# 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/Methanococcoides_burtonii_DSM_6242_uid58023/NC_007955.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/Methanococcoides_burtonii_DSM_6242_uid58023/NC_007955.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanococcoides_burtonii_DSM_6242_uid58023/NC_007955.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|91772083|ref|YP_564775.1|  [L=337]
Description: 50S ribosomal protein L3P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-86  289.5   0.2    4.3e-86  289.2   0.2    1.1  1  Ribosomal_L3  Ribosomal protein L3
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.042   14.0   0.0    1.3  1  Cass2         Integron-associated effector binding protein


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 !  289.2   0.2   4.8e-90   4.3e-86       5     365 ..       3     333 ..       1     337 [] 0.94

  Alignments for each domain:
  == domain 1  score: 289.2 bits;  conditional E-value: 4.8e-90
                                   .SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--EE CS
                  Ribosomal_L3   5 kfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetppmv 85 
                                   k ++pr+gsl ++prkR++++ ++++s+P+ d++   kl++f+GyK Gmth++  +d   s +++ e+ ++vt++etp+++
  gi|91772083|ref|YP_564775.1|   3 KGHRPRRGSLAYSPRKRSQSHIPRFRSWPESDAE--PKLQGFAGYKVGMTHVIMIDDVKHSLTEGTEISVPVTIIETPAIR 81 
                                   5579*****************************9..789****************************************** PP

                                   EEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHH.HHHHHHHSCSCEEEEEE CS
                  Ribosomal_L3  86 ivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkkliea.dleeikkeasvvrviah 165
                                   ++++++y +  +G  ++ + w++ l +++ rrl             k     ++ dv++++e+ ++   + +a  +r+i++
  gi|91772083|ref|YP_564775.1|  82 VAAIRAYGKDTYGEIAIAEAWTDVLDKDLSRRL-------------K---TAKNPDVNASLEKlETLVESGRANDIRLITY 146
                                   *********************************.............2...334468888888877777788899******* PP

                                   EECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTS CS
                  Ribosomal_L3 166 tvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkth 246
                                   t    ++++ +K ++++E+ v g  +  k+++a+  l   v++++vF++g+++Dv+++t G+G++G+vkRWg++  ++k+ 
  gi|91772083|ref|YP_564775.1| 147 TLPSTLTGVPKKVPDVMETGVSGSDVKAKFEYAKTVLGTMVEISDVFDNGKIVDVAAITTGHGTQGPVKRWGINLMKNKHS 227
                                   ********************************************************************************* PP

                                   SS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB..TSCEE CS
                  Ribosomal_L3 247 rg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGevkndfi 325
                                   r+  lR+v+++g+w pa+Vs+ v++aGq+Gyh+Rt++nk+i ++ +               +e++P GGfv+yG v++++i
  gi|91772083|ref|YP_564775.1| 228 RQgsLRQVGTLGPWTPAHVSWRVPQAGQMGYHQRTDYNKRILKMSS-------------DVDEVNPAGGFVNYGLVRGNYI 295
                                   *99*****************************************99.............3578****************** PP

                                   EEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TT CS
                  Ribosomal_L3 326 lvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidta 365
                                   l+kGsvpGp krl++lr+  +++ s   e+++   +++t+
  gi|91772083|ref|YP_564775.1| 296 LIKGSVPGPSKRLIRLREPTRSKVSSIGEPQI--MHVSTQ 333
                                   ********************999999888888..555555 PP

>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.6e-06     0.042       1      47 [.      73     120 ..      73     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
                                   EEEEE--EEEEEEEEETTCCCCH...HHHHHHHHHHHHH...HHCTTSBS CS
                         Cass2   1 rIvelpeftvaGiryegskeeedlnkeigklwreflekg...rlkkikkd 47 
                                   +I+e p+++va+ir +g++ + +    i ++w ++l k    rlk  k++
  gi|91772083|ref|YP_564775.1|  73 TIIETPAIRVAAIRAYGKDTYGE--IAIAEAWTDVLDKDlsrRLKTAKNP 120
                                   69********************7..999********99956555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1998.22
//
Query:       gi|91772084|ref|YP_564776.1|  [L=253]
Description: 50S ribosomal protein L4P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  160.8   0.8    3.3e-47  160.7   0.8    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 !  160.7   0.8   1.8e-51   3.3e-47       1     190 [.      17     249 ..      17     251 .. 0.94

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 1.8e-51
                                   EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT---S CS
                  Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargGgva 73 
                                   ++L p+vF++ +r+dli++av++ +anr q+++ +  a++++s+  +++++  G+G A v++i+        p+a+gG++a
  gi|91772084|ref|YP_564776.1|  17 IAL-PEVFSEIFRPDLIKKAVLSAQANRLQPYGTKLyAGMQTSA--HSWGS--GRGVAQVPRISngsrvarIPQAVGGRRA 92 
                                   568.9***************************************..6****..**************************** PP

                                   S---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.---..-S.........S--HHHHHHHHHHTT-......... CS
                  Ribosomal_L4  74 hgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.nle.ple.........esktkelvellkklgl......... 134
                                   h+pk+e d ++k+nkK++rlA+rsa++a+++++l+++++ +++ +++           k ke++++l++ gl         
  gi|91772084|ref|YP_564776.1|  93 HPPKTETDRTEKINKKEKRLAVRSAIAATIDADLVKARGhKFTaEVPfvaddaiegLVKIKEVISFLQAAGLyddiirake 173
                                   ***************************************86764455889999999999**********888888888888 PP

                                   .................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHH CS
                  Ribosomal_L4 135 .................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitksavekle 190
                                                    ++ksvLiv++e ++ l +aa+nlpgv+v++v+ ln++ l+++++    +v+t+sa+ ++e
  gi|91772084|ref|YP_564776.1| 174 gkhiragkgkrrgrkykNRKSVLIVTGE-ESLLSKAANNLPGVDVATVTALNAELLAPGTHagrlTVWTQSAITNME 249
                                   9999999999999999999********7.99******************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1811.17
//
Query:       gi|91772085|ref|YP_564777.1|  [L=82]
Description: 50S ribosomal protein L23P [Methanococcoides burtonii DSM 6242]
Scores for 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   54.6   2.1    5.2e-14   52.4   2.1    1.8  1  Ribosomal_L23    Ribosomal protein L23
     0.0048   16.7   0.1     0.0056   16.5   0.1    1.1  1  Pox_polyA_pol_C  Poxvirus poly(A) polymerase C-terminal domai
  ------ inclusion threshold ------
       0.05   14.2   0.1      0.056   14.1   0.1    1.2  1  Asp_protease_2   Aspartyl protease


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 !   52.4   2.1   8.6e-18   5.2e-14       2      60 ..       3      61 ..       2      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.6e-18
                                  SEEEE--SHHHHHHHTTE.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBES CS
                 Ribosomal_L23  2 vilkPvitEkstklaeknkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkr 60
                                   i+ P itEk+++l+++nk+ F V+ +anK+++ + v k++g +V++V t+   +  k+
  gi|91772085|ref|YP_564777.1|  3 AIRYPFITEKAMMLMDENKLQFVVDTRANKTQVENDVVKMYGFTVKSVCTMTTMKGLKK 61
                                  6899***********************************************98776654 PP

>> Pox_polyA_pol_C  Poxvirus poly(A) polymerase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   9.4e-07    0.0056      70     140 ..       5      78 ..       1      80 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.4e-07
                                   TT.SSSSEEEEES-HHHHHHHHHHTT-.---EE-GGGTSSEEEEETTEEEEE-S....S--EEEETTEE-HHHHH CS
               Pox_polyA_pol_C  70 ayalstkkivvylDenkLskdilklnasdeavdfeavsNskyliedntlytYFs....Ntillssedkihdisvk 140
                                   +y + t+k+++++DenkL + +++  a++++v+ + v    + +++ ++ t  +      + +++ d+ h+i+++
  gi|91772085|ref|YP_564777.1|   5 RYPFITEKAMMLMDENKL-QFVVDTRANKTQVENDVVKMYGFTVKSVCTMTTMKglkkALVTFNETDAAHEIATR 78 
                                   688999************.9999**********************997776654111144566788888888776 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   9.4e-06     0.056       6      48 ..      18      60 ..      13      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.4e-06
                Asp_protease_2  6 nGkpvrfllDTGasttlispelaeklglkvreseltvrvsgag 48
                                  ++ +++f++DT a+ t + +++++  g +v++  + ++++g+ 
  gi|91772085|ref|YP_564777.1| 18 DENKLQFVVDTRANKTQVENDVVKMYGFTVKSVCTMTTMKGLK 60
                                  45699************************99975545555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 579.41
//
Query:       gi|91772086|ref|YP_564778.1|  [L=237]
Description: 50S ribosomal protein L2P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-45  152.5   0.4    9.8e-45  151.8   0.4    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
      1e-16   60.6   0.0    2.5e-16   59.4   0.0    1.7  1  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8   0.4   1.1e-48   9.8e-45       1     120 [.      90     220 ..      90     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 1.1e-48
                                   SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT--- CS
                Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekkl 81 
                                   k+Gn+lpl++ipeG  ++nie+kp++gg++ars+G ya++v++e +kv+v++pSg  ++++ +crAtiG+v++g++ ++++
  gi|91772086|ref|YP_564778.1|  90 KPGNTLPLAEIPEGIPICNIESKPNDGGQYARSSGVYATLVSRELSKVVVRMPSGVLKWFHPKCRATIGIVAGGGRVDRPF 170
                                   68******************************************9************************************ PP

                                   -STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SSSS CS
                Ribosomal_L2_C  82 gkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksrka 120
                                   +kAg+k+++      ++p+v G+amn vdHp+GGG+    Gk  t+sr+a
  gi|91772086|ref|YP_564778.1| 171 LKAGKKYHKmkaraAKYPRVSGIAMNVVDHPFGGGNrkhpGKptTVSRNA 220
                                   *********9999999********************66666664555555 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 !   59.4   0.0   2.8e-20   2.5e-16       1      75 [.      11      81 ..      11      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.8e-20
                                  TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE CS
                  Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtv 75
                                  Gr+++ +r+++++++   + k + +d    +++++g+V+ ie+Dp+RsApiA+v++e+g+k++i+ peg++vG+++
  gi|91772086|ref|YP_564778.1| 11 GRGSPtYRAPSHKYKA--ELKHPRVDE---ESTLNGTVIGIEHDPARSAPIAMVAFENGKKQFIVVPEGISVGEKL 81
                                  9***************..889999998...789****************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.39
# Mc/sec: 1821.85
//
Query:       gi|91772087|ref|YP_564779.1|  [L=137]
Description: 30S ribosomal protein S19P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-26   90.5   0.3    6.4e-26   90.1   0.3    1.2  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
      0.066   12.3   0.0       0.07   12.2   0.0    1.1  1  Citrate_synt   Citrate synthase, C-terminal domain


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 !   90.1   0.3   7.1e-30   6.4e-26       1      81 []      44     120 ..      44     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 7.1e-30
                                   .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS---- CS
                 Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvk 80 
                                   rs+++g +  q+ +l+++r+ k     e ++th R+++I+Pem+g  ++VynGk+fv++ei +em+Gh++gE+spTr++v+
  gi|91772087|ref|YP_564779.1|  44 RSIRRGfSDSQKGVLQQFRDGK-----ESVRTHFRNMIIFPEMIGKNLEVYNGKEFVKIEIMPEMIGHRFGEYSPTRNRVS 119
                                   7889998899999999998887.....689**************************************************9 PP

                                   S CS
                 Ribosomal_S19  81 h 81 
                                   h
  gi|91772087|ref|YP_564779.1| 120 H 120
                                   9 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 ?   12.2   0.0   7.8e-06      0.07      10      66 ..       4      52 ..       1      88 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-06
                                  ESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHC CS
                  Citrate_synt 10 teisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelae 66
                                   ++s++ ++kge ++RG ++ +L   + sfe+ a lL     P ++e +++++ +++
  gi|91772087|ref|YP_564779.1|  4 KSTSRLPKRKGEYTFRGKTVAQLQ--EMSFEDFAELL-----P-AKERRSIRRGFSD 52
                                  5678888899************87..799********.....6.4555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 923.41
//
Query:       gi|91772088|ref|YP_564780.1|  [L=151]
Description: 50S ribosomal protein L22P [Methanococcoides burtonii DSM 6242]
Scores for complete 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  102.4   0.1    1.6e-29  102.2   0.1    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
      0.045   13.0   0.0      0.055   12.7   0.0    1.1  1  PNP_UDP_1      Phosphorylase superfamily


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 !  102.2   0.1   1.8e-33   1.6e-29       1     102 [.      18     147 ..      18     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.8e-33
                                   EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST..........................THHHHHHHHHHHHHH CS
                 Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk..........................aakfvlklLknaean 53 
                                   a+gs+l++s+kk re++++I+gm  + A +yL++    k+                          +a ++lklLknae+n
  gi|91772088|ref|YP_564780.1|  18 AMGSELHISPKKSRELCKAIKGMRTNAARQYLEDvvILKQavpfgrhndslghrkgpmaagrypvkVASEMLKLLKNAESN 98 
                                   6899*******************************955556**************************************** PP

                                   HH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                 Ribosomal_L22  54 aelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                   ae+kgl+++ ++I++  +n+g+ ++++++rArGr++p + +++++e+++
  gi|91772088|ref|YP_564780.1|  99 AEYKGLNPEHMFIAHTAMNRGRVIHGMRPRARGRASPENTETVNLEMII 147
                                   ***********************************************97 PP

>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-06     0.055      89     157 ..      50     130 ..      44     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-06
                                   T-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTT.............TTEEEEEEEEESESS- CS
                     PNP_UDP_1  89 GDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealg.............ikvhrGvvatadgfya 156
                                    Dvvi ++a+ f   +++ g++ + + + + y++++ +e+++llk+a +  +               + rG v+ +  ++a
  gi|91772088|ref|YP_564780.1|  50 EDVVILKQAVPFGRHNDSLGHRKG-PMAAGRYPVKVASEMLKLLKNAESNAEykglnpehmfiahTAMNRGRVIHGMRPRA 129
                                   6********************998.*********************43333355577777777777777777777766666 PP

                                   C CS
                     PNP_UDP_1 157 e 157
                                    
  gi|91772088|ref|YP_564780.1| 130 R 130
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 951.91
//
Query:       gi|91772089|ref|YP_564781.1|  [L=304]
Description: 30S ribosomal protein S3P [Methanococcoides burtonii DSM 6242]
Scores for 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-22   77.8   1.6    1.1e-21   77.2   0.2    2.0  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    3.8e-15   55.5   0.0    1.2e-14   53.9   0.0    1.9  1  KH_2            KH domain
  ------ inclusion threshold ------
       0.14   12.0   2.1       0.47   10.3   0.0    2.8  4  KH_1            KH domain
       0.57   10.1   0.1       0.57   10.1   0.1    2.3  2  KH_4            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.2   2.4e-25   1.1e-21       1      83 []      99     182 ..      99     182 .. 0.98
   2 ?   -2.0   0.1       1.2   5.5e+03      32      55 ..     223     246 ..     217     267 .. 0.55

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.4e-25
                                   HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEEE CS
                Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiGv 79 
                                   +a+++e+++ fR+a ++++r++m+aga G++i++sG+L+ ++++r ek+ +G++++  +++++ +d ++a+a  k G++G+
  gi|91772089|ref|YP_564781.1|  99 LASSIERGWYFRKAGHNTMRAVMNAGALGCEIVISGKLT-GSRSRVEKMVNGYIKHagKPVDDIVDDGFATAVKKLGTLGC 178
                                   5899***********************************.9**************************************** PP

                                   EEEE CS
                Ribosomal_S3_C  80 kVwI 83 
                                   kV+I
  gi|91772089|ref|YP_564781.1| 179 KVRI 182
                                   **98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                   EEEEC-SS.TTT--EEEEEEC--- CS
                Ribosomal_S3_C  32 iqvsGrLggaeiarsekykeGrvp 55 
                                   ++  G +  ae a  e+ ++ +  
  gi|91772089|ref|YP_564781.1| 223 VEAKGEVAEAEEAVVEETAKAEAE 246
                                   555566666666655555444333 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   2.7e-18   1.2e-14       3      78 .]      18      90 ..      16      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.7e-18
                                  HHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTGG CS
                          KH_2  3 peslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpel 78
                                  +e++a++++ ag+++++I+rt+ ++ i++++++pg+vIGk G+ i+k++ ++ +  + l + ++     +Vk+pel
  gi|91772089|ref|YP_564781.1| 18 DEYFAKQLSRAGYGGMDINRTPMGTQITVYAEKPGMVIGKAGKVIRKLTRDVDRLYD-LDNPQID--AQEVKRPEL 90
                                  689*****************************************************6.9999999..99****996 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0001      0.47       4      27 ..      44      67 ..      41      70 .. 0.81
   2 ?   -2.4   0.0      0.99   4.5e+03      47      53 ..     129     136 ..     126     148 .. 0.48
   3 ?   -1.0   0.0      0.35   1.6e+03      29      40 ..     175     186 ..     172     201 .. 0.79
   4 ?   -2.2   0.2      0.88   3.9e+03      44      64 ..     217     236 ..     204     238 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                                  EEEGGGHHHHHHTGGGHHHHHHHH CS
                          KH_1  4 ilvPsslvgriIGkgGsnIkeIre 27
                                  i+v +++ g +IGk G++I+++ +
  gi|91772089|ref|YP_564781.1| 44 ITVYAEKPGMVIGKAGKVIRKLTR 67
                                  5566666799***********986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.99
                                   EEEEEE.S CS
                          KH_1  47 evtisG.s 53 
                                   e++isG  
  gi|91772089|ref|YP_564781.1| 129 EIVISGkL 136
                                   45565422 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.35
                                   H.T-EEEEESSTT CS
                          KH_1  29 t.gakIkvpksed 40 
                                   t g+k++++  +d
  gi|91772089|ref|YP_564781.1| 175 TlGCKVRII-HPD 186
                                   669****99.443 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.88
                                   T.-EEEEEESHHHHHHHHHHH CS
                          KH_1  44 derevtisGspeavekAkeli 64 
                                    e+ v++  + e v++A+e++
  gi|91772089|ref|YP_564781.1| 217 IEELVEVEAKGE-VAEAEEAV 236
                                   566777776667.77777766 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00013      0.57      32      52 ..      43      63 ..      20      65 .. 0.87
   2 ?   -2.0   2.0      0.78   3.5e+03       8      32 ..     225     249 ..     218     280 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                          KH_4 32 elnvegedlGrvIGkrGrtld 52
                                  +++v  e+ G vIGk G++++
  gi|91772089|ref|YP_564781.1| 43 QITVYAEKPGMVIGKAGKVIR 63
                                  67888999**********985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.78
                          KH_4   8 lkalvddpeevevteeeeeeeveie 32 
                                   +k+ v ++ee  v+e+ ++e +++e
  gi|91772089|ref|YP_564781.1| 225 AKGEVAEAEEAVVEETAKAEAETVE 249
                                   5555555666666666554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1940.55
//
Query:       gi|91772090|ref|YP_564782.1|  [L=67]
Description: 50S ribosomal protein L29P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-15   54.5   0.1    1.1e-14   54.2   0.1    1.1  1  Ribosomal_L29  Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   5.9e-19   1.1e-14       1      56 [.       7      63 ..       7      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.9e-19
                                  HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHH CS
                 Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlre 56
                                  ke+r+++  e +++l++ + eL + r  +++g +++np+r+ ++R+++A ikT+++e
  gi|91772090|ref|YP_564782.1|  7 KEIRDMTPHEREDELVKIRSELIRERALASAGgAPDNPGRVGELRRTVAKIKTIQHE 63
                                  7*****************************999**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 455.66
//
Query:       gi|91772091|ref|YP_564783.1|  [L=101]
Description: ribonuclease P protein component 1 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-24   83.3   0.0    9.3e-24   83.2   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.0   5.2e-28   9.3e-24       2      83 ..       7      93 ..       6      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 5.2e-28
                                  HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE......TTEEEEEECCCCSSXHH CS
                       UPF0086  2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefev.....kdvlevevdGsqlryrpa 79
                                  +L+ ++l+G+  eV +s+np+l++i G+V++Et+n+l i+t++++ k+vpK+g++F f++     ++  +v++ G+ l+++p+
  gi|91772091|ref|YP_564783.1|  7 NLIFHELIGLYAEVFESTNPKLINICGRVIDETRNMLIIETEDTHEKMVPKNGTTFVFHLpsssaDHDQRVKIFGTLLLSQPE 89
                                  89**************************************************************967789************* PP

                                  HHHC CS
                       UPF0086 80 dRae 83
                                  +R++
  gi|91772091|ref|YP_564783.1| 90 NRVK 93
                                  **87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 630.56
//
Query:       gi|91772092|ref|YP_564784.1|  [L=109]
Description: 30S ribosomal protein S17P [Methanococcoides burtonii DSM 6242]
Scores for complete 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  100.3   2.8    5.6e-29  100.1   2.8    1.1  1  Ribosomal_S17    Ribosomal protein S17
  ------ inclusion threshold ------
      0.048   12.7   0.1      0.057   12.5   0.1    1.0  1  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.079   13.3   0.5       0.24   11.8   0.0    2.0  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   2.8   9.3e-33   5.6e-29       1      68 []      36     104 ..      36     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 9.3e-33
                                   EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                 Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                   G+Vvs+kmd+Tvv+++ r + ++ky++y+kr++k++ah+++++ +kvGDiV+i+ecrPlSktk++vvv+
  gi|91772092|ref|YP_564784.1|  36 GTVVSAKMDRTVVIQQRREKLINKYQRYEKRQSKIHAHNPPCIdAKVGDIVTIAECRPLSKTKSYVVVK 104
                                   99*****************************************************************96 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 ?   12.5   0.1   9.6e-06     0.057     125     175 ..      49      98 ..      40     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-06
                         Atg14 125 leerrkkqiaklqdaikrieqklsslssktlesrsslcselaklyglrrts 175
                                   +++rr+k+i+k+q++ kr++ k+++ ++ +++++  ++ ++a++ +l++t+
  gi|91772092|ref|YP_564784.1|  49 IQQRREKLINKYQRYEKRQS-KIHAHNPPCIDAKVGDIVTIAECRPLSKTK 98 
                                   89***********7776655.66*************************975 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 ?   11.8   0.0   4.1e-05      0.24      34      68 ..       3      33 ..       1      34 [. 0.72
   2 ?   -0.9   0.2      0.36   2.1e+03      30      32 ..      61      63 ..      42      75 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                                  ----TT----GGGGS-----TTSSSSSS----S-E CS
               Ribosomal_S17_N 34 knvglgfktPkeAiegtYiDkKCPFtGnvsirGri 68
                                  k++gl +  P +  +    D  CPF G+  +rG+i
  gi|91772092|ref|YP_564784.1|  3 KDIGLDIPEPTKECD----DINCPFHGELPVRGQI 33
                                  566665555544433....778***********98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.36
                                  --- CS
               Ribosomal_S17_N 30 kry 32
                                  +ry
  gi|91772092|ref|YP_564784.1| 61 QRY 63
                                  222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 689.54
//
Query:       gi|91772093|ref|YP_564785.1|  [L=132]
Description: 50S ribosomal protein L14P [Methanococcoides burtonii DSM 6242]
Scores for complete 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  126.4   1.7    6.9e-37  126.2   1.7    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 !  126.2   1.7   3.9e-41   6.9e-37       4     122 .]      14     132 .]      11     132 .] 0.94

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 3.9e-41
                                   SS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEES CS
                 Ribosomal_L14   4 lktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirfd 80 
                                    +++++++DN+ga++ve+i+v +++    + +++ +Gd++vvsvkk++p   ++++++++av+vr+kke+rr+dG  + f+
  gi|91772093|ref|YP_564785.1|  14 AGAKIECVDNTGARTVEIISVKKYRgvknRMPKGGIGDMCVVSVKKGTP---EMRKQILYAVIVRQKKEFRRPDGIRVAFE 91 
                                   67899*****************9887665559*****************...99*************************** PP

                                   S-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                 Ribosomal_L14  81 dnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                   dna+V++++kg p+Gt i+gpvare++e+ f+ki ++A++++
  gi|91772093|ref|YP_564785.1|  92 DNAVVIVDDKGIPKGTDIKGPVAREAAER-FPKIGTTASMIV 132
                                   ****************************9.********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 813.73
//
Query:       gi|91772094|ref|YP_564786.1|  [L=117]
Description: 50S ribosomal protein L24P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-29  100.0   0.1    9.2e-29   99.7   0.1    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    2.1e-05   24.3   1.3    6.3e-05   22.8   1.3    1.9  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.1     1e-32   9.2e-29       1      81 [.       3     115 ..       3     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 1e-32
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxx RF
                 Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gvtrek 49 
                                   s+++rkqrKa+++ap+h+++k+m apLsk Lr kyg rs  +                                 gv+++k
  gi|91772094|ref|YP_564786.1|   3 SKQPRKQRKARYEAPLHMKQKYMAAPLSKALRGKYG-RSANVIvgdtvivmrgdhagtkgkvealslksgtivveGVSVSK 82 
                                   89**********************************.7777777************************************* PP

                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                 Ribosomal_L26  50 angttvpvgihpSkvvItklkl.DkdrkkiLer 81 
                                    +gt+vp++i pS+v+It+l++ Dk+r++iL+r
  gi|91772094|ref|YP_564786.1|  83 VDGTEVPRPIYPSNVMITSLEMnDKHRDSILSR 115
                                   *******************************87 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.3     7e-09   6.3e-05       1      31 [.      45      75 ..      45      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7e-09
                                  TTSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                           KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                  +Gd+V+V++G h+G +GkV+    +  +++v
  gi|91772094|ref|YP_564786.1| 45 VGDTVIVMRGDHAGTKGKVEALSLKSGTIVV 75
                                  7******************876666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 756.35
//
Query:       gi|91772095|ref|YP_564787.1|  [L=236]
Description: 30S ribosomal protein S4e [Methanococcoides burtonii DSM 6242]
Scores for 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   64.3   0.4    1.5e-17   63.2   0.4    1.6  1  Ribosomal_S4e  Ribosomal family S4e
      3e-10   40.0   1.5    6.1e-10   39.0   1.5    1.4  1  RS4NT          RS4NT (NUC023) domain
    1.1e-08   34.6   1.2    5.8e-08   32.3   0.2    2.5  2  S4             S4 domain
    2.3e-05   24.1   0.1    7.4e-05   22.6   0.1    1.9  1  KOW            KOW motif
     0.0049   16.6   0.0      0.019   14.8   0.0    2.1  2  S4_2           S4 domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.4   4.3e-21   1.5e-17       2      75 .]      92     163 ..      91     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 4.3e-21
                                   TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                 Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                   +  yr+++d k r++l k +   a+ KLc+i++kt +k+g++q++++dG +i+ +++ ++++D++ ++++++k+
  gi|91772095|ref|YP_564787.1|  92 NVEYRVMLDGKSRLVLNKLDGTGAD-KLCRIEGKTSIKEGKIQMRLNDGVNIIGSNN-YNTKDSIILSVPDKKV 163
                                   568**********************.******************************9.**************97 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   1.5   1.7e-13   6.1e-10       6      35 ..       4      33 ..       2      34 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.7e-13
                                  -EETTTS-TTS---SSSSSEE----SSSS- CS
                         RS4NT  6 HLKrlaAPkhWpldkkegvfavkPspGPHk 35
                                  H Kr++ Pk+W+++kk++++++ ++pGPH+
  gi|91772095|ref|YP_564787.1|  4 HQKRISVPKSWQISKKSNKWITSTRPGPHN 33
                                  *****************************7 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.2   1.6e-11   5.8e-08       2      48 .]      39      86 ..      38      86 .. 0.94
   2 ?   -0.1   0.0      0.22   8.1e+02      31      43 ..     160     172 ..     160     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.6e-11
                                  EHHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                            S4  2 RLdkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                  +L ++l   lg +  r eA++  ++G VlV+G  +kd  ++V+ +D+i
  gi|91772095|ref|YP_564787.1| 39 PLAVILrDMLGVVDNRAEAKRVLSEGNVLVDGVARKDLRFPVGLMDII 86
                                  5788888889************************************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                                   TTEEE--TT-EE- CS
                            S4  31 NGkvvkdpsyrVk 43 
                                   ++kvvk  +y+V+
  gi|91772095|ref|YP_564787.1| 160 DKKVVKHIKYEVG 172
                                   78********996 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   2.1e-08   7.4e-05       1      31 [.     171     205 ..     171     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.1e-08
                                   TTSEEEESSSTTTTCEEEEEEEETTT....TEEEE CS
                           KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                   +G+  ++v+G h+G++G +++++  k    ++V++
  gi|91772095|ref|YP_564787.1| 171 VGNLAMIVGGSHAGEVGSIKEINTVKssknNTVTI 205
                                   7***********************99999999987 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.2e-06     0.019      16      43 ..      47      74 ..      33      98 .. 0.77
   2 ?   -2.6   0.0       1.4   5.2e+03      26      36 ..     123     133 ..     122     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.2e-06
                          S4_2 16 laglvesGgeaKafiaegeVkvNGevet 43
                                  ++g+v++ +eaK +++eg+V+v+G   +
  gi|91772095|ref|YP_564787.1| 47 MLGVVDNRAEAKRVLSEGNVLVDGVARK 74
                                  57999999****************8765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                          S4_2  26 aKafiaegeVk 36 
                                    K+ i+eg+++
  gi|91772095|ref|YP_564787.1| 123 GKTSIKEGKIQ 133
                                   78999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.34s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 1339.28
//
Query:       gi|91772096|ref|YP_564788.1|  [L=169]
Description: 50S ribosomal protein L5P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   88.3   0.0    3.9e-25   87.8   0.0    1.2  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    7.2e-19   67.9   0.0    1.4e-18   66.9   0.0    1.5  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 !   87.8   0.0   4.3e-29   3.9e-25       1      94 []      60     159 ..      60     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 4.3e-29
                Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak... 78 
                                   piG+kvtLrge ++ fl++ l +v++rl+      +s+fd  GnvsfG++e+++ p+++yd+++gifGmdit+v++++   
  gi|91772096|ref|YP_564788.1|  60 PIGCKVTLRGEAAEGFLETSLGIVEKRLN------ESQFDIFGNVSFGVEEHTDYPGMRYDPNIGIFGMDITVVVNRPgyr 134
                                   8****************************......*******************************************877 PP

                Ribosomal_L5_C  79 .tde..........earallkelgipf 94 
                                    + +          +++ ++ke++i f
  gi|91772096|ref|YP_564788.1| 135 vS-KrriakrkiptSHK-ITKEDTISF 159
                                   42.34677777885555.888877776 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   1.6e-22   1.4e-18       1      57 []       3      56 ..       3      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.6e-22
                                  SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                  Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                  N+M+ P++eK+v++mgvGe+g+    l  a+ +L++ItGQ+ v+++ak++ ++F i+
  gi|91772096|ref|YP_564788.1|  3 NPMRNPKVEKVVVHMGVGESGQH---LVDAEGILETITGQTVVRSYAKRTLPAFTIK 56
                                  9**********************...****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1094.64
//
Query:       gi|91772097|ref|YP_564789.1|  [L=50]
Description: 30S ribosomal protein S14P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-16   59.2   2.7    2.5e-16   59.1   2.7    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
     0.0029   17.2   1.4     0.0036   16.9   1.4    1.1  1  zf-P11         P-11 zinc finger
  ------ inclusion threshold ------
      0.015   15.2   0.3      0.018   14.9   0.3    1.2  1  DUF4428        Domain of unknown function (DUF4428)
      0.053   14.3   0.6      0.053   14.3   0.6    1.1  1  MRNIP          MRN-interacting protein
      0.089   12.8   0.5      0.097   12.7   0.5    1.1  1  DUF1451        Zinc-ribbon containing 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 !   59.1   2.7   7.1e-20   2.5e-16       7      54 .]       6      50 .]       1      50 [] 0.93

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 7.1e-20
                                  -SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                 Ribosomal_S14  7 rnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                  +n   +r+ n C+ +Gr +G++rk+g+  +R+cfRe A++   +G++K+S
  gi|91772097|ref|YP_564789.1|  6 KNF--GRGANECKRCGRKQGLVRKYGIylCRHCFREIAHD---MGFEKYS 50
                                  666..9**********************************...******8 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.4   9.9e-07    0.0036       1      28 [.      11      37 ..      11      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.9e-07
                                  -SSSBTTTSS--SSEEE-SSSEEEHHHH CS
                        zf-P11  1 GplsCksCWfkdksLveCsdHYLClrCl 28
                                  G   Ck C   +++Lv+    YLC++C+
  gi|91772097|ref|YP_564789.1| 11 GANECKRCGR-KQGLVRKYGIYLCRHCF 37
                                  6789****76.579*************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 ?   14.9   0.3   5.2e-06     0.018       2      37 ..      15      44 ..      14      50 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-06
                       DUF4428  2 CaiCgkKigllkrlkleDgyvCkdClkKl.seflsdv 37
                                  C  Cg K gl         y+C  C+ ++      d+
  gi|91772097|ref|YP_564789.1| 15 CKRCGRKQGLVR---KYGIYLCRHCFREIaH----DM 44
                                  788********9...8899*********943....33 PP

>> MRNIP  MRN-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   1.5e-05     0.053      21      46 ..      13      38 ..       2      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                         MRNIP 21 wkCkvCnekqslkkvygsgsgkdcrq 46
                                   +Ck C+ kq l + yg +  + c +
  gi|91772097|ref|YP_564789.1| 13 NECKRCGRKQGLVRKYGIYLCRHCFR 38
                                  58***************988888854 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   2.7e-05     0.097     111     138 ..       9      36 ..       2      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                       DUF1451 111 glGtlvCekCgkelalkkteeippCpkC 138
                                   g G  +C++Cg++  l +   i  C +C
  gi|91772097|ref|YP_564789.1|   9 GRGANECKRCGRKQGLVRKYGIYLCRHC 36 
                                   78999*********************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 337.29
//
Query:       gi|91772098|ref|YP_564790.1|  [L=130]
Description: 30S ribosomal protein S8P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-27   94.7   0.0    5.3e-27   94.3   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 !   94.3   0.0     3e-31   5.3e-27       1     127 []       5     130 .]       5     130 .] 0.85

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 3e-31
                                   -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEEE-SB CS
                  Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklkrvsk 77 
                                   Dp+ad+l+ i+Nae+++k+++++ paskl+ ++lkv++++Gyi dfe++ + k  +  +++ +++nk  +++ik    v  
  gi|91772098|ref|YP_564790.1|   5 DPLADALSIIKNAEAVGKDSCTIrPASKLIGNVLKVMNDRGYIGDFEFVeDGKAGVytVELIGRINK--CGAIKPRYSVGV 83 
                                   9***********************************************8444433355888889988..999996444433 PP

                                   TTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                  Ribosomal_S8  78 pgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                        + + ++     +++G++i++T+kGv+++ eAr+++vGG++l +v+
  gi|91772098|ref|YP_564790.1|  84 ---TEFERWEKQFLPAKNFGVLILTTPKGVISQYEARENNVGGQLLSFVY 130
                                   ...335555555666789*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 843.32
//
Query:       gi|91772099|ref|YP_564791.1|  [L=177]
Description: 50S ribosomal protein L6P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-28   97.5   7.0    5.8e-16   58.9   0.4    2.1  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.4   3.2e-20   5.8e-16       1      76 []      11      83 ..      11      83 .. 0.93
   2 !   42.2   1.4   5.5e-15   9.9e-11       1      76 []      95     169 ..      95     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 3.2e-20
                                  CSTTEEEEEETTTEEEEEESSEEEEEE-CTT.SEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipeg.vtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                  iP+gv+v+ ++ ++++  Gpkg+ tr +++  v++e  v+g ++ v + s  +k+k+ ++gt++s+i nm+kGV +g
  gi|91772099|ref|YP_564791.1| 11 IPEGVTVTFEK-NVLSASGPKGTNTRFLWYPgVNIE--VNGSEIIVDSASSRKKQKA-MVGTYTSHITNMMKGVVDG 83
                                  8*********5.*****************9945555..99*****************.****************887 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 5.5e-15
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                   +P+  +v++k+  ++++lG+k+++  +i  ++ v+ +     +++++vsgi+ke+v    A+i++ +++++ + +++++g
  gi|91772099|ref|YP_564791.1|  95 FPMQIKVNGKKFVINNFLGEKKPRVSNILGETSVKAS-----GDEVIVSGINKEDVgqtaANIEQKTKIKRFDPRVFQDG 169
                                   79*********************************77.....************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1346.81
//
Query:       gi|91772100|ref|YP_564792.1|  [L=148]
Description: 50S ribosomal protein L32e [Methanococcoides burtonii DSM 6242]
Scores for 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  117.3   0.0    5.1e-34  116.9   0.0    1.1  1  Ribosomal_L32e   Ribosomal protein L32
  ------ inclusion threshold ------
      0.068   13.9   0.2       0.12   13.1   0.1    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


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 !  116.9   0.0   5.7e-38   5.1e-34       1     108 []      38     143 ..      38     143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 5.7e-38
                                   ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..EE CS
                Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksyaa 81 
                                   +++F+r +s++y++l+++wr+prG++ ++r+ +k++ +++++GYgspk+++gl+psG+ +vlV+n++ +e ++ + +  a+
  gi|91772100|ref|YP_564792.1|  38 KPDFKRADSHKYKRLDSNWRRPRGLQGKQRKGIKAKGAVVQAGYGSPKAVKGLHPSGYSEVLVNNLAGIEGVDASLE--AI 116
                                   589**************************************************************************..** PP

                                   EE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                Ribosomal_L32e  82 eiahsVsskkrkeiverAaelgikVtN 108
                                   +i+++V+++k+  i+++A elgik++N
  gi|91772100|ref|YP_564792.1| 117 RIGRTVGARKKALIEAKAVELGIKILN 143
                                   *************************99 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05      0.12      74     126 ..      78     130 ..      62     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                   EEEES.HHHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE--SHHHH CS
               DXP_reductoisom  74 evlvG.eealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLANKEsLV 126
                                   +  +G ++a+k l  +  ++v+v+ + G+ G+ ++l+ai+ g+++  A K +L+
  gi|91772100|ref|YP_564792.1|  78 QAGYGsPKAVKGLHPSGYSEVLVNNLAGIEGVDASLEAIRIGRTVG-ARKKALI 130
                                   44454246777777888899************************97.6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1058.77
//
Query:       gi|91772101|ref|YP_564793.1|  [L=148]
Description: 50S ribosomal protein L19e [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-56  190.4   8.0    1.9e-56  190.2   8.0    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.2   8.0     1e-60   1.9e-56       1     141 [.       3     143 ..       3     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 1e-60
                                   -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG--S CS
                Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrkG 81 
                                   dl++qkrlaa+vl++G++rvwl+pe++++ia Aitredir li +g I+++++kg sr+rar+r++k+r+g+r+g+G+rkG
  gi|91772101|ref|YP_564793.1|   3 DLTNQKRLAAKVLGCGVHRVWLNPEASSDIAVAITREDIRGLIASGSIKAEAVKGVSRGRARARDAKRRYGHRKGHGSRKG 83 
                                   5899***************************************************************************** PP

                                   -HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT CS
                Ribosomal_L19e  82 tkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyie 141
                                   tk+aR p+ke+W+k+iRalRr+Lkelr+++++dk+ + + YrkakGge+kn a+++++++
  gi|91772101|ref|YP_564793.1|  84 TKGARNPRKEQWMKKIRALRRKLKELRADGTLDKSAFCKAYRKAKGGEYKNLAHMETHLN 143
                                   *********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1067.34
//
Query:       gi|91772102|ref|YP_564794.1|  [L=173]
Description: 50S ribosomal protein L18P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-30  104.8   2.1      9e-20   71.3   0.8    2.3  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
    1.3e-05   25.5   0.0      2e-05   24.9   0.0    1.3  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.024   14.3   0.0    1.3  1  Lipoprotein_16  Uncharacterized lipoprotein


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 !   71.3   0.8   1.5e-23     9e-20       2      98 ..       6      95 ..       5     100 .. 0.95
   2 !   32.7   0.0   1.1e-11   6.6e-08     132     163 .]     102     133 ..      96     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.5e-23
                 Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltnyaa 84
                                  r++v frrrreg+tdY++r rl+   +        R+vVr + +++ +q+++   +gd++l++a skel kyg++ +  n +a
  gi|91772102|ref|YP_564794.1|  6 RYKVAFRRRREGRTDYHQRLRLLLSRE-------DRVVVRKSARHMQIQLVAPDANGDVTLSSAISKELAKYGYEGSTGNTTA 81
                                  9*********************99755.......59*********************************************** PP

                 Ribosomal_L5e 85 aYatglllarrllk 98
                                  aY+tgll++ ++l+
  gi|91772102|ref|YP_564794.1| 82 AYLTGLLFGYKTLA 95
                                  ********998886 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.1e-11
                 Ribosomal_L5e 132 iLdvGLartttgakvfgalkgavdgglsiphs 163
                                   +Ld+G++ ++ g++v++alkg+vd+gl++ph+
  gi|91772102|ref|YP_564794.1| 102 VLDIGIQASSAGSRVYAALKGVVDSGLDVPHN 133
                                   7******************************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 !   24.9   0.0   3.4e-09     2e-05       3      94 ..      14     106 ..       8     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.4e-09
                                   CCHHHCHHHHHHTTT--TTSSS-EEEEEE-SS-EEEEEE-TTT--EEEEECS-SCCCT....S-SSSCHHHHHHHHHHHHH CS
                Ribosomal_L18p   3 kkearkrRhkRirkklsgtaerprlvvfrsnrhiyaQviddvkgktlasastlekelk....lkstknkeaakkvgeliAe 79 
                                   ++e r+  h+R+r  ls  +   r+vv +s+rh+ +Q+++  ++  ++ +s++ kel       st+n+ aa   g l+  
  gi|91772102|ref|YP_564794.1|  14 RREGRTDYHQRLRLLLSRED---RVVVRKSARHMQIQLVAPDANGDVTLSSAISKELAkygyEGSTGNTTAAYLTGLLFGY 91 
                                   66777778888888888777...****************999999999999999999877777889999999999999999 PP

                                   HHCHHCHTC-EE--T CS
                Ribosomal_L18p  80 rakekgiekvvfDrg 94 
                                   ++++ g e+ v D g
  gi|91772102|ref|YP_564794.1|  92 KTLAEGYESGVLDIG 106
                                   999999998888865 PP

>> Lipoprotein_16  Uncharacterized lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.1e-06     0.024      23      68 ..      30      75 ..      30      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-06
                Lipoprotein_16 23 sRsaqevakinegdgelallsasedvrlllqqalrqqlssqGfrig 68
                                  sR++++v++++  +++++l+ +  +  ++l +a++++l + G++ +
  gi|91772102|ref|YP_564794.1| 30 SREDRVVVRKSARHMQIQLVAPDANGDVTLSSAISKELAKYGYEGS 75
                                  69*****************************************973 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1202.53
//
Query:       gi|91772103|ref|YP_564795.1|  [L=211]
Description: 30S ribosomal protein S5P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-24   82.7   0.6    1.6e-23   81.9   0.6    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    1.4e-23   82.6   0.7    3.1e-23   81.5   0.7    1.6  1  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 !   81.9   0.6   1.8e-27   1.6e-23       2      66 ..     136     201 ..     135     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.8e-27
                                   EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                   gk g+v+v lkpaprG G+ agg++r+vle aG+kDv+++++g +r+++n++kAt++AL+++ +++
  gi|91772103|ref|YP_564795.1| 136 GKAGSVTVVLKPAPRGLGLAAGGTARKVLEKAGVKDVWTRTEGqTRTTLNFAKATYNALMNTGTVR 201
                                   99***********************************************************99876 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 !   81.5   0.7   3.4e-27   3.1e-23       1      64 [.      50     113 ..      50     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 3.4e-27
                                   XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
                  Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64 
                                   l+++vl+i++vq++t++Grr +f+a+v+vG+g+G vGlG +k  +v  AirkAi++Ak n++++
  gi|91772103|ref|YP_564795.1|  50 LEDEVLDINMVQRMTDSGRRVKFRATVIVGNGDGFVGLGQAKDVQVGPAIRKAIDNAKINITRI 113
                                   799**********************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1553.99
//
Query:       gi|91772104|ref|YP_564796.1|  [L=153]
Description: 50S ribosomal protein L30P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-14   53.7   0.1    2.3e-14   53.0   0.1    1.4  1  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1   1.3e-18   2.3e-14       2      51 .]       3      52 ..       2      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.3e-18
                                  EEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                 Ribosomal_L30  2 fVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                  +V+r+r++++v+ k+ +tL +L+L+k+n+ v++ +tp+ +Gm++k k+++
  gi|91772104|ref|YP_564796.1|  3 AVVRVRGPVNVSGKIEDTLGMLRLHKVNHCVFLQDTPNNKGMIQKSKDYI 52
                                  7***************************99999999***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1124.16
//
Query:       gi|91772105|ref|YP_564797.1|  [L=147]
Description: 50S ribosomal protein L15P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   75.4   0.3    8.1e-21   75.0   0.3    1.1  1  Ribosomal_L27A   Ribosomal proteins 50S-L15, 50S-L18e, 60S-L2
  ------ inclusion threshold ------
      0.016   14.6   0.1      0.026   13.9   0.1    1.4  1  Ribosomal_L18    Ribosomal protein 60S L18 and 50S L18e
        5.7    7.6  10.0        9.5    6.9  10.0    1.3  1  FoP_duplication  C-terminal duplication domain of Friend of P


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.3   1.4e-24   8.1e-21       2     127 ..      29     143 ..      28     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.4e-24
                                   GGGTSSTTTTTTTTT-S--.......S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--...----EEE CS
                Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkk.kpgfeGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la...deaeeid 76 
                                   G++gGrG+ G++k++ +   + g+         r  +rGf+   k   + +vvn+++Ldel+d+++++  a    +a++ d
  gi|91772105|ref|YP_564797.1|  29 GNRGGRGRSGENKHHFTRAlQLGYI--------RGSERGFSrPLKAIHDVSVVNVGELDELADQLVEDgFAkleAGAYVMD 101
                                   9*************98665566653........55559***744455788*****************987789778***** PP

                                   GGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  77 leelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                   l++l          ++ Kvlg+g++tk++ v+a +fS+ A+ kIe aGG+++
  gi|91772105|ref|YP_564797.1| 102 LADL----------EIeKVLGTGKVTKNMVVTACNFSEVARGKIETAGGSCV 143
                                   ****..........999*********************************97 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 ?   13.9   0.1   4.3e-06     0.026      96     122 ..     119     145 ..     109     147 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-06
                 Ribosomal_L18  96 klsvaALrftetararilkaGGeiltl 122
                                   ++ v+A +f+e ar +i+ aGG ++ l
  gi|91772105|ref|YP_564797.1| 119 NMVVTACNFSEVARGKIETAGGSCVEL 145
                                   4899********************876 PP

>> FoP_duplication  C-terminal duplication domain of Friend of PRMT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  10.0    0.0016       9.5       6      48 ..       4      45 ..       1      48 [. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0016
               FoP_duplication  6 rarrggggrggrrgrgrggrggrggrgrgrggrggrkkkkplt 48
                                  r+ ++++ rg r+ +g++++++rg ++rg +gr g ++k++ t
  gi|91772105|ref|YP_564797.1|  4 RKCNTKKFRGSRTCGGGTTKNRRGAGNRGGRGRSG-ENKHHFT 45
                                  56678899999999999999998888888888888.7777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1178.57
//
Query:       gi|91772106|ref|YP_564798.1|  [L=492]
Description: preprotein translocase subunit SecY [Methanococcoides burtonii DSM 6242]
Scores for 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-64  216.8  25.5    4.8e-64  216.5  25.5    1.1  1  SecY             SecY translocase
    5.5e-12   45.3   1.0    5.5e-12   45.3   1.0    2.0  2  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.5  25.5   5.4e-68   4.8e-64       1     306 []      72     470 ..      72     470 .. 0.83

  Alignments for each domain:
  == domain 1  score: 216.5 bits;  conditional E-value: 5.4e-68
                                   BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC............... CS
                          SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg............... 65 
                                   s++ LGI+P++tasI+lqLl ++    + +l+  ++++++ ++++++++++v+++++al  +++ g               
  gi|91772106|ref|YP_564798.1|  72 SLMLLGIGPIVTASIVLQLLvGA---DVIKLNMSDPADQAFFQGAQKFMVFVMIILEALPQIVG-Gyiqpdagvasalgvg 148
                                   89******************999...666677679***********************997755.4578999999999999 PP

                                   ..HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS...............-HHHH......... CS
                          SecY  66 ..lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals...............gliel......... 120
                                     +++++i++q+++g+vl+++++E ++++GiG+G+ l+i+ag+++++++ l                +   +         
  gi|91772106|ref|YP_564798.1| 149 lgAVTAIIFIQICIGGVLILFMDEIVSKWGIGSGVGLFIVAGVSQQIVTGLFnwgldttglpigilpK---Wiyivqnvgl 226
                                   997799******************************************66654777777777644441...2444444555 PP

                                   ...SS.........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETTCCCSCHHHHHHHHHH. CS
                          SecY 121 ...ale.......gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlklnyagviPiIfasslla. 189
                                      a +        i   +l+l+ t++++l+vv+ve+++++ip+ ++  r    g+++++P+kl+ya+v+P+I++++l+a 
  gi|91772106|ref|YP_564798.1| 227 dyiA-TsegvmflLIRGGILALISTVAIFLMVVFVESTRIEIPLAHSaVR----GARGRFPVKLIYASVLPMILVRALQAn 302
                                   5441.14544444333789***************************9778....9*************************7 PP

                                   .........................................HHHCCCCS.......TCCCSTHHHHHHHHHHHHHH....H CS
                          SecY 190 .........................................lpstiaqfl......lallspsvlyvvlyvlliif....F 219
                                                                            +ps + +++      +  +++  l+v++ ++++i+    F
  gi|91772106|ref|YP_564798.1| 303 lqmiglllsgrginvlgeyygstpingimyyispinspydwIPSLVRETFtgygapVPSMWQVGLHVFVDAFFLIAggiiF 383
                                   77777777777777777777776666666666666655555444444444565555222234456889998888888888* PP

                                   HHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHH CS
                          SecY 220 ayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLiv 298
                                   a f++e+t + +k +a++  +sg++ipg+r +  +++k++ ++++++t+iG++f++++++l++llg+  ig  ggt+lL++
  gi|91772106|ref|YP_564798.1| 384 ALFWIETTgMGAKPTAQKVFNSGMQIPGFRrNVGSIEKVMLRYIPKVTIIGGAFIGVLTLLASLLGT--IGGAGGTGLLLT 462
                                   ******************************9************************************..999********* PP

                                   HHHHHHHH CS
                          SecY 299 Vgvaletv 306
                                   V+++++++
  gi|91772106|ref|YP_564798.1| 463 VSIVYRLY 470
                                   ****9875 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   1.0   6.1e-16   5.5e-12       1      35 []      38      71 ..      38      71 .. 0.97
   2 ?   -2.8   0.2      0.69   6.2e+03       9      25 ..     325     343 ..     323     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 6.1e-16
                                  HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
               Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                  +lY+ l++iPL+G+s s+s+D+f+++Ra fA+++G
  gi|91772106|ref|YP_564798.1| 38 VLYFALANIPLFGLS-SDSIDLFEQYRAFFAGASG 71
                                  79************9.9***************998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.69
                                   SB-TT--..SSS-TCCHTT CS
               Plug_translocon   9 iPLyGis..sssssDpfyw 25 
                                   +P+ Gi    s ++ p+ w
  gi|91772106|ref|YP_564798.1| 325 TPINGIMyyISPINSPYDW 343
                                   7888998887788888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); 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):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3076.36
//
Query:       gi|91772107|ref|YP_564799.1|  [L=215]
Description: adenylate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-56  189.5   0.0    4.3e-56  189.2   0.0    1.0  1  ADK              Adenylate kinase
      5e-28   98.2   0.0    1.4e-27   96.8   0.0    1.6  2  AAA_17           AAA domain
    1.6e-15   56.7   3.7    1.9e-15   56.5   2.6    1.7  2  ADK_lid          Adenylate kinase, active site lid
    1.6e-05   25.2   0.0       0.19   12.0   0.0    2.2  2  Hydin_ADK        Hydin Adenylate kinase-like domain
    0.00052   20.6   0.0      0.001   19.6   0.0    1.7  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.013   15.3   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
       0.02   15.1   0.0      0.037   14.2   0.0    1.5  1  AAA_33           AAA domain
      0.024   14.9   0.0      0.033   14.4   0.0    1.3  1  AAA_28           AAA domain
      0.064   13.0   0.0       0.12   12.1   0.0    1.5  1  AAA_24           AAA domain
       0.12   12.8   0.0       0.21   12.0   0.0    1.4  1  AAA              ATPase family associated with various cellul
       0.12   12.0   0.0       0.22   11.2   0.0    1.4  1  Thymidylate_kin  Thymidylate 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 !  189.2   0.0   2.6e-59   4.3e-56       1     150 [.       5     189 ..       5     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 2.6e-59
                                   EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllDG 81 
                                   l G+PgaGKGtqa++l k+y+++h+stGd+lRa+v+ gt+lGkeak +mdkgelvpdev+++++k++l+++d+k g+llDG
  gi|91772107|ref|YP_564799.1|   5 LFGPPGAGKGTQAKELDKHYQIPHISTGDILRANVRDGTKLGKEAKGYMDKGELVPDEVLIGVIKNRLAESDCKPGYLLDG 85 
                                   68******************************************************************************* PP

                                   B-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT...................................GSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................xxxxx RF
                           ADK  82 fPRtveqaealeelleeekvkldlvleldvpeevlveRltg...................................Dneet 127
                                   +PRt++qa+al ++l e ++ l++vl++dv +e lv+Rl g                                   D+e+ 
  gi|91772107|ref|YP_564799.1|  86 YPRTTPQADALSSILVEIGMPLEVVLNIDVADEELVTRLCGryvctcgesyhmkfnppkkenvcdacgadlyqrddDKEDV 166
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK 128 vkkRletykkqtkplidyykkkg 150
                                   +++Rl+ yk++t+pli+yy +kg
  gi|91772107|ref|YP_564799.1| 167 IRQRLDSYKEKTQPLISYYGEKG 189
                                   *******************9886 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   8.7e-31   1.4e-27       1     122 [.       6     127 ..       6     135 .. 0.94
   2 ?   -1.5   0.1       1.9   3.1e+03     109     120 ..     160     171 ..     145     179 .. 0.64

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 8.7e-31
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79 
                                   +G+PG+GKgtq+++l ++y+++h+s+Gd+lr+++++g +l ++a+++m+k++l++++ l   +++++ae ++k g+l+dg+
  gi|91772107|ref|YP_564799.1|   6 FGPPGAGKGTQAKELDKHYQIPHISTGDILRANVRDGtKLgKEAKGYMDKGELVPDEVLIGVIKNRLAESDCKPGYLLDGY 86 
                                   6*********************************9995567999************************************* PP

                                   SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                        AAA_17  80 prikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                   pr+  qa++l+ + +e+   l  ++++ +++ +ee++ r+  +
  gi|91772107|ref|YP_564799.1|  87 PRTTPQADALSSILVEIGMPL--EVVLNIDVADEELVTRLCGR 127
                                   ***************988777..99999***********9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                   E--HHHHHHHHH CS
                        AAA_17 109 eadpeeilerrl 120
                                   ++d+e+++++rl
  gi|91772107|ref|YP_564799.1| 160 DDDKEDVIRQRL 171
                                   444555555554 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.5   7.4e+03      25      34 ..     114     123 ..     114     123 .. 0.80
   2 !   56.5   2.6   1.2e-18   1.9e-15       1      36 []     127     161 ..     127     161 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                                   TTT--.-B-- CS
                       ADK_lid  25 DkCGepLvqR 34 
                                   D+  e+Lv+R
  gi|91772107|ref|YP_564799.1| 114 DVADEELVTR 123
                                   566799**99 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 1.2e-18
                                   EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                       ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                   R vC  CG+sYh++fnpPk+e++CD CG +L+qR+D
  gi|91772107|ref|YP_564799.1| 127 RYVCT-CGESYHMKFNPPKKENVCDACGADLYQRDD 161
                                   99**6.*****************************9 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00016      0.27       2      41 ..       3      42 ..       2      51 .. 0.83
   2 !   12.0   0.0   0.00012      0.19     170     197 ..      58      85 ..      46      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                     Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdg 41
                                  +++ G+P +GK + a  L k+Y++  ++  +++   + dg
  gi|91772107|ref|YP_564799.1|  3 VVLFGPPGAGKGTQAKELDKHYQIPHISTGDILRANVRDG 42
                                  7899********************9999888776655554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00012
                     Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                   + P+++l+ ++  Rl  +dC  G ++Dg
  gi|91772107|ref|YP_564799.1|  58 LVPDEVLIGVIKNRLAESDCKPGYLLDG 85 
                                   68*************************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.4e-07     0.001       1      36 [.       3      43 ..       3     129 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.4e-07
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakeng 36
                                  ++l G+pG+GK t akeL k+ ++     g++lr +++++ 
  gi|91772107|ref|YP_564799.1|  3 VVLFGPPGAGKGTQAKELDKHYQIphistGDILRANVRDGT 43
                                  789***************99966687788666666555533 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   7.8e-06     0.013       3      35 ..       5      37 ..       3     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.8e-06
                                  EE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHH CS
                Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyldtgalYRa 35
                                  + GP g+GK++ a++l ++ ++  ++tg + Ra
  gi|91772107|ref|YP_564799.1|  5 LFGPPGAGKGTQAKELDKHYQIPHISTGDILRA 37
                                  56****************************997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.037       2      40 ..       3      44 ..       3     130 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrr.rlfg..t 40
                                  v+l G+pG+GK t a++l k+ +  ++s+ +++r +++   +
  gi|91772107|ref|YP_564799.1|  3 VVLFGPPGAGKGTQAKELDKHYQIPHISTGDILRaNVRDgtK 44
                                  6899***************99999999986665525555542 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05     0.033       1      44 [.       2      48 ..       2      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                        AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakged 44
                                  ++v++G++++GK t +++L ++ ++p++   ++ r  ++++++ g++
  gi|91772107|ref|YP_564799.1|  2 NVVLFGPPGAGKGTQAKELDKHyQIPHIstGDILRANVRDGTKLGKE 48
                                  59*******************98999887788888888887766654 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   7.1e-05      0.12       4      24 ..       2      21 ..       1      53 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                        AAA_24  4 kiliyGpsgiGKTtlakelgp 24
                                  +++++Gp+g+GK t+akel +
  gi|91772107|ref|YP_564799.1|  2 NVVLFGPPGAGKGTQAKEL-D 21
                                  799***************9.3 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.21       1      26 [.       3      28 ..       3      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                  EEEESSTTSSHHHHHHHHHHHHTHEE CS
                           AAA  1 vllyGppGtGKTllakavakelgvef 26
                                  v+l+GppG GK + ak + k+ +++ 
  gi|91772107|ref|YP_564799.1|  3 VVLFGPPGAGKGTQAKELDKHYQIPH 28
                                  689**************999876553 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.22       3      65 ..       7      71 ..       7      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                  ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHH CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfaadr 65
                                  G  GaGK tqa+ l ++++  +i+   +++    +gt++G+ +++++  + el +  +++   ++r
  gi|91772107|ref|YP_564799.1|  7 GPPGAGKGTQAKELDKHYQIPHIStgdILRANVRDGTKLGKEAKGYMD-KGELVPDEVLIGVIKNR 71
                                  5669***************9999888889999999***********98.76666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1560.48
//
Query:       gi|91772108|ref|YP_564800.1|  [L=206]
Description: hypothetical protein Mbur_0026 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-48  163.7   7.2    3.9e-48  163.4   7.2    1.1  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
      0.076   12.9   0.2       0.16   11.8   0.0    1.6  2  HPIH        N-terminal domain with HPIH motif
      0.099   12.8   0.3       0.15   12.3   0.3    1.2  1  RRF_GI      Ribosome recycling factor


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 !  163.4   7.2   6.6e-52   3.9e-48       2     169 ..      42     204 ..      41     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 6.6e-52
                    EMC3_TMCO1   2 lvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelme 82 
                                   +++dp + +     ++i++++++++t+l+++l+qk++id++ m+++q+r+k +qk++re+q +++  + kkle++++++m+
  gi|91772108|ref|YP_564800.1|  42 VFMDPISMMVGEGNFHIMLFIMAAITALYASLIQKYTIDWDLMRNTQERMKSFQKEFREAQLSQNTYMVKKLEEQRADMMG 122
                                   56788888888889******************************************************************* PP

                    EMC3_TMCO1  83 dqsemmmdqmkpmivtmipqiliffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqiir 163
                                   dq+em+++q+kpm+++ i+++++f+w ++++sg+  a l fp++g+   l     e++ ++++++i+wYf++s+++sq++r
  gi|91772108|ref|YP_564800.1| 123 DQMEMSKQQFKPMAYISIISLPLFMWAYHYISGHPGASLEFPFWGTQI-LV----ETVIGPIQYWIFWYFITSLAISQVVR 198
                                   *********************************************998.55....9************************* PP

                    EMC3_TMCO1 164 klLgea 169
                                   k+L+++
  gi|91772108|ref|YP_564800.1| 199 KALNIG 204
                                   ***986 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 ?   11.8   0.0   2.7e-05      0.16      19      63 ..      57      96 ..      56     131 .. 0.76
   2 ?   -2.5   0.0      0.66   3.9e+03      30      44 ..     135     149 ..     132     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                          HPIH 19 htIvvvallasttYlsvleeslfdwkldsksissagkvdvdsLle 63
                                  h++++++   ++ Y s+++++  dw l ++++        +s+++
  gi|91772108|ref|YP_564800.1| 57 HIMLFIMAAITALYASLIQKYTIDWDLMRNTQERM-----KSFQK 96
                                  8888888888999*************999887764.....34444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.66
                          HPIH  30 ttYlsvleeslfdwk 44 
                                   ++Y+s++   lf w 
  gi|91772108|ref|YP_564800.1| 135 MAYISIISLPLFMWA 149
                                   689999998888886 PP

>> RRF_GI  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   2.4e-05      0.15      42      92 ..      80     132 ..      76     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                        RRF_GI  42 nWqlkge.aeklqslleelkakeeesleylikkietalleh.adklepleekL 92 
                                   +W l+ + +e+++s+ +e ++ + ++ +y++kk+e++ ++   d++e  +++ 
  gi|91772108|ref|YP_564800.1|  80 DWDLMRNtQERMKSFQKEFREAQLSQNTYMVKKLEEQRADMmGDQMEMSKQQF 132
                                   58776651568***********************9998765157777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1593  (0.0888505); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1514.97
//
Query:       gi|91772109|ref|YP_564801.1|  [L=175]
Description: cytidylate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   75.1   0.6    1.1e-19   71.3   0.6    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    3.1e-11   43.9   0.0    4.3e-11   43.5   0.0    1.3  1  AAA_18           AAA domain
    3.3e-11   43.8   0.1    6.3e-11   42.9   0.1    1.6  1  AAA_17           AAA domain
    1.9e-08   34.3   1.5    0.00049   19.9   0.3    2.1  2  Cytidylate_kin   Cytidylate kinase
    6.8e-05   23.0   0.2    0.00042   20.4   0.0    2.1  2  ADK              Adenylate kinase
    0.00016   21.9   0.3       0.42   10.7   0.0    2.1  2  SKI              Shikimate kinase
     0.0035   17.0   1.2        1.7    8.3   0.1    2.1  2  CoaE             Dephospho-CoA kinase
  ------ inclusion threshold ------
      0.044   13.9   0.3        3.1    7.9   0.0    2.2  2  AAA_33           AAA domain
       0.13   12.1   0.8        5.8    6.7   0.1    2.1  2  dNK              Deoxynucleoside kinase
       0.16   12.3   0.1       0.29   11.5   0.0    1.4  1  Sulfotransfer_3  Sulfotransferase family


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 !   71.3   0.6     6e-23   1.1e-19       3     179 .]       4     155 ..       2     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 6e-23
               Cytidylate_kin2   3 TIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldeklddelf 82 
                                   TIs+  Gsg +t+g+ LAe++ +++++  ++++ +ake g++ +e+ ++ e  +                  d ++d e+ 
  gi|91772109|ref|YP_564801.1|   4 TISGLPGSGTTTVGKLLAEHYSVDIISAgDVFRGLAKERGVTLAEFGRLAE--S------------------DPSIDVEID 64 
                                   9*********************************************99999..2..................678999999 PP

               Cytidylate_kin2  83 eaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytgq 163
                                   ++q+++ ++    ++ ++ GR a  + k+   +l++++ aple+rvkr+ +reg s +   ++  e++  +a +yk++++ 
  gi|91772109|ref|YP_564801.1|  65 KRQSDIANSS---DNLILEGRLAGQMAKK---ALKIWIKAPLEVRVKRIVDREGSSFDVRMQETVEREASEALRYKEIHSI 139
                                   99***99988...59*********66665...************************8877788888889999********* PP

               Cytidylate_kin2 164 dwgdaenYdlvlntsk 179
                                   d++d + Ydlv+++s+
  gi|91772109|ref|YP_564801.1| 140 DIHDLSVYDLVIDSSR 155
                                   **************95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   2.4e-14   4.3e-11       3     124 ..       5     126 ..       3     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.4e-14
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlv 78 
                                   ++G pG+G tt++k L+++  +     g++ r +ake+g  l ++    ++   +d + +++ +d+ +         +nl+
  gi|91772109|ref|YP_564801.1|   5 ISGLPGSGTTTVGKLLAEHYSVdiisaGDVFRGLAKERGVTLAEFGRLAESDPSIDVEIDKRQSDIANS-------SDNLI 78 
                                   89****************965599***********************3333334444444444444444.......489** PP

                        AAA_18  79 idghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik.....ene 124
                                   ++g+la     +a +   ++++a+ e++ +R+ +R+ ++ + +     e e
  gi|91772109|ref|YP_564801.1|  79 LEGRLAGQMAKKALK---IWIKAPLEVRVKRIVDREGSSFDVRmqetvERE 126
                                   *********999987...******************998877766444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.1   3.5e-14   6.3e-11       2      97 ..       7      97 ..       6     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.5e-14
                                  E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEE CS
                        AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdghprik 83
                                  G+PGsG +t+ + l+e+y + ++saGd++r  ak++g    +++++++ + +++ e++k+   +ia+  ++++++++g    +
  gi|91772109|ref|YP_564801.1|  7 GLPGSGTTTVGKLLAEHYSVDIISAGDVFRGLAKERGVtLAEFGRLAESDPSIDVEIDKRQS-DIAN--SSDNLILEGRLAGQ 86
                                  9************************************8445667777777777777777765.4665..5889*****99654 PP

                                  ETTEEEESSHHHHH CS
                        AAA_17 84 eqagfldglpkevl 97
                                    +++l   + +++
  gi|91772109|ref|YP_564801.1| 87 MAKKAL---KIWIK 97
                                  333332...22222 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.6e-05     0.029       2      37 ..       4      39 ..       3      55 .. 0.92
   2 !   19.9   0.3   2.8e-07   0.00049      95     164 ..      56     123 ..      45     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                  EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                  +i G  gsG  +v+++lae+ ++ ++++g ++R la
  gi|91772109|ref|YP_564801.1|  4 TISGLPGSGTTTVGKLLAEHYSVDIISAGDVFRGLA 39
                                  788999***************************887 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.8e-07
                                   SHHHHHHHHHHHHTT-B.SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHH CS
                Cytidylate_kin  95 ipavRailvkklrelvk.karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleell 164
                                    p++  ++ k++ ++++ ++++++eGR  g  + +   lKi+++A  e+R+kR ++  + ++++v ++e +
  gi|91772109|ref|YP_564801.1|  56 DPSIDVEIDKRQSDIANsSDNLILEGRLAGQ-MAK-KALKIWIKAPLEVRVKRIVDR-EGSSFDVRMQETV 123
                                   577888999*******999********7775.445.55*************987665.5555665554433 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.3e-07   0.00042       1      36 [.       5      40 ..       5      55 .. 0.88
   2 ?    0.3   0.0      0.38   6.9e+02      93     135 ..      80     122 ..      70     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                                  EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                  + G Pg+G  t+ + l+++y++  +s+Gd++R   k
  gi|91772109|ref|YP_564801.1|  5 ISGLPGSGTTTVGKLLAEHYSVDIISAGDVFRGLAK 40
                                  579*****************************7665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.38
                                   HHHHHHHTSEESEEEEEE--HHHHHHHHHTGSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  93 eelleeekvkldlvleldvpeevlveRltgDneetvkkRlety 135
                                   e  l+ + +k  l + +++p ev v+R+++ +  +   R+++ 
  gi|91772109|ref|YP_564801.1|  80 EGRLAGQMAKKALKIWIKAPLEVRVKRIVDREGSSFDVRMQET 122
                                   5556666666777788888889999999885555555555543 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00024      0.42       1      23 [.       9      31 ..       9      50 .. 0.86
   2 !    9.7   0.0   0.00047      0.85      73     133 ..      78     135 ..      61     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                  TTSSHHHHHHHHHHHHTSEEEEH CS
                           SKI  1 mGaGKstvGkllAkklglefiDl 23
                                  +G+G +tvGkllA++++++ i +
  gi|91772109|ref|YP_564801.1|  9 PGSGTTTVGKLLAEHYSVDIISA 31
                                  69**************9998865 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00047
                                   GGSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCC CS
                           SKI  73 vlseenrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyee 133
                                   +l+ +    +++k++ i+++++le+ ++r+ +++    +  +++e+ ++e    +   y+e
  gi|91772109|ref|YP_564801.1|  78 ILEGRLAGQMAKKALKIWIKAPLEVRVKRIVDREG-SSFDVRMQETVEREAS--EALRYKE 135
                                   5566667778899*****************98888.4555555533333332..3333444 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00096       1.7       2      46 ..       2      47 ..       1      56 [. 0.85
   2 !    8.2   0.2     0.001       1.8     122     162 ..      91     131 ..      55     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00096
                                  EEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHH CS
                          CoaE  2 ivgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealk 46
                                  ++ ++G  +sG +tv +l+a+ ++v+i+ a  v r + ++   +l+
  gi|91772109|ref|YP_564801.1|  2 LLTISGLPGSGTTTVGKLLAEhYSVDIISAGDVFRGLAKERGVTLA 47
                                  56789999************99*******99998888777766665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                                   SSEEEEEE--HHHHHHHHHHCCTSTHH.HHHHHHHHS--HHH CS
                          CoaE 122 iervlvvdvelelqveRlvardgvsee.evkaiiaaQlseee 162
                                   +   + ++++le +v+R+v+r+g s +  +++ ++  +se+ 
  gi|91772109|ref|YP_564801.1|  91 AL-KIWIKAPLEVRVKRIVDREGSSFDvRMQETVEREASEAL 131
                                   32.3458999************98864256666666666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0017       3.1       2      41 ..       3      42 ..       2      88 .. 0.78
   2 ?    4.5   0.1     0.021        37      94     125 ..      86     118 ..      81     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtd 41
                                  + + GlpGsG +t+ + l+++  + ++s  +++r l+++ 
  gi|91772109|ref|YP_564801.1|  3 LTISGLPGSGTTTVGKLLAEHYSVDIISAGDVFRGLAKER 42
                                  5678***********9999888888888888777777654 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.021
                        AAA_33  94 rlgvpvrivvvetdeetlkeRlakRaang.ddr 125
                                   ++  + + ++++++ e+  +R+  R+ ++ d+r
  gi|91772109|ref|YP_564801.1|  86 QMAKKALKIWIKAPLEVRVKRIVDREGSSfDVR 118
                                   555566679*****************9865443 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0033       5.8       1      27 [.       3      29 ..       3      34 .. 0.89
   2 ?    4.4   0.1     0.017        30     119     186 ..      86     150 ..      63     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0033
                                  EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                  ++++G  g+G +t+ klL++++ v ++
  gi|91772109|ref|YP_564801.1|  3 LTISGLPGSGTTTVGKLLAEHYSVDII 29
                                  589*****************9988765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.017
                                   HCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TT CS
                           dNK 119 elakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidveeldlv 186
                                   ++ak  l i++ka+le+ ++ri  R+ +     + +  e+++++ +e+l+  +  ++ + d + +dlv
  gi|91772109|ref|YP_564801.1|  86 QMAKKALKIWIKAPLEVRVKRIVDREGSS---FDVRMQETVEREASEALRYKEIHSIDIHDLSVYDLV 150
                                   56678899**************9997654...444555555555555555544444555555555544 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.29       4      26 ..       5      27 ..       3      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                  EE--TTSSHHHHHHHHHTSTTEE CS
               Sulfotransfer_3  4 ivGlpRSGTTlLhrlLaahpdvr 26
                                  i Glp SGTT + +lLa+h +v 
  gi|91772109|ref|YP_564801.1|  5 ISGLPGSGTTTVGKLLAEHYSVD 27
                                  88****************98854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1149.61
//
Query:       gi|91772110|ref|YP_564802.1|  [L=331]
Description: H/ACA RNA-protein complex component Cbf5p [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-26   91.4   0.4    3.6e-22   79.4   0.4    3.1  1  TruB_N    TruB family pseudouridylate synthase (N terminal do
    2.1e-24   85.5   0.0    3.8e-24   84.6   0.0    1.5  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    7.2e-15   54.8   0.0    1.4e-14   53.9   0.0    1.4  1  DKCLD     DKCLD (NUC011) domain
    1.1e-14   54.1   0.2    2.6e-14   52.9   0.2    1.7  1  PUA       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 !   79.4   0.4   7.9e-26   3.6e-22       1     148 [.      62     174 ..      62     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 7.9e-26
                                   HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHH CS
                        TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevl 81 
                                   + +l++kk+Gh+G+LDp +tG+L+v++g+aTk+++ l  + KeY+++++l+ +                  + ++k+++++
  gi|91772110|ref|YP_564802.1|  62 RDMLGVKKAGHSGSLDPHVTGLLPVMLGRATKAVSALRLSGKEYICVMHLHDD------------------IPDRKIRKAC 124
                                   6799*********************************************9753..................3345799*** PP

                                   HHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                        TruB_N  82 kkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                   k+ftG i+q+pp++SAvk                 r+ r  +iy l++le+e +ev ++v c++GtY
  gi|91772110|ref|YP_564802.1| 125 KEFTGPIYQTPPIISAVK-----------------RQLRIRNIYYLDVLEIEGREVLMRVGCEAGTY 174
                                   ******************.................999***************************** 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 !   84.6   0.0   8.4e-28   3.8e-24       1      63 [.     176     241 ..     176     242 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 8.4e-28
                                   HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                      TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                   R+Lc+DiG++Lgcg+h+++LRRt +gpf e+ +v+l dL+da+ +++e  de+ L++l++P+e+ l
  gi|91772110|ref|YP_564802.1| 176 RKLCHDIGLVLGCGGHMKQLRRTGTGPFREDTLVSLYDLKDACVFWQEdgDESeLRKLVRPMEEGL 241
                                   9***********************************************887779*********976 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0     3e-18   1.4e-14      11      57 ..      11      57 ..       7      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3e-18
                                  XX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHH CS
                         DKCLD 11 ydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEV 57
                                  ++ ++ + ++ t+  +G+ P  Rpi eyi++Gv+n+DK  +P+SHEV
  gi|91772110|ref|YP_564802.1| 11 VNIMVEKFHATTNAAYGCLPQDRPILEYINMGVVNIDKAIGPTSHEV 57
                                  556777888899**********************************9 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.2   5.9e-18   2.6e-14       1      73 [.     245     317 ..     245     318 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 5.9e-18
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                   +++++ d+Av+a+++gasL +pG+v++ + ++++d +a+++ +ge+va+ ++ ++++el+   +g++  +erv
  gi|91772110|ref|YP_564802.1| 245 PKIIIRDSAVDAVCRGASLAVPGIVSFSKCIQKDDKIAVFTLKGEAVALCRSFMNADELENESHGIACITERV 317
                                   69**********************************************************9999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2260.12
//
Query:       gi|91772111|ref|YP_564803.1|  [L=172]
Description: death-on-curing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-07   30.3   0.3    1.5e-06   29.0   0.2    1.9  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 !   29.0   0.2   8.3e-11   1.5e-06      50      97 .]      41      87 ..       7      87 .. 0.88
   2 ?   -3.0   0.0      0.81   1.5e+04      44      57 ..     110     123 ..      95     132 .. 0.55

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8.3e-11
                                  HHHHHHHCHHT-S-HHHHHHHHHHHHHHH--SSS-HHHHHHHHHHHHH CS
                           Fic 50 eelleylnelekeeplekaaalhyefekiHPFaDGNgRtarlllnllL 97
                                  e l+e+   +++++p+  aa ++ ++++ H+F++GN+Rt++++++ lL
  gi|91772111|ref|YP_564803.1| 41 EGLFEWRV-SNDNSPIRNAALILDSITRRHAFNNGNKRTGFAVASILL 87
                                  45566666.88999*****************************99876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.81
                                   CHHHHHHHHHHHHC CS
                           Fic  44 evpaeleelleyln 57 
                                   + ++e+e+ + +l+
  gi|91772111|ref|YP_564803.1| 110 KYQMEVEDTELWLT 123
                                   33444444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 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:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1275.00
//
Query:       gi|91772112|ref|YP_564804.1|  [L=405]
Description: hypothetical protein Mbur_0030 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   42.1  17.5     0.0088   16.0   0.3    4.6  4  Cytochrome_C7    Cytochrome c7 and related cytochrome c
    3.7e-10   39.3  12.8    1.1e-07   31.1   0.1    3.5  3  Cytochrom_C552   Cytochrome c552
    1.1e-07   32.2  17.6      0.021   15.2   1.8    4.2  4  Cytochrom_c3_2   Cytochrome c3
    2.8e-05   23.7  30.1       0.08   12.7   1.3    5.7  5  Paired_CXXCH_1   Doubled CXXCH motif (Paired_CXXCH_1)
    0.00042   21.2  27.2       0.44   11.5   2.4    5.9  4  Cytochrome_C554  Cytochrome c554 and c-prime
     0.0051   17.1  17.2        1.1    9.7   6.0    3.9  3  Cytochrom_CIII   Class III cytochrome C family
  ------ inclusion threshold ------
       0.25   11.3   0.9        1.6    8.7   0.2    2.6  2  YokU             YokU-like protein, putative antitoxin
       0.96    9.1  22.9        1.2    8.8   0.2    5.6  4  Cytochrom_NNT    NapC/NirT cytochrome c family, N-terminal re


Domain annotation for each model (and alignments):
>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   3.9e-06    0.0088      48      73 .]      40      68 ..      25      68 .. 0.83
   2 !   14.9   1.0   8.7e-06     0.019      12      72 ..      91     183 ..      80     184 .. 0.64
   3 !    9.0   2.2   0.00061       1.4      48      73 .]     177     204 ..     162     204 .. 0.72
   4 !   14.3   4.1   1.4e-05     0.031      15      73 .]     198     282 ..     192     308 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                 Cytochrome_C7 48 ltCgaCHdgknaf...svakkaeCakCHt 73
                                   +Cg+CH ++ a    s ++ a+C+ CHt
  gi|91772112|ref|YP_564804.1| 40 EECGDCHGETYAVwssSPHGSASCEICHT 68
                                  46**********666688899*******7 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.7e-06
                 Cytochrome_C7  12 tgykCtdCHsklfeska.k..kkmaemekgkskkaeves.lt..........CgaCHdgknaf.................. 60 
                                   ++  C dCHs+++  ++ +  +  a+++++ + +++  + ++          C aC   +                     
  gi|91772112|ref|YP_564804.1|  91 SSEVCGDCHSGVY-DEWnEfgE--ADFDMEAIASHSEPTeVAepyvlnsgasCVACKSTDGGIlniadaepyaldeggihd 168
                                   4578********5.33323232..3333333333333332224556778888****9988886667777788888888888 PP

                 Cytochrome_C7  61 ...svakkaeCakCH 72 
                                       ++ + +Ca CH
  gi|91772112|ref|YP_564804.1| 169 levVEEWAISCAACH 183
                                   8874556999****9 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00061
                 Cytochrome_C7  48 ltCgaCHdgknaf..svakkaeCakCHt 73 
                                    +C+aCHd   +      +   C++CH+
  gi|91772112|ref|YP_564804.1| 177 ISCAACHDPHDTGprIDDSVLLCGNCHN 204
                                   5699999998886554556789999995 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 1.4e-05
                 Cytochrome_C7  15 kCtdCHskl.feska.k....kk..maemekgkskkaeveslt........CgaCHdgknaf..................s 61 
                                    C +CH++  + +   +    ++  +   ++g    +     +        C +CH  +  +                  +
  gi|91772112|ref|YP_564804.1| 198 LCGNCHNTEgVVMDGnTpvvrHAqwELVSTSGY---V-----DgshptsigCVDCHMVQISNdevvetghtfdfdaerlsN 270
                                   699999998542222123332112211112222...2.....133334467*****9888877778888888888888875 PP

                 Cytochrome_C7  62 vakkaeCakCHt 73 
                                     + ++C+ CH+
  gi|91772112|ref|YP_564804.1| 271 PDSGNNCSLCHQ 282
                                   667999999996 PP

>> Cytochrom_C552  Cytochrome c552
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.6      0.13     3e+02     233     284 ..      50     100 ..      42     115 .. 0.63
   2 !   13.6   0.1   1.1e-05     0.024      85     142 ..     135     193 ..     112     200 .. 0.72
   3 !   31.1   0.1     5e-11   1.1e-07     228     367 ..     217     358 ..     210     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                   HHHHHTSHHHHTT--HHHHHS-EEETTSEEEE----S-GG.GGCCCTGGGT-- CS
                Cytochrom_C552 233 fElysegvHakngvsCaDCHmPkvkegakkvtdHkvtsPl.ksiekaCksCHk 284
                                   + ++s++ H++  +sC  CH +      ++++      P  +  ++ C  CH+
  gi|91772112|ref|YP_564804.1|  50 YAVWSSSPHGS--ASCEICHTASPGGFDAHISAPFTSAPNvSLSSEVCGDCHS 100
                                   56677777775..4777777666655555555555555541333366777775 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.1e-05
                                   SSBGGGGTTT-THHHHHHHHHHH.HHHCSSBCCCCTTT--S-S-HHHHB-TTTHHB--- CS
                Cytochrom_C552  85 kqpaaCltCkspdvprlieekge.edyfstkyaevgkeivnsvgCadCHdpkdmeLrit 142
                                   + +a+C+ Cks d   l  +++e  ++ ++  ++++   + +++Ca CHdp+d+  ri 
  gi|91772112|ref|YP_564804.1| 135 NSGASCVACKSTDGGILNIADAEpYALDEGGIHDLEVVEEWAISCAACHDPHDTGPRID 193
                                   7899***********988888873344455555555555567**********9987776 PP

  == domain 3  score: 31.1 bits;  conditional E-value: 5e-11
                                   ----HHHHHHTS..HHHH..TT--HHHHHS-EEETTSEEEE----S-GGGGCC.....CTGGGT--S-HHHHHHHHHHHHH CS
                Cytochrom_C552 228 iqHPefElyseg..vHak..ngvsCaDCHmPkvkegakkvtdHkvtsPlksie.....kaCksCHkqseeeLkeqveaiqe 299
                                   ++H ++El s++  v ++    + C+DCHm ++++++ + t H      ++++     + C  CH+ s + L e+ +a  e
  gi|91772112|ref|YP_564804.1| 217 VRHAQWELVSTSgyVDGShpTSIGCVDCHMVQISNDEVVETGHTFDFDAERLSnpdsgNNCSLCHQSSLASLIEDKQAPIE 297
                                   789999997754122332114699*******************98744443333336689********9999999999999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHHHHHSSTTHHHHSHHHHHHHH CS
                Cytochrom_C552 300 rvaelklraedalvkahkeakkaedagateeelkearelirkaqwrldfvaAensagfHaPeealrvl 367
                                   ++++  + ++++  +a + ++ ++  +         r ++ ++q+ l  ++ + s g+H+ e +++ l
  gi|91772112|ref|YP_564804.1| 298 SHISALNSLKEKAGNALESINGTDSYE-------AQRANYNNGQFYLTKIENDGSLGIHNLETVTNDL 358
                                   999999998888888888887775544.......4688999999999999999999999988776655 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.8   9.6e-06     0.021       8      67 ..      41     101 ..      37     109 .. 0.77
   2 !   14.1   4.0   2.2e-05      0.05      28      80 .]     118     204 ..      95     204 .. 0.59
   3 !   11.9   8.9    0.0001      0.23       7      73 ..     177     253 ..     173     284 .. 0.73
   4 !    7.1   2.7    0.0032       7.3       7      37 ..     239     285 ..     234     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-06
                                   TGGGTSSSST.-SSTTHHHHHHHHHHH--HHHCHTTSST.TSSBTTSSCTSSS-GGGTS-T CS
                Cytochrom_c3_2   8 kCadCHtkek.pkkdkaveeekClsCHgkleelakktkeakeanphkshekeleCteCHke 67 
                                   +C dCH+++  + +++ + +++C+ CH       +++ +a  +++ +   ++  C +CH++
  gi|91772112|ref|YP_564804.1|  41 ECGDCHGETYaVWSSSPHGSASCEICHTASPGGFDAHISAPFTSAPNVSLSSEVCGDCHSG 101
                                   7******7763445669999********99877777766555555566678889*****86 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.2e-05
                                   H.....................HHHHH--HHHCHTTSST.....TSSBTTSSC...TSSS-GGGTS-TTT......SBT-G CS
                Cytochrom_c3_2  28 k.....................ClsCHgkleelakktkea....keanphksh...ekeleCteCHkeHk......ksekv 74 
                                   +                     C++C ++   + + ++ +    +e   h+     e  ++C++CH  H+      +s+ +
  gi|91772112|ref|YP_564804.1| 118 AiashseptevaepyvlnsgasCVACKSTDGGILNIADAEpyalDEGGIHDLEvveEWAISCAACHDPHDtgpridDSVLL 198
                                   1445555555555555555566999988887665544433344533344443222247789*********888877778** PP

                                   GGGT-S CS
                Cytochrom_c3_2  75 CaeCHe 80 
                                   C +CH+
  gi|91772112|ref|YP_564804.1| 199 CGNCHN 204
                                   *****6 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.0001
                                   .TGGGTSSSST-SSTTHHHHHHHHHHH--HHHCHTTSST...........TSSBTTSSCTSSS-GGGTS-TTTSBT- CS
                Cytochrom_c3_2   7 vkCadCHtkekpkkdkaveeekClsCHgkleelakktkea..........keanphkshekeleCteCHkeHkksek 73 
                                   ++Ca CH  +++  + + +   C +CH++   + + ++            ++  ++ sh +++ C +CH+   ++ +
  gi|91772112|ref|YP_564804.1| 177 ISCAACHDPHDTGPRIDDSVLLCGNCHNTEGVVMDGNTPVvrhaqwelvsTSGYVDGSHPTSIGCVDCHMVQISNDE 253
                                   78******88877667777888******99987775554467888888877777888999*********98764333 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0032
                                   .TGGGTSSSST-SSTTHHHHHH.................HHHHH--HH CS
                Cytochrom_c3_2   7 vkCadCHtkekpkkdkaveeek.................ClsCHgkle 37 
                                   + C dCH  + + +d+ ve+ +                 C  CH++  
  gi|91772112|ref|YP_564804.1| 239 IGCVDCHMVQIS-NDEVVETGHtfdfdaerlsnpdsgnnCSLCHQSSL 285
                                   678888887775.45666666667788888888888888999988653 PP

>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.3   3.6e-05      0.08       9      38 ..      42     100 ..      35     102 .. 0.66
   2 ?   -3.5   0.2         4   8.9e+03       8      12 ..     139     143 ..     134     145 .. 0.68
   3 !   12.2   6.0   5.1e-05      0.11       8      39 ..     178     205 ..     171     208 .. 0.83
   4 !    6.5   2.3    0.0032       7.2       7      39 ..     240     283 ..     235     286 .. 0.65
   5 ?    2.9   0.5     0.042        93       7      14 ..     275     282 ..     270     294 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                Paired_CXXCH_1   9 ClsCH.........nphgsdnpkll....................kkakgaalCysCHd 38 
                                   C +CH         +phgs+   +                      ++  +++C +CH+
  gi|91772112|ref|YP_564804.1|  42 CGDCHgetyavwssSPHGSASCEIChtaspggfdahisapftsapNVSLSSEVCGDCHS 100
                                   55565555555555555555555555555555555558888888888999********7 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4
                Paired_CXXCH_1   8 eClsC 12 
                                   +C +C
  gi|91772112|ref|YP_564804.1| 139 SCVAC 143
                                   58887 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 5.1e-05
                Paired_CXXCH_1   8 eClsCHnphgsdnpkllkkakgaalCysCHde 39 
                                   +C +CH+ph +  p++   ++   lC +CH++
  gi|91772112|ref|YP_564804.1| 178 SCAACHDPHDT-GPRI---DDSVLLCGNCHNT 205
                                   5********99.5554...6999*******87 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0032
                Paired_CXXCH_1   7 geClsCH.............nphgsdnpkllkkakgaalCysCHde 39 
                                   g C +CH             ++   d ++l  + +  + C  CH++
  gi|91772112|ref|YP_564804.1| 240 G-CVDCHmvqisndevvetgHTFDFDAERL-SNPDSGNNCSLCHQS 283
                                   5.*****77777666665332223334444.58999999****986 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.042
                Paired_CXXCH_1   7 geClsCHn 14 
                                   ++C+ CH+
  gi|91772112|ref|YP_564804.1| 275 NNCSLCHQ 282
                                   45777775 PP

>> Cytochrome_C554  Cytochrome c554 and c-prime
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   4.3    0.0014       3.1       2      22 ..      42      62 ..      41      70 .. 0.87
   2 !   11.5   2.4   0.00019      0.44       1      83 [.      94     183 ..      94     184 .. 0.54
   3 !    7.1   4.3    0.0047        11       2      84 .]     199     282 ..     198     282 .. 0.57
   4 ?    3.7   0.3     0.053   1.2e+02       2      44 ..     277     325 ..     276     357 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                  HHHHTHHHHHHHTTSTGGGTT CS
               Cytochrome_C554  2 CaeCHeeqyeswkkskhakal 22
                                  C +CH e y+ w++s+h +a 
  gi|91772112|ref|YP_564804.1| 42 CGDCHGETYAVWSSSPHGSAS 62
                                  *****************9875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00019
                                   HHHHHTHHHHHHHTTSTGGG.TTGGGSTTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTT...........STT---SSS CS
               Cytochrome_C554   1 aCaeCHeeqyeswkkskhak.aleslkkekkaeakkkakldpakdaeeapeClkCHatgag...........kdkgfvlke 69 
                                   +C +CH   y++w++   a+  +e + +++  e  +++  +p    ++ + C++C  t  g            d+g   + 
  gi|91772112|ref|YP_564804.1|  94 VCGDCHSGVYDEWNEFGEADfDMEAIASHS--E-PTEV-AEP-YVLNSGASCVACKSTDGGilniadaepyaLDEGGIHDL 169
                                   6************98876652233333322..2.2222.222.3356789******9976433333222222223223333 PP

                                   --GGGBSS-HHHHH CS
               Cytochrome_C554  70 ktkllagVqCesCH 83 
                                   +   +  ++C +CH
  gi|91772112|ref|YP_564804.1| 170 EVVEEWAISCAACH 183
                                   33333477888888 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0047
                                   HHHHTHHHHHHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTTSTT---SSS--GGGB....... CS
               Cytochrome_C554   2 CaeCHeeqyeswkkskhakaleslkkekkaeakkkakldpakdaeeapeClkCHatgagkdkgfvlkektklla....... 75 
                                   C +CH+++     ++      ++++  +     ++     + ++ ++  C++CH+  +++d++++  ++++  a       
  gi|91772112|ref|YP_564804.1| 199 CGNCHNTEGVVMDGNTPVVRHAQWELVS-----TSG--YVDGSHPTSIGCVDCHMVQISNDEVVETGHTFDFDAerlsnpd 272
                                   6666766666655544333333333222.....222..22345667899**********9999876655433222233444 PP

                                   .SS-HHHHH- CS
               Cytochrome_C554  76 .gVqCesCHg 84 
                                    g +C  CH+
  gi|91772112|ref|YP_564804.1| 273 sGNNCSLCHQ 282
                                   5999999995 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.053
                                   HHHHTHHHH......HHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS- CS
               Cytochrome_C554   2 CaeCHeeqy......eswkkskhakaleslkkekkaeakkkakldpakd 44 
                                   C+ CH++++      ++    +h +al+slk+++ +  ++  ++d  + 
  gi|91772112|ref|YP_564804.1| 277 CSLCHQSSLasliedKQAPIESHISALNSLKEKAGNALESINGTDSYEA 325
                                   999**98663333324444567888999998877666555555554444 PP

>> Cytochrom_CIII  Class III cytochrome C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   3.3    0.0008       1.8      32      87 ..      40     103 ..      34     149 .. 0.81
   2 !    9.7   6.0   0.00048       1.1      33      91 ..     178     253 ..     166     281 .. 0.61
   3 ?    4.1   1.6     0.026        58      49      86 ..     240     284 ..     230     300 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0008
                                   HTHHHTSTT.....CTTSCSTS-CTCTS-SSS...TTTSTTCHHHHHHCSSTTTCHHHHHHHHH CS
                Cytochrom_CIII  32 keCeeCHhk.....eeekeeiekcstcHaeek...ekkekkslekavHkkkaaksCvgCHkkkk 87 
                                   +eC +CH +      ++ +  ++c+ cH+ +    + + +  +++a   + +++ C +CH+   
  gi|91772112|ref|YP_564804.1|  40 EECGDCHGEtyavwSSSPHGSASCEICHTASPggfDAHISAPFTSAPNVSLSSEVCGDCHSGVY 103
                                   58*****9999985555667789999***99777766667777888887777799*****8665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00048
                                   THHHTSTT....CTTSCSTS-CTCTS-SSS..TTTSTTCHHHHHHCSSTT..............TCHHHHHHHHHHTSH CS
                Cytochrom_CIII  33 eCeeCHhk....eeekeeiekcstcHaeek..ekkekkslekavHkkkaa..............ksCvgCHkkkkkekk 91 
                                   +C++CH         ++++  c +cH++e       + ++  + H++ +                 Cv+CH  + ++++
  gi|91772112|ref|YP_564804.1| 178 SCAACHDPhdtgPRIDDSVLLCGNCHNTEGvvM---DGNTPVVRHAQWELvstsgyvdgshptsIGCVDCHMVQISNDE 253
                                   8*****983333334556667999****96552...344444444433333445555666665568*****98876554 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.026
                                   -CTCTS-SSSTTTSTTCH.......HHHHHCSSTTTCHHHHHHHH CS
                Cytochrom_CIII  49 kcstcHaeekekkekksl.......ekavHkkkaaksCvgCHkkk 86 
                                    c +cH  + ++ e  ++        + + + ++ ++C  CH++ 
  gi|91772112|ref|YP_564804.1| 240 GCVDCHMVQISNDEVVETghtfdfdAERLSNPDSGNNCSLCHQSS 284
                                   355555555433222222111111122222333347788888765 PP

>> YokU  YokU-like protein, putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       0.5   1.1e+03      27      49 ..     168     187 ..     159     206 .. 0.68
   2 ?    8.7   0.2   0.00074       1.6      17      52 ..     220     255 ..     198     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.5
                          YokU  27 aieiketPsieCseCglvyqeee 49 
                                    +e+ e  +i+C  C+     ++
  gi|91772112|ref|YP_564804.1| 168 DLEVVEEWAISCAACH---DPHD 187
                                   5677778889999996...3444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00074
                          YokU  17 vyWelpdgtkaieiketPsieCseCglvyqeeevvk 52 
                                     Wel++ +  ++ ++  si C +C++v+++++ v 
  gi|91772112|ref|YP_564804.1| 220 AQWELVSTSGYVDGSHPTSIGCVDCHMVQISNDEVV 255
                                   46***********99999**********98655444 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.1     0.011        25      14      74 ..      17      69 ..       5      80 .. 0.71
   2 ?    8.8   0.2   0.00054       1.2     123     167 ..      58     102 ..      48     109 .. 0.87
   3 ?   -1.2  10.0      0.62   1.4e+03      68     135 ..     179     248 ..     163     282 .. 0.51
   4 ?    7.4   1.4    0.0015       3.4      39     114 ..     241     332 ..     237     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                 Cytochrom_NNT 14 vgvvvgvvflggfntaleatsteeFCvsCHemednveeykesiHysnrsgvraeCsdCHvP 74
                                  +  +v v++++ f t++  + + e C  CH   ++++ +++s H        a+C+ CH  
  gi|91772112|ref|YP_564804.1| 17 LRSIVVVTTVLLFLTTVVGAVDFEECGDCH--GETYAVWSSSPHG------SASCEICHTA 69
                                  3444555555566666666667777*****..5789999*****9......6889999965 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00054
                 Cytochrom_NNT 123 ndsreCrnCHseeamdlekqkkkaakahkkaaeeektCidCHkgi 167
                                   + s+ C+ CH+ +   ++++ +   +   ++  +++ C dCH g+
  gi|91772112|ref|YP_564804.1|  58 HGSASCEICHTASPGGFDAHISAPFTSAPNVSLSSEVCGDCHSGV 102
                                   46999********9999999999999999999999********98 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.62
                 Cytochrom_NNT  68 CsdCHvPkelvkklarkiqaskevlak..lvgkidtkekfeakrlelaerewarmkandsreCrnCHsee 135
                                   C+ CH P+++ + +   +    ++ ++  +v + +t+    a+ + + ++ + + ++  s  C +CH  +
  gi|91772112|ref|YP_564804.1| 179 CAACHDPHDTGPRIDDSVLLCGNCHNTegVVMDGNTPVVRHAQWELVSTSGYVDGSHPTSIGCVDCHMVQ 248
                                   5566666655555555555333332220023333333333334444444445555555555566666555 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0015
                 Cytochrom_NNT  39 CvsCHemednveeykesiHysn...rsg....vraeCsdCHvPk......elvkklarkiq...askevlaklvgkidtke 103
                                   Cv CH ++   +e+ e+ H      ++        +Cs CH         +  + + ++i    ++ke   +++++i+ ++
  gi|91772112|ref|YP_564804.1| 241 CVDCHMVQISNDEVVETGHTFDfdaERLsnpdSGNNCSLCHQSSlaslieDKQAPIESHISalnSLKEKAGNALESINGTD 321
                                   999**9888888888888864422122211113468999998766555543334444555511156777788899999999 PP

                 Cytochrom_NNT 104 kfeakrlelae 114
                                   ++ea+r + ++
  gi|91772112|ref|YP_564804.1| 322 SYEAQRANYNN 332
                                   99999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 2735.89
//
Query:       gi|91772113|ref|YP_564805.1|  [L=174]
Description: ThiJ/PfpI [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-39  135.7   0.5    1.4e-39  135.6   0.5    1.0  1  DJ-1_PfpI   DJ-1/PfpI family
    5.1e-05   23.0   0.0     0.0046   16.7   0.0    2.2  2  ThiJ_like   ThiJ/PfpI family-like
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.025   14.2   0.1    1.4  1  Catalase_C  C-terminal domain found in long catalases
      0.073   12.7   0.0      0.096   12.3   0.0    1.3  1  GATase_3    CobB/CobQ-like glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   0.5   3.1e-43   1.4e-39       1     164 [.       5     171 ..       5     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 3.1e-43
                                   EEEEEEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTS CS
                     DJ-1_PfpI   1 kkvlvlla.dgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperlren 80 
                                   kk+l+++a ++++d E+  p +v++  g kv+v+s ++++ kg  G kv++d s++dv+ ++yDa+ + GG    ++l++n
  gi|91772113|ref|YP_564805.1|   5 KKILMVIAqENFRDEEFLKPKKVFEDSGAKVTVASNTTKKAKGVLGKKVSPDISISDVNIDDYDAISITGGGGAKQYLWDN 85 
                                   79**999999*********************************************************************** PP

                                   HHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHH...HHTTSEE-SSSEEEETTEEEESSGGGHHHH CS
                     DJ-1_PfpI  81 ekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdkl...ekagakyvdkrvvvdgnlvTsrgpgaaief 158
                                   ++++e+v+++ e+gk+++aIC +p++La+ag+l+g+ +T +++ + ++   + + aky dk v+vdgn++T r p+aa ++
  gi|91772113|ref|YP_564805.1|  86 KELQEIVRKANEQGKIIGAICIAPVVLANAGLLEGKMTTVFKNEE-TVkilKDNDAKYRDKDVMVDGNIITGRDPNAANKY 165
                                   *********************************999888887755.444469***************************** PP

                                   HHHHHH CS
                     DJ-1_PfpI 159 alelle 164
                                   + ++++
  gi|91772113|ref|YP_564805.1| 166 GQAVIK 171
                                   999987 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0     0.006        27       2      35 ..      12      45 ..      11      56 .. 0.87
   2 !   16.7   0.0     1e-06    0.0046      79     162 ..      61     135 ..      52     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.006
                     ThiJ_like  2 adeGydvtevaipwkvlkdagfsveFvtekgkvp 35
                                  a+e +  +e   p kv++d+g +v+ ++++ k +
  gi|91772113|ref|YP_564805.1| 12 AQENFRDEEFLKPKKVFEDSGAKVTVASNTTKKA 45
                                  567788999*****************99988765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1e-06
                     ThiJ_like  79 sFsleeydlvllpGGsdkavrell.eserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlwmer 158
                                   + ++++yd++ ++GG +   +++l +++ l++        v++++e+ k++gaic   ++la+a   l+ k tt+    e 
  gi|91772113|ref|YP_564805.1|  61 DVNIDDYDAISITGGGGA--KQYLwDNKELQE----I---VRKANEQGKIIGAICIAPVVLANAGL-LEGKMTTVFKNEET 131
                                   56799**********986..466614544444....3...46677999***************998.88888888777777 PP

                     ThiJ_like 159 tsil 162
                                   + il
  gi|91772113|ref|YP_564805.1| 132 VKIL 135
                                   6655 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.6e-06     0.025      23     129 ..      24     130 ..       6     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-06
                    Catalase_C  23 laaalaaegvdvtvvaeklgsaegv.......nrTYstadaveFDaivvadgaeslfsakataasslfpagrplqlllday 96 
                                    ++ ++++g++vtv  ++ ++a+gv       + + s  +  ++Dai +++g          a++ l  +++ ++++++a 
  gi|91772113|ref|YP_564805.1|  24 PKKVFEDSGAKVTVASNTTKKAKGVlgkkvspDISISDVNIDDYDAISITGG--------GGAKQYLWDNKELQEIVRKAN 96 
                                   5788999999999999999988887554444456677788889********9........345678999************ PP

                    Catalase_C  97 rhgKpigalGsgaealkaagisa.eepGVyvads 129
                                   + gK iga+  +  +l++ag+ + +   V+ +++
  gi|91772113|ref|YP_564805.1|  97 EQGKIIGAICIAPVVLANAGLLEgKMTTVFKNEE 130
                                   **********999999999987634444444444 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05     0.096      28      82 ..      55     106 ..      43     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                      GATase_3  28 rfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiC 82 
                                     ++++d ++ +d+d++ + Gg      + l ++++l+e +++a e+g+ + +iC
  gi|91772113|ref|YP_564805.1|  55 PDISISDVNI-DDYDAISITGGGGAK--QYLWDNKELQEIVRKANEQGKIIGAIC 106
                                   4566778888.56******9998655..45667778******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1162.36
//
Query:       gi|91772114|ref|YP_564806.1|  [L=940]
Description: peptidase M1, membrane alanine aminopeptidase [Methanococcoides burtonii DSM 6242]
Scores for 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  104.5   3.3      7e-30  104.5   3.3    1.8  2  DUF3458_C       Domain of unknown function (DUF3458_C) ARM re
    8.2e-26   90.9   1.7    1.2e-25   90.3   0.3    2.0  3  Peptidase_M1    Peptidase family M1 domain
    1.2e-12   48.4   0.1    2.2e-12   47.5   0.1    1.4  1  Peptidase_M1_N  Peptidase M1 N-terminal domain
      1e-06   29.1   0.0    2.7e-06   27.7   0.0    1.7  1  DUF3458         Domain of unknown function (DUF3458) Ig-like 


Domain annotation for each model (and alignments):
>> DUF3458_C  Domain of unknown function (DUF3458_C) ARM repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.35   1.6e+03     175     223 ..     461     509 ..     451     517 .. 0.76
   2 !  104.5   3.3   1.6e-33     7e-30       1     287 [.     599     887 ..     599     921 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHCTTSHHHHHHHHHHHHH--STTHHHHHHHHHTSTTT CS
                     DUF3458_C 175 pereealadfyqrwkdealvldkWfalqAtspredtlervkallehpaF 223
                                   ++ ++al+++++++++ +   + W+++    +  d  e  k+ l++ +F
  gi|91772114|ref|YP_564806.1| 461 ETFARALDSYHTKFSHSNATGEDWLRTMEEFSGMDFSEMSKNWLKQTKF 509
                                   567899******************9987777776666666666666666 PP

  == domain 2  score: 104.5 bits;  conditional E-value: 1.6e-33
                                   HHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHH.TT----HHHHHHHHHHHT-TTS-HHHHHHHTS---HHHHCTT-SSB CS
                     DUF3458_C   1 deelafLlahdsDafnRweagqrLalrvllalva.eeaalsealvealravLedealdpalkaeaLtlPseaelaeqlkev 80 
                                   d+el++ ++ d+D  nR+ a  +L+ r+ ++l+a ++a++se +++ ++++++d++l + +  ++L++ +  e ++     
  gi|91772114|ref|YP_564806.1| 599 DDELLLQVEKDNDMINRFVAYYTLVDREKMKLIAdKDARVSEMFIDLFSELITDDELMEDVGGQFLSIFESVEDVSLS--H 677
                                   689******************************66999*****************************97766665555..5 PP

                                   -HHHHHHHHHHHHHHHHHHTHHHHHHHHHH.....HHHHC--SHHHHHHHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHS CS
                     DUF3458_C  81 dpdaihaarealrkalaealedellalyea.....laaegayspdaaaagrRaLknlaLsylaaaddeeaaelavaqfkaa 156
                                     + +++++e++ +++a++    +l++y++     + a+++ + +a  + +R+ knl+L++la++d++ +++l+++qf +a
  gi|91772114|ref|YP_564806.1| 678 RYQLLYDVKERILNEIAKNRTVSILNIYHKyltlsVPANDTLEEQARCIKARQVKNLVLRILATLDTPFVQQLCKKQFYEA 758
                                   79***************************854433333346666777799*********************9999****** PP

                                   SSHHHHHHHHHHHTTSSSHHHHHHHHHHHHHCTTSHHHHHHHHHHHHH--STTHHHHHHHHHTSTTTTTTSHHHHHHHHHH CS
                     DUF3458_C 157 dnmTdrlaALaalvnsdlpereealadfyqrwkdealvldkWfalqAtspredtlervkallehpaFdlknPNrvrsLiga 237
                                   ++ +d+laA+    ns+++++ e+l+ f ++ k+  +  ++++++ A++++ d+++ v+++ + ++F +++ N  r+L+g+
  gi|91772114|ref|YP_564806.1| 759 SCASDKLAAFDRYLNSSAEDKMELLEMFMEESKKSLVAWETFLSIVAGNSSMDAVSLVRQIEASESFRIEQANDQRALYGG 839
                                   ********************************************************************************* PP

                                   HH.T-HHHHT-TTSHHHHHHHHHHHHHHTT-HHHHHHHGGGGTTGGGB-H CS
                     DUF3458_C 238 FaaanpaaFhaadGsGYafladqvleldaiNpqvAaRlvtaltrwrryde 287
                                   Fa++ +     ++ +G ++l +++ +l ++N    + +++++ +   ++e
  gi|91772114|ref|YP_564806.1| 840 FARNRKISL--QTEAGRELLREILSKLSNVNEYSTTSMLNVFANIDLMEE 887
                                   **7777666..566899*************************99876665 PP

>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.96   4.3e+03      16      50 ..      67     101 ..      62     103 .. 0.85
   2 !   90.3   0.3   2.8e-29   1.2e-25       9     218 .]     292     503 ..     285     503 .. 0.85
   3 ?   -3.2   0.0       1.1     5e+03     111     154 ..     791     837 ..     778     882 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.96
                                   HHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGG CS
                  Peptidase_M1  16 yfkvpYplpkldlvalpdfsagAMEnwglityree 50 
                                    ++++Y++   + ++  +f+a+  En+ +++++e+
  gi|91772114|ref|YP_564806.1|  67 DYDISYDYRPDEYILSIKFPAMVPENTEIVIHTET 101
                                   577888888888899999**********9999986 PP

  == domain 2  score: 90.3 bits;  conditional E-value: 2.8e-29
                                   HHHHHHHHHTS--SSS..EEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBTTTEEES CS
                  Peptidase_M1   9 llefleeyfkvpYplp..kldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfGnlVtmk 87 
                                    l+ l++ +k+ Y+++   +  + +++  +g+MEn g +t++ + ++  pe+++    + + +v +HE+ H+  G  Vt  
  gi|91772114|ref|YP_564806.1| 292 ELKKLDSSLKMGYKYTgtVYREIGMQNSDFGGMENVGNTTITTNRIMPYPETTDP-AFEYMIRVKVHEYYHNINGSEVTGW 371
                                   556666665555555433999**************************99887766.788999******************* PP

                                   SGGGGHHHHHHHHHHHHHHHHHHSC.CCHCHHHH..HHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHHHHH CS
                  Peptidase_M1  88 wWddlwLnEGfatyleylildklep.ewevseql..lleeveealsedaldeshpitqevekpseidevFdsiaYeKGasl 165
                                   +  ++wLnE  ++ +e ++   l++ +++  +++  ll+    +++ d+ + s +i    e  ++++++ ++++Y K  ++
  gi|91772114|ref|YP_564806.1| 372 SPFEIWLNEAVTVHIEHQFHAFLFGdNYSRLANVldLLYPGVGTFAIDSGAASMSI--VPEGFNDPNDLITAVTYVKAPEF 450
                                   *************************7665444442445566666677776666666..67888999*************** PP

                                   HHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                  Peptidase_M1 166 lrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                   +rmle+l+g+e+F ++l sY ++f+++na+ ed ++++ee ++ d se+ ++w
  gi|91772114|ref|YP_564806.1| 451 VRMLETLMGKETFARALDSYHTKFSHSNATGEDWLRTMEEFSGMDFSEMSKNW 503
                                   ************************************************99999 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.1
                                   SCCCHCHHHHHHHCHHHHHHHHTSTTHHHSS....GG-GSHHHHHHTS CS
                  Peptidase_M1 111 epewevseqllleeveealsedaldeshpit....qevekpseidevF 154
                                   +++   +e++ l+ v  + s+da++  ++i+     ++e++++   ++
  gi|91772114|ref|YP_564806.1| 791 KKSLVAWETF-LSIVAGNSSMDAVSLVRQIEasesFRIEQANDQRALY 837
                                   4444467777.6777777778888777777655433555555555555 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.1     5e-16   2.2e-12      20     186 .]      33     197 ..       9     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 5e-16
                                   EEEEEEEEES...S-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTC.EEEEECCEEETTCEEEEEEEEEEE- CS
                Peptidase_M1_N  20 Gsvtitlqlk...eatseivldakdlkiksvslsaevksesvkidfkieqkdeel.ltiklkeslqqtskytLeieyegel 96 
                                   + vt +l++k   ++++++ l+++dl+ik++s        +   d +++++ +e+ l+ik++ ++   ++ ++ i  e+  
  gi|91772114|ref|YP_564806.1|  33 TYVTSDLKVKtleNSIDHLDLNCRDLEIKDISCK------D--YDISYDYRPDEYiLSIKFPAMVP--ENTEIVIHTETIC 103
                                   33444444444459**************555554......4..44555566655559999999776..4555555554522 PP

                                   ...BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTS.EEEESSECCCEE.EETTCEE CS
                Peptidase_M1_N  97 ...ndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkee.talSnmpeeese.klengqk 172
                                      ++ l+Gly  +  +  ++ ++ +Tq++   + +++PC+D   +K t+t++i+a++ +  ++Sn++++++    +ng++
  gi|91772114|ref|YP_564806.1| 104 rptSNVLEGLYYDE--TPAGAPPQQITQCQQWGFQRIVPCIDDMTAKCTYTTTIIADERYtNLISNGDVIDERySIGNGRS 182
                                   4449999***9655..344566999***********************************7799***99976514459999 PP

                                   EEEEEEE.ESBEGGG CS
                Peptidase_M1_N 173 iteFeqt.pkmstYL 186
                                   +  ++++  +m tYL
  gi|91772114|ref|YP_564806.1| 183 KIIYDNSiTPMATYL 197
                                   666655426899998 PP

>> DUF3458  Domain of unknown function (DUF3458) Ig-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   6.1e-10   2.7e-06       3      92 ..     510     593 ..     509     596 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.1e-10
                                   -EEEEEEEEETTTTEEEEEEEEE---BSSBSS-----EEEEEEEEETTS-BECEEEEEEE-SSEEEEEEC---S-EEEEES CS
                       DUF3458   3 PevtvsesydeaaktytltlsQktpptagqkekkplviPiklalldekGeelelekvlelteaeqsftfenvaekpvpSll 83 
                                   P +++++syd+++++++ +l Q +p+ +     +    P+ +al+d++G++++ e +  + ++++++ +env+  +++S++
  gi|91772114|ref|YP_564806.1| 510 PVLNINTSYDSSNRSFKFDLAQVVPEGS-----THWEFPFVAALVDNEGTDIA-EFTEWIASEKAEVLVENVDLPAFISVN 584
                                   99**********************9443.....5789***************9.8888999******************** PP

                                   TT--SSSEE CS
                       DUF3458  84 rdFSAPvkl 92 
                                   r++S++ k+
  gi|91772114|ref|YP_564806.1| 585 RGYSFYGKV 593
                                   ****99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (940 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 6049.89
//
Query:       gi|91772115|ref|YP_564807.1|  [L=221]
Description: HAD family hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-33  115.6   0.2    3.5e-33  115.2   0.2    1.2  1  HAD_2            Haloacid dehalogenase-like hydrolase
    4.9e-17   62.9   0.2    7.2e-16   59.1   0.2    2.2  1  Hydrolase        haloacid dehalogenase-like hydrolase
    8.3e-11   41.8   0.0    1.4e-10   41.1   0.0    1.4  1  Hydrolase_like   HAD-hyrolase-like
      4e-06   27.4   0.0    5.2e-06   27.0   0.0    1.2  1  HAD              haloacid dehalogenase-like hydrolase
     0.0008   18.9   0.1     0.0013   18.2   0.1    1.3  1  Put_Phosphatase  Putative Phosphatase
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.46   10.6   0.0    1.7  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.2   1.2e-36   3.5e-33       1     176 [.       8     188 ..       8     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 1.2e-36
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeygls...elseeelrkliglslrellrklgeseeeee.....kieellrkyneek 73 
                                   ++FD+D+Tl d  e+ + a ++++e+ g +    + +  lr+  g+++ e ++ +  ++   +     +++   + y + k
  gi|91772115|ref|YP_564807.1|   8 VLFDMDNTLFDFLEAKLIACQRIVEHLGTGdaeAMLQYFLRENTGFEDLENIQDYLLDN---KlysedNYAISCDLYDKVK 85 
                                   79*************************88732133344456666665544444333322...2344579999999999999 PP

                         HAD_2  74 kkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkee 154
                                    +  + +y+gv+e+L++Lke+++ +++vT+ ++ ++ + +e+++i +yFd++vt+++++ kKPdp+v++ al+ lk+ +++
  gi|91772115|ref|YP_564807.1|  86 VE-ALVLYPGVIETLQKLKEQRLDIALVTDAQSYNAIKRIERTQIGNYFDTVVTTDMTGAKKPDPKVFHYALNILKIPPSK 165
                                   99.****************************************************************************** PP

                         HAD_2 155 viyvGDsp.tDieaakkagikvi 176
                                   +++vGDsp +Die a+k+g++++
  gi|91772115|ref|YP_564807.1| 166 ALFVGDSPrRDIEPARKIGMQTA 188
                                   ********************997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.2   2.4e-19   7.2e-16       1     210 []       5     184 ..       5     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.4e-19
                                   SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHETTTEHHHHTHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.sgaltgfatfigrgayaigkpewltal 80 
                                   i +v+fD+d+TL +   + + + +++   +          ++g   ++a  +    + tgf+        +++ +++l ++
  gi|91772115|ref|YP_564807.1|   5 IQAVLFDMDNTLFDFL-EAKLIACQR---I--------VEHLGTGDAEAMLQYfLRENTGFED-------LENIQDYLLDN 66 
                                   6799999999999777.223333333...1........1223444433333334444466766.......66666666666 PP

                                   HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH.HHHHH.TTGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxx RF
                     Hydrolase  81 dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae.raanq.lGddy 159
                                              ++ s++  ++ +  +++  ++++    ++p++ e++++Lk++ ++++l+t  ++ +a  r+ +  +G +y
  gi|91772115|ref|YP_564807.1|  67 -----------KLYSEDNYAISC--DLYDKVKVEAL-VLYPGVIETLQKLKEQRLDIALVTDAQSYNAIkRIERTqIG-NY 132
                                   ...........666666677777..66666666543.6***************************9999566666666.** PP

                                   ESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Hydrolase 160 fdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                   fd v+++d ++ +kp+p+ +++a++ L+++p++ ++VGD++  D++ +++ g
  gi|91772115|ref|YP_564807.1| 133 FDTVVTTDMTGAKKPDPKVFHYALNILKIPPSKALFVGDSPRrDIEPARKIG 184
                                   *********************************************9988765 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.7e-14   1.4e-10       3      67 ..     145     206 ..     143     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.7e-14
                                   STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT- CS
                Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkpty 67 
                                    KP p ++ +al+ l+++p++ l++GD+++ Di+ A+++G++++  + G +r+     ++ ++++
  gi|91772115|ref|YP_564807.1| 145 KKPDPKVFHYALNILKIPPSKALFVGDSPRRDIEPARKIGMQTAYAAYGDKRENG---QKVEADI 206
                                   6*********************************************999988743...2344555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.8e-09   5.2e-06       1     181 [.       8     173 ..       8     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.8e-09
                           HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfvaevi 81 
                                   +lfD+D TL+d   + l++ +++    ++l++  +e+ l++++re   +++++  + +    + +se+  a  ++++++v+
  gi|91772115|ref|YP_564807.1|   8 VLFDMDNTLFDFLEAKLIACQRIV---EHLGTGDAEAMLQYFLRENTGFEDLENIQDYLLDNKLYSEDNYAISCDLYDKVK 85 
                                   79**********888877774444...455777777777777666666655555555554456666999999999999999 PP

                           HAD  82 rpk.lldpgalellaahraaGdrvvvvSgg.lrplvepll.aelg..adevlatelevddrltgelglegkpvrgegkvaa 157
                                    ++ +l+pg+ e l++ +++   +++v+ +     ++++   + g  +d+v+ t      ++tg  + +++ v+      a
  gi|91772115|ref|YP_564807.1|  86 VEAlVLYPGVIETLQKLKEQRLDIALVTDAqSYNAIKRIErTQIGnyFDTVVTT------DMTGA-KKPDPKVFH----YA 155
                                   9996488*********************99455567777744888999999999......99999.888888888....88 PP

                           HAD 158 lrewlaaegegidleevvayGDsp 181
                                   l+        +i++++  ++GDsp
  gi|91772115|ref|YP_564807.1| 156 LNI------LKIPPSKALFVGDSP 173
                                   888......888999999999998 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   4.2e-07    0.0013       3     121 ..       8     138 ..       6     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.2e-07
               Put_Phosphatase   3 vvfDFDktiided.....sdnwvvdelpatelfeelretlrkglwnelmdrvlkelheqgvsead...i......kkvlrs 69 
                                   v+fD D+t+ d       + + +v+ l++ +  + l+  lr+++  e ++++  +l +++  ++d   i      k  ++ 
  gi|91772115|ref|YP_564807.1|   8 VLFDMDNTLFDFLeakliACQRIVEHLGTGDAEAMLQYFLRENTGFEDLENIQDYLLDNKLYSEDnyaIscdlydKVKVEA 88 
                                   789999999885411111345688999999999999999998888888888888887776444331221222222335788 PP

               Put_Phosphatase  70 iplspglvelikslakkkleldliiiSDaNsffieeileaagledlFseift 121
                                   + l pg++e +++l  k+++ld+ ++ Da s+   + +e +++ ++F+ + t
  gi|91772115|ref|YP_564807.1|  89 LVLYPGVIETLQKL--KEQRLDIALVTDAQSYNAIKRIERTQIGNYFDTVVT 138
                                   9999**********..5779**************9*************9887 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2   3.5e+03       1      12 [.       8      19 ..       8      50 .. 0.78
   2 ?   10.6   0.0   0.00015      0.46      15      49 ..      91     125 ..      81     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                                  EEEESTTTSEET CS
                   Hydrolase_6  1 flfDidGvLwrg 12
                                  +lfD+d +L ++
  gi|91772115|ref|YP_564807.1|  8 VLFDMDNTLFDF 19
                                  689999888764 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00015
                                   E-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHH CS
                   Hydrolase_6  15 aipgaaealnalraagkpvvllTNnsskseeeyak 49 
                                   ++pg+ e+l+ l+++  +++l+T   s +  ++++
  gi|91772115|ref|YP_564807.1|  91 LYPGVIETLQKLKEQRLDIALVTDAQSYNAIKRIE 125
                                   79*********************998877555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1625.80
//
Query:       gi|91772116|ref|YP_564808.1|  [L=88]
Description: hypothetical protein Mbur_0034 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 623.58
//
Query:       gi|91772117|ref|YP_564809.1|  [L=300]
Description: hypothetical protein Mbur_0035 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-28   98.9  40.0    5.4e-16   59.0  16.5    2.0  2  EamA      EamA-like transporter family
     0.0024   17.3  18.7      0.017   14.4  17.4    2.0  1  TPT       Triose-phosphate Transporter family
  ------ inclusion threshold ------
        3.4    7.8  12.7        1.4    8.9   3.6    2.6  2  TMEM234   Putative transmembrane family 234
        4.4    5.5  33.7     0.0078   14.6  16.7    2.0  2  DUF2070   Predicted membrane protein (DUF2070)


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 !   46.2  15.4   1.1e-15   4.7e-12       2     136 ..       7     139 ..       6     140 .. 0.89
   2 !   59.0  16.5   1.2e-19   5.4e-16       3     136 ..     156     286 ..     154     287 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.1e-15
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkd.wllllllgllgtvlafll 81 
                                   +g+l + ++++++++ +v+  +l++++ +l + f+ +li+ i+l  +  l+++ +  ++ k+  + llllg++  +   ++
  gi|91772117|ref|YP_564809.1|   7 KGYLEITTGCIVYGMVGVFL-VLINDMGTLPIIFYKLLIGVIFLAGYVYLTGKMD-LIKIKGkRKHLLLLGIFKLMTI-YF 84 
                                   678889999***********.779**********************999999999.4554442366788888777666.69 PP

                          EamA  82 ffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   +f+ + +++ s+a l+++++P++++++s ++l+e +t + ++g++l+++G++l++
  gi|91772117|ref|YP_564809.1|  85 YFTCILYSGLSIAILLLYTAPMYVTLFSPFVLKEIPTRLGIVGLLLSMAGIVLVV 139
                                   *****************************************************96 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 1.2e-19
                          EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllff 83 
                                   g++  +l+ +++++ ++ +++l  ++s ++ +f+ ++++ i+ll++a     +     + ++ llll+g+++t +  +l+f
  gi|91772117|ref|YP_564809.1| 156 GLIAGILSGISFSFLIMNARYLRDEYSGFAQFFWATVFCVIVLLPFASDVTVPV---LKDNFMLLLLFGVVNTSISGVLYF 233
                                   8999******************************************99999999...56667888**************** PP

                          EamA  84 yalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   ++l+k+  ++as++  +ePv  +++ ++ll+  +   ++lg+v+i++G+ll +
  gi|91772117|ref|YP_564809.1| 234 TGLSKVRTQTASILAMFEPVSGIFFDYALLHSVIFAETVLGCVFIIAGALLAV 286
                                   **************************************************986 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4  17.4   3.9e-06     0.017      37     288 ..      40     284 ..      28     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-06
                           TPT  37 vqllvgsvlil.vlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgek 116
                                    +ll+g+++++  ++ +g  +  ki+    k +l l+++k+++  +    +     S +  +  ++P++  ++s ++l+e 
  gi|91772117|ref|YP_564809.1|  40 YKLLIGVIFLAgYVYLTGKMDLIKIKG-KRKHLLLLGIFKLMTIYFYFTCILYSGLSIAILLLYTAPMYVTLFSPFVLKEI 119
                                   567788877541344445555555554.689999*********************************************** PP

                           TPT 117 lsllvylsLlpivgGval....asvtElsF...nligfisAlisnltfslrnifsKkllkklkdldalnlfaiitilslll 190
                                   ++ l ++ Ll  ++G++l    + +  + F    ++g+i+ ++s ++fs+  i++ + l++  + +   +f+  t++ +++
  gi|91772117|ref|YP_564809.1| 120 PTRLGIVGLLLSMAGIVLvvdpSNLVGAGFsdmHFVGLIAGILSGISFSFL-IMNARYLRD--EYSGFAQFFWATVFCVIV 197
                                   ****999999999999883333345555552224689***********995.899999999..59**************** PP

                           TPT 191 llPvallvegvlktpsllkstkvslkevllllllsgvlfhlynqva.ymvLervspvthsvantvKrvvvIvlsvlvfknp 270
                                   llP+a  v+     p+ lk       + ++llll gv++ + + v  ++ L++v   t s+      v  I +   +++  
  gi|91772117|ref|YP_564809.1| 198 LLPFASDVTV----PV-LK-------DNFMLLLLFGVVNTSISGVLyFTGLSKVRTQTASILAMFEPVSGIFFDYALLHSV 266
                                   ***8766555....33.33.......336788888888887776551567******************************* PP

                           TPT 271 vsllnaiGtavaivGvfl 288
                                   +   +++G++  i+G++l
  gi|91772117|ref|YP_564809.1| 267 IFAETVLGCVFIIAGALL 284
                                   ***************987 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.7     0.013        56      60     116 .]      84     139 ..      58     139 .. 0.78
   2 ?    8.9   3.6   0.00032       1.4      52     115 ..     222     285 ..     157     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                       TMEM234  60 lfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialcv 116
                                   ++f  +    ls+a  +  +  + +T+    +l+e + ++  ++g+ll ++gi+l+v
  gi|91772117|ref|YP_564809.1|  84 FYFTCILYSGLSIAILLLYTAPMYVTLFSPFVLKE-IPTRLGIVGLLLSMAGIVLVV 139
                                   45556788899999999999999999998888876.66777899**********986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00032
                       TMEM234  52 llNqsgS.vlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                   ++N s S vl+f  l+k+   +a+++a   + v  +  +++l   v+ ++tvlg++++++g  l 
  gi|91772117|ref|YP_564809.1| 222 VVNTSISgVLYFTGLSKVRTQTASILA-MFEPVSGIFFDYALLHSVIFAETVLGCVFIIAGALLA 285
                                   478876659*********988777655.7999*****************************9885 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.9  17.1         4   1.8e+04      28     170 ..      22     170 ..       6     172 .. 0.50
   2 ?   14.6  16.7   1.7e-06    0.0078      21     180 ..     127     293 ..     114     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: -6.9 bits;  conditional E-value: 4
                       DUF2070  28 igllaflssk......lfgillfglpalvaflltlpvlrilggrltykrs.lflalltelivviisllaillsallqalvl 101
                                   +g+  +l++       +f  ll+g+ +l+  + ++  +++++  ++ kr+ l+l  ++ l+ + +++  il+s        
  gi|91772117|ref|YP_564809.1|  22 VGVFLVLINDmgtlpiIFYKLLIGVIFLAGYVYLTGKMDLIK--IKGKRKhLLLLGIFKLMTIYFYFTCILYSG------- 93 
                                   333333444323333444555566666666555555555553..556666466666666666666666666663....... PP

                       DUF2070 102 lalvlslalvfalrllvlvavsdesllkav.....lpaliqpllailllvly.......fspesfllllllslifalavyl 170
                                       ls+a+ + ++  ++v++++  +lk +     ++ l+ ++++i+l+v         fs+ +f+ l++ +l  + +++l
  gi|91772117|ref|YP_564809.1|  94 ----LSIAILLLYTAPMYVTLFSPFVLKEIptrlgIVGLLLSMAGIVLVVDPsnlvgagFSDMHFVGLIAGILSGISFSFL 170
                                   ....33444444444444444444444444221114444444444444444477777776666666666666666555555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.7e-06
                       DUF2070  21 iillalligllaflssk.....lfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall 96 
                                    +ll+++  +l+++ s+     +  + ++gl a +   +   +l +  ++l  + s f  ++ ++++++i+ll+ +  + +
  gi|91772117|ref|YP_564809.1| 127 GLLLSMAGIVLVVDPSNlvgagFSDMHFVGLIAGILSGISFSFLIMNARYLRDEYSGFAQFFWATVFCVIVLLPFASDVTV 207
                                   44444444444444444777789999999999988888888999888888999999******************9999877 PP

                       DUF2070  97 ...qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfivv 174
                                      ++ ++l l+++++ + +  +l ++ +s+ ++ +a+++a+  p+++i++ ++++ +  f+   +l ++f++a +l+ v+
  gi|91772117|ref|YP_564809.1| 208 pvlKDNFMLLLLFGVVNTSISGVLYFTGLSKVRTQTASILAMFEPVSGIFFDYALLHSVIFAE-TVLGCVFIIAGALLAVM 287
                                   999****************************************************65555555.55555666666666665 PP

                       DUF2070 175 vdrplk 180
                                    ++ ++
  gi|91772117|ref|YP_564809.1| 288 ENISFR 293
                                   555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2176.14
//
Query:       gi|91772118|ref|YP_564810.1|  [L=148]
Description: 30S ribosomal protein S13P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.6e-40  136.3   0.4    8.9e-40  136.0   0.4    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.021   13.6   0.0      0.022   13.6   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
       0.79    9.7   3.4         11    6.0   0.0    2.5  2  Nup54_C        Nup54 C-terminal interacting domain


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 !  136.0   0.4   1.5e-43   8.9e-40       1     128 []      11     138 ..      11     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 1.5e-43
                 Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdGk 80 
                                   Ri++td++gkk v++alt i+GiG r++++i+  +++d +++ig l++e+i+k+  +++++ + + p+w+ nrq d  +G+
  gi|91772118|ref|YP_564810.1|  11 RIMNTDLQGKKPVKYALTGIRGIGLRTSRVIVDSTGIDPNAVIGYLSDEDIKKLDSTIDKFEE-QLPKWMlNRQFDPLTGE 90 
                                   9***********************************************************555.5555555********** PP

                 Ribosomal_S13  81 dshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                   ++h++ +d+  +l+ed++ lkk r+yrGlRH+rGlkvRGQrTk+tgR+
  gi|91772118|ref|YP_564810.1|  91 NKHLLGQDIILTLKEDLNDLKKSRAYRGLRHERGLKVRGQRTKSTGRR 138
                                   ***********************************************7 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 ?   13.6   0.0   3.6e-06     0.022     184     244 ..      15      77 ..       2     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-06
                                   H..S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX. CS
                          FbpA 184 k..kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelleelee 244
                                   +  + k+ vk  ++ ++G++  +++ ++ ++g+d++  +  ls+ed+++l +++ ++ e+l +
  gi|91772118|ref|YP_564810.1|  15 TdlQGKKPVKYALTGIRGIGLRTSRVIVDSTGIDPNAVIGYLSDEDIKKLDSTIDKFEEQLPK 77 
                                   345678889999999*****************************************9999974 PP

>> Nup54_C  Nup54 C-terminal interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0018        11      22      34 ..       6      18 ..       1      20 [. 0.90
   2 ?    3.4   1.1     0.012        72      25      37 ..      99     111 ..      97     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0018
                       Nup54_C 22 lkhLIeIIkdDls 34
                                  + hL+ I ++Dl+
  gi|91772118|ref|YP_564810.1|  6 IRHLVRIMNTDLQ 18
                                  89*********97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                       Nup54_C  25 LIeIIkdDlsdLk 37 
                                   +I + k+Dl+dLk
  gi|91772118|ref|YP_564810.1|  99 IILTLKEDLNDLK 111
                                   57789*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 985.59
//
Query:       gi|91772119|ref|YP_564811.1|  [L=184]
Description: 30S ribosomal protein S4P [Methanococcoides burtonii DSM 6242]
Scores for 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   57.1   0.1    2.4e-15   56.0   0.1    1.6  1  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 !   56.0   0.1   1.3e-19   2.4e-15       1      46 [.     108     153 ..     108     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.3e-19
                                   EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                            S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                   rRL++ ++rlgla + r+Arq+I hG++ ++Gk+v+ p+++V+ + 
  gi|91772119|ref|YP_564811.1| 108 RRLQTQVHRLGLARTARQARQFITHGHIAIDGKRVTVPGMMVTREQ 153
                                   8*****************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1287.47
//
Query:       gi|91772120|ref|YP_564812.1|  [L=126]
Description: 30S ribosomal protein S11P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  158.8   2.2    7.2e-47  158.3   2.2    1.2  1  Ribosomal_S11  Ribosomal protein S11
    0.00085   19.1   0.1     0.0011   18.8   0.1    1.2  1  Pilus_CpaD     Pilus biogenesis CpaD protein (pilus_cpaD)
  ------ inclusion threshold ------
      0.016   15.5   0.1      0.037   14.3   0.0    1.6  2  CBM_25         Carbohydrate binding domain (family 25)


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 !  158.3   2.2   1.2e-50   7.2e-47       1     110 []       7     125 ..       7     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 1.2e-50
                 Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pG 72 
                                   Gvahi++sfnntiit+tdl+Gae+++ks+Gg++vka+r +ssPy+a+++a + a+ + dkG++ v++kv++        pG
  gi|91772120|ref|YP_564812.1|   7 GVAHIKCSFNNTIITVTDLTGAETIAKSSGGMVVKAARdESSPYTAMQMATQLADILRDKGLEGVHIKVRApggnkqrsPG 87 
                                   9******************************************************************************** PP

                 Ribosomal_S11  73 pGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                   pG++aa+ra+araG++igriedvtP+Phdg+r++++rr
  gi|91772120|ref|YP_564812.1|  88 PGAQAAIRAFARAGVRIGRIEDVTPVPHDGTRPKGGRR 125
                                   ***********************************998 PP

>> Pilus_CpaD  Pilus biogenesis CpaD protein (pilus_cpaD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.8e-07    0.0011      69     122 ..      31      84 ..      22     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-07
                    Pilus_CpaD  69 rregagaivisvpsgssneaaaaaaaaeiravlaaaGvpaseisvrayqaaape 122
                                    ++++g +v+++ +++s++ +a+++a++++++l ++G+++ +i+vra  +++++
  gi|91772120|ref|YP_564812.1|  31 IAKSSGGMVVKAARDESSPYTAMQMATQLADILRDKGLEGVHIKVRAPGGNKQR 84 
                                   57889999**************************************98887764 PP

>> CBM_25  Carbohydrate binding domain (family 25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.68     4e+03      79      91 ..      14      26 ..       3      42 .. 0.57
   2 ?   14.3   0.0   6.1e-06     0.037      13      66 ..      64     117 ..      54     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.68
                        CBM_25 79 slsaGvstvadnt 91
                                  s++  + tv+d t
  gi|91772120|ref|YP_564812.1| 14 SFNNTIITVTDLT 26
                                  4444444444433 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.1e-06
                        CBM_25  13 rkkGftsayihyrpaGGswtavpGvkmrdaeaGyakkdvdlGaassleaafndG 66 
                                   r kG +  +i+ r  GG     pG + ++a   +a+  v +G   +++    dG
  gi|91772120|ref|YP_564812.1|  64 RDKGLEGVHIKVRAPGGNKQRSPGPGAQAAIRAFARAGVRIGRIEDVTPVPHDG 117
                                   899***************************************988877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 761.16
//
Query:       gi|91772121|ref|YP_564813.1|  [L=267]
Description: DNA-directed RNA polymerase subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-24   85.1   0.0    1.3e-23   83.4   0.0    1.8  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    1.8e-15   56.1   0.0    3.6e-15   55.1   0.0    1.5  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    2.9e-07   30.0  13.9    0.00015   21.5   4.3    2.9  3  Fer4           4Fe-4S binding domain
    2.7e-05   24.2   6.6    2.7e-05   24.2   6.6    2.3  2  Fer4_10        4Fe-4S dicluster domain
    4.3e-05   24.0   7.0    4.3e-05   24.0   7.0    2.5  3  Fer4_7         4Fe-4S dicluster domain
    4.4e-05   23.5  19.1    0.00035   20.7   9.4    3.0  4  Fer4_9         4Fe-4S dicluster domain
     0.0013   19.7  12.6      0.018   15.9   0.7    2.9  3  Fer4_16        4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.014   15.5  11.1      0.014   15.5  11.1    2.4  2  Fer4_21        4Fe-4S dicluster domain
      0.022   14.8   2.7      0.022   14.8   2.7    3.5  3  Fer4_2         4Fe-4S binding domain
      0.099   13.2   1.7      0.099   13.2   1.7    3.3  3  Fer4_4         4Fe-4S binding domain
       0.14   13.2   2.6       0.14   13.2   2.6    3.3  2  Fer4_3         4Fe-4S binding domain
       0.17   12.4  14.4       0.31   11.5   0.5    2.7  3  Fer4_8         4Fe-4S dicluster domain
       0.17   12.0   0.0        0.6   10.2   0.0    1.9  2  OapA           Opacity-associated protein A LysM-like domain
        4.9    7.8  19.8          4    8.1   2.0    2.8  2  Fer4_17        4Fe-4S dicluster 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 !   83.4   0.0   1.1e-26   1.3e-23       1     112 []      44     156 ..      44     156 .. 0.92
   2 ?   -1.2   0.0         2   2.6e+03      48      69 ..     226     245 ..     189     263 .. 0.55

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 1.1e-26
                                   EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC....EEGGGCBESSSSCE CS
                 RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge....vtagdlkledadve 77 
                                   V+i++ntsvl+DE +a rlglipl+++ +++      ++   +  g++ ++v+l+L+v+  +     v +gd++++d++v+
  gi|91772121|ref|YP_564813.1|  44 VNIYNNTSVLYDEQLALRLGLIPLTTSFDDF--VPQDKC-TCDGAGCPACTVSLTLSVETDESgqtiVHSGDIVSSDPNVQ 121
                                   89***********************998888..333334.24679**************999999**************** PP

                                   ESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                 RNA_pol_A_bac  78 ivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                   +++++i+I+ Lr gq++ lea++  G+G +hak++
  gi|91772121|ref|YP_564813.1| 122 PADKNIPIIDLRVGQKVVLEAIAHMGYGNKHAKWQ 156
                                   **********************************6 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                                   TCSEEEEEEEEESSECEEGGGC CS
                 RNA_pol_A_bac  48 eeksvelkLnvkgpgevtagdl 69 
                                   +ek  ++  +++  g  ta++l
  gi|91772121|ref|YP_564813.1| 226 DEK--SFIFTMESDGSYTAQQL 245
                                   333..23333333333445554 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 !   55.1   0.0   2.8e-18   3.6e-15       1      68 [.      14     256 ..      14     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 2.8e-18
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                     RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea................................................... 30 
                                   +f l++++++++N  Rr +l++vp++ai+                                                    
  gi|91772121|ref|YP_564813.1|  14 KFILSNTTAAFANGVRRAMLADVPTLAIDDvniynntsvlydeqlalrlgliplttsfddfvpqdkctcdgagcpactvsl 94 
                                   699*********************************************************999999999999999999999 PP

                                   ........................................................................xx....... RF
                     RNA_pol_L  31 ........................................................................pv....... 32 
                                                                                                           p+       
  gi|91772121|ref|YP_564813.1|  95 tlsvetdesgqtivhsgdivssdpnvqpadknipiidlrvgqkvvleaiahmgygnkhakwqagvacgykimPIvtfegcd 175
                                   999999999999999999999998888888888777777777777777776666666666666666666666115555555 PP

                                   .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_L  33 .............................................vkvntdkdklilevetdgslkPeealkeAlkiLkek 68 
                                                                                + v++d++ +i++ e+dgs+++++++++A++ +k k
  gi|91772121|ref|YP_564813.1| 176 gcgicinscprniiqlidgsamvadedllkcslcrlcqdscdinaITVSADEKSFIFTMESDGSYTAQQLILNAVNTIKGK 256
                                   5555555555566666666666666666666666666666666668999***************************99976 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.5   1.1e+04       5       9 ..      77      81 ..      76      81 .. 0.79
   2 !   21.5   4.3   1.1e-07   0.00015       2      24 .]     168     190 ..     167     190 .. 0.88
   3 !   14.6   0.5   1.7e-05     0.021       5      24 .]     203     222 ..     200     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.5
                                  TTTSS CS
                          Fer4  5 eekCi 9 
                                  ++kC+
  gi|91772121|ref|YP_564813.1| 77 QDKCT 81
                                  58996 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.1e-07
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   ++  e C gCG+C++ CP + I+
  gi|91772121|ref|YP_564813.1| 168 IVTFEGCDGCGICINSCPRNIIQ 190
                                   566789**************995 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.7e-05
                                   TTTSSS-THHHHHSTTTEEE CS
                          Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                     kC  C +C + C  +AIt
  gi|91772121|ref|YP_564813.1| 203 LLKCSLCRLCQDSCDINAIT 222
                                   569****************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 ?    0.8   0.2      0.41   5.2e+02      15      23 ..      82      91 ..      74     124 .. 0.67
   2 !   24.2   6.6   2.1e-08   2.7e-05       6      55 ..     171     216 ..     166     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.41
                       Fer4_10 15 Cvka.CPadl 23
                                  C  a CPa+ 
  gi|91772121|ref|YP_564813.1| 82 CDGAgCPACT 91
                                  3333455533 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.1e-08
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaC 55 
                                    + C +Cg C ++CP      + ++ ++++++v + ++ kC  c  C+++C
  gi|91772121|ref|YP_564813.1| 171 FEGCDGCGICINSCPR-----NIIQLIDGSAMVADeDLLKCSLCRLCQDSC 216
                                   578*************.....888888888877777*************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.4       3.5   4.4e+03      39      44 ..      81      90 ..      73      95 .. 0.56
   2 !   24.0   7.0   3.3e-08   4.3e-05       2      51 ..     174     219 ..     173     220 .. 0.89
   3 !   10.6   1.9   0.00052      0.67       1      22 [.     205     226 ..     205     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.5
                        Fer4_7 39 l....gCgaC 44
                                  +    gC aC
  gi|91772121|ref|YP_564813.1| 81 TcdgaGCPAC 90
                                  4333334444 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 3.3e-08
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   C gCg C + Cp + i+l +       + ++ d  kC+ C+ C++ C  +
  gi|91772121|ref|YP_564813.1| 174 CDGCGICINSCPRNIIQLIDG----SAMVADEDLLKCSLCRLCQDSCDIN 219
                                   ******************886....3477899999************766 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00052
                        Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                   +C  C+ C++ C  +ai++  +
  gi|91772121|ref|YP_564813.1| 205 KCSLCRLCQDSCDINAITVSAD 226
                                   7999************998765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.43   5.5e+02       5      21 ..      80      96 ..      71     108 .. 0.66
   2 !   15.7   2.1     1e-05     0.013      33      51 .]     165     189 ..     144     189 .. 0.69
   3 !   20.7   9.4   2.7e-07   0.00035       2      51 .]     174     221 ..     173     221 .. 0.90
   4 !   11.2   1.3   0.00025      0.32       1      29 [.     205     233 ..     205     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.43
                        Fer4_9  5 CgaCvea.Cpagvvveda 21
                                  C+ C  a Cpa++v+   
  gi|91772121|ref|YP_564813.1| 80 CT-CDGAgCPACTVSLTL 96
                                  44.533337777766555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1e-05
                        Fer4_9  33 e......eaCigCgaCveaCpkgai 51 
                                          e C gCg C++ Cp+++i
  gi|91772121|ref|YP_564813.1| 165 ImpivtfEGCDGCGICINSCPRNII 189
                                   034444456************9965 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 2.7e-07
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C gCg C+++Cp ++++  ++  +++ +     +C  C+ C + C  +ai
  gi|91772121|ref|YP_564813.1| 174 CDGCGICINSCPRNIIQLIDGSAMVADEDL--LKCSLCRLCQDSCDINAI 221
                                   ********************9999998766..57***********87766 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00025
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlr 29 
                                   kC  C+ C+++C  ++++ +a e+    +
  gi|91772121|ref|YP_564813.1| 205 KCSLCRLCQDSCDINAITVSADEKSFIFT 233
                                   7***************9999888776655 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   1.0       7.3   9.3e+03      54      61 ..      82      91 ..      70      92 .. 0.65
   2 !   15.9   0.7   1.4e-05     0.018       2      19 ..     174     191 ..     173     202 .. 0.86
   3 !   11.9   0.2   0.00026      0.33       1      23 [.     205     227 ..     205     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.3
                       Fer4_16 54 i..tgCdiCq 61
                                  +  +gC +C+
  gi|91772121|ref|YP_564813.1| 82 CdgAGCPACT 91
                                  2347888885 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.4e-05
                       Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                   C +Cg C+++CP n i+ 
  gi|91772121|ref|YP_564813.1| 174 CDGCGICINSCPRNIIQL 191
                                   99************9985 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00026
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkek 23 
                                   +C  C+ C ++C  nai+  +++
  gi|91772121|ref|YP_564813.1| 205 KCSLCRLCQDSCDINAITVSADE 227
                                   599**************977443 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5       1.8   2.4e+03      43      47 ..      86      90 ..      73     108 .. 0.63
   2 ?   15.5  11.1   1.1e-05     0.014       6      58 ..     172     222 ..     167     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                       Fer4_21 43 GCnlC 47
                                  GC  C
  gi|91772121|ref|YP_564813.1| 86 GCPAC 90
                                  44444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.1e-05
                       Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   + C gCg C+ +C+ + +q i+++ + v+     +C  C lC + C + ++i+
  gi|91772121|ref|YP_564813.1| 172 EGCDGCGICINSCPRNIIQLIDGS-AMVADEDLLKCSLCRLCQDSCDI-NAIT 222
                                   6799**********9999999875.3444555569************8.8887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.8       1.2   1.6e+03       9      17 ..      81      91 ..      73      93 .. 0.56
   2 ?   14.8   2.7   1.7e-05     0.022       8      21 ..     172     185 ..     166     186 .. 0.87
   3 ?   10.9   1.5   0.00032      0.41       4      20 ..     198     216 ..     195     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                        Fer4_2  9 rCig..CgaCv 17
                                  +C g  C aC+
  gi|91772121|ref|YP_564813.1| 81 TCDGagCPACT 91
                                  56554455664 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.7e-05
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                   + C gCg+C+++CP
  gi|91772121|ref|YP_564813.1| 172 EGCDGCGICINSCP 185
                                   56************ PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00032
                        Fer4_2   4 vvdtd..rCigCgaCvsaC 20 
                                   v+d+d  +C  C+ C+++C
  gi|91772121|ref|YP_564813.1| 198 VADEDllKCSLCRLCQDSC 216
                                   6677777***********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 ?    4.4   3.6      0.05        64       1      11 [.      77      91 ..      77      93 .. 0.85
   2 ?   13.2   1.7   7.8e-05     0.099       2      16 ..     172     186 ..     171     191 .. 0.90
   3 ?    5.4   2.4     0.024        31       3      14 ..     205     216 ..     203     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.05
                        Fer4_4  1 qerCi....gCgsCv 11
                                  q++C+    gC++C+
  gi|91772121|ref|YP_564813.1| 77 QDKCTcdgaGCPACT 91
                                  799988888*****8 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.8e-05
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   e C gCg C+++CP 
  gi|91772121|ref|YP_564813.1| 172 EGCDGCGICINSCPR 186
                                   56************6 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.024
                        Fer4_4   3 rCigCgsCvaaC 14 
                                   +C  C+ C ++C
  gi|91772121|ref|YP_564813.1| 205 KCSLCRLCQDSC 216
                                   799********* 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   2.6   0.00011      0.14       1      14 [.     174     187 ..     174     188 .. 0.94
   2 ?    6.3   2.0     0.017        22       1      15 []     206     220 ..     206     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+gCg C ++CP +
  gi|91772121|ref|YP_564813.1| 174 CDGCGICINSCPRN 187
                                   ************87 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C  C++C ++C  +A
  gi|91772121|ref|YP_564813.1| 206 CSLCRLCQDSCDINA 220
                                   999********7776 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   8.3     0.089   1.1e+02      47      65 .]     170     188 ..      78     188 .. 0.78
   2 ?    7.3  11.2    0.0049       6.3       2      64 ..     171     219 ..     170     220 .. 0.80
   3 ?   11.5   0.5   0.00024      0.31       2      17 ..     203     218 ..     202     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.089
                        Fer4_8  47 alwsCttcgaCtevCpvgi 65 
                                   +++ C +cg C + Cp +i
  gi|91772121|ref|YP_564813.1| 170 TFEGCDGCGICINSCPRNI 188
                                   5667777777777777765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0049
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +e C +Cg C ++Cp     ++ ++   g a+  + e+        l +C+ c+ C++ C ++
  gi|91772121|ref|YP_564813.1| 171 FEGCDGCGICINSCP-----RNIIQLIDGSAMV-ADED--------LLKCSLCRLCQDSCDIN 219
                                   577***********9.....6777888888777.4443........569***********875 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00024
                        Fer4_8   2 lekCieCgaCqsaCpv 17 
                                   l kC  C +Cq++C +
  gi|91772121|ref|YP_564813.1| 203 LLKCSLCRLCQDSCDI 218
                                   6799999999999952 PP

>> OapA  Opacity-associated protein A LysM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.5     7e+03      39      50 ..     128     139 ..     120     143 .. 0.70
   2 ?   10.2   0.0   0.00047       0.6      55      83 ..     214     242 ..     203     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.5
                          OapA  39 plSnlksGqkvr 50 
                                   p+ +l+ Gqkv 
  gi|91772121|ref|YP_564813.1| 128 PIIDLRVGQKVV 139
                                   666788888875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00047
                          OapA  55 aqgkvdelqlekgaksvlftRqsDGsfkr 83 
                                   ++ ++++++++ ++ks +ft +sDGs++ 
  gi|91772121|ref|YP_564813.1| 214 DSCDINAITVSADEKSFIFTMESDGSYTA 242
                                   5678999********************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 ?    7.4  11.3     0.005       6.4       2      56 ..     174     216 ..     173     219 .. 0.82
   2 ?    8.1   2.0    0.0031         4       1      19 [.     205     223 ..     205     262 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.005
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkC 56 
                                   C +Cg C+++Cp++++   +   ++++            e   +C+ C++C+ +C
  gi|91772121|ref|YP_564813.1| 174 CDGCGICINSCPRNIIQLIDGSAMVAD------------EDLLKCSLCRLCQDSC 216
                                   ***************988755544444............5678999999999999 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                       Fer4_17   1 rCiqCgyClpeCpsyeayd 19 
                                   +C+ C+ C ++C  ++++ 
  gi|91772121|ref|YP_564813.1| 205 KCSLCRLCQDSCDINAITV 223
                                   6999999999999877743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1576.16
//
Query:       gi|91772122|ref|YP_564814.1|  [L=283]
Description: UDP pyrophosphate synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-68  228.3   0.1    9.7e-68  228.0   0.1    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.0   0.1   5.4e-72   9.7e-68       1     219 [.      32     254 ..      32     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 228.0 bits;  conditional E-value: 5.4e-72
                                   EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH..HHHHHHHHHHH CS
                  Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk..eellkeelkel 79 
                                   imDGNrR+A k g +++ +Gh++Ga+  ++++e+++e+gvk +tvYafSteNf+R+++e   l+el++   ++++++ +++
  gi|91772122|ref|YP_564814.1|  32 IMDGNRRFAGKLG-KRVDYGHSRGADITERVIEWSYEIGVKELTVYAFSTENFNRTDDETVRLFELIAnkFDYMRKN-ERT 110
                                   9************.99999************************************************8554466555.799 PP

                                   HHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT...SSSGGGHSHHHHHCT CS
                  Prenyltransf  80 lkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkeks.eekkkeeideetlekh 159
                                   +++++rvr++Gd+ ll+++++ea +++eeatk+ +k ++ln+a++Yg+r++iv+av+++++++  +e   e+i+e+t+++h
  gi|91772122|ref|YP_564814.1| 111 HEREIRVRAVGDIGLLSKELQEATRRIEEATKDYRK-FKLNVAIAYGGRQDIVQAVKKMADKVLiNELMPEDISENTVAEH 190
                                   999*****************************6555.**********************988862444558999******* PP

                                   STT..T..SSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHC CS
                  Prenyltransf 160 lytaka..lpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkr 219
                                   ly  ++  + ++Dl+iRt+G+eR+SnFl wq+  +e   yf+  +WP+f+k dll+ ++ yq+r
  gi|91772122|ref|YP_564814.1| 191 LYPIESpsVSNVDLIIRTGGNERISNFLPWQANGNEcaAYFCAPFWPEFRKIDLLRSIRIYQTR 254
                                   **88778899*********************99999999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1794.94
//
Query:       gi|91772123|ref|YP_564815.1|  [L=103]
Description: hypothetical protein Mbur_0042 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-31  106.9   0.2    5.3e-31  106.7   0.2    1.1  1  DUF2551   Protein of unknown function (DUF2551)
  ------ inclusion threshold ------
      0.072   13.2   0.0      0.095   12.9   0.0    1.1  1  FUR       Ferric uptake regulator family


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.2   5.9e-35   5.3e-31       1      83 []      15      96 ..      15      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 5.9e-35
                       DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkek.fdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeeyadl 82
                                  L kyl rD++GiR+ vLk+fl+++++t++++y++l+ek fdvsy+gv++mvGl+++rlGIl++  +++g++n Y Lke+y+ +
  gi|91772123|ref|YP_564815.1| 15 LIKYLGRDDTGIREVVLKMFLDGGTFTTSDVYKHLHEKeFDVSYRGVSAMVGLMNTRLGILSI--DVTGDHNLYLLKEDYKPV 95
                                  679**********************************99************************..***************988 PP

                       DUF2551 83 v 83
                                  v
  gi|91772123|ref|YP_564815.1| 96 V 96
                                  7 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05     0.095       7      73 ..      24      89 ..      21      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                  HHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEES CS
                           FUR  7 TkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryela 73
                                  T  Re +l+++ +  ++ +  +vyk+l e++ ++s   V  ++ l++ +  + +++++++++ y l+
  gi|91772123|ref|YP_564815.1| 24 TGIREVVLKMFLDGGTF-TTSDVYKHLHEKEFDVSYRGVSAMVGLMNTRLGILSIDVTGDHNLYLLK 89
                                  56699999999998886.5689************************999999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 677.09
//
Query:       gi|91772124|ref|YP_564816.1|  [L=348]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   30.0   0.0    8.4e-07   29.1   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
      6e-07   30.0   0.2    2.2e-06   28.2   0.1    1.9  2  Radical_SAM  Radical SAM superfamily
    0.00036   20.8   0.1     0.0007   19.9   0.1    1.4  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.4e-10   8.4e-07       1      90 [.      31     118 ..      31     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.4e-10
                       Fer4_14   1 lfvrlsgCnlsCkgCdnketwks..elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey. 78 
                                   lf+ ++ C   C  C  +e+ k    + ++++ e+ e++l   +++ +++ g  +tGGePL   +k+++++ ++ lk e+ 
  gi|91772124|ref|YP_564816.1|  31 LFI-TGICDRGCFYCPLSEDRKRdtVYANEKAVETDEDVL--CEAHTMDALGTGITGGEPL--LKKEKVIHYIELLKAEFg 106
                                   578.999********9444444311344444444444566..88888889999********..88***************7 PP

                       Fer4_14  79 pekkiwletngt 90 
                                   + ++i+l+t+  
  gi|91772124|ref|YP_564816.1| 107 KAHHIHLYTSIA 118
                                   77*******865 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   3.6e-10   2.2e-06       3     106 ..      33     136 ..      31     139 .. 0.85
   2 ?   -1.6   0.0      0.51     3e+03      49      73 ..     271     294 ..     238     330 .. 0.42

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.6e-10
                                   EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEEEE CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgirit 81 
                                   +t  C ++C +C+ +e+ +r+++++ ++ ve  ++ + e+ + +++ +  ++ggepll +++v  + +l k +  +  +i+
  gi|91772124|ref|YP_564816.1|  33 ITGICDRGCFYCPLSEDrKRDTVYANEKAVETDEDVLCEA-HTMDALGTGITGGEPLLKKEKVIHYIELLKAEfGKAHHIH 112
                                   6789*************88888888888888888888888.6888*************************99977777777 PP

                                   EEECSSCHGHHHHHHHHHTT-SEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelgvdrvs 106
                                   + t+    ++e le+l+ +g+d + 
  gi|91772124|ref|YP_564816.1| 113 LYTSIAP-SKETLEALASAGLDEIR 136
                                   7776555.5***********99875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.51
                                   EEEEESSTGGGSTTHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  49 evilgggepllypdfvellerlakl 73 
                                     +l+ g   + +d++el+  l ++
  gi|91772124|ref|YP_564816.1| 271 DGTLLYGSIEA-SDIEELVSFLNEI 294
                                   33333333333.3333333333333 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.2e-07    0.0007       4      92 ..      25     115 ..      17     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-07
                       Fer4_12   4 eGvrlslfvsg.CnlsCkgCfnketwsfk..sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevke 81 
                                   +G  ++lf++g C++ C +C   e ++ +  + +e   e+ e ++ +++     g  ++GGEPll  ++e+++  ++ +k+
  gi|91772124|ref|YP_564816.1|  25 QGAKMVLFITGiCDRGCFYCPLSEDRKRDtvYANEKAVETDEDVLCEAHTMDALGTGITGGEPLL--KKEKVIHYIELLKA 103
                                   466679996655********8666665553355555566666666677778889999********..************** PP

                       Fer4_12  82 ekp.ekdiwlyt 92 
                                   e+     i lyt
  gi|91772124|ref|YP_564816.1| 104 EFGkAHHIHLYT 115
                                   *99555555666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2017.93
//
Query:       gi|91772125|ref|YP_564817.1|  [L=63]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   35.4  15.0    1.6e-05   24.8   4.3    2.2  2  Fer4_6    4Fe-4S binding domain
    1.5e-08   34.1  13.4    3.4e-05   23.5   3.6    2.1  2  Fer4      4Fe-4S binding domain
    2.9e-07   30.9  10.5      4e-07   30.5  10.5    1.2  1  Fer4_7    4Fe-4S dicluster domain
    1.8e-06   27.9  11.7    2.1e-06   27.7  11.7    1.1  1  Fer4_21   4Fe-4S dicluster domain
    1.9e-05   24.7  10.5    2.8e-05   24.2  10.5    1.3  1  Fer4_9    4Fe-4S dicluster domain
    4.1e-05   24.4   9.2     0.0031   18.4   0.5    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    9.7e-05   22.4   8.9      0.005   16.9   2.0    2.1  2  Fer4_10   4Fe-4S dicluster domain
     0.0039   17.2  16.9      0.052   13.7   4.4    2.2  2  Fer4_2    4Fe-4S binding domain
     0.0076   16.7  12.8      0.043   14.3   1.2    2.2  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   16.7  15.6       0.28   12.2   3.8    2.2  2  Fer4_3    4Fe-4S binding domain
      0.014   15.8  12.1       0.35   11.4   2.5    2.1  2  Fer4_8    4Fe-4S dicluster domain
       0.21   12.2  13.5       0.68   10.5   2.6    2.1  2  Fer4_17   4Fe-4S dicluster domain
        1.1   10.1  12.0       0.33   11.7   4.2    2.1  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.9   4.5e-06    0.0062       9      24 .]      15      30 ..      15      30 .. 0.96
   2 !   24.8   4.3   1.2e-08   1.6e-05       2      19 ..      37      54 ..      36      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-06
                        Fer4_6  9 CigCgdCvrvCPegai 24
                                  C+ Cg+C+ +C ++a+
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICSHDAL 30
                                  *************996 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.2e-08
                        Fer4_6  2 veidpdkCigCgdCvrvC 19
                                  v+id d+C+ C+dC++vC
  gi|91772125|ref|YP_564817.1| 37 VTIDHDRCVLCMDCAKVC 54
                                  89**************** PP

>> Fer4  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   3.9e-06    0.0054       8      24 .]      15      31 ..      14      31 .. 0.94
   2 !   23.5   3.6   2.5e-08   3.4e-05       1      23 [.      37      59 ..      37      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-06
                                  SSS-THHHHHSTTTEEE CS
                          Fer4  8 CigCGaCvevCPvgAIt 24
                                  C +CG+C+ +C ++A++
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICSHDALE 31
                                  **************985 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 2.5e-08
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  v+id ++C+ C+ C++vC   AI
  gi|91772125|ref|YP_564817.1| 37 VTIDHDRCVLCMDCAKVCFIKAI 59
                                  68****************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 !   30.5  10.5   2.9e-10     4e-07       2      48 ..      15      54 ..      14      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.9e-10
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48
                                  C +Cg+C+  C+++a+e++++       +v+id+++C+ C  C++vC
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICSHDALEFHND-------RVTIDHDRCVLCMDCAKVC 54
                                  ******************775.......69***************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7  11.7   1.5e-09   2.1e-06       8      55 ..      15      58 ..       9      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.5e-09
                       Fer4_21  8 CigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55
                                  C +CgkC++ C+   h+a+e+++++v ++ +d+Cv C  C++vC ++ 
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICS---HDALEFHNDRV-TIDHDRCVLCMDCAKVCFIKA 58
                                  99*********9...9*****97776.99***************9843 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2  10.5   2.1e-08   2.8e-05       2      49 ..      15      57 ..      14      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.1e-08
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                  C++Cg+C   C +++ + ++ + ++ ++     +C+ C++C+++C  +
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICSHDALEFHNDRVTIDHD-----RCVLCMDCAKVCFIK 57
                                  *****************99999999985.....5***********655 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5   2.2e-06    0.0031       2      23 ..      15      36 ..      14      43 .. 0.83
   2 !   10.5   2.7   0.00067      0.92       1      18 [.      43      60 ..      43      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.2e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikekkek 23
                                  C +CgkCa +C ++a++  +++
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICSHDALEFHNDR 36
                                  ****************988544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00067
                       Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                  rC+ C  Ca+vC  +ai 
  gi|91772125|ref|YP_564817.1| 43 RCVLCMDCAKVCFIKAIV 60
                                  6***********999985 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.7   0.00045      0.62      44      55 ..      14      25 ..       3      34 .. 0.71
   2 !   16.9   2.0   3.6e-06     0.005       2      19 ..      37      54 ..      36      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                       Fer4_10 44 kCtgcgaCveaC 55
                                   C +cg+C+ +C
  gi|91772125|ref|YP_564817.1| 14 GCNNCGKCALIC 25
                                  455555555555 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.6e-06
                       Fer4_10  2 vvidddtCirCgkCvkaC 19
                                  v id d+C+ C +C k+C
  gi|91772125|ref|YP_564817.1| 37 VTIDHDRCVLCMDCAKVC 54
                                  789*************** 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   4.6   0.00079       1.1      10      21 ..      15      26 ..      14      27 .. 0.90
   2 !   13.7   4.4   3.7e-05     0.052       2      20 ..      36      54 ..      35      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00079
                        Fer4_2 10 CigCgaCvsaCP 21
                                  C++Cg+C   C 
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICS 26
                                  ********9996 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.7e-05
                        Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                  +v +d drC+ C  C ++C
  gi|91772125|ref|YP_564817.1| 36 RVTIDHDRCVLCMDCAKVC 54
                                  6889*************** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.2   3.1e-05     0.043       4      15 ..      15      26 ..      13      35 .. 0.94
   2 !    7.6   4.5    0.0044         6       2      14 ..      42      54 ..      41      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                        Fer4_4  4 CigCgsCvaaCP 15
                                  C++Cg+C  +C+
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICS 26
                                  ***********6 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0044
                        Fer4_4  2 erCigCgsCvaaC 14
                                  +rC+ C+ C  +C
  gi|91772125|ref|YP_564817.1| 42 DRCVLCMDCAKVC 54
                                  8**********99 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.0    0.0007      0.97       1      15 []      15      29 ..      15      29 .. 0.93
   2 ?   12.2   3.8   0.00021      0.28       1      15 []      44      58 ..      44      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0007
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C++Cg C   C  +A
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICSHDA 29
                                  ***********8877 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00021
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ C+ C +vC+ +A
  gi|91772125|ref|YP_564817.1| 44 CVLCMDCAKVCFIKA 58
                                  ***********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 ?   10.3   2.2   0.00055      0.76      45      62 ..       9      26 ..       2      29 .. 0.76
   2 ?   11.4   2.5   0.00025      0.35      49      62 ..      42      55 ..      29      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                        Fer4_8 45 eealwsCttcgaCtevCp 62
                                  + a+  C++cg+C+  C 
  gi|91772125|ref|YP_564817.1|  9 HMAIIGCNNCGKCALICS 26
                                  556778999999999986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                        Fer4_8 49 wsCttcgaCtevCp 62
                                  ++C+ c+ C++vC 
  gi|91772125|ref|YP_564817.1| 42 DRCVLCMDCAKVCF 55
                                  78999999999996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.6    0.0005      0.68      41      59 ..      10      28 ..       1      30 [. 0.78
   2 ?    8.0   3.2     0.003       4.2      44      56 ..      42      54 ..      29      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                       Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                  +++  C++Cg+C+  C ++
  gi|91772125|ref|YP_564817.1| 10 MAIIGCNNCGKCALICSHD 28
                                  67889********999876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                       Fer4_17 44 slCieCgeCerkC 56
                                  ++C+ C  C+++C
  gi|91772125|ref|YP_564817.1| 42 DRCVLCMDCAKVC 54
                                  7899999998888 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9     0.083   1.1e+02       8      19 ..      15      27 ..      13      36 .. 0.74
   2 ?   11.7   4.2   0.00024      0.33       1      18 [.      37      54 ..      37      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.083
                       Fer4_15  8 CigcglCvaea.p 19
                                  C  cg C+  +  
  gi|91772125|ref|YP_564817.1| 15 CNNCGKCALICsH 27
                                  999*****99944 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00024
                       Fer4_15  1 VvvDrdaCigcglCvaea 18
                                  V++D+d+C  c  C++++
  gi|91772125|ref|YP_564817.1| 37 VTIDHDRCVLCMDCAKVC 54
                                  89*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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):              13  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 457.02
//
Query:       gi|91772126|ref|YP_564818.1|  [L=111]
Description: hypothetical protein Mbur_0046 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.057   12.9   1.0      0.069   12.7   1.0    1.1  1  E1-E2_ATPase  E1-E2 ATPase


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 ?   12.7   1.0   3.9e-06     0.069     110     163 ..      54     104 ..      25     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTH CS
                  E1-E2_ATPase 110 plqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaL 163
                                   p++  + ++++++++++ll+++ ++l+++++++   +++l  +++l++++Pc +
  gi|91772126|ref|YP_564818.1|  54 PFETVMFSYVGTFATLALLLLFDTLLFQITTFD---RTILTLVVVLTITLPCVF 104
                                   455555555566666666665555555555444...78**************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 725.71
//
Query:       gi|91772127|ref|YP_564819.1|  [L=514]
Description: type II secretion system protein E [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-32  112.6   0.0    2.6e-32  112.0   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.066   13.6   0.0       0.47   10.8   0.0    2.2  2  AAA_16    AAA ATPase domain
       0.16   11.4   0.0       0.33   10.5   0.0    1.4  1  AAA_7     P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.0   4.4e-36   2.6e-32       3     254 ..      92     356 ..      90     371 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 4.4e-36
                         T2SSE   3 illeallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrv 82 
                                    +le +l d++v+d+ ++ p +   v+  +dg e  +  +l+++ l  ++sr+ a +++   e  p+++ +l+e gvr+ v
  gi|91772127|ref|YP_564819.1|  92 GILEDILSDTRVTDVYINAPADkNPVHVLIDGDECITNIFLSQDDLDSMVSRFRAISGRPFGEATPILEMELKEFGVRVSV 172
                                   57899*************9988799999****99*********************************************** PP

                         T2SSE  83 vllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivt 162
                                   +  P++a+  a++ Rk+s +  tl +l+a+++ ++  a +l+  +  + +ilv+G    GKt ll a++ ei+++  ri+t
  gi|91772127|ref|YP_564819.1| 173 IGDPLSANgLAYAFRKHSRRPWTLPKLIATGSISPLTAGLLSFLMDGETSILVAGEVRAGKTSLLSAMIMEIPQK-YRILT 252
                                   *****99989*****************************************************************.***** PP

                         T2SSE 163 vEDpvEiqleganqvqlnak...........kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgs..lsT 230
                                   +ED++Ei +e+ + +  + +           + ++  + +lra+LRl    +++GE+R++e+  + +A++ G  g   l+T
  gi|91772127|ref|YP_564819.1| 253 IEDTREIPIEDLQELGWKMQgmssrssilntNLEIRPEVALRATLRLGNSSLVIGEVRGEEVKVLYEAMQVGAAGNseLGT 333
                                   **************99999999999****7777778889*********************************9884449** PP

                         T2SSE 231 lHansaagalerLe.qlgaeveaae 254
                                   +H  sa  + er+  +lg  v++a 
  gi|91772127|ref|YP_564819.1| 334 IHGASASAVYERIVhTLG--VPPAS 356
                                   ************851566..55555 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   7.8e-05      0.47      16      53 ..     213     249 ..     205     265 .. 0.76
   2 ?   -0.4   0.0      0.22   1.3e+03       5      35 ..     310     340 ..     309     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.8e-05
                        AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdgg 53 
                                   l+ + +g+  ++l+ Ge   GK+sl+ +   ++ +++ 
  gi|91772127|ref|YP_564819.1| 213 LSFLMDGE-TSILVAGEVRAGKTSLLSAMIMEIPQKYR 249
                                   55555666.79***************887778888853 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.22
                        AAA_16   5 ReeeleqLlsalervrsgrpelvllsGesGv 35 
                                   R+ee++ L +a++  ++g +el  ++G+s++
  gi|91772127|ref|YP_564819.1| 310 RGEEVKVLYEAMQVGAAGNSELGTIHGASAS 340
                                   99*************************9975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.5e-05      0.33      25      79 ..     212     265 ..     206     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.5e-05
                         AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlq 79 
                                   ll+ l++ + ++l+ G++  GKt++++ ++ +++ +ky +lti+ +     ++lq
  gi|91772127|ref|YP_564819.1| 212 LLSFLMDGETSILVAGEVRAGKTSLLSAMIMEIP-QKYRILTIEDTREIPIEDLQ 265
                                   788999****************************.9**99999877766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3370.19
//
Query:       gi|91772128|ref|YP_564820.1|  [L=142]
Description: hypothetical protein Mbur_0048 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 932.18
//
Query:       gi|91772129|ref|YP_564821.1|  [L=476]
Description: UDP-glucose/GDP-mannose dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  123.9   0.0      1e-35  123.1   0.0    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      2e-21   76.0   0.3    2.6e-20   72.4   0.0    2.5  2  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    6.5e-20   71.5   0.1    2.2e-19   69.8   0.0    1.9  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.046   13.0   0.1        7.3    5.9   0.0    2.6  2  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase


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 !  123.1   0.0   2.2e-39     1e-35       2     184 ..      17     208 ..      16     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 2.2e-39
                                   EEEEE--STTHHHHHHHHHHCT..SEEEEE-S-H....HHHHHHCTTS-SS..--TTHHHHHHHHCHTTTEEEES-HHHHH CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeig..hevigvDide....ekvdklnsgkipi..yepgLeelvkkavesgrlsfttdvekav 74 
                                   ki v+G+GYvG++ aa++a       v+g   d+     k+++ln+g++p+  +epgLe+l++k+v++++++ t d+++ +
  gi|91772129|ref|YP_564821.1|  17 KIGVLGMGYVGIPAAALFADSEkfDLVLGFQRDSpssgYKIEMLNKGDSPLkgEEPGLEDLLRKVVDANKFECTPDFSR-I 96 
                                   8******************887634577877665333369*********99556************************9.* PP

                                   HC-SEEEE-----B-T.TTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEEE-- CS
                UDPG_MGDP_dh_N  75 eeadvifiaVgTPskk.kgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvvsnP 153
                                   +e d++ +a+ TP+ + +  ++D +++ + +r+++++lk+g +vv++ST+ +gt++ l+++ilee+s  k g+df +++ P
  gi|91772129|ref|YP_564821.1|  97 SEVDAVALAIQTPFLDpASLQPDFSALIEGIRNVGKYLKEGMLVVLESTITPGTTDTLARQILEEESGLKaGEDFALAHAP 177
                                   **************9988999********************************************999888********** PP

                                   ----TTSHHHHHHS-S-EEEEESSCHHHHHH CS
                UDPG_MGDP_dh_N 154 EflregsavkdllnpdrvviGveekkaeaal 184
                                   E++  g  +k++++ dr+v+G ++++++ a+
  gi|91772129|ref|YP_564821.1| 178 ERVMVGRLLKNIQEHDRIVGGIDDNSTKRAV 208
                                   *************************999554 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 !   72.4   0.0   5.8e-24   2.6e-20       2      82 ..     227     309 ..     226     318 .. 0.89
   2 ?    0.5   0.1      0.16     7e+02      39      61 ..     447     469 ..     430     472 .. 0.79

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 5.8e-24
                  UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldpr..igpkflkpglGvGGsclpkDvkaLvalaeelgl 80 
                                   +AE++K a+N+f++++I+ iN+la +cea+gi+v +V+ ++ + +   i++++l+pg+GvGG+cl kD++ L + + + + 
  gi|91772129|ref|YP_564821.1| 227 AAEVTKTAENTFRDLQIAAINQLALYCEAMGINVYDVRAGIDSLKGegITRAVLYPGAGVGGHCLTKDTYHLERGVTTSNG 307
                                   79***************************************9987667999********************9887766665 PP

                  UDPG_MGDP_dh  81 ea 82 
                                   ++
  gi|91772129|ref|YP_564821.1| 308 DL 309
                                   55 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.16
                  UDPG_MGDP_dh  39 ieavgldprigpkflkpglGvGG 61 
                                   ++++  d +ig+ f+++g+G G+
  gi|91772129|ref|YP_564821.1| 447 RNVLDPDAFIGNGFVYKGIGRGD 469
                                   566778999***********997 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   4.6e+03      54      87 ..     228     246 ..     202     263 .. 0.61
   2 !   69.8   0.0   4.8e-23   2.2e-19       1     105 []     354     452 ..     354     452 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                   CEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHH CS
                UDPG_MGDP_dh_C  54 vevvdsleealkgadaiviltehdefkeldlakl 87 
                                   +ev++               t+ + f++l++a +
  gi|91772129|ref|YP_564821.1| 228 AEVTK---------------TAENTFRDLQIAAI 246
                                   44444...............44455555544444 PP

  == domain 2  score: 69.8 bits;  conditional E-value: 4.8e-23
                                   EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGG CS
                UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefke 81 
                                   ailG+af +d+dD R+ p+    + L e+gaev ++DP+v + +        +ve++++++e +++ad++ +lt h+++ +
  gi|91772129|ref|YP_564821.1| 354 AILGWAFINDSDDARNPPSEPYRNLLIENGAEVMVHDPHVLNYP--------EVEIMKNIDEVIENADVVAVLTGHSDYFK 426
                                   8***************************************9955........5889************************* PP

                                   S-HHHHHHCC..SS-EEEESSS-CCC CS
                UDPG_MGDP_dh_C  82 ldlaklkelm..kpavvfDgrnvldp 105
                                   ld a l++l   k+ v++Dgrnvldp
  gi|91772129|ref|YP_564821.1| 427 LDPAYLRSLTekKNTVIVDGRNVLDP 452
                                   *********998889*********96 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 ?    5.9   0.0    0.0016       7.3     112     146 ..     190     226 ..     177     239 .. 0.83
   2 ?    4.2   0.0    0.0054        24      49      94 ..     372     426 ..     337     457 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0016
                                   C-TTEEE-SB-HHHHCTTSSEE--T..TTSCHHHHHH CS
                 THF_DHG_CYH_C 112 vekgklvGDvdfeevkevasaitPv..pgGVGpmTva 146
                                   +e++++vG +d ++ k+ +++++Pv  +g + pmT++
  gi|91772129|ref|YP_564821.1| 190 QEHDRIVGGIDDNSTKRAVELYSPVltKGQIIPMTAT 226
                                   37899*******************96679999**986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0054
                                   HHHHHHHHHCTT-EEEEE-TTS.........CCHHHHHCCSSEEEE-SS-TT-B- CS
                 THF_DHG_CYH_C  49 gkplallLleknatVtvchskt.........kdlaeitreadivvvavGkpelik 94 
                                    +p   lL e++a V+v + +          k+++e++++ad+v v +G+ +  k
  gi|91772129|ref|YP_564821.1| 372 SEPYRNLLIENGAEVMVHDPHVlnypeveimKNIDEVIENADVVAVLTGHSDYFK 426
                                   456777777777777766555444445555589999*********9999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3154.01
//
Query:       gi|91772130|ref|YP_564822.1|  [L=80]
Description: hypothetical protein Mbur_0050 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-38  129.9   9.1    2.9e-38  129.9   9.1    1.3  2  DUF5371   Family of unknown function (DUF5371)


Domain annotation for each model (and alignments):
>> DUF5371  Family of unknown function (DUF5371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       0.9   1.6e+04      41      46 ..       6      11 ..       6      12 .. 0.78
   2 !  129.9   9.1   1.6e-42   2.9e-38       1      65 []      13      77 ..      13      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.9
                       DUF5371 41 eCeYtd 46
                                  +C+Y d
  gi|91772130|ref|YP_564822.1|  6 KCPYGD 11
                                  699976 PP

  == domain 2  score: 129.9 bits;  conditional E-value: 1.6e-42
                       DUF5371  1 mvKivHAqtvLaeeeLeeLKkKtnesstkdAlsiAveHYleCeYtdlneemwtkKlEkvvqKKkk 65
                                  ++KivHAqtvLaee+L +LK+K+n++stk+Al+iAveHY+eCeYtd+neemwtkKlEk+vqKKk+
  gi|91772130|ref|YP_564822.1| 13 KMKIVHAQTVLAEEQLLALKDKCNNTSTKEALIIAVEHYIECEYTDMNEEMWTKKLEKIVQKKKE 77
                                  59*************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1462  (0.0815439); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 459.29
//
Query:       gi|91772131|ref|YP_564823.1|  [L=150]
Description: N-acetylglutamate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-12   46.4   0.0    9.7e-12   45.2   0.0    1.6  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.3e-11   43.9   0.0    3.4e-11   43.4   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      7e-09   35.7   0.0    8.6e-09   35.4   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.4e-05   23.0   0.0    8.6e-05   22.6   0.0    1.2  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    0.00057   20.0   0.0      0.016   15.3   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0016   18.6   0.0     0.0041   17.3   0.0    1.6  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0064   17.2   0.0      0.019   15.7   0.0    1.8  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.34   11.0   0.1    1.7  1  HTH_16           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         4     9e+03      66      71 ..      17      22 ..       4      23 .. 0.58
   2 !   45.2   0.0   4.3e-15   9.7e-12       4      76 .]      40     117 ..      37     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                                  HHHHHH CS
                Acetyltransf_7 66 ikfYek 71
                                  i+fY+k
  gi|91772131|ref|YP_564823.1| 17 ISFYAK 22
                                  459988 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 4.3e-15
                                   EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEE.EEEETHHHHHHHHHHTTEE CS
                Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.....aekgiile.qlelnaekaikfYeklGFe 75 
                                   +++V+e dg +vG+++l++l+   aei  +a++peyrgk iG++Ll+a     +   ++ + + +l  ++a  f+ek+ F+
  gi|91772131|ref|YP_564823.1|  40 NFYVYEIDGDVVGCCGLQVLWadlAEILSFAILPEYRGKCIGTQLLNAclddaR--ELKATsVFTL--TYAPVFFEKNHFK 116
                                   79******************998888888******************8443321..2222222233..26778*******8 PP

                                   E CS
                Acetyltransf_7  76 e 76 
                                   +
  gi|91772131|ref|YP_564823.1| 117 R 117
                                   5 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.5e-14   3.4e-11      31      99 ..      38     102 ..       8     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.5e-14
                                   TTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE CS
                Acetyltransf_1  31 eaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivl 99 
                                   +   ++v+e dg ++G+++l   +    + a+i s+a+ peyrgk +G++Ll+a+++ are  ++ ++ 
  gi|91772131|ref|YP_564823.1|  38 IR-NFYVYEIDGDVVGCCGLQVLWA---DLAEILSFAILPEYRGKCIGTQLLNACLDDARELKATSVFT 102
                                   33.48889*****************...9********************************98877643 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   3.8e-12   8.6e-09      28     112 ..      36     121 ..       9     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.8e-12
               Acetyltransf_10  28 egealllvaeeggkivGvielrdgs....hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYekl 104
                                   e+   ++v+e +g +vG+++l+  +    +i  +++ peyrg+ ig++Ll+a+++ a++   k +++v   +ya  f+ek 
  gi|91772131|ref|YP_564823.1|  36 ESIRNFYVYEIDGDVVGCCGLQVLWadlaEILSFAILPEYRGKCIGTQLLNACLDDAREL--K-ATSVFTLTYAPVFFEKN 113
                                   556679*************9888877888***************************9655..4.89*************** PP

               Acetyltransf_10 105 GFkavgee 112
                                    Fk+v++ 
  gi|91772131|ref|YP_564823.1| 114 HFKRVDKA 121
                                   ****9875 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.9e-08   8.6e-05      23      75 ..      62     114 ..      40     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.9e-08
               Acetyltransf_CG  23 gvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvptCsyvaaylekhp 75 
                                   +  ++    + +e+rGk i+ +L +a+lddare + + v t +y+  ++ek++
  gi|91772131|ref|YP_564823.1|  62 DLAEILSFAILPEYRGKCIGTQLLNACLDDARELKATSVFTLTYAPVFFEKNH 114
                                   55667777788**************************************9986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     7e-06     0.016       2     122 ..       2     112 ..       1     118 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7e-06
                                   EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEE.TTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE CS
                Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaed.ngelvgqlallplelnvpGktlkaagvtgVav 81 
                                   ir++t +d+d+++++ +  F  +++    +++++++l+e+ r + +++ +g++vg+++l  l         + a + + a 
  gi|91772131|ref|YP_564823.1|   2 IRKATLNDVDAIKSIIS--FYAKQELM--LHRSVSELYESIRNFYVYEiDGDVVGCCGLQVL-------WADLAEILSFAI 71 
                                   78888888888888875..55555553..557788888876555555448888888876443.......345688999999 PP

                                   -CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHT CS
                Acetyltransf_9  82 apehrgrgvlskLlaraleemreegqplsllfPssipiYrr 122
                                    pe+rg+ + ++Ll++ l+++re +++ ++   +++ ++++
  gi|91772131|ref|YP_564823.1|  72 LPEYRGKCIGTQLLNACLDDARELKATSVFTLTYAPVFFEK 112
                                   ***********************999999988888888776 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0041       1     121 [.       2     107 ..       2     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkrakdwkael 80 
                                   ir at++D ++i+ i ++y      ++   + sv e+   + +        f v+e ++++vG + l+ + +   d + +l
  gi|91772131|ref|YP_564823.1|   2 IRKATLNDVDAIKSIISFYAK----QELMLHRSVSELYESIRN--------FYVYEiDGDVVGCCGLQ-VLW--ADLAEIL 67 
                                   899**************9544....233344566666555555........455566**********9.556..699999* PP

                Acetyltransf_4  81 svylaerdnnkeglgrelidaleqvlkeqnienllaeiasp 121
                                   s+ +     + + +g +l++a+ + ++e   ++ ++ +++p
  gi|91772131|ref|YP_564823.1|  68 SFAIL-PEYRGKCIGTQLLNACLDDARELKATSVFTLTYAP 107
                                   ****8.679*****************999999999998876 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.3e-06     0.019       5     117 ..       3     100 ..       1     118 [. 0.66
   2 ?   -1.0   0.0       1.2   2.6e+03      62      79 ..     125     142 ..     106     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.3e-06
                Acetyltransf_3   5 rplteeDleal.f..elrsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeae 82 
                                   r++t  D++a+    ++++ +e+m     +++++e +e ++++         y + i   d++v+G++gl+ l  +  +  
  gi|91772131|ref|YP_564823.1|   3 RKATLNDVDAIkSiiSFYAKQELML----HRSVSELYESIRNF---------YVYEI---DGDVVGCCGLQVLWAD-LAEI 66 
                                   5555555555521122455555553....45555555555532.........44555...6769*******55444.4245 PP

                Acetyltransf_3  83 lgymlapsfwgkGyateavralleyafeelglerl 117
                                   l++ + p+++gk ++t  ++a+l+ a +el+++ +
  gi|91772131|ref|YP_564823.1|  67 LSFAILPEYRGKCIGTQLLNACLDDA-RELKATSV 100
                                   6799********************99.55555544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                Acetyltransf_3  62 dtgv.iGsvglrdleeede 79 
                                   + ++ iG++ ++++++ de
  gi|91772131|ref|YP_564823.1| 125 H-KIwIGCIKCHKFPDCDE 142
                                   3.37799999999988765 PP

>> HTH_16  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00015      0.34       4      38 ..       2      38 ..       1      52 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                        HTH_16  4 ieaAvnGDeeAieeiLkhY..egyIrklSlrklyded 38
                                  i +A+ +D +Ai+ i+++Y  + ++ + S   ly++ 
  gi|91772131|ref|YP_564823.1|  2 IRKATLNDVDAIKSIISFYakQELMLHRSVSELYESI 38
                                  89*****************333566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 907.31
//
Query:       gi|91772132|ref|YP_564824.1|  [L=309]
Description: hypothetical protein Mbur_0052 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00011   22.4   0.2    0.00038   20.7   0.0    1.9  2  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.051   13.7   0.2       0.27   11.3   0.1    2.2  2  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.32   2.9e+03      65      80 ..      77      92 ..      44     106 .. 0.52
   2 !   20.7   0.0   4.2e-08   0.00038      14      48 ..     115     160 ..     101     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.32
                                  ECTTEEEEEECEEECC CS
                  NTP_transf_2 65 ellglevdlvtrekle 80
                                  +  +++v l++ +++ 
  gi|91772132|ref|YP_564824.1| 77 PEDQVKVILHPSDPIS 92
                                  3334444444444444 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.2e-08
                                   TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH...........H CS
                  NTP_transf_2  14 vakvvlfGSyarGtalkgSDiDllvvlpeevsre...........k 48 
                                   + k+ ++GS+  G+ +  SD+D++v+++++++             +
  gi|91772132|ref|YP_564824.1| 115 IEKMGVTGSFLPGLQNDMSDVDFVVYGKDWFNARdviavakakggF 160
                                   67999*************************8766544443333331 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.33     3e+03      27      42 ..      49      64 ..      44      87 .. 0.68
   2 ?   11.3   0.1     3e-05      0.27      14      47 ..     116     149 ..      89     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.33
                                  -----EEEEEEEESS- CS
                       Polbeta 27 areeSDiDlavllkek 42
                                    ++ D+D+a+ + ++
  gi|91772132|ref|YP_564824.1| 49 NYRKYDFDVAFDFMRN 64
                                  5566799999887766 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3e-05
                                   HSTTEEEEEE-S------EEEEEEEESS---HHH CS
                       Polbeta  14 elaylFGSrakgkareeSDiDlavllkekldlee 47 
                                   e + + GS++ g +++ SD+D+ v+ k+  +  +
  gi|91772132|ref|YP_564824.1| 116 EKMGVTGSFLPGLQNDMSDVDFVVYGKDWFNARD 149
                                   555677********************99844444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1731.61
//
Query:       gi|91772133|ref|YP_564825.1|  [L=103]
Description: hypothetical protein Mbur_0053 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   86.3   2.4    1.5e-24   86.2   2.4    1.0  1  DUF2098   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.025   14.3   0.4      0.057   13.2   0.4    1.5  1  DUF2733   Protein of unknown function (DUF2733)


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 !   86.2   2.4   1.6e-28   1.5e-24       1      94 []      14     103 .]      14     103 .] 0.93

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 1.6e-28
                       DUF2098   1 eievGsvVrYinTgTvGkVvdikkeedgevwvkLdstdLyYrvdtLevidekekkkekeekekedleelekkekeleeevd 81 
                                   +i+vGs VrYinT+T+G ++di+++++g+ w++Ld+t+LyYr+dtL+++++ ++k +++  +ke+++el k ++e+    +
  gi|91772133|ref|YP_564825.1|  14 PINVGSNVRYINTDTIGVIEDITTDDEGT-WALLDTTQLYYRIDTLQITEKVSTKGKEHVLTKEEAKELIKAHSETG---Q 90 
                                   599********************999999.********************999***********************9...3 PP

                       DUF2098  82 eeketdesceGGG 94 
                                   e+ e+  +++GGG
  gi|91772133|ref|YP_564825.1|  91 EKVEDVFQATGGG 103
                                   3336778999998 PP

>> DUF2733  Protein of unknown function (DUF2733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   6.3e-06     0.057      13      25 ..       6      17 ..       5      20 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-06
                       DUF2733 13 npvkDVdGepINv 25
                                   pv D+dG+pINv
  gi|91772133|ref|YP_564825.1|  6 KPV-DIDGKPINV 17
                                  79*.********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 662.32
//
Query:       gi|91772134|ref|YP_564826.1|  [L=317]
Description: GTP cyclohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-84  281.4   2.6    7.7e-84  281.2   2.6    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2


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 !  281.2   2.6   4.3e-88   7.7e-84       2     259 .]       9     301 ..       8     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 281.2 bits;  conditional E-value: 4.3e-88
                                   XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG..GGHHH CS
                        GCHY-1   2 pDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee..kslee 79 
                                   pDvq+++++++i+l+rVGv+gvk++v++k+k+k+++ l++++++fvdLp+++kG+++SR++e+++   e++++   +++e+
  gi|91772134|ref|YP_564826.1|   9 PDVQANRPKIPINLTRVGVTGVKKLVEIKRKDKRPIVLISTFEIFVDLPSDRKGANLSRNFEAMDeVLEKAINLpvYEIEK 89 
                                   9****************************************************************4445555547855555 PP

                                   ....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE...TT.E..EEEEEEEEEEEEEE-HHHHH CS
                        GCHY-1  80 ....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaeler.ke.e..vkltvgvevpvttlCPCske 152
                                       ++++ll+++eya+r+ev++k+ey+++++ap ++++++e +++++ea+++r ++ +  vk+ +g+ev+++t+CPC++e
  gi|91772134|ref|YP_564826.1|  90 lcndVAKSLLRRHEYATRSEVRMKSEYVVKREAPSTKMKCQEVVDIFAEATATRlEDgDidVKKLIGAEVVGMTACPCAQE 170
                                   5556************************************************998544356******************** PP

                                   HS.........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHH CS
                        GCHY-1 153 isrell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavt 212
                                   i+r+++                     ++++HnQR++  +++e+ + + +v++e++i+++ess+ss++ ellKR+DE+ v+
  gi|91772134|ref|YP_564826.1| 171 IMRDNAktalrelgvgletvmnflnkvPMATHNQRGRGIISLEV-SGDVDVSLETIIRIIESSMSSSIVELLKRADEALVV 250
                                   ***999*************************************6.58999******************************* PP

                                   HHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                        GCHY-1 213 ekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                   e+a++npkFvED+vR++a+++     v+ef         ++++ neESiH+Hna+A
  gi|91772134|ref|YP_564826.1| 251 ERAHQNPKFVEDCVRTMAQNI-----VSEFahvpdsalvTIKQINEESIHRHNAFA 301
                                   *********************.....6666666889999****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2018.63
//
Query:       gi|91772135|ref|YP_564827.1|  [L=98]
Description: nucleoid protein MC1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-38  129.5   1.0    4.9e-38  129.3   1.0    1.0  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 !  129.3   1.0   2.7e-42   4.9e-38       1      91 [.       3      89 ..       3      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 2.7e-42
                           MC1  1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWledkit 83
                                  ++rnf+lrde+G+e++vf+GkqPrqaaLk+a+r++++    + k ++i Lre+Gtkk+h++ g++e+++aP++kpdW++dki 
  gi|91772135|ref|YP_564827.1|  3 ETRNFVLRDEKGNESGVFTGKQPRQAALKVANRGKGT----KKKPDNIMLRERGTKKIHVFVGWKEMVDAPKNKPDWMPDKIN 81
                                  68**********************************9....677899************************************ PP

                           MC1 84 kanvskqg 91
                                  k+ v+kq+
  gi|91772135|ref|YP_564827.1| 82 KPFVKKQK 89
                                  *****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 639.02
//
Query:       gi|91772136|ref|YP_564828.1|  [L=304]
Description: acetylglutamate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   5.0    2.4e-46  158.3   5.0    1.0  1  AA_kinase    Amino acid kinase family
  ------ inclusion threshold ------
      0.045   13.7   0.0      0.077   12.9   0.0    1.3  1  RNaseH_like  Ribonuclease H-like


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   5.0   2.7e-50   2.4e-46       2     241 .]      31     278 ..      30     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 2.7e-50
                                   EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHHH CS
                     AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrdal 82 
                                   + V+K+GG+++ d++   + +++++i  l+  g+++v+VhGgg+ + + +++ +g +s+++  glr t++e++e+a+++++
  gi|91772136|ref|YP_564828.1|  31 VMVIKVGGHAMVDPQV--MSDIVQDIVLLRFVGIHPVIVHGGGPEITEKMDR-MGKKSEFIG-GLRITDDETMEIARMVLV 107
                                   57**************..**********************************.*********.****************** PP

                                   HHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.................HHHTTTCEEECCHHHHHHHTT-EEEEESEEE CS
                     AA_kinase  83 aslgerlvaallaaglpavglsaaaldateagr...............degsdgnvesvdaeaieelleagvvpvltgfig 148
                                   + +++r+v+ + ++g + vgls+++ +++ a++               d g +g+ e ++ e i+   ++g++pv+++++ 
  gi|91772136|ref|YP_564828.1| 108 GNINTRIVSLISKHGGKGVGLSGKDGNMILAKKkptqkiliediehdvDLGWVGDTEIINPEIINIVTANGYIPVISPIA- 187
                                   ******************************************************************************76. PP

                                   EETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHHH CS
                     AA_kinase 149 ldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGmkvkhpaala 228
                                   +d eg  +++++Dt+a  lA al+A+kli++tdV+GV+ +  ++    +++++i vde+e+ ++++  +gGm++k+++a a
  gi|91772136|ref|YP_564828.1| 188 MDSEGNALNINADTVAGDLADALNAKKLILMTDVPGVLRDQTDIS---TRISRIGVDEVEQlIEDGVLSGGMIPKMRSAKA 265
                                   ******99************************************9...********************************* PP

                                   HHHCTT-EEEEEE CS
                     AA_kinase 229 aarrggipvvItn 241
                                    +++g+ +v++++
  gi|91772136|ref|YP_564828.1| 266 SVEGGVDRVHVID 278
                                   **********986 PP

>> RNaseH_like  Ribonuclease H-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.6e-06     0.077      94     134 ..     148     188 ..     116     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-06
                   RNaseH_like  94 elkleihiDiGengktkelikevvgmvegsgfeakiKPesf 134
                                     ++e ++D G  g+t+ +  e++++v+++g+ + i P ++
  gi|91772136|ref|YP_564828.1| 148 IEDIEHDVDLGWVGDTEIINPEIINIVTANGYIPVISPIAM 188
                                   458999********************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 1668.43
//
Query:       gi|91772137|ref|YP_564829.1|  [L=347]
Description: hypothetical protein Mbur_0057 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00068   20.1   0.3     0.0025   18.2   0.1    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 !   18.2   0.1   1.4e-07    0.0025       4     140 ..      48     195 ..      45     254 .. 0.74
   2 ?   -1.3   0.0      0.14   2.5e+03       8      31 ..     292     313 ..     288     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-07
                                   ESEESS-....-TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE....SSTGGGSTTHHHHHHHHHHT CS
                                   xxxxxxx....xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   4 trgCnlr....CsfCarpet...vrregrgrslsveeileevkelkaekgvkevilg....ggepllypdfvellerlakl 73 
                                   t gC  +    C+ C + ++     + + + +++ ++ +++ +++ ++  vk +++g      e+++  +   l       
  gi|91772137|ref|YP_564829.1|  48 TSGCWWGkaggCTMCGFVYDsakIPPQPEELERQFDNAMRKGEKF-ERFMVKIFTSGsfldENEVTAETRANILN------ 121
                                   66777777777*******984444444444444444444444444.33324444444555555555544333333...... PP

                                   C....CCTEEEEEEECSSCHGHHHHHHHHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHT CS
                                   x....xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  74 a....vpgiritvetngtlpdeeklerllelg...vdrvslgleaaddekvlklmnrghtfeevlealeklrea 140
                                   +    ++ +++ ve+ +  ++ee l++ +e+       v++gle+ +d   ++ +n+g tfe+++ a   ++++
  gi|91772137|ref|YP_564829.1| 122 KlaadERIFKVLVESRPEFVTEETLKACKEALgktAFEVAIGLETSSDNIRKNSINKGFTFEDYITASNVAKNN 195
                                   3444459***********************99999**************6666777999999999888777765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.14
                                   SS--TTTSCCTTHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   8 nlrCsfCarpetvrregrgrslsv 31 
                                   +++C+ C+r  +  + ++  s+++
  gi|91772137|ref|YP_564829.1| 292 PHNCKICSRDVS--DAVHLFSRTQ 313
                                   79*******986..7777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2506.22
//
Query:       gi|91772138|ref|YP_564830.1|  [L=304]
Description: GMP synthase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-27   94.5   0.0    5.8e-27   93.6   0.0    1.5  1  GMP_synt_C       GMP synthase C terminal domain
      8e-12   44.8   0.0      2e-11   43.5   0.0    1.6  1  NAD_synthase     NAD synthase
     0.0007   19.1   0.0     0.0012   18.4   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC
     0.0011   17.8   0.0      0.014   14.2   0.0    2.1  2  tRNA_Me_trans    tRNA methyl transferase
     0.0025   17.2   0.4     0.0039   16.5   0.1    1.4  2  Arginosuc_synth  Arginosuccinate synthase
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.022   14.8   0.0    1.3  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
        0.1   12.4   0.0       0.15   11.8   0.0    1.4  1  ATP_bind_3       PP-loop family
       0.15   11.6   0.1       0.35   10.4   0.1    1.6  1  ThiI             Thiamine biosynthesis protein (ThiI)
       0.19   11.3   0.0       0.34   10.5   0.0    1.4  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 !   93.6   0.0   2.9e-30   5.8e-27      11      92 .]     223     303 ..     211     303 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 2.9e-30
                                   GSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS-S- CS
                    GMP_synt_C  11 kiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpatiE 91 
                                   k wQ+fa+++  k +Gv+gd R +++++a+Rav s+D+mta++ elp+e+L ki sri  e+ +v+rv+yd++ kPpatiE
  gi|91772138|ref|YP_564830.1| 223 KPWQTFAAVIG-KGTGVKGDVRVHGWIIAVRAVGSRDGMTAEALELPWETLMKIESRISGEIASVARVLYDLSPKPPATIE 302
                                   56*******98.99******************************************************************* PP

                                   - CS
                    GMP_synt_C  92 w 92 
                                   +
  gi|91772138|ref|YP_564830.1| 303 F 303
                                   7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0     1e-14     2e-11      11     177 ..      13     185 ..       1     193 [. 0.80

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1e-14
                                   HHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHH CS
                  NAD_synthase  11 eyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeqe 91 
                                   + +k++   + ++ lSGGvDSs+ a+la +a+ k+  + +++ +    + ++e  +++  +  ++ +tid k+        
  gi|91772138|ref|YP_564830.1|  13 DRIKEQAKGKTIIALSGGVDSSVCAVLAYQAI-KDDLIPIYIDTGLMRKGETERIKEIFAD--MNLQTIDAKDRFLDALVG 90 
                                   35666777899*********************.**********99999999***9999999..999999999876555544 PP

                                   HHHHH........-HHHHHHHHHHHHHHHHHHHHHHH..TEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHHHH CS
                  NAD_synthase  92 lkeak........edlakgNlkaRiRmailyaiankl..nllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevkeL 162
                                   +k+ +        + ++    +aR+  +++y i +    +++    g ks   vG    + D  + ++pi +l+K ev+e 
  gi|91772138|ref|YP_564830.1|  91 IKDPEekrkvvgeTFIRVFEEEARE-INAQYLIQGTIypDRIESDGGIKSHHNVGGLPEHIDFKGIIEPIDDLYKDEVREV 170
                                   4433324445653333334455664.6788888776533677788899********************************* PP

                                   HHHTT--HHHHCS-- CS
                  NAD_synthase 163 akelnvPervlkkpP 177
                                   a +l  Pe++ ++ P
  gi|91772138|ref|YP_564830.1| 171 AWALDLPEEICERMP 185
                                   *************98 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.1e-07    0.0012       1      57 [.      22      78 ..      22     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.1e-07
                                  EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EE CS
                          QueC  1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehk 57
                                  k ++ lSGG+DS+++++la +++ + ++ + +d g  +k e+e  k+i++++++ ++ 
  gi|91772138|ref|YP_564830.1| 22 KTIIALSGGVDSSVCAVLAYQAIkDDLIPIYIDTGLMRKGETERIKEIFADMNL-QTI 78
                                  57999**************999846899**********************9999.333 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.3e-06     0.014       3      24 ..      23      44 ..      21      91 .. 0.81
   2 ?    1.6   0.0     0.049        98     164     186 ..     155     177 ..     148     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.3e-06
                 tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqg 24
                                   ++alSgGVDSsv a+l  ++ 
  gi|91772138|ref|YP_564830.1| 23 TIIALSGGVDSSVCAVLAYQAI 44
                                  689************9987765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.049
                 tRNA_Me_trans 164 llfPlgeltKeevrkiAkeagla 186
                                   ++ P+ +l K+evr++A + +l+
  gi|91772138|ref|YP_564830.1| 155 IIEPIDDLYKDEVREVAWALDLP 177
                                   677**************988775 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     2e-06    0.0039       1      65 [.      24      86 ..      24      92 .. 0.81
   2 ?   -3.7   0.0       2.8   5.6e+03     192     242 ..     158     213 ..     155     216 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-06
               Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqeee.dldevkekalklgavksvvvDakeefve 65
                                  ++a sGG+D sv+  l  + ++++ i + +d G  ++ + +++k   + +++++  ++Dak+ f +
  gi|91772138|ref|YP_564830.1| 24 IIALSGGVDSSVCAVLAYQAIKDDLIPIYIDTGLMRKgETERIK---EIFADMNLQTIDAKDRFLD 86
                                  6899*****************************88431333333...446788999*******986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.8
               Arginosuc_synth 192 ppediye.ltkdpakapdepeev..eiefe.kGvPvaldgeelsv.lelieklnei 242
                                   p++d+y+  ++++a a d pee+  ++ f   G+ v + ge ++  +++++++n i
  gi|91772138|ref|YP_564830.1| 158 PIDDLYKdEVREVAWALDLPEEIceRMPFPgPGLSVRIIGEVTEEkVDVVREANAI 213
                                   66666652355666666666666333555424778887776655448888888766 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.1e-05     0.022       3      61 ..      24      81 ..      22     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                  EEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-S CS
                   PAPS_reduct  3 vvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdeleeryglrlkvyepe 61
                                  +++ sgG ds+V   La +a k+    +++dtg   +  +e ++e+   ++l+ +  + +
  gi|91772138|ref|YP_564830.1| 24 IIALSGGVDSSVCAVLAYQAIKDDlIPIYIDTGLMRKGETERIKEIFADMNLQTI--DAK 81
                                  7899*******************6258*******999999999999888866633..333 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.8e-05      0.15       2      53 ..      23      69 ..      22     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
                                  EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHH CS
                    ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkel 53
                                  +++A+SgG+DS +  +l+++  k+   +l+ i++d gl  + +  +e +ke+
  gi|91772138|ref|YP_564830.1| 23 TIIALSGGVDSSVCAVLAYQAIKD---DLIPIYIDTGLMRKGE--TERIKEI 69
                                  79*********9988888877554...7788888888764332..3334444 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00018      0.35       3     115 ..      20     124 ..      18     128 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                          ThiI   3 qgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv 83 
                                   +gk++  lSgG+DS V a l+ +  ++ +l+ +  +  t+   ++  e++ e++a+ +      l ++d k+   + l  +
  gi|91772138|ref|YP_564830.1|  20 KGKTIIALSGGVDSSVCAVLAYQ-AIKDDLIPI--YIDTGLMRKGETERIKEIFADMN------LQTIDAKDRFLDALVGI 91 
                                   799999***********998876.456566555..33444445555566666666544......56666665544444443 PP

                          ThiI  84 .kekltivllkrkmlriAekvaeeegakalvtG 115
                                    +++ +  ++  +++r+ e+ a+e +a+ l++G
  gi|91772138|ref|YP_564830.1|  92 kDPEEKRKVVGETFIRVFEEEAREINAQYLIQG 124
                                   222333334455677777777777777777766 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.34      22      40 ..      25      43 ..      10      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                  Asn_synthase 22 alLSGGlDSSliaalaarq 40
                                  + LSGG+DSS+ a la + 
  gi|91772138|ref|YP_564830.1| 25 IALSGGVDSSVCAVLAYQA 43
                                  68********999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1935.20
//
Query:       gi|91772139|ref|YP_564831.1|  [L=444]
Description: hypothetical protein Mbur_0059 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-09   37.6   4.6      2e-09   37.6   4.6    2.5  2  DUF11      Domain of unknown function DUF11
    0.00014   21.2   4.0    0.00073   18.9   0.2    3.2  4  Lactonase  Lactonase, 7-bladed beta-propeller
     0.0044   16.2   0.1      0.015   14.5   0.1    1.8  1  DUF5128    6-bladed beta-propeller
     0.0044   16.6   3.8        0.1   12.2   0.1    3.4  4  SGL        SMP-30/Gluconolactonase/LRE-like region
  ------ inclusion threshold ------
          3    8.5  16.7          2    9.0   1.1    5.2  5  PQQ_3      PQQ-like 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 ?   -1.4   1.1      0.81   2.9e+03      61      78 ..      81      99 ..      24     113 .. 0.41
   2 !   37.6   4.6   5.6e-13     2e-09       3      80 ..     300     379 ..     298     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.81
                         DUF11 61 v.gsLeagesatlsftvrv 78
                                  + g+L   + +t++++ +v
  gi|91772139|ref|YP_564831.1| 81 SsGQLYLVNGTTMTAAGTV 99
                                  2333333333333333333 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 5.6e-13
                         DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatlsftvrvtr 80 
                                   K   ++ v +G ++ty+l   Nt p+  ++v +tDt P g+++vs++ s  ++++ +++++g+L  ges  +++tv+ + 
  gi|91772139|ref|YP_564831.1| 300 KDDGSTSVVAGSQITYNLSYINTNPTGVTNVEITDTIPVGTTFVSATGSyvESAGVVTWTIGDLVSGESGSVTMTVQESS 379
                                   66678899*****************************************998888999999***********99998655 PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.053   1.9e+02      48     110 ..      23      85 ..      20      91 .. 0.73
   2 !   18.9   0.2     2e-07   0.00073     209     309 ..      79     172 ..      39     177 .. 0.74
   3 ?    1.2   0.1      0.05   1.8e+02      36     114 ..     194     266 ..     177     277 .. 0.60
   4 ?   -0.8   0.0      0.19   6.9e+02      25      98 ..     267     340 ..     250     383 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.053
                                   SSEEEEEET.S.TTTEEEEEEEETTTTEEEEEEEEE.SSS-EEEEEE-TTSSEEEEEETTTTEE CS
                     Lactonase  48 gktlYavnetg.eeggvsafaidkdsgeltllnkvssegaspchlsvdedgkllavAnYsggsv 110
                                   +k lY++++t+  +  + a++++ +     +  +++ +g   + +++d +  +l++ + s+g++
  gi|91772139|ref|YP_564831.1|  23 AKSLYVLSNTNsASSPIQAYDVNVAG-ISYQATHNTGSGWGEVGVAIDSNSGYLFITHESSGQL 85 
                                   67788888888778888888888874.4444444555888888889999999999888777765 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2e-07
                                   ETTTTEEEEEEEE-TTTEEEEEEEEESS-T...SS-S---EEEEEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEE CS
                     Lactonase 209 nELsstvsvfsydeatgaleelqtvstlpe...gftgknsaaeIrlspdgkflyvSnRgadsiavfavdeadgtltlveev 286
                                   +E              g+l  ++ ++++++   ++ g++ +a I++ ++ + +y+ nRg++++ v++ d++  tl  v+  
  gi|91772139|ref|YP_564831.1|  79 HES------------SGQLYLVNGTTMTAAgtvTAPGASNLAGIVVDEEKQRVYAVNRGTSNLYVYDWDSSAKTLIAVTGS 147
                                   333............44444444444443333346678999******************************9999999875 PP

                                   E..-SSS.--EEEE-TTSSEEEEEE CS
                     Lactonase 287 s..tegkfPRdfaldpsgklllvan 309
                                   +   +g++   +ald++++ll+va 
  gi|91772139|ref|YP_564831.1| 148 PftLTGANAYGIALDEANDLLYVAS 172
                                   5115788899999999999999986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.05
                                   SS---SEEE-TTSSEEEEEET.STTTEEEEEEEETTTTEEEEEEEEE.SSS-EEEEEE-TTSSEEEEEETTTTEEEEEE CS
                     Lactonase  36 lenPsyLalspdgktlYavnetgeeggvsafaidkdsgeltllnkvssegaspchlsvdedgkllavAnYsggsvsvfp 114
                                   ++++  +a+ +dgk+lY+ +    ++ +s++++ ++    t+ n +++ g     ++ +e+g++ a+  Y+g+ v+vf+
  gi|91772139|ref|YP_564831.1| 194 GQKAIGIAV-EDGKYLYTGSGFAGSNVLSQYDLVAK----TESNITNTYGIMGLAVD-QETGRVYATTGYTGDMVQVFD 266
                                   444444555.67777777777767777777777766....33343333333333333.256666777777777777776 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.19
                                   S-EEEEEEEEESS---SEEE-TTSSEEEEEET.S.TTTEEEEEEEETTTTEEEEEEEEE.SSS-EEEEEE-TTSS CS
                     Lactonase  25 gkltplelvaelenPsyLalspdgktlYavnetg.eeggvsafaidkdsgeltllnkvssegaspchlsvdedgk 98 
                                    +lt + ++ ++++P+ L + p + + Y     + ++g+ s +a ++ + +l+ +n+++++ +++   ++ + g 
  gi|91772139|ref|YP_564831.1| 267 SSLTLIDSTGDIGDPTGLCV-PRTGVSYNPLGFDkDDGSTSVVAGSQITYNLSYINTNPTGVTNVEITDTIPVGT 340
                                   47788888888888888888.888888888777778888888888888888888888887766665555555554 PP

>> DUF5128  6-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.2e-06     0.015      61     184 ..     115     237 ..     105     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-06
                       DUF5128  61 vdkrifvlDsaknnlfvFdkkGkfvrkIgaqGe.....GPgEYlqindfiidksnesIyildfmknkiltYdLegykfiee 136
                                    ++r++ +++ ++nl+v+d +   ++ I  +G+     G++ Y     +++d+ n+ +y+ +  +n + +Yd  ++   ++
  gi|91772139|ref|YP_564831.1| 115 EKQRVYAVNRGTSNLYVYDWDSSAKTLIAVTGSpftltGANAY----GIALDEANDLLYVASY-NNIVRYYDTATWTQQGT 190
                                   46899999***********999**********74444477766....7899********7777.99999****99888888 PP

                       DUF5128 137 kkldllvsdvaqlekdklifdssrie.dekrskfnlvvtdeegneisgs 184
                                   ++l  ++   +++e++k+++  s+++ ++  s++ lv++ e  n+++++
  gi|91772139|ref|YP_564831.1| 191 ITLGQKAI-GIAVEDGKYLYTGSGFAgSNVLSQYDLVAKTES-NITNTY 237
                                   88888855.689**************5446677777776665.776654 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.14     5e+02     147     208 ..      25      86 ..      20     108 .. 0.65
   2 !   12.2   0.1   2.8e-05       0.1       4      75 ..     109     188 ..     107     222 .. 0.73
   3 ?    1.9   0.0      0.04   1.4e+02     186     216 ..     239     271 ..     203     276 .. 0.71
   4 ?   -0.2   0.1      0.17   6.2e+02      67      96 ..     366     394 ..     313     413 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                           SGL 147 tlYl...aDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDa.eGnvwvAvwgggkvv 208
                                    lY+   ++s+   i+aydv+  g   s + +  ++  g ge  G+a+D+ +G++++++ ++g++ 
  gi|91772139|ref|YP_564831.1|  25 SLYVlsnTNSASSPIQAYDVNVAGI--SYQATH-NTGSGWGE-VGVAIDSnSGYLFITHESSGQLY 86 
                                   5666667888888899999964444..444433.33333332.38999988888888877777655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.8e-05
                           SGL   4 GpvwdeeegaLlwvDilgqrihrldpatgketvldtpe.........svGaiaprkdgrlvvasksglall.dlasgelet 74 
                                   G+v+dee+++++ v+  +++++ +d+++ ++t + + +           G++ + +++ l+vas ++++++ d+a+  +++
  gi|91772139|ref|YP_564831.1| 109 GIVVDEEKQRVYAVNRGTSNLYVYDWDSSAKTLIAVTGspftltganAYGIALDEANDLLYVASYNNIVRYyDTAT--WTQ 187
                                   8899****************************96666666666667788888887779999999999999966555..444 PP

                           SGL  75 l 75 
                                    
  gi|91772139|ref|YP_564831.1| 188 Q 188
                                   3 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.04
                           SGL 186 pDGlavDa.eGnvwvAvw.gggkvvrfdpdGkl 216
                                   + GlavD+ +G+v++++   g+ v++fd   +l
  gi|91772139|ref|YP_564831.1| 239 IMGLAVDQeTGRVYATTGyTGDMVQVFDSSLTL 271
                                   448999998899998876355678888766555 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.17
                           SGL  67 lasgeletladeeedekpllrfNDgvvdpd 96 
                                    +sg+++  ++e  + + ++  ND+ +d+d
  gi|91772139|ref|YP_564831.1| 366 GESGSVTMTVQES-SGVLRTITNDATIDSD 394
                                   3567888888875.5559999999999987 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.31   1.1e+03      16      37 ..      65      89 ..      54     101 .. 0.70
   2 ?    0.1   0.1      0.34   1.2e+03      15      37 ..     108     133 ..      89     137 .. 0.61
   3 ?    9.0   1.1   0.00057         2      11      40 .]     153     184 ..     143     184 .. 0.76
   4 ?    2.5   0.1     0.063   2.2e+02      16      29 ..     199     213 ..     185     224 .. 0.69
   5 ?    3.3   0.2     0.035   1.2e+02      13      30 ..     238     266 ..     232     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.31
                         PQQ_3 16 spavd..gglvyvgtg.dGtlyAlD 37
                                  ++a+d   g+++++ +  G ly ++
  gi|91772139|ref|YP_564831.1| 65 GVAIDsnSGYLFITHEsSGQLYLVN 89
                                  4577643489999999988888665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.34
                         PQQ_3  15 sspavdgg..lvyvgtg.dGtlyAlD 37 
                                   ++ +vd+   +vy++     +ly +D
  gi|91772139|ref|YP_564831.1| 108 AGIVVDEEkqRVYAVNRgTSNLYVYD 133
                                   55577764224777766666666666 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00057
                         PQQ_3  11 gpvnsspavd..gglvyvgtgdGtlyAlDaet 40 
                                   g+  ++ a+d  ++l+yv+++++ ++ +D++t
  gi|91772139|ref|YP_564831.1| 153 GANAYGIALDeaNDLLYVASYNNIVRYYDTAT 184
                                   33345668874469***************987 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.063
                         PQQ_3  16 spav.dgglvyvgtg 29 
                                   + av dg ++y+g+g
  gi|91772139|ref|YP_564831.1| 199 GIAVeDGKYLYTGSG 213
                                   457735568*****9 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.035
                         PQQ_3  13 vnsspavd..gglvyvgtg.........d 30 
                                   +  ++avd   g+vy++tg         d
  gi|91772139|ref|YP_564831.1| 238 GIMGLAVDqeTGRVYATTGytgdmvqvfD 266
                                   4567899966799*****98755555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2868.64
//
Query:       gi|91772140|ref|YP_564832.1|  [L=468]
Description: hypothetical protein Mbur_0060 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   30.8   6.8    2.6e-07   30.8   6.8    2.4  3  DUF11         Domain of unknown function DUF11
    3.4e-06   26.6   0.1    1.5e-05   24.5   0.0    2.1  2  Lactonase     Lactonase, 7-bladed beta-propeller
    2.5e-05   24.4   1.5       0.21   11.8   0.0    4.7  5  Arylesterase  Arylesterase
    0.00092   18.9   0.8      0.041   13.4   0.6    2.9  2  SGL           SMP-30/Gluconolactonase/LRE-like region
     0.0049   17.1   0.1       0.14   12.5   0.0    2.5  2  Chlam_OMP6    Chlamydia cysteine-rich outer membrane protein 


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       4.8   1.7e+04      21      35 ..      96     110 ..      89     111 .. 0.73
   2 ?   -1.7   0.2         1   3.6e+03      25      28 ..     240     243 ..     199     286 .. 0.61
   3 !   30.8   6.8   7.3e-11   2.6e-07       2      86 ..     320     410 ..     319     416 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.8
                         DUF11  21 tvtNtgpasangvvv 35 
                                   tvt +g+++++g+vv
  gi|91772140|ref|YP_564832.1|  96 TVTAPGAKNLAGIVV 110
                                   888888888888877 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                         DUF11  25 tgpa 28 
                                   +g++
  gi|91772140|ref|YP_564832.1| 240 PGGV 243
                                   2222 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 7.3e-11
                         DUF11   2 tKtvdksevrpGdtvtytltvtNtgpasa.ngvvvtDtlPaglayvsvsas....qgtasaltsvgsLeage.satlsftv 76 
                                    Kt + ++v  G+t+ty +   N  +++  n v + D lP  +++vs+s s    + t ++++++g+L+ag+ s  +s+tv
  gi|91772140|ref|YP_564832.1| 320 AKTDSVTQVYQGGTLTYAISYDNALNNNPvNSVMIVDSLPVEVTFVSASDSgvynSTTHTVTWTIGTLAAGApSDSVSVTV 400
                                   6999999******************999889********************66555555555555****998678899999 PP

                         DUF11  77 rvtrtaasga 86 
                                   +v +++  g+
  gi|91772140|ref|YP_564832.1| 401 NVGASTPIGT 410
                                   9988765555 PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.1e-09   1.5e-05     229     310 ..      87     170 ..      69     194 .. 0.83
   2 ?   -1.8   0.0       0.4   1.4e+03      28      76 ..     183     233 ..     172     264 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.1e-09
                                   EEEEEESS-T.SS-S---EEEEEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS..--EEEE-TTSSEEEE CS
                     Lactonase 229 elqtvstlpe.gftgknsaaeIrlspdgkflyvSnRgadsiavfavdeadgtltlveevstegkf.PRdfaldpsgklllv 307
                                   + +t+  l   ++ g++ +a I++ +d + +y+ +Rga si +++ d+ ++tltl +++s  g++    +ald++++ll+v
  gi|91772140|ref|YP_564832.1|  87 DAKTLAVLGTvTAPGAKNLAGIVVDQDKQQVYTNDRGAKSIYIYDWDATTSTLTLNKIQSLVGTTqIYGIALDEANDLLYV 167
                                   45566666665788999*******************************************988763678999999999999 PP

                                   EET CS
                     Lactonase 308 anq 310
                                   ++ 
  gi|91772140|ref|YP_564832.1| 168 GDL 170
                                   864 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.4
                                   EEEEEEEESS---SEEE-TTSSEEEEEET.S...TTTEEEEEEEETTTTEEE CS
                     Lactonase  28 tplelvaelenPsyLalspdgktlYavnetg...eeggvsafaidkdsgelt 76 
                                   +++++    +++  +a+++++ ++Y+ n      + g +s++++++  +e+t
  gi|91772140|ref|YP_564832.1| 183 SSAGSFPVSQKVMGIAVDATNGYVYTGNAYPnagSIGLLSQYDLGTS-TEVT 233
                                   55555555566666777777777777777764434444555655554.3333 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   4.3e+03      57      71 ..      62      76 ..      51      77 .. 0.86
   2 !   11.8   0.0     6e-05      0.21      52      82 ..     101     131 ..      95     135 .. 0.86
   3 ?    3.2   0.0     0.029     1e+02      56      76 ..     153     173 ..     141     180 .. 0.77
   4 ?   -0.5   0.1      0.41   1.5e+03      57      72 ..     195     210 ..     190     214 .. 0.85
   5 ?    3.6   0.0     0.022        79      52      71 ..     244     263 ..     240     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                  Arylesterase 57 nGInidadkkyiyva 71
                                   G++id+d   ++v+
  gi|91772140|ref|YP_564832.1| 62 AGLGIDTDSETLFVT 76
                                  6999******99997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6e-05
                  Arylesterase  52 glssanGInidadkkyiyvadilresihvmk 82 
                                   g +   GI++d+dk+ +y  d  ++si++++
  gi|91772140|ref|YP_564832.1| 101 GAKNLAGIVVDQDKQQVYTNDRGAKSIYIYD 131
                                   556668***********************97 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.029
                  Arylesterase  56 anGInidadkkyiyvadilre 76 
                                     GI +d  +  +yv+d++ +
  gi|91772140|ref|YP_564832.1| 153 IYGIALDEANDLLYVGDLTTQ 173
                                   569**************9864 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.41
                  Arylesterase  57 nGInidadkkyiyvad 72 
                                    GI +da + y+y ++
  gi|91772140|ref|YP_564832.1| 195 MGIAVDATNGYVYTGN 210
                                   59***********876 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.022
                  Arylesterase  52 glssanGInidadkkyiyva 71 
                                   +l+ a GI +d+    +yv+
  gi|91772140|ref|YP_564832.1| 244 SLDNAVGIAVDPATGLVYVT 263
                                   67899**************8 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.6   1.2e-05     0.041     137     201 ..     106     169 ..      95     218 .. 0.85
   2 ?    2.1   0.0     0.033   1.2e+02     158     214 ..     221     283 ..     196     288 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                           SGL 137 NGlawspdgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDa.eGnvwvAv 201
                                    G+ +++d++++Y++D  +++i+ yd+da++++l+  +    + +++  + G+a+D+ ++ ++v  
  gi|91772140|ref|YP_564832.1| 106 AGIVVDQDKQQVYTNDRGAKSIYIYDWDATTSTLTLNKIQSLVGTTQ--IYGIALDEaNDLLYVGD 169
                                   5999****************************999888776666665..77999998666666664 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.033
                           SGL 158 iwaydvdaeggklsnrrvf.adlkkgegepDGlavDa.eGnvwvAvw.....gggkvvrfdpd.G 214
                                   +++yd+ ++++   n r++   +     +  G+avD  +G v+v++      g++++ +f+p  G
  gi|91772140|ref|YP_564832.1| 221 LSQYDLGTSTEVTVNTRTLpG-GVSL-DNAVGIAVDPaTGLVYVTTGnqasgGSDRILVFNPSlG 283
                                   667777777776666666621.2222.22448999988899999888665555558888887655 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 !   12.5   0.0   3.8e-05      0.14      27      83 ..     335     393 ..     315     403 .. 0.70
   2 ?    1.9   0.0     0.076   2.7e+02       3      28 ..     426     452 ..     424     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                    Chlam_OMP6  27 pypieitavgkkdcvd.vvitqqlpcevefvr.sdpastptadgklvwkidrlgqgeks 83 
                                    y i    + +++ v+ v+i + lp+ev fv+ sd     ++   + w+i  l  g  s
  gi|91772140|ref|YP_564832.1| 335 TYAISYDNALNNNPVNsVMIVDSLPVEVTFVSaSDSGVYNSTTHTVTWTIGTLAAGAPS 393
                                   56666554444455542889***********8467777778888999*****9998755 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.076
                    Chlam_OMP6   3 svkvnddrnveisq.avpeyatvgspy 28 
                                   +++ +dd++v +++  +pe+ tv  p 
  gi|91772140|ref|YP_564832.1| 426 TTQHDDDTEVILTDnEIPEFPTVALPI 452
                                   67889999999986269******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 2438.83
//
Query:       gi|91772141|ref|YP_564833.1|  [L=647]
Description: ATP-dependent DNA helicase RecQ [Methanococcoides burtonii DSM 6242]
Scores for complete 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  104.6   0.1    1.5e-29  102.0   0.0    2.3  3  RQC            RQC domain
    2.9e-23   82.5   0.0    2.9e-22   79.3   0.0    2.1  2  DEAD           DEAD/DEAH box helicase
    3.4e-23   82.1   0.0    4.6e-19   68.8   0.0    2.6  2  Helicase_C     Helicase conserved C-terminal domain
    4.4e-19   69.0   2.0    1.2e-18   67.6   2.0    1.8  1  RecQ_Zn_bind   RecQ zinc-binding
    6.3e-19   67.7   0.0    1.1e-18   67.0   0.0    1.4  1  HRDC           HRDC domain
    5.8e-06   26.3   0.1    1.2e-05   25.3   0.1    1.4  1  Helicase_Sgs1  Sgs1 RecQ helicase
    0.00056   20.0   0.0     0.0011   19.1   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   3.8e+03      72      98 ..     151     177 ..     119     186 .. 0.62
   2 ?   -2.1   0.0       1.3   3.2e+03      40      65 ..     242     267 ..     239     272 .. 0.80
   3 !  102.0   0.0     6e-33   1.5e-29       1     106 [.     395     499 ..     395     506 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                                   HHTTSEEEE..SSSBEEE-CCGHHHHT CS
                           RQC  72 iaegyLeedveeygvlkltekarevlk 98 
                                      g+L+++   ++v+ lt  a + +k
  gi|91772141|ref|YP_564833.1| 151 RRMGFLKKKYPDVPVIALTATATAKVK 177
                                   556777777777777777776644443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                   CCCCCTTGGGSTTTTTTTTS-HHHHH CS
                           RQC  40 kkirqlghdklstfGigkdlskkewr 65 
                                    k+ + g++ l+++  ++d ++++ +
  gi|91772141|ref|YP_564833.1| 242 TKLNREGFHALPYHAGLNDAKRQDNQ 267
                                   6888999*******999998887754 PP

  == domain 3  score: 102.0 bits;  conditional E-value: 6e-33
                                   ---EEE-HHHHHHHHHHHHHTTS-SBHHHHHHHHHT---CCCCCTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE. CS
                           RQC   1 ppetvDvteeaqkilscvyrtgqrfgaghivdvLrGsktkkirqlghdklstfGigkdlskkewrrlirqLiaegyLeedv 81 
                                   p++t+D+++ a++ lscv ++++rfg++hivd+L+Gsk+kki +++hd+l+ +G g+++ k+ew +++r++i  g +++++
  gi|91772141|ref|YP_564833.1| 395 PRDTYDASDVARTFLSCVDEVNERFGLTHIVDILTGSKSKKIISYKHDRLKSYGTGEGYIKSEWVEMAREMIRLGHVDVKE 475
                                   5789***************************************************************************** PP

                                   .SSSBEEE-CCGHHHHTSSS--EEE CS
                           RQC  82 eeygvlkltekarevlkgeekvklr 106
                                   ++y++l l++++revl g  +v+l+
  gi|91772141|ref|YP_564833.1| 476 GKYPILLLNKNSREVLGGS-EVHLT 499
                                   ****************998.56655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   0.0   1.2e-25   2.9e-22       2     175 ..      16     178 ..      15     179 .. 0.84
   2 ?    0.7   0.0      0.15   3.8e+02      43     105 ..     220     282 ..     208     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.2e-25
                                   HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.lrvlli 81 
                                   + Q+ +i+ +l+++dv+v ++TG GK+ +++ip+l  +          a++v+P+ +L++++++ l + +  +  l+  l 
  gi|91772141|ref|YP_564833.1|  16 PLQEDIINDVLNKKDVFVLMPTGGGKSICYQIPAL--I------MDGLAVVVSPLISLMKDQVDGLVSNGISAAyLNSTLS 88 
                                   78*********************************..4......2459******************988887442555555 PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHHCTTSTTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlpqitcdgklqr 160
                                   +++v++   ++ ++ +vdi++  p+rl    +++ l+  +v+++ +DEa++++++  +f+++++r +  l++++ d +   
  gi|91772141|ref|YP_564833.1|  89 YNEVQK-ITRAIVEGNVDILYVAPERLCMKSTQELLSHVNVSLFAIDEAHCISEWghDFRPEYRR-MGFLKKKYPDVP--- 164
                                   554443.444444566************8666777889999**************999*******.889989999998... PP

                                   EEEEEESSBSHHHHH CS
                                   xxxxxxxxxxxxxxx RF
                          DEAD 161 qvivlSATlpkdvkk 175
                                    vi+l+AT++ +vk+
  gi|91772141|ref|YP_564833.1| 165 -VIALTATATAKVKE 178
                                   .********988875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.15
                                   TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH.HTTCSEEEEEH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                          DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl.dngvdivvgtp 105
                                   kg++g+  +i + +r+ +e + ++l++ + +  l +++ +++ +++d+++++ + +vdi+v+t 
  gi|91772141|ref|YP_564833.1| 220 KGQRGNSGIIYCNSRKSVESVSTKLNREGFH-ALPYHAGLNDAKRQDNQERFiRDDVDIIVATV 282
                                   6667777777777777777777777776664.477887788777766666662677*****995 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 !   10.4   0.0   0.00025      0.64      17      70 ..      54     107 ..      42     111 .. 0.80
   2 !   68.8   0.0   1.8e-22   4.6e-19      13     110 ..     221     318 ..     212     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                                   SEEEEEESSHHHHHH..HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEE CS
                    Helicase_C  17 gkilifvntidrlek..vklllekkgikvavlhgelpqnereeileqfnkgesdvL 70 
                                   g ++++++ i+ +++    l+  ++gi++a+l+++l+ ne ++i ++  +g++d+L
  gi|91772141|ref|YP_564833.1|  54 GLAVVVSPLISLMKDqvDGLV--SNGISAAYLNSTLSYNEVQKITRAIVEGNVDIL 107
                                   567777888885543433555..88*****************************98 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 1.8e-22
                                   TTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSS CS
                    Helicase_C  13 eeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdl 93 
                                    ++g+  +i++n+++++e+v+  l+++g++++++h+ l+  +r++  e+f ++++d+++at + ++Gid p+v++Vi++dl
  gi|91772141|ref|YP_564833.1| 221 GQRGNSGIIYCNSRKSVESVSTKLNREGFHALPYHAGLNDAKRQDNQERFIRDDVDIIVATVAFGMGIDKPNVRFVIHYDL 301
                                   5678888**********9855555788****************************************************** PP

                                   SSSHHHHHHHHTTSSST CS
                    Helicase_C  94 prnvtsyiqriGRtgRa 110
                                   p+n++ y q  GR gR 
  gi|91772141|ref|YP_564833.1| 302 PKNLEGYYQETGRGGRD 318
                                   ****************6 PP

>> RecQ_Zn_bind  RecQ zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   2.0   4.6e-22   1.2e-18       2      66 .]     331     393 ..     330     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 4.6e-22
                  RecQ_Zn_bind   2 qDvsrlrrlieqseesekekeaelekleamlaycentteCrrkllleyFgeeaaeeeCgnCDnCl 66 
                                   +D  ++++li+q+  +++e++ +++kl++m++yce+t+ Crrk+ll+yFgee ++++Cg+CD+Cl
  gi|91772141|ref|YP_564833.1| 331 ADWYKIKYLIDQKP-KKSERDIAMTKLQEMIDYCESTS-CRRKALLHYFGEELESDNCGSCDVCL 393
                                   69999*****8775.788999*************9999.*************************6 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   4.2e-22   1.1e-18       2      68 .]     573     639 ..     572     639 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 4.2e-22
                                   HHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHHHHHH CS
                          HRDC   2 lallkaLrewReelAreedvppyvvfpdktLleiAeklPttleeLlqiegvgkrklekygeeileai 68 
                                   ++l+++Lre+R++lA e +vppy++f d  L+++A+  P +++e+  i+gvg+ kl+kyg  +++ i
  gi|91772141|ref|YP_564833.1| 573 KKLFDKLRELRKRLAVEANVPPYIIFADTSLRQMAANFPNNEKEFIGITGVGEVKLKKYGSVFMKEI 639
                                   579***********************************************************99876 PP

>> Helicase_Sgs1  Sgs1 RecQ helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   4.6e-09   1.2e-05       7      65 ..     574     632 ..     572     644 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.6e-09
                                   HHHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHHGG CS
                 Helicase_Sgs1   7 vayerlravainlgnrmnlpvdtylpdnilkkiAaiLPatedeFislvgnndkarrkyk 65 
                                   + +++lr++   l+   n+p    + d+ l+++Aa  P +e+eFi+++g+ + + +ky 
  gi|91772141|ref|YP_564833.1| 574 KLFDKLRELRKRLAVEANVPPYIIFADTSLRQMAANFPNNEKEFIGITGVGEVKLKKYG 632
                                   679******************************************************95 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 !   19.1   0.0   4.1e-07    0.0011       3     169 ..      13     172 ..      11     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.1e-07
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG.GGGTGG.. CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef.kkflseay 82 
                                   e+r+ Qe++i+++l      ++k +++ m+TG GK++++ ++ + ++       ++++ p +sl++   + + ++ +s ay
  gi|91772141|ref|YP_564833.1|  13 EFRPLQEDIINDVL------NKKDVFVLMPTGGGKSICY-QIPALIMDG----LAVVVSPLISLMKDQVDGLvSNGISAAY 82 
                                   78999********8......56789**********9876.555555554....579********98777665266666777 PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS......TTTHHH...HH CS
                        ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak.....kswrei...le 155
                                    + + ++++ +k+ +++ + n +il +  ++l  +s     ++e l++ +  ++ iDEaH +++       ++r+    ++
  gi|91772141|ref|YP_564833.1|  83 LNSTLSYNEVQKITRAIVEGNVDILYVAPERLCMKS-----TQELLSHVNVSLFAIDEAHCISEWghdfrPEYRRMgflKK 158
                                   667777777777778889999999999999999999.....88888888899***********976555449999888788 PP

                                   T---SEEEEEESS- CS
                        ResIII 156 kfkeavllglTATp 169
                                   k+++  +++lTAT 
  gi|91772141|ref|YP_564833.1| 159 KYPDVPVIALTATA 172
                                   889999******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.55
# Mc/sec: 3559.30
//
Query:       gi|91772142|ref|YP_564834.1|  [L=252]
Description: peptidase A24B, FlaK-like [Methanococcoides burtonii DSM 6242]
Scores for complete 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  108.9   0.1    1.3e-31  108.9   0.1    2.6  3  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
    1.9e-13   50.7   7.8    3.8e-13   49.8   7.8    1.5  1  Peptidase_A24  Type IV leader peptidase family
  ------ inclusion threshold ------
          5    5.9  14.4         14    4.4  10.2    2.2  2  LptF_LptG      Lipopolysaccharide export system permease LptF


Domain annotation for each model (and alignments):
>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.5      0.15     9e+02      71      89 ..      50      68 ..      33      69 .. 0.93
   2 ?   -3.0   0.5       1.8   1.1e+04      69      90 ..     102     123 ..     101     124 .. 0.74
   3 !  108.9   0.1   2.2e-35   1.3e-31       1      92 []     151     242 ..     151     242 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                   Arc_PepC_II 71 ygvPflipitaGfiialvl 89
                                  yg+P++   +++fi+ +v+
  gi|91772142|ref|YP_564834.1| 50 YGIPYVKWTLISFIFIFVF 68
                                  9*************99987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                   Arc_PepC_II  69 vtygvPflipitaGfiialvlG 90 
                                   ++y +P+  +  +G+ ++ v+G
  gi|91772142|ref|YP_564834.1| 102 ISYHLPVAGMPPIGLFTFSVFG 123
                                   7899998666666888888887 PP

  == domain 3  score: 108.9 bits;  conditional E-value: 2.2e-35
                   Arc_PepC_II   1 kkllymligyrvkvkellkkflflleefeekdgkikrkfisvekeldeelrkelkkykkkglieetvWvtygvPflipita 81 
                                   k+++ym+igyr  +k+l++ +++l+e++ee+dg ++++f++ +++lde++++++k+y k+glie++ Wvt+g+Pf+ipita
  gi|91772142|ref|YP_564834.1| 151 KRPHYMFIGYRSLIKDLERPHIRLIEQYEENDGIVSHRFTTGGMQLDEDTIAMMKEYDKNGLIEKRTWVTPGLPFMIPITA 231
                                   6899***************************************************************************** PP

                   Arc_PepC_II  82 GfiialvlGDl 92 
                                   Gfi a+++GDl
  gi|91772142|ref|YP_564834.1| 232 GFISAVIYGDL 242
                                   **********6 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   7.8   6.3e-17   3.8e-13       1      92 [.       8     106 ..       8     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 6.3e-17
                 Peptidase_A24   1 lvlltillvlsviDldtrtlpdeltlpllllgvlfa..qllllglpnlaqavlgalvgalvlllislvdeqamGgGDvkla 79 
                                   lv+l++ll+ +++D++tr+++++l+ ++l     +   +++  g+p +++ +++++ +++++++  l++ +a+Gg+D+k++
  gi|91772142|ref|YP_564834.1|   8 LVCLLFLLYSCYSDIKTRRVTNKLWPIMLGAAAPLIiyDIARYGIPYVKWTLISFIFIFVFVYI--LFYFGAFGGADAKIL 86 
                                   6899***********************9999888777877888*********************..*************** PP

                 Peptidase_A24  80 avlgaflgwerl.......l 92 
                                   +v++++l+++         l
  gi|91772142|ref|YP_564834.1|  87 MVISLILPIYPAlelisyhL 106
                                   ********988744444440 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1    0.0036        21     306     345 ..       7      46 ..       4      50 .. 0.90
   2 ?    4.4  10.2    0.0023        14       8      64 ..      52     110 ..      46     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0036
                     LptF_LptG 306 liaillfvlyyvllslgkalaengvlppilaawlpnilfl 345
                                   +++ llf+ly   + ++     n ++p +l+a  p+i++ 
  gi|91772142|ref|YP_564834.1|   7 VLVCLLFLLYSCYSDIKTRRVTNKLWPIMLGAAAPLIIYD 46 
                                   567789999****************************985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0023
                     LptF_LptG   8 lkpfllvllvllfllllqdllryldllvgkglpvgdllelil..ynlpyilelalPlav 64 
                                   ++++  +l+ ++f+++++ +l y++ ++g  +++  +++lil  y +++++ + lP+a 
  gi|91772142|ref|YP_564834.1|  52 IPYVKWTLISFIFIFVFVYILFYFGAFGGADAKILMVISLILpiYPALELISYHLPVAG 110
                                   56667899*********************************888999999******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1545.06
//
Query:       gi|91772143|ref|YP_564835.1|  [L=109]
Description: hypothetical protein Mbur_0064 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.9   0.3      0.042   13.5   0.3    1.6  1  DUF842    Eukaryotic protein of unknown function (DUF842)


Domain annotation for each model (and alignments):
>> DUF842  Eukaryotic protein of unknown function (DUF842)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   2.3e-06     0.042      39     114 ..      18      97 ..      15     107 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-06
                        DUF842  39 rkasresveqCvekCseplqkaqkvvqqEleqfqe.....rLqrcvmvCqdkakdklgpnssekqtakaekelekCvakCv 114
                                   +++++e++e+C+ + s++++++++v+++E  +f+e       +  + ++  ++k+  ++ + ++++ k++++  kC+ k v
  gi|91772143|ref|YP_564835.1|  18 NDEDKEQIEHCIVSLSKKARSFESVLETETMTFEEakgifDKTAGLLRAVMDLKEI-DELPGPERMTKFKEDAMKCTVKDV 97 
                                   67889****************************99332221111222222222222.234577777778888887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 661.51
//
Query:       gi|91772144|ref|YP_564836.1|  [L=308]
Description: aspartate carbamoyltransferase catalytic subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-46  156.2   0.0    1.3e-45  155.0   0.0    1.6  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    1.2e-29  103.5   0.0    1.6e-29  103.0   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 !  155.0   0.0   1.5e-49   1.3e-45       2     147 ..       7     147 ..       6     148 .. 0.95
   2 ?   -2.4   0.0       0.5   4.4e+03      52      77 ..     167     191 ..     151     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 1.5e-49
                                   -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTG CS
                      OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssv 82 
                                   h++s++++s++ i+++l++a+ l+   k + k++llkgk+l++lF+epStRTr+Sfe+A+ rlGg+vlsl++    + ss+
  gi|91772144|ref|YP_564836.1|   7 HIISMKSFSRDMIDHVLNTAEMLEPIAKGKTKSDLLKGKILGVLFFEPSTRTRMSFETAMMRLGGDVLSLGSV---DASSI 84 
                                   89***********************9999******************************************44...68999 PP

                                   GSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                      OTCace_N  83 skgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                   +kg  E+l+Dt+rv+++y++aiv+Rh+++  ++   +++svp++Nagdg+g+HPtQ+++Dl+tir
  gi|91772144|ref|YP_564836.1|  85 AKG--ETLADTIRVVNGYANAIVLRHNKEGAAQLASEFSSVPILNAGDGAGHHPTQTFLDLYTIR 147
                                   9**..**********************555577778889*************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.5
                                   HHHHHHHHHHHHTTSEEEEEESTTTS CS
                      OTCace_N  52 RTrvSfevAakrlGgkvlslseaedi 77 
                                   RT  S   A +  G++ + +s ++++
  gi|91772144|ref|YP_564836.1| 167 RTVHSLCYALSLYGAEITLVS-PKEL 191
                                   777777778887777777766.4333 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 !  103.0   0.0   1.8e-33   1.6e-29       1     156 [.     153     302 ..     153     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1.8e-33
                                   CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--S CS
                        OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvw 80 
                                   +glkia+ Gd k++++++sl ++l+ +g++++lv+Pk+l+   +++e +++     + ++t  e +e+a++++Dv+y +++
  gi|91772144|ref|YP_564836.1| 153 DGLKIALAGDlKYGRTVHSLCYALSLYGAEITLVSPKELRLPADIIEDLRSR----NIKLTEIEYIEDAIENVDVLYVTRI 229
                                   69************************************99999999877765....6788888899*************** PP

                                   SETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                        OTCace  81 vsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                   +     ker+   ++++k+++   +  ell++ak++++v+H+LP  r +E++  V++ +++ +f+q  +++ +++All+l
  gi|91772144|ref|YP_564836.1| 230 Q-----KERFpdpAEYRKVANsLLISPELLEKAKPELKVMHPLP--RTNEIDPRVDNTKHACYFKQSFYGVPIRMALLAL 302
                                   *.....8888888889999988**********************..********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1981.58
//
Query:       gi|91772145|ref|YP_564837.1|  [L=159]
Description: aspartate carbamoyltransferase regulatory subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  104.1   3.6    5.6e-30  103.4   3.6    1.3  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    7.7e-18   64.1   2.6    7.7e-18   64.1   2.6    1.5  2  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me
  ------ inclusion threshold ------
       0.21   11.7   1.3        0.4   10.7   0.2    1.9  2  zf-BED    BED zinc finger


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 !  103.4   3.6   9.4e-34   5.6e-30       2      93 ..      12     101 ..      11     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 9.4e-34
                                   -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEE CS
                          PyrI   2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniI 82 
                                   +v++ienG+ViDHI+ag+al+vlk+L++ + +s++ v++++n++s + g+Kd++kieg+el+ ee+dk+aliapnatiniI
  gi|91772145|ref|YP_564837.1|  12 RVHPIENGTVIDHINAGQALNVLKILNIPT-SSSRVVSVLINAPSVH-GRKDVVKIEGRELNVEEVDKIALIAPNATINII 90 
                                   799**************************7.66669*********97.9******************************** PP

                                   ETTEEEEEE-- CS
                          PyrI  83 kdgevveKkkv 93 
                                   +d+ev +K  v
  gi|91772145|ref|YP_564837.1|  91 RDFEVSDKDIV 101
                                   *******9765 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 ?   -3.8   0.0       2.2   1.3e+04      20      30 ..      89      99 ..      85     102 .. 0.68
   2 !   64.1   2.6   1.3e-21   7.7e-18       1      46 [.     106     153 ..     106     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.2
                                  -.-EEEEEETT CS
                        PyrI_C 20 veskFkvedke 30
                                  +   F+v+dk+
  gi|91772145|ref|YP_564837.1| 89 IIRDFEVSDKD 99
                                  55678877665 PP

  == domain 2  score: 64.1 bits;  conditional E-value: 1.3e-21
                                   EEESSS--S-TTBGGGT.TS-.-EEEE.EETTTTEEEETTT--EEEHH CS
                        PyrI_C   1 eiegvlkCpNpnCItnn.epveskFkv.edkekvklkCkYCekeisee 46 
                                   +iegv++C NpnCI+n+ epv+skF v ++ ++++l+C YCe++is +
  gi|91772145|ref|YP_564837.1| 106 QIEGVVRCINPNCISNSnEPVTSKFAVsSNGQRTILRCSYCERIISDD 153
                                   69***************99********889999************986 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.32   1.9e+03       9      21 ..     103     115 ..     101     129 .. 0.71
   2 ?   10.7   0.2   6.7e-05       0.4      11      29 ..     135     153 ..     128     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.32
                                   ---GGSS--EETT CS
                        zf-BED   9 pvslkeqkavCry 21 
                                   ++s  e++++C+ 
  gi|91772145|ref|YP_564837.1| 103 IHSQIEGVVRCIN 115
                                   5667789999985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.7e-05
                                   -GGSS--EETTTTEE---- CS
                        zf-BED  11 slkeqkavCryCgkilsrg 29 
                                   + +++  +C yC++i+s++
  gi|91772145|ref|YP_564837.1| 135 NGQRTILRCSYCERIISDD 153
                                   4789999*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1055.30
//
Query:       gi|91772146|ref|YP_564838.1|  [L=302]
Description: cell surface protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-37  128.1  83.7    1.1e-23   83.8  49.7    2.6  3  Beta_helix       Right handed beta helix region
    1.9e-27   96.1  63.5    2.7e-17   62.9  27.9    2.1  2  NosD             Periplasmic copper-binding protein (NosD)
    1.2e-06   28.1  39.4     0.0061   15.9  16.1    3.9  2  DUF1565          Protein of unknown function (DUF1565)
    0.00042   20.2  33.1      0.061   13.2   8.0    3.1  3  Pectate_lyase_3  Pectate lyase superfamily protein
    0.00066   18.5   0.4      0.001   17.8   0.4    1.4  1  Pectinesterase   Pectinesterase


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 !   57.7  26.0   3.4e-19   1.2e-15       8     113 ..      99     206 ..      92     207 .. 0.71
   2 !   83.8  49.7   3.1e-27   1.1e-23       1     156 [.     118     268 ..     118     270 .. 0.95
   3 ?    2.5   0.1     0.032   1.2e+02      79      99 ..     262     282 ..     258     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 3.4e-19
                                   S-E.EEESEEEES-...SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES- CS
                    Beta_helix   8 ssnvtiknntisns...ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienn 85 
                                   s+nvt+ +++i+++    ++Giyl+g ++++i nn +++ +++Gi++ +ssnnt+ nn+i+ n   gi l+ +snn ++nn
  gi|91772146|ref|YP_564838.1|  99 SDNVTVIGFKITGThgpTKAGIYLDGVEKCTIANNILSK-NEDGIGLVSSSNNTLINNNINSNSFEGIDLERSSNNELSNN 178
                                   344577777777777777777777777777777777777.77777777777777777777777777777777777777777 PP

                                   EEES-SS-SEE-TT-S--EEES-EEEST CS
                    Beta_helix  86 eitdnggsGiylnyssnntienNiidnn 113
                                   +i+ n  +Gi+l+ s+nn+++nNii++n
  gi|91772146|ref|YP_564838.1| 179 TISSNIWNGIFLEASNNNRFSNNIINSN 206
                                   7777766677777777777777777776 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 3.1e-27
                                   -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                    Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                   +gi+++g++ +ti nn++s+ + +Gi l +ssn+++ nn+i++ns++Gi++++ssnn +snntis n   gi l++++nn 
  gi|91772146|ref|YP_564838.1| 118 AGIYLDGVEKCTIANNILSK-NEDGIGLVSSSNNTLINNNINSNSFEGIDLERSSNNELSNNTISSNIWNGIFLEASNNNR 197
                                   59******************.6*********************************************************** PP

                                   EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                    Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                   ++nn i+ n  +Gi++ +s+n +i+nN+i++n+++Gi++d s+ n+t ++N + nn+ +Gi   ++   ++++ N
  gi|91772146|ref|YP_564838.1| 198 FSNNIINSNHLNGISFINSNNSKINNNTINSNGQNGIFLDISN-NNTLNDNFLLNNS-KGIRADYTE--NHIYDN 268
                                   *******************************************.************8.***555554..577777 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.032
                                   --EEES-EEES-SS-SEE-TT CS
                    Beta_helix  79 nnlienneitdnggsGiylny 99 
                                    n i++n+i+d++  Gi + +
  gi|91772146|ref|YP_564838.1| 262 ENHIYDNHINDREVPGIPFVN 282
                                   577888888888888887765 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9  27.9   7.5e-21   2.7e-17      30     148 ..      82     206 ..      46     207 .. 0.80
   2 !   46.6  27.6   6.9e-16   2.5e-12      60     155 ..     185     280 ..     182     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 7.5e-21
                          NosD  30 snneisn.srdgilldnssnntitgntienl....ryGihlensesntiedntlssnesGialmsssnntlenNtisnnen 105
                                   +++ ++   ++++++ +s+n+t+ g +i+      ++Gi+l++ e++ti +n+ls+ne+Gi l sssnntl nN+i++n+ 
  gi|91772146|ref|YP_564838.1|  82 NDTVVQAgKNSHVFHITSDNVTVIGFKITGThgptKAGIYLDGVEKCTIANNILSKNEDGIGLVSSSNNTLINNNINSNSF 162
                                   3333443034455999**********999989999*********************************************9 PP

                          NosD 106 yGillsdssnntisnNtis.nnnkGiflensssntitgNriesn 148
                                    Gi l++ssnn++snNtis n  +Gifle+s++n++++N i+sn
  gi|91772146|ref|YP_564838.1| 163 EGIDLERSSNNELSNNTISsNIWNGIFLEASNNNRFSNNIINSN 206
                                   *******************99*********************99 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 6.9e-16
                          NosD  60 ryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssnt 139
                                    +Gi+le s++n+ ++n+++sn+ +Gi++ +s+n+ ++nNti++n ++Gi+l+ s+nnt+++N  +nn+kGi+ +  ++n 
  gi|91772146|ref|YP_564838.1| 185 WNGIFLEASNNNRFSNNIINSNHlNGISFINSNNSKINNNTINSNGQNGIFLDISNNNTLNDNFLLNNSKGIRADY-TENH 264
                                   4799999999999999999999999999999999999999999999999999999999999999999999999998.7999 PP

                          NosD 140 itgNriesnqkiGill 155
                                   i +N+i++ +  Gi +
  gi|91772146|ref|YP_564838.1| 265 IYDNHINDREVPGIPF 280
                                   9999999998888865 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  16.1   1.7e-06    0.0061      11     189 ..      35     206 ..      28     208 .. 0.44
   2 !    5.9  18.6    0.0019       6.8     107     185 ..     202     283 ..     201     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                       DUF1565  11 ksaPfktiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGnea.gKGlskslyagkkvgplisgggddlsgvq 90 
                                   ++a +  i  A+  a++g++i + pGtY e+   + Pl+i    +   ++  + G+++ ++                    
  gi|91772146|ref|YP_564838.1|  35 REANYANIQDAIDNANSGDIILVNPGTYRENVNVNKPLTIISRSENPNDTVvQAGKNSHVFHI------------------ 97 
                                   566677888899999999999999999999999999998854444333332123333333332.................. PP

                       DUF1565  91 nvtivlaneatiaGvtitNpnilkgtgvliesa.sakianNtitg......................niadGievsiyeak 148
                                        + +++t+ G++it ++   + g+++ ++   +ianN +++                      n  +Gi  +   ++
  gi|91772146|ref|YP_564838.1|  98 -----TSDNVTVIGFKITGTHGPTKAGIYLDGVeKCTIANNILSKnedgiglvsssnntlinnninsNSFEGIDLERS-SN 172
                                   .....3334444444444443334444444444444444444444000000000000000000000033344444433.23 PP

                       DUF1565 149 tgaggniisGnsilfeknGiaisgasaavenkienNiivkN 189
                                   ++  +n+is n      nGi  + +    +n+  nNii  N
  gi|91772146|ref|YP_564838.1| 173 NELSNNTISSNI----WNGIFLEAS---NNNRFSNNIINSN 206
                                   333333333332....234443322...2235555555444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0019
                       DUF1565 107 itNpnilkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGnsilfeknGiaisgasaa.venkien... 183
                                   i N n l+g   +i+s ++ki+nNti+ n+++Gi+ +i +      +n+   n++l++ +Gi  + +++  + n+i++   
  gi|91772146|ref|YP_564838.1| 202 IINSNHLNGI-SFINSNNSKINNNTINSNGQNGIFLDISN------NNTLNDNFLLNNSKGIRADYTENHiYDNHINDrev 275
                                   6677766666.589999********************996......78888899999999999888777735567755555 PP

                       DUF1565 184 ......Ni 185
                                         N+
  gi|91772146|ref|YP_564838.1| 276 pgipfvNT 283
                                   55555554 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0016       5.6      12      45 ..      33      63 ..      29      75 .. 0.86
   2 !   13.2   8.0   1.7e-05     0.061     125     213 ..      97     187 ..      69     189 .. 0.79
   3 !    8.5  13.3   0.00047       1.7     123     213 ..     191     277 ..     185     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0016
                                  EEEEE-HHHHHHHH......HTSS-EEE-SEEEE CS
               Pectate_lyase_3 12 DGvtDdtaaiqkaiscasatttgavVYfPaGtYl 45
                                  D++  + a iq+ai   ++ ++g+++ + +GtY+
  gi|91772146|ref|YP_564838.1| 33 DDREANYANIQDAI---DNANSGDIILVNPGTYR 63
                                  677778899*****...9999************8 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.7e-05
                                   EEEEEEES-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEEE CS
               Pectate_lyase_3 125 aqatslenvefemseasgtkhqgifiengsggfl.ndlvfsglgdigiavgnqqftvrnitfnnattgievlwgwgwtlkn 204
                                    + ++++ + f+++  +g ++ gi+++  ++ ++ n++  ++ ++ig+  ++++  ++n+  +n+ +gi+++++++  l+n
  gi|91772146|ref|YP_564838.1|  97 ITSDNVTVIGFKITGTHGPTKAGIYLDGVEKCTIaNNILSKNEDGIGLVSSSNNTLINNNINSNSFEGIDLERSSNNELSN 177
                                   4455566667788888888999****9999988878888888888888889999999***********************9 PP

                                   EEE.ESSSEE CS
               Pectate_lyase_3 205 vki.nncegG 213
                                   ++i +n  +G
  gi|91772146|ref|YP_564838.1| 178 NTIsSNIWNG 187
                                   9884444445 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00047
                                   EEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEE CS
               Pectate_lyase_3 123 qtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtl 202
                                   + + +  ++n+++++++ +     gi   n++++ +n+ +++ +g+ gi +  +++ t++++   n++ gi+++++++ ++
  gi|91772146|ref|YP_564838.1| 191 EASNNNRFSNNIINSNHLN-----GISFINSNNSKINNNTINSNGQNGIFLdISNNNTLNDNFLLNNSKGIRADYTENHIY 266
                                   4566677777777777777.....899999999999999999999999999668888999988888899999998777777 PP

                                   EEEEEESSSE.E CS
               Pectate_lyase_3 203 knvkinnceg.G 213
                                    ++ in+ e+ G
  gi|91772146|ref|YP_564838.1| 267 -DNHINDREVpG 277
                                   .67777766655 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.4   2.9e-07     0.001       2      74 ..      29      96 ..      28     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-07
                                  EEE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES-TTTEEEEE---TTTT- CS
                Pectinesterase  2 vvvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvGdGkektvitgsknvvdgk 74
                                  ++v +d ++++  i++a++++++      +i v+ G+Y+env+v+k    ++   +  + tv+ + kn+   +
  gi|91772146|ref|YP_564838.1| 29 ITVDDDREANYANIQDAIDNANS----GDIILVNPGTYRENVNVNKP-LTIISRSENPNDTVVQAGKNSHVFH 96
                                  78999*************98874....359**************985.5677788889999998865554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1806.21
//
Query:       gi|91772147|ref|YP_564839.1|  [L=815]
Description: plasma-membrane proton-efflux P-type ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-52  176.2   2.0    4.6e-52  176.2   2.0    3.5  5  E1-E2_ATPase     E1-E2 ATPase
    1.3e-22   81.2   1.8    2.3e-22   80.4   1.8    1.4  1  Hydrolase        haloacid dehalogenase-like hydrolase
      7e-16   57.7   0.0      7e-16   57.7   0.0    2.0  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
      4e-08   33.3   0.4    0.00018   21.3   0.2    2.8  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.037   14.1   0.1      0.079   13.1   0.1    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)


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 !  176.2   2.0   1.3e-55   4.6e-52       4     181 .]     119     296 ..     116     296 .. 0.98
   2 ?   -0.8   0.0      0.26   9.5e+02      46      70 ..     481     506 ..     477     515 .. 0.81
   3 ?   -2.9   0.0       1.1     4e+03      27      42 ..     592     607 ..     591     622 .. 0.90
   4 ?   -3.6   0.6         2     7e+03     122     146 ..     625     649 ..     599     659 .. 0.48
   5 ?   -3.0   2.2       1.2   4.4e+03     109     170 ..     748     768 ..     685     795 .. 0.62

  Alignments for each domain:
  == domain 1  score: 176.2 bits;  conditional E-value: 1.3e-55
                                   --EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEE CS
                  E1-E2_ATPase   4 pptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvekekgdmvfsGtvvvsgeaka 83 
                                   + +a+v+rd+++ e+ a+e+vpGD++ l+ gd+ paD++++ g    vdes LTGEslpvek+  d ++sG+v+ +ge+ a
  gi|91772147|ref|YP_564839.1| 119 AVEARVLRDNKWLEVTAREIVPGDVIRLRLGDILPADVKLIGGDYlLVDESTLTGESLPVEKHVLDVAYSGSVIRQGEMDA 199
                                   6789***************************************************************************** PP

                                   EEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHH CS
                  E1-E2_ATPase  84 vVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLp 164
                                    V+atg++t++gk a+lveea ++++++qk + k+g +l++++l++++l+f++ l++ +s  + + +al+l+vaaiP aLp
  gi|91772147|ref|YP_564839.1| 200 LVVATGMSTYFGKTAKLVEEA-KTQSHFQKAVIKIGDYLIAFALVLVVLIFFVVLYRHESMLNFFQFALVLIVAAIPAALP 279
                                   *********************.9********************************************************** PP

                                   HHHHHHHHHHHHHHHHT CS
                  E1-E2_ATPase 165 lavplalalgarrlakk 181
                                   +++++++a+ga +lak+
  gi|91772147|ref|YP_564839.1| 280 AVLSVTMAVGAISLAKE 296
                                   **************995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.26
                                   E-S.EEE-TTTS---S-EE-G-TTEE CS
                  E1-E2_ATPase  46 gsa.evdesaLTGEslpvekekgdmv 70 
                                    ++  v+  ++TG++l++ ke  ++v
  gi|91772147|ref|YP_564839.1| 481 AQSmGVNVKMVTGDHLAIAKEISKQV 506
                                   55568999***********9866655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                                   SEEEEETT-B--SEEE CS
                  E1-E2_ATPase  27 DivllkagdrvpaDgr 42 
                                   Divl k+g +v +D++
  gi|91772147|ref|YP_564839.1| 592 DIVLTKPGLSVIIDAI 607
                                   9*********999975 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHS-STTTSSTTH CS
                  E1-E2_ATPase 122 lvpvvlliallvflialllgkslae 146
                                   ++ ++ +++++++ i ++ + +++ 
  gi|91772147|ref|YP_564839.1| 625 IAETIRILLFITLSIIVFQFYPVTA 649
                                   4444444444444444444444433 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 1.2
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHH CS
                  E1-E2_ATPase 109 tplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavpla 170
                                   +                                         al l++a+i   L++++ ++
  gi|91772147|ref|YP_564839.1| 748 P-----------------------------------------ALPLFIAVITTQLIATIITV 768
                                   3.........................................44444444444443332222 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   1.8   6.3e-26   2.3e-22       1     210 []     312     575 ..     312     575 .. 0.77

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 6.3e-26
                                   SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH.......HHCHHHHHHHHHHHHH........HHHHHHHHHETTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx........xxxxxxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg.......sehpigkalvaaakar........sgaltgfatfigr 66 
                                   ++ ++ Dk+GT+t+ e ++ +v   ++  ++ +l ++        + pi +a+v + k +        s ++  f +f   
  gi|91772147|ref|YP_564839.1| 312 MDILCSDKTGTITKNEVVLAEVKLFNDFIEKDVLLFAslasreeDQDPIDNAIVTKTKTMqevaeiigSYKVVAFKAF--- 389
                                   578999**********888888777744444444444467779999********999999777766653333333332... PP

                                   E..................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH................TTHHHHHHHH CS
                                   x..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxx RF
                     Hydrolase  67 g..................ayaigkpewltaldippdlgaaigsaqsqgrtvall................qaralavfti 113
                                                      ++ +g p+ + +l       ++i+saq +     +                 + +  +++++
  gi|91772147|ref|YP_564839.1| 390 DpvskrteatiehtnsnsfKVTKGAPQVILSL----VDSKDISSAQVDEDVNNFAakgyralgvartddegNWHFAGLIAL 466
                                   14445557777777899999999999988888....4444444444444444444666777777888877788******** PP

                                   HHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..........GGGE.SEEEEHHCES......STTTSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxx.xxxxxxxxxx......xxxxxxx RF
                     Hydrolase 114 adplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..........ddyf.daviasdiet......vakpspe 177
                                    dp  ++++ +e++++ +++g++v ++tgd+ + a+++ +q++          +  + d + +    +      +a + pe
  gi|91772147|ref|YP_564839.1| 467 YDP--PREDSKETIKKAQSMGVNVKMVTGDHLAIAKEISKQVNlnpeivlatsFLDMpDRKAQE---VvetangFAQVFPE 542
                                   ***..**************************************999999965522222444444...3445999******* PP

                                   HHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   +k ++++ Lq k++ v m GDgvnDa+al++A+
  gi|91772147|ref|YP_564839.1| 543 HKYHIVELLQRKGHIVGMTGDGVNDAPALKKAD 575
                                   *******************************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 !   57.7   0.0     2e-19     7e-16       3      69 .]      13      77 ..      11      77 .. 0.96
   2 ?   -3.3   0.7       2.2   7.8e+03      58      67 ..     265     274 ..     264     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 2e-19
               Cation_ATPase_N  3 alsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                  + +++e+lekL  ++e G++ +ea+er ++yGpNe+  +kk+s +vk+l+ f+ p++++ ++aa++s
  gi|91772147|ref|YP_564839.1| 13 NATINELLEKLS-SSEIGISASEAEERFQQYGPNEI-TEKKTSSIVKFLSYFWGPIPWMIEIAAILS 77
                                  57899******6.9**********************.****************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
               Cation_ATPase_N  58 lvilLlvaal 67 
                                   + ++L+vaa+
  gi|91772147|ref|YP_564839.1| 265 FALVLIVAAI 274
                                   789*****97 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00031       1.1      18      58 ..     472     512 ..     468     517 .. 0.89
   2 !   21.3   0.2   5.1e-08   0.00018     201     245 ..     553     597 ..     544     607 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                   Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                   e +ke+ikk+++ g++v   TG +l  ++++ ++++l+  +
  gi|91772147|ref|YP_564839.1| 472 EDSKETIKKAQSMGVNVKMVTGDHLAIAKEISKQVNLNPEI 512
                                   6799********************************99444 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 5.1e-08
                                   --GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE-- CS
                   Hydrolase_3 201 isleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtks 245
                                    +   v   GDg ND + L++a+ g+A++ a++ +k+aAd v ++
  gi|91772147|ref|YP_564839.1| 553 RKGHIVGMTGDGVNDAPALKKADAGIAVAGATDAAKSAADIVLTK 597
                                   555556677*******************************99876 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 ?   13.1   0.1   2.2e-05     0.079      22      86 ..     358     420 ..     341     424 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                 Cation_ATPase  22 nktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilk 86 
                                   ++ + A++  ++ + +++ e+  ++k v+   F+ + Kr    ++ + +++   ++KGAp++il+
  gi|91772147|ref|YP_564839.1| 358 DPIDNAIVTKTKTM-QEVAEIIGSYKVVAFKAFDPVSKRTEATIEHT-NSNSFKVTKGAPQVILS 420
                                   78899999999999.999************************99995.77788899*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (815 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1327  (0.0740142); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 5024.49
//
Query:       gi|91772148|ref|YP_564840.1|  [L=433]
Description: amino acid transporter [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-37  129.7  49.5    1.5e-37  129.5  49.5    1.1  1  AA_permease_2  Amino acid permease
    3.1e-34  118.4  45.6    5.2e-34  117.7  45.6    1.3  1  AA_permease    Amino acid permease
      0.009   15.1  32.0     0.0088   15.1  28.6    2.2  2  Trp_Tyr_perm   Tryptophan/tyrosine permease family


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5  49.5   2.5e-41   1.5e-37       1     418 [.      10     407 ..      10     414 .. 0.79

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 2.5e-41
                 AA_permease_2   1 lsllsafalvigsvigsgifvkn.laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf.gkkvafl 79 
                                   +++lsa+ + ig ++g gif++  la   g+  + + ++ ++i+ l+ ++ ya ls + p++gG + ++ +af + +v   
  gi|91772148|ref|YP_564840.1|  10 IGYLSAVSIGIGGMVGGGIFAVLgLAVEIGKGGTPIAFGLAGIVALITSYSYAKLSVRYPSEGGTVEFLNQAFgSGLVTGG 90 
                                   799******************98744457777777778888888899*********99***************55777788 PP

                 AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliili 160
                                     +++w++yv++l++++++++sy  +++ pd   + +l  ++ ++i++ ++++ni+g k ++k+ ++++ +k+  +l+i+i
  gi|91772148|ref|YP_564840.1|  91 LNILLWLSYVVMLSLYAYAFGSYGSTFF-PDS-MQAVLRHVLTSIIIVSLTVVNIVGAKVVGKLETWIVGFKVA-ILLIFI 168
                                   88888******99888888888877765.754.346799999*******************************5.888888 PP

                 AA_permease_2 161 ilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvn 238
                                    +g++ v+ + f+         + + +p+  ++g +i+++++ Gfe +an ++ vk+  k++p a  +++++v+vly+l++
  gi|91772148|ref|YP_564840.1| 169 GVGIWSVKSQPFQ--------PTISSNPLqLVAGGMIIFLAYEGFELIANTAKDVKNpgKTLPCAYYSAVVFVIVLYVLIA 241
                                   8999999888885........35556665444455569******************9989********************* PP

                 AA_permease_2 239 iaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvnkfg 319
                                   +  +  v++d+i + ++  +++a+ ++ + g +++ ++++++ ls + ain+ ++g+srv + +a+dg+lP+ +     ++
  gi|91772148|ref|YP_564840.1| 242 FITVETVSIDSIIQAKD--YALAVAAKPFLGNFGFNLIAVAALLSTASAINATLYGASRVSFTIAKDGELPEILEE-KIWN 319
                                   *********99977677..3467777777789***************************************99975.4677 PP

                 AA_permease_2 320 spiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkr..pgkilvaiigalfllfl 398
                                   +pi ++ +t  ++li++              ++++s++++ s ++l+i + ++  +   +++   +++ ++i+g++++ ++
  gi|91772148|ref|YP_564840.1| 320 RPIEGLLITSALTLIVANT------------FNLASISIMGSAGFLLIFGAVNASNACLYQKtaSYRW-ISITGIIVCSIA 387
                                   8************765433............3444444444444444444444444333322237778.677777777777 PP

                 AA_permease_2 399 lvalffppkgpatqssliyt 418
                                   l++l++++ + + ++ +i++
  gi|91772148|ref|YP_564840.1| 388 LFTLIWYTLNNSPKDIFILA 407
                                   77777666555544445554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7  45.6   8.6e-38   5.2e-34       2     421 ..      15     396 ..      14     416 .. 0.85

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 8.6e-38
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfviGln 81 
                                   ++ i +gg++G g+f  lg ++  +G +g+ +a+ lag+v +++ +s + +++ +p+ gg+  +  +  g+  + +  +++
  gi|91772148|ref|YP_564840.1|  15 AVSIGIGGMVGGGIFAVLGLAVE-IGKGGTPIAFGLAGIVALITSYSYAKLSVRYPSEGGTVEFLNQAFGSgLVTGGLNIL 94 
                                   5789***************9885.6666****************************9999999999999984444555555 PP

                   AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvt....gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgi 158
                                   +++s+++ l l   a +++ +    ++d + + v      ++++v l+++n+vg+kv g+ e+++  +k+ ++++fi vgi
  gi|91772148|ref|YP_564840.1|  95 LWLSYVVMLSLYAYAFGSYGSTF--FPDSM-QAVLrhvlTSIIIVSLTVVNIVGAKVVGKLETWIVGFKVAILLIFIGVGI 172
                                   9*****99999888888776666..56655.3333455599***************************************7 PP

                   AA_permease 159 illaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqv 239
                                   +++ ++  ++                 ++++         ++ +++ +i+++a+ G+el+a++a++vk+P k++P a  ++
  gi|91772148|ref|YP_564840.1| 173 WSVKSQPFQPT----------------ISSN--------PLQLVAGGMIIFLAYEGFELIANTAKDVKNPGKTLPCAYYSA 229
                                   55444443333................4455........67888889999******************************* PP

                   AA_permease 240 viritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslak 320
                                   v+ ++++Yvl++++ + +v+ ++    +d a    + v +  ++g+ +++ li+++ l+++ s++n+ ly asRv ++ ak
  gi|91772148|ref|YP_564840.1| 230 VVFVIVLYVLIAFITVETVSIDSIIQAKDYA----LAVAAKPFLGNFGFN-LIAVAALLSTASAINATLYGASRVSFTIAK 305
                                   *******************999955555444....88*********9997.56777788999******************* PP

                   AA_permease 321 dglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsi 401
                                   dg +P +l+  + +++P+ ++l+++++ l++   + +nla       ++ +  + +l++++++++s + + ++  ++ r+i
  gi|91772148|ref|YP_564840.1| 306 DGELPEILEE-KIWNRPIEGLLITSALTLIVA--NTFNLA------SISIMGSAGFLLIFGAVNASNACLYQK-TASYRWI 376
                                   ********97.679************999888..******......445566677889**********77777.4666779 PP

                   AA_permease 402 eelgfkaallplgvilvlaa 421
                                   +  g++ + + l++ ++ ++
  gi|91772148|ref|YP_564840.1| 377 SITGIIVCSIALFTLIWYTL 396
                                   9************9999876 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  28.6   1.5e-06    0.0088       5     292 ..      12     295 ..       8     297 .. 0.80
   2 ?    2.0   4.0     0.014        84      82     174 ..     227     318 ..     219     337 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-06
                  Trp_Tyr_perm   5 llggvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaakeeasfttlakkllGkkg.....n 80 
                                    l++v++ +g ++G+G++a+   + ++g   + +++ l+ +++l + + ++ +++ +++e +  ++ ++ +G+       n
  gi|91772148|ref|YP_564840.1|  12 YLSAVSIGIGGMVGGGIFAVLGLAVEIGKGGTPIAFGLAGIVALITSYSYAKLSVRYPSEGGTVEFLNQAFGSGLvtgglN 92 
                                   689999******************************************************************975111225 PP

                  Trp_Tyr_perm  81 iivalvllfllyiLlvAyisggGsilselleeasgialsarlavliftlvlgalvvlstkavdrinrvllflklvafvlll 161
                                   i+ +l+++++l    +A     Gs  s  +++++  a+ +++ + i+++ l ++ ++++k+v ++ + ++ +k+  + +++
  gi|91772148|ref|YP_564840.1|  93 ILLWLSYVVMLSLYAYA----FGSYGSTFFPDSM-QAVLRHVLTSIIIVSLTVVNIVGAKVVGKLETWIVGFKVAILLIFI 168
                                   66666665555544444....4555566666666.5667999999999999999999************************ PP

                  Trp_Tyr_perm 162 alllskvksdvLlsaksdtskvslvlsalPvlllsfGFhgivpslvkyldknvkkvkkailiGtliaLvlyllWelivlGn 242
                                    +++++vks+     + + + ++lv   + ++l+  GF  i  +  k + +  k++  a     ++ +vly+l  +i++ +
  gi|91772148|ref|YP_564840.1| 169 GVGIWSVKSQPFQP-TISSNPLQLVAGGMIIFLAYEGFELIANT-AKDVKNPGKTLPCAYYSAVVFVIVLYVLIAFITVET 247
                                   *********99888.54556666666666666666699876655.555555889999999999999*************** PP

                  Trp_Tyr_perm 243 lpreelariiakggnldtlveallelleskslelavelFsflAlatSflG 292
                                   ++  +++++++ +  l ++ + +l+ +  + +++a  l   +A+ + + G
  gi|91772148|ref|YP_564840.1| 248 VSIDSIIQAKDYA--LAVAAKPFLGNFGFNLIAVAALLSTASAINATLYG 295
                                   **99999988877..88888888888888887777777777777666655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.014
                  Trp_Tyr_perm  82 ivalvllfllyiLlvAyisggGsilselleeasg...ialsarlavliftlvlgalvvlstkavdrinrvllflklvafvl 159
                                     a+v++++ly+L+ A+i+     + ++++       +a++++l ++ f l++ a ++   + ++ in+ l  +  v+f++
  gi|91772148|ref|YP_564840.1| 227 YSAVVFVIVLYVLI-AFITVETVSIDSIIQAKDYalaVAAKPFLGNFGFNLIAVAALL---STASAINATLYGASRVSFTI 303
                                   56788899999986.5555444334444433221113777888888888877544443...34567889999999999999 PP

                  Trp_Tyr_perm 160 llalllskvksdvLl 174
                                   +  + l+++ ++++ 
  gi|91772148|ref|YP_564840.1| 304 AKDGELPEILEEKIW 318
                                   988888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); 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:                         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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2804.25
//
Query:       gi|91772149|ref|YP_564841.1|  [L=279]
Description: amino acid transporter, partial [Methanococcoides burtonii DSM 6242]
Scores for complete 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-20   71.2  22.1    2.5e-19   69.4  22.1    1.7  1  AA_permease_2    Amino acid permease
    5.3e-17   61.6  17.9    9.3e-17   60.8  17.8    1.4  1  AA_permease      Amino acid permease
  ------ inclusion threshold ------
       0.17   11.5   0.2       0.32   10.5   0.2    1.4  1  NDUF_B5          NADH:ubiquinone oxidoreductase, NDUFB5/SGDH 
        6.1    6.5  16.0       0.77    9.5   9.8    2.1  2  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4  22.1   5.6e-23   2.5e-19     148     416 ..       2     250 ..       1     276 [. 0.75

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 5.6e-23
                 AA_permease_2 148 gilkillpliiliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvsee..vkkkdvpkaifi 225
                                   + +k+ ++l ++ ++gl+++++            +++   +  +l g +iv+++++Gf  ++n +e   +++k++pka+ +
  gi|91772149|ref|YP_564841.1|   2 VSIKV-GILMLFALAGLFFIKPENL--------AVMNFPKTPnILYGAGIVFLAYQGFGLITNAAEDmdDPRKTLPKALYL 73 
                                   56788.5667777788888765333........345454443479999*******************5444599******* PP

                 AA_permease_2 226 gllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardg 306
                                   ++liv+++y+lv++a++g ++++ei++ ++   ++a+ ++ + g++++ i++i++ ls   ain+ ++g + v + +a++g
  gi|91772149|ref|YP_564841.1|  74 SVLIVICIYVLVSLAVIGNLSISEISTAKDY--ALAAAAKPFLGPIGFKIMAIAALLSTSSAINASLYGGANVSYLIAKEG 152
                                   **************************98883..466666666689************************************ PP

                 AA_permease_2 307 vlPrffa.kvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrpgkil 386
                                   +lP ff  kv+k+   + ++++t  ++ il+           + ll++  +g++ s  ll+i+  ++  + +  ++ g+ +
  gi|91772149|ref|YP_564841.1| 153 ELPGFFErKVWKR--STESLFITSGLV-ILC-----------TNLLNLERIGMLASASLLVIYIAVNTAHLRLSGETGAKP 219
                                   ***8886155688..778899999998.543...........568888888888888888888888888877666655432 PP

                 AA_permease_2 387 .vaiigalfllfllvalffppkgpatqssli 416
                                    + + +++++l+++ +l ++   +++ + + 
  gi|91772149|ref|YP_564841.1| 220 yLIWASLFSSLIFFGILVYYELIHSIITLIV 250
                                   1444445555555555554432222333333 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8  17.8   2.1e-20   9.3e-17     199     431 ..      34     252 ..      16     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 2.1e-20
                   AA_permease 199 knfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvif 279
                                    n+++++ iv++a++G++l++++a++++dP+k++Pka    v++++ +Yvl++l+++  ++ +  +  +d a    +   +
  gi|91772149|ref|YP_564841.1|  34 PNILYGAGIVFLAYQGFGLITNAAEDMDDPRKTLPKALYLSVLIVICIYVLVSLAVIGNLSISEISTAKDYA----LAAAA 110
                                   68999***********************************************************99988877....66999 PP

                   AA_permease 280 ikesgvsvlaplinaviltaalssansslysasRvlyslakdglaPkvlk.kvskrgvPlraillsmiisllalllaslnl 359
                                     ++g ++++ +++++ l+++ s++n+sly +  v y  ak+g +P +++ kv kr     ++++++ ++ l+   + lnl
  gi|91772149|ref|YP_564841.1| 111 KPFLGPIGFK-IMAIAALLSTSSAINASLYGGANVSYLIAKEGELPGFFErKVWKRS--TESLFITSGLVILCT--NLLNL 186
                                   9999999996.89*********************************66650444443..466666666666666..66677 PP

                   AA_permease 360 aapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilal 431
                                   +       +  ++ ++ l++++++++++lr+  +  ++   i  + f +  ++ ++++  ++ +ii+li++ 
  gi|91772149|ref|YP_564841.1| 187 E------RIGMLASASLLVIYIAVNTAHLRLSGETGAKPYLIWASLFSSLIFFGILVYYELIHSIITLIVFA 252
                                   7......55667778899***********8877765555444444444444444444444444443333332 PP

>> NDUF_B5  NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   7.2e-05      0.32      36      87 ..     203     253 ..     177     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.2e-05
                       NDUF_B5  36 kaekvavrlsgdHgkrlfvikpsrfydkrflkllkfYilltgiPvavlvtlv 87 
                                    ++++ +rlsg+ g +  +i +s f    f  +l +Y l+  i ++++v+ v
  gi|91772149|ref|YP_564841.1| 203 AVNTAHLRLSGETGAKPYLIWASLFSSLIFFGILVYYELIHSI-ITLIVFAV 253
                                   3456889********************************9999.77777665 PP

>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4     0.089     4e+02     158     171 ..      72      85 ..      35     139 .. 0.62
   2 ?    9.5   9.8   0.00017      0.77     189     248 ..     207     274 ..     154     275 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.089
               PhoLip_ATPase_C 158 ftalvlvvnlkval 171
                                   + ++++v++++v++
  gi|91772149|ref|YP_564841.1|  72 YLSVLIVICIYVLV 85 
                                   22222222222221 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
               PhoLip_ATPase_C 189 l...........lyflflllyssllpsssefygvleelfsspsfwlvlllvvvvallpdllikvlkrtffp 248
                                   +            y+++  l+ssl++    ++ v++el++s+ + +v+++v++++++++++++ + r++ +
  gi|91772149|ref|YP_564841.1| 207 AhlrlsgetgakPYLIWASLFSSLIF---FGILVYYELIHSIITLIVFAVVLTLCFIVEWAYRKYSRRILK 274
                                   12333333444467777778877765...46668899**************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1769.21
//
Query:       gi|91772150|ref|YP_564842.1|  [L=118]
Description: hypothetical protein Mbur_0071 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.8   0.0      0.069   13.1   0.0    1.3  1  HTH_12    Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-06     0.069      32      51 ..      70      89 ..      56      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-06
                        HTH_12 32 eravRyrLrkleergltrrv 51
                                  e ++Ry+L+k+e ++l++ +
  gi|91772150|ref|YP_564842.1| 70 ETSMRYHLQKIELDQLIEHN 89
                                  569*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 824.01
//
Query:       gi|91772151|ref|YP_564843.1|  [L=257]
Description: alpha/beta hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-12   45.9   0.1      4e-06   26.7   0.0    2.6  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0099   14.6   0.2      0.019   13.7   0.2    1.7  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.062   13.9   0.0       0.34   11.5   0.0    2.0  1  Abhydrolase_6  Alpha/beta hydrolase family
      0.072   12.4   0.8          5    6.4   0.1    2.7  3  DUF915         Alpha/beta hydrolase of unknown function (DUF9
        0.1   11.9   0.0       0.19   10.9   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.1e-09     4e-06       3     106 ..      21     113 ..      19     126 .. 0.86
   2 !   16.5   0.0   1.4e-06     0.005     193     254 ..     182     238 ..     143     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.1e-09
                                   EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHH CS
                 Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmG 83 
                                   + ++hG++gs+  w +   ++ ++k ++ +++l +  +         in++ ++++v+ +++  ld+++++  + vG+S+ 
  gi|91772151|ref|YP_564843.1|  21 ITFIHGFGGSARTWKK--QIEFFSK-HYNLLVLEMHKNK--------INEELNLDNVCIFINNTLDHYKIKTSHFVGFSFS 90 
                                   6689999999999999..8888888.9999999885444........446777899************************* PP

                                   HHHHHHHHHHHGGGEEEEEEESE CS
                 Abhydrolase_1  84 GmialayaaeyperVkalvllga 106
                                   ++i+l +a +ype++++l++ g+
  gi|91772151|ref|YP_564843.1|  91 SLICLRFAVLYPEKINSLIMGGG 113
                                   ******************98666 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.4e-06
                                   HHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHH CS
                 Abhydrolase_1 193 pttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafl 254
                                   +t+ s  +l++l++     + +l++sg++D+l+  + l+ +++  ++ ++++i+++gH   +
  gi|91772151|ref|YP_564843.1| 182 QTKKSLTWLDELNK----DIQVLYVSGNEDHLFLKDTLRHSKKISNS-QVEIIEHCGHVCSI 238
                                   55566666666666....559********************977666.**********7655 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   5.3e-06     0.019      80     129 ..      61     110 ..      51     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-06
                                   --HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEE CS
                           Ndr  80 pslddladqllavldhfklksviglGvgaGAyilarfalkhperveglvL 129
                                     ld+++  +++ ldh+k+k+   +G      i +rfa+ +pe++ +l++
  gi|91772151|ref|YP_564843.1|  61 LNLDNVCIFINNTLDHYKIKTSHFVGFSFSSLICLRFAVLYPEKINSLIM 110
                                   56899*******************************************97 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.4e-05      0.34       3     218 ..      23     245 ..      21     247 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.4e-05
                                   EE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT..TTSEEEEEETCHHHHHHHH CS
                 Abhydrolase_6   3 llHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaagggpvvlvGHSlGGalalaa 82 
                                   ++HG+g+sa+ W      +++++++  l++    +       l+l+++  +  ++ld+ +   +  + vG S+  ++ l++
  gi|91772151|ref|YP_564843.1|  23 FIHGFGGSARTWK--KQIEFFSKHYNLLVLEMHKN--KINEELNLDNVCIFiNNTLDHYK--IKTSHFVGFSFSSLICLRF 97 
                                   8999999999994..33344577777788888666..47777888775444777888886..77779*********99995 PP

                                   HHCC....EEEEES-..----TTTS----TTHH.......HHHHTT-CCCCH.CCH....S-HSCCCCHHHC..CCCHCHC CS
                 Abhydrolase_6  83 apla..lvvgvlldppptalpagllaaalelll.......allallrllawl.sre....plprlfladeda..daawrar 147
                                   a l    + ++++ +  ++  +  + ++l +l+        ++ l+ ++a+  +       ++r ++ +e++   ++  + 
  gi|91772151|ref|YP_564843.1|  98 AVLYpeKINSLIMGG--GIIKFNIRTRFLLFLAikfkkiiNYMILYKFFAYIiM-PkqnhKRSRAIFVNEAKklGYDEFCK 175
                                   555577556655555..2555554333333333222111122223333444431.24556344444444442357777777 PP

                                   CCGHHHHCCHHCHTTCCHHTT-TTGCEEECTT-C.HHHHCHHCCCHSTTEEETCE...SSS-HHHHSHHHHH CS
                 Abhydrolase_6 148 larlaallaglgllpaaawadlpvpllvlggeDp.lvprllerllaqagarlpvvlpgaGHlphleepdeva 218
                                   + +l +++++  ++  +  +d+ v++ v g eD   ++++l++   +   ++ ++++++GH+  +e+ d+++
  gi|91772151|ref|YP_564843.1| 176 WVDLVPQTKKSLTWLDELNKDIQVLY-VSGNEDHlFLKDTLRHSKKISNSQV-EIIEHCGHVCSIEQYDKFN 245
                                   77777777777777677777777777.7245555544444444444788888.9*******55554878775 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.005        18      14      37 ..      21      44 ..      15      62 .. 0.80
   2 ?    6.4   0.1    0.0014         5      67     125 ..      45     102 ..      42     107 .. 0.79
   3 ?   -1.7   0.0      0.39   1.4e+03     180     193 ..     192     205 ..     182     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.005
                        DUF915 14 tifihGyggtaeslnemvkqlenk 37
                                  + fihG+gg+a++ ++ ++ + ++
  gi|91772151|ref|YP_564843.1| 21 ITFIHGFGGSARTWKKQIEFFSKH 44
                                  569***********9999888644 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0014
                        DUF915  67 nPiikvgfednrdaslkkqakwlkkvlseLkkkYnikkfnavGhSmGglaltsYleeya 125
                                   + + ++++++n+  + + +   + + +++   +Y+ik   +vG+S   l +++++  y 
  gi|91772151|ref|YP_564843.1|  45 YNLLVLEMHKNK-INEELNLDNVCIFINNTLDHYKIKTSHFVGFSFSSLICLRFAVLYP 102
                                   556667777777.4777777777778888889*************99999999987775 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.39
                        DUF915 180 kipkdlevlniaGd 193
                                   +++kd++vl + G+
  gi|91772151|ref|YP_564843.1| 192 ELNKDIQVLYVSGN 205
                                   56788888888887 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.4e-05      0.19      61     232 ..      65     234 ..      57     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.4e-05
                   Hydrolase_4  61 DlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv.. 139
                                    +  f+++  ++++ +    +G S  +li l+++  yp+k++ li+ +  +k + +++   +l +l+  ++k++  + +  
  gi|91772151|ref|YP_564843.1|  65 NVCIFINNTLDHYKIKTSHFVGFSFSSLICLRFAVLYPEKINSLIMGGGIIKFNIRTR---FLLFLAIKFKKIINYMILyk 142
                                   555677888888888888899********************************98753...33333333344433333344 PP

                   Hydrolase_4 140 .......snnlkadslsrd..pevvaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasr 211
                                          +  +++++ sr     + +++  d+++++   v    + l+ +++l+++ +     +l ++G +D++  ++  r
  gi|91772151|ref|YP_564843.1| 143 ffayiimP--KQNHKRSRAifVNEAKKLGYDEFCKWVDLVPQTKKSLTWLDELNKDIQ-----VLYVSGNEDHLFLKDTLR 216
                                   45566443..344444443113455677777777764444444444444444444333.....678888888877744333 PP

                   Hydrolase_4 212 elyerlgskdktlklypglyH 232
                                      ++++  + ++++++++ H
  gi|91772151|ref|YP_564843.1| 217 -HSKKIS--NSQVEIIEHCGH 234
                                   .233333..346666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1713.21
//
Query:       gi|91772152|ref|YP_564844.1|  [L=422]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for 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   55.4   0.2    3.2e-14   53.6   0.1    1.9  2  Radical_SAM  Radical SAM superfamily
    2.9e-09   37.1   0.2    8.1e-09   35.6   0.2    1.7  1  Fer4_14      4Fe-4S single cluster domain
    6.2e-09   36.3   0.1    1.3e-08   35.2   0.1    1.5  1  Fer4_12      4Fe-4S single cluster domain
    2.6e-06   27.8   0.4    6.8e-05   23.3   0.0    3.1  3  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 !   53.6   0.1   7.2e-18   3.2e-14       3     142 ..      64     192 ..      62     216 .. 0.83
   2 ?   -1.1   0.0      0.49   2.2e+03      11      20 ..     298     317 ..     296     375 .. 0.68

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 7.2e-18
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                   +t  Cnl+C+ C+       ++ g+++s  +  ++++++ ++ g+  ++++ggepll++   e++++l+k++ +++++   
  gi|91772152|ref|YP_564844.1|  64 PTSDCNLKCKGCWSQD----YESGHNISYKKFDDILDQA-ENLGIMDCLMTGGEPLLRK---EDILKLCKKH-DKMTFGAF 135
                                   6889***********6....6666666666666666666.6667*************88...4455555543.79****** PP

                                   ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                   tn+tl+dee+++++++lg   v +++e + +e    +  + + +++ ++++++l+++ i
  gi|91772152|ref|YP_564844.1| 136 TNATLIDEEFADEMAKLGNLNVFISIEGTKEE-NDFRR-GAGVYDKAIRSMDILKSREI 192
                                   ********************************.66666.88999999999999998765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.49
                                   -TTTSCCTT..........H CS
                                   xxxxxxxxx..........x RF
                   Radical_SAM  11 CsfCarpet..........v 20 
                                   C fC+ + +           
  gi|91772152|ref|YP_564844.1| 298 CAFCHYSDSnihevslaeaL 317
                                   99999998655555544440 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 !   35.6   0.2   1.8e-12   8.1e-09       5      78 ..      65     131 ..      62     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.8e-12
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                   +s Cnl+CkgC  ++    e+g+  +++  ++il+++++  i      +tGGePL   +k+++lkl+k+  + +
  gi|91772152|ref|YP_564844.1|  65 TSDCNLKCKGCWSQD---YESGHNISYKKFDDILDQAENLGI--MDCLMTGGEPL--LRKEDILKLCKKHDKMT 131
                                   689*********999...78999999********55555555..7799*******..89*********987766 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   2.8e-12   1.3e-08      12      85 ..      65     133 ..      54     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.8e-12
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                   +s+Cnl+CkgC     ++ +sg++++ +  + i++++++  i +  ++GGEPll   +e++l+l+k+  +  + 
  gi|91772152|ref|YP_564844.1|  65 TSDCNLKCKGCW---SQDYESGHNISYKKFDDILDQAENLGIMDCLMTGGEPLL--RKEDILKLCKKHDKMTFG 133
                                   799*******99...788999*********************************..*********998887773 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.22   9.7e+02      16      67 ..      19      75 ..      14      76 .. 0.52
   2 ?   -2.2   0.3       1.4   6.1e+03      25      45 ..      75      96 ..      68     100 .. 0.59
   3 !   23.3   0.0   1.5e-08   6.8e-05       5      64 ..     284     339 ..     279     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                         SPASM 16 VvpCcvd....kktyveelklGnireesleeIwnseeyqe..fr...kskkfplielCrnC 67
                                  ++ C        k+  + l++Gn    +l+e++n+ + +    r        +++  C+ C
  gi|91772152|ref|YP_564844.1| 19 IYRC--KqfflAKRLTTHLTMGNFV--TLKELYNGFKNKSsiPRvllVDPTSDCNLKCKGC 75
                                  5667..1123333444449999995..5999998876666542222212233334447777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                         SPASM 25 tyveelklG.nireesleeIwn 45
                                  ++++++  G ni+ +++++I+ 
  gi|91772152|ref|YP_564844.1| 75 CWSQDYESGhNISYKKFDDILD 96
                                  4555543332677778888875 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 1.5e-08
                         SPASM   5 srslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefr..kskkfplielC 64 
                                      + In++GdV pC +        ++  ni+e sl+e ++s+ +++fr  + + +++ ++C
  gi|91772152|ref|YP_564844.1| 284 IGFVHINAKGDVEPCAFC------HYSDSNIHEVSLAEALRSKFFTAFRaaQPFSQNPLRPC 339
                                   55679**********444......38999********************4433344444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2570.51
//
Query:       gi|91772153|ref|YP_564845.1|  [L=244]
Description: hypothetical protein Mbur_0074 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1658.40
//
Query:       gi|91772154|ref|YP_564846.1|  [L=343]
Description: major facilitator transporter [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-35  122.9  26.6    2.1e-35  122.3  26.6    1.3  1  MFS_1       Major Facilitator Superfamily
    1.3e-05   24.3  18.2    1.7e-05   23.9  18.2    1.0  1  MFS_1_like  MFS_1 like family
    0.00018   20.5   5.3    0.00018   20.5   5.3    1.7  1  Sugar_tr    Sugar (and other) transporter
  ------ inclusion threshold ------
      0.047   12.5  23.1       0.13   11.0   9.4    2.1  2  LacY_symp   LacY proton/sugar symporter
      0.093   12.4   1.9       0.26   10.9   1.9    1.8  1  CPP1-like   Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3  26.6   5.9e-39   2.1e-35       1     280 [.      16     303 ..      16     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 5.9e-39
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                   lll+ f+ al+++i++p+l  +l +++g ++ ++g++ ++y +++++++++lGr+sd +Gr+++l+++ ++++l+ ++++ 
  gi|91772154|ref|YP_564846.1|  16 LLLISFIDALGFGIVIPFLV-FLVDQFGGNAIVYGFIGAMYPAFQLIGAPILGRWSDIHGRKKILFITQAGTLLS-WIIFl 94 
                                   6899****************.******************************************************.77776 PP

                         MFS_1  81 fa..ss....................lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpl 139
                                   fa  ++                    l +l+++r + Gl+ g+ +++++a++ad++ +++r++ +g +s++++lG+i+gp+
  gi|91772154|ref|YP_564846.1|  95 FAvfTPlktlievdsavlgtfiitipLLILFIARSFDGLT-GGNIAVANAYLADITEEKDRNKNFGKMSISTNLGFIIGPG 174
                                   64442233455555566666666643557**********9.8*************************************** PP

                         MFS_1 140 lgglla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllf 219
                                   l+gll+ + +    + +++a++sl++ +++ll+lpe++  + r ++k              ++++   + + ++l+  +l+
  gi|91772154|ref|YP_564846.1| 175 LAGLLSiTIYKELIPVLAAALISLVGTIVILLYLPESRQCKIRTTKKIS------------FREVIGIKNIPYMLLLYFLI 243
                                   ******7777766669999999999999988999999999999888777............66666666664355555555 PP

                         MFS_1 220 ffgfsglltllplylqevlglsglllaglllallalvgail.allagrlsdrlgrrrrllla 280
                                   ffgf++++t +pl +   l ++ + ++g+++++l+++++i+ +++++r +++++    l +a
  gi|91772154|ref|YP_564846.1| 244 FFGFNIFYTAFPLHAIRSLQWT-VAEMGIYFSVLGILMIIVqGPILSRAVKKYSD-VHLAIA 303
                                   57********************.***************99999999999999776.222222 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 !   23.9  18.2   4.7e-09   1.7e-05      15     324 ..      27     332 ..      20     339 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.7e-09
                    MFS_1_like  15 lgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkk..vvilslllsavlflsllfippskerqe 93 
                                   +g ++P+l    ++ g +a   g+i ++ p+++++++pi+g  +D  g++k   +  +++lls ++fl  +f p       
  gi|91772154|ref|YP_564846.1|  27 FGIVIPFLVFLVDQFGGNAIVYGFIGAMYPAFQLIGAPILGRWSDIHGRKKIlfITQAGTLLSWIIFLFAVFTP------L 101
                                   68899******************************************999984455667788888888666667......3 PP

                    MFS_1_like  94 esklevsvaqdvd.aektfwilfllvvlasfflaailvlldaatlkel..gedrkdyGrqrlfGsvGyaifafitGilidh 171
                                   ++ +ev +a     + ++  +++++   ++ ++ + +++++a     +  ++++k++G+  +   +G++i   + G+l  +
  gi|91772154|ref|YP_564846.1| 102 KTLIEVDSAVLGTfIITIPLLILFIARSFDGLTGGNIAVANAYLADITeeKDRNKNFGKMSISTNLGFIIGPGLAGLLSIT 182
                                   33333333332221222222223333345677788888888877666664455566**********************999 PP

                    MFS_1_like 172 ysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL 252
                                   ++ +l+p+   l+ +++ lv +++++l l+e ++  k+  tk + ++ +++  +++ ++ll  +++ + ++i+++ + l+ 
  gi|91772154|ref|YP_564846.1| 183 IYKELIPV---LAAALISLVGTIVILLYLPESRQC-KIRTTK-KISFREVIGIKNIPYMLLLYFLIFFGFNIFYTAFPLHA 258
                                   9999*993...222222233333333334443333.233332.23466666666666666666666677899999999998 PP

                    MFS_1_like 253 .kelgasntllGslv.algvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhg 324
                                     +l+ +   +G++  +lg ++ i+   + ++ ++k++ v l i++ ++    ++++   + +  +l +  Lh 
  gi|91772154|ref|YP_564846.1| 259 iRSLQWTVAEMGIYFsVLGILMIIVQGPILSRAVKKYSDVHLAIAGSVVLGTNLSYLHQGTLPLHILQLHSLHL 332
                                   8***********9762678888888889999999***********99999999988877777666666666664 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   5.3   4.9e-08   0.00018      45     195 ..      45     212 ..       4     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.9e-08
                                   ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT...................SS-TGGG CS
                      Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk...................nsvevli 106
                                   ++ +g+i +++ + ++iG+ ++g ++d+ GRkk+l i+ + ++ + ++  +a  +                     + +l+
  gi|91772154|ref|YP_564846.1|  45 AIVYGFIGAMYPAFQLIGAPILGRWSDIHGRKKILFITQAGTLLSWIIFLFAVFTplktlievdsavlgtfiitIPLLILF 125
                                   5778999999***************************999999999999999998999*********99999877788889 PP

                                   GGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                      Sugar_tr 107 vgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                   ++R + G+  G+  +++  y++ i+ +k R +  +    ++ +G++++ ++   l+ t + ++    l+ +l++ +  +++
  gi|91772154|ref|YP_564846.1| 126 IARSFDGLT-GGNIAVANAYLADITEEKDRNKNFGKMSISTNLGFIIGPGLAGLLSITIY-KELIPVLAAALISLVGTIVI 204
                                   99*****95.8888999********************************99988866666.46666677777777788888 PP

                                   GGGS---H CS
                      Sugar_tr 188 llflPESP 195
                                   ll lPES 
  gi|91772154|ref|YP_564846.1| 205 LLYLPESR 212
                                   999***95 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   9.4   3.6e-05      0.13      31     194 ..      34     213 ..      10     232 .. 0.67
   2 ?    7.6   5.7   0.00041       1.5      11      60 ..     235     284 ..     226     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                     LacY_symp  31 pvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfliyvfepllqlnilvGalvGg 111
                                    v+l ++ g      G + ++   f ++  p++G  sd  G kk l+ + +  l+    fl  vf+pl  l  +  a++G+
  gi|91772154|ref|YP_564846.1|  34 LVFLVDQFGGNAIVYGFIGAMYPAFQLIGAPILGRWSDIHGRKKILFITQAGTLLSWIIFLFAVFTPLKTLIEVDSAVLGT 114
                                   466666666666667777778888899999*************************************97665444445554 PP

                     LacY_symp 112 ....vflGlvysaga.........gaieayiekvs..raskfeyGkarvfGclGyalcaslaGil.fsidpslvfwlasgf 176
                                       + l + + a++         ++ +ay+  ++  ++ + ++Gk  ++  lG+ ++  laG+l  +i ++l   la+  
  gi|91772154|ref|YP_564846.1| 115 fiitIPLLILFIARSfdgltggniAVANAYLADITeeKDRNKNFGKMSISTNLGFIIGPGLAGLLsITIYKELIPVLAAAL 195
                                   11115555677776544333322235689998886223456789*******************985577777665554433 PP

                     LacY_symp 177 .alilllllllskpdksss 194
                                    +l+ +++ ll    +s++
  gi|91772154|ref|YP_564846.1| 196 iSLVGTIVILLYL-PESRQ 213
                                   0333222222222.23334 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00041
                     LacY_symp  11 lfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfq 60 
                                   ++ l +f++ff + ++++ fp+     l+ + +e+Gi fsv+ ++ i+ q
  gi|91772154|ref|YP_564846.1| 235 YMLLLYFLIFFGFNIFYTAFPLHAIRSLQWTVAEMGIYFSVLGILMIIVQ 284
                                   456789999999******************************99999876 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.9   7.3e-05      0.26     104     191 ..     119     205 ..      96     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.3e-05
                     CPP1-like 104 lvlavltlvapaes..vpalllalglgasiyflnrKekklgravlltlvgLvvGlllGsllasllqvd.valsglsseell 181
                                   + l++l ++ + +   + ++++a + +a i   ++++k++g+  + t +g+++G  l++ll+  + ++ +++    + + l
  gi|91772154|ref|YP_564846.1| 119 IPLLILFIARSFDGltGGNIAVANAYLADITEEKDRNKNFGKMSISTNLGFIIGPGLAGLLSITIYKElIPVL---AAA-L 195
                                   334444444444447778899999***************************************9999775555...444.4 PP

                     CPP1-like 182 vslvtlvllw 191
                                    slv  ++++
  gi|91772154|ref|YP_564846.1| 196 ISLVGTIVIL 205
                                   4444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2221.54
//
Query:       gi|91772155|ref|YP_564847.1|  [L=72]
Description: class H tetracycline resistance efflux protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-08   34.5   6.9    1.2e-08   34.4   6.9    1.0  1  MFS_1       Major Facilitator Superfamily
    0.00016   20.7   1.8    0.00017   20.6   1.8    1.1  1  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.013   15.2   0.1    1.0  1  DUF647      Vitamin B6 photo-protection and homoeostasis


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   6.9   1.9e-12   1.2e-08     102     164 ..       1      63 [.       1      71 [. 0.89

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.9e-12
                         MFS_1 102 lfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   ++p+++++i++++ ++++g + g++s+++sl++ilg +lgg++++ +g ra  +++ i++ ++
  gi|91772155|ref|YP_564847.1|   1 MWPSILSIISKIAGENNQGAVQGFASSFSSLASILGLILGGFFYEIFGGRAFIVAAVIIYTVV 63 
                                   79************************************************7666666666655 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 !   20.6   1.8   2.8e-08   0.00017     330     380 ..       1      50 [.       1      63 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.8e-08
                    MFS_1_like 330 lwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksai 380
                                   +w ++ + +skia+++ ++ +qg+ s++  +l + lG ++GG+++++++ +
  gi|91772155|ref|YP_564847.1|   1 MWPSILSIISKIAGENNQGAVQGFASSF-SSLASILGLILGGFFYEIFGGR 50 
                                   7999*******************99998.89***************99976 PP

>> DUF647  Vitamin B6 photo-protection and homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.1e-06     0.013     151     208 ..       7      63 ..       3      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-06
                        DUF647 151 slsahfArkgnlgevnAKdssqetvvsllGlllgivvvslisskaaltwlllilllal 208
                                   s+    A ++n g v+  +ss + ++s+lGl+lg ++ ++++ +a  +++++i+ +++
  gi|91772155|ref|YP_564847.1|   7 SIISKIAGENNQGAVQGFASSFSSLASILGLILGGFFYEIFGGRAF-IVAAVIIYTVV 63 
                                   66778899***********************************999.56666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 515.41
//
Query:       gi|91772156|ref|YP_564848.1|  [L=160]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Methanococcoides burtonii DSM 6242]
Scores for 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-37  127.8   0.0    2.4e-37  127.6   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    4.5e-21   75.1   0.0    5.3e-21   74.9   0.0    1.0  1  Redoxin        Redoxin
    5.1e-05   23.2   0.0    0.00012   22.0   0.0    1.6  1  SCO1-SenC      SCO1/SenC
  ------ inclusion threshold ------
       0.04   14.3   0.0      0.059   13.7   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
       0.11   12.0   0.0       0.13   11.8   0.0    1.1  1  DUF899         Bacterial protein of unknown function (DUF899)


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 !  127.6   0.0   6.7e-41   2.4e-37       2     122 ..       9     135 ..       8     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 6.7e-41
                                   TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H. CS
                      AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekesl 82 
                                   g+kap+ +l++ +g++v+l+d+kgk+vvl+fyp+d++ +C  e+ ++ kl ++f+++g+ ++gvs ds++shkkfiek++l
  gi|91772156|ref|YP_564848.1|   9 GEKAPNLCLPDSEGNDVTLNDLKGKWVVLYFYPRDNTSGCSIEAMEFTKLKDDFEKEGAFILGVSKDSQASHKKFIEKKEL 89 
                                   89******************************************************************************* PP

                                   SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEE CS
                      AhpC-TSA  83 nfpllsDeegkvakaygvlkee......kglalratfvidkegkir 122
                                    ++llsDe  ++ ++y+v++++      +++++r+tf+id+eg+++
  gi|91772156|ref|YP_564848.1|  90 GITLLSDEGTELQQSYDVWHQKkmagkeYMGTVRTTFLIDPEGNLA 135
                                   ********************99*********************987 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   1.5e-24   5.3e-21       2     130 ..       8     137 ..       7     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.5e-24
                                   TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH CS
                       Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk 82 
                                   ag+kaP++ lp+  ++gn+v+l ++kgk vv++f+p+  +  Cs e+ +++kl++ ++++g  +++v+ d+ a  k+f++k
  gi|91772156|ref|YP_564848.1|   8 AGEKAPNLCLPD--SEGNDVTLNDLKGKWVVLYFYPRDNTSGCSIEAMEFTKLKDDFEKEGAFILGVSKDSQASHKKFIEK 86 
                                   89*******999..******************************************************************* PP

                                   TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG....EEE-EEEEEEETTEEEEE CS
                       Redoxin  83 eglkfpvlsDgsaaftkalGlrleedaseg....lrtpryavidedgkvvyl 130
                                   ++l +++lsD++ +++++++  + +++ +g       +++++id +g++ ++
  gi|91772156|ref|YP_564848.1|  87 KELGITLLSDEGTELQQSYD-VWHQKKMAGkeymGTVRTTFLIDPEGNLAKV 137
                                   ********************.5677777778996678999*******99886 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.3e-08   0.00012       6     133 ..      17     133 ..      13     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.3e-08
                     SCO1-SenC   6 lvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafdpri 86 
                                   l d++g+ vt +dl+gk+++++f     ++ C ++  + +++ d++++e++ +          +D+++  k+++e+ +  i
  gi|91772156|ref|YP_564848.1|  17 LPDSEGNDVTLNDLKGKWVVLYFYPRDNTSGCSIEAMEFTKLKDDFEKEGAFIL------GVSKDSQASHKKFIEKKELGI 91 
                                   56899********************************************54333......3358999********999999 PP

                     SCO1-SenC  87 igltGskeeiakaakefrvyvekvedeesdytvdHsssvyLvdpdgr 133
                                   + l+++ +e++   +++ v ++k+   ++   +    +++L+dp+g+
  gi|91772156|ref|YP_564848.1|  92 TLLSDEGTELQ---QSYDVWHQKKMAGKE--YMGTVRTTFLIDPEGN 133
                                   98988887766...567777777766666..5778889999999997 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.059       1      94 [.      32     133 ..      32     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                   .SEEEEEE--S.SSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S-- CS
                 Thioredoxin_8   1 gkvvlLyfgas.wcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynv 80 
                                   gk+v+Lyf+   + + c     + ++l+++++ k +  i+ vs d+ + + +k+++k     l ++  +++  +l++ y+v
  gi|91772156|ref|YP_564848.1|  32 GKWVVLYFYPRdNTSGCSIEAMEFTKLKDDFE-KEGAFILGVSKDS-QASHKKFIEKK---ELGITLLSDEGTELQQSYDV 107
                                   79******97626667***************9.79999*******9.58899999999...77778888889999999999 PP

                                   TT............-SEEEEE-TT-B CS
                 Thioredoxin_8  81 ka............iPtlvvldknge 94 
                                    +            + t++++d++g+
  gi|91772156|ref|YP_564848.1| 108 WHqkkmagkeymgtVRTTFLIDPEGN 133
                                   88888888999999999999999887 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.6e-05      0.13      86     175 ..      46     138 ..      35     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                        DUF899  86 pgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpgl..svf 164
                                   +gCs+ a ++ +   ++e+++  +  vs+  +++ +++ +++   + + s+ ++++++ + v  +++ a +e  g+  ++f
  gi|91772156|ref|YP_564848.1|  46 SGCSIEAMEFTKLKDDFEKEGAFILGVSKDSQASHKKFIEKKELGITLLSDEGTELQQSYDVWHQKKMAGKEYMGTvrTTF 126
                                   79********99999************************************************999998888888755677 PP

                        DUF899 165 lrdd.grvfhtY 175
                                   l d  g+  + +
  gi|91772156|ref|YP_564848.1| 127 LIDPeGNLAKVW 138
                                   766656666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); 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:                         5  (0.000278878); expected 0.2 (1e-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: 1160.82
//
Query:       gi|91772157|ref|YP_564849.1|  [L=404]
Description: hypothetical protein Mbur_0078 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   88.7   1.9    6.1e-25   88.7   1.9    2.1  3  MacB_PCD  MacB-like periplasmic core domain
    2.6e-10   40.6   5.8    2.6e-10   40.6   5.8    3.2  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
       0.12   11.1   1.9         37    2.9   6.9    2.0  2  DUF2207   Predicted membrane protein (DUF2207)


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 !   88.7   1.9     1e-28   6.1e-25       1     194 [.      22     238 ..      22     239 .. 0.78
   2 ?   -3.8   2.2       2.3   1.4e+04       5      34 ..     280     310 ..     276     321 .. 0.60
   3 ?   -5.3   3.2         3   1.8e+04       6      17 ..     374     385 ..     369     387 .. 0.67

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1e-28
                      MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv....tvr 76 
                                   s+lt LGi+iG+aav+a vslg+++++ + +++ + g ++ + +++ + + + d+++ea+r + p ve+v+p+      v+
  gi|91772157|ref|YP_564849.1|  22 SALTTLGIIIGIAAVVANVSLGASFNQFFVDELGSQGSNF-IVIYNEDINLFYDNQLEAIR-NTPkVEGVSPIRqqlaGVT 100
                                   89********************************888655.55666677778888888875.6799******876666334 PP

                      MacB_PCD  77 gggsgeeevtvvgvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlfpvGdtirl.................k 140
                                   + ++  +++ ++g ++dy k+ +++l++G ff+++    +++++v+g+++a + f   ++i                    
  gi|91772157|ref|YP_564849.1| 101 YIST-IRQIDIQGSSADYEKIGNIQLEAGNFFSDQ----DKYAAVLGSDVAYEKF--DQKISYrnsidiefirrdgtpveH 174
                                   4433.34589***999********9999****775....5789********8878..555544444455888999988889 PP

                      MacB_PCD 141 pftVvGvledpp....gsgsalg....ddavylplttlqrrs.........itvrlkdgadleaaaaelek 194
                                   +f+V+G++++p+    +          d ++++p++t+  ++         + ++++d +++  +++e++k
  gi|91772157|ref|YP_564849.1| 175 SFKVIGIIDSPDttfiQ-----TgaesDVRIFIPINTM--NEmlgiedyggFSITVEDAESVRPVSDEIDK 238
                                   9******9664334542.....13344899****9999..2334666667799999***********9986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.3
                      MacB_PCD   5 vLGiaiG.vaaviaivslgeglqasvlsqis 34 
                                    L i ++ +  +++ +++++ ++ +v+++ +
  gi|91772157|ref|YP_564849.1| 280 SLFISVAlISLIVGSIGIMNIMLVTVTERTK 310
                                   4444444344445555777777777776655 PP

  == domain 3  score: -5.3 bits;  conditional E-value: 3
                      MacB_PCD   6 LGiaiGvaavia 17 
                                   +Gia+Gv+ + +
  gi|91772157|ref|YP_564849.1| 374 VGIAVGVGLIAG 385
                                   577888877765 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    0.0031        19      16      57 ..      19      60 ..       4     103 .. 0.73
   2 ?   -1.3   1.8      0.51     3e+03      22      36 ..     282     296 ..     273     306 .. 0.46
   3 !   40.6   5.8   4.4e-14   2.6e-10       2      96 .]     310     397 ..     309     397 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0031
                          FtsX 16 qvlllllteillitlvalviGlglgllaaqllsdvllssvfs 57
                                  +++  l+t +++i++ a v+ + lg+ + q++ d l+s+ ++
  gi|91772157|ref|YP_564849.1| 19 KLRSALTTLGIIIGIAAVVANVSLGASFNQFFVDELGSQGSN 60
                                  445555566666666666666999999999999999988664 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.51
                          FtsX  22 lteillitlvalviG 36 
                                   ++ ++li+l+   iG
  gi|91772157|ref|YP_564849.1| 282 FISVALISLIVGSIG 296
                                   222333333333333 PP

  == domain 3  score: 40.6 bits;  conditional E-value: 4.4e-14
                          FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllall 82 
                                   +eig+lr+lG+++  +l l++te+++++l++ ++G+ lgl+ +++  + l        l++ ++   +++++++++ + l+
  gi|91772157|ref|YP_564849.1| 310 KEIGLLRSLGFTRSNILSLFITESIILGLIGGILGTFLGLVGSYAAVTIL-------GLPYIFPMYLFVLGVGIAVGVGLI 383
                                   8**********************************999999988866664.......6899******************** PP

                          FtsX  83 agllsiskilkkep 96 
                                   ag++++ k++k +p
  gi|91772157|ref|YP_564849.1| 384 AGVYPANKASKLDP 397
                                   ***********987 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.019   1.2e+02     381     409 ..      22     275 ..      14     320 .. 0.47
   2 ?    2.9   6.9    0.0062        37     381     439 ..     331     389 ..     308     403 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.019
                       DUF2207 381 kklsalglgliilglilillallllvll..................................................... 408
                                     l +lg++++i+++++++ + ++++ +                                                     
  gi|91772157|ref|YP_564849.1|  22 SALTTLGIIIGIAAVVANVSLGASFNQFfvdelgsqgsnfiviynedinlfydnqleairntpkvegvspirqqlagvtyi 102
                                   444555555555555555555544444466666655555555555555555555555555555555554444444444444 PP

                       DUF2207 409 ................................................................................. 408
                                                                                                                    
  gi|91772157|ref|YP_564849.1| 103 stirqidiqgssadyekigniqleagnffsdqdkyaavlgsdvayekfdqkisyrnsidiefirrdgtpvehsfkvigiid 183
                                   444444444444444444444444444444444444444444444444444444444444444444444444444444444 PP

                       DUF2207 409 ................................................................................. 408
                                                                                                                    
  gi|91772157|ref|YP_564849.1| 184 spdttfiqtgaesdvrifipintmnemlgiedyggfsitvedaesvrpvsdeidkkiarslgvsereldnedvkpytifnq 264
                                   444444444444444444444444444444444444444444444444444444444444444444444444444444444 PP

                       DUF2207 409 ..........l 409
                                             +
  gi|91772157|ref|YP_564849.1| 265 adildqldelS 275
                                   44444444440 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0062
                       DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrte 439
                                   +++++lgl+++ilg++l+l++ +++v++l + +i+ + l+++++++++    + g + +
  gi|91772157|ref|YP_564849.1| 331 TESIILGLIGGILGTFLGLVGSYAAVTILGLPYIFPMYLFVLGVGIAVGVGLIAGVYPA 389
                                   45778888888888888888888888884444444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2856.35
//
Query:       gi|91772158|ref|YP_564850.1|  [L=404]
Description: cell division protein FtsX [Methanococcoides burtonii DSM 6242]
Scores for complete 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   87.5   8.5    1.5e-24   87.5   8.5    2.2  2  MacB_PCD     MacB-like periplasmic core domain
    2.5e-16   59.9  16.2    1.1e-15   57.9   3.8    3.3  3  FtsX         FtsX-like permease family
  ------ inclusion threshold ------
       0.37   11.1   3.0        5.1    7.5   0.0    3.1  2  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   8.5   2.5e-28   1.5e-24       1     193 [.      22     237 ..      22     239 .. 0.81
   2 ?   -1.2   4.0      0.36   2.2e+03       3      37 ..     279     313 ..     276     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 2.5e-28
                      MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevpveavapvv....tvrg 77 
                                   s+lt LGi+iGvaavi+ +slg g++++++++i + g +++v  + ++++ ++d+++e +r  ++veav+pv     t ++
  gi|91772158|ref|YP_564850.1|  22 SALTTLGIIIGVAAVIVNISLGVGFSQNFEDDIGAVGSNFIVVFT-QKNNVFTDNQLEVVRNTQGVEAVSPVNgqigTLTY 101
                                   89********************************99876655444.678999**99976654556******9777774455 PP

                      MacB_PCD  78 ggsgeeevtvvgvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf....pvGdtirl...........kpft 143
                                   ++s ++++t++gv+++y +v ++ +++G+f+t++    ++ v+vig+++a + f     v  +i +           ++ft
  gi|91772158|ref|YP_564850.1| 102 QSS-SRSATINGVSSEYEEVGNIVMEKGQFLTDQ----DQFVAVIGSDIAYDKFernlSVKNSINIsinnieggvstRKFT 177
                                   554.44589*****9********6699****885....688*********887888888899998899999****9999** PP

                      MacB_PCD 144 VvGvledppgsgsalg....ddavylplttlqrrs.......itvrlkdgadleaaaaele 193
                                   V G+++dp+ +++ +     + +v++pl  +q+ +       +++++++ + le++ +e++
  gi|91772158|ref|YP_564850.1| 178 VKGIVQDPD-ATFISPevdpRVRVFIPLGVMQEMQgvsdiggFFIKAESLEVLESVTDEVD 237
                                   *****8863.2333336645666****6666443355678899999999999999999987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.36
                      MacB_PCD   3 ltvLGiaiGvaaviaivslgeglqasvlsqisdlg 37 
                                    ++L+++  +a +++ +++++ ++ +v+++ ++ g
  gi|91772158|ref|YP_564850.1| 279 TSILTVIALIALLVGSIGITNIMLVTVTERTKEIG 313
                                   4788888889**************99999887554 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.2    0.0024        14      13      57 ..      16      60 ..       7     104 .. 0.83
   2 ?    3.7   0.7     0.015        89      18      85 ..     275     297 ..     257     307 .. 0.53
   3 !   57.9   3.8   1.8e-19   1.1e-15       2      96 .]     310     397 ..     309     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0024
                          FtsX 13 kkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs 57
                                  ++++++  l+t +++i++ a ++ + lg+ ++q + d ++++ ++
  gi|91772158|ref|YP_564850.1| 16 RSAKIRSALTTLGIIIGVAAVIVNISLGVGFSQNFEDDIGAVGSN 60
                                  568899999999999999999999999999999999998888553 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.015
                          FtsX  18 lllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagl 85 
                                      l++ + +i+l+al++G                                              +g+
  gi|91772158|ref|YP_564850.1| 275 STALTSILTVIALIALLVG---------------------------------------------SIGI 297
                                   3333333344444444444.............................................3322 PP

  == domain 3  score: 57.9 bits;  conditional E-value: 1.8e-19
                          FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllall 82 
                                   +eigil++lG++ +++l l+++e+++i++++ ++G++lg++a+++++++       + +++ ++++ v+++++++l++ ++
  gi|91772158|ref|YP_564850.1| 310 KEIGILKSLGFTYRDILTLFVVEAAIIGFLGGIFGVILGFIASYFVNQY-------IDVPFVFPISLVFLGFGIALFVGVA 383
                                   8*******************************************99999.......5899********************* PP

                          FtsX  83 agllsiskilkkep 96 
                                   ag++++ k++k++p
  gi|91772158|ref|YP_564850.1| 384 AGVYPANKAAKMDP 397
                                   ************98 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00085       5.1       3      31 ..      14      42 ..      13      55 .. 0.88
   2 ?    1.9   1.0     0.047   2.8e+02      13      34 ..     274     295 ..     269     313 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00085
                   Sigma_reg_N  3 ilkkakrksilrivlislivlllifvilv 31
                                  +++ ak +s l++  i+++v+ +i+ i++
  gi|91772158|ref|YP_564850.1| 14 SIRSAKIRSALTTLGIIIGVAAVIVNISL 42
                                  6899********************99984 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.047
                   Sigma_reg_N  13 lrivlislivlllifvilvvtl 34 
                                   ++++l+s++++++++++lv ++
  gi|91772158|ref|YP_564850.1| 274 ISTALTSILTVIALIALLVGSI 295
                                   4555555555555554443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2751.68
//
Query:       gi|91772159|ref|YP_564851.1|  [L=415]
Description: hypothetical protein Mbur_0080 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   15.6   0.3       0.47   10.8   0.4    2.5  2  DUF11          Domain of unknown function DUF11
      0.071   13.4   0.3        2.8    8.2   0.0    3.4  4  NPCBM_assoc    NPCBM-associated, NEW3 domain of alpha-galacto
      0.082   12.6   3.7        2.5    7.8   1.0    2.3  2  Cation_efflux  Cation efflux family


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 ?    1.8   0.0      0.05     3e+02       7      35 ..      44      72 ..      30      74 .. 0.87
   2 ?   10.8   0.4   7.8e-05      0.47       8      85 ..     162     243 ..     145     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.05
                         DUF11  7 ksevrpGdtvtytltvtNtgpasangvvv 35
                                  + ++  G+ v++ + v N    +a++v++
  gi|91772159|ref|YP_564851.1| 44 PYPAEIGAYVDVWIKVENFASGTAEDVTI 72
                                  447899******************99987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.8e-05
                         DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv......gsLeagesatlsftvrvtrta 82 
                                   + + pGd+ ++  t+tNt ++s   + + D+    +a v++ + +gt   ++++      g L +g   ++++ ++v+ + 
  gi|91772159|ref|YP_564851.1| 162 EVFMPGDEGSVSFTLTNTAQQST--ILIDDVNYDTFARVQSATLTGTDMITVTSqpyegkGVLGPGDFVQVTYNIKVSDSI 240
                                   5788***************9999..88888776666555555555777776666777778999999999999999999887 PP

                         DUF11  83 asg 85 
                                   ++g
  gi|91772159|ref|YP_564851.1| 241 EDG 243
                                   665 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.46   2.8e+03      16      32 ..      64      80 ..      48     118 .. 0.49
   2 ?   -2.0   0.0      0.76   4.5e+03      11      23 ..     144     156 ..     133     162 .. 0.61
   3 ?    0.0   0.0      0.17     1e+03       3      20 ..     166     183 ..     164     186 .. 0.87
   4 ?    8.2   0.0   0.00047       2.8      38      73 ..     212     248 ..     210     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.46
                   NPCBM_assoc 16 dgtaaatnvslslslPe 32
                                  +gta    ++++ + P 
  gi|91772159|ref|YP_564851.1| 64 SGTAEDVTIKIEPDYPL 80
                                  33444444444444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.76
                   NPCBM_assoc  11 ltvtndgtaaatn 23 
                                   +t+ ++gt a++n
  gi|91772159|ref|YP_564851.1| 144 TTFDSKGTVALSN 156
                                   4566666666665 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.17
                   NPCBM_assoc   3 pGetvtltltvtndgtaa 20 
                                   pG++ ++ +t+tn+ +++
  gi|91772159|ref|YP_564851.1| 166 PGDEGSVSFTLTNTAQQS 183
                                   899**********99875 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00047
                   NPCBM_assoc  38 evspasaa.slapGetveatvkVtppagaaaGdyevt 73 
                                   +++p +++  l pG+ v++t +++++++++ G+y + 
  gi|91772159|ref|YP_564851.1| 212 TSQPYEGKgVLGPGDFVQVTYNIKVSDSIEDGTYFLD 248
                                   56677777789**********************9765 PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.0   0.00042       2.5       2      32 ..      10      40 ..       9      42 .. 0.94
   2 ?    5.2   0.1    0.0026        16      96     130 ..     376     410 ..     367     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00042
                 Cation_efflux  2 ilsllanlilalvelivglltnSlalladaf 32
                                  il+ll+++++al+ + +g+ + S++l ad +
  gi|91772159|ref|YP_564851.1| 10 ILVLLMVFFVALAPILAGAASSSSTLRADLL 40
                                  7899*************************76 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0026
                 Cation_efflux  96 egereihaglalvvalvslvvnlalllilrragrk 130
                                   ++++e++ + +l+v+l+++++ +a ++++r++g +
  gi|91772159|ref|YP_564851.1| 376 KHVDEDNDHTTLIVLLAGVLIVVAAYYLYRKKGLR 410
                                   57788899999999999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2505.75
//
Query:       gi|91772160|ref|YP_564852.1|  [L=240]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-33  113.7   0.0    1.2e-32  113.3   0.0    1.2  1  ABC_tran     ABC transporter
      2e-09   37.7   0.1    3.6e-05   23.7   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.6e-06   26.6   0.1      0.062   12.7   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00035   20.3   0.1    0.00063   19.4   0.1    1.3  1  AAA_29       P-loop containing region of AAA domain
    0.00038   20.4   0.1    0.00083   19.3   0.1    1.6  1  RsgA_GTPase  RsgA GTPase
     0.0039   17.5   0.3      0.031   14.6   0.2    2.0  2  AAA_22       AAA domain
     0.0058   15.8   0.0     0.0074   15.5   0.0    1.1  1  G-alpha      G-protein alpha subunit
     0.0098   16.4   0.1      0.024   15.1   0.0    1.6  2  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.014   15.8   0.1    1.5  1  AAA_16       AAA ATPase domain
       0.02   14.6   0.1        0.1   12.3   0.0    1.8  2  AAA_30       AAA domain
      0.022   14.4   0.0       0.05   13.2   0.0    1.5  1  AAA_25       AAA domain
      0.028   14.5   0.2      0.071   13.2   0.1    1.7  2  MMR_HSR1     50S ribosome-binding GTPase
      0.048   13.4   0.0       0.19   11.4   0.0    1.8  2  AAA_24       AAA domain
      0.052   13.2   0.0        6.6    6.3   0.0    2.1  2  AAA_15       AAA ATPase domain
      0.056   12.8   0.1          8    5.7   0.0    2.1  2  ATPase       KaiC
      0.074   13.0   0.2        0.7    9.8   0.1    2.0  2  ATPase_2     ATPase domain predominantly from Archaea
      0.087   12.9   0.2       0.25   11.4   0.1    1.7  2  DUF87        Helicase HerA, central domain
       0.11   13.0   0.0       0.31   11.6   0.0    1.8  2  AAA_18       AAA domain
       0.13   12.0   0.0        0.5   10.1   0.0    1.8  2  IstB_IS21    IstB-like ATP binding protein
       0.14   11.3   0.2       0.25   10.5   0.2    1.4  1  NB-ARC       NB-ARC domain
       0.14   12.3   0.2       0.34   11.1   0.2    1.9  1  AAA_33       AAA domain
       0.18   11.3   0.1       0.29   10.6   0.1    1.3  1  AAA_7        P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.0   1.4e-35   1.2e-32       1     136 [.      34     182 ..      34     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 1.4e-35
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCH.CEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrk.eigvlpqepqlfpeltvr 77 
                                   lknv+l +k+ge vai+G++G+GKStL++l+  l +pt G++ l g+d+++   +el +lr  eig+++q  +l p+lt+ 
  gi|91772160|ref|YP_564852.1|  34 LKNVNLVVKKGEFVAIMGPSGSGKSTLMNLIGCLDRPTCGSVSLMGTDVSTisdDELARLRGlEIGFVFQSFNLVPRLTAL 114
                                   79***********************************************999885555555449***************** PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   en             + +++++++l+ +gl++    +++++p++LSgGq qrva+ar+l+++p+l+l+DEpt
  gi|91772160|ref|YP_564852.1| 115 ENvelptyansrpgvDTRKRAKELLELVGLED----RINYRPTELSGGQSQRVAVARSLINDPSLILADEPT 182
                                   *******8888877767777888888888777....667899*****************************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 !   12.0   0.1   0.00016      0.13       1      22 [.      46      67 ..      46     104 .. 0.83
   2 !   23.7   0.0   4.5e-08   3.6e-05     231     301 ..     149     216 ..     124     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                        AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                  + ++ Gp gsGKS+L+ ++ +l
  gi|91772160|ref|YP_564852.1| 46 FVAIMGPSGSGKSTLMNLIGCL 67
                                  57899**************988 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 4.5e-08
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                   +  ++elS G+ +  a++ +l+ ++   sl+l DEp  +L+ k  +++++l+ el+++g  vi+ TH+p l
  gi|91772160|ref|YP_564852.1| 149 NYRPTELSGGQSQRVAVARSLINDP---SLILADEPTGNLDSKTGKEIMDLFTELNKKGRTVIMITHDPNL 216
                                   5567889999999989999999999...*****************************************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 !   11.8   0.1   0.00015      0.12      24      44 ..      44      64 ..      33      68 .. 0.83
   2 !   12.7   0.0   7.6e-05     0.062     129     209 ..     147     225 ..     106     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                  SSEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                   +f ai+Gp GSGKs l++ i
  gi|91772160|ref|YP_564852.1| 44 GEFVAIMGPSGSGKSTLMNLI 64
                                  4699************99755 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.6e-05
                                   CTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xx RF
                         SMC_N 129 sagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.dk 207
                                   + +  +++LSgG+ + va+a       ++  +l l De   +LD k  k++ +l+ e +k+   +i+i+++ ++ +   d+
  gi|91772160|ref|YP_564852.1| 147 RINYRPTELSGGQSQRVAVAR----SLINDPSLILADEPTGNLDSKTGKEIMDLFTELNKKgRTVIMITHDPNLAKVYaDR 223
                                   44455669*****99888764....4578889************************99988678999***99988764355 PP

                                   EE CS
                                   xx RF
                         SMC_N 208 lv 209
                                   ++
  gi|91772160|ref|YP_564852.1| 224 VI 225
                                   55 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   0.1   7.7e-07   0.00063      19      39 ..      41      61 ..      34      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.7e-07
                        AAA_29 19 idlkg.atlltGpsGsGKSTll 39
                                  ++ kg ++ ++GpsGsGKSTl+
  gi|91772160|ref|YP_564852.1| 41 VK-KGeFVAIMGPSGSGKSTLM 61
                                  44.45599*************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1     1e-06   0.00083      96     121 ..      40      66 ..      21      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1e-06
                                   HCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallp 121
                                   ++k+ ++++++G+SG GKStL+n +  
  gi|91772160|ref|YP_564852.1|  40 VVKKgEFVAIMGPSGSGKSTLMNLIGC 66 
                                   5555599****************8855 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   3.8e-05     0.031       4      24 ..      43      63 ..      40      84 .. 0.90
   2 ?    0.9   0.0      0.63   5.2e+02      52     104 ..     130     186 ..     100     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-05
                        AAA_22  4 tagilvvtGesGtGKTtllrr 24
                                  +  +++++G+sG+GK+tl++ 
  gi|91772160|ref|YP_564852.1| 43 KGEFVAIMGPSGSGKSTLMNL 63
                                  56799*************986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.63
                        AAA_22  52 sskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr 104
                                   + ++ ++ell+ +gle    + +  el   + ++ + ar+    ++l++ DE    l+
  gi|91772160|ref|YP_564852.1| 130 DTRKRAKELLELVGLEDRI-NYRPTELSgGQSQRVAVARSLindPSLILADEPTGnLD 186
                                   5666677888888877777.66777777778888888888788888888888655565 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     9e-06    0.0074      26     157 ..      47     229 ..      34     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9e-06
                                   EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHH..HHHHHHTT......... CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsikti..lealesleselsesf.. 89 
                                   + ++G s+SGKsT+++ + +l +++             +s++ela +r + +  + +s++++  l ale+   el + +  
  gi|91772160|ref|YP_564852.1|  47 VAIMGPSGSGKSTLMNLIGCLDRPTcgsvslmgtdvstISDDELARLRGLEIGFVFQSFNLVprLTALEN--VEL-PTYan 124
                                   5689**********************************9999*****************99833445555..333.22244 PP

                                   .....HHHC-SS-SCCCS-HCHHHH........................................HHCCHHC-HCHHH... CS
                       G-alpha  90 .....elqelkerldplkkveasliaklssateee..............................qeiefnpraevge... 132
                                        + +++ ++l +l  +e++++ + ++ +  +                                          +   
  gi|91772160|ref|YP_564852.1| 125 srpgvDTRKRAKELLELVGLEDRINYRPTELSGGQsqrvavarslindpsliladeptgnldsktG-----------Keim 194
                                   567778888888888888888887765444443335556666666666555555554444444430...........1333 PP

                                   ...........HHHHHCCSHHHHHHHCCGCCTT--T CS
                       G-alpha 133 ...........dikaLwndpgiqelyerrnkikled 157
                                               ++++ +dp++ ++y+ r  i+l+d
  gi|91772160|ref|YP_564852.1| 195 dlftelnkkgrTVIMITHDPNLAKVYADR-VINLKD 229
                                   34444444444***************988.677655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     3e-05     0.024      20      39 ..      45      64 ..      31      66 .. 0.82
   2 ?   -2.3   0.0       6.3   5.2e+03     133     133 ..     171     171 ..     123     212 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                        AAA_23 20 gltlItGpNGaGKTTildAi 39
                                   +++I Gp G+GK+T+++ i
  gi|91772160|ref|YP_564852.1| 45 EFVAIMGPSGSGKSTLMNLI 64
                                  5789*************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.3
                        AAA_23 133 n 133
                                   n
  gi|91772160|ref|YP_564852.1| 171 N 171
                                   1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   1.7e-05     0.014      24      44 ..      44      64 ..      20     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                        AAA_16 24 pelvllsGesGvGKsslvrel 44
                                  +e v + G+sG+GKs+l++ +
  gi|91772160|ref|YP_564852.1| 44 GEFVAIMGPSGSGKSTLMNLI 64
                                  389**************9765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013       0.1      13      38 ..      40      64 ..      35      85 .. 0.82
   2 ?   -0.1   0.0      0.79   6.4e+02      87     129 ..     171     217 ..     127     227 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                        AAA_30 13 lltsgdrvavltGpAGtGKttalkal 38
                                  ++++g  ++++ Gp G+GK+t+++ +
  gi|91772160|ref|YP_564852.1| 40 VVKKG-EFVAIMGPSGSGKSTLMNLI 64
                                  45555.599**************977 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.79
                        AAA_30  87 epgtllivDE.agmvdtkq...laallkaaekagakvilvGDerQla 129
                                   ++ +l++ DE +g +d+k+   + +l+++++k+g +vi++  +  la
  gi|91772160|ref|YP_564852.1| 171 NDPSLILADEpTGNLDSKTgkeIMDLFTELNKKGRTVIMITHDPNLA 217
                                   44466666664455555440003345555556666666665554444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.1e-05      0.05      25      50 ..      36      61 ..      26      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                        AAA_25 25 lvkgllpagelallaGapgtGKttla 50
                                   v  ++ +ge+++++G++g+GK+tl 
  gi|91772160|ref|YP_564852.1| 36 NVNLVVKKGEFVAIMGPSGSGKSTLM 61
                                  5667899*****************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 ?   13.2   0.1   8.7e-05     0.071       2      19 ..      47      64 ..      46      84 .. 0.90
   2 ?   -2.1   0.0       4.9     4e+03      75      75 ..     202     202 ..     157     229 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
                                  EEEEESTTSSHHHHHHHH CS
                      MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                  vai+G + +GKStL+n +
  gi|91772160|ref|YP_564852.1| 47 VAIMGPSGSGKSTLMNLI 64
                                  89**************76 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.9
                                   C CS
                      MMR_HSR1  75 e 75 
                                   +
  gi|91772160|ref|YP_564852.1| 202 K 202
                                   2 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      0.19       5      22 ..      47      64 ..      43      94 .. 0.85
   2 ?   -0.8   0.0       1.3     1e+03     108     130 ..     190     212 ..     183     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                        AAA_24  5 iliyGpsgiGKTtlakel 22
                                  ++i+Gpsg+GK+tl++ +
  gi|91772160|ref|YP_564852.1| 47 VAIMGPSGSGKSTLMNLI 64
                                  79************9876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                        AAA_24 108 aeefrrllkklqelrknvifiah 130
                                   ++e+++l + l++ + +vi+i h
  gi|91772160|ref|YP_564852.1| 190 GKEIMDLFTELNKKGRTVIMITH 212
                                   56677777777777779999988 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0081       6.6      15      43 ..      35      64 ..      33     100 .. 0.87
   2 ?    5.1   0.0     0.019        15     321     368 ..     170     216 ..     159     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0081
                        AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                  k+v + +++  +  + G+ +sGKS++++++
  gi|91772160|ref|YP_564852.1| 35 KNVNLVVKKGeFVAIMGPSGSGKSTLMNLI 64
                                  66666666666999*************998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.019
                        AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    +++ ++l +EP  +L  +  k++++l+ el ++++  vi+ TH p +
  gi|91772160|ref|YP_564852.1| 170 INDPSLILADEPTGNLDSKTGKEIMDLFTELNKKGR-TVIMITHDPNL 216
                                   57899999***************************9.9*******986 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.018        15      18      35 ..      43      60 ..      39      63 .. 0.88
   2 ?    5.7   0.0    0.0098         8     139     166 ..     188     215 ..     181     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.018
                        ATPase 18 egrvvlitGepGtGKtif 35
                                  +g+ v i+G +G+GK+++
  gi|91772160|ref|YP_564852.1| 43 KGEFVAIMGPSGSGKSTL 60
                                  7899***********987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0098
                        ATPase 139 vaReilrqlvrvlkklgvTailvsekss 166
                                   ++ ++++ l+++l+k+g T i+++  ++
  gi|91772160|ref|YP_564852.1| 188 KTGKEIMDLFTELNKKGRTVIMITHDPN 215
                                   677899*****************98655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00086       0.7      20      38 ..      44      62 ..      34      67 .. 0.83
   2 ?    1.1   0.0      0.38   3.1e+02     102     126 ..     189     213 ..     130     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00086
                      ATPase_2 20 neiyfiYGpegsGKtaLlk 38
                                   e++ i Gp gsGK++L++
  gi|91772160|ref|YP_564852.1| 44 GEFVAIMGPSGSGKSTLMN 62
                                  67899************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.38
                      ATPase_2 102 vfkaielllekikkkgkkiiiiiDe 126
                                     k i +l+ +++kkg+ +i+i  +
  gi|91772160|ref|YP_564852.1| 189 TGKEIMDLFTELNKKGRTVIMITHD 213
                                   456788999999**99999988655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00031      0.25      26      43 ..      47      64 ..      25      66 .. 0.84
   2 ?   -1.3   0.0       2.4   1.9e+03     135     205 ..     140     208 ..     121     223 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                         DUF87 26 lAilgsTGsGKSntvavL 43
                                  +Ai+g +GsGKS+++ ++
  gi|91772160|ref|YP_564852.1| 47 VAIMGPSGSGKSTLMNLI 64
                                  8**************997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                         DUF87 135 eklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf..snsstdliallleklekegkiti 205
                                   e +  ++ +++   el     + ++++   +++l+++ + +l ++ +   ++++ + i +l+ +l+k+g+ +i
  gi|91772160|ref|YP_564852.1| 140 ELVGLEDRINYRPTELS----GGQSQRVAVARSLINDPSLILADEPTGnlDSKTGKEIMDLFTELNKKGRTVI 208
                                   55555555555555555....4444444444444443333333333333323333333334455556665555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00038      0.31       1      18 [.      47      64 ..      47     111 .. 0.83
   2 ?   -1.8   0.0       5.1   4.1e+03      60      85 ..     193     215 ..     167     228 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                        AAA_18  1 IlltGtpGvGKttlakeL 18
                                  ++++G++G+GK+tl + +
  gi|91772160|ref|YP_564852.1| 47 VAIMGPSGSGKSTLMNLI 64
                                  689***********8876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.1
                        AAA_18  60 lldaleenssaleegknlvidghlae 85 
                                   ++d++ e ++   +g ++++  h  +
  gi|91772160|ref|YP_564852.1| 193 IMDLFTELNK---KGRTVIMITHDPN 215
                                   4444444433...4455554444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00062       0.5      44      67 ..      41      64 ..      18      69 .. 0.83
   2 ?   -1.0   0.0       1.5   1.2e+03     111     148 ..     174     213 ..     156     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00062
                     IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                  ++k e ++++GpsG GKs l   +
  gi|91772160|ref|YP_564852.1| 41 VKKGEFVAIMGPSGSGKSTLMNLI 64
                                  6788999***********997655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                     IstB_IS21 111 llilDdlgllpldqaeaellfeviekry..errsiiitsn 148
                                    lil d  + +ld++  ++++++  +    +r+ i+it +
  gi|91772160|ref|YP_564852.1| 174 SLILADEPTGNLDSKTGKEIMDLFTELNkkGRTVIMITHD 213
                                   4566666666777777776666666543115556666654 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   0.2   0.00031      0.25      21      39 ..      45      63 ..      30      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                  EEEEEEESTTSSHHHHHHH CS
                        NB-ARC 21 lvvalvGmgGvGKttlakq 39
                                   +va++G  G+GK+tl++ 
  gi|91772160|ref|YP_564852.1| 45 EFVAIMGPSGSGKSTLMNL 63
                                  489*************975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00042      0.34       2      17 ..      47      62 ..      46     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                        AAA_33  2 vllvGlpGsGKstlae 17
                                  v + G++GsGKstl  
  gi|91772160|ref|YP_564852.1| 47 VAIMGPSGSGKSTLMN 62
                                  5678*********976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00035      0.29      26      51 ..      37      62 ..      23      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                         AAA_7 26 lelllknkkpvllvGptGtGKtviik 51
                                  ++l++k++  v ++Gp+G+GK+++++
  gi|91772160|ref|YP_564852.1| 37 VNLVVKKGEFVAIMGPSGSGKSTLMN 62
                                  57899******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1662.05
//
Query:       gi|91772161|ref|YP_564853.1|  [L=763]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  106.1   0.2    3.3e-30  104.9   0.2    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.3e-20   72.3   3.3    5.3e-20   72.3   3.3    2.7  3  dCache_1     Cache domain
    1.4e-18   66.6   0.1    1.4e-18   66.6   0.1    3.1  3  HisKA        His Kinase A (phospho-acceptor) domain
    6.5e-15   55.2   0.1    1.4e-14   54.2   0.1    1.5  1  PAS_3        PAS fold
    1.6e-05   24.8   0.1    3.9e-05   23.5   0.1    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      8e-05   22.5   0.6    0.00022   21.1   0.6    1.8  1  HATPase_c_5  GHKL domain
    0.00013   22.2   0.0    0.00082   19.6   0.0    2.5  1  PAS_9        PAS domain
     0.0073   16.3   0.0      0.017   15.1   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.086   12.7   0.0    1.5  1  sCache_2     Single Cache domain 2
      0.061   13.0   0.4        1.2    8.8   0.0    2.8  3  DUF383       Domain of unknown function (DUF383)
      0.072   12.8   0.2        4.5    7.0   0.0    2.3  2  Neurensin    Neurensin
      0.092   12.3   1.3       0.13   11.9   0.1    1.8  2  CAMP_factor  CAMP factor (Cfa)
       0.11   12.3   0.0       0.42   10.5   0.0    1.9  1  WVELL        WVELL protein
       0.17   11.5   0.0       0.44   10.2   0.0    1.7  1  NOD          NOTCH protein


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 !  104.9   0.2   2.6e-33   3.3e-30       2     109 ..     644     752 ..     643     755 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 2.6e-33
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d+++++qi+ nl++Na+kf++++g+i++e   +++  +i ++DnGiGi ke+++klf++f+q d++++r+++gtGlGl++v
  gi|91772161|ref|YP_564853.1| 644 DKIKIKQILYNLLSNAIKFTNENGTISIEAIFDDKLMQICIKDNGIGIEKENIEKLFQPFQQiDSAASRKYQGTGLGLALV 724
                                   78899**************779999999999877799999***************************************** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlp 109
                                   k++ve++gG+iwv+se g+G+ ftft+p
  gi|91772161|ref|YP_564853.1| 725 KNFVEMHGGNIWVDSEMGKGSAFTFTIP 752
                                   **************************98 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   3.3   4.1e-23   5.3e-20       4     247 ..      41     293 ..      38     296 .. 0.80
   2 ?   -2.5   0.1       2.8   3.6e+03      18      43 ..     330     354 ..     328     400 .. 0.71
   3 ?    0.9   0.0      0.25   3.2e+02      53      90 ..     444     483 ..     415     527 .. 0.73

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 4.1e-23
                      dCache_1   4 eeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksn............. 71 
                                   ee a+ ++ ++a+ +an++++++ +  ++ +t+a + ++          +e +r++++  l++il  n             
  gi|91772161|ref|YP_564853.1|  41 EEYAYLNSVETAKKYANQFNSDMIRSHSIGKTIAYSMTVD---------TERDRDKANMVLREILVQNpeligtyacfepn 112
                                   67788889999************88889999999975442.........477*************9996666666666665 PP

                      dCache_1  72 ....pdi..sgvylvdadGqviassdpssppnleg....tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavp 142
                                        di   + +  d+ G++i   +++++ n+      ++d+ + d+y  +++ +    vi++py  ++ ++ +i++++p
  gi|91772161|ref|YP_564853.1| 113 afdgKDIeyANTSAHDSTGRFI---PYWNKLNGSLtldpLQDYEEFDYYALPKSLK--TDVITEPYW-YD-DQIIISYSTP 186
                                   5555333224789999*****8...66765565559999*************9999..556999994.35.9********* PP

                      dCache_1 143 iyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpdkdl.........lgknlrdelkaqealekal 214
                                   i++d  +fiG+ ++d++l++l++++s+i + ++gy+f+ +++G i++hp ++          + +n++        ++k++
  gi|91772161|ref|YP_564853.1| 187 IFSD-DEFIGISGVDVSLNYLDNIVSDITIFDSGYAFLSSNKGVILTHPTEKVwignnslceFDGNVY-------EMSKDI 259
                                   **97.8*******************************************8655777777777666666.......488999 PP

                      dCache_1 215 akiesgvssvklng..eeylvayapiptglgWylv 247
                                    + +sg  +++ +   +e  ++y p+ +  +++ v
  gi|91772161|ref|YP_564853.1| 260 EDGKSGHIETIDSTtgKEVVIYYEPLTE-GNYSFV 293
                                   9999999888754444888888**9984.444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                      dCache_1  18 lanniedvldslenlaetlasnpslq 43 
                                   +an i++ ++ +    e++ s+++l+
  gi|91772161|ref|YP_564853.1| 330 TANTINRRIEDIVDDFEQI-SDSALN 354
                                   6777777777777777777.333343 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.25
                      dCache_1  53 neasreslqallksilksn..pdisgvylvdadGqviass 90 
                                    +++  +++++l + lk++  ++is   +++++G+++++ 
  gi|91772161|ref|YP_564853.1| 444 HPDDVGRVEDRLGESLKRHvpNFISQYRIISKSGEIFWVE 483
                                   5667778888898888777766779***********9964 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 ?   -0.2   0.0      0.81     1e+03      49      62 ..     336     349 ..     328     352 .. 0.82
   2 ?   -1.8   0.1       2.7   3.4e+03      38      55 ..     380     397 ..     369     399 .. 0.64
   3 !   66.6   0.1   1.1e-21   1.4e-18       2      67 .]     530     597 ..     529     597 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.81
                                   HHHHHHHHHHHHHC CS
                         HisKA  49 rrldhlvedlLdls 62 
                                   rr++++v+d+ ++s
  gi|91772161|ref|YP_564853.1| 336 RRIEDIVDDFEQIS 349
                                   79*******97776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHHHHHHHH CS
                         HisKA  38 keyletiesearrldhlv 55 
                                    ++le+ ++  + +++++
  gi|91772161|ref|YP_564853.1| 380 LRNLEKSHELNEEMNNII 397
                                   455666666666666666 PP

  == domain 3  score: 66.6 bits;  conditional E-value: 1.1e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   +++fla+++HELrtPL++i+g++e+L ++  g+ + ++++y+  i  ++++l++l++++Ld+s+ e+g
  gi|91772161|ref|YP_564853.1| 530 KSEFLANMSHELRTPLNSIIGFSELLLEKtiGDINNKQERYISNILTGGQHLLSLINEILDISKVESG 597
                                   89***********************98888*77779****************************9987 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   1.1e-17   1.4e-14      10      89 .]     424     503 ..     416     503 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.1e-17
                         PAS_3  10 eilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkpvrvigva 89 
                                   + +Gy ++++l+k  +++d++hp+D  rv++ l e+lk+    +  +yRi+ k+Ge++wve+++  + d+ng   ++ g++
  gi|91772161|ref|YP_564853.1| 424 Q-FGYNADDFLSKQMDYADIIHPDDVGRVEDRLGESLKRHVpNFISQYRIISKSGEIFWVEEQTLSHADQNGDTKYLHGII 503
                                   4.5**************************************999*****************************99999985 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 !   23.5   0.1     3e-08   3.9e-05       5      76 ..     650     720 ..     646     761 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-08
                   HATPase_c_3   5 kAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiG 76 
                                   + l  l+ N++    en  ++ie+ +++ k  +i+i+D+G G+++e++++ +++ ++  +a   s+++   G+G
  gi|91772161|ref|YP_564853.1| 650 QILYNLLSNAIKFTNENgtISIEAIFDD-KLMQICIKDNGIGIEKENIEKLFQPFQQIDSA--ASRKYQGTGLG 720
                                   56889999**997777644777777765.689********************987776663..34444444455 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.6   1.7e-07   0.00022       4      92 ..     646     742 ..     643     754 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                   HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNs...yegek........kkless.kskkeehGiGlk 72 
                                   + +  il nlL NAi   ++    +  I++++  ++k + i i+ +   +e+e+        +++ s  ++k +  G+Gl 
  gi|91772161|ref|YP_564853.1| 646 IKIKQILYNLLSNAIKFTNE----NGTISIEAIFDDKLMQICIKDNgigIEKENieklfqpfQQIDSAaSRKYQGTGLGLA 722
                                   67889**********87766....5689999999998888888765333333335445555555554437788999***** PP

                   HATPase_c_5  73 sireivkkykgnlsieaedg 92 
                                    +++ v+ ++gn++++ e g
  gi|91772161|ref|YP_564853.1| 723 LVKNFVEMHGGNIWVDSEMG 742
                                   **************998765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.4e-07   0.00082       7     104 .]     408     508 ..     401     508 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.4e-07
                         PAS_9   7 dnpdgril.yaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwvl.lt 81 
                                    n++g  +  ++e   ++ Gy+++++l k+  + d++ ++++  + ++++ e++++  + +  ++ +i k+ge fwv+  t
  gi|91772161|ref|YP_564853.1| 408 KNEKGWPVeLVSENITQF-GYNADDFLSKQmdYADII-HPDDVGRVEDRLGESLKRhvPNFISQYRIISKSGEIFWVEeQT 486
                                   678885555899999988.**********99999***.6666666666666666668999********************* PP

                         PAS_9  82 aspvkdd.dgelvgiivilrDite 104
                                   +s+  ++ d ++ +  +i+++it+
  gi|91772161|ref|YP_564853.1| 487 LSHADQNgDTKYLH--GIIVNITK 508
                                   ****6655777777..******95 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-05     0.017      13     110 ..     629     729 ..     619     738 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                   HATPase_c_2  13 evaeavlrraglseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep.. 91 
                                   e+++++ +r  l  ++  +i+  +  +++Na++  +++   g++++++  d++ ++++++D+G g + e++++  ++ +  
  gi|91772161|ref|YP_564853.1| 629 EIITDIDKRLSLINADKIKIKQILYNLLSNAIKFTNEN---GTISIEAIFDDKLMQICIKDNGIGIEKENIEKLFQPFQqi 706
                                   56666666655555555688888888999*****9985...7799**999**************98777777665554478 PP

                   HATPase_c_2  92 ....keslkegGrGlalikglvD 110
                                       + + +  G+Glal+k++v+
  gi|91772161|ref|YP_564853.1| 707 dsaaSRKYQGTGLGLALVKNFVE 729
                                   89888899999********9985 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.8e-05     0.086      43      87 ..     208     251 ..     203     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-05
                      sCache_2  43 elvnglkfgdGkgYffvldedgtllvhPfnpqleGknasnlkDan 87 
                                   ++v++++  d +gY f+  ++g +l hP+++ ++G n     D n
  gi|91772161|ref|YP_564853.1| 208 NIVSDITIFD-SGYAFLSSNKGVILTHPTEKVWIGNNSLCEFDGN 251
                                   6778888888.**************************98888877 PP

>> DUF383  Domain of unknown function (DUF383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.27   3.5e+02      71      95 ..     202     226 ..     150     239 .. 0.85
   2 ?    8.8   0.0   0.00094       1.2      12      89 ..     498     598 ..     428     631 .. 0.74
   3 ?   -1.6   0.1       1.4   1.8e+03       8      59 ..     647     704 ..     640     717 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                        DUF383  71 nydylayvfanlsqlpegRelllep 95 
                                   +++yl +++++++ +++g  +l ++
  gi|91772161|ref|YP_564853.1| 202 SLNYLDNIVSDITIFDSGYAFLSSN 226
                                   58***************99988665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00094
                        DUF383  12 lacmLLsNltkeesiaaqlleaklkvsqtpeess...........ksvkalekLldlfvkgatkdlnksan.y........ 72 
                                   ++  +++N+tk ++ ++ +++akl+ ++t++++s           +  + +  + +l+++ +  d+n++++ y        
  gi|91772161|ref|YP_564853.1| 498 YLHGIIVNITKRKKAEDMVIQAKLDAEATNRTKSeflanmshelrTPLNSIIGFSELLLEKTIGDINNKQErYisniltgg 578
                                   455588999999999999999888888877666677887777776444555555555555555566655332455555666 PP

                        DUF383  73 dylayv...fanlsqlpegR 89 
                                   ++l ++   + ++s++++g+
  gi|91772161|ref|YP_564853.1| 579 QHLLSLineILDISKVESGK 598
                                   55544412234555555555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                        DUF383   8 lladlacmLLsNltkeesiaaqlleaklkvsqtpeess...........ksvkalekLldlfv 59 
                                   + ++++  LLsN  k  + + ++  ++++ ++                  +++++ekL++ f 
  gi|91772161|ref|YP_564853.1| 647 KIKQILYNLLSNAIKFTNENGTISIEAIFDDK-----LmqicikdngigIEKENIEKLFQPFQ 704
                                   55667777888887777665544432222221.....01223344455577777777777776 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.051        65      44     101 ..      16      72 ..      11      77 .. 0.91
   2 ?    7.0   0.0    0.0035       4.5      43     100 ..     312     367 ..     282     372 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.051
                     Neurensin  44 slvvgtlvlllGvtallvGylvprrlelvksegelvvvDkqaiefnnaLdtlklaGav 101
                                    +v+gt ++l+  + l+++ ++ ++ e   + +++    k a +fn  +   + +G +
  gi|91772161|ref|YP_564853.1|  16 YIVIGTFLVLIASSSLIISASTAQHEEYA-YLNSVETAKKYANQFNSDMIRSHSIGKT 72 
                                   6899*********************9999.*****************99999999865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0035
                     Neurensin  43 vslvvgtlvlllGvtallvGylvprrlelvksegelvvvDkqaiefnnaLdtlklaGa 100
                                   ++l +++ ++ +G++a l+  ++ rr+e +   +++  + ++a++ n ++++ + +G+
  gi|91772161|ref|YP_564853.1| 312 LALFSALAIMFMGIVAFLTANTINRRIEDI--VDDFEQISDSALNGNLKVRANTKIGI 367
                                   4899999*********************99..89999999999999888888888876 PP

>> CAMP_factor  CAMP factor (Cfa)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001      0.13      49     114 ..     314     378 ..     299     401 .. 0.79
   2 ?   -2.4   0.2       2.4     3e+03      53      80 ..     608     635 ..     606     649 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                   CAMP_factor  49 lkealeaiakgkvtlydlksIlaRvellvdivdtiktaattLqdKvqkAhvelgleitkavirlin 114
                                   l +al+ +  g v+++ +++I  R+e +vd  + i+ +a + + Kv+ A++++g+++ +  i l +
  gi|91772161|ref|YP_564853.1| 314 LFSALAIMFMGIVAFLTANTINRRIEDIVDDFEQISDSALNGNLKVR-ANTKIGIDLKRIPIGLNE 378
                                   5678888999************************************6.99*****99997665544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                   CAMP_factor  53 leaiakgkvtlydlksIlaRvellvdiv 80 
                                   ++++++  v l+++  I+ R+e+++di 
  gi|91772161|ref|YP_564853.1| 608 ISSMISDIVILLNPLAITNRIEIITDID 635
                                   6677778888899999999999999875 PP

>> WVELL  WVELL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00033      0.42      26      64 ..     696     734 ..     689     738 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                         WVELL  26 vElLweDFestyAkaGreYkGkevtekivkqwienyGsk 64 
                                   +E L++ F+     a r+Y+G+ +   +vk+++e +G +
  gi|91772161|ref|YP_564853.1| 696 IEKLFQPFQQIDSAASRKYQGTGLGLALVKNFVEMHGGN 734
                                   899**********************************86 PP

>> NOD  NOTCH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00034      0.44       9      39 ..     515     545 ..     512     546 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                           NOD   9 LvlvVlidpeellnnskeFLrelsalLrtnv 39 
                                   +v+   +d e   ++++eFL ++s+ Lrt +
  gi|91772161|ref|YP_564853.1| 515 MVIQAKLDAEATNRTKSEFLANMSHELRTPL 545
                                   77888889999999***************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (763 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 5513.24
//
Query:       gi|91772162|ref|YP_564854.1|  [L=208]
Description: methyltransferase type 11 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-23   81.8   0.0    5.7e-23   81.4   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    9.4e-23   80.7   0.0    1.4e-22   80.1   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
      1e-21   77.4   0.0    1.6e-21   76.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    2.5e-16   59.8   0.0    4.1e-16   59.0   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      6e-16   58.7   0.0    7.4e-16   58.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    2.1e-14   54.0   0.0      3e-14   53.5   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    6.6e-06   26.0   0.0    1.2e-05   25.2   0.0    1.4  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.3e-05   24.0   0.0    0.00095   18.7   0.0    2.1  2  MTS              Methyltransferase small domain
    7.7e-05   22.1   0.0    9.7e-05   21.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00024   20.1   0.0    0.00031   19.8   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00027   20.1   0.0    0.00052   19.2   0.0    1.4  1  Fibrillarin      Fibrillarin
    0.00038   19.8   0.0    0.00057   19.3   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
    0.00049   19.6   0.0     0.0017   17.8   0.0    1.8  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0023   17.6   0.0      0.003   17.2   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0023   17.4   0.1        0.1   12.1   0.0    2.3  2  Methyltransf_4   Putative methyltransferase
     0.0058   16.5   0.1      0.044   13.6   0.1    2.2  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.029   14.0   0.0    1.5  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.016   14.9   0.1       0.62    9.7   0.0    2.3  2  N6_N4_Mtase      DNA methylase
      0.021   14.8   0.0      0.033   14.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.04   14.3   0.0      0.063   13.6   0.0    1.3  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
      0.055   13.0   0.0       0.28   10.7   0.0    1.9  2  DOT1             Histone methylation protein DOT1
      0.061   12.8   0.0       0.14   11.6   0.0    1.6  2  Methyltransf_5   MraW methylase family


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 !   81.4   0.0     7e-26   5.7e-23       4     126 ..      45     171 ..      43     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 7e-26
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre.naqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                   + ++lD+GCG G+ +  la el +k++++G+D s++++ lA+e n+++ g+ +v+  ++++ el+  +  +kfDl++++e+
  gi|91772162|ref|YP_564854.1|  45 DSSILDVGCGGGRAVSILA-ELAEKGKIYGVDHSQDMVDLATEyNSKEIGIGRVTIMESSVSELP--FPYDKFDLVTAFET 122
                                   5689***************.999********************9*********************..999*********** PP

               Methyltransf_31  84 lnaladpdkileeiervlkpggilliedpr......llaelpakveees 126
                                   ++  +d+++ l+ei+rvlk+gg lli +        ++++ p++  + +
  gi|91772162|ref|YP_564854.1| 123 CYFWPDLEEGLREIKRVLKKGGTLLIVNEMydhelfAERNTPYNTAKGM 171
                                   ***********************99877663444433333334444444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   1.7e-25   1.4e-22       1      96 []      49     148 ..      49     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.7e-25
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                   LdvGcG+Gr +  la+ +  ++++gvD s+ m++la e +s+e    +v+++++++++lpf+ ++fDlv+++e+  +++d+
  gi|91772162|ref|YP_564854.1|  49 LDVGCGGGRAVSILAELAekGKIYGVDHSQDMVDLATEYNSKEIGigRVTIMESSVSELPFPYDKFDLVTAFETCYFWPDL 129
                                   8**************888889***************8888887769*********************************** PP

                                   HHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                   e+ l+ei+RvLk+gG+l+i
  gi|91772162|ref|YP_564854.1| 130 EEGLREIKRVLKKGGTLLI 148
                                   ***************9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0     2e-24   1.6e-21       1      97 []      48     144 ..      48     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 2e-24
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                   +Ld+GcG Gr +  la+  +k+k++gvD s++m++ a e +++e +   +v++++ ++++lpf+ ++fDlv+++ + ++++
  gi|91772162|ref|YP_564854.1|  48 ILDVGCGGGRAVSILAELAEKGKIYGVDHSQDMVDLATEYNSKE-IgigRVTIMESSVSELPFPYDKFDLVTAF-ETCYFW 126
                                   8***************99989*****************999774.3469************************5.668998 PP

                                   HHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                    +dle+ l+ei+rvLk+gG
  gi|91772162|ref|YP_564854.1| 127 -PDLEEGLREIKRVLKKGG 144
                                   .79***************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 !   59.0   0.0     5e-19   4.1e-16      42     153 ..      39     150 ..      23     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 5e-19
                                   H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHH.HHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
               Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgek.klkeegkinieflqanaeeLpfeddsfDvvt 121
                                    v+v + +++lDv +G g  a++++ ++ ekgk+ ++D +++m++ + +   ke g  ++  + ++  eLpf  d fD+vt
  gi|91772162|ref|YP_564854.1|  39 HVSVEPDSSILDVGCGGGR-AVSILAELAEKGKIYGVDHSQDMVDLATEyNSKEIGIGRVTIMESSVSELPFPYDKFDLVT 118
                                   456778899*******886.77888888899**************9866268899999*********************** PP

                                   EES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
               Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                           +D +++L+e+ rvlk GG+l++++
  gi|91772162|ref|YP_564854.1| 119 AFETCYFWPDLEEGLREIKRVLKKGGTLLIVN 150
                                   98888899*******************98874 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   9.1e-19   7.4e-16      21     163 ..      43     191 ..      25     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 9.1e-19
               Methyltransf_23  21 raggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae..........kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                   ++++++Ld+GcG G+  ++l+e     +++gvD s  +v++a               ++++     e ++p +kfdl++++
  gi|91772162|ref|YP_564854.1|  43 EPDSSILDVGCGGGRAVSILAELAEkgKIYGVDHSQDMVDLATeynskeigigRVTIMESSVS---ELPFPYDKFDLVTAF 120
                                   57889*********9999997764448**************9899988887753333333333...899999********* PP

               Methyltransf_23  90 evlehvpdppellrqiatllkpgGylllseplaslkedrllld.wlylvpagrhisffsarslkelleeaGlevv 163
                                   e+++  pd++e lr i++ lk gG ll+       +  +l+ + ++  ++a + ++ +sa++++++l+ aG+  v
  gi|91772162|ref|YP_564854.1| 121 ETCYFWPDLEEGLREIKRVLKKGGTLLIVNEM---YDHELFAErNTPYNTA-KGMNIYSAEEYRKALNSAGFLAV 191
                                   ***********************999887652...4445544413333445.899*****************666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   3.7e-17     3e-14       1      99 []      49     146 ..      49     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 3.7e-17
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlk 80 
                                   L++GcG G+ ++ l+e  +  +++gvD s+++++ a e  +k+++    +v++ + ++++l+ + ++fDlv+a++++  ++
  gi|91772162|ref|YP_564854.1|  49 LDVGCGGGRAVSILAELAEKGKIYGVDHSQDMVDLATEYNSKEIG--IGRVTIMESSVSELPFPyDKFDLVTAFETCYFWP 127
                                   8********************************777777777776..779999999998888889**************** PP

               Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                   d++e l++i+++Lk+gG l
  gi|91772162|ref|YP_564854.1| 128 DLEEGLREIKRVLKKGGTL 146
                                   *****************86 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 !   25.2   0.0   1.5e-08   1.2e-05      63     129 ..      34     100 ..      13     121 .. 0.83
   2 ?   -3.1   0.0       6.6   5.4e+03     162     171 ..     139     148 ..     131     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.5e-08
                                   HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH.HHHHCTTCSEEEE CS
                          PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr.nlkkldlenvivv 129
                                   +  l+++++++ +++L+vG+G G    +la+l  ekg++ ++++++++v+ a++ n k+ ++ +v+++
  gi|91772162|ref|YP_564854.1|  34 GWGLNHVSVEPDSSILDVGCGGGRAVSILAEL-AEKGKIYGVDHSQDMVDLATEyNSKEIGIGRVTIM 100
                                   566788999*********************97.57899***********9886526666666677665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.6
                                   TEEEEEEEEE CS
                          PCMT 162 QLkeGGrlvv 171
                                    Lk+GG l++
  gi|91772162|ref|YP_564854.1| 139 VLKKGGTLLI 148
                                   5888888877 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06   0.00095      25     100 ..      38     116 ..      37     120 .. 0.77
   2 ?    3.1   0.0     0.074        61     123     140 ..     134     151 ..     128     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                                   HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHH.HHHHTTGC.EEEEE-STTTTST.TS-EEE CS
                           MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesake.nleankle.vevvasdvleeve.ekkfdl 100
                                   ++++ e + ++lD+GcG G     la+  ++ ++  vd +   +++a+e n ++ ++  v++++s+v e     +kfdl
  gi|91772162|ref|YP_564854.1|  38 NHVSVEPDSSILDVGCGGGRAVSILAELAEKGKIYGVDHSQDMVDLATEyNSKEIGIGrVTIMESSVSELPFpYDKFDL 116
                                   5677778889***********************************9865266666665677777777653322456665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.074
                                   HHHHHHEEEEEEEEEEEE CS
                           MTS 123 aeAkeaLkegGeLliVan 140
                                   +e k++Lk+gG+LliV +
  gi|91772162|ref|YP_564854.1| 134 REIKRVLKKGGTLLIVNE 151
                                   56789**********964 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.2e-07   9.7e-05      55     167 ..      37     151 ..      27     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                                   HTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEE CS
                          CMAS  55 leklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsv 134
                                   l+ ++++p + +Ld+GcG G  v   +e     k+ g+  S++   la +   ++    +v++  +   +l+ ++d+   v
  gi|91772162|ref|YP_564854.1|  37 LNHVSVEPDSSILDVGCGGGRAVSILAELAeKGKIYGVDHSQDMVDLATEYNSKEIGIGRVTIMESSVSELPFPYDKFDLV 117
                                   677899**************98876665431589*************99987766667889******************** PP

                                   S-GGGTSG.GGHHHHHHHHHHHS-TT-EEEEEEE CS
                          CMAS 135 gafehvgk.enydtffkklkkllkedGllllhti 167
                                    afe   +   +++  +++k++lk++G+ll+   
  gi|91772162|ref|YP_564854.1| 118 TAFETCYFwPDLEEGLREIKRVLKKGGTLLIVNE 151
                                   ****98652689999*************998654 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 !   19.8   0.0   3.8e-07   0.00031     104     265 ..      33     193 ..      22     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.8e-07
                                   HHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-S..EEEEE---HHHH.HHHHHHHCCTTTTSSEEEE---GGGS-T.- CS
                Methyltransf_9 104 WdrvlphlsdlkgrtildvGcgnGyhlwrmvgegak..lvvGidPselfl.iqfeavrkllgedqrahllplgieqlpe.l 180
                                   W   l+h+s   + +ildvGcg G  +  +++e a+   + G+d s+  + +  e   k +g   r++ +  ++ +lp   
  gi|91772162|ref|YP_564854.1|  33 WGWGLNHVSVEPDSSILDVGCGGGRAVS-ILAELAEkgKIYGVDHSQDMVdLATEYNSKEIGI-GRVTIMESSVSELPFpY 111
                                   555689999999**********997664.555544312689***9998762444555555655.56777889******889 PP

                                   --EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-TT-EE--SS-BTTBSS---EEBHHHHHHHHHHTT-E CS
                Methyltransf_9 181 eafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvletlvieGdenavlvPedryakmrnvyfiPsaaalkvWlekvgfv 261
                                   + fd v +    y      + l+++k  l+kgG+l++   + + +  a        ak  n+y   sa+  ++ l+ +gf 
  gi|91772162|ref|YP_564854.1| 112 DKFDLVTAFETCYFWPDLEEGLREIKRVLKKGGTLLIVNEMYDHELFAERNTPYNTAKGMNIY---SAEEYRKALNSAGFL 189
                                   ***************99999**************99877766655433322222224444444...667777777777776 PP

                                   EEEE CS
                Methyltransf_9 262 dvri 265
                                    v+i
  gi|91772162|ref|YP_564854.1| 190 AVEI 193
                                   6665 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.4e-07   0.00052      62     108 ..      36      81 ..      32      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.4e-07
                                   T-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                   Fibrillarin  62 glkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                   gl+++ ++++s++L +G + G++vs ++++ + +g++y+v++s+ ++
  gi|91772162|ref|YP_564854.1|  36 GLNHVSVEPDSSILDVGCGGGRAVSILAELAE-KGKIYGVDHSQDMV 81 
                                   8999**************************99.9********99765 PP

>> Methyltransf_2  O-methyltransferase 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   0.00057      55     209 ..      37     188 ..      19     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.9e-07
                                   HHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS---.--TTEEEEES-TTTS---..--SEE CS
                Methyltransf_2  55 leafdleglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsag.eeervefvgGdffkdslP..eaDai 131
                                   l+++ +e+ +s++DvG G G ++   +++  + k+   D + + v  A e+ s +    rv+ ++ ++ + + P  + D++
  gi|91772162|ref|YP_564854.1|  37 LNHVSVEPDSSILDVGCGGGRAVSILAELAEKGKIYGVDHSqDMVDLATEYNSKEiGIGRVTIMESSVSELPFPydKFDLV 117
                                   55666777789*******************999999999862589999999644314689*********999999889*** PP

                                   EEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHHHHHHCSS---.--HHHHHHHHHHCT- CS
                Methyltransf_2 132 llkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdlimlvqteGke.RteaeyeellseaGf 209
                                        ++ w d    + L+++k+ l++gG +++v+ + +++  +e +t          ++G++  +++ey++ l++aGf
  gi|91772162|ref|YP_564854.1| 118 TAFETCYFWPD--LEEGLREIKRVLKKGGTLLIVNEMYDHELFAERNTPYNT------AKGMNiYSAEEYRKALNSAGF 188
                                   *********98..5688********************999888887777632......233331577888888888888 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     2e-06    0.0017     159     232 ..      42     119 ..      35     150 .. 0.71
   2 ?   -0.5   0.0      0.82   6.6e+02      82     100 ..     186     204 ..     153     208 .] 0.64

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
                          PrmA 159 vkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvake.NaelNkvea.klevalseellk.eekadviva 232
                                   v++++++lDvG+G G   +i a + +  k+++vD  +  v+ a e N +  ++ +  ++    +el+    k+d++ a
  gi|91772162|ref|YP_564854.1|  42 VEPDSSILDVGCGGGrAVSILAELAEKGKIYGVDHSQDMVDLATEyNSKEIGIGRvTIMESSVSELPFpYDKFDLVTA 119
                                   78899********99779*******************99998876255554554422211222333313566666655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.82
                          PrmA  82 lekgkvkveeveeedWaee 100
                                       +v+++ev e +W + 
  gi|91772162|ref|YP_564854.1| 186 AGFLAVEIDEVPEDNWITV 204
                                   2333677777888888765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.7e-06     0.003      11      53 ..      42      85 ..      37     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                          MetW 11 ikpgsrvldlGcGdGellellkeek.qvdgrGleldeegvaecv 53
                                  ++p s +ld+GcG G  +++l+e   + + +G++++++ v  ++
  gi|91772162|ref|YP_564854.1| 42 VEPDSSILDVGCGGGRAVSILAELAeKGKIYGVDHSQDMVDLAT 85
                                  899*************9999988541456799999999987554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00013       0.1       4      45 ..      47      88 ..      44     106 .. 0.87
   2 ?    3.1   0.0      0.07        57      99     120 ..     132     153 ..     129     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                  EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHH CS
                Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkki 45
                                   +l++GcG G++++ lA+   + ++ G++ ++++v+ + +  
  gi|91772162|ref|YP_564854.1| 47 SILDVGCGGGRAVSILAELAEKGKIYGVDHSQDMVDLATEYN 88
                                  689*******************************99887755 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.07
                                   HHHHHHHHEEEEEEEEEEESHH CS
                Methyltransf_4  99 llkelarvLkkgGvlelaTDve 120
                                    l e++rvLkkgG l ++  ++
  gi|91772162|ref|YP_564854.1| 132 GLREIKRVLKKGGTLLIVNEMY 153
                                   5889**********99987633 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   5.4e-05     0.044      74     157 ..      46     149 ..      37     203 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                   S-EEEES-TT-HHH...HH--S-..E....EEEESS-SSTT............EEES-TTS-S--TT-EE.EEEEES---S CS
                Methyltransf_8  74 lvvadlGcGeakia...eavrekekv....rsfdlvavner............vvacdlakvPledesvd.vavfclslmg 134
                                    ++ d+GcG  +      +  ek k+    +s d+v +  +            ++   ++++P   +  d v+ f      
  gi|91772162|ref|YP_564854.1|  46 SSILDVGCGGGRAVsilAELAEKGKIygvdHSQDMVDLATEynskeigigrvtIMESSVSELPFPYDKFDlVTAFETCYFW 126
                                   567777777766432223444455553334455555444330001111111112233445556555555623456667778 PP

                                   S-HHHHHHHHHHHEEEEEEEEEE CS
                Methyltransf_8 135 tnladflkeanrvlkvGGllkva 157
                                    +l++ l+e++rvlk+GG l + 
  gi|91772162|ref|YP_564854.1| 127 PDLEEGLREIKRVLKKGGTLLIV 149
                                   899***************98764 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-05     0.029       7      72 ..      43     108 ..      38     123 .. 0.84
   2 ?   -3.0   0.0       5.9   4.8e+03     123     135 ..     135     147 ..     129     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHH.HHHHTT--SEEEEES-CTCCH CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvae.nlkrLgvtntivleaDarkid 72 
                                   +++  ilD+ ++ G   + +ael ++kg+++ vd+++  ++  +e n k +g+  ++++e  +++ +
  gi|91772162|ref|YP_564854.1|  43 EPDSSILDVGCGGGRAVSILAEL-AEKGKIYGVDHSQDMVDLATEyNSKEIGIGRVTIMESSVSELP 108
                                   66788*******99999999999.99************999765439999***99999999888875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.9
                                   HHCCCEEEEEEEE CS
               Methyltr_RsmB-F 123 aaidllkkgGvlv 135
                                    +  +lkkgG+l+
  gi|91772162|ref|YP_564854.1| 135 EIKRVLKKGGTLL 147
                                   5566789999887 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.089        72     188     230 ..      41      85 ..      39      86 .. 0.85
   2 ?    9.7   0.0   0.00076      0.62      34      64 ..     128     160 ..     111     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.089
                                   HS-TT-EEEETT-TTTHHHHHHHHTT-E..EEEEESSHHHHHHHH CS
                   N6_N4_Mtase 188 stkkgdivlDpFaGSGtTavaakelgrk..fiGieieeeyvelae 230
                                   s ++++++lD  +G G  + + +el +k   +G++ ++  v+la 
  gi|91772162|ref|YP_564854.1|  41 SVEPDSSILDVGCGGGRAVSILAELAEKgkIYGVDHSQDMVDLAT 85 
                                   67899************999888887766699***9999999876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00076
                                   HHHHHHHHHHHHEEEEEEEEEEE-CCCHHT...H CS
                   N6_N4_Mtase  34 flekvlkevrrvLkddgsifiniddseikk...e 64 
                                    le+ l+e++rvLk++g+++i   +++ ++   e
  gi|91772162|ref|YP_564854.1| 128 DLEEGLREIKRVLKKGGTLLIV-NEMYDHElfaE 160
                                   578899*************997.44444443442 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     4e-05     0.033      25      73 ..      44      90 ..      37     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
               Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraek 73
                                  ++ +++DvG+G g   ++la      k k++g+d ++++v+ a + ++k
  gi|91772162|ref|YP_564854.1| 44 PDSSILDVGCGGGRAVSILAE--LAEKGKIYGVDHSQDMVDLATEYNSK 90
                                  56789**************99..5589*************999888765 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.7e-05     0.063      54      88 ..      40      76 ..      22      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-05
                  AdoMet_MTase 54 rseeketsfvdvgcgngllvyvlaaegykg..ygidl 88
                                   s e + s+ dvgcg g  v +la    kg  yg+d 
  gi|91772162|ref|YP_564854.1| 40 VSVEPDSSILDVGCGGGRAVSILAELAEKGkiYGVDH 76
                                  45578899***************86555553388885 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00034      0.28      35      85 ..      37      87 ..      26      99 .. 0.89
   2 ?   -0.2   0.0      0.74     6e+02     116     141 ..     136     161 ..     125     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                                  HHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHH CS
                          DOT1 35 ldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekq 85
                                  l++v +++++  +D G G G+ v   a  ++  + +Gv+ +++  +la + 
  gi|91772162|ref|YP_564854.1| 37 LNHVSVEPDSSILDVGCGGGRAVSILAELAEKGKIYGVDHSQDMVDLATEY 87
                                  6899***********************9999999*********99999764 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.74
                                   HHHHGGG-SEEEE--TT--HHHHHHH CS
                          DOT1 116 veeiieeadvilvNNfaFdaelnkql 141
                                   +++++++   +l+ N ++d+el ++ 
  gi|91772162|ref|YP_564854.1| 136 IKRVLKKGGTLLIVNEMYDHELFAER 161
                                   56778888888888899999987664 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.14      14      89 ..      38     115 ..      26     130 .. 0.79
   2 ?   -1.6   0.0       1.9   1.5e+03     219     239 ..     129     149 ..     125     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                   HHT---TT-EEEES--TTSHHHHHHHTT--TT.EEEEEES-HHHHHHHTT.....-..--EEEEES-GGGHHHHHHHTT CS
                Methyltransf_5  14 ellepkedgvyiDaTlGaggHsealLeqlsel.rligidrDksalarakerLkefe..krltlvkgnfkelkealaean 89 
                                   + +++++d   +D+  G gg +  +L +l e+ +++g+d+ +++++ a+e  ++ +   r+t+++++ +el   +++ +
  gi|91772162|ref|YP_564854.1|  38 NHVSVEPDSSILDVGCG-GGRAVSILAELAEKgKIYGVDHSQDMVDLATEYNSKEIgiGRVTIMESSVSELPFPYDKFD 115
                                   55667888888998887.789999***999999****************976665444679999999888876666655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHEEEEEEEEEE CS
                Methyltransf_5 219 leelleaalellakggrlavi 239
                                   lee l+++ ++l+kgg l ++
  gi|91772162|ref|YP_564854.1| 129 LEEGLREIKRVLKKGGTLLIV 149
                                   8889999999******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1369.81
//
Query:       gi|91772163|ref|YP_564855.1|  [L=247]
Description: sugar fermentation stimulation protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-41  139.1   0.0    1.1e-40  138.8   0.0    1.1  1  SfsA      Sugar fermentation stimulation protein RE domain
    1.6e-24   85.8   0.0    3.6e-24   84.7   0.0    1.6  2  SfsA_N    SfsA N-terminal OB domain


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8   0.0   1.2e-44   1.1e-40       2     134 ..      94     226 ..      93     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 1.2e-44
                                   HHHHHHHHHHEE...........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHH CS
                          SfsA   2 lpnklveealesgli.elagyeeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhleeLae 81 
                                   ++++++e+a+++++   ++++ e+ +e+k+g+sr+Dfll+k+ +++++vEVK++tl  g++a fPdapt+Rg++h+ eL +
  gi|91772163|ref|YP_564855.1|  94 FHRRIAEWAIANKVCsCFENVLEVIPEQKFGDSRLDFLLKKS-DTELWVEVKGCTLIYGNTATFPDAPTTRGKRHVGELKK 173
                                   5899********9997899999******************98.**************988********************* PP

                                   HHHTT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE CS
                          SfsA  82 lvkegyravvlfvvqredarefkpnkeidpefaealreaaeaGVevlaydckv 134
                                   ++++g +a++l+++ r+da +fk n++idp+fae +++a++aGV+v+++ + +
  gi|91772163|ref|YP_564855.1| 174 ALESGSEALILIIILRKDALCFKANASIDPDFAEVFKDAVNAGVQVCPLVFGY 226
                                   ***********************************************998765 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 !   84.7   0.0     4e-28   3.6e-24       1      63 []      19      90 ..      19      90 .. 0.90
   2 ?   -3.4   0.0       1.3   1.2e+04      23      37 ..     169     183 ..     167     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 4e-28
                                  EEEEETTEEEEEEE...........EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEETTEEEE- CS
                        SfsA_N  1 lrRpnRFladveldg.t........vHvpntGrlkelllpGarvllsksdnpkrKtkytleavekegtwvgi 63
                                  l+RpnRFl+ ve+d+ t        vH++++Grl++ll+pG+r+ll+k++npkrKt ++++a++++++w++i
  gi|91772163|ref|YP_564855.1| 19 LSRPNRFLGIVEMDEsTssgpfqekVHIHDPGRLEDLLYPGNRLLLRKATNPKRKTGWDVIAAKADDGWILI 90
                                  79**********9954133445556*********************************************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                   S--TTT--TT-EEEE CS
                        SfsA_N  23 GrlkelllpGarvll 37 
                                   G lk+ l+ G+++l+
  gi|91772163|ref|YP_564855.1| 169 GELKKALESGSEALI 183
                                   889999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1829.69
//
Query:       gi|91772164|ref|YP_564856.1|  [L=111]
Description: hypothetical protein Mbur_0086 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-06   28.0  27.9    2.2e-06   27.8  27.9    1.1  1  DUF5518   Family of unknown function (DUF5518)
  ------ inclusion threshold ------
        8.3    6.4   6.7        1.9    8.4   3.4    1.7  2  Caveolin  Caveolin


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 !   27.8  27.9   2.5e-10   2.2e-06       3     117 ..       2     106 ..       1     107 [. 0.84

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.5e-10
                       DUF5518   3 aaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglvaaiggla 83 
                                   +++ Ga++  + +l+l+  +  v+  l++++gG    y+a+++s  g+ +G+l++l+ a+p+++l++v+++  +    +++
  gi|91772164|ref|YP_564856.1|   2 NIIKGALIRSICTLVLY--MVPVLNALSPFFGG----YVAKEGSIGGVKVGLLMTLLFAVPGVLLSGVFVA--LMSEIPVI 74 
                                   57778888888888888..77779999999985....8899**************************9994..55566666 PP

                       DUF5518  84 gfvallvalllvvllllvvllvilgaiGGaiGgl 117
                                   g+++++ +++++  + ++++++i+g+iGG++Gg+
  gi|91772164|ref|YP_564856.1|  75 GTILAGSGIIIT--IGIIIYTAIFGIIGGVVGGV 106
                                   666666666666..8999**************97 PP

>> Caveolin  Caveolin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       0.3   2.7e+03     101     119 ..      13      24 ..       1      34 [. 0.40
   2 ?    8.4   3.4   0.00021       1.9      60      86 ..      48      74 ..      43     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.3
                      Caveolin 101 liqkvwsllvdalvdPlfe 119
                                   +   ++ +       P+++
  gi|91772164|ref|YP_564856.1|  13 CTLVLYMV-------PVLN 24 
                                   22222222.......3333 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00021
                      Caveolin 60 lltallaiPlalilgilfallsalhiw 86
                                  l+t+l+a+P  l++g+++al+s + + 
  gi|91772164|ref|YP_564856.1| 48 LMTLLFAVPGVLLSGVFVALMSEIPVI 74
                                  799*******************88764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 843.92
//
Query:       gi|91772165|ref|YP_564857.1|  [L=173]
Description: hypothetical protein Mbur_0088 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-48  162.2   0.0    5.4e-48  161.9   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    1.1e-15   57.2   1.1    1.7e-15   56.5   1.1    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor
  ------ inclusion threshold ------
      0.014   15.0   0.0       0.02   14.5   0.0    1.2  1  RNA_Me_trans   Predicted SAM-dependent RNA methyltransferase


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 !  161.9   0.0   9.1e-52   5.4e-48       1     127 []      49     173 .]      49     173 .] 0.96

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 9.1e-52
                                   EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E.....EB--S-B--STTTTT-BS---HHHHHHHHHHHT CS
                 Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkak.eerlLPyLvAaNpvnYgkplkLscvEAlaaalyil 80 
                                   i+l+p+ak++lspaD+   ++++i+v+dcsW+++eev  + ++ + ++r+LPyLvA+Npvn+g+p+kL++vEA+aaalyil
  gi|91772165|ref|YP_564857.1|  49 ILLDPMAKQALSPADK---HEQNITVLDCSWETVEEVFPHLMRLHlQHRALPYLVATNPVNFGRPFKLTSVEAFAAALYIL 126
                                   79*************5...5799**************9888888789********************************** PP

                                   T-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                 Ribo_biogen_C  81 glkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                   g k++ae++lskf+wg+ Fl++nke+le+Y+k+kds+e++++q+ey+
  gi|91772165|ref|YP_564857.1| 127 GNKKQAEKILSKFNWGHVFLDMNKEPLEDYSKAKDSNEIIKIQSEYM 173
                                   ********************************************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 !   56.5   1.1   2.8e-19   1.7e-15       1      34 [.       9      46 ..       9      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.8e-19
                                  --EEEES---------TTHHHHHTTSEEE....ESS-- CS
                           RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrl....vrtgk 34
                                  ++l+i++a+qCdPKKCtgkk+arf+++r+    +++++
  gi|91772165|ref|YP_564857.1|  9 YHLHIFHAKQCDPKKCTGKKMARFELARIfdkvQKIPR 46
                                  79**************************9888777776 PP

>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.3e-06      0.02      60      98 ..      33      70 ..       5      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                  RNA_Me_trans 60 sveellkelkevkkekvclLDpkaekelspedaeefdvf 98
                                  ++ +++++ +++  +  +lLDp a+++lsp+d++e ++ 
  gi|91772165|ref|YP_564857.1| 33 ELARIFDKVQKI-PRGSILLDPMAKQALSPADKHEQNIT 70
                                  555666666555.56789**************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1165.13
//
Query:       gi|91772166|ref|YP_564858.1|  [L=73]
Description: SirA-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-23   82.1   0.3      2e-23   82.0   0.3    1.0  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.3   1.1e-27     2e-23       2      70 .]       5      73 .]       4      73 .] 0.99

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.1e-27
                                  EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                          TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                  e+D+rG+ CP+Pl++++kal+k+ eg+++ +l ++pa+++ ip  +k lg+e++++ee+++e++i irk
  gi|91772166|ref|YP_564858.1|  5 EIDTRGETCPVPLVECRKALRKASEGDEVTILGTHPASKKEIPMACKALGLEVIDIEEDGKEWKIKIRK 73
                                  8******************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 484.34
//
Query:       gi|91772167|ref|YP_564859.1|  [L=126]
Description: hypothetical protein Mbur_0090 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-33  115.0   1.6    2.6e-21   76.1   0.2    2.0  2  DrsE_2    DsrE/DsrF/DrsH-like family
    7.2e-06   26.4   0.0    1.1e-05   25.8   0.0    1.3  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.1   8.5e-14   7.6e-10      15      49 ..       2      36 ..       1      40 [. 0.92
   2 !   76.1   0.2   2.9e-25   2.6e-21      70     153 .]      40     125 ..      36     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 8.5e-14
                                  .HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-G CS
                        DrsE_2 15 dkalaalilAsgAaalglevtiFftFwGLnilrke 49
                                  dk + ali+++gA a+g++v+++ftFwGL+ l+k 
  gi|91772167|ref|YP_564859.1|  2 DKLYSALIVGNGALAMGMDVSMYFTFWGLQRLKKG 36
                                  6889****************************996 PP

  == domain 2  score: 76.1 bits;  conditional E-value: 2.9e-25
                                   SS--SSS-GGGHHHHHHHHHHHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-..EEE-HHHHHHHHHC- CS
                        DrsE_2  70 ksklskmnmagigtkmmkkvmkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgv..eiagaatylkeaeea 148
                                   k +lskm+m g+g+ m+kk mk+++vasle L++  ke g k+ aC+mtm++mg+k +el  +   e++ + ty++ea +a
  gi|91772167|ref|YP_564859.1|  40 KGPLSKMHMLGLGKWMIKKRMKQANVASLERLMNDYKELGGKILACEMTMEIMGVKADELRSEWidEYGAVGTYINEARDA 120
                                   569*********************************************************9997799************** PP

                                   SEEEE CS
                        DrsE_2 149 dvnLf 153
                                   +++Lf
  gi|91772167|ref|YP_564859.1| 121 QITLF 125
                                   ****9 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.2e-09   1.1e-05      18     103 ..       5     112 ..       1     124 [. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.2e-09
                                   HHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS.....................---TGGGTS---GGGGGGCGGGT-EEEEE CS
                          DrsE  18 realelalaaaalghevsvffygdGvllllk.....................gqtanpadeknlaellkalkeygvklyvC 77 
                                   ++al + + a+a+g +vs+ f+  G + l+k                     ++  ++a+  +l  l++ +ke g k+ +C
  gi|91772167|ref|YP_564859.1|   5 YSALIVGNGALAMGMDVSMYFTFWGLQRLKKgglekgplskmhmlglgkwmiKKRMKQANVASLERLMNDYKELGGKILAC 85 
                                   7899999*********************************************788888999******************** PP

                                   HHHHHHTT--GGGE-..T--EEEE-HHH CS
                          DrsE  78 gqaakargldededl..gvgvevsglge 103
                                   +++++ +g+++d +l  +   e +++g+
  gi|91772167|ref|YP_564859.1|  86 EMTMEIMGVKAD-ELrsEWIDEYGAVGT 112
                                   **********65.553222444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 752.34
//
Query:       gi|91772168|ref|YP_564860.1|  [L=53]
Description: rubredoxin-type Fe(Cys)4 protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   59.0   4.0    3.7e-16   58.9   4.0    1.0  1  Rubredoxin       Rubredoxin
     0.0043   17.1   3.9      0.022   14.9   3.9    1.9  1  Zn-ribbon_8      Zinc ribbon domain
     0.0094   15.7   0.5        1.4    8.7   0.0    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
  ------ inclusion threshold ------
      0.014   15.4   1.3       0.58   10.2   0.1    2.1  2  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
      0.022   14.2   1.9       0.35   10.3   0.3    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.023   14.3   1.0        4.3    7.1   0.5    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.023   14.0   3.9      0.058   12.7   0.3    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
      0.026   14.6   1.8      0.057   13.5   1.8    1.6  1  PHD_4            PHD-finger
      0.033   14.0   1.1        2.7    7.9   0.3    2.2  2  zf-CCHC_2        Zinc knuckle
      0.033   13.6   0.5      0.077   12.4   0.0    1.8  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
      0.072   13.4   1.3         10    6.6   0.5    2.1  2  C1_2             C1 domain
       0.09   12.5   1.6       0.26   11.1   0.3    2.0  2  zf-MIZ           MIZ/SP-RING zinc finger
       0.12   12.1   2.2        2.3    8.0   0.1    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.19   12.4   0.1       0.21   12.2   0.1    1.2  1  RbpA             RNA polymerase-binding protein
       0.48   10.5   2.7        8.1    6.6   0.6    2.3  2  zf-C2H2_6        C2H2-type zinc finger
        1.9    9.0   5.0        9.1    6.8   1.2    2.2  2  zf-met           Zinc-finger of C2H2 type
        4.5    7.1   8.0        8.1    6.3   1.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   4.0   3.5e-19   3.7e-16       2      45 ..       4      48 ..       3      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 3.5e-19
                                  EEETTT-.BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGG CS
                    Rubredoxin  2 yeCkvCg.yvYdpakGdpdegiapgTkFedlPddWvCPdCgveke 45
                                  y+C+vC+ ++Yd+a+G+ + gi pgTk ed PddW+CP Cg++k+
  gi|91772168|ref|YP_564860.1|  4 YRCNVCNvFEYDDAEGNTELGIVPGTKPEDFPDDWKCPICGADKT 48
                                  9*****7589*********************************97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   3.9   2.1e-05     0.022       5      38 ..       3      50 ..       3      52 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                   Zn-ribbon_8  5 eYrCeeCghefe.............vlqsisdaplta.CPeCgs.evrr 38
                                  eYrC+ C+ +fe             +  +  d p+   CP Cg+ ++++
  gi|91772168|ref|YP_564860.1|  3 EYRCNVCN-VFEyddaegntelgivPGTKPEDFPDDWkCPICGAdKTHQ 50
                                  8*******.**********9996543333334456667*****977665 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.013        14      43      52 ..       2      11 ..       1      13 [. 0.86
   2 !    8.7   0.0    0.0013       1.4      32      52 ..      23      45 ..      19      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                zinc_ribbon_10 43 vkyrCpkCga 52
                                  ++yrC  C++
  gi|91772168|ref|YP_564860.1|  2 TEYRCNVCNV 11
                                  68******97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                zinc_ribbon_10 32 nGlapkeeleev..kyrCpkCga 52
                                   G +p  ++e++   ++Cp Cga
  gi|91772168|ref|YP_564860.1| 23 LGIVPGTKPEDFpdDWKCPICGA 45
                                  588997777777779******97 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.034        36      24      30 ..       4      10 ..       2      14 .. 0.81
   2 ?   10.2   0.1   0.00055      0.58      23      31 ..      37      45 ..      29      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                zf-Sec23_Sec24 24 wiCnfCn 30
                                  ++Cn Cn
  gi|91772168|ref|YP_564860.1|  4 YRCNVCN 10
                                  68***98 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00055
                zf-Sec23_Sec24 23 rwiCnfCnh 31
                                   w+C++C+ 
  gi|91772168|ref|YP_564860.1| 37 DWKCPICGA 45
                                  5******97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.04        42       2       9 ..       3      10 ..       2      16 .. 0.89
   2 ?   10.3   0.3   0.00033      0.35      17      24 ..      38      45 ..      35      52 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.04
                   zf-ribbon_3  2 tvrCPnCG 9 
                                  ++rC+ C+
  gi|91772168|ref|YP_564860.1|  3 EYRCNVCN 10
                                  68*****7 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00033
                   zf-ribbon_3 17 nvCpyCGt 24
                                   +Cp CG+
  gi|91772168|ref|YP_564860.1| 38 WKCPICGA 45
                                  56666665 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5     0.004       4.3       7      12 ..       4       9 ..       1      13 [. 0.86
   2 ?    5.9   0.0    0.0091       9.6       7      13 ..      38      44 ..      35      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.004
                                  EE-TTT CS
               Desulfoferrod_N  7 YkCevC 12
                                  Y+C+vC
  gi|91772168|ref|YP_564860.1|  4 YRCNVC 9 
                                  ****** PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0091
                                  EE-TTT- CS
               Desulfoferrod_N  7 YkCevCG 13
                                  +kC +CG
  gi|91772168|ref|YP_564860.1| 38 WKCPICG 44
                                  7****** 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   0.3     0.068        72       7      12 ..       6      11 ..       5      12 .. 0.76
   2 ?   12.7   0.3   5.5e-05     0.058       3      12 ..      36      45 ..      34      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.068
                                  -SSS-- CS
                      zf-RanBP  7 CskClv 12
                                  C++C+v
  gi|91772168|ref|YP_564860.1|  6 CNVCNV 11
                                  888887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.5e-05
                                  SSEE-SSS-- CS
                      zf-RanBP  3 gdWdCskClv 12
                                  +dW+C+ C++
  gi|91772168|ref|YP_564860.1| 36 DDWKCPICGA 45
                                  6899999986 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.8   5.4e-05     0.057      32      67 ..       5      43 ..       1      44 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                         PHD_4 32 eCsvCyeivHpeClkek...egegvvnedlpnsWeCpkC 67
                                   C+vC+     +   ++     +g+  ed p +W+Cp C
  gi|91772168|ref|YP_564860.1|  5 RCNVCNVFEYDDAEGNTelgIVPGTKPEDFPDDWKCPIC 43
                                  5888888877777777644456788899**********9 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   0.3    0.0025       2.7       4      11 ..       4      11 ..       3      13 .. 0.87
   2 ?    5.0   0.0     0.021        22       1      11 [.      35      45 ..      35      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0025
                     zf-CCHC_2  4 YvChiCgk 11
                                  Y C++C++
  gi|91772168|ref|YP_564860.1|  4 YRCNVCNV 11
                                  9******8 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                     zf-CCHC_2  1 PpgYvChiCgk 11
                                  P++ +C iCg+
  gi|91772168|ref|YP_564860.1| 35 PDDWKCPICGA 45
                                  88999****96 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.98     1e+03      11      16 ..       5      10 ..       1      14 [. 0.68
   2 ?   12.4   0.0   7.3e-05     0.077       4      17 ..      32      45 ..      29      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.98
                   Vps36-NZF-N 11 vCpICs 16
                                   C +C 
  gi|91772168|ref|YP_564860.1|  5 RCNVCN 10
                                  577775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.3e-05
                   Vps36-NZF-N  4 eavtatWvCpICsf 17
                                  e+   +W CpIC  
  gi|91772168|ref|YP_564860.1| 32 EDFPDDWKCPICGA 45
                                  566679******86 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5    0.0095        10      32      40 ..       3      11 ..       1      17 [. 0.72
   2 ?    6.3   0.0     0.011        12      12      27 ..      31      46 ..      21      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0095
                          C1_2 32 fYsCseCdf 40
                                  +Y+C+ C++
  gi|91772168|ref|YP_564860.1|  3 EYRCNVCNV 11
                                  499988984 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                          C1_2 12 gedssesfnCsaCgrk 27
                                  +ed  ++++C +Cg +
  gi|91772168|ref|YP_564860.1| 31 PEDFPDDWKCPICGAD 46
                                  5677789999999987 PP

>> zf-MIZ  MIZ/SP-RING zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.34   3.6e+02      42      48 ..       4      10 ..       1      12 [. 0.79
   2 ?   11.1   0.3   0.00025      0.26      41      48 ..      37      44 ..      29      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.34
                                  -B-TTT- CS
                        zf-MIZ 42 WnCPvCs 48
                                   +C vC+
  gi|91772168|ref|YP_564860.1|  4 YRCNVCN 10
                                  6899**8 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00025
                                  --B-TTT- CS
                        zf-MIZ 41 tWnCPvCs 48
                                   W+CP+C 
  gi|91772168|ref|YP_564860.1| 37 DWKCPICG 44
                                  5******6 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 ?    4.2   0.5     0.032        34       6      20 ..       5      19 ..       2      21 .. 0.80
   2 ?    8.0   0.1    0.0022       2.3       4      13 ..      37      46 ..      34      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.032
                       zf-RRN7  6 pCgvCgcrsftlddG 20
                                  +C vC+  +++ ++G
  gi|91772168|ref|YP_564860.1|  5 RCNVCNVFEYDDAEG 19
                                  7****9777777666 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0022
                       zf-RRN7  4 gppCgvCgcr 13
                                   + C++Cg++
  gi|91772168|ref|YP_564860.1| 37 DWKCPICGAD 46
                                  578*****94 PP

>> RbpA  RNA polymerase-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0002      0.21      27      59 ..      12      46 ..       2      51 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                          RbpA 27 vsYacakghet..evtfaaeaevPetwecrrcGke 59
                                   +Y  a+g++    v+  +  + P+ w+c+ cG+ 
  gi|91772168|ref|YP_564860.1| 12 FEYDDAEGNTElgIVPGTKPEDFPDDWKCPICGAD 46
                                  5677777764311344445569***********86 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 ?    6.6   0.6    0.0076       8.1       2       8 ..       4      10 ..       3      14 .. 0.91
   2 ?    4.0   0.1     0.048        51       3       9 ..      39      45 ..      38      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0076
                     zf-C2H2_6  2 heCsvCs 8 
                                  ++C+vC+
  gi|91772168|ref|YP_564860.1|  4 YRCNVCN 10
                                  9*****9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.048
                     zf-C2H2_6  3 eCsvCsk 9 
                                  +C++C++
  gi|91772168|ref|YP_564860.1| 39 KCPICGA 45
                                  7****97 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.2    0.0086       9.1       1       8 [.       4      11 ..       4      12 .. 0.91
   2 ?    4.0   0.1     0.068        72       1       6 [.      38      43 ..      38      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0086
                        zf-met  1 fyCelCnv 8 
                                  + C++Cnv
  gi|91772168|ref|YP_564860.1|  4 YRCNVCNV 11
                                  78*****8 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.068
                        zf-met  1 fyCelC 6 
                                  + C++C
  gi|91772168|ref|YP_564860.1| 38 WKCPIC 43
                                  89**** PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.9     0.022        23       1       7 [.       4      10 ..       4      13 .. 0.82
   2 ?    6.3   1.1    0.0077       8.1      15      22 ..      38      45 ..      38      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.022
                  Rubredoxin_2  1 YvCsqCG 7 
                                  Y+C+ C+
  gi|91772168|ref|YP_564860.1|  4 YRCNVCN 10
                                  8999996 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0077
                  Rubredoxin_2 15 GrCpsCgs 22
                                  ++Cp Cg+
  gi|91772168|ref|YP_564860.1| 38 WKCPICGA 45
                                  9*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 295.00
//
Query:       gi|91772169|ref|YP_564861.1|  [L=496]
Description: glutamate synthase (NADPH) GltB2 subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-92  310.6   0.0    1.9e-92  310.2   0.0    1.1  1  Glu_synthase  Conserved region in glutamate synthase
    5.3e-15   55.2   4.7    1.3e-14   54.0   4.7    1.7  1  Rubredoxin    Rubredoxin
    2.1e-07   30.3   0.2    9.2e-07   28.2   0.1    2.0  2  FMN_dh        FMN-dependent dehydrogenase
      2e-05   23.8   0.1      4e-05   22.8   0.1    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0015   17.9   0.6     0.0037   16.6   0.6    1.6  1  Vps36-NZF-N   Vacuolar protein sorting 36 NZF-N zinc-finger d
      0.003   17.6   0.4      0.003   17.6   0.4    2.0  2  Elf1          Transcription elongation factor Elf1 like
     0.0035   16.8   0.4      0.014   14.8   0.2    2.0  2  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.039   14.8   0.9        0.1   13.5   0.9    1.7  1  Ima1_N        Ima1 N-terminal domain
      0.086   12.3   0.0       0.16   11.4   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein
       0.18   11.3   0.1       0.27   10.7   0.1    1.2  1  LrgB          LrgB-like family
       0.19   11.9   5.6        1.3    9.2   2.6    2.9  2  Zn-ribbon_8   Zinc ribbon domain
       0.38   11.1   3.1        0.3   11.4   0.5    2.2  2  zf-Di19       Drought induced 19 protein (Di19), zinc-binding
       0.86    9.7   6.6       0.61   10.2   1.1    2.6  2  PHD_4         PHD-finger
        3.1    7.3   6.2         18    4.9   0.4    3.1  3  zf-ribbon_3   zinc-ribbon 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 !  310.2   0.0   1.5e-95   1.9e-92      53     366 ..     159     468 ..     112     470 .. 0.94

  Alignments for each domain:
  == domain 1  score: 310.2 bits;  conditional E-value: 1.5e-95
                                   --GGGS--HHHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHH CS
                  Glu_synthase  53 ikleevepalkikkriltsamSyGalseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLn 133
                                   i  +  +p l i++++ +++mS+Gals+e ++al+k+   + t++ +GEGG+ +e+++ta ++ i  + + ++ vtee L+
  gi|91772169|ref|YP_564861.1| 159 IGPHAKYP-LVIETPVFITHMSFGALSKEVKQALSKGSAAVRTAMCSGEGGILKENMETAYKY-IFEYVPNKYSVTEENLK 237
                                   55566666.78****************************************************.***************** PP

                                   H-SEEEEE---TTSTTS--EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEEEEEEE-ST CS
                  Glu_synthase 134 nakaleikiaQGakpgeGgqlpgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeakvsvKlvaea 214
                                   + +a+eiki+Q akpg+Gg+lp+eKv++e+a+iR+ ++ +d++SPa++ di++++dl++++e L+e +  +++++K++a++
  gi|91772169|ref|YP_564861.1| 238 KVDAIEIKIGQSAKPGMGGHLPAEKVTSELAEIRGFPESTDIVSPANFDDIRNKDDLKKKVEWLRETSGGKPIGIKIAAGN 318
                                   ********************************************************************************* PP

                                   THHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHH CS
                  Glu_synthase 215 gvetiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalal 295
                                    + ++++ +  a++d+i+idG  G T A+ k + + + +P++ al ++ + l e+g++d +sli++Gg++ + d +kalal
  gi|91772169|ref|YP_564861.1| 319 IEADLEV-AIYAKPDFITIDGRPGATAAALKFVKNSTSIPTIFALWRARRYLDEKGIKD-ISLIITGGFRISPDYAKALAL 397
                                   *******.999**********************************************86.9******************** PP

                                   T-SEEE-SHHHHHHTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT CS
                  Glu_synthase 296 GAdavgigtaalialgCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalg 366
                                   GAda+ igtaal+a  C++ r+C t++CpvGv+tqdpeLr rlk++ +a+++ n++k+ ++e++ ++   g
  gi|91772169|ref|YP_564861.1| 398 GADAIAIGTAALMACACQQYRLCDTGKCPVGVTTQDPELRSRLKIDISAKKLENFLKVSTKELEAFARLTG 468
                                   ***************************************************************99887666 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   4.7   9.9e-18   1.3e-14       2      45 ..       4      48 ..       3      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 9.9e-18
                                  EEETTT-.BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGG CS
                    Rubredoxin  2 yeCkvCg.yvYdpakGdpdegiapgTkFedlPddWvCPdCgveke 45
                                  y+C+vC+ ++Yd+ +Gd +++++pgTk ed PddW+CP Cg++k+
  gi|91772169|ref|YP_564861.1|  4 YRCNVCNvFEYDDTRGDSNTEMKPGTKPEDFPDDWRCPICGADKN 48
                                  9*****7589*********************************97 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.53   6.7e+02      57     136 ..     169     243 ..     129     246 .. 0.61
   2 !   28.2   0.1   7.2e-10   9.2e-07     252     310 ..     353     415 ..     265     418 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.53
                                   ESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCT CS
                        FMN_dh  57 lslPvliaPvglaklahpdgelalaraaakagipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaag 136
                                   +++Pv+i  +++  l + + + al ++ a+  + ++ ++      e++       + +  yvp++ ++tee lk++ a +
  gi|91772169|ref|YP_564861.1| 169 IETPVFITHMSFGALSK-EVKQALSKGSAAVRTAMCSGEG-GILKENMET--A-YKYIFEYVPNKYSVTEENLKKVDAIE 243
                                   44566666666666554.5666677777777777776665.333333333..2.23344477778888888888877765 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 7.2e-10
                                   TT---HHHCHHHHHHHH......SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHH CS
                        FMN_dh 252 dgapatidvLpeiveavgg....rievlvDgGirrGsDvlkAlalGAdavllGRpflyglaag 310
                                    ++++ti +L + ++++++    +i +++ gG+r   D +kAlalGAda+++G ++l++ a++
  gi|91772169|ref|YP_564861.1| 353 STSIPTIFALWRARRYLDEkgikDISLIITGGFRISPDYAKALALGADAIAIGTAALMACACQ 415
                                   578899999999999998666768***********************************9975 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   3.1e-08     4e-05     133     237 ..     295     406 ..     289     415 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.1e-08
                                   HHHHHHHHHHTT...T.SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHH.HHH.CSB---HHHHHHHHHHHHCTCT CS
                                   xxxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 133 leavkeikkkve...e.veviaGnvataegakaLieagadavkvGiGpGsiCtt.rvv.agvGvpqltAvaevaeaakkag 207
                                    ++v++++++       +++ aGn+      +  i a  d++ +   pG+     + v  ++ +p + A+ ++ ++ +++g
  gi|91772169|ref|YP_564861.1| 295 KKKVEWLRETSGgkpIgIKIAAGNIEA--DLEVAIYAKPDFITIDGRPGATAAAlKFVkNSTSIPTIFALWRARRYLDEKG 373
                                   566777777664333248889999965..45566778889999988888876542445157899***********999987 PP

                                   ...-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 208 ...vpviaDGGikysgdivkAlaaGadavmlGs 237
                                      + +i  GG + s d +kAla+Gada+ +G 
  gi|91772169|ref|YP_564861.1| 374 ikdISLIITGGFRISPDYAKALALGADAIAIGT 406
                                   44578999***********************97 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   2.9e-06    0.0037       4      47 ..      32      80 ..      29      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                   Vps36-NZF-N  4 eavtatWvCpICsfs.Ne.vpsnfdp...nastplPpClaCGvkpdlel 47
                                  e+   +W CpIC  + N+ +p + +      s+++  C+ CG k+ +++
  gi|91772169|ref|YP_564861.1| 32 EDFPDDWRCPICGADkNHqMPAEKKEvehVTSKEIVTCVKCGTKSKITV 80
                                  556679******996243144443336667899***********98875 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2         3   3.9e+03      21      28 ..       3      10 ..       1      13 [. 0.59
   2 !   17.6   0.4   2.3e-06     0.003      13      64 ..      29      85 ..      17      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                          Elf1 21 kFdCpfCn 28
                                  +++C +Cn
  gi|91772169|ref|YP_564861.1|  3 EYRCNVCN 10
                                  45566665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.3e-06
                          Elf1 13 kkkkklptkFdCpfCnheksvevkldkkek.....iaevsCkvCgesfetkvnalse 64
                                   k++ +p  ++Cp C+++k  ++  +kke      + +v+C +Cg++ +++v+al++
  gi|91772169|ref|YP_564861.1| 29 TKPEDFPDDWRCPICGADKNHQMPAEKKEVehvtsKEIVTCVKCGTKSKITVSALED 85
                                  44566999***************99999988999899***************99986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.75   9.6e+02     286     312 ..     182     208 ..     133     223 .. 0.67
   2 !   14.8   0.2   1.1e-05     0.014     193     231 ..     376     414 ..     369     422 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.75
                           NMO 286 elakkiraalveagnteegllwagqgi 312
                                    l k++++al+++  +  +++ +g+g+
  gi|91772169|ref|YP_564861.1| 182 ALSKEVKQALSKGSAAVRTAMCSGEGG 208
                                   455667777777777777777777766 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.1e-05
                           NMO 193 diPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkes 231
                                   di +i +GG+    + a aLalGA +++igt+ L++  +
  gi|91772169|ref|YP_564861.1| 376 DISLIITGGFRISPDYAKALALGADAIAIGTAALMACAC 414
                                   68899***************************9998766 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.9   7.8e-05       0.1      19     119 ..       3     108 ..       1     112 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-05
                        Ima1_N  19 sfeCpsCeayNgfdedGdindeipeqeeeslneaakkaaasksksks.......eeaessssssllCskClknqelkvskl 92 
                                   +++C+ C+ + + d +Gd n+e+++ ++ +  ++  ++    +++++       e ++ +s++ + C kC +++++ vs+l
  gi|91772169|ref|YP_564861.1|   3 EYRCNVCNVFEYDDTRGDSNTEMKPGTKPEDFPDDWRCPICGADKNHqmpaekkEVEHVTSKEIVTCVKCGTKSKITVSAL 83 
                                   69*******************999999888887766665555555556677765667778889999*************99 PP

                        Ima1_N  93 aeylpkededdpeyeekeealeeykke 119
                                   ++     +++  e +++++++e + ++
  gi|91772169|ref|YP_564861.1|  84 EDADV--KSYLGEWKRTKDEFETFMED 108
                                   98644..55555555566666666555 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.16      73     111 ..     376     414 ..     370     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                   SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THH CS
                  His_biosynth  73 fipvqvGGGIrsledveelleagadkviigtaavknpel 111
                                   +i + + GG r   d +++l +gad + igtaa+     
  gi|91772169|ref|YP_564861.1| 376 DISLIITGGFRISPDYAKALALGADAIAIGTAALMACAC 414
                                   48899***************************9976655 PP

>> LrgB  LrgB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00021      0.27     157     189 ..     384     416 ..     377     432 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                          LrgB 157 llrikdpvarGlalGtashaiGtakalelgeea 189
                                    +ri+ + a+ lalG+ + aiGta+++    ++
  gi|91772169|ref|YP_564861.1| 384 GFRISPDYAKALALGADAIAIGTAALMACACQQ 416
                                   6899999*******************9876665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.6     0.001       1.3       5      34 ..       3      45 ..       3      52 .. 0.77
   2 ?    2.2   0.1      0.15     2e+02      26      35 ..      65      75 ..      53      87 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                   Zn-ribbon_8  5 eYrCeeCghefe..........vlqsisdap...lta.CPeCgs 34
                                  eYrC+ C+ +fe          ++ + ++++   +   CP Cg+
  gi|91772169|ref|YP_564861.1|  3 EYRCNVCN-VFEyddtrgdsntEMKPGTKPEdfpDDWrCPICGA 45
                                  8*******.***99999998885555554436666667*****8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                   Zn-ribbon_8 26 lta.CPeCgse 35
                                  +++ C +Cg +
  gi|91772169|ref|YP_564861.1| 65 EIVtCVKCGTK 75
                                  44448888764 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 ?   -2.9   0.1       7.1   9.1e+03       3      10 ..       4      11 ..       2      18 .. 0.51
   2 ?   11.4   0.5   0.00023       0.3       3      41 ..      38      76 ..      36      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.1
                       zf-Di19  3 ftCPyCgk 10
                                  + C  C+ 
  gi|91772169|ref|YP_564861.1|  4 YRCNVCNV 11
                                  44555544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00023
                       zf-Di19  3 ftCPyCgkeltvkeLveHvedeHrveskevvCPvCaekv 41
                                    CP Cg + + +   e  e+eH  +++ v C  C +k+
  gi|91772169|ref|YP_564861.1| 38 WRCPICGADKNHQMPAEKKEVEHVTSKEIVTCVKCGTKS 76
                                  68******9999999******************998764 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1   0.00048      0.61      33      67 ..       6      43 ..       2      44 .. 0.72
   2 ?    6.7   3.7     0.006       7.6       4      37 ..      37      73 ..      34      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00048
                         PHD_4 33 CsvCyeivHpeClkek...egegvvnedlpnsWeCpkC 67
                                  C+vC+     +    +    ++g+  ed p +W+Cp C
  gi|91772169|ref|YP_564861.1|  6 CNVCNVFEYDDTRGDSnteMKPGTKPEDFPDDWRCPIC 43
                                  77776666655554443335678999***********9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.006
                         PHD_4  4 taaCivCgedgkedevv...eeesetpsslmeCsvCy 37
                                     C +Cg d ++++++   e e+ t++++++C  C 
  gi|91772169|ref|YP_564861.1| 37 DWRCPICGADKNHQMPAekkEVEHVTSKEIVTCVKCG 73
                                  56799********999865544567788899999996 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      0.72   9.2e+02       2       9 ..       3      10 ..       3      15 .. 0.89
   2 ?    4.9   0.4     0.014        18       4      10 ..      39      45 ..      38      48 .. 0.82
   3 ?    3.6   0.1     0.036        47       3      11 ..      67      75 ..      65      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.72
                   zf-ribbon_3  2 tvrCPnCG 9 
                                  ++rC+ C+
  gi|91772169|ref|YP_564861.1|  3 EYRCNVCN 10
                                  689****6 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                   zf-ribbon_3  4 rCPnCGa 10
                                  rCP CGa
  gi|91772169|ref|YP_564861.1| 39 RCPICGA 45
                                  7999997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.036
                   zf-ribbon_3  3 vrCPnCGap 11
                                  v+C +CG++
  gi|91772169|ref|YP_564861.1| 67 VTCVKCGTK 75
                                  689999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.56
# Mc/sec: 2687.72
//
Query:       gi|91772170|ref|YP_564862.1|  [L=92]
Description: fumarate hydratase class II [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   28.6   0.0      1e-06   28.4   0.0    1.0  1  Lyase_1   Lyase


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 !   28.4   0.0   5.6e-11     1e-06       1      66 [.      14      87 ..      14      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.6e-11
                                  CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHH CS
                       Lyase_1  1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegkl 66
                                  g+++v+ d ++g +t r + nf++s ++       a aa+k a a an+++     e+a+aii+a++ev+e g+l
  gi|91772170|ref|YP_564862.1| 14 GEIEVPEDVYYGPQTVRTINNFKISRQRLPssfirAQAAIKLASARANLEAgklePEIAKAIISAASEVRE-GNL 87
                                  799**********************666559999999999999999999999999**************99.765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 600.86
//
Query:       gi|91772171|ref|YP_564863.1|  [L=180]
Description: succinate dehydrogenase subunit B, partial [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   36.5   0.0    8.3e-09   35.4   0.0    1.6  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
     0.0032   17.9   0.5     0.0061   17.0   0.5    1.5  1  Fer4_8    4Fe-4S dicluster domain
     0.0054   16.8   0.7       0.01   15.9   0.7    1.5  1  Fer4_10   4Fe-4S dicluster domain
     0.0078   16.7   0.6      0.014   15.9   0.6    1.5  1  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.2   2.0      0.029   14.2   2.0    1.5  1  Fer4      4Fe-4S binding domain
      0.017   16.0   0.2      0.046   14.6   0.2    1.7  1  Fer4_16   4Fe-4S double cluster binding domain
      0.018   15.7   0.5      0.061   13.9   0.3    1.9  2  Fer4_7    4Fe-4S dicluster domain
      0.024   14.7   0.9      0.024   14.7   0.9    1.6  2  Fer4_21   4Fe-4S dicluster domain
       0.07   13.7   1.2       0.19   12.3   1.2    1.7  1  Fer4_4    4Fe-4S binding domain
       0.31   11.2   4.3       0.13   12.4   1.4    1.7  3  Fer4_9    4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> 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 !   35.4   0.0   4.7e-12   8.3e-09      62     108 ..       1      66 [.       1      67 [. 0.95

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4.7e-12
                        Fer2_3  62 vainGkptlaCtatikdlakqkse...................ieleplpkfpvirDLvvDideml 108
                                   + in  p+laC+ +i+++ k++++                   i +eplp+++virDLvvD+++++
  gi|91772171|ref|YP_564863.1|   1 MLINRIPRLACKMQISEMRKEPTNeenlevlitnkrteldnsvILIEPLPTLRVIRDLVVDMEPFY 66 
                                   789*****************9984689***********************************9986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   3.4e-06    0.0061       3      29 ..     101     127 ..      99     158 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldar 29 
                                    +Ci C +C  +Cpv+ + k+    a 
  gi|91772171|ref|YP_564863.1| 101 TNCILCALCHGSCPVAAKDKQYYGPAA 127
                                   69***********97776443333322 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.7   5.7e-06      0.01       5      28 ..      99     122 ..      95     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.7e-06
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvga 28 
                                   +   Ci C+ C  +CP+ ++ +++
  gi|91772171|ref|YP_564863.1|  99 QYTNCILCALCHGSCPVAAKDKQY 122
                                   5567*************5533333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   7.8e-06     0.014       1      47 [.     102     149 ..      77     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                       Fer4_17   1 rCiqCgyClpeCpsyeaydne..pkkllraaklglleeaekeekaslCi 47 
                                   +Ci C+ C  +Cp  ++ +++  p+ l++a+++  l+  ekee  ++Ci
  gi|91772171|ref|YP_564863.1| 102 NCILCALCHGSCPVAAKDKQYygPAALAKAWRFY-LDPREKEESKQECI 149
                                   6999999999999999988865688888888883.44555566666666 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.0   1.6e-05     0.029       6      22 ..     101     117 ..      99     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                   TTSSS-THHHHHSTTTE CS
                          Fer4   6 ekCigCGaCvevCPvgA 22 
                                     Ci C +C   CPv A
  gi|91772171|ref|YP_564863.1| 101 TNCILCALCHGSCPVAA 117
                                   57*************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   2.6e-05     0.046      30      66 ..      77     115 ..      64     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                       Fer4_16  30 cisyntaekkdlaedeekck..kqeaitgCdiCqdvCPa 66 
                                   ++++n++ek++l+++  + k  ++++++ C+ C   CP+
  gi|91772171|ref|YP_564863.1|  77 EMKENVPEKENLIDRDTQVKieQYTNCILCALCHGSCPV 115
                                   667788888888877765553266999***********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 ?   -1.5   0.0       2.2     4e+03      11      28 ..      10      27 ..       9      47 .. 0.70
   2 ?   13.9   0.3   3.4e-05     0.061      29      52 .]      93     117 ..      69     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.2
                        Fer4_7 11 aCpvkaieldeeenekgt 28
                                  aC+++  e+++e  ++++
  gi|91772171|ref|YP_564863.1| 10 ACKMQISEMRKEPTNEEN 27
                                  788888888876555543 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.4e-05
                        Fer4_7  29 ekvei.dpekClgCgaCvavCPtga 52 
                                    +v+i ++++C+ C  C   CP+ a
  gi|91772171|ref|YP_564863.1|  93 TQVKIeQYTNCILCALCHGSCPVAA 117
                                   5566624789************976 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9   1.4e-05     0.024      33      53 ..      94     115 ..      85     120 .. 0.67
   2 ?   -3.8   0.0       8.5   1.5e+04       7       9 ..     147     149 ..     142     154 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                       Fer4_21  33 vlkvv.edeCvGCnlCssvCPv 53 
                                   ++k+    +C+ C+lC+  CPv
  gi|91772171|ref|YP_564863.1|  94 QVKIEqYTNCILCALCHGSCPV 115
                                   4444324678888888888887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.5
                       Fer4_21   7 kCi 9  
                                   +Ci
  gi|91772171|ref|YP_564863.1| 147 ECI 149
                                   333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.2   0.00011      0.19       3      16 ..     102     115 ..     100     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +Ci C  C+ +CP+
  gi|91772171|ref|YP_564863.1| 102 NCILCALCHGSCPV 115
                                   8************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 ?   -3.3   0.0       6.2   1.1e+04      11      19 ..      10      18 ..       9      26 .. 0.59
   2 ?   12.4   1.4   7.3e-05      0.13      27      49 ..      94     116 ..      75     118 .. 0.68
   3 ?    9.3   2.8   0.00072       1.3       1      32 [.     102     133 ..     102     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.2
                        Fer4_9 11 aCpagvvve 19
                                  aC++++ ++
  gi|91772171|ref|YP_564863.1| 10 ACKMQISEM 18
                                  566665544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.3e-05
                        Fer4_9  27 rlraaseeaCigCgaCveaCpkg 49 
                                   +++++++++Ci C  C   Cp  
  gi|91772171|ref|YP_564863.1|  94 QVKIEQYTNCILCALCHGSCPVA 116
                                   233333389***********976 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00072
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraas 32 
                                   +C+ C  C+ +Cp  +  ++  +  a  +a++
  gi|91772171|ref|YP_564863.1| 102 NCILCALCHGSCPVAAKDKQYYGPAALAKAWR 133
                                   59999999999999888887777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1197.97
//
Query:       gi|91772172|ref|YP_564864.1|  [L=743]
Description: DNA topoisomerase I [Methanococcoides burtonii DSM 6242]
Scores for complete 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-124  414.6   0.0     6e-124  414.2   0.0    1.2  1  Topoisom_bac     DNA topoisomerase
    3.6e-15   56.0   0.3    9.3e-15   54.7   0.3    1.7  1  Toprim           Toprim domain
    2.2e-13   49.7   2.2    2.2e-13   49.7   2.2    2.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    5.6e-05   23.7   0.1    0.00016   22.2   0.1    1.8  1  HHH_5            Helix-hairpin-helix domain
    0.00017   21.3   0.0    0.00052   19.8   0.0    1.7  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00047   20.3   0.0     0.0011   19.1   0.0    1.6  1  Cdd1             Pathogenicity locus
    0.00069   19.8   0.0     0.0021   18.3   0.0    1.9  1  IMS_HHH          IMS family HHH motif
  ------ inclusion threshold ------
      0.019   15.1   0.2       0.16   12.1   0.1    2.4  2  TfoX_C           TfoX C-terminal domain
      0.041   14.4   0.8        0.1   13.1   0.8    1.7  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.042   13.7   0.0       0.13   12.2   0.0    1.9  1  HHH              Helix-hairpin-helix motif
      0.084   13.1   0.1       0.18   12.1   0.1    1.5  1  DUF4332          Domain of unknown function (DUF4332)
       0.15   12.3   0.1       0.42   10.9   0.1    1.8  1  DUF2283          Protein of unknown function (DUF2283)


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 !  414.2   0.0    4e-127    6e-124       2     412 ..     156     557 ..     155     558 .. 0.95

  Alignments for each domain:
  == domain 1  score: 414.2 bits;  conditional E-value: 4e-127
                  Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekkek 80 
                                   i+++l+da+++R+++D+++G++l+r+l+ ++ +  k +ls+GRVq+ptLaliv++e+e+++Fv+++ywev+atlk++++  
  gi|91772172|ref|YP_564864.1| 156 IDFDLADAGHSRQVIDLVWGASLTRYLSISAGRlgKLFLSVGRVQSPTLALIVDKEKERQAFVSKPYWEVNATLKDNDDAL 236
                                   7899************************95555658999***********************************8888887 PP

                  Topoisom_bac  81 ekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYekagli 161
                                     + ++k++++++keea+a++e + + +a v+sv++++k+++ p+pf+tt++  +as++ g++a+++++ia++LY++ g+i
  gi|91772172|ref|YP_564864.1| 237 V-NVQHKNSKFWEKEEADAVMEVIGD-KASVSSVDSSKKTDKVPTPFNTTEFIGAASSI-GFTASNAMRIAESLYTN-GFI 313
                                   5.9*********************55.6******************************8.****************7.*** PP

                  Topoisom_bac 162 tYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkelsddekklYel 242
                                   +YpRTd+t+++ + +l+a +e ++k   + ++e+a+kll+k +   ++++k++++H++I+P  +l+k++el+++++klYel
  gi|91772172|ref|YP_564864.1| 314 SYPRTDNTVYPASIDLRAQIEIFSKG--P-FREYAQKLLAKDELVPTRGKKETTDHPPIYPA-SLAKKSELNEQDWKLYEL 390
                                   *************77*********96..4.88999999987664448889999*********.777679************ PP

                  Topoisom_bac 243 IvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkTkpp 323
                                   +vrrf+a+++++a++e+++v++++++eefka+g +++ +G++ +y+++  +++   lp+l+eg++++v++ e+ +k+T+pp
  gi|91772172|ref|YP_564864.1| 391 VVRRFFATFADEAEWETMKVRFDISGEEFKANGARLVHQGWRWYYPYNAPQDRL--LPALSEGDILDVTGKEMLDKETQPP 469
                                   ***************************************************986..************************* PP

                  Topoisom_bac 324 kryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTaeleekLdeIae 403
                                    ry +++Lik+me+ g+Gt+aTr+eii+kl++r Yv+ +   l+pt++++a++e+lek+ +++++ ++T++lee++d Iae
  gi|91772172|ref|YP_564864.1| 470 GRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYVHGNP--LQPTKTSFAVIEALEKYaPTITKHDMTSQLEEDMDSIAE 548
                                   **************************************66..**************9999********************* PP

                  Topoisom_bac 404 gkadakevl 412
                                   gk ++++vl
  gi|91772172|ref|YP_564864.1| 549 GKVKEDNVL 557
                                   *****9998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.3   6.2e-18   9.3e-15       2     101 ..       3     139 ..       2     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 6.2e-18
                                   EEEESSHHHHHHHHHTHT......................STEEEEEEESSSSEEEHS.....TTEEEEE........... CS
                        Toprim   2 lvivEgpsdaktiakalg......................sgfqavtaslGhildlet.....efkpvye........... 44 
                                   l+i+E+  +ak iak+l                       ++  +v+ ++Ghi++l++     +     +           
  gi|91772172|ref|YP_564864.1|   3 LIIAEKHIAAKRIAKILApkepkqvrvsgmdtfeyknpdaEDRIIVMGLSGHIVQLDFpkaynN-----Wqkidanelida 78 
                                   8***************************************99****************665551.....044444666667 PP

                                   ...ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEES CS
                        Toprim  45 ...eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefs 101
                                        ++  k+++al++l k+a ++ +atD DreGe i+ e+l+ +++ +++ ++ rv+ s
  gi|91772172|ref|YP_564864.1|  79 eviTTPTHVKIVAALRKLGKEATHVTIATDYDREGELIGVEALNIIRKVNPDvEFDRVFYS 139
                                   66699999999999*****************************999988888777777665 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 !   49.7   2.2   1.5e-16   2.2e-13       2      38 ..     593     630 ..     592     631 .. 0.95
   2 ?    0.6   0.2      0.34     5e+02       4      34 ..     663     670 ..     661     675 .. 0.59

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.5e-16
                                   EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                   ++C +Cg++L+++r+k+G +F+GC+ YP+C+f  +l+k
  gi|91772172|ref|YP_564864.1| 593 GECSECGSKLMVRRSKRGsRFIGCNGYPDCNFSLPLPK 630
                                   79*********************************998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                                   -SSS--EEEEEE-SSSEEEEESST.T----E CS
                zf-C4_Topoisom   4 CPkCggdLvlkrgkkGkFvGCsnYPeCkftk 34 
                                   CP+                       C+f++
  gi|91772172|ref|YP_564864.1| 663 CPQ-----------------------CNFIE 670
                                   555.......................55555 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.1e-07   0.00016       3      40 ..     690     727 ..     688     734 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                                   HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTS CS
                         HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLaki 40 
                                   ++++v+GiG++tA +l +a i+++++l +a++ eL+k+
  gi|91772172|ref|YP_564864.1| 690 KITDVPGIGKVTAEKLKNAEINTIDELRQANAIELSKA 727
                                   689***************************99999886 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 !   19.8   0.0   3.4e-07   0.00052       4      38 ..     692     727 ..     690     730 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.4e-07
               DNA_pol_lambd_f   4 tkvyGVGpktAkkwyakGirtledlra.krakLtre 38 
                                   t v G+G +tA+k+ ++ i t+++lr+ + ++L+++
  gi|91772172|ref|YP_564864.1| 692 TDVPGIGKVTAEKLKNAEINTIDELRQaNAIELSKA 727
                                   7899***********************766999876 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   7.4e-07    0.0011       7      49 ..     690     732 ..     687     737 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.4e-07
                          Cdd1   7 elqdiPniGkalaedlvelGirsveelkgedpeelyekleklt 49 
                                   +++d+P+iGk +ae+l +  i++++el++ ++ el ++ +  +
  gi|91772172|ref|YP_564864.1| 690 KITDVPGIGKVTAEKLKNAEINTIDELRQANAIELSKATSLPA 732
                                   789*******************************998876655 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.4e-06    0.0021      12      30 ..     690     708 ..     690     710 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                       IMS_HHH  12 pitkipGiGgklgekLekl 30 
                                   +it++pGiG++++ekL++ 
  gi|91772172|ref|YP_564864.1| 690 KITDVPGIGKVTAEKLKNA 708
                                   59**************975 PP

>> TfoX_C  TfoX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0         1   1.5e+03      24      43 ..      87     106 ..      79     112 .. 0.84
   2 ?   12.1   0.1    0.0001      0.16       3      36 ..     689     722 ..     687     727 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                        TfoX_C  24 IktveeLrelGaveaylkik 43 
                                   +k v++Lr+lG ++ ++ i 
  gi|91772172|ref|YP_564864.1|  87 VKIVAALRKLGKEATHVTIA 106
                                   677999*****999998875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                        TfoX_C   3 nrLkdLpNlglklerlLkkaGIktveeLrelGav 36 
                                   +++ d+p +g+ +++ Lk+a+I+t++eLr+  a+
  gi|91772172|ref|YP_564864.1| 689 DKITDVPGIGKVTAEKLKNAEINTIDELRQANAI 722
                                   7899*************************98776 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   6.8e-05       0.1       8      32 ..     595     619 ..     592     651 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
               Zn_ribbon_recom   8 CgeCGspmtrrkrkgkrhyYrCsty 32 
                                   C eCGs++ +r++k++ +   C++y
  gi|91772172|ref|YP_564864.1| 595 CSECGSKLMVRRSKRGSRFIGCNGY 619
                                   ************9999999999998 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.7e-05      0.13      11      27 ..     689     705 ..     688     708 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
                                   HHHHTSTT-SHHHHHHH CS
                           HHH  11 eeLlalPGVGpktAeaI 27 
                                   + ++++PG+G+ tAe+ 
  gi|91772172|ref|YP_564864.1| 689 DKITDVPGIGKVTAEKL 705
                                   56899**********87 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012      0.18       1      52 [.     695     741 ..     695     743 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                       DUF4332   1 pgigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanl 52 
                                   pgigk  aekLk+a i+t ++L ++++ e ++     ++ + + ++ k+++l
  gi|91772172|ref|YP_564864.1| 695 PGIGKVTAEKLKNAEINTIDELRQANAIELSK-----ATSLPAGKIMKWQEL 741
                                   7999******************9997665555.....778888899998876 PP

>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00028      0.42      30      47 ..     105     122 ..      96     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                       DUF2283  30 iilDfDedGrlvGIEiLn 47 
                                   i  D+D++G+l+G+E Ln
  gi|91772172|ref|YP_564864.1| 105 IATDYDREGELIGVEALN 122
                                   668************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (743 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 5296.01
//
Query:       gi|91772173|ref|YP_564865.1|  [L=411]
Description: beta-lactamase-like [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-12   48.0   0.0    2.6e-12   47.0   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    1.5e-10   40.8   0.1    8.8e-10   38.4   0.0    2.2  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    2.4e-09   37.0   0.1    4.4e-09   36.1   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.8e-07   31.4   0.8    0.00012   22.2   0.2    2.4  2  Lactamase_B    Metallo-beta-lactamase superfamily
      3e-06   26.8   0.0    9.8e-06   25.1   0.0    1.9  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    6.1e-05   23.0   0.1    0.00018   21.4   0.1    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0021   18.0   0.1      0.011   15.7   0.0    1.9  2  Endopep_inhib  IseA DL-endopeptidase inhibitor


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0     1e-15   2.6e-12      21     108 ..     233     327 ..     221     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1e-15
                                   S-EEEEE-HHHHHHHHHGGGGGG..............E-SHH....HHHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHH CS
                     Beta-Casp  21 klpiyldsplaskatevYkeyae..............veakslewmeskkeelnsskgpkvilassgmlegGrsrellkkl 87 
                                    +p y+d+ ++ ++ ++  +++e                    + ++ +k+  n + +  vi+++ gml+gG++ +++++l
  gi|91772173|ref|YP_564865.1| 233 GIPAYVDG-MGVRIYKLLMNHPEylkdpeklkhafdnA-----TIVKGRKR-ENIPLNGTVIVTTAGMLNGGPVLHYINRL 306
                                   37999999.99999999888888987777664442221.....22222222.34556889********************* PP

                                   TTSTTSEEEESS---TTSHHH CS
                     Beta-Casp  88 ledprntvilvgyqaegTlgr 108
                                    +dp++ ++l+gyq+egT gr
  gi|91772173|ref|YP_564865.1| 307 YTDPKSKIMLTGYQVEGTNGR 327
                                   *******************98 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.95   2.4e+03      30      46 ..      43      59 ..      39      65 .. 0.81
   2 !   38.4   0.0   3.4e-13   8.8e-10       4      62 .]     344     403 ..     342     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.95
                         RMMBL 30 kprnvilvHGeeeatsa 46
                                   p+ v + HG+ +++ a
  gi|91772173|ref|YP_564865.1| 43 HPKAVLISHGHLDHCGA 59
                                  58889999**9888876 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 3.4e-13
                         RMMBL   4 vkarieeidfSgHadknellelirklkprn...vilvHGeeeatsalarllkeeegidvfiP 62 
                                   ++++ie++dfS+H++  el+ +++ +  +    v+  HGe   t+++a++ ++e g+++++P
  gi|91772173|ref|YP_564865.1| 344 IRMKIEQYDFSAHSGDKELKAMVSEFCDKGgekVFAMHGEN--TEQFAQWVTDEIGVEAYAP 403
                                   89***************************************..9*******9999****998 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 !   36.1   0.1   1.7e-12   4.4e-09      28     174 ..      41     191 ..      23     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.7e-12
                                   ..SEEEEE-SS--HHHHGGGGCCCC......C--EE...EEEEEEHHHHHHCCTTCGHHHCHTT............TTEEE CS
                 Lactamase_B_2  28 lppidaVllthaHyDHlaglltlre......lrpkk...lplyapkgvlavleanfvylaleee............pavnv 87 
                                     + +aVl++h+H DH+  ++ l        ++p     ++++  k++l++ e++                       +n+
  gi|91772173|ref|YP_564865.1|  41 YVHPKAVLISHGHLDHCGAVPNLMDmdpelfMTPPTadlAQVL-AKDTLKIAERE--------GtsipfdereiqqMVLNT 112
                                   467799***********99999999333443222222322222.23333344443........233333333587888888 PP

                                   EEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE- CS
                 Lactamase_B_2  88 heldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip....eeigerlggadlllldi 164
                                   +++d+g +f+ +  g + ++  a h  g           +  +e++gk+++y+gD  + +    +  +++l  ad l+ + 
  gi|91772173|ref|YP_564865.1| 113 RTFDTGVEFHTH--GYTAQFYNAGHIPGS---------SAIYLEKDGKSIVYTGDISTQEtylvP-SADELPEADALITES 181
                                   999999988888..778888888887777.........99999**************77755533.45799********** PP

                                   S-SSTTHHHH CS
                 Lactamase_B_2 165 tayeddemir 174
                                   t++ +d + r
  gi|91772173|ref|YP_564865.1| 182 TYFGEDHPTR 191
                                   ****999876 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   4.6e-08   0.00012      19      65 ..      24      64 ..      15      67 .. 0.77
   2 !    7.4   0.0    0.0016       4.1     125     155 ..     131     161 ..      82     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.6e-08
                                  EES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCT CS
                   Lactamase_B 19 LiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglv 65
                                  L+D G+ + ++ +        ++   ++av+++H+HlDH+G+++ l+
  gi|91772173|ref|YP_564865.1| 24 LVDYGLKPGEEPLY------PVDYVHPKAVLISHGHLDHCGAVPNLM 64
                                  55555555555554......46666799****************997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                                   HECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                   Lactamase_B 125 vtggpghghghgvveygggkvlftGDallag 155
                                      g+ +g++ + +e +g+++++tGD + ++
  gi|91772173|ref|YP_564865.1| 131 YNAGHIPGSSAIYLEKDGKSIVYTGDISTQE 161
                                   56799*********************99744 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 !   25.1   0.0   3.8e-09   9.8e-06       8     167 ..      22     162 ..      17     181 .. 0.77
   2 ?   -2.9   0.0       1.5     4e+03     102     141 ..     258     294 ..     246     302 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.8e-09
                 Lactamase_B_6   8 kiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlya 88 
                                   +iL+D G +      e+ l +++ v p   ++L+sh  l+h Ga + l+        ++ + + t p++ L++v+  d+ +
  gi|91772173|ref|YP_564865.1|  22 EILVDYGLKPG----EEPLYPVDYVHP--KAVLISHGHLDHCGAVPNLM-------DMDPELFMTPPTADLAQVLAKDTLK 89 
                                   68888888876....445666666655..69************965444.......568899****************988 PP

                 Lactamase_B_6  89 skgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhake 167
                                    ++ +g+  s  ++  +i+++  +  t  +   +e+++  +g t   ynaGh +G +   ++k  ++ivY  d++ +  
  gi|91772173|ref|YP_564865.1|  90 IAEREGT--SIPFDEREIQQMVLN--TRTFDTGVEFHT--HGYTAQFYNAGHIPGSSAIYLEKDGKSIVYTGDISTQET 162
                                   6655433..345666666666554..555777887775..79999**************************99987654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                 Lactamase_B_6 102 eledideafdkiktlkYsQklelkskldgltitaynaGht 141
                                   + e+ ++afd+ + +k   + +++ +   ++     aG  
  gi|91772173|ref|YP_564865.1| 258 DPEKLKHAFDNATIVKGRKRENIPLNGTVIVT---TAGML 294
                                   45778888999888888888777754443333...34555 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 !   21.4   0.1   7.1e-08   0.00018      17     119 ..      21     162 ..      15     180 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.1e-08
                 Lactamase_B_3  17 arilvDPfka...nlgyeppaeeaDlvlisqaledHahl.etlkql.................aenvkvlee......... 67 
                                    +ilvD++ +   +  y  + +++ +vlis+++ dH+ + ++l  +                 a       +         
  gi|91772173|ref|YP_564865.1|  21 DEILVDYGLKpgeEPLYPVDYVHPKAVLISHGHLDHCGAvPNLMDMdpelfmtpptadlaqvlA-------Kdtlkiaere 94 
                                   579*****6555566677777***************9651444444888888888844444441.......3333333334 PP

                 Lactamase_B_3  68 geslevggleiravatsh.................davggsergenngflleqdgltiyhlGhlahels 119
                                   g s+ +++ ei+++  ++                     g+ +g   ++l e+dg +i++ G+++++ +
  gi|91772173|ref|YP_564865.1|  95 GTSIPFDEREIQQMVLNTrtfdtgvefhthgytaqFYNAGHIPGSSAIYL-EKDGKSIVYTGDISTQET 162
                                   33344444444444333333434434333333222122466668777775.67899*******998644 PP

>> Endopep_inhib  IseA DL-endopeptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.43   1.1e+03      37      97 ..      97     160 ..      79     167 .. 0.65
   2 !   15.7   0.0   4.1e-06     0.011      59     104 ..     300     345 ..     297     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.43
                                   EEEETTEEEEE--TTSSSHHHHHHHHTTTB-HHHHHHHH...HTTT-EEETTEEEEE------- CS
                 Endopep_inhib  37 sievkgkeYaklkddintkeklfnYLneyfTkeaiekii...kdlkfkeidgklavpvgdggsl 97 
                                   si  +++e + +  +  t +  +++ +  +T ++ +++    ++  + e dgk  v  gd+++ 
  gi|91772173|ref|YP_564865.1|  97 SIPFDEREIQQMVLNTRTFDTGVEFHTHGYTAQFYNAGHipgSSAIYLEKDGKSIVYTGDISTQ 160
                                   5555566666666677777777778888888888888762223455778888888888888776 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.1e-06
                                   HHHHTTTB-HHHHHHHHHTTT-EEETTEEEEE-------B-GGG-E CS
                 Endopep_inhib  59 fnYLneyfTkeaiekiikdlkfkeidgklavpvgdggslldikkak 104
                                     Y n  +T+ +++ +++ ++++  +g++a   g++++   i++ +
  gi|91772173|ref|YP_564865.1| 300 LHYINRLYTDPKSKIMLTGYQVEGTNGRMALDTGNIDNDGIIQNIR 345
                                   57***********************************987777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.43
# Mc/sec: 2895.31
//
Query:       gi|91772174|ref|YP_564866.1|  [L=181]
Description: hypothetical protein Mbur_0098 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  107.2   1.2    6.1e-31  106.3   1.2    1.5  1  DUF2148     Uncharacterized protein containing a ferredoxin d
    2.7e-05   23.7   2.4    8.1e-05   22.2   2.4    1.9  1  FeS         Putative Fe-S cluster
  ------ inclusion threshold ------
      0.086   12.4   0.0       0.14   11.7   0.0    1.3  1  LDcluster4  SLOG cluster4 family


Domain annotation for each model (and alignments):
>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   1.2     1e-34   6.1e-31       2      68 .]     115     180 ..     114     180 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 1e-34
                       DUF2148   2 gplCafkaiDlGiAlgsavkvaadlrvDnRvmysvGaaAkslgllkeasvvlgiplsvsgKsifFDR 68 
                                   gp+Cafk+iDlGiAlgsa+++a+dl++DnR+my++Ga+A + gl++ a++++g+pls++gK+ifFDR
  gi|91772174|ref|YP_564866.1| 115 GPKCAFKYIDLGIALGSAAAKAKDLCIDNRIMYTIGAGALAAGLFD-ADIACGMPLSIKGKNIFFDR 180
                                   9*********************************************.*******************9 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   2.4   1.4e-08   8.1e-05       3      17 ..      89     103 ..      87     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                           FeS   3 gtNCgaCGypgCmaf 17 
                                   g+NCgaCG+p+C+++
  gi|91772174|ref|YP_564866.1|  89 GLNCGACGFPTCKEM 103
                                   89**********975 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.14      52     106 ..      27      83 ..      16      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                    LDcluster4  52 akeagGltvGilpassekehsnkyvdiiiyT...GlglagRnlilvlssdvviaiggr 106
                                   ak ++ ++ G+l  ++ k  +n+ +d +      G+g+  Rn  +v+ +d+vi+ig +
  gi|91772174|ref|YP_564866.1|  27 AKGKDSIVTGLLEPTDIKILANS-MDAMAEKkgeGFGFFNRNSQNVRDADAVILIGLK 83 
                                   44445567777777666666666.66655546669*******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1209.09
//
Query:       gi|91772175|ref|YP_564867.1|  [L=295]
Description: serine/threonine protein kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-39  134.9   0.1    3.3e-39  134.5   0.1    1.2  1  RIO1      RIO1 family
    1.5e-25   89.2   0.3    3.6e-25   88.0   0.1    1.8  2  Rio2_N    Rio2, N-terminal
    6.4e-05   22.4   0.6      0.021   14.2   0.1    2.5  2  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family
      0.002   17.5   0.0     0.0039   16.6   0.0    1.5  1  Pkinase   Protein kinase domain
  ------ inclusion threshold ------
      0.032   14.1   0.0       0.22   11.4   0.0    1.9  2  APH       Phosphotransferase enzyme family
       0.13   11.9   0.1       0.39   10.3   0.1    1.9  2  FTA2      Kinetochore Sim4 complex subunit FTA2


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.1   1.1e-42   3.3e-39      11     184 ..     123     284 ..     107     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 1.1e-42
                                   EEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EET CS
                          RIO1  11 kevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefiged 91 
                                   + v+iK+++ ++t+Fk++k+ ++  +     +++ ++ + ++l+a++Ef+++++l+++ +++Pkp++++rh++vm   +  
  gi|91772175|ref|YP_564867.1| 123 ATVIIKFHREGRTSFKSVKRGREHLAY----REHFSWIYAARLSAKREFDIMEQLYSE-ISIPKPLDYNRHAIVMAPAK-- 196
                                   4799****************9999888....689***********************9.*****************999.. PP

                                   TEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHHHHHH CS
                          RIO1  92 gvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDvenii 172
                                   g  ++k k +e     + ++ee+l++m+k+    g++H DLSeyN++v+e++v +ID++Q+v+ldh na+++L+rD  n+ 
  gi|91772175|ref|YP_564867.1| 197 GSLLVKTKLTE----PNWVLEEILSQMAKVH-SLGIIHSDLSEYNIFVSEEGVEFIDWPQYVTLDHLNAEDLLRRDAFNVL 272
                                   99888888877....7789******999988.************************************************* PP

                                   HHHHTTC----- CS
                          RIO1 173 kfFrrkgvekvd 184
                                   + F+rk+  + d
  gi|91772175|ref|YP_564867.1| 273 THFKRKYNIEKD 284
                                   *****9976555 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.1   1.2e-28   3.6e-25       1      82 []       9      90 ..       9      90 .. 0.98
   2 ?   -3.2   0.0       3.5     1e+04      24      39 ..     210     225 ..     206     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1.2e-28
                        Rio2_N  1 lryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvkr 82
                                  +r+L+++d+r+L ++E+gm+++e+Vp+e++ +++r + ++++++l +l++ ++++ ++++y+GY++ + GyD+LAL+t+vkr
  gi|91772175|ref|YP_564867.1|  9 FRQLDSKDLRILMGIEIGMKHYEWVPVEEVRKYTRFSYSQLEYKLLQLFRSNMVVGTKTPYEGYQIYFDGYDALALNTFVKR 90
                                  589*****************************************************************************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.5
                        Rio2_N  24 vVptelieeisrlkee 39 
                                   +V +e +++++++++ 
  gi|91772175|ref|YP_564867.1| 210 WVLEEILSQMAKVHSL 225
                                   6667777777776643 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       1.9   5.8e+03      10      40 ..      32      61 ..      28      62 .. 0.71
   2 !   14.2   0.1   6.9e-06     0.021      45     161 ..     149     244 ..     124     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.9
                           Kdo 10 vveeaegRrttwfvvaekvnaalrkyyrggl 40
                                  +v   e R+ t+f+  +  + +l +++r ++
  gi|91772175|ref|YP_564867.1| 32 WVPVEEVRKYTRFSYSQL-EYKLLQLFRSNM 61
                                  555566788888888777.888888888766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.9e-06
                           Kdo  45 skdlyrfk.lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrall 124
                                   +++++++  + r+ a rEf+++++L++  + +pkp+ ++  ++        ++   +g   +++ l+          +  l
  gi|91772175|ref|YP_564867.1| 149 YREHFSWIyAARLSAKREFDIMEQLYS-EISIPKPLDYNRHAI--------VMAPAKGSLLVKTKLT--------EPNWVL 212
                                   678888888888888888888888887.488888887765443........3333333333333333........345566 PP

                           Kdo 125 kavgrliaklhragvnHadlyaknillqqeeeeeaei 161
                                   +++   +ak h++g+ H dl   ni++ +e+     +
  gi|91772175|ref|YP_564867.1| 213 EEILSQMAKVHSLGIIHSDLSEYNIFVSEEG-----V 244
                                   6777778899999999999999999999987.....4 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-06    0.0039     103     137 ..     211     244 ..     157     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEE CS
                       Pkinase 103 iakqilegleylHskgiiHrDlKpeNiLidekgel 137
                                   ++++il+ ++ +Hs giiH Dl   Ni+++e+g +
  gi|91772175|ref|YP_564867.1| 211 VLEEILSQMAKVHSLGIIHSDLSEYNIFVSEEG-V 244
                                   67899*************************554.4 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.2   6.1e+02      34      61 ..     160     186 ..     128     194 .. 0.87
   2 ?   11.4   0.0   7.5e-05      0.22     156     199 ..     215     256 ..     194     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHTT-B--B-CTTB CS
                           APH  34 aeeirrevallrlLakagvpvPevlagd 61 
                                     ++ re++++ +L    +++P++l++ 
  gi|91772175|ref|YP_564867.1| 160 RLSAKREFDIMEQLYSE-ISIPKPLDYN 186
                                   578899*********99.99*****974 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.5e-05
                                   HHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---.TT-EEE CS
                           APH 156 laallpgelptvllHgDlhpgNllvdpddgrvtGviDf.edaglg 199
                                   ++  +++  + +++H Dl+  N+ v  ++g    +iD+ ++++l 
  gi|91772175|ref|YP_564867.1| 215 ILSQMAKVHSLGIIHSDLSEYNIFVS-EEGVE--FIDWpQYVTLD 256
                                   444444456799**************.55555..9***6666665 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.2   3.7e+03      50      81 ..       6      41 ..       5      49 .. 0.62
   2 ?   10.3   0.1   0.00013      0.39     177     203 ..     211     237 ..     125     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                          FTA2 50 LKlFrfleaeele....eaeedlkiprealkelasy 81
                                  +KlFr+l+ ++l+     + ++++ ++  ++e+++y
  gi|91772175|ref|YP_564867.1|  6 VKLFRQLDSKDLRilmgIEIGMKHYEWVPVEEVRKY 41
                                  799999988887777774444444444444444444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                          FTA2 177 qlpkllrdlkklhklgIvvrDlkeeny 203
                                    l+++l+++ k+h+lgI++ Dl+e n+
  gi|91772175|ref|YP_564867.1| 211 VLEEILSQMAKVHSLGIIHSDLSEYNI 237
                                   5789******************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1956.38
//
Query:       gi|91772176|ref|YP_564868.1|  [L=130]
Description: hypothetical protein Mbur_0100 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  115.1   2.4    1.4e-33  114.8   2.4    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 !  114.8   2.4     8e-38   1.4e-33       2      83 .]      23     103 ..      22     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 8e-38
                       DUF2111   2 helvgklPvtirsknkkGvriekgkvvdedYtgpvLeevleegkvikkvpkeGaYkGvpvvvaPikekegkviaaiGvVDi 82 
                                   h ++g +P+tirskn +G+r+e+g v+d++YtgpvLeev+ ++k+i+k+p+eG+YkG++vvvaPi+++ g+v++a+GvVD+
  gi|91772176|ref|YP_564868.1|  23 HGVLG-IPITIRSKNLRGLRMERGVVMDDNYTGPVLEEVILTNKIIRKIPTEGVYKGKAVVVAPIRTSGGEVVGALGVVDL 102
                                   78888.**************************************************************************8 PP

                       DUF2111  83 t 83 
                                   +
  gi|91772176|ref|YP_564868.1| 103 V 103
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 837.23
//
Query:       gi|91772177|ref|YP_564869.1|  [L=306]
Description: thioredoxin reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-44  150.3   2.6    7.7e-44  150.1   2.6    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    7.3e-27   94.4   1.0      5e-19   68.7   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      7e-14   52.2   6.4    8.4e-13   48.7   0.2    3.0  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    9.4e-08   31.2   1.9      0.004   15.9   0.1    3.1  3  HI0933_like    HI0933-like protein
    1.4e-07   30.9   4.4      2e-05   23.8   0.5    3.4  4  FAD_binding_2  FAD binding domain
    8.4e-07   28.9   6.4      0.021   14.4   1.9    3.0  3  DAO            FAD dependent oxidoreductase
    1.8e-06   27.6   6.0    8.7e-05   22.0   1.0    2.4  2  FAD_oxidored   FAD dependent oxidoreductase
    6.3e-06   25.5   3.9    0.00035   19.8   0.2    3.1  3  GIDA           Glucose inhibited division protein A
    2.5e-05   23.7   1.2      0.005   16.1   0.2    2.3  2  FAD_binding_3  FAD binding domain
    0.00018   21.7   2.2    0.00062   19.9   0.2    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00044   19.6   5.2     0.0062   15.8   0.5    2.5  2  Thi4           Thi4 family
     0.0029   16.8   0.8       0.15   11.2   0.0    2.3  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.014   15.8   1.6      0.038   14.4   0.2    2.3  2  NAD_binding_7  Putative NAD(P)-binding
      0.047   12.1   0.0      0.065   11.6   0.0    1.2  1  FMO-like       Flavin-binding monooxygenase-like
       0.33   10.0   2.3        5.5    5.9   0.2    2.8  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 !  150.1   2.6   6.4e-47   7.7e-44       1     294 []       3     287 ..       3     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 150.1 bits;  conditional E-value: 6.4e-47
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCCHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgielllge 73 
                                   +d+++iGgGp+Gl+a +++ ++g++++++  e+ ++ g+++ +  +++++++++i          e+ k   +g+ +   +
  gi|91772177|ref|YP_564869.1|   3 YDLIIIGGGPGGLSAGIYAVRYGLNTLVL--EKGFVSGQISTTGDVENYPGFPSIGGmelmdkfaEHAK--AAGVVVED-R 78 
                                   689**********************7777..999*******************9999*77755543322..22333333.4 PP

                                   TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiG 154
                                    v+++ + ++++k+ +++egd   i++ ++++AtG++p+ lgipG++e  gk+v++++++++     ++  ++vvGgG  +
  gi|91772177|ref|YP_564869.1|  79 DVLEV-RSEGDMKIVHTSEGD---IEASSVIIATGAEPKHLGIPGEEEFRGKGVSYCATCDGPFFSGRN--VIVVGGGESA 153
                                   79999.666799998888665...***************************************999988..********** PP

                                   HHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE....EEE.EEETTSCEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxx RF
                   Pyr_redox_2 155 vElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge....kle.vvledgeeidad 229
                                   +  A  l+++++ v +v++rd+l       +s++l+++  ++ ++e+ +gt+ +ei g++      ++     +  +++ d
  gi|91772177|ref|YP_564869.1| 154 ITDALILSDMAASVCVVHRRDELR------ASKILQDRAFARsNIEFLWGTTLEEIVGDSVvreaVIRdINAAEVCRVPID 228
                                   ***********************7......8999998766666*****************95543333555555555**** PP

                                   EEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 230 lvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                    v+v vGv+pst      + +  d+ g+i ++e+++ + +g++a+GD+     +++++++A + G
  gi|91772177|ref|YP_564869.1| 229 GVFVYVGVKPST----GFVDVDKDKYGFIITNERMECSEKGVFAVGDCR--NAILRQVVTAASDG 287
                                   ***********9....5679999**************************..99*******99876 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 !   23.8   1.0   1.9e-08   2.2e-05       1      34 [.       6      38 ..       6      43 .. 0.89
   2 !   68.7   0.0   4.2e-22     5e-19      82     305 .]      59     270 ..      47     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.9e-08
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                  iIiG+GP Gl+a+i + + gl + l+lEkg ++ 
  gi|91772177|ref|YP_564869.1|  6 IIIGGGPGGLSAGIYAVRYGL-NTLVLEKGFVSG 38
                                  8********************.689*****7654 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 4.2e-22
                   Pyr_redox_3  82 ealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkef 159
                                   e+++ ++e ak   + + ++ +V +v +e++  +v+ts++++eA++viiAtG    P+ l+ipGee+   + + y    + 
  gi|91772177|ref|YP_564869.1|  59 ELMDKFAEHAKAAGV-VVEDRDVLEVRSEGDMKIVHTSEGDIEASSVIIATGA--EPKHLGIPGEEEfrgKGVSYCATCDG 136
                                   555555666666666.77899*******************************9..***********864445555555566 PP

                   Pyr_redox_3 160 hkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeike 240
                                     ++g++v+V+Gg++Sa+  Al l ++ a+V vv+r++e+++++   +    +  ++++e l+ ++  +++ ++ v+e   
  gi|91772177|ref|YP_564869.1| 137 PFFSGRNVIVVGGGESAITDALILSDMAASVCVVHRRDELRASKILQDR---AFARSNIEFLWGTTLEEIVGDSVVRE--- 211
                                   5688**********************************99998644443...34444444443332123445544433... PP

                   Pyr_redox_3 241 keeeykvktedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                     +  ++++++  +v +  d v++ +G kp++ f++   +++d+ g   +t+e +e   +g+f +G
  gi|91772177|ref|YP_564869.1| 212 -AVIRDINAAEVCRVPI--DGVFVyVGVKPSTGFVD---VDKDKYG-FIITNERMECSEKGVFAVG 270
                                   .3344566666444444..4444449*********9...5554444.5677788999999999998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.029        35       2      29 ..       5      32 ..       4      35 .. 0.89
   2 ?    0.2   0.1      0.98   1.2e+03      11      63 ..      57     112 ..      55     122 .. 0.64
   3 !   48.7   0.2     7e-16   8.4e-13       1      74 [.     143     210 ..     143     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.029
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvve 29
                                  ++++GgG  gl ++ ++ ++g ++ v+e
  gi|91772177|ref|YP_564869.1|  5 LIIIGGGPGGLSAGIYAVRYGLNTLVLE 32
                                  68******************99887776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.98
                                   HHHHHHHHHHTTSEE.EEEESSSSSS..TTSSHHHHHHHHHHHHHTTEEEECSEEE CS
                     Pyr_redox  11 glElAgalaelgkkV.tvversdkll..rllDeeaskilqeklekngievllntkv 63 
                                   g+El   +ae++k    vve +d l   +  D ++    +  +e+  + + +++++
  gi|91772177|ref|YP_564869.1|  57 GMELMDKFAEHAKAAgVVVEDRDVLEvrSEGDMKIVHTSEGDIEASSVIIATGAEP 112
                                   67777788888777745666666665634445556666666666666666666665 PP

  == domain 3  score: 48.7 bits;  conditional E-value: 7e-16
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgve 74 
                                   +v+vvGgG +++  A +l++++++V vv+r+d+l+      askilq++  ++ +ie+l++t++eei+g++  v+
  gi|91772177|ref|YP_564869.1| 143 NVIVVGGGESAITDALILSDMAASVCVVHRRDELR------ASKILQDRAFARsNIEFLWGTTLEEIVGDSV-VR 210
                                   599********************************......********97777**************9987.55 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   0.1   3.3e-06     0.004       2      33 ..       4      35 ..       3      45 .. 0.87
   2 !   10.3   0.0   0.00017       0.2     110     164 ..      59     110 ..      52     115 .. 0.81
   3 ?    3.1   0.1     0.027        32       2      35 ..     143     176 ..     142     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                  d+i+iGgG+ Gl a i a + g ++l+lek+ 
  gi|91772177|ref|YP_564869.1|  4 DLIIIGGGPGGLSAGIYAVRYGLNTLVLEKGF 35
                                  89***************************984 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                   HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                   +++d + +++k+agv ++ +++v +v++e d    v+t se+ +ea+++++AtG 
  gi|91772177|ref|YP_564869.1|  59 ELMDKFAEHAKAAGVVVE-DRDVLEVRSEGDM-KIVHT-SEGDIEASSVIIATGA 110
                                   677888899999999886.5689999665555.88899.9*************97 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.027
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                   +viv+GgG + +  A+ +++  ++V ++ + ++l
  gi|91772177|ref|YP_564869.1| 143 NVIVVGGGESAITDALILSDMAASVCVVHRRDEL 176
                                   79************************99887765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.5   1.7e-08     2e-05       1      35 [.       4      38 ..       4      44 .. 0.91
   2 ?    1.7   0.0     0.089   1.1e+02     160     204 ..      66     113 ..      57     141 .. 0.66
   3 !    5.2   0.1    0.0076         9       2      35 ..     144     177 ..     143     217 .. 0.91
   4 ?   -3.2   0.0       2.8   3.4e+03     379     404 ..     256     275 ..     253     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.7e-08
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                  D+i+iG+G +GL+A++ a + Gl+++v+ek+++ g
  gi|91772177|ref|YP_564869.1|  4 DLIIIGGGPGGLSAGIYAVRYGLNTLVLEKGFVSG 38
                                  89*****************************9844 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.089
                                   ESEEEEEEEECTTEEEEEEEEETTTTCEE.....EEEESEEEE-----GG CS
                 FAD_binding_2 160 erteadeLivedgrvtGavvenpesgrev.....rirakavvlatgGfgr 204
                                   e+++a+ ++ved++v  +  e   ++++v      i+a  v++atg+ ++
  gi|91772177|ref|YP_564869.1|  66 EHAKAAGVVVEDRDVLEVRSE--GDMKIVhtsegDIEASSVIIATGAEPK 113
                                   444555555555555555444..33333344555899********98765 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0076
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                   viV+G+G +  + Al +++  ++v+vv   +e +
  gi|91772177|ref|YP_564869.1| 144 VIVVGGGESAITDALILSDMAASVCVVHRRDELR 177
                                   9**************************9887765 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 2.8
                                   ETTSBESTTEEESSBTEEE-STCEES CS
                 FAD_binding_2 379 dengrvldadgqpipGLYAaGevaag 404
                                   +e+++         +G +A+G + ++
  gi|91772177|ref|YP_564869.1| 256 NERMEC------SEKGVFAVGDCRNA 275
                                   555555......5689*****99865 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.9   1.7e-05     0.021       1      36 [.       4      42 ..       4      46 .. 0.85
   2 !   13.9   0.0   2.5e-05      0.03     147     205 ..      59     113 ..      49     137 .. 0.75
   3 ?    1.0   0.2       0.2   2.4e+02       2      32 ..     144     176 ..     143     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SG CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.ga 36
                                  d++iiGGG  Gls+  ++ r g  +++lekg   g+  +
  gi|91772177|ref|YP_564869.1|  4 DLIIIGGGPGGLSAGIYAVRYGlnTLVLEKGFVSGQiST 42
                                  789****************************55554444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH CS
                           DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd 205
                                   +l+  +a+ a+a+Gv +  +  v +++  +g+ + v  +t+ g + +a  v++a+Ga  +
  gi|91772177|ref|YP_564869.1|  59 ELMDKFAEHAKAAGVVVEDR-DVLEVRS-EGDMKIV--HTSeGDI-EASSVIIATGAEPK 113
                                   689999*******9977777.****954.5666666..6666764.3466******9865 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.2
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdia 32 
                                   v+++GGG   ++ A+ L+     V+++ ++d++
  gi|91772177|ref|YP_564869.1| 144 VIVVGGGESAITDALILSDMAasVCVVHRRDEL 176
                                   9****************7443469999999775 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.0   7.3e-08   8.7e-05       1      39 [.       4      42 ..       4      80 .. 0.83
   2 !    8.0   0.2    0.0013       1.6       2      34 ..     144     176 ..     143     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.3e-08
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                  D++++GGgp+G+ A i A r G ++l++e+  v G  +t
  gi|91772177|ref|YP_564869.1|  4 DLIIIGGGPGGLSAGIYAVRYGLNTLVLEKGFVSGQIST 42
                                  99************************9998766554444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvl 34 
                                   v+VvGGg + ++ A+    + a+v++v++r+ l
  gi|91772177|ref|YP_564869.1| 144 VIVVGGGESAITDALILSDMAASVCVVHRRDEL 176
                                   9****************************9865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2     3e-07   0.00035       1      58 [.       4      80 ..       4      85 .. 0.90
   2 ?    3.3   0.1      0.03        35     119     150 ..      81     110 ..      69     131 .. 0.67
   3 ?    3.3   0.1      0.03        36       1      32 [.     143     173 ..     143     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3e-07
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE........ES-GGGTT--SSSSEEE-T...........THHHHHHHHHH CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi........thkldtiaelsCnpsiggi...........akgllvrEida 58
                                  d+i+iGgG  G+ A + a r G+++l +           ++++ + +  psigg+           a+g +v++ d 
  gi|91772177|ref|YP_564869.1|  4 DLIIIGGGPGGLSAGIYAVRYGLNTLVLekgfvsgqISTTGDVENYPGFPSIGGMelmdkfaehakAAGVVVEDRDV 80
                                  689********************************9999***************99888888888888888877665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.03
                                   EEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA 119 eeliveekkvkgvvtedgetikakavviatGt 150
                                    e+   e+ +k +v +++  i+a++v+iatG+
  gi|91772177|ref|YP_564869.1|  81 LEVRS-EGDMK-IVHTSEGDIEASSVIIATGA 110
                                   44422.44444.4555556799*********8 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.03
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkl 32 
                                   +viV+GgG + +  Al ++ + a+v  + h+ 
  gi|91772177|ref|YP_564869.1| 143 NVIVVGGGESAITDALILSDMAASVCVV-HRR 173
                                   59**********************9988.444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   4.2e-06     0.005       3      32 ..       4      33 ..       2      99 .. 0.91
   2 !    6.6   0.0    0.0034       4.1       3      35 ..     143     175 ..     142     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                  d +I+G+Gp Gl+++    ++G +++++ek
  gi|91772177|ref|YP_564869.1|  4 DLIIIGGGPGGLSAGIYAVRYGLNTLVLEK 33
                                  679**************************9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0034
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                   +V++VG+G + ++ al+Ls    +v++v +r++
  gi|91772177|ref|YP_564869.1| 143 NVIVVGGGESAITDALILSDMAASVCVVHRRDE 175
                                   69*******************9******99976 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   5.2e-07   0.00062       1      38 [.       7      43 ..       7      71 .. 0.80
   2 ?    1.1   0.1      0.39   4.7e+02       1      30 [.     146     175 ..     146     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.2e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  I+G+G +Gl+a  ++ ++g++ l+lek+  ++G++++ 
  gi|91772177|ref|YP_564869.1|  7 IIGGGPGGLSAGIYAVRYGLNTLVLEKG-FVSGQISTT 43
                                  9**************************9.556666654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.39
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                   +vG+G s+ + A  L++  ++v ++ +rd 
  gi|91772177|ref|YP_564869.1| 146 VVGGGESAITDALILSDMAASVCVVHRRDE 175
                                   8*********99999998888888877765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   5.2e-06    0.0062      17      54 ..       2      38 ..       1      46 [. 0.87
   2 !    5.3   0.3    0.0084        10      18      49 ..     142     172 ..     137     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.2e-06
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                  + D++i+G+G+ GL+a+ y  +  +l++++le+    G
  gi|91772177|ref|YP_564869.1|  2 VYDLIIIGGGPGGLSAGIYAVRY-GLNTLVLEKGFVSG 38
                                  67*****************9998.********976655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0084
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                          Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailer 49 
                                    +v++vG+G s +t a +l+      v+++ r
  gi|91772177|ref|YP_564869.1| 142 RNVIVVGGGESAITDALILSDM-AASVCVVHR 172
                                   589****************998.778888766 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.021        25       2      34 ..       2      32 ..       1      35 [. 0.77
   2 !   11.2   0.0   0.00012      0.15     132     230 ..      80     178 ..      59     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.021
                   K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalfle 34
                                  ++Dli+iG Gp  Ls  i +      l++l+le
  gi|91772177|ref|YP_564869.1|  2 VYDLIIIGGGPGGLSAGIYAVRYG--LNTLVLE 32
                                  79**********999776655544..7777776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                   K_oxygenase 132 lltveskd....aegeeeelearnlvlgvGtepk...iPevleklegkervvHsseylerkeellakkriaVvGsGqSaae 205
                                   +l+v+s+      + +e  +ea ++++++G epk   iP   e ++g + v   ++         ++++++VvG+G Sa  
  gi|91772177|ref|YP_564869.1|  80 VLEVRSEGdmkiVHTSEGDIEASSVIIATGAEPKhlgIPGEEE-FRG-KGVSYCATCDGP---FFSGRNVIVVGGGESA-- 153
                                   4555443322223456778899999999999986333554433.332.444444444443...5899***********9.. PP

                   K_oxygenase 206 ifedllrrqkkvelklvtrsealep 230
                                   i++ l+ +  ++++ +v r+++l++
  gi|91772177|ref|YP_564869.1| 154 ITDALILSDMAASVCVVHRRDELRA 178
                                   8999999999999**9999998876 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 ?    0.3   0.1      0.78   9.3e+02      12      49 ..       7      41 ..       4     113 .. 0.47
   2 ?   14.4   0.2   3.2e-05     0.038       5      44 ..     139     176 ..     138     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.78
                 NAD_binding_7 12 vvGgGevAarkvrklleagakvtvvapevkeeleelvk 49
                                  ++GgG+ +++     +++g +  v+ +    +++++++
  gi|91772177|ref|YP_564869.1|  7 IIGGGPGGLSAGIYAVRYGLNTLVLEKG---FVSGQIS 41
                                  6666666666555555555555555444...3332222 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.2e-05
                 NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeel 44 
                                   ++g++v+vvGgGe A + +  l +  a v vv  +   el
  gi|91772177|ref|YP_564869.1| 139 FSGRNVIVVGGGESAITDALILSDMAASVCVVHRRD--EL 176
                                   689*****************************9984..22 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05     0.065     158     260 ..     116     218 ..      78     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                      FMO-like 158 sfpGiekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGswvlsrvsdsGypwdmllvtrf 238
                                     pG e+f+G+ +      +   f+g+ v+v+G G+s+   a  ls +a+ v +  r+     s++ ++       +   +
  gi|91772177|ref|YP_564869.1| 116 GIPGEEEFRGKGVSYCATCDGPFFSGRNVIVVGGGESAITDALILSDMAASVCVVHRRDELRASKILQDRAFARSNIEFLW 196
                                   579********999988899999*******************************999998888888766555555555556 PP

                      FMO-like 239 ksllknilptalsnwlvekkln 260
                                    + l++i++ +++   v + +n
  gi|91772177|ref|YP_564869.1| 197 GTTLEEIVGDSVVREAVIRDIN 218
                                   6666666666666666666666 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0046       5.5       1      32 [.       4      33 ..       4      39 .. 0.81
   2 ?    2.2   0.0     0.062        74      95     145 ..      66     113 ..      48     132 .. 0.72
   3 ?   -0.6   0.1      0.43   5.1e+02       2      34 ..     144     174 ..     143     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0046
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                  D+++iG+Gp gls        ++gl+ +++e 
  gi|91772177|ref|YP_564869.1|  4 DLIIIGGGPGGLSAGIYA--VRYGLNTLVLEK 33
                                  9***********966555..778888777765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.062
                 Lycopene_cycl  95 erlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                   e+   +gv   +  v +v+ e +    +v   +  i+a+ v+ a+g a++k
  gi|91772177|ref|YP_564869.1|  66 EHAKAAGVVVEDRDVLEVRSEGD--MKIVHTSEGDIEASSVIIATG-AEPK 113
                                   45555677777777888887777..6677777778***********.5555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.43
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasp 34 
                                   v+v+G+G   +  A  l  + ++ +v+++   +
  gi|91772177|ref|YP_564869.1| 144 VIVVGGGESAITDALIL--SDMAASVCVVHRRD 174
                                   89*****9999988888..88888999886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2111.67
//
Query:       gi|91772178|ref|YP_564870.1|  [L=80]
Description: hypothetical protein Mbur_0102 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-12   47.1   0.0    2.1e-12   46.9   0.0    1.1  1  Thioredoxin_3  Thioredoxin domain
    4.1e-06   26.9   0.0    5.4e-06   26.5   0.0    1.1  1  Glutaredoxin   Glutaredoxin
    0.00024   21.0   0.1    0.00028   20.8   0.1    1.1  1  Thioredoxin    Thioredoxin
    0.00058   20.1   0.1      0.018   15.4   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
     0.0064   16.9   0.0     0.0066   16.8   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.025   14.4   0.0    1.2  1  DSBA           DSBA-like thioredoxin domain
      0.083   13.3   0.3       0.38   11.2   0.3    1.9  1  Thioredoxin_2  Thioredoxin-like domain


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 !   46.9   0.0     8e-16   2.1e-12       5      75 ..       7      79 ..       1      80 [] 0.81

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 8e-16
                                  EESSSSTTCHHHHHHHHHHCHCCTCEC.EEECC.TTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                 Thioredoxin_3  5 vlgpgCakCpklekavkeaaaekgika.evekv.tdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                  v  + C+ Cp+++k+++++ +  ++++ ev+    + e++ e+y +msvP+++idgkv ++G vp++e+  ++l
  gi|91772178|ref|YP_564870.1|  7 VHASWCHVCPAAKKLWQSLKEGHDFDYdEVDFDtPEGEKLaEEYSIMSVPTTIIDGKVAFVG-VPNKEKAVSML 79
                                  23555**************9999999955554434556779*********************.*****987766 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.1e-09   5.4e-06       2      59 ..       5      64 ..       2      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.1e-09
                                  EEEESTSSHHHHHHHHHHHHTT..GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                  Glutaredoxin  2 vlftkptCpyCkkakrlLkelg..vkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59
                                  +l   ++C  C++ak+l ++l+   +f++ +vd d  + e+l e   +++vP+  idgk+
  gi|91772178|ref|YP_564870.1|  5 ILVHASWCHVCPAAKKLWQSLKegHDFDYDEVDFDTPEGEKLAEEYSIMSVPTTIIDGKV 64
                                  555669************9988775566666666668889999999************97 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.1e-07   0.00028      22      78 ..       4      60 ..       2      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                                  EEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                   Thioredoxin 22 lveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78
                                  ++   A+wC  C a +  +++l+e +  +   +  d+ e e+la++y++ ++Pt ++
  gi|91772178|ref|YP_564870.1|  4 VILVHASWCHVCPAAKKLWQSLKEGHDFDYDEVDFDTPEGEKLAEEYSIMSVPTTII 60
                                  55668*******77777777777666656666666777899*************855 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.038        98       6      21 ..       5      20 ..       2      30 .. 0.68
   2 !   15.4   0.0   6.9e-06     0.018      59      88 ..      31      60 ..      18      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.038
                                  EEE--SSSHHHHHHHH CS
                 Thioredoxin_8  6 Lyfgaswcppckaftp 21
                                  + ++aswc+ c a  +
  gi|91772178|ref|YP_564870.1|  5 ILVHASWCHVCPAAKK 20
                                  568999***9965444 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.9e-06
                                  TTSEE.EE-TT-HHHHTT-S--TT-SEEEE CS
                 Thioredoxin_8 59 kpwlsvpfddkkrnklkkkynvkaiPtlvv 88
                                  ++  +v+fd ++ +kl+++y ++++Pt+++
  gi|91772178|ref|YP_564870.1| 31 FDYDEVDFDTPEGEKLAEEYSIMSVPTTII 60
                                  577899*********************987 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.6e-06    0.0066       2      48 ..       4      52 ..       3      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                                  EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETT..T-CCCHCCCCT CS
                        DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIa..kdeeleakYgl 48
                                  ++L     Ch+C  ak++ + lk+ ++++ +++D +  ++e+l ++Y  
  gi|91772178|ref|YP_564870.1|  4 VILVHASWCHVCPAAKKLWQSLKEGHDFDYDEVDFDtpEGEKLAEEYSI 52
                                  78888889****************************7666779999975 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.7e-06     0.025     148     187 ..      35      74 ..      13      80 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.7e-06
                                   HHHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHH CS
                          DSBA 148 avkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrldt 187
                                   +v  +  e +++a+++ +  vPt+++dgk++++G+++ ++
  gi|91772178|ref|YP_564870.1|  35 EVDFDTPEGEKLAEEYSIMSVPTTIIDGKVAFVGVPNKEK 74 
                                   55556667899******************99999987665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00015      0.38      12      89 ..       7      63 ..       2      79 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                 Thioredoxin_2 12 ftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldg 89
                                  +++++C  C + kk  ++l            k+  ++ + +++ +         + e ++la++y + ++Pt+++  +
  gi|91772178|ref|YP_564870.1|  7 VHASWCHVCPAAKKLWQSL------------KEGHDFDYDEVDFD---------TPEGEKLAEEYSIMSVPTTIIDGK 63
                                  5555555555544422222............22223333333333.........445588************987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 525.13
//
Query:       gi|91772179|ref|YP_564871.1|  [L=316]
Description: hypothetical protein Mbur_0103 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00017   21.8   0.2    0.00042   20.5   0.2    1.6  1  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
     0.0019   18.5   0.1     0.0053   17.0   0.0    1.7  2  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
       0.03   14.6   0.3       0.16   12.3   0.2    2.2  2  DUF4878      Domain of unknown function (DUF4878)


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 !   20.5   0.2   6.9e-08   0.00042       4      62 ..     226     283 ..     223     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.9e-08
                   NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtpp 62 
                                   G++v +++ v+n  +++ +n  + +++P G + v++++ s+  + pGe+v+ t+kVtp+
  gi|91772179|ref|YP_564871.1| 226 GQSVGVDVWVKNFYQQPYENFVIIATFPTGVN-VKKATLSFGNINPGESVKRTWKVTPN 283
                                   999*****************************.999999999***************95 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.99   5.9e+03      54      54 ..     130     130 ..      81     159 .. 0.53
   2 !   17.0   0.0   8.9e-07    0.0053       9      80 ..     222     284 ..     209     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.99
                         DUF11  54 t 54 
                                   +
  gi|91772179|ref|YP_564871.1| 130 S 130
                                   1 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 8.9e-07
                         DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                   +  +G+ v + + v+N ++++ ++ v+  t P+g++  +++ s         +g++++ges + + +v++++
  gi|91772179|ref|YP_564871.1| 222 QCPSGQSVGVDVWVKNFYQQPYENFVIIATFPTGVNVKKATLS---------FGNINPGESVKRTWKVTPNV 284
                                   56689*******************************9999999.........78999999999888888775 PP

>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.7e-05      0.16      10      51 ..      35      73 ..      24     132 .. 0.74
   2 ?    0.0   0.1      0.17     1e+03      57      92 ..     124     159 ..      92     170 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                       DUF4878 10 eeavknFleavkeGdvedaikyltestreedalaeklkgkfk 51
                                  +++v nFl++++eG+++ a +y   ++ +     e    +fk
  gi|91772179|ref|YP_564871.1| 35 NDTVLNFLNSFNEGEFDTAFSYYVGNDFKVPVSLEG---MFK 73
                                  689*******************98877666555544...444 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                       DUF4878  57 aekkkekqgnlkeveikdeeesgdtAvvtVkvtlkd 92 
                                      k+ +q+ +++v     + + dtA ++V+v  + 
  gi|91772179|ref|YP_564871.1| 124 RTQKSGSQWIITKVNFDTPISQSDTALINVTVSPTH 159
                                   556667777777777777777778898888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2273.20
//
Query:       gi|91772180|ref|YP_564872.1|  [L=259]
Description: flagellin [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-32  113.3  12.7    1.9e-32  112.7  12.7    1.3  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
        8.9    6.6   5.9        5.2    7.3   1.0    2.8  3  DUF2749         Protein of unknown function (DUF2749)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7  12.7   2.2e-36   1.9e-32       1     161 [.      14     241 ..      14     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 2.2e-36
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.....EEE-SSSSSEEEEEEE-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.....dsatngtineitiyvkln 76 
                                   ++ gigtlI+fIAmVlVAAvaa vli+t+g lq++aqstg+++ ++vss+l i g+ g      ++t++t++ + + v+ln
  gi|91772180|ref|YP_564872.1|  14 AQAGIGTLIIFIAMVLVAAVAAAVLIQTSGVLQERAQSTGKQAAQEVSSNLLIKGIEGvrasgSGTTSETVDLLKVKVALN 94 
                                   689*****************************************************99988877777777777******** PP

                                   TTS--EEGGG-EEEEEESS.--EE--E...................................................... CS
                Arch_flagellin  77 aGsspidlnkttisvtddg.qetlltad.......................................efgivvisdtdgsl 117
                                    Gss+idln+++i+vtd +  + l++a                                         f++  i d+d s+
  gi|91772180|ref|YP_564872.1|  95 IGSSEIDLNQVVITVTDGDsINDLVYAGnskaygdamtnfsstassaanmivlatenttdmgnnsrfFFTVEQIRDEDESF 175
                                   *******************555566665*************************************9999************ PP

                                   ...T-EE-TT-EEEEEEE--......................TTT---TT-EEEEEEE-SSS--EE CS
                Arch_flagellin 118 tngdevlekgekvelevnvn......................eddgitagdevsvevvpenGastt 161
                                   ++  +++++g++v + + +                           + ++++v++ ++pe G++t+
  gi|91772180|ref|YP_564872.1| 176 SQAEPIMNQGDLVNIYISTVsttasagshttldevalsglkdSGITVSPRSTVNLILTPEAGSTTS 241
                                   *****************9878999999999999999999965333466888888889999999887 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.0   0.00059       5.2       5      38 ..      22      58 ..      19      68 .. 0.64
   2 ?   -3.9   0.0       1.8   1.6e+04      36      50 ..     166     180 ..     163     181 .. 0.77
   3 ?    0.1   0.1       0.1   9.2e+02      20      34 ..     227     241 ..     219     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00059
                       DUF2749  5 ilIvlviavaagagtil...wlvvqpragtsgsgeaq 38
                                  i+ + +++vaa+a+ +l     v+q ra + g ++aq
  gi|91772180|ref|YP_564872.1| 22 IIFIAMVLVAAVAAAVLiqtSGVLQERAQSTGKQAAQ 58
                                  3334445577666665411145788888888888877 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.8
                       DUF2749  36 eaqRehrerFfgadk 50 
                                   e+ R++ e F +a++
  gi|91772180|ref|YP_564872.1| 166 EQIRDEDESFSQAEP 180
                                   566889999988775 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.1
                       DUF2749  20 ilwlvvqpragtsgs 34 
                                    + l++ p+ag+ +s
  gi|91772180|ref|YP_564872.1| 227 TVNLILTPEAGSTTS 241
                                   577999***998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1510.33
//
Query:       gi|91772181|ref|YP_564873.1|  [L=262]
Description: hypothetical protein Mbur_0105 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        4.6    7.2  31.7          6    6.8  31.7    1.1  1  HisKA_7TM       N-terminal 7TM region of histidine kinase


Domain annotation for each model (and alignments):
>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  31.7   0.00034         6       3     208 ..      13     225 ..       9     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00034
                     HisKA_7TM   3 lisallslvlaiyaw......rrrskpg..araflllllavalw.slgyalellattl...eakllwaklqylgivfipv. 70 
                                   +++a++sl +a ++       +++skp+  a   ++ll+++  + +   al+++a+ l   +  + ++++  ++++f+ v 
  gi|91772181|ref|YP_564873.1|  13 FAIAVISLTFAWVLAknenleKQNSKPTlyALITFWLLVSFTYYpT---ALRMIAAYLdnaQVDIAMYYIASIPFAFVSVp 90 
                                   5667777777766645766654455666444444444444444443...55555555410055555555655555555552 PP

                     HisKA_7TM  71 lwllfaleytgkrrwltrrrlallll.vpvltlilvltnpl.hhlf..yvsagsfvvlefehGplf.wvhlaysyllliag 146
                                   + ++++   tg++   ++ ++ ++++ + + +l+++ltn+    l+  +   +s+  ++ +  +    + l+++ + +i+g
  gi|91772181|ref|YP_564873.1|  91 VAYFIIYVITGNK-QASS-YVSIIFAmFGASYLMFLLTNRVvEPLVtyW---SSIININSNIAINIyLIGLFVIPTAMILG 166
                                   3333444566653.3344.44445554889999999**99734455535...44444444333333134555667788999 PP

                     HisKA_7TM 147 vvlliralirssglyrrqalllligllvPwlanllyllglsplpgidltplafaltglllai 208
                                   ++lli  l++ s++ r +++lll+++ + + + l  +  ++++  + +++  f+l g +la+
  gi|91772181|ref|YP_564873.1| 167 ILLLI-LLRKISKKIRYRTVLLLVSISFVIDFMLTDM--ITTFDMLQFVARIFVLIGTVLAY 225
                                   99999.8999****************99643333333..34444567777788888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1685.08
//
Query:       gi|91772182|ref|YP_564874.1|  [L=120]
Description: hypothetical protein Mbur_0106 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.4   0.1       0.61   10.3   0.0    2.1  2  Mrr_N     Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.033   5.8e+02       7      26 ..      33      54 ..      30      60 .. 0.81
   2 ?   10.3   0.0   3.4e-05      0.61      61      82 ..      72      93 ..      68      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.033
                         Mrr_N  7 plLealad..gsehrlkeirer 26
                                   +L +l++  g+++  +eire+
  gi|91772182|ref|YP_564874.1| 33 LILLVLKKneGKITEFAEIREY 54
                                  5788898888999999999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 3.4e-05
                         Mrr_N 61 LkkagllespkrgvwkiTekGr 82
                                   + +gl ++ +rg + iTe+G 
  gi|91772182|ref|YP_564874.1| 72 FQLEGLAKKIQRGGYIITERGL 93
                                  56689****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 769.18
//
Query:       gi|91772183|ref|YP_564875.1|  [L=271]
Description: indole-3-glycerol phosphate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  226.1   1.8    4.4e-67  225.9   1.8    1.0  1  IGPS           Indole-3-glycerol phosphate synthase
    1.4e-06   27.7   3.8    8.8e-05   21.8   0.0    3.4  4  NanE           Putative N-acetylmannosamine-6-phosphate epime
    0.00022   20.8   0.1    0.00037   20.0   0.1    1.4  1  His_biosynth   Histidine biosynthesis protein
    0.00054   19.5   0.8    0.00086   18.8   0.1    1.7  2  PcrB           PcrB family
    0.00065   19.1   0.0     0.0017   17.7   0.0    1.7  1  ThiG           Thiazole biosynthesis protein ThiG
     0.0009   18.5   0.0     0.0036   16.6   0.0    2.0  2  DHO_dh         Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.018   15.4   0.4       0.11   12.9   0.3    2.4  2  Radical_SAM    Radical SAM superfamily
      0.059   12.4   0.0       0.14   11.2   0.0    1.6  2  FMN_dh         FMN-dependent dehydrogenase
      0.095   11.9   0.0       0.23   10.7   0.0    1.7  1  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like


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 !  225.9   1.8   2.2e-70   4.4e-67       4     254 .]       8     262 ..       5     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 225.9 bits;  conditional E-value: 2.2e-70
                                   CHHHHHHHHHHHHCCS-GGCCCCG..-SS-SS-HHHHCHCH..TTS-EEEEEE-SEETTTEESBSS.--HHHHHHHHTTT. CS
                          IGPS   4 ivaekkeevaeakkrqsladleaavklakpkrsfaeaLres..ekklaliaEvKkaSPskglired.fdpaeiAkkyeeag 81 
                                   i+++++++v++  ++++   l+ +   ++   +++ea++++  + k+ +iaEvK aSPs   ++    ++ +iA ++e+ag
  gi|91772183|ref|YP_564875.1|   8 IINSTEKRVKALYEAEDHPILKGD---TQGIEKIIEAIHSKkdSGKVPIIAEVKPASPSMKIMDISpEEAGKIAMDMENAG 85 
                                   555556666665555554444444...3556677788877766899*************9887654136789********* PP

                                   -SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEE CS
                          IGPS  82 AsaiSVLteekyFqGsledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevL 162
                                   A aiSVLte+++F+Gs+++L++vr+a+slpvlrKdFiid++q +e   + +d+iLLi+ +l +++ eel e+a+s ++e+L
  gi|91772183|ref|YP_564875.1|  86 AIAISVLTEPEFFEGSIDNLKAVREAISLPVLRKDFIIDKVQFDE---VRSDLILLIAGLLGEKL-EELIEYARSKEFEPL 162
                                   ********************************************6...568********999875.*************** PP

                                   EEESSHHHHHHHH.HTT-SEEEEESEETTTTEE-CHHHHHHCHCC-.......TTSEEEEESSS-SHHHHHHHCCTT-SEE CS
                          IGPS 163 vEvhdeeeleral.klgakiiGvNnRnLktlevdlntteeLaklvp.......kdvllvaeSGiktredveklkeegvnaf 235
                                   vEvh++eel+ +l ++ aki+G+NnR+L+tlevd+ tteeL++ ++       ++ l+++eSG++t+ed++++ ++g++a+
  gi|91772183|ref|YP_564875.1| 163 VEVHNKEELTYVLeNSSAKIVGINNRDLTTLEVDIATTEELIPIIKkydrrtgEEHLVISESGVHTPEDARRMMRAGADAI 243
                                   *************999****************************998888877789************************* PP

                                   EESHHHHC-TTHHHHHHHH CS
                          IGPS 236 LvGeslmrqedvekairel 254
                                   L+G+s++++ed  ++++el
  gi|91772183|ref|YP_564875.1| 244 LIGTSIVKDEDIYRKTKEL 262
                                   ***********99999986 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.52     1e+03      22      47 ..      40      65 ..      33      80 .. 0.68
   2 ?    3.7   0.1     0.015        30       5      36 ..      78     117 ..      74     132 .. 0.73
   3 ?    0.4   0.0      0.16   3.2e+02      29      53 ..     176     200 ..     163     207 .. 0.78
   4 !   21.8   0.0   4.4e-08   8.8e-05     145     188 ..     218     261 ..     203     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.52
                                  HHHHHHHTT--S-EEEE-B---TTS- CS
                          NanE 22 edikaikavvdlPiiGivkrdlpdse 47
                                  e i+  k   ++Pii  vk   p  +
  gi|91772183|ref|YP_564875.1| 40 EAIHSKKDSGKVPIIAEVKPASPSMK 65
                                  45555666667788877776665554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.015
                                   HHHHHHHT-SEEEE........ESHHHHHHHHTT--S-EE CS
                          NanE   5 akaaeqaGavgiri........egvedikaikavvdlPii 36 
                                   a+  e+aGa++i +         +++++ka++++++lP++
  gi|91772183|ref|YP_564875.1|  78 AMDMENAGAIAISVltepeffeGSIDNLKAVREAISLPVL 117
                                   6666777777776544333332489*************86 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.16
                                   TT--S-EEEE-B---TTS---BS-S CS
                          NanE  29 avvdlPiiGivkrdlpdsevritat 53 
                                   +  +  i+Gi  rdl   ev i++t
  gi|91772183|ref|YP_564875.1| 176 ENSSAKIVGINNRDLTTLEVDIATT 200
                                   5556779*********999999876 PP

  == domain 4  score: 21.8 bits;  conditional E-value: 4.4e-08
                                   --EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHH CS
                          NanE 145 lkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfve 188
                                     vi e  ++tPe a+++++ G+da+ +G++i + e+i +k  e
  gi|91772183|ref|YP_564875.1| 218 HLVISESGVHTPEDARRMMRAGADAILIGTSIVKDEDIYRKTKE 261
                                   569**********************************9988665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.9e-07   0.00037      62     116 ..     204     260 ..     167     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                                   HHHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                  His_biosynth  62 ldlveeiaeevf..ipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                   + ++++  +++     v   +G+ + ed++++++agad + igt+ vk+ ++ ++  
  gi|91772183|ref|YP_564875.1| 204 IPIIKKYDRRTGeeHLVISESGVHTPEDARRMMRAGADAILIGTSIVKDEDIYRKTK 260
                                   555555554444213455679*****************************9988765 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   2.3e+03      39      65 ..      32      57 ..      10      68 .. 0.54
   2 !   18.8   0.1   4.3e-07   0.00086     171     219 ..     207     259 ..     167     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                  STCHHHHHHHHHH.HHHCTSSS-EEEEE CS
                          PcrB 39 sqsvtldntvrll.kkvsriklPivlep 65
                                  +q+   +++++++ +k    k+Pi+ e+
  gi|91772183|ref|YP_564875.1| 32 TQG--IEKIIEAIhSKKDSGKVPIIAEV 57
                                  332..23444444134445678888765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.3e-07
                                   HHHHHHHHSSSE.EEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..HCHH CS
                          PcrB 171 vialkkklekar.livGGGirsaEkAkevvea.ADvivvGnvveekd..erki 219
                                   +++  ++  +++ +i   G++ +E+A+++++a AD+i++G+ + +++   rk 
  gi|91772183|ref|YP_564875.1| 207 IKKYDRRTGEEHlVISESGVHTPEDARRMMRAgADAILIGTSIVKDEdiYRKT 259
                                   445555544444156679***********************998776233344 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.6e-07    0.0017     178     220 ..     220     262 ..     198     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.6e-07
                                   BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHH CS
                          ThiG 178 vivDAGigspsdaaqamelGadavllntavaeakdpvamAraf 220
                                   vi + G+ +p+da   m  Gada+l+ t++ + +d+ +  + +
  gi|91772183|ref|YP_564875.1| 220 VISESGVHTPEDARRMMRAGADAILIGTSIVKDEDIYRKTKEL 262
                                   78899****************************9998766655 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.37   7.4e+02     254     276 ..      73      95 ..      32     106 .. 0.73
   2 !   16.6   0.0   1.8e-06    0.0036     233     283 ..     206     255 ..     161     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.37
                                   -SHHHHHHHHHHTECEEEESHHH CS
                        DHO_dh 254 esgeDalekieaGAslvqvytal 276
                                   e+g+ a+++ +aGA ++ v t+ 
  gi|91772183|ref|YP_564875.1|  73 EAGKIAMDMENAGAIAISVLTEP 95 
                                   45666777788888877777765 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.8e-06
                                   HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCH CS
                        DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpki 283
                                   +i +  +r+ +e  +I+  G+++ eDa  +++aGA ++ ++t +v+++  i
  gi|91772183|ref|YP_564875.1| 206 IIKKYDRRTGEEHLVISESGVHTPEDARRMMRAGADAILIGTSIVKDE-DI 255
                                   56667778888999*****************************96554.44 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.22   4.4e+02     145     162 ..     135     152 ..      12     157 .. 0.61
   2 ?   12.9   0.3   5.5e-05      0.11      74     122 ..     207     260 ..      60     271 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                                   EEEEEEEBTTTSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 145 vvdrivglpGendeelee 162
                                    +  i gl Ge  eel e
  gi|91772183|ref|YP_564875.1| 135 LILLIAGLLGEKLEELIE 152
                                   334444444444444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.5e-05
                                   C......CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT CS
                                   x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  74 a......vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn 122
                                            + +++++ +g++  +e ++r+ ++g d + +g  ++ de++ ++++
  gi|91772183|ref|YP_564875.1| 207 IkkydrrTGEEHLVISESGVHT-PEDARRMMRAGADAILIGTSIVKDEDIYRKTK 260
                                   0333455678999999999998.*************************9988884 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.89   1.8e+03     198     221 ..      92     118 ..      54     122 .. 0.62
   2 ?   11.2   0.0     7e-05      0.14     223     243 ..     225     245 ..     182     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.89
                                   HB-TC-...-HHHHHHHHHHHSSEEEE CS
                        FMN_dh 198 qldpsl...twddikwlreqtklplvv 221
                                     +p++   + d++k +re+ +lp++ 
  gi|91772183|ref|YP_564875.1|  92 LTEPEFfegSIDNLKAVREAISLPVLR 118
                                   334444444677888888888888875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7e-05
                                   EE-SHHHHHHHHHTTESEEEE CS
                        FMN_dh 223 GvltaedakraveaGvdgivv 243
                                   Gv t+eda+r+++aG+d+i++
  gi|91772183|ref|YP_564875.1| 225 GVHTPEDARRMMRAGADAILI 245
                                   788888888888888888876 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.23     156     194 ..     226     264 ..     213     271 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                 PEP_hydrolase 156 vfneeearamaeaGadvivahlGlttggsigaktalsle 194
                                   v ++e+ar+m++aGad+i +   + ++ +i  kt++ ++
  gi|91772183|ref|YP_564875.1| 226 VHTPEDARRMMRAGADAILIGTSIVKDEDIYRKTKELVD 264
                                   7899****************9999999988877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1909.80
//
Query:       gi|91772184|ref|YP_564876.1|  [L=393]
Description: tryptophan synthase subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  136.2   0.7    1.7e-39  136.0   0.7    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0   0.7   9.8e-44   1.7e-39       4     294 .]      50     377 ..      47     377 .. 0.84

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 9.8e-44
                                   CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE CS
                          PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtiv 84 
                                   + ++TPl ++++lsk++g++++lK+E+l ++g++K++      + +k   + + v+e+++G+hg a+A+a+  lG++ +++
  gi|91772184|ref|YP_564876.1|  50 AGRETPLYHARNLSKKYGTKIYLKREDLVHGGAHKLNNTIGQALLAKYMGKSRLVAETGAGQHGTATAMAGTNLGFETHVY 130
                                   6789*********************************999555555555499***************************** PP

                                   EETTS-H...HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH......STTCEE--TTT.SHH...HHHHHHTHHHHHHH CS
                          PALP  85 vpadasp...ekvallrllGaevvevggdydeavaaaaelaae......gegaylvsqfd.npt...viegygtiglEile 152
                                   + a++ +    +v +++ +G ev+ v+++  + ++a++e++++      ++++++ s  + +p+   v + ++ ig E+++
  gi|91772184|ref|YP_564876.1| 131 MGAKDMErqrMNVYRMEIMGTEVHPVESGSRTLKDAINEALRDwvsnveNTHYLIGSVVGpHPYpmmVRDFQSVIGNEVKQ 211
                                   ****9954559******************999999999999999999963333333333354445545555********95 PP

                                   HTT....TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B................. CS
                          PALP 153 qlg....gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs................ 213
                                   q+     + pd +v+++GgG++++Gi +++ e   dv++i+ve+ g    ++  +a +  +++v+                
  gi|91772184|ref|YP_564876.1| 212 QIIkkegRYPDSIVACAGGGSNAMGIFHPFIE--EDVKLIAVEAGGKGMEYTKDAALHSASLSVGedgvlqgartrilqde 290
                                   5555666************************9..68********9555555555466666666667888999999999999 PP

                                   .......SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCE CS
                          PALP 214 .......dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegd 286
                                          ++i  gl+ + ++++   l+d        v+d+ alea  +l r egi++   s +a+a + +++e gel+e  
  gi|91772184|ref|YP_564876.1| 291 ygqilesSSISAGLDYSGVGPELAHLADIGRILPRVVNDDLALEAFHELSRVEGIIPALESSHAVAHVmEAAESGELGEL- 370
                                   9999999**********666666666666666669************************9999999999********999. PP

                                   EEEEEE-B CS
                          PALP 287 rvvviltg 294
                                    vv+ l+g
  gi|91772184|ref|YP_564876.1| 371 -VVINLSG 377
                                   .9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2747.96
//
Query:       gi|91772185|ref|YP_564877.1|  [L=259]
Description: tryptophan synthase subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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-92  308.4   0.1      3e-92  308.1   0.1    1.0  1  Trp_syntA      Tryptophan synthase alpha chain
      1e-05   25.1   0.4    1.9e-05   24.3   0.4    1.4  1  His_biosynth   Histidine biosynthesis protein
    0.00013   21.5   0.9     0.0034   16.9   0.4    2.3  2  PcrB           PcrB family
     0.0087   15.4   0.2      0.012   15.0   0.2    1.2  1  ThiG           Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.032   13.4   0.8       0.13   11.5   0.4    2.2  3  NanE           Putative N-acetylmannosamine-6-phosphate epime
      0.043   13.0   0.6      0.059   12.6   0.6    1.2  1  DHO_dh         Dihydroorotate dehydrogenase
       0.05   12.8   0.1          1    8.5   0.0    2.6  3  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
      0.053   12.5   0.5       0.14   11.2   0.3    1.7  2  IMPDH          IMP dehydrogenase / GMP reductase domain
      0.075   12.1   0.3       0.12   11.3   0.3    1.4  1  FMN_dh         FMN-dependent dehydrogenase


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 !  308.1   0.1   1.5e-95     3e-92       1     251 [.       7     252 ..       7     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 308.1 bits;  conditional E-value: 1.5e-95
                                   HHHHHCTTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHH CS
                     Trp_syntA   1 faklkaenraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveev 81 
                                   f+++k++n++a+++yv agdpd++++  i+++l k+gad+iElGlpfsdP+adGP+Iqaa++raL++g+++++ +elv+++
  gi|91772185|ref|YP_564877.1|   7 FNEIKNRNETALLAYVCAGDPDIDSTPRIVDSLIKGGADIIELGLPFSDPVADGPTIQAASERALTAGMNPDRYFELVANL 87 
                                   77899**************************************************************************** PP

                                   HHHCSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH CS
                     Trp_syntA  82 rkkevevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveq 162
                                   +   v+vP+v++ty+nl++++g+e+f++++   g+ gli+pDlP+ee+++l + ++++g++l+flvap t+der+++++++
  gi|91772185|ref|YP_564877.1|  88 D---VQVPLVCMTYYNLIYKRGIEKFVKDCISSGISGLIIPDLPAEESADLANCCSQEGVDLIFLVAPITTDERIEMILSK 165
                                   *...***************************************************************************** PP

                                   --S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCTTTSHHH CS
                     Trp_syntA 163 aegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkieeeaeekeq 242
                                   ++gfvY+vsr GvTg+++ v+a ++++++r++  t+ P+avGFGis++eq+++++ ++adGvivGSa v++i+ + ++ e+
  gi|91772185|ref|YP_564877.1| 166 TSGFVYIVSRSGVTGTRSDVTAATSDIISRVR--TDIPKAVGFGISNAEQAAKIIdAGADGVIVGSAFVDIIA-SGNDVEK 243
                                   *******************************8..789******************9*****************.6667777 PP

                                   HHHHHHHHH CS
                     Trp_syntA 243 alekleela 251
                                    le+l++ +
  gi|91772185|ref|YP_564877.1| 244 RLEDLTAEI 252
                                   777766654 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.4   9.3e-09   1.9e-05      60     107 ..     188     233 ..     176     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.3e-09
                                   HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                  His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                   a  d++++++    ip  vG GI++ e+++++++agad vi+g+a v+
  gi|91772185|ref|YP_564877.1| 188 ATSDIISRVRTD--IPKAVGFGISNAEQAAKIIDAGADGVIVGSAFVD 233
                                   456788888877..*******************************987 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.032        65       8      37 ..      21      50 ..      10      60 .. 0.87
   2 !   16.9   0.4   1.7e-06    0.0034     157     211 ..     170     231 ..     159     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.032
                                  EEEEE-TTSS-CHHHHHHHHCTT-SEEEEE CS
                          PcrB  8 hltklDPeeenpdEiveiviesgtDavmig 37
                                  ++   DP+ + +  iv+ +i++g+D + +g
  gi|91772185|ref|YP_564877.1| 21 YVCAGDPDIDSTPRIVDSLIKGGADIIELG 50
                                  77888********************98665 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.7e-06
                                   EEEE-.TTSSS-H.HHHHHHH....HHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHH CS
                          PcrB 157 iYlEa.sGaledv.eevialk....kklekarlivGGGirsaEkAkevvea.ADvivvGnvv 211
                                   +Y+   sG+++   + ++a++    ++ +++   vG Gi +aE+A++++ a AD ++vG + 
  gi|91772185|ref|YP_564877.1| 170 VYIVSrSGVTGTRsDVTAATSdiisRVRTDIPKAVGFGISNAEQAAKIIDAgADGVIVGSAF 231
                                   6776668877766455555541111445566779*************************875 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   5.8e-06     0.012     153     207 ..     177     231 ..     124     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.8e-06
                                   SSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHH CS
                          ThiG 153 apiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntav 207
                                      G+   +++++   i + ++++P  v  Gi ++++aa+ ++ Gad+v++ +a 
  gi|91772185|ref|YP_564877.1| 177 GVTGTRSDVTAATSDIISRVRTDIPKAVGFGISNAEQAAKIIDAGADGVIVGSAF 231
                                   55555555544444334445669****************************9994 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         1     2e+03      52      70 ..      31      49 ..      25      51 .. 0.74
   2 ?   -1.5   0.0      0.59   1.2e+03     155     181 ..     132     158 ..     109     168 .. 0.65
   3 ?   11.5   0.4   6.4e-05      0.13     153     176 ..     208     231 ..     144     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                  -SHHHHHHHHTTT-SEEEE CS
                          NanE 52 atlkdideLaaagadiial 70
                                  +t + +d L++ gadii l
  gi|91772185|ref|YP_564877.1| 31 STPRIVDSLIKGGADIIEL 49
                                  5555689999999999965 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.59
                                   SHHHHHHHHTT--SEEEE-HHHH-HHH CS
                          NanE 155 tPekakkaieiGvdavvvGsaitrlee 181
                                   + ++a+ + + Gvd++ + + it  e+
  gi|91772185|ref|YP_564877.1| 132 SADLANCCSQEGVDLIFLVAPITTDER 158
                                   445566666777777766666665555 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 6.4e-05
                                   --SHHHHHHHHTT--SEEEE-HHH CS
                          NanE 153 intPekakkaieiGvdavvvGsai 176
                                   i   e+a+k+i+ G+d v+vGsa 
  gi|91772185|ref|YP_564877.1| 208 ISNAEQAAKIIDAGADGVIVGSAF 231
                                   66789*****************97 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   2.9e-05     0.059     169     279 ..     123     233 ..     102     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                                   E-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CT..TCCGCCCCTT.SSEEEEEGGGHHHHHHHHHHHHHHTTT.S- CS
                        DHO_dh 169 laPdltdeekkdiadvllelkldgiivtNttvqrlaid..lkseknvkan.ktGGlsGkalkdialkvirelykrlkkeip 246
                                   + Pdl +ee +d a+   + ++d i  +  ++  ++i+  l +++      +  G+ G    +  ++   ++ +r++ +ip
  gi|91772185|ref|YP_564877.1| 123 IIPDLPAEESADLANCCSQEGVDLIFLVAPITTDERIEmiLSKTSGFVYIvSRSGVTGTR--SDVTAATSDIISRVRTDIP 201
                                   77****************999999877765555444441144444433334677799985..5556667889999999999 PP

                                   EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                        DHO_dh 247 iIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                        Gi+ +e a   i aGA  v v++a+  +
  gi|91772185|ref|YP_564877.1| 202 KAVGFGISNAEQAAKIIDAGADGVIVGSAF-VD 233
                                   655559**********************98.34 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.15     3e+02      78     107 ..      13      43 ..       3      48 .. 0.74
   2 ?   -0.8   0.0      0.35     7e+02     207     242 ..     139     169 ..     129     195 .. 0.64
   3 ?    8.5   0.0   0.00051         1     156     204 ..     208     256 ..     201     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.15
                 PEP_hydrolase  78 vketpvlaGvcatDpf.rkleeflkelkelG 107
                                    +et++la vca Dp   ++++++++l + G
  gi|91772185|ref|YP_564877.1|  13 RNETALLAYVCAGDPDiDSTPRIVDSLIKGG 43 
                                   467999*********8344567777776655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.35
                 PEP_hydrolase 207 akevnpdvivlvhGGpiaepedaeyvlertkgvkGf 242
                                   +++   d i lv   pi++ e +e++l++t+g   f
  gi|91772185|ref|YP_564877.1| 139 CSQEGVDLIFLV--APITTDERIEMILSKTSG---F 169
                                   344444444444..588888888888855544...3 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00051
                 PEP_hydrolase 156 vfneeearamaeaGadvivahlGlttggsigaktalsleeavelvqeia 204
                                   + n+e+a+++++aGad +++   +    + g + ++ le+ ++++++++
  gi|91772185|ref|YP_564877.1| 208 ISNAEQAAKIIDAGADGVIVGSAFVDIIASGNDVEKRLEDLTAEIKSVC 256
                                   6799*********************999**********99999998875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.69   1.4e+03     155     173 ..      32      50 ..       6      52 .. 0.77
   2 ?   11.2   0.3   6.8e-05      0.14     131     173 ..     188     228 ..     149     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.69
                                   SHHHHHHHHHTT-SEEEE- CS
                                   xxxxxxxxxxxxxxxxxxx RF
                         IMPDH 155 taegakaLieagadavkvG 173
                                   t   + +Li+ gad++  G
  gi|91772185|ref|YP_564877.1|  32 TPRIVDSLIKGGADIIELG 50 
                                   5556778999999999888 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.8e-05
                                   HHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 131 kvleavkeikkkveeveviaGnvataegakaLieagadavkvG 173
                                    + + +++++++++  + ++  + +ae+a+++i+agad+v vG
  gi|91772185|ref|YP_564877.1| 188 ATSDIISRVRTDIP--KAVGFGISNAEQAAKIIDAGADGVIVG 228
                                   34455666666665..457778999999999999999999998 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   0.3   6.2e-05      0.12     257     328 ..     189     254 ..     159     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.2e-05
                                   HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        FMN_dh 257 tidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraeler 328
                                   t d    i  +v+ +i+  v  Gi++ + ++k +  GAd+v++G +f+    a G + ve+ le l+ae+++
  gi|91772185|ref|YP_564877.1| 189 TSD----IISRVRTDIPKAVGFGISNAEQAAKIIDAGADGVIVGSAFVDI-IASG-NDVEKRLEDLTAEIKS 254
                                   444....4444555556677779999999999999999999999999544.4444.4588888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1644.67
//
Query:       gi|91772186|ref|YP_564878.1|  [L=366]
Description: signal recognition particle-docking protein FtsY [Methanococcoides burtonii DSM 6242]
Scores for complete 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-73  244.2   0.7    1.1e-72  243.7   0.7    1.2  1  SRP54            SRP54-type protein, GTPase domain
    4.1e-11   42.9   5.5    4.4e-11   42.8   1.6    2.5  2  SRP54_N          SRP54-type protein, helical bundle domain
    1.6e-05   25.3   0.5    3.8e-05   24.1   0.2    1.8  1  AAA_17           AAA domain
      7e-05   22.6   0.5    0.00013   21.7   0.5    1.4  1  AAA_30           AAA domain
    8.9e-05   21.9   0.2    0.00018   20.8   0.2    1.5  1  Zeta_toxin       Zeta toxin
    0.00018   21.2   0.1     0.0057   16.4   0.0    2.6  2  Thymidylate_kin  Thymidylate kinase
    0.00022   21.6   0.2     0.0013   19.2   0.2    2.2  1  AAA              ATPase family associated with various cellul
    0.00036   20.8   0.1     0.0012   19.2   0.1    1.9  1  AAA_28           AAA domain
     0.0005   19.7   0.5      0.001   18.7   0.5    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0019   18.1   0.0     0.0037   17.2   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
     0.0024   18.1   0.1      0.009   16.2   0.1    2.1  2  AAA_33           AAA domain
     0.0025   18.1   0.0     0.0079   16.5   0.0    1.8  1  AAA_22           AAA domain
      0.003   18.0   0.0     0.0068   16.8   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0033   17.0   0.0     0.0071   15.9   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.012   14.8   0.5       0.02   14.1   0.5    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.016   15.3   0.4      0.071   13.2   0.4    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
      0.021   15.3   0.1      0.057   13.9   0.0    1.7  2  ABC_tran         ABC transporter
      0.021   14.5   0.1      0.034   13.8   0.1    1.4  1  Peripla_BP_6     Periplasmic binding protein
      0.028   14.8   0.5      0.063   13.6   0.5    1.6  1  AAA_19           AAA domain
      0.032   13.2   0.1      0.059   12.3   0.1    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.044   13.7   3.1       0.22   11.4   0.3    2.3  2  MobB             Molybdopterin guanine dinucleotide synthesis
       0.06   13.3   1.6       0.38   10.7   1.4    2.2  1  NTPase_1         NTPase
      0.076   13.1   0.2       0.26   11.3   0.2    2.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.082   12.6   0.0       0.15   11.8   0.0    1.5  1  AAA_24           AAA domain
      0.093   12.2   0.0        0.2   11.1   0.0    1.5  1  Arf              ADP-ribosylation factor family
        0.1   12.6   0.2       0.17   11.8   0.2    1.5  1  ResIII           Type III restriction enzyme, res subunit
       0.11   12.4   1.0       0.21   11.5   0.1    2.0  2  ATPase_2         ATPase domain predominantly from Archaea
       0.16   12.5   0.4       0.57   10.7   0.1    2.0  2  AAA_18           AAA domain
       0.17   11.8   1.5       0.86    9.5   0.2    2.2  2  AAA_31           AAA domain
       0.19   11.2   0.7       0.36   10.2   0.0    1.8  2  KTI12            Chromatin associated protein KTI12


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 !  243.7   0.7   1.9e-75   1.1e-72       2     195 ..     172     365 ..     171     366 .] 0.99

  Alignments for each domain:
  == domain 1  score: 243.7 bits;  conditional E-value: 1.9e-75
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHT CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakee 82 
                                     i+++G++G+GKTtt++K+a++lk+++++v+++a DtfRa+A++Q++++ae++gv++ik++e+ dpaav+++av++ak++
  gi|91772186|ref|YP_564878.1| 172 VHIVFIGINGTGKTTTISKMAKRLKDMKYSVVIAAGDTFRAGAIDQIAIHAERIGVKLIKHQEGGDPAAVVYDAVQHAKAH 252
                                   5699***************************************************************************** PP

                                   TSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHH CS
                         SRP54  83 kidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsia 163
                                   ++dvvl DTaGr++++ +lm++l+k+ +v +pd +++v +a++g++av+ a++F+ av i g iltk D+d+kgGaa+sia
  gi|91772186|ref|YP_564878.1| 253 NVDVVLSDTAGRMHTNVNLMAQLEKVCRVSSPDLIIFVDEAVAGNDAVERAQQFNTAVPIHGSILTKTDADSKGGAAISIA 333
                                   ********************************************************************************* PP

                                   HHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                         SRP54 164 aelklPikfigvGekiedleefdperlvsrll 195
                                   + +++Pi f+g+G+ ++dl++fdpe++v++l+
  gi|91772186|ref|YP_564878.1| 334 YITGKPILFLGMGQGYDDLKKFDPEWFVDQLF 365
                                   ******************************97 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.86   5.2e+02       2      24 ..       6      26 ..       5      37 .. 0.63
   2 !   42.8   1.6   7.4e-14   4.4e-11      17      73 ..      89     148 ..      77     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.86
                                  HHHHHHHHHHHCCSSCGHHHHHH CS
                       SRP54_N  2 gkklnsalkklsgkskideedle 24
                                  ++kl s+ +++  +++ide+++e
  gi|91772186|ref|YP_564878.1|  6 KEKLGSFKQSI--GKTIDEKAVE 26
                                  67777777775..6679999955 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 7.4e-14
                                   CGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHH CS
                       SRP54_N  17 kideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkd 73 
                                    +d  d+e+ l+ele+aLle+D++++v++ ++e+vk++ vg++k    ++++ v+++++ 
  gi|91772186|ref|YP_564878.1|  89 ILDGSDIEDSLWELEMALLESDIAINVAEAIVESVKEELVGSRKklgKNTGELVENALRS 148
                                   47999************************************88899999*****999986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   6.3e-08   3.8e-05       1     109 [.     177     291 ..     177     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.3e-08
                                   EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHTTTSHSS.HHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEE CS
                        AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakrgglaka.rdemrklpleekkelqkeaaekiaeea..kkkgv 74 
                                   +G+ G GK+t ++k+++++   +++ ++ aGd +r+ a ++ ++ a r  ++  +++e  +  + + +++++++  + + v
  gi|91772186|ref|YP_564878.1| 177 IGINGTGKTTTISKMAKRLkdmKYSvVIAAGDTFRAGAIDQIAIHAeRIGVKLIKHQEGGDPAAVVYDAVQHAKahNVDVV 257
                                   59**************86655566615799*******99997643303333344666666777777888877763233558 PP

                                   EEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                        AAA_17  75 lvdghprikeqagfldglpkevleelkpdaiille 109
                                   l d+  r+ ++  ++++l+k v++  +pd+ii+++
  gi|91772186|ref|YP_564878.1| 258 LSDTAGRMHTNVNLMAQLEK-VCRVSSPDLIIFVD 291
                                   999999*9999999998885.9***********98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.5   2.2e-07   0.00013      21     114 ..     174     281 ..     165     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-07
                        AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............grarlep 88 
                                    v  G  GtGKtt+++++++ +++ +++v+++A     A ++  ++ i+a++i   l +++             ++a+ ++
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRLKDMKYSVVIAAGDTFRAGAID-QIAIHAERIGVKLIKHQeggdpaavvydavQHAKAHN 253
                                   56789*********************************99999.89999*9999888788889999999999885566667 PP

                        AAA_30  89 gtllivDEagmv..dtkqlaallkaaek 114
                                    ++++ D ag +  + + +a+l k ++ 
  gi|91772186|ref|YP_564878.1| 254 VDVVLSDTAGRMhtNVNLMAQLEKVCRV 281
                                   7889889998883333456666555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2     3e-07   0.00018      10     119 ..     164     277 ..     156     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-07
                    Zeta_toxin  10 ypsq.erPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilka..dpkkaseltqkdaselvek 86 
                                   y+++ e+P+ i+  G  G GK++++++++++l+ ++ +vv   +D++R+   +  +i ++   +k    +   d   +v  
  gi|91772186|ref|YP_564878.1| 164 YIRDaEKPVHIVFIGINGTGKTTTISKMAKRLKdMKYSVVIAAGDTFRAGAIDQIAIHAEriGVKLIKHQEGGDPAAVVYD 244
                                   56666***************************988888888899****976555555554346677777777777788888 PP

                    Zeta_toxin  87 llqeaiengyniivegtlrspdvvkklaealkk 119
                                   ++q+a  + +++++  t    ++  +l+ +l+k
  gi|91772186|ref|YP_564878.1| 245 AVQHAKAHNVDVVLSDTAGRMHTNVNLMAQLEK 277
                                   888888888888887777777777766666665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.5e-06    0.0057       3      29 ..     178     204 ..     176     225 .. 0.89
   2 ?    1.8   0.0      0.27   1.6e+02     106     136 ..     271     304 ..     261     310 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.5e-06
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEE CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvl 29 
                                   G++G+GKtt + ++++rlk+++++vv+
  gi|91772186|ref|YP_564878.1| 178 GINGTGKTTTISKMAKRLKDMKYSVVI 204
                                   9**********************9776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.27
                                   HHHHHGGGTTS.E-SEEEEEE..SSHHHHHTSCC CS
               Thymidylate_kin 106 lvlslnedvll.kPdltflld..vdpevalkRla 136
                                   l+ +l++     +Pdl++++d  v  + a++R++
  gi|91772186|ref|YP_564878.1| 271 LMAQLEKVCRVsSPDLIIFVDeaVAGNDAVERAQ 304
                                   5555555544479*******96666777777776 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 !   19.2   0.2   2.1e-06    0.0013       2      71 ..     175     297 ..     174     354 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.1e-06
                                   EEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS.......................................... CS
                           AAA   2 llyGppGtGKTllakavakelg...vefleisgsellsk.......................................... 37 
                                   +++G  GtGKT++++ +ak l+    +++   g +++                                            
  gi|91772186|ref|YP_564878.1| 175 VFIGINGTGKTTTISKMAKRLKdmkYSVVIAAGDTFR-Agaidqiaihaerigvklikhqeggdpaavvydavqhakahnv 254
                                   799*****************86542555555555555.3478888888888888899999888888888888888888888 PP

                                   ......STTHHHHHHHHHHHHHHHTS..TS.EEEEEETGGGHH CS
                           AAA  38 ......yvgesekkirelfkeakeka..kp.silfiDEidala 71 
                                         + g +  +++ + +  k  +  +p  i+f+DE+ a +
  gi|91772186|ref|YP_564878.1| 255 dvvlsdTAGRMHTNVNLMAQLEKVCRvsSPdLIIFVDEAVAGN 297
                                   8877777777777766666654433355677899999976554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.9e-06    0.0012       2     121 ..     174     296 ..     173     321 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.9e-06
                        AAA_28   2 ivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedalpwv.edllafaervleeqleeeaaa.aankvl 76 
                                   iv++G  +tGKTt+++++a+r    +y+vv  a+ ++     ++   +++    +l++ +e+     ++   +a +  k  
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRlkdmKYSVVIAAGDTFRAGAIDQIAIHAERIgVKLIKHQEG--GDPAAVVYDAvQHAKAH 252
                                   9******************8888889999988888777666655555555443333333333..22222233333455555 PP

                        AAA_28  77 fcDrglldtlaYarayggeaeaeleaaarekrydlvfllppapei 121
                                    +D  l dt+  +++  +  +a+le+ +r +  dl++++++a   
  gi|91772186|ref|YP_564878.1| 253 NVDVVLSDTAGRMHTNVNL-MAQLEKVCRVSSPDLIIFVDEAVAG 296
                                   5555555555556666655.6666666666666666666666655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   1.7e-06     0.001       3     132 ..     174     303 ..     172     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                                   EEEEESTTCCHHHHHHHHHCT--SS-EEEEE..SS.-SSCHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHHHHHHH CS
                          cobW   3 tvltGflGsGKTtLlnhllenraglklaviv..Ne.fgevsiDaellret..gveivelenGciCctlredllkelealee 78 
                                   +v+ G  G+GKTt ++++ ++ +++k+ v++  ++ f   +iD+  ++++  gv++++ ++G+ + ++  d++++++a   
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRLKDMKYSVVIaaGDtFRAGAIDQIAIHAEriGVKLIKHQEGGDPAAVVYDAVQHAKA--- 251
                                   6788999************99999999998733452555899**99998878889************88888877665... PP

                                   HHTT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHH CS
                          cobW  79 reerldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekie 132
                                     +++dv+l  t G ++ +   + + e++++    d +++v +a +  ++  + +
  gi|91772186|ref|YP_564878.1| 252 --HNVDVVLSDTAGRMHTNVNlMAQLEKVCRVSSPDLIIFVDEAVAG-NDAVERA 303
                                   ..37999*******555555536667777777777777776666332.2333333 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.2e-06    0.0037       2      50 ..     171     219 ..     170     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.2e-06
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
                    APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                                   +v + + G+ g+GK+t   +++k+L+++++sv++  Gd+ R g   +++
  gi|91772186|ref|YP_564878.1| 171 PVHIVFIGINGTGKTTTISKMAKRLKDMKYSVVIAAGDTFRAGAIDQIA 219
                                   678999***********************************98776665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         8   4.8e+03      46      77 ..      60      92 ..      44     132 .. 0.61
   2 !   16.2   0.1   1.5e-05     0.009       2      78 ..     174     261 ..     174     318 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8
                        AAA_33 46 tdytrvldrlyqilnelarkalsag..rnvilda 77
                                   d t+++++l+q + ++a+ka +    r vild 
  gi|91772186|ref|YP_564878.1| 60 LDKTEASPSLKQKI-GFAQKAKALVfeREVILDG 92
                                  44556666666666.6666554443114455554 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.5e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg.....tdqqskt.......dytrvldrlyqilnelark 65 
                                   ++++G +G+GK+t + +++k+l+     +v+ + dt+r                +       + ++  d +   + + ++ 
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRLKdmkysVVIAAGDTFRAGAIDqiaihA-----ErigvkliKHQEGGDPAA-VVYDAVQH 248
                                   68*********************99974444556665553332122221.....122222222222333333.44455666 PP

                        AAA_33  66 alsagrnvildat 78 
                                   a +++ +v+l  t
  gi|91772186|ref|YP_564878.1| 249 AKAHNVDVVLSDT 261
                                   6666666666444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-05    0.0079       7     100 ..     173     293 ..     167     313 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee......................erpevvfvtlpsstsskdllrellralg 65 
                                   ++v +G  GtGKTt++ +++++l+     ++                      er +v +++ +++++++ +  + ++  +
  gi|91772186|ref|YP_564878.1| 173 HIVFIGINGTGKTTTISKMAKRLKDM---KYsvviaagdtfragaidqiaihaERIGVKLIKHQEGGDPAAVVYDAVQHAK 250
                                   799*******************9522...2244456666666666666665544444445555555555555333333333 PP

                        AAA_22  66 lelka........erlsseellealeqalraravielliiDEa 100
                                     + +        + +++  l+++le+ +r  +   ++ +DEa
  gi|91772186|ref|YP_564878.1| 251 AHNVDvvlsdtagRMHTNVNLMAQLEKVCRVSSPDLIIFVDEA 293
                                   3333356666666666666666666666666666555666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.1e-05    0.0068      13     143 ..     162     292 ..     156     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                        AAA_16  13 lsalervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrqlldeaes 91 
                                    ++++++    p  ++++G  G+GK++ + + +++l++ +  +  ++g++ + ++    ++ a+ +   +l++  +  + +
  gi|91772186|ref|YP_564878.1| 162 DDYIRDAE--KPVHIVFIGINGTGKTTTISKMAKRLKDMKYSVviAAGDTFRAGAIDQIAIHAERI-GVKLIKHQEGGDPA 239
                                   55566554..348999*********************99644413555555553333335578888.55777777776444 PP

                        AAA_16  92 aeleawrekleealaavpelagaea...srllellkrllallsrderp.lvlvlDd 143
                                    ++ +++ +  +a + v+ + ++ a   +   +l+++l + ++  ++p l++++D+
  gi|91772186|ref|YP_564878.1| 240 -AVVYDAVQHAKAHN-VDVVLSDTAgrmHTNVNLMAQLEKVCRV-SSPdLIIFVDE 292
                                   .67777777777766.4444444445666666777777788887.44559999997 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05    0.0071      34      65 ..     172     203 ..     164     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                         AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsl 65 
                                    +++++G  GtGKt++i+++ k+l++ ky+++
  gi|91772186|ref|YP_564878.1| 172 VHIVFIGINGTGKTTTISKMAKRLKDMKYSVV 203
                                   6899*********************9999876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   3.3e-05      0.02       7     132 ..     177     292 ..     172     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                       DUF2075   7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeep 87 
                                    G  GtGKt   ++++ +l   ++ +++v++     +++    ++a ++  ++++ ++ k ++   ++   ++a ++++  
  gi|91772186|ref|YP_564878.1| 177 IGINGTGKTTTISKMAKRL---KDMKYSVVIAAGDTFRAGAIDQIAIHA--ERIGVKLIKHQEGGDPAAVVYDAVQHAKAH 252
                                   3999***************...777788888888899999989998888..8888888888888888886689999***** PP

                       DUF2075  88 kedvvivDEAhrlltksdqaekqseenqlkelmkr.akvvvalvDe 132
                                   ++dvv+ D A r+ t      + +  +ql+++ +  +  ++++vDe
  gi|91772186|ref|YP_564878.1| 253 NVDVVLSDTAGRMHT------NVNLMAQLEKVCRVsSPDLIIFVDE 292
                                   ***************......5555789999999955588888887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   0.00012     0.071       2      86 ..     174     294 ..     173     319 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                   EEEEESTTSSHHHHHHHHHT..............STEEESSSTTSSSSEEEEEEEETTEE..................... CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg..............ekaivsdkpgtTrdinegrvklkgke..................... 47 
                                   ++++G   +GK+t i+++ +              ++ +++++ +  ++ +++ vk                          
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKrlkdmkysvviaagDTFRAGAIDQIAIHAERIGVK----Likhqeggdpaavvydavqhak 250
                                   89*****************855444442222221233333333333333333333....0333345556666666666677 PP

                                   .....EEEEECGGCSSHHHHHHHHHHHHHHHHC..T.SEEEEEEETT CS
                      MMR_HSR1  48 .....ielvDtpGliegaseekglgkaflalee..a.dlillvvdas 86 
                                        ++l Dt+G ++   ++ +l  +++++ +  + dli++v +a 
  gi|91772186|ref|YP_564878.1| 251 ahnvdVVLSDTAGRMH---TNVNLMAQLEKVCRvsSpDLIIFVDEAV 294
                                   77777********555...4444555555433332239999987765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       7.8   4.7e+03      58      58 ..      77      77 ..      18     140 .. 0.59
   2 ?   13.9   0.0   9.5e-05     0.057      13      80 ..     173     249 ..     165     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.8
                                  C CS
                                  x RF
                      ABC_tran 58 r 58
                                  +
  gi|91772186|ref|YP_564878.1| 77 Q 77
                                  2 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.5e-05
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.....B-HHHCCHCEEEE-SS--S-TTSBHHHH...H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                      ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.....qeleslrkeigvlpqepqlfpeltvren...e 80 
                                    ++++G nG+GK+t ++ +a+ lk+ + ++ +  g+ ++      + ++  r  ++ +++++  +p   v++    +
  gi|91772186|ref|YP_564878.1| 173 HIVFIGINGTGKTTTISKMAKRLKDMKYSVVIAaGDTFRAgaidqIAIHAERIGVKLIKHQEGGDPAAVVYDAvqhA 249
                                   5789*******************998888866534433335554477777777777777777777777666665541 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.7e-05     0.034     105     205 ..     167     268 ..     115     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
                                   CTTSTTEEESS--HHHHHHHHHHHHHHHTT.SCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHH CS
                  Peripla_BP_6 105 ekcspyvfslgpsysaqasalveylakelg.gkkvalvyadyafgregiaalkaaakaaGgevvgeepvplgttdfsaqvl 184
                                   ++ +p ++++++ + +  ++++  +ak l+  k  ++++a + f + +i++++  a++ G++++ + +   +++ +  +v+
  gi|91772186|ref|YP_564878.1| 167 DAEKPVHIVFIGINGTGKTTTISKMAKRLKdMKYSVVIAAGDTFRAGAIDQIAIHAERIGVKLIKHQEGGDPAAVVYDAVQ 247
                                   56667777777777788888899999999856666777888*********************99888877788888889** PP

                                   HHHTTT-SEEEEESSHHHHHH CS
                  Peripla_BP_6 185 qikaagadavllagtgadlaa 205
                                    +ka+++d+vl  ++g + ++
  gi|91772186|ref|YP_564878.1| 248 HAKAHNVDVVLSDTAGRMHTN 268
                                   ***********9888887654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   0.00011     0.063      12     110 ..     173     292 ..     163     306 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                        AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillv..aftgrAakelrerlaalgae...................... 68 
                                   +++ ++  GtGKT+++ ++ + l++++      ++++  +f   A ++++   + +g++                      
  gi|91772186|ref|YP_564878.1| 173 HIVFIGINGTGKTTTISKMAKRLKDMKYS---VVIAAgdTFRAGAIDQIAIHAERIGVKlikhqeggdpaavvydavqhak 250
                                   56678999***************999932...3333311344445555555554455555555566666555554444322 PP

                        AAA_19  69 atTiHrlal..ldfddlltealelleeaeeekklqeee.llivDE 110
                                   a+ +    +   d+ +++++ ++l+ + e+   + + + +++vDE
  gi|91772186|ref|YP_564878.1| 251 AHNVD---VvlSDTAGRMHTNVNLMAQLEKVCRVSSPDlIIFVDE 292
                                   22222...1224444444444455555555555555555666666 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.9e-05     0.059      16      48 ..     172     204 ..     164     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.9e-05
                 TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraiv 48 
                                    hi+++G  G+GKt++++k+ + ++  +  +++
  gi|91772186|ref|YP_564878.1| 172 VHIVFIGINGTGKTTTISKMAKRLKDMKYSVVI 204
                                   6********************999998888887 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 ?   11.4   0.3   0.00037      0.22       2      30 ..     174     202 ..     173     209 .. 0.91
   2 ?    2.2   0.2      0.26   1.6e+02      26      95 ..     223     288 ..     217     291 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                          MobB   2 lgivgksgsGKTtLleklipelkarglrv 30 
                                   + ++g +g+GKTt ++k+ + lk+ +++v
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRLKDMKYSV 202
                                   6799********************99998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.26
                          MobB  26 rglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeaelsleellarlsevDlvl 95 
                                   + + v +iKh++ g d      D+ +h+kA    v+++       ++   +   +le++++  s+ Dl++
  gi|91772186|ref|YP_564878.1| 223 ERIGVKLIKHQE-GGDPAAVVYDAVQHAKAHNVDVVLSDTAGR--MHTNVNLMAQLEKVCRV-SSPDLII 288
                                   566788899975.567778889999999988777776544333..33322324455555443.4556665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   0.00063      0.38       2      30 ..     174     202 ..     173     293 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                   ++  G  G+GKtT ++k+++ lk+  ++v
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRLKDMKYSV 202
                                   6667999***************9998887 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00044      0.26       9      37 ..     181     209 ..     174     341 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDp 37 
                                   G+GKTt+  ++a+ l++ ++ V+    D+
  gi|91772186|ref|YP_564878.1| 181 GTGKTTTISKMAKRLKDMKYSVVIAAGDT 209
                                   9*********************9876555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.15       3      23 ..     172     199 ..     170     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                        AAA_24   3 lkiliyGpsgiGKTtlakel.......g 23 
                                   + i+ +G +g+GKTt+++++       +
  gi|91772186|ref|YP_564878.1| 172 VHIVFIGINGTGKTTTISKMakrlkdmK 199
                                   67999**************965555444 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033       0.2      10      36 ..     167     193 ..     159     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                                   T.TTEEEEEEEESTTSSHHHHHHHHHH CS
                           Arf  10 lkkkelrilllGLDnaGKtTilkklkl 36 
                                    ++k ++i+++G+ ++GKtT + k+ +
  gi|91772186|ref|YP_564878.1| 167 DAEKPVHIVFIGINGTGKTTTISKMAK 193
                                   56899***************9999865 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00029      0.17      21      65 ..     155     209 ..     113     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                                   ...............TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHH CS
                        ResIII  21 s.............krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprks 65 
                                   s             ++  ++++    GtGKT ++ k+++rl+  ++    ++++ + +
  gi|91772186|ref|YP_564878.1| 155 SanvfdlddyirdaEKPVHIVFIGINGTGKTTTISKMAKRLKDMKY---SVVIAAGDT 209
                                   155555566666556666999********************99755...456665555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1         3   1.8e+03      97      97 ..     111     111 ..      46     160 .. 0.48
   2 ?   11.5   0.1   0.00036      0.21      18      55 ..     170     205 ..     157     300 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3
                      ATPase_2  97 e 97 
                                    
  gi|91772186|ref|YP_564878.1| 111 I 111
                                   1 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00036
                      ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyi 55 
                                   +p +i+fi G  g GKt+ + +++++l+d ++ v+ + 
  gi|91772186|ref|YP_564878.1| 170 KPVHIVFI-GINGTGKTTTISKMAKRLKDMKYSVV-IA 205
                                   34455555.*******************9988765.33 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.2   2.5e+03      11      54 ..      62     121 ..      62     157 .. 0.53
   2 ?   10.7   0.1   0.00095      0.57       1      25 [.     174     203 ..     174     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.2
                        AAA_18  11 KttlakeLskrlgf................gvnlrdvakenglllevdpealdeskrlde 54 
                                   Kt+ +  L+++ gf                g  + d ++e ++ l + + a++  + ++e
  gi|91772186|ref|YP_564878.1|  62 KTEASPSLKQKIGFaqkakalvferevildGSDIEDSLWELEMALLESDIAINVAEAIVE 121
                                   555556665555555555555555555666666666666666666666663333333222 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00095
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....g 25 
                                   I+  G+ G+GKtt     +krl  +    +
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRLkDMkysvV 203
                                   8899*****************866665553 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.54   3.2e+02      66     120 ..     112     164 ..      70     171 .. 0.70
   2 ?    9.5   0.2    0.0014      0.86      12      88 ..     181     261 ..     172     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.54
                        AAA_31  66 eknikeaiiktkvenldlipssidLaeaeielvelekkeeilkellekvkdeYDy 120
                                    +n++eai+  ++ + +l+ s  +L +   elve   +  i+k +  +v d  Dy
  gi|91772186|ref|YP_564878.1| 112 AINVAEAIV--ESVKEELVGSRKKLGKNTGELVENALRSAIYKVMSANVFDLDDY 164
                                   456677777..55577899999999999999998888888777666666555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0014
                        AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevl...ieeknikeaiiktkvenldlipssi 88 
                                   G GKTTt  ++a+ l  +++ v +   D+  + ++ ++ i+ ++i  +l++        + + +a++++k +n+d++ s++
  gi|91772186|ref|YP_564878.1| 181 GTGKTTTISKMAKRLKDMKYSVVIAAGDTFRAGAIdQIAIHAERIGVKLIKHQeggDPAAVVYDAVQHAKAHNVDVVLSDT 261
                                   89*********************9999986554442667777777777777753422445566777777777777777765 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       5.4   3.2e+03     157     198 ..      22      63 ..      18      73 .. 0.78
   2 ?   10.2   0.0    0.0006      0.36       4      41 ..     174     211 ..     172     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.4
                                   TS---HHHHHHHHHHHHTS--SSSTT-------HHHHHHHHH CS
                         KTI12 157 eeklpldeilkaliekkklkpnqatlskplaeanflqeLdke 198
                                   e++++l+e ++ ++e ++ ++  +t + +++ ++f ++Ldk+
  gi|91772186|ref|YP_564878.1|  22 EKAVELKEPVEEIVEIEPAEKPVSTPEVSENVSSFEDQLDKT 63 
                                   667777777888888888888888888888888888888875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0006
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                   +v+ G+  +GK+t  +++ak l++ k+svv+   ++++
  gi|91772186|ref|YP_564878.1| 174 IVFIGINGTGKTTTISKMAKRLKDMKYSVVIAAGDTFR 211
                                   899****************************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 2406.32
//
Query:       gi|91772187|ref|YP_564879.1|  [L=138]
Description: prefoldin subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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   84.3   0.6    8.3e-24   83.8   0.3    1.3  1  Prefoldin      Prefoldin subunit
    1.2e-06   28.5   4.0     0.0033   17.3   0.1    2.1  2  Prefoldin_2    Prefoldin subunit
     0.0059   16.8   0.4        2.7    8.3   0.0    2.2  2  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
     0.0061   16.6   1.4        1.9    8.6   0.3    2.2  2  DUF148         Domain of unknown function DUF148
     0.0072   16.4   1.6        2.2    8.3   0.1    2.2  2  DUF1664        Protein of unknown function (DUF1664)
  ------ inclusion threshold ------
      0.017   13.7   0.0      0.017   13.7   0.0    1.2  1  KAR9           Yeast cortical protein KAR9
      0.017   15.6   1.3        1.5    9.3   0.1    2.2  2  NPV_P10        Nucleopolyhedrovirus P10 protein
      0.017   15.3   2.3        3.2    7.9   1.1    2.2  2  Med30          Mediator complex subunit 30
      0.026   15.0   0.8       0.09   13.3   0.7    1.8  1  DUF16          Protein of unknown function DUF16
      0.054   13.3   2.4        2.6    7.9   0.1    2.2  2  CdvA           CdvA-like coiled-coil domain
      0.058   13.7   3.4       0.24   11.8   0.1    2.7  3  Flagellin_C    Bacterial flagellin C-terminal helical region
      0.076   13.2   1.1        4.3    7.6   0.0    2.1  2  Cortex-I_coil  Cortexillin I, coiled coil
      0.077   13.6   0.6        8.6    7.0   0.2    2.2  2  Syntaxin-6_N   Syntaxin 6, N-terminal
       0.13   11.2   2.1        4.5    6.1   0.6    2.0  2  IFT57          Intra-flagellar transport protein 57
        1.3    7.8   4.4        7.8    5.3   1.4    2.0  2  Spc7           Spc7 kinetochore protein


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 !   83.8   0.3     7e-27   8.3e-24       1     112 [.      19     130 ..      19     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 7e-27
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHH CS
                     Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiel 81 
                                   l++++es++++l+ ++ +ie++++++ tl++lk +   +++++plgag+ + a++ d dk++v++Gag++vek+  eAie+
  gi|91772187|ref|YP_564879.1|  19 LQQNAESVNQQLGMVQMSIEDCTRAILTLEELKSASGAINTMIPLGAGALIHANIADVDKIVVSVGAGISVEKTPTEAIET 99 
                                   6899***************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittlea 112
                                   l +++eel k +e l+  l+++ +++ ++e 
  gi|91772187|ref|YP_564879.1| 100 LTQRKEELGKVVERLNGTLTQIGQRLASIES 130
                                   **********************999999886 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.7   7.3e-05     0.087       2      43 ..      11      52 ..      10      79 .. 0.90
   2 !   17.3   0.1   2.8e-06    0.0033      56      97 ..      89     130 ..      71     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                   Prefoldin_2  2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelellde 43
                                  +l+++ ++lqq  + + qq+ ++++ ++++  ++ +le+l++
  gi|91772187|ref|YP_564879.1| 11 NLAAQHRELQQNAESVNQQLGMVQMSIEDCTRAILTLEELKS 52
                                  5789999*******************************9987 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.8e-06
                                   EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  56 vkqdkeevkeeLeerketlekeiktlekqleklekeleelke 97 
                                   v+++ +e++e+L +rke+l k++++l+  l+++ ++l+ +++
  gi|91772187|ref|YP_564879.1|  89 VEKTPTEAIETLTQRKEELGKVVERLNGTLTQIGQRLASIES 130
                                   889999*******************************99886 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.2    0.0065       7.7      32      66 ..      10      44 ..       2      64 .. 0.58
   2 !    8.3   0.0    0.0022       2.7      60     108 .]      88     136 ..      81     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0065
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT CS
                  Seryl_tRNA_N 32 leldekrrelqveleelqaerNelskeIgkakkkk 66
                                    l ++ relq+ +e+++++   ++ +I+ + ++ 
  gi|91772187|ref|YP_564879.1| 10 RNLAAQHRELQQNAESVNQQLGMVQMSIEDCTRAI 44
                                  34555666666666666666666666665555554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0022
                                   CCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS---- CS
                  Seryl_tRNA_N  60 gkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPNip 108
                                   +  k   e +e l ++ +el++ +++l+ +l+++ ++l ++ +a++N p
  gi|91772187|ref|YP_564879.1|  88 SVEKTPTEAIETLTQRKEELGKVVERLNGTLTQIGQRLASIESAVGNRP 136
                                   5556666999*******************************99999965 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.3    0.0016       1.9      37      71 ..       5      39 ..       1      62 [. 0.87
   2 !    7.2   0.0    0.0043       5.2      51      91 ..      89     129 ..      85     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                        DUF148 37 ykefeakvkaqkeevkknvtavisnLssvqeklea 71
                                   ++  ++++aq+ e+++n+++v ++L  vq ++e+
  gi|91772187|ref|YP_564879.1|  5 SEQDARNLAAQHRELQQNAESVNQQLGMVQMSIED 39
                                  57778999*******************99988876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0043
                        DUF148  51 vkknvtavisnLssvqekleaIldnkslTrkeqkeaieelk 91 
                                   v+k  t++i++L++ +e+l ++++  + T  +  +++ +++
  gi|91772187|ref|YP_564879.1|  89 VEKTPTEAIETLTQRKEELGKVVERLNGTLTQIGQRLASIE 129
                                   789999******************99999999999888776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.2    0.0031       3.7      54      92 ..       9      47 ..       1      63 [. 0.65
   2 !    8.3   0.1    0.0019       2.2      49      87 ..      92     130 ..      67     134 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                       DUF1664 54 seslaatkrhLssridrvdkkldeqkeiskeikeevtev 92
                                    +laa+ r+L+++ ++v+++l  ++  +++ ++ + ++
  gi|91772187|ref|YP_564879.1|  9 ARNLAAQHRELQQNAESVNQQLGMVQMSIEDCTRAILTL 47
                                  566777777777777777777776666666666655554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0019
                       DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeike 87 
                                     ++  e+l++ k++L + ++r++ +l +  +  ++i++
  gi|91772187|ref|YP_564879.1|  92 TPTEAIETLTQRKEELGKVVERLNGTLTQIGQRLASIES 130
                                   334444555555555555555555555555444444444 PP

>> KAR9  Yeast cortical protein KAR9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.017     125     169 ..      24      80 ..      11     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                          KAR9 125 ELwnsvlgdlgeEiedliklileleekrlss............pkkgldifeLetiv 169
                                   E +n+ lg +++ ied+++ il lee + +s            +  + +i + ++iv
  gi|91772187|ref|YP_564879.1|  24 ESVNQQLGMVQMSIEDCTRAILTLEELKSASgaintmiplgagALIHANIADVDKIV 80 
                                   446889************************988777777776666666666666666 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.023        27      12      37 ..      22      47 ..       6      62 .. 0.46
   2 ?    9.3   0.1    0.0013       1.5       8      66 ..      68     126 ..      67     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.023
                       NPV_P10 12 dikavddkVdalqqqvddvqenlpdv 37
                                  + + v++++  +q +++d +  + ++
  gi|91772187|ref|YP_564879.1| 22 NAESVNQQLGMVQMSIEDCTRAILTL 47
                                  22233333333333333333333333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0013
                       NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   +I a+i++vd+ V ++ + +   ++  + ++ l+++ +++ + ++ l+ ++++I + L 
  gi|91772187|ref|YP_564879.1|  68 LIHANIADVDKIVVSVGAGISVEKTPTEAIETLTQRKEELGKVVERLNGTLTQIGQRLA 126
                                   68999*************99888888999999999999999999999999999977665 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.1    0.0027       3.2     100     134 ..       3      37 ..       1      61 [. 0.86
   2 ?    6.9   0.0    0.0058       6.9      98     136 ..      89     127 ..      71     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
                         Med30 100 rkkseevkqlkeerkelleklkeknkqLkeimdql 134
                                   +++ +++++l ++++el+++ + +n+qL +++  +
  gi|91772187|ref|YP_564879.1|   3 ETSEQDARNLAAQHRELQQNAESVNQQLGMVQMSI 37 
                                   4567899*********************9887655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0058
                         Med30  98 eerkkseevkqlkeerkelleklkeknkqLkeimdqlrk 136
                                    e++++e +++l+++++el + ++  n  L +i ++l +
  gi|91772187|ref|YP_564879.1|  89 VEKTPTEAIETLTQRKEELGKVVERLNGTLTQIGQRLAS 127
                                   577888999999999999999999999999999888765 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   7.6e-05      0.09      22     104 .]      16     130 ..      10     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
                                   HHHHHHB-..BHHHHHHHHHHHH................................HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DUF16  22 rkqlnefkdsnkqrLkkieakvd.............................klgeqinkleqkvekqgekikelkveqka 73 
                                   +++l++  +s +q+L  ++  ++                                 +i+ + ++v   g+ i+  k   +a
  gi|91772187|ref|YP_564879.1|  16 HRELQQNAESVNQQLGMVQMSIEdctrailtleelksasgaintmiplgagaLIHANIADVDKIVVSVGAGISVEKTPTEA 96 
                                   899999999999999999999999999999999999999999999999999877788999999999999999877776666 PP

                                   HHH..........HHHHHHHHHHHHHHHHHHHC- CS
                         DUF16  74 qgeeln...kvdetleliletLqkinkRlDsieg 104
                                    +   +   ++++ +e +  tL++i++Rl sie+
  gi|91772187|ref|YP_564879.1|  97 IETLTQrkeELGKVVERLNGTLTQIGQRLASIES 130
                                   6654444447777888888899999999999996 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.012        15      24      66 ..       9      47 ..       1      59 [. 0.48
   2 ?    7.9   0.1    0.0022       2.6      29      62 ..      98     131 ..      88     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                          CdvA 24 kekleealkklkekakelkeklkkrlkeledqikslekalanl 66
                                   ++l  + ++l+++a+     ++++l+ ++  i+  ++a+++l
  gi|91772187|ref|YP_564879.1|  9 ARNLAAQHRELQQNAE----SVNQQLGMVQMSIEDCTRAILTL 47
                                  4444444444444444....44555555555555555554444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0022
                          CdvA  29 ealkklkekakelkeklkkrlkeledqiksleka 62 
                                   e+l++ ke+  ++ e+l+  l+++ + ++s+e+a
  gi|91772187|ref|YP_564879.1|  98 ETLTQRKEELGKVVERLNGTLTQIGQRLASIESA 131
                                   5677888888888888888888888888888876 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 ?   -1.0   0.1         2   2.4e+03      66      81 ..       7      22 ..       3      26 .. 0.66
   2 ?    1.8   0.2      0.27   3.2e+02      12      37 ..      24      49 ..      16      61 .. 0.72
   3 ?   11.8   0.1    0.0002      0.24       5      43 ..      94     132 ..      91     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                                  HHHHHHHHHCTCCHHH CS
                   Flagellin_C 66 qasyallaqanqlpqs 81
                                  q +  l aq ++l+q+
  gi|91772187|ref|YP_564879.1|  7 QDARNLAAQHRELQQN 22
                                  5556677777777776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.27
                                  HHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Flagellin_C 12 dkvrselGavqnRlesaitnlkaqse 37
                                  ++v  +lG+vq  +e+ + ++ +  e
  gi|91772187|ref|YP_564879.1| 24 ESVNQQLGMVQMSIEDCTRAILTLEE 49
                                  56777899999999888877766554 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH CS
                   Flagellin_C   5 deaitdldkvrselGavqnRlesaitnlkaqsenlkaae 43 
                                   +eai++l++ + elG v +Rl+ + t++ +    +++a+
  gi|91772187|ref|YP_564879.1|  94 TEAIETLTQRKEELGKVVERLNGTLTQIGQRLASIESAV 132
                                   58**************************99999888876 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.034        40      40      74 ..      10      44 ..       2      54 .. 0.76
   2 ?    7.6   0.0    0.0036       4.3      31      67 ..      96     132 ..      69     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil 40 delesllasleseaaerekrlreleakldealknl 74
                                   +l    + l+++a+  +++l  ++  +++  + +
  gi|91772187|ref|YP_564879.1| 10 RNLAAQHRELQQNAESVNQQLGMVQMSIEDCTRAI 44
                                  46677778899999999999999999999988875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil  31 sreelikqkdelesllasleseaaerekrlreleakl 67 
                                   + e l ++k+el +++  l++   +  +rl+ +e+ +
  gi|91772187|ref|YP_564879.1|  96 AIETLTQRKEELGKVVERLNGTLTQIGQRLASIESAV 132
                                   34679999*************************9976 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0072       8.6      35      64 ..       8      37 ..       1      61 [. 0.52
   2 ?    5.2   0.0     0.027        32      34      64 ..      99     132 ..      69     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0072
                  Syntaxin-6_N 35 tseeldetrteLrkalrsiewdledLeetv 64
                                     +l  +++eL+++ +s++++l   + ++
  gi|91772187|ref|YP_564879.1|  8 DARNLAAQHRELQQNAESVNQQLGMVQMSI 37
                                  345555566666666666666665555555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.027
                  Syntaxin-6_N  34 s...tseeldetrteLrkalrsiewdledLeetv 64 
                                   +   ++eel +  + L+ +l +i + l  +e +v
  gi|91772187|ref|YP_564879.1|  99 TltqRKEELGKVVERLNGTLTQIGQRLASIESAV 132
                                   1333799999999999999999999999999888 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.6    0.0038       4.5     271     312 ..       8      49 ..       4      59 .. 0.82
   2 ?    4.7   0.0      0.01        12     236     271 ..      97     131 ..      88     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0038
                         IFT57 271 qleellqeyreaqeelsevkekykqlsegvseltrelaeise 312
                                     ++l +++re+q++ ++v++++ +++ +++++tr   +++e
  gi|91772187|ref|YP_564879.1|   8 DARNLAAQHRELQQNAESVNQQLGMVQMSIEDCTRAILTLEE 49 
                                   567889999*******************99999997766644 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                         IFT57 236 ieeslpetksqlkklhedisktlekiesrEkylnsq 271
                                   ie+ l++ k++l k+ e ++ tl++i +r   ++s 
  gi|91772187|ref|YP_564879.1|  97 IET-LTQRKEELGKVVERLNGTLTQIGQRLASIESA 131
                                   443.44448888888888888888888887777665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.4    0.0065       7.8     212     257 ..       6      51 ..       2      59 .. 0.76
   2 ?    3.6   0.1     0.021        25     156     188 ..      98     130 ..      88     135 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0065
                          Spc7 212 kaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervl 257
                                   +++ +++ +++ elq++ e++++++  ++ +++++  +i   e+++
  gi|91772187|ref|YP_564879.1|   6 EQDARNLAAQHRELQQNAESVNQQLGMVQMSIEDCTRAILTLEELK 51 
                                   5667777888888888888888888888888888888887777665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                          Spc7 156 elLekqeeeldellpeleeekaeleeeleklqe 188
                                   e+L++++eel +++++l+   +++ ++l+++++
  gi|91772187|ref|YP_564879.1|  98 ETLTQRKEELGKVVERLNGTLTQIGQRLASIES 130
                                   456666666666666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 954.22
//
Query:       gi|91772188|ref|YP_564880.1|  [L=58]
Description: 50S ribosomal protein LX [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-10   40.3   0.2    3.3e-10   40.1   0.2    1.1  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 !   40.1   0.2   1.9e-14   3.3e-10      67     120 ..       2      55 ..       1      56 [. 0.97

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.9e-14
                                   ............TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEE CS
                Ribosomal_L18A  67 knygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekv 120
                                   +ny++   ++  +++++f+k++++ +e++a +++ s++gs+hr+ r  I+Ie+v
  gi|91772188|ref|YP_564880.1|   2 QNYVVKGTFKAGHSWEKFTKNVESQNEKNARDKTLSTFGSKHRIVRALIKIESV 55 
                                   7999999*********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 470.34
//
Query:       gi|91772189|ref|YP_564881.1|  [L=217]
Description: translation initiation factor IF-6 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-66  221.1   4.8    9.8e-66  220.9   4.8    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 !  220.9   4.8   5.5e-70   9.8e-66       2     197 .]       5     196 ..       4     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 220.9 bits;  conditional E-value: 5.5e-70
                                   E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHHH CS
                         eIF-6   2 lsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklkes 82 
                                   ++i++++ +Gvfa++t+++a+vp g++ + ++ ++e+L+v+v++t i+gs +vGsl  gNsng+l+++ ++ ++l+ ++  
  gi|91772189|ref|YP_564881.1|   5 VNIYDNPVLGVFATCTEDVAIVPIGTAGKAIDLLAEQLDVKVISTLINGSIVVGSLSKGNSNGFLISRDANVSDLKDVE-- 83 
                                   789****************************************************************999888888887.. PP

                                   HH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT--HHHH CS
                         eIF-6  83 lkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkateeel 163
                                     ++ve+l++ ltA+GNvilaND++Alvhp+++++++e+i+ vLgv+v rgtiag+ tvG+a+vvtn+gllvhp +t +el
  gi|91772189|ref|YP_564881.1|  84 --VPVEVLPDMLTAVGNVILANDTAALVHPEMTDSSIEVISRVLGVDVHRGTIAGLGTVGMAGVVTNRGLLVHPMVTPDEL 162
                                   ..78999************************************************************************** PP

                                   HHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                         eIF-6 164 eeleellkveveagTvNrGsklvgsglvaNdkga 197
                                   + le+++ +++e gT N+Gs+ vgsgl+aN+kg+
  gi|91772189|ref|YP_564881.1| 163 SVLEDVFALPIELGTTNYGSQAVGSGLLANSKGY 196
                                   ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1771.06
//
Query:       gi|91772190|ref|YP_564882.1|  [L=88]
Description: 50S ribosomal protein L31e [Methanococcoides burtonii DSM 6242]
Scores for 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-08   32.2   0.1    1.1e-07   32.0   0.1    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 !   32.0   0.1   5.9e-12   1.1e-07       7      71 ..      11      76 ..       5      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.9e-12
                Ribosomal_L31e  7 ytInihkrihgvgfkkraprAlkeikkfamkemg..tpdvridtrLnkavwakgirnvpyrirvrls 71
                                  ytI   +  + + + kr  rA+  i+k+  ++m+   +  +id+++n  +w++g +++p  ir+r +
  gi|91772190|ref|YP_564882.1| 11 YTIP-LREAKLAPRWKRTGRAMSLIRKYLVRHMKadPSQIKIDATINHRIWERGSQKPPSSIRIRAA 76
                                  7787.66777888899******************533445***********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 644.06
//
Query:       gi|91772191|ref|YP_564883.1|  [L=51]
Description: 50S ribosomal protein L39e [Methanococcoides burtonii DSM 6242]
Scores for complete 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   75.7   8.7    1.8e-21   75.5   8.7    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   8.7     1e-25   1.8e-21       2      41 ..       9      48 ..       8      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1e-25
                 Ribosomal_L39  2 KlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkL 41
                                  K+rLaKa +qN++vP Wv++kt+rkv ++pkrRhWRr++L
  gi|91772191|ref|YP_564883.1|  9 KIRLAKAHNQNQRVPTWVIIKTNRKVVSHPKRRHWRRNSL 48
                                  9*************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 00:00:00.39
# Mc/sec: 391.84
//
Query:       gi|91772192|ref|YP_564884.1|  [L=197]
Description: hypothetical protein Mbur_0116 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.17   11.5   0.0    1.3  1  Asn_synthase  Asparagine synthase
       0.12   12.4   0.2       0.32   11.0   0.0    1.8  2  DUF3969       Protein of unknown function (DUF3969)


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.9e-05      0.17      22      82 ..       5      61 ..       2      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
                  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvltee 82
                                  +l+SGG DSSl a l++ +   ++  ++++f     +    ak +a++lg  h+ l+l+  
  gi|91772192|ref|YP_564884.1|  5 VLFSGGKDSSLSAILLDPFF--DIELVTCTF--SILPVGNIAKVTADELGFSHRVLELDLT 61
                                  789****************9..79*******..9999999*************99888655 PP

>> DUF3969  Protein of unknown function (DUF3969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.28   2.5e+03      49      60 ..      63      74 ..      36     100 .. 0.67
   2 ?   11.0   0.0   3.6e-05      0.32      32      77 ..     147     192 ..     117     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.28
                       DUF3969 49 lsdelveiihkg 60
                                  l+  l  ii++g
  gi|91772192|ref|YP_564884.1| 63 LETALNTIIEDG 74
                                  444455555554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.6e-05
                       DUF3969  32 esllFslemlelieelelsdelveiihkgmeLEDvesliPeeLeds 77 
                                   ++l+      + i +++++ el+e+i + ++ E v ++ P++L+  
  gi|91772192|ref|YP_564884.1| 147 KHLVIDEGQSDSIAKADYETELRELIRQQYGNEKVIDIFPQHLQSR 192
                                   55555555667899*****************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1419.36
//
Query:       gi|91772193|ref|YP_564885.1|  [L=114]
Description: hypothetical protein Mbur_0117 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-28   99.1  20.9    1.9e-28   98.9  20.9    1.0  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.066   12.7   2.1      0.071   12.6   2.1    1.1  1  MTBP_N          MDM2-binding
       0.08   13.1   0.1       0.17   12.1   0.1    1.7  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
        2.4    7.8   9.4       0.42   10.3   2.2    2.1  2  PAXX            PAXX, PAralog of XRCC4 and XLF, also called C


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 !   98.9  20.9   4.3e-32   1.9e-28       1     107 [.       7     112 ..       7     114 .] 0.91

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 4.3e-32
                                   XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS CS
                    dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGql 81 
                                   ir++rlaelq+q++s +++++a+ qqeq ++a+++e+ +a+L+q+++peAreRL+r+rl+++e +e++e++L++laq+G+l
  gi|91772193|ref|YP_564885.1|   7 IRQKRLAELQQQQSSPQNDAQAAYQQEQ-AQAERDEQVKAVLRQVMTPEARERLTRLRLSRKELVEQLESQLVMLAQNGRL 86 
                                   9***********9988876654444444.44479*********************************************** PP

                                   -----HHHHHHHHHHHS---XXXXX. CS
                    dsDNA_bind  82 rskvteeqLkeLLeqvaekkketkiv 107
                                   ++k+++e+Lk LL+q++ +k++t+i+
  gi|91772193|ref|YP_564885.1|  87 QTKIDDEKLKVLLTQMQPQKRQTSIT 112
                                   ***********************995 PP

>> MTBP_N  MDM2-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.1   1.6e-05     0.071      73     142 ..      14      83 ..       6     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                        MTBP_N  73 gsfQfcsSdWeelsadsekedseeslqtaleeclsalqeleeedsnsrdslsltdlleeaAeslhqLsdk 142
                                   +  Q  sS  ++ +a+ ++e+ + + +++++++l+++ + e+++  +r +ls ++l+e+   +l++L+++
  gi|91772193|ref|YP_564885.1|  14 ELQQQQSSPQNDAQAAYQQEQAQAERDEQVKAVLRQVMTPEARERLTRLRLSRKELVEQLESQLVMLAQN 83 
                                   56788899999********************************************************975 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 ?   12.1   0.1   3.7e-05      0.17       2      28 ..      41      67 ..      40     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                  HHHHHHHTT-B-TTTSSBCCCCT---E CS
                FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvre 28
                                  e+v a+Lr+V++Pe    l+ l+l r+
  gi|91772193|ref|YP_564885.1| 41 EQVKAVLRQVMTPEARERLTRLRLSRK 67
                                  89***************9999988665 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 ?    2.2   1.7     0.028   1.3e+02     127     157 ..       9      39 ..       2      51 .. 0.73
   2 ?   10.3   2.2   9.3e-05      0.42      99     136 ..      46      83 ..      37     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.028
                                   HHHHHTHHT-XXXXXXXXXXXXXXXXXXXXX CS
                          PAXX 127 ekrlaaveesavsPrKksqragaefePdkdq 157
                                   +krla+++++  sP+ + q a ++ + + ++
  gi|91772193|ref|YP_564885.1|   9 QKRLAELQQQQSSPQNDAQAAYQQEQAQAER 39 
                                   5899************999998874443333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.3e-05
                                   EEEE--HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHT- CS
                          PAXX  99 eLskledpeaaerlkaLllelAervaqlekrlaavees 136
                                    L ++  pea+erl  L l+  e v qle++l  ++++
  gi|91772193|ref|YP_564885.1|  46 VLRQVMTPEARERLTRLRLSRKELVEQLESQLVMLAQN 83 
                                   588999*************************9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2634  (0.146913); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 777.53
//
Query:       gi|91772194|ref|YP_564886.1|  [L=149]
Description: 30S ribosomal protein S19e [Methanococcoides burtonii DSM 6242]
Scores for complete 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  191.5   0.0    5.6e-57  191.3   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e


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 !  191.3   0.0   3.1e-61   5.6e-57       1     136 [.       3     137 ..       3     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.3 bits;  conditional E-value: 3.1e-61
                                   TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS---- CS
                Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgkkrr 81 
                                   t++dVpa+++i++lae+Lk+++++++Pewa++vKtg++ke +p d+dW+y+R+A+i+R +y++gpvGverlr+vYGgkk+r
  gi|91772194|ref|YP_564886.1|   3 TAYDVPASDIIAKLAENLKENDQIKPPEWAAFVKTGVHKEHSPVDKDWWYIRCAAIMRTIYMQGPVGVERLRSVYGGKKNR 83 
                                   689****************************************************************************** PP

                                   ---THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                Ribosomal_S19e  82 gvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                   g +ps+++k+sgsv+r+++qqLe++g+v+k  k+gr+++++Gq+lld++++ev++
  gi|91772194|ref|YP_564886.1|  84 GANPSRKAKGSGSVVREAFQQLETAGFVRKL-KSGRVIAPAGQSLLDNLSTEVKN 137
                                   ****************************888.55******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 983.55
//
Query:       gi|91772195|ref|YP_564887.1|  [L=423]
Description: adenylosuccinate synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-163  544.4   0.0     2e-163  544.2   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 !  544.2   0.0  1.1e-167    2e-163       2     418 ..       4     420 ..       3     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 544.2 bits;  conditional E-value: 1.1e-167
                                   EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHHHTT CS
               Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleEiee 82 
                                   ++ G+q+GDEGKGkivDll++++d+vvRfqGG+nAGHtvvv++  yklhl+pSG l  + + +iG+g+v++pe+l+eEi++
  gi|91772195|ref|YP_564887.1|   4 ILTGSQFGDEGKGKIVDLLSKDYDLVVRFQGGDNAGHTVVVGDDVYKLHLIPSGFLL-DSRVLIGPGTVLNPEVLAEEIDM 83 
                                   789*****************************************************7.6677******************* PP

                                   SS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHHHHHHHHHH CS
               Adenylsucc_synt  83 leakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeeleeklekll 163
                                   le+ gve+s+++l i++++ +++pyh++lD+l+e+ ++ +kiGtTkkGiG ay dk+ar  +r+ dl+d+e l ++l++++
  gi|91772195|ref|YP_564887.1|  84 LEKTGVEVSSDKLGIDAKTSIIMPYHVELDSLRESLRK-EKIGTTKKGIGFAYVDKIARDEVRMSDLVDSEILMNRLTEMA 163
                                   ***********************************885.9***************************************** PP

                                   HHTHHHHHHT.....T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SH CS
               Adenylsucc_synt 164 elknkllekldk..eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSntta 242
                                   + k++ +++l    + ++ +el++++ k+ +rl+pyv+d+++++n+a++egk+vL EGaqgt+lD+ hGt  fvTsS+t+a
  gi|91772195|ref|YP_564887.1| 164 ASKEAAIRELGGdpSIVTDSELMDKYVKLGQRLAPYVTDVSYEINKAISEGKNVLAEGAQGTFLDVIHGTQKFVTSSSTIA 244
                                   *********977665555589************************************************************ PP

                                   HHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHHHT-SE CS
               Adenylsucc_synt 243 ggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwlDlvllryavrvngvte 323
                                   g+a++ lg++p+k+devlg+vKAy+trvGeGp+ptel+de+g +l+++G+Efgtttgr RrcGw+Dl+ll++a+++ng+t+
  gi|91772195|ref|YP_564887.1| 245 GSACANLGVGPTKVDEVLGIVKAYITRVGEGPLPTELHDEAGAHLHDVGHEFGTTTGRSRRCGWFDLPLLKKAINLNGYTS 325
                                   ********************************************************************************* PP

                                   EEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT---GGGS-HHHHHHHHHHHHHHTS CS
               Adenylsucc_synt 324 laltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgvrsfedlpenakkyvefieellgv 404
                                   +altklDvl++ld +kvcvaY+l+g++ld+ p++++ l+ ++p+y el+gW++d++gv+++ed+ ++a++yve +e ++gv
  gi|91772195|ref|YP_564887.1| 326 VALTKLDVLSDLDVVKVCVAYDLNGERLDYPPEDTSLLSMCKPIYDELEGWSDDLTGVKRYEDIARAAHDYVEKLEGMMGV 406
                                   ********************************************************************************* PP

                                   -EEEEE-SSSTT-E CS
               Adenylsucc_synt 405 pvkiisvGpereqt 418
                                   p+k++svGp+reqt
  gi|91772195|ref|YP_564887.1| 407 PIKYVSVGPGREQT 420
                                   ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2962.02
//
Query:       gi|91772196|ref|YP_564888.1|  [L=221]
Description: hexapaptide repeat-containing transferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-30  103.2  25.8    3.9e-08   32.7   3.5    5.4  5  Hexapep     Bacterial transferase hexapeptide (six repeats)
    3.1e-17   62.0  28.4    2.1e-06   27.3   7.1    5.6  5  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.069   13.4   0.6      0.069   13.4   0.6    2.5  3  Bactofilin  Polymer-forming cytoskeletal
       0.13   10.7   0.2       0.18   10.3   0.2    1.2  1  DUF3686     ATPase involved in DNA repair


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 !    9.8   0.1   0.00015      0.66       2      29 ..       5      32 ..       4      33 .. 0.59
   2 !   13.4   0.0   1.1e-05     0.047      18      34 ..      55      71 ..      53      73 .. 0.86
   3 !   29.8   2.3   7.4e-11   3.3e-07       1      35 [.      74     108 ..      74     109 .. 0.93
   4 !   32.7   3.5   8.6e-12   3.9e-08       1      35 [.     110     144 ..     110     145 .. 0.96
   5 !   30.0   0.7     6e-11   2.7e-07       2      36 .]     159     193 ..     158     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                                  EEEETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIg 29
                                  t I+s ++I   + ig+n ++ +nv++g
  gi|91772196|ref|YP_564888.1|  5 TNIHSSAKIYGTSFIGDNSVVLENVILG 32
                                  5566666666666666666666666655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.1e-05
                                  TTEEE-TTEEEETTEEE CS
                       Hexapep 18 gnVkIGdnvkIgagvvi 34
                                   +++IG n+ I ++++i
  gi|91772196|ref|YP_564888.1| 55 TGCTIGANSFIRPNTTI 71
                                  68999999999999998 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 7.4e-11
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   ++++G+n   g++++i++n++IGdnv Ig +v i 
  gi|91772196|ref|YP_564888.1|  74 NVRTGDNFRTGHNCMIRENTTIGDNVLIGTNVIID 108
                                   5899****************************996 PP

  == domain 4  score: 32.7 bits;  conditional E-value: 8.6e-12
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   +++IG+nv I  +++i  +V+I dnv Ig+++v++
  gi|91772196|ref|YP_564888.1| 110 NVKIGNNVSIQGNVYIPTHVIIEDNVFIGPCAVLA 144
                                   689******************************97 PP

  == domain 5  score: 30.0 bits;  conditional E-value: 6e-11
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   +vI +++ Ig++a+i+++V+IG+++ ++ g+ +++
  gi|91772196|ref|YP_564888.1| 159 PVIRKGASIGANATILPGVEIGEGAMVAGGALVTK 193
                                   79*****************************9985 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   0.00051       2.3       8      32 ..       5      31 ..       3      33 .. 0.86
   2 !    6.5   0.4    0.0016       7.1       3      16 ..      58      71 ..      55      89 .. 0.61
   3 !   27.3   7.1   4.8e-10   2.1e-06       1      32 [.      92     125 ..      92     126 .. 0.95
   4 !   11.9   0.1   3.1e-05      0.14       2      14 ..     129     141 ..     128     144 .. 0.88
   5 !   21.2   0.6   4.1e-08   0.00018       9      34 .]     166     193 ..     161     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00051
                                  -EE-TT-EE.SEE.E-TT-EE-TT-EE CS
                     Hexapep_2  8 CliGanagi.Gvs.lGdncvvgaGvvi 32
                                  ++i+++a i G+s +Gdn+vv  +v++
  gi|91772196|ref|YP_564888.1|  5 TNIHSSAKIyGTSfIGDNSVVLENVIL 31
                                  68999999999988*******888876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0016
                                  EE-TT-EE-TT-EE CS
                     Hexapep_2  3 iIGdnCliGanagi 16
                                  +IG+n++i +n +i
  gi|91772196|ref|YP_564888.1| 58 TIGANSFIRPNTTI 71
                                  45555555555555 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 4.8e-10
                                   .EEE-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                     Hexapep_2   1 pviIGdnCliGanagi.G.vslGdncvvgaGvvi 32 
                                   +++IGdn+liG n +i G v++G+n+ ++ +v+i
  gi|91772196|ref|YP_564888.1|  92 NTTIGDNVLIGTNVIIdGnVKIGNNVSIQGNVYI 125
                                   589*************979**************9 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 3.1e-05
                                   EEE-TT-EE-TT- CS
                     Hexapep_2   2 viIGdnCliGana 14 
                                   viI+dn++iG+ a
  gi|91772196|ref|YP_564888.1| 129 VIIEDNVFIGPCA 141
                                   9*********966 PP

  == domain 5  score: 21.2 bits;  conditional E-value: 4.1e-08
                                   EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                     Hexapep_2   9 liGanagi..GvslGdncvvgaGvvita 34 
                                    iGana+i  Gv++G+++ v+ G  +t+
  gi|91772196|ref|YP_564888.1| 166 SIGANATIlpGVEIGEGAMVAGGALVTK 193
                                   59*********************99996 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.95   4.3e+03      69      79 ..       6      16 ..       2      30 .. 0.64
   2 ?   13.4   0.6   1.5e-05     0.069       3      70 ..      65     137 ..      47     146 .. 0.48
   3 ?   -0.2   0.0      0.28   1.3e+03      44      56 ..     174     187 ..     157     209 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.95
                    Bactofilin 69 elkktakveGd 79
                                  +++++ak+ G+
  gi|91772196|ref|YP_564888.1|  6 NIHSSAKIYGT 16
                                  55566666554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.5e-05
                    Bactofilin   3 igegtkikGelevegdlri..dGkveGdieakgklvvgeggkvegnika.eevvvaGtvk..Gnveaeekvel 70 
                                   i ++t+i  ++++ +++r   +  ++ + + ++++ +g +  ++gn+k  ++v+++G+v     v +e++v +
  gi|91772196|ref|YP_564888.1|  65 IRPNTTIFSNVRTGDNFRTghNCMIRENTTIGDNVLIGTNVIIDGNVKIgNNVSIQGNVYipTHVIIEDNVFI 137
                                   4444444444444444444333334444444455555555555555555444555555432233333333333 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.28
                    Bactofilin  44 egnika.eevvvaG 56 
                                      ++  e + vaG
  gi|91772196|ref|YP_564888.1| 174 LPGVEIgEGAMVAG 187
                                   33333322233333 PP

>> DUF3686  ATPase involved in DNA repair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2     4e-05      0.18      27      59 ..      78     110 ..      64     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4e-05
                       DUF3686  27 tervrtenncvardivavgdlllfGynvklglk 59 
                                    +  rt +nc+ r+  ++gd +l+G nv ++ +
  gi|91772196|ref|YP_564888.1|  78 GDNFRTGHNCMIRENTTIGDNVLIGTNVIIDGN 110
                                   56789**********************988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1641.77
//
Query:       gi|91772197|ref|YP_564889.1|  [L=358]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-138  462.0   0.2   1.8e-138  461.8   0.2    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.5e-07   28.2   0.1      1e-06   27.5   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    8.4e-07   28.6   0.8    3.7e-06   26.4   0.8    1.8  1  Beta_elim_lyase  Beta-eliminating lyase
    4.4e-06   25.9   0.9    1.5e-05   24.1   0.9    1.8  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.8   0.2    4e-142  1.8e-138       2     360 ..       9     353 ..       8     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 461.8 bits;  conditional E-value: 4e-142
                                   HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHH CS
               DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavle 82 
                                   i+eee+eav +vl+sg++ +g++v+eFE++fa y+g++ha+av+sGtaAlh aL a g+g+gdeVI++s++F+atan++++
  gi|91772197|ref|YP_564889.1|   9 IGEEEIEAVCKVLRSGMIAEGKRVAEFEEEFASYIGTEHAVAVNSGTAALHAALLAHGIGNGDEVITTSFSFIATANSIMY 89 
                                   789****************************************************************************** PP

                                   TT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSS CS
               DegT_DnrJ_EryC1  83 lgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgd 163
                                   +gakpvfvD+ pdt+nidp  +e++it +tkaI+pVhlyG++a+m+a+++ia++h+l++ieDa++A+Ga y gkkvG++g 
  gi|91772197|ref|YP_564889.1|  90 TGAKPVFVDIVPDTFNIDPTLVEEKITDNTKAIMPVHLYGHPAEMKAITDIAKDHDLILIEDACQAHGAAYGGKKVGSFG- 169
                                   ********************************************************************************. PP

                                   EEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHH CS
               DegT_DnrJ_EryC1 164 aavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarR 244
                                   +++fSFyptKn+tt eGG+++tndee+a+ka+++r+hG++    +ry +e+ +Gyn+r+t+i AAigl+qL++l + ++ R
  gi|91772197|ref|YP_564889.1| 170 TGAFSFYPTKNMTTSEGGMMTTNDEEVAKKAKMIRAHGSQ----QRYLHEM-IGYNLRMTDIGAAIGLTQLKKLPSYNSLR 245
                                   899***********************************99....8******.***************************** PP

                                   HHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCC CS
               DegT_DnrJ_EryC1 245 reiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerkeea 325
                                   +++a+l++++L++ +g++ + +++  + h +h+y+++++     +rde++++l ++gigt v+yp+p+h+qp+y++  ++ 
  gi|91772197|ref|YP_564889.1| 246 QRNASLLSKGLRNTDGITIPVVKEGCE-HMFHQYTIRLN-----NRDEMLTKLGQAGIGTGVYYPIPIHMQPIYKDAGYT- 319
                                   ***************986666666666.***********.....89*******************************766. PP

                                   CHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
               DegT_DnrJ_EryC1 326 sgdlpnaerlaervlsLplypelteedvdrVveal 360
                                    ++lp  e+++++vlsLp++p+++e++++++++a+
  gi|91772197|ref|YP_564889.1| 320 -DKLPECEKASKEVLSLPVHPGVSEDEIQQIIDAV 353
                                   .46*****************************997 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   0.1   2.3e-10     1e-06      56     178 ..      34     156 ..      29     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.3e-10
                                   HHHHHHHHHHT-SEEEEESSHHHHHHHHHHT.TS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST..TSHHHHHHH CS
               Cys_Met_Meta_PP  56 vleeriaaLeggeaalavssGmaAiaaaila.llkaGdeivvsddlYggtqrllkkvlkklgievkfvdt..sdleeleka 133
                                    +ee+ a   g+e+a+av+sG+aA++aa+la  + +Gde+++++  +  t + + ++  k      + dt   d+  +e++
  gi|91772197|ref|YP_564889.1|  34 EFEEEFASYIGTEHAVAVNSGTAALHAALLAhGIGNGDEVITTSFSFIATANSIMYTGAKPVFVDIVPDTfnIDPTLVEEK 114
                                   6899999999***************99877516999****************9999988843332233332347889**** PP

                                   CCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTH CS
               Cys_Met_Meta_PP 134 ikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfas 178
                                   i++ntk++    p     + + +++i+++ak+++++++ D++ a 
  gi|91772197|ref|YP_564889.1| 115 ITDNTKAIM---PVHLYGHPAEMKAITDIAKDHDLILIEDACQAH 156
                                   *******96...677777778899999999999999998887665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.8   8.3e-10   3.7e-06      29     280 ..      27     267 ..      23     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 8.3e-10
                                   T--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.T CS
               Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.G 107
                                   +e k v ++e+++a ++g+e+a+ v +GtaA + +l ++    g+evi t+ +   f  t +   + g+k++ +++  +  
  gi|91772197|ref|YP_564889.1|  27 AEGKRVAEFEEEFASYIGTEHAVAVNSGTAALHAALLAHGiGNGDEVITTSFS---FIATANSIMYTGAKPVFVDIVPDtF 104
                                   6778999*****************************99988999999888765...5556677788999998888665337 PP

                                   BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTT CS
               Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsy 188
                                   ++d+  +e++i++      ++k+i+      +  G    ++e++++++iak++++ l+ D++    aa   g +v +   +
  gi|91772197|ref|YP_564889.1| 105 NIDPTLVEEKITD------NTKAIMPVHL--Y--GH---PAEMKAITDIAKDHDLILIEDACQAHGAA-YGGKKVGSFGTG 171
                                   8888888888888......6777765433..3..44...67889999***************999988.777777777665 PP

                                   SSEEEEESSSTT--SS-EEEEE-HH...........HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHHH CS
               Beta_elim_lyase 189 vDsvtmslkKdllanvGgvlafrddel.......edylaerveqrkylggglrqagvlaaleagiraleeglaslerdhkt 262
                                      +++  +K++++  Gg++ ++d+e            ++ + +++++g +lr  ++ aa   g+  l++     +  +++
  gi|91772197|ref|YP_564889.1| 172 --AFSFYPTKNMTTSEGGMMTTNDEEVakkakmiRAHGSQQRYLHEMIGYNLRMTDIGAA--IGLTQLKKLPSYNSLRQRN 248
                                   ..589999****************988888444422223334446777888888888888..8888888775555555667 PP

                                   HHHHHHHHHHCT--.EEEC CS
               Beta_elim_lyase 263 aeqlaeklelvrla.iprr 280
                                   a+ l ++l++++++ ip  
  gi|91772197|ref|YP_564889.1| 249 ASLLSKGLRNTDGItIPVV 267
                                   7777777777776524444 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.9   3.4e-09   1.5e-05      43     181 ..      30     157 ..      23     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.4e-09
                                   HHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE. CS
                   Aminotran_5  43 kaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipld. 122
                                   k v e +e++a  i++e     + + ++t a+ +++l+    + +gde+++t+    a+    + ++  tgak +++ +  
  gi|91772197|ref|YP_564889.1|  30 KRVAEFEEEFASYIGTEH--A-VAVNSGTAALHAALLAH--GIGNGDEVITTSFSFIATA---NSIM-YTGAKPVFVDIVp 101
                                   567899999******996..4.55555565777766655..48*********98776666...7776.7888877776651 PP

                                   TTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
                   Aminotran_5 123 eegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                                   ++ ++d+  +e++++++tk+++  h     G   ++++i+++ak+++ +++ Da+qa g
  gi|91772197|ref|YP_564889.1| 102 DTFNIDPTLVEEKITDNTKAIMPVHL---YGHPAEMKAITDIAKDHDLILIEDACQAHG 157
                                   5679***************9998885...8**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.40
# Mc/sec: 2715.95
//
Query:       gi|91772198|ref|YP_564890.1|  [L=313]
Description: oxidoreductase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-29  102.5   0.4    5.4e-29  101.5   0.4    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    3.1e-05   24.0   0.0    5.4e-05   23.2   0.0    1.4  1  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta
    3.4e-05   24.4   0.1    7.3e-05   23.3   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      9e-05   22.6   0.4     0.0023   18.0   0.1    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00011   22.3   3.2     0.0017   18.5   0.9    2.7  3  DapB_N           Dihydrodipicolinate reductase, N-terminus
    0.00017   21.8   1.1    0.00053   20.2   1.1    1.9  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0015   19.2   0.6     0.0046   17.6   0.6    1.8  1  CoA_binding      CoA binding domain
     0.0026   17.2   0.3     0.0076   15.6   0.1    1.8  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.042   13.2   2.2       0.12   11.7   1.2    2.1  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.049   12.6   0.2      0.084   11.8   0.2    1.4  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
       0.05   13.0   0.1      0.082   12.3   0.1    1.3  1  Rota_VP4_MID     Rotavirus VP4 membrane interaction domain
      0.051   13.9   0.1       0.14   12.5   0.1    1.9  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
       0.11   13.0   1.0       0.82   10.1   1.0    2.2  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


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 !  101.5   0.4   3.9e-32   5.4e-29       1     120 []       4     121 ..       4     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 3.9e-32
                                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelaka 81 
                                   +rv++iG+G +g++h+r + e  ++ e+v++ d d++r +++a+++gv+a++d+++ll+ +  dav++++p+++h++++++
  gi|91772198|ref|YP_564890.1|   4 IRVGVIGVGAMGQHHVRIYSEM-EEVELVGISDVDQKRVQELADQYGVKAFTDHNKLLD-EGLDAVSIVVPTTLHKKVTLD 82 
                                   69**************777777.999*********************************.66******************* PP

                                   HHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                  GFO_IDH_MocA  82 aleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                   a++ + +vl+EKP+a+t+e a+ ++e+aek+g +++vg+
  gi|91772198|ref|YP_564890.1|  83 AINSNTNVLVEKPIADTLENADIMIEAAEKAGLTLMVGH 121
                                   *************************************97 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.9e-08   5.4e-05       1     100 [.     133     217 ..     133     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.9e-08
                                   HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSC CS
                GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaede 81 
                                   Ke Ie+g lG++vs++     tr+  ++ +r +     + G+  dlg+HdiD   +   ++ s+v+a+    + ++ +ed 
  gi|91772198|ref|YP_564890.1| 133 KEIIESGLLGRIVSIS-----TRRVGPYNPRIR-----DVGIILDLGVHDIDAISYMYASNVSEVYAIA--GKDVHSQEDH 201
                                   89*************7.....999999999999.....67****************************6..4555455444 PP

                                   SEEEEEEEEEEETTEEEEE CS
                GFO_IDH_MocA_C  82 daavmsvlnlekgsgevit 100
                                        + l++e+++  v++
  gi|91772198|ref|YP_564890.1| 202 AS---IMLRFEDNRAGVAN 217
                                   44...47777777766655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   5.3e-08   7.3e-05       1      81 [.       5      83 ..       5     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.3e-08
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81
                                  ++g+iG G mg+  ++  ++   + + +  +++ ++++++ela+++gvk+++ +n+ + e  d v + v+++ +++v  ++
  gi|91772198|ref|YP_564890.1|  5 RVGVIGVGAMGQHHVRIYSEME-EVELVG-ISDVDQKRVQELADQYGVKAFTDHNKLLDEGLDAVSIVVPTTLHKKVTLDA 83
                                  69**************777776.555566.66********************8888888899********99999987555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.7e-06    0.0023      14      90 ..       5      81 ..       2      90 .. 0.86
   2 ?    4.9   0.1     0.018        25      31     103 ..      59     130 ..      56     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                                  EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB CS
                  Shikimate_DH 14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepil 90
                                  +v +iG G m++  ++  ++  +v+ v +   +++r++ela+++ g+++ + + + l+e l+++ +v+  t ++++ l
  gi|91772198|ref|YP_564890.1|  5 RVGVIGVGAMGQHHVRIYSEMeEVELVGISDVDQKRVQELADQY-GVKAFTDHNKLLDEGLDAVSIVVPTTLHKKVTL 81
                                  799*************999865899999****************.555777777888999999****99999988766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                                   HHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCHHH.S CS
                  Shikimate_DH  31 LlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeeveealkkrk 103
                                   Ll++g+++v ++  t  + k   + ++++ +++l  + + + l++ad++i a       l  +++e+ + +++
  gi|91772198|ref|YP_564890.1|  59 LLDEGLDAVSIVVPTTLHKKVTLDAINSN-TNVLVEKPIADTLENADIMIEAAEKAGLTLMVGHIERFNPATS 130
                                   77777777777766666666666666444.7777778899**************9999999999999876654 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.9   1.2e-06    0.0017       1      75 [.       4      74 ..       4      86 .. 0.77
   2 ?    3.6   0.1     0.049        68      51      78 ..      85     113 ..      66     123 .. 0.79
   3 ?   -3.0   0.0       5.6   7.8e+03      59      90 ..     193     224 ..     175     236 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH....-SEEEE-S CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek....advliDFT 75
                                  i+v+v+G+ G mG++ v+  +e e++elv+  d ++     k + el++  + gv+ ++d +++l++    + +++  T
  gi|91772198|ref|YP_564890.1|  4 IRVGVIGV-GAMGQHHVRIYSEMEEVELVGISDVDQ-----KRVQELAD--QYGVKAFTDHNKLLDEgldaVSIVVPTT 74
                                  79*****9.**********************99987.....34444443..6899999999998888743344666555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.049
                                   S.--S-BEBSSHHHHHHH-SEEEE-S-HH CS
                        DapB_N  51 g.klgvavtddleevlekadvliDFTtpe 78 
                                   + +++v v++ ++++le+ad++i+    +
  gi|91772198|ref|YP_564890.1|  85 NsNTNVLVEKPIADTLENADIMIEAAEKA 113
                                   33899******************987665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.6
                                   SSHHHHHHH-SEEEE-S-HHHHHHHHHHHHHT CS
                        DapB_N  59 ddleevlekadvliDFTtpeavlenlklalek 90 
                                   +d+++  ++a +++ F    a ++n+++++ +
  gi|91772198|ref|YP_564890.1| 193 KDVHSQEDHASIMLRFEDNRAGVANTNWLTPH 224
                                   34444444455555555555555555555544 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 !   20.2   1.1   3.8e-07   0.00053       1      87 [.       5     107 ..       5     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.8e-07
                                   EEEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHC.SEEEE-SSSHHHHHHHHHS.. CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnl..lkagykvavynrtkekveelvae.gakaaesieelvasl.dvvitmvkagkavdevieg.. 75 
                                   ++g+iG+G MG++ ++    +++   v + ++++++v+el+++ g+ka+++ ++l+++  d+v ++v+ + + + +++   
  gi|91772198|ref|YP_564890.1|   5 RVGVIGVGAMGQHHVRIYseMEEVELVGISDVDQKRVQELADQyGVKAFTDHNKLLDEGlDAVSIVVPTTLHKKVTLDAin 85 
                                   58***********999884344555677889**********9956999999999997655*******99888777776644 PP

                                   ..........HCCC--TT-EEE CS
                 NAD_binding_2  76 ..........llealkkgdili 87 
                                             ++++l++ di+i
  gi|91772198|ref|YP_564890.1|  86 sntnvlvekpIADTLENADIMI 107
                                   4555555555555555555555 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6   3.3e-06    0.0046       5      89 ..       5      90 ..       2      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                                  EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET..TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHT CS
                   CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl..glpvyksvdeleektevdvavitvPaesaqeavdelvea 85
                                  +v+viG+g +g+  +   +e+ +++++ + +v+ + v +  +  g++++++ ++l ++ + d+  i+vP +  +++++++++ 
  gi|91772198|ref|YP_564890.1|  5 RVGVIGVGAMGQHHVRIYSEMEEVELVGISDVDQKRVQELADqyGVKAFTDHNKLLDE-GLDAVSIVVPTTLHKKVTLDAINS 86
                                  89*********************************888555566*****999999999.9********************998 PP

                                  T-SE CS
                   CoA_binding 86 gikg 89
                                  + ++
  gi|91772198|ref|YP_564890.1| 87 NTNV 90
                                  7765 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 !   15.6   0.1   5.5e-06    0.0076      38     106 ..       5      78 ..       3      88 .. 0.79
   2 ?   -1.9   0.0       1.3   1.8e+03     145     160 ..     187     202 ..     179     225 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                                   EEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH..CHHHHTC.EECSHHHHHHH.-SEEEE-S--STTTT CS
                  2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgm.kviaydrskkkee..eeeelgv.elvsleellae.sDivslhlpltpetr 106
                                   +vG+iG+G++Gq+  ++ ++++  ++++++   +k+    ++++gv  +++ ++ll e  D vs+++p t + +
  gi|91772198|ref|YP_564890.1|   5 RVGVIGVGAMGQHHVRIYSEMEEvELVGISDVDQKRVqeLADQYGVkAFTDHNKLLDEgLDAVSIVVPTTLHKK 78 
                                   79*****************88644988887776655545577888866779999998736********987665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                   SCCEEEES--SSSSSG CS
                  2-Hacid_dh_C 145 kiagaalDvfeeeplp 160
                                     a a+ Dv+++e+  
  gi|91772198|ref|YP_564890.1| 187 VYAIAGKDVHSQEDHA 202
                                   5678899999999544 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 ?   11.7   1.2   8.6e-05      0.12      30      99 ..       5     110 ..       2     136 .. 0.75
   2 ?   -0.5   0.0      0.45   6.1e+02      38      71 ..     231     267 ..     230     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                                   EEEEESTSHHHHHHHHHHHHTT-E..EEEEESSHHHHHHHHH.TTTCECEE.............................. CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgak..VtvlDvrparleqles.lgakfvev.............................. 77 
                                   +v viG+G  G++ +++ ++++ +  V + Dv+++r ++l + +g k ++                               
  gi|91772198|ref|YP_564890.1|   5 RVGVIGVGAMGQHHVRIYSEMEEVelVGISDVDQKRVQELADqYGVKAFTDhnklldegldavsivvpttlhkkvtldain 85 
                                   799******************975559999******999999788774443566666666666666666666666666666 PP

                                   ...HCHHHHHHHHHHHH-SEEEE-- CS
                   AlaDh_PNT_C  78 ...lksqeellaeavkeadvvigtv 99 
                                          e+ +a+++++ad++i ++
  gi|91772198|ref|YP_564890.1|  86 sntNVLVEKPIADTLENADIMIEAA 110
                                   5555555566666666666666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.45
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH...TT CS
                   AlaDh_PNT_C  38 vaGlqAiatakglgakVtvlDvrparleqles...lg 71 
                                   v G+  +     ++++Vt++D +  r  ++e+   l 
  gi|91772198|ref|YP_564890.1| 231 VIGVDGVGYLDYIDQTVTIHDANWVRDAKVEKgepLA 267
                                   5677777777788999999999999999988766433 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 ?   11.8   0.2   6.1e-05     0.084     132     209 ..       6      82 ..       4     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                                   EEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCH....HHHTTSSEEEE----SS-SB CS
               OCD_Mu_crystall 132 laiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsacksee....eavegadivvtvTaakapil 208
                                   +++iG G++ + ++++ +++ +++ v i d+d++  + +a++       v+a ++ +    e  + + ivv +T+ k+  l
  gi|91772198|ref|YP_564890.1|   6 VGVIGVGAMGQHHVRIYSEMEEVELVGISDVDQKRVQELADQYG-----VKAFTDHNklldEGLDAVSIVVPTTLHKKVTL 81 
                                   79*********************************999999876.....67777765111134455678888888888555 PP

                                   - CS
               OCD_Mu_crystall 209 k 209
                                    
  gi|91772198|ref|YP_564890.1|  82 D 82 
                                   4 PP

>> Rota_VP4_MID  Rotavirus VP4 membrane interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     6e-05     0.082      50     126 ..     182     263 ..     164     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                  Rota_VP4_MID  50 vnytysytrdgeevta...hvtisvnnvkeray..ggslptdfkvskfevldedsyvyidywddseifknvvyvrdlaadl 125
                                    n +  y+ +g++v +   h++i +   ++ra        t  kv k+ev+  d   y+dy d++  +++  +vrd + + 
  gi|91772198|ref|YP_564890.1| 182 SNVSEVYAIAGKDVHSqedHASIMLRFEDNRAGvaNTNWLTPHKVRKMEVIGVDGVGYLDYIDQTVTIHDANWVRDAKVEK 262
                                   4666677777777754333666666555555432355667889*********************************98876 PP

                  Rota_VP4_MID 126 g 126
                                   g
  gi|91772198|ref|YP_564890.1| 263 G 263
                                   6 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1    0.0001      0.14       1      37 [.       4      39 ..       4      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                  CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HH CS
                       Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindltdle 37
                                  ++v++ G G +G+  +r+  e +e+e+v i d+   +
  gi|91772198|ref|YP_564890.1|  4 IRVGVIGVGAMGQHHVRIYSEMEEVELVGISDVD-QK 39
                                  69*****************************953.33 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 ?   10.1   1.0    0.0006      0.82       1      83 [.       5      80 ..       5     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0006
                                  EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHH CS
                Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskela 83
                                  +v+++G  G++Gq  +r+ +e  evelv ++  +++  ++la+ ++  + +   k+ d      +++d v   +p   +k+++
  gi|91772198|ref|YP_564890.1|  5 RVGVIG-VGAMGQHHVRIYSEMEEVELVGISDVDQKRVQELADQYGVKAFTDHNKLLD------EGLDAVSIVVPTTLHKKVT 80
                                  79****.9*********************99999966666666666222222222222......4444444444555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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 0.22s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2407.65
//
Query:       gi|91772199|ref|YP_564891.1|  [L=165]
Description: VanZ like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-17   62.2   2.5    9.8e-17   61.8   2.5    1.1  1  VanZ      VanZ like family
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.043   13.6   0.0    1.5  1  DUF2238   Predicted membrane protein (DUF2238)
          9    6.5   7.1        5.4    7.2   0.0    2.8  3  Pox_A9    A9 protein conserved region


Domain annotation for each model (and alignments):
>> VanZ  VanZ like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   2.5   1.6e-20   9.8e-17       3     124 ..      14     149 ..      11     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.6e-20
                          VanZ   3 lylllllyliffpssqnaeessslsglvsklinlipfkeikrllkere......lea.li..vgnvalfvp...lGfllpl 71 
                                   ++ ll + +if+ s+q++ e  s+s++    + l ++ ++k+     +      ++   i  + +va++v    lG+ll +
  gi|91772199|ref|YP_564891.1|  14 AFSLLYAGFIFYLSAQSSIELPSSSSIPF--YDL-LLDSVKNS----NipylvdIAHySIdnFDKVAHMVLyfgLGILLHV 87 
                                   56678888********9988766654443..333.33444444....122223333334477**********999****** PP

                          VanZ  72 llkkk....flk......vlllgfllslsiElhQlfvpgRsfdvdDvilntlGallGillyll 124
                                   +++++    + k      ++l+g+ + +++E+hQ++vpgR+++++D++ + +G++l+ +++++
  gi|91772199|ref|YP_564891.1|  88 TFRHSdnlkL-KkyapifAILIGITYGITDEIHQMYVPGRASSFNDLVADGIGIALAQIVFWV 149
                                   **99997643.2689999**************************************9999985 PP

>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.2e-06     0.043      48     109 ..      58     121 ..      48     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.2e-06
                       DUF2238  48 lkelfglernkYDrlvHfaqGlllalvvrelllrkkkl..rkwllllavlvvlaisalYEliEw 109
                                   l ++ + + +++D+++H++ ++ l +++   ++++ +l  +k++ ++a+l+ ++ + + E+ ++
  gi|91772199|ref|YP_564891.1|  58 LVDIAHYSIDNFDKVAHMVLYFGLGILLHVTFRHSDNLklKKYAPIFAILIGITYGITDEIHQM 121
                                   567889999**************99999888888888866667777777777777666666555 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.93   5.5e+03      25      32 ..       7      14 ..       6      27 .. 0.71
   2 ?    7.2   0.0    0.0009       5.4      30      49 ..      72      91 ..      69      95 .. 0.79
   3 ?    2.2   1.0     0.034     2e+02      22      31 ..     147     156 ..     141     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.93
                        Pox_A9 25 Vvlksiis 32
                                  Vv++++++
  gi|91772199|ref|YP_564891.1|  7 VVFRILVA 14
                                  78888775 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0009
                        Pox_A9 30 iisMvmyLvlGvaLlyissn 49
                                  +  Mv+y+ lG+ L   + +
  gi|91772199|ref|YP_564891.1| 72 VAHMVLYFGLGILLHVTFRH 91
                                  678*********99766655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.034
                        Pox_A9  22 fafVvlksii 31 
                                   f+ V+lks++
  gi|91772199|ref|YP_564891.1| 147 FWVVILKSVF 156
                                   9******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1193.19
//
Query:       gi|91772200|ref|YP_564892.1|  [L=326]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-26   91.3  15.8    6.3e-26   91.3  15.8    2.0  3  Glycos_transf_4  Glycosyl transferase family 4
  ------ inclusion threshold ------
       0.95    9.5   7.1       0.18   11.8   1.7    2.6  2  SHP              Small hydrophobic protein


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 ?   -2.0   0.1      0.35   3.1e+03     114     114 ..      61      61 ..       7      82 .. 0.53
   2 !   91.3  15.8     7e-30   6.3e-26       3     158 ..      86     238 ..      84     240 .. 0.93
   3 ?   -3.0   0.1       0.7   6.2e+03     107     127 ..     299     319 ..     288     322 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.35
               Glycos_transf_4 114 l 114
                                   +
  gi|91772200|ref|YP_564892.1|  61 I 61 
                                   1 PP

  == domain 2  score: 91.3 bits;  conditional E-value: 7e-30
               Glycos_transf_4   3 lllltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNavNl 83 
                                   ++l++i+l+++ G+lDD+ ++  + Kl+l   ++ +li ++  + t l l+++ + ielg++++ +++  ++++++N vN+
  gi|91772200|ref|YP_564892.1|  86 VVLIVISLFGIFGILDDMIDIGRVSKLFLMYYCSYPLIQYA--THTALVLPSF-GHIELGILYLQFIVPTYVLVASNLVNM 163
                                   6899********************************97764..4555555555.78****99999**************** PP

               Glycos_transf_4  84 iDGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlail 158
                                     G++Gla+g+s+i++ +l++ +++ g+ e +++++a+ gallG++l+ ryp+++F G++gsl++G+++++++++
  gi|91772200|ref|YP_564892.1| 164 HSGYNGLASGLSAIVLSSLIIKSILLGDVENIYTIIAITGALLGYFLYDRYPSHIFWGNVGSLTIGATIGAFIVI 238
                                   *********************************************************************998876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.7
               Glycos_transf_4 107 avdgrsellllalallgallG 127
                                   +++++ +++++al+  + l+G
  gi|91772200|ref|YP_564892.1| 299 LTEKQATYAMYALTGFFCLIG 319
                                   444445555553333333355 PP

>> SHP  Small hydrophobic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.27   2.5e+03      26      37 ..      18      29 ..       3      40 .. 0.58
   2 ?   11.8   1.7     2e-05      0.18       6      37 ..      69     100 ..      66     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.27
                           SHP 26 tlislliiitim 37
                                   l+  li++ti 
  gi|91772200|ref|YP_564892.1| 18 NLLLPLILVTIS 29
                                  333345555553 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2e-05
                           SHP   6 itieftskfwpyftlihmiltlislliiitim 37 
                                   ++i fts f+ y t  +++l +isl+ i  i+
  gi|91772200|ref|YP_564892.1|  69 LAISFTSLFFKYSTTNYVVLIVISLFGIFGIL 100
                                   5799*********************9998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1873.69
//
Query:       gi|91772201|ref|YP_564893.1|  [L=418]
Description: hypothetical protein Mbur_0125 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-10   39.2   6.2    1.9e-09   37.9   6.2    1.8  1  Cohesin   Cohesin domain


Domain annotation for each model (and alignments):
>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   6.2     1e-13   1.9e-09      12     119 ..      46     148 ..      35     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1e-13
                                   TTSEEEEEEEEESECTTEEEEEEEEEE.TTTEEEEEEEE-TTS.SSGGHCEEEEEEC.GTTEEEEEEE.TTSSSTTCBEES CS
                       Cohesin  12 vGdtvtvpvtvsnvskkvaaaqftikYDpavlevvsvkaGsiv.knssvnfgsnlle.epgkikflfldlaslgssgiaek 90 
                                    G++vtv + v+     v++aqf++ +D  +l v+s+++G+i+    s+ f+  +++  +g i  ++ +l   g++ ++ k
  gi|91772201|ref|YP_564893.1|  46 IGSNVTVIIYVDPDVP-VSGAQFDLDFDGDILSVISISEGDIFtNGVSTLFSGGTIDnLEGNIMNVYGALF--GKNEVI-K 122
                                   59*************9.**************************8777888877655545677777766666..9999**.* PP

                                   SEEEEEEEEEESTTS-TCEEEEEEEEEEE CS
                       Cohesin  91 dgvlatitfkvkskaaegttaikisdtls 119
                                   +g++ati+f  ks+    +++ ++s++++
  gi|91772201|ref|YP_564893.1| 123 SGTFATIVFETKSSG---SSSLQLSNVVV 148
                                   **************9...44444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3079.94
//
Query:       gi|91772202|ref|YP_564894.1|  [L=313]
Description: TPR repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   53.0   4.5    1.1e-05   25.0   0.1    3.4  3  TPR_1       Tetratricopeptide repeat
    1.5e-11   43.4   2.2     0.0003   20.7   0.1    3.5  3  TPR_2       Tetratricopeptide repeat
    1.1e-09   37.8   2.6     0.0018   18.3   0.2    3.3  3  TPR_8       Tetratricopeptide repeat
    1.4e-07   31.0   0.0     0.0003   20.6   0.0    2.6  2  TPR_7       Tetratricopeptide repeat
    4.5e-07   29.8   0.1     0.0026   18.0   0.1    2.7  2  TPR_17      Tetratricopeptide repeat
    5.6e-07   29.8   0.0     0.0061   16.8   0.0    2.4  2  TPR_12      Tetratricopeptide repeat
    1.7e-05   25.3   0.5       0.12   12.9   0.0    2.7  3  TPR_19      Tetratricopeptide repeat
    2.8e-05   24.6   0.0       0.76   10.8   0.0    3.3  3  TPR_14      Tetratricopeptide repeat
    5.5e-05   23.2   0.0      0.032   14.4   0.0    2.3  2  TPR_9       Tetratricopeptide repeat
    0.00011   22.6   0.5       0.41   11.4   0.1    2.8  2  TPR_6       Tetratricopeptide repeat
    0.00032   21.3   0.0    0.00059   20.4   0.0    1.5  1  TPR_16      Tetratricopeptide repeat
    0.00052   19.8   0.9     0.0038   17.0   0.1    2.4  2  TPR_10      Tetratricopeptide repeat
     0.0007   19.2   1.0     0.0066   16.1   0.0    3.0  4  TPR_11      TPR repeat
     0.0095   16.0   2.8       0.13   12.3   0.4    2.8  3  Fis1_TPR_C  Fis1 C-terminal 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 !    6.2   0.0    0.0075       9.6      22      34 .]     109     121 ..     108     121 .. 0.92
   2 !   25.0   0.1     9e-09   1.1e-05       2      25 ..     123     146 ..     122     151 .. 0.91
   3 !   22.1   0.2   7.1e-08   9.1e-05       3      33 ..     160     190 ..     158     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0075
                                   HHHHHHHHHSTTH CS
                         TPR_1  22 eyyekALelnPnn 34 
                                    y++ AL+++P+n
  gi|91772202|ref|YP_564894.1| 109 HYFKMALQIQPKN 121
                                   79*********98 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 9e-09
                                   HHHHHHHHHHHHTT-HHHHHHHHH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyye 25 
                                   +al+n+G++++++g++ eA++yye
  gi|91772202|ref|YP_564894.1| 123 RALNNMGLLLQQKGEFREAIKYYE 146
                                   79*********************8 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 7.1e-08
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                    +yn+++++  lg+++ A  y ++AL   P+
  gi|91772202|ref|YP_564894.1| 160 LYYNIAVCLKLLGNLEGAKTYINRALAKKPD 190
                                   6**************************9997 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.28   3.6e+02      22      34 .]     109     121 ..     108     121 .. 0.90
   2 !   19.0   0.1   8.1e-07     0.001       2      25 ..     123     146 ..     122     151 .. 0.90
   3 !   20.7   0.1   2.4e-07    0.0003       3      33 ..     160     190 ..     158     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.28
                         TPR_2  22 eafekAleldPnn 34 
                                   ++f+ Al++ P+n
  gi|91772202|ref|YP_564894.1| 109 HYFKMALQIQPKN 121
                                   69*********97 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 8.1e-07
                         TPR_2   2 ealynlGlayyklgdyeeAleafe 25 
                                   +al+n+Gl++ ++g++ eA++++e
  gi|91772202|ref|YP_564894.1| 123 RALNNMGLLLQQKGEFREAIKYYE 146
                                   69*********************9 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 2.4e-07
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   ++yn++ ++  lg++e A+ + ++Al+  P+
  gi|91772202|ref|YP_564894.1| 160 LYYNIAVCLKLLGNLEGAKTYINRALAKKPD 190
                                   69*************************9997 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.6   3.3e+03      23      34 .]     110     121 ..     104     121 .. 0.86
   2 !   18.3   0.2   1.4e-06    0.0018       2      25 ..     123     146 ..     122     151 .. 0.93
   3 !   17.8   0.1     2e-06    0.0026       2      29 ..     159     186 ..     158     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHH. CS
                         TPR_8  23 yyekaleldpdn 34 
                                   y++ al+++p+n
  gi|91772202|ref|YP_564894.1| 110 YFKMALQIQPKN 121
                                   89999****986 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.4e-06
                                   CHHHHHHHHHHHTT-HHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyye 25 
                                   +a++n+g++++++g++ eA++yye
  gi|91772202|ref|YP_564894.1| 123 RALNNMGLLLQQKGEFREAIKYYE 146
                                   89*********************9 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2e-06
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                   ++yyn++ +++ lg++e Ak y+++al 
  gi|91772202|ref|YP_564894.1| 159 PLYYNIAVCLKLLGNLEGAKTYINRALA 186
                                   78************************95 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.3e-07    0.0003       1      24 [.     124     147 ..     124     157 .. 0.91
   2 !    7.9   0.0    0.0027       3.5       2      34 ..     161     191 ..     160     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeq 24 
                                   aL+n++ l ++ G+++eAi++ye 
  gi|91772202|ref|YP_564894.1| 124 ALNNMGLLLQQKGEFREAIKYYEI 147
                                   89********************95 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0027
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                   ++n+a++   lG+ e A ++  +  al+k p++
  gi|91772202|ref|YP_564894.1| 161 YYNIAVCLKLLGNLEGAKTYINR--ALAKKPDE 191
                                   89*********************..77766654 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     2e-06    0.0026       2      34 .]     111     143 ..     110     143 .. 0.93
   2 !    9.0   0.0    0.0016         2      13      33 ..     158     178 ..     156     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   ++ al++ P+n  a+nn++ ll ++G++++A++
  gi|91772202|ref|YP_564894.1| 111 FKMALQIQPKNIRALNNMGLLLQQKGEFREAIK 143
                                   6779***************************85 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0016
                        TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                   +++y+n A++l+ +G+l+ A+
  gi|91772202|ref|YP_564894.1| 158 SPLYYNIAVCLKLLGNLEGAK 178
                                   689**************9986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.8e-06    0.0061      44      69 ..     121     146 ..     108     150 .. 0.80
   2 !   10.4   0.0   0.00047       0.6       6      31 ..     161     186 ..     157     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.8e-06
                        TPR_12  44 tattlrnLgrlyralgryeeAlelle 69 
                                    +++l+n+g l+++ g+++eA++++e
  gi|91772202|ref|YP_564894.1| 121 NIRALNNMGLLLQQKGEFREAIKYYE 146
                                   47888888888888888888888887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00047
                        TPR_12   6 lnnlaavlrrlgrydeAlellekale 31 
                                   ++n+a++l  lg+++ A ++ ++al+
  gi|91772202|ref|YP_564894.1| 161 YYNIAVCLKLLGNLEGAKTYINRALA 186
                                   66888888888888888888888875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00087       1.1      13      46 ..     110     143 ..     108     149 .. 0.93
   2 !   12.9   0.0   9.5e-05      0.12      27      59 ..     160     192 ..     151     201 .. 0.87
   3 ?   -2.1   0.0       4.6   5.9e+03      43      67 ..     219     241 ..     217     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00087
                        TPR_19  13 lleqalqedpknaearllLAeallalgqldeAea 46 
                                   +++ alq  pkn +a+ ++  +l + g++ eA++
  gi|91772202|ref|YP_564894.1| 110 YFKMALQIQPKNIRALNNMGLLLQQKGEFREAIK 143
                                   6899****************************97 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.5e-05
                        TPR_19  27 arllLAeallalgqldeAealLdalpeedpdda 59 
                                   + ++ A +l  lg+l+ A+  ++++++++pd++
  gi|91772202|ref|YP_564894.1| 160 LYYNIAVCLKLLGNLEGAKTYINRALAKKPDEE 192
                                   78999**************************54 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.6
                        TPR_19  43 eAealLdalpeedpddaryasLlAk 67 
                                   +A ++ d+++e+dp   ++a+L  +
  gi|91772202|ref|YP_564894.1| 219 KASDVADPYGEWDPP--AIATLASQ 241
                                   788889999999997..66666655 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      0.31   3.9e+02      23      42 ..     110     129 ..     103     131 .. 0.85
   2 !    8.8   0.0    0.0025       3.2       7      30 ..     128     151 ..     122     167 .. 0.85
   3 !   10.8   0.0   0.00059      0.76       8      35 ..     165     192 ..     157     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.31
                        TPR_14  23 llrralalaPddaeawllla 42 
                                   +++ al+ +P++ +a+  ++
  gi|91772202|ref|YP_564894.1| 110 YFKMALQIQPKNIRALNNMG 129
                                   7999*********9987665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                        TPR_14   7 laeallalGdpdeAiallrralal 30 
                                   ++ +l + G+++eAi++++ +++l
  gi|91772202|ref|YP_564894.1| 128 MGLLLQQKGEFREAIKYYEIIISL 151
                                   67788899***********99986 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00059
                        TPR_14   8 aeallalGdpdeAiallrralalaPdda 35 
                                   a  l  lG++++A ++ +rala+ Pd++
  gi|91772202|ref|YP_564894.1| 165 AVCLKLLGNLEGAKTYINRALAKKPDEE 192
                                   5556779******************976 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.5e-05     0.032      10      53 ..     103     146 ..      99     155 .. 0.89
   2 !    6.5   0.0    0.0071       9.1      31      69 ..     160     198 ..     149     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                   d er   +  + l+++P+ ++ +   Glll+q G +++A++  e
  gi|91772202|ref|YP_564894.1| 103 DVERKEHYFKMALQIQPKNIRALNNMGLLLQQKGEFREAIKYYE 146
                                   67777888999****************************99877 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0071
                         TPR_9  31 errdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                   +++  +++l  lG+l++A    +++la+ pd +    ++
  gi|91772202|ref|YP_564894.1| 160 LYYNIAVCLKLLGNLEGAKTYINRALAKKPDEEIFLELK 198
                                   56777889999********************98877666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0026       3.3       5      27 ..     127     149 ..     124     151 .. 0.88
   2 !   11.4   0.1   0.00032      0.41       3      32 ..     161     190 ..     160     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                   +++l++++ g+ ++A++++e +i
  gi|91772202|ref|YP_564894.1| 127 NMGLLLQQKGEFREAIKYYEIII 149
                                   6999999988**********887 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                   +y++a +++ lg+ + A+++ +r + + Pd
  gi|91772202|ref|YP_564894.1| 161 YYNIAVCLKLLGNLEGAKTYINRALAKKPD 190
                                   7*********99**********99988665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.6e-07   0.00059       3      67 ..     128     191 ..     126     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.6e-07
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   +++++ + g++++A++++e+ + ++ +       +++ ++++  +g+l++A  ++++al+  pd+
  gi|91772202|ref|YP_564894.1| 128 MGLLLQQKGEFREAIKYYEIIISLGVVAK-PSPLYYNIAVCLKLLGNLEGAKTYINRALAKKPDE 191
                                   7999*********************5555.99*******************************97 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     3e-06    0.0038       3      26 ..     123     146 ..     122     149 .. 0.95
   2 ?    0.5   0.1      0.47     6e+02       5      30 ..     161     186 ..     160     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                        TPR_10   3 sslnNLanalrqrgrydeAealle 26 
                                   ++lnN++ +l+q g++ eA +++e
  gi|91772202|ref|YP_564894.1| 123 RALNNMGLLLQQKGEFREAIKYYE 146
                                   69********************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.47
                        TPR_10   5 lnNLanalrqrgrydeAealleeala 30 
                                   + N+a+ l  +g++++A  +  +ala
  gi|91772202|ref|YP_564894.1| 161 YYNIAVCLKLLGNLEGAKTYINRALA 186
                                   56888889999******999999987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.6   3.4e+03       5      17 ..      82      94 ..      81      95 .. 0.84
   2 !   16.1   0.0   5.2e-06    0.0066      19      42 .]     113     136 ..     111     136 .. 0.94
   3 ?    1.3   0.0      0.21   2.7e+02       6      17 ..     134     145 ..     133     146 .. 0.89
   4 ?   -0.9   0.0       1.1   1.4e+03       7      26 ..     171     190 ..     168     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                        TPR_11  5 yeqGkyeeAieaY 17
                                  +++ +++ A+e+Y
  gi|91772202|ref|YP_564894.1| 82 MAKDDINSAVERY 94
                                  67889999***99 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.2e-06
                        TPR_11  19 kAlkldPdnaeayynLGlayykqG 42 
                                    Al++ P+n +a++n+Gl+++++G
  gi|91772202|ref|YP_564894.1| 113 MALQIQPKNIRALNNMGLLLQQKG 136
                                   59********************98 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.21
                        TPR_11   6 eqGkyeeAieaY 17 
                                   ++G++ eAi+ Y
  gi|91772202|ref|YP_564894.1| 134 QKGEFREAIKYY 145
                                   79*******988 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.1
                        TPR_11   7 qGkyeeAieaYkkAlkldPd 26 
                                   +G++e+A +  ++Al+ +Pd
  gi|91772202|ref|YP_564894.1| 171 LGNLEGAKTYINRALAKKPD 190
                                   57788887777889988887 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   1.5e+02      23      37 ..     110     124 ..     107     126 .. 0.85
   2 ?   -2.8   0.0       5.4     7e+03      15      27 ..     136     148 ..     135     150 .. 0.82
   3 !   12.3   0.4    0.0001      0.13       5      45 ..     162     202 ..     160     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                   HHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  23 yvdalLeiEPenrQa 37 
                                   y ++ L+i+P+n  a
  gi|91772202|ref|YP_564894.1| 110 YFKMALQIQPKNIRA 124
                                   899*********766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.4
                                   T-HHHHHHHHHHH CS
                    Fis1_TPR_C  15 geYseArryvdal 27 
                                   ge++eA +y + +
  gi|91772202|ref|YP_564894.1| 136 GEFREAIKYYEII 148
                                   7999999998865 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
                    Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPenrQaqsLkelie 45 
                                   Y +A+    lg+ + A+ y+++ L++ P+ +  ++Lke i 
  gi|91772202|ref|YP_564894.1| 162 YNIAVCLKLLGNLEGAKTYINRALAKKPDEEIFLELKEEIL 202
                                   7889988889***************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2219.21
//
Query:       gi|91772203|ref|YP_564895.1|  [L=105]
Description: hypothetical protein Mbur_0128 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.1   0.0    3.1e-05   23.5   0.0    1.3  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.003   17.2   0.0     0.0053   16.4   0.0    1.4  1  Sigma70_r4_2  Sigma-70, region 4
     0.0078   15.8   0.0      0.012   15.2   0.0    1.3  1  GntR          Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.018   14.9   0.0    1.1  1  MarR_2        MarR family
      0.044   13.3   0.0      0.091   12.3   0.0    1.6  1  Sigma70_r4    Sigma-70, region 4


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 !   23.5   0.0   8.6e-09   3.1e-05      17      47 ..      24      54 ..      15      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.6e-09
                        HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   ++q+e+Ae++ l+p t+++ l rL++e ++
  gi|91772203|ref|YP_564895.1| 24 LLTQKEIAEQSYLPPRTIRYALGRLKDEDFL 54
                                  49*************************9875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-06    0.0053       5      49 ..       2      47 ..       1      50 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                                  HHHHTTS-HHHHHHHHHHHTS-.--HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2  5 realaeLperqreifllryleg.lsykEIAellgisegtVksrlsR 49
                                  r+a++ Lp+  + +f   ++ g l++kEIAe+  ++++t++++l R
  gi|91772203|ref|YP_564895.1|  2 RKAIEGLPPSAKLVFKVLEYGGlLTQKEIAEQSYLPPRTIRYALGR 47
                                  79*************999999955******************9987 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.4e-06     0.012      15      55 ..      16      55 ..      11      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-06
                                  TTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          GntR 15 sgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                   ++l+ G  L +++e+a++      t+R AL rL+ e+ ++
  gi|91772203|ref|YP_564895.1| 16 FKVLEYGGLL-TQKEIAEQSYLPPRTIRYALGRLKDEDFLQ 55
                                  567999****.**************************9887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.1e-06     0.018       2      54 ..       7      57 ..       6      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.1e-06
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  gl+p+   v  +L  ++   lt++e+a+   l++ ++ ++l rL +  ++++r
  gi|91772203|ref|YP_564895.1|  7 GLPPSAKLVFKVLEYGGL--LTQKEIAEQSYLPPRTIRYALGRLKDEDFLQER 57
                                  677777777777877877..8************************99988776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05     0.091       1      38 [.       4      42 ..       4      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                  HHHHS-HHHHHHHH.HHHTTT--HHHHHHHHTS-HHHHH CS
                    Sigma70_r4  1 aLasLpererevle.lrfgeglTleEIgerlgiSrerVr 38
                                  a++ Lp+  + v++ l +g  lT++EI+e+  ++  ++r
  gi|91772203|ref|YP_564895.1|  4 AIEGLPPSAKLVFKvLEYGGLLTQKEIAEQSYLPPRTIR 42
                                  688999999999972556999********9999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 650.50
//
Query:       gi|91772204|ref|YP_564896.1|  [L=171]
Description: hypothetical protein Mbur_0129 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.3   1.9      0.038   14.0   0.0    2.8  3  DUF3741   Protein of unknown function (DUF3741)
  ------ inclusion threshold ------
      0.035   13.9   0.4      0.054   13.3   0.4    1.3  1  Poxvirus  dsDNA Poxvirus


Domain annotation for each model (and alignments):
>> DUF3741  Protein of unknown function (DUF3741)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2     0.084   7.5e+02      28      41 ..       7      22 ..       6      23 .. 0.75
   2 !   14.0   0.0   4.2e-06     0.038      21      40 ..      46      65 ..      44      67 .. 0.84
   3 ?   -1.9   0.0      0.36   3.3e+03      30      40 ..     119     129 ..     112     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.084
                       DUF3741 28 vlssN..kdLFlklLq 41
                                   l+sN  k+ +l +Lq
  gi|91772204|ref|YP_564896.1|  7 ALNSNdeKEILLLYLQ 22
                                  6788866889999998 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.2e-06
                       DUF3741 21 eflDALevlssNkdLFlklL 40
                                  ef DALe+lss+ d   ++L
  gi|91772204|ref|YP_564896.1| 46 EFRDALEILSSDSDRHAMIL 65
                                  9***********99666665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.36
                       DUF3741  30 ssNkdLFlklL 40 
                                   +++++L+ +++
  gi|91772204|ref|YP_564896.1| 119 NTDENLLKEIF 129
                                   77888887776 PP

>> Poxvirus  dsDNA Poxvirus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4     6e-06     0.054      74     105 ..      95     129 ..      85     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-06
                      Poxvirus  74 kiGklFkeLmkyddlAikkygkdli....klikdll 105
                                   ++  +F+e+mky+++A++ y   +     +l+k+++
  gi|91772204|ref|YP_564896.1|  95 SYYEIFSEIMKYEIFARDAYE-TIAntdeNLLKEIF 129
                                   5568****************4.44412224444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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 0.29s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1193.17
//
Query:       gi|91772205|ref|YP_564897.1|  [L=257]
Description: UBA/THIF-type NAD/FAD binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  206.6   0.0      5e-61  206.2   0.0    1.0  1  ThiF             ThiF family
    0.00014   22.1   0.1    0.00033   20.9   0.1    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0068   16.5   0.1      0.021   14.9   0.0    1.9  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.075   13.7   0.1       0.15   12.7   0.1    1.6  1  PglD_N           PglD N-terminal domain
       0.13   11.8   0.1        0.2   11.2   0.1    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.2   0.0   1.4e-64     5e-61       3     240 ..      13     240 ..      10     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 1.4e-64
                                   HHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHH CS
                                   xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF   3 rqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaeal 81 
                                   +++++  +ge+gq++L +s+vl vGaGglGs+++++La++Gvg l +vD+D++e+sNl+Rq++    + Gk+K+ +a++ +
  gi|91772205|ref|YP_564897.1|  13 KHIVMkqMGEEGQKRLLSSRVLCVGAGGLGSPVIQYLAAAGVGTLGIVDDDVVEMSNLQRQVI-HAGNLGKQKVWSARQYV 92 
                                   5554466899*****************************************************.899************** PP

                                   HHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  82 qeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeC 162
                                   +++ p+++v a+ +r+++++ +e l++++D+Vvd++Dn+++r+l+n+acv + +pl +++   fegqv++i+p++ +cy+C
  gi|91772205|ref|YP_564897.1|  93 ERLDPGINVLAYDMRVGPDN-VEGLIKDYDVVVDCSDNFATRYLLNDACVLQNKPLFHGSIFMFEGQVMTILPHEGPCYRC 172
                                   ******************98.68********************************************************** PP

                                   S-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHH..TTBCGGGCCEEEECCTTTTEEEEECCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 163 ldpsstedptekkvplctsiagnipaiatttavvaglaalellkll..sgkeklenslltqvdllesrfenvelerakks 240
                                    +      p+++ +       g   +++ +++vv+ ++a+e++k+l      +l +++  ++d+l +rf+++ +++++++
  gi|91772205|ref|YP_564897.1| 173 IFA---CSPSNDAAKDA----G---VMGILPGVVGTMQATEVVKHLvrL-GAPLIGRMI-YYDALGMRFDEITVRKNPEC 240
                                   *96...77777777777....7...99*******************643.334777777.9*************998854 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 !   20.9   0.1   9.2e-08   0.00033       1      90 [.      33     141 ..      33     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.2e-08
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH....................TTTCEEEEE--TTTHHH CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka....................lgvrfeaialdaenyea 61 
                                   vl++GaG+ G++v+++la+ +    ++ ++d +  ++ +l  ++                    l + ++  a d    ++
  gi|91772205|ref|YP_564897.1|  33 VLCVGAGGLGSPVIQYLAAAGVG--TLGIVDDDVVEMSNLQRQVihagnlgkqkvwsarqyverLDPGINVLAYDMRVGPD 111
                                   79******************976..9*******99999999888999*****************99999999999999999 PP

                                   HHHHHHTTSSEEEE-SSGGGHH.HHHHHHH CS
               Sacchrp_dh_NADP  62 vLaallkegdlvvnlsppissl.dvlkaCi 90 
                                    ++ l+k++d+vv++s ++ ++  + +aC+
  gi|91772205|ref|YP_564897.1| 112 NVEGLIKDYDVVVDCSDNFATRyLLNDACV 141
                                   9******************55515556776 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.7e-06     0.021       9      76 ..      27      95 ..      19     127 .. 0.82
   2 ?   -2.2   0.0       1.1   3.8e+03      68      83 ..     112     127 ..     100     142 .. 0.80
   3 ?   -2.8   0.0       1.7   6.2e+03      23      35 ..     200     212 ..     195     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-06
                                  ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT- CS
                  Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaea 76
                                  +l +++vl +GaG +++ v+++L+a+gv  + ++  ++  +++l +++ ++ ++  +k+ + ++++++ 
  gi|91772205|ref|YP_564897.1| 27 RLLSSRVLCVGAGGLGSPVIQYLAAAGVGTLGIVDDDVVEMSNLQRQViHAGNLGKQKVWSARQYVERL 95
                                  67789****************************999999999998887555556666666666666655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                   GHHHHHHT-SEEEE-S CS
                  Shikimate_DH  68 elkellaeadvvisat 83 
                                   +++ l++++dvv+ + 
  gi|91772205|ref|YP_564897.1| 112 NVEGLIKDYDVVVDCS 127
                                   6777899999998764 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHCCT CS
                  Shikimate_DH  23 maelvakhLlakg 35 
                                    a++v+khL++ g
  gi|91772205|ref|YP_564897.1| 200 QATEVVKHLVRLG 212
                                   4788999999765 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.3e-05      0.15       2      34 ..      33      64 ..      32      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                        PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdnk 34
                                  ++ +GaGG g  v++ + a g    +g++Dd+ 
  gi|91772205|ref|YP_564897.1| 33 VLCVGAGGLGSPVIQYLAAAG-VGTLGIVDDDV 64
                                  6779*****************.9********86 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   5.6e-05       0.2       2      59 ..      32      90 ..      31     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.6e-05
                                  EEEEE--STTHHHHHHHHHHCTSEEE.EE-S-HHHHHHHCTTS-SS--TTHHHHHHHHC CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevi.gvDideekvdklnsgkipiyepgLeelvkkav 59
                                  ++ ++G+G +G +    la++g+  + +vD d    ++l+++ i+  + g +++  ++ 
  gi|91772205|ref|YP_564897.1| 32 RVLCVGAGGLGSPVIQYLAAAGVGTLgIVDDDVVEMSNLQRQVIHAGNLGKQKVWSARQ 90
                                  799*******************7655168**************9999988888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1888.13
//
Query:       gi|91772206|ref|YP_564898.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91772206|ref|YP_564898.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772206|ref|YP_564898.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772206|ref|YP_564898.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772206|ref|YP_564898.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772206|ref|YP_564898.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772206|ref|YP_564898.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772206|ref|YP_564898.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772206|ref|YP_564898.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2070.99
//
Query:       gi|91772207|ref|YP_564899.1|  [L=788]
Description: monovalent cation/H+ antiporter subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-70  236.0  18.9    5.1e-70  236.0  18.9    2.8  3  Proton_antipo_M  Proton-conducting membrane transporter
    1.1e-18   67.1   8.2    1.1e-18   67.1   8.2    3.6  3  DUF4040          Domain of unknown function (DUF4040)
    3.3e-09   36.7   1.1    3.3e-09   36.7   1.1    4.2  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   1.9      0.99   5.9e+03     131     170 ..      13      53 ..       6     124 .. 0.47
   2 !  236.0  18.9   8.5e-74   5.1e-70       1     286 [.     130     420 ..     130     427 .. 0.93
   3 ?  -10.4  13.6         3   1.8e+04     119     259 ..     592     727 ..     584     757 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.99
               Proton_antipo_M 131 llirlllllavssneisqlllilaiismllg.slvalaqtd 170
                                   l + +  l+ v+++ ++q + + a++++l   +l+++a t+
  gi|91772207|ref|YP_564899.1|  13 LPFIFAGLVPVMEKLLKQRVGWFAAATALASfALIGMAATE 53 
                                   55555555555555555555555555555332444444443 PP

  == domain 2  score: 236.0 bits;  conditional E-value: 8.5e-74
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal...elglns 78 
                                   +++ ++l++++El+++ +++Lig+w++kp+s++ + k++llt+ g l++L g+lll n+tg+ e+ ++++     ++ ++ 
  gi|91772207|ref|YP_564899.1| 130 SGNTIQLFIFWELTSITSFMLIGYWRHKPESIYGATKSLLLTASGGLAMLAGFLLLGNITGSFELAAILNDPqviNAIKEH 210
                                   6789****************************************************************9977776888888 PP

               Proton_antipo_M  79 lelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllilaiism 158
                                     +l+ l+l+l+g+++Ksaq p+  Wlp+a +eaPtpvsa+l +at+vkag++l++r++++++  ++++ +l+   +ii+m
  gi|91772207|ref|YP_564899.1| 211 ELFLITLILILIGAAAKSAQGPFYIWLPNA-MEAPTPVSAFLhSATMVKAGIYLVARIHPIFS-GTEAWFILVSGTGIITM 289
                                   88999999**********************.********************************.999999*********** PP

               Proton_antipo_M 159 llgslvalaqtdiKrllAySsishlGymlialavatq....ygveaaiihllthalfkallFllagsviyerektrdiray 235
                                   l+++++a +qtdiK +lAyS+is+l+ym+   + +t     +gv+aa +hll ha fka lFl+ag v +e   trdir++
  gi|91772207|ref|YP_564899.1| 290 LVAGFLAFRQTDIKGILAYSTISQLAYMMTMYGYTTHhepgIGVAAATFHLLNHAAFKACLFLVAGIVAHE-AATRDIRKL 369
                                   ******************************9999665333379**********************777555.59******* PP

               Proton_antipo_M 236 ggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla 286
                                   ggL+  mPi++++  ++ l++aG+Pp+ gFlsk +  e+++++++ +  ++
  gi|91772207|ref|YP_564899.1| 370 GGLRREMPITFIIACIAGLAMAGIPPLNGFLSKEMFYESSIEMGASIGGIF 420
                                   ***********************************9999999987766555 PP

  == domain 3  score: -10.4 bits;  conditional E-value: 3
               Proton_antipo_M 119 ll.AatlvkagvlllirlllllavssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygv 198
                                   l+ A ++  a++l+   + + l +  + ++ +ll+l i+++l    +a+  t + +++A S ++  G+ l+ + +   ++ 
  gi|91772207|ref|YP_564899.1| 592 LMiALIAIPAAILATNIMPSQLNFDIPPYEAILLLLLIVAALS---AAILPTYLPSIIALSALGY-GVSLLFIYL---KAP 665
                                   3346666777777766666666677788888888777777775...4666788999999988653.444444444...678 PP

               Proton_antipo_M 199 eaaiihllthalfkallFllagsviye.rektrdirayggLakkmPilalvllvlllslaGl 259
                                   ++a++++l+  l+++   l++  + ++ +ek      ++ +  ++ + a v++vll ++ G+
  gi|91772207|ref|YP_564899.1| 666 DLALTQILVETLSTIIFLLAITKIPQKyKEKISISVFTRDILIAITVAASVFVVLLNATQGI 727
                                   99999999998888887777777766644455556667788888888888888888888776 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.6   9.6e+03       3       9 ..     289     295 ..     280     317 .. 0.55
   2 !   67.1   8.2   1.9e-22   1.1e-18       1      67 []     626     691 ..     626     691 .. 0.98
   3 ?   -3.4   0.4       1.9   1.1e+04      20      47 ..     710     713 ..     701     723 .. 0.44

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                       DUF4040   3 lvlaala 9  
                                   +++a ++
  gi|91772207|ref|YP_564899.1| 289 MLVAGFL 295
                                   2222222 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 1.9e-22
                       DUF4040   1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlpr 67 
                                   lll++aal a++ +  l ++i+l+++G++v+llf++l+APD+AlTq+ +ve+l+t+++lla+ ++p+
  gi|91772207|ref|YP_564899.1| 626 LLLIVAALSAAILPTYLPSIIALSALGYGVSLLFIYLKAPDLALTQI-LVETLSTIIFLLAITKIPQ 691
                                   689********************************************.****************995 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.9
                       DUF4040  20 villgvvGllvallfvllgAPDvAlTqa 47 
                                   +                          a
  gi|91772207|ref|YP_564899.1| 710 IT------------------------VA 713
                                   22........................11 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 !   36.7   1.1   5.5e-13   3.3e-09       3      57 ..      65     117 ..      63     118 .. 0.94
   2 ?   -2.2   0.2      0.74   4.4e+03      23      39 ..     465     481 ..     464     483 .. 0.87
   3 ?    1.7   0.4     0.046   2.8e+02      23      39 ..     518     533 ..     503     536 .. 0.70
   4 ?   -2.3   0.6       0.8   4.8e+03      21      34 ..     586     599 ..     579     609 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 5.5e-13
               Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                   +W+++ g  ++++++ D+l  +  ++ +++++l++ YS gYM++ e  +R++ yl
  gi|91772207|ref|YP_564899.1|  65 SWIPSAG--VNFTIYADGLATMIGFIASGIGVLIMSYSNGYMSRTEDLTRYYQYL 117
                                   7999885..9*********************************999********9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.74
               Proton_antipo_N  23 almllvvtfvsllvhlY 39 
                                   ++ml+   f+++lv+l+
  gi|91772207|ref|YP_564899.1| 465 MTMLIPPAFLAFLVILF 481
                                   689999999*****998 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.046
               Proton_antipo_N  23 almllvvtfvsllvhlY 39 
                                    lm+++vtf+ l +++Y
  gi|91772207|ref|YP_564899.1| 518 SLMMTIVTFI-LGILIY 533
                                   5788888887.344455 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.8
               Proton_antipo_N  21 lsalmllvvtfvsl 34 
                                   +sa+ ll++ +++ 
  gi|91772207|ref|YP_564899.1| 586 MSAMLLLMIALIAI 599
                                   57777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4987.34
//
Query:       gi|91772208|ref|YP_564900.1|  [L=139]
Description: monovalent cation/H+ antiporter subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-32  112.3  12.0      2e-32  112.1  12.0    1.0  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1  12.0   1.1e-36     2e-32       1     123 [.       5     128 ..       5     129 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 1.1e-36
                          MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafgleelekllrvklaprileglglllavltgll 81 
                                   i++t++++++pl++l+s++lll+Ghn+PGGGF+gG+++a+ ++l y++fgl++ + + + +  + +++g+gl+la +t++ 
  gi|91772208|ref|YP_564900.1|   5 ITKTITKICIPLVILFSISLLLAGHNNPGGGFIGGVMFASVIALAYVVFGLKDIKTFFNPD--WAKWFGFGLTLASFTAFS 83 
                                   789**************************************************99999999..559*************** PP

                          MnhB  82 glllg..fltslflelel.llgevelgtallfdlgVylvVvggll 123
                                   ++++g  f++s++ +++l l+ge el +a lfd+gVy+vV+g+ll
  gi|91772208|ref|YP_564900.1|  84 AMMFGhnFFRSAVEFVHLpLFGEIELVSAGLFDIGVYFVVIGSLL 128
                                   ***********9999999*99*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 946.06
//
Query:       gi|91772209|ref|YP_564901.1|  [L=140]
Description: monovalent cation/H+ antiporter subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-36  121.8   5.0    1.1e-35  121.4   5.0    1.1  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 !  121.4   5.0   6.3e-40   1.1e-35       2     105 .]       6     137 ..       5     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 6.3e-40
                                   HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.................................. CS
                   Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi............................ 54 
                                   l l+i +lf+iG++++l rr+++kv+igl+++s+avnll+v agvf++g ++i                            
  gi|91772209|ref|YP_564901.1|   6 LTLTISILFGIGTFLIL-RRDMIKVIIGLSVLSHAVNLLIVSAGVFENGKVPIitgsghggevtgtiyndniaegilapiv 85 
                                   6799*************.*******************************9999**************************** PP

                                   ........TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG--X CS
                   Oxidored_q2  55 .tnpatefadplpqalvLtaivigaaetavgLallvrlyreygtddvqelrr 105
                                      +  ef+dpl+qalvLtaivi++a+ta++L l++r+y+eygt+d++elrr
  gi|91772209|ref|YP_564901.1|  86 sAGTHVEFVDPLVQALVLTAIVISLATTAFILILAYRIYEEYGTTDIRELRR 137
                                   999999*******************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1075.80
//
Query:       gi|91772210|ref|YP_564902.1|  [L=513]
Description: monovalent cation/H+ antiporter subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  234.3  29.5    1.6e-69  234.3  29.5    2.9  3  Proton_antipo_M  Proton-conducting membrane transporter
    1.4e-05   24.5   7.4    1.4e-05   24.5   7.4    2.6  2  NADHdeh_related  NADH dehydrogenase I, subunit N related prot
     0.0013   18.8   0.5     0.0013   18.8   0.5    3.5  6  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.6     0.048   2.9e+02     128     168 ..      14      54 ..       4      96 .. 0.79
   2 !  234.3  29.5   2.7e-73   1.6e-69       2     293 .]     130     431 ..     129     431 .. 0.94
   3 ?    1.1   0.6     0.031   1.8e+02     202     263 ..     427     488 ..     422     496 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.048
               Proton_antipo_M 128 gvlllirlllllavssneisqlllilaiismllgslvalaq 168
                                   +v +l+  l+++  s+ +++++l +  +++m+l s++ l q
  gi|91772210|ref|YP_564902.1|  14 AVPILMSALMIFLRSNANVQKWLNVSVSLAMMLISIILLLQ 54 
                                   44455555555556788888888888888888888887776 PP

  == domain 2  score: 234.3 bits;  conditional E-value: 2.7e-73
               Proton_antipo_M   2 ndLlllylglElvllplylLiglwk.....kkpksleAslklflltllgsliLLlgilllynltgtlefeelskal....e 73 
                                   +d++ +++++E+ ll++  L+  ++     k+ +++eA++k+++l+++gs+++L++++ ly+  gtl++ +ls  +     
  gi|91772210|ref|YP_564902.1| 130 GDIFNMFVFFEILLLASCGLVIANEkggvtKSSDKMEATFKYLILNMIGSFVMLIAVASLYATVGTLNMADLSVKIstmsA 210
                                   58999*************99987652222268899************************************9988878778 PP

               Proton_antipo_M  74 lglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllil 153
                                   +g   + + +++ll++v +  K+a +p+h Wlpd++  aP p+sa+l++++ k+g+++++r+++l++  +   ++ ++++l
  gi|91772210|ref|YP_564902.1| 211 AGTLPWHIYAIALLFIVVFGNKAAIFPMHYWLPDVHPTAPSPISAMLSGVMIKVGAYGILRIFFLIFrDALFLLQPIIILL 291
                                   89999************************************************************997788889999**** PP

               Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdira 234
                                   a++++++g++ a+ q+d+K+llAySs+s++Gy++++++++++y+++aa++++  ha+ k++lFl +g++i++   trd+r 
  gi|91772210|ref|YP_564902.1| 292 ALVTIIIGAVSAVGQNDVKKLLAYSSVSQIGYVFLGIGIGSVYALAAALVYMANHAIAKSMLFLTSGGIIHHA-GTRDMRH 371
                                   *********************************************************************9998.9****** PP

               Proton_antipo_M 235 yggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                   +gg+ k+ Pi+++++l++++s+aGlPp+ gF++kf ++ a ++++ ++ v++ ++ +v+t
  gi|91772210|ref|YP_564902.1| 372 MGGMNKTSPIMSIAFLIGAMSIAGLPPMGGFVAKFILFDAGLRAEYYIPVAIaLFFAVFT 431
                                   **********************************************99999988888876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.031
               Proton_antipo_M 202 iihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPpta 263
                                   ++ ++++ +f a l ++ g +   +e  ++     +L+ + Pi++l+ lv+++++ + P+ a
  gi|91772210|ref|YP_564902.1| 427 FAVFTLFYMFRAWLLMFWGETRDVEEYGEYSSHKPSLMIALPIVSLAALVFIFGVYAEPLIA 488
                                   45556666777777777777755566667777777888999999999999999998888765 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   7.4   2.4e-09   1.4e-05      83     175 ..     124     230 ..     108     242 .. 0.74
   2 !    3.7  10.5    0.0058        35      73     186 ..     290     405 ..     283     431 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-09
               NADHdeh_related  83 lgavvtgdvfnftlflaliGianiGivaavkkefv......leaafnyGlvaliatlplfggaalilastGtlsifelakl 157
                                    g+ +tgd+fn  +f  ++ +a  G+v a +k  v      +ea+f+y ++ +i++  ++ + a + a+ Gtl + +l+  
  gi|91772210|ref|YP_564902.1| 124 NGTFLTGDIFNMFVFFEILLLASCGLVIANEKGGVtkssdkMEATFKYLILNMIGSFVMLIAVASLYATVGTLNMADLSVK 204
                                   47889**********************7765543322222389**************999999999***********9865 PP

               NADHdeh_related 158 ......agd..vlliaklllvlGvvG 175
                                         ag+    ++a +ll + v G
  gi|91772210|ref|YP_564902.1| 205 istmsaAGTlpWHIYAIALLFIVVFG 230
                                   33333222212235555555555555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0058
               NADHdeh_related  73 llaivcg.latlgavvtgdvfnftlflal..iGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtls 150
                                   lla+v+  + ++ av   dv +   + ++  iG + +Gi  ++ + ++l aa  y     ia   lf +++ i+ ++Gt  
  gi|91772210|ref|YP_564902.1| 290 LLALVTIiIGAVSAVGQNDVKKLLAYSSVsqIGYVFLGI--GIGSVYALAAALVYMANHAIAKSMLFLTSGGIIHHAGTRD 368
                                   566665414566777778877766665542255555555..78899*********************************** PP

               NADHdeh_related 151 ifelaklagdvlliaklllvlGvvGetGvaPf..yaak 186
                                   +  + +++++ + i  + +++G +  +G+ P+  ++ak
  gi|91772210|ref|YP_564902.1| 369 MRHMGGMNKTSP-IMSIAFLIGAMSIAGLPPMggFVAK 405
                                   *******99655.5567778899999999986334555 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 ?   -3.8   0.9       2.5   1.5e+04      21      31 ..      40      50 ..      36      55 .. 0.62
   2 !   18.8   0.5   2.1e-07    0.0013      15      47 ..      74     106 ..      65     118 .. 0.85
   3 ?   -3.5   0.1       1.9   1.1e+04      28      38 ..     173     183 ..     162     189 .. 0.56
   4 ?   -3.9   0.5       2.6   1.5e+04      22      32 ..     288     297 ..     282     301 .. 0.53
   5 ?   -4.1   0.2       2.9   1.7e+04      33      44 ..     424     435 ..     422     438 .. 0.68
   6 ?   -2.8   0.3       1.2     7e+03      22      39 ..     462     479 ..     460     482 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
               Proton_antipo_N 21 lsalmllvvtf 31
                                  +s+ m+l+  +
  gi|91772210|ref|YP_564902.1| 40 VSLAMMLISII 50
                                  46666665443 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.1e-07
               Proton_antipo_N  15 gfllDklsalmllvvtfvsllvhlYSigYMadd 47 
                                    +  D ls  m+++ ++vs+l +lYS+ Y ++ 
  gi|91772210|ref|YP_564902.1|  74 VLVADLLSSGMVVLSSIVSFLALLYSLDYIEGR 106
                                   577899***********************9865 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.9
               Proton_antipo_N  28 vvtfvsllvhl 38 
                                   +  +++++v+l
  gi|91772210|ref|YP_564902.1| 173 ILNMIGSFVML 183
                                   44455555554 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 2.6
               Proton_antipo_N  22 salmllvvtfv 32 
                                     + l++vt++
  gi|91772210|ref|YP_564902.1| 288 I-ILLALVTII 297
                                   3.445555555 PP

  == domain 5  score: -4.1 bits;  conditional E-value: 2.9
               Proton_antipo_N  33 sllvhlYSigYM 44 
                                   +l+  ++++ YM
  gi|91772210|ref|YP_564902.1| 424 ALFFAVFTLFYM 435
                                   555667777787 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 1.2
               Proton_antipo_N  22 salmllvvtfvsllvhlY 39 
                                   s++ +l +  +++lv ++
  gi|91772210|ref|YP_564902.1| 462 SLMIALPIVSLAALVFIF 479
                                   677777788888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); 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:                        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: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 3175.19
//
Query:       gi|91772211|ref|YP_564903.1|  [L=164]
Description: monovalent cation/H+ antiporter subunit E [Methanococcoides burtonii DSM 6242]
Scores for complete 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  148.2   0.0    1.6e-43  148.0   0.0    1.0  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.0   0.0   8.6e-48   1.6e-43       3     145 ..      10     161 ..       8     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 8.6e-48
                          MNHE   3 llflvWllltgs..lgelllGlllallvalllrrll........lplrrvllrllayllvflweivkanldVakrvlrpkl 73 
                                   ++ l+W+++ g+  l+++l+G+ll+ +v+  +r+l+        +++ r++ +l++++ v+++ei+kan+ +ak++l+pk+
  gi|91772211|ref|YP_564903.1|  10 FFGLIWCFVHGTvnLNNFLIGALLGPIVIRPFRPLYgfenkisyKKVIRKIPKLIKFFYVLFIEIIKANIMMAKIILQPKM 90 
                                   6779*****************************999*9999888555555555**************************** PP

                          MNHE  74 pirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvedeeeeareeikgrlErrlle 145
                                   +i+pgi++vp+r+k+++++t++an+itltPGTlt+dv+++++vlyvH++d++d ++ ++++i+++lE+++le
  gi|91772211|ref|YP_564903.1|  91 DIKPGIIAVPIRTKTNTGITAIANTITLTPGTLTIDVSDNKEVLYVHAIDASD-PQGLCDSIRDDLEEYVLE 161
                                   *****************************************************.***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1054.54
//
Query:       gi|91772212|ref|YP_564904.1|  [L=88]
Description: monovalent cation/H+ antiporter subunit F [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-20   71.4   5.5    6.1e-20   71.4   5.5    1.9  2  MrpF_PhaF      Multiple resistance and pH regulation protein 
  ------ inclusion threshold ------
      0.065   13.2   1.4      0.065   13.2   1.4    1.6  2  DUF2393        Protein of unknown function (DUF2393)


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       0.1   9.4e+02      31      42 ..       6      17 ..       2      22 .. 0.60
   2 !   71.4   5.5   6.8e-24   6.1e-20       1      52 [.      31      82 ..      31      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                     MrpF_PhaF 31 ldvalvlAllgF 42
                                  +d+ + + +++ 
  gi|91772212|ref|YP_564904.1|  6 FDISITFMVIAI 17
                                  666666655554 PP

  == domain 2  score: 71.4 bits;  conditional E-value: 6.8e-24
                     MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                  +DRv+A+D+++t+++++l++++ ++++++++dvalvlA+++Fvgtv ++++l
  gi|91772212|ref|YP_564904.1| 31 PDRVIAVDAMTTVIIVILGIYSYMQESAFFMDVALVLAIISFVGTVTISKYL 82
                                  8**************************************************9 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4      0.27   2.4e+03      24      35 ..       6      17 ..       2      26 .. 0.48
   2 ?   13.2   1.4   7.3e-06     0.065       2      45 ..      43      83 ..      42      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.27
                       DUF2393 24 lsllilflapfv 35
                                  +++ i+f+++++
  gi|91772212|ref|YP_564904.1|  6 FDISITFMVIAI 17
                                  344444444333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.3e-06
                       DUF2393  2 llllllglllkkrsavalfliflsllilflapfvvhliidkylk 45
                                  +++++lg++   ++ +   +++   l+l++ +fv+ ++i+kyl 
  gi|91772212|ref|YP_564904.1| 43 VIIVILGIYSYMQESA---FFMDVALVLAIISFVGTVTISKYLD 83
                                  799***********53...5667778889999**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 577.17
//
Query:       gi|91772213|ref|YP_564905.1|  [L=115]
Description: monovalent cation/H+ antiporter subunit G [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-25   88.8   9.9    2.6e-25   88.5   9.9    1.1  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   9.9   1.5e-29   2.6e-25       1      79 []      15      94 ..      15      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1.5e-29
                PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaaslkllliilfllltaPvaahliaraay 79
                                  lll+Ga+fv+lg++gl+rlpdvy+Rlha+tk+ tlG++ ++l+++ ++  +   +k++ + +f+lltaPvaah+i+raa+
  gi|91772213|ref|YP_564905.1| 15 LLLVGAFFVFLGMVGLIRLPDVYNRLHATTKIGTLGAFGVMLSIVAKLgLEPIGVKAITVGFFILLTAPVAAHMIGRAAH 94
                                  79********************************************9966666*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 836.13
//
Query:       gi|91772214|ref|YP_564906.1|  [L=350]
Description: translation factor SUA5 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-60  201.5   0.0    1.5e-59  200.5   0.0    1.5  1  Sua5_yciO_yrdC  Telomere recombination
    2.3e-31  109.1   0.0    3.9e-31  108.4   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin


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 !  200.5   0.0   1.7e-63   1.5e-59       2     179 .]      25     200 ..      24     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 1.7e-63
                                   HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEEE CS
                Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitlll 82 
                                   ++++Ggiva+ptetvYgL+++a +++av++++++Kgrp+d+pl+v+vas ++ ++la+ ++++ a+kl+++fwPGp+tl+l
  gi|91772214|ref|YP_564906.1|  25 IIKEGGIVAFPTETVYGLGANALDPDAVKKIFKAKGRPADNPLIVHVASKDQCNDLAK-NISQTAFKLMDEFWPGPLTLIL 104
                                   79*******************************************************9.********************** PP

                                   E..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS--- CS
                Sua5_yciO_yrdC  83 krskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvds 163
                                   k++k  +p+  ++gl+tvG+r+P++++a++++++ g+pl+a+San sg+ps+t+ae+v ++l++++d+i+dgg +++g +s
  gi|91772214|ref|YP_564906.1| 105 KAKKV-VPEITTGGLDTVGLRMPANEIALEFIRRSGTPLAAPSANTSGRPSPTSAEHVTQDLEGKIDAIIDGGMVEIGLES 184
                                   *7444.*************************************************************************** PP

                                   EEEETTSSTSSECEXX CS
                Sua5_yciO_yrdC 164 tVvdltegkpkilRrG 179
                                   tVvd+t++ p ilR+G
  gi|91772214|ref|YP_564906.1| 185 TVVDITGDIPAILRPG 200
                                   **************98 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.0   4.4e-35   3.9e-31       1     133 [.     202     344 ..     202     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 4.4e-35
                                   .-HHHHHHHS......---.........-------------S-SSEEEEE--GGGHHHH......HHHHHTTS-EEEEEEG CS
                          SUA5   1 itleeleevl......davek.....keekpraPGmkyrHYaPkapvvlveaeeeeeaake.ekleekkksgkkvgvlats 69 
                                   +++e+++e+           +      +e+ r+PGmky+HY+P+++v+l+e+++++ +++  + + + +k+gk+vg+lat+
  gi|91772214|ref|YP_564906.1| 202 VSAEDIRECAgnveigY---TdktleGNETARSPGMKYTHYSPETKVILIEGSSASVENTMvNLITNCHKKGKRVGLLATE 279
                                   789******84433320...12345578899**********************999888779999***************9 PP

                                   GGTGGTSEEEEE..E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----S.TTHHHHHHHHHHHT CS
                          SUA5  70 eskeaassvlslslgsrsdleeaarnLFaaLrelDeegvdlilvegvpee.glglAvmnRLrkAA 133
                                   e  +  +s ++ slg+++++++aar +F +Lr+lD++++d+ilv+g  ++ g+g+A+ nRLrkAA
  gi|91772214|ref|YP_564906.1| 280 EILDSINSDVTYSLGKKDEPNQAARSIFMGLRHLDNKEIDIILVDGTLKTdGIGAAIFNRLRKAA 344
                                   99999777666679*********************99********766554*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2586.55
//
Query:       gi|91772215|ref|YP_564907.1|  [L=81]
Description: hypothetical protein Mbur_0140 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.6   0.4      0.058   13.3   0.4    1.0  1  DUF4077   Domain of unknown function (DUF4077)


Domain annotation for each model (and alignments):
>> DUF4077  Domain of unknown function (DUF4077)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   3.3e-06     0.058      38      89 ..      16      65 ..       9      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-06
                       DUF4077 38 tyfslldeialkfaiadlsvvaittlfllikrlekavkyevmlfmlllvsyi 89
                                    ++ +++++ k+a ad+ v++ ++l+ ++++ e   ++  m   +++++y+
  gi|91772215|ref|YP_564907.1| 16 QEYYAITKRNKKIATADMLVLGTGLLLKFFNQAEIGKHF--MWLGFIIMVYV 65
                                  356889***************************998888..44334444453 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 619.56
//
Query:       gi|91772216|ref|YP_564908.1|  [L=439]
Description: signal recognition particle protein Srp54 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  232.7   0.0    4.7e-69  232.0   0.0    1.4  1  SRP54            SRP54-type protein, GTPase domain
    2.6e-27   95.3   2.3    2.6e-27   95.3   2.3    2.3  2  SRP_SPB          Signal peptide binding domain
      8e-23   80.5   0.9    8.1e-22   77.2   0.3    2.6  2  SRP54_N          SRP54-type protein, helical bundle domain
    6.2e-05   22.7   0.2    0.00081   19.0   0.2    2.2  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00038   19.8   0.0    0.00073   18.9   0.0    1.5  1  Zeta_toxin       Zeta toxin
    0.00059   19.9   0.0     0.0035   17.4   0.0    2.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0007   19.0   0.0     0.0012   18.2   0.0    1.3  1  6PF2K            6-phosphofructo-2-kinase
     0.0022   17.9   0.0     0.0054   16.6   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
     0.0032   17.8   0.0       0.01   16.1   0.0    1.5  1  AAA_19           AAA domain
     0.0051   15.8   0.1      0.013   14.5   0.0    1.7  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0064   16.3   0.0      0.018   14.8   0.0    1.8  1  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.046   14.0   0.0    1.9  1  AAA_22           AAA domain
      0.018   14.8   0.1      0.059   13.1   0.1    1.9  1  AAA_24           AAA domain
      0.026   14.8   0.0       0.05   13.9   0.0    1.6  1  AAA_28           AAA domain
      0.027   14.6   0.0      0.058   13.6   0.0    1.5  1  AAA_33           AAA domain
      0.027   14.2   0.1      0.067   12.9   0.1    1.6  1  Thymidylate_kin  Thymidylate kinase
      0.031   14.0   0.0       0.09   12.5   0.0    1.8  1  AAA_30           AAA domain
      0.035   14.7   0.2       0.17   12.4   0.2    2.2  1  AAA_18           AAA domain
      0.037   13.9   0.1      0.071   13.0   0.1    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.049   14.1   2.4        3.5    8.1   0.4    3.3  2  AAA_17           AAA domain
      0.056   12.3   0.0       0.11   11.3   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.072   13.2   0.3       0.71   10.0   0.3    2.5  1  MMR_HSR1         50S ribosome-binding GTPase
      0.074   13.1   0.0      0.074   13.1   0.0    2.4  1  TFIIA_gamma_N    Transcription initiation factor IIA, gamma s
      0.075   13.0   0.3       0.41   10.6   0.1    2.0  2  DUF4919          Domain of unknown function (DUF4919)
      0.084   12.3   0.0       0.19   11.2   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
       0.09   13.1   0.1       0.24   11.8   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.091   11.8   0.1       0.16   11.0   0.1    1.3  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
        0.1   12.6   0.3        1.5    8.8   0.0    2.7  3  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.1   0.0       0.27   10.9   0.0    1.6  1  PRK              Phosphoribulokinase / Uridine kinase family


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 !  232.0   0.0   7.6e-72   4.7e-69       2     196 .]      98     290 ..      97     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.0 bits;  conditional E-value: 7.6e-72
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHT CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakee 82 
                                   + i+++GlqG+GKTtt++KL+++++++g k+++++aDtfR++A++QLktl +kl+vp++++  + d++ ++++++ +  + 
  gi|91772216|ref|YP_564908.1|  98 QTIMMIGLQGSGKTTTTSKLSRYFQRKGLKPAVICADTFRPGAYQQLKTLCDKLNVPFYGEVGNPDAVGIVERGLAELGK- 177
                                   789***********************************************************999**********99988. PP

                                   TSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHH CS
                         SRP54  83 kidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsia 163
                                     dv++vDTaGr+  +++l++e+++i+++++pd +llvld+++gq+a +qa+aF+++vgi+gv+++klDg+akgG+als++
  gi|91772216|ref|YP_564908.1| 178 -NDVLIVDTAGRHSLEADLIDEMEQIHEIAQPDYKLLVLDGAIGQQASEQARAFNDSVGISGVVISKLDGTAKGGGALSAV 257
                                   .79****************************************************************************** PP

                                   HHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                         SRP54 164 aelklPikfigvGekiedleefdperlvsrllg 196
                                   +e+++ i+figvGe+ +dle+f+p+r++srllg
  gi|91772216|ref|YP_564908.1| 258 SETNSAIAFIGVGETPDDLEKFEPDRFISRLLG 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 ?   -2.1   0.1        10   6.2e+03      13      27 ..     287     301 ..     283     316 .. 0.69
   2 !   95.3   2.3   4.2e-30   2.6e-27       2      99 .]     320     420 ..     319     420 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 10
                                   HHHCCCCCCHHHHCC CS
                       SRP_SPB  13 qikkmGplskllsmi 27 
                                   ++  mG++++l+++ 
  gi|91772216|ref|YP_564908.1| 287 RLLGMGDIKSLIEKA 301
                                   567899999998875 PP

  == domain 2  score: 95.3 bits;  conditional E-value: 4.2e-30
                                   SCTHHHHHHHHHHHCCCCCCHHHHCCC.........H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHH CS
                       SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiP..gmsae..akae..eeaekklkrieaiidSMTkeErdspekllkesRkrRiAr 76 
                                   ftl+d+++ql+ ++kmGp++++++m+P  gm+a+     +  + +e+k+k + +++dSMT+eE+ +p+ ll +sR++Ri+ 
  gi|91772216|ref|YP_564908.1| 320 FTLKDMYSQLEAMNKMGPMKQIMQMLPlgGMGAKlsD--DayKVTEDKMKGYRVLMDSMTEEELLNPR-LLGSSRIKRISL 397
                                   9************************996666666643..2458889**********************.8879******** PP

                                   HTTS-HHHHHHHHHHHHHHHHHT CS
                       SRP_SPB  77 GsGtsvqevnellkqfeqmkkmm 99 
                                   GsG s + v+ellk +++m++ m
  gi|91772216|ref|YP_564908.1| 398 GSGSSPDAVRELLKYYKMMQNAM 420
                                   ********************987 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 !   77.2   0.3   1.3e-24   8.1e-22       1      75 []       6      83 ..       6      83 .. 0.97
   2 ?    0.6   0.0       1.1   6.9e+02      23      45 ..     294     316 ..     285     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 1.3e-24
                                  HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHHH CS
                       SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkdeL 75
                                  Lg++l++alkkl g+++ide+++ e++k++++aLl+aDV+vk+v+++ + +k++a++ ++    ++p+++v+kiv++eL
  gi|91772216|ref|YP_564908.1|  6 LGSSLQDALKKLVGAGRIDEKTVTEVVKDIQRALLQADVNVKLVMQMSSHIKERALK-EEvppgMNPREHVIKIVYQEL 83
                                  899**************************************************9999.555*****************8 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHTT--HHHHH CS
                       SRP54_N  23 leealkeleeaLleaDVgvkvvk 45 
                                   ++ ++++ ee+L e D+ +++ +
  gi|91772216|ref|YP_564908.1| 294 IKSLIEKAEETLSEEDIDMEAMM 316
                                   55566667888888888877765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   1.3e-06   0.00081       3     156 ..     100     250 ..      98     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                                   EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHHT CS
                          cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeeree 81 
                                   +++ G  GsGKTt  ++l    +r+glk avi  +    +  ++l + +++  v    G +      d++  +e+ +++ +
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSryFQRKGLKPAVICADTFRPGAYQQLKTLCDKLNVP-FYGEVGNP---DAVGIVERGLAELG 176
                                   5678999*********99988899*************888888877777543333.34665555...99999999888888 PP

                                   T-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                          cobW  82 rldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee 156
                                   + dv+++ t G  +  a ++ + e++++ ++ d ++ v+D+ ++ ++ +++++ ++d +  + + v++K D   + 
  gi|91772216|ref|YP_564908.1| 177 KNDVLIVDTAGrHSLEADLIDEMEQIHEIAQPDYKLLVLDG-AIGQQASEQARAFNDSVGISGV-VISKLDGTAKG 250
                                   ***********8666666657799*****************.7779999***********9975.67999977665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06   0.00073      15      57 ..      96     139 ..      88     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                    Zeta_toxin  15 rPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRel 57 
                                   +P  i++ G +G+GK+++ ++l ++++ ++ +  ++ +D++R+ 
  gi|91772216|ref|YP_564908.1|  96 KPQTIMMIGLQGSGKTTTTSKLSRYFQrKGLKPAVICADTFRPG 139
                                   8**************************88889**********74 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 !   17.4   0.0   5.6e-06    0.0035       9      88 ..     107     248 ..     102     332 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.6e-06
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.................................. RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep.................................. 54 
                                   G+GKTt++ +L r+++r+gl+ +++ aD+ ++ +   l++l  d  +                                  
  gi|91772216|ref|YP_564908.1| 107 GSGKTTTTSKLSRYFQRKGLKPAVICADTFRPGAYQqLKTL-CD--Klnvpfygevgnpdavgiverglaelgkndvlivd 184
                                   99***********************9999888766432222.22..13357777777777788888888888888888888 PP

                                   ................................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS. CS
                                   ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ................................................dlkrllellealgkkkalllkiagvvlnrvdge 87 
                                                                                   +                  + i gvv+ + dg 
  gi|91772216|ref|YP_564908.1| 185 tagrhsleadlidemeqiheiaqpdykllvldgaigqqaseqarafndS------------------VGISGVVISKLDGT 247
                                   8888888888888777777777777777777655433333333333330..................44555555555554 PP

                                   . CS
                                   x RF
                          CbiA  88 n 88 
                                   +
  gi|91772216|ref|YP_564908.1| 248 A 248
                                   4 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     2e-06    0.0012      13      51 ..      97     135 ..      90     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                         6PF2K  13 klvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgk 51 
                                   +  i+++GL   gKt++++kl+ry +  g++  v  +  
  gi|91772216|ref|YP_564908.1|  97 PQTIMMIGLQGSGKTTTTSKLSRYFQRKGLKPAVICADT 135
                                   5679*********************98888765544444 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.7e-06    0.0054       2      49 ..      97     144 ..      96     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.7e-06
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                    APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                   + ++++ Gl gsGK+t + +l+++ ++kg +  ++  d+ R g +++L
  gi|91772216|ref|YP_564908.1|  97 PQTIMMIGLQGSGKTTTTSKLSRYFQRKGLKPAVICADTFRPGAYQQL 144
                                   689************************************999888776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-05      0.01       8      69 ..      95     173 ..      89     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                        AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae..................a 69 
                                   lk +++++++  G+GKT+++ +  +++++ g +kp+ i + +f   A ++l++ +++l+++                  a
  gi|91772216|ref|YP_564908.1|  95 LKPQTIMMIGLQGSGKTTTTSKLSRYFQRKG-LKPAVICADTFRPGAYQQLKTLCDKLNVPfygevgnpdavgiverglA 173
                                   67789999***********998888877776.88999999999999*******999999997777777774433333330 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 !   14.5   0.0   2.1e-05     0.013      30      66 ..      98     134 ..      79     152 .. 0.89
   2 ?   -2.9   0.1       4.3   2.6e+03     123     141 ..     179     197 ..     163     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                                   EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                   q + + G+ G+Gk t++++l   ++r+G + av+  D
  gi|91772216|ref|YP_564908.1|  98 QTIMMIGLQGSGKTTTTSKLSRYFQRKGLKPAVICAD 134
                                   567789****************************988 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                                   SEEEEEEESSTTHHHHHHT CS
                          MeaB 123 DvvlietvGvGqsevdvae 141
                                   Dv++++t G    e d+++
  gi|91772216|ref|YP_564908.1| 179 DVLIVDTAGRHSLEADLID 197
                                   7788888887777777765 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 !   14.8   0.0   2.9e-05     0.018       2      33 ..     103     134 ..     102     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                    ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                   +G  GsGKtt +++ls +++ +g ++av+  D
  gi|91772216|ref|YP_564908.1| 103 IGLQGSGKTTTTSKLSRYFQRKGLKPAVICAD 134
                                   899**********************9998665 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   7.5e-05     0.046       7     103 ..      99     189 ..      95     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-05
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                    ++ +G  G+GKTt+  +l + +++       +p v+  +   ++  ++l + l+ +l+++  + +  + + +  +e+ l 
  gi|91772216|ref|YP_564908.1|  99 TIMMIGLQGSGKTTTTSKLSRYFQRK----GLKPAVICADTFRPGAYQQL-KTLCDKLNVPFYG-EVGNPDAVGIVERGLA 173
                                   57889****************99643....35888898888888855555.9999999999999.8888899999999999 PP

                        AAA_22  88 aravielliiDEaqhl 103
                                   + ++  +li+D a + 
  gi|91772216|ref|YP_564908.1| 174 ELGKNDVLIVDTAGRH 189
                                   9999999999977654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.5e-05     0.059       2      76 ..      97     188 ..      96     229 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                        AAA_24   2 klkiliyGpsgiGKTtlakel.........gpkplfidtek.Glksldadkfpdie.......swedfldevvelaaelad 65 
                                   ++ i+++G +g+GKTt+ ++l         +p +++ dt++ G+ +   +  ++++       + +d +  v+   ael +
  gi|91772216|ref|YP_564908.1|  97 PQTIMMIGLQGSGKTTTTSKLsryfqrkglKPAVICADTFRpGAYQQLKTLCDKLNvpfygevGNPDAVGIVERGLAELGK 177
                                   5789*****************999999976666666677665554333333333333344444222222222222444444 PP

                        AAA_24  66 yktlviDtide 76 
                                    ++l++Dt++ 
  gi|91772216|ref|YP_564908.1| 178 NDVLIVDTAGR 188
                                   44455554443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     8e-05      0.05       2      81 ..     100     186 ..      99     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar......gypvv.pEaareileeklakgedalpwv.edllafaervleeqleeeaaaaank 74 
                                   i+++G +++GKTt++++L++       +  v+ ++++r    ++l++  d+l+   +  +   ++ +    + +a+  +n+
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSRYfqrkglKPAVIcADTFRPGAYQQLKTLCDKLNVPfYGEVGNPDA-VGIVERGLAELGKND 179
                                   889****************6555575545577899999999999988888888774444444443.455667777778888 PP

                        AAA_28  75 vlfcDrg 81 
                                   vl++D+ 
  gi|91772216|ref|YP_564908.1| 180 VLIVDTA 186
                                   8888875 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   9.3e-05     0.058       2      21 ..     100     119 ..     100     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                        AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                   ++++Gl+GsGK+t   +l +
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSR 119
                                   79***********9988843 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   0.00011     0.067       3      28 ..     104     130 ..     103     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                   ESTTSSHHHHHHHHHHHHHHTTE..EE CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.vv 28 
                                   Gl G+GKtt + +l ++++++g+k +v
  gi|91772216|ref|YP_564908.1| 104 GLQGSGKTTTTSKLSRYFQRKGLKpAV 130
                                   999*******************98654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.09      21     123 ..     100     217 ..      95     245 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                        AAA_30  21 avltGpAGtGKttalkalreaweaag.grviglAptgk..aAkvLae...elgi....eastiakllkrlk......grar 85 
                                    ++ G  G+GKtt+ ++l + ++++g ++ +++A t +  a ++L++   +l++    e  + +      +      g a+
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSRYFQRKGlKPAVICADTFRpgAYQQLKTlcdKLNVpfygEVGNPD------AvgiverGLAE 174
                                   57889********************867888888887633556676411133322233333333......13344447778 PP

                        AAA_30  86 lepgtllivDEagmv.....dtkqlaallkaaekagakvilvG 123
                                   l ++++livD ag        +++++++ ++a+ +   ++l G
  gi|91772216|ref|YP_564908.1| 175 LGKNDVLIVDTAGRHsleadLIDEMEQIHEIAQPDYKLLVLDG 217
                                   8889999999999884433334567777777777545555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00027      0.17       1      22 [.     100     121 ..     100     231 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                        AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                   I+  G +G+GKtt +  Ls+  
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSRYF 121
                                   7889**************8853 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00012     0.071       2      33 ..     100     131 ..      99     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                          MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                   + ++g +gsGKTt  +kl + ++++gl+ ++i
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSRYFQRKGLKPAVI 131
                                   6789************************9998 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0056       3.5       1     103 [.     103     209 ..     103     221 .. 0.55
   2 ?    2.9   0.1      0.22   1.4e+02      53      94 ..     293     334 ..     278     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0056
                                   EE-TTSSHHHHHHHHHHHHTEEEEE....HHHHHHHHHHTTTSHSSHHHHCTS.....HHHHHHHHHHHHHHHHHHHHHSS CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthls....aGdllreeakrgglakardemrkl.....pleekkelqkeaaekiaeeakkk 72 
                                   +G+ GsGK+t  +kl + ++ + l       d +r  a     ++ +   +kl      ++ + +   ++++ +ae  k++
  gi|91772216|ref|YP_564908.1| 103 IGLQGSGKTTTTSKLSRYFQRKGLKpaviCADTFRPGA----YQQLKTLCDKLnvpfyGEVGNPDAVGIVERGLAELGKND 179
                                   5999***********98774443330000334444222....222222222221112244445555566666666666666 PP

                                   EEEEEE-SEEEETTEEEESSHHHHHHHH..S CS
                        AAA_17  73 gvlvdghprikeqagfldglpkevleelkpd 103
                                    ++vd+  r   +a+++d++++ + e ++pd
  gi|91772216|ref|YP_564908.1| 180 VLIVDTAGRHSLEADLIDEMEQ-IHEIAQPD 209
                                   6777777777777777777764.66666665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHH CS
                        AAA_17  53 ekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpk 94 
                                   + k l ++a+e++ ee+ ++++++ g +++k++  +l+ + k
  gi|91772216|ref|YP_564908.1| 293 DIKSLIEKAEETLSEEDIDMEAMMRGRFTLKDMYSQLEAMNK 334
                                   567899************************999988888765 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.11      16      50 ..      98     134 ..      88     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                 TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairarg..draivlD 50 
                                   q i+++G +GsGKt++++kl r  +++g    +i +D
  gi|91772216|ref|YP_564908.1|  98 QTIMMIGLQGSGKTTTTSKLSRYFQRKGlkPAVICAD 134
                                   679******************9999998544455555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3    0.0011      0.71       2      87 ..     100     221 ..      99     243 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                   EEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSE.EEEEEE..ET...........................T CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdi.negrvk..lk...........................g 45 
                                   ++ +G   +GK+t  ++l++       +    + +   T  +  + ++k   +                           +
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSRyfqrkglK---PAVICADTFRPgAYQQLKtlCDklnvpfygevgnpdavgiverglaelgK 177
                                   6778888888888888888733322221...22222223333222222222112223333333333333344444444435 PP

                                   EEEEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT..T CS
                      MMR_HSR1  46 keielvDtpGliegaseek...glgkaflaleeadlillvvdas..e 87 
                                   +++ +vDt+G  +  s e    ++ ++++++ + d  llv+d +  +
  gi|91772216|ref|YP_564908.1| 178 NDVLIVDTAG-RH--SLEAdliDEMEQIHEIAQPDYKLLVLDGAigQ 221
                                   66********.44..45551134444555555569999999944331 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00012     0.074      10      36 ..       6      32 ..       5      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                 TFIIA_gamma_N 10 lGtaLtdaLDeliqegkIspqlamkVL 36
                                  lG +L+daL  l+ +g+I+++ + +V 
  gi|91772216|ref|YP_564908.1|  6 LGSSLQDALKKLVGAGRIDEKTVTEVV 32
                                  8*******************9999886 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5     9e+02      56     109 ..      12      64 ..       7      80 .. 0.81
   2 ?   10.6   0.1   0.00066      0.41      69     142 ..     290     364 ..     273     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                       DUF4919  56 ekleelkldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkee 109
                                   + l++l +    ++e+++ e+++  ++al +  +++k  + ++   k++  kee
  gi|91772216|ref|YP_564908.1|  12 DALKKL-VGAGRIDEKTVTEVVKDIQRALLQADVNVKLVMQMSSHIKERALKEE 64 
                                   556666.67788999*****************9****99999998888877766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00066
                       DUF4919  69 seeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkllkailssGdGlt.eetawvvisv 142
                                    + ++k++i+ aee l+++ +d+++++   + +k    + ea +    ++++++++   G G++  + a++v++ 
  gi|91772216|ref|YP_564908.1| 290 GMGDIKSLIEKAEETLSEEDIDMEAMMRGRFTLKDMYSQLEAMNKMGPMKQIMQMLPLGGMGAKlSDDAYKVTED 364
                                   56799*************************************999*****************8745788888764 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   0.0    0.0003      0.19       4      41 ..     100     137 ..      98     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                   +++ Gl  sGK+t +++L+++++ ++ +  vi  ++++
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSRYFQRKGLKPAVICADTFR 137
                                   7899**********************999999877765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00039      0.24      25      69 ..      98     155 ..      81     235 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                        AAA_16  25 elvllsGesGvGKsslvrellralekd..............ggif.lrgkcdqlesaipy 69 
                                   + ++ +G +G+GK++   +l r+++++              g++  l++ cd+l  ++p+
  gi|91772216|ref|YP_564908.1|  98 QTIMMIGLQGSGKTTTTSKLSRYFQRKglkpavicadtfrpGAYQqLKTLCDKL--NVPF 155
                                   678899****************99999766655555555443333444444444..4554 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00026      0.16      46      71 ..     106     131 ..      94     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                                   S-HSHHHHHHHHHHHTTTS..-EEEE CS
                          LpxK  46 GGtGKTPlvialvkllqarglkvgvl 71 
                                    G+GKT ++  l +++q++glk++v+
  gi|91772216|ref|YP_564908.1| 106 QGSGKTTTTSKLSRYFQRKGLKPAVI 131
                                   69***********************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 ?    0.0   0.0       1.3   7.9e+02      13      48 ..      29      68 ..       8      87 .. 0.76
   2 ?    8.8   0.0    0.0025       1.5       2      26 ..     100     124 ..      99     135 .. 0.89
   3 ?   -2.0   0.0       5.4   3.3e+03      30      48 ..     370     388 ..     360     396 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.3
                                  HHHHHHGGGGB....S--EEEEE--TT--HHHHH--B--. CS
                         AAA_5 13 selaerlaaal....nreveyvqltrdtteedlkgrreik 48
                                  +e+++ + +al     +  +++q+++ ++e+ lk ++ + 
  gi|91772216|ref|YP_564908.1| 29 TEVVKDIQRALlqadVNVKLVMQMSSHIKERALKEEVPPG 68
                                  5677777777776655556788999999999998877665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                                   EEEE--SSSSHHHHHHHGGGGBS-- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnre 26 
                                   ++++G +G+gK++ + +l++ ++r+
  gi|91772216|ref|YP_564908.1| 100 IMMIGLQGSGKTTTTSKLSRYFQRK 124
                                   689*****************99765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.4
                                   EE--TT--HHHHH--B--. CS
                         AAA_5  30 vqltrdtteedlkgrreik 48 
                                     l +++tee+l+ +r + 
  gi|91772216|ref|YP_564908.1| 370 RVLMDSMTEEELLNPRLLG 388
                                   5667789999999998775 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00044      0.27       4      38 ..     102     136 ..      99     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                           PRK   4 vagsSGaGkttvarklekifgrekvkaaeiegdsf 38 
                                   + g  G+Gktt++ kl   f+r+++k+a+i  d f
  gi|91772216|ref|YP_564908.1| 102 MIGLQGSGKTTTTSKLSRYFQRKGLKPAVICADTF 136
                                   55778**********************99977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2670.70
//
Query:       gi|91772217|ref|YP_564909.1|  [L=137]
Description: hypothetical protein Mbur_0142 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-47  159.5   0.3    6.6e-47  159.1   0.3    1.1  1  DUF2072      Zn-ribbon containing protein
  ------ inclusion threshold ------
      0.059   13.3   0.7       0.11   12.4   0.7    1.5  1  Prok-RING_1  Prokaryotic RING finger family 1
      0.087   13.0   1.2       0.19   11.9   1.2    1.5  1  Zn-ribbon_8  Zinc ribbon domain
       0.13   12.4   0.1       0.25   11.5   0.1    1.6  1  DGC          DGC domain


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 !  159.1   0.3   1.5e-50   6.6e-47       1     133 []       2     131 ..       2     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 159.1 bits;  conditional E-value: 1.5e-50
                       DUF2072   1 PHkCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseekeelvaeaeeeieevldaeeteeeklekk..ekeka 79 
                                   PHkCt+Cek+fedg+++il+GCp+CG++kFlyvk++e +++v+ + e     + +++++ + ae+  +e+ ++   e++++
  gi|91772217|ref|YP_564909.1|   2 PHKCTRCEKIFEDGAEVILSGCPNCGWNKFLYVKDMEPEKEVQVQPE-----TVDSVDDDIPAEQFIREIDDIIgiEHKER 77 
                                   9************************************9999888887.....33444444455555555444434345555 PP

                       DUF2072  80 ekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsvlkk 133
                                   e+ +ee++rvesvril+pGsYelNl++L+er+e+vma+k++g+Y+vdl+s+++k
  gi|91772217|ref|YP_564909.1|  78 ETVEEEGERVESVRILGPGSYELNLNSLFEREEIVMAIKQDGTYAVDLSSAFRK 131
                                   568899*********************************************985 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 ?   12.4   0.7   2.5e-05      0.11       5      27 ..       3      27 ..       1      30 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                   Prok-RING_1  5 kkCpvCgkelkeedDiVv..CpeCg 27
                                  +kC+ C+k ++++  ++   Cp+Cg
  gi|91772217|ref|YP_564909.1|  3 HKCTRCEKIFEDGAEVILsgCPNCG 27
                                  69*************99777****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 ?   11.9   1.2   4.3e-05      0.19       7      33 ..       4      27 ..       3      30 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCg 33
                                  +C++C + fe  +++    l  CP+Cg
  gi|91772217|ref|YP_564909.1|  4 KCTRCEKIFEDGAEVI---LSGCPNCG 27
                                  7*********777666...777****9 PP

>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.6e-05      0.25      44      98 ..       9      61 ..       3      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                           DGC 44 velaksarkiiaidGCpleCakkilekagvkpdehlvvtdlgikkeekldlseee 98
                                   ++++++   +++ GCp +  +k l  ++++p+++++v+   +   ++ d+ +e+
  gi|91772217|ref|YP_564909.1|  9 EKIFEDG-AEVILSGCPNCGWNKFLYVKDMEPEKEVQVQPETVDSVDD-DIPAEQ 61
                                  5566666.66889*************************9867766665.666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 888.34
//
Query:       gi|91772218|ref|YP_564910.1|  [L=253]
Description: hypothetical protein Mbur_0143 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-72  242.0  13.1    6.1e-72  241.8  13.1    1.0  1  DUF1624        Protein of unknown function (DUF1624)
    2.9e-10   39.8  20.8    2.9e-06   26.6   5.2    2.3  2  Acyl_transf_3  Acyltransferase family
      5e-05   22.3   6.8    0.00019   20.5   3.1    2.5  2  OpgC_C         OpgC protein
    0.00037   20.5   2.3    0.00037   20.5   2.3    2.2  2  DUF418         Protein of unknown function (DUF418)


Domain annotation for each model (and alignments):
>> DUF1624  Protein of unknown function (DUF1624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.8  13.1   1.4e-75   6.1e-72       1     223 []       7     234 ..       7     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.8 bits;  conditional E-value: 1.4e-75
                       DUF1624   1 RieeiDalRGiAlilMiifHflfdLeffgylavslatsglwvvfarliaslFlfiaGvslvlahskslrw.......rkfl 74 
                                   R +eiD+lRGiA+ lM++fH+l+dL +fgy++ +++ +g +++++r++a+lF+f+aG+sl+l++sk+l++        k++
  gi|91772218|ref|YP_564910.1|   7 RKWEIDLLRGIAITLMVFFHLLYDLYYFGYYDNDIR-TGEVFLIGRAAAFLFIFVAGISLTLSFSKQLEMeqtkpkfIKYV 86 
                                   89**********************************.8999999999**********************9****9999*** PP

                       DUF1624  75 kRglkilaaallitaatylllpdsfivFGiLhlialalllallflrlpkalllllallilalglllreaifdlplllwlgl 155
                                   kRg ki++++++ita++y++l++++i+FG Lh+i++a++l ++fl+ + a+l++ a+l +++g+ lr+ + ++p+llw+g+
  gi|91772218|ref|YP_564910.1|  87 KRGSKIFLWGMAITAGSYIFLREGIIIFGALHFIGVAIILSYPFLKQRSASLVA-AFLTIIAGIPLRTITIEQPWLLWIGI 166
                                   **************************************************9999.8888889******************* PP

                       DUF1624 156 ssekfetndYvplfPWfgvvllGialgkllyekgkrrlklpslpkaklvrplallGrhsLliYlihqp 223
                                   ++++f++ dY+pl+PWfgv+l+Gi++g++ly+++kr++ l+++++ +++++l+++G++sL iYl+hqp
  gi|91772218|ref|YP_564910.1| 167 QPTGFRSYDYFPLIPWFGVMLMGIFTGNVLYPQYKRKFILSDISELTHIKVLTYMGKRSLRIYLLHQP 234
                                   *******************************************************************9 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   5.2   6.5e-10   2.9e-06       3      91 ..      10     101 ..       8     118 .. 0.72
   2 !   16.1  11.8     1e-06    0.0045     199     311 ..     117     243 ..      86     252 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.5e-10
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
                 Acyl_transf_3   3 ylDllRgiAillVvflHali.ayspdagrgspiqasqssqiaflggfgvplFFllSGffla......amlyrrrglsklik 76 
                                   ++DllRgiAi l+vf+H l+ +y  ++  +   +  ++    ++g+ +  lF+++ G  l+       + + +++ +  ++
  gi|91772218|ref|YP_564910.1|  10 EIDLLRGIAITLMVFFHLLYdLYYFGYYDNDIRTGEVF----LIGRAAAFLFIFVAGISLTlsfskqLEMEQTKPKFIKYV 86 
                                   69******************844444444444444443....*******************9**98866666666666666 PP

                                   xxxxxxxxxxxxxxx RF
                 Acyl_transf_3  77 rRilrlliplliwll 91 
                                   +R  +++++ ++ + 
  gi|91772218|ref|YP_564910.1|  87 KRGSKIFLWGMAITA 101
                                   666677654444333 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-06
                                   xxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 199 llfflfGalladaddrdrnlsr.....glkislllsllllalillalfgqtdggglvasvliqsaslllvslgimllllll 274
                                   l f+++ ++l++ + ++r+ s+       ++ ++l  +++  ++l++ g    ++++ +  + ++ l+ ++  +++ + + 
  gi|91772218|ref|YP_564910.1| 117 LHFIGVAIILSYPFLKQRSASLvaaflTIIAGIPLRTITIEQPWLLWIG----IQPTGFRSYDYFPLIPWFGVMLMGIFTG 193
                                   4444444455444444444444333334444444444444444444444....5577777777777666666666655555 PP

                                   xxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 275 falpsrsafk.............llrylgkiSygiYliHlpllmllqkll 311
                                   ++l +  ++k             +l y+gk S+ iYl+H+p+l ++ ++ 
  gi|91772218|ref|YP_564910.1| 194 NVLYPQYKRKfilsdiselthikVLTYMGKRSLRIYLLHQPILIAIFYIT 243
                                   55555555555********************************9998875 PP

>> OpgC_C  OpgC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   3.1   4.2e-08   0.00019       1      87 [.       7     101 ..       7     143 .. 0.84
   2 !    3.4   0.2    0.0065        29     295     321 ..     213     239 ..     116     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.2e-08
                        OpgC_C   1 RdlrlDlfRGlalvlivvdHi......pgsvlskltlrnfGfsd..aAevFVflSGlavglvYgraaeregalaaaarilr 73 
                                   R++++Dl+RG+a+ l+v+ H+       g + + + + ++ ++   aA +F+f++G+++ l +++  e e+ +    + ++
  gi|91772218|ref|YP_564910.1|   7 RKWEIDLLRGIAITLMVFFHLlydlyyFGYYDNDIRTGEVFLIGraAAFLFIFVAGISLTLSFSKQLEMEQTKPKFIKYVK 87 
                                   89*******************877665455555666666656542267799****************************** PP

                        OpgC_C  74 RawelYvahiallv 87 
                                   R  ++++  +a+++
  gi|91772218|ref|YP_564910.1|  88 RGSKIFLWGMAITA 101
                                   *****998887765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0065
                        OpgC_C 295 avlrplillGrhsLavFvvgvvlslll 321
                                      ++l+ +G++sL ++ ++  + +++
  gi|91772218|ref|YP_564910.1| 213 THIKVLTYMGKRSLRIYLLHQPILIAI 239
                                   456788999999999999886655554 PP

>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.077   3.4e+02      16      76 ..      13      71 ..       2     108 .. 0.62
   2 !   20.5   2.3   8.2e-08   0.00037      18     115 ..     138     246 ..     113     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.077
                        DUF418 16 llrrllligllvglplnlllavlaeaaeesallelllsvlrylaglllalgyvalilllla 76
                                  llr +++ +++ + +l+ l++   ++ +++  ++ ++ + r++a l++ ++ ++l l + +
  gi|91772218|ref|YP_564910.1| 13 LLRGIAITLMVFFHLLYDLYY--FGYYDNDIRTGEVFLIGRAAAFLFIFVAGISLTLSFSK 71
                                  444444444333333333333..56666666666666666666666655555555555544 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 8.2e-08
                        DUF418  18 rrllligllvglplnllla....vlaeaaeesallelllsvlrylaglllalgyvalillllakekrrr.......llral 87 
                                    + +++++++g+pl  +++    +l+  ++ +  ++   + l  ++g++l+ ++ + +l+  +k+k           +++l
  gi|91772218|ref|YP_564910.1| 138 LVAAFLTIIAGIPLRTITIeqpwLLWIGIQPTGFRSYDYFPLIPWFGVMLMGIFTGNVLYPQYKRKFILsdiseltHIKVL 218
                                   445666789999999999998877788888889999999999999999988888777777666666633466665559*** PP

                        DUF418  88 aavGRmALTnYllqslictllfygyglg 115
                                   +++G+++L  Yll+  i++++fy  g+ 
  gi|91772218|ref|YP_564910.1| 219 TYMGKRSLRIYLLHQPILIAIFYITGFA 246
                                   **********************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1935.81
//
Query:       gi|91772219|ref|YP_564911.1|  [L=354]
Description: DNA-directed DNA polymerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-48  164.1   0.1    3.7e-48  163.3   0.1    1.4  1  IMS              impB/mucB/samB family
    1.2e-16   61.4   1.1    2.2e-16   60.6   1.1    1.4  1  IMS_C            impB/mucB/samB family C-terminal domain
    1.4e-05   25.3   0.0    3.1e-05   24.2   0.0    1.6  1  DUF4332          Domain of unknown function (DUF4332)
    0.00032   20.8   0.0    0.00095   19.4   0.0    1.9  1  IMS_HHH          IMS family HHH motif
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.057   13.7   0.0    1.8  1  Cdd1             Pathogenicity locus
      0.027   15.1   0.2       0.16   12.6   0.0    2.4  2  HHH_5            Helix-hairpin-helix domain
      0.038   14.3   1.4      0.058   13.8   0.2    1.9  2  PfUIS3           Plasmodium falciparum UIS3 membrane protein
       0.08   12.8   0.0       0.29   11.0   0.0    2.0  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   0.1   1.6e-51   3.7e-48       1     150 []       5     155 ..       5     155 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 1.6e-51
                                   EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHHHHHH CS
                           IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyrrask 78 
                                   iDmd+Fy sve a+dp+Lkg Pvvv++   +   rg+v ++syeAr++G+k++m+i++a++lcp++++++v++++y+++s+
  gi|91772219|ref|YP_564911.1|   5 IDMDSFYSSVEVAADPKLKGLPVVVGSDPLQgvgRGVVSTCSYEAREFGIKSAMAISKAYHLCPEAVYLRVNMPLYKKVSN 85 
                                   8**************************9555999*********************************************** PP

                                   HHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHHH CS
                           IMS  79 kileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlase 150
                                   +i+e+l+++ s k +++s+DEayld++ +++ +++  ++la +++k+++++ g+t+s+Gi++nk +AK+as+
  gi|91772219|ref|YP_564911.1|  86 SIMELLRNY-SSKFQQVSVDEAYLDVSYIVSGFDEA-KKLAMQIKKDVFQKEGITCSVGIGPNKSIAKIASD 155
                                   *********.55**********************96.*********************************96 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   1.1   9.9e-20   2.2e-16       3     115 ..     236     348 ..     234     351 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 9.9e-20
                         IMS_C   3 earpepksissektfpepydesk...lkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtreil 79 
                                   +++ e ksis+e+tf+++++  +   l++++  L+e ++  L +k+ + +t+t+k+r  df+  +r +tL+  ++d  +i 
  gi|91772219|ref|YP_564911.1| 236 QESGEIKSISKEDTFDKDTS--DmeyLESVVDTLSEHVHTSLSKKKYLFKTVTIKVRLEDFTtYTRAKTLAAHSDDLVTIR 314
                                   677899***********333..23369******************************999999****************** PP

                         IMS_C  80 eaalkLlrrlidepglpirligvsasnlvekaesqa 115
                                   ++a+ Ll++ +   + ++rl+gv++++l++ +e q+
  gi|91772219|ref|YP_564911.1| 315 KTAKGLLQEFNG--KNKLRLLGVGVTKLDKLDERQT 348
                                   *******99999..***************9888876 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.4e-08   3.1e-05      41     100 ..     165     224 ..     140     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.4e-08
                       DUF4332  41 isernvlklanlAdLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqklkrlnrskk 100
                                   +s +nv+++    d +ri gig++ + +L + G++++ eLa  n+++L +k +++    +
  gi|91772219|ref|YP_564911.1| 165 VSPENVRSFLYPLDVSRISGIGKKTSVMLGQMGIRTIGELAIHNVQDLREKFGKFGLVMH 224
                                   567788888888899************************************999866655 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.2e-07   0.00095       1      23 [.     167     189 ..     167     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.2e-07
                       IMS_HHH   1 pddvkefLwplpitkipGiGgkl 23 
                                   p++v++fL+pl+++ i GiG+k+
  gi|91772219|ref|YP_564911.1| 167 PENVRSFLYPLDVSRISGIGKKT 189
                                   799*******************9 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.057       9      45 ..     180     216 ..     176     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                          Cdd1   9 qdiPniGkalaedlvelGirsveelkgedpeelyekl 45 
                                    +i +iGk+++ +l ++Gir++ el+ ++ ++l ek+
  gi|91772219|ref|YP_564911.1| 180 SRISGIGKKTSVMLGQMGIRTIGELAIHNVQDLREKF 216
                                   6899*************************99998876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         8   1.8e+04      11      21 ..      53      63 ..      53      64 .. 0.74
   2 ?   12.6   0.0     7e-05      0.16       3      37 ..     178     212 ..     176     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8
                                  -HHHHHHHHTT CS
                         HHH_5 11 GpktAlallsa 21
                                  G k A+a+ +a
  gi|91772219|ref|YP_564911.1| 53 GIKSAMAISKA 63
                                  67888888765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7e-05
                                   HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHH CS
                         HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeL 37 
                                   ++ ++sGiG+kt + l   Gi+++ +la  +v++L
  gi|91772219|ref|YP_564911.1| 178 DVSRISGIGKKTSVMLGQMGIRTIGELAIHNVQDL 212
                                   6779**********************997777766 PP

>> PfUIS3  Plasmodium falciparum UIS3 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.7   3.8e+03      78      86 ..     104     112 ..      71     130 .. 0.50
   2 ?   13.8   0.2   2.6e-05     0.058      23      86 ..     225     289 ..     206     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                                   HHHHHHHHH CS
                        PfUIS3  78 dkavldlky 86 
                                   d a ld+ y
  gi|91772219|ref|YP_564911.1| 104 DEAYLDVSY 112
                                   233333333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHHHHHHHHHHS-HHH.HHHHTT-HHHHHHHHHHHHHHTT----HHHHHHHHHHHHH CS
                        PfUIS3  23 rynifvdivklaiqkhfedlsndq.kdslvndyeylrkivqtldesrdvslskaqedkavldlky 86 
                                   +  + vd  k+     ++ +s ++  d    d+eyl+ +v+tl e  + slsk +     + +k 
  gi|91772219|ref|YP_564911.1| 225 QLANGVDGRKVQESGEIKSISKEDtFDKDTSDMEYLESVVDTLSEHVHTSLSKKKYLFKTVTIKV 289
                                   555666777777777777788654158899***********************886655555555 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 ?   11.0   0.0   0.00013      0.29       5      29 ..     181     205 ..     179     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
               DNA_pol_lambd_f   5 kvyGVGpktAkkwyakGirtledlr 29 
                                   ++ G+G kt  ++ ++Girt+ +l 
  gi|91772219|ref|YP_564911.1| 181 RISGIGKKTSVMLGQMGIRTIGELA 205
                                   89******************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2716.41
//
Query:       gi|91772220|ref|YP_564912.1|  [L=96]
Description: hypothetical protein Mbur_0145 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       589  (0.0328518); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 783.21
//
Query:       gi|91772221|ref|YP_564913.1|  [L=64]
Description: 30S ribosomal protein S17e [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-12   46.1   0.2    4.6e-12   45.9   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 !   45.9   0.2   2.6e-16   4.6e-12       1      58 [.       1      58 [.       1      61 [. 0.97

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 2.6e-16
                                  XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHH CS
                Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlm 58
                                  mg++r+  +K  a  ++e+y   +t+dF++nk ++++ ++i+ k +rn++aGyvt+ +
  gi|91772221|ref|YP_564913.1|  1 MGNIRQTHIKNIAFRLVENYGDVFTTDFDKNKLLVSQYTTIEGKVIRNRVAGYVTRKI 58
                                  99*****************************************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 440.34
//
Query:       gi|91772222|ref|YP_564914.1|  [L=291]
Description: dihydrodipicolinate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-99  331.9   0.5    2.4e-99  331.7   0.5    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
       0.07   13.1   0.1       0.19   11.8   0.1    1.8  1  PA        PA domain


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.7   0.5  2.6e-103   2.4e-99       2     288 ..       2     286 ..       1     287 [. 0.97

  Alignments for each domain:
  == domain 1  score: 331.7 bits;  conditional E-value: 2.6e-103
                                   -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSH CS
                         DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnst 82 
                                   f+g+++al+tpf +d ++d+  l k+ief  n  v g+vv+GttGEsatlst+e+++++ iave+a+  +pv+ag+Gsn+t
  gi|91772222|ref|YP_564914.1|   2 FEGVLPALITPFTKDDTIDRTGLIKNIEFAENGKVTGVVVCGTTGESATLSTAEHMEVIDIAVECAN--VPVVAGTGSNNT 80 
                                   89*****************************999*******************************95..************ PP

                                   HHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEEE- CS
                         DHDPS  83 seaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivgvKea 163
                                   +ea++l+k+aeeaGa g+l++ PYYnkp+++gl++hf++i+ea + p++lYnvpsrtg+d+s+e++++La+++nivg+Kea
  gi|91772222|ref|YP_564914.1|  81 AEAVELTKHAEEAGASGALVISPYYNKPNKAGLISHFRTIAEAVEIPIVLYNVPSRTGQDISLEVITELAKIDNIVGIKEA 161
                                   ********************************************************************************* PP

                                   SS-CTHHHHHHC.CCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHC CS
                         DHDPS 164 vgdleevikikk.evgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllplikil 243
                                   +g+l++  +i++ ++++d+ + sGdd l+l+++s+G+ Gvisv +ni++ rm  l++a +eGd+a+a++l+ ++ pli +l
  gi|91772222|ref|YP_564914.1| 162 SGNLDKASQIIEnTMDEDFKVTSGDDGLTLPIMSIGGCGVISVVANIVPDRMSRLVNAFNEGDTATAQQLHYEIAPLIRAL 242
                                   ****99999886156889*************************************************************** PP

                                   CCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                         DHDPS 244 faepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                   f e+n++++k a++l+Gl++++ lr+Pl+p++ e+++ l++ lk+
  gi|91772222|ref|YP_564914.1| 243 FTETNPVPIKRAMNLVGLNAGH-LRPPLAPISAENNKLLANCLKE 286
                                   **********************.************9999998886 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.1e-05      0.19      36      79 ..      84     129 ..      36     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                            PA  36 aeKarnAqaaGAagviiv....ndgelgaatgasgnegepdgitiPav 79 
                                   +e +++A++aGA g++++    n++   +a+  s   + ++ ++iP+v
  gi|91772222|ref|YP_564914.1|  84 VELTKHAEEAGASGALVIspyyNKP--NKAGLISHFRTIAEAVEIPIV 129
                                   67789*************5554333..233333444445555666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1797.90
//
Query:       gi|91772223|ref|YP_564915.1|  [L=263]
Description: dihydrodipicolinate reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-46  155.0   0.2    1.2e-45  154.4   0.2    1.3  1  DapB_C           Dihydrodipicolinate reductase, C-terminus
    1.4e-27   96.3   3.5    2.2e-27   95.6   3.5    1.3  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0041   16.2   3.5      0.089   11.8   3.5    2.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
      0.044   12.3   0.5      0.063   11.8   0.5    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !  154.4   0.2   2.7e-49   1.2e-45       1     121 []     131     261 ..     131     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 2.7e-49
                                   HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH.................-S-ETTCCCEEEETTT CS
                        DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia..egke...........arkkkeigihsvRggg 68 
                                   Gvn+++k+++e ak+l+e yd+eiiE+Hhn+K+DaPSGTA++ ae i+                 a ++keigih+vRgg+
  gi|91772223|ref|YP_564915.1| 131 GVNVFFKILQETAKYLSE-YDIEIIEAHHNQKKDAPSGTAMKAAEVISetL--GgkdfvygreglAPRDKEIGIHAVRGGD 208
                                   9***************99.*****************************550..24556666667777889*********** PP

                                   --CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                        DapB_C  69 vvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                   +vg+h+vlfag+ge+ieikh+a+sr+ Fa+Ga++aa w++++ +g+ +m+d+L
  gi|91772223|ref|YP_564915.1| 209 IVGDHTVLFAGDGERIEIKHQAHSRNAFASGAVKAAIWINNAGPGIHTMDDIL 261
                                   ***************************************9999********97 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   3.5   4.9e-31   2.2e-27       2     124 .]       3     128 ..       2     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 4.9e-31
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE-S-HH CS
                        DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliDFTtpe 78 
                                   + +v+GasGrmGk +++ + + e+++l++a+d  +   +gkd+ge++++gkl+v+++  +d+++vl++  ++v+iDFT   
  gi|91772223|ref|YP_564915.1|   3 NAGVTGASGRMGKLIIENIIKMEGIQLSSAFDLMN---IGKDVGEVAQTGKLDVNISdvADMATVLKEskTNVVIDFTIAP 80 
                                   568******************************99...9******************888999999998999********* PP

                                   HHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTT..SEEEE-S-- CS
                        DapB_N  79 avlenlklalekgvklViGTTGlseeelaeleelakk..igvviapNf 124
                                   a+++n+ +++ +gv+l+iGTTG+s+e++a++e +  k  +++vi+pN+
  gi|91772223|ref|YP_564915.1|  81 ATVANAPVVAGAGVDLIIGTTGFSDEQRATIEGAIIKngTSAVISPNY 128
                                   ********************************9776659********7 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   3.5     2e-05     0.089       2      73 ..       6      74 ..       5     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                     3Beta_HSD  2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihl 73
                                  vtG++G +G+ ++++++++e ++   ++Dl +  +   e+ +++  +v   Dv d ++   +l++++ ++++
  gi|91772223|ref|YP_564915.1|  6 VTGASGRMGKLIIENIIKMEGIQLSSAFDLMNIGKDVGEVAQTGKLDVNISDVADMAT---VLKESKTNVVI 74
                                  9*******************9999999**77666665666666666565666655544...44444433333 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 ?   11.8   0.5   1.4e-05     0.063     151     219 ..      53     123 ..      47     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                                   T----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT..-SEEEEETTTTTTCSSS--EEEEEESSCHHH CS
               Cys_Met_Meta_PP 151 lkvvDiekiaklakkagvlvvvDntfasp.llqrplklg..aDivvhSaTKylgGhsdvvaGvivvkgkeel 219
                                   +++ D++++a + k+ ++ vv+D t+a   +   p+  g  +D+++  +T + + +  ++ G+i+++g  ++
  gi|91772223|ref|YP_564915.1|  53 VNISDVADMATVLKESKTNVVIDFTIAPAtVANAPVVAGagVDLII-GTTGFSDEQRATIEGAIIKNGTSAV 123
                                   789**********************987747777998882245544.6789999999********9986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1620.12
//
Query:       gi|91772224|ref|YP_564916.1|  [L=195]
Description: hypothetical protein Mbur_0149 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   2.2    2.3e-14   53.9   2.2    1.8  2  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
        1.6    9.0   7.4       0.42   10.9   1.2    2.7  2  DUF3392      Protein of unknown function (DUF3392)
          4    8.2   9.0        1.9    9.2   2.1    2.2  2  DUF4029      Protein of unknown function (DUF4029)


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   2.2   3.9e-18   2.3e-14       1     119 [.      32     155 ..      32     156 .. 0.91
   2 ?   -1.9   0.6      0.76   4.5e+03      11      29 ..     169     187 ..     164     190 .. 0.58

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.9e-18
                   SNARE_assoc   1 lPsevllvaaGvlf.....glllgtlvtslgallGaslayllgrylgr..kalrrkllsekrvkalerlverygflallll 74 
                                   lP evll++ G+++     +l ++++v++++ + G++l y+l++   +    l  + ++ek++ ++e l++ ++ +++++l
  gi|91772224|ref|YP_564916.1|  32 LPEEVLLLTIGYFVslgfgNLGIVIVVSLIAGCSGDILLYWLSKNGSKlfLHL-NRNINEKKIVKYENLMQTHDGKTVFVL 111
                                   699***********887777777********************9999884444.55678888888**************** PP

                   SNARE_assoc  75 rllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                   rl+ ++ r + ++vaG ++v +++F+++ +++ ++    +++lG+
  gi|91772224|ref|YP_564916.1| 112 RLIVGL-RFFGPVVAGSANVAWRKFLFYDLLALLIYYPSLIFLGY 155
                                   ******.****************************9999999997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.76
                   SNARE_assoc  11 Gvlfglllgtlvtslgall 29 
                                   G++ +++  ++v + g+ +
  gi|91772224|ref|YP_564916.1| 169 GIFSHIIFFIVVGLFGIAI 187
                                   5555555555555555554 PP

>> DUF3392  Protein of unknown function (DUF3392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.6      0.11   6.9e+02      11      36 ..       5      30 ..       3      62 .. 0.76
   2 ?   10.9   1.2     7e-05      0.42      20      66 ..     141     187 ..     128     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                       DUF3392 11 rllrpylseislalvatlLvvygddi 36
                                  +++ pyl+ +s a +  +L v+g+ i
  gi|91772224|ref|YP_564916.1|  5 QFSIPYLEHLSYAGIFITLAVLGHFI 30
                                  66778888888888877777777654 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7e-05
                       DUF3392  20 islalvatlLvvygddinrllkrllsslkfvlrvlvfvllcafGyGl 66 
                                   ++l +    L+ +g ++++ l++l+s+  ++  +++f+++  fG ++
  gi|91772224|ref|YP_564916.1| 141 LALLIYYPSLIFLGYHFHNNLRNLISEVGIFSHIIFFIVVGLFGIAI 187
                                   677888889***********************************876 PP

>> DUF4029  Protein of unknown function (DUF4029)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.7     0.027   1.6e+02       6      86 ..      36     116 ..      33     120 .. 0.77
   2 ?    9.2   2.1   0.00031       1.9       9      47 ..     151     189 ..     145     195 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.027
                       DUF4029   6 lmalflgyvfi..fsnlnriqeqsileiclfsisielfsivsivllnelflrihsfelmkfgnvvlqvicayivfvvldki 84 
                                   ++ l +gy +   f nl  +   s++  c   i +  +s     l+  l + i   +++k+ n++ q+     vfv l+ i
  gi|91772224|ref|YP_564916.1|  36 VLLLTIGYFVSlgFGNLGIVIVVSLIAGCSGDILLYWLSKNGSKLFLHLNRNINEKKIVKYENLM-QTHDGKTVFV-LRLI 114
                                   56677787542238899999999999999999999999999889999999999999999999974.6666777775.5556 PP

                       DUF4029  85 vg 86 
                                   vg
  gi|91772224|ref|YP_564916.1| 115 VG 116
                                   55 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00031
                       DUF4029   9 lflgyvfifsnlnriqeqsileiclfsisielfsivsiv 47 
                                   +flgy f     n i e  i+   +f i + lf i   +
  gi|91772224|ref|YP_564916.1| 151 IFLGYHFHNNLRNLISEVGIFSHIIFFIVVGLFGIAISI 189
                                   79*****9888899*******************996444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1182.51
//
Query:       gi|91772225|ref|YP_564917.1|  [L=263]
Description: hypothetical protein Mbur_0155 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.9    8.9  16.1          5    7.6   0.1    4.4  4  FlaC_arch      Flagella accessory protein C (FlaC)
        2.7    8.0  13.2       0.86    9.6   2.9    2.8  2  DUF1664        Protein of unknown function (DUF1664)
        4.6    7.0   9.1       0.35   10.6   0.4    2.6  2  Lectin_N       Hepatic lectin, N-terminal domain


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.016        97      34      52 ..       4      22 ..       2      22 .. 0.92
   2 ?    1.5   1.0     0.067     4e+02       2      31 ..      20      49 ..      19      60 .. 0.79
   3 ?    7.6   0.1   0.00083         5       3      25 ..      68      90 ..      67     115 .. 0.80
   4 ?    4.9   1.8    0.0059        35       3      40 ..     206     243 ..     205     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.016
                     FlaC_arch 34 kenVkdllsLYEvVsnqvN 52
                                  +e++++l+++ E Vsn +N
  gi|91772225|ref|YP_564917.1|  4 NERIENLMKIAEEVSNVKN 22
                                  799*************888 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.067
                     FlaC_arch  2 idelEnklsklsteletvkkeneelsksve 31
                                  +++++n+++k  ++l  + ++ e+ +k++ 
  gi|91772225|ref|YP_564917.1| 20 VKNIQNEMKKSTIKLLELDEKYESAKKDLS 49
                                  789999999999988888887777777664 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00083
                     FlaC_arch  3 delEnklsklsteletvkkenee 25
                                  ++lEnk+ +l+t+++ ++ e   
  gi|91772225|ref|YP_564917.1| 68 KDLENKIRDLDTKIADIRLEARR 90
                                  79*************99877654 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.0059
                     FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                   +++E++++ +++ + ++ +++ + +  +++lken +++
  gi|91772225|ref|YP_564917.1| 206 EKIEKEIEAHQVLIRSANSNIHSERMHLNNLKENLERI 243
                                   579***********999999999999999999998654 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.9   0.00014      0.86      37     120 ..      21     102 ..      17     108 .. 0.83
   2 ?    3.4   2.4     0.013        76      59     114 ..     187     241 ..     155     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                       DUF1664  37 rslsdavesvskqleqvseslaatkrhLss.ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                   +++++ +++ + +l ++ e+ +++k++Ls+ +++ v+       e++k++++++ ++  ++++i+ + + + +    l + 
  gi|91772225|ref|YP_564917.1|  21 KNIQNEMKKSTIKLLELDEKYESAKKDLSDyNLKLVELDNSRELEMTKDLENKIRDLDTKIADIRLEARRLFTP---LSKA 98 
                                   7888899999999999************9757888999999999*********************999877654...3334 PP

                       DUF1664 117 leri 120
                                   ++r+
  gi|91772225|ref|YP_564917.1|  99 ISRM 102
                                   4444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.013
                       DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                   + k++L+s+++ +     e ++i kei+++   +r+  s+i+++  +++++ e+le
  gi|91772225|ref|YP_564917.1| 187 SEKDKLTSELNGLSIY-REREKIEKEIEAHQVLIRSANSNIHSERMHLNNLKENLE 241
                                   5567777777766654.344556666666666666666666666666666555555 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.6     0.074   4.4e+02      58     128 ..      11      81 ..       6      95 .. 0.71
   2 ?   10.6   0.4   5.8e-05      0.35      67     120 ..     204     257 ..     186     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.074
                      Lectin_N  58 etLketfsnfssstlaeiqalssqggslsekvtsleaklekkqqdl.kadhselllhvkqlvkdLrtLsCql 128
                                     + e++sn+ ++++ e+++ + +  +l+ek +s +  l   + +l + d s  l   k l + +r L  ++
  gi|91772225|ref|YP_564917.1|  11 MKIAEEVSNV-KNIQNEMKKSTIKLLELDEKYESAKKDLSDYNLKLvELDNSRELEMTKDLENKIRDLDTKI 81 
                                   5555666665.4677777888888888888888888888777665524577777777777777777776555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.8e-05
                      Lectin_N  67 fssstlaeiqalssqggslsekvtsleaklekkqqdlkadhselllhvkqlvkd 120
                                     ++++ ei+a +   +s++ +++s + +l++ +++l+   s lll v+++  d
  gi|91772225|ref|YP_564917.1| 204 EREKIEKEIEAHQVLIRSANSNIHSERMHLNNLKENLERIRSVLLLDVRHFFGD 257
                                   4578999*******************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2076  (0.11579); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); 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):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 1453.20
//
Query:       gi|91772226|ref|YP_564918.1|  [L=150]
Description: hypothetical protein Mbur_0156 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.059   14.0   0.3      0.093   13.3   0.3    1.4  1  TetR_C_37  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_37  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   5.2e-06     0.093       8      60 ..       2      51 ..       1      67 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-06
                                  HHH.......HHHHHHS-HHHHHHGGGGS-GGGHHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_37  8 klierLFSkkwnelfddgvfYsyyalvfrekeikekykkildsLrevLksklk 60
                                  k+ierLF kk ++    +  Y+++ lv   +++k+++kk+ + Lr v+k+k +
  gi|91772226|ref|YP_564918.1|  2 KFIERLFGKKQEK---KESHYVVFELVELSSTVKAEIKKQEEILRPVIKDKFE 51
                                  89********986...7999****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 1173.85
//
Query:       gi|91772227|ref|YP_564919.1|  [L=382]
Description: AAA ATPase [Methanococcoides burtonii DSM 6242]
Scores for 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-18   64.7   0.0    1.4e-17   64.1   0.0    1.3  1  AlbA_2    Putative DNA-binding domain
  ------ inclusion threshold ------
      0.058   13.9   0.3       0.83   10.2   0.2    2.4  2  DUF1279   Protein of unknown function (DUF1279)
        3.9    7.8   9.9       0.75   10.1   4.0    2.2  3  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


Domain annotation for each model (and alignments):
>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   2.4e-21   1.4e-17       1     120 [.     236     366 ..     236     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2.4e-21
                        AlbA_2   1 EdellEfKeslgnklkkrers......iakticAfaNsegGtlliGVeDdgkvvGvecsdqeedqlrlelksiikrfkpk. 74 
                                   E ++lEfK++l+ +l++++ +      + kti+A +Ns+gG+ll+GV Dd+++ G+  ++++ +++++ + ++ +++  + 
  gi|91772227|ref|YP_564919.1| 236 EGQKLEFKSTLRMNLHTSKPDkriehaVTKTIVAYLNSNGGHLLVGVCDDKTILGI--EEDNFQNNDKFNLHFTNLIGRSi 314
                                   889*********99999888899999******************************..88888888888888888888887 PP

                        AlbA_2  75 .....vlpdiervelkgkkvlvvkvekskkkp.lyeneegvvyiRrggsskr 120
                                        + +d e v+++g+ vl v + +s+ ++ l+e +++++yiR+ + + +
  gi|91772227|ref|YP_564919.1| 315 gneflPYIDSELVNVQGRFVLRVDCSPSDIPVfLKEGDKEEFYIRSAAATIE 366
                                   778888888888*****************9999999999******9877665 PP

>> DUF1279  Protein of unknown function (DUF1279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00014      0.83       6      34 ..      83     115 ..      78     152 .. 0.84
   2 ?    1.0   0.0       0.1   6.2e+02      52      73 ..     217     271 ..     171     273 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                       DUF1279   6 lfkkYGkvalgvy....lsislidlgicYllvk 34 
                                   l+++Y++++l+v+    ++i  i +++ Yll++
  gi|91772227|ref|YP_564919.1|  83 LIQRYWWWYLFVHalsaFVIGAIGFSLAYLLFR 115
                                   79***********44444555677888888876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.1
                       DUF1279  52 v.................................sskkvekksksswgefaiAYa 73 
                                                                     +++k +k+ +  +++ ++AY+
  gi|91772227|ref|YP_564919.1| 217 RyheqtdpsekllklinkgegqklefkstlrmnlHTSKPDKRIEHAVTKTIVAYL 271
                                   1455555555555555555555555555555555788888889999999999996 PP

>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.14   8.2e+02      65     117 ..      17      70 ..       3      81 .. 0.55
   2 ?    0.3   0.4      0.14   8.4e+02      53      94 ..      50      91 ..      21     102 .. 0.59
   3 ?   10.1   4.0   0.00013      0.75      36     120 ..     101     186 ..      96     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                          MnhB  65 rileglglllavltgllglllg..fltslflelelllg.evelgtallfdlgVylv 117
                                    +l+++g++++v   +l l+l    lt +fl++ + ++ e e+ +  lf++++ + 
  gi|91772227|ref|YP_564919.1|  17 ALLAAAGVIAVVRNDWLNLVLAlfALTLTFLPT-I-IEkEWEFDFPSLFETLILIF 70 
                                   356667777777777777777665455444444.2.22134455555555544443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                          MnhB 53 elekllrvklaprileglglllavltgllglllg..fltslfle 94
                                    ek  +++  +  l+ + +l+++ + +++  +g  + ++++++
  gi|91772227|ref|YP_564919.1| 50 IIEKEWEFD--FPSLFETLILIFIYLSIFPETMGplIQRYWWWY 91
                                  233333444..447778888888888888888887444444444 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00013
                          MnhB  36 lilaaalillylafgleelekllrvklaprileglglllavltgllglllgfltslflel.elllgevelgtallfdlgVy 115
                                   +i+a+++ l yl f  +++   l   + + + + l++++a+++ ++ + ++fl +++++  ++ +++  l + l ++l+V 
  gi|91772227|ref|YP_564919.1| 101 VIGAIGFSLAYLLFRERRTTTGLTPAIVAAFSFCLSFTIATIMEIFIFTMEFLFEFNVQRyDMRTTTLDLIIYLGINLAVT 181
                                   899************999544444443335666666666666666666666888887766333333344777777777777 PP

                          MnhB 116 lvVvg 120
                                   l V+ 
  gi|91772227|ref|YP_564919.1| 182 LSVAV 186
                                   77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2209.89
//
Query:       gi|91772228|ref|YP_564920.1|  [L=197]
Description: phosphoesterase, PA-phosphatase related [Methanococcoides burtonii DSM 6242]
Scores for complete 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   51.0  21.1    4.9e-13   49.2  21.1    1.7  1  PAP2_3    PAP2 superfamily
    1.5e-09   37.7  13.9    1.5e-09   37.7  13.9    2.1  2  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
       0.25   10.4   7.7      0.095   11.7   4.0    1.9  2  DUF973    Protein of unknown function (DUF973)
        6.7    7.0  18.0      0.084   13.1   3.8    2.4  2  TctB      Tripartite tricarboxylate transporter TctB family
          7    7.3  16.7       0.33   11.5   9.6    2.3  3  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2  21.1   1.4e-16   4.9e-13      24     190 .]      16     174 ..       7     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.4e-16
                        PAP2_3  24 ahpalavilalaYaslhfqvtl.lvlvllflrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaasla 103
                                   a+p+l+++ a++Y + +  +++ ++l++++ ++ + l+ef +++ l+ l+++ +y++fP+     +      ++   ++l+
  gi|91772228|ref|YP_564920.1|  16 ATPWLTYLSAFVYLIGFTGLLIgTFLLFAYKKDEKSLQEFTIAFTLIYLIAYPFYTWFPVYVTSKV---LPNMAPLLYTLD 93 
                                   79************9887666516677777*****************************9998444...222223333333 PP

                        PAP2_3 104 galrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvala 184
                                      +  ++ ++ ++    +   +fPSlH a++++++l++++  ++  ++++a+++ +++ ++++++g H ++D+i+G++la
  gi|91772228|ref|YP_564920.1|  94 P--SIVSFIHICAP----SLNNCFPSLHSALSFMTMLIIISRTSHISFKAIAVVVTIAIHFTILYLGIHWITDMIGGILLA 168
                                   3..22222344444....44788***************998888889********************************** PP

                        PAP2_3 185 lvaial 190
                                   + ++++
  gi|91772228|ref|YP_564920.1| 169 FTSYYI 174
                                   **9985 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.24   8.8e+02     114     129 ..      32      47 ..      31      54 .. 0.82
   2 !   37.7  13.9   4.3e-13   1.5e-09       5     130 ..      59     178 ..      53     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                          PAP2 114 laGlliGialaalayr 129
                                   ++GlliG++l++++++
  gi|91772228|ref|YP_564920.1|  32 FTGLLIGTFLLFAYKK 47 
                                   6799****99998865 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 4.3e-13
                          PAP2   5 lllalalaalltsvlKdlvg.rpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkkigl 84 
                                   + l++++a+ + +++  +v+ +  P+++    +ld++  ++ +    + +++fPS Hsa +f+ +l++++      +k   
  gi|91772228|ref|YP_564920.1|  59 FTLIYLIAYPFYTWFPVYVTsKVLPNMAPLLYTLDPSIVSFIHICAPSLNNCFPSLHSALSFMTMLIIISRTSHISFK--- 136
                                   55666666667777777777567788888888888888777765558999******************9999999999... PP

                          PAP2  85 vllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrl 130
                                       +i++++++ + ++ lylg+H+ +D ++G+l++++  ++a+r+
  gi|91772228|ref|YP_564920.1| 137 ----AIAVVVTIAIHFTILYLGIHWITDMIGGILLAFTSYYIATRY 178
                                   ....9**********************************9999875 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.12   4.2e+02     131     152 ..      22      43 ..       8      68 .. 0.69
   2 ?   11.7   4.0   2.6e-05     0.095     108     168 ..     122     184 ..     115     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                        DUF973 131 llgviilligiilaliGqillg 152
                                    l+++++lig+  +liG  ll+
  gi|91772228|ref|YP_564920.1|  22 YLSAFVYLIGFTGLLIGTFLLF 43 
                                   4566666666666666666553 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.6e-05
                        DUF973 108 aiiiiigvilaivsllslilslillgviilligi..ilaliGqillglsfyklGevYnnglik 168
                                   +++iii+    i++   ++ + i++ ++il++gi  i  +iG ill+++ y + ++Y + +++
  gi|91772228|ref|YP_564920.1| 122 TMLIIISRTSHISFKAIAVVVTIAIHFTILYLGIhwITDMIGGILLAFTSYYIATRYCEHIVE 184
                                   456777877777766677777788888888888888*********************998876 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.8   2.4e-05     0.084      73     132 ..      19      75 ..       4      77 .. 0.79
   2 ?   -0.4   6.3      0.35   1.3e+03      86     125 ..     137     174 ..      88     194 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                          TctB  73 llaalllyallleplGfilatalflllllg.reerkwlkalilavvlallvyllFtklLgv 132
                                   +l  l +++ l+++ G++++t+l++    + ++ +k l+ + +a+ l  l+ + F +++ v
  gi|91772228|ref|YP_564920.1|  19 WLTYLSAFVYLIGFTGLLIGTFLLF----AyKKDEKSLQEFTIAFTLIYLIAYPFYTWFPV 75 
                                   3457888999************888....44566777999999999999999999999877 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.35
                          TctB  86 plGfilatalflllll.greerkwlkalilavvlallvyll 125
                                    +  ++++a+ +++l+ g    +w+++ i +++la+ +y++
  gi|91772228|ref|YP_564920.1| 137 AIAVVVTIAIHFTILYlG---IHWITDMIGGILLAFTSYYI 174
                                   222233333222222221...23555555555555555554 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         1   3.6e+03      37      37 ..      32      32 ..       8      51 .. 0.53
   2 ?   -0.8   0.2      0.62   2.2e+03      41      41 ..      64      64 ..      31     103 .. 0.64
   3 ?   11.5   9.6   9.2e-05      0.33       8      71 ..     113     174 ..     109     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                        PAP2_C 37 l 37
                                  +
  gi|91772228|ref|YP_564920.1| 32 F 32
                                  2 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.62
                        PAP2_C 41 l 41
                                  l
  gi|91772228|ref|YP_564920.1| 64 L 64
                                  1 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 9.2e-05
                        PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvfll 71 
                                   S H++  ++++l+i + +++    +k i++++++ + f i++   H+  D++ g++++++ +++
  gi|91772228|ref|YP_564920.1| 113 SLHSALSFMTMLIIISRTSHIS--FKAIAVVVTIAIHFTILYLGIHWITDMIGGILLAFTSYYI 174
                                   5599999999999999999998..********************************99988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1209.49
//
Query:       gi|91772229|ref|YP_564921.1|  [L=81]
Description: hypothetical protein Mbur_0159, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-06   28.2   0.0    1.9e-06   28.1   0.0    1.0  1  Resolvase  Resolvase, N terminal domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0     1e-10   1.9e-06      84     145 ..       1      66 [.       1      67 [. 0.86

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1e-10
                                   HHHHHHHHHTT-EEEESS......SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHHHHHHHHH CS
                     Resolvase  84 ltlleelrekgvslvsld.eg...idtstpmgrlllqilaalaeferelirertkeglaaakakGk 145
                                   ++l+ ++++kg+++vsl+ ++     +++  +rll  +++++ e e++ ++er+k g+++ k++++
  gi|91772229|ref|YP_564921.1|   1 MNLVMDFEDKGIRVVSLSpSEswsTIEDSHYRRLLTSLFGWVTENEKRILQERIKVGIERYKKEND 66 
                                   6899**************54367533455669******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 496.18
//
Query:       gi|91772230|ref|YP_564922.1|  [L=120]
Description: hypothetical protein Mbur_0160 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-18   66.4   0.1      4e-18   66.2   0.1    1.0  1  SpoIIAA-like  SpoIIAA-like


Domain annotation for each model (and alignments):
>> SpoIIAA-like  SpoIIAA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.1   2.3e-22     4e-18       1      95 [.      12     118 ..      12     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.3e-22
                                   .EEEEEEEEE-HHHHHH.HHHHHHHHC.CSSSEEEEEEE.............HHHHHHHCCCGGECEEEEE-SSCCCCCC. CS
                  SpoIIAA-like   1 iiaveisgkitaedykevliellekal.ahgkirllvdl.............ediklglahlsrfrrvAvvtdkkwikalv 67 
                                   ++av+++g +  edy++ l++++e+++ ++gkir+l+ l             ed++lg +++  f+r+Avv+d +w+ ++ 
  gi|91772230|ref|YP_564922.1|  12 VVAVRLTGVVKGEDYDNILVPVIEDKVkEYGKIRVLYQLgpdyekfsrkamlEDMELGVKNITSFDRIAVVSDVEWMNHA- 91 
                                   699*********************99977**************999977777777777799*******************. PP

                                   CCHHCCH.-CCEEEEE..SSHHHHHHHH CS
                  SpoIIAA-like  68 allasalflslevkvFkleeeeeAlaWL 95 
                                   ++l +++++  +vk+++ ee+ eA aW+
  gi|91772230|ref|YP_564922.1|  92 MELFKYMIP-GQVKTYNNEELSEAKAWI 118
                                   999999955.9****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 724.73
//
Query:       gi|91772231|ref|YP_564923.1|  [L=331]
Description: hypothetical protein Mbur_0161 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-05   23.5   1.1      6e-05   22.8   1.1    1.4  1  DDE_Tnp_1  Transposase DDE domain
     0.0064   16.6   4.2       0.14   12.3   0.2    2.6  2  TetR_C_8   Transcriptional regulator C-terminal region


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.1   6.7e-09     6e-05      26     182 ..      84     250 ..      33     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.7e-09
                     DDE_Tnp_1  26 gykggk..ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleekgvdy 102
                                   g+ +++  ++y y   +++d   ++ +sv  + + ++ +++lk ++d+++++  k  ++   + + s++++ +l+e+ v +
  gi|91772231|ref|YP_564923.1|  84 GQAKKStnSFYSYISLCIIDKDERVTISVLPVEKGNSKTDYLKYFIDQIKQIklKINVLCLNREFYSRDVFSFLQENEVAH 164
                                   3332224599**********************999********************************************** PP

                     DDE_Tnp_1 103 iirl.kkntklyrk........................gaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntn 158
                                   i+++ k  ++l++                          ++ k+r+  r+++ ++ l  +    +                
  gi|91772231|ref|YP_564923.1| 165 IVPVvKMGKRLKEIidgtkkrcdtytmnstkgkvelvlAIDVKYRKGKRGKNGCENLGFVVYGIDW--------------- 230
                                   ****95555555556677776666666666666666666888888888888888888888888888............... PP

                     DDE_Tnp_1 159 sellsaeevaelyrlRwqiErvFk 182
                                       ++++v + yr++  iE++ +
  gi|91772231|ref|YP_564923.1| 231 ----DPRKVSDTYRKKFAIESSYR 250
                                   ....99999999999999999876 PP

>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.5    0.0026        23      22      78 ..      46     102 ..      32     104 .. 0.84
   2 !   12.3   0.2   1.6e-05      0.14      29      87 ..     261     322 ..     247     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0026
                                   HHHHHH-.THHHHHHHHHHHHHHHHHHHHHH-TT--S-HHHHHHHHHHHHHHHHHHH CS
                      TetR_C_8  22 knllssngresfekylkelikelilkvieelsegkelseedkefiadfysygfvgvi 78 
                                   +  l++  +++ +++  +++++++++ i++ ++ + ++ + k+   +fysy  + +i
  gi|91772231|ref|YP_564923.1|  46 QSSLETLKQKKKHDFAIDYTNDQYYGSIDDSNNRYVIRGQAKKSTNSFYSYISLCII 102
                                   5556666677778888899*************999****************888776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.6e-05
                                   .THHHHHHHHHHHHHHHHHHHHHH-TT-..-S-HHHHHHHHHHH.HHHHHHHHHHHHHTTS- CS
                      TetR_C_8  29 gresfekylkelikelilkvieelsegk..elseedkefiadfy.sygfvgvildWlengmk 87 
                                   +++s+ +y++ li+ l+++ + ++++ +  +++  +k + +d++    fv++i++W++++ k
  gi|91772231|ref|YP_564923.1| 261 SKDSMLRYFYALISFLFKNAWVSIQRMHfiKVKRGPKTIESDMFrFDMFVHLIVEWVRRKLK 322
                                   568999***************8888666789999**********556**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2053.02
//
Query:       gi|91772232|ref|YP_564924.1|  [L=388]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-53  181.6   1.5    4.4e-53  180.6   0.0    1.9  2  DDE_Tnp_IS66   Transposase IS66 family
      2e-05   24.8   0.4      0.039   14.2   0.2    2.7  3  DDE_Tnp_IS240  DDE domain
    3.6e-05   24.3   0.7     0.0001   22.8   0.7    1.7  1  SlyX           SlyX
  ------ inclusion threshold ------
       0.19   12.3   3.6       0.21   12.2   1.4    2.2  2  BST2           Bone marrow stromal antigen 2
       0.28   11.8   3.6       0.34   11.5   0.2    2.6  3  PLATZ          PLATZ transcription factor
       0.35   11.4   4.8       0.37   11.3   0.2    2.5  3  DUF16          Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3      0.18   5.5e+02     174     225 ..      20      69 ..       4      85 .. 0.63
   2 !  180.6   0.0   1.5e-56   4.4e-53      48     280 ..     122     350 ..     106     352 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.18
                  DDE_Tnp_IS66 174 larigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   ++ + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772232|ref|YP_564924.1|  20 VTLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   4447777777666532..3466666666666666667776766665555444 PP

  == domain 2  score: 180.6 bits;  conditional E-value: 1.5e-56
                  DDE_Tnp_IS66  48 raaelleplvealkaallasevihaDETtlrvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkG 126
                                   ++ + le + +++k+ l +s+vi++DET++r       +gk+++l+v++t+k   +++++ +++Rg+e+++a+  L +f+G
  gi|91772232|ref|YP_564924.1| 122 NCERSLEDFEQQIKNFLIESPVINCDETGMR------IEGKRQWLHVASTNK---MTCYYPHQKRGSEAMNAMgiLPNFNG 193
                                   56677**************************......99***********99...****************9955666*** PP

                  DDE_Tnp_IS66 127 vlvsDgyagYnklaeeqvthalCwaHlrRkfvdaeeakkksqaaaealarigklyaierearea....eaeerlalrqees 203
                                   ++v+D +++Y k+   +++h +C aHl+R++++++e+++  q +++a++ +  + + +  +re+    ++e+ ++ +  + 
  gi|91772232|ref|YP_564924.1| 194 TVVHDFWKSYYKY---DCDHSICNAHLLRELTSVSENDD--QLWSKAMNILLLMSKNQLTIREMsgcmKPERIKEFEDWYG 269
                                   ************9...7*******************977..*********99999999999855568888*********** PP

                  DDE_Tnp_IS66 204 rpllaeleawleeql....kkvlpksklgkairyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   + ++  +e++ + q     ++ +++++++++++++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91772232|ref|YP_564924.1| 270 QIIHIGIEENPQLQAkskkRGRTKQTTAKNLLDRFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 350
                                   *********998554567799***********************************************************9 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.9   5.8e+03      20      36 ..      26      42 ..      24      67 .. 0.59
   2 !    7.8   0.0    0.0012       3.6       5      45 ..     145     183 ..     141     186 .. 0.84
   3 !   14.2   0.2   1.3e-05     0.039      85     139 ..     313     367 ..     287     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                 DDE_Tnp_IS240 20 lyravDkegrildflvs 36
                                  ly ++ +++ri++ +  
  gi|91772232|ref|YP_564924.1| 26 LYDIIAEQQRIIELQAA 42
                                  56677777777766654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0012
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91772232|ref|YP_564924.1| 145 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSEAMN 183
                                   68************99866..77779999999999998875 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkgh 139
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  +l+  + ++ ++k++
  gi|91772232|ref|YP_564924.1| 313 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFLRVRSYISTVKKNQ 367
                                   55667899******************************99999988888888876 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.7   3.5e-08    0.0001      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.5e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772232|ref|YP_564924.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   7.1e-05      0.21      45      87 ..      21      63 ..       3      67 .. 0.81
   2 ?   -1.7   0.0       1.5   4.6e+03      14      30 ..     119     135 ..     115     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91772232|ref|YP_564924.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHH CS
                          BST2  14 ecrnvtrlLerqLtqaq 30 
                                   +c+n +r Le   +q +
  gi|91772232|ref|YP_564924.1| 119 KCSNCERSLEDFEQQIK 135
                                   56666666654433333 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.45   1.4e+03      16      52 ..      25      63 ..      18      72 .. 0.59
   2 ?   11.5   0.2   0.00012      0.34      34      71 ..      73     130 ..      69     134 .. 0.83
   3 ?   -3.3   0.0       5.1   1.5e+04      38      50 ..     278     290 ..     249     299 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.45
                         PLATZ 16 klldvseiQtYvi..nsakvvflnerpqarsakakakek 52
                                  +l+d+   Q+ +i    a++  l+er ++ +++ k++++
  gi|91772232|ref|YP_564924.1| 25 TLYDIIAEQQRIIelQAARITELEERVKKLEEQLKKNSR 63
                                  556666656655411467888888886665555544443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772232|ref|YP_564924.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDF 130
                                   9*********99998888743.33333568999***********************985 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.1
                         PLATZ  38 erpqarsakakak 50 
                                   e pq + +++k+ 
  gi|91772232|ref|YP_564924.1| 278 ENPQLQAKSKKRG 290
                                   4444443333332 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00012      0.37      45      82 ..      25      62 ..      16      75 .. 0.82
   2 ?   -3.8   0.0         6   1.8e+04      56      64 ..     126     134 ..     110     141 .. 0.52
   3 ?    1.5   0.2      0.14   4.3e+02      10      58 ..     286     341 ..     277     369 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772232|ref|YP_564924.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6
                                   HHHHHHHHH CS
                         DUF16  56 kvekqgeki 64 
                                     e  +++i
  gi|91772232|ref|YP_564924.1| 126 SLEDFEQQI 134
                                   222222222 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.14
                                   XXX.X.XTTB-BHHHHHH....B-.....BHHHHH.HHHHHHH...HHHHHHHHHHH CS
                         DUF16  10 vKkiPvkteYVTrkqlne....fkds...nkqrLk.kieakvdklgeqinkleqkve 58 
                                    Kk  ++t+  T k+l +    +k++      +Lk  +e++++ +++++ k++qk++
  gi|91772232|ref|YP_564924.1| 286 SKK-RGRTKQTTAKNLLDrfigYKNDilrFMHDLKvPFENNLAERDVRMMKVQQKIS 341
                                   455.46788888888877788899998883344442356666666666666665553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1677  (0.0935356); expected 358.6 (0.02)
Passed bias filter:                      923  (0.0514808); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 2419.38
//
Query:       gi|91772233|ref|YP_564925.1|  [L=113]
Description: hypothetical protein Mbur_0164 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.026   14.8   1.2      0.026   14.8   1.2    1.9  1  Dpoe2NT    DNA polymerases epsilon N terminal
      0.051   13.3   0.5      0.064   13.0   0.5    1.1  1  DUF3440    Domain of unknown function (DUF3440)
      0.062   13.6   1.8       0.08   13.2   1.8    1.2  1  FliS       Flagellar protein FliS
       0.23   11.5   4.6         12    6.0   2.9    2.5  2  DUF1192    Protein of unknown function (DUF1192)
       0.28   11.3   7.1       0.35   11.0   7.1    1.2  1  DUF2120    Uncharacterized protein conserved in archaea (DUF2
          1    9.8   9.0       0.81   10.1   1.4    2.9  3  FlaC_arch  Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> Dpoe2NT  DNA polymerases epsilon N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.2   8.8e-06     0.026      35      66 ..      41      76 ..      27      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.8e-06
                       Dpoe2NT 35 ldeeeledwlekiieavekQp..Lssnlier..svv 66
                                  +++ee +  +e+i+++v+kQ+  L+ n+ie+  s++
  gi|91772233|ref|YP_564925.1| 41 MSKEEGKMLVEDIVSEVKKQKfdLEKNIIEKvhSTI 76
                                  789999**************8446789999733444 PP

>> DUF3440  Domain of unknown function (DUF3440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   2.1e-05     0.064      75     148 ..      20      98 ..      16     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                       DUF3440  75 LstlpeelrenylkklkvsikfWrekGgalseetikelkeaeikieveek.....snyktekkvvrlkeylddidikef 148
                                   L++l ee  ++y+k    + +  +e+G +l e+ ++e+k++++++e++       + +  +k+ v+l++ +d+++i+e 
  gi|91772233|ref|YP_564925.1|  20 LAALSEERIREYVKDKIEAGTMSKEEGKMLVEDIVSEVKKQKFDLEKNIIekvhsTIKMADKELVELSDKIDEMKIQEL 98 
                                   5677777667777666666778899**************9999877664422332555667899***999999999986 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.8   2.7e-05      0.08      18      77 ..      46     105 ..      28     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHTCCTTTSCHHHHHHHHH CS
                          FliS  18 vlmLydgalkflkrakeaieekdiekkgeaiskaqdIiseLrasLdlekggeiaknLaal 77 
                                     mL++ +++++k+ k  +e++ iek +  i+ a + + eL++ +d  k +e+ ++L+++
  gi|91772233|ref|YP_564925.1|  46 GKMLVEDIVSEVKKQKFDLEKNIIEKVHSTIKMADKELVELSDKIDEMKIQELEAELERI 105
                                   57*****************9999**********************998889999999875 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0093        28      10      30 ..      13      33 ..       2      37 .. 0.84
   2 ?    6.0   2.9     0.004        12      27      45 ..      93     111 ..      77     113 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0093
                       DUF1192 10 theigqDLslLSveELeerIa 30
                                  t++ig+ L +LS e ++e+++
  gi|91772233|ref|YP_564925.1| 13 TALIGAGLAALSEERIREYVK 33
                                  789***************997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.004
                       DUF1192  27 erIalLeaEIaRleaaiak 45 
                                     I++LeaE +R++  +++
  gi|91772233|ref|YP_564925.1|  93 MKIQELEAELERIKSLREA 111
                                   469**********998876 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   7.1   0.00012      0.35      35     100 ..      40     105 ..      26     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                       DUF2120  35 keeleeleskleellekldaeevdleseeakkliekldesireveeieeevdafglerlkeslEal 100
                                   +++ ee +  +e+++++++++++dle++ ++k+ +++    +e +e+ +++d++ ++ l  +lE +
  gi|91772233|ref|YP_564925.1|  40 TMSKEEGKMLVEDIVSEVKKQKFDLEKNIIEKVHSTIKMADKELVELSDKIDEMKIQELEAELERI 105
                                   45578888899***************998888888888888899999*****************98 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 ?   -0.0   0.3       0.4   1.2e+03      19      36 ..      50      67 ..      32      70 .. 0.63
   2 ?   10.1   1.4   0.00027      0.81       8      34 ..      68      94 ..      63      95 .. 0.87
   3 ?    5.0   0.2     0.011        33       1      14 [.      94     107 ..      94     113 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.4
                     FlaC_arch 19 vkkeneelsksveelken 36
                                  v++  +e++k+  +l++n
  gi|91772233|ref|YP_564925.1| 50 VEDIVSEVKKQKFDLEKN 67
                                  444455555555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00027
                     FlaC_arch  8 klsklsteletvkkeneelsksveelk 34
                                   ++k+ ++++++ ke+ els++++e+k
  gi|91772233|ref|YP_564925.1| 68 IIEKVHSTIKMADKELVELSDKIDEMK 94
                                  4799*********************97 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.011
                     FlaC_arch   1 ridelEnklsklst 14 
                                   +i+elE +l+++++
  gi|91772233|ref|YP_564925.1|  94 KIQELEAELERIKS 107
                                   899*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1960  (0.10932); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 678.93
//
Query:       gi|91772234|ref|YP_564926.1|  [L=283]
Description: UbiE/COQ5 methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   74.8   0.1    1.3e-20   73.9   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    2.5e-20   72.9   0.0    4.5e-20   72.1   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    3.1e-20   72.5   0.0    4.1e-20   72.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.1e-12   47.9   0.0    1.8e-12   47.1   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.7e-11   42.8   0.0    1.2e-10   42.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    4.3e-10   39.7   0.0    6.2e-10   39.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.3e-05   24.3   0.0      5e-05   23.2   0.0    1.5  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.8e-05   23.6   0.0    4.2e-05   23.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00059   19.6   0.0     0.0014   18.3   0.0    1.5  2  UPF0020          Putative RNA methylase family UPF0020
    0.00069   19.6   0.0     0.0012   18.8   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0024   17.1   0.0     0.0034   16.6   0.0    1.2  1  Methyltransf_3   O-methyltransferase
     0.0035   16.9   0.0     0.0049   16.4   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0048   16.6   0.1      0.008   15.9   0.1    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0067   17.4   0.0      0.016   16.2   0.0    1.5  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.017   14.5   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.014   15.2   0.0      0.025   14.4   0.0    1.4  1  Methyltransf_8   Hypothetical methyltransferase
      0.025   14.0   0.0      0.037   13.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.094   12.5   0.1       0.18   11.6   0.1    1.4  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
       0.11   12.5   0.0       0.18   11.8   0.0    1.3  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   1.4e-23   1.3e-20       1      97 []      51     145 ..      51     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.4e-23
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                   vL +Gc tG  +  +a+r+g ++v+gvDi+e  +++a+ ra++ gl   vef+ gda dlpfe g++D+v+  ++ ++l+ 
  gi|91772234|ref|YP_564926.1|  51 VLMVGCSTGFSACFVAERFG-CSVVGVDIAEISIRKAKGRAKSLGLgdGVEFHIGDAYDLPFEPGTYDVVITEFVAQFLD- 129
                                   899****************8.**********************99999************************88877765. PP

                                   HHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                     ++ka++e+ rvLkpgG
  gi|91772234|ref|YP_564926.1| 130 --MDKAFREFVRVLKPGG 145
                                   ..889************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   4.8e-23   4.5e-20       1      94 [.      52     147 ..      52     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4.8e-23
                                   EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                   L vGc tG  a+ +a+r+ ++vvgvD+++  ++ ak +a+  gl   vef+ +da +lpfe +++D+v+  +v +++ d++
  gi|91772234|ref|YP_564926.1|  52 LMVGCSTGFSACFVAERFgCSVVGVDIAEISIRKAKGRAKSLGLgdGVEFHIGDAYDLPFEPGTYDVVITEFVAQFL-DMD 131
                                   679************6666**********************999**99*****************************.7** PP

                                   HHHHHHHHHEEEEEEE CS
               Methyltransf_11  79 kalkeiaRvLkpgGll 94 
                                   ka++e++RvLkpgG++
  gi|91772234|ref|YP_564926.1| 132 KAFREFVRVLKPGGMV 147
                                   **************86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   4.3e-23   4.1e-20       2     130 ..      46     171 ..      45     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4.3e-23
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                   +k+ +vl +GC tG+ +   ae+  +++ vvG+Di e +i++A+ +a++lgl   veF++gd+ +l+  +e+ ++D++++ 
  gi|91772234|ref|YP_564926.1|  46 NKASKVLMVGCSTGFSACFVAER--FGCSVVGVDIAEISIRKAKGRAKSLGLGdGVEFHIGDAYDLP--FEPGTYDVVIT- 121
                                   78999****************66..579************************99*************..***********. PP

               Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedprllaelpakveeeskay.e 130
                                   e+++ + d+dk+++e  rvlkpgg + i+++   a+ p  +ee+ ++  +
  gi|91772234|ref|YP_564926.1| 122 EFVAQFLDMDKAFREFVRVLKPGGMVGINEMYRDADIPPAIEEDIQEAeR 171
                                   8999****************************999999777776665431 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   1.9e-15   1.8e-12      42     154 ..      42     152 ..      17     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.9e-15
                                   H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEE CS
               Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvt 121
                                   l    +++kvl v + tg  a  +++  g    vv++Di e  ++ ++ ++k  g    +ef  ++a +Lpfe +++Dvv 
  gi|91772234|ref|YP_564926.1|  42 LCQINKASKVLMVGCSTGFSACFVAERFGC--SVVGVDIAEISIRKAKGRAKSLGLGdGVEFHIGDAYDLPFEPGTYDVVI 120
                                   4455678899********999988887775..69*********************9978*********************9 PP

                                   EES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
               Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                     f +  + D++ka++e  rvlkpGG + + e+
  gi|91772234|ref|YP_564926.1| 121 TEF-VAQFLDMDKAFREFVRVLKPGGMVGINEM 152
                                   999.7889*******************988776 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.3e-13   1.2e-10       2      98 ..      53     146 ..      52     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.3e-13
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlkd 81 
                                    +Gc tG  +  ++e+  +++++gvDi + +i +ak + ++ +  +  ++++ +  +l  + + +++D+v+  +v + l d
  gi|91772234|ref|YP_564926.1|  53 MVGCSTGFSACFVAER-FGCSVVGVDIAEISIRKAKGRAKSLGLGDGVEFHIGDAYDL--PFEpGTYDVVITEFVAQFL-D 129
                                   69*****999999999.89***********************9988777777666544..33347*************8.* PP

               Methyltransf_12  82 irevldnirklLkpgGr 98 
                                   ++++++++ ++LkpgG+
  gi|91772234|ref|YP_564926.1| 130 MDKAFREFVRVLKPGGM 146
                                   ****************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   6.6e-13   6.2e-10      14     164 ..      40     202 ..      33     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 6.6e-13
               Methyltransf_23  14 erllpklraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeqeaaepqgkf 83 
                                   ++l +  ++ ++vL +Gc tG + + v++++g+sv+gvD+ ++ + +a+          +  + + d +   + +++ g++
  gi|91772234|ref|YP_564926.1|  40 AELCQ-INKASKVLMVGCSTGfSACFVAERFGCSVVGVDIAEISIRKAKgrakslglgdGVEFHIGDAY---DLPFEPGTY 116
                                   33443.688899*********8889999********************999999987665555555555...888899*** PP

               Methyltransf_23  84 dlIvlrevlehvpdppellrqiatllkpgGylllseplasl.......kedrllldwlylvpagrhi..sffsarslkell 155
                                   d+++  +v   + d+ +++r + + lkpgG + + e  +++       +  + ++ +  + ++   +  s  s +++++ l
  gi|91772234|ref|YP_564926.1| 117 DVVITEFV-AQFLDMDKAFREFVRVLKPGGMVGINEMYRDAdippaieEDIQEAERIFGELTQ---LpfSISSPEEWEQRL 193
                                   *9986655.678899*********************888776676444233333333333333...345777888888888 PP

               Methyltransf_23 156 eeaGlevve 164
                                   e+aGl+ v+
  gi|91772234|ref|YP_564926.1| 194 ERAGLSEVH 202
                                   888887664 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.3e-08     5e-05      65     168 ..      39     146 ..      28     154 .. 0.81
   2 ?   -3.2   0.0       6.1   5.8e+03      17      33 ..     245     261 ..     236     281 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.3e-08
                                   HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEE CS
                          PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYd 144
                                   + el +++k ++vL vG+ +G+ +  +a+ +g    vv+++  +  +++ak + k l+l   v +++gD +    e   Yd
  gi|91772234|ref|YP_564926.1|  39 LAELCQINKASKVLMVGCSTGFSACFVAERFGC--SVVGVDIAEISIRKAKGRAKSLGLGdGVEFHIGDAYDLPFEPGTYD 117
                                   578999*******************99*99985..56****999999***********9769*******998878888899 PP

                                   EEEESSBB.....SS--HHHHHTEEEEEE CS
                          PCMT 145 aihvgaaa.....peiPealidQLkeGGr 168
                                   ++++   a     ++  +++++ Lk+GG 
  gi|91772234|ref|YP_564926.1| 118 VVITEFVAqfldmDKAFREFVRVLKPGGM 146
                                   98876554122224455666777777775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.1
                                   --HHHHHHHHHS-GGGG CS
                          PCMT  17 ksdkvaealeevdReef 33 
                                    s+k+++ ++++ R++ 
  gi|91772234|ref|YP_564926.1| 245 SSKKIRNRFKQISRGKR 261
                                   67788888888888653 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   4.5e-08   4.2e-05      53     164 ..      38     149 ..      33     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                                   HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SE CS
                          CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdr 130
                                   ++ e  ++++ +++L +Gc  G  +   +er++ +vvg+ + +   ++ak r ++l+l + ve ++ d  dl+     +d 
  gi|91772234|ref|YP_564926.1|  38 RLAELCQINKASKVLMVGCSTGFSACFVAERFGCSVVGVDIAEISIRKAKGRAKSLGLGDGVEFHIGDAYDLPFepgTYDV 118
                                   55677789999*********************************************************9999854556775 PP

                                   EEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                          CMAS 131 vvsvgafehvgkenydtffkklkkllkedGllll 164
                                   v+  + + ++     d+ f+++ ++lk++G++ +
  gi|91772234|ref|YP_564926.1| 119 VI-TEFVAQF--LDMDKAFREFVRVLKPGGMVGI 149
                                   54.4444443..4567788899999999999865 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.5e-06    0.0014      77     128 ..      71     122 ..      58     123 .. 0.92
   2 ?   -3.0   0.0       5.1   4.8e+03     151     193 ..     168     210 ..     166     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                                   --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS
                       UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128
                                    +++g+D+ +  +++a+  a++ g+gd +ef   da +L+ + g +dv++t+
  gi|91772234|ref|YP_564926.1|  71 CSVVGVDIAEISIRKAKGRAKSLGLGDGVEFHIGDAYDLPFEPGTYDVVITE 122
                                   4699************************************88889*****96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.1
                                   HHHHH-TT..-EEEEEESSHHHHHCC---ESEEEEEEETTEEE CS
                       UPF0020 151 elkrvlrgggrlvlltsenkalekaleeralrkvkeknvklgl 193
                                   e++r++ +   l + +s+ ++ e+ le++ l +v++++ +l+ 
  gi|91772234|ref|YP_564926.1| 168 EAERIFGELTQLPFSISSPEEWEQRLERAGLSEVHVYRHHLSV 210
                                   5666666666677777788888888888889899888888775 PP

>> Methyltransf_18  Methyltransferase 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    0.0012       2      86 ..      36     119 ..      35     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
               Methyltransf_18   2 skRLkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk.ee 81 
                                   +kRL+++++ ++k s+v+ +G+  g+ +++++++  + +v+ +Di+e +++kak  +++ gl d +e++++d  +    ++
  gi|91772234|ref|YP_564926.1|  36 TKRLAELCQ-INKASKVLMVGCSTGFSACFVAERFGC-SVVGVDIAEISIRKAKGRAKSLGLGDGVEFHIGDAYDLPFePG 114
                                   589999887.667999999************998888.99*******************************9987543144 PP

               Methyltransf_18  82 evdtv 86 
                                    +d+v
  gi|91772234|ref|YP_564926.1| 115 TYDVV 119
                                   45555 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.7e-06    0.0034      38     158 ..      38     152 ..      26     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                                   HHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHH.HHHHHT CS
                Methyltransf_3  38 fLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkv.Leelvk 117
                                    L  L ++  a +vl +G  tG+s+  +a  +     ++ +di +     a+   +  g+++ +e++ gda    +e  + 
  gi|91772234|ref|YP_564926.1|  38 RLAELCQINKASKVLMVGCSTGFSACFVAERFG--CSVVGVDIAEISIRKAKGRAKSLGLGDGVEFHIGDAYDLpFEPGTY 116
                                   5777999**********************9985..68**********************************9974677888 PP

                                   SSS---EEEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE-T CS
                Methyltransf_3 118 dkklpefDfifvDaDkssyvnyyeklleLvkvGgliaiDnt 158
                                   d   +ef   f+D Dk      +++ ++++k Gg+++i+  
  gi|91772234|ref|YP_564926.1| 117 DVVITEFVAQFLDMDKA-----FREFVRVLKPGGMVGINEM 152
                                   888************96.....5667889999999998765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.2e-06    0.0049      20     103 ..      36     121 ..      27     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.2e-06
                                   HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTTS- CS
                           MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.eveekk 97 
                                   +k L+e  + +++ kvl +Gc +G+ ++ +a++    +v+ vd+   +++ ak  +++ +l   ve++  d+++  +e++ 
  gi|91772234|ref|YP_564926.1|  36 TKRLAELCQINKASKVLMVGCSTGFSACFVAERFGC-SVVGVDIAEISIRKAKGRAKSLGLGdgVEFHIGDAYDlPFEPGT 115
                                   566677777778999****************99887.8**********************999**********9456799* PP

                                   EEEEEE CS
                           MTS  98 fdlivs 103
                                   +d++++
  gi|91772234|ref|YP_564926.1| 116 YDVVIT 121
                                   ****98 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   8.5e-06     0.008      27      76 ..      37      87 ..      25     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.5e-06
                                  HHHHHT.T-S--EEEEEET-TT-HHHHHH-BT.TEEEEEE-S-HHHHHHHH CS
                          TPMT 27 kkfldalkakaglrvlvPlCGkaldlvwlAeq.grevvGvelselAvekff 76
                                  k++ +  + ++  +vl+ +C  +  +   Ae+ g +vvGv+++e+ ++k+ 
  gi|91772234|ref|YP_564926.1| 37 KRLAELCQINKASKVLMVGCSTGFSACFVAERfGCSVVGVDIAEISIRKAK 87
                                  44555556667779*****************9899*************964 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.7e-05     0.016       3     101 ..      54     147 ..      52     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
               Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDgghaae 82 
                                   +G++ G+s+++++   +r g  ++v vd  +   ++a+  a+++gl d v+++ +d+ ++   ++ g++D+++  + ++  
  gi|91772234|ref|YP_564926.1|  54 VGCSTGFSACFVA---ERFGC-SVVGVDIAEIsIRKAKGRAKSLGLGDGVEFHIGDAYDL--PFEPGTYDVVITEFVAQFL 128
                                   79*********99...56665.899****88766667788889****************9..67889************** PP

               Methyltransf_24  83 avledleallprlapggvv 101
                                   +  ++++ + ++l+pgg+v
  gi|91772234|ref|YP_564926.1| 129 DMDKAFREFVRVLKPGGMV 147
                                   *****************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 ?   14.5   0.0   1.8e-05     0.017     159     256 ..      45     147 ..      33     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleval..seell.keekadvivaNILa 236
                                   +++ ++vl vG+ +G  a  +a     +vv+vDi e++++ ak  a+  ++ + +e ++  + +l+ + +++dv++   +a
  gi|91772234|ref|YP_564926.1|  45 INKASKVLMVGCSTGFSACFVAERFGCSVVGVDIAEISIRKAKGRAKSLGLGDGVEFHIgdAYDLPfEPGTYDVVITEFVA 125
                                   456679**********9975555445689*********************999777764215555555899********** PP

                          PrmA 237 evli..elaedikklvkeggll 256
                                   + l   +   ++ +++k+gg++
  gi|91772234|ref|YP_564926.1| 126 QFLDmdKAFREFVRVLKPGGMV 147
                                   *985226778888999999986 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-05     0.025     109     159 ..     102     152 ..      64     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                                   EES-TTS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEEEEEEEEE CS
                Methyltransf_8 109 vacdlakvPledesvdvavfclslmgtnladflkeanrvlkvGGllkvaev 159
                                      d   +P e ++ dv++  +     ++ +  +e  rvlk+GG++ + e+
  gi|91772234|ref|YP_564926.1| 102 HIGDAYDLPFEPGTYDVVITEFVAQFLDMDKAFREFVRVLKPGGMVGINEM 152
                                   4568889****************9**********************99987 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.9e-05     0.037      23     112 ..      40     132 ..      27     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                                   HHHCCCS-S-EEEEES-TTSHHHHHHH.HTT-EEEEEES-HHHHHHHHHHHHHTT-.TTEEEEE--GGG----.S-EEEEE CS
                          TehB  23 veavkivkpgkvldlgcgqgrnslyls.llgydvtawdknensiafleeikekenl.knistalydineakld.erydfil 100
                                    e  +i k +kvl +gc  g  + +++   g  v  +d  e si   +  ++   l ++++  + d  ++ ++   yd ++
  gi|91772234|ref|YP_564926.1|  40 AELCQINKASKVLMVGCSTGFSACFVAeRFGCSVVGVDIAEISIRKAKGRAKSLGLgDGVEFHIGDAYDLPFEpGTYDVVI 120
                                   56778999***************9997357**************99886555555438899999999999998358***** PP

                                   EESSGGGS-GGG CS
                          TehB 101 stvvlmfleaer 112
                                   +  v  fl+ ++
  gi|91772234|ref|YP_564926.1| 121 TEFVAQFLDMDK 132
                                   *******99764 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00019      0.18      36      69 ..      45      76 ..      33      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                  ---.-SEEEEESTSSHHHHHHHHHHHHSS--EEE CS
               Eno-Rase_NADH_b 36 iekgpkkvLviGaStGYGLAsriaaafgagadti 69
                                  i+ ++ kvL +G+StG+  A+ +a  fg+ + ++
  gi|91772234|ref|YP_564926.1| 45 IN-KASKVLMVGCSTGFS-ACFVAERFGCSVVGV 76
                                  44.4789**********6.777777777766555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.18      19      84 ..      41     101 ..      34     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
               Methyltransf_32  19 elakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsf 84 
                                   el++ ++a +v+ vG+  g+ +  +a    +++++vvg+d+ e  ++ka+ ra+ lg  + + ++f
  gi|91772234|ref|YP_564926.1|  41 ELCQINKASKVLMVGCSTGFSACFVAE---RFGCSVVGVDIAEISIRKAKGRAKSLG--LGDGVEF 101
                                   4466788999999*********99999...9************************99..6566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1791.31
//
Query:       gi|91772235|ref|YP_564927.1|  [L=184]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-11   42.8   0.0    5.5e-11   42.4   0.0    1.2  1  HTH_20    Helix-turn-helix domain
    5.3e-08   32.6   0.1    8.4e-08   32.0   0.1    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
    2.2e-05   24.3   0.3    4.2e-05   23.4   0.3    1.4  1  MarR      MarR family
    3.1e-05   24.1   0.1    5.4e-05   23.3   0.1    1.4  1  HTH_34    Winged helix DNA-binding domain
     0.0003   20.6   0.1    0.00054   19.8   0.1    1.3  1  HxlR      HxlR-like helix-turn-helix
      0.001   18.9   0.0     0.0016   18.3   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0012   18.7   0.0     0.0018   18.1   0.0    1.2  1  MarR_2    MarR family
     0.0046   16.9   0.0      0.007   16.3   0.0    1.3  1  PadR      Transcriptional regulator PadR-like family
     0.0052   16.6   0.2       0.01   15.7   0.2    1.6  1  DUF3116   Protein of unknown function (DUF3116)
     0.0087   16.5   0.1      0.013   15.9   0.1    1.4  1  HTH_27    Winged helix DNA-binding domain
     0.0099   15.8   0.6      0.017   15.1   0.6    1.4  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.047   14.2   2.0      0.075   13.5   2.0    1.3  1  FtsX      FtsX-like permease family
      0.047   14.2   0.2      0.081   13.4   0.2    1.4  1  PH_12     Pleckstrin homology domain
      0.078   13.3   0.0       0.11   12.8   0.0    1.4  1  DUF2513   Hypothetical protein (DUF2513)


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 !   42.4   0.0   4.3e-14   5.5e-11       4      58 ..      23      76 ..      20      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.3e-14
                                  HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  + A++  +R +il+ L   + +t sel +++d++k+tl ++L+++e+ag++ev r
  gi|91772235|ref|YP_564927.1| 23 LAAISTNTRIKILKTL-VSRQMTISELSRCMDCAKSTLLKNLKIMEDAGFIEVKR 76
                                  5688999*********.***********************************987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   6.6e-11   8.4e-08       3      46 ..      30      73 ..      28      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 6.6e-11
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  tR+kILk L +++++++el++ ++  +st+   Lk++++aG++e
  gi|91772235|ref|YP_564927.1| 30 TRIKILKTLVSRQMTISELSRCMDCAKSTLLKNLKIMEDAGFIE 73
                                  9*****************************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   3.3e-08   4.2e-05       2      54 ..      28      79 ..      28      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.3e-08
                                  -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT CS
                          MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspe 54
                                  t t+++iL +l  + ++++seL + + + kst+ + l+ +e++G+ie +++++
  gi|91772235|ref|YP_564927.1| 28 TNTRIKILKTLV-SRQMTISELSRCMDCAKSTLLKNLKIMEDAGFIEVKRNEN 79
                                  667788888885.467**********************************975 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 !   23.3   0.1   4.2e-08   5.4e-05       2      71 ..      31      96 ..      30     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.2e-08
                        HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71
                                  R+++l +L+s ++++ +el+ ++   ++ L ++lk++e+ag+iev+ + ++      +++T +G++  ++
  gi|91772235|ref|YP_564927.1| 31 RIKILKTLVS-RQMTISELSRCMDCAKSTLLKNLKIMEDAGFIEVKRNENK---WVYYKLTHDGKALLQS 96
                                  8899999976.789*******************************877655...499*******987765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   4.2e-07   0.00054       8      72 ..      32      93 ..      26      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.2e-07
                                  HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGG CS
                          HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsl 72
                                  + il +l++ ++  sel+r + ++++++L ++L+ +e  g+ie +   +  + v Y+lt+ G++l
  gi|91772235|ref|YP_564927.1| 32 IKILKTLVSRQMTISELSRCM-DCAKSTLLKNLKIMEDAGFIEVKR--NENKWVYYKLTHDGKAL 93
                                  56999***************9.9*******************8655..555678*********98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0016      11      62 ..      32      83 ..      28      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                  CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EE CS
                          TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lY 62
                                  +k+ ++L+ + ++t++e++++ +  +s+  + L+ +ed+G++e+++ + k +Y
  gi|91772235|ref|YP_564927.1| 32 IKILKTLV-SRQMTISELSRCMDCAKSTLLKNLKIMEDAGFIEVKRNENKwVY 83
                                  67888899.789********************************997644355 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.4e-06    0.0018       6      58 ..      30      79 ..      24      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-06
                                  HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                  +   +L  L  r    +t++el r ++  ks++ + lk +++aG++e +++++
  gi|91772235|ref|YP_564927.1| 30 TRIKILKTLVSRQ---MTISELSRCMDCAKSTLLKNLKIMEDAGFIEVKRNEN 79
                                  5566777777777...8*******************************99865 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.4e-06     0.007      21      74 ..      47      95 ..      39      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.4e-06
                                  CCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 21 elsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  els   ++  +++l ++Lk +e+ g++e +++e+    +  yY+lT +G++ l+
  gi|91772235|ref|YP_564927.1| 47 ELSR-CMDCAKSTLLKNLKIMEDAGFIEVKRNEN----KWVYYKLTHDGKALLQ 95
                                  5543.47888999***************998875....99**********9886 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   7.9e-06      0.01      30      82 ..      47      96 ..      11      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.9e-06
                       DUF3116 30 eldeksvkkltkneLLytvYWLElkgyilRkeekannkkrYelTekGellyke 82
                                  el  ++ ++  k +LL  +  +E  g+i  k+++ n+  +Y+lT++G+ l+++
  gi|91772235|ref|YP_564927.1| 47 EL--SRCMDCAKSTLLKNLKIMEDAGFIEVKRNE-NKWVYYKLTHDGKALLQS 96
                                  22..4456779*****************988885.8999***********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 !   15.9   0.1     1e-05     0.013       8      68 .]      34      90 ..      20      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  +L ++    r++++++l++ +++ +s+  ++lk ++ +G++e ++ e   + + ++lT  G
  gi|91772235|ref|YP_564927.1| 34 ILKTLV--SRQMTISELSRCMDCAKSTLLKNLKIMEDAGFIEVKRNE--NKWVYYKLTHDG 90
                                  677777..899******************************777766..777888888665 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.6   1.3e-05     0.017      10      68 ..      33      96 ..      27     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                        HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlellek 68
                                   IL+ + + + + +++    +   ++l k L+++ + g+i     +++   Y+lT+ G+ ll++
  gi|91772235|ref|YP_564927.1| 33 KILKTLVSRQMTISELSRCMDCAKSTLLKNLKIMEDAGFIevkrnENKWVYYKLTHDGKALLQS 96
                                  68888888889999999999999999**************99887777888**********986 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.0   5.9e-05     0.075      23      94 ..     109     178 ..     100     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-05
                          FtsX  23 teillitlvalviG.lglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsiskilkk 94 
                                   + + + ++v+l +G ++l++l+++++s+  +s+   ++l+  i++  ++ +++++ ++ ll+ +  i+k +k 
  gi|91772235|ref|YP_564927.1| 109 IVLGFSSIVSLSFGiIALLNLILKPVSNSSDSI---DSLPAAINPTFYVYFFFFFGFVSLLIFWKYIFKKRKS 178
                                   445566778888886667889999999998888...9999999999999999999999999989999998776 PP

>> PH_12  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.4e-05     0.081      21      52 ..      73     104 ..      51     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-05
                         PH_12  21 sgkrekkkwrfvkLspnrkvLhygdfeekspq 52 
                                   + kr+++kw+++kL ++ k+L+   + ek++q
  gi|91772235|ref|YP_564927.1|  73 EVKRNENKWVYYKLTHDGKALLQSNYPEKTNQ 104
                                   5677889*******************999986 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.9e-05      0.11      33      84 ..      50      96 ..      15     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                       DUF2513 33 aidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLds 84
                                  +  +  k ++   lk++++ag+ie++ ++ k     +v+++Lt +G  +L+s
  gi|91772235|ref|YP_564927.1| 50 RCMDCAKSTLLKNLKIMEDAGFIEVKRNENK-----WVYYKLTHDGKALLQS 96
                                  6667778899999**********98765544.....67999*****999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1184.96
//
Query:       gi|91772236|ref|YP_564928.1|  [L=305]
Description: hypothetical protein Mbur_0167 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-05   23.8   1.9        0.3   11.7   0.2    4.2  3  PepSY     Peptidase propeptide and YPEB domain
  ------ inclusion threshold ------
      0.022   14.3   0.1      0.048   13.1   0.1    1.5  1  DUF1248   Protein of unknown function (DUF1248)


Domain annotation for each model (and alignments):
>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.031   2.8e+02       2      60 ..      50     109 ..      49     112 .. 0.53
   2 !   11.7   0.2   3.3e-05       0.3       1      62 [.     126     200 ..     126     201 .. 0.85
   3 !    6.4   0.0    0.0015        14      43      62 ..     281     300 ..     268     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.031
                                   S-HHHHHHHHHHHSTTEEEEEEEEEEE..TTEEEEEEEEE.EE.TTEEEEEEEETTT--EE CS
                         PepSY   2 iseeqAlaiAlaavpgkiieieleded..dgrlvYevelstaepegpeyevfiDAkTGkvl 60 
                                   +++e+A++  + ++p +++e+ +  +   d+   Y   +++ + +g+ +   iD+++G+ +
  gi|91772236|ref|YP_564928.1|  50 LTLEKAKEQMKSENP-DVLENSITGGLveDDIFGYIWMFTSKNLDGGAVLSGIDPYNGDTI 109
                                   677777777777743.222333333333344444444444455677777777888888765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.3e-05
                                   SS-HHHHHHHHHHHSTTE.EEEEEEEEEE........TTEEEEEEEEE.......EE.TTEEEEEEEETTT--EEEE CS
                         PepSY   1 kiseeqAlaiAlaavpgk.iieieleded........dgrlvYevelst......aepegpeyevfiDAkTGkvlkk 62 
                                   +is ++A++iA++ +++k  i+  + +          +  + Y v +++      + ++g+      DA+TG+v+++
  gi|91772236|ref|YP_564928.1| 126 PISSKEANEIANDYLEKKsNIDGTIFSSVifhsstgeNLPATYAVHYDRvinginSLSDGIILN--LDAETGEVVSY 200
                                   69*********99977666777777777777778999888899999888889999999***999..********975 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0015
                                   .TTEEEEEEEETTT--EEEE CS
                         PepSY  43 pegpeyevfiDAkTGkvlkk 62 
                                   +e p  +  iD ++G+vl++
  gi|91772236|ref|YP_564928.1| 281 NEEPIPIAWIDVHSGEVLSV 300
                                   4555566679********86 PP

>> DUF1248  Protein of unknown function (DUF1248)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.4e-06     0.048      59      98 ..     228     267 ..     222     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-06
                       DUF1248  59 iatshtitfkplkeskdknlvflGlaWidpdyRgkeilkl 98 
                                   i  +h+  + pl ++ d +++ + l+Wid +yR +++ ++
  gi|91772236|ref|YP_564928.1| 228 ILNKHMSSWTPLSKNDDVEIQSMDLFWIDYNYRENQVHDI 267
                                   6778999**************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1937.96
//
Query:       gi|91772237|ref|YP_564929.1|  [L=232]
Description: hypothetical protein Mbur_0168 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   2.9       0.14   12.1   1.8    1.7  1  DUF2028   Domain of unknown function (DUF2028)


Domain annotation for each model (and alignments):
>> DUF2028  Domain of unknown function (DUF2028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.8   7.6e-06      0.14      41      99 ..      21      76 ..      19     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-06
                       DUF2028 41 icqldesdfaeenrdsslfqfdeissstsqsddlaaveqseksalfqfaeissdtsqtq 99
                                  ic +++s  +++  d s  qf +is+st     + +  +  ks lf  ++iss t   q
  gi|91772237|ref|YP_564929.1| 21 ICTISASATPDAIIDRSRTQFPDISASTISY--INSKCNDVKSDLFLISDISSITDY-Q 76
                                  8************************999654..334445679***********9973.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1530.85
//
Query:       gi|91772238|ref|YP_564930.1|  [L=244]
Description: hypothetical protein Mbur_0169 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1638.66
//
Query:       gi|91772239|ref|YP_564931.1|  [L=422]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for 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   55.4   0.2    3.2e-14   53.6   0.1    1.9  2  Radical_SAM  Radical SAM superfamily
    2.9e-09   37.1   0.2    8.1e-09   35.6   0.2    1.7  1  Fer4_14      4Fe-4S single cluster domain
    6.2e-09   36.3   0.1    1.3e-08   35.2   0.1    1.5  1  Fer4_12      4Fe-4S single cluster domain
    2.6e-06   27.8   0.4    6.8e-05   23.3   0.0    3.1  3  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 !   53.6   0.1   7.2e-18   3.2e-14       3     142 ..      64     192 ..      62     216 .. 0.83
   2 ?   -1.1   0.0      0.49   2.2e+03      11      20 ..     298     317 ..     296     375 .. 0.68

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 7.2e-18
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                   +t  Cnl+C+ C+       ++ g+++s  +  ++++++ ++ g+  ++++ggepll++   e++++l+k++ +++++   
  gi|91772239|ref|YP_564931.1|  64 PTSDCNLKCKGCWSQD----YESGHNISYKKFDDILDQA-ENLGIMDCLMTGGEPLLRK---EDILKLCKKH-DKMTFGAF 135
                                   6889***********6....6666666666666666666.6667*************88...4455555543.79****** PP

                                   ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                   tn+tl+dee+++++++lg   v +++e + +e    +  + + +++ ++++++l+++ i
  gi|91772239|ref|YP_564931.1| 136 TNATLIDEEFADEMAKLGNLNVFISIEGTKEE-NDFRR-GAGVYDKAIRSMDILKSREI 192
                                   ********************************.66666.88999999999999998765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.49
                                   -TTTSCCTT..........H CS
                                   xxxxxxxxx..........x RF
                   Radical_SAM  11 CsfCarpet..........v 20 
                                   C fC+ + +           
  gi|91772239|ref|YP_564931.1| 298 CAFCHYSDSnihevslaeaL 317
                                   99999998655555544440 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 !   35.6   0.2   1.8e-12   8.1e-09       5      78 ..      65     131 ..      62     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.8e-12
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                   +s Cnl+CkgC  ++    e+g+  +++  ++il+++++  i      +tGGePL   +k+++lkl+k+  + +
  gi|91772239|ref|YP_564931.1|  65 TSDCNLKCKGCWSQD---YESGHNISYKKFDDILDQAENLGI--MDCLMTGGEPL--LRKEDILKLCKKHDKMT 131
                                   689*********999...78999999********55555555..7799*******..89*********987766 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   2.8e-12   1.3e-08      12      85 ..      65     133 ..      54     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.8e-12
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                   +s+Cnl+CkgC     ++ +sg++++ +  + i++++++  i +  ++GGEPll   +e++l+l+k+  +  + 
  gi|91772239|ref|YP_564931.1|  65 TSDCNLKCKGCW---SQDYESGHNISYKKFDDILDQAENLGIMDCLMTGGEPLL--RKEDILKLCKKHDKMTFG 133
                                   799*******99...788999*********************************..*********998887773 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.22   9.7e+02      16      67 ..      19      75 ..      14      76 .. 0.52
   2 ?   -2.2   0.3       1.4   6.1e+03      25      45 ..      75      96 ..      68     100 .. 0.59
   3 !   23.3   0.0   1.5e-08   6.8e-05       5      64 ..     284     339 ..     279     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                         SPASM 16 VvpCcvd....kktyveelklGnireesleeIwnseeyqe..fr...kskkfplielCrnC 67
                                  ++ C        k+  + l++Gn    +l+e++n+ + +    r        +++  C+ C
  gi|91772239|ref|YP_564931.1| 19 IYRC--KqfflAKRLTTHLTMGNFV--TLKELYNGFKNKSsiPRvllVDPTSDCNLKCKGC 75
                                  5667..1123333444449999995..5999998876666542222212233334447777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                         SPASM 25 tyveelklG.nireesleeIwn 45
                                  ++++++  G ni+ +++++I+ 
  gi|91772239|ref|YP_564931.1| 75 CWSQDYESGhNISYKKFDDILD 96
                                  4555543332677778888875 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 1.5e-08
                         SPASM   5 srslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefr..kskkfplielC 64 
                                      + In++GdV pC +        ++  ni+e sl+e ++s+ +++fr  + + +++ ++C
  gi|91772239|ref|YP_564931.1| 284 IGFVHINAKGDVEPCAFC------HYSDSNIHEVSLAEALRSKFFTAFRaaQPFSQNPLRPC 339
                                   55679**********444......38999********************4433344444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2772.68
//
Query:       gi|91772240|ref|YP_564932.1|  [L=257]
Description: alpha/beta hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-12   45.9   0.1      4e-06   26.7   0.0    2.6  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0099   14.6   0.2      0.019   13.7   0.2    1.7  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.062   13.9   0.0       0.34   11.5   0.0    2.0  1  Abhydrolase_6  Alpha/beta hydrolase family
      0.072   12.4   0.8          5    6.4   0.1    2.7  3  DUF915         Alpha/beta hydrolase of unknown function (DUF9
        0.1   11.9   0.0       0.19   10.9   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.1e-09     4e-06       3     106 ..      21     113 ..      19     126 .. 0.86
   2 !   16.5   0.0   1.4e-06     0.005     193     254 ..     182     238 ..     143     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.1e-09
                                   EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHH CS
                 Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmG 83 
                                   + ++hG++gs+  w +   ++ ++k ++ +++l +  +         in++ ++++v+ +++  ld+++++  + vG+S+ 
  gi|91772240|ref|YP_564932.1|  21 ITFIHGFGGSARTWKK--QIEFFSK-HYNLLVLEMHKNK--------INEELNLDNVCIFINNTLDHYKIKTSHFVGFSFS 90 
                                   6689999999999999..8888888.9999999885444........446777899************************* PP

                                   HHHHHHHHHHHGGGEEEEEEESE CS
                 Abhydrolase_1  84 GmialayaaeyperVkalvllga 106
                                   ++i+l +a +ype++++l++ g+
  gi|91772240|ref|YP_564932.1|  91 SLICLRFAVLYPEKINSLIMGGG 113
                                   ******************98666 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.4e-06
                                   HHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHH CS
                 Abhydrolase_1 193 pttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafl 254
                                   +t+ s  +l++l++     + +l++sg++D+l+  + l+ +++  ++ ++++i+++gH   +
  gi|91772240|ref|YP_564932.1| 182 QTKKSLTWLDELNK----DIQVLYVSGNEDHLFLKDTLRHSKKISNS-QVEIIEHCGHVCSI 238
                                   55566666666666....559********************977666.**********7655 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   5.3e-06     0.019      80     129 ..      61     110 ..      51     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-06
                                   --HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEE CS
                           Ndr  80 pslddladqllavldhfklksviglGvgaGAyilarfalkhperveglvL 129
                                     ld+++  +++ ldh+k+k+   +G      i +rfa+ +pe++ +l++
  gi|91772240|ref|YP_564932.1|  61 LNLDNVCIFINNTLDHYKIKTSHFVGFSFSSLICLRFAVLYPEKINSLIM 110
                                   56899*******************************************97 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.4e-05      0.34       3     218 ..      23     245 ..      21     247 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.4e-05
                                   EE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT..TTSEEEEEETCHHHHHHHH CS
                 Abhydrolase_6   3 llHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaagggpvvlvGHSlGGalalaa 82 
                                   ++HG+g+sa+ W      +++++++  l++    +       l+l+++  +  ++ld+ +   +  + vG S+  ++ l++
  gi|91772240|ref|YP_564932.1|  23 FIHGFGGSARTWK--KQIEFFSKHYNLLVLEMHKN--KINEELNLDNVCIFiNNTLDHYK--IKTSHFVGFSFSSLICLRF 97 
                                   8999999999994..33344577777788888666..47777888775444777888886..77779*********99995 PP

                                   HHCC....EEEEES-..----TTTS----TTHH.......HHHHTT-CCCCH.CCH....S-HSCCCCHHHC..CCCHCHC CS
                 Abhydrolase_6  83 apla..lvvgvlldppptalpagllaaalelll.......allallrllawl.sre....plprlfladeda..daawrar 147
                                   a l    + ++++ +  ++  +  + ++l +l+        ++ l+ ++a+  +       ++r ++ +e++   ++  + 
  gi|91772240|ref|YP_564932.1|  98 AVLYpeKINSLIMGG--GIIKFNIRTRFLLFLAikfkkiiNYMILYKFFAYIiM-PkqnhKRSRAIFVNEAKklGYDEFCK 175
                                   555577556655555..2555554333333333222111122223333444431.24556344444444442357777777 PP

                                   CCGHHHHCCHHCHTTCCHHTT-TTGCEEECTT-C.HHHHCHHCCCHSTTEEETCE...SSS-HHHHSHHHHH CS
                 Abhydrolase_6 148 larlaallaglgllpaaawadlpvpllvlggeDp.lvprllerllaqagarlpvvlpgaGHlphleepdeva 218
                                   + +l +++++  ++  +  +d+ v++ v g eD   ++++l++   +   ++ ++++++GH+  +e+ d+++
  gi|91772240|ref|YP_564932.1| 176 WVDLVPQTKKSLTWLDELNKDIQVLY-VSGNEDHlFLKDTLRHSKKISNSQV-EIIEHCGHVCSIEQYDKFN 245
                                   77777777777777677777777777.7245555544444444444788888.9*******55554878775 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.005        18      14      37 ..      21      44 ..      15      62 .. 0.80
   2 ?    6.4   0.1    0.0014         5      67     125 ..      45     102 ..      42     107 .. 0.79
   3 ?   -1.7   0.0      0.39   1.4e+03     180     193 ..     192     205 ..     182     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.005
                        DUF915 14 tifihGyggtaeslnemvkqlenk 37
                                  + fihG+gg+a++ ++ ++ + ++
  gi|91772240|ref|YP_564932.1| 21 ITFIHGFGGSARTWKKQIEFFSKH 44
                                  569***********9999888644 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0014
                        DUF915  67 nPiikvgfednrdaslkkqakwlkkvlseLkkkYnikkfnavGhSmGglaltsYleeya 125
                                   + + ++++++n+  + + +   + + +++   +Y+ik   +vG+S   l +++++  y 
  gi|91772240|ref|YP_564932.1|  45 YNLLVLEMHKNK-INEELNLDNVCIFINNTLDHYKIKTSHFVGFSFSSLICLRFAVLYP 102
                                   556667777777.4777777777778888889*************99999999987775 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.39
                        DUF915 180 kipkdlevlniaGd 193
                                   +++kd++vl + G+
  gi|91772240|ref|YP_564932.1| 192 ELNKDIQVLYVSGN 205
                                   56788888888887 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.4e-05      0.19      61     232 ..      65     234 ..      57     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.4e-05
                   Hydrolase_4  61 DlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv.. 139
                                    +  f+++  ++++ +    +G S  +li l+++  yp+k++ li+ +  +k + +++   +l +l+  ++k++  + +  
  gi|91772240|ref|YP_564932.1|  65 NVCIFINNTLDHYKIKTSHFVGFSFSSLICLRFAVLYPEKINSLIMGGGIIKFNIRTR---FLLFLAIKFKKIINYMILyk 142
                                   555677888888888888899********************************98753...33333333344433333344 PP

                   Hydrolase_4 140 .......snnlkadslsrd..pevvaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasr 211
                                          +  +++++ sr     + +++  d+++++   v    + l+ +++l+++ +     +l ++G +D++  ++  r
  gi|91772240|ref|YP_564932.1| 143 ffayiimP--KQNHKRSRAifVNEAKKLGYDEFCKWVDLVPQTKKSLTWLDELNKDIQ-----VLYVSGNEDHLFLKDTLR 216
                                   45566443..344444443113455677777777764444444444444444444333.....678888888877744333 PP

                   Hydrolase_4 212 elyerlgskdktlklypglyH 232
                                      ++++  + ++++++++ H
  gi|91772240|ref|YP_564932.1| 217 -HSKKIS--NSQVEIIEHCGH 234
                                   .233333..346666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1531.01
//
Query:       gi|91772241|ref|YP_564933.1|  [L=527]
Description: hypothetical protein Mbur_0172 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-33  117.6  17.7    4.4e-33  115.5  17.7    2.0  1  AAA_15    AAA ATPase domain
    6.7e-17   62.2   5.9    4.7e-11   43.1   0.3    2.5  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.3e-07   31.1   0.2    5.1e-07   30.0   0.2    1.6  1  DUF3696   Protein of unknown function (DUF3696)
    5.7e-07   30.2   2.1    1.6e-06   28.8   2.1    1.9  1  AAA_23    AAA domain
    5.5e-06   25.8   0.0    1.2e-05   24.7   0.0    1.5  1  G-alpha   G-protein alpha subunit
      1e-05   25.1   0.7    2.1e-05   24.1   0.7    1.6  1  SMC_N     RecF/RecN/SMC N terminal domain
    0.00091   18.9   0.1     0.0022   17.7   0.1    1.6  1  AAA_29    P-loop containing region of AAA domain
     0.0074   15.9   0.1      0.012   15.3   0.1    1.3  1  AAA_27    AAA domain
     0.0086   15.4   1.2       0.17   11.1   0.1    2.8  3  DUF2813   Protein of unknown function (DUF2813)


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5  17.7   2.2e-36   4.4e-33       1     369 []       1     452 [.       1     452 [. 0.69

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 2.2e-36
                        AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn.......kkvikiekedleifenise 73 
                                   M Ik+++++NF+ lkd  +idl++ lt+l+G N+sGKSsi++ l  ++++ e+ +       +  ++   ++++i +n+  
  gi|91772241|ref|YP_564933.1|   1 M-IKQLHLENFKGLKDsKKIDLKP-LTLLCGSNSSGKSSIIQSLLMLKQTFESQSryrkvvlNGQFTHLGSFINIIHNKTL 79 
                                   8.9*************99******.*******************888887777779999***9999999************ PP

                        AAA_15  74 skdikIdvef............aek..ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvek 140
                                   s+++ ++++             +++  +   +++ +  s+e ++++ll +++  +  k ++  + ++++ ++  ++ ++++
  gi|91772241|ref|YP_564933.1|  80 SNEVMLKFQIspstpainggnkKYSfiDYHLNDFNFGSSSENNSNKLLDIELGLKVLKDSNAMEPYVNTFNVLAKSNDLQE 160
                                   **********87777777766533355455555666666666666666777777777777777777777777777666666 PP

                        AAA_15 141 kkskkelpkekeeklekekeelkidkedlkklikkleeslkkee...................elknvlksaiiklllisa 202
                                   + s     ++++ +   +k++lk ++ +    ++  e  ++  +                     k+ ++ +++k    + 
  gi|91772241|ref|YP_564933.1| 161 NHSDGTSISLSRIST--DKYNLKWKNIKSGYFLNFVEDPVPIPKsiisyvcpkcgishrsnsgIGKKHYSYHFYKHNGAEV 239
                                   666444444444433..3455555555555555544444444448888889999999998887444555555555555555 PP

                        AAA_15 203 kRnvsd.edsekkssllgklkekileealqekl...........................................eeelt 239
                                   k ++s+     k++++  k+++ i++++++ k                                            +    
  gi|91772241|ref|YP_564933.1| 240 KASFSNlMPIIKQQDYSVKALYPIVHSINSLKElihtefsnlyyigplreeparryiheaefidigirgenapfilS---- 316
                                   55555555555666666777777777654444455555555566888888887777555555555554433332220.... PP

                        AAA_15 240 eklkeiqeklkeidkklaeelk...................kilkkkidkikkfnykgkkneeieik.............. 287
                                                   ++ ++k                   ++l++ +                  +              
  gi|91772241|ref|YP_564933.1| 317 ----------------IEGNKKispyrfyneplnewqsiddDNLEDAV------------------Nrwlrymgiseyele 363
                                   ................22222233332222222223333332222222..................022233344444444 PP

                        AAA_15 288 ...............ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelan 353
                                                   d++++l+++G+Gv+++l+++++ l++ ++        +l++E+PE+hLHp++q++l++ + +++ 
  gi|91772241|ref|YP_564933.1| 364 akddiirlnmssiqdKDVKVTLADVGFGVSQILPILVEGLRIGDG-------QTLILEQPEIHLHPKLQMQLADFFVSMVL 437
                                   4566678889999999*****************************.......***************************** PP

                        AAA_15 354 dnktQviitTHSphii 369
                                   ++k  v+i+THS+hi+
  gi|91772241|ref|YP_564933.1| 438 SGK-RVLIETHSDHIV 452
                                   **9.***********7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.0   9.2e-08   0.00018       1      68 [.      24     111 ..      24     187 .. 0.83
   2 !   43.1   0.3   2.3e-14   4.7e-11     177     303 .]     349     453 ..     286     453 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.2e-08
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarl......................drdvegltdelsggggirkipslldlydpeipfe 59 
                                   l++l G N+sGKS++++ l +l+++                      ++ +++ t ++    ++++ ps +  +  +++  
  gi|91772241|ref|YP_564933.1|  24 LTLLCGSNSSGKSSIIQSLLMLKQTfesqsryrkvvlngqfthlgsfINIIHNKTLSNEVMLKFQISPSTPAINGGNKKYS 104
                                   699*********************999999999888888888888888888888888888888888888888888877777 PP

                        AAA_21  60 feieeflsq 68 
                                   f ++  +++
  gi|91772241|ref|YP_564933.1| 105 FIDY--HLN 111
                                   7777..333 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 2.3e-14
                        AAA_21 177 gfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkk 257
                                   + + +   +++++ + k++ i+l ++ ++                     +++ ++++++++ G+ ++l++l+  lr  + 
  gi|91772241|ref|YP_564933.1| 349 NRWLRYMGISEYELEAKDDIIRLNMSSIQ---------------------DKDVKVTLADVGFGVSQILPILVEGLRIGDG 408
                                   33333344455555666666666666544.....................4678899********************9999 PP

                        AAA_21 258 gsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpllld 303
                                     +l+++ pE +LHPkl+  l++++ +    g  v++ THS ++++
  gi|91772241|ref|YP_564933.1| 409 -QTLILEQPEIHLHPKLQMQLADFFVSMVLSGKRVLIETHSDHIVN 453
                                   .************************6666667***********986 PP

>> DUF3696  Protein of unknown function (DUF3696)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2   2.6e-10   5.1e-07       5      49 ..     470     510 ..     469     514 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.6e-10
                       DUF3696   5 dvalyfferdegkdsaidtevlspiddnGrisnWPeGFFDqaekd 49 
                                   +++l+ffe  +g  ++ + e    id n  i nWP+GFFDq+ ++
  gi|91772241|ref|YP_564933.1| 470 KTNLLFFENIDGYPALNPVE----IDSNRGIVNWPKGFFDQSADE 510
                                   6899****************....*****************9776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   2.1   7.9e-10   1.6e-06       1      42 [.       4      45 ..       4     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.9e-10
                        AAA_23  1 kLkienfrsfrd.qeidFskgltlItGpNGaGKTTildAikla 42
                                  +L++enf+ ++d ++id++ +ltl++G N +GK++i++ +   
  gi|91772241|ref|YP_564933.1|  4 QLHLENFKGLKDsKKIDLK-PLTLLCGSNSSGKSSIIQSLLML 45
                                  59********88356***9.*****************999776 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0     6e-09   1.2e-05      26     210 ..      25     389 ..       3     393 .. 0.56

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6e-09
                                   EEEEESTTSSHHHHHHHHHHHCS----HHHHHCCHHHHHHHHHHHHHHHHHHHHH.....TT................... CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkgfseeelatwraviqlnivrsiktileales.....leselsesf............ 89 
                                    ll+G+++SGKs+i+++l +l+ ++f+ +    +r+v+ +   +++ ++++++ +     +       +            
  gi|91772241|ref|YP_564933.1|  25 TLLCGSNSSGKSSIIQSLLMLK-QTFESQ--SRYRKVVLNGQFTHLGSFINIIHNktlsnE-------Vmlkfqispstpa 95 
                                   599**************99666.889999..779*******************99443330.......2334466665566 PP

                                   .............................................HHHC-SS-SCCCS-HCHHHH..........HHCCHH CS
                       G-alpha  90 .............................................elqelkerldplkkveasliaklssateeeqeiefn 125
                                                                                                                    
  gi|91772241|ref|YP_564933.1|  96 inggnkkysfidyhlndfnfgsssennsnklldielglkvlkdsnA----------------------------------- 141
                                   6666666666666666666555444444433333333333322221................................... PP

                                   C-HCHHHHHHHHCCSHHHHHHHCCGCCTT..--TTHHHHHCTHHHHCSTT---............................ CS
                       G-alpha 126 praevgedikaLwndpgiqelyerrnkik..lednaeyFlddleritspdYlp............................ 176
                                              +    +  ++++++n+++  ++d++ +   +l+ri++ +Y                              
  gi|91772241|ref|YP_564933.1| 142 -----------MEPYVNTFNVLAKSNDLQenHSDGTSI---SLSRISTDKYNLkwkniksgyflnfvedpvpipksiisyv 208
                                   ...........111112222222222222111111111...1222222222222222222222222222222333333333 PP

                                   ................................................................................. CS
                       G-alpha 177 ................................................................................. 176
                                                                                                                    
  gi|91772241|ref|YP_564933.1| 209 cpkcgishrsnsgigkkhysyhfykhngaevkasfsnlmpiikqqdysvkalypivhsinslkelihtefsnlyyigplre 289
                                   333333333333333333333333333333333333333344444444467777777777777777777777777777777 PP

                                   .....................................................-CHHHHCS-----SEEEEEEEC...... CS
                       G-alpha 177 .....................................................tddDilkarlktvGisetkfev...... 198
                                                                                        + +D ++  l+ +Gise+++e       
  gi|91772241|ref|YP_564933.1| 290 eparryiheaefidigirgenapfilsiegnkkispyrfyneplnewqsidddNLEDAVNRWLRYMGISEYELEAkddiir 370
                                   777777777777777777777777777777777777777777777776665555588888889999999999988888888 PP

                                   .......T-TEEEEEEEE- CS
                       G-alpha 199 .......dsklefrivdvg 210
                                          d+++++++ dvg
  gi|91772241|ref|YP_564933.1| 371 lnmssiqDKDVKVTLADVG 389
                                   8888888778888888887 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   0.7   1.1e-08   2.1e-05       1      48 [.       1      45 [.       1     127 [. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.1e-08
                                  EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvL 48
                                  ++k+l +enFk ++ +++++++++ +t + G+N SGKs++++++l +L
  gi|91772241|ref|YP_564933.1|  1 MIKQLHLENFKGLK-DSKKIDLKP-LTLLCGSNSSGKSSIIQSLL-ML 45
                                  69***********8.899999999.9*****************93.33 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.1e-06    0.0022       3      43 ..       4      43 ..       2      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                        AAA_29  3 rlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiq 43
                                  +l+l N   +++ ++i+++    tll G + sGKS+++ ++ 
  gi|91772241|ref|YP_564933.1|  4 QLHLENFKGLKDsKKIDLK--PLTLLCGSNSSGKSSIIQSLL 43
                                  6777777778777777776..569*************94443 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.8e-06     0.012       3      60 ..       2      56 ..       1      77 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.8e-06
                        AAA_27  3 lerLdLeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdn 60
                                  +++L+Le +  ++d+ ++d++     l+l+ G+N +GKs++++++  l   ++ ++++ 
  gi|91772241|ref|YP_564933.1|  2 IKQLHLENFKGLKDSkKIDLK----PLTLLCGSNSSGKSSIIQSLLMLKQTFESQSRYR 56
                                  799******888875379998....8**********************99999999886 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   8.3e-05      0.17       4      45 ..       3      45 ..       1      57 [. 0.83
   2 ?   -1.2   0.0      0.47   9.4e+02      52      92 ..     105     145 ..      94     181 .. 0.67
   3 ?    1.6   0.0     0.067   1.3e+02     287     304 ..     411     428 ..     404     459 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                       DUF2813  4 erieisGFRGinr.LSlsleentvLiGENaWGKSSLldALsli 45
                                  +++ +  F+G++    + l+++t L G N+ GKSS+++ L ++
  gi|91772241|ref|YP_564933.1|  3 KQLHLENFKGLKDsKKIDLKPLTLLCGSNSSGKSSIIQSLLML 45
                                  78888899999862579*********************99765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.47
                       DUF2813  52 lyqFtlkDFhvdeseeeeqekhlqlvltfkeeekeeekarr 92 
                                   +  ++l+DF + +s+e++++k l + l  k  +  + ++  
  gi|91772241|ref|YP_564933.1| 105 FIDYHLNDFNFGSSSENNSNKLLDIELGLKVLKDSNAMEPY 145
                                   33457899999999999999999887766655554444444 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.067
                       DUF2813 287 lllEdpearLHPtmlaia 304
                                   l+lE+pe +LHP+   ++
  gi|91772241|ref|YP_564933.1| 411 LILEQPEIHLHPKLQMQL 428
                                   89**********865444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 2895.78
//
Query:       gi|91772242|ref|YP_564934.1|  [L=294]
Description: hypothetical protein Mbur_0173 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1723.43
//
Query:       gi|91772243|ref|YP_564935.1|  [L=544]
Description: acetolactate synthase, large subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  177.1   0.0    1.8e-51  174.2   0.0    2.0  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    7.6e-38  129.7   0.1      2e-37  128.3   0.0    1.8  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    3.8e-32  110.9   0.1    1.1e-31  109.4   0.0    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


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 !  174.2   0.0     3e-55   1.8e-51       1     170 [.       1     167 [.       1     169 [. 0.98
   2 ?    0.4   0.0     0.072   4.3e+02     113     162 ..     482     526 ..     438     530 .. 0.84

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 3e-55
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   m+++e++v++L+++gv+++fg+pG++ l+l+++ls+++ i+++++rhEq+aaf+Ad   r+tg+pgv+l t gpGatn++t
  gi|91772243|ref|YP_564935.1|   1 MKGSELFVKCLENEGVKYIFGIPGEETLDLMESLSRSD-IEFIVVRHEQSAAFMADVCGRLTGRPGVCLPTLGPGATNLMT 80 
                                   79***********************************6.****************************************** PP

                                   HHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                   ++a+A++dr Pl++++g+ + ++  ++  q  ld +++f  +t ++ +vt ++++pe++ +A+++a ++ pg++++elp+d
  gi|91772243|ref|YP_564935.1|  81 GVADAHLDRAPLVAITGQGSLDRAYKESHQ-FLDVAGMFSRITSWNATVTAANQIPELIGKAFDIA-TDVPGAAHIELPED 159
                                   *************************88888.99*********************************.************** PP

                                   HCC-EEEH CS
                  TPP_enzyme_N 163 vlleevde 170
                                   v ++e+d+
  gi|91772243|ref|YP_564935.1| 160 VSTQETDA 167
                                   *****996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.072
                                   -T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                  TPP_enzyme_N 113 eldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                   + d ++l++++     r++s++ l  al+ A+++      g+ ++++p d
  gi|91772243|ref|YP_564935.1| 482 NPDFVGLANSFGAKGIRINSADGLGDALQSAFKEG-----GVWLIDVPVD 526
                                   45778888888888999999999999999999887.....7777777777 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         1   6.2e+03      38      57 ..      80     100 ..      75     102 .. 0.73
   2 !  128.3   0.0   3.3e-41     2e-37       1     153 []     377     523 ..     377     523 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                                   HHHHHHST.TSEEEEEEEHHH CS
                  TPP_enzyme_C  38 iGaklakp.drevvaivGDGg 57 
                                   +G++ a+  +++ vai+G G+
  gi|91772243|ref|YP_564935.1|  80 TGVADAHLdRAPLVAITGQGS 100
                                   5666665315699*****998 PP

  == domain 2  score: 128.3 bits;  conditional E-value: 3.3e-41
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvln 81 
                                   d+G ++lw+ rl+ +  p+++l+s+gl++mG+glpa+i+a+l +p+++vv i+GD g+lm++q+l+tavr n ++++++++
  gi|91772243|ref|YP_564935.1| 377 DVGAHKLWIGRLYLALAPNTVLMSNGLASMGFGLPAGIAACLIHPEKKVVTIAGDAGILMNIQDLETAVRLNCDLVIIIFD 457
                                   89******************************************************************************* PP

                                   -SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  82 NegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                   +++yg+++++++ ++g+++ + +   +k++df+ la ++Gakg+r+++a  + l +al+ a++++g+ li+v
  gi|91772243|ref|YP_564935.1| 458 DASYGLIEWESNTKFGESFGT-S---FKNPDFVGLANSFGAKGIRINSA--DGLGDALQSAFKEGGVWLIDV 523
                                   **********99999877655.5...8999*******************..*******************97 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 !  109.4   0.0   1.8e-35   1.1e-31       2     136 ..     187     319 ..     186     320 .. 0.93
   2 ?   -2.9   0.0      0.87   5.2e+03      76      84 ..     447     455 ..     417     467 .. 0.67

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 1.8e-35
                                   HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEE CS
                  TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvl 82 
                                    ka+el++ a +p+i++G+gv+r++as el++++++ +i vvtt+mgkg+ip d+++++g++g+  +++    l+ aD+v+
  gi|91772243|ref|YP_564935.1| 187 HKAIELISGATKPLIIAGNGVIRENASLELEQFVDAANIGVVTTFMGKGAIPADNDHFIGSMGMSEKDYIICGLNAADVVI 267
                                   69******************************************************************************* PP

                                   EES-SSSTCCCTTTTT.TTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
                  TPP_enzyme_M  83 alGarfddirttgsep.efapeakiihididpaeigknyqvdlaivgdvketlea 136
                                   a+G  fd    +++++ ++   + iih++  + ei  +y ++ a++g +k+tl+a
  gi|91772243|ref|YP_564935.1| 268 AIG--FDS-VEYSPDHwNMDHSKSIIHVQNRHPEIETSYIPECALLGTLKTTLRA 319
                                   ***..888.566666645555559*****************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.87
                                   HH-SEEEEE CS
                  TPP_enzyme_M  76 eeaDlvlal 84 
                                    ++Dlv+++
  gi|91772243|ref|YP_564935.1| 447 LNCDLVIII 455
                                   367777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 3159.61
//
Query:       gi|91772244|ref|YP_564936.1|  [L=455]
Description: succinate-semialdehyde dehydrogenase (NAD(P)+) [Methanococcoides burtonii DSM 6242]
Scores for complete 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-144  480.4   0.1   5.2e-144  480.2   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.2   0.1  2.9e-148  5.2e-144       8     462 .]       3     452 ..       1     452 [. 0.98

  Alignments for each domain:
  == domain 1  score: 480.2 bits;  conditional E-value: 2.9e-148
                                   EEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH CS
                        Aldedh   8 tievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara 88 
                                   +i ++nPatgev  +++  ++e +++ + +A+ +f +w++l+++eRa +L++aa+ l+++k+el +++t+e+Gkp++e+  
  gi|91772244|ref|YP_564936.1|   3 KIVSMNPATGEVNEEIELYSEERINRTITKARTTFLEWKNLDISERAHYLKTAATQLRKDKDELGRIITIEMGKPIKESVP 83 
                                   57899**************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHH CS
                        Aldedh  89 eveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetpls 168
                                   eve+++  l+yyae ae+ l+ e+++++   ++ v  eP Gv+++I+PWNfP+  a++ +apal+ GNtv+lK a+ +p++
  gi|91772244|ref|YP_564936.1|  84 EVEKCAWALEYYAENAENfLAPEAVETD-ALESGVSFEPKGVILSIMPWNFPFWQALRFAAPALVGGNTVILKHASSVPMC 163
                                   ******************8999*99995.88999999******************************************** PP

                                   HHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSH CS
                        Aldedh 169 alllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaD 249
                                   al++ ++f++aglP+g+++ +  +g++++e +++ +e+++v+ftGs + grk+a+aa++n+k+ +lElGG +p+ivl+da+
  gi|91772244|ref|YP_564936.1| 164 ALAIEKVFADAGLPEGAFQTLIIDGRTASELIAR-DEIAAVTFTGSLTAGRKVAEAAGRNMKKAVLELGGSDPFIVLDDAN 243
                                   ***********************9*987777666.69******************************************** PP

                                   HHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHT CS
                        Aldedh 250 ldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakee 330
                                   ++ a++a v++ f n GQ Ciaa+r++v e ++def+  ++  a+kl+vgdp+d++tdvGPl++++q++ ++++v++ +++
  gi|91772244|ref|YP_564936.1| 244 VEMAAKAGVNSRFQNGGQSCIAAKRFIVTEAVADEFLRIFIGSARKLQVGDPMDPQTDVGPLVNAQQVDIIDAQVKDSVDK 324
                                   ********************************************************************************* PP

                                   TSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHH CS
                        Aldedh 331 gaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdleraer 411
                                   ga+lll+g    + ++ g f++P++l+nv+++mr+++eE+FGPV++vi +kdeeeai++a ++++GL+a+++t+d e+a++
  gi|91772244|ref|YP_564936.1| 325 GAELLLEG---GRLDRLGSFYAPVILSNVNENMRVLKEETFGPVAPVIIVKDEEEAIRVAGNSDFGLGASLWTEDREHAME 402
                                   ******88...6789****************************************************************** PP

                                   HHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                        Aldedh 412 vaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                   + +++e G + +N++ ++++   pfgGvk+Sg+Gre  k+gl e++++k++
  gi|91772244|ref|YP_564936.1| 403 IEKHIESGILSVNSMVASDPRL-PFGGVKKSGIGRELYKYGLYEFMNIKSI 452
                                   ********************99.**************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 3342.57
//
Query:       gi|91772245|ref|YP_564937.1|  [L=116]
Description: hypothetical protein Mbur_0176 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   29.1   0.3    1.1e-06   28.7   0.3    1.1  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      6e-05   22.9   0.1    8.5e-05   22.4   0.1    1.2  1  MarR            MarR family
     0.0031   17.4   0.0     0.0048   16.8   0.0    1.3  1  MarR_2          MarR family
     0.0047   16.5   0.7     0.0065   16.0   0.7    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0062   16.4   0.2     0.0079   16.0   0.2    1.2  1  TFIIE_alpha     TFIIE alpha subunit
  ------ inclusion threshold ------
      0.025   13.4   0.1       0.03   13.1   0.1    1.0  1  HTH_micro       HTH-like
      0.046   14.2   0.0      0.065   13.7   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain
      0.057   13.3   0.0      0.073   13.0   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> 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 !   28.7   0.3   4.8e-10   1.1e-06      16      66 ..      15      61 ..       3      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.8e-10
                B-block_TFIIIC 16 ysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksistsl 66
                                  ++G++q++L+k++++d+r+   +l++L k  LI + s      ++++st+l
  gi|91772245|ref|YP_564937.1| 15 KDGVFQNELWKLLEIDSRKCSRILNKLIKAELISRESS----VNNGASTYL 61
                                  68**********************************99....566666665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   3.8e-08   8.5e-05      18      55 ..      18      55 ..       5      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.8e-08
                                  EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTS CS
                          MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRskspeD 55
                                    + eL+k l++++   +r+l +L+k++li+R+ s ++
  gi|91772245|ref|YP_564937.1| 18 VFQNELWKLLEIDSRKCSRILNKLIKAELISRESSVNN 55
                                  5577******************************9998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.1e-06    0.0048      18      56 ..      16      52 ..       8      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                                  TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  +g  + ++el + l ++    sril++L +a L+ r+++
  gi|91772245|ref|YP_564937.1| 16 DG--VFQNELWKLLEIDSRKCSRILNKLIKAELISRESS 52
                                  45..88999999***********************9987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   2.9e-06    0.0065       4      47 ..       3      47 ..       2      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                        HTH_24  4 tdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  ++ k L+++q+ + +  q+eL + l + +  ++r l++L++++lI
  gi|91772245|ref|YP_564937.1|  3 IEEKTLKIIQDsKDGVFQNELWKLLEIDSRKCSRILNKLIKAELI 47
                                  7789999****9999****************************99 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   0.2   3.5e-06    0.0079      27      70 ..      17      60 ..       2      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.5e-06
                                  SEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEE CS
                   TFIIE_alpha 27 evteedlakelkidlnelrklLnrLyearlvkykrrrdeekswy 70
                                   v  ++l k+l+id  +  ++Ln+L +a l++   +++++ s+y
  gi|91772245|ref|YP_564937.1| 17 GVFQNELWKLLEIDSRKCSRILNKLIKAELISRESSVNNGASTY 60
                                  466789**************************999999988876 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.3e-05      0.03     100     152 ..      11      66 ..       6      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                     HTH_micro 100 lvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeak...ivikink 152
                                   +  +kd v + el + l+id++k + +++kL k +li  + + ++    ++iki +
  gi|91772245|ref|YP_564937.1|  11 IQDSKDGVFQNELWKLLEIDSRKCSRILNKLIKAELISRESSVNNGastYLIKIVA 66 
                                   44567999999**************************9776544434478888876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.9e-05     0.065      12      61 ..      11      60 ..       6      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                        HTH_27 12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                  i+   +++ + +l + l +++   s +l+kL++++L+ r+ +  ++ ++ 
  gi|91772245|ref|YP_564937.1| 11 IQDSKDGVFQNELWKLLEIDSRKCSRILNKLIKAELISRESSVNNGASTY 60
                                  5556666667889999*********************9999977776654 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.3e-05     0.073      26      67 ..      21      67 ..       4      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
                                  CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TTEEEE--H CS
                          TrmB 26 deiaeelgvprskvYevLrsLedkGlVerekgr.....pklYravdp 67
                                  +e+ + l+++  k+ ++L++L+++ l+ re +      ++l + v p
  gi|91772245|ref|YP_564937.1| 21 NELWKLLEIDSRKCSRILNKLIKAELISRESSVnngasTYLIKIVAP 67
                                  5788899**********************986556777667766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 740.35
//
Query:       gi|91772246|ref|YP_564938.1|  [L=65]
Description: small ribonucleoprotein [Methanococcoides burtonii DSM 6242]
Scores for 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-19   66.9   0.2      1e-18   66.8   0.2    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 !   66.8   0.2   5.7e-23     1e-18       7      67 .]       2      62 ..       1      62 [. 0.96

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 5.7e-23
                                  TTSEEEEEETTS.EEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                           LSM  7 inkkvtvelkng.relrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                  i++kv+ve+k++ + l+GtL++ D+++Nl+L d++e+ +++ + r+lg v++RGnni+li++
  gi|91772246|ref|YP_564938.1|  2 IGSKVQVEMKGDqHILEGTLQSADDYLNLHLVDTTEIADGQ-RLRSLGSVVLRGNNIILIVP 62
                                  899********8799***********************999.******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 406.10
//
Query:       gi|91772247|ref|YP_564939.1|  [L=123]
Description: hypothetical protein Mbur_0178 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   64.0   0.0    1.3e-17   63.7   0.0    1.1  1  DUF3467   Protein of unknown function (DUF3467)


Domain annotation for each model (and alignments):
>> DUF3467  Protein of unknown function (DUF3467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   7.4e-22   1.3e-17       3      90 ..       4     101 ..       1     102 [. 0.89

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 7.4e-22
                       DUF3467   3 kdekaagkkiralrie.vdesvaggsYsngaivmtspsEfiidF....lqlvpgrpearvksr.....vvlspaaakqlva 73 
                                   ++ + +g+  ++l+ie ++ ++++++Y++ga   +sp++f+i F    ++ +++ ++++v++r     v++sp aa +l +
  gi|91772247|ref|YP_564939.1|   4 EKTTPEGNVTKKLKIEvIKPEDFKQTYAIGALGGHSPYDFRIGFyndsPKGFEKSSNSQVIQRsieteVIMSPLAALELSQ 84 
                                   344445555588****99**************************77776689999999****9****************** PP

                       DUF3467  74 aLqknldlyetrfGeik 90 
                                   +L+++++++e+ fG+i+
  gi|91772247|ref|YP_564939.1|  85 WLEQHIRDFEAMFGPIT 101
                                   ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 743.03
//
Query:       gi|91772248|ref|YP_564940.1|  [L=825]
Description: DEAD/DEAH box helicase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-24   84.7   0.0    1.4e-23   83.6   0.0    1.6  1  DEAD          DEAD/DEAH box helicase
    3.6e-16   59.5   0.1    1.6e-15   57.4   0.0    2.2  2  Helicase_C    Helicase conserved C-terminal domain
      2e-09   37.7   0.1    5.5e-09   36.3   0.1    1.8  1  ResIII        Type III restriction enzyme, res subunit
     0.0015   17.3   0.0     0.0021   16.8   0.0    1.2  1  SNF2_N        SNF2 family N-terminal domain
  ------ inclusion threshold ------
       0.07   12.5   0.0       0.13   11.6   0.0    1.4  1  APO_RNA-bind  APO RNA-binding


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 !   83.6   0.0   3.9e-27   1.4e-23       2     170 ..     220     385 ..     219     390 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 3.9e-27
                                   HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   ++Q+ +i+  l + ++ lv   T++GKTl+  i+ +++++      + k+l+++P+ +La+q +++++k+ + i+l+++  
  gi|91772248|ref|YP_564940.1| 220 PVQSLSIEKGLlERRNQLVTSVTATGKTLIGEIAGIENIL----HGHGKMLYLVPLVALANQKYDQFNKRYSGIGLNTSIR 296
                                   789999999887999************************6....57889*****************************988 PP

                                   ETTSSH.HHHHHHHHTT..CSEEEEEHHHHHHHHHCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTT CS
                                   xxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaa.rdqlskldng..vdivvgtpgrlddllstgkln.lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgkl 158
                                   +g+++  +++ +k+++g  +di+vgt + ld +l+tg  + l q+ ++V+DE++++ d++++  ++ ++ +l+   +    
  gi|91772248|ref|YP_564940.1| 297 VGSSKIrTSKTKKMKRGldADIIVGTYEGLDVILRTGDADlLGQIGTVVIDEVHMIEDSERGHRLDGVIGRLKYVASG--- 374
                                   9977762566667766699******************99999******************************654443... PP

                                   TSEEEEEESSBS CS
                                   xxxxxxxxxxxx RF
                          DEAD 159 qrqvivlSATlp 170
                                     q+i lSAT+ 
  gi|91772248|ref|YP_564940.1| 375 -AQFIYLSATVA 385
                                   .35*******97 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1         3   1.1e+04       6      35 ..      62      89 ..      59     120 .. 0.59
   2 !   57.4   0.0   4.6e-19   1.6e-15      11     109 ..     436     535 ..     420     537 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3
                                  HHHHHHHTTTTSEEEEEESSHHHHHH.HHHH CS
                    Helicase_C  6 llellkleeeggkilifvntidrlek.vkll 35
                                  ++ell   ++ ++ili +++ ++ e  v+ l
  gi|91772248|ref|YP_564940.1| 62 FIELL---RISERILIDIESEKSSEAaVREL 89
                                  45555...77888888888888665452222 PP

  == domain 2  score: 57.4 bits;  conditional E-value: 4.6e-19
                                   HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEES CS
                    Helicase_C  11 kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinf 91 
                                   +++ ++g+++if+n+++++   + + +  +i + ++h+ l+ +er+++ ++f kg++ v+++t +++ G+d+p ++ Vi+ 
  gi|91772248|ref|YP_564940.1| 436 SSKGHRGQTIIFTNSRRNC---HSIAQAISIPASPYHAGLSMEERKKVERRFEKGDIPVVVTTAALAAGVDFP-ASQVIFE 512
                                   567899*************...56656669******************************************9.5666666 PP

                                   SSS.....SSHHHHHHHHTTSSS CS
                    Helicase_C  92 dlp.....rnvtsyiqriGRtgR 109
                                   +l       n++++ q+ GR+gR
  gi|91772248|ref|YP_564940.1| 513 SLAmgiewLNMQEFLQMLGRAGR 535
                                   66657777789************ 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 !   36.3   0.1   1.5e-12   5.5e-09      23     169 ..     232     384 ..     188     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.5e-12
                                   TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG..........GEEEESSS-B-- CS
                        ResIII  23 rdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke......igkkvsgdkkka 96 
                                   ++++ l+   T tGKTl+  ++ ie++l+ ++  k+l lvp  +l +q +++f+k +s    +       +k+       +
  gi|91772248|ref|YP_564940.1| 232 ERRNQLVTSVTATGKTLIGeIAGIENILHGHG--KMLYLVPLVALANQKYDQFNKRYSGIGLNtsirvgSSKI-------R 303
                                   5667789999******************9877..*******************99999887655555432222.......2 PP

                                   ............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHH...HHT-.--SEEEEE CS
                        ResIII  97 .....kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swrei...lekf.keavllgl 165
                                        k+k+  +++i+v t++ ld ++    ++ +  l +++  ++iDE+H + +++       +   l+++ + a  ++l
  gi|91772248|ref|YP_564940.1| 304 tsktkKMKRGLDADIIVGTYEGLDVIL----RTGDADLLGQIGTVVIDEVHMIEDSErghRLDGVigrLKYVaSGAQFIYL 380
                                   23333468999****************....88999999****************85333333334555555244889999 PP

                                   ESS- CS
                        ResIII 166 TATp 169
                                   +AT 
  gi|91772248|ref|YP_564940.1| 381 SATV 384
                                   9997 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 !   16.8   0.0   5.9e-07    0.0021      98     193 ..     220     356 ..      24     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-07
                                   -............................................EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHH CS
                                   x............................................xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N  98 p............................................tLivvPa.slldqWeneierhvsssalrvlvyggqk 133
                                   p                                            +L +vP  +l++q ++++++  s+  l+  +  g++
  gi|91772248|ref|YP_564940.1| 220 PvqslsiekgllerrnqlvtsvtatgktligeiagienilhghgkMLYLVPLvALANQKYDQFNKRYSGIGLNTSIRVGSS 300
                                   0555555555555555555555556666666666666666666668999**99********************99999998 PP

                                   H-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 134 kmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknst 193
                                   k + + ++ + k   d+d+++ tY+ l     +    + l q+    vv+DE h+++ s+
  gi|91772248|ref|YP_564940.1| 301 KIRTS-KTKKMKRGLDADIIVGTYEGLDVIL-RTGDADLLGQIG--TVVIDEVHMIEDSE 356
                                   76666.445778889*************555.667788888875..7*********9885 PP

>> APO_RNA-bind  APO RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.7e-05      0.13     105     180 ..     435     505 ..     426     509 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                  APO_RNA-bind 105 vgkvGheikdckGpssskrkglheWvkgsiedvlvpiesyhlydrlgkrikheerfsidripavvel.ciqaGvdlp 180
                                   v+++Gh+ ++     +++r+  h+ +    + + +p   yh    +++r k e+rf+   ip vv    + aGvd+p
  gi|91772248|ref|YP_564940.1| 435 VSSKGHRGQTII--FTNSRRNCHSIA----QAISIPASPYHAGLSMEERKKVERRFEKGDIPVVVTTaALAAGVDFP 505
                                   556666655554..345677777655....5688*****************************997626899***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (825 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 4578.39
//
Query:       gi|91772249|ref|YP_564941.1|  [L=300]
Description: hypothetical protein Mbur_0180 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.001   18.5   0.1     0.0024   17.3   0.1    1.6  1  ATPase         KaiC
     0.0061   15.7   0.6       0.01   15.0   0.6    1.3  1  Lipoprotein_9  NLPA lipoprotein
  ------ inclusion threshold ------
      0.023   13.9   0.0      0.035   13.2   0.0    1.3  1  PAXNEB         PAXNEB 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 !   17.3   0.1     4e-07    0.0024       2     226 ..      71     293 ..      70     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4e-07
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwd.....lekl 77 
                                   +tgI  lD+ l gG+p  ++v  + +p +    +++ Fl++  ++  +++ + t+  +++ +++++ +   d     + ++
  gi|91772249|ref|YP_564941.1|  71 PTGIYVLDRSLGGGLPLSSMVYFSADPRS----MSEVFLYEFTQS--RKTYYFTTGRRPKYIQRDIINQNLDpsriiFVDI 145
                                   8**************************87....99999*999777..99**********7777777666666111114555 PP

                        ATPase  78 eeegklaiidasesaeesaee.kdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvl.kkl 154
                                    +e  ++ +  + ++ +  +e  d++ +e    +l+++ ++ +    +++ D+ t +   ++ +v    l++l++++ ++ 
  gi|91772249|ref|YP_564941.1| 146 YSEYYFTPLGDMIDNVG--NEhIDSKIIEFTEYNLQNIQNDAGDedINIIFDNFTFF---MNLNVNPGLLKRLTNIIyENS 221
                                   55544444433333333..22256666677777999999999994446778*****9...444455555666666665555 PP

                        ATPase 155 gvTailvsekss..seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikv 226
                                   + T+ ++       s++   +++v +  +d ++ ++++ +++++v  l i k+Rg   +++++ f+I+e g+++
  gi|91772249|ref|YP_564941.1| 222 KETNSMTYLYALkgSQDDLIENEVLN-TSDVIFDVKVDHNADHIVSKLTIPKIRGMVPNSDVLKFNISE-GVQI 293
                                   566666654433448899999*****.****************************************97.4554 PP

>> Lipoprotein_9  NLPA lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.6   1.7e-06      0.01      21      76 ..     161     216 ..     149     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-06
                                   HHTTTEEEEEEEESSSSHHHHHHHTTSSSEEE.EEEHHHHHHHHHHTT-.EEEEEEE CS
                 Lipoprotein_9  21 lkkkgldleiveFtdyvqpNkaladgeiDana.FQhlpyLeqfnkekgkklvavgnt 76 
                                   + ++++d +i+eFt+y+ +N + ++g+ D+n+ F+   ++ + n + g  l++++n+
  gi|91772249|ref|YP_564941.1| 161 VGNEHIDSKIIEFTEYNLQNIQNDAGDEDINIiFDNFTFFMNLNVNPGL-LKRLTNI 216
                                   56788999***********************559****99998887666.6666655 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.9e-06     0.035       3      41 ..      54      92 ..      52     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-06
                        PAXNEB  3 kpipGtrpSphdgqlltStGtpsLDklLgGGLplGsill 41
                                  ++ip +++ + ++ ++  tG+  LD+ LgGGLpl s++ 
  gi|91772249|ref|YP_564941.1| 54 NQIPEMQTPVYTAPIISPTGIYVLDRSLGGGLPLSSMVY 92
                                  677888888889999999****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1808.39
//
Query:       gi|91772250|ref|YP_564942.1|  [L=254]
Description: methylthioadenosine phosphorylase [Methanococcoides burtonii DSM 6242]
Scores for 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-37  126.5   0.2    9.6e-37  126.5   0.2    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.2   5.4e-41   9.6e-37      42     228 ..      41     226 ..       4     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 5.4e-41
                                   EEEEEEE--......SSHHHHHHHHHHHHHHHC--SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCC CS
                     PNP_UDP_1  42 kpvvivstG......iGkpnaavvaeirllkefgvkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyf 116
                                   k + ++s        + +++++++a i+++ e gvk+ii+++++G + +d ++G +v++dd+i++   + +++++     +
  gi|91772250|ref|YP_564942.1|  41 KSIAMISRHsgaaehVPPHMINYRAIIWAIREIGVKRIIATNSVGTM-KDHPIGSFVVTDDFIDLNKSRISTFYDKN-TVH 119
                                   44444333345888899******************************.****************8888888888887.*** PP

                                   CTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEE CS
                     PNP_UDP_1 117 pdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvv 197
                                   +d++++ +++ + ++l  ++ ++g ++ rG++++++g+++et+ae+++++++g d+v+M++ ++++lArel++++a+i+++
  gi|91772250|ref|YP_564942.1| 120 VDMTEP-YCHIISKCLMDSLDKKGLNYTRGTYVCTEGPRFETRAEIAMMSTFG-DVVGMTGLPEVVLARELELCYASICTI 198
                                   ******.**********************************************.*************************** PP

                                   EETTTBETTCTCH.HCCCHHHHHHHHHHHHH CS
                     PNP_UDP_1 198 sdlaaggadaeatheeveefaqeaaknaaal 228
                                   +++a g +d++ t +ev e     a++  +l
  gi|91772250|ref|YP_564942.1| 199 TNQACGMTDNKITADEVVEK---LATTQDIL 226
                                   **999988877555555444...44444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1538.56
//
Query:       gi|91772251|ref|YP_564943.1|  [L=378]
Description: hypothetical protein Mbur_0183 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     2e-120  402.3   8.3   2.3e-120  402.1   8.3    1.0  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
       0.03   14.5   0.1       0.06   13.6   0.1    1.6  1  NusG_add  NusG additional domain


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 !  402.1   8.3  2.5e-124  2.3e-120       1     335 []       2     350 ..       2     350 .. 0.99

  Alignments for each domain:
  == domain 1  score: 402.1 bits;  conditional E-value: 2.5e-124
                        DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgvea 81 
                                   +tLv+c+DrD+Dlg+ka+v++P++Gre++++aav+la++dPeDSD+N++fg+++v +eL+++g d+e+++ +Gd++vg+ +
  gi|91772251|ref|YP_564943.1|   2 RTLVICIDRDNDLGEKANVSSPIIGREDNIKAAVELATVDPEDSDSNTIFGGVNVLNELHSKGIDAEIVTFAGDKNVGIIS 82 
                                   69******************************************************************************* PP

                        DUF373  82 drkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrktiLvplG 162
                                   d+ki  qld  l++ ++++ai++sDGaeDe++lpi+qsr+k+dsvkr+vV+qs n+Estyy+lk+a++dp++++t++vp+G
  gi|91772251|ref|YP_564943.1|  83 DQKIVVQLDAFLEENDITNAIFISDGAEDETLLPIVQSRIKIDSVKRIVVQQSANLESTYYILKNAFNDPKISQTFFVPIG 163
                                   ********************************************************************************* PP

                        DUF373 163 lllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligiisgyisle 243
                                   l+ liya++ll+++pe a++ i++++G+y+l+rGf+ld+ ++ l e++k s++eg++tfvt+++a++l++i+++ g i+l+
  gi|91772251|ref|YP_564943.1| 164 LTALIYAIFLLANYPEGAIIGISAAIGAYMLYRGFNLDQPFALLRERMKGSFYEGQMTFVTNTIAIILAVIATMIGAITLW 244
                                   ********************************************************************************* PP

                        DUF373 244 svss..asvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvlygasaylls... 319
                                   ++ +  + +++gl+tl+++fi+ +v+w+++ail+a +gk++d     ++++  + ++  ++++a+gl+++gas+y+l    
  gi|91772251|ref|YP_564943.1| 245 KYFTtgGGWYYGLITLFTVFINVTVWWYVIAILFANIGKMVDLKR--NDHFSLKDVSPSLFITAMGLLFWGASTYILTiga 323
                                   ***99999**********************************655..778999***********************99*** PP

                        DUF373 320 ...........lsilalslvvgivval 335
                                              ++++++s+v++i++al
  gi|91772251|ref|YP_564943.1| 324 fpgatdspnfsIQYFIYSVVGAIIIAL 350
                                   ************************986 PP

>> NusG_add  NusG additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.7e-06      0.06      74     107 ..     122     155 ..      78     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-06
                      NusG_add  74 veveklkrivvkredneldvyvipldvfdsaavk 107
                                   ++ + +krivv+++ n +  y+i +++f+  ++ 
  gi|91772251|ref|YP_564943.1| 122 IKIDSVKRIVVQQSANLESTYYILKNAFNDPKIS 155
                                   78899************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2389.03
//
Query:       gi|91772252|ref|YP_564944.1|  [L=207]
Description: hypothetical protein Mbur_0184 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-31  107.8   0.1    5.6e-31  107.5   0.1    1.1  1  MAF_flag10     Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.025   14.4   0.1       0.05   13.5   0.1    1.6  1  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
      0.038   14.0   0.1      0.063   13.3   0.1    1.3  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 !  107.5   0.1   9.4e-35   5.6e-31      15     169 ..      46     187 ..      31     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 9.4e-35
                    MAF_flag10  15 lkellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgd 94 
                                   l+el+   +g k+++++g+ P+L ++l+++k   ++ v+i+ad+a+ +L+++gI+P ++v+ lD+   + e   +a+k+g+
  gi|91772252|ref|YP_564944.1|  46 LEELI---SG-KDVLVCGNAPTLAQELDQVK--IEDHVVITADGATATLVDRGIIPAVIVTdLDG---DVEKEIQANKEGS 117
                                   34444...57.*******************9..5789999*************************...666668888888* PP

                    MAF_flag10  95 iplvfasgvnpellkkykgpkiflvtgstqa.lelleeekneilfgGgsvantaldlAvklgfkeIiliGqDlayt 169
                                   i +++a+g+n+el+ ky ++ ++++ +++ a + ++       +fgG+++++++++lA ++++ +I+l+G+D+  +
  gi|91772252|ref|YP_564944.1| 118 IAVIHAHGDNIELILKYAPRFKNIIGTTQAApFGNI------YNFGGFTDGDRCVFLAGEFNAASITLAGFDFDDE 187
                                   **********************97775444356666......8******************************876 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   0.1   8.4e-06      0.05      26      64 ..      52      92 ..      32     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-06
                                  -SEEEEEE.EEEGGGCS-TTT.HHHHTTB-EEEEEEEEEEE CS
                   ACP_syn_III 26 akrvLvig.aetlskilDwkd.rstavlfGDGAgAvvleas 64
                                   k vLv+g a tl++ lD+ + ++ +v+ +DGA+A+++ ++
  gi|91772252|ref|YP_564944.1| 52 GKDVLVCGnAPTLAQELDQVKiEDHVVITADGATATLVDRG 92
                                  499****867899******88799999***********886 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.063       7      62 ..      74     124 ..      68     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                 TPK_catalytic   7 naslrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefyeskgteivkkp 62 
                                   + ++++ aDg++  l+     +++++p viv DlD   ++  +  ++  +++++ +
  gi|91772252|ref|YP_564944.1|  74 EDHVVITADGATATLV-----DRGIIPAVIVTDLDGDVEKEIQANKEGSIAVIHAH 124
                                   56899***********.....99************999988888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1346.90
//
Query:       gi|91772253|ref|YP_564945.1|  [L=1058]
Description: isoleucyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for 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-198  660.5   4.1   2.2e-198  660.3   3.3    1.4  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    5.3e-33  114.1   0.4    1.6e-32  112.6   0.4    1.9  1  Anticodon_1   Anticodon-binding domain of tRNA
    2.4e-26   92.4   7.5    2.3e-12   46.4   0.3    4.0  3  tRNA-synt_1g  tRNA synthetases class I (M)
    4.7e-06   26.2   0.0    2.4e-05   23.8   0.0    2.0  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
     0.0031   16.5   0.2       0.04   12.8   0.0    2.5  3  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.084   12.9   0.2       0.42   10.6   0.0    2.3  3  Thioredoxin   Thioredoxin


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 !  660.3   3.3  7.5e-202  2.2e-198       2     601 ..      18     635 ..      17     636 .. 0.97
   2 ?   -3.6   0.0      0.79   2.3e+03     398     417 ..     762     781 ..     744     782 .. 0.79

  Alignments for each domain:
  == domain 1  score: 660.3 bits;  conditional E-value: 7.5e-202
                   tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvek 82 
                                   + e+We+++++++ +e++k +k+f +vdgPPy tG++H+G a++k++kd + ry +m+ ++ l + GwD++Gl+ie kve 
  gi|91772253|ref|YP_564945.1|  18 VHEFWEANNAYRSVREHRKGAKKFYFVDGPPYTTGHIHLGTAWNKIIKDSILRYMSMNDHDILDRAGWDMHGLPIEVKVEG 98 
                                   679****************************************************************************** PP

                   tRNA-synt_1  83 klgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklv 163
                                    lg + kk+ + +g+ +f+ek++e++ ++++++++q++ lGv++D++++y+Tl++e+ ea ++++++  dk l+  gk++v
  gi|91772253|ref|YP_564945.1|  99 ALGFESKKDIETYGVGNFIEKCKEFALRQKDDMTEQFQTLGVWLDWEDPYMTLKDEYIEAAWWTLKQAQDKNLLETGKRVV 179
                                   ********************************************************************************* PP

                   tRNA-synt_1 164 nwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv........itkeklila 236
                                   nw+++++ta++++Evey+d +d++++++f+l+d++++ +vi+TTtP+T++++ avav+pe++y+           e li+a
  gi|91772253|ref|YP_564945.1| 180 NWCPRCETAIADAEVEYEDREDPSTYIKFKLKDEDNTFVVIWTTTPWTIPSNIAVAVHPEFEYSkvkaisenSATEILIIA 260
                                   ***************************************************************999*9998878899**** PP

                   tRNA-synt_1 237 eallkslvkke..sekkiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                   + l++++++     +++il ++ gk+Leg  +e+pl       ++ + +i + dyv++++ tG+V+iaP+h+ dD+evg k
  gi|91772253|ref|YP_564945.1| 261 SELVENVLRIGryLDYEILSTMSGKDLEGTVYEHPLadlvplqAEIEHRICNADYVTADS-TGCVHIAPGHGVDDFEVGVK 340
                                   *******998766899***********************999999999*********997.******************** PP

                   tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkelad 389
                                   ++ ++ +++  +g +t+ea+++ g+++ da++ v+++l e+gll+ +  i+h +++c+r k+ iiy ateqWf ++ el++
  gi|91772253|ref|YP_564945.1| 341 NEFPIFCPVGPNGSYTHEAGKYCGMNILDANRVVMDDLLERGLLMAERMISHRYGHCWRCKTAIIYLATEQWFLKIGELKE 421
                                   ********************************************************************************* PP

                   tRNA-synt_1 390 aalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekea 469
                                   ++l++++kv+++p++ + +r+++w+e ++dWciSRqr+WG +ip++  ++ + ++v+   kel +     ++ + +l++  
  gi|91772253|ref|YP_564945.1| 422 DMLEEIKKVNWTPEWaGSARFKDWIEGARDWCISRQRYWGIPIPVWKCSSCNSLTVVGTRKELIE--RSGADPHIELHRPY 500
                                   ***************99***************************************999999988..56666777889999 PP

                   tRNA-synt_1 470 kdkl...kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePf 547
                                   +dk+    +  g+++++edv+DvWF+S+    +tl +p++ +e++++ +pad+++eG D++rgW+++ +  s+  +g++P+
  gi|91772253|ref|YP_564945.1| 501 VDKVtipCECGGTMKRVEDVFDVWFDSAVASWATLRFPHQ-KEKFNEWWPADFITEGHDQTRGWFYSQLGASMVAFGKAPY 580
                                   999988666679****************************.9*************************************** PP

                   tRNA-synt_1 548 kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                   k+vl+hg+++d+ G+KmSKs+gNvi+p +vi+k gad lR +++  s   +d+++
  gi|91772253|ref|YP_564945.1| 581 KNVLMHGFTLDGSGKKMSKSIGNVIQPAEVIDKFGADTLRSYVLsASAPWEDLKF 635
                                   ****************************************999966777777765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.79
                   tRNA-synt_1 398 vqfvpkskekryaswleniq 417
                                   + f+p+ +e++y+++++ni 
  gi|91772253|ref|YP_564945.1| 762 APFMPHLAEEMYQNLVRNID 781
                                   5699**************97 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 !  112.6   0.4   5.4e-36   1.6e-32       1     149 [.     684     835 ..     684     839 .. 0.90

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 5.4e-36
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPf 80 
                                   d+wils+++ +++ev++a++   ++ka +++ ef+++dl++wy++l++pr + e +++++  +++vl++v+ t  +l+aPf
  gi|91772253|ref|YP_564945.1| 684 DKWILSRMQTVIAEVNKAMDARLLHKAMRSINEFVLEDLSRWYIQLIRPRTWVEADNPDKLaVYRVLYDVFVTTAKLIAPF 764
                                   9****************************************************99988866689***************** PP

                   Anticodon_1  81 mPfitEelwqr.....eeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselk 149
                                   mP+++Ee++q+          + + +i+l++wp  +e l ++ l e++++++++iv+a  ++r++ + k +++++
  gi|91772253|ref|YP_564945.1| 765 MPHLAEEMYQNlvrniD---ENAPVTIHLCDWPVVNEALvDTSL-EAQMKVARSIVEASSNARQKVGRKLRWPVS 835
                                   ***********875331...256699*******95545557777.99******************9999998865 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   9.1e-10   2.7e-06       8      58 ..      48      98 ..      42     198 .. 0.66
   2 !   21.2   0.2   3.4e-08    0.0001     168     238 ..     396     465 ..     387     474 .. 0.87
   3 !   46.4   0.3   7.8e-16   2.3e-12     242     381 ..     518     652 ..     502     655 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 9.1e-10
                                  B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH CS
                  tRNA-synt_1g  8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek 58
                                  pY++g++HlG + + i+ D + Ry  ++++++l  +g D+hG pie+k e 
  gi|91772253|ref|YP_564945.1| 48 PYTTGHIHLGTAWNKIIKDSILRYMSMNDHDILDRAGWDMHGLPIEVKVEG 98
                                  9*********************************************99763 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 3.4e-08
                                   .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                  tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                   ++  ++++ ++  te++f+k+ ++++++ e i++ + + e   +   k+w++   +d++isr+  wGip+P
  gi|91772253|ref|YP_564945.1| 396 HCWRCKTAIIYLATEQWFLKIGELKEDMLEEIKKVNWTPEWAGSARFKDWIEG-ARDWCISRQRYWGIPIP 465
                                   6888999999999*******************7777556666677889**976.9***************9 PP

  == domain 3  score: 46.4 bits;  conditional E-value: 7.8e-16
                                   CEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEE..EGGGHH..HHHTHHHHHHHHTT----S-EEEE CS
                  tRNA-synt_1g 242 kkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfi..gkdiik..FHtifwPaillgaelklpkkvvah 318
                                   + v+ VW+d  +   +++        ++ek++e+W +        fi  g d ++  F +  + a + + +    k+v  h
  gi|91772253|ref|YP_564945.1| 518 EDVFDVWFDSAVASWATLRFPH----QKEKFNEWWPA-------DFIteGHDQTRgwFYSQ-LGASMVAFGKAPYKNVLMH 586
                                   67899****9998777777665....679******44.......45522566654324444.456667778888899**** PP

                                   --.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHH..HHHHHHHCCC CS
                  tRNA-synt_1g 319 ey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedf..vervNseLad 381
                                   ++ l  +gkK+SkS g+v+++ e+++++ ad+lR y+++++   +Dl+f+w+++  v+r+N+ L +
  gi|91772253|ref|YP_564945.1| 587 GFtLDGSGKKMSKSIGNVIQPAEVIDKFGADTLRSYVLSASAPWEDLKFNWDELatVHRTNNILWN 652
                                   *956789*********************************************97335677877665 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 ?   -0.8   0.0      0.26   7.6e+02      21      48 ..      52      79 ..      34      80 .. 0.84
   2 !   23.8   0.0     8e-09   2.4e-05     228     296 ..     570     640 ..     554     645 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.26
                                  S--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdv 48
                                   ++hlG a + ++ D + r++ + ++d+
  gi|91772253|ref|YP_564945.1| 52 GHIHLGTAWNKIIKDSILRYMSMNDHDI 79
                                  679*****************99988776 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 8e-09
                                   HHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-.TTS-EEE-HHHH CS
                  tRNA-synt_1e 228 qseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsah.yrsqldfkeell 296
                                    s+ af+  ++ +  +h   l   g+kmsks++n+i+  +v+ kf + +lR ++lsa    + l+f+ ++l
  gi|91772253|ref|YP_564945.1| 570 ASMVAFGkAPYKNVLMHGFTLDGSGKKMSKSIGNVIQPAEVIDKFGADTLRSYVLSASaPWEDLKFNWDEL 640
                                   577788867899999**999*******************************99987641234566665555 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 ?    0.5   0.0     0.075   2.2e+02       5      57 ..      24      74 ..      20      84 .. 0.68
   2 ?   -4.2   0.2         2   6.1e+03     212     227 ..     422     437 ..     417     438 .. 0.78
   3 !   12.8   0.0   1.3e-05      0.04     269     322 ..     584     638 ..     551     645 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.075
                  tRNA-synt_1f  5 dklaeklieerkkkka.ekdevvvesGispSGliHiGnlrevltadlvaralrk 57
                                   + a + ++e+   ++  k+ + v+    + G+iH+G++ + +  d + r ++ 
  gi|91772253|ref|YP_564945.1| 24 ANNAYRSVREH---RKgAKKFYFVDGPPYTTGHIHLGTAWNKIIKDSILRYMSM 74
                                  44444434333...33256777888778899*******9988888888776655 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 2
                  tRNA-synt_1f 212 diregngKLqWkvdwa 227
                                   d+ e   K +W  +wa
  gi|91772253|ref|YP_564945.1| 422 DMLEEIKKVNWTPEWA 437
                                   666778999******8 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 1.3e-05
                  tRNA-synt_1f 269 vvYelillkggekmssSkGnvltledwlevaepevlr.flilrrkPkkakkldld 322
                                   ++  + l+  g+kms+S Gnv+ ++++++    ++lr +++  + P + +k++ d
  gi|91772253|ref|YP_564945.1| 584 LMHGFTLDGSGKKMSKSIGNVIQPAEVIDKFGADTLRsYVLSASAPWEDLKFNWD 638
                                   455566666777****************999999888244555678888887776 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3   6.8e+03      28      34 ..     180     186 ..     177     198 .. 0.82
   2 ?   -3.9   0.0       4.8   1.4e+04      34      51 ..     759     776 ..     756     782 .. 0.78
   3 ?   10.6   0.0   0.00014      0.42      43      78 ..    1018    1054 ..    1014    1058 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                   TTSHHHH CS
                   Thioredoxin  28 pwCghCk 34 
                                   +wC+ C 
  gi|91772253|ref|YP_564945.1| 180 NWCPRCE 186
                                   7*****6 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.8
                                   HCHHHHHHHHHHHCTTTS CS
                   Thioredoxin  34 kalaPeleklaeelkdkv 51 
                                   k +aP++ +laee+ +++
  gi|91772253|ref|YP_564945.1| 759 KLIAPFMPHLAEEMYQNL 776
                                   789999999999987654 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00014
                                    HHHHCTTTSEEEEEETTTSHHHHHHTT-SSSS.EEEE CS
                   Thioredoxin   43 laeelkdkvklakvdvdenedlakkyevegiP.tlkl 78  
                                    +a+e++++v ++ +dv++  +lak+++vegiP t+ +
  gi|91772253|ref|YP_564945.1| 1018 IAKEVRANVLVIGLDVETTGELAKEWNVEGIPmTIAI 1054
                                    7899999*************************44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1058 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.49
# Mc/sec: 6487.57
//
Query:       gi|91772254|ref|YP_564946.1|  [L=441]
Description: L-lysine 2,3-aminomutase [Methanococcoides burtonii DSM 6242]
Scores for 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   23.4   0.0    0.00011   22.3   0.0    1.6  1  Fer4_14         4Fe-4S single cluster domain
    0.00021   21.6   0.0    0.00039   20.7   0.0    1.6  1  Fer4_12         4Fe-4S single cluster domain
    0.00031   21.2   0.0     0.0013   19.1   0.0    2.0  1  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.019   15.0   0.4        5.6    7.1   0.0    3.0  4  Colicin_Pyocin  Colicin immunity protein / pyocin immunity pr
      0.077   12.8   0.1       0.25   11.2   0.0    1.8  2  Sigma54_CBD     Sigma-54 factor, core binding domain


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.1e-08   0.00011       7      91 ..     152     230 ..     145     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.1e-08
                       Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwlet 87 
                                    C+  C++C++ +++      +++++++e+ ++ l+++  +++ + +tGG+P+         +l+kr+ e + e +i+   
  gi|91772254|ref|YP_564946.1| 152 TCHTFCTFCFRWAQFTGMKDLKFASREIETLVSYLQEHPEVKD-VLFTGGDPMTM-----SANLLKRYIEPILEADIRTIE 226
                                   69**************999999999999999988888877666.*********44.....667888888888777777665 PP

                       Fer4_14  88 ngtl 91 
                                   n  +
  gi|91772254|ref|YP_564946.1| 227 NIRI 230
                                   5544 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 !   20.7   0.0   1.1e-07   0.00039      12      82 ..     150     220 ..     132     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpenaeallelvkevkee 82 
                                    + C   C +Cf  +     +  +f +  +e ++  l++ ++++++ ++GG+P+  + a+ l + ++ + e+
  gi|91772254|ref|YP_564946.1| 150 GQTCHTFCTFCFRWAQFTGMKDLKFASREIETLVSYLQEhPEVKDVLFTGGDPMT-MSANLLKRYIEPILEA 220
                                   478*********6666666666677899999****99964899***********9.6666666666666555 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.7e-07    0.0013       5      83 ..     151     233 ..     148     312 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.7e-07
                                   SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.....TTHHHHHHHHHHTCCCTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.....pdfvellerlaklavpgir 79 
                                   + C+  C+fC r+    ++ +      +ei+ +v +l +e+  vk v+++gg+p+       ++++e ++++  +  ++ir
  gi|91772254|ref|YP_564946.1| 151 QTCHTFCTFCFRWAQ-FTGMKDLKFASREIETLVSYL-QEHPeVKDVLFTGGDPMTMsanllKRYIEPILEADIRTIENIR 229
                                   57***********94.555555555667888888888.66666***********987444442333333222222244444 PP

                                   EEEE CS
                                   xxxx RF
                   Radical_SAM  80 itve 83 
                                   i   
  gi|91772254|ref|YP_564946.1| 230 IGTK 233
                                   4444 PP

>> Colicin_Pyocin  Colicin immunity protein / pyocin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         2     7e+03      26      47 ..      96     118 ..      89     120 .. 0.63
   2 ?   -3.5   0.0       3.4   1.2e+04      43      60 ..     136     153 ..     130     155 .. 0.78
   3 ?    4.6   0.0    0.0097        35      37      56 ..     182     201 ..     165     213 .. 0.78
   4 ?    7.1   0.0    0.0016       5.6      25      75 ..     242     292 ..     236     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                                   -SHHHHHHHHHHHH.HHH--TTT CS
                Colicin_Pyocin  26 kteeeedslvkefe.kitehPsg 47 
                                   ++eee +++++++   +  hP+g
  gi|91772254|ref|YP_564946.1|  96 ASEEEVQQAIHKIRlTLNPHPAG 118
                                   45666677777765246677776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.4
                                   --TTTTHHHHS--TTS-S CS
                Colicin_Pyocin  43 ehPsgsdlifypeedeed 60 
                                   +h   + ++f p +++++
  gi|91772254|ref|YP_564946.1| 136 QHKYNETVLFFPTQGQTC 153
                                   566677899999998875 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0097
                                   HHHHHH--TTTTHHHHS--T CS
                Colicin_Pyocin  37 efekitehPsgsdlifypee 56 
                                    ++ + ehP+ +d++f   +
  gi|91772254|ref|YP_564946.1| 182 LVSYLQEHPEVKDVLFTGGD 201
                                   467899**********8665 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0016
                                   --SHHHHHHHHHHHHHHH--TTTTHHHHS--TTS-SSHHHHHHHHHHHHHH CS
                Colicin_Pyocin  25 lkteeeedslvkefekitehPsgsdlifypeedeedspegilkeiKeWRak 75 
                                   + ++++++++++ f+++t+h +   ++ + ++  e +   + + iK+ Ra 
  gi|91772254|ref|YP_564946.1| 242 FVSDKDSEDILSLFSNVTDHNKHMAIMGHFNHPVELTTDTVKEAIKNIRAT 292
                                   567788899********************9****************99985 PP

>> Sigma54_CBD  Sigma-54 factor, core binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.9e-05      0.25     107     142 ..      84     122 ..      69     128 .. 0.79
   2 ?   -2.2   0.0      0.87   3.1e+03     115     131 ..     275     291 ..     251     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.9e-05
                   Sigma54_CBD 107 dlkklakklgl..seeelqealelIk.kLnPkPgrefss 142
                                   ++k++++ l+   seee+q+a+++I+ +LnP+P+ ++++
  gi|91772254|ref|YP_564946.1|  84 HYKEMKHLLHTaaSEEEVQQAIHKIRlTLNPHPAGQLDK 122
                                   677777766655599**********559******99864 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.87
                   Sigma54_CBD 115 lglseeelqealelIkk 131
                                   ++l+ ++++ea++ I++
  gi|91772254|ref|YP_564946.1| 275 VELTTDTVKEAIKNIRA 291
                                   45677777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3018.52
//
Query:       gi|91772255|ref|YP_564947.1|  [L=182]
Description: RNA-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-19   67.9   1.7    9.2e-19   67.2   1.7    1.3  1  PUA       PUA domain
    5.5e-05   23.8   0.3    0.00019   22.1   0.3    1.8  1  Pre-PUA   Pre-PUA-like domain
  ------ inclusion threshold ------
      0.018   15.3   0.1       0.03   14.6   0.1    1.4  1  UPF0113   UPF0113 PUA domain
      0.021   15.1   0.0      0.036   14.4   0.0    1.5  1  DUF1947   Domain of unknown function (DUF1947)


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 !   67.2   1.7     2e-22   9.2e-19       2      72 ..     101     171 ..     100     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2e-22
                                   EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                           PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveier 72 
                                    v+vd+gAvk++++ga++++pG+v+v++ + egd V iv e  g+++a+G+a++ + e+     gk+++ ++
  gi|91772255|ref|YP_564947.1| 101 VVTVDAGAVKFVVNGADIMCPGIVKVDDGLNEGDLVIIVEEThGKPLAIGRALVPATEMVGR-SGKAIKSIH 171
                                   599**************************************88****************988.456666555 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3   4.2e-08   0.00019       5      82 ..      23      91 ..      20      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.2e-08
                       Pre-PUA  5 fkvksntqlksSdrrkLraklleqfpslseeqleellpkkeevkvvklqgehvelyvvdgeplffqdregellPtlyt 82
                                   kvks+ ql++S + kL ++l ++f  +    ++++   k e    +   +  ++++vdg++lffq   +  +Pt++ 
  gi|91772255|ref|YP_564947.1| 23 LKVKSRVQLRKSAKNKLFKSLRSTFGDV----IDRISEYKLE----SAMADDFKIIIVDGKVLFFQM-GEVSFPTVRG 91
                                  589*******************999999....7777766555....33348999*************.8899****85 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   6.6e-06      0.03       3      53 ..     103     154 ..     101     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-06
                       UPF0113   3 vvkekaeklFLYGrdvlkesilkitesvkenqvvvV.lnengeplGiGkirk 53 
                                    v+  a k ++ G d++  +i+k++++++e++ v++   + g+pl+iG++  
  gi|91772255|ref|YP_564947.1| 103 TVDAGAVKFVVNGADIMCPGIVKVDDGLNEGDLVIIvEETHGKPLAIGRALV 154
                                   566667777788*****************777655427889*******9966 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.9e-06     0.036      12      61 ..      38      90 ..      27      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.9e-06
                                  HHHHHHHTTT--.-TT--...-EEEE-SS-EEEEETTEEEEEE.SSSEEE-HH CS
                       DUF1947 12 eileklkekyis.islesdk.iEieeekkeklYlingvpilfe.eekliPtLk 61
                                  ++++ l++   + i+  s+  +E +  +++k++ ++g+ ++f+ +e  +Pt++
  gi|91772255|ref|YP_564947.1| 38 KLFKSLRSTFGDvIDRISEYkLESAMADDFKIIIVDGKVLFFQmGEVSFPTVR 90
                                  55555555443314545544499999*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1196.52
//
Query:       gi|91772256|ref|YP_564948.1|  [L=126]
Description: hypothetical protein Mbur_0188 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-12   46.9   0.7    3.4e-12   46.5   0.7    1.2  1  SepF            Cell division protein SepF
     0.0071   16.0   0.1     0.0087   15.7   0.1    1.1  1  Transposase_31  Putative transposase, YhgA-like


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 !   46.5   0.7   3.8e-16   3.4e-12       1      72 []      43     116 ..      43     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.8e-16
                                   EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                          SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                   + v+e++++++ +++++++++g+i+++++++++     + r+++ l+ vv +++Gdi+ ++++ +l+tP++v+i
  gi|91772256|ref|YP_564948.1|  43 IRVAELTNLNELPDLKKEIYNGNILMIDISNIKAdkLMLDRALKDLKDVVVDVHGDIAGIKDDQVLVTPTGVRI 116
                                   7899**************************999877889*********************************98 PP

>> Transposase_31  Putative transposase, YhgA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   9.7e-07    0.0087     127     182 ..      45      99 ..      38     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.7e-07
                Transposase_31 127 slslldlfddpelakelykseflLvDltkvpddeilekrrlallllvqkhirqrdl 182
                                     +l +l + p+l+ke+y+ ++l++D+++++ d+++ +r l+ l  v+ +++  d+
  gi|91772256|ref|YP_564948.1|  45 VAELTNLNELPDLKKEIYNGNILMIDISNIKADKLMLDRALKDLKDVVVDVHG-DI 99 
                                   56778888899****************************99988888888874.54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 898.85
//
Query:       gi|91772257|ref|YP_564949.1|  [L=221]
Description: ZPR1-like zinc finger protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-37  126.9   0.0    9.1e-37  126.4   0.0    1.3  1  zf-ZPR1     ZPR1 zinc-finger domain
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.18   11.4   0.0    1.3  1  DUF2321     Uncharacterized protein conserved in bacteria (DU
       0.15   11.9   0.1        8.9    6.2   0.0    2.3  2  DUF3943     Domain of unknown function (DUF3943)


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 !  126.4   0.0   1.5e-40   9.1e-37       2     158 ..      20     173 ..      19     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1.5e-40
                       zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatveipe 82 
                                   +Cp C+ e+ + +    +iPyf+ev+ +s++C +Cg++ ++++++ ++e+  +r++lkve  edln +v++S+++t++ipe
  gi|91772257|ref|YP_564949.1|  20 SCPLCQ-EDLIIKWQGDEIPYFGEVMYISTSCCNCGFRFTDTMILAQKEP--MRFELKVEGLEDLNARVIRSTSGTIRIPE 97 
                                   7****6.99**999999*********************************..***************************** PP

                       zf-ZPR1  83 leleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegeepftlildDpagnSfi 158
                                   l+++++pg  +++++t++EG+L+++++ + +++g  ++++ +++++  e+ +++e++i+g+ p+t+i++Dp+gnS+i
  gi|91772257|ref|YP_564949.1|  98 LGIDVEPGsVSDSYVTNIEGILQRVQSVVVTATGWVKDDD-DAYARGLELQDQIEKAIAGDFPLTVIIEDPLGNSAI 173
                                   ********999******************65444444443.69********************************98 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.18      35      87 ..      16      66 ..      11     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                       DUF2321 35 ktitkcpkCsteirGkyyvegvislgkeyevpsyCkkCgkpyPWtkakleaak 87
                                  +t t+cp C+ ++  k + +++ ++g+ +++ + C +Cg ++  t++ + a k
  gi|91772257|ref|YP_564949.1| 16 ETRTSCPLCQEDLIIKWQGDEIPYFGEVMYISTSCCNCGFRF--TDTMILAQK 66
                                  57799**********************************887..555555554 PP

>> DUF3943  Domain of unknown function (DUF3943)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0015       8.9      17      54 ..      38      78 ..      36      93 .. 0.84
   2 ?    3.4   0.0     0.011        68      49      72 ..      97     119 ..      85     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0015
                       DUF3943 17 pyaGslyylaa..RsaglsfwesllyallgStlwElgvE.f 54
                                  py+G+++y +    ++g++f++++++a    + +El vE  
  gi|91772257|ref|YP_564949.1| 38 PYFGEVMYISTscCNCGFRFTDTMILAQKEPMRFELKVEgL 78
                                  9*******76522689************99999***99933 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.011
                       DUF3943  49 ElgvEfaekpSinDlivTplgGvv 72 
                                   Elg+   e+ S+ D +vT + G++
  gi|91772257|ref|YP_564949.1|  97 ELGID-VEPGSVSDSYVTNIEGIL 119
                                   88999.99**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1557.29
//
Query:       gi|91772258|ref|YP_564950.1|  [L=478]
Description: prolyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-26   93.1   0.0      3e-26   92.5   0.0    1.2  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.1e-21   76.8   0.0      2e-21   75.9   0.0    1.4  1  HGTP_anticodon  Anticodon binding domain
    2.8e-15   56.3   0.1    1.2e-14   54.2   0.0    2.1  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.52   10.5   0.0    1.9  1  ProRS-C_2       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 !   92.5   0.0   6.6e-30     3e-26       9     177 ..     106     274 ..      95     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 6.6e-30
                                   EEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES.GGGHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxx RF
                  tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha.easlddslrdlika 86 
                                    +++L+Pt+e++++ ++r + +rs  +LPlklyqi   +R+E++ +r+L+R+re++  k+++ +ha  +++ +++++ i++
  gi|91772258|ref|YP_564950.1| 106 VKLALRPTSETAIYPMYRLW-VRShADLPLKLYQIVNTFRYETKHTRPLIRLREITSfKEAHTVHAtWDEAASQVEEAIRL 185
                                   5799**************88.9**778*****************9**********8659*******7799*********** PP

                                   HHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  87 isriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaai 166
                                   + ++++rl +++   ++  +++  + ++++  ++ +++  +k++++gt++ lg+++++++++++ d ++++   + +c+++
  gi|91772258|ref|YP_564950.1| 186 YIEFYKRLAIPVLPSKRPsWDK-FPGADYTIAVDSLMP-DGKTLQVGTAHHLGDNFAKTFDIKYEDVDGEQVYAHQTCYGV 264
                                   **********986555555664.489999999999999.9***************************************** PP

                                   EHHHHHHHHHH CS
                                   xxxxxxxxxxx RF
                  tRNA-synt_2b 167 gveRllsaile 177
                                   + eR ++ +l+
  gi|91772258|ref|YP_564950.1| 265 S-ERCIATLLS 274
                                   *.****99886 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   4.4e-25     2e-21       1      92 [.     292     384 ..     292     386 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 4.4e-25
                                   SEEEEESSSS.HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                HGTP_anticodon   1 qvvviplnek.aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                   qvv+ip+  k  e++++ ++++++eL+aag+rv +dds++++g k+ +++++g+p+++++G+++l+++   + +rdt+e+e
  gi|91772258|ref|YP_564950.1| 292 QVVIIPIIFKePEAVLNACNDVKAELEAAGVRVTIDDSDKRPGSKYYKWEMKGVPLRIEIGPRDLKNEAAMLARRDTGEKE 372
                                   8******999766688***************************************************************** PP

                                   EEETTHHHHHHH CS
                HGTP_anticodon  81 rvsldelveklk 92 
                                   +v+l+++++++ 
  gi|91772258|ref|YP_564950.1| 373 QVPLASIKDEVL 384
                                   ********9986 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.64   2.9e+03       9      28 ..     163     183 ..     159     197 .. 0.77
   2 !   54.2   0.0   2.7e-18   1.2e-14       2      69 .]     413     478 .]     412     478 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.64
                                   HTT-EEEEEESS.GHHHHHHH CS
                     ProRS-C_1   9 ekkgfvlapWcg.eeecEekI 28 
                                   ++ + v a W++  ++ Ee I
  gi|91772258|ref|YP_564950.1| 163 KEAHTVHATWDEaASQVEEAI 183
                                   566789999999445777777 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 2.7e-18
                                   HHHHHHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                     ProRS-C_1   2 eefkealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                   +++ke++++ g++l+pWcgee+c  ++ e++ga +l+ip+d   ++++ kC +c k++ ++v+++r+Y
  gi|91772258|ref|YP_564950.1| 413 DDVKEKVQD-GIALVPWCGEEKCGLDLDEQVGAGILGIPTDM-DEDGTYKCPICSKETRTRVYVARTY 478
                                   788999976.8******************************7.68999*******************9 PP

>> ProRS-C_2  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.52      11      51 ..     410     449 ..     401     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                                   ..HHHHHHHCTTT-SEEEEE-.-GGG-SHHHHHHHSS-EEEE CS
                     ProRS-C_2  11 lllenikeklsekkGvvLvPf.neeiYneefeeeidasvLGe 51 
                                   + ++++kek+++  G+ LvP+  ee    +++e+++a +LG 
  gi|91772258|ref|YP_564950.1| 410 STVDDVKEKVQD--GIALVPWcGEEKCGLDLDEQVGAGILGI 449
                                   56899***9975..9*****956899999************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3065.44
//
Query:       gi|91772259|ref|YP_564951.1|  [L=347]
Description: hypothetical protein Mbur_0191 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.1   0.1        9.1    6.2   0.0    2.3  2  VirD1     T-DNA border endonuclease VirD1


Domain annotation for each model (and alignments):
>> VirD1  T-DNA border endonuclease VirD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0   0.00051       9.1      96     136 ..     102     142 ..      92     146 .. 0.88
   2 ?    3.3   0.0    0.0042        75      73     111 ..     244     287 ..     232     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00051
                         VirD1  96 npttdlealraeriafgkafadldgllrsilsvsrrridgc 136
                                    p  dl+a   e i    a  d++g++++ lsv  r  d  
  gi|91772259|ref|YP_564951.1| 102 VPFEDLGARYGEDIRNDVAVHDVEGIIKAALSVGERVRDDH 142
                                   5889*****************************99977755 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0042
                         VirD1  73 eailksigtlssniaallsayaenpttd.....lealraeriaf 111
                                    a +k +gt  sn++ + ++y  n  t      +eal+a+  a+
  gi|91772259|ref|YP_564951.1| 244 YAFMKHMGTDLSNVSIVTTSYVANDETAnfneiIEALEADMFAI 287
                                   577899***************87765422223367888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2555.54
//
Query:       gi|91772260|ref|YP_564952.1|  [L=197]
Description: 50S ribosomal protein L15e [Methanococcoides burtonii DSM 6242]
Scores for complete 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-84  280.1  11.2    9.4e-84  279.9  11.2    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
       0.25   12.0  10.9        0.1   13.3   2.6    2.1  2  FXMRP1_C_core   Fragile X-related 1 protein core C terminal


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 !  279.9  11.2     1e-87   9.4e-84       1     191 []       4     191 ..       4     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 279.9 bits;  conditional E-value: 1e-87
                                   -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS-- CS
                Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgr 81 
                                   ++y y+r++wk+++++++r l +erl+ +r+e +v+rverptr+drAr+LGYkakqGivv+rv+vrrG+++k  s++++gr
  gi|91772260|ref|YP_564952.1|   4 SFYGYIRDAWKNPDETYVRDLRWERLQVWRKEGSVTRVERPTRIDRARSLGYKAKQGIVVARVKVRRGSMRK--SRYIRGR 82 
                                   689*********************************************************************..******* PP

                                   -GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGGGT CS
                Ribosomal_L15e  82 kpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRelrG 162
                                   +++++g nk++  ks+q+i+eer++rk+pn++vLnSYwvgeDg++k+yEvilvDpsh++i++dk++nwic k h +R++rG
  gi|91772260|ref|YP_564952.1|  83 RTQHTGKNKITVGKSIQRISEERAARKYPNMEVLNSYWVGEDGKQKWYEVILVDPSHPVIKSDKNLNWICGKAHSGRVFRG 163
                                   ********************************************************************************* PP

                                   -SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                Ribosomal_L15e 163 ltsagkksRGlrkkglkgaekirgsrran 191
                                   +tsag+k+RG++++g +g+ek+r+s+r+n
  gi|91772260|ref|YP_564952.1| 164 KTSAGRKGRGMQTRG-TGTEKTRPSVRSN 191
                                   ***************.9********9985 PP

>> FXMRP1_C_core  Fragile X-related 1 protein core C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.6   1.1e-05       0.1       8      95 ..      21     107 ..      19     126 .. 0.77
   2 ?    4.0   1.3    0.0082        74      58      83 ..     162     191 ..     137     197 .] 0.50

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                 FXMRP1_C_core   8 VeqLrlErLqIDeqLRqigggsrppesnrsdkek..gystDeesgessssslggsrsysgRGrGrRGagatsgkygtnsea 86 
                                   V  Lr ErLq+    R+ g  +r   ++r d+++  gy + ++   +  + ++gs   s+  rGrR+++ +++k  + ++ 
  gi|91772260|ref|YP_564952.1|  21 VRDLRWERLQVW---RKEGSVTRVERPTRIDRARslGYKAKQGIVVARVKVRRGSMRKSRYIRGRRTQHTGKNKITVGKSI 98 
                                   5679******96...666666666666787777777*******9999988888888888889*****99987765555555 PP

                 FXMRP1_C_core  87 snasetese 95 
                                   +  se+   
  gi|91772260|ref|YP_564952.1|  99 QRISEERAA 107
                                   555555544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0082
                 FXMRP1_C_core  58 ggsrsysgRGrGr..RGagatsg..kygtn 83 
                                   +g+ s +++GrG   RG g +++  + ++n
  gi|91772260|ref|YP_564952.1| 162 RGKTSAGRKGRGMqtRGTGTEKTrpSVRSN 191
                                   222233445555544555555443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1361.36
//
Query:       gi|91772261|ref|YP_564953.1|  [L=151]
Description: hypothetical protein Mbur_0193 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-34  118.0   0.0    3.2e-34  117.7   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 !  117.7   0.0   1.8e-38   3.2e-34       1     119 []       4     132 ..       4     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 1.8e-38
                                   EEEEEEEE-TTC-HHHHHHHHHTTSTTS.........E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCC CS
                   RNA_binding   1 kievrafvhaTEdeekVlealsnllpee.........eveieeeeaeGhygnpitileaelekkka.kkvlkkllellree 71 
                                   +i+vr+ +haTEde++V++al+ +l ++         ++ +e+  +eG++gnpit+++  +++k + k+++ +++ +++ e
  gi|91772261|ref|YP_564953.1|   4 YISVRVSAHATEDESRVRSALDLFLLNSfdkgkctdtDKYVESLVVEGYHGNPITMFSSAIKRKPDtKAFAAFVRPKMTPE 84 
                                   69***********************9999*******98899**************************************** PP

                                   CHHHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEEE CS
                   RNA_binding  72 eikeLlkeleervdekgklylrldKQaaylgklslvegddvIkvkikv 119
                                   +++ L++e+++r+d++++++lr+dKQaa++g+++l++++d+I vk+k+
  gi|91772261|ref|YP_564953.1|  85 DVELLREEMPDRLDDDQMFHLRFDKQAAFNGRIKLSSSSDAIIVKVKI 132
                                   *********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1021.96
//
Query:       gi|91772262|ref|YP_564954.1|  [L=241]
Description: ribonuclease P protein component 3 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-49  166.8   0.0    5.5e-49  166.5   0.0    1.1  1  RNase_P_p30     RNase P subunit p30
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.036   13.7   0.0    1.4  1  SelB-wing_3     Elongation factor SelB, winged helix
       0.13   12.1   0.0       0.93    9.4   0.0    2.0  2  Staphostatin_A  Staphostatin A
       0.14   12.0   0.0        0.2   11.4   0.0    1.3  1  Amidohydro_2    Amidohydrolase


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 !  166.5   0.0   1.2e-52   5.5e-49       1     214 [.       7     208 ..       7     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 1.2e-52
                                   EEEEE-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.. CS
                   RNase_P_p30   1 ydlnipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl. 80 
                                   ydl i++ +d++++ +++i+ +++lg+ g+ ++++  ae + k + +              +g+++++ v+lv+s+pskl 
  gi|91772262|ref|YP_564954.1|   7 YDLSIHYVPDGKNTAEELISMAKHLGFAGIGLSNHSTAEGPLKSDGT--------------EGFDIFRTVELVASNPSKLh 73 
                                   8*************99********************95555554444..............59****************99 PP

                                   HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHHHHHH CS
                   RNase_P_p30  81 qrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaRrnfi 161
                                   + + k+r+k+d+lav++++e ++raa+en +vDi+++++t  + +gl+h+++++A+e++va+ +++  l+ ++g++R++ +
  gi|91772262|ref|YP_564954.1|  74 GLVGKYRNKVDVLAVHGGDEGINRAAVENSNVDILIHPFTP-KGSGLNHVLAKSASENNVAIAFDIDSLIMSRGGRRVHSL 153
                                   ***************************************98.99************************************* PP

                                   HHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTTH CS
                   RNase_P_p30 162 snarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeavse 214
                                   s++r++l l+r+   +++++S+A s ++lR+p++ii+L++++G+e+d+a  a+se
  gi|91772262|ref|YP_564954.1| 154 SHFRDYLALSRKydVPMLLTSNALSIFGLRAPREIIALAALFGMEKDEAIMALSE 208
                                   ****************************************************987 PP

>> SelB-wing_3  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     8e-06     0.036      11      29 ..     153     171 ..     151     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-06
                                   HHHHHHHHT--HHHHHHHH CS
                   SelB-wing_3  11 aaefRdllgtSRKyaiplL 29 
                                   ++ fRd l +SRKy +p+L
  gi|91772262|ref|YP_564954.1| 153 LSHFRDYLALSRKYDVPML 171
                                   789***********99987 PP

>> Staphostatin_A  Staphostatin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.17   7.8e+02      29      54 ..     109     134 ..      98     144 .. 0.80
   2 ?    9.4   0.0   0.00021      0.93      33      55 ..     205     227 ..     187     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.17
                Staphostatin_A  29 whpveledsplkiilskeidsdyvck 54 
                                    hp   + s l+ +l+k+ + + v  
  gi|91772262|ref|YP_564954.1| 109 IHPFTPKGSGLNHVLAKSASENNVAI 134
                                   68999999999999999999988865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00021
                Staphostatin_A  33 eledsplkiilskeidsdyvckl 55 
                                    l ++plki+ +k  d +yvc+ 
  gi|91772262|ref|YP_564954.1| 205 ALSETPLKIVQKKRHDKNYVCEG 227
                                   57899****************85 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.5e-05       0.2      93     127 ..      15      49 ..      10     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.5e-05
                                   SSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTT CS
                  Amidohydro_2  93 ldpedaaaeleraveelgfkGvrlnphvggddllg 127
                                   +d++++a+el+  +++lgf G+ l+ h   + +l 
  gi|91772262|ref|YP_564954.1|  15 PDGKNTAEELISMAKHLGFAGIGLSNHSTAEGPLK 49 
                                   699*********************99987666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1698.59
//
Query:       gi|91772263|ref|YP_564955.1|  [L=122]
Description: ribonuclease P-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-16   60.4   0.0    1.9e-16   60.1   0.0    1.1  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 !   60.1   0.0   1.1e-20   1.9e-16       1     102 [.      15     109 ..      15     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-20
                                   EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT--EETT CS
                 RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlitkieg 81 
                                   RY+++e++  +    +++++ll++i   +++l+Gd gl+++g   ++  f++  s +i+Rc r+ +++ +a+L+ +t+++g
  gi|91772263|ref|YP_564955.1|  15 RYFAFELIGGN---IVDRSDLLREIFLCASSLVGDNGLSECGV--RLLDFED--SKGIVRCLRDRMDMTRAVLASVTSVNG 88 
                                   9*********9...3678***********************99..6777777..9************************** PP

                                   EEEEEEEEEEESSHHHHHHHT CS
                 RNase_P_Rpp14  82 rpvvfrvvrvsGTikkaeeea 102
                                   +pv+++v+++sGT++ a  ++
  gi|91772263|ref|YP_564955.1|  89 KPVIIHVLGISGTVHGATTKY 109
                                   **************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1070.67
//
Query:       gi|91772264|ref|YP_564956.1|  [L=263]
Description: proteasome subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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  200.5   0.5    2.4e-59  200.0   0.5    1.2  1  Proteasome      Proteasome subunit
    1.4e-14   53.4   0.5    4.4e-14   51.8   0.1    2.0  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 !  200.0   0.5   2.7e-63   2.4e-59       1     189 [.      32     215 ..      32     216 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 2.7e-63
                                   HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                    Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                   vk+Gtt+ Gik+kdgvvl++dkr+t  s l++ +++eKif+id+higva++Gl+aDar+lv+rar+eaq    +y++pi v
  gi|91772264|ref|YP_564956.1|  32 VKRGTTAAGIKAKDGVVLIVDKRIT--SRLIEAESIEKIFQIDEHIGVATSGLVADARALVDRARVEAQINMATYDEPIGV 110
                                   79***********************..****************************************************** PP

                                   HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                    Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                   ++l +++++++q ytq++g+rp+g +lliagvd++  p+L++ dpsG+++e+k a+aiG g+++ ++ +e+  ++d+t+ee
  gi|91772264|ref|YP_564956.1| 111 KVLSKKICDHKQTYTQYGGVRPYGTALLIAGVDDNL-PRLFESDPSGALLEYK-ATAIGAGRNVFMETFEEMHRDDMTMEE 189
                                   *********************************777.***************8.*************************** PP

                                   HHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                    Proteasome 163 avelavkalkealerdklsgknievav 189
                                   av l  +al+ a++  k+ + ++ev+ 
  gi|91772264|ref|YP_564956.1| 190 AVMLGMEALYRASD-VKIDPATLEVGM 215
                                   *************9.779998888876 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.1   4.9e-18   4.4e-14       1      23 []       9      31 ..       9      31 .. 0.99
   2 ?   -1.0   0.0      0.16   1.5e+03      13      18 ..      67      72 ..      67      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.9e-18
                Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                  YDr++t+FSPdGRLfQVEYA +A
  gi|91772264|ref|YP_564956.1|  9 YDRAITVFSPDGRLFQVEYAREA 31
                                  *********************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.16
                Proteasome_A_N 13 RLfQVE 18
                                  ++fQ++
  gi|91772264|ref|YP_564956.1| 67 KIFQID 72
                                  79**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1557.85
//
Query:       gi|91772265|ref|YP_564957.1|  [L=230]
Description: RNA-associated protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-23   82.0   0.2    3.7e-23   81.4   0.2    1.3  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.8e-21   76.3   0.0    2.5e-21   75.8   0.0    1.2  1  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
      0.084   12.9   0.0       0.18   11.9   0.0    1.4  1  EFG_C     Elongation factor G C-terminus


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.2   6.1e-27   3.7e-23       4      88 .]       9      93 ..       6      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 6.1e-27
                                  EEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--HHH CS
                          SBDS  4 ivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsaee 86
                                  ++r+kkg+k++e++v+++ +le+++g +++++++l++e+iF+++ +G+ a +s+l +af+t+++ ei+  I+k+Geiq+++e+
  gi|91772265|ref|YP_564957.1|  9 VARLKKGSKHYEVLVDPDGALEFKKGGNVKIEDILAVESIFEDSGRGDHAAESDLTNAFQTDDVFEIAAYIIKHGEIQLTKEQ 91
                                  789*******************************************************************************9 PP

                                  HH CS
                          SBDS 87 rk 88
                                  rk
  gi|91772265|ref|YP_564957.1| 92 RK 93
                                  97 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 !   75.8   0.0   4.3e-25   2.5e-21       2     115 ..     100     217 ..      99     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 4.3e-25
                                   HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CCCHHH CS
                        SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikdkilk 82 
                                    +++i+ +a++++npqt++p+++++Ieka++e+++++++ k +++Q+  v+ka++ +ipi+++++++++++p    +++ k
  gi|91772265|ref|YP_564957.1| 100 TRQVISTIARNAINPQTRAPHPPGRIEKAMEEAKVHIDPLKGVDEQVNIVMKAIRPIIPIRFEEVEIAVKIP---SEYAGK 177
                                   689*********************************************************************...666666 PP

                                   HHHHH.HH.....S.EE......EEEEEEGGGHHHHHHHH CS
                        SBDS_C  83 lieqv.esqkvaekewe......vvvliePgaykeleefv 115
                                    + ++ +   +  ++we       vv i++g+++++  +v
  gi|91772265|ref|YP_564957.1| 178 SYGDIaKFGTMLRDNWEndgswvAVVKIPAGMQNDFYGLV 217
                                   666664444444444444444426777****999887665 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 ?   11.9   0.0     3e-05      0.18       8      71 ..     165     227 ..     163     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                                   EEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EE CS
                         EFG_C   8 kveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsf 71 
                                   ++ +++p+ey gk ++d+++    + d  ++++++v    +iP+    +f+  ++ lTkG ++ 
  gi|91772265|ref|YP_564957.1| 165 EIAVKIPSEYAGKSYGDIAKFGTMLRDNWENDGSWV-AVVKIPAGMQNDFYGLVNHLTKGDAET 227
                                   6789***************98888888888855555.558***99999************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1424.76
//
Query:       gi|91772266|ref|YP_564958.1|  [L=263]
Description: exosome complex RNA-binding protein Rrp4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   36.8   0.0    5.3e-09   35.7   0.0    1.6  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    6.1e-09   36.1   0.4    1.2e-08   35.1   0.4    1.6  1  KH_6      KH domain
    6.5e-05   22.7   0.4    0.00015   21.6   0.4    1.6  1  KH_1      KH domain
    0.00011   22.0   0.3    0.00032   20.4   0.3    1.9  1  KH_2      KH domain
     0.0008   19.7   0.2     0.0023   18.2   0.2    1.8  1  S1        S1 RNA binding domain
     0.0054   15.7   0.2     0.0075   15.2   0.2    1.2  1  DUF759    Borrelia burgdorferi protein of unknown function (D


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.8e-12   5.3e-09       1      34 [.       5      37 ..       5      40 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.8e-12
                                  EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEE CS
                        ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGt 34
                                  iV+PG+ l ++ + m+G+GTYv++g+iy+ + G+
  gi|91772266|ref|YP_564958.1|  5 IVIPGQLL-SEKKEMAGPGTYVKNGNIYSLLYGI 37
                                  9*******.***********************97 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.4   4.1e-12   1.2e-08       1      44 [.     137     183 ..     137     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 4.1e-12
                          KH_6   1 GmlfeVslslvrRll....nhvLeeLgkagpfeiavGlNGriWvkses 44 
                                   G ++eV +s+v+R++    + v + L+k+  +++ vG+NGriW+++++
  gi|91772266|ref|YP_564958.1| 137 GRIIEVVPSKVPRVIghggSMV-SILKKESNCDVFVGKNGRIWINGKD 183
                                   6689***********5553333.55567777**************987 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.4   4.9e-08   0.00015       5      63 ..     142     195 ..     138     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.9e-08
                                   EEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHH..HHHHHHH CS
                          KH_1   5 lvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.spea..vekAkel 63 
                                    vPs+ v+r+IG gGs++  +++e+++ + v k       +  + i G +++      A+e+
  gi|91772266|ref|YP_564958.1| 142 VVPSK-VPRVIGHGGSMVSILKKESNCDVFVGK-------NGRIWINGkDKDMdrLTTAIEM 195
                                   46766.************************753.......3468888866553345555555 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   1.1e-07   0.00032       5      69 ..     119     180 ..      97     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-07
                                   HHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                          KH_2   5 slaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                                   + +ve+++ + ++  +    ++ ii +  s+  +vIG+gGs++  ++ke + d+ + +++++++n
  gi|91772266|ref|YP_564958.1| 119 AMKVELSMREQGSRAL---SKGRIIEVVPSKVPRVIGHGGSMVSILKKESNCDVFVGKNGRIWIN 180
                                   5566666555555555...477899999**************************99999999998 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   7.7e-07    0.0023      11      75 .]      64     127 ..      58     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.7e-07
                                   EEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                            S1  11 eVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                   +V++vt+ + + e g + +g++++se + +++ ++  +   vGd v v+v +v k+ + + ls++
  gi|91772266|ref|YP_564958.1|  64 NVIDVTPSNWIMETGSPYDGLLHVSEFPKRVDSSEMRKFMDVGDCVIVRVKDVSKAMK-VELSMR 127
                                   6999999999999*****************8888888999****************99.999986 PP

>> DUF759  Borrelia burgdorferi protein of unknown function (DUF759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.5e-06    0.0075     245     329 ..     122     209 ..     105     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-06
                        DUF759 245 vefaamlkssgamssedavkavns....vlggdgselfdllkksgvgdkyiedakmawqsgaqvdldsritkmmemfkd.f 320
                                   ve++   + s a+s    +  v s    v  g g  +  +lkk    d ++    + w +g + d+d r+t  +em++   
  gi|91772266|ref|YP_564958.1| 122 VELSMREQGSRALSKGRIIEVVPSkvprV-IGHGGSMVSILKKESNCDVFVGKNGRIWINGKDKDMD-RLTTAIEMIESeS 200
                                   56666666777888877777776622213.46777899****************************8.899999*998615 PP

                        DUF759 321 ksfgltkkv 329
                                   +  glt kv
  gi|91772266|ref|YP_564958.1| 201 HMSGLTDKV 209
                                   567999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1535.69
//
Query:       gi|91772267|ref|YP_564959.1|  [L=343]
Description: exosome complex exonuclease Rrp41 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-30  106.2   0.0    3.5e-30  105.2   0.0    1.5  1  RNase_PH    3' exoribonuclease family, domain 1
    1.6e-17   63.3   0.3    3.2e-17   62.3   0.3    1.6  1  RNase_PH_C  3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
      0.086   12.7   0.1       0.21   11.5   0.1    1.6  1  Big_2       Bacterial Ig-like domain (group 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 !  105.2   0.0   5.9e-34   3.5e-30       1     132 []      23     152 ..      23     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 5.9e-34
                                   EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHH CS
                      RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeielsr 80 
                                   e+R++++e+gvls+a+GS+yle G++kvla+v+gp+e +p++ + + +e  +  ++++a f+ ++r r   ps++++e+s+
  gi|91772267|ref|YP_564959.1|  23 EIRPMTVEMGVLSRADGSCYLEWGNNKVLAAVYGPRELHPRRLQrP-SEALVRYRYNMAAFSVEDRIR-PGPSRRSTEISK 101
                                   79************************************88888644.455599999999***999944.34********** PP

                                   HHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  81 lleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                   +  +a++ +++ + +p   id++++vl++d  ++  a+inaa+lAL+dagip
  gi|91772267|ref|YP_564959.1| 102 VSGEAFETVVMKQFYPGAVIDVFAEVLQADA-GTRTAAINAATLALVDAGIP 152
                                   *******************************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.3   5.4e-21   3.2e-17       2      66 ..     156     218 ..     155     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 5.4e-21
                                   --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                    RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                   +v+a++vgkvd+q+v+D++k E++++++dl++a+++++e+ tl++++g+ l+++++ +++e+  k
  gi|91772267|ref|YP_564959.1| 156 LVAACAVGKVDGQLVIDLNKPEDNYGDADLPIAMTEDGEI-TLLQMDGN-LTADEIAKGVEMVRK 218
                                   89************************************99.********.*********999776 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 ?   11.5   0.1   3.5e-05      0.21      24      63 ..     125     166 ..     115     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                                   EEEESTT-S---EEEEECC-SSEEEE....TCCEECCCSSEEEE CS
                         Big_2  24 vevtpssasdkkvtwtssngsvAtVs....atGlVtavaaGkat 63 
                                   +ev +++a++   t ++ + ++A V+    ++GlV a a+Gk++
  gi|91772267|ref|YP_564959.1| 125 AEVLQADAGT--RTAAINAATLALVDagipMKGLVAACAVGKVD 166
                                   7778888876..899***************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2151.45
//
Query:       gi|91772268|ref|YP_564960.1|  [L=259]
Description: exosome complex RNA-binding protein Rrp42 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  100.7   0.0    1.4e-28  100.1   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    5.5e-09   35.9   0.1    1.1e-08   35.0   0.1    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.0   1.5e-32   1.4e-28       1     132 []      30     165 ..      30     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.5e-32
                                   EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHH CS
                      RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeielsr 80 
                                   e R+l iet+v+ +a+GSa + lGdt+vl++v++++ + p++++ d  +g++ + +e+ p+as++++  g p +++ie++r
  gi|91772268|ref|YP_564960.1|  30 ETRDLIIETNVIDKAEGSAKVLLGDTQVLVGVKLQVGS-PFADSaD--KGVIITSMELNPIASPNFEA-GPPREKAIEMAR 106
                                   679*********************************98.6666434..588***************55.9*********** PP

                                   HHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  81 lleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                   +++r +r+s+ +        e++  + + id++vl+++g +llda++++a++AL++a ip
  gi|91772268|ref|YP_564960.1| 107 VVDRGIRESGAIdlnklcitEGEEVWIVFIDVHVLNDSG-NLLDAASLGAIAALMTATIP 165
                                   ***********8899999999999***************.******************99 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 !   35.0   0.1   1.2e-12   1.1e-08       3      62 ..     183     242 ..     181     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.2e-12
                                   -EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHH CS
                    RNase_PH_C   3 viavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaie 62 
                                   +++ ++  +++++v+D+t++Ee++s+ +lt++ + ++++++++k+g + l+ee++l+ +e
  gi|91772268|ref|YP_564960.1| 183 PVSLSFIDIGGELVIDATNNEESVSDLRLTIVTNQDGSICAMQKSGPGTLSEENFLRSVE 242
                                   5555555678********************************************998666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2018.02
//
Query:       gi|91772269|ref|YP_564961.1|  [L=95]
Description: 50S ribosomal protein L37Ae [Methanococcoides burtonii DSM 6242]
Scores for complete 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  108.6   6.9    1.5e-31  108.3   6.9    1.1  1  Ribosomal_L37ae  Ribosomal L37ae protein family
  ------ inclusion threshold ------
      0.013   15.4   2.0      0.022   14.7   2.0    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.02   14.8   2.1       0.03   14.2   2.1    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
       0.02   13.8   0.2       0.02   13.7   0.2    1.0  1  Pestivirus_E2    Pestivirus envelope glycoprotein E2
       0.03   14.2   1.3       0.03   14.2   1.3    2.3  2  HalOD2           Halobacterial output domain 2
      0.072   12.8   0.3      0.096   12.4   0.3    1.2  1  Rep_fac-A_C      Replication factor-A C terminal domain
      0.094   12.8   0.3         13    6.0   0.0    2.2  2  Zn-ribbon_8      Zinc ribbon domain
       0.52   10.8   5.4       0.55   10.8   1.0    2.3  2  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   6.9   6.9e-35   1.5e-31       3      84 ..      10      91 ..       8      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 6.9e-35
                                  XXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-XXXXX CS
               Ribosomal_L37ae  3 kkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksairrlk 84
                                  ++ ++aG++gtrYG++ rk v+++e+++ha+++C++c + +vkR+++giwkCkkcg+t+aGg+y+p tt +ktv +++++++
  gi|91772269|ref|YP_564961.1| 10 RVSRSAGRFGTRYGRRDRKLVADLEEKMHAAHKCASCARLTVKRVGTGIWKCKKCGYTFAGGTYIPATTVGKTVLRTVKKAT 91
                                  66789*************************************************************************9976 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.0   9.7e-06     0.022      19      46 .]      41      67 ..      33      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.7e-06
                 Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrkq 46
                                  + C  C+  ++ r+ t g ++Ck+C+++
  gi|91772269|ref|YP_564961.1| 41 HKCASCARLTVKRVGT-GIWKCKKCGYT 67
                                  6799***889999999.********985 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.1   1.3e-05      0.03       9      38 ..      38      68 ..      33      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                  SS--B-TTT-SB--S.SSS-EEEETTT--EE CS
                          C1_1  9 kqptfCkhCgeflwg.kekqglkCswCkllv 38
                                     ++C+ C+ +  +  ++ ++kC+ C++++
  gi|91772269|ref|YP_564961.1| 38 HAAHKCASCARLTVKrVGTGIWKCKKCGYTF 68
                                  56789********888************985 PP

>> Pestivirus_E2  Pestivirus envelope glycoprotein E2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     9e-06      0.02     153     228 ..      10      85 ..       1      91 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9e-06
                                   EEEEE-S-B---TT---EEEETTEEEEEEE-STTT-EEEEE-B--..SS-EEEEEETTEEESSSTTSSSSS-SEEEES CS
                 Pestivirus_E2 153 rtyrrskpfphrqgcitqknlgedlhncilggnwtcvpgdqllyk..ggsiesckwcgyqfkeseglphypigkckle 228
                                   r  r +  f  r g    ++l  dl + +  +   c    +l  k  g  i  ck cgy f     +p   +gk  l 
  gi|91772269|ref|YP_564961.1|  10 RVSRSAGRFGTRYGRRD-RKLVADLEEKMH-AAHKCASCARLTVKrvGTGIWKCKKCGYTFAGGTYIPATTVGKTVLR 85 
                                   55566666777777654.456678877654.4567888888877655889************************8775 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.23   5.1e+02      32      37 ..      41      46 ..       7      50 .. 0.57
   2 ?   14.2   1.3   1.3e-05      0.03      24      44 ..      51      71 ..      47      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.23
                        HalOD2 32 WkCtrC 37
                                   kC+ C
  gi|91772269|ref|YP_564961.1| 41 HKCASC 46
                                  355555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.3e-05
                        HalOD2 24 yrqLGayvWkCtrCGevqaaA 44
                                  +++ G+ +WkC +CG + a+ 
  gi|91772269|ref|YP_564961.1| 51 VKRVGTGIWKCKKCGYTFAGG 71
                                  6889***********998875 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   4.3e-05     0.096      11      48 ..      33      69 ..      27      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                  EETTTTEEEB--STT---B-EEE.TTTEEEETTTTEEES CS
                   Rep_fac-A_C 11 ikkdnlvYkACpsedCnkKvvee.edgewrCekCdkeve 48
                                  +++++ + + C+   C +  v++ + g w+C+kC  +++
  gi|91772269|ref|YP_564961.1| 33 LEEKMHAAHKCA--SCARLTVKRvGTGIWKCKKCGYTFA 69
                                  555666667788..9***99999889********88775 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.012        26      26      39 ..      40      54 ..      29      54 .. 0.73
   2 ?    6.0   0.0    0.0058        13       7      15 ..      60      68 ..      59      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                   Zn-ribbon_8 26 ltaCPeCgs.evrrv 39
                                    +C +C   +v+rv
  gi|91772269|ref|YP_564961.1| 40 AHKCASCARlTVKRV 54
                                  345****99999996 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0058
                   Zn-ribbon_8  7 rCeeCghef 15
                                  +C++Cg +f
  gi|91772269|ref|YP_564961.1| 60 KCKKCGYTF 68
                                  7*****999 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 ?    2.1   0.2      0.13     3e+02      15      22 ..      41      48 ..      34      52 .. 0.75
   2 ?   10.8   1.0   0.00024      0.55      14      25 ..      58      69 ..      50      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                     zf-H2C2_2 15 yeCplCdk 22
                                  ++C +C+ 
  gi|91772269|ref|YP_564961.1| 41 HKCASCAR 48
                                  89****86 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                     zf-H2C2_2 14 pyeCplCdkaFk 25
                                  +++C++C+++F+
  gi|91772269|ref|YP_564961.1| 58 IWKCKKCGYTFA 69
                                  68*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 636.05
//
Query:       gi|91772270|ref|YP_564962.1|  [L=46]
Description: DNA-directed RNA polymerase subunit P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-08   34.5   8.2    1.8e-08   33.9   8.2    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
    0.00015   21.2   1.3       0.23   11.1   0.0    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
    0.00084   18.7   0.8     0.0095   15.3   0.1    2.1  2  zf-ribbon_3     zinc-ribbon domain
     0.0026   17.6   1.2     0.0035   17.2   1.2    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0029   17.5   0.8      0.038   13.9   0.1    2.1  2  Cys_rich_CPXG   Cysteine-rich CPXCG
     0.0031   17.0   1.4      0.004   16.6   1.4    1.3  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0066   16.5   2.7      0.014   15.5   2.7    1.5  1  Zn-ribbon_8     Zinc ribbon domain
     0.0083   16.1   0.7     0.0097   15.9   0.7    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.011   15.4   3.9      0.033   13.9   3.9    1.7  1  zinc_ribbon_2   zinc-ribbon domain
      0.013   15.2   0.5        1.7    8.5   0.1    2.1  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.024   14.6   0.8       0.05   13.6   0.8    1.5  1  DZR             Double zinc ribbon
      0.025   14.3   0.3       0.35   10.6   0.0    2.0  2  Ribosomal_S27e  Ribosomal protein S27
      0.049   13.6   3.7       0.36   10.8   0.1    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.051   13.1   2.1        2.1    8.0   0.3    2.1  2  Sgf11           Sgf11 (transcriptional regulation protein)
      0.059   13.3   0.2      0.063   13.3   0.2    1.1  1  RNHCP           RNHCP domain
      0.074   12.9   2.0        3.4    7.6   0.1    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.18   11.7   4.5        8.2    6.4   4.5    2.3  1  zinc_ribbon_4   zinc-ribbon domain
       0.28   11.3   2.0         12    6.1   0.1    2.1  2  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
        7.4    6.8   8.2         44    4.3   8.2    2.0  1  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   8.2   1.9e-11   1.8e-08       1      32 []       3      35 ..       3      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.9e-11
                                  -B-SSS--B----SS.S----SSS-----B--- CS
                DNA_RNApol_7kD  1 YiCgeCgaevslkkg.dpiRCkeCGhRilYKkR 32
                                  Y+C +C+ +v+++ g   iRC +CGhRil K+R
  gi|91772270|ref|YP_564962.1|  3 YKCTRCKRPVEIDYGyTGIRCPYCGHRILVKER 35
                                  9**********9988356**************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 !    9.5   0.3   0.00076      0.72       3      14 ..       3      14 ..       2      16 .. 0.87
   2 !   11.1   0.0   0.00024      0.23       3      18 ..      21      36 ..      19      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00076
                        zf_UBZ  3 ylCerCgkeipe 14
                                  y C rC++++++
  gi|91772270|ref|YP_564962.1|  3 YKCTRCKRPVEI 14
                                  99******9986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00024
                        zf_UBZ  3 ylCerCgkeipeselq 18
                                  + C+ Cg++i++ e++
  gi|91772270|ref|YP_564962.1| 21 IRCPYCGHRILVKERP 36
                                  68**********9998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.15   1.5e+02       4      13 ..       4      13 ..       2      15 .. 0.70
   2 !   15.3   0.1     1e-05    0.0095       3      11 ..      21      30 ..      20      35 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
                   zf-ribbon_3  4 rCPnCGapls 13
                                  +C +C+ p++
  gi|91772270|ref|YP_564962.1|  4 KCTRCKRPVE 13
                                  6888887766 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1e-05
                   zf-ribbon_3  3 vrCPnCGa.p 11
                                  +rCP+CG+ +
  gi|91772270|ref|YP_564962.1| 21 IRCPYCGHrI 30
                                  7899999987 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 !   17.2   1.2   3.7e-06    0.0035       9      38 ..       2      30 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                OrfB_Zn_ribbon  9 eykakeyGikveevnpayTSktCseCgskn 38
                                   yk+++  ++v e++  yT  +C+ Cg++ 
  gi|91772270|ref|YP_564962.1|  2 DYKCTRCKRPV-EIDYGYTGIRCPYCGHRI 30
                                  79999888887.69**************86 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.13   1.2e+02      27      37 ..       5      15 ..       3      19 .. 0.68
   2 !   13.9   0.1   4.1e-05     0.038       1      12 [.      21      32 ..      21      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                 Cys_rich_CPXG 27 CqvCCrPivlq 37
                                  C  C rP++++
  gi|91772270|ref|YP_564962.1|  5 CTRCKRPVEID 15
                                  67777777664 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.1e-05
                 Cys_rich_CPXG  1 iqCPyCgeeiev 12
                                  i CPyCg++i v
  gi|91772270|ref|YP_564962.1| 21 IRCPYCGHRILV 32
                                  78******9865 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.4   4.2e-06     0.004       1      27 [.       3      28 ..       3      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.2e-06
                                  EEETTTTCEECHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                  ykC  C+ + ++ D+  + ++C+ CG 
  gi|91772270|ref|YP_564962.1|  3 YKCTRCKRP-VEIDYGYTGIRCPYCGH 28
                                  8******87.8***************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 !   15.5   2.7   1.4e-05     0.014       5      34 ..       2      28 ..       2      35 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                   Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgs 34
                                  +Y+C++C++  e+    +    + CP Cg+
  gi|91772270|ref|YP_564962.1|  2 DYKCTRCKRPVEIDYGYT---GIRCPYCGH 28
                                  8***********777665...889*****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 !   15.9   0.7     1e-05    0.0097      71      99 ..       3      32 ..       1      45 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                  EEETTTS-EEECHH.H.HHS-TTTSSS-EEE CS
                          HypA 71 vrCreCgkefelee.k.alrCpkCgsadvei 99
                                  ++C++C++ +e++  +  +rCp Cg++ + +
  gi|91772270|ref|YP_564962.1|  3 YKCTRCKRPVEIDYgYtGIRCPYCGHR-ILV 32
                                  79*********99864688*****985.444 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   3.9   3.5e-05     0.033       1      22 [.       4      29 ..       4      30 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                 zinc_ribbon_2  1 fCpnCGaelqdnakF....CpyCGtp 22
                                  +C++C ++++ +  +    CpyCG+ 
  gi|91772270|ref|YP_564962.1|  4 KCTRCKRPVEIDYGYtgirCPYCGHR 29
                                  8***********************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 ?    8.5   0.1    0.0018       1.7       3      15 ..       2      14 ..       1      18 [. 0.88
   2 ?    5.5   0.0     0.016        15       6      18 ..      23      34 ..      21      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                 A2L_zn_ribbon  3 lkvCsvCggngil 15
                                  +++C+ C++++++
  gi|91772270|ref|YP_564962.1|  2 DYKCTRCKRPVEI 14
                                  69*******9987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                 A2L_zn_ribbon  6 CsvCggngilnse 18
                                  C +Cg+  ++ +e
  gi|91772270|ref|YP_564962.1| 23 CPYCGHRILV-KE 34
                                  99****9888.76 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   5.3e-05      0.05      15      36 ..       5      28 ..       2      36 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-05
                           DZR 15 CseCgtklkavaa..edrCpsCge 36
                                  C +C+ +++       +rCp Cg+
  gi|91772270|ref|YP_564962.1|  5 CTRCKRPVEIDYGytGIRCPYCGH 28
                                  666666664332255666666665 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.16   1.5e+02       6      14 ..       1       9 [.       1      14 [. 0.73
   2 ?   10.6   0.0   0.00037      0.35       8      28 ..      21      41 ..      16      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.16
                                  EEEE-TTTS CS
                Ribosomal_S27e  6 ldvkCpdCe 14
                                  +d kC  C+
  gi|91772270|ref|YP_564962.1|  1 MDYKCTRCK 9 
                                  567888886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00037
                                  EE-TTTS-EEEEESS-SS-EE CS
                Ribosomal_S27e  8 vkCpdCenetvvFshaatvvk 28
                                  ++Cp C++   v +++++ +k
  gi|91772270|ref|YP_564962.1| 21 IRCPYCGHRILVKERPQSSIK 41
                                  89***************9987 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7     0.051        48      38      45 ..       3      10 ..       2      11 .. 0.89
   2 ?   10.8   0.1   0.00038      0.36      18      27 ..      20      29 ..      18      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                 Zn_Tnp_IS1595 38 fqCkeCrk 45
                                  ++C +C++
  gi|91772270|ref|YP_564962.1|  3 YKCTRCKR 10
                                  99****97 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00038
                 Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                  g +CP+Cg+r
  gi|91772270|ref|YP_564962.1| 20 GIRCPYCGHR 29
                                  789*****87 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3    0.0023       2.1       4      14 ..       2      12 ..       1      14 [. 0.86
   2 ?    5.2   0.1     0.016        15       5      14 ..      21      30 ..      18      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                                  EEE-TTTSSEE CS
                         Sgf11  4 yvtCpnCgRqi 14
                                  +++C  C+R++
  gi|91772270|ref|YP_564962.1|  2 DYKCTRCKRPV 12
                                  689******99 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                                  EE-TTTSSEE CS
                         Sgf11  5 vtCpnCgRqi 14
                                  ++Cp+Cg  i
  gi|91772270|ref|YP_564962.1| 21 IRCPYCGHRI 30
                                  68****9766 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   6.7e-05     0.063       3      41 ..       2      38 ..       1      45 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                         RNHCP  3 sftCeeCgkeveklaagsakrnHCpsCLlskHvdeepgd 41
                                  +++C++C++ ve + +g  +   Cp+C + + v+e+p+ 
  gi|91772270|ref|YP_564962.1|  2 DYKCTRCKRPVEID-YGY-TGIRCPYCGHRILVKERPQS 38
                                  689********965.555.4677****999999999876 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.017        16      29      35 ..       3       9 ..       1      11 [. 0.85
   2 ?    7.6   0.1    0.0037       3.4       1      10 [.      21      30 ..      21      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                       TFIIS_C 29 ykCtkCg 35
                                  ykCt C+
  gi|91772270|ref|YP_564962.1|  3 YKCTRCK 9 
                                  8999997 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0037
                       TFIIS_C  1 akCpkCgsre 10
                                  ++Cp Cg+r 
  gi|91772270|ref|YP_564962.1| 21 IRCPYCGHRI 30
                                  5799999985 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.5    0.0087       8.2       1      35 [.       1      30 [.       1      31 [. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0087
                 zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                  M+  C +Ck   eid      + + +rC+ Cgh +
  gi|91772270|ref|YP_564962.1|  1 MDYKCTRCKRPVEIDY-----GYTGIRCPYCGHRI 30
                                  5556666666666666.....45679999999975 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 ?    5.7   0.2     0.017        16      54      66 ..       4      16 ..       1      21 [. 0.84
   2 ?    6.1   0.1     0.013        12      29      39 ..      22      32 ..      18      36 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                     DiS_P_DiS 54 rCraCkakislry 66
                                  +C +Ck+++++ y
  gi|91772270|ref|YP_564962.1|  4 KCTRCKRPVEIDY 16
                                  8999999999988 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                     DiS_P_DiS 29 rCpkCghklkw 39
                                  rCp Cgh++ +
  gi|91772270|ref|YP_564962.1| 22 RCPYCGHRILV 32
                                  68888888755 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   8.2     0.046        44      15      23 ..      21      29 ..       4      29 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.046
                       UPF0547 15 qfCphCGyv 23
                                   +Cp+CG++
  gi|91772270|ref|YP_564962.1| 21 IRCPYCGHR 29
                                  58*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 304.62
//
Query:       gi|91772271|ref|YP_564963.1|  [L=155]
Description: ribosomal biogenesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       325  (0.0181271); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1182.92
//
Query:       gi|91772272|ref|YP_564964.1|  [L=84]
Description: hypothetical protein Mbur_0204 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   32.5   0.0    8.1e-08   32.3   0.0    1.1  1  Pcc1      Transcription factor Pcc1
  ------ inclusion threshold ------
      0.079   13.5   0.0       0.12   12.9   0.0    1.3  1  Spec3     Ectodermal ciliogenesis protein


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0     9e-12   8.1e-08      12      72 ..      12      73 ..       6      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 9e-12
                                  HHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                          Pcc1 12 rlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                  ++A++++r + ++     +  + +++++++  L+++++A +  ++R ++n++l++++++ ++
  gi|91772272|ref|YP_564964.1| 12 EDAEAIYRCILPELGTMVSGrSIVDIKVNNHSLVMNITADDIISMRSTLNTWLRMVQIAHDV 73
                                  48***********88888777999*********************************99877 PP

>> Spec3  Ectodermal ciliogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05      0.12      16      69 ..      17      76 ..      13      79 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                         Spec3 16 ilNillPGlGTilsgllvlclgkerlkkke.......klktflvnvlvgvlQlltvlfllv 69
                                  i  ++lP lGT++sg +++ ++ ++ +           ++  ++n++  ++Q++   ++ v
  gi|91772272|ref|YP_564964.1| 17 IYRCILPELGTMVSGRSIVDIKVNNHSLVMnitaddiISMRSTLNTWLRMVQIAH-DVCAV 76
                                  67799************99865554433222344544445567888888888854.35555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 638.33
//
Query:       gi|91772273|ref|YP_564965.1|  [L=117]
Description: prefoldin, beta subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-23   80.9  20.9    6.5e-23   80.7  20.9    1.0  1  Prefoldin_2   Prefoldin subunit
  ------ inclusion threshold ------
      0.016   15.2   4.3      0.016   15.2   4.3    2.1  2  DHR10         Designed helical repeat protein 10 domain
      0.097   13.1   0.5      0.097   13.1   0.5    2.6  2  FlaC_arch     Flagella accessory protein C (FlaC)
       0.12   12.0  12.6       0.17   11.5  12.6    1.2  1  DUF4795       Domain of unknown function (DUF4795)
       0.25    9.2   7.2       0.31    8.9   7.2    1.1  1  V_ATPase_I    V-type ATPase 116kDa subunit family
       0.37   10.4  10.5       0.48   10.1  10.5    1.1  1  SMP_2         Bacterial virulence factor haemolysin
       0.38   11.2  14.1        1.1    9.7   1.9    2.1  2  DUF16         Protein of unknown function DUF16
       0.47   10.5   4.6       0.59   10.2   4.6    1.1  1  DUF87         Helicase HerA, central domain
       0.48   10.5  17.0       0.62   10.2  17.0    1.2  1  Mod_r         Modifier of rudimentary (Mod(r)) protein
       0.52   10.5   2.9       0.55   10.4   0.8    2.0  2  CinA_KH       Damage-inducible protein CinA KH domain
          1    9.5  17.6         26    4.9  17.6    2.1  1  Nup54         Nucleoporin complex subunit 54
        1.2    7.7  11.1          2    6.9  11.0    1.3  1  FapA          Flagellar Assembly Protein A
        2.2    8.6   8.5        9.3    6.6   0.5    2.5  2  DUF948        Bacterial protein of unknown function (DUF948)
        2.3    8.6  15.5        1.1    9.6   5.7    2.1  2  TSNAXIP1_N    Translin-associated factor X-interacting N-term
        3.4    6.9  23.6        4.4    6.5  10.7    2.0  1  HemX          HemX, putative uroporphyrinogen-III C-methyltra
        4.2    7.9  10.3       0.25   11.8   1.4    2.1  2  SecD-TM1      SecD export protein N-terminal TM region
        4.2    7.4  14.1         46    4.0  14.1    2.0  1  Laminin_II    Laminin Domain II
        6.5    6.8  26.8        1.3    9.1  11.1    2.5  2  FlxA          FlxA-like protein
          7    5.9  11.3        9.3    5.5  11.3    1.2  1  DUF4407       Domain of unknown function (DUF4407)
        7.3    5.4  19.2         23    3.7  19.3    1.6  1  Spc7          Spc7 kinetochore protein


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 !   80.7  20.9   7.2e-26   6.5e-23       1     105 [.      10     114 ..      10     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 7.2e-26
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktl 81 
                                   q++++++qq qqq q+la+q++q+e  +ke+e +leele+l +d+ vy+ vGd+ ++ +k+++ ++L+er+etl+ +++++
  gi|91772273|ref|YP_564965.1|  10 QNQLAQLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLSDDAIVYRAVGDLQIQSNKDDTVAKLKERLETLSLRLQSI 90 
                                   89******************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHCCTS- CS
                   Prefoldin_2  82 ekqleklekeleelkeelqkklqq 105
                                   ++q+e++ k++++l+e+l++++++
  gi|91772273|ref|YP_564965.1|  91 TRQEERISKRFTQLQEQLKQAMGT 114
                                   ********************9987 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 ?    5.3   6.6     0.021        19      45      85 ..       9      49 ..       6      54 .. 0.56
   2 ?   15.2   4.3   1.8e-05     0.016      49      97 ..      63     111 ..      57     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                         DHR10 45 ieaelakleeakkklkelrdaleekeielrelerkeerlqr 85
                                  ++++la+l+++++++++l  + +++e  ++e e+  e l++
  gi|91772273|ref|YP_564965.1|  9 VQNQLAQLQQVQQQAQALAMQKNQMESMKKESEMALEELEK 49
                                  45555555555555555555555555555555555555554 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.8e-05
                         DHR10  49 lakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerl 97 
                                   l+ +   ++++++l+++le+++ +l+ ++r+eer+ ++  + +e+l ++
  gi|91772273|ref|YP_564965.1|  63 LQIQSNKDDTVAKLKERLETLSLRLQSITRQEERISKRFTQLQEQLKQA 111
                                   5556677899***********************************9876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.6      0.12     1e+02      11      33 ..      28      50 ..       7      55 .. 0.57
   2 ?   13.1   0.5   0.00011     0.097       3      40 ..      74     111 ..      72     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                     FlaC_arch 11 klsteletvkkeneelsksveel 33
                                    + ++e++kke e   +++e+l
  gi|91772273|ref|YP_564965.1| 28 MQKNQMESMKKESEMALEELEKL 50
                                  22235555555555555555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                     FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                    +l ++l+ ls +l+++ ++ e +sk  ++l+e+ k+ 
  gi|91772273|ref|YP_564965.1|  74 AKLKERLETLSLRLQSITRQEERISKRFTQLQEQLKQA 111
                                   67899****************************99875 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  12.6   0.00019      0.17      30     126 ..       9     112 ..       2     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                       DUF4795  30 vkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeakkeLekmleellekle..... 105
                                   v++   +l++ +++ +al  q ++ e+ k+++e   eel+  +d   + + v + q+++ k++   +l+e le l+     
  gi|91772273|ref|YP_564965.1|   9 VQNQLAQLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLSDDAIVYRAVGDLQIQSNKDDTVAKLKERLETLSlrlqs 89 
                                   555566788999999999999999999999999999999999**************6655555444444444443333335 PP

                       DUF4795 106 ..eqeealkkaldtLqeelkekl 126
                                      qee++ k   +Lqe+lk+ +
  gi|91772273|ref|YP_564965.1|  90 itRQEERISKRFTQLQEQLKQAM 112
                                   55999999999999998888754 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 ?    8.9   7.2   0.00035      0.31      21     106 ..      22     108 ..       5     116 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00035
                    V_ATPase_I  21 fqrkfvkevrrcdemerklrfleeeieklekavikeeea.eesleapeekeldeleeelekleeelkelnenleklkkeln 100
                                     ++ + +  +++ m+++ ++  ee+ekl++  i ++   + + ++++++++ +l+e+le+l  +l+++++++e+++k+++
  gi|91772273|ref|YP_564965.1|  22 QAQALAMQKNQMESMKKESEMALEELEKLSDDAIVYRAVgDLQIQSNKDDTVAKLKERLETLSLRLQSITRQEERISKRFT 102
                                   222222333344444444444444444444444443333567888999999****************************** PP

                    V_ATPase_I 101 elvelk 106
                                   +l+e+ 
  gi|91772273|ref|YP_564965.1| 103 QLQEQL 108
                                   **9975 PP

>> SMP_2  Bacterial virulence factor haemolysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  10.5   0.00054      0.48      35     133 ..       9     110 ..       5     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00054
                         SMP_2  35 lgsqlarvnQveeLsklLvrQvanslskllvdnakeeklkelldqltkeslvlDAsvYskdGellAqseeale...lrdrl 112
                                   +++qla+ +Qv++ ++ L+ Q  +  s+  +++   e+l++l d     + v D ++ s++  ++A+ +e+le   lr + 
  gi|91772273|ref|YP_564965.1|   9 VQNQLAQLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLSDDAIVYRAVGDLQIQSNKDDTVAKLKERLEtlsLRLQS 89 
                                   689******************99988887777777777777777777777888999**********999876521155554 PP

                         SMP_2 113 aldgkkagssfnqQiVepies 133
                                      +++  s++  Q+ e +++
  gi|91772273|ref|YP_564965.1|  90 ITRQEERISKRFTQLQEQLKQ 110
                                   455555555566666666655 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.7    0.0069       6.2      55      97 ..      10      52 ..       2      55 .. 0.66
   2 ?    9.7   1.9    0.0013       1.1      24      75 ..      64     116 ..      56     117 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0069
                                  HHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHH CS
                         DUF16 55 qkvekqgekikelkveqkaqgeelnkvdetleliletLqkink 97
                                  q+  +q ++++++ +    q+++++++++  e+ le L+k+++
  gi|91772273|ref|YP_564965.1| 10 QNQLAQLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLSD 52
                                  3334455566666666666777777888888888888887765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                   HHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH.HHHHHHHHH CS
                         DUF16  24 qlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekike.lkveqkaqg 75 
                                   q++  kd++ ++Lk+  ++++ + ++i ++e+ ++k   +++e lk+ + +qg
  gi|91772273|ref|YP_564965.1|  64 QIQSNKDDTVAKLKERLETLSLRLQSITRQEERISKRFTQLQEqLKQAMGTQG 116
                                   77888999999999999999999999999999999999998762455556665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.6   0.00066      0.59     111     195 ..       6     103 ..       2     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                         DUF87 111 kpaaavqrsvleealdqaka....keekeklssdepveklleelk...........kekeelrklknqaiarlldkledll 176
                                   +p+ ++q + l+++ +qa+a    k++ e+++ ++ ++  leel+            ++++++++k+++ a+l+++le l 
  gi|91772273|ref|YP_564965.1|   6 PPQVQNQLAQLQQVQQQAQAlamqKNQMESMKKESEMA--LEELEklsddaivyraVGDLQIQSNKDDTVAKLKERLETLS 84 
                                   57888888888888888888877644444444444333..555555666777777666667*******************9 PP

                         DUF87 177 rkggsfsnsstdliallle 195
                                   ++ +s++ +++++ +   +
  gi|91772273|ref|YP_564965.1|  85 LRLQSITRQEERISKRFTQ 103
                                   9999995555555555433 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  17.0    0.0007      0.62       6     103 ..      11     111 ..       8     117 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0007
                         Mod_r   6 eeLqelledeeklealvktlpevkqlkeekeellaeneslaeknlslep....eleelrselqekle.elkelekefeeke 81 
                                   ++L +l + +++ +al+ + ++++++k+e e++l+e e+l ++ +  +     +++ +++++ +kl+  l++l+ +++  +
  gi|91772273|ref|YP_564965.1|  11 NQLAQLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLSDDAIVYRAvgdlQIQSNKDDTVAKLKeRLETLSLRLQSIT 91 
                                   799**************************************6666666666666666666666666633666666666666 PP

                         Mod_r  82 qeldellqkfspdallarLqta 103
                                   ++ ++++++f++  l+++L++a
  gi|91772273|ref|YP_564965.1|  92 RQEERISKRFTQ--LQEQLKQA 111
                                   666666666654..33344433 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.98   8.8e+02      38      55 ..      19      36 ..       8      56 .. 0.56
   2 ?   10.4   0.8   0.00061      0.55      17      68 ..      59     113 ..      38     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.98
                                  EEEEEE...EEHHHHHHH CS
                       CinA_KH 38 vtvRltakaaneeeaeal 55
                                  v+ +  a a ++++ e +
  gi|91772273|ref|YP_564965.1| 19 VQQQAQALAMQKNQMESM 36
                                  333334444444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00061
                                   HHGGG.S-B.SSSEEEEEEET.TEEEEEEE...EEHHHHHHHHH....HHHHHTT CS
                       CinA_KH  17 kladl.idr.enptlAiyake.gevtvRltakaaneeeaealiapveeeirerlg 68 
                                   +++dl i++ +++t+A + ++ +  ++Rl    ++ee   ++  +++e++++++g
  gi|91772273|ref|YP_564965.1|  59 AVGDLqIQSnKDDTVAKLKERlETLSLRLQSITRQEERISKRFTQLQEQLKQAMG 113
                                   5677744443556*****9998899**************************9988 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  17.6     0.029        26      41     129 ..      15     114 ..       8     117 .] 0.54

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.029
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH............HHHHHHHHHHHHHHHHTT-SS---SSH CS
                         Nup54  41 Qqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhv............elshRllrllrkleilrsrgyaldaeE 109
                                   Q ++v+q+ ++l   ++++e+++ k++  ++++lek+    +            +    + +l  +le l+ r ++++ +E
  gi|91772273|ref|YP_564965.1|  15 QLQQVQQQAQALAMQKNQMESMK-KESEMALEELEKLSDDAIvyravgdlqiqsNKDDTVAKLKERLETLSLRLQSITRQE 94 
                                   44555555555555555555555.4444455555554443320000000000002233455566666666666779999** PP

                                   HHHHHHHHHHHHHHS-HHH. CS
                         Nup54 110 eelrarletleaqlndpaql 129
                                   e++++r+ +l++ql++  + 
  gi|91772273|ref|YP_564965.1|  95 ERISKRFTQLQEQLKQAMGT 114
                                   **************986544 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  11.0    0.0023         2     336     414 ..      30     106 ..      11     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0023
                          FapA 336 keklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkee 414
                                   k++++ +++e e   eelekl ++ +  ++   + q++s+k ++++kl+e +e l+ +l++++++ +++++++ +  +e
  gi|91772273|ref|YP_564965.1|  30 KNQMESMKKESEMALEELEKLSDDAIVYRA-VGDLQIQSNKDDTVAKLKERLETLSLRLQSITRQEERISKRFTQL-QE 106
                                   444588888888889999999999888888.4567899*********************************99988.33 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 ?    5.3   2.1     0.026        23      28      62 ..      19      53 ..       5      57 .. 0.72
   2 ?    6.6   0.5      0.01       9.3      27      65 ..      72     110 ..      56     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.026
                        DUF948 28 ldeaaatieelekqvdpilkevedllakvnelled 62
                                  +++ a++++  ++q++++ ke+e +l++ ++l +d
  gi|91772273|ref|YP_564965.1| 19 VQQQAQALAMQKNQMESMKKESEMALEELEKLSDD 53
                                  34444455555699999999999999999998887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                        DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvne 65 
                                   t+ ++++++e+l  ++++i+++ e++ +   +l+e++++
  gi|91772273|ref|YP_564965.1|  72 TVAKLKERLETLSLRLQSITRQEERISKRFTQLQEQLKQ 110
                                   555555555555555555555555555555555554444 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.7    0.0013       1.1      69     110 ..      10      50 ..       2      51 .. 0.76
   2 ?    4.8   2.1      0.04        36      48      92 ..      66     111 ..      63     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                    TSNAXIP1_N  69 kaklktlsessdkraleleekreelralekeskalleeidkl 110
                                   +++l+ l++ + ++a++l ++++++++++kes+ +lee++kl
  gi|91772273|ref|YP_564965.1|  10 QNQLAQLQQVQ-QQAQALAMQKNQMESMKKESEMALEELEKL 50 
                                   66776666644.44448888888*****************98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.04
                    TSNAXIP1_N  48 KkEYelyiahllesqreaqylkaklktlsessdkraleleek.ree 92 
                                    +  ++++a l+e+ +++ +  + ++  +e+ +kr  +l+e+ ++ 
  gi|91772273|ref|YP_564965.1|  66 QSNKDDTVAKLKERLETLSLRLQSITRQEERISKRFTQLQEQlKQA 111
                                   5555899999********9999999999999999999999996665 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 ?    6.5  10.7    0.0049       4.4      39      82 ..       8      51 ..       2      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0049
                          HemX 39 elqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekel 82
                                  ++q+qla+l+q ++q++a++ qk+++e+  ++ + +le+lek++
  gi|91772273|ref|YP_564965.1|  8 QVQNQLAQLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLS 51
                                  68999999999999999999999999999999999999998876 PP

>> SecD-TM1  SecD export protein N-terminal TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.0      0.48   4.3e+02      47      69 ..      16      38 ..       2      62 .. 0.55
   2 ?   11.8   1.4   0.00028      0.25      45      86 ..      68     109 ..      56     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.48
                      SecD-TM1 47 eatlskveqaLkeagievksiel 69
                                   + +++  qaL+ ++ +++s++ 
  gi|91772273|ref|YP_564965.1| 16 LQQVQQQAQALAMQKNQMESMKK 38
                                  22233334444444444444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00028
                      SecD-TM1  45 vdeatlskveqaLkeagievksielenesllvrfestdqqlk 86 
                                    +++t++k+++ L++ +++ +si+ ++e++  rf++ ++qlk
  gi|91772273|ref|YP_564965.1|  68 NKDDTVAKLKERLETLSLRLQSITRQEERISKRFTQLQEQLK 109
                                   35668899********************************97 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  14.1     0.052        46      16     102 ..      30     111 ..       2     113 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.052
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                    Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96 
                                   ++q++ ++++ e   e+l+++ ++ + +   v d  ++     + v kL++ ++ L  +l+++  +ee    +s+   +++
  gi|91772273|ref|YP_564965.1|  30 KNQMESMKKESEMALEELEKLSDD-AIVYRAVGD-LQIQSNKDDTVAKLKERLETLSLRLQSITRQEER---ISKRFTQLQ 105
                                   233344444444444444444444.222222333.3445556788999999999999999999999999...********* PP

                                   HHHHHH CS
                    Laminin_II  97 elIaqA 102
                                   e+ +qA
  gi|91772273|ref|YP_564965.1| 106 EQLKQA 111
                                   ***998 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  11.1    0.0014       1.3      60      91 ..       8      40 ..       2      53 .. 0.53
   2 ?    3.4   7.7     0.083        75      12      67 ..      66     110 ..      59     117 .] 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                          FlxA 60 qlqaQIaqlqqqqaekaqekqqse.keeksksk 91
                                  q+q+Q+aqlqq q++ ++ + q++ +e+++k++
  gi|91772273|ref|YP_564965.1|  8 QVQNQLAQLQQVQQQAQALAMQKNqMESMKKES 40
                                  566777777665555444443333033333333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.083
                          FlxA  12 ssgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaq 67 
                                   +s+ ++ +a+L++ +++l+  L++++ ++e       k+  ++q+Q+       +q
  gi|91772273|ref|YP_564965.1|  66 QSNKDDTVAKLKERLETLSLRLQSITRQEERIS----KRFTQLQEQL-------KQ 110
                                   566677777777777777777777777733322....2333333333.......33 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  11.3      0.01       9.3     128     224 ..      10     109 ..       2     117 .] 0.59

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.01
                       DUF4407 128 aaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakl 206
                                   +++    +++++  + +a  ++++++ +++ + + +e++k  d    +   +  G+ ++  +k++  ++++++l++l+ +l
  gi|91772273|ref|YP_564965.1|  10 QNQlaQLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLSDD---AIVYRAVGDLQIQSNKDDTVAKLKERLETLSLRL 87 
                                   33322334444444444455555556666666666666655554...344558999999******************9998 PP

                       DUF4407 207 d....atarlaalraelaelea 224
                                   +    +++r++++ ++l+e  +
  gi|91772273|ref|YP_564965.1|  88 QsitrQEERISKRFTQLQEQLK 109
                                   8877744444444333333222 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  19.3     0.025        23     147     239 ..      15     111 ..       7     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.025
                          Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqe....aaeelesidkeeLeelreelaelkaeieekkkela 223
                                   +l++++++++ L+ q+++++++++e e   +ele+  ++          +++s + + +++l+e+l++l+  +++  ++ +
  gi|91772273|ref|YP_564965.1|  15 QLQQVQQQAQALAMQKNQMESMKKESEMALEELEKLSDDAIVyravGDLQIQSNKDDTVAKLKERLETLSLRLQSITRQEE 95 
                                   6899999****************9999999999988888776444434466777789999999999999999998888888 PP

                          Spc7 224 elqeqleeleekieel 239
                                   +  ++ ++l+e+++++
  gi|91772273|ref|YP_564965.1|  96 RISKRFTQLQEQLKQA 111
                                   8888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3450  (0.192426); expected 358.6 (0.02)
Passed bias filter:                      872  (0.0486363); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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):              20  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.56
# Mc/sec: 626.44
//
Query:       gi|91772274|ref|YP_564966.1|  [L=321]
Description: phosphoesterase, RecJ-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   40.1   0.8      6e-10   39.3   0.8    1.4  1  DHH       DHH family
    4.2e-10   40.2   1.9    8.9e-10   39.1   1.9    1.5  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
       0.31   10.1   0.2       0.43    9.6   0.2    1.1  1  eIF-4B    Plant specific eukaryotic initiation factor 4B


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 !   39.3   0.8     1e-13     6e-10       2     101 .]      18     150 ..      17     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1e-13
                                   EEEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCHHCCCS CS
                                   xxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxx RF
                           DHH   2 ilivghknpDtDsigSaialan.......................................llvDhneksqavegeakeea 43 
                                   il ++h+n D D+i Sa+al++                                       ++vD+++++q  +     + 
  gi|91772274|ref|YP_564966.1|  18 ILYLCHRNADPDAISSAFALSEavggkvglvdgcnrvatllvdkleiavinnpdpkdydlvVVVDTSTSAQLNDI----KL 94 
                                   67789*****************9999999888888888888888888888888888888877*******999976....88 PP

                                   EEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  44 edviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                    +  ++DHH+    + t +  ++l+ ++ s aeiv+++l   ++ i +++a  l++gi
  gi|91772274|ref|YP_564966.1|  95 TNYCVVDHHATT--ALTENASFYLHRNATSVAEIVYDVLICMGAPIMHRMALGLMTGI 150
                                   8999*******7..55555789999**************9999999999999999998 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   1.9   1.5e-13   8.9e-10      59     122 ..     228     293 ..     220     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.5e-13
                                   HHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEE CS
                         DHHA1  59 aadklksklkkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagi 122
                                   a ++l +      ++fv + + d+++vs+r+k+d    gv++g++++e++++  g GGGH+ AaG  +
  gi|91772274|ref|YP_564966.1| 228 ASSMLIN--IGGDVAFVGTARSDNIRVSGRAKRDavnaGVNLGKIMEEISSHYEGTGGGHAGAAGIDV 293
                                   6667777..77899999999999******************************************876 PP

>> eIF-4B  Plant specific eukaryotic initiation factor 4B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   7.2e-05      0.43     146     223 ..     194     273 ..     186     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 7.2e-05
                        eIF-4B 146 esrvsdfdqpsrad..evddWakakkslasfdsgrqsrygslGgggglggasradevdnWaagkkplpvrsstlGsgfrd 223
                                   + r++ ++ +srad   v dW     +++sf  + +s     Gg+  ++g++r+d++   +++k+++     +lG  + +
  gi|91772274|ref|YP_564966.1| 194 SMRIAMLKTASRADveRVGDWLVVTSNVSSFGGSASSMLINIGGDVAFVGTARSDNIRVSGRAKRDAVNAGVNLGKIMEE 273
                                   567888999****954588*********************************************9998888888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1980.84
//
Query:       gi|91772275|ref|YP_564967.1|  [L=434]
Description: phenylacetate-CoA ligase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-31  108.6   0.7    2.8e-31  107.7   0.7    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    7.3e-15   54.5   0.1    1.7e-14   53.3   0.0    1.6  2  AMP-binding      AMP-binding enzyme
    1.4e-05   24.3   0.0    0.00085   18.4   0.0    2.5  2  LuxE             Acyl-protein synthetase, LuxE
     0.0014   17.6   0.1       0.12   11.2   0.0    2.1  2  GH3              GH3 auxin-responsive promoter
  ------ inclusion threshold ------
      0.039   14.2   0.0       0.07   13.4   0.0    1.4  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati


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 !  107.7   0.7   7.8e-35   2.8e-31       1      96 []     336     432 ..     336     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 7.8e-35
                                   TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEEE-TT CS
               AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvelvepg 80 
                                   G+nvfPsq+e+vl++i+ev+++++i+v+r +elD ++v++E+++ +fsd++++  +lekk+a++lk +l++ vkvelve+g
  gi|91772275|ref|YP_564967.1| 336 GINVFPSQVESVLMKIPEVGEHFMIIVDRVNELDIMKVQIEMTDlAFSDKVNDIINLEKKVAAALKGVLNIAVKVELVEHG 416
                                   99******************************************99*********************************** PP

                                   -S---------EEE-S CS
               AMP-binding_C_2  81 tlprsegKakrviDkR 96 
                                   +lprs gKak+viD+R
  gi|91772275|ref|YP_564967.1| 417 SLPRSMGKAKKVIDNR 432
                                   ***************9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   4.7e-18   1.7e-14     158     370 ..      83     287 ..      15     289 .. 0.78
   2 ?   -2.0   0.1      0.28     1e+03     410     423 .]     322     335 ..     300     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 4.7e-18
                                   TTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT-EEEE-TT CS
                   AMP-binding 158 pddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvv.lsilplahifglilelllallsGatvvllpk 236
                                   ++ l+ +  +SGTTGkP  V ++ + + + ++sl+   t  +++++d + + +    +  gl    ++a   G+tv   + 
  gi|91772275|ref|YP_564967.1|  83 NNKLVRFHVSSGTTGKPTVVGYTDNDIKSWTTSLArALTSIGIGRNDIMqIGYGYGLFTGGL-GMHYGAEETGCTVLPTS- 161
                                   5666667779**************99966666665422235566788885555555555565.66677777777665555. PP

                                   CGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHC.HHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEE CS
                   AMP-binding 237 daaldpklllelieklkvtviagvPrvlealle.sgalka.akkakdlsslrlvllggeplspellrffralfgeevlegY 315
                                   +  +d  + +el+++l+ +vi ++P+ +  ++e +++    +++  d   lr+ ++g+ep s+e+ +++++  g + ++++
  gi|91772275|ref|YP_564967.1| 162 SGNTD--RQIELMQDLGTSVIGCTPSYFLFMIEaAKEAGIsFQE--D-TNLRIGVFGAEPWSEEMRKRIEESSGIKAYDIF 237
                                   44444..448*******************998845444432332..3.34************************9****** PP

                                   EEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                   AMP-binding 316 GlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                   G +E +g ++  +++e+    g +        v+++D+etgepv+dge Gel++ 
  gi|91772275|ref|YP_564967.1| 238 GTSELSGPLF-TECREQ---NG-IHVWADQFLVEVIDPETGEPVADGERGELVIT 287
                                   ********98.554444...33.667778999********************995 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.28
                                   EEEEEECCCEEEET CS
                   AMP-binding 410 leivgRkkdliklr 423
                                   ++++gR++d++++r
  gi|91772275|ref|YP_564967.1| 322 MRVLGRADDMLIVR 335
                                   789*******9986 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.012        44      31     128 ..      24     124 ..      11     134 .. 0.78
   2 !   18.4   0.0   2.4e-07   0.00085     207     360 ..     186     330 ..     167     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.012
                          LuxE  31 flldelvnhykhneeyrkycqknkvddlvtegevddiPviPvsvfkai....gtkllsvsedeikaklqssatsGlkstvl 107
                                    l + +   y+h+  yrk      + +  ++  +dd+  +P    k +     t +  v ++++     ss+t+G ++ v 
  gi|91772275|ref|YP_564967.1|  24 KLCNLIIYVYEHSPFYRKQFDDAGIRPEDIK-GLDDVTKLPFTYKKDLrdtyPTGMFCVPNNKLVRFHVSSGTTGKPTVVG 103
                                   5556667789999999998888888887777.4899999998877765111146788899999999999***********9 PP

                          LuxE 108 ldklsierllravarvmkevl 128
                                        i+  + ++ar++  ++
  gi|91772275|ref|YP_564967.1| 104 YTDNDIKSWTTSLARALTSIG 124
                                   999999999999999998776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.4e-07
                          LuxE 207 yllyqtvyktlkdknisfqldknlqvitiGGWkklekekldkidfnrdladvlnlsiddvvdiygfteqvelntpdfkdel 287
                                   y l+    ++ k+ +isfq d nl++   G    + +e  ++i+      +  +++     di+g +e  +  ++++++  
  gi|91772275|ref|YP_564967.1| 186 YFLFM--IEAAKEAGISFQEDTNLRIGVFGA-EPWSEEMRKRIE------ESSGIK---AYDIFGTSELSGPLFTECRE-Q 253
                                   44444..456899999999999998766554.445555555544......444553...57999988888877777764.4 PP

                          LuxE 288 krkrvysdviir...deetlkvvgdGkvGlleyvdalstsyPafvvltddlGvieeslcegqkaGkl.vkvlrrvkk 360
                                   + ++v +d ++    d+et ++v+dG  G l     + ++ P       d+ v++  +ce++++  + ++vl+r++ 
  gi|91772275|ref|YP_564967.1| 254 NGIHVWADQFLVeviDPETGEPVADGERGELVITTLVKEALPLIRYRIGDITVLNWDECECGRTHPRiMRVLGRADD 330
                                   678888875544456***************************999999**************98755279****976 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   3.5e-05      0.12      74     115 ..      84     121 ..      79     165 .. 0.79
   2 !    4.4   0.0    0.0039        14     354     419 ..     276     350 ..     264     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                                   SS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHH CS
                           GH3  74 epiklfalsSGTtsgksKliPvteeslkelallvlallaall 115
                                   +++++f  sSGTt gk+ ++ +t++  k+++  +++   al+
  gi|91772275|ref|YP_564967.1|  84 NKLVRFHVSSGTT-GKPTVVGYTDNDIKSWTTSLAR---ALT 121
                                   68899********.**************98766444...333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0039
                                   S-TTSEEEEEEES....TTS-SSEEECEEEEE....EEEETTEE.EEEEEECCTEEE-SSSS-CCHHHHHHHHH. CS
                           GH3 354 vevGkeYelvvTt....faGLyRYrigDvvrv....tgfynkaP.rleFvgRknvvlsidgeklteeelqkavee 419
                                   v  G++ elv+Tt    +  L RYrigD+        +   + P +++++gR + +l ++g  +  +++++++ +
  gi|91772275|ref|YP_564967.1| 276 VADGERGELVITTlvkeALPLIRYRIGDITVLnwdeCECGRTHPrIMRVLGRADDMLIVRGINVFPSQVESVLMK 350
                                   66788899999995544568********85431111234456787778888888888888888888888877764 PP

>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05      0.07       5      30 ..     174     199 ..     170     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                   HHHHHHTTTHHHHHHHHHHHHHHHHH CS
                    P5CR_dimer   5 davtalsGsgpAyvflliealadagv 30 
                                   d  t + G++p y++++iea  +ag+
  gi|91772275|ref|YP_564967.1| 174 DLGTSVIGCTPSYFLFMIEAAKEAGI 199
                                   77899*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 2856.15
//
Query:       gi|91772276|ref|YP_564968.1|  [L=145]
Description: amino acid-binding (ACT) protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   55.9   1.2    1.2e-06   28.1   0.1    2.5  2  ACT       ACT domain
    5.8e-07   30.0   0.1      0.008   16.8   0.0    2.3  2  ACT_4     ACT domain
    0.00033   20.4   0.1       0.46   10.3   0.0    2.8  2  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   6.7e-10     4e-06       3      49 ..       9      52 ..       7      62 .. 0.81
   2 !   28.1   0.1   2.1e-10   1.2e-06       2      55 ..      74     125 ..      73     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.7e-10
                                  EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEE CS
                           ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvviv 49
                                  ++++++++PG La v+  + ++giNi+  ++++ +d   gi+ +v v
  gi|91772276|ref|YP_564968.1|  9 ISLFAENKPGRLASVADKFKNAGINIRAFTIAEAGD--FGIIRMV-V 52
                                  8899******************************99..3333333.2 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.1e-10
                                   EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHH CS
                           ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedl 55 
                                   vl v+++D+PG L+ ++ +l++ +iNid +  + ++    + + +v v d +++
  gi|91772276|ref|YP_564968.1|  74 VLGVEMEDVPGQLGMIADVLGEKNINIDYAYAFVTRT--EKAFLIVRVNDIRGA 125
                                   6889********************************9..477777766666655 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06     0.008       8      54 ..       8      52 ..       2      59 .. 0.86
   2 !   11.3   0.0   6.7e-05       0.4       9      46 ..      75     112 ..      72     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                         ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitv 54
                                  ++++ ae+++g La++++ ++++++ni++ ++ +  +  +  i++ v
  gi|91772276|ref|YP_564968.1|  8 QISLFAENKPGRLASVADKFKNAGINIRAFTIAE--AGDFGIIRMVV 52
                                  799*****************************99..45577777765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.7e-05
                         ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdg 46 
                                   l ve+ed +g L+ i++v+ e+++ni    a  +++++
  gi|91772276|ref|YP_564968.1|  75 LGVEMEDVPGQLGMIADVLGEKNINIDYAYAFVTRTEK 112
                                   56999*********************876666554444 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   7.7e-05      0.46      20      44 ..      16      41 ..       7      64 .. 0.86
   2 !    7.4   0.0   0.00064       3.8      12      63 ..      75     129 ..      68     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.7e-05
                                  S--HHHHHHHHHHTTT---EEEE.-S CS
                         ACT_7 20 vtGivaklaspLaeagIsifqiS.ty 44
                                   +G++a++a +  +agI+i +++  +
  gi|91772276|ref|YP_564968.1| 16 KPGRLASVADKFKNAGINIRAFTiAE 41
                                  69*****************8887555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00064
                                   -S-.---SS--HHHHHHHHHHTTT---EEEE....-SS-EEEEEEGGGHHHHHHHH CS
                         ACT_7  12 vgsglpfdvtGivaklaspLaeagIsifqiS....tyrtdyiLVpeedlekAveaL 63 
                                    g  +  dv+G +  +a +L e +I+i +         + +++V+ +d+  Av++L
  gi|91772276|ref|YP_564968.1|  75 LGVEME-DVPGQLGMIADVLGEKNINIDYAYafvtRTEKAFLIVRVNDIRGAVRIL 129
                                   556664.59******************66542332444567777777877777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 906.05
//
Query:       gi|91772277|ref|YP_564969.1|  [L=116]
Description: hypothetical protein Mbur_0209 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  121.9   1.0    9.9e-36  121.7   1.0    1.0  1  DUF2103   Predicted metal-binding protein (DUF2103)


Domain annotation for each model (and alignments):
>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   1.0   5.5e-40   9.9e-36       2      97 ..      13     110 ..      12     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 5.5e-40
                       DUF2103   2 pkeklggsHstiiggreGkkllekiakhpevkkviPgvikakg.sssggglrvkvt.raderGnlrlllrdgssvQevfiv 80 
                                   +k+kl+g+H+t+ig+r+Gkk+l +i++h++vk ++P+vi+++g ss+gg+l++kv+ ++de+Gnlrlll++g+s+Qe++iv
  gi|91772277|ref|YP_564969.1|  13 LKDKLHGAHTTVIGERQGKKILGTISQHEKVKGIVPSVITVRGkSSPGGNLAAKVLpHPDEHGNLRLLLTHGTSAQEIRIV 93 
                                   689****************************************88999******9879*********************** PP

                       DUF2103  81 ttakdreegeriaeeLn 97 
                                   tt+++re+g+ ++eeLn
  gi|91772277|ref|YP_564969.1|  94 TTVATREDGALLMEELN 110
                                   ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 762.32
//
Query:       gi|91772278|ref|YP_564970.1|  [L=325]
Description: hypothetical protein Mbur_0210 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2036.42
//
Query:       gi|91772279|ref|YP_564971.1|  [L=270]
Description: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-49  169.0   0.0    1.4e-49  168.8   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase
     0.0033   16.2   0.0      0.036   12.8   0.0    2.0  2  Peptidase_M8  Leishmanolysin


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 !  168.8   0.0   1.5e-53   1.4e-49       1     260 [.      11     255 ..      11     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 1.5e-53
                                   EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEE CS
                  CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvig 81 
                                   ++A++Q+ +  +++++n++k+l +++eA +kgad+ivlPE+f tg+ + ++    Ae g  +t++ l   ++kn++++v+ 
  gi|91772279|ref|YP_564971.1|  11 KIAAIQMDICHCNKQKNIKKALHFSEEAISKGADIIVLPEVFSTGF-CYEELENIAESGSYPTIKELEVFSKKNKCIIVGS 90 
                                   69*******99***********************************.9999999*************************** PP

                                   EEEEEC.CTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTE..EEEEEEGGGGGSH CS
                  CN_hydrolase  82 lierel.tngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvg..kiGaaiCyeigfp 159
                                   +ie+   +n    + n +++l +dg+lvg y K+h f          e+e+f +gd i+++ ++     +G++iCye++fp
  gi|91772279|ref|YP_564971.1|  91 IIEKHSsKNRET-YTNLGFCL-EDGELVGTYTKTHPF--------GKEKEYFTSGDVIEPIHLKERdlTVGLQICYEMRFP 161
                                   ****76444444.56666666.89999********66........89*********75555444335599*********** PP

                                   HHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECC CS
                  CN_hydrolase 160 ellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglg 240
                                   e++r+l l ga+il +++       ++ + qw +l+ ara+en++f ia+n+ g   +    ++g+S+iidp G+++a++ 
  gi|91772279|ref|YP_564971.1| 162 EIARKLCLSGADILMTIA----EFPNPREHQWRTLATARAIENQVFHIACNRSGS--DPTSTFFGGSMIIDPLGNVIADAK 236
                                   **************9933....5668999**************************..************************ PP

                                   SSSTEEEEEEEEHHHHHHHH CS
                  CN_hydrolase 241 eeeegvliaeidladvratr 260
                                     e  v+i eid + +++tr
  gi|91772279|ref|YP_564971.1| 237 DGEC-VIIEEIDTSIMKKTR 255
                                   *995.*******88777776 PP

>> Peptidase_M8  Leishmanolysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0     4e-06     0.036     417     469 ..      50     110 ..      11     123 .. 0.83
   2 ?    1.3   0.0     0.012   1.1e+02     144     177 ..     151     184 ..     140     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-06
                  Peptidase_M8 417 egysngaC.....nqdsssadpslkefevfsdasRCl.dgalrpkqstgiteeyng..lCa 469
                                   e +s+g+C     n   s + p++ke evfs+  +C+  g++++k+s++  e+y++   C 
  gi|91772279|ref|YP_564971.1|  50 EVFSTGFCyeeleNIAESGSYPTIKELEVFSKKNKCIiVGSIIEKHSSKNRETYTNlgFCL 110
                                   568999999999888999999***************7369*******99988888744665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.012
                  Peptidase_M8 144 dgdvCsefkvPekhvtvGvsdaDlvlyvasvPse 177
                                     ++C e + Pe      +s+aD+++ +a +P  
  gi|91772279|ref|YP_564971.1| 151 GLQICYEMRFPEIARKLCLSGADILMTIAEFPNP 184
                                   6789**************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1666.54
//
Query:       gi|91772280|ref|YP_564972.1|  [L=429]
Description: hypothetical protein Mbur_0212 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-09   35.2   0.9      4e-08   32.7   0.9    1.9  1  Dus           Dihydrouridine synthase (Dus)
    2.8e-06   27.0   0.3     0.0002   20.9   0.1    2.2  2  His_biosynth  Histidine biosynthesis protein
      7e-06   25.3   1.0    9.5e-06   24.8   1.0    1.1  1  IMPDH         IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.9   6.7e-12     4e-08      55     219 ..     140     293 ..      70     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6.7e-12
                                   CEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESST CS
                           Dus  55 plavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigidd 135
                                    + + + + + + l++aA +v+d    + +l + C ++++ + g+G aL+++   + + +k+++  +++ ++vk+r  + d
  gi|91772280|ref|YP_564972.1| 140 AVGFNVRAVSLEPLLKAATIVKD-AGGILELDAHCRQEEMVSIGVGEALMKDLPRLNEWIKKIK-ETGVVLSVKVRANVVD 218
                                   5555666777889**********.77889*********************************96.58999*******9996 PP

                                   TTC.HHHHHHHHHHCT-SEEEEESSECCCTT-C.G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCH CS
                           Dus 136 eeenalelakiveaaGaqaltvHgRtraqnyeg.tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrg 215
                                   +      la+ +e+aGa+ l v +     + eg  ad++aI  ++++ ++ +i+N  I d+ da+++ ++ Gad + ++r 
  gi|91772280|ref|YP_564972.1| 219 DI----ALARSIENAGADILHVDA-----MKEGaGADLRAILRIRDSTRLLLIGNNSIMDIMDARDMFSK-GADMISVSRV 289
                                   55....59**********998854.....555559***********************************.*****99999 PP

                                   HCCS CS
                           Dus 216 algn 219
                                    l++
  gi|91772280|ref|YP_564972.1| 290 VLED 293
                                   8876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0048        29      80     133 ..     164     215 ..     154     219 .. 0.84
   2 !   20.9   0.1   3.3e-08    0.0002      32     118 ..     220     303 ..     216     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0048
                                   SSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEEC CS
                  His_biosynth  80 GGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrg 133
                                   GGI +l+  ++  +  +  + +g a +k+   ++e+++k+ +  +v+++ +r++
  gi|91772280|ref|YP_564972.1| 164 GGILELD--AHCRQEEMVSIGVGEALMKDLPRLNEWIKKIKETGVVLSVKVRAN 215
                                   7777777..66666667788999**************************99986 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.3e-08
                                   HHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHH CS
                  His_biosynth  32 velakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpeli 112
                                   ++la++ e++gad lhv   da keg +a+l ++ +i++++++ +     I ++ d++++++ gad ++++ +++++  +i
  gi|91772280|ref|YP_564972.1| 220 IALARSIENAGADILHV---DAMKEGAGADLRAILRIRDSTRLLLIGNNSIMDIMDARDMFSKGADMISVSRVVLEDDGFI 297
                                   67999**********97...999*****************9999999999******************************* PP

                                   HHHHHH CS
                  His_biosynth 113 kelaek 118
                                   ++l+e 
  gi|91772280|ref|YP_564972.1| 298 DSLVED 303
                                   *99986 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   1.0   1.6e-09   9.5e-06      31     172 ..      63     286 ..      46     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.6e-09
                                   EEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-.SSS-HHHHHHHHHHHHTS............................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx............................ RF
                         IMPDH  31 iklniPlvsaamdtvtesemAialareGgigvih.knlsieeqaeevkkvkrs............................ 82 
                                   ++ + P+  a+m  +t+s  A + a++ g++vi   nl+ e++a+  k v r                             
  gi|91772280|ref|YP_564972.1|  63 VTFRNPIALAPMAGITDSVFASKNAKNAGLAVIGgYNLDEETNAAAAKLVERGrqeflsdapleffetevnavdtggavgf 143
                                   67788****************************73589999999999999988999************************* PP

                                   ......................................................TTSXBXTTSXB-EEEEE-SSTTHHHHH CS
                                   ......................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH  83 ......................................................pnaakdekgrllvgaavgvkedalerv 109
                                                                                          ++ k++   l v    +v  d+++ +
  gi|91772280|ref|YP_564972.1| 144 nvravslepllkaativkdaggileldahcrqeemvsigvgealmkdlprlnewIKKIKETGVVLSVKVRANVV-DDIALA 223
                                   ************************************************99654434444444444444444444.677888 PP

                                   HHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEE.E-SHHHHHHHHHTT-SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 110 kalveagvdvlvvdsahghsekvleavkeikkkveeveviaGn.vataegakaLieagadavkv 172
                                   + + +ag+d+l vd+ +      l+a+ +i++++ ++ +i+ n + +   a+++++ gad++ v
  gi|91772280|ref|YP_564972.1| 224 RSIENAGADILHVDAMKEGAGADLRAILRIRDST-RLLLIGNNsIMDIMDARDMFSKGADMISV 286
                                   99***************999************99.676776555999**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.36s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2803.72
//
Query:       gi|91772281|ref|YP_564973.1|  [L=315]
Description: triphosphoribosyl-dephospho-CoA protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-74  251.6   0.0    1.3e-74  251.4   0.0    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 !  251.4   0.0     7e-79   1.3e-74       1     280 [.      17     307 ..      17     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 251.4 bits;  conditional E-value: 7e-79
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH.. CS
                          CitG   1 aelavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa.. 79 
                                   a +a+lA++lEvs +pKPG++dr++++  +D+++e+FlaSa++++p++e+aa          ++  ++G+l++ a+ ++  
  gi|91772281|ref|YP_564973.1|  17 ACCAQLAMILEVSSSPKPGNIDRHHDY--EDTRYEHFLASAVSVHPVIEAAA----------RNDSRVGTLLKSAVCHSns 85 
                                   579************************..***********************..........899**************** PP

                                   .------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--.......---...... CS
                          CitG  80 .tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv.......eel...... 145
                                    ++g+NTh+Ga++ll++l++aag+  +++++++++elv++a+e++++++++da++f +a+r a v         +      
  gi|91772281|ref|YP_564973.1|  86 wQSGGNTHFGAFLLLIPLSMAAGELLGSGNKFDMDELVARAHEIVSSTDTDDAIDFyKAFRSAGVrvndvdeF-Dlqddss 165
                                   ***********************9999**************************************99877640.2554344 PP

                                   HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SS......HHHHHHHHHHHHHHS--HHHH CS
                          CitG 146 kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadl......ndalvqallallaelpDtnil 220
                                     +l+e ++ltl++ + +s+g+d+i++e++sgF +++++a  +l + ++ ++d       n+a+v  +l+ll+e pDt+i 
  gi|91772281|ref|YP_564973.1| 166 FVSLRE-NGLTLYDLMVISQGYDQIANEWVSGFGDCVKCAQ-MLDRFMDVSRDGalipdiNHAVVFSFLKLLSERPDTFIR 244
                                   444455.9******************************887.677776544222356777********************* PP

                                   HHHHHHHHHHHHHHHH............H-.SHHHHHHHHHHHHHHT---HHHHHHHHHHHHH CS
                          CitG 221 rrgGaegaeevqeeArallaa..ggvaaea.glealeeldrelvernisPGgsADllaatlfl 280
                                   ++ ++++aeev+++A+ ++++  g+  + + +++ +  +d+ l e++++PG++AD+++a+lf+
  gi|91772281|ref|YP_564973.1| 245 TKTDEKTAEEVSHQAKCIVERleGSGYHMSpFWDDVGIFDELLLEKGLNPGSTADIVIAGLFI 307
                                   ******************9999955556666*******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1997.23
//
Query:       gi|91772282|ref|YP_564974.1|  [L=198]
Description: hypothetical protein Mbur_0214 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-56  190.0   0.0    3.4e-56  189.8   0.0    1.0  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   0.0   1.9e-60   3.4e-56       1     175 [.      16     191 ..      16     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 1.9e-60
                                   EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETTTC.TT CS
                        DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetkpa.ki 80 
                                   +EvivtT++ ++pnaaPiG+i+kgd+v++rlfkgs+T++N+++++ lv+n+++Dpl+f+++++g+++es+f+    ++ ++
  gi|91772282|ref|YP_564974.1|  16 SEVIVTTYQGWSPNAAPIGIIRKGDDVFVRLFKGSQTYKNVKAERMLVANLVYDPLIFVRSTFGNITESEFKVLSYGGrAF 96 
                                   6********99****************************************************************999899 PP

                                   .EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCCSHHHHHHHHHHHHHHHHHH CS
                        DUF447  81 avlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldiedkeklleeieylssvikk 161
                                   a+++++ +wv +e++e +++s a++++l p ++++ +++++++nRg+++v+E +V+atR++++++ek+++ ie +s++++k
  gi|91772282|ref|YP_564974.1|  97 ATVRDSSCWVVFECDEFKETSGAIVAKLIPRHAHVGRCIFNSINRGFNLVVESCVHATRYELTNNEKYMRLIEAYSITVNK 177
                                   9******************************************************************************** PP

                                   H--HHHHHHHHHHH CS
                        DUF447 162 tggerekealellk 175
                                   +g+ r+kea+ell 
  gi|91772282|ref|YP_564974.1| 178 CGSGRDKEAMELLL 191
                                   ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1556.66
//
Query:       gi|91772283|ref|YP_564975.1|  [L=159]
Description: CMP/dCMP deaminase, zinc-binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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   88.3   0.0    3.8e-25   87.7   0.0    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
      1e-21   77.1   0.0    1.2e-21   76.9   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.054   13.6   0.1    1.8  1  APOBEC3          APOBEC3
      0.043   13.9   0.0      0.073   13.2   0.0    1.3  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
      0.054   12.9   0.3      0.072   12.5   0.3    1.1  1  DUF2162          Predicted transporter (DUF2162)


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 !   87.7   0.0   1.1e-28   3.8e-25       4     101 .]       6     105 ..       3     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.1e-28
                                   HHHHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHH.TSSCETTEEEEEEE--B CS
               dCMP_cyt_deam_1   4 dekllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaakn.ggsklegatlyvtlePC 82 
                                    e++++ a+k+a++   + +  ++Gavivk++ iis+g+n+    +++ +HAE++Ai+ka    +  +l g+ ly t+ PC
  gi|91772283|ref|YP_564975.1|   6 MEYFMDAAVKEAQKGMrNNEGGPFGAVIVKDDTIISKGHNEVLGTNDPSAHAEIVAIRKASAAlEDFDLSGCELYATTMPC 86 
                                   589**********************************************************997799************** PP

                                   HHHHHHHHHHT-SEEEEEE CS
               dCMP_cyt_deam_1  83 smCakaiiqsgikkvvvgt 101
                                   +mC  ai +++i k+++gt
  gi|91772283|ref|YP_564975.1|  87 PMCLSAIMWARIGKIYYGT 105
                                   ****************985 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   3.3e-25   1.2e-21       6     110 ..       9     136 ..       4     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 3.3e-25
                   MafB19-deam   6 afrkalaevekatkike.dkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlepCdmC 85 
                                   ++  a++e++k++  +e  + gavivkd+ +i +g+ne  + +++ aHaEi a+++A+ +l++  l+++ ly t  pC+mC
  gi|91772283|ref|YP_564975.1|   9 FMDAAVKEAQKGMRNNEgGPFGAVIVKDDTIISKGHNEVLGTNDPSAHAEIVAIRKASAALEDFDLSGCELYATTMPCPMC 89 
                                   57778899999987765279************************************************************* PP

                   MafB19-deam  86 agaivqaglkklvygagnpks......................lnkL 110
                                   + ai+ a++ k+ yg++ ++                       l+++
  gi|91772283|ref|YP_564975.1|  90 LSAIMWARIGKIYYGTSTEDVaslgfddgdiyamlregvdtsvLSEV 136
                                   ****************9887666666666655555555555555555 PP

>> APOBEC3  APOBEC3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.5e-05     0.054      27      70 ..      51      93 ..      34     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                       APOBEC3 27 nkekkHAEerfidkirslnldslkqykitcylswsPcpkCaeel 70
                                  n  + HAE+++i+k     l++ +     +y +  Pcp C + +
  gi|91772283|ref|YP_564975.1| 51 NDPSAHAEIVAIRKASA-ALEDFDLSGCELYATTMPCPMCLSAI 93
                                  45689*********877.99999999**************7765 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 ?   13.2   0.0     2e-05     0.073      18      61 ..      50      94 ..      34      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                         SNAD4 18 knkke.haEllflekikseldpsqeyrvtwylswsPCaeCaekia 61
                                  +n+ + haE++ ++k ++ l+        +y ++ PC+ C ++i+
  gi|91772283|ref|YP_564975.1| 50 TNDPSaHAEIVAIRKASAALEDFDLSGCELYATTMPCPMCLSAIM 94
                                  333346**********9999988888999************9985 PP

>> DUF2162  Predicted transporter (DUF2162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3     2e-05     0.072      92     113 ..      73      94 ..      57      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                       DUF2162  92 dvssrtflalvlPCPvCltail 113
                                   d+s    +a ++PCP+Cl+ai+
  gi|91772283|ref|YP_564975.1|  73 DLSGCELYATTMPCPMCLSAIM 94 
                                   5555567999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1058.25
//
Query:       gi|91772284|ref|YP_564976.1|  [L=296]
Description: TPR repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-40  135.8  18.1    5.5e-09   35.5   0.3    7.3  7  TPR_1            Tetratricopeptide repeat
    1.7e-36  121.3  18.0      2e-07   30.6   0.3    7.9  8  TPR_2            Tetratricopeptide repeat
    7.7e-28   95.9  12.8    1.1e-07   31.4   0.0    5.6  5  TPR_11           TPR repeat
    6.7e-24   82.1  21.2    4.6e-05   23.3   0.1    8.0  8  TPR_8            Tetratricopeptide repeat
    3.9e-20   70.7   8.1     0.0025   18.1   0.2    7.2  7  TPR_17           Tetratricopeptide repeat
      9e-20   70.8  19.7     0.0002   21.6   0.9    6.8  6  TPR_12           Tetratricopeptide repeat
    2.9e-19   68.1   7.5    4.3e-05   24.0   0.0    6.9  7  TPR_14           Tetratricopeptide repeat
    3.1e-18   66.1   1.9    5.4e-05   23.8   0.0    4.4  4  TPR_16           Tetratricopeptide repeat
    7.1e-18   64.9  13.6      2e-05   25.0   0.1    5.5  5  TPR_19           Tetratricopeptide repeat
    1.6e-13   50.5   0.0    9.6e-06   25.7   0.0    4.3  4  TPR_9            Tetratricopeptide repeat
    1.4e-12   47.0  12.7     0.0095   15.8   0.2    6.8  7  TPR_10           Tetratricopeptide repeat
    1.7e-12   47.4  11.2    4.7e-05   23.5   0.1    5.4  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    4.3e-12   45.2   5.5      0.034   14.2   0.0    6.6  7  TPR_7            Tetratricopeptide repeat
    1.1e-09   38.8   3.3      0.048   14.1   0.0    3.8  4  BTAD             Bacterial transcriptional activator domain
    1.6e-09   38.0   2.9       0.11   12.5   0.2    5.6  5  DUF3856          Domain of Unknown Function (DUF3856)
    6.2e-09   35.9   1.9    0.00012   22.0   0.3    4.4  4  SRP_TPR_like     Putative TPR-like repeat
    9.3e-09   34.9   0.8      0.044   13.0   0.1    3.1  3  TPR_15           Tetratricopeptide repeat
    1.4e-07   31.7  11.7         35    5.3   0.2    8.0  7  TPR_6            Tetratricopeptide repeat
    3.3e-07   29.6   9.3       0.32    9.8   0.4    4.9  5  NARP1            NMDA receptor-regulated protein 1
    6.2e-06   26.3   0.0         15    6.6   0.0    5.4  4  TPR_4            Tetratricopeptide repeat
    1.6e-05   24.9  18.7       0.69   10.0   0.3    5.6  5  MIT              MIT (microtubule interacting and transport) 
    5.4e-05   23.1   0.4         11    6.2   0.0    4.5  4  TPR_3            Tetratricopeptide repeat
    0.00021   20.8   0.2    0.00097   18.7   0.3    1.9  2  RIBIOP_C         40S ribosome biogenesis protein Tsr1 and BMS
    0.00056   19.9   4.8       0.18   11.9   0.0    4.9  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0023   17.0   0.2       0.35    9.8   0.0    2.3  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
     0.0039   16.9   2.5         11    5.6   0.3    4.3  4  TPR_21           Tetratricopeptide repeat-like domain
     0.0041   17.4   0.1         11    6.5   0.0    4.1  4  TPR_20           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.016   14.2   0.1      0.034   13.2   0.1    1.5  1  SRP68            RNA-binding signal recognition particle 68
      0.021   15.1   1.4        1.9    8.7   0.0    3.7  3  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
      0.022   15.0  10.2         77    3.9   0.1    6.8  7  PPR              PPR repeat
      0.023   15.2   0.7        1.7    9.1   0.0    3.4  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.034   13.6   1.6         32    4.1   0.2    3.8  3  SHNi-TPR         SHNi-TPR
       0.04   14.1   0.6        1.8    8.8   0.6    2.3  1  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
      0.055   13.4   0.0       0.18   11.8   0.0    2.0  1  Phage_term_smal  Phage small terminase subunit
      0.087   12.9   0.2       0.26   11.4   0.2    1.8  1  TFR_dimer        Transferrin receptor-like dimerisation domai
        0.2   11.5   1.5          9    6.1   0.0    3.5  4  PvlArgDC         Pyruvoyl-dependent arginine decarboxylase (P
       0.31   11.1   1.5         29    4.8   0.0    3.1  3  zf-CW            CW-type Zinc Finger
       0.96    9.1   8.7        7.1    6.3   0.1    4.8  4  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 !   15.5   0.1   2.4e-05     0.011       4      30 ..      27      53 ..      24      56 .. 0.88
   2 !    7.2   0.0    0.0099       4.7       4      34 .]      81     111 ..      79     111 .. 0.86
   3 !   18.3   0.0   3.1e-06    0.0015       6      34 .]     117     145 ..     115     145 .. 0.94
   4 !   35.5   0.3   1.2e-11   5.5e-09       1      29 [.     146     174 ..     146     176 .. 0.95
   5 !   33.3   0.2   5.8e-11   2.7e-08       3      32 ..     204     233 ..     203     235 .. 0.95
   6 !   23.7   0.0   6.1e-08   2.9e-05       2      32 ..     237     267 ..     236     269 .. 0.93
   7 !    9.6   0.4    0.0017      0.82       3      22 ..     272     291 ..     270     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1  4 lynlGnayfklgkydeAleyyekALel 30
                                   y++G+++++ g+++eAle y++A ++
  gi|91772284|ref|YP_564976.1| 27 TYGKGYVLHEIGRFEEALEKYDEAASI 53
                                  599********************9765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0099
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                    +n+  ++fkl k +eAl   e  ++  P++
  gi|91772284|ref|YP_564976.1|  81 RFNKCFILFKLDKKEEALTIIENTIQKKPDD 111
                                   58999*************9888888888875 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 3.1e-06
                                   HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   6 nlGnayfklgkydeAleyyekALelnPnn 34 
                                    +G ++f+ g+ydeAl   + A++l+P++
  gi|91772284|ref|YP_564976.1| 117 SKGFILFNIGRYDEALRMLDLAISLEPEY 145
                                   689************************86 PP

  == domain 4  score: 35.5 bits;  conditional E-value: 1.2e-11
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                   ++a+  ++n++++l++++eAle+yekA+e
  gi|91772284|ref|YP_564976.1| 146 PDAWSCKANTLYQLERFEEALECYEKAIE 174
                                   68**************************9 PP

  == domain 5  score: 33.3 bits;  conditional E-value: 5.8e-11
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                   ++y ++n++ klgk++eA+++y+ ALe+ P
  gi|91772284|ref|YP_564976.1| 204 IWYCKANTLEKLGKHKEAIDAYNSALEIKP 233
                                   6****************************9 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 6.1e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                   +a+y +G ++ +lg+ + Al +y+ ALe++ 
  gi|91772284|ref|YP_564976.1| 237 DAWYCMGTTLEELGENENALNAYSNALEVER 267
                                   8***************************975 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHHTT-HHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAle 22 
                                   al n++n+++klg+ +eA e
  gi|91772284|ref|YP_564976.1| 272 ALENKANLLYKLGREEEAKE 291
                                   778***************87 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.5e-05     0.007       5      29 ..      28      52 ..      24      53 .. 0.89
   2 ?    0.7   0.0       1.6   7.6e+02      13      30 ..      63      80 ..      60      83 .. 0.84
   3 !    8.0   0.0    0.0071       3.4       4      34 .]      81     111 ..      78     111 .. 0.89
   4 !   17.1   0.0   8.9e-06    0.0042       6      34 .]     117     145 ..     114     145 .. 0.92
   5 !   30.6   0.3   4.3e-10     2e-07       1      30 [.     146     175 ..     146     177 .. 0.94
   6 !   25.7   0.1   1.6e-08   7.4e-06       3      32 ..     204     233 ..     202     235 .. 0.95
   7 !   17.8   0.1   5.4e-06    0.0026       2      30 ..     237     265 ..     236     269 .. 0.93
   8 !   11.7   0.4   0.00048      0.23       3      23 ..     272     292 ..     270     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-05
                         TPR_2  5 ynlGlayyklgdyeeAleafekAle 29
                                  y  G+++ + g++eeAle +++A +
  gi|91772284|ref|YP_564976.1| 28 YGKGYVLHEIGRFEEALEKYDEAAS 52
                                  889********************86 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.6
                         TPR_2 13 klgdyeeAleafekAlel 30
                                  ++g  +eA++a+++ le+
  gi|91772284|ref|YP_564976.1| 63 QNGMEDEAKNALNRELEI 80
                                  78889*******998876 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0071
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                    +n   +++kl++ eeAl   e  ++  P++
  gi|91772284|ref|YP_564976.1|  81 RFNKCFILFKLDKKEEALTIIENTIQKKPDD 111
                                   689999*************999999999986 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 8.9e-06
                         TPR_2   6 nlGlayyklgdyeeAleafekAleldPnn 34 
                                     G ++++ g+y+eAl+ ++ A++l+P++
  gi|91772284|ref|YP_564976.1| 117 SKGFILFNIGRYDEALRMLDLAISLEPEY 145
                                   5799***********************85 PP

  == domain 5  score: 30.6 bits;  conditional E-value: 4.3e-10
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                   ++a+ + ++ +y+l ++eeAle++ekA+e 
  gi|91772284|ref|YP_564976.1| 146 PDAWSCKANTLYQLERFEEALECYEKAIEF 175
                                   689*************************95 PP

  == domain 6  score: 25.7 bits;  conditional E-value: 1.6e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                   ++y+ ++ ++klg+++eA++a++ Ale+ P
  gi|91772284|ref|YP_564976.1| 204 IWYCKANTLEKLGKHKEAIDAYNSALEIKP 233
                                   7***************************99 PP

  == domain 7  score: 17.8 bits;  conditional E-value: 5.4e-06
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                   +a+y++G  +++lg+ e Al+a+  Ale 
  gi|91772284|ref|YP_564976.1| 237 DAWYCMGTTLEELGENENALNAYSNALEV 265
                                   79*************************96 PP

  == domain 8  score: 11.7 bits;  conditional E-value: 0.00048
                         TPR_2   3 alynlGlayyklgdyeeAlea 23 
                                   al n ++++yklg+ eeA+e+
  gi|91772284|ref|YP_564976.1| 272 ALENKANLLYKLGREEEAKEL 292
                                   899****************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.5e-05     0.012       1      22 [.      31      52 ..      31      55 .. 0.93
   2 !   23.5   0.0   6.7e-08   3.2e-05       3      41 ..     121     159 ..     119     159 .. 0.94
   3 !   20.4   0.4   6.5e-07   0.00031       2      23 ..     154     175 ..     153     176 .. 0.93
   4 !   31.4   0.0   2.4e-10   1.1e-07       6      42 .]     214     250 ..     209     250 .. 0.93
   5 !   17.2   1.5   6.5e-06    0.0031       6      42 .]     248     284 ..     245     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                        TPR_11  1 GdayyeqGkyeeAieaYkkAlk 22
                                  G++++e G++eeA+e+Y +A  
  gi|91772284|ref|YP_564976.1| 31 GYVLHEIGRFEEALEKYDEAAS 52
                                  899****************976 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 6.7e-08
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   +++  G+y+eA+  +  A+ l P++++a+++ ++++y++
  gi|91772284|ref|YP_564976.1| 121 ILFNIGRYDEALRMLDLAISLEPEYPDAWSCKANTLYQL 159
                                   67889********************************86 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 6.5e-07
                        TPR_11   2 dayyeqGkyeeAieaYkkAlkl 23 
                                   + +y++ ++eeA+e+Y+kA+++
  gi|91772284|ref|YP_564976.1| 154 NTLYQLERFEEALECYEKAIEF 175
                                   899*****************95 PP

  == domain 4  score: 31.4 bits;  conditional E-value: 2.4e-10
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++Gk +eAi aY+ Al+++P + +a+y++G ++ ++G
  gi|91772284|ref|YP_564976.1| 214 KLGKHKEAIDAYNSALEIKPAFSDAWYCMGTTLEELG 250
                                   79****************************9999988 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 6.5e-06
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   e+G++e+A++aY++Al+    +  a+ n ++++yk+G
  gi|91772284|ref|YP_564976.1| 248 ELGENENALNAYSNALEVERGFTAALENKANLLYKLG 284
                                   79*********************************99 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0049       2.3       5      30 ..      28      53 ..      24      53 .. 0.85
   2 ?    1.2   0.1       1.2   5.5e+02      13      31 ..      63      81 ..      62      84 .. 0.81
   3 ?    1.5   0.0      0.94   4.4e+02       9      25 ..      86     102 ..      78     106 .. 0.79
   4 !   14.4   0.0   6.7e-05     0.032       5      33 ..     116     144 ..     114     145 .. 0.93
   5 !   19.9   0.1   1.2e-06   0.00057       7      30 ..     152     175 ..     146     177 .. 0.88
   6 !   23.3   0.1   9.7e-08   4.6e-05       3      33 ..     204     234 ..     202     235 .. 0.94
   7 !   12.0   0.0   0.00041      0.19       2      31 ..     237     266 ..     236     269 .. 0.92
   8 !   10.2   0.3    0.0016      0.74       3      23 ..     272     292 ..     270     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0049
                                  HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8  5 ynlgsiylklgdyeeAkeyyekalel 30
                                  y +g+++++ g++eeA e y +a ++
  gi|91772284|ref|YP_564976.1| 28 YGKGYVLHEIGRFEEALEKYDEAASI 53
                                  889**************999988775 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.2
                                  HTT-HHHHHHHHHHHHHHH CS
                         TPR_8 13 klgdyeeAkeyyekaleld 31
                                  + g  +eAk ++++ le++
  gi|91772284|ref|YP_564976.1| 63 QNGMEDEAKNALNRELEIR 81
                                  78999*******9877765 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.94
                                   HHHHHTT-HHHHHHHHH CS
                         TPR_8   9 siylklgdyeeAkeyye 25 
                                    i++kl ++eeA   +e
  gi|91772284|ref|YP_564976.1|  86 FILFKLDKKEEALTIIE 102
                                   5899********87665 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 6.7e-05
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   + +g i+++ g+y+eA   +  a++l+p+
  gi|91772284|ref|YP_564976.1| 116 FSKGFILFNIGRYDEALRMLDLAISLEPE 144
                                   56899**********************97 PP

  == domain 5  score: 19.9 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekalel 30 
                                   +++++ +l+++eeA e+yeka+e 
  gi|91772284|ref|YP_564976.1| 152 KANTLYQLERFEEALECYEKAIEF 175
                                   799*******************96 PP

  == domain 6  score: 23.3 bits;  conditional E-value: 9.7e-08
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++y ++++++klg+++eA+ +y+ ale++p+
  gi|91772284|ref|YP_564976.1| 204 IWYCKANTLEKLGKHKEAIDAYNSALEIKPA 234
                                   78999************************97 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 0.00041
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   +a+y +g ++++lg+ e+A  +y  ale +
  gi|91772284|ref|YP_564976.1| 237 DAWYCMGTTLEELGENENALNAYSNALEVE 266
                                   79999**********************986 PP

  == domain 8  score: 10.2 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHHTT-HHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkey 23 
                                   a+ n+++++ klg+ eeAke 
  gi|91772284|ref|YP_564976.1| 272 ALENKANLLYKLGREEEAKEL 292
                                   6779***************95 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.057        27      11      34 .]      22      45 ..      22      45 .. 0.93
   2 !   10.0   0.0     0.002      0.95       3      33 ..     102     132 ..     100     133 .. 0.93
   3 !   14.4   0.0   7.7e-05     0.036       5      34 .]     138     167 ..     134     167 .. 0.94
   4 ?    0.4   0.2       2.3   1.1e+03       1       7 [.     168     174 ..     168     176 .. 0.89
   5 !   10.2   0.0    0.0017       0.8      13      33 ..     202     222 ..     195     223 .. 0.88
   6 !   18.1   0.2   5.3e-06    0.0025       2      32 ..     225     255 ..     224     257 .. 0.92
   7 !    9.5   0.3    0.0029       1.4       2      34 .]     259     291 ..     258     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.057
                        TPR_17 11 nnadaynnLAelllknGdlmtArq 34
                                  +na++ + ++++l+++G++++A++
  gi|91772284|ref|YP_564976.1| 22 KNAESTYGKGYVLHEIGRFEEALE 45
                                  69999****************985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.002
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   ++ +++ P++ ++ + ++ +l ++G++++A+
  gi|91772284|ref|YP_564976.1| 102 ENTIQKKPDDMKPIFSKGFILFNIGRYDEAL 132
                                   778999***********************96 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 7.7e-05
                        TPR_17   5 aleldPnnadaynnLAelllknGdlmtArq 34 
                                   a+ l+P ++da+  +A++l+++ ++++A++
  gi|91772284|ref|YP_564976.1| 138 AISLEPEYPDAWSCKANTLYQLERFEEALE 167
                                   899************************985 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 2.3
                        TPR_17   1 lylkale 7  
                                   +y+ka+e
  gi|91772284|ref|YP_564976.1| 168 CYEKAIE 174
                                   8*****9 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0017
                        TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                   +  ++ +A++l+k+G++++A+
  gi|91772284|ref|YP_564976.1| 202 SGIWYCKANTLEKLGKHKEAI 222
                                   678****************97 PP

  == domain 6  score: 18.1 bits;  conditional E-value: 5.3e-06
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   y  ale+ P  +da++ ++++l+++G+ + A
  gi|91772284|ref|YP_564976.1| 225 YNSALEIKPAFSDAWYCMGTTLEELGENENA 255
                                   888***********************99887 PP

  == domain 7  score: 9.5 bits;  conditional E-value: 0.0029
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   y +ale +     a+ n+A+ll+k+G+ ++A++
  gi|91772284|ref|YP_564976.1| 259 YSNALEVERGFTAALENKANLLYKLGREEEAKE 291
                                   7889999999999*****************986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   6.9e-06    0.0032       5      36 ..      27      57 ..      23      60 .. 0.88
   2 ?   -1.4   0.0       6.1   2.9e+03      58      75 ..      64      81 ..      62      81 .. 0.80
   3 !    9.4   0.0    0.0028       1.3      10      32 ..     119     141 ..     115     148 .. 0.86
   4 !   19.8   0.3   1.5e-06   0.00071       5      33 ..     148     176 ..     144     177 .. 0.89
   5 !   21.6   0.9   4.2e-07    0.0002       5      66 ..     204     264 ..     201     264 .. 0.92
   6 !   13.6   2.4   0.00013     0.063       4      67 ..     237     292 ..     234     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.9e-06
                        TPR_12  5 alnnlaavlrrlgrydeAlellekaleiarrl 36
                                  ++   + vl++ gr++eAle +++a  i+++l
  gi|91772284|ref|YP_564976.1| 27 TY-GKGYVLHEIGRFEEALEKYDEAASIWEEL 57
                                  44.899***********************997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.1
                        TPR_12 58 lgryeeAlelleealaia 75
                                   g  +eA ++l++ l+i+
  gi|91772284|ref|YP_564976.1| 64 NGMEDEAKNALNRELEIR 81
                                  577799999999998885 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0028
                        TPR_12  10 aavlrrlgrydeAlellekalei 32 
                                   + +l+  grydeAl++l+ a+ +
  gi|91772284|ref|YP_564976.1| 119 GFILFNIGRYDEALRMLDLAISL 141
                                   889999***********998765 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 1.5e-06
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleia 33 
                                   a++  a++l++l+r++eAle++eka+e a
  gi|91772284|ref|YP_564976.1| 148 AWSCKANTLYQLERFEEALECYEKAIEFA 176
                                   78889********************9975 PP

  == domain 5  score: 21.6 bits;  conditional E-value: 4.2e-07
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                   +++  a++l +lg++ eA++ ++ alei   ++ + +++  ttl  Lg+   al+ y  Ale
  gi|91772284|ref|YP_564976.1| 204 IWYCKANTLEKLGKHKEAIDAYNSALEIK-PAFSDAWYCMGTTLEELGENENALNAYSNALE 264
                                   67899************************.788899**************999999999985 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 0.00013
                        TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                    a++ ++++l +lg+ + Al  +  ale+ r           ++l n + l+++lgr eeA el
  gi|91772284|ref|YP_564976.1| 237 DAWYCMGTTLEELGENENALNAYSNALEVERGF----T----AALENKANLLYKLGREEEAKEL 292
                                   57889*************************755....3....4677777777777777777666 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1      0.08        38       8      31 ..      31      54 ..      24      63 .. 0.72
   2 ?    0.0   0.0       4.5   2.1e+03      11      26 ..      61      76 ..      54      81 .. 0.81
   3 !   17.9   0.0   8.1e-06    0.0038      10      42 ..     121     153 ..     118     155 .. 0.89
   4 !   15.3   0.1   5.6e-05     0.026       1      29 [.     146     174 ..     146     178 .. 0.94
   5 !   24.0   0.0   9.2e-08   4.3e-05       3      42 ..     204     243 ..     202     244 .. 0.95
   6 !   14.9   0.0   7.3e-05     0.034       2      42 ..     237     277 ..     236     279 .. 0.88
   7 ?   -0.2   0.1       5.4   2.5e+03       8      24 ..     277     293 ..     270     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.08
                        TPR_14  8 aeallalGdpdeAiallrralala 31
                                  + +l + G+++eA++ +++a + +
  gi|91772284|ref|YP_564976.1| 31 GYVLHEIGRFEEALEKYDEAASIW 54
                                  667777888888888888887655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 4.5
                        TPR_14 11 llalGdpdeAiallrr 26
                                  + ++G  deA ++l+r
  gi|91772284|ref|YP_564976.1| 61 MIQNGMEDEAKNALNR 76
                                  5689999******998 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 8.1e-06
                        TPR_14  10 allalGdpdeAiallrralalaPddaeawllla 42 
                                   +l++ G++deA+++l+ a++l P+ ++aw   a
  gi|91772284|ref|YP_564976.1| 121 ILFNIGRYDEALRMLDLAISLEPEYPDAWSCKA 153
                                   57888************************7655 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 5.6e-05
                        TPR_14   1 peallalaeallalGdpdeAiallrrala 29 
                                   p+a+ + a  l++l++++eA++++++a++
  gi|91772284|ref|YP_564976.1| 146 PDAWSCKANTLYQLERFEEALECYEKAIE 174
                                   789************************98 PP

  == domain 5  score: 24.0 bits;  conditional E-value: 9.2e-08
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    +++ a  l+ lG+++eAi++++ al+  P++ +aw+ ++
  gi|91772284|ref|YP_564976.1| 204 IWYCKANTLEKLGKHKEAIDAYNSALEIKPAFSDAWYCMG 243
                                   69**********************************9987 PP

  == domain 6  score: 14.9 bits;  conditional E-value: 7.3e-05
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   +a+++++  l++lG+ + A++++  al+   ++ +a+   a
  gi|91772284|ref|YP_564976.1| 237 DAWYCMGTTLEELGENENALNAYSNALEVERGFTAALENKA 277
                                   69*************************99888877776655 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 5.4
                        TPR_14   8 aeallalGdpdeAiall 24 
                                   a +l+ lG+ +eA +ll
  gi|91772284|ref|YP_564976.1| 277 ANLLYKLGREEEAKELL 293
                                   77899999999999987 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00034      0.16      33      61 ..      23      51 ..      11      57 .. 0.90
   2 !   23.8   0.0   1.1e-07   5.4e-05       7      63 ..     122     175 ..     117     177 .. 0.94
   3 !   11.0   0.0    0.0011      0.53      36      65 ..     204     233 ..     196     238 .. 0.87
   4 !   14.7   0.2   7.8e-05     0.037       4      53 ..     243     289 ..     242     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00034
                        TPR_16 33 aaeAllllgdaalrqgrlaeAaalyraal 61
                                  +ae+ +++g ++ + gr++eA++ y++a+
  gi|91772284|ref|YP_564976.1| 23 NAESTYGKGYVLHEIGRFEEALEKYDEAA 51
                                  6899******************9999987 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.1e-07
                        TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                   +++ g+yd+A+++l+ a+ +    P+ ++A+  +++ ++++ r++eA++ y++a++ 
  gi|91772284|ref|YP_564976.1| 122 LFNIGRYDEALRMLDLAISLE---PEYPDAWSCKANTLYQLERFEEALECYEKAIEF 175
                                   7889*****************...***************************999865 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0011
                        TPR_16  36 AllllgdaalrqgrlaeAaalyraalraap 65 
                                    ++ +++ + ++g ++eA+++y++al+  p
  gi|91772284|ref|YP_564976.1| 204 IWYCKANTLEKLGKHKEAIDAYNSALEIKP 233
                                   67888999******************9887 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 7.8e-05
                        TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                   ++ + ++g+ + A++a+  al+         +Al +++++++++gr +eA
  gi|91772284|ref|YP_564976.1| 243 GTTLEELGENENALNAYSNALEVE---RGFTAALENKANLLYKLGREEEA 289
                                   6678899*****************...9999***************9998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.32   1.5e+02      18      46 ..      17      45 ..       6      53 .. 0.76
   2 !    8.1   0.5    0.0082       3.9      13      50 ..      39      76 ..      37     116 .. 0.76
   3 !   25.0   0.1   4.2e-08     2e-05       5      51 ..     126     172 ..     123     176 .. 0.95
   4 !   15.1   0.0   5.3e-05     0.025       5      44 ..     216     255 ..     212     255 .. 0.92
   5 !   20.9   2.1   8.1e-07   0.00038       5      48 ..     250     293 ..     246     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.32
                        TPR_19 18 lqedpknaearllLAeallalgqldeAea 46
                                  l++  knae  ++   +l + g+++eA +
  gi|91772284|ref|YP_564976.1| 17 LKQIVKNAESTYGKGYVLHEIGRFEEALE 45
                                  45556788888889999999999999976 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0082
                        TPR_19 13 lleqalqedpknaearllLAeallalgqldeAealLda 50
                                  ++e+al+++ + a ++  L + ++++g  deA+++L++
  gi|91772284|ref|YP_564976.1| 39 RFEEALEKYDEAASIWEELQQEMIQNGMEDEAKNALNR 76
                                  67778888777888888888888888888888888876 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 4.2e-08
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                   g+y+eAl++l  a++ +p++++a+   A+ l++l +++eA ++ +++
  gi|91772284|ref|YP_564976.1| 126 GRYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEEALECYEKA 172
                                   89***********************99***************98876 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 5.3e-05
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                   g++ eA++++ +al+ +p  ++a++ +   l +lg+ + A
  gi|91772284|ref|YP_564976.1| 216 GKHKEAIDAYNSALEIKPAFSDAWYCMGTTLEELGENENA 255
                                   99**************************999999997765 PP

  == domain 5  score: 20.9 bits;  conditional E-value: 8.1e-07
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                   g  ++Al+++++al+ + +  +a+ + A++l++lg+ +eA++lL
  gi|91772284|ref|YP_564976.1| 250 GENENALNAYSNALEVERGFTAALENKANLLYKLGREEEAKELL 293
                                   67789*************************************99 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.44   2.1e+02      35      56 ..      30      51 ..      22      66 .. 0.83
   2 !   25.7   0.0     2e-08   9.6e-06       9      65 ..      92     148 ..      86     153 .. 0.93
   3 !   23.2   0.7   1.2e-07   5.6e-05      10      59 ..     127     176 ..     127     180 .. 0.94
   4 !    9.1   0.0    0.0029       1.4       9      59 ..     216     266 ..     209     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.44
                         TPR_9 35 RGlllaqlGclsaAladLeayl 56
                                   G +l++ G++++Al+  + ++
  gi|91772284|ref|YP_564976.1| 30 KGYVLHEIGRFEEALEKYDEAA 51
                                  68999**********9887766 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 2e-08
                         TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                   ++ e+al ++e  ++ +Pdd   ++  G++l+  G++ +Al+ L+ +++l+p+ pda
  gi|91772284|ref|YP_564976.1|  92 DKKEEALTIIENTIQKKPDDMKPIFSKGFILFNIGRYDEALRMLDLAISLEPEYPDA 148
                                   67799***********************************************99998 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.2e-07
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   ++++al+++++ + l P+ p+ +   +  l+ql+++++Al++ e +++ a
  gi|91772284|ref|YP_564976.1| 127 RYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEEALECYEKAIEFA 176
                                   5899*****************************************99865 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0029
                         TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                    ++ +a+ ++++ l ++P   + ++  G  l++lG  + Al++   +l+++
  gi|91772284|ref|YP_564976.1| 216 GKHKEAIDAYNSALEIKPAFSDAWYCMGTTLEELGENENALNAYSNALEVE 266
                                   57889***************************************9999886 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00065      0.31       9      35 ..      31      57 ..      30      57 .. 0.94
   2 ?   -0.1   0.0       1.9   9.1e+02      12      30 ..      88     106 ..      86     107 .. 0.80
   3 !    9.3   0.0    0.0022         1       9      30 ..     119     140 ..     119     141 .. 0.88
   4 !   15.8   0.2     2e-05    0.0095       9      30 ..     153     174 ..     152     176 .. 0.95
   5 ?    3.7   0.0      0.13        61       9      31 ..     209     231 ..     208     232 .. 0.91
   6 ?    1.2   0.1      0.76   3.6e+02       9      31 ..     243     265 ..     241     267 .. 0.83
   7 ?    7.1   0.2     0.011         5       3      25 ..     271     293 ..     270     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                        TPR_10  9 analrqrgrydeAealleealairrrl 35
                                  + +l++ gr++eA++ ++ea +i+++l
  gi|91772284|ref|YP_564976.1| 31 GYVLHEIGRFEEALEKYDEAASIWEEL 57
                                  67999********************96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                        TPR_10  12 lrqrgrydeAealleeala 30 
                                   l+++ + +eA+ + e +++
  gi|91772284|ref|YP_564976.1|  88 LFKLDKKEEALTIIENTIQ 106
                                   7788899999999887775 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0022
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   + +l++ grydeA+++l+ a++
  gi|91772284|ref|YP_564976.1| 119 GFILFNIGRYDEALRMLDLAIS 140
                                   5689999**********99986 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 2e-05
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   an+l+q+ r++eA++ +e+a++
  gi|91772284|ref|YP_564976.1| 153 ANTLYQLERFEEALECYEKAIE 174
                                   89******************98 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.13
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   an+l ++g+++eA + +  al+i
  gi|91772284|ref|YP_564976.1| 209 ANTLEKLGKHKEAIDAYNSALEI 231
                                   899999********999999987 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.76
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   + +l ++g+ + A++ +  al++
  gi|91772284|ref|YP_564976.1| 243 GTTLEELGENENALNAYSNALEV 265
                                   78889999999999999888876 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.011
                        TPR_10   3 sslnNLanalrqrgrydeAeall 25 
                                   ++l N an+l+++gr +eA +ll
  gi|91772284|ref|YP_564976.1| 271 AALENKANLLYKLGREEEAKELL 293
                                   589999*************9986 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 ?    4.6   0.0     0.079        37      15      49 ..      16      50 ..      10      62 .. 0.72
   2 ?    6.9   0.0     0.016       7.3      54      81 ..      76     103 ..      62     104 .. 0.79
   3 !   23.5   0.1   9.9e-08   4.7e-05       7      82 .]      96     172 ..      95     172 .. 0.95
   4 !   13.9   0.1    0.0001     0.047      53      80 ..     199     226 ..     192     228 .. 0.86
   5 !   15.5   0.5   3.2e-05     0.015      27      81 ..     206     261 ..     202     262 .. 0.86
   6 ?    4.9   0.4     0.064        30      36      80 ..     249     294 ..     229     296 .] 0.58

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.079
                                  HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                        ANAPC3 15 llaaetespedayllAlclylngqykrAyellrka 49
                                   l++  +++e++y ++++l + g++++A+e +++a
  gi|91772284|ref|YP_564976.1| 16 KLKQIVKNAESTYGKGYVLHEIGRFEEALEKYDEA 50
                                  44466677777777777777777777777766655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.016
                                   C-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  54 kslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   + l++r+ +   l+kL+k eeA++++e+
  gi|91772284|ref|YP_564976.1|  76 RELEIRFNKCFILFKLDKKEEALTIIEN 103
                                   55666666677899***********997 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 9.9e-08
                                   HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                        ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                   +A+ ++e   ++++++ + ++ ++  l++ g+y++A++ l+ a  l+++ + ++ ++A +l++L+++eeA+ ++ek+
  gi|91772284|ref|YP_564976.1|  96 EALTIIENTIQKKPDDMKPIFSKGFILFNIGRYDEALRMLDLAiSLEPEYPDAWSCKANTLYQLERFEEALECYEKA 172
                                   7999999999899999999******************************************************9985 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 0.0001
                                   HC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  53 skslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   ++  g++y++A +l kL+k++eAi+a+ 
  gi|91772284|ref|YP_564976.1| 199 KNASGIWYCKANTLEKLGKHKEAIDAYN 226
                                   456799*******************986 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  27 yllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   y +A +l ++g++k+A++ +++a ++++    ++y+++ +l +L++ e A++a+++
  gi|91772284|ref|YP_564976.1| 206 YCKANTLEKLGKHKEAIDAYNSAlEIKPAFSDAWYCMGTTLEELGENENALNAYSN 261
                                   45688999999999999999999999999999999999999999999999998875 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.064
                                   TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   +g+ + A++ +++a + +    +++  +A  l+kL++ eeA  +L+
  gi|91772284|ref|YP_564976.1| 249 LGENENALNAYSNAlEVERGFTAALENKANLLYKLGREEEAKELLG 294
                                   5555555555555545555555555566666666666666655554 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.017       7.9       8      31 ..      33      56 ..      28      61 .. 0.80
   2 ?   -0.5   0.0       3.6   1.7e+03      10      35 ..      89     112 ..      87     113 .. 0.80
   3 ?    4.4   0.0     0.099        46       9      30 ..     122     141 ..     121     146 .. 0.77
   4 !   14.2   0.0   7.3e-05     0.034       6      29 ..     153     176 ..     152     196 .. 0.87
   5 !    9.4   0.0    0.0023       1.1       6      31 ..     209     234 ..     208     239 .. 0.86
   6 ?    5.4   0.1     0.045        21       5      29 ..     242     266 ..     238     270 .. 0.85
   7 ?   -0.5   0.1       3.5   1.7e+03       1      21 [.     272     292 ..     272     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                         TPR_7  8 lysrlGdyeeAielyeqsLaltkd 31
                                  + ++ G++eeA+e y ++  ++++
  gi|91772284|ref|YP_564976.1| 33 VLHEIGRFEEALEKYDEAASIWEE 56
                                  56789**********997766655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.6
                         TPR_7  10 srlGdyeeAielyeqsLaltkdpeda 35 
                                   ++l + eeA+++ e    + k p+d+
  gi|91772284|ref|YP_564976.1|  89 FKLDKKEEALTIIEN--TIQKKPDDM 112
                                   6777889****9999..888888876 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.099
                         TPR_7   9 ysrlGdyeeAielyeqsLaltk 30 
                                    ++ G+y+eA++ +    a+  
  gi|91772284|ref|YP_564976.1| 122 LFNIGRYDEALRMLDL--AISL 141
                                   6789*******99988..5554 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 7.3e-05
                         TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                   a++  +l ++eeA+e+ye++++++
  gi|91772284|ref|YP_564976.1| 153 ANTLYQLERFEEALECYEKAIEFA 176
                                   6788899************77765 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0023
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                   a++ ++lG+++eAi+ y  +L++  +
  gi|91772284|ref|YP_564976.1| 209 ANTLEKLGKHKEAIDAYNSALEIKPA 234
                                   8999*************998888765 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.045
                         TPR_7   5 LarlysrlGdyeeAielyeqsLalt 29 
                                   ++ + ++lG+ e+A+  y  +L+++
  gi|91772284|ref|YP_564976.1| 242 MGTTLEELGENENALNAYSNALEVE 266
                                   78899*************9966655 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 3.5
                         TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                   aL n a+l  +lG+ eeA el
  gi|91772284|ref|YP_564976.1| 272 ALENKANLLYKLGREEEAKEL 292
                                   688999**99***99999877 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0014      0.64      11      93 ..      29     109 ..      21     111 .. 0.81
   2 !   14.1   0.0    0.0001     0.048      73     122 ..     123     172 ..     118     176 .. 0.94
   3 !   11.6   0.1   0.00059      0.28      74     123 ..     214     263 ..     206     267 .. 0.92
   4 ?    0.9   0.1       1.2   5.6e+02      57      83 ..     265     291 ..     261     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                                   HHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          BTAD  11 aagraalaagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealaelealvae 91 
                                    +g  +++ g++eea+e++++A+++w++   + ++  + +e+e++   ++ le+    +  +++l + eeal+  e+ +++
  gi|91772284|ref|YP_564976.1|  29 GKGYVLHEIGRFEEALEKYDEAASIWEELQQEMIQ--NGMEDEAKNALNRELEIRFNKCFILFKLDKKEEALTIIENTIQK 107
                                   5666788899****************987666655..58888888888888999888888899999999999988888887 PP

                                   ST CS
                          BTAD  92 hP 93 
                                   +P
  gi|91772284|ref|YP_564976.1| 108 KP 109
                                   77 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.0001
                                   HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                   + +Gr++eal+ l+ +++++P   +++      l++++r +eALe Ye++
  gi|91772284|ref|YP_564976.1| 123 FNIGRYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEEALECYEKA 172
                                   679********************************************987 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00059
                                   HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                   +lG+++ea++ ++++++ +P   +++  + + l  +G+++ AL++Y ++ 
  gi|91772284|ref|YP_564976.1| 214 KLGKHKEAIDAYNSALEIKPAFSDAWYCMGTTLEELGENENALNAYSNAL 263
                                   79********************************************9875 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                          BTAD  57 leelrlealealaeaelrlGraeeala 83 
                                   +e+ + +ale  a+++ +lGr+eea +
  gi|91772284|ref|YP_564976.1| 265 VERGFTAALENKANLLYKLGREEEAKE 291
                                   56778999*************999876 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0024       1.1     104     139 ..      28      63 ..      20      67 .. 0.88
   2 ?    4.7   0.0     0.064        30     102     126 ..     114     138 ..     109     144 .. 0.85
   3 !   12.5   0.2   0.00024      0.11      61     129 ..     152     231 ..     147     233 .. 0.71
   4 ?    5.1   0.1     0.048        23     106     129 ..     242     265 ..     235     279 .. 0.82
   5 ?    0.5   0.0       1.2   5.7e+02     100     120 ..     270     290 ..     264     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S--TT CS
                       DUF3856 104 fsravaleelGrkdealkafrmagemiaerkGelkg 139
                                   + ++  l+e+Gr +eal+++  a+ + +e + e+ +
  gi|91772284|ref|YP_564976.1|  28 YGKGYVLHEIGRFEEALEKYDEAASIWEELQQEMIQ 63 
                                   678999*******************99999988865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.064
                                   HHHHHHHHHHHTT-HHHHHHHHHHH CS
                       DUF3856 102 avfsravaleelGrkdealkafrma 126
                                    +fs++  l ++Gr+deal+++  a
  gi|91772284|ref|YP_564976.1| 114 PIFSKGFILFNIGRYDEALRMLDLA 138
                                   589999999999****999988776 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00024
                                   HHHHHHHTT-HHHHHHHHHHHHHH.....HH..HH--TTSTHH...HHHHH.HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  61 lsealaklgrydealesadkalry.....fn..rrGeleqdeG...klWia.avfsravaleelGrkdealkafrmagem 129
                                    +++l +l r++eale+ +ka+++     fn  r   l+ +     k+  + + + +a +le+lG+++ea++a++ a e+
  gi|91772284|ref|YP_564976.1| 152 KANTLYQLERFEEALECYEKAIEFadimhFNfpRYSFLNMNPDptiKKNASgIWYCKANTLEKLGKHKEAIDAYNSALEI 231
                                   57788899999999999999976544444443377766654321123333315689*******************99885 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.048
                                   HHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856 106 ravaleelGrkdealkafrmagem 129
                                    +++leelG +++al+a+  a e+
  gi|91772284|ref|YP_564976.1| 242 MGTTLEELGENENALNAYSNALEV 265
                                   6789**************999986 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHTT-HHHHH CS
                       DUF3856 100 iaavfsravaleelGrkdeal 120
                                    aa+ ++a  l +lGr++ea 
  gi|91772284|ref|YP_564976.1| 270 TAALENKANLLYKLGREEEAK 290
                                   688999************996 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3   2.6e-07   0.00012      24      98 ..      34     135 ..      14     144 .. 0.74
   2 !   20.8   0.1   6.5e-07    0.0003      19      96 ..      82     167 ..      63     169 .. 0.75
   3 !    9.3   0.1    0.0023       1.1      20      65 ..     152     222 ..     139     244 .. 0.78
   4 ?    1.4   0.1      0.64     3e+02      48      69 ..     273     294 ..     244     296 .] 0.67

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-07
                  SRP_TPR_like  24 liklekyeeaLkllkkgs.......................alsedvrfEkaYvlYklkkykkalkilkkveaee..kvkv 79 
                                   l +++++eeaL+  +++                        + + ++rf k ++l+kl k ++al i++++ +++   +k 
  gi|91772284|ref|YP_564976.1|  34 LHEIGRFEEALEKYDEAAsiweelqqemiqngmedeaknalNRELEIRFNKCFILFKLDKKEEALTIIENTIQKKpdDMKP 114
                                   45667777777766666667777779***********99555556799********************9876664346776 PP

                  SRP_TPR_like  80 lksq..vlYrlgsyekAYklL 98 
                                   + s+  +l+ +g y++A ++L
  gi|91772284|ref|YP_564976.1| 115 IFSKgfILFNIGRYDEALRML 135
                                   66644499*********9998 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 6.5e-07
                  SRP_TPR_like  19 f.kvvaliklekyeeaLkllkkgs.alsedv..rfEkaYvlYklkkykkalkilkkveaee....kvkvlksqvlYrlgsy 91 
                                   f k   l kl+k eeaL++++++  +  +d+  +f k ++l+ + +y +al++l+ + + e     +   k+  lY l+ +
  gi|91772284|ref|YP_564976.1|  82 FnKCFILFKLDKKEEALTIIENTIqKKPDDMkpIFSKGFILFNIGRYDEALRMLDLAISLEpeypDAWSCKANTLYQLERF 162
                                   357888999********999876524445552269*****************99866554432256678899999999999 PP

                  SRP_TPR_like  92 ekAYk 96 
                                   e+A +
  gi|91772284|ref|YP_564976.1| 163 EEALE 167
                                   99976 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0023
                  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs.........................alsedvrfEkaYvlYklkkykkal 65 
                                   k+ +l +le++eeaL+  +k+                          + ++ + + ka  l kl k k+a 
  gi|91772284|ref|YP_564976.1| 152 KANTLYQLERFEEALECYEKAIefadimhfnfprysflnmnpdptikKNASGIWYCKANTLEKLGKHKEAI 222
                                   788899***********999986777777777777777777777776566667777777777777777776 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.64
                  SRP_TPR_like  48 rfEkaYvlYklkkykkalkilk 69 
                                      ka  lYkl + ++a ++l 
  gi|91772284|ref|YP_564976.1| 273 LENKANLLYKLGREEEAKELLG 294
                                   3358999999999999988775 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   9.4e-05     0.044      89     240 ..      13     172 ..       4     179 .. 0.77
   2 !   10.3   0.0   0.00061      0.29     138     180 ..     193     236 ..     186     239 .. 0.83
   3 !    9.2   0.1    0.0014      0.64     148     203 ..     238     293 ..     236     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-05
                        TPR_15  89 ydaepkeaarlaekgwrrf...rsprlLssalellera.kdydria.ellksle...eeeaaeqsaafllaraelyrqegq 161
                                   y+++ k+ ++ ae+++ +    ++  ++++ale +++a   +++++ e++++ +   +++a++++  + +    +  + ++
  gi|91772284|ref|YP_564976.1|  13 YKRKLKQIVKNAESTYGKGyvlHEIGRFEEALEKYDEAaSIWEELQqEMIQNGMedeAKNALNRELEIRFNKCFILFKLDK 93 
                                   6777777777777777774344888889999998876515688886257777552323445888888888888899999** PP

                        TPR_15 162 tdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkq 240
                                   +++Al+++++ ++++pd+ + +    ++l + gr++e+ ++l      + + ++ w   a  l  L+r ++ALe ++k 
  gi|91772284|ref|YP_564976.1|  94 KEEALTIIENTIQKKPDDMKPIFSKGFILFNIGRYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEEALECYEKA 172
                                   ******************99988888888889****96666655555558999999999***************99985 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00061
                        TPR_15 138 eeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                   ++++ + + + +++  a+  ++ g++++A+ +y  Al+ +p+ s
  gi|91772284|ref|YP_564976.1| 193 PDPTIKkNASGIWYCKANTLEKLGKHKEAIDAYNSALEIKPAFS 236
                                   566655356789****************************9865 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0014
                        TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrell 203
                                    ++ ++   ++ g++++Al++y +Al+++ + +++ ++   ll  lgr++e++ell
  gi|91772284|ref|YP_564976.1| 238 AWYCMGTTLEELGENENALNAYSNALEVERGFTAALENKANLLYKLGREEEAKELL 293
                                   599999999*********************99999999999999999999999987 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.092        43       1      28 [.      32      59 ..      28      76 .. 0.85
   2 ?    2.2   0.0      0.74   3.5e+02      10      32 ..      88     110 ..      86     111 .. 0.86
   3 ?    4.0   0.0       0.2        94       8      31 ..     120     143 ..     116     145 .. 0.81
   4 ?    5.0   0.2     0.095        45      10      28 ..     156     174 ..     152     174 .. 0.80
   5 ?    5.1   0.0     0.087        41       9      28 ..     211     230 ..     208     233 .. 0.85
   6 ?    4.5   0.0      0.14        65       1      27 [.     237     263 ..     237     265 .. 0.86
   7 ?    5.3   0.2     0.074        35       2      23 ..     272     293 ..     271     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.092
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  1 dAlyklalsyrklgdtdkAlealerlik 28
                                  ++l  +++  ++l ++d+A  ++e+l +
  gi|91772284|ref|YP_564976.1| 32 YVLHEIGRFEEALEKYDEAASIWEELQQ 59
                                  5677888888887799999999988866 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.74
                                   HHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                                   ++kl+++++Al++ e+ i++ Pd
  gi|91772284|ref|YP_564976.1|  88 LFKLDKKEEALTIIENTIQKKPD 110
                                   678889*********99998776 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   8 lsyrklgdtdkAlealerlikeYP 31 
                                     +++ g++d+Al++l+  i+  P
  gi|91772284|ref|YP_564976.1| 120 FILFNIGRYDEALRMLDLAISLEP 143
                                   5678878*********98888766 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.095
                                   HHHHHHHHHHHHHHHHHHH CS
                         TPR_6  10 yrklgdtdkAlealerlik 28 
                                   +++l + ++Ale +e+ i+
  gi|91772284|ref|YP_564976.1| 156 LYQLERFEEALECYEKAIE 174
                                   566559**********986 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.087
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAlealerlik 28 
                                    ++klg++ +A++a+++ ++
  gi|91772284|ref|YP_564976.1| 211 TLEKLGKHKEAIDAYNSALE 230
                                   678899*********99876 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerli 27 
                                   dA y ++  +++lg+ ++Al a+ + +
  gi|91772284|ref|YP_564976.1| 237 DAWYCMGTTLEELGENENALNAYSNAL 263
                                   577779999***99*********8876 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.074
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAleal 23 
                                   Al + a +++klg+ ++A+e+l
  gi|91772284|ref|YP_564976.1| 272 ALENKANLLYKLGREEEAKELL 293
                                   566779999**99*******98 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.2    0.0091       4.3      18      70 ..      11      63 ..       5      67 .. 0.89
   2 ?    4.3   0.1     0.032        15      34      72 ..      74     112 ..      64     118 .. 0.83
   3 !    9.8   0.0   0.00071      0.33     205     252 ..     125     172 ..     120     178 .. 0.90
   4 ?    0.8   0.0      0.38   1.8e+02      44      69 ..     208     233 ..     203     241 .. 0.79
   5 !    9.8   0.4   0.00069      0.32      12      60 ..     244     292 ..     235     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0091
                                  THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                         NARP1 18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpe 70
                                   ++++ l+++ +++++   k  v+   ++++ +L++++eA++++e+L +   +
  gi|91772284|ref|YP_564976.1| 11 ASYKRKLKQIVKNAESTYGKGYVLHEIGRFEEALEKYDEAASIWEELQQEMIQ 63
                                  56788999***************************************987655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.032
                                   ---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                         NARP1  34 ivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                   +  +l+++ +k  +l+kL++keeA +++e+ +++ p+++
  gi|91772284|ref|YP_564976.1|  74 LNRELEIRFNKCFILFKLDKKEEALTIIENTIQKKPDDM 112
                                   4456888889999*********************99976 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00071
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                   +g++++Al+++d ai+ +p+  + +  Ka+ l +   +++A e+ e+a
  gi|91772284|ref|YP_564976.1| 125 IGRYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEEALECYEKA 172
                                   68899*************************999999999999999888 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.38
                                   HHHHHHHTT-HHHHHHHHHHHHHH-T CS
                         NARP1  44 kaelllkLgrkeeAeatyeaLlernp 69 
                                   ka+ l kLg+++eA  +y++ le  p
  gi|91772284|ref|YP_564976.1| 208 KANTLEKLGKHKEAIDAYNSALEIKP 233
                                   78888899999999999988887765 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00069
                                   HHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHH CS
                         NARP1  12 qiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeat 60 
                                   + +ee g++e+Al+  +++ +      a +e+ka+ll kLgr+eeA+++
  gi|91772284|ref|YP_564976.1| 244 TTLEELGENENALNAYSNALEVERGFTAALENKANLLYKLGREEEAKEL 292
                                   578999************99999999********************986 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.24   1.1e+02       3      22 ..      26      45 ..      24      45 .. 0.83
   2 ?    5.7   0.0     0.062        29      15      25 ..     126     136 ..     121     136 .. 0.94
   3 ?    2.8   0.0      0.52   2.5e+02       5      25 ..     150     170 ..     146     171 .. 0.82
   4 ?    6.6   0.0     0.032        15       2      24 ..     271     293 ..     270     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.24
                         TPR_4  3 allaLArallalGdldeAra 22
                                   +++ + +l++ G+++eA++
  gi|91772284|ref|YP_564976.1| 26 STYGKGYVLHEIGRFEEALE 45
                                  567788999999******85 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.062
                         TPR_4  15 GdldeAralle 25 
                                   G++deA+++l+
  gi|91772284|ref|YP_564976.1| 126 GRYDEALRMLD 136
                                   9********96 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.52
                         TPR_4   5 laLArallalGdldeAralle 25 
                                   +  A +l++l +++eA++  e
  gi|91772284|ref|YP_564976.1| 150 SCKANTLYQLERFEEALECYE 170
                                   55688999999******9877 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.032
                         TPR_4   2 rallaLArallalGdldeArall 24 
                                   +al + A +l+ lG+ +eA +ll
  gi|91772284|ref|YP_564976.1| 271 AALENKANLLYKLGREEEAKELL 293
                                   578899*************9998 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2    0.0031       1.5      18      50 ..      38      75 ..      31      81 .. 0.70
   2 ?    1.0   0.0      0.98   4.6e+02      26      40 ..     127     142 ..     125     158 .. 0.76
   3 !    8.8   0.3    0.0034       1.6      18      32 ..     160     174 ..     150     178 .. 0.87
   4 !   10.0   0.3    0.0015      0.69      10      32 ..     208     230 ..     206     231 .. 0.91
   5 ?    5.7   0.2     0.032        15      13      33 ..     245     265 ..     241     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                           MIT 18 gnyeeAlelYkealelLlqalke..kne...errellr 50
                                  g +eeAle+Y ea  ++ ++ +e  +n    e +++l 
  gi|91772284|ref|YP_564976.1| 38 GRFEEALEKYDEAASIWEELQQEmiQNGmedEAKNALN 75
                                  789***********999998884443322224455444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.98
                           MIT  26 lYkealelLlqalk.e 40 
                                    Y eal+ L +a++ e
  gi|91772284|ref|YP_564976.1| 127 RYDEALRMLDLAISlE 142
                                   5889999998888754 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0034
                           MIT  18 gnyeeAlelYkeale 32 
                                   + +eeAle+Y++a+e
  gi|91772284|ref|YP_564976.1| 160 ERFEEALECYEKAIE 174
                                   689***********8 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0015
                           MIT  10 kAveeDnagnyeeAlelYkeale 32 
                                   kA  +++ g+ +eA+++Y +ale
  gi|91772284|ref|YP_564976.1| 208 KANTLEKLGKHKEAIDAYNSALE 230
                                   688899***************98 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.032
                           MIT  13 eeDnagnyeeAlelYkealel 33 
                                    +++ g+ e Al++Y++ale+
  gi|91772284|ref|YP_564976.1| 245 TLEELGENENALNAYSNALEV 265
                                   6789999************96 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.023        11       4      25 ..      27      48 ..      25      53 .. 0.85
   2 ?    6.1   0.0     0.024        11       5      34 ..     116     143 ..     112     144 .. 0.80
   3 ?    5.0   0.1     0.054        25      10      27 ..     155     170 ..     153     175 .. 0.87
   4 ?   -1.9   0.0       7.5   3.5e+03      16      26 ..     217     225 ..     215     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.023
                                  HHHHHHHHHHTT-HHHHHHH.. CS
                         TPR_3  4 lysyAaefynkkkyqeArelfs 25
                                   y+ +++++  ++++eA+e ++
  gi|91772284|ref|YP_564976.1| 27 TYGKGYVLHEIGRFEEALEKYD 48
                                  56669*************9866 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.024
                                   HHHHHHHHHTT-HHHHHHH..HHHHHHH-T CS
                         TPR_3   5 ysyAaefynkkkyqeArelfsYallaildk 34 
                                   +s ++ ++n ++y+eA+  ++  l+  l++
  gi|91772284|ref|YP_564976.1| 116 FSKGFILFNIGRYDEALRMLD--LAISLEP 143
                                   55578899*********9999..8876665 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.054
                                   HHHHTT-HHHHHHH..HH CS
                         TPR_3  10 efynkkkyqeArelfsYa 27 
                                   ++y+ ++++eA+e   Y+
  gi|91772284|ref|YP_564976.1| 155 TLYQLERFEEALEC--YE 170
                                   89***********9..64 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 7.5
                                   -HHHHHHH..H CS
                         TPR_3  16 kyqeArelfsY 26 
                                   k  eA+++  Y
  gi|91772284|ref|YP_564976.1| 217 KHKEAIDA--Y 225
                                   55689999..4 PP

>> RIBIOP_C  40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3     2e-06   0.00097      38     133 ..       5     126 ..       2     130 .. 0.70
   2 ?   -1.3   0.0       2.5   1.2e+03      95     133 ..     246     284 ..     228     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-06
                      RIBIOP_C  38 arifefenfketkkrvlkeale........................eregveg......Gtyvrleiknvpeelveek... 85 
                                   +++f+ +++k++ k+++k+a++                        +             ++++  +++  ++        
  gi|91772284|ref|YP_564976.1|   5 KDMFQQASYKRKLKQIVKNAEStygkgyvlheigrfeealekydeaA-----SiweelqQEMIQNGMEDEAKNA---Lnre 77 
                                   57899999999999999977776788888888777766554432110.....1221222222222222222222...1333 PP

                      RIBIOP_C  86 .nfdekkplivfgllphEekvsvvnvrikrhreyekpikskdplifsvG 133
                                    +   +k +i+f+l + Ee +++++ +i+++++  kpi sk  ++f++G
  gi|91772284|ref|YP_564976.1|  78 lEIRFNKCFILFKLDKKEEALTIIENTIQKKPDDMKPIFSKGFILFNIG 126
                                   56678899**************************************999 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                      RIBIOP_C  95 vfgllphEekvsvvnvrikrhreyekpikskdplifsvG 133
                                   + +l ++E+ +  ++  ++ +r +++ +++k +l+ ++G
  gi|91772284|ref|YP_564976.1| 246 LEELGENENALNAYSNALEVERGFTAALENKANLLYKLG 284
                                   567888999999999999999999999****99999998 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       8.5     4e+03      18      33 ..      95     110 ..      89     112 .. 0.70
   2 !   11.9   0.0   0.00039      0.18      13      36 ..     124     147 ..     122     152 .. 0.89
   3 ?   -0.8   0.1       3.4   1.6e+03      12      28 ..     157     173 ..     153     176 .. 0.81
   4 ?    4.4   0.0     0.084        40      13      37 ..     214     238 ..     206     239 .. 0.92
   5 ?    0.4   0.1       1.5   7.3e+02      14      37 ..     249     272 ..     248     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.5
                                   HHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  18 seArryvdalLeiEPe 33 
                                   +eA+  ++  +++ P+
  gi|91772284|ref|YP_564976.1|  95 EEALTIIENTIQKKPD 110
                                   6777788887777776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00039
                                   HHT-HHHHHHHHHHHHHHTTS-HH CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQ 36 
                                    +g+Y+eA+r +d  +++EPe   
  gi|91772284|ref|YP_564976.1| 124 NIGRYDEALRMLDLAISLEPEYPD 147
                                   689*****************9765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.4
                                   HHHT-HHHHHHHHHHHH CS
                    Fis1_TPR_C  12 yklgeYseArryvdalL 28 
                                   y l +++eA+++ +  +
  gi|91772284|ref|YP_564976.1| 157 YQLERFEEALECYEKAI 173
                                   88999999999987665 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.084
                                   HHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                                   klg+++eA    +  Lei P ++ a
  gi|91772284|ref|YP_564976.1| 214 KLGKHKEAIDAYNSALEIKPAFSDA 238
                                   9*******************99766 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 1.5
                                   HT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                                   lge ++A++     Le+E ++  a
  gi|91772284|ref|YP_564976.1| 249 LGENENALNAYSNALEVERGFTAA 272
                                   678899999999999999887665 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00074      0.35     209     289 ..      87     167 ..      13     172 .. 0.93
   2 ?    5.2   0.1     0.019       8.8     236     290 ..     204     258 ..     189     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00074
                                   HHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                         ChAPs 209 vllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALl 289
                                   +l+  d+  +a+ +++++++++++d++ +  +   l +  +++ Al++ + a+++ P     W + +++  +le +e+AL 
  gi|91772284|ref|YP_564976.1|  87 ILFKLDKKEEALTIIENTIQKKPDDMKPIFSKGFILFNIGRYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEEALE 167
                                   5677899999*******************999999********************************************95 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                         ChAPs 236 lLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALlt 290
                                   +  ++a+ l +  k++ A+++ ++a ++ P  +  W+++  +  +l++ enAL +
  gi|91772284|ref|YP_564976.1| 204 IWYCKANTLEKLGKHKEAIDAYNSALEIKPAFSDAWYCMGTTLEELGENENALNA 258
                                   56677888888889999***********************************965 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3     0.024        11     152     188 ..      30      66 ..       7      74 .. 0.84
   2 ?    3.1   0.0      0.14        68     122     174 ..     121     174 ..      87     190 .. 0.74
   3 ?    2.8   0.1      0.18        83     156     174 ..     212     230 ..     207     236 .. 0.86
   4 ?    1.8   0.0      0.35   1.7e+02     154     176 ..     244     266 ..     240     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                        TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleekarellqlKl 188
                                   +G +l + g+++eA ++Y++A +  ee ++e++q  +
  gi|91772284|ref|YP_564976.1|  30 KGYVLHEIGRFEEALEKYDEAASIWEELQQEMIQNGM 66 
                                   89999****************9999999999998655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                        TPR_21 122 vllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                   +l++ + ydeAl++L+ + + e     +   + + l++ ++++eA + Y++A++
  gi|91772284|ref|YP_564976.1| 121 ILFNIGRYDEALRMLDLAISlEPEYPDAWSCKANTLYQLERFEEALECYEKAIE 174
                                   567778999999999654321222234445788889999999999999999986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.18
                        TPR_21 156 lvaqgkldeAraaYqaAla 174
                                   l + gk +eA +aY+ Al+
  gi|91772284|ref|YP_564976.1| 212 LEKLGKHKEAIDAYNSALE 230
                                   6688*************97 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.35
                        TPR_21 154 DilvaqgkldeAraaYqaAlaal 176
                                     l + g++++A +aY++Al+  
  gi|91772284|ref|YP_564976.1| 244 TTLEELGENENALNAYSNALEVE 266
                                   5677889************9865 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.37   1.7e+02      12      44 ..      14      46 ..       6      80 .. 0.79
   2 ?    6.5   0.0     0.023        11       5      45 ..      95     135 ..      92     148 .. 0.89
   3 ?   -1.6   0.0       7.7   3.6e+03      22      43 ..     146     167 ..     135     168 .. 0.76
   4 ?    2.9   0.1       0.3   1.4e+02       5      55 ..     219     269 ..     216     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.37
                        TPR_20 12 eaalaanpddldarldlAlallaagryeeAleq 44
                                  +++l++  ++ +  +    +l++ gr eeAle+
  gi|91772284|ref|YP_564976.1| 14 KRKLKQIVKNAESTYGKGYVLHEIGRFEEALEK 46
                                  667777778888888888889999999999885 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                        TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqL 45 
                                   ++ l+ +e++++++pdd++  +     l+  gry+eAl  L
  gi|91772284|ref|YP_564976.1|  95 EEALTIIENTIQKKPDDMKPIFSKGFILFNIGRYDEALRML 135
                                   56778899*****************************9877 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 7.7
                        TPR_20  22 ldarldlAlallaagryeeAle 43 
                                    da    A+ l++ +r eeAle
  gi|91772284|ref|YP_564976.1| 146 PDAWSCKANTLYQLERFEEALE 167
                                   5555566889999999999997 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.3
                        TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                   ++ +++  +al+ +p+  da + + + l + g++e Al++  + l+ +r++
  gi|91772284|ref|YP_564976.1| 219 KEAIDAYNSALEIKPAFSDAWYCMGTTLEELGENENALNAYSNALEVERGF 269
                                   567788888899999999999999999999999999999888888888777 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 ?   13.2   0.1   7.2e-05     0.034     128     181 ..      30      83 ..      22     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-05
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH.....TTTHHHHHHHTHH...HHHHHH CS
                         SRP68 128 rGallfekqqWekalesyskaraiyeaLakvt.....seefkdllsetveelePsiRYc 181
                                   +G +l+e  ++e+ale+y +a +i+e+L + +     ++e+k+ l++++e     iR++
  gi|91772284|ref|YP_564976.1|  30 KGYVLHEIGRFEEALEKYDEAASIWEELQQEMiqngmEDEAKNALNRELE-----IRFN 83 
                                   799999**********************9987733355566666665555.....7776 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 ?    1.1   0.0         1   4.8e+02      20      39 ..      36      55 ..      26      81 .. 0.78
   2 ?    8.7   0.0    0.0041       1.9      12      37 ..     150     175 ..     146     186 .. 0.86
   3 ?    0.8   0.1       1.2   5.7e+02      14      35 ..     208     229 ..     205     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1
                     NRBF2_MIT 20 aaGkyeeaischkkaaayls 39
                                    G++eea+  +  aa++  
  gi|91772284|ref|YP_564976.1| 36 EIGRFEEALEKYDEAASIWE 55
                                  56899999988888887654 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0041
                     NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaay 37 
                                   s ka+ l    ++eea+ c++ka ++
  gi|91772284|ref|YP_564976.1| 150 SCKANTLYQLERFEEALECYEKAIEF 175
                                   679999999*************9875 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.2
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaa 35 
                                   ka+ l   Gk++eai  ++ a 
  gi|91772284|ref|YP_564976.1| 208 KANTLEKLGKHKEAIDAYNSAL 229
                                   78889999*******9988775 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0         1   4.7e+02      14      25 ..      38      49 ..      36      51 .. 0.88
   2 ?    2.7   0.1       0.4   1.9e+02      15      28 ..      46      59 ..      43      66 .. 0.84
   3 ?   -0.5   0.0         4   1.9e+03      12      21 ..      63      72 ..      59      76 .. 0.72
   4 ?    3.0   0.0       0.3   1.4e+02      13      24 ..     125     136 ..     121     141 .. 0.84
   5 ?    3.9   0.1      0.16        77      12      27 ..     158     173 ..     154     175 .. 0.82
   6 ?    1.2   0.0       1.1   5.4e+02      12      24 ..     214     226 ..     206     231 .. 0.84
   7 ?    3.1   0.1      0.29   1.3e+02      10      23 ..     280     293 ..     278     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1
                           PPR 14 GkleeAlelfke 25
                                  G++eeAle ++e
  gi|91772284|ref|YP_564976.1| 38 GRFEEALEKYDE 49
                                  99*****98887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.4
                           PPR 15 kleeAlelfkeMke 28
                                  k++eA ++++e+++
  gi|91772284|ref|YP_564976.1| 46 KYDEAASIWEELQQ 59
                                  79999999999986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4
                           PPR 12 knGkleeAle 21
                                  +nG+ +eA+ 
  gi|91772284|ref|YP_564976.1| 63 QNGMEDEAKN 72
                                  6888888876 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.3
                           PPR  13 nGkleeAlelfk 24 
                                    G+++eAl++++
  gi|91772284|ref|YP_564976.1| 125 IGRYDEALRMLD 136
                                   59********98 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.16
                           PPR  12 knGkleeAlelfkeMk 27 
                                   +  ++eeAle++++ +
  gi|91772284|ref|YP_564976.1| 158 QLERFEEALECYEKAI 173
                                   6789********9865 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 1.1
                           PPR  12 knGkleeAlelfk 24 
                                   k Gk++eA++ ++
  gi|91772284|ref|YP_564976.1| 214 KLGKHKEAIDAYN 226
                                   8999999999876 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.29
                           PPR  10 ycknGkleeAlelf 23 
                                   + k G+ eeA+el+
  gi|91772284|ref|YP_564976.1| 280 LYKLGREEEAKELL 293
                                   7799********98 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       5.7   2.7e+03      86     109 ..      56      79 ..      17     107 .. 0.63
   2 ?    9.1   0.0    0.0036       1.7      78     122 ..     121     165 ..      84     171 .. 0.85
   3 ?    1.6   0.0      0.75   3.5e+02     104     128 ..     203     227 ..     167     232 .. 0.66
   4 ?   -0.1   0.1       2.4   1.2e+03      83     122 ..     250     289 ..     237     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.7
                                   HHHHHHHHHHHHHSTT-HHHHHHH CS
               Alkyl_sulf_dimr  86 rwaaellnhlvfadpenaeakelk 109
                                   ++ +e++++ ++ + +na  +el+
  gi|91772284|ref|YP_564976.1|  56 ELQQEMIQNGMEDEAKNALNRELE 79 
                                   333445555555566666666664 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0036
                                   HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
               Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                     ++ g y  a+ +l+ ++  +pe  +a + ka++l ql +++e+
  gi|91772284|ref|YP_564976.1| 121 ILFNIGRYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEEA 165
                                   568999**********************************99986 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.75
                                   HHHHHHHHHHHHHHHH-SSHHHHHH CS
               Alkyl_sulf_dimr 104 eakelkadaleqlgyqaesatwRni 128
                                        ka++le+lg+++e+  + n 
  gi|91772284|ref|YP_564976.1| 203 GIWYCKANTLEKLGKHKEAIDAYNS 227
                                   334459**********999877665 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2.4
                                   T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
               Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                   g+ + a++  +++++ +   ++a e ka+ l +lg+++e+
  gi|91772284|ref|YP_564976.1| 250 GENENALNAYSNALEVERGFTAALENKANLLYKLGREEEA 289
                                   4555566666666777777777777888888888887765 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.068        32      13      33 ..      36      56 ..      35      60 .. 0.80
   2 ?    4.0   0.2     0.073        34      15      29 ..     160     174 ..     159     175 .. 0.92
   3 ?    1.7   0.0      0.39   1.8e+02      18      31 ..     219     232 ..     216     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.068
                      SHNi-TPR 13 EnenFpqAveDlrkaLeLreq 33
                                  E ++F++A+e +++a  + e+
  gi|91772284|ref|YP_564976.1| 36 EIGRFEEALEKYDEAASIWEE 56
                                  6789******99999666555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.073
                      SHNi-TPR  15 enFpqAveDlrkaLe 29 
                                   e+F++A+e ++ka+e
  gi|91772284|ref|YP_564976.1| 160 ERFEEALECYEKAIE 174
                                   9**********9987 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.39
                      SHNi-TPR  18 pqAveDlrkaLeLr 31 
                                   ++A+  +++aLe++
  gi|91772284|ref|YP_564976.1| 219 KEAIDAYNSALEIK 232
                                   789999******97 PP

>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6    0.0038       1.8      45      90 ..       9      58 ..       2     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0038
               Gluconate_2-dh3 45 eqeayrkglaaldayaraeygksFveldgaqqdalLealekeaea....k 90
                                  +q  y+++l+++ + a+++ygk +v  +  + ++ Le++++ a      +
  gi|91772284|ref|YP_564976.1|  9 QQASYKRKLKQIVKNAESTYGKGYVLHEIGRFEEALEKYDEAASIweelQ 58
                                  58899999*****************9999999999999999876544330 PP

>> Phage_term_smal  Phage small terminase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00037      0.18      57      99 ..     122     164 ..      89     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
               Phage_term_smal  57 liDvgdyeqALdiaeyaiahglelPdrfkrtlatvvaeeiada 99 
                                   l+ +g y++AL++ + ai+ + e Pd ++ ++ t+   e ++ 
  gi|91772284|ref|YP_564976.1| 122 LFNIGRYDEALRMLDLAISLEPEYPDAWSCKANTLYQLERFEE 164
                                   799*************************999988874444444 PP

>> TFR_dimer  Transferrin receptor-like dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00056      0.26       8      58 ..      35      87 ..      31     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00056
                     TFR_dimer  8 eaikkfkkaaeefdkwadkwed.vggaessllavrkrrkiNdkl.mrferafl 58
                                  + i +f++a e++d+ a+ we+ ++++ ++ ++ +  +++N+ l +rf+++f+
  gi|91772284|ref|YP_564976.1| 35 HEIGRFEEALEKYDEAASIWEElQQEMIQNGMEDEAKNALNRELeIRFNKCFI 87
                                  67999****************864789999999999999***99559999998 PP

>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.93   4.4e+02     106     129 ..      45      66 ..      21     111 .. 0.64
   2 ?    6.1   0.0     0.019         9      15      39 ..     163     187 ..     159     188 .. 0.90
   3 ?   -0.7   0.0       2.2   1.1e+03      12      25 ..     216     229 ..     210     231 .. 0.90
   4 ?   -0.3   0.0       1.7   8.1e+02      12      26 ..     250     264 ..     246     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.93
                      PvlArgDC 106 eseeeaeeeaeelaaemlattrgl 129
                                   e+ +ea +  eel +em++   g+
  gi|91772284|ref|YP_564976.1|  45 EKYDEAASIWEELQQEMIQN--GM 66 
                                   34466666666777777663..44 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                      PvlArgDC  15 keelasFdlALldAgIenfNLvkvS 39 
                                   +e+l+++++A   A+I++fN  ++S
  gi|91772284|ref|YP_564976.1| 163 EEALECYEKAIEFADIMHFNFPRYS 187
                                   5789****************98887 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.2
                      PvlArgDC  12 geskeelasFdlAL 25 
                                   g++ke++ ++++AL
  gi|91772284|ref|YP_564976.1| 216 GKHKEAIDAYNSAL 229
                                   99***********9 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.7
                      PvlArgDC  12 geskeelasFdlALl 26 
                                   ge++++l+++ +AL 
  gi|91772284|ref|YP_564976.1| 250 GENENALNAYSNALE 264
                                   8999*********95 PP

>> zf-CW  CW-type Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.062        29      12      34 ..     133     155 ..     132     170 .. 0.71
   2 ?    3.0   0.0      0.22     1e+02      27      36 ..     204     212 ..     191     224 .. 0.71
   3 ?    0.4   0.1       1.4   6.7e+02      25      32 ..     236     243 ..     218     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.062
                         zf-CW  12 Rrlptev.dkselipekWvCsmnp 34 
                                   R+l   +  + e +p+ W C+ n+
  gi|91772284|ref|YP_564976.1| 133 RMLDLAIsLEPE-YPDAWSCKANT 155
                                   556666644555.49******998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.22
                         zf-CW  27 kWvCsmnpsd 36 
                                    W+C+ n+  
  gi|91772284|ref|YP_564976.1| 204 IWYCKANT-L 212
                                   7*****99.3 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.4
                         zf-CW  25 pekWvCsm 32 
                                    + W+C  
  gi|91772284|ref|YP_564976.1| 236 SDAWYCMG 243
                                   379***75 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.72   3.4e+02       1      14 [.     127     140 ..     127     143 .. 0.89
   2 ?    3.3   0.0      0.13        62       1      15 [.     161     175 ..     161     176 .. 0.90
   3 ?    6.3   0.1     0.015       7.1      29      47 ..     205     223 ..     203     225 .. 0.89
   4 ?   -2.3   0.0       7.5   3.6e+03      30      44 ..     240     254 ..     239     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.72
                                   -HHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAie 14 
                                   rY+eaL   + Ai 
  gi|91772284|ref|YP_564976.1| 127 RYDEALRMLDLAIS 140
                                   7*******999986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.13
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   r+eeaLe  +kAie 
  gi|91772284|ref|YP_564976.1| 161 RFEEALECYEKAIEF 175
                                   689**********95 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHTT--HHHHH CS
                      HTH_Bact  29 yYqkgecleklgfseeeIk 47 
                                   +Y k++ leklg  +e I 
  gi|91772284|ref|YP_564976.1| 205 WYCKANTLEKLGKHKEAID 223
                                   8*************99996 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 7.5
                                   HHHHHHHHHTT--HH CS
                      HTH_Bact  30 Yqkgecleklgfsee 44 
                                   Y  g  le+lg +e+
  gi|91772284|ref|YP_564976.1| 240 YCMGTTLEELGENEN 254
                                   777999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 1787.87
//
Query:       gi|91772285|ref|YP_564977.1|  [L=852]
Description: multi-sensor protein [Methanococcoides burtonii DSM 6242]
Scores for 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-51  171.3   5.3    1.5e-17   63.6   0.1    3.9  3  PAS_3     PAS fold
    3.3e-34  118.2   0.0    2.8e-20   73.0   0.0    2.4  2  GAF_2     GAF domain
    4.5e-19   68.5   0.5    4.6e-06   26.6   0.0    4.5  4  PAS       PAS fold
    1.1e-18   67.5   0.1     0.0014   18.9   0.0    4.8  5  PAS_4     PAS fold
    6.8e-10   39.1   1.2      0.023   15.0   0.0    4.5  4  PAS_9     PAS domain
    2.9e-08   34.4   0.0     0.0047   17.6   0.0    2.4  2  GAF       GAF domain
    2.8e-06   27.7   0.0     0.0004   20.7   0.0    2.5  2  GAF_3     GAF domain
     0.0056   16.9   2.2       0.81    9.8   0.1    2.9  3  LicD      LicD family
  ------ inclusion threshold ------
      0.011   15.7   4.1       0.54   10.3   0.2    4.5  5  PAS_8     PAS domain
       0.34   11.3   2.6         70    3.9   0.2    3.6  3  SUKH_6    SMI1-KNR4 cell-wall


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   1.3e-17   2.4e-14       3      89 .]      42     128 ..      40     128 .. 0.92
   2 !   63.6   0.1   8.5e-21   1.5e-17       8      89 .]     181     262 ..     174     262 .. 0.94
   3 !   54.7   0.1   5.1e-18   9.2e-15       3      88 ..     479     564 ..     477     565 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.3e-17
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqeal.kkgepyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +vse++++  Gy++ +l++ + +++d++hp+D + v ++   ++ +k++ ++  yRi++k Ge+rwv++r++ ++d++g +
  gi|91772285|ref|YP_564977.1|  42 FVSENISQF-GYDAKDLISGKFRYADIIHPDDVDGVISESSLHVcDKDRNFNLRYRILTKTGEVRWVDERTSSHYDDSGSI 121
                                   788888887.**********************99999999977757777******************************** PP

                         PAS_3  83 vrvigva 89 
                                   +++ g++
  gi|91772285|ref|YP_564977.1| 122 QFYHGIV 128
                                   ***9985 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 8.5e-21
                         PAS_3   8 veeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkpvrvig 87 
                                   + +++Gys  ++++ +  + d+vhp+D++rvr+ + ++ ++g  ++ +eyRi++k Ge+rwv++r+++ +d +g++ +++g
  gi|91772285|ref|YP_564977.1| 181 I-DMFGYSVGDFISGKLVYGDIVHPDDIDRVRAGVSKCTEGGYsDFFQEYRILTKAGEVRWVDERTQIQHDPQGNVKYLQG 260
                                   4.89***********999************************9************************************** PP

                         PAS_3  88 va 89 
                                   ++
  gi|91772285|ref|YP_564977.1| 261 II 262
                                   85 PP

  == domain 3  score: 54.7 bits;  conditional E-value: 5.1e-18
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +vse+v +  Gys +++++    ++d+vhp D+erv+++l + ++ g  ++++eyR+++k G++rwv++r+++ +de g++
  gi|91772285|ref|YP_564977.1| 479 FVSENVIQF-GYSVDDFISGRFVYADIVHPYDLERVQRELSKRIDAGFmDFNQEYRVLTKFGDIRWVDERTFIKHDEIGNV 558
                                   667777666.**********999********************************************************** PP

                         PAS_3  83 vrvigv 88 
                                    +++g 
  gi|91772285|ref|YP_564977.1| 559 AYMQGL 564
                                   ****96 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   1.6e-23   2.8e-20       2     137 ..     294     436 ..     293     436 .. 0.91
   2 !   42.9   0.0   3.2e-14   5.8e-11       1     137 [.     591     729 ..     591     730 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 1.6e-23
                                   HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEE...EEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEES- CS
                         GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrla...awgeaeeefgaaldrpl.....geglvgealrtgrpvilnd 73 
                                   a+++++ d++ +e+v+l+ + +gy++++ dd++       +w+e   + ++ l+++l     + gl+ eal+++ p+i+nd
  gi|91772285|ref|YP_564977.1| 294 ASIQDIIDFAREEVVRLTeSKMGYLAFISDDES--AItddSWSENVTNECSLLEKKLqshvvDVGLWSEALKQRLPIIVND 372
                                   799*************966********998877..33455*************99667778899***************** PP

                                   .GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                         GAF_2  74 .leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                    + e+ +kkg+p+gh  + +fl+vP+++++++v+ +++ ank  ++d +d++++++l++ ++ ++
  gi|91772285|ref|YP_564977.1| 373 ySYESTSKKGYPEGHMEIDRFLSVPIFDREKIVALVGV-ANKALDYDHSDVRQVTLLMQGMWSIL 436
                                   655599**********************889******8.9**********************876 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 3.2e-14
                                   HHHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG-S- CS
                         GAF_2   1 aadleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleedpd 79 
                                   a++lee+++++l+  +++  ++ g ++l+d+ +g l l a  +  e+f   ++  + +++  + ++tg+pv+ +++e ++ 
  gi|91772285|ref|YP_564977.1| 591 AHSLEETFEQMLEFSLKVEpVDSGRLYLIDESTGdLMLMAHKGLSERFVKDTSLFVKNSVQNRLVMTGQPVYKHHSELSAI 671
                                   689**************955****999999776656666888888888888844447779************888899999 PP

                                   HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                         GAF_2  80 kkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                     g+  +++gl+++ ++P+ ++g+++++l+l+++ +++  +  +  Le++a+qi+++i
  gi|91772285|ref|YP_564977.1| 672 TTGESSQYEGLHATGIIPVKHDGKIIAALCLSSHAEYEIPANARNSLETIATQIGVVI 729
                                   99999***************************************************99 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.2e-07    0.0004       4     113 .]      19     131 ..      17     131 .. 0.84
   2 !   26.6   0.0   2.6e-09   4.6e-06       3     113 .]     152     265 ..     150     265 .. 0.96
   3 ?    5.2   0.0     0.011        20      32     102 ..     485     557 ..     458     568 .. 0.79
   4 !   11.2   0.0   0.00016      0.29       1      62 [.     743     803 ..     743     833 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                                   HHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCT.TSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECCCCEEE CS
                           PAS   4 raileslpdpifvvD.edgrilyvNaaaeellGlsreevl.gkslldliheedda...elaelleqlleqgeesrageisf 79 
                                   +++++s+p+ +f+++ e g+ +++ ++  +++G+++++++ gk  + +i+++dd    +  + l+ + ++++ +  ++i  
  gi|91772285|ref|YP_564977.1|  19 KSVINSSPAVVFIWReEAGWPVEFVSENISQFGYDAKDLIsGKFRYADIIHPDDVdgvISESSLHVCDKDRNFNLRYRILT 99 
                                   689*********************************888726666899999999877777777777777777777777766 PP

                                   ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                   k+  g++++++ r+s+ +d +g i  + g++ di
  gi|91772285|ref|YP_564977.1| 100 KT--GEVRWVDERTSSHYDDSGSIQFYHGIVLDI 131
                                   66..******************998777777765 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 2.6e-09
                                   HHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEE CS
                           PAS   3 lraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfk 80 
                                   l+++++s+p+ +f+++ e  + +++ ++  +++G+s  + ++gk ++++i+++dd   +++ ++++ e g +   +e ++ 
  gi|91772285|ref|YP_564977.1| 152 LQTVINSSPVVVFLWRaETDWPVEFVSNNIDMFGYSVgDFISGKLVYGDIVHPDDIdRVRAGVSKCTEGGYSDFFQEYRIL 232
                                   6899************999999***************999****************899999999999999********** PP

                                   CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                   ++ g++++++ r+    d++g+++++ g++ di
  gi|91772285|ref|YP_564977.1| 233 TKAGEVRWVDERTQIQHDPQGNVKYLQGIILDI 265
                                   ******************************998 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.011
                                   HHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEE CS
                           PAS  32 ellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdagge 102
                                    ++G+s  + ++g+ ++ +i++++d   ++++l++++ +g +  ++e ++ ++ g +++++ r+    d+ g+
  gi|91772285|ref|YP_564977.1| 485 IQFGYSVdDFISGRFVYADIVHPYDLeRVQRELSKRIDAGFMDFNQEYRVLTKFGDIRWVDERTFIKHDEIGN 557
                                   589****88899***********999999*******************9999888888888776666555555 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHH CS
                           PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaell 62 
                                   edl++++e  +d  +v D  g ilyvN+  ++ + ls  +++  ++l+l h+ d++ + +e +
  gi|91772285|ref|YP_564977.1| 743 EDLQSLVEMVDDILVVMDMEGYILYVNKVVADRFELSDVDISDMHYLEL-HP-DREwDNVESM 803
                                   6899*****************************************9955.44.3444555555 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.4e-06    0.0026       2     109 ..      23     135 ..      22     136 .. 0.80
   2 !   17.3   0.0   2.4e-06    0.0042       2     108 ..     157     268 ..     156     270 .. 0.89
   3 !    7.0   0.0    0.0037       6.7       3     109 ..     461     572 ..     459     573 .. 0.87
   4 ?   -1.5   0.0       1.6   2.9e+03      62     102 ..     657     703 ..     651     705 .. 0.55
   5 !   18.9   0.0   7.7e-07    0.0014       4      79 ..     752     827 ..     749     834 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                         PAS_4   2 dslpdalavl..dpdgrvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll..pg 76 
                                   +s+p++++++   +   v+++++++ + fg+++++l+  +++  ++  ++d +++ +     +  +++ + l ++ l   g
  gi|91772285|ref|YP_564977.1|  23 NSSPAVVFIWreEAGWPVEFVSENISQ-FGYDAKDLISGKFRyaDIIHPDDVDGVISESSLHVCDKDRNFNLRYRILtkTG 102
                                   678888888876667778888888888.899999999888888887666677777666666666666666666666669** PP

                         PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                   e r+++ r +   d+sG ++++ +i+ DiTe+r
  gi|91772285|ref|YP_564977.1| 103 EVRWVDERTSSHYDDSGSIQFYHGIVLDITEQR 135
                                   *******************************97 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.4e-06
                         PAS_4   2 dslpdalavl..dpdgrvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll..pg 76 
                                   +s+p++++ +   +d  v++++++  ++fg++  +++  +l   +++ ++d +r+++ + ++ eg+ + +f+e++ l   g
  gi|91772285|ref|YP_564977.1| 157 NSSPVVVFLWraETDWPVEFVSNN-IDMFGYSVGDFISGKLVygDIVHPDDIDRVRAGVSKCTEGGYSDFFQEYRILtkAG 236
                                   689999999999999999999998.567999999988666666**99999***********************99999*** PP

                         PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTer 108
                                   e r+++ r    +d++G v  + +i+ DiT  
  gi|91772285|ref|YP_564977.1| 237 EVRWVDERTQIQHDPQGNVKYLQGIILDITGK 268
                                   ********96667*****************65 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0037
                         PAS_4   3 slpdalavl..dpdgrvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll..pge 77 
                                   ++p++++ +   pd  v++++++  + fg++ ++++  ++   +++ + d +r++r l + ++ +   + +e+++l   g+
  gi|91772285|ref|YP_564977.1| 461 NSPAVVFLWraEPDWPVEFVSENVIQ-FGYSVDDFISGRFVyaDIVHPYDLERVQRELSKRIDAGFMDFNQEYRVLtkFGD 540
                                   78888888888999999999999666.8888888775555559999999**************9998888888888999** PP

                         PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                    r+++ r +  +de G v    ++++D+T+r+
  gi|91772285|ref|YP_564977.1| 541 IRWVDERTFIKHDEIGNVAYMQGLIVDVTDRK 572
                                   ********9999******************97 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.6
                         PAS_4  62 geepiefleelll....pgeerhyelrl...lPlrdesGevigvlvis 102
                                   +++p++ ++  l     + + ++  l++   +P+ +++G++i++l++s
  gi|91772285|ref|YP_564977.1| 657 TGQPVYKHHSELSaittGESSQYEGLHAtgiIPV-KHDGKIIAALCLS 703
                                   4444444444444466533333333333444999.5799999999876 PP

  == domain 5  score: 18.9 bits;  conditional E-value: 7.7e-07
                         PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                   + d+l+v d +g +ly+N+  a+ f +++ ++ ++++ el+p++  +++e+ l  v  g++ +++++ l+ +g+  
  gi|91772285|ref|YP_564977.1| 752 VDDILVVMDMEGYILYVNKVVADRFELSDVDISDMHYLELHPDREWDNVESMLSSVRVGNKLVYETIMLDVGGSLD 827
                                   67899999*****************************************999999999988888887665566555 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05     0.023       5     104 .]      30     133 ..      26     133 .. 0.76
   2 !    8.2   0.0    0.0016       2.9      22     103 ..     182     266 ..     164     267 .. 0.78
   3 !    7.2   0.0    0.0033       5.9       7     104 .]     471     570 ..     463     570 .. 0.84
   4 ?    4.2   0.0     0.028        50       3      58 ..     755     808 ..     753     825 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                         PAS_9   5 li.dnpdgril.yaNeaalrllGyspeevlgks..itdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                   +i   + g  + +++e   ++ Gy++++++  +  + d++   + d    e   ++ +  r   ++  + + +k+ge  wv
  gi|91772285|ref|YP_564977.1|  30 FIwREEAGWPVeFVSENISQF-GYDAKDLISGKfrYADIIhpdDVDGVISESSLHVCDKDR--NFNLRYRILTKTGEVRWV 107
                                   555556674455999999999.********9997778888666444444455555555555..8***************** PP

                         PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                   + + s  +dd+g ++++ +i+ Dite
  gi|91772285|ref|YP_564977.1| 108 DERTSSHYDDSGSIQFYHGIVLDITE 133
                                   *66656668999999999*******8 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                         PAS_9  22 rllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltaspvkdddgelvgiiv 97 
                                   +++Gys  +++  +  + d++  +p++ +r+ra +   ++   + + +e+ + +k ge  wv+ +    +d +g+++ + +
  gi|91772285|ref|YP_564977.1| 182 DMFGYSVGDFISGKlvYGDIV--HPDDIDRVRAGVSKCTEggySDFFQEYRILTKAGEVRWVDERTQIQHDPQGNVKYLQG 260
                                   688888888777665556666..555555555555555559********************99866555555******99* PP

                         PAS_9  98 ilrDit 103
                                   i+ Dit
  gi|91772285|ref|YP_564977.1| 261 IILDIT 266
                                   *****9 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0033
                         PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgks..itdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltas 83 
                                     pd ++++++e ++++ Gys ++++  +  + d++  ++ ++ +++l++ +++g    +++e+   +k g   wv+ + +
  gi|91772285|ref|YP_564977.1| 471 AEPDWPVEFVSENVIQF-GYSVDDFISGRfvYADIVhpYDLERVQRELSKRIDAGF-MDFNQEYRVLTKFGDIRWVDERTF 549
                                   557778899******99.*********99888888888888888888888888888.99****************997777 PP

                         PAS_9  84 pvkdddgelvgiivilrDite 104
                                     +d+ g++  + ++++D+t+
  gi|91772285|ref|YP_564977.1| 550 IKHDEIGNVAYMQGLIVDVTD 570
                                   777888888889999999996 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.028
                         PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgr 58 
                                     ++ +++g ily+N+ +++ +  s  ++   ++ +l   ++++ ++++ +l + r
  gi|91772285|ref|YP_564977.1| 755 ILVVMDMEGYILYVNKVVADRFELSDVDISDMHYLELH--PDREWDNVESMLSSVR 808
                                   455667**************999999999999988888..8877777777777777 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-06    0.0047       3     119 ..     297     422 ..     295     430 .. 0.63
   2 !   14.6   0.0   2.2e-05     0.039      42     133 .]     638     729 ..     593     729 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                                   HHHHHHHHHHHHHHHTESEEEE.EEEEETTEEECEEEEECC..........EEEETTSHHHH.....HHHHHSSSEEESTG CS
                           GAF   3 eelldtvveelrellgadrval.ylpdydGlhydipqasrw..........lfmkngrgicg.....qvlatgqplvipds 67 
                                   +++ d + ee+ +l++   + l +++d +         ++w          l+ k  + +++     ++l+++ p++++d+
  gi|91772285|ref|YP_564977.1| 297 QDIIDFAREEVVRLTESKMGYLaFISDDES----AITDDSWsenvtnecslLEKKLQSHVVDvglwsEALKQRLPIIVNDY 373
                                   666777778888888887766645522222....122222212223333325555555566688889************96 PP

                                   GTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHH CS
                           GAF  68 tpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreel 119
                                   + ++   +       ++m+i  +l+vP+++++++++l+ + n+   ++ +++
  gi|91772285|ref|YP_564977.1| 374 SYESTSKK---GYPEGHMEIDRFLSVPIFDREKIVALVGVANKALDYDHSDV 422
                                   53333333...234599***********************994334555554 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.2e-05
                                   C.....EEEET.TSHHHHHHHHHSSSEEESTGG....TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS CS
                           GAF  42 w.....lfmkn.grgicgqvlatgqplvipdst....pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp 112
                                   +     lf kn +++   + + tgqp+  ++s     +++  +qy         g ++   +P+++dg+++++l+l ++ +
  gi|91772285|ref|YP_564977.1| 638 FvkdtsLFVKNsVQN---RLVMTGQPVYKHHSElsaiTTGESSQY--------EGLHATGIIPVKHDGKIIAALCLSSHAE 707
                                   233333666665555...777788998888533334455555554........48999999*****************777 PP

                                   .CSHHHHHHHHHHHHHHHHHHH CS
                           GAF 113 .pftreelellqvladqvaval 133
                                    +   ++++ l+++a+q++v +
  gi|91772285|ref|YP_564977.1| 708 yEIPANARNSLETIATQIGVVI 729
                                   66799*************9975 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.025        45       2     121 ..     296     430 ..     295     432 .. 0.66
   2 !   20.7   0.0   2.2e-07    0.0004       1     127 [.     593     729 ..     593     731 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.025
                         GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse.........sldedsalarralssgevvsepsfa 73 
                                   ++++++ + +++v+l+ ++ g l    +d +++ +  +w  +++ +e         s + d  l+++al+++ +++++++ 
  gi|91772285|ref|YP_564977.1| 296 IQDIIDFAREEVVRLTESKMGYLAFISDD-ESAITDDSW-SENVTNEcsllekklqSHVVDVGLWSEALKQRLPIIVNDYS 374
                                   78888888888888888888888877744.566566667.44444445333343333334445555999999999997776 PP

                         GAF_3  74 eedg.........lpdraalavPLvagrqviGvlalastkprafdaedlelleslAr 121
                                    e++         ++    l vP+ ++++ + ++++a +   ++d +d++ +  l++
  gi|91772285|ref|YP_564977.1| 375 YESTskkgypeghMEIDRFLSVPIFDREKIVALVGVANKA-LDYDHSDVRQVTLLMQ 430
                                   6655344444444666777999999977777777777755.7799999998888887 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.2e-07
                         GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse..sldedsalarralssgevvse........ps 71 
                                   sl+e++e+ l++  k+  +++g l+l de   +l  +a+++ ++++++  sl  ++++  r++++g++v++        ++
  gi|91772285|ref|YP_564977.1| 593 SLEETFEQMLEFSLKVEPVDSGRLYLIDESTGDLMLMAHKGLSERFVKdtSLFVKNSVQNRLVMTGQPVYKhhselsaiTT 673
                                   689*************************************99999999899986666666777778888886766655544 PP

                         GAF_3  72 faeedglpdraalavPLvagr.qviGvlalastkprafdaedlelleslArqiatai 127
                                   ++  ++  ++a  ++P+++ + + i  l+l s+ + ++ a  +  le++A+qi+  i
  gi|91772285|ref|YP_564977.1| 674 GESSQYEGLHATGIIPVKH-DgKIIAALCLSSHAEYEIPANARNSLETIATQIGVVI 729
                                   4555678889999******.66********************************888 PP

>> LicD  LicD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.2   2.1e+03      71     100 ..     104     133 ..      86     145 .. 0.83
   2 !    9.8   0.1   0.00045      0.81      71     126 ..     238     288 ..     222     359 .. 0.69
   3 !    5.4   0.0    0.0099        18      70     212 ..     538     684 ..     509     693 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                          LicD  71 aklldkntsiterkngngkndsglyiDIfp 100
                                   + ++d++ts +  + g  ++ +g+ +DI+ 
  gi|91772285|ref|YP_564977.1| 104 VRWVDERTSSHYDDSGSIQFYHGIVLDITE 133
                                   67889999999999998899********96 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00045
                          LicD  71 aklldkntsiterkngngkndsglyiDIfpldyvpkskllikkkkekeklkkklal 126
                                   + ++d++t+i+   +gn k+ +g+ +DI++ ++v++       + e+++++ +l+l
  gi|91772285|ref|YP_564977.1| 238 VRWVDERTQIQHDPQGNVKYLQGIILDITGKKKVENVL-----HSEERRIEALLRL 288
                                   7899***************************9999732.....2223333333333 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0099
                          LicD  70 f..aklldkntsiterkngngkndsglyiDIfpldyvpkskll........ikkkkekeklkkklalkkslskkdkkelkk 140
                                   f    ++d++t+i   + gn ++ +gl +D++  +  ++   +        ++++ ++e+++++l+    + k ++ +  +
  gi|91772285|ref|YP_564977.1| 538 FgdIRWVDERTFIKHDEIGNVAYMQGLIVDVTDRKHSDDFMHMqfdldsvlSSAHSLEETFEQMLE---FSLKVEPVDSGR 615
                                   3357899*************************8865555433344444333223332333322222...244444444444 PP

                          LicD 141 killkkksfklkklnkkkklkkleklekkkeydlkkseyiavlksgklrnkeilpleelsplkkvkFegvev 212
                                    +l  ++   l+ + +k   +++ k ++    +++ ++++ +  +    +k+  +l+ ++  +  ++eg  +
  gi|91772285|ref|YP_564977.1| 616 LYLIDESTGDLMLMAHKGLSERFVKDTSL-FVKNSVQNRLVMTGQP--VYKHHSELSAITTGESSQYEGLHA 684
                                   44444444444444444444444433332.4444444443333332..367777777777777777777665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.78   1.4e+03       3      18 ..      18      33 ..      17      72 .. 0.83
   2 ?    2.6   0.1      0.08   1.4e+02       3      45 ..     152     196 ..     150     215 .. 0.62
   3 ?   -3.3   0.0       5.7     1e+04      34      54 ..     487     507 ..     486     520 .. 0.63
   4 ?   -3.3   0.0       5.5   9.9e+03      29      46 ..     597     612 ..     596     625 .. 0.68
   5 ?   10.3   0.2    0.0003      0.54       3      43 ..     745     786 ..     743     807 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.78
                         PAS_8  3 lralfesspdgiavvd 18
                                  ++++++ssp  ++++ 
  gi|91772285|ref|YP_564977.1| 18 FKSVINSSPAVVFIWR 33
                                  7899999999999864 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.08
                         PAS_8   3 lralfesspdgiavvd..lgd..rivdvNqaalellGys.adlkgell 45 
                                   l+++++ssp+ ++++   +++   +v  N   ++++Gys  d++  +l
  gi|91772285|ref|YP_564977.1| 152 LQTVINSSPVVVFLWRaeTDWpvEFVSNN---IDMFGYSvGDFISGKL 196
                                   67888888888888553222344454444...6677777666665555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.7
                         PAS_8  34 lGys.adlkgellgqllpvlrp 54 
                                   +Gys +d++   + ++ + ++p
  gi|91772285|ref|YP_564977.1| 487 FGYSvDDFISGRF-VYADIVHP 507
                                   8999998888777.44444333 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 5.5
                         PAS_8  29 aalellGysadlkgellg 46 
                                   +++++l +s  lk e+++
  gi|91772285|ref|YP_564977.1| 597 TFEQMLEFS--LKVEPVD 612
                                   799999988..7766664 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.0003
                         PAS_8   3 lralfesspdgiavvd.lgdrivdvNqaalellGys.adlkge 43 
                                   l++l+e ++d ++v d +g  i++vN+  ++ + +s  d++++
  gi|91772285|ref|YP_564977.1| 745 LQSLVEMVDDILVVMDmEGY-ILYVNKVVADRFELSdVDISDM 786
                                   89**************8999.************9886665553 PP

>> SUKH_6  SMI1-KNR4 cell-wall
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.039        70      95     120 ..      25      50 ..       9      50 .. 0.82
   2 ?    3.6   0.0     0.049        87      91     120 ..     156     184 ..      91     184 .. 0.65
   3 ?    1.3   0.1      0.25   4.4e+02      94     120 ..     461     487 ..     454     487 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.039
                        SUKH_6  95 depkvvfwdseedgevekvadsFeeF 120
                                   +   v++w +e ++ ve+v+++ ++F
  gi|91772285|ref|YP_564977.1|  25 SPAVVFIWREEAGWPVEFVSENISQF 50 
                                   34456666***************998 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.049
                        SUKH_6  91 yeendepkvvfw.dseedgevekvadsFeeF 120
                                   +  n++p vvf+   e d+ ve+v+++ + F
  gi|91772285|ref|YP_564977.1| 156 I--NSSPVVVFLwRAETDWPVEFVSNNIDMF 184
                                   3..5666666667**************9877 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.25
                        SUKH_6  94 ndepkvvfwdseedgevekvadsFeeF 120
                                   n+   v++w  e d+ ve+v+++  +F
  gi|91772285|ref|YP_564977.1| 461 NSPAVVFLWRAEPDWPVEFVSENVIQF 487
                                   455556667************997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (852 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 5782.38
//
Query:       gi|91772286|ref|YP_564978.1|  [L=281]
Description: hypothetical protein Mbur_0218 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.29   11.3   0.0    1.3  1  DUF2802   Protein of unknown function (DUF2802)


Domain annotation for each model (and alignments):
>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.6e-05      0.29      13      50 ..     162     199 ..     158     200 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
                       DUF2802  13 lkqleerleeleqqdpqsklYsqAiklvrqGasveela 50 
                                    ++le+ l+ +e + ++s  +s+ ++ v+ Gas+++++
  gi|91772286|ref|YP_564978.1| 162 QDRLEDALDVMEGDANASSDFSRVMEFVEPGASIQQVM 199
                                   56899999999**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1943.82
//
Query:       gi|91772287|ref|YP_564979.1|  [L=117]
Description: 50S ribosomal protein L7Ae [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-27   93.5   1.0    5.6e-27   93.3   1.0    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
      0.001   18.9   0.0     0.0016   18.3   0.0    1.3  1  PELOTA_1        PELOTA RNA binding domain
  ------ inclusion threshold ------
      0.065   13.8   4.5        4.2    8.0   0.7    2.1  2  YtxH            YtxH-like protein


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 !   93.3   1.0   9.4e-31   5.6e-27       2      94 ..      13     105 ..      12     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 9.4e-31
                                   HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSE CS
                Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsa 82 
                                   ++ e++++a+++gk+++G++e+tka+erg  kl ++A+d+ep e++++++alc+ek+ py++vk +keLG+++g  + ++a
  gi|91772287|ref|YP_564979.1|  13 KALEAIELARDTGKIKKGTNEATKAIERGITKLAVIAADIEPSEIVAHIPALCEEKNTPYIFVKQQKELGAACGIGVGCAA 93 
                                   67899**************************************************************************** PP

                                   EEEEESTTTHHH CS
                Ribosomal_L7Ae  83 laikdegdskdl 94 
                                   ++i+d+g+ ++l
  gi|91772287|ref|YP_564979.1|  94 VVITDAGKGSEL 105
                                   ******986665 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.6e-07    0.0016      17      71 ..      22      78 ..      11      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.6e-07
                      PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                  +d+  iK g  EaT+++ R + +  +++++ e  + +ah+ +L++ek++p+  v+++
  gi|91772287|ref|YP_564979.1| 22 RDTGKIKKGTNEATKAIERGITKLAVIAADIEpsEIVAHIPALCEEKNTPYIFVKQQ 78
                                  68899****************9987777755533779************98777655 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2     0.001       6.1      34      70 ..       7      45 ..       5      49 .. 0.86
   2 ?    8.0   0.7   0.00071       4.2       2      38 ..      81     117 .]      81     117 .] 0.92

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.001
                          YtxH 34 addlkekakelleeakeka..kekaedlkekvkekadel 70
                                   d+l++ka e++e a++++  k+ +++++++++ ++ +l
  gi|91772287|ref|YP_564979.1|  7 PDELADKALEAIELARDTGkiKKGTNEATKAIERGITKL 45
                                  5899***************99888999999998887776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00071
                          YtxH   2 lglliGaavGaaaglLlAPksGketRkdlkekaddlk 38 
                                   lg+  G+ vG aa + +   +G+e+ +d+++k+ +lk
  gi|91772287|ref|YP_564979.1|  81 LGAACGIGVGCAAVVITDAGKGSELVEDVAQKVAALK 117
                                   58899*************************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 825.68
//
Query:       gi|91772288|ref|YP_564980.1|  [L=71]
Description: 30S ribosomal protein S28e [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-27   95.7   0.4    1.2e-27   95.6   0.4    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 !   95.6   0.4   6.8e-32   1.2e-27       5      64 .]       9      68 ..       5      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 6.8e-32
                                  EEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                Ribosomal_S28e  5 lAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                  +AeVi+v+g+tG++Ge+ q+++++leg+dkgrii+Rn+ GPvr GD+ +L+Et rEA++L
  gi|91772288|ref|YP_564980.1|  9 AAEVIDVIGNTGMHGEASQIQCRVLEGRDKGRIITRNCVGPVRIGDVFMLMETSREAKKL 68
                                  7*********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 517.71
//
Query:       gi|91772289|ref|YP_564981.1|  [L=62]
Description: 50S ribosomal protein L24e [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.2    6.2e-19   68.0   0.2    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    8.4e-07   28.8   2.3    1.2e-06   28.3   2.3    1.2  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
      9e-06   25.7   0.6    1.2e-05   25.2   0.6    1.2  1  YHS             YHS domain
  ------ inclusion threshold ------
      0.029   14.2   4.7      0.057   13.3   4.7    1.5  1  VATC            Vms1-associating treble clef domain
       0.19   10.5   0.0       0.19   10.5   0.0    1.0  1  SerH            Cell surface immobilisation antigen SerH


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   0.2   1.7e-22   6.2e-19       1      61 [.       1      61 [.       1      62 [] 0.96

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.7e-22
                                  XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXX CS
                Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkk 61
                                  m+ +kCsF+g+  +PG+G +f ++Dg+++ F+ssKc+ +f+  r Pr++ WT++ R   kk
  gi|91772289|ref|YP_564981.1|  1 MEQRKCSFCGELLEPGTGLLFAKRDGSTYYFCSSKCKGNFDLGRLPRRTVWTEQGRIYLKK 61
                                  7889****************************************************88877 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 !   28.3   2.3   3.3e-10   1.2e-06       3      40 ..       3      39 ..       2      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.3e-10
                        zf-FCS  3 kkrCwfCkkyikgkpeftyvlendgvvgqFCStsClds 40
                                  +++C+fC+++++ +++      +dg++++FCS+ C+  
  gi|91772289|ref|YP_564981.1|  3 QRKCSFCGELLEPGTG-LLFAKRDGSTYYFCSSKCKGN 39
                                  589************5.6777778***********875 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.6   3.5e-09   1.2e-05       6      38 ..       9      41 ..       8      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.5e-09
                           YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkdkFe 38
                                  cg  +++++     +++G++YyFcS +Ck  F+
  gi|91772289|ref|YP_564981.1|  9 CGELLEPGTGLLFAKRDGSTYYFCSSKCKGNFD 41
                                  6666666766677789**************998 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.7   1.6e-05     0.057       4      31 ..       4      36 ..       1      39 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                          VATC  4 lrCsiCgeslegkv..yFekfd...frYCstkC 31
                                  ++Cs+Cge le+ +   F k d   + +Cs kC
  gi|91772289|ref|YP_564981.1|  4 RKCSFCGELLEPGTglLFAKRDgstYYFCSSKC 36
                                  79*********977779**97644489****** PP

>> SerH  Cell surface immobilisation antigen SerH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.2e-05      0.19     239     274 ..       4      39 ..       1      56 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.2e-05
                          SerH 239 sdCnaCattaspstkllfAnaagssCvassasctts 274
                                    +C  C++   p t llfA+ +gs+    s +c+++
  gi|91772289|ref|YP_564981.1|   4 RKCSFCGELLEPGTGLLFAKRDGSTYYFCSSKCKGN 39 
                                   678888888888888888888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 440.60
//
Query:       gi|91772290|ref|YP_564982.1|  [L=149]
Description: nucleoside diphosphate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  183.4   0.0      2e-54  183.2   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.0   1.1e-58     2e-54       1     135 []       2     136 ..       2     136 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 1.1e-58
                                   EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHH CS
                           NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaie 81 
                                   ert+v++KPd+v+r l+gei+sr+e+kglki+al+m  +te+ a+ehY+eh+++pff +lv+f+tsgp v +v+eg++ai+
  gi|91772290|ref|YP_564982.1|   2 ERTYVMVKPDGVQRCLVGEIVSRIEKKGLKIAALRMNVMTEAAAKEHYKEHSERPFFGSLVSFVTSGPSVSMVIEGNNAIK 82 
                                   89******************************************************************************* PP

                                   HHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
                           NDK  82 kvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                                    +r++ Gatnp +a pgtiR+d +v++g+N+vH+Sd +esaerei+l F+e+ei
  gi|91772290|ref|YP_564982.1|  83 IMRAINGATNPVDALPGTIRGDLAVDMGRNVVHASDAPESAEREIGLHFEESEI 136
                                   **************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 884.42
//
Query:       gi|91772291|ref|YP_564983.1|  [L=591]
Description: translation initiation factor IF-2 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-30  105.9   0.2    8.9e-29  100.4   0.0    2.5  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.1e-27   95.8   3.8    1.1e-27   95.8   3.8    2.7  3  GTP_EFTU_D4  Elongation factor Tu domain 4
    1.2e-23   83.3   4.3    1.3e-23   83.1   1.5    2.3  2  IF-2         Translation-initiation factor 2
    2.1e-08   34.2   0.0    6.4e-08   32.7   0.0    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
    1.2e-06   28.8   0.3    1.2e-06   28.8   0.3    3.7  4  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0087   15.9   0.0      0.022   14.5   0.0    1.6  1  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.011   15.6   0.5          6    6.7   0.0    3.0  3  RsgA_GTPase  RsgA GTPase
      0.014   15.4   0.1        0.4   10.7   0.0    2.6  2  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0     4e-32   8.9e-29       4     190 ..      10     216 ..       7     220 .. 0.77
   2 ?   -3.1   0.1       2.1   4.8e+03      44      60 ..     346     362 ..     326     377 .. 0.64

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 4e-32
                                   EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE...TTCSSEEEEEEEESSSG CS
                      GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle...ketkkylinliDtPGHv 81 
                                     ++++ghvDhGKt+L+d +  ++    ++g+ +       ++    e  i+  ++ +      ++     + +iDtPGH 
  gi|91772291|ref|YP_564983.1|  10 PIVCVMGHVDHGKTSLLDMIRGSAVVSGEAGAIT-------QHIGATEVPISAIVEKCGNPgllDKFMVPGLLFIDTPGHH 83 
                                   579*****************97766666644333.......233333333443333333336546888999********** PP

                                   GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHH CS
                      GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqkls 151
                                    F+   +rg + +D+av++vd++eG +pqt e l++++++++p++v+ NK+D++            ++++++ e v+ +l+
  gi|91772291|ref|YP_564983.1|  84 AFTTLRSRGGALADLAVVIVDINEGFKPQTIESLNILQQHKTPFVVVANKIDKIhgwnpqkgapfMTSYNKQSEHVRGSLD 164
                                   *************************************************************99996777777777777775 PP

                                   HH.............HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHH CS
                      GTP_EFTU 152 rk.............eeklekygekge.........kevpvvfgSalkgegvktllealve 190
                                   +k                       ++         +++ v+++Sa++geg+ +ll +l  
  gi|91772291|ref|YP_564983.1| 165 TKfyevvgelynhgfS---------SDrydrvndfqHNIGVIPISAITGEGIPDLLMVLLG 216
                                   5555553333333331.........3366666666689****************9988765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                                   CHSHHHHHHTSCSSCEE CS
                      GTP_EFTU  44 DtlkeErergiTiksaa 60 
                                   D + +  + giTik+ +
  gi|91772291|ref|YP_564983.1| 346 DVQIDTDQSGITIKADT 362
                                   44445556677777655 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 ?   -3.7   0.0       5.2   1.2e+04      39      53 ..     230     244 ..     227     245 .. 0.81
   2 ?   -1.3   0.1      0.91     2e+03      10      68 ..     257     311 ..     253     325 .. 0.61
   3 !   95.8   3.8   4.7e-31   1.1e-27       1      85 [.     463     547 ..     463     548 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.2
                                   TTE.EEEEEEEEEET CS
                   GTP_EFTU_D4  39 edGrevGeilqiqdk 53 
                                   ++G  vG++l+++++
  gi|91772291|ref|YP_564983.1| 230 AEGPGVGTVLEVKEE 244
                                   688999*99999876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.91
                                   EEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEE CS
                   GTP_EFTU_D4  10 gvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevai 68 
                                   + v ++ d ++vG   lg  i+++v+ +  + r + ei +++dk k++++++a   v i
  gi|91772291|ref|YP_564983.1| 257 DGVLKKGDTIVVG--CLGEPIQTKVRAVL-KPRALSEI-NVEDKFKQVSKVTAAVGVKI 311
                                   5566777777777..66666776666554.33455555.35666666666555444444 PP

  == domain 3  score: 95.8 bits;  conditional E-value: 4.7e-31
                                   S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--T CS
                   GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqike 81 
                                   +P+ ++i+p++vfr+s+pa+vGv+v+gG+ik++v++ + dG+ vG ++ +q++g+++++a+ G+eva+sieg++vGrqi+e
  gi|91772291|ref|YP_564983.1| 463 KPAMFTIMPDCVFRQSKPAVVGVRVIGGTIKTKVDVATGDGTVVGIVKGLQSRGENVSVATIGMEVAMSIEGPTVGRQINE 543
                                   79******************************************************************************* PP

                                   T-EE CS
                   GTP_EFTU_D4  82 gdil 85 
                                   gdil
  gi|91772291|ref|YP_564983.1| 544 GDIL 547
                                   **99 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   1.5   5.7e-27   1.3e-23       3     104 ..     342     442 ..     338     443 .. 0.92
   2 ?   -0.6   0.1      0.63   1.4e+03      40      65 ..     526     552 ..     503     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 5.7e-27
                                   CHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH....STEEEEEESSSCTHH CS
                          IF-2   3 elfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa....snaiiigFnvkvskk 79 
                                   +++e+++ ++++ ++ ikaD+ GsleAl + L+k       +++ +++vG+i+++D++ a a     +++i+gFnv++ ++
  gi|91772291|ref|YP_564983.1| 342 NEIEDVQIDTDQSGITIKADTIGSLEALVNELKKE-----DIPIRKANVGDISNRDIMEAFAiedpFHSVIVGFNVNILPD 417
                                   677888888899**********************8.....5*******************88655556************* PP

                                   HHHCCCCCTSEEEEESSHHHHHHHH CS
                          IF-2  80 akklaekegvkirlynvIYkliddv 104
                                   ak+++++ gvk++ ++vIY+lidd+
  gi|91772291|ref|YP_564983.1| 418 AKEKVRSTGVKVFMNDVIYRLIDDY 442
                                   ***********************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.63
                                   SSTEEEECEEEESS.B-HHHHHHHHHS CS
                          IF-2  40 eevkvkvihsgvGa.itesDvelasas 65 
                                    ev +++    vG  i+e D+ +a+  
  gi|91772291|ref|YP_564983.1| 526 MEVAMSIEGPTVGRqINEGDILHANIP 552
                                   57888888888995599****999875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.9e-11   6.4e-08       2     114 .]      12     133 ..      11     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.9e-11
                                   EEEEESTTSSHHHHHHHHHTS......TEEESSSTTSSSSEEEEEEEETTEE..........EEEEECGGCSSHHHHHHHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge......kaivsdkpgtTrdinegrvklkgke..........ielvDtpGliegaseekgl 66 
                                   v+++G+   GK++L+  + g+      +  ++++ g+T  ++ + v++ g++          + ++DtpG  +        
  gi|91772291|ref|YP_564983.1|  12 VCVMGHVDHGKTSLLDMIRGSavvsgeAGAITQHIGATEVPISAIVEKCGNPglldkfmvpgLLFIDTPG-HH----AFTT 87 
                                   89****************98533223244777777888888888888555447777777777********.44....2222 PP

                                   HHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  67 gkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    ++       adl++++vd++ e++kp+  e  ++l+++k p+++v+nk
  gi|91772291|ref|YP_564983.1|  88 LRSRG--GAlADLAVVIVDIN-EGFKPQTIESLNILQQHKTPFVVVANK 133
                                   22222..2247********99.88*************9**********8 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 !   28.8   0.3   5.2e-10   1.2e-06       1      69 [.     248     322 ..     248     326 .. 0.88
   2 ?    0.7   0.1      0.31     7e+02      25      57 ..     350     388 ..     339     390 .. 0.57
   3 ?   -3.3   0.0       5.5   1.2e+04      18      44 ..     411     433 ..     408     434 .. 0.66
   4 ?    1.7   6.4      0.16   3.5e+02       3      73 ..     482     547 ..     481     548 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5.2e-10
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE.........ETTSEEEEEEEESSCCSGSST CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea.........vaganaGvivaikgledaiiv 69 
                                   Gt+ + ++y+G+lkkGd++++ g ++    +i+t++++++++++  ++           + a++Gv++ ++ l+ a+  
  gi|91772291|ref|YP_564983.1| 248 GTTLDLILYDGVLKKGDTIVV-GcLGE---PIQTKVRAVLKPRALSEINvedkfkqvsKVTAAVGVKISAPHLDGALSG 322
                                   899999***************.66876...899*********9987777999****99999999999999999887443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.31
                                   CTTSEE......EEEEEEEEEEETEEESEEETTSEEEEE CS
                   GTP_EFTU_D2  25 dtskke......ivtrissletfhededeavaganaGvi 57 
                                   dt++++       ++   +l  + ++ed+++  an+G+i
  gi|91772291|ref|YP_564983.1| 350 DTDQSGitikadTIGSLEALVNELKKEDIPIRKANVGDI 388
                                   445555555444445555556666666666777777776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.5
                                   EEEEECTCTTSEEEEEEEEEEEEETEE CS
                   GTP_EFTU_D2  18 evrilgndtskkeivtrissletfhed 44 
                                   +v il++  ++k   +r +++ +f++d
  gi|91772291|ref|YP_564983.1| 411 NVNILPDA-KEK---VRSTGVKVFMND 433
                                   57777733.256...888888888876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.16
                                   EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   v+++rv+ Gt+k+   v     d  +   v+ +++l+   e++  a  g  +   + ++ +   i  Gd+l
  gi|91772291|ref|YP_564983.1| 482 VVGVRVIGGTIKTKVDVAT--GD--G-TVVGIVKGLQSRGENVSVATIGMEVAMSIEGPTVGRQINEGDIL 547
                                   99**********9888887..43..2.3789*********************9999999999999999988 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   9.8e-06     0.022      93     233 ..      74     212 ..      63     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.8e-06
                    ATP_bind_1  93 yllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek. 172
                                   +l +DtPG   + t+++ +           a  +v++vD +   +p +     + +l+++ ++++P+vvv nk+D +    
  gi|91772291|ref|YP_564983.1|  74 LLFIDTPGHHAFTTLRSRGG--------ALADLAVVIVDINEGFKPQT-----IESLNILQQHKTPFVVVANKIDKIHGWn 141
                                   67799999999999999999........56678999999887666544.....4448*******************98767 PP

                    ATP_bind_1 173 lekeleffedvealslllekee.........ekykk.laeaiaelleefalvlrflplssekeesiedlls 233
                                    +k   f++  ++ s+               e y++   ++  + +++f++++ ++p+s+ ++e+i dll 
  gi|91772291|ref|YP_564983.1| 142 PQKGAPFMTSYNKQSEHVRGSLdtkfyevvgELYNHgFSSDRYDRVNDFQHNIGVIPISAITGEGIPDLLM 212
                                   77888888866655554433325677888874444404445667899999999999999999999988875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0027         6      93     124 ..       3      34 ..       1      62 [. 0.83
   2 ?   -1.5   0.0      0.88     2e+03     150     164 ..      72      85 ..      66      88 .. 0.77
   3 ?    5.6   0.0    0.0059        13      13      60 ..      93     138 ..      82     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0027
                                   HHHHCTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  93 lkellkdktsvlvGqSGvGKStLinallpele 124
                                   +k++l+  +++++G+   GK++L++++++++ 
  gi|91772291|ref|YP_564983.1|   3 VKDNLRTPIVCVMGHVDHGKTSLLDMIRGSAV 34 
                                   67899999*******************99854 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.88
                                   TTTEEEESS-SSSS- CS
                   RsgA_GTPase 150 aegglliDtPGfrel 164
                                   + g l iDtPG +++
  gi|91772291|ref|YP_564983.1|  72 P-GLLFIDTPGHHAF 85 
                                   4.6788*****8776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0059
                                   EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG-- CS
                   RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlle 60 
                                    a  d ++++v ++ + +++++++  L ++++++ + v+v nKiD ++
  gi|91772291|ref|YP_564983.1|  93 GALADLAVVIVDIN-EGFKPQTIE-SLNILQQHKTPFVVVANKIDKIH 138
                                   5678999******9.9*******8.68999999************986 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018       0.4       1      34 [.      12      45 ..      12      51 .. 0.90
   2 ?    1.8   0.0     0.095   2.1e+02      98     114 ..      69      85 ..      65     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                                  EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                  ++v+G++ +GK+S+l+ + g+++   +++ +T+ 
  gi|91772291|ref|YP_564983.1| 12 VCVMGHVDHGKTSLLDMIRGSAVVSGEAGAITQH 45
                                  78********************998888888875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.095
                                   TTS-SEEEEE---B-SS CS
                     Dynamin_N  98 llvkgltlvDlPGldsv 114
                                   + v+gl ++D+PG +  
  gi|91772291|ref|YP_564983.1|  69 FMVPGLLFIDTPGHHAF 85 
                                   6789999******8864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 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:                        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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3848.63
//
Query:       gi|91772292|ref|YP_564984.1|  [L=135]
Description: 30S ribosomal protein S6e [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-38  129.6   0.0    6.8e-38  129.5   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 !  129.5   0.0   3.8e-42   6.8e-38       1     124 [.       4     123 ..       4     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 3.8e-42
                                   -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSS CS
                 Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggv 81 
                                   +k+++sdp+t k++++++++++++++ig++ig++vdg+++G  l+gy+l itgg+d++Gf m +++++p+r+++L+++ gv
  gi|91772292|ref|YP_564984.1|   4 FKIVVSDPKT-KTYQFDITGAEANQFIGRSIGQTVDGATVG--LDGYTLTITGGTDNSGFVMSPTLPGPRRQKVLIAN-GV 80 
                                   79*******8.99****************************..***********************************.** PP

                                   SS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTS CS
                 Ribosomal_S6e  82 gyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieglt 124
                                   gy    kG r+rk +rG++v+ di q+n++++ + +k ie+++
  gi|91772292|ref|YP_564984.1|  81 GYSAVAKGVRRRKFLRGSEVAPDITQINTKVTGYSDKAIEEIL 123
                                   *****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1054.22
//
Query:       gi|91772293|ref|YP_564985.1|  [L=414]
Description: TPR repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  195.0  15.7    1.7e-09   37.1   0.7   11.2 11  TPR_1            Tetratricopeptide repeat
      1e-55  181.4  14.8    5.1e-08   32.4   0.6   11.3 11  TPR_2            Tetratricopeptide repeat
    2.4e-41  139.1  31.8    6.1e-07   29.0   2.8   10.9 11  TPR_11           TPR repeat
    8.1e-39  128.6  22.1    1.4e-05   24.9   0.0   11.0 11  TPR_8            Tetratricopeptide repeat
    6.3e-38  129.1  11.4    1.1e-08   35.6   0.5    6.3  6  TPR_16           Tetratricopeptide repeat
    3.7e-25   86.5   9.9      0.024   15.0   0.0   10.4 10  TPR_17           Tetratricopeptide repeat
    5.1e-24   84.6  14.7    2.3e-05   24.8   3.9    6.6  7  TPR_19           Tetratricopeptide repeat
    1.9e-23   81.1  10.3      0.016   16.0   0.1   10.2 10  TPR_14           Tetratricopeptide repeat
    9.1e-22   77.2  21.3    6.9e-06   26.3   1.6    8.5  8  TPR_12           Tetratricopeptide repeat
    3.9e-20   71.8   2.5    0.00026   21.1   0.1    5.9  6  TPR_9            Tetratricopeptide repeat
    5.3e-16   58.1  17.7      0.012   16.3   0.4    9.5 10  TPR_6            Tetratricopeptide repeat
    1.5e-13   49.7  11.3      0.052   13.6   0.1    9.0  9  TPR_7            Tetratricopeptide repeat
      2e-11   44.0  10.1    0.00022   21.4   0.3    4.8  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.1e-07   31.8   0.8        2.8    8.1   0.1    6.0  6  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    7.5e-06   25.6  19.3      0.042   13.7   0.2    8.2 10  TPR_10           Tetratricopeptide repeat
    5.3e-05   22.3   1.5     0.0055   15.7   0.3    3.8  6  NARP1            NMDA receptor-regulated protein 1
     0.0013   18.7  22.4       0.91    9.6   0.4    8.0  9  TPR_3            Tetratricopeptide repeat
     0.0023   18.4   2.8         90    4.2   0.2    5.7  5  TPR_4            Tetratricopeptide repeat
     0.0028   17.4  17.5       0.67    9.6   0.3    5.6  6  TPR_21           Tetratricopeptide repeat-like domain
     0.0033   17.4   1.5        3.3    7.7   0.0    3.9  3  SRP_TPR_like     Putative TPR-like repeat
  ------ inclusion threshold ------
      0.013   15.5   2.8         14    5.8   0.1    4.8  5  DUF627           Protein of unknown function (DUF627)
      0.019   15.1  13.9         33    4.5   0.7    6.9  5  DUF3856          Domain of Unknown Function (DUF3856)
      0.022   15.2   0.5        3.8    8.0   0.0    3.0  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.029   14.4   0.1          8    6.6   0.1    3.6  3  MCC-bdg_PDZ      PDZ domain of MCC-2 bdg protein for Usher sy
          5    6.9   6.1        1.1    9.0   0.3    2.6  2  UPF0730          UPF0730 unknown protein family


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 ?    5.0   0.0     0.032        23      14      33 ..       4      23 ..       2      24 .. 0.90
   2 !   37.1   0.7   2.3e-12   1.7e-09       2      33 ..      26      57 ..      25      58 .. 0.96
   3 !   10.6   0.2   0.00054      0.39       2      28 ..      60      86 ..      59      89 .. 0.92
   4 !   22.2   0.0   1.2e-07   8.3e-05       1      34 []      93     126 ..      93     126 .. 0.98
   5 !   10.3   0.1   0.00071      0.51       4      30 ..     130     156 ..     127     160 .. 0.83
   6 !   24.9   0.0   1.6e-08   1.2e-05       3      34 .]     163     194 ..     161     194 .. 0.95
   7 !   18.5   0.0   1.8e-06    0.0013       3      34 .]     197     228 ..     195     228 .. 0.93
   8 !    7.4   0.0    0.0056         4       2      29 ..     230     257 ..     229     262 .. 0.89
   9 !   12.0   0.0    0.0002      0.15       1      31 [.     263     293 ..     263     296 .. 0.94
  10 !   25.8   0.1     9e-09   6.4e-06       1      34 []     297     330 ..     297     330 .. 0.95
  11 !   20.5   0.1     4e-07   0.00029       3      34 .]     333     364 ..     332     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.032
                                  TT-HHHHHHHHHHHHHHSTT CS
                         TPR_1 14 lgkydeAleyyekALelnPn 33
                                   g++  Al ++e A+  +Pn
  gi|91772293|ref|YP_564985.1|  4 EGDHAGALNAFETAIMYQPN 23
                                  699************99998 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.3e-12
                                  HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPn 33
                                   a+y++G  +f+lg+y+ A+++y+ AL+ +Pn
  gi|91772293|ref|YP_564985.1| 26 AAWYGKGDSHFYLGDYEAAIQAYDMALQYDPN 57
                                  79*****************************9 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00054
                                  HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_1  2 kalynlGnayfklgkydeAleyyekAL 28
                                  +a+ +++  + k gk deA   yekA 
  gi|91772293|ref|YP_564985.1| 60 NAYAGKADSLAKIGKSDEARTLYEKAT 86
                                  5999*********************96 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a+++ ++G +++ lg y e + +y+kA++l+P+n
  gi|91772293|ref|YP_564985.1|  93 AEIWSRKGSTLYGLGYYSESVNAYDKAISLDPTN 126
                                   799*****************************98 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00071
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALel 30 
                                   + ++G+ +    +y +Ale++e+AL  
  gi|91772293|ref|YP_564985.1| 130 YVGKGYSLIGIAQYSDALEAFEEALVF 156
                                   6778888888889***********965 PP

  == domain 6  score: 24.9 bits;  conditional E-value: 1.6e-08
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++ ++G +y+ lg y+ A+ +y+ AL+++P++
  gi|91772293|ref|YP_564985.1| 163 SWVGKGDCYYGLGGYEAAISAYDMALSIDPTF 194
                                   6999**************************96 PP

  == domain 7  score: 18.5 bits;  conditional E-value: 1.8e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a+ ++G+ +++ g+++ A+ +++ AL + P++
  gi|91772293|ref|YP_564985.1| 197 AWSGKGYSLYEIGDHEGAIVAFDTALFHSPKY 228
                                   9*************************998876 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0056
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                   kal +++ ++f l++yd  l ++++ + 
  gi|91772293|ref|YP_564985.1| 230 KALSGKAFTLFALEEYDLSLIAFNETID 257
                                   89******************99999776 PP

  == domain 9  score: 12.0 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                   aka+ ++G ++ + gk ++A + y+  ++l+
  gi|91772293|ref|YP_564985.1| 263 AKAWSGKGDVLSQIGKAEQATASYRMSVQLY 293
                                   89************************99997 PP

  == domain 10  score: 25.8 bits;  conditional E-value: 9e-09
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a+alynlG  +f++g + eAle++e  L +n +n
  gi|91772293|ref|YP_564985.1| 297 ADALYNLGRELFEMGLFSEALEAFEASLNVNSEN 330
                                   89**************************999876 PP

  == domain 11  score: 20.5 bits;  conditional E-value: 4e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   al ++G+a+++lg+y+ A  ++++A+ ++P +
  gi|91772293|ref|YP_564985.1| 333 ALVGKGYALYELGDYKGASVAFDQAIAVQPGY 364
                                   7889*************************975 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0021       1.5      13      33 ..       3      23 ..       1      24 [. 0.92
   2 !   32.4   0.6   7.1e-11   5.1e-08       1      33 [.      25      57 ..      25      58 .. 0.96
   3 !   12.4   0.2   0.00018      0.13       3      30 ..      61      88 ..      60      92 .. 0.90
   4 !   26.8   0.0   4.5e-09   3.2e-06       1      34 []      93     126 ..      93     126 .. 0.98
   5 !   10.7   0.1   0.00063      0.45       5      31 ..     131     157 ..     128     160 .. 0.84
   6 !   18.4   0.0   2.2e-06    0.0016       3      33 ..     163     193 ..     161     194 .. 0.93
   7 !   15.6   0.0   1.7e-05     0.012       3      33 ..     197     227 ..     195     228 .. 0.93
   8 ?    5.1   0.0     0.042        30       2      29 ..     230     257 ..     229     261 .. 0.89
   9 !    7.2   0.0    0.0084         6       1      32 [.     263     294 ..     263     296 .. 0.93
  10 !   21.9   0.2   1.7e-07   0.00012       1      33 [.     297     329 ..     297     330 .. 0.93
  11 !   19.8   0.1     8e-07   0.00057       3      33 ..     333     363 ..     332     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0021
                         TPR_2 13 klgdyeeAleafekAleldPn 33
                                    gd++ Al+afe A+ + Pn
  gi|91772293|ref|YP_564985.1|  3 DEGDHAGALNAFETAIMYQPN 23
                                  579****************98 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 7.1e-11
                         TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPn 33
                                  + a+y  G+++++lgdye A++a++ Al++dPn
  gi|91772293|ref|YP_564985.1| 25 PAAWYGKGDSHFYLGDYEAAIQAYDMALQYDPN 57
                                  579*****************************9 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00018
                         TPR_2  3 alynlGlayyklgdyeeAleafekAlel 30
                                  a+   +++++k g+ +eA+ ++ekA ++
  gi|91772293|ref|YP_564985.1| 61 AYAGKADSLAKIGKSDEARTLYEKATAI 88
                                  788899*******************876 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 4.5e-09
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ae++ + G  +y lg y e ++a++kA++ldP+n
  gi|91772293|ref|YP_564985.1|  93 AEIWSRKGSTLYGLGYYSESVNAYDKAISLDPTN 126
                                   799*****************************98 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00063
                         TPR_2   5 ynlGlayyklgdyeeAleafekAleld 31 
                                      G++++   +y +Aleafe+Al  d
  gi|91772293|ref|YP_564985.1| 131 VGKGYSLIGIAQYSDALEAFEEALVFD 157
                                   56789999999************9765 PP

  == domain 6  score: 18.4 bits;  conditional E-value: 2.2e-06
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                    +   G++yy lg ye A+ a++ Al++dP+
  gi|91772293|ref|YP_564985.1| 163 SWVGKGDCYYGLGGYEAAISAYDMALSIDPT 193
                                   58899*************************8 PP

  == domain 7  score: 15.6 bits;  conditional E-value: 1.7e-05
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   a+   G+++y+ gd+e A+ af+ Al + P+
  gi|91772293|ref|YP_564985.1| 197 AWSGKGYSLYEIGDHEGAIVAFDTALFHSPK 227
                                   899***********************88887 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.042
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                   +al   +  +++l +y+  l af++ + 
  gi|91772293|ref|YP_564985.1| 230 KALSGKAFTLFALEEYDLSLIAFNETID 257
                                   689999*****************99765 PP

  == domain 9  score: 7.2 bits;  conditional E-value: 0.0084
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                   a+a+   G+++ + g+ e+A + ++ +++l+ 
  gi|91772293|ref|YP_564985.1| 263 AKAWSGKGDVLSQIGKAEQATASYRMSVQLYS 294
                                   79***********************9999986 PP

  == domain 10  score: 21.9 bits;  conditional E-value: 1.7e-07
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                   a+alynlG+ ++++g + eAleafe++l  + +
  gi|91772293|ref|YP_564985.1| 297 ADALYNLGRELFEMGLFSEALEAFEASLNVNSE 329
                                   79*************************998866 PP

  == domain 11  score: 19.8 bits;  conditional E-value: 8e-07
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   al   G+a+y+lgdy+ A  af++A++  P+
  gi|91772293|ref|YP_564985.1| 333 ALVGKGYALYELGDYKGASVAFDQAIAVQPG 363
                                   67889**********************9997 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05    0.0086       6      38 ..       3      35 ..       2      36 .. 0.93
   2 !   29.0   2.8   8.5e-10   6.1e-07       1      42 []      32      73 ..      32      73 .. 0.94
   3 !   20.9   0.0     3e-07   0.00022       2      42 .]      67     107 ..      66     107 .. 0.94
   4 !   23.0   0.1   6.3e-08   4.5e-05       1      36 [.     100     135 ..     100     138 .. 0.90
   5 ?    4.4   0.0     0.042        30       9      25 ..     142     158 ..     142     161 .. 0.92
   6 !   21.8   0.2   1.5e-07   0.00011       1      42 []     168     209 ..     168     209 .. 0.96
   7 !   14.2   0.0   3.6e-05     0.026       1      40 [.     202     241 ..     202     243 .. 0.92
   8 !    6.8   0.0    0.0073       5.3       4      42 .]     239     277 ..     238     277 .. 0.93
   9 !   16.1   0.0   9.5e-06    0.0068       1      41 [.     270     310 ..     270     311 .. 0.91
  10 !    6.9   0.0    0.0069         5       1      27 [.     304     330 ..     304     333 .. 0.95
  11 !   16.0   0.5   9.6e-06    0.0069       1      25 [.     338     362 ..     338     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                        TPR_11  6 eqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                  + G+  +A++a+++A+ + P+ + a+y+ G+ +
  gi|91772293|ref|YP_564985.1|  3 DEGDHAGALNAFETAIMYQPNVPAAWYGKGDSH 35
                                  689*************************99877 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8.5e-10
                        TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                  Gd  + +G+ye+Ai+aY  Al++dP+  +ay + ++ ++k G
  gi|91772293|ref|YP_564985.1| 32 GDSHFYLGDYEAAIQAYDMALQYDPNLLNAYAGKADSLAKIG 73
                                  999****************************99998888876 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 3e-07
                        TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   d + + Gk +eA + Y+kA ++  d+ae+++  G ++y +G
  gi|91772293|ref|YP_564985.1|  67 DSLAKIGKSDEARTLYEKATAIGADDAEIWSRKGSTLYGLG 107
                                   677889********************************988 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 6.3e-08
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                   G  +y +G y e+++aY kA+ ldP+n   y + G+
  gi|91772293|ref|YP_564985.1| 100 GSTLYGLGYYSESVNAYDKAISLDPTNILSYVGKGY 135
                                   6778999*********************99988775 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.042
                        TPR_11   9 kyeeAieaYkkAlkldP 25 
                                   +y +A+ea+++Al +d+
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEALVFDN 158
                                   89***********9985 PP

  == domain 6  score: 21.8 bits;  conditional E-value: 1.5e-07
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   Gd yy +G ye+Ai aY  Al +dP++  a+++ G+ +y+ G
  gi|91772293|ref|YP_564985.1| 168 GDCYYGLGGYEAAISAYDMALSIDPTFSPAWSGKGYSLYEIG 209
                                   899**********************************99987 PP

  == domain 7  score: 14.2 bits;  conditional E-value: 3.6e-05
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                   G+ +ye G+ e+Ai a+ +Al  +P+++ a+++ ++++++
  gi|91772293|ref|YP_564985.1| 202 GYSLYEIGDHEGAIVAFDTALFHSPKYVKALSGKAFTLFA 241
                                   889***************************9998888775 PP

  == domain 8  score: 6.8 bits;  conditional E-value: 0.0073
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++++ +y+ ++ a+++ ++ d ++a a+++ G+++ + G
  gi|91772293|ref|YP_564985.1| 239 LFALEEYDLSLIAFNETIDADASYAKAWSGKGDVLSQIG 277
                                   78999*****************************98876 PP

  == domain 9  score: 16.1 bits;  conditional E-value: 9.5e-06
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   Gd++ + Gk e+A ++Y+  ++l + +a+a+ynLG  ++++
  gi|91772293|ref|YP_564985.1| 270 GDVLSQIGKAEQATASYRMSVQLYSGDADALYNLGRELFEM 310
                                   89999******************************666665 PP

  == domain 10  score: 6.9 bits;  conditional E-value: 0.0069
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdn 27 
                                   G++++e G + eA+ea+++ l+ +++n
  gi|91772293|ref|YP_564985.1| 304 GRELFEMGLFSEALEAFEASLNVNSEN 330
                                   899*******************99987 PP

  == domain 11  score: 16.0 bits;  conditional E-value: 9.6e-06
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldP 25 
                                   G+a+ye+G+y++A  a+ +A++  P
  gi|91772293|ref|YP_564985.1| 338 GYALYELGDYKGASVAFDQAIAVQP 362
                                   99********************998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.086        62      13      33 ..       3      23 ..       2      24 .. 0.92
   2 !   24.1   0.2   3.6e-08   2.6e-05       3      33 ..      27      57 ..      25      58 .. 0.96
   3 !   12.6   0.3   0.00017      0.12       2      29 ..      60      87 ..      59      91 .. 0.92
   4 !   24.9   0.0     2e-08   1.4e-05       1      34 []      93     126 ..      93     126 .. 0.96
   5 ?    5.3   0.1     0.038        27       3      28 ..     129     154 ..     128     158 .. 0.94
   6 !   17.7   0.0   4.1e-06    0.0029       3      33 ..     163     193 ..     162     194 .. 0.95
   7 ?    6.7   0.0     0.013       9.4       2      28 ..     196     222 ..     195     222 .. 0.92
   8 ?    0.7   0.1       1.2   8.3e+02       5      32 ..     233     260 ..     229     262 .. 0.81
   9 !    8.7   0.0    0.0031       2.2       1      25 [.     263     287 ..     263     295 .. 0.89
  10 !   17.4   0.1   4.9e-06    0.0035       1      33 [.     297     329 ..     297     330 .. 0.93
  11 !   11.6   0.0   0.00037      0.27       4      32 ..     334     362 ..     333     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.086
                                  HTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8 13 klgdyeeAkeyyekaleldpd 33
                                  + gd+  A  ++e a+ ++p+
  gi|91772293|ref|YP_564985.1|  3 DEGDHAGALNAFETAIMYQPN 23
                                  689**************9997 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 3.6e-08
                                  HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                  a+y +g+ ++ lgdye+A+++y  al++dp+
  gi|91772293|ref|YP_564985.1| 27 AWYGKGDSHFYLGDYEAAIQAYDMALQYDPN 57
                                  8*****************************7 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00017
                                  CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8  2 eayynlgsiylklgdyeeAkeyyekale 29
                                   ay  +++ + k g+ +eA   yeka+ 
  gi|91772293|ref|YP_564985.1| 60 NAYAGKADSLAKIGKSDEARTLYEKATA 87
                                  58999*********************86 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 2e-08
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   ae++ ++gs++  lg y e++ +y ka++ldp+n
  gi|91772293|ref|YP_564985.1|  93 AEIWSRKGSTLYGLGYYSESVNAYDKAISLDPTN 126
                                   799*****************************86 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.038
                                   HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekal 28 
                                   +y+ +g+ ++   +y  A e++e+al
  gi|91772293|ref|YP_564985.1| 129 SYVGKGYSLIGIAQYSDALEAFEEAL 154
                                   68999*******************98 PP

  == domain 6  score: 17.7 bits;  conditional E-value: 4.1e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +++ +g++y  lg ye+A+++y  al++dp+
  gi|91772293|ref|YP_564985.1| 163 SWVGKGDCYYGLGGYEAAISAYDMALSIDPT 193
                                   6999*************************96 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.013
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                   +a+  +g+ + + gd+e A+ ++  al
  gi|91772293|ref|YP_564985.1| 196 PAWSGKGYSLYEIGDHEGAIVAFDTAL 222
                                   78999*****************99886 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                     ++ +++ l++y+ +  ++++ +++d 
  gi|91772293|ref|YP_564985.1| 233 SGKAFTLFALEEYDLSLIAFNETIDADA 260
                                   56788999***********999887775 PP

  == domain 9  score: 8.7 bits;  conditional E-value: 0.0031
                                   CCHHHHHHHHHHHTT-HHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyye 25 
                                   a+a+  +g+++++ g+ e+A ++y+
  gi|91772293|ref|YP_564985.1| 263 AKAWSGKGDVLSQIGKAEQATASYR 287
                                   7899********************8 PP

  == domain 10  score: 17.4 bits;  conditional E-value: 4.9e-06
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   a+a+ynlg+ ++++g + eA e++e  l  + +
  gi|91772293|ref|YP_564985.1| 297 ADALYNLGRELFEMGLFSEALEAFEASLNVNSE 329
                                   789************************998876 PP

  == domain 11  score: 11.6 bits;  conditional E-value: 0.00037
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldp 32 
                                   ++ +g+++ +lgdy+ A  ++ +a+  +p
  gi|91772293|ref|YP_564985.1| 334 LVGKGYALYELGDYKGASVAFDQAIAVQP 362
                                   6679*********************9988 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.5   1.5e-11   1.1e-08       9      62 ..       3      53 ..       2      57 .. 0.93
   2 !   20.8   0.0   6.1e-07   0.00044       3      66 ..      65     125 ..      63     127 .. 0.94
   3 !   23.2   0.0   1.1e-07   8.1e-05       4      65 ..     134     192 ..     132     193 .. 0.86
   4 !   10.9   0.0   0.00078      0.56      36      66 ..     197     227 ..     195     229 .. 0.92
   5 !   12.0   0.1   0.00036      0.26       7      67 ..     239     296 ..     235     297 .. 0.93
   6 !   28.1   0.4   3.2e-09   2.3e-06       1      66 [.     301     363 ..     301     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.5e-11
                        TPR_16  9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62
                                  + gd + A++a+e+a+ ++   P  ++A++++gd+++ +g++++A+++y+ al+
  gi|91772293|ref|YP_564985.1|  3 DEGDHAGALNAFETAIMYQ---PNVPAAWYGKGDSHFYLGDYEAAIQAYDMALQ 53
                                  779****************...*****************************996 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 6.1e-07
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   +a+++++ g+ d+A+ ++e a++ +    d+ae +  +g  ++ +g + e + +y++a+  +p 
  gi|91772293|ref|YP_564985.1|  65 KADSLAKIGKSDEARTLYEKATAIG---ADDAEIWSRKGSTLYGLGYYSESVNAYDKAISLDPT 125
                                   699**********************...************************999999988886 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.1e-07
                        TPR_16   4 araalragdyddAaaal.eaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                   +++++   +y dA++a+ ea++ ++        ++ ++gd+++ +g +++A+ +y+ al  +p
  gi|91772293|ref|YP_564985.1| 134 GYSLIGIAQYSDALEAFeEALVFDN----GYSISWVGKGDCYYGLGGYEAAISAYDMALSIDP 192
                                   566667779********66666666....499**************************98887 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00078
                        TPR_16  36 AllllgdaalrqgrlaeAaalyraalraapd 66 
                                   A+ ++g ++++ g++++A+ +++ al ++p+
  gi|91772293|ref|YP_564985.1| 197 AWSGKGYSLYEIGDHEGAIVAFDTALFHSPK 227
                                   8999***************999999999996 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00036
                        TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   ++++ +yd  + a+++++++d      a A+ ++gd++ + g  + A a yr  ++ ++++
  gi|91772293|ref|YP_564985.1| 239 LFALEEYDLSLIAFNETIDAD---ASYAKAWSGKGDVLSQIGKAEQATASYRMSVQLYSGD 296
                                   678899999999*********...***************************9999999887 PP

  == domain 6  score: 28.1 bits;  conditional E-value: 3.2e-09
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   ++l+r++++ g + +A++a+ea l  +   +++  Al ++g a++++g++++A  +++ a++  p+
  gi|91772293|ref|YP_564985.1| 301 YNLGRELFEMGLFSEALEAFEASLNVN---SENLFALVGKGYALYELGDYKGASVAFDQAIAVQPG 363
                                   89*************************...55555*******************888777777776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.04        29       2      34 .]      14      46 ..      13      46 .. 0.92
   2 !   15.0   0.4   3.4e-05     0.024       2      33 ..      48      79 ..      47      80 .. 0.95
   3 ?    4.8   0.0     0.061        44       1      25 [.      81     105 ..      81     111 .. 0.91
   4 !   12.6   0.0    0.0002      0.14       1      33 [.     115     147 ..     115     148 .. 0.87
   5 !    7.9   0.0    0.0063       4.5       2      33 ..     150     181 ..     149     182 .. 0.95
   6 !   15.0   0.0   3.4e-05     0.024       2      33 ..     184     215 ..     183     216 .. 0.94
   7 ?    0.4   0.0       1.5   1.1e+03       8      30 ..     224     246 ..     217     249 .. 0.81
   8 ?    7.0   0.0     0.012       8.7       2      32 ..     252     282 ..     251     284 .. 0.92
   9 ?    6.4   0.0     0.019        14       3      27 ..     287     311 ..     285     318 .. 0.76
  10 ?    6.6   0.1     0.016        11       2      32 ..     320     350 ..     319     351 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.04
                        TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                  ++ a+ + Pn + a++ ++  +  +Gd++ A+q
  gi|91772293|ref|YP_564985.1| 14 FETAIMYQPNVPAAWYGKGDSHFYLGDYEAAIQ 46
                                  78888899***********************97 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.4e-05
                        TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                  y  al++dPn  +ay  +A  l+k+G++++Ar
  gi|91772293|ref|YP_564985.1| 48 YDMALQYDPNLLNAYAGKADSLAKIGKSDEAR 79
                                  888****************************8 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.061
                        TPR_17   1 lylkaleldPnnadaynnLAelllk 25 
                                   ly+ka ++  ++a+ +  ++ +l+ 
  gi|91772293|ref|YP_564985.1|  81 LYEKATAIGADDAEIWSRKGSTLYG 105
                                   7********************9975 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.0002
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +y ka+ ldP+n  +y  +++ l  + ++ +A+
  gi|91772293|ref|YP_564985.1| 115 AYDKAISLDPTNILSYVGKGYSLIGIAQYSDAL 147
                                   59******************9998887777775 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0063
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +++al  d  ++ ++  ++ +++ +G+++ A+
  gi|91772293|ref|YP_564985.1| 150 FEEALVFDNGYSISWVGKGDCYYGLGGYEAAI 181
                                   89***************************997 PP

  == domain 6  score: 15.0 bits;  conditional E-value: 3.4e-05
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   y  al +dP+ ++a+  +++ l+++Gd++ A+
  gi|91772293|ref|YP_564985.1| 184 YDMALSIDPTFSPAWSGKGYSLYEIGDHEGAI 215
                                   8889************************9986 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 1.5
                        TPR_17   8 ldPnnadaynnLAelllknGdlm 30 
                                   + P++++a+  +A +l  + +++
  gi|91772293|ref|YP_564985.1| 224 HSPKYVKALSGKAFTLFALEEYD 246
                                   78************998888776 PP

  == domain 8  score: 7.0 bits;  conditional E-value: 0.012
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   + + ++ d ++a+a+  ++ +l+++G+ ++A
  gi|91772293|ref|YP_564985.1| 252 FNETIDADASYAKAWSGKGDVLSQIGKAEQA 282
                                   6788999********************9998 PP

  == domain 9  score: 6.4 bits;  conditional E-value: 0.019
                        TPR_17   3 lkaleldPnnadaynnLAelllknG 27 
                                   + +++l+  +ada++nL++ l + G
  gi|91772293|ref|YP_564985.1| 287 RMSVQLYSGDADALYNLGRELFEMG 311
                                   557788899*********9666555 PP

  == domain 10  score: 6.6 bits;  conditional E-value: 0.016
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   ++ +l  +  n  a+  ++++l+++Gd++ A
  gi|91772293|ref|YP_564985.1| 320 FEASLNVNSENLFALVGKGYALYELGDYKGA 350
                                   899999**********************977 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00015      0.11       2      30 ..       2      30 ..       1      36 [. 0.92
   2 !   24.8   3.9   3.1e-08   2.3e-05       4      63 ..      38      97 ..      35     102 .. 0.95
   3 !   16.8   0.0     1e-05    0.0073       6      61 ..     142     198 ..     137     201 .. 0.91
   4 !   10.8   0.0   0.00075      0.54       4      53 ..     208     257 ..     205     271 .. 0.83
   5 ?    1.8   0.2      0.48   3.5e+02      15      46 ..     253     284 ..     249     299 .. 0.83
   6 !   14.5   0.3   5.4e-05     0.039       5      53 ..     277     325 ..     273     337 .. 0.90
   7 !   16.8   0.1   9.9e-06    0.0071       1      56 [.     307     362 ..     307     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                        TPR_19  2 laegdyaeAlalleqalqedpknaearll 30
                                  l+egd+a Al+++e a+ + p+ ++a+++
  gi|91772293|ref|YP_564985.1|  2 LDEGDHAGALNAFETAIMYQPNVPAAWYG 30
                                  89*************************97 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 3.1e-08
                        TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63
                                   gdy++A++++  alq+dp+ ++a ++ A+ l + g  deA+ l +++ +  +dda+++s
  gi|91772293|ref|YP_564985.1| 38 LGDYEAAIQAYDMALQYDPNLLNAYAGKADSLAKIGKSDEARTLYEKATAIGADDAEIWS 97
                                  59*****************************************************99886 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1e-05
                        TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ary 61 
                                   +y +Al+++e+al  d++++  + +  ++++ lg +++A+ + d ++  dp   +++
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEALVFDNGYSISWVGKGDCYYGLGGYEAAISAYDMALSIDPTFsPAW 198
                                   899*******************************************99999843555 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00075
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                    gd++ A+ ++  al ++pk+  a+ + A  l+al ++d    + ++  +
  gi|91772293|ref|YP_564985.1| 208 IGDHEGAIVAFDTALFHSPKYVKALSGKAFTLFALEEYDLSLIAFNETID 257
                                   59************************************966655555555 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.48
                        TPR_19  15 eqalqedpknaearllLAeallalgqldeAea 46 
                                    + +++d+ +a a+ +  ++l + g  ++A a
  gi|91772293|ref|YP_564985.1| 253 NETIDADASYAKAWSGKGDVLSQIGKAEQATA 284
                                   55678889999999999999999999999976 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 5.4e-05
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                   g+ ++A a ++   q + ++a+a+++L + l+++g + eA ++ +a ++
  gi|91772293|ref|YP_564985.1| 277 GKAEQATASYRMSVQLYSGDADALYNLGRELFEMGLFSEALEAFEASLN 325
                                   7889999999999*****************************9998776 PP

  == domain 7  score: 16.8 bits;  conditional E-value: 9.9e-06
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                   l+++g + eAl+++e+ l  + +n+ a+ +   al++lg+++ A  + d++ + +p
  gi|91772293|ref|YP_564985.1| 307 LFEMGLFSEALEAFEASLNVNSENLFALVGKGYALYELGDYKGASVAFDQAIAVQP 362
                                   7899*********************************************9987766 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0038       2.8      13      42 ..       3      32 ..       1      34 [. 0.90
   2 !   15.6   0.4   2.9e-05     0.021       1      41 [.      25      65 ..      25      68 .. 0.89
   3 !   16.0   0.1   2.2e-05     0.016       3      41 ..      61      99 ..      59     102 .. 0.88
   4 !   10.1   0.0    0.0017       1.2       2      35 ..      94     127 ..      93     136 .. 0.90
   5 ?    2.0   0.0      0.69     5e+02      16      30 ..     142     156 ..     132     170 .. 0.83
   6 ?    7.0   0.0     0.017        12      14      38 ..     174     198 ..     163     204 .. 0.84
   7 ?    6.4   0.0     0.027        20       5      38 ..     199     232 ..     196     238 .. 0.83
   8 !    9.2   0.0    0.0034       2.5       2      43 ..     264     305 ..     263     306 .. 0.93
   9 !    8.3   0.1    0.0063       4.5       2      31 ..     298     327 ..     297     339 .. 0.85
  10 !    9.1   0.0    0.0037       2.6       8      35 ..     338     365 ..     331     375 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                        TPR_14 13 alGdpdeAiallrralalaPddaeawllla 42
                                    Gd+++A+++++ a+  +P+ ++aw+  +
  gi|91772293|ref|YP_564985.1|  3 DEGDHAGALNAFETAIMYQPNVPAAWYGKG 32
                                  68************************8765 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.9e-05
                        TPR_14  1 peallalaeallalGdpdeAiallrralalaPddaeawlll 41
                                  p+a++  ++ ++ lGd+++Ai++++ al+ +P+ + a+   
  gi|91772293|ref|YP_564985.1| 25 PAAWYGKGDSHFYLGDYEAAIQAYDMALQYDPNLLNAYAGK 65
                                  789**************************999988777655 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.2e-05
                        TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawlll 41
                                  a++  a+ l+  G+ deA++l+++a a + ddae+w + 
  gi|91772293|ref|YP_564985.1| 61 AYAGKADSLAKIGKSDEARTLYEKATAIGADDAEIWSRK 99
                                  777778899999************************776 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0017
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda 35 
                                   e + + ++ l+ lG + e+++++++a++l+P++ 
  gi|91772293|ref|YP_564985.1|  94 EIWSRKGSTLYGLGYYSESVNAYDKAISLDPTNI 127
                                   67899999***********************985 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.69
                        TPR_14  16 dpdeAiallrralal 30 
                                   ++ +A++++++al  
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEALVF 156
                                   788999999999865 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.017
                        TPR_14  14 lGdpdeAiallrralalaPddaeaw 38 
                                   lG +++Ai +++ al+ +P++  aw
  gi|91772293|ref|YP_564985.1| 174 LGGYEAAISAYDMALSIDPTFSPAW 198
                                   566899**************99999 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.027
                        TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeaw 38 
                                      +  l++ Gd+++Ai +++ al + P+   a+
  gi|91772293|ref|YP_564985.1| 199 SGKGYSLYEIGDHEGAIVAFDTALFHSPKYVKAL 232
                                   5556778899******************998876 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0034
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   +a+   +++l + G+ ++A a +r  ++l+ +da+a++ l++
  gi|91772293|ref|YP_564985.1| 264 KAWSGKGDVLSQIGKAEQATASYRMSVQLYSGDADALYNLGR 305
                                   68888899*****************************99987 PP

  == domain 9  score: 8.3 bits;  conditional E-value: 0.0063
                        TPR_14   2 eallalaeallalGdpdeAiallrralala 31 
                                   +al+ l++ l++ G + eA++++++ l  +
  gi|91772293|ref|YP_564985.1| 298 DALYNLGRELFEMGLFSEALEAFEASLNVN 327
                                   79999*******************998655 PP

  == domain 10  score: 9.1 bits;  conditional E-value: 0.0037
                        TPR_14   8 aeallalGdpdeAiallrralalaPdda 35 
                                   + al++lGd+++A  ++++a+a +P+ +
  gi|91772293|ref|YP_564985.1| 338 GYALYELGDYKGASVAFDQAIAVQPGYE 365
                                   7899********************9876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.5    0.0003      0.22      45      73 ..      25      53 ..       2      55 .. 0.61
   2 !   26.3   1.6   9.7e-09   6.9e-06       4      74 ..      26      88 ..      23      90 .. 0.92
   3 !    8.8   0.1    0.0026       1.9       3      72 ..      93     154 ..      91     158 .. 0.74
   4 !   16.2   0.2   1.3e-05    0.0093      23      75 ..     140     191 ..     139     193 .. 0.86
   5 ?    5.0   0.0     0.043        31      44      72 ..     228     256 ..     194     259 .. 0.53
   6 !   13.8   0.1   7.5e-05     0.054       5      75 ..     231     293 ..     227     294 .. 0.83
   7 !   24.5   0.4   3.4e-08   2.4e-05       3      74 ..     263     326 ..     261     329 .. 0.92
   8 !   15.4   0.9   2.4e-05     0.017       4      73 ..     298     359 ..     296     363 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                        TPR_12 45 attlrnLgrlyralgryeeAlelleeala 73
                                   ++ ++ g+ +++lg+ye+A++++  al+
  gi|91772293|ref|YP_564985.1| 25 PAAWYGKGDSHFYLGDYEAAIQAYDMALQ 53
                                  44555555555555566666555555554 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 9.7e-09
                        TPR_12  4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                  +a++  ++ +++lg+y+ A++ ++ al+       p   ++++++ + ++ + + g+ +eA+ l+e+a+ai
  gi|91772293|ref|YP_564985.1| 26 AAWYGKGDSHFYLGDYEAAIQAYDMALQYD-----P---NLLNAYAGKADSLAKIGKSDEARTLYEKATAI 88
                                  68889*********************7666.....6...49***************************997 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0026
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                   a ++++ +++l+ lg y e+   ++ka+ +      p++   + ++ + g  +    +y +Ale++eeal
  gi|91772293|ref|YP_564985.1|  93 AEIWSRKGSTLYGLGYYSESVNAYDKAISLD-----PTN---ILSYVGKGYSLIGIAQYSDALEAFEEAL 154
                                   7889999999999999999999999998888.....544...5566666666666666666666666665 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 1.3e-05
                        TPR_12  23 lellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                   ++ +  ale+++++l     +++++  + g++y+ lg ye+A++++  al i+
  gi|91772293|ref|YP_564985.1| 140 IAQYSDALEAFEEALV-FDNGYSISWVGKGDCYYGLGGYEAAISAYDMALSID 191
                                   5678899999977764.4458*****************************986 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.043
                        TPR_12  44 tattlrnLgrlyralgryeeAlelleeal 72 
                                   ++ +l + + +++al++y+  l +++e++
  gi|91772293|ref|YP_564985.1| 228 YVKALSGKAFTLFALEEYDLSLIAFNETI 256
                                   45555555555555555555555555544 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 7.5e-05
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                   al+  a +l++l++yd +l  +++ +++         + +a +  + g+++++ g+ e+A + ++ +++++
  gi|91772293|ref|YP_564985.1| 231 ALSGKAFTLFALEEYDLSLIAFNETIDAD--------ASYAKAWSGKGDVLSQIGKAEQATASYRMSVQLY 293
                                   66677888888888888888888886666........258999**********************999987 PP

  == domain 7  score: 24.5 bits;  conditional E-value: 3.4e-08
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   a+a++  ++vl + g+ ++A + ++ +++++    G      a +l+nLgr ++++g + eAle++e +l++
  gi|91772293|ref|YP_564985.1| 263 AKAWSGKGDVLSQIGKAEQATASYRMSVQLY---SG-----DADALYNLGRELFEMGLFSEALEAFEASLNV 326
                                   889999*************************...33.....5889***********************9986 PP

  == domain 8  score: 15.4 bits;  conditional E-value: 2.4e-05
                        TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                    al+nl+  l+++g + eAle +e++l++       ++   + +l + g ++++lg+y+ A  ++ +a+a
  gi|91772293|ref|YP_564985.1| 298 DALYNLGRELFEMGLFSEALEAFEASLNVN-----SEN---LFALVGKGYALYELGDYKGASVAFDQAIA 359
                                   455566666666666666666666666666.....333...56777777777777777777777777776 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   3.6e-07   0.00026       6      61 ..       2      57 ..       1      72 [. 0.89
   2 !   12.2   0.0   0.00021      0.15      11      62 ..      75     126 ..      66     131 .. 0.90
   3 !    9.3   0.0    0.0017       1.2      10      60 ..     142     192 ..     136     197 .. 0.91
   4 !    9.7   0.0    0.0013      0.93      11      61 ..     177     227 ..     176     236 .. 0.94
   5 !   13.8   0.1   6.8e-05     0.049      10      57 ..     278     325 ..     272     331 .. 0.90
   6 !    7.7   0.1    0.0053       3.8      36      60 ..     338     362 ..     333     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.6e-07
                         TPR_9  6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                                  + e d++ al + e  ++ +P+ p  ++  G  ++ lG+++aA+++ + +l+ +p+
  gi|91772293|ref|YP_564985.1|  2 LDEGDHAGALNAFETAIMYQPNVPAAWYGKGDSHFYLGDYEAAIQAYDMALQYDPN 57
                                  5689***********************************************99994 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00021
                         TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                   +++a   +e   ++  dd+e +   G  l+ lG +s+ +++ + +++l+p +
  gi|91772293|ref|YP_564985.1|  75 SDEARTLYEKATAIGADDAEIWSRKGSTLYGLGYYSESVNAYDKAISLDPTN 126
                                   567777888899999**********************************975 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0017
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                   +++ al++ e  l+++      +   G +++ lG ++aA+ + + +l+++p
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEALVFDNGYSISWVGKGDCYYGLGGYEAAISAYDMALSIDP 192
                                   677899999999999999999999**********************99998 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0013
                         TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   +e+a+ ++++ l ++P     +   G  l++ G+ ++A+ +++++l ++p+
  gi|91772293|ref|YP_564985.1| 177 YEAAISAYDMALSIDPTFSPAWSGKGYSLYEIGDHEGAIVAFDTALFHSPK 227
                                   689*******************************************99995 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 6.8e-05
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                   ++e+a a + + ++l + d++ ++  G+ l+++G +s+Al+++ea l 
  gi|91772293|ref|YP_564985.1| 278 KAEQATASYRMSVQLYSGDADALYNLGRELFEMGLFSEALEAFEASLN 325
                                   67899999************************************9775 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0053
                         TPR_9  36 GlllaqlGclsaAladLeaylalap 60 
                                   G +l++lG++++A  ++++++a++p
  gi|91772293|ref|YP_564985.1| 338 GYALYELGDYKGASVAFDQAIAVQP 362
                                   889********************99 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.5     1e+03      13      27 ..       4      18 ..       1      23 [. 0.81
   2 !   16.3   0.4   1.6e-05     0.012       2      32 ..      27      57 ..      26      58 .. 0.95
   3 ?    6.8   0.1     0.017        12       6      26 ..      65      85 ..      60      88 .. 0.83
   4 ?   -0.9   0.0       4.6   3.3e+03      16      31 ..     109     124 ..     101     126 .. 0.70
   5 ?    3.0   0.0      0.27     2e+02       7      26 ..     134     153 ..     129     155 .. 0.80
   6 !    8.9   0.0    0.0036       2.6       7      31 ..     168     192 ..     164     193 .. 0.89
   7 ?    3.7   0.0      0.16   1.1e+02       7      25 ..     202     220 ..     200     222 .. 0.87
   8 ?   -1.9   0.0       9.9   7.1e+03      14      30 ..     277     293 ..     261     295 .. 0.67
   9 !   12.4   0.1   0.00027       0.2       1      24 [.     298     321 ..     298     325 .. 0.94
  10 !    8.6   0.1    0.0043       3.1       2      31 ..     333     362 ..     332     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.5
                                  HHHHHHHHHHHHHHH CS
                         TPR_6 13 lgdtdkAlealerli 27
                                   gd++ Al a+e  i
  gi|91772293|ref|YP_564985.1|  4 EGDHAGALNAFETAI 18
                                  47*********9887 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYPd 32
                                  A y  + s++ lgd+++A++a++  ++  P+
  gi|91772293|ref|YP_564985.1| 27 AWYGKGDSHFYLGDYEAAIQAYDMALQYDPN 57
                                  899********99**************9998 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.017
                                  HHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  6 lalsyrklgdtdkAlealerl 26
                                   a s+ k g++d+A++++e+ 
  gi|91772293|ref|YP_564985.1| 65 KADSLAKIGKSDEARTLYEKA 85
                                  688999988**********96 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 4.6
                                   HHHHHHHHHHHHHH-T CS
                         TPR_6  16 tdkAlealerlikeYP 31 
                                   +++++ a+++ i+  P
  gi|91772293|ref|YP_564985.1| 109 YSESVNAYDKAISLDP 124
                                   5667777887777666 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.27
                                   HHHHHH.HHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrk.lgdtdkAlealerl 26 
                                   ++s++  + ++++Alea+e+ 
  gi|91772293|ref|YP_564985.1| 134 GYSLIGiA-QYSDALEAFEEA 153
                                   77778756.*********986 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                   + +y+ lg +++A+ a++  ++  P
  gi|91772293|ref|YP_564985.1| 168 GDCYYGLGGYEAAISAYDMALSIDP 192
                                   89****99**********9988776 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealer 25 
                                   ++s+++ gd++ A+ a++ 
  gi|91772293|ref|YP_564985.1| 202 GYSLYEIGDHEGAIVAFDT 220
                                   899***88*******9986 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 9.9
                                   HHHHHHHHHHHHHHHH- CS
                         TPR_6  14 gdtdkAlealerlikeY 30 
                                   g++++A + ++  ++ Y
  gi|91772293|ref|YP_564985.1| 277 GKAEQATASYRMSVQLY 293
                                   67888877777665555 PP

  == domain 9  score: 12.4 bits;  conditional E-value: 0.00027
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   1 dAlyklalsyrklgdtdkAleale 24 
                                   dAly+l++ ++++g  ++Alea+e
  gi|91772293|ref|YP_564985.1| 298 DALYNLGRELFEMGLFSEALEAFE 321
                                   8**********************9 PP

  == domain 10  score: 8.6 bits;  conditional E-value: 0.0043
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                   Al   ++++++lgd+  A  a+++ i   P
  gi|91772293|ref|YP_564985.1| 333 ALVGKGYALYELGDYKGASVAFDQAIAVQP 362
                                   88899******99***********998666 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.14     1e+02      11      35 ..       3      25 ..       2      26 .. 0.90
   2 !   13.6   0.1   7.2e-05     0.052       5      33 ..      31      57 ..      27      59 .. 0.87
   3 ?    6.2   0.1     0.017        12       6      29 ..      66      87 ..      61      95 .. 0.78
   4 ?    5.9   0.0     0.021        15       6      34 ..     100     126 ..      93     128 .. 0.79
   5 ?    3.6   0.0      0.12        84      14      29 ..     142     157 ..     134     162 .. 0.86
   6 ?    3.6   0.0      0.11        79       6      29 ..     168     191 ..     163     197 .. 0.80
   7 ?   -1.3   0.0       4.1     3e+03       5      24 ..     269     288 ..     265     296 .. 0.78
   8 !   10.0   0.1     0.001      0.72       1      27 [.     299     325 ..     299     331 .. 0.90
   9 ?    0.7   0.0      0.93   6.7e+02       6      31 ..     338     361 ..     333     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                         TPR_7 11 rlGdyeeAielyeqsLaltkdpeda 35
                                  ++Gd++ A+  +e   a+ ++p+++
  gi|91772293|ref|YP_564985.1|  3 DEGDHAGALNAFET--AIMYQPNVP 25
                                  68************..****99976 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.2e-05
                         TPR_7  5 LarlysrlGdyeeAielyeqsLaltkdpe 33
                                   ++ ++ lGdye Ai+ y    al +dp+
  gi|91772293|ref|YP_564985.1| 31 KGDSHFYLGDYEAAIQAYDM--ALQYDPN 57
                                  6899****************..9999986 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.017
                         TPR_7  6 arlysrlGdyeeAielyeqsLalt 29
                                  a+   + G+ +eA +lye+  a++
  gi|91772293|ref|YP_564985.1| 66 ADSLAKIGKSDEARTLYEK--ATA 87
                                  6777889************..665 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.021
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                   +++   lG+y+e +  y +  a+  dp++
  gi|91772293|ref|YP_564985.1| 100 GSTLYGLGYYSESVNAYDK--AISLDPTN 126
                                   5555669************..99998876 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.12
                         TPR_7  14 dyeeAielyeqsLalt 29 
                                   +y++A+e +e++L+++
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEALVFD 157
                                   79*********88776 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.11
                         TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                   +++y  lG ye Ai+ y  +L ++
  gi|91772293|ref|YP_564985.1| 168 GDCYYGLGGYEAAISAYDMALSID 191
                                   788888999**********66554 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 4.1
                         TPR_7   5 LarlysrlGdyeeAielyeq 24 
                                    +++ s+ G+ e+A   y+ 
  gi|91772293|ref|YP_564985.1| 269 KGDVLSQIGKAEQATASYRM 288
                                   58899999999999888886 PP

  == domain 8  score: 10.0 bits;  conditional E-value: 0.001
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                                   aL+nL+r  +++G ++eA+e +e+sL 
  gi|91772293|ref|YP_564985.1| 299 ALYNLGRELFEMGLFSEALEAFEASLN 325
                                   79**********************985 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 0.93
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                   + +  +lGdy+ A   + q  a++ +
  gi|91772293|ref|YP_564985.1| 338 GYALYELGDYKGASVAFDQ--AIAVQ 361
                                   6677789***999888888..66655 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.3     3e-07   0.00022       3      82 .]       5      85 ..       3      85 .. 0.92
   2 ?    3.4   0.1      0.13        93      31      81 ..     101     152 ..      91     153 .. 0.87
   3 ?    5.6   0.2     0.025        18       4      78 ..     142     183 ..     107     187 .. 0.58
   4 !    8.0   0.1    0.0047       3.4       4      80 ..     142     219 ..     140     221 .. 0.84
   5 ?    1.7   0.0      0.44   3.1e+02      30      73 ..     202     246 ..     197     255 .. 0.80
   6 !   16.7   0.3   8.9e-06    0.0064      20      80 ..     294     355 ..     275     357 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3e-07
                                  T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                        ANAPC3  3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82
                                  +++  A+  +e +  ++++ p + y ++ +++ +g+y+ A++ ++ a + +++ l++   +A +l k++k +eA++++ek+
  gi|91772293|ref|YP_564985.1|  5 GDHAGALNAFETAIMYQPNVPAAWYGKGDSHFYLGDYEAAIQAYDMAlQYDPNLLNAYAGKADSLAKIGKSDEARTLYEKA 85
                                  6788899999999999*******************************8888888899999*****************9985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                                   HHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  31 lclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    +ly +g y +  + ++ka  l+++++ + + ++ +l+ + +y +A+ a+e+
  gi|91772293|ref|YP_564985.1| 101 STLYGLGYYSESVNAYDKAiSLDPTNILSYVGKGYSLIGIAQYSDALEAFEE 152
                                   5678888888889999999999999999999999***************997 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.025
                                   -HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                        ANAPC3   4 nyknAiflaerllaaetespedayl..lAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaa 78 
                                   +y +A+  +e +l    ++ +++ +  ++ c+y +g y+ A+                                 +a
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEAL--VFDNGYSISWvgKGDCYYGLGGYEAAI---------------------------------SA 183
                                   4555555555555..444455555522355555555555555.................................44 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0047
                                   -HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3   4 nyknAiflaerllaaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   +y +A+  +e +l    ++ +++ +  ++ c+y +g y+ A+  ++ a  ++++   ++  ++ +l++++ +e Ai a++
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEAL--VFDNGYSISWvgKGDCYYGLGGYEAAISAYDMAlSIDPTFSPAWSGKGYSLYEIGDHEGAIVAFD 219
                                   7999999999999..88888899994459*************99999988888888888888888888888888888775 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.44
                                   HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HH CS
                        ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkye 73 
                                   +++ly+ g+++ A+  +++a    +k  +++  +A +l++L++y+
  gi|91772293|ref|YP_564985.1| 202 GYSLYEIGDHEGAIVAFDTAlFHSPKYVKALSGKAFTLFALEEYD 246
                                   678888899999999999888888888888888999999999998 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 8.9e-06
                                   H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   + +++++y l+  l+++g + +A+e ++ + + ns++l +++ ++ +l++L+ y+ A  a++
  gi|91772293|ref|YP_564985.1| 294 SGDADALYNLGRELFEMGLFSEALEAFEASlNVNSENLFALVGKGYALYELGDYKGASVAFD 355
                                   779999*************************************************9998876 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 !    8.1   0.1    0.0038       2.8      11      37 ..      35      61 ..      34      64 .. 0.89
   2 ?    3.2   0.0      0.13        94      12      34 ..     104     126 ..     102     127 .. 0.94
   3 ?   -2.6   0.0       8.5   6.1e+03      14      27 ..     140     153 ..     138     156 .. 0.76
   4 ?    6.4   0.0     0.013       9.2      11      35 ..     171     195 ..     170     199 .. 0.92
   5 ?    1.4   0.0      0.48   3.4e+02       2      35 ..     298     331 ..     297     334 .. 0.85
   6 ?    4.6   0.0     0.047        34       9      46 ..     339     376 ..     338     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0038
                                  HHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C 11 hyklgeYseArryvdalLeiEPenrQa 37
                                  h+ lg+Y+ A +  d+ L+ +P+  +a
  gi|91772293|ref|YP_564985.1| 35 HFYLGDYEAAIQAYDMALQYDPNLLNA 61
                                  5669******************97766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                   HHHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                   y lg Yse+ +  d  ++++P n
  gi|91772293|ref|YP_564985.1| 104 YGLGYYSESVNAYDKAISLDPTN 126
                                   889******************98 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 8.5
                                   HT-HHHHHHHHHHH CS
                    Fis1_TPR_C  14 lgeYseArryvdal 27 
                                   + +Ys+A++  +  
  gi|91772293|ref|YP_564985.1| 140 IAQYSDALEAFEEA 153
                                   56899999887765 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.013
                                   HHHHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenr 35 
                                   +y lg Y+ A    d+ L+i+P ++
  gi|91772293|ref|YP_564985.1| 171 YYGLGGYEAAISAYDMALSIDPTFS 195
                                   799*******************875 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.48
                                   HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEPenr 35 
                                   + lY l    + +g +seA++  +a L++  en 
  gi|91772293|ref|YP_564985.1| 298 DALYNLGRELFEMGLFSEALEAFEASLNVNSENL 331
                                   567777777888999************9998885 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.047
                                   HHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHH CS
                    Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQaqsLkelied 46 
                                   ++ y lg+Y+ A    d+ ++++P+ +   + k+l e 
  gi|91772293|ref|YP_564985.1| 339 YALYELGDYKGASVAFDQAIAVQPGYERSIEGKQLAET 376
                                   68899*******************98766665555555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.86   6.2e+02      16      29 ..       5      18 ..       2      18 .. 0.90
   2 ?    1.2   0.0       0.5   3.6e+02      13      30 ..      36      53 ..      32      56 .. 0.72
   3 ?    4.9   0.1     0.035        25      12      31 ..      69      88 ..      58      89 .. 0.81
   4 ?    3.5   0.0     0.097        70       9      30 ..     100     121 ..      99     122 .. 0.91
   5 ?   -0.1   0.2       1.3   9.6e+02      17      29 ..     142     154 ..     141     155 .. 0.89
   6 ?   -2.4   0.0       6.9   4.9e+03      12      30 ..     171     189 ..     171     191 .. 0.64
   7 ?   -2.0   0.0         5   3.6e+03      11      29 ..     204     222 ..     202     222 .. 0.79
   8 ?   -1.0   0.0       2.5   1.8e+03      11      32 ..     272     293 ..     270     293 .. 0.85
   9 !   13.7   0.2   5.8e-05     0.042       2      31 ..     297     326 ..     297     332 .. 0.92
  10 ?    6.5   0.1     0.011       7.8       9      31 ..     338     360 ..     337     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.86
                        TPR_10 16 grydeAealleeal 29
                                  g++++A++ +e a+
  gi|91772293|ref|YP_564985.1|  5 GDHAGALNAFETAI 18
                                  99*********997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                        TPR_10 13 rqrgrydeAealleeala 30
                                  + +g+y++A + ++ al+
  gi|91772293|ref|YP_564985.1| 36 FYLGDYEAAIQAYDMALQ 53
                                  667888888887777765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.035
                        TPR_10 12 lrqrgrydeAealleealai 31
                                  l + g+ deA+ l+e+a ai
  gi|91772293|ref|YP_564985.1| 69 LAKIGKSDEARTLYEKATAI 88
                                  5667899*********9765 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.097
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   + +l+ +g y e+++ +++a++
  gi|91772293|ref|YP_564985.1| 100 GSTLYGLGYYSESVNAYDKAIS 121
                                   67899***************97 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.3
                        TPR_10  17 rydeAealleeal 29 
                                   +y +A++ +eeal
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAFEEAL 154
                                   6889*******98 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 6.9
                        TPR_10  12 lrqrgrydeAealleeala 30 
                                   ++ +g y++A   ++ al+
  gi|91772293|ref|YP_564985.1| 171 YYGLGGYEAAISAYDMALS 189
                                   5666777777777766665 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 5
                        TPR_10  11 alrqrgrydeAealleeal 29 
                                    l++ g++++A   ++ al
  gi|91772293|ref|YP_564985.1| 204 SLYEIGDHEGAIVAFDTAL 222
                                   68999*****988877775 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 2.5
                        TPR_10  11 alrqrgrydeAealleealair 32 
                                   +l+q g+ ++A a ++ +++++
  gi|91772293|ref|YP_564985.1| 272 VLSQIGKAEQATASYRMSVQLY 293
                                   7999999999999999988876 PP

  == domain 9  score: 13.7 bits;  conditional E-value: 5.8e-05
                        TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                                   A +l NL++ l+++g + eA++ +e +l++
  gi|91772293|ref|YP_564985.1| 297 ADALYNLGRELFEMGLFSEALEAFEASLNV 326
                                   789************************987 PP

  == domain 10  score: 6.5 bits;  conditional E-value: 0.011
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   + al+++g+y++A   +++a+a+
  gi|91772293|ref|YP_564985.1| 338 GYALYELGDYKGASVAFDQAIAV 360
                                   789******************97 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   7.6e-06    0.0055     179     259 ..       6      92 ..       1     100 [. 0.85
   2 ?   -0.1   0.0      0.45   3.2e+02     207     256 ..     108     157 ..     101     159 .. 0.84
   3 ?    1.0   0.0      0.21   1.5e+02     205     252 ..     174     221 ..     169     237 .. 0.77
   4 ?   -1.9   0.0       1.6   1.2e+03     214     248 ..     251     285 ..     241     296 .. 0.57
   5 ?   -0.6   0.0      0.67   4.8e+02      14      71 ..     273     330 ..     261     339 .. 0.71
   6 ?   -1.0   0.0      0.89   6.4e+02      16      65 ..     309     358 ..     299     376 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.6e-06
                                   G.GSS----SSHHHHHHHHHHHHHHH......HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         NARP1 179 dnedsekepesallwvlyflAqhydk......lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                   d++ + + +e+a+++  +  A +y k      lg++e A++  d a++ +p+l++ y  Ka  l + G  ++A ++ e+a 
  gi|91772293|ref|YP_564985.1|   6 DHAGALNAFETAIMYQPNVPAAWYGKgdshfyLGDYEAAIQAYDMALQYDPNLLNAYAGKADSLAKIGKSDEARTLYEKAT 86 
                                   55556677888888888888888887666666899********************************************98 PP

                                   HCTTT- CS
                         NARP1 254 klDlaD 259
                                   ++   D
  gi|91772293|ref|YP_564985.1|  87 AIGADD 92 
                                   876655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.45
                                   -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                         NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                    ++++++  dkai+ +pt +  y+ K+  l    + ++A e+ eea  +D
  gi|91772293|ref|YP_564985.1| 108 YYSESVNAYDKAISLDPTNILSYVGKGYSLIGIAQYSDALEAFEEALVFD 157
                                   567888999***************99998888888888888888887666 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.21
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                   lg +e A++  d a++ +pt+   +  K+  l   Gd ++A+ + ++a
  gi|91772293|ref|YP_564985.1| 174 LGGYEAAISAYDMALSIDPTFSPAWSGKGYSLYEIGDHEGAIVAFDTA 221
                                   566788888888888888888888888888888888888887777765 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.6
                                   HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                         NARP1 214 yidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                                     ++ i+ + +    +  K+ +l + G  ++A++ 
  gi|91772293|ref|YP_564985.1| 251 AFNETIDADASYAKAWSGKGDVLSQIGKAEQATAS 285
                                   55555555555555555555555555555555443 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.67
                                   HHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                         NARP1  14 ieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                                   +++ gk+e+A +  + + +        + + ++ l+++g ++eA +++ea l+ n+en
  gi|91772293|ref|YP_564985.1| 273 LSQIGKAEQATASYRMSVQLYSGDADALYNLGRELFEMGLFSEALEAFEASLNVNSEN 330
                                   5555666666666666555555555556666777778888888888888888888887 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 0.89
                                   HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLl 65 
                                   e g   eAle +e++ +   ++l  +  k+  l +Lg+++ A+ ++ + +
  gi|91772293|ref|YP_564985.1| 309 EMGLFSEALEAFEASLNVNSENLFALVGKGYALYELGDYKGASVAFDQAI 358
                                   55666677777777777777777777777777777777777766666655 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.5     0.014        10      15      35 ..      39      57 ..      34      58 .. 0.86
   2 ?    2.4   0.0      0.23   1.6e+02      15      35 ..      73      91 ..      68      92 .. 0.82
   3 ?   -2.3   0.1       6.9   4.9e+03      17      21 ..     116     120 ..     102     123 .. 0.58
   4 ?   -1.0   0.2       2.7   1.9e+03      16      24 ..     142     150 ..     142     154 .. 0.86
   5 ?   -0.0   0.0       1.3   9.2e+02      12      31 ..     172     189 ..     171     192 .. 0.74
   6 ?    3.1   0.0      0.14        99       8      34 ..     202     224 ..     198     225 .. 0.88
   7 ?   -1.7   0.0       4.2     3e+03       2      18 ..     227     246 ..     226     248 .. 0.78
   8 ?    6.2   0.0     0.014        10       2      31 ..     298     325 ..     297     330 .. 0.82
   9 !    9.6   0.4    0.0013      0.91       1      30 [.     328     358 ..     328     362 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                                  T-HHHHHHH..HHHHHHH-TT CS
                         TPR_3 15 kkyqeArelfsYallaildke 35
                                  ++y+ A+++++   +  +d++
  gi|91772293|ref|YP_564985.1| 39 GDYEAAIQAYD--MALQYDPN 57
                                  9********77..99999876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.23
                                  T-HHHHHHH..HHHHHHH-TT CS
                         TPR_3 15 kkyqeArelfsYallaildke 35
                                  +k +eAr l  Y+ ++++ ++
  gi|91772293|ref|YP_564985.1| 73 GKSDEARTL--YEKATAIGAD 91
                                  6779*****..9899998766 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.9
                                   HHHHH CS
                         TPR_3  17 yqeAr 21 
                                   y++A+
  gi|91772293|ref|YP_564985.1| 116 YDKAI 120
                                   55555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.7
                                   -HHHHHHH. CS
                         TPR_3  16 kyqeArelf 24 
                                   +y++A+e+f
  gi|91772293|ref|YP_564985.1| 142 QYSDALEAF 150
                                   7******95 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 1.3
                                   HHTT-HHHHHHH..HHHHHH CS
                         TPR_3  12 ynkkkyqeArelfsYallai 31 
                                   y  + y+ A+ +++   +  
  gi|91772293|ref|YP_564985.1| 172 YGLGGYEAAISAYD--MALS 189
                                   667889******77..6665 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.14
                                   HHHHHHTT-HHHHHHH..HHHHHHH-T CS
                         TPR_3   8 AaefynkkkyqeArelfsYallaildk 34 
                                   ++++y  ++ + A+ +f+    ++l++
  gi|91772293|ref|YP_564985.1| 202 GYSLYEIGDHEGAIVAFD----TALFH 224
                                   89***************9....77776 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 4.2
                                   HHHHHH...HHHHHHTT-HH CS
                         TPR_3   2 dylysy...Aaefynkkkyq 18 
                                   +y +++   A++++  ++y+
  gi|91772293|ref|YP_564985.1| 227 KYVKALsgkAFTLFALEEYD 246
                                   67778887788888888886 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHTT-HHHHHHH..HHHHHH CS
                         TPR_3   2 dylysyAaefynkkkyqeArelfsYallai 31 
                                   d ly ++ e++ ++ ++eA+e+  ++ + +
  gi|91772293|ref|YP_564985.1| 298 DALYNLGRELFEMGLFSEALEA--FEASLN 325
                                   669*******************..556655 PP

  == domain 9  score: 9.6 bits;  conditional E-value: 0.0013
                                   HHHHHHH...HHHHHHTT-HHHHHHH..HHHHH CS
                         TPR_3   1 ldylysy...AaefynkkkyqeArelfsYalla 30 
                                   ++ l+++   ++++y  ++y  A  +f+  ++ 
  gi|91772293|ref|YP_564985.1| 328 SENLFALvgkGYALYELGDYKGASVAFD--QAI 358
                                   6789999999****************88..875 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       1.4     1e+03      12      25 ..       2      15 ..       1      16 [. 0.81
   2 ?    1.0   0.0       1.4   9.7e+02       1      20 [.      25      44 ..      25      49 .. 0.79
   3 ?    3.5   0.0      0.21   1.5e+02       4      25 ..      62      83 ..      59      84 .. 0.80
   4 ?    4.2   0.2      0.13        90       3      25 ..     299     321 ..     297     322 .. 0.91
   5 ?    3.1   0.0      0.27   1.9e+02       3      20 ..     333     350 ..     331     356 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.4
                         TPR_4 12 lalGdldeAralle 25
                                  l+ Gd++ A+ ++e
  gi|91772293|ref|YP_564985.1|  2 LDEGDHAGALNAFE 15
                                  678******97766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.4
                         TPR_4  1 arallaLArallalGdldeA 20
                                  ++a ++ +  ++ lGd+++A
  gi|91772293|ref|YP_564985.1| 25 PAAWYGKGDSHFYLGDYEAA 44
                                  56778888888889*****9 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.21
                         TPR_4  4 llaLArallalGdldeAralle 25
                                  +++ A  l+  G +deAr+l e
  gi|91772293|ref|YP_564985.1| 62 YAGKADSLAKIGKSDEARTLYE 83
                                  5666777888899******998 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.13
                         TPR_4   3 allaLArallalGdldeAralle 25 
                                   al++L+r l++ G + eA++++e
  gi|91772293|ref|YP_564985.1| 299 ALYNLGRELFEMGLFSEALEAFE 321
                                   89*****************9988 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.27
                         TPR_4   3 allaLArallalGdldeA 20 
                                   al++ + al++lGd+  A
  gi|91772293|ref|YP_564985.1| 333 ALVGKGYALYELGDYKGA 350
                                   7788899*******9988 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.034        24     151     175 ..      30      54 ..       1      62 [. 0.72
   2 !    6.7   0.3    0.0075       5.4     154     178 ..      67      91 ..      60     103 .. 0.84
   3 ?    3.2   0.2     0.087        62     160     179 ..      73      92 ..      71     126 .. 0.85
   4 ?    2.8   0.0      0.12        86     152     174 ..     167     189 ..     141     194 .. 0.88
   5 !    9.6   0.3   0.00094      0.67     126     179 ..     242     296 ..     204     312 .. 0.76
   6 ?    3.2   0.1     0.086        62     121     179 ..     305     364 ..     299     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                        TPR_21 151 lrGDilvaqgkldeAraaYqaAlaa 175
                                    +GD ++  g+ + A +aY+ Al+ 
  gi|91772293|ref|YP_564985.1|  30 GKGDSHFYLGDYEAAIQAYDMALQY 54 
                                   59********************985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0075
                        TPR_21 154 DilvaqgkldeAraaYqaAlaalee 178
                                   D l++ gk deAr+ Y++A a +++
  gi|91772293|ref|YP_564985.1|  67 DSLAKIGKSDEARTLYEKATAIGAD 91 
                                   88999**************986655 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.087
                        TPR_21 160 gkldeAraaYqaAlaaleek 179
                                   gk deAr+ Y++A a ++++
  gi|91772293|ref|YP_564985.1|  73 GKSDEARTLYEKATAIGADD 92 
                                   89999999999998766554 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.12
                        TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                   +GD ++  g  + A +aY+ Al+
  gi|91772293|ref|YP_564985.1| 167 KGDCYYGLGGYEAAISAYDMALS 189
                                   9*******************996 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.00094
                        TPR_21 126 ekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                    ++yd  l +  e+ +++a  a++   +GD+l++ gk ++A a Y+ +++  + +
  gi|91772293|ref|YP_564985.1| 242 LEEYDLSLIAFnETIDADASYAKAWSGKGDVLSQIGKAEQATASYRMSVQLYSGD 296
                                   556666666662334455566777778*******************998866655 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.086
                        TPR_21 121 rvllaekkydeAlktLeakkeeafaalvael.rGDilvaqgkldeAraaYqaAlaaleek 179
                                   r l++++ + eAl++ ea+ + + + l+a + +G +l++ g+ + A  a+++A+a +   
  gi|91772293|ref|YP_564985.1| 305 RELFEMGLFSEALEAFEASLNVNSENLFALVgKGYALYELGDYKGASVAFDQAIAVQPGY 364
                                   567777888888888888888877777776559********************9876655 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.031        22       3      41 ..     114     154 ..     112     191 .. 0.71
   2 ?    0.1   0.0       1.1     8e+02      20      52 ..     235     265 ..     210     293 .. 0.63
   3 !    7.7   0.0    0.0046       3.3      25      70 ..     308     356 ..     306     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.031
                  SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs 41 
                                   ++y+k + l+ +++  +  k  +li + +y++aL++ +++ 
  gi|91772293|ref|YP_564985.1| 114 NAYDKAISLDPTNILSYvgKGYSLIGIAQYSDALEAFEEAL 154
                                   67899999998888888899999999999999999998876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsalsedvrfEka 52 
                                   k+ +l  le y+ +L++ +++   + d  + ka
  gi|91772293|ref|YP_564985.1| 235 KAFTLFALEEYDLSLIAFNETI--DADASYAKA 265
                                   6777777888876666665544..444444443 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0046
                  SRP_TPR_like  25 iklekyeeaLkllkkgsalsedvrf...EkaYvlYklkkykkalkilkk 70 
                                    +++ ++eaL++ +   +++++  f    k Y+lY l  yk a   +++
  gi|91772293|ref|YP_564985.1| 308 FEMGLFSEALEAFEASLNVNSENLFalvGKGYALYELGDYKGASVAFDQ 356
                                   6788999****9999988887765422279***********99876665 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.57   4.1e+02       6      27 ..       2      23 ..       1      32 [. 0.83
   2 ?    3.1   0.0      0.13        95      61      98 ..      43      87 ..      35      92 .. 0.88
   3 ?    0.3   0.0      0.94   6.7e+02      58      88 ..     108     145 ..     101     158 .. 0.58
   4 ?   -1.3   0.0       2.9   2.1e+03      61      94 ..     179     219 ..     177     231 .. 0.73
   5 ?    5.8   0.1     0.019        14      64     106 ..     284     326 ..     280     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.57
                        DUF627  6 largnhikALeiiedlisrhge 27
                                  l++g+h  AL  +e +i  + +
  gi|91772293|ref|YP_564985.1|  2 LDEGDHAGALNAFETAIMYQPN 23
                                  689***********99987766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                        DUF627 61 asvecfseavels.......rfyArsLfelasqlgsklyYkkavk 98
                                  a+++++ +a +         ++ A sL ++++  + +  Y+ka +
  gi|91772293|ref|YP_564985.1| 43 AAIQAYDMALQYDpnllnayAGKADSLAKIGKSDEARTLYEKATA 87
                                  78999999988889999999999*********999999***9975 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.94
                        DUF627  58 yllasvecfseavels.......rfyArsLfelasqlg 88 
                                   y   sv+++ +a +l         +   sL+ +a+  +
  gi|91772293|ref|YP_564985.1| 108 YYSESVNAYDKAISLDptnilsyVGKGYSLIGIAQYSD 145
                                   66778888888888875555544444444555554333 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.9
                        DUF627  61 asvecfseavels.......rfyArsLfelasqlgsklyYk 94 
                                   a+++++ +a ++        ++   sL+e++++ g  + + 
  gi|91772293|ref|YP_564985.1| 179 AAISAYDMALSIDptfspawSGKGYSLYEIGDHEGAIVAFD 219
                                   67777777777777777877778889999998877665555 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.019
                        DUF627  64 ecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                    +++++v+l ++ A  L++l+++l     + +a++  + +L+v
  gi|91772293|ref|YP_564985.1| 284 ASYRMSVQLYSGDADALYNLGRELFEMGLFSEALEAFEASLNV 326
                                   689*******************998888888888877777766 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7     0.046        33      65     123 ..      35      82 ..      25      92 .. 0.63
   2 ?    1.0   0.0      0.58   4.2e+02      57      82 ..      95     120 ..      89     125 .. 0.68
   3 ?    2.8   0.1      0.16   1.2e+02      47      82 ..     153     188 ..     151     191 .. 0.79
   4 ?    4.4   0.2      0.05        36      74     129 ..     241     292 ..     199     302 .. 0.74
   5 ?    1.3   0.0      0.45   3.2e+02     100     123 ..     331     354 ..     292     373 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.046
                                   HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                       DUF3856  65 laklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkaf 123
                                      lg+y++a+++ d al+y               ++a   +a +l+++G++dea   +
  gi|91772293|ref|YP_564985.1|  35 HFYLGDYEAAIQAYDMALQYDP-----------NLLNAYAGKADSLAKIGKSDEARTLY 82 
                                   5668888888888888888832...........12334444555555555555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856  57 chaglsealaklgrydealesadkal 82 
                                   +++   ++l +lg y e++++ dka+
  gi|91772293|ref|YP_564985.1|  95 IWSRKGSTLYGLGYYSESVNAYDKAI 120
                                   55555666777777777777777765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.16
                                   ---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856  47 afdheGfdalchaglsealaklgrydealesadkal 82 
                                   a+ ++   ++ + g  + + +lg y++a+++ d al
  gi|91772293|ref|YP_564985.1| 153 ALVFDNGYSISWVGKGDCYYGLGGYEAAISAYDMAL 188
                                   55555555788889999999********99999998 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.05
                                   HHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  74 alesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                   ale  d +l  fn   + +    k W      ++  l+++G+ ++a  ++rm++++
  gi|91772293|ref|YP_564985.1| 241 ALEEYDLSLIAFNETIDADASYAKAW----SGKGDVLSQIGKAEQATASYRMSVQL 292
                                   56666667777777666666666666....579999****************9865 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.45
                                   HHHHHHHHHHHHHTT-HHHHHHHH CS
                       DUF3856 100 iaavfsravaleelGrkdealkaf 123
                                   + a++ ++ al elG ++ a  af
  gi|91772293|ref|YP_564985.1| 331 LFALVGKGYALYELGDYKGASVAF 354
                                   234445555555555555555555 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0053       3.8      78     123 ..      34      79 ..      26     115 .. 0.90
   2 ?    4.0   0.0     0.091        65      75     124 ..     235     284 ..     223     294 .. 0.80
   3 ?    0.7   0.0       0.9   6.5e+02      49     101 ..     272     329 ..     261     348 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0053
                                   HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
               Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                   +++  gdy++a++  +++++ dp+  +a + kad+l ++g+  e+ 
  gi|91772293|ref|YP_564985.1|  34 SHFYLGDYEAAIQAYDMALQYDPNLLNAYAGKADSLAKIGKSDEAR 79 
                                   566779**********************************988865 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.091
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
               Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                   ka + ++ ++y +++   n  + ad + a+a + k d+l q+g+++++++
  gi|91772293|ref|YP_564985.1| 235 KAFTLFALEEYDLSLIAFNETIDADASYAKAWSGKGDVLSQIGKAEQATA 284
                                   55666778899999999999999999999999999999999999887654 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.9
                                   GTS---HHHHHHHHHHH.....TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
               Alkyl_sulf_dimr  49 nLnplppeekakrlvel.....mGgaekvlekakealkegdyrwaaellnhlvfadpe 101
                                    L ++ ++e+a+   ++      G+a+++ +  +e ++ g +  a+e  +  +  ++e
  gi|91772293|ref|YP_564985.1| 272 VLSQIGKAEQATASYRMsvqlySGDADALYNLGRELFEMGLFSEALEAFEASLNVNSE 329
                                   4444444444433322211112567777777777777777777777766666665555 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.011         8      34      58 ..      38      62 ..      36      65 .. 0.93
   2 ?    0.3   0.0         1   7.2e+02      34      49 ..     174     189 ..     171     204 .. 0.87
   3 ?    2.1   0.0      0.27   1.9e+02      32      58 ..     274     301 ..     248     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                   MCC-bdg_PDZ 34 lgkaEsnatALvlALeyserlkeay 58
                                  lg +E+   A+ +AL+y  +l++ay
  gi|91772293|ref|YP_564985.1| 38 LGDYEAAIQAYDMALQYDPNLLNAY 62
                                  899*****************99999 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1
                   MCC-bdg_PDZ  34 lgkaEsnatALvlALe 49 
                                   lg +E+  +A+ +AL+
  gi|91772293|ref|YP_564985.1| 174 LGGYEAAISAYDMALS 189
                                   899***********97 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.27
                   MCC-bdg_PDZ  32 ldlgkaEsnatALvlALe.yserlkeay 58 
                                    ++gkaE  ++ +++ ++ ys  +  +y
  gi|91772293|ref|YP_564985.1| 274 SQIGKAEQATASYRMSVQlYSGDADALY 301
                                   5899999777779999998888877776 PP

>> UPF0730  UPF0730 unknown protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3    0.0015       1.1      23      35 ..     100     112 ..      96     118 .. 0.84
   2 ?   -1.2   1.1       2.4   1.8e+03      22      30 ..     167     175 ..     159     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                       UPF0730  23 enalYGvGYsssh 35 
                                   +++lYG+GY s+ 
  gi|91772293|ref|YP_564985.1| 100 GSTLYGLGYYSES 112
                                   89*******9975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
                       UPF0730  22 senalYGvG 30 
                                    + + YG+G
  gi|91772293|ref|YP_564985.1| 167 KGDCYYGLG 175
                                   589*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2470.82
//
Query:       gi|91772294|ref|YP_564986.1|  [L=118]
Description: hypothetical protein Mbur_0226 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-19   68.3   2.7    5.3e-19   67.9   2.7    1.1  1  DUF4389   Domain of unknown function (DUF4389)
  ------ inclusion threshold ------
       0.11   12.5   0.2       0.19   11.8   0.2    1.3  1  GIIM      Group II intron, maturase-specific domain


Domain annotation for each model (and alignments):
>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   2.7     6e-23   5.3e-19       2      72 ..      19      89 ..      18      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 6e-23
                       DUF4389  2 eavwlRlllmllfaivlslaslvlwvvvvvqflivLvtgrpnepLrdfgksllrYiarilrfltlnseekP 72
                                   ++++Rl+++++++i+lsl+sl++++++++q+ ++Lv+gr+ e+L++++k++l+Y+++i+++ +l ++++P
  gi|91772294|ref|YP_564986.1| 19 FELFVRLFYSIPVVIILSLYSLLMIICLLFQLPFILVLGRRFETLNNVIKGYLEYYTHIAGYFYLTTDKRP 89
                                  589*******************************************************************9 PP

>> GIIM  Group II intron, maturase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.1e-05      0.19      22      42 ..      57      77 ..      54      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                          GIIM 22 eelirklnpilrGWanYyrlg 42
                                  + + + ln +++G+ +Yy + 
  gi|91772294|ref|YP_564986.1| 57 GRRFETLNNVIKGYLEYYTHI 77
                                  567899************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 876.33
//
Query:       gi|91772295|ref|YP_564987.1|  [L=130]
Description: thioredoxin-related [Methanococcoides burtonii DSM 6242]
Scores for complete 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   73.1   0.0    1.8e-20   72.8   0.0    1.1  1  Thioredoxin    Thioredoxin
    5.6e-07   30.0   0.5    1.1e-05   25.9   0.5    2.1  1  Thioredoxin_2  Thioredoxin-like domain
    0.00019   21.3   0.0    0.00023   21.1   0.0    1.1  1  TraF           F plasmid transfer operon protein
    0.00096   19.3   0.1     0.0015   18.6   0.1    1.5  1  Thioredoxin_7  Thioredoxin-like
     0.0014   19.0   0.1      0.052   13.9   0.1    2.2  2  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.032   14.0   1.2       0.53   10.0   0.0    2.1  2  DSBA           DSBA-like thioredoxin domain
      0.037   13.7   0.0      0.044   13.5   0.0    1.2  1  Redoxin        Redoxin
       0.04   14.0   0.0      0.058   13.4   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
      0.041   14.0   0.3        8.3    6.5   0.0    2.1  2  Thioredoxin_4  Thioredoxin
      0.053   13.4   0.1       0.12   12.3   0.1    1.6  1  AhpC-TSA       AhpC/TSA family
       0.19   11.7   0.0       0.28   11.2   0.0    1.3  1  HyaE           Hydrogenase-1 expression protein HyaE


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   1.1e-23   1.8e-20       5     102 ..       9     106 ..       5     107 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.1e-23
                                   SSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEE CS
                   Thioredoxin   5 ltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkev 85 
                                   + + n+e  v+k+ k+vlv Fy + C hCka+ P + ++ae++kd  k+ +++++ n+ +a++y+veg Pt++++ +gk +
  gi|91772295|ref|YP_564987.1|   9 VGDGNWEIMVEKQPKPVLVMFYLNTCSHCKAIDPYFREFAETYKDSCKFFRLNAELNPWVAERYGVEGTPTFIFTCAGKMI 89 
                                   56789**************************************************************************** PP

                                   EEEESS-HHHHHHHHHH CS
                   Thioredoxin  86 kkyegarekeklaaflk 102
                                   + + g ++ ++l+++++
  gi|91772295|ref|YP_564987.1|  90 RGMAGVSHPSELKKNIE 106
                                   ******999****9987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.5   6.5e-09   1.1e-05       2     105 ..      19     101 ..      18     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.5e-09
                 Thioredoxin_2   2 kgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82 
                                   +++ kpvlv+f+ ++C  Ck++   ++e     ++     +k+s   k++++  + ++           ++a++ygv+gtP
  gi|91772295|ref|YP_564987.1|  19 EKQPKPVLVMFYLNTCSHCKAIDPYFREF---AET-----YKDS--CKFFRLNAELNP-----------WVAERYGVEGTP 78 
                                   6788*****************99988888...556.....8888..677777777777...........699********* PP

                 Thioredoxin_2  83 tivfldgkeivarlpGyvpaeel 105
                                   t++f  + +++  + G   + el
  gi|91772295|ref|YP_564987.1|  79 TFIFTCAGKMIRGMAGVSHPSEL 101
                                   *7755554466666666666665 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.4e-07   0.00023     132     222 ..      25     104 ..      15     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
                          TraF 132 gLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpvaaG 212
                                    L++Fy ++c+ c+a  p  ++fa++y+ + ++  ++ + +p +++         r+gv+ tP++++      k++  +aG
  gi|91772295|ref|YP_564987.1|  25 VLVMFYLNTCSHCKAIDPYFREFAETYKDSCKFFRLNAELNPWVAE---------RYGVEGTPTFIFTCAG--KMIRGMAG 94 
                                   69***************************************99888.........*********9987665..55555556 PP

                          TraF 213 llsldeleer 222
                                   +   +el+++
  gi|91772295|ref|YP_564987.1|  95 VSHPSELKKN 104
                                   6555555555 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   9.4e-07    0.0015      14      38 ..      19      43 ..      17      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.4e-07
                                  HHHT--EEEEE--TT-HHHHHHHHH CS
                 Thioredoxin_7 14 aergkpvlvffgaswcftCqalerd 38
                                  +++ kpvlv+f  ++c++C+a++  
  gi|91772295|ref|YP_564987.1| 19 EKQPKPVLVMFYLNTCSHCKAIDPY 43
                                  5899*****************9855 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   3.2e-05     0.052       2      36 ..      23      55 ..      21      62 .. 0.88
   2 !    6.0   0.0    0.0089        15      55      87 ..      52      81 ..      46      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                  SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSE CS
                 Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkv 36
                                  k vl++f+ + c++cka+ p   e+ e++k  + +
  gi|91772295|ref|YP_564987.1| 23 KPVLVMFYLNTCSHCKAIDPYFREFAETYK--DSC 55
                                  78***************************9..444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0089
                                  GGS-TTSEE.EE-TT-HHHHTT-S--TT-SEEE CS
                 Thioredoxin_8 55 kknkkpwlsvpfddkkrnklkkkynvkaiPtlv 87
                                  k+   ++ +++ + + + +++++y+v++ Pt++
  gi|91772295|ref|YP_564987.1| 52 KD---SCKFFRLNAELNPWVAERYGVEGTPTFI 81
                                  33...59999999999***************97 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4      0.04        65       4      33 ..      28      58 ..      25      68 .. 0.80
   2 ?   10.0   0.0   0.00032      0.53     160     182 ..      69      92 ..      65     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.04
                                  EEEBTTBHHHHHHHHHHHHHHHHCCT.EEEE CS
                          DSBA  4 effDvlCPyCylgkerleklaarspd.vkvv 33
                                  +f+   C +C++ ++ +++ a+ ++d +k+ 
  gi|91772295|ref|YP_564987.1| 28 MFYLNTCSHCKAIDPYFREFAETYKDsCKFF 58
                                  566668******************7779886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00032
                                   HHHTT-SSSSEEEE..TTCEEEESS CS
                          DSBA 160 aqslgvtGvPtvvv..dgkrmvfGa 182
                                   a+++gv G+Pt+++   gk m+ G 
  gi|91772295|ref|YP_564987.1|  69 AERYGVEGTPTFIFtcAGK-MIRGM 92 
                                   899**********999898.66553 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-05     0.044      29      89 ..      23      81 ..      10     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                  SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEE CS
                       Redoxin 29 kkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpv 89
                                  k+v+v f+   +c  C+a  py++++ae +k++  +++ ++a  ++ v e  g eg + ++
  gi|91772295|ref|YP_564987.1| 23 KPVLVMFYLN-TCSHCKAIDPYFREFAETYKDS-CKFFRLNAELNPWVAERYGVEGTPTFI 81
                                  7788888888.******************8887.888888888888888877776665555 PP

>> Thioredoxin_3  Thioredoxin 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     0.058       8      54 ..      32      81 ..      25     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                                  SSSTTCHHHHHHHHHHCHCCT..CECEEECCTTHHHH.HHCT-SSSSEEE CS
                 Thioredoxin_3  8 pgCakCpklekavkeaaaekg..ikaevekvtdfeei.ekygVmsvPalv 54
                                   +C +C++++  ++e a++ +   k+   +++ ++ + e+ygV+ +P+ +
  gi|91772295|ref|YP_564987.1| 32 NTCSHCKAIDPYFREFAETYKdsCKFFRLNAELNPWVaERYGVEGTPTFI 81
                                  47*****************9625666666677777778*********986 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5    0.0097        16      15      42 ..      24      51 ..      19      64 .. 0.76
   2 ?    6.5   0.0    0.0051       8.3     133     165 ..      69     106 ..      59     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0097
                                  EEEEEEE-TT-HHHHHHHHHHHHHHHHH CS
                 Thioredoxin_4 15 vtvieyedlrCphCakfeeeveklleey 42
                                   +++ +   +C+hC++ +    ++ e y
  gi|91772295|ref|YP_564987.1| 24 PVLVMFYLNTCSHCKAIDPYFREFAETY 51
                                  5677777779*****9988777777776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0051
                                   HHHHT--SS-EEEE..TTEEE...-TT--HHHHHHHHT CS
                 Thioredoxin_4 133 akkagiestPtfii..ngekv...eepqtyeelkalid 165
                                   a++ g+e+tPtfi    g+++   ++ + ++elk+ i+
  gi|91772295|ref|YP_564987.1|  69 AERYGVEGTPTFIFtcAGKMIrgmAGVSHPSELKKNIE 106
                                   5899********97666777534456666666666665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.3e-05      0.12      25      60 ..      22      55 ..      11      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
                                  TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTE CS
                      AhpC-TSA 25 gkpvvlffypkdwcpvCttelpalaklyeefkergv 60
                                   kpv+++fy +  c +C++  p +++ +e +k+  +
  gi|91772295|ref|YP_564987.1| 22 PKPVLVMFYLN-TCSHCKAIDPYFREFAETYKD-SC 55
                                  39*********.****************99995.45 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.28      70     104 ..      63      97 ..      43     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                   HHHHHHHHCCT-TSSSEEEEEETTEEEEEEESSST CS
                          HyaE  70 eqeealaerfgvlktPsllflrdgeylgvlakird 104
                                   e +  +aer+gv  tP+++f   g+++  +a++  
  gi|91772295|ref|YP_564987.1|  63 ELNPWVAERYGVEGTPTFIFTCAGKMIRGMAGVSH 97 
                                   5566789*******************999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1138.40
//
Query:       gi|91772296|ref|YP_564988.1|  [L=402]
Description: transposase, IS204/IS1001/IS1096/IS1165 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-70  237.8   4.3    2.3e-70  237.0   4.3    1.3  1  DDE_Tnp_ISL3  Transposase
    2.4e-14   52.5   0.1    4.1e-14   51.7   0.1    1.4  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
    5.6e-11   42.9   1.3    1.5e-10   41.6   1.3    1.8  1  zf-ISL3       zinc-finger of transposase IS204/IS1001/IS1096/
     0.0011   17.7   0.3     0.0026   16.5   0.2    1.6  1  UPF0236       Uncharacterised protein family (UPF0236)
     0.0042   16.8   0.0      0.024   14.4   0.0    2.2  2  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.056   13.5   0.0       0.13   12.3   0.0    1.6  1  HTH_29        Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.0   4.3   7.8e-74   2.3e-70       1     234 [.     156     382 ..     156     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 237.0 bits;  conditional E-value: 7.8e-74
                  DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkafleslsek.erekveavvmDmsaayksavkealPnAkiv 80 
                                   +g+DEis+kkgh+yvt ++dl  +++r+++i +g+k++++k+f e ls+k +++++++++mDm++a+k  ++e++PnAkiv
  gi|91772296|ref|YP_564988.1| 156 IGVDEISVKKGHSYVTLFYDL--NKSRIIHIENGKKRSVFKKFREYLSKKiDPDNIKYISMDMYPAFKGGAREYFPNAKIV 234
                                   8********************..**********************997778****************************** PP

                  DDE_Tnp_ISL3  81 vDrFHvvklanealdevRrreqkelreekrkklkrsrrlllknpenlteeqkqrldelleaspelekaYelkeelrevfrk 161
                                   +D+FH+vk++n+a+d+vRr e ++ ++     l ++r+++lknpenl++++ ++++++ +++++++kaY++k +l+++++ 
  gi|91772296|ref|YP_564988.1| 235 YDKFHIVKMMNDAIDKVRRSEYQSNKD-----LGKTRFMWLKNPENLSDREIAKIQSIKDLDTKTAKAYKFKLALQRLWEI 310
                                   ***********************8765.....************************************************* PP

                  DDE_Tnp_ISL3 162 kdkeearkalkewiekaersglkefkklaktlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayGfrnfe 234
                                   k+ + ar+++++w+ + ++s++ke+ +lak++k++ ++Il++++ ++sng+vEg+Nnkik++ +r+yG ++ e
  gi|91772296|ref|YP_564988.1| 311 KNMDVAREYIEKWHYWGTHSNIKEVITLAKMIKRNSHGILESIKGNISNGVVEGLNNKIKTAFKRSYGLKT-E 382
                                   ********************************************99**********************964.4 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 !   51.7   0.1   1.4e-17   4.1e-14       2      52 .]      92     141 ..      91     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.4e-17
                  HTH_Tnp_ISL3   2 elPwarrrsriTlrleayilelllesrsvkavArqlgvSwtTVwrildryv 52 
                                   ++Pw+r + ++Tl +ea i++ ++e+ +v+a+A++ ++++++Vwril +yv
  gi|91772296|ref|YP_564988.1|  92 NVPWTRQNTGFTLFFEALIVAISKEM-TVSAIAEMINIHEDSVWRILTHYV 141
                                   79************************.**********************97 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   1.3   4.9e-14   1.5e-10       4      47 .]      44      86 ..      41      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.9e-14
                       zf-ISL3  4 rCPnCgsktvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47
                                   CP C++ +   h++k+  +rhl+++++++yL++r++R +C+e+
  gi|91772296|ref|YP_564988.1| 44 SCPVCNKLS-ELHDTKKKVWRHLDFFHYETYLHARVPRTKCNEH 86
                                  7*******8.889999*************************987 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   8.7e-07    0.0026     232     306 ..     186     259 ..     161     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.7e-07
                       UPF0236 232 aekeeDvWedleeyleeeYklekiekviinGDaasWikegle.wikkalfqlDRfhlkkelrkvlskePryrekvr 306
                                   + k++ v++++ eyl ++ + ++i   +i+ D  +  k g   +++ a  + D+fh+ k ++ ++ k  r   + +
  gi|91772296|ref|YP_564988.1| 186 NGKKRSVFKKFREYLSKKIDPDNI--KYISMDMYPAFKGGAReYFPNAKIVYDKFHIVKMMNDAIDKVRRSEYQSN 259
                                   367899******************..59999**9999998655********************9988766555555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   8.1e-06     0.024      17      45 ..     116     144 ..     108     151 .. 0.83
   2 ?   -1.9   0.0       1.1   3.2e+03      17      25 ..     275     283 ..     267     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.1e-06
                        HTH_23  17 GlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                    ++v++IA++ ++++  v+r+l  y+++ 
  gi|91772296|ref|YP_564988.1| 116 EMTVSAIAEMINIHEDSVWRILTHYVNKA 144
                                   589*******************9997665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                        HTH_23  17 GlsvreIAr 25 
                                    ls reIA+
  gi|91772296|ref|YP_564988.1| 275 NLSDREIAK 283
                                   6899****8 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.2e-05      0.13       6      38 ..     111     142 ..     108     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                        HTH_29   6 lllaeGvstvsqiAkllglsrrtvyrwlkrfee 38 
                                    ++++++ tvs iA++ ++++++v r+l  +++
  gi|91772296|ref|YP_564988.1| 111 VAISKEM-TVSAIAEMINIHEDSVWRILTHYVN 142
                                   4567778.9*****************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3058.93
//
Query:       gi|91772297|ref|YP_564989.1|  [L=202]
Description: hypothetical protein Mbur_0229 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-57  195.0   8.2    2.5e-57  194.3   8.2    1.3  1  DUF1673   Protein of unknown function (DUF1673)


Domain annotation for each model (and alignments):
>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.3   8.2   1.4e-61   2.5e-57       2     229 ..       5     197 ..       4     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 1.4e-61
                       DUF1673   2 fietIrKlmGWCPnakaletrksispenleadnysrakeenesseenpgwvdkrsnrillvslfftllsllvltqlGi.nl 81 
                                   ++etIrK+mGWCPn  a+e+rk+++++nl  +++++++e+n   +++++w++k++n il+ s+f+t++ ++++ ++G  n+
  gi|91772297|ref|YP_564989.1|   5 IAETIRKVMGWCPNLGAMEARKAMQFDNLVVNAPDKSREPN---HKTMTWRNKYRNLILIGSIFGTIGPINMFISWGGkNM 82 
                                   79***************************************...*********************************99** PP

                       DUF1673  82 ialliglllsllliiltwkkqmqiyddikralvektvdkisikrilfkpvvIiikievtenenpvlrwllrllllviflli 162
                                    ++l+g++l +l++++twk++++++d+i+ ++ +k+++k+sikri++                         ++++if+++
  gi|91772297|ref|YP_564989.1|  83 GIVLAGTFLGILISKITWKTTWHSLDRIAIRIPRKAATKLSIKRIVV-------------------------FGIIIFIYV 138
                                   ***********************************************.........................********* PP

                       DUF1673 163 avllillsyvesiagelqlgevvssfisgllllllwliylqviywekkNkktivrkrygkkilvite 229
                                   av+++++s++  +        +v++f++g++++llw++y+q+++we+kN+kt+v+++y++ i+v+++
  gi|91772297|ref|YP_564989.1| 139 AVITHFMSIYGLR--------SVVAFLGGCGMSLLWSHYMQIVQWERKNQKTLVKSGYATPIVVVSN 197
                                   **********999........99*****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1421.01
//
Query:       gi|91772298|ref|YP_564990.1|  [L=116]
Description: hypothetical protein Mbur_0230 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.7   0.0      0.037   13.8   0.0    1.5  1  HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
      0.043   13.4   0.1      0.052   13.1   0.1    1.2  1  HNHc_6     Putative HNHc nuclease
       0.14   12.5   0.0       0.22   11.8   0.0    1.4  1  SAM_DrpA   DNA processing protein A sterile alpha motif domai


Domain annotation for each model (and alignments):
>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.1e-06     0.037      18      39 ..      18      39 ..      14      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-06
                     HTH_Tnp_4 18 lnltyqdLayrFgvsestvsri 39
                                   +l++  +a++F++s+  vsr 
  gi|91772298|ref|YP_564990.1| 18 GGLPNINIAHSFNISRQAVSRA 39
                                  579999**************95 PP

>> HNHc_6  Putative HNHc nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.8e-06     0.052      81     129 ..      59     107 ..      22     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.8e-06
                        HNHc_6  81 klarelielliatlfeydiplavktldllredkallyfaikyrrcvicg 129
                                   ++  e +    ++lf + +pl v tl  ++e+++++++      c  c+
  gi|91772298|ref|YP_564990.1|  59 QIEMESMSSERGILFGHLVPLNVSTLIFVSEKYGVQVWYEHEGDCGKCS 107
                                   44555555566899*************************9999999886 PP

>> SAM_DrpA  DNA processing protein A sterile alpha motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.6e-05      0.22       3      22 ..       9      28 ..       8      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                      SAM_DrpA  3 nFelykLKkAGLtNlnilni 22
                                  +Fe +kL++ GL N ni + 
  gi|91772298|ref|YP_564990.1|  9 QFEFWKLRRGGLPNINIAHS 28
                                  7****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 845.31
//
Query:       gi|91772299|ref|YP_564991.1|  [L=277]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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   68.5   0.2    7.9e-13   47.7   0.3    2.4  2  HTH_24           Winged helix-turn-helix DNA-binding
    2.9e-11   43.3   0.0    2.5e-05   24.3   0.0    2.2  2  HTH_20           Helix-turn-helix domain
    2.3e-09   37.0   0.0    0.00011   22.0   0.0    2.5  2  HTH_5            Bacterial regulatory protein, arsR family
    2.8e-06   27.2   0.0     0.0012   18.7   0.0    2.4  2  MarR             MarR family
    3.3e-06   26.8   0.1    5.4e-05   22.9   0.1    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.1e-05   25.2   0.0      0.053   13.4   0.0    2.3  2  MarR_2           MarR family
    1.7e-05   24.5   0.0       0.27   11.1   0.0    2.4  2  HTH_IclR         IclR helix-turn-helix domain
    0.00098   19.0   0.0      0.027   14.3   0.0    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0024   17.7   0.0      0.013   15.3   0.0    2.2  2  HTH_10           HTH DNA binding domain
     0.0027   17.6   0.0        2.9    7.9   0.0    3.0  2  HTH_36           Helix-turn-helix domain
     0.0033   17.6   0.0        1.9    8.7   0.0    2.4  2  HTH_34           Winged helix DNA-binding domain
     0.0034   17.7   0.1       0.64   10.4   0.0    2.3  2  Penicillinase_R  Penicillinase repressor
     0.0055   16.9   0.0      0.017   15.3   0.0    1.8  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0077   16.2   0.0        4.7    7.2   0.0    2.8  3  HTH_11           HTH domain
  ------ inclusion threshold ------
       0.03   14.1   0.0         13    5.7   0.0    2.5  2  TetR_N           Bacterial regulatory proteins, tetR family
       0.03   13.9   0.1        0.4   10.3   0.1    2.3  2  GerE             Bacterial regulatory proteins, luxR family
      0.051   13.0   0.0       0.58    9.6   0.0    2.2  2  RepL             Firmicute plasmid replication protein (RepL)
       0.06   13.0   0.0        1.1    8.9   0.0    2.1  2  RP-C             Replication protein C N-terminal domain
      0.063   13.3   1.8        1.3    9.2   0.1    3.2  3  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
      0.069   13.1   0.2       0.65   10.0   0.0    2.2  2  HTH_45           Winged helix-turn-helix
       0.11   12.5   0.2       0.37   10.8   0.0    2.0  2  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.21   11.3   1.3       0.52   10.1   0.2    2.3  3  HTH_38           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.3e-06    0.0011       2      47 ..     114     159 ..     113     160 .. 0.89
   2 !   47.7   0.3   9.7e-16   7.9e-13       1      48 []     189     236 ..     189     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                        HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                   + +++k++  +q  ++   +e+ +r+gl ++tv+++++ Le +  I
  gi|91772299|ref|YP_564991.1| 114 NLNRKKLYGFIQSRSGAYFNEIVKRTGLNRGTVRYHVDVLETQHMI 159
                                   5678899999999999999*********************977665 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 9.7e-16
                        HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   +d++dr+I  ++  n+  ++  LAer+g+S st +++++rL+e+++++
  gi|91772299|ref|YP_564991.1| 189 RDDIDRRIVLEILNNGCNTNGALAERIGVSASTMSWHIRRLMEQEIVR 236
                                   69********************************************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 !   16.7   0.0     7e-06    0.0057       7      50 ..     112     155 ..     107     164 .. 0.88
   2 !   24.3   0.0     3e-08   2.5e-05      12      60 ..     194     241 ..     190     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7e-06
                                   HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                        HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLee 50 
                                   L++  R +++  + ++ g+ ++e+ +r +l + t++yH++vLe 
  gi|91772299|ref|YP_564991.1| 112 LDNLNRKKLYGFIQSRSGAYFNEIVKRTGLNRGTVRYHVDVLET 155
                                   7788899999999*****************************96 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3e-08
                                   HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                   Rr +l  L  +++ t ++laer+++s +t+s H+r L e ++v++ +eg
  gi|91772299|ref|YP_564991.1| 194 RRIVLEIL-NNGCNTNGALAERIGVSASTMSWHIRRLMEQEIVRGDKEG 241
                                   66677777.9999999*****************************9997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00013      0.11      16      41 ..     130     155 ..     123     159 .. 0.87
   2 !   22.0   0.0   1.4e-07   0.00011       3      45 ..     193     235 ..     191     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                   EEHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_5  16 lcvcelaeelglsqstvShHLkkLre 41 
                                   +++ e+++ +gl+++tv++H  +L+ 
  gi|91772299|ref|YP_564991.1| 130 AYFNEIVKRTGLNRGTVRYHVDVLET 155
                                   6789****************999985 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.4e-07
                                   HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5   3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                    R+ +L +L++g  + + lae +g+s st S H ++L+e+ +V
  gi|91772299|ref|YP_564991.1| 193 DRRIVLEILNNGCNTNGALAERIGVSASTMSWHIRRLMEQEIV 235
                                   59999*************************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.015        12      17      47 ..     129     159 ..     124     163 .. 0.84
   2 !   18.7   0.0   1.5e-06    0.0012       8      48 ..     196     236 ..     194     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                                   TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  17 plsvseLakklgvskstvtrvldrLekkGli 47 
                                   +++  e+ k+ g++++tv   +d Le + +i
  gi|91772299|ref|YP_564991.1| 129 GAYFNEIVKRTGLNRGTVRYHVDVLETQHMI 159
                                   566789********************88666 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                   i+  + ++g+ ++  La+++gvs st++  ++rL +++ ++
  gi|91772299|ref|YP_564991.1| 196 IVLEILNNGCNTNGALAERIGVSASTMSWHIRRLMEQEIVR 236
                                   66778899999*************************99885 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.37     3e+02      20      36 ..     132     148 ..     119     154 .. 0.82
   2 !   22.9   0.1   6.6e-08   5.4e-05       2      41 ..     190     229 ..     188     230 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.37
                 HTH_AsnC-type  20 yaeLAervGlSestvlr 36 
                                   + e+ +r+Gl + tv+ 
  gi|91772299|ref|YP_564991.1| 132 FNEIVKRTGLNRGTVRY 148
                                   678889*********96 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 6.6e-08
                 HTH_AsnC-type   2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41 
                                   D+iDr+I+ ++  ++  ++ +LAer+G+S+st    +rrL
  gi|91772299|ref|YP_564991.1| 190 DDIDRRIVLEILNNGCNTNGALAERIGVSASTMSWHIRRL 229
                                   9******************************977666666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0011       0.9      17      51 ..     127     159 ..     120     166 .. 0.84
   2 !   13.4   0.0   6.5e-05     0.053       8      52 ..     194     236 ..     186     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                   TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                        MarR_2  17 rpgrdltvgelarrlglsksavsrilkrLvaaGLv 51 
                                   r g     +e+++r+gl +++v ++++ L+ + ++
  gi|91772299|ref|YP_564991.1| 127 RSG--AYFNEIVKRTGLNRGTVRYHVDVLETQHMI 159
                                   555..5679********************998666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.5e-05
                                   HHHHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2   8 arvLaaLgrrpgrdl.tvgelarrlglsksavsrilkrLvaaGLve 52 
                                   +r+ +++ +++   + t g+la+r g+s s++s +++rL ++  v+
  gi|91772299|ref|YP_564991.1| 194 RRIVLEILNNG---CnTNGALAERIGVSASTMSWHIRRLMEQEIVR 236
                                   67777787887...55999***********************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00034      0.28      21      45 ..     132     156 ..     123     161 .. 0.83
   2 !   11.1   0.0   0.00033      0.27      20      51 ..     207     238 ..     197     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                   HHHHHHHHTS-HHHHHHHHHHHHHT CS
                      HTH_IclR  21 lselArrtglpkStvhRlLqtLvel 45 
                                   + e+ +rtgl++ tv+ ++  L+ +
  gi|91772299|ref|YP_564991.1| 132 FNEIVKRTGLNRGTVRYHVDVLETQ 156
                                   78**************999999865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00033
                                   BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR  20 tlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                   t+  lA+r+g++ St + +++ L+e+ +v+ d
  gi|91772299|ref|YP_564991.1| 207 TNGALAERIGVSASTMSWHIRRLMEQEIVRGD 238
                                   6899**********************999866 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.22   1.8e+02      21      58 ..     128     165 ..     116     172 .. 0.79
   2 !   14.3   0.0   3.4e-05     0.027      15      63 ..     198     247 ..     190     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.22
                                   CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                     a  +ei +++g+ r +v   +  Le   ++   k +
  gi|91772299|ref|YP_564991.1| 128 SGAYFNEIVKRTGLNRGTVRYHVDVLETQHMIVSHKVN 165
                                   5566789************9999999998888777766 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.4e-05
                                   HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEE CS
                          TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYr 63 
                                   l +l++g  t   +ae++gv+ s+    +r+L++  +V+  k+  +++Yr
  gi|91772299|ref|YP_564991.1| 198 LEILNNGCNTNGALAERIGVSASTMSWHIRRLMEQEIVRGDKEGcYTIYR 247
                                   67899999********************************9988788998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.6   3.7e+03      27      44 ..     133     150 ..     130     154 .. 0.83
   2 !   15.3   0.0   1.6e-05     0.013      27      48 ..     209     230 ..     206     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.6
                        HTH_10  27 keLAkelGIskstlsehL 44 
                                   +e+ k+ G+ + t+ +h+
  gi|91772299|ref|YP_564991.1| 133 NEIVKRTGLNRGTVRYHV 150
                                   578899999999999996 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.6e-05
                        HTH_10  27 keLAkelGIskstlsehLrkae 48 
                                    +LA+++G+s+st+s h+r+ +
  gi|91772299|ref|YP_564991.1| 209 GALAERIGVSASTMSWHIRRLM 230
                                   57*****************976 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0035       2.9       8      52 ..     118     156 ..      76     159 .. 0.69
   2 !    6.9   0.0    0.0072       5.9      27      52 ..     207     232 ..     157     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0035
                        HTH_36   8 klllgslasfanknggcfpsqetlakrlglsknTvsraikeLeql 52 
                                   k l+g++ s +  + +    +  + kr+gl++ Tv+ +++ Le+ 
  gi|91772299|ref|YP_564991.1| 118 KKLYGFIQSRS--GAY----FNEIVKRTGLNRGTVRYHVDVLETQ 156
                                   55555555555..444....99**************999999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0072
                        HTH_36  27 sqetlakrlglsknTvsraikeLeql 52 
                                   ++  la+r g+s +T s +i+ L++ 
  gi|91772299|ref|YP_564991.1| 207 TNGALAERIGVSASTMSWHIRRLMEQ 232
                                   4778*******************986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0023       1.9      12      48 ..     127     163 ..     119     169 .. 0.88
   2 ?    6.3   0.0     0.013        10      20      78 ..     211     265 ..     197     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                        HTH_34  12 vdeadfvelkealeatdgnLsvhlkkLekagYievdk 48 
                                    + a f+e+ + ++++ g    h+++Le++  i+ +k
  gi|91772299|ref|YP_564991.1| 127 RSGAYFNEIVKRTGLNRGTVRYHVDVLETQHMIVSHK 163
                                   6789*************************99998777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                        HTH_34  20 lkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78 
                                   l e ++++++ +s h++ L +++ +  dke       t++ri ++ +e  +kyv++++s
  gi|91772299|ref|YP_564991.1| 211 LAERIGVSASTMSWHIRRLMEQEIVRGDKEG----CYTIYRINSNYLESVEKYVQTMDS 265
                                   678899****************999888864....367888888888888888888876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.032        26      26      65 ..     134     173 ..     119     197 .. 0.82
   2 !   10.4   0.0   0.00078      0.64      27      77 ..     211     261 ..     207     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.032
                                   T--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
               Penicillinase_R  26 eleeekelaysTVktllrrLvkKgllsrekegrafiYspl 65 
                                   e+ +++ l++ TV+  +  L+ ++++ ++k + +++Y  +
  gi|91772299|ref|YP_564991.1| 134 EIVKRTGLNRGTVRYHVDVLETQHMIVSHKVNGKIRYFQN 173
                                   4445567889*********************999999765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00078
                                   --GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXX CS
               Penicillinase_R  27 leeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavk 77 
                                   l+e+  ++ sT    +rrL+++++++ +keg  +iY+ + +  e v++ v+
  gi|91772299|ref|YP_564991.1| 211 LAERIGVSASTMSWHIRRLMEQEIVRGDKEGCYTIYRINSNYLESVEKYVQ 261
                                   78888999****************************987776666666555 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.1e-05     0.017      24      53 ..     207     236 ..     197     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLekdGyve 53 
                                   ++  laer++vs+s+ s  +++L +++ v 
  gi|91772299|ref|YP_564991.1| 207 TNGALAERIGVSASTMSWHIRRLMEQEIVR 236
                                   6789*********************99886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.1     5e+03      20      29 ..      49      58 ..      48      59 .. 0.86
   2 ?    5.8   0.0     0.016        13      11      43 ..     125     157 ..     116     166 .. 0.78
   3 !    7.2   0.0    0.0058       4.7      17      41 ..     207     231 ..     194     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.1
                        HTH_11 20 eLAeeLnvSr 29
                                  +L+ e++vS 
  gi|91772299|ref|YP_564991.1| 49 TLSNEFGVSV 58
                                  6999****96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                        HTH_11  11 eargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                   ++r+    +e+ +++++ r tvr +++ Le++ 
  gi|91772299|ref|YP_564991.1| 125 QSRSGAYFNEIVKRTGLNRGTVRYHVDVLETQH 157
                                   666666678999*****************9875 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0058
                        HTH_11  17 sgeeLAeeLnvSrrtvrrdIkaLee 41 
                                   +   LAe+++vS +t   +I++L e
  gi|91772299|ref|YP_564991.1| 207 TNGALAERIGVSASTMSWHIRRLME 231
                                   6678***********9999999855 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 ?    5.7   0.0     0.016        13      19      36 ..     132     149 ..     128     149 .. 0.87
   2 ?    5.7   0.0     0.016        13      21      36 ..     210     225 ..     207     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                                   HHHHHHHHTSSHHHHHHH CS
                        TetR_N  19 vreIAkrAGvskgalYry 36 
                                   ++eI+kr G+++g++ ++
  gi|91772299|ref|YP_564991.1| 132 FNEIVKRTGLNRGTVRYH 149
                                   589***********9666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                                   HHHHHHTSSHHHHHHH CS
                        TetR_N  21 eIAkrAGvskgalYry 36 
                                   ++A+r Gvs++++ ++
  gi|91772299|ref|YP_564991.1| 210 ALAERIGVSASTMSWH 225
                                   79**********9998 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.56   4.5e+02      20      38 ..     132     150 ..     128     155 .. 0.84
   2 ?   10.3   0.1   0.00049       0.4      10      43 ..     197     231 ..     195     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.56
                                   HHHHHHHHTS-HHHHHHHH CS
                          GerE  20 nkeIAeelniSekTVkvhk 38 
                                    +eI ++ ++   TV++h+
  gi|91772299|ref|YP_564991.1| 132 FNEIVKRTGLNRGTVRYHV 150
                                   57999999999*******7 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00049
                                   HHHHHCTT.S-HHHHHHHHTS-HHHHHHHHHHHHH CS
                          GerE  10 vLrllaeG.ksnkeIAeelniSekTVkvhksnimk 43 
                                   vL+ l +G ++n   Ae+ ++S+ T + h++++m+
  gi|91772299|ref|YP_564991.1| 197 VLEILNNGcNTNGALAERIGVSASTMSWHIRRLME 231
                                   777777774588899******************97 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.31   2.6e+02      80     111 ..     134     166 ..      90     170 .. 0.79
   2 ?    9.6   0.0   0.00071      0.58      75     115 ..     205     245 ..     192     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.31
                          RepL  80 elaeetgislktvsetlkileeanilk.kkanG 111
                                   e+ ++tg+   tv+  + +le   ++  +k nG
  gi|91772299|ref|YP_564991.1| 134 EIVKRTGLNRGTVRYHVDVLETQHMIVsHKVNG 166
                                   79999**********999999887664145555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00071
                          RepL  75 iatnRelaeetgislktvsetlkileeanilkkkanGvlvi 115
                                     tn  lae+ g+s  t+s  ++ l+e +i++   +G + i
  gi|91772299|ref|YP_564991.1| 205 CNTNGALAERIGVSASTMSWHIRRLMEQEIVRGDKEGCYTI 245
                                   579999***************************99999876 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 ?    1.7   0.0      0.22   1.8e+02      77     110 ..     135     167 ..     132     178 .. 0.74
   2 ?    8.9   0.0    0.0013       1.1      74     101 ..     208     235 ..     205     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
                          RP-C  77 LsralglsestlrrhlaaLveaGliirrDspngk 110
                                   + +++gl + t+r+h+  L    +i+     ngk
  gi|91772299|ref|YP_564991.1| 135 IVKRTGLNRGTVRYHVDVLETQHMIVSH-KVNGK 167
                                   67899***********999877777654.34444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                          RP-C  74 NaqLsralglsestlrrhlaaLveaGli 101
                                   N +L++++g+s+st++ h+++L+e  ++
  gi|91772299|ref|YP_564991.1| 208 NGALAERIGVSASTMSWHIRRLMEQEIV 235
                                   889********************98876 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.5   1.2e+03      10      20 ..      32      42 ..      26      48 .. 0.85
   2 ?    1.1   0.0      0.52   4.2e+02      11      36 ..     122     147 ..     112     167 .. 0.77
   3 ?    9.2   0.1    0.0016       1.3      10      48 ..     197     235 ..     192     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                Sulfolobus_pRN 10 illilsrrcat 20
                                  +ll++s  cat
  gi|91772299|ref|YP_564991.1| 32 LLLSISTACAT 42
                                  799******99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.52
                Sulfolobus_pRN  11 llilsrrcatleeleektGiekeell 36 
                                    +i sr  a ++e+  +tG+++ ++ 
  gi|91772299|ref|YP_564991.1| 122 GFIQSRSGAYFNEIVKRTGLNRGTVR 147
                                   5678999999999*******998865 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
                Sulfolobus_pRN  10 illilsrrcatleeleektGiekeellvyltrlykrGli 48 
                                   +l il ++c t   l e+ G+   ++  ++ rl ++ ++
  gi|91772299|ref|YP_564991.1| 197 VLEILNNGCNTNGALAERIGVSASTMSWHIRRLMEQEIV 235
                                   6779**********************9999999988776 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.78   6.4e+02      19      53 ..     129     163 ..     123     183 .. 0.79
   2 ?   10.0   0.0    0.0008      0.65      11      72 ..     197     259 ..     193     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.78
                        HTH_45  19 eakkTkimykanLsykllnkYLdmLvekglikksk 53 
                                   +a   +i+++  L+  +++  +d L  + +i  +k
  gi|91772299|ref|YP_564991.1| 129 GAYFNEIVKRTGLNRGTVRYHVDVLETQHMIVSHK 163
                                   56667899999999999999999999999994433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0008
                        HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli.kkskekYvlTekGlelleklkel 72 
                                   +Le++++g+++  ++  +   s ++++  +  L+e++++  ++++ Y++    +++le+++++
  gi|91772299|ref|YP_564991.1| 197 VLEILNNGCNTNGALAERIGVSASTMSWHIRRLMEQEIVrGDKEGCYTIYRINSNYLESVEKY 259
                                   466666*********************************666889999977777777777766 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.2   5.8e+03      30      52 ..     138     160 ..     133     169 .. 0.68
   2 ?   10.8   0.0   0.00046      0.37      23      53 ..     207     239 ..     195     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.2
                                   HTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2  30 mlGltretvsrilseLkreglis 52 
                                   + Gl+r tv      L+ + +i 
  gi|91772299|ref|YP_564991.1| 138 RTGLNRGTVRYHVDVLETQHMIV 160
                                   67888888877777777777776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00046
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E CS
                     HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglis..r 53 
                                   t+  lA+++G++ +t+s  +++L ++ +++  +
  gi|91772299|ref|YP_564991.1| 207 TNGALAERIGVSASTMSWHIRRLMEQEIVRgdK 239
                                   6778*************************9632 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.1   4.2e+03      24      41 ..     133     150 ..     129     150 .. 0.77
   2 ?   10.1   0.2   0.00064      0.52      11      43 ..     195     228 ..     192     229 .. 0.75
   3 ?   -2.6   0.0       6.2     5e+03      12      26 ..     233     248 ..     232     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                        HTH_38  24 reIArrLgrspsTIsREl 41 
                                    eI +r g +++T+ +++
  gi|91772299|ref|YP_564991.1| 133 NEIVKRTGLNRGTVRYHV 150
                                   567788888999998865 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00064
                        HTH_38  11 eeIerllaeG.lslreIArrLgrspsTIsRElkR 43 
                                   +     l+ G  ++ + A r+g+s sT s +++R
  gi|91772299|ref|YP_564991.1| 195 RIVLEILNNGcNTNGALAERIGVSASTMSWHIRR 228
                                   444444555538888************9999998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.2
                        HTH_38  12 eIerllaeG.lslreI 26 
                                   eI r+ +eG +++++I
  gi|91772299|ref|YP_564991.1| 233 EIVRGDKEGcYTIYRI 248
                                   6667777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1939.55
//
Query:       gi|91772300|ref|YP_564992.1|  [L=50]
Description: hypothetical protein Mbur_0232 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 381.06
//
Query:       gi|91772301|ref|YP_564993.1|  [L=99]
Description: hypothetical protein Mbur_0233 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        1.6    8.4  13.8        5.2    6.7  13.8    1.9  1  PAP2_3        PAP2 superfamily
        6.1    7.2   8.7         14    6.1   8.7    1.6  1  DUF4064       Protein of unknown function (DUF4064)
        9.8    5.7   6.1         12    5.4   6.1    1.1  1  E1-E2_ATPase  E1-E2 ATPase


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  13.8   0.00086       5.2      29     133 ..       3      99 .]       1      99 [] 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00086
                        PAP2_3  29 avilalaYaslhfqvtllvlvllf.lrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaaslagalrd 108
                                   + i a++Y + + ++++ +++ll+ +++ + l+e+ ++++++ l++l +y+ +P++   +      + t   ++l+     
  gi|91772301|ref|YP_564993.1|   3 TCISAIVYLVGFSLLLVFTFFLLMqTQNLKVLQEYTIAFIAIYLIALPFYIYLPVTVTGYT---LPTVTPLLYNLSP---- 76 
                                   5678999*99888777777777778*****************************9988444...1122222222222.... PP

                        PAP2_3 109 gasravllrgtienglaa..fPSlHva 133
                                        + +   i +++    fPSlH+a
  gi|91772301|ref|YP_564993.1|  77 ----IISQGVRIVDPFLDncFPSLHAA 99 
                                   ....23333334455544458888875 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   8.7    0.0023        14       7      73 ..       1      50 [.       1      61 [. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0023
                       DUF4064  7 iLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaiv 73
                                  +L+ I++i++++++ lll+f+f+l                   +++ l +l++++i+++ i lia+ 
  gi|91772301|ref|YP_564993.1|  1 MLTCISAIVYLVGFSLLLVFTFFL-----------------LMQTQNLKVLQEYTIAFIAIYLIALP 50
                                  7999********999999998877.................34677889999999999999998875 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   6.1     0.002        12     121     170 ..       8      60 ..       1      64 [. 0.66

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.002
                                   HHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHHHHS-TTHHHHHHHH CS
                  E1-E2_ATPase 121 vlvpvvlliallvflialllgksla...eallralallvaaiPcaLplavpla 170
                                   ++ +v++ ++l++ +++l+ +++l    e+ + ++a+ ++a+P  + l v+++
  gi|91772301|ref|YP_564993.1|   8 IVYLVGFSLLLVFTFFLLMQTQNLKvlqEYTIAFIAIYLIALPFYIYLPVTVT 60 
                                   433444444444444444444444467899999**********9999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 749.36
//
Query:       gi|91772302|ref|YP_564994.1|  [L=248]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-18   63.4   0.1    1.5e-09   37.3   0.1    2.3  2  HTH_24           Winged helix-turn-helix DNA-binding
    2.1e-13   49.9   0.0    1.9e-06   27.6   0.0    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
    8.9e-12   44.9   0.0      2e-05   24.5   0.0    2.2  2  HTH_20           Helix-turn-helix domain
    1.5e-08   34.4   0.0    5.1e-06   26.3   0.1    2.3  2  MarR             MarR family
    5.4e-08   32.6   0.0    0.00021   21.1   0.0    2.2  2  MarR_2           MarR family
    1.7e-06   28.4   0.0    6.5e-06   26.6   0.0    1.8  2  HTH_27           Winged helix DNA-binding domain
    2.2e-06   27.1   0.5    9.8e-05   21.8   0.1    2.3  2  GerE             Bacterial regulatory proteins, luxR family
    5.8e-05   22.8   0.0       0.13   12.1   0.0    2.3  2  HTH_IclR         IclR helix-turn-helix domain
    0.00027   21.1   0.0       0.33   11.2   0.1    2.4  2  HTH_34           Winged helix DNA-binding domain
     0.0003   20.9   0.0     0.0049   17.0   0.0    2.2  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00063   19.6   0.0        1.3    9.0   0.0    2.5  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0027   17.5   0.0       0.18   11.6   0.0    2.3  2  HTH_10           HTH DNA binding domain
     0.0048   16.7   0.0      0.009   15.8   0.0    1.4  1  HTH_23           Homeodomain-like domain
      0.005   16.5   0.0          1    9.1   0.0    2.4  2  Sigma70_r4_2     Sigma-70, region 4
      0.005   16.8   0.0      0.058   13.3   0.1    2.2  2  HTH_11           HTH domain
     0.0056   17.1   0.1        2.4    8.7   0.0    2.3  2  HTH_40           Helix-turn-helix domain
     0.0077   16.6   0.0       0.18   12.2   0.0    2.3  2  FaeA             FaeA-like protein
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.27   10.9   0.0    2.1  2  RP-C             Replication protein C N-terminal domain
      0.016   15.1   0.0      0.063   13.3   0.0    1.8  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.019   15.3   0.1      0.097   13.0   0.1    1.9  2  Penicillinase_R  Penicillinase repressor
      0.036   13.6   0.0       0.18   11.4   0.0    1.9  2  Sigma70_r4       Sigma-70, region 4
       0.04   13.7   0.0       0.28   11.0   0.0    2.0  2  HTH_38           Helix-turn-helix domain
      0.049   13.7   0.0       0.49   10.5   0.0    2.0  2  HTH_Tnp_IS630    Transposase
      0.058   13.7   0.2       0.52   10.6   0.0    2.1  2  DUF2513          Hypothetical protein (DUF2513)
       0.09   12.5   0.0       0.42   10.3   0.0    2.1  2  HTH_41           Helix-turn-helix domain
       0.13   12.0   0.0         16    5.4   0.0    2.3  2  HTH_30           PucR C-terminal 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 !   24.1   0.0   2.7e-08   1.9e-05       4      47 ..     100     143 ..      98     144 .. 0.88
   2 !   37.3   0.1   2.2e-12   1.5e-09       2      46 ..     174     218 ..     173     220 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.7e-08
                        HTH_24   4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                   ++ ++ e++  np++s ++++  l l ++t +++lk+L +e  I
  gi|91772302|ref|YP_564994.1| 100 NRNNVFEYIVSNPGCSVADISHGLELNRGTAKYHLKKLHNEHKI 143
                                   5556778999****************************998776 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2.2e-12
                        HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46 
                                   d ++++IL  ++++p+++++e+++ l ++ stv+++lk+++ ++l
  gi|91772302|ref|YP_564994.1| 174 DANQKQILLMIRDKPGMTNNEISQTLCITNSTVSYHLKKMTTNEL 218
                                   889*************************************98876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.7e-07   0.00039       3      41 ..     100     139 ..      98     140 .. 0.85
   2 !   27.6   0.0   2.8e-09   1.9e-06       3      44 ..     176     218 ..     174     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.7e-07
                                   HHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_5   3 tRlkILklLaege.lcvcelaeelglsqstvShHLkkLre 41 
                                   +R  +  +  +++ ++v +++  l+l+++t  +HLkkL++
  gi|91772302|ref|YP_564994.1| 100 NRNNVFEYIVSNPgCSVADISHGLELNRGTAKYHLKKLHN 139
                                   566666677778889***********************98 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.8e-09
                                   HHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                         HTH_5   3 tRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGL 44 
                                   ++ +IL + ++++ ++  e++  l ++ stvS+HLkk+    L
  gi|91772302|ref|YP_564994.1| 176 NQKQILLMIRDKPgMTNNEISQTLCITNSTVSYHLKKMTTNEL 218
                                   5679*********************************977666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.7e-06    0.0018       7      49 ..      96     138 ..      91     148 .. 0.93
   2 !   24.5   0.0   2.9e-08     2e-05       9      61 .]     174     226 ..     165     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                                   HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                        HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLe 49 
                                   +a++ R  ++ ++ ++ g +++++ + l+l + t+ yHL++L 
  gi|91772302|ref|YP_564994.1|  96 FANKNRNNVFEYIVSNPGCSVADISHGLELNRGTAKYHLKKLH 138
                                   6899999**********************************95 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 2.9e-08
                                   -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                        HTH_20   9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                   +  +  il +++++ g+t +e+ ++l ++ +t+syHL+++   +L+  ++ gr
  gi|91772302|ref|YP_564994.1| 174 DANQKQILLMIRDKPGMTNNEISQTLCITNSTVSYHLKKMTTNELLQAEKDGR 226
                                   567889**********************************9999998888775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.02        14      14      41 ..     110     137 ..     106     149 .. 0.90
   2 !   26.3   0.1   7.5e-09   5.1e-06       4      51 ..     176     223 ..     174     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                                   HSTTEEHHHHHHHHTS-HHHHHHHHHHH CS
                          MarR  14 eqgplsvseLakklgvskstvtrvldrL 41 
                                   +++++sv+++   l+++++t+   l++L
  gi|91772302|ref|YP_564994.1| 110 SNPGCSVADISHGLELNRGTAKYHLKKL 137
                                   5799***********************9 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 7.5e-09
                                   HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                   +q  iL ++++++++++ e+   l++++stv+  l+++  ++l++ +k
  gi|91772302|ref|YP_564994.1| 176 NQKQILLMIRDKPGMTNNEISQTLCITNSTVSYHLKKMTTNELLQAEK 223
                                   67789**************************************98665 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    0.0015         1      10      46 ..     104     138 ..     101     140 .. 0.91
   2 !   21.1   0.0     3e-07   0.00021       6      56 ..     176     224 ..     172     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                        MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLv 46 
                                   v  ++  +pg  ++v+++   l l ++++ ++lk+L 
  gi|91772302|ref|YP_564994.1| 104 VFEYIVSNPG--CSVADISHGLELNRGTAKYHLKKLH 138
                                   56689999**..***********************96 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3e-07
                                   HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2   6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                    q ++L+ +++ pg  +t +e+ ++l ++ s+vs++lk++    L++ +++
  gi|91772302|ref|YP_564994.1| 176 NQKQILLMIRDKPG--MTNNEISQTLCITNSTVSYHLKKMTTNELLQAEKD 224
                                   5779**********..*****************************988875 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 ?   -1.2   0.0       4.3     3e+03      22      44 ..     117     139 ..     111     143 .. 0.83
   2 !   26.6   0.0   9.4e-09   6.5e-06       4      64 ..     176     232 ..     174     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.3
                        HTH_27  22 adlcgrlnvedshisyslkkLte 44 
                                   ad++  l ++  ++ y lkkL++
  gi|91772302|ref|YP_564994.1| 117 ADISHGLELNRGTAKYHLKKLHN 139
                                   78888889999999999***987 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 9.4e-09
                        HTH_27   4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64 
                                   +q ++L  ir    +++  +++++l ++ s++sy lkk+t ++L+   + e+d+r kr++l
  gi|91772302|ref|YP_564994.1| 176 NQKQILLMIR-DKPGMTNNEISQTLCITNSTVSYHLKKMTTNELL---QAEKDGRFKRYSL 232
                                   6789999999.9999999***************************...77799******98 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.088        61      17      41 ..     113     137 ..     102     144 .. 0.87
   2 !   21.8   0.1   1.4e-07   9.8e-05       8      41 ..     178     213 ..     174     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.088
                                   TS-HHHHHHHHTS-HHHHHHHHHHH CS
                          GerE  17 GksnkeIAeelniSekTVkvhksni 41 
                                   G s+ +I+  l++   T k+h++ +
  gi|91772302|ref|YP_564994.1| 113 GCSVADISHGLELNRGTAKYHLKKL 137
                                   8899*****************9976 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.4e-07
                                   HHHHHHHCT..TS-HHHHHHHHTS-HHHHHHHHHHH CS
                          GerE   8 revLrllae..GksnkeIAeelniSekTVkvhksni 41 
                                   +++L ++ +  G++n+eI++ l i + TV++h++ +
  gi|91772302|ref|YP_564994.1| 178 KQILLMIRDkpGMTNNEISQTLCITNSTVSYHLKKM 213
                                   56666665444**********************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 !    8.3   0.0    0.0029         2      15      44 ..     111     139 ..     103     141 .. 0.84
   2 !   12.1   0.0   0.00018      0.13       7      48 ..     179     219 ..     178     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0029
                                   TBSS-BHHHHHHHHTS-HHHHHHHHHHHHH CS
                      HTH_IclR  15 apqeltlselArrtglpkStvhRlLqtLve 44 
                                     ++ +++++++ + l++ t+  +L+ L++
  gi|91772302|ref|YP_564994.1| 111 N-PGCSVADISHGLELNRGTAKYHLKKLHN 139
                                   3.4579****************99999976 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                   +iL +++  p+ +t+ e+++ + ++ Stv+ +L+ ++   ++
  gi|91772302|ref|YP_564994.1| 179 QILLMIRDKPG-MTNNEISQTLCITNSTVSYHLKKMTTNELL 219
                                   68888888888.9********************999887776 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 !    7.4   0.0    0.0071       4.9       4      46 ..     103     145 ..     101     152 .. 0.92
   2 !   11.2   0.1   0.00048      0.33      11      50 ..     186     225 ..     179     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0071
                        HTH_34   4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46 
                                   +v+ y +s+   + ++++  le++ g    hlkkL +   i+v
  gi|91772302|ref|YP_564994.1| 103 NVFEYIVSNPGCSVADISHGLELNRGTAKYHLKKLHNEHKITV 145
                                   6899*******************************99988876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00048
                        HTH_34  11 svdeadfvelkealeatdgnLsvhlkkLekagYievdkef 50 
                                   ++  ++ +e++++l +t++  s hlkk+ +++ ++ +k+ 
  gi|91772302|ref|YP_564994.1| 186 DKPGMTNNEISQTLCITNSTVSYHLKKMTTNELLQAEKDG 225
                                   46677889************************99999975 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 ?    1.3   0.0       0.6   4.1e+02      24      48 ..     115     139 ..     110     143 .. 0.91
   2 !   17.0   0.0   7.1e-06    0.0049      19      57 ..     186     224 ..     178     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.6
                                   -HHHHHHHHTS-HHHHHHHHHHHHH CS
                Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLek 48 
                                   +++d++  L+    ++   lkkL++
  gi|91772302|ref|YP_564994.1| 115 SVADISHGLELNRGTAKYHLKKLHN 139
                                   6899*******************97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.1e-06
                                   HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                Fe_dep_repress  19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57 
                                   +k   ++ ++++ L +  s+Vs  lkk+  +++++ ek+
  gi|91772302|ref|YP_564994.1| 186 DKPGMTNNEISQTLCITNSTVSYHLKKMTTNELLQAEKD 224
                                   55567899**************************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.004       2.7      13      49 ..     104     140 ..      99     156 .. 0.89
   2 !    9.0   0.0    0.0019       1.3      19      63 ..     186     231 ..     175     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.004
                                   HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHC CS
                          TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedk 49 
                                   v+ +++++   ++ +i++ l++ r ++   L++L + 
  gi|91772302|ref|YP_564994.1| 104 VFEYIVSNPGCSVADISHGLELNRGTAKYHLKKLHNE 140
                                   8999******************************875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                          TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                    +  +t +ei++ l +  s+v   L+++    l + ek gr k+Y+
  gi|91772302|ref|YP_564994.1| 186 DKPGMTNNEISQTLCITNSTVSYHLKKMTTNELLQAEKdGRFKRYS 231
                                   567899*******************************945566775 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       0.1        71      24      47 ..     114     137 ..     112     141 .. 0.90
   2 !   11.6   0.0   0.00027      0.18      25      47 ..     191     213 ..     189     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
                        HTH_10  24 vtlkeLAkelGIskstlsehLrka 47 
                                   +++++++  l + + t+++hL+k 
  gi|91772302|ref|YP_564994.1| 114 CSVADISHGLELNRGTAKYHLKKL 137
                                   7899*****************985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00027
                        HTH_10  25 tlkeLAkelGIskstlsehLrka 47 
                                   t +e++++l I++st+s+hL+k 
  gi|91772302|ref|YP_564994.1| 191 TNNEISQTLCITNSTVSYHLKKM 213
                                   5689****************996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-05     0.009       9      40 ..     179     212 ..     172     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                        HTH_23   9 rillllae..GlsvreIAreLgvsrrTvyrwlkr 40 
                                   +ill+ ++  G++  eI++ L ++ +Tv+  lk+
  gi|91772302|ref|YP_564994.1| 179 QILLMIRDkpGMTNNEISQTLCITNSTVSYHLKK 212
                                   79**************************976665 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 ?    5.0   0.0     0.029        20      26      49 ..     113     136 ..     113     137 .. 0.94
   2 !    9.1   0.0    0.0015         1      14      49 ..     176     212 ..     174     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.029
                                   ---HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2  26 glsykEIAellgisegtVksrlsR 49 
                                   g+s ++I+  l+++ gt k++l++
  gi|91772302|ref|YP_564994.1| 113 GCSVADISHGLELNRGTAKYHLKK 136
                                   89*******************986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHTS.---HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2  14 rqreifllryle.glsykEIAellgisegtVksrlsR 49 
                                    q++i+l+++ + g++  EI++ l i+ +tV ++l++
  gi|91772302|ref|YP_564994.1| 176 NQKQILLMIRDKpGMTNNEISQTLCITNSTVSYHLKK 212
                                   5899999998888*********************975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.71   4.9e+02      16      41 ..     114     139 ..     101     146 .. 0.81
   2 !   13.3   0.1   8.4e-05     0.058       2      40 ..     177     214 ..     176     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.71
                        HTH_11  16 isgeeLAeeLnvSrrtvrrdIkaLee 41 
                                    s ++++  L++ r t   ++k+L  
  gi|91772302|ref|YP_564994.1| 114 CSVADISHGLELNRGTAKYHLKKLHN 139
                                   789999999*********9*999965 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.4e-05
                        HTH_11   2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLe 40 
                                   ++qil +++++ g ++ +e+++ L ++ +tv  ++k+++
  gi|91772302|ref|YP_564994.1| 177 QKQILLMIRDKPG-MTNNEISQTLCITNSTVSYHLKKMT 214
                                   7899999955555.*******************999975 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.015        10      12      47 ..     113     147 ..     107     187 .. 0.78
   2 !    8.7   0.0    0.0034       2.4      11      39 ..     188     216 ..     176     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                        HTH_40  12 glsieeIAkerglkesTIegHLaelieegeeidler 47 
                                   g+s+++I++  +l+++T   HL +l +e + i + +
  gi|91772302|ref|YP_564994.1| 113 GCSVADISHGLELNRGTAKYHLKKLHNEHK-ITVYD 147
                                   89***********************99965.55543 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
                        HTH_40  11 eglsieeIAkerglkesTIegHLaeliee 39 
                                    g++  eI++   ++ sT+  HL ++  +
  gi|91772302|ref|YP_564994.1| 188 PGMTNNEISQTLCITNSTVSYHLKKMTTN 216
                                   5999*******************998766 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00026      0.18       2      45 ..     101     143 ..     100     148 .. 0.95
   2 ?    1.8   0.0      0.45   3.1e+02       4      43 ..     179     217 ..     176     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                   HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                          FaeA   2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegki 45 
                                   ++++ ey+ s + +c  ++i   l l    a+y L++L+ e ki
  gi|91772302|ref|YP_564994.1| 101 RNNVFEYIVS-NPGCSVADISHGLELNRGTAKYHLKKLHNEHKI 143
                                   699*******.******************************998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.45
                                   HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHS CS
                          FaeA   4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekeg 43 
                                   +Il  + + k + + +ei + l ++   + y L+++    
  gi|91772302|ref|YP_564994.1| 179 QILLMIRD-KPGMTNNEISQTLCITNSTVSYHLKKMTTNE 217
                                   56666666.67777789********999999999887655 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 ?    1.6   0.0      0.28   1.9e+02      75     115 ..     117     157 ..     113     165 .. 0.84
   2 ?   10.9   0.0   0.00039      0.27      73     113 ..     191     231 ..     189     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.28
                          RP-C  75 aqLsralglsestlrrhlaaLveaGliirrDspngkRyarr 115
                                   a++s  l l + t ++hl++L +   i+  D+    R+ + 
  gi|91772302|ref|YP_564994.1| 117 ADISHGLELNRGTAKYHLKKLHNEHKITVYDHGSSPRFFQN 157
                                   56777888999***********9999999999998888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00039
                          RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirrDspngkRya 113
                                    N+++s+ l++++st+++hl+++    l+        kRy 
  gi|91772302|ref|YP_564994.1| 191 TNNEISQTLCITNSTVSYHLKKMTTNELLQAEKDGRFKRYS 231
                                   599***************************99999*****6 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 ?   -1.3   0.0       3.3   2.3e+03      24      52 ..     116     144 ..     106     149 .. 0.80
   2 ?   13.3   0.0   9.2e-05     0.063      20      53 ..     188     222 ..     168     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.3
                                   HHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2  24 qeelAsmlGltretvsrilseLkreglis 52 
                                    +++++ l l+r t    l++L +e  i+
  gi|91772302|ref|YP_564994.1| 116 VADISHGLELNRGTAKYHLKKLHNEHKIT 144
                                   56888888899999999999998887665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.2e-05
                                   EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                     HTH_Crp_2  20 lpltqeelAsmlGltretvsrilseLkreglis.r 53 
                                     +t+ e+++ l +t +tvs  l+++    l++  
  gi|91772302|ref|YP_564994.1| 188 PGMTNNEISQTLCITNSTVSYHLKKMTTNELLQaE 222
                                   469*************************9999963 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.56   3.9e+02       8     105 ..     104     194 ..     100     197 .. 0.57
   2 ?   13.0   0.1   0.00014     0.097       6      63 ..     178     231 ..     175     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.56
                                   HHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXXXXXX CS
               Penicillinase_R   8 vmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkqlldklfegsv 88 
                                   v e++ ++  ++v+++   le    l++ T k  l++L++ + ++ + +g + ++     +++ v s+  q+l  +++   
  gi|91772302|ref|YP_564994.1| 104 VFEYIVSNPGCSVADISHGLE----LNRGTAKYHLKKLHNEHKITVYDHGSSPRF----FQNNSVCSEQAQILAPFLQDAN 176
                                   555666666666666666555....447777777888877777777777765444....4444455555555555555555 PP

                                   XXXXXXXXXXX.XXXXXX CS
               Penicillinase_R  89 kelvaafveee.klsedd 105
                                   ++ ++ +++++  +++++
  gi|91772302|ref|YP_564994.1| 177 QKQILLMIRDKpGMTNNE 194
                                   555555555544555555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00014
                                   SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
               Penicillinase_R   6 aevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYs 63 
                                   ++++ ++++k  +t +e+ + l  +    +sTV   l++++  +ll++ek+gr  +Ys
  gi|91772302|ref|YP_564994.1| 178 KQILLMIRDKPGMTNNEISQTLCIT----NSTVSYHLKKMTTNELLQAEKDGRFKRYS 231
                                   6777788888888888888877766....************************99997 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.7   1.2e+03      20      42 ..     113     135 ..     103     137 .. 0.80
   2 ?   11.4   0.0   0.00026      0.18       7      43 ..     175     212 ..     174     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                                   T--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4  20 glTleEIgerlgiSrerVrqiek 42 
                                   g + ++I+  l + r++++ ++k
  gi|91772302|ref|YP_564994.1| 113 GCSVADISHGLELNRGTAKYHLK 135
                                   567889999999****9997776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                                   HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                    Sigma70_r4   7 ererevlelrf.geglTleEIgerlgiSrerVrqiekr 43 
                                   ++++++l + +   g+T  EI+++l i+ ++V+ ++k+
  gi|91772302|ref|YP_564994.1| 175 ANQKQILLMIRdKPGMTNNEISQTLCITNSTVSYHLKK 212
                                   5799*****99999******************987775 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.2   8.5e+02      20      41 ..     113     134 ..     101     136 .. 0.79
   2 ?   11.0   0.0   0.00041      0.28      18      42 ..     187     211 ..     172     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
                        HTH_38  20 GlslreIArrLgrspsTIsREl 41 
                                   G+s+++I   L  +++T  ++l
  gi|91772302|ref|YP_564994.1| 113 GCSVADISHGLELNRGTAKYHL 134
                                   99*****988888888755555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00041
                        HTH_38  18 aeGlslreIArrLgrspsTIsRElk 42 
                                   + G+++ eI + L+   sT+s++lk
  gi|91772302|ref|YP_564994.1| 187 KPGMTNNEISQTLCITNSTVSYHLK 211
                                   469********************99 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.69   4.7e+02      59     102 ..     102     145 ..      97     158 .. 0.77
   2 ?   10.5   0.0   0.00071      0.49      57      97 ..     176     216 ..     169     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.69
                 HTH_Tnp_IS630  59 kelkedvkknpdallkerakkfgvtpasllyalkklkitrkkks 102
                                   +++ e +  np   + ++   ++++  +  y lkkl   +k ++
  gi|91772302|ref|YP_564994.1| 102 NNVFEYIVSNPGCSVADISHGLELNRGTAKYHLKKLHNEHKITV 145
                                   55556677788888888888888999999999999987776655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00071
                 HTH_Tnp_IS630  57 drkelkedvkknpdallkerakkfgvtpasllyalkklkit 97 
                                   ++k++   ++++p +   e+ + + +t ++++y lkk+  +
  gi|91772302|ref|YP_564994.1| 176 NQKQILLMIRDKPGMTNNEISQTLCITNSTVSYHLKKMTTN 216
                                   66777778999***************************865 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.1   7.3e+02      41      64 ..     129     152 ..     116     163 .. 0.81
   2 ?   10.6   0.0   0.00076      0.52       9      65 ..     179     229 ..     177     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.1
                       DUF2513  41 eiiyhlkllaeagLieaekkkaks 64 
                                   +  yhlk+l+++  i ++++ ++ 
  gi|91772302|ref|YP_564994.1| 129 TAKYHLKKLHNEHKITVYDHGSSP 152
                                   678******999999888887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00076
                       DUF2513   9 diLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakss 65 
                                   +iLl +++++  +++         +    ++ +++yhlk++  ++L++aek+ + ++
  gi|91772302|ref|YP_564994.1| 179 QILLMIRDKPGMTNNEIS------QTLCITNSTVSYHLKKMTTNELLQAEKDGRFKR 229
                                   677777777777666333......556678899*****************9987665 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00062      0.42       8      42 ..     115     149 ..     114     151 .. 0.90
   2 ?   -1.6   0.0       3.3   2.3e+03      22      43 ..     205     226 ..     193     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                        HTH_41   8 tIeelakeleLSvGlvQkALklLeddkaislerrG 42 
                                   ++ ++++ leL +G+    Lk+L ++  i++   G
  gi|91772302|ref|YP_564994.1| 115 SVADISHGLELNRGTAKYHLKKLHNEHKITVYDHG 149
                                   58899*********************999987665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                        HTH_41  22 lvQkALklLeddkaislerrGr 43 
                                   +v   Lk++  +   + e+ Gr
  gi|91772302|ref|YP_564994.1| 205 TVSYHLKKMTTNELLQAEKDGR 226
                                   6667799999999998888887 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 ?    5.4   0.0     0.023        16      12      37 ..     113     138 ..     107     147 .. 0.91
   2 ?    4.2   0.0     0.054        37      16      36 ..     193     213 ..     189     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.023
                                   TT-HHHHHHHHTS-HHHHHHHHHHHH CS
                        HTH_30  12 ggnisatAkaLhvHrnTlryRLrrie 37 
                                   g+++++ +  L + r T +y L++++
  gi|91772302|ref|YP_564994.1| 113 GCSVADISHGLELNRGTAKYHLKKLH 138
                                   799********************986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.054
                                   HHHHHHHTS-HHHHHHHHHHH CS
                        HTH_30  16 satAkaLhvHrnTlryRLrri 36 
                                   ++ +++L +   T++y L++ 
  gi|91772302|ref|YP_564994.1| 193 NEISQTLCITNSTVSYHLKKM 213
                                   578899*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1742.07
//
Query:       gi|91772303|ref|YP_564995.1|  [L=360]
Description: hypothetical protein Mbur_0235 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   55.6   0.1    1.3e-14   54.3   0.1    1.6  2  LolA_like  Outer membrane lipoprotein-sorting protein
    1.1e-07   31.6   0.0    2.7e-07   30.3   0.0    1.6  1  MucB_RseB  MucB/RseB N-terminal domain
    1.2e-07   32.2   1.6    4.4e-07   30.3   0.0    2.8  3  DUF4367    Domain of unknown function (DUF4367)
    3.4e-07   30.1   0.3    5.9e-07   29.3   0.3    1.4  1  LolA       Outer membrane lipoprotein carrier protein LolA
    2.1e-05   24.0   0.1     0.0033   16.8   0.1    2.3  1  DUF2092    Predicted periplasmic protein (DUF2092)
     0.0012   18.4   0.0     0.0024   17.3   0.0    1.5  1  DUF1571    Protein of unknown function (DUF1571)
     0.0047   16.3   0.2      0.079   12.2   0.0    2.1  2  DUF1329    Protein of unknown function (DUF1329)
  ------ inclusion threshold ------
      0.016   14.9   0.2        2.1    8.0   0.0    2.4  2  DUF3394    Domain of unknown function (DUF3394)


Domain annotation for each model (and alignments):
>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.1     6e-18   1.3e-14       2     137 ..      71     203 ..      70     210 .. 0.88
   2 ?    0.3   0.0      0.22   4.9e+02     160     177 ..     196     213 ..     194     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 6e-18
                                   TTEEEEEEEESTTTTT-EEEEESSSTTEEEEEETTTTCEEEE-GGGTTSECCTTC.EHHHHC--SCCCEEEEEEEEEEETT CS
                     LolA_like   2 ddkslivftePadvkGtafLtlkekdddlWlYlPalkrvrrisssdksqsfmGsdfsyeDlssrevedythellgeeevgg 82 
                                   +dk+  v+++Pa+++Gt + +    ++ +W Y+P+ ++v  +   + + ++  ++++y+D+  +++++ ++++ g ++++g
  gi|91772303|ref|YP_564995.1|  71 KDKMRSVTKQPAEQAGTIVVSN---GETMWTYDPQQNSVVAME--MPDIDLY-QEINYGDIIAQFLNESDVSFSGMKKIEG 145
                                   6789999***************...**************9999..5555555.666************************* PP

                                   EEEEEEEEEESS....TTSS...ECEEEEEEETTT--EEEEEEEETTS-EEEEEEEEEEEE CS
                     LolA_like  83 kdcyvleltpkd...aadvs...YskivlwvdketylplkvefydksgkllKtltvsdiek 137
                                   ++++++ l+pk+   +   +    + i++wvd et++plk+++yd +g+ + +++v++++ 
  gi|91772303|ref|YP_564995.1| 146 RNTFIMNLEPKEevpS---AgpfTGNIKVWVDAETWMPLKYDMYDTDGNVIVSVEVRNLQV 203
                                   ************6533...3343679************************99999998875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.22
                                   EEEEEEEE--.--GGGCS CS
                     LolA_like 160 leisevefdkglpdklFt 177
                                   +e++++++++g++d++F+
  gi|91772303|ref|YP_564995.1| 196 VEVRNLQVNTGISDEVFE 213
                                   6899*************6 PP

>> MucB_RseB  MucB/RseB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.2e-10   2.7e-07      58     173 ..      89     211 ..      82     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.2e-10
                     MucB_RseB  58 virrndevscfepeskavsvesrkikdslpallpadle.aleehYefrllGreRvAgreaqvvrilPkDql......RYgy 131
                                   v+ +++++ ++ p++++v+  +    d   ++ + d+  ++ +  +++  G +++ gr++ +++++Pk++         ++
  gi|91772303|ref|YP_564995.1|  89 VVSNGETMWTYDPQQNSVVAMEMPDIDLYQEINYGDIIaQFLNESDVSFSGMKKIEGRNTFIMNLEPKEEVpsagpfTGNI 169
                                   7788899999999999988888777788888888876448999999***********************962222114579 PP

                     MucB_RseB 132 rlwiDeetgLlLksdlldedgevLEqfaftslelgeelekae 173
                                   ++w+D et ++Lk+d++d dg+v+  +++ +l++++ ++++ 
  gi|91772303|ref|YP_564995.1| 170 KVWVDAETWMPLKYDMYDTDGNVIVSVEVRNLQVNTGISDEV 211
                                   ***********************************9998875 PP

>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.5       1.9   4.3e+03      60      60 ..      84      84 ..      30     143 .. 0.59
   2 ?   -2.2   0.0       2.6   5.7e+03      29      51 ..     186     206 ..     177     212 .. 0.56
   3 !   30.3   0.0     2e-10   4.4e-07       3     110 .]     251     359 ..     249     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                       DUF4367 60 e 60
                                  +
  gi|91772303|ref|YP_564995.1| 84 Q 84
                                  1 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                       DUF4367  29 Ykdengelisfsiskqskeesqk 51 
                                   Y  + ++ +++s+++++ + +++
  gi|91772303|ref|YP_564995.1| 186 Y--DTDGNVIVSVEVRNLQVNTG 206
                                   2..45555555555555555555 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 2e-10
                       DUF4367   3 eptylPeGy.........kfkktnisedsesalleYkdengelisfsiskqskeesqklsidtedaevekieingikatyy 74 
                                    p+y+P+Gy           +  + s+  ++++l +++++++l ++     +  +   + +      +e +++ng  + ++
  gi|91772303|ref|YP_564995.1| 251 LPSYVPDGYeldhaslfdNSEFASGSQVLQRVTLVFINDDSQLHITE---VESGFPGPTEFP----GSESVDVNGSPGDFV 324
                                   599******88888877777777777777788888887776666666...666666666666....8999*********** PP

                       DUF4367  75 ekedgeyvlvwedegvvytlsgniskeelikiaesi 110
                                   e  ++ ++l w+ +++  ++s+ ++k+e++k+aes+
  gi|91772303|ref|YP_564995.1| 325 EVYGN-KMLRWYVDDIELMISASLDKDEIVKVAESM 359
                                   *8887.9****************************8 PP

>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   2.6e-10   5.9e-07      31     165 .]      68     215 ..      66     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.6e-10
                                   EETTTEEEEEE-TTS-EE...EEEETTEEEEEETTTTEEEEEE.......HHHHTTT-GGGGGGS-HHHHTTTEEEEEEEE CS
                          LolA  31 ikrPgkfrweytsPdeql...ivsdgktvwlydpdleqvties.......lkqalsktplvlLledkaklskdynvsvkke 101
                                   +++ +k+r  +++P eq+   +vs+g+t+w ydp+ + v++++       ++ + +  ++ +L e+++++s   +++    
  gi|91772303|ref|YP_564995.1|  68 FQKKDKMRSVTKQPAEQAgtiVVSNGETMWTYDPQQNSVVAMEmpdidlyQEINYGDIIAQFLNESDVSFSGMKKIE---G 145
                                   677789999999999984444******************99888888877788888999999999999999998888...7 PP

                                   TTEEEEEEEESSS-SS....ECEEEEEE.ETTE.EEEEEEEETT--EE.EEEEEEEEES----GGGG--- CS
                          LolA 102 qdldtltlkpkakdan....lsritigfdkkgl.lkqlkvvdaqGqrt.titfsnvkenakladdlFkft 165
                                    +++ + l+pk+++ +    + +i++++d+++  + +  ++d +G+ + +++++n++ n  ++d++F+f+
  gi|91772303|ref|YP_564995.1| 146 RNTFIMNLEPKEEVPSagpfTGNIKVWVDAETWmPLKYDMYDTDGNVIvSVEVRNLQVNTGISDEVFEFD 215
                                   888888999996655422336899**********************7538******************96 PP

>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.5e-06    0.0033      47     206 ..      69     220 ..      55     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                       DUF2092  47 qrPdklrvdt..sgdekdrefyyDGktftlydkaenvYaqapapgtidelldklqekygielPladlllsdpyedlteevk 125
                                   q+ dk+r+ t   ++++ + ++++G+t+ +yd+++n +  ++ p+       +l++    e+   d++ + ++e      +
  gi|91772303|ref|YP_564995.1|  69 QKKDKMRSVTkqPAEQAGTIVVSNGETMWTYDPQQNSVVAMEMPD------IDLYQ----EINYGDIIAQFLNE------S 133
                                   8899***9995556699999************************9......22333....34444444443333......3 PP

                       DUF2092 126 sakyvgtskvngqecehl.........afrnkdvdwqlWIsqgdkpLprkivityktdpgapqytaefsdWnldpeipedt 197
                                   ++++ g++k++g ++  +          +   + ++ +W+ ++   +p+k+ + +++  g+   ++e+++ ++++ i++++
  gi|91772303|ref|YP_564995.1| 134 DVSFSGMKKIEGRNTFIMnlepkeevpSAGPFTGNIKVWVDAETW-MPLKYDMYDTD--GNVIVSVEVRNLQVNTGISDEV 211
                                   567889999999999999888888777556666789999966655.89999877665..4577889999999999999999 PP

                       DUF2092 198 FrftpPkgA 206
                                   F+f  P+g 
  gi|91772303|ref|YP_564995.1| 212 FEFDIPEGV 220
                                   999999986 PP

>> DUF1571  Protein of unknown function (DUF1571)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-06    0.0024     112     204 ..     128     217 ..     116     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                       DUF1571 112 ea.eeaevelkreerldgrrvtalevehpskeeq.vef.skaelllDeelklpirveaydwPaaeddseelvEeyeyadlk 189
                                   +  +e++v+++  ++ +gr+ +++++e +++ ++  +f    ++++D e+ +p+++  y      d +++++ + e ++l+
  gi|91772303|ref|YP_564995.1| 128 QFlNESDVSFSGMKKIEGRNTFIMNLEPKEEVPSaGPFtGNIKVWVDAETWMPLKYDMY------DTDGNVIVSVEVRNLQ 202
                                   4468999*****************9999998887535515889****************......99************** PP

                       DUF1571 190 lnvgltdadFdpanp 204
                                   +n+g++d  F+ + p
  gi|91772303|ref|YP_564995.1| 203 VNTGISDEVFEFDIP 217
                                   *******99987655 PP

>> DUF1329  Protein of unknown function (DUF1329)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.049   1.1e+02     130     161 ..      61      92 ..      24     110 .. 0.67
   2 !   12.2   0.0   3.5e-05     0.079     283     333 ..     170     217 ..     164     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.049
                       DUF1329 130 kpekkedenvlryyllavtaParlaGtallvh 161
                                   +  +++  +++ ++++ +++Pa++aGt+++  
  gi|91772303|ref|YP_564995.1|  61 SVMEQDMFQKKDKMRSVTKQPAEQAGTIVVSN 92 
                                   33445556777889999**********99853 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.5e-05
                       DUF1329 283 vfYlDedswqivaadqYDarGeLwrvseahlinaydvpagwstlevlyDlq 333
                                   ++++D+ +w+++ +d+YD  G++     +  + + +v++g+s+ ++ +D+ 
  gi|91772303|ref|YP_564995.1| 170 KVWVDAETWMPLKYDMYDTDGNVIV---SVEVRNLQVNTGISDEVFEFDIP 217
                                   58*******************9876...44445555666666666666665 PP

>> DUF3394  Domain of unknown function (DUF3394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.012        28      33     138 ..       8     111 ..       2     132 .. 0.69
   2 ?    8.0   0.0   0.00095       2.1      67     131 ..     237     301 ..     226     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                       DUF3394  33 vlLLlvaftLfrPgffldlisppyeelepselvevveelpkgselrlkvegenlegeeiektvalplge.eatgeer.Lea 111
                                   ++LLl++ +Lf  g + ++++ ++ + ++++ ++ +e+ +    +++++ g++     +  + +++ ++ + ++ ++  e+
  gi|91772303|ref|YP_564995.1|   8 LVLLLMCCALFSAGCVDEQLTAEEIAEKMQQKNDLIEDSSFTLYMTMSLMGQES----VMEQDMFQKKDkMRSVTKQpAEQ 84 
                                   799*************99999999999999988888888777777777777662....22222233333233333331477 PP

                       DUF3394 112 aGltlleedgkvlvdevefgspaekag 138
                                   aG  ++++++++    ++ +s ++ + 
  gi|91772303|ref|YP_564995.1|  85 AGTIVVSNGETMWTYDPQQNSVVAMEM 111
                                   788777778777777777777766554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00095
                       DUF3394  67 vveelpkgselrlkvegenlegeeiektvalplgeeatgeerLeaaGltlleedgkvlvdevefg 131
                                   ++ee++++ ++ + +    ++g e++    ++ +e a+g++ L+++ l+ +++d ++ + eve+g
  gi|91772303|ref|YP_564995.1| 237 TLEEAQDKADFHILLPSYVPDGYELDHASLFDNSEFASGSQVLQRVTLVFINDDSQLHITEVESG 301
                                   578899999999999999999*****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2230.47
//
Query:       gi|91772304|ref|YP_564996.1|  [L=86]
Description: hypothetical protein Mbur_0236 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   1.9      0.023   14.8   1.9    1.3  1  DUF4870   Domain of unknown function (DUF4870)
      0.091   13.2   4.2       0.11   12.9   4.2    1.1  1  FtsX      FtsX-like permease family
        2.9    8.2   6.1        4.1    7.8   6.1    1.3  1  2TM       2TM domain


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.9   3.8e-06     0.023      34      86 ..       6      77 ..       1      82 [. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-06
                       DUF4870 34 kdksefvdeqgkealNFqislliysiilivlsllvli......................gflllllllllllnlv 86
                                  k+++ +++e gk  +N+ i  l++++i++ l +l+ i                      gf   + ++ll+++++
  gi|91772304|ref|YP_564996.1|  6 KKDDDLMNEPGKIQINYIIYALVCGVIGANL-FLTSIgqmltsnifyqeylfgplltwtGF--GVGFVLLVASIF 77
                                  4555899999999999999999999888888.77777677777777777766655555533..333444444444 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.2   1.9e-05      0.11      23      84 ..      20      76 ..      16      82 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                          FtsX 23 teillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallag 84
                                  + +++++lv+ viG   ++l++  + ++l s+ f     + + ++  +++++++++l+++++
  gi|91772304|ref|YP_564996.1| 20 INYIIYALVCGVIG---ANLFLTSIGQMLTSNIF--YQEYLFGPLLTWTGFGVGFVLLVASI 76
                                  67899999999999...99999999999999986..44455555555555555555555543 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.1   0.00069       4.1      18      63 ..      23      84 ..      12      86 .] 0.63

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00069
                           2TM 18 vvYlivni......flilinl.......gsswflwpilfW...giglllhalkvFgtekffg 63
                                  ++Y++v        fl  i +       ++++ + p+l W   g+g++l ++++F+++  fg
  gi|91772304|ref|YP_564996.1| 23 IIYALVCGviganlFLTSIGQmltsnifYQEYLFGPLLTWtgfGVGFVLLVASIFFVKDSFG 84
                                  55555544222222666664367766655555555888877779999999999998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 607.18
//
Query:       gi|91772305|ref|YP_564997.1|  [L=227]
Description: hypothetical protein Mbur_0237 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1537.03
//
Query:       gi|91772306|ref|YP_564998.1|  [L=153]
Description: cell surface protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-06   27.3   4.3    2.7e-06   26.8   4.3    1.2  1  NosD            Periplasmic copper-binding protein (NosD)
    4.3e-05   23.0   5.0       0.03   13.7   3.7    2.1  2  DUF1565         Protein of unknown function (DUF1565)
    0.00018   20.3   0.8    0.00023   20.0   0.8    1.2  1  Pectinesterase  Pectinesterase
    0.00033   20.5  13.7    0.00087   19.2  13.8    1.8  1  Beta_helix      Right handed beta helix region
  ------ inclusion threshold ------
       0.19   11.5   2.8       0.19   11.4   0.2    2.0  2  Rrp44_CSD1      Rrp44-like cold shock 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 !   26.8   4.3   7.5e-10   2.7e-06       2      91 ..      43     148 ..      42     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7.5e-10
                          NosD   2 nnaisgdevlvsa.........rgngiqlens.......egseisnneisnsrdgilldnssnntitgntienl....... 59 
                                   +na +gd +lv+          ++       s        + e +  e  n++d++ + +s++++i+g t+  +       
  gi|91772306|ref|YP_564998.1|  43 DNANEGDVILVQPgsymenidiSK-------SltlmsqsGNPEDTIVEAANNQDHVIHVSSDSVNISGFTVMGGiknttmy 116
                                   666777777777555333334222.......23333332444446778889999999************887777888999 PP

                          NosD  60 ryGihlensesntiedntlssnesGialmsss 91 
                                   + Gi+++++++++i++n++s+n++Gi+l +  
  gi|91772306|ref|YP_564998.1| 117 KGGIYIDEASNCIIQNNIVSNNGNGIYLFYPA 148
                                   9**************************98766 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0002      0.71      11      41 ..      31      61 ..      20      76 .. 0.87
   2 !   13.7   3.7   8.4e-06      0.03      89     141 ..      88     143 ..      64     151 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0002
                       DUF1565 11 ksaPfktiTkAlllakageviqlapGtYsea 41
                                   +a + ti kA+  a+ g+vi + pG Y e+
  gi|91772306|ref|YP_564998.1| 31 DEANYATIQKAVDNANEGDVILVQPGSYMEN 61
                                  567799**********************886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.4e-06
                       DUF1565  89 vqnvtivlaneatiaGvt....itNpnilkgtgvliesa.sakianNtitgniadGie 141
                                   +++v  v  ++++i G+t    i+N+  +++ g++i +a +  i+nN +++n ++Gi 
  gi|91772306|ref|YP_564998.1|  88 QDHVIHVSSDSVNISGFTvmggIKNT-TMYKGGIYIDEAsNCIIQNNIVSNN-GNGIY 143
                                   33344466788999999933334666.456777***9995566666666665.88885 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.8   6.5e-08   0.00023       2      87 ..      25     104 ..      24     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-08
                                   EEE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES-TTTEEEEE---TTTT--SGGG-SE CS
                Pectinesterase   2 vvvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvGdGkektvitgsknvvdgkttfktatv 82 
                                   ++v + +++++ ti++av++++e      vi v+ G Y en++++k+ t +   G+  e t++ +  n +d++   ++ +v
  gi|91772306|ref|YP_564998.1|  25 IIVGAGDEANYATIQKAVDNANEG----DVILVQPGSYMENIDISKSLTLMSQSGN-PEDTIVEAA-NNQDHVIHVSSDSV 99 
                                   78999999**********998754....59**************997665555554.566777775.55555555555556 PP

                                   EE-ST CS
                Pectinesterase  83 avvge 87 
                                    ++g 
  gi|91772306|ref|YP_564998.1| 100 NISGF 104
                                   55554 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 !   19.2  13.8   2.4e-07   0.00087       3      53 ..      92     146 ..      16     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.4e-07
                                   EEE-SS-E.EEESEEEES-......SS-SEEE-SSS-.EEES-EEES-SS-SEEE-T CS
                    Beta_helix   3 isingssnvtiknntisns......ggyGiylrgssnvvienneiannsgsGiyilg 53 
                                   i+++++s+ +i+++t+++       ++ Giy++++sn++i+nn ++n +g+Giy+ +
  gi|91772306|ref|YP_564998.1|  92 IHVSSDSV-NISGFTVMGGiknttmYKGGIYIDEASNCIIQNNIVSN-NGNGIYLFY 146
                                   33444444.66666666666666666666666666666666555555.666666544 PP

>> Rrp44_CSD1  Rrp44-like cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.11     4e+02      53     112 ..      39      99 ..      27     104 .. 0.62
   2 ?   11.4   0.2   5.4e-05      0.19      10      32 ..     103     125 ..      98     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                   HHHHTS--TT-EEEEEE--GGG.-B---SS-B-CCCSSTT--TT-B--SSS-.-SSSSS-SS CS
                    Rrp44_CSD1  53 qknlnrafngdqvivellpqse.wkapssivldsehfdvndnpdieagdddd.nnesssntt 112
                                   qk ++ a +gd ++v+     e      s+ l s+  + +d   +ea +++d     ss++ 
  gi|91772306|ref|YP_564998.1|  39 QKAVDNANEGDVILVQPGSYMEnIDISKSLTLMSQSGNPEDTI-VEAANNQDhVIHVSSDSV 99 
                                   7888888888888887655544134556777777766665554.454444440445555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.4e-05
                                   HHHHHHHHHTTSEEEEEEEEESS CS
                    Rrp44_CSD1  10 tarvmgglkngvlyqgniqisey 32 
                                      vmgg+kn  +y+g i i e 
  gi|91772306|ref|YP_564998.1| 103 GFTVMGGIKNTTMYKGGIYIDEA 125
                                   5679***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1079.99
//
Query:       gi|91772307|ref|YP_564999.1|  [L=342]
Description: hypothetical protein Mbur_0240 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-13   49.9  30.9    7.3e-13   48.3  31.0    1.7  1  NosD             Periplasmic copper-binding protein (NosD)
    1.2e-09   38.2  41.7      2e-07   31.0  24.2    2.8  3  Beta_helix       Right handed beta helix region
  ------ inclusion threshold ------
       0.06   13.7   1.2        0.1   12.9   0.1    1.9  2  DUF5376          Family of unknown function (DUF5376)
        0.1   12.0   0.1       0.39   10.1   0.0    1.8  2  Transcrip_reg    Transcriptional regulator
        4.5    7.1  20.0          3    7.6   4.7    2.6  3  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3  31.0     2e-16   7.3e-13      57     184 ..       3     131 ..       1     142 [. 0.83

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2e-16
                          NosD  57 enlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflenss 136
                                   +n + Gi ++ s+ nti++n++++n sGia++ s+nn++e N++snne+ Gi++ + + nt ++N ++ n+n+Gi +++ s
  gi|91772307|ref|YP_564999.1|   3 SNIYDGILVSFSNYNTINGNIVFDNPSGIAIHGSNNNIVEHNNASNNEI-GISVGGDN-NTPAGNIVTmNENRGIVISG-S 80 
                                   4557899999999999999999999999999999999999999999999.99988776.56889999889999999999.5 PP

                          NosD 137 sntitgNriesn...qkiGilllsssegntiynNyFinnsenvkydgsnnn 184
                                   +n++ +N i s+    + Gi++ s+s+gn + nN+  nn+ n++ d++ +n
  gi|91772307|ref|YP_564999.1|  81 GNKLLNNVILSKigdYGFGIFVSSGSNGNILLNNTIRNNNCNLYLDERVDN 131
                                   788888888887666688899999999999999999999999998887654 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 !   31.0  24.2   5.7e-11     2e-07      69     158 .]       6      89 ..       1      90 [. 0.70
   2 !   18.0  11.2   5.5e-07     0.002       2      89 ..      74     141 ..      74     159 .. 0.45
   3 ?   -1.1   0.0      0.42   1.5e+03      74      95 ..     231     252 ..     204     281 .. 0.61

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.7e-11
                                   SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS CS
                    Beta_helix  69 gggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss 149
                                   ++gi ++ +++n+i++n ++dn + Gi +++s+nn++e+N+++nn+  Gi++   +  +t  +N++t n + Gi v+++s+
  gi|91772307|ref|YP_564999.1|   6 YDGILVSFSNYNTINGNIVFDNPS-GIAIHGSNNNIVEHNNASNNE-IGISVGGDN--NTPAGNIVTMNENRGI-VISGSG 81 
                                   577788888888888888888876.888888888888888888888.666666665..6668888888888888.555555 PP

                                   --EEES-E. CS
                    Beta_helix 150 nvtvrnNti 158
                                    +++ nN+i
  gi|91772307|ref|YP_564999.1|  82 -NKLLNNVI 89 
                                   .67777765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.5e-07
                                   SEEE-SS-E.EEESEEEES-..SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S CS
                    Beta_helix   2 gisingssnvtiknntisns..ggyGiylrgssn.vvienneiannsgsGiyilgssnntisnntisdnngggialf.gas 78 
                                   gi+i+gs+n  ++n+++s++  +g Gi++ ++sn +++ nn+i n                       nn   ++l+   +
  gi|91772307|ref|YP_564999.1|  74 GIVISGSGNKLLNNVILSKIgdYGFGIFVSSGSNgNILLNNTIRN-----------------------NN-CNLYLDeRVD 130
                                   444444444223333333334444444444444433333455555.......................44.4444444444 PP

                                   --EEES-EEES CS
                    Beta_helix  79 nnlienneitd 89 
                                   n++i++n+i++
  gi|91772307|ref|YP_564999.1| 131 NTTIRDNDISE 141
                                   44444444443 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.42
                                   TT--S--EEES-EEES-SS-SE CS
                    Beta_helix  74 lfgasnnlienneitdnggsGi 95 
                                   +  ++ ++  ++ i+ + ++G+
  gi|91772307|ref|YP_564999.1| 231 FHPNGSVIWTGCGINGCVEVGV 252
                                   3333334444444444433333 PP

>> DUF5376  Family of unknown function (DUF5376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.9e-05       0.1      31     100 ..     110     179 ..      91     198 .. 0.83
   2 ?   -1.5   0.1      0.86   3.1e+03      52      83 ..     258     308 ..     243     324 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                       DUF5376  31 sylaeylsdldlelakkvldklkdkeieeedigse..awdaeieedkvkigfllddeedekevlidrkeliY 100
                                   ++l++ +++ + +   +  +++ +++i+++di+ e  ++d  +e  +v+i+  +++ + +++  i rk l +
  gi|91772307|ref|YP_564999.1| 110 ILLNNTIRNNNCN--LYLDERVDNTTIRDNDISEEllGYDKIVERSRVRIEKEMENFSTDDHNSIGRKSLEF 179
                                   5666667666655..4555789999*******998668999***************99999999***99877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.86
                       DUF5376  52 lkdkeieeedigseawdaeieedkvkigfll...................d 83 
                                   + +++++e +  +e+ + ++  ++v + f++                   +
  gi|91772307|ref|YP_564999.1| 258 IDNSTLDEIYEIFEEQGKKVGIEEVPVAFMYdgfivldeeiveesnvdpvE 308
                                   455555555544555555666667777777766666665555555544443 PP

>> Transcrip_reg  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.26   9.2e+02     138     183 ..     155     204 ..     151     209 .. 0.70
   2 ?   10.1   0.0   0.00011      0.39      83     140 ..     237     294 ..     219     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.26
                                   EEEECCH....CT-HHHHHHHHHHHHTESEEEEE.TTTC.EEEEEEGGGHH CS
                 Transcrip_reg 138 ivveeke....eevdedelleaaieaGaeDveed.eeeevievitepedla 183
                                   +++e+ e    +++d +++  + +e G e ++e  +e++vi+ ++ + +++
  gi|91772307|ref|YP_564999.1| 155 VRIEK-EmenfSTDDHNSIGRKSLEFGPETFKELrNETNVITTYCRMPSFE 204
                                   55533.335666778888889999999999998743366888888887776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00011
                                   EEEEEEETTT.EEEEEEEEES-HHHHHHHHHHHHHHTT-EEE.-TTSSGGGEEEEEEEEE CS
                 Transcrip_reg  83 vtyegygpgg.vavivealTdnknrtaaevrsifsknggnlg.esgsvsflFerkgvivv 140
                                   v++ g+g +g v v v   Td  n t+ e+ +if+++g ++g e+ +v+f+++  g+iv+
  gi|91772307|ref|YP_564999.1| 237 VIWTGCGINGcVEVGVLEGTDIDNSTLDEIYEIFEEQGKKVGiEEVPVAFMYD--GFIVL 294
                                   5566667655466778888*********************9966778888877..55555 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.2    0.0011       3.8     147     213 ..       8      74 ..       2      76 .. 0.59
   2 ?    7.6   4.7   0.00085         3     143     208 ..      70     140 ..      58     147 .. 0.72
   3 ?   -2.2   0.1      0.88   3.1e+03     189     214 ..     226     252 ..     216     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                                   T---SS--EEEE.ES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEE.EEEEESSSEE CS
               Pectate_lyase_3 147 gifiengsggfl.ndlvfsglgdigiavgnqqftvrnitfnnattgievlwgwgwtlk.nvkinncegG 213
                                   gi+++ ++ +++  ++vf++ ++i+i  +n++++ +n++ nn + gi+v+   + t + n+   n ++G
  gi|91772307|ref|YP_564999.1|   8 GILVSFSNYNTInGNIVFDNPSGIAIHGSNNNIVEHNNASNN-EIGISVGG-DNNTPAgNIVTMNENRG 74 
                                   666666666777678888886666666667777777777777.88888874.44444413333333334 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00085
                                   ---TT---SS--EEEEES-EEES-SS-SEEE.S...-EEEEEES-EEE-S--SEEE-TT-E.EEEEEEEEE CS
               Pectate_lyase_3 143 tkhqgifiengsggflndlvfsglgdigiav.g...nqqftvrnitfnnattgievlwgwg.wtlknvkin 208
                                   +++ gi+i+ + ++ ln+++ s++gd+g+ +     ++  ++ n+t+ n++   ++++  +  t++++ i+
  gi|91772307|ref|YP_564999.1|  70 NENRGIVISGSGNKLLNNVILSKIGDYGFGIfVssgSNGNILLNNTIRNNNCNLYLDERVDnTTIRDNDIS 140
                                   4555887766666777**********998874368888888899999998888888875555888887765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.88
                                   --SEEE-TT-EEEEEEEEEESSSE.EE CS
               Pectate_lyase_3 189 ttgievlwgwgwtlknvkinnceg.Gi 214
                                   +t ++++ + ++++ ++ in+c + G+
  gi|91772307|ref|YP_564999.1| 226 ETEVYFHPNGSVIWTGCGINGCVEvGV 252
                                   566677766679999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2546.60
//
Query:       gi|91772308|ref|YP_565000.1|  [L=108]
Description: hypothetical protein Mbur_0241 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.9   0.3       0.14   12.3   0.2    1.3  1  Cuticle_3  Pupal cuticle protein C1


Domain annotation for each model (and alignments):
>> Cuticle_3  Pupal cuticle protein C1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   8.1e-06      0.14      29      57 ..      30      58 ..      26      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-06
                     Cuticle_3 29 tpyssvskvDsritnnvytPkvlysaPvp 57
                                    y  ++ +D+ i+nnvy   + y  P +
  gi|91772308|ref|YP_565000.1| 30 SGYVTIHASDADISNNVYDDDIYYETPST 58
                                  57999********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 763.98
//
Query:       gi|91772309|ref|YP_565001.1|  [L=98]
Description: hypothetical protein Mbur_0243 [Methanococcoides burtonii DSM 6242]
Scores for 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-07   28.7   0.0    9.9e-07   28.6   0.0    1.0  1  SnoaL     SnoaL-like polyketide cyclase
    0.00089   19.9   0.0     0.0011   19.6   0.0    1.1  1  SnoaL_2   SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.1e-10   9.9e-07      40     126 .]       7      95 ..       2      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.1e-10
                                   HHHHHHHHHHHHHHCTTCEEEEEEEEEET..TEEEEEEEEEEEESSEBTTBE-TT-EEEEEEEEEEEEETTEEEEEEEEEC CS
                         SnoaL  40 legfrafveelfkafPDlkvevedlvaeg..dkvaarltftGthtgeflGipptGkkvkfeeitllrvedGkIveewdviD 118
                                   +eg+ + +++l++ +PD + e   l +++    vaa ++f Gt  g+ + +pptGk+ +   + l+ +e   I++  ++++
  gi|91772309|ref|YP_565001.1|   7 VEGYTEWMKNLLTPIPDGHYELLFLAEDEerNSVAACAVFHGTQIGPGGPVPPTGKTAAADYTYLMIFEGNLIKHMTKIWN 87 
                                   7999****************9988887664478************************************************ PP

                                   HHHHHHHC CS
                         SnoaL 119 llgllrQl 126
                                    + +l+Q+
  gi|91772309|ref|YP_565001.1|  88 DMITLQQI 95 
                                   ******97 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-07    0.0011      36     101 ..       7      81 ..       2      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHHHHHHEEEEEEEEEEEEEET..TEEEEEEEEEEE.......EETTSSEEEEEEEEEEEEETTEEEE CS
                       SnoaL_2  36 reairaffralfaafpdlrfeihdvvadg..drvavewtvtgt.......ipatgrgvtvrgvdvfrvrdGkive 101
                                    e++ ++++ l+  +pd ++e+  +++d+  + va+   ++gt       +p+tg++   +++ ++ +++ +i++
  gi|91772309|ref|YP_565001.1|   7 VEGYTEWMKNLLTPIPDGHYELLFLAEDEerNSVAACAVFHGTqigpggpVPPTGKTAAADYTYLMIFEGNLIKH 81 
                                   578999*******************77772267777799999999*************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 649.57
//
Query:       gi|91772310|ref|YP_565002.1|  [L=105]
Description: hypothetical protein Mbur_0244 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-05   24.6   0.0    3.7e-05   24.1   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00032   20.7   0.0    0.00038   20.4   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0011   19.2   0.0     0.0017   18.6   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   6.2e-09   3.7e-05      26      72 ..      18      72 ..       4      73 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.2e-09
                                  CTEE.EEE-GGGTTSSHHHHHHHH..TT...SEEEEE.EEEE...THHHHHHHHHHT CS
                Acetyltransf_7 26 eitr.laVdpeyrgkGiGraLlea..ae...kgiile.qlel...naekaikfYekl 72
                                  +i + + Vd + ++  iG++Ll +  +e   +g + + ++e+   n+ +a++fY+k+
  gi|91772310|ref|YP_565002.1| 18 DIVHlIMVDVDLQRESIGSQLLVHsgKElsgHGAT-TlHVETfeiNN-QAVNFYKKN 72
                                  4444699***************9865225444532.33344444444.9******97 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.3e-08   0.00038      54     114 ..      20      81 ..       7     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.3e-08
               Acetyltransf_10  54 isllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeqe 114
                                   ++l++Vd + ++  ig++Ll +  +e++ +g  + +++  + + +av+fY+k     + ++ +
  gi|91772310|ref|YP_565002.1|  20 VHLIMVDVDLQRESIGSQLLVHSGKELSGHGATTlHVETFEINnQAVNFYKKNDCILTRKQ-K 81 
                                   7899***********************99999989887777766********998776443.3 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.8e-07    0.0017      62     114 ..      19      71 ..       3      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.8e-07
                                   EEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH CS
                Acetyltransf_1  62 yieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek 114
                                   +++ ++V+ + ++  +Gs+Ll +  +++  +g++ + ++++e n++a+++Y+k
  gi|91772310|ref|YP_565002.1|  19 IVHLIMVDVDLQRESIGSQLLVHSGKELSGHGATTLHVETFEINNQAVNFYKK 71 
                                   67889**********************************************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 703.26
//
Query:       gi|91772311|ref|YP_565003.1|  [L=463]
Description: DEAD/DEAH box helicase-like protein [Methanococcoides burtonii DSM 6242]
Scores for 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  174.2   0.1    8.8e-51  172.1   0.0    1.9  2  DEAD           DEAD/DEAH box helicase
    3.1e-31  108.0   0.2    1.5e-30  105.8   0.3    2.1  2  Helicase_C     Helicase conserved C-terminal domain
    3.9e-08   32.5   0.2     0.0002   20.3   0.1    3.4  3  UTP25          Utp25, U3 small nucleolar RNA-associated SSU p
    9.3e-08   32.3   0.0    3.3e-07   30.5   0.0    1.9  2  ResIII         Type III restriction enzyme, res subunit
    0.00014   22.2   0.1      0.018   15.4   0.0    2.3  2  AAA_19         AAA domain
     0.0013   18.9   0.0      0.061   13.5   0.0    2.8  3  RraA-like      Aldolase/RraA
     0.0016   18.2   0.0     0.0039   16.9   0.0    1.6  1  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.015   15.5   0.5       0.13   12.6   0.5    2.4  1  AAA_22         AAA domain
      0.019   14.2   0.0      0.031   13.5   0.0    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.036   13.5   0.0      0.062   12.8   0.0    1.4  1  DUF2608        Protein of unknown function (DUF2608)
      0.042   13.8   0.0       0.13   12.2   0.0    1.9  1  Flavi_DEAD     Flavivirus DEAD domain
       0.12   11.7   0.0       0.12   11.7   0.0    2.2  2  CMS1           U3-containing 90S pre-ribosomal complex subuni


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 !  172.1   0.0   5.9e-54   8.8e-51       1     174 [.      25     194 ..      25     196 .. 0.96
   2 ?   -0.6   0.1      0.64   9.5e+02      64     104 ..     257     301 ..     247     309 .. 0.73

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 5.9e-54
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                   t+iQ+ +ip++l+++d+++ a+TG+GKT+af++p+lq+++      + ++p++l+++PtreLa q+ + + +++ky++++ 
  gi|91772311|ref|YP_565003.1|  25 TPIQELSIPHLLDNRDMIGIAQTGTGKTAAFILPILQNMSAIhkkATPKKPRVLVLAPTRELAAQIGESFATYGKYTRYKH 105
                                   89***********************************9976687668999******************************* PP

                                   EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                    +++ggv ++ q+++l++gvd++v+tpgrl+dl+++g+++ls+v+++VlDEadr+ld+gf +++n+i+  l       +++
  gi|91772311|ref|YP_565003.1| 106 TVVFGGVGQTPQVRALSRGVDCLVATPGRLLDLIQQGHIKLSNVEYFVLDEADRMLDMGFLNDVNKIVDML-------PKK 179
                                   ****************999****************************************************.......677 PP

                                   SEEEEEESSBSHHHH CS
                                   xxxxxxxxxxxxxxx RF
                          DEAD 160 rqvivlSATlpkdvk 174
                                   rq +++SAT++ +++
  gi|91772311|ref|YP_565003.1| 180 RQSLFFSATMSPEIS 194
                                   89********97765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.64
                                   HHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT....CSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                          DEAD  64 lnnlkkfkkyidlrvlliiggvaardqlskldng....vdivvgt 104
                                   +n++++++++ ++++ +i g++++++  ++l+n     ++++v+t
  gi|91772311|ref|YP_565003.1| 257 ANKVTEMLNKSNINAGAIHGSKSQTHRTKTLQNFksgqLRVLVAT 301
                                   567777777777888899998888888888842222367888777 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       3.5   5.2e+03      13      57 ..      71     119 ..      59     131 .. 0.53
   2 !  105.8   0.3   9.9e-34   1.5e-30       2     111 .]     231     339 ..     230     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.5
                                   TTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHH CS
                    Helicase_C  13 eeeggkilifvntidrlek.vklllekk...gikvavlhgelpqneree 57 
                                   + ++ ++l+ ++t++ + +  + + +      +k +v+ g   q  + +
  gi|91772311|ref|YP_565003.1|  71 TPKKPRVLVLAPTRELAAQiGESFATYGkytRYKHTVVFGGVGQTPQVR 119
                                   5566777888888874433322221111223555555555555555544 PP

  == domain 2  score: 105.8 bits;  conditional E-value: 9.9e-34
                                   HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                    Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                   k e ll+ll + e+ + +l+f++t+ r++kv+ +l+k++i++ ++hg+ +q +r ++l++f++g+ +vL+atd+a+rGidi
  gi|91772311|ref|YP_565003.1| 231 KNELLLHLL-RGEHLDCVLVFTRTKHRANKVTEMLNKSNINAGAIHGSKSQTHRTKTLQNFKSGQLRVLVATDIAARGIDI 310
                                   677888888.7888999***********99666668889****************************************** PP

                                   TTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRag 111
                                   +++++Vin+dlp  ++sy++riGRt+Rag
  gi|91772311|ref|YP_565003.1| 311 EDISHVINYDLPNIPESYVHRIGRTARAG 339
                                   ***************************97 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0092        14      74      95 ..      73      94 ..      32     108 .. 0.85
   2 ?   -1.6   0.0      0.57   8.5e+02     189     218 ..     146     176 ..     136     179 .. 0.80
   3 !   20.3   0.1   1.3e-07    0.0002     246     418 ..     180     330 ..     167     348 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0092
                         UTP25 74 trpkvLillptreaalevvell 95
                                  ++p+vL+l+ptre a ++ e++
  gi|91772311|ref|YP_565003.1| 73 KKPRVLVLAPTRELAAQIGESF 94
                                  69*************9986665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.57
                         UTP25 189 LsSiEvlivdqadvl.emQnwehvetvlkhl 218
                                   Ls +E +++d+ad +  m   + v++++++l
  gi|91772311|ref|YP_565003.1| 146 LSNVEYFVLDEADRMlDMGFLNDVNKIVDML 176
                                   899*********9652677778888888776 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 1.3e-07
                         UTP25 246 RQtlvfssyetpeinslfnskleNlaGkvkvkkvvkggslekvglkvrqvFqrfdaesivdepdarfkfftekilpqlkks 326
                                   RQ+l+fs+ ++pei +l ++ l+N   +v+v+++ ++      + +++q    +d+++             +++l +l + 
  gi|91772311|ref|YP_565003.1| 180 RQSLFFSATMSPEISTLARKMLSNP-AQVEVTPQATT------VERIEQFIFFVDSDN------------KNELLLHLLR- 240
                                   6777777777777777765555554.35555555555......234445443444444............2456667777. PP

                         UTP25 327 sskssgiliyipsyfdfvrvrnylkeekvsfaaiseysskkevsraRelFfkgkkkvlLyteRlhffrRykikgvkkvilY 407
                                    ++ + +l++  +     +v++ l++++++ +ai+ ++s+++ +++ + F++g+ +vl+ t+ +   r  +i+++++vi Y
  gi|91772311|ref|YP_565003.1| 241 GEHLDCVLVFTRTKHRANKVTEMLNKSNINAGAIHGSKSQTHRTKTLQNFKSGQLRVLVATDIAA--RGIDIEDISHVINY 319
                                   5788999999999999**********************************************885..99************ PP

                         UTP25 408 klPenpefyse 418
                                   +lP+ pe y  
  gi|91772311|ref|YP_565003.1| 320 DLPNIPESYVH 330
                                   ******98864 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 !   30.5   0.0   2.2e-10   3.3e-07      29     169 ..      43     189 ..      22     191 .. 0.83
   2 ?   -2.1   0.0       2.2   3.4e+03      56      67 ..     221     232 ..     210     301 .. 0.49

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.2e-10
                                   EEESTTSTHHHHHHHHHHHH-S...........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--....... CS
                        ResIII  29 ikmaTGtGKTlvaaklierllkkgkee......kflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kekdst 102
                                     + TGtGKT   +  i + +++ +++      ++l+l+p+++l  q  e f+ + + ++ +++ ++ g ++++  +  s 
  gi|91772311|ref|YP_565003.1|  43 GIAQTGTGKTAAFILPILQNMSAIHKKatpkkpRVLVLAPTRELAAQIGESFATYGKYTRYKHTVVFGGVGQTPqVRALSR 123
                                   4678*******99888877777777777999*************************9999986666666666664566888 PP

                                   .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT-.--SEEEEEESS- CS
                        ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekf.keavllglTATp 169
                                     + lv+t  +l   +     ++ + + ++ ++++ DEa r+ ++   + +++i++++ k+   l ++AT+
  gi|91772311|ref|YP_565003.1| 124 GVDCLVATPGRLLDLI-----QQGHIKLSNVEYFVLDEADRMLDMgflNDVNKIVDMLpKKRQSLFFSATM 189
                                   99************99.....78888888899************97777999999999455777999**97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                   -EEEEESSHHHH CS
                        ResIII  56 kflflvprksll 67 
                                   +f+f+v++ +  
  gi|91772311|ref|YP_565003.1| 221 QFIFFVDSDNKN 232
                                   555555554322 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.018       9     115 ..      37     162 ..      28     187 .. 0.65
   2 ?    4.8   0.1     0.022        32      39      77 ..     241     279 ..     230     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                        AAA_19   9 kekvllvtaGpGtGKTr.vlkhivallvelggvkp...eeillvaftgrAakelrerlaalgaeatTiHrlal........ 77 
                                    ++ ++ +a  GtGKT   +  i++ + ++++ +     ++l++a+t+  a ++ e+ a++g+ ++  H + +        
  gi|91772311|ref|YP_565003.1|  37 DNRDMIGIAQTGTGKTAaFILPILQNMSAIHKKATpkkPRVLVLAPTRELAAQIGESFATYGKYTRYKHTVVFggvgqtpq 117
                                   5666777999******734666666666666544344489******************99999877777664466677777 PP

                        AAA_19  78 .....ldfddlltealelle.eaeeekklqeeellivDEfq.dvd 115
                                         ++d l+ ++  ll+  ++ + kl + e+++ DE+  ++d
  gi|91772311|ref|YP_565003.1| 118 vralsRGVDCLVATPGRLLDlIQQGHIKLSNVEYFVLDEADrMLD 162
                                   777774445555555555555335566675666888888752444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.022
                        AAA_19  39 gvkpeeillvaftgrAakelrerlaalgaeatTiHrlal 77 
                                   g++++ +l+ + t++ a++++e l++ + +a  iH+   
  gi|91772311|ref|YP_565003.1| 241 GEHLDCVLVFTRTKHRANKVTEMLNKSNINAGAIHGSKS 279
                                   3455889999***************99********8822 PP

>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   4.1e-05     0.061      46     112 ..      69     132 ..      27     145 .. 0.78
   2 ?   -0.5   0.0      0.81   1.2e+03      27      67 ..     211     257 ..     190     276 .. 0.72
   3 ?    1.2   0.0      0.25   3.8e+02      92     118 ..     356     382 ..     355     393 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                                   HTS--TTEEEEEESTT.SSSSSECE-HHHHHHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-S CS
                     RraA-like  46 leeagpgdvlVvdgggdeslraallGgllataakangvaGvvvdGavRDvaelreldfpvfargvtp 112
                                    +++++ +vlV+  +   +l+a + G+  at+ k+   + +vv+G v  + ++r+l+ +v ++ +tp
  gi|91772311|ref|YP_565003.1|  69 KATPKKPRVLVLAPTR--ELAAQI-GESFATYGKYTRYKHTVVFGGVGQTPQVRALSRGVDCLVATP 132
                                   34677889****9777..545555.***********************************9998887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.81
                                   EEEEEEEESS..........BGHHHHHHHTS--TTEEEEEESTT.SSSSS CS
                     RraA-like  27 GpavTvkvvea.........dnslvkealeeagpgdvlVvdgggdeslra 67 
                                    +a+Tv+ +e+         +n+l+ ++l   + + vlV + +++   ra
  gi|91772311|ref|YP_565003.1| 211 PQATTVERIEQfiffvdsdnKNELLLHLLRGEHLDCVLVFTRTKH---RA 257
                                   578888888888888888767799999999999999999986663...22 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.25
                                   ES-HHHHTTSSSEEEEEEE-SSB-B-S CS
                     RraA-like  92 vRDvaelreldfpvfargvtprkkpkk 118
                                   +RD+++l ++++ v  ++ +  k +++
  gi|91772311|ref|YP_565003.1| 356 LRDIEKLTDMEIEVAEHNYHSEKAKNA 382
                                   6*************9999988764443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.6e-06    0.0039       7      97 ..      29     157 ..      25     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                        AAA_30   7 aaavealltsgdrvavltGpAGtGKtta.....lkalreaweaag...grviglAptgkaAkvLaeelgieastiakllkr 79 
                                   +  + +ll ++d  ++  +  GtGKt a     l+ + +++++a     rv++lApt + A++++e++ + ++ +  + ++
  gi|91772311|ref|YP_565003.1|  29 ELSIPHLLDNRD--MIGIAQTGTGKTAAfilpiLQNMSAIHKKATpkkPRVLVLAPTRELAAQIGESFATYGKYTR-YKHT 106
                                   555667777777..889999******85443335555555555535679****************98765322211.1111 PP

                        AAA_30  80 lk.................................grarlepgtllivDEa 97 
                                                                      g+ +l++ + ++ DEa
  gi|91772311|ref|YP_565003.1| 107 VVfggvgqtpqvralsrgvdclvatpgrlldliqqGHIKLSNVEYFVLDEA 157
                                   113344455555555555556666666666666665566666677777777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   8.4e-05      0.13      70     128 ..     100     188 ..      41     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.4e-05
                        AAA_22  70 a...........................erlsseellealeqalraravielliiDEaqh.lrseealeeLrsllnl...s 119
                                   +                             ++  +ll++++q   + + +e +++DEa++ l  +  l+++ ++++    +
  gi|91772311|ref|YP_565003.1| 100 YtrykhtvvfggvgqtpqvralsrgvdcLVATPGRLLDLIQQGHIKLSNVEYFVLDEADRmL-DMGFLNDVNKIVDMlpkK 179
                                   34445555555666556666666666665567778888888877777778**********77.8*******9999988666 PP

                        AAA_22 120 rkgvqliLv 128
                                   r+++ +   
  gi|91772311|ref|YP_565003.1| 180 RQSLFFSAT 188
                                   655555555 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.1e-05     0.031      57     131 ..     241     319 ..     215     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                 ERCC3_RAD25_C  57 ekrgDkiivfsDnvfaLkeyakklkkpy.....iyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqi 131
                                    ++ D ++vf+   +  ++++++l+k       i+G+ s+++r+k lq+fk+  ++++++   ++   iD+ + + +i  
  gi|91772311|ref|YP_565003.1| 241 GEHLDCVLVFTRTKHRANKVTEMLNKSNinagaIHGSKSQTHRTKTLQNFKSG-QLRVLVATDIAARGIDIEDISHVINY 319
                                   456799999999999999999999887522222789**************976.8999999**********998888765 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-05     0.062     157     228 ..     223     292 ..     185     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                       DUF2608 157 vlftsglnKGeaLlklLdkigrepksviFiDDkkknlasveealksadidflglhYtkieekekktqqqiak 228
                                   ++f++  nK e+Ll+lL   g++ + v+    +k+  ++v e l++++i+  ++h +k++ ++ kt q+ + 
  gi|91772311|ref|YP_565003.1| 223 IFFVDSDNKNELLLHLLR--GEHLDCVLVFTRTKHRANKVTEMLNKSNINAGAIHGSKSQTHRTKTLQNFKS 292
                                   9***************96..8999***9999*********************************98888765 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.8e-05      0.13      14      65 ..      48     108 ..      39     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.8e-05
                                   TS-TTTTHHH.......HHHHHHHHTT--EEEEESSHHHHHHHHHHTT..TS-EEE----- CS
                    Flavi_DEAD  14 GaGktrkvlp.......elvkeaierrlrtlvLaPtrvvlaemeealk..glevryktsav 65 
                                   G+Gkt  ++         + k+a+ ++ r lvLaPtr  +a + e+++  g+  ryk+++v
  gi|91772311|ref|YP_565003.1|  48 GTGKTAAFILpilqnmsAIHKKATPKKPRVLVLAPTRELAAQIGESFAtyGKYTRYKHTVV 108
                                   7777776544011111145678888999***************997652256677776665 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.7     4e+03     118     134 ..      66      82 ..      53     109 .. 0.76
   2 ?   11.7   0.0     8e-05      0.12     181     209 ..     128     156 ..     111     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                          CMS1 118 vksaksngsPelLvltl 134
                                   +++ +++ +P++Lvl+ 
  gi|91772311|ref|YP_565003.1|  66 IHKKATPKKPRVLVLAP 82 
                                   45578899999999975 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 8e-05
                          CMS1 181 avGtpgRildLleeeslsvdeLkrivlDa 209
                                    v tpgR+ldL++++ ++++++++ vlD 
  gi|91772311|ref|YP_565003.1| 128 LVATPGRLLDLIQQGHIKLSNVEYFVLDE 156
                                   589************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 2501.43
//
Query:       gi|91772312|ref|YP_565004.1|  [L=257]
Description: hypothetical protein Mbur_0246 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-48  163.3  35.6    9.3e-48  162.9  35.6    1.1  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9  35.6   5.2e-52   9.3e-48       2     235 ..       7     250 ..       6     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 5.2e-52
                          TauE   2 llagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGallGa 81 
                                   ++++ll +++ ++lG+Gg++i+vPl+++l ++  +a+a++l+++v+t++s++++++r+++vd++++ +++l+s+i+a+lGa
  gi|91772312|ref|YP_565004.1|   7 VALVLLLSVLFSFLGMGGAVIYVPLFYWLgIDLITAIAMALMLNVVTTASASVTYLRKKTVDLPTAAPFILSSAIAAPLGA 87 
                                   688999**********************6589999********************************************** PP

                          TauE  82 llllllpsellkllfgvlllllallmllrkkr..srak..grerrptaillvliggl.vGllsGllGiGgGfllvplllll 157
                                   ++++++p+e+++  f+v+++++++lm+l k +  +  +  ++ + + ++++++i gl +G+++GllGiGgG++lvp+l++ 
  gi|91772312|ref|YP_565004.1|  88 YVSTSVPEEFVLHTFSVVVAAAGVLMILLKDIgeN--DttSNLDIKERLAIGIISGLfIGFIAGLLGIGGGIFLVPILVF- 165
                                   **************************997777552..234567777777777776666*********************7. PP

                          TauE 158 lglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarl.......arrlsertlrrlfallllv 231
                                   +g+ +++a ats+l++l++sl+g+l++++++++ +++l++l++ +++G++lG++l        + + er+++++f+lll++
  gi|91772312|ref|YP_565004.1| 166 MGFGVRRAPATSALVVLFSSLSGFLSHISNAQIEFRTLAILGIVSFIGGQLGSHLmylrfpsLSGFFERYFQKIFGLLLIL 246
                                   7*****************************************************7544433333334589**********9 PP

                          TauE 232 lgvk 235
                                   +++ 
  gi|91772312|ref|YP_565004.1| 247 ISMM 250
                                   9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); 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:                        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: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1465.34
//
Query:       gi|91772313|ref|YP_565005.1|  [L=584]
Description: peptidase M50 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-23   82.9   0.0    1.7e-22   79.9   0.0    2.1  1  Peptidase_M50   Peptidase family M50
    6.3e-16   58.5   3.4    4.2e-07   30.2   0.2    2.3  2  PDZ_2           PDZ domain
    9.2e-08   31.8   0.1    0.00051   19.8   0.0    2.4  2  PDZ_6           PDZ domain
    1.4e-05   25.3   6.2    0.00048   20.4   0.3    2.8  2  PDZ             PDZ domain
     0.0077   16.2   1.3        3.9    7.6   0.1    2.4  2  PDZ_1           PDZ-like domain
  ------ inclusion threshold ------
      0.035   13.7   0.2      0.035   13.7   0.2    2.9  4  Peptidase_M50B  Peptidase M50B-like
      0.065   13.3   0.1       0.17   11.9   0.1    1.6  1  GP3             Equine arteritis virus GP3


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 !   79.9   0.0   6.7e-26   1.7e-22       3     246 ..     126     563 ..     124     567 .. 0.81

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 6.7e-26
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                 Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka..... 78 
                                   +++l++ +vvHE+ H+++ + +g++v++++i++                a++p+GG+ + ++ee    ++e+++       
  gi|91772313|ref|YP_565005.1| 126 VIALLVTLVVHEFSHAILCRVEGIRVKSMGILL----------------AIVPIGGFAEPDEEELFGVKKEDTEGLgantt 190
                                   89***************************9999................*************99665544444444999** PP

                                   .................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................................. CS
                                   .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                 Peptidase_M50  79 .................flkkspwqrllivlAGplanfilailvfvv.................................. 108
                                                     + +s  qr++i++AG + nf++a+++f++                                  
  gi|91772313|ref|YP_565005.1| 191 dgpierrilgtekevmpKKVASREQRARILAAGVMSNFVVALIAFILffgpvlgaiapmsdtmiinvtsdssaniagleng 271
                                   **************9887788889********************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Peptidase_M50 109 ................................................................................. 108
                                                                                                                    
  gi|91772313|ref|YP_565005.1| 272 mvitqiddtsiqkandiilymnnieagavvqvhaskdhnllvydvevgndtddgikgmyvnnvvtdspaeamglesgmlii 352
                                   ****************************************************************99999999999999999 PP

                                   .....................................................-EEECECTTTSCEE-SEEEC-....... CS
                                   .....................................................xxxxxxxxxxxxxxxxxxxxx....... RF
                 Peptidase_M50 109 .....................................................pkkskeseeekrgviGvspkp....... 129
                                                                                        p     +  +++g++G++  p       
  gi|91772313|ref|YP_565005.1| 353 kiddtaisssedfvtfmnftktgqvisvetviagkatgdnvsseifeielashP-----EGGSEKGFLGIYYRPneieiei 428
                                   999999999999999999999999999999999888888777777665433332.....6777888888888889999999 PP

                                   ...............XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX...X CS
                                   ...............xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                 Peptidase_M50 130 ...............vkkegllealkegvektlkvvvltvk.algklitg.klslktlggpisiaqlaseaaeagls...s 190
                                                    + +++ ++ +g++  + +  l +    g+ + g + +l ++  pi+ ++  +    +g+    +
  gi|91772313|ref|YP_565005.1| 429 vplgmsigefpakdyLAALKAIPSMLGGFTGWIIILGLPIFgFAGEGFPGfSGQLAQFYSPIGWGEPLG----IGIFwiaN 505
                                   888888887555443333333333333333333333332222334445555555666666666666665....44445579 PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                 Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghllfalleairrkplserk..eevanlvglal 246
                                   +l ++ ++++ +g++N lP  +LDGgh+++  l a+  + +s ++  +ev + + + +
  gi|91772313|ref|YP_565005.1| 506 TLLWVGWLNFYVGLFNCLPAVPLDGGHVFRDYLHALISRFISDEAkaKEVSSAIAASF 563
                                   9***********************************9999887651145555555555 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.3   4.3e-10   1.1e-06       3      82 .]     243     318 ..     241     318 .. 0.90
   2 !   30.2   0.2   1.6e-10   4.2e-07      14      68 ..     327     381 ..     319     391 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.3e-10
                                   ..XX------..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE- CS
                         PDZ_2   3 lGvsvsdeedtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevkl 82 
                                   lG+   ++++     +++V++++ a+ agl+ g vi+++d++ +++  d+i ++++ ++G  V++  + d++ + ++v++
  gi|91772313|ref|YP_565005.1| 243 LGAIAPMSDT----MIINVTSDSSANIAGLENGMVITQIDDTSIQKANDIILYMNNIEAGAVVQVHASKDHNLLVYDVEV 318
                                   5555555554....899********************************************************9999986 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.6e-10
                                   .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEE CS
                         PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVklt 68 
                                   +g++v +V  ++Pa++ gl++g  i+k+d+++++s+ed+ + ++++k G+ ++++
  gi|91772313|ref|YP_565005.1| 327 KGMYVNNVVTDSPAEAMGLESGMLIIKIDDTAISSSEDFVTFMNFTKTGQVISVE 381
                                   699***********************************************99996 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00029      0.75       4      43 ..     256     293 ..     253     303 .. 0.84
   2 !   19.8   0.0     2e-07   0.00051       2      52 ..     331     380 ..     330     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                         PDZ_6   4 aVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr 43 
                                    V  +s A  AGl+ G +i++++++++  ++ +d++ ++ 
  gi|91772313|ref|YP_565005.1| 256 NVTSDSSANIAGLENGMVITQIDDTSI--QKANDIILYMN 293
                                   678899999******************..99999986665 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2e-07
                         PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvl 52 
                                   V  V+++sPA+ +Gl+ G +i++++++ +   s +d++  +  +++g+ +++
  gi|91772313|ref|YP_565005.1| 331 VNNVVTDSPAEAMGLESGMLIIKIDDTAI--SSSEDFVTFMNfTKTGQVISV 380
                                   899**************************..*****9998887777777766 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   1.5    0.0052        13      29      61 ..     253     285 ..     246     303 .. 0.89
   2 !   20.4   0.3   1.9e-07   0.00048      18      61 ..     318     362 ..     300     382 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0052
                                   EEEEECTTSHHHHHTSSTTEEEEEETTEETTTS CS
                           PDZ  29 fvsevlpggaaeadglkvGDkIlsvNgvdvenv 61 
                                    + +v  +++a+ +gl+ G +I++++++++ + 
  gi|91772313|ref|YP_565005.1| 253 MIINVTSDSSANIAGLENGMVITQIDDTSIQKA 285
                                   6999****99*****************999876 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.9e-07
                                   EETTSS.SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTS CS
                           PDZ  18 ggsdqr.gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenv 61 
                                    g+d + g kg +v++v+ +++aea gl+ G  I++++++ +++ 
  gi|91772313|ref|YP_565005.1| 318 VGNDTDdGIKGMYVNNVVTDSPAEAMGLESGMLIIKIDDTAISSS 362
                                   444444589******************************999986 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0015       3.9      38      75 ..     259     295 ..     247     297 .. 0.81
   2 !    7.1   0.1    0.0021       5.3      30      73 ..     326     370 ..     320     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
                         PDZ_1  38 asgsfklsskekkgviitsinnqptpnLdefievvkki 75 
                                   +  s ++++  ++g++it+i+++ ++  ++ i  +++i
  gi|91772313|ref|YP_565005.1| 259 SDSSANIAG-LENGMVITQIDDTSIQKANDIILYMNNI 295
                                   344555566.9*********************999998 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0021
                         PDZ_1  30 vkgvyvseasg.sfklsskekkgviitsinnqptpnLdefievvk 73 
                                   +kg+yv++    s++ + + ++g++i +i+++ +++ ++f+++++
  gi|91772313|ref|YP_565005.1| 326 IKGMYVNNVVTdSPAEAMGLESGMLIIKIDDTAISSSEDFVTFMN 370
                                   67888886544044445669**********************997 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.4       1.3   3.4e+03      97     108 ..      70      81 ..      50      93 .. 0.51
   2 ?   13.7   0.2   1.4e-05     0.035      17      47 ..     124     155 ..     112     158 .. 0.80
   3 ?   -4.0   0.2       3.7   9.6e+03     101     107 ..     229     235 ..     214     247 .. 0.48
   4 ?   -0.6   0.4      0.33   8.4e+02     127     191 ..     498     569 ..     495     577 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                Peptidase_M50B  97 lvllvllllvll 108
                                   l+++ +l ++l+
  gi|91772313|ref|YP_565005.1|  70 LMFVGMLAMFLI 81 
                                   112222222222 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.4e-05
                Peptidase_M50B  17 lrpfk.llvvffHElGHalaalLtGgrvkgie 47 
                                   + ++  l++ ++HE++Ha+ + + G rvk++ 
  gi|91772313|ref|YP_565005.1| 124 WGVIAlLVTLVVHEFSHAILCRVEGIRVKSMG 155
                                   555440455679****************9985 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.7
                Peptidase_M50B 101 vllllvl 107
                                   v++l+++
  gi|91772313|ref|YP_565005.1| 229 VVALIAF 235
                                   1222221 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.33
                Peptidase_M50B 127 lllvlllaedelleflllflgvflllgsvr.d...i..ddl.irrkapesDasqlakltgvpallwvvlwll 191
                                   + ++++ ++  ++ +l  ++g+f++l +v  d   +  d+l    ++  sD ++ +++    a  + +l+l+
  gi|91772313|ref|YP_565005.1| 498 IGIFWIANTLLWVGWLNFYVGLFNCLPAVPlDgghVfrDYLhALISRFISDEAKAKEVSSAIAASFTMLILA 569
                                   556777777788888899999999886654243332444442122444666666666665555555554444 PP

>> GP3  Equine arteritis virus GP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.6e-05      0.17       8      84 ..     229     306 ..     223     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
                           GP3   8 pvallcfflyfcficgsvgsnntticmhttsdtsvhlfyaanvtfpshfq.rhfaaaqdfvvhtgyeyagvtmlvhlf 84 
                                    val++f+l+f  + g++     t+ +  tsd+s  +    n  + ++++   +  a+d++++     ag  + vh  
  gi|91772313|ref|YP_565005.1| 229 VVALIAFILFFGPVLGAIAPMSDTMIINVTSDSSANIAGLENGMVITQIDdTSIQKANDIILYMNNIEAGAVVQVHAS 306
                                   59*********************************9998888776666651567889999999999899988888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); 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:                         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: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3619.76
//
Query:       gi|91772314|ref|YP_565006.1|  [L=150]
Description: hypothetical protein Mbur_0249 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   91.5   0.0    4.1e-26   91.2   0.0    1.1  1  SnoaL     SnoaL-like polyketide cyclase
    3.4e-12   46.9   0.0    4.5e-12   46.5   0.0    1.1  1  SnoaL_2   SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.0   4.6e-30   4.1e-26      19     125 ..      38     142 ..      25     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 4.6e-30
                                   HHGTEEEEEEETCCTT.TCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEESSEBTTBE-TT-EEEEE CS
                         SnoaL  19 ldelvaedvvdhnpee.eparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGthtgeflGipptGkkvkfe 98 
                                   l e ++ d++ h     +++  leg+ +f+ +   a+P+l +e+ d++aegdkv++r++++Gth g+f+G+ pt k+v f+
  gi|91772314|ref|YP_565006.1|  38 LSEKCSVDYHMH---FgGSTLDLEGLIEFMGAIHYALPNLVFEIYDVIAEGDKVVTRWSASGTHLGKFQGVIPTKKPVHFT 115
                                   444555555555...3589999*********************************************************** PP

                                   EEEEEEEETTEEEEEEEEECHHHHHHH CS
                         SnoaL  99 eitllrvedGkIveewdviDllgllrQ 125
                                   +it+ r+e+G Ive w+ +D+l  ++Q
  gi|91772314|ref|YP_565006.1| 116 GITISRIENGMIVEDWEEVDQLNFAQQ 142
                                   ***********************9999 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0     5e-16   4.5e-12      24     101 ..      44     129 ..      36     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 5e-16
                                   EEEEET.TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE.......EETTSSEEEEEEEEEEEEET CS
                       SnoaL_2  24 vvwedp.ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt.......ipatgrgvtvrgvdvfrvrd 96 
                                   v ++ + gg++   e++ +f+ a + a+p l fei dv+a+gd+v+++w ++gt       + +t ++v+++g+++ r+++
  gi|91772314|ref|YP_565006.1|  44 VDYHMHfGGSTLDLEGLIEFMGAIHYALPNLVFEIYDVIAEGDKVVTRWSASGThlgkfqgVIPTKKPVHFTGITISRIEN 124
                                   45677777789999******************************************************************* PP

                                   TEEEE CS
                       SnoaL_2  97 Gkive 101
                                   G ive
  gi|91772314|ref|YP_565006.1| 125 GMIVE 129
                                   ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 928.71
//
Query:       gi|91772315|ref|YP_565007.1|  [L=276]
Description: fumarate hydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-95  319.5   0.0      2e-95  319.3   0.0    1.0  1  Fumerase  Fumarate hydratase (Fumerase)
  ------ inclusion threshold ------
      0.083   12.7   0.1        2.1    8.2   0.0    2.4  2  RPAP1_N   RPAP1-like, N-terminal


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 !  319.3   0.0   2.3e-99     2e-95       2     269 ..       9     270 ..       8     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: 319.3 bits;  conditional E-value: 2.3e-99
                      Fumerase   2 eaveealkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetgdlee 82 
                                   ea+ +++kea+t+lp+dv++alk+a ++E+s++a ++++++l+N++iA+++++plCqDTGi +++v+ig+e++  + dl+ 
  gi|91772315|ref|YP_565007.1|   9 EATVDIIKEAETQLPDDVIDALKNARQNESSDVAISQIDAILKNIDIASNNNIPLCQDTGILIFYVEIGRELK-LDIDLKG 88 
                                   678899******************************************************************7.899**** PP

                      Fumerase  83 aineGvreaykegplRksvvadplerkntgd....nlPavihielvpgdeleitvlakGgGsenksklkmlnpsdglegvk 159
                                   ai e+ r a++e plR+++v +p++r n++d    +lP  i++e+v+gd+l+itv++kG+Gsen+s+lkm+np++ l++v+
  gi|91772315|ref|YP_565007.1|  89 AIIEASRIATQEVPLRPNAV-HPITRSNSSDntgdGLP-DIKYEFVEGDQLKITVAPKGAGSENMSALKMMNPTE-LKDVR 166
                                   ********************.9999999888777799*.**********************************77.***** PP

                      Fumerase 160 kfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiGpqGlGGkttvld 240
                                   kf+letv +ag+++CpP+++gvgiGg++++aa+lak  llre+ +        + e+++l++in+lgiGp+GlGG+tt+l+
  gi|91772315|ref|YP_565007.1| 167 KFILETVLNAGGRPCPPIIVGVGIGGSFDKAARLAKATLLREVTDMT------DEEKSILKDINSLGIGPMGLGGDTTALA 241
                                   ******************************************96655......5689************************ PP

                      Fumerase 241 vkierlprhiAslpvavnvsCsadRrakv 269
                                   v++ + ++h+Aslpva+n++C+a+R+a+v
  gi|91772315|ref|YP_565007.1| 242 VHLATSYCHTASLPVAINIQCWANRHASV 270
                                   **************************986 PP

>> RPAP1_N  RPAP1-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.022     2e+02      27      44 ..      19      36 ..      15      38 .. 0.83
   2 ?    8.2   0.0   0.00023       2.1       5      29 ..     148     172 ..     147     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.022
                       RPAP1_N 27 lesLdPkllefLlkRank 44
                                    +L +++++ L++ +++
  gi|91772315|ref|YP_565007.1| 19 ETQLPDDVIDALKNARQN 36
                                  57899*********9886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00023
                       RPAP1_N   5 eENrarLasMspeEIeeereeLles 29 
                                    EN+  L+ M+p E ++ r+ +le+
  gi|91772315|ref|YP_565007.1| 148 SENMSALKMMNPTELKDVRKFILET 172
                                   5*******************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1515.88
//
Query:       gi|91772316|ref|YP_565008.1|  [L=190]
Description: fumarate hydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  158.4   0.0    1.6e-46  158.2   0.0    1.0  1  Fumerase_C       Fumarase C-terminus
  ------ inclusion threshold ------
       0.14   12.2   0.0        0.5   10.4   0.0    1.8  2  tRNA_anti-codon  OB-fold nucleic acid binding domain


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 !  158.2   0.0   1.8e-50   1.6e-46      31     205 ..       4     178 ..       1     179 [. 0.94

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 1.8e-50
                    Fumerase_C  31 dLnqketeeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPv..ktpedeavgsaGPTT 109
                                   +Ln++  +e ++++++g+ + +sG++l+aRD aH+r+ e  e+g+elp  ++l++ +iY++GP   +t ++++v +aGPTT
  gi|91772316|ref|YP_565008.1|   4 HLNTPLKKEYIEELNTGDIVYISGTVLTARDEAHARILELKEEGKELP--FSLEGAAIYHCGPLmqQTDGKWKVIAAGPTT 82 
                                   68999999****************************************..9999*********98788899********** PP

                    Fumerase_C 110 atRmdkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGGaAilakkaikkvevvefeelGm.EAiyeievedf 189
                                   + Rm k +  ll+++++++ ++Kg++++ v +++ k+++vYL   GG A la+++ik+v+ v++ +lGm EA++e+ev++f
  gi|91772316|ref|YP_565008.1|  83 SDRMSKMTPALLENFNVRVLIGKGGMTN-VADSM-KEKCVYLAYTGGCAALASESIKNVTNVHWLDLGMpEAVWELEVHEF 161
                                   *************************986.55666.5689****************************************** PP

                    Fumerase_C 190 .pafvvvddkGndlfke 205
                                    p +v +d+kG+d+f++
  gi|91772316|ref|YP_565008.1| 162 gPLIVGIDAKGKDFFTS 178
                                   778888*********86 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.6e-05       0.5      39      63 ..      10      34 ..       6      50 .. 0.83
   2 ?   -1.5   0.0      0.28   2.5e+03      30      54 ..      99     123 ..      95     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.6e-05
                                  HHHHHTTS-TTSEEEEEEEEEECTT CS
               tRNA_anti-codon 39 atklaenlkeGdvvrvtGrvkrrpg 63
                                  ++++ e+l  Gd+v+++G+v + ++
  gi|91772316|ref|YP_565008.1| 10 KKEYIEELNTGDIVYISGTVLTARD 34
                                  57899**************977655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.28
                                   EEEEEETHHHHHHHTTS-TTSEEEE CS
               tRNA_anti-codon  30 iqvvlfreeatklaenlkeGdvvrv 54 
                                   ++v + ++++t++a++ ke +v+ +
  gi|91772316|ref|YP_565008.1|  99 VRVLIGKGGMTNVADSMKEKCVYLA 123
                                   7777778899999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1123.57
//
Query:       gi|91772317|ref|YP_565009.1|  [L=328]
Description: type II secretion system protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-19   69.0   1.8    3.5e-19   69.0   1.8    1.6  2  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.044   13.9   0.1      0.087   13.0   0.1    1.5  1  SRTM1     Serine-rich and transmembrane domain-containing pro
       0.39   11.1   3.0        1.2    9.6   0.1    2.4  2  COX7a     Cytochrome c oxidase subunit VII


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.7       1.9   1.1e+04     101     114 ..      63      76 ..      61      79 .. 0.72
   2 !   69.0   1.8   5.8e-23   3.5e-19       1     123 [.     122     247 ..     122     249 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.9
                                   HHHTTXXXXXXXXX CS
                         T2SSF 101 allepllllvvall 114
                                   a+ +p++++++++ 
  gi|91772317|ref|YP_565009.1|  63 AFSGPAAIIFMIAG 76 
                                   67788888888876 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 5.8e-23
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-H CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeggnL 77 
                                   flr +a +++aG++l +++e++a+   +g++++e++ + + l++G+s+++ le    r+++  +++ v+ +++a ++gg++
  gi|91772317|ref|YP_565009.1| 122 FLRDIAEMSRAGLTLPASVETVAKGE-YGEMTKEIRMMDASLSWGISFEDTLEnfgkRMNTHLITRSVALITQANRAGGRV 201
                                   89************************.**************************99998887677***************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                         T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                   + vLe++a++  e   l+r+++ +++ ++++ ++ ++v+++++++l
  gi|91772317|ref|YP_565009.1| 202 SFVLEAAARDASEIKTLERERRGNMAVYVVISYMSFFVFIFVILML 247
                                   *******************************************997 PP

>> SRTM1  Serine-rich and transmembrane domain-containing protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.087      33      84 ..     221     271 ..     193     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                         SRTM1  33 grlsnvyvyvsi.flsllaflllllvialqrlkniisssssypecssdaGssf 84 
                                    r +n+ vyv i ++s+++f++++l++a + +  +    +s+   ss aG sf
  gi|91772317|ref|YP_565009.1| 221 ERRGNMAVYVVIsYMSFFVFIFVILMLATRFVPTMHM--ASVASSSSPAGGSF 271
                                   678999999988689************9877665533..34455566666666 PP

>> COX7a  Cytochrome c oxidase subunit VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0002       1.2      14      47 ..      41      74 ..      38      78 .. 0.87
   2 ?    0.9   0.7       0.1     6e+02      26      49 ..     227     250 ..     219     257 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0002
                         COX7a 14 dkkplwlrgprsklylypyyalfavgllgslygm 47
                                  d+ + +++ p+  +  ypyya+++ g +++ +++
  gi|91772317|ref|YP_565009.1| 41 DRLRDFMKDPKGSFSTYPYYAMAFSGPAAIIFMI 74
                                  566778999*****************99998876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                         COX7a  26 klylypyyalfavgllgslygmyr 49 
                                   ++y++  y  f+v ++++l  ++r
  gi|91772317|ref|YP_565009.1| 227 AVYVVISYMSFFVFIFVILMLATR 250
                                   455555577777777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2158.15
//
Query:       gi|91772318|ref|YP_565010.1|  [L=306]
Description: type II secretion system protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   57.3   0.1    1.5e-15   57.3   0.1    2.9  4  T2SSF     Type II secretion system (T2SS), protein F
     0.0052   16.1   0.0     0.0081   15.5   0.0    1.3  1  HlyE      Haemolysin E (HlyE)
  ------ inclusion threshold ------
        2.4    6.8  12.0        2.9    6.6   0.4    2.3  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3     0.024   1.4e+02     106     123 ..      49      66 ..      21      71 .. 0.54
   2 ?   -3.5   0.5       1.6   9.5e+03     105     119 ..      92     106 ..      91     110 .. 0.68
   3 !   57.3   0.1   2.5e-19   1.5e-15       2     124 ..     138     265 ..     137     266 .. 0.95
   4 ?   -5.0   3.0         3   1.8e+04     108     124 ..     287     303 ..     281     304 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.024
                                   XXXXXXXXXXXXXXXXXX CS
                         T2SSF 106 llllvvallvllillail 123
                                   + +l++++++ll++++i+
  gi|91772318|ref|YP_565010.1|  49 ISILATLGILLLFFFVIV 66 
                                   333333333333333333 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.6
                                   TXXXXXXXXXXXXXX CS
                         T2SSF 105 pllllvvallvllil 119
                                   p+l++v+++l++++l
  gi|91772318|ref|YP_565010.1|  92 PILVAVFGGLFFAAL 106
                                   777777777777766 PP

  == domain 3  score: 57.3 bits;  conditional E-value: 2.5e-19
                                   HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-H CS
                         T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnL 77 
                                   +++++ +++aGv +v+ +++l+++  +g++  e k+++r+l+  g +l  a++    +tps+ + e+++  i+++ +gg L
  gi|91772318|ref|YP_565010.1| 138 INYMSAMSGAGVLPVDLFRALSNNEIYGEMCVESKYLVRDLEVLGsNLVSAMKnlasSTPSPMLQEFLQGAITVVTSGGEL 218
                                   789***************************************8775788888899999999999***************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                   + +++  ae++  ++++++k+++++l+ l + +v+++v+++l++i++
  gi|91772318|ref|YP_565010.1| 219 ESYFKIKAEQYIIDNRQKQKEFLETLGLLGETYVTAFVAGPLFLIIT 265
                                   ********************************************985 PP

  == domain 4  score: -5.0 bits;  conditional E-value: 3
                                   XXXXXXXXXXXXXXXXX CS
                         T2SSF 108 llvvallvllillaill 124
                                   l++v+++++l++++ ++
  gi|91772318|ref|YP_565010.1| 287 LIPVGSAMFLVIITLIT 303
                                   56667777777666665 PP

>> HlyE  Haemolysin E (HlyE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-06    0.0081     151     206 ..     217     269 ..     175     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-06
                                   HHHHH......HHHHHHHHHHHHHHHHGGGG...........SS-HHHHHHHHHHH CS
                          HlyE 151 ekssygmqkaalksavdkirkeakaliivGvigliftaitafvaGPiGlilalaia 206
                                   e  sy ++  a +  +d+ +k++  l   G++g   t +tafvaGP+ li+++ai 
  gi|91772318|ref|YP_565010.1| 217 ELESY-FKIKAEQYIIDNRQKQKEFLETLGLLG--ETYVTAFVAGPLFLIITIAIV 269
                                   55556.466677999****************55..6889*************9986 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.3    0.0019        11     362     442 ..      14      88 ..       2     134 .. 0.53
   2 ?    6.6   0.4   0.00048       2.9     367     431 ..     225     299 ..     154     305 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0019
                       DUF2207 362 savkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGa 442
                                   + + +k+++yf+ +    + +l++ +  ++  +l++++la       l +ll+++++++li++ v+   +  ++++t+ ++
  gi|91772318|ref|YP_565010.1|  14 KYYVDKRSKYFNLRRDLLRSRLNMGYDRYLSGVLLISILAT------LGILLLFFFVIVLIGVPVIEANRFGFPAWTAAYR 88 
                                   44445566666666655555555544444444444443333......2333333333333333333333344445554443 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00048
                       DUF2207 367 kergyfdkkgkkklkklsalglgliilglilillallllvll..........lvfllilllillliaiivlllfs 431
                                   k+++y+ ++ +k++  l +lgl++   +++++ + l+l++++           vfl+il+++l+ ++++++l++ 
  gi|91772318|ref|YP_565010.1| 225 KAEQYIIDNRQKQKEFLETLGLLGETYVTAFVAGPLFLIITIaivslmggadQVFLYILVYGLIPVGSAMFLVII 299
                                   555555555555544444444444333333332222222222334555555777777777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1951.66
//
Query:       gi|91772319|ref|YP_565011.1|  [L=654]
Description: type II secretion system protein E [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  169.8   0.0      1e-49  169.1   0.0    1.2  1  T2SSE       Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.042   13.6   0.8          3    7.6   0.1    2.7  2  ATP_bind_1  Conserved hypothetical ATP binding protein
      0.067   12.9   0.0       0.16   11.7   0.0    1.6  1  AAA_29      P-loop containing region of AAA domain
        0.3   12.0   2.0        0.3   12.0   0.2    1.9  2  DUF4065     Protein of unknown function (DUF4065)


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 !  169.1   0.0   2.2e-53     1e-49       6     262 ..     273     534 ..     269     544 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 2.2e-53
                         T2SSE   6 eallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvll 85 
                                   +a+++d ++ di    p++ v v  ++ +   ++v + e++ l++li r+a+  +++is  +pl+da+lp +g r+++ l 
  gi|91772319|ref|YP_565011.1| 273 DAIMRDLEIEDISGDGPNTpVYVYHKKYESIPSNVIFDEEDGLNALIIRLAQICGKHISIANPLLDATLP-DGSRIQMTLG 352
                                   6888999999**99999999999777777799999999********************************.*******998 PP

                         T2SSE  86 Pvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvE 164
                                     + +   +++iR+ +++ +t +dl   +++++++ + l  av +  +++++GgT sGKtt ++a+ ++i+ +  +iv +E
  gi|91772319|ref|YP_565011.1| 353 REITTrgSTFTIRRFNENPITPSDLLSYHTFSNAMLAYLWLAVDSSRSLIFAGGTASGKTTAMNAVSTFIQPE-MKIVSIE 432
                                   766665599***************************************************************9.******* PP

                         T2SSE 165 DpvEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaag 238
                                   D++E++l+++n +  +++       k+++++ +ll+aaLR+rP  i+vGE+R++e++ + +A++TGH   +sT+Ha+s+++
  gi|91772319|ref|YP_565011.1| 433 DTRELNLAHPNWIPGVTReafggenKGSIEMYELLKAALRQRPEFILVGEVRGAEAYVLFQAMSTGHTT-FSTMHADSVQS 512
                                   **************99999*****99*******************************************.*********** PP

                         T2SSE 239 alerLeqlgaeveaaelkssilav 262
                                    ++rLe+   +v++  +  + l++
  gi|91772319|ref|YP_565011.1| 513 IVHRLENPPINVPR--IMIQALDI 534
                                   ******98744443..33333444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.011        50     160     237 ..      59     138 ..      52     141 .. 0.78
   2 ?    7.6   0.1   0.00067         3       2      27 ..     404     426 ..     403     435 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                    ATP_bind_1 160 vvvlnkfDllkek.lekeleffedvealslllekee...ekykklaeaiaelleefalvlrflplssekeesiedllslid 236
                                   v + ++++ll+++ le ++  + ++++ +   ++++   e  +  +++++e+++e  +  ++lpl+ + e+ i+++l++++
  gi|91772319|ref|YP_565011.1|  59 VEADSQTELLSQEeLESDIGELLNFKKKNID-KSTNlsgEISSAWEKTLKEIVSEHPIP-EVLPLEIKPESFIQKFLNMVR 137
                                   5556777788777777777777777554443.33335778899999**********999.*****************9997 PP

                    ATP_bind_1 237 e 237
                                   +
  gi|91772319|ref|YP_565011.1| 138 A 138
                                   5 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00067
                    ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsv 27 
                                   +G+  sGKtt ++a+s +++ +   +
  gi|91772319|ref|YP_565011.1| 404 AGGTASGKTTAMNAVSTFIQPE---M 426
                                   79***************99876...4 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   3.6e-05      0.16      20      50 ..     396     426 ..     378     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                        AAA_29  20 dlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                   d + + +++G + sGK+T + A+++ + p+ 
  gi|91772319|ref|YP_565011.1| 396 DSSRSLIFAGGTASGKTTAMNAVSTFIQPEM 426
                                   44457899*****************999976 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.5   1.1e+04      79      86 ..      66      74 ..       4     108 .. 0.58
   2 ?   12.0   0.2   6.7e-05       0.3      18     104 ..     139     224 ..     128     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                       DUF4065 79 e.lseeeke 86
                                  e ls+ee+e
  gi|91772319|ref|YP_565011.1| 66 ElLSQEELE 74
                                  144444443 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.7e-05
                       DUF4065  18 kpitglkyiawkyGPVvp......evydeikelgskpieekeeeisdeklekkekkeveeleddkeaelseeekevidkvi 92 
                                   k++  ++y    +GP v+      +vydei+ ++ +p    ++   + ++ +   ++v e e      lseee ++ ++v 
  gi|91772319|ref|YP_565011.1| 139 KSFEMDDYDIAIHGPLVEitlpedSVYDEIEFYNVNPPYSYIRVVYNPEIHEY-LYQVLEPE------LSEEETKLFKMVK 212
                                   555668899999****99999999******99988876555555555555443.33333333......************* PP

                       DUF4065  93 kkykdlsaseLs 104
                                   ++++++  + L 
  gi|91772319|ref|YP_565011.1| 213 ERLGEVMDTHLK 224
                                   ***998777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 4464.55
//
Query:       gi|91772320|ref|YP_565012.1|  [L=506]
Description: thymidine phosphorylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   61.6   0.6    1.2e-16   60.3   0.6    1.7  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    2.5e-13   49.5   0.0    6.5e-13   48.1   0.0    1.8  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    2.5e-12   46.9   0.3    1.8e-11   44.2   0.3    2.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
      1e-05   25.5   0.1    2.6e-05   24.2   0.1    1.6  2  Molydop_binding  Molydopterin dinucleotide binding domain
    0.00067   19.8   0.1     0.0014   18.7   0.1    1.6  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      0.004   16.0   0.0     0.0058   15.5   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
  ------ inclusion threshold ------
      0.037   14.0   0.1      0.079   13.0   0.1    1.5  1  DUF1160          Protein of unknown function (DUF1160)
       0.04   13.7   1.2      0.093   12.5   0.1    2.2  2  RPN6_C_helix     26S proteasome subunit RPN6 C-terminal helix


Domain annotation for each model (and alignments):
>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.6   5.3e-20   1.2e-16       3      63 .]      90     150 ..      88     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 5.3e-20
                                   HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
               Glycos_trans_3N   3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                   ii+k +dg++Lt+eei  ++++i++ ++ +++iaAfL+A +++ +t +E+  l++Am++sg
  gi|91772320|ref|YP_565012.1|  90 IIRKTMDGQKLTKEEIDILVKDIVEENLAEIEIAAFLTATYINDMTDDETEWLTRAMIDSG 150
                                   9**********************************************************97 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 !   48.1   0.0   2.9e-16   6.5e-13       1      70 [.     424     486 ..     424     490 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.9e-16
                                   EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHH CS
                        PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkk 70 
                                   y+ e+d++++  +a+ +GA       p d+++Gi lh+k G+  k+G+p++tiYa+k++kle+avk +k+
  gi|91772320|ref|YP_565012.1| 424 YILEMDNKRLVQIARLAGA-------PNDKGAGILLHRKQGEPLKEGDPVMTIYAEKKSKLENAVKSAKE 486
                                   6789***************.......****************************************9997 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.3   7.9e-15   1.8e-11       3     253 .]     159     387 ..     157     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 7.9e-15
                                   TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE..EH CS
               Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl..fa 81 
                                   +++D+++ GG+  n   iS+   ++vAa G+ ++k + r+++  +G+aD++e l   +e ++ e++++ eevg +++  +a
  gi|91772320|ref|YP_565012.1| 159 PIMDKHSIGGVPGNK--ISLLIVPIVAANGLLIPKTSSRAITGAGGTADLMEIL-APVEFDAAEIKRMTEEVGGVLVwgGA 236
                                   799***********9..***********************************98.5899*************977773346 PP

                                   HSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHHHHHH CS
               Glycos_transf_3  82 peyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsllaktt 162
                                   ++  +a ++ ++v   l i            p    + l ++++k+ a ++++v+++++++ +  +++  + e + la  +
  gi|91772320|ref|YP_565012.1| 237 TNIAPADDKLIKVEYPLSI-----------DP--HCQMLASIMAKKGAIGADHVVMDIPTGPGTKIKN--VQEGRKLARDL 302
                                   7777777777777766666...........34..3345789***************************..*********** PP

                                   HHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHH CS
               Glycos_transf_3 163 vaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvak 242
                                   +   +  g     +l+    +++r  + ale+    e++++l++  eg++s +  +  + +ag++l + + +   ++g + 
  gi|91772320|ref|YP_565012.1| 303 INLGDrLGMDVDCALTYGASPVGRTIGPALEV---IEALKVLESF-EGPNSLI--EKSASLAGMLLEMGN-VAGKDKGYDL 376
                                   *****99999**********************...9999999986.9999996..777778887776655.888999**** PP

                                   HHHHHHTSHHH CS
               Glycos_transf_3 243 aeevidsGkAl 253
                                   a e++++GkAl
  gi|91772320|ref|YP_565012.1| 377 AIETLKNGKAL 387
                                   *********95 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.2e-08   2.6e-05      31      82 ..      16      67 ..       7      84 .. 0.84
   2 ?   -3.0   0.0       3.4   7.5e+03      74     102 ..     122     143 ..     106     145 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                                  EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC CS
               Molydop_binding 31 vveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe 82
                                   v +n  dA++lG+ +Gd+V+++++   +    ++++++ pG++ +++   e
  gi|91772320|ref|YP_565012.1| 16 KVILNTIDAKELGVHEGDRVRIKNHVTLTAIVDFTEDMISPGMIGLYHEVKE 67
                                  6899********************98766555577777******99997655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                                   EEEESSHCC.....S-GHCTS--SCSTTT CS
               Molydop_binding  74 vfmpfgwweagekggnaNaltddatdpls 102
                                   +++   +       + +N+ tdd+t+ l+
  gi|91772320|ref|YP_565012.1| 122 IAAFLTA-------TYINDMTDDETEWLT 143
                                   4444444.......449999999887765 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   6.4e-07    0.0014       2      83 ..       3      82 ..       2      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.4e-07
                                  EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                       CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrka 83
                                  L+V+ +    vg+ +v++++ d +elg+++gd v+i+++  T   ++   ++  ++g I +   + + +     ++V+V +a
  gi|91772320|ref|YP_565012.1|  3 LKVQPID-VKVGKYKVILNTIDAKELGVHEGDRVRIKNHV-TLTAIVDFTEDMISPGMIGLYHEVKEALSKEWTETVEVFPA 82
                                  5666664.469**************************877.555555555555599*9999999999999999999998776 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.6e-06    0.0058     187     256 ..     409     483 ..     385     489 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                       DUF2254 187 seeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkgeplakvwgeeddeelaeklre 256
                                   s  e ++ i a+++Gy+ + d ++Lv++a+      ++++ i l+++ G+ + +g+p+++++ e+ +++l++++++
  gi|91772320|ref|YP_565012.1| 409 SVGEFTEDIIAPNNGYILEMDNKRLVQIARlagapnDKGAGILLHRKQGEPLKEGDPVMTIYAEK-KSKLENAVKS 483
                                   5556678899******************9744444477899*********************888.5566665554 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.5e-05     0.079      31      96 ..      65     128 ..      35     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
                       DUF1160  31 rdetfrkklvkvlkmFiereievediyeiveavdgikLtkkQidylvkqvyeneki.isilqkfvde 96 
                                     e ++k +++ +++F +++   ++ y i +++dg kLtk+ id lvk ++e++   i+i   f   
  gi|91772320|ref|YP_565012.1|  65 VKEALSKEWTETVEVFPAEKP--KSTYIIRKTMDGQKLTKEEIDILVKDIVEENLAeIEI-AAFLTA 128
                                   567889999999999998875..5567788******************999765331333.344433 PP

>> RPN6_C_helix  26S proteasome subunit RPN6 C-terminal helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.89     2e+03       8      15 ..     331     338 ..     331     338 .. 0.89
   2 ?   12.5   0.1   4.1e-05     0.093       1      14 [.     370     383 ..     370     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.89
                  RPN6_C_helix   8 ALeTIknm 15 
                                   ALe+I+++
  gi|91772320|ref|YP_565012.1| 331 ALEVIEAL 338
                                   8****986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.1e-05
                  RPN6_C_helix   1 kDktYeaALeTIkn 14 
                                   kDk+Y+ A+eT+kn
  gi|91772320|ref|YP_565012.1| 370 KDKGYDLAIETLKN 383
                                   7************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3489.69
//
Query:       gi|91772321|ref|YP_565013.1|  [L=178]
Description: tRNA 2'-O-methylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-48  162.2   0.0    5.2e-48  161.9   0.0    1.1  1  Trm56           tRNA ribose 2'-O-methyltransferase, aTrm56
     0.0083   16.3   0.0      0.011   15.9   0.0    1.2  1  SpoU_methylase  SpoU rRNA Methylase family
  ------ inclusion threshold ------
      0.048   13.6   0.0       0.08   12.9   0.0    1.4  1  rRNA_methylase  Putative rRNA methylase


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   8.8e-52   5.2e-48       1     119 []      55     172 ..      55     172 .. 0.99

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 8.8e-52
                                   H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS---H CS
                         Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnqPhse 81 
                                   wGg+f ve+++++k+ i+++k+egg+v+hl+myG+n+ ++  eik ++k l++vvGaekvp+e+y+lad+nv++gnqPhse
  gi|91772321|ref|YP_565013.1|  55 WGGDFYVENDVNWKSEIEKWKEEGGKVCHLSMYGINLPDAAGEIKLCDK-LMIVVGAEKVPTEIYDLADWNVAIGNQPHSE 134
                                   ********************************************99987.******************************* PP

                                   HHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                         Trm56  82 vaalaifldrllegkelekefedaklkviPsergkkvv 119
                                   vaa+a+++dr+++++ l++ef  a+l+++P+ergk+v+
  gi|91772321|ref|YP_565013.1| 135 VAAVALTMDRIAQEEPLKREFGYAELTIVPMERGKRVI 172
                                   ************************************95 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.9e-06     0.011      21     127 ..      26     132 ..      20     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                                   HHHHTT-SEEEEESGSSCTCGSHHHHHHCT..THHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC....CSHHHT CS
                SpoU_methylase  21 takafgaselvlvkprsadllnpeakraaa..galevlelkvvdsleealkelkeegfalvatslkgksls....eidlke 95 
                                   ta+a+ga++++l ++++   +++ +  +a   g  +++e     ++++ ++++keeg +++ +s +g +l     ei+l +
  gi|91772321|ref|YP_565013.1|  26 TARALGAEGMLLASNDKG--IKNAIEDVAErwGGDFYVE--NDVNWKSEIEKWKEEGGKVCHLSMYGINLPdaagEIKLCD 102
                                   677888888888775554..5555555554115555555..67799999*******************999555555777* PP

                                   TEEEEEEBTTTBS-HHHHCTSSEEEE----TT CS
                SpoU_methylase  96 kvalvfGnEdkGlsnelleladrlvkIpmsge 127
                                   k ++v+G E+  +++e+ +lad  v I  +++
  gi|91772321|ref|YP_565013.1| 103 KLMIVVGAEK--VPTEIYDLADWNVAIGNQPH 132
                                   *********7..99********9999977665 PP

>> rRNA_methylase  Putative rRNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05      0.08      46      82 ..       3      39 ..       1      44 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                  EEEEEEESB-CTS-TTSB--HHHHHHHHHHHHHHEEE CS
                rRNA_methylase 46 kavifNLGYLPggdksivTkaettlkAlekalelLkk 82
                                  k+vi  LG+ P+ dk+i+T+   t +Al +   lL++
  gi|91772321|ref|YP_565013.1|  3 KIVILRLGHRPERDKRITTHVGLTARALGAEGMLLAS 39
                                  678999**********************998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 1057.08
//
Query:       gi|91772322|ref|YP_565014.1|  [L=362]
Description: hypothetical protein Mbur_0257 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-11   42.2   1.1    1.8e-10   41.3   1.1    1.5  1  PDDEXK_4  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.069   12.5   0.1        0.1   11.9   0.1    1.2  1  MTD       methylene-5,6,7,8-tetrahydromethanopterin dehydroge


Domain annotation for each model (and alignments):
>> PDDEXK_4  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   1.1     2e-14   1.8e-10      36     164 ..      35     170 ..      10     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2e-14
                      PDDEXK_4  36 flkafldllrerlfssdeisasvadlesaevere....nasekngriDlll....qenkivvlIEnKvaAkdqkeQlarYe 108
                                   f   fl ++++ +    e       + +++ ++      + ++ +r D+ +     +++ ++++E K+++++ ++Ql+rY+
  gi|91772322|ref|YP_565014.1|  35 FFLSFLTHFKITEA--IEP------IATIWTQQTykalDYHFSDSRPDICIeinnASHNELIFVESKIGSSEGYDQLKRYA 107
                                   44444444444444..112......22222222244456666677777777667699999********************* PP

                      PDDEXK_4 109 efakkkakkkdivvvyLtldgeapsedslee....dekeayktisyeqilewleecvkk...i 164
                                   e +++ ++ ++  +vy t+d e+++e ++ +    +++ ++ +i + +i+++l++  k+    
  gi|91772322|ref|YP_565014.1| 108 EQLDQLNHFGKKKLVYITRDHENKDENKIFAgcnnEDELYFIQIRWYEIYNFLSTYYKQtdsE 170
                                   *********************99999999889988889999*************999993330 PP

>> 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 ?   11.9   0.1   1.2e-05       0.1     115     185 ..     171     242 ..     168     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                                   S------TTT--HHHHHHHHH.HHHHHHHHTTHHHHHHHHHHHHHHHHTTT-.GGGS-EEEESGGGGGGSS-- CS
                           MTD 115 DpliGarrefLDptemalfna.dvlkvLaatGavRlvqeeldkviekvkagk.eielPkividaekaveaaef 185
                                   D li    +f++  +ma+ n  + + +La t  +R vq+ +d++i  + ++k e+e+ k+   a   ++  +f
  gi|91772322|ref|YP_565014.1| 171 DILIRETLNFMEEHNMATNNCfNTIDILALT-NFRKVQQMMDETIYGIVSDKfETEIGKVSQRASCLTQLRDF 242
                                   667777789*********997689*****99.59*****************9999999988777766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2198.64
//
Query:       gi|91772323|ref|YP_565015.1|  [L=246]
Description: hypothetical protein Mbur_0258 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-59  199.9   0.3      6e-59  199.6   0.3    1.0  1  NIF3      NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   0.3   3.4e-63     6e-59       1     243 [.       5     231 ..       5     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 3.4e-63
                          NIF3   1 eivevleelaplelae..swDnvGlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddykkr 79 
                                   ++ve+lee+ap+elae  + D +Gl + d ++++k++++ald+te vle+A + gad++ithH lif++++ + ++   + 
  gi|91772323|ref|YP_565015.1|   5 KVVETLEEIAPPELAEdfDIDRIGLTL-DLDNDIKRIAVALDPTEYVLERAAQIGADMLITHHTLIFHSVNLISKE--LAG 82 
                                   589*************6777899****.7***********************************************..*** PP

                          NIF3  80 llkkliknnislysaHtnlDaapgGvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelakklkkklgl 160
                                   llk +  n+islys+Htn+D+a+gGvnd+la++lgl+++             e g+grig+++e + l+ ++++++k+l+ 
  gi|91772323|ref|YP_565015.1|  83 LLKIAFDNEISLYSMHTNYDSAKGGVNDVLAQRLGLNDVY------------EVGMGRIGTIDE-CPLDVFIDHVAKSLNT 150
                                   ************************************9754............679********9.**************66 PP

                          NIF3 161 ekvrvagdldkkvkkvaicaGsGa..slieeakakgaDlliTGelkhhealdakekgiavidvgHyatErvflealaelLk 239
                                    +++++  ++ ++kkv++++GsG   ++++ a+++++D+++++elkh+   ++ +  + ++d+ HyatE++++e+l e+Lk
  gi|91772323|ref|YP_565015.1| 151 -HLQYV-GEKDTIKKVMVFGGSGFkdDYLDIARDNDVDAYVSAELKHDVLRSYDD--LLLVDATHYATENPAMETLCERLK 227
                                   .*****.89999***********8889**************************77..57*********************9 PP

                          NIF3 240 eklk 243
                                   + lk
  gi|91772323|ref|YP_565015.1| 228 DLLK 231
                                   8765 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:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1566.83
//
Query:       gi|91772324|ref|YP_565016.1|  [L=263]
Description: nicotinate-nucleotide diphosphorylase (carboxylating) [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-30  103.8   0.0    1.3e-29  103.2   0.0    1.3  1  QRPTase_C      Quinolinate phosphoribosyl transferase, C-term
    3.8e-13   49.3   0.0    6.3e-13   48.6   0.0    1.4  1  QRPTase_N      Quinolinate phosphoribosyl transferase, N-term
  ------ inclusion threshold ------
      0.018   15.0   0.1       0.21   11.5   0.0    2.5  3  Lactamase_B_3  Beta-lactamase superfamily domain
      0.043   13.8   0.0       0.64   10.1   0.0    2.2  2  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   2.8e-33   1.3e-29       1     166 [.     101     256 ..     101     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 2.8e-33
                                   HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTT CS
                     QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdk 79 
                                   iAt+t++mv++a+++   + i+  Rkt+Pg+r+ e ++v +GGgd+hr +Lsd +li +nh +++gs  +    +r     
  gi|91772324|ref|YP_565016.1| 101 IATKTRKMVDKAREVnpDIMIATSRKTHPGFRKYELRSVHAGGGDHHRNSLSDSILITQNHFNVVGSFDK----LR----A 173
                                   9**************9999***********************************************7654....33....3 PP

                                   TSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHT CS
                     QRPTase_C  80 evkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalths 160
                                   + kie+e +++ee+ + +    di +LD  ++eelk+++ +l+++n+++++ v Gg++ en+ +ya s+ d++ v+++  +
  gi|91772324|ref|YP_565016.1| 174 MRKIEIEPRTKEEVFQYAPIA-DILLLDHYTPEELKEVAPKLRQINPKLELAV-GGISFENIPKYAASV-DFV-VTTAPFY 250
                                   447************988876.*************************999966.99**********998.766.6666777 PP

                                   B----E CS
                     QRPTase_C 161 vkalDi 166
                                   +++ D+
  gi|91772324|ref|YP_565016.1| 251 AEPFDL 256
                                   777776 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 !   48.6   0.0   1.4e-16   6.3e-13       1      89 []      13      99 ..      13      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.4e-16
                                  CTT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHH CS
                     QRPTase_N  1 igrgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLn 83
                                  +++gD tte l + e +++ +i ++++g+ ++ +  +e++e+  gl+v+++ + G++++++++l+e+eG++r+l + +R+ + 
  gi|91772324|ref|YP_565016.1| 13 CPYGDETTELLGI-EGEGSLTIRSRDPGIASCADDLAEFYEKK-GLKVNMHLENGKEFTENAILFEAEGDLRKLFKLWRISQT 93
                                  589*****66666.56889************************.*************************************** PP

                                  HHHHHH CS
                     QRPTase_N 84 llqrlS 89
                                  +l++++
  gi|91772324|ref|YP_565016.1| 94 FLSMTC 99
                                  **9865 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 ?    0.0   0.0      0.15   6.9e+02     142     162 ..     103     123 ..      91     124 .. 0.87
   2 ?   -1.8   0.0      0.57   2.5e+03      35      47 ..     150     162 ..     134     166 .. 0.74
   3 ?   11.5   0.0   4.6e-05      0.21      46      87 ..     198     239 ..     176     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                 Lactamase_B_3 142 lgqeealelakrLkpklvlPm 162
                                    +++++++ a++++p++++ +
  gi|91772324|ref|YP_565016.1| 103 TKTRKMVDKAREVNPDIMIAT 123
                                   577899************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.57
                 Lactamase_B_3  35 eeaDlvlisqale 47 
                                      D +li+q++ 
  gi|91772324|ref|YP_565016.1| 150 SLSDSILITQNHF 162
                                   4568888888885 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 4.6e-05
                 Lactamase_B_3  46 ledHahletlkqlaenvkvleegeslevggleiravatshda 87 
                                   l dH+++e+lk++a + + ++++ +l+vgg+++++++ ++ +
  gi|91772324|ref|YP_565016.1| 198 LLDHYTPEELKEVAPKLRQINPKLELAVGGISFENIPKYAAS 239
                                   57**********************************999865 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.08   3.6e+02      41      58 ..     106     124 ..      91     134 .. 0.72
   2 ?   10.1   0.0   0.00014      0.64      66     109 ..     205     244 ..     194     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.08
                   B12-binding  41 edivaairaekpdv.vglS 58 
                                    ++v+++r+ +pd+ ++ S
  gi|91772324|ref|YP_565016.1| 106 RKMVDKAREVNPDImIATS 124
                                   5677888888888755554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                   B12-binding  66 eavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvv 109
                                   e+ ke++  l++i+p++ ++vGG+ ++  p+    a   +d+vv
  gi|91772324|ref|YP_565016.1| 205 EELKEVAPKLRQINPKLELAVGGISFENIPKY---A-ASVDFVV 244
                                   678999999****************9999999...6.6778876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1662.24
//
Query:       gi|91772325|ref|YP_565017.1|  [L=183]
Description: hemerythrin HHE cation binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-18   66.5   5.8    4.6e-18   66.1   1.9    2.1  2  Hemerythrin  Hemerythrin HHE cation binding domain
     0.0071   16.4   0.3      0.014   15.4   0.1    1.6  2  HTH_16       Helix-turn-helix domain
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.23   11.7   0.0    1.3  1  Reo_sigmaC   Reovirus sigma C capsid protein C-terminal domai


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   1.9   7.8e-22   4.6e-18       2     131 .]       3     137 ..       2     137 .. 0.86
   2 ?    2.4   0.1     0.039   2.3e+02      77      92 ..     163     179 ..     139     183 .] 0.81

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 7.8e-22
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC....HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH...CCC.HHHHHHH CS
                   Hemerythrin   2 ivealdeeHralrallerlraladaaaevhga....lrklaelldelvdeleaHhaaEEellfPlle..drpggravldvl 76 
                                   +++ l+eeH+a+  +l+ l+ + +++++  +     l  + e+l+ +vd    Hh++EEe+lfP+++  + pg ++++d+l
  gi|91772325|ref|YP_565017.1|   3 PTDDLKEEHHAVTLMLKILDGICTDLESGKEVkhehLGNVVEFLKVFVDK--CHHTKEEEYLFPAMKkaEIPGSEDMIDSL 81 
                                   6789***************7777774433333456799999999999998..***************************** PP

                                   HHHHHHHHHHHHHHHHHCHTCGGSTCHHHHH...HHHHHHHHHHHHHHHHHHTHHHHH CS
                   Hemerythrin  77 ereHdeirelleelrellkgleepsaaafae...lleeladllreHiakEesilfpll 131
                                    +eH+  r+ ++ + e++ g    +++a+       +++++ll +Hi kEe+ lfp++
  gi|91772325|ref|YP_565017.1|  82 LEEHEHGRRNVRMISEAVSGNM--DSEALSTivrSSRDYIELLTQHINKEENNLFPMA 137
                                   ********99999997777765..4555555777**********************97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                                   HHHHHHHHHHHHHHH.H CS
                   Hemerythrin  77 ereHdeirelleelr.e 92 
                                   e+ H+e+++ll+ lr  
  gi|91772325|ref|YP_565017.1| 163 EGKHEEFHKLLHSLRdV 179
                                   57899999999888844 PP

>> HTH_16  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       2.2   1.3e+04      11      20 ..      10      19 ..       7      22 .. 0.59
   2 !   15.4   0.1   2.3e-06     0.014       3      60 ..      94     152 ..      92     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.2
                        HTH_16 11 DeeAieeiLk 20
                                  ++ A+  +Lk
  gi|91772325|ref|YP_565017.1| 10 EHHAVTLMLK 19
                                  5566666665 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.3e-06
                        HTH_16   3 vieaAvnG..DeeAieeiLkhYegyIrklSlrklydedgnvngyvdedlkqeleikliea 60 
                                    i  Av+G  D eA+ +i++  ++yI  l    + +e++n+    de l qe+++ l+++
  gi|91772325|ref|YP_565017.1|  94 MISEAVSGnmDSEALSTIVRSSRDYIELLTQ-HINKEENNLFPMADEHLAQEIQVDLLKS 152
                                   5788888866789*************99988.6777999******************986 PP

>> Reo_sigmaC  Reovirus sigma C capsid protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.8e-05      0.23      12      51 ..      72     111 ..      61     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                    Reo_sigmaC  12 dgssdsidmtvnahchgrrtdylmsstesltvtsnavslv 51 
                                    gs d id  ++ h hgrr   ++s   s  + s+a s +
  gi|91772325|ref|YP_565017.1|  72 PGSEDMIDSLLEEHEHGRRNVRMISEAVSGNMDSEALSTI 111
                                   599**********************988877777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1129.91
//
Query:       gi|91772326|ref|YP_565018.1|  [L=120]
Description: alkylhydroperoxidase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   62.5   0.0    3.6e-17   62.2   0.0    1.1  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.013   15.5   0.3       0.03   14.4   0.3    1.6  1  SapB_1    Saposin-like type B, region 1
      0.041   14.2   0.0      0.061   13.7   0.0    1.4  1  UXS1_N    UDP-glucuronate decarboxylase N-terminal
      0.057   12.3   0.0      0.059   12.3   0.0    1.1  1  PA26      PA26 p53-induced protein (sestrin)


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 !   62.2   0.0     8e-21   3.6e-17       1      84 [.      35     117 ..      35     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 8e-21
                                   HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHH CS
                           CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAla 81 
                                   p++l+ +++ ++ ll+ +g L++k + L+alav a+ +c+ C  + ++ Al++G+t+eei+e++ +  +++g pa+ + ++
  gi|91772326|ref|YP_565018.1|  35 PDFLKKYNRCNHKLLS-DGTLPAKMKILMALAVVASKQCDRCTVVQMQSALKNGATKEEIMETMEVIYITSGAPAVASCRE 114
                                   99*************9.9**********************************************************99999 PP

                                   HHH CS
                           CMD  82 aae 84 
                                   a++
  gi|91772326|ref|YP_565018.1| 115 ALK 117
                                   987 PP

>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   6.6e-06      0.03      10      31 ..      77      98 ..      76      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                                  HHHHHHHH-SS--HHHHHHHHH CS
                        SapB_1 10 VkeveklLkdNkTeeeIieaLe 31
                                  V ++++ Lk+ +T+eeI+e +e
  gi|91772326|ref|YP_565018.1| 77 VVQMQSALKNGATKEEIMETME 98
                                  889***************9876 PP

>> UXS1_N  UDP-glucuronate decarboxylase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.061      14      48 ..      57      91 ..      28     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                        UXS1_N 14 rmklLlalaliaYvasvwGtfvnmrsiqenGdvKv 48
                                  +mk+L+ala++a   +   t v+m+s   nG  K 
  gi|91772326|ref|YP_565018.1| 57 KMKILMALAVVASKQCDRCTVVQMQSALKNGATKE 91
                                  4****************9*********99*99985 PP

>> PA26  PA26 p53-induced protein (sestrin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.3e-05     0.059      25     101 ..      13      89 ..       1     101 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                          PA26  25 leeaflssgrvdqvtqvlgl.HPqylesflrtqnfllrgdgpLpleyRhYiailaaaRhqcsyLvklhekeFlekggd 101
                                   l++   + g   ++ +++g   P++l+++ r+++ ll  dg Lp++++  +a+   a  qc     +++++ l++g  
  gi|91772326|ref|YP_565018.1|  13 LDSMSDKLGFTPRILETVGDlDPDFLKKYNRCNHKLLS-DGTLPAKMKILMALAVVASKQCDRCTVVQMQSALKNGAT 89 
                                   4444444455566666666349*************995.9**********9999999999998777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 754.87
//
Query:       gi|91772327|ref|YP_565019.1|  [L=523]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   88.6   0.0    8.2e-25   87.7   0.0    1.5  1  GAF_2        GAF domain
    5.9e-22   78.3   0.0    1.2e-21   77.2   0.0    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.3e-07   30.3   0.0      8e-07   29.1   0.0    1.7  1  PAS          PAS fold
      1e-06   28.9   0.0    1.8e-06   28.2   0.0    1.4  1  PAS_4        PAS fold
    2.2e-06   27.8   0.1    8.6e-06   26.0   0.0    2.1  2  PAS_9        PAS domain
    6.6e-05   22.9   0.7    0.00014   21.8   0.1    1.9  2  HisKA        His Kinase A (phospho-acceptor) domain
    0.00087   19.3   0.0     0.0029   17.6   0.0    2.0  1  PAS_8        PAS domain
    0.00089   19.2   0.0     0.0019   18.1   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0024   18.5   0.0      0.017   15.7   0.0    2.4  2  PAS_10       PAS domain
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.12   12.6   0.0    2.5  2  PAS_7        PAS fold
      0.038   14.0   0.2       0.12   12.4   0.2    1.9  2  CARD         Caspase recruitment domain
       0.12   13.1   0.0       0.22   12.2   0.0    1.4  1  GAF          GAF domain


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   5.5e-28   8.2e-25       3     136 ..     143     283 ..     141     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 5.5e-28
                                   HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEES-.GG CS
                         GAF_2   3 dleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrpl.....geglvgealrtgrpvilnd.le 75 
                                    +++++d+v++++v+l+ +++gyi+++ +d++ l++++w++  ++ +  +d+++     + gl+ge +r+++p+i+nd l+
  gi|91772327|ref|YP_565019.1| 143 PMQQIADFVHEQAVRLTqSTIGYIAFLSEDESlLTMHTWSNSVMQKCTIPDKKFvypvkNIGLWGEPIRQRKPIIVNDyLA 223
                                   6799***********955********99888879999*************995556679*******************888 PP

                                   G-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHH CS
                         GAF_2  76 edpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaia 136
                                    dp kkg p gh+ + + l +P+++++r+v+  ++ +nk++++d++d+++L++l++ ++  
  gi|91772327|ref|YP_565019.1| 224 PDPLKKGFPPGHVEMFNYLTIPVFEGERIVATAGV-GNKDEDYDRSDVRQLTLLMQGLWNL 283
                                   8************************99*******8.89999****************9986 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 !   77.2   0.0   8.3e-25   1.2e-21       6     110 ..     419     522 ..     415     523 .] 0.94

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 8.3e-25
                                   HHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHH CS
                     HATPase_c   6 LrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklve 86 
                                   +++++ n+++Na+k++++++++ + i  s+d+ +++v+D G Gi  ed +klfe+f +   +k+g +gtGlGl+i+kk++e
  gi|91772327|ref|YP_565019.1| 419 IEEVFVNFLSNAIKYSPEKERVIIDILDSDDEWKVTVTDFGSGIADEDKPKLFERFKR--VDKSGVKGTGLGLAIAKKITE 497
                                   67899**********99***99999997779***************************..789999*************** PP

                                   HTTTEEEEEEET.TTEEEEEEEEES CS
                     HATPase_c  87 lmgGeiwvesep.grGttftftlpl 110
                                   l+gG+i ve++p  +G+ f++t+++
  gi|91772327|ref|YP_565019.1| 498 LHGGHIGVENNPdAKGSVFWVTIKK 522
                                   ********9999999******9985 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   5.3e-10     8e-07       2     113 .]       6     113 ..       5     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.3e-10
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                   d+r i+es+p +i+  De g i+++N++ +++l+ +  ++ g ++ d +  e    ++ ++ +  +  +   +++   +  
  gi|91772327|ref|YP_565019.1|   6 DYRMIIESSPLGIIYFDETGMITFCNEKLTSILNMQKMDIFGLNMADIFTDE---GMQNIIGKTFLGESAHYQVNFHPPG- 82 
                                   8999******************************************666544...5**************9999999999. PP

                                   TSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  83 dgrpihlevraspvrdaggeilgflgvlrdi 113
                                   +   i++e+ +sp ++++g ++g +++l d+
  gi|91772327|ref|YP_565019.1|  83 KDDAIEIEIYCSPGISGQGSPHGTVCILEDV 113
                                   ****************************997 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.2e-09   1.8e-06       2     108 ..      12     116 ..      11     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.2e-09
                         PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhy 81 
                                   +s+p +++++d+ g ++++N+   +++ ++  ++ G  +a+++++   ++ ++++ +   ge +++++ ++ +  ++   +
  gi|91772327|ref|YP_565019.1|  12 ESSPLGIIYFDETGMITFCNEKLTSILNMQKMDIFGLNMADIFTD---EGMQNIIGKTFLGESAHYQVNFHPPgKDDAIEI 89 
                                   89******************************************9...999******************999955555556 PP

                         PAS_4  82 elrllPlrdesGevigvlvisrDiTer 108
                                   e+ ++P    +G ++g+++i+ D+T r
  gi|91772327|ref|YP_565019.1|  90 EIYCSPGISGQGSPHGTVCILEDVTSR 116
                                   6677999999999************98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.7e-09   8.6e-06       3     103 ..      17     114 ..      15     115 .. 0.85
   2 ?   -2.8   0.0       5.1   7.6e+03      43      59 ..     334     350 ..     317     368 .. 0.55

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.7e-09
                         PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltas 83 
                                   gi+  ++ g+i+++Ne++  +l +++ ++ g ++ d+f td+  ++ + + +   +   ++v+ +   k++  + +++ +s
  gi|91772327|ref|YP_565019.1|  17 GIIYFDETGMITFCNEKLTSILNMQKMDIFGLNMADIF-TDEGMQNIIGKTFLGES-AHYQVNFHPPGKDD-AIEIEIYCS 94 
                                   677656********************************.77777777777776666.56777777777765.8888***** PP

                         PAS_9  84 pvkdddgelvgiivilrDit 103
                                   p ++++g   g ++il+D+t
  gi|91772327|ref|YP_565019.1|  95 PGISGQGSPHGTVCILEDVT 114
                                   *******************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.1
                         PAS_9  43 dpeanerlraaleqgrk 59 
                                   ++e++e++ ++l+++++
  gi|91772327|ref|YP_565019.1| 334 ESEEDEEKMKILQTIDR 350
                                   44455555555554443 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 ?   -3.4   0.0       7.2   1.1e+04      25      44 ..     282     300 ..     277     304 .. 0.47
   2 !   21.8   0.1   9.3e-08   0.00014       2      66 ..     307     370 ..     306     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.2
                                   HHHHC.....T-HSSCHHHHHHH CS
                         HisKA  25 eaLkre...gklteelkeyleti 44 
                                    +++r+   +    +l+e  e++
  gi|91772327|ref|YP_565019.1| 282 NLMQRRegiE----KLREHTEQL 300
                                   5665553332....444444443 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 9.3e-08
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                   +  f+  + H+L +P  +++g++++L ++ + +ee ++ l+ti ++ + l +++     ++++++
  gi|91772327|ref|YP_565019.1| 307 KDLFTDILRHDLLNPAGVVKGYTDILLES-EEDEEKMKILQTIDRNNEKLIEMIRSAASFAKLDT 370
                                   66788899*****************9775.679*********************99999999885 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.9e-06    0.0029       3      40 ..       7      40 ..       5      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                         PAS_8  3 lralfesspdgiavvd.lgdrivdvNqaalellGysadl 40
                                  +r ++essp gi+ +d +g  i+++N++   +l     +
  gi|91772327|ref|YP_565019.1|  7 YRMIIESSPLGIIYFDeTGM-ITFCNEKLTSILN----M 40
                                  899*************6776.******9988885....4 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.3e-06    0.0019      31     109 ..     414     496 ..     381     515 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                   HATPase_c_2  31 eirlaveEactNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpetlpdpteeep...keslkegGrGlalik 106
                                   +++  +eE+++N    a +  p +++v + + +++++ +v+v+D G g  d   +p+  e  +   k   k  G+Gla+ k
  gi|91772327|ref|YP_565019.1| 414 KVNPMIEEVFVNFLSNAIKYSPeKERVIIDILDSDDEWKVTVTDFGSGiADED-KPKLFERFKrvdKSGVKGTGLGLAIAK 493
                                   6777899********999999989************************55554.4444332225668999999*****999 PP

                   HATPase_c_2 107 glv 109
                                   +++
  gi|91772327|ref|YP_565019.1| 494 KIT 496
                                   875 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.017       3     106 .]       9     114 ..       8     114 .. 0.82
   2 ?   -1.3   0.0       2.2   3.3e+03      54      90 ..     384     420 ..     367     424 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                        PAS_10   3 nlLnstpieltflDdnlqirrFtpaakklfklipadv.Grpladihpkkavknveeviealrtgekdevevvvp...kngk 79 
                                   ++++s p++++++D++  i++ +++ ++++++++ d+ G ++adi +++    ++++i +   ge+ + +v      k++ 
  gi|91772327|ref|YP_565019.1|   9 MIIESSPLGIIYFDETGMITFCNEKLTSILNMQKMDIfGLNMADIFTDE---GMQNIIGKTFLGESAHYQVNFHppgKDDA 86 
                                   67899******************************987*******6655...55667888888888777777753465555 PP

                        PAS_10  80 w.vlvrylpyrdedgeiaGvvetfvDit 106
                                   + + ++ +p    +g+ +G+v ++ D+t
  gi|91772327|ref|YP_565019.1|  87 IeIEIYCSPGISGQGSPHGTVCILEDVT 114
                                   5588888999999999999999999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                        PAS_10  54 nveeviealrtgekdevevvvp.kngkwvlvrylpyrd 90 
                                    ++ ++e+l+  + de e+ ++ +++  ++ ++ p+ +
  gi|91772327|ref|YP_565019.1| 384 MLRMIVESLKL-QIDEREMDIEvMPDGAYMAKVNPMIE 420
                                   44455555554.45667788887889999999999976 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-05      0.12       2     113 ..      12     119 ..      11     121 .. 0.80
   2 ?   -2.0   0.0       2.5   3.8e+03      91     107 ..     315     331 ..     281     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-05
                         PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsferer 82 
                                   e+ + Gi+ fD+++ ++++N++  ++l++ +  +  g ++++++     ++ +g+    + ++  ++    gk +++e e 
  gi|91772327|ref|YP_565019.1|  12 ESSPLGIIYFDETGMITFCNEKLTSILNMQKMDI-FGLNMADIFTDEGMQNIIGKTFLGESAHYQVNFHPPGKDDAIEIEI 91 
                                   66678************************99988.9******999999999998777777777777777777777777777 PP

                         PAS_7  83 pdgrvievrgnplpdgGfVttytDiTerrra 113
                                        i+ +g+p    G+V + +D+T r++ 
  gi|91772327|ref|YP_565019.1|  92 YCSPGISGQGSP---HGTVCILEDVTSRIEL 119
                                   777667666666...5788888888888775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                         PAS_7  91 rgnplpdgGfVttytDi 107
                                   r+  l   G+V  ytDi
  gi|91772327|ref|YP_565019.1| 315 RHDLLNPAGVVKGYTDI 331
                                   55556778889999998 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   8.1e-05      0.12       7      78 ..     314     381 ..     308     386 .. 0.82
   2 ?   -3.8   0.0       9.1   1.4e+04      46      61 ..     435     450 ..     432     451 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                                   THHHHHHHSSHHHHHHHHHHHTTSS-HHHHHHHHTSSSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHSHHH CS
                          CARD   7 nrkrLverlkslsglldyLlekkVLteeeeekikakttrlskareLldlvqkkgekacqaflealkegqpdl 78 
                                    r+ L++  ++++g++d Lle     ee+eek k + t  ++ ++L++++++  + a+   +e ++++++d 
  gi|91772327|ref|YP_565019.1| 314 LRHDLLNPAGVVKGYTDILLES----EEDEEKMKILQTIDRNNEKLIEMIRSAASFAKLDTIENIEFKDMDI 381
                                   577777777799*********9....*************************888777666666666666665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.1
                                   HHHHHHHHHHHHTSCH CS
                          CARD  46 lskareLldlvqkkge 61 
                                   ++k r+++d++ + +e
  gi|91772327|ref|YP_565019.1| 435 PEKERVIIDILDSDDE 450
                                   5788999999987665 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.22      39     123 ..     193     274 ..     143     280 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                   EECCEEEETTSHHHHHHHHHSSSEEEST.GGTSTT...HHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSH CS
                           GAF  39 asrwlfmkngrgicgqvlatgqplvipd.stpdpr...faqynrrdllenmgirsslvvPlvndgelwGllvlhnpsppft 115
                                      +++++ + g+ g+ +++++p++++d ++pdp    f +       ++ ++ ++l++P++ +++++++  + n+++ ++
  gi|91772327|ref|YP_565019.1| 193 DKKFVYPVKNIGLWGEPIRQRKPIIVNDyLAPDPLkkgFPP-------GHVEMFNYLTIPVFEGERIVATAGVGNKDEDYD 266
                                   33344444444455588999********6668888555555.......566677*********************877899 PP

                                   HHHHHHHH CS
                           GAF 116 reelellq 123
                                   r++++ l+
  gi|91772327|ref|YP_565019.1| 267 RSDVRQLT 274
                                   99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2985.16
//
Query:       gi|91772328|ref|YP_565020.1|  [L=67]
Description: hypothetical protein Mbur_0263 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 428.59
//
Query:       gi|91772329|ref|YP_565021.1|  [L=73]
Description: redox-active disulfide protein 2 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-24   86.3   1.0    1.2e-24   86.2   1.0    1.0  1  Thioredoxin_3  Thioredoxin domain
     0.0059   16.8   0.2      0.013   15.7   0.2    1.6  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.072   13.2   0.0      0.082   13.1   0.0    1.1  1  FtsK_alpha     FtsK alpha domain
      0.088   12.4   0.1       0.11   12.1   0.1    1.1  1  DUF953         Eukaryotic protein of unknown function (DUF953
       0.13   12.3   0.1        9.4    6.2   0.0    2.0  2  DUF1223        Protein of unknown function (DUF1223)


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   1.0   3.3e-28   1.2e-24       1      73 [.       1      73 []       1      73 [] 0.98

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 3.3e-28
                                  EEEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHH CS
                 Thioredoxin_3  1 meikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirk 73
                                  m+i++lg+gCakC k++++v++a++e+g++aev+kv+d+e+i +ygVm +P+lvidg+  ++G+vps++ ++k
  gi|91772329|ref|YP_565021.1|  1 MKIEILGTGCAKCIKAKEIVEKALQESGLQAEVVKVEDYETILSYGVMITPGLVIDGEAMIAGRVPSVDNVKK 73
                                  89*******************************************************************9986 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   3.6e-06     0.013       7      58 ..       8      58 ..       1      60 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                                  TSSHHHHHHHHHH....HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTE CS
                  Glutaredoxin  7 ptCpyCkkakrlL....kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgk 58
                                  ++C  C kak++     +e g++ e++ v++     e + ++ gv+  P ++idg+
  gi|91772329|ref|YP_565021.1|  8 TGCAKCIKAKEIVekalQESGLQAEVVKVEDY----ETILSY-GVMITPGLVIDGE 58
                                  79*********997666888899******997....666667.9999999999997 PP

>> FtsK_alpha  FtsK alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.3e-05     0.082      23      62 ..      14      53 ..       8      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                    FtsK_alpha 23 ekkaklieetleefgieakvveisvGPvvtqyevepapgv 62
                                   k ++++e++l+e g +a+vv+++   ++  y v + pg 
  gi|91772329|ref|YP_565021.1| 14 IKAKEIVEKALQESGLQAEVVKVEDYETILSYGVMITPGL 53
                                  567899****************************998875 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.2e-05      0.11      38      64 ..      10      36 ..       4      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                                  SHHHHHHHHHHHHHHHH-SS-EEEEEE CS
                        DUF953 38 CPdCvkaepvieealkeapedvklvrv 64
                                  C +C+ka +++e+al+e   ++++v+v
  gi|91772329|ref|YP_565021.1| 10 CAKCIKAKEIVEKALQESGLQAEVVKV 36
                                  99***************9888888877 PP

>> DUF1223  Protein of unknown function (DUF1223)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0072        26       9      27 ..       9      27 ..       6      38 .. 0.79
   2 ?    6.2   0.0    0.0026       9.4      60      86 ..      38      64 ..      33      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0072
                                  T-TT-HHHHHHHHHH.HHH CS
                       DUF1223  9 GCssCPpAdallselaaed 27
                                  GC++C +A++++++  +e+
  gi|91772329|ref|YP_565021.1|  9 GCAKCIKAKEIVEKALQES 27
                                  9***********9986654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0026
                                  HHHHHTT-S---SSEEEETTTEEEETT CS
                       DUF1223 60 ayaealglrsvYTPqvvvnGreevvgs 86
                                  +y + l    + TP +v++G++ + g+
  gi|91772329|ref|YP_565021.1| 38 DYETILSYGVMITPGLVIDGEAMIAGR 64
                                  688888889999*********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 492.08
//
Query:       gi|91772330|ref|YP_565022.1|  [L=537]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   95.2   0.1    6.6e-27   94.6   0.1    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.3e-26   93.1   0.0    3.2e-26   91.9   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-24   86.7   0.0    2.9e-24   86.0   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.3e-18   68.0   0.0    1.8e-18   67.5   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.6e-14   54.2   0.7      2e-12   47.3   0.7    2.3  1  Glyco_transf_5   Starch synthase catalytic domain
      4e-09   36.6   0.0    8.6e-09   35.6   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0026   18.1   0.0     0.0058   17.0   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.1   2.6e-30   6.6e-27       1     166 [.      20     190 ..      20     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 2.6e-30
                Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaf.....lrrlrrllkre.kpDv 75 
                                   vGG++ hv eLa+aLa+ Gh V+++t++ + +++ e +++v  +rv + l+++  + + +     ++r+  + k++ k+D+
  gi|91772330|ref|YP_565022.1|  20 VGGIAPHVSELAEALAKTGHSVHIFTRNNGLEPYGE-VNGVHYHRVDHSLSGGIVQQMDSmcdsmYSRFLDVTKEYgKFDI 99 
                                   7***********************************.7778888888777777666554412222568888888889**** PP

                Glyco_transf_4  76 vHahspaalgaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrviavSeatadelrerygvp 155
                                   +Hah+++++  a+ +++ + gip+ +t+H+++  +   k+ ++++   +   e+++   + +vi +S+++ de++ +y++p
  gi|91772330|ref|YP_565022.1| 100 LHAHDWHPF-NAVSRIKYEFGIPFMFTYHSTEWgRNGNKYGNWWEAEEISHREWKAGYESVKVISTSQQLTDEIKFLYQIP 179
                                   ********8.555666668*************77333444444444444445777788999******************** PP

                Glyco_transf_4 156 pekitVipnGv 166
                                    ekit+ipnG+
  gi|91772330|ref|YP_565022.1| 180 DEKITIIPNGI 190
                                   **********8 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 ?   -3.6   0.0       2.6   6.8e+03      65      86 ..     162     183 ..     155     186 .. 0.68
   2 !   91.9   0.0   1.3e-29   3.2e-26      15     170 ..     214     363 ..     202     365 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.6
                                   HHHHHCTTCGGGEEECCHSSSH CS
               Glycos_transf_1  65 laeelelsdnviflgevsredl 86 
                                    + + +l d+++fl ++++e++
  gi|91772330|ref|YP_565022.1| 162 ISTSQQLTDEIKFLYQIPDEKI 183
                                   5556677788888888886655 PP

  == domain 2  score: 91.9 bits;  conditional E-value: 1.3e-29
                                   -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESE CS
               Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadi 95 
                                    +++l++gr++++Kg+dll++a++++ +  + ++k+v++G+ge++   ++la + ++sdn++flg+v++e    +++++di
  gi|91772330|ref|YP_565022.1| 214 APVVLFIGRMSYQKGPDLLVEAIPEVIDH-RWDTKFVFIGEGEMRPPCEALANAEKISDNCHFLGYVDDETARDWINACDI 293
                                   689***********************887.*************************************************** PP

                                   EEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
               Glycos_transf_1  96 fvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                                   +++ps++E+fGiv+lE   a   ++a++a    +++++ ++G+lv +n + ++a +i+ +l+d  ++  ++++++
  gi|91772330|ref|YP_565022.1| 294 LCIPSRNEPFGIVVLEGWDAERTIVATDA---VQIINNFVDGILVYKN-PNSIAWGINYVLDDL-SNSSMRKAGK 363
                                   ****************************5...689***********99.*************96.7777777776 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 !   86.0   0.0   1.1e-27   2.9e-24       2     134 .]     215     352 ..     214     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.1e-27
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---TH..HHHHHHH-SE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfved..laellaaadv 75 
                                   pv+lf+Gr+   +kg dll+ea+p++ ++  d ++v++G+g+ rp  +e+la+  +++++++f+G+v+d   +++++a+d+
  gi|91772330|ref|YP_565022.1| 215 PVVLFIGRM-SYQKGPDLLVEAIPEVIDHrwDTKFVFIGEGEmRP-PCEALANaeKISDNCHFLGYVDDetARDWINACDI 293
                                   89*******.667**********9999774559********9766.666555446999*********4456********** PP

                                   EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.T.TSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv.g.engllvppgdpealaeailrLled 134
                                   +++Ps  e fg+++lE   a++ +Vatd+    +++ + ++g+lv  ++p+++a  i  +l+d
  gi|91772330|ref|YP_565022.1| 294 LCIPSrnEPFGIVVLEGWDAERTIVATDAV---QIInNfVDGILVY-KNPNSIAWGINYVLDD 352
                                   *****999*******************994...45543489****5.68****9999999887 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 !   67.5   0.0   6.9e-22   1.8e-18       1     160 []      21     189 ..      21     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 6.9e-22
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladla.....alralrrllrqrrerpdv 76 
                                   gGi+ +v ela+aLa+ Gh+V+++t++   +++  e +gv++hr++ + +++ +  ++     ++ ++ ++   +  ++d+
  gi|91772330|ref|YP_565022.1|  21 GGIAPHVSELAEALAKTGHSVHIFTRNNGLEPY-GEVNGVHYHRVDHSLSGGIVQQMDsmcdsMYSRFLDVT-KEYGKFDI 99 
                                   8*************************8888877.8899******9866555545544411122558888887.89****** PP

               Glyco_trans_4_4  77 vhahsptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyraler......rllrradavlvvseaeaeelra.lgvp 150
                                   +hah+++   a+ +++   gip+++t+h++++ r  g ++  ++++e        +      v+++s+++ +e+   + +p
  gi|91772330|ref|YP_565022.1| 100 LHAHDWHPFNAVSRIKYEFGIPFMFTYHSTEWGRN-GNKYGNWWEAEEishrewKAGYESVKVISTSQQLTDEIKFlYQIP 179
                                   ******87777777777***********9776544.44444444444411112255555777**************888** PP

               Glyco_trans_4_4 151 adrvvvvpng 160
                                   +++++++png
  gi|91772330|ref|YP_565022.1| 180 DEKITIIPNG 189
                                   *********8 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.7     8e-16     2e-12       1     221 [.       6     164 ..       6     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 8e-16
                Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkvaklkk 81 
                                   ki ++++E    +k+GG+a +v++L++aLak gh v++++ + g  +          e                       
  gi|91772330|ref|YP_565022.1|   6 KIGMFSWESLHSIKVGGIAPHVSELAEALAKTGHSVHIFTRNNGLEPY--------GE----------------------V 56 
                                   788*************************************77744333........23......................3 PP

                Glyco_transf_5  82 dgvdvyfldnpeffdreglYgdkgedyednaerfa..lfsraalelleklgw.kpdvihahDWhtalvpallkelykergl 159
                                   +gv+++ +d+       g+         ++ + +   ++sr  l++ ++  + k+d++hahDWh   +   +k        
  gi|91772330|ref|YP_565022.1|  57 NGVHYHRVDHSL---SGGIV--------QQMDSMCdsMYSRF-LDVTKE--YgKFDILHAHDWHPFNAVSRIKYEF----- 118
                                   5***********...23333........22222222244444.777777..437***********99977777653..... PP

                Glyco_transf_5 160 fkkiktvftiHNlayqgrfp..kdelaalglpaedfekldglefygkvnflk.agivyadavttV 221
                                      i+++ft H++++ ++ +   ++ +a +                 ++  +  + +++ +v+  
  gi|91772330|ref|YP_565022.1| 119 --GIPFMFTYHSTEWGRNGNkyGNWWEAEE-----------------ISHREwKAGYESVKVIST 164
                                   ..3*************99994322222222.................333332334444444444 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 !   35.6   0.0   3.4e-12   8.6e-09      11     110 ..      25     130 ..      20     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.4e-12
               Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg....pleyl...kafklkklikki.kPDvvhahya 83 
                                   +h+++la++Lak g+ Vh++t+++g + + e +g+h hr++ + +g    ++  +   ++ ++ ++ k+  k+D++hah  
  gi|91772330|ref|YP_565022.1|  25 PHVSELAEALAKTGHSVHIFTRNNGLEPYGEVNGVHYHRVDHSLSGgivqQMDSMcdsMYSRFLDVTKEYgKFDILHAHDW 105
                                   79**************************************98855553433333333145799999999648********9 PP

               Glyco_trans_4_2  84 kpygllgslaarlsgvipvvlsvwGld 110
                                    p + + ++   ++  ip+ ++ + + 
  gi|91772330|ref|YP_565022.1| 106 HPFNAVSRIKYEFG--IPFMFTYHSTE 130
                                   99998888855555..99999988665 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.3e-06    0.0058       5      89 ..     297     378 ..     290     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
               Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                   psr+e +  +++E   + ++++++da ++ + f +g  ++++++++++a  i+y+l ++   +++++a++e +++++++ +
  gi|91772330|ref|YP_565022.1| 297 PSRNEPFGIVVLEGWDAERTIVATDAVQIINNFVDG--ILVYKNPNSIAWGINYVL-DDLSNSSMRKAGKELIETRYNWLN 374
                                   8999**********************8899999999..***************987.5666699***************99 PP

               Glyco_trans_1_2  86 raeq 89 
                                    ae+
  gi|91772330|ref|YP_565022.1| 375 IAEN 378
                                   9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3475.29
//
Query:       gi|91772331|ref|YP_565023.1|  [L=867]
Description: S-layer-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-199  658.4  34.9   2.2e-103  344.8  12.6    3.0  3  S-layer   S-layer protein
      3e-06   27.4   1.1    1.6e-05   25.1   1.1    2.3  1  CARDB     CARDB
     0.0028   17.9   2.4       0.36   11.1   0.4    3.3  2  DUF4362   Domain of unknown function (DUF4362)
  ------ inclusion threshold ------
      0.011   16.1   2.0        5.5    7.3   0.0    4.0  4  DUF4198   Domain of unknown function (DUF4198)
      0.012   15.4   0.1       0.57   10.1   0.0    3.2  2  PEGA      PEGA domain
       0.13   12.1   0.1         23    4.9   0.0    2.7  2  A2M       Alpha-2-macroglobulin family
       0.15   11.4   3.8       0.41   10.0   0.1    3.0  4  DUF5462   Family of unknown function (DUF5462)
       0.69   10.4   6.5         33    5.0   0.2    5.0  6  CBM60     Ca-dependent carbohydrate-binding module xylan-bind


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 !  344.8  12.6  9.7e-107  2.2e-103       3     258 .]      38     291 ..      36     291 .. 0.98
   2 !  322.3   9.7  7.3e-100   1.6e-96       2     258 .]     313     563 ..     312     563 .. 0.98
   3 ?   -0.4   0.1      0.22   4.9e+02     135     158 ..     781     804 ..     771     836 .. 0.81

  Alignments for each domain:
  == domain 1  score: 344.8 bits;  conditional E-value: 9.7e-107
                       S-layer   3 neeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy 83 
                                   +e+++ e+twta+++sgfyydid+g+ssE+lt++l+s+sdr+i++g+lvYst+p+e++fe++ wgsY+vigf+ae+Yfagy
  gi|91772331|ref|YP_565023.1|  38 DENMTLEYTWTAQSYSGFYYDIDSGKSSETLTINLDSDSDRSIDDGDLVYSTKPIETDFEHNGWGSYQVIGFMAERYFAGY 118
                                   67788999****************************99******************************************* PP

                       S-layer  84 .dnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskads 163
                                    d+s++++ddvsl+s+++L+kvl+d+d++k++++gssl LeegY+l+i ++D+dg+kv+++Ltkdg++v+s++++s    +
  gi|91772331|ref|YP_565023.1| 119 tDDSDFVRDDVSLISEGQLAKVLTDDDDKKSFFAGSSLVLEEGYKLSIVEVDMDGNKVLVSLTKDGKQVESAILTS---RD 196
                                   877779**********************************************************************...** PP

                       S-layer 164 tyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemenddsitLsrdk 244
                                   +yvyekdlg+++dv+iiavh+de+frgte+++++++gifqisd+++e++ gd+fg+mev++vs nei men+d+i+Lsr+k
  gi|91772331|ref|YP_565023.1| 197 DYVYEKDLGSAEDVPIIAVHFDEIFRGTETNAIFVRGIFQISDQYVEVDGGDDFGRMEVQTVSANEISMENNDDISLSRGK 277
                                   ********************************************************************************* PP

                       S-layer 245 tieimddlkfkvaD 258
                                    i+im++lkf vaD
  gi|91772331|ref|YP_565023.1| 278 IISIMGKLKFIVAD 291
                                   *************8 PP

  == domain 2  score: 322.3 bits;  conditional E-value: 7.3e-100
                       S-layer   2 eneeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfag 82 
                                   ++++e+e++twt+ nF+gfyy+id+g+++Esl++   s +++tie+g+lvYst ++e++fe+ +wg+++v+gf+aekYfag
  gi|91772331|ref|YP_565023.1| 313 GTITEEENMTWTPLNFEGFYYNIDEGIGTESLEVV--SLDGKTIEKGDLVYSTVAEEVSFEYGQWGKFRVVGFMAEKYFAG 391
                                   578999****************************8..679***************************************** PP

                       S-layer  83 ydnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskads 163
                                   y ++   +ddvs+ls+++Lskvlid+d+++t+ +gssl LeegYe+ei ++D+ gdk++++L+k+g++vds+vi+s   + 
  gi|91772331|ref|YP_565023.1| 392 YPENR-FTDDVSMLSEGQLSKVLIDNDKKSTVVAGSSLVLEEGYEIEIVEVDISGDKILVTLMKNGKKVDSEVIKS---NA 468
                                   *6555.599*******************************************************************...** PP

                       S-layer 164 tyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemenddsitLsrdk 244
                                   + v ekdlg+++ v+ii+vh++e+frgte+++v+++g+fqis++++e+++gd+++kmevk++++++iemend+sitLsrdk
  gi|91772331|ref|YP_565023.1| 469 DLVFEKDLGSAESVPIIVVHFEEIFRGTETNAVFMKGMFQISEKFVEVNNGDSYDKMEVKRINSQMIEMENDKSITLSRDK 549
                                   ********************************************************************************* PP

                       S-layer 245 tieimddlkfkvaD 258
                                   ti im+d+++kvaD
  gi|91772331|ref|YP_565023.1| 550 TIPIMGDISLKVAD 563
                                   *************8 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.22
                       S-layer 135 vdgdkvwleLtkdgeevdskviss 158
                                   +d   v ++L  +ge vdsk ++ 
  gi|91772331|ref|YP_565023.1| 781 TDEGDVNVQLNINGEVVDSKSVTL 804
                                   688899*************98876 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   1.1   7.2e-09   1.6e-05       7      86 ..     756     832 ..     749     837 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.2e-09
                                   .EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEEST CS
                         CARDB   7 tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvDp 86 
                                   + +++p+e+ +ge++ti v v N+Gt+ +g+++v+l ++ge+v++ +v  L  +e++tv+ft t + ++ge+ +++ +++
  gi|91772331|ref|YP_565023.1| 756 NLIITPAEVGTGEAVTIMVDVMNTGTD-EGDVNVQLNINGEVVDSKSV-TLGVDEESTVEFTRTES-EAGEYLVQIGIES 832
                                   456799*******************95.79******************.8***************9.****999887776 PP

>> DUF4362  Domain of unknown function (DUF4362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.4   0.00016      0.36      31      70 ..     163     202 ..     118     213 .. 0.91
   2 ?    4.8   0.1     0.015        34      31      57 ..     435     461 ..     428     477 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                       DUF4362  31 kirivsyTeeGdpiledleydgkklkyilDnrrDefasde 70 
                                   k+ iv+   +G+ +l  l++dgk+++++  ++rD++  ++
  gi|91772331|ref|YP_565023.1| 163 KLSIVEVDMDGNKVLVSLTKDGKQVESAILTSRDDYVYEK 202
                                   678999******************************8543 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                       DUF4362  31 kirivsyTeeGdpiledleydgkklky 57 
                                   +i iv+  + Gd il +l ++gkk+ +
  gi|91772331|ref|YP_565023.1| 435 EIEIVEVDISGDKILVTLMKNGKKVDS 461
                                   799*******************99876 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.081   1.8e+02      36     165 ..     336     460 ..     310     475 .. 0.70
   2 ?    7.3   0.0    0.0025       5.5     144     210 ..     588     644 ..     583     647 .. 0.78
   3 ?    3.2   0.1     0.043        97     131     204 ..     650     726 ..     634     736 .. 0.67
   4 ?   -0.7   0.0      0.68   1.5e+03      19      89 ..     770     837 ..     757     845 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.081
                       DUF4198  36 heplkleklkvlapdg...ektdlgkylstfdvallkpekegtyklaaakkpgdwkeygdpklakevp.aeaaelkvvkys 112
                                    e +  e+l+v++ dg   ek+dl  y ++ + ++++  + g ++++ ++   ++  y + ++ ++v    + +l+ v + 
  gi|91772331|ref|YP_565023.1| 336 DEGIGTESLEVVSLDGktiEKGDLV-YSTVAEEVSFEYGQWGKFRVVGFMAEKYFAGYPENRFTDDVSmLSEGQLSKVLID 415
                                   3555556889999999766666666.5555555555556688999998888899999999996666663333336677777 PP

                       DUF4198 113 qyaktfvtvgkpsetwdkpvglglEivPlthpydlkageelevqvlldGkPla 165
                                   +  k+ v +g+    ++++ g+++Eiv      d+ +g+++ v+++ +Gk + 
  gi|91772331|ref|YP_565023.1| 416 NDKKSTVVAGSS--LVLEE-GYEIEIVE----VDI-SGDKILVTLMKNGKKVD 460
                                   777777777765..55553.88899986....344.69999999999999876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
                       DUF4198 144 pydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleae 210
                                   p+ l++g+++ ++v+++G  +++a ve+        ++ +     t ++G +++++++ G++ ++ae
  gi|91772331|ref|YP_565023.1| 588 PSVLVQGDSIDIKVTFRGATVSEALVEFDG------KEVG----LTSDEGMISYRPTRLGTFSVSAE 644
                                   8889******************99999632......2333....57778888888888888877776 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.043
                       DUF4198 131 pvglglEivPlthpydlkageelevqvlldGkPlagaeveveyggtryrdapdeikv.....ktdadGvvtftlpkaGl 204
                                    + +++E +  ++ +  +a e+ +++v+++G   +  +++++ ++   + +++  +       t a+G  +f++ ++G+
  gi|91772331|ref|YP_565023.1| 650 SADKEVEVISTDDVTRKVAIEVTPFEVVYEGDTITISTIKAIGADP--VAEAQILYDgvsigNTSAKGTLSFKVIESGV 726
                                   36788999999999999999999********988877777765432..2222222224556777777777777777765 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.68
                       DUF4198  19 ewvtvdlafghdpfeadheplklekl.kvlapdgektdlg.kylstfdvallkpekegtyklaaakkpgdwke 89 
                                    ++ vd++ +    e+d + ++l+   +v++ +  +++lg +++st++++++ ++++g y ++   ++g+++ 
  gi|91772331|ref|YP_565023.1| 770 VTIMVDVMNTG-TDEGD-VNVQLNINgEVVDSK--SVTLGvDEESTVEFTRT-ESEAGEYLVQIGIESGTYTV 837
                                   44555555554.33444.444444333666666..45555588899998884.56679999998877787775 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.57      11      67 ..     609     670 ..     605     673 .. 0.82
   2 ?    1.3   0.0      0.15   3.3e+02      11      44 ..     697     735 ..     690     749 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                          PEGA  11 eGatVyidGkylG....kTPvtls.leaGnyslrvekeGYedlektvtvtagetvklnltLe 67 
                                   ++a V +dGk++G    +  +++     G+ s+  eke ++ + k+v+v +++ v++++ +e
  gi|91772331|ref|YP_565023.1| 609 SEALVEFDGKEVGltsdEGMISYRpTRLGTFSVSAEKEEFASADKEVEVISTDDVTRKVAIE 670
                                   7899*********444444477777889*********************9998888887765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                          PEGA  11 eGatVyidGkylGkTP....vtls.leaGnyslrvekeG 44 
                                   ++a++  dG+++G+T     ++   +e+G ++++ + eG
  gi|91772331|ref|YP_565023.1| 697 AEAQILYDGVSIGNTSakgtLSFKvIESGVHKITSQSEG 735
                                   578999999999977511114566678888888877777 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.019        42      58      77 ..     583     602 ..     573     614 .. 0.88
   2 ?    4.9   0.0      0.01        23      62      92 .]     760     790 ..     756     790 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                                   EEEE--SEEETTSEEEEEEE CS
                           A2M  58 vdlnlPysvrrgeqveikav 77 
                                   +++++P+ +++g+++ ik++
  gi|91772331|ref|YP_565023.1| 583 LTIEMPSVLVQGDSIDIKVT 602
                                   7899**************98 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                                   --SEEETTSEEEEEEEEEE-SSS-EEEEEEE CS
                           A2M  62 lPysvrrgeqveikavvfNyldkeikvrvel 92 
                                    P  v  ge v+i + v+N  ++e +v+v+l
  gi|91772331|ref|YP_565023.1| 760 TPAEVGTGEAVTIMVDVMNTGTDEGDVNVQL 790
                                   5999*******************99999986 PP

>> DUF5462  Family of unknown function (DUF5462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.12   2.8e+02      98     122 ..     167     191 ..     153     199 .. 0.78
   2 ?   -2.8   0.1       1.6   3.6e+03      96     114 ..     448     466 ..     438     473 .. 0.67
   3 ?   -3.4   0.0       2.4   5.4e+03      99     120 ..     589     610 ..     576     626 .. 0.63
   4 ?   10.0   0.1   0.00018      0.41      59     115 ..     753     810 ..     747     819 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                       DUF5462  98 veLvvdgkkvsisvkqrgedvvitv 122
                                   ve+ +dg kv +s ++ g++v+ ++
  gi|91772331|ref|YP_565023.1| 167 VEVDMDGNKVLVSLTKDGKQVESAI 191
                                   7788899999999999999887655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                       DUF5462  96 lkveLvvdgkkvsisvkqr 114
                                   + v+L+ +gkkv  +v ++
  gi|91772331|ref|YP_565023.1| 448 ILVTLMKNGKKVDSEVIKS 466
                                   4577777777776665555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.4
                       DUF5462  99 eLvvdgkkvsisvkqrgedvvi 120
                                   ++ v g  + i+v+ rg++v+ 
  gi|91772331|ref|YP_565023.1| 589 SVLVQGDSIDIKVTFRGATVSE 610
                                   4667777777777777777754 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00018
                       DUF5462  59 llksLvirnAelrkasggevlvtvketlpdgsearvtlkve.Lvvdgkkvsisvkqrg 115
                                    l++L+i  Ae+ + +  +++v v +t  d+++++v+l+++  vvd+k v++ v +++
  gi|91772331|ref|YP_565023.1| 753 ELSNLIITPAEVGTGEAVTIMVDVMNTGTDEGDVNVQLNINgEVVDSKSVTLGVDEES 810
                                   5789***********************************973689******9988765 PP

>> CBM60  Ca-dependent carbohydrate-binding module xylan-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   2.4e+02      13      58 ..     173     218 ..     166     226 .. 0.80
   2 ?   -1.4   0.0       1.5   3.3e+03      20      43 ..     347     371 ..     340     374 .. 0.80
   3 ?   -3.9   0.0         8   1.8e+04      18      31 ..     450     463 ..     442     483 .. 0.64
   4 ?   -1.4   0.0       1.5   3.3e+03       4      46 ..     601     645 ..     598     670 .. 0.52
   5 ?    1.7   0.0      0.16   3.5e+02      11      35 ..     692     716 ..     682     729 .. 0.71
   6 ?    5.0   0.2     0.015        33       3      46 ..     773     818 ..     771     838 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                         CBM60  13 deppefrllvdGqkvgeadvasteaktytftadltagahklqiryl 58 
                                   ++++ + l  dG++v++a ++s++   y+ ++  +++   + ++++
  gi|91772331|ref|YP_565023.1| 173 GNKVLVSLTKDGKQVESAILTSRDDYVYEKDLGSAEDVPIIAVHFD 218
                                   4567889999*********888888888877777788778888887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                         CBM60  20 llvdGqkvgead.vasteaktytft 43 
                                   + +dG++++++d v st a++++f+
  gi|91772331|ref|YP_565023.1| 347 VSLDGKTIEKGDlVYSTVAEEVSFE 371
                                   5899999999998888888887776 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 8
                         CBM60  18 frllvdGqkvgead 31 
                                   ++l+ +G+kv +  
  gi|91772331|ref|YP_565023.1| 450 VTLMKNGKKVDSEV 463
                                   67888888887433 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.5
                         CBM60   4 VrAagdqagdeppefrllvdGqkvg......eadvasteaktytftadl 46 
                                   V  +g++  +      +  dG++vg       ++ + t   t++++a+ 
  gi|91772331|ref|YP_565023.1| 601 VTFRGATVSE----ALVEFDGKEVGltsdegMISYRPTRLGTFSVSAEK 645
                                   5555555544....55677999999777755333444444444444443 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.16
                         CBM60  11 agdeppefrllvdGqkvgeadvast 35 
                                     d  +e ++l+dG+ +g++++++t
  gi|91772331|ref|YP_565023.1| 692 GADPVAEAQILYDGVSIGNTSAKGT 716
                                   33445799**********9985543 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.015
                         CBM60   3 vVrAagdqagdeppefrllvdGqkvg..eadvasteaktytftadl 46 
                                    V +  +  ++  ++++l ++G++v   ++++  +e  t++ft + 
  gi|91772331|ref|YP_565023.1| 773 MVDVMNTGTDEGDVNVQLNINGEVVDskSVTLGVDEESTVEFTRTE 818
                                   55555555544459***********966333333444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (867 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 5810.11
//
Query:       gi|91772332|ref|YP_565024.1|  [L=306]
Description: TM helix protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-24   85.2  25.4    5.9e-11   42.2   1.3    5.0  5  TM_helix  Conserved TM helix


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   4.0   2.9e-12   5.2e-08       6      49 ..      13      56 ..       8      57 .. 0.94
   2 ?   -2.0   1.5       0.2   3.6e+03       6      24 ..      77      95 ..      75      97 .. 0.77
   3 !   36.2   5.0   2.4e-13   4.3e-09       2      49 ..     102     149 ..     101     150 .. 0.97
   4 ?   -3.7   3.8      0.69   1.2e+04      18      30 ..     170     182 ..     170     190 .. 0.82
   5 !   42.2   1.3   3.3e-15   5.9e-11       1      48 [.     194     241 ..     194     243 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.9e-12
                                  XXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                      TM_helix  6 llnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49
                                  + +++++f+P L++ i++ +vG +++k   ++  k+l+k+g+dd
  gi|91772332|ref|YP_565024.1| 13 IMDQFIAFIPILIAVIVLMIVGKFVGKAFGKIGAKILDKIGLDD 56
                                  679****************************************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.2
                                  XXHHHHTTHSHHHHHHHHH CS
                      TM_helix  6 llnellsflPnLvgAilIL 24
                                  + + ++   + ++ A++I 
  gi|91772332|ref|YP_565024.1| 77 MFDGIIRWFIYIIFAVIII 95
                                  6777888888899999985 PP

  == domain 3  score: 36.2 bits;  conditional E-value: 2.4e-13
                                   XXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                      TM_helix   2 plnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49 
                                    + n+l++++ flP +  A++ L++G++i  f+  l++k+  ++gid+
  gi|91772332|ref|YP_565024.1| 102 IVANFLTQIILFLPLIASALITLVIGLLIVDFLVELIKKVAMASGIDE 149
                                   689********************************************7 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 0.69
                                   HHHHHHHHHHHHH CS
                      TM_helix  18 vgAilILlvGwii 30 
                                   ++A +I + G+ii
  gi|91772332|ref|YP_565024.1| 170 IIAGIIKAFGYII 182
                                   6789999999998 PP

  == domain 5  score: 42.2 bits;  conditional E-value: 3.3e-15
                                   XXXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS- CS
                      TM_helix   1 nplnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgid 48 
                                   n ++n+l ++l+++PnL++  lIL+vG++ + f+++ ++ +++ + ++
  gi|91772332|ref|YP_565024.1| 194 NVVSNFLVSILNYIPNLFAGMLILVVGLLAIDFLTDYLKGIMEGMEVE 241
                                   579****************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); 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:                         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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2145.47
//
Query:       gi|91772333|ref|YP_565025.1|  [L=260]
Description: hypothetical protein Mbur_0270 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-06   26.7  20.8        1.5    9.5   0.1    5.9  6  DUF883           Bacterial protein of unknown function (DUF88
    3.5e-05   23.9  17.6      0.026   14.5   0.7    3.8  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    9.9e-05   22.3  11.5     0.0033   17.3   6.0    2.5  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
    0.00071   19.5   0.8        2.3    8.2   0.0    3.5  3  T2SSF            Type II secretion system (T2SS), protein F
      0.002   18.2  20.1       0.23   11.5   4.0    3.6  4  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
     0.0078   16.2  16.9        1.1    9.3   0.2    3.5  3  NYD-SP28         Sperm tail
     0.0086   16.8   5.8       0.19   12.5   0.3    3.5  3  Occludin_ELL     Occludin homology domain
  ------ inclusion threshold ------
      0.011   16.2  26.8        4.5    7.9   0.7    5.9  3  YtxH             YtxH-like protein
      0.033   13.9   0.7        1.9    8.2   0.1    2.8  2  Peptidase_M9_N   Peptidase family M9 N-terminal
      0.079   13.3  22.8        1.2    9.5   1.3    4.8  4  Syntaxin_2       Syntaxin-like protein
       0.12   13.1  11.8        1.6    9.4   0.2    4.1  4  Cytochrom_B562   Cytochrome b562
       0.14   12.3   0.1         25    5.1   0.0    3.6  4  DprA_WH          DprA winged helix domain
       0.24   11.3   6.7        2.2    8.3   0.2    4.0  4  GnsAB_toxin      GnsA/GnsB toxin of bacterial toxin-antitoxin
       0.71    9.2   8.8       0.32   10.4   0.4    2.8  3  ZYG-11_interact  Interactor of ZYG-11
        1.4    8.5  14.5        4.7    6.7   1.3    4.0  4  Fzo_mitofusin    fzo-like conserved region
        2.4    8.2  15.8         11    6.0   0.2    4.1  4  DUF1451          Zinc-ribbon containing domain
        2.7    8.4  18.9        8.1    6.9   1.1    4.8  6  V-SNARE          Vesicle transport v-SNARE protein N-terminus
        2.8    6.4  14.6        1.4    7.4   4.7    2.4  2  Zw10             Centromere/kinetochore Zw10
        5.3    7.2   9.9        1.4    9.0   2.4    2.9  3  ASL_C            Adenylosuccinate lyase C-terminal
        5.5    6.6   5.8        2.6    7.7   0.2    3.2  3  YvrJ             YvrJ protein family
        7.4    7.2  11.8         34    5.1   0.2    4.2  4  Syntaxin-6_N     Syntaxin 6, N-terminal


Domain annotation for each model (and alignments):
>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.5    0.0019       1.6       4      44 ..       2      42 ..       1      43 [. 0.86
   2 ?    6.4   0.2     0.016        14       3      39 ..      46      82 ..      44      87 .. 0.90
   3 ?    5.8   0.3     0.025        21       3      44 ..      88     129 ..      86     131 .. 0.89
   4 ?    5.3   0.0     0.035        30       2      35 ..     132     165 ..     131     169 .. 0.89
   5 ?    2.0   0.0      0.39   3.3e+02       3      38 ..     175     210 ..     173     217 .. 0.73
   6 !    9.5   0.1    0.0018       1.5       2      42 ..     219     259 ..     218     260 .] 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                        DUF883  4 eaeleslladleellkeaadeageeaeelRerleerlerar 44
                                  e+ le++ +d+++l++++++ea+   e+++ rl++ +++++
  gi|91772333|ref|YP_565025.1|  2 EKLLEEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLK 42
                                  56789999999999999999999999999999999888765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.016
                        DUF883  3 leaeleslladleellkeaadeageeaeelRerleer 39
                                  ++ae+++l  ++++l+++++++a+  a+e+++++++ 
  gi|91772333|ref|YP_565025.1| 46 IKAEVKKLGVKVDQLVDRTGSSAKMLASEVKQEITAI 82
                                  789****************************999875 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.025
                        DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlerar 44 
                                   l++ +++l  dl+el+ ++++ea +   ++++ +++ +++++
  gi|91772333|ref|YP_565025.1|  88 LHKHMDDLSRDLDELAVKTGSEATKLGTKVKQDMRSLASSVK 129
                                   6778999************************99999888776 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.035
                        DUF883   2 eleaeleslladleellkeaadeageeaeelRer 35 
                                   ++++e+++++a +++l++++++ a+   +e++++
  gi|91772333|ref|YP_565025.1| 132 DIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKDE 165
                                   5789******************999999988876 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.39
                        DUF883   3 leaeleslladleellkeaadeageeaeelRerlee 38 
                                   l++ le l ++++el+ e+++ea +   +++e++++
  gi|91772333|ref|YP_565025.1| 175 LNNRLEILSNSINELAVETGSEASKLGMNVKEEMKS 210
                                   556677888888888888888888888888877665 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0018
                        DUF883   2 eleaeleslladleellkeaadeageeaeelRerleerler 42 
                                   ++++e+e++++++e l+++++++a++ a e+ e +++ l++
  gi|91772333|ref|YP_565025.1| 219 DIKEEIEAIISKVERLVDSTGESAKKLAIEINEDIKNLLKK 259
                                   5799************************9999999988875 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 !    9.2   1.1    0.0014       1.2      55      95 ..       2      42 ..       1      62 [. 0.89
   2 !   14.5   0.7   3.1e-05     0.026      19     108 ..      73     158 ..      45     164 .. 0.68
   3 !    8.0   3.7    0.0033       2.8      29     101 ..     170     238 ..     160     260 .] 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                  Baculo_PEP_C 55 ksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsilt 95
                                  ++ll+e+++++d+l++n  +  + l+++++++L+++ ++l 
  gi|91772333|ref|YP_565025.1|  2 EKLLEEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLK 42
                                  78999*******************************99986 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.1e-05
                  Baculo_PEP_C  19 tnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLls 99 
                                   ++v + i + +  i  +l + +d++ + L++l+ +  s  ++l t++++ +  L ++++++   +r+e++n+ + +  L  
  gi|91772333|ref|YP_565025.1|  73 SEVKQEITAITDRI--ALHKHMDDLSRDLDELAVKTGSEATKLGTKVKQDMRSLASSVKSID--IRKEIDNIIARVDKLID 149
                                   44444444444445..6777777777777777777777777777788888888888888887..89999999888888888 PP

                  Baculo_PEP_C 100 svtNinstL 108
                                   s +   +tL
  gi|91772333|ref|YP_565025.1| 150 STGEAAKTL 158
                                   877777776 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0033
                  Baculo_PEP_C  29 nvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssv 101
                                   n+ i  +l++ l+ + +++n+l+ +  s  ++l  ++++ ++ ++d+++++   +++e++++ s++  L+ s 
  gi|91772333|ref|YP_565025.1| 170 NSRI--DLNNRLEILSNSINELAVETGSEASKLGMNVKEEMKSISDSIKSID--IKEEIEAIISKVERLVDST 238
                                   4445..6677777777777777777777777777777777777777777776..7777777777777776554 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   6.0   3.9e-06    0.0033      46     165 ..       1     123 [.       1     132 [. 0.74
   2 !    7.7   0.2    0.0035         3       6     108 ..     137     238 ..     132     260 .] 0.52

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
                                   HHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHH.CHHCCHHCHCCHCHHHHHHHHHH....HHHHHHHHCH CS
                Apolipoprotein  46 leevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaa.daeelqeqlavyaeelrerlerh....vealkarlap 121
                                   +e + + + +++d + e+ g++++ l++++++ ++ +++ l+  ++++  ++l v+ ++l +r+ ++    ++++k+ +++
  gi|91772333|ref|YP_565025.1|   1 MEKLLEEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLKYiNIKAEVKKLGVKVDQLVDRTGSSakmlASEVKQEITA 81 
                                   799999*********************************666666666666666666666666666666669999999999 PP

                                   HHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-T CS
                Apolipoprotein 122 yveelrqklaerleelkeslaphaeeveerlssrveelreklee 165
                                   +++++   l++++++l++ l++ a + ++++++  + +++ +  
  gi|91772333|ref|YP_565025.1|  82 ITDRIA--LHKHMDDLSRDLDELAVKTGSEATKLGTKVKQDMRS 123
                                   999998..789999999988888766664444444444444433 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                                   CCCHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHH CS
                Apolipoprotein   6 ldelkayaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerl 86 
                                   +d++ a++++l +  +++a++l   + +el  +  r+  +l++  + l++ ++e+  + g+++ +l   +++  + + +++
  gi|91772333|ref|YP_565025.1| 137 IDNIIARVDKLIDSTGEAAKTLGSEIKDELVLINSRI--DLNNRLEILSNSINELAVETGSEASKLGMNVKEEMKSISDSI 215
                                   5566666666666666666666666666666666666..666666666666666666666666666666666555555544 PP

                                   HH.CHHCCHHCHCCHCHHHHHHH CS
                Apolipoprotein  87 aa.daeelqeqlavyaeelrerl 108
                                   +  d++e  e++ ++ e l +++
  gi|91772333|ref|YP_565025.1| 216 KSiDIKEEIEAIISKVERLVDST 238
                                   43333333333333333333333 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.65   5.5e+02      12      46 ..      54      90 ..      50     115 .. 0.73
   2 !    8.2   0.0    0.0027       2.3      12      65 ..     114     167 ..     104     181 .. 0.79
   3 !    6.5   0.0    0.0092       7.8       8      46 ..     197     235 ..     190     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.65
                                  T--HHHHHHHHHHHHS..SHHHHHHHHHHHHHHHTTS CS
                         T2SSF 12 GvplveaLellaeeae..ngplaeelkriarrlraGg 46
                                  Gv +++ +++ +++a+    ++++e+ +i +r++  +
  gi|91772333|ref|YP_565025.1| 54 GVKVDQLVDRTGSSAKmlASEVKQEITAITDRIALHK 90
                                  7777777777777777778888899999988888766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                                   T--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHCT-TT.TS-HHHH CS
                         T2SSF  12 GvplveaLellaeeaengplaeelkriarrlraGgslsealertpssefpelvv 65 
                                   G  + + +++la++ +++ +++e+++i++r++  ++     ++t  se+++ +v
  gi|91772333|ref|YP_565025.1| 114 GTKVKQDMRSLASSVKSIDIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKDELV 167
                                   5666777999************************97764444444458866555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0092
                                   HHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS CS
                         T2SSF   8 llsaGvplveaLellaeeaengplaeelkriarrlraGg 46 
                                   +++ G+++ e +++++++ +++ ++ee+++i+ +++   
  gi|91772333|ref|YP_565025.1| 197 ASKLGMNVKEEMKSISDSIKSIDIKEEIEAIISKVERLV 235
                                   5678*****************************998765 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 !   11.5   4.0   0.00027      0.23      40     122 ..       7      87 ..       1     103 [. 0.80
   2 !    7.1   0.2    0.0062       5.3      41     117 ..      95     169 ..      88     176 .. 0.80
   3 ?    4.3   1.9     0.045        38      27      94 ..     133     206 ..     110     217 .. 0.52
   4 !    9.0   3.1    0.0016       1.4      36     117 ..     177     256 ..     170     260 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                     ApoLp-III  40 qvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakek 120
                                   ++ + ++  + ++ +e++ + + +k+ ++ +a++l+    ++k ++++l  kv + v  + ++++ la+++k+++ ++++ 
  gi|91772333|ref|YP_565025.1|   7 EINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLKY--INIKAEVKKLGVKVDQLVDRTGSSAKMLASEVKQEITAITDR 85 
                                   44445555555556666666677999*********99..899**********************************99998 PP

                     ApoLp-III 121 la 122
                                   +a
  gi|91772333|ref|YP_565025.1|  86 IA 87 
                                   75 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0062
                     ApoLp-III  41 vikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqea 117
                                   ++  l+e + k+ +e++++ + vk+++   a ++++   ++ k++++  + v + + s+ + +++l++++k++   +
  gi|91772333|ref|YP_565025.1|  95 LSRDLDELAVKTGSEATKLGTKVKQDMRSLASSVKS--IDIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKDELVLI 169
                                   566677777788889999999999999999999888..889999999999999999999999999999999887655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.045
                     ApoLp-III  27 iKensenlvdqlkqvikslqeelkkksdeleealk......evkkkieetadklseenPevkkkaqelqekvQs 94 
                                   i+++ +n++ ++ ++i+s+ e++k+  +e++  l       ++++ +e   ++++e   e+  +a++l  +v +
  gi|91772333|ref|YP_565025.1| 133 IRKEIDNIIARVDKLIDSTGEAAKTLGSEIKDELVlinsriDLNNRLEILSNSINELAVETGSEASKLGMNVKE 206
                                   55666666777777777777777775555554332111111344444444444444444444444444444444 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0016
                     ApoLp-III  36 dqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqe 116
                                   ++l+ +++s++e + ++ +e+ ++  +vk++++ + d++++   ++k+++++  +kv   v s+ ++++kla +++e++++
  gi|91772333|ref|YP_565025.1| 177 NRLEILSNSINELAVETGSEASKLGMNVKEEMKSISDSIKS--IDIKEEIEAIISKVERLVDSTGESAKKLAIEINEDIKN 255
                                   56777788888888899999999999999999999999998..89999999999999999999999999999999998876 PP

                     ApoLp-III 117 a 117
                                    
  gi|91772333|ref|YP_565025.1| 256 L 256
                                   5 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   2.2    0.0031       2.7      14      86 ..       6      78 ..       2      95 .. 0.88
   2 !    9.3   0.2    0.0013       1.1      29      85 ..     108     164 ..      83     166 .. 0.81
   3 !    7.1   2.7    0.0062       5.3      36      85 ..     202     251 ..     170     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0031
                      NYD-SP28 14 eelrqerkekleeeaksseekfeeinekWreilrknkpqeLrkeleeqkqaceelideKdklikelqeeLkek 86
                                  ee++q   +  e+  ++++  +e+i+ + +++ +  k   +++e++++  + ++l+d+  +  k+l  e+k+ 
  gi|91772333|ref|YP_565025.1|  6 EEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLKYINIKAEVKKLGVKVDQLVDRTGSSAKMLASEVKQE 78
                                  677888888889999999999**************************************99999999998874 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0013
                      NYD-SP28  29 ksseekfeeinekWreilrknkpqeLrkeleeqkqaceelideKdklikelqeeLke 85 
                                   +++ +   ++++ +r++    k+ ++rke+++  ++ ++lid+  +  k+l  e+k+
  gi|91772333|ref|YP_565025.1| 108 SEATKLGTKVKQDMRSLASSVKSIDIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKD 164
                                   4555556789999*******************************9999999999986 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0062
                      NYD-SP28  36 eeinekWreilrknkpqeLrkeleeqkqaceelideKdklikelqeeLke 85 
                                    +++e++++i +  k+ ++++e+e   ++ e+l+d+  +  k+l  e++e
  gi|91772333|ref|YP_565025.1| 202 MNVKEEMKSISDSIKSIDIKEEIEAIISKVERLVDSTGESAKKLAIEINE 251
                                   57899999***************************998888888777765 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.3   0.00022      0.19      37      91 ..       4      59 ..       1      68 [. 0.88
   2 ?    3.4   0.1      0.14   1.2e+02      27      69 ..      88     124 ..      74     174 .. 0.59
   3 ?    2.4   0.1      0.31   2.6e+02      34      88 ..     175     230 ..     168     243 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                  Occludin_ELL 37 kfseLerelkelkegsk.eykkieeeilqeykklkkdpeyqekkkrceyLkekLsh 91
                                   ++e+++++++l+e++  e k ++e+i  +++++ kd +y + k+++++L  k + 
  gi|91772333|ref|YP_565025.1|  4 LLEEINQDVDKLAENTGeEAKVLNEKIKTRLNSVAKDLKYINIKAEVKKLGVKVDQ 59
                                  5778999999**9999978888999************************9888665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                  Occludin_ELL  27 lhaeleevskkfseLerelkelkegsk.eykkieeeilqeykkl 69 
                                   lh++++++s+++ eL  ++         e +k+  ++ q+ ++l
  gi|91772333|ref|YP_565025.1|  88 LHKHMDDLSRDLDELAVKT-------GsEATKLGTKVKQDMRSL 124
                                   6666666666666666333.......223333333333333322 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.31
                  Occludin_ELL  34 vskkfseLerelkelkegsk.eykkieeeilqeykklkkdpeyqekkkrceyLkek 88 
                                   ++++++ L++ ++el+ ++  e +k+  ++ +e k+++ + +  + k+++e + +k
  gi|91772333|ref|YP_565025.1| 175 LNNRLEILSNSINELAVETGsEASKLGMNVKEEMKSISDSIKSIDIKEEIEAIISK 230
                                   56667777777777776666677777777777777777777777777666666655 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.087        74      29      62 ..     132     165 ..     131     167 .. 0.88
   2 ?    6.4   0.1     0.015        13      27      74 ..     172     215 ..     170     217 .. 0.67
   3 ?    7.9   0.7    0.0053       4.5      29      68 ..     219     258 ..     218     260 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.087
                          YtxH  29 dlkekaddlkekakelleeakekakekaedlkek 62 
                                   d++++ d++  ++++l++++ e ak  ++++k++
  gi|91772333|ref|YP_565025.1| 132 DIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKDE 165
                                   7899999999999999999999999999999886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                          YtxH  27 Rkdlkekaddlkekakelleeakekakekaedlkekvkekadelkekv 74 
                                   R dl+++++ l+++++el+ e+     ++a++l  +vke+ +++++++
  gi|91772333|ref|YP_565025.1| 172 RIDLNNRLEILSNSINELAVET----GSEASKLGMNVKEEMKSISDSI 215
                                   6689999999999999998888....4555555555555555555544 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0053
                          YtxH  29 dlkekaddlkekakelleeakekakekaedlkekvkekad 68 
                                   d+ke+ +++  k+++l++++ e ak+ a ++ e++k+  +
  gi|91772333|ref|YP_565025.1| 219 DIKEEIEAIISKVERLVDSTGESAKKLAIEINEDIKNLLK 258
                                   89******************99998888888888887554 PP

>> Peptidase_M9_N  Peptidase family M9 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0022       1.9      94     142 ..     111     159 ..      64     166 .. 0.94
   2 ?    3.1   0.1      0.08        69      94     140 ..     198     244 ..     190     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0022
                Peptidase_M9_N  94 salsqavaqaldaflanpnakdvtdeqgevlaelliliDsakqnaetls 142
                                   ++l ++v+q + +++ + ++ d  +e ++++a + +liDs+ ++a+tl 
  gi|91772333|ref|YP_565025.1| 111 TKLGTKVKQDMRSLASSVKSIDIRKEIDNIIARVDKLIDSTGEAAKTLG 159
                                   57889999************************************99986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.08
                Peptidase_M9_N  94 salsqavaqaldaflanpnakdvtdeqgevlaelliliDsakqnaet 140
                                   s+l  +v++ ++++  + ++ d ++e + +++ +  l+Ds+ + a+ 
  gi|91772333|ref|YP_565025.1| 198 SKLGMNVKEEMKSISDSIKSIDIKEEIEAIISKVERLVDSTGESAKK 244
                                   6778899999999***************************9998875 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   8.5       1.8   1.5e+03      14      14 ..      45      45 ..       1     136 [. 0.51
   2 ?    7.4   2.5    0.0066       5.6       7      63 ..     116     172 ..     109     192 .. 0.58
   3 ?    5.1   1.5     0.035        30       4      59 ..     140     203 ..     137     216 .. 0.76
   4 ?    9.5   1.3    0.0015       1.2      14      62 ..     203     251 ..     195     260 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                    Syntaxin_2 14 t 14
                                  +
  gi|91772333|ref|YP_565025.1| 45 N 45
                                  1 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0066
                    Syntaxin_2   7 kinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnss 63 
                                   k+ + +++l + vk++  +k+ +++  ++++li+++ e +k+  + +k+   l+ns 
  gi|91772333|ref|YP_565025.1| 116 KVKQDMRSLASSVKSIDIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKDELVLINSR 172
                                   445556666666666666666666666666666666666666666666655555554 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.035
                    Syntaxin_2   4 nlqkinsnvstleklvkqLgtk.kd.......teelreklhelieeinelikktnellkklsql 59 
                                    + ++ +++ + ++  k+Lg+  kd         +l+++l+ l ++inel+ +t +  +kl  +
  gi|91772333|ref|YP_565025.1| 140 IIARVDKLIDSTGEAAKTLGSEiKDelvlinsRIDLNNRLEILSNSINELAVETGSEASKLGMN 203
                                   5667777888888888999998756677776688888999999999999999998888887654 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0015
                    Syntaxin_2  14 tleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldns 62 
                                   + ++ +k+++++  + +++e+++ +i+++ +l+  t e+ kkl+  +n 
  gi|91772333|ref|YP_565025.1| 203 NVKEEMKSISDSIKSIDIKEEIEAIISKVERLVDSTGESAKKLAIEINE 251
                                   567788999999999***************************9986665 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.7       0.4   3.5e+02      61      92 ..       1      32 [.       1      42 [. 0.90
   2 ?   -0.4   0.0       2.1   1.8e+03       2      20 ..      88     106 ..      87     115 .. 0.73
   3 ?    6.3   0.0     0.018        16       2      49 ..     117     164 ..     116     192 .. 0.86
   4 ?    9.4   0.2    0.0019       1.6       1      48 [.     203     250 ..     203     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.4
                Cytochrom_B562 61 ldklidqldkaealakagkleeakaalkelkd 92
                                  ++kl++++++   +++++  eeak + +++k+
  gi|91772333|ref|YP_565025.1|  1 MEKLLEEINQDVDKLAENTGEEAKVLNEKIKT 32
                                  8999****999999999*******99999986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                Cytochrom_B562   2 lkeeMkqmkkalkqvakad 20 
                                   l+++M+++++ l ++a  +
  gi|91772333|ref|YP_565025.1|  88 LHKHMDDLSRDLDELAVKT 106
                                   7899999999888887444 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.018
                Cytochrom_B562   2 lkeeMkqmkkalkqvakaddaeelkkalkelraaaedakeatpsklek 49 
                                   +k++M +++ ++k++   ++++++ + +++l+    +a ++  s++++
  gi|91772333|ref|YP_565025.1| 117 VKQDMRSLASSVKSIDIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKD 164
                                   89*****************************99999999888777775 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0019
                Cytochrom_B562   1 dlkeeMkqmkkalkqvakaddaeelkkalkelraaaedakeatpskle 48 
                                   ++keeMk++++++k++   +++e++ +++++l     ++ ++ + +++
  gi|91772333|ref|YP_565025.1| 203 NVKEEMKSISDSIKSIDIKEEIEAIISKVERLVDSTGESAKKLAIEIN 250
                                   69*****************************99888777777665555 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.1   9.6e+02      21      42 ..       5      26 ..       3      28 .. 0.74
   2 ?    5.1   0.0     0.029        25      26      44 ..      55      73 ..      50      75 .. 0.88
   3 ?    1.4   0.0      0.41   3.5e+02      19      40 ..      90     111 ..      76     115 .. 0.72
   4 ?   -2.1   0.0       4.9   4.2e+03      27      42 ..     143     158 ..     135     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                       DprA_WH 21 LgpePvhvDqLvrrtglpaaev 42
                                  L+     vD L++ tg +a ++
  gi|91772333|ref|YP_565025.1|  5 LEEINQDVDKLAENTGEEAKVL 26
                                  5556668999999999888766 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.029
                       DprA_WH 26 vhvDqLvrrtglpaaevsa 44
                                  v vDqLv rtg +a  +++
  gi|91772333|ref|YP_565025.1| 55 VKVDQLVDRTGSSAKMLAS 73
                                  789********99988776 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.41
                       DprA_WH  19 aaLgpePvhvDqLvrrtglpaa 40 
                                    ++   ++ +D+L+ +tg +a 
  gi|91772333|ref|YP_565025.1|  90 KHMDDLSRDLDELAVKTGSEAT 111
                                   5556667889999999997765 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.9
                       DprA_WH  27 hvDqLvrrtglpaaev 42 
                                    vD L+  tg  a ++
  gi|91772333|ref|YP_565025.1| 143 RVDKLIDSTGEAAKTL 158
                                   5788888887766655 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 ?   -0.0   0.1         1   8.6e+02      18      33 ..       8      23 ..       2      27 .. 0.83
   2 ?    3.3   0.0      0.09        77      19      48 ..      96     125 ..      89     130 .. 0.82
   3 ?    8.3   0.2    0.0025       2.2      17      46 ..     181     210 ..     177     221 .. 0.89
   4 ?   -1.0   0.1         2   1.7e+03      12      31 ..     222     240 ..     215     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1
                                  HHHHHHHHHHHHSSEE CS
                   GnsAB_toxin 18 iakKiaELkKkTGkEV 33
                                  i + +  L  +TG E 
  gi|91772333|ref|YP_565025.1|  8 INQDVDKLAENTGEEA 23
                                  889999999****995 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                                   HHHHHHHHHHHSSEEEEEEEEEEEETTEEE CS
                   GnsAB_toxin  19 akKiaELkKkTGkEVseieFtaREkmtGLE 48 
                                   ++ + EL  kTG E +++    +  m+ L 
  gi|91772333|ref|YP_565025.1|  96 SRDLDELAVKTGSEATKLGTKVKQDMRSLA 125
                                   667789**********99888888887775 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHHHHSSEEEEEEEEEEEETTE CS
                   GnsAB_toxin  17 liakKiaELkKkTGkEVseieFtaREkmtG 46 
                                    ++  i EL  +TG E s++    +E m+ 
  gi|91772333|ref|YP_565025.1| 181 ILSNSINELAVETGSEASKLGMNVKEEMKS 210
                                   578899**********************96 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHHHHSS CS
                   GnsAB_toxin  12 eeiaeliakKiaELkKkTGk 31 
                                   eei + i+ K+  L   TG 
  gi|91772333|ref|YP_565025.1| 222 EEIEAIIS-KVERLVDSTGE 240
                                   67777666.57777777775 PP

>> ZYG-11_interact  Interactor of ZYG-11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.28   2.4e+02      42      83 ..       6      54 ..       1      73 [. 0.56
   2 ?   10.4   0.4   0.00037      0.32      13      88 ..      69     146 ..      57     173 .. 0.75
   3 ?    3.2   0.4     0.056        48      37      96 ..     182     241 ..     146     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.28
               ZYG-11_interact 42 rdleqave.......krlkklpeegerlleqllssifsqkskdslnelv 83
                                  ++++q v+       +++k+l+e+ +  l+ + ++++  + k ++++l 
  gi|91772333|ref|YP_565025.1|  6 EEINQDVDklaentgEEAKVLNEKIKTRLNSVAKDLKYINIKAEVKKLG 54
                                  4444444433335556777777777777777777776666666666654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00037
               ZYG-11_interact  13 sditeavknegseeeavirlvirtysklgrdleqave...krlkklpeegerlleqllssifsqkskdslnelvnalvd 88 
                                   + +++ vk+e ++ +  i+l  +++ +l+rdl++ +     ++ kl  ++++ +  l ss++s   ++++ +++  +  
  gi|91772333|ref|YP_565025.1|  69 KMLASEVKQEITAITDRIAL-HKHMDDLSRDLDELAVktgSEATKLGTKVKQDMRSLASSVKSIDIRKEIDNIIARVDK 146
                                   45667777777887777765.699*********97765667899*****************888888877777655443 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.056
               ZYG-11_interact  37 ysklgrdleqavekrlkklpeegerlleqllssifsqkskdslnelvnalvdlsppekls 96 
                                   +s+  ++l   +  ++ kl  ++++ ++ +  si+s   k++++ +++ +  l   ++ s
  gi|91772333|ref|YP_565025.1| 182 LSNSINELAVETGSEASKLGMNVKEEMKSISDSIKSIDIKEEIEAIISKVERLVDSTGES 241
                                   333333333333489999****************999*********99887776555555 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.3    0.0055       4.7      99     146 ..       1      49 [.       1      60 [. 0.87
   2 ?    1.2   0.2      0.28   2.4e+02     110     138 ..      68      99 ..      50     119 .. 0.44
   3 ?    6.1   0.2    0.0084       7.2      84     150 ..     122     191 ..     111     199 .. 0.78
   4 ?    2.2   0.2      0.13   1.1e+02      92     120 ..     217     245 ..     195     260 .] 0.45

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0055
                 Fzo_mitofusin  99 lsstfarlcqqvdetekeleeeikelekeie.kleevqkkakllrnkas 146
                                   +++ +++++q+vd+  ++  ee k l+++i+ +l++v k +k +  ka+
  gi|91772333|ref|YP_565025.1|   1 MEKLLEEINQDVDKLAENTGEEAKVLNEKIKtRLNSVAKDLKYINIKAE 49 
                                   567788999*********************648*********9999986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.28
                 Fzo_mitofusin 110 vdetekeleeeikelekei...ekleevqkka 138
                                    ++  +e+++ei++++ +i   ++++++++ +
  gi|91772333|ref|YP_565025.1|  68 AKMLASEVKQEITAITDRIalhKHMDDLSRDL 99 
                                   33333344444444444441111222222222 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0084
                 Fzo_mitofusin  84 vsltsancshqvqqelsstfarlcqqvd...etekeleeeikelekeiekleevqkkakllrnkaslles 150
                                    sl s+  s  +++e+++ +ar+ + +d   e+ k+l +eik+    i++  ++++++++l n  ++l+ 
  gi|91772333|ref|YP_565025.1| 122 RSLASSVKSIDIRKEIDNIIARVDKLIDstgEAAKTLGSEIKDELVLINSRIDLNNRLEILSNSINELAV 191
                                   4678888999999999999998887777211557889999999999999888889999999888887765 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.13
                 Fzo_mitofusin  92 shqvqqelsstfarlcqqvdetekeleee 120
                                   s  +++e++  ++++++ vd t ++ ++ 
  gi|91772333|ref|YP_565025.1| 217 SIDIKEEIEAIISKVERLVDSTGESAKKL 245
                                   23333344444444444444333333333 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.0     0.034        29      15      97 ..       2      85 ..       1      94 [. 0.45
   2 ?    6.0   0.2     0.013        11      13      56 ..      87     130 ..      80     140 .. 0.86
   3 ?    4.0   0.2     0.053        45      12      86 ..     142     214 ..     131     219 .. 0.71
   4 ?    2.0   0.2      0.22   1.9e+02      13      52 ..     219     258 ..     215     260 .] 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.034
                       DUF1451 15 eelvekakeklseaeeltkeelelvaeylkrDleeaarsleeske.eleewlsldlelieesllealasiaDktqvelaelae 96
                                  e+l+e+ ++ ++++ e t ee++ ++e +k  l+++a++l+  +     ++l ++++ + ++  ++   +a + + e++++++
  gi|91772333|ref|YP_565025.1|  2 EKLLEEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLKYINIkAEVKKLGVKVDQLVDRTGSSAKMLASEVKQEITAITD 84
                                  45555555555555555555555555555555555555554433322233444444444444444444444444444444333 PP

                       DUF1451 97 d 97
                                  +
  gi|91772333|ref|YP_565025.1| 85 R 85
                                  3 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                       DUF1451  13 eleelvekakeklseaeeltkeelelvaeylkrDleeaarslee 56 
                                   +l++ +++  + l+e+   t +e+ ++   +k+D++++a+s+++
  gi|91772333|ref|YP_565025.1|  87 ALHKHMDDLSRDLDELAVKTGSEATKLGTKVKQDMRSLASSVKS 130
                                   68899999999999999999999999999999999999998875 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.053
                       DUF1451  12 eeleelvekakeklseaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldlelieesllealasiaDk 86 
                                    ++++l++++ e ++ ++   k+el l+++  + Dl++  + l++s +el+ +   + + +   + e++ si+D 
  gi|91772333|ref|YP_565025.1| 142 ARVDKLIDSTGEAAKTLGSEIKDELVLINS--RIDLNNRLEILSNSINELAVETGSEASKLGMNVKEEMKSISDS 214
                                   567777777777777777777777777776..4577777777777777777777777777777777777777775 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.22
                       DUF1451  13 eleelvekakeklseaeeltkeelelvaeylkrDleeaar 52 
                                   +++e++e    k++ + + t e ++++a  +++D++++ +
  gi|91772333|ref|YP_565025.1| 219 DIKEEIEAIISKVERLVDSTGESAKKLAIEINEDIKNLLK 258
                                   6889999999999999999*********999999999876 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.1    0.0095       8.1       2      42 ..       2      42 ..       1      51 [. 0.87
   2 ?   -1.0   0.0       2.7   2.3e+03       5      35 ..      50      80 ..      46      86 .. 0.70
   3 ?    5.1   0.1     0.035        30       3      46 ..      90     133 ..      88     140 .. 0.90
   4 ?    0.0   0.0       1.3   1.1e+03       5      34 ..     137     166 ..     132     185 .. 0.67
   5 ?    1.1   0.3      0.62   5.3e+02       8      46 ..     182     220 ..     175     223 .. 0.86
   6 ?    4.1   0.3     0.071        61       3      37 ..     222     256 ..     220     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0095
                       V-SNARE  2 kellaeiksklarlsslageerkaalreiekkldeaeelld 42
                                  ++ll+ei++ +++l++++gee k +  +i+++l+++ + l+
  gi|91772333|ref|YP_565025.1|  2 EKLLEEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLK 42
                                  5799***************************9999877666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                       V-SNARE  5 laeiksklarlsslageerkaalreiekkld 35
                                  ++++  k+++l   +g++ k + +e+++++ 
  gi|91772333|ref|YP_565025.1| 50 VKKLGVKVDQLVDRTGSSAKMLASEVKQEIT 80
                                  5566677777777777888888888888776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.035
                       V-SNARE   3 ellaeiksklarlsslageerkaalreiekkldeaeelldqMel 46 
                                   ++++++++ l+ l+ ++g+e  ++  +++++  ++ + +++ ++
  gi|91772333|ref|YP_565025.1|  90 KHMDDLSRDLDELAVKTGSEATKLGTKVKQDMRSLASSVKSIDI 133
                                   5789****************************999999998887 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.3
                       V-SNARE   5 laeiksklarlsslageerkaalreiekkl 34 
                                   +++i  ++++l  ++ge  k + +ei+ +l
  gi|91772333|ref|YP_565025.1| 137 IDNIIARVDKLIDSTGEAAKTLGSEIKDEL 166
                                   444444555555666677777777776654 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.62
                       V-SNARE   8 iksklarlsslageerkaalreiekkldeaeelldqMel 46 
                                   +++ ++ l+ ++g+e +++  +++++ +++ + +++ ++
  gi|91772333|ref|YP_565025.1| 182 LSNSINELAVETGSEASKLGMNVKEEMKSISDSIKSIDI 220
                                   678899999999999999999999999999999998886 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.071
                       V-SNARE   3 ellaeiksklarlsslageerkaalreiekkldea 37 
                                   e ++ i sk++rl  ++ge+ k++  ei ++++++
  gi|91772333|ref|YP_565025.1| 222 EEIEAIISKVERLVDSTGESAKKLAIEINEDIKNL 256
                                   66777888999999999999999999999888875 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.7      0.02        17      56     135 ..      44     123 ..       2     132 .. 0.71
   2 ?    7.4   4.7    0.0016       1.4      55     149 ..     130     225 ..     115     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.02
                          Zw10  56 eslskeidalkkkveneieqdlkaaveelaelkqqlkekevvlellealkkieealeelkealknkaflvaadlleelks 135
                                    +++ e+  l  kv++ ++++  +a     e kq++   +  + l +++ +++  l el  ++ + a     ++ ++++s
  gi|91772333|ref|YP_565025.1|  44 INIKAEVKKLGVKVDQLVDRTGSSAKMLASEVKQEITAITDRIALHKHMDDLSRDLDELAVKTGSEATKLGTKVKQDMRS 123
                                   46677777777778888887777777667788888888888888888888888888888888877766666666666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                          Zw10  55 veslskeidalkkkveneieqdlkaaveelaelkqqlkekevvlellealkkieealeelkealknkaflvaadlleelks 135
                                   +  + keid +  +v++ i+++ +aa +   e+k +l   +  ++l ++l+ +++ ++el   + + a     ++ ee+ks
  gi|91772333|ref|YP_565025.1| 130 SIDIRKEIDNIIARVDKLIDSTGEAAKTLGSEIKDELVLINSRIDLNNRLEILSNSINELAVETGSEASKLGMNVKEEMKS 210
                                   34578****************************************************************99*********9 PP

                          Zw10 136 lldlekvekafq.lk 149
                                   + d++k+  +++ ++
  gi|91772333|ref|YP_565025.1| 211 ISDSIKSIDIKEeIE 225
                                   999999987777666 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.4    0.0016       1.4      31     110 ..       2      83 ..       1      86 [. 0.87
   2 ?   -1.4   0.0       2.8   2.4e+03      82     104 ..     117     139 ..      95     150 .. 0.67
   3 ?    1.6   0.3      0.32   2.7e+02      47     107 ..     174     229 ..     160     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                                   HHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHHHHHHHTTS---HHHHHHHHHCS.-.S-HHHHHHHHC- CS
                         ASL_C  31 lkglsklevneealaedLdenwevlaEaiqtvlrregiekpYeklkeltrgkkitkeslkefiesl.e.vseeakeeLkal 109
                                    k l++++ + ++lae+  e+ +vl E i+t l + + +  Y ++k+ +++  ++ ++l +   s  + + +e+k+e++a+
  gi|91772333|ref|YP_565025.1|   2 EKLLEEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLKYINIKAEVKKLGVKVDQLVDRTGSSaKmLASEVKQEITAI 82 
                                   57799999999************************************9999999988887776655334899999999998 PP

                                   - CS
                         ASL_C 110 t 110
                                   t
  gi|91772333|ref|YP_565025.1|  83 T 83 
                                   7 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                                   S---HHHHHHHHHCS-S-HHHHH CS
                         ASL_C  82 kkitkeslkefieslevseeake 104
                                    k++ +sl++ ++s+++++e+ +
  gi|91772333|ref|YP_565025.1| 117 VKQDMRSLASSVKSIDIRKEIDN 139
                                   34555666666666666666554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.32
                                   HHHT-GGGGHHHHHHHHHHTT-TTHHHHHHHHHTTS---HHHHHHHHHCS-S-HHHHHHHH CS
                         ASL_C  47 dLdenwevlaEaiqtvlrregiekpYeklkeltrgkkitkeslkefieslevseeakeeLk 107
                                   dL++  e+l+ +i  +  ++g e    +  +l  + k + +s+++ i+s++++ee+++ ++
  gi|91772333|ref|YP_565025.1| 174 DLNNRLEILSNSINELAVETGSE----A-SKLGMNVKEEMKSISDSIKSIDIKEEIEAIIS 229
                                   66666666666665544333332....2.24455556677788888888888888777665 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.96   8.2e+02      19      35 ..       1      17 [.       1      18 [. 0.88
   2 ?   -2.5   0.0       4.7     4e+03      26      35 ..      88      97 ..      87     103 .. 0.64
   3 ?    7.7   0.2     0.003       2.6      19      34 ..     175     190 ..     173     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.96
                          YvrJ 19 iEkkLdeLtksIeeLse 35
                                  +Ek L+e ++ +++L+e
  gi|91772333|ref|YP_565025.1|  1 MEKLLEEINQDVDKLAE 17
                                  79999**9999999986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                          YvrJ 26 LtksIeeLse 35
                                  L k++++Ls+
  gi|91772333|ref|YP_565025.1| 88 LHKHMDDLSR 97
                                  5666666664 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.003
                          YvrJ  19 iEkkLdeLtksIeeLs 34 
                                   ++++L+ L++sI+eL+
  gi|91772333|ref|YP_565025.1| 175 LNNRLEILSNSINELA 190
                                   689************7 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.095        81      18      58 ..       2      42 ..       1      45 [. 0.75
   2 ?    5.1   0.2      0.04        34       3      61 ..      43     103 ..      42     132 .. 0.72
   3 ?    1.8   2.4      0.41   3.5e+02       7      62 ..     134     191 ..     116     251 .. 0.65
   4 ?    0.9   0.1      0.77   6.6e+02       7      39 ..     221     246 ..     218     260 .] 0.46

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.095
                  Syntaxin-6_N 18 eslyrrwerlledtssstseeldetrteLrkalrsiewdle 58
                                  e+l+++ ++  ++  ++t ee + +++++++ l+s+ +dl+
  gi|91772333|ref|YP_565025.1|  2 EKLLEEINQDVDKLAENTGEEAKVLNEKIKTRLNSVAKDLK 42
                                  66666676545555556799999999999999999999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.04
                  Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrw.erlledtssstseeldetrt..eLrkalrsiewdledLe 61 
                                   ++++k+eV+k   k+ +l++r  ++ + ++s+  ++e+   ++   L+k +++++ dl++L 
  gi|91772333|ref|YP_565025.1|  43 YINIKAEVKKLGVKVDQLVDRTgSSAKMLASE-VKQEITAITDriALHKHMDDLSRDLDELA 103
                                   67889999999999999999995454455544.35666655542268999999999999985 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.41
                  Syntaxin-6_N   7 keeVqkslnkaeslyrrw.erlledtss.stseeldetrteLrkalrsiewdledLee 62 
                                   ++e+ + + ++ +l+++  e  ++++s+ + +  l + r +L++ l+ +++ +++L  
  gi|91772333|ref|YP_565025.1| 134 RKEIDNIIARVDKLIDSTgEAAKTLGSEiKDELVLINSRIDLNNRLEILSNSINELAV 191
                                   5666666666666666664344444444444444455666666666666666666643 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.77
                  Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtssstseel 39 
                                   kee++  ++k+e l+++         +s ++  
  gi|91772333|ref|YP_565025.1| 221 KEEIEAIISKVERLVDST-------GESAKKLA 246
                                   555555555555555554.......33223333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1789  (0.0997825); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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):              21  [number of targets reported over threshold]
# CPU time: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 1507.84
//
Query:       gi|91772334|ref|YP_565026.1|  [L=223]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-12   46.9   4.4    3.3e-12   46.5   4.4    1.2  1  DDE_Tnp_1       Transposase DDE domain
  ------ inclusion threshold ------
      0.043   12.7   1.5       0.07   12.0   1.5    1.3  1  Lentivirus_VIF  Lentivirus virion infectivity factor (VIF)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   4.4   3.7e-16   3.3e-12       4     214 .]      35     204 ..      32     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.7e-16
                     DDE_Tnp_1   4 revlivDattvrvpgtkedarwgykggkykygy.klhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgklvla 82 
                                   ++++++D+t ++    +   ++++  +k+++ y k  i vd    +i++++++ + vhd k++k+ll +++ + +++++++
  gi|91772334|ref|YP_565026.1|  35 IDITAIDSTGFTSGYCS--NYYSWRIKKWRRSYvKTSISVDVSKFVITGYKVSGKPVHDAKHAKTLLLQCHCNrRSRYYVT 113
                                   6899*******965555..566778889888888************************************999******** PP

                     DDE_Tnp_1  83 DaGYasaelldtle.ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsell 162
                                   D++Y+s+++++  + + g   i++l               r+ +rk+++++ ++k  ++++                    
  gi|91772334|ref|YP_565026.1| 114 DKAYDSENIHELTReKLGSIAIVPL---------------RQLERKRIKGRYRKKMIHEFDN------------------- 160
                                   **************55555555655...............6666666666666666665555................... PP

                     DDE_Tnp_1 163 saeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                          +y+ R   E+ F+ lkrk+g  ++++r+++  + ++ ++ + +nl
  gi|91772334|ref|YP_565026.1| 161 ------KIYSMRNLSETMFSVLKRKYG--KTYVRKYRNQVKEVKFKVILHNL 204
                                   ......6*****************777..99999999999999999998887 PP

>> Lentivirus_VIF  Lentivirus virion infectivity factor (VIF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.5   7.8e-06      0.07      32      82 ..     139     189 ..     126     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.8e-06
                Lentivirus_VIF  32 dekekekkkkdlkkrlkdledkfikrlrkaeGikwslhtrdyhvgyvkelv 82 
                                    + e+++ k  ++k++ +  d+ i+ +r+     +s+  r+y  +yv++  
  gi|91772334|ref|YP_565026.1| 139 RQLERKRIKGRYRKKMIHEFDNKIYSMRNLSETMFSVLKRKYGKTYVRKYR 189
                                   6899*******************************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 1315.74
//
Query:       gi|91772335|ref|YP_565027.1|  [L=214]
Description: multiple antibiotic resistance (MarC)-related proteins [Methanococcoides burtonii DSM 6242]
Scores for complete 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-54  184.0  16.0    2.5e-54  183.8  16.0    1.0  1  MarC       MarC family integral membrane protein
  ------ inclusion threshold ------
       0.62   10.0  12.9       0.12   12.4   1.5    2.6  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
        2.8    8.2   8.7        0.3   11.4   2.7    2.1  2  DUF1772    Domain of unknown function (DUF1772)


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 !  183.8  16.0   4.1e-58   2.5e-54       2     201 ..       5     204 ..       4     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.8 bits;  conditional E-value: 4.1e-58
                          MarC   2 kaiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillfl 82 
                                   +++i++f++L++i+ p++ v  f++l++  s +e++ ia+k + la++i ++f+++G +il+++gis+d+lk+aGg+ll++
  gi|91772335|ref|YP_565027.1|   5 SYFINSFITLFVIVSPITGVITFITLTNGLSLREKNVIAKKSVTLAFIISMFFIFTGTIILDVLGISLDSLKVAGGLLLLT 85 
                                   6899***************************************************************************** PP

                          MarC  83 iaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllilll 163
                                   +a+dm++ak ++++   +e ++s+e+d+i ++P+A+P++aGP++itt ++l+++a+ +++k++++la ++ ++++++++l 
  gi|91772335|ref|YP_565027.1|  86 VAFDMMHAKISRQSITDKEINASYERDDIWIFPIAMPILAGPATITTAIILTETAEVVQQKMLLILAAVITYSVAMVTFLF 166
                                   ********************************************************************************* PP

                          MarC 164 sslilrllgktginaleRlmGllLvalavqlivdGike 201
                                   s  i +++g +g+ +l+Rl+Gl+L a++v++i  G+ +
  gi|91772335|ref|YP_565027.1| 167 SRRIHKKMGYNGMLVLTRLFGLFLGAISVDMIASGVWG 204
                                   ***********************************976 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 ?   12.4   1.5     2e-05      0.12      60     114 ..      38      94 ..      33     107 .. 0.81
   2 ?    3.0   3.2     0.015        89      58     115 ..     144     199 ..     131     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                     RseC_MucC  60 eksll..kaallvYllPllllilgallgsallgssellaalgallglvlgflivrll 114
                                   ek+++  k++ l++++ ++++++g+++ ++l++s + l ++g+ll+l ++f +++  
  gi|91772335|ref|YP_565027.1|  38 EKNVIakKSVTLAFIISMFFIFTGTIILDVLGISLDSLKVAGGLLLLTVAFDMMHAK 94 
                                   5555433799**********************9**************9999777654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.015
                     RseC_MucC  58 ieeksllkaallvYllPllllilgallgsallgssellaalgallglvlgflivrlls 115
                                    ++  l+ aa++ Y + +++++++  + + +  + +++ +l+ l+gl+lg + v +++
  gi|91772335|ref|YP_565027.1| 144 QQKMLLILAAVITYSVAMVTFLFSRRIHKKM--GYNGMLVLTRLFGLFLGAISVDMIA 199
                                   4555567788888888888888888888888..6888888888888888888877766 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.5      0.16   9.8e+02      40      85 ..      20      64 ..       4      91 .. 0.57
   2 ?   11.4   2.7     5e-05       0.3      38      91 ..     120     173 ..      80     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.16
                       DUF1772 40 pplallsalafa.ylaaraasrgarllylaaaallllsivp.yTllvm 85
                                  p +++++ + ++  l+ r ++  a + + ++a +++  +++ +T +++
  gi|91772335|ref|YP_565027.1| 20 PITGVITFITLTnGLSLREKNVIAKKSV-TLAFIIS--MFFiFTGTII 64
                                  3344444444444444555555555555.3244433..4433555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5e-05
                       DUF1772  38 vfpplallsalafa.ylaaraasrgarllylaaaallllsivpyTllvmvPtNnk 91 
                                   ++p la  +++ +a  l+   a   + +++l++aa+++ s++ +T+l+ + + +k
  gi|91772335|ref|YP_565027.1| 120 AMPILAGPATITTAiILT-ETAEVVQQKMLLILAAVITYSVAMVTFLFSRRIHKK 173
                                   466677777777774444.566666666666779999999*******98877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1554.92
//
Query:       gi|91772336|ref|YP_565028.1|  [L=279]
Description: GCN5-related N-acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-08   35.2   0.0    1.9e-08   34.6   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-07   30.8   0.0    4.2e-07   30.0   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    9.7e-07   28.9   0.1    1.6e-05   25.0   0.1    2.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00047   20.5   0.0     0.0009   19.6   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.031   14.2   0.0      0.055   13.4   0.0    1.4  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   5.2e-12   1.9e-08       5     117 .]     143     250 ..     136     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.2e-12
                                   HHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHH CS
                Acetyltransf_1   5 vellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLleal 85 
                                   ++   e++++p +d+++    +    ++  ++ a +++++i+  s  + +     ++++ ++a  pe+rgkGl s Ll ++
  gi|91772336|ref|YP_565028.1| 143 YNKTFETYPFPIHDPDYLLKTIE---DNVVYFGAFKEDQIIALSSSEIEYG--HLNVEMTDFATLPEFRGKGLSSYLLGKM 218
                                   33334444444444444443333...5557777******************..7899************************ PP

                                   HHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  86 eerareegikkivlaveedndaairlYeklGF 117
                                   e++++ +gik  +   +++  ++  ++ k+G+
  gi|91772336|ref|YP_565028.1| 219 EDEMKAKGIKTAYTIARASSYGMNIVFAKCGY 250
                                   *********77665344444444444447776 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) 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   4.2e-07      15     118 ..     153     262 ..     133     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.2e-10
               Acetyltransf_10  15 efispealrerieegealllvaeeggkivGviel.rdgs....hisllfVdpeyrgqGigkaLleaveeeaekdgikl.el 89 
                                    +++p+ l + i e ++++++a+++++i+   +   + +    +++ ++  pe+rg+G+++ Ll ++e+e++ +gik+  +
  gi|91772336|ref|YP_565028.1| 153 PIHDPDYLLKTI-EDNVVYFGAFKEDQIIALSSSeIEYGhlnvEMTDFATLPEFRGKGLSSYLLGKMEDEMKAKGIKTaYT 232
                                   556667777888.88999***********7664433333355688999******************************999 PP

               Acetyltransf_10  90 tvnasp.yavpfYeklGFkavgeeqeenGi 118
                                    ++as+     ++ k+G++ +g+  + ++i
  gi|91772336|ref|YP_565028.1| 233 IARASSyGMNIVFAKCGYEYCGRLVNNTNI 262
                                   999999666779*********999887776 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   4.4e-09   1.6e-05       2     117 ..     128     239 ..     127     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.4e-09
                                   EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE- CS
                Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVava 82 
                                   ir  +++d+ ++++l ++ F+  + p+++ ++ ++ + ++  ++ga++++++++   l + e+  +  ++++   t+ a+ 
  gi|91772336|ref|YP_565028.1| 128 IRICDKSDISQMADLYNKTFETYPFPIHDPDYLLKTIEDNVVYFGAFKEDQIIA---LSSSEIEYGHLNVEM---TDFATL 202
                                   788899****************9999954557777777777999********87...556788877777776...89**** PP

                                   CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSH CS
                Acetyltransf_9  83 pehrgrgvlskLlaraleemreegqplsllfP..ssi 117
                                   pe rg+g+ s Ll ++ +em+++g++ ++ ++  ss+
  gi|91772336|ref|YP_565028.1| 203 PEFRGKGLSSYLLGKMEDEMKAKGIKTAYTIAraSSY 239
                                   *****************************99966444 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.5e-07    0.0009       7      75 ..     172     251 ..     163     252 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.5e-07
                                   EEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEEEEEEEE...THH.HHHH.HHHHTT CS
                Acetyltransf_7   7 VaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea..ae...kgiileqlel...nae.kaik.fYeklG 73 
                                    a ++++i+   + +++      e t +a++pe+rgkG+ + Ll     e   kgi+ + +++   + + +  +  ++k+G
  gi|91772336|ref|YP_565028.1| 172 GAFKEDQIIALSSSEIEYghlnVEMTDFATLPEFRGKGLSSYLLGKmeDEmkaKGIK-T-AYTiarA-SsYGMNiVFAKCG 249
                                   455556666433333332443344455****************96434114457754.2.3443221.1222335888888 PP

                                   EE CS
                Acetyltransf_7  74 Fe 75 
                                   +e
  gi|91772336|ref|YP_565028.1| 250 YE 251
                                   87 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.055      23      78 ..     195     251 ..     171     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                                   SEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEE.ETT-HHHHHHHHHHT-E CS
                          FR47  23 elgalqvlpehrrrGlgsrlvkalakeiaergktvllvv.vasNtpsirlyeklGfe 78 
                                   e+    +lpe+r++Gl s l  ++  e+ ++g++    + +as      ++ k G+e
  gi|91772336|ref|YP_565028.1| 195 EMTDFATLPEFRGKGLSSYLLGKMEDEMKAKGIKTAYTIaRASSYGMNIVFAKCGYE 251
                                   5666789************************98765554044544555577777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1966.19
//
Query:       gi|91772337|ref|YP_565029.1|  [L=435]
Description: L-lysine 2,3-aminomutase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-44  151.4   0.0    2.4e-44  150.6   0.0    1.4  1  LAM_C        Lysine-2,3-aminomutase
      2e-12   47.8   0.0      8e-12   45.9   0.0    2.0  1  Radical_SAM  Radical SAM superfamily
    0.00046   20.3   0.4     0.0061   16.7   0.0    2.7  3  Fer4_14      4Fe-4S single cluster domain
     0.0043   17.3   0.1      0.017   15.4   0.0    1.9  2  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> LAM_C  Lysine-2,3-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0   5.3e-48   2.4e-44       1     107 [.     322     434 ..     322     435 .] 0.97

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 5.3e-48
                         LAM_C   1 ieglrGhtsGyavPtfvvdaPgGGGkialqPnyllsqsedkvvlrnfeGvitsypePeny....vkgkaddyfkevypdte 77 
                                   +e+l+GhtsG++vPt+v+daP+GGGki+++Pny++s+s+++v+lrn+eGvitsy+ePe y    ++ +++++  ++  d +
  gi|91772337|ref|YP_565029.1| 322 MENLIGHTSGFSVPTYVIDAPHGGGKIPVMPNYIISWSTNRVILRNYEGVITSYKEPESYkqiyCDRNCEKCDLQLKLDDA 402
                                   799********************************************************99999999************** PP

                         LAM_C  78 kkkeevGisalled..eelsltPenlkrlerr 107
                                   ++++ +Gis+ll+d  +++sl+Pe+++r+err
  gi|91772337|ref|YP_565029.1| 403 TEYKAIGISKLLADydDTTSLVPEDNERMERR 434
                                   ************9876899************9 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   1.8e-15     8e-12       3     158 ..     131     278 ..     129     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.8e-15
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla...vpgir 79 
                                   +++ C++ C++C+r+++   ++  ++  +e+ile +++++ +   ++ v+l+gg+pl+ +d   ++     +    v+ ir
  gi|91772337|ref|YP_565029.1| 131 ISNVCSMYCRHCTRKRK--VGDIDYIPEKEKILEGIEYIR-NTPqIRDVLLSGGDPLMLSDDFLDWILTEINSiphVEVIR 208
                                   6789***********96..9*******************8.4444**************8888888888887667777777 PP

                                   EEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                   xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  80 itvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                   i    + +lp+   +e ++ l++ ++ +++ + +++ +           tf+ + +al+kl++agi+   + +v+l G+nd
  gi|91772337|ref|YP_565029.1| 209 IGSRMPVVLPYritDELVDVLKKHHPIWLNTHFNHPREM----------TFSSR-QALKKLADAGIP-LGNQTVLLAGVND 277
                                   77777777776999*********9999999999999994..........35555.9***********.************9 PP

                                   H CS
                                   x RF
                   Radical_SAM 158 e 158
                                    
  gi|91772337|ref|YP_565029.1| 278 C 278
                                   6 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.4e-06    0.0061       2      69 ..     129     192 ..     128     211 .. 0.67
   2 ?   -1.9   0.0      0.76   3.4e+03      69      90 ..     224     242 ..     219     259 .. 0.65
   3 ?   -0.3   0.1      0.25   1.1e+03       8      22 ..     386     400 ..     383     422 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-06
                       Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellk 69 
                                   f   + C++ C+ C +k +  +    p++e++l + ++   ++   i+ + l+GG+PL+    +++l+
  gi|91772337|ref|YP_565029.1| 129 FHISNVCSMYCRHCTRKRKVGDIDYIPEKEKIL-EGIEYIRNTPQ-IRDVLLSGGDPLML--SDDFLD 192
                                   555688*********999777766666666666.45544444444.567*********65..344443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.76
                       Fer4_14  69 klvkrlkeeypekkiwletngt 90 
                                   +lv+ lk++   ++iwl+t   
  gi|91772337|ref|YP_565029.1| 224 ELVDVLKKH---HPIWLNTHFN 242
                                   455555544...5999999755 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.25
                       Fer4_14   8 CnlsCkgCdnketwk 22 
                                   C  +C  Cd + + +
  gi|91772337|ref|YP_565029.1| 386 CDRNCEKCDLQLKLD 400
                                   999*****9665443 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.8e-06     0.017      12      66 ..     132     186 ..     117     201 .. 0.69
   2 ?   -1.7   0.1      0.71   3.2e+03      15      22 ..     386     393 ..     384     415 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllp 66 
                                    + C++ C+ C  ++ +  +     +ke + e ie + + ++i+++ l+GG+Pl+ 
  gi|91772337|ref|YP_565029.1| 132 SNVCSMYCRHCT-RKRKVGDIDYIPEKEKILEGIEYIRNtPQIRDVLLSGGDPLML 186
                                   667*******99.444444444444455555555566554999***********93 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.71
                       Fer4_12  15 CnlsCkgC 22 
                                   C+++C+ C
  gi|91772337|ref|YP_565029.1| 386 CDRNCEKC 393
                                   ******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2936.07
//
Query:       gi|91772338|ref|YP_565030.1|  [L=103]
Description: hypothetical protein Mbur_0275 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 765.53
//
Query:       gi|91772339|ref|YP_565031.1|  [L=124]
Description: hypothetical protein Mbur_0277 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   12.9   0.0       0.11   12.3   0.0    1.3  1  DUF1353   Protein of unknown function (DUF1353)
       0.36    9.0  16.4       0.38    9.0  16.4    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF1353  Protein of unknown function (DUF1353)
   #    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      15      41 ..      25      51 ..      13      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                       DUF1353 15 tvvtvpkgfrtDlASiPrllwalipte 41
                                     tv+ +f+tD +SiP +l ++  t+
  gi|91772339|ref|YP_565031.1| 25 LFATVRYCFKTDRSSIPDYLLIFAGTF 51
                                  5568999************99988665 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  16.4   4.3e-05      0.38      39     148 ..       9     119 ..       1     124 [] 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 4.3e-05
                       DUF2070  39 fgillfglpalvaflltlpvlrilggrltykrs....lflalltelivviisllaillsall..qalvllalvlslalvfa 113
                                   + +l+++++++v + ++  ++r+    +++ rs    + l +++ +++++ s+l++l ++l    +++++ ++++ ++v+ 
  gi|91772339|ref|YP_565031.1|   9 NFLLALLVTLIVETTILFATVRYC---FKTDRSsipdY-LLIFAGTFSSF-STLPYLWFVLPmfIRSYSHLIAIGEVSVVL 84 
                                   456888889999999999999988...99999988744.44444444444.5666666544466999************** PP

                       DUF2070 114 lrllvlvavsdesllkavlpaliqpllailllvly 148
                                   +  +++ +v + s+ ka+++++i +l+++l+ +++
  gi|91772339|ref|YP_565031.1|  85 VEAVIYCFVLKVSMNKALFLSFICNLVSFLIGLAL 119
                                   ***************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 875.55
//
Query:       gi|91772340|ref|YP_565032.1|  [L=230]
Description: hypothetical protein Mbur_0278 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1624.86
//
Query:       gi|91772341|ref|YP_565033.1|  [L=458]
Description: parallel beta-helix repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-30  105.3  54.1    3.2e-20   72.4  27.3    2.2  2  NosD            Periplasmic copper-binding protein (NosD)
      5e-21   75.2  52.0    7.2e-15   55.2  31.6    2.4  2  Beta_helix      Right handed beta helix region
     0.0011   17.8   0.3     0.0023   16.7   0.2    1.7  1  Pectinesterase  Pectinesterase
  ------ inclusion threshold ------
       0.22   11.0  14.0      0.017   14.7   3.6    2.3  2  DUF3169         Protein of unknown function (DUF3169)


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 !   72.4  27.3   7.1e-24   3.2e-20      25     154 ..      88     219 ..      63     222 .. 0.90
   2 !   46.8  18.8   4.8e-16   2.2e-12      54     153 ..     187     287 ..     187     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 7.1e-24
                          NosD  25 egseisnneisnsrdgi..lldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnn 103
                                   +g++i + ++s++ +g   +ld+  n+ i++n i+++++G+ l+ se+nt+ +n++++n++Gi++ +s +n+l+nNt+++n
  gi|91772341|ref|YP_565033.1|  88 SGFTIIGASTSKYDSGSgiYLDEVVNAFISNNIITKNNAGVILVRSENNTLVNNVAYMNRNGISIGDSDHNVLNNNTVKQN 168
                                   6777766666655544444************************************************************** PP

                          NosD 104 enyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGil 154
                                   + +Gi l +s+nn++ nN++s n ++Gi+le+s++n++  N ++sn  +G+ 
  gi|91772341|ref|YP_565033.1| 169 KFNGIVLGYSDNNSLINNNASsNYDSGIRLESSNDNELIVNVVNSN-RYGFE 219
                                   ********************99************************.99986 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 4.8e-16
                          NosD  54 ntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflen 134
                                   n+ +n+++Gi+le+s++n +  n+++sn++G+ ++ss nntl++Nt+++n+  Gi+ +ds+nn++++N  s+n k i+ ++
  gi|91772341|ref|YP_565033.1| 187 NASSNYDSGIRLESSNDNELIVNVVNSNRYGFEFKSSFNNTLSDNTVNSNSAVGIYFKDSANNKVEGNLLSKNLKNIHEDS 267
                                   5678999**********************************************************************9887 PP

                          NosD 135 s..ssntitgNriesnqkiGi 153
                                   +  ++n i +N+i+++ +iG 
  gi|91772341|ref|YP_565033.1| 268 DrsDKNHIYDNEINDS-TIGN 287
                                   7779**********99.7774 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 !   55.2  31.6   1.6e-18   7.2e-15      32     156 ..      83     209 ..      37     211 .. 0.84
   2 !   31.8  24.1   2.5e-11   1.1e-07      12     121 ..     182     292 ..     180     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.6e-18
                                   S-.EEES-EEES......-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEE CS
                    Beta_helix  32 snvvienneian......nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntie 106
                                   +nv+i++ +i +      +sgsGiy+ ++ n+ isnn i+ nn  g+ l  + nn++ nn  ++n++ Gi++ +s++n+++
  gi|91772341|ref|YP_565033.1|  83 DNVTISGFTIIGastskyDSGSGIYLDEVVNAFISNNIITKNN-AGVILVRSENNTLVNNVAYMNRN-GISIGDSDHNVLN 161
                                   3345555444445666669999****999**********9999.9999999999***********98.9*9999999**** PP

                                   S-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                    Beta_helix 107 nNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                   nN+++ n+ +Giv+ +s+ n+   nN++++n + Gi + +s++ +++  N
  gi|91772341|ref|YP_565033.1| 162 NNTVKQNKFNGIVLGYSD-NNSLINNNASSNYDSGIRLESSND-NELIVN 209
                                   *******999*******9.888899999999999996666666.777666 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 2.5e-11
                                   EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS CS
                    Beta_helix  12 tiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdngg 92 
                                   ++ nn+ s+++++Gi l++s+++ +  n++++ + +G++ ++s nnt+s+nt++ n ++gi+++++ nn +e+n  ++n +
  gi|91772341|ref|YP_565033.1| 182 SLINNNASSNYDSGIRLESSNDNELIVNVVNS-NRYGFEFKSSFNNTLSDNTVNSNSAVGIYFKDSANNKVEGNLLSKNLK 261
                                   57788888889999999999999888777777.999999999999999999999999999999999999999999999988 PP

                                   -SEE-TT..-S--EEES-EEESTT.--SEE-- CS
                    Beta_helix  93 sGiylny..ssnntienNiidnna.gsGivid 121
                                     i+ ++  s+ n i +N i++ + g+ ++i 
  gi|91772341|ref|YP_565033.1| 262 -NIHEDSdrSDKNHIYDNEINDSTiGNILFII 292
                                   .6877734566699999999887755555555 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.2e-07    0.0023       1      65 [.      10      69 ..      10      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.2e-07
                                  SEEE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES-TTTEEEE CS
                Pectinesterase  1 dvvvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvGdGkektvit 65
                                  d++v +dg +kf +i+eav+  ++       i v  G+Y env+v k+ t v   Gd ++ t+i 
  gi|91772341|ref|YP_565033.1| 10 DITVDDDGFAKFMSIDEAVKYSKT----GDTIIVYPGTYFENVDVYKEITLVSYSGDPND-TIIQ 69
                                  789****************87553....33466889****************99999765.5554 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.6   3.7e-06     0.017      77     157 ..     259     338 ..     254     346 .. 0.70
   2 ?    1.5   2.7      0.04   1.8e+02       3      33 ..     409     439 ..     408     456 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-06
                       DUF3169  77 llkkwdeeddeeseeeyeqiekklsiglilssvslilsfllilasyslkiyeeesssklvlif.liaivlfliilflkiii 156
                                    lk++ e+ d +   ++  +++ ++  +i + +++i sf++i ++ ++ + +++ ++k++li  ++++++  +i+f  +i+
  gi|91772341|ref|YP_565033.1| 259 NLKNIHEDSDRSD--KNHIYDNEINDSTIGNILFIISSFFVIVLVAVFRVLKDKINTKKLLISlIASLFVSALIIFTAVIF 337
                                   3444444433333..33778889*******************999999988777666666655466777777777777776 PP

                       DUF3169 157 q 157
                                    
  gi|91772341|ref|YP_565033.1| 338 F 338
                                   5 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.04
                       DUF3169   3 allkfillmliggliGgiiGfllgafeaekg 33 
                                   +++ +i +  i+ ++Gg +G++ +  + e+ 
  gi|91772341|ref|YP_565033.1| 409 KFIELIFYYGIYSIVGGLAGYFASKRKIEYL 439
                                   5788899999999****99999955444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3400.66
//
Query:       gi|91772342|ref|YP_565034.1|  [L=282]
Description: formate dehydrogenase family accessory protein FdhD [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  206.9   0.0    4.2e-61  206.7   0.0    1.0  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 !  206.7   0.0   2.3e-65   4.2e-61       1     236 [.      49     281 ..      49     282 .] 0.88

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 2.3e-65
                                   E--EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S.........----...----- CS
                     FdhD-NarQ   1 veEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatrakaedkeerrt...akrvv 78 
                                   ++E+++++++n+ +la+++atp++ eela+Gfl++eg+i++a di s+ev++d+  ++ +    +  k ++r+    +r  
  gi|91772342|ref|YP_565034.1|  49 IVEKEFHLSLNDVPLASFFATPQEFEELAVGFLICEGFIDHAIDIISVEVKDDRLICEADICTDRIGK-TKRNidpDSRFD 128
                                   689**************************************************877444433322222.334411133444 PP

                                   ------.---...--H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHHHHHH CS
                     FdhD-NarQ  79 tsgCglcgkesleelletlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnAlDkv 159
                                     +C + g++      +++ ++ sd++++ + l++++++l++ ++++++tgg+H++ + d+d+++la++eDv+R  A+Dk+
  gi|91772342|ref|YP_565034.1| 129 FCSCAI-GSRPC---KKKVGNV-SDIRFDRKVLFNAVEHLKTDAKTWRRTGGTHSVIITDNDSNILAFCEDVSRASAVDKA 204
                                   555555.55544...4555555.59******************************************************** PP

                                   HHHHHT.TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE-GGGE CS
                     FdhD-NarQ 160 iGaallegldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtgaeRi 236
                                   +G+a+l+g+d+s++++v +gRls+ mv Ka++ag++vl+s+++p + +++lA+++gl lvgfvr  ++ vY+g eRi
  gi|91772342|ref|YP_565034.1| 205 VGKAALAGVDMSKCAIVATGRLSVTMVSKAVNAGVSVLASKAGPINEGIDLARAVGLSLVGFVRPPHMYVYNGIERI 281
                                   ****************************************************************************9 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:                      314  (0.0175135); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1814.52
//
Query:       gi|91772343|ref|YP_565035.1|  [L=435]
Description: formylmethanofuran dehydrogenase, subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   61.8   0.0    2.1e-16   59.9   0.0    1.7  1  Molybdopterin  Molybdopterin oxidoreductase
  ------ inclusion threshold ------
      0.028   14.2   0.0      0.047   13.5   0.0    1.3  1  CO_dh          CO dehydrogenase beta subunit/acetyl-CoA synth
      0.089   12.5   0.0       0.28   10.9   0.0    1.8  2  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   3.6e-20   2.1e-16       1     418 [.      48     415 ..      48     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 3.6e-20
                                   B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCG CS
                 Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwya 81 
                                   Rlk+P+v+   + +Gk++++ WdeAl+  a+ l++    + p    +f  g+ +s+e+  ++   ++ lgg    + d++a
  gi|91772343|ref|YP_565035.1|  48 RLKDPLVK---K-NGKLEKAAWDEALTKAAEMLVN---AKRP----LFFLGSETSCEAQEVGLHIAEYLGG----VADSNA 113
                                   9*******...6.8*********************...9999....99999********************....9***** PP

                                   GGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHH........HHHHHHHHHTTC.........-EEE CS
                 Molybdopterin  82 dlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpil........narirkaalkkk.........akvi 145
                                     +++ +   + + + s ++ s++ +    +d+ i wG+N+   +p                     +          kvi
  gi|91772343|ref|YP_565035.1| 114 TICHGPT---VMGIQESGCAGSTAGQVKNRADVNIYWGTNPLASMPRHmskyavfpR----------GywskrgrfdRKVI 181
                                   ****994...56666777777777665667************999988555422222..........2344445888**** PP

                                   EECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHH CS
                 Molybdopterin 146 vigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariare 226
                                    ++pr ++++   d+++ +kp++d +l+ a+  + + ++k   ++                      ++++++v++   +e
  gi|91772343|ref|YP_565035.1| 182 TVDPRRTDTAVASDLHIQLKPNSDYELLSALL-T-ILNGKRPHPS----------------------VEEITGVPISAMDE 238
                                   ********9999***************55554.3.3355555544......................5568899999999* PP

                                   HHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTTH CS
                 Molybdopterin 227 larnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslkee 307
                                   +++ + +++    i+vG gl  +     +++  +nL++ +   ++++G  + l     l g+ + +g +    +v s+ ++
  gi|91772343|ref|YP_565035.1| 239 MIDVMVNANF-GSISVGLGLGSSMGKHRNVELGLNLVKEL---NNNHGTKFVLG---ALRGHCNVAGFN----QVASYLYG 308
                                   *******999.77778*******************98855...45666666666...788877777777....88888899 PP

                                   HHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHH....CSSEEEEEESCSSHHHHTSS CS
                 Molybdopterin 308 kikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekale....kldlvvvldgrltstalyaD 384
                                    ++ ++  +g   ++p+++ +   +ll+++++++ ++++       ad ++ + a+           +ld+    t  ++D
  gi|91772343|ref|YP_565035.1| 309 YPFGIDFSRGYPRYNPGETTT--VDLLRDKDVDAAFVMC-------ADLVNHIPADAasylAEIPMTCLDIAPCPTTTASD 380
                                   9999999*******9999998..9***************.......444444444443333778999************** PP

                                   EEEEBE-.CCGSEEEEE-TTSEEEEEEESSS-STT CS
                 Molybdopterin 385 iiLPaat.wyEkedlytndegrfqhlkqavsppge 418
                                   ++LP+    +E ++++   +   + +k+++ +p+e
  gi|91772343|ref|YP_565035.1| 381 VVLPGVIdAMENDGTFYRLDNVPMYFKPFTTSPFE 415
                                   ****975489******9999999999999999998 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 ?   13.5   0.0   7.9e-06     0.047      17      46 ..      61      90 ..      50     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-06
                                  X--EEE--SHHHHHHHHHSSSEEEEE-S-- CS
                         CO_dh 17 kkatleealkvvakmikkakrPllivGpqv 46
                                  +ka   eal+ +a+m+  akrPl ++G + 
  gi|91772343|ref|YP_565035.1| 61 EKAAWDEALTKAAEMLVNAKRPLFFLGSET 90
                                  67888999*******************876 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.7e-05      0.28       2      29 ..      70      96 ..      69     108 .. 0.79
   2 ?   -2.2   0.0      0.53   3.2e+03      96     116 ..     169     190 ..     126     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                                  HHHHHHHHH-SSEEEEE-CHHCHTTGHH CS
                  TPP_enzyme_M  2 ekaaellkaakrpvilvGggvarsgase 29
                                   kaae+l +akrp++++G++++  +a+e
  gi|91772343|ref|YP_565035.1| 70 TKAAEMLVNAKRPLFFLGSETS-CEAQE 96
                                  69*****************998.45555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.53
                                   TTTTTTTT-.EEEEEESSCCCC CS
                  TPP_enzyme_M  96 sepefapea.kiihididpaei 116
                                   ++++  + + k+i +d+ +++ 
  gi|91772343|ref|YP_565035.1| 169 YWSKRGRFDrKVITVDPRRTDT 190
                                   3443333355777777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3053.97
//
Query:       gi|91772344|ref|YP_565036.1|  [L=129]
Description: formylmethanofuran dehydrogenase, subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-07   29.8   0.0    6.1e-07   29.5   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 !   29.5   0.0   3.4e-11   6.1e-07       2     109 ..       4     102 ..       3     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.4e-11
                                   EEEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTE..EEEEEEEEESSB-TTEEEEESSH CS
               Molydop_binding   2 rLitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrG..svevrakvtervrpGvvfmpfgw 80 
                                    L+tg++ ++       ++ +++++ e++v++++p     lG  +  +V+v+s+    s+ v  k t+ ++ G vfmp + 
  gi|91772344|ref|YP_565036.1|   4 LLNTGSTINEGRLAKGGNKYSEEYRLECAVCWLSPSNFGSLGCPE--KVKVTSKDKkhSIIVYTKCTDVMMDGDVFMPRAI 82 
                                   58999999999999999*************************655..55555555544999999***************** PP

                                   CC.....S-GHCTS--SCSTTT--CSTT- CS
               Molydop_binding  81 weagekggnaNaltddatdplsgtpefks 109
                                   w+        N+++ d+ +  +g+p +k+
  gi|91772344|ref|YP_565036.1|  83 WS--------NVII-DPYTFSTGSPLYKG 102
                                   **........9999.77778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1004.64
//
Query:       gi|91772345|ref|YP_565037.1|  [L=269]
Description: formylmethanofuran dehydrogenase, subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-06   25.5  25.0    0.00089   18.9  16.1    2.7  2  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   2.5   1.4e-05      0.26     123     165 ..      67     113 ..      55     122 .. 0.70
   2 !   18.9  16.1     5e-08   0.00089      39     148 ..     112     216 ..     109     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.4e-05
                                   EEESEB...-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE.-S CS
                         GXGXG 123 avvegv...gdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvl.de 165
                                   +v++g     + ++e mt G + v g++++++++ m gG + v  d 
  gi|91772345|ref|YP_565037.1|  67 IVIKGDsarVKRIGEKMTVGNITVEGSVSMHVGSQMVGGEILVKgDA 113
                                   55555422235678888888888888888888888888888886443 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 5e-08
                                   EE-TTTTTT--TTEEEEEEEEE-STTT.....T..T-ESSEEEEE--TT-SS-GGGSB-S-SSTTTT--SEEEEESSB--S CS
                         GXGXG  39 saGqslgaflakGltleleGdandyvG.....k..glsgGkivikpskeskfkaeeniivGnvvlygatgGklfirgkage 112
                                    a    g+ +  G  +++eG+and vG     k  g+sgG+ivi +++             n +  g+ gG++ + g++g+
  gi|91772345|ref|YP_565037.1| 112 DADSWAGMEM-VGGLIHIEGNANDHVGcayrgKwiGMSGGRIVIDGDA------------NNNLGGGISGGEIIVGGNVGH 179
                                   5555556666.556699999*999887443333668999999999999............477888999999999999999 PP

                                   STTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B- CS
                         GXGXG 113 Rfavrnsgatavvegv.gdhgceYmtGGvvvvLgktg 148
                                    +++r +g  + v+g+    ++  mt G++vv g+  
  gi|91772345|ref|YP_565037.1| 180 YTGIRQNGGLIAVKGNaIRAVAAEMTAGTMVVNGTIE 216
                                   9999999999999998677788889999999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1681.38
//
Query:       gi|91772346|ref|YP_565038.1|  [L=584]
Description: formylmethanofuran dehydrogenase, subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-91  308.6   0.0    1.5e-91  308.3   0.0    1.1  1  Amidohydro_3  Amidohydrolase family
    6.9e-07   28.9   0.1     0.0034   16.8   0.0    2.7  3  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.3   0.0   1.6e-95   1.5e-91       1     472 [.      46     518 ..      46     519 .. 0.95

  Alignments for each domain:
  == domain 1  score: 308.3 bits;  conditional E-value: 1.6e-95
                  Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpyal 80 
                                   +viDa+G++v+PG+vDsH+H+ag++vn  r++r++d ++t+  ++  a             ++g+G ++++++ e++ y++
  gi|91772346|ref|YP_565038.1|  46 KVIDATGKTVMPGGVDSHSHIAGAKVNTgRMMRPEDGYKTTRTKTAIA-------------HSGSGETVPSVYMEGYEYSK 113
                                   69**********************************777644222222.............3566778************* PP

                  Amidohydro_3  81 aeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlaplareaeaaa 161
                                    ++++++e+a ++++a++tH+++r++++ld+            g++l+ +n+++ +++l+eg           + +  aa+
  gi|91772346|ref|YP_565038.1| 114 LGYTTAFEAAVPPMEARHTHEEMRSIPMLDM------------GGYLVLGNNWFMMRYLKEG-----------DMDRAAAY 171
                                   ******************************8............*******************...........******** PP

                  Amidohydro_3 162 vaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls..........pg 225
                                   va++++ ++ yGi++v       +++g+nvssld+ +++fe++ +e      ii +l +++e+lg p s          pg
  gi|91772346|ref|YP_565038.1| 172 VAWMMRTHKTYGIKCVnpggvenWGWGKNVSSLDEQNIHFEISSRE------IIDGLTEVNEMLGMPMSmhlhannlghPG 246
                                   **********************************************......99*************************** PP

                  Amidohydro_3 226 seeltigavklfad................gvlgsrtalltepyf.....tgwpdfedea..laelvaaadergldvaiha 283
                                   ++++t++++ +  +                 + + ++++lt+ +f     t+w+dfe+++  la+++++ad++ +d +++ 
  gi|91772346|ref|YP_565038.1| 247 NYRTTKESLGISSKtkakqnmsvnwaetkiDASRDQSVYLTHMMFnafagTSWRDFESGVkpLADYINNADHVVIDSGCVP 327
                                   **************77777766555555554559*********************************************** PP

                  Amidohydro_3 284 igdaavd..dvldafeaa...aekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrlgperarg 356
                                   +g+a+ +  d++   +     + k++n+d+ +le ++gv   t+ + ++v++ q+a+g++                     
  gi|91772346|ref|YP_565038.1| 328 FGEATCMtgDGPSIHDLSvltGGKWSNTDV-ELECGSGVcpfTYLKSNPVHSTQWAMGLE--------------------- 386
                                   *********9*999999999*********9.*****************************..................... PP

                  Amidohydro_3 357 stpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg.............evlrpdeelsleealalyTrgpAk 423
                                      + +l+++++k+++++D +++gpf+++p +++++m++++r++             ++ + d+e+sl++++ l+++++Ak
  gi|91772346|ref|YP_565038.1| 387 ---CLLLIDDPWKTIMTTDsPNGGPFTKYPLVMSWLMSEKFREQtfsechkwandrsTLGGVDREMSLYDLAILTRANTAK 464
                                   ...****************************************************************************** PP

                  Amidohydro_3 424 algledrkGtLevGadADlvvldadpldvdppelaear......vrltvvdGrvv 472
                                   ++g+ +rkG+ ++Gad+D++++d+dp ++d+ + ++++      +++t+++G+vv
  gi|91772346|ref|YP_565038.1| 465 TIGMAHRKGSFGIGADGDVTIYDIDPTKIDT-REYSDLinkfstAEYTIKGGEVV 518
                                   ******************************5.7888889***************9 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   8.3e-05      0.74       1      17 [.      54      70 ..      54     129 .. 0.77
   2 ?   -1.5   0.0      0.14   1.2e+03     130     156 ..     215     241 ..     208     268 .. 0.70
   3 !   16.8   0.0   3.8e-07    0.0034     271     340 ..     441     513 ..     364     518 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 8.3e-05
                                  EEEE-EEEEEEECETTE CS
                  Amidohydro_1  1 ivlPGlIDaHvHleqsl 17
                                  +v+PG++D+H H+ +  
  gi|91772346|ref|YP_565038.1| 54 TVMPGGVDSHSHIAGAK 70
                                  69***********8553 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHTTEEEEEE.TSSC CS
                  Amidohydro_1 130 sdeelkealkeakkrdlpvaiHa.letk 156
                                   s+e ++ + ++ +  ++p+++H+ + ++
  gi|91772346|ref|YP_565038.1| 215 SREIIDGLTEVNEMLGMPMSMHLhA-NN 241
                                   4555666666666669999999952.32 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 3.8e-07
                                   CCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT....CGGGTTTCTSEEEEEEEET CS
                  Amidohydro_1 271 llyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi....laafvglkkdgnvkkvivk 340
                                    l ++ +  +sl+++  ++  n+Ak +g+++++Gs+  G d D ++ d d+    + ++  l ++++++   +k
  gi|91772346|ref|YP_565038.1| 441 TLGGV-DREMSLYDLAILTRANTAKTIGMAHRKGSFGIGADGDVTIYDIDPtkidTREYSDLINKFSTAEYTIK 513
                                   34433.455999998888889**************************996666785555555555555443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3960.73
//
Query:       gi|91772347|ref|YP_565039.1|  [L=340]
Description: formylmethanofuran dehydrogenase, subunit F [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-54  178.5  84.6    3.6e-09   36.1   2.7    8.2  8  Fer4          4Fe-4S binding domain
    3.1e-37  126.9  69.1    1.4e-10   41.6   7.5    5.6  6  Fer4_7        4Fe-4S dicluster domain
    1.5e-34  118.8  61.4    3.7e-10   40.6   6.3    7.2  7  Fer4_16       4Fe-4S double cluster binding domain
    9.2e-34  114.1  85.3    2.6e-05   24.1   1.9    8.2  8  Fer4_6        4Fe-4S binding domain
    2.6e-32  110.8  64.1    4.3e-11   42.8   6.5    5.6  7  Fer4_9        4Fe-4S dicluster domain
    1.2e-27   95.8  77.9    1.5e-07   31.4  12.6    6.8  6  Fer4_21       4Fe-4S dicluster domain
    1.4e-27   95.6  78.5    3.7e-07   30.2  10.2    7.4  8  Fer4_10       4Fe-4S dicluster domain
    2.2e-27   93.4  81.8    6.4e-06   25.9   2.3    8.3  8  Fer4_2        4Fe-4S binding domain
    8.2e-21   72.8  79.0    0.00025   21.3   1.6    8.3  8  Fer4_4        4Fe-4S binding domain
    9.6e-20   70.8  67.4    6.1e-06   26.6   7.4    6.6  7  Fer4_8        4Fe-4S dicluster domain
    3.1e-15   56.4  67.4    0.00026   21.5  13.9    6.7  6  Fer4_17       4Fe-4S dicluster domain
    3.2e-13   49.6 109.2      0.011   16.6   5.6    8.4  8  Fer4_3        4Fe-4S binding domain
    6.1e-07   29.9  89.1       0.25   11.9   3.6    8.9  8  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    6.4e-06   26.9  74.2      0.086   13.7   1.1    8.1 11  Fer4_22       4Fe-4S dicluster domain
    3.6e-05   23.9  72.6       0.28   11.4   4.3    8.1  8  Fer4_18       4Fe-4S dicluster domain
    6.3e-05   23.6  71.0      0.061   14.1   3.3    8.9  7  Fer4_15       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.018   15.0   0.3      0.086   12.8   0.3    2.3  1  Integrase_Zn  Integrase Zinc 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 !   28.9   3.1   6.2e-10   6.6e-07       2      22 ..      15      35 ..      14      37 .. 0.88
   2 !   26.8   2.2   2.8e-09     3e-06       5      24 .]      57      76 ..      54      76 .. 0.92
   3 !   26.8   3.9   2.9e-09   3.1e-06       5      24 .]     100     119 ..      96     119 .. 0.91
   4 !   36.1   2.7   3.4e-12   3.6e-09       2      24 .]     137     159 ..     136     159 .. 0.96
   5 !   18.4   6.1   1.2e-06    0.0013       5      23 ..     172     190 ..     170     191 .. 0.93
   6 !   28.9   5.1   6.3e-10   6.7e-07       5      24 .]     208     227 ..     205     227 .. 0.94
   7 !   29.9   3.2   3.1e-10   3.2e-07       2      22 ..     262     282 ..     261     284 .. 0.92
   8 !   26.6   3.4   3.3e-09   3.5e-06       2      23 ..     311     332 ..     310     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.2e-10
                                  EEETTTSSS-THHHHHSTTTE CS
                          Fer4  2 videekCigCGaCvevCPvgA 22
                                  v+ +ekCigCG+C +vCP + 
  gi|91772347|ref|YP_565039.1| 15 VYLPEKCIGCGTCTMVCPKDT 35
                                  6779**************985 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 2.8e-09
                                  TTTSSS-THHHHHSTTTEEE CS
                          Fer4  5 eekCigCGaCvevCPvgAIt 24
                                   + Ci CG C +vCP+gA++
  gi|91772347|ref|YP_565039.1| 57 RDTCITCGMCTKVCPTGALE 76
                                  699***************85 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 2.9e-09
                                   TTTSSS-THHHHHSTTTEEE CS
                          Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                    + C++CG C+++CP gAI+
  gi|91772347|ref|YP_565039.1| 100 NDNCVHCGVCEQICPQGAIE 119
                                   699****************6 PP

  == domain 4  score: 36.1 bits;  conditional E-value: 3.4e-12
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   +id+e C++CG C evCP++AIt
  gi|91772347|ref|YP_565039.1| 137 IIDQETCVHCGWCSEVCPTNAIT 159
                                   79********************7 PP

  == domain 5  score: 18.4 bits;  conditional E-value: 1.2e-06
                                   TTTSSS-THHHHHSTTTEE CS
                          Fer4   5 eekCigCGaCvevCPvgAI 23 
                                   e+ C +C +Cv+vCP +A+
  gi|91772347|ref|YP_565039.1| 172 EDVCQACRTCVDVCPCNAL 190
                                   799***************7 PP

  == domain 6  score: 28.9 bits;  conditional E-value: 6.3e-10
                                   TTTSSS-THHHHHSTTTEEE CS
                          Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                   ++ Ci+CGaC+  CPv+AI+
  gi|91772347|ref|YP_565039.1| 208 PDACIYCGACAVSCPVNAID 227
                                   89****************95 PP

  == domain 7  score: 29.9 bits;  conditional E-value: 3.1e-10
                                   EEETTTSSS-THHHHHSTTTE CS
                          Fer4   2 videekCigCGaCvevCPvgA 22 
                                   v de+ C gCG+Cv +CPv+A
  gi|91772347|ref|YP_565039.1| 262 VTDEDACLGCGNCVIMCPVNA 282
                                   67******************9 PP

  == domain 8  score: 26.6 bits;  conditional E-value: 3.3e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   v+d+e C  CGaC+ +CPv AI
  gi|91772347|ref|YP_565039.1| 311 VVDQEACGSCGACALICPVSAI 332
                                   79*******************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 !   21.1   2.0   3.2e-07   0.00034      26      51 ..       9      34 ..       2      35 .. 0.84
   2 !   35.7  15.6   9.4e-12   9.9e-09       1      52 []      59     117 ..      59     117 .. 0.80
   3 !   38.6  13.7   1.2e-12   1.2e-09       2      52 .]     103     157 ..     102     157 .. 0.86
   4 !   30.2  17.2   4.7e-10   4.9e-07       1      52 []     142     189 ..     142     189 .. 0.93
   5 !   41.6   7.5   1.3e-13   1.4e-10       1      52 []     210     282 ..     210     282 .. 0.68
   6 !   17.8   0.1   3.5e-06    0.0036      34      52 .]     313     331 ..     284     340 .] 0.71

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.2e-07
                        Fer4_7 26 kgtekveidpekClgCgaCvavCPtg 51
                                  k +++v++ pekC+gCg C  vCP++
  gi|91772347|ref|YP_565039.1|  9 KDNKQVVYLPEKCIGCGTCTMVCPKD 34
                                  456789999***************86 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 9.4e-12
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..gtekv........eidpekClgCgaCvavCPtga 52 
                                   +Ci Cg C+++Cp++a+e++e+ ++   +            + + ++C++Cg+C++ CP ga
  gi|91772347|ref|YP_565039.1|  59 TCITCGMCTKVCPTGALEMREDGKPVcdE---NflcsslapTTVNDNCVHCGVCEQICPQGA 117
                                   5******************9984443331...134444455999***************997 PP

  == domain 3  score: 38.6 bits;  conditional E-value: 1.2e-12
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgt....ekveidpekClgCgaCvavCPtga 52 
                                   C++Cg C++ Cp++aie+++   ++g      ++ id+e+C++Cg C +vCPt+a
  gi|91772347|ref|YP_565039.1| 103 CVHCGVCEQICPQGAIETRQWLANDGSaridGETIIDQETCVHCGWCSEVCPTNA 157
                                   *******************987788773344455889****************97 PP

  == domain 4  score: 30.2 bits;  conditional E-value: 4.7e-10
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C++Cg C ++Cp++ai++++        ++e  ++ C+ C+ Cv+vCP +a
  gi|91772347|ref|YP_565039.1| 142 TCVHCGWCSEVCPTNAITVQKPF----EGTWERAEDVCQACRTCVDVCPCNA 189
                                   5******************9874....369*******************987 PP

  == domain 5  score: 41.6 bits;  conditional E-value: 1.3e-13
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..........gtekv..............eidpekClgCgaCvavCPtga 52 
                                   +Ci CgaC++ Cpv+ai++++ +  +          +   +              + d++ ClgCg+Cv  CP++a
  gi|91772347|ref|YP_565039.1| 210 ACIYCGACAVSCPVNAIDVQKTAIVPdmnkkavfekK---LlnkpsatpvltsvlVTDEDACLGCGNCVIMCPVNA 282
                                   5*****************9974322222222333330...033334444455555999****************97 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 3.5e-06
                        Fer4_7  34 dpekClgCgaCvavCPtga 52 
                                   d+e C +CgaC+  CP+ a
  gi|91772347|ref|YP_565039.1| 313 DQEACGSCGACALICPVSA 331
                                   5666666666666666544 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 !   15.9   0.9   1.8e-05     0.019      52      65 ..      19      32 ..       6      40 .. 0.65
   2 !   19.8   4.5   1.1e-06    0.0011       1      23 [.      59      81 ..      59      96 .. 0.84
   3 !   19.8   0.6   1.1e-06    0.0012       1      25 [.     102     123 ..     102     140 .. 0.82
   4 !   21.9   1.1   2.5e-07   0.00026       1      22 [.     142     163 ..     142     173 .. 0.81
   5 !   15.2   3.4   2.9e-05      0.03       2      29 ..     175     199 ..     174     208 .. 0.81
   6 !   40.6   6.3   3.5e-13   3.7e-10       2      67 .]     211     281 ..     210     281 .. 0.81
   7 !   19.2   1.3   1.7e-06    0.0017       2      21 ..     317     336 ..     316     340 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                       Fer4_16 52 eaitgCdiCqdvCP 65
                                  e+++gC++C++vCP
  gi|91772347|ref|YP_565039.1| 19 EKCIGCGTCTMVCP 32
                                  55666666666666 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.1e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkek 23
                                  +C+tCg C++vCPt+a++++++ 
  gi|91772347|ref|YP_565039.1| 59 TCITCGMCTKVCPTGALEMREDG 81
                                  5****************988544 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1.1e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekei 25 
                                   +C+ Cg C ++CP++ai+++   ++
  gi|91772347|ref|YP_565039.1| 102 NCVHCGVCEQICPQGAIETR---QW 123
                                   6****************998...44 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 2.5e-07
                       Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                   +C+ Cg C evCPtnai+ +k 
  gi|91772347|ref|YP_565039.1| 142 TCVHCGWCSEVCPTNAITVQKP 163
                                   5****************98743 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 2.9e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare 29 
                                   C+ C+ C++vCP na+ ++   e+++ e
  gi|91772347|ref|YP_565039.1| 175 CQACRTCVDVCPCNALFNP---EWAPGE 199
                                   ***************9888...666555 PP

  == domain 6  score: 40.6 bits;  conditional E-value: 3.5e-13
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkq.......eaitgCdiCqdvCPan 67 
                                   C+ Cg+Ca +CP+nai+ + ++ i +++++++ + ekk l++ +++            a+ gC++C+ +CP+n
  gi|91772347|ref|YP_565039.1| 211 CIYCGACAVSCPVNAIDVQ-KTAIVPDMNKKA-VFEKKLLNKPSATPVLTsvlvtdeDACLGCGNCVIMCPVN 281
                                   *****************99.677777777766.777777777777766555666666999***********98 PP

  == domain 7  score: 19.2 bits;  conditional E-value: 1.7e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                   Cg+Cg+Ca +CP++ai  +k
  gi|91772347|ref|YP_565039.1| 317 CGSCGACALICPVSAIWLEK 336
                                   ****************8874 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   1.9   2.4e-08   2.6e-05       3      21 ..      15      33 ..      14      38 .. 0.86
   2 !   23.4   2.6     4e-08   4.2e-05       6      24 .]      57      75 ..      56      75 .. 0.94
   3 !   18.7   3.5   1.2e-06    0.0013       6      24 .]     100     118 ..      96     118 .. 0.92
   4 !   22.0   2.5   1.2e-07   0.00012       4      24 .]     138     158 ..     137     158 .. 0.97
   5 !   10.9   7.9   0.00037      0.39       7      24 .]     173     190 ..     170     190 .. 0.90
   6 !   15.3   5.3   1.5e-05     0.015       6      24 .]     208     226 ..     204     226 .. 0.95
   7 !   21.1   3.5   2.1e-07   0.00022       4      23 ..     263     282 ..     260     282 .. 0.91
   8 !   21.7   3.5   1.4e-07   0.00014       3      24 .]     311     332 ..     309     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.4e-08
                        Fer4_6  3 eidpdkCigCgdCvrvCPe 21
                                  ++ p+kCigCg C++vCP 
  gi|91772347|ref|YP_565039.1| 15 VYLPEKCIGCGTCTMVCPK 33
                                  6679**************5 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 4e-08
                        Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                  +d Ci Cg C++vCP+ga+
  gi|91772347|ref|YP_565039.1| 57 RDTCITCGMCTKVCPTGAL 75
                                  89***************97 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.2e-06
                        Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                    d+C++Cg C+ +CP gai
  gi|91772347|ref|YP_565039.1| 100 NDNCVHCGVCEQICPQGAI 118
                                   69*************9998 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 1.2e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   id++ C++Cg C  vCP++ai
  gi|91772347|ref|YP_565039.1| 138 IDQETCVHCGWCSEVCPTNAI 158
                                   8*******************8 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00037
                        Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                   d C  C+ Cv+vCP +a+
  gi|91772347|ref|YP_565039.1| 173 DVCQACRTCVDVCPCNAL 190
                                   67************9996 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 1.5e-05
                        Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                   pd+Ci Cg+C++ CP +ai
  gi|91772347|ref|YP_565039.1| 208 PDACIYCGACAVSCPVNAI 226
                                   89***************98 PP

  == domain 7  score: 21.1 bits;  conditional E-value: 2.1e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPega 23 
                                    d+d+C+gCg+Cv+ CP +a
  gi|91772347|ref|YP_565039.1| 263 TDEDACLGCGNCVIMCPVNA 282
                                   69***************987 PP

  == domain 8  score: 21.7 bits;  conditional E-value: 1.4e-07
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   ++d+++C +Cg+C+ +CP  ai
  gi|91772347|ref|YP_565039.1| 311 VVDQEACGSCGACALICPVSAI 332
                                   79*****************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 !   42.8   6.5   4.1e-14   4.3e-11       1      50 [.      20      74 ..      20      75 .. 0.96
   2 !   18.2   4.6     2e-06    0.0021      18      51 .]      91     118 ..      78     118 .. 0.72
   3 !   17.3   2.5   3.8e-06     0.004      30      51 .]     137     158 ..     120     158 .. 0.72
   4 !   22.2  16.7   1.1e-07   0.00012       2      50 ..     143     189 ..     142     190 .. 0.87
   5 !   24.1  14.5   2.9e-08   3.1e-05       2      51 .]     175     226 ..     174     226 .. 0.87
   6 !   26.2  10.4   6.1e-09   6.4e-06       1      49 [.     210     281 ..     210     283 .. 0.93
   7 !   30.7   6.0   2.5e-10   2.6e-07       1      51 []     267     332 ..     267     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 4.1e-14
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50
                                  kC+gCg+C+ +Cp+++ +  +++  ar  + +e     + Ci+Cg C+++Cp+ga
  gi|91772347|ref|YP_565039.1| 20 KCIGCGTCTMVCPKDTLIIGSVGPVARGLINKEyldirDTCITCGMCTKVCPTGA 74
                                  7***************************99999*****99*************97 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2e-06
                        Fer4_9  18 vedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                     + a+++++      ++C++Cg C+++Cp+gai
  gi|91772347|ref|YP_565039.1|  91 CSSLAPTTVN------DNCVHCGVCEQICPQGAI 118
                                   4444444444......47**************97 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 3.8e-06
                        Fer4_9  30 aaseeaCigCgaCveaCpkgai 51 
                                   + ++e C++Cg C e+Cp++ai
  gi|91772347|ref|YP_565039.1| 137 IIDQETCVHCGWCSEVCPTNAI 158
                                   333478*************987 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 1.1e-07
                        Fer4_9   2 CtgCgaCveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   C+ Cg C e+Cp++++ v++ +e++++  ++    C  C++Cv++Cp +a
  gi|91772347|ref|YP_565039.1| 143 CVHCGWCSEVCPTNAItVQKPFEGTWERAED---VCQACRTCVDVCPCNA 189
                                   ***************9678888999886543...6************986 PP

  == domain 5  score: 24.1 bits;  conditional E-value: 2.9e-08
                        Fer4_9   2 CtgCgaCveaCpagvv.vedaaerkarlraase.eaCigCgaCveaCpkgai 51 
                                   C  C++Cv++Cp ++  ++++a++++  + a+  +aCi CgaC+  Cp +ai
  gi|91772347|ref|YP_565039.1| 175 CQACRTCVDVCPCNALfNPEWAPGERVDKVAQRpDACIYCGACAVSCPVNAI 226
                                   ************99876888888888777666689*************9987 PP

  == domain 6  score: 26.2 bits;  conditional E-value: 6.1e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.......................eaCigCgaCveaCpkg 49 
                                   +C+ CgaC  +Cp +++  ++ +    ++++                         +aC+gCg Cv  Cp +
  gi|91772347|ref|YP_565039.1| 210 ACIYCGACAVSCPVNAIDVQKTAIVPDMNKKAVfekkllnkpsatpvltsvlvtdeDACLGCGNCVIMCPVN 281
                                   6****************9999999999877666999********************9*************87 PP

  == domain 7  score: 30.7 bits;  conditional E-value: 2.5e-10
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCgaCveaCpkgai 51 
                                   +C gCg+Cv +Cp ++ + ++ +    ++ +++               eaC +CgaC+ +Cp  ai
  gi|91772347|ref|YP_565039.1| 267 ACLGCGNCVIMCPVNAKSSKDLAAGSLNDLDEKpllevrngtvkvvdqEACGSCGACALICPVSAI 332
                                   6****************999998888887776699***************************9887 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   1.9   2.9e-07    0.0003      27      54 ..       7      34 ..       2      39 .. 0.74
   2 !   17.0   3.2   4.5e-06    0.0047      37      59 .]      56      77 ..      46      77 .. 0.82
   3 !   20.8  17.6     3e-07   0.00032       5      58 ..      57     119 ..      56     120 .. 0.76
   4 !   31.4  12.6   1.4e-10   1.5e-07       2      53 ..     137     187 ..     136     191 .. 0.83
   5 !   25.3  12.9   1.2e-08   1.3e-05       5      54 ..     208     281 ..     204     286 .. 0.72
   6 !   23.7  12.9   3.7e-08   3.9e-05       4      56 ..     264     331 ..     262     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                       Fer4_21 27 eidaktvlkvvedeCvGCnlCssvCPve 54
                                  ++++++++ ++ ++C+GC  C+ vCP +
  gi|91772347|ref|YP_565039.1|  7 QTKDNKQVVYLPEKCIGCGTCTMVCPKD 34
                                  445556666679**************54 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.5e-06
                       Fer4_21 37 vedeCvGCnlCssvCPvedciem 59
                                  + d+C+ C +C++vCP+ +++em
  gi|91772347|ref|YP_565039.1| 56 IRDTCITCGMCTKVCPT-GALEM 77
                                  5799************6.88887 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 3e-07
                       Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvl...........kvvedeCvGCnlCssvCPvedcie 58 
                                   +d+Ci Cg C+++C++++ +    d+k v            ++v+d+Cv C +C ++CP +++ie
  gi|91772347|ref|YP_565039.1|  57 RDTCITCGMCTKVCPTGALEMR-EDGKPVCdenflcsslapTTVNDNCVHCGVCEQICP-QGAIE 119
                                   589************8776655.333333334445666776789***************.79986 PP

  == domain 4  score: 31.4 bits;  conditional E-value: 1.4e-10
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieid..aktvlkvvedeCvGCnlCssvCPv 53 
                                   +id+++C++Cg C  +C++   +ai+++   + +++  ed C +C  C++vCP 
  gi|91772347|ref|YP_565039.1| 137 IIDQETCVHCGWCSEVCPT---NAITVQkpFEGTWERAEDVCQACRTCVDVCPC 187
                                   69****************5...6665551145678999***************7 PP

  == domain 5  score: 25.3 bits;  conditional E-value: 1.2e-08
                       Fer4_21   5 edkCigCgkCliaCedtshqai......eidaktvl....................kvvedeCvGCnlCssvCPve 54 
                                   +d Ci Cg C+++C+ ++++        ++++k  +                     + ed C GC  C+++CPv+
  gi|91772347|ref|YP_565039.1| 208 PDACIYCGACAVSCPVNAIDVQktaivpDMNKK--AvfekkllnkpsatpvltsvlVTDEDACLGCGNCVIMCPVN 281
                                   689************766553333334422233..14466677777888888765455699*************94 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 3.7e-08
                       Fer4_21   4 dedkCigCgkCliaCedtshqai................eidaktvlkvvedeCvGCnlCssvCPvedc 56 
                                   ded C+gCg+C+i+C+ ++                    e+ + tv  v ++ C  C  C+ +CPv  +
  gi|91772347|ref|YP_565039.1| 264 DEDACLGCGNCVIMCPVNAKSSKdlaagslndldekpllEVRNGTVKVVDQEACGSCGACALICPV-SA 331
                                   89**************88777665567777766665555555555657779**************9.55 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5  13.8   1.1e-09   1.2e-06       2      56 .]      14      71 ..      13      71 .. 0.88
   2 !   20.9  17.6   2.7e-07   0.00028       6      56 .]      57     114 ..      52     114 .. 0.96
   3 !   13.7   3.0   4.7e-05     0.049       6      23 ..     100     117 ..      95     134 .. 0.75
   4 !   25.6  14.2   9.1e-09   9.6e-06       3      56 .]     137     186 ..     135     186 .. 0.80
   5 !   19.1  16.8   9.6e-07     0.001       3      56 .]     169     222 ..     167     222 .. 0.74
   6 !   17.1   2.7   4.2e-06    0.0044       3      29 ..     205     231 ..     203     247 .. 0.70
   7 !   30.2  10.2   3.5e-10   3.7e-07       3      56 .]     262     328 ..     260     328 .. 0.90
   8 !   13.7   2.3   4.7e-05     0.049       3      21 ..     311     329 ..     309     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  vv+ +++Ci+Cg+C+ +CP d     svg  +   ++++  +  + C++cg+C+++CP
  gi|91772347|ref|YP_565039.1| 14 VVYLPEKCIGCGTCTMVCPKDTliiGSVGPVARGLINKEYLDIRDTCITCGMCTKVCP 71
                                  67889***************999977777777777888888899*************9 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.7e-07
                       Fer4_10   6 ddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +dtCi Cg C+k+CP+ +       + v  +++   + a  ++ ++C +cg C ++CP
  gi|91772347|ref|YP_565039.1|  57 RDTCITCGMCTKVCPTGAlemredgKPVCDENFLCSSLAPTTVNDNCVHCGVCEQICP 114
                                   69**************99*******99******************************9 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 4.7e-05
                       Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                    d C++Cg C + CP+ +
  gi|91772347|ref|YP_565039.1| 100 NDNCVHCGVCEQICPQGA 117
                                   589************954 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 9.1e-09
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +id++tC++Cg C ++CP+    +  + ++  e++ + + + C++c  Cv++CP
  gi|91772347|ref|YP_565039.1| 137 IIDQETCVHCGWCSEVCPT----NAITVQKPFEGTWERAEDVCQACRTCVDVCP 186
                                   79*****************....5555555555555555566***********9 PP

  == domain 5  score: 19.1 bits;  conditional E-value: 9.6e-07
                       Fer4_10   3 vidddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++ +d C  C++Cv++CP ++  +   a    ++ ++v   +++C+ cgaC+ +CP
  gi|91772347|ref|YP_565039.1| 169 ERAEDVCQACRTCVDVCPCNAlfNPEWA--PGERVDKVAQRPDACIYCGACAVSCP 222
                                   56789**************663333333..333444444578*************9 PP

  == domain 6  score: 17.1 bits;  conditional E-value: 4.2e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgak 29 
                                      +d Ci Cg+C  +CP+++  v+++
  gi|91772347|ref|YP_565039.1| 205 AQRPDACIYCGACAVSCPVNAIDVQKT 231
                                   56789**************66333333 PP

  == domain 7  score: 30.2 bits;  conditional E-value: 3.5e-10
                       Fer4_10   3 vidddtCirCgkCvkaCPadl............tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                   v d+d C++Cg+Cv +CP+++            + +++   + ++++v++ + e+C  cgaC+ +CP
  gi|91772347|ref|YP_565039.1| 262 VTDEDACLGCGNCVIMCPVNAksskdlaagslnDLDEKPLLEVRNGTVKVvDQEACGSCGACALICP 328
                                   6899***************99***********97777777777777777779**************9 PP

  == domain 8  score: 13.7 bits;  conditional E-value: 4.7e-05
                       Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                   v+d++ C  Cg+C   CP+
  gi|91772347|ref|YP_565039.1| 311 VVDQEACGSCGACALICPV 329
                                   68999*************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 !   25.9   2.3   6.1e-09   6.4e-06       3      21 ..      14      32 ..      12      33 .. 0.93
   2 !   20.2   2.3     4e-07   0.00042       6      22 .]      56      72 ..      51      72 .. 0.88
   3 !   14.2   4.7   3.3e-05     0.035       8      22 .]     101     115 ..      95     115 .. 0.86
   4 !   16.3   2.8   7.4e-06    0.0078       5      22 .]     138     155 ..     135     155 .. 0.94
   5 !   12.1   5.7   0.00015      0.16       7      21 ..     172     186 ..     170     186 .. 0.95
   6 !   13.5   4.1   5.6e-05     0.059       5      21 ..     206     222 ..     202     223 .. 0.85
   7 !   18.1   2.5   1.9e-06     0.002       4      21 ..     262     279 ..     259     280 .. 0.89
   8 !   16.2   3.0   7.5e-06    0.0079       4      21 ..     311     328 ..     309     329 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.1e-09
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  vv+ +++CigCg+C+ +CP
  gi|91772347|ref|YP_565039.1| 14 VVYLPEKCIGCGTCTMVCP 32
                                  6899**************9 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4e-07
                        Fer4_2  6 dtdrCigCgaCvsaCPa 22
                                   +d+Ci Cg C+++CP+
  gi|91772347|ref|YP_565039.1| 56 IRDTCITCGMCTKVCPT 72
                                  489*************7 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.3e-05
                        Fer4_2   8 drCigCgaCvsaCPa 22 
                                   d+C++Cg C + CP+
  gi|91772347|ref|YP_565039.1| 101 DNCVHCGVCEQICPQ 115
                                   88************6 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 7.4e-06
                        Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                   +d ++C++Cg C  +CP+
  gi|91772347|ref|YP_565039.1| 138 IDQETCVHCGWCSEVCPT 155
                                   89***************7 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00015
                        Fer4_2   7 tdrCigCgaCvsaCP 21 
                                   +d C +C++Cv++CP
  gi|91772347|ref|YP_565039.1| 172 EDVCQACRTCVDVCP 186
                                   689***********9 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 5.6e-05
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                   + +d+Ci CgaC  +CP
  gi|91772347|ref|YP_565039.1| 206 QRPDACIYCGACAVSCP 222
                                   5589************* PP

  == domain 7  score: 18.1 bits;  conditional E-value: 1.9e-06
                        Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                   v d+d+C+gCg Cv  CP
  gi|91772347|ref|YP_565039.1| 262 VTDEDACLGCGNCVIMCP 279
                                   679**************9 PP

  == domain 8  score: 16.2 bits;  conditional E-value: 7.5e-06
                        Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                   vvd ++C +CgaC   CP
  gi|91772347|ref|YP_565039.1| 311 VVDQEACGSCGACALICP 328
                                   79**************** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.6   2.3e-07   0.00025       1      16 [.      18      33 ..      18      40 .. 0.93
   2 !   15.3   3.8     2e-05     0.021       2      17 .]      58      73 ..      57      73 .. 0.93
   3 !   19.8   4.1   7.4e-07   0.00078       2      17 .]     101     116 ..     100     116 .. 0.94
   4 !    9.5   3.9    0.0015       1.5       1      17 []     140     156 ..     140     156 .. 0.93
   5 !   13.8   3.6   5.9e-05     0.062       2      15 ..     173     186 ..     170     201 .. 0.91
   6 !   12.4   2.2   0.00017      0.18       1      17 []     208     224 ..     208     229 .. 0.92
   7 !   14.0   2.2     5e-05     0.053       2      17 .]     266     281 ..     265     283 .. 0.92
   8 !    8.8   3.3    0.0024       2.6       1      16 [.     314     329 ..     314     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.3e-07
                        Fer4_4  1 qerCigCgsCvaaCPq 16
                                  +e+CigCg C+ +CP 
  gi|91772347|ref|YP_565039.1| 18 PEKCIGCGTCTMVCPK 33
                                  69*************5 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2e-05
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  ++Ci Cg C+ +CP+g
  gi|91772347|ref|YP_565039.1| 58 DTCITCGMCTKVCPTG 73
                                  79************86 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 7.4e-07
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   ++C++Cg+C+ +CPqg
  gi|91772347|ref|YP_565039.1| 101 DNCVHCGVCEQICPQG 116
                                   89************96 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0015
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   qe+C++Cg C  +CP++
  gi|91772347|ref|YP_565039.1| 140 QETCVHCGWCSEVCPTN 156
                                   79*************86 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 5.9e-05
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   + C+ C+ Cv++CP
  gi|91772347|ref|YP_565039.1| 173 DVCQACRTCVDVCP 186
                                   67***********9 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00017
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   ++ Ci Cg+C  +CP++
  gi|91772347|ref|YP_565039.1| 208 PDACIYCGACAVSCPVN 224
                                   689************75 PP

  == domain 7  score: 14.0 bits;  conditional E-value: 5e-05
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   + C+gCg Cv+ CP++
  gi|91772347|ref|YP_565039.1| 266 DACLGCGNCVIMCPVN 281
                                   78************75 PP

  == domain 8  score: 8.8 bits;  conditional E-value: 0.0024
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   qe C  Cg+C  +CP+
  gi|91772347|ref|YP_565039.1| 314 QEACGSCGACALICPV 329
                                   688999*********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 !   11.7   3.9   0.00027      0.28      48      63 ..      18      33 ..       3      35 .. 0.72
   2 !   16.7  14.7   7.2e-06    0.0075       3      64 ..      19      73 ..      17      74 .. 0.65
   3 !   26.1   8.3   8.5e-09   8.9e-06       3      64 ..     101     156 ..     100     157 .. 0.77
   4 !    8.0   4.4    0.0036       3.8      47      64 ..     171     188 ..     159     189 .. 0.80
   5 !   26.6   7.4   5.8e-09   6.1e-06       3      64 ..     209     281 ..     207     282 .. 0.72
   6 !   19.1  10.3   1.2e-06    0.0013       3      64 ..     266     330 ..     264     332 .. 0.63
   7 !   12.2   2.1   0.00018      0.19       2      20 ..     314     332 ..     313     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                        Fer4_8 48 lwsCttcgaCtevCpv 63
                                   ++C +cg Ct vCp+
  gi|91772347|ref|YP_565039.1| 18 PEKCIGCGTCTMVCPK 33
                                  5678888888888887 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.2e-06
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtk...khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  ekCi+Cg C+  Cp  ++t         arg  ++  +  +      + ++C tcg+Ct+vCp+g
  gi|91772347|ref|YP_565039.1| 19 EKCIGCGTCTMVCP--KDTLiigSVGPVARGLINK--EYLD------IRDTCITCGMCTKVCPTG 73
                                  69***********9..3333111222233333333..3333......469*************87 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 8.5e-09
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ++C++Cg C++ Cp    +  ++l +    +++  ++          ++C++cg C+evCp++
  gi|91772347|ref|YP_565039.1| 101 DNCVHCGVCEQICPQGAIETrQWLANDGSARID-GETIID------QETCVHCGWCSEVCPTN 156
                                   68************8877773665555555555.444444......68*************97 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0036
                        Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                   a + C++c+ C++vCp +
  gi|91772347|ref|YP_565039.1| 171 AEDVCQACRTCVDVCPCN 188
                                   5577************86 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 5.8e-09
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvlee...........eealwsCttcgaCtevCpvg 64 
                                   ++Ci CgaC  +Cpv     +     ++++++ v e++ l++            +  ++C++cg+C+  Cpv+
  gi|91772347|ref|YP_565039.1| 209 DACIYCGACAVSCPVNAIDVQKTAIVPDMNKKAVFEKKLLNKpsatpvltsvlVTDEDACLGCGNCVIMCPVN 281
                                   58************77776666666666666623333333336666677777777779*************97 PP

  == domain 6  score: 19.1 bits;  conditional E-value: 1.2e-06
                        Fer4_8   3 ekCieCgaCqsaCp............vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ++C +Cg C  +Cp            +l++ + k ll+ r++  + v+           ++C +cgaC+  Cpv+
  gi|91772347|ref|YP_565039.1| 266 DACLGCGNCVIMCPvnaksskdlaagSLNDLDeKPLLEVRNGTVK-VV---------DQEACGSCGACALICPVS 330
                                   68************4444444444444444443333333333333.32.........3468************96 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.00018
                        Fer4_8   2 lekCieCgaCqsaCpvlrr 20 
                                    e+C+ CgaC   Cpv   
  gi|91772347|ref|YP_565039.1| 314 QEACGSCGACALICPVSAI 332
                                   5799999999999998765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.9   7.2e-06    0.0076      41      59 ..      16      34 ..       1      35 [. 0.75
   2 !   21.5  13.9   2.5e-07   0.00026       2      59 ..      60     116 ..      59     118 .. 0.87
   3 !   16.6  11.6   7.9e-06    0.0083       2      59 ..     103     156 ..     103     158 .. 0.74
   4 !    7.6  14.9    0.0052       5.5       2      58 ..     175     223 ..     174     225 .. 0.78
   5 !   17.9   8.8   3.2e-06    0.0034       1      59 [.     210     281 ..     210     283 .. 0.62
   6 !   13.6   7.8   6.8e-05     0.072       1      57 [.     267     328 ..     267     332 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.2e-06
                       Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                     ++Ci+Cg C+++CP++
  gi|91772347|ref|YP_565039.1| 16 YLPEKCIGCGTCTMVCPKD 34
                                  45689************86 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.5e-07
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   Ci Cg+C+++Cp+++    e  k++ + ++ l+      ++ ++C++Cg Ce+ CPqg
  gi|91772347|ref|YP_565039.1|  60 CITCGMCTKVCPTGALEMREDGKPVCDENF-LCSSLAPTTVNDNCVHCGVCEQICPQG 116
                                   ***************988888888888566.566666679****************97 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 7.9e-06
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   C +Cg C++ Cp++++     + l+++ ++  ++++ +    ++C++Cg C+++CP +
  gi|91772347|ref|YP_565039.1| 103 CVHCGVCEQICPQGAIETR--QWLANDGSAR-IDGE-TIIDQETCVHCGWCSEVCPTN 156
                                   9*************99554..5566664443.3331.2246699************86 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0052
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl.glleeaekeekaslCieCgeCerkCPq 58 
                                   C+ C+ C+++Cp ++  +        ++++ ++++++   ++ + Ci Cg C+ +CP 
  gi|91772347|ref|YP_565039.1| 175 CQACRTCVDVCPCNALFNP-------EWAPgERVDKV--AQRPDACIYCGACAVSCPV 223
                                   *************999776.......23331345554..57899*************6 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 3.2e-06
                       Fer4_17   1 rCiqCgyClpeCpsyea..........ydne.....pkkllraaklglleeaeke.......ekaslCieCgeCerkCPqg 59 
                                   +Ci Cg+C+ +Cp +++          +  +     +kkll++ +++               +  + C++Cg+C+  CP +
  gi|91772347|ref|YP_565039.1| 210 ACIYCGACAVSCPVNAIdvqktaivpdM--NkkavfEKKLLNKPSAT-------PvltsvlvTDEDACLGCGNCVIMCPVN 281
                                   6************998855444443321..21122233444443333.......123334447889*************75 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 6.8e-05
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepk.........kllraaklglleeaekeekaslCieCgeCerkCP 57 
                                   +C +Cg C+ +Cp +++ +++ +         k+l ++++g ++        + C +Cg C+  CP
  gi|91772347|ref|YP_565039.1| 267 ACLGCGNCVIMCPVNAKSSKDLAagslndldeKPLLEVRNGTVKV----VDQEACGSCGACALICP 328
                                   5*************9996664331111111113444444433333....46689***********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 !   11.8   5.5   0.00037      0.39       1      14 [.      21      34 ..      21      34 .. 0.95
   2 !   14.5   5.8   4.9e-05     0.052       1      15 []      60      74 ..      60      74 .. 0.98
   3 !   13.8   7.0   8.3e-05     0.087       1      15 []     103     117 ..     103     117 .. 0.98
   4 !   16.6   5.6   1.1e-05     0.011       1      15 []     143     157 ..     143     157 .. 0.98
   5 ?    6.1  10.5     0.025        26       1      15 []     175     189 ..     175     189 .. 0.94
   6 !   12.6   6.6   0.00019       0.2       1      15 []     211     225 ..     211     225 .. 0.98
   7 !   12.2   6.4   0.00027      0.28       1      15 []     268     282 ..     268     282 .. 0.98
   8 ?    6.7   5.9     0.015        16       3      15 .]     319     331 ..     317     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+gCg+C  vCP++
  gi|91772347|ref|YP_565039.1| 21 CIGCGTCTMVCPKD 34
                                  ************85 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.9e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C +vCP+gA
  gi|91772347|ref|YP_565039.1| 60 CITCGMCTKVCPTGA 74
                                  **************9 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 8.3e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C++Cg C++ CP gA
  gi|91772347|ref|YP_565039.1| 103 CVHCGVCEQICPQGA 117
                                   *************99 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 1.1e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C++Cg C evCP++A
  gi|91772347|ref|YP_565039.1| 143 CVHCGWCSEVCPTNA 157
                                   *************98 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.025
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C++Cv+vCP +A
  gi|91772347|ref|YP_565039.1| 175 CQACRTCVDVCPCNA 189
                                   999*********998 PP

  == domain 6  score: 12.6 bits;  conditional E-value: 0.00019
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ CgaC ++CPv+A
  gi|91772347|ref|YP_565039.1| 211 CIYCGACAVSCPVNA 225
                                   9************99 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.00027
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gCg Cv  CPv+A
  gi|91772347|ref|YP_565039.1| 268 CLGCGNCVIMCPVNA 282
                                   *************99 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.015
                        Fer4_3   3 gCgaCvevCPvgA 15 
                                    CgaC   CPv A
  gi|91772347|ref|YP_565039.1| 319 SCGACALICPVSA 331
                                   5*********977 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 !   10.9   3.5   0.00049      0.52       4      18 ..      19      33 ..      18      33 .. 0.93
   2 !   11.8   4.3   0.00026      0.28       3      18 ..      57      72 ..      54      88 .. 0.82
   3 ?   -2.6   0.0       7.8   8.2e+03       9      18 ..      88      97 ..      80      98 .. 0.77
   4 !   10.0   3.2   0.00094      0.99       1      18 [.      99     115 ..      99     116 .. 0.93
   5 !   11.9   3.6   0.00024      0.25       1      18 [.     138     155 ..     138     156 .. 0.95
   6 ?   -1.4  20.7       3.3   3.5e+03       4      58 .]     173     228 ..     172     228 .. 0.83
   7 !   10.8   2.0   0.00051      0.54       2      17 ..     264     279 ..     262     287 .. 0.94
   8 !   10.4   3.2   0.00071      0.74       1      17 [.     312     328 ..     312     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  ++Ci+cg+C +++P+
  gi|91772347|ref|YP_565039.1| 19 EKCIGCGTCTMVCPK 33
                                  79************5 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00026
                       Fer4_13  3 rdtCiacgaCvelaPd 18
                                  rdtCi cg C +++P 
  gi|91772347|ref|YP_565039.1| 57 RDTCITCGMCTKVCPT 72
                                  79*************6 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.8
                       Fer4_13  9 cgaCvelaPd 18
                                    +C +laP 
  gi|91772347|ref|YP_565039.1| 88 NFLCSSLAPT 97
                                  55799**996 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00094
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   V+ d+C+ cg+C +++P+
  gi|91772347|ref|YP_565039.1|  99 VN-DNCVHCGVCEQICPQ 115
                                   67.9*************6 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 0.00024
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   +D++tC+ cg C e++P 
  gi|91772347|ref|YP_565039.1| 138 IDQETCVHCGWCSEVCPT 155
                                   8****************6 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 3.3
                       Fer4_13   4 dtCiacgaCvelaP..dvFeeddeggasvvaeqptseeekadaeeAadaCPvesIgv 58 
                                   d C ac +Cv+++P   +F  +   g  +v +  + ++    + + a +CPv++I v
  gi|91772347|ref|YP_565039.1| 173 DVCQACRTCVDVCPcnALFNPEWAPG-ERVDKVAQRPDACIYCGACAVSCPVNAIDV 228
                                   78************444566666544.7888889999999***************86 PP

  == domain 7  score: 10.8 bits;  conditional E-value: 0.00051
                       Fer4_13   2 DrdtCiacgaCvelaP 17 
                                   D+d C +cg+Cv ++P
  gi|91772347|ref|YP_565039.1| 264 DEDACLGCGNCVIMCP 279
                                   89*************9 PP

  == domain 8  score: 10.4 bits;  conditional E-value: 0.00071
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   VD++ C +cgaC+ ++P
  gi|91772347|ref|YP_565039.1| 312 VDQEACGSCGACALICP 328
                                   9***************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   1.1   8.2e-05     0.086       1      13 [.      20      32 ..       5      35 .. 0.71
   2 !    9.0   5.3    0.0023       2.4       1      16 [.      59      74 ..      59      89 .. 0.84
   3 ?    6.4   3.8     0.015        16      79      94 ..     100     115 ..      90     118 .. 0.74
   4 ?    5.6   3.5     0.027        29       2      14 ..     103     115 ..     102     130 .. 0.75
   5 !   10.1   2.2    0.0011       1.2      78      94 ..     139     155 ..     117     157 .. 0.72
   6 !    8.5   2.7    0.0034       3.6       2      15 ..     143     156 ..     142     174 .. 0.82
   7 ?   -1.1   6.1       3.2   3.4e+03       2      13 ..     175     186 ..     158     190 .. 0.71
   8 ?    0.3   5.3       1.3   1.3e+03       2      16 ..     175     189 ..     174     210 .. 0.76
   9 ?    6.2   3.1     0.018        19       2      14 ..     211     223 ..     210     247 .. 0.76
  10 !   13.5   0.8   9.5e-05       0.1      77      95 ..     263     281 ..     229     282 .. 0.70
  11 !    7.8   0.8    0.0055       5.8       2      14 ..     317     329 ..     304     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.2e-05
                       Fer4_22  1 rClsCgaCtlvCp 13
                                  +C++Cg+Ct+vCp
  gi|91772347|ref|YP_565039.1| 20 KCIGCGTCTMVCP 32
                                  4666666666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0023
                       Fer4_22  1 rClsCgaCtlvCptCs 16
                                  +C++Cg Ct vCpt  
  gi|91772347|ref|YP_565039.1| 59 TCITCGMCTKVCPTGA 74
                                  5************965 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.015
                       Fer4_22  79 esgCvGCgRCieacpv 94 
                                   +  Cv Cg C++ cp+
  gi|91772347|ref|YP_565039.1| 100 NDNCVHCGVCEQICPQ 115
                                   5678888888888876 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.027
                       Fer4_22   2 ClsCgaCtlvCpt 14 
                                   C++Cg C  +Cp 
  gi|91772347|ref|YP_565039.1| 103 CVHCGVCEQICPQ 115
                                   6666666666664 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0011
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                   ++++Cv Cg C+e+cp+
  gi|91772347|ref|YP_565039.1| 139 DQETCVHCGWCSEVCPT 155
                                   67777888888877776 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0034
                       Fer4_22   2 ClsCgaCtlvCptC 15 
                                   C++Cg C+ vCpt 
  gi|91772347|ref|YP_565039.1| 143 CVHCGWCSEVCPTN 156
                                   99999999999985 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 3.2
                       Fer4_22   2 ClsCgaCtlvCp 13 
                                   C +C +C  vCp
  gi|91772347|ref|YP_565039.1| 175 CQACRTCVDVCP 186
                                   556666666665 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 1.3
                       Fer4_22   2 ClsCgaCtlvCptCs 16 
                                   C +C +C  vCp   
  gi|91772347|ref|YP_565039.1| 175 CQACRTCVDVCPCNA 189
                                   888999999998654 PP

  == domain 9  score: 6.2 bits;  conditional E-value: 0.018
                       Fer4_22   2 ClsCgaCtlvCpt 14 
                                   C+ CgaC++ Cp 
  gi|91772347|ref|YP_565039.1| 211 CIYCGACAVSCPV 223
                                   9999999999996 PP

  == domain 10  score: 13.5 bits;  conditional E-value: 9.5e-05
                       Fer4_22  77 fgesgCvGCgRCieacpvk 95 
                                   ++e +C GCg C+ +cpv+
  gi|91772347|ref|YP_565039.1| 263 TDEDACLGCGNCVIMCPVN 281
                                   48899********999986 PP

  == domain 11  score: 7.8 bits;  conditional E-value: 0.0055
                       Fer4_22   2 ClsCgaCtlvCpt 14 
                                   C sCgaC+l+Cp 
  gi|91772347|ref|YP_565039.1| 317 CGSCGACALICPV 329
                                   6667777777764 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.9   0.00062      0.65      47      74 ..       6      34 ..       1      40 [. 0.72
   2 !   11.4   4.3   0.00027      0.28      59      80 ..      58      80 ..      48      99 .. 0.78
   3 !    8.7   2.5    0.0018       1.9      58      78 ..     100     121 ..      92     128 .. 0.80
   4 !    9.5   2.3     0.001       1.1      57      74 ..     139     156 ..     125     165 .. 0.81
   5 ?    5.2   6.0     0.022        24      55      73 ..     169     187 ..     157     190 .. 0.80
   6 !    9.0   0.9    0.0015       1.6      55      79 ..     205     230 ..     196     241 .. 0.80
   7 !    6.8   2.0    0.0069       7.3      57      75 ..     264     282 ..     250     294 .. 0.83
   8 ?    4.2   1.6     0.045        48      54      74 ..     310     330 ..     291     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00062
                       Fer4_18 47 lkekeerkekg.agdcidcescvkvcPtg 74
                                  +++k++++      +ci c++c  vcP +
  gi|91772347|ref|YP_565039.1|  6 VQTKDNKQVVYlPEKCIGCGTCTMVCPKD 34
                                  556666665541568************76 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00027
                       Fer4_18 59 gdcidcescvkvcPtg.idirkG 80
                                    ci+c++c kvcPtg +++r+ 
  gi|91772347|ref|YP_565039.1| 58 DTCITCGMCTKVCPTGaLEMRED 80
                                  67*************84577765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0018
                       Fer4_18  58 agdcidcescvkvcPtg.idir 78 
                                   + +c++c++c ++cP g i+ r
  gi|91772347|ref|YP_565039.1| 100 NDNCVHCGVCEQICPQGaIETR 121
                                   679************9745665 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.001
                       Fer4_18  57 gagdcidcescvkvcPtg 74 
                                   ++  c++c+ c +vcPt+
  gi|91772347|ref|YP_565039.1| 139 DQETCVHCGWCSEVCPTN 156
                                   5678************96 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.022
                       Fer4_18  55 ekgagdcidcescvkvcPt 73 
                                   e+++  c +c++cv+vcP 
  gi|91772347|ref|YP_565039.1| 169 ERAEDVCQACRTCVDVCPC 187
                                   566778************7 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0015
                       Fer4_18  55 ekgagdcidcescvkvcPtg.idirk 79 
                                   ++    ci c++c   cP++ id++k
  gi|91772347|ref|YP_565039.1| 205 AQRPDACIYCGACAVSCPVNaIDVQK 230
                                   455567************85489987 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.0069
                       Fer4_18  57 gagdcidcescvkvcPtgi 75 
                                   ++  c+ c+ cv +cP++ 
  gi|91772347|ref|YP_565039.1| 264 DEDACLGCGNCVIMCPVNA 282
                                   5678************975 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.045
                       Fer4_18  54 kekgagdcidcescvkvcPtg 74 
                                   k  ++  c +c++c  +cP+ 
  gi|91772347|ref|YP_565039.1| 310 KVVDQEACGSCGACALICPVS 330
                                   4566788************85 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   1.2    0.0038         4       6      20 ..      19      33 ..      14      36 .. 0.90
   2 !   14.1   3.3   5.8e-05     0.061       3      32 ..      54      85 ..      53      99 .. 0.84
   3 ?   -2.0  13.9       5.9   6.2e+03       6      66 .]     101     160 ..      98     160 .. 0.50
   4 ?    0.8   3.9      0.81   8.6e+02       6      19 ..     173     186 ..     171     193 .. 0.88
   5 ?    4.8   3.8     0.046        48       6      21 ..     209     223 ..     208     245 .. 0.78
   6 !   13.1   0.3   0.00011      0.12       3      30 ..     263     289 ..     261     306 .. 0.77
   7 !   11.9   1.2   0.00027      0.29       2      19 ..     311     328 ..     311     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0038
                       Fer4_15  6 daCigcglCvaeape 20
                                  ++Cigcg C  ++p+
  gi|91772347|ref|YP_565039.1| 19 EKCIGCGTCTMVCPK 33
                                  79***********96 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.8e-05
                       Fer4_15  3 vD.rdaCigcglCvaea.pevfeldedglasv 32
                                  +D rd+Ci cg+C +++ +   e+ edg+++ 
  gi|91772347|ref|YP_565039.1| 54 LDiRDTCITCGMCTKVCpTGALEMREDGKPVC 85
                                  5669*************446899999**9954 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.9
                       Fer4_15   6 daCigcglCvaea.....pevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66 
                                   d+C  cg+C + +     +++  l++dg a++++      e+ ++++   +     ++CP+ AI+v
  gi|91772347|ref|YP_565039.1| 101 DNCVHCGVCEQICpqgaiETRQWLANDGSARIDG------ETIIDQETCVHCGWCSEVCPTNAITV 160
                                   6677777777777333333333334444443332......34444444444445567777777765 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.81
                       Fer4_15   6 daCigcglCvaeap 19 
                                   d C+ c  Cv+++p
  gi|91772347|ref|YP_565039.1| 173 DVCQACRTCVDVCP 186
                                   78**********98 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.046
                       Fer4_15   6 daCigcglCvaeapev 21 
                                   daCi cg+C+  +p v
  gi|91772347|ref|YP_565039.1| 209 DACIYCGACAVSCP-V 223
                                   89*********998.3 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 0.00011
                       Fer4_15   3 vDrdaCigcglCvaeapevfeldedgla 30 
                                    D+daC gcg+Cv  +p v  + +++la
  gi|91772347|ref|YP_565039.1| 263 TDEDACLGCGNCVIMCP-VNAKSSKDLA 289
                                   59**************9.5555555655 PP

  == domain 7  score: 11.9 bits;  conditional E-value: 0.00027
                       Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                   vvD++aC +cg+C+  +p
  gi|91772347|ref|YP_565039.1| 311 VVDQEACGSCGACALICP 328
                                   69*************998 PP

>> Integrase_Zn  Integrase Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   8.2e-05     0.086      11      36 ..     156     181 ..     155     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-05
                  Integrase_Zn  11 NakaLrkkFgitrkqAreIVqsCptC 36 
                                   Na + +k F  t++ A+++ q+C tC
  gi|91772347|ref|YP_565039.1| 156 NAITVQKPFEGTWERAEDVCQACRTC 181
                                   88889999****************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2280.24
//
Query:       gi|91772348|ref|YP_565040.1|  [L=196]
Description: formylmethanofuran dehydrogenase, subunit E [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-26   91.1   0.0    7.9e-26   90.7   0.0    1.2  1  FmdE           FmdE, Molybdenum formylmethanofuran dehydrogen
  ------ inclusion threshold ------
      0.033   14.2   1.7      0.051   13.6   1.7    1.3  1  DZR            Double zinc ribbon
      0.074   12.8   0.7          5    7.0   0.1    2.4  2  zinc_ribbon_2  zinc-ribbon domain
       0.15   11.7   0.0       0.15   11.7   0.0    1.7  2  zf_C2H2_13     Zinc finger domain
        0.8    9.4   3.6        5.6    6.7   0.1    2.3  2  GATA           GATA zinc finger


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   2.2e-29   7.9e-26       1     125 [.      28     155 ..      28     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 2.2e-29
                                   HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEET..... CS
                          FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkr..... 76 
                                   fHG+l+ g+++G++m  +a++ l++k  e +e++++++et++C +D +q+l g+t+G++ ++++dygk+a+t++kr     
  gi|91772348|ref|YP_565040.1|  28 FHGYLSSGAMIGLQMLTMAKRLLDVK--E-GERIYVTAETSNCVPDPFQILEGATIGNKGMKIKDYGKMAVTVNKRgapge 105
                                   9**********************985..4.5*********************************************97776 PP

                                   TT-EEEEEEE-....CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS CS
                          FmdE  77 ktgkavrlklk....eelpelreklakgkakeekeeeeleeeleeaikkilna 125
                                       avr++l+    e++p+l++++++    e++++ee+   l ea++ki++ 
  gi|91772348|ref|YP_565040.1| 106 MIMPAVRIYLDaektEAYPRLHAWFMNL---EKVRHEEILPILLEAGEKIYSY 155
                                   55678**********************7...8888899999999999999876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.7   1.4e-05     0.051      10      36 ..     168     194 ..     163     196 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                           DZR  10 pdarfCseCgtklkavaaedrCpsCge 36 
                                   ++ r C++Cg++  +++ e  C +C +
  gi|91772348|ref|YP_565040.1| 168 KQVRLCEKCGESFIQYEGEALCEACRH 194
                                   67799********************87 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0014         5      13      22 ..     170     179 ..     165     180 .. 0.79
   2 ?    4.1   0.1     0.011        39      11      22 ..     184     195 ..     181     196 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                 zinc_ribbon_2  13 akFCpyCGtp 22 
                                   ++ C++CG+ 
  gi|91772348|ref|YP_565040.1| 170 VRLCEKCGES 179
                                   6789999985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                 zinc_ribbon_2  11 dnakFCpyCGtp 22 
                                   +++  C+ C+++
  gi|91772348|ref|YP_565040.1| 184 EGEALCEACRHE 195
                                   68899*****97 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.15       7      24 ..     160     177 ..     157     181 .. 0.90
   2 ?   -4.1   0.5       3.7   1.3e+04      19      23 ..     188     192 ..     188     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                    zf_C2H2_13   7 iedpLdtnlnYRvCnkCG 24 
                                   ie p+ ++ + R+C+kCG
  gi|91772348|ref|YP_565040.1| 160 IEVPVKKSKQVRLCEKCG 177
                                   88899************* PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.7
                    zf_C2H2_13  19 vCnkC 23 
                                   +C++C
  gi|91772348|ref|YP_565040.1| 188 LCEAC 192
                                   6**99 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0016       5.6      17      30 ..     167     180 ..     165     185 .. 0.80
   2 ?    3.5   0.6     0.015        54      18      27 ..     185     193 ..     182     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0016
                          GATA  17 dgnksLCnaCGlyy 30 
                                   +++ +LC+ CG  +
  gi|91772348|ref|YP_565040.1| 167 SKQVRLCEKCGESF 180
                                   57889******876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.015
                          GATA  18 gnksLCnaCG 27 
                                   g+  LC+aC 
  gi|91772348|ref|YP_565040.1| 185 GEA-LCEACR 193
                                   777.*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1334.17
//
Query:       gi|91772349|ref|YP_565041.1|  [L=95]
Description: hypothetical protein Mbur_0287, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   15.2   0.0      0.016   15.1   0.0    1.3  1  TBP       Transcription factor TFIID (or TATA-binding protein


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   9.1e-07     0.016      44      82 ..      56      94 ..      18      95 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.1e-07
                                  EETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHH CS
                           TBP 44 rlrepkvtaliFssGkvvitGakseeelreaakkiapil 82
                                  r+ +  +++li+ sGk+++  a     +r+ ++++a+++
  gi|91772349|ref|YP_565041.1| 56 RFTSGAMMVLIYGSGKITVRHAPDDGTARQLLERVAELV 94
                                  55666889***************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 770.56
//
Query:       gi|91772350|ref|YP_565042.1|  [L=211]
Description: nitrogen-fixing NifU-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-42  145.2   0.0    1.8e-42  144.5   0.0    1.4  1  NifU_N          NifU-like N terminal domain
    2.2e-10   40.6   2.8    4.2e-10   39.7   1.1    2.3  3  FeS_assembly_P  Iron-sulfur cluster assembly protein
       0.01   15.6   0.1       0.87    9.3   0.0    2.1  2  Pilus_CpaD      Pilus biogenesis CpaD protein (pilus_cpaD)
  ------ inclusion threshold ------
      0.041   14.1   0.0      0.086   13.0   0.0    1.5  1  CO_deh_flav_C   CO dehydrogenase flavoprotein C-terminal doma


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 !  144.5   0.0     4e-46   1.8e-42       2     126 ..       5     126 ..       4     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 4e-46
                                   SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSBH CS
                        NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgktl 82 
                                   y+++vl+h++nP+nvG++e+ d   g g  g+pacGD+v +++kv+ +t +ied++F+++GC+s iA++s++te+ kgktl
  gi|91772350|ref|YP_565042.1|   5 YTKEVLEHFRNPQNVGKMEDPD---GKGLEGSPACGDMVAVYLKVNPDTLVIEDISFESYGCASNIATASMITEMAKGKTL 82 
                                   99********************...8******************************************************* PP

                                   HHHCCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                        NifU_N  83 eealkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakk 126
                                   eea+kit ke+a++lgglp++k hcsvla + l+ a+++Y++k+
  gi|91772350|ref|YP_565042.1|  83 EEAKKITWKEAANALGGLPPVKAHCSVLAVEGLRSAIRDYEEKH 126
                                   *****************************************997 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.82   3.7e+03      56      68 ..      92     104 ..      90     110 .. 0.82
   2 ?   -2.7   0.0       1.6   7.1e+03      45      58 ..     105     120 ..     102     121 .. 0.74
   3 !   39.7   1.1   9.3e-14   4.2e-10       4      72 ..     140     207 ..     138     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.82
                                   HHHHHHC.STT-- CS
                FeS_assembly_P  56 daeaalralpgve 68 
                                   +a +al+ lp+v+
  gi|91772350|ref|YP_565042.1|  92 EAANALGGLPPVK 104
                                   7889999999964 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.6
                                   TT-T..THHHHHHHHH CS
                FeS_assembly_P  45 pacs..laeairadae 58 
                                   ++cs  ++e++r++++
  gi|91772350|ref|YP_565042.1| 105 AHCSvlAVEGLRSAIR 120
                                   6888777788888776 PP

  == domain 3  score: 39.7 bits;  conditional E-value: 9.3e-14
                                   HHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                FeS_assembly_P   4 vlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpgvevveV 72 
                                   v + L++V+ P  g+d++ + lv ++++e+g+V++ + ++    ++a ai++d+ ++l++l+ ve+v+V
  gi|91772350|ref|YP_565042.1| 140 VSKRLKHVMNPMAGLDIIRTELVLKVVVEEGTVRIVLDIP-STHQFAVAIKEDIVDKLESLWDVESVTV 207
                                   7889***********************************9.55556*****************888877 PP

>> Pilus_CpaD  Pilus biogenesis CpaD protein (pilus_cpaD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0059        26     155     173 ..      56      74 ..      33      83 .. 0.78
   2 !    9.3   0.0   0.00019      0.87      22      87 ..     116     185 ..     103     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0059
                    Pilus_CpaD 155 esysnfGCAvqaNlAamva 173
                                    s + +GCA++   A m+ 
  gi|91772350|ref|YP_565042.1|  56 ISFESYGCASNIATASMIT 74 
                                   56789************96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00019
                    Pilus_CpaD  22 tgsi.dyrsrhpivveeaeasldlkvasgdggLtaaqrarl...ealaeeyrregagaivisvpsgssne 87 
                                    ++i dy+++h +vve+++ ++++  ++ +  +++++  ++   e +++ + +eg+ +iv+++ps  + +
  gi|91772350|ref|YP_565042.1| 116 RSAIrDYEEKHGMVVENEATTVEVVSKRLKHVMNPMAGLDIirtELVLKVVVEEGTVRIVLDIPSTHQFA 185
                                   456689******************9988888888888776633345778888899999999999887665 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05     0.086      18      62 ..      40      85 ..      38     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                  EEEEEEEETTC.EECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHH CS
                 CO_deh_flav_C 18 aAfrveleedg.kiedariafggvaptpvraekaeaaLiGkplsee 62
                                  +A+ +++++d+ +ied+++   g+a+   +a+ + ++ +Gk l+e+
  gi|91772350|ref|YP_565042.1| 40 VAVYLKVNPDTlVIEDISFESYGCASNIATASMITEMAKGKTLEEA 85
                                  89****************************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1437.96
//
Query:       gi|91772351|ref|YP_565043.1|  [L=389]
Description: aminotransferase, class V [Methanococcoides burtonii DSM 6242]
Scores for complete 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-70  236.9   0.0    3.9e-70  236.7   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    9.3e-06   25.2   0.2    1.4e-05   24.6   0.2    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.004   16.5   0.1     0.0059   15.9   0.1    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.022   14.3   0.0      0.067   12.8   0.0    1.8  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
      0.061   11.9   0.3      0.097   11.2   0.3    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.14   12.1   0.2       0.47   10.3   0.1    1.9  2  Transketolase_C  Transketolase, C-terminal domain


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 !  236.7   0.0   1.3e-73   3.9e-70       1     370 [.       6     367 ..       6     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 236.7 bits;  conditional E-value: 1.3e-73
                                   EEEBTTTS----HHHHHHHHHHHHCTCCSSSS.SSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHH CS
                   Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhr.svhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvals 80 
                                   iyld+aA+t++ +eVl+a++ y+ d +a +++   +++g +a++ +e  r+ +a  ++a+   ei+ftsG+te+ n+++++
  gi|91772351|ref|YP_565043.1|   6 IYLDNAASTRLDEEVLEAMKPYFFDAYAVATSeFGYSMGIDAKEGLERSRKVIASRLGAQA-GEIVFTSGSTESSNMAIKG 85 
                                   8*******************************55789***********************6.******************* PP

                                   CCCC..-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HH CS
                   Aminotran_5  81 lars..lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpve 159
                                   ++ +   k++d+ +v+++e  + l+++++l  ++g+kv++i++d eg ld+d ++++++ +t+lv+i++++ ++Gt+q+++
  gi|91772351|ref|YP_565043.1|  86 VLSAlkGKKDDHLIVSRLEDFSVLNTAKKLD-KQGYKVDFINVDGEGVLDIDMFTDTITSQTALVSIQQANQEIGTLQDLK 165
                                   *999777899********************8.67*********************************************** PP

                                   HHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEE CS
                   Aminotran_5 160 eigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsleett 240
                                   +i +++ +k++l+++Da+ ++   p+dv+kl vD++++s+h ++gP GiG+ly+r+     + +++ gg        +e+ 
  gi|91772351|ref|YP_565043.1| 166 AISDICEDKDVLLHTDATHSFTRVPLDVSKLPVDLVTMSAHTIHGPRGIGALYIRE--GTPIDKWMDGGF-------QESD 237
                                   ********************************************************..99**********.......7777 PP

                                   EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSH CS
                   Aminotran_5 241 faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvha 321
                                           +aG +n+++++g+++a+e++   + e+ ++  ++    ++ +++++ +v+l+g + + r ++  +++f++v+ 
  gi|91772351|ref|YP_565043.1| 238 -------RRAGVENIPSAVGFAKAVELVTPEENERLAAMRDRV---IERAMSDISHVTLNG-SATSRLPQNANMTFHYVEG 307
                                   .......89*******************777777666666655...556677788888988.5789*************** PP

                                   HHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHH CS
                   Aminotran_5 322 edvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdr 370
                                   e +   Ld  g av++G++c     + ++++l++        g++R+S+++ nt e+ d+
  gi|91772351|ref|YP_565043.1| 308 ESITLHLDMLGFAVSTGSACFsrslEASHVILGIGgnherahGSLRFSFGRFNTIEDADA 367
                                   ********************9777766666666668889999***************986 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 !   24.6   0.2   4.8e-09   1.4e-05      44     149 ..      76     186 ..      58     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.8e-09
                                   ESSHHHHHHHHHHHTTTTTT-EEEEE...SSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-G. CS
               DegT_DnrJ_EryC1  44 vssGtaAlhlaLralgvgpgdeVIvp...sltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhl. 120
                                   + s   A+  +L+al+ +++d +Iv     ++ + ta+   + g+k+ f++vd     +d ++    it++t+ + +  + 
  gi|91772351|ref|YP_565043.1|  76 TESSNMAIKGVLSALKGKKDDHLIVSrleDFSVLNTAKKLDKQGYKVDFINVD-GEGVLDIDMFTDTITSQTALVSIQQAn 155
                                   4566678888999************933346777788888899**********.6789**************776655442 PP

                                   ..GGB---HHHHHHHHHHCT-EEEEE-TT-T CS
               DegT_DnrJ_EryC1 121 ..yGqvadmdalkaiaakhglkvieDaAhAl 149
                                      G   d++a+ +i++++++ +  Da h++
  gi|91772351|ref|YP_565043.1| 156 qeIGTLQDLKAISDICEDKDVLLHTDATHSF 186
                                   237999***********************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 !   15.9   0.1     2e-06    0.0059      92     169 ..     116     183 ..      45     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                                   HCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
               Beta_elim_lyase  92 elagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                     +g k+  ++ + +G +d++ + + i+       +++l+s+ ++n+     + +l+ l+++++i++++++ lh D++
  gi|91772351|ref|YP_565043.1| 116 DKQGYKVDFINVDGEGVLDIDMFTDTITS------QTALVSIQQANQE----IGTLQDLKAISDICEDKDVLLHTDAT 183
                                   4466777777777779***********99......599*********5....779*********************97 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   3.7e+03      59      75 ..      81      97 ..      64     126 .. 0.68
   2 ?   12.8   0.0   2.2e-05     0.067      43      85 ..     237     279 ..     212     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                                  HHHHHHSGGGTTTEEEE CS
                       Gp_dh_C 59 kavglVlpelkgkldgl 75
                                   a++ Vl  lkgk d +
  gi|91772351|ref|YP_565043.1| 81 MAIKGVLSALKGKKDDH 97
                                  58888888888886555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.2e-05
                                   TSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEEEEESSSSEE CS
                       Gp_dh_C  43 araaaeniiptstgaakavglVlpelkgkldglAvrVPtpnvs 85 
                                    r a+ + ip+  g akav+lV pe + +l ++  rV    +s
  gi|91772351|ref|YP_565043.1| 237 DRRAGVENIPSAVGFAKAVELVTPEENERLAAMRDRVIERAMS 279
                                   355677889**********************998888666665 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 ?   11.2   0.3   3.2e-05     0.097      78     196 ..      81     205 ..      51     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT-- CS
               Cys_Met_Meta_PP  78 aAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvylEtptnpllkv 153
                                    Ai+ ++ al  + d+ ++ + l + +     k l k g +v+f+++      d++ +   i+++t lv +         +
  gi|91772351|ref|YP_565043.1|  81 MAIKGVLSALKGKKDDHLIVSRLEDFSVLNTAKKLDKQGYKVDFINVdgegvLDIDMFTDTITSQTALVSIQQANQEIGTL 161
                                   244444445544444444445565666666677788888999998875555579999****************999999** PP

                                   --HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEET CS
               Cys_Met_Meta_PP 154 vDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSa 196
                                    D+++i++++ +++vl+  D+t +   +     kl +D+v+ Sa
  gi|91772351|ref|YP_565043.1| 162 QDLKAISDICEDKDVLLHTDATHSFTrVPLDVSKLPVDLVTMSA 205
                                   **********************8744365666677799998887 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00016      0.47      23      77 ..     107     161 ..      94     181 .. 0.92
   2 ?   -2.4   0.0       1.4   4.2e+03      61      86 ..     254     279 ..     248     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
               Transketolase_C  23 ealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                    +l+ a++L k+g++++ +++     lD +++ + + +   lv +++a+++ G  
  gi|91772351|ref|YP_565043.1| 107 SVLNTAKKLDKQGYKVDFINVDGEGVLDIDMFTDTITSQTALVSIQQANQEIGTL 161
                                   5899*********************************999***999999999875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                   HSEEEEEEEEESTTSHHHHHHHHHHH CS
               Transketolase_C  61 tgrlvvveeavkrgGigsevaaalae 86 
                                     +lv+ ee+ +  ++ + v+++ + 
  gi|91772351|ref|YP_565043.1| 254 AVELVTPEENERLAAMRDRVIERAMS 279
                                   56789999999999888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2455.44
//
Query:       gi|91772352|ref|YP_565044.1|  [L=107]
Description: hypothetical protein Mbur_0290 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00055   19.9   0.0    0.00089   19.3   0.0    1.3  1  HTH_3           Helix-turn-helix
     0.0045   16.5   0.0     0.0078   15.8   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0074   16.1   0.1      0.023   14.5   0.0    1.7  2  HTH_23          Homeodomain-like domain
     0.0093   16.0   0.0      0.018   15.1   0.0    1.5  1  HTH_7           Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.015   14.7   0.0        0.1   12.0   0.0    2.0  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.016   15.5   0.0      0.032   14.5   0.0    1.5  1  DUF2811         Protein of unknown function (DUF2811)
      0.018   14.9   0.0      0.035   14.0   0.0    1.5  1  MarR_2          MarR family
      0.029   14.5   0.1      0.065   13.4   0.0    1.6  2  HTH_28          Helix-turn-helix domain
      0.036   13.9   0.0        4.4    7.3   0.0    2.3  2  HTH_5           Bacterial regulatory protein, arsR family
       0.04   13.6   0.0      0.082   12.6   0.0    1.6  1  Sigma70_r4_2    Sigma-70, region 4
       0.05   13.5   0.0      0.084   12.7   0.0    1.5  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.059   13.7   0.0       0.13   12.6   0.0    1.7  2  HTH_31          Helix-turn-helix domain
      0.079   12.9   0.0        0.2   11.6   0.0    1.6  2  HTH_37          Helix-turn-helix domain
       0.09   12.6   0.0       0.22   11.4   0.0    1.6  2  P22_Cro         DNA-binding transcriptional regulator Cro
       0.11   12.6   0.0       0.15   12.1   0.0    1.3  1  Cro             Cro


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.5e-07   0.00089       7      34 ..      28      55 ..      22      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.5e-07
                                  HTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                         HTH_3  7 qlglsqeeLAeklGvsrstisriEnGer 34
                                   +g+ q+e+A++ G+ +s++s+++  +r
  gi|91772352|ref|YP_565044.1| 28 NNGIAQKEVARLFGMAPSAVSQYMTKKR 55
                                  689********************98765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.5e-06    0.0078      15      39 ..      28      52 ..      22      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.5e-06
                        HTH_24 15 nprisqreLAerlglSpstvnrrlk 39
                                  n +i q+e+A+  g+ ps+v++++ 
  gi|91772352|ref|YP_565044.1| 28 NNGIAQKEVARLFGMAPSAVSQYMT 52
                                  889********************96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.9e-05     0.023       6      38 ..      19      51 ..      15      60 .. 0.80
   2 ?   -1.2   0.0       1.6   1.9e+03      19      27 ..      87      95 ..      69      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                        HTH_23  6 eRlrillllaeGlsvreIAreLgvsrrTvyrwl 38
                                  + ++++ l+ +G+ ++e+Ar++g+ ++ v+++ 
  gi|91772352|ref|YP_565044.1| 19 RAALAVELVNNGIAQKEVARLFGMAPSAVSQYM 51
                                  44567777778******************9984 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                        HTH_23 19 svreIAreL 27
                                   + +I+r+L
  gi|91772352|ref|YP_565044.1| 87 KICDICRHL 95
                                  345566655 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 !   15.1   0.0   1.5e-05     0.018      12      44 ..      21      53 ..      15      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                  GGGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                         HTH_7 12 nrvvkLleeGisiskIAkevnisRsTvYRylad 44
                                  + +v+L+++Gi+ +++A+ ++ ++s v +y ++
  gi|91772352|ref|YP_565044.1| 21 ALAVELVNNGIAQKEVARLFGMAPSAVSQYMTK 53
                                  789**********************99888765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.5e-05       0.1      18      48 ..      21      51 ..      19      53 .. 0.86
   2 ?    0.0   0.0      0.48   5.7e+02      32      42 ..      90     100 ..      90     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.5e-05
                  HTH_Tnp_ISL3 18 ayilelllesrsvkavArqlgvSwtTVwril 48
                                  a ++el+ ++++ k+vAr++g  ++ V  ++
  gi|91772352|ref|YP_565044.1| 21 ALAVELVNNGIAQKEVARLFGMAPSAVSQYM 51
                                  6688888888***************998765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.48
                  HTH_Tnp_ISL3  32 avArqlgvSwt 42 
                                   +++r+l+++++
  gi|91772352|ref|YP_565044.1|  90 DICRHLRTGDD 100
                                   799*****997 PP

>> DUF2811  Protein of unknown function (DUF2811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.7e-05     0.032      24      52 ..      12      40 ..       7      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                       DUF2811 24 WDqdrllqaALslFLlqngssdravarvY 52
                                  WD    + aAL+  L++ng  +++var++
  gi|91772352|ref|YP_565044.1| 12 WDVLPAIRAALAVELVNNGIAQKEVARLF 40
                                  999999********************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.9e-05     0.035       5      40 ..      16      49 ..      11      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                                  HHHHHHHHH.HHCTTTSEEEHHHHHHHHTSSHHHHHH CS
                        MarR_2  5 paqarvLaa.Lgrrpgrdltvgelarrlglsksavsr 40
                                  pa++ +La+ L +++   ++++e+ar +g+ +savs+
  gi|91772352|ref|YP_565044.1| 16 PAIRAALAVeLVNNG---IAQKEVARLFGMAPSAVSQ 49
                                  666677776577776...9*****************8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.5e-05     0.065       5      31 ..      23      49 ..      19      60 .. 0.88
   2 ?   -2.4   0.0       4.6   5.5e+03      18      24 ..      91      97 ..      75     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                        HTH_28  5 iikllaaGhsvreaArelgisrrtvyr 31
                                  +++l+ +G +++e+Ar++g+ ++ v++
  gi|91772352|ref|YP_565044.1| 23 AVELVNNGIAQKEVARLFGMAPSAVSQ 49
                                  788999999***************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                        HTH_28 18 aArelgi 24
                                  ++r+l +
  gi|91772352|ref|YP_565044.1| 91 ICRHLRT 97
                                  6777655 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0037       4.4      20      35 ..      35      50 ..      32      53 .. 0.88
   2 ?    4.5   0.0     0.027        32      16      26 ..      86      96 ..      82      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0037
                                  HHHHHHTS-HHHHHHH CS
                         HTH_5 20 elaeelglsqstvShH 35
                                  e a+ +g+ +s+vS++
  gi|91772352|ref|YP_565044.1| 35 EVARLFGMAPSAVSQY 50
                                  77999*********97 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                                  EEHHHHHHHHT CS
                         HTH_5 16 lcvcelaeelg 26
                                  +++c+++++l+
  gi|91772352|ref|YP_565044.1| 86 AKICDICRHLR 96
                                  689******96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.9e-05     0.082      25      48 ..      29      52 ..      17      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.9e-05
                                  S---HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2 25 eglsykEIAellgisegtVksrls 48
                                  +g  +kE+A+l+g+ +++V +++ 
  gi|91772352|ref|YP_565044.1| 29 NGIAQKEVARLFGMAPSAVSQYMT 52
                                  66779***************9986 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.1e-05     0.084      10      43 ..      32      65 ..      21      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpaervpeI 43
                                   qk++A++ g++++aVsq +  k++  +e   eI
  gi|91772352|ref|YP_565044.1| 32 AQKEVARLFGMAPSAVSQYMTKKRGYRIEFDNEI 65
                                  59******************98888766655555 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011      0.13      13      40 ..      22      56 ..      12      74 .. 0.82
   2 ?   -1.9   0.0       3.8   4.6e+03      47      57 ..      88      98 ..      76     101 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                        HTH_31 13 a.......GLsqeevAerlgvsestlsrlEqGrrg 40
                                          G+ q+evA++ g+ +s +s++++ +rg
  gi|91772352|ref|YP_565044.1| 22 LavelvnnGIAQKEVARLFGMAPSAVSQYMTKKRG 56
                                  45566666999*******************98875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                        HTH_31 47 lealaralgld 57
                                  +  ++r l++ 
  gi|91772352|ref|YP_565044.1| 88 ICDICRHLRTG 98
                                  44566666664 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017       0.2      26      53 ..      25      52 ..      17      63 .. 0.80
   2 ?   -1.9   0.0       2.8   3.4e+03      50      60 ..      75      85 ..      64      87 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                  HHHHCT--HHHHHHHHT--HHHHHHHHT CS
                        HTH_37 26 liekrelsqseaaqllgiaqPkvsrllr 53
                                   +  ++++q+e+a+l+g+a + vs+ + 
  gi|91772352|ref|YP_565044.1| 25 ELVNNGIAQKEVARLFGMAPSAVSQYMT 52
                                  5567899*****************9764 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                                  HHHTT--TT-- CS
                        HTH_37 50 rllrgklsrfs 60
                                  +++ gk++++s
  gi|91772352|ref|YP_565044.1| 75 EIQEGKIDNVS 85
                                  35556666655 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 ?   -3.0   0.0       5.6   6.7e+03      29      39 ..      12      21 ..      10      31 .. 0.65
   2 ?   11.4   0.0   0.00019      0.22      12      42 ..      33      60 ..      32      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.6
                                  HHTC--HHHHH CS
                       P22_Cro 29 WgeeiPelray 39
                                  W + +P  ra 
  gi|91772352|ref|YP_565044.1| 12 W-DVLPAIRAA 21
                                  6.677777653 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00019
                                  HHHHHHHHTS-HHHHHHHHTC--HHHHHHHH CS
                       P22_Cro 12 vekvAkalgvtksAVsqWgeeiPelrayqie 42
                                  ++ vA++ g ++sAVsq      ++r y+ie
  gi|91772352|ref|YP_565044.1| 33 QKEVARLFGMAPSAVSQY---MTKKRGYRIE 60
                                  678**************9...6678888887 PP

>> Cro  Cro
   #    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      13      38 ..      31      56 ..      20      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                  HHHHHHHHHHTS-HHHHHHHHHCT-E CS
                           Cro 13 vGQaktAkdlgvkqsaIsKAlkakRn 38
                                  + Q+ +A+ +g+++sa+s  + +kR 
  gi|91772352|ref|YP_565044.1| 31 IAQKEVARLFGMAPSAVSQYMTKKRG 56
                                  569******************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 636.79
//
Query:       gi|91772353|ref|YP_565045.1|  [L=63]
Description: XRE family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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-18   65.4   0.0    3.8e-18   65.3   0.0    1.0  1  HTH_3           Helix-turn-helix
    8.6e-09   35.3   0.1      1e-08   35.1   0.1    1.0  1  HTH_19          Helix-turn-helix domain
    2.7e-08   34.1   0.0    3.3e-08   33.9   0.0    1.1  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    1.7e-07   31.5   0.0    1.9e-07   31.3   0.0    1.0  1  HTH_31          Helix-turn-helix domain
      8e-05   22.4   0.1    9.9e-05   22.1   0.1    1.2  1  HTH_25          Helix-turn-helix domain
    0.00021   21.2   0.1    0.00032   20.6   0.1    1.2  1  HTH_11          HTH domain
     0.0096   15.9   0.1       0.01   15.8   0.1    1.1  1  Translin        Translin family
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.024   14.5   0.0    1.2  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.026   14.5   0.0      0.035   14.1   0.0    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.032   13.7   0.1      0.048   13.2   0.1    1.2  1  Sigma70_r4      Sigma-70, region 4
      0.036   13.6   0.0      0.049   13.2   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding


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 !   65.3   0.0   2.3e-21   3.8e-18       1      54 [.       5      58 ..       5      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 2.3e-21
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                  lk +R +++++qe+LA+k+ v+r+ti++iE+G+  Ps++ ++k+a+++ +s+++
  gi|91772353|ref|YP_565045.1|  5 LKVWRAKKDITQEQLAKKIEVTRQTINAIERGKYDPSIKLAFKMARFFECSIED 58
                                  56689**********************************************997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   6.2e-12     1e-08       3      60 ..       4      60 ..       3      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.2e-12
                        HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                  +Lk  R ++ +tqe+la+++ ++r  i+aiE gk+ +ps++l  k a++++ ++e ++
  gi|91772353|ref|YP_565045.1|  4 NLKVWRAKKDITQEQLAKKIEVTRQTINAIERGKY-DPSIKLAFKMARFFECSIEDIF 60
                                  677779999*************************9.***************9998765 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     2e-11   3.3e-08       1      61 [.       4      63 .]       4      63 .] 0.96

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2e-11
                        HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleye 61
                                  +L+++ a+++it+ +La++++++++t++ +  gk   +s++   k ++ ++c+++D++ ye
  gi|91772353|ref|YP_565045.1|  4 NLKVWRAKKDITQEQLAKKIEVTRQTINAIERGK-YDPSIKLAFKMARFFECSIEDIFLYE 63
                                  799******************************9.69********************9886 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.2e-10   1.9e-07       6      55 ..       5      53 ..       4      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.2e-10
                        HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                  L+ +R++  ++qe++A+ + v++ t++ +E+G+ + ps     ++ar + 
  gi|91772353|ref|YP_565045.1|  5 LKVWRAKKDITQEQLAKKIEVTRQTINAIERGKYD-PSIKLAFKMARFFE 53
                                  889*******************************7.***99999999876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   6.1e-08   9.9e-05       3      36 ..       6      39 ..       4      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.1e-08
                                  HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                        HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                  +  R ++ ++ e++ak++ +  +++ a+E++++d
  gi|91772353|ref|YP_565045.1|  6 KVWRAKKDITQEQLAKKIEVTRQTINAIERGKYD 39
                                  55699***************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.9e-07   0.00032      11      32 ..       9      30 ..       5      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                        HTH_11 11 eargpisgeeLAeeLnvSrrtv 32
                                  +a+++i+ e+LA++++v+r+t+
  gi|91772353|ref|YP_565045.1|  9 RAKKDITQEQLAKKIEVTRQTI 30
                                  57889****************9 PP

>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.4e-06      0.01     164     204 ..       2      43 ..       1      44 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.4e-06
                                   HHHHHTS----HH....HHHHHTTHHHHHHHHHHHHHHHHHH CS
                      Translin 164 ragfellnlknds.akdlrkKldvlkqsvkKvEdvvYdlsvR 204
                                   +++++++  k d+ +++l kK++v++q ++ +E+  Yd s++
  gi|91772353|ref|YP_565045.1|   2 KNNLKVWRAKKDItQEQLAKKIEVTRQTINAIERGKYDPSIK 43 
                                   56788899998886679********************98875 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.024       9      32 ..      14      37 ..       9      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                YdaS_antitoxin  9 GgqkaLAealgvsqqaVsqWlkgk 32
                                   +q +LA++++v++q+++   +gk
  gi|91772353|ref|YP_565045.1| 14 ITQEQLAKKIEVTRQTINAIERGK 37
                                  5799**************987665 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 ?   14.1   0.0   2.2e-05     0.035      21      40 ..      13      32 ..       3      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                                  EHHHHHHHHHTTSSHHHHHH CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsr 40
                                  ++tqe+lA  + +tr+t++ 
  gi|91772353|ref|YP_565045.1| 13 DITQEQLAKKIEVTRQTINA 32
                                  69****************96 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   2.9e-05     0.048      19      42 ..      12      35 ..       7      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                  TT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4 19 eglTleEIgerlgiSrerVrqiek 42
                                  ++ T+e+++++  ++r ++  ie+
  gi|91772353|ref|YP_565045.1| 12 KDITQEQLAKKIEVTRQTINAIER 35
                                  789*******************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 ?   13.2   0.0     3e-05     0.049      16      36 ..      12      32 ..       6      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                        HTH_24 16 prisqreLAerlglSpstvnr 36
                                   +i+q +LA+++ ++++t+n+
  gi|91772353|ref|YP_565045.1| 12 KDITQEQLAKKIEVTRQTINA 32
                                  57*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 409.37
//
Query:       gi|91772354|ref|YP_565046.1|  [L=130]
Description: hypothetical protein Mbur_0293 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-26   92.7   5.6    1.6e-26   92.5   5.6    1.0  1  DUF2178   Predicted membrane protein (DUF2178)
  ------ inclusion threshold ------
       0.11   12.9   2.7       0.16   12.4   2.7    1.5  1  DUF3796   Protein of unknown function (DUF3796)
       0.21   11.5   1.4        8.6    6.3   0.1    2.1  2  SLATT_1   SMODS and SLOG-associating 2TM effector domain 1
       0.87   10.1   5.2       0.25   11.8   0.7    2.0  2  MerC      MerC mercury resistance protein


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   5.6   3.7e-30   1.6e-26       2     104 ..       9     117 ..       8     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 3.7e-30
                       DUF2178   2 liivavialvglgiwa.....aignvllaviavaaGvllaillkkkve.....evveDERlariaekAsrktlqillflia 72 
                                   l+i+++++l+g+g+++     +i+++++ +++++aGv+l+i++ ++++     ++veDER ++iaekAs+ktl il++l++
  gi|91772354|ref|YP_565046.1|   9 LVIGFILTLIGIGFRIfepswTIDPTGASGAFIGAGVVLIIITFRDIRfrnkgTIVEDERIFHIAEKASHKTLLILIILEG 89 
                                   89************7789999************************************************************ PP

                       DUF2178  73 llgvvlivlksdfpeytrvgfllafsalllli 104
                                   +l+++l+v++s++++y+ v++l+a+++    i
  gi|91772354|ref|YP_565046.1|  90 TLIAFLGVTASNIKAYPIVSLLFAITI----I 117
                                   *************************94....4 PP

>> DUF3796  Protein of unknown function (DUF3796)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.7   3.6e-05      0.16      46     105 ..      61     120 ..       9     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                       DUF3796  46 stvllDErfeenvkraaaiafk.vaileiiiavlislilsrvelsevllalllaslilafG 105
                                    t++ DEr  + +++a   +   + ile ++++++ + +s++   + +++ll+a++i+ ++
  gi|91772354|ref|YP_565046.1|  61 GTIVEDERIFHIAEKASHKTLLiLIILEGTLIAFLGVTASNI-KAYPIVSLLFAITIISYA 120
                                   57899**9877777777776651567899*************.788999*******99996 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0061        28      30      66 ..      11      45 ..       2      52 .. 0.84
   2 ?    6.3   0.1    0.0019       8.6      29      70 ..      87     127 ..      64     130 .] 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0061
                       SLATT_1 30 llillellalllaalrafgelsvdlvgvlaavaaall 66
                                  + ++l+l+++ + +++  +++++d++g+  a+++a++
  gi|91772354|ref|YP_565046.1| 11 IGFILTLIGIGFRIFE--PSWTIDPTGASGAFIGAGV 45
                                  4567889999999999..9**************9987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0019
                       SLATT_1  29 lllillellalllaalrafgelsvdlvgvlaavaaallaWle 70 
                                   l   l+ +l++++  ++a++ +s+ l+++++   a ++ W +
  gi|91772354|ref|YP_565046.1|  87 LEGTLIAFLGVTASNIKAYPIVSL-LFAITIISYAGFFHWYK 127
                                   444567788899999999998888.99999999999999975 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.24   1.1e+03      74      84 ..      13      23 ..       4      56 .. 0.40
   2 ?   11.8   0.7   5.5e-05      0.25      33      84 ..      72     124 ..      67     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                          MerC 74 llillvalflg 84
                                  +++ l++  + 
  gi|91772354|ref|YP_565046.1| 13 FILTLIGIGFR 23
                                  33333332222 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.5e-05
                          MerC  33 lasellhqvllilvvaigllalvvgy.rrhrktsvlvlgalGllillvalflg 84 
                                   +a+++ h++llil+++ g l  ++g+  +  k +++v ++++++i+ +a f++
  gi|91772354|ref|YP_565046.1|  72 IAEKASHKTLLILIILEGTLIAFLGVtASNIKAYPIVSLLFAITIISYAGFFH 124
                                   668899**********99999999995677899******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 855.19
//
Query:       gi|91772355|ref|YP_565047.1|  [L=259]
Description: hypothetical protein Mbur_0295 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-19   70.2   0.0    1.9e-19   69.6   0.0    1.2  1  META      META domain
    0.00067   19.5   0.1        6.5    6.8   0.0    3.5  3  DUF1344   Protein of unknown function (DUF1344)
     0.0056   17.0   0.0       0.02   15.3   0.0    2.0  2  DUF3221   Protein of unknown function (DUF3221)


Domain annotation for each model (and alignments):
>> META  META domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   3.2e-23   1.9e-19       3     108 ..      46     155 ..      44     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 3.2e-23
                                   TTTTEEEEEE......EECSSCS-BTT---EEEECCCEEEEE-SSSEEEEEEEECTTEEEESSEEE-----SCHHHHCHHH CS
                          META   3 plagteWelt......svdgkavaasapatltfaedgrvsgsagCNrfsGsytleggrltlgalasTrmaCspalmelEqa 77 
                                   ++a+ eW+++      s +++ v++++++t+++++d+++s +a CN  sG+ytleg++ltl++   T  +C    ++l+++
  gi|91772355|ref|YP_565047.1|  46 TVANIEWQWSglieteSGSQSVVPDPENYTIVLNSDETYSIKADCNVGSGGYTLEGSNLTLSSGPITLAYC--GSDSLDTQ 124
                                   678889999988887777789999999999*****************************************..9******* PP

                                   HHHCCCH-CEEEE-SSEEEEE-TTS.-EEEE CS
                          META  78 llkaLqavtsyriegdrLtLtdadgeelltf 108
                                   +l++L++vt++++++d+L+L   ++ +++ f
  gi|91772355|ref|YP_565047.1| 125 YLSLLNNVTTVSMDNDQLVLGIGENGDRMLF 155
                                   ********************97777788776 PP

>> DUF1344  Protein of unknown function (DUF1344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0015         9      12      35 ..      70      93 ..      61      94 .. 0.92
   2 ?    2.1   0.0     0.031   1.9e+02      19      41 ..     180     206 ..     171     217 .. 0.68
   3 !    6.8   0.0    0.0011       6.5      32      47 ..     224     239 ..     221     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0015
                       DUF1344 12 dkkalsitLdDGktYklpeefdid 35
                                  d+++ +i+L+  +tY++ ++ +++
  gi|91772355|ref|YP_565047.1| 70 DPENYTIVLNSDETYSIKADCNVG 93
                                  89******************9987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.031
                       DUF1344  19 tLdDGktYkl....peefdidgLkvGv 41 
                                   +L+DG +Y +    +ee+  +g + G 
  gi|91772355|ref|YP_565047.1| 180 SLEDGDSYPMflleSEEISSSGYTKGI 206
                                   69****997544445555555555555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0011
                       DUF1344  32 fdidgLkvGvkVvVfY 47 
                                   fd ++Lk G++V+Vf+
  gi|91772355|ref|YP_565047.1| 224 FDSENLKEGMNVRVFF 239
                                   7899**********98 PP

>> DUF3221  Protein of unknown function (DUF3221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.58   3.5e+03      45      45 ..     175     175 ..     148     214 .. 0.59
   2 !   15.3   0.0   3.3e-06      0.02      47      81 ..     225     259 .]     191     259 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.58
                       DUF3221  45 s 45 
                                   +
  gi|91772355|ref|YP_565047.1| 175 N 175
                                   1 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.3e-06
                       DUF3221  47 kvsnlevGqkVrVwfdgkileSyPaqakakkievv 81 
                                   + +nl++G+ VrV f   +  S P+ ++a+ i+ +
  gi|91772355|ref|YP_565047.1| 225 DSENLKEGMNVRVFFGPALTKSIPPIGQAELIQLI 259
                                   5689*************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1562.46
//
Query:       gi|91772356|ref|YP_565048.1|  [L=145]
Description: hypothetical protein Mbur_0296 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.0   1.3        1.4    9.1   0.2    2.4  2  YjcQ      YjcQ protein


Domain annotation for each model (and alignments):
>> YjcQ  YjcQ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2     8e-05       1.4      37      68 ..      67     100 ..      64     120 .. 0.74
   2 ?    3.0   0.2    0.0067   1.2e+02      28      49 ..     124     144 ..      99     145 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 8e-05
                                   HHHHHHHHTSEE--EESSS.....SEE--SS--E CS
                          YjcQ  37 iiemlveegyikGvkvkktkk..geivisidnvr 68 
                                   +   l+eeg+ikG++  ++++   +   +++ v+
  gi|91772356|ref|YP_565048.1|  67 TFLALCEEGMIKGITKGNYTNsrKNKEYALKAVK 100
                                   56789***********999883223344444444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0067
                                   TS-HHHHHHHHHHHHHHTSEE- CS
                          YjcQ  28 disesrfndiiemlveegyikG 49 
                                   +i++ +  d+i  l ++gyi+G
  gi|91772356|ref|YP_565048.1| 124 KIHNGQM-DVIIALWKNGYIDG 144
                                   4555554.6777899*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 941.65
//
Query:       gi|91772357|ref|YP_565049.1|  [L=188]
Description: hypothetical protein Mbur_0297 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.6   0.3      0.038   13.9   0.2    1.5  1  DUF4756   Domain of unknown function (DUF4756)


Domain annotation for each model (and alignments):
>> DUF4756  Domain of unknown function (DUF4756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.1e-06     0.038      61     139 ..      83     161 ..      58     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-06
                       DUF4756  61 dkkrksliekfieelnpissskartsakasgnldvlqerviyrk.aiseksdeeivalvikqrteaalefqrsveqsleq 139
                                   ++   sli++f   ln +s+  a+ +ak   +  ++++ ++  k   +eks ++ + +++ +  +  +ef+  +e  +++
  gi|91772357|ref|YP_565049.1|  83 ERFTPSLIKNFPRILNFVSEN-AQDTAKLFFKTTQFKNIIVLSKlPATEKSRNQTIQFLKENGVDHVIEFKAIIEFIVKE 161
                                   56678**************99.77778888888888887766652789***********************999976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1147.11
//
Query:       gi|91772358|ref|YP_565050.1|  [L=541]
Description: hypothetical protein Mbur_0298 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-12   47.9   0.9    1.6e-07   31.5   0.2    3.6  3  DUF11         Domain of unknown function DUF11
    1.5e-08   34.8   8.2      0.011   15.9   0.1    3.7  3  CARDB         CARDB
    3.7e-08   32.6   7.1     0.0049   15.7   0.4    3.8  4  BatD          Oxygen tolerance
     0.0015   18.6   4.7        1.4    9.0   0.4    4.3  3  Cupredoxin_1  Cupredoxin-like domain
     0.0021   17.5   4.4        0.1   12.0   0.1    3.5  3  TRAP_beta     Translocon-associated protein beta (TRAPB)
     0.0072   17.0   0.2         13    6.5   0.0    3.9  4  N_BRCA1_IG    Ig-like domain from next to BRCA1 gene
     0.0081   16.2   1.8        1.6    8.8   0.1    3.1  3  DUF1573       Protein of unknown function (DUF1573)
  ------ inclusion threshold ------
      0.013   15.4   0.4        3.9    7.4   0.2    3.6  3  Big_2         Bacterial Ig-like domain (group 2)
      0.013   15.7   0.3        5.2    7.4   0.1    3.3  3  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
      0.064   13.5   0.2         43    4.3   0.0    3.9  4  bMG10         Bacterial Alpha-2-macroglobulin MG10 domain
      0.069   13.1   0.1       0.13   12.3   0.1    1.5  1  PGF-CTERM     PGF-CTERM motif
       0.11   12.5   1.1        5.7    6.9   0.2    2.9  3  DUF2393       Protein of unknown function (DUF2393)
       0.81   10.0   4.2          2    8.7   0.2    3.0  3  A2M_BRD       Alpha-2-macroglobulin bait region domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.069        96      14      35 ..     164     185 ..     154     211 .. 0.85
   2 !    9.4   0.0   0.00095       1.3       1      47 [.     264     309 ..     264     365 .. 0.66
   3 !   31.5   0.2   1.2e-10   1.6e-07       2      52 ..     376     430 ..     375     462 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.069
                         DUF11  14 dtvtytltvtNtgpasangvvv 35 
                                   + ++ t tv+Ntg++  +++++
  gi|91772358|ref|YP_565050.1| 164 QRISATFTVKNTGTSEGKNIKL 185
                                   5666799*******99888776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00095
                         DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvs 47 
                                   ltK+ +k+ + + +t  + +  +N+g  s n v+v+D   +g+++  
  gi|91772358|ref|YP_565050.1| 264 LTKSITKE-IYMDETAHVLVSIRNSGIYSINSVTVKDSIIEGVELKD 309
                                   68999998.9999************************9855555332 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 1.2e-10
                         DUF11   2 tKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas....q 52 
                                   t  +dk++++pG++v++t+t++N g+++a++ v +D  P++ +++s+        
  gi|91772358|ref|YP_565050.1| 376 TQIFDKTTLQPGQEVKVTVTARNEGNRDASTRVTSDQFPESATFISGDKNldavL 430
                                   67799*****************************************998844441 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.8   1.4e-05     0.019       2      96 ..     142     251 ..     141     256 .. 0.73
   2 !    6.5   0.2    0.0073        10       6      77 ..     264     339 ..     259     358 .. 0.70
   3 !   15.9   0.1   8.3e-06     0.011       2      71 ..     371     444 ..     363     455 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                   --EEE......EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEE...EEEEEEE CS
                         CARDB   2 pDLtv.....tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagest...tvsftwt 70 
                                   p L++     + ++ p++++  + ++ t+tvkN+Gt + +++k+++  +  +      + ++ sL+ ge +   tv+f+++
  gi|91772358|ref|YP_565050.1| 142 PELEItigtdKDEYDPKTMSSPQRISATFTVKNTGTSEGKNIKLSIEPNLLELtdgkLEYEIYSLEKGEVAepiTVKFKVP 222
                                   666666687788899999******************999999998877766664444456669*****9862114555555 PP

                                   -S-S-CEEEEEEEE...STT-SS--SSCC CS
                         CARDB  71 teategevtltvvv...DpdnevaEsnEt 96 
                                     ++e e+++++ v   D +n+  E++E+
  gi|91772358|ref|YP_565050.1| 223 HLWEETEIEINAIVeakDINNDFYETDES 251
                                   55999999999999333445666666664 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0073
                                   E.EEEC-SEEETTSEEEEEEEEEE-SSS-..EEEEEEEEEETTEEEEEEEE...SEE-CTEEEEE.EEEEE-S-S-CE CS
                         CARDB   6 vtntlnpseafvgeentitvtvkNqGtaa..sgatkvalyldgelvgtvtv...psLaagesttv.sftwtteatege 77 
                                   + +++  +e +  e+  + v+++N+G  +  s ++k +++   el++++t+    + ++ge+++v s++ ++ ++eg+
  gi|91772358|ref|YP_565050.1| 264 L-TKSITKEIYMDETAHVLVSIRNSGIYSinSVTVKDSIIEGVELKDSITLeknLNFEPGETKEVfSYSLKP-LKEGT 339
                                   4.56777899999*************8773255555566666666688888866566788877762333333.35555 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 8.3e-06
                                   --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEE.EEEEETTEEE.EEEEE.SEE-CTEEEEEEEEEE- CS
                         CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaa.sgatk.valyldgelv.gtvtv.psLaagesttvsftwtt 71 
                                   pD ++t+++  +++ +g+e+++tvt +N+G+ + s+ ++  ++  + +   g+ ++ + L a++s++ ++t ++
  gi|91772358|ref|YP_565050.1| 371 PDIVITQIFDKTTLQPGQEVKVTVTARNEGNRDaSTRVTsDQFPESATFIsGDKNLdAVLGADQSSSYTYTLKM 444
                                   77777**************************9944433303333344433666666667777777777777666 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.55   7.6e+02     239     253 ..     107     121 ..      71     198 .. 0.60
   2 !   10.9   0.1    0.0001      0.14      66      98 ..     318     349 ..     269     362 .. 0.69
   3 !   15.7   0.4   3.6e-06    0.0049      12      97 ..     375     458 ..     366     470 .. 0.83
   4 !    7.4   0.0    0.0012       1.7     368     445 ..     469     537 ..     466     541 .] 0.55

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.55
                          BatD 239 vkkrvsspavtitVk 253
                                   + +++s+++vt++V 
  gi|91772358|ref|YP_565050.1| 107 QDIKISAKTVTLNVD 121
                                   444444444444443 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                          BatD  66 nGkssssssktwtytLapkkeGtltIpaatiev 98 
                                   n++  ++++  ++y+L+p keGt+t p+at+++
  gi|91772358|ref|YP_565050.1| 318 NFEPGETKE-VFSYSLKPLKEGTFTAPEATASF 349
                                   444444333.68999999999999999998754 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.6e-06
                          BatD  12 ftasvdknevevgetfrLtftvngasgepdfsapslekdfevlsg..sqssstqiinGkssssssktwtytLapkkeGtlt 90 
                                   +t  +dk++++ g+++++t+t+ ++ g+ d s    +++f    +  s  +++  + G  +s ss  +tytL+ ++ G ++
  gi|91772358|ref|YP_565050.1| 375 ITQIFDKTTLQPGQEVKVTVTARNE-GNRDASTRVTSDQFPESATfiSGDKNLDAVLGADQS-SS--YTYTLKMNELGIFK 451
                                   67778********************.777777666656776666667667888889999888.46..************** PP

                          BatD  91 Ipaatie 97 
                                   + +at++
  gi|91772358|ref|YP_565050.1| 452 LSPATAT 458
                                   ****986 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0012
                          BatD 368 etatlpeitikVekgaaaasspasst.saspaqkeevkllgkdirfikgeaslkkkgsff.lfw.lllllplllfvvllll 445
                                   ++ + p+it++V +g++++s+p +++ s++p+++ ++++  +d +   +e+++        +f  +l++++++    ++ll
  gi|91772358|ref|YP_565050.1| 469 KISNMPSITVDVPPGPEETSNPDTQSdSNTPSENTNINTDVHDQN---DEEKV------QpGFGsILVIATIAG---VYLL 537
                                   567899*******9*977777766665666666666665555432...12222......123331333333333...2444 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.4     0.001       1.4      22      56 ..     145     198 ..     132     258 .. 0.76
   2 ?    0.9   0.1      0.35   4.8e+02      56      89 ..     302     341 ..     270     350 .. 0.74
   3 !    6.7   0.0    0.0054       7.5      36      96 ..     381     446 ..     376     450 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                  Cupredoxin_1  22 tveitvkdggfePskievkagekvklkiknkdkt...................p 56 
                                   +++i   +++++P+++  ++  ++++++kn++++                    
  gi|91772358|ref|YP_565050.1| 145 EITIGTDKDEYDPKTMSSPQRISATFTVKNTGTSegkniklsiepnlleltdgK 198
                                   577778899************************966666666554444444431 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                  Cupredoxin_1  56 peefesed...lgeekvlapgkttti...tiaplkpGeYe 89 
                                    e +e +d   l+++ + +pg+t+++    ++plk+G+++
  gi|91772358|ref|YP_565050.1| 302 IEGVELKDsitLEKNLNFEPGETKEVfsySLKPLKEGTFT 341
                                   4555566665577777778888877633368899999885 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0054
                  Cupredoxin_1  36 kievkagekvklkiknkdkt..p..eefesedlgee.kvlapgktttitiaplkpGeYeftcdmhm 96 
                                   k +++ g++vk++++++ +      + ++s+++ e+ + +  +k+  + + +++  +Y++t +m++
  gi|91772358|ref|YP_565050.1| 381 KTTLQPGQEVKVTVTARNEGnrDasTRVTSDQFPESaTFISGDKNLDAVLGADQSSSYTYTLKMNE 446
                                   66778888888766555444224569999999887757788889999****************996 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 ?    2.3   0.0      0.07        97      32      84 ..     161     210 ..     155     240 .. 0.74
   2 ?    2.5   0.5      0.06        83      19     114 ..     261     354 ..     246     367 .. 0.68
   3 !   12.0   0.1   7.3e-05       0.1      32     113 ..     385     463 ..     368     484 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.07
                     TRAP_beta  32 vegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapge 84 
                                   +  ++++ ++t+ N G+s+  +++l   s++++  e+  g+l+ ++ +l+ ge
  gi|91772358|ref|YP_565050.1| 161 SSPQRISATFTVKNTGTSEGKNIKL---SIEPNLLELTDGKLEYEIYSLEKGE 210
                                   556899*****************99...5777777777777777777777665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.06
                     TRAP_beta  19 rvlvkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvs.hsfvvepkksg 98 
                                   +++  K+i +++   +e   v ++i N G  +   V+++D  ++    e+    +  k    +pge+ + +s+ ++p k+g
  gi|91772358|ref|YP_565050.1| 261 ELILTKSITKEIYM-DETAHVLVSIRNSGIYSINSVTVKDSIIEG--VELKDSITLEKNLNFEPGETKEvFSYSLKPLKEG 338
                                   56666666666666.566677777777777777777777765533..3555554444455566776655378999999999 PP

                     TRAP_beta  99 sfngtaavvtYresek 114
                                    f +  a+ ++ +s+ 
  gi|91772358|ref|YP_565050.1| 339 TFTAPEATASFVASNG 354
                                   9999999999966654 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 7.3e-05
                     TRAP_beta  32 vegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepkksgsfngtaavvtYres 112
                                     g+++ v++t  N G+  A   +++ d fpe+a +++sg  ++  ++l + ++ s++++++    g+f+ ++a+ t+ + 
  gi|91772358|ref|YP_565050.1| 385 QPGQEVKVTVTARNEGNRDAS-TRVTSDQFPESA-TFISGDKNLD-AVLGADQSSSYTYTLKMNELGIFKLSPATATFIDM 462
                                   5699***************96.5999*****999.7788866665.68****************************99665 PP

                     TRAP_beta 113 e 113
                                   e
  gi|91772358|ref|YP_565050.1| 463 E 463
                                   5 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.57   7.8e+02      26      67 ..      38      80 ..      36     115 .. 0.79
   2 ?    4.2   0.0     0.052        72       7      73 ..     159     223 ..     155     236 .. 0.73
   3 ?   -1.4   0.0       2.9     4e+03      56      79 ..     318     341 ..     270     356 .. 0.66
   4 !    6.5   0.0    0.0097        13       2      39 ..     378     422 ..     377     456 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.57
                    N_BRCA1_IG 26 eaWpagtklvfvgGdkmgs.asaeessvsvpavapgeevevsv 67
                                  ++W+++t+  + +Gd+m++ + ++  +++ ++   +  v++s+
  gi|91772358|ref|YP_565050.1| 38 VEWESSTSSTLYWGDTMVNgGDSDGYTIKAEDFTKDGYVHISL 80
                                  689999***********84455566666666666666666654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.052
                    N_BRCA1_IG   7 vvppgteftktWrlrNtGseaWpagtklvfvgGdkmgsasaeessvsvpavapgeeve.vsvelkaPs 73 
                                   +++  +++  t++++NtG+++  +++kl +    ++ + +  + ++++ +++ ge++e ++v++k+P+
  gi|91772358|ref|YP_565050.1| 159 TMSSPQRISATFTVKNTGTSE-GKNIKLSIEP--NLLELTDGKLEYEIYSLEKGEVAEpITVKFKVPH 223
                                   6677788999*********97.4777776655..4444445566777888888888873588888885 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                    N_BRCA1_IG  56 avapgeevevsvelkaPskpgryi 79 
                                   + +pge+ ev    + P k+g+++
  gi|91772358|ref|YP_565050.1| 318 NFEPGETKEVFSYSLKPLKEGTFT 341
                                   367788888855555577777654 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0097
                    N_BRCA1_IG   2 ipdgtvvppgteftktWrlrNtGseaWpagtklv.........fvgG 39 
                                   i d+t+++pg+e + t + rN+G+++   +t++          f++G
  gi|91772358|ref|YP_565050.1| 378 IFDKTTLQPGQEVKVTVTARNEGNRDA--STRVTsdqfpesatFISG 422
                                   7799********************965..555543344444444444 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0011       1.6       3      31 ..     150     178 ..     148     183 .. 0.92
   2 ?   -2.4   0.0       3.7   5.2e+03       3      13 ..     225     235 ..     199     257 .. 0.58
   3 ?    5.2   0.1     0.016        22      48      79 ..     378     406 ..     374     420 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                       DUF1573   3 feettidfgkieegekvtatFeftNtgka 31 
                                    +++++d +++++ ++++atF+++Ntg++
  gi|91772358|ref|YP_565050.1| 150 TDKDEYDPKTMSSPQRISATFTVKNTGTS 178
                                   6899***********************86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                       DUF1573   3 feettidfgki 13 
                                   +eet+i+++ i
  gi|91772358|ref|YP_565050.1| 225 WEETEIEINAI 235
                                   33444444444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.016
                       DUF1573  48 eypkepiapGesgkikvtfnakgrpgefnktv 79 
                                    ++k++++pG++ k++vt  ++g   + + + 
  gi|91772358|ref|YP_565050.1| 378 IFDKTTLQPGQEVKVTVTARNEG---NRDAST 406
                                   578999*****999999877776...333344 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 ?    3.3   0.0     0.054        74       6      44 ..       5      46 ..       3      47 .. 0.85
   2 ?   -1.7   0.0       1.9   2.7e+03       8      46 ..     171     209 ..     165     218 .. 0.50
   3 ?    7.4   0.2    0.0028       3.9      11      41 ..     381     411 ..     373     421 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.054
                                  EEEEC-CEEETT-EEEEEEEEESTT-S-...--EEEEECC-S CS
                         Big_2  6 tvsptevtvkkgatqqltvevtpssasd...kkvtwtssngs 44
                                   vsp++ ++++  ++  +    p++as    ++v+w+ss +s
  gi|91772358|ref|YP_565050.1|  5 AVSPRSISLLVVSALLISLCLLPFNASAyslDDVEWESSTSS 46
                                  5888888888888888899999999999999*******8765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                                   EEC-CEEETT-EEEEEEEEESTT-S---EEEEECC-SSE CS
                         Big_2   8 sptevtvkkgatqqltvevtpssasdkkvtwtssngsvA 46 
                                   + +++   +g++ +l+ e      +d+k ++++ + +++
  gi|91772358|ref|YP_565050.1| 171 TVKNTGTSEGKNIKLSIEPNLLELTDGKLEYEIYSLEKG 209
                                   333334444555555555555555555555555555555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0028
                                   -CEEETT-EEEEEEEEESTT-S---EEEEEC CS
                         Big_2  11 evtvkkgatqqltvevtpssasdkkvtwtss 41 
                                   ++t++ g+ +++tv+ + ++++d +++ ts+
  gi|91772358|ref|YP_565050.1| 381 KTTLQPGQEVKVTVTARNEGNRDASTRVTSD 411
                                   79**************************995 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 ?    4.5   0.0     0.031        43       8      29 ..     167     188 ..     162     189 .. 0.88
   2 ?   -2.1   0.0       3.6   4.9e+03      21      39 ..     212     230 ..     200     239 .. 0.74
   3 ?    7.4   0.1    0.0038       5.2       2      24 ..     385     408 ..     384     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.031
                   NPCBM_assoc   8 tltltvtndgtaaatnvslsls 29 
                                   + t+tv+n+gt+  +n++ls++
  gi|91772358|ref|YP_565050.1| 167 SATFTVKNTGTSEGKNIKLSIE 188
                                   5799***************986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                   NPCBM_assoc  21 atnvslslslPeGWtvvev 39 
                                   a+ + ++ ++P  W+ +e+
  gi|91772358|ref|YP_565050.1| 212 AEPITVKFKVPHLWEETEI 230
                                   5667888999999985554 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0038
                   NPCBM_assoc   2 epGetvtltltvtndg.taaatnv 24 
                                   +pG++v++t+t+ n+g ++a t+v
  gi|91772358|ref|YP_565050.1| 385 QPGQEVKVTVTARNEGnRDASTRV 408
                                   79**************55555555 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       4.4     6e+03      75     101 ..     184     210 ..     165     217 .. 0.68
   2 ?    4.3   0.0     0.031        43     101     124 ..     325     348 ..     318     351 .. 0.89
   3 ?    2.1   0.0      0.15   2.1e+02      18      41 ..     381     402 ..     368     420 .. 0.78
   4 ?    1.4   0.0      0.25   3.4e+02     101     123 ..     435     457 ..     430     459 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.4
                         bMG10  75 eeltefsyreirddrvvffadylpkgt 101
                                   + ++e++  e++d + ++ +++l+kg+
  gi|91772358|ref|YP_565050.1| 184 KLSIEPNLLELTDGKLEYEIYSLEKGE 210
                                   445677777888888888888888886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.031
                         bMG10 101 tytfeylvravtpGtfsvppakae 124
                                   + +f+y ++   +Gtf++p a+a+
  gi|91772358|ref|YP_565050.1| 325 KEVFSYSLKPLKEGTFTAPEATAS 348
                                   5689*****************996 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.15
                         bMG10  18 ksdaklkvGdkvrvrltvttprdl 41 
                                   k+  +l+ G++v+v++t + +  +
  gi|91772358|ref|YP_565050.1| 381 KT--TLQPGQEVKVTVTARNEGNR 402
                                   33..89**********99866544 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.25
                         bMG10 101 tytfeylvravtpGtfsvppaka 123
                                   + +++y+++++  G f++ pa+a
  gi|91772358|ref|YP_565050.1| 435 SSSYTYTLKMNELGIFKLSPATA 457
                                   5689*****************98 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.3e-05      0.13       1      23 []     519     540 ..     519     541 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.3e-05
                     PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                   +PGFG++l +a ++++ +L+RRr
  gi|91772358|ref|YP_565050.1| 519 QPGFGSILVIATIAGV-YLLRRR 540
                                   7**************6.666665 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.086   1.2e+02      55      85 ..     158     188 ..     153     193 .. 0.87
   2 ?    6.9   0.2    0.0041       5.7      51     125 ..     266     341 ..     259     344 .. 0.75
   3 ?   -1.8   0.0         2   2.7e+03      54      76 ..     381     403 ..     374     426 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.086
                       DUF2393  55 krllyteafvvdgtitNeGkftikeCkleik 85 
                                   k +++ + +++++t++N+G  + k+ kl+i+
  gi|91772358|ref|YP_565050.1| 158 KTMSSPQRISATFTVKNTGTSEGKNIKLSIE 188
                                   56777889999***********999999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0041
                       DUF2393  51 ilsqkrllyteafvvdgtitNeGkftikeCkleiklvnkshnkkskellkklkpl.vsksevikedlkpgeskeFr 125
                                   ++  k + ++e+  v ++i+N G + i+ ++++ ++++  + k s  l k l+++  +++ev++  lkp ++ +F+
  gi|91772358|ref|YP_565050.1| 266 KSITKEIYMDETAHVLVSIRNSGIYSINSVTVKDSIIEGVELKDSITLEKNLNFEpGETKEVFSYSLKPLKEGTFT 341
                                   5556778889999999*****************9999988888555555555544235556888888887776665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2
                       DUF2393  54 qkrllyteafvvdgtitNeGkft 76 
                                   ++ l+  + + v++t +NeG+++
  gi|91772358|ref|YP_565050.1| 381 KTTLQPGQEVKVTVTARNEGNRD 403
                                   55556666666666777777654 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.7   6.5e+03      83     107 ..     111     137 ..      92     156 .. 0.59
   2 ?    1.1   0.6      0.33   4.5e+02      13     100 ..     180     307 ..     169     342 .. 0.48
   3 ?    8.7   0.2    0.0015         2       5      26 ..     379     402 ..     375     516 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.7
                                   EEEEEEE----.-GGGB-EEEEE.E.E CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.x.x RF
                       A2M_BRD  83 vvadsvqlpvekdfenklsvsle.s.y 107
                                   + a +v+l+v+++  n  +   e + y
  gi|91772358|ref|YP_565050.1| 111 ISAKTVTLNVDEWTGNMEDPNAEiEiY 137
                                   455556666665544444444433334 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.33
                                   TSEEEEEEE-SS-EE-TT-.....BSS..-----.-S.......................................S.... CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxx....................................xxxxxx RF
                       A2M_BRD  13 Getakltvkstfatverdstl.ylvls..rgnivssgek....................................veeids 54 
                                   G+++kl+++ +   + +d++l y+++s  +g++ ++                                       +  +  
  gi|91772358|ref|YP_565050.1| 180 GKNIKLSIEPNL-LELTDGKLeYEIYSleKGEV-AEP-ItvkfkvphlweeteieinaiveakdinndfyetdesK-TVTV 256
                                   555566666555.34444444566644223333.122.12333344444444444444444444444443333320.2333 PP

                                   -EEEEEE--TT-----E......EEEEE..E--CEEEEEEE----.-GGGB- CS
                                   xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       A2M_BRD  55 stsfsfpvtadmaPnar......vvvyyirrdgevvadsvqlpvekdfenkl 100
                                   ++++++ +t++   +++      v+v  ir++g + ++sv+++    +  +l
  gi|91772358|ref|YP_565050.1| 257 EPKVELILTKSITKEIYmdetahVLVS-IRNSGIYSINSVTVKDSIIEGVEL 307
                                   334444333333333332222214433.366677777777766555555555 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0015
                                   ESSSS--TTSEEEEEEE-SS-..E CS
                                   xxxxxxxxxxxxxxxxxxxxx..x RF
                       A2M_BRD   5 pdkeeykvGetakltvkstfa..t 26 
                                    dk+++++G+++k+tv+++ +   
  gi|91772358|ref|YP_565050.1| 379 FDKTTLQPGQEVKVTVTARNEgnR 402
                                   5999*************9885442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3245.02
//
Query:       gi|91772359|ref|YP_565051.1|  [L=417]
Description: hypothetical protein Mbur_0299 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.046   13.8   0.7        1.1    9.4   0.0    2.9  3  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 ?   -2.0   0.0      0.22     4e+03       2      20 ..       7      25 ..       6      34 .. 0.67
   2 ?    1.4   0.1      0.02   3.5e+02      64      89 ..     193     219 ..     123     221 .. 0.67
   3 ?    9.4   0.0   6.1e-05       1.1      45     104 .]     268     328 ..     263     328 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.22
                  Cupredoxin_1  2 laalavllllsskaaaaae 20
                                  +++l+++l+l+++  aa++
  gi|91772359|ref|YP_565051.1|  7 ILLLIFILALTNTPTAAED 25
                                  6677777777776655544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.02
                  Cupredoxin_1  64 lgeekvlapgktttit..iaplkpGeYe 89 
                                   +++  +l+p ++++i+  +++l+pG Y+
  gi|91772359|ref|YP_565051.1| 193 INI-SDLNPYSKKVIQysVKALYPGNYT 219
                                   444.556665555553338999999997 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 6.1e-05
                  Cupredoxin_1  45 vklkiknkdktpeefesed..lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                                   + +++kn++++++++ ++d  l e+k ++ + ++ + + p +    +++  m++  +G++iV
  gi|91772359|ref|YP_565051.1| 268 IAVNVKNEGDRAAHIRIQDemLVESKLIDGKTSADLVLLPNNTTNLSYIVHMNKI-QGNMIV 328
                                   6799***************988888888888899999988888888887777776.9*9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2747.06
//
Query:       gi|91772360|ref|YP_565052.1|  [L=207]
Description: GTP-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-16   59.8   0.1    3.3e-16   59.4   0.1    1.2  1  MMR_HSR1     50S ribosome-binding GTPase
    1.2e-11   44.4   0.3    1.5e-10   40.8   0.3    2.0  1  FeoB_N       Ferrous iron transport protein B
    0.00028   20.8   2.2      0.073   13.0   0.4    2.9  3  RsgA_GTPase  RsgA GTPase
     0.0024   17.4   0.1      0.021   14.4   0.0    2.1  2  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0048   17.0   1.7      0.032   14.3   1.2    1.9  2  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.039   14.5   0.1       0.09   13.3   0.0    1.6  1  AAA_18       AAA domain
       0.07   13.3   0.4       0.28   11.4   0.1    2.0  2  Roc          Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.1   1.3e-19   3.3e-16       1     114 []      13     141 ..      13     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.3e-19
                                   EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC.....SSHHHHHHHHHHHHHH.... CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGl.....iegaseekglgkafla.... 72 
                                   e++i Gr+NvGKS++i+ ltg++++v+++pg+T++++++ ++    ++ ++D+pG+     ++ ++++  +++++ +    
  gi|91772360|ref|YP_565052.1|  13 EIIISGRSNVGKSSIIRELTGKQVKVGKRPGVTLKPTQILLS----DMLITDLPGFgfmsgVK-DRKQDIVKDQIVRyien 88 
                                   689************************************997....69*******54332222.22222344444432212 PP

                                   HHC.TSEEEEEEETT............TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  73 lee.adlillvvdas............eeklkpldeeleelleeakkplilvlnk 114
                                   + +  +++++v d+             +    p+d e+ ++ +e + ++i+++nk
  gi|91772360|ref|YP_565052.1|  89 NADrIKIAVIVTDSVsfvdvverwesrN--EIPIDIEIFDFFNELGFDTIIAVNK 141
                                   3334788888888557877777766422..3477788888777777777777776 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 !   40.8   0.3     6e-14   1.5e-10       2     123 ..      13     150 ..      12     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6e-14
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSS.SHHHHHHHHHHH...... CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsay.seeekvardfll...... 75 
                                   ++++ G  nvGk++++ +ltg++ kvg  pGvt + ++  l+    ++ i+DlPG   +s +  + + +++d ++      
  gi|91772360|ref|YP_565052.1|  13 EIIISGRSNVGKSSIIRELTGKQVKVGKRPGVTLKPTQILLS----DMLITDLPGFGFMSGVkDRKQDIVKDQIVryienn 89 
                                   68899*******************************999999....9********97774431334455555554444333 PP

                                   CTSSSEEEEEEEGGGH.........HHHHHHHHHHH....HTTSSEEEEEETHHHHHHTTE CS
                        FeoB_N  76 eeepdvvvnvvdatnl.........ernLyLtlqll....elgvpvvlalnmideaekkgi 123
                                    +++++ v v d+ ++         + ++ + ++++    elg ++++a+n++d +++ + 
  gi|91772360|ref|YP_565052.1|  90 ADRIKIAVIVTDSVSFvdvverwesRNEIPIDIEIFdffnELGFDTIIAVNKMDRIKDIHH 150
                                   3444555556665543222211111446777777653333688999999999999887555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   2.9e-05     0.073     102     128 ..      14      39 ..       2      68 .. 0.81
   2 ?   -1.9   0.0         1   2.7e+03      55      83 ..      74     101 ..      72     118 .. 0.69
   3 !    6.4   0.0     0.003       7.7      43      99 ..     129     193 ..     122     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                                   EEEECSTTSSHHHHHHHHCTT-----S CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktg 128
                                   +++ G S vGKS++i +l+++ ++k+g
  gi|91772360|ref|YP_565052.1|  14 IIISGRSNVGKSSIIRELTGK-QVKVG 39 
                                   5789***************98.55555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                                   -GGG--HHHHHHHHHHHHHHTTSEEEE-- CS
                   RsgA_GTPase  55 KiDlleeeeeleelkeelealgyevllvs 83 
                                   K D+++++  ++ ++++  ++ ++v++++
  gi|91772360|ref|YP_565052.1|  74 KQDIVKDQI-VRYIENNADRIKIAVIVTD 101
                                   667777777.7777777777777776664 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.003
                                   HHTT-EEEEEEE-GGG--HHH.........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  43 eekgiepvivlnKiDlleeee.........eleelkeelealgyevllvsaktkegleelkellkd 99 
                                   +e g + +i++nK+D +++ +         e   l++  ++++y +  +sak k ++++lk ll++
  gi|91772360|ref|YP_565052.1| 129 NELGFDTIIAVNKMDRIKDIHhderldaivEKFGLSSPWKQWNYIIAPTSAK-KGDIKSLKGLLRK 193
                                   56677899********999886676666554445667778888988888888.5577888777776 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 ?    1.5   0.0     0.074   1.9e+02       6      33 ..      14      41 ..      10     108 .. 0.84
   2 !   14.4   0.0   8.2e-06     0.021     113     178 ..     123     182 ..      86     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.074
                                  EEEEESTTSSHHHHHHHHHHHTTSSCHH CS
                      GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskk 33
                                  i+i g  + GK++++ +L+ k  ++ k+
  gi|91772360|ref|YP_565052.1| 14 IIISGRSNVGKSSIIRELTGKQVKVGKR 41
                                  7889999999999999999887777665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.2e-06
                                   HHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTT CS
                      GTP_EFTU 113 evlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkg 178
                                   e++   +++g  +i+++NKmDr+ +   +e  +++ +k+      l++ + +   ++ ++++Sa+kg
  gi|91772360|ref|YP_565052.1| 123 EIFDFFNELGFDTIIAVNKMDRIkDIHHDERLDAIVEKF-----GLSSPWKQW--NYIIAPTSAKKG 182
                                   566677888999***********9555556666666666.....333333332..455666666665 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.2   1.3e-05     0.032       1      42 [.      14      55 ..      14      94 .. 0.74
   2 !    6.0   0.1    0.0043        11      92     131 ..      45      92 ..      43     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                  EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECC CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlge 42
                                  i++ G  + GKSS++  L+g+++ + +   +T +p+++ l++
  gi|91772360|ref|YP_565052.1| 14 IIISGRSNVGKSSIIRELTGKQVKVGKRPGVTLKPTQILLSD 55
                                  6788999***************99999999********9943 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0043
                                   EEEEEETTS-SEEEEE---B-S...SSGTTS....HHHHHHH.STTEE CS
                     Dynamin_N  92 llkilsllvkgltlvDlPGlds...vnkrdq....elvkeyi.kkadi 131
                                   +lk++++l +++ + DlPG+     v++r+q    + + +yi ++ad 
  gi|91772360|ref|YP_565052.1|  45 TLKPTQILLSDMLITDLPGFGFmsgVKDRKQdivkDQIVRYIeNNADR 92 
                                   688999999*********985421255555666665555666555554 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   3.5e-05      0.09       1      68 [.      14      90 ..      14     125 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf...........gvnlrdvakenglllevdpealdeskrldedkldklldaleens 68
                                  I+++G + vGK+++ +eL  +  ++            + l+d++  + + +++     d+++ +++d+   +++ +e+n+
  gi|91772360|ref|YP_565052.1| 14 IIISGRSNVGKSSIIRELTGKQvKVgkrpgvtlkptQILLSDMLITDLPGFGFMSGVKDRKQDIVKDQ---IVRYIENNA 90
                                  9*****************76654557777666666666666666665555555555444444444444...444444443 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   0.1   0.00011      0.28       2      29 ..      14      41 ..      13      56 .. 0.83
   2 ?   -0.3   0.0      0.47   1.2e+03      21      38 ..      87     104 ..      71     143 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                  EEEESSTTSSHHHHHHCHCT-CCC-EEE CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkfsekek 29
                                  +++ G s+vGK+s++++++ ++++  ++
  gi|91772360|ref|YP_565052.1| 14 IIISGRSNVGKSSIIRELTGKQVKVGKR 41
                                  7899***************999876554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                                   T-CCC-EEETTTTEEEEE CS
                           Roc  21 edkfsekekstigvdflt 38 
                                   e++ ++ + + i  d ++
  gi|91772360|ref|YP_565052.1|  87 ENNADRIKIAVIVTDSVS 104
                                   444444443333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1266.09
//
Query:       gi|91772361|ref|YP_565053.1|  [L=206]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-19   71.1   0.1    1.6e-19   70.9   0.1    1.1  1  Radical_SAM  Radical SAM superfamily
    3.3e-08   33.7   0.0    5.1e-08   33.1   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.1   1.8e-23   1.6e-19       2     152 ..      27     184 ..      26     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.8e-23
                                   EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                   xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                   ++t+ C+ +C+fC+r  +    +++ +  ++ s++eil+++ +l  e   ++v+ g gep+ + d+v ++ r  k+   g+
  gi|91772361|ref|YP_565053.1|  27 NITNRCSANCVFCIRDISdgiyGSNLRLTKEPSLDEILDKLGSLDLEIYREVVFTGFGEPTIRLDIVLEVTRWLKE--HGM 105
                                   799*****************************************97777***************************..7** PP

                                   EEEEEECSSCHG....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpd....eeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdrivgl 152
                                   ++++ tng+       ++++ +l+++g+d vs++l+a ++e++ +l+     + +e+ le ++ + +agi+ +  ++vg+
  gi|91772361|ref|YP_565053.1| 106 KVRIDTNGHAQLlhpeRDVISELKDAGLDEVSVSLNAESKERYDELCQpdLENAYEAMLEFTKEAVNAGIE-SRMTVVGF 184
                                   *********9669999*******************************877777788899999999999888.55555554 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   5.7e-12   5.1e-08       3      97 ..      27     121 ..      25     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 5.7e-12
                       Fer4_14   3 vrlsgCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseiki.qglvltG.GePLhyenkkellklvkrlkeeyp 79 
                                   + +++C+ +C++C    ++    +     +e  l++il++l   + +i +++v+tG GeP    + + +l++ ++lke++ 
  gi|91772361|ref|YP_565053.1|  27 NITNRCSANCVFCIrdISDGIYGSNLRLTKEPSLDEILDKLGSLDLEIyREVVFTGfGEPT--IRLDIVLEVTRWLKEHG- 104
                                   5689*********95423333445556677777888888665554443267**********..78***************. PP

                       Fer4_14  80 ekkiwletngtleielek 97 
                                    +k+++ tng +++ + +
  gi|91772361|ref|YP_565053.1| 105 -MKVRIDTNGHAQLLHPE 121
                                   .**********9976653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1405.84
//
Query:       gi|91772362|ref|YP_565054.1|  [L=122]
Description: hypothetical protein Mbur_0302 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   74.9   0.0    9.1e-21   74.7   0.0    1.0  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like


Domain annotation for each model (and alignments):
>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   5.1e-25   9.1e-21       1     120 [.       4     114 ..       4     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 5.1e-25
                                   EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.ETTTEEEETTSSE..EEEEEEEE-HHHHHHHHHCT.TTTTSE CS
                         GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlydlggkypalvpgdge.kVkGelyevddeelarLDelEpeepseY 80 
                                   +FvYGtLkrg+ nh+ ll +  +  +++ t k++++ d  g++pa+v++    ++ Gel++vdd++l+ +D++E   ++++
  gi|91772362|ref|YP_565054.1|   4 LFVYGTLKRGYVNHH-LLER-STFVLETCTEKKFQILDM-GDFPAVVKDVPVsTIDGELFNVDDSTLSDIDAFE---GEWF 78 
                                   7*************9.7767.45557777********96.79*****555556*********************...**** PP

                                   EEEEEEEEC.TTS-EEEEEEEEETT...GGGCCS-S-SS-- CS
                         GGACT  81 ereevkvevledgeqveawvYvyag.eeeegdrliesgdWr 120
                                    re  +v +  +++++ aw+Y+  +  ++eg + i sg W+
  gi|91772362|ref|YP_565054.1|  79 SRE--EVVL--QDSSI-AWMYFLSEyVSHEGCPSITSGTWQ 114
                                   ***..9999..66677.******77688888888******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 845.33
//
Query:       gi|91772363|ref|YP_565055.1|  [L=396]
Description: geranylgeranyl reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-12   45.8   3.8    7.4e-10   38.6   0.6    3.0  2  FAD_binding_3   FAD binding domain
    3.5e-09   36.8   0.0      6e-08   32.8   0.0    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.2e-08   33.6   5.3    2.1e-05   24.3   0.5    2.7  2  DAO             FAD dependent oxidoreductase
    3.5e-08   33.2   1.3    4.9e-08   32.7   0.4    1.6  2  FAD_oxidored    FAD dependent oxidoreductase
    1.6e-07   30.4   0.6    2.7e-07   29.6   0.6    1.4  1  HI0933_like     HI0933-like protein
    3.6e-07   29.6   0.0    3.6e-07   29.6   0.0    1.6  1  GIDA            Glucose inhibited division protein A
    4.6e-07   29.4   0.2    4.7e-06   26.0   0.1    2.5  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.3e-06   26.9   1.8    5.2e-06   25.8   1.8    1.5  1  FAD_binding_2   FAD binding domain
    5.7e-06   25.7   0.0    1.2e-05   24.7   0.0    1.4  1  Thi4            Thi4 family
    6.2e-06   25.3   0.9     0.0005   19.0   0.1    2.5  2  Trp_halogenase  Tryptophan halogenase
      1e-05   24.8   2.0     0.0077   15.3   0.4    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    0.00039   19.8   0.7     0.0014   17.9   1.1    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0018   18.8   0.0      0.061   13.9   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.024   14.0   0.1      0.024   14.0   0.1    1.9  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.093   12.6   0.2       0.25   11.2   0.2    1.7  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.14   12.5   0.1        0.5   10.6   0.0    1.9  2  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.6   6.6e-13   7.4e-10       2     175 ..       7     171 ..       6     217 .. 0.79
   2 !    5.1   0.1    0.0098        11     287     325 ..     284     322 ..     278     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 6.6e-13
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHH..HHHHSEECCCCEEEEEEEC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledr..ilaegapnelmgealynel 80 
                                   +d++IVGaGpaG ++a   ++aG +v+l+ek ++     + +g+ +  +++l++l   ++  +l e+ p + ++++ + + 
  gi|91772363|ref|YP_565055.1|   7 YDIIIVGAGPAGSTAAAYAAKAGASVLLIEKKKDIGLPLQCGGFLP-HLDTLQELVPNAQlpYLLEDIPADCIHTTSSVQ- 85 
                                   689****************************877655558777766.478888886666522577888999999999999. PP

                                   CCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                 FAD_binding_3  81 sdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                    +   a+  ++ +    +  ++   +++++L+++a ++g++v  +t+v+ ++ +   v+ ++     g++  ++ k l+Ga
  gi|91772363|ref|YP_565055.1|  86 -RF-IAPNGYS-KEFEVDADAIDRRRFDKYLAKEAGRCGADVMIGTNVLEVNGTSVDVDGVF-----GTH-SISGKVLIGA 157
                                   .33.3444444.45556788999**************************4444444444443.....445.8********* PP

                                   -GTT-HHHHHHTGG CS
                 FAD_binding_3 162 DGgrStvrktlgie 175
                                   DG +Stv ++ g+ 
  gi|91772363|ref|YP_565055.1| 158 DGPNSTVGRAKGLV 171
                                   *******9998875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0098
                                   EE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTS CS
                 FAD_binding_3 287 flaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGe 325
                                   ++aGDAa     t+G G+ ta+      +   a++l+G+
  gi|91772363|ref|YP_565055.1| 284 LVAGDAAGHIIATNGGGISTAMVGGKIAGQTAAEFLEGK 322
                                   79********************99888888888888865 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   5.3e-11     6e-08       1      33 [.      11      43 ..      11      88 .. 0.91
   2 ?    1.2   0.0      0.41   4.6e+02       2      16 ..     306     320 ..     305     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 5.3e-11
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                  IvGaG +G++aA+++akag++vll+ek  ++G 
  gi|91772363|ref|YP_565055.1| 11 IVGAGPAGSTAAAYAAKAGASVLLIEKKKDIGL 43
                                  9******************************96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                                   E--SHHHHHHHHHHH CS
                 NAD_binding_8   2 vGaGlsGlvaAylLa 16 
                                   vG+ ++G +aA +L 
  gi|91772363|ref|YP_565055.1| 306 VGGKIAGQTAAEFLE 320
                                   9***********997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   1.9e-08   2.1e-05       1      33 [.       8      42 ..       8      48 .. 0.96
   2 !   10.9   0.4   0.00022      0.25     135     348 ..      97     310 ..      53     314 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.9e-08
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  d++i+G+G +G+++A ++a++g  V+l+ek++++g
  gi|91772363|ref|YP_565055.1|  8 DIIIVGAGPAGSTAAAYAAKAGasVLLIEKKKDIG 42
                                  8*****************************98887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                                   EEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH..HHHTTCTT CS
                           DAO 135 lfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd..llgllkel 213
                                   + ++    +d +++ ++la++a + G+++  gt+v +++ ++ +v gv+ t   +  + + ++ a G+ s+   +   k l
  gi|91772363|ref|YP_565055.1|  97 FEVDA-DAIDRRRFDKYLAKEAGRCGADVMIGTNVLEVNGTSVDVDGVFGTH-SI--SGKVLIGADGPNSTvgRA---KGL 170
                                   44444.566*****************************55555677776332.22..347799999***975444...333 PP

                                   ....TSEEEEEEEEEEEEEECCT.HSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESSEEETTCSS.TSCSHHHHHH CS
                           DAO 214 ....dlpispvrgqvlvlkplse.klvspaailpvpe.tdddgrgvyvtprkdgrvlvGgtadeesgddd.pevdeedide 287
                                       d p+    g+ + + ++s+   +++a +  ++     +g++  ++   +++  +G       ++ + ++    ++d+
  gi|91772363|ref|YP_565055.1| 171 vrdhD-PMGT--GTAFEY-EVSCvDIDREA-VEMYFGkDYVPGGYAWIISQGGDTANIGVGI----RE-VlFRNGLSARDY 241
                                   22113.3222..333333.22220111111.1111111222222223333222222233221....11.134555556666 PP

                                   HHHHHHHHSGG...G..CGEEEEEEEEEEETTSSEEEEEEE......TEEEEEEEEECTTTHHHHHHHHHHH CS
                           DAO 288 llealrklfPq...l..gdvlrkwaGlrplpdglpligetp......gvkglylatGhsghGltlapatGkl 348
                                   l + + ++  +   l  +++ +  +Gl p + g p +  t          g+++at+  g G+++a++ Gk+
  gi|91772363|ref|YP_565055.1| 242 LERFMYEHPIAsrkLdgASIISVVSGLVP-VGGAPKVTATKdtlvagDAAGHIIATN--GGGISTAMVGGKI 310
                                   66666665533333244557778888888.666666666434444433446666654..4788888887776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.4   4.4e-11   4.9e-08       1      35 [.       8      42 ..       8      52 .. 0.97
   2 ?   -2.3   0.0       1.9   2.2e+03     401     420 ..     305     324 ..     299     371 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.4e-11
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                  D+++vG+gpaG +AA  Aa+aGa+vlL+e+++ +G
  gi|91772363|ref|YP_565055.1|  8 DIIIVGAGPAGSTAAAYAAKAGASVLLIEKKKDIG 42
                                  9*****************************99887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                  FAD_oxidored 401 malGqAaGvaAalaleegva 420
                                   m+ G+ aG  Aa  le ++a
  gi|91772363|ref|YP_565055.1| 305 MVGGKIAGQTAAEFLEGKCA 324
                                   44444444444444444444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.6   2.4e-10   2.7e-07       1      39 [.       7      45 ..       7      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.4e-10
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHH CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKi 39
                                  +d+i++G+G+AG  aA+ aak+g++Vll+ek+k +g  +
  gi|91772363|ref|YP_565055.1|  7 YDIIIVGAGPAGSTAAAYAAKAGASVLLIEKKKDIGLPL 45
                                  589*******************************99655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.3e-10   3.6e-07       1      34 [.       8      41 ..       8     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.3e-10
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34
                                  d+i++G+G AG+ AA+ aa++Ga+vlLi +k d 
  gi|91772363|ref|YP_565055.1|  8 DIIIVGAGPAGSTAAAYAAKAGASVLLIEKKKDI 41
                                  79**************************555443 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 !   26.0   0.1   4.2e-09   4.7e-06       1      33 [.       7      39 ..       7      62 .. 0.90
   2 ?   -0.1   0.0      0.38   4.2e+02     188     217 ..     112     141 ..     101     206 .. 0.55
   3 ?   -2.0   0.0       1.5   1.7e+03       5      20 ..     305     320 ..     302     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.2e-09
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                  +d++++G+GpAG +aa ++a+aga v+l+e+++
  gi|91772363|ref|YP_565055.1|  7 YDIIIVGAGPAGSTAAAYAAKAGASVLLIEKKK 39
                                  69***************************8554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.38
                                   HHHHHHHHTTEEEEESCEEEEEEETTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 188 aleealekeGvevklgtsvkeidgngekle 217
                                   +l+++  + G +v+ gt+v e++g + +++
  gi|91772363|ref|YP_565055.1| 112 YLAKEAGRCGADVMIGTNVLEVNGTSVDVD 141
                                   455555555555555555555555554333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.5
                                   EE--SHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   5 viGgGpAGlaaaltla 20 
                                    +Gg +AG +aa++l 
  gi|91772363|ref|YP_565055.1| 305 MVGGKIAGQTAAEFLE 320
                                   6888888888888875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   1.8   4.6e-09   5.2e-06       1      35 [.       8      42 ..       8      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.6e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                  D+i++G+G AG +AA+ aa+aG++v+++ek++  g
  gi|91772363|ref|YP_565055.1|  8 DIIIVGAGPAGSTAAAYAAKAGASVLLIEKKKDIG 42
                                  9*****************************98766 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.1e-08   1.2e-05      18      63 ..       7      51 ..       4      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                                   D++ivGaG++G taa y ak+ +  v+++e++  +G     GG l
  gi|91772363|ref|YP_565055.1|  7 YDIIIVGAGPAGSTAAAYAAKA-GASVLLIEKKKDIGLPLQCGGFL 51
                                  59*******************9.**********9999888888865 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   4.5e-07    0.0005       1      37 [.       8      42 ..       8      61 .. 0.80
   2 ?    4.7   0.1      0.01        12     150     208 ..     103     159 ..      72     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.5e-07
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S.SS- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese.eig 37
                                  +i+ivG+G+aG++aAa+ aka+   ++v+l+e++ +ig
  gi|91772363|ref|YP_565055.1|  8 DIIIVGAGPAGSTAAAYAAKAG---ASVLLIEKKkDIG 42
                                  69********************...89*****861465 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                                   EE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SG CS
                Trp_halogenase 150 hldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsG 208
                                    +d+++++k+L + a + G +++ g+ v  +   + +v+++     +++++   i + G
  gi|91772363|ref|YP_565055.1| 103 AIDRRRFDKYLAKEAGRCGADVMIGTNVLEVNGTSVDVDGVFG--THSISGKVLIGADG 159
                                   5899****************99988765444444555555544..45555555555555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   6.9e-06    0.0077       1      36 [.       8      41 ..       8      47 .. 0.91
   2 !    8.9   0.0    0.0006      0.67     225     322 ..     251     349 ..     230     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.9e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                  D++++GaGpAg   Aa    ak+g +v+lie  +++
  gi|91772363|ref|YP_565055.1|  8 DIIIVGAGPAGSTAAAYA--AKAGASVLLIEKKKDI 41
                                  9***********999999..**********987776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0006
                 Lycopene_cycl 225 lralglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres...slsa 301
                                   ++   l  +++++   g++Pv  gg ++ ++ k +l +G aag +  + G  +  ++   ++  +  a+ l+ +   + ++
  gi|91772363|ref|YP_565055.1| 251 IASRKLDGASIISVVSGLVPV--GGAPKVTATKdTLVAGDAAGHIIATNGGGISTAMVGGKIAGQTAAEFLEGKcalQDYE 329
                                   4456788899999999*****..99999999988999********************999988888888888666777888 PP

                 Lycopene_cycl 302 rawatlwprerkrqreffrll 322
                                   + w++ ++ e+k   ++ r l
  gi|91772363|ref|YP_565055.1| 330 ERWRREMGLEIKTA-VYVRKL 349
                                   88888888887754.444444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.1   1.3e-06    0.0014       1      31 [.      10      39 ..      10      44 .. 0.92
   2 ?   -2.7   0.0       2.5   2.8e+03      67     108 ..      93     134 ..      84     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                  iI+GaGPaG +aa  + kag  ++l +Ek++
  gi|91772363|ref|YP_565055.1| 10 IIVGAGPAGSTAAAYAAKAGA-SVLLIEKKK 39
                                  8********************.7*****984 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                   Pyr_redox_3  67 tspafslkeeklsrkealeYlrevaksfelpiklfeeVesvk 108
                                    s +f ++ + + r+ + +Yl++ a +   +++  ++V +v+
  gi|91772363|ref|YP_565055.1|  93 YSKEFEVDADAIDRRRFDKYLAKEAGRCGADVMIGTNVLEVN 134
                                   466778888888888888999988888888888888888886 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.4e-05     0.061       2      35 ..       9      42 ..       8      47 .. 0.92
   2 ?    1.6   0.0      0.37   4.1e+02      43      75 ..     110     142 ..     101     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  +++vG+G  g  +A+++a+ g++V ++e ++ + 
  gi|91772363|ref|YP_565055.1|  9 IIIVGAGPAGSTAAAYAAKAGASVLLIEKKKDIG 42
                                  89**************************998876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHTTEEEECSEEEEEEEEETTSEEE CS
                     Pyr_redox  43 skilqeklekngievllntkveeiegsedgves 75 
                                    k+l+++  + g +v+ +t+v e++g++  v +
  gi|91772363|ref|YP_565055.1| 110 DKYLAKEAGRCGADVMIGTNVLEVNGTSVDVDG 142
                                   4455555555599************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 ?   14.0   0.1   2.1e-05     0.024      31      61 ..       9      39 ..       5      46 .. 0.91
   2 ?   -3.1   0.7       3.6     4e+03      31      46 ..     303     318 ..     288     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                  EEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                  ++++G+G aG  A+a a++ ga+V ++++++
  gi|91772363|ref|YP_565055.1|  9 IIIVGAGPAGSTAAAYAAKAGASVLLIEKKK 39
                                  89**********************9999876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.6
                                   EEEESTSHHHHHHHHH CS
                   AlaDh_PNT_C  31 vlviGgGvaGlqAiat 46 
                                   +  +Gg +aG+ A++ 
  gi|91772363|ref|YP_565055.1| 303 TAMVGGKIAGQTAAEF 318
                                   4567888999998875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00022      0.25       2      33 ..       9      40 ..       8      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                  + ++GaG  G+  aa +a+ag +V l++ +++
  gi|91772363|ref|YP_565055.1|  9 IIIVGAGPAGSTAAAYAAKAGASVLLIEKKKD 40
                                  679************************99876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00044       0.5       1      32 [.       9      40 ..       9      43 .. 0.90
   2 ?   -3.0   0.0       7.7   8.6e+03      21      35 ..     185     198 ..     178     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                                  EEEES-SHHHHHHHHHHHHTTEEEEEEESSHH CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdee 32
                                  iii+G+G  G++ a +  ++g +v++i+k+++
  gi|91772363|ref|YP_565055.1|  9 IIIVGAGPAGSTAAAYAAKAGASVLLIEKKKD 40
                                  8******************6657*****9875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.7
                                   TEEEEEEESSHHHHH CS
                        TrkA_N  21 gkdvvvidkdeerve 35 
                                   + +v+ +d d+e+ve
  gi|91772363|ref|YP_565055.1| 185 Y-EVSCVDIDREAVE 198
                                   4.4999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2785.67
//
Query:       gi|91772364|ref|YP_565056.1|  [L=68]
Description: hypothetical protein Mbur_0304 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   66.6   1.3    1.6e-18   66.4   1.3    1.0  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 !   66.4   1.3   8.9e-23   1.6e-18       3      61 ..      12      66 ..      10      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 8.9e-23
                                  XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                          TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                  + G+t+eV++e+ + +eg+gi+r+  g+vvfvp+++   Gd+V++k+tkv r++++Ge+
  gi|91772364|ref|YP_565056.1| 12 EAGETYEVTIEDIA-REGDGIARVS-GFVVFVPNTSV--GDEVTIKVTKVMRKFAFGEV 66
                                  67***********9.**********.********999..******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 599.80
//
Query:       gi|91772365|ref|YP_565057.1|  [L=152]
Description: hypothetical protein Mbur_0305 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.056   13.9   2.4      0.086   13.3   2.4    1.3  1  Ago_N_1    Fungal Argonaute N-terminal domain
        0.2   11.1   0.0        1.8    8.0   0.0    2.0  1  adh_short  short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Ago_N_1  Fungal Argonaute N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.4   9.5e-06     0.086      11      82 ..      30     100 ..      27     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-06
                                   HHH-TT----HHHHHHHHHHHHHHHHSTTTS----CCHHHHHHHH-HHHHCCCTT-EEE-TT---------- CS
                       Ago_N_1  11 fkenekeqytlldWilecykqaeaarkaktkgkpsakdlnlfveknkdikdllkGlkvyrpyinysvnpdGt 82 
                                   +k + ++ y + d +++ y+      k    ++ s+k++ ++ +k ++ k+l+  lk y   +++ vn++ +
  gi|91772365|ref|YP_565057.1|  30 LKRDADKLYKIYDELVDQYNAYPYMSKDWYVENSSSKSIHMC-SKWQEFKELVDFLKAYSDDLDFLVNNNNN 100
                                   67888999**************988888899999*****987.8999********************98765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0002       1.8      18      85 ..      18      98 ..      14     141 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0002
                                  HHHHHTT-EEEEEESCHHHHHHHHHHHHHT......TSEEEEEE-T.......TTSHHHHHHHHHHHHHHHSSESEEEE-- CS
                     adh_short 18 kelakeGakvvvvdrseekleevakelkee......gakalaiqvD.......vtdreevealvekavkklgkldvLvnNA 85
                                    +a++G+k v ++r ++kl ++++el ++       +k ++++          ++++e ++lv+  ++  + ld LvnN 
  gi|91772365|ref|YP_565057.1| 18 SYFAQQGWKWVNLKRDADKLYKIYDELVDQynaypyMSKDWYVENSssksihmCSKWQEFKELVDFLKAYSDDLDFLVNNN 98
                                  556667777777777777776666666665322222122222221111111113578899999999999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1023.55
//
Query:       gi|91772366|ref|YP_565058.1|  [L=489]
Description: dihydropteroate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-09   37.1   0.0    5.4e-09   36.1   0.0    1.5  1  DUF4346      Domain of unknown function (DUF4346)
      4e-09   36.5   1.0    7.3e-09   35.7   1.0    1.5  1  Pterin_bind  Pterin binding enzyme
     0.0019   17.0   0.1      0.003   16.3   0.1    1.2  1  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun


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 !   36.1   0.0     9e-13   5.4e-09      63     118 .]     434     486 ..     419     486 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 9e-13
                       DUF4346  63 eaekvyrgrtakelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                   +++ + +grtake+   i+       ++kldha YlG e+++ae+aL  g++Y qD
  gi|91772366|ref|YP_565058.1| 434 HEDVTVTGRTAKEVIDTIIKM---GLISKLDHAGYLGCEIKKAEIALRLGRSYSQD 486
                                   4566889*******9999876...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 !   35.7   1.0   1.2e-12   7.3e-09      26     126 ..     164     253 ..     150     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.2e-12
                                   HHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEEEETTTTSSS CS
                   Pterin_bind  26 qarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadivNdvsgeerd 106
                                   ++ + +++GAdi+D+g+  t        ++++++  v v +   + ++vp+siDt +++ ++aAl++g+d+v + +  +  
  gi|91772366|ref|YP_565058.1| 164 KVTEFIKKGADIIDLGASLT-------ASAKDVRNTVRVAR---KVSTVPVSIDTLDPDLLKAALDEGVDLVLSLNSSN-I 233
                                   67899***************.......33444444444444...3338***************************9999.7 PP

                                   TTHHHHHHHHT-EEEEESEC CS
                   Pterin_bind 107 pkmlelvaeagaavvvmhmr 126
                                     + + vaeag++ vv    
  gi|91772366|ref|YP_565058.1| 234 DIVGNDVAEAGVTAVVIPDA 253
                                   78899999999999987555 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 !   16.3   0.1   5.1e-07     0.003      70     195 ..     173     297 ..     156     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-07
                                   --EEEEE--SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE CS
                          CdhD  70 ldaiairlistdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvll 150
                                   +d+i + +  t  ak ++++v+   k   vp+ + ++dp+ lkaal++  d   l+ + +  + + + +   e +v  v++
  gi|91772366|ref|YP_565058.1| 173 ADIIDLGASLTASAKDVRNTVRVARKVSTVPVSIDTLDPDLLKAALDEGVD---LVLSLNSSNIDIVGNDVAEAGVTAVVI 250
                                   55665555555556666777766666678*****************87775...777778888888887777777766665 PP

                                   -.SSHHHHHHHHHHHHC...TT---EEEE---SH.....HHHHHHHHH CS
                          CdhD 151 sindleelkelarkllk...agvkdivldPttaalGegleetidnvvr 195
                                        ++  +l++++ +   ag+ +++ dP+  ++G+g  ++i + vr
  gi|91772366|ref|YP_565058.1| 251 P-DAGNSFESLVHNIQAardAGIANLIADPVLDPIGHGFVDSIVRYVR 297
                                   5.444566666665554333999******************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3701.51
//
Query:       gi|91772367|ref|YP_565059.1|  [L=394]
Description: cell division protein FtsZ [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-38  130.6   0.2    1.4e-37  129.8   0.2    1.4  1  Tubulin   Tubulin/FtsZ family, GTPase domain
    2.3e-34  117.5   0.4    9.9e-34  115.5   0.1    2.2  2  FtsZ_C    FtsZ family, C-terminal domain


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.2   1.6e-41   1.4e-37       1     195 [.      35     193 ..      35     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 1.6e-41
                                   EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                       Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                   +i ++g+G++Gn+++n+l++      gi             +g +e+i    ai+td+q+l++i+a+      +k+l+gk+
  gi|91772367|ref|YP_565059.1|  35 RITIVGCGGAGNNTINRLYN-----IGI-------------EG-AETI----AINTDKQHLDHIRAD------KKILVGKT 86 
                                   5899****************.....599.............88.7787....***************......******** PP

                                   CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G CS
                       Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefse 162
                                    ++++gaggypevg++aae  +  +++ ++++d+   +fita++gGGTG+G++pv++e++ke+  +a+vv++v  P++   
  gi|91772367|ref|YP_565059.1|  87 LTRGLGAGGYPEVGAKAAELARGTLEEIFKESDL---VFITAGMGGGTGTGVAPVVAEIAKEQ--GAIVVGMVSSPFRV-- 160
                                   **********************************...**************************..************98.. PP

                                   -HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                       Tubulin 163 vvvepynailalkelieesdavividNdaLlki 195
                                   +  +  +a+++l ++++ +d+viv+dN++Ll+ 
  gi|91772367|ref|YP_565059.1| 161 ERARTVKAEEGLDTFRSAADTVIVLDNNRLLDY 193
                                   7899**************************986 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 ?   -1.6   0.0       0.4   3.6e+03      55      75 ..     133     153 ..     115     166 .. 0.65
   2 !  115.5   0.1   1.1e-37   9.9e-34       1      95 []     242     336 ..     242     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHS-TTSEEEEEE CS
                        FtsZ_C  55 eevaetireevdeeanvivGa 75 
                                     va +++e ++e+  ++vG 
  gi|91772367|ref|YP_565059.1| 133 TGVAPVVAEIAKEQGAIVVGM 153
                                   346666777777777777775 PP

  == domain 2  score: 115.5 bits;  conditional E-value: 1.1e-37
                                   EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT- CS
                        FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavideel 81 
                                   GvA+m vG ++++d++++++++a+++pLLdvd++gA+g lv+itgg+dl+lkE+ee+a  ++ e++++anvi+Ga+i +++
  gi|91772367|ref|YP_565059.1| 242 GVAVMLVGDSKNQDKSTDVVRTALNHPLLDVDYRGATGSLVHITGGPDLSLKEAEEIAASLTYELSPDANVIWGARIRDDF 322
                                   99******************************************************************************* PP

                                   -SEEEEEEEEES-X CS
                        FtsZ_C  82 edeirvtvvatglk 95 
                                   e+++rv++++tg++
  gi|91772367|ref|YP_565059.1| 323 EGKVRVMAIMTGVQ 336
                                   ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2923.42
//
Query:       gi|91772368|ref|YP_565060.1|  [L=231]
Description: hypothetical protein Mbur_0308 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  124.4   0.2    5.6e-36  124.2   0.2    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 !  124.2   0.2   3.1e-40   5.6e-36       9     200 ..      29     220 ..      23     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 3.1e-40
                                   -EEEEEE-TT-EEEE-CCGEEEEETTEEEEE......--------------EEEEEEES.SS-EEEEE--SSSE.EEEEEE CS
                         AIM24   9 sllsvtLspgeelyaerGalvamsgkvemet......gllkalkrlltgeslfllkftakissgtvllapklpg.tivtle 82 
                                   ++l+++L  + +++++rG++va+ g+v+++       g++k lk+++tge+++l+k +++   g+v+la   ++ +i++l+
  gi|91772368|ref|YP_565060.1|  29 RMLELNL--NGRVWTKRGSMVAYLGNVKFTRegilehGVGKLLKKAVTGEGISLTKAEGQ---GKVYLADAGKKiSIINLD 104
                                   6788888..568*****************99***************************66...********9998999999 PP

                                   GGTT.EEEEEGGGEEEEETT-EEEEEEEE--SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEEGGGEEEEE CS
                         AIM24  83 lgggdwlivqkdafLAatgnveldikfqkglkglfggeglflqkltGrGlvalsgyGaiyeielkageelvvdpghlvafs 163
                                      ++ ++v+ + +LA+++++ +dik+ k+++g+++g glf+ kl+G+G+va++ + ++++++++++ +++ dp++ va+s
  gi|91772368|ref|YP_565060.1| 105 ---NEAIFVNGNDLLAFEETIGWDIKMMKKVTGIMAG-GLFNVKLEGTGMVAITTHYDPVTLKVTKDTPVFTDPNATVAWS 181
                                   ...679***********************99999976.9****************************************** PP

                                   TTEEEEEEEE...TT---STTTTS-EEEEEEEEEEEEEES CS
                         AIM24 164 gslkfdierv...gglkrrligGeglflkltGpgtvllqs 200
                                   g+l+ d+++    +++++r  +Ge++++ ++G+g v++q+
  gi|91772368|ref|YP_565060.1| 182 GNLSPDLKTDvslKSFVGRS-SGESIQMSFKGEGFVVIQP 220
                                   ****9999998888999999.******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1522.03
//
Query:       gi|91772369|ref|YP_565061.1|  [L=237]
Description: hypothetical protein Mbur_0309 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   15.8   0.1     0.0075   15.8   0.1    1.7  2  ApbE      ApbE family


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 !   15.8   0.1   4.2e-07    0.0075     115     189 ..      70     148 ..      11     152 .. 0.75
   2 ?   -4.4   1.0      0.64   1.1e+04     219     235 ..     163     180 ..     159     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-07
                                   T..-----TTTHHHHHHHHHHHHHHH.TT-EEEEEETTEEEEEC-ECT-EEEEEE-TT.S..SEEEEEEESSS..EEEEEE CS
                          ApbE 115 gpgmkLDlggiaKGyavdrvaellka.giksalvnlGGdiralGpdgkpwrvgiedPr.a..ellavlslsdd..avaTSG 189
                                   g+ + +   +   G ++  ++  + + g +sa+v+ GGdi+ l  d +p  +gi   + +  ++  +l+ sd   +++TS+
  gi|91772369|ref|YP_565061.1|  70 GNSVGIGPMSAVAGTIAALAVGSMVDaGATSAIVDNGGDIAFLN-D-RPIVIGIYAGQsSirNIGFTLEPSDHirGICTSS 148
                                   555566555566677777777777777**************999.5.7******988742445555788776688899987 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 0.64
                                   EEEEESC.HHHHHHHHHH CS
                          ApbE 219 vtViads.alADalaTal 235
                                   + V++d+  lAD +aT l
  gi|91772369|ref|YP_565061.1| 163 AVVFSDDvSLADSAATEL 180
                                   566687779999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1618.10
//
Query:       gi|91772370|ref|YP_565062.1|  [L=128]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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   61.5  11.6    5.2e-09   35.5   1.0    2.2  2  Fer4             4Fe-4S binding domain
      4e-12   46.5  23.2    7.2e-09   36.1  12.7    1.9  2  Fer4_7           4Fe-4S dicluster domain
    4.5e-12   45.3  12.4    1.1e-06   28.4   1.4    2.3  2  Fer4_2           4Fe-4S binding domain
    6.6e-12   45.0  11.0    6.6e-07   29.1   0.9    2.3  2  Fer4_6           4Fe-4S binding domain
    6.3e-10   39.1  20.3    1.1e-06   28.6  12.5    2.1  2  Fer4_9           4Fe-4S dicluster domain
    8.4e-10   38.6   8.2    0.00017   21.7   1.1    2.2  2  Fer4_10          4Fe-4S dicluster domain
    1.5e-09   37.8   9.0     0.0002   21.4   1.2    2.2  2  Fer4_21          4Fe-4S dicluster domain
    2.1e-09   38.2   7.8    0.00027   21.8   0.3    2.3  2  Fer4_16          4Fe-4S double cluster binding domain
    1.4e-08   35.0   5.0      0.001   19.5   0.1    2.2  2  Fer4_8           4Fe-4S dicluster domain
    1.2e-07   32.1   3.6     0.0062   17.0   0.9    2.2  2  Fer4_17          4Fe-4S dicluster domain
    9.3e-07   29.6   1.9      0.016   16.0   0.1    2.1  2  Fer4_22          4Fe-4S dicluster domain
    1.2e-06   29.0  11.8     0.0043   17.6   3.2    2.3  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    2.3e-06   27.7  12.8     0.0013   19.1   3.8    2.2  2  Fer4_4           4Fe-4S binding domain
    5.8e-05   23.3  12.1     0.0012   19.0   2.1    2.5  2  Fer4_18          4Fe-4S dicluster domain
    0.00011   22.9  20.0      0.033   15.1   6.7    2.2  2  Fer4_3           4Fe-4S binding domain
     0.0076   17.0  11.3        0.1   13.3   1.6    2.6  2  Fer4_15          4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.036   12.9   0.1      0.043   12.7   0.1    1.1  1  Trp_syntA        Tryptophan synthase alpha chain
      0.065   13.4   3.1       0.17   12.1   3.1    1.7  1  ETF_QO           Electron transfer flavoprotein-ubiquinone ox
        1.7    8.5   9.3        9.4    6.1   0.5    2.3  2  zf-C2H2_11       zinc-finger C2H2-type
        5.9    7.2   8.2        6.7    7.0   1.1    2.2  2  c-SKI_SMAD_bind  c-SKI Smad4 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 !   31.0   3.7   1.6e-10   1.4e-07       3      23 ..      74      94 ..      72      95 .. 0.90
   2 !   35.5   1.0   5.8e-12   5.2e-09       2      23 ..     103     124 ..     102     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.6e-10
                                  EETTTSSS-THHHHHSTTTEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAI 23
                                   dee C+ CGaC++vCPvg+ 
  gi|91772370|ref|YP_565062.1| 74 RDEEECVECGACISVCPVGVF 94
                                  69****************985 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 5.8e-12
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   ++d++kCi CG+C  +CP++A+
  gi|91772370|ref|YP_565062.1| 103 EVDTDKCIQCGTCLTMCPHNAL 124
                                   69*******************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   2.7   1.6e-07   0.00014      32      52 .]      73      93 ..      48      93 .. 0.78
   2 !   36.1  12.7     8e-12   7.2e-09       2      52 .]      79     123 ..      78     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-07
                        Fer4_7 32 eidpekClgCgaCvavCPtga 52
                                    d+e+C+ CgaC++vCP+g+
  gi|91772370|ref|YP_565062.1| 73 SRDEEECVECGACISVCPVGV 93
                                  56889**************96 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 8e-12
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   C++CgaC ++Cpv+++++ ++       ++e+d +kC++Cg C + CP++a
  gi|91772370|ref|YP_565062.1|  79 CVECGACISVCPVGVFSFADD------WSLEVDTDKCIQCGTCLTMCPHNA 123
                                   ******************997......4689*****************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   3.8   1.2e-07   0.00011       3      21 ..      72      90 ..      70      91 .. 0.88
   2 !   28.4   1.4   1.2e-09   1.1e-06       3      22 .]     102     121 ..     100     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  +  d++ C++CgaC+s+CP
  gi|91772370|ref|YP_565062.1| 72 ISRDEEECVECGACISVCP 90
                                  5679999************ PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.2e-09
                        Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    +vdtd+Ci+Cg+C++ CP+
  gi|91772370|ref|YP_565062.1| 102 LEVDTDKCIQCGTCLTMCPH 121
                                   689****************7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   3.5   3.7e-07   0.00033       4      23 ..      74      93 ..      71      94 .. 0.88
   2 !   29.1   0.9   7.3e-10   6.6e-07       3      24 .]     103     124 ..     101     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-07
                        Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                   d++ C+ Cg+C++vCP g+
  gi|91772370|ref|YP_565062.1| 74 RDEEECVECGACISVCPVGV 93
                                  68999************997 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 7.3e-10
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   e+d dkCi+Cg C + CP++a+
  gi|91772370|ref|YP_565062.1| 103 EVDTDKCIQCGTCLTMCPHNAL 124
                                   89******************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 !   21.5   0.9   2.2e-07    0.0002      33      49 ..      70      92 ..      42      94 .. 0.73
   2 !   28.6  12.5   1.3e-09   1.1e-06       1      50 [.      78     123 ..      78     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-07
                        Fer4_9 33 e......eaCigCgaCveaCpkg 49
                                         e+C++CgaC+ +Cp g
  gi|91772370|ref|YP_565062.1| 70 TpisrdeEECVECGACISVCPVG 92
                                  144444578************87 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.3e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   +C++CgaC+++Cp gv++  +       +     +Ci+Cg+C+  Cp++a
  gi|91772370|ref|YP_565062.1|  78 ECVECGACISVCPVGVFSFADDWSLEVDTD----KCIQCGTCLTMCPHNA 123
                                   5***************97666555544433....7************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 !   21.0   1.0     3e-07   0.00027       3      21 ..      73      91 ..      71      99 .. 0.87
   2 !   21.7   1.1   1.9e-07   0.00017       3      21 ..     103     121 ..     101     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                       Fer4_10  3 vidddtCirCgkCvkaCPa 21
                                   +d++ C++Cg+C ++CP+
  gi|91772370|ref|YP_565062.1| 73 SRDEEECVECGACISVCPV 91
                                  679999************9 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.9e-07
                       Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                   ++d+d+Ci+Cg+C ++CP 
  gi|91772370|ref|YP_565062.1| 103 EVDTDKCIQCGTCLTMCPH 121
                                   5799**************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.2   2.3e-07    0.0002      34      53 ..      72      91 ..      57      96 .. 0.82
   2 !   20.8   1.3   3.6e-07   0.00032       3      22 ..     104     123 ..     101     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.3e-07
                       Fer4_21 34 lkvvedeCvGCnlCssvCPv 53
                                  +   e+eCv C  C+svCPv
  gi|91772370|ref|YP_565062.1| 72 ISRDEEECVECGACISVCPV 91
                                  456799*************9 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.6e-07
                       Fer4_21   3 idedkCigCgkCliaCedts 22 
                                   +d dkCi+Cg Cl++C+ ++
  gi|91772370|ref|YP_565062.1| 104 VDTDKCIQCGTCLTMCPHNA 123
                                   8999************9765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.1e-07   0.00027       2      20 ..      79      97 ..      78     107 .. 0.83
   2 !   19.5   2.4   1.5e-06    0.0014       1      18 [.     108     125 ..     108     128 .] 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-07
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++Cg+C++vCP+++++  
  gi|91772370|ref|YP_565062.1| 79 CVECGACISVCPVGVFSFA 97
                                  **************99876 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.5e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                   +C++Cg C+ +CP+na+ 
  gi|91772370|ref|YP_565062.1| 108 KCIQCGTCLTMCPHNALV 125
                                   6***************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 !   19.5   0.1   1.1e-06     0.001      49      64 ..      77      92 ..      29      95 .. 0.75
   2 !   17.0   1.7   6.7e-06     0.006       2      16 ..     106     120 ..     105     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                        Fer4_8 49 wsCttcgaCtevCpvg 64
                                  ++C++cgaC +vCpvg
  gi|91772370|ref|YP_565062.1| 77 EECVECGACISVCPVG 92
                                  5677777777777766 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.7e-06
                        Fer4_8   2 lekCieCgaCqsaCp 16 
                                    +kCi+Cg C ++Cp
  gi|91772370|ref|YP_565062.1| 106 TDKCIQCGTCLTMCP 120
                                   579***********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.6e-05     0.015      44      60 ..      77      93 ..      32      94 .. 0.84
   2 !   17.0   0.9     7e-06    0.0062       1      59 [.     108     122 ..     100     125 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                       Fer4_17 44 slCieCgeCerkCPqgl 60
                                  ++C+eCg C ++CP g+
  gi|91772370|ref|YP_565062.1| 77 EECVECGACISVCPVGV 93
                                  78999999999999765 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7e-06
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   +CiqCg Cl +Cp                                            ++
  gi|91772370|ref|YP_565062.1| 108 KCIQCGTCLTMCP--------------------------------------------HN 122
                                   3555555555555............................................43 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.8e-05     0.016      61      95 ..      53      92 ..      29      93 .. 0.65
   2 !   13.4   0.4   0.00012      0.11      73      94 ..     100     121 ..      94     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-05
                       Fer4_22 61 rlrqrllhklsefkekf.....gesgCvGCgRCieacpvk 95
                                  ++r  l++k +e++        +e+ Cv Cg Ci++cpv+
  gi|91772370|ref|YP_565062.1| 53 KIRDSLVKKGAEVVVLDtpisrDEEECVECGACISVCPVG 92
                                  5566666665543322223444889999999999999986 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                       Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                   +  ++++ +C+ Cg C ++cp+
  gi|91772370|ref|YP_565062.1| 100 WSLEVDTDKCIQCGTCLTMCPH 121
                                   5556677777777777777776 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.4   1.1e-05      0.01       2      22 ..      75      96 ..      72     101 .. 0.82
   2 !   17.6   3.2   4.8e-06    0.0043       1      18 [.     104     121 ..     104     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                       Fer4_13  2 DrdtCiacgaCvelaP.dvFee 22
                                  D+++C++cgaC +++P  vF  
  gi|91772370|ref|YP_565062.1| 75 DEEECVECGACISVCPvGVFSF 96
                                  89**************336655 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.8e-06
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   VD d+Ci cg+C  ++P+
  gi|91772370|ref|YP_565062.1| 104 VDTDKCIQCGTCLTMCPH 121
                                   9****************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 !   19.1   3.8   1.4e-06    0.0013       2      17 .]      77      92 ..      76      93 .. 0.92
   2 !   13.8   1.7   7.3e-05     0.066       2      15 ..     107     120 ..     106     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  e C++Cg+C+++CP+g
  gi|91772370|ref|YP_565062.1| 77 EECVECGACISVCPVG 92
                                  78************86 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.3e-05
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   ++Ci+Cg C   CP
  gi|91772370|ref|YP_565062.1| 107 DKCIQCGTCLTMCP 120
                                   89*******99999 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.1   1.3e-06    0.0012      47      75 ..      65      93 ..      28     103 .. 0.74
   2 !    9.9   2.1   0.00092      0.83      56      73 ..     104     121 ..      94     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                       Fer4_18 47 lkekeerkekgagdcidcescvkvcPtgi 75
                                  +   ++  ++++ +c++c++c++vcP+g+
  gi|91772370|ref|YP_565062.1| 65 VVVLDTPISRDEEECVECGACISVCPVGV 93
                                  4445566678899**************97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00092
                       Fer4_18  56 kgagdcidcescvkvcPt 73 
                                    ++ +ci+c++c+++cP 
  gi|91772370|ref|YP_565062.1| 104 VDTDKCIQCGTCLTMCPH 121
                                   56778************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 !   15.1   6.7   3.7e-05     0.033       1      14 [.      79      92 ..      79      93 .. 0.96
   2 !   13.8   5.4   9.8e-05     0.088       1      15 []     109     123 ..     109     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+ CgaC  vCPvg
  gi|91772370|ref|YP_565062.1| 79 CVECGACISVCPVG 92
                                  ************98 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9.8e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C++Cg+C+  CP +A
  gi|91772370|ref|YP_565062.1| 109 CIQCGTCLTMCPHNA 123
                                   ************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 !    8.9   1.9    0.0029       2.6       4      25 ..      75      97 ..      72     100 .. 0.79
   2 !   13.3   1.6   0.00012       0.1       2      19 ..     103     120 ..     102     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                       Fer4_15  4 DrdaCigcglCvaeap.evfeld 25
                                  D+++C  cg+C+ ++p  vf ++
  gi|91772370|ref|YP_565062.1| 75 DEEECVECGACISVCPvGVFSFA 97
                                  99*************73566555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                       Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                   +vD d+Ci cg C++ +p
  gi|91772370|ref|YP_565062.1| 103 EVDTDKCIQCGTCLTMCP 120
                                   69**************99 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.7e-05     0.043     109     154 ..      31      76 ..      10      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                                   HHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HH CS
                     Trp_syntA 109 aelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsde 154
                                    +++    +g +v+D+P e+  ++++ + kkg e+v l +p ++de
  gi|91772370|ref|YP_565062.1|  31 SQAHYDTTHGEVVADIPSEQFGKIRDSLVKKGAEVVVLDTPISRDE 76 
                                   55566677899******************************88876 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 ?   12.1   3.1   0.00019      0.17      45      87 ..      84     121 ..      60     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                   THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT CS
                        ETF_QO  45 peqryCPagvyeivedeeakekklqinaqnCvhCktCdikdps 87 
                                    +  +CP gv+ +++d       l++++  C+ C tC    p+
  gi|91772370|ref|YP_565062.1|  84 ACISVCPVGVFSFADDW-----SLEVDTDKCIQCGTCLTMCPH 121
                                   56679*******99665.....7**************766665 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5     0.011       9.4       7      13 ..      79      85 ..      77      88 .. 0.88
   2 ?    6.0   2.9     0.011       9.8       4      15 ..     106     117 ..     104     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                    zf-C2H2_11  7 CleCGlc 13
                                  C+eCG c
  gi|91772370|ref|YP_565062.1| 79 CVECGAC 85
                                  ******* PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                    zf-C2H2_11   4 tcqCleCGlcft 15 
                                   t +C +CG c t
  gi|91772370|ref|YP_565062.1| 106 TDKCIQCGTCLT 117
                                   669*******76 PP

>> c-SKI_SMAD_bind  c-SKI Smad4 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.0     0.059        53      22      37 ..      73      88 ..      59      97 .. 0.78
   2 ?    7.0   1.1    0.0074       6.7      24      44 ..     105     125 ..      96     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
               c-SKI_SMAD_bind 22 ssseakCikCleCkll 37
                                  s +e +C++C  C  +
  gi|91772370|ref|YP_565062.1| 73 SRDEEECVECGACISV 88
                                  667899*******766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0074
               c-SKI_SMAD_bind  24 seakCikCleCkllfspqkFv 44 
                                   ++ kCi+C +C ++   +  v
  gi|91772370|ref|YP_565062.1| 105 DTDKCIQCGTCLTMCPHNALV 125
                                   5789*******9998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 912.95
//
Query:       gi|91772371|ref|YP_565063.1|  [L=500]
Description: hypothetical protein Mbur_0311 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-142  474.3   0.2   1.8e-142  474.3   0.2    1.6  2  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    5.6e-26   90.8   2.0    7.3e-12   45.6   0.0    2.7  2  CBS       CBS domain
  ------ inclusion threshold ------
      0.017   13.8   1.6       0.13   11.0   0.3    2.2  2  DUF5018   Domain of unknown function (DUF5018)
        0.5   10.7   2.0        2.8    8.3   0.0    2.9  3  IF3_N     Translation initiation factor IF-3, N-terminal doma


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 !  474.3   0.2  4.1e-146  1.8e-142       2     346 ..      19     354 ..      18     355 .. 0.98
   2 ?   -2.2   0.4      0.32   1.4e+03       3      31 ..     424     454 ..     422     460 .. 0.70

  Alignments for each domain:
  == domain 1  score: 474.3 bits;  conditional E-value: 4.1e-146
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio   2 vVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayaglaavdlylgataese 82 
                                    V+taee++++v e g++ aa+evDVVttgTfg+m+ssg+ ln+g++ep+i+i+k+wLn+v+ay+g+aavd+ylgat+ s+
  gi|91772371|ref|YP_565063.1|  19 NVVTAEEMVDIVGELGAEGAAKEVDVVTTGTFGAMCSSGVWLNFGHSEPPIRINKLWLNDVEAYSGVAAVDAYLGATQASR 99 
                                   69******************************************************************************* PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio  83 ddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNsseetiytymge 163
                                   +  ++ eyGG+hviedL++g++++++ ++ +tdcypr+ i+t+i++ dln+ai++npRnayq+Ynaa+Ns+++t+ tymg+
  gi|91772371|ref|YP_565063.1| 100 S--KGLEYGGAHVIEDLIRGRSIDVHGTSPGTDCYPRTVIDTTINIYDLNQAIMLNPRNAYQKYNAATNSTNHTLNTYMGT 178
                                   3..456*************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 164 lkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLavigdlkeMspey 244
                                   l pn gn+t+sgaG lsP+ nDp+++tig+Gtri+LgGa+Gy++geGTq+spe+          +gtL+++gdlkeMs+ey
  gi|91772371|ref|YP_565063.1| 179 LLPNHGNVTFSGAGVLSPMHNDPNYETIGTGTRIFLGGAQGYIVGEGTQHSPESG---------FGTLMLKGDLKEMSSEY 250
                                   ***************************************************8776.........***************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                        HcyBio 245 lrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael..Gkieiegkevktarl 323
                                   +r+a++++yG++l+vg+gipiPvl+e++++++av+d+di+++++D+++++ +r+ + +v+Y+el  G+i+++gkev+t++l
  gi|91772371|ref|YP_565063.1| 251 IRAASFEGYGTSLYVGMGIPIPVLNEDIAKATAVTDDDIVTNLLDYGIPSSNRPAIRSVTYGELrsGSIDVNGKEVTTSSL 331
                                   ********************************************************************************* PP

                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 324 sslkrareiaeeLkewiekgefl 346
                                   ss+k++r+ia+eLk+wi++gef+
  gi|91772371|ref|YP_565063.1| 332 SSFKKSRQIANELKDWIKSGEFF 354
                                   **********************7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.32
                                   xxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                        HcyBio   3 Vltaeelkklvrekgekkaaeev...DVVttg 31 
                                   ++ta +++k v++  e   ++++   DVVtt+
  gi|91772371|ref|YP_565063.1| 424 IVTAWDISKAVAKA-EYDLVKDImtkDVVTTS 454
                                   79999999999984.44444443344****97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   1.6e-15   7.3e-12       1      56 [.     380     435 ..     380     436 .. 0.95
   2 !   44.0   0.5   5.1e-15   2.3e-11       1      56 [.     442     497 ..     442     498 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.6e-15
                                   HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   Vgdimt+dv  +  +++  +a+++ m +k +s+lPVVd+d+ lvGivt  D+ +a++
  gi|91772371|ref|YP_565063.1| 380 VGDIMTSDVSIIQAEASFNDAAKTiM-DKQFSHLPVVDKDNSLVGIVTAWDISKAVA 435
                                   89**********************66.999**********************98876 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 5.1e-15
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V+dimt+dvvt +pd+ +  a+ ++ +++vs+lPV+d  +++vGi+t  D+ ++l+
  gi|91772371|ref|YP_565063.1| 442 VKDIMTKDVVTTSPDEAIDIAAFKLDSNNVSALPVIDAKKQVVGIITSDDISKLLA 497
                                   89***********************7777*******88889**********88875 PP

>> DUF5018  Domain of unknown function (DUF5018)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.02        91     148     172 ..     413     437 ..     401     444 .. 0.89
   2 ?   11.0   0.3   2.8e-05      0.13     133     171 ..     458     498 ..     443     500 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.02
                       DUF5018 148 gvidedkktisLisaddlsevladv 172
                                    v+d+d+  +++++a d+s+ +a++
  gi|91772371|ref|YP_565063.1| 413 PVVDKDNSLVGIVTAWDISKAVAKA 437
                                   59*******************9986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.8e-05
                       DUF5018 133 kcellefslpekgisg..videdkktisLisaddlsevlad 171
                                   + ++  f+l+++++s+  vid +k+ +++i+ dd+s+ la 
  gi|91772371|ref|YP_565063.1| 458 AIDIAAFKLDSNNVSAlpVIDAKKQVVGIITSDDISKLLAR 498
                                   67899*********98669******************9986 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 ?    0.3   0.1       0.2   8.8e+02       1      23 [.       9      30 ..       9      46 .. 0.76
   2 ?    8.3   0.0   0.00062       2.8       9      41 ..     411     443 ..     403     450 .. 0.91
   3 ?   -2.1   0.0       1.1   4.8e+03      12      31 ..     476     495 ..     471     499 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                                  ETTS--SSEEEEE-SSS-EEEEE CS
                         IF3_N  1 iNeqIrarevrlvdedGeqlGvi 23
                                  iN +Ir   v +v+++ e++ ++
  gi|91772371|ref|YP_565063.1|  9 INGRIRDGSVNVVTAE-EMVDIV 30
                                  799**********988.666665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00062
                                   EEEEE-SSS-EEEEEEHHHHHHHHHHHTSEEEE CS
                         IF3_N   9 evrlvdedGeqlGvistreAlrlaeekgldLVe 41 
                                   +  +vd+d+  +G+++ +++ +   +++ dLV+
  gi|91772371|ref|YP_565063.1| 411 HLPVVDKDNSLVGIVTAWDISKAVAKAEYDLVK 443
                                   5679****999********************96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.1
                                   EE-SSS-EEEEEEHHHHHHH CS
                         IF3_N  12 lvdedGeqlGvistreAlrl 31 
                                   ++d++ + +G+i+ +++ +l
  gi|91772371|ref|YP_565063.1| 476 VIDAKKQVVGIITSDDISKL 495
                                   89999899999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3658.87
//
Query:       gi|91772372|ref|YP_565064.1|  [L=556]
Description: GAF sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  101.2   1.4      2e-28   99.2   0.3    2.2  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.9e-15   55.6   0.2    2.3e-13   50.0   0.0    3.1  3  HisKA        His Kinase A (phospho-acceptor) domain
    3.8e-14   52.7   0.1    8.4e-14   51.6   0.1    1.6  1  PAS_3        PAS fold
    3.2e-08   34.0   0.0    7.7e-08   32.7   0.0    1.7  1  GAF_3        GAF domain
    8.1e-06   26.1   0.1    1.9e-05   24.9   0.1    1.6  1  DUF3369      Domain of unknown function (DUF3369)
    9.8e-05   22.2   0.1     0.0002   21.2   0.1    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    0.00096   19.8   0.0     0.0018   18.9   0.0    1.5  1  GAF          GAF domain
    0.00097   19.4   0.0      0.041   14.2   0.0    2.7  2  GAF_2        GAF domain
     0.0083   16.0   0.0      0.027   14.3   0.0    1.9  2  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.043   13.8   0.0    1.8  1  PAS          PAS fold


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 ?    0.4   0.0      0.49   8.8e+02       2      25 ..      90     112 ..      89     167 .. 0.73
   2 !   99.2   0.3   1.1e-31     2e-28       1     109 [.     447     555 ..     447     556 .] 0.96

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.49
                                   HHHHHHHHHHHHHHHHHHHHSTTT CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkag 25 
                                   d ++++ iis+ v + +++  +++
  gi|91772372|ref|YP_565064.1|  90 DRDGVKDIISESVNAGIDE-FNCE 112
                                   7889999***********8.4333 PP

  == domain 2  score: 99.2 bits;  conditional E-value: 1.1e-31
                                   EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHH CS
                     HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsi 80 
                                   gde+rL+ +++n++dNavkf   +ge+ v+++ + d+++++++DnGiGipk++++k+f++f+q d+s +r +ggtG+Gl +
  gi|91772372|ref|YP_565064.1| 447 GDEERLTTALNNILDNAVKF-MLEGEVIVSVQDEADHIHLRIKDNGIGIPKNKVDKVFDSFYQvDGSLTRMYGGTGIGLHV 526
                                   79******************.9999999**995559********************************************* PP

                                   HHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlp 109
                                   +k++++ ++G+iw++s +g Gtt+++ lp
  gi|91772372|ref|YP_565064.1| 527 SKRIIDVHNGKIWLKSLEGFGTTVHILLP 555
                                   *************************9887 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.8   3.2e+03      33      55 ..      15      40 ..       7      42 .. 0.74
   2 !   50.0   0.0   1.3e-16   2.3e-13       2      60 ..     334     394 ..     333     400 .. 0.96
   3 ?    1.7   0.0      0.15   2.6e+02      34      60 ..     435     461 ..     417     463 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                                  -HSSCHHHHHHHHHHHH...HHHHHH CS
                         HisKA 33 lteelkeyletiesear...rldhlv 55
                                  l   l++ le i+ +a+   rl++++
  gi|91772372|ref|YP_565064.1| 15 LESALRQSLEEIKLSAEtkiRLESVI 40
                                  56778899999998888777777666 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 1.3e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLd 60 
                                   +++f+a+++HEL+tP+ +i+g++e+L +   g+l+ e+k++ + ++++a+rl +l++ lL 
  gi|91772372|ref|YP_565064.1| 334 KNEFFANLSHELKTPMISIKGFSELLGDGkfGPLNVEQKKANDAVVRNAERLKDLIDSLLY 394
                                   789*******************************************************986 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.15
                                   HSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                         HisKA  34 teelkeyletiesearrldhlvedlLd 60 
                                   ++e  e++ +i   ++rl+  ++++Ld
  gi|91772372|ref|YP_565064.1| 435 RDEIPENIPVIYGDEERLTTALNNILD 461
                                   567789999****************98 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.1   4.7e-17   8.4e-14       5      88 ..      62     145 ..      58     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 4.7e-17
                         PAS_3   5 serveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkpvr 84 
                                    +++e+ +Gys+e++      + +++hp+Dr+ v++ + e+++ g  ++++eyRi++ + ++ wv ++++++r  ++ +++
  gi|91772372|ref|YP_565064.1|  62 TDNIER-FGYSKEDFVTGTLLYDSIIHPDDRDGVKDIISESVNAGIdEFNCEYRIVTESNDIKWVYETTVIHRTTDSTVDH 141
                                   555644.6**********9999*********************************************************** PP

                         PAS_3  85 vigv 88 
                                   + g+
  gi|91772372|ref|YP_565064.1| 142 FYGI 145
                                   *998 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   4.3e-11   7.7e-08       1     129 []     181     313 ..     181     313 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.3e-11
                         GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesld..edsalar.......ralssgevvsepsf 72 
                                   ++d+ll+++l +l +l++ ++g +++ d d+ k++ +a+++  ++l  ++    ++ +++       +++ s+e +  +++
  gi|91772372|ref|YP_565064.1| 181 DIDDLLAEILMELGDLFKIDAGGVYIIDHDQYKANLRANIGTDDVLASTIHysQNEDMFKnvtnlpkNTIVSDELI-RQGS 260
                                   689************************************9555555443333355555552211111333333322.2333 PP

                         GAF_3  73 aeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                   +      ++++++  L ++++v+G+++l  +++ ++++++l+ le+++ +i++aie+
  gi|91772372|ref|YP_565064.1| 261 RF---VTKTNLTFY-LHSRDKVVGFVLLVLPPGYPLSEKNLQVLEHVGKHIGIAIEN 313
                                   33...344555554.77777************************************8 PP

>> DUF3369  Domain of unknown function (DUF3369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.1e-08   1.9e-05      34     167 ..     179     319 ..     167     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                       DUF3369  34 lrsleefaegvltqlasllnlkkdglvcaskakaaaske.....lkvlaatgkfesligk..pleeladeelrellerale 107
                                   + +++++++++l +l  l+++++ g++++++++ +a+ +       vla+t ++++ ++   ++ +l  ++ +   ++ ++
  gi|91772372|ref|YP_565064.1| 179 SLDIDDLLAEILMELGDLFKIDAGGVYIIDHDQYKANLRanigtDDVLASTIHYSQNEDMfkNVTNL--PKNTIVSDELIR 257
                                   45799***********************999988887778999999**********77764444444..444555567777 PP

                       DUF3369 108 skkslfeddfvvlyfktkegsegvlyle..ttrplseldrkLlevFannvavafeNvllnee 167
                                   + + ++++  +++y++++++  g+++l      plse + + le   + +++a+eN++l+e+
  gi|91772372|ref|YP_565064.1| 258 QGSRFVTKTNLTFYLHSRDKVVGFVLLVlpPGYPLSEKNLQVLEHVGKHIGIAIENAQLFEK 319
                                   7777777788888******888877766346789*************************985 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.1e-07    0.0002       4      79 ..     453     526 ..     450     531 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-07
                   HATPase_c_3   4 ekAlaelvdNsldAdaen.vkievnknrgktgeivieDdGkGmseeelknalr.latsskeakrkstslGkkGiGlkl 79 
                                   ++Al  ++dN++    e  v ++v+++  ++  ++i+D+G G++++++++++  + + + +     + +G  GiGl  
  gi|91772372|ref|YP_565064.1| 453 TTALNNILDNAVKFMLEGeVIVSVQDE-ADHIHLRIKDNGIGIPKNKVDKVFDsFYQVDGS---LTRMYGGTGIGLHV 526
                                   68999********88775277777776.589*******************99626666666...58999999999865 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     1e-06    0.0018       1     133 []     181     311 ..     181     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-06
                                   SHHHHHHHHHHHHHHHHTESEEEEEEEEETTEEE..........CEEEEECCEEEETTSHHHHHHHHHSSSEEESTGGTST CS
                           GAF   1 dleelldtvveelrellgadrvalylpdydGlhy..........dipqasrwlfmkngrgicgqvlatgqplvipdstpdp 71 
                                   d+++ll++++ el++l++ d + +y+ d+d   y          d   as+  + +n ++ +  v + ++  +++d    +
  gi|91772372|ref|YP_565064.1| 181 DIDDLLAEILMELGDLFKIDAGGVYIIDHDQ--YkanlranigtDDVLASTIHYSQNEDM-FKNVTNLPKNTIVSD----E 254
                                   799**********************944444..233445566666666777777777777.454555555556663....3 PP

                                   THHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                           GAF  72 rfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                      q       +++ +++ l+  l+++++++G + l+ p   p ++  l++l++++ ++++a+
  gi|91772372|ref|YP_565064.1| 255 LIRQ------GSRFVTKTNLTFYLHSRDKVVGFVLLVLPPGyPLSEKNLQVLEHVGKHIGIAI 311
                                   3333......45677799********************744899*****************98 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.3e-05     0.041       2     138 .]     180     312 ..     179     312 .. 0.65
   2 ?   -3.2   0.0       5.4   9.7e+03       4      21 ..     452     469 ..     450     498 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-.GGG-S- CS
                         GAF_2   2 adleelldlvldelvel.gaalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilnd.leedpd 79 
                                   +d+++ll ++l el +l  +++g ++++d+d++   l+a  ++++ + + ++ + +e  +  +    + +i++d l +   
  gi|91772372|ref|YP_565064.1| 180 LDIDDLLAEILMELGDLfKIDAGGVYIIDHDQYkANLRANIGTDDVLASTIHYSQNEDMFKNVTNLPKNTIVSDeLIR--- 257
                                   678888888888888866777776667776665322224445555555555445555555555555555555552111... PP

                                   HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                         GAF_2  80 kkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                      +  ++   ++ l + l s+++vvG++ l+    ++++e +l++Le ++ +i+iaie
  gi|91772372|ref|YP_565064.1| 258 ---Q-GSRFVTKTNLTFYLHSRDKVVGFVLLVLPPGYPLSEKNLQVLEHVGKHIGIAIE 312
                                   ...1.2333333448888888889***999988888889*******************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.4
                                   HHHHHHHHHHHHHHSS.. CS
                         GAF_2   4 leelldlvldelvelgaa 21 
                                   l++ l+++ld +v++  +
  gi|91772372|ref|YP_565064.1| 452 LTTALNNILDNAVKFMLE 469
                                   566778888888775333 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.5   9.9e+03      10      17 ..     307     314 ..     304     328 .. 0.68
   2 !   14.3   0.0   1.5e-05     0.027       5      92 ..     451     545 ..     448     555 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.5
                   HATPase_c_5  10 lgnlLdNA 17 
                                   +g++++NA
  gi|91772372|ref|YP_565064.1| 307 IGIAIENA 314
                                   57788887 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.5e-05
                   HATPase_c_5   5 dlcvilgnlLdNAieacsk......ieeekrfIrltvrekkksliisieNsyegekkkle....sskskkeehGiGlksir 75 
                                    l++ l n+LdNA+  + +      +++e   I+l ++ +    i + +N++++  +++     s ++  +  GiGl+  +
  gi|91772372|ref|YP_565064.1| 451 RLTTALNNILDNAVKFMLEgevivsVQDEADHIHLRIKDNG---IGIPKNKVDKVFDSFYqvdgSLTRMYGGTGIGLHVSK 528
                                   68999*********999885665555555555555554332...3345666666443333233366788899********* PP

                   HATPase_c_5  76 eivkkykgnlsieaedg 92 
                                   +i++ ++g+++++  +g
  gi|91772372|ref|YP_565064.1| 529 RIIDVHNGKIWLKSLEG 545
                                   *********99887655 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.043      34     112 ..      68     148 ..      35     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                   HSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                           PAS  34 lGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrd 112
                                   +G+s  + v g  l+d+i+++dd+  +++++++  ++g ++ + e ++ +  + ++++  +++  r  ++++ +f g+l d
  gi|91772372|ref|YP_565064.1|  68 FGYSKeDFVTGTLLYDSIIHPDDRdGVKDIISESVNAGIDEFNCEYRIVTESNDIKWVYETTVIHRTTDSTVDHFYGILFD 148
                                   899997889*****************************************9999999999999999999998888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3810.52
//
Query:       gi|91772373|ref|YP_565065.1|  [L=243]
Description: peptidylprolyl isomerase, FKBP-type [Methanococcoides burtonii DSM 6242]
Scores for complete 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   39.3   0.0    1.4e-09   37.9   0.0    1.8  2  FKBP26_C  FKBP26_C-terminal
    4.3e-09   36.6   0.4    4.4e-08   33.3   0.2    2.2  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         1   9.1e+03      40      49 ..      92     101 ..      87     102 .. 0.77
   2 !   37.9   0.0   1.6e-13   1.4e-09       3      71 ..     157     221 ..     155     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                   GSTTHHHHHH CS
                      FKBP26_C  40 Fieniqlakl 49 
                                   ++eni l+k+
  gi|91772373|ref|YP_565065.1|  92 LVENISLTKF 101
                                   6788988887 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 1.6e-13
                                   HHHHHHHHHH..-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEE CS
                      FKBP26_C   3 ekikelIkry..iPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdef 71 
                                   ek+k+l  +y  +P ++     + ied++v+Ie+p + +F +   +ak r+A ++++ + + ekV++++ +
  gi|91772373|ref|YP_565065.1| 157 EKVKGLLALYtgVPDLE-----VAIEDNKVSIEVPAMLSFNQRWLMAKGRVASELIEHL-GLEKVSYIESY 221
                                   9********86667777.....*************************************.*********87 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2     5e-12   4.4e-08       5      76 ..       6      90 ..       5     115 .. 0.89
   2 ?    1.1   0.0     0.056     5e+02       8      73 ..     126     193 ..     119     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5e-12
                                  B-TTCEEEEEEEEEETTSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTTT CS
                        FKBP_C  5 akegdtVtvhykgkledgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYgek 74
                                  +++gd+++v y+gk+ ++++fd++             r ++    + vG+g+ i G++e   g +vG   t++i pe ++ge+
  gi|91772373|ref|YP_565065.1|  6 IEKGDIIKVSYTGKFGGDQIFDTTdeelakaneiynpRGMYGGDVVIVGAGHTIAGLDEDFAGKEVGHSGTVIIAPEKGFGEH 88
                                  579************99*******99999999996655588889999**********************************97 PP

                                  TB CS
                        FKBP_C 75 gl 76
                                  + 
  gi|91772373|ref|YP_565065.1| 89 DP 90
                                  65 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.056
                                   TCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBT...T-EEEEEEEGGGTTTT CS
                        FKBP_C   8 gdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkv...GekrtltippelaYge 73 
                                   g +V+v+++  l  gk +  ++s  +++e  +++ + + +++ ++  ++v   + k  +++p  l + +
  gi|91772373|ref|YP_565065.1| 126 GRRVRVDFNHPL-AGKDINYEYSIDEKIEEPIEKVKGLLALYTGVPDLEVaieDNKVSIEVPAMLSFNQ 193
                                   778888988888.67777777778888888888877788888888776653336677777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1646.43
//
Query:       gi|91772374|ref|YP_565066.1|  [L=1021]
Description: cadherin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   33.2   0.2    5.3e-08   33.2   0.2    3.4  4  Cadherin         Cadherin domain
    6.4e-07   29.5   6.6    6.4e-07   29.5   6.6    5.5  6  Big_3_5          Bacterial Ig-like domain (group 3)
  ------ inclusion threshold ------
      0.066   13.2   0.1       0.16   12.0   0.1    1.7  1  Gram_pos_anchor  LPXTG cell wall anchor motif
        1.1    8.7   5.9        1.2    8.7   1.5    2.5  2  DUF1189          Protein of unknown function (DUF1189)
          3    7.8   9.0        1.4    8.8   0.1    4.8  6  PKD              PKD domain


Domain annotation for each model (and alignments):
>> Cadherin  Cadherin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         1   3.8e+03      14      48 ..     362     401 ..     353     409 .. 0.72
   2 !   33.2   0.2   1.5e-11   5.3e-08       3      92 ..     397     491 ..     395     492 .. 0.73
   3 ?   -3.6   0.1       4.4   1.6e+04      37      55 ..     692     710 ..     685     712 .. 0.68
   4 ?   -1.4   0.1      0.94   3.4e+03      13      40 ..     791     818 ..     782     822 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                                   EEEEECECCCSTSTTTSEEEEEEECTT.....TTSEEEET CS
                      Cadherin  14 evltvtatdaDlgpnsrirysilegne.....ggkFridt 48 
                                   +  t+t++d D +  s  ++ ++ gn+     ++++++ +
  gi|91772374|ref|YP_565066.1| 362 RTYTITVKDGDGELASGTSTLFVYGNApvfnsADNYSVAE 401
                                   5678899999999999888888888866666556666555 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.5e-11
                                   EEEETTS-TCCEEEEECECCCS..TSTTTSEEEEEEECTTTTSEEEETTTTEEEESST....C-TTTSSEEEEEEEEEECT CS
                      Cadherin   3 asvpEnapvgtevltvtatdaD..lgpnsrirysilegneggkFridtetgdlsttkp....LdrEsqgeYeLtveatDes 77 
                                    sv En+++    l  t  d+     + s+i+y +++g+ +  F+id+++g++++t+     Ld+E + +Y+L+v++tD+ 
  gi|91772374|ref|YP_565066.1| 397 YSVAENETSLALMLYDTQADNGdgGLNDSNITYLFAGGDGQSLFAIDSDDGEIRLTSLgtvtLDYEAKTNYTLQVLVTDQ- 476
                                   577777665444444444444344445689*********9************7776533356******************. PP

                                   GCCEEEEEEEEEEEE CS
                      Cadherin  78 gspplsstttvtvtV 92 
                                   +  + +   +vtv+V
  gi|91772374|ref|YP_565066.1| 477 QAANNTLIENVTVNV 491
                                   566666666777766 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.4
                                   ECTTTTSEEEETTTTEEEE CS
                      Cadherin  37 egneggkFridtetgdlst 55 
                                   + n ++ F i+ ++ d+++
  gi|91772374|ref|YP_565066.1| 692 ASNDSEVFYINITKRDIEV 710
                                   3444688888888888876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.94
                                   CEEEEECECCCSTSTTTSEEEEEEECTT CS
                      Cadherin  13 tevltvtatdaDlgpnsrirysilegne 40 
                                   + v  vt++d+++ +n+  +++ l++++
  gi|91772374|ref|YP_565066.1| 791 SAVSLVTVSDPQTSDNGVRVHTKLGQPS 818
                                   567889******9888887777777764 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.9     1e+04      24      67 ..      94     123 ..      84     128 .. 0.43
   2 ?   -1.7   0.2      0.97   3.5e+03      37      71 ..     201     223 ..     188     227 .. 0.54
   3 ?    2.4   0.2     0.049   1.7e+02      11      37 ..     363     390 ..     350     415 .. 0.79
   4 ?    3.6   0.3     0.021        77       6      52 ..     463     512 ..     458     533 .. 0.76
   5 ?   -0.9   1.0      0.53   1.9e+03      15      81 ..     631     698 ..     621     705 .. 0.52
   6 !   29.5   6.6   1.8e-10   6.4e-07       2      89 ..     717     802 ..     716     803 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.9
                                   S--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEE CS
                       Big_3_5  24 ptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAtY 67 
                                    +G +++   ++ +gt + + + G+              i AtY
  gi|91772374|ref|YP_565066.1|  94 SNGEISINGSDVFVGTGSGVVKIGI--------------INATY 123
                                   4444444433333344333333333..............33444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.97
                                   -SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TT CS
                       Big_3_5  37 lgtavllsanGtAtltvsalaaGthsitAtYsGda 71 
                                   +           At+++ a ++Gt+s++ +  G++
  gi|91772374|ref|YP_565066.1| 201 F-----------ATADTDA-SQGTYSLKLSNRGTT 223
                                   3...........3333333.466666655555554 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.049
                                   EEEEE--CCCCTTS--EEEEEE.TTEE- CS
                       Big_3_5  11 tltatVtaasggtptGtVtftd.ggttl 37 
                                   t t+tV++++g+ ++Gt t+++ g++++
  gi|91772374|ref|YP_565066.1| 363 TYTITVKDGDGELASGTSTLFVyGNAPV 390
                                   7899999999999****99988455555 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.021
                                   TTSEEEEEEE--CCCCTTS-....-EEEEEETTEE-SS-EE--TTSEEEEE CS
                       Big_3_5   6 agqtvtltatVtaasggtpt....GtVtftdggttlgtavllsanGtAtlt 52 
                                   a++++tl++ Vt++++++ t     tV++ d +++  +a++ls +G ++ t
  gi|91772374|ref|YP_565066.1| 463 AKTNYTLQVLVTDQQAANNTlienVTVNVIDANDPAIAASPLS-QGAVNGT 512
                                   78999*******9887655555446777888999999999999.6766544 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 0.53
                                   E--CCCCTTS--EEEEEE...TTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S--EEE CS
                       Big_3_5  15 tVtaasggtptGtVtftd...ggttlgtavllsanGtAtltvsalaaGthsitAtYsGdanyaastssav 81 
                                   +Vt++++ + + +Vt  +   +g +lg+  + +   + + t+ +  + + ++  +Ys +++ +as++s+v
  gi|91772374|ref|YP_565066.1| 631 SVTSTETDADNVNVTYNVpwlTGSSLGSINTDD-LKWCNHTLLNS-TVAENVIRVYSNTTQTSASNDSEV 698
                                   444443333333333333444555555544433.23333333333.334556667888888888888876 PP

  == domain 6  score: 29.5 bits;  conditional E-value: 1.8e-10
                                   S-EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S--EEEE CS
                       Big_3_5   2 tsvtagqtvtltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAtYsGdanyaastssavt 82 
                                   +s++ g+t+ ++atV +  g+t  G+  f  +g  +gt+++++ +G+A+++++  + Gth    ++  ++ y   ++  + 
  gi|91772374|ref|YP_565066.1| 717 QSIAPGATIWVSATVEGEYGETFIGNAVFLRDGIGIGTTQAVT-DGNASFNTTESSLGTHIFSIEFYNTTLYHNTSAV-SL 795
                                   57899**************************************.9**********************99998776555.55 PP

                                   EEEES-- CS
                       Big_3_5  83 vtVtkaa 89 
                                   vtV+ ++
  gi|91772374|ref|YP_565066.1| 796 VTVSDPQ 802
                                   9998876 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.4e-05      0.16      14      42 ..     993    1021 .]     993    1021 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Gram_pos_anchor   14 engnifltaaGllallggllLlvkrRKke 42  
                                    e++ ++l ++G++++lg++ + v++R+k+
  gi|91772374|ref|YP_565066.1|  993 EKDKPILAVFGIAIVLGMATVIVSKRNKK 1021
                                    67789****************99998875 PP

>> DUF1189  Protein of unknown function (DUF1189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.5   0.00033       1.2      29     111 ..      14      99 ..      12     141 .. 0.80
   2 ?    1.2   0.2     0.062   2.2e+02      87     153 ..     623     715 ..     613     735 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00033
                       DUF1189  29 lllLslilalpisiiifyefnskinqleelieeeipdFtiedGelqieekepiiiqedgitiifDtsgetdeedlekynn. 108
                                   l++L++++ +++ i++  ++ s  n ++++iee+  +++i d+ l i +++++ + + +i +i+ +s+++d+ dl++  + 
  gi|91772374|ref|YP_565066.1|  14 LIVLVFVILVVLGISVQASVPSFTNLDNSTIEEQ--NISIMDNDLAITNSDGTGYGDGYIEFILSNSNSYDDFDLNSSSSp 92 
                                   6899999999999999999999999999999776..799************9999999999**********9998876655 PP

                       DUF1189 109 ....gil 111
                                        i 
  gi|91772374|ref|YP_565066.1|  93 nsngEIS 99 
                                   5555444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.062
                       DUF1189  87 gitiifDtsgetdeedlekynn............................gililkdkivi.knggttqsysysdledqkl 138
                                   gi++ +D s +++e+d ++ n                             +  + ++ i + +n+++t+  + s++  +++
  gi|91772374|ref|YP_565066.1| 623 GINFNIDHSVTSTETDADNVNVtynvpwltgsslgsintddlkwcnhtllNSTVAENVIRVySNTTQTSASNDSEVFYINI 703
                                   555666666665555532222233344555555555555555555423332333333333368888888888888888899 PP

                       DUF1189 139 tkedlrefl.ssvksi 153
                                   tk d++ ++       
  gi|91772374|ref|YP_565066.1| 704 TKRDIEVVIsP----S 715
                                   99999999942....2 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4     5e+03      10      35 ..     343     371 ..     339     383 .. 0.57
   2 ?    8.8   0.1    0.0004       1.4      23      70 ..     424     481 ..     403     482 .. 0.83
   3 ?   -1.1   0.0      0.48   1.7e+03      28      34 ..     520     526 ..     517     549 .. 0.78
   4 ?   -1.2   0.1      0.53   1.9e+03      13      36 ..     631     655 ..     626     665 .. 0.72
   5 ?   -0.4   0.0       0.3   1.1e+03       2      20 ..     713     731 ..     712     738 .. 0.85
   6 ?   -3.9   0.0       3.6   1.3e+04      23      36 ..     834     846 ..     831     863 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                                   SSEEEEEEEES.-SS-S...EEEEE--SS CS
                           PKD  10 pgatvaftaavpdganv...tysWdfgdg 35 
                                   +  t++ t ++p+g+ +   ty+ ++ dg
  gi|91772374|ref|YP_565066.1| 343 RSLTYNYTDSSPSGDVIsgrTYTITVKDG 371
                                   55666666666666665333455666665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0004
                                   SS-SEEEEE--SS..........--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD  23 ganvtysWdfgdg..........svvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                   ++n+ty++  gdg          +    +s  tvt+ Y++  +Y+++v++++   + +
  gi|91772374|ref|YP_565066.1| 424 DSNITYLFAGGDGqslfaidsddGEIRLTSLGTVTLDYEAKTNYTLQVLVTDQQAANN 481
                                   689999999999999999999864444455569*******************977665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.48
                                   EEEE--S CS
                           PKD  28 ysWdfgd 34 
                                   +sW+f d
  gi|91772374|ref|YP_565066.1| 520 FSWTFSD 526
                                   89***99 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.53
                                   EEEEEEES.-SS-SEEE..EE--SS- CS
                           PKD  13 tvaftaavpdganvtys..Wdfgdgs 36 
                                   +v+ t + +d +nvty   W +g  s
  gi|91772374|ref|YP_565066.1| 631 SVTSTETDADNVNVTYNvpWLTGS-S 655
                                   566666778899999987787776.5 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.3
                                   E---S--BSSEEEEEEEES CS
                           PKD   2 sasptvlvpgatvaftaav 20 
                                   s+s+++++pgat+  +a+v
  gi|91772374|ref|YP_565066.1| 713 SPSSQSIAPGATIWVSATV 731
                                   788999***********99 PP

  == domain 6  score: -3.9 bits;  conditional E-value: 3.6
                                   SS-SEEEEE--SS- CS
                           PKD  23 ganvtysWdfgdgs 36 
                                   g+ v +++  gd  
  gi|91772374|ref|YP_565066.1| 834 GNKVEFTFSAGD-A 846
                                   445555555555.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1021 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.24s 00:00:00.96 Elapsed: 00:00:00.41
# Mc/sec: 7400.32
//
Query:       gi|91772375|ref|YP_565067.1|  [L=492]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-63  214.8   0.8      4e-63  213.5   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
    9.5e-11   41.9   3.8    2.7e-10   40.5   3.8    1.8  1  zf-IS66          zinc-finger binding domain of transposase IS
    0.00012   22.3   0.1       0.16   12.2   0.2    2.6  2  DDE_Tnp_IS240    DDE domain
    0.00014   22.4   0.6    0.00039   21.0   0.6    1.7  1  SlyX             SlyX
  ------ inclusion threshold ------
      0.029   14.9   1.6       0.13   12.9   1.6    2.2  1  BST2             Bone marrow stromal antigen 2
      0.067   12.9   1.5        0.6    9.8   0.7    2.4  2  YkyA             Putative cell-wall binding lipoprotein
       0.15   12.5   2.7       0.58   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.53   10.7   7.7        1.2    9.6   5.8    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.62   10.8   8.8          5    7.9   1.0    3.9  4  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.4    8.8   6.4       0.79   10.4   1.3    2.8  1  PLATZ            PLATZ transcription factor
        3.8    7.6   8.1       0.83    9.7   0.8    3.0  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       0.5   8.2e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  213.5   0.0   2.5e-66     4e-63       2     280 ..     179     454 ..     178     456 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.5
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e +  +  e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772375|ref|YP_565067.1|  21 TLVTTLYDIIAEQQ--TIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   44677777766653..24466666666666666666766766665555444 PP

  == domain 2  score: 213.5 bits;  conditional E-value: 2.5e-66
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+ a++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91772375|ref|YP_565067.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELRADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+e+++a+  L +f+G++v+  +++Y k+   +++h +C aHl+R+++++
  gi|91772375|ref|YP_565067.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSEAMNAMgiLPNFNGTVVHYFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...****************9955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealarigklyaierearea....eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkairy 233
                                   +e+++  q +++a++ +  + + +  +re+    ++e+ ++ +  + + ++  +e++ + q     ++ ++++++++++++
  gi|91772375|ref|YP_565067.1| 329 SENDD--QLWSKAMNILLLMSKNQLTIREMsgcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLDR 407
                                   **977..*********99999999999855568888********************998554567799************* PP

                  DDE_Tnp_IS66 234 llkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   +   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91772375|ref|YP_565067.1| 408 FIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 454
                                   **********************************************9 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 !   40.5   3.8   1.7e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.7e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91772375|ref|YP_565067.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0031       5.1       5      45 ..     249     287 ..     245     289 .. 0.84
   2 !   12.2   0.2    0.0001      0.16      85     138 ..     417     470 ..     392     472 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0031
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91772375|ref|YP_565067.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSEAMN 287
                                   68************99866..77779999999999998865 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0001
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91772375|ref|YP_565067.1| 417 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 470
                                   45667899*****************************98777776666666665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.6   2.4e-07   0.00039      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq  i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772375|ref|YP_565067.1| 22 LVTTLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.6     8e-05      0.13      44      87 ..      20      63 ..       3      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 44 nqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                     v tL + + ++++  + q a++ el++ +kkL+++L++ + 
  gi|91772375|ref|YP_565067.1| 20 VTLVTTLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNSR 63
                                  56788999999999**************************9876 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7   0.00037       0.6      49      99 ..      16      66 ..       3      76 .. 0.85
   2 ?    0.6   0.0      0.23   3.8e+02      33      58 ..     367     392 ..     362     396 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00037
                          YkyA 49 fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeel 99
                                   +++++l+  + +++ e+++++e + + i e +e ++k++e++++   ++ 
  gi|91772375|ref|YP_565067.1| 16 PEAVVTLVTTLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNSRNSS 66
                                  5679999*************************************9866554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.23
                          YkyA  33 keqelyeeiielgmdefdkikklsde 58 
                                   + ++ y +ii  g++e+ +++++s++
  gi|91772375|ref|YP_565067.1| 367 EFEDWYGQIIHIGIEENPQLQAKSKK 392
                                   556789****************9986 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00036      0.58      45      82 ..      25      62 ..      16      73 .. 0.80
   2 ?    1.1   0.1      0.35   5.7e+02      11      58 ..     391     445 ..     382     476 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772375|ref|YP_565067.1| 25 TLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNS 62
                                  55566788889999999999999999999999988654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.35
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91772375|ref|YP_565067.1| 391 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 445
                                   44.467888888888777888999988854444440......55555555555555555543 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.5   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?    9.6   5.8   0.00072       1.2       2      36 ..     156     213 ..     155     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91772375|ref|YP_565067.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00072
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91772375|ref|YP_565067.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCelrADvCGC 213
                                   79***************99987555588888888888888888875555444445666 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 ?   -3.0   0.0       7.5   1.2e+04      29      42 ..      31      44 ..      30      45 .. 0.81
   2 ?    3.3   0.1     0.081   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   3 ?    7.9   1.0    0.0031         5       4      13 ..     159     168 ..     158     183 .. 0.69
   4 ?    2.0   0.1       0.2   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.5
                       zf-ISL3 29 ggkrvyLrlrkrRy 42
                                  ++++++++l+  R+
  gi|91772375|ref|YP_565067.1| 31 AEQQTIIELQAARI 44
                                  7899****998775 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.081
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91772375|ref|YP_565067.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0031
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91772375|ref|YP_565067.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.2
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91772375|ref|YP_565067.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00048      0.79      34      71 ..      73     130 ..      19     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772375|ref|YP_565067.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************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 ?    0.6   0.0      0.34   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00051      0.83      21      34 ..     160     174 ..     153     181 .. 0.80
   3 ?   -1.5   0.3       1.6   2.6e+03      29      45 ..     301     319 ..     297     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.34
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91772375|ref|YP_565067.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00051
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91772375|ref|YP_565067.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.6
                 Zn_Tnp_IS1595  29 ayriktrglfqCke..Crk 45 
                                   +y+ k+  ++ C +  C++
  gi|91772375|ref|YP_565067.1| 301 HYFWKSYYKYDCDHsiCNA 319
                                   68888888999*9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1604  (0.089464); expected 358.6 (0.02)
Passed bias filter:                      848  (0.0472977); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3152.04
//
Query:       gi|91772376|ref|YP_565068.1|  [L=843]
Description: bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-91  305.5   0.0    4.5e-91  304.0   0.0    1.7  2  Aconitase_2_N    Aconitate hydratase 2 N-terminus
    1.3e-57  194.2   0.0      2e-57  193.6   0.0    1.3  1  Aconitase_B_N    Aconitate B N-terminal domain
    2.1e-38  132.5   0.0    1.6e-36  126.3   0.0    2.5  1  Aconitase        Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.039   14.0   0.0       0.14   12.2   0.0    1.9  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
       0.11   12.7   0.0       0.32   11.2   0.0    1.8  1  PAS_7            PAS fold


Domain annotation for each model (and alignments):
>> 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 !  304.0   0.0   1.2e-94   4.5e-91       1     199 [.     167     365 ..     167     371 .. 0.98
   2 ?   -2.6   0.0         1   3.6e+03      71      98 ..     537     565 ..     526     569 .. 0.82

  Alignments for each domain:
  == domain 1  score: 304.0 bits;  conditional E-value: 1.2e-94
                                   EEEEEEEEEEEHHHHS-GGGGGGTTSHHHHHCCTT-S-BTTSHHHHHHHHTTSS-EEEEEEEEEES---THHHHHHHHHHS CS
                 Aconitase_2_N   1 vtvfkveGetntDdlsPasdAwsRsDiplHakamlkkkaeeelkaieelkkkgvplayvgdvvGtGssRksavnsvlWtig 81 
                                   v vfkv+Ge+ntDd+sPas AwsR+DiplHa  m +++ ++ +++i++++ +g+++a+v dvvGtGssRksa+nsvlW+ig
  gi|91772376|ref|YP_565068.1| 167 VRVFKVDGEINTDDFSPASAAWSRPDIPLHALEMGTTRFPGGIEEIAKWRGEGHEVAFVADVVGTGSSRKSACNSVLWHIG 247
                                   579****************************************************************************** PP

                                   EEETTEEEEEE--EEEEEEE-HHHHHHHHHTT-EEEE---TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHH CS
                 Aconitase_2_N  82 edipyvPnkraggvvlGgkiaPiFfntvedsGalpieadvskletGdvieikpkegkikkeegevvsefklkpetlldevr 162
                                   +dip+vPnkr+ +v++G+ iaPiFfnt+edsGalp+++d+skl++Gd+i+i++++g++++eeg+v+s+  l+p+tl de+r
  gi|91772376|ref|YP_565068.1| 248 KDIPHVPNKRRDCVIIGTAIAPIFFNTAEDSGALPLQMDISKLQHGDIITINTVKGEVTDEEGNVLSTLYLNPNTLPDEYR 328
                                   ********************************************************************************* PP

                                   HTSHHHHHHHHHHHHHHHHHTT-----SS-------- CS
                 Aconitase_2_N 163 aggripliigrgltekarealgleasdvFakpkepae 199
                                   aggripliigr+lt+++re+lgl+++d+F+kp++p  
  gi|91772376|ref|YP_565068.1| 329 AGGRIPLIIGRSLTTRTREVLGLPETDIFVKPDNPIP 365
                                   ********************************99865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                                   HHHHHH.HHHHSEEETTEEEEEE--EEEE CS
                 Aconitase_2_N  71 savnsv.lWtigedipyvPnkraggvvlG 98 
                                     vns+  ++i++ + +vP k++  +  G
  gi|91772376|ref|YP_565068.1| 537 DVVNSIpYYAIQQGLMTVPKKNKINIFNG 565
                                   56899988999999******998877666 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 !  193.6   0.0   5.5e-61     2e-57       2     154 .]       5     155 ..       4     155 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.6 bits;  conditional E-value: 5.5e-61
                 Aconitase_B_N   2 yrkhveeraalgipplPLdaeqtaelvellknpkageeellleLltnrvppGvdeaayvKAefLaaiakgeaesplispee 82 
                                   y  h eer+a+gip+lPL+ eqt+el+ell+np+a++ee+ll+L+t+r++pGv +aa+vKA+fL +i++g+a+spli+++e
  gi|91772376|ref|YP_565068.1|   5 YLIHEEERKAQGIPALPLNPEQTSELCELLQNPPAEQEEFLLHLFTERISPGVGPAAKVKADFLGNILTGDASSPLIDKKE 85 
                                   8889***************************************************************************** PP

                 Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekdeelaeeaaeaLkktllvydafedveelakenaaakevleswaeaewF 154
                                   A+ +LgtM+GGynvk Li++l   d+e+a+ea+ aL+ + lvy+af++v el+++n+aa++vleswa+aewF
  gi|91772376|ref|YP_565068.1|  86 AIGILGTMIGGYNVKYLIEALG--DSEVADEATCALSGITLVYEAFDEVLELSETNEAARKVLESWANAEWF 155
                                   **********************..***********************************************9 PP

>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.0   4.5e-40   1.6e-36      88     457 ..     447     803 ..     389     807 .. 0.82

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 4.5e-40
                     Aconitase  88 efLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvg 168
                                   ++L ++ ++ g    +pg GI+H   l+  l++p+++  g+DSHT+   g   + ++ G+  ++ + +   + l +p++v 
  gi|91772376|ref|YP_565068.1| 447 RTLPDFVSDRGGVSLNPGDGIIHSW-LNR-LLVPDTVGTGGDSHTRFPIG---ISFPAGSGLVAFAGALGFMPLDMPESVL 522
                                   4555666666555789********9.566.7****9**********9999...89999999999999999999******** PP

                     Aconitase 169 vkltGklkegvtakDlvlavigklrkkgvv.....gkvvEffG.....egvesLsledraTiaNMaaEvGAttglfpvdek 239
                                   v+++Gkl++g+t +D+v  +     ++g +     +k+  f G     eg+ +L++e+ + +++ aaE  A +g ++ dek
  gi|91772376|ref|YP_565068.1| 523 VRFSGKLNSGITLRDVVNSIPYYAIQQGLMtvpkkNKINIFNGrileiEGLPDLTAEQAFELTDSAAERSAAAGCIQLDEK 603
                                   *****************88766555555444555588888888777778999****************************6 PP

                     Aconitase 240 .tleYLkatgr..........eeaavlveaydkaqalf.e....laadedaeydkvleldlstl.epsvagpkrPqdavpl 303
                                    + +YL+ +            ++a++l ++++ a++ + e    l+ad++a+y+ v+ +dl+++ ep +a p+ P+d+  l
  gi|91772376|ref|YP_565068.1| 604 pVATYLRSNVAlmkkmigngySDAQTLQKRIE-AVEEWlEdpklLKADPNADYAAVIGIDLADIkEPILACPNDPDDVKLL 683
                                   3778***6555555666665522222222222.3334442355689******************6699*********8888 PP

                     Aconitase 304 selvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGS 384
                                    ++v+                      gt     +++ ++igSC+ +++ ++raaa++ +     ++k +++v+t++ P +
  gi|91772376|ref|YP_565068.1| 684 -SEVA----------------------GT-----PIQDVFIGSCM-TNIGHFRAAAEIWR-----DQKFNSDVRTWICPPT 730
                                   .3332......................33.....46699*****8.678***********.....99************** PP

                     Aconitase 385 evvkayleaeGlleiLekaGfevvgagCstCignsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaa 457
                                   +  +a+l++e + ++  ++G+ +  agCs C+gn+ r+++++++ s+s+RNF +R+g +++ yL S el +++
  gi|91772376|ref|YP_565068.1| 731 RMDQAKLREESVFSVYGQVGARIEIAGCSLCMGNQARVPDESTVFSTSTRNFDNRVGDGAQVYLGSAELGAVI 803
                                   *******************************************************************997665 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 ?   -3.3   0.0       2.4   8.7e+03      19      48 ..     609     638 ..     603     639 .. 0.81
   2 ?   12.2   0.0   3.8e-05      0.14      57      96 ..     675     712 ..     673     731 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                                   TSTTHHHHHHHHHHHHHHHT--GGGEEEEE CS
               Ketoacyl-synt_C  19 tapngeaqaraiekalaeagvdpedvdyve 48 
                                    + n + ++++i + +++a++  ++++ ve
  gi|91772376|ref|YP_565068.1| 609 LRSNVALMKKMIGNGYSDAQTLQKRIEAVE 638
                                   566778888999999999999999999887 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.8e-05
                                   HHHHHHHHHHHHHGGGGGSCTSEEE-THHHH-B-GGGHHH CS
               Ketoacyl-synt_C  57 gDpiElealkkvfgekarkqplavgSvKsniGHleaAaGv 96 
                                   +Dp  +++l++v g+    q +++gS+ +niGH  aAa +
  gi|91772376|ref|YP_565068.1| 675 NDPDDVKLLSEVAGTPI--QDVFIGSCMTNIGHFRAAAEI 712
                                   799999999***99987..67****************966 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.8e-05      0.32       4      75 ..     547     621 ..     545     643 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.8e-05
                         PAS_7   4 msqGisvfDadlrLvawNrrylelldlpeelvqvgvp.leellrynaergefg..agdveaeverrlaaaragkp 75 
                                   ++qG++ + +++++ ++N r+le+ +lp+  +++  +  ++  +  a+ g ++  ++ v+ +++  +a +++   
  gi|91772376|ref|YP_565068.1| 547 IQQGLMTVPKKNKINIFNGRILEIEGLPDLTAEQAFElTDSAAERSAAAGCIQldEKPVATYLRSNVALMKKMIG 621
                                   89******************************9999944455666688888886555577778888877777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (843 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5557.89
//
Query:       gi|91772377|ref|YP_565069.1|  [L=110]
Description: hypothetical protein Mbur_0318 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   28.9   2.8    9.6e-07   28.3   2.8    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    1.4e-06   27.5   2.9    2.5e-06   26.7   2.9    1.3  1  zf-ribbon_3     zinc-ribbon domain
    0.00013   22.0   0.5    0.00017   21.5   0.5    1.2  1  DZR             Double zinc ribbon
    0.00061   19.8   0.1     0.0009   19.3   0.1    1.2  1  PRC             PRC-barrel domain
     0.0011   19.6   0.2     0.0015   19.3   0.2    1.3  1  zinc_ribbon_15  zinc-ribbon family
  ------ inclusion threshold ------
      0.021   14.9   1.1      0.032   14.3   1.1    1.2  1  UPF0547         Uncharacterised protein family UPF0547
      0.036   14.3   0.7       0.38   11.1   0.1    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
      0.068   13.1   0.5       0.11   12.5   0.5    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.081   12.8   0.0      0.097   12.6   0.0    1.1  1  DUF1826         Protein of unknown function (DUF1826)
       0.25   11.3   2.1        2.5    8.1   0.1    2.4  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   2.8   5.4e-10   9.6e-07       1      23 []      87     109 ..      87     109 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.4e-10
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                   +Cp+C  e+  +a FC++CGt l
  gi|91772377|ref|YP_565069.1|  87 RCPSCNSEIGGGAMFCTNCGTDL 109
                                   6********************87 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   2.9   1.4e-09   2.5e-06       4      26 .]      87     109 ..      86     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                   zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGtkl 26 
                                   rCP+C++ +   ++++C++CGt+l
  gi|91772377|ref|YP_565069.1|  87 RCPSCNSeI-GGGAMFCTNCGTDL 109
                                   8******77.************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.5   9.4e-08   0.00017       1      22 [.      88     109 ..      69     110 .] 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.4e-08
                           DZR   1 CpqCgeelppdarfCseCgtkl 22 
                                   Cp+C++e+  +a fC +Cgt+l
  gi|91772377|ref|YP_565069.1|  88 CPSCNSEIGGGAMFCTNCGTDL 109
                                   7777777777777777777776 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1     5e-07    0.0009       7      74 ..      12      72 ..       6      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5e-07
                                  ---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.CEECCCTEEEETT CS
                           PRC  7 sdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfdlavkigkdriivda 74
                                   ++iG++V++++G + GkVk++ +  +e + +alv+++       ++e + P+  ++++ +d+i++++
  gi|91772377|ref|YP_565069.1| 12 EKIIGMQVIDSSGYIRGKVKELSLVVGEPD-QALVIEDED-----GNESEAPWS-RISAAGDVILLKS 72
                                  68********************99884444.566666654.....39*******.*********9986 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   8.2e-07    0.0015      56      86 .]      76     106 ..      51     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.2e-07
                zinc_ribbon_15  56 eiekkessekkeCknCgkeveeefkyCpkCg 86 
                                   + +k++ss +++C++C++e+     +C++Cg
  gi|91772377|ref|YP_565069.1|  76 SANKSSSSMSHRCPSCNSEIGGGAMFCTNCG 106
                                   3334444559********************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.1   1.8e-05     0.032       2      22 ..      87     107 ..      86     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                       UPF0547   2 vCPeCeakvPvaaqfCphCGy 22 
                                   +CP C +++   a fC  CG+
  gi|91772377|ref|YP_565069.1|  87 RCPSCNSEIGGGAMFCTNCGT 107
                                   6*******************9 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00021      0.38      51      67 ..      80      96 ..      76      97 .. 0.85
   2 ?    1.6   0.1      0.19   3.3e+02      58      64 ..     101     107 ..      99     110 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                 zf-LITAF-like 51 slkdvehyCpnCgallg 67
                                  s   + h+Cp+C++ +g
  gi|91772377|ref|YP_565069.1| 80 SSSSMSHRCPSCNSEIG 96
                                  567789*******9997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.19
                 zf-LITAF-like  58 yCpnCga 64 
                                   +C+nCg+
  gi|91772377|ref|YP_565069.1| 101 FCTNCGT 107
                                   5777776 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 ?   12.5   0.5   5.9e-05      0.11       5      28 ..      86     107 ..      82     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                   Prok-RING_1   5 kkCpvCgkelkeedDiVvCpeCgt 28 
                                   ++Cp C+ e+  +  +  C++Cgt
  gi|91772377|ref|YP_565069.1|  86 HRCPSCNSEIGGG--AMFCTNCGT 107
                                   78********999..9*******9 PP

>> DUF1826  Protein of unknown function (DUF1826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.4e-05     0.097     150     188 ..      53      93 ..      29      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                       DUF1826 150 akeaairql.eagdvaLlKGerwpgneg.rglvHRSPpvag 188
                                   ++ea++ ++ +agdv+LlK e+++ n+  + + HR P+ ++
  gi|91772377|ref|YP_565069.1|  53 ESEAPWSRIsAAGDVILLKSEEYSANKSsSSMSHRCPSCNS 93 
                                   455555544168***********9887615789****9765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.076   1.4e+02      23      29 ..      86      92 ..      83      93 .. 0.87
   2 ?    8.1   0.1    0.0014       2.5       2      10 ..     101     109 ..     100     110 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.076
                                  EEETTTT CS
                     Nudix_N_2 23 lvCpaCg 29
                                  ++Cp+C+
  gi|91772377|ref|YP_565069.1| 86 HRCPSCN 92
                                  78****7 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                                   B-TTT--B- CS
                     Nudix_N_2   2 FCsqCGtpv 10 
                                   FC++CGt +
  gi|91772377|ref|YP_565069.1| 101 FCTNCGTDL 109
                                   9*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 704.18
//
Query:       gi|91772378|ref|YP_565070.1|  [L=235]
Description: hypothetical protein Mbur_0320 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   26.0   5.0    1.2e-05   24.8   5.0    1.6  1  zinc_ribbon_2   zinc-ribbon domain
     0.0002   21.3   0.4    0.00041   20.3   0.4    1.5  1  DZR             Double zinc ribbon
     0.0032   18.2   4.4     0.0053   17.5   4.4    1.7  1  zinc_ribbon_15  zinc-ribbon family
     0.0041   16.5   3.7     0.0041   16.5   3.7    2.1  2  zf-ribbon_3     zinc-ribbon domain
     0.0079   16.1   2.6       0.72    9.8   0.3    2.7  2  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
       0.74    9.7   6.3       0.64    9.9   0.9    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        4.2    7.6   7.2         97    3.2   0.6    2.8  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   5.0   4.7e-09   1.2e-05       1      22 [.     212     233 ..     212     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.7e-09
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtp 22 
                                   fC nCG ++ +++kFC++CG  
  gi|91772378|ref|YP_565070.1| 212 FCNNCGLKVIPGSKFCSKCGNR 233
                                   9*******************86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   1.6e-07   0.00041      29      49 .]     211     231 ..     185     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.6e-07
                           DZR  29 drCpsCgekvdpearfCpeCG 49 
                                   ++C +Cg kv p+++fC +CG
  gi|91772378|ref|YP_565070.1| 211 NFCNNCGLKVIPGSKFCSKCG 231
                                   567777777777777777776 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   4.4   2.1e-06    0.0053      54      86 .]     199     231 ..      97     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                zinc_ribbon_15  54 gkeiekkessekkeCknCgkeveeefkyCpkCg 86 
                                   +++ ++k+++  + C+nCg +v + +k+C+kCg
  gi|91772378|ref|YP_565070.1| 199 NNKNNNKKKVIINFCNNCGLKVIPGSKFCSKCG 231
                                   233334444449********************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 ?   -1.9   0.1      0.97   2.5e+03       6      10 ..      97     101 ..      95     105 .. 0.64
   2 !   16.5   3.7   1.6e-06    0.0041       4      26 .]     212     234 ..     211     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.97
                   zf-ribbon_3   6 PnCGa 10 
                                   +nC++
  gi|91772378|ref|YP_565070.1|  97 NNCNK 101
                                   47777 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.6e-06
                   zf-ribbon_3   4 rCPnCGaplssddnvCpyCGtkl 26 
                                   +C+nCG ++ ++ ++C +CG +l
  gi|91772378|ref|YP_565070.1| 212 FCNNCGLKVIPGSKFCSKCGNRL 234
                                   7******88***********987 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1    0.0057        15       1      10 [.     211     220 ..     211     222 .. 0.85
   2 !    9.8   0.3   0.00028      0.72       1      10 [.     225     234 ..     225     235 .] 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0057
                                   -B-TTT--B- CS
                     Nudix_N_2   1 kFCsqCGtpv 10 
                                   +FC++CG +v
  gi|91772378|ref|YP_565070.1| 211 NFCNNCGLKV 220
                                   7******776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00028
                                   -B-TTT--B- CS
                     Nudix_N_2   1 kFCsqCGtpv 10 
                                   kFCs+CG+++
  gi|91772378|ref|YP_565070.1| 225 KFCSKCGNRL 234
                                   9******986 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 ?    1.9   0.4     0.079     2e+02       2       8 ..     211     217 ..     204     218 .. 0.89
   2 ?    9.9   0.9   0.00025      0.64       2      12 ..     225     235 .]     225     235 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.079
                                   EBESTTT CS
                RNA_POL_M_15KD   2 kFCpkCg 8  
                                    FC  Cg
  gi|91772378|ref|YP_565070.1| 211 NFCNNCG 217
                                   7999998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
                                   EBESTTTSBEE CS
                RNA_POL_M_15KD   2 kFCpkCgNlLl 12 
                                   kFC+kCgN Ll
  gi|91772378|ref|YP_565070.1| 225 KFCSKCGNRLL 235
                                   7*******775 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.6     0.038        97      24      32 ..     211     219 ..     199     223 .. 0.80
   2 ?    2.5   7.0     0.064   1.6e+02      11      33 ..     213     234 ..     205     235 .] 0.64

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.038
                  NOB1_Zn_bind  24 kFCpkCGnk 32 
                                   +FC++CG k
  gi|91772378|ref|YP_565070.1| 211 NFCNNCGLK 219
                                   7******76 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.064
                  NOB1_Zn_bind  11 ChaCfkvtkdmtkkFCpkCGnkt 33 
                                   C  C   +     kFC+kCGn+ 
  gi|91772378|ref|YP_565070.1| 213 CNNCGLKV-IPGSKFCSKCGNRL 234
                                   55554322.24568******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1113  (0.0620782); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1591.79
//
Query:       gi|91772379|ref|YP_565071.1|  [L=405]
Description: nicotinate phosphoribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-59  199.6   0.0      8e-59  199.2   0.0    1.1  1  NAPRTase    Nicotinate phosphoribosyltransferase (NAPRTase) f
    1.5e-33  115.9   0.1    2.4e-33  115.2   0.1    1.3  1  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


Domain annotation for each model (and alignments):
>> NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   0.0     9e-63     8e-59       3     237 ..     175     396 ..     173     399 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 9e-63
                                   EEE-TSTTSSSHHHHHHHHHHHHHHHTTTEEEESBHHHHHHHT--B--HHHHHHHHHHHHHHCHHHHHCCHHHHHHHHHHH CS
                      NAPRTase   3 lhDFGtRrrsslesqeivvkalkkahlvnflGtdnvlaaakysikaaetsahealgkeqelsafrnnlkqfqkdaldlwva 83 
                                   +++FGtRrr+ ++ ++ vv++l++  l +f+Gt+nv++a+ky++ +++t+ he+++++ +l      l++++k a d wv+
  gi|91772379|ref|YP_565071.1| 175 FSEFGTRRRRGFKLHDKVVEVLHE--LDSFSGTSNVYFAKKYGVRPIGTIGHEWIMGNSALVG----LRNANKFAFDNWVK 249
                                   79******************9999..***********************************97....************** PP

                                   HHCCHIIEEECHCCTHHHHHCCS-CC.HHHSEEEEE-SS-HHHHHHHHHHHHHCTCTTTCCCSEEEEESS-SHHHHHHHHH CS
                      NAPRTase  84 iekgnlgiaLtdlvltdaflkdfrle.akaylgvRpDSGdpvevieklaahygstlnskgytkrlifsDgldvekiieile 163
                                   ++kg+l iaL+d+++++ f ++f    ak y+gvR+DSGdp++  + +++hy+++ ++++++k+l+fsD+l v+ ++++ e
  gi|91772379|ref|YP_565071.1| 250 VYKGDLSIALSDTFGSKPFFQNFSIGlAKIYDGVRHDSGDPIKFADEVIEHYKKL-GIDPMKKVLVFSDSLHVSDAVKLKE 329
                                   ************************99*****************************.************************* PP

                                   HHHHTTCEEEEEESHHHHSSECTTCTTTCCEEEEEEEEEEEEEETTEETTBGGSSCCGSBGSGHHHHHHHHHHC CS
                      NAPRTase 164 alkkkgfniaFGiGtnltqdlnrdtlefavkasalniviklvevnkdpvakisdrskkgrlgdkefvkllrtvf 237
                                   ++++ ++n +FGiGt+lt++ +     f++   +ln+vikl+++ + pv+k+sd+ +k++ gdk++++ +  +f
  gi|91772379|ref|YP_565071.1| 330 YCSG-RINCSFGIGTTLTNNPDF----FSY-NPPLNMVIKLHKIDGIPVVKLSDSVEKAT-GDKDALRVANYIF 396
                                   ****.**************9887....554.479**************************.9998877766666 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.1   2.7e-37   2.4e-33       1     125 []       6     127 ..       6     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 2.7e-37
                    NAPRTase_N   1 LdtDlYkltmaqavfkkgpdvevvfelffRkkpfkgeyaivagleevie.ylenlrfteeeieyLkrklpyfkedfleyLr 80 
                                   Ld+DlYk+tm+ av++ +p++++++++++R ++  ++ ++v++l++ i+  ++++ ++e+e+ +Lk+++p+fk++++eyL+
  gi|91772379|ref|YP_565071.1|   6 LDNDLYKFTMQMAVLELFPNARAEYRFINRGAQ-SFTNDFVNELRRIINkDISKIALSEDEYIWLKDNCPFFKPSYIEYLK 85 
                                   89*******************************.**************857****************************** PP

                    NAPRTase_N  81 tfrfkpsevaveeeevvfpgepeirveGpwieaillEtplLaivn 125
                                   +frf+p+ev++   e   ++e+e+ +eGpw++ il+E+ l+++++
  gi|91772379|ref|YP_565071.1|  86 NFRFNPEEVKIVLTE---DNELELCIEGPWHSSILWEIVLMSTIS 127
                                   ***********9996...************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2799.19
//
Query:       gi|91772380|ref|YP_565072.1|  [L=374]
Description: transposase, mutator type [Methanococcoides burtonii DSM 6242]
Scores for 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-113  376.9   3.9   1.2e-112  376.6   3.9    1.0  1  Transposase_mut  Transposase, Mutator family
    3.1e-10   40.4   0.0    8.9e-10   38.9   0.0    1.8  1  MULE             MULE transposase domain
    0.00019   21.0   0.7    0.00039   20.0   0.7    1.5  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.033   13.9   0.3       0.12   12.1   0.1    2.1  2  DUF4423          Domain of unknown function (DUF4423)
      0.041   14.1   5.7        5.7    7.2   4.1    2.9  2  DDE_Tnp_IS240    DDE domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.6   3.9  3.3e-116  1.2e-112      22     380 ..      14     365 ..       4     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 376.6 bits;  conditional E-value: 3.3e-116
               Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykRreka 102
                                   ++  lk l++ +l+e++e+e+ e+ ga ++ers +r+ +RnG+r+r+l+Tr g+l+l+ P++R+  F ++++ery R+eka
  gi|91772380|ref|YP_565072.1|  14 SNVSLKPLITYFLNEVMEQEAIEQSGAGKHERSITRTAHRNGYRDRSLTTRHGELTLKKPQLRDFPFTTQVFERYSRTEKA 94 
                                   55678999************************************************************************* PP

               Transposase_mut 103 leavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrvvsk 183
                                   +e++++e yv+Gvstrkvek++ +l++ +s+S+s vS+i+++ld++v+ f ++++e++   +l++Da+ylkvR+  r v+k
  gi|91772380|ref|YP_565072.1|  95 IENAIVESYVQGVSTRKVEKIISQLGV-ESISRSRVSRIAQDLDKTVHGFMNKPIEHE-IKYLYVDATYLKVRDRVRYVNK 173
                                   ***************************.77***************************9.********************** PP

               Transposase_mut 184 avliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrvHllrnll 264
                                   av+i  gv+ dG+reiLg+++adsE++ fW++++++Lk+rGl+gvelv+sD+hkG+++a+++ f +a++Q C+vHl r +l
  gi|91772380|ref|YP_565072.1| 174 AVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKERGLRGVELVISDGHKGIQRAVERQFLGASWQMCIVHLERLIL 254
                                   ********************************************************************************* PP

               Transposase_mut 265 akvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafpeqirrkikstNllErLN 344
                                   +k+p+k+ ++ +e++k + +       + +l  ++ ++ +  + k+ae++++ +  ++++ afp++++++ik+tN++ErLN
  gi|91772380|ref|YP_565072.1| 255 KKLPRKHHKEAMESFKEVQDD------QTKLLGLMVEWDRpGFEKAAETIERFQHGLTNYQAFPKEHWKRIKTTNMIERLN 329
                                   **************9987543......345555666677789*************************************** PP

               Transposase_mut 345 keirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                   ke++Rr++vvg FPn+es++rlv avl +++++w++
  gi|91772380|ref|YP_565072.1| 330 KEVKRRSKVVGAFPNDESLMRLVIAVLIDQNENWIT 365
                                   **********************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.5e-13   8.9e-10       2      94 ..     155     250 ..     154     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.5e-13
                          MULE   2 vvlDgTyktnkykl.....plltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnal 77 
                                   + +D+Ty++ + ++       ++v gv++ g   +l++ + +se+   +e ++++l+e+ +  r  + +i+D +k++++a+
  gi|91772380|ref|YP_565072.1| 155 LYVDATYLKVRDRVryvnkAVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKER-GL-RGVELVISDGHKGIQRAV 233
                                   679****99865441122167889**********************************5.44.7***************** PP

                          MULE  78 eevfpeakhrlClfHia 94 
                                   e++f +a  ++C+ H++
  gi|91772380|ref|YP_565072.1| 234 ERQFLGASWQMCIVHLE 250
                                   ***************97 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.7   1.1e-07   0.00039      11     238 ..      97     336 ..      88     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                  DDE_Tnp_IS66  11 eilvlkyadhlPlyRqeeilarlGv.elsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkks 90 
                                   +++v+ y+++++ +++e+i+++lGv  +sr+ +++  ++  +++  ++++  ++  + +++ +D T l+v +  r +  ++
  gi|91772380|ref|YP_565072.1|  97 NAIVESYVQGVSTRKVEKIISQLGVeSISRSRVSRIAQDLDKTVHGFMNKPIEH--EIKYLYVDATYLKVRD--RVRYVNK 173
                                   6799*********************569***99999988888888888776654..55799********877..6888888 PP

                  DDE_Tnp_IS66  91 ylWvyvtdkr...kpavlfeyspsRggevaealLag.....fkG..vlvsDgyagYnklae...eqvthalCwaHlrRkfv 158
                                    +++++  k+   +++   ++++s  +   e+++++      +G   ++sDg++g ++  e    ++  ++C +Hl R + 
  gi|91772380|ref|YP_565072.1| 174 AVFIVAGVKNdgyREILGVKIADSEEAMFWEEMFTDlkergLRGveLVISDGHKGIQRAVErqfLGASWQMCIVHLERLIL 254
                                   88888887777899*************999999777664665556679*********976657778888*********887 PP

                  DDE_Tnp_IS66 159 daeeakkk...sqaaaealar.igklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgkairyll 235
                                   +   +k +    +  +e +++   kl  +  e+  ++  e++a   e+ +  l++++a  +e+ k+++  + ++++ ++++
  gi|91772380|ref|YP_565072.1| 255 KKLPRKHHkeaMESFKE-VQDdQTKLLGLMVEWD-RPGFEKAAETIERFQHGLTNYQAFPKEHWKRIKTTNMIERLNKEVK 333
                                   66655432232222222.2222555555555553.2456677777777777777777766666566655555555555555 PP

                  DDE_Tnp_IS66 236 krw 238
                                   +r 
  gi|91772380|ref|YP_565072.1| 334 RRS 336
                                   555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.48   1.7e+03     106     130 ..     121     128 ..      86     148 .. 0.55
   2 ?   12.1   0.1   3.3e-05      0.12      92     145 ..     252     305 ..     247     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.48
                       DUF4423 106 iealervpkeeRdissltlaisked 130
                                   +e                 +is++ 
  gi|91772380|ref|YP_565072.1| 121 VE-----------------SISRSR 128
                                   33.................344444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.3e-05
                       DUF4423  92 eavrsyhkqmlelAiealervpkeeRdissltlaiskedyekikkeirefrkki 145
                                   + ++++ ++  ++A+e++++v+ ++ ++ +l++  ++  +ek+++ i++f++ +
  gi|91772380|ref|YP_565072.1| 252 LILKKLPRKHHKEAMESFKEVQDDQTKLLGLMVEWDRPGFEKAAETIERFQHGL 305
                                   567788888999**************************************9866 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.4e+03      64      96 ..      82      97 ..      48     124 .. 0.58
   2 ?    7.2   4.1    0.0016       5.7      84     124 ..     292     350 ..     153     360 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                 DDE_Tnp_IS240 64 tDkasayasalkelkregelfdevshvqvkyln 96
                                  t                    ++ s+ ++  +n
  gi|91772380|ref|YP_565072.1| 82 TQVF-----------------ERYSRTEKAIEN 97
                                  3222.................222333333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0016
                 DDE_Tnp_IS240  84 f...................devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                                        + +h+++    n+iE+ ++++K+r ++++ f + +s+ +
  gi|91772380|ref|YP_565072.1| 292 EkaaetierfqhgltnyqafPK-EHWKRIKTTNMIERLNKEVKRRSKVVGAFPNDESLMR 350
                                   0333333333344444444333.7888888999999999999999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2402.62
//
Query:       gi|91772381|ref|YP_565073.1|  [L=187]
Description: hypothetical protein Mbur_0327 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-07   32.2   0.0    4.4e-07   31.0   0.0    1.6  2  Cytochrom_C      Cytochrome c
    3.4e-07   30.5   0.3    9.4e-07   29.1   0.3    1.7  1  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
     0.0047   17.3   0.6     0.0076   16.7   0.6    1.3  1  LPAM_1           Prokaryotic membrane lipoprotein lipid attac


Domain annotation for each model (and alignments):
>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   1.8e+04      36      51 ..      25      40 ..      23      53 .. 0.61
   2 !   31.0   0.0   7.3e-11   4.4e-07      11      91 ..      93     187 .]      87     187 .] 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                                  HHTTT-HHHHHHHHTT CS
                   Cytochrom_C 36 erasaasigasvanpa 51
                                  + ++  s++ ++++p 
  gi|91772381|ref|YP_565073.1| 25 DSYDRPSQEYFWHEPG 40
                                  5566666777777763 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 7.3e-11
                                   TGGGTB-SSSBSSS........................--HHHHHHHTTT-HHHHHHHHTTSS--SSSHHHHHHHGGGGGG CS
                   Cytochrom_C  11 nCaaCHgvegggakqgg....................gptlsgaaerasaasigasvanpaavsaprddfekkkltaempa 71 
                                    C++CHgv g+g  + +                    +   +g +++++a  ++ ++++ +   +p+    +++    mp 
  gi|91772381|ref|YP_565073.1|  93 SCVSCHGVSGKGGIPIMmgtdipsdirystltaedepANEVAGGHDEHPAYTDETIKEAIRDGIEPDGEELDYT----MPR 169
                                   7**********9987779*********77777776666666666666666666666665543333333333333....444 PP

                                   G.TT--HHHHHHHHHHHHTT CS
                   Cytochrom_C  72 rkerlteqeiadlaaYLksl 91 
                                       +++++i+dl++YLk+l
  gi|91772381|ref|YP_565073.1| 170 --WDMSDDDIEDLINYLKTL 187
                                   ..48**************96 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.3   1.6e-10   9.4e-07      13      67 .]      93     184 ..      87     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.6e-10
               Cytochrome_CBB3  13 nCasCHg.kggag......................pslagrdwep................dalvdiiknGk...g..... 46 
                                   +C+sCHg +g++g                               p                ++++++i++G+   g     
  gi|91772381|ref|YP_565073.1|  93 SCVSCHGvSGKGGipimmgtdipsdirystltaedE--------PanevagghdehpaytdETIKEAIRDGIepdGeeldy 165
                                   8******77777798888888876666655544440........14445555555566777**********9554155666 PP

               Cytochrome_CBB3  47 aMpafggqlsdeelwalvaYl 67 
                                    Mp +  ++sd+++++l++Yl
  gi|91772381|ref|YP_565073.1| 166 TMPRW--DMSDDDIEDLINYL 184
                                   8****..69***********7 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 !   16.7   0.6   1.3e-06    0.0076       1      17 [.       1      19 [.       1      19 [. 0.99

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                        LPAM_1  1 MKKi..llalgalllLsGC 17
                                  MK++  l++lg++ ++sGC
  gi|91772381|ref|YP_565073.1|  1 MKRPilLFLLGIAIVVSGC 19
                                  ******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1319.78
//
Query:       gi|91772382|ref|YP_565074.1|  [L=226]
Description: hypothetical protein Mbur_0328 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  222.8   0.0    4.6e-66  222.7   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 !  222.7   0.0   2.6e-70   4.6e-66       2     205 ..      13     220 ..      12     221 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.7 bits;  conditional E-value: 2.6e-70
                        DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklksg... 79 
                                   L+++l+lkt+PVav ++ +   +pe++ek++e++r+Cqmv ++r+ g+ +++ta++++C+gG+a++G++e+p+kl +g   
  gi|91772382|ref|YP_565074.1|  13 LTKKLNLKTKPVAVSLIPKGYAIPEGIEKLDESTRHCQMVDMVRKTGREFYATADEQACKGGSAIMGLNEMPSKLSTGqty 93 
                                   899****************************************************************************** PP

                        DUF169  80 ..egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvsfpgngaaC 158
                                     ++ +++++aa++++es++rlea ++k+vv+ pLe+a+f Pdv+v++++p+q+m+L+q++ y++gg r++ sf+g++++C
  gi|91772382|ref|YP_565074.1|  94 lnLNRFDTINAARRTMESVTRLEANSIKAVVYGPLENATFAPDVIVIITTPKQVMQLSQALIYKHGG-RVETSFAGIQSVC 173
                                   *****************************************************************99.************* PP

                        DUF169 159 adivaypykegepniglgdpgarkfaklkddelafgiPyelleemve 205
                                   ad v++pykeg+ +++lg+ g+rkfa++ +de+++giP+e++ +++e
  gi|91772382|ref|YP_565074.1| 174 ADGVVKPYKEGKVSVTLGCGGSRKFANIAEDEMIIGIPVERAHDLLE 220
                                   ******************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1589.60
//
Query:       gi|91772383|ref|YP_565075.1|  [L=110]
Description: hypothetical protein Mbur_0329 [Methanococcoides burtonii DSM 6242]
Scores for 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-32  109.4   4.4    9.9e-32  109.3   4.4    1.0  1  CGGC      CGGC domain


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   4.4   5.5e-36   9.9e-32       1     106 []       2     110 .]       2     110 .] 0.95

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 5.5e-36
                          CGGC   1 kiaiirCekvedvCpgvkClkalkerkgaFeeyeeevelvgfvtCggCpgkkvveklkelkkegvdvihlssCiktk.kak 80 
                                   ki+iirC+++ed+Cpg+ ++k ++e+k aFe ++e++e++g+v+CggCpgkkvv+++ke++k+g+d+i+l+sCi++   + 
  gi|91772383|ref|YP_565075.1|   2 KIGIIRCRQTEDMCPGTMDFKIIREKKCAFEGIKENIEIIGMVSCGGCPGKKVVTRAKEMVKRGADTIVLASCITRGnPIG 82 
                                   8************************************************************************94444899 PP

                          CGGC  81 keCpeieeikeaieekl..gievvegth 106
                                    +Cp+++ i+e +++kl  +++++++th
  gi|91772383|ref|YP_565075.1|  83 FPCPHAAIIEESVKNKLgeKVQIINYTH 110
                                   9****************7778999***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 724.22
//
Query:       gi|91772384|ref|YP_565076.1|  [L=87]
Description: hypothetical protein Mbur_0330 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-28   97.7   1.6    3.1e-28   97.6   1.6    1.0  1  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   1.6   1.7e-32   3.1e-28       1      76 [.       5      80 ..       5      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 1.7e-32
                        HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleela 76
                                  rR kleIi+dIL+++++++a+kT+i+y+anL+++++n+YL m+++ gl++k+ +kY++T+ G+e+l+k+++++++ 
  gi|91772384|ref|YP_565076.1|  5 RRGKLEIIVDILNVVRKSDATKTAIVYNANLNFNRANQYLIMMMCIGLVEKDINKYSITDLGSEYLHKINDVNMMF 80
                                  8***********************************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 607.46
//
Query:       gi|91772385|ref|YP_565077.1|  [L=326]
Description: hypothetical protein Mbur_0331 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.09   12.8   0.0       0.15   12.0   0.0    1.2  1  MNE1      Mitochondrial splicing apparatus component
       0.15   12.1   0.0       0.26   11.4   0.0    1.3  1  DUF1419   Protein of unknown function (DUF1419)


Domain annotation for each model (and alignments):
>> MNE1  Mitochondrial splicing apparatus component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05      0.15      51     129 ..     143     220 ..     135     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                          MNE1  51 eknfggvvsaleklvkelnlqsllnssnligsldnsgfhillksvsnSssakltsltLFkfLkks..kfeltksdYlllik 129
                                   + +++ ++ +l  l++  + + +  ++ l++  + + + + +k+v    +a + ++t+F+++  +  +  +t+ +Y  ++ 
  gi|91772385|ref|YP_565077.1| 143 QAEYDNLLWMLDPLKQ--QAKMFKVANTLTNHDEPGNYSVYFKAVDTG-GAYMIGYTYFDYMALKaiELDFTQVNYGPIMV 220
                                   5566677777777777..3345556677888888999********999.************86654488899999977665 PP

>> DUF1419  Protein of unknown function (DUF1419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.26      30      80 ..     122     172 ..     118     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                       DUF1419  30 rpereeaddsalyaGeWfeiseaehdymleilPPlflrgdmfalrefltgs 80 
                                    ++++++d++ l a e   i++ae+d +l +l Pl ++++mf + + lt++
  gi|91772385|ref|YP_565077.1| 122 ITNTADQDAALLAALEMGLITQAEYDNLLWMLDPLKQQAKMFKVANTLTNH 172
                                   5667777777888888889*************************9999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2243.42
//
Query:       gi|91772386|ref|YP_565078.1|  [L=383]
Description: hypothetical protein Mbur_0332 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2754.17
//
Query:       gi|91772387|ref|YP_565079.1|  [L=308]
Description: cell surface glycoprotein (s-layer protein) [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-34  118.6  52.1    3.8e-21   75.4  22.6    1.9  2  NosD            Periplasmic copper-binding protein (NosD)
    5.2e-12   45.9  22.3    5.2e-12   45.9  22.3    1.5  1  Beta_helix      Right handed beta helix region
  ------ inclusion threshold ------
      0.036   12.8   0.4        0.3    9.7   0.1    2.3  3  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 !   56.6  21.5   3.7e-19   2.2e-15       1     154 [.      47     200 ..      47     208 .. 0.81
   2 !   75.4  22.6   6.4e-25   3.8e-21      82     239 ..     110     256 ..     105     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3.7e-19
                          NosD   1 vnnaisgdevlvsargngiqlens..egsei...snneisnsrdgi..lldnssnntitgntienlryGihlensesntie 74 
                                   vnna +gd+v+v    +gi+ en+  ++  i    +  i++++     l  ++++  + g ++ n+r+G ++++ + n+++
  gi|91772387|ref|YP_565079.1|  47 VNNANEGDKVIVH---SGIYEENVilDKQIIlqgVGSPIIDGMGVGnsLSLYAESLVVDGFVLCNGRSGSYVVSDN-NILT 123
                                   6899999999999...788888877433333444555555555444777889999**************8888655.5*** PP

                          NosD  75 dntlssnesGialmsssnntlenNtisnnenyGills.dssnntisnNtisnnnkGiflensssntitgNriesnqkiGil 154
                                   +nt+++n++G++l  s++n++e+N+i +n++yG++l  +s+nn i++N+i nn+ Gi++ +s++n++  N+i +n    ++
  gi|91772387|ref|YP_565079.1| 124 NNTFKGNQYGVYLFGSKGNVIEQNVIEHNQRYGVYLLfKSDNNIITDNMINNNGGGIRIISSDDNKLYLNSIIEN----VV 200
                                   **********************************766156677899**************************999....33 PP

  == domain 2  score: 75.4 bits;  conditional E-value: 6.4e-25
                          NosD  82 esGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGifl.ensssntitgNriesnqkiGilllssse 160
                                   +sG ++ s + n+l+nNt+++n++ G++l +s++n i++N+i  n+ +G++l  +s++n it+N i++n + Gi  + ss+
  gi|91772387|ref|YP_565079.1| 110 RSGSYVVSDN-NILTNNTFKGNQY-GVYLFGSKGNVIEQNVIEhNQRYGVYLlFKSDNNIITDNMINNN-GGGIR-IISSD 186
                                   5666665555.9**********99.******************9******972566999**********.*****.***** PP

                          NosD 161 gntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg.....eDadgDGigDtpYeindgv.iDyl 235
                                   +n++y N+ i+n   v  +g  nn+W+               +GN++s +d       D+d+D ++D+pY+i+ ++ +D++
  gi|91772387|ref|YP_565079.1| 187 DNKLYLNSIIENV--VISNG--NNQWDDGV-----------DKGNHYSFFDEesegfIDKDHDDVSDVPYKIPVKNeVDNY 252
                                   *********6665..44444..9***8888...........78*****************************977779*** PP

                          NosD 236 plvn 239
                                   pl++
  gi|91772387|ref|YP_565079.1| 253 PLAS 256
                                   **86 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9  22.3   8.7e-16   5.2e-12      44     138 ..     108     204 ..      83     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 8.7e-16
                                   -SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---T CS
                    Beta_helix  44 nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiyln.yssnntienNiidnnagsGividds 123
                                   n+ sG y+ + +nn+++nnt+ +n  +g++lfg+++n+ie n i++n ++G+yl   s+nn+i++N i+nn+  Gi i +s
  gi|91772387|ref|YP_565079.1| 108 NGRSGSYVVS-DNNILTNNTFKGNQ-YGVYLFGSKGNVIEQNVIEHNQRYGVYLLfKSDNNIITDNMINNNG-GGIRIISS 185
                                   4777777765.9**********999.**************************99989999********9999.9****999 PP

                                   T....---EEES-EEES-S CS
                    Beta_helix 124 s....snvtvtnNtitnnk 138
                                   +    + + +  N++ +n+
  gi|91772387|ref|YP_565079.1| 186 DdnklYLNSIIENVVISNG 204
                                   9544522223344444443 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   5.1e-05       0.3      10      56 ..      38      77 ..      29      97 .. 0.78
   2 ?   -2.2   0.0      0.23   1.4e+03     112     135 ..     115     138 ..     112     151 .. 0.83
   3 ?    0.0   0.0     0.047   2.8e+02     227     249 ..     190     212 ..     187     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 5.1e-05
                                  SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEE CS
                Pectinesterase 10 gkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvG 56
                                   +++ i++av++++e  +    + v++G+Yeenv ++k+   ++l G
  gi|91772387|ref|YP_565079.1| 38 QEYSHIQDAVNNANEGDK----VIVHSGIYEENVILDKQ---IILQG 77
                                  46999*****99986654....4589********99984...55555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.23
                                   E--TTEEEES-EEE-STT-EEE-S CS
                Pectinesterase 112 vdsDlsvfyrcslegyqDtlyvhs 135
                                   v sD+ ++ + +++g+q  +y + 
  gi|91772387|ref|YP_565079.1| 115 VVSDNNILTNNTFKGNQYGVYLFG 138
                                   568999999999999999999765 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.047
                                   EEES-EE-TTB-TT-S--SSTTT CS
                Pectinesterase 227 vimeskiedvidpeGwleWngdf 249
                                   ++++s ie+v+ ++G  +W++ +
  gi|91772387|ref|YP_565079.1| 190 LYLNSIIENVVISNGNNQWDDGV 212
                                   6899***************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2052.29
//
Query:       gi|91772388|ref|YP_565080.1|  [L=241]
Description: thioredoxin-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-26   90.7   1.7    5.3e-26   90.7   1.7    1.6  2  FeThRed_B      Ferredoxin thioredoxin reductase catalytic bet
    1.1e-21   76.7   0.1    1.7e-21   76.1   0.1    1.3  1  Thioredoxin    Thioredoxin
    1.1e-08   35.5   0.1    2.3e-08   34.5   0.1    1.6  1  Thioredoxin_2  Thioredoxin-like domain
    1.1e-05   25.4   0.0      2e-05   24.5   0.0    1.5  1  Thioredoxin_3  Thioredoxin domain
    1.1e-05   25.0   0.1    1.5e-05   24.5   0.1    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family
    1.2e-05   24.4   0.0    1.6e-05   24.0   0.0    1.2  1  Phosducin      Phosducin
    0.00042   20.2   0.2     0.0011   18.9   0.0    1.6  2  TraF           F plasmid transfer operon protein
     0.0032   17.4   0.0     0.0059   16.6   0.0    1.5  1  HyaE           Hydrogenase-1 expression protein HyaE
     0.0033   17.4   0.1     0.0096   15.8   0.1    1.8  2  Thioredoxin_6  Thioredoxin-like domain
     0.0083   15.9   0.1       0.63    9.8   0.1    2.2  2  DSBA           DSBA-like thioredoxin domain
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.029   14.5   0.1    1.5  1  Thioredoxin_4  Thioredoxin
      0.026   13.8   0.1       0.13   11.6   0.0    1.9  2  T4_deiodinase  Iodothyronine deiodinase
      0.027   14.7   0.2       0.12   12.6   0.1    2.1  2  Glutaredoxin   Glutaredoxin
      0.087   13.0   0.0       0.16   12.2   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like


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 ?   -3.1   0.1         6   7.7e+03      67      71 ..      62      66 ..      55      78 .. 0.50
   2 !   90.7   1.7   4.2e-29   5.3e-26       3      88 ..     156     239 ..     154     241 .] 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6
                                  -HHHH CS
                     FeThRed_B 67 Cvplr 71
                                  C+ + 
  gi|91772388|ref|YP_565080.1| 62 CKKMG 66
                                  33332 PP

  == domain 2  score: 90.7 bits;  conditional E-value: 4.2e-29
                                   HHHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HHHHHH....---TTS CS
                     FeThRed_B   3 ektrkflekvakklgtkfnpdeevtevvieglarnkeeyGkrlCPCrlvedkeeeekkavwnCPCvplreeldeekeChCg 83 
                                   e +++ + k+a+k g+++npdee  + v+eglarn+++ Gk++CPCr+v+++e+e+kk++  CPC+++++e++  ++ChC 
  gi|91772388|ref|YP_565080.1| 156 EDMHAWTAKYADKAGYMLNPDEESLHLVLEGLARNRNKHGKNYCPCRIVTGDEQEDKKII--CPCIYHKDEINDGGSCHCD 234
                                   67999*******************************************************..******************* PP

                                   SSB-T CS
                     FeThRed_B  84 lfvtk 88 
                                   lf +k
  gi|91772388|ref|YP_565080.1| 235 LFFKK 239
                                   **976 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.1   1.3e-24   1.7e-21       6     102 ..      35     131 ..      30     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.3e-24
                                   SHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEE CS
                   Thioredoxin   6 tkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevk 86 
                                   ++ +Fe+ev++++ +v+v+++ + C++Ck++  ++ek+a+e++ kvk++k+d ++++ + k++++ g+Ptl++fk+g+ ++
  gi|91772388|ref|YP_565080.1|  35 NTFAFEAEVEHSNLPVVVDCFTKTCPPCKKMGQVFEKVASEYESKVKFIKIDLKASPAIGKRFNILGVPTLLFFKDGNLQN 115
                                   5668***************************************************************************** PP

                                   EEESS-HHHHHHHHHH CS
                   Thioredoxin  87 kyegarekeklaaflk 102
                                   +++g  +++k++++l+
  gi|91772388|ref|YP_565080.1| 116 NVVGFTNEDKFREHLD 131
                                   *****99999998876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   1.8e-11   2.3e-08       4     109 .]      46     130 ..      43     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.8e-11
                 Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt. 83 
                                   ++ pv+v+  + +Cp Ckk+ ++++++    +      +  +++ k+++i+ +++++            ++++++ g+Pt 
  gi|91772388|ref|YP_565080.1|  46 SNLPVVVDCFTKTCPPCKKMGQVFEKV---ASE-----Y--ESKVKFIKIDLKASPA-----------IGKRFNILGVPTl 105
                                   6789***********************...333.....4..5668999999999997...........9***********6 PP

                 Thioredoxin_2  84 ivfldgkeivarlpGyvpaeeleall 109
                                   ++f dg+  +++++G+++++++++ l
  gi|91772388|ref|YP_565080.1| 106 LFFKDGN-LQNNVVGFTNEDKFREHL 130
                                   6699999.999***********9865 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.6e-08     2e-05       5      57 ..      54     111 ..      50     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.6e-08
                                   EESSSSTTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEE..ECTT CS
                 Thioredoxin_3   5 vlgpgCakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPal..vidg 57 
                                    ++++C+ C+k+ ++++++a e + k++++k+  + ++ i +++++  vP+l  + dg
  gi|91772388|ref|YP_565080.1|  54 CFTKTCPPCKKMGQVFEKVASEYESKVKFIKIdlKASPAIgKRFNILGVPTLlfFKDG 111
                                   4799*******************8777777666699***************9644455 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 !   24.5   0.1   1.2e-08   1.5e-05      44     132 ..      57     133 ..      52     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
                     OST3_OST6  44 fkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp.................kkg 107
                                   + C +C+++ + fe+va+ + ++       + F+k+d++ ++ + +++++  +P ll+f+                  +  
  gi|91772388|ref|YP_565080.1|  57 KTCPPCKKMGQVFEKVASEYESK-------VKFIKIDLKASPAIGKRFNILGVPTLLFFKDgnlqnnvvgftnedkfrE-- 128
                                   57****************99998.......88***************************99444444444433332220.. PP

                     OST3_OST6 108 pkeskkkdtydfsrggfdaealakf 132
                                                       +l + 
  gi|91772388|ref|YP_565080.1| 129 --------------------HLDNL 133
                                   ....................22222 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.2e-08   1.6e-05     143     237 ..      44     137 ..      24     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.2e-08
                                   S-TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-T.TSEEEEEEHHHH.--TTSS-TTT-SEEEEEETTEEEEEETTGGGGS CS
                     Phosducin 143 eqkitlivvhiyedgvkgtealnssliclaaeyp.tvkfckvkasvi.gasdrfsrdvlpallvykagellsnfvrvtdql 221
                                   e     +vv  +    + ++ +   +  +a+ey   vkf k+   +    ++rf    +p+ll +k g+l +n v  t+  
  gi|91772388|ref|YP_565080.1|  44 EHSNLPVVVDCFTKTCPPCKKMGQVFEKVASEYEsKVKFIKIDLKASpAIGKRFNILGVPTLLFFKDGNLQNNVVGFTN-- 122
                                   55556689999999*******************637*****97655415699***********************9996.. PP

                                   -TT--HHHHHHHHHTT CS
                     Phosducin 222 aedffavdleaflqef 237
                                    ed f   l+ +l++ 
  gi|91772388|ref|YP_565080.1| 123 -EDKFREHLDNLLEQL 137
                                   .778888888877765 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   8.5e-07    0.0011     138     210 ..      56     119 ..      52     122 .. 0.91
   2 ?   -2.0   0.0         2   2.5e+03      40      65 ..     153     180 ..     140     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.5e-07
                          TraF 138 rgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpva 210
                                    ++cp c+++ ++ +++a +y+ +v+++++d + +p + +         r+++  +P+l++++  + +  +v+
  gi|91772388|ref|YP_565080.1|  56 TKTCPPCKKMGQVFEKVASEYESKVKFIKIDLKASPAIGK---------RFNILGVPTLLFFKDGNLQNNVVG 119
                                   679********************************99999.........************999987766776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                          TraF  40 esaaelrkeleelldkAi..lnPteenv 65 
                                    + +++++++ ++ dkA   lnP ee +
  gi|91772388|ref|YP_565080.1| 153 STKEDMHAWTAKYADKAGymLNPDEESL 180
                                   5567888889999999955588888865 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.6e-06    0.0059      66      99 ..      83     117 ..      63     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                                   EE.THHHHHHHHHCCT-TSSSEEEEEETTEEEEEE CS
                          HyaE  66 va.dreqeealaerfgvlktPsllflrdgeylgvl 99 
                                   ++ d + + a+++rf++l +P+llf++dg++   +
  gi|91772388|ref|YP_565080.1|  83 IKiDLKASPAIGKRFNILGVPTLLFFKDGNLQNNV 117
                                   334789999********************987665 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.5e-06    0.0096      88     159 ..      41     109 ..      26     136 .. 0.79
   2 ?   -1.3   0.0       1.4   1.8e+03      55      70 ..     146     161 ..     114     168 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.5e-06
                                   HHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEE CS
                 Thioredoxin_6  88 eelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivd 159
                                    e+ +++lp+++ +f+ k+    +k+ +++ekva e++ k++f+ +d+k+ + + +++++    +P++ +++
  gi|91772388|ref|YP_565080.1|  41 AEVEHSNLPVVVDCFT-KTCPPCKKMGQVFEKVASEYESKVKFIKIDLKASPAIGKRFNIL--GVPTLLFFK 109
                                   5677888885555555.688899**************************888877777776..667666655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                   EEEETHT--HHHHHHH CS
                 Thioredoxin_6  55 vkydgekitvddlkkf 70 
                                   + +++++ t++d+  +
  gi|91772388|ref|YP_565080.1| 146 INMTDNESTKEDMHAW 161
                                   2233333444444444 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00049      0.63       9      44 ..      58      91 ..      51      96 .. 0.88
   2 ?    4.6   0.0     0.019        25     160     192 ..      94     130 ..      92     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                                  TBHHHHHHHHHHHHHHHHCCTEEEEEEE-SSSCHHH CS
                          DSBA  9 lCPyCylgkerleklaarspdvkvvlrpfelagakk 44
                                   CP C+ + +++ek+a+ + + kv++  ++l+++ +
  gi|91772388|ref|YP_565080.1| 58 TCPPCKKMGQVFEKVASEY-ESKVKFIKIDLKAS-P 91
                                  6******************.9******9999987.4 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                                   HHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHHH CS
                          DSBA 160 aqslgvtGvPtvvv..dgk..rmvfGadrldtladal 192
                                   +++ ++ GvPt ++  dg   + v+G ++ d+++++l
  gi|91772388|ref|YP_565080.1|  94 GKRFNILGVPTLLFfkDGNlqNNVVGFTNEDKFREHL 130
                                   578899*****999887766799**********9998 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.3e-05     0.029      14      55 ..      49      87 ..      45     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                                  SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE- CS
                 Thioredoxin_4 14 pvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdf 55
                                  pv+v+ ++  +Cp C+k+ +  ek+ +ey  + kvkfi +d+
  gi|91772388|ref|YP_565080.1| 49 PVVVDCFTK-TCPPCKKMGQVFEKVASEY--ESKVKFIKIDL 87
                                  788888875.8******************..99*****9887 PP

>> T4_deiodinase  Iodothyronine deiodinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.9e-05      0.13     100     141 ..      45      86 ..       9      95 .. 0.90
   2 ?   -0.1   0.0      0.35   4.5e+02      70     120 ..     189     239 ..     171     241 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.9e-05
                 T4_deiodinase 100 qgnrPlvlnfGsatcPpflaklsafkrlveefssvadfliiy 141
                                   ++n P+v++  + tcPp     + f+++  e+ s++ f+ i 
  gi|91772388|ref|YP_565080.1|  45 HSNLPVVVDCFTKTCPPCKKMGQVFEKVASEYESKVKFIKID 86 
                                   5789*************9988899**************8775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.35
                 T4_deiodinase  70 ykqvkeGgdaPnsevvrvsgteschildfaqgnrPlvlnfGsatcPpflak 120
                                    ++ k+G++   + +v  + +e ++i+     ++  + + Gs+ c  f  k
  gi|91772388|ref|YP_565080.1| 189 RNRNKHGKNYCPCRIVTGDEQEDKKIICPCIYHKDEINDGGSCHCDLFFKK 239
                                   467788888889999999999999999888888888888999999888765 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.7e-05      0.12       7      41 ..      57      97 ..      50     110 .. 0.72
   2 ?   -1.3   0.0       2.1   2.7e+03      24      44 ..     141     161 ..     131     168 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-05
                                  TSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHH CS
                  Glutaredoxin  7 ptCpyCkkakrlLkelg......vkfeeidvdkdeeireel 41
                                  +tCp Ckk+ +++++        vkf  id+ + ++i +  
  gi|91772388|ref|YP_565080.1| 57 KTCPPCKKMGQVFEKVAseyeskVKFIKIDLKASPAIGKRF 97
                                  89***********6666455555778888888877766655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                                   GGEEEEEGCCSHHHHHHHHHH CS
                  Glutaredoxin  24 vkfeeidvdkdeeireelkel 44 
                                    + e+i+ +++e+ +e++ + 
  gi|91772388|ref|YP_565080.1| 141 SPSEVINMTDNESTKEDMHAW 161
                                   456899999999999998765 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.16      12      81 ..      42     108 ..      38     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                   HHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG..-TT---SSEEEEE CS
                 Thioredoxin_7  12 kaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani.leldeqgvPvvafl 81 
                                   + + ++ pv v+    +c++C+++ ++f++     + + +k+ + ++d   + a i  ++   gvP+++f+
  gi|91772388|ref|YP_565080.1|  42 EVEHSNLPVVVDCFTKTCPPCKKMGQVFEKV--ASE-YESKVKFIKIDLKASPA-IgKRFNILGVPTLLFF 108
                                   55677889********************876..666.99999999999988887.6334344789999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1624.03
//
Query:       gi|91772389|ref|YP_565081.1|  [L=152]
Description: formylmethanofuran dehydrogenase, subunit G [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   54.1   2.2    8.8e-15   54.1   2.2    2.4  2  FeS       Putative Fe-S cluster
    2.5e-09   36.5  21.3    3.4e-08   33.0   5.3    3.4  3  Fer4      4Fe-4S binding domain
      1e-07   32.0  24.9    4.5e-06   26.7   6.7    2.7  2  Fer4_9    4Fe-4S dicluster domain
    2.1e-07   30.7  20.7    7.1e-06   25.9   3.8    3.5  3  Fer4_6    4Fe-4S binding domain
    2.4e-07   30.8  13.7    1.5e-06   28.2   8.5    2.9  2  Fer4_10   4Fe-4S dicluster domain
    2.6e-06   27.8  22.7    0.00036   20.9   7.3    2.5  2  Fer4_8    4Fe-4S dicluster domain
    9.7e-06   26.1  24.8    0.00024   21.6   4.3    3.0  3  Fer4_7    4Fe-4S dicluster domain
    1.4e-05   24.9   2.5    1.4e-05   24.9   2.5    3.5  3  Fer4_2    4Fe-4S binding domain
    5.6e-05   23.2  14.6    0.00017   21.6   1.6    3.1  3  Fer4_21   4Fe-4S dicluster domain
    0.00016   22.2   4.2    0.00016   22.2   4.2    2.5  2  Fer4_17   4Fe-4S dicluster domain
    0.00074   19.8   2.9    0.00074   19.8   2.9    3.8  3  Fer4_4    4Fe-4S binding domain
     0.0028   18.2  12.6     0.0074   16.8   7.1    3.0  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0032   18.2   0.3     0.0032   18.2   0.3    2.9  2  Fer4_15   4Fe-4S single cluster domain
     0.0044   17.9  20.5      0.012   16.6   2.7    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
     0.0048   17.7  23.6      0.012   16.5   7.3    3.7  3  Fer4_3    4Fe-4S binding domain
     0.0066   16.4   0.6     0.0066   16.4   0.6    2.2  2  YhfH      YhfH-like protein
  ------ inclusion threshold ------
      0.058   14.2   2.5      0.058   14.2   2.5    3.0  3  Fer4_22   4Fe-4S dicluster domain
      0.092   12.9   0.4      0.092   12.9   0.4    2.6  3  Fer4_18   4Fe-4S dicluster domain


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 !   54.1   2.2   8.9e-18   8.8e-15       1      33 []      11      43 ..      11      43 .. 0.99
   2 ?   -3.6   2.6       9.3   9.3e+03       6       9 ..      81      84 ..      77      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 8.9e-18
                           FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                  LP+tNC++CG ++CmafA+al++ e+ ++dCpp
  gi|91772389|ref|YP_565081.1| 11 LPKTNCKQCGKATCMAFAAALLSREVVVDDCPP 43
                                  9*******************************8 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.3
                           FeS  6 CgaC 9 
                                  Cg C
  gi|91772389|ref|YP_565081.1| 81 CGNC 84
                                  7777 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.43   4.2e+02       7      12 ..      15      20 ..      13      22 .. 0.64
   2 !   33.0   5.3   3.4e-11   3.4e-08       2      22 ..      72      92 ..      71      94 .. 0.92
   3 !   11.8   2.3   0.00016      0.16       9      24 .]     135     150 ..     135     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.43
                                  TSSS-T CS
                          Fer4  7 kCigCG 12
                                   C  CG
  gi|91772389|ref|YP_565081.1| 15 NCKQCG 20
                                  466666 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 3.4e-11
                                  EEETTTSSS-THHHHHSTTTE CS
                          Fer4  2 videekCigCGaCvevCPvgA 22
                                  ++++ekCigCG+Cv +CPv++
  gi|91772389|ref|YP_565081.1| 72 IVHTEKCIGCGNCVVACPVNV 92
                                  789****************96 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00016
                                   SS-THHHHHSTTTEEE CS
                          Fer4   9 igCGaCvevCPvgAIt 24 
                                   i C+ C+  CP+ AI+
  gi|91772389|ref|YP_565081.1| 135 ILCNGCIVTCPTKAIE 150
                                   78*************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 !   17.7  10.2     3e-06     0.003       3      49 ..      14      91 ..      14      93 .. 0.78
   2 !   26.7   6.7   4.6e-09   4.5e-06       1      51 []      77     149 ..      77     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-06
                        Fer4_9  3 tgCgaCvea.C........pagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49
                                  t+C++C +a C          +vvv+d+ + k    ++++                      e+CigCg Cv aCp +
  gi|91772389|ref|YP_565081.1| 14 TNCKQCGKAtCmafaaallSREVVVDDCPPLKEDKFKDKYeklseiitpageasesgmivhtEKCIGCGNCVVACPVN 91
                                  6899995555988888888667777776666655544444788889999999999*********************87 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 4.6e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkgai 51 
                                   kC+gCg+Cv aCp +v+++ ++++  r    ++                      e+ i C+ C+  Cp++ai
  gi|91772389|ref|YP_565081.1|  77 KCIGCGNCVVACPVNVAEDPHGAGSGRAPTSDNvilrvedgvvrlsnvsqcrrfgENKILCNGCIVTCPTKAI 149
                                   7***********************999877777***************988888866788999*******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 ?    3.6   1.3     0.079        79       8      16 ..      15      25 ..      13      26 .. 0.84
   2 !   25.9   3.8   7.1e-09   7.1e-06       5      23 ..      74      92 ..      71      93 .. 0.88
   3 !   11.5   1.2   0.00024      0.24      10      24 .]     135     149 ..     125     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.079
                        Fer4_6  8 kCigCgd..Cv 16
                                  +C +Cg+  C+
  gi|91772389|ref|YP_565081.1| 15 NCKQCGKatCM 25
                                  8*****98887 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 7.1e-09
                        Fer4_6  5 dpdkCigCgdCvrvCPega 23
                                    +kCigCg+Cv++CP ++
  gi|91772389|ref|YP_565081.1| 74 HTEKCIGCGNCVVACPVNV 92
                                  579*************975 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00024
                        Fer4_6  10 igCgdCvrvCPegai 24 
                                   i C+ C++ CP++ai
  gi|91772389|ref|YP_565081.1| 135 ILCNGCIVTCPTKAI 149
                                   58***********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 ?    4.1   0.2     0.052        51       7      17 ..      14      26 ..      10      59 .. 0.70
   2 !   28.2   8.5   1.5e-09   1.5e-06       2      56 .]      71     145 ..      70     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.052
                       Fer4_10  7 dtCirCg..kCvk 17
                                    C +Cg  +C++
  gi|91772389|ref|YP_565081.1| 14 TNCKQCGkaTCMA 26
                                  3455555444544 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.5e-09
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl.............tsvgakgeaseeeavrkkvekCtg.......cgaCveaCP 56 
                                   +++ +++Ci+Cg+Cv aCP+++             ts++++   +++ +   +v++C +       c  C+  CP
  gi|91772389|ref|YP_565081.1|  71 MIVHTEKCIGCGNCVVACPVNVaedphgagsgrapTSDNVILRVEDGVVRLSNVSQCRRfgenkilCNGCIVTCP 145
                                   567889**************99************999999998888888888*******999999999******9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   7.5   1.2e-06    0.0012       4      65 .]      15      92 ..      13      92 .. 0.78
   2 !   20.9   7.3   3.6e-07   0.00036       3      64 ..      76     147 ..      74     148 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                        Fer4_8  4 kCieCg..aCq.............saCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                  +C +Cg   C+             + Cp l++ k k+++++  e +  + e  +       ++C +cg+C+++Cpv++
  gi|91772389|ref|YP_565081.1| 15 NCKQCGkaTCMafaaallsrevvvDDCPPLKEDKfKDKYEKLSEIITPAGEASESGMIVHTEKCIGCGNCVVACPVNV 92
                                  79999977899999999999999999**9999887777777777666333333333367899*************986 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.6e-07
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae........dvqeeqvlee...eealwsC.......ttcgaCtevCpvg 64 
                                   ekCi+Cg C  aCpv  +++ h   +    +         d        +     ++ +C         c+ C + Cp++
  gi|91772389|ref|YP_565081.1|  76 EKCIGCGNCVVACPVNVAEDPHGAGSGRAPTSdnvilrveD--------GvvrLSNVSQCrrfgenkILCNGCIVTCPTK 147
                                   79************877776554433333333455433320........23445667888666666688999******87 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  12.6   7.7e-06    0.0077       4      52 .]      15      92 ..      11      92 .. 0.53
   2 !   21.6   4.3   2.4e-07   0.00024       1      18 [.      77      94 ..      77     129 .. 0.84
   3 !   11.1   0.6   0.00047      0.47       4      19 ..     136     151 ..     135     152 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-06
                        Fer4_7  4 gCgaCvaa.Cpvkaieldeeenek............................gtekveidpekClgCgaCvavCPtga 52
                                  +C++C +a C++ a  l  +e+                                  + ++ ekC+gCg+Cv +CP+++
  gi|91772389|ref|YP_565081.1| 15 NCKQCGKAtCMAFAAALLSREVVVddcpplkedkfkdkyeklseiitpageaSESGMIVHTEKCIGCGNCVVACPVNV 92
                                  7888985548644444332211111233333333333333344444433322113358899**************986 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.4e-07
                        Fer4_7  1 rCigCgaCvaaCpvkaie 18
                                  +CigCg+Cv+aCpv++ e
  gi|91772389|ref|YP_565081.1| 77 KCIGCGNCVVACPVNVAE 94
                                  7************99976 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00047
                        Fer4_7   4 gCgaCvaaCpvkaiel 19 
                                    C+ C ++Cp+kaie+
  gi|91772389|ref|YP_565081.1| 136 LCNGCIVTCPTKAIEF 151
                                   6************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.042        42       9      16 ..      15      24 ..       8      27 .. 0.79
   2 !   24.9   2.5   1.4e-08   1.4e-05       5      21 ..      73      89 ..      69      90 .. 0.89
   3 ?    3.6   1.8     0.081        81      13      22 .]     137     146 ..     123     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                        Fer4_2  9 rCigCg..aC 16
                                  +C +Cg  +C
  gi|91772389|ref|YP_565081.1| 15 NCKQCGkaTC 24
                                  6999998888 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.4e-08
                        Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                  v t++CigCg Cv aCP
  gi|91772389|ref|YP_565081.1| 73 VHTEKCIGCGNCVVACP 89
                                  679************** PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.081
                        Fer4_2  13 CgaCvsaCPa 22 
                                   C+ C+  CP+
  gi|91772389|ref|YP_565081.1| 137 CNGCIVTCPT 146
                                   988*999*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 ?    0.7   0.4      0.59   5.9e+02       7      14 ..      15      22 ..      10      42 .. 0.66
   2 !   21.6   1.6   1.7e-07   0.00017      35      53 ..      72      90 ..      58      95 .. 0.67
   3 !    9.0   0.6    0.0015       1.5       9      23 ..     135     149 ..     120     152 .] 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.59
                       Fer4_21  7 kCigCgkC 14
                                  +C +Cgk 
  gi|91772389|ref|YP_565081.1| 15 NCKQCGKA 22
                                  56666552 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.7e-07
                       Fer4_21 35 kvvedeCvGCnlCssvCPv 53
                                   v +++C+GC  C+  CPv
  gi|91772389|ref|YP_565081.1| 72 IVHTEKCIGCGNCVVACPV 90
                                  4455666666666666666 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0015
                       Fer4_21   9 igCgkCliaCedtsh 23 
                                   i C+ C+++C+++++
  gi|91772389|ref|YP_565081.1| 135 ILCNGCIVTCPTKAI 149
                                   667777777776544 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   4.2   1.6e-07   0.00016       1      60 [.      15      92 ..      15      93 .. 0.76
   2 ?    3.8   0.5     0.087        87      48      58 ..     136     146 ..     115     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.6e-07
                       Fer4_17  1 rCiqCgy..Clp.............eCpsyeaydnepk..kllraaklglleeaekee..kaslCieCgeCerkCPqgl 60
                                  +C qCg   C++              Cp +++ +++ k  kl + ++++  e+ e  +    ++Ci+Cg+C+ +CP ++
  gi|91772389|ref|YP_565081.1| 15 NCKQCGKatCMAfaaallsrevvvdDCPPLKEDKFKDKyeKLSEIITPA-GEASESGMivHTEKCIGCGNCVVACPVNV 92
                                  6****9666***9999999999999999999876654433677777764.333333332489**************886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.087
                       Fer4_17  48 eCgeCerkCPq 58 
                                    C++C   CP 
  gi|91772389|ref|YP_565081.1| 136 LCNGCIVTCPT 146
                                   68888888885 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.4     0.059        59       3      13 ..      15      27 ..      13      27 .. 0.73
   2 !   19.8   2.9   7.4e-07   0.00074       2      17 .]      76      91 ..      75      94 .. 0.93
   3 ?    3.2   2.6      0.15   1.5e+02       6      16 ..     136     146 ..     125     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.059
                        Fer4_4  3 rCigCgs..Cvaa 13
                                  +C +Cg+  C+a+
  gi|91772389|ref|YP_565081.1| 15 NCKQCGKatCMAF 27
                                  7999996668875 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 7.4e-07
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  e+CigCg Cv aCP++
  gi|91772389|ref|YP_565081.1| 76 EKCIGCGNCVVACPVN 91
                                  89************75 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.15
                        Fer4_4   6 gCgsCvaaCPq 16 
                                    C  C+ +CP+
  gi|91772389|ref|YP_565081.1| 136 LCNGCIVTCPT 146
                                   5888*****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 ?    2.3   0.2      0.25   2.5e+02       8      23 ..      15      30 ..      14      60 .. 0.77
   2 !   16.8   7.1   7.4e-06    0.0074       3      57 ..      75     150 ..      73     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.25
                       Fer4_13  8 acgaCvelaPdvFeed 23
                                  +c++C+++    F+  
  gi|91772389|ref|YP_565081.1| 15 NCKQCGKATCMAFAAA 30
                                  7999999998888765 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7.4e-06
                       Fer4_13   3 rdtCiacgaCvelaPdvFeeddeggasvvaeqpts.......................eeekadaeeAadaCPvesIg 57 
                                    ++Ci+cg+Cv ++P   +ed++g  s   + pts                        e k +++  + +CP+++I+
  gi|91772389|ref|YP_565081.1|  75 TEKCIGCGNCVVACPVNVAEDPHGAGSG--RAPTSdnvilrvedgvvrlsnvsqcrrfGENKILCNGCIVTCPTKAIE 150
                                   689*******************987665..444444477777778888888888999988899************996 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   3.2e-06    0.0032       5      30 ..      75     100 ..      72     120 .. 0.82
   2 ?    2.0   0.5      0.35   3.5e+02      58      65 ..     143     150 ..     136     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.2e-06
                       Fer4_15   5 rdaCigcglCvaeapevfeldedgla 30 
                                    ++Cigcg+Cv ++p  + +d  g  
  gi|91772389|ref|YP_565081.1|  75 TEKCIGCGNCVVACPVNVAEDPHGAG 100
                                   589************99999988765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.35
                       Fer4_15  58 aCPvdAIr 65 
                                   +CP++AI+
  gi|91772389|ref|YP_565081.1| 143 TCPTKAIE 150
                                   6*****97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  13.5     0.019        19      23      67 .]      36      91 ..      14      91 .. 0.46
   2 !   16.6   2.7   1.2e-05     0.012       1      20 [.      77      96 ..      77     111 .. 0.84
   3 !   12.1   0.9   0.00028      0.28       5      18 ..     137     150 ..     135     152 .] 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                       Fer4_16 23 keiearecisy...........ntaekkdlaedeekckkqeaitgCdiCqdvCPan 67
                                   +++ +   ++           + +   + a ++      e+++gC++C+ +CP+n
  gi|91772389|ref|YP_565081.1| 36 VVVDDCPPLKEdkfkdkyeklsEIITPAGEASESGMIVHTEKCIGCGNCVVACPVN 91
                                  44444443333333332232322333333333333333458899999999999988 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++Cg+C+ +CP+n+ + +
  gi|91772389|ref|YP_565081.1| 77 KCIGCGNCVVACPVNVAEDP 96
                                  5*************998776 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00028
                       Fer4_16   5 CgkCaevCPtnaik 18 
                                   C+ C+ +CPt+ai+
  gi|91772389|ref|YP_565081.1| 137 CNGCIVTCPTKAIE 150
                                   *************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 ?    1.9   1.4      0.54   5.4e+02       1       8 [.      16      25 ..      14      27 .. 0.75
   2 !   16.5   7.3   1.2e-05     0.012       1      14 [.      78      91 ..      78      92 .. 0.95
   3 !    9.1   0.8    0.0027       2.7       3      15 .]     136     148 ..     135     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.54
                        Fer4_3  1 CtgCg..aCv 8 
                                  C +Cg  +C+
  gi|91772389|ref|YP_565081.1| 16 CKQCGkaTCM 25
                                  8888866687 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+gCg Cv++CPv+
  gi|91772389|ref|YP_565081.1| 78 CIGCGNCVVACPVN 91
                                  ************98 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0027
                        Fer4_3   3 gCgaCvevCPvgA 15 
                                    C+ C + CP++A
  gi|91772389|ref|YP_565081.1| 136 LCNGCIVTCPTKA 148
                                   7988*******98 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.6   6.6e-06    0.0066       1      22 [.       1      22 [.       1      25 [. 0.93
   2 ?   -3.0   2.9       7.6   7.5e+03      15      21 ..      77      83 ..      75      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.6e-06
                          YhfH  1 lekiveFfrnLPkKkCteCGke 22
                                  + + +e+++ LPk  C +CGk 
  gi|91772389|ref|YP_565081.1|  1 MANALEIYQLLPKTNCKQCGKA 22
                                  7899****************95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.6
                          YhfH 15 kCteCGk 21
                                  kC  CG+
  gi|91772389|ref|YP_565081.1| 77 KCIGCGN 83
                                  7999997 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.9       3.6   3.6e+03       2      15 ..      16      24 ..      13      45 .. 0.65
   2 ?   14.2   2.5   5.8e-05     0.058      78      95 ..      74      91 ..      44      92 .. 0.81
   3 ?    2.5   1.4      0.27   2.7e+02       3      14 ..     135     146 ..     125     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.6
                       Fer4_22  2 ClsCgaCtlvCptC 15
                                  C +Cg+ t     C
  gi|91772389|ref|YP_565081.1| 16 CKQCGKAT-----C 24
                                  33333332.....2 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.8e-05
                       Fer4_22 78 gesgCvGCgRCieacpvk 95
                                  ++++C+GCg C+ acpv+
  gi|91772389|ref|YP_565081.1| 74 HTEKCIGCGNCVVACPVN 91
                                  7889***********987 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.27
                       Fer4_22   3 lsCgaCtlvCpt 14 
                                   + C+ C ++Cpt
  gi|91772389|ref|YP_565081.1| 135 ILCNGCIVTCPT 146
                                   569999999998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3         4     4e+03      87      93 ..      15      21 ..       8      41 .. 0.63
   2 ?   12.9   0.4   9.2e-05     0.092      56      75 ..      73      92 ..      46      95 .. 0.81
   3 ?    5.0   0.4     0.028        28      60      74 ..     133     147 ..     112     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                       Fer4_18 87 scllcid 93
                                  +c +c  
  gi|91772389|ref|YP_565081.1| 15 NCKQCGK 21
                                  2333322 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.2e-05
                       Fer4_18 56 kgagdcidcescvkvcPtgi 75
                                    + +ci c+ cv  cP+++
  gi|91772389|ref|YP_565081.1| 73 VHTEKCIGCGNCVVACPVNV 92
                                  56778************987 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.028
                       Fer4_18  60 dcidcescvkvcPtg 74 
                                   + i c+ c+  cPt+
  gi|91772389|ref|YP_565081.1| 133 NKILCNGCIVTCPTK 147
                                   4689*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 961.69
//
Query:       gi|91772390|ref|YP_565082.1|  [L=414]
Description: formylmethanofuran dehydrogenase, subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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      0.014   15.1   0.0    2.7  2  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.014   14.3   0.0       0.41    9.5   0.0    2.5  3  Molybdopterin  Molybdopterin oxidoreductase
       0.18   11.3   1.7       0.58    9.7   1.7    1.9  1  TF_Zn_Ribbon   TFIIB zinc-binding
       0.19   11.5   0.1          1    9.1   0.0    2.0  2  CO_dh          CO dehydrogenase beta subunit/acetyl-CoA synth


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 !   15.1   0.0   3.2e-06     0.014       3      54 ..      65     116 ..      63     187 .. 0.69
   2 !    8.6   0.0   0.00033       1.5       3      39 ..     230     267 ..     228     284 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-06
                                   HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE.EEEGGGTTSS-T CS
                  TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPv.vttlmgkgvipe 54 
                                   +aa +lk+ak pvi+ G g ++s+a++ + e+a+k+++ +  t+  ++g i e
  gi|91772390|ref|YP_565082.1|  65 EAARILKEAKSPVIF-GMGNSTSQAQKNAIEVAKKTDAYFdDTSSFCQGPIVE 116
                                   89***********96.9999999**************9884333444555554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00033
                                   HHHHHHHH-SSEEEEE-CHHCHT.TGHHHHHHHHHHHT CS
                  TPP_enzyme_M   3 kaaellkaakrpvilvGggvars.gaseelrelaeklg 39 
                                   ++a++lk+a+  vi vG g  +s +  e l++l +kl+
  gi|91772390|ref|YP_565082.1| 230 ELANMLKKAEFGVICVGLGLVYSlEEIEPLVRLMDKLN 267
                                   789********************9999******99987 PP

>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.03   1.3e+02     318     363 ..      54      97 ..      41     103 .. 0.79
   2 ?    9.5   0.0   9.1e-05      0.41     110     178 ..     133     210 ..     101     218 .. 0.83
   3 ?   -1.0   0.0      0.15   6.5e+02     333     392 ..     318     374 ..     222     399 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.03
                                   CSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHH CS
                 Molybdopterin 318 nlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekal 363
                                   n++ + +  ++e+++ lk+ +  v++ +gn+ +++++++ ev  a+
  gi|91772390|ref|YP_565082.1|  54 NEPATLEAAIIEAARILKEAKSPVIFGMGNSTSQAQKNAIEV--AK 97 
                                   5566667889999****************8888877777777..33 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.1e-05
                                   GG-SEEEEESS-HHHHSHHH........HHHHHHHHHTTC-EEEEECSSB-HCGGGC.SEEEEEHTTTHHHHHHHHHH CS
                 Molybdopterin 110 ensdliilwGsNvreerpil........narirkaalkkkakvivigpryaellkfa.dewlaikpgtdaalalamgh 178
                                   +++d+i+ wG+++ + +p           +++r++  +++   i+i+ r++++++ + d+   i p+ d +l++a+ +
  gi|91772390|ref|YP_565082.1| 133 DKADVIVYWGADPSNSHPRHlskytyfpRGKERQRGWEEDRTAICIDVRKSDTATICgDKFYQIPPQADEELLNALTN 210
                                   79****************9988888888777777777777889*********888775788899********999876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.15
                                   HHHTTSSSEEEEESH.HHHHSTTSCCCHCHHH.CSSEEEEEESCSSHHHHTSSEEEEBE-C CS
                 Molybdopterin 333 llkssgkkvlyllgnnpevdhadenevekale.kldlvvvldgrltstalyaDiiLPaatw 392
                                   ll++  +++  ++g++p+ + +         e     v+++d   t t ++a +  Paat 
  gi|91772390|ref|YP_565082.1| 318 LLRKRTVDAALIIGSDPMSSLPGSIAK----ElLDIPVITIDPCNTLTSRKAKVSIPAATA 374
                                   555555555555555555554444444....312345777777777777777777777765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.7   0.00013      0.58      17      36 ..       3      22 ..       1      28 [. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                  TTCEEESSSSBEEEECCCCC CS
                  TF_Zn_Ribbon 17 rgelvCtdCGlVlednside 36
                                  +  +vCt CGl+ +d  i+ 
  gi|91772390|ref|YP_565082.1|  3 TEYYVCTGCGLLCDDIEIEL 22
                                  5566********99988765 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 ?    9.1   0.0   0.00023         1      14      58 ..      52      96 ..      43     103 .. 0.77
   2 ?   -0.7   0.0      0.23     1e+03      27      49 ..     230     252 ..     220     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00023
                                  XXXX--EEE--SHHHHHHHHHSSSEEEE.E-S--.-HH.HHHHHHH CS
                         CO_dh 14 anskkatleealkvvakmikkakrPlli.vGpqvlkaeneeakekk 58
                                  +n++ atle a+ ++a+++k ak P+++ +G+   +  ++ a+e++
  gi|91772390|ref|YP_565082.1| 52 INNEPATLEAAIIEAARILKEAKSPVIFgMGNSTSQ-AQKNAIEVA 96
                                  68999**********************944555544.435555544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.23
                                   HHHHHHHHSSSEEEEE-S--.-H CS
                         CO_dh  27 vvakmikkakrPllivGpqvlka 49 
                                   + a+m+kka+  ++ vG  + + 
  gi|91772390|ref|YP_565082.1| 230 ELANMLKKAEFGVICVGLGLVYS 252
                                   56899999998888888665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2817.56
//
Query:       gi|91772391|ref|YP_565083.1|  [L=132]
Description: formylmethanofuran dehydrogenase, subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-05   22.4   0.0    0.00011   22.1   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 !   22.1   0.0   6.4e-09   0.00011       4     108 ..      17     113 ..      14     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.4e-09
                                   EEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS..B-TTEEEEESSHCC CS
               Molydop_binding   4 itgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvter..vrpGvvfmpfgwwe 82 
                                   it+r + q  +   ++   ++a+++  v+++   d++++ +k G + ++++ +G+v+v  + ++    ++G  +m+   w+
  gi|91772391|ref|YP_565083.1|  17 ITYRDVFQSTALESSGCGDEYAERSA-VILLDKGDMKKMVLKAGRKAVLKNNFGRVVVHLRPSDYekGHEGIGYMTNSPWS 96 
                                   67777777666666666666666665.*********************************887644499************ PP

                                   .....S-GHCTS--SCSTTT--CSTT CS
               Molydop_binding  83 agekggnaNaltddatdplsgtpefk 108
                                           Nal+ ++ +  sg p+fk
  gi|91772391|ref|YP_565083.1|  97 --------NALV-SSETGGSGVPKFK 113
                                   ........****.6666778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 924.80
//
Query:       gi|91772392|ref|YP_565084.1|  [L=282]
Description: hypothetical protein Mbur_0338 [Methanococcoides burtonii DSM 6242]
Scores for 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-114  381.1   3.3   2.3e-114  380.9   3.3    1.0  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20
     0.0033   17.6   0.0     0.0095   16.1   0.0    1.7  1  FlaG      FlaG protein


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 !  380.9   3.3  2.6e-118  2.3e-114       1     257 []       3     256 ..       3     256 .. 1.00

  Alignments for each domain:
  == domain 1  score: 380.9 bits;  conditional E-value: 2.6e-118
                       DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGasEil 81 
                                   H++e+lgk++vvv++gkvvevgep+i++CPlf+k+rgik+it+ea+k+n+efrik+fGlftk+R le++  fv+fGasE++
  gi|91772392|ref|YP_565084.1|   3 HVMEILGKTKVVVENGKVVEVGEPEIDWCPLFEKARGIKKITREAVKENMEFRIKDFGLFTKDRMLEMD-VFVGFGASEVM 82 
                                   9********************************************************************.*********** PP

                       DUF2099  82 stalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveGvkkAiekg 162
                                   +t+l ++++d++v+vcdgaGtvi++np lvqg+g+risGlveTePi+evi+rie++ggivl++++a id++ Gv kAie g
  gi|91772392|ref|YP_565084.1|  83 MTGLGRDILDTTVTVCDGAGTVITNNPVLVQGMGARISGLVETEPIDEVIDRIEKMGGIVLEPSKAIIDPIGGVLKAIELG 163
                                   ********************************************************************************* PP

                       DUF2099 163 ykkiavtvaeaedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkkallqvgksvpvfa 243
                                   +k+iavtv+++e+a+ lre+e+e++++++i+++httg+s+e+a e+v+++D++++cAsk+ir+i+k  +l+qvg++vp+fa
  gi|91772392|ref|YP_565084.1| 164 FKRIAVTVVDPETARILREIESENNLEMMIIGAHTTGLSREDALEIVKYLDIIASCASKAIRDIIK--PLAQVGTAVPLFA 242
                                   ******************************************************************..9************ PP

                       DUF2099 244 ltekGkelilerlk 257
                                   lt+kGkel+ler+k
  gi|91772392|ref|YP_565084.1| 243 LTQKGKELLLERAK 256
                                   ***********986 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-06    0.0095      61      88 ..     165     192 ..     160     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                                   TEEEEEEEETTT-SEEEEE-HHHHHHHH CS
                          FlaG  61 krvvVkviDketgevIrqiPseevldla 88 
                                   kr+ V+v+D et +++r+i se  l+++
  gi|91772392|ref|YP_565084.1| 165 KRIAVTVVDPETARILREIESENNLEMM 192
                                   799************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2241.68
//
Query:       gi|91772393|ref|YP_565085.1|  [L=433]
Description: phenylacetate-CoA ligase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.6    4.5e-28   97.4   0.6    1.6  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    4.3e-17   61.8   0.1    4.7e-16   58.4   0.1    1.9  1  AMP-binding      AMP-binding enzyme
     0.0047   16.0   0.0      0.028   13.5   0.0    2.1  3  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 !   97.4   0.6   7.6e-32   4.5e-28       1      96 []     333     430 ..     333     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 7.6e-32
                                   TEEE-HHHHHHHHHT-TTEEEEEEEEEEEET.TEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEEE-T CS
               AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtreg.elDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvelvep 79 
                                   G+nvfPsqie+vl +ie+++++++i+++r++ +lDe++v+vE++e +f+ e+k+le++++ ++ +lks+l+++++velve+
  gi|91772393|ref|YP_565085.1| 333 GINVFPSQIENVLVRIEKITDQFEIYLDRNKnKLDEITVRVELDEgAFTGEIKDLESTRRLVEGELKSVLNIRANVELVEK 413
                                   99***************************8537************78899******************************* PP

                                   T-S---------EEE-S CS
               AMP-binding_C_2  80 gtlprsegKakrviDkR 96 
                                   gt+pr++gKakrv+D+R
  gi|91772393|ref|YP_565085.1| 414 GTIPRTTGKAKRVFDRR 430
                                   ***************99 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   7.8e-20   4.7e-16     156     422 ..      80     331 ..      52     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 7.8e-20
                                   -BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-T CS
                   AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGatvvllp 235
                                   + + d++ i  +SGT GkP  V ++ + + + +  ++ + +  +l+++dv+   + +   +g   + +++   Ga  v  +
  gi|91772393|ref|YP_565085.1|  80 VPKRDVVRIHASSGTSGKPTVVGYTANDIETWANMMARNFTmVGLDANDVFQNAVNYGLFTGGLGFHYGIEQLGAMAVP-S 159
                                   55788999999***********9999998554344332222356778**********9999987888888888885555.5 PP

                                   TCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEE CS
                   AMP-binding 236 kdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegY 315
                                   ++     ++ +e++++++vt i+++P+   +l+e  ++ +      d  slr+  +g+ep s+++ +++++ f  + +++Y
  gi|91772393|ref|YP_565085.1| 160 GTGN--TARQIEMMQDFGVTAIHCTPSYGLYLAEtVREMN----IIDQLSLRVGCFGAEPWSSSTRKELEDAFNIKAYDSY 234
                                   5555..23458*********************99665555....568899***999*****************99****** PP

                                   EEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCC CS
                   AMP-binding 316 GlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegr 394
                                   Gl+E+ g  + ++++e+       G  ++  +  v+++De+ ge v++ge+Gel++             ++t+ea+     
  gi|91772393|ref|YP_565085.1| 235 GLSEMMGPGIAFECQEQ---D---GLHIWsdHYLVEVLDED-GEQVAEGEKGELVLT------------SLTKEALP-MI- 294
                                   ********985554444...3...4444324999******9.9************86............46888884.32. PP

                                   EEEEEEEEEEETTS.........EEEEEEECCCEEEE CS
                   AMP-binding 395 wlrTGDlgrldedG.........yleivgRkkdlikl 422
                                    +rTGD+ rl +             +i+gR++d++++
  gi|91772393|ref|YP_565085.1| 295 RYRTGDITRLLKSEcacgrtsnrISRILGRADDMLIV 331
                                   6999999997643333446665447899999999887 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.26   1.5e+03     244     268 ..      30      54 ..      20      76 .. 0.79
   2 ?   -1.3   0.0      0.14   8.5e+02      93     128 ..      88     123 ..      55     131 .. 0.83
   3 !   13.5   0.0   4.6e-06     0.028     255     360 ..     222     327 ..     216     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.26
                          LuxE 244 ekldkidfnrdladvlnlsiddvvd 268
                                      + + f r+ ++ l+++++d++ 
  gi|91772393|ref|YP_565085.1|  30 SAYNNVHFYREKFEALGITPEDIRS 54 
                                   5567788999999999999999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.14
                          LuxE  93 klqssatsGlkstvlldklsierllravarvmkevl 128
                                      ss+tsG ++ v      ie   + +ar    v+
  gi|91772393|ref|YP_565085.1|  88 IHASSGTSGKPTVVGYTANDIETWANMMARNFTMVG 123
                                   5689*****999999999999999988888877775 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 4.6e-06
                          LuxE 255 ladvlnlsiddvvdiygfteqvelntpdfkdelkrkrvysdviir..deetlkvvgdGkvGlleyvdalstsyPafvvltd 333
                                   l d +n++     d yg++e ++   ++  +e    ++ sd ++    +e+ + v++G  G l   + + ++ P     t 
  gi|91772393|ref|YP_565085.1| 222 LEDAFNIK---AYDSYGLSEMMGPGIAFECQEQDGLHIWSDHYLVevLDEDGEQVAEGEKGELVLTSLTKEALPMIRYRTG 299
                                   55666664...4689***********999999999*****999876645677999************************** PP

                          LuxE 334 dlGvieeslcegqkaGklv.kvlrrvkk 360
                                   d+  + +s+c ++++  ++ ++l+r++ 
  gi|91772393|ref|YP_565085.1| 300 DITRLLKSECACGRTSNRIsRILGRADD 327
                                   **************999874799**976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2820.65
//
Query:       gi|91772394|ref|YP_565086.1|  [L=312]
Description: prenyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   55.7  26.9    3.6e-14   52.7  26.0    2.2  1  UbiA           UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7  26.0     2e-18   3.6e-14       9     244 ..      42     278 ..      34     290 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 2e-18
                          UbiA   9 lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnR..PlvsGrispkealifaivllilglllla.l 86 
                                   +a+ a   + +++ + ++l+++l+  ++++++ +  +e+D+   +   R   l ++    +++li  i   i+++++ + +
  gi|91772394|ref|YP_565086.1|  42 VAIMASIIFAIPITWDFMLIIYLIFYSIYVYDYFTGAEEDKG--NYSSRseYLQKN---DEKMLIGTIYGSIVAIAFTYlI 117
                                   555556667777888889999999999999999999999999..666660033333...3344444444444444444405 PP

                          UbiA  87 llnpltallgllalllyvvYt..g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialand 164
                                   +     +l+g+ +l+l+++Y       +K++++++++++++++gl++ + + +++ ++++ a++++++vfl  ++i ++ d
  gi|91772394|ref|YP_565086.1| 118 FSDIKNMLIGFSILILGLMYHshFkSITKKFPAFKNLFVSLVWGLLIYIMFIYYGYQIDMSAMVISAFVFLRMMGIQIMFD 198
                                   66677777777777777****97357******************************************************* PP

                          UbiA 165 lrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrdakkaak 244
                                   +rd+egDr  g+ t+p+++G  +++ +l +l +v+l++l++ +++  l++++l+ +l++a+ + +  +++ +r+++++  
  gi|91772394|ref|YP_565086.1| 199 IRDMEGDRIKGLLTIPAIFGHGKSMSFLKMLNIVTLILLAFGVYMKILPIFVLMIMLVMAYSIKYKDKVLMSRNDHRCYI 278
                                   *******************88888887555666666666689***********************999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2021.06
//
Query:       gi|91772395|ref|YP_565087.1|  [L=429]
Description: hypothetical protein Mbur_0342 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   29.2   0.6      2e-06   27.5   0.6    1.9  1  Peptidase_M1  Peptidase family M1 domain
  ------ inclusion threshold ------
      0.076   12.8   1.6       0.25   11.1   0.1    2.3  2  DUF2510       Protein of unknown function (DUF2510)


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.6   2.2e-10     2e-06      70     213 ..     290     423 ..     231     428 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.2e-10
                                   HHHHHHHHHHBTTTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHH CS
                  Peptidase_M1  70 viaHElaHqWfGnlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpsei 150
                                   + +HElaH W+      ++ ++lw++EG+a++++ ++l+kl+p   ++e   l+e+ e   ++ + ++ +i +e+ +    
  gi|91772395|ref|YP_565087.1| 290 TLIHELAHYWT----ESCSFEQLWMDEGYANFYALMVLEKLDPVQATKELDRLYEIGEPEMNEGSLTDWSIPSELVS---- 362
                                   568*******8....56899***********************6665555556666555555555555556544443.... PP

                                   HHTSS.HHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHT CS
                  Peptidase_M1 151 devFd.siaYeKGasllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdise 213
                                    ++++ + +Y+K + l  +l k +  + F+++  ++++  + +n ++ +++++++   +k++++
  gi|91772395|ref|YP_565087.1| 363 GNAYQtKRNYKKAFILTYSLYKEVDIDIFKDANIEFINMGHVGNNDHISIMESIS---GKELDA 423
                                   3556537899999999999999999999999999999988888888777777776...345555 PP

>> DUF2510  Protein of unknown function (DUF2510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1     0.086   7.7e+02      12      19 ..      68      74 ..      64      75 .. 0.78
   2 ?   11.1   0.1   2.8e-05      0.25      13      28 ..     218     234 ..     212     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.086
                       DUF2510 12 gllRyWDG 19
                                  +  RyW G
  gi|91772395|ref|YP_565087.1| 68 S-TRYWQG 74
                                  4.8***98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.8e-05
                       DUF2510  13 llRyWDGa.rWTehtap 28 
                                   ++ yWDG+ +W eh+  
  gi|91772395|ref|YP_565087.1| 218 TVKYWDGEeQWAEHVMD 234
                                   589****649****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3321.94
//
Query:       gi|91772396|ref|YP_565088.1|  [L=334]
Description: hypothetical protein Mbur_0343 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2522.32
//
Query:       gi|91772397|ref|YP_565089.1|  [L=101]
Description: hypothetical protein Mbur_0344 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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 0.20s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 863.08
//
Query:       gi|91772398|ref|YP_565090.1|  [L=62]
Description: hypothetical protein Mbur_0345 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0066   16.3   0.7     0.0097   15.8   0.7    1.2  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.7   3.0      0.017   15.2   3.0    1.2  1  Zn-ribbon_8     Zinc ribbon domain
      0.024   14.3   2.5      0.065   12.9   2.5    1.7  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.058   13.5   0.1      0.073   13.1   0.1    1.1  1  ArfGap          Putative GTPase activating protein for Arf
      0.059   13.4   1.5       0.39   10.8   1.6    1.9  2  zinc_ribbon_6   Zinc-ribbon


Domain annotation for each model (and alignments):
>> 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 !   15.8   0.7   2.7e-06    0.0097       4      32 ..      25      54 ..      25      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
                Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhn.YrCrrCkg 32
                                  +++C +Cg+e ++++  ++ +  +C+ C +
  gi|91772398|ref|YP_565090.1| 25 KAKCADCGQETEVPFVPDPDRpVYCKECYQ 54
                                  589************************965 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   3.0   4.8e-06     0.017       7      34 ..      27      54 ..      24      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.8e-06
                   Zn-ribbon_8  7 rCeeCghefe.vlqsisdaplta.CPeCgs 34
                                  +C +Cg+e e ++++  d++ ++ C+eC +
  gi|91772398|ref|YP_565090.1| 27 KCADCGQETEvPFVP--DPDRPVyCKECYQ 54
                                  7*********55654..8889999****65 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.5   1.8e-05     0.065       2      23 ..      27      52 ..      27      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                  B-SSS--B---....-SSS----SSS CS
                DNA_RNApol_7kD  2 iCgeCgaevsl....kkgdpiRCkeC 23
                                  +C++Cg+e+++    ++  p+ CkeC
  gi|91772398|ref|YP_565090.1| 27 KCADCGQETEVpfvpDPDRPVYCKEC 52
                                  6*******99744445889******* PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     2e-05     0.073      12      44 ..      24      57 ..      16      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                  CCCB-TTT.-SBS--EEETTTTEEE-HHHHHHHC CS
                        ArfGap 12 enkvCaDC.gakeptWaslnlgvflCieCsgvHr 44
                                  + ++CaDC +++e+ ++      + C eC   Hr
  gi|91772398|ref|YP_565090.1| 24 HKAKCADCgQETEVPFVPDPDRPVYCKECYQSHR 57
                                  5679****777889999999999**********9 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.6   0.00011      0.39      27      43 ..      23      39 ..      17      53 .. 0.79
   2 ?    1.1   0.2      0.12   4.1e+02      30      38 ..      47      55 ..      42      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                 zinc_ribbon_6 27 kvkilCnDCekksevkf 43
                                  + k  C DC++++ev+f
  gi|91772398|ref|YP_565090.1| 23 MHKAKCADCGQETEVPF 39
                                  56778**********99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                 zinc_ribbon_6 30 ilCnDCekk 38
                                  ++C+ C ++
  gi|91772398|ref|YP_565090.1| 47 VYCKECYQS 55
                                  788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 467.89
//
Query:       gi|91772399|ref|YP_565091.1|  [L=190]
Description: flagellin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-42  144.4   7.4    4.1e-42  144.1   7.4    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.1   7.4   2.3e-46   4.1e-42       1     164 []      13     175 ..      13     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 2.3e-46
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE..EEE-SSSSSEEEEEEE--TTS CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg..dsatngtineitiyvklnaGs 79 
                                   +f+g++++Iv++A+V+VAAv+++v+++++++++qk+q++++++++q+ss++++ gdv+  + +++g++++it+y+ ++aG+
  gi|91772399|ref|YP_565091.1|  13 AFTGLEAAIVLVAFVVVAAVFSYVMLGAGFYTTQKSQEVVHTGVAQASSSVAVAGDVVakGHTSDGSVANITFYISTTAGG 93 
                                   79********************************************************555555566666*********** PP

                                   --EEGGG-EEEEEESS.--EE--E..................T-EE-TT-EEEEEEE--.....TTT---TT-EEEEEEE- CS
                Arch_flagellin  80 spidlnkttisvtddg.qetlltadefgivvisdtdgsltngdevlekgekvelevnvn.....eddgitagdevsvevvp 154
                                   sp+dl+k+++++td++ +++++++         +t++ + ++de++ekgek++++ ++      +++ ++ ++++++e++p
  gi|91772399|ref|YP_565091.1|  94 SPVDLSKSILTYTDSDnFVANCNW---------STSAIIGDSDELVEKGEKYQITAELGaggslVTTMPGVNEKIKIELKP 165
                                   ****************88888888.........6667777779*********************9999************* PP

                                   SSS--EEEEE CS
                Arch_flagellin 155 enGasttief 164
                                   ++Ga +++e+
  gi|91772399|ref|YP_565091.1| 166 PTGAVLIVER 175
                                   ****999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1422.89
//
Query:       gi|91772400|ref|YP_565092.1|  [L=186]
Description: flagellin [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-46  156.2   3.8    9.5e-46  156.0   3.8    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.027   14.0   0.0      0.041   13.4   0.0    1.3  1  DUF3153         Protein of unknown function (DUF3153)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   3.8   1.1e-49   9.5e-46       1     164 []      11     173 ..      11     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 1.1e-49
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE..EEE-SSSSSEEEEEEE--TTS CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg..dsatngtineitiyvklnaGs 79 
                                   +f+g++++Iv++A+V+VAAv+++v+++++++++qk+q++++++++q+ss+le++gdv+  ++ t +ti+++t+ v+l+aG+
  gi|91772400|ref|YP_565092.1|  11 AFTGLEAAIVLVAFVVVAAVFSYVMLGAGFYTTQKSQEVVHTGVAQASSSLEVSGDVIasGNITANTIENVTVFVQLTAGG 91 
                                   79********************************************************553334445777*********** PP

                                   --EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--E CS
                Arch_flagellin  80 spidlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGast 160
                                   spid+n+t+i++td +  +++t d+ ++ v+ ++  +  + d++lek ek+e+ ++++ +++i a+de++ e++p++Gas+
  gi|91772400|ref|YP_565092.1|  92 SPIDMNRTIITYTDLNNHASFTMDDPEMTVPAKY--GGADADNLLEKFEKFEVRIDLS-SYSISANDEFQFEIKPPEGASY 169
                                   ****************555555534444444333..3333378**************6.999******************* PP

                                   EEEE CS
                Arch_flagellin 161 tief 164
                                   t+++
  gi|91772400|ref|YP_565092.1| 170 TLQR 173
                                   9985 PP

>> DUF3153  Protein of unknown function (DUF3153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.6e-06     0.041      92     138 ..     131     177 ..     106     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-06
                       DUF3153  92 nlllgveqqlsldlDLrelsgtprldLelaLetpggarninseetae 138
                                   + ll + +++++ +DL++ s++ + ++++++++p ga+ + + ++ +
  gi|91772400|ref|YP_565092.1| 131 DNLLEKFEKFEVRIDLSSYSISANDEFQFEIKPPEGASYTLQRSAPP 177
                                   667778899***************************99877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1393.48
//
Query:       gi|91772401|ref|YP_565093.1|  [L=254]
Description: hypothetical protein Mbur_0348 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1859.00
//
Query:       gi|91772402|ref|YP_565094.1|  [L=157]
Description: hypothetical protein Mbur_0349 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   1.7    3.3e-11   43.7   1.7    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.083   13.0   2.0       0.14   12.3   2.0    1.5  1  Nuc_recep-AF1   Nuclear/hormone receptor activator site AF-1


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   1.7   3.6e-15   3.3e-11       4     161 ..       5     152 ..       2     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 3.6e-15
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--EEG CS
                Arch_flagellin   4 gigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspidl 84 
                                   ++ t I+ IA +++  +++ +++ +   l+ ++++  +e+ ++v+++++i+ +   +      n+i+++vk n Gss+i l
  gi|91772402|ref|YP_565094.1|   5 VLTTSILTIASIVAVIALINTVVPSINELSRSYSAISHEMGTEVKTDIDIIFIST-Q-E----NNISLWVK-NVGSSRIPL 78 
                                   689************************************************9988.2.2....349*****.********* PP

                                   GG-EEE.EEESS--EE--E....................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--EE CS
                Arch_flagellin  85 nkttis.vtddgqetlltad.efgivvisdtdgsltng.devlekgekvelevnvneddgitagdevsvevvpenGastt 161
                                   +   +s +++  ++++      f+  +  ++d +l ng   +++ ge+++  +++    +  ++d++++++v  nG+s++
  gi|91772402|ref|YP_565094.1|  79 SYLGMSdIFITSSSNSW--HpYFENASAPTWDYTLENGdGSTWDAGETIKTSIEL----DTLPSDTYNINFVLYNGVSGS 152
                                   *9888853333322222..24799999999999999997789************9....589**************9986 PP

>> Nuc_recep-AF1  Nuclear/hormone receptor activator site AF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.0   1.5e-05      0.14      13      89 ..       2      74 ..       1      96 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                 Nuc_recep-AF1 13 sslelhpsllesavsasrsLpspistlsspinglgspysVIssslgspslslpstpglnfgtlespqlns.lnsvsss 89
                                  ss +l +s+l  ++++  ++ + i+t+  +in l  +ys Is  +g+      +   + f +++  +++  +++v ss
  gi|91772402|ref|YP_565094.1|  2 SSEVLTTSIL--TIASIVAVIALINTVVPSINELSRSYSAISHEMGTEV---KTDIDIIFISTQENNISLwVKNVGSS 74
                                  5556666666..456666677789**********************954...57778888888888888788888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 876.74
//
Query:       gi|91772403|ref|YP_565095.1|  [L=157]
Description: flagellar protein FlaF [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-06   27.2   0.7      5e-06   26.8   0.7    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.7   2.8e-10     5e-06       7     158 ..       9     147 ..       1     150 [. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.8e-10
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--E.EGGG CS
                Arch_flagellin   7 tlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspi.dlnk 86 
                                   +  v+  m++VA +++  +    +   + +++   ++ +++++++ei ++  +s+ n    ++ + v  n+G +++ +++ 
  gi|91772403|ref|YP_565095.1|   9 AFFVITTMLVVANTLVFGMNEFIDSSFDGYSAMHTTTIDKMQTDIEIQNIWFNSTEN----HLHFMVE-NTGETKLsEFDL 84 
                                   444666899999999999999888889999999999***************965555....5******.*****6537999 PP

                                   -EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS- CS
                Arch_flagellin  87 ttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGa 158
                                    +i+v+++g  + ++    g  +  d  ++  n  ++l++ e +e+e+     +++++gd++ ++v+++nG 
  gi|91772403|ref|YP_565095.1|  85 WDIIVIKNG-TADYMG---GNRWALDVYDGQLNP-NILDPLEEMEIEIM----EEYNNGDAIILKVITPNGI 147
                                   9********.333333...555555555555555.9*************....58****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 966.05
//
Query:       gi|91772404|ref|YP_565096.1|  [L=238]
Description: flagellar accessory protein FlaH [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   87.7   0.0    8.2e-25   87.5   0.0    1.0  1  ATPase         KaiC
    3.4e-10   39.6   0.8    6.8e-07   28.7   0.1    2.1  2  PAXNEB         PAXNEB protein
    3.4e-07   29.8   0.1    7.2e-07   28.7   0.1    1.5  1  Rad51          Rad51
    0.00014   21.5   0.0    0.00026   20.6   0.0    1.4  1  AAA_25         AAA domain
    0.00043   20.0   0.2    0.00082   19.1   0.2    1.4  1  DUF835         Protein of unknown function (DUF835)
     0.0026   17.1   0.1      0.074   12.4   0.0    2.5  2  DnaB_C         DnaB-like helicase C terminal domain
     0.0041   17.2   0.3      0.077   13.1   0.0    2.2  2  Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
     0.0079   16.5   0.1      0.012   15.9   0.1    1.3  1  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.017   15.6   0.0      0.027   14.9   0.0    1.4  1  AAA            ATPase family associated with various cellular
      0.021   14.9   0.2       0.39   10.8   0.2    2.3  1  AAA_14         AAA domain
       0.04   13.4   0.0       0.14   11.6   0.0    1.8  2  RecA           recA bacterial DNA recombination protein
      0.054   13.3   0.1        1.3    8.9   0.0    2.6  3  S4_2           S4 domain
      0.069   12.6   0.0      0.094   12.2   0.0    1.2  1  Elong_Iki1     Elongator subunit Iki1


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 !   87.5   0.0   5.9e-28   8.2e-25       3     229 ..      13     233 ..      11     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 5.9e-28
                        ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegkl 83 
                                   +g +++D+ l +Gip g+ vli Ge +tGK+++++q +  g+++   +  + ++e + ++l ++++sl  d+ ++ + g l
  gi|91772404|ref|YP_565096.1|  13 SGNNEIDKKLGEGIPLGSLVLIEGENDTGKSVLCQQLVHGGLNQ-LHRMAYYSTENTIKSLLKQMESLSLDVSDFYSWGYL 92 
                                   677899*******************************9999988.89999******************************* PP

                        ATPase  84 aiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvsek 164
                                    i+ +   + +     ++e+++  ++ +ae ik+++++ + iDs+t ++++++e+ +   l +l++   + g T  ++   
  gi|91772404|ref|YP_565096.1|  93 RILPVQLAGVDW----TSEQMKGTLNLMAENIKNMREQVIFIDSLTMFTTYSDEDSILGFLTKLKNLC-DQGHTIFITLH- 167
                                   ***999999884....58999999999*********************999999999999***99866.55677666666. PP

                        ATPase 165 ssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskke.hpfeIte.egikvlee 229
                                   ++  ++ +  ++   ++d+ + L++++ +++   ++e+ k+Rg+k+++   + fe+++  g k+++ 
  gi|91772404|ref|YP_565096.1| 168 QHAFKEDTLVRIRS-ACDCHLFLRKEQLSDRYISVMEVAKIRGAKIRTGNiVSFEVQPgYGLKIIPI 233
                                   45557777889999.*******************************9965167*****99***9985 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1     5e-10   6.8e-07      14      85 ..       6      76 ..       3      85 .. 0.87
   2 !    9.7   0.1   0.00031      0.42     212     281 ..     129     189 ..     102     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5e-10
                        PAXNEB 14 dgqlltStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlreL 85
                                  d + + S+G++++Dk Lg G+plGs++lie + +++ ++vL++  +  G+ q h++ + s +++ +++l+++
  gi|91772404|ref|YP_565096.1|  6 DKKNILSSGNNEIDKKLGEGIPLGSLVLIEGE-NDTGKSVLCQQLVHGGLNQLHRMAYYSTENTIKSLLKQM 76
                                  567799***********99**********976.556699******************999988888877765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00031
                        PAXNEB 212 vipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieL 281
                                    i sL   +        s++ ++l FL++L+ l  +   +++itl  + +  ++  + +i++ +D+ + L
  gi|91772404|ref|YP_565096.1| 129 FIDSLTMFTT------YSDEDSILGFLTKLKNLCDQG-HTIFITLHQHAF--KEDTLVRIRSACDCHLFL 189
                                   5555555555......467899**********99765.588*********..666677899999987765 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   5.2e-10   7.2e-07      19     155 ..      11     145 ..       3     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.2e-10
                                   E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--S..SEEEEEESSS---G..GGGHHHH... CS
                         Rad51  19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGge..gkavyidtegtfrp..erlveia... 92 
                                   l+ G++++D+ Lg Gi+ gs+  i Ge+ +Gk+ lc++l          gG +   +++y +te t+++  +++ ++    
  gi|91772404|ref|YP_565096.1|  11 LSSGNNEIDKKLGEGIPLGSLVLIEGENDTGKSVLCQQLV--------HGGLNqlHRMAYYSTENTIKSllKQMESLSldv 83 
                                   789**********************************985........3444411578999*****987445565555555 PP

                                   .HHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------T CS
                         Rad51  93 .erykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgel 155
                                    + y+    ++l        +t+e+ +  l+ +a+ +++ + +++ +Ds+t    t +s+ + +
  gi|91772404|ref|YP_565096.1|  84 sDFYSWGYLRILPVQLAGVDWTSEQMKGTLNLMAENIKNMREQVIFIDSLTMF--TTYSDEDSI 145
                                   47778888888887777778999999999999999999999999999998753..456666554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.9e-07   0.00026      25     188 ..      22     168 ..       6     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                        AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllv 105
                                   l +g+ p+g+l+l+ G  +tGK++l+ +l++  +              +  y+s+E++ + l + ++ +  +++d   +  
  gi|91772404|ref|YP_565096.1|  22 LGEGI-PLGSLVLIEGENDTGKSVLCQQLVHGGLNQL----------HRMAYYSTENTIKSLLKQMESLSLDVSDFYSWGY 91 
                                   55565.***********************99988644..........3899*******************99943333333 PP

                        AAA_25 106 ldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllv 186
                                   l +    +++L+  d  +++ ++ ++ +++ i+ + + +++ iD+l+ ++  + +  + +  ++++l++++++ + +++ +
  gi|91772404|ref|YP_565096.1|  92 LRI---LPVQLAGVDWTSEQMKGTLNLMAENIKNM-REQVIFIDSLTMFTTYSDE--DSILGFLTKLKNLCDQGHTIFITL 166
                                   333...24456666666666778888899999995.589********99887544..467899999999999999888877 PP

                        AAA_25 187 hH 188
                                   h+
  gi|91772404|ref|YP_565096.1| 167 HQ 168
                                   75 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2     6e-07   0.00082      68     132 ..     116     179 ..     106     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6e-07
                        DUF835  68 ivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalL 132
                                   + +++k+  ++v++iD+l + +++++ +s+l fl++lk  +  ++ t+ +++ ++a++e  l  +
  gi|91772404|ref|YP_565096.1| 116 MAENIKNMREQVIFIDSLTMFTTYSDEDSILGFLTKLKN-LCDQGHTIFITLHQHAFKEDTLVRI 179
                                   55677777888***************************6.6899999999*******99876655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   5.4e-05     0.074       2      75 ..      11      84 ..      11     169 .. 0.74
   2 ?    2.2   0.0     0.066        92      58      87 ..     189     220 ..     157     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                                  BXSSTHHHH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXX CS
                                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  2 lstgfkdLD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeid 75
                                  ls+g +++D kl +G+  g l++i +   +Gk++l+ ++++   + + +++a++s e + ++l++++ s   +++
  gi|91772404|ref|YP_565096.1| 11 LSSGNNEIDkKLGEGIPLGSLVLIEGENDTGKSVLCQQLVHGGLN-QLHRMAYYSTENTIKSLLKQMESLSLDVS 84
                                  57888999944557**************************98775.5568**************99987666654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.066
                                   SXHHHHHHHHHH..HHHTXXHHHHHHTTSXHH CS
                                   xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                        DnaB_C  58 msaeqlvqRlls..seaeidskklrtgklkee 87 
                                     +eql +R +s  + a+i+  k+rtg++ + 
  gi|91772404|ref|YP_565096.1| 189 LRKEQLSDRYISvmEVAKIRGAKIRTGNIVSF 220
                                   57899999999844567999999999998665 PP

>> Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.15     2e+02      23      51 ..      62      93 ..      44     102 .. 0.69
   2 !   13.1   0.0   5.6e-05     0.077       6      59 ..     119     173 ..     115     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
                 Mad3_BUB1_I_2 23 lYkktkd.lkilfLmkl..KkIskfyyfvYle 51
                                  +Y +++    +l  m     ++s+fy++ Yl 
  gi|91772404|ref|YP_565096.1| 62 YYSTENTiKSLLKQMESlsLDVSDFYSWGYLR 93
                                  444444434466667641146899****9986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.6e-05
                 Mad3_BUB1_I_2   6 dipyfrnnpsyiekwkelYkktkdlkil.fLmklKkIskfyyfvYlelsryFlkk 59 
                                   +i+ +r++  +i+ ++ +  ++++  il fL klK++ +  + +++ l+++  k 
  gi|91772404|ref|YP_565096.1| 119 NIKNMREQVIFIDSLTMFTTYSDEDSILgFLTKLKNLCDQGHTIFITLHQHAFKE 173
                                   7899***********99977666666666**********************7665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   8.7e-06     0.012       6     125 ..      30     163 ..      28     173 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.7e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.............erpevvfvtlpsst.sskdllre.llralglelka. 70 
                                   +++++ Ge  tGK++l+++l++   ++  +++             +       ++ s++ + +d++++  lr+l ++l + 
  gi|91772404|ref|YP_565096.1|  30 SLVLIEGENDTGKSVLCQQLVHGGLNQ-LHRMayystentiksllK-------QMESLSlDVSDFYSWgYLRILPVQLAGv 102
                                   578999***************997554.444458866633333333.......4444445666664433556666666556 PP

                        AAA_22  71 ..erlsseellealeqalraravielliiDEaqhlr..s.....eealeeLrsllnlsrkgvql 125
                                        + +  l+++++++++ +  +++ iD    ++  s        l++L++l +  + ++ +
  gi|91772404|ref|YP_565096.1| 103 dwTSEQMKGTLNLMAENIKNMRE-QVIFIDSLTMFTtySdedsiLGFLTKLKNLCD--QGHTIF 163
                                   66668888999************.******99999777356556667777777777..554444 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 ?   14.9   0.0     2e-05     0.027       1     120 [.      32     178 ..      32     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                                   EEEESSTTSSHHHHHHHHHHH................HTHEEEEEETTTCSSS............................ CS
                           AAA   1 vllyGppGtGKTllakavake................lgvefleisgsellsk............................ 37 
                                   vl+ G   tGK+ l++++++                 +         ++ll k                            
  gi|91772404|ref|YP_565096.1|  32 VLIEGENDTGKSVLCQQLVHGglnqlhrmayystentI---------KSLL-Kqmeslsldvsdfyswgylrilpvqlagv 102
                                   68999*************99965554443322222220.........2222.12334444444455568999999999988 PP

                                   .STTHHHH.HHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                           AAA  38 .yvgesek.kirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkld 116
                                    + +e++k  ++ + +++k+++   ++fiD +  +++ +       +e+ +  +lt+l+++ ++ + +i+i+  ++  k d
  gi|91772404|ref|YP_565096.1| 103 dWTSEQMKgTLNLMAENIKNMR-EQVIFIDSLTMFTTYS-------DEDSILGFLTKLKNLCDQGH-TIFITLHQHAFKED 174
                                   8555555505555556688887.8*******99887777.......66667777777777777544.77776666655555 PP

                                   HHHH CS
                           AAA 117 pall 120
                                     ++
  gi|91772404|ref|YP_565096.1| 175 TLVR 178
                                   5555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00028      0.39       4      43 ..      31      70 ..      29     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                  +++i+G   +GK++l++ql++  l +  ++ y++ ++  +
  gi|91772404|ref|YP_565096.1| 31 LVLIEGENDTGKSVLCQQLVHGGLNQLHRMAYYSTENTIK 70
                                  68999***************99996777777777777544 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.14      32      94 ..       9      70 ..       2      87 .. 0.81
   2 ?   -1.0   0.0      0.72   9.9e+02     165     190 ..     109     134 ..     101     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                  -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS---- CS
                          RecA 32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehald 94
                                  + +ssG+  +d  lG  G+p G ++ i G + +Gk+ l+ +++    ++   +a+  +e ++ 
  gi|91772404|ref|YP_565096.1|  9 NILSSGNNEIDKKLG-EGIPLGSLVLIEGENDTGKSVLCQQLVHGGLNQLHRMAYYSTENTIK 70
                                  679************.79********************9999887777777777777766665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.72
                                   HHHHHHHHHHHHTTT--EEEEEEE-- CS
                          RecA 165 msqalrkltgaisksntvvifinqir 190
                                   m  +l  ++ +i++++  vifi+ + 
  gi|91772404|ref|YP_565096.1| 109 MKGTLNLMAENIKNMREQVIFIDSLT 134
                                   56667778888999999999998765 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.2   7.2e+03      34      44 ..      31      41 ..      23      43 .. 0.68
   2 ?    1.1   0.0      0.25   3.4e+02      10      26 ..     146     162 ..     140     175 .. 0.78
   3 ?    8.9   0.0   0.00095       1.3      40      59 ..     203     222 ..     191     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.2
                          S4_2 34 eVkvNGevetr 44
                                   V++ Ge +t 
  gi|91772404|ref|YP_565096.1| 31 LVLIEGENDTG 41
                                  57777777765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                          S4_2  10 LgqlLKlaglvesGgea 26 
                                   Lg l Kl +l+++G+  
  gi|91772404|ref|YP_565096.1| 146 LGFLTKLKNLCDQGHTI 162
                                   6667899******9876 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00095
                          S4_2  40 evetrRgkKlraGdvVeidg 59 
                                   ev + Rg+K+r G +V+++ 
  gi|91772404|ref|YP_565096.1| 203 EVAKIRGAKIRTGNIVSFEV 222
                                   67889************975 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.8e-05     0.094      81     135 ..     119     170 ..      96     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-05
                    Elong_Iki1  81 alspkssekk..kkalviiDslnplaslikeeslaaflssllssp..svslvavYHtdv 135
                                   ++       k  ++++++iDsl++  ++ +e+s+  fl++l +      ++  ++H+  
  gi|91772404|ref|YP_565096.1| 119 NI-------KnmREQVIFIDSLTMFTTYSDEDSILGFLTKLKNLCdqGHTIFITLHQHA 170
                                   22.......123789********998999********9998752244889999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1357.93
//
Query:       gi|91772405|ref|YP_565097.1|  [L=610]
Description: type II secretion system protein E [Methanococcoides burtonii DSM 6242]
Scores for complete 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-43  146.6   0.0    9.9e-43  146.2   0.0    1.1  1  T2SSE     Type II/IV secretion system protein
     0.0097   16.4   0.0      0.025   15.1   0.0    1.6  1  ABC_tran  ABC transporter
  ------ inclusion threshold ------
      0.013   15.2   0.1       0.03   14.1   0.1    1.6  1  AAA_29    P-loop containing region of AAA domain
      0.067   13.5   0.0       0.16   12.3   0.0    1.6  1  AAA_22    AAA domain
      0.072   13.6   0.2       0.22   12.0   0.2    1.8  1  AAA_23    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 !  146.2   0.0   2.8e-46   9.9e-43       5     259 ..     225     490 ..     221     500 .. 0.91

  Alignments for each domain:
  == domain 1  score: 146.2 bits;  conditional E-value: 2.8e-46
                         T2SSE   5 leallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvll 85 
                                   l +++ d+++ di  +  ++++++ +v +   + +e+ +++ l+ +i ++a   ++ i  + p++da+lp +g r+++v  
  gi|91772405|ref|YP_565097.1| 225 LAPYICDSNIEDITCNGLGSIFLEHKVFDGLRSVLEFTDNDVLNHFIIKLAERIGKPITFKDPIVDATLP-DGSRINIVYG 304
                                   56677899************999998877577778889999*****************************.******9987 PP

                         T2SSE  86 Pvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvE 164
                                     v +   +++iRk +   +++ +++ +++++ k+a+ +   ++e ++  + G T sGKtt+l+al ++i  +  ++v +E
  gi|91772405|ref|YP_565097.1| 305 TDVSKngSNFTIRKFNDIPFSILQVIDRGTMDYKVAAYIWILLSEGMSGFICGETASGKTTSLNALTTFISPD-AKLVSIE 384
                                   766665799*************************************************************999.******* PP

                         T2SSE 165 DpvEiqleganqvqlnak............kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHa 233
                                   D+ E+q+ ++n ++ +++              +vt+ dll+a LR+rP  i+vGEiR+ e   + +A++TGH++ +sT Ha
  gi|91772405|ref|YP_565097.1| 385 DTPELQIPHKNWTREVTRgstrgggvgegtGSDVTMFDLLKAGLRQRPNYILVGEIRGVEGNVAFQAMQTGHPV-VSTFHA 464
                                   **************99999********999999*****************************************.****** PP

                         T2SSE 234 nsaagalerLeqlgaeveaaelkssi 259
                                    s+ + ++r+      ++++ + +  
  gi|91772405|ref|YP_565097.1| 465 ASVEKLIQRITAEPISIPKTYVDNLN 490
                                   *********98765556666665554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.9e-06     0.025       9      61 ..     348     400 ..     344     405 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.9e-06
                                   ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkei 61 
                                   +eg    i Ge+ +GK+t l++l+   +p++  + +++++  +++++ + +e+
  gi|91772405|ref|YP_565097.1| 348 SEGMSGFICGETASGKTTSLNALTTFISPDAKLVSIEDTPELQIPHKNWTREV 400
                                   67777789*****************************9998888888877766 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 ?   14.1   0.1   8.4e-06      0.03      21      51 ..     348     379 ..     325     382 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-06
                        AAA_29  21 lkg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                                    +g + ++ G++ sGK+T l A+++ + p+ k
  gi|91772405|ref|YP_565097.1| 348 SEGmSGFICGETASGKTTSLNALTTFISPDAK 379
                                   4567889*******************999875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05      0.16       6      29 ..     351     374 ..     347     399 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                        AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                    +++++Ge+ +GKTt+l+ l+   
  gi|91772405|ref|YP_565097.1| 351 MSGFICGETASGKTTSLNALTTFI 374
                                   6899**************998765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   6.1e-05      0.22      24      41 ..     355     372 ..     347     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                        AAA_23  24 ItGpNGaGKTTildAikl 41 
                                   I+G++ +GKTT l+A++ 
  gi|91772405|ref|YP_565097.1| 355 ICGETASGKTTSLNALTT 372
                                   9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.36s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 3259.71
//
Query:       gi|91772406|ref|YP_565098.1|  [L=539]
Description: flagellar assembly protein J [Methanococcoides burtonii DSM 6242]
Scores for complete 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-13   48.8   2.7    8.6e-06   25.7   0.2    3.4  4  T2SSF         Type II secretion system (T2SS), protein F
      0.004   17.3   0.3         15    5.6   0.1    3.4  3  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.53   4.8e+03      36      64 ..       7      38 ..       6      40 .. 0.65
   2 !   21.4   0.0     2e-08   0.00018       2     124 ..      47     173 ..      46     174 .. 0.93
   3 !   25.7   0.2   9.6e-10   8.6e-06       1     120 [.     300     425 ..     300     431 .. 0.80
   4 ?   -6.9   3.7         2   1.8e+04     112     124 ..     509     521 ..     500     522 .. 0.45

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.53
                                  HHHHHHHHTTS...SHHHHHCT-TT.TS.-HHH CS
                         T2SSF 36 kriarrlraGg...slsealertpssef.pelv 64
                                  k+i +r+++G    sls+ ++r   + f ++l+
  gi|91772406|ref|YP_565098.1|  7 KNIFKRIDEGNssnSLSKMWSRKV-ENFkKDLY 38
                                  678889999986666667776654.47756555 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2e-08
                                   HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHH.HHHC....T-TT.TS-HHHHHHHHHHHHHT-H CS
                         T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgsls.eale....rtpssefpelvvqlirageeggnL 77 
                                   l+++a+ + a v+ +++++ ++e + +      +k++++  + ++    +a e    + ++ +++el+ ++++++ +g + 
  gi|91772406|ref|YP_565098.1|  47 LTYMASISTANVSRDKIFTNISEKT-EYCPHTYFKKVKDLAQDWHYDYaQACElvsvKIKNAKLHELFNRFSNSIASGEPD 126
                                   689**********************.*******************775155559999666679****************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                    e+L++ ++ +   r+ + ++ ++++  +  +++allv+  l++i++
  gi|91772406|ref|YP_565098.1| 127 VEFLKKEWKLFKTIRKDEFERNLETTKEWSNAYTALLVSTSLVSIIV 173
                                   ********************************************998 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 9.6e-10
                                   HHHHHHHHHH.TT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT CS
                         T2SSF   1 flrqlatlls.aGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageegg 75 
                                   f+r+l++ +s +G++l +aL  +      g+l+e+  ++ r+l  G++ +  +      ++ s + +++ + ++ ++  gg
  gi|91772406|ref|YP_565098.1| 300 FIRSLGSIVSgSGLTLPKALMKIDPKN-LGELREITIELHRKLTIGMDSKLCWNqfveDSG-SYLiHKFTSVFVDSINLGG 378
                                   89999999999****************.*******************99999997775444.4555*************** PP

                                   -HHHHHHHHHHHHHHHHHHH..HHHHHHHHTTXXXXXXXXXXXXXXX CS
                         T2SSF  76 nLaevLerlaeyleeerelr..rkllaallepllllvvallvllill 120
                                   + ++v e +++   e   lr  r++ +a++  l++ + +++v+l+l+
  gi|91772406|ref|YP_565098.1| 379 DAEAVGELVSSSNLELVLLRmkRERISASFTFLVVPLHLAMVALLLF 425
                                   ***************99888435555555544444333333333333 PP

  == domain 4  score: -6.9 bits;  conditional E-value: 2
                                   XXXXXXXXXXXXX CS
                         T2SSF 112 allvllillaill 124
                                   ++++++ +++ ++
  gi|91772406|ref|YP_565098.1| 509 IFFIFSGIMMLIV 521
                                   3444444444444 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1    0.0017        15      66     106 ..       6      43 ..       2      55 .. 0.81
   2 ?    2.7   0.0     0.013   1.2e+02      52     169 ..      61     174 ..      41     175 .. 0.59
   3 !    5.4   0.0    0.0019        17       1      96 [.     265     358 ..     265     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHH CS
                  Spore_III_AB  66 lseffeevaerleekegesfeeaweeavekllkklaLkked 106
                                   l+++f+++ e    ++ +s++++w+++ve+ +k+l+++++ 
  gi|91772406|ref|YP_565098.1|   6 LKNIFKRIDEG---NSSNSLSKMWSRKVENFKKDLYISNDM 43 
                                   55666666666...8*******************9998765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.013
                                   HHHHHHHHHCS-TTHHHHHHHHHHHHH..S.TSS-HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHH..T--SHHHHHHH CS
                  Spore_III_AB  52 pealeklaeksesplseffeevaerlee.k.egesfeeaweeavekllkklaLkkedkeilkelgesl..gysdregqlka 128
                                    +++ +++ek+e+    +f++v +  ++ + +  ++ e+ + ++++        ++  e++ ++ +s+  g+ d+e  +k 
  gi|91772406|ref|YP_565098.1|  61 DKIFTNISEKTEYCPHTYFKKVKDLAQDwHyDYAQACELVSVKIKN--------AKLHELFNRFSNSIasGEPDVEFLKKE 133
                                   5688888888888777777777665444323444444444444444........344556666666553355566666666 PP

                                   HHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                  Spore_III_AB 129 lelaleeleeeieeareeakkkeklyrtlGvlaGlflvilL 169
                                    +l++   ++e e+  e  k+ +  y++l v   l+ +i+L
  gi|91772406|ref|YP_565098.1| 134 WKLFKTIRKDEFERNLETTKEWSNAYTALLVSTSLVSIIVL 174
                                   66666666666666666666666666666666666666666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0019
                                   XXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.ST CS
                  Spore_III_AB   1 KligallillactgiGfalakrlkrrlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerleeke 81 
                                   K +g++l  l++  +G+a+ ++  +  k+ e +  +++ l + ++ +  +Lp+al k+  k  ++l+e+  e+ ++l    
  gi|91772406|ref|YP_565098.1| 265 KGFGMILAGLIMLPVGLAARTDVIKVNKRDESYTTFIRSLGSIVSGSGLTLPKALMKIDPKNLGELREITIELHRKLT--I 343
                                   56788888888899999999999*******************9999***********************999999987..7 PP

                                   SS-HHHHHHHHHHHH CS
                  Spore_III_AB  82 gesfeeaweeavekl 96 
                                   g++ + +w++ ve +
  gi|91772406|ref|YP_565098.1| 344 GMDSKLCWNQFVEDS 358
                                   888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.36s 00:00:01.14 Elapsed: 00:00:00.54
# Mc/sec: 3013.00
//
Query:       gi|91772407|ref|YP_565099.1|  [L=314]
Description: hypothetical protein Mbur_0354 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.4   0.2       0.19   11.6   0.1    1.9  2  NuA4      Histone acetyltransferase subunit NuA4


Domain annotation for each model (and alignments):
>> NuA4  Histone acetyltransferase subunit NuA4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.1e-05      0.19      40      76 ..      26      61 ..      23      64 .. 0.86
   2 ?   -1.4   0.0      0.12   2.2e+03      39      50 ..      65      80 ..      61     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                          NuA4 40 iikGFdnylkssssssaaerrkrkvtdedriFSlSSv 76
                                  i  G+d+y + +++++ ++  +  v+ ++r FSlSS+
  gi|91772407|ref|YP_565099.1| 26 IAVGYDKYKE-GGATDPNTSISNPVSGSERQFSLSSL 61
                                  677*******.7777777777999************7 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.12
                          NuA4 39 NiikGFdnylk....s 50
                                  Ni+ G d+ +k     
  gi|91772407|ref|YP_565099.1| 65 NILVGLDKKIKklikR 80
                                  9999999999944321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1974.17
//
Query:       gi|91772408|ref|YP_565100.1|  [L=53]
Description: hypothetical protein Mbur_0355 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 404.76
//
Query:       gi|91772409|ref|YP_565101.1|  [L=652]
Description: chemotaxis sensory transducer [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-41  140.9  44.5    1.6e-39  135.5  17.0    4.3  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    2.7e-18   66.0   0.0    1.5e-17   63.6   0.0    2.4  1  PAS_3            PAS fold
    2.9e-11   43.6   0.0    5.8e-06   26.5   0.0    2.7  2  PAS_4            PAS fold
    2.7e-10   40.4   2.0    0.00057   20.1   0.0    3.5  3  PAS_9            PAS domain
    2.4e-08   34.1  34.2    2.5e-05   24.5   2.1    7.2  7  DUF948           Bacterial protein of unknown function (DUF94
    1.1e-05   25.4   0.0       0.11   12.5   0.0    2.7  2  PAS              PAS fold
     0.0028   16.8   3.2     0.0028   16.8   3.2    2.8  2  FH2              Formin Homology 2 Domain
  ------ inclusion threshold ------
      0.013   15.3  21.8       0.84    9.5   0.1    6.4  6  DASH_Duo1        DASH complex subunit Duo1
      0.017   15.1  34.1      0.045   13.8   2.7    5.7  5  Laminin_II       Laminin Domain II
      0.067   13.8   0.6       0.92   10.1   0.0    3.1  3  PAS_10           PAS domain
       0.14   12.6   0.9         68    4.0   0.0    4.1  4  HAMP             HAMP domain
       0.22   11.0  14.4        1.8    7.9   3.0    3.3  3  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.22   11.6  25.0        2.2    8.4   1.0    5.3  5  DUF1664          Protein of unknown function (DUF1664)
        0.3   11.2  12.0       0.14   12.3   0.7    3.4  3  Cob_adeno_trans  Cobalamin adenosyltransferase
       0.58   10.3  23.0        0.7   10.1   2.6    5.0  5  Fib_alpha        Fibrinogen alpha/beta chain family
       0.59   10.2   5.1        5.8    7.0   0.4    3.3  3  AAA_14           AAA domain
        1.2    9.0  16.9        1.1    9.1   1.5    4.9  5  Sec34            Sec34-like family
        2.5    8.4   7.3          5    7.5   0.6    4.1  4  Rx_N             Rx N-terminal domain
        2.6    8.6  24.3        2.3    8.7   1.5    6.1  6  NPV_P10          Nucleopolyhedrovirus P10 protein
        3.7    7.9  33.2       0.32   11.3   0.6    5.5  6  BLOC1_2          Biogenesis of lysosome-related organelles co


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   3.8   2.9e-05     0.026     113     168 ..     331     386 ..     313     404 .. 0.57
   2 !    8.1   0.7    0.0025       2.2      84     153 ..     390     462 ..     385     463 .. 0.61
   3 !  135.5  17.0   1.8e-42   1.6e-39       5     170 ..     429     598 ..     422     599 .. 0.89
   4 !   16.6   7.7   5.9e-06    0.0053     100     171 ..     563     634 ..     560     635 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                                   HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 113 rqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                   +  ve+  ++v+ t ++++   ++v++ ++ v+++++  e++s+++e+++++ e++
  gi|91772409|ref|YP_565101.1| 331 NGFVENLNKIVQATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIATGSENL 386
                                   44455555555555555555555555555555555555555555555555554443 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHHH...............HHHHH..HHHHHH.HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  84 saqaakeiealiieiqkei.ndsvesleetrq..rveegs.elveetgealkeiveavaevadlvqeiaaasee 153
                                   +  aa +++a   +i ke  + +++s + + q  +++ gs +l++++ ++l+ i ++++++a +v+ +  a+++
  gi|91772409|ref|YP_565101.1| 390 ANTAALDVKASE-QIFKELsEAATKSASFSAQavEMSDGSqKLANSALKDLEVIMNEIEQLAGIVTSLDGAVDN 462
                                   555555555433.34443313333333333330044455515688999*******************9999886 PP

  == domain 3  score: 135.5 bits;  conditional E-value: 1.8e-42
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHH CS
                     MCPsignal   5 eeaseeAeeggkevanvvkqmeeieks....skeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLA 81 
                                   ++  ++A ++ +++ n ++q+  i +s    +++i ++++ i++iadQTNlLALNAaiEAARAGe+GrGFaVVAdEVrkLA
  gi|91772409|ref|YP_565101.1| 429 QKLANSALKDLEVIMNEIEQLAGIVTSldgaVDNIDKVTDKIKSIADQTNLLALNAAIEAARAGEHGRGFAVVADEVRKLA 509
                                   4444555555555555555555555557777************************************************** PP

                                   HHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  82 ersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevn 162
                                   e+s  ++ ei+ +++++qke+++++e++e ++++v +g + +  +  +  ei+ +v+++++++  +++ +ee  + ie++n
  gi|91772409|ref|YP_565101.1| 510 EESRSSTAEINGIVVNVQKETKKVTEAIERAKEQVISGNKDIGGALGKSGEITGMVDKINSMLGSLNKKAEEGMEKIESIN 590
                                   ********************************************************************************* PP

                                   HHHHHHHH CS
                     MCPsignal 163 qaveevak 170
                                   +++ eva+
  gi|91772409|ref|YP_565101.1| 591 ENIGEVAS 598
                                   ***99875 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 5.9e-06
                                   ..........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 100 keindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevakv 171
                                     +++  ++l + ++++eeg+e++e+ +e++ e++++++e a+  +e +aa eeq+a++e+v+ ++++v+++
  gi|91772409|ref|YP_565101.1| 563 GMVDKINSMLGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAASEQVSGSIKNVNDL 634
                                   45566677888999*****************************************************99976 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   1.7e-20   1.5e-17       3      88 ..      52     137 ..      50     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.7e-20
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpv 83 
                                   y+s++v++++G+ + ++lgk+ +w d+v peD +++ +a++ a+k+++py++ yRi++k+G+++++++ ++ ++d++g+  
  gi|91772409|ref|YP_565101.1|  52 YISKNVYDLTGHPKTDFLGKKLTWSDVVFPEDVPKIDAAIDIAMKNNAPYKVNYRIKTKNGDTVYIREEGKLVNDDEGNAA 132
                                   89*****************************************************************************99 PP

                         PAS_3  84 rvigv 88 
                                   ++ gv
  gi|91772409|ref|YP_565101.1| 133 YLDGV 137
                                   99887 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.2e-05     0.037       2     107 ..      33     143 ..      32     145 .. 0.90
   2 !   26.5   0.0   6.5e-09   5.8e-06       5     107 ..     162     277 ..     156     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                         PAS_4   2 dslpdalavl..dpdgrvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll.pge 77 
                                   d+lp+ ++ +  ++   + y++++  +l g+p  ++lGk+l   +++ +ed + +++a++ +++ ++p++     ++ +g+
  gi|91772409|ref|YP_565101.1|  33 DNLPVTIFRCdiNASWDIYYISKNVYDLTGHPKTDFLGKKLTwsDVVFPEDVPKIDAAIDIAMKNNAPYKVNYRIKTkNGD 113
                                   7899999999778888999********************99998977778***************************9*** PP

                         PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTe 107
                                   ++++  +   + d++G +  + +++  iTe
  gi|91772409|ref|YP_565101.1| 114 TVYIREEGKLVNDDEGNAAYLDGVFLNITE 143
                                   999999999999999998888888888887 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 6.5e-09
                         PAS_4   5 pdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpee.........daarleralrrvlegeepiefleelll. 74 
                                   p++ +++dp+g+v ++N  + +     ++e+++G+++ e+  +            ++ +++++ vl+++e++e+le     
  gi|91772409|ref|YP_565101.1| 162 PALAIFVDPEGKVKHINDYYVKlSQFQSDEDVIGRSPSEIIGKTtlvgdnsnmKLGASQTIVESVLDTRESVESLEAIIKl 242
                                   5667777************999778888999999999998888888888888889999****************9988888 PP

                         PAS_4  75 .pgeerhyelrl.lPlrdesGevigvlvisrDiTe 107
                                    + +++ y ++  +P++de+G   g+l++++D+T+
  gi|91772409|ref|YP_565101.1| 243 hGLDHELYTISSaSPIFDEEGVFEGILEVLTDLTD 277
                                   8888888887777*********************7 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.4e-06     0.003      13     104 .]      50     143 ..      37     143 .. 0.85
   2 !   20.1   0.0   6.4e-07   0.00057       3     104 .]     165     277 ..     162     277 .. 0.70
   3 ?   -1.5   0.1       3.4     3e+03      13      58 ..     571     618 ..     561     637 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                         PAS_9  13 ilyaNeaalrllGyspeevlgks..itdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkddd 89 
                                   i y+++ + +l+G  + ++lgk+  ++d++  ++ p+ +  ++ a+++    ++ v++ + +kng t++++     v dd+
  gi|91772409|ref|YP_565101.1|  50 IYYISKNVYDLTGHPKTDFLGKKltWSDVVfpEDVPKIDAAIDIAMKNNA--PYKVNYRIKTKNGDTVYIREEGKLVNDDE 128
                                   679********************555555577777777777777777777..*************************9999 PP

                         PAS_9  90 gelvgiivilrDite 104
                                   g+   + +++ +ite
  gi|91772409|ref|YP_565101.1| 129 GNAAYLDGVFLNITE 143
                                   998887799998887 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.4e-07
                         PAS_9   3 gilidnpdgrilyaNeaalrllG.yspeevlgksitdlf...........vtdpeanerlraaleqgrkkerevevvlirk 71 
                                   +i+ ++p+g++ ++N+   +l + +s e+v+g+s ++++            +   ++  ++ +l++ + ++++ e ++   
  gi|91772409|ref|YP_565101.1| 165 AIF-VDPEGKVKHINDYYVKLSQfQSDEDVIGRSPSEIIgkttlvgdnsnMKLGASQTIVESVLDTRE-SVESLEAIIKLH 243
                                   455.56***888*********99556999**********88776666665444444444444444444.344444333333 PP

                         PAS_9  72 ng.etfwvlltaspvkdddgelvgiivilrDite 104
                                       ++++  +asp++d++g + gi+ +l+D+t+
  gi|91772409|ref|YP_565101.1| 244 GLdHELYTISSASPIFDEEGVFEGILEVLTDLTD 277
                                   332455566899********************96 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.4
                         PAS_9  13 il.yaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgr 58 
                                   +l + N++a++   + + e ++ +i ++    ++++ + e+ +aa+e+ +
  gi|91772409|ref|YP_565101.1| 571 MLgSLNKKAEEG--MEKIESINENIGEVAstaEENAANSEETSAAIEEQT 618
                                   566778888887..778888999998888666444444444444444444 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 ?    2.1   0.1      0.27   2.4e+02      49      88 ..     198     237 ..     175     238 .. 0.79
   2 ?    0.6   0.1      0.76   6.9e+02      42      61 ..     278     297 ..     262     320 .. 0.66
   3 !   24.5   2.1   2.8e-08   2.5e-05      25      85 ..     324     387 ..     310     391 .. 0.82
   4 ?    6.0   0.8     0.016        14      34      84 ..     431     477 ..     402     486 .. 0.66
   5 !    8.1   0.7    0.0036       3.2      36      78 ..     499     541 ..     479     546 .. 0.83
   6 !    7.2   0.1    0.0069       6.2      47      83 ..     559     599 ..     548     604 .. 0.71
   7 !    8.7   3.2    0.0022         2      23      88 ..     567     632 ..     561     644 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.27
                        DUF948  49 vedllakvnelledvneklekvdplteavadlgesvseln 88 
                                     +++ k+  + ++ n kl + ++++e+v d+ esv++l+
  gi|91772409|ref|YP_565101.1| 198 PSEIIGKTTLVGDNSNMKLGASQTIVESVLDTRESVESLE 237
                                   45666777777777788*******************9996 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.76
                        DUF948  42 vdpilkevedllakvnelle 61 
                                   +++  kev++ll+ +n+ l+
  gi|91772409|ref|YP_565101.1| 278 IKQKEKEVNELLDYTNDCLS 297
                                   44444566666666665443 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 2.8e-08
                        DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvne...klekvdplteavadlgesvs 85 
                                   +kt+de++ ++e+l+k v++++++++++l++v++ +e vn+    +e++ +  e++a+ +e++s
  gi|91772409|ref|YP_565101.1| 324 GKTFDEFNGFVENLNKIVQATMRDMNATLDEVKQSTEAVNQmntGMEQISTAAEQIATGSENLS 387
                                   89********************************999888855566666666666666666665 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.016
                        DUF948  34 tieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                     ++  k+++ i++e+e+l   v      + + ++++d++t++++ ++++ 
  gi|91772409|ref|YP_565101.1| 431 LANSALKDLEVIMNEIEQLAGIVTS----LDGAVDNIDKVTDKIKSIADQT 477
                                   4444445666666666666655555....5567777777777777776654 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0036
                        DUF948  36 eelekqvdpilkevedllakvnelledvneklekvdplteava 78 
                                   +++ ++v+++ +e++  +a++n ++ +v+++++kv + +e ++
  gi|91772409|ref|YP_565101.1| 499 AVVADEVRKLAEESRSSTAEINGIVVNVQKETKKVTEAIERAK 541
                                   5677889999999999999999999999999999988888776 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.0069
                        DUF948  47 kevedllakvnelledvne....klekvdplteavadlges 83 
                                    e++++++k+n +l  +n+     +ek++++ e++++++ +
  gi|91772409|ref|YP_565101.1| 559 GEITGMVDKINSMLGSLNKkaeeGMEKIESINENIGEVAST 599
                                   67888888888888887774443566777777777776655 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0022
                        DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                   k++++l ++++  ee ++++++i +++ ++ ++++e +++ +e ++++++ t+a ++++ s++++n
  gi|91772409|ref|YP_565101.1| 567 KINSMLGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAASEQVSGSIKNVN 632
                                   566777777777777778888888888888888888888888888888888888888888888887 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00076      0.68       6     103 ..      31     131 ..      26     140 .. 0.84
   2 !   12.5   0.0   0.00012      0.11      11     110 ..     162     272 ..     153     275 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                                   HHHHSSSEEEEEE..TTSBEEEECHHHHHHHSSTHHHCTTSBG..GGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                           PAS   6 ileslpdpifvvD..edgrilyvNaaaeellGlsreevlgksl..ldliheeddaelaelleqlleqgeesrageisfklr 82 
                                   ++++lp+ if  D  ++ +i y++++  +l+G +  + lgk+l  +d++++ed  +  +++  +++++ + + ++ ++k++
  gi|91772409|ref|YP_565101.1|  31 LIDNLPVTIFRCDinASWDIYYISKNVYDLTGHPKTDFLGKKLtwSDVVFPEDVPKIDAAIDIAMKNNAPYK-VNYRIKTK 110
                                   799999999887766999***********************9966799999986688888888888887776.57778888 PP

                                   TSSEEEEEEEEEEEEETTEEE CS
                           PAS  83 dgrpihlevraspvrdaggei 103
                                   +g +++++ + + v d +g+ 
  gi|91772409|ref|YP_565101.1| 111 NGDTVYIREEGKLVNDDEGNA 131
                                   ******999999999988875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                                   SSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.........HHHHHHHHHHHHTT-ECCCCEEEEC CS
                           PAS  11 pdpifvvDedgrilyvNaaaeellGlsr.eevlgkslldliheedda.........elaelleqlleqgeesrageisfkl 81 
                                   p+  + vD  g++ ++N+ + +l +++  e+v+g+s ++ i  ++             + ++e +l ++e+ ++ e  +kl
  gi|91772409|ref|YP_565101.1| 162 PALAIFVDPEGKVKHINDYYVKLSQFQSdEDVIGRSPSEIIGKTTLVgdnsnmklgASQTIVESVLDTRESVESLEAIIKL 242
                                   3445679*******************************6655544448888888888888999999999999999998888 PP

                                   TTSSEEEEEE..EEEEEEETTEEEEEEEEEE CS
                           PAS  82 rdgrpihlev..raspvrdaggeilgflgvl 110
                                    +g   +l +   asp++d++g   g+l vl
  gi|91772409|ref|YP_565101.1| 243 -HGLDHELYTisSASPIFDEEGVFEGILEVL 272
                                   .665544443227788888888777777665 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   3.2   3.1e-06    0.0028     227     345 ..     269     415 ..     268     426 .. 0.95
   2 ?    0.2   4.0      0.36   3.2e+02     244     304 ..     570     630 ..     429     652 .] 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                                   GGGGGGCCCSB-STTTSB.HHHHHHHHHHT...........................TSGGGGGHHHHTTTHHHCCTS-HH CS
                           FH2 227 LssLlkLsdvKstdnktt.LLHylvkiire...........................klpevldfsseLknvkkaakvnle 279
                                   L+ L+ L d+K ++++++ LL+y  ++++                             ++e+++f + L+++ +a+  +++
  gi|91772409|ref|YP_565101.1| 269 LEVLTDLTDIKQKEKEVNeLLDYTNDCLSAlgngikmvgegnlnvklekikdddfgkTFDEFNGFVENLNKIVQATMRDMN 349
                                   899**********999988************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FH2 280 slekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkelv 345
                                   +  +evk+ ++ + ++++ +e+ ++++e+  + +e l++  ++a+ ++k  e+  ke+ e++++ +
  gi|91772409|ref|YP_565101.1| 350 ATLDEVKQSTEAVNQMNTGMEQISTAAEQIATGSENLSRHANTAALDVKASEQIFKELSEAATKSA 415
                                   *************************99999***************999999999999988877755 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.36
                                   BHHHHHHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                           FH2 244 tLLHylvkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessek 304
                                   ++L  l k  +e++++++  ++ + +v ++a+ n  + e++  ++e++ ++ e+   s ++
  gi|91772409|ref|YP_565101.1| 570 SMLGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAASEQVSGSIKN 630
                                   3444444444445555555555555555555555555554444444444444444444444 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.84   7.6e+02      18      45 ..     263     290 ..     245     297 .. 0.77
   2 ?    4.9   0.3     0.025        22      15      35 ..     344     364 ..     325     388 .. 0.52
   3 ?    9.5   0.1   0.00094      0.84       4      38 ..     444     478 ..     442     480 .. 0.94
   4 ?    3.5   0.7     0.067        60      11      41 ..     518     548 ..     508     549 .. 0.89
   5 ?    5.9   0.2     0.012        11       9      38 ..     565     594 ..     562     599 .. 0.90
   6 ?    1.6   0.2      0.26   2.3e+02      21      53 ..     612     644 ..     608     650 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.84
                     DASH_Duo1  18 nviesLkkaksniervketvestntLLd 45 
                                   +v e + ++ +++  +k++ +++n+LLd
  gi|91772409|ref|YP_565101.1| 263 GVFEGILEVLTDLTDIKQKEKEVNELLD 290
                                   5566677777888888888888888887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.025
                     DASH_Duo1  15 vienviesLkkaksniervke 35 
                                   +  +++++L+++k+ +e v++
  gi|91772409|ref|YP_565101.1| 344 TMRDMNATLDEVKQSTEAVNQ 364
                                   233333333333333333332 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00094
                     DASH_Duo1   4 kEleqLrkinevienviesLkkaksniervketve 38 
                                   +E+eqL  i + +++ +++++k++++i++++ +++
  gi|91772409|ref|YP_565101.1| 444 NEIEQLAGIVTSLDGAVDNIDKVTDKIKSIADQTN 478
                                   79****************************99875 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.067
                     DASH_Duo1  11 kinevienviesLkkaksniervketvestn 41 
                                   +in ++ nv+++ kk+++ ier ke+v s n
  gi|91772409|ref|YP_565101.1| 518 EINGIVVNVQKETKKVTEAIERAKEQVISGN 548
                                   79************************98866 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.012
                     DASH_Duo1   9 LrkinevienviesLkkaksniervketve 38 
                                   ++kin+++ +++++ ++  ++ie+++e++ 
  gi|91772409|ref|YP_565101.1| 565 VDKINSMLGSLNKKAEEGMEKIESINENIG 594
                                   89***********************99875 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.26
                     DASH_Duo1  21 esLkkaksniervketvestntLLdkWirIlsq 53 
                                   +++++ +   e+v+ +++++n L +k +++l +
  gi|91772409|ref|YP_565101.1| 612 AAIEEQTAASEQVSGSIKNVNDLAQKTTDMLMK 644
                                   678888888999999999999999988887766 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.092        82      15      59 ..     264     308 ..     251     322 .. 0.81
   2 ?    4.6   5.1     0.033        29      28     106 ..     336     415 ..     324     425 .. 0.61
   3 ?    2.5   0.6      0.15   1.3e+02      16      57 ..     446     489 ..     428     492 .. 0.56
   4 ?   13.8   2.7     5e-05     0.045       1      80 [.     512     591 ..     502     592 .. 0.93
   5 ?   11.1   5.2   0.00034       0.3       3      73 ..     570     640 ..     568     647 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.092
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArr 59 
                                   v e + ++ ++l  +k+k +e+n+ ++ tn+ ++++ ++i+ +++
  gi|91772409|ref|YP_565101.1| 264 VFEGILEVLTDLTDIKQKEKEVNELLDYTNDCLSALGNGIKMVGE 308
                                   6677788899999******************99999988888775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.033
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHH CS
                    Laminin_II  28 ntkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss..lsdniseikelIaqARkaA 106
                                   n+++ ++   r+++ t ++vk++++a+++ ++ + ++   a+q+    ++l  + +  ++  ++++ +  kel ++A k A
  gi|91772409|ref|YP_565101.1| 336 NLNKIVQATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIATGSENLSRHANT-AAldVKASEQIFKELSEAATKSA 415
                                   444444555555666666666777777777777777777777776666666665555.33355555555566666665555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.15
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXX CS
                    Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvk..dankairdA 57 
                                    eqla++ + l+   +++ ++ ++++ + ++ +  ++n ai+ A
  gi|91772409|ref|YP_565101.1| 446 IEQLAGIVTSLDGAVDNIDKVTDKIKSIADQTNllALNAAIEAA 489
                                   35566666777777777777777776666666555556555555 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 5e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                    Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                   s++  ae+n ++++v++ ++++ + +e+ ke++ + n+++     k  + + +++  ++    L+k+a++ ++k++++++
  gi|91772409|ref|YP_565101.1| 512 SRSSTAEINGIVVNVQKETKKVTEAIERAKEQVISGNKDIGGALGKSGEITGMVDKINSMLGSLNKKAEEGMEKIESINE 591
                                   5677899**************************999999999999999999*************************9986 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00034
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                    Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                   +++ + n++a+e  e+++ +++n+ ++ + ++e +++ eet + +++ + a ++++ s+k+++ la++  d
  gi|91772409|ref|YP_565101.1| 570 SMLGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAASEQVSGSIKNVNDLAQKTTD 640
                                   688899******************************99*************************99987655 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0     0.001      0.92      51     106 .]     219     276 ..     162     276 .. 0.51
   2 ?   -1.4   0.1       3.9   3.5e+03      27      50 ..     336     360 ..     313     380 .. 0.45
   3 ?   -1.3   0.0       3.8   3.4e+03      41      73 ..     468     500 ..     463     530 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.001
                        PAS_10  51 avknveeviealrtgekdevevvvp......kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                   +    + ++e++ ++++ +++ +          + + +   +p+ de+g+++G++e+++D+t
  gi|91772409|ref|YP_565101.1| 219 S----QTIVESVLDTRESVESLEAIiklhglDHELYTISSASPIFDEEGVFEGILEVLTDLT 276
                                   2....4455554444443333322222447344445556789******************86 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                        PAS_10  27 aakklfklipadvGrpladihpk.k 50 
                                   + +k+++ +  d+  +l++++++ +
  gi|91772409|ref|YP_565101.1| 336 NLNKIVQATMRDMNATLDEVKQStE 360
                                   2223333333333333333332222 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.8
                        PAS_10  41 rpladihpkkavknveeviealrtgekdevevv 73 
                                   +++++i  + ++  ++  iea r ge  +   v
  gi|91772409|ref|YP_565101.1| 468 DKIKSIADQTNLLALNAAIEAARAGEHGRGFAV 500
                                   677777777777777777777777776543333 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.098        88      16      52 ..     302     338 ..     296     339 .. 0.89
   2 ?    4.0   0.0     0.076        68       8      28 ..     367     389 ..     361     400 .. 0.77
   3 ?   -2.0   0.0       5.3   4.8e+03      23      41 ..     434     450 ..     418     455 .. 0.56
   4 ?   -0.6   0.0       2.1   1.9e+03      26      52 ..     556     576 ..     531     577 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.098
                                   HHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                          HAMP  16 aarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    ++ +++G+l++ l+   +D +G     fN ++++L+
  gi|91772409|ref|YP_565101.1| 302 GIKMVGEGNLNVKLEKIKDDDFGKTFDEFNGFVENLN 338
                                   578899**********9*****************997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.076
                                   HHHHHHHHHHHHHTTT..BTSST CS
                          HAMP   8 rPLrrLaraarriaaG..dldtr 28 
                                     ++++++aa++ia G  +l+ +
  gi|91772409|ref|YP_565101.1| 367 TGMEQISTAAEQIATGseNLSRH 389
                                   56799**********98776655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.3
                                   T...BTSSTCCTTSSSHHHHHH CS
                          HAMP  23 G...dldtrlpvsgrDEiGeLa 41 
                                       dl++       +Ei +La
  gi|91772409|ref|YP_565101.1| 434 SalkDLEVIM-----NEIEQLA 450
                                   1444555554.....6777776 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.1
                                   SSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                          HAMP  26 dtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    ++       Ei  ++  +N Ml +L+
  gi|91772409|ref|YP_565101.1| 556 GKS------GEITGMVDKINSMLGSLN 576
                                   455......8999999999***99997 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.8    0.0024       2.2      31      99 ..     321     389 ..     319     395 .. 0.91
   2 ?    7.9   3.0     0.002       1.8      35     168 ..     360     498 ..     356     509 .. 0.81
   3 ?    6.5   1.4    0.0056         5      35     117 ..     563     645 ..     551     648 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                     Mce4_CUP1  31 erlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdal 99 
                                   + +G++ +++n ++++lN+ +    +d+++  d  +  ++a +++ + +++++t ++ i++ +++L++ 
  gi|91772409|ref|YP_565101.1| 321 DDFGKTFDEFNGFVENLNKIVQATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIATGSENLSRH 389
                                   689**************************9999999999********************9999999765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.002
                     Mce4_CUP1  35 esltdlnevLdelNprlpqlr...edireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgad 112
                                   e+++++n+ ++++ +  +q+    e++++ a++a++  +a++++++ L++a+t s++  +q+ e+++  +++++ + +  +
  gi|91772409|ref|YP_565101.1| 360 EAVNQMNTGMEQISTAAEQIAtgsENLSRHANTAALDVKASEQIFKELSEAATKSASFSAQAVEMSDGSQKLANSALKDLE 440
                                   678899999999999988886222566667777777789****************************************** PP

                     Mce4_CUP1 113 llerngdnLirlaadlrptlelLakYspeltCllrnla..dvepkvakalggtngysl 168
                                   ++ +  ++L+ ++++l+ +++ ++k  +++  + ++++   ++ ++++a++g++g+++
  gi|91772409|ref|YP_565101.1| 441 VIMNEIEQLAGIVTSLDGAVDNIDKVTDKIKSIADQTNllALNAAIEAARAGEHGRGF 498
                                   ***********99999999998888888888777665511344555666777777766 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0056
                     Mce4_CUP1  35 esltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqa...eLdalllaavglsntgad 112
                                    +++++n++L  lN++ ++    +++++++++  +++a+   +  +n+  ts++i+eq a   +++  + ++  l+++++d
  gi|91772409|ref|YP_565101.1| 563 GMVDKINSMLGSLNKKAEE---GMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAaseQVSGSIKNVNDLAQKTTD 640
                                   3688999******998765...6666666777777888888888999********99965222777789999999****** PP

                     Mce4_CUP1 113 llern 117
                                   +l +n
  gi|91772409|ref|YP_565101.1| 641 MLMKN 645
                                   99988 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   0.0       4.9   4.4e+03      93     111 ..     272     290 ..     264     308 .. 0.47
   2 ?    8.4   1.0    0.0024       2.2      57     114 ..     323     380 ..     310     390 .. 0.69
   3 ?    4.9   0.3     0.028        25      79     121 ..     422     464 ..     397     471 .. 0.80
   4 ?    6.4   1.1    0.0095       8.6      46     123 ..     501     578 ..     496     581 .. 0.72
   5 ?    8.0   1.7    0.0032       2.9      38     112 ..     563     637 ..     562     645 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.9
                       DUF1664  93 redlseigedvesvkeave 111
                                     dl++i+++ ++v+e+  
  gi|91772409|ref|YP_565101.1| 272 LTDLTDIKQKEKEVNELLD 290
                                   4444444444444444332 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0024
                       DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                     +t ++++  +++++k ++++++  +++ +ev++  e ++++++ +e++++a e+++
  gi|91772409|ref|YP_565101.1| 323 FGKTFDEFNGFVENLNKIVQATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIA 380
                                   5556666677777777777777777777777777777777777777777777777765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.028
                       DUF1664  79 keiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                    e+s   ++  +++ +dl+ i +++e++  +v++l++ +++i+
  gi|91772409|ref|YP_565101.1| 422 VEMSDGSQKLANSALKDLEVIMNEIEQLAGIVTSLDGAVDNID 464
                                   5666666666677889999999999999999999999999986 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0095
                       DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                   v+ ++ ++ e+ ++   +++  + +v+k+ ++++e+++  ke+v + ++d+     ++ ++  +v +++s l ++++k
  gi|91772409|ref|YP_565101.1| 501 VADEVRKLAEESRSSTAEINGIVVNVQKETKKVTEAIERAKEQVISGNKDIGGALGKSGEITGMVDKINSMLGSLNKK 578
                                   566666666777777777777777778888888888888888888888888777777788888888887777777655 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0032
                       DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                   ++ d ++s+  +l++  e+  +  + ++++i +v ++ +e+++ s+e+++ ++e     ++++  +++v+++ ++
  gi|91772409|ref|YP_565101.1| 563 GMVDKINSMLGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAASEQVSGSIKNVNDLAQK 637
                                   577778888888888888888888899999************************999999999999999988765 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.9     0.059        53      32     112 ..     327     421 ..     277     460 .. 0.65
   2 ?   -0.6   0.1       1.4   1.3e+03      54      54 ..     506     506 ..     439     554 .. 0.45
   3 ?   12.3   0.7   0.00016      0.14      27      99 ..     560     632 ..     557     648 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.059
                                   HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT................-BTCCG-S--.HHHHHHHHHHHH CS
               Cob_adeno_trans  32 vDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatp...............ekkkekkkit.eeeveelekeid 96 
                                    De+n ++  + ++++++ ++++++L e++++   + +   t                e + ++++ t + +v++ e+ ++
  gi|91772409|ref|YP_565101.1| 327 FDEFNGFVENLNKIVQATMRDMNATLDEVKQSTEAVNQMN-TGmeqistaaeqiatgsE-NLSRHANTaALDVKASEQIFK 405
                                   5666666666666665554455555544443322222111.111112222334444333.333333332446888888888 PP

                                   HHHHHS--EESEEES- CS
               Cob_adeno_trans  97 eleaelpplksfilpg 112
                                   el++  ++ +sf  + 
  gi|91772409|ref|YP_565101.1| 406 ELSEAATKSASFSAQA 421
                                   8888888888776665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                   H CS
               Cob_adeno_trans  54 k 54 
                                   +
  gi|91772409|ref|YP_565101.1| 506 R 506
                                   1 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT...-BTCCG-S--HHHH...HHHHHHHHHHH CS
               Cob_adeno_trans  27 eayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatp..ekkkekkkiteeev...eelekeidele 99 
                                   e+ G vD++ns++g + + +    ee +e++e+i +++ ++ ++   +  ++++++ +i+e+ +   e++   i++++
  gi|91772409|ref|YP_565101.1| 560 EITGMVDKINSMLGSLNKKA----EEGMEKIESINENIGEVASTAEENaaNSEETSAAIEEQ-TaasEQVSGSIKNVN 632
                                   678***********999544....56678899999998888887754443333333333333.311123333444444 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 ?    0.3   0.0      0.81   7.2e+02      35      65 ..     266     296 ..     260     301 .. 0.82
   2 ?   10.1   2.6   0.00078       0.7      22      82 ..     330     390 ..     316     426 .. 0.82
   3 ?    2.1   0.7      0.22     2e+02      36     115 ..     396     474 ..     383     489 .. 0.55
   4 ?    0.8   0.2      0.58   5.2e+02      28      63 ..     507     542 ..     500     552 .. 0.46
   5 ?    7.4   2.1    0.0052       4.7      33     110 ..     561     637 ..     553     647 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.81
                                   HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHH CS
                     Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdsl 65 
                                   + + ++  +l++i++++ke++el  +++d l
  gi|91772409|ref|YP_565101.1| 266 EGILEVLTDLTDIKQKEKEVNELLDYTNDCL 296
                                   5667778899*************99998876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00078
                                   HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikks 82 
                                    ++++++ +k v+ ++++++ +l+e+++st+ ++++ + ++++ +++++ +++++n+ ++ 
  gi|91772409|ref|YP_565101.1| 330 FNGFVENLNKIVQATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIATGSENLSRHA 390
                                   57889999999******************************99999999888877665544 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.22
                                   HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHH CS
                     Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesne 115
                                   d++  e+ ++e+s+  +++ + + +  ++    qk ++   + ++ + +e+e + + +  ++d  + ni + ++ ++s  
  gi|91772409|ref|YP_565101.1| 396 DVKASEQIFKELSEAATKSASFSAQAVEMSDGSQKLANSALKDLEVIMNEIE-QLAGIVTSLDGAVDNIDKVTDKIKSIA 474
                                   5555555555555555555555555555555555555554555555555555.555555555555566665555555544 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.58
                                   CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHH CS
                     Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikd 63 
                                   k  ++ + + ++++  + +++++tk++ e +++ k+
  gi|91772409|ref|YP_565101.1| 507 KLAEESRSSTAEINGIVVNVQKETKKVTEAIERAKE 542
                                   333344444444444444444444444444444433 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0052
                                   CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                     Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                   ++  ++k+++ l +++++ +e  e +++i++ + e  +++++n    ++ s  +e e++   e+++  ++n++ L + 
  gi|91772409|ref|YP_565101.1| 561 ITGMVDKINSMLGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIE-EQTAASEQVSGSIKNVNDLAQK 637
                                   566799999999999*****************99999999999999999999999.8888899999999999988654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.11        94      13      90 ..     202     279 ..     201     287 .. 0.68
   2 ?    7.0   0.4    0.0064       5.8      48     105 ..     329     388 ..     307     403 .. 0.65
   3 ?   -0.3   0.1       1.1     1e+03      51      89 ..     437     476 ..     398     495 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                        AAA_14  13 vGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqevpewekalkslvdeg 90 
                                   +GKTtl+ +  + +l  ++ i++  ld+ +  ++ +   kl+ l  e+++       ++DE    +++ ++l +l d +
  gi|91772409|ref|YP_565101.1| 202 IGKTTLVGDNSNMKLGASQTIVESVLDTRESVESLEAIiKLHGLDHELYTI-SSASPIFDEEGVFEGILEVLTDLTDIK 279
                                   6******99999999778888888888877755443322233222222333.455679999999999999998888854 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0064
                        AAA_14  48 dpe...kllelileklke.ekktylflDEiqevpewekalkslvdeg.knldvivtGSnskll 105
                                   +++   ++l+ i +   +  ++    lDE+++++e+ + ++  +++  +  + i+tGS ++  
  gi|91772409|ref|YP_565101.1| 329 EFNgfvENLNKIVQ---AtMRDMNATLDEVKQSTEAVNQMNTGMEQIsTAAEQIATGSENLSR 388
                                   22222222222222...133445589*******************7657889******98765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.1
                        AAA_14  51 kllelileklkeekktylflDE.iqevpewekalkslvde 89 
                                   k le+i++++++    +  lD  + +++++ + +ks+ d+
  gi|91772409|ref|YP_565101.1| 437 KDLEVIMNEIEQLAGIVTSLDGaVDNIDKVTDKIKSIADQ 476
                                   2233444443333344444443234445555555555554 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.88   7.9e+02       3      27 ..     276     300 ..     274     307 .. 0.85
   2 ?    9.1   1.5    0.0013       1.1      13      85 ..     342     418 ..     331     433 .. 0.66
   3 ?    4.3   0.1     0.037        33       7      44 ..     444     481 ..     436     488 .. 0.84
   4 ?   -2.1   0.1       3.6   3.2e+03      26      49 ..     516     539 ..     501     550 .. 0.51
   5 ?    2.8   0.5      0.11        99      12      65 ..     572     625 ..     556     650 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.88
                         Sec34   3 dqLeskeeecdelleqtdealeqLe 27 
                                   + +++ke+e++ell+ t+++l+ L 
  gi|91772409|ref|YP_565101.1| 276 TDIKQKEKEVNELLDYTNDCLSALG 300
                                   5688999*************99886 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                         Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelae....eieekLkyFeeldpitrkLnspg 85 
                                   ++ +++++++l+++++ +e ++++++ ++++++a+eq+ +  ++l++ a+    ++++  ++F+el ++ +k  s +
  gi|91772409|ref|YP_565101.1| 342 QATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIATGSENLSRHANtaalDVKASEQIFKELSEAATKSASFS 418
                                   44556666677777777777777777777777777777776666655444222278888889999988877655555 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.037
                         Sec34   7 skeeecdelleqtdealeqLeeleekfksvsektsslh 44 
                                   ++ e++  +++++d a ++++++++k ks++++t+ l 
  gi|91772409|ref|YP_565101.1| 444 NEIEQLAGIVTSLDGAVDNIDKVTDKIKSIADQTNLLA 481
                                   56788999999999999999999999999999999775 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.6
                         Sec34  26 Leeleekfksvsektsslheaceq 49 
                                    +e++  + +v+++t+++ ea e+
  gi|91772409|ref|YP_565101.1| 516 TAEINGIVVNVQKETKKVTEAIER 539
                                   334444444455555555444443 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.11
                         Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                   + +l ++++e +e++e+++e+  +v++  ++  +++e+  +  ++ +  +e+++
  gi|91772409|ref|YP_565101.1| 572 LGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAASEQVS 625
                                   344445555555555555555555555555555444444444444444444444 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         7   6.3e+03      37      59 ..     268     290 ..     265     295 .. 0.77
   2 ?    1.1   0.0      0.53   4.7e+02      30      65 ..     341     376 ..     323     393 .. 0.75
   3 ?   -0.2   0.1       1.3   1.2e+03      18      30 ..     461     473 ..     407     520 .. 0.61
   4 ?    7.5   0.6    0.0056         5       6      72 ..     565     642 ..     561     649 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7
                          Rx_N  37 iqavLedaeerqikdeavkeWlk 59 
                                   i  vL d  + ++k+++v+e l+
  gi|91772409|ref|YP_565101.1| 268 ILEVLTDLTDIKQKEKEVNELLD 290
                                   66788899998899999988887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.53
                          Rx_N  30 lkdeLesiqavLedaeerqikdeavkeWlkelrdla 65 
                                    + +++ ++a L+++ +  +  +++++ ++++  +a
  gi|91772409|ref|YP_565101.1| 341 VQATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAA 376
                                   467889999999998887777777777777766665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.3
                          Rx_N  18 kllkgvkeelekl 30 
                                     + +v ++++++
  gi|91772409|ref|YP_565101.1| 461 DNIDKVTDKIKSI 473
                                   3344444444444 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0056
                          Rx_N   6 lqkLadllaeeakllkgvkeeleklkdeLesiqavLedaee.............rqi.kdeavkeWlkelrdlaydaeDvl 72 
                                   ++k+ ++l +   l k+ +e +ek+++  e+i  v + aee              q+  +e+v   +k++ dla +  D+l
  gi|91772409|ref|YP_565101.1| 565 VDKINSMLGS---LNKKAEEGMEKIESINENIGEVASTAEEnaanseetsaaieEQTaASEQVSGSIKNVNDLAQKTTDML 642
                                   5566666665...89999999999999999999999999997777766666665333356888889999999988888876 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.2   2.9e+03      19      56 ..     215     254 ..     211     280 .. 0.64
   2 ?    1.5   0.2      0.45   4.1e+02      26      57 ..     274     314 ..     264     321 .. 0.61
   3 ?    5.2   0.4     0.033        29      22      55 ..     347     380 ..     331     404 .. 0.63
   4 ?    8.7   1.5    0.0026       2.3       6      43 ..     439     476 ..     429     490 .. 0.72
   5 ?    2.9   0.1      0.17   1.5e+02      11      56 ..     528     577 ..     513     596 .. 0.54
   6 ?    3.3   0.7      0.13   1.2e+02      19      64 ..     585     634 ..     580     642 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                       NPV_P10  19 kVdalqqqvddvqenlpdvtelne..kLdaqsaqLaelet 56 
                                   k+ a q+ v++v +  + v+ l++  kL ++  +L ++++
  gi|91772409|ref|YP_565101.1| 215 KLGASQTIVESVLDTRESVESLEAiiKLHGLDHELYTISS 254
                                   6666677777777777777766644467777777666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.45
                       NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaelet............k 57 
                                    ++d++++    +e+ne Ld  ++ L +l +            k
  gi|91772409|ref|YP_565101.1| 274 DLTDIKQKE---KEVNELLDYTNDCLSALGNgikmvgegnlnvK 314
                                   344444444...45777788888888888884444444444444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.033
                       NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                    +++ +d+v++  + v+++n+ ++++s++ +++ 
  gi|91772409|ref|YP_565101.1| 347 DMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIA 380
                                   3444555555555555555555555555555544 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0026
                       NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnek 43 
                                   L vI ++i+++   V++l+ +vd++++   +++ + ++
  gi|91772409|ref|YP_565101.1| 439 LEVIMNEIEQLAGIVTSLDGAVDNIDKVTDKIKSIADQ 476
                                   56788888888888888888888888777777777655 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.17
                       NPV_P10  11 adikavddkVdalqqqv....ddvqenlpdvtelnekLdaqsaqLaelet 56 
                                   ++ k+v + ++  ++qv    +d+   l +  e++  +d+++  L +l++
  gi|91772409|ref|YP_565101.1| 528 KETKKVTEAIERAKEQVisgnKDIGGALGKSGEITGMVDKINSMLGSLNK 577
                                   44444444444444444444455555555555666666666666666666 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.13
                       NPV_P10  19 kVdalqqqv....ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                   k++++++++       +en  + +e ++ +++q+a+ ++++ +++n++d+
  gi|91772409|ref|YP_565101.1| 585 KIESINENIgevaSTAEENAANSEETSAAIEEQTAASEQVSGSIKNVNDL 634
                                   666666666333344567888889999**************999999986 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   0.1         3   2.7e+03      61      82 ..     220     241 ..     210     242 .. 0.76
   2 ?   -1.9   0.1       4.7   4.2e+03      49      65 ..     274     290 ..     269     294 .. 0.69
   3 ?    9.1   2.7    0.0017       1.5      24      79 ..     333     388 ..     314     402 .. 0.83
   4 ?   11.3   0.6   0.00035      0.32      32      91 ..     410     470 ..     396     474 .. 0.76
   5 ?   -1.5   0.1       3.5   3.1e+03      31      54 ..     511     534 ..     498     546 .. 0.46
   6 ?    5.1   3.9      0.03        27       3      77 ..     564     641 ..     562     644 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
                       BLOC1_2  61 qpylqqidqiekqvteLeeavs 82 
                                   q  ++++ +  ++v++Le++++
  gi|91772409|ref|YP_565101.1| 220 QTIVESVLDTRESVESLEAIIK 241
                                   5667778888999999999875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.7
                       BLOC1_2  49 kleklnekyeelqpylq 65 
                                   +l ++++k++e++++l+
  gi|91772409|ref|YP_565101.1| 274 DLTDIKQKEKEVNELLD 290
                                   56777777777777765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0017
                       BLOC1_2  24 lLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                   ++e+lN+ +++   +++  +++++++ e++n+++  +++  +  +qi +  + L  
  gi|91772409|ref|YP_565101.1| 333 FVENLNKIVQATMRDMNATLDEVKQSTEAVNQMNTGMEQISTAAEQIATGSENLSR 388
                                   57999999999999999999999999999999999999988888888777766655 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00035
                       BLOC1_2  32 asekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                   a++k ++ + +a ++++ ++kl +     l+  +++i+q+   vt+L  av+ +D+ + ++
  gi|91772409|ref|YP_565101.1| 410 AATKSASFSAQAVEMSDGSQKLANSALkDLEVIMNEIEQLAGIVTSLDGAVDNIDKVTDKI 470
                                   5566666677777777777777665544899999999999999999999999999998877 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 3.5
                       BLOC1_2  31 aasekykklkdvaaslekklekln 54 
                                   ++ +  ++++ ++ +++k+ +k+ 
  gi|91772409|ref|YP_565101.1| 511 ESRSSTAEINGIVVNVQKETKKVT 534
                                   333333333344444444444333 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.03
                       BLOC1_2   3 mfekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekye...elqpylqqidqiekqvteL 77 
                                   m++k++++l +  + + e ++ +e +Ne+  e     +++aa+ e+++ +++e+ +   +++  +++++++ +++t++
  gi|91772409|ref|YP_565101.1| 564 MVDKINSMLGSLNKKAEEGMEKIESINENIGEVASTAEENAANSEETSAAIEEQTAaseQVSGSIKNVNDLAQKTTDM 641
                                   778888888888888999999999999999999999999999988888888888762225555566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2156  (0.120252); expected 358.6 (0.02)
Passed bias filter:                      764  (0.0426125); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); 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: 1.22u 0.36s 00:00:01.58 Elapsed: 00:00:00.59
# Mc/sec: 3338.79
//
Query:       gi|91772410|ref|YP_565102.1|  [L=159]
Description: CheW-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-37  127.5   0.5    3.1e-37  127.3   0.5    1.0  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   0.5   1.7e-41   3.1e-37       1     137 [.      15     152 ..      15     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 1.7e-41
                                   EEEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEEETTEEE CS
                          CheW   1 qlllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivvelgnqvv 81 
                                   q+++f lgee y++++++v+ei+++++it+ip++p++++gv+nlrG++  +i+Lr++lg +++e +++tr+ivve++n v+
  gi|91772410|ref|YP_565102.1|  15 QVIVFALGEEIYGVDISQVKEIIRPTKITRIPNSPEFIEGVVNLRGQITTIINLRKRLGKETKETDNETRIIVVEYENAVI 95 
                                   789****************************************************************************** PP

                                   EEEESEEEEEEEEECCGEETT..TSSTSSTCCCEEEEEECTTSEEEEEE-CCCHHHHH CS
                          CheW  82 GllVdevkgiqeivikqiepp..lglssdlagyisGatklgdgrlvliLDveallrsl 137
                                   G++Vd v+++  ++ k+i++   + +s d +++++G+ kl+dg l++++D++++++++
  gi|91772410|ref|YP_565102.1|  96 GMIVDTVNEVKYLSSKNIDELpsIITSRDDSKFLTGVGKLDDG-LLTLMDLDKVFSEE 152
                                   *********************996669999**********666.**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1111.76
//
Query:       gi|91772411|ref|YP_565103.1|  [L=266]
Description: hypothetical protein Mbur_0358 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-14   52.3   0.1    9.2e-13   48.4   0.1    2.1  1  CheF-arch  Chemotaxis signal transduction system protein F fr


Domain annotation for each model (and alignments):
>> CheF-arch  Chemotaxis signal transduction system protein F from archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.1   5.1e-17   9.2e-13     100     215 ..      74     188 ..       4     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 5.1e-17
                     CheF-arch 100 iekFetkLfkalLngkevlvkhpAvvGGvvq.dtewekgklkvekkaielatkkgsfveielsdvgdvereektvdgeerp 179
                                    + F+   f++  +   v++   A vGGvv+  ++wekg ++v+++   + + + +  +i  ++vg+v++  ++v g++r+
  gi|91772411|ref|YP_565103.1|  74 PQVFRFLAFNLKSDRFAVYYLDSATVGGVVTsGSQWEKGYFSVTDEGFWFISPQKQQ-KILFDNVGTVSKDVRNVGGKQRK 153
                                   45566666666666677888889*************************888888776.5********************** PP

                     CheF-arch 180 vlevehtedgesvttylagkdkrkvslLerylreey 215
                                   vl++  +edg+  t++l  ++  ++++Le+ l++++
  gi|91772411|ref|YP_565103.1| 154 VLVISKVEDGQVATSLLMCPE-TTLEMLENHLNLVI 188
                                   *********************.99999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1736.99
//
Query:       gi|91772412|ref|YP_565104.1|  [L=120]
Description: CheY like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-31  108.0   0.7      3e-31  107.9   0.7    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.7   1.7e-35     3e-31       1     111 [.       4     114 ..       4     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 1.7e-35
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESST CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahs 81 
                                   vlivdD   +r+ll+++l  +gy   +eae+gk+a+e++k+ ++d++++D+ mp+m+G+++lk+i++ ++e +v+++ta +
  gi|91772412|ref|YP_565104.1|   4 VLIVDDTAFMRKLLKNILFGAGYDIAGEAENGKQAVEMYKALNPDVVTMDVVMPEMNGIDALKNIKTINKEAKVVMCTAIG 84 
                                   8**********************7777****************************************************** PP

                                   SHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  82 eeedavealkagaddflsKpfdpeeLlkal 111
                                   +e+ ++ alk+ga++++ Kpf+  ++++ +
  gi|91772412|ref|YP_565104.1|  85 QEKIVKTALKLGAKGYIIKPFQAPKVVEEI 114
                                   ***********************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 954.36
//
Query:       gi|91772413|ref|YP_565105.1|  [L=351]
Description: chemotaxis-specific methylesterase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-55  186.5   0.2    5.5e-55  185.7   0.2    1.4  1  CheB_methylest  CheB methylesterase
    2.9e-26   91.8   2.1    1.5e-25   89.6   1.0    2.2  2  Response_reg    Response regulator receiver domain


Domain annotation for each model (and alignments):
>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   0.2   6.1e-59   5.5e-55       1     170 []     160     340 ..     160     340 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 6.1e-59
                                   EEEEE-TTHHHHHTTTGGGS-TT-SS-EEEEE---T.T-HHHHHHHHHHH-SSEEEE--TT-B--TTEEEE--TTSEEEEE CS
                CheB_methylest   1 vvigaStGGlealkellaalpedfpaavvvvqhmpp.sftsslaelLnresslkVkeaedgeelepgrvyvapgdkhllie 80 
                                   ++ig+StGG+ +l++++++lp d+pa+v++vqhmp+ +f s+la +L+++s+l+Vkeae++e+++ g +y+apg++h++i+
  gi|91772413|ref|YP_565105.1| 160 ILIGSSTGGPSSLEQIIPRLPGDLPASVFIVQHMPEgNFCSQLAARLDAISELEVKEAENNEKVKIGVAYIAPGGYHMEIR 240
                                   68********************************883579***************************************** PP

                                   ...........E.....E.-.-SS-HHHHHHHHHHHH.GGEEEEE-SBSS-TTHHHHHHHHHTT-EEEEE-GGG-SSBSHH CS
                CheB_methylest  81 .......lalsa.....k.kgerpsiDvlfesaaeaygeraigviLtGmgsDGaeGlkaikeaggltiaqdpesavvpgmP 148
                                          +   +     + ++  ps+Dv+ es  ++yg++ +++iLtGmg DGa G k+i+e++g tia +++++vv+gmP
  gi|91772413|ref|YP_565105.1| 241 kaldvtrI---KiikgkPmHAVMPSVDVTVESFVKVYGNNSVAIILTGMGVDGASGFKKINESNGATIACSEDTCVVFGMP 318
                                   77666442...13334354666*********************************************************** PP

                                   HHHHHTT--SEEE-GGGHHHHH CS
                CheB_methylest 149 kaaieagavdevlpleeiaeel 170
                                   kaaieaga d v p+ ei+e++
  gi|91772413|ref|YP_565105.1| 319 KAAIEAGAIDVVKPIFEIPEQI 340
                                   *******999*******99886 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   1.0   1.6e-29   1.5e-25       2     109 ..       5     114 ..       4     116 .. 0.92
   2 ?    0.9   0.0     0.054   4.9e+02      55     101 ..     287     332 ..     266     345 .. 0.68

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.6e-29
                                   EEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEE..S CS
                  Response_reg   2 livdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilt..a 79 
                                   l+vdD+ l+r+++r++le  +++e++++a++gkea+e++++ k+ +i++D+nmp mdGl ++k i ++   +p+i+++  +
  gi|91772413|ref|YP_565105.1|   5 LVVDDSALMRRAIRDMLEsADDIEVIGTAKNGKEAVENTNKLKPEVIVMDVNMPIMDGLAAVKAIMKTT-PIPIIMFSslT 84 
                                   89****************7799*******************************************8877.79999999543 PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlk 109
                                   ++ + +a eal++ga df++Kp   +e+ k
  gi|91772413|ref|YP_565105.1|  85 KKGSIEALEALRLGAIDFITKPSGLQEISK 114
                                   44488999***************9999865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.054
                                   SSEHHHHHHHHHHCTTTSEEEEEESSTS..HHHHHHHHHCTESEEEESS CS
                  Response_reg  55 gmdGlellkeireedpelpviiltahse..eedavealkagaddflsKp 101
                                   g+dG   +k+i+e +     i+++  +     + ++a++aga d++ Kp
  gi|91772413|ref|YP_565105.1| 287 GVDGASGFKKINESN--GATIACSEDTCvvFGMPKAAIEAGAIDVV-KP 332
                                   457777777787755..67777775554224567889999999976.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2646.84
//
Query:       gi|91772414|ref|YP_565106.1|  [L=897]
Description: CheW-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-23   80.3  15.8      3e-13   49.6   4.6    4.6  5  P2            P2 response regulator binding domain
    8.3e-23   80.6   1.8    8.3e-23   80.6   1.8    2.3  2  CheW          CheW-like domain
    2.5e-19   69.9   1.3    6.9e-19   68.4   0.2    2.3  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    2.6e-16   59.6   0.0    8.4e-16   58.0   0.0    2.0  1  Hpt           Hpt domain
    6.8e-15   55.2   6.7    2.8e-12   46.9   1.0    3.9  3  H-kinase_dim  Signal transducing histidine kinase, homodimeri
    7.6e-06   25.8   0.3      4e-05   23.5   0.3    2.3  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
     0.0048   16.8   4.2      0.013   15.4   0.1    3.2  2  HATPase_c_5   GHKL domain
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.068   13.1   0.0    1.7  1  HATPase_c_2   Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       1.9   4.2e+03      29      76 ..     128     143 ..     109     152 .. 0.57
   2 !   49.6   4.6   1.3e-16     3e-13       5      79 ..     170     241 ..     167     243 .. 0.97
   3 !   45.4   3.3   2.8e-15   6.3e-12       5      79 ..     279     350 ..     276     352 .. 0.96
   4 ?   -3.7   1.8       5.9   1.3e+04      33      64 ..     452     482 ..     445     489 .. 0.56
   5 ?   -2.1   0.1       1.9   4.2e+03      28      55 ..     769     797 ..     762     812 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                                   TTEEEEEES-HHHHHTT-SSSEEEEEEEESS-HHHHHHHHHTSSS-SE CS
                            P2  29 lgeiiksiPsvedieeekfdegfevvlltkeskeeikealasiseies 76 
                                     e ++++P                                +i ei++
  gi|91772414|ref|YP_565106.1| 128 QKEAVNCVP--------------------------------EIIEIQE 143
                                   234444555................................4444443 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 1.3e-16
                                   EEE--TT-SSHHHHHHHHHHHHHHTTEEEEEES-HHHHHTT-SSSEEEEEEEESS-HHHHHHHHHTSSS-SEEEE CS
                            P2   5 kvkldedclmksvRaflvfkaLeelgeiiksiPsvedieeekfdegfevvlltkeskeeikealasiseiesvev 79 
                                   +vk+++d++   ++a+l++++L+e+g++ik++P++e+i++ +f+++++ ++  + ++e++ e++++isei+++e+
  gi|91772414|ref|YP_565106.1| 170 NVKISPDSDIMELKAILIIESLKEVGSVIKTEPTEEEIDN-TFKGSLKAFI--QSDAEKVDEVMNKISEIDHFEI 241
                                   79**************************************.9*********..********************98 PP

  == domain 3  score: 45.4 bits;  conditional E-value: 2.8e-15
                                   EEE--TT-SSHHHHHHHHHHHHHHTTEEEEEES-HHHHHTT-SSSEEEEEEEESS-HHHHHHHHHTSSS-SEEEE CS
                            P2   5 kvkldedclmksvRaflvfkaLeelgeiiksiPsvedieeekfdegfevvlltkeskeeikealasiseiesvev 79 
                                   +v ++ d++ k ++a+lv+++L+e+g++ik++P +e+i++ +f+++++ ++    ++e+++ ++++isei ++e+
  gi|91772414|ref|YP_565106.1| 279 NVIIAHDSDIKELKAILVIESLKEVGQVIKTEPIEEEIDS-TFKGSLKAFI--RGDAEKVEGVMNKISEIANFEI 350
                                   78999***********************************.9*********..********************98 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 5.9
                                   EEEES-HHHHHTT-S.SSEEEEEEEESS-HHHH CS
                            P2  33 iksiPsvedieeekf.degfevvlltkeskeei 64 
                                    + iP  e i ee   ++++  +++ +++++e+
  gi|91772414|ref|YP_565106.1| 452 QEIIP--EIIAEEIEkQDEIPEIMVEEKNQQEV 482
                                   55666..44444333455665566566665555 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 1.9
                                   HTTEEEEEES-HHHHHTT-S.SSEEEEEE CS
                            P2  28 elgeiiksiPsvedieeekf.degfevvl 55 
                                   e g+ i+ iP    +e+ ++ +++f+++ 
  gi|91772414|ref|YP_565106.1| 769 ESGNEIYAIPISNVVEALDVnKDNFKLIR 797
                                   77999999997777777555588888875 PP

>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.4   3.2e+03      57      79 ..     430     452 ..     427     479 .. 0.74
   2 !   80.6   1.8   3.7e-26   8.3e-23       3     134 ..     766     891 ..     764     893 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                                   HCTSSSSTTSTCEEEEEEE.ETTE CS
                          CheW  57 llglgpeesrentrvivve.lgnq 79 
                                   +lg+g++++ e+t+viv e +++q
  gi|91772414|ref|YP_565106.1| 430 VLGVGSNQQ-EETPVIVAEvFEKQ 452
                                   677777775.99999998855554 PP

  == domain 2  score: 80.6 bits;  conditional E-value: 3.7e-26
                                   EEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTT.STCEEEEEEEETTEEEE CS
                          CheW   3 llfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpees.rentrvivvelgnqvvG 82 
                                   l+++ g+e yaip+++v e l+v++  + +  +++   ++ +r++++p i+L+e++ +g+     e+++ i+ve++n+ v+
  gi|91772414|ref|YP_565106.1| 766 LIIESGNEIYAIPISNVVEALDVNK-DNFKLIRDQ--PLLYVREKLLPAIRLKEFFDIGEHVTqLEKEVGIIVERENEEVA 843
                                   7788999******************.*********..***********************9998999************** PP

                                   EEESEEEEEEEEECCGEETTTSSTSSTCCCEEEEEECTTSEEEEEE-CCCHH CS
                          CheW  83 llVdevkgiqeivikqiepplglssdlagyisGatklgdgrlvliLDveall 134
                                   llVd+++++qeivik++++ l+   +++g + G+t+lgdg++++iLDv al+
  gi|91772414|ref|YP_565106.1| 844 LLVDSIIDQQEIVIKPLGSILS---KVKG-FIGVTILGDGKVIPILDVSALV 891
                                   ********************99...99**.99******************97 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 ?   -1.3   0.0       1.4   3.1e+03      37      63 ..     560     586 ..     509     603 .. 0.65
   2 !   68.4   0.2   3.1e-22   6.9e-19       3     111 ..     619     759 ..     617     760 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                                   EEEEEEEESSSSSTTHHHTGTCSTTCH CS
                     HATPase_c  37 dlvisveDnGiGipkedlkklfekfsq 63 
                                   +   s +D    i + +++k+f+kf +
  gi|91772414|ref|YP_565106.1| 560 KSITSLQDEVMMIRMVKIEKVFKKFPR 586
                                   444467777777888899999999988 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 3.1e-22
                                   HHHHHHHHHHHHHHHHHH........HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.................... CS
                     HATPase_c   3 ekrLrqiisnlvdNavkf........atkageieveikaseddlvisveDnGiGipkedlk.................... 55 
                                   ++ L ++++n vd+ v+         ++k+g+i+++ k++++++ i++eD+G+G++ e +k                    
  gi|91772414|ref|YP_565106.1| 619 SDPLVHLVRNCVDHGVESpeerakagKSKTGHIKLSAKREKNNVIIEIEDDGKGLDLERIKskalekgilslaeldklged 699
                                   6789**************999988544477777777776669*************************************** PP

                                   ....GTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                     HATPase_c  56 ....klfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGttftftlple 111
                                       ++f+  +s+ ++++++ +g+G+G+  vk  ve++gG+i++ s++g+Gt+++++lp +
  gi|91772414|ref|YP_565106.1| 700 eissLIFTsGLST-KDNATEISGRGVGMDAVKTTVEKLGGKIKIYSKKGKGTKMRINLPPT 759
                                   *******999999.9999999************************************9975 PP

>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   3.7e-19   8.4e-16       4      83 ..      10      97 ..       7     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 3.7e-19
                                  HHHHHHHHHHHHHHHHHH......SCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHH..HCTSCHHHHHHHHHHHHH CS
                           Hpt  4 elfleeaeelleqleqal......dqedlqelaraaHtLKGsagmlGltelaelahelEdlld..ragelelepellealkal 78
                                  ++fl+e+ e+le  +qa+      d ++l+e++r+aHt+KG+ag lG+  l++l+h++E++l   + +e  +++ l++ +   
  gi|91772414|ref|YP_565106.1| 10 DDFLQEVNEYLEIFNQAFvdlengDTAALDEIFRVAHTIKGMAGFLGYASLERLCHRMEEVLSgiKCNEITIDGNLIDIMLST 92
                                  78*******************977777***********************************999999999999999966655 PP

                                  HHHHH CS
                           Hpt 79 lealr 83
                                  +++++
  gi|91772414|ref|YP_565106.1| 93 VDRIN 97
                                  55554 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.015        33       7      21 ..     222     236 ..     217     236 .. 0.90
   2 ?    4.1   0.2     0.028        63       4      52 ..     328     380 ..     325     393 .. 0.72
   3 !   46.9   1.0   1.2e-15   2.8e-12       2      69 .]     513     572 ..     512     572 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.015
                  H-kinase_dim   7 dakrlDyLlnlvGEl 21 
                                   da+++D+ +n ++E+
  gi|91772414|ref|YP_565106.1| 222 DAEKVDEVMNKISEI 236
                                   9************95 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                  H-kinase_dim   4 lRVdakrlDyLlnlvGEl.....VitkarLnqsleefrfenglkasvtelkssl 52 
                                   +R da++++  +n ++E+     +  k+++ + +++++  +++k+  ++ + sl
  gi|91772414|ref|YP_565106.1| 328 IRGDAEKVEGVMNKISEIanfeiISCKKEVPETIDSLN-LEEMKNISQNENNSL 380
                                   899*************8522222677777777777777.666666666655555 PP

  == domain 3  score: 46.9 bits;  conditional E-value: 1.2e-15
                  H-kinase_dim   2 stlRVdakrlDyLlnlvGElVitkarLnqsleefrfenglkasvtelksslqnlgrisgeLQegvmki 69 
                                   +t+RV ++ +D  +nlvGElVi+k  L q+++e +          el+++++ l++ ++ LQ++vm+i
  gi|91772414|ref|YP_565106.1| 513 DTIRVRVSNIDSIMNLVGELVINKGCLLQISQEHK--------IPELEEATSILDKSITSLQDEVMMI 572
                                   79*********************************........***********************87 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 !   23.5   0.3   1.8e-08     4e-05       7     101 ..     622     752 ..     617     786 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-08
                   HATPase_c_3   7 laelvdNsldAdaen..............vkievnknrgktgeivieDdGkGmseeelkn......alrlatsskeakr.. 65 
                                   l+ lv+N++d   e+              +k+++++++ ++  i ieDdGkG++ e +k+       l+la+ +k  +   
  gi|91772414|ref|YP_565106.1| 622 LVHLVRNCVDHGVESpeerakagksktghIKLSAKREK-NNVIIEIEDDGKGLDLERIKSkalekgILSLAELDKLGEDei 701
                                   7889******8888888888888899999999999986.6899**********9998876511124456777777766544 PP

                   HATPase_c_3  66 .............kstslGkkGiGl...klAslslgkkltvitkkegesstl 101
                                                ++t ++ +G+G+   k+ + +lg k+++++kk  + +++
  gi|91772414|ref|YP_565106.1| 702 ssliftsglstkdNATEISGRGVGMdavKTTVEKLGGKIKIYSKKG-KGTKM 752
                                   44555555444444666999****8888999************864.33333 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.8      0.31   6.9e+02      22      68 ..     461     508 ..     458     512 .. 0.74
   2 !   15.4   0.1   5.6e-06     0.013       6      92 ..     622     747 ..     619     754 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.31
                   HATPase_c_5  22 skieeekrfIrltvrekkksliisieNsyegek.kklesskskkeehG 68 
                                   ++ie+++++ ++ v+ek+++ ++ + N+ + ++ +++ + ++kk++ G
  gi|91772414|ref|YP_565106.1| 461 EEIEKQDEIPEIMVEEKNQQEVVDFRNTESTQEnDTVIQDTTKKGYVG 508
                                   567776777789999999999999***977766344445566777766 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.6e-06
                   HATPase_c_5   6 lcvilgnlLdNAieacsk...iee.ekrfIrltvrekkksliisieNsyeg.............................. 52 
                                   l+ ++ n  d  +e+ ++     + ++  I+l+++++k+++ii+ie   +g                              
  gi|91772414|ref|YP_565106.1| 622 LVHLVRNCVDHGVESPEErakAGKsKTGHIKLSAKREKNNVIIEIEDDGKGldlerikskalekgilslaeldklgedeis 702
                                   56677788888888776632222335678*******************999999****************99999988665 PP

                   HATPase_c_5  53 .....ekkklesskskkeehGiGlksireivkkykgnlsieaedg 92 
                                        +  + +++ ++ + +G+G+  ++ +v+k +g+++i  ++g
  gi|91772414|ref|YP_565106.1| 703 sliftSGLSTKDNATEISGRGVGMDAVKTTVEKLGGKIKIYSKKG 747
                                   44432112233445667889*******************998875 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.068      53     104 ..     642     726 ..     601     754 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                   HATPase_c_2  53 e......gpvevrlesdeealtvevaDsGpgfdpetlpdpteeep...........................keslkegGr 100
                                   +      g+++++++++++ + +e++D+G+g d+e ++ +++e+                            ++  +++Gr
  gi|91772414|ref|YP_565106.1| 642 KagksktGHIKLSAKREKNNVIIEIEDDGKGLDLERIKSKALEKGilslaeldklgedeissliftsglstkDNATEISGR 722
                                   0333334999999*********************99998888766999999999999999999999999999999999999 PP

                   HATPase_c_2 101 Glal 104
                                   G+ +
  gi|91772414|ref|YP_565106.1| 723 GVGM 726
                                   9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (897 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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):               8  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 5856.09
//
Query:       gi|91772415|ref|YP_565107.1|  [L=200]
Description: CheC-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-23   81.8   0.2    4.5e-12   45.7   0.0    2.5  2  CheC      CheC-like family
      1e-07   32.0   1.2    0.00057   20.0   0.1    2.5  2  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0     5e-16   4.5e-12       5      38 .]      14      47 ..      10      47 .. 0.93
   2 !   33.9   0.1   2.4e-12   2.1e-08       1      35 [.     106     140 ..     106     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 5e-16
                                  HHHHHHHHHHHHHHHHHHTCCTS-EEE---EEEE CS
                          CheC  5 AlgEigNIlaGsaatalatllnfkidisPPtvvy 38
                                  +l+E+gNI++G+aat+l++lln+ i++++P+v++
  gi|91772415|ref|YP_565107.1| 14 VLKELGNIGTGHAATSLSKLLNKYIEMTVPEVKI 47
                                  89*****************************985 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 2.4e-12
                                   HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---E CS
                          CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPt 35 
                                   m +SA++E+gNIl++ +++a a++l++ + +sPP 
  gi|91772415|ref|YP_565107.1| 106 MYASAVMEAGNILSSAFCDAAADFLDIILLPSPPN 140
                                   568*******************************5 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   6.6e-05       0.6      43      72 ..      12      45 ..       3      53 .. 0.84
   2 !   20.0   0.1   6.3e-08   0.00057       5      57 ..      70     122 ..      66     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.6e-05
                          CheX 43 ndavgEltNmiaGnakskl....geevklspPlv 72
                                   +++ El N+ +G+a + l    ++ +++++P+v
  gi|91772415|ref|YP_565107.1| 12 VEVLKELGNIGTGHAATSLskllNKYIEMTVPEV 45
                                  6899************7774446779******97 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.3e-08
                          CheX   5 iglaGdisGliilsadeelalkiasal.gedeeeieedvndavgEltNmiaGna 57 
                                    +l+G  sG+++++++ ++a  +++++ g d+ + +e+  +av+E  N+++ ++
  gi|91772415|ref|YP_565107.1|  70 EDLEGVNSGYLYVMLPVKSADILVKEMyGTDDVD-DEMYASAVMEAGNILSSAF 122
                                   5789999*******************97888888.*************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1220.19
//
Query:       gi|229220840|ref|YP_565108.2|  [L=220]
Description: chemoreceptor glutamine deamidase CheD [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   94.7   0.1      5e-27   94.1   0.1    1.2  1  CheD      CheD chemotactic sensory transduction


Domain annotation for each model (and alignments):
>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.1   2.8e-31     5e-27      12     108 ..     117     211 ..     112     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 2.8e-31
                                    -TTSCCCBHHHHHHHHHHHHHTTT--GGG-EEEEEE----S.....---SS-HHHHHHHHHHHHHHHTT--EEEEEE-SS CS
                           CheD  12 sasnpakyadtaielLinellklgakkerleaklaGGAqmfafessksdvlniGerNveavkelLkeegipivaedvggn 91 
                                    s++ ++k+a+tai +++++++++ga+++++ ak aGGAq+f+ +s   d+l+iG+rN++ v+e+L++e+i+i+a+dvgg+
  gi|229220840|ref|YP_565108.2| 117 SSDGKTKHAETAITTMLEDMVSNGARRRHICAKFAGGAQIFKHMS--LDILKIGDRNIKSVEETLAKEKIKILATDVGGD 194
                                    456789***********************************9966..79******************************* PP

                                    S-EEEEEETTTTEEEEE CS
                           CheD  92 ygRtvlfdpatgkvlvk 108
                                     gR+vlf++ +g ++vk
  gi|229220840|ref|YP_565108.2| 195 MGRNVLFNTIDGSLIVK 211
                                    *************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1244.80
//
Query:       gi|91772417|ref|YP_565109.1|  [L=270]
Description: protein-glutamate O-methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-56  189.9   0.1      4e-56  189.6   0.1    1.1  1  CheR             CheR methyltransferase, SAM binding domain
    1.1e-10   41.0   1.0    2.1e-10   40.2   1.0    1.5  1  CheR_N           CheR methyltransferase, all-alpha domain
    1.1e-05   26.1   0.0      9e-05   23.1   0.0    2.2  1  Methyltransf_25  Methyltransferase domain
    3.7e-05   24.4   0.0    0.00019   22.1   0.0    2.1  1  Methyltransf_12  Methyltransferase domain
    0.00087   19.1   0.0     0.0016   18.2   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
     0.0024   17.3   0.1     0.0063   16.0   0.0    1.7  2  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.016   15.1   0.0       0.02   14.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.019   15.6   0.0      0.083   13.5   0.0    2.0  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   0.1   1.8e-59     4e-56       1     193 [.      72     264 ..      72     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 1.8e-59
                                   SS--TTTTCHHHHHHHHCCH.HHHHHHHTS..SSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHH CS
                          CheR   1 neTeffreakhfeelekevlepllakakne..krvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlek 79 
                                   n+Tef+r++++f  ++++++ + +++++++  k vr+wsagcs+GeEpYs+ +++ke+lpk  +  ++i+AtDid k+l++
  gi|91772417|ref|YP_565109.1|  72 NVTEFMRDKTPFVYFKDKLIADIIERKQSSqsKLVRFWSAGCSNGEEPYSIGICAKEALPKDWN--ISIYATDIDVKCLKN 150
                                   79******************99888887776456***********************8887766..*************** PP

                                   HHHTEEECCHHTTS-HHHHHHHEEEEETTCEEE-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHH CS
                          CheR  80 AkagvykeeeleglseelleryfekseddsykvkkeikelvkFeklnllekksvlgklDvifcrnvliYfdeetqekvler 160
                                   A++gvy ++++e+l + l+++yfe+sed ++k+k+      +F++++l+++++v++++D +fcrnv+iYf+e ++ k++++
  gi|91772417|ref|YP_565109.1| 151 ASEGVYCQDKIEKLDPILKDKYFERSED-NFKIKNIQNLSYRFKNYDLTNDSPVSKHFDTVFCRNVMIYFNEGQKVKMISN 230
                                   ***********************66666.**************************************************** PP

                                   HHCCEEEEEEEEE-TTB--S.SSCCCCCEEEECT CS
                          CheR 161 faeklkpgglLllGhsEslk.klkdkfevvkstk 193
                                   f+e+l +gg+L++G+sE+l+ +++  fe+v+++ 
  gi|91772417|ref|YP_565109.1| 231 FHESLTKGGYLIIGKSETLPpEVRSLFETVSVRD 264
                                   ********************99999999998765 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   1.0   9.4e-14   2.1e-10       3      52 ..       9      58 ..       7      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 9.4e-14
                                  HHHHHHHHHHTT-EE--SSTHHHHHTHHHHHHHTTT-SSSHHHHHHTSHS CS
                        CheR_N  3 ferlleliyertGidlsdyKrallkrRlsrRmralglksfeeYldlLrsd 52
                                  f++l + i +++Gi l +y+ ++lkrR++ Rmra  ++++++Y +lL ++
  gi|91772417|ref|YP_565109.1|  9 FNLLTKKISKSSGIILDGYRDSYLKRRIDLRMRAIEVSDYKDYSQLLDKN 58
                                  899********************************************998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     4e-08     9e-05      44      97 .]     186     239 ..     111     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4e-08
                                   TTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  44 eglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                   ++l+ +f + d+++ +  +++fD v++++++ ++++ +  k+++++++ L++gG
  gi|91772417|ref|YP_565109.1| 186 QNLSYRFKNYDLTNDSPVSKHFDTVFCRNVMIYFNEGQKVKMISNFHESLTKGG 239
                                   556999******99999999*******999***********************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.3e-08   0.00019      43      99 .]     182     241 ..     121     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.3e-08
               Methyltransf_12  43 rennnnnnvelealdlldldgg.ssfDlvvasnvlhhl..kdirevldnirklLkpgGrl 99 
                                   ++n +n  +++++ dl ++++  ++fD+v++ nv+ ++   ++ ++++n+++ L++gG+l
  gi|91772417|ref|YP_565109.1| 182 IKNIQNLSYRFKNYDLTNDSPVsKHFDTVFCRNVMIYFneGQKVKMISNFHESLTKGGYL 241
                                   444456667777777766666689**************988899**************87 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   7.3e-07    0.0016      58     124 ..     180     255 ..     103     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.3e-07
               Methyltransf_31  58 Feqgdieeleklled..........ekfDlilsnevlnaladpdki..leeiervlkpggilliedprllaelpakvee 124
                                   F++ +i++l+  ++           + fD +++++v+ ++++ +k+  + + ++ l++gg+l+i        lp +v++
  gi|91772417|ref|YP_565109.1| 180 FKIKNIQNLSYRFKNydltndspvsKHFDTVFCRNVMIYFNEGQKVkmISNFHESLTKGGYLIIGKSE---TLPPEVRS 255
                                   444444444422222334444444499**********8888776652266*************99888...55555555 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.96   2.1e+03      97     121 ..      75      99 ..      47     104 .. 0.64
   2 !   16.0   0.0   2.8e-06    0.0063      70     132 ..     181     243 ..     168     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.96
                                   EEEEEESSGGGS-GGGHHHHHHHHH CS
                          TehB  97 dfilstvvlmfleaeripsiienmq 121
                                   +f+     +++++ + i++iie  q
  gi|91772417|ref|YP_565109.1|  75 EFMRDKTPFVYFKDKLIADIIERKQ 99 
                                   3444455566777777777776655 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.8e-06
                                   HHHHHTT-TTEEEEE--G.GG----S-EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEE CS
                          TehB  70 eikekenlknistalydi.neaklderydfilstvvlmfleaeripsiienmqectkvggynli 132
                                   +ik+++nl+  + + yd+ n+  +++++d ++   v++++++ +  ++i+n++e    ggy +i
  gi|91772417|ref|YP_565109.1| 181 KIKNIQNLS-YRFKNYDLtNDSPVSKHFDTVFCRNVMIYFNEGQKVKMISNFHESLTKGGYLII 243
                                   467777777.6778899856788**************999999999***************554 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     9e-06      0.02      37     117 ..     126     243 ..      73     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9e-06
               Methyltransf_23  37 levl..rengfsvtgvDlspeaveiae.................................kakkaqkdqfdeqeaaepqgk 82 
                                   ++++  +++  s+++ D++ ++ + a+                                 +   ++++++d  ++++ +++
  gi|91772417|ref|YP_565109.1| 126 AKEAlpKDWNISIYATDIDVKCLKNASegvycqdkiekldpilkdkyfersednfkikniQNLSYRFKNYDLTNDSPVSKH 206
                                   44444566777999999988888888889999998888888888888888888887777766667777777778888899* PP

               Methyltransf_23  83 fdlIvlrevlehvp..dppellrqiatllkpgGylll 117
                                   fd++ +r+v+  +      + ++++++ l  gGyl++
  gi|91772417|ref|YP_565109.1| 207 FDTVFCRNVMIYFNegQKVKMISNFHESLTKGGYLII 243
                                   **************55599****************97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.7e-05     0.083      44      96 .]     189     243 ..     120     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                   EEEETTEECCC.TSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  44 kvefvvadaek.lpfednsfDlvvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                   + +f   d+++  p+ +  fD v++++v+ ++   +  k +++++  L +gG+l+i
  gi|91772417|ref|YP_565109.1| 189 SYRFKNYDLTNdSPVSK-HFDTVFCRNVMIYFneGQKVKMISNFHESLTKGGYLII 243
                                   45667777775246655.9*************55467789**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1640.28
//
Query:       gi|91772418|ref|YP_565110.1|  [L=388]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  150.1   5.0    7.1e-44  150.1   5.0    1.5  2  Y2_Tnp         Putative transposase
    7.3e-22   77.2   6.8    7.3e-22   77.2   6.8    2.1  2  Zn_Tnp_IS91    Transposase zinc-binding domain
     0.0023   17.9   0.1        1.9    8.6   0.0    2.5  2  Proho_convert  Prohormone convertase enzyme
     0.0066   16.4   1.3      0.018   15.0   0.2    2.2  2  Armet          Degradation arginine-rich protein for mis-fold
  ------ inclusion threshold ------
       0.45   10.3  10.0       0.78    9.5   1.9    3.4  3  zf-C2H2_11     zinc-finger C2H2-type
        7.8    6.7   8.4         16    5.7   6.2    2.3  2  Zn-ribbon_8    Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Y2_Tnp  Putative transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.8   8.5e+03      22      43 ..      78     100 ..      77     108 .. 0.62
   2 !  150.1   5.0   2.4e-47   7.1e-44       1     180 [.     152     323 ..     152     326 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.8
                        Y2_Tnp  22 lvpdGgleedgewkaskks.ffl 43 
                                   + ++ gl+++++w +s k+ +f 
  gi|91772418|ref|YP_565110.1|  78 ICTNCGLNHTEKWSKSLKRaMFN 100
                                   56677777778888766663443 PP

  == domain 2  score: 150.1 bits;  conditional E-value: 2.4e-47
                        Y2_Tnp   1 GavavlhtfgsalnlhpHvHvlvpdGgleedgewkaskksfflpvkalsrlfrgklletlrkavaraklkrgllerdeefs 81 
                                   Ga++vlh f++++ ++pH+H+l+++G +++ g+     ++ f+++k++++++++++l+++++a       +++++++++  
  gi|91772418|ref|YP_565110.1| 152 GAIVVLHPFSKDMGFNPHLHILLTEGRFDMYGKF---IHQKFIHFKTMRKTWQYQVLTRFKDA-------LSKVQAFSHLV 222
                                   99******************************44...4479**********************.......7789999**** PP

                        Y2_Tnp  82 sllkkaskkgfvvhakkave..kerkvleyLarYisrpaisnkRlvstdeekvtfrlkdkrrkktktvtlepeefirrlla 160
                                   + l k++ +gf+vh+ k+ +  +++++ +y++rYi++pai+n+Rl+s+d+++vtf+++d++ + ++ vt+e +efir l++
  gi|91772418|ref|YP_565110.1| 223 NQLFKEYPDGFYVHMPKNSRitNKQRMAQYVGRYIRHPAIANSRLYSYDGKSVTFWYNDHE-GVRHFVTMELQEFIRALIQ 302
                                   ****************998887999***********************************7.78899************** PP

                        Y2_Tnp 161 hVppkgfkriRyyGvla.rvk 180
                                   h+p+++fk+iRyyG ++ +vk
  gi|91772418|ref|YP_565110.1| 303 HIPDRNFKMIRYYGAYSrKVK 323
                                   *****************4444 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 !   77.2   6.8   2.4e-25   7.3e-22       4      91 .]      22     110 ..      19     110 .. 0.95
   2 ?   -2.1   0.1       1.3     4e+03      60      74 ..     353     367 ..     347     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.4e-25
                   Zn_Tnp_IS91   4 dhleeflek.kkklrpsqrkavekilrCrtaalGfaryeCeeCghekivyfsCksrhCpsCqkkateewlekqqeellpvp 83 
                                   +++++f+   ++ lr++++++v+k+l+C++++ Gf +y+Ce+Cg+ k+vyf C+s  C++C+ ++te+w +++++ +++v 
  gi|91772418|ref|YP_565110.1|  22 NNWDQFCIDhEDILRNVEIEEVNKMLSCKDKSRGFFTYQCESCGNYKTVYFGCNSCICTNCGLNHTEKWSKSLKRAMFNVV 102
                                   78999988867788******************************************************************* PP

                   Zn_Tnp_IS91  84 yrhvvfTl 91 
                                   +rh v+T+
  gi|91772418|ref|YP_565110.1| 103 HRHAVLTI 110
                                   *******7 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                   Zn_Tnp_IS91  60 CpsCqkkateewlek 74 
                                   C+ C+ k +  w ek
  gi|91772418|ref|YP_565110.1| 353 CSFCGGKMKFVWYEK 367
                                   888888888888876 PP

>> Proho_convert  Prohormone convertase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00063       1.9      21      30 ..     141     150 ..     138     157 .. 0.87
   2 !    6.7   0.0    0.0024       7.2       6      20 ..     223     237 ..     219     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00063
                 Proho_convert  21 pYrHRDdrLL 30 
                                    ++HR+drLL
  gi|91772418|ref|YP_565110.1| 141 SFKHRNDRLL 150
                                   58*******9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0024
                 Proho_convert   6 dslYsdYsDgFYrik 20 
                                   ++l+ +Y DgFY   
  gi|91772418|ref|YP_565110.1| 223 NQLFKEYPDGFYVHM 237
                                   78**********765 PP

>> Armet  Degradation arginine-rich protein for mis-folding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.44   1.3e+03     110     136 ..      13      39 ..       2      47 .. 0.78
   2 !   15.0   0.2   6.1e-06     0.018     101     132 ..     332     363 ..     284     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.44
                         Armet 110 eLkkiledWgeeCkgCieksdfikrie 136
                                    +k+i++d ++  + Ci+ +d ++ +e
  gi|91772418|ref|YP_565110.1|  13 TVKRIFKDNNNWDQFCIDHEDILRNVE 39 
                                   578999888888889999999988775 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.1e-06
                         Armet 101 vdlkklkvkeLkkiledWgeeCkgCieksdfi 132
                                     +k+   k+ kk+l++W  +C+ C  k  f+
  gi|91772418|ref|YP_565110.1| 332 RSIKQTNLKDFKKVLNKWAPQCSFCGGKMKFV 363
                                   46789999*********************998 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.028        84       4      11 ..      58      65 ..      57      67 .. 0.92
   2 ?    9.5   1.9   0.00026      0.78       3      25 ..      75      99 ..      74     104 .. 0.78
   3 ?    1.1   0.1      0.11   3.4e+02       4      11 ..     350     357 ..     347     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.028
                    zf-C2H2_11  4 tcqCleCG 11
                                  t+qC  CG
  gi|91772418|ref|YP_565110.1| 58 TYQCESCG 65
                                  89*****9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00026
                    zf-C2H2_11  3 stcqCleCGlcftSql..sLsRHlf 25
                                  ++c C+ CGl+ t +   sL+R +f
  gi|91772418|ref|YP_565110.1| 75 NSCICTNCGLNHTEKWskSLKRAMF 99
                                  79***********864227999888 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.11
                    zf-C2H2_11   4 tcqCleCG 11 
                                   ++qC  CG
  gi|91772418|ref|YP_565110.1| 350 APQCSFCG 357
                                   79*****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.2    0.0053        16       4      38 ..      57      89 ..      56      90 .. 0.77
   2 ?   -0.2   0.0      0.37   1.1e+03      27      35 ..     351     359 ..     341     363 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0053
                   Zn-ribbon_8  4 YeYrCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                  + Y+Ce+Cg+  +v    +      C +Cg  ++++
  gi|91772418|ref|YP_565110.1| 57 FTYQCESCGNYKTVYFGCN---SCICTNCGLnHTEK 89
                                  78*******8888887655...455****9866665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.37
                   Zn-ribbon_8  27 taCPeCgse 35 
                                   ++C  Cg++
  gi|91772418|ref|YP_565110.1| 351 PQCSFCGGK 359
                                   557777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2430.25
//
Query:       gi|91772419|ref|YP_565111.1|  [L=192]
Description: hypothetical protein Mbur_0366 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1114.58
//
Query:       gi|91772420|ref|YP_565112.1|  [L=160]
Description: formaldehyde-activating enzyme [Methanococcoides burtonii DSM 6242]
Scores for complete 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-70  234.7   0.5    4.8e-70  234.6   0.5    1.0  1  Fae       Formaldehyde-activating enzyme (Fae)
  ------ inclusion threshold ------
      0.034   13.3   0.0      0.046   12.8   0.0    1.2  1  ECSIT     Evolutionarily conserved signalling intermediate in


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 !  234.6   0.5   5.4e-74   4.8e-70       1     158 [.       2     159 ..       2     160 .] 0.99

  Alignments for each domain:
  == domain 1  score: 234.6 bits;  conditional E-value: 5.4e-74
                           Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfGpaQa 81 
                                   +GEalvgeg+evAhid+++G+k+++v+tAf+++la++++gh+pllavl+pn+l kPatl+vnkvtikn++qa l+fGpaQa
  gi|91772420|ref|YP_565112.1|   2 IGEALVGEGPEVAHIDIVVGTKGSAVETAFMTSLASPRQGHSPLLAVLEPNVLPKPATLLVNKVTIKNANQAILMFGPAQA 82 
                                   8******************************************************************************** PP

                           Fae  82 avakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdkakhpf 158
                                   ++akav+d+veegiipkeea+ l+iivsvf++++a+dk+kiyeynyeAtklA+krA++++P++de l++kd+a+hpf
  gi|91772420|ref|YP_565112.1|  83 SIAKAVMDSVEEGIIPKEEAEYLLIIVSVFLQWDATDKAKIYEYNYEATKLALKRAIEGTPTVDEALAKKDSAEHPF 159
                                   ****************************************************************************9 PP

>> ECSIT  Evolutionarily conserved signalling intermediate in Toll pathway
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.1e-06     0.046      97     144 ..      63     109 ..      52     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-06
                         ECSIT  97 evfiprnllqaeFlhyprqqecgvdvLeqmeengvlPdketeallvqi 144
                                   ++++ +n  qa+ ++ p q  ++ +v++ +ee g++P +e e ll+ +
  gi|91772420|ref|YP_565112.1|  63 NKVTIKNANQAILMFGPAQASIAKAVMDSVEE-GIIPKEEAEYLLIIV 109
                                   578899***********************985.*********998743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 943.15
//
Query:       gi|91772421|ref|YP_565113.1|  [L=125]
Description: HxlR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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   79.3   0.0    1.9e-22   78.9   0.0    1.2  1  HxlR      HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.019   14.9   0.4      0.037   14.0   0.1    1.7  2  HTH_45    Winged helix-turn-helix
      0.072   13.1   0.1       0.24   11.4   0.0    1.8  2  PadR      Transcriptional regulator PadR-like family
      0.085   13.0   0.0       0.13   12.4   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
      0.096   12.4   0.1        0.2   11.4   0.1    1.5  1  VD10_N    Viral D10 N-terminal


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   5.3e-26   1.9e-22       1      84 [.      15      98 ..      15     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 5.3e-26
                                  HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHHH CS
                          HxlR  1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkwg 83
                                  +i++kW+l i++ +++gkk f+e+ +  pk+s k+L+ +Lr+Leqd lie+ +++++P  +eY+lt kGr+l+++l e++ ++
  gi|91772421|ref|YP_565113.1| 15 IISKKWTLNIIRDMFCGKKQFNEFLKSNPKLSSKVLSDKLRQLEQDDLIEKLIVSKTPLSIEYHLTSKGRNLNKLLYEISGFA 97
                                  699*************************************************************************9998876 PP

                                  H CS
                          HxlR 84 e 84
                                   
  gi|91772421|ref|YP_565113.1| 98 Y 98
                                  4 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     1e-05     0.037      30      73 ..      44      94 ..      22      98 .. 0.85
   2 ?   -2.3   0.0       1.3   4.6e+03      53      60 ..     111     118 ..     101     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                        HTH_45 30 nLsykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkele 73
                                   Ls k+l+  L +L + +li       +  + +Y lT kG++l + l e+ 
  gi|91772421|ref|YP_565113.1| 44 KLSSKVLSDKLRQLEQDDLIeklivskTPLSIEYHLTSKGRNLNKLLYEIS 94
                                  689999999999******998888863337899**********99999886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                        HTH_45  53 kekYvlTe 60 
                                   +++Y+lT+
  gi|91772421|ref|YP_565113.1| 111 EHSYKLTK 118
                                   45666665 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.6e-05      0.24      31      71 ..      47      85 ..      32      88 .. 0.79
   2 ?   -1.3   0.0      0.59   2.1e+03      11      17 ..     112     118 ..      95     122 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                                  HHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                          PadR 31 eGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                     l + L++Le+++l+e+  +   ++p    Y+lT +Gr+
  gi|91772421|ref|YP_565113.1| 47 SKVLSDKLRQLEQDDLIEKLIVS--KTPLSIEYHLTSKGRN 85
                                  55566789************997..69************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.59
                                   EHHHHHH CS
                          PadR  11 yGyeiik 17 
                                   + y+++k
  gi|91772421|ref|YP_565113.1| 112 HSYKLTK 118
                                   4444444 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 ?   12.4   0.0   3.7e-05      0.13      18      67 ..      37      85 ..      22      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                        HTH_34 18 velkealeatdgnLsvhlkkLekagYievdkefkgkkpr.tllriTpeGre 67
                                  ++lk+  ++++  Ls +l+ Le+ + ie  k  ++k+p  + + +T++Gr+
  gi|91772421|ref|YP_565113.1| 37 EFLKSNPKLSSKVLSDKLRQLEQDDLIE--KLIVSKTPLsIEYHLTSKGRN 85
                                  57999999*****************985..777888886267********8 PP

>> VD10_N  Viral D10 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.5e-05       0.2       2      20 ..      29      47 ..      28      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                        VD10_N  2 lyySslfsyitknNrkLsk 20
                                  ++  + f++ +k+N+kLs+
  gi|91772421|ref|YP_565113.1| 29 FCGKKQFNEFLKSNPKLSS 47
                                  666788***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 871.47
//
Query:       gi|91772422|ref|YP_565114.1|  [L=408]
Description: geranylgeranyl reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   57.7   2.2    6.1e-14   52.0   2.2    2.7  1  FAD_binding_3   FAD binding domain
    2.8e-11   43.4   2.7    9.9e-11   41.6   2.7    1.7  1  FAD_oxidored    FAD dependent oxidoreductase
    1.8e-10   40.5   2.2    5.4e-07   29.0   0.6    2.2  2  FAD_binding_2   FAD binding domain
    9.1e-09   34.9   0.4    1.3e-08   34.3   0.4    1.3  1  GIDA            Glucose inhibited division protein A
    4.3e-08   32.3   0.9    1.3e-07   30.6   0.1    2.1  3  HI0933_like     HI0933-like protein
    5.3e-07   29.0   0.4    0.00056   19.1   0.4    2.4  2  Lycopene_cycl   Lycopene cyclase protein
    7.3e-07   28.7   3.4    2.7e-05   23.5   0.3    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.7e-07   29.3   0.3      3e-06   27.4   0.1    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.1e-06   27.0   0.8     0.0023   17.6   0.2    2.1  2  DAO             FAD dependent oxidoreductase
    1.3e-05   24.3   0.7       0.11   11.4   0.5    2.3  2  Trp_halogenase  Tryptophan halogenase
    5.7e-05   22.5   3.2      0.001   18.4   3.2    2.3  1  Thi4            Thi4 family
     0.0012   18.1   0.2     0.0019   17.5   0.2    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.023   14.0   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.055   13.4   0.1       0.12   12.2   0.1    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.058   14.0   0.4       0.51   10.9   0.1    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
        0.2   10.7   0.0       0.32   10.0   0.0    1.3  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 !   52.0   2.2   5.5e-17   6.1e-14       2     337 ..       5     326 ..       4     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 5.5e-17
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaegapnelmgealynels 81 
                                   +d ++VGaGpaG ++a+  +++G +v+++ekr++  +  r a+g+ ++ ++  +++ l+++ l   ++++   ++  n   
  gi|91772422|ref|YP_565114.1|   5 YDLVVVGAGPAGSIAATTAAKKGLSVLMLEKRQEIGEPVRcAEGVGKKRLR--QHIELDEKWLCGEVSSAK--IISPNG-- 79 
                                   5779****************************9988777648888888665..788899998887755553..333333.. PP

                                   CCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE-- CS
                 FAD_binding_3  82 dtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaD 162
                                         +  e++++ e  +v+  + ++r Lve   e+g+++  k++v++l  +e++v  +   +  g+++ +r+k ++GaD
  gi|91772422|ref|YP_565114.1|  80 ---TTLTMAEEDAGSEVGYVLDRKIFDRTLVELSGEAGVDIMVKARVTGLIIEENTVCGVEMMH-LGKTYSIRSKLVIGAD 156
                                   ...22333334688888899999*********************************99988888.5*************** PP

                                   GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTC.CEEEEECCTTEE..EEEECCETEEEEEEEEECCE-GGGS CS
                 FAD_binding_3 163 GgrStvrktlgiefegeetvyeagvldvlfda.dlsdivep.lvlilsaesrgv..mviPlentlerfyvqvearaekeer 239
                                   G+ S+v + +gi+ + + +  + + ++ l++  d+++  +   ++++++  +g    v P  n+  ++ + +  ++  e++
  gi|91772422|ref|YP_565114.1| 157 GVESKVGRWAGIDTSLKPSH-IETCAQFLVSGvDIDQ--SScYFYMGNKVAPGGyvWVFPKGNNMANVGIGILGSRAGEKK 234
                                   *************6655544.4566666655557772..223466666655555448899999555554444445555666 PP

                                   CCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHH CS
                 FAD_binding_3 240 sekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaa 320
                                   + ++ ++ v a++++ + ++++   +        a+   ek   + ++l+GDAa    P +G G+  a+    + +   a+
  gi|91772422|ref|YP_565114.1| 235 PIEYLTDFVEANYPNGSIIEQVAGAVP-------ASGPIEKTIANGLMLVGDAARQSDPFTGGGISNAMDAGLYAGEVAAE 308
                                   999999999999999888777766554.......445566777789**********************9999999988888 PP

                                   HH.TTSS-GGGGHHHHHH CS
                 FAD_binding_3 321 vl.kGeAkeelLdtYeee 337
                                   ++ + + +e++L+ Ye++
  gi|91772422|ref|YP_565114.1| 309 AIaQDDVSEKILQKYEKR 326
                                   762566788899999875 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   2.7   8.8e-14   9.9e-11       1     156 [.       6     170 ..       6     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 8.8e-14
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG..Glltsglvatdignkaee...qvvtg.iareflerlrqrgga.. 73 
                                   D+vVvG+gpaG +AA +Aa++G +vl++e+r+ +G     + g++   + +++e    ++++     ++++ +        
  gi|91772422|ref|YP_565114.1|   6 DLVVVGAGPAGSIAATTAAKKGLSVLMLEKRQEIGepVRCAEGVGKKRLRQHIELdekWLCGEvSSAKIISPNGT---Tlt 83 
                                   99********************************94412344444444444444344444444123344444433...122 PP

                  FAD_oxidored  74 .rlkkrskwn...tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg.dGdla 149
                                     ++++ + +   + + +++ ++l e+  eagv+++ ++r+++ + e++++ +v++ +  +++ ir+k++i A g + +++
  gi|91772422|ref|YP_565114.1|  84 mAEEDAGS-EvgyVLDRKIFDRTLVELSGEAGVDIMVKARVTGLIIEENTVCGVEMMHLGKTYSIRSKLVIGADGvESKVG 163
                                   11122222.13559*********************************99*******77667**********9976567777 PP

                  FAD_oxidored 150 alaGvpy 156
                                    +aG+ +
  gi|91772422|ref|YP_565114.1| 164 RWAGIDT 170
                                   7777765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.6   4.8e-10   5.4e-07       1      43 [.       6      48 ..       6      52 .. 0.93
   2 !   10.9   0.0   0.00016      0.17     146     200 ..     105     157 ..      80     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.8e-10
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                  D++V+G+G AG  AA++aa++Gl+v+++ek qe g    +++G
  gi|91772422|ref|YP_565114.1|  6 DLVVVGAGPAGSIAATTAAKKGLSVLMLEKRQEIGEPVRCAEG 48
                                  89******************************99888777777 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00016
                                   HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                 FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                   +lve   +agvd++ +++++ Li+e++ v G++++  + g++  ir+k v+ a g
  gi|91772422|ref|YP_565114.1| 105 TLVELSGEAGVDIMVKARVTGLIIEENTVCGVEMM--HLGKTYSIRSKLVIGADG 157
                                   4566666788*************************..999999999999988876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.4   1.2e-11   1.3e-08       1     147 [.       6     155 ..       6     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.2e-11
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--S.SSSEEE-T.THHHHHHHHHHHT-SH..HHHHHHHEEEEEEE CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaels.Cnpsiggi.akgllvrEidalggli..ikaadkagiqfril 77 
                                   d++V+G+G AG+ AA +aa++G++vl++ +k ++i+e + C + +g +  + ++  + + l g++  +k++  +g  + + 
  gi|91772422|ref|YP_565114.1|   6 DLVVVGAGPAGSIAATTAAKKGLSVLML-EKRQEIGEPVrCAEGVGKKrLRQHIELDEKWLCGEVssAKIISPNGTTLTMA 85 
                                   689************************9.8999999964387777766533444433344555442267788888878887 PP

                                   STTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEE.ES-EEEEEECTTEEEEEEE.TTS-EEEEC..EEEE- CS
                          GIDA  78 NrskGpavralraqvdrelyskevteklenepnleii.eeeveeliveekkvkgvvt.edgetikak..avvia 147
                                    +  G  v++     dr+ + +++ e l+ e  ++i+ +++v+ li+ee++v+gv + + g+t++ +   v+ a
  gi|91772422|ref|YP_565114.1|  86 EEDAGSEVGYV---LDRKIFDRTLVE-LSGEAGVDIMvKARVTGLIIEENTVCGVEMmHLGKTYSIRskLVIGA 155
                                   77777777777...*******99875.78889999963789*************96515566655433155555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   1.2e-10   1.3e-07       2      43 ..       6      48 ..       5      64 .. 0.90
   2 ?   -1.4   0.0      0.63     7e+02     115     155 ..     106     147 ..     100     161 .. 0.69
   3 ?   -2.5   0.0       1.4   1.5e+03     307     343 ..     333     366 ..     306     370 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.2e-10
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC.G CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis.G 43
                                  d++v+G+G+AG  aA +aak+g +Vl+lek +++g+ ++ + G
  gi|91772422|ref|YP_565114.1|  6 DLVVVGAGPAGSIAATTAAKKGLSVLMLEKRQEIGEPVRCAeG 48
                                  89*********************************99987645 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.63
                                   HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEE CS
                   HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvkt.kseeelea 155
                                   l++   eagv+++++ +v+++  ee+ +  v++ + +++++ 
  gi|91772422|ref|YP_565114.1| 106 LVELSGEAGVDIMVKARVTGLIIEENTVCGVEMmHLGKTYSI 147
                                   555667899************999999999988543443332 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.4
                                   HHHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE- CS
                   HI0933_like 307 evlleealieeedkklaqlskkelkklaealkaltvk 343
                                   + ++++ l    +++  +ls+++l++la ++k++ +k
  gi|91772422|ref|YP_565114.1| 333 NEIANN-L--IVKETFFSLSDEDLDSLALSIKDVDFK 366
                                   444444.2..345678899999999999999998886 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4     5e-07   0.00056       1     142 [.       6     159 ..       6     192 .. 0.59
   2 !    7.5   0.0    0.0017       1.9     234     313 ..     251     336 ..     236     358 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5e-07
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecve..hsWsgtivyldd.....gkk 74 
                                   D+vv+GaGpAg   A     ak+gl+v+++e  +++   ++ v + e+ + ++l + +e   +W   +v  ++     g +
  gi|91772422|ref|YP_565114.1|   6 DLVVVGAGPAGSIAATTA--AKKGLSVLMLEKRQEI---GEPVRCAEGVGKKRLRQHIEldEKWLCGEVSSAKiispnGTT 81 
                                   9**********6666555..**********999999...777888888888887776542256754444433210000222 PP

                 Lycopene_cycl  75 illg.......raYgrvsskrlkeellerlvengv.klleakves..veeeea.geslvvleggrkirarlvvdargla 142
                                    ++          Y  + +k + + l e   e+gv ++++a+v+   +ee+++ g  ++ l     ir++lv+ a g+ 
  gi|91772422|ref|YP_565114.1|  82 LTMAeedagseVGY-VLDRKIFDRTLVELSGEAGVdIMVKARVTGliIEENTVcGVEMMHLGKTYSIRSKLVIGADGVE 159
                                   22224555533333.3455555555555555666633567777652133333323333333333377777777777744 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0017
                 Lycopene_cycl 234 evveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres........slsarawa 305
                                   +++e+  g +P    g+++++ ++  + +G aa    P TG  + +++ +   +a  +aa +  +        + +++ w+
  gi|91772422|ref|YP_565114.1| 251 SIIEQVAGAVPA--SGPIEKTIANgLMLVGDAARQSDPFTGGGISNAMDAGL-YAGEVAAEAIAQddvsekilQKYEKRWR 328
                                   78999999***9..88888888876999*******************97654.6666665554433555667766677777 PP

                 Lycopene_cycl 306 tlwprerk 313
                                    + ++e++
  gi|91772422|ref|YP_565114.1| 329 GSFGNEIA 336
                                   66666665 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   2.4e-08   2.7e-05       1      33 [.       5      37 ..       5      56 .. 0.89
   2 !    5.6   0.2    0.0071         8     163     239 ..      88     160 ..      76     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                  +d+vv+G+GpAG  aa+t+a++g+ v+++e+++
  gi|91772422|ref|YP_565114.1|  5 YDLVVVGAGPAGSIAATTAAKKGLSVLMLEKRQ 37
                                  689**************************7443 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0071
                                   HHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE...EEE.EEETTSCEEEESEEEE-S-EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx.xxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 163 klgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge...kle.vvledgeeidadlvvvavGvrp 239
                                   ++g+ev +v +r+++         ++l e   + Gv+++++++v+ ++ +++    +e ++l++  +i  +lv+ a Gv+ 
  gi|91772422|ref|YP_565114.1|  88 DAGSEVGYVLDRKIF--------DRTLVELSGEAGVDIMVKARVTGLIIEENtvcGVEmMHLGKTYSIRSKLVIGADGVES 160
                                   444444444444444........34444555566***********8777777679888999999999*******9999986 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   0.1   2.7e-09     3e-06       1      32 [.       9      40 ..       9      60 .. 0.90
   2 ?   -1.7   0.0       3.2   3.5e+03       7      26 ..     302     321 ..     298     330 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.7e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  +vGaG +G+ aA ++ak+g++vl lekr+ +G
  gi|91772422|ref|YP_565114.1|  9 VVGAGPAGSIAATTAAKKGLSVLMLEKRQEIG 40
                                  8******************************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHCCTEEEEEE- CS
                 NAD_binding_8   7 sGlvaAylLakagfdvllle 26 
                                   +G vaA ++a+++++  +l+
  gi|91772422|ref|YP_565114.1| 302 AGEVAAEAIAQDDVSEKILQ 321
                                   67789999999877533333 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2     2e-06    0.0023       1      33 [.       6      40 ..       6      44 .. 0.95
   2 !    7.6   0.0    0.0022       2.4     152     351 ..     106     308 ..      91     309 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  d+v++G+G +G+ +A  +a++g  V+ lek+ ++g
  gi|91772422|ref|YP_565114.1|  6 DLVVVGAGPAGSIAATTAAKKGlsVLMLEKRQEIG 40
                                  89*****************************9888 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
                                   HHHHHHHTT-EEEESECEEEEEEEETCEEEEE...EECTEEEEEEEE..EEE--GGGHH..HHHTTCTTTSEEEEEEEEEE CS
                           DAO 152 laraaealGveilegtevtgleeedgkvwgve...rttpgendaada..vVnaaGawsd..llgllkeldlpispvrgqvl 225
                                   l +   ++Gv+i  +++vtgl  e++ v gve       g + +++   v+ a G+ s+   +     +d   + ++ +++
  gi|91772422|ref|YP_565114.1| 106 LVELSGEAGVDIMVKARVTGLIIEENTVCGVEmmhL---GKTYSIRSklVIGADGVESKvgRW---AGID---TSLKPSHI 177
                                   55666689************8666678899966642...5443334455********985544...3332...55666666 PP

                                   EEEECCTHSTGSGCSEEEEE......EEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGC CS
                           DAO 226 vlkplseklvspaailpvpe......tdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlg 300
                                    ++   +  vs   i++         ++ +g++v v+p  ++   vG         ++ + + + i++l + +++ +P+ g
  gi|91772422|ref|YP_565114.1| 178 ETCAQFL--VSGVDIDQSSCyfymgnKVAPGGYVWVFPKGNNMANVGIG-----ILGSRAGEKKPIEYLTDFVEANYPN-G 250
                                   6644333..3331111111122333466666666666655443333432.....2223566777899999999999999.9 PP

                                   GEEEEEEEEEE.......E.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                           DAO 301 dvlrkwaGlrp.......l.pdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                   ++ ++ aG  p       +  +gl l+g + + ++ +   G+ ++++  ++ +G+++ae
  gi|91772422|ref|YP_565114.1| 251 SIIEQVAGAVPasgpiekTiANGLMLVGDAARQSDPFTGGGI-SNAMDAGLYAGEVAAE 308
                                   999999999995443322133556666665444455555555.6666666666666665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.5   9.5e-05      0.11       2      35 ..       7      37 ..       6      70 .. 0.85
   2 !   10.9   0.0   0.00013      0.15     142     365 ..      88     325 ..      60     341 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                                  EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                  +v+vG+G+aG++aA++ ak +   l+v+++e+ +
  gi|91772422|ref|YP_565114.1|  7 LVVVGAGPAGSIAATTAAKKG---LSVLMLEKRQ 37
                                  79**************99999...9999999854 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                   -B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-IIIIIIT- CS
                Trp_halogenase 142 lsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgllieqaLk 219
                                    ++ + +y ld++ +++ L + + ++Gv+++    v+  + e++ v ++++       ++   l+i + G ++++   a  
  gi|91772422|ref|YP_565114.1|  88 DAGSEVGYVLDRKIFDRTLVELSGEAGVDIMVKARVTGLIIEENTVCGVEMMHlgkTYSIRSKLVIGADGVESKVGRWAGI 168
                                   4677889**********************9877777777777788888877766225566778*********997655533 PP

                                   --EEE-TTT----EEEEEEEE--H.---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--TTT CS
                Trp_halogenase 220 tgfedwsdvLltdrAlavqvesee.lvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgklea 298
                                    +  + s++  + + l+  v+ ++     y +      G +W  P  +++ n G+    ++a + + ++ l+  ++++  +
  gi|91772422|ref|YP_565114.1| 169 DTSLKPSHIETCAQFLVSGVDIDQsSCYFYMGNKVAPGGYVWVFPKGNNMANvGIGILGSRAGEKKPIEYLTDFVEANYPN 249
                                   333333444444444444444443334445556666667777777666666666666666665555555555444433222 PP

                                   S-EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHH CS
                Trp_halogenase 299 eprkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnr 365
                                     + i+  +G        +++  ++++++G+a+   +P  + +i  ++     a +  ++ ++++ +++  ++++++
  gi|91772422|ref|YP_565114.1| 250 G-SIIEQVAGAvpasgpIEKTIANGLMLVGDAARQSDPFTGGGISNAMDaglyAGEVAAEAIAQDDVSEKILQKYEK 325
                                   2.333333333333333666666666666666666666666666665544333344445555555555555555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   3.2   9.2e-07     0.001      18     173 ..       5     163 ..       3     172 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.2e-07
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT...TTTSTTBSEEEEETTTHHHHHHTT---EEESSEEEESE CS
                          Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGa...wlGGqlfsaivvrkpakelLdelgikyedegdyvvvkd 95 
                                    D+v+vGaG++G  aa + akk +l v++le++  +G  +    + G+   +  ++ + k l  e+  +   + ++ +   
  gi|91772422|ref|YP_565114.1|   5 YDLVVVGAGPAGSIAATTAAKK-GLSVLMLEKRQEIGEPVrcaEGVGKKRLRQHIELDEKWLCGEVSSAKIISPNGTTLTM 84 
                                   69********************.**********999975411123344333444556666777777766666666666655 PP

                                   HHHHHHHHHHHHHTSTTEEEEESEEEE.......EEEEETBTEEEEEEEEEHH...HHTCTTTSS.-B-EEEEEEEEEE-- CS
                          Thi4  96 aalftstllskvlqlanvkllnavave.......DlivregegvaGvvinwtl...velahdtqscvDPlvirakvvvdat 166
                                   a +     +  vl+    k+++ + ve       D++v+   +v+G++i+  +   ve+ h          ir+k+v+ a 
  gi|91772422|ref|YP_565114.1|  85 AEEDAGSEVGYVLD---RKIFDRTLVElsgeagvDIMVKA--RVTGLIIEENTvcgVEMMH----LGKTYSIRSKLVIGAD 156
                                   55555555555555...45555555555555555777777..8888887765511245556....3445677777777777 PP

                                   GSSSTTT CS
                          Thi4 167 Ghdgeiv 173
                                   G +++++
  gi|91772422|ref|YP_565114.1| 157 GVESKVG 163
                                   7777665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   1.7e-06    0.0019       1      34 [.       8      41 ..       8      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.7e-06
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nign 34
                                  +++GaGPaG  aa+++ k+gl ++l lEk  +ig+
  gi|91772422|ref|YP_565114.1|  8 VVVGAGPAGSIAATTAAKKGL-SVLMLEKRqEIGE 41
                                  79*******************.7******867776 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.1e-05     0.023      31      69 ..       7      45 ..       3      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                  EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                   +v+G+G aG  A+ ta++ g +V +l++r++  e ++ 
  gi|91772422|ref|YP_565114.1|  7 LVVVGAGPAGSIAATTAAKKGLSVLMLEKRQEIGEPVRC 45
                                  69****************************998887765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.12       3      36 ..       8      41 ..       6      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                  EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHH CS
                       3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseeale 36
                                   v+GaG  G+  a+ +a++gl+V +++ ++e+ e
  gi|91772422|ref|YP_565114.1|  8 VVVGAGPAGSIAATTAAKKGLSVLMLEKRQEIGE 41
                                  69*************************9998755 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00046      0.51       2      38 ..       7      41 ..       6      60 .. 0.83
   2 ?    0.2   0.0         1   1.2e+03      41      76 ..     100     136 ..      88     148 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrll 38
                                  +vvvG+G  g  +A+++a+ g +V ++e + ++   +
  gi|91772422|ref|YP_565114.1|  7 LVVVGAGPAGSIAATTAAKKGLSVLMLEKRQEIG--E 41
                                  79****************************9998..3 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEE CS
                     Pyr_redox  41 easkilqeklekn.gievllntkveeiegsedgvesv 76 
                                   ++ +++  +l+ + g++++ +++v+ +  +e++v +v
  gi|91772422|ref|YP_565114.1| 100 KIFDRTLVELSGEaGVDIMVKARVTGLIIEENTVCGV 136
                                   4433333344333477777777777665555444444 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00029      0.32     126     165 ..     268     306 ..     250     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00029
                            SE 126 knekkGlillGDalnmRHPltggGmtvalnDivllskllk 165
                                   k+  +Gl+l+GDa     P tggG+  a+ D+ l++  + 
  gi|91772422|ref|YP_565114.1| 268 KTIANGLMLVGDAARQSDPFTGGGISNAM-DAGLYAGEVA 306
                                   55569*******************98775.5666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2729.60
//
Query:       gi|91772423|ref|YP_565115.1|  [L=353]
Description: hypothetical protein Mbur_0370 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-51  174.9   3.3    2.2e-51  174.7   3.3    1.1  1  NMD3            NMD3 family
  ------ inclusion threshold ------
       0.22   11.4   1.5       0.39   10.6   0.6    2.0  2  DUF2797         Protein of unknown function (DUF2797)
       0.26   11.3  10.0       0.12   12.4   3.3    3.2  3  DZR             Double zinc ribbon
        5.8    6.6   5.8         42    3.8   0.1    3.5  3  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7   3.3   4.9e-55   2.2e-51       1     243 []       6     238 ..       6     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 4.9e-55
                          NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvseevee 81 
                                   C++CG+++e+l+++ C++C+lk++ ++e +  ++ ++C++Cg+ + ++kW         +l+e++ ++ve++L +++e+++
  gi|91772423|ref|YP_565115.1|   6 CPKCGVKTEKLYKNTCRECFLKSFTLAELPLVLHANICAKCGARFDRNKW-----RDVGDLDEIVIRTVEDALLIHNEAKD 81 
                                   *********************************************999**.....45589999999999************ PP

                          NMD3  82 vkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk.relteee 161
                                   v++  v+++   +++  + +kv+v+v++ v+g   + l+q+++ ev+v r  C+rCsr+aggy+e+i+Q+R++ r +t ee
  gi|91772423|ref|YP_565115.1|  82 VEIY-VNPH---QMT-PHFYKVRVEVDAMVEG---ESLHQDLRAEVRVIRGACDRCSRMAGGYFEGILQIRATnRVPTAEE 154
                                   ***9.9999...454.577999999999*966...5699****************************************** PP

                          NMD3 162 hkrtfelleqli....lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkevyrlt 238
                                    + ++ +   ++    +k+d+ afi++ ++ k+G D+y+gs +a+r++++ +++e+gg+++es +l s+ k+ gk+ yr+t
  gi|91772423|ref|YP_565115.1| 155 IDSCKMICAVMVeklwKKGDRLAFITNSSDSKDGADLYLGSCNACRHICKSISNELGGSFTESATLHSH-KE-GKDIYRMT 233
                                   **99998776666767*****************************************************.66.******** PP

                          NMD3 239 ysvrl 243
                                   y++rl
  gi|91772423|ref|YP_565115.1| 234 YAMRL 238
                                   ***97 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   8.8e-05      0.39      11      40 ..       3      31 ..       1      66 [. 0.78
   2 ?   -2.4   0.0      0.79   3.6e+03     196     215 ..     289     308 ..     263     318 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.8e-05
                       DUF2797 11 errCvnCgrktkksfsqgvCakCfkklaea 40
                                  ++ C +Cg kt+k + +  C +Cf k+ + 
  gi|91772423|ref|YP_565115.1|  3 QIICPKCGVKTEKLY-KNTCRECFLKSFTL 31
                                  789************.779****9876554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.79
                       DUF2797 196 ekeaeveGtllGikGqylil 215
                                   + +++v+ +l+++ G ++++
  gi|91772423|ref|YP_565115.1| 289 NRKDAVAAVLVAVEGDDIMV 308
                                   55677888888888888775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.3   2.8e-05      0.12       1      41 [.       6      53 ..       6      57 .. 0.79
   2 ?    0.3   0.0      0.17   7.5e+02      28      37 ..     123     132 ..      87     136 .. 0.79
   3 ?   -0.3   0.3      0.24   1.1e+03      29      39 ..     194     204 ..     153     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                           DZR  1 CpqCgeelppdar.fCseCgtk......lkavaaedrCpsCgekvdpe 41
                                  Cp+Cg ++++  + +C eC  k      l+ v +++ C +Cg+  d +
  gi|91772423|ref|YP_565115.1|  6 CPKCGVKTEKLYKnTCRECFLKsftlaeLPLVLHANICAKCGARFDRN 53
                                  *******9988777*****999666555444555********997655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                           DZR  28 edrCpsCgek 37 
                                     +C++C+++
  gi|91772423|ref|YP_565115.1| 123 RGACDRCSRM 132
                                   6789999876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.24
                           DZR  29 drCpsCgekvd 39 
                                     C +C + ++
  gi|91772423|ref|YP_565115.1| 194 GSCNACRHICK 204
                                   56777776654 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.021        95       2       9 ..       3      10 ..       2      13 .. 0.86
   2 ?    3.8   0.1    0.0094        42       4      14 ..      42      52 ..      40      56 .. 0.83
   3 ?    0.3   0.3      0.12   5.5e+02       5      10 ..     126     131 ..     124     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.021
                        zf_UBZ  2 tylCerCg 9 
                                  +++C++Cg
  gi|91772423|ref|YP_565115.1|  3 QIICPKCG 10
                                  789****8 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0094
                        zf_UBZ  4 lCerCgkeipe 14
                                  +C++Cg+++  
  gi|91772423|ref|YP_565115.1| 42 ICAKCGARFDR 52
                                  7******9975 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.12
                        zf_UBZ   5 CerCgk 10 
                                   C+rC +
  gi|91772423|ref|YP_565115.1| 126 CDRCSR 131
                                   ****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2020.43
//
Query:       gi|91772424|ref|YP_565116.1|  [L=290]
Description: hypothetical protein Mbur_0371 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-36  125.0   0.0    3.7e-36  124.6   0.0    1.1  1  ATP-grasp_3      ATP-grasp domain
    1.7e-13   50.5   0.0    6.5e-07   29.1   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    5.8e-09   35.8   0.0    2.8e-08   33.6   0.0    1.9  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    1.7e-06   27.5   0.0    3.1e-06   26.7   0.0    1.4  1  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    0.00011   21.8   0.0    0.00053   19.6   0.0    1.9  1  ATP-grasp        ATP-grasp domain
    0.00031   20.3   0.0     0.0061   16.1   0.0    2.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0059   16.4   0.0        3.5    7.4   0.0    2.4  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
  ------ inclusion threshold ------
      0.016   14.8   0.0       0.11   12.1   0.0    1.9  2  RimK             RimK-like ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   0.0   1.7e-39   3.7e-36       1     161 []      11     184 ..      11     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 1.7e-39
                                   HTSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE..................EEEE-- CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...........lvqefi 70 
                                   +sdK  ++k ++  g++ P     +e+e   ++l vKp  ++gg  +rvv+++ e+++ +ee+            ++qef+
  gi|91772424|ref|YP_565116.1|  11 VSDKSSFAKDMESMGIPHPVSGIVDEAEDIGYPLMVKPKCAGGGRLNRVVQDESELNTVLEELPvmdptlelddiMIQEFL 91 
                                   69*****************999999********************************999998899*************** PP

                                   -SEEEEEEEEE.SSSEEEEEEEEEEEET.......TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.S CS
                   ATP-grasp_3  71 eGkplSvsllsdgekvlvlavnrqliekaeke...fvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdee 148
                                   +G p+Svsl+++g+  +++avn+qli+  +++   f+y+Gn+tp++t  +++++e+ e++ e++ gl+G++GvD++l+d++
  gi|91772424|ref|YP_565116.1|  92 SGFPASVSLIANGKCSVPIAVNEQLIGVPWLSslpFSYCGNITPYRTPYTSQMYEISEKLAENF-GLVGSNGVDFLLTDKG 171
                                   *******************************99*******************************.**************** PP

                                   EEEEEEESS--GG CS
                   ATP-grasp_3 149 pyviEvNPRltts 161
                                   p viE N+R+++s
  gi|91772424|ref|YP_565116.1| 172 PFVIELNARFQGS 184
                                   ***********97 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.9e-10   6.5e-07      28      92 ..      31      94 ..      13     112 .. 0.80
   2 !   19.4   0.0   2.7e-07    0.0006     140     201 ..     143     202 ..     137     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.9e-10
                                  HHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSS CS
                   CPSase_L_D2 28 eealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgp 92
                                     ++ a++igyP ++k+  ++GG+  rv+++e+el+ ++++   +   ++  + ++++++l+g+
  gi|91772424|ref|YP_565116.1| 31 SGIVDEAEDIGYPLMVKPKCAGGGRLNRVVQDESELNTVLEELPVMD-PTLELDDIMIQEFLSGF 94
                                  3445889******************************9998876666.47788888888888765 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.7e-07
                                   HHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHH CS
                   CPSase_L_D2 140 alreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaak 201
                                   ++ e + k++++ g+vg   v+fll    k  +viE+N+R + +    e aTGl+l  + +k
  gi|91772424|ref|YP_565116.1| 143 QMYEISEKLAENFGLVGSNGVDFLLTD--KGPFVIELNARFQGSLDSVEIATGLNLFDMHVK 202
                                   577888999****************95..77789**********************999888 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 !   33.6   0.0   1.2e-11   2.8e-08       3     115 ..      83     212 ..      81     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.2e-11
                  ATPgrasp_Ter   3 pallvmeyLegpEySvDvlae.k.......gevlaavpRrKe.....kgglq..elekdeelielaerlaeefgldglvnv 68 
                                   ++++++e+L+g   Sv  +a+ k       +e l+ vp   +      g+++  ++ +++++ e++e+lae+fgl g ++v
  gi|91772424|ref|YP_565116.1|  83 DDIMIQEFLSGFPASVSLIANgKcsvpiavNEQLIGVPWLSSlpfsyCGNITpyRTPYTSQMYEISEKLAENFGLVGSNGV 163
                                   567788888888888888877555555555555555555554544443444477788999********************* PP

                  ATPgrasp_Ter  69 QvrededgpkLLEiNpRasGGlgy.salaGvnlpylalklllgl.etee 115
                                    +  +++gp ++E N+R++G l+   +++G+nl ++ +k + g  +t +
  gi|91772424|ref|YP_565116.1| 164 DFLLTDKGPFVIELNARFQGSLDSvEIATGLNLFDMHVKSFNGIlPTGT 212
                                   **********************8615777***********999754433 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 !   26.7   0.0   1.4e-09   3.1e-06     216     281 ..     132     198 ..      98     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                   ATPgrasp_ST 216 klsglqiPnweevlelaakaaeklpglgylGwDivldeekgplllElNar..pglaivqiangegllp 281
                                   +++ ++ P+ +++ e+  k+ae++  +g  G+D+ l++++ p ++ElNar   +l+ v+ia g  l++
  gi|91772424|ref|YP_565116.1| 132 NITPYRTPYTSQMYEISEKLAENFGLVGSNGVDFLLTDKG-PFVIELNARfqGSLDSVEIATGLNLFD 198
                                   6777889*******************************99.*********844688888888877665 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.4e-07   0.00053      22     156 ..      35     177 ..      28     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.4e-07
                                   HHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.......GTTCEEEEE---.-SEEEEEEEEEETTC-EEE-- CS
                     ATP-grasp  22 eaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal.......keekvivEefvp.fekElsvlvvrsaeGetafyp 94 
                                   + ae++g+p++vK ++ +  G+ + vv++e++l+++le+l       +   +++ ef + f   +s+++    +G   ++p
  gi|91772424|ref|YP_565116.1|  35 DEAEDIGYPLMVK-PKCAGGGRLNRVVQDESELNTVLEELpvmdptlELDDIMIQEFLSgFPASVSLIA----NG-KCSVP 109
                                   66899********.99999*********************99999997788888888755999999995....88.66788 PP

                                   EEEEEEETTEEEEEEECEE-SCH.......HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEE CS
                     ATP-grasp  95 vvetvqedgilrlsvapaevsek.......aqkkaeeiakkiveeLggvGvfavElFvledgellvnEl 156
                                   +  + q  g+  ls  p +   +          +  ei +k++e++g vG  +v + ++++g  +v El
  gi|91772424|ref|YP_565116.1| 110 IAVNEQLIGVPWLSSLPFSYCGNitpyrtpYTSQMYEISEKLAENFGLVGSNGVDFLLTDKGP-FVIEL 177
                                   88899999998888777665544334444478999********************99996554.33354 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 !   16.1   0.0   2.7e-06    0.0061      31     172 ..      36     177 ..      28     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
                                   HHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-.....SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE- CS
               Dala_Dala_lig_C  31 veeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd.....ekvlvEeaiegreievavlgneklevsevgeivv 106
                                   + e +gyp++VKp  +G       v+ e+el+  +ee   +d      ++++ e+++g    v+++ n+k  v  +++ ++
  gi|91772424|ref|YP_565116.1|  36 EAEDIGYPLMVKPKCAGGGRLNRVVQDESELNTVLEELPVMDptlelDDIMIQEFLSGFPASVSLIANGKCSVPIAVNEQL 116
                                   56889*************9999999************9999933333469*****************99988765555444 PP

                                   SS..SSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEE CS
               Dala_Dala_lig_C 107 kk..gfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEv 172
                                    +   +      y ++ + +          ++++ e++ k  ++ +l G+  vDf+lt++g +v+ E+
  gi|91772424|ref|YP_565116.1| 117 IGvpWLSSLPFSYCGNITPYRT------PYTSQMYEISEKLAENFGLVGSNGVDFLLTDKGPFVI-EL 177
                                   4422333444455444443333......3456677777777788888888888888887776655.55 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 !    6.6   0.0    0.0026       5.9      37     109 ..      41     111 ..      12     116 .. 0.79
   2 !    7.4   0.0    0.0016       3.5     167     190 ..     159     182 ..     139     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0026
                                   SSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE-- CS
                        GARS_A  37 takalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelleGeEvsllalvdgktvkplp 109
                                   + +   vK++   +g+   v+++e+e  ++++e+ +        + ++i e+l+G   s+  + +gk  +p++
  gi|91772424|ref|YP_565116.1|  41 GYPL-MVKPKCAGGGRLNRVVQDESELNTVLEELPVMDPTL-ELDDIMIQEFLSGFPASVSLIANGKCSVPIA 111
                                   4444.899999999999999999999999999986644443.5789********************9887765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                                   EEEEEEEEEETTEEEEEEEESS-- CS
                        GARS_A 167 GvLyaglmlvedgpkvlefnvRfg 190
                                   G   ++++l+++gp v+e n+Rf 
  gi|91772424|ref|YP_565116.1| 159 GSNGVDFLLTDKGPFVIELNARFQ 182
                                   55556899**************96 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.21   4.7e+02      37      82 ..      37      91 ..      20     115 .. 0.79
   2 ?   12.1   0.0   4.8e-05      0.11     131     179 ..     144     195 ..     129     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.21
                                  T-..-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH........GGG--EEEEE- CS
                          RimK 37 ik.lrfPvvvKsvegsqGikvvlakkeqklkqvlea........lkeailvqeyi 82
                                   + ++ P++vK   +  G    + ++e +l+ vle             i++qe++
  gi|91772424|ref|YP_565116.1| 37 AEdIGYPLMVKPKCAGGGRLNRVVQDESELNTVLEElpvmdptlELDDIMIQEFL 91
                                  4446789999999999998888999999999999987776665333567899987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.8e-05
                                   HHHHHHHHHHHCT-S.EEEEEEEEETTEEEEEEEESS--..SHHHHHHHT-- CS
                          RimK 131 ekelAikaakamelv.vaGvDllrakrgllvlEvnsspg..lekiektlgid 179
                                     e+  k a+  +lv   GvD l +++g++v+E+n+  +  l+ +e  +g++
  gi|91772424|ref|YP_565116.1| 144 MYEISEKLAENFGLVgSNGVDFLLTDKGPFVIELNARFQgsLDSVEIATGLN 195
                                   556666777777776357******************8763356666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); 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:                         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 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1668.23
//
Query:       gi|91772425|ref|YP_565117.1|  [L=165]
Description: transcription factor IIE (TFIIE), alpha subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-13   50.3   1.8    2.1e-13   50.1   0.4    1.7  2  TFIIE_alpha  TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.4   1.2e-17   2.1e-13       9     103 ..      15     108 ..       8     110 .. 0.93
   2 ?   -1.0   0.0     0.091   1.6e+03      90     102 ..     148     160 ..     140     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.2e-17
                                   HCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHH CS
                   TFIIE_alpha   9 kfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkl 89 
                                   +  gee +++++ +  +gevt+e++a+  ++ ln++r+ L+ + e  l+ ++r+rd + +w +y w+++   +   + +++
  gi|91772425|ref|YP_565117.1|  15 QLIGEEGIEMIENMP-EGEVTDEQIAEASGVMLNIVRRTLFIMNENNLAVCRRERDSSSGWLTYLWQLDLSDIESHLVKEK 94 
                                   567999999999988.**********************************************************9999999 PP

                                   HHHHHHHHHHHCCC CS
                   TFIIE_alpha  90 eevvkkLeekleke 103
                                   +++ k+Le   ++e
  gi|91772425|ref|YP_565117.1|  95 KRITKNLEIRYNFE 108
                                   99***999777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.091
                                   HHHHHHHHHHHCC CS
                   TFIIE_alpha  90 eevvkkLeeklek 102
                                   + +vkkL++ l++
  gi|91772425|ref|YP_565117.1| 148 SVMVKKLRDRLDA 160
                                   5688888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1035.80
//
Query:       gi|91772426|ref|YP_565118.1|  [L=168]
Description: hypothetical protein Mbur_0373 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-14   53.7   0.7    3.3e-14   53.2   0.7    1.3  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.7   1.8e-18   3.3e-14       2     120 ..      21     130 ..      20     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.8e-18
                                   HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHH CS
                            HD   2 leHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldle 79 
                                   + H+  V + a  +a +l+e     d +l++++aLlHD+G  +++              +H+++ga+i++++ +++     
  gi|91772426|ref|YP_565118.1|  21 IRHCQVVSETAVSIACELQEkgqKVDIQLVEVGALLHDLGRSRTHG------------IKHAIEGASIAEKLDLDP----- 84 
                                   78999999***********9***********************775............68****************..... PP

                                   HHHHHHHTTCCHHHHHHHHH.....HHHCCTSCHHHHHHHHHHHHH CS
                            HD  80 dvaklirehheswegkkrpr.....glaerqlslearivklaDrla 120
                                    ++++i++h +   ++++ +     + +  ++s e++iv+ aD+l 
  gi|91772426|ref|YP_565118.1|  85 RIIQIIKNHIGAGITSEEAKvmglpEVDHLPISTEEKIVAHADNLV 130
                                   *************999888455677******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1082.21
//
Query:       gi|91772427|ref|YP_565119.1|  [L=210]
Description: proteasome endopeptidase complex [Methanococcoides burtonii DSM 6242]
Scores for complete 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-55  186.4   1.7    4.4e-55  186.1   1.7    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 !  186.1   1.7   2.5e-59   4.4e-55       3     190 .]       8     189 ..       7     189 .. 0.97

  Alignments for each domain:
  == domain 1  score: 186.1 bits;  conditional E-value: 2.5e-59
                                   HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHH CS
                    Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipver 83 
                                   kGtt+vGi ++dgvvla+++rat+g+ + +++t++Ki++idd +g+++aG+++Da+++vr++++e +l+++r ++ i+++ 
  gi|91772427|ref|YP_565119.1|   8 KGTTTVGIVCTDGVVLATEQRATMGHFI-ASKTAKKIYQIDDLVGMTTAGSVGDAQQIVRIISVESKLFKMRRQESITIK- 86 
                                   7***************************.55559**********************************************. PP

                                   HHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHH CS
                    Proteasome  84 lvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeav 164
                                       ++++l++++  ++  p++v+lli+gvd++g p +y++d  G  iee +av++Gsgs +a+++le++y+ed+t+ e+v
  gi|91772427|ref|YP_565119.1|  87 ---GITTLLSNMLSGQRYYPLMVQLLIGGVDKNG-PAIYSLDALGGNIEETRAVSTGSGSPMAYGVLEDRYTEDMTVVEGV 163
                                   ...888899999999999*************888.********************************************** PP

                                   HHHHHHHHHHHHHBTTSCSSEEEEEE CS
                    Proteasome 165 elavkalkealerdklsgknievavi 190
                                   +la++al++a++rd++sg+ni+v+vi
  gi|91772427|ref|YP_565119.1| 164 DLAIRALHNAMKRDSASGENIDVVVI 189
                                   ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1375.80
//
Query:       gi|91772428|ref|YP_565120.1|  [L=636]
Description: beta-lactamase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-32  109.3   1.5    9.1e-30  102.4   0.6    3.0  2  KH_7           KH domain
    1.3e-25   89.8   0.0    5.2e-25   87.9   0.0    2.1  2  Beta-Casp      Beta-Casp domain
    2.8e-14   52.8   0.0    9.7e-14   51.1   0.0    2.0  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    5.3e-13   48.8   0.0    9.5e-13   48.0   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    5.7e-13   49.3   0.3      4e-11   43.3   0.4    3.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.9e-09   37.4   0.1    4.5e-09   36.1   0.1    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.4e-05   24.8   1.9    9.4e-05   22.2   0.0    3.1  3  KH_2           KH domain
    0.00012   22.1   0.0    0.00025   21.0   0.0    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0047   16.7   1.4      0.057   13.3   0.3    2.8  2  KH_1           KH domain
     0.0049   16.7   0.0      0.024   14.5   0.0    2.2  2  KH_4           KH domain
  ------ inclusion threshold ------
      0.037   13.4   0.0      0.093   12.1   0.0    1.6  1  Peptidase_M55  D-aminopeptidase


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 !  102.4   0.6   5.6e-33   9.1e-30       1      68 []       4      71 ..       4      71 .. 0.98
   2 ?    4.4   0.0     0.023        37       6      55 ..      76     128 ..      73     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 5.6e-33
                          KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                  e+vl +lk+kieek+P++++it+veFEGP+lV+Yt++pk fa+ng+++r+lAk+lr Riv+RpDp+vl
  gi|91772428|ref|YP_565120.1|  4 EDVLADLKKKIEEKVPDNTTITSVEFEGPQLVVYTEDPKNFADNGQIVRTLAKTLRTRIVVRPDPKVL 71
                                  6899**************************************************************98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
                          KH_7   6 elkekieeklPkevkitdveFEG..PelViYtknpklfa.engdlirklAkel 55 
                                   e   ki++++Pk++ +++ +F     e+Vi ++ p l++ ++g+ +r++ k++
  gi|91772428|ref|YP_565120.1|  76 EAIGKIKDTVPKDAVLSNFHFDPdvGEVVIEAEKPGLVIgKHGETLREITKKI 128
                                   56679****************84225899999999998878899999998876 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   3.2e-28   5.2e-25       2     110 .]     422     546 ..     421     546 .. 0.87
   2 ?   -3.1   0.0       5.7   9.2e+03      48      71 ..     584     614 ..     562     617 .. 0.47

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 3.2e-28
                                   HHHHHHH..HCTT..TTS-S.-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....HHHH CS
                     Beta-Casp   2 qellylLeelwkekkledlk.lpiyldsplaskatevYkeyae.........................veakslewmeskk 56 
                                   qe++++Le++++++    ++ +p+yld+ ++ +at+++ +y+e                         v++++       +
  gi|91772428|ref|YP_565120.1| 422 QEVMIVLEDAIRRGI---IDdVPVYLDG-MIWEATAIHATYPEylnnnlrklifqkgqnpflaecfkpVDSND------LR 492
                                   9**********9944...3448******.************99999999999999999988877765444333......23 PP

                                   ..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                     Beta-Casp  57 eelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                   +++ +++ p+vil++sgm+++G++ e++k++++dp+nt+++vgyqa gTlgr++
  gi|91772428|ref|YP_565120.1| 493 KKIIEDPHPCVILSTSGMMNAGPVMEYFKAFAPDPNNTLVFVGYQADGTLGRRI 546
                                   3456789*********************************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                                   H.....HHH....H....HHHS-SSEEEEES CS
                     Beta-Casp  48 s.lewmesk....ke..elnsskgpkvilas 71 
                                   + +e+++++    ++  + + +++ ++ las
  gi|91772428|ref|YP_565120.1| 584 QlMEYFKKMkpqpERvfTEHGDERSCIDLAS 614
                                   3333333332112112222244455555555 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 !   51.1   0.0   5.9e-17   9.7e-14       2      56 ..     564     621 ..     563     627 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 5.9e-17
                         RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeeg 56 
                                   +++++ +e +d fSgH+d+ +l+e+ +k+kp++  v+  HG+e+++ +la+ l++++ 
  gi|91772428|ref|YP_565120.1| 564 VKMNMGVEVVDgFSGHSDRKQLMEYFKKMKPQPerVFTEHGDERSCIDLASSLHKKYR 621
                                   789*************************************************987765 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 !   48.0   0.0   5.8e-16   9.5e-13       1     162 [.     198     353 ..     198     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5.8e-16
                 Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekv..iptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLG 79 
                                   lL+  + ki++D+G++  +++  +   +l +v  ++++d+++++ha l+h G  +lly+     ++ + p+y+t p+  + 
  gi|91772428|ref|YP_565120.1| 198 LLSTPESKIMIDCGVNVGSDDNMTPYLYLPEVqpLNQIDAVVITHAHLDHQGLVPLLYK-----YGYEGPIYCTSPTRDIM 273
                                   5677789*********66555555566677664589****************6666664.....67899*******99999 PP

                 Lactamase_B_6  80 rvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..WkiskesekivY 158
                                    ++ ld +  +  +g++     e  +++ a ++ ++l Y+  +++     ++ +t +naGh +G +i  ++i ++++++v 
  gi|91772428|ref|YP_565120.1| 274 TLLQLDFIDVAAKEGKKP--PYESTNVRDALKHTIALDYEEVTDIAP---DVKLTFHNAGHIIGSAIshFHIGDGLHNVVV 349
                                   999988888777766554..4466899**************999985...899************8866888999999987 PP

                 Lactamase_B_6 159 avdw 162
                                     d+
  gi|91772428|ref|YP_565120.1| 350 TGDY 353
                                   7666 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.7   1.1e+03      58      92 ..     128     162 ..     128     176 .. 0.88
   2 !   43.3   0.4   2.5e-14     4e-11       4     162 ..     192     363 ..     189     399 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.7
                                   HTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHH CS
                   Lactamase_B  58 iGglgglveatdvpvgavaeeapalfmeeaddaas 92 
                                   iG+ +++v++ +++++ v+ + + ++++++d+ + 
  gi|91772428|ref|YP_565120.1| 128 IGWTPKVVRTPPIKSRTVKNIREFMRTNHKDRKEI 162
                                   79999**********************99987665 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 2.5e-14
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                   ++ +++l+ ++++ i+iD+G+    ++ +   ++  +  +++++dav++TH+HlDH G ++ l +     ++++   ++  
  gi|91772428|ref|YP_565120.1| 192 VGRSCFLLSTPESKIMIDCGVNVGSDDNMTpyLYLPEVQPLNQIDAVVITHAHLDHQGLVPLLYKYGYEGPIYCTSPTRDI 272
                                   6789***********************99998888999999**********************999999888888887777 PP

                                   HCHHHHHHHHHCCHH............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTT CS
                   Lactamase_B  83 fmeeaddaasrkgll............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDa 151
                                    +    d       +            +a  + ++ d  e  +   +    +  + ++ g+  +h+++++g  +v++tGD 
  gi|91772428|ref|YP_565120.1| 273 MTLLQLDFIDVAAKEgkkppyestnvrDALKHTIALDYEEVTDIAPDVKLTFHNAGHIIGSAISHFHIGDGLHNVVVTGDY 353
                                   777764444433333799****9977644444444444444444444444444455677888899**************** PP

                                   TSSHHCCCCCC CS
                   Lactamase_B 152 llagetgridl 162
                                    + +   ++d+
  gi|91772428|ref|YP_565120.1| 354 KYGPT-RLFDP 363
                                   99554.44444 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 !   36.1   0.1   2.7e-12   4.5e-09       3     150 ..     206     360 ..     204     388 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.7e-12
                                   EEES--TTHHHH..HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCH CS
                 Lactamase_B_2   3 iLiDagpdlrqq..alral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylale 80 
                                   i iD+g ++     ++++l  P   ++ l++idaV++thaH DH  gl  l   ++ + p+y++  ++++++   + ++ +
  gi|91772428|ref|YP_565120.1| 206 IMIDCGVNVGSDdnMTPYLyLP--EVQPLNQIDAVVITHAHLDHQ-GLVPLLYKYGYEGPIYCTSPTRDIMTLL-QLDFID 282
                                   99******87778899999555..5677889**************.8888888666679*****9998854433.444444 PP

                                   TT................TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S- CS
                 Lactamase_B_2  81 ee................pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgy 145
                                   ++                +  ++  ld +e ++++ +++++t++ a h  g         +  + i++g ++v+ +gD +y
  gi|91772428|ref|YP_565120.1| 283 VAakegkkppyestnvrdALKHTIALDYEEVTDIA-PDVKLTFHNAGHIIGS-------AISHFHIGDGLHNVVVTGDYKY 355
                                   44445566555555555555555566677777778.5899999999999888.......7888999999999999999999 PP

                                   --HHH CS
                 Lactamase_B_2 146 ipeei 150
                                    p ++
  gi|91772428|ref|YP_565120.1| 356 GPTRL 360
                                   99543 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.46   7.5e+02      43      63 ..      47      67 ..       9      77 .. 0.73
   2 !   22.2   0.0   5.7e-08   9.4e-05      28      67 ..     102     141 ..      85     152 .. 0.85
   3 ?   -1.7   0.0       1.6   2.7e+03      48      65 ..     391     408 ..     389     444 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.46
                                  GGHHHHHHHHHHHHHHHHHHT CS
                          KH_2 43 gGsnikkigkelrkdiekleg 63
                                  +G+ ++++ k+lr +i +  +
  gi|91772428|ref|YP_565120.1| 47 NGQIVRTLAKTLRTRIVVRPD 67
                                  688888888888888865555 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 5.7e-08
                                   EEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                          KH_2  28 iiviresqpgivIGkgGsnikkigkelrkdieklegkkVk 67 
                                   ++vi +++pg+vIGk G+++++i+k+++   ++++  ++k
  gi|91772428|ref|YP_565120.1| 102 EVVIEAEKPGLVIGKHGETLREITKKIGWTPKVVRTPPIK 141
                                   69************************98777777766666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHHTTC CS
                          KH_2  48 kkigkelrkdieklegkk 65 
                                   k+ +k+l+++i++ ++ k
  gi|91772428|ref|YP_565120.1| 391 KEAEKNLQQIIKNTLNNK 408
                                   667777777776655555 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 !   21.0   0.0   1.5e-07   0.00025       5      52 ..     192     250 ..     190     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                 Lactamase_B_3   5 lghnsflletagarilvDPfkanlgyeppa............eeaDlvlisqaledHahl 52 
                                   +g ++fll+t++ +i++D +  n+g + +              ++D+v+i++a+ dH  l
  gi|91772428|ref|YP_565120.1| 192 VGRSCFLLSTPESKIMIDCGV-NVGSDDNMtpylylpevqplNQIDAVVITHAHLDHQGL 250
                                   589***************984.33333333446677778888***************765 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.25     4e+02      18      40 ..      47      68 ..      46      83 .. 0.74
   2 !   13.3   0.3   3.5e-05     0.057       4      28 ..     103     127 ..     101     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.25
                                  GGHHHHHHHHHH.T-EEEEESSTT CS
                          KH_1 18 gGsnIkeIreet.gakIkvpksed 40
                                  +G+ ++ + + t  ++I+v  +++
  gi|91772428|ref|YP_565120.1| 47 NGQIVRTLAK-TlRTRIVVR-PDP 68
                                  7999******.88*****86.443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.5e-05
                                   EEEGGGHHHHHHTGGGHHHHHHHHH CS
                          KH_1   4 ilvPsslvgriIGkgGsnIkeIree 28 
                                   + + +++ g++IGk G++++eI ++
  gi|91772428|ref|YP_565120.1| 103 VVIEAEKPGLVIGKHGETLREITKK 127
                                   566777779*************984 PP

>> KH_4  KH 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     0.024      32      52 ..     102     122 ..      94     124 .. 0.88
   2 ?   -2.9   0.0         4   6.5e+03      30      45 ..     317     332 ..     302     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                          KH_4  32 elnvegedlGrvIGkrGrtld 52 
                                   e+ +e e+ G+vIGk+G+tl+
  gi|91772428|ref|YP_565120.1| 102 EVVIEAEKPGLVIGKHGETLR 122
                                   677899*************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4
                          KH_4  30 eielnvegedlGrvIG 45 
                                     ++++  ++ G +IG
  gi|91772428|ref|YP_565120.1| 317 APDVKLTFHNAGHIIG 332
                                   5567778889999999 PP

>> Peptidase_M55  D-aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.7e-05     0.093     158     210 ..     359     413 ..     343     435 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                 Peptidase_M55 158 alceeakellpevetvavkeglgrfaakslspeeaeeaireavkeavekake..a 210
                                   +l + a + +p+vetv + +++g  +a+  s +eae+++++ +k+++++++   +
  gi|91772428|ref|YP_565120.1| 359 RLFDPAVNKFPRVETVITESTYGAASAVQPSLKEAEKNLQQIIKNTLNNKGIvlI 413
                                   4566677889************************************999876444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.54
# Mc/sec: 3575.99
//
Query:       gi|91772429|ref|YP_565121.1|  [L=213]
Description: HAD family hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   89.4   0.0    3.9e-25   89.0   0.0    1.2  1  HAD_2           Haloacid dehalogenase-like hydrolase
    3.1e-13   50.5   0.0    1.7e-12   48.1   0.0    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00016   21.7   0.0    0.00032   20.7   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
    0.00073   19.3   0.0     0.0036   17.1   0.0    1.9  1  NIF             NLI interacting factor-like phosphatase
     0.0021   18.5   0.0     0.0031   18.0   0.0    1.3  1  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.0   1.1e-28   3.9e-25       1     178 []       5     183 ..       5     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.1e-28
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee...kieellrkyneekkk.ke 77 
                                   +iFD Dg+l+++ +++++a+ +++ e g+ ++ ++++  + g +   +++ ++++   +    +ie+l+ + +e   k ++
  gi|91772429|ref|YP_565121.1|   5 LIFDADGVLVNSMPFHADAWIQTFSEVGI-DVIRQDIYDIEGSNFVGIIELIFKKAGRDAdpeLIEKLRVRKRELFFKyEK 84 
                                   69*************************98.99999999999999999999999988877778899999888888888899* PP

                         HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyv 158
                                    + ++g+ ++L+e k+ +y+l++v+ ++r  +++++++l   ++Fd  +++ dv + KP+pe+++ka+e ++++ke+++++
  gi|91772429|ref|YP_565121.1|  85 ATAFEGMYDFLNE-KKDKYNLAVVSGSDRPIIDKMFNKLY-PDIFDLLISGADVAHGKPHPEPYLKAVEYFGVDKEKCLVI 163
                                   *************.89***********************9.7*************************************** PP

                         HAD_2 159 GDsptDieaakkagikviav 178
                                   +  p ++e+ak+a + ++av
  gi|91772429|ref|YP_565121.1| 164 ENAPLGVESAKNASLYCVAV 183
                                   ***************99987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   4.8e-16   1.7e-12       2     209 ..       3     176 ..       2     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 4.8e-16
                                   SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.sgaltgfatfigrgayaigkpewltald 81 
                                   +t++fD dG+L+++ p + d++ +                    + +   ++ + ++ +++         +g  e++ +  
  gi|91772429|ref|YP_565121.1|   3 NTLIFDADGVLVNSMPFHADAWIQT-------------------FSEVGIDViRQDIYDIEG-----SNFVGIIELIFKK- 58 
                                   8************************...................333333334555566666.....7788888888888. PP

                                   CHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  82 ippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfda 162
                                          a  +a  +  +   +  r +++f   ++ + ++++ +++++ k+ ++++++++g+++   ++  n+l  d+fd 
  gi|91772429|ref|YP_565121.1|  59 -------AGRDADPELIEKLRV--RKRELFFKYEKATAFEGMYDFLNE-KKDKYNLAVVSGSDRPIIDKMFNKLYPDIFDL 129
                                   .......888999999999999..9999999999999***********.667799******************777***** PP

                                   EEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 163 viasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                    i++ +++++kp+pe +++a++ +++++e++++++  + +++ +++A
  gi|91772429|ref|YP_565121.1| 130 LISGADVAHGKPHPEPYLKAVEYFGVDKEKCLVIENAPLGVESAKNA 176
                                   ************************************99999999987 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.9e-08   0.00032       3      57 ..     139     192 ..     137     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.9e-08
                                   STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTT CS
                Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrped 57 
                                   gKP+pe y  a+e +g+d+e++l+i       +++A+na + +v+V t v+ ++ 
  gi|91772429|ref|YP_565121.1| 139 GKPHPEPYLKAVEYFGVDKEKCLVIENA-PLGVESAKNASLYCVAVSTHVNPKGL 192
                                   9*************************99.899****************9977755 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     1e-06    0.0036       2     148 ..       4     208 ..       3     212 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                           NIF   2 tLVLDLDetLvhskleksk........................................klkvegek......vevsvlkR 36 
                                   tL++D D++Lv s     +                                        +      +       + +v kR
  gi|91772429|ref|YP_565121.1|   4 TLIFDADGVLVNSMPF--HadawiqtfsevgidvirqdiydiegsnfvgiielifkkagR------DadpeliEKLRVRKR 76 
                                   6777777777755521..112344445555566665555555555555544443322220......122233333444444 PP

                           NIF  37 ............pgldefLkelsklyevvifTasseeyaeavidildpekkllshrlyrescv..kk.kgeyvKdLsllgr 102
                                                g+ +fL+e   +y++ + + s +  ++++ ++l p+   ++  ++  +++  k   + y+K ++++g 
  gi|91772429|ref|YP_565121.1|  77 elffkyekatafEGMYDFLNEKKDKYNLAVVSGSDRPIIDKMFNKLYPDI--FDLLISGADVAhgKPhPEPYLKAVEYFGV 155
                                   555555566667899*******************************9995..566666666643222255*********** PP

                           NIF 103 dlsrvvivDdspdsfelqpe...ngipiksffs....dkkDneLlkllpllke 148
                                   d ++ +++++ p  +e+ ++     + +++ ++    +k D+ + + ++ll+ 
  gi|91772429|ref|YP_565121.1| 156 DKEKCLVIENAPLGVESAKNaslYCVAVSTHVNpkglEKADKVFNNHSELLEF 208
                                   ************98887554213445555554344566666666655555554 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.5e-07    0.0031       2     130 ..       6     133 ..       5     179 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.5e-07
                           HAD   2 lfDfDgTLldgdslelllrfllrrgaprlwralreklllal...frellrldraglaelleallaglseelaaelerfv.a 78 
                                   +fD Dg L+++ +++  ++++++++++   + +r+ ++ +    f  + +l    ++++ + +   l e+l  + ++++  
  gi|91772429|ref|YP_565121.1|   6 IFDADGVLVNSMPFH--ADAWIQTFSEVGIDVIRQDIYDIEgsnFVGIIEL---IFKKAGRDADPELIEKLRVRKRELFfK 81 
                                   8**********5555..4555556444445555555444443333333333...222333333333332222222222222 PP

                           HAD  79 evirpklldpgalellaahraaGdrvvvvSgglrplvepll.aelg..adevlat 130
                                    ++++ ++ +g++++l++  +  + ++vvSg+ rp++  +  +++   +d +++ 
  gi|91772429|ref|YP_565121.1|  82 YEKAT-AF-EGMYDFLNEK-KDKYNLAVVSGSDRPIIDKMFnKLYPdiFDLLISG 133
                                   22222.36.9*******55.66689*************99955555755555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1335.89
//
Query:       gi|91772430|ref|YP_565122.1|  [L=70]
Description: hypothetical protein Mbur_0377 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   15.4   0.2      0.027   15.1   0.2    1.2  1  ThiS      ThiS family
      0.034   14.2   0.1      0.072   13.2   0.1    1.7  1  TGS       TGS domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2     3e-06     0.027      13      77 .]      16      70 .]       7      70 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-06
                                  CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                          ThiS 13 eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   + + +++gst ++ll+ ++ ++      + v+++ +g+ vp    d ++ +g +v il +++GG
  gi|91772430|ref|YP_565122.1| 16 GQAINVPDGSTYEDLLNVMDINQ------ELVILLNDGKAVPI---DDVVIEG-TVTILKAISGG 70
                                  478999*****************......999999999****9...9999999.699******99 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     8e-06     0.072       5      24 ..      13      32 ..       7      65 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-06
                                  ETTSSEEEEETTB-HHHHHH CS
                           TGS  5 tPdGkvpdlprgatveDfAy 24
                                  tPdG+++++p g+t eD+ +
  gi|91772430|ref|YP_565122.1| 13 TPDGQAINVPDGSTYEDLLN 32
                                  8****************855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 471.48
//
Query:       gi|91772431|ref|YP_565123.1|  [L=124]
Description: hypothetical protein Mbur_0378 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0084   16.3   0.0      0.013   15.7   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.058   13.4   0.0       0.13   12.2   0.0    1.7  1  PadR      Transcriptional regulator PadR-like family
      0.065   13.1   0.0       0.11   12.4   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB


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 !   15.7   0.0   2.2e-06     0.013       6      59 ..      33      88 ..      30      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-06
                        HTH_34  6 lsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkk..prtll 59
                                  ++yL+ v+ea+ +e+  ++++ + + sv ++ + + ++i+++ e++ +k  p  ++
  gi|91772431|ref|YP_565123.1| 33 VAYLSNVSEASSQEIEMKTGLRQPEVSVAMRSMREHDWISIHNEKVTGKgrPTKIY 88
                                  79*************************************99877765541155555 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05      0.13      37      65 ..      61      90 ..      38      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                  HHHHHHHTTSEEEEEE-S.TSSS-EEEEEE CS
                          PadR 37 aLkrLekeglvesewees.gegpprkyYrl 65
                                  a+++++++++++ ++e+  g+g+p+k+Y+l
  gi|91772431|ref|YP_565123.1| 61 AMRSMREHDWISIHNEKVtGKGRPTKIYTL 90
                                  67899*******9999988*********98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.9e-05      0.11       2      63 ..      21      89 ..      18      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                  HHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                          TrmB  2 qklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63
                                  + lG++ + a + ++L +  +a+ +ei  ++g+ ++ v  ++rs+ + +++ +  ++       +k+Y 
  gi|91772431|ref|YP_565123.1| 21 KSLGMTRNLATTVAYLSNVSEASSQEIEMKTGLRQPEVSVAMRSMREHDWISIHNEKvtgkgrpTKIYT 89
                                  566666666666677777889999****************************99999888888555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 784.08
//
Query:       gi|91772432|ref|YP_565124.1|  [L=330]
Description: aspartate semialdehyde dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-47  161.2   0.0    3.8e-47  160.7   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    6.1e-33  113.8   0.0    1.2e-32  112.9   0.0    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.036   14.2   0.0       0.07   13.3   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.058   12.9   0.0      0.092   12.3   0.0    1.3  1  NmrA             NmrA-like family


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 !  160.7   0.0   8.5e-51   3.8e-47       2     184 .]     137     317 ..     136     317 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 8.5e-51
                                   HHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHH CS
               Semialdhyde_dhC   2 kPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkava 82 
                                    +L+++ ++l++vi++tyqa+SGaG++g++eL +++++ ++++e+k++vf  pia+N ip+id++++++  +tree+k v+
  gi|91772432|ref|YP_565124.1| 137 YALHKK-YGLKKVIISTYQATSGAGAAGMSELTEETKNYLEGKEVKNKVFAHPIAFNTIPHIDSFQEND--YTREEMKVVW 214
                                   689998.99************************************************************..********** PP

                                   HHHHHCTESC.SEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCSTTEEEEESS.HCHHSSHHHHTTCSSSEEEE CS
               Semialdhyde_dhC  83 etkkilefte.kvsatcvrVPvlrGhseavtiklklkdveveeveellaaapevkvvvne.eedrPtpaavaggtnsvsVG 161
                                   et+ki++ ++ ++s tcvr+P +r h e++ i++ ++ ++  ++++ll + +++++ ++  ++ +P+p+++++ +++v VG
  gi|91772432|ref|YP_565124.1| 215 ETRKIFSEPDiPISCTCVRIPTMRVHGESIVIET-ERSIDPVDAKKLLGQVEGIELKDDIeHNIYPMPLNATK-KYDVEVG 293
                                   **********************************.599*********************99***********9.8****** PP

                                   EEEEETTCTT.EEEEEEEEETTTT CS
               Semialdhyde_dhC 162 Rirkdemgde.glklvvvgDNllk 184
                                   Rir++ ++ + gl+++v gD++lk
  gi|91772432|ref|YP_565124.1| 294 RIRQNLVFGDhGLEFFVCGDQILK 317
                                   ***99876554***********97 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 !  112.9   0.0   2.6e-36   1.2e-32       1     120 [.       4     118 ..       4     119 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 2.6e-36
                                   EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80 
                                   +v+i GatG+vG+e++++L+e +++ve ++l++s+rsaGk+++ +++       +++e++d+++ ++++i+f+a +++ sk
  gi|91772432|ref|YP_565124.1|   4 NVGIMGATGAVGKEIIEVLHErNFPVEQLRLFASERSAGKTIDTLFG------SITIENADMADYSQLNIAFFAISGDWSK 78 
                                   79*******************************************77......9*************************** PP

                                   HHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGGG CS
                Semialdhyde_dh  81 elapklaeagvkviDlssdfRlkddavyvlpevnreaikk 120
                                   + a+k+ +a+++viD+ss+fR++d++++v+pe+n++ai +
  gi|91772432|ref|YP_565124.1|  79 KNAEKATSADCYVIDNSSAFRYDDKVPLVVPEINADAIGN 118
                                   ************************************9965 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.6e-05      0.07       2      24 ..       4      26 ..       3      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                                  EEEEETTTSHHHHHHHHHHHHST CS
                        DapB_N  2 kvavvGasGrmGkevvkaveeae 24
                                  +v+++Ga+G +Gke++++++e++
  gi|91772432|ref|YP_565124.1|  4 NVGIMGATGAVGKEIIEVLHERN 26
                                  79*****************9962 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05     0.092       3      28 ..       7      32 ..       5      77 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                                  ESSTTSHHHHHHHHHHHHHT-EEEEE CS
                          NmrA  3 viGaTGrqGksvvrallkaghkvral 28
                                  ++GaTG+ Gk ++++l +++++v  l
  gi|91772432|ref|YP_565124.1|  7 IMGATGAVGKEIIEVLHERNFPVEQL 32
                                  89********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1885.21
//
Query:       gi|91772433|ref|YP_565125.1|  [L=235]
Description: histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-28   98.5   0.1      5e-28   97.8   0.1    1.3  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-15   57.0   0.0      2e-15   56.5   0.0    1.2  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0003   20.7   0.1    0.00062   19.6   0.0    1.6  1  HATPase_c_5  GHKL domain
     0.0049   16.7   0.0     0.0084   15.9   0.0    1.3  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.056   13.0   0.0       0.12   12.0   0.0    1.5  1  ATP-synt_J   ATP synthase j chain


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 !   97.8   0.1   1.4e-31     5e-28       2     110 ..     124     233 ..     123     235 .] 0.94

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1.4e-31
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGls 79 
                                   de ++++i+ nlv Na+kf++++ ++++e k  +  +  ++ v+D+GiGi + ++ klfe f+q d+st+r++gg GlGl 
  gi|91772433|ref|YP_565125.1| 124 DEFKFKHILYNLVHNAIKFTPDGRHVTIETK--KcgKSMCFFVKDTGIGILPTNQIKLFEQFYQvDSSTTRKYGGIGLGLN 202
                                   77789**************88999*****99..3347999***************************************** PP

                                   HHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                     HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlpl 110
                                   ivkk+ve +gG++w+ese ++G+tf f++p 
  gi|91772433|ref|YP_565125.1| 203 IVKKFVEIHGGKVWIESEVEKGSTFGFSIPD 233
                                   ***************************9986 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 !   56.5   0.0   5.7e-19     2e-15       1      67 []      10      77 ..      10      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 5.7e-19
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA  1 slgrflagvaHELrtPLsailgnaeaLkre.gklteelkeyletiesearrldhlvedlLdlsrieag 67
                                  s+++f+ +++HE rtPL++++g++++L ++ g+ +e++ +yl+ i  ++++l+++ +++L +s+ie+g
  gi|91772433|ref|YP_565125.1| 10 SKSEFIMNMSHEVRTPLNSVIGFSSVLLDKpGNRDESQVRYLHNILFNGKHLLEIFNEILAISKIESG 77
                                  799************************99998889*******************************97 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.7e-07   0.00062       5      90 ..     127     220 ..     123     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-07
                   HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..........ek..kklesskskkeehGiGlks 73 
                                    +  il nl  NAi      ++  r ++++ ++  ks+++ ++ +  g          e+  +   s+++k +  G+Gl+ 
  gi|91772433|ref|YP_565125.1| 127 KFKHILYNLVHNAIKFT---PD-GRHVTIETKKCGKSMCFFVKDTGIGilptnqiklfEQfyQVDSSTTRKYGGIGLGLNI 203
                                   56789999999999764...43.7899999999999999999999666666654444422434444778888889999*** PP

                   HATPase_c_5  74 ireivkkykgnlsieae 90 
                                   +++ v+ ++g+++ie e
  gi|91772433|ref|YP_565125.1| 204 VKKFVEIHGGKVWIESE 220
                                   *************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 !   15.9   0.0   2.3e-06    0.0084       4      77 ..     129     201 ..     126     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-06
                   HATPase_c_3   4 ekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGl 77 
                                   +  l  lv N++    d ++v+ie +k  gk+  + ++D G G+ + + ++ + ++ + + +   + +++G  G+Gl
  gi|91772433|ref|YP_565125.1| 129 KHILYNLVHNAIKftPDGRHVTIETKKC-GKSMCFFVKDTGIGILPTNQIKLFeQFYQVDSS---TTRKYGGIGLGL 201
                                   556889*****98668999999999996.789999************999988457777777...689999999996 PP

>> ATP-synt_J  ATP synthase j chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.4e-05      0.12       9      38 ..      98     127 ..      94     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                                   SSHHHHHHHHHHHHHHHHHHHHSTTSSSSS CS
                    ATP-synt_J   9 pmwPFfaaglivlygvnkaqnammnsdEfk 38 
                                    m+PF    +i+l  +  ++na mn dEfk
  gi|91772433|ref|YP_565125.1|  98 SMMPFALEKGIILTHIIDVENAIMNADEFK 127
                                   599**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1496.17
//
Query:       gi|91772434|ref|YP_565126.1|  [L=276]
Description: bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE [Methanococcoides burtonii DSM 6242]
Scores for 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   82.8   0.1    3.4e-23   82.1   0.1    1.4  1  MoaE      MoaE protein
    9.2e-17   61.2   0.1      2e-16   60.1   0.1    1.6  1  MobB      Molybdopterin guanine dinucleotide synthesis protei
     0.0025   17.8   0.0     0.0072   16.4   0.0    1.8  1  AAA_14    AAA domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.074   13.1   0.1    1.9  1  MMR_HSR1  50S ribosome-binding GTPase
      0.036   13.8   0.0      0.067   12.9   0.0    1.6  1  AAA_24    AAA domain
      0.071   12.0   0.0       0.11   11.3   0.0    1.3  1  DUF463    YcjX-like family, DUF463


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 !   82.1   0.1   1.2e-26   3.4e-23      13     112 ..     152     255 ..     141     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.2e-26
                                   HHH-.-TT...--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTSEEEEE CS
                          MoaE  13 alva.spk...aGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevgeasvvv 89 
                                   + v+ +p+   aG++ +F+G+vR ++++ +++ Le+e y+++a +++++i ee++++ ++ +v+++H+ G++ + e +v++
  gi|91772434|ref|YP_565126.1| 152 EKVRsNPEivkAGGIGTFIGIVRTDNEDYETRMLEFEKYDKVADASIQKIREEMMQQDGIIDVLIHHKAGRIMPLEDIVYI 232
                                   44443333333************9999****************************************************** PP

                                   EEEESSHHHHHHHHHHHHHHHHH CS
                          MoaE  90 avssahRkeafeaceylidelKk 112
                                   ++++ hR++ f+a ++ +d++K+
  gi|91772434|ref|YP_565126.1| 233 VIAAGHRQQLFAALSETLDRVKS 255
                                   **********************7 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   6.6e-20     2e-16       1     110 [.       5     110 ..       5     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 6.6e-20
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeaelsl 81 
                                   v++++g++++GKTt+++++++el + g rvgt+K    ++ +d+p+ D+ +h ++GA+ v+ +++++l  i++     +s+
  gi|91772434|ref|YP_565126.1|   5 VISVIGYKNTGKTTFVTRMVKELLELG-RVGTVKLML-DHRLDDPNTDTGKHFDSGADMVTAVTDRELVTISRN----PSF 79 
                                   689**********************99.9*****865.679***************************999994....566 PP

                          MobB  82 eellarlse..vDlvlvEGfkkealpkievl 110
                                   e+ l+ l++  +D+ +vEG k++++pk+++ 
  gi|91772434|ref|YP_565126.1|  80 EKALDELADagMDFAIVEGAKDSEVPKVVLG 110
                                   66666664446****************9875 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   2.4e-06    0.0072       2      90 ..       3      90 ..       2     108 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikell.vkkesilyinldderd....kkladpekllelileklkeekktylflDEiqevpew 79
                                   k++ + G + +GKTt++ +++kell   +  ++ + ld+  d    ++ +++++  +++ + ++  +++++    i++ p++
  gi|91772434|ref|YP_565126.1|  3 MKVISVIGYKNTGKTTFVTRMVKELLeLGRVGTVKLMLDHRLDdpntDTGKHFDSGADMVTA-VT--DRELVT---ISRNPSF 79
                                  6899**********************844444555555544441111444444322223222.22..233333...5666666 PP

                        AAA_14 80 ekalkslvdeg 90
                                  ekal +l d g
  gi|91772434|ref|YP_565126.1| 80 EKALDELADAG 90
                                  66666666666 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   2.5e-05     0.074       2      23 ..       6      27 ..       5      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                                  EEEEESTTSSHHHHHHHHHTST CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltgek 23
                                  + ++G+ N+GK+t++ ++++e 
  gi|91772434|ref|YP_565126.1|  6 ISVIGYKNTGKTTFVTRMVKEL 27
                                  789***************9974 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.3e-05     0.067       4      48 ..       5      57 ..       2     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                        AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie........s 48
                                   i ++G   +GKTt+++++ ++ l +   + +k + +++++d++        s
  gi|91772434|ref|YP_565126.1|  5 VISVIGYKNTGKTTFVTRMVKELLELGRVGTVKLMLDHRLDDPNtdtgkhfdS 57
                                  6889***************8899988666666666666666666555554443 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.8e-05      0.11       3      38 ..       6      38 ..       5      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
                        DUF463  3 lavTGLsraGKtvfitsLvnqLlaaekkarlplfea 38
                                  ++v G    GKt+f+t +v++Ll+    +r+ + + 
  gi|91772434|ref|YP_565126.1|  6 ISVIGYKNTGKTTFVTRMVKELLEL---GRVGTVKL 38
                                  6899*******************54...44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1877.27
//
Query:       gi|91772435|ref|YP_565127.1|  [L=229]
Description: DNA repair protein RadC [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-44  150.6   0.1    2.7e-44  150.0   0.1    1.3  1  RadC      RadC-like JAB domain
    0.00021   21.0   0.0    0.00057   19.6   0.0    1.8  2  HHH       Helix-hairpin-helix motif
      0.001   19.1   0.0      0.002   18.2   0.0    1.4  1  HHH_2     Helix-hairpin-helix motif
     0.0024   17.6   0.0     0.0037   17.0   0.0    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain
     0.0038   17.8   0.0     0.0088   16.6   0.0    1.7  1  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.032   14.5   0.1      0.079   13.2   0.1    1.6  1  HHH_3     Helix-hairpin-helix motif
       0.14   12.2   0.0        0.3   11.1   0.0    1.6  1  HRDC      HRDC domain


Domain annotation for each model (and alignments):
>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.0   0.1   1.1e-47   2.7e-44       1     121 [.     107     226 ..     107     227 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 1.1e-47
                                   -SSHHHHHHHHTTTSS-TTS-EEEEEEE-TTSBEEEEEEEEESTT-GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S-- CS
                          RadC   1 lsspedvaeylkeeladleqEefvvllLdsknrliadeelseGtlnstlvdprevfkealklnAaavilaHnhPsgdlepS 81 
                                   ++s++dv+++l ++ ++l++E++ +l+Ld+kn++i++e++s G+ln+ +v+prevfk+al +++a+vil+HnhPsgd+ pS
  gi|91772435|ref|YP_565127.1| 107 IRSANDVYSLLYPRHRELKKEHLTALYLDTKNNIIKEEVISIGSLNANIVHPREVFKSALMESSASVILTHNHPSGDPAPS 187
                                   67999**************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHT-EEEEEEEEESSE.EEETCCCT CS
                          RadC  82 eeDieltkrlkealkllgiellDhiIigdeeeyySfaeeg 121
                                   +eDi++t++l e +k+lgi++lDh+Iigd++ y+S++eeg
  gi|91772435|ref|YP_565127.1| 188 REDIAVTEKLVEGGKILGISVLDHVIIGDGR-YVSLKEEG 226
                                   ****************************666.*****987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.2e-07   0.00057       3      28 ..      62      87 ..      60      89 .. 0.90
   2 ?   -3.7   0.0       5.3   1.4e+04       5      13 ..     183     191 ..     182     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.2e-07
                                  HHHHTSSHHHHHTSTT-SHHHHHHHH CS
                           HHH  3 eglipasreeLlalPGVGpktAeaIl 28
                                  + l  a++ +L+++ G+Gp++A +I+
  gi|91772435|ref|YP_565127.1| 62 KQLSQANISQLTKIRGIGPAKASQIA 87
                                  67889******************997 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.3
                                   HHTSSHHHH CS
                           HHH   5 lipasreeL 13 
                                   + + sre++
  gi|91772435|ref|YP_565127.1| 183 DPAPSREDI 191
                                   567899997 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   7.7e-07     0.002      25      57 ..      60      92 ..      52      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.7e-07
                         HHH_2 25 sldaLkkasleeLlevddiGeeiAqsivefFen 57
                                  +l +L++a++ +L+++++iG+  A++i   Fe 
  gi|91772435|ref|YP_565127.1| 60 NLKQLSQANISQLTKIRGIGPAKASQIAALFEL 92
                                  799*************************99985 PP

>> 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 !   17.0   0.0   1.4e-06    0.0037      51      98 ..     157     208 ..     114     224 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                      Prok-JAB  51 dpedslarlkfearerglevvgiwHSHpggsarPSetDrrdaaalar........v 98 
                                    p++ ++    +a  +    v   H Hp g + PS++D++  ++l++        v
  gi|91772435|ref|YP_565127.1| 157 HPREVFK----SALMESSASVILTHNHPSGDPAPSREDIAVTEKLVEggkilgisV 208
                                   3333333....566777788889*****************9999998766655542 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.5e-06    0.0088      17      51 ..      54      86 ..      49      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-06
                                  HHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHH CS
                         HHH_5 17 allsaGiesvedlaaadveeLakipGiGkktAeri 51
                                  ++ls     + +l +a++ +L+ki GiG+ +A +i
  gi|91772435|ref|YP_565127.1| 54 RILSE--YNLKQLSQANISQLTKIRGIGPAKASQI 86
                                  78999..99***********************999 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   0.1   3.1e-05     0.079       9      32 ..      65      88 ..      63      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                         HHH_3  9 NtAsaeeLqklpGlgpklAknIva 32
                                   +A  ++L+k+ G+gp++A +I a
  gi|91772435|ref|YP_565127.1| 65 SQANISQLTKIRGIGPAKASQIAA 88
                                  679999999999999999999976 PP

>> HRDC  HRDC 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      24      63 ..      53      89 ..      44      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                  HHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHH CS
                          HRDC 24 yvvfpdktLleiAeklPttleeLlqiegvgkrklekygee 63
                                  ++++++  L++++++   + ++L++i+g+g++k+ + ++ 
  gi|91772435|ref|YP_565127.1| 53 SRILSEYNLKQLSQA---NISQLTKIRGIGPAKASQIAAL 89
                                  689999999999998...9***************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1500.95
//
Query:       gi|91772436|ref|YP_565128.1|  [L=129]
Description: hypothetical protein Mbur_0383 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 994.11
//
Query:       gi|91772437|ref|YP_565129.1|  [L=426]
Description: hypothetical protein Mbur_0384 [Methanococcoides burtonii DSM 6242]
Scores for 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-07   29.2   0.2    7.3e-06   26.3   0.1    2.4  3  Hint_2           Hint domain
    1.2e-05   25.2   0.0    3.1e-05   23.9   0.0    1.7  1  Intein_splicing  Intein splicing domain
    2.6e-05   24.5   0.1      0.035   14.3   0.0    2.4  2  PT-HINT          Pretoxin HINT domain
     0.0012   19.0   0.0     0.0024   17.9   0.0    1.5  1  Terminase_6C     Terminase RNaseH-like domain
     0.0025   17.7   0.0     0.0048   16.7   0.0    1.4  1  Vint             Hint-domain


Domain annotation for each model (and alignments):
>> Hint_2  Hint domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1     2e-09   7.3e-06       2      50 ..      73     120 ..      72     128 .. 0.88
   2 ?   -0.9   0.0      0.53   1.9e+03      14      45 ..     144     175 ..     140     190 .. 0.77
   3 ?   -2.1   0.0       1.2   4.2e+03      59      81 ..     273     295 ..     243     340 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2e-09
                        Hint_2   2 CflagtliatpeGevaveeLrvGdlVvtadgglqpvrwigsrtlsaadl 50 
                                   C+++gt+++t+ G +++e++r+G+ V+t+ +g+++v+  g+++ s+ ++
  gi|91772437|ref|YP_565129.1|  73 CLAEGTMVMTDVGGIPIENIREGMFVLTR-EGYKRVLAAGQTSSSSDTM 120
                                   9***************************9.6788999999988776555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.53
                        Hint_2  14 GevaveeLrvGdlVvtadgglqpvrwigsrtl 45 
                                   G   +++L   d+V+t +++l +++    + +
  gi|91772437|ref|YP_565129.1| 144 GFTNIDALVWYDRVITCEENLSNIKESRLQDI 175
                                   66788999999*******99999987665555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
                        Hint_2  59 vriragalgegvpardLlvspqh 81 
                                    r+++g+l ++  + +L+ s+q 
  gi|91772437|ref|YP_565129.1| 273 ARVMNGMLSMESGHGKLVTSRQG 295
                                   45566666666666666666554 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.5e-09   3.1e-05      38     134 .]     107     390 ..      80     390 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.5e-09
                                   EEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE........................ CS
                                   xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
               Intein_splicing  38 vkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavp........................ 93 
                                   v ++ ++  +   ++++ ++g ++  T++H++ v   +g   ++ d L   d +++                         
  gi|91772437|ref|YP_565129.1| 107 VLAAGQTSSSsDTMTVHFSNGVTLNGTGNHPVYVE-GKGF--TNIDALVWYDRVITCeenlsnikesrlqdirrlkaypaa 184
                                   555555655568999*****************998.5777..999**********99************************ PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|91772437|ref|YP_565129.1| 185 dtsirsskkrterksklftkrygkmrtgrypmgtisttetatlptirlitsnvyrkrntlsatttdvathrgntstkyahl 265
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|91772437|ref|YP_565129.1| 266 rrsgmlrarvmngmlsmesghgklvtsrqgyvsnvganmkqsalgmisdsvlanvltntmsrpknimrsesaryvdqssks 346
                                   ********************************************************************************9 PP

                                   ....HSCEEEEEEEEEEEEEC.EEEEEEEEETTT-EEEECTTEEE- CS
                                   ....xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  94 ....dadvvwdkvksievede.eeyVYdltvednhNFvangiivHN 134
                                              +v      +  +++VY ltve+ + ++angi+vHN
  gi|91772437|ref|YP_565129.1| 347 rsqkS--RQHAHVSVLGSYGAgKRKVYNLTVEECNEYFANGILVHN 390
                                   98543..344444444444334556********************9 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   9.8e-06     0.035       1     110 [.      79     181 ..      79     188 .. 0.84
   2 !    7.7   0.1    0.0011         4     107     136 ..     368     390 ..     352     391 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.8e-06
                       PT-HINT   1 lvktadGykaiarikaGdrvlakdeasgkvaekpvlar.ygneyqelvylkisdgignsevlisnkihPfysk.gkfieak 79 
                                   +v t  G   i++i+ G  vl+++      ++k vla   +    +++ ++ s+g+    +l  +  hP y++  +f + +
  gi|91772437|ref|YP_565129.1|  79 MVMTDVGGIPIENIREGMFVLTRE------GYKRVLAAgQTSSSSDTMTVHFSNGV----TLNGTGNHPVYVEgKGFTNID 149
                                   778888888999999999999765......89999986245567788888888865....8999*********6679**** PP

                       PT-HINT  80 elkvGdklldesGkvlvveeiklk.dePlkay 110
                                    l   d++++ + +   ++e +l+  + lkay
  gi|91772437|ref|YP_565129.1| 150 ALVWYDRVITCEENLSNIKESRLQdIRRLKAY 181
                                   **********************9944788998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                       PT-HINT 107 lkaynlkvadfhtyfvkgnraeteGvlvhn 136
                                    k+ynl+v++   yf +       G+lvhn
  gi|91772437|ref|YP_565129.1| 368 RKVYNLTVEECNEYFAN-------GILVHN 390
                                   59*************87.......999998 PP

>> Terminase_6C  Terminase RNaseH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.8e-07    0.0024      64     130 ..       3      61 ..       1      71 [. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.8e-07
                                   CHHHHHHHHHHCCT--S-SCEESSH..HHHHHHHHHHHHHHHTTSEEEETHHCECCCCCCHCC-EEH CS
                  Terminase_6C  64 saGesvaellkrdlesealavkpepaskdkatrvskvkdliesgrlkvdkgaecaksfealegfhtd 130
                                   ++G  v ++l++ ++s  +++k+ +as++k tr+++++ ++e+gr+ ++ +      f ale +++d
  gi|91772437|ref|YP_565129.1|   3 NGGDLVEANLRSVDPS--IPYKAVRASRGKQTRAEPISSYYEQGRIHHVGT------FPALEDQMCD 61 
                                   6788899999999998..9******************************98......9999999887 PP

>> Vint  Hint-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-06    0.0048       2      69 ..      73     143 ..      72     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                          Vint   2 Cfagesrvklaegktvkiselrkgmkvqtpkgarkvaavlktkveeeelcrl...g.ellvTpwHPvrlegk 69 
                                   C+a  ++v +++   ++i+++r+gm v t +g ++v a  +t+ ++ ++      g +l  T  HPv +egk
  gi|91772437|ref|YP_565129.1|  73 CLAEGTMV-MTDVGGIPIENIREGMFVLTREGYKRVLAAGQTSSSSDTMTVHfsnGvTLNGTGNHPVYVEGK 143
                                   77777777.5666789***************************999666433465347888*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3275.97
//
Query:       gi|91772438|ref|YP_565130.1|  [L=137]
Description: hypothetical protein Mbur_0385 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 887.66
//
Query:       gi|91772439|ref|YP_565131.1|  [L=115]
Description: transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00071   20.1   0.7    0.00099   19.6   0.7    1.1  1  FlgN          FlgN protein
     0.0042   17.1   0.0     0.0062   16.6   0.0    1.3  1  HTH_20        Helix-turn-helix domain
     0.0095   15.9   0.9      0.014   15.4   0.1    1.6  2  HTH_45        Winged helix-turn-helix
  ------ inclusion threshold ------
      0.012   15.0   0.7      0.013   14.9   0.7    1.1  1  Endonuc-MspI  Restriction endonuclease MspI
      0.033   14.3   1.4      0.039   14.1   1.4    1.1  1  MRP-L28       Mitochondrial ribosomal protein L28
      0.064   13.3   0.9      0.079   13.0   0.9    1.1  1  SdrG_C_C      C-terminus of bacterial fibrinogen-binding adhe
       0.16   11.9   0.0       0.29   11.0   0.0    1.5  1  HTH_5         Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.7   3.9e-07   0.00099      40     138 ..       6      97 ..       4     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.9e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                          FlgN  40 LeelleekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelkelleelkelnelNgrlieqslef 120
                                   L+e +++kq+l+e+++++ +kr  + +++          ++l+++++ ++ e +++  + l+++k++ +lN++  + +l++
  gi|91772439|ref|YP_565131.1|   6 LDENNRKKQKLIEQMKEAGKKRNPSEDHAVAL-------KILQNPTRRKIIEFMKDGPKSLDQIKDKYDLNNMQARLNLDM 79 
                                   89999*****************9999999999.......89999************************************* PP

                                   HHHHHHHCCHXXXX.XXX CS
                          FlgN 121 nqrllnllqgaanksntY 138
                                   ++ +  + +  ++++ +Y
  gi|91772439|ref|YP_565131.1|  80 LEDSFYIAKTDSSDKINY 97 
                                   **9999999888887777 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   2.4e-06    0.0062       3      54 ..      36      86 ..      34      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                                  HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                        HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                  ++++L +P+Rr+i      +++ ++ ++++  dl   +++ +L+ Le+  ++
  gi|91772439|ref|YP_565131.1| 36 ALKILQNPTRRKIIEFM-KDGPKSLDQIKDKYDLNNMQARLNLDMLEDSFYI 86
                                  578999***********.****************999999999999986555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   4.8e+03      38      43 ..      15      20 ..       2      27 .. 0.58
   2 !   15.4   0.1   5.5e-06     0.014      11      70 ..      48     111 ..      45     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                        HTH_45 38 kYLdmL 43
                                  k ++++
  gi|91772439|ref|YP_565131.1| 15 KLIEQM 20
                                  222332 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.5e-06
                        HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklk 70 
                                   I e +++g ++  +i  k +L+  +++  LdmL +  +i    + +k +Y+lT +G  +le+++
  gi|91772439|ref|YP_565131.1|  48 IIEFMKDGPKSLDQIKDKYDLNNMQARLNLDMLEDSFYIaktdSSDKINYELTIRGDAFLENVR 111
                                   7788888888999999999********************9887779999************987 PP

>> Endonuc-MspI  Restriction endonuclease MspI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.7   5.3e-06     0.013     138     206 ..       6      71 ..       2     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.3e-06
                  Endonuc-MspI 138 ldlsdsdlrellkkfqevGskkklkektpdsikvleeeLkpynkkliqwaiaGlhspglvdekiqlady 206
                                   ld ++ + ++l+++++e+G k++  e +    k+l++   p ++k+i+++  G +s + +++k  l ++
  gi|91772439|ref|YP_565131.1|   6 LDENNRKKQKLIEQMKEAGKKRNPSEDHAVALKILQN---PTRRKIIEFMKDGPKSLDQIKDKYDLNNM 71 
                                   5566677999***************999999999985...899***************99999988876 PP

>> MRP-L28  Mitochondrial ribosomal protein L28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.4   1.5e-05     0.039      24     104 ..       9      87 ..       2      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXSXSXXTTSSTTX..XSXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       MRP-L28  24 akkrlekqirkleksakelkPveelivplksvdsakrrqrkllelskeelerrallekqwaryrqqekekdeqlirqqlea 104
                                   + ++++k i +++ + k+ +P e+  v lk++++    +rk +e  k+  ++ + ++ ++ ++ +q +++ + l +  + a
  gi|91772439|ref|YP_565131.1|   9 NNRKKQKLIEQMKEAGKKRNPSEDHAVALKILQNP--TRRKIIEFMKDGPKSLDQIKDKYDLNNMQARLNLDMLEDSFYIA 87 
                                   4567788889*************************..78899999999999999999999999999998776666666655 PP

>> SdrG_C_C  C-terminus of bacterial fibrinogen-binding adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   3.1e-05     0.079      31     126 ..       7      94 ..       4     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                   TSS-EEEEEEEEEEECTS...EETTTTT-EEEEEEESSGGGS-TT----T-CCCCEE-GGGHGCCEEEECTTEEEEEEEEE CS
                      SdrG_C_C  31 skkslksaevvgnlseaeesnskvnknntkvkIYkvnkgqdLpeSygvnedsskledvtnqfdgkislgdnnsakinfgnl 111
                                   ++++ k++++  +++ea+++ ++ ++++  +kI +++   ++ e ++     + l  + +    k++l++ + a++n+  l
  gi|91772439|ref|YP_565131.1|   7 DENNRKKQKLIEQMKEAGKKRNPSEDHAVALKILQNPTRRKIIEFMKDG--PKSLDQIKD----KYDLNNMQ-ARLNLDML 80 
                                   578889999999********************************88887..999*99999....55576666.******** PP

                                   .SSS-EEEEEEEEE- CS
                      SdrG_C_C 112 qkdksYivkvegkyd 126
                                    +d+ Yi k ++  +
  gi|91772439|ref|YP_565131.1|  81 -EDSFYIAKTDSSDK 94 
                                   .89999988776544 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 ?   11.0   0.0   0.00011      0.29       1      23 [.      42      64 ..      42      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                  SHHHHHHHHHHTTSSEEHHHHHH CS
                         HTH_5  1 dptRlkILklLaegelcvcelae 23
                                  +ptR+kI+ ++ +g+++  ++ +
  gi|91772439|ref|YP_565131.1| 42 NPTRRKIIEFMKDGPKSLDQIKD 64
                                  69**************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 856.67
//
Query:       gi|91772440|ref|YP_565132.1|  [L=249]
Description: ABC efflux pump, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-37  128.4  23.3    2.3e-37  128.4  23.3    1.5  2  ABC2_membrane    ABC-2 type transporter
    1.3e-14   54.1  29.3    1.3e-14   54.1  29.3    1.5  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.3e-05   24.7  16.4    1.3e-05   24.7  16.4    1.6  2  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4  23.3   3.9e-41   2.3e-37       3     209 ..       4     214 ..       3     215 .. 0.93
   2 ?   -2.3   0.3       0.4   2.4e+03      28      33 ..     232     237 ..     221     247 .. 0.37

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 3.9e-41
                 ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn...lg.nsedglnr..pgllffsvlflafsaltsvapvfer 77 
                                   i++++ r++++++r++s + l +l +p++++lv+g+   +   l+  +++++ +  pg++ +svlf++   ++++ +++++
  gi|91772440|ref|YP_565132.1|   4 IYTIWLRNVKRYLRSKSRL-LGSLGMPVFFLLVLGFGLNSvvvLPgMEQGYIGFiiPGIISMSVLFTS--VFSGMEIIWDK 81 
                                   6899************999.******************986554454444444478************..6666667**** PP

                 ABC2_membrane  78 ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls...rfflflllllltalaasslgllisala 155
                                   + g+l++ lv+p+ s+ +++l+++++ ++ +++q+li++++++f+ gl++s    f++++++++l++l + ++g++i++ +
  gi|91772440|ref|YP_565132.1|  82 QFGFLKETLVAPV-SRTEIMLGQTFGGATTAVIQGLIIFILSVFM-GLKISsipGFVIAIVFMVLIGLSFAAFGIAIASRM 160
                                   *************.*******************************.*****99888************************* PP

                 ABC2_membrane 156 psfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                   ++++ +++++++v++p++ lsG+++pids+p  ++++  l Plty+ve++r++l
  gi|91772440|ref|YP_565132.1| 161 EDMHGFQLIMNFVIFPIFGLSGALFPIDSLPANMRFLTLLDPLTYGVEGIRYGL 214
                                   *******************************9*******************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.4
                 ABC2_membrane  28 qpllla 33 
                                   +++l+ 
  gi|91772440|ref|YP_565132.1| 232 FTILMV 237
                                   111111 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 !   54.1  29.3   2.2e-18   1.3e-14     157     343 ..      51     240 ..      45     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.2e-18
               ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afgl.gip 234
                                   +++  f+++ i+ +++++t++f  ++i+ +k+ + ++  lv++vs+++++l+  +g ++ +++q l+i++l  + gl   +
  gi|91772440|ref|YP_565132.1|  51 QGYIGFIIPGIISMSVLFTSVFSGMEIIWDKQFGFLKETLVAPVSRTEIMLGQTFGGATTAVIQGLIIFILsvFMGLkISS 131
                                   6788899998888889999999999***********99********************************87555643344 PP

               ABC2_membrane_3 235 fg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgll 314
                                      ++++++++++l gl+++a+g ++ s + ++   q+++ +vi++++g++g+lfp+++lp  ++ ++ + P+++  +g+ 
  gi|91772440|ref|YP_565132.1| 132 -IpGFVIAIVFMVLIGLSFAAFGIAIASRMEDMHGFQLIMNFVIFPIFGLSGALFPIDSLPANMRFLTLLDPLTYGVEGIR 211
                                   .369****************************************************************************5 PP

               ABC2_membrane_3 315 rlitgdplweillsliilalfavvyllla 343
                                     +   + ++  +s+++l +f++++++++
  gi|91772440|ref|YP_565132.1| 212 YGLLESSQIDPVISFVVLSGFTILMVVIG 240
                                   55544433566789999999999999987 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 ?   -1.6   0.2      0.22   1.3e+03      22     150 ..      26      40 ..       6      74 .. 0.53
   2 !   24.7  16.4   2.1e-09   1.3e-05     101     285 ..      81     246 ..      51     249 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.22
               ABC2_membrane_2  22 vllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstimavlipviaalfgadaiagEke 102
                                   + +p++                                                                           
  gi|91772440|ref|YP_565132.1|  26 LGMPVF--------------------------------------------------------------------------- 31 
                                   444444........................................................................... PP

               ABC2_membrane_2 103 rgTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiil 150
                                                                          +ll l++ l
  gi|91772440|ref|YP_565132.1|  32 ---------------------------------------FLLVLGFGL 40 
                                   .......................................233333333 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.1e-09
               ABC2_membrane_2 101 kergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllv.vflal 180
                                   k  g lk  L  PvsR ei lg   gg++     ++  l++      +il++ + l+++++  +v+a+v+++l++  f+a+
  gi|91772440|ref|YP_565132.1|  81 KQFGFLKETLVAPVSRTEIMLGQTFGGATT---AVIQGLII------FILSVFMGLKISSIPGFVIAIVFMVLIGlSFAAF 152
                                   555668999*********************...33333333......4555667788888888999999999988899*** PP

               ABC2_membrane_2 181 glllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlnalgst 261
                                   g++++s +       +l   ++++  +  +++l+++ +l+a + +       l+ll+p  +   +++  l  s   +++  
  gi|91772440|ref|YP_565132.1| 153 GIAIASRME-DMHGFQLIMNFVIFPIFGLSGALFPIDSLPANMRF-------LTLLDPLTYGVEGIRYGLLES---SQIDP 222
                                   ********9.7788888888888888999999*999999995555.......777777666555555555555...47888 PP

               ABC2_membrane_2 262 atnllilllllavllvlgyvlFkr 285
                                   + ++++l + ++ ++v+g +lF++
  gi|91772440|ref|YP_565132.1| 223 VISFVVLSGFTILMVVIGSYLFRK 246
                                   99********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1659.12
//
Query:       gi|91772441|ref|YP_565133.1|  [L=327]
Description: daunorubicin resistance ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-35  120.9   0.0    9.9e-35  120.0   0.0    1.4  1  ABC_tran         ABC transporter
    6.4e-12   45.9   1.1    6.6e-08   32.7   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.8e-09   38.2   0.3    4.4e-09   36.9   0.3    1.7  1  DUF4162          Domain of unknown function (DUF4162)
    2.7e-07   30.6   1.1     0.0089   15.8   0.0    2.5  3  AAA_15           AAA ATPase domain
    3.8e-06   27.5   0.7    9.4e-06   26.3   0.3    1.7  2  AAA_23           AAA domain
      1e-05   26.0   0.4    0.00013   22.4   0.2    2.6  2  AAA              ATPase family associated with various cellul
      0.001   19.0   0.0     0.0021   18.0   0.0    1.5  1  Rad17            Rad17 P-loop domain
      0.001   18.5   0.1     0.0082   15.6   0.1    2.2  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0034   17.1   0.6     0.0064   16.2   0.6    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0038   16.9   0.1      0.012   15.2   0.1    1.8  1  SRP54            SRP54-type protein, GTPase domain
     0.0054   16.3   0.1     0.0092   15.6   0.1    1.3  1  AAA_27           AAA domain
  ------ inclusion threshold ------
      0.023   14.3   0.1      0.073   12.7   0.1    1.9  1  Nbl1_Borealin_N  Nbl1 / Borealin N terminal
      0.027   13.8   0.2      0.096   11.9   0.0    1.9  2  DUF2813          Protein of unknown function (DUF2813)
      0.028   13.9   0.1      0.052   13.0   0.1    1.3  1  AAA_7            P-loop containing dynein motor region
      0.037   13.7   0.2       0.71    9.6   0.0    2.3  2  AAA_24           AAA domain
      0.042   13.6   0.1      0.083   12.7   0.1    1.4  1  MukB             MukB N-terminal
      0.048   13.4   0.0      0.088   12.5   0.0    1.5  1  AAA_30           AAA domain
      0.053   13.8   2.4      0.095   13.0   0.1    2.4  3  T3RM_EcoP15I_C   Type III R-M EcoP15I C-terminal domain
      0.069   13.1   1.1       0.21   11.5   0.0    2.2  2  AAA_31           AAA domain
      0.072   13.0   0.1       0.94    9.4   0.0    2.3  2  NTPase_1         NTPase
      0.083   12.4   0.0        4.5    6.8   0.0    2.4  2  GTP_EFTU         Elongation factor Tu GTP binding domain
        0.1   12.6   0.1       0.53   10.3   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.6   0.3       0.98    9.7   0.3    2.1  1  AAA_22           AAA domain
       0.13   12.0   0.1         23    4.7   0.1    2.5  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 !  120.0   0.0   1.3e-37   9.9e-35       1     136 [.      19     162 ..      19     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 1.3e-37
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   ++n+s+++k+ge+ +++G+nGaGK+t +++l+ +lkp +G+  ++g d+++ ++  +rk+ig+++q+++l++elt++en  
  gi|91772441|ref|YP_565133.1|  19 VNNLSFSIKQGEVFGLLGPNGAGKTTTMSMLSTMLKPSSGKASVNGFDIQT-NEDDVRKSIGIVFQDQSLDEELTAYENmd 98 
                                   589************************************************.99*************************** PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               ++e+i ++l+ ++l+++kd++v    +++SgG+++r+++ar ll +pk+l+lDEpt
  gi|91772441|ref|YP_565133.1|  99 fhgrlyripknIRQEKIMELLELVELDGKKDNIV----KTYSGGMRRRLEIARGLLHEPKVLFLDEPT 162
                                   ********88777777888888888888899998....*****************************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 !   12.4   0.2   0.00013       0.1       2      24 ..      32      54 ..      31     115 .. 0.73
   2 !   32.7   0.1   8.9e-11   6.6e-08     228     298 ..     125     194 ..      65     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                        AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                   +l GpNg+GK++ +  l+ +  
  gi|91772441|ref|YP_565133.1| 32 FGLLGPNGAGKTTTMSMLSTMLK 54
                                  689***********999977753 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 8.9e-11
                        AAA_21 228 dgqelparel.SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                   dg++ ++ +  S G++r l ++  ll  +   ++l++DEp +gL+P+   +l++ +++l++ +g+ +iltTH 
  gi|91772441|ref|YP_565133.1| 125 DGKKDNIVKTySGGMRRRLEIARGLLHEP---KVLFLDEPTLGLDPQTRNHLWKYIEKLNKeKGITIILTTHY 194
                                   44444444444888888888888888777...9***********************666666**********5 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.3   5.8e-12   4.4e-09       4      78 ..     220     301 ..     218     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 5.8e-12
                                   HHHHTTS-SSEEEEE....--.-----..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHH CS
                       DUF4162   4 eeiKrsygknrieve....ad.aeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIF 77 
                                   +++K+  g+++i++     ++  + ++++p+++ +e ++++l++ l++ e+   ++ + + ++ ++i s++ ++P+L+d+F
  gi|91772441|ref|YP_565133.1| 220 DKLKNDVGGDIITIVssenNKlYSVIRSLPEIKNIELHDSSLTIDLQNaEKHVAQIVTMAsDNSIPIDSISIHKPTLEDVF 300
                                   789**********776643225666667799*****************9***********77******************* PP

                                   H CS
                       DUF4162  78 i 78 
                                   +
  gi|91772441|ref|YP_565133.1| 301 L 301
                                   7 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05    0.0089      25      83 ..      31      84 ..      20     136 .. 0.61
   2 !   13.2   0.0   7.2e-05     0.054     323     364 ..     152     193 ..     139     194 .. 0.93
   3 ?   -2.7   0.1       4.8   3.6e+03     267     275 ..     247     255 ..     205     289 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                        AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83
                                  +  l G+N++GK++ + +l  +l+ ++     +  ++  d++++ +++  k+i I ++ 
  gi|91772441|ref|YP_565133.1| 31 VFGLLGPNGAGKTTTMSMLSTMLKPSSG----KASVNGFDIQTN-EDDVRKSIGIVFQD 84
                                  55688*******************9933....334444444444.44444444444444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.2e-05
                        AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   ++++l+++EP + L pq  ++l+k++ +l +++   +i+tTH
  gi|91772441|ref|YP_565133.1| 152 EPKVLFLDEPTLGLDPQTRNHLWKYIEKLNKEKGITIILTTH 193
                                   5789*************************999988******* PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.8
                        AAA_15 267 kidkikkfn 275
                                   ++ +ik+++
  gi|91772441|ref|YP_565133.1| 247 SLPEIKNIE 255
                                   222222222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   1.3e-08   9.4e-06       6     174 ..      12     192 ..      10     224 .. 0.66
   2 ?   -1.0   0.0       2.8   2.1e+03      80     144 ..     236     308 ..     203     324 .. 0.52

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.3e-08
                        AAA_23   6 nfrsfrdqe.idF...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenk 82 
                                    f+ f  ++ + F      ++ + GpNGaGKTT +  +  +L   +++ s +        d+   +e++v++++ + f+++
  gi|91772441|ref|YP_565133.1|  12 KFGGFTAVNnLSFsikQGEVFGLLGPNGAGKTTTMSMLSTMLKPSSGKASVN------GFDIQT-NEDDVRKSIGIVFQDQ 85 
                                   5777744433555555557***********************9866555543......234432.2347777788888887 PP

                        AAA_23  83 dgry....trsiererelskkkgkttkkaklellei....deleqfisellgskkiilnlilflgqerfeefel....... 148
                                   + ++    ++++++   l++  ++ +++++ elle      +++++++++ g   ++l++   l  e +  f++       
  gi|91772441|ref|YP_565133.1|  86 SLDEeltaYENMDFHGRLYRIPKNIRQEKIMELLELveldGKKDNIVKTYSGGMRRRLEIARGLLHEPKVLFLDeptlgld 166
                                   777778887777777777777666677776666666334433445555566666666666666555555455553333433 PP

                        AAA_23 149 kdkkerleelekeleeledekkllek 174
                                    ++ + l +++++l++++ +   l +
  gi|91772441|ref|YP_565133.1| 167 PQTRNHLWKYIEKLNKEKGITIILTT 192
                                   44555888888888888776666555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.8
                        AAA_23  80 enkdgry........trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfe 144
                                   + +++ y         ++ie   +    + ++  k   ++++++  + +  +++++ k+ l+ ++++  +r+ 
  gi|91772441|ref|YP_565133.1| 236 SENNKLYsvirslpeIKNIELHDSSLTIDLQNAEKHVAQIVTMASDNSIPIDSISIHKPTLEDVFLYFTGRTI 308
                                   4444433333333333333333333333333444444555555555555555666666666666666666654 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 !   22.4   0.2   1.7e-07   0.00013       3     121 ..      34     204 ..      32     211 .. 0.76
   2 ?   -2.6   0.0       9.1   6.8e+03      39      57 ..     265     283 ..     241     290 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-07
                                   EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS.SS........................................... CS
                           AAA   3 lyGppGtGKTllakavakelg..vefleisgsell.sk........................................... 37 
                                   l Gp G GKT++++ + + l+  +   +++g ++  ++                                           
  gi|91772441|ref|YP_565133.1|  34 LLGPNGAGKTTTMSMLSTMLKpsSGKASVNGFDIQtNEddvrksigivfqdqsldeeltayenmdfhgrlyripknirqek 114
                                   78*****************97433334444444442224555566777777777777777777777777777777777777 PP

                                   ................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSS CS
                           AAA  38 ................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkes 101
                                                   +v+  +  +r  ++ a+    +p++lf+DE       +          + n+L + +++++k+++
  gi|91772441|ref|YP_565133.1| 115 imellelveldgkkdnIVKTYSGGMRRRLEIARGLLhEPKVLFLDEPTLGLDPQ----------TRNHLWKYIEKLNKEKG 185
                                   777777777777777799999999999999999888999*******87776666..........89************766 PP

                                   TEEEEEEESSGGGSTHHHHS CS
                           AAA 102 kvivigatnrpdkldpallr 121
                                    +++i++t+++++ d+   r
  gi|91772441|ref|YP_565133.1| 186 -ITIILTTHYMEEADKLCHR 204
                                   .***********99987664 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.1
                                   TTHHHHHHHHHHHHHHHTS CS
                           AAA  39 vgesekkirelfkeakeka 57 
                                   ++++ek+++++++ a+ ++
  gi|91772441|ref|YP_565133.1| 265 LQNAEKHVAQIVTMASDNS 283
                                   5677888888888877665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.9e-06    0.0021      47     139 ..      31     120 ..      17     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                         Rad17  47 iLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklqklG 126
                                   +  + GP G gk+t++ +Ls  l ++  +  +n+  ++  +  +    g++ +++++   + +++++  ++  y +     
  gi|91772441|ref|YP_565133.1|  31 VFGLLGPNGAGKTTTMSMLSTMLKPSSgKASVNGFDIQTNEDDVRKSIGIVFQDQSLDEELTAYENMDFHGRLY-R---IP 107
                                   66788******************997626689****99998889888999999999999999999998888888.4...45 PP

                         Rad17 127 ddlrtdkklilve 139
                                   +++r +k + l+e
  gi|91772441|ref|YP_565133.1| 108 KNIRQEKIMELLE 120
                                   8899888887777 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 !   15.6   0.1   1.1e-05    0.0082      27     209 ..      32     202 ..      12     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                   EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkg 107
                                     ++GpNG+GK+  +  ++ +L  +s     +++++      ++++   + ++ i+f++++ +     ee++   ++  +g
  gi|91772441|ref|YP_565133.1|  32 FGLLGPNGAGKTTTMSMLSTMLKPSSG----KASVNGFDI--QTNEDDVRKSIGIVFQDQSLD-----EELTAYENMDFHG 101
                                   5689*********99988777765444....333443322..334455556799999888877.....8899999999999 PP

                                   EEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 108 eseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                   +  y+i  k++++++++elle ++++ +      + SgG +  + +a        +p+   +lDe    LD + ++ + ++
  gi|91772441|ref|YP_565133.1| 102 R-LYRIP-KNIRQEKIMELLELVELDGKkdnivkTYSGGMRRRLEIARG---LLHEPKV-LFLDEPTLGLDPQTRNHLWKY 176
                                   8.89996.6889999999999999998777888799***9986666543...2245555.569****************** PP

                                   HHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 183 lkeksknaQfivislreemlekadklv 209
                                   +++ +k+   i i l+++ +e+adkl+
  gi|91772441|ref|YP_565133.1| 177 IEKLNKEK-GITIILTTHYMEEADKLC 202
                                   **999665.566678888899998875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   8.5e-06    0.0064      15      55 ..      22      63 ..      13      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                        AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                   +++i++ +++ l Gp+G+GK+T +  ++++L p++ k++ N
  gi|91772441|ref|YP_565133.1| 22 LSFSIKQGEVFGLLGPNGAGKTTTMSMLSTMLKPSSgKASVN 63
                                  445566444999**********************99777776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.6e-05     0.012       5      38 ..      33      66 ..      30      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                   l+G++GaGKTtt++ L+ +lk +  k+ +   D
  gi|91772441|ref|YP_565133.1| 33 GLLGPNGAGKTTTMSMLSTMLKPSSGKASVNGFD 66
                                  589******************9987776666555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.2e-05    0.0092       9      50 ..      11      53 ..       5      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                        AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                  +++G ft  ++l+fs ++ ++  ++GpN AGK+t+++ +s +l
  gi|91772441|ref|YP_565133.1| 11 KKFGGFTAvNNLSFSIKQGEVFGLLGPNGAGKTTTMSMLSTML 53
                                  68****98358*****9999999*************9988776 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 ?   12.7   0.1   9.8e-05     0.073      35      56 ..      99     120 ..      95     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
               Nbl1_Borealin_N  35 felellriPkavRkmtmkelle 56 
                                   f  +l riPk +R+ +++elle
  gi|91772441|ref|YP_565133.1|  99 FHGRLYRIPKNIRQEKIMELLE 120
                                   67799***************98 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013     0.096      10      81 ..      15      85 ..      11     136 .. 0.79
   2 ?   -0.8   0.1      0.94     7e+02     286     315 ..     155     184 ..     110     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                       DUF2813 10 GFRGinrLSlsleentv..LiGENaWGKSSLldALslilnvekelyqFtlkDFhvdeseeeeqekhlqlvltfk 81
                                  GF  +n LS s+++  v  L+G N  GK   ++ Ls +l++++   + +  D     ++e++ +k++ +v+  +
  gi|91772441|ref|YP_565133.1| 15 GFTAVNNLSFSIKQGEVfgLLGPNGAGKTTTMSMLSTMLKPSSGKASVNGFDIQ---TNEDDVRKSIGIVFQDQ 85
                                  9************9998667********************99987666555544...55777788888887543 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.94
                       DUF2813 286 illlEdpearLHPtmlaiaWellellPlQk 315
                                   +l l++p   L P++   +W+++e l   k
  gi|91772441|ref|YP_565133.1| 155 VLFLDEPTLGLDPQTRNHLWKYIEKLNKEK 184
                                   788899999999999999999999887666 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 ?   13.0   0.1     7e-05     0.052      29      82 ..      25      78 ..      19      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                         AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                                   +k++  + l Gp G GKt++++ l + l++++ +  +  f  qt+  ++++ i
  gi|91772441|ref|YP_565133.1| 25 SIKQGEVFGLLGPNGAGKTTTMSMLSTMLKPSSGKASVNGFDIQTNEDDVRKSI 78
                                  5778888889***********************9999999******99999877 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00095      0.71       5      24 ..      32      50 ..      28      88 .. 0.85
   2 ?    2.0   0.1       0.2   1.5e+02     109     138 ..     171     201 ..     168     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                        AAA_24  5 iliyGpsgiGKTtlakelgp 24
                                  + + Gp+g+GKTt++++l  
  gi|91772441|ref|YP_565133.1| 32 FGLLGPNGAGKTTTMSML-S 50
                                  5789***********999.3 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                        AAA_24 109 eefrrllkklqelrk.nvifiahektrkded 138
                                   + ++++++kl++ ++ ++i++ h  ++ d+ 
  gi|91772441|ref|YP_565133.1| 171 NHLWKYIEKLNKEKGiTIILTTHYMEEADKL 201
                                   5678888888888889*******99998875 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011     0.083      27      53 ..      30      56 ..      12      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                  HHHHHHS--SHHHHHHHHHHHHHHS-- CS
                          MukB 27 lvttlsGgnGaGksttmaafvtaliPd 53
                                   v  l G nGaGk+ttm  + t l P 
  gi|91772441|ref|YP_565133.1| 30 EVFGLLGPNGAGKTTTMSMLSTMLKPS 56
                                  578899**************9999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.088      19      46 ..      30      58 ..      22     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g 46
                                   v  l Gp G+GKtt+++ l  +++ + g
  gi|91772441|ref|YP_565133.1| 30 EVFGLLGPNGAGKTTTMSMLSTMLKPSsG 58
                                  478899**************998877644 PP

>> T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00013     0.095      15      61 ..      79     125 ..      76     136 .. 0.86
   2 ?   -1.0   0.0       2.9   2.2e+03       2      26 ..     185     209 ..     169     222 .. 0.67
   3 ?   -2.2   0.0       7.3   5.4e+03      45      72 ..     266     292 ..     252     297 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                T3RM_EcoP15I_C  15 gygltekveevdlegYtayliekkLYliekglesealkaLieklded 61 
                                   g+ ++++  + +l  Y+ +  + +LY i k++++e++++L+e ++ d
  gi|91772441|ref|YP_565133.1|  79 GIVFQDQSLDEELTAYENMDFHGRLYRIPKNIRQEKIMELLELVELD 125
                                   5667777778899*****************************98844 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                T3RM_EcoP15I_C   2 gketiLttwlvkDgygltekveevd 26 
                                   g+  iLtt+ ++   +l +++  +d
  gi|91772441|ref|YP_565133.1| 185 GITIILTTHYMEEADKLCHRIAIMD 209
                                   5556777777777666666666555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.3
                T3RM_EcoP15I_C  45 glesealkaLiekldedkefniekivlf 72 
                                   +  ++++++++ +   d+++ i+ i + 
  gi|91772441|ref|YP_565133.1| 266 QNAEKHVAQIVTMAS-DNSIPIDSISIH 292
                                   445667777776665.777777777665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.21      12      47 ..      39      77 ..      37     136 .. 0.70
   2 ?   -0.2   0.3       1.1     8e+02      43      43 ..     215     215 ..     144     291 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                        AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt...g 47
                                  G GKTTt  +l+ +l  +  k  +  +D Q+n      +
  gi|91772441|ref|YP_565133.1| 39 GAGKTTTMSMLSTMLKPSSGKASVNGFDIQTNEDDvrkS 77
                                  89***************999************8664442 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                        AAA_31  43 n 43 
                                   +
  gi|91772441|ref|YP_565133.1| 215 A 215
                                   0 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0013      0.94       4      39 ..      34      71 ..      31     118 .. 0.82
   2 ?    1.0   0.0      0.48   3.6e+02      42      90 ..     223     277 ..     198     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                                  EE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE- CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGfyteevr 39
                                  + Gp G GKtT ++ ++ +lk s    +v+Gf  +   
  gi|91772441|ref|YP_565133.1| 34 LLGPNGAGKTTTMSMLSTMLKPSsgKASVNGFDIQTNE 71
                                  679*****************976446789999766554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.48
                                   ----EEEEEET.T--EEEEEETT......---SSEETTEEE-HHHHHHHHHHHHH CS
                      NTPase_1  42 grrigFkivdlasgeegiLarve......akreprvgkyvvdvesfeelalealr 90 
                                   ++ +g +i+++ s e++ L +v       ++ e + ++ ++d++++e+ ++++++
  gi|91772441|ref|YP_565133.1| 223 KNDVGGDIITIVSSENNKLYSVIrslpeiKNIELHDSSLTIDLQNAEKHVAQIVT 277
                                   5567888999999999999888755555444444555666666666666666555 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 ?    6.8   0.0    0.0061       4.5       6      62 ..      32      86 ..      28     106 .. 0.75
   2 ?    3.1   0.0     0.081        60      47      79 ..     179     212 ..     163     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0061
                                  EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEE CS
                      GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaais 62
                                  +g++g   +GKtT++  L + ++  s k+++++ +  + t++++ ++ i i  +  s
  gi|91772441|ref|YP_565133.1| 32 FGLLGPNGAGKTTTMSMLSTMLKPSSGKASVNGFD--IQTNEDDVRKSIGIVFQDQS 86
                                  67889999*************99999988888633..56666666666666555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.081
                                   HHHHHHTSCSSCEEEEEET.TCSSEEEEEEEESS CS
                      GTP_EFTU  47 keErergiTiksaaislek.etkkylinliDtPG 79 
                                   k  +e+giTi  ++ ++e+ ++  ++i+++D  G
  gi|91772441|ref|YP_565133.1| 179 KLNKEKGITIILTTHYMEEaDKLCHRIAIMDKGG 212
                                   66799*************5466677888888766 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 ?   10.3   0.0    0.0007      0.53       4      60 ..      34      88 ..      32     179 .. 0.83
   2 ?   -1.4   0.0       2.9   2.2e+03      13      46 ..     171     206 ..     163     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0007
                                  EE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........---- CS
                         AAA_5  4 LvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplv 60
                                  L+Gp G gK++ +  l+ +l     +  +  +  +t+e+d++ ++ i     +++d++l 
  gi|91772441|ref|YP_565133.1| 34 LLGPNGAGKTTTMSMLSTMLkpsSGKASVNGFDIQTNEDDVRKSIGI-----VFQDQSLD 88
                                  89******************987777777788889999999998887.....56655554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                                   HHHHHHGGGGB.S--EEEEE--TT--HHH.HH--B- CS
                         AAA_5  13 selaerlaaal.nreveyvqltrdtteed.lkgrre 46 
                                   + l++++ ++  ++ +++++ t +++e+d l  r+ 
  gi|91772441|ref|YP_565133.1| 171 NHLWKYIEKLNkEKGITIILTTHYMEEADkLCHRIA 206
                                   567777777776666777777777776542444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0013      0.98      10      31 ..      34      55 ..      27     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                        AAA_22 10 vtGesGtGKTtllrrlleqlde 31
                                  + G+ G+GKTt++ +l   l+ 
  gi|91772441|ref|YP_565133.1| 34 LLGPNGAGKTTTMSMLSTMLKP 55
                                  67*************9999853 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.031        23      41      62 ..      22      44 ..      14      56 .. 0.81
   2 ?    4.6   0.0     0.033        24     106     145 ..     150     188 ..     134     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.031
                     IstB_IS21 41 lsf.iekkenivllGpsGvGKsh 62
                                  lsf i++ e + llGp G+GK+ 
  gi|91772441|ref|YP_565133.1| 22 LSFsIKQGEVFGLLGPNGAGKTT 44
                                  555478889999*********95 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.033
                     IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiii 145
                                   l ++++l lD+   l ld + +++l++ iek  + + i i
  gi|91772441|ref|YP_565133.1| 150 LHEPKVLFLDEPT-LGLDPQTRNHLWKYIEKLNKEKGITI 188
                                   567899****975.689**************987765433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2190.47
//
Query:       gi|91772442|ref|YP_565134.1|  [L=633]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Methanococcoides burtonii DSM 6242]
Scores for 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-68  228.6   0.1    1.3e-67  228.1   0.1    1.2  1  GatB_N       GatB/GatE catalytic domain
    3.4e-20   72.4   2.2    4.6e-20   72.0   0.2    2.1  2  GatB_Yqey    GatB domain
    3.3e-17   62.5   0.0    9.4e-17   61.0   0.0    1.8  1  GAD          GAD domain
     0.0015   18.6   0.2     0.0047   17.0   0.0    1.9  2  YqeY         Yqey-like protein
  ------ inclusion threshold ------
      0.044   13.0   0.0      0.079   12.2   0.0    1.4  1  HIGH_NTase1  HIGH Nucleotidyl Transferase


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 !  228.1   0.1   3.5e-71   1.3e-67       2     272 ..      13     444 ..      12     445 .. 0.96

  Alignments for each domain:
  == domain 1  score: 228.1 bits;  conditional E-value: 3.5e-71
                                   EEEEEEEEEB--SB-SSSSSBSS...SSCE...........STTSS--TTTTTS..........................T CS
                                   xxxxxxxxxxxxxxxxxxxxxxx...xxxx...........xxxxxxxxxxxxx..........................x RF
                        GatB_N   2 viGlEiHaqlktksKlFssaste...eege...........epnsevsevdlal..........................P 42 
                                   ++GlEiH+ql++k+K+F++++t+   +  +            + se++e+d a+                          P
  gi|91772442|ref|YP_565134.1|  13 KCGLEIHQQLDSKEKMFCKCPTTirnT--DesnfeffrylrPTASEMGETDKAAleqtkvnrkyiykaydttcliendeeP 91 
                                   89*******************885431..2356778888844889999999999***********************9998 PP

                                   T..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE---E CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                        GatB_N  43 GtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDaak 121
                                      P+ ln+e++++a+++++ l++   e+++++RK+++++++++g+Q+t+    la++G+l++ e +v+i+ i++Ee+aa+
  gi|91772442|ref|YP_565134.1|  92 ---PRkLNREVLDIALSISKLLHMVPVEQLHMMRKIVVDGSNTSGFQRTA---FLANGGNLDTsEGTVGIDVICVEEEAAQ 166
                                   ...989********************************************...688******97889************** PP

                                   EEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 122 svheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtr 202
                                   +++++ ++ +++l+R+G+pL+Ei+t+pd+ sp++ar+++ k+++llr++g++++++  G++R+DvN+S+++       g+r
  gi|91772442|ref|YP_565134.1| 167 KIEDAGDSIIYSLDRLGIPLVEIATNPDIISPSHARETAAKIGMLLRSTGKVKRGI--GTIRQDVNISIAK-------GAR 238
                                   ********************************************************..************4.......59* PP

                                   EEEEEE-SHHHHHHHHHHHHHHHHHHH...................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                        GatB_N 203 vEiKnlnslksiekaieyeierqiell...................................................... 229
                                   vEiK+++ l+ ie+++e e+erq++ll                                                      
  gi|91772442|ref|YP_565134.1| 239 VEIKGVQALDLIETIVEREVERQVNLLeirrslnernasvhdeifdvtelfkgteskvikrsnkkgkvfavllpgfaghvg 319
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                        GatB_N 230 ................................................................................. 229
                                                                                                                    
  gi|91772442|ref|YP_565134.1| 320 mevqpgrrlgtefsdraktsgvggifhtdelpnygitedevttlrefvgagkndavimvadkekrargamesvliraaeal 400
                                   ********************************************************************************* PP

                                   ....-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHH CS
                                   ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 230 ....qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseeli 272
                                       +eTrk  +d g++ ++R+ + a   r++pe+d+p++eis+e++
  gi|91772442|ref|YP_565134.1| 401 efipEETRKGLPD-GNSAYMRPLPGA--SRMYPETDVPQVEISREYF 444
                                   *************.**********88..6**************9987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.33   1.2e+03      21      62 ..     264     302 ..     245     311 .. 0.75
   2 !   72.0   0.2   1.3e-23   4.6e-20       2     148 .]     482     627 ..     481     627 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                                   HTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHH CS
                     GatB_Yqey  21 lnellgelnkegleieelkltpeqlaellkliaegkIskkia 62 
                                   l e+ ++ln+++ ++++   +  +++el+k  +++ I  +  
  gi|91772442|ref|YP_565134.1| 264 LLEIRRSLNERNASVHD---EIFDVTELFKGTESKVIKRSNK 302
                                   56888999999999999...6677888888877777766554 PP

  == domain 2  score: 72.0 bits;  conditional E-value: 1.3e-23
                                   HHHHHHHHSS.HHHHHHHH....HTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHH CS
                     GatB_Yqey   2 ffeevvkegadaklaanwl....lnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspe 77 
                                   +fee+++  +  k++++ l    ++ +++el++ g+++e+  +t+e+++++++ i++g+++k++++++l+++++  +  ++
  gi|91772442|ref|YP_565134.1| 482 LFEELISRFSADKIITATLivrtITGTVSELKRDGVDVEK--ITDEHFKQMFEVISSGEVAKEAIEKILRHVAQRpDTFVR 560
                                   6888888886655555554011145567899********9..9********************************9***** PP

                                   HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                     GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                   +++ee gL+   d+ ++e+++e+ ++e ++ +    ++   a++ l+G vM + +Gk+d+k+++ellk+k+
  gi|91772442|ref|YP_565134.1| 561 DLLEELGLTGT-DTTKIEAFIEKLVEERQDFI---TEKGPGAVGPLMGLVMGEFRGKVDGKVLSELLKQKI 627
                                   ********876.78**************4443...3444499**************************996 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   2.6e-20   9.4e-17       6      95 .]     301     389 ..     297     389 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2.6e-20
                                   HSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEEEEEEE CS
                           GAD   6 ksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDillfvA 85 
                                   +++g+v a+ +pg +a+ +++e+++++++++e+++++++  +v+g ++t++++ + +te+ev +l+e vga ++D++++vA
  gi|91772442|ref|YP_565134.1| 301 NKKGKVFAVLLPG-FAGHVGMEVQPGRRLGTEFSDRAKTS-GVGGIFHTDELPNYgITEDEVTTLREFVGAGKNDAVIMVA 379
                                   689**********.8************************9.**************************************** PP

                                   EEHHHHHHHH CS
                           GAD  86 dkkktvnkal 95 
                                   dk+k +  a+
  gi|91772442|ref|YP_565134.1| 380 DKEKRARGAM 389
                                   ***9998776 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.8     1e+04     112     131 ..     300     319 ..     285     321 .. 0.73
   2 !   17.0   0.0   1.3e-06    0.0047      95     142 ..     575     626 ..     569     627 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                                   GGGHHHHHHHHHHHHTTTS- CS
                          YqeY 112 mkdmGkvmkalkpkvkGkaD 131
                                   +++ Gkv ++l p ++G++ 
  gi|91772442|ref|YP_565134.1| 300 SNKKGKVFAVLLPGFAGHVG 319
                                   45569999999998888775 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHHHHHT....T--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                          YqeY  95 eiealvkeaiaev....gaesmkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                   +iea++++ ++e      ++++ ++G +m++++ +++Gk+Dgk +s+l+k+k
  gi|91772442|ref|YP_565134.1| 575 KIEAFIEKLVEERqdfiTEKGPGAVGPLMGLVMGEFRGKVDGKVLSELLKQK 626
                                   566677777766533337889*****************************97 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05     0.079     242     340 ..     437     539 ..     405     583 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                   HIGH_NTase1 242 aslsledlskllkykllteskeelkkildvsegLenrikkalkkaesleelleklk.tKrytytriqRillhillnikked 321
                                   +++s e ++++   +llte++++++k + ++e+L+++i    ++ + +eel+++ +  K +t t i R+++ ++ ++k++ 
  gi|91772442|ref|YP_565134.1| 437 VEISREYFESIPVPELLTERAKRFSKEYGLNEELAQKIVY-SQDLTLFEELISRFSaDKIITATLIVRTITGTVSELKRDG 516
                                   566788899999999***********************99.6999********87626999*************9999885 PP

                   HIGH_NTase1 322 lk..klkkkk.p.ylrvLGfnkk 340
                                   ++  k+++++ + ++ v+   + 
  gi|91772442|ref|YP_565134.1| 517 VDveKITDEHfKqMFEVISSGEV 539
                                   54004444445335555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4342.55
//
Query:       gi|91772443|ref|YP_565135.1|  [L=354]
Description: WD40-like beta propeller protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-40  136.8   9.4    4.3e-13   48.8   0.2    6.3  6  PD40             WD40-like Beta Propeller Repeat
    2.9e-11   42.7   5.7      0.011   14.5   0.0    5.0  4  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    4.6e-10   39.2   0.3    1.2e-09   37.9   0.2    1.6  1  DUF5050          Domain of unknown function (DUF5050)
    6.5e-06   26.1   0.1     0.0063   16.3   0.0    2.9  3  Gmad1            Lipoprotein LpqB beta-propeller domain
      7e-05   21.7   0.2       0.23   10.1   0.1    2.6  2  Pectate_lyase22  Oligogalacturonate lyase
    7.6e-05   21.7   4.1     0.0023   16.8   0.0    3.0  3  Peptidase_S9_N   Prolyl oligopeptidase, N-terminal beta-prope
     0.0089   16.4   0.4       0.18   12.2   0.1    2.5  2  Inhibitor_I42    Chagasin family peptidase inhibitor I42


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   8.1e-08   0.00021      10      30 ..      45      65 ..      40      80 .. 0.78
   2 !    8.9   0.1   0.00055       1.4      11      28 ..      86     103 ..      70     109 .. 0.90
   3 !   27.0   0.0   1.2e-09   2.9e-06       5      38 .]     128     160 ..     125     160 .. 0.91
   4 !   23.8   0.0   1.2e-08     3e-05       2      29 ..     169     196 ..     168     200 .. 0.91
   5 !    7.9   0.0    0.0012       3.1      11      38 .]     218     244 ..     208     244 .. 0.91
   6 !   48.8   0.2   1.7e-16   4.3e-13       2      37 ..     253     287 ..     252     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.1e-08
                                  .EEEEEE-TTSSEEEEEEECT CS
                          PD40 10 negaPsfSPDGkrlaFsSdRg 30
                                  n  aP++SPD  r+++sS+++
  gi|91772443|ref|YP_565135.1| 45 NQVAPAWSPDSDRIVYSSEQT 65
                                  6679***************98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00055
                                   EEEEEE-TTSSEEEEEEE CS
                          PD40  11 egaPsfSPDGkrlaFsSd 28 
                                   +g+P f  DG rl+F+S+
  gi|91772443|ref|YP_565135.1|  86 DGEPVFNTDGDRLYFASE 103
                                   89999999*********7 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 1.2e-09
                                   -SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                          PD40   5 tntpgnegaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                   ++ ++++ aP++SPDG+ la+ S  + G+++I+v
  gi|91772443|ref|YP_565135.1| 128 ITKNADMRAPAVSPDGTQLAYLSKLS-GNYEIWV 160
                                   5667899*******************.******8 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 1.2e-08
                                   EE--SSSS.EEEEEE-TTSSEEEEEEEC CS
                          PD40   2 krltntpgnegaPsfSPDGkrlaFsSdR 29 
                                   +++t ++ +eg P++SPDGk +++s ++
  gi|91772443|ref|YP_565135.1| 169 TQITDSDIDEGVPAWSPDGKHIIYSLEG 196
                                   699*********************9775 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0012
                                   EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                          PD40  11 egaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                    ++P f P G++ a++ + + G  dI++
  gi|91772443|ref|YP_565135.1| 218 SYNPVFNPEGTKVAYVLETN-GVKDIWI 244
                                   5799999*************.******7 PP

  == domain 6  score: 48.8 bits;  conditional E-value: 1.7e-16
                                   EE--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEE CS
                          PD40   2 krltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIy 37 
                                   k+lt+++++e++P++SPDGk++a+sS++  G ++I+
  gi|91772443|ref|YP_565135.1| 253 KQLTFSDQDEIDPAWSPDGKSIAYSSNKA-GEFNIW 287
                                   89***************************.****** PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1   0.00035       0.9      44      73 ..      45      74 ..      31      96 .. 0.76
   2 !   14.5   0.0   4.4e-06     0.011       4      93 ..      95     183 ..      92     183 .. 0.74
   3 !   12.5   0.0   1.7e-05     0.044      20      69 ..     153     202 ..     150     211 .. 0.89
   4 !   10.9   0.4   5.3e-05      0.14      48     137 ..     221     296 ..     209     308 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00035
                                  .BSEEEEESSTTEEEEEETTEEEEESTTTS CS
                       DPPIV_N 44 klqlakwSPagdklafvrnnnLyvrelatg 73
                                   +  + wSP++d++++  ++ ++  ++   
  gi|91772443|ref|YP_565135.1| 45 NQVAPAWSPDSDRIVYSSEQTIWTMNSDGT 74
                                  466799*****************9987655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.4e-06
                                   SSEEEEEECEEEESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEE....TTEEEEESTTTSEEEECES CS
                       DPPIV_N   4 gkflllatnaeknwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafvr....nnnLyvrelatgkeiqlTs 80 
                                   g++l++a+++ + + +++  + +++d+   + ++++++ ++   + +SP+g++la+      n +++v ++  ++++q+T+
  gi|91772443|ref|YP_565135.1|  95 GDRLYFASEHVNPYSAKFI-SIHVVDIDGLNRTQITKN-ADMRAPAVSPDGTQLAYLSklsgNYEIWVMDIDGSNQTQITD 173
                                   5555555555555555443.456778888788888888.9999*************96444479****************7 PP

                                   -STTTEEESB--H CS
                       DPPIV_N  81 dgsagifnGvadW 93 
                                        i  Gv+ W
  gi|91772443|ref|YP_565135.1| 174 SD---IDEGVPAW 183
                                   55...55666666 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 1.7e-05
                                   EETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEETTEEEEES CS
                       DPPIV_N  20 sytaeyyiydletneveelspgeeklqlakwSPagdklafvrnnnLyvre 69 
                                   s+  e ++ d+   + +++++++ +  ++ wSP+g+ +++  + n++  +
  gi|91772443|ref|YP_565135.1| 153 SGNYEIWVMDIDGSNQTQITDSDIDEGVPAWSPDGKHIIYSLEGNIWKVN 202
                                   67889999****9999999999999**********************665 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 5.3e-05
                                   EEEESSTTEEEEEETTE....EEEESTTTSEEEECES-STTTEEESB--HHHHHHTSSSSBEEEE-TTSSEEEEEEEECTT CS
                       DPPIV_N  48 akwSPagdklafvrnnn....LyvrelatgkeiqlTsdgsagifnGvadWvyeEEvlgsnsavwWspdgsrlaylrfdese 124
                                   + ++P+g+k+a+v + n    +++ +   + ++qlT+               ++E        +Wspdg+ +ay +    e
  gi|91772443|ref|YP_565135.1| 221 PVFNPEGTKVAYVLETNgvkdIWIMNADGKGTKQLTFSD-------------QDE-----IDPAWSPDGKSIAYSSNKAGE 283
                                   667888888888877533333888888777888888776.............566.....455677777777777777777 PP

                                   S-EEEEEESSSSC CS
                       DPPIV_N 125 Vpeitlpsytdee 137
                                    +++++   + e+
  gi|91772443|ref|YP_565135.1| 284 FNIWKMELSMTEA 296
                                   7766666655554 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.2   4.5e-13   1.2e-09      75     258 ..      60     261 ..      52     266 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.5e-13
                                   S-.SEEEEEEETTS---EEEE-S-EEE....EEEETTEEEEEEE....SSSS-EEEEEEETTS---EEEESS...----SE CS
                       DUF5050  75 sl.ltglyriktdGtertklsddksle....vslvgnwiYYqhy....dekdglklykikidgkektklsde...aiepls 143
                                      ++ +  ++ dGt++++++d+ +++     +  g+ +Y+ +      + + ++++ ++idg ++t+++++   ++  +s
  gi|91772443|ref|YP_565135.1|  60 YSsEQTIWTMNSDGTNKNEIYDSIVWDgepvFNTDGDRLYFASEhvnpYSAKFISIHVVDIDGLNRTQITKNadmRAPAVS 140
                                   444889999***************9975554677899****86333446789999**************665221444556 PP

                                   EETTEEEEE-T..TT--EEEEETTTTEEEEEE-S-EEE....EEEEETTEEEEEGGGTT-EEEE-SSS---EE-S-S-EEE CS
                       DUF5050 144 vkdgwiYytge.sedhslykldtdgksiskvseenlyl....lvvegdyiYyidlsknyaLyrvklsgsekevltedkvdn 219
                                    ++ ++ y+++ s + +++ +d+dg+++++++++++       + +g++i y   s + ++++v++  +  ++l+e+  + 
  gi|91772443|ref|YP_565135.1| 141 PDGTQLAYLSKlSGNYEIWVMDIDGSNQTQITDSDIDEgvpaWSPDGKHIIY---SLEGNIWKVNIGPKVPSILKENYYTS 218
                                   66777766666155569****************9999876334457788888...78899**************9999877 PP

                                   EE....EETTEEEEEE-SSS-E.EEEEETTS---EEEEES-EE CS
                       DUF5050 220 yN....vtgnwiYyqkesdeekalyrikldGsekeklaegnvs 258
                                   yN     +g+++ y  e++  k++  ++ dG++++ l+  + +
  gi|91772443|ref|YP_565135.1| 219 YNpvfnPEGTKVAYVLETNGVKDIWIMNADGKGTKQLTFSDQD 261
                                   66321157999988888888999**********9998766655 PP

>> Gmad1  Lipoprotein LpqB beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.17   4.4e+02       9      56 ..      30      73 ..      20      85 .. 0.67
   2 !   16.3   0.0   2.4e-06    0.0063      22      81 ..     131     201 ..     124     214 .. 0.78
   3 !    6.0   0.0    0.0035       8.9      13      77 ..     206     272 ..     196     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.17
                         Gmad1  9 grvepvpGplgegavdlrsaAvSrdgqqvaavtapdggrtLvvgsygg 56
                                  g+v+ ++ ++    +++ ++A S+d+++++  +    ++t+++++ +g
  gi|91772443|ref|YP_565135.1| 30 GAVTVTDHYQLTEGINQVAPAWSPDSDRIVYSS----EQTIWTMNSDG 73
                                  555555556666667888888888888887766....66666665444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.4e-06
                         Gmad1  22 avdlrsaAvSrdgqqvaavtapdggrtLvvgsyggeasevleggsltr..pSwd.........rdgalWvv 81 
                                   ++d+r++AvS+dg+q+a +++ +g+ +++v++ +g  ++ ++++++ +  p w+         ++g++W v
  gi|91772443|ref|YP_565135.1| 131 NADMRAPAVSPDGTQLAYLSKLSGNYEIWVMDIDGSNQTQITDSDIDEgvPAWSpdgkhiiysLEGNIWKV 201
                                   5689*******************************999999888776544999955555555444555555 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0035
                         Gmad1  13 pvpGplgegavdlrsaAvSrdgqqvaavtapdggrtLvvgsyggeasevl..eggsltrpSwdrdga 77 
                                   +vp +l e   +  ++   ++g++va v +++g + +++++ +g+ ++ l  ++++  +p w++dg+
  gi|91772443|ref|YP_565135.1| 206 KVPSILKENYYTSYNPVFNPEGTKVAYVLETNGVKDIWIMNADGKGTKQLtfSDQDEIDPAWSPDGK 272
                                   577777777777777888899******************9887777776668999999*****9974 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   8.8e-05      0.23     179     271 ..      75     165 ..      60     174 .. 0.83
   2 !    8.1   0.0   0.00036      0.93     183     261 ..     210     283 ..     197     299 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.8e-05
               Pectate_lyase22 179 eaevilkenqwlghpiyrpfdds.tvafchegphdlvdarmwlinedgsnlrkvkehaegescthevwvpdgsalayvsyl 258
                                   + + i++   w g p++    d    a  h  p+      + +++ dg n  ++ + a+  + +     pdg+ lay+s l
  gi|91772443|ref|YP_565135.1|  75 NKNEIYDSIVWDGEPVFNTDGDRlYFASEHVNPYSAKFISIHVVDIDGLNRTQITKNADMRAPA---VSPDGTQLAYLSKL 152
                                   5567888899******98765541567778999999999****************999987765...57************ PP

               Pectate_lyase22 259 kgsterviysadp 271
                                    g+ e  ++++d 
  gi|91772443|ref|YP_565135.1| 153 SGNYEIWVMDIDG 165
                                   **99998888775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00036
               Pectate_lyase22 183 ilkenqwlgh.piyrpfddstvafchegphdlvdarmwlinedgsnlrkvkehaegescthevwvpdgsalayvsylkgs 261
                                   ilken +  + p++ p   + va++ e    +    +w++n dg   +++    + e      w pdg ++ay s   g+
  gi|91772443|ref|YP_565135.1| 210 ILKENYYTSYnPVFNPE-GTKVAYVLETNG-V--KDIWIMNADGKGTKQLTFSDQDE--IDPAWSPDGKSIAYSSNKAGE 283
                                   55555555432555553.344555555322.2..23566666666665554444333..345566666666666655444 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.059   1.5e+02     160     203 ..      37      77 ..      31     103 .. 0.77
   2 !   16.8   0.0   9.1e-07    0.0023     125     187 ..     133     193 ..     123     201 .. 0.87
   3 !    3.8   0.2    0.0079        20     131     190 ..     223     280 ..     212     290 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.059
                                   TEEEEEEEEEEESEEEEECTTSSEEEEEESS-SSS-TSTSB-S- CS
                Peptidase_S9_N 160 gedlpdeledvkfsgivWaadekgffYtrydkedersdtdtnln 203
                                     +l++ +++v ++   W +d++ + Y+++++    ++++tn+n
  gi|91772443|ref|YP_565135.1|  37 HYQLTEGINQVAPA---WSPDSDRIVYSSEQTIWTMNSDGTNKN 77 
                                   55677777777777...**********99886555555444444 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.1e-07
                                   EEEEEEE-TTSSEEEEEEEETTSSEEEEEEEETTTTEEEEEEEEEEESEEEEECTTSSEEEEE CS
                Peptidase_S9_N 125 algefavsedgkllAyslsksGsdwytirvkdietgedlpdeledvkfsgivWaadekgffYt 187
                                   ++++ avs+dg+ lAy  + sG+  y+i v+di+  ++++ + +d+     +W +d+k ++Y+
  gi|91772443|ref|YP_565135.1| 133 DMRAPAVSPDGTQLAYLSKLSGN--YEIWVMDIDGSNQTQITDSDIDEGVPAWSPDGKHIIYS 193
                                   577789****************8..************77666666666669***********7 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0079
                                   E-TTSSEEEEEEEETTSSEEEEEEEETTTTEEEEEEEEEEESEEEEECTTSSEEEEEESS CS
                Peptidase_S9_N 131 vsedgkllAyslsksGsdwytirvkdietgedlpdeledvkfsgivWaadekgffYtryd 190
                                   ++++g+ +Ay l+++G  ++ i +++++ + + + +++d      +W +d+k + Y++ +
  gi|91772443|ref|YP_565135.1| 223 FNPEGTKVAYVLETNG--VKDIWIMNADGKGTKQLTFSDQDEIDPAWSPDGKSIAYSSNK 280
                                   6788888888888887..566777777777766777777777778888888888887644 PP

>> Inhibitor_I42  Chagasin family peptidase inhibitor I42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.16   4.1e+02      29      63 ..      41      74 ..      20      93 .. 0.81
   2 !   12.2   0.1     7e-05      0.18      19      73 ..     196     260 ..     192     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.16
                                  TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSS CS
                 Inhibitor_I42 29 seglkllseeyipdesdelvGaggthvwtfkalkp 63
                                  +eg++++   ++pd++  +v ++ +++wt+++ ++
  gi|91772443|ref|YP_565135.1| 41 TEGINQVAPAWSPDSDR-IVYSSEQTIWTMNSDGT 74
                                  47888999999999998.999999****9988754 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7e-05
                                   T-EEEEEE--TTTEEE-TTTCECCECCE...........STTSSEEEEEEEEESSSEEEEEEEEEE CS
                 Inhibitor_I42  19 GYsWtvdasdseglkllseeyipdesde...........lvGaggthvwtfkalkpGettiefkya 73 
                                   G  W+v+ + +++  +l+e+y +++++            l + g++++w ++a ++G+ +++f+ +
  gi|91772443|ref|YP_565135.1| 196 GNIWKVNIG-PKVPSILKENYYTSYNPVfnpegtkvayvLETNGVKDIWIMNADGKGTKQLTFSDQ 260
                                   778999998.7999999999999999889999******8888888*****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2259.48
//
Query:       gi|91772444|ref|YP_565136.1|  [L=512]
Description: sulphate transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-54  185.4  41.9    1.3e-54  185.4  41.9    2.6  2  Sulfate_transp  Sulfate permease family
    1.4e-07   31.1   0.0    2.7e-07   30.2   0.0    1.4  1  STAS            STAS domain
    0.00036   20.9   8.6    0.00036   20.9   8.6    4.3  4  MFS_MOT1        Molybdate transporter of MFS superfamily
     0.0055   17.0   0.0       0.01   16.1   0.0    1.4  1  STAS_2          STAS domain
  ------ inclusion threshold ------
      0.018   15.1   0.2      0.072   13.2   0.2    2.1  1  RAMP4           Ribosome associated membrane protein RAMP4


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4  41.9   3.7e-58   1.3e-54       1     379 [.      14     367 ..      14     368 .. 0.90
   2 !    3.5   1.4     0.007        25     322     354 ..     360     392 ..     359     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 3.7e-58
                Sulfate_transp   1 lkgDliaGitvallaiPqalayallaglppiygLyssvvpqlvyalfGtsrqlavGpvavlslivgeiiakvaeeepekgi 81 
                                   +k+++++G+tv l ++P a a++++a++ p++gLys+++ +l+ a++G+ + +++G++++++++v +++ +        g+
  gi|91772444|ref|YP_565136.1|  14 FKNEVLSGLTVSLALVPEAVAFSIIANVSPLVGLYSAFIIGLITAILGGRPGMISGATGAIAVVVVALVIQH-------GV 87 
                                   7899*********************************************************99999998866.......9* PP

                Sulfate_transp  82 eiattltllaGviqvllGllRLgflveflseavlsGfiaGaaivillsqikvllglervskkeslvsvlsslftnlekvnl 162
                                   e ++++++l G+iq+++G l+Lg+ ++++++av+ Gf+ G aivi+++q++++  ++        ++ + + +     + l
  gi|91772444|ref|YP_565136.1|  88 EYLFAAVVLMGIIQMIIGALKLGKFIRLVPHAVMFGFVNGLAIVIFMAQLAQFKVTD--------INGIEHWLGGQ--ALL 158
                                   **************************************************9986665........22222222222..123 PP

                Sulfate_transp 163 akvvlgllllvvLlvtkellkklkkllvipapaelvavivatlvsaifelkreagvkivgeipsglpelslp..kvdwsll 241
                                   + + + +l+++++++  +        +   +pa l+a+iv  +++++f+ ++++ v  + +i  g+p+++lp   ++ +++
  gi|91772444|ref|YP_565136.1| 159 VMLGFVGLTMAIIYLLPR--------FTKAVPASLAAIIVVSTIVIYFQIQTRT-VGDIASIAGGFPKFHLPkvPLNLETI 230
                                   444445555666666666........88999*****************655554.4445699**********44455666* PP

                Sulfate_transp 242 sallpdalaialvglleaiavsksldkkkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGaktqlsglvs 322
                                   + ++p +l++alvgl+e++++  ++d++++++  +nkE vA+G++N+++++fgg+   + + +s++ni++Ga++++sg+v 
  gi|91772444|ref|YP_565136.1| 231 KIIFPYSLIMALVGLIESLLTLTVIDEMTETRSRGNKESVAQGVANLVCGFFGGMGGCAMIGQSLININSGARNRISGIVA 311
                                   ********************************************************************************* PP

                Sulfate_transp 323 alvvllvllvltplleyiPkavLaaiiivagkglLvelkelkklwklskldflilla 379
                                   al +l+++lv+++l+e iP+a+L ++++v+++g   e+++lk ++k+   d+l++++
  gi|91772444|ref|YP_565136.1| 312 ALGLLFFVLVGSSLIEKIPMAALVGVMFVVAIG-TFEWASLKIFRKVPITDVLVMVV 367
                                   *********************************.99******************997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.007
                Sulfate_transp 322 salvvllvllvltplleyiPkavLaaiiivagk 354
                                   + ++v++v+  +t + +++  av+a++ii+a+ 
  gi|91772444|ref|YP_565136.1| 360 TDVLVMVVVASITVIYHNLAAAVIAGVIISALA 392
                                   5689*************************9986 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   7.6e-11   2.7e-07       3     100 ..     405     491 ..     403     504 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.6e-11
                                   EEEECTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EE CS
                          STAS   3 daeeiegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvev 83 
                                   ++ + +gi+ +++ gp++f+++ +f++k +   + +            +i+dl++  + D s+++aL++i +++ + g +v
  gi|91772444|ref|YP_565136.1| 405 EIVDDNGIKHYEFFGPLFFGSVTEFQSKFDVLNDPD-----------EIIIDLKESRVADHSAIEALNKITERYAKVGKTV 474
                                   5677899**********************9888877...........6********************************* PP

                                   EEES--HHHHHHHHHTT CS
                          STAS  84 vlvnikpevreklektg 100
                                    l  ++++ r  l+++ 
  gi|91772444|ref|YP_565136.1| 475 HLRHLSEDCRVLLDNAS 491
                                   *********99998875 PP

>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9  15.1   0.00027      0.96      12     109 ..      26     130 ..      19     132 .. 0.86
   2 ?    3.6   3.0     0.023        82      73     105 ..     159     191 ..     153     195 .. 0.90
   3 !   20.9   8.6     1e-07   0.00036      29     109 ..     265     343 ..     234     345 .. 0.85
   4 ?    1.3   0.6      0.12   4.4e+02      35      64 ..     365     393 ..     344     404 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                      MFS_MOT1  12 lTllnlvialaalaslsltalllsvGlmnlltglfggvPmc......hgAgglaaqyrf..gartgaagillGlvllllgl 84 
                                   l l++ ++a +++a++s+   l s+ ++ l+t+++gg P        ++A +++a + +   + + aa++l+G++ +++g+
  gi|91772444|ref|YP_565136.1|  26 LALVPEAVAFSIIANVSPLVGLYSAFIIGLITAILGGRPGMisgatgAIAVVVVALVIQhgVEYLFAAVVLMGIIQMIIGA 106
                                   6789999********99999999999*************87777777666666555444679999**************** PP

                      MFS_MOT1  85 tgllerllrliPksvlgglllgaGl 109
                                   +  l ++ rl+P++v+ g + g+++
  gi|91772444|ref|YP_565136.1| 107 LK-LGKFIRLVPHAVMFGFVNGLAI 130
                                   *7.99************99988875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.023
                      MFS_MOT1  73 illGlvllllgltgllerllrliPksvlgglll 105
                                   ++lG v l+++++ ll r+++++P s+  ++++
  gi|91772444|ref|YP_565136.1| 159 VMLGFVGLTMAIIYLLPRFTKAVPASLAAIIVV 191
                                   799***********************9999987 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 1e-07
                      MFS_MOT1  29 ltalllsvGlmnlltglfggvPmchgAgglaaqyrfgartgaagillGlvllllgltgllerllrliPksvlgglllgaGl 109
                                    ++ ++  G++nl++g+fgg+  c++ g  + + ++gar   +gi+ +l ll++ l+g  + l + iP++ l g+++++++
  gi|91772444|ref|YP_565136.1| 265 GNKESVAQGVANLVCGFFGGMGGCAMIGQSLININSGARNRISGIVAALGLLFFVLVG--SSLIEKIPMAALVGVMFVVAI 343
                                   45668899****************999999999999******************9999..899********9999999886 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.12
                      MFS_MOT1  35 svGlmnlltglfggvPmchgAgglaaqyrf 64 
                                   +v ++  +t+++ ++  + +Ag++++  +f
  gi|91772444|ref|YP_565136.1| 365 MV-VVASITVIYHNLAAAVIAGVIISALAF 393
                                   33.333445555555555555555555444 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.9e-06      0.01      12      75 ..     426     488 ..     419     491 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.9e-06
                        STAS_2  12 aaelreqllealaagaevvvDlsgvervDsaalalLlalartarargrrlvlrglppalrrlld 75 
                                   ++e++++++ +l +++e+ +Dl + + +D++a+ +L    ++ ++ g+++ lr+l+++ r lld
  gi|91772444|ref|YP_565136.1| 426 VTEFQSKFD-VLNDPDEIIIDLKESRVADHSAIEALNKITERYAKVGKTVHLRHLSEDCRVLLD 488
                                   556666666.456667******************************************999987 PP

>> RAMP4  Ribosome associated membrane protein RAMP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     2e-05     0.072      40      59 ..     312     331 ..     303     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                         RAMP4  40 lLglfiFVViGSaifqiirt 59 
                                   +Lgl+ FV +GS++++ i +
  gi|91772444|ref|YP_565136.1| 312 ALGLLFFVLVGSSLIEKIPM 331
                                   8**************98866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1198  (0.0668191); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.83u 0.35s 00:00:01.18 Elapsed: 00:00:00.56
# Mc/sec: 2759.55
//
Query:       gi|91772445|ref|YP_565137.1|  [L=65]
Description: hypothetical protein Mbur_0395 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-30  102.7   6.0    8.4e-30  102.6   6.0    1.0  1  DUF2196   Uncharacterized conserved protein (DUF2196)


Domain annotation for each model (and alignments):
>> DUF2196  Uncharacterized conserved protein (DUF2196)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   6.0   4.7e-34   8.4e-30       2      61 .]       4      63 ..       3      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 4.7e-34
                       DUF2196  2 gktrkdikpGleVeivlkkdqrtGklteGiVkdilTnssthphGIKVrLedGeVGRVqei 61
                                  g+tr++ik+G++V ivlk+dqr+Gk t+G+Vk+ilT+ssthphGIKV+LedG+VGRV+ei
  gi|91772445|ref|YP_565137.1|  4 GNTRANIKVGANVGIVLKNDQRSGKITQGVVKRILTKSSTHPHGIKVQLEDGQVGRVKEI 63
                                  789*******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 411.95
//
Query:       gi|91772446|ref|YP_565138.1|  [L=254]
Description: GTP-binding protein YlqF [Methanococcoides burtonii DSM 6242]
Scores for complete 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   57.3   1.1      2e-12   47.2   0.1    2.7  3  MMR_HSR1      50S ribosome-binding GTPase
    9.8e-10   38.6   0.1    1.5e-09   38.0   0.1    1.2  1  RsgA_GTPase   RsgA GTPase
    6.1e-09   35.6   1.8     0.0016   18.0   0.1    2.3  2  FeoB_N        Ferrous iron transport protein B
    7.3e-06   25.7   0.8      0.004   16.7   0.1    2.4  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    0.00011   22.3   2.9        0.8    9.7   0.0    3.3  2  Dynamin_N     Dynamin family
     0.0018   17.6   0.1     0.0028   17.0   0.1    1.4  1  AIG1          AIG1 family
     0.0024   17.9   0.1     0.0039   17.2   0.1    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
       0.19   11.3   2.3       0.18   11.4   0.2    1.9  2  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0017       3.8      73     114 .]      12      52 ..       3      52 .. 0.71
   2 ?   -0.6   0.0       0.6   1.4e+03      23      55 ..      68     100 ..      58     106 .. 0.78
   3 !   47.2   0.1   8.9e-16     2e-12       3     100 ..     106     207 ..     104     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                                   HHCTSEEEEEEETT..TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  73 leeadlillvvdas..eeklkpldeeleelleeakkplilvlnk 114
                                   +++ad++l vvda+  +e     + e+e+  ++++kpli+vl+k
  gi|91772446|ref|YP_565138.1|  12 IKQADILLEVVDARfpDE-T--RNLEVERDVKRSGKPLIIVLSK 52 
                                   3459********887533.2..3356666666789******987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.6
                                   TEEESSSTTSSSSEEEEEEEETTEEEEEEECGG CS
                      MMR_HSR1  23 kaivsdkpgtTrdinegrvklkgkeielvDtpG 55 
                                    ++v+ + ++  + ++g+  l++k +e++D+ G
  gi|91772446|ref|YP_565138.1|  68 LSKVAPTVFVSSKERYGTTMLRHKILEIADIQG 100
                                   578888899999999998888888889999887 PP

  == domain 3  score: 47.2 bits;  conditional E-value: 8.9e-16
                                   EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS.....HHHHHH...HHHHHHHHHH CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGlie.....gaseek...glgkaflale 74 
                                   + +G+pN+GKS++in   g+ ka +s++ g T+ ++  +     ++i+++DtpG+i      + +  +   g+++a + ++
  gi|91772446|ref|YP_565138.1| 106 GSLGYPNTGKSSVINGVAGKnKAGTSSISGHTKGVQIVKAG---SRIVFIDTPGVIPfgdndEYR--QgllGVKDATHLND 181
                                   668****************989***************9885...89********98554322233..24467777777644 PP

                                   C....TSEEEEEEETTTTCSHHHHHHHHHH CS
                      MMR_HSR1  75 e....adlillvvdaseeklkpldeeleel 100
                                        +++i++++d + +    + ee+ ++
  gi|91772446|ref|YP_565138.1| 182 PigvaMKIIAHICDNN-K---SVLEEFYNI 207
                                   3555369999999944.2...233333333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.1   6.6e-13   1.5e-09      44     161 ..      41     157 ..      22     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 6.6e-13
                                   HTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.....SEEEEECSTT...SSHHHHH CS
                   RsgA_GTPase  44 ekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd.....ktsvlvGqSG...vGKStLi 116
                                   ++g +++ivl+K+Dl+++e+ l++ k++l+++  ++++vs+k++ g++ l++++ +        +l+G+ G    GKS++i
  gi|91772446|ref|YP_565138.1|  41 RSGKPLIIVLSKCDLVSKET-LQKAKSRLSKV-APTVFVSSKERYGTTMLRHKILEiadiqGRNILIGSLGypnTGKSSVI 119
                                   5667899*************.***********.66777777778888888776543221335689***9995556****** PP

                                   HHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                   RsgA_GTPase 117 nallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                   n +++++++ t+++s +       T+ v++++  +  + iDtPG+
  gi|91772446|ref|YP_565138.1| 120 NGVAGKNKAGTSSISGH-------TKGVQIVKAGSRIVFIDTPGV 157
                                   ***************96.......78899****99999******8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     7e-07    0.0016      77     155 ..      13      91 ..       4      92 .. 0.86
   2 !   17.1   0.2   1.4e-06    0.0031       5      57 ..     107     157 ..     103     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7e-07
                                   TSSSEEEEEEEGGGH..HHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                        FeoB_N  77 eepdvvvnvvdatnl..ernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                   +++d++++vvda      rnL +  ++   g+p++++l ++d ++k+ ++  +++Ls+    p v +s+k++ g+  l+++
  gi|91772446|ref|YP_565138.1|  13 KQADILLEVVDARFPdeTRNLEVERDVKRSGKPLIIVLSKCDLVSKETLQKAKSRLSKV--APTVFVSSKERYGTTMLRHK 91 
                                   589*********865227**************************************997..68888899998888888776 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.4e-06
                                   EEESTTSSHHHHHHHHHTTSEE.EEESTTSSSEEEEEEEEETTEEEEEEE---- CS
                        FeoB_N   5 lvGnpnvGkttlfnaltgakqk.vgNwpGvtvekkegklklkgkeveivDlPGi 57 
                                    +G pn+Gk++++n ++g+++   +  +G t   k +++  +g+++ ++D PG+
  gi|91772446|ref|YP_565138.1| 107 SLGYPNTGKSSVINGVAGKNKAgTSSISGHT---KGVQIVKAGSRIVFIDTPGV 157
                                   689***************9864256666666...5555555789*********8 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 !   16.7   0.1   1.8e-06     0.004      87     150 ..       8      72 ..       2     130 .. 0.78
   2 !    7.5   0.1    0.0012       2.7      54      86 ..     133     163 ..     115     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-06
                                   HHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHH CS
                      GTP_EFTU  87 virglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqkl 150
                                   v   ++++D+ + vvda+   e++  ev r +++ g p+i+++ K+D + k++l++ ++ +++  
  gi|91772446|ref|YP_565138.1|   8 VKDVIKQADILLEVVDARFPDETRNLEVERDVKRSGKPLIIVLSKCDLVsKETLQKAKSRLSKVA 72 
                                   566689*******************************************7777777777776443 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                                   SCSSCEEEEEETTCSSEEEEEEEESSSGGGHHH CS
                      GTP_EFTU  54 iTiksaaisleketkkylinliDtPGHvdFske 86 
                                   i+ +++ +++   ++  +i +iDtPG + F ++
  gi|91772446|ref|YP_565138.1| 133 ISGHTKGVQIV--KAGSRIVFIDTPGVIPFGDN 163
                                   66667778888..999***********999876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00036       0.8     121     167 ..       7      52 ..       3      53 .. 0.92
   2 !    8.4   1.3   0.00094       2.1       5      40 ..     109     145 ..     105     218 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                                   HHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                     Dynamin_N 121 lvkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                                   +vk  ik+adi+l v++a      +++l+++r v+  gk  i+vl k
  gi|91772446|ref|YP_565138.1|   7 MVKDVIKQADILLEVVDARFPDE-TRNLEVERDVKRSGKPLIIVLSK 52 
                                   899****************9655.899*****************998 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00094
                                   EBTTTTHHHHHHHHHTS--S---SS.S---S-EEEEE CS
                     Dynamin_N   5 GsqSsGKSSvlnaLlgedilprgpn.ptTrrplelql 40 
                                   G  + GKSSv+n + g++   ++++   T  + +++ 
  gi|91772446|ref|YP_565138.1| 109 GYPNTGKSSVINGVAGKNKAGTSSIsGHTKGVQIVKA 145
                                   66689***********998877766344555544444 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.3e-06    0.0028       6      67 ..     108     165 ..     101     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                                   ESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHH CS
                          AIG1   6 vGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsad 67 
                                   +G   +GkS+ +N + gk+   ++    s+  + + ++ +++g +i+ iDTPg++   ++++
  gi|91772446|ref|YP_565138.1| 108 LGYPNTGKSSVINGVAGKNKAGTS----SISGHTKGVQIVKAGSRIVFIDTPGVIPFGDNDE 165
                                   566679***********9976665....6888888888899************987776655 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 !   17.2   0.1   1.7e-06    0.0039      56     102 ..      44      94 ..       5      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                  MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare....pnsvviSaekelnldeLkekiwe 102
                                   +p ++vl K+Dl+s+e+l++ +++      +v++S++++++   L +ki e
  gi|91772446|ref|YP_565138.1|  44 KPLIIVLSKCDLVSKETLQKAKSRlskvAPTVFVSSKERYGTTMLRHKILE 94 
                                   799*****************9996666568999*********999999965 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2     8e-05      0.18     112     172 ..      15      74 ..       6      78 .. 0.75
   2 ?   -1.3   0.1      0.62   1.4e+03       7      26 ..     109     129 ..     102     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8e-05
                                   ECEEEEEEETTTH.CCHCCHHHHHHHHHHTSS...EEEEE-HHHHCHC..HHHHHHHHHHHHTT CS
                          cobW 112 ldavvavvDaknleaeeekieekaedqlaaad...llvlnKtDlldeeallekleerlrqlnpe 172
                                   +d+++ vvDa ++   +e+ + ++e+ ++ +    ++vl+K+Dl+++e+l +k ++rl+++ p+
  gi|91772446|ref|YP_565138.1|  15 ADILLEVVDA-RFP--DETRNLEVERDVKRSGkplIIVLSKCDLVSKETL-QKAKSRLSKVAPT 74 
                                   6888999999.663..4555556666666664343899**********76.9999999998875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.62
                                   ESTTCCHHHHHHHHH.CT--S CS
                          cobW   7 GflGsGKTtLlnhll.enrag 26 
                                   G++ +GK++++n +  +n+ag
  gi|91772446|ref|YP_565138.1| 109 GYPNTGKSSVINGVAgKNKAG 129
                                   56669******9998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1706.91
//
Query:       gi|91772447|ref|YP_565139.1|  [L=353]
Description: hypothetical protein Mbur_0397 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.9   0.0    3.2e-05   23.9   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.8e-09   3.2e-05      13     229 ..      34     295 ..      30     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.8e-09
               Glyco_tranf_2_3  13 eedvlgevlesllaqeyprvevvvvvdesdaetle....vaeelaaalpdvrvrvvvnarnlgstgksralnealra.... 85 
                                    e +lg+ +esl+  e  ++e+vv v ++  e +e     ++ + + +++++vrv    +  g+ +  ++l e+l+     
  gi|91772447|ref|YP_565139.1|  34 SEGTLGRAIESLVILEDTDFELVVLVAPNNMEIAEqveqKVRDVIRSSSNADVRV----HMFGP-SHLEKLHEVLKKdgmg 109
                                   567899******9999999*******87775554411113444445566777775....44576.7777777777777777 PP

               Glyco_tranf_2_3  86 ....................vk....sdlvllvDdDtvv.ePdtlkrllqff.ltpkvgavgtpv..fll.nrstlvsalg 137
                                                       v     sd+ ll+DdD v  +P ++ ++  f+ ++++ +++ +    +l+ n++++v +  
  gi|91772447|ref|YP_565139.1| 110 eycdllsltgysnirnmclfVPhimgSDVALLIDDDEVFeDPQFISKAKEFIgKYHEGRFINAVAgyYLQpNGDYHVEVPE 190
                                   77777888888776666555115557*************9*************9998888886653234446888866665 PP

               Glyco_tranf_2_3 138 alefaerhlrflaar..........ralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaa 208
                                   +  ++ ++ +++             r + ++++ G  ++i r+++     +dp  + ++D+++   +r+ g+     +++a
  gi|91772447|ref|YP_565139.1| 191 NPWTKYWDKNICMNEafdeiidtspRLKETPFVFGGNMVIHRDLFMKV-PFDPMVSRGEDIDYLINARMFGHSFLLDNELA 270
                                   555555555433333333666666555568888898889999988888.799999999*********************** PP

               Glyco_tranf_2_3 209 vrevfp....sslkayikqrnRwvy 229
                                   + ++ p    +++k+++    R+vy
  gi|91772447|ref|YP_565139.1| 271 IKHLPPakshPTWKRVREDIYRFVY 295
                                   ****773332557777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2426.52
//
Query:       gi|91772448|ref|YP_565140.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-22   76.9   0.0    1.8e-21   75.9   0.0    1.5  1  DUF772       Transposase domain (DUF772)
    1.8e-16   60.4   2.1    5.5e-16   58.9   2.1    1.8  1  DDE_Tnp_1    Transposase DDE domain
     0.0038   17.4   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.037   13.7   0.0      0.067   12.9   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   5.1e-25   1.8e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.1e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+++    +++++e
  gi|91772448|ref|YP_565140.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERIAQsgkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   2.1   1.5e-19   5.5e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.5e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772448|ref|YP_565140.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772448|ref|YP_565140.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772448|ref|YP_565140.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772448|ref|YP_565140.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772448|ref|YP_565140.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772448|ref|YP_565140.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.067      72     132 ..     213     276 ..     160     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772448|ref|YP_565140.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2243.15
//
Query:       gi|91772449|ref|YP_565141.1|  [L=820]
Description: MCP methyltransferase, CheR-type, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-56  190.8   0.1    3.2e-56  189.7   0.1    1.6  1  CheB_methylest  CheB methylesterase
    6.5e-52  175.8   0.0    1.7e-51  174.5   0.0    1.8  1  CheR            CheR methyltransferase, SAM binding domain
    3.6e-19   69.3   2.9    2.3e-18   66.7   0.7    2.8  3  PAS_10          PAS domain
    9.6e-11   41.2   0.7    1.9e-10   40.3   0.7    1.5  1  CheR_N          CheR methyltransferase, all-alpha domain
     0.0089   16.0   0.2        1.6    8.7   0.0    2.5  2  InvH            InvH outer membrane lipoprotein
  ------ inclusion threshold ------
      0.011   16.3   9.5      0.021   15.3   9.5    1.4  1  APG6_N          Apg6 coiled-coil region
      0.013   15.5  11.2      0.013   15.5  11.2    1.8  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
      0.031   14.3   2.3      0.093   12.8   2.3    1.9  1  Prefoldin_3     Prefoldin subunit
       0.06   13.0   0.6       0.36   10.5   0.1    2.4  2  DUF4264         Protein of unknown function (DUF4264)
       0.26   10.7   8.6       0.51    9.7   8.6    1.4  1  DUF3552         Domain of unknown function (DUF3552)
       0.58   10.6  11.7        2.8    8.4  11.7    2.2  1  ZapB            Cell division protein ZapB
        0.8    9.9   3.4        1.2    9.3   0.1    2.6  2  EF-hand_2       EF hand
        5.7    7.1   7.1        9.8    6.4   5.6    2.3  1  bZIP_1          bZIP transcription factor


Domain annotation for each model (and alignments):
>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.7   0.1   2.3e-59   3.2e-56       1     170 []       6     180 ..       6     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: 189.7 bits;  conditional E-value: 2.3e-59
                                   EEEEE-TTHHHHHTTTGGGS-TT-SS-EEEEE---TT-HHHHHHHHHHH-SSEEEE--TT-B--TTEEEE--TTSEEEEE. CS
                CheB_methylest   1 vvigaStGGlealkellaalpedfpaavvvvqhmppsftsslaelLnresslkVkeaedgeelepgrvyvapgdkhllie. 80 
                                   v+igaS+GGlea+ e+++++p + ++a++vvqh++p+++s ++e+L+++++++V  ae+g+ +ep++vy++p++k+l+i  
  gi|91772449|ref|YP_565141.1|   6 VGIGASAGGLEAIAEFFENMPHNSGMAFIVVQHLSPDYKSLMVEILSKHTQMEVLRAEEGMLVEPNKVYLIPPKKNLSIFn 86 
                                   79*****************************************************************************86 PP

                                   ........E.E.-.-SS-HHHHHHHHHHHH.GGEEEEE-SBSS-TTHHHHHHHHHTT-EEEEE-GGG-SSBSHHHHHHHTT CS
                CheB_methylest  81 ..lals..a.k.kgerpsiDvlfesaaeaygeraigviLtGmgsDGaeGlkaikeaggltiaqdpesavvpgmPkaaieag 155
                                     l     + + + ++ ++D+lf+s+a++ +e+ai++iL+G+gsDG+ G+ +ike+gg++i+q+pesa+ +gmP++ai ++
  gi|91772449|ref|YP_565141.1|  87 qrL--LieQsSsTLPNYPVDILFRSLAQDQAEKAIAIILSGTGSDGSLGIHHIKENGGIVIVQNPESAKLSGMPENAISTE 165
                                   542..2322222445999*************************************************************** PP

                                   --SEEE-GGGHHHHH CS
                CheB_methylest 156 avdevlpleeiaeel 170
                                   +vd++l++++++++l
  gi|91772449|ref|YP_565141.1| 166 LVDFILTPAQMPSQL 180
                                   ***********9876 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.5   0.0   1.2e-54   1.7e-51       2     194 ..     269     459 ..     268     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.5 bits;  conditional E-value: 1.2e-54
                                   S--TTTTCHHHHHHHHCCH.HHHHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS.-EEEEEEESSCHHHHHHH CS
                          CheR   2 eTeffreakhfeelekevlepllakaknekrvriwsagcssGeEpYslAmllketlpkaakl.kvkilAtDidlkvlekAk 81 
                                   +T+ffr++  f+el+++ l+  l + k+ k++r+w +gcs+GeE+Ys+A++lke + k  ++ +vki+AtDi++++++ A+
  gi|91772449|ref|YP_565141.1| 269 VTSFFRDESAFDELQNKWLP-ILFSEKKDKNLRLWVVGCSTGEEAYSVAIVLKELMDKLNNYfNVKIFATDINQEAINSAS 348
                                   69*****************5.66666679*************************999988888****************** PP

                                   HTEEECCHHTTS-HHHHHHHEEEEETTCEEE-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHH CS
                          CheR  82 agvykeeeleglseelleryfekseddsykvkkeikelvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfa 162
                                    g+++++ l ++s e+l +yf   +d +++++ +i+++v F+++++++ +++++++D+i+crn+liY+++  q+kvl+ ++
  gi|91772449|ref|YP_565141.1| 349 VGFFPKSILGNISSERLSKYFV-PKDSGFQISRDIRQMVIFAQHDIIK-DPPFNNIDMITCRNMLIYMQPVLQTKVLDLLN 427
                                   *********************5.5555*********************.******************************** PP

                                   CCEEEEEEEEE-TTB--SSSCCCCCEEEECTT CS
                          CheR 163 eklkpgglLllGhsEslkklkdkfevvkstka 194
                                    +lk++g+L+lG+ E+   l ++fe+++s+++
  gi|91772449|ref|YP_565141.1| 428 YSLKKKGILFLGSCETSGALVEYFETLSSKWK 459
                                   ****************9999999999998876 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.44     6e+02      15      75 ..     524     584 ..     520     601 .. 0.70
   2 ?   -2.4   0.0       5.2   7.2e+03      38      64 ..     621     648 ..     611     679 .. 0.48
   3 !   66.7   0.7   1.6e-21   2.3e-18       2     104 ..     714     816 ..     713     818 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.44
                        PAS_10  15 lDdnlqirrFtpaakklfklipadvGrpladihpkkavknveeviealrtgekdevevvvp 75 
                                   + +++ +r+   +++ +fkl ++++  ++++++pk+ +  +   ++++ ++e+d +   + 
  gi|91772449|ref|YP_565141.1| 524 VGSDMTLRYLVGNSEDYFKLPAGKLEYNITKMVPKELIIPLSTGLKKVFQNEEDLSYNNIH 584
                                   667888899999999********************77766666666666666554433333 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.2
                        PAS_10  38 dvGrpladihpk.kavknveeviealrt 64 
                                   d G++ +d++ + ++  ++++ i++l +
  gi|91772449|ref|YP_565141.1| 621 DKGNNFNDVNLEyDIGRETKQHINDLEQ 648
                                   5555555554333333333333332222 PP

  == domain 3  score: 66.7 bits;  conditional E-value: 1.6e-21
                        PAS_10   2 nnlLnstpieltflDdnlqirrFtpaakklfklipadvGrpladihpk.kavknveeviealrtgekdevevvvpkngkwv 81 
                                   +nlL++++i+++flD+nl++r+Ft   ++lf l ++d+G ++ ++++k   ++ v+++++  +t +++e ev+ +k+g  +
  gi|91772449|ref|YP_565141.1| 714 KNLLSTVQIGTLFLDENLNVRKFTAPMDNLFALDNSDIGKSIYNLKNKtTVEDLVNKFVQVHKTIKSQEIEVK-TKDGIEF 793
                                   89********************************************996666677999999999999999955.78***** PP

                        PAS_10  82 lvrylpyrdedgeiaGvvetfvD 104
                                    +++ py   ++++ Gv++t +D
  gi|91772449|ref|YP_565141.1| 794 ELKIIPYDIGQNNYSGVMITALD 816
                                   ********************998 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.7   1.4e-13   1.9e-10       1      53 []     203     255 ..     203     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.4e-13
                                   HHHHHHHHHHHHTT-EE--SSTHHHHHTHHHHHHHTTT-SSSHHHHHHTSHSS CS
                        CheR_N   1 edferlleliyertGidlsdyKrallkrRlsrRmralglksfeeYldlLrsdp 53 
                                   ++f+ +l+ +++r ++d+s+y+ +++ rR++rRm  ++++++++Y+  L+++p
  gi|91772449|ref|YP_565141.1| 203 NEFDIILSILRNRNNFDFSEYRSNTILRRIERRMIMNQVTNLKDYIMILQNNP 255
                                   59************************************************997 PP

>> InvH  InvH outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0011       1.6     100     138 ..      52      89 ..      28      96 .. 0.81
   2 ?    4.6   0.0     0.021        28      73     114 ..     745     786 ..     729     815 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                          InvH 100 qehpqymrskedeeqlmtefkkvllepgsknlsiyqtll 138
                                    +h q m     ee ++ e +kv l p  knlsi++  l
  gi|91772449|ref|YP_565141.1|  52 SKHTQ-MEVLRAEEGMLVEPNKVYLIPPKKNLSIFNQRL 89 
                                   55665.667778999*******************96543 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                          InvH  73 asknsaisssifcekykqtkeqaltffqehpqymrskedeeq 114
                                   a  ns i  si+  k k t e+ +  f +  + ++s+e e +
  gi|91772449|ref|YP_565141.1| 745 ALDNSDIGKSIYNLKNKTTVEDLVNKFVQVHKTIKSQEIEVK 786
                                   678******************999877666678899887754 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   9.5   1.6e-05     0.021      44     122 ..     627     716 ..     587     723 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                        APG6_N  44 k...........qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlell 113
                                   +           +++ +++le++l  ++++ ++++eeL+   +e ++ ++el a  eel+  +ee ++  +ey+ + +el+
  gi|91772449|ref|YP_565141.1| 627 NdvnleydigreTKQHINDLEQDLLLTKETLHAAIEELETSNEELQSTNEELLASNEELQSTNEELHNVNSEYQLKIIELT 707
                                   355555555555677888888888888888888888888888888888888888888888888888888888888888888 PP

                        APG6_N 114 eleeeldsl 122
                                   el+++ + l
  gi|91772449|ref|YP_565141.1| 708 ELNNDFKNL 716
                                   888887766 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 ?   15.5  11.2   9.6e-06     0.013      40     112 ..     647     719 ..     634     731 .. 0.78
   2 ?   -3.8   0.3       8.4   1.2e+04      92     116 ..     760     784 ..     758     789 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.6e-06
                CENP-F_leu_zip  40 qekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenllee 112
                                    +++ l +Et  a++e+l++  eel+++ +el +  ++l+s +eeL++   + q ++ eL +ln +++nll+ 
  gi|91772449|ref|YP_565141.1| 647 EQDLLLTKETLHAAIEELETSNEELQSTNEELLASNEELQSTNEELHNVNSEYQLKIIELTELNNDFKNLLST 719
                                   34567777888888888888888888888888888888888888888888889999*************9975 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.4
                CENP-F_leu_zip  92 kqervseLeslnsslenlleekEqe 116
                                   ++ +v++L +  ++++++++ +E e
  gi|91772449|ref|YP_565141.1| 760 NKTTVEDLVNKFVQVHKTIKSQEIE 784
                                   4556677777777777777766655 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.3   6.7e-05     0.093       3      54 ..     660     711 ..     658     722 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
                   Prefoldin_3   3 slyklreweaeydglkeeisalkeeddateedllriardfegslvtekEvee 54 
                                    +++l+++++e+++ +ee+ a +ee ++t+e+l +++ +++ ++++  E+++
  gi|91772449|ref|YP_565141.1| 660 AIEELETSNEELQSTNEELLASNEELQSTNEELHNVNSEYQLKIIELTELNN 711
                                   67899*****************************************999875 PP

>> DUF4264  Protein of unknown function (DUF4264)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00026      0.36      18      34 ..     421     437 ..     419     441 .. 0.96
   2 ?   -0.8   0.0      0.87   1.2e+03      40      51 ..     484     495 ..     481     496 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                       DUF4264  18 kvVDfLNktLKdkdlmF 34 
                                   kv D+LN +LK+k+++F
  gi|91772449|ref|YP_565141.1| 421 KVLDLLNYSLKKKGILF 437
                                   9**************99 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.87
                       DUF4264  40 kkkekmvitIYe 51 
                                   +k++++ i+IY+
  gi|91772449|ref|YP_565141.1| 484 DKEKQVSINIYK 495
                                   46799******7 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   8.6   0.00037      0.51      74     149 ..     637     712 ..     628     719 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                       DUF3552  74 kerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLerisgLtke 149
                                   +e +++++ le+ ll  +etL    e+le  +e+l+++++el + +++l++++eel+++ +e + ++ ++ +L+++
  gi|91772449|ref|YP_565141.1| 637 RETKQHINDLEQDLLLTKETLHAAIEELETSNEELQSTNEELLASNEELQSTNEELHNVNSEYQLKIIELTELNND 712
                                   678999********************************************************99999999998765 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  11.7     0.002       2.8      19      58 ..     653     692 ..     646     722 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                          ZapB  19 titlLqmeieeLkeeneelkeenreleeeneqlkeereaw 58 
                                   t ++L   ieeL+  neel++ n+el ++ne+l+ + e++
  gi|91772449|ref|YP_565141.1| 653 TKETLHAAIEELETSNEELQSTNEELLASNEELQSTNEEL 692
                                   5567777777777777777777777777777777555543 PP

>> EF-hand_2  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00086       1.2       5      37 ..     210     242 ..     206     303 .. 0.82
   2 ?   -0.6   1.0      0.98   1.4e+03      24     110 ..     692     783 ..     685     788 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00086
                     EF-hand_2   5 kslkqfnairfaaYRtalKLralqkelcldsvs 37 
                                   + l++ n++ f++YR    Lr++ +++ +++v+
  gi|91772449|ref|YP_565141.1| 210 SILRNRNNFDFSEYRSNTILRRIERRMIMNQVT 242
                                   557899*********************999885 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.98
                     EF-hand_2  24 Lralqkelcldsvsisivaevlkeigls....sdefdrllsvsqledvLldlysalekkk.sslgqvkvevcvdlllnwLl 99 
                                   L+ +  e +l+ ++++ + + +k+        +   d+ l+v + ++ + +l+   +++  +s  ++k +++v+ l+n ++
  gi|91772449|ref|YP_565141.1| 692 LHNVNSEYQLKIIELTELNNDFKNLLSTvqigTLFLDENLNVRKFTAPMDNLFALDNSDIgKSIYNLKNKTTVEDLVNKFV 772
                                   566677778888888888887777655566668888999999999999999997655332122233344444444445455 PP

                     EF-hand_2 100 nvyDrkrkgki 110
                                   +v  + ++++i
  gi|91772449|ref|YP_565141.1| 773 QVHKTIKSQEI 783
                                   55555555555 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.6    0.0071       9.8      26      60 ..     659     693 ..     655     697 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0071
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                   a ieeLe+  ++L++ N++L   +eel+ ++e+L 
  gi|91772449|ref|YP_565141.1| 659 AAIEELETSNEELQSTNEELLASNEELQSTNEELH 693
                                   56889999999999999999999999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (820 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1532  (0.0854482); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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):              13  [number of targets reported over threshold]
# CPU time: 0.80u 0.29s 00:00:01.09 Elapsed: 00:00:00.45
# Mc/sec: 5508.17
//
Query:       gi|91772450|ref|YP_565142.1|  [L=436]
Description: PAS sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-28   98.9   0.4      7e-28   97.4   0.1    2.0  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.8e-18   65.7   0.0      6e-18   64.6   0.0    1.6  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0013   18.6   0.8     0.0057   16.5   0.4    2.3  2  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.028   14.3   0.0    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.025   14.6   0.1      0.076   13.1   0.0    1.9  2  PAS_8        PAS domain
      0.041   12.9   0.0      0.072   12.1   0.0    1.4  1  Herpes_UL31  Herpesvirus UL31-like protein
      0.061   13.6   0.1       0.12   12.6   0.1    1.6  1  PAS_9        PAS domain
       0.16   12.2   0.1       0.38   11.0   0.1    1.6  1  DUF3925      Protein of unknown function (DUF3925)


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       6.3   1.4e+04       7      32 ..     287     311 ..     285     318 .. 0.71
   2 !   97.4   0.1   3.1e-31     7e-28       2     109 ..     322     430 ..     321     432 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.3
                                   HHHHHHHHHHHHHHHSTTTEEEEEEE CS
                     HATPase_c   7 rqiisnlvdNavkfatkageieveik 32 
                                     +i ++v+ ++ f +++++ie+e++
  gi|91772450|ref|YP_565142.1| 287 NLLIHEVVESLAPF-ANKKSIELEMT 311
                                   56788899988888.77777777665 PP

  == domain 2  score: 97.4 bits;  conditional E-value: 3.1e-31
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d ++++qi+ nl+ N++kf++ +g+i +++ ++e+++ is++DnGiGi k + +++fe+f q d   + +++gtGlGlsi+
  gi|91772450|ref|YP_565142.1| 322 DRTKIKQILLNLLNNSIKFTPACGKIMLTVGVDEENINISISDNGIGIAKYNYDRIFEPFNQaDMLLTKQYEGTGLGLSIA 402
                                   78899**************88*****999999899***************************776777778********** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlp 109
                                   kk+ve+++G+iwv+se g Gttf +++p
  gi|91772450|ref|YP_565142.1| 403 KKYVEMHKGQIWVKSELGVGTTFNIKIP 430
                                   *****999****************9987 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 !   64.6   0.0   2.7e-21     6e-18       2      67 .]     208     275 ..     207     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2.7e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   ++ f+ +v+HELrtPL++i+g++++Lk+   ++lte++ +y   +e ++++l++l++d+Ld+s+ie+g
  gi|91772450|ref|YP_565142.1| 208 KSNFIGNVSHELRTPLNSIIGFSHILKENneNNLTENQLKYCSNVEISGKHLLALINDVLDISKIESG 275
                                   789***********************999999**********************************97 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.2     5e+03      19      42 ..     295     317 ..     287     322 .. 0.70
   2 !   16.5   0.4   2.5e-06    0.0057       4      92 ..     324     420 ..     321     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.2
                   HATPase_c_5  19 eacskieeekrfIrltvrekkksl 42 
                                   e+   +  +k++I+l+++ k+k++
  gi|91772450|ref|YP_565142.1| 295 ESLAPFA-NKKSIELEMTLKHKNI 317
                                   4555555.4899999998888765 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.5e-06
                   HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.............ekkklesskskkeehGiGl 71 
                                   + +  il nlL+N+i    ++     +I ltv  +++++ isi+ +  g             ++  +   +++ e  G+Gl
  gi|91772450|ref|YP_565142.1| 324 TKIKQILLNLLNNSIKFTPACG----KIMLTVGVDEENINISISDNGIGiakynydrifepfNQADMLL-TKQYEGTGLGL 399
                                   567889**********999999....5***********9999987744445566666665543333333.3568899**** PP

                   HATPase_c_5  72 ksireivkkykgnlsieaedg 92 
                                   +  ++ v+ +kg+++++ e g
  gi|91772450|ref|YP_565142.1| 400 SIAKKYVEMHKGQIWVKSELG 420
                                   ***************999866 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 ?   14.3   0.0   1.2e-05     0.028       5      64 ..     328     388 ..     324     422 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                   HATPase_c_3   5 kAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeak 64 
                                   + l+ l++Ns+     + ++ ++v  ++ ++ +i+i D+G G+ + + ++ +++ +++    
  gi|91772450|ref|YP_565142.1| 328 QILLNLLNNSIKftPACGKIMLTVGVDE-ENINISISDNGIGIAKYNYDRIFEPFNQADMLL 388
                                   5688999999986566777888887765.689********************9999888754 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.4e-05     0.076       3      34 ..      69     100 ..      67     129 .. 0.79
   2 ?   -2.5   0.0       2.5   5.6e+03       1       9 [.     126     134 ..     126     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                         PAS_8   3 lralfesspdgiavvd.lgdrivdvNqaalell 34 
                                   + +lf+ +p+g +++d +   i+ +N+++ ++ 
  gi|91772450|ref|YP_565142.1|  69 YFTLFNKIPVGYVLLDvNAS-IIRMNETFSKMI 100
                                   789*************9999.********9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                         PAS_8   1 erlralfes 9  
                                   +r+ra+fe+
  gi|91772450|ref|YP_565142.1| 126 SRYRAFFEN 134
                                   59*****96 PP

>> Herpes_UL31  Herpesvirus UL31-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.2e-05     0.072     139     224 ..     280     361 ..     242     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                                   -HHHHHHHHHHHCCTTSEEEEEEEETTCEEEEEEESSS-EEE-HHHHHHHHHHTTTEEEEEEEETTEEEEEEEC------- CS
                   Herpes_UL31 139 QpelfyiyyvlkagvsdifpilfaedgklamyviFkgsslHlseklirqlldnlegYkvvadvvkdtfvlsvlceaateas 219
                                    pelf ++++++++v++  p+  ++  +l m +  k+  +H   + i+q+l nl + ++      ++ +l+v      +++
  gi|91772450|ref|YP_565142.1| 280 EPELFKLNLLIHEVVESLAPFANKKSIELEMTLKHKNIGVHADRTKIKQILLNLLNNSIKFTPACGKIMLTVG--V--DEE 356
                                   59****************************************************9999999999999999993..2..333 PP

                                   ----- CS
                   Herpes_UL31 220 svkid 224
                                   +++i+
  gi|91772450|ref|YP_565142.1| 357 NINIS 361
                                   44443 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.5e-05      0.12       1      70 [.      77     146 ..      77     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                         PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlir 70 
                                   p+g+++ + +  i+++Ne++ +++    + vl k ++d++   +++   +r ra++e+ +   +  e+ + +
  gi|91772450|ref|YP_565142.1|  77 PVGYVLLDVNASIIRMNETFSKMIFKEIDKVLFKGLSDFIydLDKQIFLSRYRAFFENPT--NKKMEIRFNK 146
                                   68999989***************9455677**********77777777777777777777..5555544444 PP

>> DUF3925  Protein of unknown function (DUF3925)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.38       1      47 [.      55     100 ..      55     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                       DUF3925   1 mktaqreklsnrefyfvlymmllfvvGWv.ldvnGlflskyftlagmi 47 
                                   +kt+q e l+++e yf l+  +   vG+v ldvn   +    t++ mi
  gi|91772450|ref|YP_565142.1|  55 LKTSQIELLAQKEAYFTLFNKI--PVGYVlLDVNASIIRMNETFSKMI 100
                                   69****************9875..356552799988776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2871.63
//
Query:       gi|91772451|ref|YP_565143.1|  [L=389]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  178.8   1.7    2.7e-52  178.0   0.0    1.9  2  DDE_Tnp_IS66   Transposase IS66 family
    3.4e-05   24.4   0.7     0.0001   22.8   0.7    1.8  1  SlyX           SlyX
    6.1e-05   23.3   0.4       0.12   12.6   0.2    2.8  3  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.067   13.3   2.1       0.76    9.9   0.0    2.7  3  GutM           Glucitol operon activator protein (GutM)
      0.085   13.5   1.8       0.35   11.5   0.2    2.5  2  PLATZ          PLATZ transcription factor
       0.12   12.3   0.1        1.2    9.0   0.0    2.6  3  BBS2_N         Ciliary BBSome complex subunit 2, N-terminal
       0.16   12.5   3.6       0.21   12.2   1.4    2.3  2  BST2           Bone marrow stromal antigen 2
       0.26   11.8   4.8       0.37   11.3   0.2    2.7  3  DUF16          Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3      0.25   5.5e+02     174     225 ..      20      69 ..       4      85 .. 0.63
   2 !  178.0   0.0   1.2e-55   2.7e-52      48     280 ..     122     351 ..     106     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.25
                  DDE_Tnp_IS66 174 larigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   ++ + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772451|ref|YP_565143.1|  20 VTLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   4447777777666532..3466666666666666667776766665555444 PP

  == domain 2  score: 178.0 bits;  conditional E-value: 1.2e-55
                  DDE_Tnp_IS66  48 raaelleplvealkaallasevihaDETtlrvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkG 126
                                   ++ + le + +++k+ l +s+vi++DET++r       +gk+++l+v++t+k   +++++ +++Rg+e+++a+  L +f+G
  gi|91772451|ref|YP_565143.1| 122 NCERSLEDFEQQIKNFLIESPVINCDETGMR------IEGKRQWLHVASTNK---MTCYYPHQKRGSEAMNAMgiLPNFNG 193
                                   56677**************************......99***********99...****************9955666*** PP

                  DDE_Tnp_IS66 127 vlvsDgyagYnklaeeqvthalCwaHlrRkfvdaeeakkksqaaaealar.igklyaierearea....eaeerlalrqee 202
                                   ++v+  +++Y k+   +++h +C aHl+R++++++e+++  q +++a++  + ++++  +++r++    ++e+ ++ +  +
  gi|91772451|ref|YP_565143.1| 194 TVVHYFWKSYYKY---DCDHSICNAHLLRELTSVSENDN--QLWSKAMNIlLIDVKKSVDQIRKMsgcmKPERIKEFEDWY 269
                                   ************9...7*******************976..*********************955568888********** PP

                  DDE_Tnp_IS66 203 srpllaeleawleeql....kkvlpksklgkairyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeG 279
                                    + ++  +e++ + q     ++ +++++++++++++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++G
  gi|91772451|ref|YP_565143.1| 270 GQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLDRFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQG 350
                                   **********998554567799*********************************************************** PP

                  DDE_Tnp_IS66 280 a 280
                                   a
  gi|91772451|ref|YP_565143.1| 351 A 351
                                   9 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.7   4.6e-08    0.0001      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.6e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772451|ref|YP_565143.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.9   6.5e+03      21      36 ..      27      42 ..      25      67 .. 0.57
   2 !    7.8   0.0    0.0016       3.6       5      45 ..     145     183 ..     141     186 .. 0.84
   3 !   12.6   0.2   5.3e-05      0.12      85     138 ..     314     367 ..     288     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.9
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91772451|ref|YP_565143.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0016
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91772451|ref|YP_565143.1| 145 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSEAMN 183
                                   68************99866..77779999999999998875 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 5.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91772451|ref|YP_565143.1| 314 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 367
                                   55667899*****************************98777776666666665 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       4.1   9.1e+03      75     103 ..      31      58 ..      28      61 .. 0.63
   2 ?    9.9   0.0   0.00034      0.76      41      90 ..     226     275 ..     216     293 .. 0.80
   3 ?    2.3   0.1      0.08   1.8e+02      64      82 ..     344     362 ..     326     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.1
                          GutM  75 arfkeleelegksleeieeeklkkkdklt 103
                                   a  +++ el+  +++e+ee+ +kk ++++
  gi|91772451|ref|YP_565143.1|  31 AEQQRIIELQAARITELEER-VKKLEEQL 58 
                                   55566667777777777666.66666655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00034
                          GutM  41 rkkgrfragvivllavdedgiivearvmkGvTvfarfkeleelegkslee 90 
                                   ++ +++ ++++ +l +d ++ + ++r+m+G     r+ke+e+  g+ ++ 
  gi|91772451|ref|YP_565143.1| 226 ENDNQLWSKAMNILLIDVKKSVDQIRKMSGCMKPERIKEFEDWYGQIIHI 275
                                   6778889999*********************9999999999999988764 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.08
                          GutM  64 earvmkGvTvfarfkelee 82 
                                    +r m+G  +f+r+++  +
  gi|91772451|ref|YP_565143.1| 344 TFRSMQGALIFSRVRSYIS 362
                                   5689**********98654 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       0.6   1.4e+03      16      52 ..      25      63 ..      18      72 .. 0.59
   2 ?   11.5   0.2   0.00015      0.35      34      71 ..      73     130 ..      69     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.6
                         PLATZ 16 klldvseiQtYvi..nsakvvflnerpqarsakakakek 52
                                  +l+d+   Q+ +i    a++  l+er ++ +++ k++++
  gi|91772451|ref|YP_565143.1| 25 TLYDIIAEQQRIIelQAARITELEERVKKLEEQLKKNSR 63
                                  556666656655411467888888886665555544443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772451|ref|YP_565143.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDF 130
                                   9*********99998888743.33333568999***********************985 PP

>> BBS2_N  Ciliary BBSome complex subunit 2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00055       1.2      17      82 ..     108     171 ..      94     177 .. 0.83
   2 ?   -2.6   0.0       2.2     5e+03      69      89 ..     228     248 ..     214     260 .. 0.58
   3 ?   -1.1   0.0      0.76   1.7e+03      41      55 ..     328     342 ..     316     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00055
                        BBS2_N  17 tagkvlihnphekeqklkserlsasesevslLninkevtalaagklkekqekdiLligtqtnllaY 82 
                                     ++v+ih+ h+ ++  +  +l++ e++++ + i++ v+      ++ + +++ L +++ +++++Y
  gi|91772451|ref|YP_565143.1| 108 VPDEVIIHKVHKCSNCER--SLEDFEQQIKNFLIESPVINCDETGMRIEGKRQWLHVASTNKMTCY 171
                                   5679*******9985443..45556***********99999888899999**************99 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                        BBS2_N  69 diLligtqtnllaYdveeNsd 89 
                                   d  l +++ n+l+ dv++  d
  gi|91772451|ref|YP_565143.1| 228 DNQLWSKAMNILLIDVKKSVD 248
                                   333334444444444444433 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.76
                        BBS2_N  41 sesevslLninkevt 55 
                                    e++v++++++++++
  gi|91772451|ref|YP_565143.1| 328 AERDVRMMKVQQKIS 342
                                   3899********997 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   9.5e-05      0.21      45      87 ..      21      63 ..       3      67 .. 0.81
   2 ?   -1.7   0.0       2.1   4.6e+03      14      30 ..     119     135 ..     115     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91772451|ref|YP_565143.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHHHHHH CS
                          BST2  14 ecrnvtrlLerqLtqaq 30 
                                   +c+n +r Le   +q +
  gi|91772451|ref|YP_565143.1| 119 KCSNCERSLEDFEQQIK 135
                                   56666666654433333 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00017      0.37      45      82 ..      25      62 ..      16      75 .. 0.82
   2 ?   -3.8   0.0         8   1.8e+04      56      64 ..     126     134 ..     110     141 .. 0.52
   3 ?    1.6   0.2      0.17   3.8e+02      10      58 ..     287     342 ..     278     373 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772451|ref|YP_565143.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8
                                   HHHHHHHHH CS
                         DUF16  56 kvekqgeki 64 
                                     e  +++i
  gi|91772451|ref|YP_565143.1| 126 SLEDFEQQI 134
                                   222222222 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
                                   XXX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  10 vKkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                    Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91772451|ref|YP_565143.1| 287 SKK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 342
                                   455.467888888888777888999988854444440......55555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1698  (0.0947069); expected 358.6 (0.02)
Passed bias filter:                      915  (0.0510346); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); 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: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 2344.60
//
Query:       gi|91772452|ref|YP_565144.1|  [L=97]
Description: hypothetical protein Mbur_0402 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 601.27
//
Query:       gi|91772453|ref|YP_565145.1|  [L=307]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-06   26.5   1.3    6.7e-06   25.9   1.3    1.3  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
       0.05   13.1   0.1       0.11   12.0   0.1    1.5  1  DUF4283    Domain of unknown function (DUF4283)
      0.062   13.3   0.0       0.22   11.6   0.0    2.0  2  DUF772     Transposase domain (DUF772)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.3   1.1e-09   6.7e-06      10     185 ..      83     259 ..      75     287 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-09
                     DDE_Tnp_1  10 Dattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYas 88 
                                   D+t++++ + +  ++  y+ +  ++  k+hi +   + l++ +  t g +hds+ lk  +d+l ++  + +++  D+GY+s
  gi|91772453|ref|YP_565145.1|  83 DSTPLEASRYD--KYADYNPHYNCKMDKAHITM--IGPLPIYMTHTKGASHDSPELKKHIDALVEMgvDIDTYALDGGYDS 159
                                   88888888888..44444444445555888888..4457***********************9999*************** PP

                     DDE_Tnp_1  89 aelldtle.ekgvdyiirlkkntklyrk.....................gaeskrrgrlrkhdrnkiltksqkrrnkskke 147
                                    +++ ++  + +++++i++++++k++                        + +++ ++l  ++r+k++    + +n     
  gi|91772453|ref|YP_565145.1| 160 FRNHADIWyKLNAKPVIAYSSDSKVQYEgmmeridhwvnkmwklggsihMKYEEKLHFLYENGREKQVGMHLRNKNI---- 236
                                   888888888**********9999999888887777777666666555541333344444444444444444444444.... PP

                     DDE_Tnp_1 148 kgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlk 185
                                                  +   + e y++R ++Erv+  +k
  gi|91772453|ref|YP_565145.1| 237 ---------------KDDGFDEDYSHRGECERVHNHIK 259
                                   ...............556669************99888 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.8e-05      0.11      24      59 ..     190     225 ..     169     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                       DUF4283  24 lsalrrvlakaWklkggvkikelgdglflfrfssee 59 
                                   ++++ ++++k+Wkl+g +++k+ ++ +fl++   e+
  gi|91772453|ref|YP_565145.1| 190 MERIDHWVNKMWKLGGSIHMKYEEKLHFLYENGREK 225
                                   678999***********************9866655 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.6e-05      0.22      10      70 ..       1      64 [.       1      67 [. 0.79
   2 ?   -2.8   0.0       1.1   6.8e+03      21      37 ..     244     260 ..     243     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                        DUF772 10 mlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70
                                  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f k rl++  l++++
  gi|91772453|ref|YP_565145.1|  1 MIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVKyRLGKtgLDEVM 64
                                  89999999999999998888762566666666664333.89*****************9977776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                        DUF772  21 glSdreleealrenlsf 37 
                                   ++S r  +e++++++ +
  gi|91772453|ref|YP_565145.1| 244 DYSHRGECERVHNHIKW 260
                                   56888899****99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2017.74
//
Query:       gi|91772454|ref|YP_565146.1|  [L=200]
Description: alkylhydroperoxidase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-09   37.6   0.0    2.6e-09   37.0   0.0    1.3  1  CMD          Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.047   13.9   0.0        1.1    9.5   0.0    2.3  2  SelB-wing_2  Elongation factor SelB, winged helix


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 !   37.0   0.0     3e-13   2.6e-09       6      66 ..      22      83 ..      19      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3e-13
                                  HHHHHHHHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHH CS
                           CMD  6 altalrealla.reggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaq 66
                                  a++ +++ l+a +++ L+    e i lav  +ngce C  aHt++AleaG++ eei+  la 
  gi|91772454|ref|YP_565146.1| 22 AFFSTYDLLYAkKNELLSQHFLERIMLAVTEVNGCEVCSYAHTKMALEAGMSNEEIQSMLAG 83
                                  56666666777789999****************************************88875 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 ?    9.5   0.0   0.00012       1.1       8      31 ..      63      89 ..      62      97 .. 0.76
   2 ?    1.6   0.0     0.037   3.3e+02      31      49 ..     178     196 ..     171     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                                  HHH-TTS--EEHHHHHHHCS...SSS- CS
                   SelB-wing_2  8 HrenPlrpGmskeeLrsrla...prlp 31
                                  H +  l+ Gms ee  s+la    ++p
  gi|91772454|ref|YP_565146.1| 63 HTKMALEAGMSNEEIQSMLAgisDDVP 89
                                  78889*************884443555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.037
                                   -HCCHHHHHHHHHHTTSEE CS
                   SelB-wing_2  31 paklfqallealvargila 49 
                                   p +l++all++l +r  ++
  gi|91772454|ref|YP_565146.1| 178 PIALIHALLAKLFNRSTIK 196
                                   66899*******9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1293.82
//
Query:       gi|91772455|ref|YP_565147.1|  [L=55]
Description: hypothetical protein Mbur_0407 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 359.68
//
Query:       gi|91772456|ref|YP_565148.1|  [L=377]
Description: Na+/proline symporter-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-13   47.9  11.7    1.4e-12   47.2  11.7    1.3  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
       0.15   11.4   0.5       0.27   10.6   0.5    1.4  1  DUF4191   Domain of unknown function (DUF4191)


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 !   47.2  11.7   1.5e-16   1.4e-12       1     119 [.      36     158 ..      36     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.5e-16
                           SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvlle.lgalllvlllllllaerlr....nagalTlpdyls 76 
                                   y+lagr++ ++ l+ls +a  is a ++G  G+  + Gl++++l  +++ +++ +++++++ r r    n+ga+T+p+++ 
  gi|91772456|ref|YP_565148.1|  36 YMLAGRKVNPYILALSYGAAFISTAAIIGFGGVTGTLGLGTLWLVfMNIFVGIFIAFVVFGARTRriglNLGAVTFPELIG 116
                                   99***************************************99863788899999999999999999************** PP

                           SSF  77 kRfkgkrilvylsalslllvitlklsvdlvggaklielalGln 119
                                    Rf+++ i+ y  al+ l ++ l+    l+gga+++e+al ++
  gi|91772456|ref|YP_565148.1| 117 RRFQSRFIQGYSGALIAL-FMPLYAGIVLIGGARFMETALCMS 158
                                   *******88887777665.5667777779***********986 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5     3e-05      0.27      19      75 ..      41     101 ..      27     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3e-05
                       DUF4191  19 rkedkkllwlllaaflvvvvvfvvlglllg....slilllilgillgllvalivltrraek 75 
                                   rk ++ +l l  +a+ + +++++ +g ++g    ++++l+++ i++g+ +a++v++ r+++
  gi|91772456|ref|YP_565148.1|  41 RKVNPYILALSYGAAFISTAAIIGFGGVTGtlglGTLWLVFMNIFVGIFIAFVVFGARTRR 101
                                   66777777777776666666666666665333346888899****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2200.80
//
Query:       gi|91772457|ref|YP_565149.1|  [L=138]
Description: hypothetical protein Mbur_0409 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   33.3   0.4    8.8e-08   32.8   0.4    1.2  1  Peptidase_C39_2  Peptidase_C39 like family


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.4   4.9e-12   8.8e-08      23     144 .]       1     123 [.       1     123 [. 0.68

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.9e-12
               Peptidase_C39_2  23 mvlsyl...gk.k.vtqnelakelktnssgdpntgfvgnitdksglgvynepivklaekyglkvsdtrgssi...eevkke 95 
                                   mvl+y+   g+ +    ++l +el++ + g  ++g+ g     ++ ++    i+++ ++yg++   +++ +    +e   e
  gi|91772457|ref|YP_565149.1|   1 MVLEYWdenGYsNfSYGDTLIEELADAM-GTNENGING-----TKISHIDDGIEEVCDYYGYSDFTIVNDDNlfmSETMFE 75 
                                   8899996665542433455555555554.222334322.....233444555888889999944444444333559***** PP

               Peptidase_C39_2  96 idagkPvvvsvttfkplndgeikftssgHlvvitGYdekg.krvyvnDPa 144
                                   idag+P+v+s+ +   + ++ ++  +++H+v+++GY+e++ ++++++D++
  gi|91772457|ref|YP_565149.1|  76 IDAGNPFVLSMIYG--GLGSGYTNPYNNHSVTCMGYSEGTiDYLFLHDTW 123
                                   ***********543..24789*****************998999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 837.81
//
Query:       gi|91772458|ref|YP_565150.1|  [L=86]
Description: hypothetical protein Mbur_0412 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 574.95
//
Query:       gi|91772459|ref|YP_565151.1|  [L=309]
Description: cysteine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  233.0   0.1    5.3e-69  232.9   0.1    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 !  232.9   0.1     3e-73   5.3e-69       2     294 .]       9     295 ..       8     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 3e-73
                                   GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                          PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallGl 79 
                                   t  +g+TPlvrl+r++  + + +++K E +np+gS+KdR a ++++++++    +++  v+e +sGN+g++lA+++a  G+
  gi|91772459|ref|YP_565151.1|   9 TKTVGKTPLVRLNRITVGCYATVLVKVEAFNPLGSIKDRIALNMIETAEKDgmlKKGAIVIEPTSGNTGIGLAFVCATKGY 89 
                                   7789***********9555555*************************77777***************************** PP

                                   EEEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTTTT CS
                          PALP  80 kvtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlggk 157
                                   ++++ +p+++s e++  l+ lGae+v++  +++ + a + a+++ +e+++ ++ +qf np++ +    t++ Ei++++ggk
  gi|91772459|ref|YP_565151.1|  90 RLILTMPETMSVERRNILKVLGAEIVLTpgPNGMKGAIEEAERIGKETPDSFIPHQFMNPANPDIhRCTTAGEIWDDTGGK 170
                                   ****************************88778************************************************ PP

                                   EEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHHHHSEEE CS
                          PALP 158 pdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselafelldrlv 237
                                   +d +v++vG+Gg+i+G++  lk+r+p  + i+vep+ s+ l ++          +++++++g+++g +p +l+++++    
  gi|91772459|ref|YP_565151.1| 171 VDILVAGVGTGGTITGVSEELKSRKPGFKAIAVEPKDSAVLSGGS---------PGPHMIQGIGAGfVPDVLNVDII---- 238
                                   *********************************************.........88**********99*****9999.... PP

                                   EEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                          PALP 238 deivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                   dei+tvs+e+a+e+ r+la++egi+++ ss+aal a+ + ++++e +++  +vv+l++
  gi|91772459|ref|YP_565151.1| 239 DEIITVSNEDAFETTRELAKKEGILAGISSGAALFAAlDVARRKENEGK-MIVVVLPD 295
                                   67888***********************888887777566666666666.99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1967.52
//
Query:       gi|91772460|ref|YP_565152.1|  [L=320]
Description: Serine O-acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-11   41.5   7.7    2.8e-05   23.7   1.4    2.7  2  Hexapep      Bacterial transferase hexapeptide (six repeats)
    1.8e-06   27.6   5.5     0.0021   17.8   0.7    3.6  3  Hexapep_2    Hexapeptide repeat of succinyl-transferase
    0.00065   20.0   0.0     0.0016   18.8   0.0    1.7  1  SATase_N     Serine acetyltransferase, N-terminal
  ------ inclusion threshold ------
      0.033   13.3   0.1      0.049   12.7   0.1    1.2  1  Cas_St_Csn2  CRISPR-associated protein Csn2 subfamily St


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 !   23.7   1.4   6.2e-09   2.8e-05       1      35 [.     206     242 ..     206     243 .. 0.96
   2 !   20.9   0.6   4.7e-08   0.00021       1      35 [.     261     296 ..     261     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.2e-09
                                   TEEEETTEEE-T..TEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgp..faviggnVkIGdnvkIgagvvig 35 
                                   +++IG++ +I++  ++vig+  +IGdnv+I  gv++g
  gi|91772460|ref|YP_565152.1| 206 GAKIGKGFFIDHgtGVVIGETSEIGDNVRIYQGVTLG 242
                                   589********************************97 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.7e-08
                                   TEEEETTEEE-T.TEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgp.faviggnVkIGdnvkIgagvvig 35 
                                   +++I+++v+I +  +++gg+++IG +++Ig +v ++
  gi|91772460|ref|YP_565152.1| 261 HPTIEDDVVIYSnSTILGGDTVIGARSVIGGNVWLT 296
                                   679*********888999**************9887 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.019        83      13      33 ..     196     216 ..     195     217 .. 0.88
   2 !    6.6   0.7    0.0014       6.4      19      32 ..     228     241 ..     218     243 .. 0.71
   3 !   17.8   0.7   4.7e-07    0.0021       3      34 .]     263     297 ..     263     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.019
                                   T-EESEEE-TT-EE-TT-EE- CS
                     Hexapep_2  13 nagiGvslGdncvvgaGvvit 33 
                                    +++G+++  ++++g G +i+
  gi|91772460|ref|YP_565152.1| 196 HSVVGIDIHPGAKIGKGFFID 216
                                   699************998886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0014
                                   EE-TT-EE-TT-EE CS
                     Hexapep_2  19 slGdncvvgaGvvi 32 
                                   ++Gdn+ ++ Gv++
  gi|91772460|ref|YP_565152.1| 228 EIGDNVRIYQGVTL 241
                                   58888888888876 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 4.7e-07
                                   EE-TT-EE-TT-EE..S.EEE-TT-EE-TT-EE-S CS
                     Hexapep_2   3 iIGdnCliGanagi..G.vslGdncvvgaGvvita 34 
                                   +I+d+++i +n++i  G + +G ++v+g +v +t+
  gi|91772460|ref|YP_565152.1| 263 TIEDDVVIYSNSTIlgGdTVIGARSVIGGNVWLTR 297
                                   6************99637*************9985 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.6e-07    0.0016      67     103 ..     125     170 ..      73     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.6e-07
                                   T.........HHHHHHHHHHHHHHHH-TT---THHHHHH-HHHHHH CS
                      SATase_N  67 p.........eiveaaraDlkAvlerDpAcksylepllyfKGFhAl 103
                                   +         +i++ ++aD+ A +e+DpA+k y e++  + G  Al
  gi|91772460|ref|YP_565152.1| 125 EtvmllrkipQIRSLLAADIIAAYEHDPAAKGYDEIIFSYPGIFAL 170
                                   0444444444*************************99999998776 PP

>> Cas_St_Csn2  CRISPR-associated protein Csn2 subfamily St
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.1e-05     0.049      68     133 ..      46     113 ..      37     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                                   EEEESSHHHHHHCTS-STTSHHHHHH.HHHHSSCCCHHHH.HHHHHHHHHHHHHHHCC---EETTEE- CS
                   Cas_St_Csn2  68 svdissreDlikileisksslmqkYl.ekiltkvdivvdl.ekiseqlerifeamneeikenigkvel 133
                                   s +i sre +++i+++ k  l  +Y+ ++ + + ++  ++ ++i+e  e++ +++ ++i++ + + e 
  gi|91772460|ref|YP_565152.1|  46 SAVIPSRESIVEIIDLFKDVLFPGYFgDQTVERSNLIYHIgNEINELFEKLSKQVTNSILHECRRTEE 113
                                   6789**********************56899999*99998568*****************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1877.11
//
Query:       gi|91772461|ref|YP_565153.1|  [L=486]
Description: hypothetical protein Mbur_0415 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2820.48
//
Query:       gi|91772462|ref|YP_565154.1|  [L=310]
Description: transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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   31.1   0.5    2.2e-07   31.1   0.5    3.4  3  Gate            Nucleoside recognition
  ------ inclusion threshold ------
          2    8.7   4.3        1.7    9.0   0.0    2.6  3  FA_hydroxylase  Fatty acid hydroxylase superfamily


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 !   31.1   0.5   2.5e-11   2.2e-07       1      99 [.      13     102 ..      13     118 .. 0.84
   2 ?   -0.5   0.3      0.17   1.5e+03       5      32 ..     119     146 ..     104     158 .. 0.62
   3 ?    2.4   8.2     0.021   1.9e+02       2      91 ..     178     258 ..     177     309 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.5e-11
                          Gate   1 llkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtl.ytsalgellqgfd 80 
                                   l+k++p i+++++ + +l + +++ ++g+l +p+++  g  l  ++  s+lt+f++ +++ +++++l y         ++ 
  gi|91772462|ref|YP_565154.1|  13 LIKVLPPIVIGTLAMAILVEMGWVNKFGFLASPLMHY-G-HLRQEIGLSFLTSFGSSTAGNSMIAKLhY--------DKHI 83 
                                   689**********************************.4.6**************************55........7888 PP

                          Gate  81 tpksalafllfvllytpcv 99 
                                   ++k+ +++ +++++ ++ v
  gi|91772462|ref|YP_565154.1|  84 DRKETIIATMVNSFPSSIV 102
                                   8888888888888877554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                          Gate   5 gpiillasiliwflssssllgrigklle 32 
                                   g i l +++li+f +   +l ++  +l+
  gi|91772462|ref|YP_565154.1| 119 GLIYLGIVVLIGFVKTLIALVAARLFLT 146
                                   4455556666666555544444444444 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.021
                          Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplg.qeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdt 81 
                                   ++++ +  ++si i  l +++++++i+++++  f      ++  +++++++++ +a  +++g+l +          ++  +
  gi|91772462|ref|YP_565154.1| 178 IRMILTTTIVSIAIFQLMETGIFDMIANIMKSSFLVNYvPPEALPIIAGWFASNIAAYTIAGNLLS----------AQLLS 248
                                   6788888999999999999**************999444555555555555555555555555544..........46666 PP

                          Gate  82 pksalafllf 91 
                                   +k+ + +ll+
  gi|91772462|ref|YP_565154.1| 249 TKDIILALLI 258
                                   6665544444 PP

>> FA_hydroxylase  Fatty acid hydroxylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.09   8.1e+02      59     111 ..      15      51 ..       2      69 .. 0.46
   2 ?    9.0   0.0   0.00019       1.7      25      84 ..      73     134 ..      67     157 .. 0.74
   3 ?   -1.9   0.1      0.45     4e+03      67      67 ..     195     195 ..     165     238 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.09
                FA_hydroxylase  59 llllllllgplsalll.....vlvlaallelliHsglhvslgwllerllatpraHrlH 111
                                    +l+ +++g+l +++l     v  +++l   l H+g                     H
  gi|91772462|ref|YP_565154.1|  15 KVLPPIVIGTLAMAILvemgwVNKFGFLASPLMHYG---------------------H 51 
                                   344444444433333333221233333333345554.....................2 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00019
                FA_hydroxylase  25 lwrrlHkvHHsseaptalaalrahpleallla.llllllllllgplsalll.vlvlaallel 84 
                                   + ++lH   H +++ t +a++ +++ ++++l   ll ++++llg++ +++l ++vl  ++++
  gi|91772462|ref|YP_565154.1|  73 MIAKLHYDKHIDRKETIIATMVNSFPSSIVLSrDLLPIMVALLGTTGLIYLgIVVLIGFVKT 134
                                   7788**************99999988888888766666667777555555544554444443 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.45
                FA_hydroxylase  67 g 67 
                                    
  gi|91772462|ref|YP_565154.1| 195 M 195
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2066.83
//
Query:       gi|91772463|ref|YP_565155.1|  [L=363]
Description: hypothetical protein Mbur_0417 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-05   23.6   0.6    5.8e-05   22.8   0.6    1.4  1  DDE_Tnp_1  Transposase DDE domain
     0.0014   18.7   0.6     0.0034   17.5   0.6    1.6  1  Hit1_C     Hit1 C-terminal
  ------ inclusion threshold ------
      0.013   15.6   0.8      0.035   14.2   0.8    1.8  1  Mg296      Mg296 protein


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.6   9.7e-09   5.8e-05      27     182 ..     128     293 ..      97     296 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.7e-09
                     DDE_Tnp_1  27 ykggk..ykygyklhiavdtrsglilsvvitpgnvhd...skglkqlldelrprkgklvlaDaGYasaelldtleekgvdy 102
                                   + +++  ++y y   ++++  +++ +s+  + + +      k++++++d ++  k  ++  D+ + s++++ +l+e+ + +
  gi|91772463|ref|YP_565155.1| 128 QAKKStnSFYSYISLCIINKYTRFTISMLPVEKGKTKtdyLKYFIDVVDKINL-KINIICLDREFYSRDVFTFLQENDIPH 207
                                   33222458999999999999999999999864444440115666667777777.*************************** PP

                     DDE_Tnp_1 103 iirl.kkntklyrk........................gaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntn 158
                                   i ++ +k +++++                          ++ k+ +  r+++ ++ l  +    +                
  gi|91772463|ref|YP_565155.1| 208 ITPVvRKGKRIKDIldgnnkryekyvmknkkgdvgldiAIDVKYLKGKRGKNGCENLGFVVYGIDW--------------- 273
                                   ****97777777666766664443444444444444444555555555555555555555555555............... PP

                     DDE_Tnp_1 159 sellsaeevaelyrlRwqiErvFk 182
                                       ++ ++  +yr+R  iE++ +
  gi|91772463|ref|YP_565155.1| 274 ----EPGKISMIYRKRFAIESSYR 293
                                   ....9999999*****99998765 PP

>> Hit1_C  Hit1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.6   5.8e-07    0.0034      20      67 ..      67     118 ..      58     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.8e-07
                        Hit1_C  20 vkfhlakv.yrilttsegn...ggssdtlsseakkqlavdylntlryGGvhy 67 
                                   +++hl+k+ +  l  ++++   ++s++tl s+ k +la+dy n   yG v y
  gi|91772463|ref|YP_565155.1|  67 MRYHLHKIdFDQLIENNAKillQSSHKTLDSNKKYDLAIDYTNDPYYGEVNY 118
                                   68*****965666655554232466677*********************999 PP

>> Mg296  Mg296 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   5.9e-06     0.035       9      68 ..      65     124 ..      58     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.9e-06
                                   HHHHHHHHTS-HHHHHHHHHHHHHHHHT-SSGGGSS---.S-HHHHHHHHHHHHHHHHHHH CS
                         Mg296   9 tflkeilekvdlekliqnynlileretstlliyedddye.eidffeksieselfyvksklv 68 
                                   t ++  l+k+d+++li+n  +il ++ +  l   +  y+  id+ + +  +e++yv+++ v
  gi|91772463|ref|YP_565155.1|  65 TSMRYHLHKIDFDQLIENNAKILLQSSHKTL-DSNKKYDlAIDYTNDPYYGEVNYVNENYV 124
                                   5678899****************99998776.5566777579**************87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2614.62
//
Query:       gi|91772464|ref|YP_565156.1|  [L=202]
Description: hypothetical protein Mbur_0418 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-09   38.4   0.0      2e-09   38.0   0.0    1.2  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.1e-13     2e-09       1      59 [.      64     147 ..      64     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.1e-13
                                   EEE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCC........................CTSEEEEEEEEEEEEE CS
                          ASCH   1 lsfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalk........................ptgralgivevtkvev 57 
                                   l+++q++asli++G K +e+r++++    vrg + i+a                           ptg+++g v++++++ 
  gi|91772464|ref|YP_565156.1|  64 LAIRQPWASLIIRGLKNIEVRSKNTY---VRGTIAIYASRSiirkkdlklvnenydipieqlddlPTGMIIGTVNLVECKE 141
                                   689***********************...********5555**************************************88 PP

                                   E....H CS
                          ASCH  58 k....p 59 
                                   +    +
  gi|91772464|ref|YP_565156.1| 142 YesdfH 147
                                   866443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1474.78
//
Query:       gi|91772465|ref|YP_565157.1|  [L=632]
Description: DNA gyrase subunit B [Methanococcoides burtonii DSM 6242]
Scores for 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-60  201.0   0.7    1.5e-59  200.4   0.7    1.3  1  DNA_gyraseB    DNA gyrase B
    8.8e-32  109.1   0.1    1.8e-31  108.1   0.1    1.6  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    8.5e-22   77.8   0.1    2.6e-21   76.2   0.1    1.9  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    1.4e-16   60.6   0.0    2.9e-16   59.5   0.0    1.6  1  Toprim         Toprim domain
    0.00084   19.2   0.1     0.0017   18.2   0.1    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.4   0.7   4.1e-63   1.5e-59       1     173 [.     221     389 ..     221     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 4.1e-63
                   DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlneyak 81 
                                   G+ +fve+ln+++++l+k+++++e+ek  e    ve+a+q+t+sy e ++sF+Nni+t eGGtH+ gfk+alt++ n+y+k
  gi|91772465|ref|YP_565157.1| 221 GIISFVEHLNQSRTALHKTPIYFEREK--EG-TIVEIAMQYTDSYGEYVYSFANNINTYEGGTHLIGFKTALTRVANDYIK 298
                                   899************************..77.99*********************************************** PP

                   DNA_gyraseB  82 kkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakkilekaveaa 162
                                   k++++k +e k++gediregl a++svk++epqFeGQTK+kLgnse k+iv+++vse l++++een+++a  i +ka++a+
  gi|91772465|ref|YP_565157.1| 299 KNNVVKGDE-KLTGEDIREGLAAIISVKLTEPQFEGQTKTKLGNSELKGIVDSMVSEGLSEYMEENPKVAVIIFQKALDAR 378
                                   ***999987.*********************************************************************** PP

                   DNA_gyraseB 163 kareaarkare 173
                                   +areaa+kare
  gi|91772465|ref|YP_565157.1| 379 RAREAAKKARE 389
                                   *********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 !  108.1   0.1   5.1e-35   1.8e-31       2      63 .]     560     621 ..     559     621 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 5.1e-35
                 DNA_gyraseB_C   2 kkveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                   +++ +qR+KGLGEmnpeqLweTTm+p+tR+Llqvt++da++ade+fs+LmG++v+pR++fi+
  gi|91772465|ref|YP_565157.1| 560 NNTYVQRYKGLGEMNPEQLWETTMNPDTRTLLQVTMDDAAAADEMFSVLMGDEVAPRKAFIQ 621
                                   5788*********************************************************7 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   7.4e-25   2.6e-21       2     109 ..      31     171 ..      30     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 7.4e-25
                                   HHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTTCHHCS CS
                     HATPase_c   2 dekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekfsqdds 66 
                                   d ++L++++ ++vdN++++  a+ +++i+v+i+    d +++v D+G+Gip+++++              + ++kf++ ++
  gi|91772465|ref|YP_565157.1|  31 DTRGLHHLVYEVVDNSIDEalAGFCKNIDVSIN--A-DGSVTVVDDGRGIPVDNHPkykksalevvltvlHAGGKFDK-SN 107
                                   7899***************7666**********..5.9******************************877777****.** PP

                                   TCHTSTSSSHHHHHHHHHHHHTTTEEEE.....................EEETTTEEEEEEEEE CS
                     HATPase_c  67 tkrggggtGlGlsivkklvelmgGeiwv.....................esepgrGttftftlp 109
                                   +k++gg +G+G+s+v++l+e m+ e+++                      + +g Gt+ tf ++
  gi|91772465|ref|YP_565157.1| 108 YKVSGGLHGVGVSVVNALSEWMEVEVKRdgklyyqryergaptsdvtviGDAKGTGTKSTFMPD 171
                                   ***********************98888888887877777765555554444477888888776 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   8.2e-20   2.9e-16       1     102 [.     418     529 ..     418     530 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 8.2e-20
                                   EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEECSSS CS
                        Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiilatDpD 73 
                                   e+++vEg+s+ +++++ +++ fqa+++ +G+i+++e+ ++++v++  e+ + ++++++      + ++ r++++i++tD+D
  gi|91772465|ref|YP_565157.1| 418 EVYLVEGDSAGGSAKQGRNRRFQAILPFRGKIINVEKaRLSKVLKnnEVLSLITAMGTgiaedYNIEKARYHKVIIMTDAD 498
                                   589**********************************7677777677666666666669999999999************* PP

                                   HHHHHHHHHHHHHHT....HHHTTTEEEEEESS CS
                        Toprim  74 reGeaiawellevlk....ellenkigrvefse 102
                                   ++G +i++++l+++     +l+++  g+v++++
  gi|91772465|ref|YP_565157.1| 499 VDGAHIRTLILTFFFrymaPLIDA--GYVYIAQ 529
                                   ************999666666666..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 !   18.2   0.1   4.9e-07    0.0017       7      49 ..      39      81 ..      34     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.9e-07
                   HATPase_c_3  7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGmseee 49
                                  + e+vdNs+d    + ++n+++++n +    g++++ DdG G++ ++
  gi|91772465|ref|YP_565157.1| 39 VYEVVDNSIDealaGFCKNIDVSINAD----GSVTVVDDGRGIPVDN 81
                                  88********97755678899999996....69**********8764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4535.30
//
Query:       gi|91772466|ref|YP_565158.1|  [L=830]
Description: DNA gyrase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-157  523.3   1.0   6.1e-157  522.9   1.0    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    8.9e-73  239.6  18.5    4.9e-15   54.7   0.5    6.5  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
       0.06   13.2   0.6       0.12   12.2   0.1    1.8  2  ANTAR          ANTAR domain


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 !  522.9   1.0    1e-160  6.1e-157       1     425 [.      54     493 ..      54     494 .. 0.98

  Alignments for each domain:
  == domain 1  score: 522.9 bits;  conditional E-value: 1e-160
                 DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGnfGsi 80 
                                   Ra+P++rDGlKPv+RriLyam++  ++ dk +kK+a++vG+vlgkYhPHGd+++yd++vr+ q+f++++pl+d+qGnfGsi
  gi|91772466|ref|YP_565158.1|  54 RALPDARDGLKPVHRRILYAMKEAgMTYDKAYKKSARVVGDVLGKYHPHGDTAVYDSLVRMVQEFSLRYPLIDGQGNFGSI 134
                                   9******************************************************************************** PP

                 DNA_topoisoIV  81 ldgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipphnlkeiid 161
                                    dgd++Aa+RY+e r+ +i++e+l++idketv y++nyDgs kEP+vlp+++PnlL+nG++GIavGmat+++phnl+e+id
  gi|91772466|ref|YP_565158.1| 135 -DGDSAAAMRYTESRMDRISNEMLADIDKETVLYRPNYDGSLKEPTVLPARLPNLLINGSTGIAVGMATNMAPHNLGEVID 214
                                   .******************************************************************************** PP

                 DNA_topoisoIV 162 aliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie....e.ktivitElPigvntskli 234
                                   a+  l++++e+   +l+e+v+gPdfptgg+i+g+++ik+ayetgrG ik+ra ++ie    + k+iv++ElP++vn+s+li
  gi|91772466|ref|YP_565158.1| 215 ATLMLIEDPETpisSLMEIVKGPDFPTGGVILGHQGIKSAYETGRGPIKIRAVTSIEemknDkKRIVVSELPYQVNKSRLI 295
                                   *********9999****************************************99999*9956****************** PP

                 DNA_topoisoIV 235 ekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkpkylslkeilkefl 313
                                   e+i++lv++kki  isd+rdesdr g+r+ iel+r++++e++l++lyk+t++++++ + nl+l+d+ p+ l+lke+l+ +l
  gi|91772466|ref|YP_565158.1| 296 ENIAALVREKKIVgISDLRDESDRdGIRVSIELTRNTNPEVILNQLYKHTQMQTTFGIINLALVDNIPRELTLKELLQIYL 376
                                   *******9999999*********99******************************************************** PP

                 DNA_topoisoIV 314 evrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqaeyllemrlrrLtkee 392
                                   e+r++v+ +r+ ++++k++e+++il+gl++al++idevi++ir+s+  ++ak+ L+++  l+e qa+++l+mrl++Lt +e
  gi|91772466|ref|YP_565158.1| 377 EHRIDVILKRSMFDMRKADEKAHILKGLMIALDHIDEVIALIRGSNAVDEAKEGLMTRfgLDEVQAKAILDMRLQKLTGLE 457
                                   *********************************************99********************************** PP

                 DNA_topoisoIV 393 veklekeieelekeikelekllak...lkklikeel 425
                                   ++k+e+e+ el k i++l++++++     ++ikeel
  gi|91772466|ref|YP_565158.1| 458 RQKIEDEHGELVKLIEDLKDIIESderKYSIIKEEL 493
                                   **********************99776666666665 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 !   47.5   0.1   1.5e-16   9.2e-13       3      46 ..     527     570 ..     525     572 .. 0.94
   2 !   23.8   0.0   3.7e-09   2.2e-05       1      47 [.     575     624 ..     575     625 .. 0.96
   3 !   35.2   0.0   1.1e-12   6.4e-09       2      47 ..     632     675 ..     631     676 .. 0.95
   4 !   46.0   0.2   4.3e-16   2.6e-12       2      48 .]     680     726 ..     679     726 .. 0.97
   5 !   41.0   0.7   1.6e-14   9.3e-11       2      38 ..     730     768 ..     729     777 .. 0.87
   6 !   54.7   0.5   8.2e-19   4.9e-15       1      47 [.     780     826 ..     780     827 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.5e-16
                                   EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                 DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                   +++iT+ Gy+kr+p++++++q+Rg+kGv+g+ +ke d + ++++
  gi|91772466|ref|YP_565158.1| 527 IVTITNSGYIKRMPVDTYSQQHRGGKGVIGMETKEQDVVEDIFI 570
                                   89***********************************9998887 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.7e-09
                                   SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEEEE CS
                 DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvlvv 47 
                                   d+l+++T++G+v + +++ lpe +R +kG+ ++   +l e++++++ + v
  gi|91772466|ref|YP_565158.1| 575 DYLMFFTNRGKVHWKKVYGLPEGSRQSKGKAVVnllDLAENESVTATITV 624
                                   8*******************************************998876 PP

  == domain 3  score: 35.2 bits;  conditional E-value: 1.1e-12
                                   EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                 DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                    l+++T+ G vk++pls++++ +++  G+++ kl+egd+lv+v+++
  gi|91772466|ref|YP_565158.1| 632 FLFMATRMGTVKKTPLSDFSNVRKA--GIIALKLDEGDELVNVALT 675
                                   599********************99..****************987 PP

  == domain 4  score: 46.0 bits;  conditional E-value: 4.3e-16
                                   EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                 DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                   e+++++++G+++rf + +++++gR+a+Gv+g++l+ +d +vs+ +v+
  gi|91772466|ref|YP_565158.1| 680 EIMMVSRHGKAIRFCERDVRPMGRTARGVRGMRLTGDDIVVSLDIVD 726
                                   89*****************************************9985 PP

  == domain 5  score: 41.0 bits;  conditional E-value: 1.6e-14
                                   EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS..ETTTT CS
                 DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgi..klkeg 38 
                                   +ll+iT+nGy+kr+  +e++ ++Rg++Gv+ i   l++g
  gi|91772466|ref|YP_565158.1| 730 KLLTITENGYGKRTTFDEYRGMKRGGQGVITIvtSLRNG 768
                                   69******************************6666554 PP

  == domain 6  score: 54.7 bits;  conditional E-value: 8.2e-19
                                   SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                 DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                   de+++ +s G  +r+p+ ++++qgR+++Gvk+++ ++gdk+v+v+ +
  gi|91772466|ref|YP_565158.1| 780 DEVMVTSSEGIFIRIPVKDIRAQGRNTQGVKIMNVRPGDKVVGVARI 826
                                   89******************************************987 PP

>> ANTAR  ANTAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1       2.5   1.5e+04      21      33 ..      74      86 ..      74      86 .. 0.90
   2 ?   12.2   0.1     2e-05      0.12      10      35 ..     421     446 ..     417     448 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.5
                                  HHHHT--HHHHHH CS
                         ANTAR 21 meryglsedeAfr 33
                                  m+  g++ d A++
  gi|91772466|ref|YP_565158.1| 74 MKEAGMTYDKAYK 86
                                  8999******995 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHHHHHT--HHHHHHHH CS
                         ANTAR  10 RklieqAkgiLmeryglsedeAfrlL 35 
                                    ++++ Ak  Lm+r gl+e +A + L
  gi|91772466|ref|YP_565158.1| 421 SNAVDEAKEGLMTRFGLDEVQAKAIL 446
                                   589******************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (830 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 5020.36
//
Query:       gi|91772467|ref|YP_565159.1|  [L=298]
Description: pyridoxal biosynthesis lyase PdxS [Methanococcoides burtonii DSM 6242]
Scores for complete 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-103  343.9   8.9   5.2e-103  343.2   8.9    1.3  1  SOR_SNZ       SOR/SNZ family
    3.3e-10   39.7   6.3    9.5e-08   31.6   1.6    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
    0.00013   21.2   2.6     0.0026   17.0   0.1    2.6  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0013   18.2   0.5     0.0013   18.2   0.5    2.1  2  NMO           Nitronate monooxygenase
     0.0039   17.2   0.0       0.04   14.0   0.0    2.3  2  TetR_C_27     Tetracyclin repressor-like, C-terminal domain
     0.0055   16.2   0.6      0.024   14.1   0.1    2.1  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.01   15.5   0.3        2.3    7.7   0.0    2.4  2  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
      0.021   14.0   0.1       0.17   11.0   0.0    2.1  2  IGPS          Indole-3-glycerol phosphate synthase
      0.031   13.6   2.1       0.76    9.1   0.2    2.4  2  TMP-TENI      Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.2   8.9  2.6e-106  5.2e-103       3     207 .]      12     216 ..      10     216 .. 0.99

  Alignments for each domain:
  == domain 1  score: 343.2 bits;  conditional E-value: 2.6e-106
                                   HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HH CS
                       SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfv 83 
                                    +k+g+a+m+kgGvimdv+++e+akiaeeaGavavmal+ vp+dirkeggvarm+dp++  +i+++v+ipvmak+riGhfv
  gi|91772467|ref|YP_565159.1|  12 LIKRGFAKMQKGGVIMDVTTPEEAKIAEEAGAVAVMALHAVPSDIRKEGGVARMADPQVTADIIASVTIPVMAKARIGHFV 92 
                                   68******************************************************************************* PP

                                   HHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHHHH CS
                       SOR_SNZ  84 eaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrkike 164
                                   ea+il+alg d+iDesevltpadee+hidk++f+vpfvcGarnlgealrri+eGaamirtkGeagtGdv eavrh+++i  
  gi|91772467|ref|YP_565159.1|  93 EAEILQALGSDMIDESEVLTPADEEFHIDKTQFTVPFVCGARNLGEALRRINEGAAMIRTKGEAGTGDVREAVRHMKQILG 173
                                   ********************************************************************************* PP

                                   HHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                       SOR_SNZ 165 eirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                   eir+lk +++eel+ +a++++ap+elv e+ae++rlpvvnfaa
  gi|91772467|ref|YP_565159.1| 174 EIRTLKGMTKEELIMAARDIEAPIELVMETAEMQRLPVVNFAA 216
                                   *****************************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00013      0.26     118     201 ..      11     105 ..       2     144 .. 0.74
   2 !   31.6   1.6   4.8e-11   9.5e-08     164     225 ..     196     260 ..     174     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                   HHHHTT-EEEEE..E-S-...HHHHHHHHHTT-SEBEEBSS...STTS----S...-HHHHHHHHHH-SS-BEEES---SH CS
                          ThiG 118 iLvkeGFevlpY..vsdD...lvlarrleevGcaavmPlaa...piGsglGll...nkealkiiieeakvPvivDAGigsp 187
                                    L+k GF+ +    v  D   +  a+  ee+G+ avm l a    i    G++   ++++   ii+++++Pv+  A ig+ 
  gi|91772467|ref|YP_565159.1|  11 ELIKRGFAKMQKggVIMDvttPEEAKIAEEAGAVAVMALHAvpsDIRKEGGVArmaDPQVTADIIASVTIPVMAKARIGHF 91 
                                   56666666664322333411134588899********9975222577777765111567778899***************9 PP

                                   HHHHHHHHTT-SEE CS
                          ThiG 188 sdaaqamelGadav 201
                                    +a     lG d +
  gi|91772467|ref|YP_565159.1|  92 VEAEILQALGSDMI 105
                                   99999888898865 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 4.8e-11
                                   HHHHHHHHHH-.SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                          ThiG 164 kealkiiieea.kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                   +  l + ++e+ ++Pv+  A  Gi +p daa  m lGad+v++ + + +a+ p  mA+a+  av+
  gi|91772467|ref|YP_565159.1| 196 PIELVMETAEMqRLPVVNFAagGIATPADAALMMRLGADGVFVGSGIFKAEKPEVMAKAIVEAVN 260
                                   44444444455589999654459****************************************97 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 ?    3.4   0.1     0.018        37     153     171 ..      29      47 ..      10      65 .. 0.75
   2 !   17.0   0.1   1.3e-06    0.0026     119     191 ..     177     260 ..     140     261 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.018
                                   --SHHHHHHHHTT--SEEE CS
                          NanE 153 intPekakkaieiGvdavv 171
                                   + tPe+ak a e G++av+
  gi|91772467|ref|YP_565159.1|  29 VTTPEEAKIAEEAGAVAVM 47 
                                   5688888888888888886 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-06
                                   TTTTSSTTS-..SS--....HHHHHHHHH.TT--..EEEES---SHHHHHHHHTT--SEEEE-HHHH-...HHHHHHHHHH CS
                          NanE 119 tlsGytkeeek.aepD....falvkalse.aglk..viaeGrintPekakkaieiGvdavvvGsaitr...leeiakkfve 188
                                   tl G tkee   a  D    ++lv +  e + l     a G i tP+ a+ ++++G+d v vGs i +   +e +ak  ve
  gi|91772467|ref|YP_565159.1| 177 TLKGMTKEELImAARDieapIELVMETAEmQRLPvvNFAAGGIATPADAALMMRLGADGVFVGSGIFKaekPEVMAKAIVE 257
                                   6777777665444444111144554433313344224699*************************9751115566777777 PP

                                   HT- CS
                          NanE 189 aik 191
                                   a++
  gi|91772467|ref|YP_565159.1| 258 AVN 260
                                   765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.9      0.24   4.8e+02     139     198 ..      25      84 ..      17      99 .. 0.63
   2 !   18.2   0.5   6.6e-07    0.0013     182     229 ..     197     246 ..     179     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                           NMO 139 liptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                                   +i+ +++ +ea+++e++Ga a+ +        + +  v+     ++ + +   v iPv+A
  gi|91772467|ref|YP_565159.1|  25 VIMDVTTPEEAKIAEEAGAVAVMALHAVPSDIRKEGGVARMADPQVTADIIASVTIPVMA 84 
                                   566788889999999999777665332222222111222233445666666666677776 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6.6e-07
                           NMO 182 faLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltk 229
                                   ++Lv + ++   +Pv+  AaGGi +  + a +++lGA gv +g+    ++
  gi|91772467|ref|YP_565159.1| 197 IELVMETAEMQRLPVVnfAAGGIATPADAALMMRLGADGVFVGSGIFKAE 246
                                   5677777777779**877*************************9877665 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 ?   -0.1   0.0      0.47   9.3e+02      66      97 ..      64      95 ..      59     101 .. 0.76
   2 !   14.0   0.0     2e-05      0.04      61      95 ..     239     273 ..     230     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.47
                                  TT--HHHHHHHHHHHSGGGTSHHHHHHHGGG- CS
                     TetR_C_27 66 kaadpeaaaravfdatarfhhPalaaewsdpe 97
                                  + adp+++a  ++ +t  ++  a + +  + e
  gi|91772467|ref|YP_565159.1| 64 RMADPQVTADIIASVTIPVMAKARIGHFVEAE 95
                                  56899999999999998888877776666555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2e-05
                                   HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGG CS
                     TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaewsd 95 
                                    +G Fka+ pe++a+a+++a++++ +P ++ae s+
  gi|91772467|ref|YP_565159.1| 239 GSGIFKAEKPEVMAKAIVEAVNNYNNPEVLAEVSK 273
                                   689***************************99875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.25     5e+02     163     197 ..      50      85 ..      13     105 .. 0.63
   2 !   14.1   0.1   1.2e-05     0.024      57     115 ..     192     254 ..     185     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.25
                                   EEEEEETTTTT.TSS---HHHHHHHHHHHSSEEEEE CS
                  His_biosynth 163 eilltdidrdG.tlsGpdleltkelaeavkipvias 197
                                   + +  di ++G +    d ++t ++ ++v+ipv+a 
  gi|91772467|ref|YP_565159.1|  50 HAVPSDIRKEGgVARMADPQVTADIIASVTIPVMAK 85 
                                   345567777651444456778999999999999885 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                                   THHHHHHHHHHHHHH-SSEE..EEESSSSSHHHHHHHHHCT-SEEEESHHHH..H-THHHHHH CS
                  His_biosynth  57 greanldlveeiaeevfipv..qvGGGIrsledveelleagadkviigtaav..knpelikel 115
                                     ea ++lv e+ae  ++pv     GGI +  d++ ++++gad v +g+  +  ++pe++ ++
  gi|91772467|ref|YP_565159.1| 192 DIEAPIELVMETAEMQRLPVvnFAAGGIATPADAALMMRLGADGVFVGSGIFkaEKPEVMAKA 254
                                   5566789999999999988833589************************96622567775544 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 ?    6.1   0.2    0.0037       7.4      81     157 ..     141     216 ..     134     227 .. 0.85
   2 ?    7.7   0.0    0.0012       2.3     194     224 ..     224     254 ..     215     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0037
                                   HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTTESEEEC CS
                     OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkaedfvmGfva 157
                                    ri e+a ++   + aG++ v+++++ +++     +  l  m+ ++  m +++ ++  ++v + +e+++   v+ f a
  gi|91772467|ref|YP_565159.1| 141 RRINEGAAMIRTKGEAGTGDVREAVRHMKQIL-GEIRTLKGMTKEELIMAARDiEAPIELVMETAEMQRL-PVVNFAA 216
                                   699****************************9.79999************99779999999999999954.4444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                                   HHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                     OMPdecase 194 pekligiagadiiivGRgIlkagdpveeaer 224
                                     +l+ + gad + vG gI+ka++p+  a++
  gi|91772467|ref|YP_565159.1| 224 DAALMMRLGADGVFVGSGIFKAEKPEVMAKA 254
                                   556777789****************999987 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.16   3.2e+02      61      86 ..      22      47 ..      16      53 .. 0.86
   2 ?   11.0   0.0   8.6e-05      0.17     203     251 ..     204     252 ..     189     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.16
                                  TEESBSS--HHHHHHHHTTT.-SEEE CS
                          IGPS 61 kgliredfdpaeiAkkyeeagAsaiS 86
                                  kg + +d+  +e Ak  eeagA a+ 
  gi|91772467|ref|YP_565159.1| 22 KGGVIMDVTTPEEAKIAEEAGAVAVM 47
                                  7889999999999******9999875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.6e-05
                                   CHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHH CS
                          IGPS 203 aklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekai 251
                                   a++ +  v+  a  Gi+t++d+  + + g++++ vG+ + ++e+ e + 
  gi|91772467|ref|YP_565159.1| 204 AEMQRLPVVNFAAGGIATPADAALMMRLGADGVFVGSGIFKAEKPEVMA 252
                                   5555556888899***************************999877655 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.015        30     103     156 ..      29      85 ..      23     100 .. 0.85
   2 ?    9.1   0.2   0.00038      0.76     139     181 .]     197     242 ..     181     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.015
                      TMP-TENI 103 vhsleeaeeaealgadYigvGpifpTdtKkda...eplgleglkelaealeiPvvai 156
                                   v ++eea+ ae++ga  +++ +  p+d +k+    ++++ +  +++ ++++iPv+a 
  gi|91772467|ref|YP_565159.1|  29 VTTPEEAKIAEEAGAVAVMALHAVPSDIRKEGgvaRMADPQVTADIIASVTIPVMAK 85 
                                   56899**********999999999**9999875557778889999999999***995 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00038
                      TMP-TENI 139 leglkelaealeiPvv..aiGGi.tlenvaevleagadgvavvsai 181
                                   +e++ e+ae+ ++Pvv  a GGi t++++a +++ gadgv v s+i
  gi|91772467|ref|YP_565159.1| 197 IELVMETAEMQRLPVVnfAAGGIaTPADAALMMRLGADGVFVGSGI 242
                                   677888888888888544999*967899**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2100.83
//
Query:       gi|91772468|ref|YP_565160.1|  [L=198]
Description: glutamine amidotransferase subunit PdxT [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-55  186.7   0.1    4.2e-55  186.5   0.1    1.0  1  SNO            SNO glutamine amidotransferase family
    4.3e-10   39.5   0.0    7.2e-10   38.8   0.0    1.3  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    7.8e-10   38.8   0.0    1.2e-09   38.3   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    3.6e-06   26.8   0.0    4.8e-06   26.4   0.0    1.2  1  Peptidase_S51  Peptidase family S51
      0.003   17.3   0.3      0.063   13.0   0.3    2.5  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.019   14.8   0.1    1.4  1  DJ-1_PfpI      DJ-1/PfpI family


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 !  186.5   0.1   1.4e-58   4.2e-55       1     186 [.       5     196 ..       5     198 .] 0.92

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 1.4e-58
                                   EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEET CS
                           SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtC 75 
                                   v+a+qG+v ehve ++++lae        ++k+k  +  +d+l+ PGGest++++li r g+  ++++  +++  +++GtC
  gi|91772468|ref|YP_565160.1|   5 VIAIQGDVSEHVESLERALAERgataeiVNIKHKGIVPTCDGLVFPGGESTTLGRLILREGIDAEIKDAKEQG-IPIMGTC 84 
                                   89*******************999999999*******************************777776666665.******* PP

                                   HHHHHHCC....EETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTT CS
                           SNO  76 aGlillsk....elenelvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeldg 152
                                   aGlil +k    ++e+ + + l+l+++kv+rnafGrq +sfe  l+++ l+ +++avfiraP i e++  e vkvl   dg
  gi|91772468|ref|YP_565160.1|  85 AGLILTAKagdsQVEKTHQHLLGLMDIKVNRNAFGRQFQSFEVGLEISFLDSPYNAVFIRAPAITEAG--EGVKVLASIDG 163
                                   ******9833334555567779**********************************************..99********* PP

                                   EEEEEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
                           SNO 153 eivvakqkkilatsfhPelaeddirvhdyfveev 186
                                   +iv+a+q+++la +fhPel++d +rvh+yf++++
  gi|91772468|ref|YP_565160.1| 164 KIVAAEQDNVLAFAFHPELTDD-MRVHQYFLDKL 196
                                   ********************98.*******9875 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 !   38.8   0.0   2.4e-13   7.2e-10      19     119 ..      23     117 ..      13     141 .. 0.80
   2 ?   -3.5   0.0       2.1   6.3e+03     169     187 ..     160     178 ..     144     180 .. 0.49

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.4e-13
                      GATase_3  19 LeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegve 99 
                                   L++++    ++v++k++ + + +d +++pGg++t+    +lre g+d +ik+a e+g+p++g C+Gl+ L  +  d++ v 
  gi|91772468|ref|YP_565160.1|  23 LAERG-ATAEIVNIKHKGIVPTCDGLVFPGGESTTLGRLILRE-GIDAEIKDAKEQGIPIMGTCAGLI-LTAKAGDSQ-V- 98 
                                   44444.4456777788888899********************9.**********************96.555556654.3. PP

                      GATase_3 100 geageveglglLdietefek 119
                                    e++    lgl+di+++ + 
  gi|91772468|ref|YP_565160.1|  99 -EKTHQHLLGLMDIKVNRNA 117
                                   .35578899*****998665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                      GATase_3 169 ekdGavkksedgnvlGtYl 187
                                   + dG +   e++nvl+  +
  gi|91772468|ref|YP_565160.1| 160 SIDGKIVAAEQDNVLAFAF 178
                                   3344444444555555444 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   3.9e-13   1.2e-09      10     186 ..      16     195 ..      11     198 .] 0.79

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 3.9e-13
                                   HHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHH CS
                        GATase  10 tenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQlla 85 
                                   +e+l++al+e+g++ e+v+i+++         ++dg++++gG  +       +eg  + ik a e++iPi+G C G+ l+a
  gi|91772468|ref|YP_565160.1|  16 VESLERALAERGATAEIVNIKHKGIVP-----TCDGLVFPGGESTTLgrlilREGIDAEIKDAKEQGIPIMGTCAGLILTA 91 
                                   689*****************9755555.....8*********99888899*88999999******************9999 PP

                                   HHTTTEEEEEECEEEEEEEEEEEETTT............CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                        GATase  86 iefgrkvvkekekehhggtmrlgddet............allyglknevierhrHryevnpkelepaglevtakseddeel 154
                                   ++   +v+k +  +h+ g m ++ +++             +++ l++++++ +    ++++     +g++v+a   d+ ++
  gi|91772468|ref|YP_565160.1|  92 KAGDSQVEKTH--QHLLGLMDIKVNRNafgrqfqsfevgLEISFLDSPYNAVFIRAPAITE---AGEGVKVLASI-DG-KI 165
                                   99999999877..788888999887778887776555553444444566666666666666...77889997777.66.57 PP

                                   EEEEEETTTEEEESSBTTSTTSTTHHHHHHHH CS
                        GATase 155 meiiekknpfvgvQFHPEststpegpellfnf 186
                                   +++ +++  + ++ FHPE t   + ++++ ++
  gi|91772468|ref|YP_565160.1| 166 VAAEQDN--VLAFAFHPELTDDMRVHQYFLDK 195
                                   7665544..8999******9888877776655 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.6e-09   4.8e-06      43     136 ..      10      97 ..       6     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.6e-09
                                   -S--HHHHHHHHHHHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEET CS
                 Peptidase_S51  43 gdddeyvekvrkaleklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvS 123
                                   gd+ e ve+ ++al++ g+  ++++++  ++  + +     d+++  GG+   L +l+ ++g+d+ +++a +qg++++G+ 
  gi|91772468|ref|YP_565160.1|  10 GDVSEHVESLERALAERGATAEIVNIK--HKGIVPT----CDGLVFPGGESTTLGRLILREGIDAEIKDAKEQGIPIMGTC 84 
                                   7889999*****************998..6777888....***************************************** PP

                                   HHHHTTSSB-GGG CS
                 Peptidase_S51 124 AGaivagesiett 136
                                   AG i +++ + ++
  gi|91772468|ref|YP_565160.1|  85 AGLILTAKAGDSQ 97 
                                   **99988877654 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.3   2.1e-05     0.063      98     216 .]      70     181 ..      13     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                 Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqai 178
                                   i+ a e+g+Pi+g+C Gl l + a   ++ +  ++  gl+d + +++ + ++  ++e g  + ++l  +  +   +   ai
  gi|91772468|ref|YP_565160.1|  70 IKDAKEQGIPIMGTCAGLILTAKAGDSQVEKTHQHLLGLMDIKVNRNAFGRQFQSFEVGLEI-SFLD-SPYNAVFIRAPAI 148
                                   68899************977754444444444445677888777765444444444433222.2222.2333344556788 PP

                 Peptidase_C26 179 kelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   +e +e+++v A   Dg i a e  +    vl+  +HPE
  gi|91772468|ref|YP_565160.1| 149 TEAGEGVKVLAS-IDGKIVAAEQDN----VLAFAFHPE 181
                                   999999888874.477777777666....788888887 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   6.4e-06     0.019      62     117 ..      44     100 ..      22     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.4e-06
                                   -SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSE CS
                     DJ-1_PfpI  62 yDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrr 117
                                    D lv pGG++    rl   e + + +k++ e+g ++   Cag +l a+ag  + ++
  gi|91772468|ref|YP_565160.1|  44 CDGLVFPGGESTTlGRLILREGIDAEIKDAKEQGIPIMGTCAGLILTAKAGDSQVEK 100
                                   79*******985336899999****************************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 1192.73
//
Query:       gi|91772469|ref|YP_565161.1|  [L=306]
Description: TM helix protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   90.4  27.1    5.7e-10   39.0   7.7    5.2  6  TM_helix         Conserved TM helix


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   5.3   4.8e-14   8.6e-10       5      49 ..      12      56 ..       9      57 .. 0.96
   2 ?   -0.5   1.2      0.07   1.3e+03       5      24 ..      76      95 ..      74      97 .. 0.85
   3 !   39.0   7.7   3.2e-14   5.7e-10       2      49 ..     102     149 ..     101     150 .. 0.97
   4 ?   -2.7   0.0      0.33   5.9e+03      37      48 ..     155     166 ..     153     167 .. 0.84
   5 ?   -3.8   2.0      0.75   1.3e+04      19      30 ..     171     182 ..     170     190 .. 0.69
   6 !   37.5   0.4   9.1e-14   1.6e-09       3      48 ..     196     241 ..     194     242 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.8e-14
                                  SXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                      TM_helix  5 nllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49
                                  ++++++++f+P Lv+ i + +vG++++k++ ++  k+l+k+g+dd
  gi|91772469|ref|YP_565161.1| 12 GMVDQFIAFIPILVAVIMLMIVGMFVGKILGKIGAKVLDKIGLDD 56
                                  79******************************************8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.07
                                  SXXHHHHTTHSHHHHHHHHH CS
                      TM_helix  5 nllnellsflPnLvgAilIL 24
                                  ++ ++++   + ++ A++I 
  gi|91772469|ref|YP_565161.1| 76 AMFGSIIKWFVYIIFAVIII 95
                                  68899999999999999996 PP

  == domain 3  score: 39.0 bits;  conditional E-value: 3.2e-14
                                   XXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                      TM_helix   2 plnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49 
                                    + n+l +++ flP ++ A++IL++G++i  f++  ++ +l ++gid+
  gi|91772469|ref|YP_565161.1| 102 IVANFLAQIILFLPLVISAAVILIIGLLIVDFLTGFIKTILIASGIDE 149
                                   689********************************************7 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.33
                                   HHHHHHHHHTS- CS
                      TM_helix  37 lvtkllaktgid 48 
                                   +++k l++++++
  gi|91772469|ref|YP_565161.1| 155 GIGKGLEAANLK 166
                                   7999****9986 PP

  == domain 5  score: -3.8 bits;  conditional E-value: 0.75
                                   HHHHHHHHHHHH CS
                      TM_helix  19 gAilILlvGwii 30 
                                   +A ++ + G++i
  gi|91772469|ref|YP_565161.1| 171 IAGIVKAFGYLI 182
                                   677777777776 PP

  == domain 6  score: 37.5 bits;  conditional E-value: 9.1e-14
                                   XXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS- CS
                      TM_helix   3 lnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgid 48 
                                   ++ +l+++l+++P L++ +lIL+vG+++  ++++ ++ +++ + ++
  gi|91772469|ref|YP_565161.1| 196 VSKFLTDILNYIPSLFAGVLILIVGLLVLDLLTDYLKGIMEGMEVE 241
                                   899**************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 1787.30
//
Query:       gi|91772470|ref|YP_565162.1|  [L=55]
Description: hypothetical protein Mbur_0424 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.1   0.0      0.096   12.0   0.0    1.0  1  CCB1      Cofactor assembly of complex C subunit B


Domain annotation for each model (and alignments):
>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.4e-06     0.096      64      97 ..      11      44 ..       5      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-06
                          CCB1 64 eketvtfeGlvapslflAifLtllaalgllclaL 97
                                  + +++t+ G+  p+++lA +L +++alg++  +L
  gi|91772470|ref|YP_565162.1| 11 KWQVITMLGIDDPQIWLAYILCIVSALGCMVYGL 44
                                  5689************************999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 325.97
//
Query:       gi|91772471|ref|YP_565163.1|  [L=530]
Description: Na+/solute symporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  208.7  43.3    1.6e-61  208.4  43.3    1.1  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
        4.2    7.8   5.5          2    8.8   0.2    3.4  3  ATP19     ATP synthase subunit K


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.4  43.3   1.8e-65   1.6e-61       1     406 []      36     454 ..      36     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 208.4 bits;  conditional E-value: 1.8e-65
                           SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvlle.lgalllvlllllllaerlr....nagalTlpdyls 76 
                                   y+lagr++ ++ l+ls +a  is a ++G  G+  + Gl++++l  +++ +++ +++++++ r r    n+ga+T+p+++ 
  gi|91772471|ref|YP_565163.1|  36 YMLAGRKVNPYILALSYGAAFISTAAIIGFGGVTGTLGLGTLWLVfMNIFVGIFIAFVVFGARTRriglNLGAVTFPELIG 116
                                   99***************************************99863788899999999999999999************** PP

                           SSF  77 kRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvg 157
                                    Rf+++ i+ y  al+ l ++ l+    l+gga+++e+al+++y++avl+l++++a Y+++GGllAv+ytd +q++lm vg
  gi|91772471|ref|YP_565163.1| 117 RRFQSRFIQGYSGALIAL-FMPLYAGIVLIGGARFMETALSIDYNIAVLILIVIVAAYVITGGLLAVMYTDALQGTLMFVG 196
                                   *******88887777665.5667777779**************************************************** PP

                           SSF 158 alilliivllevGgleslveklkeaapkv.vdl..........ltpdslkllrdpltalslwlglvlGvaglphilvRfla 227
                                    +ill+++ +++Gg+ ++ + l++ ap v   l          +   +  +    ++++   lg+++Gv  +p  +vRf++
  gi|91772471|ref|YP_565163.1| 197 MSILLVLTYTKLGGVVEAHQALTNLAPLVpESLaagghqgwtaMPVFGSPIWWTMVSTI--ILGVGIGVLAQPQLAVRFMT 275
                                   ***************************99544444443332221111112222222332..35888999999********* PP

                           SSF 228 akdakailkgvlkltivlilvligm.isiilfaiklagavpkavgt.evgvsniaypeLvvkllpnllaGlllavmlAaim 306
                                   ++++k++ ++v+ + ++++++   + i+ +l   ++++ v+ + +  + g+ ++++pe ++  +p+l+  +++   lAa m
  gi|91772471|ref|YP_565163.1| 276 VDSKKSLNRAVFAGGPFILMMAGVAyIVGGLSNVHFFNTVGMISIDvAKGNLDLIMPEYINSAMPELFVIFFMITLLAAAM 356
                                   *************99988776544326678999********66665156788***************************** PP

                           SSF 307 stltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavill 387
                                   stl+s++    +a+ +D+Y +++ k++a ++  v    iiv ++ s+  l+ + + +  ++   ++ f+  a+a+l++ + 
  gi|91772471|ref|YP_565163.1| 357 STLSSQFHTMGTAIGHDFYREFLMKGNAGNTVTVTKFGIIVTIIFSVI-LAYILPISI-IARATAIFFGLCAAAFLPMYIG 435
                                   *************************99998888888777777777764.556667777.99999999************** PP

                           SSF 388 alfwkrvneqGAlagliiG 406
                                   alfwkr++++GA+a+l++G
  gi|91772471|ref|YP_565163.1| 436 ALFWKRMTKEGAIASLVVG 454
                                   ****************998 PP

>> ATP19  ATP synthase subunit K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2   0.00023         2       4      21 ..      35      52 ..      33      71 .. 0.75
   2 ?   -2.6   0.0      0.81   7.2e+03      16      27 ..      71      82 ..      67      86 .. 0.78
   3 ?   -2.2   0.4      0.63   5.6e+03      19      35 ..     161     177 ..     160     178 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00023
                                  X---STTSS--S-SHHHH CS
                         ATP19  4 aYtIaGravkshyLAlgt 21
                                   Y +aGr+v++ +LAl+ 
  gi|91772471|ref|YP_565163.1| 35 DYMLAGRKVNPYILALSY 52
                                  69**************75 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.81
                                  -SHHHHHHHHH- CS
                         ATP19 16 yLAlgtLgttgl 27
                                   L lgtL ++++
  gi|91772471|ref|YP_565163.1| 71 TLGLGTLWLVFM 82
                                  578999998886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.63
                                   HHHHHHHH--XXXXXXX CS
                         ATP19  19 lgtLgttglivylamgg 35 
                                   +++L++++ ++++  +g
  gi|91772471|ref|YP_565163.1| 161 IAVLILIVIVAAYVITG 177
                                   56677766666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 3245.50
//
Query:       gi|91772472|ref|YP_565164.1|  [L=269]
Description: hypothetical protein Mbur_0426 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  133.4   0.0      1e-38  133.0   0.0    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 !  133.0   0.0   5.6e-43     1e-38       1     160 [.      77     252 ..      77     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 5.6e-43
                       DUF1638   1 fleaglHnrpeeLrealqeeidrakadydqIllgYGlCggalagl....rsdecpveilkg......ddCislllgseeay 71 
                                   +le +lH+ p++L+++++++++ + + +d+Ill+YGlCg+ l ++       +c++ ilk+      ddCi+++lg+++ay
  gi|91772472|ref|YP_565164.1|  77 ILEFALHAIPQNLKSEVYKAVEDMADFSDGILLFYGLCGNVLGKVeeelGDLDCRICILKEengeivDDCIGAVLGGRDAY 157
                                   5899*****************************************88888889**************************** PP

                       DUF1638  72 aeelkdekg..tffltpgwvkewdrlv.lekygeelarmifgk...llkgYkrlvyidtgltddpeleeraeefaarlgle 146
                                    e+lk+ kg  tffltp+w+++w +++   ++g++ ++ ++ k      gYk++++++tgl++++e+++ ++efa++++++
  gi|91772472|ref|YP_565164.1| 158 LEQLKSFKGvgTFFLTPMWAANWGDMLvAGGFGKDPTDVKTSKwvfDSIGYKKVAKLNTGLHYEKEFDNIVKEFANIFEFD 238
                                   **************************987777888888888887666689******************************* PP

                       DUF1638 147 levipgglgllekl 160
                                   +  i+g+l+l+e++
  gi|91772472|ref|YP_565164.1| 239 ILNIEGTLDLVERC 252
                                   ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1753.94
//
Query:       gi|91772473|ref|YP_565165.1|  [L=143]
Description: cytidyltransferase-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-21   75.6   0.0    5.1e-21   75.4   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.043   13.7   0.2       0.13   12.1   0.2    2.1  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   5.6e-25   5.1e-21       1     143 []       5     133 ..       5     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 5.6e-25
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
               CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                   la GtFD++H GH   l+qa++ ++e l+v+v+ d   k+k +p++++ +Rl+m+ ++  vd+++  ++ ++  e lk+++
  gi|91772473|ref|YP_565165.1|   5 LATGTFDLLHPGHVFFLRQARSFGDE-LYVLVARDSMIKHKAQPIVPEGQRLKMISAFGVVDKALLGSESDIF-EPLKEIN 83 
                                   689***********************.*************99*******************************.6****** PP

                                   TTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
               CTP_transf_like  82 pdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                   pd  ++v+g+d++ d   + ele+ lg++++  ++++       ++++ +++ +Ss +i++r
  gi|91772473|ref|YP_565165.1|  84 PD--IIVLGHDQFFD---TGELEKNLGERGFKAKVVR-------IDDAMKCELCSSGRIIKR 133
                                   **..**********9...59**************998.......99999999****999986 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.5e-05      0.13       8      38 ..       3      33 ..       1     115 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                       FAD_syn  8 avvtlGnFDGvHlGHqallkkaveaakekgl 38
                                   v++ G FD +H GH   l++a++  +e  +
  gi|91772473|ref|YP_565165.1|  3 RVLATGTFDLLHPGHVFFLRQARSFGDELYV 33
                                  58999*****************999877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1033.72
//
Query:       gi|91772474|ref|YP_565166.1|  [L=380]
Description: aspartate aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-68  230.5   0.0    3.8e-68  230.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.9e-05   23.5   0.0    4.5e-05   22.9   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00047   19.2   0.0    0.00086   18.4   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
     0.0025   16.4   0.0     0.0042   15.7   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.006   15.9   0.0      0.013   14.8   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.068   13.2   0.0    2.1  2  Rsbr_N           Rsbr N terminal


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.0   1.3e-71   3.8e-68       2     363 .]      30     375 ..      29     375 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 1.3e-71
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   d+i ++ +e+++     t++++ ka+++  ++ ++ + y p++g pel+ea+a  l++++kl+++ +  v+v++Ga+++i 
  gi|91772474|ref|YP_565166.1|  30 DIISFSLGEPDFN----TPDHICKAAAD--AMYRGDTHYAPSTGIPELREAIANKLQTENKLEVTSD-DVLVTPGAKQAIF 103
                                   7899*********....***********..999**********************************.************* PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    +++   l+  de +++dp++ sy+++++ +g+  v  p++  +d +    ++ee++++      ktk+i+v+sp NPtG 
  gi|91772474|ref|YP_565166.1| 104 EVMMSV-LDDNDEAILSDPSWVSYSPCIKFAGANPVWAPTD--PDNGFMPYGIEELITN------KTKLIVVNSPCNPTGG 175
                                   ******.********************************66..66678899********......**************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsql 243
                                   v++ e l++++dla  + ll+++De+Y++  +++ ++++    ++   + +++v+++sKa++++G+R+Gy+++ +++ +  
  gi|91772474|ref|YP_565166.1| 176 VFDNEMLKTVADLAVDHDLLVLSDEIYEKIIYDK-KHIS-MGSLDGMHErTITVNGFSKAYAMTGWRLGYVTAIPELMKGF 254
                                   ********************************95.5556.66677766679****************************** PP

                                   HHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH.CHHHHH CS
                 Aminotran_1_2 244 rklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae.takels 321
                                   +k++++  s  ++ +q   +aal+ +++    +++m +++++rr+ l ++L+ +g+k+  ++++++ + d+s+  + ++++
  gi|91772474|ref|YP_565166.1| 255 KKIHSHSVSsaTTFAQFGGVAALEGPQE---PVNDMLKEFKARRDILINGLNTIGIKCKRPDGAFYAFADVSEFgDGDAVA 332
                                   *********999***************7...8****************************************989999*** PP

                                   HHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                 Aminotran_1_2 322 kkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                   +kLl+  +v+vtpg+ f++  + ++Ri++ ++++e ++++++++
  gi|91772474|ref|YP_565166.1| 333 EKLLQDAHVAVTPGSAFGLsgKDFVRISY-ATSQERIKQALQRI 375
                                   *******************9999******.************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 !   22.9   0.0   1.5e-08   4.5e-05      60     144 ..     110     199 ..      80     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                                   TTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB---...HHHHHHHH CS
               DegT_DnrJ_EryC1  60 vgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhlyGqvad...mdalkaia 134
                                   ++++de I    ++v+   ++  +ga+pv +  dpd   + p  ie++it++tk I+   p +  G v+d   ++ + ++a
  gi|91772474|ref|YP_565166.1| 110 LDDNDEAILSDPSWVSYSPCIKFAGANPVWAPTDPDNGFM-PYGIEELITNKTKLIVvnsPCNPTGGVFDnemLKTVADLA 189
                                   4467*******************************99876.999************9444567788888644467788899 PP

                                   HHCT-EEEEE CS
               DegT_DnrJ_EryC1 135 akhglkvieD 144
                                    +h+l v++D
  gi|91772474|ref|YP_565166.1| 190 VDHDLLVLSD 199
                                   99*****998 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.9e-07   0.00086      47     173 ..      70     197 ..      55     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHHHHT-STG.....GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE CS
                   Aminotran_5  47 earekvaelinaese.....eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipld 122
                                   e re +a+ +++e++     +++++t G+ +ai  v++s+   l++ de+++++    +   p+ +     ga+ +++p d
  gi|91772474|ref|YP_565166.1|  70 ELREAIANKLQTENKlevtsDDVLVTPGAKQAIFEVMMSV---LDDNDEAILSDPSWVSYS-PCIKF---AGANPVWAPTD 143
                                   56666666666665311111789*****************...***********9999888.66555...59********* PP

                                   TTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHH...HHHHHTT-EEE CS
                   Aminotran_5 123 eegeldldelekllnektklvaithvsnvtGtiqpveeig...klakkkgalvl 173
                                   ++    +  +e+l+++ktkl+ ++   n tG +++ e ++   +la +++ lvl
  gi|91772474|ref|YP_565166.1| 144 PDNGFMPYGIEELITNKTKLIVVNSPCNPTGGVFDNEMLKtvaDLAVDHDLLVL 197
                                   ********************************9986655400044555555555 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   1.4e-06    0.0042      64     174 ..      85     200 ..      73     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-06
                                   HHT-.SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEE CS
               Cys_Met_Meta_PP  64 Legg.eaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvy 142
                                   Le + + +l+++    Ai+ +++++l   de ++sd  + + +  +k    + +   ++  +   +  +e+ i+++tkl+ 
  gi|91772474|ref|YP_565166.1|  85 LEVTsDDVLVTPGAKQAIFEVMMSVLDDNDEAILSDPSWVSYSPCIKFAGANpVWAPTDPDNGFMPYGIEELITNKTKLIV 165
                                   5555244555666678999999************999999888888887666466778888888999************** PP

                                   EESS-TTTT----...HHHHHHHHHHTT-EEEEEG CS
               Cys_Met_Meta_PP 143 lEtptnpllkvvD...iekiaklakkagvlvvvDn 174
                                   + +p np+  v D   ++++a+la ++++lv+ D 
  gi|91772474|ref|YP_565166.1| 166 VNSPCNPTGGVFDnemLKTVADLAVDHDLLVLSDE 200
                                   *************5555678888888888887775 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.3e-06     0.013      17     167 ..      50     199 ..      42     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
                                   HH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEE.......ES-HHHHHHHHH...HHH--TTEEEEEETT-HHHHSS CS
               Beta_elim_lyase  17 aq.aaamlGdesYgedktvnrLedavaelfgkeaalf.......vpqGtaAnsill...killqrgeevivtepahihfde 86 
                                   a   a+  Gd  Y+ ++++ +L +a+a+ + +e  l        v    +A +  +   + +l  ++e i+++p+ +    
  gi|91772474|ref|YP_565166.1|  50 AAaDAMYRGDTHYAPSTGIPELREAIANKLQTENKLEvtsddvlV--TPGAKQAIFevmMSVLDDNDEAILSDPSWVSYSP 128
                                   44367789********************99999998744455332..3345666554446667899999999999988877 PP

                                   TTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase  87 tgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                   +     +ag++++ ++++ ++ + +  +e++i++      k+kli++   +n   G v   e l+ va++a ++++ ++ D
  gi|91772474|ref|YP_565166.1| 129 C---IKFAGANPVWAPTDPDNGFMPYGIEELITN------KTKLIVVNSPCNP-TGGVFDNEMLKTVADLAVDHDLLVLSD 199
                                   6...66799999999999999999*********9......699*********6.7889******************99888 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.57   1.7e+03      78      97 ..      66      85 ..      61     115 .. 0.73
   2 ?   13.2   0.0   2.3e-05     0.068      10      78 ..     179     246 ..     176     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.57
                                  HHHHHHHHHHHHHHHH..T- CS
                        Rsbr_N 78 kgLqefrkvvlellseeddv 97
                                  +g+ e+r+++ ++l+ e+++
  gi|91772474|ref|YP_565166.1| 66 TGIPELREAIANKLQTENKL 85
                                  67778888888888777633 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHHHTTSSS-.--HHHHHHHHHHHHHHHHH-SS.-SSTTHHHHHHHHHHHHHTT--HHHHHH CS
                        Rsbr_N  10 kewlkelkelrkeeslqtisdevyektskefvdlilssveegneeleekleefaerlvqlGwpLkyltk 78 
                                   +e lk++++l+ +++l ++sde+yek+  +  ++ + s++ g +e + +++ f++    +Gw L y+t 
  gi|91772474|ref|YP_565166.1| 179 NEMLKTVADLAVDHDLLVLSDEIYEKIIYDKKHISMGSLD-GMHERTITVNGFSKAYAMTGWRLGYVTA 246
                                   567889999999999*************************.66667799******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2713.81
//
Query:       gi|91772475|ref|YP_565167.1|  [L=138]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-30  106.3   0.5    1.2e-30  106.1   0.5    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


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 !  106.1   0.5     7e-35   1.2e-30       2     138 ..       7     136 ..       6     138 .] 0.95

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 7e-35
                                   EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHH CS
                 DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyv 82 
                                   +r+++Vva+fn+++t ++    ++++k +g+  e ++++ VPG++++pla+kkl+   + +davi++G+vi+G+t+h+e+v
  gi|91772475|ref|YP_565167.1|   7 IRLGFVVAEFNRDLTYQMELMGIEHAKFLGA--EVTETILVPGVYDMPLAIKKLCLM-DDIDAVITIGIVIEGATKHDEIV 84 
                                   589***************************7..59********************95.447******************** PP

                                   HHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHH CS
                 DMRL_synthase  83 aeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaaleman 138
                                   +++++++++++sl++++Pv+ g+  +  t+ +a++r+     +++++a+eaa+++++
  gi|91772475|ref|YP_565167.1|  85 VQQAARKIIDLSLEYDKPVTLGIAGPGmTRMEAHQRV-----DYAKRAVEAAVKLVR 136
                                   ***************************9*********.....899999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 961.59
//
Query:       gi|91772476|ref|YP_565168.1|  [L=348]
Description: K+-dependent Na+/Ca+ exchanger related-protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  199.4  45.0    2.4e-30  105.5  19.7    2.0  2  Na_Ca_ex    Sodium/calcium exchanger protein
  ------ inclusion threshold ------
       0.26   10.1   5.6       0.57    8.9   5.6    1.5  1  DUF2254     Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5  19.7   2.7e-34   2.4e-30       3     149 ..       5     143 ..       3     144 .. 0.93
   2 !  100.1  17.3   1.2e-32   1.1e-28       4     149 ..     203     341 ..     200     343 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 2.7e-34
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHH CS
                      Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllvi 83 
                                   +++++++l+l++ ++d++vssa++iak+lg+s+ ++Gltl+A+g+s+pEl+ssi+a l+++  ++ign++Gsni+n+ l++
  gi|91772476|ref|YP_565168.1|   5 VFILLIGLILLVKGSDIFVSSASSIAKKLGVSEFIIGLTLVAIGTSIPELASSIAASLSHSSGIVIGNIVGSNIANIALIV 85 
                                   6899***************************************************************************** PP

                                   HHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  84 GlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                                   G++a+i+ +k +s  lk+d  ++l+++ l++l  +++        +l++ e+++l+l+Y++y++++
  gi|91772476|ref|YP_565168.1|  86 GCAAIISVVKTESDMLKRDGYIMLFASTLFFL--FAFD------LQLSRTEAFILVLFYIAYIFFL 143
                                   ******88999999999999888888877744..5555......9*******************97 PP

  == domain 2  score: 100.1 bits;  conditional E-value: 1.2e-32
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHH CS
                      Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviG 84 
                                   +++++s  +++++a+++v+ a  +a+ + ++++++G+tl+A+g+slpEl+++i+aa++g++++aignv+Gsni n++lv+G
  gi|91772476|ref|YP_565168.1| 203 LILAFSGTAVIFGAKYFVEEAIFFAQFFQLPDTLIGVTLVAIGTSLPELMVTISAARKGYGNIAIGNVIGSNITNIFLVLG 283
                                   78999999******************9****************************************************** PP

                                   HHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  85 lialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                                   l+a++ +l + ++s++l+++++++++++ll+++ +        +++ ++eg++l+llY+++l+l+
  gi|91772476|ref|YP_565168.1| 284 LSAFVFPLEITGLSIMLTIPFMIMISVVLLWFIHT-H------WEIRRVEGIALILLYVIFLLLL 341
                                   *******************9999999999775555.4......9******************986 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.6   6.4e-05      0.57      50     152 ..     234     326 ..     227     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 6.4e-05
                       DUF2254  50 stiagsmltvagfvfSitvvalqlassqfsPRllrnfmrdrvtqvvLGtfigtfvYsllvlrairteeevpqlsvlvalll 130
                                    t++g +l  +g+++  ++v+++ a + ++  ++ n++ +++t + L + +++fv+ l           + +ls+++++ +
  gi|91772476|ref|YP_565168.1| 234 DTLIGVTLVAIGTSLPELMVTISAARKGYGNIAIGNVIGSNITNIFLVLGLSAFVFPLE----------ITGLSIMLTIPF 304
                                   589999999*********************************************99873..........44699******* PP

                       DUF2254 131 aivsvllLiyFihhlarsiqvs 152
                                   +i++ ++L++Fih   ++ +v+
  gi|91772476|ref|YP_565168.1| 305 MIMISVVLLWFIHTHWEIRRVE 326
                                   *************877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2349.77
//
Query:       gi|91772477|ref|YP_565169.1|  [L=871]
Description: cation transporting P-type ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-51  173.2   0.2    3.6e-51  173.2   0.2    3.4  4  E1-E2_ATPase     E1-E2 ATPase
      1e-42  145.9   4.3      1e-42  145.9   4.3    2.3  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    6.6e-20   72.3   1.4    6.9e-19   69.0   1.4    2.4  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.9e-15   56.1   0.0    6.5e-15   55.0   0.0    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)
    4.9e-10   39.6   1.2    4.8e-05   23.2   1.2    2.4  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    1.8e-07   30.8   0.2    6.3e-07   29.0   0.0    2.1  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
     0.0011   19.4   0.0      0.011   16.1   0.0    2.3  2  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
        4.8    7.4   9.9       0.64   10.1   4.7    2.3  2  SPC12            Microsomal signal peptidase 12 kDa subunit (


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.86   1.9e+03     107     153 ..      23      67 ..      14      76 .. 0.71
   2 !  173.2   0.2   1.6e-54   3.6e-51       2     181 .]      96     286 ..      95     286 .. 0.98
   3 ?   -1.4   0.2      0.65   1.4e+03     143     169 ..     656     681 ..     628     691 .. 0.60
   4 ?   -1.9   5.5      0.92   2.1e+03      96     167 ..     778     849 ..     767     850 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.86
                                   ---HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHH CS
                  E1-E2_ATPase 107 kktplqkkldklgkvlvpvvlliallvflialllgkslaeallrala 153
                                   +++ l+k  +++ ++++++ ++ all ++  ll  ++ +  l+ a+a
  gi|91772477|ref|YP_565169.1|  23 SESALKKYFKQFHNFFSFLLIAGALLSYASELLDPGKGN--LYIAIA 67 
                                   567788888999999999999999998888877665544..333333 PP

  == domain 2  score: 173.2 bits;  conditional E-value: 1.6e-54
                                   SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-..........G-TTEE- CS
                  E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek..........ekgdmvf 71 
                                   l pp akv+rdg+++ei a elv+GD++++++gd+vpaDgr++e+++ +vd+s+LTGE++p  +          e ++mvf
  gi|91772477|ref|YP_565169.1|  96 LIPPVAKVLRDGEIKEILAPELVVGDVIFIEEGDKVPADGRLIEENTlKVDNSSLTGEAEPQLRslecthpnilECRNMVF 176
                                   789********************************************************************9999****** PP

                                   TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHH CS
                  E1-E2_ATPase  72 sGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallral 152
                                   sGt v+ g+ kavV+ tg++t++gk+a+l+e+++s +tpl k+l++++++++++++++++ +f i +++++     l++a+
  gi|91772477|ref|YP_565169.1| 177 SGTLVLTGNGKAVVYGTGQNTQMGKLATLTERTTSVETPLRKELNNFIRIISIIAIFLGISFFTIGFVTQDLFLLNLIFAI 257
                                   ******************************************************************99999999******* PP

                                   HHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                  E1-E2_ATPase 153 allvaaiPcaLplavplalalgarrlakk 181
                                   +++va +P++L  +v+l+l+l+ +r+ak+
  gi|91772477|ref|YP_565169.1| 258 GIIVANVPEGLLPTVTLSLSLASKRMAKR 286
                                   ***************************96 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.65
                                   STTHHHHHHHHHHHHHS-TTHHHHHHH CS
                  E1-E2_ATPase 143 slaeallralallvaaiPcaLplavpl 169
                                   ++   +l ++a+++ +iP  + + + l
  gi|91772477|ref|YP_565169.1| 656 NI-PEILPFIAFVLLSIPLPMNVQLIL 681
                                   22.456666666666666666555555 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.92
                                   TTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHH CS
                  E1-E2_ATPase  96 kiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplav 167
                                   +ia+l+ + ++ ++ l +++     +l +vv  +++l ++++    ++++ +   ++  +v a+P a+ l+v
  gi|91772477|ref|YP_565169.1| 778 QIANLLVSRTRIESALSRNMFTNKIILLAVVSELVILSMIMFHPFANKIFGTAPISMEYIVLAMPFAILLFV 849
                                   788888888888899999888877776666666666655555555555557777799999999999998876 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   0.2       1.6   3.5e+03     124     146 ..      60      82 ..      32      91 .. 0.69
   2 ?   -1.6   0.4      0.86   1.9e+03      54      74 ..     226     247 ..     208     279 .. 0.66
   3 !  145.9   4.3   4.6e-46     1e-42       1     181 [.     672     856 ..     672     857 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
               Cation_ATPase_C 124 snkllllaillslllqvlivyvp 146
                                    n ++ +a+++ ++l +++++++
  gi|91772477|ref|YP_565169.1|  60 GNLYIAIALFGVVILNATFTFIQ 82 
                                   57777777777777777777765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.86
               Cation_ATPase_C  54 i.liqgllqalvtllvffltll 74 
                                   i  i++++++++ +++ f+t+ 
  gi|91772477|ref|YP_565169.1| 226 IiSIIAIFLGISFFTIGFVTQD 247
                                   3244445555555544444444 PP

  == domain 3  score: 145.9 bits;  conditional E-value: 4.6e-46
               Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrri.liqgllqalvtllvffltlllfgise 80 
                                   plp+++ +iL i+L+tD+lpalaLa+e+ e dimkrpPr+k e l+++ +l+ + ++ g + al++++ +f++ll  g++ 
  gi|91772477|ref|YP_565169.1| 672 PLPMNVQLILAIDLGTDILPALALAVEKGEGDIMKRPPRSKYERLLTPQILLTSyGMKGPIEALAGFTCYFAVLLDGGWTW 752
                                   79****************************************************9********************888888 PP

               Cation_ATPase_C  81 kenkls....snyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtapl 157
                                    ++ ls    +++a  ++F +++++qi+n+l++r+r es+++ +++f+nk++lla++ +l+++ +i++ p+ n++fgtap+
  gi|91772477|ref|YP_565169.1| 753 GQALLSndllYRQAIMAFFAAVIVCQIANLLVSRTRIESALS-RNMFTNKIILLAVVSELVILSMIMFHPFANKIFGTAPI 832
                                   7766668899********************************.************************************** PP

               Cation_ATPase_C 158 sleewlialllalvvllvdelvKl 181
                                   s+e  ++a+++a+++++ de++K+
  gi|91772477|ref|YP_565169.1| 833 SMEYIVLAMPFAILLFVQDEIRKY 856
                                   ***********************8 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   1.4   3.1e-22   6.9e-19       2     210 .]     303     603 ..     302     603 .. 0.62

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 3.1e-22
                                   SEEEEESBTTTBCHHHHHHHHHHHH..............CHHHHHHHHHH...............HHCHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxx...............xxxxxxxxxxxxxxxx RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa..............alalaaaletg...............sehpigkalvaaakar 53 
                                   ++++ Dk+GTLt+ ++ ++  +                  ++       +                  p            
  gi|91772477|ref|YP_565169.1| 303 TVICTDKTGTLTQNKMAIHSMTLGFeqidvsngevppdiLMKV------AvlcnnsrlvegpsryKGDPTE---------- 367
                                   57999**********9999988777333444443333331111......1222122333334444444444.......... PP

                                   HHHHHHHHHETTTE..............................................HHHHTHHHHHHHHHCHHHHHH CS
                                   xxxxxxxxxxxxxx..............................................xxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  54 sgaltgfatfigrg..............................................ayaigkpewltaldippdlga 88 
                                                g                                               y++g  e +           
  gi|91772477|ref|YP_565169.1| 368 -------------GallmyaskftdidlmrenntrlkeysfdslkermqviyhtdpgeqeSYLKGATEVVI---------- 425
                                   .............3333333333333222222232222224444444444444444455555555555555.......... PP

                                   HHHHHHHHCHHHHHH...................................................TTHHHHHHHHH...H CS
                                   xxxxxxxxxxxxxxx...................................................xxxxxxxxxxx...x RF
                     Hydrolase  89 aigsaqsqgrtvall...................................................qaralavftia...d 115
                                                 +                                                          + +a   d
  gi|91772477|ref|YP_565169.1| 426 --------------KmcdhvlmngdevpiteddrnklldmhlkiagrgervlalayrraeeeieydT--GFTFIGFAgavD 490
                                   ..............35555555555555555555555566667777788888999999999887532..344444445569 PP

                                   THHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT...............GGGESEEEEHHCES........... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxx........... RF
                     Hydrolase 116 plkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG...............ddyfdaviasdiet........... 170
                                   p   +pe+++a+++ ++agi+vv++tgd+p ta ++a+++G                d           +           
  gi|91772477|ref|YP_565169.1| 491 P--HRPEVKDAIHKCHQAGIKVVMITGDHPVTALSIAKNVGfssngnepvmitgaeLD-----------Klsvdelskklk 558
                                   9..**************************************99877766555543312...........123223434455 PP

                                   .....STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 171 .....vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        +a  sp +k+++++ +q ++e v m GDgvnDa+a+++A+
  gi|91772477|ref|YP_565169.1| 559 apyiiFARTSPVQKLKIVQAFQSRGEIVTMTGDGVNDAPAIKNAD 603
                                   578888888*************88888****************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   2.9e-18   6.5e-15       2      91 .]     348     431 ..     347     431 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.9e-18
                 Cation_ATPase   2 lcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApe 82 
                                   lcN++++     ++   + G++tE ALl +a+k+  d++ +re++++++e+ F+s + rm v++ + + ++   y KGA e
  gi|91772477|ref|YP_565169.1| 348 LCNNSRL----VEGPSRYKGDPTEGALLMYASKF-TDIDLMRENNTRLKEYSFDSLKERMQVIYHT-DPGEQESYLKGATE 422
                                   8999999....6777889****************.9*****************************9.69999********* PP

                 Cation_ATPase  83 iilkrCthv 91 
                                   +++k C+hv
  gi|91772477|ref|YP_565169.1| 423 VVIKMCDHV 431
                                   *******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 !   13.9   0.0   1.5e-05     0.035      18      55 ..     494     531 ..     490     558 .. 0.87
   2 !   23.2   1.2   2.1e-08   4.8e-05     195     253 ..     575     633 ..     570     635 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                   Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                   ++ k+ai+k++++gikvv  TG +++++l++++++g++
  gi|91772477|ref|YP_565169.1| 494 PEVKDAIHKCHQAGIKVVMITGDHPVTALSIAKNVGFS 531
                                   6899******************************9976 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.1e-08
                                   HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHH CS
                   Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVak 253
                                   +++ ++   e v   GDg ND + ++ a++gvAmg++++ + + Ad++  + n   +++
  gi|91772477|ref|YP_565169.1| 575 IVQAFQSRGEIVTMTGDGVNDAPAIKNADMGVAMGSGTDVARESADMILLDDNFATIVN 633
                                   556667777778889*********************************99888766665 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 !   29.0   0.0   2.8e-10   6.3e-07      24      69 .]       4      49 ..       1      49 [. 0.95
   2 ?   -3.4   0.0       3.6   8.1e+03       3      14 ..     547     558 ..     546     559 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.8e-10
               Cation_ATPase_N 24 aeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                  + a erl+ +G+N++++   +s+++k++kqf n++  lL+++al+s
  gi|91772477|ref|YP_565169.1|  4 SGALERLEICGRNIFENIGSESALKKYFKQFHNFFSFLLIAGALLS 49
                                  6789****************************************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
               Cation_ATPase_N   3 alsleevlekLe 14 
                                   +ls++e+++kL+
  gi|91772477|ref|YP_565169.1| 547 KLSVDELSKKLK 558
                                   689*******97 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.39   8.7e+02     109     151 ..      91     135 ..      88     149 .. 0.81
   2 !   16.1   0.0   5.1e-06     0.011      78     186 ..     486     598 ..     434     600 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
                           HAD 109 gglrplvepllaelg...adevlatelevdd.rltgelglegkpvrg 151
                                   +++r+l+ p+++ l    ++e+la el v d  +  e  ++  p  g
  gi|91772477|ref|YP_565169.1|  91 ASFRQLIPPVAKVLRdgeIKEILAPELVVGDvIFIEE--GDKVPADG 135
                                   78999******988889***********999876666..66666555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.1e-06
                           HAD  78 aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg.......adevlatelevdd..rltgelglegkpv 149
                                   a ++ p  ++p+++++++++++aG++vv+++g +   +  +++++g       +  + + el++     l+++l+ +  + 
  gi|91772477|ref|YP_565169.1| 486 AGAVDP--HRPEVKDAIHKCHQAGIKVVMITGDHPVTALSIAKNVGfssngnePVMITGAELDKLSvdELSKKLKAPYIIF 564
                                   444555..469*******999*************************76666433333444444444666666655555555 PP

                           HAD 150 rgegkvaalrewl.aaegegidleevvayGDspsDlpl 186
                                   ++   v++l+    ++   +i    v   GD+++D p+
  gi|91772477|ref|YP_565169.1| 565 ARTSPVQKLKIVQaFQSRGEI----VTMTGDGVNDAPA 598
                                   554444444442203333333....7777999999887 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.7   0.00029      0.64      11      48 ..     225     262 ..     221     264 .. 0.89
   2 ?   -2.4   0.2       2.3   5.2e+03      16      37 ..     761     782 ..     755     785 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                         SPC12  11 kllqvilvlsaviafivGyitqdlkltlyillagvvlt 48 
                                   +++++i ++ ++  f +G++tqdl l+ +i+++g++++
  gi|91772477|ref|YP_565169.1| 225 RIISIIAIFLGISFFTIGFVTQDLFLLNLIFAIGIIVA 262
                                   5778888899999999******************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                         SPC12  16 ilvlsaviafivGyitqdlklt 37 
                                   +l+  a++af++  i+ ++ ++
  gi|91772477|ref|YP_565169.1| 761 LLYRQAIMAFFAAVIVCQIANL 782
                                   5666677777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (871 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 5793.03
//
Query:       gi|91772478|ref|YP_565170.1|  [L=156]
Description: hypothetical protein Mbur_0432 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.29   10.8   7.1       0.69    9.6   7.1    1.7  1  Archaeal_AmoA  Archaeal ammonia monooxygenase subunit A (AmoA


Domain annotation for each model (and alignments):
>> Archaeal_AmoA  Archaeal ammonia monooxygenase subunit A (AmoA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   7.1   3.9e-05      0.69       6     105 ..      15     125 ..      10     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 3.9e-05
                 Archaeal_AmoA   6 tlltinagdyifytdwawtsfvvfsisqslmlvvgaiyyllftgvpgtatyya...li...mtvyv......wvakgawfa 74 
                                    l  i  g y  yt  +  +  + s+  s ++ + +  +l ++gv gt+  +    li   +t+        +v   +w  
  gi|91772478|ref|YP_565170.1|  15 ILNGISRGLYAPYTGEIL-AHQISSVNFSAVIFIITYIFLKYSGVSGTSMQFIyvgLIwlcLTMSFeflfghFVIGHSWHR 94 
                                   566778888888888765.456788888888888888899********975541113322222211222222577789*** PP

                 Archaeal_AmoA  75 lgypydfivvpvwlpsamlldlaywatkrnk 105
                                   l y y+++   +wl   ++l  + w+ ++n 
  gi|91772478|ref|YP_565170.1|  95 LLYDYNIVEGRIWLLVLIVLATSPWTCQQNA 125
                                   *************************999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1015.32
//
Query:       gi|91772479|ref|YP_565171.1|  [L=601]
Description: hypothetical protein Mbur_0433 [Methanococcoides burtonii DSM 6242]
Scores for 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   56.4   1.4    1.3e-07   30.6   0.0    2.7  2  Glycogen_syn     Glycogen synthase
    1.4e-07   31.7   0.0    2.7e-07   30.7   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00046   19.8   0.1     0.0022   17.5   0.0    2.1  2  Glycos_transf_1  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.44   11.0   0.0    1.8  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.7   4.3e-09   1.9e-05     122     337 ..     170     406 ..      14     416 .. 0.69
   2 !   30.6   0.0   2.9e-11   1.3e-07     441     535 ..     454     549 ..     435     595 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.3e-09
                                   HHHHHHHHHHHHHHHCT--..................--EEEEEEETGGGHHHHHHHHHTT-..SEEEEEEESS-HHHHHH CS
                  Glycogen_syn 122 iilGflvalflkefrelee..................kkavvahfhewlaGvgliltrkrkl..dvatvftthatllGryl 182
                                   + l + +++f++ +++l e                   +++   +h    Gv   ++r +k+   + tv t hat+ Gr  
  gi|91772479|ref|YP_565171.1| 170 LNLSYAISEFVHTLVSLREetavayedklisefasslMPTLYVSLHCHEFGVFYAIARLKKIgvTINTVATYHATIPGRV- 249
                                   5555666666555555444455555555555555555444444455555677777777777611678************6. PP

                                   HHTT---TTSTTS--HHHHHHHTT-HHHHHHHHHHHHHSSEEEESSHHHHHHHHHHSS---SEE----B-GGGT--TTTHH CS
                  Glycogen_syn 183 cagavdfynnldkfdvdkeaGkrqiyhrycleraaahtadvfttvseitaleaehllkrkpdvvlpnGlnvkkfsalhefq 263
                                    ag + +       + d   G+        le  +   adv t+v + t  e + l+     +v+ nG+++   + + e+ 
  gi|91772479|ref|YP_565171.1| 250 -AGHLSIKK---IRENDSSLGNGTPKNMVTLESLS-SYADVVTAVGDSTKKEIK-LFYGIDSIVVRNGIDLE-IEDIDELL 323
                                   .66655543...23457777777777788888765.679***********9987.5556678999****985.899***** PP

                                   HHHHHHHHHHHHHHHHHTTT.-..--S-GGGEEEEEEESSS-TTTTTHHHHHHHHHHHHHHHHC---......T-EEEEEE CS
                  Glycogen_syn 264 nlhalkkekindfvrGhfyG.h..ldfdldktlyffiaGryefsnkGadifieslarlnyllkveks......kktvvafl 335
                                   + + + + ki+++   ++y  h  +++  +k + +f   r e +nkG   +++sl  l+ ++++e +      +  vv+f+
  gi|91772479|ref|YP_565171.1| 324 DKKFKCRTKIQELTASKLYNtHhsVELLPEKIIPIFSISRIEIENKGYPDLLDSLLLLDRMVRIEIKagrldkNYRVVCFI 404
                                   ***************998853412455569******************999*****9999999876555666577888888 PP

                                   E- CS
                  Glycogen_syn 336 il 337
                                   i 
  gi|91772479|ref|YP_565171.1| 405 IT 406
                                   86 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.9e-11
                                   SEEEEEE-S---TTSSSS---HHHHHHH-SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHHHH-T.TGGGGTEE CS
                  Glycogen_syn 441 rvkvvfhpeflsstspllgldyeefvrGchlGvfpsyyepwGytpaectvmGipsvttnlsGfGcfmeelie.dakdyGiy 520
                                    v  v++p++ls  +  + ++ +ef+ Gc  G+fps yep+  t  e      ps+ + + Gf   +           G+ 
  gi|91772479|ref|YP_565171.1| 454 YVSAVLYPQWLSDHDGGFNMNVDEFMAGCIAGIFPSRYEPFLLTGLEAGKEATPSIVSKVCGFSDALSTAKRlVMGMGGVL 534
                                   4889***********************************************************866554433133445566 PP

                                   EE--SSS-HHHHHHH CS
                  Glycogen_syn 521 ivdrrfkslddsveq 535
                                   +vd    +  +++ +
  gi|91772479|ref|YP_565171.1| 535 VVDNIDLAYLETIAD 549
                                   666655555555555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0     6e-11   2.7e-07      76     169 ..     214     315 ..     202     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 6e-11
                Glyco_transf_4  76 vHahspaalgaallalrr.rlgiplVltvHglye...........krllkarlkplsrllralerrllrradrviavSeat 144
                                   +H+h ++ + +a ++l++    i +V+t+H + +            r   + l+++++ +   ++ l + ad v+av ++t
  gi|91772479|ref|YP_565171.1| 214 LHCHEFGVF-YAIARLKKiGVTINTVATYHATIPgrvaghlsikkIRENDSSLGNGTPKNMVTLESLSSYADVVTAVGDST 293
                                   499997665.777777777999*************99999999764445566667788888889999************** PP

                Glyco_transf_4 145 adelrerygvppekitVipnGvDle 169
                                   ++e++  yg+++    V+ nG+Dle
  gi|91772479|ref|YP_565171.1| 294 KKEIKLFYGIDS---IVVRNGIDLE 315
                                   ***********7...8*******98 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.39   1.8e+03       7      42 ..     347     383 ..     343     401 .. 0.79
   2 !   17.5   0.0     5e-07    0.0022      82     143 ..     473     538 ..     469     552 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                                   HHTTTTTT-EEEEEESS-TTT.TTHHHHHHHHHCCCC CS
               Glycos_transf_1   7 kklgknekkkiilsvgrleke.Kgvdllikafallkk 42 
                                     + ++ek   i+s++r+e e Kg+  l++++ ll +
  gi|91772479|ref|YP_565171.1| 347 SVELLPEKIIPIFSISRIEIEnKGYPDLLDSLLLLDR 383
                                   55667778888999****9988999999998877754 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5e-07
                                   HSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......SEEEE-TT CS
               Glycos_transf_1  82 sredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......tGllvkpn 143
                                   +  +++e++  + + ++ps++E+f ++ lEA +  +p i+s+++g+++ +  ++       G+lv  n
  gi|91772479|ref|YP_565171.1| 473 M--NVDEFMAGCIAGIFPSRYEPFLLTGLEAGKEATPSIVSKVCGFSDALSTAKrlvmgmGGVLVVDN 538
                                   4..799*****************************************999888866666666666655 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 ?   11.0   0.0   9.8e-05      0.44      65     116 ..     474     535 ..     450     552 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.8e-05
                                   HHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--........TTSSEE- CS
               Glyco_trans_1_4  65 dlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv........gengllv 116
                                   +++e++a +   ++Ps  e f l+ lEa   ++p ++++v g+++++        g  g+lv
  gi|91772479|ref|YP_565171.1| 474 NVDEFMAGCIAGIFPSryEPFLLTGLEAGKEATPSIVSKVCGFSDALstakrlvmGMGGVLV 535
                                   68999***********999*********************9999866433222244555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 3442.59
//
Query:       gi|91772480|ref|YP_565172.1|  [L=329]
Description: sulfate adenylyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-15   55.6   0.0    2.2e-11   43.2   0.0    2.8  2  DUF4921          Domain of unknown function (DUF4921)
    2.1e-10   41.4   0.0    3.7e-09   37.3   0.0    2.1  1  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    5.3e-07   29.2   0.6    1.8e-06   27.4   0.0    2.1  2  DUF4931          Domain of unknown function (DUF4931)
    1.1e-05   25.8   0.4      7e-05   23.3   0.0    2.2  3  DcpS_C           Scavenger mRNA decapping enzyme C-term bindi
    1.3e-05   25.0   0.0    2.1e-05   24.3   0.0    1.4  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
    2.9e-05   24.7   0.0       0.13   13.0   0.0    2.3  2  HIT              HIT domain
     0.0065   17.0   0.4      0.014   16.0   0.4    1.5  1  PY_rept_46       Plasmodium yoelii repeat (PY_rept_46)
  ------ inclusion threshold ------
      0.082   13.4   0.0       0.16   12.5   0.0    1.4  1  DUF4406          Domain of unknown function (DUF4406)


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 !    8.6   0.0   0.00031       0.7      21     111 ..      18      97 ..      13     105 .. 0.77
   2 !   43.2   0.0   9.7e-15   2.2e-11     215     389 ..     140     316 ..     119     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00031
                       DUF4921  21 pgrgnrPlsekaeetapleeedreeacafcedrkletpPekarlvkeegdakilrgllaeeledtvaefrrvpnLfeivsy 101
                                   pgr++rP   kae++     e+ +++c fc+ +  +tp      v +  + +il++ +++++  t +++r++pnL+  ++ 
  gi|91772480|ref|YP_565172.1|  18 PGRSKRPSVFKAEKK-----EKDSNKCVFCAGEEDKTPLA--TAVYK--NGSILKDSESSRV--TGWDVRCMPNLYPALAP 87 
                                   888888877666543.....456789********999964..44664..4568888888777..78999*******99998 PP

                       DUF4921 102 dyWkknygfe 111
                                   d  + n ++e
  gi|91772480|ref|YP_565172.1|  88 DAGEVNSDHE 97 
                                   8888887776 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 9.7e-15
                       DUF4921 215 ykrnryvrYvavfqnWLkpaGasfdhlhkqlvaiDergvqaeaeiarlrenPnl.ynelavdyaakhnlviaendhavafa 294
                                   y++  +++Yv+ f+nW ++aGas++h h ql+a+  +     +e++ + +     y ++ v+  +k + ++ en+h +++a
  gi|91772480|ref|YP_565172.1| 140 YETFDKIEYVSLFKNWGEKAGASLEHTHSQLIAMPIKPPLLMEEMKIIGSFSICpYCDI-VEKESKGERLLYENEHFMVIA 219
                                   888899****************************9999888888888776554427776.777778888899********* PP

                       DUF4921 295 gfGhryp.tlevysksatkePweqseeevravsdlvhalhaaaga...dvpcneeWhhrpidvdvpmpwrilikwrvstla 371
                                    +  + p  l +  k + ++    ++++++++   + ++  +  +   ++p n  +++  +  +    + + ++  +++ a
  gi|91772480|ref|YP_565172.1| 220 PYCSKVPyELWILPKEHINHISGFDQDHLDSLGIAIRSALSCLRDnmgEIPYNYMFYQ--LRDEPEYHFNLKLQPVTTKTA 298
                                   ******9558999999999999999999999988777655444331115666654443..33344445555555667889* PP

                       DUF4921 372 GfeggtkiylntisPael 389
                                   Gfe +t++y+nt+ P++ 
  gi|91772480|ref|YP_565172.1| 299 GFEKNTEVYINTMPPETA 316
                                   **************9875 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 !   37.3   0.0   1.7e-12   3.7e-09      15     181 ..       5     174 ..       1     177 [. 0.72

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.7e-12
               GalP_UDP_transf  15 rfnpltgewvlvsphrtkrpwqgqqekiskdtlpekDklkcyLcPgnsra.............ngefnpky...kstfvft 79 
                                   r + +++e+ +++p r krp   + ek      +ekD+ kc++c+g++                ++++++     ++    
  gi|91772480|ref|YP_565172.1|   5 RKHYFLDEYCIIAPGRSKRPSVFKAEK------KEKDSNKCVFCAGEEDKtplatavykngsiLKDSESSRvtgWDVRCMP 79 
                                   666778888889999999988555554......466666677776666551111112221111111111111233455566 PP

               GalP_UDP_transf  80 ndFpalsedsnyikteaiaknilfkaepayGrceviifsskheltladlspkdikavvaaWqektaelkakeypkcvlifE 160
                                   n +pal +d+ +++          ++ p yG  evi+  + he  l+dls +++   ++ ++++    +  +++++v  f 
  gi|91772480|ref|YP_565172.1|  80 NLYPALAPDAGEVNS-------DHEVFPGYGFHEVIVETPTHENMLPDLSDEEMSLLMKVYRDRVIHYETFDKIEYVSLFK 153
                                   777777777777766.......346779***************************************999*********** PP

               GalP_UDP_transf 161 NkGaamgvsnphPHgqiwaee 181
                                   N G++ g+s+ h H+q+ a +
  gi|91772480|ref|YP_565172.1| 154 NWGEKAGASLEHTHSQLIAMP 174
                                   ****************87765 PP

>> DUF4931  Domain of unknown function (DUF4931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   8.1e-10   1.8e-06      53     121 ..     105     173 ..      99     178 .. 0.95
   2 ?   -1.9   0.1      0.75   1.7e+03      18      25 ..     191     198 ..     182     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 8.1e-10
                       DUF4931  53 qtvlietdeceedistyseehlrellrfgvkhwlelekseeyksvllfknhGPlsGGsikhahmqivGl 121
                                     v++et + e+ +++ s+e +  l++   ++ ++ e  ++ + v lfkn+G  +G s++h+h q++ +
  gi|91772480|ref|YP_565172.1| 105 HEVIVETPTHENMLPDLSDEEMSLLMKVYRDRVIHYETFDKIEYVSLFKNWGEKAGASLEHTHSQLIAM 173
                                   679***************************************************************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.75
                       DUF4931  18 tacPfcdr 25 
                                   + cP+cd 
  gi|91772480|ref|YP_565172.1| 191 SICPYCDI 198
                                   56777763 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 ?   -3.4   0.0       6.1   1.4e+04       1      20 [.      38      58 ..      38      65 .. 0.68
   2 ?   -0.1   0.1      0.55   1.2e+03      44     107 ..     114     178 ..      97     185 .. 0.61
   3 !   23.3   0.0   3.1e-08     7e-05       2      76 ..     193     268 ..     192     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.1
                                  T-HHHHHHTTSS-B-E.EEE- CS
                        DcpS_C  1 kwvfnilakgkeperv.vyed 20
                                  k+vf+  +++k p +  vy++
  gi|91772480|ref|YP_565172.1| 38 KCVFCAGEEDKTPLATaVYKN 58
                                  699999888888654436655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.55
                                   ---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T..-EEEEE--SCCCT--S-S--EEEEE...... CS
                        DcpS_C  44 dikslrdLtkehlpllkemrekakkvieekyne..vdaeelrvgvhyqPsvyhlHlHvisldfesp 107
                                   + + l dL++e+++ll +++++     e    +  + + + + g ++  s++h H  +i+   + p
  gi|91772480|ref|YP_565172.1| 114 HENMLPDLSDEEMSLLMKVYRDRVIHYETFD-KieYVSLFKNWGEKAGASLEHTHSQLIAMPIKPP 178
                                   5555666666666666666654333333222.1346666777788888888888877777666555 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 3.1e-08
                                   -HHHHHHTTSS.-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                        DcpS_C   2 wvfnilakgke.pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                   + +++++++++  er++ye+e+f+v+  +  k ++ l ++pk++i+++  ++++hl+ l    + a + +++++ e
  gi|91772480|ref|YP_565172.1| 193 CPYCDIVEKESkGERLLYENEHFMVIAPYCSKVPYELWILPKEHINHISGFDQDHLDSLGIAIRSALSCLRDNMGE 268
                                   6789999998878999*******************************************99999999999888865 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 !   24.3   0.0   9.5e-09   2.1e-05      26      94 ..     202     271 ..     149     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.5e-09
                                   HHH-TTEEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHH.HHHHHHHHHCTS-- CS
                 GalP_UDP_tr_C  26 laekervvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailk.klarkydnlfetsf 94 
                                     + er++ ++++f++++py  k P+e  +l+k+++++++ + + + + l  +++  l   +dn+ e   
  gi|91772480|ref|YP_565172.1| 202 ESKGERLLYENEHFMVIAPYCSKVPYELWILPKEHINHISGFDQDHLDSLGIAIRsALSCLRDNMGEIPY 271
                                   456799************************************9987777765554146667777766555 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     6e-05      0.13      20      90 ..      97     168 ..      90     173 .. 0.89
   2 !    9.5   0.0   0.00071       1.6       6      64 ..     206     264 ..     201     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                                   -SS-SSSSEEEEEESS.TGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EE CS
                           HIT  20 didpkapghlLvipkk.hlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHi 90 
                                   +++p +  h  ++    h + l dl++ee++ l+++ +  + + ++  k + + +++n g++ag s  h H 
  gi|91772480|ref|YP_565172.1|  97 EVFPGYGFHEVIVETPtHENMLPDLSDEEMSLLMKVYRDRVIHYETFDKIEYVSLFKNWGEKAGASLEHTHS 168
                                   67899999999999988999999**************999999998678999*******************6 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00071
                                   CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHT CS
                           HIT   6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqk 64 
                                   ++++ye+++++++    +k+p  l ++pk+h+++++ ++++ l  l  a++   + l++
  gi|91772480|ref|YP_565172.1| 206 ERLLYENEHFMVIAPYCSKVPYELWILPKEHINHISGFDQDHLDSLGIAIRSALSCLRD 264
                                   5789**********************************999888887777666665555 PP

>> PY_rept_46  Plasmodium yoelii repeat (PY_rept_46)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   6.1e-06     0.014       4      23 ..      20      39 ..      18      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-06
                    PY_rept_46  4 kSrFpsMFKrdKkDkDsdks 23
                                  +S+ ps FK +Kk kDs+k 
  gi|91772480|ref|YP_565172.1| 20 RSKRPSVFKAEKKEKDSNKC 39
                                  9*****************95 PP

>> DUF4406  Domain of unknown function (DUF4406)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05      0.16      51      88 ..     138     175 ..     116     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                       DUF4406  51 iclalllkcdaivmLpgweeSkGAtlElelakklglai 88 
                                   i ++  +k + + ++++w e +GA lE++  + + ++i
  gi|91772480|ref|YP_565172.1| 138 IHYETFDKIEYVSLFKNWGEKAGASLEHTHSQLIAMPI 175
                                   6778899999*******************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2249.10
//
Query:       gi|91772481|ref|YP_565173.1|  [L=389]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   94.3   0.0    1.6e-26   92.9   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    7.5e-27   94.4   0.1    1.2e-26   93.7   0.1    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    9.2e-25   87.6   0.0    1.5e-24   86.9   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.9e-18   65.6   0.0    9.7e-18   65.1   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    9.9e-15   54.9   1.2    1.6e-12   47.7   1.2    2.2  1  Glyco_transf_5   Starch synthase catalytic domain
    3.5e-09   36.8   0.0    7.2e-09   35.8   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0014   19.0   0.0     0.0031   17.9   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         1   2.6e+03      64      86 ..     161     183 ..     150     189 .. 0.62
   2 !   92.9   0.0   6.3e-30   1.6e-26      15     170 ..     214     363 ..     201     365 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                   HHHHHHCTTCGGGEEECCHSSSH CS
               Glycos_transf_1  64 klaeelelsdnviflgevsredl 86 
                                     + + +l d+++fl +++++++
  gi|91772481|ref|YP_565173.1| 161 VISTSQQLTDEIKFLYQIPDKKI 183
                                   44555566666666666665544 PP

  == domain 2  score: 92.9 bits;  conditional E-value: 6.3e-30
                                   -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESE CS
               Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadi 95 
                                    +++l++gr++++Kg+dll++a++++ +  + ++k+v++G+ge++   ++la + ++sdn++flg+v++e    +++++di
  gi|91772481|ref|YP_565173.1| 214 APVVLFIGRMSYQKGPDLLVEAIPEVIDH-RWDTKFVFIGEGEMRPPCEALANAEKISDNCHFLGYVDDETARDWINACDI 293
                                   689***********************887.*************************************************** PP

                                   EEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
               Glycos_transf_1  96 fvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                                   +++ps++E+fGiv+lE   a   ++a++a    +++++ ++G+lv +n + ++a +i+ +l+d  ++  ++++++
  gi|91772481|ref|YP_565173.1| 294 LCIPSRNEPFGIVVLEGWDAERTIVATDA---VQIINNFVDGILVYKN-PNSIAWGINYVLDDL-SNSSMRKAGK 363
                                   ****************************5...689***********99.*************96.7777777776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.1   4.8e-30   1.2e-26       1     166 [.      20     190 ..      20     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 4.8e-30
                Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaf.....lrrlrrllkre.kpDv 75 
                                   vGG++ hv eLa+aLa+ Gh V+++t++ + +++ e +++v  +rv + l+++  + + +     ++r+  + k++ k+D+
  gi|91772481|ref|YP_565173.1|  20 VGGIAPHVSELAEALAKTGHSVHIFTRNNGLEPYGE-VNGVHYHRVDHSLSGGIVQQMDSmcdsmYSRFLDVTKEYgKFDI 99 
                                   7***********************************.7778888888777777666554412222568888888889**** PP

                Glyco_transf_4  76 vHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl..lrradrviavSeatadelrerygv 154
                                   +Hah+++++  a+ +++ + gip+ +t+H+++ +++ ++ +++++ +++   r +     + +vi +S+++ de++ +y++
  gi|91772481|ref|YP_565173.1| 100 LHAHDWHPF-NAVSRIKYEFGIPFMFTYHSTE-WGRNGNIHGNWWEAEEISHREWkaGYESVKVISTSQQLTDEIKFLYQI 178
                                   ********8.555666668*************.56666655555555554444444378888******************* PP

                Glyco_transf_4 155 ppekitVipnGv 166
                                   p +ki +ipnG+
  gi|91772481|ref|YP_565173.1| 179 PDKKISIIPNGI 190
                                   ***********8 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0     6e-28   1.5e-24       2     134 .]     215     352 ..     214     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 6e-28
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---TH..HHHHHHH-SE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfved..laellaaadv 75 
                                   pv+lf+Gr+   +kg dll+ea+p++ ++  d ++v++G+g+ rp  +e+la+  +++++++f+G+v+d   +++++a+d+
  gi|91772481|ref|YP_565173.1| 215 PVVLFIGRM-SYQKGPDLLVEAIPEVIDHrwDTKFVFIGEGEmRP-PCEALANaeKISDNCHFLGYVDDetARDWINACDI 293
                                   89*******.667**********9999774559********9766.666555446999*********4456********** PP

                                   EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.T.TSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv.g.engllvppgdpealaeailrLled 134
                                   +++Ps  e fg+++lE   a++ +Vatd+    +++ + ++g+lv  ++p+++a  i  +l+d
  gi|91772481|ref|YP_565173.1| 294 LCIPSrnEPFGIVVLEGWDAERTIVATDAV---QIInNfVDGILVY-KNPNSIAWGINYVLDD 352
                                   *****999*******************994...45543489****5.68****9999999887 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 !   65.1   0.0   3.8e-21   9.7e-18       1     160 []      21     189 ..      21     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 3.8e-21
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladla.....alralrrllrqrrerpdv 76 
                                   gGi+ +v ela+aLa+ Gh+V+++t++   +++  e +gv++hr++ + +++ +  ++     ++ ++ ++   +  ++d+
  gi|91772481|ref|YP_565173.1|  21 GGIAPHVSELAEALAKTGHSVHIFTRNNGLEPY-GEVNGVHYHRVDHSLSGGIVQQMDsmcdsMYSRFLDVT-KEYGKFDI 99 
                                   8*************************8888877.8899******9866555545544411122558888887.89****** PP

               Glyco_trans_4_4  77 vhahsptaglaarlarrrrgiplvvtlhglllrrg.....sgavrrlyralerrllrradavlvvseaeaeelra.lgvpa 151
                                   +hah+++   a+ +++   gip+++t+h++++ r      + +++  +   e  +      v+++s+++ +e+   + +p+
  gi|91772481|ref|YP_565173.1| 100 LHAHDWHPFNAVSRIKYEFGIPFMFTYHSTEWGRNgnihgNWWEAEEISHREWKAGYESVKVISTSQQLTDEIKFlYQIPD 180
                                   ******87777777777***********977655513332334444444445566666888**************888*** PP

               Glyco_trans_4_4 152 drvvvvpng 160
                                    ++ ++png
  gi|91772481|ref|YP_565173.1| 181 KKISIIPNG 189
                                   ********8 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   1.2   6.1e-16   1.6e-12       1     219 [.       6     162 ..       6     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 6.1e-16
                Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkvaklkk 81 
                                   ki ++++E    +k+GG+a +v++L++aLak gh v++++ + g  +          e                       
  gi|91772481|ref|YP_565173.1|   6 KIGMFSWESLHSIKVGGIAPHVSELAEALAKTGHSVHIFTRNNGLEPY--------GE----------------------V 56 
                                   788*************************************77744333........23......................3 PP

                Glyco_transf_5  82 dgvdvyfldnpeffdreglYgdkgedyednaerfa..lfsraalelleklgw.kpdvihahDWhtalvpallkelykergl 159
                                   +gv+++ +d+       g+         ++ + +   ++sr  l++ ++  + k+d++hahDWh   +   +k        
  gi|91772481|ref|YP_565173.1|  57 NGVHYHRVDHSL---SGGIV--------QQMDSMCdsMYSRF-LDVTKE--YgKFDILHAHDWHPFNAVSRIKYEF----- 118
                                   5***********...23333........22222222244444.777777..437***********99977777653..... PP

                Glyco_transf_5 160 fkkiktvftiHNlayqgrfp..kdelaalglpaedfekldglefygkvnflk.agivyadavt 219
                                      i+++ft H++++ ++ +   ++ +a ++                    +  + +++ +v+
  gi|91772481|ref|YP_565173.1| 119 --GIPFMFTYHSTEWGRNGNihGNWWEAEEIS-----------------HREwKAGYESVKVI 162
                                   ..3*************9998443222333333.................22223334444444 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 !   35.8   0.0   2.8e-12   7.2e-09      11     109 ..      25     129 ..      19     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.8e-12
               Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg....pleyl...kafklkklikki.kPDvvhahya 83 
                                   +h+++la++Lak g+ Vh++t+++g + + e +g+h hr++ + +g    ++  +   ++ ++ ++ k+  k+D++hah  
  gi|91772481|ref|YP_565173.1|  25 PHVSELAEALAKTGHSVHIFTRNNGLEPYGEVNGVHYHRVDHSLSGgivqQMDSMcdsMYSRFLDVTKEYgKFDILHAHDW 105
                                   79**************************************98855553433333333145799999999648********9 PP

               Glyco_trans_4_2  84 kpygllgslaarlsgvipvvlsvwGl 109
                                    p + + ++   ++  ip+ ++ + +
  gi|91772481|ref|YP_565173.1| 106 HPFNAVSRIKYEFG--IPFMFTYHST 129
                                   99998888854555..8998888855 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.2e-06    0.0031       5      89 ..     297     378 ..     289     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
               Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                   psr+e +  +++E   + ++++++da ++ + f +g  ++++++++++a  i+y+l ++   +++++a++e +++++++ +
  gi|91772481|ref|YP_565173.1| 297 PSRNEPFGIVVLEGWDAERTIVATDAVQIINNFVDG--ILVYKNPNSIAWGINYVL-DDLSNSSMRKAGKELIETRYNWIN 374
                                   8999**********************8899999999..***************987.5666699***************99 PP

               Glyco_trans_1_2  86 raeq 89 
                                    ae+
  gi|91772481|ref|YP_565173.1| 375 IAEN 378
                                   9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 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:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2881.39
//
Query:       gi|91772482|ref|YP_565174.1|  [L=376]
Description: glycoside hydrolase family protein [Methanococcoides burtonii DSM 6242]
Scores for 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-42  143.3   1.5    9.9e-41  140.0   1.5    2.3  2  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   1.5   5.5e-45   9.9e-41      92     321 ..      54     281 ..       6     285 .. 0.89
   2 ?    0.4   0.0     0.016   2.9e+02     164     192 ..     294     322 ..     285     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 5.5e-45
                                   H......HHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHH CS
                Glyco_hydro_57  92 k......ldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkarelyee 166
                                   +      +d  + ++++isg +l q+ kw n+ v+e+f+el+++g   + +spyyH++ +l+pd +++++qv ++r+ ++e
  gi|91772482|ref|YP_565174.1|  54 NealldsIDNGAKYTFDISGIFLDQC-KW-NPAVIESFKELKDRGA-GFSASPYYHSISSLFPDTKEFKEQVSMHRDKIKE 131
                                   0444555777789***********99.99.9**************7.5********************************* PP

                                   HHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--CHH-TTTSGGG-... CS
                Glyco_hydro_57 167 yfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdreLsddigFrys... 244
                                   +f+++Pr+f ++El++++e+ +il+e+ f++l++++++++l +    +p+ +y   n+ i  ++R+  Ls+di+ r+s   
  gi|91772482|ref|YP_565174.1| 132 IFNVNPRTFINTELILTKELSAILKEMKFKCLISEGSENLLYGN---DPNQVYD--NH-IPTLLRHIPLSEDIEIRFSdqk 206
                                   ********************************************...******8..44.*******************888 PP

                                   .............TTSB..........-TT---TT.T-.-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHSS-EE CS
                Glyco_hydro_57 245 .eqypleavddfinwlkkvkkaksevvtialdgEn.wg.hypetgkkeFleklyeeleenglielvtpsefikklkpkgl 321
                                      ypl  +d+f+ w+ ++   +++v t++ ++   +  + + + +++Fl +l+ ++e+ g i ++tp+e++k +k+k+l
  gi|91772482|ref|YP_565174.1| 207 wISYPL-IADKFASWIANM---EGDVTTLHFKYSSiLShQHNRSDILQFLIDLPASFEKYG-ISMITPEEALKNFKTKEL 281
                                   766999.9*********99...*************8667777778888*************.**************9987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.016
                                   HHHHHSS--SBEE-GGG-B--SHHHHHHH CS
                Glyco_hydro_57 164 yeeyfgqePrgfwlpElavspeileilae 192
                                   +++++g +P+ ++l El+   eil++++ 
  gi|91772482|ref|YP_565174.1| 294 MHNLMGNHPQHLYLHELISIGEILQSIKS 322
                                   6899**************99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2548.52
//
Query:       gi|91772483|ref|YP_565175.1|  [L=400]
Description: Alpha-amylase [Methanococcoides burtonii DSM 6242]
Scores for 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-65  220.6   0.0      4e-65  220.1   0.0    1.1  1  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.1   0.0   2.2e-69     4e-65       3     323 ..       7     289 ..       5     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 220.1 bits;  conditional E-value: 2.2e-69
                                   EEEE-----TTS-SSSSSHHHHHHH.HHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHHHHHHH CS
                Glyco_hydro_57   3 vfhqHqplykkpgkgeytlpwvreh.aaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateellelie 82 
                                   +f+ Hqp++ k         w +   + e+Y+++a +  +f+kv+                     k+ylpat++l el  
  gi|91772483|ref|YP_565175.1|   7 YFQLHQPYRLKWF-------WPDDSkGFERYFDVAINRSIFEKVA--------------------RKCYLPATTLLAELV- 59 
                                   7889999998777.......8876449******************....................**************8. PP

                                   HHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHH CS
                Glyco_hydro_57  83 eglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkarel 163
                                      ++ +++k      f+++i+g+ll+q++kw n++vl+ f +l++s++vE++ ++ yH+l+ l+ d+ ++++q+ +++el
  gi|91772483|ref|YP_565175.1|  60 --DQHEGNFK------FSVSITGTLLSQCEKW-NPDVLDIFTQLADSKRVEFIDETNYHSLAGLFDDKNEFREQILEHHEL 131
                                   ..78889999......****************.************************************************ PP

                                   HHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--CHH-TTTSGGG- CS
                Glyco_hydro_57 164 yeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdreLsddigFrys 244
                                     +++g++P++f+++El++++ i+e++  +G++ ++t++++++l+ +   sp+ +y++k+ g+ v++R++++sddig+r+s
  gi|91772483|ref|YP_565175.1| 132 TSDLLGVKPQVFRNTELLYNNSIAETVSSMGYKAILTEGVDQLLDSR---SPNHVYKAKDCGLPVLLRNYKMSDDIGYRFS 209
                                   ***********************************************...******************************* PP

                                   ................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHSS- CS
                Glyco_hydro_57 245 ....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleenglielvtpsefikklkpk 319
                                       e ypl ++d+++nw ++    ++++++i++d+E++g  +++ +g+++Fl++l+ e+  +g +e+ tpse+++k++p 
  gi|91772483|ref|YP_565175.1| 210 arwwEEYPL-TADKWANWASTE---QGDCMNIFMDYETFGehQWSDSGIFDFLRALPGEVLGKG-LEFNTPSEIVEKYEPV 285
                                   ****99***.**********74...***************************************.*************999 PP

                                   EEEE CS
                Glyco_hydro_57 320 glik 323
                                   g ++
  gi|91772483|ref|YP_565175.1| 286 GEVD 289
                                   8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 3241.93
//
Query:       gi|91772484|ref|YP_565176.1|  [L=647]
Description: glycoside hydrolase 15-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-16   59.2   0.0    1.6e-06   27.2   0.1    3.5  2  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.026   14.7   0.0        0.1   12.9   0.0    1.9  2  DUF3938         Protein of unknown function (DUF3938)


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 !   22.1   0.0   6.3e-09   5.7e-05       6      63 ..     274     335 ..     271     345 .. 0.82
   2 !   27.2   0.1   1.8e-10   1.6e-06     116     445 ..     365     636 ..     337     639 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.3e-09
                                   HHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.....B--SEEHHHHHHHHHHHH.......HHH CS
                Glyco_hydro_15   6 lylrnvktlilleqnpvtGlliASpstsdp.....DYrytWvRDsvyvilavwglgyrdedra 63 
                                   ly+r++ +l  l + p+ G ++ASp+ + +     +Y ++W RDsv v+la++++gy + + +
  gi|91772484|ref|YP_565176.1| 274 LYVRSLLSL-NLLNDPYEGSFVASPEFDPAfemcgGYGFCWNRDSVEVVLALLNAGYPEFAAK 335
                                   577777776.456789**********8888**************************9744444 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 1.8e-10
                                   S-..-S--BTTHHHHHHHHHHHH.....HCTTHCHCCCCHHHHTHHHHHHH....HHHHTTS-EE-TTS--ECEEHH..HH CS
                Glyco_hydro_15 116 GddewghlQlDatslyllalaqm.....tasglqiistldevafvqnlvdY....ieaayktpdfglWEenqgeselnass 187
                                   G+ + +  Q+D t+  l+a+  +     +a+ +++ ++++e   v+   +Y    + +    p+  lWE  +g+  +  + 
  gi|91772484|ref|YP_565176.1| 365 GN-FDDSTQIDETGSTLYAIDHYylkleVAERSEFLKNMWET--VRGGAEYlmgrTVQGLHDPCRCLWESDKGIFSY--TN 440
                                   44.55667************999999988888*********9..666666611115667788999*********999..** PP

                                   HHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHH CS
                Glyco_hydro_15 188 vgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgsfaedkeqvqeyrealdaslll 268
                                   ++  ++l  a+ +a+ +g+   a+++++ ++ + ++      +++  w +++++ +   +        ++    +d+s+  
  gi|91772484|ref|YP_565176.1| 441 AAIYAGLKGAAHLARNNGEPVLAKKWSDRAELVRKET-----IEK-LWLEEGYFSRGIID--------NNIHRTVDSSM-- 505
                                   ***************************9999999999.....444.77777777765555........34677888888.. PP

                                   HHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHHHHHH CS
                Glyco_hydro_15 269 lpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkpdklglsGrpyylctlwtvetll 349
                                     + +f+p++        p+ p   a +l  ++ ++++ ++ v+e ++ ++Ry++d++      +G+p+ ++tlw  + ll
  gi|91772484|ref|YP_565176.1| 506 --IGTFIPFAL-----ISPNDPNEKAMILSMIEHIERALRIPVNEYFG-IKRYENDNYI-----DGNPWVVTTLWLSRALL 573
                                   ..667777777.....33444555555666666667777778889899.9********7.....***********777777 PP

                                   HHHHHHHHHTE-EEEECCCHHHH.HHHTTTTTGGGSSEEETCHHHHHHHHHHHHHHHHHHHHHHS-TTS---SEE-TTT-- CS
                Glyco_hydro_15 350 delyekagkgrlwglvryalgll.eklveskqltvGlpperesvisaplpveeladliveaveednslgvLteevdvylge 429
                                   + +   +++          ++ll +k++e                            i  +++ + s+g+L+e+vd+++g+
  gi|91772484|ref|YP_565176.1| 574 TLAFSLEKRDD-------KYDLLvNKAIEY---------------------------IKWTIRSTTSTGLLSEQVDKNTGQ 620
                                   77777777643.......333321233333...........................444455599999999999999999 PP

                                   EESSTT-HHHHHHHHH CS
                Glyco_hydro_15 430 liraqpllfsealllr 445
                                      a+pl +s al+++
  gi|91772484|ref|YP_565176.1| 621 AAWARPLGWSCALFIE 636
                                   9999999999998886 PP

>> DUF3938  Protein of unknown function (DUF3938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.74   6.7e+03      50      74 ..     377     403 ..     375     406 .. 0.78
   2 ?   12.9   0.0   1.1e-05       0.1       6      57 ..     490     542 ..     486     561 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.74
                       DUF3938  50 gclsysitnyalvlqls..saffhglw 74 
                                   g   y+i  y l l+++  s f++ +w
  gi|91772484|ref|YP_565176.1| 377 GSTLYAIDHYYLKLEVAerSEFLKNMW 403
                                   556799999999999864478888888 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.1e-05
                       DUF3938   6 khivlnsieslvsalllgrlvlf.lldseesaqktvlltmigivggclsysit 57 
                                   + i+ n+i   v ++++g ++ f l+ +++  +k+++l+mi  +  +l   + 
  gi|91772484|ref|YP_565176.1| 490 RGIIDNNIHRTVDSSMIGTFIPFaLISPNDPNEKAMILSMIEHIERALRIPVN 542
                                   56899****************8846789999**********988777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 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:                        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: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4049.64
//
Query:       gi|91772485|ref|YP_565177.1|  [L=660]
Description: glycogen debranching protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-132  440.6   0.0   6.4e-132  440.1   0.0    1.1  1  GDE_C            Amylo-alpha-1,6-glucosidase
    1.8e-72  243.3   0.0    2.7e-72  242.8   0.0    1.2  1  GDE_N            Glycogen debranching enzyme N terminal
    1.8e-05   24.1   1.0      3e-05   23.4   1.0    1.2  1  DUF608           Glycosyl-hydrolase family 116, catalytic reg
    0.00011   21.1   0.1       0.12   11.0   0.0    2.4  2  Glyco_hydro_100  Alkaline and neutral invertase
  ------ inclusion threshold ------
       0.19   11.2   0.0       0.44   10.0   0.0    1.5  2  CAF1-p150_C2     CAF1 complex subunit p150, region binding to


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 !  440.1   0.0  1.8e-135  6.4e-132       2     383 .]     284     650 ..     283     650 .. 0.96

  Alignments for each domain:
  == domain 1  score: 440.1 bits;  conditional E-value: 1.8e-135
                         GDE_C   2 asdqflvrrkseslkeeekgvsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNllde.gqea 81 
                                   a+d+f+v+r+      +++ +s++AG++wF+dWGRD++I+L+Gl+Lvtgrf++A++il+tF++++++GliPN++++ g+ +
  gi|91772485|ref|YP_565177.1| 284 AADAFIVHRN------STASKSILAGYHWFADWGRDAMISLPGLTLVTGRFNDAKAILTTFSEQCSQGLIPNRFSDdGISP 358
                                   6788888886......6789******************************************************9988888 PP

                         GDE_C  82 l.yntvdaslwlieaiekYleyagdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmDakvkgepv 161
                                   + yntvdaslw+i+++e+Y++y+ d e+++++++++ +il++y++Gt y i++d +dgli ++    qlTWmD+k+ ++ +
  gi|91772485|ref|YP_565177.1| 359 TdYNTVDASLWFIHSLERYYSYTRDIEFVKKMWDTVGSILHNYIEGTLYGIRMD-DDGLIEQKG---QLTWMDVKIGDREI 435
                                   77****************************************************.*****9999...9************* PP

                         GDE_C 162 tPRdGkaveinaLwyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDvlkssee....kd 238
                                   tPR+Gka+einaLwy++L i++ + e  +g  ++++y e+ + +k++f  +Fw+      +  ++l+D+++ +e     kd
  gi|91772485|ref|YP_565177.1| 436 TPRAGKACEINALWYNSLCIANLFGE-LIGA-DTKQYLEISRLAKSNFVDTFWN------STDKCLYDCVSVDEDmaviKD 508
                                   ************************99.4444.8*********************......999******9988777789** PP

                         GDE_C 239 lslRpNflialslapellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvWvwllgsyvea 319
                                   +s+RpN+++a+sl++++l+++k+k ++ek+ eeLltp+Gl+tL+p+d +Y g+Y+g++dsrd aYH+GtvW+wllg +v+a
  gi|91772485|ref|YP_565177.1| 509 ASIRPNQIFAVSLPYTMLNPDKEKMIVEKVVEELLTPYGLRTLSPADSQYIGRYRGDRDSRDRAYHNGTVWPWLLGPFVTA 589
                                   ********************************************************************************* PP

                         GDE_C 320 llkfgeklgkskealeevkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvaellr 383
                                   ++k++++   s ++le  ++lL ++  h  eag+g++sE+fdgd+++ p+gci QAWSvae+lr
  gi|91772485|ref|YP_565177.1| 590 YTKVHNR---SPSSLEYSRQLLLNFGPHFDEAGIGTISEIFDGDTPHRPDGCISQAWSVAEILR 650
                                   ******7...888899999*******************************************97 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 !  242.8   0.0   7.4e-76   2.7e-72       1     209 [.      19     225 ..      19     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 242.8 bits;  conditional E-value: 7.4e-76
                         GDE_N   1 REwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLesFel 81 
                                   REwl+TNg+GGYas+t++g n+R+yhGlL+a+ npp++R +lls+lde+++v++kv++L+ ++yp++++p+G++yLe+F+ 
  gi|91772485|ref|YP_565177.1|  19 REWLITNGIGGYASSTIIGDNSRKYHGLLIASANPPVDRRVLLSSLDEEIIVGNKVYHLAAHRYPDTLYPSGFKYLERFSA 99 
                                   9******************************************************************************** PP

                         GDE_N  82 epvptwtyrvgdvllekqivmpkgentvliaYrlen.adepatLrlrpllafRdfheltkanellqksqeeglveiqasea 161
                                   +p+pt+ y++g+++l+k i+m +g+nt++++Y+l n ++e++ +r+ pl++ Rdfh+l +a+ ++++s+ ++   +q    
  gi|91772485|ref|YP_565177.1| 100 SPLPTFEYSIGNIKLKKNIFMIHGQNTTIVRYKLINpDNEDLVFRILPLVTNRDFHQLKRAD-AISFSERHDASGVQLRTV 179
                                   *************************************999********************87.555555655667788888 PP

                         GDE_N 162 epslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfev 209
                                   +  l+l++  + +f++ep+wyyn+ey++E+erG  ++edly+pg+fe 
  gi|91772485|ref|YP_565177.1| 180 DGVLQLRS--NMQFVQEPHWYYNLEYDTERERGEAYQEDLYNPGHFER 225
                                   88888888..589*********************************85 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 !   23.4   1.0   8.3e-09     3e-05      99     213 ..     365     488 ..     359     507 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.3e-09
                        DUF608  99 DlnlkfvLqvYRdyvitedkeflkemypkvkkvleklle.....fDkdkdglienegf...adqtYDa...wsvkGvsayc 168
                                   D  l f+ ++ R y  t d ef+k+m+++v ++l++ +e       +d+dglie++g    +d        +   G    +
  gi|91772485|ref|YP_565177.1| 365 DASLWFIHSLERYYSYTRDIEFVKKMWDTVGSILHNYIEgtlygIRMDDDGLIEQKGQltwMDVKIGDreiTPRAGKACEI 445
                                   66677888999********************99988776433134699********9522234333223557778****** PP

                        DUF608 169 gglwlaaLeaaiemaellgdkkdaeeykellekakkvyekkLwnG 213
                                   + lw+ +L +a  + el+g   d+++y e+ + ak+ + +++wn 
  gi|91772485|ref|YP_565177.1| 446 NALWYNSLCIANLFGELIGA--DTKQYLEISRLAKSNFVDTFWNS 488
                                   ******************75..55669****************95 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 !    7.7   0.1   0.00035       1.2     112     140 ..     362     390 ..     328     479 .. 0.78
   2 !   11.0   0.0   3.3e-05      0.12     348     379 ..     565     596 ..     527     649 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00035
                                   --HHHHHHHHHHHHHHHHHH---HHHHSH CS
               Glyco_hydro_100 112 apvDsslWWiillraYvkatgdlslaeee 140
                                    +vD+slW+i  l+ Y   t+d+++++++
  gi|91772485|ref|YP_565177.1| 362 NTVDASLWFIHSLERYYSYTRDIEFVKKM 390
                                   68***********************9874 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.3e-05
                                   -GGG-TTBTTBT-B-GGGHHHHHHHHHHTT-H CS
               Glyco_hydro_100 348 DpkntpwsYhngGsWpvllWllvaaalkterk 379
                                   D+  +  +Yhng  Wp ll  +v+a  k++++
  gi|91772485|ref|YP_565177.1| 565 DRDSRDRAYHNGTVWPWLLGPFVTAYTKVHNR 596
                                   66677789*****************9998764 PP

>> CAF1-p150_C2  CAF1 complex subunit p150, region binding to CAF1-p60 at C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00012      0.44      76     112 ..     321     357 ..     311     377 .. 0.77
   2 ?   -3.4   0.0       1.5   5.2e+03      47      93 ..     493     538 ..     489     543 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                  CAF1-p150_C2  76 lpllhGnvngskviirefqehcrrgllskdtgspasp 112
                                   l l+ G  n +k+i+  f e c +gl+ +  +    +
  gi|91772485|ref|YP_565177.1| 321 LTLVTGRFNDAKAILTTFSEQCSQGLIPNRFSDDGIS 357
                                   78999*********************98776553333 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                  CAF1-p150_C2  47 lletvpaeeeqtp.kaskrekrdeqilaqllpllhGnvngskviiref 93 
                                   l + v ++e+ +  k++    r +qi+a  lp    n +  k+i+ + 
  gi|91772485|ref|YP_565177.1| 493 LYDCVSVDEDMAViKDA--SIRPNQIFAVSLPYTMLNPDKEKMIVEKV 538
                                   55555555554330222..34678999999999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4202.69
//
Query:       gi|91772486|ref|YP_565178.1|  [L=117]
Description: hypothetical protein Mbur_0440 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 882.56
//
Query:       gi|91772487|ref|YP_565179.1|  [L=182]
Description: hypothetical protein Mbur_0441 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-08   32.1  18.4    0.00017   20.5  10.5    2.5  2  GPDPase_memb     Membrane domain of glycerophosphoryl diester
  ------ inclusion threshold ------
      0.011   15.8   1.8      0.011   15.8   1.8    2.9  4  DUF624           Protein of unknown function, DUF624
       0.29   10.5   5.8       0.49    9.8   5.8    1.6  1  DUF92            Integral membrane protein DUF92
        1.6    8.9  14.8       0.63   10.2   1.2    3.3  3  NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit 
        2.4    8.2  14.3         35    4.4  14.3    2.2  1  Sensor           Putative sensor
        9.4    6.1  15.1        1.1    9.1   0.9    3.1  3  DUF4118          Domain of unknown function (DUF4118)


Domain annotation for each model (and alignments):
>> GPDPase_memb  Membrane domain of glycerophosphoryl diester phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   6.4     3e-05      0.09     198     241 ..       5      48 ..       1      89 [. 0.72
   2 !   20.5  10.5   5.6e-08   0.00017     165     239 ..      87     161 ..      71     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                  GPDPase_memb 198 eAlkeSwqltkknflrlllklllliliivivltvilsllllllq 241
                                    Alk+Sw+++k+n+++++++ll+ ++  ++++t++   ++++ +
  gi|91772487|ref|YP_565179.1|   5 IALKNSWNVVKGNLVTFIVGLLIAVVGSIFIVTIAPLAYGFISM 48 
                                   69***************9*9999999999999998887777665 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.6e-08
                  GPDPase_memb 165 vllylifylivfylaiRliftLPliilekkslkeAlkeSwqltkknflrlllklllliliivivltvilslllll 239
                                    +l  i+ ++ ++++i ++ft+Pl+++++++  e +keS +++kk  ++ ++ +++++++  i   +++++ll+ 
  gi|91772487|ref|YP_565179.1|  87 TILGQIASILSTIVGILFMFTMPLLVIKGYNGIEGIKESIEIIKKAPVECVIVYVIMLVLNLIGTLLLGIGLLVT 161
                                   344567789999**************************************9999888888776665555555443 PP

>> DUF624  Protein of unknown function, DUF624
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.12   3.6e+02      49      72 ..      11      33 ..       5      36 .. 0.53
   2 ?   15.8   1.8   3.7e-06     0.011      13      73 ..      30      89 ..      13      91 .. 0.91
   3 ?   -2.5   0.2       1.9   5.6e+03      61      69 ..      99     107 ..      93     115 .. 0.51
   4 ?   -1.3   3.1       0.8   2.4e+03       6      22 ..     141     157 ..     136     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.12
                        DUF624 49 weaYKknfkksnllglillligli 72
                                  w+  K n++    +gl+++++g i
  gi|91772487|ref|YP_565179.1| 11 WNVVKGNLVTFI-VGLLIAVVGSI 33
                                  666667766544.44444444444 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.7e-06
                        DUF624 13 llglvvfglfPAtaAlfavvrkwirkeedssifktFweaYKknfkksnllglillliglil 73
                                  + ++++++++P      ++  k +r+e ++ i   F+   K+ f++s ++ li+++i  il
  gi|91772487|ref|YP_565179.1| 30 VGSIFIVTIAPLAYGFISMAVKGARGE-QIEISDVFVGFNKDDFIRSWTFMLIYIVIATIL 89
                                  67899**********************.*****************************9997 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.9
                        DUF624  61 llglillli 69 
                                   ++g++++++
  gi|91772487|ref|YP_565179.1|  99 IVGILFMFT 107
                                   334444433 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.8
                        DUF624   6 llwllftllglvvfglf 22 
                                   +++l+++l+g +++g++
  gi|91772487|ref|YP_565179.1| 141 VIMLVLNLIGTLLLGIG 157
                                   67777777777777765 PP

>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.8   0.00016      0.49     146     194 ..      22     104 ..      18     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                         DUF92 146 llGllasllGalliall.....avlllllel..................................lillltlaGllGsllD 187
                                   ++Gll++++G+++i+++        +    +                                  +i+++t+ G ++s+l 
  gi|91772487|ref|YP_565179.1|  22 IVGLLIAVVGSIFIVTIaplayG--F---ISmavkgargeqieisdvfvgfnkddfirswtfmliYIVIATILGQIASILS 97 
                                   58*************88555321..2...223446799************************99888999999******** PP

                         DUF92 188 SlLGatl 194
                                   +++G ++
  gi|91772487|ref|YP_565179.1|  98 TIVGILF 104
                                   **99876 PP

>> NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.6    0.0077        23      66      94 ..      11      39 ..       3      52 .. 0.79
   2 ?    2.1   0.8     0.072   2.1e+02      10      34 ..      87     112 ..      72     118 .. 0.53
   3 ?   10.2   1.2   0.00021      0.63       3      48 ..     129     174 ..     127     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0077
               NiFe_hyd_3_EhaA 66 veiydGlllaiiiGvlsalfskyllekvf 94
                                   ++++G l+++i+G+l a++   ++ ++ 
  gi|91772487|ref|YP_565179.1| 11 WNVVKGNLVTFIVGLLIAVVGSIFIVTIA 39
                                  45679999999999999998776666655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.072
               NiFe_hyd_3_EhaA  10 llisYlvaiivsiivali..LrlPllp 34 
                                   +++   +a i s iv+++    +Pll+
  gi|91772487|ref|YP_565179.1|  87 TILGQ-IASILSTIVGILfmFTMPLLV 112
                                   33333.344444455543115677765 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00021
               NiFe_hyd_3_EhaA   3 ilvnvldllisYlvaiivsiivaliLrlPllpekParqsftisvif 48 
                                   i+   ++ +i Y++ ++  +i +l+L++ ll+  P+   f +++ f
  gi|91772487|ref|YP_565179.1| 129 IKKAPVECVIVYVIMLVLNLIGTLLLGIGLLVTVPISSVFLANATF 174
                                   55666899****************************9999998877 PP

>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  14.3     0.012        35      75     151 ..      60     170 ..      12     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                        Sensor  75 larlrallrdpatwrdllylllhfplglvlfvvavvl..lalalalltaPlw....................t........ 125
                                   ++ +   + +  ++r+  ++l+ ++++++l+ +a +l  +++ l+++t+Pl+                    +        
  gi|91772487|ref|YP_565179.1|  60 ISDVFVGFNKDDFIRSWTFMLIYIVIATILGQIASILstIVGILFMFTMPLLvikgyngiegikesieiikkApvecvivy 140
                                   45677788899999*************9999998888889999********757777776666666666555055555565 PP

                        Sensor 126 ....lpeallvavlGlllllvllwvvrgla 151
                                       +++ +++++lG++ll++++    +la
  gi|91772487|ref|YP_565179.1| 141 vimlVLNLIGTLLLGIGLLVTVPISSVFLA 170
                                   555578888888999999888876665555 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4     0.018        54      75      95 ..      16      36 ..       9      43 .. 0.82
   2 ?    9.1   0.9   0.00037       1.1      30      57 ..      77     104 ..      64     117 .. 0.87
   3 ?    2.0   1.5     0.059   1.8e+02      27      62 ..     139     174 ..     130     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.018
                       DUF4118 75 eylltlvvflvvallvstlva 95
                                  ++l+t++v l++a++ s ++ 
  gi|91772487|ref|YP_565179.1| 16 GNLVTFIVGLLIAVVGSIFIV 36
                                  799999999999999887665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00037
                       DUF4118  30 lfllavllvallgglgpgllaallsvll 57 
                                   +f+l  +++a ++g ++++l++++++l 
  gi|91772487|ref|YP_565179.1|  77 TFMLIYIVIATILGQIASILSTIVGILF 104
                                   79**********************9984 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.059
                       DUF4118  27 ivllfllavllvallgglgpgllaallsvllfnyff 62 
                                   +++++l++ l+ +ll+g+g  + + + sv+l n  f
  gi|91772487|ref|YP_565179.1| 139 VYVIMLVLNLIGTLLLGIGLLVTVPISSVFLANATF 174
                                   566777888888888899999999999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1259.66
//
Query:       gi|91772488|ref|YP_565180.1|  [L=377]
Description: hypothetical protein Mbur_0443 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   18.1   1.2          2    8.7   0.1    2.4  2  BEN       BEN domain
  ------ inclusion threshold ------
      0.061   13.2   3.2       0.12   12.3   0.6    2.7  2  DUF4488   Domain of unknown function (DUF4488)
      0.076   12.2   3.2       0.12   11.6   3.2    1.3  1  TMPIT     TMPIT-like protein
      0.087   13.2   0.6       0.28   11.5   0.6    1.8  1  DUF2935   Domain of unknown function (DUF2935)
        4.1    7.5   8.8       0.33   11.0   1.2    2.7  3  COG2      COG (conserved oligomeric Golgi) complex component,


Domain annotation for each model (and alignments):
>> BEN  BEN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00056         2      32      70 ..      72     108 ..      61     113 .. 0.74
   2 !    7.9   0.1     0.001       3.6      19      58 ..     279     322 ..     269     333 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00056
                                   ---EE--HHHHHHHHHHHHHHH--..........-HHHH CS
                           BEN  32 ppkkaLDpnklsaIrnyveerypsekededwwrecldqI 70 
                                     ++++D++++  Ir+++ + + s+++   + +e++++I
  gi|91772488|ref|YP_565180.1|  72 KITQGIDSKHILEIRDTILDTCSSVSS--SKDNEIVEKI 108
                                   5689********************333..3334445544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.001
                                   EESS----GGGTT...---EE--HHHHHHHHHHHHHHH--.... CS
                           BEN  19 ssvtGkrsrafkr...ppkkaLDpnklsaIrnyveeryps.eke 58 
                                   +  +   s++ +r   ++k+a+D n++ + ++++++ y++ +ke
  gi|91772488|ref|YP_565180.1| 279 MFSGSVESKKLTRillDNKNAMDDNRILDCLKIIANKYGEiIKE 322
                                   4444455667777888***********************94333 PP

>> DUF4488  Domain of unknown function (DUF4488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.33   1.2e+03      60      81 ..      99     120 ..      86     127 .. 0.78
   2 ?   12.3   0.6   3.3e-05      0.12      26      79 ..     221     274 ..     190     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.33
                       DUF4488  60 ksdsvyvEsveksvhlpqlegk 81 
                                   ++d+ +vE++e+  +l+q e k
  gi|91772488|ref|YP_565180.1|  99 SKDNEIVEKIEEKTKLAQHEVK 120
                                   6799999999999888776655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.3e-05
                       DUF4488  26 pslKilsddgkf.vnlvleeksgasiiigyGeYelksdsvyvEsveksvhlpqle 79 
                                    +lK + +d+     +++   ++ + ii yGeY ++ d+v ++s++ +  +   +
  gi|91772488|ref|YP_565180.1| 221 ENLKAVIEDKDSeHKFTISGDEN-TYIIHYGEYDITGDNVLADSINMNYVDIIAK 274
                                   67887766655415566666655.59*******************9987766555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.2   3.3e-05      0.12       4      91 ..      38     128 ..      21     142 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                         TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikk..qkkrlkelkssl.kklkksvkeeeeeeveelkeelkerkkv 81 
                                   +++++ke ke     ++++q++++ +k  +++ ++i++   +k++ e+++++ +++++ ++++++e+ve+++e++k +++ 
  gi|91772488|ref|YP_565180.1|  38 ATKIKKENKEDVVILENIIQEIDKFQKDTTDFIEKITQgiDSKHILEIRDTIlDTCSSVSSSKDNEIVEKIEEKTKLAQHE 118
                                   333344444333334445555555555555555555442234555555555414444445599****************** PP

                         TMPIT  82 lkevesllpk 91 
                                   +k++es + +
  gi|91772488|ref|YP_565180.1| 119 VKDLESKMLS 128
                                   ****998766 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   7.8e-05      0.28      32     100 ..      17      84 ..      11      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                       DUF2935  32 likeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekvlscklfs 100
                                   +i+ +++f k  +++     ++++   + ++e++  ++++++e+ k  +  ++F ++++++++s+ +  
  gi|91772488|ref|YP_565180.1|  17 FIQDLQNFMKVSKEVIPLEKSATKIK-KENKEDVVILENIIQEIDKFQKDTTDFIEKITQGIDSKHILE 84 
                                   55566655444444443333333344.88999********************************99975 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 ?   11.0   1.2   9.1e-05      0.33      52     131 ..      19      98 ..       3     100 .. 0.88
   2 ?    2.9   0.2     0.029     1e+02      79     114 ..      83     125 ..      79     136 .. 0.70
   3 ?   -1.6   0.1      0.73   2.6e+03      44      56 ..     258     270 ..     251     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.1e-05
                          COG2  52 edyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevveklea 131
                                   +d+++F+++S++ + l+++  +++++ ++ +  +e++++++++ +++ ++ +e+ ++  + + +l++   + ++++++++
  gi|91772488|ref|YP_565180.1|  19 QDLQNFMKVSKEVIPLEKSATKIKKENKEDVVILENIIQEIDKFQKDTTDFIEKITQGIDSKHILEIRDTILDTCSSVSS 98 
                                   89*******************************************99999999999999999999999999999998865 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.029
                          COG2  79 aaarkkvesvrekls.ereeeveskleeakeleekr......e 114
                                   +++r+ + ++ +++s  + +e+ +k+ee+++l++++      +
  gi|91772488|ref|YP_565180.1|  83 LEIRDTILDTCSSVSsSKDNEIVEKIEEKTKLAQHEvkdlesK 125
                                   677788877777776156789999*****99999875544333 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.73
                          COG2  44 kellelvnedyad 56 
                                   + l++++n++y d
  gi|91772488|ref|YP_565180.1| 258 NVLADSINMNYVD 270
                                   66899******88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1556  (0.0867868); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2725.31
//
Query:       gi|91772489|ref|YP_565181.1|  [L=175]
Description: Na-K-Cl cotransporter [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1334.61
//
Query:       gi|91772490|ref|YP_565182.1|  [L=246]
Description: hypothetical protein Mbur_0445 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-05   24.6   0.7    2.7e-05   23.6   0.1    1.7  2  NucS       Endonuclease NucS
  ------ inclusion threshold ------
      0.042   13.8   0.0       0.11   12.4   0.0    1.7  1  PDDEXK_10  PD-(D/E)XK nuclease superfamily
        0.1   12.6   0.0       0.27   11.2   0.0    1.8  1  DUF1967    Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.13   7.7e+02      88     110 ..      30      52 ..      17     126 .. 0.61
   2 !   23.6   0.1   4.5e-09   2.7e-05     104     211 ..     132     240 ..     106     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.13
                          NucS  88 ehasayeledveelvldGseael 110
                                   eh++ y +   e+l  d +ea  
  gi|91772490|ref|YP_565182.1|  30 EHECDYSIVAIEDLSEDEQEAIR 52 
                                   56666666666666666665532 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4.5e-09
                          NucS 104 dGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklviv..elkrrkaevdaveqLkr.yvellkedsvl 181
                                   + se +++ +i   p+Lie G +  + e  v  G +d +  d ++k  ++  e+  r  ++  v+++k  y e++  d   
  gi|91772490|ref|YP_565182.1| 132 HISEDDISRMISSIPELIEPGLTFHEVEVEVEGGRIDAVFTDSQDKHFLIeiEINARDNDIGQVQRFKLpYAEKYGVDVE- 211
                                   55899*************************************99998766115677878887777776336666665543. PP

                          NucS 182 dkvrGvlvapsittdaekllkeeglefkel 211
                                    ++r  +v+ +i +  +   +  g+e+ +l
  gi|91772490|ref|YP_565182.1| 212 -DIRLGIVCADIDSSRMTACRGAGIEVFRL 240
                                   .55544555667777777777777776655 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05      0.11      12      57 ..     176     223 ..     161     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                     PDDEXK_10  12 gkvilvEiksslkrgDlavikrkkelYekakgvkvd..rlivvtpfid 57 
                                    k+ l+Ei+ + +  D+ +++r k  Y  + gv v+  rl +v + id
  gi|91772490|ref|YP_565182.1| 176 DKHFLIEIEINARDNDIGQVQRFKLPYAEKYGVDVEdiRLGIVCADID 223
                                   479******************************998233456666666 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.4e-05      0.27      31      60 ..     109     138 ..      93     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                                   GGGHHHHHHHHHHTTHHHHHHTTT--TT-E CS
                       DUF1967  31 eeavrrfarrLkklGvedaLrkaGakeGdt 60 
                                     a+++++ ++++ +vedaL+ + + e+d 
  gi|91772490|ref|YP_565182.1| 109 TTAIQYLNLIMRSPNVEDALESKHISEDDI 138
                                   5699**********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1651.14
//
Query:       gi|91772491|ref|YP_565183.1|  [L=259]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for 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-16   58.3   5.7    9.6e-16   58.1   5.7    1.1  1  DDE_Tnp_1    Transposase DDE domain
     0.0021   18.4   1.6     0.0027   18.0   0.8    1.7  2  DDE_Tnp_1_2  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   5.7   1.1e-19   9.6e-16       4     214 .]      19     189 ..      16     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.1e-19
                     DDE_Tnp_1   4 revlivDattvrvpgtkedarwgykggkykygy.klhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgklvla 82 
                                   ++++++D+t ++    +   ++++  +k+++ y k  i vd +  +i++++i+ + vhd k++k+ll +++++ +++++++
  gi|91772491|ref|YP_565183.1|  19 IDITAIDSTGFTSGYCS--NYYSWRIKKWRRSYvKTSISVDVHKFVITGYKISGKPVHDAKHAKALLSQCHHNrRSRYYVV 97 
                                   6899*******965555..566778889888888*********************************************** PP

                     DDE_Tnp_1  83 DaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                   D++Y+s+++++  +ek ++  i +               r+r+rk+++++ ++k  ++++                     
  gi|91772491|ref|YP_565183.1|  98 DKAYDSENIHELTREKLGSIAIVP--------------LRQRERKRIKGRYRKKMIHEFDS-------------------- 144
                                   **************6555555555..............599********************.................... PP

                     DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                         +y+ R   E+ F+ lkr++g d+lr+r+++  + ++ ++ + +nl
  gi|91772491|ref|YP_565183.1| 145 -----KIYSMRNLSETMFSVLKRRYG-DNLRARKYRNQVKEVKFKVILHNL 189
                                   .....******************777.**************9999999997 PP

>> DDE_Tnp_1_2  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.7   1.6e+04      22      35 ..      67      80 ..      62      90 .. 0.62
   2 !   18.0   0.8     3e-07    0.0027       3      65 ..      97     166 ..      95     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                   DDE_Tnp_1_2 22 rasipplgrpaknk 35
                                  ++s++p+++ +  k
  gi|91772491|ref|YP_565183.1| 67 KISGKPVHDAKHAK 80
                                  66777777666533 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-07
                   DDE_Tnp_1_2   3 aDrgYrsralrealker.gIrasipplgrpakn......kaapkkqarederarnvvErsfgwlkrrrsl 65 
                                   +D++Y+s+ + e+ +e  g  a +p ++r+ k+      k+   +++ +++  rn+ E  f+ lkrr++ 
  gi|91772491|ref|YP_565183.1|  97 VDKAYDSENIHELTREKlGSIAIVPLRQRERKRikgryrKKMIHEFDSKIYSMRNLSETMFSVLKRRYGD 166
                                   8*********99998875777777777777777*99888888899**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 00:00:00.41
# Mc/sec: 1897.89
//
Query:       gi|91772492|ref|YP_565184.1|  [L=540]
Description: phenylalanyl-tRNA synthetase subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete 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-43  147.7   0.1    4.8e-43  147.1   0.1    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.7e-16   60.3   0.6    5.3e-16   58.7   0.1    2.2  2  B5               tRNA synthetase B5 domain
    3.3e-14   53.0   0.0      6e-14   52.1   0.0    1.4  1  B3_4             B3/4 domain
    0.00047   20.3   0.5       0.47   10.7   0.0    3.4  4  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
     0.0011   18.5   0.2     0.0023   17.5   0.2    1.5  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.16   11.9   0.1        4.8    7.2   0.0    2.8  4  DUF4265          Domain of unknown function (DUF4265)


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 !  147.1   0.1   1.6e-46   4.8e-43       1     214 []     345     538 ..     345     538 .. 0.99

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 1.6e-46
               tRNA_synthFbeta   1 IpstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpg 81 
                                   I+s +Pk +t +   ++   +r  +r++++++G++Ev+ ++++s+k+  +++++++ +++  +++P+sedq+++Rt++lp+
  gi|91772492|ref|YP_565184.1| 345 IKSEFPKSATIGC-AHPISVTRGVMREIMVSLGYSEVMPFTLTSQKVHFEWMNREETDDVTFVLHPISEDQTMVRTTILPN 424
                                   899*********9.88************************************99999************************ PP

               tRNA_synthFbeta  82 lLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekv 162
                                   l+e  + N++++++  rlFE+g+v+ +       +++ hla++  + +           ++f ++ ++++a++++  i ++
  gi|91772492|ref|YP_565184.1| 425 LIEIFSLNQHHELP-QRLFEVGEVVVNS------KNRLHLAAASIHAQ-----------ANFTEIREVLDAVMRERDI-EY 486
                                   **************.*************......9*************...........*******************.** PP

               tRNA_synthFbeta 163 efepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                   e++ +e+pa+  gr A+i v+g++vG++Gel pev  +f+l q++++fE+dl
  gi|91772492|ref|YP_565184.1| 487 EVVVSEDPAFIEGRRADILVNGEKVGMMGELYPEVIINFGLGQPIVGFEIDL 538
                                   **************************************************98 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.5   1.3e+04      27      38 ..      28      39 ..      15      53 .. 0.49
   2 !   58.7   0.1   1.8e-19   5.3e-16       3      67 .]     277     342 ..     275     342 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.5
                                  HTT-E.EESSTT CS
                                  xxxxxxxxxxxx RF
                            B5 27 rlgceriekdkd 38
                                   +g +++  +k+
  gi|91772492|ref|YP_565184.1| 28 MIGADIERIEKE 39
                                  333333333333 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 1.8e-19
                                   EEHHHHHHHHTS---HHHHHHHHHHTT-E..EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5   3 lrvekinkllGidlseeeiikiLkrlgce.riekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                   +  + i +l+Gi+l+++eii+ Lkr+ ++   ++d+d +++ vP++R D+++  D++E++a+ yG+
  gi|91772492|ref|YP_565184.1| 277 VPRSDIDSLIGIKLTDDEIINELKRMRFDaSVLEDGDMFEISVPTYRADILHNFDIVEDIAIGYGF 342
                                   67789***********************854599*******************************7 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0     2e-17     6e-14       3     158 ..      95     255 ..      93     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 2e-17
                                   SEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTEEEEB CS
                          B3_4   3 pryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakegeklvt 78 
                                   p   +++++g+++t +s               i+++ D+++ ++  lg+      ++++D+ +i+++++ +    ++++v+
  gi|91772492|ref|YP_565184.1|  95 PVLGCAIVKGINFTSSS---------------IKSLMDLQEDLHWGLGRnrkkvSIGVHDMTNIEPPFKYQAVSPDFEFVP 160
                                   55667888888887777...............************************************************* PP

                                   TTS-EEEE.-T...................TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHHHHHH CS
                          B3_4  79 ldgkerel.de...................edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirktarr 138
                                   ld +e    de                   ++++i+dse++v s +++++g  ++v+e+T++ f+ ++++ +      a  
  gi|91772492|ref|YP_565184.1| 161 LDFTEPMTmDEvlekhpkgvrfanilegmeKYPLITDSEGKVlSFPPIINGTLTRVEESTTDLFIDVTGLGD------AVY 235
                                   *9998777577*********************************************************9655......556 PP

                                   TT---HHHHHHHH---TTTH CS
                          B3_4 139 lglrseaskrfergvdpekl 158
                                   + l+   s   erg + e +
  gi|91772492|ref|YP_565184.1| 236 TALSIVVSALAERGGKIESV 255
                                   66666666666666665555 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 ?   -2.5   0.0         2   6.1e+03       1      15 [.       1      15 [.       1      24 [. 0.82
   2 !   10.7   0.0   0.00016      0.47      49      81 ..      34      66 ..      18      68 .. 0.88
   3 ?   -4.0   0.0       5.9   1.8e+04      33      41 ..      84      92 ..      84      95 .. 0.84
   4 !    6.1   0.1    0.0044        13      36      77 ..     293     336 ..     273     341 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                     PhetRS_B1  1 MPtisvkkeaLfkal 15
                                  MP+i+++ e+L +++
  gi|91772492|ref|YP_565184.1|  1 MPIITLQYEDLESLT 15
                                  9*****999998765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                     PhetRS_B1 49 kkseeviykidipAnryDLLcleglaralkvFl 81
                                  ++ e++ + i+    r+DL ++eg+ara++ F 
  gi|91772492|ref|YP_565184.1| 34 ERIEKEAIDIEFFPDRPDLYSVEGVARAMRGFM 66
                                  56678899999999***************9996 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 5.9
                     PhetRS_B1 33 lElDeivee 41
                                  +ElDe ++e
  gi|91772492|ref|YP_565184.1| 84 IELDEKIKE 92
                                  79**99987 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0044
                     PhetRS_B1  36 Deiveeee..kkkadkkseeviykidipAnryDLLcleglaral 77 
                                   Dei++e +  +  a+  ++  ++ i +p  r D+L    +++ +
  gi|91772492|ref|YP_565184.1| 293 DEIINELKrmRFDASVLEDGDMFEISVPTYRADILHNFDIVEDI 336
                                   677777773333577888999*************9876666655 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   7.7e-07    0.0023       9     111 ..     351     448 ..     344     474 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.7e-07
                                   SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHH CS
                  tRNA-synt_2d   9 krieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthtta 89 
                                   k+ + g+ hp++ ++  ++ei+++lg++ev    + s+   f+ +n ++ +       tF+l +p +  e+++++Rt   +
  gi|91772492|ref|YP_565184.1| 351 KSATIGCAHPISVTRGVMREIMVSLGYSEVMPFTLTSQKVHFEWMNREETDD-----VTFVL-HPIS--EDQTMVRTTILP 423
                                   6778899***************************************998754.....37777.7777..889*******99 PP

                                   HHHHHH...TTS-SSEEEEEEEEEE CS
                  tRNA-synt_2d  90 vqirtl...ekkkppikiisigrvf 111
                                     i      +++++p++++ +g+v 
  gi|91772492|ref|YP_565184.1| 424 NLIEIFslnQHHELPQRLFEVGEVV 448
                                   9888877799999********9985 PP

>> DUF4265  Domain of unknown function (DUF4265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.2   9.4e+03      67      89 ..      20      42 ..      13      49 .. 0.74
   2 ?   -3.3   0.0       2.8   8.3e+03      28      51 ..     231     251 ..     224     267 .. 0.64
   3 ?    1.2   0.0      0.12   3.5e+02      67      94 ..     293     321 ..     280     325 .. 0.88
   4 ?    7.2   0.0    0.0016       4.8      67     113 ..     435     483 ..     424     486 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
                       DUF4265 67 sevreeLealgceveglsaklla 89
                                  + +++++ ++g+++e ++++ + 
  gi|91772492|ref|YP_565184.1| 20 DTIIDRVPMIGADIERIEKEAID 42
                                  78899999999999988887665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.8
                       DUF4265  28 gDvvevdedeerlafervvkesGn 51 
                                   gD v++     + +++ +++++G+
  gi|91772492|ref|YP_565184.1| 231 GDAVYT---ALSIVVSALAERGGK 251
                                   566665...555566666666664 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.12
                       DUF4265  67 sevreeLealgceveglsa.kllavdvpa 94 
                                   +e+++eL+++  +  +l++ +++ ++vp+
  gi|91772492|ref|YP_565184.1| 293 DEIINELKRMRFDASVLEDgDMFEISVPT 321
                                   89***************999*******96 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0016
                       DUF4265  67 sevreeLealgceveglsa..kllavdvpadvdleaikelLaeleeegv 113
                                   +e+ ++L ++g  v  +++   l a +++a++++ +i+e+L+++ +e  
  gi|91772492|ref|YP_565184.1| 435 HELPQRLFEVGEVVVNSKNrlHLAAASIHAQANFTEIREVLDAVMRERD 483
                                   466677777765555555458999******************9666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3909.57
//
Query:       gi|91772493|ref|YP_565185.1|  [L=797]
Description: type II secretion system protein E [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  159.9   0.0    9.5e-47  159.3   0.0    1.2  1  T2SSE     Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   0.0   5.3e-51   9.5e-47       7     256 ..     421     676 ..     416     687 .. 0.91

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 5.3e-51
                         T2SSE   7 allddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllP 86 
                                    l++d++  di  + + + +++   +  +++++    ++++l  +i ++a+ ++++is   p++da++p +g r+++ l  
  gi|91772493|ref|YP_565185.1| 421 SLMNDDSLEDISGNGHSKpIFL-YHKTYLNIATNIIFDEEELDSFIIQLAQRSGKHISVADPMVDATMP-DGSRIQMTLGT 499
                                   6778888888888888888888.666666888888899999****************************.99999998876 PP

                         T2SSE  87 vvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvED 165
                                   +v +   +++iRk ++  +t  dl + ++++++  + l   ++++++++ +GgT sGKt +l+a+  +i+++  +i+ +ED
  gi|91772493|ref|YP_565185.1| 500 SVTThgSTFTIRKFNEVPITPVDLLKWGTFSPEAMAYLWLCIENNKSLIYAGGTASGKTSSLNAVSLFIPEK-AKIISLED 579
                                   66555599****************************************************************.******** PP

                         T2SSE 166 pvEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaaga 239
                                   ++E++l + n +  +++       ++ v++ dll+aaLR+rP  ++vGE+R+ke+l++ +A++TGH   +sT+Ha+s+ +a
  gi|91772493|ref|YP_565185.1| 580 TRELKLPHLNWIPGVTRdsftsdeRGAVDMYDLLKAALRQRPEYLLVGEVRGKEALTLFQAMSTGHTT-FSTMHADSVPSA 659
                                   ************999999*****99*******************************************.************ PP

                         T2SSE 240 lerLeqlgaeveaaelk 256
                                   ++rLe+    v++++++
  gi|91772493|ref|YP_565185.1| 660 IHRLENPPISVPRNMIQ 676
                                   ****9976666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 5609.04
//
Query:       gi|91772494|ref|YP_565186.1|  [L=716]
Description: type II secretion system protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-36  125.4   3.1    3.2e-19   69.1   0.0    4.5  5  T2SSF            Type II secretion system (T2SS), protein F
     0.0036   16.3   0.0        1.6    7.6   0.0    2.6  2  Pex24p           Integral peroxisomal membrane peroxin
  ------ inclusion threshold ------
      0.016   15.4   0.1       0.39   10.8   0.0    2.7  3  Spore_III_AB     Stage III sporulation protein AB (spore_III_
       0.11   12.8   0.1        1.6    9.0   0.0    2.5  2  RNA_binding      RNA binding
       0.17   12.1   0.1       0.35   11.1   0.1    1.5  1  Fer4_12          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.2      0.81   2.9e+03     100     121 ..      97     118 ..      92     121 .. 0.80
   2 ?   -4.2   1.5       4.3   1.5e+04     102     115 ..     149     162 ..     143     171 .. 0.51
   3 !   69.1   0.0   8.9e-23   3.2e-19       2     124 ..     193     321 ..     192     322 .. 0.96
   4 ?   -6.5   6.1         5   1.8e+04     107     125 .]     342     360 ..     335     360 .. 0.83
   5 !   64.8   1.2     2e-21   7.1e-18       1     123 [.     509     634 ..     509     636 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.81
                                   HHHHTTXXXXXXXXXXXXXXXX CS
                         T2SSF 100 aallepllllvvallvllilla 121
                                    a+++ ll+ v++l++++++  
  gi|91772494|ref|YP_565186.1|  97 NAIFYSLLSCVFGLIIGIFVAY 118
                                   5778899999999999998875 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 4.3
                                   HHTTXXXXXXXXXX CS
                         T2SSF 102 llepllllvvallv 115
                                   + + l++l++a+ +
  gi|91772494|ref|YP_565186.1| 149 FVGFLIMLFFAASL 162
                                   33344444444444 PP

  == domain 3  score: 69.1 bits;  conditional E-value: 8.9e-23
                                   HHHHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT- CS
                         T2SSF   2 lrqlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggn 76 
                                   ++ ++ l+++G+++ e+++ll+++ + +g++++e+++i+r++++ g ++++a++    r+ps+ f el+++li+++++gg+
  gi|91772494|ref|YP_565186.1| 193 VTFMYALSKGGMNIIEVFRLLSRSGStYGEVSKEINAIIREMDYFGyDMKTAISniseRSPSDRFNELMDNLITIIDSGGS 273
                                   56799**************************************988688999999999*********************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                   ++ ++++ ae++ ++  +  k ++++l+ l++ +v+++v+++l++i++
  gi|91772494|ref|YP_565186.1| 274 IPRYFQDKAEQYLQKTSIDEKGFLETLGLLAESYVTAFVAGPLFIIIM 321
                                   **********************************************98 PP

  == domain 4  score: -6.5 bits;  conditional E-value: 5
                                   XXXXXXXXXXXXXXXXXXX CS
                         T2SSF 107 lllvvallvllillaillp 125
                                   ++l++++l+++++++i++p
  gi|91772494|ref|YP_565186.1| 342 AVLPIGSLMFVVMISIITP 360
                                   6789999999999999887 PP

  == domain 5  score: 64.8 bits;  conditional E-value: 2e-21
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC......T-TT.TS-HHHHHHHHHHHHHT CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale......rtpssefpelvvqlirageegg 75 
                                   fl  la+  ++G++l ++++l+a+++ +g l+ e++ i +++++G++++++l       rt   ++++ ++ ++ a e++g
  gi|91772494|ref|YP_565186.1| 509 FLKKLASTNETGMTLRDSIKLMAKSK-SGHLGNEIRMIWADISWGMNVNDSLIrfanrlRT--QVIARSLTLITKANESSG 586
                                   8999**********************.**************************88874433..477*************** PP

                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                         T2SSF  76 nLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                   +++evL  +a++   e+ ++r+++ +++ +++++++ +lv++ ++ ++
  gi|91772494|ref|YP_565186.1| 587 DVGEVLLVAARDAASEQSMKRERAMSMMIYIVIIYISFLVFVGVIYVI 634
                                   ********************************************9987 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00046       1.6      49     185 ..      99     343 ..      90     363 .. 0.69
   2 ?    3.1   3.0     0.011        39     143     180 ..     603     640 ..     437     645 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00046
                        Pex24p  49 lvytficlvpylelvvlplllllfvvmvpaylyrhplrksslik..................................... 92 
                                   ++y+++ +v  l++ ++++ + ++vv +p +++                                                
  gi|91772494|ref|YP_565186.1|  99 IFYSLLSCVFGLIIGIFVAYISIYVVGLPEAITKL--------Efsessawilqfkgifvgflimlffaaslgggiygmfm 171
                                   44444444444444444444445555555555554........03333344568888888888888888888888888888 PP

                        Pex24p  93 ......................................................................keesknestse 103
                                                                                                         k++ +n+s ++
  gi|91772494|ref|YP_565186.1| 172 lypkfqaserkgdidrqlpyavtfmyalskggmniievfrllsrsgstygevskeinaiiremdyfgydmKTAISNIS-ER 251
                                   888888888888888888888888888888888888888888888888777777777777777777776322222222.22 PP

                        Pex24p 104 gptldeaskeivlnLr...........dlqnkmedllnpidalekflkelagfkdenlstllfltllltpililllsrlip 173
                                   +p+ +   +e++ nL             +q+k+e++l+  +  ek + e+ g+ +e++ t ++ + l ++i+ ++++++  
  gi|91772494|ref|YP_565186.1| 252 SPSDR--FNELMDNLItiidsggsiprYFQDKAEQYLQKTSIDEKGFLETLGLLAESYVTAFVAGPLFIIIMGVMMAVMGS 330
                                   22222..467777777899999999999***********************************999999999998877666 PP

                        Pex24p 174 wrlillvlg.ail 185
                                    + +++ +   ++
  gi|91772494|ref|YP_565186.1| 331 GSEVMVYAIiYAV 343
                                   6555555543333 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                        Pex24p 143 agfkdenlstllfltllltpililllsrlipwrlillv 180
                                   + +k+e+  +++++++++ ++++++++++  +++++l+
  gi|91772494|ref|YP_565186.1| 603 QSMKRERAMSMMIYIVIIYISFLVFVGVIYVISTTFLA 640
                                   359***********************999999999885 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.8     1e+04     136     167 ..      83     114 ..      23     116 .. 0.58
   2 ?   10.8   0.0   0.00011      0.39      31     105 ..     221     294 ..     209     305 .. 0.87
   3 ?    1.1   0.0      0.11   3.8e+02      52     112 ..     492     548 ..     483     557 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXX CS
                  Spore_III_AB 136 leeeieeareeakkkeklyrtlGvlaGlflvi 167
                                   ++++i    e + +++  y+ l+ + Gl++ i
  gi|91772494|ref|YP_565186.1|  83 FQARIPLSYEMYVSNAIFYSLLSCVFGLIIGI 114
                                   33333333344444444555555555555554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-T.THHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HH CS
                  Spore_III_AB  31 eelkralellegeirygatpLpealeklaekses.plseffeevaerleekegesfeeaweeavekllkklaLkke 105
                                    e+ + ++ + +e+ y    ++ a+++++e+s s +++e++ ++   ++  +g+s+ + +++++e++l+k++++++
  gi|91772494|ref|YP_565186.1| 221 GEVSKEINAIIREMDYFGYDMKTAISNISERSPSdRFNELMDNLITIID--SGGSIPRYFQDKAEQYLQKTSIDEK 294
                                   67788899999******************98888688888888888775..9****************99998775 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.11
                                   HHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHHHHHHH CS
                  Spore_III_AB  52 pealeklaeksesplseffeevaerleekegesfeeaweeavekllkklaLkkedkeilke 112
                                    e++++ +++ e ++ +f++++a+   +++g+++++ ++  +++  k+ +L +e + i+++
  gi|91772494|ref|YP_565186.1| 492 HEIMSRKKKHLERNFPDFLKKLAST--NETGMTLRDSIKLMAKS--KSGHLGNEIRMIWAD 548
                                   6899999999999999999999998..45999999999888887..477888777777665 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18   6.3e+02      58     108 ..     242     293 ..     213     296 .. 0.76
   2 ?    9.0   0.0   0.00045       1.6      29      80 ..     526     581 ..     499     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHCCCCHHHHHHCCHCCB-TTSEEEEEE.EHHHHHTT---BES CS
                   RNA_binding  58 kkvlkkllellreeeikeLlkeleervdekgklylrl.dKQaaylgklslve 108
                                   k +++++ e+  +++++eL+++l   +d +g++   + dK + yl k s+ e
  gi|91772494|ref|YP_565186.1| 242 KTAISNISERSPSDRFNELMDNLITIIDSGGSIPRYFqDKAEQYLQKTSIDE 293
                                   7788899999999999999999999999888887666577777777777765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00045
                                   E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCH...HHHHHCC CS
                   RNA_binding  29 eveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeei...keLlkel 80 
                                   ++++  ++ +Gh gn+i+++ a ++   + +++l +++++lr + i     L  + 
  gi|91772494|ref|YP_565186.1| 526 SIKLMAKSKSGHLGNEIRMIWADISWGMNvNDSLIRFANRLRTQVIarsLTLITKA 581
                                   567888999****************99999************99887663343333 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   9.8e-05      0.35      76     136 ..      28      84 ..      17      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.8e-05
                       Fer4_12  76 vkevkeekpekdiwlytgytleelskkekeellkeidvlvdGkfeesledeslrfrgssnq 136
                                   + ++k++++    ++++g+++ + +++ + ++lk++ +++ G ++++++d+  +++++ +q
  gi|91772494|ref|YP_565186.1|  28 LTRLKSKFS----VSSNGTSYSKEKASTYLNILKKLPFTLLGDYVQERKDKYENLQLKLFQ 84 
                                   555555555....89**********99************************9999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); 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:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.42
# Mc/sec: 5136.56
//
Query:       gi|91772495|ref|YP_565187.1|  [L=213]
Description: ribonuclease HII [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  161.3   0.0    2.9e-47  161.1   0.0    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 !  161.1   0.0   1.6e-51   2.9e-47       1     197 [.       4     207 ..       4     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 1.6e-51
                                   EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH...SEEEEEEE-HHHHH.HHTTTS-HH CS
                     RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik...kkiekrklvaeeikyaseneinln 78 
                                   iGiDEaG+Gpv+Gp+ + +v +++++ + lk+lgv+DSKkLs+++r  La +ik         +++ ++i+ +  + ++ n
  gi|91772495|ref|YP_565187.1|   4 IGIDEAGKGPVIGPMCIGGVRIDEDKSNALKNLGVADSKKLSPKRRVHLAAQIKkyaDGWFVYEVSPNQID-ELRKLMSMN 83 
                                   8*****************************************************55444567888889898.77999**** PP

                                   HHHHHHHHHHHHHHHHTCEECCECCCE--SS....HHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHH CS
                     RNase_HII  79 eikaaltlaviklleklgvkvdeilvdgvtt....peslkkkleqiikikvtvekkadekyllvaaASiiAkverdeelel 155
                                   +i + ++  vi++l  ++++ d+ +v+  +      +++ +k  ++ + +v+ ++ ad ++++v+aASi+Akv+rde +e+
  gi|91772495|ref|YP_565187.1|  84 DIMVLAFGSVIEELPSDKIYADAADVKEERFgkrlFDNYMEKHPDVSPPEVISKHGADDLFPVVSAASILAKVRRDELIEK 164
                                   **************************977766576677777777788899******************************* PP

                                   HHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                     RNase_HII 156 lkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                   +k ++g +d+gsGy+sd+kt+++l+++  +    pdivr+s+kt
  gi|91772495|ref|YP_565187.1| 165 IKVDMG-VDIGSGYPSDPKTKKFLENWYREnsSFPDIVRHSWKT 207
                                   ****96.********************9998899*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1494.14
//
Query:       gi|91772496|ref|YP_565188.1|  [L=310]
Description: methylcobalamin:coenzyme M methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-75  253.6   0.0    3.2e-75  253.4   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.4   0.0   1.8e-79   3.2e-75      36     346 .]       2     303 ..       1     303 [. 0.97

  Alignments for each domain:
  == domain 1  score: 253.4 bits;  conditional E-value: 1.8e-79
                                   HHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGGT-EEEEET.TTEEEEE--S-.....GGGS----GG CS
                         URO-D  36 eragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaealGlevefee.gegPvvekpvr.taedveklevpddv 114
                                   + +g++++e++ n e++a ++++ ++ +gl+ + +++d + +a+ lG+++  ++ +++P++++ ++ t+edv++l+vp+++
  gi|91772496|ref|YP_565188.1|   2 QASGTQWPEAHFNSEKMATLAIAGHEIAGLEGIRYPFDGTAIAQTLGCTMGEGTyDTQPSIHDFPFeTIEDVKDLTVPENF 82 
                                   5679**********************************************99995556**********************9 PP

                                   G..G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH CS
                         URO-D 115 ee.grlpyvleaikllkkelggevpligfvgaPftlasylveGgskgfekllkllykdpeevhklldkltdvvieylkaqi 194
                                    e +r++++l+a++++kk+ ++++p+i+++ +P  +  +lv     g++++l++++++p+++++l+ + td++iey +a++
  gi|91772496|ref|YP_565188.1|  83 LEsERIKTILDATEIIKKRADEDIPIIAGHLGPAAITLSLV-----GVRNYLMWFISHPDTIKELITFSTDICIEYSNALL 158
                                   7788*************************************.....*********************************** PP

                                   HTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHH CS
                         URO-D 195 eagAdaiqifD..swagllspedfeefvlpylkrivdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtvdlke 273
                                   e gAd+++i D  + ++l++pe fe++++p +kr+ +e+k+     + i +i+g++a ile++a +g+d++s++++vd++ 
  gi|91772496|ref|YP_565188.1| 159 ERGADVVCIPDseAGPELIPPEFFETMIFPEYKRLNREIKG-----KTIAHICGDSADILEKVAISGFDGISIEEKVDVQY 234
                                   ***********999999************************.....79********99*********************99 PP

                                   HHHSS....EEE--B-G.GGGG.S-HHHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT- CS
                         URO-D 274 aarevgdkvalqGnldPialLl.gspeeiekevkeilekgaggkkgyilnlGhgippetppenvkalveavkey 346
                                   a++++gdk++l+Gn++P+++Ll  +pe++++e+k+++e+g++     il++G+g++p+t+++n+ka+v a++ey
  gi|91772496|ref|YP_565188.1| 235 AKSAIGDKACLIGNVSPVHTLLgMKPEKVKEEAKQCIEDGVD-----ILAPGCGLAPHTSLNNLKAFVAARDEY 303
                                   999*******************99******************.....***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1682.40
//
Query:       gi|91772497|ref|YP_565189.1|  [L=274]
Description: nitroreductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-26   91.6   0.0    7.1e-26   91.3   0.0    1.1  1  Nitroreductase   Nitroreductase family
    6.8e-09   35.2  13.3      3e-05   23.7   2.6    2.4  2  Fer4             4Fe-4S binding domain
    3.1e-08   33.4   0.7    0.00093   18.8   0.0    3.0  3  TM1586_NiRdase   Putative TM nitroreductase
    4.9e-08   33.0   7.0    8.7e-08   32.2   7.0    1.4  1  Fer4_9           4Fe-4S dicluster domain
    7.6e-08   32.8   5.5     0.0051   17.4   2.3    2.5  2  Fer4_7           4Fe-4S dicluster domain
    2.9e-07   31.3   3.6     0.0066   17.4   0.1    2.4  2  Fer4_16          4Fe-4S double cluster binding domain
    1.5e-06   28.0  15.0     0.0015   18.6   3.7    2.4  2  Fer4_6           4Fe-4S binding domain
    2.3e-06   27.6   7.1     0.0026   17.9  11.5    2.3  2  Fer4_10          4Fe-4S dicluster domain
     0.0002   21.6   9.2      0.031   14.8   1.8    2.3  2  Fer4_4           4Fe-4S binding domain
    0.00056   20.3  10.3      0.022   15.2   1.0    2.4  2  Fer4_8           4Fe-4S dicluster domain
    0.00072   19.6   9.7      0.051   13.7   3.4    2.3  2  Fer4_21          4Fe-4S dicluster domain
     0.0016   18.4  14.1     0.0032   17.5   3.2    2.5  2  Fer4_2           4Fe-4S binding domain
     0.0071   16.9  12.8       0.58   10.7   3.1    2.4  2  Fer4_17          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.057   14.3   3.8        1.1   10.1   0.1    2.3  2  Fer4_22          4Fe-4S dicluster domain
        0.1   13.2  11.6       0.13   12.9   3.1    2.5  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
       0.16   13.0  17.9        1.6    9.8   5.3    2.4  2  Fer4_3           4Fe-4S binding domain
       0.19   11.4   0.0        6.5    6.4   0.0    2.1  2  CAP59_mtransfer  Cryptococcal mannosyltransferase 1
       0.67   10.2   7.8       0.42   10.8   1.4    2.3  2  Fer4_18          4Fe-4S dicluster 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 !   91.3   0.0   7.1e-29   7.1e-26       3     170 .]      90     255 ..      88     255 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 7.1e-29
                                   H--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG.....H CS
                Nitroreductase   3 kRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke.....e 78 
                                    RrS+R+++de+v+k ++e+il+ ar+aPs++n qp++ ++v++ e+ +k+  +  +++++  a++ +++ +        +
  gi|91772497|ref|YP_565189.1|  90 MRRSVRNYKDEKVEKSTIEEILDIARYAPSGMNNQPVHWTIVHNPEEVKKITSLTIDWMREVVADDIEHPLKPLMptlisV 170
                                   6*****************************************************************999998766****** PP

                                   HHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH...HHHHHHT- CS
                Nitroreductase  79 lklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaae...evrkllgl 156
                                   ++++ ++  +ga  l ++          +ae ++++ + d+ +a+  + LaA+a+++g+c+ g++ +aa     + + l+l
  gi|91772497|ref|YP_565189.1| 171 YENGSDPICRGALHLAFA----------HAEAENPTGYTDSIIALSWFELAAQAFDIGACWAGFLAIAATsyqPLIDELDL 241
                                   ******************..........**************************************77766669******* PP

                                   S..SEEEEEEEEE- CS
                Nitroreductase 157 pdeeeivvliavGy 170
                                   p+e+ +++ +++G+
  gi|91772497|ref|YP_565189.1| 242 PQEHVVQYSMMFGH 255
                                   *999999*****97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   2.6     3e-08     3e-05       2      23 ..       5      26 ..       4      27 .. 0.90
   2 !   16.8   3.1   4.4e-06    0.0044       8      24 .]      45      61 ..      43      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3e-08
                                  EEETTTSSS-THHHHHSTTTEE CS
                          Fer4  2 videekCigCGaCvevCPvgAI 23
                                   +++e+C++C  Cve CP   I
  gi|91772497|ref|YP_565189.1|  5 SVNPELCTNCDVCVELCPMSII 26
                                  69****************8766 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.4e-06
                                  SSS-THHHHHSTTTEEE CS
                          Fer4  8 CigCGaCvevCPvgAIt 24
                                  C +CG C+  CP gAI+
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPEGAIS 61
                                  ***************96 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   1.7e-05     0.017       2      29 ..      84     111 ..      83     112 .. 0.89
   2 !   18.8   0.0   9.4e-07   0.00093     159     187 ..     106     134 ..     103     151 .. 0.78
   3 ?    1.6   0.0      0.18   1.8e+02      92     108 ..     209     225 ..     189     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                   HHHHHHH--B---B--S---HHHHHHHH CS
                TM1586_NiRdase   2 lyeaiekRhsvRkYkdealeeelleelk 29 
                                   + + + +R+svR+Ykde++e++++ee+ 
  gi|91772497|ref|YP_565189.1|  84 IGKYMVMRRSVRNYKDEKVEKSTIEEIL 111
                                   567899******************9985 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 9.4e-07
                                   HHHHHHHHHHTS--GGG----EEE.E-SS CS
                TM1586_NiRdase 159 wfkeileaarlAPsAlNqqpwrfelkddd 187
                                    ++eil++ar+APs +N+qp++ +++ + 
  gi|91772497|ref|YP_565189.1| 106 TIEEILDIARYAPSGMNNQPVHWTIVHNP 134
                                   689******************99988853 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                                   HHHHHHTT-EEEEES-- CS
                TM1586_NiRdase  92 vLkltalGlgtcWvggt 108
                                    L ++a ++g cW g+ 
  gi|91772497|ref|YP_565189.1| 209 ELAAQAFDIGACWAGFL 225
                                   5889999******9975 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   7.0   8.7e-11   8.7e-08       2      51 .]      11      60 ..      10      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 8.7e-11
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  Ct+C+ Cve Cp+ ++ +++ +++    ++    C +Cg C+  Cp+gai
  gi|91772497|ref|YP_565189.1| 11 CTNCDVCVELCPMSIILPSEEGGTPYSPEEATVYCSKCGHCEVFCPEGAI 60
                                  *******************999999998888899*************997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.3   5.1e-06    0.0051      30      51 ..       3      24 ..       1      25 [. 0.87
   2 !   16.3   0.1   1.1e-05     0.011       2      19 ..      45      62 ..      33     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.1e-06
                        Fer4_7 30 kveidpekClgCgaCvavCPtg 51
                                   + ++pe C++C++Cv+ CP  
  gi|91772497|ref|YP_565189.1|  3 VISVNPELCTNCDVCVELCPMS 24
                                  57899***************75 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-05
                        Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                  C +Cg C++ Cp +ai++
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPEGAIST 62
                                  888999999999888875 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 !   14.4   0.8   5.7e-05     0.057       2      21 ..      11      30 ..      10      41 .. 0.85
   2 !   17.4   0.1   6.6e-06    0.0066       2      19 ..      45      62 ..      44     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-05
                       Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                  C++C  C+e CP + i   +
  gi|91772497|ref|YP_565189.1| 11 CTNCDVCVELCPMSIILPSE 30
                                  9***********99998774 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 6.6e-06
                       Fer4_16  2 CgtCgkCaevCPtnaike 19
                                  C +Cg C   CP++ai++
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPEGAIST 62
                                  ****************95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   3.7   1.5e-06    0.0015       1      24 []       3      26 ..       3      26 .. 0.93
   2 !   14.9   3.5   2.2e-05     0.022       9      24 .]      45      60 ..      44      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  v+ ++p++C+ C+ Cv  CP+ +i
  gi|91772497|ref|YP_565189.1|  3 VISVNPELCTNCDVCVELCPMSII 26
                                  689*****************9876 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.2e-05
                        Fer4_6  9 CigCgdCvrvCPegai 24
                                  C  Cg C++ CPegai
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPEGAI 60
                                  99*************8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  11.5   2.6e-06    0.0026       3      56 .]       5      56 ..       3      56 .. 0.74
   2 !   13.1   0.3   8.1e-05     0.081       8      24 ..      44      70 ..      37     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-06
                       Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   ++++ C++C  Cv+ CP+++     ++e       +++   C +cg C   CP
  gi|91772497|ref|YP_565189.1|  5 SVNPELCTNCDVCVELCPMSI--ILPSEEGGTPYSPEEATVYCSKCGHCEVFCP 56
                                  6799***************55..3333333344444455566***********9 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.1e-05
                       Fer4_10  8 tCirCgkCvkaCPadl..........t 24
                                   C +Cg C  +CP  +          +
  gi|91772497|ref|YP_565189.1| 44 YCSKCGHCEVFCPEGAistlfdstyyQ 70
                                  6************97666555544440 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.8   3.1e-05     0.031       1      16 [.       8      23 ..       8      26 .. 0.92
   2 !   10.9   0.9   0.00054      0.54       4      16 ..      45      57 ..      39      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                        Fer4_4  1 qerCigCgsCvaaCPq 16
                                  +e C++C++Cv  CP+
  gi|91772497|ref|YP_565189.1|  8 PELCTNCDVCVELCPM 23
                                  588************6 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00054
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C  Cg C+ +CP 
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPE 57
                                  99**********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 !    9.4   2.6    0.0014       1.4      49      65 .]       9      25 ..       5      25 .. 0.89
   2 !   15.2   1.0   2.2e-05     0.022      45      64 ..      39      58 ..      28      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                        Fer4_8 49 wsCttcgaCtevCpvgi 65
                                  + Ct+c  C+e Cp++i
  gi|91772497|ref|YP_565189.1|  9 ELCTNCDVCVELCPMSI 25
                                  57************987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.2e-05
                        Fer4_8 45 eealwsCttcgaCtevCpvg 64
                                  eea  +C+ cg+C++ Cp+g
  gi|91772497|ref|YP_565189.1| 39 EEATVYCSKCGHCEVFCPEG 58
                                  68889*************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 !   13.7   3.4   5.1e-05     0.051      33      53 ..       3      23 ..       1      27 [. 0.84
   2 !    9.5   0.4    0.0011       1.1       8      25 ..      45      62 ..      40      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                       Fer4_21 33 vlkvvedeCvGCnlCssvCPv 53
                                  v+ v  + C+ C++C++ CP+
  gi|91772497|ref|YP_565189.1|  3 VISVNPELCTNCDVCVELCPM 23
                                  5678899*************7 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                       Fer4_21  8 CigCgkCliaCedtshqa 25
                                  C +Cg+C + C+++++  
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPEGAIST 62
                                  888999999999877654 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.2   3.2e-06    0.0032       3      21 ..       4      22 ..       2      23 .. 0.92
   2 ?    6.2   3.3     0.012        12      10      22 .]      45      57 ..      43      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.2e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  + v+++ C++C  Cv  CP
  gi|91772497|ref|YP_565189.1|  4 ISVNPELCTNCDVCVELCP 22
                                  679**************** PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                        Fer4_2 10 CigCgaCvsaCPa 22
                                  C  Cg C   CP+
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPE 57
                                  999****999**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 !   10.7   3.1   0.00058      0.58      44      60 ..       9      25 ..       4      26 .. 0.85
   2 !    9.8  13.0    0.0011       1.1       2      59 ..      11      58 ..      10      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                       Fer4_17 44 slCieCgeCerkCPqgl 60
                                  +lC++C  C++ CP+++
  gi|91772497|ref|YP_565189.1|  9 ELCTNCDVCVELCPMSI 25
                                  68999999999999976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                  C++C  C++ Cp+ ++ ++e+  + +   +        ee+   C++Cg Ce  CP+g
  gi|91772497|ref|YP_565189.1| 11 CTNCDVCVELCPMSIILPSEEGGTPYS--P--------EEATVYCSKCGHCEVFCPEG 58
                                  *******************99999988..2........346789************87 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.9     0.061        61      80      95 ..       9      24 ..       3      26 .. 0.71
   2 ?   10.1   0.1    0.0011       1.1       2      25 ..      45      70 ..      44     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.061
                       Fer4_22 80 sgCvGCgRCieacpvk 95
                                  + C+ C  C+e cp++
  gi|91772497|ref|YP_565189.1|  9 ELCTNCDVCVELCPMS 24
                                  5677777777777765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
                       Fer4_22  2 ClsCgaCtlvCptCsCfdvedet..k 25
                                  C +Cg+C + Cp     ++ d+t  +
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPEGAISTLFDSTyyQ 70
                                  99**********99999988887431 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.1   0.00013      0.13       1      18 [.       6      23 ..       6      24 .. 0.93
   2 ?    4.7   1.4     0.045        45       6      18 ..      45      57 ..      43      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  V+ + C++c++Cvel+P 
  gi|91772497|ref|YP_565189.1|  6 VNPELCTNCDVCVELCPM 23
                                  78999************5 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.045
                       Fer4_13  6 CiacgaCvelaPd 18
                                  C+ cg C  ++P+
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPE 57
                                  ************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 ?    8.9   4.7    0.0033       3.3       1      12 [.      11      22 ..      11      25 .. 0.94
   2 ?    9.8   5.3    0.0016       1.6       1      15 []      45      59 ..      45      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0033
                        Fer4_3  1 CtgCgaCvevCP 12
                                  Ct+C  Cve CP
  gi|91772497|ref|YP_565189.1| 11 CTNCDVCVELCP 22
                                  ************ PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0016
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C  Cg C++ CP+gA
  gi|91772497|ref|YP_565189.1| 45 CSKCGHCEVFCPEGA 59
                                  999***********9 PP

>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.069        69      34      59 ..     166     191 ..     136     204 .. 0.77
   2 ?    6.4   0.0    0.0065       6.5     192     213 ..     212     233 ..     197     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.069
               CAP59_mtransfer  34 vfvSiyesgskdgtkeaLraleaele 59 
                                   + +S+ye+gs+   + aL+ + a+ e
  gi|91772497|ref|YP_565189.1| 166 TLISVYENGSDPICRGALHLAFAHAE 191
                                   679*********99999996545444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0065
               CAP59_mtransfer 192 ldpvpVksCWnGmvaldaepfl 213
                                    +++ + +CW G  a+ a+ + 
  gi|91772497|ref|YP_565189.1| 212 AQAFDIGACWAGFLAIAATSYQ 233
                                   36999*************9883 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.4   0.00042      0.42      61      75 ..      11      25 ..       4      32 .. 0.89
   2 ?    2.8   0.7      0.13   1.3e+02      56      74 ..      40      58 ..      33      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                       Fer4_18 61 cidcescvkvcPtgi 75
                                  c++c++cv++cP+ i
  gi|91772497|ref|YP_565189.1| 11 CTNCDVCVELCPMSI 25
                                  *************98 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                       Fer4_18 56 kgagdcidcescvkvcPtg 74
                                  +++  c +c++c   cP g
  gi|91772497|ref|YP_565189.1| 40 EATVYCSKCGHCEVFCPEG 58
                                  56678************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1695.51
//
Query:       gi|91772498|ref|YP_565190.1|  [L=124]
Description: hypothetical protein Mbur_0455 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 922.96
//
Query:       gi|91772499|ref|YP_565191.1|  [L=106]
Description: translation initiation factor IF-1A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-17   61.9   0.2    4.8e-17   61.5   0.2    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.2   2.7e-21   4.8e-17       1      64 []      28      90 ..      28      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 2.7e-21
                                  EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                        eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                  +e+ ++V+ +lg+ +++ +++d g  ++++ipg  ++++w+++Gd+V++ +++++++k++++++
  gi|91772499|ref|YP_565191.1| 28 NEILATVSALLGGKRVTLQCMD-GIVRMGRIPGSKKKRMWVREGDIVIITPWDFQDSKAEVIWK 90
                                  6889*****************6.***************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 848.81
//
Query:       gi|91772500|ref|YP_565192.1|  [L=447]
Description: L-threonine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-25   90.0   0.0      5e-25   88.5   0.0    1.6  1  PALP            Pyridoxal-phosphate dependent enzyme
    7.4e-21   74.2   0.1    3.7e-20   71.9   0.0    2.3  2  Thr_synth_N     Threonine synthase N terminus
  ------ inclusion threshold ------
      0.029   13.7   0.0      0.049   13.0   0.0    1.3  1  DUF3387         Domain of unknown function (DUF3387)
       0.17   12.4   0.0        1.1    9.8   0.0    2.3  2  Peptidase_S66C  LD-carboxypeptidase C-terminal domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.0   1.1e-28     5e-25      19     285 ..      88     386 ..      81     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1.1e-28
                                   CCCCEEEEEEGGGSTTSBTTHHHHHHHHHH....HHTTTTTSEEEEEBSSHHHHHHHHHHHHH.T-EEEEEEETTS-.HHH CS
                          PALP  19 elgvplflKlEslnptgSfKdRgaeyllar....lkegtgaktvveassGNhgralAaaaall.Glkvtivvpadas.pek 93 
                                   e+  + ++ + +  pt SfKd +a  +       lk+++++ t+++a+sG++g a+A+a   l ++kv++++p++   + +
  gi|91772500|ref|YP_565192.1|  88 EVDENTYIMRLDRGPTASFKDFAARMMARLmqfyLKKENKNLTILTATSGDTGSAVAHAFYDLdNIKVIVLFPETEVsERQ 168
                                   66777899999**************44444889988888************************99*********9984577 PP

                                   HHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTT.SHHHHHH...HHTHHHHHHHHTTTTEE..EEEEE-S CS
                          PALP  94 vallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfd.nptvieg...ygtiglEileqlggkpd..avvvpvG 166
                                   ++++  l  ++  +  +g +d+++a+++++ a+ ++  +++ ++ n+ +i     ++   +  + +l + p+      p G
  gi|91772500|ref|YP_565192.1| 169 RKQMTTLDGNISAIamDGKFDDCQALVKQAFAD-PDLKHLNLSSaNSINIGRlipQSIYYFYAYLKLREFPEeiIYSIPSG 248
                                   8889999999999988*****************.99999999988777555441344444444455555555222467777 PP

                                   SSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B....................SSS.CCSTCS...CG CS
                          PALP 167 gGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs...................dtiadglavg...sp 225
                                   + g+++G++ + + + p ++ i + ++++d +  ++ +g+++++++s                    ti  g         
  gi|91772500|ref|YP_565192.1| 249 NFGNMMGCVLAKRMGVP-IKKILASVNENDEVPVFFNTGEYSKIEPSkncisnamnvghpsnlarlVTIYGGEMDEtghIT 328
                                   77***********9888.8999999**********************9777777777777666666444444444423333 PP

                                   TTCCHHHHSEEEE..EEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTC CS
                          PALP 226 selafelldrlvd..eivtvsdeealeamrllarregivvepssaaalaalklreagelkeg 285
                                      ++++l          +v+dee+ + +++++++ gi++ep++a+++ +l l  +++ +++
  gi|91772500|ref|YP_565192.1| 329 KMPDMDVLN---NdiFSTSVTDEETTAIVKEFYEDYGIFIEPHGAVGIKGL-LDYRAASNDD 386
                                   333333333...3445889********************************.6655555555 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 !   71.9   0.0   8.2e-24   3.7e-20       3      79 .]       4      80 ..       2      80 .. 0.98
   2 ?   -2.4   0.0       1.3   5.8e+03      47      62 ..     103     118 ..      96     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 8.2e-24
                   Thr_synth_N  3 iSTRgeaeklsfeeallkGlAeDgGLyvPeeiPklsaeeleelrklsYaelafevlklfiedeipeedLkeliekaY 79
                                  +ST  +a+++sfe+al++GlA+D GLy+P+ +P++s+eel++l++  Y+e+af++l++ +e ei+e+ Lke++ +aY
  gi|91772500|ref|YP_565192.1|  4 YSTNLKADEVSFETALITGLAPDKGLYMPKDLPHFSEEELSSLKDEPYPEIAFRLLSRILEGEIDEASLKEITYDAY 80
                                  69*************************************************************************99 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                   Thr_synth_N  47 klsYaelafevlklfi 62 
                                   + s+++ a++++++ +
  gi|91772500|ref|YP_565192.1| 103 TASFKDFAARMMARLM 118
                                   6789999999988765 PP

>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.049     149     191 ..      33      75 ..      21      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                       DUF3387 149 pdisiLseefleevkkmkeknlavelLkklLadeikarsrkNl 191
                                   +d+ ++see l+ +k+ +++++a+ lL ++L+ ei + s k++
  gi|91772500|ref|YP_565192.1|  33 KDLPHFSEEELSSLKDEPYPEIAFRLLSRILEGEIDEASLKEI 75 
                                   48999*******************************9987765 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00024       1.1      23      70 ..     149     202 ..     128     248 .. 0.81
   2 ?   -0.6   0.0      0.42   1.9e+03      86     104 ..     266     284 ..     245     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                                   -.-TT..EEEEEE-.-TT....HHHHHHHHHHHHCTSTTGGG--EEEEEE--.. CS
                Peptidase_S66C  23 e.kdlkgkILflEd.vse....spyridrmLtqlkeagvldkvkGivlGrftkp 70 
                                   + ++ k ++Lf E+ vse    ++  +d +++++++ g++d+++++v   f +p
  gi|91772500|ref|YP_565192.1| 149 DlDNIKVIVLFPETeVSErqrkQMTTLDGNISAIAMDGKFDDCQALVKQAFADP 202
                                   33567889******88889999************************98777766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.42
                                   HHHHHHT-GGGTTS-EEEE CS
                Peptidase_S66C  86 leevlaeiledlkiPvlyn 104
                                   ++++la++ e+ ++Pv++n
  gi|91772500|ref|YP_565192.1| 266 IKKILASVNENDEVPVFFN 284
                                   88999999999*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3209.33
//
Query:       gi|91772501|ref|YP_565193.1|  [L=374]
Description: hypothetical protein Mbur_0458 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-06   26.1   0.7      1e-05   25.3   0.7    1.4  1  DDE_Tnp_1  Transposase DDE domain
     0.0014   18.7   0.6     0.0036   17.4   0.6    1.6  1  Hit1_C     Hit1 C-terminal
  ------ inclusion threshold ------
      0.014   15.5   0.8      0.037   14.2   0.8    1.8  1  Mg296      Mg296 protein


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.7   1.7e-09     1e-05      27     182 ..     128     293 ..      97     296 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-09
                     DDE_Tnp_1  27 ykggk..ykygyklhiavdtrsglilsvvitpgnvhd...skglkqlldelrprkgklvlaDaGYasaelldtleekgvdy 102
                                   + +++  ++y y   ++++  +++ +s+  + + +      k++++++d ++  k  ++  D+ + s++++ +l+e+ + +
  gi|91772501|ref|YP_565193.1| 128 QAKKStnSFYSYISLCIINKYTRFTISMLPVEKGKTKtdyLKYFIDVVDKINL-KINILCLDREFYSRDVFTFLQENDIPH 207
                                   33222458999999999999999999999864444440115666667777777.*************************** PP

                     DDE_Tnp_1 103 iirl.kkntklyrk........................gaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntn 158
                                   i ++ +k +++++                          ++ k+ +  r+++ ++ l  +    +                
  gi|91772501|ref|YP_565193.1| 208 ITPVvRKGKRIKDIldgnnkryekyvmknkkgdvgldiAIDVKYLKGKRGKNGCENLGFVVYGIDW--------------- 273
                                   ****97777777666776664443444444444444444666666666666666666666666666............... PP

                     DDE_Tnp_1 159 sellsaeevaelyrlRwqiErvFk 182
                                       ++ ++  +yr+R +iE++ +
  gi|91772501|ref|YP_565193.1| 274 ----EPGKISTIYRKRFTIESSYR 293
                                   ....****************9875 PP

>> Hit1_C  Hit1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.6     6e-07    0.0036      20      67 ..      67     118 ..      58     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6e-07
                        Hit1_C  20 vkfhlakv.yrilttsegn...ggssdtlsseakkqlavdylntlryGGvhy 67 
                                   +++hl+k+ +  l  ++++   ++s++tl s+ k +la+dy n   yG v y
  gi|91772501|ref|YP_565193.1|  67 MRYHLHKIdFDQLIENNAKillQSSHKTLDSNKKYDLAIDYTNDPYYGEVNY 118
                                   68*****965666655554232466677*********************999 PP

>> Mg296  Mg296 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   6.1e-06     0.037       9      68 ..      65     124 ..      58     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-06
                                   HHHHHHHHTS-HHHHHHHHHHHHHHHHT-SSGGGSS---.S-HHHHHHHHHHHHHHHHHHH CS
                         Mg296   9 tflkeilekvdlekliqnynlileretstlliyedddye.eidffeksieselfyvksklv 68 
                                   t ++  l+k+d+++li+n  +il ++ +  l   +  y+  id+ + +  +e++yv+++ v
  gi|91772501|ref|YP_565193.1|  65 TSMRYHLHKIDFDQLIENNAKILLQSSHKTL-DSNKKYDlAIDYTNDPYYGEVNYVNENYV 124
                                   5678899****************99998776.5566777579**************87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2663.88
//
Query:       gi|91772502|ref|YP_565194.1|  [L=373]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   12.6   0.1       0.14   11.6   0.1    1.5  1  DUF4283   Domain of unknown function (DUF4283)
       0.12   12.5   0.0       0.51   10.4   0.0    2.1  2  DUF772    Transposase domain (DUF772)


Domain annotation for each model (and alignments):
>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.6e-05      0.14      24      59 ..     256     291 ..     235     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                       DUF4283  24 lsalrrvlakaWklkggvkikelgdglflfrfssee 59 
                                   ++++ ++++k+Wkl+g +++k+ ++ +fl++   e+
  gi|91772502|ref|YP_565194.1| 256 MERIDHWVNKMWKLGGSIHMKYEEKLHFLYENGREK 291
                                   678999***********************9866655 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.7e-05      0.51       5      70 ..      62     130 ..      61     133 .. 0.80
   2 ?   -3.3   0.0       1.1   9.7e+03      21      37 ..     310     326 ..     309     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.7e-05
                        DUF772   5 yppelmlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70 
                                   y +  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f   rl++  l++++
  gi|91772502|ref|YP_565194.1|  62 YKVSSMIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVIyRLGKtgLDEVM 130
                                   67889*************9999998772566667666664433.89**********99999999977766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                        DUF772  21 glSdreleealrenlsf 37 
                                   ++S r  +e++++++ +
  gi|91772502|ref|YP_565194.1| 310 DYSHRGECERVHNHIKW 326
                                   568888999***99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2342.72
//
Query:       gi|91772503|ref|YP_565195.1|  [L=73]
Description: hypothetical protein Mbur_0460 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 542.76
//
Query:       gi|91772504|ref|YP_565196.1|  [L=231]
Description: phosphoribosylformylglycinamidine synthase I [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  161.8   0.0    1.9e-47  161.6   0.0    1.1  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    1.2e-10   41.5   0.0    1.8e-10   40.8   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
    2.1e-10   40.5   0.0    4.2e-10   39.5   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.8e-08   34.4   0.0    2.7e-08   33.8   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    4.9e-06   26.5   0.0    2.7e-05   24.1   0.0    1.9  2  SNO            SNO glutamine amidotransferase family
    0.00041   20.2   0.0     0.0012   18.7   0.0    1.7  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 !  161.6   0.0   6.4e-51   1.9e-47       3     259 ..       2     227 ..       1     228 [. 0.92

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 6.4e-51
                      GATase_5   3 kvailreeGvngeyemaaafeka.GfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklreal 82 
                                    +ai+ + G+n++ ++ + +e+  G ea+ v       ++ +ld++ ++++pGGfsygD l +g+++++     + + +++
  gi|91772504|ref|YP_565196.1|   2 TIAIIQFGGSNCDLDVLHVLEDVvGTEAELVWY-----KEHDLDKYDGVIIPGGFSYGDYLRAGAIASR-----TPIMDSI 72 
                                   589*****************9853777777766.....5569**********************98873.....5679*** PP

                      GATase_5  83 ekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvfl.kgmeglslpvah 161
                                   +k+ ++ ++ ++GiCnGfq+L++ gl++g          +lt N+  +f+++++++ v +++sp     k++e++++p+ah
  gi|91772504|ref|YP_565196.1|  73 KKMADE-GKPIMGICNGFQILTESGLLDG----------ALTTNEYPKFRCEWTNLrVETNDSPFTSAfKKGEVIRIPIAH 142
                                   *99999.**********************..........9****************999999**99777************ PP

                      GATase_5 162 GeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervveavqksiipeee 242
                                    eG+f + +e++l+++e+n +va+rYvd+++++t +  +NPNgS+e+iagi s +  v++lmpHper++e++  s      
  gi|91772504|ref|YP_565196.1| 143 MEGNFYA-DEATLSNMEDNDLVAFRYVDNAKHVTDD--VNPNGSQENIAGILSGNRNVMGLMPHPERASEEILGS------ 214
                                   *******.9**********************99986..7******************************999988...... PP

                      GATase_5 243 eeevspwlrlFenavky 259
                                       ++++r+Fe++++y
  gi|91772504|ref|YP_565196.1| 215 ----NDGVRMFESMIEY 227
                                   ....4678888888888 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 !   40.8   0.0   6.2e-14   1.8e-10      54     123 ..      34     109 ..      22     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.2e-14
                                   GGGCTCCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--.SGG CS
                     DJ-1_PfpI  54 lddvkaaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTs.ypa 123
                                   +++ + ++yD +++pGG +  ++lr+ +      +++ +k++a++gk++  IC g q+L + g+l+g  +T  yp+
  gi|91772504|ref|YP_565196.1|  34 YKEHDLDKYDGVIIPGGFSYGDYLRAGAiasrtPIMDSIKKMADEGKPIMGICNGFQILTESGLLDGALTTNeYPK 109
                                   5677889****************9975433333899******************************9987742455 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 !   39.5   0.0   1.4e-13   4.2e-10      15      91 ..      14      95 ..       3     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.4e-13
                      GATase_3 15 dldpLeaepevrvrfvpl...kdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                  dld+L+  ++v +  ++l   k+ +l++ +d vi+pGg+++   +++ a++ ++ + ++ik++a +g+p++giC G+q+L e+
  gi|91772504|ref|YP_565196.1| 14 DLDVLHVLEDVVGTEAELvwyKEHDLDK-YDGVIIPGGFSYgdyLRAGAIASRTPIMDSIKKMADEGKPIMGICNGFQILTES 95
                                  7787777777766555432228999965.*********97611166677889999*************************986 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   9.1e-12   2.7e-08      21     109 ..      26     151 ..      12     214 .. 0.64

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 9.1e-12
                                   T-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT.. CS
                        GATase  21 gvkvevvpidasaeeilellknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQllaiefgr.. 90 
                                   g + e+v++++ +      l+++dg++++gG+ +           ++  ++ ik+++++++Pi+GIC G+Q+l+++     
  gi|91772504|ref|YP_565196.1|  26 GTEAELVWYKEHD------LDKYDGVIIPGGFSYGDylragaiasRTPIMDSIKKMADEGKPIMGICNGFQILTESGLLdg 100
                                   5677778877544......4569*********999899888887767777888899999*************987644455 PP

                                   .................................EEEEEECEEEEEEEEEEEE CS
                        GATase  91 .................................kvvkekekehhggtmrlgd 109
                                                                    +v++     h+ g+   ++
  gi|91772504|ref|YP_565196.1| 101 alttneypkfrcewtnlrvetndspftsafkkgEVIRIP-IAHMEGNFYADE 151
                                   666666665555555555555555555555555555555.555555555555 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     9e-09   2.7e-05      25      83 ..      33      94 ..      16     105 .. 0.80
   2 ?   -0.0   0.0      0.23   6.8e+02     135     176 ..     171     211 ..     146     223 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9e-09
                                  E-SGGGGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCC CS
                           SNO 25 vkrkedlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlillsk 83
                                    +++dl++ d++iiPGG s       + ++ rt +++++++++ ++ k+++G C G+ +l++
  gi|91772504|ref|YP_565196.1| 33 WYKEHDLDKYDGVIIPGGFSYGdylrAGAIASRTPIMDSIKKMADEG-KPIMGICNGFQILTE 94
                                  345679***********998642222689***********9999988.*********988875 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.23
                                   EEEE-.TTTCEEEEECTTEEEEEE..ETTEEEESS-GGGSTTHC CS
                           SNO 135 ieeilddeavkvlyeldgeivvak..qkkilatsfhPelaeddi 176
                                    +++ dd + +  +e   +i ++    ++++++  hPe a ++i
  gi|91772504|ref|YP_565196.1| 171 AKHVTDDVNPNGSQE---NIAGILsgNRNVMGLMPHPERASEEI 211
                                   444444333333333...23333321559999999999988766 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.9e-07    0.0012      97     131 ..      71     103 ..      32     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.9e-07
                 Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtlyqdie 131
                                    i+++ ++g+Pi+giC G+q+l  +  G l  ++ 
  gi|91772504|ref|YP_565196.1|  71 SIKKMADEGKPIMGICNGFQIL--TESGLLDGALT 103
                                   47999****************9..55566655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1682.87
//
Query:       gi|91772505|ref|YP_565197.1|  [L=82]
Description: phosphoribosylformylglycinamidine synthase subunit PurS [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-25   89.1   0.0    1.7e-25   89.0   0.0    1.0  1  PurS           Phosphoribosylformylglycinamidine (FGAM) synth
  ------ inclusion threshold ------
      0.087   12.7   0.0        0.1   12.4   0.0    1.2  1  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
       0.16   12.6   0.0       0.21   12.2   0.0    1.3  1  ThiS           ThiS family


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 !   89.0   0.0   2.9e-29   1.7e-25       2      76 ..       5      78 ..       4      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 2.9e-29
                                  EEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEE CS
                          PurS  2 akveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeie 76
                                  a+v+++ K+g+lDp+G+++k+al++lgy+  +d+++ k++ + le+e+ e a+++v+emc+kl+aNp+i++y+i+
  gi|91772505|ref|YP_565197.1|  5 AEVTIERKSGMLDPEGTTIKRALEHLGYH-TNDIKTSKRYIIYLEGESPEMAKTKVDEMCQKLIANPMIHNYTID 78
                                  89**************************9.*******************************************97 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.7e-05       0.1      14      56 ..      20      62 ..       9      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                 DAHP_snth_FXD 14 ieevierieelGlkvhvskGeertViGviGdtskldkeqleal 56
                                     + + +e lG+ ++ +k ++r +i + G++ ++ k +++++
  gi|91772505|ref|YP_565197.1| 20 GTTIKRALEHLGYHTNDIKTSKRYIIYLEGESPEMAKTKVDEM 62
                                  5678899************************999999888766 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.6e-05      0.21      16      52 ..      15      51 ..       2      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                                  EEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEE CS
                          ThiS 16 lelaegstvaelleaLgerypelalerrvavavNgei 52
                                   +++eg+t++ +le+Lg++ + ++ ++r ++++ ge 
  gi|91772505|ref|YP_565197.1| 15 MLDPEGTTIKRALEHLGYHTNDIKTSKRYIIYLEGES 51
                                  6789****************99998899999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 534.89
//
Query:       gi|91772506|ref|YP_565198.1|  [L=165]
Description: CDP-alcohol phosphatidyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   35.7   3.2    1.1e-08   35.7   3.2    2.6  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
       0.68    9.9   6.3        1.1    9.2   0.6    2.8  3  DUF4083          Domain of unknown function (DUF4083)


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 !   35.7   3.2   1.2e-12   1.1e-08      11      66 .]       3      57 ..       1      57 [. 0.82
   2 ?   -0.8   3.5       0.3   2.7e+03      26      39 ..     127     149 ..      62     155 .. 0.56

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.2e-12
                                  HHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
               CDP-OH_P_transf 11 lllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                  l +s+la++ +++   l+++++l+++++++D lDG +AR  ++ + +G +lDs++D
  gi|91772506|ref|YP_565198.1|  3 LGISFLAAIEFAA-GDLIMGAVLIMLSGIFDVLDGAVARSSGMMTPFGGVLDSVCD 57
                                  5566677755533.33789999999******************999*********9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                                   ...........HHHHHHHHHHHH CS
               CDP-OH_P_transf  26 p.........lvlailllliasl 39 
                                             + ++i+++lia+l
  gi|91772506|ref|YP_565198.1| 127 LiilvlgaltYQIMIAVVLIAIL 149
                                   03333333222223333344444 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.52   4.7e+03       6      14 ..      19      27 ..      16      41 .. 0.58
   2 ?    3.1   0.1      0.01        94       6      24 ..      87     105 ..      81     107 .. 0.87
   3 ?    9.2   0.6   0.00013       1.1       2      27 ..     132     157 ..     131     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.52
                       DUF4083  6 iyliivivL 14
                                  i   ++i+L
  gi|91772506|ref|YP_565198.1| 19 IMGAVLIML 27
                                  443333333 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.01
                       DUF4083   6 iyliivivLilllvfsftl 24 
                                   ++l+ vi Li+  ++s t+
  gi|91772506|ref|YP_565198.1|  87 LWLLCVIALIGSYMVSYTR 105
                                   88999**********9986 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00013
                       DUF4083   2 lgdliyliivivLilllvfsftlfiR 27 
                                   lg+l y+i++ v++++++  +tl+ R
  gi|91772506|ref|YP_565198.1| 132 LGALTYQIMIAVVLIAILTHITLLQR 157
                                   89********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1089.83
//
Query:       gi|91772507|ref|YP_565199.1|  [L=205]
Description: TPR repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for 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-35  118.6   9.0    7.2e-08   31.9   0.1    4.9  5  TPR_1         Tetratricopeptide repeat
    9.2e-32  106.6   0.4    4.5e-07   29.5   0.1    4.7  4  TPR_2         Tetratricopeptide repeat
    1.6e-27   94.9   9.2      2e-09   37.0   0.1    4.7  4  TPR_11        TPR repeat
    5.1e-24   82.4   5.6      2e-06   27.6   0.1    4.8  4  TPR_8         Tetratricopeptide repeat
      1e-20   72.5   2.2    0.00026   21.1   0.0    5.2  5  TPR_17        Tetratricopeptide repeat
    1.5e-18   66.9   0.4    2.1e-05   24.7   0.0    3.9  3  TPR_12        Tetratricopeptide repeat
    2.8e-17   61.4   0.3     0.0026   17.7   0.0    4.7  4  TPR_7         Tetratricopeptide repeat
    2.9e-12   46.3   0.0      0.042   14.7   0.0    5.0  5  TPR_14        Tetratricopeptide repeat
    3.2e-11   43.7   0.0     0.0003   21.4   0.0    4.0  4  TPR_16        Tetratricopeptide repeat
    4.2e-10   40.0   0.0    0.00029   21.3   0.2    3.6  4  TPR_19        Tetratricopeptide repeat
    8.2e-10   38.7   0.0     0.0074   16.4   0.0    3.8  4  TPR_9         Tetratricopeptide repeat
    1.8e-07   30.8   0.3       0.38   10.7   0.0    4.9  5  TPR_10        Tetratricopeptide repeat
    2.4e-06   27.8   0.0       0.19   12.4   0.0    4.5  4  TPR_6         Tetratricopeptide repeat
      3e-05   24.0   0.6       0.45   10.6   0.0    3.6  3  MIT           MIT (microtubule interacting and transport) dom
    0.00015   21.3   0.3      0.018   14.5   0.5    2.1  2  Coatomer_E    Coatomer epsilon subunit
    0.00017   21.7   2.3       0.14   12.4   0.9    2.7  3  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    0.00074   19.5   1.7        2.5    8.2   0.0    4.0  4  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
     0.0029   17.7   0.0        2.6    8.1   0.0    3.1  3  DUF3856       Domain of Unknown Function (DUF3856)
      0.004   16.1   1.9       0.77    8.6   0.0    2.2  2  NARP1         NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.015   15.5   0.2         35    4.9   0.0    3.7  3  PPR           PPR repeat
       0.02   15.1   0.2       0.11   12.7   0.1    2.3  2  Gla           Vitamin K-dependent carboxylation/gamma-carboxy
      0.022   14.8   1.6       0.96    9.5   0.1    2.7  2  SRP_TPR_like  Putative TPR-like repeat
      0.054   12.5   0.0       0.38    9.7   0.1    1.9  2  Paf67         RNA polymerase I-associated factor PAF67
      0.064   13.5   1.6        9.1    6.6   0.1    3.1  3  NRBF2_MIT     MIT domain of nuclear receptor-binding factor 2


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 ?   -2.0   0.1         5   3.7e+03      21      29 ..      25      33 ..      25      33 .. 0.86
   2 !   30.1   0.1   3.7e-10   2.7e-07       1      32 [.      48      79 ..      48      81 .. 0.93
   3 !   27.7   0.0   2.1e-09   1.6e-06       1      34 []      82     115 ..      82     115 .. 0.96
   4 !   31.3   0.1   1.5e-10   1.1e-07       3      27 ..     118     142 ..     117     144 .. 0.93
   5 !   31.9   0.1   9.7e-11   7.2e-08       3      34 .]     155     186 ..     153     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5
                                  HHHHHHHHH CS
                         TPR_1 21 leyyekALe 29
                                  +eyy+ +Le
  gi|91772507|ref|YP_565199.1| 25 IEYYSAVLE 33
                                  89**99987 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 3.7e-10
                                  HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                         TPR_1  1 akalynlGnayfklgkydeAleyyekALelnP 32
                                  a ++ n G ay  l +y++A+ ++e+ Lel+ 
  gi|91772507|ref|YP_565199.1| 48 ALVWTNTGIAYCDLSNYEKAIYCFERGLELDT 79
                                  679***************************95 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 2.1e-09
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++++yn+G a+ + g+++e +  y+k L ++P++
  gi|91772507|ref|YP_565199.1|  82 PDIWYNKGIAHSYVGDHEESIISYSKTLDIDPKY 115
                                   589*****************************97 PP

  == domain 4  score: 31.3 bits;  conditional E-value: 1.5e-10
                                   HHHHHHHHHHHTT-HHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                   a+ n+G +y  lg+y+eAle+ye +
  gi|91772507|ref|YP_565199.1| 118 AWINKGIIYDILGRYEEALECYENV 142
                                   9*********************975 PP

  == domain 5  score: 31.9 bits;  conditional E-value: 9.7e-11
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a++ +G+ay++l ky+eA+ ++ k+L  +P++
  gi|91772507|ref|YP_565199.1| 155 AWNKKGVAYHHLDKYEEAITCFAKVLNADPDY 186
                                   9*****************************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   5.8e-09   4.4e-06       1      34 []      48      81 ..      48      81 .. 0.94
   2 !   21.0   0.0   3.2e-07   0.00024       1      34 []      82     115 ..      82     115 .. 0.95
   3 !   24.3   0.0   2.8e-08   2.1e-05       3      27 ..     118     142 ..     116     146 .. 0.93
   4 !   29.5   0.1   6.1e-10   4.5e-07       3      34 .]     155     186 ..     153     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.8e-09
                         TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                  a ++ n G ay  l +ye+A+ +fe+ leld +n
  gi|91772507|ref|YP_565199.1| 48 ALVWTNTGIAYCDLSNYEKAIYCFERGLELDTDN 81
                                  6799**************************9876 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 3.2e-07
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ++++yn G a+ + gd+ee +  + k l +dP++
  gi|91772507|ref|YP_565199.1|  82 PDIWYNKGIAHSYVGDHEESIISYSKTLDIDPKY 115
                                   579*****************************85 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 2.8e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekA 27 
                                   a+ n G +y  lg+yeeAle++e +
  gi|91772507|ref|YP_565199.1| 118 AWINKGIIYDILGRYEEALECYENV 142
                                   8*********************975 PP

  == domain 4  score: 29.5 bits;  conditional E-value: 6.1e-10
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   a++  G ay +l++yeeA+ +f k+l  dP++
  gi|91772507|ref|YP_565199.1| 155 AWNKKGVAYHHLDKYEEAITCFAKVLNADPDY 186
                                   9*****************************85 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   2.6e-12     2e-09       3      38 ..      57      92 ..      55      93 .. 0.95
   2 !   18.2   0.0   1.9e-06    0.0014       8      38 ..      96     126 ..      95     127 .. 0.97
   3 !   17.5   0.2   3.3e-06    0.0025       7      40 ..     129     165 ..     128     167 .. 0.90
   4 !   27.6   0.9   2.3e-09   1.7e-06       3      41 ..     162     200 ..     160     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.6e-12
                        TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                  ay+++ +ye+Ai ++++ l+ld dn++++yn G a+
  gi|91772507|ref|YP_565199.1| 57 AYCDLSNYEKAIYCFERGLELDTDNPDIWYNKGIAH 92
                                  8********************************997 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.9e-06
                        TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                   G+ ee+i +Y+k l++dP++ +a+ n G +y
  gi|91772507|ref|YP_565199.1|  96 GDHEESIISYSKTLDIDPKYDNAWINKGIIY 126
                                   899*************************998 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 3.3e-06
                        TPR_11   7 qGkyeeAieaYkkA...lkldPdnaeayynLGlayyk 40 
                                   +G+yeeA+e+Y++     +l++++  a+++ G+ay+ 
  gi|91772507|ref|YP_565199.1| 129 LGRYEEALECYENVhstMELNSKYTIAWNKKGVAYHH 165
                                   7************966679****************95 PP

  == domain 4  score: 27.6 bits;  conditional E-value: 2.3e-09
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   ay+ + kyeeAi+++ k l+ dPd+ +a +nL++a+ k+
  gi|91772507|ref|YP_565199.1| 162 AYHHLDKYEEAITCFAKVLNADPDYEDAKNNLAAAMGKL 200
                                   899999*****************************9886 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00031      0.23       3      34 .]      50      81 ..      48      81 .. 0.88
   2 !   20.4   0.0   5.3e-07    0.0004       2      33 ..      83     114 ..      82     115 .. 0.95
   3 !   22.3   0.1   1.3e-07   9.5e-05       3      25 ..     118     140 ..     116     142 .. 0.94
   4 !   27.6   0.1   2.7e-09     2e-06       3      34 .]     155     186 ..     154     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                  HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                  ++ n g +y +l +ye+A+ ++e+ leld dn
  gi|91772507|ref|YP_565199.1| 50 VWTNTGIAYCDLSNYEKAIYCFERGLELDTDN 81
                                  57777888999*****************9775 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.3e-07
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +++yn+g +++  gd+ee++ +y k l++dp+
  gi|91772507|ref|YP_565199.1|  83 DIWYNKGIAHSYVGDHEESIISYSKTLDIDPK 114
                                   69*****************************8 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.3e-07
                                   HHHHHHHHHHHTT-HHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyye 25 
                                   a+ n+g iy+ lg+yeeA e+ye
  gi|91772507|ref|YP_565199.1| 118 AWINKGIIYDILGRYEEALECYE 140
                                   8*********************9 PP

  == domain 4  score: 27.6 bits;  conditional E-value: 2.7e-09
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   a++++g +y+ l +yeeA+ ++ k+l +dpd+
  gi|91772507|ref|YP_565199.1| 155 AWNKKGVAYHHLDKYEEAITCFAKVLNADPDY 186
                                   8*****************************85 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.016        12      13      33 ..      48      68 ..      37      69 .. 0.93
   2 !   19.6   0.0   1.1e-06   0.00079       1      31 [.      70     100 ..      70     102 .. 0.94
   3 !   21.1   0.0   3.5e-07   0.00026       2      34 .]     105     137 ..     104     137 .. 0.95
   4 !   12.6   0.0   0.00018      0.13       6      33 ..     146     173 ..     145     174 .. 0.94
   5 !    8.1   0.2    0.0052       3.9       1      28 [.     175     202 ..     175     205 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                        TPR_17 13 adaynnLAelllknGdlmtAr 33
                                  a +++n + +++ + ++++A+
  gi|91772507|ref|YP_565199.1| 48 ALVWTNTGIAYCDLSNYEKAI 68
                                  789****************97 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.1e-06
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                   ++++ leld +n+d ++n++ +++  Gd+++
  gi|91772507|ref|YP_565199.1|  70 CFERGLELDTDNPDIWYNKGIAHSYVGDHEE 100
                                   89***********************999987 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 3.5e-07
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   y k l++dP++ +a+ n++ ++  +G++++A++
  gi|91772507|ref|YP_565199.1| 105 YSKTLDIDPKYDNAWINKGIIYDILGRYEEALE 137
                                   7899***************************85 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00018
                        TPR_17   6 leldPnnadaynnLAelllknGdlmtAr 33 
                                   +el+ ++  a+n ++++++++ ++++A+
  gi|91772507|ref|YP_565199.1| 146 MELNSKYTIAWNKKGVAYHHLDKYEEAI 173
                                   6999**********************97 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0052
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGd 28 
                                   ++ k+l  dP++ da nnLA ++ k+++
  gi|91772507|ref|YP_565199.1| 175 CFAKVLNADPDYEDAKNNLAAAMGKLKG 202
                                   7889****************99876654 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.8e-08   2.1e-05       3      76 ..      48     113 ..      44     114 .. 0.92
   2 !   17.2   0.0   6.3e-06    0.0047       4      32 ..     117     145 ..     114     152 .. 0.83
   3 !   19.4   0.1   1.3e-06   0.00099       4      48 ..     154     197 ..     151     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.8e-08
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                   a +++n + +++ l +y++A+ ++e+ le+      +d+p+   + +n g+++++ g++ee +  + ++l+i++
  gi|91772507|ref|YP_565199.1|  48 ALVWTNTGIAYCDLSNYEKAIYCFERGLELD-----TDNPD---IWYNKGIAHSYVGDHEESIISYSKTLDIDP 113
                                   567779*************************.....88888...7**************************986 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.3e-06
                        TPR_12   4 talnnlaavlrrlgrydeAlellekalei 32 
                                   +a+ n + ++  lgry+eAle++e ++  
  gi|91772507|ref|YP_565199.1| 117 NAWINKGIIYDILGRYEEALECYENVHST 145
                                   67889999999999999999999988765 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1.3e-06
                        TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattl 48 
                                   +a+n+ ++++++l +y+eA++++ k+l++    +++ + ++a+++
  gi|91772507|ref|YP_565199.1| 154 IAWNKKGVAYHHLDKYEEAITCFAKVLNADP-DYEDAKNNLAAAM 197
                                   57888**********************9983.3334444566665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.5e-06    0.0026       4      34 ..      53      81 ..      50      83 .. 0.83
   2 !    7.5   0.0    0.0062       4.6       2      29 ..      85     110 ..      84     116 .. 0.83
   3 !   14.2   0.0   4.6e-05     0.034       1      24 [.     118     141 ..     118     148 .. 0.89
   4 !   16.5   0.0     8e-06     0.006       2      31 ..     156     185 ..     155     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                         TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkdped 34
                                  n + +y++l +ye+Ai ++e+  +l+ d ++
  gi|91772507|ref|YP_565199.1| 53 NTGIAYCDLSNYEKAIYCFER--GLELDTDN 81
                                  55889****************..88777655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0062
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                   ++n + ++s +Gd+ee i  y +   l+
  gi|91772507|ref|YP_565199.1|  85 WYNKGIAHSYVGDHEESIISYSK--TLD 110
                                   67999*************99988..444 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 4.6e-05
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeq 24 
                                   a+ n + +y  lG+yeeA+e+ye 
  gi|91772507|ref|YP_565199.1| 118 AWINKGIIYDILGRYEEALECYEN 141
                                   56788999999***********96 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 8e-06
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   ++  +++y+ l +yeeAi+++ ++L  + d
  gi|91772507|ref|YP_565199.1| 156 WNKKGVAYHHLDKYEEAITCFAKVLNADPD 185
                                   66679******************7766655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.39   2.9e+02      15      38 ..      19      42 ..       8      51 .. 0.82
   2 !   12.4   0.0   0.00031      0.23       8      41 ..      55      88 ..      49      91 .. 0.89
   3 ?    5.6   0.0     0.047        35      10      41 ..      91     122 ..      86     125 .. 0.87
   4 ?    6.1   0.0     0.033        25       8      29 ..     123     144 ..     118     152 .. 0.84
   5 !   14.7   0.0   5.6e-05     0.042       3      43 ..     155     195 ..     153     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.39
                        TPR_14 15 GdpdeAiallrralalaPddaeaw 38
                                  + pde i+++ ++l+ + +d+ +w
  gi|91772507|ref|YP_565199.1| 19 EYPDEKIEYYSAVLESGSKDPLLW 42
                                  568999*********999999998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00031
                        TPR_14  8 aeallalGdpdeAiallrralalaPddaeawlll 41
                                  + a+  l ++++Ai +++r l+l+ d++++w+  
  gi|91772507|ref|YP_565199.1| 55 GIAYCDLSNYEKAIYCFERGLELDTDNPDIWYNK 88
                                  56788899***********************876 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.047
                        TPR_14  10 allalGdpdeAiallrralalaPddaeawlll 41 
                                   a+   Gd++e+i  + + l+ +P+ + aw+  
  gi|91772507|ref|YP_565199.1|  91 AHSYVGDHEESIISYSKTLDIDPKYDNAWINK 122
                                   666779***********************876 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.033
                        TPR_14   8 aeallalGdpdeAiallrrala 29 
                                   + ++  lG+++eA+++++ + +
  gi|91772507|ref|YP_565199.1| 123 GIIYDILGRYEEALECYENVHS 144
                                   678889***********98766 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 5.6e-05
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   a+ + + a+ +l++++eAi+++ ++l ++Pd ++a   la 
  gi|91772507|ref|YP_565199.1| 155 AWNKKGVAYHHLDKYEEAITCFAKVLNADPDYEDAKNNLAA 195
                                   66777889**************************9988885 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.1     8e+02      18      33 ..      26      41 ..      25      53 .. 0.77
   2 !   21.4   0.0     4e-07    0.0003       4      66 ..      55     114 ..      52     116 .. 0.91
   3 !    7.6   0.0    0.0078       5.8      24      55 ..     109     137 ..     105     144 .. 0.80
   4 !   15.4   0.0     3e-05     0.022      10      67 ..     129     186 ..     120     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
                        TPR_16 18 aaleaalkrdpssPda 33
                                  +++ a+l++++++P+ 
  gi|91772507|ref|YP_565199.1| 26 EYYSAVLESGSKDPLL 41
                                  78999*****999983 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 4e-07
                        TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   + a+ ++ +y++A+  +e+ l++d    d+++ ++++g a+   g+++e +  y + l+ +p+
  gi|91772507|ref|YP_565199.1|  55 GIAYCDLSNYEKAIYCFERGLELD---TDNPDIWYNKGIAHSYVGDHEESIISYSKTLDIDPK 114
                                   6788899*****************...66777**********************999999997 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0078
                        TPR_16  24 lkrdpssPdaaeAllllgdaalrqgrlaeAaa 55 
                                   l+ d   P    A+ ++g ++  +gr++eA++
  gi|91772507|ref|YP_565199.1| 109 LDID---PKYDNAWINKGIIYDILGRYEEALE 137
                                   5556...8888999999999999999999986 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 3e-05
                        TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   +g+y++A++ +e +       +    A++ +g+a+ ++  ++eA+  +++ l a+pd+
  gi|91772507|ref|YP_565199.1| 129 LGRYEEALECYENVHSTMELNSKYTIAWNKKGVAYHHLDKYEEAITCFAKVLNADPDY 186
                                   69*********999888888899**********************9999999999986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0094         7       6      29 ..      63      86 ..      25      89 .. 0.72
   2 !    7.9   0.0    0.0056       4.2       6      35 ..      63      92 ..      60     102 .. 0.84
   3 !   13.9   0.0   7.9e-05     0.059       5      48 ..      96     139 ..      94     145 .. 0.88
   4 !   21.3   0.2   3.9e-07   0.00029       5      62 ..     130     190 ..     128     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0094
                        TPR_19  6 dyaeAlalleqalqedpknaearl 29
                                  +y+ A+  +e+ l+ d +n+++++
  gi|91772507|ref|YP_565199.1| 63 NYEKAIYCFERGLELDTDNPDIWY 86
                                  455555555555555555555555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0056
                        TPR_19  6 dyaeAlalleqalqedpknaearllLAeal 35
                                  +y+ A+  +e+ l+ d +n++++++  +a+
  gi|91772507|ref|YP_565199.1| 63 NYEKAIYCFERGLELDTDNPDIWYNKGIAH 92
                                  7999********************877665 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.9e-05
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                   gd++e +  +++ l+ dpk+++a+++  +++  lg+++eA ++ 
  gi|91772507|ref|YP_565199.1|  96 GDHEESIISYSKTLDIDPKYDNAWINKGIIYDILGRYEEALECY 139
                                   6666666678999***************************9986 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 3.9e-07
                        TPR_19   5 gdyaeAlalleq...alqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   g+y+eAl+ +e+    ++ + k+  a+     a+  l  ++eA+ + ++++++dpd ++++
  gi|91772507|ref|YP_565199.1| 130 GRYEEALECYENvhsTMELNSKYTIAWNKKGVAYHHLDKYEEAITCFAKVLNADPDYEDAK 190
                                   89**********4444488*************************************66655 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.1   8.3e+02      15      40 ..      25      50 ..      18      53 .. 0.84
   2 !   14.5   0.0   3.8e-05     0.028       9      61 ..      62     114 ..      55     118 .. 0.89
   3 ?    6.0   0.0     0.018        14      30      53 ..     117     140 ..     109     143 .. 0.84
   4 !   16.4   0.0   9.9e-06    0.0074      10      66 ..     131     190 ..     130     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                         TPR_9 15 lavverllllaPddpeerrdRGllla 40
                                  ++++  +l   ++dp ++ + +++l+
  gi|91772507|ref|YP_565199.1| 25 IEYYSAVLESGSKDPLLWSEEAIALV 50
                                  6788889999999*****99999875 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.8e-05
                         TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    ++e+a+ + er l l+ d p+ ++  G+++  +G+ ++ +      l+++p+
  gi|91772507|ref|YP_565199.1|  62 SNYEKAIYCFERGLELDTDNPDIWYNKGIAHSYVGDHEESIISYSKTLDIDPK 114
                                   689*********************************99999999999998885 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.018
                         TPR_9  30 eerrdRGlllaqlGclsaAladLe 53 
                                     +   G+++  lG++++Al++ e
  gi|91772507|ref|YP_565199.1| 117 NAWINKGIIYDILGRYEEALECYE 140
                                   67999****************987 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 9.9e-06
                         TPR_9  10 dweralavverl...lllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                   ++e+al+++e +   + l+++    +   G+++++l+ +++A+ ++   l  +pd +da 
  gi|91772507|ref|YP_565199.1| 131 RYEEALECYENVhstMELNSKYTIAWNKKGVAYHHLDKYEEAITCFAKVLNADPDYEDAK 190
                                   5677777777652226679999999*****************************998885 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     0.055        41       9      30 ..      55      76 ..      52      78 .. 0.88
   2 ?    2.2   0.0      0.25   1.8e+02       7      21 ..      87     101 ..      86     111 .. 0.82
   3 !   10.7   0.0   0.00051      0.38       7      31 ..     121     145 ..     120     147 .. 0.85
   4 !    6.9   0.0    0.0079       5.9       9      30 ..     160     181 ..     157     182 .. 0.90
   5 ?   -0.5   0.0       1.7   1.3e+03       4      11 ..     189     196 ..     188     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.055
                        TPR_10  9 analrqrgrydeAealleeala 30
                                  ++a++++ +y++A   +e+ l+
  gi|91772507|ref|YP_565199.1| 55 GIAYCDLSNYEKAIYCFERGLE 76
                                  99***********999999776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                        TPR_10   7 NLanalrqrgrydeA 21 
                                   N ++a++ +g+++e+
  gi|91772507|ref|YP_565199.1|  87 NKGIAHSYVGDHEES 101
                                   6699********997 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00051
                        TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                   N ++++  +gry+eA++ +e + ++
  gi|91772507|ref|YP_565199.1| 121 NKGIIYDILGRYEEALECYENVHST 145
                                   6699999************987665 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0079
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   ++a++++ +y+eA   + ++l+
  gi|91772507|ref|YP_565199.1| 160 GVAYHHLDKYEEAITCFAKVLN 181
                                   89*************9999987 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.7
                        TPR_10   4 slnNLana 11 
                                   + nNLa+a
  gi|91772507|ref|YP_565199.1| 189 AKNNLAAA 196
                                   679***87 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.58   4.3e+02       7      25 ..      55      73 ..      53      73 .. 0.85
   2 ?    1.3   0.0      0.87   6.5e+02       4      32 ..      86     114 ..      83     115 .. 0.80
   3 ?    5.8   0.0     0.033        25      13      27 ..     129     143 ..     118     145 .. 0.84
   4 !   12.4   0.0   0.00025      0.19       7      32 ..     160     185 ..     158     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.58
                                  HHHHHHHHHHHHHHHHHHH CS
                         TPR_6  7 alsyrklgdtdkAlealer 25
                                  + +y  l +++kA+  +er
  gi|91772507|ref|YP_565199.1| 55 GIAYCDLSNYEKAIYCFER 73
                                  78899988******99997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.87
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                   y+ + ++   gd+++++  + + ++  P+
  gi|91772507|ref|YP_565199.1|  86 YNKGIAHSYVGDHEESIISYSKTLDIDPK 114
                                   77777777756*******99999988886 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.033
                                   HHHHHHHHHHHHHHH CS
                         TPR_6  13 lgdtdkAlealerli 27 
                                   lg++++Ale +e++ 
  gi|91772507|ref|YP_565199.1| 129 LGRYEEALECYENVH 143
                                   68**********985 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00025
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                   + +y  l+++++A++ + ++++  Pd
  gi|91772507|ref|YP_565199.1| 160 GVAYHHLDKYEEAITCFAKVLNADPD 185
                                   89999*99**************9998 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.064        48      18      33 ..      62      77 ..      46      79 .. 0.87
   2 !   10.6   0.0   0.00061      0.45       8      29 ..     120     141 ..     118     142 .. 0.90
   3 ?    5.4   0.0     0.025        19      24      46 ..     166     190 ..     159     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.064
                           MIT 18 gnyeeAlelYkealel 33
                                   nye+A+ +++ +lel
  gi|91772507|ref|YP_565199.1| 62 SNYEKAIYCFERGLEL 77
                                  69********999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00061
                           MIT   8 vkkAveeDnagnyeeAlelYke 29 
                                   ++k + +D  g yeeAle+Y++
  gi|91772507|ref|YP_565199.1| 120 INKGIIYDILGRYEEALECYEN 141
                                   7889999*************85 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.025
                           MIT  24 lelYkealelLlqalk.e.kneerr 46 
                                   l++Y+ea+  + ++l+   + e  +
  gi|91772507|ref|YP_565199.1| 166 LDKYEEAITCFAKVLNaDpDYEDAK 190
                                   689***********99333222334 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0023       1.7     181     255 ..      62     136 ..      42     153 .. 0.81
   2 !   14.5   0.5   2.4e-05     0.018     181     245 ..     130     197 ..     114     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                                   THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                    Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                   ++++ A y f+   e    +p++   k +++  +g++ee   +  ++Ld d+k+ ++ iN  +    lg+ +e+ 
  gi|91772507|ref|YP_565199.1|  62 SNYEKAIYCFERGLELDTDNPDIWYNKGIAHSYVGDHEESIISYSKTLDIDPKYDNAWINKGIIYDILGRYEEAL 136
                                   67889999999988888899999999**********************************999999999885543 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.4e-05
                                   THHHHHHHHHHHHHHHS---...HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                    Coatomer_E 181 ekiqdAyyifqelsekykst...plllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaa 245
                                   +++++A+  ++++  +++ +   ++  n k v+  +l++yeeA +   + L+ d+ +e++  Nl  a+
  gi|91772507|ref|YP_565199.1| 130 GRYEEALECYENVHSTMELNskyTIAWNKKGVAYHHLDKYEEAITCFAKVLNADPDYEDAKNNLAAAM 197
                                   78999999999999888766111456799*******************************99998765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0076       5.7      32      68 ..      57      94 ..      40     108 .. 0.68
   2 !   11.3   0.1   0.00043      0.32       3      81 ..      62     141 ..      60     142 .. 0.93
   3 !   12.4   0.9   0.00019      0.14      37      81 ..     130     178 ..     125     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0076
                                  HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHH CS
                        ANAPC3 32 clylngqykrAyellrka.klnskslgcrylfAqcllk 68
                                  +++ +++y++A++ +++  +l+  ++ ++y ++ +   
  gi|91772507|ref|YP_565199.1| 57 AYCDLSNYEKAIYCFERGlELDTDNPDIWYNKGIAHSY 94
                                  67777777777777777777777777777766555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00043
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    ny++Ai ++er l+ +t++p+  y ++ ++   g++++ +  ++k+ ++++k  ++++ ++  +  L++yeeA+ ++e+
  gi|91772507|ref|YP_565199.1|  62 SNYEKAIYCFERGLELDTDNPDIWYNKGIAHSYVGDHEESIISYSKTlDIDPKYDNAWINKGIIYDILGRYEEALECYEN 141
                                   69*************************9999999**999998888888**************999999********9987 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00019
                                   T-HHHHHHHHHCTSHHHC-HHHHHHHH.....HHHHHTT-HHHHHHHH-S CS
                        ANAPC3  37 gqykrAyellrkaklnskslgcrylfA.....qcllkLkkyeeAiaaLek 81 
                                   g+y++A+e +++       l++ y++A      ++  L+kyeeAi+++ k
  gi|91772507|ref|YP_565199.1| 130 GRYEEALECYENV-HSTMELNSKYTIAwnkkgVAYHHLDKYEEAITCFAK 178
                                   7888888888888.445555888888888886788899999999999876 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 ?    4.5   0.1     0.049        37       8      34 ..      55      81 ..      53      84 .. 0.89
   2 ?    2.3   0.0      0.25   1.9e+02       3      37 ..      84     118 ..      82     119 .. 0.88
   3 ?    0.6   0.0      0.83   6.2e+02      14      25 ..     129     140 ..     129     143 .. 0.85
   4 !    8.2   0.0    0.0034       2.5       9      38 ..     161     190 ..     160     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.049
                                  HHHHHHHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  8 AlGhyklgeYseArryvdalLeiEPen 34
                                   +++  l +Y++A  + ++ Le++ +n
  gi|91772507|ref|YP_565199.1| 55 GIAYCDLSNYEKAIYCFERGLELDTDN 81
                                  689999**************9999888 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C   3 clYylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                     Y   ++h  +g+++e+       L i+P+  +a
  gi|91772507|ref|YP_565199.1|  84 IWYNKGIAHSYVGDHEESIISYSKTLDIDPKYDNA 118
                                   678999************99999999999998765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.83
                                   HT-HHHHHHHHH CS
                    Fis1_TPR_C  14 lgeYseArryvd 25 
                                   lg+Y+eA+++ +
  gi|91772507|ref|YP_565199.1| 129 LGRYEEALECYE 140
                                   79******9876 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0034
                                   HHHHHHT-HHHHHHHHHHHHHHTTS-HHHH CS
                    Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQaq 38 
                                   +++  l +Y+eA  +   +L+ +P+ + a+
  gi|91772507|ref|YP_565199.1| 161 VAYHHLDKYEEAITCFAKVLNADPDYEDAK 190
                                   789999********************9997 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0035       2.6      75     126 ..      61     108 ..      44     114 .. 0.84
   2 ?    3.4   0.0       0.1        75     103     127 ..     119     143 ..     112     151 .. 0.78
   3 ?    3.8   0.0     0.076        56      69     125 ..     130     178 ..     127     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                                   HHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                       DUF3856  75 lesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                   l+  +ka++ f+r  el+ d+  +W    ++++ a + +G ++e++ ++ ++
  gi|91772507|ref|YP_565199.1|  61 LSNYEKAIYCFERGLELDTDNPDIW----YNKGIAHSYVGDHEESIISYSKT 108
                                   5566899999**999**********....79999999999999999888765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856 103 vfsravaleelGrkdealkafrmag 127
                                    ++++  ++ lGr++eal+ ++ + 
  gi|91772507|ref|YP_565199.1| 119 WINKGIIYDILGRYEEALECYENVH 143
                                   5678888889999999999887765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.076
                                   T-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                       DUF3856  69 grydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                   gry+eale+ ++         el++     +  a  +++va++ l +++ea+  f +
  gi|91772507|ref|YP_565199.1| 130 GRYEEALECYENVH----STMELNSK----YTIAWNKKGVAYHHLDKYEEAITCFAK 178
                                   55555555444322....22234333....233346788888888888888888766 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.001      0.77     186     261 ..      44     115 ..       4     123 .. 0.81
   2 !    7.1   0.6     0.003       2.2      17      82 ..     129     197 ..     118     205 .] 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                   --SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HH CS
                         NARP1 186 epesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRy 261
                                   e + al+w+++ +A  y  l ++ekA+ + ++ +e +    +++++K+  +   Gd ++ +  +  ++ lD   +y
  gi|91772507|ref|YP_565199.1|  44 EEAIALVWTNTGIA--YCDLSNYEKAIYCFERGLELDTDNPDIWYNKGIAHSYVGDHEESI--ISYSKTLDIDPKY 115
                                   55668889988887..77899***********************************99864..5566666665555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.003
                                   HTHHHHHHHHHHHHGGG-...--HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT CS
                         NARP1  17 agkleeAlehLeekekqi...vDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak 82 
                                    g++eeAle  e++++++          ++k+  + +L+++eeA + + + l+  p+ ++  ++l +a 
  gi|91772507|ref|YP_565199.1| 129 LGRYEEALECYENVHSTMelnSKYTIAWNKKGVAYHHLDKYEEAITCFAKVLNADPDYEDAKNNLAAAM 197
                                   6889999999888777652112223334788999999*******************9999888888776 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.047        35       9      25 ..      57      73 ..      51      78 .. 0.91
   2 ?    4.3   0.0     0.076        57      14      24 ..     130     140 ..     128     144 .. 0.88
   3 ?    1.5   0.0       0.6   4.5e+02      10      25 ..     163     178 ..     162     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.047
                           PPR  9 gycknGkleeAlelfke 25
                                  +yc   ++e+A+ +f++
  gi|91772507|ref|YP_565199.1| 57 AYCDLSNYEKAIYCFER 73
                                  8*************997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.076
                           PPR  14 GkleeAlelfk 24 
                                   G++eeAle+++
  gi|91772507|ref|YP_565199.1| 130 GRYEEALECYE 140
                                   9*******997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.6
                           PPR  10 ycknGkleeAlelfke 25 
                                   y +  k+eeA+ +f +
  gi|91772507|ref|YP_565199.1| 163 YHHLDKYEEAITCFAK 178
                                   667889*****99966 PP

>> Gla  Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014      0.11      19      41 .]     131     153 ..     129     153 .. 0.94
   2 ?   -1.5   0.0       3.9   2.9e+03      20      28 ..     169     177 ..     168     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                   SSSHHHHSC-SSCTTTTTSSSSX CS
                           Gla  19 syEEArEiFeddektkeFWkkYt 41 
                                    yEEA E++e+ + t+e  +kYt
  gi|91772507|ref|YP_565199.1| 131 RYEEALECYENVHSTMELNSKYT 153
                                   59***************999997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                                   SSHHHHSC- CS
                           Gla  20 yEEArEiFe 28 
                                   yEEA  +F 
  gi|91772507|ref|YP_565199.1| 169 YEEAITCFA 177
                                   999998886 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 ?    4.2   0.2     0.057        43      20      41 ..     122     143 ..      50     156 .. 0.72
   2 ?    9.5   0.1    0.0013      0.96      20      52 ..     159     189 ..     145     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.057
                  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs 41 
                                   k + +  l++yeeaL+  ++ +
  gi|91772507|ref|YP_565199.1| 122 KGIIYDILGRYEEALECYENVH 143
                                   5555556778888887776655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsalsedvrfEka 52 
                                   k va+ +l+kyeea++  +k    + d  +E a
  gi|91772507|ref|YP_565199.1| 159 KGVAYHHLDKYEEAITCFAKVL--NADPDYEDA 189
                                   89*************9998865..667777765 PP

>> Paf67  RNA polymerase I-associated factor PAF67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.34   2.6e+02     169     189 ..      53      73 ..      33      79 .. 0.85
   2 ?    9.7   0.1   0.00051      0.38     134     192 ..     128     181 ..     120     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.34
                         Paf67 169 yvGfaylmlrrYkDAirtlsq 189
                                     G+ay  l +Y+ Ai ++++
  gi|91772507|ref|YP_565199.1|  53 NTGIAYCDLSNYEKAIYCFER 73 
                                   579***************987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00051
                         Paf67 134 llGdYttalkvlenidlskkallskvpaahvsllYyvGfaylmlrrYkDAirtlsqill 192
                                   +lG Y++al++ en++ +  +l sk + a        G+ay  l +Y++Ai ++ ++l+
  gi|91772507|ref|YP_565199.1| 128 ILGRYEEALECYENVHSTM-ELNSKYTIA----WNKKGVAYHHLDKYEEAITCFAKVLN 181
                                   6899**********98876.444444443....3468*******************997 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.8   1.3e+03      23      35 ..      63      75 ..      59      82 .. 0.79
   2 ?    4.0   0.1     0.077        57      22      36 ..     130     144 ..     126     160 .. 0.81
   3 ?    6.6   0.1     0.012       9.1      22      34 ..     167     179 ..     156     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.8
                     NRBF2_MIT 23 kyeeaischkkaa 35
                                   ye+ai c ++  
  gi|91772507|ref|YP_565199.1| 63 NYEKAIYCFERGL 75
                                  79******98765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.077
                     NRBF2_MIT  22 Gkyeeaischkkaaa 36 
                                   G+yeea+ c++   +
  gi|91772507|ref|YP_565199.1| 130 GRYEEALECYENVHS 144
                                   9********987655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                     NRBF2_MIT  22 Gkyeeaischkka 34 
                                    kyeeai+c  k 
  gi|91772507|ref|YP_565199.1| 167 DKYEEAITCFAKV 179
                                   69*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 1080.03
//
Query:       gi|91772508|ref|YP_565200.1|  [L=468]
Description: asparagine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-42  146.5   0.1    6.4e-23   82.0   0.0    2.1  2  Asn_synthase  Asparagine synthase
    7.4e-09   35.6   0.0    2.3e-08   34.0   0.0    1.9  1  GATase_7      Glutamine amidotransferase domain
    0.00021   21.5   0.0    0.00089   19.5   0.0    2.2  2  GATase_6      Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.013   14.6   0.0      0.025   13.7   0.0    1.4  1  NAD_synthase  NAD synthase
       0.07   12.5   0.0       0.11   11.9   0.0    1.2  1  DUF3458_C     Domain of unknown function (DUF3458_C) ARM repe


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   1.8e-26   6.4e-23       3     144 ..     207     353 ..     205     357 .. 0.89
   2 !   64.6   0.0   3.4e-21   1.2e-17     204     307 ..     350     451 ..     348     462 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.8e-26
                  Asn_synthase   3 relLedaVkrrlradvpvGalLSGGlDSSliaalaarqsk...splktFsigf.eekgsdeakyakevaehlgtehtelvl 79 
                                    +lL++aV +r+  d  +G+++S G+DS+++a l + +++    + + +++g+  +  s++++ a+++a++l++e    ++
  gi|91772508|ref|YP_565200.1| 207 LSLLKEAVSKRV-PDEDFGVMFSAGIDSTILALLCKGFAEakgVKCNYYTVGLsGQVPSPDIACARKLADELELELNVHEI 286
                                   579******998.9**********************999988888999*****44599*********************** PP

                  Asn_synthase  80 teeelldalpdviyhlee...pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaals 144
                                     + ++++l  v+  +e+   p +   a+ +y ++r+ak++g+ v++ G GaDElf+GY+ f + +++
  gi|91772508|ref|YP_565200.1| 287 GLDTVEEYLSTVVPLIEDatvPKT-GVALTMYAACRAAKEDGINVLFAGAGADELFAGYNRFKSSESV 353
                                   ******************765533.44589******************************77666555 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 3.4e-21
                  Asn_synthase 204 edelhrelyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegy.lPeeileR 283
                                    + +++ +++d+ ++++ +  r D  ++  g  +R+P+lD ++ve+al++p e+k++++ +K +LR+a e + lP+ ++eR
  gi|91772508|ref|YP_565200.1| 350 SESVNEDCIRDIMEMHKVNTYRDDTVAAFTGTIVRYPYLDENFVEYALAIPKEYKISDEMNKIVLRKAGEELgLPKYVVER 430
                                   6789999****************************************************************99******** PP

                  Asn_synthase 284 pKegfsapvgewklkgelrelaee 307
                                    K+++++  g++ ++++l++la++
  gi|91772508|ref|YP_565200.1| 431 GKKAAQY--GSS-FDQALKKLAKR 451
                                   *****98..666.88899998876 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   6.3e-12   2.3e-08      13     122 ..      44     156 ..      32     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 6.3e-12
                      GATase_7  13 aQPmvssedgrlvivfnGeiyNykelreeLeakghrf.....rtksDtevllallea...ewgeealerlnGmfAfaiwde 85 
                                   + P++ s+++++ +v +  iyN +e   e+   +++      r   Dt  l ++ ++   +  ++ l+ ++G +A+a++  
  gi|91772508|ref|YP_565200.1|  44 SSPLS-SSSDKFELVGDIDIYNSDEFACEFHCGNVENmsiltRFLQDTFGLEKCSDDemfQRFDSSLKAIRGVYAIACHIG 123
                                   55666.455566667677777777776666544322111111333444444444333666788999*************99 PP

                      GATase_7  86 eekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                   ++  ++laRD +G+k+L y  ++  +++faSe k l+
  gi|91772508|ref|YP_565200.1| 124 DK--VFLARDLIGVKSLWYDVSS--GFAFASEKKFLE 156
                                   99..******************5..7*******9885 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.5e-07   0.00089      88     134 .]     108     151 ..      21     151 .. 0.84
   2 ?   -2.1   0.0       1.2   4.1e+03      42      62 ..     374     394 ..     367     461 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                      GATase_6  88 vlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                    l+++rG++a+a   +  ++++lard +gvk l+y+v  sg+afase
  gi|91772508|ref|YP_565200.1| 108 SLKAIRGVYAIA--CHIGDKVFLARDLIGVKSLWYDV-SSGFAFASE 151
                                   467889988885..34899*****************9.9*******8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                      GATase_6  42 lllvhNGeiynykelreelpa 62 
                                    + ++ G+i  y+ l e++ +
  gi|91772508|ref|YP_565200.1| 374 TVAAFTGTIVRYPYLDENFVE 394
                                   566778888888877776655 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.9e-06     0.025      10      86 ..     211     292 ..     204     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-06
                                   HHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHH....TCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---H.HH CS
                  NAD_synthase  10 keyvkkaga.kgvvlGlSGGvDSslvaalavkal....gkenvlalllPssvsseedvedalalaenlgievktidik.pi 84 
                                   ke v+k+   + + +  S G+DS++ a l++        k n+ ++ l s + +  d+  a++la++l++e ++ +i  ++
  gi|91772508|ref|YP_565200.1| 211 KEAVSKRVPdEDFGVMFSAGIDSTILALLCKGFAeakgVKCNYYTVGL-SGQVPSPDIACARKLADELELELNVHEIGlDT 290
                                   55555544335566668*************988755544678889999.8888899***********99998888875344 PP

                                   HH CS
                  NAD_synthase  85 vr 86 
                                   v+
  gi|91772508|ref|YP_565200.1| 291 VE 292
                                   44 PP

>> DUF3458_C  Domain of unknown function (DUF3458_C) ARM repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05      0.11      15      80 ..     344     412 ..     342     455 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHHHHHHHHHHHH..TT----HHHHHHH.HHHHT-TTS-HHHHHHHTS---HHHHCTT-SSB CS
                     DUF3458_C  15 fnRweagqrLalrvllalva..eeaalsealveal.ravLedealdpalkaeaLtlPseaelaeqlkev 80 
                                   +nR+ ++++  ++++ + ++  +  +  ++ v+a+ +++++ + ld+ ++++aL++P+e +++++++++
  gi|91772508|ref|YP_565200.1| 344 YNRFKSSESVNEDCIRDIMEmhKVNTYRDDTVAAFtGTIVRYPYLDENFVEYALAIPKEYKISDEMNKI 412
                                   678888888877777777755444455555666551567778999*********************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2974.39
//
Query:       gi|91772509|ref|YP_565201.1|  [L=231]
Description: hypothetical protein Mbur_0466 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.4   0.1    1.7e-67  227.1   0.1    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.25   10.8   0.0    1.4  1  Proteasome       Proteasome subunit


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 !  227.1   0.1   1.9e-71   1.7e-67       1     210 [.       1     215 [.       1     224 [. 0.95

  Alignments for each domain:
  == domain 1  score: 227.1 bits;  conditional E-value: 1.9e-71
               Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgt 80 
                                   mk  vl+s GkDs++aL+   ++   +e L+++ s+n++symfh++n+++  l+ae++G p+ ++ t+Ge+e e +dLk+ 
  gi|91772509|ref|YP_565201.1|   1 MKLGVLFSSGKDSCYALHIMQEKgNSIECLITIKSKNPDSYMFHTPNIDMSRLQAEAMGFPFLETFTEGEKELELDDLKNA 81 
                                   8999**************99888899*****************************************************99 PP

               Diphthami_syn_2  81 lkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrrid 157
                                   + + +     e++v+Ga++s+yqk rie++C elGl  + PLW+ d e+ +   ++++f+ i  +++a+gld  ++G+ i+
  gi|91772509|ref|YP_565201.1|  82 ILEAQkkygLEGIVTGALYSNYQKDRIEKICDELGLDVFSPLWHMDQEQEMRDLLDNGFRFIFSSIAAYGLDSGWVGKEIT 162
                                   855544555************************************************************************ PP

               Diphthami_syn_2 158 kklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrg 210
                                      +d+l +l+ek g++ agegGe+e++v+DaP+fkk++++++++  + +++ 
  gi|91772509|ref|YP_565201.1| 163 TSEVDKLVRLNEKIGLNIAGEGGEFESFVIDAPMFKKKIQINKYDLVERDEYT 215
                                   *********************************************98877765 PP

>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.8e-05      0.25      29      61 ..     160     191 ..     150     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                                   EEEESSSSTSEEEEETTEEEEEEESHHHHHHHH CS
                    Proteasome  29 kllskstveKifkiddhigvafaGlaaDartlv 61 
                                   ++ ++s+v+K+ +++++ig+ +aG+ ++++ +v
  gi|91772509|ref|YP_565201.1| 160 EI-TTSEVDKLVRLNEKIGLNIAGEGGEFESFV 191
                                   44.6778*********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1405.75
//
Query:       gi|91772510|ref|YP_565202.1|  [L=464]
Description: hydroxylamine oxidase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-37  128.8  17.1      2e-35  122.3   4.0    3.0  3  Multi-haem_cyto  Seven times multi-haem cytochrome CxxCH
    4.4e-11   42.6  32.3    3.6e-05   23.7   5.1    4.6  3  Cytochrome_C7    Cytochrome c7 and related cytochrome c
    8.8e-08   32.5  36.3      0.096   13.2   8.9    5.6  4  Cytochrom_c3_2   Cytochrome c3
    2.1e-07   31.8  31.4     0.0015   19.4   1.1    5.9  6  Cytochrome_C554  Cytochrome c554 and c-prime
    4.6e-06   26.3  34.5       0.34   10.7   6.5    6.8  6  Paired_CXXCH_1   Doubled CXXCH motif (Paired_CXXCH_1)
     0.0067   16.1  26.4       0.12   12.1   1.3    5.2  4  Cytochrom_NNT    NapC/NirT cytochrome c family, N-terminal re
  ------ inclusion threshold ------
      0.077   11.9  28.1      0.054   12.4   8.1    3.7  3  Cytochrom_C552   Cytochrome c552
      0.083   13.2  38.2       0.86   10.0   7.2    5.5  6  Cytochrom_CIII   Class III cytochrome C family
        3.8    7.9  38.4        2.2    8.7   0.5    7.8  5  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III


Domain annotation for each model (and alignments):
>> Multi-haem_cyto  Seven times multi-haem cytochrome CxxCH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.2     0.024        48       4      38 ..      31      68 ..      28      72 .. 0.66
   2 !   13.4   1.5   1.8e-05     0.035       3      95 ..      59     154 ..      57     162 .. 0.68
   3 !  122.3   4.0     1e-38     2e-35      97     268 ..     182     363 ..     177     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.024
                                  -HHHHHT-TT-..S-EETTTS----.-HHHHHTT-HHH CS
               Multi-haem_cyto  4 gcidchvdvga..ekaehkkdlrlp.daaacgtchlqe 38
                                  +c+dch ++++    ++  ++ +      +c +ch  e
  gi|91772510|ref|YP_565202.1| 31 SCLDCHSSMNKfpAVIDDWENSKHAeAGITCENCHTAE 68
                                  79999999998654555555554440456888888765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.8e-05
                                   --HHHHHT-TT-..S-EETTTS----..-HHHHHTT-HHHHHHHHTHHHH--..-TT-SS-TT-SSSTTHHHHHHTSHHHH CS
               Multi-haem_cyto   3 vgcidchvdvga..ekaehkkdlrlp..daaacgtchlqefaereserdtle..wpnkqwpkgrpshaldyeanvelavwa 77 
                                   ++c +ch++ +   + + h+   + p  +aa cg+ch+  f e+    ++l   + + +  +g+   +l+ e  + l  ++
  gi|91772510|ref|YP_565202.1|  59 ITCENCHTAEADdpDAIAHMGLYMTPvvSAADCGNCHVAAFEENTRSLHSLGtlYYEVD-FDGQKLPSLESE--ITLDEYT 136
                                   6899***9876545778887655555446899*********998876666541122333.355555556555..5555666 PP

                                   H-S-HHHHHHHHHTS-TT CS
               Multi-haem_cyto  78 ameqrevaegcdmchtnq 95 
                                   + ++ +  +gc+ ch ++
  gi|91772510|ref|YP_565202.1| 137 TASHNATVNGCQACHGTN 154
                                   777888999******765 PP

  == domain 3  score: 122.3 bits;  conditional E-value: 1e-38
                                   -STSSSTTTT--HHHHHSTHHHHTTS-STT--HHHHHHHSHHHHHHHHHTTTS-TTS-GGGTTTTS---S--HHHHHSEET CS
               Multi-haem_cyto  97 kcdschtrhefsaaearkpeacatchngvdhnefenyllskhgtvyevlgdkwnfevplkdalakggqtaptcalchleye 177
                                    c schtrh fs+ earkpeac +ch g dh + e y  skhg++y ++gd+wn+     d  a + + aptca+ch+   
  gi|91772510|ref|YP_565202.1| 182 SCASCHTRHVFSVEEARKPEACQQCHLGPDHPQTEIYFESKHGSIYGTEGDDWNWTEG--DWKAGEDYRAPTCAVCHMSGT 260
                                   7******************************************************865..6666788***********976 PP

                                   TEE..-S--TTT-SS-S-T.STTHHHHT..........TSHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHHHHH CS
               Multi-haem_cyto 178 gey..shnlvrkvrwafnp.vpeiadnl..........ehewfeerkeswvetctkchsesfarsyldvvdkgtleglkke 245
                                    e   +h++  ++ w  +p v + +dn              w e ++e   + c +chse++ ++y + +d ++    kk+
  gi|91772510|ref|YP_565202.1| 261 DELkaTHDVSSRLSWELEPpVSRHTDNTanilgtpisdGTTWQE-KRERMTSVCEQCHSETWVNNYYENADATVELYNKKY 340
                                   654339**********9987555444432223555443345655.5578999*******************9998889999 PP

                                   HHHHHHHHHHHHHT-STTTTTS- CS
               Multi-haem_cyto 246 keakkvveklyedglltgqktnr 268
                                    ++ ++v++l +dgllt q  + 
  gi|91772510|ref|YP_565202.1| 341 ADSSSIVDSLRKDGLLTEQDFDE 363
                                   *****************998665 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   5.1   1.8e-08   3.6e-05      12      72 ..      28      95 ..      20      96 .. 0.79
   2 !   20.5   7.4   1.8e-07   0.00036       6      72 ..     138     207 ..     133     208 .. 0.62
   3 !    6.4   4.0    0.0045       8.9      49      56 ..     301     319 ..     212     347 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.8e-08
                 Cytochrome_C7 12 tgykCtdCHsklfeskakkkmaemekgkskkaeves.ltCgaCHdgknaf............svakkaeCakCH 72
                                  ++ +C dCHs++      +k  ++ +++ ++++ e+  tC +CH+ +  +             v ++a+C++CH
  gi|91772510|ref|YP_565202.1| 28 VSDSCLDCHSSM------NKFPAVIDDWENSKHAEAgITCENCHTAEADDpdaiahmglymtPVVSAADCGNCH 95
                                  4679********......3344556667777888999**********99888888999999866679******* PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.8e-07
                 Cytochrome_C7   6 kshlkatgykCtdCHsklfeskakkk...maemekgkskkaeves.ltCgaCHdgknaf..svakkaeCakCH 72 
                                   +sh + t + C++CH++ ++ k++++       ++g  + +   s  +C++CH++   +  + +k ++C++CH
  gi|91772510|ref|YP_565202.1| 138 ASHNA-TVNGCQACHGTNMTGKSTDDpdvW--PNNGIGRINPDGSsGSCASCHTRHVFSveEARKPEACQQCH 207
                                   55654.6789******99533333222121..2222222222233355******9988777677899****** PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0045
                 Cytochrome_C7  49 t...........CgaCHdg 56 
                                   t           C +CH +
  gi|91772510|ref|YP_565202.1| 301 TwqekrermtsvCEQCHSE 319
                                   0222223333445555544 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   7.7   8.4e-05      0.17      22      79 ..      25      95 ..      20      95 .. 0.72
   2 !   11.2  21.7   0.00019      0.38       2      79 ..      54     207 ..      53     208 .. 0.80
   3 !   13.2   8.9   4.8e-05     0.096       8      65 ..     182     256 ..     177     258 .. 0.65
   4 !    7.6   3.0    0.0026       5.3      18      80 .]     241     318 ..     235     345 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.4e-05
                                  THHHHHHHHHHH--HHHCHTTSST.TSSBTTSSCTSSS-GGGTS-TTT................SBT-GGGGT- CS
                Cytochrom_c3_2 22 kaveeekClsCHgkleelakktkeakeanphkshekeleCteCHkeHk................ksekvCaeCH 79
                                  +a+ +++Cl CH++++++ +  ++    +++k+ e  ++C++CH+                    s + C +CH
  gi|91772510|ref|YP_565202.1| 25 SAAVSDSCLDCHSSMNKFPAVIDD---WENSKHAEAGITCENCHTAEAddpdaiahmglymtpvVSAADCGNCH 95
                                  5677899**********9999885...44555557899******988766666666666655444447777777 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00019
                                   HHCCT.TGGGTSSSST-SSTTHHHHHH...................................................... CS
                Cytochrom_c3_2   2 HakegvkCadCHtkekpkkdkaveeek...................................................... 28 
                                   Ha++g++C++CHt e  + d+ +++                                                        
  gi|91772510|ref|YP_565202.1|  54 HAEAGITCENCHTAEADDPDAIAHMGLymtpvvsaadcgnchvaafeentrslhslgtlyyevdfdgqklpsleseitlde 134
                                   9999999999999888655554444447899999999999999999999999999************************** PP

                                   ............HHHHH--HHHCHTTSST.....TSSBTTSSCTSSS-GGGTS-TTT......SBT-GGGGT- CS
                Cytochrom_c3_2  29 ............ClsCHgkleelakktkea....keanphkshekeleCteCHkeHk......ksekvCaeCH 79 
                                               C++CHg+  + +++++      + +   ++  ++ +C++CH+ H       ++ + C++CH
  gi|91772510|ref|YP_565202.1| 135 yttashnatvngCQACHGTNMTGKSTDDPDvwpnNGIGRINPDGSSGSCASCHTRHVfsveeaRKPEACQQCH 207
                                   ******************999887777755343222222233347889********9555544444******* PP

  == domain 3  score: 13.2 bits;  conditional E-value: 4.8e-05
                                   TGGGTSSSST-SSTTHHHHHHHHHHH--HHHCHTTSST.................TSSBTTSSC.TSSS-GGGTS CS
                Cytochrom_c3_2   8 kCadCHtkekpkkdkaveeekClsCHgkleelakktkea................keanphksh.ekeleCteCH 65 
                                   +Ca+CHt++ ++ ++a + e+C++CH   ++ +++   +                +e ++++   ++  +C+ CH
  gi|91772510|ref|YP_565202.1| 182 SCASCHTRHVFSVEEARKPEACQQCHLGPDHPQTEIYFEskhgsiygtegddwnwTEGDWKAGEdYRAPTCAVCH 256
                                   8**********999************8666555543333334566777666555533333332213555677777 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0026
                                   -SSTTHHHHHHHHHHH--HHHCHTTSST.............................TSSBTTSSCTSSS-GGGTS-TTTS CS
                Cytochrom_c3_2  18 pkkdkaveeekClsCHgkleelakktkea............................keanphkshekeleCteCHkeHkk 70 
                                   +k+ +++++ +C  CH + ++  k+t++                             +              t+  ++ ++
  gi|91772510|ref|YP_565202.1| 241 WKAGEDYRAPTCAVCHMSGTDELKATHDVssrlsweleppvsrhtdntanilgtpisD-------------GTTWQEKRER 308
                                   5566677777888888766544444443447788877777665333333333333332.............3333333333 PP

                                   BT-GGGGT-S CS
                Cytochrom_c3_2  71 sekvCaeCHe 80 
                                    ++vC++CH+
  gi|91772510|ref|YP_565202.1| 309 MTSVCEQCHS 318
                                   3355555553 PP

>> Cytochrome_C554  Cytochrome c554 and c-prime
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.1   7.4e-07    0.0015      47      84 .]      28      66 ..      20      66 .. 0.81
   2 ?    4.0   0.1     0.049        97      48      63 ..      88     103 ..      76     117 .. 0.75
   3 ?   -0.9  10.5       1.7   3.3e+03       2      62 ..      91     158 ..      90     188 .. 0.50
   4 ?   -0.4   1.1       1.1   2.2e+03       2       8 ..     183     189 ..     182     197 .. 0.71
   5 !   16.4   0.8   6.6e-06     0.013       1      64 [.     202     265 ..     202     274 .. 0.75
   6 !    6.2   0.1    0.0097        19       1      29 [.     312     339 ..     301     358 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.4e-07
                                  T-TTTGGGSBSTTTSTT---SSS--GG.GBSS-HHHHH- CS
               Cytochrome_C554 47 eapeClkCHatgagkdkgfvlkektkl.lagVqCesCHg 84
                                   +  Cl+CH ++ + + ++   e++k+ +ag++Ce+CH+
  gi|91772510|ref|YP_565202.1| 28 VSDSCLDCHSSMNKFPAVIDDWENSKHaEAGITCENCHT 66
                                  5679*******9999998877777666378********5 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.049
                                   -TTTGGGSBSTTTSTT CS
               Cytochrome_C554  48 apeClkCHatgagkdk 63 
                                   a++C +CH+++++++ 
  gi|91772510|ref|YP_565202.1|  88 AADCGNCHVAAFEENT 103
                                   6788888888887765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.7
                                   HHHHTHHHHHHHTTSTGGGTTGGGST..TSSHHHHHHTT--TT.....S--TT-TTTGGGSBSTTTST CS
               Cytochrome_C554   2 CaeCHeeqyeswkkskhakaleslkk..ekkaeakkkakldpa.....kdaeeapeClkCHatgagkd 62 
                                   C +CH   +e+  +s h+  +   +   + ++  + +++++ +     ++  + + C +CH t++  +
  gi|91772510|ref|YP_565202.1|  91 CGNCHVAAFEENTRSLHSLGTLYYEVdfDGQKLPSLESEITLDeyttaSHNATVNGCQACHGTNMTGK 158
                                   99999999999999999876544443003333323333332222222133457799*****9998532 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.1
                                   HHHHTHH CS
               Cytochrome_C554   2 CaeCHee 8  
                                   Ca+CH  
  gi|91772510|ref|YP_565202.1| 183 CASCHTR 189
                                   7777765 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 6.6e-06
                                   HHHHHT....HHHHHHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTTSTT- CS
               Cytochrome_C554   1 aCaeCH....eeqyeswkkskhakaleslkkekkaeakkkakldpakdaeeapeClkCHatgagkdkg 64 
                                   aC++CH    + q+e++ +skh + + +   + +    ++ + +  +d  +ap+C  CH++g ++ k+
  gi|91772510|ref|YP_565202.1| 202 ACQQCHlgpdHPQTEIYFESKHGSIYGTEGDDWN---WTEGDWKAGED-YRAPTCAVCHMSGTDELKA 265
                                   7*****666557************9998776543...33344554444.589**********998775 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.0097
                                   HHHHHTHH.HHHHHTTSTGGGTTGGGSTTS CS
               Cytochrome_C554   1 aCaeCHee.qyeswkkskhakaleslkkek 29 
                                   +C++CH e  ++++ +   a+a+ +l ++k
  gi|91772510|ref|YP_565202.1| 312 VCEQCHSEtWVNNYYE--NADATVELYNKK 339
                                   6999997624577754..455555554443 PP

>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.6    0.0023       4.6      28      40 ..      27      39 ..      20      41 .. 0.71
   2 !    5.9   5.8    0.0052        10       6      40 ..      29      68 ..      25      70 .. 0.82
   3 ?    3.7   0.8     0.026        51       8      17 ..      60      69 ..      52      77 .. 0.71
   4 !    6.0   4.8    0.0049       9.7       4      41 ..      86     155 ..      83     156 .. 0.85
   5 !   10.7   6.5   0.00017      0.34       6      37 ..     180     207 ..     178     211 .. 0.85
   6 !    8.6   0.0   0.00075       1.5       9      39 ..     252     319 ..     245     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0023
                Paired_CXXCH_1 28 kgaalCysCHdek 40
                                    ++ C++CH+++
  gi|91772510|ref|YP_565202.1| 27 AVSDSCLDCHSSM 39
                                  5667788888765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0052
                Paired_CXXCH_1  6 egeClsCHnphgsdnpkll......kkakgaalCysCHdek 40
                                  +++Cl+CH+     +p+ +      k a+   +C +CH+++
  gi|91772510|ref|YP_565202.1| 29 SDSCLDCHSSMNK-FPAVIddwensKHAEAGITCENCHTAE 68
                                  456*****99876.888889999998899999999999876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.026
                Paired_CXXCH_1  8 eClsCHnphg 17
                                   C++CH + +
  gi|91772510|ref|YP_565202.1| 60 TCENCHTAEA 69
                                  5899997765 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0049
                Paired_CXXCH_1   4 vaegeClsCHnphgsdnpkll................................kkakgaalCysCHdeka 41 
                                   v++ +C +CH +  ++n + l                                  + + + C+ CH +++
  gi|91772510|ref|YP_565202.1|  86 VSAADCGNCHVAAFEENTRSLhslgtlyyevdfdgqklpsleseitldeyttaSHNATVNGCQACHGTNM 155
                                   55668*****999999999999999999999999999999999999999988877888889999998766 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00017
                Paired_CXXCH_1   6 egeClsCHnphgsdnpkllkkakgaalCysCH 37 
                                   +g+C sCH +h       + +a++++ C++CH
  gi|91772510|ref|YP_565202.1| 180 SGSCASCHTRHVF----SVEEARKPEACQQCH 207
                                   689********54....5558999******** PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.00075
                Paired_CXXCH_1   9 ClsCH.........................nphgsdnpkll............kkakgaalCysCHde 39 
                                   C  CH                         ++h  + +++l            k+++ + +C +CH+e
  gi|91772510|ref|YP_565202.1| 252 CAVCHmsgtdelkathdvssrlsweleppvSRHTDNTANILgtpisdgttwqeKRERMTSVCEQCHSE 319
                                   777887777777777777777777777777889999999999999999999999999*********97 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.3     6e-05      0.12      16      75 ..      10      68 ..       2      82 .. 0.63
   2 !    9.0   6.2   0.00054       1.1      39     166 ..      61     189 ..      61     197 .. 0.68
   3 ?   -1.7   6.6       1.1   2.1e+03      67      91 ..     182     206 ..     171     278 .. 0.55
   4 !    5.3   3.2    0.0072        14     112     148 ..     297     333 ..     248     349 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                 Cytochrom_NNT 16 vvvgvvflggfntaleatsteeFCvsCHemednveeykesiHysnrsgvraeCsdCHvPk 75
                                  +++++++l+++ +  +a+  ++ C+ CH+ ++++ ++ ++   s +     +C++CH  +
  gi|91772510|ref|YP_565202.1| 10 TIIAILILIIVPVSASAA-VSDSCLDCHSSMNKFPAVIDDWENSKHAEAGITCENCHTAE 68
                                  444454444444444333.3456*****977776666655555555556679*****876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00054
                 Cytochrom_NNT  39 CvsCHemedn.veeykesiHysnrsgvraeCsdCHvPkelvkklarkiqaskevlaklvgkidtkekfeakrlelaerewa 118
                                   C +CH+ e    +++ +   y       a+C +CHv    ++  +r ++++  ++ ++  ++d ++    + +   ++ ++
  gi|91772510|ref|YP_565202.1|  61 CENCHTAEADdPDAIAHMGLYMTPVVSAADCGNCHVAA--FEENTRSLHSLGTLYYEV--DFDGQKLPSLESEITLDEYTT 137
                                   89999988875666666666777777789*******85..677788888999999999..666554444333333444444 PP

                 Cytochrom_NNT 119 rmkandsreCrnCHseeamdlekqkkkaakahkkaa....eeektCidCHkg 166
                                     ++   + C++CH ++ +  ++ +++   +          ++ +C +CH+ 
  gi|91772510|ref|YP_565202.1| 138 ASHNATVNGCQACHGTNMTGKSTDDPDVWPNNGIGRinpdGSSGSCASCHTR 189
                                   455556789*******977777776665444333224444445599999975 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.1
                 Cytochrom_NNT  67 eCsdCHvPkelvkklarkiqaskev 91 
                                   +C++CH  + +    ark +a +++
  gi|91772510|ref|YP_565202.1| 182 SCASCHTRHVFSVEEARKPEACQQC 206
                                   4444444444444444444433332 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0072
                 Cytochrom_NNT 112 laerewarmkandsreCrnCHseeamdlekqkkkaak 148
                                      + w++ ++   + C++CHse+ ++   ++++a+ 
  gi|91772510|ref|YP_565202.1| 297 SDGTTWQEKRERMTSVCEQCHSETWVNNYYENADATV 333
                                   4567788888888888999998886655544444433 PP

>> Cytochrom_C552  Cytochrome c552
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.9   7.2e-05      0.14     236     285 ..      49      97 ..      42     108 .. 0.82
   2 ?   -0.4   1.6      0.21   4.1e+02     238     285 ..     137     189 ..     132     196 .. 0.57
   3 ?   12.4   8.1   2.7e-05     0.054      76     219 ..     189     364 ..     183     395 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.2e-05
                                   HHTSHHHHTT--HHHHHS-EEETTSEEEE----S-GGGGCCCTGGGT--S CS
                Cytochrom_C552 236 ysegvHakngvsCaDCHmPkvkegakkvtdHkvtsPlksiekaCksCHkq 285
                                   ++++ Ha++g++C +CH +      +       + P+ s    C +CH  
  gi|91772510|ref|YP_565202.1|  49 WENSKHAEAGITCENCHTAEADDPDAIAHMGLYMTPVVSA-ADCGNCHVA 97 
                                   99***************98877665555555688999888.89*****64 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.21
                                   TSHHHHTT--HHHHHS-EEETTSEEEE----S-GGGGCC.....CTGGGT--S CS
                Cytochrom_C552 238 egvHakngvsCaDCHmPkvkegakkvtdHkvtsPlksie.....kaCksCHkq 285
                                   ++ H +    C  CH   ++ ++++  d + ++ + +i+      +C+sCH++
  gi|91772510|ref|YP_565202.1| 137 TASHNATVNGCQACHGTNMTGKSTDDPDVWPNNGIGRINpdgssGSCASCHTR 189
                                   55566666666666666666555555555555555555444444567777764 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 2.7e-05
                                   ---SSTT-SSSBGGGGTTT.-THHHHHHHHHHH..........HHHCSSBCCCCTTT--...S-S-HHHHB-TTTHHB--- CS
                Cytochrom_C552  76 gapkeaeegkqpaaCltCk.spdvprlieekge..........edyfstkyaevgkeiv...nsvgCadCHdpkdmeLrit 142
                                   ++ ++ ee+ +p aC +C+ +pd p+      +          +   + +++e   +     ++ +Ca CH + + eL+ t
  gi|91772510|ref|YP_565202.1| 189 RHVFSVEEARKPEACQQCHlGPDHPQTEIYFESkhgsiygtegD---DWNWTEGDWKAGedyRAPTCAVCHMSGTDELKAT 266
                                   5556778999********97789996532222222235553332...2233333333323334489***********9988 PP

                                   -HHHHHHHHHTT-..................--CTTS-HHHHHHHHHCTTSS--EEECCCECCCCEEE-S-TT-SSHHHHH CS
                Cytochrom_C552 143 rptlkralealgv..................devkkatrqekrtlvCaqCHveYyfkkdeekkskkvtfPWdkgktvenie 205
                                    +  +r   +l+                   d ++ ++++e+ t vC qCH e  +++  e+ +++v +  +k  +  +i 
  gi|91772510|ref|YP_565202.1| 267 HDVSSRLSWELEPpvsrhtdntanilgtpisDGTTWQEKRERMTSVCEQCHSETWVNNYYENADATVELYNKKYADSSSIV 347
                                   8766665555555666777888888998877656667888888**********9999999999999999888888888888 PP

                                   HHHHHTT...--SEE-T CS
                Cytochrom_C552 206 kyydeie...fadwthk 219
                                   + +++++    +d+ + 
  gi|91772510|ref|YP_565202.1| 348 DSLRKDGlltEQDFDEP 364
                                   88888877665565554 PP

>> Cytochrom_CIII  Class III cytochrome C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.2   0.00043      0.86      47     102 .]      29      95 ..      22      95 .. 0.83
   2 ?    7.1   2.3    0.0034       6.8      32      92 ..      89     160 ..      82     169 .. 0.67
   3 ?    7.5  11.2    0.0026       5.2      43     102 .]     140     207 ..     117     207 .. 0.71
   4 ?    8.5   5.4    0.0013       2.6      33      57 ..     182     210 ..     173     229 .. 0.69
   5 ?   -0.6   4.3      0.85   1.7e+03      69      69 ..     301     301 ..     240     323 .. 0.42
   6 ?    3.0   0.5     0.064   1.3e+02      32      40 ..     311     319 ..     280     347 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00043
                                   TS-CTCTS-SSS.TTTSTTCHHHHHHCSSTTTCHHHHHHHHHHTSHH...........HCHHSHHHHC CS
                Cytochrom_CIII  47 iekcstcHaeek.ekkekkslekavHkkkaaksCvgCHkkkkkekke...........keptkCaech 102
                                    ++c +cH++ +   +  + +e+  H++    +C +CH+++++++              + + C++ch
  gi|91772510|ref|YP_565202.1|  29 SDSCLDCHSSMNkFPAVIDDWENSKHAEAGI-TCENCHTAEADDPDAiahmglymtpvVSAADCGNCH 95 
                                   57999***99975456668999999*97666.*********988777999999999888889999998 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0034
                                   HTHHHTSTT..CTTSCSTS-CTCTS-SSS..........TTTSTTCHHHHHHCSSTTTCHHHHHHHHHHTSHH CS
                Cytochrom_CIII  32 keCeeCHhk..eeekeeiekcstcHaeek..........ekkekkslekavHkkkaaksCvgCHkkkkkekke 92 
                                   ++C +CH +  ee+++++++  t   e +          ++ + +++++a H+++  + C+ CH ++ + k++
  gi|91772510|ref|YP_565202.1|  89 ADCGNCHVAafEENTRSLHSLGTLYYEVDfdgqklpsleSEITLDEYTTASHNATV-NGCQACHGTNMTGKST 160
                                   47888888877677777777777555554445556555444444566888898554.5999999887766655 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0026
                                   TSCSTS-CTCTS-SSS..TTTSTTCH..HHHHHCSSTT...TCHHHHHHHHHHTSHH.HCHHSHHHHC CS
                Cytochrom_CIII  43 ekeeiekcstcHaeek..ekkekksl..ekavHkkkaa...ksCvgCHkkkkkekke.keptkCaech 102
                                   ++ +++ c++cH ++   +++++  +  ++ + + + +    sC +CH+++  + +e ++p +C++ch
  gi|91772510|ref|YP_565202.1| 140 HNATVNGCQACHGTNMtgKSTDDPDVwpNNGIGRINPDgssGSCASCHTRHVFSVEEaRKPEACQQCH 207
                                   456788999999887645333333334533333322224448********9987766699*******9 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0013
                                   THHHTSTT....CTTSCSTS-CTCTS-SS CS
                Cytochrom_CIII  33 eCeeCHhk....eeekeeiekcstcHaee 57 
                                   +C++CH      +ee ++ e+c++cH   
  gi|91772510|ref|YP_565202.1| 182 SCASCHTRhvfsVEEARKPEACQQCHLGP 210
                                   67777765557777777777777777666 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.85
                                   H CS
                Cytochrom_CIII  69 a 69 
                                   +
  gi|91772510|ref|YP_565202.1| 301 T 301
                                   1 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.064
                                   HTHHHTSTT CS
                Cytochrom_CIII  32 keCeeCHhk 40 
                                   + Ce+CH +
  gi|91772510|ref|YP_565202.1| 311 SVCEQCHSE 319
                                   257777766 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.2   9.9         9   1.8e+04      13      24 ..      60      71 ..      23     111 .. 0.72
   2 ?    8.7   0.5    0.0011       2.2      13      33 ..     146     167 ..     137     180 .. 0.73
   3 ?   -4.9  10.1         9   1.8e+04      13      21 ..     182     190 ..     177     238 .. 0.70
   4 ?    7.3   0.0     0.003         6       9      24 ..     246     262 ..     239     294 .. 0.64
   5 ?    4.2   0.0     0.026        53       7      20 ..     306     319 ..     300     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: -5.2 bits;  conditional E-value: 9
               Cytochrome_CBB3 13 nCasCHgkggag 24
                                  +C  CH++++  
  gi|91772510|ref|YP_565202.1| 60 TCENCHTAEADD 71
                                  566666655544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
               Cytochrome_CBB3  13 nCasCHgkggagpslagr.dwe 33 
                                    C++CHg+++ g+s  +   w+
  gi|91772510|ref|YP_565202.1| 146 GCQACHGTNMTGKSTDDPdVWP 167
                                   6******998887666332454 PP

  == domain 3  score: -4.9 bits;  conditional E-value: 9
               Cytochrome_CBB3  13 nCasCHgkg 21 
                                   +CasCH+ +
  gi|91772510|ref|YP_565202.1| 182 SCASCHTRH 190
                                   577777633 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.003
               Cytochrome_CBB3   9 lykk.nCasCHgkggag 24 
                                    y++ +Ca CH +g   
  gi|91772510|ref|YP_565202.1| 246 DYRApTCAVCHMSGTDE 262
                                   46666******966433 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.026
               Cytochrome_CBB3   7 aalykknCasCHgk 20 
                                   ++++++ C +CH +
  gi|91772510|ref|YP_565202.1| 306 RERMTSVCEQCHSE 319
                                   678999******84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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):               9  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.51
# Mc/sec: 2726.65
//
Query:       gi|91772511|ref|YP_565203.1|  [L=85]
Description: hypothetical protein Mbur_0468 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-05   23.3   0.9    3.5e-05   23.3   0.9    1.0  1  MPS2            Monopolar spindle protein 2
    9.5e-05   21.9   0.1    0.00011   21.7   0.1    1.1  1  FAM76           FAM76 protein
     0.0035   17.1   0.6     0.0055   16.4   0.6    1.3  1  DivIC           Septum formation initiator
     0.0042   16.3   0.3     0.0048   16.2   0.3    1.0  1  HAP1_N          HAP1 N-terminal conserved region
     0.0063   16.5   0.9     0.0082   16.1   0.9    1.2  1  Sec2p           GDP/GTP exchange factor Sec2p
     0.0072   16.7   1.1       0.01   16.2   1.1    1.3  1  Syntaxin_2      Syntaxin-like protein
     0.0082   16.0   0.2     0.0087   15.9   0.2    1.0  1  Spc29           Spindle Pole Component 29
  ------ inclusion threshold ------
      0.014   15.2   0.4      0.017   14.9   0.4    1.2  1  Phage_GP20      Phage minor structural protein GP20
      0.015   15.0   0.2      0.016   14.9   0.2    1.1  1  Med4            Vitamin-D-receptor interacting Mediator subun
      0.017   14.0   0.2      0.017   14.0   0.2    1.1  1  Spc7            Spc7 kinetochore protein
      0.021   15.1   0.2      0.039   14.3   0.2    1.6  1  HalX            HalX domain
      0.022   14.9   0.8      0.024   14.7   0.8    1.2  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
      0.033   14.5   2.2      0.046   14.0   2.1    1.3  1  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.035   14.7   1.5       0.86   10.3   1.1    2.0  2  SlyX            SlyX
      0.037   14.3   0.0      0.043   14.1   0.0    1.1  1  ATG16           Autophagy protein 16 (ATG16)
       0.04   14.2   0.0      0.054   13.8   0.0    1.1  1  DUF948          Bacterial protein of unknown function (DUF948
       0.08   12.8   0.2      0.095   12.5   0.2    1.1  1  DUF724          Protein of unknown function (DUF724)
       0.13   12.5   0.1        3.4    8.0   0.0    2.0  2  Sterile         Male sterility protein
       0.27   11.5   2.5       0.45   10.8   2.0    1.4  1  XhlA            Haemolysin XhlA
       0.32   11.0   4.3        1.3    9.1   4.2    1.8  1  FlxA            FlxA-like protein
        2.1    8.3   4.8        5.1    7.1   0.9    2.8  3  Pox_A_type_inc  Viral A-type inclusion protein repeat


Domain annotation for each model (and alignments):
>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.9     4e-08   3.5e-05     156     218 ..       3      66 ..       1      85 [] 0.76

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4e-08
                          MPS2 156 nrklkaLevrveslkdELeakdevlrekeRelleLkkrlseykekYellqrefs.lykarrvek 218
                                   n   k+++ ++++lk+ L++kde + + + +++eL++ ++ ++e++   + e + l+ a   +k
  gi|91772511|ref|YP_565203.1|   3 NDPFKQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNERFSGHSDEMNqLFDANPSQK 66 
                                   667899***************************************9877776654544444333 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.3e-07   0.00011     222     274 ..       7      59 ..       5      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                         FAM76 222 tqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekea 274
                                   +q++++i +lk+ql++kd+++++ d +i el++     +++   +  e+++ +
  gi|91772511|ref|YP_565203.1|   7 KQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNERFSGHSDEMNQLF 59 
                                   799****************************9988777777666666666555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.6   6.4e-06    0.0055      20      53 ..       7      40 ..       5      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                         DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksd 53
                                  kq++++i++l+++l+++ +++ +L+ ++ +L+s 
  gi|91772511|ref|YP_565203.1|  7 KQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSY 40
                                  799***************************9754 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 !   16.2   0.3   5.6e-06    0.0048     211     263 ..       6      58 ..       3      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-06
                        HAP1_N 211 lseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneel 263
                                   +++ ++qi+el+ +l++k e++     +i +L++ i  l++++  ++ e ++l
  gi|91772511|ref|YP_565203.1|   6 FKQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNERFSGHSDEMNQL 58 
                                   78899*****************************************9999887 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.9   9.6e-06    0.0082      46      86 ..       7      47 ..       2      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.6e-06
                                  HHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXX CS
                         Sec2p 46 ealekkneklkeqLkeketlleslqeqLkeLkevlekmeee 86
                                  ++++k+ ++lk+qL+ek++ + +l+ q  eL + ++ ++e+
  gi|91772511|ref|YP_565203.1|  7 KQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNER 47
                                  689****************************9999888775 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.1   1.2e-05      0.01      13      67 ..      11      66 ..       3      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                    Syntaxin_2 13 stleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldnsssdsq 67
                                  +++++l +qL  k     +l+ ++ el+++in l ++ + +  +++ql + +++++
  gi|91772511|ref|YP_565203.1| 11 KQIDELKRQLDEKDeKIVDLDGQIIELTSYINMLNERFSGHSDEMNQLFDANPSQK 66
                                  455555566655542599******************************99997652 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2     1e-05    0.0087     130     185 ..      10      67 ..       2      82 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                         Spc29 130 kleIkeLkreleqqrtvnseLqekvaeleeevkrl..aalehSnrkfrsyssapsnst 185
                                   + +I eLkr+l+++   +  L  ++ el + +++l  +   hS++  + +   ps++ 
  gi|91772511|ref|YP_565203.1|  10 QKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLneRFSGHSDEMNQLFDANPSQKR 67 
                                   5678888888888888888888888888888887732234577777777777777664 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 ?   14.9   0.4     2e-05     0.017      18      71 ..       4      54 ..       1      63 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                    Phage_GP20 18 akldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakae 71
                                  + +++++++ d+lk ql+++d+++ dL ++     eL+  i+ l++ +   ++e
  gi|91772511|ref|YP_565203.1|  4 DPFKQIQKQIDELKRQLDEKDEKIVDLDGQ---IIELTSYINMLNERFSGHSDE 54
                                  6799***********************888...888888888888877665555 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   1.8e-05     0.016      24      69 ..       6      57 ..       2      81 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                          Med4 24 hqknearilqLraeveslDekikeivksLkeyekeLkavp......dqensk 69
                                  +++++++i++L+ +  ++Deki ++ +++ e+ + ++ +       ++e+++
  gi|91772511|ref|YP_565203.1|  6 FKQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNerfsghSDEMNQ 57
                                  899**********************988777777666554333544344444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2     2e-05     0.017     202     251 ..       7      56 ..       1      68 [. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                          Spc7 202 eelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeia 251
                                   ++++++++elk +++ek +++ +l  q+ el++ i+ l+e+ s + +e++
  gi|91772511|ref|YP_565203.1|   7 KQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNERFSGHSDEMN 56 
                                   55566666666666666666666666666666666666666555555554 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.6e-05     0.039      33      57 ..       2      26 ..       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                          HalX 33 dseeYqeLearleelraqldetlde 57
                                  +++ + +++ +++el++qlde  + 
  gi|91772511|ref|YP_565203.1|  2 ENDPFKQIQKQIDELKRQLDEKDEK 26
                                  7999****************98766 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 ?   14.7   0.8   2.9e-05     0.024     151     183 ..       6      38 ..       2      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                       UPF0242 151 lqeyqetieeqrsvlekrqdqieqLeskVrDln 183
                                   +++ q++i e++  l++++++i +L+ ++  l+
  gi|91772511|ref|YP_565203.1|   6 FKQIQKQIDELKRQLDEKDEKIVDLDGQIIELT 38 
                                   67899*********************9998876 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.1   5.3e-05     0.046      45      87 ..       8      47 ..       2      56 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-05
                       BLOC1_2 45 slekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87
                                  +++k++++l++   +l+++ ++i +++ q+ eL++ +++L+e 
  gi|91772511|ref|YP_565203.1|  8 QIQKQIDELKR---QLDEKDEKIVDLDGQIIELTSYINMLNER 47
                                  44444444444...66666666666666666666666666654 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1     0.001      0.86      28      52 ..       8      32 ..       3      35 .. 0.84
   2 ?    6.0   0.0     0.022        19       3      35 ..      25      57 ..      23      67 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                                  HHHHHHHHHHHHHHHHHHT-XXXXX CS
                          SlyX 28 eqqqqidrlqrqlrllaerlkelee 52
                                  + q+qid+l+rql++  e++ +l+ 
  gi|91772511|ref|YP_565203.1|  8 QIQKQIDELKRQLDEKDEKIVDLDG 32
                                  789***********99999988765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.022
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SlyX  3 erleeLEiklafqedtieeLndvvaeqqqqidr 35
                                  e++++L  ++  +   i+ Ln+    + +++ +
  gi|91772511|ref|YP_565203.1| 25 EKIVDLDGQIIELTSYINMLNERFSGHSDEMNQ 57
                                  445555555555555555555544444444444 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     5e-05     0.043      99     149 ..       8      58 ..       6      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                         ATG16  99 elaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                   + ++++ el+ +l++++ek+   + ++ el++ ++ l+++ + + +e++++
  gi|91772511|ref|YP_565203.1|   8 QIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNERFSGHSDEMNQL 58 
                                   7899************************************99999999876 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 ?   13.8   0.0   6.3e-05     0.054      20      76 ..       5      61 ..       4      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.3e-05
                        DUF948 20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76
                                  ++++++k +de++++++e  +++  +  ++ +l++ +n l e  +++++++++l++a
  gi|91772511|ref|YP_565203.1|  5 PFKQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNERFSGHSDEMNQLFDA 61
                                  5899**************************************************987 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00011     0.095     132     183 ..       6      57 ..       2      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                        DUF724 132 idelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFea 183
                                   +++++k+i el+rql+ + ek  + d +i +l s  ++l+e+ +   +e ++
  gi|91772511|ref|YP_565203.1|   6 FKQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSYINMLNERFSGHSDEMNQ 57 
                                   68999***********999********************9999888777765 PP

>> Sterile  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.004       3.4      48      80 ..      10      42 ..       5      45 .. 0.91
   2 ?    3.0   0.0      0.14   1.2e+02      43      69 ..      47      73 ..      42      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                       Sterile 48 ndnlekLldrlseedrkiFnfdvrsidwedYfe 80
                                  ++++++L  +l+e+d+ki + d + i+ ++Y++
  gi|91772511|ref|YP_565203.1| 10 QKQIDELKRQLDEKDEKIVDLDGQIIELTSYIN 42
                                  578999*************************86 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                       Sterile 43 ewkfdndnlekLldrlseedrkiFnfd 69
                                   ++ ++d++++L+d+  +++r i+  d
  gi|91772511|ref|YP_565203.1| 47 RFSGHSDEMNQLFDANPSQKRGIYARD 73
                                  5667899*******9999999988765 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.0   0.00052      0.45      14      47 ..       7      40 ..       4      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                          XhlA 14 dnleervdkleekaaeaeekiknleedlkklesn 47
                                  + +++++d+l++  +e +eki  l  ++ +l+s 
  gi|91772511|ref|YP_565203.1|  7 KQIQKQIDELKRQLDEKDEKIVDLDGQIIELTSY 40
                                  5678899999999999999999999999999985 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.2    0.0015       1.3      20      60 ..       7      36 ..       2      58 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                          FlxA 20 asLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqq 60
                                  +++qkQi++l+ qL+e           k +++  +  QI  
  gi|91772511|ref|YP_565203.1|  7 KQIQKQIDELKRQLDE-----------KDEKIVDLDGQIIE 36
                                  4455555555555444...........33334444444433 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.9    0.0059       5.1       8      19 ..      11      22 ..       7      22 .. 0.85
   2 ?    1.6   0.0      0.33   2.8e+02       8      14 ..      25      31 ..      25      33 .. 0.84
   3 ?   -1.6   0.0       3.4   2.9e+03       2       6 ..      54      58 ..      53      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0059
                Pox_A_type_inc  8 sRIsDLErqLse 19
                                    I +L+rqL+e
  gi|91772511|ref|YP_565203.1| 11 KQIDELKRQLDE 22
                                  5699******97 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.33
                Pox_A_type_inc  8 sRIsDLE 14
                                  ++I+DL+
  gi|91772511|ref|YP_565203.1| 25 EKIVDLD 31
                                  69****7 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.4
                Pox_A_type_inc  2 Emsrl 6 
                                  Em++l
  gi|91772511|ref|YP_565203.1| 54 EMNQL 58
                                  9*997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1464  (0.0816554); expected 358.6 (0.02)
Passed bias filter:                     1002  (0.0558871); expected 358.6 (0.02)
Passed Vit filter:                       206  (0.0114898); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 496.50
//
Query:       gi|91772512|ref|YP_565204.1|  [L=477]
Description: pyruvate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-118  395.4   2.0   2.4e-118  395.0   2.0    1.1  1  PK         Pyruvate kinase, barrel domain
    2.3e-23   82.6   0.0    1.7e-22   79.9   0.0    2.4  2  PK_C       Pyruvate kinase, alpha/beta domain
     0.0014   17.8   0.2       0.01   15.0   0.1    2.1  2  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
     0.0024   16.9   0.0      0.045   12.7   0.0    2.4  3  IMPDH      IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.0   2.0  5.3e-122  2.4e-118       2     340 ..       6     338 ..       5     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 395.0 bits;  conditional E-value: 5.3e-122
                                   --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTTCSS CS
                            PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkdgkk 82 
                                   ++tkivct+GPas+s e+l++li aG+nv+r+nfshGs+e+h+++i  +++  ++l+  v+++ D+ Gp+ir+g +kd  +
  gi|91772512|ref|YP_565204.1|   6 HKTKIVCTIGPASSSEEMLRELIFAGMNVARINFSHGSFEDHSKVIRLIKKLCDELNVIVSVMADLPGPKIRVGEIKD--S 84 
                                   59****************************************************************************..5 PP

                                   SEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-BEE CS
                            PK  83 dielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvlgskkgvn 163
                                    i+l++gdk+k+++++ + +   ++li +d+ ++   +   + ++ +DG ++++   + +++  e+ev ++g+l+s+kgvn
  gi|91772512|ref|YP_565204.1|  85 PINLQKGDKVKLTTKRIVGS---KDLIPVDFDKLPYCIAKKSDVYFNDGFIQMRCSGICSNE-AECEVIVGGQLSSHKGVN 161
                                   7************9998876...69********************************99888.9***************** PP

                                   -TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTHHHHHHHSSEEE CS
                            PK 164 lpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenldeileasDgim 244
                                   lpg ++ l+ ++ekD + l f++++gv+   +sf+ ++sD++++r+ + ++g+++ ++akie+ ++v n+d+i+ea+D++m
  gi|91772512|ref|YP_565204.1| 162 LPGIDLLLDPVTEKDLKILDFALDEGVNCFSVSFIEQGSDIQKIRDHATKKGRSVFLVAKIERGHSVGNIDDIMEATDALM 242
                                   ********************************************************************************* PP

                                   EEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHTSS-HH CS
                            PK 245 varGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetakGkyPv 325
                                   +arGDlG+eip e+v++vqk li+k+nl g pvitat+mlesm+ n rptrae++Dvana+lDGtDa+mLsgeta GkyP 
  gi|91772512|ref|YP_565204.1| 243 IARGDLGVEIPIEEVPIVQKELIHKANLRGMPVITATHMLESMTDNVRPTRAEATDVANAILDGTDAIMLSGETAVGKYPL 323
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHH CS
                            PK 326 eavkamaevaleaek 340
                                   eav++m ++a+++e+
  gi|91772512|ref|YP_565204.1| 324 EAVHTMVRIARKTEA 338
                                   ************997 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.32   1.4e+03      22      41 ..     209     228 ..     208     318 .. 0.67
   2 !   79.9   0.0   3.7e-26   1.7e-22       3     117 .]     365     470 ..     363     470 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                                   E-SSSHHHHHHHHT-TSSEE CS
                          PK_C  22 ltesGetArliskyrpkvpi 41 
                                   +t++G+++ l++k+ ++  +
  gi|91772512|ref|YP_565204.1| 209 ATKKGRSVFLVAKIERGHSV 228
                                   57777777777777665444 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 3.7e-26
                                   HHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHHHHHH CS
                          PK_C   3 iakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellreavk 83 
                                   i+  + +a ++l ++++v++t+sG t+r+is+++p+ +iia+++ elt+ qla + Gvyp+ v     ++s ++l ++++ 
  gi|91772512|ref|YP_565204.1| 365 ISLQVYDAIRKLSIELVVTPTHSGATPRRISRFKPDNWIIAMSHVELTCEQLAYSYGVYPISV-----SDSSEDLEKKMLG 440
                                   77889999*****************************************************87.....45667777799** PP

                                   HHHHTTSS-STSEEEEEE-SSSS..SS--EEEEE CS
                          PK_C  84 vakeaglvkkgdevvvtaGtpkgesgttNtlrVv 117
                                   +++++g+ k+g ++v+t+G++ g    tN+l+++
  gi|91772512|ref|YP_565204.1| 441 ALLSRGIGKSGNTIVLTQGSSGG----TNLLKII 470
                                   *******************9988....*****97 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.3e-06      0.01      72     154 ..     171     248 ..     164     281 .. 0.84
   2 ?    0.2   0.0     0.075   3.4e+02      14      33 ..     299     318 ..     291     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-06
                                   HHHHHHGG....HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEE CS
                     HpcH_HpaI  72 elikqdle....vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgv 147
                                   ++ ++dl+    +ld+g++ + v ++e+  +++++     +          ++ l+a iE  + v n+++I+ a++   ++
  gi|91772512|ref|YP_565204.1| 171 PVTEKDLKildfALDEGVNCFSVSFIEQGSDIQKIRDHATKKG-------RSVFLVAKIERGHSVGNIDDIMeATD---AL 241
                                   66778888788899******************99998888877.......89********************5555...45 PP

                                   EE-HHHH CS
                     HpcH_HpaI 148 flGaeDl 154
                                   +++  Dl
  gi|91772512|ref|YP_565204.1| 242 MIARGDL 248
                                   5555555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.075
                                   HHHHCTC--SEEEEESSTSS CS
                     HpcH_HpaI  14 aekaaiagaDsvliDlEdav 33 
                                   + +a + g D++++ +E av
  gi|91772512|ref|YP_565204.1| 299 VANAILDGTDAIMLSGETAV 318
                                   66788889999999999999 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0     1e-05     0.045      93     154 ..       8      69 ..       2      75 .. 0.88
   2 ?    1.1   0.0     0.036   1.6e+02      20     116 ..     147     245 ..     125     277 .. 0.70
   3 ?   -2.5   0.0      0.44     2e+03     219     236 ..     296     313 ..     270     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                                   B-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH  93 llvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnva 154
                                     +  ++g  ++++e +++l+ ag++v  ++ +hg  e   ++++ ikk ++e++vi+  +a
  gi|91772512|ref|YP_565204.1|   8 TKIVCTIGPASSSEEMLRELIFAGMNVARINFSHGSFEDHSKVIRLIKKLCDELNVIVSVMA 69 
                                   455668999999***************************************99*99986655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.036
                                   GSB--EESSTTEEESSSEEE-SSTTT-SHHHHH.HHHHTTSEEEE-SSS-HHHHHHHHHHHHTSTTSXBXTT.....SXB- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx RF
                         IMPDH  20 evdlktkltkkiklniPlvsaamdtvtesemAi.alareGgigvihknlsieeqaeevkkvkrspnaakdek.....grll 94 
                                   ev +  +l+++  +n+P +   +d vte+++ i  +a   g+ +   ++s  eq + ++k++ +  a+k+ +      ++ 
  gi|91772512|ref|YP_565204.1| 147 EVIVGGQLSSHKGVNLPGIDLLLDPVTEKDLKIlDFALDEGVNCF--SVSFIEQGSDIQKIRDH--ATKKGRsvflvAKIE 223
                                   5566678888899999999999*******9987468888888765..56777888888888844..444433001113444 PP

                                   EEEEE-SSTTHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH  95 vgaavgvkedalervkalveag 116
                                    g +vg  +d +e  +al+ a+
  gi|91772512|ref|YP_565204.1| 224 RGHSVGNIDDIMEATDALMIAR 245
                                   4667777777777777776665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.44
                                   HHHHHHHHHTT-SEEEES CS
                                   xxxxxxxxxxxxxxxxxx RF
                         IMPDH 219 sgdivkAlaaGadavmlG 236
                                     d++ A+  G+da+ml 
  gi|91772512|ref|YP_565204.1| 296 ATDVANAILDGTDAIMLS 313
                                   578999999999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2865.21
//
Query:       gi|91772513|ref|YP_565205.1|  [L=361]
Description: hypothetical protein Mbur_0470 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.0   0.7    3.1e-13   49.7   0.1    2.7  2  CCG       Cysteine-rich domain
    1.2e-09   38.4   2.6    1.2e-09   38.4   2.6    2.3  2  Fer4_8    4Fe-4S dicluster domain
    2.5e-06   28.3   5.4    2.9e-06   28.1   3.3    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    4.3e-06   27.2   3.1    4.3e-06   27.2   3.1    2.4  3  Fer4_17   4Fe-4S dicluster domain
     0.0003   20.9   8.7      0.069   13.3   0.2    3.3  4  Fer4_9    4Fe-4S dicluster domain
     0.0013   19.3  11.2     0.0046   17.5   7.9    3.1  3  Fer4_7    4Fe-4S dicluster domain
     0.0016   18.5  19.5      0.018   15.2   0.8    4.0  4  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   16.0   1.9      0.013   16.0   1.9    4.2  4  Fer4_4    4Fe-4S binding domain
      0.025   14.7   4.2      0.025   14.7   4.2    3.4  3  Fer4_6    4Fe-4S binding domain
       0.97    9.4  25.9       0.15   11.9   2.0    3.5  4  Fer4      4Fe-4S binding domain
        1.2    9.3   9.4        4.9    7.4   0.6    2.5  2  Fer4_18   4Fe-4S dicluster domain
        6.6    7.1  22.5       0.26   11.5   2.5    3.6  3  Fer4_2    4Fe-4S binding domain
        6.7    6.9  15.4         13    6.0  10.9    3.3  3  Fer4_21   4Fe-4S dicluster domain
        9.6    7.4  15.2          4    8.6   0.8    3.4  2  Fer4_3    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 !   49.7   0.1   2.5e-16   3.1e-13       1      85 []     134     217 ..     134     217 .. 0.98
   2 !   24.0   0.0   2.6e-08   3.3e-05      20      84 ..     270     336 ..     256     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2.5e-16
                           CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCl 81 
                                   vay +gC ++  a+++  +++ kll+++g+      +e+CCG   + +g+ e+a+++ak+ ve +e++  ++i++ cpgC+
  gi|91772513|ref|YP_565205.1| 134 VAYMTGC-WIAFAHQDIARSTIKLLNKAGIAPRAIPEEKCCGLFLIDNGHMEEAKEYAKEYVEYLESLRIKKIIVSCPGCY 213
                                   79*****.*************************99********************************************** PP

                           CCG  82 lqlk 85 
                                   + lk
  gi|91772513|ref|YP_565205.1| 214 IVLK 217
                                   9885 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.6e-08
                           CCG  20 alkkllealgveleel..ekesCCGagggrsgkee.laealakrnvetaeetgadaivtacpgCllql 84 
                                   + +++l+ + ve++e+   k+ CCG ++g++ + + ++ +++   +e  +++ +d +v+ cp+C+ +l
  gi|91772513|ref|YP_565205.1| 270 IPREILRSMQVEIKEMfgGKHGCCGGPAGVKPNFPeISSKVGMITIEKTKDY-PDGVVSYCPFCYHHL 336
                                   55778888889988887789*********9999888***************8.************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 !   38.4   2.6   9.6e-13   1.2e-09       2      65 .]       8      74 ..       7      74 .. 0.77
   2 ?   -0.6   0.1       1.4   1.8e+03      17      54 ..     175     212 ..     169     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 9.6e-13
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae........dvqeeqvlee..eealwsCttcgaCtevCpvgi 65
                                  +++Ci Cg C + C++++ t++  +++r + +         +        +   + ++  t cgaC+++Cp++i
  gi|91772513|ref|YP_565205.1|  8 VSYCIDCGKCYDVCHIAKVTDNK-YTPRSKIMLlqkliegdE----LD--QdeVDDVYLSTRCGACDDACPMNI 74
                                  689*****************855.567777776566654431....22..133678***************997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                        Fer4_8  17 vlrrtkkhlldargeaaedvqeeqvleeeealwsCttc 54 
                                   ++   + h  +a++ a+e+v+  + l  ++++ sC +c
  gi|91772513|ref|YP_565205.1| 175 LFLIDNGHMEEAKEYAKEYVEYLESLRIKKIIVSCPGC 212
                                   45555567777777777755555554448999999888 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   3.3   2.3e-09   2.9e-06       2      67 .]      11      73 ..      10      73 .. 0.78
   2 ?   -2.5   0.0       8.5   1.1e+04      54      60 ..     206     212 ..     179     222 .. 0.56

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.3e-09
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy..ntaekkdlaedeekckkqeaitgCdiCqdvCPan 67
                                  C++CgkC +vC  + ++ +   ++ +r +i    + +e ++l +de  +   +  t C++C d+CP+n
  gi|91772513|ref|YP_565205.1| 11 CIDCGKCYDVCHIAKVTDN---KYTPRSKIMLlqKLIEGDELDQDEVDDV--YLSTRCGACDDACPMN 73
                                  ***********99999999...5556665555336777777777776666..777***********98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.5
                       Fer4_16  54 itgCdiC 60 
                                   i  C  C
  gi|91772513|ref|YP_565205.1| 206 IVSCPGC 212
                                   3444333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   3.1   3.4e-09   4.3e-06       2      61 .]      11      75 ..      10      75 .. 0.74
   2 ?   -2.9   0.0       8.4   1.1e+04      45      49 ..     208     212 ..     181     228 .. 0.69
   3 ?   -3.1   0.4       9.6   1.2e+04      12      19 ..     329     336 ..     326     346 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.4e-09
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraakl....glleeaeke..ekaslCieCgeCerkCPqgld 61
                                  Ci Cg C ++C   + +dn + +++ +++l     + +e  ++  + + l + Cg C+ +CP++++
  gi|91772513|ref|YP_565205.1| 11 CIDCGKCYDVCHIAKVTDN-KYTPRSKIMLlqklIEGDELDQDevDDVYLSTRCGACDDACPMNIP 75
                                  ****************999.445555555554223344444444469999*************985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.4
                       Fer4_17  45 lCieC 49 
                                   +C +C
  gi|91772513|ref|YP_565205.1| 208 SCPGC 212
                                   33333 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 9.6
                       Fer4_17  12 Cpsyeayd 19 
                                   Cp+++ + 
  gi|91772513|ref|YP_565205.1| 329 CPFCYHHL 336
                                   66666654 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   5.4e-05     0.069      36      47 ..      11      22 ..       3      52 .. 0.80
   2 !   11.4   0.5   0.00022      0.28       3      26 ..      61      84 ..      59     103 .. 0.81
   3 ?   -2.5   0.0       4.7     6e+03      34      39 ..     207     212 ..     179     215 .. 0.65
   4 ?   -2.3   0.1       4.1   5.3e+03      34      41 ..     327     334 ..     304     343 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                        Fer4_9 36 CigCgaCveaCp 47
                                  Ci+Cg+C+++C 
  gi|91772513|ref|YP_565205.1| 11 CIDCGKCYDVCH 22
                                  777777777774 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00022
                        Fer4_9  3 tgCgaCveaCpagvvvedaaerka 26
                                  t+CgaC +aCp+++ + d  +r++
  gi|91772513|ref|YP_565205.1| 61 TRCGACDDACPMNIPITDIIQRER 84
                                  579999999999998887766655 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.7
                        Fer4_9  34 eaCigC 39 
                                    +C gC
  gi|91772513|ref|YP_565205.1| 207 VSCPGC 212
                                   445555 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.1
                        Fer4_9  34 eaCigCga 41 
                                   + C +C  
  gi|91772513|ref|YP_565205.1| 327 SYCPFCYH 334
                                   44666654 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   7.9   3.6e-06    0.0046       2      52 .]      11      74 ..      10      74 .. 0.60
   2 !   10.8   1.4   0.00046      0.59       4      19 ..      62      77 ..      60     104 .. 0.75
   3 ?   -0.7   0.1       1.8   2.3e+03      28      47 ..     319     339 ..     296     343 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenek......gtekv.........ei.dpekClgCgaCvavCPtga 52
                                  Ci Cg+C ++C    ++ ++++  +      +   +         e+ d    + CgaC ++CP ++
  gi|91772513|ref|YP_565205.1| 11 CIDCGKCYDVCHIAKVTDNKYTPRSkimllqK---LiegdeldqdEVdDVYLSTRCGACDDACPMNI 74
                                  ***********866666555533332333320...13333223323313456899*********875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00046
                        Fer4_7  4 gCgaCvaaCpvkaiel 19
                                   CgaC +aCp++   +
  gi|91772513|ref|YP_565205.1| 62 RCGACDDACPMNIPIT 77
                                  7*********987655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.8
                        Fer4_7  28 tekveidpekClgCga.Cvav 47 
                                   +++++++ ++C +C++  ++v
  gi|91772513|ref|YP_565205.1| 319 KDYPDGVVSYCPFCYHhLEDV 339
                                   455677788888887643444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.9   6.2e-05     0.079       7      29 ..       9      29 ..       4      57 .. 0.74
   2 !   15.2   0.8   1.4e-05     0.018      10      37 ..      61      94 ..      52     109 .. 0.75
   3 ?   -0.2   0.1      0.84   1.1e+03      28      48 ..     192     212 ..     168     217 .. 0.80
   4 ?    0.8   0.4      0.43   5.6e+02      24      49 ..     308     333 ..     289     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-05
                       Fer4_10  7 dtCirCgkCvkaCPadltsvgak 29
                                  + Ci CgkC ++C  ++ +v  +
  gi|91772513|ref|YP_565205.1|  9 SYCIDCGKCYDVC--HIAKVTDN 29
                                  6799999999999..77433333 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                       Fer4_10 10 irCgkCvkaCPadl......tsvgakgeaseeea 37
                                  +rCg+C +aCP+++      ++ +++ ++ ++e+
  gi|91772513|ref|YP_565205.1| 61 TRCGACDDACPMNIpitdiiQRERTILAEQGKEP 94
                                  79**********8888777655555555544444 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.84
                       Fer4_10  28 akgeaseeeavrkkvekCtgc 48 
                                    + e+ e+ +++k + +C+gc
  gi|91772513|ref|YP_565205.1| 192 EYVEYLESLRIKKIIVSCPGC 212
                                   566777778888999999999 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.43
                       Fer4_10  24 tsvgakgeaseeeavrkkvekCtgcg 49 
                                   ++vg + +++ ++  +++v+ C++c 
  gi|91772513|ref|YP_565205.1| 308 SKVGMITIEKTKDYPDGVVSYCPFCY 333
                                   566777777888888999999**996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   1.9     1e-05     0.013       3      15 ..      10      22 ..       9      32 .. 0.90
   2 ?    8.5   1.4    0.0025       3.2       5      17 .]      61      73 ..      61      73 .. 0.90
   3 ?   -0.4   0.3       1.8   2.3e+03       6      12 ..     208     214 ..     207     215 .. 0.77
   4 ?   -0.8   0.4       2.4   3.1e+03      12      16 ..     327     331 ..     326     334 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                        Fer4_4  3 rCigCgsCvaaCP 15
                                   Ci+Cg+C+++C 
  gi|91772513|ref|YP_565205.1| 10 YCIDCGKCYDVCH 22
                                  5***********6 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0025
                        Fer4_4  5 igCgsCvaaCPqg 17
                                  ++Cg+C +aCP++
  gi|91772513|ref|YP_565205.1| 61 TRCGACDDACPMN 73
                                  68*********85 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                        Fer4_4   6 gCgsCva 12 
                                    C+ C++
  gi|91772513|ref|YP_565205.1| 208 SCPGCYI 214
                                   6999986 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.4
                        Fer4_4  12 aaCPq 16 
                                   ++CP+
  gi|91772513|ref|YP_565205.1| 327 SYCPF 331
                                   67774 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   4.2   1.9e-05     0.025       8      19 ..      10      21 ..       8      26 .. 0.90
   2 ?    3.8   2.4     0.053        68      11      23 ..      62      74 ..      61      75 .. 0.88
   3 ?   -0.9   0.2       1.6     2e+03       8      13 ..     208     213 ..     207     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                        Fer4_6  8 kCigCgdCvrvC 19
                                   Ci+Cg+C++vC
  gi|91772513|ref|YP_565205.1| 10 YCIDCGKCYDVC 21
                                  6*********** PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.053
                        Fer4_6 11 gCgdCvrvCPega 23
                                   Cg+C ++CP+++
  gi|91772513|ref|YP_565205.1| 62 RCGACDDACPMNI 74
                                  5*********986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                        Fer4_6   8 kCigCg 13 
                                   +C gC+
  gi|91772513|ref|YP_565205.1| 208 SCPGCY 213
                                   69***7 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   5.8    0.0002      0.25       6      18 ..       9      21 ..       8      21 .. 0.93
   2 ?   11.9   2.0   0.00012      0.15       9      22 ..      61      74 ..      61      76 .. 0.88
   3 ?   -2.7   0.5         5   6.4e+03       5      10 ..     169     174 ..     167     174 .. 0.76
   4 ?   -2.8   0.1       5.3   6.8e+03      15      20 ..     326     331 ..     326     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                  TTSSS-THHHHHS CS
                          Fer4  6 ekCigCGaCvevC 18
                                  + Ci CG+C++vC
  gi|91772513|ref|YP_565205.1|  9 SYCIDCGKCYDVC 21
                                  57*********** PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                                  SS-THHHHHSTTTE CS
                          Fer4  9 igCGaCvevCPvgA 22
                                  ++CGaC ++CP + 
  gi|91772513|ref|YP_565205.1| 61 TRCGACDDACPMNI 74
                                  58*********986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5
                                   TTTSSS CS
                          Fer4   5 eekCig 10 
                                   eekC g
  gi|91772513|ref|YP_565205.1| 169 EEKCCG 174
                                   899976 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.3
                                   HHHSTT CS
                          Fer4  15 vevCPv 20 
                                   v+ CP+
  gi|91772513|ref|YP_565205.1| 326 VSYCPF 331
                                   678**6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.4    0.0099        13      85      96 ..      11      22 ..       4      42 .. 0.64
   2 ?    7.4   0.6    0.0039       4.9      55      83 ..      54      82 ..      27      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0099
                       Fer4_18 85 ciscllcidacd 96
                                  ci c++c d c+
  gi|91772513|ref|YP_565205.1| 11 CIDCGKCYDVCH 22
                                  777777777774 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0039
                       Fer4_18 55 ekgagdcidcescvkvcPtgidirkGlql 83
                                   +++   + c++c + cP++i i + +q 
  gi|91772513|ref|YP_565205.1| 54 VDDVYLSTRCGACDDACPMNIPITDIIQR 82
                                  344444689**************998886 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.5    0.0002      0.26      10      20 ..      11      21 ..       6      22 .. 0.94
   2 ?    9.1   2.0    0.0011       1.5      11      21 ..      61      71 ..      61      72 .. 0.93
   3 ?   -3.0   0.3       8.3   1.1e+04      10      14 ..     209     213 ..     208     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                        Fer4_2 10 CigCgaCvsaC 20
                                  Ci Cg+C+++C
  gi|91772513|ref|YP_565205.1| 11 CIDCGKCYDVC 21
                                  *********** PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                        Fer4_2 11 igCgaCvsaCP 21
                                  ++CgaC +aCP
  gi|91772513|ref|YP_565205.1| 61 TRCGACDDACP 71
                                  69********* PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.3
                        Fer4_2  10 CigCg 14 
                                   C gC 
  gi|91772513|ref|YP_565205.1| 209 CPGCY 213
                                   88885 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  10.9      0.01        13       6      53 ..       9      72 ..       5      82 .. 0.60
   2 ?   -3.0   0.0       6.6   8.5e+03      35      43 ..     166     174 ..     143     175 .. 0.56
   3 ?   -2.0   0.0       3.3   4.2e+03       9      16 ..     207     214 ..     194     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                       Fer4_21  6 dkCigCgkCliaCedtshqaieidaktvl...............kvve.deCvGCnlCssvCPv 53
                                  + Ci+CgkC+ +C+ + ++  ++++++++               +v +    + C  C + CP+
  gi|91772513|ref|YP_565205.1|  9 SYCIDCGKCYDVCHIAKVTDNKYTPRSKImllqkliegdeldqdEVDDvYLSTRCGACDDACPM 72
                                  57***********976666555555443344555555555554333221245566666666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.6
                       Fer4_21  35 kvvedeCvG 43 
                                   ++ e++C G
  gi|91772513|ref|YP_565205.1| 166 AIPEEKCCG 174
                                   334777766 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.3
                       Fer4_21   9 igCgkCli 16 
                                   ++C  C+i
  gi|91772513|ref|YP_565205.1| 207 VSCPGCYI 214
                                   34555544 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   3.5     0.027        35       1      11 [.      11      21 ..      11      23 .. 0.95
   2 ?    8.6   0.8    0.0031         4       3      14 ..      62      73 ..      61      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.027
                        Fer4_3  1 CtgCgaCvevC 11
                                  C+ Cg C +vC
  gi|91772513|ref|YP_565205.1| 11 CIDCGKCYDVC 21
                                  9********** PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                        Fer4_3  3 gCgaCvevCPvg 14
                                   CgaC ++CP +
  gi|91772513|ref|YP_565205.1| 62 RCGACDDACPMN 73
                                  5*********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2158.59
//
Query:       gi|91772514|ref|YP_565206.1|  [L=418]
Description: gluconate transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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   80.1  31.4    7.5e-22   77.6  31.4    1.8  1  GntP_permease  GntP family permease
  ------ inclusion threshold ------
        2.1    8.2   9.2        1.1    9.1   1.1    2.9  2  FixP_N         N-terminal domain of cytochrome oxidase-cbb3, 


Domain annotation for each model (and alignments):
>> GntP_permease  GntP family permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6  31.4   8.4e-26   7.5e-22       3     429 ..       4     406 ..       2     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 8.4e-26
                 GntP_permease   3 llivligvilllllviklklnafvaLllvsllvglvsGmpldkvvksiekGlGgtlGslaiiiglGamlGklledsGaaer 83 
                                   ll+ +++++ + +l+i++++ +f++L+ +++l g++sGm+   +++ ++ G G  +  l+i i  Ga++ +ll +    e+
  gi|91772514|ref|YP_565206.1|   4 LLLFVLTIVFISVLTIRYHITPFLTLIAAAFLFGTFSGMDW--LIQYVTGGAGRIFSLLGIPIYCGAVIAQLLRHGHFIEK 82 
                                   788999*********************************86..89************************************ PP

                 GntP_permease  84 ialtlikklgkkkvqwalvlagfivgialFfe.vglvlLiplvfaiakeakisllklgiplvaalavvhgllpPhPgplav 163
                                   i   + +++     ++a  ++g++++i+l     + v+++pl+ ++ ke       + ++ +++++   +l+ P P    +
  gi|91772514|ref|YP_565206.1|  83 IVEDVKHTIKA--PDLAAGVVGYLLSIPLMCClTTYVVMLPLIEQMEKEQSSGGRLFYMAAFGSVLS-FVLILPLPVVYSM 160
                                   ***99888755..59999**********98761578***********99888777777777777665.5677899999999 PP

                 GntP_permease 164 aellgadiGkvllyGli.vaiptvii.agpllkk.flkevvkeeeelaeeaeeksreekelPsfglslltillPvvlmlvk 241
                                    +++g+    ++ + li v +  +++ +g +++k +    ++  +el+  +e     +  lP    + l i lP++l+ + 
  gi|91772514|ref|YP_565206.1| 161 TTAFGVSNSDTFSINLItVPLSLFLLgTGYVVAKrLSGGSQHLLPELSGLVEP---AMLSLPRWK-VWLPIALPIILISIG 237
                                   99999877777666554144555555666666662555555555555544444...357788754.567888999999876 PP

                 GntP_permease 242 tiaelllpkesaalevvefiGnpvvalliallvaiytlglrrgksikkvldileealksiaiilliigaGGafkqvlvdsg 322
                                    +            + +++i +  +al+i+++v++ ++      + +k+   le++ k+++iil+ + + Ga++ v+  s+
  gi|91772514|ref|YP_565206.1| 238 YL-----------FSPLSIISDVNIALVISVFVSLLLVEE----KPRKIA--LEKGTKNAGIILFDLCGAGALGFVIAASS 301
                                   43...........34578999************9865533....234455..89*************************** PP

                 GntP_permease 323 vgkalaellsnlelspillaflvaallrialGsatVaaltaaglva..piiaqlpgvnlallvlaigaGslilshvnDagF 401
                                     + +  l++++ +++++++f++a+l++ a+Gs  V+a+ ++++va  +i++++p+v    l l i+aG+li+s+v D+ F
  gi|91772514|ref|YP_565206.1| 302 FPDDVFALINGV-FPVVIVPFVLAVLIQTAQGSRIVTAVITSTIVAgtDIVTSVPTVP---LILMISAGTLIVSYVSDPYF 378
                                   *****9998765.89******************************9666777776666...6677899************* PP

                 GntP_permease 402 Wlvkeylgltvketlktwtvletilsvv 429
                                   Wl+++ +g ++   ++ +t+    ++v+
  gi|91772514|ref|YP_565206.1| 379 WLIQRSTGDSIPTVVRRFTLPLAGAGVL 406
                                   *********9999999999876544444 PP

>> FixP_N  N-terminal domain of cytochrome oxidase-cbb3, FixP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.1   0.00012       1.1      24      46 ..       4      26 ..       3      28 .. 0.92
   2 ?    2.2   1.6     0.017   1.5e+02      19      39 ..     218     240 ..     214     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00012
                        FixP_N 24 lylFyativfavvYlilYpalgl 46
                                  l+lF++tivf+ v +i+Y++ ++
  gi|91772514|ref|YP_565206.1|  4 LLLFVLTIVFISVLTIRYHITPF 26
                                  689****************9986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.017
                        FixP_N  19 lPrWWlylFyat..ivfavvYli 39 
                                   lPrW ++l +a+  i+++++Yl+
  gi|91772514|ref|YP_565206.1| 218 LPRWKVWLPIALpiILISIGYLF 240
                                   9***8888777533888999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2629.36
//
Query:       gi|91772515|ref|YP_565207.1|  [L=174]
Description: ADP-ribose binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-45  153.4   0.3    3.8e-45  152.7   0.3    1.3  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.7   0.3   2.1e-49   3.8e-45       1     118 []      22     134 ..      22     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 2.1e-49
                                   EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHHHHHH CS
                         Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeellaka 81 
                                   VnAaN++llggggv+gaih+aag++l+eeck+l     gcl+Gea++t++y+lpakyvihtvgp+++ ++  +e ++lak+
  gi|91772515|ref|YP_565207.1|  22 VNAANNSLLGGGGVDGAIHKAAGPQLLEECKYL----DGCLTGEAKITSGYHLPAKYVIHTVGPIWK-EGASGEGNKLAKC 97 
                                   9********************************....78***************************8.7999********* PP

                                   HHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                         Macro  82 yknalelaeekgiksvafPaistGifgvpweeaarva 118
                                   y+n+l+ a ++g++++afP+istG +g+p+e+aa +a
  gi|91772515|ref|YP_565207.1|  98 YRNSLKVAVKNGVRTIAFPSISTGAYGFPVEKAATIA 134
                                   **********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.36s 00:00:00.91 Elapsed: 00:00:00.53
# Mc/sec: 982.37
//
Query:       gi|91772516|ref|YP_565208.1|  [L=71]
Description: hypothetical protein Mbur_0473 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 453.38
//
Query:       gi|91772517|ref|YP_565209.1|  [L=320]
Description: MscS mechanosensitive ion channel [Methanococcoides burtonii DSM 6242]
Scores for complete 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-33  114.8   1.9    3.8e-33  114.8   1.9    1.7  2  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.064   13.4   0.0    2.0  1  DUF2023          Protein of unknown function (DUF2023)
       0.36   10.1  11.0       0.62    9.3  11.0    1.3  1  AgrB             Accessory gene regulator B
       0.42   11.0   7.2       0.63   10.4   6.6    1.6  1  DUF4199          Protein of unknown function (DUF4199)
       0.77    9.6  11.6        1.2    9.0  11.6    1.4  1  DUF4271          Domain of unknown function (DUF4271)
        1.9    8.9   8.6        2.6    8.5   3.6    2.8  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
        8.4    6.1   9.1        3.7    7.3   0.4    2.2  2  TMEM208_SND2     SRP-independent targeting protein 2/TMEM208


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 ?   -4.3   0.7       4.4   1.1e+04       7      27 ..       9      29 ..       7      31 .. 0.62
   2 !  114.8   1.9   1.5e-36   3.8e-33       2     194 ..      75     288 ..      74     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 4.4
                                  HHHHHHHHHHHHTTT--SCCH CS
                    MS_channel  7 liivvgilivlsllgvnvsal 27
                                  +++++ i i++ ++++ +  l
  gi|91772517|ref|YP_565209.1|  9 IVVLLSIAIFIAYINYFTDHL 29
                                  556666677777777666555 PP

  == domain 2  score: 114.8 bits;  conditional E-value: 1.5e-36
                                   .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SS CS
                    MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglr 82 
                                   k+++i+i ++++   + ++  +++ l+++ G+l++++++al+dl++++++G+i+ +++pf+ GD++e+gdi+G V+di+ +
  gi|91772517|ref|YP_565209.1|  75 KAVSIIITFLVLASLFAVWFRETTGLIVAYGILSAGVAIALQDLLKSIAGGLIIFISRPFRAGDRIEVGDIIGDVIDIKNF 155
                                   5666777777777777777777********************************************************999 PP

                                   EEEE.........EETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS CS
                    MS_channel  83 ttki.........rtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdk 154
                                   +t+i          + +griv  Pns +++ +++N+++     +++v+i + y+s+ kk+e+++ ++ + +  + e+  +k
  gi|91772517|ref|YP_565209.1| 156 STTImeirewvdgDQYTGRIVQLPNSFILSGTVKNYTKDFSFIWDEVQIMLVYGSNWKKAEEIAIKVTKDAIYDFEDSAKK 236
                                   99984443333333569*********************99**********************998888888888888889* PP

                                   -EEEEEEEE-SSSEEEEEEEEEET...............TTHHHHHHHHHHH CS
                    MS_channel 155 ellvvldefgdsslnfevrvfvkt............vvpeeylsvqseinlr 194
                                   ell++ +++ ++s ++e + +++t            v+p+++ ++++ ++++
  gi|91772517|ref|YP_565209.1| 237 ELLNMSEKYFITSYDVETKLYMTTrdnwidmrvryvVDPRQRRKIKHMLVQK 288
                                   **********************996666444444444445555555555555 PP

>> DUF2023  Protein of unknown function (DUF2023)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.5e-05     0.064      63      94 ..     281     312 ..     221     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                                   HHHHHHTS-GGG--HHHHHHHHHHTT--HHHH CS
                       DUF2023  63 vvrslvkkplneltpeeDfilGilLGYdilkq 94 
                                   + ++lv+k ++++ peeD ilG+ +G di++ 
  gi|91772517|ref|YP_565209.1| 281 IKHMLVQKLFQAFEPEEDIILGTAVGIDIMRS 312
                                   334566777899****************9875 PP

>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  11.0   0.00024      0.62      86     177 ..      12     111 ..       7     116 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                          AgrB  86 flllillakllslsls.......lllillliilliisliiilllaPvdtpnkpisskekkkklki.lsiivllilliiall 158
                                   +l++++++ ++++ ++       ll+ ll  ++++  ++ +++    d  + ++++++++ +l++  sii+++++l+ ++ 
  gi|91772517|ref|YP_565209.1|  12 LLSIAIFIAYINYFTDhligyetLLTKLLHSVIIV-LVFYVIKNIAEDIIKIKVHDNKERYTLRKaVSIIITFLVLASLFA 91 
                                   33333334444333334345654333333333333.334444555557777777788888888884555555554444444 PP

                          AgrB 159 l.knekisnaillglllvav 177
                                   +  +e+   ++++g+l++ v
  gi|91772517|ref|YP_565209.1|  92 VwFRETTGLIVAYGILSAGV 111
                                   47677777788888886655 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.6   0.00024      0.63       5      87 ..       9      94 ..       8     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                       DUF4199  5 ilglvwilifll.ilyllglhqi.lstgpllglla.llllllvpflvylalkky.......rkknlgGfisfgqafgfgflis 77
                                  i+ l++i+if++ i y+++   i ++      ll+ ll +++ ++lv++ +k+        + +++++ ++ ++a ++ +   
  gi|91772517|ref|YP_565209.1|  9 IVVLLSIAIFIAyINYFTDHL-IgYE-----TLLTkLLHSVI-IVLVFYVIKNIaediikiKVHDNKERYTLRKAVSIIITFL 84
                                  678999*****9888888774.3222.....22333555555.6779999999955555443333577*************** PP

                       DUF4199 78 lvagllsavf 87
                                  ++a+l+ ++f
  gi|91772517|ref|YP_565209.1| 85 VLASLFAVWF 94
                                  *****99887 PP

>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  11.6   0.00048       1.2      54     169 ..       7     116 ..       1     135 [. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00048
                       DUF4271  54 lllltclllglllylllsefgslfgsylassllllliiflilllylllKlllykllgwlFfdkkkirqwifsylsylsllg 134
                                   l+++++l++++++ ++    + l g+  ++ l+ ll  ++i+l+++++K +++ ++     d k+     +     +s++ 
  gi|91772517|ref|YP_565209.1|   7 LNIVVLLSIAIFIAYINYFTDHLIGY--ETLLTKLLHSVIIVLVFYVIKNIAEDIIKIKVHDNKERYTLRKA----VSIII 81 
                                   55666666666555555554444444..49*************************99988888887655555....45555 PP

                       DUF4271 135 lllfplvlllvyfplssqillililiillliklll 169
                                   ++l++++l+ v f + +  ++ ++++  +++ +l+
  gi|91772517|ref|YP_565209.1|  82 TFLVLASLFAVWFRETTGLIVAYGILSAGVAIALQ 116
                                   55666666666677766666666666555544444 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.3      0.17   4.3e+02      25      71 ..      10      59 ..       8      62 .. 0.61
   2 ?    8.5   3.6     0.001       2.6      29      74 ..      76     121 ..      45     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
               Phage_holin_5_2 25 lilgiiGiilgvvivfta...dfqaedilifgaiiqGilsggastglnQl 71
                                  ++l+ i i+++ + +ft+    ++   + ++ ++i+ ++   +   + ++
  gi|91772517|ref|YP_565209.1| 10 VVLLSIAIFIAYINYFTDhliGYETLLTKLLHSVIIVLVFYVIKNIAEDI 59
                                  68899999999999999635444443444444666665555555555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
               Phage_holin_5_2  29 iiGiilgvvivfta..dfqaedilifgaiiqGilsggastglnQliKQ 74 
                                   +++ii++ +++      +  e + +  +++ Gils+g+++ l++l K 
  gi|91772517|ref|YP_565209.1|  76 AVSIIITFLVLASLfaVWFRETTGL--IVAYGILSAGVAIALQDLLKS 121
                                   4666666444443245666666777..9****************9995 PP

>> TMEM208_SND2  SRP-independent targeting protein 2/TMEM208
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.7     0.032        83      17      69 ..       4      57 ..       2      63 .. 0.90
   2 ?    7.3   0.4    0.0014       3.7      10      68 ..      64     123 ..      56     125 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.032
                  TMEM208_SND2 17 Lknlrlislavnalylllrlll.rsslrprslllylllslpalllyyvlekmgr 69
                                  L+ l +++l++ a++++++ ++  +   +++ll+ ll s++ +l+ yv++++++
  gi|91772517|ref|YP_565209.1|  4 LRGLNIVVLLSIAIFIAYINYFtDHLIGYETLLTKLLHSVIIVLVFYVIKNIAE 57
                                  6778999************9998888899999999**************99986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                  TMEM208_SND2  10 aeeNkatLknlrlislavnalylllrlllrsslrprsllly.lllslpalllyyvlekmg 68 
                                   ++ Nk++ +  + +s+++++l+l+  + ++ + +   ++ y +l++ +a++l+ +l++++
  gi|91772517|ref|YP_565209.1|  64 VHDNKERYTLRKAVSIIITFLVLASLFAVWFRETTGLIVAYgILSAGVAIALQDLLKSIA 123
                                   556666555555555555555555555554455555556551566679999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1283  (0.07156); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1859.72
//
Query:       gi|91772518|ref|YP_565210.1|  [L=235]
Description: hypothetical protein Mbur_0475 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-46  156.6   0.7    4.4e-46  156.1   0.7    1.3  1  DUF432    Protein of unknown function (DUF432)


Domain annotation for each model (and alignments):
>> DUF432  Protein of unknown function (DUF432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   0.7   2.4e-50   4.4e-46       1     123 []      56     178 ..      56     178 .. 1.00

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 2.4e-50
                        DUF432   1 PvnlpkeitkyllveleeplvvepkseveiyvkvpveigvfikskkeveliDvfslskkkYaLYGspesGviaryvksevy 81 
                                   P+n pk+it++ll+e++++++++p ++v++y+k+pve+g+fi++k+eve+iD+++l+k+k++LYG+p++G+i++y+ksevy
  gi|91772518|ref|YP_565210.1|  56 PLNKPKKITSNLLIEFDKTVTIAPMARVKVYIKFPVEMGIFISDKDEVEIIDILTLAKNKFTLYGNPSDGMICKYWKSEVY 136
                                   99******************************************************************************* PP

                        DUF432  82 seppeldpleeavveleikNetdevvevskivfdalglklyy 123
                                   s++p++dp++e+++el+i N+t+++vevs+ vf+a+g+k+yy
  gi|91772518|ref|YP_565210.1| 137 STIPSSDPMYEGIMELSIINSTNRWVEVSQSVFNANGMKIYY 178
                                   *****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1445.95
//
Query:       gi|91772519|ref|YP_565211.1|  [L=279]
Description: MscS mechanosensitive ion channel [Methanococcoides burtonii DSM 6242]
Scores for complete 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-51  174.3   6.5    3.2e-51  173.8   6.5    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 !  173.8   6.5   1.8e-55   3.2e-51       4     206 .]      61     257 ..      58     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 173.8 bits;  conditional E-value: 1.8e-55
                                   HHHHHHHHH.HHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSE CS
                    MS_channel   4 lkiliivvg.ilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrt 83 
                                    +++i++++ + i+l  lgv++s+ll++  + gl++g+a+++++ nl++G++l+fe+p+k+G+ v+i +  G+Vedi+l +
  gi|91772519|ref|YP_565211.1|  61 SYYGIVAITfVFIILPILGVETSSLLVAGSIFGLVIGFASQSIVGNLISGLFLIFERPIKLGNQVNIDGNVGIVEDISLIS 141
                                   5677766651568899***************************************************************** PP

                                   EEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE- CS
                    MS_channel  84 tkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefg 164
                                   t irt dg +v iPn++++t++i+N+   + +rr+++++gv+ys d   +++++ ++k+ ++e++  lk++e+ v+++e+g
  gi|91772519|ref|YP_565211.1| 142 TIIRTYDGLYVRIPNENVFTTTITNYVA-NVARRFEYVVGVRYSDD---ADQAIGIIKNLIEEHSFALKNPEPVVFVGELG 218
                                   ****************************.*****************...9******************************* PP

                                   SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                    MS_channel 165 dsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                   ++s+n++v++++++    +++++++e+  +ikk lee+giei
  gi|91772519|ref|YP_565211.1| 219 NNSVNITVKIWAPS---TDWYALKTELLWKIKKTLEENGIEI 257
                                   **************...9**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1724.50
//
Query:       gi|91772520|ref|YP_565212.1|  [L=144]
Description: hypothetical protein Mbur_0477 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-11   43.3   5.6    3.5e-11   43.3   5.6    2.0  2  PsiE        Phosphate-starvation-inducible E
  ------ inclusion threshold ------
      0.071   13.5   1.5      0.071   13.5   1.5    2.5  3  DUF3852     Protein of unknown function (DUF3852)
       0.63    9.8   5.3          7    6.4   0.5    3.0  3  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like


Domain annotation for each model (and alignments):
>> PsiE  Phosphate-starvation-inducible E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.2      0.44   2.6e+03      54      66 ..      20      32 ..      10      34 .. 0.57
   2 !   43.3   5.6   5.9e-15   3.5e-11       3      68 .]      61     127 ..      59     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.44
                          PsiE 54 ltllglaaailaL 66
                                  l++l+la+++ +L
  gi|91772520|ref|YP_565212.1| 20 LYILLLAVIVGVL 32
                                  4556666665555 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 5.9e-15
                          PsiE   3 diLllLillEllrtivaylkehriavrlvieaaiiavaRklIil.dlkdggyltllglaaailaLgl 68 
                                   ++L++++l++++ ++++y ++ ri+++++ +a+i+ v R++ i  + ++++y+ +l+l+a++l+Lg+
  gi|91772520|ref|YP_565212.1|  61 SVLTVFVLIDFFKAFIDYREHERIRLTYITDATILIVMREIAIGiYDQKIEYEFMLSLSAVLLVLGA 127
                                   69****************9999*******************************************96 PP

>> DUF3852  Protein of unknown function (DUF3852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.7       0.1   6.1e+02      49      69 ..       8      28 ..       4      45 .. 0.73
   2 ?   13.5   1.5   1.2e-05     0.071      54      86 ..      56      88 ..      48     106 .. 0.75
   3 ?   -0.5   0.2      0.26   1.6e+03      65     100 ..      97     132 ..      86     136 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.1
                       DUF3852 49 vnnvvfpvidvilavllfvkl 69
                                   + v+  v+ +il +ll++ +
  gi|91772520|ref|YP_565212.1|  8 FDIVIRYVTTLILYILLLAVI 28
                                  566777777777777777665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.2e-05
                       DUF3852 54 fpvidvilavllfvklatayldYrkhgqlefaa 86
                                  + ++  +l+v+++    +a++dYr+h+++  + 
  gi|91772520|ref|YP_565212.1| 56 TNIVFSVLTVFVLIDFFKAFIDYREHERIRLTY 88
                                  5677889999*****************876432 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.26
                       DUF3852  65 lfvklatayldYrkhgqlefaapailfagLvfsltA 100
                                   +++ +a    d + + ++  +  a+l++   + ++A
  gi|91772520|ref|YP_565212.1|  97 VMREIAIGIYDQKIEYEFMLSLSAVLLVLGAIRVLA 132
                                   445566666566666666666666666655555555 PP

>> 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 ?    6.4   0.5    0.0012         7     132     165 ..       2      35 ..       1      40 [. 0.85
   2 ?    1.1   0.2     0.048   2.9e+02      96     118 ..      55      77 ..      46     102 .. 0.79
   3 ?    3.4   0.0    0.0094        56       4      32 ..     106     134 ..     103     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
                    EMC3_TMCO1 132 llqrglesldvrfvssiswYflcsfglsqiirkl 165
                                   l++ ++ + ++r+v+ +++Y+l +  + ++++++
  gi|91772520|ref|YP_565212.1|   2 LTHDKIFDIVIRYVTTLILYILLLAVIVGVLKIF 35 
                                   68888889999***********999999998876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.048
                    EMC3_TMCO1  96 ivtmipqiliffwlnsffsgfvv 118
                                   ++++++++l+ f+l  ff+ f+ 
  gi|91772520|ref|YP_565212.1|  55 FTNIVFSVLTVFVLIDFFKAFID 77 
                                   66778888888888888876654 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0094
                    EMC3_TMCO1   4 ldplirdwvllPivivillvgiltgllse 32 
                                    d +i++ ++l ++ v+l++g+++ l+ +
  gi|91772520|ref|YP_565212.1| 106 YDQKIEYEFMLSLSAVLLVLGAIRVLAVK 134
                                   588999******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 897.89
//
Query:       gi|91772521|ref|YP_565213.1|  [L=389]
Description: hypothetical protein Mbur_0479 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  184.2   1.0    8.2e-54  183.0   0.0    1.8  2  DDE_Tnp_IS66   Transposase IS66 family
    0.00011   22.7   0.6    0.00035   21.1   0.6    1.8  1  SlyX           SlyX
    0.00016   21.9   0.3       0.12   12.6   0.2    2.8  3  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.053   13.6   0.2        2.3    8.3   0.0    2.6  2  GutM           Glucitol operon activator protein (GutM)
       0.16   11.9   0.0        1.5    8.8   0.0    2.5  3  BBS2_N         Ciliary BBSome complex subunit 2, N-terminal
       0.34   11.6   3.4       0.34   11.5   0.2    2.4  3  PLATZ          PLATZ transcription factor
       0.36   11.4   3.3       0.49   11.0   1.2    2.3  2  BST2           Bone marrow stromal antigen 2
       0.43   11.1   5.0       0.52   10.8   0.2    2.7  3  DUF16          Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.29   6.4e+02     174     227 ..      20      71 ..       4      84 .. 0.67
   2 !  183.0   0.0   3.7e-57   8.2e-54      48     280 ..     122     351 ..     106     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                  DDE_Tnp_IS66 174 larigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpkskl 227
                                   ++ + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ + +
  gi|91772521|ref|YP_565213.1|  20 VTLVTTLYDIIAEQQR--IIELQAVRITELEERVKKLEEQLKKNSRNSSKPPST 71 
                                   4447778887766633..457778888888888888888888777665555544 PP

  == domain 2  score: 183.0 bits;  conditional E-value: 3.7e-57
                  DDE_Tnp_IS66  48 raaelleplvealkaallasevihaDETtlrvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkG 126
                                   ++ + le + +++k+ l +s+vi++DET++r       +gk+++l+v++t+k   ++++  +++Rg+e+++a+  L +f+G
  gi|91772521|ref|YP_565213.1| 122 NCERSLEDFEQQIKNFLIESPVINCDETGMR------IEGKRQWLHVASTNK---MTCYCPHQKRGSEAMNAMgiLPNFNG 193
                                   56677**************************......99***********99...****************9955666*** PP

                  DDE_Tnp_IS66 127 vlvsDgyagYnklaeeqvthalCwaHlrRkfvdaeeakkksqaaaealar.igklyaierearea....eaeerlalrqee 202
                                   ++v+D +++Y k+   +++h +C aHl+R++++++e+++  q +++a++  + ++++  +++re+    ++e+ ++ +  +
  gi|91772521|ref|YP_565213.1| 194 TVVHDFWKSYYKY---DCDHSICNAHLLRELTSVSENDD--QLWSKAMNIlLIDVKKSVDQIREMsgcmKPERIKEFEDWY 269
                                   ************9...7*******************977..*********************955678888********** PP

                  DDE_Tnp_IS66 203 srpllaeleawleeql....kkvlpksklgkairyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeG 279
                                    + ++  +e++ + q     ++ +++++++++++++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++G
  gi|91772521|ref|YP_565213.1| 270 GQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLDRFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQG 350
                                   **********998554567799*********************************************************** PP

                  DDE_Tnp_IS66 280 a 280
                                   a
  gi|91772521|ref|YP_565213.1| 351 A 351
                                   9 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.6   1.5e-07   0.00035      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ +  ++ +l+er+k+lee+ +++ ++  +PP
  gi|91772521|ref|YP_565213.1| 22 LVTTLYDIIAEQQRIIELQAVRITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.5   5.6e+03      21      36 ..      27      42 ..      24      67 .. 0.54
   2 !    6.3   0.0    0.0046        10       5      44 ..     145     182 ..     141     185 .. 0.79
   3 !   12.6   0.2   5.3e-05      0.12      85     138 ..     314     367 ..     288     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.5
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91772521|ref|YP_565213.1| 27 YDIIAEQQRIIELQAV 42
                                  6666666666665543 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0046
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaa 44 
                                   + DET ++i+Gk ++l  a  ++ ++ ++   ++R+ +a 
  gi|91772521|ref|YP_565213.1| 145 NCDETGMRIEGKRQWLHVA--STNKMTCYCPHQKRGSEAM 182
                                   68************99866..6666778888888887775 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 5.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91772521|ref|YP_565213.1| 314 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 367
                                   55667899*****************************98777776666666665 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.001       2.3      42      90 ..     227     275 ..     218     293 .. 0.79
   2 ?    2.3   0.1      0.08   1.8e+02      64      82 ..     344     362 ..     326     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.001
                          GutM  42 kkgrfragvivllavdedgiivearvmkGvTvfarfkeleelegkslee 90 
                                   +  ++ ++++ +l +d ++ + ++r+m+G     r+ke+e+  g+ ++ 
  gi|91772521|ref|YP_565213.1| 227 NDDQLWSKAMNILLIDVKKSVDQIREMSGCMKPERIKEFEDWYGQIIHI 275
                                   66677889999*******************9999999999999988764 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.08
                          GutM  64 earvmkGvTvfarfkelee 82 
                                    +r m+G  +f+r+++  +
  gi|91772521|ref|YP_565213.1| 344 TFRSMQGALIFSRVRSYIS 362
                                   5689**********98654 PP

>> BBS2_N  Ciliary BBSome complex subunit 2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00066       1.5      17      82 ..     108     171 ..      94     176 .. 0.83
   2 ?   -3.1   0.0       3.3   7.3e+03      42      54 ..     235     247 ..     219     260 .. 0.55
   3 ?   -1.1   0.0      0.76   1.7e+03      41      55 ..     328     342 ..     316     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00066
                        BBS2_N  17 tagkvlihnphekeqklkserlsasesevslLninkevtalaagklkekqekdiLligtqtnllaY 82 
                                     ++v+ih+ h+ ++  +  +l++ e++++ + i++ v+      ++ + +++ L +++ +++++Y
  gi|91772521|ref|YP_565213.1| 108 VPDEVIIHKVHKCSNCER--SLEDFEQQIKNFLIESPVINCDETGMRIEGKRQWLHVASTNKMTCY 171
                                   5679*******9985443..45556***********99999888899999**************99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                        BBS2_N  42 esevslLninkev 54 
                                   + ++ l++++k+v
  gi|91772521|ref|YP_565213.1| 235 AMNILLIDVKKSV 247
                                   3344444444444 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.76
                        BBS2_N  41 sesevslLninkevt 55 
                                    e++v++++++++++
  gi|91772521|ref|YP_565213.1| 328 AERDVRMMKVQQKIS 342
                                   3899********997 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         1   2.3e+03      17      51 ..      26      62 ..      19      72 .. 0.50
   2 ?   11.5   0.2   0.00015      0.34      34      71 ..      73     130 ..      69     134 .. 0.83
   3 ?   -3.7   0.0         8   1.8e+04      39      51 ..     280     292 ..     268     300 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                         PLATZ 17 lldvseiQtYvinsa..kvvflnerpqarsakakake 51
                                  l+d+   Q+ +i  +  ++  l+er ++ +++ k+++
  gi|91772521|ref|YP_565213.1| 26 LYDIIAEQQRIIELQavRITELEERVKKLEEQLKKNS 62
                                  5555555555554331144566666444444433333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772521|ref|YP_565213.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDF 130
                                   9*********99998888743.33333568999***********************985 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 8
                         PLATZ  39 rpqarsakakake 51 
                                    pq + +++k+ +
  gi|91772521|ref|YP_565213.1| 280 NPQLQAKSKKRGR 292
                                   4444433333332 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.2   0.00022      0.49      45      87 ..      21      63 ..       3      67 .. 0.80
   2 ?   -1.7   0.0       2.1   4.6e+03      14      30 ..     119     135 ..     115     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q  ++ el++ +kkL+++L++ + 
  gi|91772521|ref|YP_565213.1| 21 TLVTTLYDIIAEQQRIIELQAVRITELEERVKKLEEQLKKNSR 63
                                  5677888888888888899999*****************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHHHHHH CS
                          BST2  14 ecrnvtrlLerqLtqaq 30 
                                   +c+n +r Le   +q +
  gi|91772521|ref|YP_565213.1| 119 KCSNCERSLEDFEQQIK 135
                                   56666666654433333 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00023      0.52      45      82 ..      25      62 ..      16      74 .. 0.80
   2 ?   -3.8   0.0         8   1.8e+04      56      64 ..     126     134 ..     110     141 .. 0.52
   3 ?    1.6   0.2      0.17   3.8e+02      10      58 ..     287     342 ..     278     373 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q  +i+el++++k+ +e+l+k  
  gi|91772521|ref|YP_565213.1| 25 TLYDIIAEQQRIIELQAVRITELEERVKKLEEQLKKNS 62
                                  55666888899999999999999999999999998654 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8
                                   HHHHHHHHH CS
                         DUF16  56 kvekqgeki 64 
                                     e  +++i
  gi|91772521|ref|YP_565213.1| 126 SLEDFEQQI 134
                                   222222222 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
                                   XXX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  10 vKkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                    Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91772521|ref|YP_565213.1| 287 SKK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 342
                                   455.467888888888777888999988854444440......55555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1614  (0.0900218); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2323.43
//
Query:       gi|91772522|ref|YP_565214.1|  [L=163]
Description: hypothetical protein Mbur_0481 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-17   63.0   0.0      5e-17   62.6   0.0    1.2  1  TIR_2            TIR domain
      1e-06   29.1   0.1    4.1e-06   27.1   0.1    2.0  1  DUF1863          MTH538 TIR-like domain (DUF1863)
     0.0011   19.3   0.2     0.0025   18.2   0.2    1.6  1  DUF4062          Domain of unknown function (DUF4062)
     0.0055   16.7   0.0     0.0069   16.4   0.0    1.3  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
  ------ inclusion threshold ------
      0.024   14.4   0.3      0.029   14.2   0.3    1.4  1  TIR              TIR domain
      0.036   13.9   0.1       0.24   11.3   0.1    2.0  2  Dioxygenase_N    Catechol dioxygenase N terminus


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 !   62.6   0.0   1.7e-20     5e-17       1     117 [.       5     122 ..       5     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.7e-20
                         TIR_2   1 VFiSyssedkewaeklaeaLeaag.irvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreeleaaleaae 80 
                                   +F+Sys++d e ++ + ++ +     + ++  + l pg+++ ++i + i ++dv+++++s+ + +s+++++e+  a++   
  gi|91772522|ref|YP_565214.1|   5 IFVSYSTKDVEEIKPILQQIQTIKdTEFFFADETLNPGDHISQRIINYITNCDVFIFFYSKFAYDSTYVQHEIGVAKA--- 82 
                                   8*******************87763667777779*******************************************8... PP

                         TIR_2  81 egkkrlipvllepekpp..laslqyidlskk..deealerL 117
                                    ++k +ip+ll++ kp+  l++++y+++ ++  +++++ rL
  gi|91772522|ref|YP_565214.1|  83 -NDKLIIPILLDETKPDgmLQGINYLNFYNQnkKQQEFVRL 122
                                   .5566*******65676678********9777544777665 PP

>> DUF1863  MTH538 TIR-like domain (DUF1863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.4e-09   4.1e-06       2     112 ..       4      97 ..       3     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.4e-09
                       DUF1863   2 kvFiSysheddkerlnklkkllaesyrkiagkraglgeasgnalepirdrdedsaaedikeairdaldrssvliVLvgset 82 
                                   k+F+Sys +d + +   +k +l++  ++i+++++            +  +++++  + i+++i +++++ +v i + ++ +
  gi|91772522|ref|YP_565214.1|   4 KIFVSYSTKDVE-E---IKPILQQ-IQTIKDTEF------------FFADETLNPGDHISQRIINYITNCDVFIFFYSKFA 67 
                                   789999888777.3...3344444.344445333............223334445668*********************** PP

                       DUF1863  83 atsrWvdwEIaaslkkgkrllgvsldrlkq 112
                                   ++s +v++EI  +  ++k ++ + ld++k 
  gi|91772522|ref|YP_565214.1|  68 YDSTYVQHEIGVAKANDKLIIPILLDETKP 97 
                                   *************************99984 PP

>> DUF4062  Domain of unknown function (DUF4062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   8.3e-07    0.0025       1      61 [.       4      64 ..       4      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.3e-07
                       DUF4062  1 rvFiSStfrdlkeeRealieallelglepvgme.efaardqsqlelcleevdecdifililg 61
                                  ++F+S   +d++e    l +++++ + +++ +  e  ++ ++  + +++ +++cd+fi+++ 
  gi|91772522|ref|YP_565214.1|  4 KIFVSYSTKDVEEIKPIL-QQIQTIKDTEFFFAdETLNPGDHISQRIINYITNCDVFIFFYS 64
                                  8*********99776666.5555566666666636999999*****************9986 PP

>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.3e-06    0.0069      44     102 ..      37      93 ..       6     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-06
                                   .--SSHHHHHHHHHHHHHC-SEEEEE--SSSSSS--HHHH.HHHHHHHHCT-EEEEE-S- CS
               Nuc_deoxyrib_tr  44 paeetaraiyeadialirqaDavianldpfrgpeaDsGta.fEvGyavalgkpvlayttd 102
                                   +  ++   i ++ i+ i ++D+ i+ +++f     Ds  +  E+G+a a  k ++    d
  gi|91772522|ref|YP_565214.1|  37 ETLNPGDHISQRIINYITNCDVFIFFYSKFA---YDSTYVqHEIGVAKANDKLIIPILLD 93 
                                   5566777899999******************...99986538**********88755544 PP

>> TIR  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   9.8e-06     0.029      19      76 ..      18      74 ..       2     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.8e-06
                                  HCHHHHHTTCCTTSEEEESSTT--SSS-HHHHHHHHHHCSSEEEEEE-TTHHHHCCCC CS
                           TIR 19 shllkellekqkgiklfiddrdlepGeaiadelksaIkkSrrlivvlSknyasskwcl 76
                                    +l+++ +  k  + f+ d+ l+pG+ i++ + + I ++ + i+  Sk    s+ + 
  gi|91772522|ref|YP_565214.1| 18 KPILQQI-QTIKDTEFFFADETLNPGDHISQRIINYITNCDVFIFFYSKFAYDSTYVQ 74
                                  5566666.56677889999**************************9998666666333 PP

>> Dioxygenase_N  Catechol dioxygenase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0025       7.4      26      54 ..      97     123 ..      93     126 .. 0.86
   2 ?   11.3   0.1     8e-05      0.24      26      72 ..     116     160 ..     112     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHHHHHHH.....TT-HHHHH CS
                 Dioxygenase_N  26 eeEwwaavdfLtrvGqisddkrqEfiLls 54 
                                   ++ + +++++L+   q  ++k+qEf+ l 
  gi|91772522|ref|YP_565214.1|  97 PDGMLQGINYLNFYNQ--NKKQQEFVRLY 123
                                   566789**********..*******9986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8e-05
                                   HHHHHHHHHHHHHHHH.....TT-HHHHHHHTTHHHHHHHHHHHHHH CS
                 Dioxygenase_N  26 eeEwwaavdfLtrvGqisddkrqEfiLlsdvLGlehlvdaindakea 72 
                                   ++E+    +++++  q   ++r+ +   ++ LGle ++   +d++e+
  gi|91772522|ref|YP_565214.1| 116 QQEFVRLYNYINQNVQ--RKNRNSALSTLALLGLEYFLLKSDDEQEE 160
                                   79***********888..99******************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 940.59
//
Query:       gi|91772523|ref|YP_565215.1|  [L=475]
Description: divergent AAA ATP [Methanococcoides burtonii DSM 6242]
Scores for complete 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   77.1   0.8    2.7e-21   76.2   0.1    1.9  1  AlbA_2          Putative DNA-binding domain
    1.6e-14   53.8   0.0      4e-14   52.5   0.0    1.7  1  HATPase_c_4     Putative ATP-dependent DNA helicase recG C-te
    1.2e-11   44.0   0.4    2.9e-11   42.7   0.1    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    5.7e-05   23.0   0.5    0.00029   20.7   0.1    2.2  2  HTH_11          HTH domain
     0.0001   22.1   0.0    0.00017   21.3   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0009   19.6   0.1     0.0034   17.7   0.0    1.9  2  FaeA            FaeA-like protein
     0.0011   18.9   0.0     0.0023   18.0   0.0    1.4  1  HTH_20          Helix-turn-helix domain
     0.0083   16.1   0.0      0.024   14.6   0.0    1.8  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.4   0.1        4.2    7.6   0.0    3.3  3  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.038   13.8   0.0      0.098   12.5   0.0    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.043   13.5   0.2       0.18   11.6   0.0    1.9  2  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.066   13.6   0.0       0.14   12.5   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.077   12.9   0.5       0.45   10.5   0.1    2.1  2  MarR            MarR family
       0.11   12.2   0.0       0.22   11.3   0.0    1.4  1  HTH_39          Helix-turn-helix domain
       0.12   12.2   0.0       0.49   10.3   0.0    1.9  2  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   2.2e-24   2.7e-21       1     121 [.      14     131 ..      14     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.2e-24
                        AlbA_2   1 EdellEfKeslgnklkkrersiakticAfaNsegGtlliGVeD...dgkvvGvecsdqeedqlrlelksiikrfkpkvlpd 78 
                                   E+e+ E+Ke++++  k+      +t++Af N++gG+l++GVe+   d +++Gve+ ++ e+++++ l    ++f++k++++
  gi|91772523|ref|YP_565215.1|  14 EWEDFEVKEAKSSIPKS----SFETVSAFSNTNGGWLVFGVEQlnkDFEITGVEDAERIEQNFTTALR--GDKFNQKIRVK 88 
                                   78999**********98....89*******************9866777****665555555555555..9********** PP

                        AlbA_2  79 iervelkgkkvlvvkvekskkkplyeneegvvyiRrggsskrl 121
                                    ++++++gk vl+++v+ s++kp+y n++++ +iR+g+ ++r+
  gi|91772523|ref|YP_565215.1|  89 STKYDFDGKIVLAFYVPASEQKPVYFNSRKNTFIRTGSGDQRA 131
                                   ****************************************997 PP

>> 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 !   52.5   0.0   3.3e-17     4e-14       3      88 .]     306     389 ..     305     389 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 3.3e-17
                   HATPase_c_4   3 kvqieifdDRleItspGglpggvtveskllegrssaRNelLasllerlrlmeergsGiqrilealeeaglpepefredgss 83 
                                   k +i++f DR+e  +pG+lp   ++es ++e  +  RN++++++++ ++l e+ gsG+++++   + +  +ep +++d + 
  gi|91772523|ref|YP_565215.1| 306 KPRIRVFLDRIEFLNPGSLP--KDIESIMKEDFTMPRNPIITRIFRVIKLSENAGSGFDKMFTGWKSYYETEPVVSNDIDF 384
                                   679*****************..77888779999********************************************9998 PP

                   HATPase_c_4  84 ftvtl 88 
                                    ++t+
  gi|91772523|ref|YP_565215.1| 385 YKITF 389
                                   88775 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 ?   -2.5   0.0       3.3   3.9e+03      18      27 ..     184     193 ..     182     195 .. 0.83
   2 !   42.7   0.1   2.5e-14   2.9e-11       2      48 .]     414     460 ..     413     460 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.3
                        HTH_24  18 isqreLAerl 27 
                                   +s++eL e+l
  gi|91772523|ref|YP_565215.1| 184 LSMKELLEKL 193
                                   8999999987 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 2.5e-14
                        HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    +t+ kIL ++ + p+i+ +eLAe +g++   v +++k+L++eGl+k
  gi|91772523|ref|YP_565215.1| 414 EKTREKILDIMSQTPKITTAELAELTGITAKGVEWHIKKLKDEGLLK 460
                                   6899****************************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.4e+03      12      27 ..     179     195 ..     178     195 .. 0.86
   2 !   20.7   0.1   2.5e-07   0.00029       2      51 ..     417     467 ..     416     469 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                        HTH_11  12 argp.isgeeLAeeLnv 27 
                                   +r + +s +eL e+L v
  gi|91772523|ref|YP_565215.1| 179 HRYNkLSMKELLEKLQV 195
                                   778889********987 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.5e-07
                        HTH_11   2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg..vpIesepg 51 
                                   +++il +  +++++i+ +eLAe ++++ + v  +Ik+L++ g   +I +++g
  gi|91772523|ref|YP_565215.1| 417 REKILDIM-SQTPKITTAELAELTGITAKGVEWHIKKLKDEGllKRIGADKG 467
                                   68999999.66666****************************8888888877 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 !   21.3   0.0   1.5e-07   0.00017       2      46 ..     415     460 ..     414     461 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                                   HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5   2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                   +tR kIL ++++ +  +  elae +g++   v  H kkL+++GL++
  gi|91772523|ref|YP_565215.1| 415 KTREKILDIMSQTPkITTAELAELTGITAKGVEWHIKKLKDEGLLK 460
                                   7999********7769****************************85 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.3   3.9e+03      26      43 ..     164     179 ..     156     186 .. 0.75
   2 !   17.7   0.0   2.8e-06    0.0034       3      60 ..     418     472 ..     416     474 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.3
                                   TS-HHHHHHHHHHHHHHS CS
                          FaeA  26 glsaYQaRyYLeqLekeg 43 
                                    +s+Y  R YLe+ + e 
  gi|91772523|ref|YP_565215.1| 164 TISDY--RTYLENVNPEH 179
                                   57777..89999987665 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.8e-06
                                   HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-EEEE CS
                          FaeA   3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstlWel 60 
                                   e+Il+ + +     +T+e+A+ +g++a  +   +++L+ eg +kr  + +G  ++We+
  gi|91772523|ref|YP_565215.1| 418 EKILDIMSQ-TPKITTAELAELTGITAKGVEWHIKKLKDEGLLKRIGADKG--GMWEV 472
                                   788888877.7779************************************9..77876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.9e-06    0.0023      11      57 ..     416     462 ..     413     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                                   HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                        HTH_20  11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                   +R +il+  ++    t +elae+ +++ + +  H+++L + gL+++ 
  gi|91772523|ref|YP_565215.1| 416 TREKILDIMSQTPKITTAELAELTGITAKGVEWHIKKLKDEGLLKRI 462
                                   666778888888889*****************************975 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 !   14.6   0.0     2e-05     0.024      20      54 ..     428     463 ..     410     475 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                   EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.T CS
                     HTH_Crp_2  20 lpltqeelAsmlGltretvsrilseLkreglisr.g 54 
                                    ++t +elA++ G+t   v   +++Lk+egl++r g
  gi|91772523|ref|YP_565215.1| 428 PKITTAELAELTGITAKGVEWHIKKLKDEGLLKRiG 463
                                   4799****************************9434 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 ?   -1.7   0.0       2.7   3.2e+03      30      43 ..       1      14 [.       1      29 [. 0.88
   2 ?    2.5   0.1      0.14   1.7e+02      38      69 ..     180     209 ..     178     304 .. 0.63
   3 ?    7.6   0.0    0.0035       4.2      19      51 ..     430     462 ..     430     467 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.7
                B-block_TFIIIC 30 qdprslfyrlksLe 43
                                  +d+ +lf rl+ Le
  gi|91772523|ref|YP_565215.1|  1 MDKTKLFNRLDDLE 14
                                  7999*******997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                B-block_TFIIIC  38 rlksLekkgLIvkqsiidsatkksistsllvl 69 
                                   r ++L+ k L +k+++  + +++++ + llv+
  gi|91772523|ref|YP_565215.1| 180 RYNKLSMKELLEKLQV--VVDGRITIGGLLVF 209
                                   6788888888888888..55555555555554 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0035
                B-block_TFIIIC  19 itqsdLakeskqdprslfyrlksLekkgLIvkq 51 
                                   it+ +La ++++ ++ +  ++k+L++ gL +++
  gi|91772523|ref|YP_565215.1| 430 ITTAELAELTGITAKGVEWHIKKLKDEGLLKRI 462
                                   6899*************************9986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.2e-05     0.098       7      34 ..     419     446 ..     418     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-05
                 HTH_AsnC-type   7 kILeaLqedaRisyaeLAervGlSestv 34 
                                   kIL+++ + ++i+ aeLAe +G+++  v
  gi|91772523|ref|YP_565215.1| 419 KILDIMSQTPKITTAELAELTGITAKGV 446
                                   8**********************99766 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 ?   -1.5   0.0       1.9   2.2e+03      14      26 ..     183     195 ..     180     197 .. 0.85
   2 ?   11.6   0.0   0.00015      0.18       3      47 ..     418     462 ..     417     465 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                      HTH_DeoR  14 klsveelvellgv 26 
                                   kls +el e l+v
  gi|91772523|ref|YP_565215.1| 183 KLSMKELLEKLQV 195
                                   7999999999998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                      HTH_DeoR   3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47 
                                   e+il+   q  k+++ el+el g++ + +   +++L+ +gll+R+
  gi|91772523|ref|YP_565215.1| 418 EKILDIMSQTPKITTAELAELTGITAKGVEWHIKKLKDEGLLKRI 462
                                   89***************************************9996 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.14      22      65 ..     426     469 ..     419     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                   TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCE CS
                          Rrf2  22 eeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGy 65 
                                   +  +++++e+ae ++i ++ +e  ++kL+ +gl+k +   +GG+
  gi|91772523|ref|YP_565215.1| 426 QTPKITTAELAELTGITAKGVEWHIKKLKDEGLLKRIGADKGGM 469
                                   34459*****************************9988888886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.8   9.5e+02      40      58 ..     183     201 ..     180     202 .. 0.83
   2 ?   10.5   0.1   0.00038      0.45       7      49 ..     419     461 ..     415     463 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.8
                                   HHHHTTSEEEEEETTSTTS CS
                          MarR  40 rLekkGlieRskspeDrRe 58 
                                   +L  k+l+e+ +   D R+
  gi|91772523|ref|YP_565215.1| 183 KLSMKELLEKLQVVVDGRI 201
                                   7889999999999999886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00038
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49 
                                   +iL i ++ + ++ +eLa+  g++   v   +++L ++Gl++R
  gi|91772523|ref|YP_565215.1| 419 KILDIMSQTPKITTAELAELTGITAKGVEWHIKKLKDEGLLKR 461
                                   69999************************************99 PP

>> HTH_39  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   0.00018      0.22       3      41 ..     417     457 ..     415     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                        HTH_39   3 carilaaLrqhgsittleamrelditr..laaRIkeLrekG 41 
                                   + +il+++ q+ +itt e+ +  +it       Ik L+++G
  gi|91772523|ref|YP_565215.1| 417 REKILDIMSQTPKITTAELAELTGITAkgVEWHIKKLKDEG 457
                                   679**********************9866666777777777 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9   3.5e+03      20      33 ..     181     195 ..     170     195 .. 0.74
   2 ?   10.3   0.0   0.00041      0.49      17      54 ..     427     462 ..     416     467 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                                   S.EEEHHHHHHHHTS CS
                        MarR_2  20 r.dltvgelarrlgl 33 
                                   + +l+++el ++l++
  gi|91772523|ref|YP_565215.1| 181 YnKLSMKELLEKLQV 195
                                   156999999999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00041
                                   TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                    p   +t +ela+ +g++   v  ++k+L + GL+ r 
  gi|91772523|ref|YP_565215.1| 427 TPK--ITTAELAELTGITAKGVEWHIKKLKDEGLLKRI 462
                                   454..9*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2811.09
//
Query:       gi|91772524|ref|YP_565216.1|  [L=568]
Description: N-6 DNA methylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-118  395.7   0.1   1.9e-118  395.3   0.1    1.2  1  N6_Mtase  N-6 DNA Methylase
    4.6e-21   75.9   4.5    1.3e-20   74.4   4.5    1.9  1  HsdM_N    HsdM N-terminal domain
     0.0011   19.4   0.0     0.0065   17.0   0.0    2.4  3  Eco57I    Eco57I restriction-modification methylase
  ------ inclusion threshold ------
      0.079   13.0   0.3       0.73    9.9   0.0    2.6  2  DUF2487   Protein of unknown function (DUF2487)


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 !  395.3   0.1  4.3e-122  1.9e-118       2     311 ..     200     527 ..     199     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 395.3 bits;  conditional E-value: 4.3e-122
                      N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee........dgk 74 
                                   skd+lG+vYEy+l++fa +egk+gG+++TP+++++live+lep++g+ vyDpa+Gsgg++v+++k+++++        +++
  gi|91772524|ref|YP_565216.1| 200 SKDILGHVYEYFLGQFALAEGKQGGQYYTPKSIVTLIVEMLEPYKGR-VYDPAMGSGGFFVSSDKFIENHanvkhynaSEQ 279
                                   79********************************************8.********************99*******9999 PP

                      N6_Mtase  75 tkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekderfreav 155
                                   +k++s+yGqe+n+tt++La mN++++gi+ + ++++++d++ ++++  d ++d+v+aNppfn kew++++l++d+r+++++
  gi|91772524|ref|YP_565216.1| 280 KKQISVYGQESNPTTWKLAAMNMAIRGIDFN-FGKKNADSFLDDQHP-DLRADFVMANPPFNMKEWWHEKLADDPRWKYGT 358
                                   *******************************.***************.********************************* PP

                      N6_Mtase 156 apksnadlafllhiieslkpkGraavvlangvLfr.ggkegkIrkalvekdlveavialpeklFyntsiptcilvlkkeka 235
                                   +pk+na++a+++h++++l+p+G +a++lang++++ +++egkIrk+lve+d ve+++alp +lF+nt+ip+ci +l+k+ka
  gi|91772524|ref|YP_565216.1| 359 PPKNNANFAWMQHMLHHLAPTGSMALLLANGSMSSnTNNEGKIRKTLVENDIVECMVALPGQLFTNTQIPACICFLTKDKA 439
                                   **********************************999*******************************************9 PP

                      N6_Mtase 236 e......rkgkvlfidaseefkkkdrkknklteediekildtykek......skevdkfskvveleeiaendynlnvgryv 304
                                   +      r+g++lfida++   +kdr  +++++edi++i+dt++ +       k++++f+++++   i++ +++l++gryv
  gi|91772524|ref|YP_565216.1| 440 AkddkrnRHGEILFIDARNLGFMKDRVLRDFKDEDIQRIADTFHTWqhnwseDKNEPGFCFSANHATIEKHNFVLTPGRYV 520
                                   899999999*************************************99997778888************************ PP

                      N6_Mtase 305 eteeeee 311
                                   ++e+e +
  gi|91772524|ref|YP_565216.1| 521 GAEAEVD 527
                                   *998865 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   4.5     3e-24   1.3e-20       2     137 .]      13     181 ..      12     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 3e-24
                                   HHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC................................--... CS
                        HsdM_N   2 esklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereekllee......................yken...al.ee 56 
                                   e klwkaad+LR+++d ++yk ++lgL+FlK+++d +eer+++l+e                       y  +   a+  e
  gi|91772524|ref|YP_565216.1|  13 ETKLWKAADKLRSNMDVANYKHVVLGLIFLKYVSDAFEERQNELVELfkkdddeniyylpredyssteeY--QhaiAEeLE 91 
                                   789*********99*****************************988899898888888888776655332..254633244 PP

                                   --------....S-CCCSHHHHHHS.................--HH..HHHHHHHHCHHHHCT--STHHHHHHHS...... CS
                        HsdM_N  57 leeklkskeafyipeelrWkelakk.................kddd..elgenlnkafpaleelnkslkgvfmkddfnafa 118
                                    ++ +++k+ f++p+++rW+ l++k                    +  ++   +++a++++e++n++lkg+++ +      
  gi|91772524|ref|YP_565216.1|  92 IRDYYAEKNVFWVPKTARWDILKEKsvlslntviwqneqgkdV--KlkSVSWLIDNALDEIEKANPKLKGILN-R-----I 164
                                   44555666*************9999999999999766444331..13356666777****************5.4.....3 PP

                                   S-----SSHHHHHHHHHHH CS
                        HsdM_N 119 lgeitkkspalLskviekf 137
                                    +   + ++++L  +i+ f
  gi|91772524|ref|YP_565216.1| 165 GQ--YQLDSEKLIGLINNF 181
                                   43..458999999999876 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.7   1.2e+04      50      69 ..     259     278 ..     256     290 .. 0.59
   2 !   17.0   0.0   1.5e-06    0.0065       3     104 ..     329     438 ..     327     440 .. 0.85
   3 ?   -3.5   0.0       3.3   1.5e+04      49      60 ..     513     525 ..     499     552 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.7
                        Eco57I  50 iiparflasgkglkefrekl 69 
                                   + + +f+++   +k+++++ 
  gi|91772524|ref|YP_565216.1| 259 VSSDKFIENHANVKHYNASE 278
                                   66677776555555555443 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.5e-06
                        Eco57I   3 fdviiGNPPYqeseakkelkaleek........akdiyqkFvekalkle.dkylaliiparfl.asgkglkefrekllkdk 73 
                                    d ++ NPP+ ++e  +e  a+  +        +++ +   ++   +l+  + +al++ +  + ++ +   ++r++l+++ 
  gi|91772524|ref|YP_565216.1| 329 ADFVMANPPFNMKEWWHEKLADDPRwkygtppkNNANFAWMQHMLHHLApTGSMALLLANGSMsSNTNNEGKIRKTLVEND 409
                                   6999********9966666656665899999988888999999999999778999****999988999999******9998 PP

                        Eco57I  74 klkklvefedskevFkdveikggilvflkdk 104
                                    ++ +v ++ +   F++++i  +i++++kdk
  gi|91772524|ref|YP_565216.1| 410 IVECMVALPGQ--LFTNTQIPACICFLTKDK 438
                                   88888888765..5***************98 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.3
                        Eco57I  49 liiparfl.asgk 60 
                                   +++p r++ a+++
  gi|91772524|ref|YP_565216.1| 513 VLTPGRYVgAEAE 525
                                   5678888744443 PP

>> DUF2487  Protein of unknown function (DUF2487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.25   1.1e+03      51     101 ..      68     115 ..      48     146 .. 0.71
   2 ?    9.9   0.0   0.00016      0.73      86     138 ..     430     482 ..     421     489 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                       DUF2487  51 vlllPaftYlkeeekeeeverlkeweeelkeegfkhvvfitsdeewkelee 101
                                   ++ lP   Y ++ee ++++++  e+++ + e+   +v+++   ++w  l+e
  gi|91772524|ref|YP_565216.1|  68 IYYLPREDYSSTEEYQHAIAEELEIRDYYAEK---NVFWVPKTARWDILKE 115
                                   55667777777777777666666666555554...7777777777766555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00016
                       DUF2487  86 hvvfitsdeewkeleeelegkliwvpaiplesldesqkqkiveeqvkqvlell 138
                                    ++f+t d+  k  +++ +g+++++ a +l  +++++ + + +e ++ + +++
  gi|91772524|ref|YP_565216.1| 430 CICFLTKDKAAKDDKRNRHGEILFIDARNLGFMKDRVLRDFKDEDIQRIADTF 482
                                   59***********************************9999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 4159.65
//
Query:       gi|91772525|ref|YP_565217.1|  [L=941]
Description: DEAD/DEAH box helicase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   95.4   0.0    5.2e-27   94.7   0.0    1.3  1  DEAD        DEAD/DEAH box helicase
    1.5e-18   67.3   0.1    6.3e-18   65.3   0.1    2.2  1  DUF1998     Domain of unknown function (DUF1998)
    3.7e-17   61.0   1.1    3.2e-06   26.8   0.1    4.2  3  TPR_2       Tetratricopeptide repeat
    1.1e-15   56.7   9.3    1.6e-06   27.6   0.1    4.3  4  TPR_1       Tetratricopeptide repeat
      7e-12   45.7   0.0      2e-11   44.2   0.0    1.8  1  Helicase_C  Helicase conserved C-terminal domain
    9.8e-11   41.2   0.2    0.00012   21.7   0.0    2.9  2  TPR_11      TPR repeat
    1.1e-08   35.2   0.0     0.0002   21.5   0.0    2.8  2  TPR_12      Tetratricopeptide repeat
    4.7e-08   32.6   0.8       0.28   11.5   0.0    4.1  3  TPR_8       Tetratricopeptide repeat
    7.4e-07   29.3   0.0      2e-06   27.9   0.0    1.7  2  ResIII      Type III restriction enzyme, res subunit
    1.6e-05   24.9   0.1      0.005   17.0   0.0    3.3  3  TPR_9       Tetratricopeptide repeat
    3.2e-05   24.0   1.8     0.0018   18.5   0.1    3.8  3  TPR_17      Tetratricopeptide repeat
    0.00011   22.7   0.0        0.7   10.9   0.1    3.3  2  TPR_14      Tetratricopeptide repeat
    0.00015   22.2   0.2     0.0092   16.5   0.0    2.7  2  TPR_19      Tetratricopeptide repeat
    0.00061   20.3   0.5        1.8    9.4   0.0    4.2  3  TPR_6       Tetratricopeptide repeat
     0.0026   17.0   0.0        0.1   11.8   0.0    2.2  2  TPR_15      Tetratricopeptide repeat
     0.0045   17.6   0.0       0.04   14.6   0.0    2.6  3  TPR_16      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.045   14.0   1.5      0.091   13.0   1.5    1.5  1  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
       0.13   12.3   2.2        8.8    6.6   0.0    3.5  4  TPR_7       Tetratricopeptide repeat
        1.3    8.9   3.7         10    6.0   0.6    3.1  3  RelB_N      RelB Antitoxin alpha helical 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 !   94.7   0.0   5.5e-30   5.2e-27       3     174 ..      57     230 ..      55     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 5.5e-30
                                   HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT..STSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky..idlrvlli 81 
                                    Qa a++++l+g++++++  T+sGK+l++++p+++++++   +++  al+++P+ +L++++l+ ++kf +   +dl+++ +
  gi|91772525|ref|YP_565217.1|  57 HQADAVKEVLDGKNIVLSTSTASGKSLCYMLPIFETLMD---DPNATALYISPLNALVNDQLESFEKFRDSmgLDLNINKF 134
                                   7************************************75...9999************************83355888888 PP

                                   ETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHH....HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldng.vdivvgtpgrlddll....stgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                   ig  + + ++s+++ g ++i++++p++++  +    ++   +  ls+++++VlDE ++++    +  + ++l++l++i+++
  gi|91772525|ref|YP_565217.1| 135 IGTMPPE-EKSAVKYGnPRILFTNPEMVHLSFlqwkQQW--KkfLSNLKYIVLDESHTYSGV-TGINMANLLRRLNRICDH 211
                                   8877775.555555555***********99665765333..245*****************9.99999999****888777 PP

                                   STTTSEEEEEESSBSHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          DEAD 156 gklqrqvivlSATlpkdvk 174
                                     ++ q i+++AT+ + v+
  gi|91772525|ref|YP_565217.1| 212 YGSSPQYICCTATIGNPVE 230
                                   779999*******986665 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.1   6.7e-21   6.3e-18       1      83 []     654     734 ..     654     734 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 6.7e-21
                       DUF1998   1 lehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCeeaGCpa 81 
                                   +ehali + pl+l  d++d+g+ +++++  +  ++ +i+iyd++ gG+G+ae+++  +ee+l+ +l+ ie c+C+  GCp+
  gi|91772525|ref|YP_565217.1| 654 IEHALIAMYPLHLLADRNDVGGISTPEHG-DIGNRSGIFIYDGHAGGVGYAEAGYAKIEEMLEVTLKAIEGCPCK-GGCPS 732
                                   69**********************96655.47899***************************************8.***** PP

                       DUF1998  82 Cl 83 
                                   C+
  gi|91772525|ref|YP_565217.1| 733 CI 734
                                   *7 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   4.4e-05     0.042      14      34 .]     830     850 ..     819     850 .. 0.92
   2 !   16.1   0.0   9.5e-06    0.0089       3      29 ..     853     879 ..     851     882 .. 0.93
   3 !   26.8   0.1   3.4e-09   3.2e-06       1      34 []     886     919 ..     886     919 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                         TPR_2  14 lgdyeeAleafekAleldPnn 34 
                                    +d+++A  +f+kAl+l+P+n
  gi|91772525|ref|YP_565217.1| 830 EKDHKKACYCFDKALQLEPDN 850
                                   5799***************98 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.5e-06
                         TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                   al+n G  y++++ y  Ale+f++ l 
  gi|91772525|ref|YP_565217.1| 853 ALFNKGITYLQMKMYPLALECFNRLLN 879
                                   8***********************997 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 3.4e-09
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   a+++ + G++++ l++ ++A+e++++Al+l P++
  gi|91772525|ref|YP_565217.1| 886 AKVWKCKGDCLRMLDNRADAIECYNEALRLKPDD 919
                                   789*****************************96 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       3.6   3.4e+03       7      15 ..     525     533 ..     524     533 .. 0.90
   2 !   10.1   0.7   0.00061      0.57      14      34 .]     830     850 ..     828     850 .. 0.91
   3 !   22.1   0.0     1e-07   9.5e-05       3      26 ..     853     876 ..     851     880 .. 0.92
   4 !   27.6   0.1   1.7e-09   1.6e-06       1      34 []     886     919 ..     886     919 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.6
                                   HHHHHHHTT CS
                         TPR_1   7 lGnayfklg 15 
                                   +G++yf++g
  gi|91772525|ref|YP_565217.1| 525 KGAIYFNQG 533
                                   799****98 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00061
                                   TT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  14 lgkydeAleyyekALelnPnn 34 
                                    +++++A  +++kAL+l+P+n
  gi|91772525|ref|YP_565217.1| 830 EKDHKKACYCFDKALQLEPDN 850
                                   58999999***********98 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 1e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyek 26 
                                   al+n+G +y+++++y  Ale++++
  gi|91772525|ref|YP_565217.1| 853 ALFNKGITYLQMKMYPLALECFNR 876
                                   99********************98 PP

  == domain 4  score: 27.6 bits;  conditional E-value: 1.7e-09
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ak+++ +G +++ l +  +A+e+y++AL+l P++
  gi|91772525|ref|YP_565217.1| 886 AKVWKCKGDCLRMLDNRADAIECYNEALRLKPDD 919
                                   89******************************96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   2.1e-14     2e-11      12     110 ..     286     390 ..     278     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.1e-14
                                   HTTTTSEEEEEESSHHHHHHHHHH..HHHT........TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                    Helicase_C  12 leeeggkilifvntidrlekvkll..lekk........gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                   + +++ ++++f++ ++++e  k++     +          ++  + g    nere+i +   kge+  +i+t+++e Gidi
  gi|91772525|ref|YP_565217.1| 286 FVQNDLQTIVFTRARQKVE--KMFveA--RnqlegrgvRKTISSYRGGYYGNEREAIEKGLSKGEIAGVISTTALELGIDI 362
                                   4578889***********9..666331..223456667789999************************************* PP

                                   TTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRa 110
                                    +++ +i+ ++p ++ s+ q++GR+gR+
  gi|91772525|ref|YP_565217.1| 363 GGLDACIIDGFPGTLMSARQQAGRAGRG 390
                                   ***************************7 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.3e-07   0.00012       7      41 ..     830     864 ..     827     865 .. 0.91
   2 !   16.2   0.1   6.4e-06     0.006      12      29 ..     904     921 ..     899     922 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                        TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                     + ++A  ++ kAl+l Pdn++a++n G +y+++
  gi|91772525|ref|YP_565217.1| 830 EKDHKKACYCFDKALQLEPDNVTALFNKGITYLQM 864
                                   56788999************************987 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.4e-06
                        TPR_11  12 eAieaYkkAlkldPdnae 29 
                                   +Aie+Y++Al+l+Pd++ 
  gi|91772525|ref|YP_565217.1| 904 DAIECYNEALRLKPDDVK 921
                                   7**************986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.2e-07    0.0002       9      74 ..     822     880 ..     819     882 .. 0.90
   2 !   10.5   0.0   0.00062      0.58      52      75 ..     893     916 ..     885     918 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-07
                        TPR_12   9 laavl.rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   l+ +  r  +++ +A+ +++kal++      pd+   +t+l+n g++y++++ y  Ale +++ l+i
  gi|91772525|ref|YP_565217.1| 822 LGIAAgRDEKDHKKACYCFDKALQLE-----PDN---VTALFNKGITYLQMKMYPLALECFNRLLNI 880
                                   6666656799****************.....*98...9*************************9987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00062
                        TPR_12  52 grlyralgryeeAlelleealaia 75 
                                   g+++r+l++ ++A+e ++eal+++
  gi|91772525|ref|YP_565217.1| 893 GDCLRMLDNRADAIECYNEALRLK 916
                                   778888888888888888888875 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    0.0025       2.3       4      34 .]     819     850 ..     819     850 .. 0.86
   2 !    8.3   0.0     0.003       2.9       2      30 ..     852     880 ..     851     880 .. 0.92
   3 !   11.5   0.0    0.0003      0.28       8      34 .]     893     919 ..     892     919 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0025
                                   HHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   4 yynlgsiy.lklgdyeeAkeyyekaleldpdn 34 
                                   +++lg +  ++ +d+++A  ++ kal+l+pdn
  gi|91772525|ref|YP_565217.1| 819 WVKLGIAAgRDEKDHKKACYCFDKALQLEPDN 850
                                   667775566899******************97 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.003
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                    a++n+g +yl+++ y  A e++++ l +
  gi|91772525|ref|YP_565217.1| 852 TALFNKGITYLQMKMYPLALECFNRLLNI 880
                                   589*********************99865 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0003
                                   HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   8 gsiylklgdyeeAkeyyekaleldpdn 34 
                                   g++++ l +   A+e+y++al+l+pd+
  gi|91772525|ref|YP_565217.1| 893 GDCLRMLDNRADAIECYNEALRLKPDD 919
                                   666677889999*************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 !   27.9   0.0   2.1e-09     2e-06       3     149 ..      53     197 ..      51     226 .. 0.76
   2 ?   -3.1   0.0       7.2   6.8e+03      54      90 ..     393     429 ..     383     450 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.1e-09
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                   el+ +Q++a++++l      + k++++   T +GK+l+++  i + l   ++  +l + p ++l++  le f+kf ++   
  gi|91772525|ref|YP_565217.1|  53 ELYTHQADAVKEVL------DGKNIVLSTSTASGKSLCYMLPIFETLMDDPNATALYISPLNALVNDQLESFEKFRDSMGL 127
                                   67899999999998......6789***************87777777778999*************************999 PP

                                   ...GEEE...ESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T..T CS
                        ResIII  84 e..igkk...vsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk..s 149
                                   +  i+k+   +  ++k  ++ +  n +il+t+ ++++ +   + +++ ++  ++ ++i+ DE+H +++ +  +
  gi|91772525|ref|YP_565217.1| 128 DlnINKFigtMPPEEK--SAVKYGNPRILFTNPEMVHLSF-LQWKQQWKKFLSNLKYIVLDESHTYSGVTgiN 197
                                   9885555332333333..3589******************.444455555556666********998863332 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                                   ..-EEEEESSHHHHHHHHHHGGGGTGG....GEEEES CS
                        ResIII  54 eekflflvprkslleqtleefkkflseaykeigkkvs 90 
                                   e+ +++++++++l +  +++  +f+ ++ +++  +vs
  gi|91772525|ref|YP_565217.1| 393 ESIVVLVADSNALDQYYMRNPGEFFVKECERAVINVS 429
                                   4578899999999887777766666665555444444 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.3   1.2e+03      36      60 ..     638     663 ..     636     675 .. 0.81
   2 !   17.0   0.0   5.3e-06     0.005       7      56 ..     829     878 ..     824     887 .. 0.93
   3 !    7.0   0.1    0.0068       6.4      13      72 ..     869     929 ..     867     930 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                         TPR_9  36 GlllaqlGclsaAladLeayl.alap 60 
                                   Gl++++  ++++++ + e++l a+ p
  gi|91772525|ref|YP_565217.1| 638 GLVEEHDRDFNGGIHAIEHALiAMYP 663
                                   99*****************9965555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.3e-06
                         TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                    e+d+ +a  + +  l+l Pd +  ++  G+ + q+  +  Al+++++ l
  gi|91772525|ref|YP_565217.1| 829 DEKDHKKACYCFDKALQLEPDNVTALFNKGITYLQMKMYPLALECFNRLL 878
                                   689*******************************************9976 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0068
                         TPR_9  13 ralavverllll.aPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqL 72 
                                    al++ +rll +   d +  +   G +l  l++ + A+++ + +l+l pd+  + ++r  L
  gi|91772525|ref|YP_565217.1| 869 LALECFNRLLNIgYRDNAKVWKCKGDCLRMLDNRADAIECYNEALRLKPDDVKIKQARDSL 929
                                   699999999999667778889999**************************99999998766 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     2e-06    0.0018       1      32 [.     839     870 ..     839     872 .. 0.89
   2 ?    0.8   0.0      0.88   8.3e+02       9      33 ..     882     906 ..     873     907 .. 0.78
   3 ?    0.8   0.1      0.87   8.2e+02       1      14 [.     908     921 ..     908     922 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   ++ kal+l+P+n+ a++n++ ++l+ + +  A
  gi|91772525|ref|YP_565217.1| 839 CFDKALQLEPDNVTALFNKGITYLQMKMYPLA 870
                                   799********************998877666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.88
                        TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                   + +na+++  ++ +l+++ + ++A+
  gi|91772525|ref|YP_565217.1| 882 YRDNAKVWKCKGDCLRMLDNRADAI 906
                                   568************9988777766 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.87
                        TPR_17   1 lylkaleldPnnad 14 
                                   +y +al+l P++++
  gi|91772525|ref|YP_565217.1| 908 CYNEALRLKPDDVK 921
                                   8**********986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0048       4.5       4      41 ..     819     857 ..     816     860 .. 0.83
   2 !   10.9   0.1   0.00074       0.7       3      37 ..     888     922 ..     886     940 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0048
                        TPR_14   4 llalaeal.lalGdpdeAiallrralalaPddaeawlll 41 
                                   + +l+ a  +   d+++A  ++++al+l Pd+ +a++  
  gi|91772525|ref|YP_565217.1| 819 WVKLGIAAgRDEKDHKKACYCFDKALQLEPDNVTALFNK 857
                                   66777665467789********************99865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00074
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaea 37 
                                   ++++ ++ l+ l++ ++Ai+++++al+l Pdd  +
  gi|91772525|ref|YP_565217.1| 888 VWKCKGDCLRMLDNRADAIECYNEALRLKPDDVKI 922
                                   68888999999********************9876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.7e-06    0.0092       3      60 ..     829     887 ..     827     895 .. 0.89
   2 ?    3.5   0.1      0.11   1.1e+02      32      58 ..     893     919 ..     881     926 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.7e-06
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ar 60 
                                   +e+d+  A   + +alq +p+n  a+ +  + +l+++ +  A ++ ++l++    d a 
  gi|91772525|ref|YP_565217.1| 829 DEKDHKKACYCFDKALQLEPDNVTALFNKGITYLQMKMYPLALECFNRLLNIGYRDnAK 887
                                   68999999999**************************************9977766555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                        TPR_19  32 AeallalgqldeAealLdalpeedpdd 58 
                                    ++l  l + ++A+++ +++++ +pdd
  gi|91772525|ref|YP_565217.1| 893 GDCLRMLDNRADAIECYNEALRLKPDD 919
                                   688889999999999999999999995 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.23   2.2e+02       5      32 ..     821     849 ..     819     850 .. 0.86
   2 !    9.4   0.0    0.0019       1.8       2      28 ..     853     879 ..     852     884 .. 0.94
   3 ?    3.1   0.0      0.19   1.8e+02       7      29 ..     893     915 ..     892     919 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.23
                                   HHHHHHHH.HHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   5 klalsyrk.lgdtdkAlealerlikeYPd 32 
                                   kl+ +  +  +d+ kA+  +++ ++  Pd
  gi|91772525|ref|YP_565217.1| 821 KLGIAAGRdEKDHKKACYCFDKALQLEPD 849
                                   67777887789**************9999 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                   Al++ +  y++++ +  Ale ++rl++
  gi|91772525|ref|YP_565217.1| 853 ALFNKGITYLQMKMYPLALECFNRLLN 879
                                   9************************97 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerlike 29 
                                   + ++r+l++ ++A+e +++ ++ 
  gi|91772525|ref|YP_565217.1| 893 GDCLRMLDNRADAIECYNEALRL 915
                                   78999999**********99876 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.053        50     142     182 ..     812     853 ..     792     856 .. 0.77
   2 !   11.8   0.0   0.00011       0.1     141     185 ..     881     925 ..     860     926 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.053
                        TPR_15 142 aeqsaafllar.aelyrqegqtdaAlrdyreAlalapdssel 182
                                    ++sa  ++ + +++ r+e ++++A  ++ +Al+l+pd+ ++
  gi|91772525|ref|YP_565217.1| 812 GSGSAGEWVKLgIAAGRDEKDHKKACYCFDKALQLEPDNVTA 853
                                   45667777654267789999******************9765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                        TPR_15 141 aaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraa 185
                                    ++++a ++   +   r  ++ ++A+++y eAl+l+pd+ ++++a
  gi|91772525|ref|YP_565217.1| 881 GYRDNAKVWKCKGDCLRMLDNRADAIECYNEALRLKPDDVKIKQA 925
                                   588999**********************************99985 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.9   3.6e+03      10      31 ..     793     815 ..     791     851 .. 0.74
   2 ?    5.0   0.0      0.04        38      20      60 ..     840     877 ..     828     881 .. 0.88
   3 !   14.6   0.0   4.2e-05      0.04       2      67 ..     856     919 ..     855     920 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.9
                        TPR_16  10 agd.yddAaaaleaalkrdpssP 31 
                                   agd +++A++++++ lk+++s +
  gi|91772525|ref|YP_565217.1| 793 AGDsPAEALNRAKRKLKKQGSGS 815
                                   67778999999999999998664 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.04
                        TPR_16  20 leaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                   ++ al +    Pd++ Al+++g  +l+ + +++A++ ++++
  gi|91772525|ref|YP_565217.1| 840 FDKALQLE---PDNVTALFNKGITYLQMKMYPLALECFNRL 877
                                   78899999...***************999999999877776 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 4.2e-05
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   +++  +l+ + y+ A++ ++++l  ++   d+a  +  +gd++  + + a+A++ y++alr  pd+
  gi|91772525|ref|YP_565217.1| 856 NKGITYLQMKMYPLALECFNRLLNIGY--RDNAKVWKCKGDCLRMLDNRADAIECYNEALRLKPDD 919
                                   6788999*******************9..55*********************************97 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 ?   13.0   1.5   9.7e-05     0.091       2      81 ..     830     911 ..     829     912 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-05
                                   TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SH.HHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.kl.nskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                    +++k+A  +++++l+ e+++  +++ ++ ++++++ y  A+e ++++ ++ +  + +++ +++ cl  L++  +Ai ++ 
  gi|91772525|ref|YP_565217.1| 830 EKDHKKACYCFDKALQLEPDNVTALFNKGITYLQMKMYPLALECFNRLlNIgYRDNAKVWKCKGDCLRMLDNRADAIECYN 910
                                   679*********************************************866145666***************999999876 PP

                                   S CS
                        ANAPC3  81 k 81 
                                   +
  gi|91772525|ref|YP_565217.1| 911 E 911
                                   5 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       8.1   7.7e+03       4      14 ..     197     207 ..     196     207 .. 0.89
   2 ?   -2.6   0.0       8.3   7.8e+03      14      31 ..     832     849 ..     828     850 .. 0.78
   3 ?    3.5   0.0     0.095        90       1      30 [.     853     882 ..     853     886 .. 0.88
   4 ?    6.6   0.0    0.0094       8.8      12      34 ..     899     919 ..     893     921 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.1
                         TPR_7   4 nLarlysrlGd 14 
                                   n+a+l +rl++
  gi|91772525|ref|YP_565217.1| 197 NMANLLRRLNR 207
                                   9*******985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.3
                         TPR_7  14 dyeeAielyeqsLaltkd 31 
                                   d+++A  ++ ++L+l+ d
  gi|91772525|ref|YP_565217.1| 832 DHKKACYCFDKALQLEPD 849
                                   889999999998888765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.095
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                   aL+n + +y ++  y  A+e++ ++L + +
  gi|91772525|ref|YP_565217.1| 853 ALFNKGITYLQMKMYPLALECFNRLLNIGY 882
                                   799*******************99887655 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0094
                         TPR_7  12 lGdyeeAielyeqsLaltkdped 34 
                                   l ++++Aie+y +  al+  p+d
  gi|91772525|ref|YP_565217.1| 899 LDNRADAIECYNE--ALRLKPDD 919
                                   6799*********..66666655 PP

>> RelB_N  RelB Antitoxin alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.011        10       8      23 ..     457     472 ..     456     473 .. 0.93
   2 ?    1.9   0.0      0.21     2e+02      10      18 ..     707     715 ..     705     716 .. 0.92
   3 ?   -1.8   0.0         3   2.9e+03      31      45 ..     742     756 ..     741     757 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                                   HHHHHHHHHH.HHHHH CS
                        RelB_N   8 eeyekIeEiLEDyGLa 23 
                                   ee+++I  +LE +GL+
  gi|91772525|ref|YP_565217.1| 457 EEFKRIVAALEEEGLL 472
                                   79*************6 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                                   HHHHHHHH. CS
                        RelB_N  10 yekIeEiLE 18 
                                   y kIeE+LE
  gi|91772525|ref|YP_565217.1| 707 YAKIEEMLE 715
                                   99******9 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3
                                   T--EEECCCHH-XXX CS
                        RelB_N  31 deepLsieeAleyye 45 
                                   ++epL+++ A   ++
  gi|91772525|ref|YP_565217.1| 742 NNEPLDKDAAIMILR 756
                                   89******9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 5750.55
//
Query:       gi|91772526|ref|YP_565218.1|  [L=255]
Description: hypothetical protein Mbur_0485 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1556.57
//
Query:       gi|91772527|ref|YP_565219.1|  [L=203]
Description: ABC proline/glycine betaine transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for 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  14.4      1e-20   74.2  14.4    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2  14.4   5.8e-25     1e-20       6     184 ..      30     198 ..      25     203 .] 0.88

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 5.8e-25
                  BPD_transp_1   6 ilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlv 84 
                                   + +a    +nk++ +++  + ++ +++Psf+++ ++v         g ++ p+++++ll a+ +++ +++ +l++++ +  
  gi|91772527|ref|YP_565219.1|  30 MPLAfgSLYNKRFGYVVIKFANLAQAVPSFAVVAIVV------PLMGIGFYPAVVAILLRALLPIIKNTYIGLSTVDPSML 104
                                   555555789999999999*******************......899999******************************** PP

                  BPD_transp_1  85 eaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviav 165
                                    +a   G+++wqi+r+v+lPna p i++g+ +af+++   a+l+ ++gs+ Glg l+++ + +++   i+     a++i  
  gi|91772527|ref|YP_565219.1| 105 DYADGIGLNEWQILRYVRLPNAYPAIFAGIKFAFILINSIAILTAYIGSG-GLGELIFQGLVAFNNEKIL-----AGAIPA 179
                                   ************************************************55.7***************555.....666666 PP

                  BPD_transp_1 166 lllnlvadilqrlldprvr 184
                                   +l+ +++di+ + ++++++
  gi|91772527|ref|YP_565219.1| 180 ILIAIAFDIIFTRIEKKLT 198
                                   6666666666666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1327.68
//
Query:       gi|91772528|ref|YP_565220.1|  [L=198]
Description: ABC proline/glycine betaine transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for 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-24   84.1  12.5    1.3e-23   83.7  12.5    1.1  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.69    9.8  10.7       0.35   10.8   3.6    2.6  2  DUF4321       Domain of unknown function (DUF4321)
        8.7    5.7  11.4       0.58    9.5   6.0    1.7  2  DUF92         Integral membrane protein DUF92


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 !   83.7  12.5   2.1e-27   1.3e-23       3     184 ..      21     192 ..      19     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 2.1e-27
                  BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpk 81 
                                   ++G++++  l+++ k+ + +++l +++ ++P + l++ll+       i+g +  p i++++l+++ +++++++ +l++++ 
  gi|91772528|ref|YP_565220.1|  21 IIGVFLGlfLYSRPKIAHPMLNLLNLVETIPDIPLLVLLL------PIFGLGSGPTIVASVLYSLLPITRNTYTGLKEVDL 95 
                                   68899999888*****************************......9********************************** PP

                  BPD_transp_1  82 dlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalv 162
                                    +v  ara+G+s++ i++kv++P++lp+i+ gl++a+++ +g  +l  +++++ Glg  l+  i+ y ++     ++l+++
  gi|91772528|ref|YP_565220.1|  96 KYVDIARAMGLSERDILFKVRIPLSLPMIVGGLRIALVFTMGVVTLGGLIAAG-GLGAALIAGIQLYKIN-----TILVAG 170
                                   ***************************************************66.7***************.....778*** PP

                  BPD_transp_1 163 iavlllnlvadilqrlldprvr 184
                                   + + ll +++d l+ ++++r+ 
  gi|91772528|ref|YP_565220.1| 171 LWTGLLAVIFDGLAGIVEKRLQ 192
                                   ********************86 PP

>> DUF4321  Domain of unknown function (DUF4321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.6   5.8e-05      0.35      29      48 .]      12      31 ..       8      31 .. 0.93
   2 ?    2.7   0.7     0.019   1.1e+02      15      44 ..     118     147 ..     104     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.8e-05
                       DUF4321 29 lsfkinlasiiGiilAiliY 48
                                  + + i lasiiG++l++++Y
  gi|91772528|ref|YP_565220.1| 12 FGIAIVLASIIGVFLGLFLY 31
                                  789999*************9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.019
                       DUF4321  15 PltlDLgvlkltFglsfkinlasiiGiilA 44 
                                   Pl+l + v  l ++l f   + ++ G+i+A
  gi|91772528|ref|YP_565220.1| 118 PLSLPMIVGGLRIALVFTMGVVTLGGLIAA 147
                                   888888899999****************98 PP

>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.25   1.5e+03     157     172 ..      20      56 ..       9      85 .. 0.45
   2 ?    9.5   6.0   9.8e-05      0.58     140     193 ..     135     187 ..     122     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.25
                         DUF92 157 lliallavlllllel.......................l 172
                                    +i++++ l+l+  +                       l
  gi|91772528|ref|YP_565220.1|  20 SIIGVFLGLFLY--SrpkiahpmlnllnlvetipdiplL 56 
                                   223322222221..0223344444444444445554442 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.8e-05
                         DUF92 140 tnGgVsllGll.asllGalliallavlllllellillltlaGllGsllDSlLGat 193
                                   t G V+l Gl+ a+ lGa+lia + +    ++++++++++ Gll+ ++D l G +
  gi|91772528|ref|YP_565220.1| 135 TMGVVTLGGLIaAGGLGAALIAGIQLYK--INTILVAGLWTGLLAVIFDGLAGIV 187
                                   6699*****9725789******886444..45577778888********998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1260.54
//
Query:       gi|91772529|ref|YP_565221.1|  [L=376]
Description: glycine betaine/L-proline ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  117.3   0.0    1.4e-33  116.4   0.0    1.5  1  ABC_tran      ABC transporter
    9.6e-09   35.5   0.3    0.00038   20.4   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.2e-05   24.8   0.2     0.0039   17.6   0.1    2.9  2  CBS           CBS domain
    0.00022   21.7   0.0    0.00034   21.0   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00039   20.2   0.2    0.00085   19.1   0.1    1.8  1  AAA_15        AAA ATPase domain
     0.0013   19.0   0.0     0.0033   17.7   0.0    1.9  1  AAA_22        AAA domain
     0.0019   18.0   0.0     0.0036   17.1   0.0    1.4  1  AAA_30        AAA domain
     0.0026   17.5   0.0     0.0052   16.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0042   17.3   0.0     0.0072   16.5   0.0    1.6  1  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.038   13.6   0.0    1.9  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.011   16.3   0.8      0.015   15.8   0.1    1.6  1  AAA_23        AAA domain
      0.018   14.8   0.0       0.66    9.7   0.0    2.2  2  AAA_24        AAA domain
       0.02   14.0   0.0      0.037   13.1   0.0    1.4  1  T2SSE         Type II/IV secretion system protein
      0.029   13.8   0.0      0.054   12.9   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.036   14.0   0.0      0.068   13.1   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.049   12.8   0.0       0.06   12.5   0.0    1.3  1  G-alpha       G-protein alpha subunit
      0.068   13.2   0.0       0.11   12.5   0.0    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
      0.082   12.7   0.0       0.36   10.6   0.0    1.9  1  DEAD          DEAD/DEAH box helicase
      0.093   12.5   0.0       0.16   11.7   0.0    1.3  1  malic         Malic enzyme, N-terminal domain
      0.094   13.1   0.0       0.33   11.4   0.0    2.1  1  AAA           ATPase family associated with various cellular 
       0.17   11.2   0.0       0.31   10.3   0.0    1.3  1  Zeta_toxin    Zeta toxin
       0.18   12.2   0.1       0.38   11.1   0.1    1.5  1  AAA_19        AAA domain
       0.18   12.0   0.0       0.39   11.0   0.0    1.5  1  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   1.7e-36   1.4e-33       2     136 ..      29     174 ..      28     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 1.7e-36
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   ++vs++++ ge+v ++G++G+GK+t l+++ +l +p++G+il++++++ e e   lr++ig++ q   lfp++t++en   
  gi|91772529|ref|YP_565221.1|  29 NDVSIDIEGGELVIFIGPSGSGKTTTLRMINRLIEPDSGTILINDQNVMELEPVALRRNIGYVIQSIGLFPHMTIAENigl 109
                                   89******************************************************************************* PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             + ++++e +l+ ++l+   +  +++ p++LSgGq+qrv larall +p+lll+DEp+
  gi|91772529|ref|YP_565221.1| 110 vaklegwnekKIKDRVEYLLDFVSLPS--EMFMDRYPHQLSGGQQQRVGLARALLMDPPLLLMDEPF 174
                                   ******998888888999999999999..88999999*****************************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 !   12.7   0.1    0.0001     0.081       2      23 ..      41      62 ..      40      82 .. 0.81
   2 !   20.4   0.0   4.9e-07   0.00038     227     298 ..     137     206 ..     112     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                        AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                   ++iGp gsGK++ L+ +  l 
  gi|91772529|ref|YP_565221.1| 41 VIFIGPSGSGKTTTLRMINRLI 62
                                  689**************98873 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4.9e-07
                        AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                   +   ++ +++lS G+++  +l+ all ++   +lll DEp   L+P l + l e + + ++  g  +i++TH+
  gi|91772529|ref|YP_565221.1| 137 EMFMDRYPHQLSGGQQQRVGLARALLMDP---PLLLMDEPFGALDPILRKQLQEEFYQIREkLGKTIIFVTHD 206
                                   555567899*********9********99...**************555555555544434356799*****8 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1     5e-06    0.0039      16      53 ..     278     314 ..     261     318 .. 0.85
   2 ?    4.0   0.0     0.088        69       8      45 ..     328     364 ..     322     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5e-06
                                   SBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHH CS
                           CBS  16 ttleealelmrekgvsrlPVV.dedgklvGivtlrDllr 53 
                                    ++e a+  m+ek++  + VV +++g ++Giv l Dllr
  gi|91772529|ref|YP_565221.1| 278 LDIESAISSMIEKNI-EIAVVsNGSG-PLGIVKLIDLLR 314
                                   4599***********.9999978788.***********8 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.088
                                   SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEE CS
                           CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGi 45 
                                   ++++++ ++ l+  l++m ++g+s  +V+  d++l G 
  gi|91772529|ref|YP_565221.1| 328 EIPSFSRNELLSSSLKIMQKNGHSMAFVMT-DEELSGF 364
                                   45788899999999****777776447984.4447765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.4e-07   0.00034      23      58 ..      37      73 ..      26     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.4e-07
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekd.ggiflrg 58
                                  ++elv+++G+sG+GK++ +r++ r +e d g i+++ 
  gi|91772529|ref|YP_565221.1| 37 GGELVIFIGPSGSGKTTTLRMINRLIEPDsGTILIND 73
                                  3499*******************99999942333333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.1e-06   0.00085      14      50 ..      28      65 ..      27     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                  + dv+id++   l ++iG+ +sGK++ l++++ +++ +
  gi|91772529|ref|YP_565221.1| 28 INDVSIDIEGGeLVIFIGPSGSGKTTTLRMINRLIEPD 65
                                  678899998777*********************99977 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.2e-06    0.0033       5      51 ..      38      77 ..      34     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-06
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51
                                    +++ +G+sG+GKTt+lr++ +  +       +++++++++ ++ +
  gi|91772529|ref|YP_565221.1| 38 GELVIFIGPSGSGKTTTLRMINRLIE-------PDSGTILINDQNVM 77
                                  567899**************999875.......46677766666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.6e-06    0.0036      18      49 ..      38      69 ..      32     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrv 49
                                    +++  Gp G+GKtt+l+ +++++e + g++
  gi|91772529|ref|YP_565221.1| 38 GELVIFIGPSGSGKTTTLRMINRLIEPDSGTI 69
                                  46999*******************99884443 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 !   16.5   0.0   6.6e-06    0.0052      15      50 ..      31      66 ..      25      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-06
                        AAA_29 15 htieidlkg..atlltGpsGsGKSTllDAiqalLvpak 50
                                   +i+i+  g   ++++GpsGsGK+T l  i+ l+ p++
  gi|91772529|ref|YP_565221.1| 31 VSIDIE--GgeLVIFIGPSGSGKTTTLRMINRLIEPDS 66
                                  445555..446999***********9977777777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.3e-06    0.0072       1      19 [.      40      58 ..      40     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.3e-06
                        AAA_33  1 lvllvGlpGsGKstlaerl 19
                                  lv+++G++GsGK+t ++ +
  gi|91772529|ref|YP_565221.1| 40 LVIFIGPSGSGKTTTLRMI 58
                                  89************98743 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.9e-05     0.038       3      49 ..      41      87 ..      39     128 .. 0.81
   2 ?   -1.9   0.0       2.7   2.1e+03     100     130 ..     201     231 ..     197     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                                  EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret 49
                                  +++ G+ GsGKTt l+ + +  +  +  +++N++  ++++   lr++
  gi|91772529|ref|YP_565221.1| 41 VIFIGPSGSGKTTTLRMINRLIEPDSGTILINDQNVMELEPVALRRN 87
                                  6788***************99999**********9888887777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                                   HTTSHHHHHCCCECEEEEEEETTTH.CCHCC CS
                          cobW 100 afteeelksdltldavvavvDaknleaeeek 130
                                   +f +++++++++l   +a++D ++l + ++ 
  gi|91772529|ref|YP_565221.1| 201 IFVTHDIEEAFKLGDRIAIMDNAKLVQIGTA 231
                                   5678889999999999999998887433333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   1.9e-05     0.015      11      39 ..      29      58 ..      12      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                        AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAi 39
                                  +d++id  +  l++++Gp G+GKTT l+ i
  gi|91772529|ref|YP_565221.1| 29 NDVSIDIeGGELVIFIGPSGSGKTTTLRMI 58
                                  67889996668***************9987 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   0.00085      0.66       6      25 ..      42      60 ..      39      85 .. 0.82
   2 ?    2.7   0.0      0.11        87     115     142 ..     190     217 ..     181     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00085
                        AAA_24  6 liyGpsgiGKTtlakelgpk 25
                                  + +Gpsg+GKTt+++++ ++
  gi|91772529|ref|YP_565221.1| 42 IFIGPSGSGKTTTLRMI-NR 60
                                  568***********999.54 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                        AAA_24 115 lkklqelrknvifiahektrkdedpege 142
                                   ++  ++l+k++if+ h  ++ ++ +++ 
  gi|91772529|ref|YP_565221.1| 190 YQIREKLGKTIIFVTHDIEEAFKLGDRI 217
                                   444578999***********99998655 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 ?   13.1   0.0   4.8e-05     0.037     130     166 ..      39      74 ..      18      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                         T2SSE 130 glilvsGgTgsGKttllyallkeinksderivtvEDp 166
                                    l+++ G+ gsGKtt+l ++   i+ +    +++ D 
  gi|91772529|ref|YP_565221.1|  39 ELVIFIGPSGSGKTTTLRMINRLIEPD-SGTILINDQ 74 
                                   578999************999999988.555566665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     7e-05     0.054      13      52 ..      29      68 ..      18     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
                  Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                  + + i + Gg  ++++Gp+GsGKt   + ++ l+ p s +
  gi|91772529|ref|YP_565221.1| 29 NDVSIDIEGGELVIFIGPSGSGKTTTLRMINRLIEPDSGT 68
                                  556788999*****************99999998776655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.8e-05     0.068      81     120 ..      19      59 ..       3      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.8e-05
                                   E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                   + + +++ ++++++  +++ ++++++G+SG GK+t + +++
  gi|91772529|ref|YP_565221.1|  19 TKKYDDRFAINDVSIDIEGgELVIFIGPSGSGKTTTLRMIN 59 
                                   555566667888888888889*************9665554 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.7e-05      0.06      26      62 ..      41      82 ..      27     261 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.7e-05
                                  EEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHH CS
                       G-alpha 26 llllGqseSGKsTilkqlkllykkg.....fseeelatwrav 62
                                  ++++G s+SGK+T+l+ + +l ++      ++++++ ++ +v
  gi|91772529|ref|YP_565221.1| 41 VIFIGPSGSGKTTTLRMINRLIEPDsgtilINDQNVMELEPV 82
                                  6899***************98877767776555555554443 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.11       2      32 ..      41      72 ..      40     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                  EEEE--SSSSHHHHHHHGGGGB.S--EEEEE- CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvql 32
                                  v+ +Gp+G+gK++  + + +++  ++ ++  +
  gi|91772529|ref|YP_565221.1| 41 VIFIGPSGSGKTTTLRMINRLIePDSGTILIN 72
                                  799******************95444444333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047      0.36      11      78 ..      35     261 ..      27     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                                   HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS............................................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                          DEAD  11 ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktg............................................ 47 
                                   i gg+ v+  ++ GsGKT+   + ++++++e  ++ +                                            
  gi|91772529|ref|YP_565221.1|  35 IEGGELVIFIGPSGSGKTTT--LRMINRLIE-PDSGTilindqnvmelepvalrrnigyviqsiglfphmtiaeniglvak 112
                                   55788999**********98..889999988.3333377778888999999999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          DEAD  48 ................................................................................. 47 
                                                                                                                    
  gi|91772529|ref|YP_565221.1| 113 legwnekkikdrveylldfvslpsemfmdryphqlsggqqqrvglarallmdpplllmdepfgaldpilrkqlqeefyqir 193
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   .....................................-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                   .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  48 .....................................pkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                                                           li  P  e++  +++  kkfk+  +l++
  gi|91772529|ref|YP_565221.1| 194 eklgktiifvthdieeafklgdriaimdnaklvqigtAEELIFHPANEMVASIVDSGKKFKHLDTLKI 261
                                   99999999999999999999999999999999999999999999999999999999999998422333 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.16      37      81 ..     263     306 ..     258     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                   HHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTTT CS
                         malic  37 eeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLGl 81 
                                   + ++  + +y++ +   +i+++++++ e++++++vv++g++ LG+
  gi|91772529|ref|YP_565221.1| 263 DLISPLECMYVHNGSL-DIESAISSMIEKNIEIAVVSNGSGPLGI 306
                                   5556667789998888.9*************************98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00043      0.33       1      22 [.      41      62 ..      41     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                                  EEEESSTTSSHHHHHHHHHHHH CS
                           AAA  1 vllyGppGtGKTllakavakel 22
                                  v+++Gp G GKT++ + + + +
  gi|91772529|ref|YP_565221.1| 41 VIFIGPSGSGKTTTLRMINRLI 62
                                  689************9997665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0004      0.31      18      59 ..      40      81 ..      32      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0004
                    Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhP 59
                                  l++  G +G+GK+++++++++ +e++++ + ++  ++ el P
  gi|91772529|ref|YP_565221.1| 40 LVIFIGPSGSGKTTTLRMINRLIEPDSGTILINDQNVMELEP 81
                                  56777899****************999999999877766655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00049      0.38      11      34 ..      39      62 ..      31      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                        AAA_19 11 kvllvtaGpGtGKTrvlkhivall 34
                                  ++++ +++ G+GKT++l++i +l+
  gi|91772529|ref|YP_565221.1| 39 ELVIFIGPSGSGKTTTLRMINRLI 62
                                  5788899**********9987765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0005      0.39       2      20 ..      41      59 ..      40      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  ++++G++++GKTt+l+ ++
  gi|91772529|ref|YP_565221.1| 41 VIFIGPSGSGKTTTLRMIN 59
                                  89*************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2313.45
//
Query:       gi|91772530|ref|YP_565222.1|  [L=308]
Description: ABC glycine betaine transporter, substrate-binding subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-59  200.5   0.8    4.2e-59  200.2   0.8    1.0  1  OpuAC     Substrate binding domain of ABC-type glycine betain


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   0.8   2.3e-63   4.2e-59       2     256 ..      34     296 ..      33     297 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 2.3e-63
                                   EEEEEEESSHHHHHHHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH..................H CS
                         OpuAC   2 tivigsknwteqevlaeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta..................y 63 
                                   ++vigsk ++e+++la++++ +le++Gy +  + +lg+t v +++l++G+iDvy+ e+tgta                  y
  gi|91772530|ref|YP_565222.1|  34 EVVIGSKLFQESYILAHMAGIMLEEAGYeVDVKEGLGGTFVNYEGLKQGSIDVYV-EYTGTAysqileepalevwdpevvY 113
                                   79**************************88888899999****************.***********************99 PP

                                   HHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT CS
                         OpuAC  64 eaykkaveekkglevlgplgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYg 144
                                   ++ +++++e+ +l+v + lg++++++lav+k  ae++++  isDL ++a+dl  g + ef  r+dg++           Yg
  gi|91772530|ref|YP_565222.1| 114 QKAEEGLKEDGVLVV-SNLGFEDAYALAVKKQWAEENNVVAISDLENHASDLIIGTDPEFALREDGLP------RISSLYG 187
                                   999999997777776.99**************************************************......******* PP

                                   -TTCEEEGSCEEEEHHHHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHHHHSCTHHHHHHH CS
                         OpuAC 145 ldkvelvegseaamdaelyaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefaekaPevaafLek 225
                                   +    +++   +++ +++y+a+k +e++v+ a+t+d ++  +dl+ Led+ +++pp y++ +v+++efae++P++ ++Lek
  gi|91772530|ref|YP_565222.1| 188 F----EFKEVKPTVATLMYEAIKLDEVDVISAYTTDTRNELFDLTILEDDMNALPP-YDAIVVMSAEFAEANPDAVTALEK 263
                                   *....55444666667****************************************.************************ PP

                                   HC..--HHHHHHHHHHHHTTTT-HHHHHHHHHH CS
                         OpuAC 226 ls..ldtetlnelnaqvdvegkdpeevAkawla 256
                                   l+  +dtet++ ln+q dv+++++e++A+++l 
  gi|91772530|ref|YP_565222.1| 264 LNgqIDTETMRGLNYQFDVDKREAEDIARDFLI 296
                                   *******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1862.80
//
Query:       gi|91772531|ref|YP_565223.1|  [L=407]
Description: SufBD [Methanococcoides burtonii DSM 6242]
Scores for 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-52  176.5   0.0    7.7e-52  176.1   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 !  176.1   0.0   4.3e-56   7.7e-52       2     218 .]     156     379 ..     155     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 176.1 bits;  conditional E-value: 4.3e-56
                       UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakleltt 70 
                                   q+++++i+vee+a++ +i   +gc            g++ei+v+++  l++++++nw++d+ + +++ +++++ a++  ++
  gi|91772531|ref|YP_565223.1| 156 QTVHNIIIVEEDAKLDVI---TGCttkkgveraihlGISEIYVKKGGILNFTMIHNWAGDVGVRPRTVIHLEEGASFVNNY 233
                                   889***************...899999999999999*********************************999999999999 PP

                       UPF0051  71 vslggk.ltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqk 150
                                   + l+    + ++p++ l+gega a+++++++a+ +++ld++++v  n+pnt+++++s+++ + +++++ rg++   ++  +
  gi|91772531|ref|YP_565223.1| 234 ILLKPVrSIQSYPTAILDGEGAFARFHTIAVAHPGSELDLGSRVLFNAPNTKAELISRTITT-GGKVIARGEM--VANKPH 311
                                   999988355669**************************************************.599*******..4448** PP

                       UPF0051 151 tdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                   +++h e++ L+l+d+++  +iP le+   dv+++H+A+vG+i+ eq+ YLm+RGlsee+A  +ivrgf
  gi|91772531|ref|YP_565223.1| 312 CKGHLECHGLVLKDGGTQLAIPALEASVADVELTHEAAVGRIAREQVEYLMARGLSEEDAVGMIVRGF 379
                                   *******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2454.05
//
Query:       gi|91772532|ref|YP_565224.1|  [L=249]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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   74.5   0.0    1.6e-20   74.0   0.0    1.3  1  ABC_tran     ABC transporter
    2.1e-06   27.8   0.1    0.00096   19.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00043   19.8   0.4       0.11   11.9   0.1    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0022   17.7   0.1     0.0046   16.7   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0072   16.8   0.1      0.012   16.1   0.1    1.4  1  AAA_23       AAA domain
     0.0078   16.1   0.1      0.013   15.5   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.043   13.5   0.0      0.087   12.5   0.0    1.4  1  AAA_15       AAA ATPase domain
      0.058   13.0   0.1      0.087   12.4   0.1    1.2  1  AAA_27       AAA domain
      0.097   12.2   0.1       0.16   11.5   0.1    1.3  1  AAA_25       AAA domain
       0.19   12.1   0.1       0.32   11.4   0.1    1.3  1  AAA_16       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   9.2e-24   1.6e-20       1     136 [.      17     158 ..      17     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 9.2e-24
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                   l++v+lk+++g++++++G+nGaGKS Ll++l+g +      G+il++g+d+++    e++++ +g+++q p    ++++++
  gi|91772532|ref|YP_565224.1|  17 LNKVNLKVEQGSTTVLFGPNGAGKSALLMTLMGFSGYdiVGGQILFKGEDITHlSVNERAERGLGIMTQRPPNLTGVKLKD 97 
                                   789******************************8765449*************99999************55555555555 PP

                                   H......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                          + + + e+a +kl+++ + d+ v      +SgG+ +r +l ++ +++p l+llDEp 
  gi|91772532|ref|YP_565224.1|  98 LvkvisnDHNFDTETASKKLDMDRFMDRDV---NVGFSGGEIKRSELLQLSAQNPCLYLLDEPE 158
                                   566654477777*************99999...679**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.4e-07   0.00096       2      24 ..      30      52 ..      29      88 .. 0.78
   2 !    6.9   0.0    0.0027       4.8     259     283 ..     150     176 ..     141     200 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.4e-07
                        AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                  +vl GpNg+GKS LL +l ++++
  gi|91772532|ref|YP_565224.1| 30 TVLFGPNGAGKSALLMTLMGFSG 52
                                  8****************966654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0027
                        AAA_21 259 sllliDEpEngLHPkllrrllell..k 283
                                    l+l+DEpE+g +   ++++ + +   
  gi|91772532|ref|YP_565224.1| 150 CLYLLDEPESGVDLVSIEEIGTTIdgL 176
                                   689**********99999999777641 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 !   11.9   0.1   6.1e-05      0.11      24      44 ..      27      47 ..       8      56 .. 0.79
   2 !    6.2   0.0    0.0034       6.1     155     184 ..     145     174 ..      90     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                                  SSEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                   s t++ GpNG+GKs ll  +
  gi|91772532|ref|YP_565224.1| 27 GSTTVLFGPNGAGKSALLMTL 47
                                  3578899********998765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0034
                                   CCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 155 kvkpaplyllDeidaaLDeknvkkvaellk 184
                                   +++  +lyllDe ++  D   ++++ + ++
  gi|91772532|ref|YP_565224.1| 145 SAQNPCLYLLDEPESGVDLVSIEEIGTTID 174
                                   45678****************999998886 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.6e-06    0.0046      15      39 ..      20      44 ..      15      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                        AAA_29 15 htieidlkg.atlltGpsGsGKSTll 39
                                    +++++ g +t+l Gp+G+GKS+ll
  gi|91772532|ref|YP_565224.1| 20 VNLKVEQ-GsTTVLFGPNGAGKSALL 44
                                  5567774.459*************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   6.8e-06     0.012      20      37 ..      28      45 ..       9      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.8e-06
                        AAA_23 20 gltlItGpNGaGKTTild 37
                                    t+++GpNGaGK+++l 
  gi|91772532|ref|YP_565224.1| 28 STTVLFGPNGAGKSALLM 45
                                  479************996 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1     7e-06     0.013      90     121 ..      17      49 ..       2      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7e-06
                                   HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   l++++ ++++ +t+vl G+ G+GKS+L+ +l++
  gi|91772532|ref|YP_565224.1|  17 LNKVNLKVEQgSTTVLFGPNGAGKSALLMTLMG 49 
                                   556666666669****************99987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.9e-05     0.087      22      48 ..      23      52 ..      15     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                        AAA_15 22 see...ltvliGkNnsGKSsilealdlFln 48
                                  + e   +tvl G+N++GKS +l+ l  F  
  gi|91772532|ref|YP_565224.1| 23 KVEqgsTTVLFGPNGAGKSALLMTLMGFSG 52
                                  3333459****************9977765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.9e-05     0.087       3      46 ..       4      47 ..       2      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                        AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAi 46
                                  ++ L++e  G++  ++++++ e+ + ++++GpN AGKs++l  +
  gi|91772532|ref|YP_565224.1|  4 IKDLTVEIGGRMILNKVNLKVEQGSTTVLFGPNGAGKSALLMTL 47
                                  667777777888888999999999**************998765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     9e-05      0.16      31      54 ..      25      48 ..      20      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9e-05
                        AAA_25 31 pagelallaGapgtGKttlaldla 54
                                    g++++l+G+ g+GK++l++ l+
  gi|91772532|ref|YP_565224.1| 25 EQGSTTVLFGPNGAGKSALLMTLM 48
                                  5799****************9886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00018      0.32      19      45 ..      24      48 ..      14      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                        AAA_16 19 vrsgrpelvllsGesGvGKsslvrell 45
                                  v +g  + ++l G+ G GKs+l+ +l+
  gi|91772532|ref|YP_565224.1| 24 VEQG--STTVLFGPNGAGKSALLMTLM 48
                                  5555..6799*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1451.54
//
Query:       gi|91772533|ref|YP_565225.1|  [L=183]
Description: hypothetical protein Mbur_0492 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1119.58
//
Query:       gi|91772534|ref|YP_565226.1|  [L=111]
Description: hypothetical protein Mbur_0493 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-24   86.1   0.1    1.1e-24   86.1   0.1    1.4  2  DUF1622          Protein of unknown function (DUF1622)
  ------ inclusion threshold ------
      0.015   14.9   0.1      0.016   14.8   0.1    1.1  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family


Domain annotation for each model (and alignments):
>> DUF1622  Protein of unknown function (DUF1622)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.4      0.94   8.4e+03      57      60 ..      14      17 ..       5      25 .. 0.45
   2 !   86.1   0.1   1.2e-28   1.1e-24       1      77 [.      29     104 ..      29     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.94
                       DUF1622 57 igvL 60
                                  i+ L
  gi|91772534|ref|YP_565226.1| 14 IASL 17
                                  2222 PP

  == domain 2  score: 86.1 bits;  conditional E-value: 1.2e-28
                       DUF1622   1 GvlvalikflkselrkkaaeayeeiRleLgrsllLgLeflvaadIlkTvvaptledigvLaaivliRtvLsyfLekE 77 
                                   G +++++k+++ e+ kk   +y+eiR +L++ +++gLef +aadIl+Tv+apt+e+++ L+a+v iRtvL yfL kE
  gi|91772534|ref|YP_565226.1|  29 GGFISTYKLIMLEIFKK-PCEYNEIRRDLTNRIIFGLEFYIAADILETVLAPTTEELILLGAVVGIRTVLGYFLGKE 104
                                   56789999999999999.9*******************************************************998 PP

>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.8e-06     0.016      78     119 ..      21      62 ..      10      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-06
               Gpr1_Fun34_YaaH  78 gatalssYGgFwlsyaailipgfgilaaYeedeeelnnalgl 119
                                     t+l +YGgF+ +y +i+++ f+   +Y+e  ++l+n + +
  gi|91772534|ref|YP_565226.1|  21 VGTVLITYGGFISTYKLIMLEIFKKPCEYNEIRRDLTNRIIF 62 
                                   579**************************8888888887644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 714.71
//
Query:       gi|91772535|ref|YP_565227.1|  [L=89]
Description: hypothetical protein Mbur_0494 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 590.92
//
Query:       gi|91772536|ref|YP_565228.1|  [L=91]
Description: hypothetical protein Mbur_0495 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 590.86
//
Query:       gi|91772537|ref|YP_565229.1|  [L=256]
Description: ABC Fe3+-siderophore transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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    6.2e-32  111.0   0.0    1.4  1  ABC_tran      ABC transporter
    1.2e-17   64.7   4.1    1.6e-12   47.9   1.3    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.2e-09   35.9   1.8    3.4e-06   26.7   1.8    2.5  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.1e-05   25.4   4.9     0.0076   16.0   1.6    2.1  2  AAA_15        AAA ATPase domain
    9.6e-05   22.8   0.1     0.0012   19.3   0.1    2.3  1  AAA           ATPase family associated with various cellular 
    0.00013   21.9   0.1    0.00023   21.1   0.1    1.3  1  RsgA_GTPase   RsgA GTPase
    0.00014   22.4   0.5    0.00023   21.7   0.5    1.3  1  AAA_23        AAA domain
     0.0005   19.8   0.0      0.001   18.8   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0034   17.1   0.0     0.0046   16.6   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
     0.0045   17.4   0.0     0.0095   16.3   0.0    1.6  2  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
       0.01   15.6   0.1       0.17   11.6   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.011   15.6   0.2      0.061   13.2   0.1    1.9  2  NACHT         NACHT domain
      0.015   15.3   0.0      0.058   13.4   0.0    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.025   14.5   0.2       0.16   11.9   0.1    2.0  2  NTPase_1      NTPase
      0.026   14.2   0.0      0.046   13.4   0.0    1.4  1  AAA_24        AAA domain
      0.036   14.0   0.0      0.048   13.6   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
      0.043   12.5   0.2        3.6    6.1   0.1    2.0  2  AAA_13        AAA domain
      0.059   13.7   0.3       0.38   11.0   0.1    2.0  2  AAA_22        AAA domain
      0.078   13.2   0.0       0.82    9.9   0.0    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.096   12.6   0.0       0.16   11.9   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.099   13.0   0.0       0.21   12.0   0.0    1.6  1  RNA_helicase  RNA helicase
        0.1   12.0   0.0       0.16   11.3   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.0   7.7e-35   6.2e-32       2     137 .]      20     168 ..      19     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 7.7e-35
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.. RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.. 79 
                                   +n+s++lk+ge++ i+G+nG GKStL+k++a+  k ++G+il+ +k++++ +++++ ++ig++pq   ++f+ + + +   
  gi|91772537|ref|YP_565229.1|  20 ENISFSLKKGETLCILGPNGIGKSTLIKCIANVFKLKNGTILIGNKNISSMSRTEVAQRIGYVPQAdMSVFSFS-ILDFvl 99 
                                   79****************************************************************55555555.888899 PP

                                   ..............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                 e  ++   +e+a+ ++g+++l d++v    +++SgG+kq   +aral+++p++lllDEpt+
  gi|91772537|ref|YP_565229.1| 100 lgraphlpffsspsE--KDiiiAENAIINVGISHLMDRPV----TEISGGEKQLALIARALAQEPDILLLDEPTS 168
                                   9*********86431..336789*****************....*****************************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 !   18.8   0.8   1.4e-06    0.0011       3      39 ..      33      71 ..      32     102 .. 0.67
   2 !   47.9   1.3   1.9e-15   1.6e-12     125     299 ..      53     199 ..      51     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                        AAA_21  3 vliGpNgsGKSnLLdaldllarl..drdvegltdelsgg 39
                                  ++ GpNg GKS+L++++  ++ l   + ++g ++++s++
  gi|91772537|ref|YP_565229.1| 33 CILGPNGIGKSTLIKCIANVFKLknGTILIGNKNISSMS 71
                                  699**************9998876644444444444444 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 1.9e-15
                        AAA_21 125 fslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgeg 205
                                   f+lk+ ++ + n++++++ +t++  r+ +  + +      ++ + +   d++   + ++l +  ++s k++ i   ++   
  gi|91772537|ref|YP_565229.1|  53 FKLKNGTILIGNKNISSMSRTEVAQRIGYVPQAD------MSVFSFSILDFVLLGRAPHLPFFSSPSEKDIIIAENAII-- 125
                                   6666666777777777777777777777777777......666666666666666666666666666666655554442.. PP

                        AAA_21 206 eeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkels 286
                                                     +  ++  ++p++e+S G k+l al++  l++ +  ++ll+DEp ++L+   + r+l l+++ls
  gi|91772537|ref|YP_565229.1| 126 -----------------NVGISHLMDRPVTEISGGEKQL-ALIARALAQEP--DILLLDEPTSHLDFGNQVRILNLIDKLS 186
                                   .................2233444567899*********.99999999887..9*************************** PP

                        AAA_21 287 rngaQviltTHSp 299
                                   r g+ vi++TH p
  gi|91772537|ref|YP_565229.1| 187 RQGTSVIMSTHYP 199
                                   ***********87 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 !   26.7   1.8   4.2e-09   3.4e-06      18     214 ..      22     214 ..      11     220 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.2e-09
                                   EEEETTSSEE.EEEESTTSSHHHHHHHHHHHCTT.TTTTT.TCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSS CS
                                   xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  18 vilpfsksft.aivGpNGSGKsnlldAilFvLGersakkl.rseklsdlihk..skekasvkkaeveitfdnedkklkiek 94 
                                   ++  ++k+ t +i+GpNG GKs l+  i  v+  ++ + l  ++++s++      ++   v +a++++ f+ +  +++   
  gi|91772537|ref|YP_565229.1|  22 ISFSLKKGETlCILGPNGIGKSTLIKCIANVFKLKNGTILiGNKNISSMSRTevAQRIGYVPQADMSV-FSFSILDFVLLG 101
                                   55555554432799**************7777766654441233344443333223333344444444.222222222222 PP

                                   SCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  95 eevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       +    ++  e ++ i ++ + +  +s+l+ +     +++SgGek+L+ +a  +A    +   + llDe  ++LD+ n
  gi|91772537|ref|YP_565229.1| 102 RAPHLPFF-SSPSEKDIIIAENAIINVGISHLMDRPV---TEISGGEKQLALIARALA----QEPDILLLDEPTSHLDFGN 174
                                   22222222.2233346778888888888888887764...468*****9987766655....4456899************ PP

                                   HHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEEE CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 176 vkkvaellkekskn.aQfivislreemlekadklvgvtkv 214
                                     ++ +l+++ s + + +i+ ++  ++   ++k+v ++ +
  gi|91772537|ref|YP_565229.1| 175 QVRILNLIDKLSRQgTSVIMSTHYPDHAFMSQKNVAIMLE 214
                                   *********9998868899999988888888888888774 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.6   9.3e-06    0.0076      15      74 ..      20      76 ..      18      80 .. 0.80
   2 !   10.6   0.1    0.0004      0.33     321     365 ..     155     198 ..     111     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.3e-06
                        AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenises 74
                                  ++++ +l++  + ++ G+N++GKS++++ +   ++ k    + +i i +++++ +  ++  
  gi|91772537|ref|YP_565229.1| 20 ENISFSLKKGeTLCILGPNGIGKSTLIKCIANVFKLK----NGTILIGNKNISSMSRTEVA 76
                                  5555566666688**********************99....88899988888888777665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                        AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    ++++ill++EP  hL   +q  + +l+ +l++++   vi++TH 
  gi|91772537|ref|YP_565229.1| 155 AQEPDILLLDEPTSHLDFGNQVRILNLIDKLSRQGT-SVIMSTHY 198
                                   45789******************************7.*******5 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 !   19.3   0.1   1.5e-06    0.0012       2     113 ..      33     200 ..      32     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                                   EEESSTTSSHHHHHHHHHHHHTHE..........EEEEETTTCSSS................................... CS
                           AAA   2 llyGppGtGKTllakavakelgve..........fleisgsellsk................................... 37 
                                   ++ Gp G+GK++l+k +a+ ++ +          + ++s +e+ +                                    
  gi|91772537|ref|YP_565229.1|  33 CILGPNGIGKSTLIKCIANVFKLKngtilignknISSMSRTEVAQRigyvpqadmsvfsfsildfvllgraphlpffssps 113
                                   789*****************8644444554445544444444443355555555555555555555555666666666666 PP

                                   .........................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                           AAA  38 .........................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                                             ++ +ek+++ + +++ ++ +p il++DE  +                +  +l+ +
  gi|91772537|ref|YP_565229.1| 114 ekdiiiaenaiinvgishlmdrpvtEISGGEKQLALIARAL-AQ-EPDILLLDEPTSHLDFG----------NQVRILNLI 182
                                   66666666666666666666666654444555555544433.33.48999999988887766..........466788888 PP

                                   HHTTTSSSTEEEEEEESSGG CS
                           AAA  94 dgvkkkeskvivigatnrpd 113
                                   d+++++   + vi+ t++pd
  gi|91772537|ref|YP_565229.1| 183 DKLSRQ--GTSVIMSTHYPD 200
                                   888884..468888888877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.8e-07   0.00023      86     129 ..      15      59 ..       5      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-07
                                   THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                   RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                   +k+ +e+++  lk+ +t +++G+ G+GKStLi+ +++  +lk g 
  gi|91772537|ref|YP_565229.1|  15 KKNVFENISFSLKKgETLCILGPNGIGKSTLIKCIANVFKLKNGT 59 
                                   46778999999*999*******************99877777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.5   2.8e-07   0.00023      11      40 ..      20      50 ..       8      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.8e-07
                        AAA_23 11 rdqeidF..skg.ltlItGpNGaGKTTildAik 40
                                  ++  i F  +kg   +I GpNG GK+T++ +i 
  gi|91772537|ref|YP_565229.1| 20 EN--ISFslKKGeTLCILGPNGIGKSTLIKCIA 50
                                  44..555546651559***************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06     0.001      12      46 ..      19      53 ..      16      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                        AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                  f++ +++++  ++  + Gp+G GKSTl+  i+ ++
  gi|91772537|ref|YP_565229.1| 19 FENISFSLKKGETLCILGPNGIGKSTLIKCIANVF 53
                                  555566777444899*************9888876 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 !   16.6   0.0   5.6e-06    0.0046       9      49 ..      24      81 ..      20     242 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-06
                                  S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.................E CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................x RF
                   ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg.................i 49
                                  f++ +G++++i+g +g+Gk+++++ +++  + ++ +i++g                  
  gi|91772537|ref|YP_565229.1| 24 FSLKKGETLCILGPNGIGKSTLIKCIANVFKLKNGTILIGnknissmsrtevaqrigY 81
                                  7889***********************9998887666665455555555555555550 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0095      24      55 ..      29      60 ..      17     124 .. 0.79
   2 ?   -2.0   0.0       5.1   4.2e+03      72      83 ..     150     161 ..     125     194 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                        AAA_16 24 pelvllsGesGvGKsslvrellralekdggif 55
                                  +e + + G+ G+GKs+l++++++ ++ ++g  
  gi|91772537|ref|YP_565229.1| 29 GETLCILGPNGIGKSTLIKCIANVFKLKNGTI 60
                                  367889***************98777665333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.1
                        AAA_16  72 laqalareellr 83 
                                   +a+ala+e  + 
  gi|91772537|ref|YP_565229.1| 150 IARALAQEPDIL 161
                                   333333322222 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 ?   11.6   0.0   0.00021      0.17      44      68 ..      26      50 ..      11      62 .. 0.86
   2 ?    1.9   0.0       0.2   1.6e+02      98     150 ..     146     199 ..     123     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                     IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                  ++k e +++lGp G+GKs l   ++
  gi|91772537|ref|YP_565229.1| 26 LKKGETLCILGPNGIGKSTLIKCIA 50
                                  57899*************9987776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.2
                     IstB_IS21  98 klaralkrllkv.dllilDdlgllpldqaeaellfeviekryer.rsiiitsnlp 150
                                   +la ++++l++  d+l+lD+  + +ld  ++  ++++i+k   + +s+i+++  p
  gi|91772537|ref|YP_565229.1| 146 QLALIARALAQEpDILLLDEP-TSHLDFGNQVRILNLIDKLSRQgTSVIMSTHYP 199
                                   55555555554339999*996.567888889999999999876625666666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.5e-05     0.061       2      22 ..      31      51 ..      30      60 .. 0.86
   2 ?   -0.1   0.0      0.92   7.5e+02      90     128 ..     163     197 ..     130     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-05
                                  CEEEEC-TTTCHHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                  ++++ G++G+GK+tL++ +a 
  gi|91772537|ref|YP_565229.1| 31 TLCILGPNGIGKSTLIKCIAN 51
                                  89**************99986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.92
                                   STT-SS-TCH.........HHHHHCTTTTT--EEEEEEE CS
                         NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeasllltvr 128
                                   lDe  ++l++      ++ + +li k + +++s++++++
  gi|91772537|ref|YP_565229.1| 163 LDEPTSHLDF----GNQVRILNLIDKLSRQGTSVIMSTH 197
                                   5777777777....6678888999998888888888765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.2e-05     0.058       2      45 ..      32      79 ..      31      96 .. 0.73
   2 ?   -0.7   0.0       1.6   1.3e+03      63      73 ..     155     165 ..     116     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                                  EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT...--HHHHH--B CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrd...tteedlkgrr 45
                                  ++++Gp G+gKs+l++ +a ++  ++ ++  ++++   ++++++ +r+
  gi|91772537|ref|YP_565229.1| 32 LCILGPNGIGKSTLIKCIANVFkLKNGTILIGNKNissMSRTEVAQRI 79
                                  79********************74444444444441115566666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                                   --G-SEEEEES CS
                         AAA_5  63 aregeilvlDE 73 
                                   a+e++il+lDE
  gi|91772537|ref|YP_565229.1| 155 AQEPDILLLDE 165
                                   34556666665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0002      0.16       3      27 ..      33      57 ..      31      81 .. 0.83
   2 ?    0.3   0.0      0.71   5.8e+02      86     103 ..     147     165 ..     128     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                  EEE--TTSSHHHHHHHHHHHH...G CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkssg 27
                                  +i Gp G+GK+Tl+k ++++ k ++
  gi|91772537|ref|YP_565229.1| 33 CILGPNGIGKSTLIKCIANVFKLKN 57
                                  688****************998665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.71
                                   HHHHHHHH.HHH-EEEE-- CS
                      NTPase_1  86 lealrkal.seadviviDE 103
                                   l+ + +al +e+d++++DE
  gi|91772537|ref|YP_565229.1| 147 LALIARALaQEPDILLLDE 165
                                   5566666668999999999 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.7e-05     0.046       4      26 ..      31      52 ..      28      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
                        AAA_24  4 kiliyGpsgiGKTtlakelgpkp 26
                                   ++i Gp+giGK+tl+k +  ++
  gi|91772537|ref|YP_565229.1| 31 TLCILGPNGIGKSTLIKCI-ANV 52
                                  689*************998.443 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 ?   13.6   0.0   5.9e-05     0.048      21      48 ..      30      57 ..      22     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                      ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkd 48
                                  e + i Gp g+GK++L+k i++  + k+
  gi|91772537|ref|YP_565229.1| 30 ETLCILGPNGIGKSTLIKCIANVFKLKN 57
                                  567899****************997655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0044       3.6      21      59 ..      34      66 ..      27      98 .. 0.69
   2 ?    4.5   0.0     0.013        11     525     569 ..     156     197 ..     136     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0044
                        AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsieitnge 59
                                  i G NG GK+tL + ++++       k++ng+i i n++
  gi|91772537|ref|YP_565229.1| 34 ILGPNGIGKSTLIKCIANV------FKLKNGTILIGNKN 66
                                  78***************98......45677777666554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                        AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTH 569
                                   ++  i  +D P S LD + +  + +li++      +   ++ +TH
  gi|91772537|ref|YP_565229.1| 156 QEPDILLLDEPTSHLDFGNQVRILNLIDKLS---RQGTSVIMSTH 197
                                   47889************************98...78888999999 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   0.00046      0.38       7      29 ..      31      53 ..      26      82 .. 0.80
   2 ?    0.4   0.0      0.91   7.4e+02      82     127 ..     150     194 ..     130     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                        AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                   l++ G+ G+GK+tl++ +++ +
  gi|91772537|ref|YP_565229.1| 31 TLCILGPNGIGKSTLIKCIANVF 53
                                  6899*************988766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.91
                        AAA_22  82 leqalraravielliiDEaqh.lr...seealeeLrsllnlsrkgvqliL 127
                                   +++al +     +l++DE    l+   + ++l+ +    +lsr+g+++i+
  gi|91772537|ref|YP_565229.1| 150 IARALAQEP--DILLLDEPTShLDfgnQVRILNLI---DKLSRQGTSVIM 194
                                   444444444..599999977768544334444444...444567777776 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   0.0     0.001      0.82      26      89 ..     133     183 ..     126     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                       SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   ++r +++ SGGek    +lal   ++al +        +++++LDE  s lD  ++ ++l+l++
  gi|91772537|ref|YP_565229.1| 133 MDRPVTEISGGEK----QLALI--ARALAQ-------EPDILLLDEPTSHLDFGNQVRILNLID 183
                                   6788899999999....33333..222333.......389999999999999999888888875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.16      43      72 ..      27      56 ..      16      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                         Rad17 43 rkkriLLisGPsGCgkstvvkvLskelgik 72
                                  +k + L i GP G gkst +k ++  +  k
  gi|91772537|ref|YP_565229.1| 27 KKGETLCILGPNGIGKSTLIKCIANVFKLK 56
                                  4556899***************99876544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.21       1      23 [.      32      54 ..      32      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                  +++ Gp+g+GKStl+k +a+ + 
  gi|91772537|ref|YP_565229.1| 32 LCILGPNGIGKSTLIKCIANVFK 54
                                  5899************9777655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.16      22      69 ..      29      76 ..      12      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                  Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkee 69
                                  g  l ++Gp G GK+ l+k++++++   + +  +  ++i+s+++++ +
  gi|91772537|ref|YP_565229.1| 29 GETLCILGPNGIGKSTLIKCIANVFKLKNGTILIGNKNISSMSRTEVA 76
                                  667999******************998888888888889888875544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1474.07
//
Query:       gi|91772538|ref|YP_565230.1|  [L=354]
Description: ABC Fe3+-siderophore transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-92  308.4  31.6    5.5e-92  308.1  31.6    1.0  1  FecCD     FecCD transport family
    0.00025   20.7  16.3    0.00025   20.7  16.3    1.6  2  ABC-3     ABC 3 transport family
  ------ inclusion threshold ------
        1.6    8.7   5.7        2.6    8.0   0.6    2.9  2  Caveolin  Caveolin
        2.2    8.6   5.1         12    6.2   5.1    2.2  1  DUF1269   Protein of unknown function (DUF1269)


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 !  308.1  31.6   1.2e-95   5.5e-92       1     310 [.      33     346 ..      32     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 308.1 bits;  conditional E-value: 1.2e-95
                         FecCD   1 llllllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadP 74 
                                   l++ll++lsl++g ++isp  ++ ++++k        +++ +++++++r+pr++aa++vG++L+vaGa++Q+++rNpL++P
  gi|91772538|ref|YP_565230.1|  33 LMILLFILSLFVGRYSISPVSIMGLIVSKFipiehtwSPNIDTVIFQIRMPRIIAAMVVGGGLSVAGASFQGLFRNPLVSP 113
                                   5789***********************9999999888888888************************************** PP

                         FecCD  75 silGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllll 155
                                   +ilG+ +ga++ga+l++l+   s +++ + l+af ++++a++l + l +  +++s+l l+L+Gi+++a+++altsl+++++
  gi|91772538|ref|YP_565230.1| 114 YILGVAAGAGFGACLGILI---SENIILIQLLAFSFGIFAAFLAYNLGKVCNQTSTLILVLSGIIIGAVFTALTSLIKYIA 191
                                   *****************98...689999***************************************************** PP

                         FecCD 156 .neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltava 235
                                      ++l +++fwl+Gsls+++w++++ +++++++++l+lll+  ++++l+lg+e+A+slG++++r++ll++++++l+t +a
  gi|91772538|ref|YP_565230.1| 192 dPYDKLPEMVFWLMGSLSSVRWDDLFYVAPAMMVSTLVLLLIGWRINVLSLGEEEARSLGIDTKRMTLLVIICATLITTSA 272
                                   8899***************************************************************************** PP

                         FecCD 236 valvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiyll 310
                                   v+++G ig+vGLivPhiar++vg+d+rkllp+s++lGa +l+++d lar++ s+te+p+gi+tal+Gapff+yll
  gi|91772538|ref|YP_565230.1| 273 VSISGLIGWVGLIVPHIARMIVGPDYRKLLPMSIFLGASFLVIVDDLARTV-SSTEIPLGILTALMGAPFFAYLL 346
                                   ***************************************************.58********************8 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.4       1.9   8.5e+03     243     256 ..      30      43 ..      24      45 .. 0.54
   2 !   20.7  16.3   5.5e-08   0.00025      44     226 ..     124     314 ..      80     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.9
                         ABC-3 243 ivlvatllfllall 256
                                   i l+++llf+l+l+
  gi|91772538|ref|YP_565230.1|  30 ILLLMILLFILSLF 43 
                                   44444455555544 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.5e-08
                         ABC-3  44 pGvalayllgvn...lllgailvgliaava...lellkrktklkedtaigivlsvflalglvlvslikk...skvdldsyL 115
                                    G +l++l++ n   + l a+ +g++aa+    l+ + ++t + + ++ gi++ +++     l+++i +      ++  +L
  gi|91772538|ref|YP_565230.1| 124 FGACLGILISENiilIQLLAFSFGIFAAFLaynLGKVCNQTSTLILVLSGIIIGAVFTALTSLIKYIADpydKLPEMVFWL 204
                                   5788888888887665566788888877651115666777777788899****9999988889999998766667888899 PP

                         ABC-3 116 fGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLviall 196
                                   +G++ ++  +dl+++a + +v  l+lll+   + ++++ ee A++ g+ +k++ ll ++   l    a+ + G+i  +  l
  gi|91772538|ref|YP_565230.1| 205 MGSLSSVRWDDLFYVAPAMMVSTLVLLLIGWRINVLSLGEEEARSLGIDTKRMTLLVIICATLITTSAVSISGLIGWVG-L 284
                                   9*********************9999999999***********************999999999999999999998777.5 PP

                         ABC-3 197 iiPaatArrltrslesllivAillglvsvv 226
                                   i+P ++ + ++ + ++ll ++i lg+ ++v
  gi|91772538|ref|YP_565230.1| 285 IVPHIARMIVGPDYRKLLPMSIFLGASFLV 314
                                   779988888899999999999999987766 PP

>> Caveolin  Caveolin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.6   0.00057       2.6      34      74 ..       5      45 ..       1      90 [. 0.76
   2 ?    2.2   0.5     0.037   1.7e+02      64     102 ..     167     205 ..     143     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00057
                      Caveolin 34 dsthsfdkvwrlshavfevvkvliYrlltallaiPlalilg 74
                                   ++  +d+vw  +h++f+ +k  i  ll ++l   l+l++g
  gi|91772538|ref|YP_565230.1|  5 VGKNIIDHVWSSTHKIFDSSKKEILILLLMILLFILSLFVG 45
                                  566778***************99888887777666666666 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.037
                      Caveolin  64 llaiPlalilgilfallsalhiwlvvPlvklllielkli 102
                                   l+ +   +i+g +f+ l++l  ++  P+ kl  + + l+
  gi|91772538|ref|YP_565230.1| 167 LILVLSGIIIGAVFTALTSLIKYIADPYDKLPEMVFWLM 205
                                   4455567999999999999999*9999999887776555 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.1    0.0028        12       8      36 ..      99     132 ..      92     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0028
                       DUF1269   8 GllvGllflnP.....llGaavGAaaGAlvgals 36 
                                   G+ +  lf nP     +lG+a+GA++GA  g l 
  gi|91772538|ref|YP_565230.1|  99 GASFQGLFRNPlvspyILGVAAGAGFGACLGILI 132
                                   4444445666622225667*********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2158.34
//
Query:       gi|91772539|ref|YP_565231.1|  [L=580]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   33.2   0.4    3.1e-07   30.9   0.3    2.0  2  Radical_SAM   Radical SAM superfamily
    2.9e-07   30.3   0.0    4.7e-07   29.6   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein
      0.001   19.4   1.1     0.0022   18.3   1.1    1.5  1  Fer4_12       4Fe-4S single cluster domain
     0.0054   16.9   0.8      0.014   15.6   0.8    1.7  1  Fer4_14       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.084   13.0   0.1         21    5.3   0.0    2.9  2  Orthopox_F7   Orthopoxvirus F7 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 !   30.9   0.3   8.7e-11   3.1e-07       4     165 ..      65     217 ..      63     219 .. 0.85
   2 ?   -1.0   0.0      0.55     2e+03      31      74 ..     412     451 ..     404     475 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 8.7e-11
                                   ESEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   4 trgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   t gCn++C  C+         + gr ++++ +++++++    ++ ++ ++++   +p++     ++l++ ak+  +++ i 
  gi|91772539|ref|YP_565231.1|  65 TIGCNFNCEGCISEILaseMDTLGRKKEITNDQVIKKA----FDEDCIGIVFCLNDPIVSFFTFKDLAEKAKE--NDLLIG 139
                                   77************888777777888888888887777....6777999999999999997666666666666..7***** PP

                                   EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                   ++tng+   e  l++l +l  d v+lg++ ++de     + + ++     ++l++l+e++++ v + ++ l+G+ de + +
  gi|91772539|ref|YP_565231.1| 140 CSTNGYYT-EAALKELIPLI-DFVNLGIKGYSDE-RYLSC-GANSSTPAFRNLKLLHESNVH-VEVSTIYLKGFEDE-VIN 214
                                   *******8.*********99.*************.66666.778888888************.9999999**99998.566 PP

                                   HHH CS
                                   xxx RF
                   Radical_SAM 163 lle 165
                                   +++
  gi|91772539|ref|YP_565231.1| 215 TAK 217
                                   666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.55
                                   HHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  31 veeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                   ++ i  evk lk       v  ++g pl+  + +++  +l++ a
  gi|91772539|ref|YP_565231.1| 412 LDFIRSEVKNLK----RPRVYYSMGYPLFSINGERIENNLVEAA 451
                                   566888999998....889999******9999999988888876 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.3e-10   4.7e-07      94     236 ..     374     520 ..     336     522 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.3e-10
                                   S.......HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHTS CS
                  Peripla_BP_2  94 g.......eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdlldal 167
                                   +       +s+ + ir +++l+++e+e+ +l+  ++ kl+ ++s ++++ ++p ++++ +++   + +      + l++a+
  gi|91772539|ref|YP_565231.1| 374 LhhdvqklDSYFDVIRHFATLTEKEAEGMELIDYMKTKLDFIRSEVKNL-KRPRVYYSMGYP--LFSINGERIENNLVEAA 451
                                   4666666799***************************************.555555554444..555555666789***** PP

                                   --EES...TTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                  Peripla_BP_2 168 gieni...aaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyalds 236
                                   g++++   ++ + ++ + +is  ++ +++p+ if+sg  ++  +  +e   +n ll  + Avkn ++y+l +
  gi|91772539|ref|YP_565231.1| 452 GGDSVnrcIERE-GKPGVNISSREFIEMNPEFIFISGLFSSPVSDSYEYCRKNALL--VDAVKNENIYGLRP 520
                                   **9984334444.9***************************************999..***********987 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 !   18.3   1.1   6.2e-07    0.0022      12     117 ..      65     167 ..      58     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.2e-07
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwl 90 
                                   + gCn++C+gC+ + +   +  +     + + +++i+++ +e  +g++++  +P++     ++ +l+++ ke+ +     +
  gi|91772539|ref|YP_565231.1|  65 TIGCNFNCEGCISEILA-SEMDTLGRkkEITNDQVIKKAFDEDCIGIVFCLNDPIV--SFFTFKDLAEKAKENDL-LIGCS 141
                                   67**********66555.4433333212556789999999****************..****************9.56778 PP

                       Fer4_12  91 ytgytleelskkekeellkeidvlvdG 117
                                   ++gy  e+ +k e  +l++ ++  ++G
  gi|91772539|ref|YP_565231.1| 142 TNGYYTEAALK-ELIPLIDFVNLGIKG 167
                                   88998888875.466666666655655 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.8   3.8e-06     0.014       5      92 ..      65     147 ..      61     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-06
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgk..pqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekki 83 
                                   + gCn++C gC  +   +se+ +   ++e + +q++k++ ++++   g+v++  +P+   +  ++ +l ++ ke+   + i
  gi|91772539|ref|YP_565231.1|  65 TIGCNFNCEGCISEI-LASEMDTlgRKKEITNDQVIKKAFDEDC--IGIVFCLNDPI--VSFFTFKDLAEKAKEND--LLI 138
                                   669*********766.3333333004455566778855445555..89*********..77899999999999988..99* PP

                       Fer4_14  84 wletngtle 92 
                                    + tng + 
  gi|91772539|ref|YP_565231.1| 139 GCSTNGYYT 147
                                   ****99876 PP

>> Orthopox_F7  Orthopoxvirus F7 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0059        21      33      65 ..     184     216 ..     177     222 .. 0.90
   2 ?    4.2   0.0     0.013        46      46      70 ..     528     552 ..     511     561 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0059
                   Orthopox_F7  33 dyknlndldeaearvefgplyiineeksdintl 65 
                                    ++nl+ l e++  ve   +y+   e   int 
  gi|91772539|ref|YP_565231.1| 184 AFRNLKLLHESNVHVEVSTIYLKGFEDEVINTA 216
                                   589*******************99999999985 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.013
                   Orthopox_F7  46 rvefgplyiineeksdintldikrr 70 
                                   r  +g +yi n+ +sdi  +di + 
  gi|91772539|ref|YP_565231.1| 528 RWILGLMYIANKIHSDIFNFDIDKE 552
                                   666899****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3644.98
//
Query:       gi|91772540|ref|YP_565232.1|  [L=218]
Description: UbiE/COQ5 methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-22   78.5   0.0    8.2e-22   77.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    7.6e-20   71.4   0.0    1.6e-19   70.4   0.0    1.5  2  Methyltransf_25  Methyltransferase domain
    4.2e-14   52.4   0.0    5.5e-14   52.1   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.4e-12   46.3   0.0    1.3e-11   45.1   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    1.5e-11   44.3   0.0    2.1e-11   43.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.6e-08   32.6   0.0    8.4e-08   32.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.2e-06   27.7   0.0    3.6e-05   23.7   0.0    2.2  1  Methyltransf_8   Hypothetical methyltransferase
    3.4e-06   27.1   0.2    7.3e-06   26.0   0.2    1.5  1  Methyltransf_18  Methyltransferase domain
    1.3e-05   24.7   0.1    1.9e-05   24.2   0.1    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00056   19.3   0.0    0.00067   19.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0016   17.7   0.0     0.0027   16.9   0.0    1.3  1  Methyltransf_3   O-methyltransferase
     0.0063   16.2   0.0       0.01   15.5   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0066   16.0   0.0      0.012   15.2   0.0    1.5  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.034   13.9   0.0    1.2  1  Met_10           Met-10+ like-protein
      0.027   14.5   0.1      0.056   13.4   0.0    1.5  2  Methyltransf_32  Methyltransferase domain
      0.037   13.7   0.0      0.069   12.8   0.0    1.5  1  SET_assoc        Histone lysine methyltransferase SET associa
      0.072   12.6   0.1       0.14   11.7   0.1    1.5  1  TrmK             tRNA (adenine(22)-N(1))-methyltransferase
      0.081   12.7   0.0       0.12   12.1   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.11   12.2   0.0       0.16   11.7   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   8.7e-25   8.2e-22       2      93 ..      52     146 ..      51     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 8.7e-25
                                   EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHH CS
               Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedpek 79 
                                   dvG+Gt +la  l +   ++++++D+s++m ++ak+++ +++l  k++ + +d++++pfed++ Dl+vs+ +l++++d++ 
  gi|91772540|ref|YP_565232.1|  52 DVGSGTAALAISLSHLIdGNIYTLDISEKMYAIAKKRIDQSNLsdKITPILEDVHNMPFEDGYADLIVSRGSLFFWQDVAT 132
                                   9*************8889************************9999999******************************** PP

                                   HHHHHHHHEEEEEE CS
               Methyltransf_11  80 alkeiaRvLkpgGl 93 
                                   a+++i+RvLkpgG+
  gi|91772540|ref|YP_565232.1| 133 AFRQIYRVLKPGGF 146
                                   *************7 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   1.7e-22   1.6e-19       1      97 []      50     145 ..      50     145 .. 0.95
   2 ?   -2.6   0.0       9.9   9.3e+03      34      43 ..     174     183 ..     150     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.7e-22
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                   ++d+G Gt  l++ l++ + +++++ +Dise+m ++a++r+++++l  +++ +  d++++pfedg  Dl+vs+g+l + + 
  gi|91772540|ref|YP_565232.1|  50 IIDVGSGTAALAISLSHLI-DGNIYTLDISEKMYAIAKKRIDQSNLsdKITPILEDVHNMPFEDGYADLIVSRGSLFF-W- 127
                                   79**************998.7**********************999**************************988665.3. PP

                                   HHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                   +d+++a+++i+rvLkpgG
  gi|91772540|ref|YP_565232.1| 128 QDVATAFRQIYRVLKPGG 145
                                   6999*************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.9
                                   HHHHHHHHHH CS
               Methyltransf_25  34 leaareraee 43 
                                   +e++++r+e+
  gi|91772540|ref|YP_565232.1| 174 IENVNKRLER 183
                                   3444444433 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   5.8e-17   5.5e-14      37     148 ..      37     146 ..       2     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 5.8e-17
                                   HHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T- CS
               Ubie_methyltran  37 kfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfedds 116
                                   + + ++ +  ++  ++Dv +Gt+ la++ls+ ++  g++  lDi+e+m  +++k++ ++  + +i  +  +  ++pfed+ 
  gi|91772540|ref|YP_565232.1|  37 QQIVQRCN-INSGIIIDVGSGTAALAISLSHLID--GNIYTLDISEKMYAIAKKRIDQSNLSdKITPILEDVHNMPFEDGY 114
                                   44444433.344479****************996..89*******************9999989***************** PP

                                   EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEE CS
               Ubie_methyltran 117 fDvvtvsfGlrnvtDklkaLkeayrvlkpGGr 148
                                    D++     l    D  +a++++yrvlkpGG 
  gi|91772540|ref|YP_565232.1| 115 ADLIVSRGSLFFWQDVATAFRQIYRVLKPGGF 146
                                   **99766668899*****************96 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.4e-14   1.3e-11       2      97 ..      52     145 ..      51     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.4e-14
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlkd 81 
                                   ++G+Gt++l+  l    +d +++ +Dis+++ + ak+++ + +  +  +++   +d+++ + + ++ Dl+v+ + l  ++d
  gi|91772540|ref|YP_565232.1|  52 DVGSGTAALAISLSHL-IDGNIYTLDISEKMYAIAKKRIDQSNLSD--KITPILEDVHNMPFEdGYADLIVSRGSLFFWQD 129
                                   9***********9777.***************99999999988744..66666666666655567**************** PP

               Methyltransf_12  82 irevldnirklLkpgG 97 
                                   ++ ++++i+++LkpgG
  gi|91772540|ref|YP_565232.1| 130 VATAFRQIYRVLKPGG 145
                                   ***************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   2.2e-14   2.1e-11       7     127 ..      50     167 ..      46     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.2e-14
               Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevlna 86 
                                   ++D+G+Gt +l++ l +++  +++++ +Dise++   A+++ ++ +l+  ++   +d+++++  +ed   Dli+s++ l  
  gi|91772540|ref|YP_565232.1|  50 IIDVGSGTAALAISLSHLI--DGNIYTLDISEKMYAIAKKRIDQSNLSdKITPILEDVHNMP--FEDGYADLIVSRGSLFF 126
                                   89**************554..79*****************999999988*************..***************** PP

               Methyltransf_31  87 ladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                     d + ++++i rvlkpgg   i    + +el+ k+++e+ 
  gi|91772540|ref|YP_565232.1| 127 WQDVATAFRQIYRVLKPGGFGYIGGGFGTSELKSKISNEMV 167
                                   *******************8777777777777776666665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   8.9e-11   8.4e-08      20     114 ..      44     146 ..      32     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 8.9e-11
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.......kakkaqkdqfdeqeaae..........pqgk 82 
                                   +  +g ++d+G Gt  l+ +l+     +++  D+s+++ +ia+                  ++++++          ++g+
  gi|91772540|ref|YP_565232.1|  44 NINSGIIIDVGSGTAALAISLSHLIDgNIYTLDISEKMYAIAKkridqsnL----------SDKITPiledvhnmpfEDGY 114
                                   5678899**************888778**************8544444441..........333333333444444499** PP

               Methyltransf_23  83 fdlIvlrevlehvpdppellrqiatllkpgGy 114
                                    dlIv+r +l   +d++ ++rqi++ lkpgG 
  gi|91772540|ref|YP_565232.1| 115 ADLIVSRGSLFFWQDVATAFRQIYRVLKPGGF 146
                                   ******************************85 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.8e-08   3.6e-05      71     164 ..      45     163 ..      26     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.8e-08
                                   -TTS-EEEES-TT-HHHHH--S-....EEEEES..............S-SSTTEEES..-TTS-S--TT-EEEEEEES--- CS
                Methyltransf_8  71 kdnlvvadlGcGeakiaeavrek..ekvrsfdl..............vavnervvac..dlakvPledesvdvavfclslm 133
                                    ++ +++d+G G a +a + ++    ++ ++d+                + +++++   d+ ++P ed+ +d++v   sl 
  gi|91772540|ref|YP_565232.1|  45 INSGIIIDVGSGTAALAISLSHLidGNIYTLDIsekmyaiakkridqSNLSDKITPIleDVHNMPFEDGYADLIVSRGSLF 125
                                   3567888888888888855554311345555541111111110000045566666545599******************97 PP

                                   .SS-HHHHHHHHHHHEEEEEEEEE......EEEGGG-S CS
                Methyltransf_8 134 .gtnladflkeanrvlkvGGllkv......aevksrfe 164
                                     +++a+  ++++rvlk+GG+ ++      +e+ks+++
  gi|91772540|ref|YP_565232.1| 126 fWQDVATAFRQIYRVLKPGGFGYIgggfgtSELKSKIS 163
                                   2689****************988833333346666665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.2   7.7e-09   7.3e-06       8      87 ..      39     119 ..      37     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.7e-09
               Methyltransf_18   8 iaslvekgs.rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtv 86 
                                   i++ ++ +s +++D+G+  + l+i l  + +  +++  Di+e+ ++ ak+ i++++l+dki+ +l d  +   e+  +d +
  gi|91772540|ref|YP_565232.1|  39 IVQRCNINSgIIIDVGSGTAALAISLS-HLIDGNIYTLDISEKMYAIAKKRIDQSNLSDKITPILEDVHNMPFEDGyADLI 118
                                   555566555599*************98.678889********************************998876544447776 PP

               Methyltransf_18  87 v 87 
                                   v
  gi|91772540|ref|YP_565232.1| 119 V 119
                                   6 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1     2e-08   1.9e-05     156     254 ..      41     145 ..      33     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2e-08
                          PrmA 156 eklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk....eekadviva 232
                                   ++ + +   ++DvG G++ Lai  + L   +++ +Di e    +ak+ +++ ++++k++  + e++ +    ++ ad+iv+
  gi|91772540|ref|YP_565232.1|  41 QRCNINSGIIIDVGSGTAALAISLSHLIDGNIYTLDISEKMYAIAKKRIDQSNLSDKITP-ILEDVHNmpfeDGYADLIVS 120
                                   4555556689**********************************************9965.44555433334899999997 PP

                          PrmA 233 N...ILaevlielaedikklvkegg 254
                                          + +     +i++++k+gg
  gi|91772540|ref|YP_565232.1| 121 RgslFFWQDVATAFRQIYRVLKPGG 145
                                   4222344555555556666666666 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.1e-07   0.00067      55     161 ..      40     146 ..      36     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.1e-07
                                   HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEE CS
                          CMAS  55 leklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvv 132
                                   +++ +++ G  ++d+G G  +l++   +  d ++  l +S++ ++ akkr+d+ +l++k +  l d ++++      d +v
  gi|91772540|ref|YP_565232.1|  40 VQRCNINSGI-IIDVGSGTAALAISLSHLIDGNIYTLDISEKMYAIAKKRIDQSNLSDKITPILEDVHNMPFedgYADLIV 119
                                   5666677774.78************************************************999999987533458899** PP

                                   EES-GGGTSGGGHHHHHHHHHHHS-TT-E CS
                          CMAS 133 svgafehvgkenydtffkklkkllkedGl 161
                                   s g +  +  +  +t f++++++lk++G 
  gi|91772540|ref|YP_565232.1| 120 SRGSL--FFWQDVATAFRQIYRVLKPGGF 146
                                   *9976..6778889999999999999996 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0027      50     106 ..      47     103 ..      37     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                                   EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES CS
                Methyltransf_3  50 rvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekielieg 106
                                     + i v  G ++La++l+   DG+i ++di ++ y+ia+k i+++ + +ki  i  
  gi|91772540|ref|YP_565232.1|  47 SGIIIDVGSGTAALAISLSHLIDGNIYTLDISEKMYAIAKKRIDQSNLSDKITPILE 103
                                   55667777899*****************************************87665 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.1e-05      0.01      32     109 ..      39     113 ..      30     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                         GCD14  32 iimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdee 109
                                   i+++ +++ G  +++ G G+++l+ +++  +   G+++t++  e+ +  a++   + +ls+ +t    Dv +  f+++
  gi|91772540|ref|YP_565232.1|  39 IVQRCNINSG-IIIDVGSGTAALAISLSHLI--DGNIYTLDISEKMYAIAKKRIDQSNLSDKITPILEDVHNMPFEDG 113
                                   6777778777.57999999999999999988..59***********************************99988655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.012      31     103 ..      46     120 ..      18     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTT.STTS-EEEEEE CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvlee.veekkfdlivs 103
                                    sg ++D+G+G+ +l+++l +  +  ++  +d++ +  ++ak+ + +++l+  ++ + +dv +  +e++  dlivs
  gi|91772540|ref|YP_565232.1|  46 NSGIIIDVGSGTAALAISLSHLIDG-NIYTLDISEKMYAIAKKRIDQSNLSdkITPILEDVHNMpFEDGYADLIVS 120
                                   67789***************99888.7999***************9999997877777888765155777788886 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05     0.034     101     170 ..      47     116 ..      17     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                                   T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EE CS
                        Met_10 101 gevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqlad 170
                                     +++dv  G   +ai++++   +  +++ d+  + +   k+ i   +++++++pileD++++   +  ad
  gi|91772540|ref|YP_565232.1|  47 SGIIIDVGSGTAALAISLSH-LIDGNIYTLDISEKMYAIAKKRIDQSNLSDKITPILEDVHNMPFeDGYAD 116
                                   45789**9**********96.56667**********************************99876445555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     6e-05     0.056      25      74 ..      46      92 ..      27     107 .. 0.83
   2 ?   -2.5   0.1       4.7   4.4e+03      71      93 ..     170     192 ..     156     203 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-05
               Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraekl 74
                                  ++  ++DvG+G + L+  l++       +++ +d++e++ + a+kr ++ 
  gi|91772540|ref|YP_565232.1| 46 NSGIIIDVGSGTAALAISLSH---LIDGNIYTLDISEKMYAIAKKRIDQS 92
                                  45679****************...99************999999887765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
               Methyltransf_32  71 aeklgkkfnkrlsfaelsieeat 93 
                                   ++   +++nkrl++++l++ e+ 
  gi|91772540|ref|YP_565232.1| 170 DKGWIENVNKRLERSNLESFEKA 192
                                   44455566666666666655554 PP

>> SET_assoc  Histone lysine methyltransferase SET associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.3e-05     0.069      11      42 ..     183     216 ..     174     218 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                     SET_assoc  11 kvtvedlkkrLkkyewer..iledktGyYivFnd 42 
                                   ++++e ++k Lk+ ++ +  i++d++G++i+F++
  gi|91772540|ref|YP_565232.1| 183 RSNLESFEKALKTAKINDyeIIDDESGFWILFKK 216
                                   6788999*****99997444************86 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00015      0.14       1      56 [.      50     104 ..      50     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                          TrmK   1 laDiGsDHAyLpiylvknnkvsvai.agevnegplesAkknvkkskleekievrlgd 56 
                                   ++D+Gs  A L+i l   + ++  i   +++e  ++ Akk + +s+l++ki+ +l d
  gi|91772540|ref|YP_565232.1|  50 IIDVGSGTAALAISL--SHLIDGNIyTLDISEKMYAIAKKRIDQSNLSDKITPILED 104
                                   58**********998..46666665368***********************988766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.12      77     124 ..      50      95 ..      18     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                   EEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
                          PCMT  77 vLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                                   +++vGsG+  l+  l++l+    ++ +++ ++++++ ak+++ +++l+
  gi|91772540|ref|YP_565232.1|  50 IIDVGSGTAALAISLSHLIDG--NIYTLDISEKMYAIAKKRIDQSNLS 95 
                                   89****************975..56899999************99987 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.16      40     101 ..      40      99 ..      21     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
               Methyltransf_16  40 lganelsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvk 101
                                   +++ + +   ++++GsGt    +++ +l  + +++  D++e +  + kk i+ ++  l++k++
  gi|91772540|ref|YP_565232.1|  40 VQRCNINSGIIIDVGSGTAALAISLSHL-IDGNIYTLDISEkMYAIAKKRIDQSN--LSDKIT 99 
                                   45667788889**************999.78899999998869999******955..888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1307.64
//
Query:       gi|91772541|ref|YP_565233.1|  [L=362]
Description: ABC Fe3+-siderophore transporter, substrate binding subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-20   73.2   0.0    2.6e-20   73.0   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 !   73.0   0.0   1.5e-24   2.6e-20      46     236 ..     103     294 ..      55     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 1.5e-24
                                   ESSSB-HHHHHHH--SEEEE-GGG.......GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                  Peripla_BP_2  46 adgeidvEklaalkPDlvilskgl....gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeid 122
                                   + ++ ++E+++   PD+++  ++     + t  + ++    ip+v  es+  +  ++++i+  g +lg+ ++ae l+ +++
  gi|91772541|ref|YP_565233.1| 103 GKQDGNYESIISICPDIIFEGYNSgediDSTINARQEKFGTIPVVGIESNIDVMTYEDSIEFMGGVLGEDERAEHLIRFYK 183
                                   46889******************995555555555555578**************************************** PP

                                   HHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--...STT-EEE-HHHHHHH--SEEE CS
                  Peripla_BP_2 123 sklaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk...kseyeeisaEqilasdpdvif 198
                                     l  + ++++++  ++++ ++++++ + g    + +s  ++l++  g+ n+a+  +   + ++ eis Eqil+++pdvi+
  gi|91772541|ref|YP_565233.1| 184 TSLNTVTTKVSEIplNERKRVYYAEGTA-GLQTDSKGSSHSQLIEVCGGINVAEC-PfleGYGRTEISIEQILKWNPDVII 262
                                   *************765555555554444.66677788889999999***999554.6688999****************** PP

                                   EEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                  Peripla_BP_2 199 vsgraeadnktgleflkenpllaelpAvkngrVyalds 236
                                     ++      t++  + +++++++++Avk + +y +++
  gi|91772541|ref|YP_565233.1| 263 TGDS------TFYNNIYSDHIWQNITAVKDHEIYLVPN 294
                                   ***9......************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2245.18
//
Query:       gi|91772542|ref|YP_565234.1|  [L=332]
Description: ABC glycine betaine/L-proline transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  102.4   0.1    5.3e-29  101.5   0.1    1.5  1  ABC_tran    ABC transporter
    4.6e-17   62.2   4.9    1.3e-07   31.9   0.2    2.9  3  CBS         CBS domain
    0.00014   21.8   0.2       0.55   10.0   0.0    2.2  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    0.00048   19.1   1.9       0.01   14.7   0.1    2.9  3  ABC_ATPase  Predicted ATPase of the ABC class
     0.0095   16.3   0.1      0.018   15.4   0.1    1.6  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.064   13.8   0.0       0.15   12.6   0.0    1.6  1  AAA_18      AAA domain
      0.067   13.5   0.4       0.27   11.5   0.4    2.0  1  AAA_22      AAA domain
       0.07   13.0   0.0       0.17   11.8   0.0    1.7  1  APS_kinase  Adenylylsulphate kinase
      0.077   13.2   1.8       0.51   10.6   1.8    2.3  1  SbcCD_C     Putative exonuclease SbcCD, C subunit
      0.096   12.4   0.0       0.17   11.6   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
       0.11   11.8   0.0       0.21   10.9   0.0    1.5  1  Zeta_toxin  Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   0.1   3.3e-32   5.3e-29      17     136 ..       1     133 [.       1     134 [. 0.97

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 3.3e-32
                                   EESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHHHH.............H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............x RF
                      ABC_tran  17 vGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvren.............e 80 
                                   +G +G+GKStLl++l +l +pt+G+i ldg+d+ +    + +e+ rk++g+++q+  l  + tv +n             e
  gi|91772542|ref|YP_565234.1|   1 MGLSGSGKSTLLRCLNRLIEPTAGHIILDGEDVATanseELREIRRKKMGMVFQNFALIHHRTVLDNvaygleiqgiskeE 81 
                                   699*******************************99998889999********************************9999 PP

                                   HHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  81 sdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   +d++ ++a++++glk+ ++++     s+LSgG++qrv laral+++p++ll+DE++
  gi|91772542|ref|YP_565234.1|  82 RDVKGKEAIETVGLKGYENSKT----SQLSGGMQQRVGLARALATDPDILLMDEAF 133
                                   9999************999999....****************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.7   9.3e+03       9      24 ..     159     172 ..     152     195 .. 0.62
   2 !   31.9   0.2   8.1e-11   1.3e-07       4      55 ..     220     271 ..     214     273 .. 0.88
   3 !   31.5   0.4   1.1e-10   1.8e-07       1      56 [.     275     328 ..     275     329 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.7
                                   CEEEETTSBHHHHHHH CS
                           CBS   9 vvtvppdttleealel 24 
                                   +v+v+ d  l eal+l
  gi|91772542|ref|YP_565234.1| 159 IVFVSHD--LDEALKL 172
                                   5555555..6666643 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 8.1e-11
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   +m r  ++v+ +++ + al+lmre+g+s+++VV+ +++l Gi++  D +r++
  gi|91772542|ref|YP_565234.1| 220 VMKRADPVVSMNSSPKVALQLMREHGISSIFVVNREKHLKGIISVDDAVRKV 271
                                   666644599999*********************99999*********99875 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 1.1e-10
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   ++d+mt+dv t +pdt+l e++ ++  ++ s + V+ +dgkl+G++ +  +l al+
  gi|91772542|ref|YP_565234.1| 275 IKDVMTSDVTTTHPDTPLNELIPII--ENSSPIAVTKDDGKLLGVIVRGSVLGALA 328
                                   68***********************..55788888899********9999999885 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00038      0.62       6      23 ..       2      19 ..       1      84 [. 0.80
   2 !   10.0   0.0   0.00033      0.55     235     299 ..     104     166 ..      75     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00038
                        AAA_21  6 GpNgsGKSnLLdaldlla 23
                                  G  gsGKS+LL++l  l 
  gi|91772542|ref|YP_565234.1|  2 GLSGSGKSTLLRCLNRLI 19
                                  5579**********9984 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00033
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSp 299
                                   ++lS G+++  +l+ al+ ++   ++ll DE  + L+P + ++   ell ++++    +++++H+ 
  gi|91772542|ref|YP_565234.1| 104 SQLSGGMQQRVGLARALATDP---DILLMDEAFSALDPLIRSEMQdELLALEEKMQKTIVFVSHDL 166
                                   478999999999999999999...9*************6666666777755555559*******95 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.059        96     255     276 ..       6      30 ..       1      50 [. 0.72
   2 !   14.7   0.1   6.2e-06      0.01     317     389 ..     100     172 ..      94     207 .. 0.79
   3 ?    0.4   0.1      0.13   2.2e+02     366     395 ..     220     252 ..     212     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.059
                                   SSHHHHHHHHHHCCSE...E-TTSS CS
                    ABC_ATPase 255 hGKsTLLeAlekGvyn...hvpgDG 276
                                    GKsTLL+ l++ + +   h++ DG
  gi|91772542|ref|YP_565234.1|   6 SGKSTLLRCLNRLIEPtagHIILDG 30 
                                   6********9986643222666666 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.2e-06
                                   TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH-- CS
                    ABC_ATPase 317 kfstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgv 389
                                   ++ t++ SG + q + +++al  + ++lL+DE  sA   +ir e+ +el++ e++  +++v   ++l + l +
  gi|91772542|ref|YP_565234.1| 100 NSKTSQLSGGMQQRVGLARALATDPDILLMDEAFSALDPLIRSEMQDELLALEEKMQKTIVFVSHDLDEALKL 172
                                   5678999*******************************************98888888888777777665544 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.13
                                   S-GGG--B--HH...HCHHHHHHHH--EEEEEE CS
                    ABC_ATPase 366 vskekepitplv...drvrelykklgvstilvv 395
                                   v k+++p+ ++    + + +l++++g+s+i vv
  gi|91772542|ref|YP_565234.1| 220 VMKRADPVVSMNsspKVALQLMREHGISSIFVV 252
                                   556667776665111456799*********998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.1e-05     0.018      31      63 ..       2      34 ..       1     172 [. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                        AAA_16 31 GesGvGKsslvrellralekdggiflrgkcdql 63
                                  G sG+GKs+l+r+l r +e + g+ +    d  
  gi|91772542|ref|YP_565234.1|  2 GLSGSGKSTLLRCLNRLIEPTAGHIILDGEDVA 34
                                  99*************999999777766655555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.1e-05      0.15       5      83 ..       2      69 ..       1      81 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.1e-05
                        AAA_18  5 GtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghl 83
                                  G +G+GK+tl + L+++       ++++ +++ + + + e   e ++++++k+  +++++  +      ++  v+d + 
  gi|91772542|ref|YP_565234.1|  2 GLSGSGKSTLLRCLNRLI--EPTAGHIILDGEDVATANSE---ELREIRRKKMGMVFQNFALI------HHRTVLDNVA 69
                                  99************9996..77777777777766666666...77777777777788777776......5666777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00017      0.27      12     117 ..       2     153 ..       1     170 [. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                        AAA_22  12 GesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdl.lrellralglelka.................... 70 
                                   G sG+GK+tllr l +  +  a +    + +v++ +  ++ + +   + ++++++ l +++                    
  gi|91772542|ref|YP_565234.1|   2 GLSGSGKSTLLRCLNRLIEPTAGHIIlDGEDVATANSEELREIRRKkMGMVFQNFALIHHRtvldnvaygleiqgiskeer 82 
                                   99*************998655555448555555555555553333335666666666666666666666666677777778 PP

                        AAA_22  71 ................erlsseellealeqalrarav....ielliiDEaqh.lr...seealeeLrslln 117
                                                   e+ ++++l   ++q +  +++    + +l+ DEa   l+   + e+  eL  l +
  gi|91772542|ref|YP_565234.1|  83 dvkgkeaietvglkgyENSKTSQLSGGMQQRVGLARAlatdPDILLMDEAFSaLDpliRSEMQDELLALEE 153
                                   88888888888888875666666665555554444444778889999998777766655777777755555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.17       9      49 ..       2      41 ..       1      69 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                  SSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                    APS_kinase  9 GlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49
                                  GlsgsGKst+ + l++ L e     ++LdG+ v +  +++L
  gi|91772542|ref|YP_565234.1|  2 GLSGSGKSTLLRCLNR-LIEPTAGHIILDGEDVATANSEEL 41
                                  9*************96.6667777789****9988776666 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 ?   10.6   1.8   0.00031      0.51      50      83 ..     110     143 ..      81     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                       SbcCD_C  50 laalyssaegrepalrlvfLDEAFsklDeesiat 83 
                                   + + ++ a++  ++++++++DEAFs lD+  +++
  gi|91772542|ref|YP_565234.1| 110 MQQRVGLARALATDPDILLMDEAFSALDPLIRSE 143
                                   555555554456789*************866655 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   0.0   0.00011      0.17      29      49 ..       2      22 ..       1      26 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                        AAA_29 29 GpsGsGKSTllDAiqalLvpa 49
                                  G sGsGKSTll  ++ l+ p+
  gi|91772542|ref|YP_565234.1|  2 GLSGSGKSTLLRCLNRLIEPT 22
                                  89*********8888887775 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.21      23      90 ..       2      67 ..       1      71 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                    Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqe 90
                                  G +G+GKs+l++ l++ +e++ + + ld+ d+ +     ee+++ + kk+  ++q++a    +++l+ 
  gi|91772542|ref|YP_565234.1|  2 GLSGSGKSTLLRCLNRLIEPTAGHIILDGEDVATAN--SEELREIRRKKMGMVFQNFALIHHRTVLDN 67
                                  568*****************************9998..5698888999******99998888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2112.97
//
Query:       gi|91772543|ref|YP_565235.1|  [L=276]
Description: ABC glycine betaine/L-proline transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-27   96.9   8.4    1.1e-27   96.9   8.4    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.22   11.9   0.5        1.9    8.9   0.1    2.3  2  BDM           Putative biofilm-dependent modulation 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 ?   -0.9   4.9      0.13   1.2e+03       5      51 ..      24      87 ..      23     108 .. 0.61
   2 !   96.9   8.4   1.3e-31   1.1e-27       1     173 [.     109     267 ..     109     276 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                  BPD_transp_1  5 GilaalnrnkkldkllrpliivllslPsfvlaillvlvf..................vilsilgh 51
                                  Gil+   ++ ++d++++++ ++ll + ++v+a+++  ++                   +++  g 
  gi|91772543|ref|YP_565235.1| 24 GILLD-IFSDVTDYIISGFNDTLLLFHPIVFALIIGIAAyfigrkdlklaigstvglLLIDNMGL 87
                                  66666.67788999999999999998888888876544455555555555455444433333333 PP

  == domain 2  score: 96.9 bits;  conditional E-value: 1.3e-31
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpk 81 
                                   +i+lGi++a  +n +  +++ pl ++++++Psfv +i+ v        +g ++ p++++++++a+p++++++  +++++pk
  gi|91772543|ref|YP_565235.1| 109 AIPLGIVSA--KNEFAYHIIKPLLDLMQTMPSFVYLIPAV------IFFGLGNVPGLVATIVFAMPPAIRLTTLGIQQVPK 181
                                   69*******..***********************999999......88********************************* PP

                  BPD_transp_1  82 dlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalv 162
                                   +l e+a a G ++wq + kv lP alp+i++g+   ++++l   v++ ++g+  Glg+++l  i+  d+ ++       ++
  gi|91772543|ref|YP_565235.1| 182 ELTEVADAFGSTPWQKLTKVELPTALPSIMAGVNQCIMLSLSMVVIAAMIGAR-GLGYQVLIGIQRVDIGQGF-----EAG 256
                                   ***************************************************66.7***************777.....444 PP

                  BPD_transp_1 163 iavlllnlvad 173
                                   + ++++ +++d
  gi|91772543|ref|YP_565235.1| 257 LGIVIIAIILD 267
                                   44444444444 PP

>> BDM  Putative biofilm-dependent modulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00021       1.9      41      71 .]      16      45 ..      11      45 .. 0.87
   2 ?    0.3   0.0       0.1     9e+02      20      41 ..     249     270 ..     246     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00021
                           BDM 41 tkwveasdndilsdiyqqtinyvvsGqhptl 71
                                    w+e  d  il di+    +y++sG   tl
  gi|91772543|ref|YP_565235.1| 16 VNWIE-DDFGILLDIFSDVTDYIISGFNDTL 45
                                  67888.5899****************98886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.1
                           BDM  20 ieqGlraelGvvteddilmelt 41 
                                   i qG+ a lG+v    il  +t
  gi|91772543|ref|YP_565235.1| 249 IGQGFEAGLGIVIIAIILDRFT 270
                                   88**********9887776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1794.96
//
Query:       gi|91772544|ref|YP_565236.1|  [L=290]
Description: ABC glycine betaine/L-proline transporter, substrate-binding subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-70  236.3   1.0    4.8e-70  236.1   1.0    1.0  1  OpuAC     Substrate binding domain of ABC-type glycine betain


Domain annotation for each model (and alignments):
>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.1   1.0   2.7e-74   4.8e-70       1     256 [.      35     277 ..      35     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 236.1 bits;  conditional E-value: 2.7e-74
                                   CEEEEEEESSHHHHHHHHHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEE CS
                         OpuAC   1 ktivigsknwteqevlaeilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgp 81 
                                   k++++g+  w+ +++ ++++ q+lekkGy+ve  ++++ ++l+ ++a+Gd+D+++++w++ ++e y+ ++ ++ + +    
  gi|91772544|ref|YP_565236.1|  35 KEVTVGYVLWDGEIASTNVIEQVLEKKGYDVEIIAVDA-GALYLGVAQGDFDFTTSAWLPVTQENYWNQYGDQLVSV--RN 112
                                   68************************************.99******************************998888..89 PP

                                   ESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSCEEEEHHHH CS
                         OpuAC  82 lgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgldkvelvegseaamdael 162
                                   + ++   gl+vp+yv    +i+si++L++++e     ++ge++g+++g+g+++ te++++aYgl +++l+++s+a+m+a+l
  gi|91772544|ref|YP_565236.1| 113 NLENCPLGLVVPAYV----EIDSIAELNDNKE----MFNGEIIGIDPGAGIMQNTENAIEAYGL-DYKLISSSTAGMTAQL 184
                                   ***************....9************....9***************************.8*************** PP

                                   HHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTSTS-SSEEEEEEEEHHHHHHSCTHHHHHHHHC--HHHHHHHHHHHHTT CS
                         OpuAC 163 yaaykrgepvvvyawtPdwaikkydlvvLedpkglfppaynvvpvvrkefaekaPevaafLeklsldtetlnelnaqvdve 243
                                    +a++++epvvv++w+P+w ++++dl++L+dp+g+f++a+nv +++r +++e+ Pev+++L +++++ e++++++ +++  
  gi|91772544|ref|YP_565236.1| 185 RKAIDDEEPVVVTLWSPHWSFGRWDLKYLDDPEGVFGQADNVETLARTGLEEDMPEVYDVLTRFHWTHEDIQSVMSDMES- 264
                                   *******************************************************************************7. PP

                                   TT-HHHHHHHHHH CS
                         OpuAC 244 gkdpeevAkawla 256
                                   g+ pe++A++w++
  gi|91772544|ref|YP_565236.1| 265 GMAPEDAAAKWIE 277
                                   ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2102.20
//
Query:       gi|91772545|ref|YP_565237.1|  [L=281]
Description: metallophosphoesterase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-17   64.5   1.4    2.4e-17   64.1   1.4    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    7.2e-13   49.1   1.3    2.6e-10   40.8   1.3    2.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   1.4   2.6e-21   2.4e-17       1     203 [.       1     213 [.       1     214 [. 0.55

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2.6e-21
                                   EEEEEEESBTB..TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH.TSEEEEEC-TTS..C CS
                   Metallophos   1 lrilvigDlHl..algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky.pipvylllGNHe..g 76 
                                   ++il+i+DlH+   + +g+   ll++++ +    ++d+v+ +GD++ +g  ++ ++e  ++l +   ++v+ + GNH+  +
  gi|91772545|ref|YP_565237.1|   1 MNILHISDLHFgpRHWDGDDKILLEMINSF----DADIVINTGDNTTDGLEDE-CAEAGRFLKAIkCKNVISTWGNHDkrN 76 
                                   79********66655556666666666555....***************5555.6666666666555788********663 PP

                                   HHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHHHHHHSCHHHHCC........ CS
                   Metallophos  77 fee.ellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklgslnleleapepg........ 147
                                    +  e ++ky ++ +              + +++ +++   +++l        ++  ++ + +n++++++ +g        
  gi|91772545|ref|YP_565237.1|  77 MRShEFFRKYIDNSEI-------------ISISETIKTRkKNIFLNREI----TKVNENFTDINFIKPISINGktvliisi 140
                                   3333444444444444.............33333333322222222222....1111222222222222222222222222 PP

                                   .............HHHHHH....HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                   Metallophos 148 .............dewlkd....lekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                                +e+l+      e+ e + ++++ ++s l +  ++l ++  l d+ +k+++++v++GHtH+
  gi|91772545|ref|YP_565237.1| 141 dtnelyndngyveKEILNAvskeIEQIEYDLPLLITHYSILGTDECPLTNSADLIDFVQKHKIQYVFCGHTHE 213
                                   22111111112224444446444555555555555555555588888889999999****************7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   1.3   2.9e-14   2.6e-10       1     154 [.       1     244 [.       1     253 [. 0.61

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.9e-14
                 Metallophos_2   1 MklaiiSDlH....snldaleavlealkevgvdaiihaGD.....leeeepevleellela...pvlaVrGNnD....... 62 
                                   M++++iSDlH     +    + +le +++ ++d +i++GD     le+e  e+ + l++      v+   GN+D       
  gi|91772545|ref|YP_565237.1|   1 MNILHISDLHfgprHWDGDDKILLEMINSFDADIVINTGDnttdgLEDECAEAGRFLKA-IkckNVISTWGNHDkrnmrsh 80 
                                   9*********9996666667777999**************4433323333333222222.257799999*****8888888 PP

                 Metallophos_2  63 .................................................eevveedvlreaaelgtdlpeeaelelagekv 94 
                                                                                                               +g++v
  gi|91772545|ref|YP_565237.1|  81 effrkyidnseiisisetiktrkkniflnreitkvnenftdinfikpisI--------------------------NGKTV 135
                                   88888888888887777777766444444444444444443333333330..........................44444 PP

                 Metallophos_2  95 lliHgdpl.........................................gvkdalaellkeaeegsd..vvvcGHtHvpev 132
                                   l+i  d++                                         + +  ++++l +  ++++  +v+cGHtH+ e+
  gi|91772545|ref|YP_565237.1| 136 LIISIDTNelyndngyvekeilnavskeieqieydlpllithysilgtdECPLTNSADLIDFVQKHKiqYVFCGHTHELEI 216
                                   444443334444444444444444444444444444444444444699955555555555545555556**********99 PP

                 Metallophos_2 133 ekeggv......lvvnPGsvgeprdgdp 154
                                    +++++      ++   Gs++   + ++
  gi|91772545|ref|YP_565237.1| 217 MRTNDQyhgfsfTHFMCGSLSSSNHPKD 244
                                   9997443444447888888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1831.16
//
Query:       gi|91772546|ref|YP_565238.1|  [L=373]
Description: hypothetical protein Mbur_0505 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   33.8  12.6      0.012   15.9   0.0    3.2  3  Bactofilin  Polymer-forming cytoskeletal
     0.0035   16.0   7.5     0.0035   16.0   7.5    2.1  2  FapA        Flagellar Assembly Protein A
  ------ inclusion threshold ------
      0.017   14.1  10.0      0.032   13.1  10.0    1.4  1  CstA        Carbon starvation protein CstA


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   4.2   6.8e-05      0.41      35      84 ..      36      84 ..      22      93 .. 0.60
   2 !   15.8   5.8   2.2e-06     0.013      16      96 ..      67     149 ..      64     151 .. 0.85
   3 !   15.9   0.0     2e-06     0.012      46      83 ..     151     189 ..     150     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.8e-05
                    Bactofilin 35 lvvgeggkvegnikaeevvvaGtvkGnveaeekvelkktakveGdikaks 84
                                  ++++e+ + +  i  ++++v+G v G+v a    +l+ t++v+Gd+ +  
  gi|91772546|ref|YP_565238.1| 36 VIINETVEDDVYIAGDTLIVNGDVLGDVVAA-GGTLQITGNVSGDLIVTA 84
                                  4444444444445557777777777777777.666666677777765544 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.2e-06
                    Bactofilin  16 egdlridGkveGdi.eakgklvvgeggkvegn..ikaeevvvaGtvkGnveaee.kvelkktakveGdikaksleieegav 92 
                                    g+l+i G+v+Gd+  ++g++++  +g +  +  + +++ +++G++ +++ + + +v+ ++ta++ Gd + +s + + g++
  gi|91772546|ref|YP_565238.1|  67 GGTLQITGNVSGDLiVTAGDVTI--TGIIGDDvrVACGTFELSGQIGDDLLVAAgTVSTTETANIGGDTTIRSGDADLGGN 145
                                   689**********9888899999..5655444337789*********99888877*********************99999 PP

                    Bactofilin  93 feGk 96 
                                   f G 
  gi|91772546|ref|YP_565238.1| 146 FGGL 149
                                   9885 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2e-06
                    Bactofilin  46 nikaeevvvaGtvkGnveaee.kvelkktakveGdikak 83 
                                   +++a+++v++G+v+G+ + ++  ++++++++v+G++++ 
  gi|91772546|ref|YP_565238.1| 151 EVSAGSLVLSGNVEGDAKLDSaDITIQPDSSVKGNLEYT 189
                                   5899***************999*************9986 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   7.5   5.8e-07    0.0035     199     255 ..      48     102 ..      38     127 .. 0.80
   2 !    3.2   0.4    0.0046        27     177     248 ..     120     204 ..     113     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.8e-07
                          FapA 199 fkG.sViikGnVeegmkVkasgditikGvvesatieAggnItikgGiigkgkskikAg 255
                                     G ++i++G+V  g  V a+g ++i G+v++  i + g++ti  Giig ++ ++ +g
  gi|91772546|ref|YP_565238.1|  48 IAGdTLIVNGDV-LGDVVAAGGTLQITGNVSGDLIVTAGDVTIT-GIIG-DDVRVACG 102
                                   567789******.5778**************************9.****.66777774 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0046
                          FapA 177 gisVdpvleikgdVdlstGnIk...........fkGsViikGnVeegmkVkasgditik..Gvv.esatieAggnItikgG 243
                                   ++s  +  +i gd  +++G+ +             Gs++ +GnVe + k  +  diti+    v  + + +A ++I i  G
  gi|91772546|ref|YP_565238.1| 120 TVSTTETANIGGDTTIRSGDADlggnfggllevSAGSLVLSGNVEGDAKLDSA-DITIQpdSSVkGNLEYTAPKEIPIPTG 199
                                   56666777788888888888888888888888889*****************9.****97544445555667777777777 PP

                          FapA 244 iigkg 248
                                   ++g++
  gi|91772546|ref|YP_565238.1| 200 TVGED 204
                                   77755 PP

>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  10.0   5.4e-06     0.032     123     228 ..     228     338 ..     224     351 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-06
                          CstA 123 elgkvakllallaillililvlavlalvvvkalaespaavfsviltipialllGvllrklrkg.....vleasvigvvlll 198
                                    +gk+a   +l+a  +i ilv    +  ++k ++++p   ++v l+i+i  ++G+++  + +      +l   ++++vl++
  gi|91772546|ref|YP_565238.1| 228 IIGKIAYYSILFALGVISILVFPQKTEKIAKNIQKEPLKKIAVGLLILIGSFMGIIVLLITIIgipiaLLLLLLLAIVLMI 308
                                   589999999999999****************************************98876643211225667789****** PP

                          CstA 199 lavvvgseveealaelltlsketlaivliv 228
                                   + +++++++ ea  e   ++ ++++++ + 
  gi|91772546|ref|YP_565238.1| 309 AKIYTAMWIGEASFEKAGFKYNQWTTLAFG 338
                                   *********666666667777777765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 2664.02
//
Query:       gi|91772547|ref|YP_565239.1|  [L=483]
Description: divergent AAA ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   64.0   0.1    3.5e-17   62.9   0.1    1.7  1  AlbA_2       Putative DNA-binding domain
     0.0033   17.5   0.0     0.0095   16.1   0.0    1.8  1  HATPase_c_4  Putative ATP-dependent DNA helicase recG C-termi
  ------ inclusion threshold ------
       0.15   11.2   2.6       0.24   10.5   2.6    1.2  1  Med3         Mediator complex subunit 3 fungal


Domain annotation for each model (and alignments):
>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   5.8e-21   3.5e-17       1     118 [.      14     125 ..      14     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 5.8e-21
                        AlbA_2   1 EdellEfKeslgnklkkrersiakticAfaNsegGtlliGVeDdgkvvGv.ecsdqeedqlrlelksiikrfkpkvlpdie 80 
                                   E  ++EfKe+ ++ +k+    +  ++cAf+N +gG++++GV Ddg v+G+ e+   +++++  +  +  ++++p++ +  e
  gi|91772547|ref|YP_565239.1|  14 EGLTVEFKECRNKLNKD----VYDSVCAFLNRSGGHIVLGVRDDGIVTGIdEDALPQIKKDLVTALNNPQKINPPLYILPE 90 
                                   7789******9999998....*****************************7666667777777777788999999999999 PP

                        AlbA_2  81 rvelkgkkvlvvkvekskkkplyeneegvvyiRrggss 118
                                   ++ +++k vl +++++s++ +   + +g+++ R+++ +
  gi|91772547|ref|YP_565239.1|  91 TIVIDEKFVLYLNIPESSQVH---HCNGKIFDRNEDGD 125
                                   9*****************999...66666666666554 PP

>> 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 !   16.1   0.0   1.6e-06    0.0095      28      79 ..     328     379 ..     311     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-06
                   HATPase_c_4  28 eskllegrssaRNelLasllerlrlmeergsGiqrilealee.aglpepefre 79 
                                    +  ++ ++  +N+++a+++++++ +ee gsG++   + ++  +g+++ +f+e
  gi|91772547|ref|YP_565239.1| 328 IN-PSNFTPYPKNPVIARVFKEIGRAEELGSGVRNLHKYTRIySGGNDTQFIE 379
                                   44.467778899**********************9998888744555666655 PP

>> Med3  Mediator complex subunit 3 fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.6   4.1e-05      0.24     199     230 ..     388     419 ..     383     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.1e-05
                          Med3 199 PrkPrqtkkaaakaaakaqaqaqaqaqaqqqv 230
                                   P  P+ t +a+a+a a+a aqa aq+ +q+ +
  gi|91772547|ref|YP_565239.1| 388 PVTPQATAQATAQATAQATAQATAQVEKQELI 419
                                   66788888888899999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3646.32
//
Query:       gi|91772548|ref|YP_565240.1|  [L=511]
Description: restriction modification system DNA specificity subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-44  150.7   0.1      5e-30  104.9   0.0    2.2  2  Methylase_S  Type I restriction modification DNA specificity 
  ------ inclusion threshold ------
        0.1   11.6   2.1       0.19   10.7   2.1    1.4  1  DUF3987      Protein of unknown function (DUF3987)
        7.2    7.1  10.0         22    5.5   0.4    3.3  3  V-SNARE      Vesicle transport v-SNARE protein N-terminus


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   8.4e-34     5e-30       2     164 ..      13     184 ..      12     187 .. 0.97
   2 !   43.6   0.2     6e-15   3.6e-11      36     162 ..     320     450 ..     286     456 .. 0.76

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 8.4e-34
                                   TT-EEEEHHHHEEEEE-----TT.GGTTT--EEEE-HHHCCT...........EE-HHHHCCTT---B-TT-EEEE-SSST CS
                   Methylase_S   2 edwevvkLgdvfeikkgktpkkk.elkengkypyiragilnn...........kvvkdglgykkkyilpkgdilissrati 70 
                                   +dw +  L+d++++ +g tpk+k  +++++++ +i++ +l++           +++  gl+++++ ++pkg++l+ssra+i
  gi|91772548|ref|YP_565240.1|  13 DDWVKGVLSDFGQVVSGGTPKTKvPEYWGEDILWITPADLSGysekyiykgrkSITHLGLKNSSARLIPKGSVLFSSRAPI 93 
                                   69******************************************************************************* PP

                                   T-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHH CS
                   Methylase_S  71 GkvayrdkkyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsq 151
                                   G++a++++++++nq++++lip  + +++ fly+yl+ +++  +    g+t+++l+ + ++++++ +Ppl+eQ  I++ ++q
  gi|91772548|ref|YP_565240.1|  94 GYIAIAGNELCTNQGFKTLIPS-EALNRDFLYYYLKSIKQLAEGRASGTTFKELSGKAFAELPLCVPPLPEQRAIVSKIEQ 173
                                   *********************8.78889************99999************************************ PP

                                   HHHHHHHHHHHHH CS
                   Methylase_S 152 ldntielekkikn 164
                                   l +  el ++i n
  gi|91772548|ref|YP_565240.1| 174 LFS--ELDNGIAN 184
                                   ***..99988765 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 6e-15
                                   -HHHCCT......EE-HHHHCCTT---B-TT-EEEE.-SSSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHH.HC CS
                   Methylase_S  36 ragilnn......kvvkdglgykkkyilpkgdilis.sratiGkvayrdkkyylnqsvivlipknkkkineflylyll.lk 108
                                   +     n      +v++d ++++k+  ++kgd+l++ +r +  kv +++++ ++++++ v++++++ ++n+  y++l+ ++
  gi|91772548|ref|YP_565240.1| 320 SK----NqgtltdEVKIDVINTVKN-SFKKGDLLYGkLRPYLNKVYLANEDGVCSTDILVFESIPSLDLNYSKYYFLSyKF 395
                                   33....2234455777888887766.566666666615699************************88888********888 PP

                                   HHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHH.HHHHHHHH CS
                   Methylase_S 109 lkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldn.tielekki 162
                                   +++++++s g++ p+++++ l+++++pl +leeQ+ I+  +++  + + + e+ i
  gi|91772548|ref|YP_565240.1| 396 VNDMTHNSSGVNLPRVSTKYLQEYPFPLFSLEEQQAIVTEIETRLSvCDKVEQDI 450
                                   99***********************************987776555555555555 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.1   3.3e-05      0.19      57     110 ..     223     280 ..     221     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.3e-05
                       DUF3987  57 lrpleeieaelreeyeeelkeyeaekkaweaelealekkaakak....eakaeealae 110
                                    ++le+i+ e +e+y+e+l e++++ k+we + ++ +k  + +k    e  +e++lae
  gi|91772548|ref|YP_565240.1| 223 KALLEQIQVEREESYNEKLDEWKRAVKEWEDAGKEGKKPTKPKKlkkiEPFTETELAE 280
                                   5799***************************999866655544443443333444433 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 ?    5.5   0.4    0.0037        22      22      62 ..     163     202 ..     158     205 .. 0.90
   2 ?    5.4   1.5     0.004        24      27      75 ..     212     253 ..     205     257 .. 0.79
   3 ?   -1.7   0.0      0.65   3.9e+03      21      38 ..     427     444 ..     415     462 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0037
                       V-SNARE  22 erkaalreiekkldeaeelldqMelEvrnlpsserasykak 62 
                                   e++a +++ie+ + e+++ + ++ l  ++l   +r+s+++k
  gi|91772548|ref|YP_565240.1| 163 EQRAIVSKIEQLFSELDNGIANLKLAQQQLK-VYRQSVLKK 202
                                   7899************************998.999999887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.004
                       V-SNARE  27 lreiekkldeaeelldqMelEvrnlpsserasykaklreykselkklkk 75 
                                    re +++l +a+ ll+q ++E +        sy++kl e+k+ +k++++
  gi|91772548|ref|YP_565240.1| 212 WREQQTDLPDAKALLEQIQVERE-------ESYNEKLDEWKRAVKEWED 253
                                   56777888888888888888866.......6799999999999999876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.65
                       V-SNARE  21 eerkaalreiekkldeae 38 
                                   ee+ a + eie++l  ++
  gi|91772548|ref|YP_565240.1| 427 EEQQAIVTEIETRLSVCD 444
                                   566666666666655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 3643.79
//
Query:       gi|91772549|ref|YP_565241.1|  [L=918]
Description: type III restriction enzyme, res subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-48  165.5   0.3    1.1e-48  165.5   0.3    3.1  4  EcoEI_R_C   EcoEI R protein C-terminal
    8.4e-40  136.6   0.0    2.5e-39  135.0   0.0    1.9  1  ResIII      Type III restriction enzyme, res subunit
    5.9e-19   68.6   0.1    5.9e-19   68.6   0.1    2.0  2  SWI2_SNF2   SWI2/SNF2 ATPase
      9e-11   42.1   0.1    1.4e-07   31.7   0.1    3.4  2  HSDR_N      Type I restriction enzyme R protein N terminus (H
    1.9e-09   37.5   0.0    8.2e-09   35.5   0.0    2.1  1  DEAD        DEAD/DEAH box helicase
    0.00014   22.2   0.1      0.001   19.4   0.0    2.5  3  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.093   13.1   0.0       0.23   11.8   0.0    1.6  1  AAA_19      AAA domain
      0.097   12.1   0.0       0.21   11.0   0.0    1.5  1  PhoH        PhoH-like protein


Domain annotation for each model (and alignments):
>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.6   8.1e+03      49     103 ..     245     295 ..     239     308 .. 0.70
   2 ?   -2.4   0.0         2   4.4e+03      66      82 ..     463     480 ..     422     494 .. 0.73
   3 ?    0.7   0.2      0.23   5.1e+02      51     101 ..     679     717 ..     610     732 .. 0.71
   4 !  165.5   0.3     5e-52   1.1e-48       2     168 ..     740     916 ..     739     917 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.6
                     EcoEI_R_C  49 itpealweayellekkvspq.ltdlidlirkiagldeeletrserverafkrwike 103
                                   ++ ++l++ y        +q   + i+ +  i+ + eel   +e+ + a k+w k+
  gi|91772549|ref|YP_565241.1| 245 YNVQRLRSNYISS----DSQvCISTIQHLYSILKG-EELDDEAETQNPAEKDWQKK 295
                                   5566667777333....334577778888888888.67888888888888888765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                     EcoEI_R_C  66 spq.ltdlidlirkiagl 82 
                                   +++ + d+i+++r+ +g+
  gi|91772549|ref|YP_565241.1| 463 TDShADDIIQIVREEFGE 480
                                   344588999999987775 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.23
                     EcoEI_R_C  51 pealweayellekkvspqltdlidlirkiagldeeletrserverafkrwi 101
                                   +++l+e             + lid+ r ++ +  el  + e v+r+ +++i
  gi|91772549|ref|YP_565241.1| 679 EQELQEQA----------QQELIDVARSTFSG--ELNEYIENVRRVHDQII 717
                                   22222222..........33788888888777..38888888888887776 PP

  == domain 4  score: 165.5 bits;  conditional E-value: 5e-52
                     EcoEI_R_C   2 eyvekfrkfieenkdsidaLqiiws....dreltkellkeLeekLkepppgitpealweayellek.kv.spq..ltdlid 74 
                                   e++ +f++++e nkd+i+aL i+++    +r++t++++ke  ekLk ++p+i+p+++w+aye+lek +  sp+  lt l++
  gi|91772549|ref|YP_565241.1| 740 ELISDFKAYMEANKDEITALNIFYNqpyqRRDVTFKMIKEVLEKLKLERPHIAPSRVWQAYEQLEKvSGnSPKneLTALVS 820
                                   67899*************************************************************877855567****** PP

                     EcoEI_R_C  75 lirkiagldeeletrserverafkrwikek.....kfteeqrewLelildhiaangvielddldeapefkqkgglgkaykl 150
                                   lir++   d  l+ ++ +v+r+f++w+++k     kf+e+q++wL++i+d++++++++el+dld++p f+++gg g++y+l
  gi|91772549|ref|YP_565241.1| 821 LIRRVTEIDPVLTAYDLTVNRNFQDWVFSKqagtlKFNEDQMNWLRMIKDYVSTSFHLELEDLDYTP-FDAMGGRGRMYQL 900
                                   *******************************************************************.************* PP

                     EcoEI_R_C 151 FGgkqeldeileelneel 168
                                   FG+  e++ +++elne+l
  gi|91772549|ref|YP_565241.1| 901 FGN--EMNVVISELNEAL 916
                                   ***..***********98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.0   1.1e-42   2.5e-39       4     170 ..     160     346 ..     157     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 1.1e-42
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                        ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke 84 
                                   lr++Q+ aienl+ ++k +++ ++l++maTG+GKT++a+ +i+rllk ++ +k+lflv++++l eq+++ef+ ++++++++
  gi|91772549|ref|YP_565241.1| 160 LRDCQIMAIENLERSFK-DNRPKALVQMATGSGKTYTAVTFIYRLLKYADAKKILFLVDTRNLGEQAEQEFMAYMPNDDNR 239
                                   89**************9.9999********************************************************988 PP

                                   .GEEEESSS-B--.......-SEEEEEHHHHHHTH...............................HHHTTT-SEEEEETG CS
                        ResIII  85 .igkkvsgdkkkakekdstnkkilvttiqsldadseee.......................eeeseellrdrfdviiiDEa 141
                                     ++ ++ ++ ++ ++ s++++++++tiq l+++++ e                         ++e    ++fd+i++DE+
  gi|91772549|ref|YP_565241.1| 240 kFTELYNVQRLRS-NYISSDSQVCISTIQHLYSILKGEelddeaetqnpaekdwqkkeplpVVYNENIPIEEFDFIVVDEC 319
                                   7778888888888.*********************8889*9999999999999999999888888888999999******* PP

                                   GGTTS.TTTHHHHHT---SEEEEEESS-S CS
                        ResIII 142 HrlgakkswreilekfkeavllglTATpe 170
                                   Hr+ + + w++ +++f+ ++l+glTATp+
  gi|91772549|ref|YP_565241.1| 320 HRSIY-NLWQQFIDYFD-SFLIGLTATPD 346
                                   *****.**********9.9*********7 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.1   2.6e-22   5.9e-19       2     207 ..     164     391 ..     163     410 .. 0.76
   2 ?   -2.3   1.3       1.3   2.8e+03     162     203 ..     731     774 ..     622     788 .. 0.44

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.6e-22
                     SWI2_SNF2   2 QyravekavervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka....geekpk 78 
                                   Q++a+e++ ++ k+ +r + ++   +GSGK++t v++  +ll+   + +k+++++D ++L +Q  ++f +     +++k +
  gi|91772549|ref|YP_565241.1| 164 QIMAIENLERSFKD-NRPKALVQMATGSGKTYTAVTFIYRLLK-YADAKKILFLVDTRNLGEQAEQEFMAYmpndDNRKFT 242
                                   88999998888887.5999************************.999**********************985544344556 PP

                     SWI2_SNF2  79 qaesrkeLkellekesekiifttiqKfe.....eeek.........................eklevlsereniivlvDEa 129
                                   +  + ++L+++  +++++++++tiq +      e  +                         +  e +  +e  +++vDE+
  gi|91772549|ref|YP_565241.1| 243 ELYNVQRLRSNYISSDSQVCISTIQHLYsilkgE--ElddeaetqnpaekdwqkkeplpvvyN--ENIPIEEFDFIVVDEC 319
                                   7888999999887889**********98677551..245567788999999998866665432..233333344899**** PP

                     SWI2_SNF2 130 HRsqygelakklrkalpnaafigFTGTPilkkdkktkevFg.eyidkYtikeaveDgavvpilYesrlaklelkeeek.l 207
                                   HRs y+  ++ +   + +  +ig+T TP    dk+t   F+ +++++Y  +eav+Dg+   + Y   ++++e++++ + +
  gi|91772549|ref|YP_565241.1| 320 HRSIYNLWQQFIDY-F-DSFLIGLTATP----DKRTFGFFNeNVVSEYGHEEAVADGVN--VGYDVYTIETEITKNGSqI 391
                                   *****988777754.4.5789*******....789*****64799************65..5566666666665554322 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                     SWI2_SNF2 162 dkktkevFgeyidkYt.ikeaveDgav.vpilYesrlaklelke 203
                                   dk+   + +e+i+ ++   ea +D+ + ++i+Y++ +++ +++ 
  gi|91772549|ref|YP_565241.1| 731 DKDAVVKADELISDFKaYMEANKDEITaLNIFYNQPYQRRDVTF 774
                                   34444444555555542346666665523466666666666655 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   6.1e-11   1.4e-07       5     193 ..       8     121 ..       4     122 .. 0.71
   2 ?   -3.6   0.0         4   9.1e+03     144     164 ..     794     814 ..     788     841 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.1e-11
                                   HHHHH.HHHHHHHHTT-EE................----SHHHHHHHHHHHHHHHH-HHHHHHHHTT--HHHHHHHHHTS- CS
                        HSDR_N   5 aeleqelidellrelGyqvlskkdveiegrrpe.vrkskaevaleknlreqlgalnikkltkrlalsdgnkefyellkegk 84 
                                   ++  ++ id+ l + G++vl+k++v ++ +r+  v++                                            
  gi|91772549|ref|YP_565241.1|   8 EQKARDSIDKKLTDSGWKVLNKNEVDWNASRGIaVKEY------------------------------------------- 45 
                                   55555566666666666666666666666655543333........................................... PP

                                   EEEETS-EEEEESS-SSSGGGS-EEEEE----SSSS---EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS---.---S. CS
                        HSDR_N  85 vkfkegrkknikLiDkknlenNrfqvvnQvtvtgnqkrrpDivlfvnglplvviElKrpgtieeAinQikryrkeksdvs. 164
                                                                     ++   +D+vlfvn  p+ +iE+K+               +e + +  
  gi|91772549|ref|YP_565241.1|  46 ---------------------------------STEVGPADYVLFVNKRPVGIIEAKK--------------NEEGHHLTv 79 
                                   .................................334459*******************..............233344445 PP

                                   .SSGGGGG-............-EEEEE-SS-EEEEE--SSSG CS
                        HSDR_N 165 .ipqlfrYl............qfgvisngketrfyaktkrre 193
                                    ++q+ +Y+            +f++ s gk tr+++++++++
  gi|91772549|ref|YP_565241.1|  80 vEEQAGEYAtsklkylkndplPFIYESTGKLTRYTDQRDPKP 121
                                   6778888888888888********************998875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4
                                   T-HHHHHHHHTSS---.---S CS
                        HSDR_N 144 gtieeAinQikryrkeksdvs 164
                                   + +++A++Q+++ + ++ +++
  gi|91772549|ref|YP_565241.1| 794 SRVWQAYEQLEKVSGNSPKNE 814
                                   478999999998887765544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.7e-12   8.2e-09       4     145 ..     164     334 ..     161     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.7e-12
                                   HHHHHHHHH.....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                   xxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   4 Qaeaiplil.....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                   Q  ai+++      +  + lv+++TGsGKT  ++  +++ +   k  +++k+l+++ tr L eq  +++  ++ + d r  
  gi|91772549|ref|YP_565241.1| 164 QIMAIENLErsfkdNRPKALVQMATGSGKTYTAVTFIYRLL---KYADAKKILFLVDTRNLGEQAEQEFMAYMPNDDNRKF 241
                                   55566666544443334899************999999777...689999************************8664544 PP

                                   EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH............................HCTSSHCTTEEEEEEETHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxx RF
                          DEAD  80 liiggvaardqlskldngvdivvgtpgrlddll............................stgklnlsqvrflVlDEadr 132
                                     + +v++    + ++++ ++ ++t + l ++l                             ++++ ++++ f+V+DE++r
  gi|91772549|ref|YP_565241.1| 242 TELYNVQR-LRSNYISSDSQVCISTIQHLYSILkgeelddeaetqnpaekdwqkkeplpvvYNENIPIEEFDFIVVDECHR 321
                                   44444444.4444555789999999999999888999999999999999999888888777667788************** PP

                                   HHHTTTHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                          DEAD 133 lldqgfsdfinri 145
                                      +  ++fi+  
  gi|91772549|ref|YP_565241.1| 322 SIYNLWQQFIDYF 334
                                   **99999988873 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 ?   -1.9   0.0       1.9   4.3e+03       5      35 ..     199     233 ..     196     263 .. 0.67
   2 !   19.4   0.0   4.6e-07     0.001      12     109 ..     450     551 ..     440     553 .. 0.84
   3 ?   -2.8   0.0       3.4   7.7e+03      40      63 ..     620     643 ..     607     649 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.9
                                   HHHHHHHHTTTTSEEEEEESSHH...HHHH..HHHH CS
                    Helicase_C   5 allellkleeeggkilifvntid...rlek..vkll 35 
                                    +++ll + ++ +kil  v t++   ++e+  + ++
  gi|91772549|ref|YP_565241.1| 199 FIYRLL-KYADAKKILFLVDTRNlgeQAEQefMAYM 233
                                   678888.78999999999999997654433445555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 4.6e-07
                                   HTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSSSTSTTESEE CS
                    Helicase_C  12 leeeggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfnkgesd.vLiatdvaerGidipkvnlV 88 
                                    +ee  k+lif++t +++++ +++++e++  g  +++       ++ + +l+qf+++    + ++ d++++G d++ ++++
  gi|91772549|ref|YP_565241.1| 450 GREEVPKTLIFAKTDSHADDiIQIVREEFgeGNAFCKKVTYKVEEDPKSVLSQFRNDYNPrIAVTVDMIATGTDVKPLECL 530
                                   567889************989999999997644444444446678889******987777899****************** PP

                                   EESSSSSSHHHHHHHHTTSSS CS
                    Helicase_C  89 infdlprnvtsyiqriGRtgR 109
                                    ++   ++   + q++GR  R
  gi|91772549|ref|YP_565241.1| 531 LFMRDVKSRNYFEQMKGRGTR 551
                                   ******************988 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.4
                                   TSTEEEESTTSTHHHHHHHHHHHH CS
                    Helicase_C  40 gikvavlhgelpqnereeileqfn 63 
                                   + + a+l+ +++ +er    e+ n
  gi|91772549|ref|YP_565241.1| 620 ASRLARLNKQITEDERATFAEKAN 643
                                   467899999999999999888876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.23      12     112 ..     181     320 ..     173     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                        AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae........................ 68 
                                     lv    G+GKT++ ++ +  l++  +   ++il +  t+   ++ +++  ++ ++                        
  gi|91772549|ref|YP_565241.1| 181 KALVQMATGSGKTYTAVTFIYRLLKYADA--KKILFLVDTRNLGEQAEQEF-MAYMPnddnrkftelynvqrlrsnyissd 258
                                   56777889*****************9965..8****999998777777776.44444689999999999999999999999 PP

                        AAA_19  69 ....atTiHrlal................ldfddlltealelleeaeeekklqeee.llivDEfq 112
                                       ++Ti +l                   + d +++e+l +    +e+ ++ ee+  ++vDE  
  gi|91772549|ref|YP_565241.1| 259 sqvcISTIQHLYSilkgeelddeaetqnpAEKDWQKKEPLPV--VYNENIPI-EEFdFIVVDECH 320
                                   999988888774477887766666665553333333334444..44788899.555599999975 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.2e-05      0.21      27      76 ..     187     241 ..     164     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.2e-05
                                   -TTSSTTHHHHHHHHHHHHTTS-SEEEE...EE-S--T..T----SS-------- CS
                          PhoH  27 paGtGKtylavalavealkkkkvkriil...trpavea..geelGflpgdleekv 76 
                                    +G+GKty av+   ++lk  + k+i++   tr+  e   +e + ++p d + k+
  gi|91772549|ref|YP_565241.1| 187 ATGSGKTYTAVTFIYRLLKYADAKKILFlvdTRNLGEQaeQEFMAYMPNDDNRKF 241
                                   69*******************9999987223466554445556788888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (918 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 5960.22
//
Query:       gi|91772550|ref|YP_565242.1|  [L=633]
Description: Cache sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-33  116.0   0.0    2.4e-33  115.0   0.0    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.6e-21   76.1   4.6    3.6e-21   76.1   4.6    2.4  2  dCache_1     Cache domain
    1.3e-16   60.4   0.4    8.7e-16   57.7   0.1    2.6  2  HisKA        His Kinase A (phospho-acceptor) domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.025   14.4   0.0    1.5  1  sCache_2     Single Cache domain 2
      0.013   15.4   0.0      0.037   13.9   0.0    1.8  1  HATPase_c_5  GHKL domain
      0.024   14.3   0.0      0.024   14.3   0.0    2.2  2  FixS         Cytochrome oxidase maturation protein cbb3-type
      0.025   13.7   1.8      0.076   12.2   0.0    2.2  2  dCache_2     Cache domain
      0.049   13.6   0.0      0.092   12.7   0.0    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain
       0.14   11.5   0.2        1.6    8.1   0.0    2.6  3  CoA_trans    Coenzyme A transferase
       0.28   10.0   2.5       0.78    8.6   0.1    2.5  3  Spc7         Spc7 kinetochore protein


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 !  115.0   0.0   1.4e-36   2.4e-33       2     110 ..     516     625 ..     515     627 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 1.4e-36
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   de rL  +++n+vdNa+kf++++g i + +  +e++l+++v+D+GiGipke +++lf+kf+q d+s +r++ggtGlGl+i+
  gi|91772550|ref|YP_565242.1| 516 DEARLVDMLNNIVDNAIKFTPPGGMIILGVFDDENYLHLTVSDTGIGIPKELIPNLFKKFYQiDSSIRRKYGGTGLGLYIC 596
                                   899****************8899999888886789********************************************** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                   kk+v+ + Geiw+esep++Gtt++++lp+
  gi|91772550|ref|YP_565242.1| 597 KKIVDAHSGEIWIESEPHKGTTVHIRLPK 625
                                   **************************996 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   4.6     2e-24   3.6e-21      11     246 ..      45     292 ..      36     294 .. 0.73
   2 ?    0.6   0.1      0.22   3.9e+02      13      71 ..     462     531 ..     453     608 .. 0.54

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 2e-24
                      dCache_1  11 llglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksn...................p 72 
                                   + + a  +an+++++++s  + a+t+as+ ++ +          ++re+++++lk+il  n                   +
  gi|91772550|ref|YP_565242.1|  45 SIEKASNYANKFNSDMQSNMAMARTIASTLTVYN---------SSDREEVNDILKEILIDNpnligtytafepnafdgkdA 116
                                   55668899********999999999999855433.........689************99933443333333333333332 PP

                      dCache_1  73 disgvylvdadGqviassdpssppnleg.......tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiydd 146
                                    + g   +d+ G+++   +++   n+ g       +  +  +d+y+ +++ +  + v ++ y +   g++++++++pi  d
  gi|91772550|ref|YP_565242.1| 117 EYAGTEGYDSTGRLV---PYW---NKIGgtifmepLLYYEISDYYQLPKQLE--QEVLTESYLY-Q-GELIVSYVSPIIRD 187
                                   223455555677664...333...22224567888667777***********..6668888974.5.79**********86 PP

                      dCache_1 147 sgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd.kdllgknlrdelkaq......ealekalakiesg 220
                                    g+fiG+ ++d++l+++++++sn+   etgy+f  +++G++++hp  kd++gk+  + l+++      +     +   ++g
  gi|91772550|ref|YP_565242.1| 188 -GEFIGIGGVDVSLNYIDEIVSNVTAFETGYAFTTSNTGMLLSHPVhKDWIGKKTLNDLNDSeitfmaD----NIRVGQGG 263
                                   .***************************************************99888888887854441....33333333 PP

                      dCache_1 221 vssvk..lngeeylvayapip.tglgWyl 246
                                     ++    +ge+ ++ y p++ ++   +l
  gi|91772550|ref|YP_565242.1| 264 HIETVdpTTGEDVIIFYEPVRtGNYSFIL 292
                                   33222126779**999*****54444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                      dCache_1  13 glaeqlanniedvldslenlaetlasnps.lqdlleepnra.............neasreslqallksilksn 71 
                                    +++  a+ ie+++++ + +a+ +++++     l+ee n +              ea++++l ++l++i++  
  gi|91772550|ref|YP_565242.1| 462 YISQAQAEIIEYDFKECY-IAKIISNTIMdTIMLVEE-N-DlhiekkipsdlptIEADEARLVDMLNNIVDNA 531
                                   567788889999998854.555555554422223333.3.235888888888888888888888888887533 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 !   57.7   0.1   4.9e-19   8.7e-16       2      66 ..     402     468 ..     401     469 .. 0.92
   2 ?   -1.4   0.0       1.4   2.4e+03      41      60 ..     510     529 ..     503     531 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 4.9e-19
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                   +  fl++v+HELrtPL++i+g+++ L +e  g+ + ++k  let+ ++a+rl++lv+ lL +s+ +a
  gi|91772550|ref|YP_565242.1| 402 KDVFLSNVSHELRTPLTSIKGYTQNLYDEslGDINGSQKTSLETVLRNADRLRRLVDSLLYISQAQA 468
                                   6679**********************77779667799**************************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHHHHHH CS
                         HisKA  41 letiesearrldhlvedlLd 60 
                                   l tie  + rl ++++++ d
  gi|91772550|ref|YP_565242.1| 510 LPTIEADEARLVDMLNNIVD 529
                                   66899999999999999865 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05     0.025      43     106 ..     205     265 ..     199     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                      sCache_2  43 elvnglkfgdGkgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggf 106
                                   e+v++ +  +  gY f + ++g ll hP+ ++++Gk+  n  + +  +++ + ++ ++  gg++
  gi|91772550|ref|YP_565242.1| 205 EIVSNVTAFE-TGYAFTTSNTGMLLSHPVHKDWIGKKTLNDLNDSEITFMADNIRVGQ--GGHI 265
                                   5666666677.9************************9877555555666666666666..5555 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.1e-05     0.037       5      92 ..     519     614 ..     515     623 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                   HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg............ekkklesskskkeehGiGlks 73 
                                    l+ +l n+ dNAi           +I l v  +++ l ++++ +  g              +   s  +k +  G+Gl  
  gi|91772550|ref|YP_565242.1| 519 RLVDMLNNIVDNAIKFTPP----GGMIILGVFDDENYLHLTVSDTGIGipkelipnlfkkFYQIDSSIRRKYGGTGLGLYI 595
                                   5778999999**9988766....346666666666666666666654444444443331033334466889999******* PP

                   HATPase_c_5  74 ireivkkykgnlsieaedg 92 
                                    ++iv+ ++g+++ie e +
  gi|91772550|ref|YP_565242.1| 596 CKKIVDAHSGEIWIESEPH 614
                                   **************98865 PP

>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.024       3      33 ..      10      40 ..       9      44 .. 0.95
   2 ?   -3.6   3.8       5.6     1e+04       7      25 ..     312     330 ..     310     331 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                          FixS  3 LylLiplSlllgllalaaFlWavksGQFDDl 33
                                  L++ i+lS+ll+++a  a + +  + Q +Dl
  gi|91772550|ref|YP_565242.1| 10 LIIYIGLSVLLVMAATTAIIISTSTSQHEDL 40
                                  7899**************************8 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.6
                          FixS   7 iplSlllgllalaaFlWav 25 
                                   ++ S+ l+++a aa l a+
  gi|91772550|ref|YP_565242.1| 312 LISSIALIFMAGAAYLVAI 330
                                   5568889999999888876 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.8      0.27   4.9e+02      34      81 ..      45      89 ..      30      98 .. 0.68
   2 ?   12.2   0.0   4.3e-05     0.076      80     138 ..     202     259 ..     199     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.27
                      dCache_2 34 lieyeknsleeslkesLksrveeaysiaeeiyekyknelseeeakkli 81
                                  +i  + ++  ++++++++s + +a++ia+ +   + +  + ee+   +
  gi|91772550|ref|YP_565242.1| 45 SI-EKASNYANKFNSDMQSNMAMARTIASTLTVYNSS--DREEVNDIL 89
                                  33.4667788899999999999999999887665444..444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.3e-05
                      dCache_2  80 likealrsirydggegyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremikl 138
                                    i e++++++  +++gy f  + +g+l+ hp +++  Gk++l+  ++++  ++ + i+ 
  gi|91772550|ref|YP_565242.1| 202 YIDEIVSNVT-AFETGYAFTTSNTGMLLSHPVHKDWIGKKTLNDLNDSEITFMADNIRV 259
                                   5778999999.999999999999999999999999999888888888888888887765 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.1e-05     0.092      39     123 ..     523     621 ..     514     623 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-05
                   HATPase_c_2  39 actNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikglvDev 112
                                   +++N+v  a +  p  g + + + +de+ l+++v+D G g + e +p+  ++ +        +    G+Gl++ k++vD  
  gi|91772550|ref|YP_565242.1| 523 MLNNIVDNAIKFTPpGGMIILGVFDDENYLHLTVSDTGIGIPKELIPNLFKKFYqidssiRRKYGGTGLGLYICKKIVDAH 603
                                   678888888888888899999999999*************999988887765559999998999999************99 PP

                   HATPase_c_2 113 ..ey.....dgegnvvtm 123
                                     e+       +g++v++
  gi|91772550|ref|YP_565242.1| 604 sgEIwiesePHKGTTVHI 621
                                   665577653334777776 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.88   1.6e+03     150     212 ..      25      95 ..      15      96 .. 0.65
   2 ?   -0.5   0.0      0.38   6.9e+02       9      45 ..     182     215 ..     177     266 .. 0.76
   3 ?    8.1   0.0    0.0009       1.6      25      67 ..     560     602 ..     548     616 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.88
                                   EEEEEECCEEETTCSEESSGGGHTTHSHHHHH.........HEEEEEEEEEEEECTTSSECCCESBTGGGHS CS
                     CoA_trans 150 dvalikaskadeegnlvfeksagnfnkpaiae.........aakvtileveeivekgkldpekvliPgvlvd 212
                                   + a+i  +  ++++ l+++ks  + + +++++         a  +ti++ + +    ++  ++ +   +l+d
  gi|91772550|ref|YP_565242.1|  25 TTAIIISTSTSQHEDLAYKKSIEKAS-NYANKfnsdmqsnmAMARTIASTLTVYNSSDREEVNDILKEILID 95 
                                   45566666666777888888777777.444445666677777888888888887777776666666666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.38
                                   CTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEE CS
                     CoA_trans   9 akeikdGmtvavGGFgligiPealiaalarsgvkdlt 45 
                                   +  i+dG+ + +G   ++    + i++++ +  + +t
  gi|91772550|ref|YP_565242.1| 182 SPIIRDGEFIGIG---GVDVSLNYIDEIVSNVTAFET 215
                                   55799********...566777778777777655555 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0009
                                   TBTHHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEE CS
                     CoA_trans  25 ligiPealiaalarsgvkdltviiseagvlglgplllngsvkk 67 
                                   +igiP++li +l +++++ +  i  + g++glg+++ ++ v++
  gi|91772550|ref|YP_565242.1| 560 GIGIPKELIPNLFKKFYQIDSSIRRKYGGTGLGLYICKKIVDA 602
                                   69*********************************99988876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00043      0.78      66     105 ..      70     109 ..      31     110 .. 0.89
   2 ?    0.2   0.1      0.15   2.7e+02     143     174 ..     373     404 ..     367     458 .. 0.65
   3 ?   -2.2   0.0      0.83   1.5e+03      93     108 ..     569     584 ..     565     586 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00043
                          Spc7  66 screLkkyisegrkiireieeetleenPpLfreYmeadpd 105
                                   + + L+ y s  r+ +++i +e+l +nP L+  Y + +p+
  gi|91772550|ref|YP_565242.1|  70 IASTLTVYNSSDREEVNDILKEILIDNPNLIGTYTAFEPN 109
                                   6778999***************************987775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                          Spc7 143 gleenlegleedkelLekqeeeldellpelee 174
                                   gl+++l++l+  ++ Lek ++el++l +  + 
  gi|91772550|ref|YP_565242.1| 373 GLNDILDSLQIYSNDLEKANKELKSLDQMKDV 404
                                   55555555555555555555555555444333 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.83
                          Spc7  93 PpLfreYmeadpdvka 108
                                   P Lf++++++d++++ 
  gi|91772550|ref|YP_565242.1| 569 PNLFKKFYQIDSSIRR 584
                                   9**********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 4028.53
//
Query:       gi|91772551|ref|YP_565243.1|  [L=50]
Description: response regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   36.9   0.1    4.8e-09   36.7   0.1    1.0  1  HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like A


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 !   36.7   0.1   2.7e-13   4.8e-09      69     111 ..       4      46 ..       1      47 [. 0.90

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.7e-13
                                   HTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                     HATPase_c  69 rggggtGlGlsivkklvelmgGeiwvesepgrGttftftlple 111
                                     ++gt lGl++vk++ve++gG+iwv+se + G+ ftft+ l+
  gi|91772551|ref|YP_565243.1|   4 KAQQGTWLGLTLVKRFVEMHGGSIWVKSEVNAGSNFTFTIHLK 46 
                                   568999********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 327.39
//
Query:       gi|91772552|ref|YP_565244.1|  [L=185]
Description: XRE family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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   60.1   3.2    7.8e-09   35.9   0.4    2.3  2  CBS             CBS domain
    8.8e-13   48.1   0.4    2.8e-12   46.5   0.1    2.0  2  HTH_3           Helix-turn-helix
    3.8e-10   39.9   0.3    9.5e-10   38.7   0.3    1.6  1  HTH_31          Helix-turn-helix domain
      3e-07   30.4   0.1      6e-07   29.4   0.1    1.5  1  HTH_19          Helix-turn-helix domain
    1.6e-05   25.3   0.4    5.1e-05   23.6   0.1    2.1  2  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00015   21.5   0.1    0.00041   20.2   0.2    1.6  2  HTH_25          Helix-turn-helix domain
     0.0017   18.3   0.2     0.0095   15.9   0.1    2.1  2  HTH_37          Helix-turn-helix domain
     0.0043   16.5   0.0        1.1    8.8   0.1    2.5  2  Sigma70_r4      Sigma-70, region 4
      0.008   15.9   0.0        0.3   10.9   0.0    2.3  2  TetR_N          Bacterial regulatory proteins, tetR family
     0.0087   16.0   0.0       0.08   12.9   0.0    2.5  2  Pou             Pou domain - N-terminal to homeobox domain
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.25   11.3   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.12   12.5   0.0        0.4   10.8   0.0    1.8  2  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.4   5.2e-12   7.8e-09       1      55 [.      66     119 ..      66     121 .. 0.94
   2 !   24.8   0.1   1.5e-08   2.2e-05       1      56 [.     132     184 ..     132     185 .] 0.91

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.2e-12
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   ++dim++ v++v+ ++++e a+ lm+e+g+s++PV+ ++g +vG +++  +++++
  gi|91772552|ref|YP_565244.1|  66 ARDIMHTLVIFVSSEDSVESAVHLMEENGFSQVPVI-DQGVPVGSISEDTIIKVM 119
                                   589****9*****************9999*******.6*************9976 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.5e-08
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   ++dim + ++tv+p+t l e+  ++ e++  +++VV e g   G vt++D++++l+
  gi|91772552|ref|YP_565244.1| 132 IRDIMGDAFPTVSPTTELNEISHML-ERN-PAVLVV-EKGVTTGFVTKHDVIKLLH 184
                                   589**********************.656.5999**.9**777**********997 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1   1.9e-15   2.8e-12       1      49 [.       9      57 ..       9      60 .. 0.96
   2 ?   -2.7   0.0       4.3   6.4e+03      17      29 ..     123     135 ..     119     136 .. 0.62

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.9e-15
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                  l+++R+ l l+q eLA+++Gvs+  i+riE G+  P+l+tl k++ a+ 
  gi|91772552|ref|YP_565244.1|  9 LRQKRLDLALTQSELAKRAGVSQPLIARIEAGDVDPRLSTLRKICTAFE 57
                                  89*******************************************9985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                                   HHHTSSHHHHHHH CS
                         HTH_3  17 eklGvsrstisri 29 
                                   +++++s+  i++i
  gi|91772552|ref|YP_565244.1| 123 KASDISQMRIRDI 135
                                   4455666666655 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.3   6.4e-13   9.5e-10       5      54 ..       8      56 ..       6      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 6.4e-13
                        HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                  +Lr+ R    L+q e+A+r+gvs+  + r+E G  + p++++l+++++a+
  gi|91772552|ref|YP_565244.1|  8 RLRQKRLDLALTQSELAKRAGVSQPLIARIEAGDVD-PRLSTLRKICTAF 56
                                  788888889**************************7.**********996 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1     4e-10     6e-07       2      54 ..       7      58 ..       7      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4e-10
                        HTH_19  2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgi 54
                                  erL++ R  l ltq ela+r+g+s+  i+ iE g   +p  ++l+ki+ a++ 
  gi|91772552|ref|YP_565244.1|  7 ERLRQKRLDLALTQSELAKRAGVSQPLIARIEAGDV-DPRLSTLRKICTAFEE 58
                                  8*********************************99.*************997 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 !   23.6   0.1   3.4e-08   5.1e-05       8      51 ..      15      57 ..       8      58 .. 0.88
   2 ?   -2.0   0.1       3.4   5.1e+03       4      16 ..     117     130 ..     114     138 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.4e-08
                        HTH_26  8 drgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                  d  +t+seLa+++g+s++ ++r+  g +  ++l+tL kiC+a++
  gi|91772552|ref|YP_565244.1| 15 DLALTQSELAKRAGVSQPLIARIEAGDV-DPRLSTLRKICTAFE 57
                                  55679**********************6.************985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                        HTH_26   4 elmadrgi.tkseL 16 
                                   ++m dr+   +s++
  gi|91772552|ref|YP_565244.1| 117 KVMTDRKAsDISQM 130
                                   67777776555555 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   2.7e-07   0.00041       1      36 [.       8      43 ..       8      45 .. 0.97
   2 ?   -3.6   0.0       7.3   1.1e+04      28      39 ..      88      99 ..      85     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                                  HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                        HTH_25  1 rLraaRearglsleevaketkIrkdylealEeddfd 36
                                  rLr++R+ + l+  e+ak+  +++ ++ ++E++d+d
  gi|91772552|ref|YP_565244.1|  8 RLRQKRLDLALTQSELAKRAGVSQPLIARIEAGDVD 43
                                  7********************************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.3
                                  HHHHCT--TTSS CS
                        HTH_25 28 ealEeddfdalp 39
                                  + +Ee+ f++ p
  gi|91772552|ref|YP_565244.1| 88 HLMEENGFSQVP 99
                                  668999998877 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.3e-06    0.0095      23      57 ..       9      43 ..       6      57 .. 0.82
   2 ?   -0.7   0.0      0.92   1.4e+03      27      50 ..     122     145 ..     113     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.3e-06
                                  HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--T CS
                        HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgkls 57
                                  +++++ ++ l+qse+a++ g++qP + r++ g+++
  gi|91772552|ref|YP_565244.1|  9 LRQKRLDLALTQSELAKRAGVSQPLIARIEAGDVD 43
                                  567777889*********************99986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.92
                                   HHHCT--HHHHHHHHT--HHHHHH CS
                        HTH_37  27 iekrelsqseaaqllgiaqPkvsr 50 
                                   +++ ++sq  +  ++g a P vs 
  gi|91772552|ref|YP_565244.1| 122 RKASDISQMRIRDIMGDAFPTVSP 145
                                   566678888888888888887776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00075       1.1      20      41 ..      17      38 ..       8      40 .. 0.81
   2 !    5.3   0.0    0.0094        14      31      45 ..     126     140 ..     123     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00075
                                  T--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4 20 glTleEIgerlgiSrerVrqie 41
                                   lT++E+++r g+S+  + +ie
  gi|91772552|ref|YP_565244.1| 17 ALTQSELAKRAGVSQPLIARIE 38
                                  69************97776666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0094
                                   TS-HHHHHHHHHHHH CS
                    Sigma70_r4  31 giSrerVrqiekrAl 45 
                                   +iS++r+r i+ +A+
  gi|91772552|ref|YP_565244.1| 126 DISQMRIRDIMGDAF 140
                                   79********98886 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0002       0.3      16      33 ..      17      34 ..      16      36 .. 0.89
   2 ?    2.7   0.0     0.075   1.1e+02       3      18 ..      84      99 ..      83     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                  T--HHHHHHHHTSSHHHH CS
                        TetR_N 16 attvreIAkrAGvskgal 33
                                  a+t +e+AkrAGvs++++
  gi|91772552|ref|YP_565244.1| 17 ALTQSELAKRAGVSQPLI 34
                                  67889**********988 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.075
                                  HHHHHHHHHHHTTT-- CS
                        TetR_N  3 daArelfaerGydatt 18
                                  + A+ l++e+G++++ 
  gi|91772552|ref|YP_565244.1| 84 ESAVHLMEENGFSQVP 99
                                  689*********9885 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   5.4e-05      0.08      11      52 ..       7      42 ..       4      52 .. 0.85
   2 ?   -1.1   0.0       1.3   1.9e+03      25      42 ..      81      98 ..      77     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.4e-05
                           Pou 11 kefkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdl 52
                                  ++++qkR+ l ltQ+++++         +Sq  I r+E+ d+
  gi|91772552|ref|YP_565244.1|  7 ERLRQKRLDLALTQSELAKR------AGVSQPLIARIEAGDV 42
                                  789***********998876......6789999999998665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                           Pou 25 advglaLgklygkefSqt 42
                                    v++a + +  + fSq 
  gi|91772552|ref|YP_565244.1| 81 DSVESAVHLMEENGFSQV 98
                                  578999999999999996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00017      0.25      16      40 ..      11      36 ..       1      37 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                  C.EEEEEHHHHHHHHHTTSSHHHHHH CS
                     HTH_Crp_2 16 g.eielpltqeelAsmlGltretvsr 40
                                  + +++l ltq elA + G+++  + r
  gi|91772552|ref|YP_565244.1| 11 QkRLDLALTQSELAKRAGVSQPLIAR 36
                                  34799***************977666 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 ?   10.8   0.0   0.00027       0.4      70     115 ..       5      50 ..       1      60 [. 0.90
   2 ?   -1.2   0.0       1.4   2.1e+03      74      94 ..     118     138 ..     103     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                MqsA_antitoxin  70 dpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvk 115
                                    p+ +++ r  l l+q+e+a+  G+     +r e+G v p l++++
  gi|91772552|ref|YP_565244.1|   5 TPERLRQKRLDLALTQSELAKRAGVSQPLIARIEAGDVDPRLSTLR 50 
                                   57888999999******************************99875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                MqsA_antitoxin  74 iarvrkkleldqreaaeifGg 94 
                                   ++  rk+ +++q  + +i+G 
  gi|91772552|ref|YP_565244.1| 118 VMTDRKASDISQMRIRDIMGD 138
                                   444467777777777777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1342.04
//
Query:       gi|91772553|ref|YP_565245.1|  [L=340]
Description: hypothetical protein Mbur_0513 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   16.5   1.9       0.38   10.7   0.1    3.0  3  Cadherin_5   Cadherin-like domain
  ------ inclusion threshold ------
       0.17   10.7   0.1       0.28   10.0   0.1    1.3  1  Say1_Mug180  Steryl acetyl hydrolase


Domain annotation for each model (and alignments):
>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   4.3e-05      0.38      45      70 ..      46      70 ..      28      76 .. 0.75
   2 !    3.7   0.0    0.0067        60      17      39 ..     105     127 ..      97     140 .. 0.88
   3 ?   -1.6   0.1      0.29   2.6e+03      55      70 ..     261     276 ..     212     299 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.3e-05
                    Cadherin_5 45 sltadaenGtvvdngdGtftftpean 70
                                  s+ a++++G+ vdngdGtftft + +
  gi|91772553|ref|YP_565245.1| 46 SIMAASNEGS-VDNGDGTFTFTQQVD 70
                                  2334555676.69*********8766 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0067
                    Cadherin_5  17 seDtaltitaaqLLanasDvdgd 39 
                                   + D +lti++ +L+ +a Dvd++
  gi|91772553|ref|YP_565245.1| 105 ATDANLTINSVKLIIKAWDVDSN 127
                                   6799*****************75 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.29
                    Cadherin_5  55 vvdngdGtftftpean 70 
                                   ++d gd t t  p+a+
  gi|91772553|ref|YP_565245.1| 261 FADRGDHTGTTVPAAD 276
                                   3355555555555555 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   3.2e-05      0.28     282     309 ..     173     200 ..     167     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.2e-05
                   Say1_Mug180 282 defvnieknfdievWseilekckllity 309
                                   + f++i++n + ++W   l+ +kl++ty
  gi|91772553|ref|YP_565245.1| 173 NVFIDIDMNHNEDTWATTLDSSKLVVTY 200
                                   679************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2421.91
//
Query:       gi|91772554|ref|YP_565246.1|  [L=380]
Description: phosphoserine aminotransferase / L-aspartate aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-45  153.7   0.0      8e-45  153.4   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
     0.0034   17.4   1.1     0.0077   16.3   0.4    2.0  2  Lin0512_fam      Conserved hypothetical protein (Lin0512_fam)
  ------ inclusion threshold ------
      0.028   13.7   0.3      0.047   13.0   0.3    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
      0.062   12.5   0.0        0.1   11.8   0.0    1.4  2  Aminotran_1_2    Aminotransferase class I and II
      0.075   12.3   0.1       0.15   11.3   0.1    1.4  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 !  153.4   0.0   2.2e-48     8e-45       3     342 ..       8     328 ..       6     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 2.2e-48
                                   EBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCC CS
                   Aminotran_5   3 ldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalsla 82 
                                   l+++++ ++ ++Vl+a++            ++ h+gke++++++++++ ++e++++e+  ++  +sG+++ ++++++ +  
  gi|91772554|ref|YP_565246.1|   8 LMMPGPVPVAPRVLRAMSRP----------MINHRGKEFSAMFDDCTTMLKEIFQTEN--DLFTISGSGTaSMEAALGCT- 75 
                                   77777777777888777777..........89*************************8..55566666654899888888. PP

                                   CC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHH CS
                   Aminotran_5  83 rslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigk 163
                                     ++++d++v+ e+++ +++   +++a r g +v+ ++ +++ ++dld +e++l+e +k+v++ h++++ G+ +p  e+g 
  gi|91772554|ref|YP_565246.1|  76 --IDKDDKVVTIENGKFGER--FKDIAARYG-QVVPVECEWGTSVDLDVVEEKLAEGAKAVTMVHNETSAGIRNPALEVGM 151
                                   ..9*****************..*****8877.666********************************************** PP

                                   HHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEEEH CS
                   Aminotran_5 164 lakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl.eettfa 242
                                   lakk+gal+++D+++++g   ++v+++gvD+++++++K + +P+G+++l+v++++ e++++  l+ + ++ + + +++  +
  gi|91772554|ref|YP_565246.1| 152 LAKKYGALFIMDGVTSIGGDDVKVDEWGVDIAVVGSQKcIAAPPGLSMLSVSERAFEAMNKENLPYY-LDLKAYqKSAAKS 231
                                   ***********************************************************88777765.8888886777788 PP

                                   CTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE..TTCSH CS
                   Aminotran_5 243 eapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf..kgvha 321
                                   ++p+     Tp v+ + gl++al++++e g++a  k++++ a+++++++++++   + + + + + +s+vs     +gv++
  gi|91772554|ref|YP_565246.1| 232 QTPY-----TPAVPLFFGLQEALKIVMEEGMDARIKRQATGAAAVRAAMDAIGIEMFPQLNATSAYSSTVSAMKspEGVDS 307
                                   8898.....*******************************************9988877666777777777665579**** PP

                                   HHHHHHHHHTTEEEEEE-TTT CS
                   Aminotran_5 322 edvatlLdeegIavrsGhhca 342
                                   +d+++ + ++gI + +G++ +
  gi|91772554|ref|YP_565246.1| 308 NDIKNGMMDKGIIIAGGQNRL 328
                                   *****************9877 PP

>> Lin0512_fam  Conserved hypothetical protein (Lin0512_fam)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4     5e+03      63      84 ..     113     134 ..     105     142 .. 0.78
   2 !   16.3   0.4   2.1e-06    0.0077       2      51 ..     251     299 ..     250     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                   Lin0512_fam  63 ekvdleavkavlPygevevevv 84 
                                   ++vdl+ v++ l  g + v++v
  gi|91772554|ref|YP_565246.1| 113 TSVDLDVVEEKLAEGAKAVTMV 134
                                   6789999999998888888776 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.1e-06
                   Lin0512_fam   2 livelGmGvdlhgqdvtkAAvrAvkdAisrnslpglaeilglpkedldem 51 
                                   +++e Gm + +++q +  AAvrA  dAi   + p+l ++  ++++ +++m
  gi|91772554|ref|YP_565246.1| 251 IVMEEGMDARIKRQATGAAAVRAAMDAIGIEMFPQLNATSAYSST-VSAM 299
                                   789********************************9999776633.5555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.3e-05     0.047      15     168 ..      21     164 ..      16     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                                   HHHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-..HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHC CS
               Beta_elim_lyase  15 sdaqaaamlGdesYgedktvnrLedavaelfgkeaalfvpq..GtaAnsillkillqrgeevivtepahihfdetgaiael 93 
                                    +a+++ m+ +   + +  + +    ++e+f +e  lf+ +  Gta+ + +l   + + ++v+  e++ +  +    +a +
  gi|91772554|ref|YP_565246.1|  21 LRAMSRPMINHRGKEFSAMFDDCTTMLKEIFQTENDLFTISgsGTASMEAALGCTIDKDDKVVTIENGKFGERFKDIAARY 101
                                   5566666666666666777777888999***********973366666777777776666665555555444444555555 PP

                                   C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
               Beta_elim_lyase  94 agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                   ++v +++++      +dl+ +e++++e ga  + + ++  ++      G   +     ev  +akkyg  +++Dg
  gi|91772554|ref|YP_565246.1| 102 GQVVPVECEWGT--SVDLDVVEEKLAE-GA--KAVTMVHNETSA----GIRNP---ALEVGMLAKKYGALFIMDG 164
                                   888777777766..9************.66..566666544444....44333...4578889999999999998 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 ?   11.8   0.0   2.8e-05       0.1      66     187 ..      52     163 ..      39     230 .. 0.82
   2 ?   -3.6   0.0       1.3   4.8e+03     274     302 ..     257     285 ..     245     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                                   TGGEGEEEESHHHHHHHHHHHHHHHTTT-E.EEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCT CS
                 Aminotran_1_2  66 kreaavvvgsGagaliealifllklnpgde.ilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapeg 145
                                   ++e  + ++sG+g +   ++  ++++++d+ + + +  +++  +++ ++ g+vv+++++   + ++dl+ +ee+l+e   g
  gi|91772554|ref|YP_565246.1|  52 QTENDLFTISGSGTASMEAALGCTIDKDDKvVTIENGKFGERFKDIAARYGQVVPVECE--WGTSVDLDVVEEKLAE---G 127
                                   56777888888887776666666689999835688999*******************99..8999**********99...4 PP

                                   TETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                 Aminotran_1_2 146 nkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                    k     +v+ +hN t + +  + le +  lakky++l + D
  gi|91772554|ref|YP_565246.1| 128 AK-----AVTMVHNETSAGIRNPALE-VGMLAKKYGALFIMD 163
                                   44.....5666777776666666654.345577777777777 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHHHHHHHHHHSTEEEECC CS
                 Aminotran_1_2 274 leemrqrlqkrrkelrdeLaelglkvlas 302
                                   ++++ +r ++ +  +r++++++g++++++
  gi|91772554|ref|YP_565246.1| 257 MDARIKRQATGAAAVRAAMDAIGIEMFPQ 285
                                   66677777777788888888888888775 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 ?   11.3   0.1   4.2e-05      0.15      45     150 ..      62     169 ..      51     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.2e-05
                                   SSHHHHHHHHHHHTTTTTT-EEEEESSS.-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-...GG CS
               DegT_DnrJ_EryC1  45 ssGtaAlhlaLralgvgpgdeVIvpslt.FvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh...ly 121
                                    sGta+++ aL  + ++++d+V++  ++ F    + ++    ++v+v+ +  t  +d + +e+++ e  ka+++Vh    +
  gi|91772554|ref|YP_565246.1|  62 GSGTASMEAALG-CTIDKDDKVVTIENGkFGERFKDIAARYGQVVPVECEWGT-SVDLDVVEEKLAEGAKAVTMVHnetSA 140
                                   599999999996.78999******99973555678888888899999999665.79********************44336 PP

                                   GB---HHHHHHHHHHCT-EEEEE-TT-TT CS
               DegT_DnrJ_EryC1 122 GqvadmdalkaiaakhglkvieDaAhAlG 150
                                   G  +   ++  +a+k+g  +i D   ++G
  gi|91772554|ref|YP_565246.1| 141 GIRNPALEVGMLAKKYGALFIMDGVTSIG 169
                                   77778888999******999999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2776.13
//
Query:       gi|91772555|ref|YP_565247.1|  [L=154]
Description: riboflavin synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   63.7   0.5    1.8e-17   63.5   0.5    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
     0.0098   16.3   0.1      0.025   15.0   0.0    1.7  2  FDX-ACB        Ferredoxin-fold anticodon binding domain


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 !   63.5   0.5     2e-21   1.8e-17       3     137 ..       3     128 ..       1     132 [. 0.87

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 2e-21
                                   EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHH CS
                 DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyva 83 
                                    i+iV ++f      ++ ++a+de++++    ++i+++tVPG+ +lp+a kkl+e++++ d vialG  + G+ ++++++a
  gi|91772555|ref|YP_565247.1|   3 TIGIVDTTF---ARFNMGSAAVDEIQQNVS--AKIKRITVPGVKDLPVASKKLIEEEGC-DIVIALG--MPGAKEQDKICA 75 
                                   689999999...7889**********9885..69*********************6445.*******..9*********** PP

                                   HHHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTCCCHHHHHHHHHHHHH CS
                 DMRL_synthase  84 eavskglmrvsldtgvPvifgvltvdteeqaleraggkagnkGeeaaeaalema 137
                                   +++s g+++++l t++ +i   +  d+ ++ +e a    + + +e+a ++++m+
  gi|91772555|ref|YP_565247.1|  76 HEASTGIIQAQLMTNTHIIEVFVHEDEGKDEKELA-FLMEMRSREHALNVVNML 128
                                   ***************98887766666666666666.335999999999999996 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.55   4.9e+03      72      86 ..      19      33 ..      15      36 .. 0.64
   2 !   15.0   0.0   2.8e-06     0.025      32      70 ..      85     123 ..      60     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.55
                                  HHHHHHHHHHHHHHH CS
                       FDX-ACB 72 eevnaaiekvveale 86
                                  + v++++++v ++++
  gi|91772555|ref|YP_565247.1| 19 AAVDEIQQNVSAKIK 33
                                  556666776666664 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.8e-06
                                   -TTEEEEEEEEEEESTTS-SSEEEEEEEEEE--SSS--- CS
                       FDX-ACB  32 gellesvqlfDvYrgkklaegkkSlalrltlqskertLt 70 
                                    +l+++ ++++v+ +++ ++++k la+ + ++s e+ L+
  gi|91772555|ref|YP_565247.1|  85 AQLMTNTHIIEVFVHEDEGKDEKELAFLMEMRSREHALN 123
                                   56999************99*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1129.15
//
Query:       gi|91772556|ref|YP_565248.1|  [L=211]
Description: hypothetical protein Mbur_0516 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-32  109.4   5.5      7e-16   58.2   1.0    2.4  2  zf-CDGSH  Iron-binding zinc finger CDGSH type
    5.5e-25   87.2   0.1    1.3e-24   86.0   0.1    1.7  1  Fer4_19   Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
       0.09   13.5   0.2        3.4    8.5   0.1    2.9  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.2   4.1e-18   2.4e-14       1      47 [.      14      57 ..      14      58 .. 0.94
   2 !   58.2   1.0   1.2e-19     7e-16       1      47 [.     159     201 ..     159     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 4.1e-18
                      zf-CDGSH  1 nGPllVeGdvelvdadgesvelregrevvaLCrCgrSknkPfCDgsH 47
                                  nGP++V+   +l +++g  +e+++    ++LCrCg S+n+PfCDg+H
  gi|91772556|ref|YP_565248.1| 14 NGPYIVKDVKTLRNSKGVFIETKHV---MSLCRCGGSSNMPFCDGTH 57
                                  9*****9999999999999999887...******************* PP

  == domain 2  score: 58.2 bits;  conditional E-value: 1.2e-19
                      zf-CDGSH   1 nGPllVeGdvelvdadgesvelregrevvaLCrCgrSknkPfCDgsH 47 
                                   +GP+ V+G v+l d+dg+  e++++   +aLCrCg+S+nkPfCDg H
  gi|91772556|ref|YP_565248.1| 159 DGPYNVTG-VRLDDSDGSVPETQDH---YALCRCGASRNKPFCDGRH 201
                                   7*****76.79**********9999...******************* 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 !   86.0   0.1   2.2e-28   1.3e-24       1      63 [.      78     140 ..      78     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 2.2e-28
                       Fer4_19   1 yegeeitiednrelCihsgnCvkglpevFdpkrkpwikpdeasteeiievverCPSGALsyve 63 
                                   y g+ iti+ +r +C+h g+C+++lp+vF+++r+pw +pd+a+ eei + +++CPSGALsy+ 
  gi|91772556|ref|YP_565248.1|  78 YVGKYITIHRDRYVCSHVGHCIRNLPSVFKKGREPWADPDAADPEEIAKLIRTCPSGALSYTV 140
                                   789**********************************************************86 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00057       3.4       4      33 ..      88     117 ..      84     138 .. 0.76
   2 ?    0.8   0.0      0.14   8.3e+02      19      50 ..     152     182 ..     147     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00057
                       Fer4_15   4 DrdaCigcglCvaeapevfeldedglasvl 33 
                                   Dr  C  +g C++++p vf++  +  a+ +
  gi|91772556|ref|YP_565248.1|  88 DRYVCSHVGHCIRNLPSVFKKGREPWADPD 117
                                   8999***************99877666555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.14
                       Fer4_15  19 pevfeldedglasvllddgeiaegevpddeee 50 
                                   pe+f+l+ dg   v++ + ++++g vp+++  
  gi|91772556|ref|YP_565248.1| 152 PEIFVLK-DGPYNVTGVRLDDSDGSVPETQDH 182
                                   7888888.555557777777888999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1529.29
//
Query:       gi|91772557|ref|YP_565249.1|  [L=120]
Description: hypothetical protein Mbur_0517 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0077   16.0   0.0      0.011   15.5   0.0    1.2  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.026   14.8   0.0      0.065   13.5   0.0    1.6  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-06     0.011       4      73 ..      33     102 ..      33     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE...EEECSSSSEEEEECT CS
               Phage_integrase   4 tedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvh...eregKgskeravpls 73 
                                   t++e++++++a+      rdk+++++l ++G+R   +  L+ ++ ++++  +++    ++++K+ ++   p++
  gi|91772557|ref|YP_565249.1|  33 TKEELDKIMNACGH---PRDKAMIAVLADSGMRSWCIGFLSHQHAEFNQYGAILYisqTSKIKKTTNAKKPMG 102
                                   689*********99...9*****************99999999999998777765434455555555666665 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.2e-06     0.065      11      44 ..       6      40 ..       2      46 .. 0.88
   2 ?   -3.4   0.0       1.4   1.2e+04      28      35 ..     106     113 ..     103     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-06
                                  TT-S-HHHHHHHHHHHHHHHHHHHH..TS--TTT- CS
               Phage_int_SAM_1 11 erglspnTlraYrrdLrrflkflae.rgkesleql 44
                                  + gl p T+r+Y+r +++f++ l   + ke l+++
  gi|91772557|ref|YP_565249.1|  6 DHGLKPGTIRTYKRMVKKFFRVLGNgDTKEELDKI 40
                                  67899******************998888888876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
                                   HHHHHHHH CS
               Phage_int_SAM_1  28 rflkflae 35 
                                   +f+++la+
  gi|91772557|ref|YP_565249.1| 106 KFQDHLAK 113
                                   45555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 902.43
//
Query:       gi|91772558|ref|YP_565250.1|  [L=328]
Description: hypothetical protein Mbur_0518 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2332.95
//
Query:       gi|91772559|ref|YP_565251.1|  [L=124]
Description: hypothetical protein Mbur_0519 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.1   0.4       0.18   11.5   0.3    1.4  1  G10       G10 protein


Domain annotation for each model (and alignments):
>> G10  G10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3     1e-05      0.18      37      70 ..      87     120 ..      50     124 .] 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1e-05
                           G10  37 skeskkkeeslWkiarinhersryvyelyykrka 70 
                                   +++  k+ ++  +i++in e +ry+++ly+ + a
  gi|91772559|ref|YP_565251.1|  87 DEDVLKSLNAPLSIYKINDEATRYIHHLYHGKGA 120
                                   3344455566679***************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 878.90
//
Query:       gi|91772560|ref|YP_565252.1|  [L=262]
Description: hypothetical protein Mbur_0520 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  105.0   0.1    7.6e-30  104.3   0.1    1.3  1  NYN       NYN domain
    1.7e-19   69.4   0.0      4e-19   68.2   0.0    1.6  1  OST-HTH   OST-HTH/LOTUS domain
  ------ inclusion threshold ------
      0.024   15.3   2.8       0.21   12.2   0.1    3.3  3  PIN7      PIN 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 !  104.3   0.1   1.3e-33   7.6e-30       1     146 [.       9     143 ..       9     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 1.3e-33
                           NYN   1 rvavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgkkavD 80 
                                   ++av+iD++n++         ++ l++ei+++g   ++r yg+w+ ++++ ++d l+ + i +++++ +++    +k+a+D
  gi|91772560|ref|YP_565252.1|   9 KLAVLIDADNVHS------SIIKGLFDEIAKYGIASVKRLYGDWTGPQLSNWKDNLHIYSIqPIQQFSYTA----KKNATD 79 
                                   68**********9......489***********************************************76....89**** PP

                           NYN  81 velavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                    +l++da++l+y++++d +++vs+D+D++ l++++re g  V++++  e++t++++++a+++fi++
  gi|91772560|ref|YP_565252.1|  80 SALIIDAMDLLYTRNLDGFCIVSSDSDYTKLCQRIRESGAFVYGFG--EKKTPEAFRAACNKFIYV 143
                                   ****************************************777777..8***************86 PP

>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   6.7e-23     4e-19       6      71 ..     183     252 ..     182     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 6.7e-23
                                   HHHHHHHHHHH......TTTTSBEHHHHHHHHHHHHSST-STCCCTSSSHHHHHHTSTTTEEEEEETTSTEE CS
                       OST-HTH   6 lkkeirelLrs......dpdgwvslsrlgslykkkygksfdprkyGfskLseLlkalpdvveveerghgqli 71 
                                    +++++ lLrs      d++gw+sl+ +g+   ++++ +fd r+yG++kLs+L++a++  +e+e+rg++ +i
  gi|91772560|ref|YP_565252.1| 183 MDTNLVTLLRSaiedsaDDNGWASLGNVGQNAMNRES-DFDSRNYGYKKLSDLIEAIDL-FEIEKRGKNSHI 252
                                   57899***********9999*****************.*******************99.********9987 PP

>> PIN7  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.6e-05      0.21       1     103 []      13     118 ..      13     118 .. 0.62
   2 ?    1.3   0.2     0.091   5.4e+02       2      45 ..     141     186 ..     140     238 .. 0.73
   3 ?   -1.4   0.0      0.61   3.7e+03      41      62 ..     229     250 ..     210     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                          PIN7   1 liDyENvqkkelelk.ellkee..dkvivflgenqkklklelvkklael..gkkielikikkkgknalDFhlasylGylia 76 
                                   liD +Nv+++ +++  ++++++  + v  ++g+ +   +l+  k+  ++   + i+ +   ++ kna D  l+     l+ 
  gi|91772560|ref|YP_565252.1|  13 LIDADNVHSSIIKGLfDEIAKYgiASVKRLYGDWTGP-QLSNWKDNLHIysIQPIQQFSY-TAKKNATDSALIIDAMDLLY 91 
                                   5677777766665431444444123444466654433.2222222222200122222233.3579**************** PP

                          PIN7  77 eekeaefviiskDkGfdplieflkekG 103
                                   + +   f i+s D+++++l + ++e+G
  gi|91772560|ref|YP_565252.1|  92 TRNLDGFCIVSSDSDYTKLCQRIRESG 118
                                   ********************9999987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.091
                          PIN7   2 iDyENvqkkelelke..llkeedkvivflgenqkklklelvkklae 45 
                                   i +EN +k+e e++e  + kee++  + ++ n++k++ ++ k  ++
  gi|91772560|ref|YP_565252.1| 141 IYVENLRKEEEEETEgkEGKEEKEGSITISTNHTKIPTNELKMDTN 186
                                   6678888877665551144566677888888888888887776655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.61
                          PIN7  41 kklaelgkkielikikkkgkna 62 
                                   kkl++l + i l++i+k gkn+
  gi|91772560|ref|YP_565252.1| 229 KKLSDLIEAIDLFEIEKRGKNS 250
                                   5666666778899999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1844.57
//
Query:       gi|91772561|ref|YP_565253.1|  [L=66]
Description: hypothetical protein Mbur_0521 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 509.54
//
Query:       gi|91772562|ref|YP_565254.1|  [L=150]
Description: hypothetical protein Mbur_0522 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.24   10.6   3.3       0.32   10.2   3.3    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.3   1.8e-05      0.32     153     251 ..      29     120 ..       7     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 1.8e-05
               ABC2_membrane_2 153 givlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindfl 233
                                    +++ +++ll+  ++sv++ +++++++ +++ Ss +  ++++  ++  +++ l i++  +  ++  +  + +        +
  gi|91772562|ref|YP_565254.1|  29 IYAPYTDELLTHQISSVIFCMVIFAVTYFFMKSSGVSGTSRQFIYVGLIWLRLTIFFEFLFGHFHHPIIEDYE-------V 102
                                   3455556666666666655554456666777777777777777777777777777777777777777777777.......8 PP

               ABC2_membrane_2 234 sllsptsayntllneila 251
                                   +llsp+sa+  +++e++a
  gi|91772562|ref|YP_565254.1| 103 LLLSPGSAIVPGVAEPSA 120
                                   999999999877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1090.29
//
Query:       gi|91772563|ref|YP_565255.1|  [L=504]
Description: catalase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-198  658.7   0.1   3.4e-198  658.4   0.1    1.0  1  Catalase      Catalase
    2.8e-21   75.5   0.1    5.9e-21   74.4   0.1    1.6  1  Catalase-rel  Catalase-related immune-responsive


Domain annotation for each model (and alignments):
>> Catalase  Catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  658.4   0.1  3.8e-202  3.4e-198       1     382 [.      10     392 ..      10     393 .. 0.99

  Alignments for each domain:
  == domain 1  score: 658.4 bits;  conditional E-value: 3.8e-202
                                   B-TTS-B-S-SSS-EEESTTS-BBTT-HHHHHHHHHHHT------SS--SEEEEEEEEEESS--TTT---GGGSSTT-EEE CS
                      Catalase   1 ttseGapvsdnqnsltagerGplllqdvhlieklahfdreripeRvvhAkGagahgeFevtkdisdltkakllskvgkktp 81 
                                   tt+ G+pv d+qnsltagerGp+l+qdvhl+ekl hf+reripeRvvhAkGaga g+Fevt+d++++tkak+ls++gk+t+
  gi|91772563|ref|YP_565255.1|  10 TTAFGIPVGDDQNSLTAGERGPVLIQDVHLLEKLGHFNRERIPERVVHAKGAGAGGYFEVTADVTKYTKAKFLSEIGKRTE 90 
                                   7999***************************************************************************** PP

                                   EEEEEE-SS--TT--SSSSS--EEEEEEEETTEEEEEEEESSSS-S-S-GGGHHHHHHHHSB-TTT-SB-HHHHHHHHHT- CS
                      Catalase  82 vlvRfStvagekgsadtaRdvrGfavkfyTeeGnwDlvgnntpvFfirDpikfpdlihsqkrepqtnlkdaamfwdflsln 162
                                   v++RfStv+gekgsad+aRd+rGfa+kfyTe+Gn+Dl gnntpvFfirDp+kfpd+ih+qkr+p+tn+kd++mfwdflsl+
  gi|91772563|ref|YP_565255.1|  91 VFARFSTVGGEKGSADAARDPRGFAIKFYTEDGNHDLTGNNTPVFFIRDPLKFPDFIHTQKRNPATNCKDPNMFWDFLSLT 171
                                   ********************************************************************************* PP

                                   GGGHHHHHHHHSGGGSBS-GGGS-EE--S-EEEE-TT--EEEEEEEEEETT---B--HHHHHHHHHH-TTHHHHHHHHHHH CS
                      Catalase 163 peslhqvlilfsdrgipksyrhmngygvhtfklvnkegevvyvkfhfktkqgvknltaeeaeklagedpdyatrdLyeaie 243
                                   pes+hqv+ilfsdrg+p+++r+mngy++ht+k++n++ge ++v++hfkt+qg+k+lt+eeaekl+g+dpd+a rdLy+aie
  gi|91772563|ref|YP_565255.1| 172 PESIHQVTILFSDRGTPATFRNMNGYSSHTYKWYNDKGEYFWVQYHFKTDQGTKTLTREEAEKLSGTDPDHAVRDLYDAIE 252
                                   ********************************************************************************* PP

                                   TT---EEEEEEEEEEHHHHTTTHHHHT-TT----TTTS--EEEEEEEEEE--S-HHHHTTT----TT---TTEE--S-HHH CS
                      Catalase 244 kgeypewelyvqvmteeeaeklrfnilDlTkvwpekevplrevGkltLnrnpenyFaevEqvafspsnlvpGiepseDklL 324
                                   kg+yp+w+l +q+mt+e+ae++rf+ilD+Tkvwp+ ++p++++Gk++Lnrnp+nyFaevEq afsp+nlvpGi++s+Dk+L
  gi|91772563|ref|YP_565255.1| 253 KGDYPSWTLEMQIMTPEQAEEYRFDILDITKVWPHGDFPTIKIGKMVLNRNPTNYFAEVEQSAFSPGNLVPGIDISPDKML 333
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHT-TTGGGSGGG---..--.-S----TT-.....S-S---SS-S-T CS
                      Catalase 325 qgRlfsYadtqryRlGvnyqqlpvNrpkakva.nyqrdGamrveankgkepnYepnsle 382
                                   q+R+fsY+d++ +RlG+ny+q+pvN+pk++ + +yqrdG+mr++an g+ pnY+pns++
  gi|91772563|ref|YP_565255.1| 334 QARVFSYHDSHVHRLGPNYHQIPVNAPKNAPEtSYQRDGFMRIDANGGSGPNYWPNSFG 392
                                   ***************************77776699*********************986 PP

>> Catalase-rel  Catalase-related immune-responsive
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.1   6.6e-25   5.9e-21       5      65 .]     420     480 ..     417     480 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 6.6e-25
                                   --SSHHHHHHHH.HS-HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH-HHHHHHHHHHH CS
                  Catalase-rel   5 ddhfsQagllyr.smseeekerlvnniafelskvedeeiqerqlehfakvDpdlgqrVaeal 65 
                                   +d+f Qag+lyr +m+++++e+lv ni  +ls+++ + iq rq + f+k+Dpd+g rVa++l
  gi|91772563|ref|YP_565255.1| 420 NDDFVQAGNLYRdVMDDQARENLVGNIISHLSGAQ-KRIQLRQTALFFKADPDYGGRVADGL 480
                                   7*********************************9.************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3577.72
//
Query:       gi|91772564|ref|YP_565256.1|  [L=285]
Description: hypothetical protein Mbur_0524 [Methanococcoides burtonii DSM 6242]
Scores for 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-20   72.4  40.4    8.1e-13   48.7  14.3    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
        4.2    7.4   6.4        2.9    8.0   0.1    3.2  4  TMEM234   Putative transmembrane family 234


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0  18.1   5.6e-11   5.1e-07       3     135 ..      11     140 ..       9     142 .. 0.92
   2 !   48.7  14.3     9e-17   8.1e-13       5     136 ..     156     284 ..     153     285 .] 0.89

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.6e-11
                          EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllff 83 
                                    +++ l +a++w+++ +    ++++ + ++++ ++ +++ +ll + a l ++k+  ++  ++l+ ++ g+  + ++ l+++
  gi|91772564|ref|YP_565256.1|  11 VVFFGLMSAICWGAGDFSGGFASKRANVYSVVLITQIVGIFLLAFSAHLMAEKM--PPFGGMLWGAVAGV-FIGIGLLALY 88 
                                   57999******************************9877777777777777777..99******888886.677888**** PP

                          EamA  84 yalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                    +l+ ++ ++++++++++ + + ++ ++++   + + q++g++++l++v+li
  gi|91772564|ref|YP_565256.1|  89 RGLSQGNMGFVAPVSAIVAASVPVIYSAFYEGLPAFHQIIGFAFALVAVWLI 140
                                   **************************************************98 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 9e-17
                          EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffya 85 
                                   +l l+a + +++ f+ +++++ +   + lt+ r+ +a+i l+i++ lk++    +++k+++ +++++ +  + ++ +f  a
  gi|91772564|ref|YP_565256.1| 156 ILPLIAGMGFGLFFISIDKVSDTAVLWPLTAARI-AAAITLIIFITLKRQVY--IPPKSVFPIIFIAGIFDTGGNTFFAFA 233
                                   6779999************999998889999886.89999999999999888..7777777777777777777889***** PP

                          EamA  86 lkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    + +   +as+ +sl P+ t++l++l+l+ekl++kq+lg++ +ll++++i+
  gi|91772564|ref|YP_565256.1| 234 SQAGRLDIASITSSLYPAGTVLLAWLILKEKLSSKQWLGLATALLAIIFIS 284
                                   ************************************************997 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.32   2.9e+03       2      10 ..      16      24 ..      16      26 .. 0.84
   2 ?   -1.7   0.0      0.33   2.9e+03      65     115 ..      91     140 ..      83     141 .. 0.65
   3 ?    1.3   0.1     0.037   3.3e+02      56     105 ..     163     215 ..     147     222 .. 0.65
   4 ?    8.0   0.1   0.00032       2.9      72     114 ..     241     282 ..     216     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.32
                       TMEM234  2 llvgilWGi 10
                                  l+ +i+WG+
  gi|91772564|ref|YP_565256.1| 16 LMSAICWGA 24
                                  6899****7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.33
                       TMEM234  65 lgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                   l++ ++ ++ p++  +a  + v+ + +  e +   ++++g ++ +v++ l+
  gi|91772564|ref|YP_565256.1|  91 LSQGNMGFVAPVSAIVAASVPVIYS-AFYEGLPAFHQIIGFAFALVAVWLI 140
                                   5555666666666666666665554.4557777788888888888877775 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.037
                       TMEM234  56 sgSvlfflllgka.dlslavpiaNs.lafvfTvltelllgekvlk.kktvlgm 105
                                   +g  lff+++ k+ d ++  p++ + +a ++T+++  +l+++v    k+v  +
  gi|91772564|ref|YP_565256.1| 163 MGFGLFFISIDKVsDTAVLWPLTAArIAAAITLIIFITLKRQVYIpPKSVFPI 215
                                   56668999998873566666665543999999999999998875414444444 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.00032
                       TMEM234  72 lavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgial 114
                                   +a  i+ sl  + Tvl ++l+ ++ l++k++lg++  +++i+ 
  gi|91772564|ref|YP_565256.1| 241 IA-SITSSLYPAGTVLLAWLILKEKLSSKQWLGLATALLAIIF 282
                                   44.58999*************************9988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1889.71
//
Query:       gi|91772565|ref|YP_565257.1|  [L=645]
Description: glycoside hydrolase 15-related [Methanococcoides burtonii DSM 6242]
Scores for complete 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   69.7   0.6    1.6e-14   53.5   0.3    2.6  2  Glyco_hydro_15   Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.021   14.1   0.0    1.3  1  Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin gly


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 !   53.5   0.3   1.8e-18   1.6e-14      21     346 ..     281     574 ..     271     585 .. 0.83
   2 !   13.6   0.0   2.4e-06     0.021     395     444 ..     582     631 ..     576     635 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.8e-18
                                   S-TT-B-S-S-BSSS.......B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHHHHHHHHCTS-BTTB CS
                Glyco_hydro_15  21 pvtGlliASpstsdp.......DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrglleamvrqagkvekfk 94 
                                    + G++iA+++ sd         Y y W RDs+y+++a+          ++ ++  q+  +  +gl++      +k ++ +
  gi|91772565|ref|YP_565257.1| 281 DYDGAIIAAND-SDIlerfnmdSYSYMWPRDSAYIAMALD--------ITRYSGTVQKFFEYCQGLIHENGYFLQKYNPTG 352
                                   577999**999.44459999989****************8........44555667777778888888887778888**** PP

                                   -TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHH...HCTTHCHCCCCHHHHTHHHHHHHHHHH......T CS
                Glyco_hydro_15  95 etqstkgLhakyftktgstvvGddewghlQlDatslyllalaqm...tasglqiistldevafvqnlvdYieaa......y 166
                                   +  s+   + +  t +g+   +      +Q D t+l++ al+     t+s  +i + + ++  +    ++  ++       
  gi|91772565|ref|YP_565257.1| 353 TLASG---WMPWLTPEGKIQLP------IQEDSTALIIVALWNHykiTKSIENIDPVYHSL--IIPAAEFMIKYrdpstgL 422
                                   *****...*******9999665......5*************9978778888888888888..888888887762222224 PP

                                   TS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH CS
                Glyco_hydro_15 167 ktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgs 247
                                    +p++ lWE +   + +  +   + ++l +a+++a   g+++ a+ +++ + ei + +      ++ ++++ + +l+  + 
  gi|91772565|ref|YP_565257.1| 423 PKPSYNLWEDKRAVHSY--TCSTVYAGLICAANFAAMYGDNDLAESYNTAAMEIKKGI-----ENHLYDKELGRFLRSISP 496
                                   567**************..8888899********************************.....445778888888888877 PP

                                   .....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CG. CS
                Glyco_hydro_15 248 faedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkp. 327
                                              +e +dasl+ +++ ++ p+dd           r++++++ +++ l+ ++ +  g     + R+ +d+++ 
  gi|91772565|ref|YP_565257.1| 497 ----------RDETVDASLYAVSQFGVLPPDD----------ARVVSTMKSVESILSVKTEV--GG----IARFYKDKYQe 551
                                   ..........79********************..........************99998774..53....67777777765 PP

                                   ....SSSBSCT--BHHHHHHHHH CS
                Glyco_hydro_15 328 ....dklglsGrpyylctlwtve 346
                                       d     G+p+++ctlw ++
  gi|91772565|ref|YP_565257.1| 552 vaqyDPEIIPGNPWFICTLWVAQ 574
                                   5554777788**********544 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.4e-06
                                   HHHHHHHHHHHHHHHHHHS-TTS---SEE-TTT--EESSTT-HHHHHHHH CS
                Glyco_hydro_15 395 aplpveeladliveaveednslgvLteevdvylgeliraqpllfsealll 444
                                    ++ +++ ++ i+ + e + ++g+L+e+++  +g +++ +pl++++a ++
  gi|91772565|ref|YP_565257.1| 582 SIDDLQKTREIILWTTERATETGMLAEQLNPFDGSPLSVSPLTWAHATFV 631
                                   567788899999999999****************************9886 PP

>> Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.3e-06     0.021      80     246 ..     357     522 ..     328     543 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-06
                                   S--BSBSS--TT--B--TTTTTHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHTSBT.TB.--S-S--STT.....- CS
               Bac_rhamnosid6H  80 gavptvaPevlgalsetaeWadaivivpwelyetygDkeilkkqYesmkryldylkqrsddgleelskfqlgDWldpeard 160
                                   g +p   Pe + +l  +   +++i+++ w+ y+ + + e ++  Y+s+     +   +++d   +l k  +  W d     
  gi|91772565|ref|YP_565257.1| 357 GWMPWLTPEGKIQLPIQEDSTALIIVALWNHYKITKSIENIDPVYHSLIIPAAEFMIKYRDPSTGLPKPSYNLWED----- 432
                                   5566666665555555555555666666777777777777777777666555555555555345666666666662..... PP

                                   SS----HHHHHHHHHHHHHHHHHHHHHHTTS..--HHHHHHHHHHHHHHHHHHB.-TTS......-BTT--HHHHHHHH.H CS
               Bac_rhamnosid6H 161 gaaktekalvataylvrslklvakiaellgkeedakkyaalaeelkaafnkkyldsetg......svandtqtanalpL.a 234
                                    ++  + ++ +t+y    l  +a++a++ g ++ a+ y++ a e+k+ ++++++d+e g      s +++t+ a +++  +
  gi|91772565|ref|YP_565257.1| 433 -KRAVHSYTCSTVY--AGLICAANFAAMYGDNDLAESYNTAAMEIKKGIENHLYDKELGrflrsiSPRDETVDASLYAVsQ 510
                                   .2233334444443..3455689*******9888***********************999998877788888888888756 PP

                                   TT-S-GGGH.HH CS
               Bac_rhamnosid6H 235 fglvpeaeraak 246
                                   fg++p +  + +
  gi|91772565|ref|YP_565257.1| 511 FGVLPPDDARVV 522
                                   898887776333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4096.30
//
Query:       gi|91772566|ref|YP_565258.1|  [L=212]
Description: multiple antibiotic resistance (MarC)-related proteins [Methanococcoides burtonii DSM 6242]
Scores for complete 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-56  189.6  17.4    4.7e-56  189.4  17.4    1.0  1  MarC       MarC family integral membrane protein
    0.00012   21.8  15.2    0.00061   19.5  14.9    2.0  1  TerC       Integral membrane protein TerC family
  ------ inclusion threshold ------
      0.023   14.9   3.4      0.023   14.9   3.4    2.4  2  Adeno_E3B  Adenovirus E3B protein
        1.1    9.2  15.2      0.067   13.1   1.7    2.9  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.4  17.4     1e-59   4.7e-56       3     202 ..       6     205 ..       4     206 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 1e-59
                          MarC   3 aiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillfli 83 
                                   ++i++f++Ll+i+ p+++v  f++l+++ + +e++ ia+k + la++i ++f+++G++il+++gis+d+lk+aGg+ll++i
  gi|91772566|ref|YP_565258.1|   6 YFIYSFITLLVIVSPITAVITFITLTNSLTLDEKNVIAKKSVALAFVIAVIFMFTGNIILDVLGISLDSLKVAGGLLLIMI 86 
                                   6899***************************************************************************** PP

                          MarC  84 aidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllillls 164
                                   a++m++ak+++e+   +e +es ++++i ++P+A+P+++GP++ittv+vl+++a  +++k++++la++l ++itl+++l s
  gi|91772566|ref|YP_565258.1|  87 AFEMMQAKTSRESITDKEMDESSKREDIWIFPIAMPILTGPATITTVIVLTETAGLVQQKTLIMLALVLTYSITLVTFLFS 167
                                   ********************************************************************************* PP

                          MarC 165 slilrllgktginaleRlmGllLvalavqlivdGikei 202
                                     i +++g +g+ +l+Rl+Gl+L a++v +i  Gi ++
  gi|91772566|ref|YP_565258.1| 168 RRIHKKMGYNGMLVLTRLFGLFLGAISVSMIASGIWGL 205
                                   **********************************9775 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  14.9   1.4e-07   0.00061      15     179 ..      24     199 ..      12     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                          TerC  15 lvviallvkklpeeqqkkalllGilgAlvlRillillavallelf....dlilligglfLlytavkellekrle.nklvke 90 
                                   ++ +++l+++l  ++++ +    +++A+v+ +++++++  +l+++    d ++++ggl+L+++a++++ +k  + + + ke
  gi|91772566|ref|YP_565258.1|  24 VITFITLTNSLTLDEKNVIAKKSVALAFVIAVIFMFTGNIILDVLgislDSLKVAGGLLLIMIAFEMMQAKTSReSITDKE 104
                                   5778889999**********************************55566*******************9887553444455 PP

                          TerC  91 ekkkkkktkstllavviqielaDlvfslDSvla.avaitsdlfivitavils..ilvlrf.lakllakllerfp..tlkyl 165
                                    ++++k+++  ++ + + i +    +    vl+  +++ ++  ++++a++l   i+++ f +++ ++k +      +l  l
  gi|91772566|ref|YP_565258.1| 105 MDESSKREDIWIFPIAMPILTGPATITTVIVLTeTAGLVQQKTLIMLALVLTysITLVTFlFSRRIHKKMGYNGmlVLTRL 185
                                   555555555556666666666666655555555245566777777777776511433333134455555544441134455 PP

                          TerC 166 alalllligvklvl 179
                                     ++l+ i+v++++
  gi|91772566|ref|YP_565258.1| 186 FGLFLGAISVSMIA 199
                                   66788889998886 PP

>> Adeno_E3B  Adenovirus E3B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.4   5.2e-06     0.023      15      39 ..       6      30 ..       3      36 .. 0.91
   2 ?   -1.3   1.0       0.6   2.7e+03      22      40 ..     147     165 ..     129     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-06
                     Adeno_E3B 15 yllygfvtlilicslvtvviafiqf 39
                                  y++y f+tl++i s +t vi+fi +
  gi|91772566|ref|YP_565258.1|  6 YFIYSFITLLVIVSPITAVITFITL 30
                                  99*********************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.6
                     Adeno_E3B  22 tlilicslvtvviafiqfi 40 
                                   tli++  ++t  i+++ f+
  gi|91772566|ref|YP_565258.1| 147 TLIMLALVLTYSITLVTFL 165
                                   7888888888888887775 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.33   1.5e+03      67      89 ..      13      35 ..      10      44 .. 0.75
   2 ?   13.1   1.7   1.5e-05     0.067      60     117 ..      38      97 ..      33     106 .. 0.84
   3 ?    2.2   3.7     0.037   1.7e+02      63     115 ..     149     199 ..     132     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.33
                     RseC_MucC 67 allvYllPllllilgallgsall 89
                                  +llv + P+ ++i+++ l ++l+
  gi|91772566|ref|YP_565258.1| 13 TLLVIVSPITAVITFITLTNSLT 35
                                  57788899999999999999886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                     RseC_MucC  60 eksll..kaallvYllPllllilgallgsallgssellaalgallglvlgflivrllskr 117
                                   ek+++  k+++l++++ ++++++g ++ ++l++s + l ++g+ll+++++f +++  ++r
  gi|91772566|ref|YP_565258.1|  38 EKNVIakKSVALAFVIAVIFMFTGNIILDVLGISLDSLKVAGGLLLIMIAFEMMQAKTSR 97 
                                   5555433799**********************9***************999888776665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.037
                     RseC_MucC  63 llkaallvYllPllllilgallgsallgssellaalgallglvlgflivrlls 115
                                   ++ a +l Y + l++++++  + + +  + +++ +l+ l+gl+lg + v +++
  gi|91772566|ref|YP_565258.1| 149 IMLALVLTYSITLVTFLFSRRIHKKM--GYNGMLVLTRLFGLFLGAISVSMIA 199
                                   45566677777777777777777777..5777888888888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1296  (0.0722851); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1415.72
//
Query:       gi|91772567|ref|YP_565259.1|  [L=422]
Description: proteinase inhibitor I4, serpin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-114  382.1   7.8   3.5e-114  382.0   7.8    1.0  1  Serpin    Serpin (serine protease inhibitor)


Domain annotation for each model (and alignments):
>> Serpin  Serpin (serine protease inhibitor)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.0   7.8    2e-118  3.5e-114       2     371 .]      47     415 ..      46     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 382.0 bits;  conditional E-value: 2e-118
                                   HHHHHHHHHHHHHHHHSTTSSEEE-HHHHHHHHHHHHHTB-HHHHHHHHHHHTGCCHCHHHHHHHHHHHHHHHCSSGGTSE CS
                        Serpin   2 antkfaldlfkalskekpskNiifSPlsistaLallllGakgetaeellevLglnesdeeelhealekllsrlneseekdk 82 
                                   an++fa+d++   ++e+ ++N++fSP+si++a++++++Ga+g+t++++++v+g++  ++  l+++ +kl+++l   e++++
  gi|91772567|ref|YP_565259.1|  47 ANNAFAFDMYSISKNEN-EGNVLFSPYSIFSAISICYEGAEGSTKKQIADVFGYP-LEKIVLEANSKKLMNELYL-EDENN 124
                                   89********9988888.************************************6.6677779999*********.9**** PP

                                   EEEEEEEEEEETTSEB-HHHHHHHHHHHS-EEEEE-TTTHHH.HHHHHHHHHHHHTTTSSSSSSSTTSS-TTECEEEEEEE CS
                        Serpin  83 elkianglfvekglklkeeflklakklykaevesvdfkddee.arkkINswvekqTngkIkdllsegsidsdtrlvlvNai 162
                                    lk+an+l+++k++ l+e+++ +++++y+  v+++df +++e +r++IN wve++T gkI+++++eg i++ t ++++N++
  gi|91772567|ref|YP_565259.1| 125 ALKTANALWIKKNYLLNEQYVFNVETFYGGLVKPLDFINKPEdSRNTINLWVEEKTSGKINEMVTEGGISPATLMMITNTV 205
                                   ********************************************************************************* PP

                                   EEEEEBSS--BGGGEEEEEEESSSSEEEEEEEEEEEEEEEEEEETTTTEEEEEEEBGG.SEEEEEEEESSTTTHHHHHHHH CS
                        Serpin 163 yFkGkWeepFqpeatreekFyvnegekvkvpmMsqegkfkyaedeelnakvlelpYkg.nlsmlillPdeekgleelekkl 242
                                   yF+G+W ++F+p++t++e+Fy+++g++++v++M  ++ f++aed+  +ak++elpY++ n+sm+i+lP+ e++++++e+++
  gi|91772567|ref|YP_565259.1| 206 YFNGTWYNQFEPRNTKQEQFYLSNGQSKTVDFMTANEVFNCAEDH--SAKIVELPYRDnNISMYIVLPK-ENNISNFESSF 283
                                   *****************************************9988..*********8879********7.567******** PP

                                   SHHHHHHHHHHGEEEEEEEEEEEE-EEEEEEEEHHHHHHHTTHCGGGSTTTB.BTTTB.....SSSSEEEEEEEEEEEEEE CS
                        Serpin 243 taerleewlsklkmkkekeevslPkfkieesidlkevLqklGlkdlFseneadlsgis.....kkeplfvsevlhkafiev 318
                                   t +++ e++ ++++++ +  ++lPkf+ +++ +l + Lq+lG++d+F+ ++a++sg+      +ke+l +s + hka+i+v
  gi|91772567|ref|YP_565259.1| 284 TIDKYTELKYNMSKQQGE--ICLPKFTYSTNSELVTSLQDLGMTDAFNIMTANFSGLYnsekyQKENLAISGINHKAVIDV 362
                                   *******99999977666..**************************************88887779*************** PP

                                   SSSEEEEEEEEEECCTTCS-SSCEEEEECSEEEEEEEETTTTEEEEEEEESSC CS
                        Serpin 319 nEeGteaaaatavatllskksspvefkvdrPFlflireektgliLFlGkvvnP 371
                                   nE+Gteaaaat v+  +  + ++ e+k+d+PF+f+i++++t++iLF+Gkv nP
  gi|91772567|ref|YP_565259.1| 363 NEQGTEAAAATLVSFFMGYSAPNWELKADHPFMFFIEDRNTECILFMGKVENP 415
                                   ***********7799***********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2953.04
//
Query:       gi|91772568|ref|YP_565260.1|  [L=402]
Description: hypothetical protein Mbur_0532 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-11   44.2   0.8    2.7e-11   44.2   0.8    2.3  3  Peptidase_C39_2  Peptidase_C39 like family
    5.2e-05   23.6   5.0      0.011   16.1   1.6    2.7  2  Peptidase_C10    Peptidase C10 family
    0.00048   20.5   0.3     0.0031   17.9   0.1    2.2  2  Inhibitor_I69    Spi protease inhibitor
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.041   14.1   0.0    1.7  1  BtrH_N           Butirosin biosynthesis protein H, N-terminal
       0.14   12.4   0.0       0.68   10.2   0.0    2.1  3  3D               3D domain


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.51   1.8e+03      71     104 ..      52      86 ..      10     142 .. 0.56
   2 ?   -2.7   0.0       2.2   7.7e+03      48      48 ..     147     147 ..     114     206 .. 0.60
   3 !   44.2   0.8   7.6e-15   2.7e-11       7     143 ..     247     378 ..     241     379 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.51
               Peptidase_C39_2  71 vklaekyglkvsdtrgssieevkkeida.gkPvvv 104
                                   +++ ++ ++++sd+ +++ie   +  d  g+P v+
  gi|91772568|ref|YP_565260.1|  52 KQQIQTSVSDFSDWENAKIECSSTLYDLeGNPTVY 86 
                                   44444444444444444443333222211333333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
               Peptidase_C39_2  48 d 48 
                                   +
  gi|91772568|ref|YP_565260.1| 147 S 147
                                   1 PP

  == domain 3  score: 44.2 bits;  conditional E-value: 7.6e-15
               Peptidase_C39_2   7 nQldelpngCeptslamvlsyl..gk.k..vtqnelakelktns....sgdpntgfvgnitdksglgvynepivklaekyg 78 
                                           gC pt++a+vl y+  g  +  ++ ++l +el+t +    +g + t     i+d  ++ ++n+ ++++ ++  
  gi|91772568|ref|YP_565260.1| 247 DY----YLGCTPTAAANVLGYWegGSySslPEGDTLISELATEMytdsDGVTYTPL---IDDGIEDVCSNHGYNNFDATND 320
                                   55....568*************9744325556666666666665210033333322...2255556666666666555544 PP

               Peptidase_C39_2  79 lkvsdtrgssieevkkeidagkPvvvsvttfkplndgeikftssgHlvvitGYdekg.krvyvnDP 143
                                   +        s++evk eid+ +P+++++++ + l ++  +  +++H+v++tGY +++ ++v+++D 
  gi|91772568|ref|YP_565260.1| 321 Y------YLSWSEVKSEIDSSRPFMINMNS-GGL-ASGRTQAYGQHSVACTGYLDSTtDYVILHDG 378
                                   4......459******************84.334.3445899***********996669*****96 PP

>> Peptidase_C10  Peptidase C10 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2   0.00067       2.4      19      36 ..     248     265 ..     226     295 .. 0.74
   2 !   16.1   1.6     3e-06     0.011      99     191 ..     286     386 ..     277     387 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00067
                                   ----HHHHHHHHHHHHHT CS
                 Peptidase_C10  19 tltGCvatAmaqilkyyk 36 
                                    + GC++tA+a +l y++
  gi|91772568|ref|YP_565260.1| 248 YYLGCTPTAAANVLGYWE 265
                                   569*************98 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3e-06
                                   --SSS-----HHHHHHHHHHTS...---TT-EEE-GGGS-HHHHHHHHHHHHHTT--EEEEE......E-SS......-EE CS
                 Peptidase_C10  99 eYtpegsgalssnvvkalndyf...gYdkeisllsrsnysssewedlvkneleagrpvlysg......vatsa.....kgH 165
                                    Yt++   ++++ + + ++d++   gY+ + + ++   y s    + vk+e++++rp+++++      +         ++H
  gi|91772568|ref|YP_565260.1| 286 MYTDSDGVTYTPLIDDGIEDVCsnhGYN-NFDATNDY-YLS---WSEVKSEIDSSRPFMINMnsgglaS---GrtqayGQH 358
                                   6788888888888888888886333666.44444433.333...5789************995555551...044567*** PP

                                   EEEEEEE..ESSS-EEEE-SSSSSS-EE CS
                 Peptidase_C10 166 afviDGy..ddegyvhvNwGwgGssdGY 191
                                   ++ + Gy  ++++yv++  Gw+G+ d Y
  gi|91772568|ref|YP_565260.1| 359 SVACTGYldSTTDYVILHDGWSGTDDHY 386
                                   *******877788***********9987 PP

>> Inhibitor_I69  Spi protease inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   8.7e-07    0.0031       4      79 ..      39     118 ..      36     139 .. 0.76
   2 ?   -0.4   0.0      0.44   1.6e+03      69      89 ..     257     275 ..     254     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.7e-07
                 Inhibitor_I69   4 vseeeAlkiAekffaqngaktaa.saasqsslsseattsasasepayYVfnygdgk...GFvIVsaddrappiLaYsdtg 79 
                                   v+ + A  iA+ + +q + + +  s+ ++++++ + t  + + +p++Y f   d k   G+ ++sa +r +piLa++++ 
  gi|91772568|ref|YP_565260.1|  39 VTIDSAELIASHYKQQIQTSVSDfSDWENAKIECSSTLYDLEGNPTVYAFEVSDKKqymGYMLISASKRNYPILAFTKNE 118
                                   5667888899888888766655414555555588888899999999999998887655599***************9876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.44
                 Inhibitor_I69  69 appiLaYsdtgsfdeenlppg 89 
                                   a+ +L+Y + gs+  ++lp+g
  gi|91772568|ref|YP_565260.1| 257 AANVLGYWEGGSY--SSLPEG 275
                                   789********99..666654 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.041      34     131 ..     287     374 ..     252     377 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                        BtrH_N  34 YlpakklnplpllagrtkpgdlekrlakrlglkvevketkdpeeawkalkeeLdaGrpvivqvdvyyLpYlpkesrlhfna 114
                                   Y ++  + ++pl++         ++++ ++g++     t+d    w+++k+e+d+ rp ++ ++   L   +   ++  ++
  gi|91772568|ref|YP_565260.1| 287 YTDSDGVTYTPLIDDG------IEDVCSNHGYNNF-DATNDYYLSWSEVKSEIDSSRPFMINMNSGGLASGR---TQAYGQ 357
                                   5555555555555544......5699999999966.79******************************9888...444699 PP

                        BtrH_N 115 HnvvvyGyddeegealv 131
                                   H v+ +Gy d   ++++
  gi|91772568|ref|YP_565260.1| 358 HSVACTGYLDSTTDYVI 374
                                   ********999999987 PP

>> 3D  3D domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         4   1.4e+04      48      69 ..      34      55 ..      31      57 .. 0.77
   2 ?   10.2   0.0   0.00019      0.68      11      58 ..     152     200 ..     148     212 .. 0.86
   3 ?   -2.2   0.0       1.4     5e+03      43      59 ..     240     257 ..     239     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4
                                  EEEEEEESHHHHHHHHTSEEEE CS
                            3D 48 iDlffgtgdeagelaGlvkkeg 69
                                  +D ff t d a+ +a ++k+++
  gi|91772568|ref|YP_565260.1| 34 LDPFFVTIDSAELIASHYKQQI 55
                                  6888888888888888777775 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                                   -TT-EEEEEECCEET.TTCCEEEEEEEEE--TT--SSEEEEEEEESHHH CS
                            3D  11 plGtpvlvegeplla.gkkpvyrlviaqDtGgaIkGnriDlffgtgdea 58 
                                    lG ++++e   l++ +  + +++++++ tG aI    +Dlf + +de 
  gi|91772568|ref|YP_565260.1| 152 YLGGTYYLEEYDLKDrNGMTKNKIIVDLITGEAISSDELDLFSNENDES 200
                                   589999999976766677999**********************999886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.4
                                   --SS.EEEEEEEESHHHH CS
                            3D  43 IkGn.riDlffgtgdeag 59 
                                   I G    D+++g   +a 
  gi|91772568|ref|YP_565260.1| 240 IAGVpYYDYYLGCTPTAA 257
                                   6666678****9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2579.18
//
Query:       gi|91772569|ref|YP_565261.1|  [L=186]
Description: hypothetical protein Mbur_0533 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.26   10.7   2.2       0.35   10.2   0.6    1.9  3  MttA_Hcf106  mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   1.9e-05      0.35       5      19 ..       9      23 ..       7      24 .. 0.91
   2 ?   -3.2   0.0       0.3   5.4e+03       2       9 ..      42      49 ..      42      49 .. 0.89
   3 ?   -2.9   0.0      0.25   4.5e+03      36      45 ..      87      96 ..      86     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 1.9e-05
                                  HHHHHHHHHHHHS-T CS
                   MttA_Hcf106  5 elliIlvValllFGp 19
                                  +lli+l+Va+l+FG+
  gi|91772569|ref|YP_565261.1|  9 KLLILLFVAFLVFGS 23
                                  799***********6 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.3
                                  -HHHHHHH CS
                   MttA_Hcf106  2 gapelliI 9 
                                  g+pe+ +I
  gi|91772569|ref|YP_565261.1| 42 GMPEWYLI 49
                                  89***998 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.25
                                  HHHHHHHHHH CS
                   MttA_Hcf106 36 Fkkavkelee 45
                                  F++a k+l +
  gi|91772569|ref|YP_565261.1| 87 FQEAKKTLHD 96
                                  8999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1327.20
//
Query:       gi|91772570|ref|YP_565262.1|  [L=128]
Description: hypothetical protein Mbur_0534 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.4   0.1      0.054   13.6   0.1    1.4  1  CHU_C     C-terminal domain of CHU protein family
      0.056   13.6   0.6      0.089   13.0   0.6    1.3  1  TMEM238   TMEM238 protein family


Domain annotation for each model (and alignments):
>> CHU_C  C-terminal domain of CHU protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     6e-06     0.054      17      79 ..      31      94 ..      27     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-06
                         CHU_C 17 vfkiegi.ekypnnsleifnrwGqlVyekknyknewdGtskgkeklpeGtYfYvlkleegekee 79
                                  vf ie+  ++ ++++++ifn   ++++ ++  +   +G +   ++   G+Y Y+++++++ ++e
  gi|91772570|ref|YP_565262.1| 31 VFAIENHgNDNHTIEVKIFNDDSDMIFAETYLSGPSTGIYVPISASALGSYKYIVTMDNKITKE 94
                                  6889986246678******************9999999988669999**********5444443 PP

>> TMEM238  TMEM238 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6     1e-05     0.089      12      37 ..       7      32 ..       4      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                       TMEM238 12 vfdvvGlvlLlvGifaellfgDllvy 37
                                  ++++vGl+l+++G++a++ ++D lv+
  gi|91772570|ref|YP_565262.1|  7 TIILVGLLLVMTGMIASIHYSDSLVF 32
                                  5789*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 983.36
//
Query:       gi|91772571|ref|YP_565263.1|  [L=373]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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      0.035   14.1   0.0    1.9  1  DUF772    Transposase domain (DUF772)
      0.072   12.6   0.1       0.14   11.6   0.1    1.5  1  DUF4283   Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.9e-06     0.035       5      70 ..      62     130 ..      61     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                        DUF772   5 yppelmlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70 
                                   y +  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f k rl++  l++++
  gi|91772571|ref|YP_565263.1|  62 YKVSSMIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVKyRLGKtgLDEVM 130
                                   67889*************9999998772566667777664433.89*****************9977776 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.6e-05      0.14      24      59 ..     256     291 ..     235     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                       DUF4283  24 lsalrrvlakaWklkggvkikelgdglflfrfssee 59 
                                   ++++ ++++k+Wkl+g +++k+ ++ +fl++   e+
  gi|91772571|ref|YP_565263.1| 256 MERIDHWVNKMWKLGGSIHMKYEEKLHFLYENGREK 291
                                   678999***********************9866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2607.81
//
Query:       gi|91772572|ref|YP_565264.1|  [L=302]
Description: hypothetical protein Mbur_0536 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   41.1   0.0    1.8e-06   28.0   0.0    3.5  2  DUF1743   Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
        0.1   12.2   0.0       0.18   11.4   0.0    1.3  1  PgdA_N    Peptidoglycan GlcNAc deacetylase N-terminal 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 !   28.0   0.0     2e-10   1.8e-06       1     113 [.     153     242 ..     153     244 .. 0.88
   2 !    4.7   0.0    0.0034        30       1      16 [.     276     290 ..     276     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2e-10
                                   TTHHHHHHHHHH-..-TT....S-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSS... CS
                       DUF1743   1 grgiiGAtaalganiale....dstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdp... 74 
                                   +++++GAt+++++nia++    +s y                                     lsh+lv+l+P ++ +   
  gi|91772572|ref|YP_565264.1| 153 DTKEEGATWSMTHNIATAlnsnESVY-------------------------------------LSHSLVQLFP-VSAKtqn 195
                                   7999***********97655544555.....................................**********.88888** PP

                                   .....EEEEEEES-H.HHHHHHHHCSEE..S-EEC..EEEEEESTTS CS
                       DUF1743  75 .....vlfGirgedp.eallkaakeilskeeesee..mavfrtnqgt 113
                                        ++fG+ +e++ e+ll+ +k++l k+++see  m+  ++++++
  gi|91772572|ref|YP_565264.1| 196 cvstvLEFGCVSEEAkEELLEDLKNALLKYSVSEEtgMVALSSFDAS 242
                                   **********999988********************99999999887 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0034
                                   TTHHHHHHHHHH-..- CS
                       DUF1743   1 grgiiGAtaalgania 16 
                                   g+g+iGA+a+l++ +a
  gi|91772572|ref|YP_565264.1| 276 GNGVIGALASLAW-FA 290
                                   689*********9.44 PP

>> PgdA_N  Peptidoglycan GlcNAc deacetylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     2e-05      0.18     131     187 ..     208     264 ..     204     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHHH-----------------------GGG--EEEETTEEEE------ CS
                        PgdA_N 131 dkakeilleeikqqLadkklseeqveqilaelkekdLsqwkFsyedsqltlklpkev 187
                                   ++ake+lle++k++L + ++see    +l ++ ++++ + +   ++++lt +++ e 
  gi|91772572|ref|YP_565264.1| 208 EEAKEELLEDLKNALLKYSVSEETGMVALSSFDASHMEEYSTMCRSGELTKDIAMEH 264
                                   78************************************9998888888886665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2081.98
//
Query:       gi|91772573|ref|YP_565265.1|  [L=511]
Description: thiamine pyrophosphate enzyme-like TPP-binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-12   46.4   0.5    1.6e-11   44.2   0.3    2.3  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    1.8e-09   37.7   1.1    2.2e-09   37.4   0.2    1.6  2  POR_N           Pyruvate flavodoxin/ferredoxin oxidoreductase
    3.7e-07   29.9   0.6    3.6e-06   26.7   0.2    2.1  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
      0.004   16.8   0.0      0.011   15.4   0.0    1.7  1  Transket_pyr    Transketolase, pyrimidine binding domain
  ------ inclusion threshold ------
      0.017   14.4   0.1      0.032   13.4   0.1    1.4  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
       0.13   12.6   0.0       0.56   10.5   0.0    2.1  2  PFOR_II         Pyruvate:ferredoxin oxidoreductase core domai


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 ?   -1.6   0.0       0.7   2.1e+03      63     122 ..      93     156 ..      64     179 .. 0.55
   2 !   44.2   0.3   5.5e-15   1.6e-11      34     100 ..     390     460 ..     373     503 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.7
                                   GGHHHHHHTT-..SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB...BS----HHHHHHHTTS CS
                  TPP_enzyme_C  63 qelatavrrnl..pitvvvlnNegygmtggqqepfggkrksgpagk..dlkpvdfaklaealGa 122
                                     l+t+v + +   ++++  ++ g  + +++q+++  +  +++a      ++  +  l++a++ 
  gi|91772573|ref|YP_565265.1|  93 DPLITSVTHTIgaGLVIIAGDDPGVKASQNEQDSRWYGEVAEVAVFdpSNPDAAYRSLIRAFEL 156
                                   5566666664443666666677666666666544444444444332223444444455555544 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 5.5e-15
                                   HHHHHHHHH..HST.TSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTT CS
                  TPP_enzyme_C  34 lpaAiGakl..akp.drevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggqqepfggkrk 100
                                   +++A+Ga++  a+  d++ va++GD g+ ++ +  l++av+ + +++v+vl+N++ +mtggq++p   +  
  gi|91772573|ref|YP_565265.1| 390 VGFALGAAIstAAGfDKKSVAVIGDFGLSHSgIVGLINAVETKRDVLVMVLDNRTAAMTGGQSTPDLTEAV 460
                                   45555555544333378*********************************************999876544 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 !   37.4   0.2   7.4e-13   2.2e-09      18     153 ..      38     168 ..      21     204 .. 0.87
   2 ?   -3.4   0.0       2.2   6.6e+03      89     113 ..     436     460 ..     431     469 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 7.4e-13
                                   TTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHHHHTT--EEEEEEEEE- CS
                         POR_N  18 PsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlglaageelPvvivvvaRal 98 
                                   P + ++e +++  + +     +++ m +E +a ++++GA+++G ra+T T   G+   ++ l+  +++ + + +v++  a+
  gi|91772573|ref|YP_565265.1|  38 PTTAVIEHFEKNSPAEV----TILWMTNEKAALETALGASVSGRRALTITKHVGMNVLSDPLITSVTHTIGAGLVII--AG 112
                                   66777777777766555....79***********************************************9999988..69 PP

                                   STTBEEEEE--TTCHHHH.S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEE CS
                         POR_N  99 pstglsirtdqsDlmaar.dtglivlasenvqeafdlalvAfnlAekvrvPvivlf 153
                                   +++g+   +  +D        +++v+ ++n   a++  ++Af l+e++++Pviv +
  gi|91772573|ref|YP_565265.1| 113 DDPGVKASQNEQDSRWYGeVAEVAVFDPSNPDAAYRSLIRAFELSESTKTPVIVRI 168
                                   9***99999999998888356899999**************************964 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                                   EEEEEEEEE-STTBEEEEE--TTCH CS
                         POR_N  89 vvivvvaRalpstglsirtdqsDlm 113
                                   +v+v+ +R+ ++tg    +d ++++
  gi|91772573|ref|YP_565265.1| 436 LVMVLDNRTAAMTGGQSTPDLTEAV 460
                                   6999999999999987777766655 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 !   26.7   0.2   1.2e-09   3.6e-06       2     160 ..      14     169 ..      13     178 .. 0.85
   2 ?    1.3   0.0     0.077   2.3e+02      78     127 ..     420     467 ..     377     483 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.2e-09
                                   EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT...TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-C.HHHHHH. CS
                  TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq..girvvlarhEqgaafaAdgyaratgkpgvvlvts.gpGatn. 78 
                                   t+ eal  a  ++gv+ + +v G   ++++++++++   +++++ + +E +a   A g   ++g+++  ++ + g ++++ 
  gi|91772573|ref|YP_565265.1|  14 TGLEALYAAAMDCGVKMITAVAGFPTTAVIEHFEKNSpaEVTILWMTNEKAALETALGA-SVSGRRALTITKHvGMNVLSd 93 
                                   788999****************************************************7.666777777776669999864 PP

                                   .CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCS.SEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                  TPP_enzyme_N  79 .altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvt.kyaervtspeelpealrrAirtalsgrpgPvyl 157
                                    ++t++   ++ +  l++++gd p  + +q+      + +  + +v+  +++ +++p+++ + l rA++ + +++++Pv +
  gi|91772573|ref|YP_565265.1|  94 pLITSV--THTIGAGLVIIAGDDPGVKASQN-----EQDSRWYGEVAeVAVFDPSNPDAAYRSLIRAFELS-ESTKTPVIV 166
                                   467777..788999**********9999944.....3344455555534489*******************.99999**99 PP

                                   EEE CS
                  TPP_enzyme_N 158 elp 160
                                    + 
  gi|91772573|ref|YP_565265.1| 167 RIT 169
                                   886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.077
                                   HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEE CS
                  TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkya 127
                                   +++ +l++A  ++  +lv++ d+ t+     + q++ d ++ ++ ++ +a
  gi|91772573|ref|YP_565265.1| 420 SGIVGLINAVETKRDVLVMVLDNRTAAMT--GGQSTPDLTEAVKALCDDA 467
                                   46889999999999999999999999888..4555778888888888665 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.8e-06     0.011      42     171 ..      47     169 ..      21     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                                   HEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGGHHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGT CS
                  Transket_pyr  42 lhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgdFangAqiyadqairsgeakgklkvgvvtrlpigvgedGp 122
                                   +++++++  i  +  E+a+l +a+Ga+++g  ++   ++  + +n   +  d+ i+  +  + + +g+v+ ++   +    
  gi|91772573|ref|YP_565265.1|  47 EKNSPAEVTILWMTNEKAALETALGASVSG--RRALTITKHVGMN---VLSDPLIT--SVTHTIGAGLVIIAGD--DPGVK 118
                                   445545666666778999999999999999..6777777777777...44455555..6777778888887776..45566 PP

                                   TTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE- CS
                  Transket_pyr 123 ehqsaeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlp 171
                                   + q  ++ +++  ++++ v+ Ps+p  +++ l ra +   ++++Pv++r +
  gi|91772573|ref|YP_565265.1| 119 ASQNEQDSRWYGEVAEVAVFDPSNPDAAYRSLIRAFELseSTKTPVIVRIT 169
                                   7788999*****************************99888899***9976 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.032     119     175 ..     392     446 ..     366     476 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                DXP_synthase_N 119 aalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsi 175
                                    alG a+++  +g +kk vaviGD +l+      +l n+ e+k+++lv++ dN+ + 
  gi|91772573|ref|YP_565265.1| 392 FALGAAIST-AAGFDKKSVAVIGDFGLSHSGI-VGLINAVETKRDVLVMVLDNRTAA 446
                                   455555544.456789***********96443.477788888999999999998765 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 ?   10.5   0.0   0.00019      0.56      22      65 ..     250     293 ..     237     317 .. 0.84
   2 ?   -3.1   0.0       3.3   9.8e+03      55      81 ..     437     463 ..     431     486 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                                   HHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT CS
                       PFOR_II  22 lReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfg 65 
                                   l e+ ++v  l l ++ P P ++l++++++ kkv+v++ + +f 
  gi|91772573|ref|YP_565265.1| 250 LSERQLEVSHLSLNVVSPLPVRKLRDFISDHKKVLVVEESEAFI 293
                                   5677889999****************************998765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                                   EEEEE-S--TT-G-HHHHHHHHHTGGG CS
                       PFOR_II  55 vvvldrnisfgseGqlveevkaalkks 81 
                                   v+vld  ++  + Gq   +  +a+k+ 
  gi|91772573|ref|YP_565265.1| 437 VMVLDNRTAAMTGGQSTPDLTEAVKAL 463
                                   667777665555577777776666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3154.47
//
Query:       gi|91772574|ref|YP_565266.1|  [L=389]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-54  183.0   1.1    2.2e-53  181.6   0.0    1.9  2  DDE_Tnp_IS66   Transposase IS66 family
    9.4e-05   23.0   0.6    0.00028   21.4   0.6    1.8  1  SlyX           SlyX
     0.0003   21.0   0.0       0.22   11.7   0.2    2.6  2  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.044   13.4   1.5       0.43   10.2   0.7    2.3  2  YkyA           Putative cell-wall binding lipoprotein
      0.078   13.6   3.9      0.093   13.3   1.6    2.3  2  BST2           Bone marrow stromal antigen 2
      0.086   12.9   1.0       0.16   12.1   0.2    1.8  2  Gly_acyl_tr_N  Aralkyl acyl-CoA:amino acid N-acyltransferase
       0.14   12.1   0.0        1.4    8.8   0.0    2.6  3  BBS2_N         Ciliary BBSome complex subunit 2, N-terminal
       0.33   11.5   4.8       0.39   11.2   0.2    2.7  3  DUF16          Protein of unknown function DUF16
       0.38   11.4   4.0       0.91   10.2   1.9    2.5  2  PLATZ          PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.28   5.6e+02     174     225 ..      20      69 ..       4      85 .. 0.63
   2 !  181.6   0.0   1.1e-56   2.2e-53      48     280 ..     122     351 ..     106     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.28
                  DDE_Tnp_IS66 174 larigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   ++ + +ly+i +e +  +  e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772574|ref|YP_565266.1|  20 VTLVTTLYDIIAEQQ--TIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   444777787776653..24566666666666666777776776665555444 PP

  == domain 2  score: 181.6 bits;  conditional E-value: 1.1e-56
                  DDE_Tnp_IS66  48 raaelleplvealkaallasevihaDETtlrvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkG 126
                                   ++ + le + +++k+ l +s+vi++DET++r       +gk+++l+v++t+k   ++++  +++Rg+++++a+  L +f+G
  gi|91772574|ref|YP_565266.1| 122 NCERSLEDFEQQIKNFLIESPVINCDETGMR------IEGKRQWLHVASTNK---MTCYCPHQKRGSDAMNAMgiLPNFNG 193
                                   56677**************************......99***********99...***************99955666*** PP

                  DDE_Tnp_IS66 127 vlvsDgyagYnklaeeqvthalCwaHlrRkfvdaeeakkksqaaaealar.igklyaierearea....eaeerlalrqee 202
                                   ++v+D +++Y k+   +++h +C aHl+R++++++e+++  q +++a++  + ++++  +++re+    ++e+ ++ +  +
  gi|91772574|ref|YP_565266.1| 194 TVVHDFWKSYYKY---DCDHSICNAHLLRELTSVSENDD--QLWSKAMNIlLIDVKKSVDQIREMsgcmKPERIKEFEDWY 269
                                   ************9...7*******************977..*********************955678888********** PP

                  DDE_Tnp_IS66 203 srpllaeleawleeql....kkvlpksklgkairyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeG 279
                                    + ++  +e++ + q     ++ +++++++++++++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++G
  gi|91772574|ref|YP_565266.1| 270 GQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLDRFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQG 350
                                   **********998554567799*********************************************************** PP

                  DDE_Tnp_IS66 280 a 280
                                   a
  gi|91772574|ref|YP_565266.1| 351 A 351
                                   9 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.6   1.4e-07   0.00028      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq  i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772574|ref|YP_565266.1| 22 LVTTLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0047       9.4       5      44 ..     145     182 ..     141     185 .. 0.79
   2 !   11.7   0.2   0.00011      0.22      85     124 ..     314     353 ..     288     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaa 44 
                                   + DET ++i+Gk ++l  a  ++ ++ ++   ++R+ +a 
  gi|91772574|ref|YP_565266.1| 145 NCDETGMRIEGKRQWLHVA--STNKMTCYCPHQKRGSDAM 182
                                   68************99866..6666778888888888776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00011
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  
  gi|91772574|ref|YP_565266.1| 314 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALI 353
                                   55667899****************************9864 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00021      0.43      49      99 ..      16      66 ..       3      76 .. 0.85
   2 ?    1.0   0.0      0.14   2.8e+02      33      58 ..     264     289 ..     259     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                          YkyA 49 fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeel 99
                                   +++++l+  + +++ e+++++e + + i e +e ++k++e++++   ++ 
  gi|91772574|ref|YP_565266.1| 16 PEAVVTLVTTLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNSRNSS 66
                                  5679999*************************************9866554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                          YkyA  33 keqelyeeiielgmdefdkikklsde 58 
                                   + ++ y +ii  g++e+ +++++s++
  gi|91772574|ref|YP_565266.1| 264 EFEDWYGQIIHIGIEENPQLQAKSKK 289
                                   556789****************9986 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.6   4.7e-05     0.093      44      87 ..      20      63 ..       3      67 .. 0.83
   2 ?   -1.7   0.0       2.3   4.6e+03      14      30 ..     119     135 ..     115     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 44 nqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                     v tL + + ++++  + q a++ el++ +kkL+++L++ + 
  gi|91772574|ref|YP_565266.1| 20 VTLVTTLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNSR 63
                                  56788999999999**************************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHHHHHHHH CS
                          BST2  14 ecrnvtrlLerqLtqaq 30 
                                   +c+n +r Le   +q +
  gi|91772574|ref|YP_565266.1| 119 KCSNCERSLEDFEQQIK 135
                                   56666666654433333 PP

>> Gly_acyl_tr_N  Aralkyl acyl-CoA:amino acid N-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   7.9e-05      0.16      81     199 ..      22     137 ..       3     138 .. 0.73
   2 ?   -1.8   0.0       1.4   2.9e+03     143     143 ..     285     285 ..     215     347 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                 Gly_acyl_tr_N  81 dlealeelleeedvinwkqvfqiqglqsslkevikevaasksvqvkklktillmveetakklessklkakklslkkkkkqe 161
                                    +++l ++++e++ i   q+  i  l++ +k++ +++++ ++ + k  +t  ++++e+ k ++ +k++   ++++ +k+++
  gi|91772574|ref|YP_565266.1|  22 LVTTLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNSRNSSKPPSTD-VFINEKPKTKSRRKKSG--KKPGGQKDHP 99 
                                   455666777777777777888888888888888888877666666555544.44444444444444333..33567789** PP

                 Gly_acyl_tr_N 162 sfklssLdvshaalvnetWsfGgnerslryierliqnF 199
                                     +l ++dv +  ++ +  + +  ersl+  e+ i+nF
  gi|91772574|ref|YP_565266.1| 100 GTTLRMVDVPDEVIIHKVHKCSNCERSLEDFEQQIKNF 137
                                   ***********************************999 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                 Gly_acyl_tr_N 143 e 143
                                   +
  gi|91772574|ref|YP_565266.1| 285 A 285
                                   2 PP

>> BBS2_N  Ciliary BBSome complex subunit 2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00071       1.4      17      82 ..     108     171 ..      94     177 .. 0.83
   2 ?   -3.1   0.0       3.7   7.3e+03      42      54 ..     235     247 ..     219     260 .. 0.55
   3 ?   -1.1   0.0      0.88   1.7e+03      41      55 ..     328     342 ..     316     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00071
                        BBS2_N  17 tagkvlihnphekeqklkserlsasesevslLninkevtalaagklkekqekdiLligtqtnllaY 82 
                                     ++v+ih+ h+ ++  +  +l++ e++++ + i++ v+      ++ + +++ L +++ +++++Y
  gi|91772574|ref|YP_565266.1| 108 VPDEVIIHKVHKCSNCER--SLEDFEQQIKNFLIESPVINCDETGMRIEGKRQWLHVASTNKMTCY 171
                                   5679*******9985443..45556***********99999888899999**************99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
                        BBS2_N  42 esevslLninkev 54 
                                   + ++ l++++k+v
  gi|91772574|ref|YP_565266.1| 235 AMNILLIDVKKSV 247
                                   3344444444444 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.88
                        BBS2_N  41 sesevslLninkevt 55 
                                    e++v++++++++++
  gi|91772574|ref|YP_565266.1| 328 AERDVRMMKVQQKIS 342
                                   3899********997 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2    0.0002      0.39      45      82 ..      25      62 ..      16      75 .. 0.80
   2 ?   -3.8   0.0         9   1.8e+04      56      64 ..     126     134 ..     110     141 .. 0.52
   3 ?    1.4   0.2      0.22   4.4e+02      10      58 ..     287     342 ..     278     369 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772574|ref|YP_565266.1| 25 TLYDIIAEQQTIIELQAARITELEERVKKLEEQLKKNS 62
                                  55566788889999999999999999999999988654 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9
                                   HHHHHHHHH CS
                         DUF16  56 kvekqgeki 64 
                                     e  +++i
  gi|91772574|ref|YP_565266.1| 126 SLEDFEQQI 134
                                   222222222 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.22
                                   XXX.X.XTTB-BHHHHHH....B-.....BHHHHH.HHHHHHH...HHHHHHHHHHH CS
                         DUF16  10 vKkiPvkteYVTrkqlne....fkds...nkqrLk.kieakvdklgeqinkleqkve 58 
                                    Kk  ++t+  T k+l +    +k++      +Lk  +e++++ +++++ k++qk++
  gi|91772574|ref|YP_565266.1| 287 SKK-RGRTKQTTAKNLLDrfigYKNDilrFMHDLKvPFENNLAERDVRMMKVQQKIS 342
                                   455.46788888888877788899998883344442356666666666666666553 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9   0.00046      0.91      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.7   0.0         9   1.8e+04      39      51 ..     280     292 ..     268     300 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00046
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772574|ref|YP_565266.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDF 130
                                   9*******9999988888743.33333568999***********************985 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9
                         PLATZ  39 rpqarsakakake 51 
                                    pq + +++k+ +
  gi|91772574|ref|YP_565266.1| 280 NPQLQAKSKKRGR 292
                                   4444433333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1674  (0.0933683); expected 358.6 (0.02)
Passed bias filter:                      926  (0.0516482); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 2579.25
//
Query:       gi|91772575|ref|YP_565267.1|  [L=59]
Description: hypothetical protein Mbur_0540 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0098   16.2   0.0      0.013   15.8   0.0    1.2  1  DUF4177   Domain of unknown function (DUF4177)
  ------ inclusion threshold ------
       0.11   13.2   0.0       0.11   13.1   0.0    1.1  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> DUF4177  Domain of unknown function (DUF4177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.4e-06     0.013      22      53 ..      15      44 ..       4      52 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-06
                       DUF4177 22 eleeyqeilnelAkeGWrlvsii.pvkesrgvg 53
                                  ++++ +e ln l+ +GW+l+ +  +     + g
  gi|91772575|ref|YP_565267.1| 15 KIDTTKEDLNSLGIDGWELIKFDgQ---LDSSG 44
                                  33444467************95543...33333 PP

>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05      0.11       4      40 ..      10      46 ..       8      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                  EEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEE CS
                          P-II  4 iirpekleevkeaLekagvkgltvtevkGrGkqkght 40
                                  +ir++k++++ke L+++g++g  +++  G+    g+t
  gi|91772575|ref|YP_565267.1| 10 MIRMDKIDTTKEDLNSLGIDGWELIKFDGQLDSSGKT 46
                                  79**********************9999976666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 442.38
//
Query:       gi|91772576|ref|YP_565268.1|  [L=184]
Description: hypothetical protein Mbur_0541 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-49  166.2   2.4    9.8e-49  166.0   2.4    1.0  1  DUF2115   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0   2.4   5.5e-53   9.8e-49       2     163 ..      11     166 ..      10     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 5.5e-53
                       DUF2115   2 kgeLleilkkeaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevideeelkef 82 
                                   ++eLl+ l+k+a++is++D+mk+++++ + +k lpeky+k++s++l++y++e++ e+k  rs+  +e     id e+++e+
  gi|91772576|ref|YP_565268.1|  11 TKELLASLEKDARRISNNDIMKARSFMLNYVKFLPEKYKKAYSTELFSYYYETFMEIKGLRSNPVIE----EIDIETYNEL 87 
                                   689********************************************************66666664....49******** PP

                       DUF2115  83 lemleeqceeekeekeerlrklyylvslYliFvleePlHpvgtpfPGgfkveekdgeyYCPvkdkqkdvekalCkfCiakq 163
                                   ++++++q++e+    e+ +++++ +v++YliF++++PlHpvg+ +PGg ++ e +geyYCP+k+kq++v+ alCk+Ci+k+
  gi|91772576|ref|YP_565268.1|  88 VKNYSQQFNEDPL--ESYFQRFMSVVTPYLIFITKKPLHPVGMILPGGMTIMEPNGEYYCPIKNKQTEVDIALCKYCICKD 166
                                   *********9877..8****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1178.04
//
Query:       gi|91772577|ref|YP_565269.1|  [L=79]
Description: hypothetical protein Mbur_0542 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   11.9   0.1       0.13   11.6   0.1    1.1  1  DUF3179   Protein of unknown function (DUF3179)


Domain annotation for each model (and alignments):
>> DUF3179  Protein of unknown function (DUF3179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.2e-06      0.13     265     285 .]       4      24 ..       1      24 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-06
                       DUF3179 265 lervaaaeafWFawaaFhpet 285
                                    e++a+ + fWFa ++Fhpet
  gi|91772577|ref|YP_565269.1|   4 GEEIAKERNFWFACYTFHPET 24 
                                   68999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 530.50
//
Query:       gi|91772578|ref|YP_565270.1|  [L=703]
Description: hypothetical protein Mbur_0543 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-72  241.4   0.4    9.9e-72  240.2   0.4    1.6  1  Thioredox_DsbH  Protein of unknown function, DUF255
    1.5e-11   44.3   0.0    3.6e-11   43.1   0.0    1.7  1  Thioredoxin_7   Thioredoxin-like
    1.2e-09   37.8   0.1    5.4e-05   22.4   0.0    2.6  2  Glyco_hydro_88  Glycosyl Hydrolase Family 88
    6.8e-07   29.1   0.3     0.0066   16.0   0.0    2.7  2  Glyco_hydro_76  Glycosyl hydrolase family 76
      1e-05   25.0   0.6      0.045   13.0   0.0    3.7  4  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
    2.5e-05   23.0   3.7     0.0094   14.6   0.0    4.3  3  LANC_like       Lanthionine synthetase C-like protein
     0.0044   17.5   0.0       0.39   11.2   0.0    2.6  2  Thioredoxin_2   Thioredoxin-like domain
     0.0046   16.5   2.4      0.031   13.8   0.1    3.1  4  C5-epim_C       D-glucuronyl C5-epimerase C-terminus
  ------ inclusion threshold ------
      0.094   12.4   0.1       0.21   11.3   0.1    1.5  1  Pox_G9-A16      Pox virus entry-fusion-complex G9/A16


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 !  240.2   0.4     5e-75   9.9e-72       1     162 [.       9     170 ..       9     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 240.2 bits;  conditional E-value: 5e-75
                Thioredox_DsbH   1 knrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDre 81 
                                   knrl++ek pYllqha++ vdWypw+eea+ekak+edkpi+lsiGys+chWChvm+kesf++++va+++n++fvs+kvDre
  gi|91772578|ref|YP_565270.1|   9 KNRLINEKNPYLLQHANDSVDWYPWTEEAFEKAKNEDKPIFLSIGYSTCHWCHVMAKESFRNKDVAKMMNDTFVSIKVDRE 89 
                                   69******************************************************************************* PP

                Thioredox_DsbH  82 erPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeelleal 162
                                   erPd+d++ym+++q ++gsggWPl++++tp++ pf+++tY+p ++  gr+g+le++  i++lw+ee++++ e++e + +al
  gi|91772578|ref|YP_565270.1|  90 ERPDIDSVYMDICQKMNGSGGWPLTIIMTPEKVPFIAATYIPLKSGFGRKGMLEIIPWIEHLWKEEHNKIVEQTELIKTAL 170
                                   *************************************************************************99888776 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.8e-14   3.6e-11       1      65 [.      29      93 ..      29     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.8e-14
                                  ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                 Thioredoxin_7  1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65
                                  +w+ + +ea++ka+ + kp+++ +g s+c+ C++++++   +++v++++++ fv  +vd +er +
  gi|91772578|ref|YP_565270.1| 29 DWYPWTEEAFEKAKNEDKPIFLSIGYSTCHWCHVMAKESFRNKDVAKMMNDTFVSIKVDREERPD 93
                                  7**********************************9998888888888************99976 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 !   12.3   0.0   3.2e-05     0.064      38     117 ..     220     319 ..     216     329 .. 0.86
   2 !   22.4   0.0   2.7e-08   5.4e-05      28     166 ..     429     593 ..     402     600 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHH--HHHHHHHHHHHHHCCCTTS-.....................CTTSGGGTGHHHHHHHHHHHH-THHHHHHH CS
                Glyco_hydro_88  38 lleayeatgdkeyldyakawadslideggk.....................telelDdidigllllllyeltkderykeaa 97 
                                   ll++++ tg+++ l++++++ + + + g                       +++  D++ +   +   y+ t++e+y ++a
  gi|91772578|ref|YP_565270.1| 220 LLRYWKRTGNPTALQMVERTLQAMRKGGIYdhigfgfhrystdsswlvphfEKMLYDQALLIIAYTEAYQATNKEEYSNTA 300
                                   6789999999999999999888888777778888888888888889999988999999999999999************** PP

                                   HHHHHHHHHCS-B.TTS.B. CS
                Glyco_hydro_88  98 eeladyvlakpprtseGgfw 117
                                   +e+++y+l+++ +  +Ggf 
  gi|91772578|ref|YP_565270.1| 301 NEIIEYILRDMTS-PDGGFY 319
                                   ********99999.788886 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.7e-08
                                   .HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-...............CTTSGGGTGHHHH.HHHHHHHH-THH CS
                Glyco_hydro_88  28 ewtnGvflsglleayeatgdkeyldyakawadslideggk...............telelDdidigll.llllyeltkder 92 
                                   +w nG++l +l       g+k+y+d+ak++ad li e  k               t   lDd + +   l+ lye t +  
  gi|91772578|ref|YP_565270.1| 429 DW-NGLMLAALSISGRVMGNKRYIDIAKRNADLLISERMKengelyhnyssnkepTIGFLDDYAFFTWgLIELYEATFEVT 508
                                   44.7888888888888999**************99999999999**99999998888889998887763577********* PP

                                   HHHHHHHHHHHHHHCS-B.TTS.B.SBTTSTTEEE...........THHHHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHH CS
                Glyco_hydro_88  93 ykeaaeeladyvlakpprtseGgfwhkkkepeqlW...........lDgLfMaipllaklskvtgepkyldeaikqfllta 162
                                   y + a +l+dy++++ ++t +Ggf+h + + e+l              g    i  l+klsk+tg+p++  eai+   ++a
  gi|91772578|ref|YP_565270.1| 509 YLAKALQLTDYMIENFKDTINGGFFHTSNKSETLLfrkkevydgaiPSGNSVEINNLLKLSKLTGNPELNSEAIDTSNAFA 589
                                   **************************5555555444555553333333334577888999999999999999999888888 PP

                                   HHHB CS
                Glyco_hydro_88 163 rhlf 166
                                   ++++
  gi|91772578|ref|YP_565270.1| 590 STIY 593
                                   7755 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2   0.00019      0.38       7     129 ..     184     312 ..     178     322 .. 0.60
   2 !   16.0   0.0   3.3e-06    0.0066      39     138 ..     432     533 ..     409     582 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHCETTECCTCTCBSCES-GHHHHHHHHHHHHHHHHHCTTCCCHHHHHHHHHCCCTCE.E-SSSTTCTCSSEH CS
                Glyco_hydro_76   7 atiakgllkyYkgnesggtpgnlpdpyywWeagalfgalidywrltgdstyndlitqallaqagen.ydympanqsrtegn 86 
                                   ++i +++ +y   n  +++ g  ++p   ++  + ++ l+ yw++tg++t  +++++ l+a+++   yd +     r++ +
  gi|91772578|ref|YP_565270.1| 184 EEIIHRTYTYLANNFDNENGGFGTSP--KFPSPHNISYLLRYWKRTGNPTALQMVERTLQAMRKGGiYDHIGFGFHRYSTD 262
                                   55666666666666333333333333..3455578899*******************999977744455444433332222 PP

                                   H............HHHHHHHHHHHHHHH.....H--HHHHHHHHHHHHHHHHCB- CS
                Glyco_hydro_76  87 D............DqafwglaamtaaernfpeptdepswLalAqavfntqasrwd 129
                                                Dqa   +a  +a++      t+++++ + A+++++++ +   
  gi|91772578|ref|YP_565270.1| 263 SswlvphfekmlyDQALLIIAYTEAYQ-----ATNKEEYSNTANEIIEYILRDMT 312
                                   223333351122255555555555555.....599999****9999999887654 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.3e-06
                                   HHHHHHHHHHHHHCTTCCCHHHHHH.......HHHCCCTCE.E-SSSTTCTCSSEHHHHHHHHHHHHHHHHH.....H--H CS
                Glyco_hydro_76  39 galfgalidywrltgdstyndlitq.......allaqagen.ydympanqsrtegnDDqafwglaamtaaernfpeptdep 111
                                   g ++ al    r++g+++y d+ ++       + + ++ge  ++y ++++ +  + DD af +   ++ +e++f+ +    
  gi|91772578|ref|YP_565270.1| 432 GLMLAALSISGRVMGNKRYIDIAKRnadllisERMKENGELyHNYSSNKEPTIGFLDDYAFFTWGLIELYEATFEVT---- 508
                                   5666666666677777777777666554444334446666625588888888889******99999*****977666.... PP

                                   HHHHHHHHHHHHHHHCB-SCSCCS-BB CS
                Glyco_hydro_76 112 swLalAqavfntqasrwdeetcgGGlr 138
                                    +La A ++ +++++ ++++  +GG  
  gi|91772578|ref|YP_565270.1| 509 -YLAKALQLTDYMIENFKDT-INGGFF 533
                                   .****************886.899975 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.37   7.3e+02     277     316 ..     162     203 ..     138     205 .. 0.70
   2 !   13.0   0.0   2.3e-05     0.045      35     125 ..     226     320 ..     219     332 .. 0.79
   3 ?    2.7   0.0     0.031        62     240     326 ..     393     479 ..     378     489 .. 0.58
   4 !    4.4   0.0    0.0093        18     286     328 ..     499     541 ..     494     553 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHHHHH..H--CHHHHHHHHHHHHHHHHTB-TTT CS
                 GlcNAc_2-epim 277 qtEalkaaaalael..tgearylewyarvaeylerhlidpek 316
                                   qtE +k+a+  +++    e+  +e+ +r   yl+++++++  
  gi|91772578|ref|YP_565270.1| 162 QTELIKTALSEKSEnsHNEEVTEEIIHRTYTYLANNFDNENG 203
                                   889999987665553256678888888888888888765544 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.3e-05
                                   HTT-TTHHHHHHHHHHHTTTTTB-TTTS.SB-SEEETTEEEE-..-EEHHHHHHHHHHHHHHHTTT-TTH.HHHHHHHHHH CS
                 GlcNAc_2-epim  35 qlgrpgwldlvehGlkflekvlrdaehg.gyfsalrdggvlda..skdaYdhaFvllalasalaageeea.kdlldetlav 111
                                   + g+p +l++ve  l++++k +  ++ g g+ +  +d   l +  +k +Yd+a  ++a+ +a++a ++e   + ++e+++ 
  gi|91772578|ref|YP_565270.1| 226 RTGNPTALQMVERTLQAMRKGGIYDHIGfGFHRYSTDSSWLVPhfEKMLYDQALLIIAYTEAYQATNKEEySNTANEIIEY 306
                                   5788889999999999999988867777566666677775555115779************999988765499999***** PP

                                   HHHHTEETTTTEE- CS
                 GlcNAc_2-epim 112 lekhlweekaglvk 125
                                   + +++ +++ g++ 
  gi|91772578|ref|YP_565270.1| 307 ILRDMTSPDGGFYC 320
                                   *****999988865 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHBS-SSSSB-S-B-TTS-BSS--EE..HHHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHTB-TTTSS CS
                 GlcNAc_2-epim 240 kLfetalakgwdkdrgglvytldaagkpvddakl..lWpqtEalkaaaalaeltgearylewyarvaeylerhlidpekGl 318
                                   +++ + +++ +++ r+ l+ t ++  +p++d+k+   W  +  l+a+ +  ++ g++ry ++++r a++l +  + +e+G+
  gi|91772578|ref|YP_565270.1| 393 NITRKEIDHIIERCRKQLFSTREKRIHPSKDDKIltDWNGLM-LAALSISGRVMGNKRYIDIAKRNADLLISE-RMKENGE 471
                                   555555555555556666666666666666666533455543.555555555566667777666666666666.5556666 PP

                                   B-SEE-TT CS
                 GlcNAc_2-epim 319 Wfdkldad 326
                                    +++++ +
  gi|91772578|ref|YP_565270.1| 472 LYHNYSSN 479
                                   66665555 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0093
                                   HHHHHH--CHHHHHHHHHHHHHHHHTB-TTTSSB-SEE-TTS- CS
                 GlcNAc_2-epim 286 alaeltgearylewyarvaeylerhlidpekGlWfdkldadge 328
                                    l+e t e  yl+ + ++ +y+ ++++d ++G  f+  ++ ++
  gi|91772578|ref|YP_565270.1| 499 ELYEATFEVTYLAKALQLTDYMIENFKDTINGGFFHTSNKSET 541
                                   5777888888888888888888888888888888888777765 PP

>> LANC_like  Lanthionine synthetase C-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.033        65     182     214 ..     178     210 ..     166     224 .. 0.72
   2 !   14.6   0.0   4.7e-06    0.0094      14      60 ..     280     324 ..     277     325 .. 0.94
   3 ?    2.2   0.1     0.026        53     170     213 ..     432     477 ..     390     485 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.033
                                   .-HHHHHHHHHHHHHHHHHTS-TGTST--SBCT CS
                     LANC_like 182 tksekllelikkllkylkslkfksegnWpdsis 214
                                    ++e ++e+i+++++yl +++++++g++ +s +
  gi|91772578|ref|YP_565270.1| 178 HNEEVTEEIIHRTYTYLANNFDNENGGFGTSPK 210
                                   36677899*************888888988766 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.7e-06
                                   HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHCCH.-S--STTT.SHH CS
                     LANC_like  14 iallllelykvtknekylklahkylekikkelselglesisffs.Gaa 60 
                                   +++++ e+y++t++e+y ++a++++e+i + + +   ++ +f++ G+a
  gi|91772578|ref|YP_565270.1| 280 LIIAYTEAYQATNKEEYSNTANEIIEYILRDMTS---PDGGFYCaGDA 324
                                   5899******************************...******98875 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.026
                                   H.HHHHHHCCCHT.-HHHHHHHHHHHHHHHHHTS-TGTST.--SBC CS
                     LANC_like 170 G.ialallalykgtksekllelikkllkylkslkfksegn.Wpdsi 213
                                   G ++ al+ ++++ +++++ +++k+ +++l s + k++g+ + ++ 
  gi|91772578|ref|YP_565270.1| 432 GlMLAALSISGRVMGNKRYIDIAKRNADLLISERMKENGElYHNYS 477
                                   6456677777888899999999999999999999887777555443 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0002      0.39       1      59 [.      41      92 ..      41     134 .. 0.73
   2 ?    3.3   0.0     0.056   1.1e+02      46      88 ..     411     488 ..     381     496 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                 Thioredoxin_2  1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakek 59
                                  ak + kp+++ +  ++C  C+ + ke + ++dv +      +++   ++++++++++ +
  gi|91772578|ref|YP_565270.1| 41 AKNEDKPIFLSIGYSTCHWCHVMAKESFRNKDVAKM-----MNDT--FVSIKVDREERP 92
                                  57789*****************************99.....6666..444444444444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.056
                 Thioredoxin_2  46 fepkavaiwcakekk..kafkd.................................ieenvelarkygvrgtPtivfld 88 
                                   f++   +i  +k+ k  +++++                                 ++en el + y  +  Pti fld
  gi|91772578|ref|YP_565270.1| 411 FSTREKRIHPSKDDKilTDWNGlmlaalsisgrvmgnkryidiakrnadlliserMKENGELYHNYSSNKEPTIGFLD 488
                                   5556666667777655555555777777777888888888888888888899999*******************9998 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 ?   -0.9   0.0      0.51     1e+03      34      74 ..     216     252 ..     212     268 .. 0.76
   2 !   13.8   0.1   1.5e-05     0.031      30      69 ..     276     317 ..     273     334 .. 0.85
   3 ?   -0.6   0.2      0.39   7.8e+02      43      63 ..     443     463 ..     431     529 .. 0.59
   4 ?   -1.4   0.1      0.71   1.4e+03      38      74 ..     497     536 ..     473     550 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.51
                     C5-epim_C  34 aisvllrAYeltgdekYlkaakkalksfkipvekGGvlktl 74 
                                    is llr ++ tg+   l++ ++ l++++    kGG+ +++
  gi|91772578|ref|YP_565270.1| 216 NISYLLRYWKRTGNPTALQMVERTLQAMR----KGGIYDHI 252
                                   68999999999999999999999998875....66666665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                     C5-epim_C  30 aqgqaisvllrAYeltgdekYlkaakkalksfk..ipvekGG 69 
                                   +q+ +i+++++AY++t++e+Y ++a++ +++++  +++ +GG
  gi|91772578|ref|YP_565270.1| 276 DQALLIIAYTEAYQATNKEEYSNTANEIIEYILrdMTSPDGG 317
                                   69999************************9986113445666 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.39
                     C5-epim_C  43 eltgdekYlkaakkalksfki 63 
                                   ++ g+++Y+++ak+  +++  
  gi|91772578|ref|YP_565270.1| 443 RVMGNKRYIDIAKRNADLLIS 463
                                   566777888888776665433 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.71
                     C5-epim_C  38 llrAYeltgdekYlkaakkalksfkipve...kGGvlktl 74 
                                   l++ Ye+t +  Yl  a ++++++  + +   +GG+ +t+
  gi|91772578|ref|YP_565270.1| 497 LIELYEATFEVTYLAKALQLTDYMIENFKdtiNGGFFHTS 536
                                   4555777777777777777666654433211156666555 PP

>> Pox_G9-A16  Pox virus entry-fusion-complex G9/A16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.21       6      53 ..     647     696 ..     644     701 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                    Pox_G9-A16   6 daekkdkrckCvfpskaiieesekvlepreCWleeCt..krdrklLltdq 53 
                                   ++ek++k++  ++p +++++++++ +  ++C  +eCt  + d +++++ +
  gi|91772578|ref|YP_565270.1| 647 KSEKNEKELERIAPYTSTLKTQNQKATAYVCQGHECTlpTTDPQIIVEIL 696
                                   67899999999**************************9888888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); 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: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4633.75
//
Query:       gi|91772579|ref|YP_565271.1|  [L=171]
Description: hypothetical protein Mbur_0544 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00079   19.3   0.2     0.0013   18.7   0.2    1.3  1  RNHCP     RNHCP domain
  ------ inclusion threshold ------
      0.062   13.4   0.6       0.19   11.9   0.8    1.8  2  DUF678    Protein of unknown function (DUF678)


Domain annotation for each model (and alignments):
>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   1.4e-07    0.0013      36      83 ..      30      76 ..       7      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-07
                         RNHCP 36 deepgdraseCkglmepiavevkkkkewvivhrCekCgelkknrvakd 83
                                  +e+  +  s+C++ + +++ +   +ke++iv +C+kC++l++n   +d
  gi|91772579|ref|YP_565271.1| 30 EENEVGTCSKCRSPIVSLSYH-AIDKEFIIVGKCTKCEKLTANIYDQD 76
                                  555666789999999999987.5599*****************99887 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   2.1e-05      0.19      19      39 ..      27      48 ..      10      71 .. 0.79
   2 ?   -2.8   0.0      0.79   7.1e+03      38      57 ..      80      99 ..      77     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                        DUF678 19 vede.ddctTCSlCqSkLvkvs 39
                                  v+ e +++ TCS C S +v++s
  gi|91772579|ref|YP_565271.1| 27 VDSEeNEVGTCSKCRSPIVSLS 48
                                  66555999**********9987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.79
                        DUF678 38 vsdvskvslsklkvavgkgn 57
                                  vs++ ++++s++   +g+++
  gi|91772579|ref|YP_565271.1| 80 VSEIPNSHFSRYVAKAGTST 99
                                  78899999998887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1201.44
//
Query:       gi|91772580|ref|YP_565272.1|  [L=106]
Description: hypothetical protein Mbur_0545 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  115.9   0.7    8.8e-34  115.6   0.7    1.1  1  DUF2551          Protein of unknown function (DUF2551)
     0.0036   17.6   0.1     0.0052   17.1   0.1    1.3  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.085   13.1   0.0       0.16   12.3   0.0    1.4  1  DUF4777          Domain of unknown function (DUF4777)


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 !  115.6   0.7   1.5e-37   8.8e-34       1      82 [.      12      93 ..      12      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.5e-37
                       DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeeyadl 82
                                  L+k++e D +G+R+ vL++fl++kk t++e+++++++k+dvs+++vasmvG+i+s+lGIl+++kes++++ vYsLkeeyadl
  gi|91772580|ref|YP_565272.1| 12 LNKFIELDVNGFRSYVLSVFLSVKKSTIDELHQAIAKKYDVSRSAVASMVGYIHSKLGILRSHKESYKTPIVYSLKEEYADL 93
                                  79******************************************************************************98 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   8.7e-07    0.0052       8      63 ..      27      85 ..      24     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.7e-07
                                  HHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHT.TS-EEEEE..TTEEEEE CS
               Penicillinase_R  8 vmeilwekgeatvkevveeleeekelaysTVktllrrLvkK.gllsreke..grafiYs 63
                                  v+ ++ + ++ t++e+++++++++++++s V+++++  + K g+l+++ke  +  ++Ys
  gi|91772580|ref|YP_565272.1| 27 VLSVFLSVKKSTIDELHQAIAKKYDVSRSAVASMVGYIHSKlGILRSHKEsyKTPIVYS 85
                                  8889999999*****************************99789999988444445555 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.7e-05      0.16       8      44 ..      26      61 ..      22      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                       DUF4777  8 lvlealkvlnrPaTldEivervaerydlseeelkkvV 44
                                   vl+++ +++++ T+dE+ +++a++yd+s + +   V
  gi|91772580|ref|YP_565272.1| 26 YVLSVFLSVKKS-TIDELHQAIAKKYDVSRSAVASMV 61
                                  699999999998.****************98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 790.16
//
Query:       gi|91772581|ref|YP_565273.1|  [L=133]
Description: hypothetical protein Mbur_0546 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.19   11.6   0.0    1.4  1  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 ?   11.6   0.0   1.1e-05      0.19      23      59 ..      68     104 ..      65     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                                   CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                          TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVerekgrp 59 
                                   ++ ++i ++l+v r++ Y++ ++L+ +Gl+  +  ++
  gi|91772581|ref|YP_565273.1|  68 SEWQDIINDLDVGRASFYSMRNKLLGAGLISNRNNEY 104
                                   56789*************************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 871.91
//
Query:       gi|91772582|ref|YP_565274.1|  [L=219]
Description: K+ transport systems NAD-binding subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-26   90.7   2.5    1.3e-25   89.9   2.5    1.4  1  TrkA_N          TrkA-N domain
    1.9e-09   37.2   0.0    6.1e-09   35.6   0.0    1.9  1  TrkA_C          TrkA-C domain
    2.7e-07   31.0   0.7      5e-07   30.1   0.7    1.4  1  NAD_binding_7   Putative NAD(P)-binding
    7.7e-05   23.2   1.3    0.00018   22.0   1.3    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    9.6e-05   22.3   0.0    0.00012   22.0   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding
    0.00025   21.1   2.5    0.00041   20.4   1.1    1.9  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0021   18.3   0.3     0.0029   17.8   0.3    1.2  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0023   17.9   0.2     0.0036   17.2   0.2    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.004   15.9   0.1     0.0051   15.6   0.1    1.2  1  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.013   14.8   0.0    1.2  1  FAD_binding_3   FAD binding domain
      0.023   14.0   0.3       0.03   13.6   0.3    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.025   15.1   0.4      0.053   14.1   0.4    1.6  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.029   13.9   0.1      0.045   13.3   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.033   13.7   0.1      0.042   13.3   0.1    1.2  1  Epimerase       NAD dependent epimerase/dehydratase family
      0.042   13.7   0.1      0.074   12.9   0.1    1.5  1  LpxI_N          LpxI N-terminal domain
      0.044   13.3   0.3      0.074   12.6   0.2    1.3  1  DAO             FAD dependent oxidoreductase
      0.045   13.7   0.0      0.075   13.0   0.0    1.4  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.06   12.8   0.4      0.083   12.3   0.4    1.2  1  adh_short       short chain dehydrogenase
      0.078   12.9   0.3       0.11   12.4   0.3    1.3  1  KR              KR domain
       0.12   12.0   0.2       0.19   11.3   0.2    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA


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 !   89.9   2.5   1.4e-28   1.3e-25       1     116 []       3     118 ..       3     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.4e-28
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                   +i++G+G +G +l++++ ++gk+v++i+kde+ ++el+e   ++v+++++t++++Le+a+i++adav+a+t +d+ nil+ 
  gi|91772582|ref|YP_565274.1|   3 VIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAETMdCTVINAEGTRPDILEKADIDNADAVVACTTNDQNNILIG 83 
                                   79*****************7768***************999999************************************* PP

                                   HHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                        TrkA_N  81 llakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                   l+a++     k+i +++d+++ ++++klg+ ++i+p
  gi|91772582|ref|YP_565274.1|  84 LIARDAKV-GKVILKIEDRQFMDIASKLGFYYMINP 118
                                   ****9666.69*********************9998 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   6.8e-12   6.1e-09       6      70 .]     151     214 ..     146     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.8e-12
                                   EE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                        TrkA_C   6 vpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                   v a  ++++++l+e+ l++ +   ++i R+ e+i++  d +L+e D+l++v++ + ++++ e+lg
  gi|91772582|ref|YP_565274.1| 151 VMATDKIINMKLSEISLPQ-NSAFIGIYRKSEFILAEKDPKLYEKDELILVTKADMISTVNEVLG 214
                                   778899*************.99999999999*****************************99875 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 !   30.1   0.7   5.6e-10     5e-07       9      84 ..       2      88 ..       1     105 [. 0.68

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.6e-10
                 NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele...elvk...laeee.....l..ekdlegadlviaatddrelneri 78
                                  +v+vvG+G+++ +  r+++++g++v+++ ++  ++++   e+++   ++  e     +  ++d+++ad v+a+t++++ n  i
  gi|91772582|ref|YP_565274.1|  2 RVIVVGAGSLGIHLTRNMIAQGKEVILIEKDE-AIAKelaETMDctvINA-EgtrpdIleKADIDNADAVVACTTNDQNNILI 82
                                  79**************************9994.44442333333222111.122223356699***************99875 PP

                 NAD_binding_7 79 aeaaka 84
                                     a++
  gi|91772582|ref|YP_565274.1| 83 GLIARD 88
                                  444443 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 !   22.0   1.3     2e-07   0.00018       2      92 ..       3      96 ..       2      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2e-07
                                  EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...-EEECECHHHHHHH-SE.....EEE-S-HHHHHH CS
                 F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...vkvtavdneeaaeeadv.....vvlavkpedvee 76
                                  + ++GaG++g  l+++++a+g   +e++++ ++++  a+elae++    +++++ +  + +e+ad+     vv +    +   
  gi|91772582|ref|YP_565274.1|  3 VIVVGAGSLGIHLTRNMIAQG---KEVILI-EKDEAIAKELAETMDctvINAEG-TRPDILEKADIdnadaVVACTTNDQNNI 80
                                  5678*****************...****89.***************88855555.6666666544433330666655555555 PP

                                  HHHHCGHHHHTTSEEE CS
                 F420_oxidored 77 vlselakdalkgklvi 92
                                  ++  +a+da+ gk+++
  gi|91772582|ref|YP_565274.1| 81 LIGLIARDAKVGKVIL 96
                                  5666678888888776 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 !   22.0   0.0   1.3e-07   0.00012       3      73 ..       8      78 ..       7     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                                  TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCC CS
                NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggk 73
                                   G+ G +l++  +a+g  ev ++  +++ ++el+++  ++v+ ++ t ++ l++a +++adaVv+++ ++++
  gi|91772582|ref|YP_565274.1|  8 AGSLGIHLTRNMIAQG-KEVILIEKDEAIAKELAETMDCTVINAEGTRPDILEKAdIDNADAVVACTTNDQN 78
                                  699************6.9***********************************9979*******99987665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.1   4.6e-07   0.00041      14      89 ..       2      79 ..       1     108 [. 0.74
   2 ?   -0.7   0.0       1.5   1.3e+03      72      99 ..     140     167 ..     128     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.6e-07
                                  EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EE..EEGCGHHHH.HHT-SEEEE-SSSSS-S CS
                  Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiea..lkleelkel.laeadvvisataseepi 89
                                  +v+++GaG ++  ++++++a+g + v+ +  + + akelae ++ + i+a  ++ + l+++ +++ad v+++t   ++ 
  gi|91772582|ref|YP_565274.1|  2 RVIVVGAGSLGIHLTRNMIAQGKE-VILIEKDEAIAKELAETMDCTVINAegTRPDILEKAdIDNADAVVACTTNDQNN 79
                                  79*****************99988.9999*************965544441144444544349999*999998766543 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                   HHHT-SEEEE-SSSSS-SB-HHHHHCCH CS
                  Shikimate_DH  72 llaeadvvisataseepilekeeveeal 99 
                                    l ++dv ++ +++++ i++ +  e +l
  gi|91772582|ref|YP_565274.1| 140 NLVRYDVRFMGVMATDKIINMKLSEISL 167
                                   4568999999999999999987766555 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 !   17.8   0.3   3.3e-06    0.0029       3      86 ..       4      95 ..       2     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                                  EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT....EEE-SSHHHHHHHC.....SEEEE-SSSHHHHHHHHHS. CS
                 NAD_binding_2  3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg....akaaesieelvasl.....dvvitmvkagkavdevieg. 75
                                   ++G G +G ++ +n++++g +v++++ +++ ++el+++     ++a  +  ++++++     d+v+ + +++++  +++ g 
  gi|91772582|ref|YP_565274.1|  4 IVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAETMdctvINAEGTRPDILEKAdidnaDAVVACTTNDQN--NILIGl 84
                                  689**********************************99888876666666688888877777888887776543..333332 PP

                                  HCCC--TT-EE CS
                 NAD_binding_2 76 llealkkgdil 86
                                  +++ +k g+++
  gi|91772582|ref|YP_565274.1| 85 IARDAKVGKVI 95
                                  55555666555 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 !   17.2   0.2     4e-06    0.0036       2      46 ..       3      47 ..       2      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHH CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksl 46
                                  v v+GaG +G  ++  ++++g eV l++ +e+++++ +e++  ++
  gi|91772582|ref|YP_565274.1|  3 VIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAETMDCTV 47
                                  88*********************************9999887644 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.7e-06    0.0051       2      40 ..       2      40 ..       1      82 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                  +viv+G+G  G+  + ++ ++gk+V+l+ek +++++ ++
  gi|91772582|ref|YP_565274.1|  2 RVIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELA 40
                                  69******************************9999775 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-05     0.013       3      35 ..       2      34 ..       1      91 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                   V++VGaG  G+ l++ +  +G +v+l+ek + 
  gi|91772582|ref|YP_565274.1|  2 RVIVVGAGSLGIHLTRNMIAQGKEVILIEKDEA 34
                                  69****************************875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   3.3e-05      0.03     144     189 ..       2      43 ..       1      95 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                                   EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaal 189
                                   r++vvG+G  G+ l+  +   gkev l+e  + +     kel++++
  gi|91772582|ref|YP_565274.1|   2 RVIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIA----KELAETM 43 
                                   67888888888888888888888888888877776....4444443 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   5.9e-05     0.053       1      40 [.       2      41 ..       2      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-05
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSH CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDe 40
                                  +v+vvG+G +g+ l  ++ + gk+V ++e  + + + l e
  gi|91772582|ref|YP_565274.1|  2 RVIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAE 41
                                  79****************************9999844444 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     5e-05     0.045       1      41 [.       1      41 [.       1      80 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                                  SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCT CS
                UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklns 41
                                  m++ v+G+G +G+     + ++g+evi++ +de+  ++l +
  gi|91772582|ref|YP_565274.1|  1 MRVIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAE 41
                                  89******************************998777765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.7e-05     0.042       2      62 ..       4      75 ..       3     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                                  EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.............EEEE--TT-HHHHHHHHHH CS
                     Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.............elveldltdrsalerlfke 62
                                  +V+Ga G +G +l++++ ++g evi + ++ +a ++++ e+               l ++d+ +++a+ +   +
  gi|91772582|ref|YP_565274.1|  4 IVVGA-GSLGIHLTRNMIAQGKEVILIEKD-EAIAKELAETMdctvinaegtrpdILEKADIDNADAVVACTTN 75
                                  67777.***********************9.5555555555589666666666666666666666666555544 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.3e-05     0.074       4      44 ..       4      44 ..       2     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.3e-05
                        LpxI_N  4 liAGsGrlPllvaeaakaagrevvvvalegeadeelekivd 44
                                  ++ G+G+l +++ +++ a+g+ev+++   +++ +el++++d
  gi|91772582|ref|YP_565274.1|  4 IVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAETMD 44
                                  899***************************99999999766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   8.2e-05     0.074       1      33 [.       2      36 ..       2      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.2e-05
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  +v+++G+G  G+   +   ++g  V+l+ek++ ++
  gi|91772582|ref|YP_565274.1|  2 RVIVVGAGSLGIHLTRNMIAQGkeVILIEKDEAIA 36
                                  59****************99999********7665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.4e-05     0.075       2      41 ..       3      42 ..       2      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-05
                                  EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeinee 41
                                  + v+GaGs G  l + +  +g+ev l+ ++e+ ++e+ e+
  gi|91772582|ref|YP_565274.1|  3 VIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAET 42
                                  789****************************666666554 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   9.3e-05     0.083       3      67 ..       3      66 ..       1      82 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.3e-05
                                  EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHH CS
                     adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreeveal 67
                                  v+v+Ga+  +G  + ++++++G +v+++++ e+ ++e+a+ +  +  +a   + D+ ++++++++
  gi|91772582|ref|YP_565274.1|  3 VIVVGAG-SLGIHLTRNMIAQGKEVILIEKDEAIAKELAETMDCTVINAEGTRPDILEKADIDNA 66
                                  7899988.7**********************9999999999888788888888888888877765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00012      0.11       4      72 ..       3      73 ..       1      94 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                  EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHH.HHHHHHHHTT-EEEE-.---TT-HHHHHHHH CS
                            KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedsk.aliaelealgaevevv.aaDvsdkdaveall 72
                                  +i+ G+G+LG +l+r ++++g++ +++   +a a+e ++    + ++a g++ +++ +aD+ ++dav a+ 
  gi|91772582|ref|YP_565274.1|  3 VIVVGAGSLGIHLTRNMIAQGKEVILIEKDEAIAKELAEtMDCTVINAEGTRPDILeKADIDNADAVVACT 73
                                  566689***************98877766665444333313566677777776654257777777776655 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   0.2   0.00022      0.19       1      76 [.       3      73 ..       3      96 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCH..SCCCCS-ESEEEE-S CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsae..ekselepidlvivtv 76
                                  + ++GaG++G  l  ++ ++g +v+li +++   a+ k+  +  +++    + + e ++++  ek+++ ++d v+ ++
  gi|91772582|ref|YP_565274.1|  3 VIVVGAGSLGIHLTRNMIAQGKEVILIEKDE---AIAKELAETMDCT----VINAEGTRPDilEKADIDNADAVVACT 73
                                  579**************************99...5555555555555....111111111122344666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1490.37
//
Query:       gi|91772583|ref|YP_565275.1|  [L=485]
Description: Trk-type K+ transport systems membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-46  157.6  25.8    2.1e-44  151.9  25.8    2.1  1  TrkH      Cation transport protein
  ------ inclusion threshold ------
        7.7    5.9   5.8         28    4.1   0.9    2.5  2  Spo7      Spo7-like 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 !  151.9  25.8   2.3e-48   2.1e-44      57     491 ..      96     468 ..      50     472 .. 0.86

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 2.3e-48
                          TrkH  57 esaslafldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelgg 137
                                       ++f+da fe+vs++tttglsv++   + +   l+ r+  q++Gg+g++ +  ++l+++g     +y+++      + 
  gi|91772583|ref|YP_565275.1|  96 LTTGMPFIDAYFESVSAVTTTGLSVAPA--DVGPVFLFARSWGQWVGGIGIILVVLSVLIRPGTTASRMYKANY----GDM 170
                                   4456788********************9..888899***************988888889**999999999888....677 PP

                          TrkH 138 kelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnkniv 218
                                   k  +++ +++++l ++y+++++++++ll           +++      +l++ ++h++S ++++Gfs+ p+ +  ++   +
  gi|91772583|ref|YP_565275.1| 171 KIKPTVISTTRTLGKVYIIITLISLILL---------LMSGM------SLFDSICHALSCVSTGGFSTRPEGIRAYQG-SL 235
                                   8889************************.........88999......******************************.66 PP

                          TrkH 219 illvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfil 299
                                   i  +++i  +lG+++F++   ++ ++  ki             +++l++r f+  +a+g +   ++ ++            
  gi|91772583|ref|YP_565275.1| 236 IPTAISISCLLGAVSFVLYPHLF-KKPEKI-------------FKNLELRYFLAFIAIGSI---VFAFT------------ 287
                                   7777777889******8766655.444444.............678******544454444...44444............ PP

                          TrkH 300 ldegslvvksipkgsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkye 379
                                   l+ g++  + i+      ++lFq + + t+ GFs++dls l+ a k +l++mm igg  gStaggI+ ++v  + + +   
  gi|91772583|ref|YP_565275.1| 288 LERGNTDYDLIQ------DSLFQIINAITTaGFSTIDLSILSEASKAVLIFMMWIGGNVGSTAGGIKVLKVILLLKVVHNV 362
                                   567888777777......9******888777************************************************** PP

                          TrkH 380 ieqekepk.avskksidgkhlerqllvdlwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknas 459
                                   + + + p+ ++ +++i    +e + +++l  ++l++++ili++++   +  +   ++  + fev Sa+ tvGLS G    +
  gi|91772583|ref|YP_565275.1| 363 LLRLFLPReTITPIKIEDHVIESDEIYNLVTFMLLYTLILIVSSFIF-MLYG--TNMSSSVFEVSSALSTVGLSAG----A 436
                                   *******************************************6655.5555..57779*****************....* PP

                          TrkH 460 lsaqlttisklvlialmirGrlrglpvlldra 491
                                   +sa ++ + klvli+ m+ Gr +++p++l+++
  gi|91772583|ref|YP_565275.1| 437 TSASMPVVLKLVLIIDMLFGRIEIIPLILLFM 468
                                   *****************************997 PP

>> Spo7  Spo7-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3    0.0039        35      54      91 ..     166     203 ..     143     205 .. 0.75
   2 ?    4.1   0.9    0.0032        28      33      95 ..     395     475 ..     382     484 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0039
                          Spo7  54 redgsgvggsvywvvevvekvlliggvvTlvLfwlsGe 91 
                                   ++ + + +  v  +++++ kv +i++++ l+L+ +sG+
  gi|91772583|ref|YP_565275.1| 166 NYGDMKIKPTVISTTRTLGKVYIIITLISLILLLMSGM 203
                                   444455666889999**********************7 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0032
                          Spo7  33 lflllLalviafflyalflapred...............gsgvggsvywvvevvekvlligg...vvTlvLfwlsGeyert 95 
                                   ++l +L+l++  f++ l+ ++ ++                  +++s  +v+++v+ + +++g   ++ l+L+++ G++ ++
  gi|91772583|ref|YP_565275.1| 395 MLLYTLILIVSSFIFMLYGTNMSSsvfevssalstvglsAGATSASMPVVLKLVLIIDMLFGrieIIPLILLFMPGTWIKR 475
                                   578899999999999999955555677777777776665333444555555555555444432237889999999999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3576.45
//
Query:       gi|91772584|ref|YP_565276.1|  [L=96]
Description: hypothetical protein Mbur_0551 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 00:00:00.40
# Mc/sec: 718.49
//
Query:       gi|91772585|ref|YP_565277.1|  [L=786]
Description: CoB--CoM heterodisulfide reductase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-56  187.5   5.3    1.7e-52  176.6   0.1    4.1  4  FlpD            Methyl-viologen-reducing hydrogenase, delta s
    9.2e-19   67.8   0.1    2.5e-18   66.3   0.1    1.7  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      3e-14   53.3  30.5    8.6e-06   26.3  12.5    5.1  4  Fer4_7          4Fe-4S dicluster domain
    3.4e-11   43.9  28.1    0.00039   21.3   2.1    5.5  4  Fer4_16         4Fe-4S double cluster binding domain
    2.4e-10   39.8  54.7    2.3e-07   30.3   3.5    5.8  4  Fer4            4Fe-4S binding domain
    8.2e-09   35.5  50.6    3.1e-05   24.0  16.9    5.8  5  Fer4_21         4Fe-4S dicluster domain
    2.1e-08   34.0   0.3    3.5e-08   33.2   0.3    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    3.7e-08   33.1  50.9    0.00018   21.4   2.8    5.6  5  Fer4_6          4Fe-4S binding domain
    4.2e-08   33.2  40.1    3.5e-05   23.8   0.1    5.2  5  Fer4_10         4Fe-4S dicluster domain
    6.8e-08   32.0   0.8    3.6e-07   29.6   0.8    2.0  2  FAD_binding_2   FAD binding domain
    8.9e-08   32.2  27.0    1.7e-05   24.9  12.2    4.4  3  Fer4_9          4Fe-4S dicluster domain
    2.3e-06   27.7  33.7      0.024   15.1   1.4    5.4  4  Fer4_4          4Fe-4S binding domain
      3e-06   26.6   0.2    6.5e-06   25.5   0.2    1.5  1  GIDA            Glucose inhibited division protein A
    7.5e-06   26.4   0.4      3e-05   24.5   0.4    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.2e-05   24.7   0.3    0.00015   21.1   0.0    2.6  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.2e-05   23.3   0.6    4.6e-05   22.3   0.6    1.5  1  HI0933_like     HI0933-like protein
    4.4e-05   23.2   0.5    0.00095   18.8   0.9    2.5  2  DAO             FAD dependent oxidoreductase
    7.9e-05   23.1  31.8    0.00035   21.0   3.8    4.7  3  Fer4_17         4Fe-4S dicluster domain
    8.8e-05   22.7   0.0     0.0002   21.5   0.0    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.8e-05   22.7  37.0       0.18   12.3   3.9    5.8  4  Fer4_8          4Fe-4S dicluster domain
    0.00042   19.7   0.0    0.00084   18.7   0.0    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00057   19.8  48.1     0.0014   18.6   2.3    5.9  5  Fer4_2          4Fe-4S binding domain
    0.00082   18.7   0.0     0.0024   17.2   0.0    1.8  1  Thi4            Thi4 family
    0.00094   19.6   0.7      0.094   13.2   0.0    3.6  3  NAD_binding_7   Putative NAD(P)-binding
     0.0011   18.3   1.3     0.0016   17.8   0.5    1.6  1  FAD_binding_3   FAD binding domain
     0.0019   17.4   0.2        2.9    6.9   0.0    3.1  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.048   12.7   0.4      0.085   11.9   0.4    1.4  1  Lycopene_cycl   Lycopene cyclase protein
      0.048   13.3   0.0         30    4.4   0.0    3.4  3  HTH_53          Zap  helix turn helix N-terminal domain
       0.08   13.8   0.3       0.08   13.8   0.3    4.9  4  Fer4_22         4Fe-4S dicluster domain
       0.11   11.3   0.5        1.1    8.1   0.4    2.0  2  Trp_halogenase  Tryptophan halogenase
       0.15   12.0   0.6         13    5.7   0.2    2.7  2  NAD_binding_9   FAD-NAD(P)-binding


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 !    8.4   0.1    0.0036       2.1      19      91 ..      27      97 ..      14     122 .. 0.69
   2 ?   -1.2   0.1       3.3   1.9e+03       8      51 ..     400     446 ..     396     450 .. 0.64
   3 ?    1.7   0.0      0.41   2.4e+02      50      64 ..     526     540 ..     521     567 .. 0.66
   4 !  176.6   0.1   2.9e-55   1.7e-52       1     123 []     651     773 ..     651     773 .. 1.00

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                          FlpD 19 vsrlqyppnvriirvpCsgrvdpefilkale.kGadgVlvlgChpgdChyvkGnekaerrveklkelleelgie 91
                                  v++++  + v+ i+ +Cs+ v ++ +++ +e +++d Vlv++C p+   +++  +k+ +r  +   lle ++i 
  gi|91772585|ref|YP_565277.1| 27 VEQMKGVELVKDIQFMCSD-VGQDALMDDIEeHDIDRVLVAACTPKL--HENTFKKVLERAGLNTYLLEIVNIR 97
                                  5666777778899****97.77777777775168**********875..3356666666666666666666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                          FlpD   8 wcayaaadlagvsrlqypp...nvriirvpCsgrvdpefilkalekG 51 
                                    c+  ++++a++ + +yp+   +++ i ++ +g++ +e+ ++    G
  gi|91772585|ref|YP_565277.1| 400 VCCMSSMKNAQMIKERYPDtevTIHYIDIRAAGEMYEEYYVRSQMMG 446
                                   56666666666666666663226888999999988887776665555 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.41
                          FlpD  50 kGadgVlvlgChpgd 64 
                                   + ++gV+++gC  g 
  gi|91772585|ref|YP_565277.1| 526 AHINGVFIAGCASGP 540
                                   5689*******9875 PP

  == domain 4  score: 176.6 bits;  conditional E-value: 2.9e-55
                          FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerrvekl 81 
                                   i+aFlCnwc+ya+adlag+sr+qyp+nvrii+v+C+grvdp+f+l+al+ GadgV+v+gC+ ++Chy+ Gn+ a++r+++l
  gi|91772585|ref|YP_565277.1| 651 IIAFLCNWCSYASADLAGTSRIQYPTNVRIIKVMCAGRVDPDFVLEALQGGADGVIVAGCRLDECHYIIGNYDAKHRMDNL 731
                                   9******************************************************************************** PP

                          FlpD  82 kelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                   ke+lee+g++++R+r+e++saaege+fa++i+++v++++eLG
  gi|91772585|ref|YP_565277.1| 732 KEVLEEIGLDQRRLRVEWISAAEGERFAKTIEDYVDELTELG 773
                                   ****************************************98 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.1   4.3e-21   2.5e-18       1     294 []     141     550 ..     141     550 .. 0.73

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 4.3e-21
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH.......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx.......... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias.......... 57 
                                   kdv+viGgG+AG++aaltla +g  v++ve           l++ +++++c++   +++++ v+ +++i +          
  gi|91772585|ref|YP_565277.1| 141 KDVLVIGGGVAGIEAALTLADSGTHVYMVEkeptiggkmalLNEVFPTNDCSIcvlAPKMTDVQNHTNIDLftyseikdis 221
                                   69***************************88899999*************98766699**********999***9998776 PP

                                   ..............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC................................ CS
                                   ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                   Pyr_redox_2  58 ..............evvkklnqgielllgeevvkidpgkkkvklekkke................................ 92 
                                                 +                +v id+ k+++   ++++                                
  gi|91772585|ref|YP_565277.1| 222 gsvgnftvkgiqnpR----------------YVIIDNCKGCIDECARVCpvdisnpfdsglgktkainmpipqaipqtafi 286
                                   544444444444440................66666666666665555566666666666666666666666666666666 PP

                                   .........................TCEEEEEESEEEE---EEE-BCTCTTC.......................TTBEEC CS
                                   .........................xxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxx RF
                   Pyr_redox_2  93 .........................gdeekiaydklvlAtGssprdlgipGv......................aenvgkl 126
                                                             +e++++ +++++AtG + +d + + +                      +++ gk+
  gi|91772585|ref|YP_565277.1| 287 nsdycvgcglckqacpadaidfnmkAEEFTFTVGAVIVATGYQGFDAKRKEEygygvfpdvltnmelerllnasGPTRGKV 367
                                   6666677777777889999999999999*******************7775544455666666666666666555555555 PP

                                   CSECHHHHHHCCSS-T...SEEEEES-SHHHHHHHHHHHHHT-.........EEEEEESSSSSSTTS-HHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 127 vrtldsaealklkllp...krivvvGgGyiGvElAaalaklgk.........evtlveardrllraldkelsaaleealek 195
                                   v ++++  + k +  +    r   vG+ y++ ++++  +k ++         evt+ +  d+  ra +++ ++++  + + 
  gi|91772585|ref|YP_565277.1| 368 VVPSTKETPKKVAFIQcvgSRDETVGNPYCSRVCCMSSMKNAQmikerypdtEVTIHYI-DI--RAAGEMYEEYYV-RSQM 444
                                   555555555555555577766699*************6555445778888888885444.33..345666666655.4566 PP

                                   TTEEEEESCEEEEEEETTE...EEEEEETTSCE...EEESEEEE-S-EEES-HHCS..HCCT-EEEETTEE.E--TTSBE. CS
                                   xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxx. RF
                   Pyr_redox_2 196 eGvevklgtsvkeidgnge...klevvledgee...idadlvvvavGvrpstelle..eklglelderggi.vvdeflrt. 266
                                   +G+++  g+++ ei+ +++    l+++++ + +   +++dlvv+a+G++ps+++ +  ++l+l+   ++++    +++r  
  gi|91772585|ref|YP_565277.1| 445 MGIDFIRGKVA-EIQIDTQgkmLLRYEDTLECTlcqENYDLVVLATGMEPSNTTEPiaRTLNLTKRTDRFLsIAHPKMRPv 524
                                   7*****77777.666666643444444444444889****************99889999999998888886667788744 PP

                                   ..SSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 267 ..nvpgiyaiGDvaggkggpelaqaAvqqG 294
                                      + g++ +G +a   +gp+ +q++++qG
  gi|91772585|ref|YP_565277.1| 525 daHINGVFIAG-CA---SGPKEIQVSIAQG 550
                                   4379******9.78...8******999998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.0   0.00026      0.15      27      52 .]     231     258 ..     189     258 .. 0.62
   2 !   21.9   0.2   3.4e-07    0.0002       2      24 ..     291     313 ..     277     339 .. 0.84
   3 ?    2.4   0.1      0.41   2.4e+02       7      45 ..     396     479 ..     383     481 .. 0.41
   4 !   26.3  12.5   1.5e-08   8.6e-06       1      52 []     579     623 ..     579     623 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00026
                        Fer4_7  27 gtekveid.pekClgCga.CvavCPtga 52 
                                   g++ ++++  ++C gC   C++vCP+++
  gi|91772585|ref|YP_565277.1| 231 GIQNPRYViIDNCKGCIDeCARVCPVDI 258
                                   44445544389*****666******985 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 3.4e-07
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeen 24 
                                   C+gCg C +aCp++ai+++ +++
  gi|91772585|ref|YP_565277.1| 291 CVGCGLCKQACPADAIDFNMKAE 313
                                   99999999999999999986644 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.41
                        Fer4_7   7 aCvaaC...............pvkaieldeeenek..........................................gtek 30 
                                   +C ++C               p            +                                          ++ k
  gi|91772585|ref|YP_565277.1| 396 YCSRVCcmssmknaqmikeryP------------DtevtihyidiraagemyeeyyvrsqmmgidfirgkvaeiqidTQGK 464
                                   8999995554333333333330............22333333333333333333333333333333322222222223345 PP

                        Fer4_7  31 veidpekClgCgaCv 45 
                                   + +++e+ l C+ C+
  gi|91772585|ref|YP_565277.1| 465 MLLRYEDTLECTLCQ 479
                                   555566666666666 PP

  == domain 4  score: 26.3 bits;  conditional E-value: 1.5e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +CigC+ C+++C  ++i++ +        k+++d+ +C++Cg+C a CP++a
  gi|91772585|ref|YP_565277.1| 579 KCIGCRMCEDTCNFNTIKVIDG-------KAVVDEISCQTCGSCSASCPVDA 623
                                   7*****************9763.......789******************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.8      0.02        11      53      66 ..     242     256 ..     228     263 .. 0.69
   2 !   18.5   0.1   4.9e-06    0.0028       2      21 ..     291     310 ..     290     341 .. 0.82
   3 !   13.7   0.7   0.00016     0.095      46      67 .]     572     593 ..     544     593 .. 0.84
   4 !   21.3   2.1   6.8e-07   0.00039       2      41 ..     609     648 ..     608     661 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.02
                       Fer4_16  53 aitgC.diCqdvCPa 66 
                                   +++gC d C++vCP+
  gi|91772585|ref|YP_565277.1| 242 NCKGCiDECARVCPV 256
                                   555553356666654 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.9e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                   C++Cg C ++CP++ai+ + 
  gi|91772585|ref|YP_565277.1| 291 CVGCGLCKQACPADAIDFNM 310
                                   ****************9872 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00016
                       Fer4_16  46 ekckkqeaitgCdiCqdvCPan 67 
                                    +c  +e+++gC++C+d+C +n
  gi|91772585|ref|YP_565277.1| 572 SACVDAEKCIGCRMCEDTCNFN 593
                                   4688899************998 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 6.8e-07
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdl 41 
                                   C+tCg C  +CP++ai++++++ ++++++i ++ + k+++
  gi|91772585|ref|YP_565277.1| 609 CQTCGSCSASCPVDAIDMPHSTDAQIKAQIRAALEVKDEF 648
                                   *******************888888888888766666555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   7.3      0.99   5.7e+02       7      21 ..     242     257 ..     237     258 .. 0.74
   2 !   30.3   3.5     4e-10   2.3e-07       2      24 .]     285     307 ..     284     307 .. 0.93
   3 !   15.3   6.7   2.3e-05     0.013       3      23 ..     575     595 ..     573     596 .. 0.86
   4 !   19.4   3.5   1.1e-06   0.00065       2      24 .]     603     625 ..     602     625 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.99
                                   TSSS-.THHHHHSTTT CS
                          Fer4   7 kCigC.GaCvevCPvg 21 
                                    C gC  +C+ vCPv+
  gi|91772585|ref|YP_565277.1| 242 NCKGCiDECARVCPVD 257
                                   55555568******98 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 4e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                    i+ + C+gCG+C ++CP +AI+
  gi|91772585|ref|YP_565277.1| 285 FINSDYCVGCGLCKQACPADAID 307
                                   599******************95 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.3e-05
                                   EETTTSSS-THHHHHSTTTEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                   +d ekCigC  C++ C ++ I
  gi|91772585|ref|YP_565277.1| 575 VDAEKCIGCRMCEDTCNFNTI 595
                                   8***************66665 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 1.1e-06
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   v+de  C  CG C   CPv+AI+
  gi|91772585|ref|YP_565277.1| 603 VVDEISCQTCGSCSASCPVDAID 625
                                   89999****************95 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.9    0.0003      0.17      36      54 ..     238     257 ..     221     259 .. 0.84
   2 !   21.8   0.4   2.6e-07   0.00015      35      58 ..     285     307 ..     269     317 .. 0.70
   3 ?   -0.1   0.8       1.8     1e+03      38      53 ..     388     403 ..     372     408 .. 0.79
   4 ?   -0.4   0.1       2.3   1.3e+03      26      48 ..     457     479 ..     452     481 .. 0.75
   5 !   24.0  16.9   5.4e-08   3.1e-05       1      59 []     573     626 ..     573     626 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                       Fer4_21  36 vvedeCvGC.nlCssvCPve 54 
                                   v+ d+C GC + C+ vCPv+
  gi|91772585|ref|YP_565277.1| 238 VIIDNCKGCiDECARVCPVD 257
                                   6789*****789******94 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.6e-07
                       Fer4_21  35 kvvedeCvGCnlCssvCPvedcie 58 
                                    + +d CvGC lC + CP  d+i+
  gi|91772585|ref|YP_565277.1| 285 FINSDYCVGCGLCKQACPA-DAID 307
                                   3446677777777777774.6654 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.8
                       Fer4_21  38 edeCvGCnlCssvCPv 53 
                                    de vG   Cs vC +
  gi|91772585|ref|YP_565277.1| 388 RDETVGNPYCSRVCCM 403
                                   688999999*****75 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.3
                       Fer4_21  26 ieidaktvlkvvedeCvGCnlCs 48 
                                   i+id++ ++ ++ ++   C+lC 
  gi|91772585|ref|YP_565277.1| 457 IQIDTQGKMLLRYEDTLECTLCQ 479
                                   67777777777788888888886 PP

  == domain 5  score: 24.0 bits;  conditional E-value: 5.4e-08
                       Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                   A +d +kCigC  C  +C+ ++++ i++    ++ v e +C  C  Cs+ CPv d+i+m
  gi|91772585|ref|YP_565277.1| 573 ACVDAEKCIGCRMCEDTCNFNTIKVIDG----KAVVDEISCQTCGSCSASCPV-DAIDM 626
                                   789****************655555554....3458899*************9.99998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.3     6e-11   3.5e-08       1      39 [.     142     180 ..     142     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 6e-11
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39 
                                   Dv+V+GGg+aG+ AA++ a +G  v +ve+++ +GG ++
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTLADSGTHVYMVEKEPTIGGKMA 180
                                   9***********************************985 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2        10   5.8e+03      11      17 ..     190     196 ..     189     197 .. 0.80
   2 !   13.1   4.4   0.00014     0.079       5      22 ..     239     257 ..     237     259 .. 0.88
   3 !   21.4   2.8   3.2e-07   0.00018       2      24 .]     284     306 ..     283     306 .. 0.94
   4 !   16.5   3.7   1.1e-05    0.0066       4      22 ..     575     593 ..     575     595 .. 0.89
   5 !   10.8   3.6    0.0007      0.41       1      24 []     601     624 ..     601     624 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 10
                        Fer4_6  11 gCgdCvr 17 
                                   +C  Cv 
  gi|91772585|ref|YP_565277.1| 190 DCSICVL 196
                                   8999*96 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                        Fer4_6   5 dpdkCigC.gdCvrvCPeg 22 
                                     d+C gC ++C+rvCP +
  gi|91772585|ref|YP_565277.1| 239 IIDNCKGCiDECARVCPVD 257
                                   569**************86 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 3.2e-07
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   + i+ d C+gCg C  +CP++ai
  gi|91772585|ref|YP_565277.1| 284 AFINSDYCVGCGLCKQACPADAI 306
                                   689******************98 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 1.1e-05
                        Fer4_6   4 idpdkCigCgdCvrvCPeg 22 
                                   +d++kCigC+ C++ C ++
  gi|91772585|ref|YP_565277.1| 575 VDAEKCIGCRMCEDTCNFN 593
                                   79**************776 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0007
                        Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                   ++++d+ +C  Cg C + CP +ai
  gi|91772585|ref|YP_565277.1| 601 KAVVDEISCQTCGSCSASCPVDAI 624
                                   5889999**************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.6    0.0015      0.87       7      23 ..     241     258 ..     235     279 .. 0.74
   2 !   23.8   0.1   6.1e-08   3.5e-05       3      24 ..     285     310 ..     283     341 .. 0.76
   3 ?   -2.1   0.6       7.5   4.3e+03      14      33 ..     396     413 ..     384     423 .. 0.68
   4 !   14.6  16.5   4.5e-05     0.026       4      56 .]     575     620 ..     572     620 .. 0.79
   5 !   15.8   3.6     2e-05     0.011       2      24 ..     602     631 ..     601     660 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                       Fer4_10   7 dtCirCg.kCvkaCPadl 23 
                                   d C +C  +C ++CP+d+
  gi|91772585|ref|YP_565277.1| 241 DNCKGCIdECARVCPVDI 258
                                   689999889999999966 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 6.1e-08
                       Fer4_10   3 vidddtCirCgkCvkaCPadl....t 24 
                                    i++d C++Cg C++aCPad+     
  gi|91772585|ref|YP_565277.1| 285 FINSDYCVGCGLCKQACPADAidfnM 310
                                   699****************6633330 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7.5
                       Fer4_10  14 kCvkaCPadltsvgakgeas 33 
                                    C ++C  +++s+++ + ++
  gi|91772585|ref|YP_565277.1| 396 YCSRVC--CMSSMKNAQMIK 413
                                   699999..445554444444 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 4.5e-05
                       Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +d+++Ci+C+ C + C       ++++ ++++++v++   +C++cg+C ++CP
  gi|91772585|ref|YP_565277.1| 575 VDAEKCIGCRMCEDTCN-----FNTIKVIDGKAVVDE--ISCQTCGSCSASCP 620
                                   699*************3.....455555555555555..89***********9 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 2e-05
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl.......t 24 
                                   +v+d+ +C  Cg C ++CP+d+       +
  gi|91772585|ref|YP_565277.1| 602 AVVDEISCQTCGSCSASCPVDAidmphstD 631
                                   789999**************8866665431 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.8   6.2e-10   3.6e-07       1      39 [.     142     180 ..     142     181 .. 0.95
   2 ?   -0.6   0.0      0.93   5.4e+02     138     184 ..     318     375 ..     301     386 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.2e-10
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                 FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                   Dv+ViG+G+AG  AAl++a+ G  v +veke+  gg  a
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTLADSGTHVYMVEKEPTIGGKMA 180
                                   9*******************************9999765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.93
                                   .HHHHHHHHHHHHHHTCT.........EEEEESEEEEEEEECTTEEEEEEEEET..TT CS
                 FAD_binding_2 138 vtghallarlvesarkag.........vdfqerteadeLivedgrvtGavvenp..es 184
                                   + g  ++a++++++++            d+++++e+++L+  +g  +G vv ++  e+
  gi|91772585|ref|YP_565277.1| 318 TVGAVIVATGYQGFDAKRkeeygygvfPDVLTNMELERLLNASGPTRGKVVVPStkET 375
                                   4566667777777744434566677777888888888888888888888888774444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   4.2      0.05        29      33      49 ..     219     257 ..     189     259 .. 0.62
   2 !   22.0   6.9   2.3e-07   0.00013       1      51 []     242     306 ..     242     306 .. 0.82
   3 !   24.9  12.2   2.9e-08   1.7e-05       1      51 []     579     624 ..     579     624 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.05
                        Fer4_9  33 e.....................eaCigCga.CveaCpkg 49 
                                   +                     ++C gC + C+ +Cp +
  gi|91772585|ref|YP_565277.1| 219 DisgsvgnftvkgiqnpryviiDNCKGCIDeCARVCPVD 257
                                   245555555556666666677778999977799999987 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.3e-07
                        Fer4_9   1 kCtgC.gaCveaCpagvvvedaaerkarlraase..............eaCigCgaCveaCpkgai 51 
                                   +C gC ++C ++Cp ++ ++ +++      +  +              + C+gCg C +aCp +ai
  gi|91772585|ref|YP_565277.1| 242 NCKGCiDECARVCPVDISNPFDSGLGKTKAIN-MpipqaipqtafinsDYCVGCGLCKQACPADAI 306
                                   599**557*****9999999888777664443.34778899999999999*************987 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 2.9e-08
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kC+gC+ C++ C++++++  +++  +        +C +Cg+C + Cp +ai
  gi|91772585|ref|YP_565277.1| 579 KCIGCRMCEDTCNFNTIKVIDGKAVVDE-----ISCQTCGSCSASCPVDAI 624
                                   7****************99998888775.....36*************987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.5      0.27   1.6e+02       2      16 ..     241     256 ..     240     260 .. 0.80
   2 !   15.1   1.4   4.2e-05     0.024       1      16 [.     288     303 ..     288     312 .. 0.91
   3 !   13.9   3.7    0.0001     0.058       2      16 ..     578     592 ..     577     593 .. 0.89
   4 !   10.8   3.4   0.00098      0.57       3      16 ..     608     621 ..     608     626 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.27
                        Fer4_4   2 erCigCg.sCvaaCPq 16 
                                   ++C gC   C ++CP+
  gi|91772585|ref|YP_565277.1| 241 DNCKGCIdECARVCPV 256
                                   6788886579999996 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.2e-05
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   ++ C+gCg C  aCP 
  gi|91772585|ref|YP_565277.1| 288 SDYCVGCGLCKQACPA 303
                                   589************5 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.0001
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   e+CigC+ C+++C +
  gi|91772585|ref|YP_565277.1| 578 EKCIGCRMCEDTCNF 592
                                   89***********65 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00098
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +C+ CgsC a+CP+
  gi|91772585|ref|YP_565277.1| 608 SCQTCGSCSASCPV 621
                                   6************7 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   1.1e-08   6.5e-06       1      31 [.     142     172 ..     142     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.1e-08
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithk 31 
                                   dv ViGgG AG+eAAl++a +G +v ++ ++
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTLADSGTHVYMVEKE 172
                                   79*************************9433 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.4   5.2e-08     3e-05       2      35 ..     143     176 ..     142     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5.2e-08
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                   v+v+GgG+ g+E+A +la+ g +V++ve ++++ 
  gi|91772585|ref|YP_565277.1| 143 VLVIGGGVAGIEAALTLADSGTHVYMVEKEPTIG 176
                                   89****************************9998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.7e-07   0.00015     163     246 ..     139     228 ..     131     240 .. 0.70
   2 ?   -1.2   0.1       1.7   9.8e+02     114     135 ..     308     329 ..     303     337 .. 0.70
   3 ?   -0.7   0.0       1.1   6.5e+02     256     305 .]     480     535 ..     434     535 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.7e-07
                   Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdie.......nrleelvkeekikvlfnaevk 236
                                   a+++v+ViGg+  +++aAl l++ g +V +v ++ +i  +      ++ p++        +++ +++++++i++ + +e+k
  gi|91772585|ref|YP_565277.1| 139 ANKDVLVIGGGVAGIEAALTLADSGTHVYMVEKEPTIGGKM-ALLNEVFPTNDcsicvlaPKMTDVQNHTNIDLFTYSEIK 218
                                   589******************************99988764.455566666541111111444444444667777777777 PP

                   Pyr_redox_3 237 eikekeeeyk 246
                                   +i+ +  +++
  gi|91772585|ref|YP_565277.1| 219 DISGSVGNFT 228
                                   7766555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                   Pyr_redox_3 114 fevetsketyeAkkviiAtGef 135
                                   f+ ++++ t++   vi+AtG+ 
  gi|91772585|ref|YP_565277.1| 308 FNMKAEEFTFTVGAVIVATGYQ 329
                                   6666666677777788888874 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                   Pyr_redox_3 256 evkddvvlatGykpd..lsflkk.slfeldedgrpvlteete...etnvpglflaG 305
                                   e++d vvlatG +p+  ++++++   +++++d++  +   ++   +  ++g+f+aG
  gi|91772585|ref|YP_565277.1| 480 ENYDLVVLATGMEPSntTEPIARtLNLTKRTDRFLSIAHPKMrpvDAHINGVFIAG 535
                                   337889999***99844566777533444455544444433312255667777776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.6     8e-08   4.6e-05       2      40 ..     142     180 ..     141     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40 
                                   dv+viGgG AG+ aA+++a+ g +V ++ek++++g K++
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTLADSGTHVYMVEKEPTIGGKMA 180
                                   8***********************************986 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.9   1.7e-06   0.00095       1      35 [.     142     177 ..     142     180 .. 0.94
   2 ?    0.8   0.0      0.51     3e+02     157     204 ..     443     493 ..     428     528 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                   dv++iGGG++G+ +A+ La  g  V  +ek++ +g g
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTLADSGthVYMVEKEPTIG-G 177
                                   8*****************99999********9998.5 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                                   HHTT-EEEESECEEEEEEEETCEEEEE.....EECT.EEEEEEEEEEE--GGGH CS
                           DAO 157 ealGveilegtevtgleeedgkvwgve.....rttp.gendaadavVnaaGaws 204
                                   +  G+++++g +v +++ +  + + ++     + t   e   +d vV+a+G   
  gi|91772585|ref|YP_565277.1| 443 QMMGIDFIRG-KVAEIQIDTQGKMLLRyedtlECTLcQE--NYDLVVLATGMEP 493
                                   5679999999.9999966442224443544443333333..4788******864 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   3.8   6.1e-07   0.00035       1      59 [.     242     304 ..     236     305 .. 0.79
   2 !   12.0   0.7   0.00041      0.24      42      57 ..     576     591 ..     544     602 .. 0.73
   3 !    9.2   1.8     0.003       1.7       2      17 ..     609     624 ..     607     661 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.1e-07
                       Fer4_17   1 rCiqCgy.ClpeCpsyeaydnepk.kllraaklglleeaeke..ekaslCieCgeCerkCPqg 59 
                                   +C +C   C+++Cp  + ++++      +a+++ + +++ +    + + C++Cg+C+++CP++
  gi|91772585|ref|YP_565277.1| 242 NCKGCIDeCARVCPVDISNPFDSGlGKTKAINMPIPQAIPQTafINSDYCVGCGLCKQACPAD 304
                                   69999867999****9999997663456666776666664442358899************86 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00041
                       Fer4_17  42 kaslCieCgeCerkCP 57 
                                    a++Ci+C++Ce  C 
  gi|91772585|ref|YP_565277.1| 576 DAEKCIGCRMCEDTCN 591
                                   5677777777777774 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.003
                       Fer4_17   2 CiqCgyClpeCpsyea 17 
                                   C+ Cg C ++Cp  ++
  gi|91772585|ref|YP_565277.1| 609 CQTCGSCSASCPVDAI 624
                                   6667777777766555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.4e-07    0.0002       1      36 [.     145     180 ..     145     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.4e-07
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                   ++G+G++G  aA +La+ g +v  +ek + +GG++a
  gi|91772585|ref|YP_565277.1| 145 VIGGGVAGIEAALTLADSGTHVYMVEKEPTIGGKMA 180
                                   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 ?    6.9   0.8     0.015       8.8      45      65 .]     237     258 ..     189     258 .. 0.77
   2 !   12.3   3.9   0.00031      0.18       3      17 ..     289     322 ..     287     480 .. 0.81
   3 ?    6.7  15.9     0.017       9.7       2      64 ..     577     622 ..     576     623 .. 0.71
   4 !    8.0   6.3    0.0069         4      50      64 ..     608     622 ..     605     661 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                        Fer4_8  45 eealwsCttcga.CtevCpvgi 65 
                                   + ++++C +c   C++vCpv+i
  gi|91772585|ref|YP_565277.1| 237 YVIIDNCKGCIDeCARVCPVDI 258
                                   5678999999655******987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00031
                        Fer4_8   3 ekCieCgaCqsaCp...................v 17 
                                   ++C++Cg+C++aCp                   v
  gi|91772585|ref|YP_565277.1| 289 DYCVGCGLCKQACPadaidfnmkaeeftftvgaV 322
                                   68999****9999966555555555554444443 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.017
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +ekCi+C +C+++C +     + ++   g+    ++ ++         sC+tcg+C+  Cpv+
  gi|91772585|ref|YP_565277.1| 577 AEKCIGCRMCEDTCNF-----NTIKVIDGK----AVVDEI--------SCQTCGSCSASCPVD 622
                                   79************42.....222233333....233344........8************96 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0069
                        Fer4_8  50 sCttcgaCtevCpvg 64 
                                   sC+tcg+C+  Cpv+
  gi|91772585|ref|YP_565277.1| 608 SCQTCGSCSASCPVD 622
                                   466666666666653 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 !   18.7   0.0   1.5e-06   0.00084      29      62 ..     141     174 ..     132     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                   AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                     vlviGgGvaG++A+ t +  g +V++++++p+
  gi|91772585|ref|YP_565277.1| 141 KDVLVIGGGVAGIEAALTLADSGTHVYMVEKEPT 174
                                   579**************************99886 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       4.4   2.5e+03      12      18 ..     190     196 ..     189     197 .. 0.77
   2 ?    5.8   3.4     0.029        17       7      21 ..     240     255 ..     235     256 .. 0.82
   3 !   18.6   2.3   2.5e-06    0.0014       4      22 .]     285     303 ..     283     303 .. 0.94
   4 !   11.5   5.7   0.00043      0.25       4      20 ..     574     590 ..     571     592 .. 0.91
   5 !    9.5   2.8    0.0019       1.1       3      21 ..     602     620 ..     600     621 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.4
                        Fer4_2  12 gCgaCvs 18 
                                    C++Cv 
  gi|91772585|ref|YP_565277.1| 190 DCSICVL 196
                                   79***86 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.029
                        Fer4_2   7 tdrCigC.gaCvsaCP 21 
                                    d+C gC   C  +CP
  gi|91772585|ref|YP_565277.1| 240 IDNCKGCiDECARVCP 255
                                   589*****88****** PP

  == domain 3  score: 18.6 bits;  conditional E-value: 2.5e-06
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   ++++d C+gCg C +aCPa
  gi|91772585|ref|YP_565277.1| 285 FINSDYCVGCGLCKQACPA 303
                                   799***************8 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00043
                        Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                    vd+++CigC+ C + C
  gi|91772585|ref|YP_565277.1| 574 CVDAEKCIGCRMCEDTC 590
                                   69*************** PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0019
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +vvd+ +C  Cg+C  +CP
  gi|91772585|ref|YP_565277.1| 602 AVVDEISCQTCGSCSASCP 620
                                   6889999*******888** PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.1e-06    0.0024      16      64 ..     139     186 ..     134     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.1e-06
                                   TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB CS
                          Thi4  16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf 64 
                                   a+ Dv+++G+G +G+ aa +la + + +v ++e++ ++GG + l   +f
  gi|91772585|ref|YP_565277.1| 139 ANKDVLVIGGGVAGIEAALTLADS-GTHVYMVEKEPTIGGKMALLNEVF 186
                                   678*********************.***************988766655 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 ?    1.1   0.1      0.95   5.5e+02      52      99 ..      48     101 ..      15     104 .. 0.70
   2 !   13.2   0.0   0.00016     0.094       7      50 ..     140     181 ..     137     229 .. 0.81
   3 ?    0.4   0.0       1.5   8.9e+02      26      80 ..     477     549 ..     453     562 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.95
                 NAD_binding_7  52 eeelekdlegad....lviaatddreln..eriaeaakarrilvnvadkpelcd 99 
                                   ++ l +d+e+ d    lv a+t++ ++n  +++ e a  +  l+ +++ +e+c+
  gi|91772585|ref|YP_565277.1|  48 QDALMDDIEEHDidrvLVAACTPKLHENtfKKVLERAGLNTYLLEIVNIREQCS 101
                                   455566777655556699999998777733468888887888999999888887 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00016
                 NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkl 50 
                                   +k vlv+GgG  + + + +l+++g +v +v +e  + + +++ l
  gi|91772585|ref|YP_565277.1| 140 NKDVLVIGGGVAGIEAALTLADSGTHVYMVEKE--PTIGGKMAL 181
                                   799***************************999..444444444 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                 NAD_binding_7  26 lleagakvtvvapev.....keeleelvklaeee.............lekdlegadlviaatddrelneriae 80 
                                   l++++ +++v+a  +     +e + ++++l++++             ++++++g++++ +a   +e++  ia+
  gi|91772585|ref|YP_565277.1| 477 LCQENYDLVVLATGMepsntTEPIARTLNLTKRTdrflsiahpkmrpVDAHINGVFIAGCASGPKEIQVSIAQ 549
                                   5666666777776654433333333444444444444444444444467778888888888888888888877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.5   2.8e-06    0.0016       3      34 ..     142     173 ..     140     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                   dVl++G+G aG+ +al L+  G  v +vek  
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTLADSGTHVYMVEKEP 173
                                   8****************************975 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     0.013       7.4     185     216 ..     134     165 ..     127     191 .. 0.85
   2 ?    0.9   0.0      0.34     2e+02     322     341 ..     310     329 ..     305     330 .. 0.85
   3 !    6.9   0.0     0.005       2.9     272     340 ..     426     491 ..     390     493 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                   K_oxygenase 185 keellakkriaVvGsGqSaaeifedllrrqkk 216
                                   +++ +a+k+++V+G+G  + e +  l+++ ++
  gi|91772585|ref|YP_565277.1| 134 IRKIKANKDVLVIGGGVAGIEAALTLADSGTH 165
                                   5678999*****************99998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                   K_oxygenase 322 esgeeetlevdavvlATGYr 341
                                   ++ ee+t +v av++ATGY+
  gi|91772585|ref|YP_565277.1| 310 MKAEEFTFTVGAVIVATGYQ 329
                                   67789999***********7 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.005
                   K_oxygenase 272 vdaelieelyeelyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGY 340
                                   +d +   e+yee y ++      + ++ + +v +++ +++g++ l ++++ + +  ++++d vvlATG 
  gi|91772585|ref|YP_565277.1| 426 IDIRAAGEMYEEYYVRSQ--MMGIDFI-RGKVAEIQIDTQGKMLLRYEDTLECTLCQENYDLVVLATGM 491
                                   555555666777776644..2334444.4579999999999***************************7 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00015     0.085       1      35 [.     142     174 ..     142     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieasps 35 
                                   Dv+viG+G Ag+  A  l  a  g +v ++e  p 
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTL--ADSGTHVYMVEKEPT 174
                                   9*****************..888999999988776 PP

>> HTH_53  Zap  helix turn helix N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.063        37      28      48 ..      72      92 ..      69     103 .. 0.84
   2 ?   -0.7   0.0         2   1.2e+03      28      44 ..     348     364 ..     347     379 .. 0.79
   3 ?    4.4   0.0     0.053        30      18      46 ..     730     759 ..     724     767 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.063
                        HTH_53 28 LseaqLkevLeeAGpeRFlll 48
                                  L e+  k+vLe+AG + +ll 
  gi|91772585|ref|YP_565277.1| 72 LHENTFKKVLERAGLNTYLLE 92
                                  788999************985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                        HTH_53  28 LseaqLkevLeeAGpeR 44 
                                   L +  L  +L++ Gp R
  gi|91772585|ref|YP_565277.1| 348 LTNMELERLLNASGPTR 364
                                   66778999*******99 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.053
                        HTH_53  18 aLeeLlgeveLseaqLk.evLeeAGpeRFl 46 
                                   +L+e l+e++L + +L+ e +++A  eRF 
  gi|91772585|ref|YP_565277.1| 730 NLKEVLEEIGLDQRRLRvEWISAAEGERFA 759
                                   599*************64889999999995 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7       1.2   6.8e+02      80      96 .]     241     258 ..     225     258 .. 0.77
   2 ?   13.8   0.3   0.00014      0.08      78      94 ..     287     303 ..     275     305 .. 0.84
   3 ?    6.0   2.9     0.038        22      71      93 ..     569     591 ..     541     595 .. 0.74
   4 ?    5.6   2.5     0.049        28      74      94 ..     601     621 ..     591     624 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                       Fer4_22  80 sgCvGC.gRCieacpvki 96 
                                     C GC   C ++cpv+i
  gi|91772585|ref|YP_565277.1| 241 DNCKGCiDECARVCPVDI 258
                                   679999668999999876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00014
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                   ++  CvGCg C++acp+
  gi|91772585|ref|YP_565277.1| 287 NSDYCVGCGLCKQACPA 303
                                   7889***********97 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.038
                       Fer4_22  71 sefkekfgesgCvGCgRCieacp 93 
                                     f + +++++C+GC  C+++c+
  gi|91772585|ref|YP_565277.1| 569 DPFSACVDAEKCIGCRMCEDTCN 591
                                   5566677999************7 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.049
                       Fer4_22  74 kekfgesgCvGCgRCieacpv 94 
                                   k+ ++e +C  Cg C+++cpv
  gi|91772585|ref|YP_565277.1| 601 KAVVDEISCQTCGSCSASCPV 621
                                   556678888888888888886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0019       1.1       1      34 [.     142     172 ..     142     184 .. 0.89
   2 ?    1.0   0.0      0.26   1.5e+02     156     210 ..     435     492 ..     374     505 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                   +++++GGG aG  aA +la  +   ++v +ve+e
  gi|91772585|ref|YP_565277.1| 142 DVLVIGGGVAGIEAALTLADSG---THVYMVEKE 172
                                   699*****************99...789999997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.....S-EEE-SEEEE-SGGG CS
                Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqldedgrveslrled.....greveadlfiDcsGfr 210
                                   y+++    ++  G++ ++gkv+e+q+d +g+   lr+ed       + ++dl++ ++G++
  gi|91772585|ref|YP_565277.1| 435 YEEYYV-RSQMMGIDFIRGKVAEIQIDTQGKM-LLRYEDtlectLCQENYDLVVLATGME 492
                                   444443.36788****************9996.477777553331222577777777765 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 ?    5.7   0.2     0.023        13       2      40 ..     145     178 ..     144     185 .. 0.85
   2 ?    3.6   0.0      0.11        61     112     155 ..     442     491 ..     410     492 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.023
                 NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagr 40 
                                   ++G+G++G+ ++  L+++      +++ +++++++ g g+
  gi|91772585|ref|YP_565277.1| 145 VIGGGVAGIEAALTLADS-----GTHVYMVEKEPTiG-GK 178
                                   8**************999.....5999****988845.54 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                 NAD_binding_9 112 pegvtvevhraevvdleeradgq.avlladgas.....laadaVvLAlGh 155
                                   ++ + ++++r++v +++ + +g   ++ +d  +       +d VvLA+G+
  gi|91772585|ref|YP_565277.1| 442 SQMMGIDFIRGKVAEIQIDTQGKmLLRYEDTLEctlcqENYDLVVLATGM 491
                                   45678999*********999997245556664333333799********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 4884.17
//
Query:       gi|91772586|ref|YP_565278.1|  [L=436]
Description: formylmethanofuran dehydrogenase, subunit F [Methanococcoides burtonii DSM 6242]
Scores for complete 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  131.9  75.3    9.4e-08   31.6   2.1    8.2  8  Fer4      4Fe-4S binding domain
    7.6e-31  106.5  62.5    1.5e-10   41.5   8.1    4.9  6  Fer4_7    4Fe-4S dicluster domain
      1e-25   89.6  57.1      8e-07   29.1   8.7    5.5  7  Fer4_9    4Fe-4S dicluster domain
    1.5e-25   88.1  76.8    5.9e-06   26.1   2.2    8.3  8  Fer4_6    4Fe-4S binding domain
    2.1e-23   82.2  66.2    5.1e-06   26.5  10.4    6.4  7  Fer4_10   4Fe-4S dicluster domain
    5.6e-23   80.8  59.1    1.5e-05   25.1  12.3    6.5  7  Fer4_21   4Fe-4S dicluster domain
    5.7e-22   78.4  59.4    0.00076   20.4   8.9    7.5  7  Fer4_16   4Fe-4S double cluster binding domain
    6.2e-16   57.4  75.5    0.00016   21.6   2.3    8.3  8  Fer4_2    4Fe-4S binding domain
      6e-12   45.8  64.8    0.00049   20.5   8.0    6.1  6  Fer4_8    4Fe-4S dicluster domain
      1e-10   41.2  73.2     0.0011   19.3   3.8    8.3  8  Fer4_4    4Fe-4S binding domain
    3.6e-09   37.0  66.2      0.018   15.5  11.3    7.5  7  Fer4_17   4Fe-4S dicluster domain
    2.4e-07   31.2  88.6      0.065   14.2   5.3    8.3  8  Fer4_3    4Fe-4S binding domain
    0.00016   22.4  63.3       0.04   14.6   1.2    9.0  8  Fer4_15   4Fe-4S single cluster domain
    0.00016   22.2  73.3       0.72   10.4   1.5    8.4  8  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.019   15.8   0.2      0.019   15.8   0.2    8.1  8  Fer4_22   4Fe-4S dicluster domain
      0.093   12.9  55.8       0.17   12.1   5.8    7.3  6  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   2.1   8.4e-11   9.4e-08       3      24 .]      36      57 ..      34      57 .. 0.92
   2 !   26.1   1.0   4.4e-09   4.9e-06       6      24 .]      78      96 ..      75      96 .. 0.93
   3 !   15.4   2.6   1.1e-05     0.012       5      24 .]     119     138 ..     115     138 .. 0.91
   4 !   17.7   4.1     2e-06    0.0023       1      18 [.     160     177 ..     160     179 .. 0.94
   5 !   25.1   3.5   9.3e-09     1e-05       2      24 .]     199     221 ..     198     221 .. 0.95
   6 !   23.2   4.8   3.7e-08   4.2e-05       1      23 [.     237     259 ..     237     260 .. 0.93
   7 !    8.3   0.7    0.0019       2.1      10      20 ..     283     293 ..     282     294 .. 0.91
   8 !   26.0   3.8   4.7e-09   5.2e-06       5      23 ..     309     327 ..     306     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 8.4e-11
                                  EETTTSSS-THHHHHSTTTEEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                  +d+ +C+gCG+Cv +CP+ A++
  gi|91772586|ref|YP_565278.1| 36 YDYKRCVGCGICVRICPTRALE 57
                                  799****************985 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 4.4e-09
                                  TTSSS-THHHHHSTTTEEE CS
                          Fer4  6 ekCigCGaCvevCPvgAIt 24
                                  +kC++C  Cv+ CPv+A++
  gi|91772586|ref|YP_565278.1| 78 DKCTFCSMCVNFCPVNALE 96
                                  9****************85 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.1e-05
                                   TTTSSS-THHHHHSTTTEEE CS
                          Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                    ekC+ C +C+  CP +AI+
  gi|91772586|ref|YP_565278.1| 119 NEKCVPCSLCEATCPEDAIE 138
                                   79*****************6 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 2e-06
                                   EEEETTTSSS-THHHHHS CS
                          Fer4   1 vvideekCigCGaCvevC 18 
                                   ++id +kC  CG+C+  C
  gi|91772586|ref|YP_565278.1| 160 IEIDNDKCNLCGICARFC 177
                                   68***************9 PP

  == domain 5  score: 25.1 bits;  conditional E-value: 9.3e-09
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   +ide+ C +C +C ++CP +AI+
  gi|91772586|ref|YP_565278.1| 199 IIDEDSCDYCTLCQDICPEDAIK 221
                                   79********************6 PP

  == domain 6  score: 23.2 bits;  conditional E-value: 3.7e-08
                                   EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                   v++d  kC++CG C  vCP++A 
  gi|91772586|ref|YP_565278.1| 237 VTVDDAKCTRCGWCDAVCPYDAV 259
                                   589******************96 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.0019
                                   S-THHHHHSTT CS
                          Fer4  10 gCGaCvevCPv 20 
                                   gC aC ++CP 
  gi|91772586|ref|YP_565278.1| 283 GCHACFNICPS 293
                                   9*********5 PP

  == domain 8  score: 26.0 bits;  conditional E-value: 4.7e-09
                                   TTTSSS-THHHHHSTTTEE CS
                          Fer4   5 eekCigCGaCvevCPvgAI 23 
                                   +++C++CGaCv++CP ++ 
  gi|91772586|ref|YP_565278.1| 309 YDLCTYCGACVNACPEDVM 327
                                   79*************9975 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   8.1   1.3e-13   1.5e-10       1      52 []      40      94 ..      40      94 .. 0.89
   2 !   29.8   6.8   6.1e-10   6.9e-07       1      48 [.     121     177 ..     121     180 .. 0.81
   3 !   20.0  10.6   6.7e-07   0.00075       2      52 .]     167     219 ..     167     219 .. 0.83
   4 !   27.3  14.3   3.7e-09   4.1e-06       2      52 .]     205     258 ..     204     258 .. 0.82
   5 !   23.1  11.6   7.4e-08   8.3e-05       1      50 [.     243     293 ..     243     295 .. 0.86
   6 !   23.9  11.1   4.1e-08   4.6e-05       4      51 ..     283     325 ..     278     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.3e-13
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52
                                  rC+gCg Cv+ Cp++a+el + ++ ++    + v ++ +kC++C +Cv+ CP++a
  gi|91772586|ref|YP_565278.1| 40 RCVGCGICVRICPTRALELGPMKEIATGldaPPVMMELDKCTFCSMCVNFCPVNA 94
                                  8********************9777744455778999****************97 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 6.1e-10
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.........gtekveidpekClgCgaCvavC 48 
                                   +C+ C  C+a+Cp +aiel++   +k            ++eid +kC  Cg C++ C
  gi|91772586|ref|YP_565278.1| 121 KCVPCSLCEATCPEDAIELEYTFPKKediaplkenAEGEIEIDNDKCNLCGICARFC 177
                                   7*****************9976555534444444344899**************999 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 6.7e-07
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek..gtekveidpekClgCgaCvavCPtga 52 
                                   C  Cg C++ C +  +  +e +  +  ++e++ id+++C +C+ C++ CP +a
  gi|91772586|ref|YP_565278.1| 167 CNLCGICARFCDAFLMLEKEPTATDpmPFEQLIIDEDSCDYCTLCQDICPEDA 219
                                   999*********88777766544442266999******************986 PP

  == domain 4  score: 27.3 bits;  conditional E-value: 3.7e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldee...enekgtekveidpekClgCgaCvavCPtga 52 
                                   C  C  C++ Cp +ai+++ e   e ++   kv++d  kC+ Cg C avCP++a
  gi|91772586|ref|YP_565278.1| 205 CDYCTLCQDICPEDAIKVKGEkpcEAPEVSGKVTVDDAKCTRCGWCDAVCPYDA 258
                                   99***************9954111223344899******************997 PP

  == domain 5  score: 23.1 bits;  conditional E-value: 7.4e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekC..lgCgaCvavCPt 50 
                                   +C+ Cg C a+Cp++a+++ +  +  + + ve + +kC  +gC+aC + CP+
  gi|91772586|ref|YP_565278.1| 243 KCTRCGWCDAVCPYDAVDMLKPFEG-ELMLVESHIQKCdaQGCHACFNICPS 293
                                   7*****************9987654.4477888889987789*********7 PP

  == domain 6  score: 23.9 bits;  conditional E-value: 4.1e-08
                        Fer4_7   4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   gC+aC + Cp++  +++++    g + ++ +++ C++CgaCv++CP +
  gi|91772586|ref|YP_565278.1| 283 GCHACFNICPSHLWYVPDD----G-KNIAAVYDLCTYCGACVNACPED 325
                                   9***************987....4.77999****************87 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.8   1.3e-06    0.0014      33      50 ..      33      55 ..       9      56 .. 0.74
   2 !   28.3   9.3   1.3e-09   1.5e-06       1      50 [.      40      94 ..      40      95 .. 0.90
   3 !   27.9   9.2   1.8e-09     2e-06       1      51 []      79     137 ..      79     137 .. 0.91
   4 !   22.5   6.7   8.7e-08   9.7e-05       1      51 []     166     220 ..     166     220 .. 0.93
   5 !   17.0  14.2   4.5e-06    0.0051       2      50 ..     205     258 ..     204     259 .. 0.89
   6 !   20.1  10.4   4.6e-07   0.00052       1      49 [.     243     294 ..     243     296 .. 0.89
   7 !   29.1   8.7   7.2e-10     8e-07       4      50 ..     283     326 ..     278     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                        Fer4_9 33 e.....eaCigCgaCveaCpkga 50
                                        ++C+gCg Cv +Cp+ a
  gi|91772586|ref|YP_565278.1| 33 TldydyKRCVGCGICVRICPTRA 55
                                  03334478************976 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.3e-09
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50
                                  +C+gCg Cv+ Cp+ + +    +++a    a       ++C++C  Cv+ Cp +a
  gi|91772586|ref|YP_565278.1| 40 RCVGCGICVRICPTRALELGPMKEIATGLDAPPvmmelDKCTFCSMCVNFCPVNA 94
                                  6****************9999999999866655999999*************986 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 1.8e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkgai 51 
                                   kCt C  Cv+ Cp ++ ++++ + + + +++          e+C+ C  C++ Cp++ai
  gi|91772586|ref|YP_565278.1|  79 KCTFCSMCVNFCPVNALEMRSEGDFPKEDQYPRleqfvrmnEKCVPCSLCEATCPEDAI 137
                                   7****************9999888888777666889********************997 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 8.7e-08
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                                   kC+ Cg C + C a ++ e++ + ++ +  ++     ++C  C  C ++Cp++ai
  gi|91772586|ref|YP_565278.1| 166 KCNLCGICARFCDAFLMLEKEPTATDPMPFEQLiideDSCDYCTLCQDICPEDAI 220
                                   7****************9999999999977666999999*************997 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 4.5e-06
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50 
                                   C  C+ C++ Cp ++++ +  +   + +  ++      +C+ Cg C ++Cp +a
  gi|91772586|ref|YP_565278.1| 205 CDYCTLCQDICPEDAIKVKGEKPCEAPEVSGKvtvddAKCTRCGWCDAVCPYDA 258
                                   99**************9998888877777777899999*************997 PP

  == domain 6  score: 20.1 bits;  conditional E-value: 4.6e-07
                        Fer4_9   1 kCtgCgaCveaCpagvv.vedaaerkarlraaseeaC..igCgaCveaCpkg 49 
                                   kCt+Cg C ++Cp+++v + + +e++  l +   ++C   gC+aC+++Cp++
  gi|91772586|ref|YP_565278.1| 243 KCTRCGWCDAVCPYDAVdMLKPFEGELMLVESHIQKCdaQGCHACFNICPSH 294
                                   7***************9888999999998887779**6667*********87 PP

  == domain 7  score: 29.1 bits;  conditional E-value: 7.2e-10
                        Fer4_9   4 gCgaCveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   gC+aC + Cp++++ v+d+++++a++       C+ CgaCv+aCp+++
  gi|91772586|ref|YP_565278.1| 283 GCHACFNICPSHLWyVPDDGKNIAAVYD----LCTYCGACVNACPEDV 326
                                   7************967777777777755....6************985 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   2.2   5.3e-09   5.9e-06       4      24 .]      36      56 ..      34      56 .. 0.92
   2 !   11.0   1.4   0.00031      0.35       7      24 .]      78      95 ..      75      95 .. 0.93
   3 !   17.9   2.8   2.1e-06    0.0023       6      24 .]     119     137 ..     115     137 .. 0.92
   4 !   16.1   3.7   7.7e-06    0.0087       2      19 ..     160     177 ..     159     180 .. 0.92
   5 !   16.7   4.4     5e-06    0.0056       4      24 .]     200     220 ..     198     220 .. 0.96
   6 !   13.8   4.5   4.2e-05     0.047       1      23 [.     236     258 ..     236     259 .. 0.95
   7 !   11.5   0.8   0.00022      0.25       7      21 ..     277     293 ..     272     296 .. 0.87
   8 !   16.5   4.1   5.6e-06    0.0063       6      23 ..     309     326 ..     305     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.3e-09
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +d+ +C+gCg Cvr+CP+ a+
  gi|91772586|ref|YP_565278.1| 36 YDYKRCVGCGICVRICPTRAL 56
                                  6899**************986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00031
                        Fer4_6  7 dkCigCgdCvrvCPegai 24
                                  dkC+ C  Cv+ CP +a+
  gi|91772586|ref|YP_565278.1| 78 DKCTFCSMCVNFCPVNAL 95
                                  89*************997 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.1e-06
                        Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                    +kC+ C  C++ CPe+ai
  gi|91772586|ref|YP_565278.1| 119 NEKCVPCSLCEATCPEDAI 137
                                   68***************98 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 7.7e-06
                        Fer4_6   2 veidpdkCigCgdCvrvC 19 
                                   +eid dkC+ Cg C+r C
  gi|91772586|ref|YP_565278.1| 160 IEIDNDKCNLCGICARFC 177
                                   89**************99 PP

  == domain 5  score: 16.7 bits;  conditional E-value: 5e-06
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   id+d+C+ C  C ++CPe+ai
  gi|91772586|ref|YP_565278.1| 200 IDEDSCDYCTLCQDICPEDAI 220
                                   8******************98 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 4.2e-05
                        Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                   +v++d+ kC+ Cg C +vCP++a
  gi|91772586|ref|YP_565278.1| 236 KVTVDDAKCTRCGWCDAVCPYDA 258
                                   69*******************98 PP

  == domain 7  score: 11.5 bits;  conditional E-value: 0.00022
                        Fer4_6   7 dkCi..gCgdCvrvCPe 21 
                                   +kC+  gC +C+++CP 
  gi|91772586|ref|YP_565278.1| 277 QKCDaqGCHACFNICPS 293
                                   79**999*********6 PP

  == domain 8  score: 16.5 bits;  conditional E-value: 5.6e-06
                        Fer4_6   6 pdkCigCgdCvrvCPega 23 
                                   +d+C+ Cg+Cv++CPe++
  gi|91772586|ref|YP_565278.1| 309 YDLCTYCGACVNACPEDV 326
                                   79*************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 !   26.5  10.4   4.5e-09   5.1e-06       4      56 .]      36      91 ..      33      91 .. 0.86
   2 !   16.3   1.6   7.2e-06     0.008       5      23 ..      76      94 ..      72     110 .. 0.73
   3 !   19.9   9.8   5.4e-07   0.00061       4      55 ..     117     177 ..     114     178 .. 0.94
   4 !   15.9   3.4   9.3e-06      0.01       2      27 ..     198     223 ..     197     234 .. 0.81
   5 !   23.2  10.6   5.1e-08   5.7e-05       2      56 .]     237     292 ..     236     292 .. 0.79
   6 !   17.5  12.3     3e-06    0.0033       7      56 .]     277     323 ..     271     323 .. 0.82
   7 !   17.2   2.1   3.7e-06    0.0042       6      31 ..     309     330 ..     304     360 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.5e-09
                       Fer4_10  4 idddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +d ++C++Cg Cv+ CP+ +     ++ ++   +  +v   ++kCt+c +Cv  CP
  gi|91772586|ref|YP_565278.1| 36 YDYKRCVGCGICVRICPTRAlelGPMKEIATGLDAPPVMMELDKCTFCSMCVNFCP 91
                                  6899**************989776677777777777777799*************9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.2e-06
                       Fer4_10  5 dddtCirCgkCvkaCPadl 23
                                  + d+C+ C  Cv++CP+++
  gi|91772586|ref|YP_565278.1| 76 ELDKCTFCSMCVNFCPVNA 94
                                  6799************944 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 5.4e-07
                       Fer4_10   4 idddtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   +  ++C+ C  C + CP d+         +++ a  +++ e++++++ +kC  cg C++ C
  gi|91772586|ref|YP_565278.1| 117 RMNEKCVPCSLCEATCPEDAieleytfpkKEDIAPLKENAEGEIEIDNDKCNLCGICARFC 177
                                   5679************************99999999***********************99 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 9.3e-06
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvg 27 
                                   ++id+d+C  C+ C++ CP d+ +v+
  gi|91772586|ref|YP_565278.1| 198 LIIDEDSCDYCTLCQDICPEDAIKVK 223
                                   589*****************664444 PP

  == domain 5  score: 23.2 bits;  conditional E-value: 5.1e-08
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvga.kgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                   v +dd +C+rCg C ++CP+  ++v+  k+++ e   v+  ++kC++  c aC  +CP
  gi|91772586|ref|YP_565278.1| 237 VTVDDAKCTRCGWCDAVCPY--DAVDMlKPFEGELMLVESHIQKCDAqgCHACFNICP 292
                                   7899****************..5555414555555555669****988899******9 PP

  == domain 6  score: 17.5 bits;  conditional E-value: 3e-06
                       Fer4_10   7 dtC..irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++C   +C +C + CP+        +  ++++ +  +++ Ct cgaCv aCP
  gi|91772586|ref|YP_565278.1| 277 QKCdaQGCHACFNICPS-----HLWYVPDDGKNIAAVYDLCTYCGACVNACP 323
                                   6785569**********.....6666667777777799*************9 PP

  == domain 7  score: 17.2 bits;  conditional E-value: 3.7e-06
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvgakge 31 
                                    d C+ Cg+Cv+aCP d+     k +
  gi|91772586|ref|YP_565278.1| 309 YDLCTYCGACVNACPEDV----MKVF 330
                                   578************944....3333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   4.8e-07   0.00054      28      55 ..      28      54 ..      19      58 .. 0.78
   2 !   16.8   1.4   5.1e-06    0.0057      38      59 .]      77      97 ..      62      97 .. 0.85
   3 !   18.4   0.9   1.6e-06    0.0018      36      58 ..     117     138 ..     107     139 .. 0.85
   4 !   21.9   9.1   1.3e-07   0.00014       2      58 ..     161     221 ..     160     222 .. 0.77
   5 !   25.1  12.3   1.3e-08   1.5e-05       2      59 .]     199     261 ..     198     261 .. 0.83
   6 !   19.5   9.5   6.9e-07   0.00077       3      52 ..     239     292 ..     237     296 .. 0.76
   7 !    9.5  12.9   0.00096       1.1       8      57 ..     281     327 ..     274     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.8e-07
                       Fer4_21 28 idaktvlkvvedeCvGCnlCssvCPved 55
                                    ++++l +  ++CvGC +C+ +CP+  
  gi|91772586|ref|YP_565278.1| 28 DRSSKTLDYDYKRCVGCGICVRICPT-R 54
                                  5556677788899************7.4 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.1e-06
                       Fer4_21 38 edeCvGCnlCssvCPvedciem 59
                                   d+C+ C +C++ CPv +++em
  gi|91772586|ref|YP_565278.1| 77 LDKCTFCSMCVNFCPV-NALEM 97
                                  59*************9.88887 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.6e-06
                       Fer4_21  36 vvedeCvGCnlCssvCPvedcie 58 
                                    ++++Cv C lC + CP ed+ie
  gi|91772586|ref|YP_565278.1| 117 RMNEKCVPCSLCEATCP-EDAIE 138
                                   4689*************.89998 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 1.3e-07
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidakt.......vlkvvedeCvGCnlCssvCPvedcie 58 
                                    id+dkC  Cg C+  C+  +   +e+++ +       +l + ed+C  C+lC ++CP ed+i+
  gi|91772586|ref|YP_565278.1| 161 EIDNDKCNLCGICARFCD--AFLMLEKEPTAtdpmpfeQLIIDEDSCDYCTLCQDICP-EDAIK 221
                                   59***************9..566776555542222222446679**************.89997 PP

  == domain 5  score: 25.1 bits;  conditional E-value: 1.3e-08
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidakt.........vlkvvedeCvGCnlCssvCPvedciem 59 
                                   +ided+C  C++C   C++   +ai++++++         +++v + +C+ C  C +vCP  d+++m
  gi|91772586|ref|YP_565278.1| 199 IIDEDSCDYCTLCQDICPE---DAIKVKGEKpceapevsgKVTVDDAKCTRCGWCDAVCPY-DAVDM 261
                                   59****************7...9999988874444444444488899*************6.99887 PP

  == domain 6  score: 19.5 bits;  conditional E-value: 6.9e-07
                       Fer4_21   3 idedkCigCgkCliaCedtshqaie.idaktvl...kvvedeCvGCnlCssvCP 52 
                                   +d++kC  Cg C  +C+  +++ ++ ++++ +l   ++++ +  GC+ C ++CP
  gi|91772586|ref|YP_565278.1| 239 VDDAKCTRCGWCDAVCPYDAVDMLKpFEGELMLvesHIQKCDAQGCHACFNICP 292
                                   89***************999999973444444432233344558********** PP

  == domain 7  score: 9.5 bits;  conditional E-value: 0.00096
                       Fer4_21   8 CigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                     gC  C+  C+  sh     d+ + ++ v d C+ C  C++ CP ed++
  gi|91772586|ref|YP_565278.1| 281 AQGCHACFNICP--SHLWYVPDDGKNIAAVYDLCTYCGACVNACP-EDVM 327
                                   468*********..68877888888889999**************.6766 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   0.7   1.5e-06    0.0016       1      24 [.      40      63 ..      40      71 .. 0.83
   2 !   17.5   0.2   5.2e-06    0.0058       1      25 [.      79     103 ..      79     119 .. 0.79
   3 !   20.4   8.9   6.8e-07   0.00076       1      64 [.     121     177 ..     121     180 .. 0.77
   4 !   14.3  14.4   5.2e-05     0.058       2      66 ..     205     256 ..     204     257 .. 0.77
   5 !   11.5   1.5   0.00039      0.44       1      19 [.     243     261 ..     243     269 .. 0.83
   6 ?    4.5   3.1      0.06        67      54      65 ..     281     292 ..     268     294 .. 0.69
   7 !   19.5   0.2   1.3e-06    0.0014       2      28 ..     312     337 ..     311     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkeke 24
                                  rC++Cg C+ +CPt+a++    ke
  gi|91772586|ref|YP_565278.1| 40 RCVGCGICVRICPTRALELGPMKE 63
                                  6****************9874444 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.2e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekei 25 
                                   +C+ C  C++ CP+na+++++e  +
  gi|91772586|ref|YP_565278.1|  79 KCTFCSMCVNFCPVNALEMRSEGDF 103
                                   59****************9955443 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 6.8e-07
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                   +C+ C  C  +CP++ai+ +  +++ ++e+i+   +e+ + ++++ ++k    +  C+iC++ C
  gi|91772586|ref|YP_565278.1| 121 KCVPCSLCEATCPEDAIELE--YTFPKKEDIAP-LKENAEGEIEIDNDK----CNLCGICARFC 177
                                   5*******************..89988888876.444444444444444....77********* PP

  == domain 4  score: 14.3 bits;  conditional E-value: 5.2e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                   C  C+ C ++CP++aik k ek  ea+e          +++ d +kc+       C+ C +vCP+
  gi|91772586|ref|YP_565278.1| 205 CDYCTLCQDICPEDAIKVKGEKPCEAPEV-------SGKVTVDDAKCT------RCGWCDAVCPY 256
                                   *******************4444444443.......445666766666......9*********8 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00039
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C++Cg C  vCP +a+++
  gi|91772586|ref|YP_565278.1| 243 KCTRCGWCDAVCPYDAVDM 261
                                   5999999999999999865 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.06
                       Fer4_16  54 itgCdiCqdvCP 65 
                                     gC +C ++CP
  gi|91772586|ref|YP_565278.1| 281 AQGCHACFNICP 292
                                   478888888888 PP

  == domain 7  score: 19.5 bits;  conditional E-value: 1.3e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                   C+ Cg+C+++CP++++k  + +++   
  gi|91772586|ref|YP_565278.1| 312 CTYCGACVNACPEDVMKVFR-TKVSHT 337
                                   ****************9883.444333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   2.3   1.4e-07   0.00016       5      22 .]      36      53 ..      34      53 .. 0.93
   2 !   11.0   2.4   0.00032      0.35       2      21 ..      72      91 ..      71      92 .. 0.88
   3 ?    3.7   4.1     0.067        76       8      22 .]     120     134 ..     116     134 .. 0.90
   4 !   14.1   2.2   3.3e-05     0.037       3      20 ..     160     177 ..     158     179 .. 0.92
   5 !   14.1   1.5   3.4e-05     0.039       4      22 .]     199     217 ..     196     217 .. 0.92
   6 !   11.8   3.7   0.00018       0.2       2      22 .]     236     256 ..     235     256 .. 0.89
   7 ?    4.7   2.3     0.032        36       9      21 ..     278     292 ..     275     293 .. 0.80
   8 !   18.5   3.3   1.3e-06    0.0015       3      22 .]     305     324 ..     303     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
                        Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                  +d  rC+gCg+Cv  CP+
  gi|91772586|ref|YP_565278.1| 36 YDYKRCVGCGICVRICPT 53
                                  7899*************7 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                  pv  + d+C+ C+ Cv+ CP
  gi|91772586|ref|YP_565278.1| 72 PVMMELDKCTFCSMCVNFCP 91
                                  677889************** PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.067
                        Fer4_2   8 drCigCgaCvsaCPa 22 
                                   ++C+ C+ C   CP+
  gi|91772586|ref|YP_565278.1| 120 EKCVPCSLCEATCPE 134
                                   78*******999**5 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 3.3e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                   +++d d+C+ Cg+C   C
  gi|91772586|ref|YP_565278.1| 160 IEIDNDKCNLCGICARFC 177
                                   7899***********999 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 3.4e-05
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                    +d+d+C  C  C++ CP+
  gi|91772586|ref|YP_565278.1| 199 IIDEDSCDYCTLCQDICPE 217
                                   58****************5 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00018
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                   +v vd ++C++Cg C  +CP+
  gi|91772586|ref|YP_565278.1| 236 KVTVDDAKCTRCGWCDAVCPY 256
                                   578999*********888**5 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.032
                        Fer4_2   9 rCig..CgaCvsaCP 21 
                                   +C +  C aC + CP
  gi|91772586|ref|YP_565278.1| 278 KCDAqgCHACFNICP 292
                                   676556****999** PP

  == domain 8  score: 18.5 bits;  conditional E-value: 1.3e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                   ++++ d C+ CgaCv+aCP+
  gi|91772586|ref|YP_565278.1| 305 IAAVYDLCTYCGACVNACPE 324
                                   567899*************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 !   20.5   8.0   4.3e-07   0.00049       3      64 ..      39      93 ..      37      94 .. 0.73
   2 !   16.8   7.6   6.2e-06    0.0069       3      62 ..     120     178 ..     118     181 .. 0.67
   3 !   13.6  12.9     6e-05     0.067       4      63 ..     204     256 ..     201     258 .. 0.85
   4 ?    3.1   2.9      0.12   1.3e+02      52      63 ..     282     293 ..     260     295 .. 0.66
   5 ?    5.4  13.0     0.023        26       7      65 .]     283     326 ..     275     326 .. 0.66
   6 !   13.7   2.5   5.9e-05     0.066       5      17 ..     312     326 ..     308     368 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.3e-07
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  ++C++Cg C   Cp+   +   ++  a g  a      +       l++Ct c +C++ Cpv+
  gi|91772586|ref|YP_565278.1| 39 KRCVGCGICVRICPTRALELgPMKEIATGLDAP--PVMM------ELDKCTFCSMCVNFCPVN 93
                                  79************7776664444444444444..2223......389*************97 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.2e-06
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                   ekC+ C++C+++Cp    + +  + ++++ a    e+ + e e   ++C+ cg C++ C 
  gi|91772586|ref|YP_565278.1| 120 EKCVPCSLCEATCPEDAIELEYTFPKKEDIAP-LKENAEGEIEIDNDKCNLCGICARFCD 178
                                   79************555555555555555444.22222222355569************7 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 6e-05
                        Fer4_8   4 kCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                   +C  C +Cq+ Cp  +++ +++ + +a++   + v  +++        +Ct cg C+ vCp 
  gi|91772586|ref|YP_565278.1| 204 SCDYCTLCQDICPedAIKVKGEKPCEAPEVSGK-VTVDDA--------KCTRCGWCDAVCPY 256
                                   799*********998999999999999988666.555555........9************7 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.12
                        Fer4_8  52 ttcgaCtevCpv 63 
                                   ++c+aC + Cp 
  gi|91772586|ref|YP_565278.1| 282 QGCHACFNICPS 293
                                   445555555555 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.023
                        Fer4_8   7 eCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                   +C aC++ Cp+            g++++      v       + Ct cgaC+++Cp+++
  gi|91772586|ref|YP_565278.1| 283 GCHACFNICPSHLW----YVPDDGKNIA-----AV------YDLCTYCGACVNACPEDV 326
                                   67788888874332....2222333223.....23......689************975 PP

  == domain 6  score: 13.7 bits;  conditional E-value: 5.9e-05
                        Fer4_8   5 CieCgaCqsaCp..v 17 
                                   C+ CgaC +aCp  v
  gi|91772586|ref|YP_565278.1| 312 CTYCGACVNACPedV 326
                                   666666666665552 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   3.8   9.6e-07    0.0011       2      17 .]      39      54 ..      38      54 .. 0.91
   2 !   12.4   1.2   0.00016      0.17       2      17 .]      78      93 ..      77      97 .. 0.92
   3 !    8.7   2.0    0.0024       2.7       2      16 ..     120     134 ..     119     141 .. 0.92
   4 ?    6.7   4.0     0.011        12       2      14 ..     165     177 ..     164     178 .. 0.95
   5 ?    4.4   2.4     0.059        66       2      16 ..     203     217 ..     202     223 .. 0.86
   6 ?    5.8   4.1      0.02        23       3      16 ..     243     256 ..     242     257 .. 0.92
   7 !    9.1   1.3    0.0018       2.1       2      15 ..     277     292 ..     276     300 .. 0.88
   8 !   15.5   1.5   1.6e-05     0.018       2      16 ..     310     324 ..     309     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.6e-07
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  +rC+gCg Cv++CP++
  gi|91772586|ref|YP_565278.1| 39 KRCVGCGICVRICPTR 54
                                  8*************85 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00016
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  ++C+ C  Cv++CP++
  gi|91772586|ref|YP_565278.1| 78 DKCTFCSMCVNFCPVN 93
                                  89************75 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0024
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   e+C+ C  C+a+CP 
  gi|91772586|ref|YP_565278.1| 120 EKCVPCSLCEATCPE 134
                                   79************5 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.011
                        Fer4_4   2 erCigCgsCvaaC 14 
                                   ++C+ Cg C ++C
  gi|91772586|ref|YP_565278.1| 165 DKCNLCGICARFC 177
                                   89*********** PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.059
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++C  C  C ++CP 
  gi|91772586|ref|YP_565278.1| 203 DSCDYCTLCQDICPE 217
                                   67888999******5 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.02
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +C++Cg C a+CP+
  gi|91772586|ref|YP_565278.1| 243 KCTRCGWCDAVCPY 256
                                   7************8 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0018
                        Fer4_4   2 erC..igCgsCvaaCP 15 
                                   ++C  +gC +C ++CP
  gi|91772586|ref|YP_565278.1| 277 QKCdaQGCHACFNICP 292
                                   678667********** PP

  == domain 8  score: 15.5 bits;  conditional E-value: 1.6e-05
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   + C+ Cg+Cv+aCP 
  gi|91772586|ref|YP_565278.1| 310 DLCTYCGACVNACPE 324
                                   78************4 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.8   8.2e-05     0.092      40      58 ..      35      53 ..       3      56 .. 0.72
   2 !   13.6  10.2   6.5e-05     0.073       1      58 [.      40      92 ..      40      95 .. 0.82
   3 !   15.5  11.3   1.6e-05     0.018       1      59 [.      79     135 ..      79     136 .. 0.79
   4 !    6.7   1.9    0.0097        11      43      57 ..     164     178 ..     147     182 .. 0.69
   5 ?    3.3  11.5      0.11   1.2e+02       1      59 [.     166     218 ..     166     220 .. 0.71
   6 ?    5.4  13.3     0.024        26       2      59 ..     205     257 ..     204     259 .. 0.74
   7 !    9.1  19.9    0.0017       1.9       1      60 [.     243     326 ..     243     327 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                       Fer4_17 40 eekaslCieCgeCerkCPq 58
                                  +   ++C++Cg C+r CP 
  gi|91772586|ref|YP_565278.1| 35 DYDYKRCVGCGICVRICPT 53
                                  4578999999999999996 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.5e-05
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                  rC +Cg C++ Cp+ +        ++++++ g l++   +++ ++C+ C +C+  CP 
  gi|91772586|ref|YP_565278.1| 40 RCVGCGICVRICPTRALELG----PMKEIATG-LDAPPVMMELDKCTFCSMCVNFCPV 92
                                  7*************999888....55555554.445556899***************6 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.6e-05
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   +C+ C++C++ Cp ++     +  + ++ ++ +le+    ++ ++C+ C +Ce+ CP++
  gi|91772586|ref|YP_565278.1|  79 KCTFCSMCVNFCPVNALEMRSEGDFPKEDQYPRLEQF--VRMNEKCVPCSLCEATCPED 135
                                   6*************99966655555555455556654..57899*************86 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0097
                       Fer4_17  43 aslCieCgeCerkCP 57 
                                    ++C+ Cg C+r C 
  gi|91772586|ref|YP_565278.1| 164 NDKCNLCGICARFCD 178
                                   567777777777774 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.11
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   +C+ Cg C++ C  +   ++ep  +   +    +e+ +     ++C  C +C+  CP++
  gi|91772586|ref|YP_565278.1| 166 KCNLCGICARFCDAFLMLEKEPTATDP-MP---FEQLII--DEDSCDYCTLCQDICPED 218
                                   6*************9998887763222.22...233322..237899999999999986 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.024
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   C  C  C + Cp  ++   + +k+ +a +++ + ++       +C+ Cg C+++CP++
  gi|91772586|ref|YP_565278.1| 205 CDYCTLCQDICPEDAIK-VKGEKPCEAPEVSGKVTV----DDAKCTRCGWCDAVCPYD 257
                                   999*********97764.445667777666433332....3368************97 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0017
                       Fer4_17   1 rCiqCgyClpeCpsyea................ydnepkkllraakl.....................glleeaekeekas 44 
                                   +C++Cg C ++Cp+ +                 +        +                            ++ +   + +
  gi|91772586|ref|YP_565278.1| 243 KCTRCGWCDAVCPYDAVdmlkpfegelmlveshI--------Q---KcdaqgchacfnicpshlwyvpD--DGKNIAAVYD 310
                                   6************966643322222222222221........1...12223333334346655433221..222334899* PP

                       Fer4_17  45 lCieCgeCerkCPqgl 60 
                                   lC+ Cg C+ +CP+++
  gi|91772586|ref|YP_565278.1| 311 LCTYCGACVNACPEDV 326
                                   *************997 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   4.9   0.00015      0.17       1      15 []      41      55 ..      41      55 .. 0.97
   2 !   12.8   5.0   0.00016      0.18       1      15 []      80      94 ..      80      94 .. 0.98
   3 ?    5.2   5.1     0.044        50       1      15 []     122     136 ..     122     136 .. 0.87
   4 ?    0.8   3.8       1.1   1.2e+03       1      11 [.     167     177 ..     167     178 .. 0.95
   5 !   10.9   1.8   0.00067      0.75       1      15 []     205     219 ..     205     219 .. 0.96
   6 !   10.3   3.5     0.001       1.2       1      15 []     244     258 ..     244     258 .. 0.97
   7 !    8.0   4.1    0.0055       6.2       1      14 [.     279     294 ..     279     294 .. 0.84
   8 !   14.2   5.3   5.8e-05     0.065       1      14 [.     312     325 ..     312     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg Cv+ CP++A
  gi|91772586|ref|YP_565278.1| 41 CVGCGICVRICPTRA 55
                                  ************998 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  Ct C+ Cv+ CPv+A
  gi|91772586|ref|YP_565278.1| 80 CTFCSMCVNFCPVNA 94
                                  *************99 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.044
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C++C+  CP++A
  gi|91772586|ref|YP_565278.1| 122 CVPCSLCEATCPEDA 136
                                   555*********998 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.1
                        Fer4_3   1 CtgCgaCvevC 11 
                                   C+ Cg C + C
  gi|91772586|ref|YP_565278.1| 167 CNLCGICARFC 177
                                   ********999 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00067
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C +C + CP++A
  gi|91772586|ref|YP_565278.1| 205 CDYCTLCQDICPEDA 219
                                   99**********998 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.001
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   Ct Cg C  vCP++A
  gi|91772586|ref|YP_565278.1| 244 CTRCGWCDAVCPYDA 258
                                   *************98 PP

  == domain 7  score: 8.0 bits;  conditional E-value: 0.0055
                        Fer4_3   1 Ct..gCgaCvevCPvg 14 
                                   C+  gC aC++ CP++
  gi|91772586|ref|YP_565278.1| 279 CDaqGCHACFNICPSH 294
                                   66669*********85 PP

  == domain 8  score: 14.2 bits;  conditional E-value: 5.8e-05
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   Ct CgaCv++CP++
  gi|91772586|ref|YP_565278.1| 312 CTYCGACVNACPED 325
                                   ************86 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.5   0.00015      0.17       3      21 ..      36      54 ..      35      63 .. 0.90
   2 !    8.3   0.4    0.0034       3.8       1      19 [.      73      91 ..      73     106 .. 0.85
   3 ?    1.8   1.5      0.37   4.1e+02       8      64 ..     122     137 ..     119     140 .. 0.55
   4 !   14.6   1.2   3.6e-05      0.04       1      27 [.     160     186 ..     160     191 .. 0.88
   5 !    8.7   2.6    0.0026       2.9       3      20 ..     200     217 ..     198     223 .. 0.92
   6 ?    3.7   4.0     0.091     1e+02       1      19 [.     237     255 ..     237     261 .. 0.93
   7 ?   -0.7   0.3       2.2   2.4e+03       9      20 ..     282     293 ..     277     308 .. 0.74
   8 !    6.9   4.6    0.0095        11       6      20 ..     310     324 ..     309     429 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                       Fer4_15  3 vDrdaCigcglCvaeapev 21
                                  +D ++C gcg Cv+ +p++
  gi|91772586|ref|YP_565278.1| 36 YDYKRCVGCGICVRICPTR 54
                                  5999************975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0034
                       Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                  V  + d+C+ c +Cv  +p
  gi|91772586|ref|YP_565278.1| 73 VMMELDKCTFCSMCVNFCP 91
                                  56788***********997 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.37
                       Fer4_15   8 CigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64 
                                   C  c lC a +                                         P+dAI
  gi|91772586|ref|YP_565278.1| 122 CVPCSLCEATC-----------------------------------------PEDAI 137
                                   55555555555.........................................55555 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.6e-05
                       Fer4_15   1 VvvDrdaCigcglCvaeapevfelded 27 
                                   +++D d+C  cg C++ ++ +  l+++
  gi|91772586|ref|YP_565278.1| 160 IEIDNDKCNLCGICARFCDAFLMLEKE 186
                                   79****************999888875 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0026
                       Fer4_15   3 vDrdaCigcglCvaeape 20 
                                   +D+d C+ c lC + +pe
  gi|91772586|ref|YP_565278.1| 200 IDEDSCDYCTLCQDICPE 217
                                   9***************96 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.091
                       Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                   V+vD  +C+ cg C a++p
  gi|91772586|ref|YP_565278.1| 237 VTVDDAKCTRCGWCDAVCP 255
                                   89************99997 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 2.2
                       Fer4_15   9 igcglCvaeape 20 
                                   +gc +C   +p 
  gi|91772586|ref|YP_565278.1| 282 QGCHACFNICPS 293
                                   699999999985 PP

  == domain 8  score: 6.9 bits;  conditional E-value: 0.0095
                       Fer4_15   6 daCigcglCvaeape 20 
                                   d+C+ cg+Cv ++pe
  gi|91772586|ref|YP_565278.1| 310 DLCTYCGACVNACPE 324
                                   89***********86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   1.5   0.00065      0.72       3      17 ..      38      52 ..      37      54 .. 0.89
   2 !    8.8   0.8    0.0022       2.4       3      17 ..      77      91 ..      75     102 .. 0.88
   3 ?    5.7   4.0      0.02        22       4      18 ..     120     134 ..     118     135 .. 0.93
   4 !    6.9   1.2     0.008         9       1      18 [.     162     179 ..     162     189 .. 0.86
   5 ?    6.5   5.5     0.011        12       1      18 [.     200     217 ..     200     218 .. 0.96
   6 ?    5.4   4.4     0.024        26       1      17 [.     239     255 ..     239     256 .. 0.95
   7 !    9.9   0.5   0.00097       1.1       8      29 ..     283     304 ..     277     309 .. 0.88
   8 !    7.7   4.1    0.0046       5.2       4      18 ..     310     324 ..     308     325 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00065
                       Fer4_13  3 rdtCiacgaCvelaP 17
                                   ++C++cg+Cv ++P
  gi|91772586|ref|YP_565278.1| 38 YKRCVGCGICVRICP 52
                                  579************ PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                       Fer4_13  3 rdtCiacgaCvelaP 17
                                   d+C+ c  Cv+++P
  gi|91772586|ref|YP_565278.1| 77 LDKCTFCSMCVNFCP 91
                                  589************ PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.02
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                   ++C+ c +C +++P+
  gi|91772586|ref|YP_565278.1| 120 EKCVPCSLCEATCPE 134
                                   89************7 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.008
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   +D+d+C  cg+C+ ++  
  gi|91772586|ref|YP_565278.1| 162 IDNDKCNLCGICARFCDA 179
                                   89************9965 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.011
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   +D+d+C  c++C +++P+
  gi|91772586|ref|YP_565278.1| 200 IDEDSCDYCTLCQDICPE 217
                                   89***************7 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.024
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   VD  +C+ cg C +++P
  gi|91772586|ref|YP_565278.1| 239 VDDAKCTRCGWCDAVCP 255
                                   899*************9 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.00097
                       Fer4_13   8 acgaCvelaPdvFeeddeggas 29 
                                   +c+aC +++P +  + +++g+ 
  gi|91772586|ref|YP_565278.1| 283 GCHACFNICPSHLWYVPDDGKN 304
                                   8*****************9985 PP

  == domain 8  score: 7.7 bits;  conditional E-value: 0.0046
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                   d C+ cgaCv+++P+
  gi|91772586|ref|YP_565278.1| 310 DLCTYCGACVNACPE 324
                                   67************7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.2   1.7e-05     0.019      67      94 ..      26      53 ..       3      55 .. 0.73
   2 ?    1.8   2.5      0.38   4.3e+02      81      94 ..      79      92 ..      71      94 .. 0.67
   3 ?    4.7   1.7     0.049        55      79      94 ..     119     134 ..     105     136 .. 0.75
   4 ?    3.1   0.3      0.16   1.7e+02      78      93 ..     163     178 ..     152     184 .. 0.75
   5 ?    2.3   0.1      0.27   3.1e+02      78      94 ..     201     217 ..     190     219 .. 0.74
   6 ?    6.7   1.1     0.012        13      79      93 ..     241     255 ..     232     258 .. 0.68
   7 ?    2.1   0.3      0.32   3.6e+02      79      95 ..     278     294 ..     265     295 .. 0.69
   8 ?    6.2   0.8     0.017        19      81      95 ..     311     325 ..     303     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                       Fer4_22 67 lhklsefkekfgesgCvGCgRCieacpv 94
                                  +   s+ +  ++ + CvGCg C++ cp+
  gi|91772586|ref|YP_565278.1| 26 ISDRSSKTLDYDYKRCVGCGICVRICPT 53
                                  44444555567999************97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.38
                       Fer4_22 81 gCvGCgRCieacpv 94
                                  +C+ C  C++ cpv
  gi|91772586|ref|YP_565278.1| 79 KCTFCSMCVNFCPV 92
                                  56666666666665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.049
                       Fer4_22  79 esgCvGCgRCieacpv 94 
                                   +++Cv C  C+++cp+
  gi|91772586|ref|YP_565278.1| 119 NEKCVPCSLCEATCPE 134
                                   4578888888888876 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.16
                       Fer4_22  78 gesgCvGCgRCieacp 93 
                                   ++ +C  Cg C + c 
  gi|91772586|ref|YP_565278.1| 163 DNDKCNLCGICARFCD 178
                                   6677777777777775 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.27
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                   +e +C  C  C++ cp+
  gi|91772586|ref|YP_565278.1| 201 DEDSCDYCTLCQDICPE 217
                                   56677777777777775 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.012
                       Fer4_22  79 esgCvGCgRCieacp 93 
                                     +C+ Cg C+++cp
  gi|91772586|ref|YP_565278.1| 241 DAKCTRCGWCDAVCP 255
                                   556666666666666 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.32
                       Fer4_22  79 esgCvGCgRCieacpvk 95 
                                   +    GC  C + cp++
  gi|91772586|ref|YP_565278.1| 278 KCDAQGCHACFNICPSH 294
                                   44456888888888865 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.017
                       Fer4_22  81 gCvGCgRCieacpvk 95 
                                    C+ Cg C++acp++
  gi|91772586|ref|YP_565278.1| 311 LCTYCGACVNACPED 325
                                   688888888888875 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00019      0.21      56      74 ..      36      54 ..       3      58 .. 0.78
   2 ?    7.8   1.5    0.0032       3.6      59      74 ..      78      93 ..      71     103 .. 0.84
   3 ?    3.0   1.8       0.1   1.2e+02      56      73 ..     117     134 ..      96     143 .. 0.79
   4 ?    0.6   2.5      0.56   6.3e+02      59      74 ..     203     218 ..     185     226 .. 0.80
   5 ?    6.9   3.7    0.0062         7      55      86 ..     238     270 ..     220     281 .. 0.72
   6 ?   12.1   5.8   0.00015      0.17      57     104 ..     277     332 ..     268     338 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                       Fer4_18 56 kgagdcidcescvkvcPtg 74
                                   +   c+ c+ cv++cPt 
  gi|91772586|ref|YP_565278.1| 36 YDYKRCVGCGICVRICPTR 54
                                  45678************95 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0032
                       Fer4_18 59 gdcidcescvkvcPtg 74
                                   +c+ c++cv+ cP++
  gi|91772586|ref|YP_565278.1| 78 DKCTFCSMCVNFCPVN 93
                                  68************85 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.1
                       Fer4_18  56 kgagdcidcescvkvcPt 73 
                                   + + +c+ c+ c + cP 
  gi|91772586|ref|YP_565278.1| 117 RMNEKCVPCSLCEATCPE 134
                                   556789******999996 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.56
                       Fer4_18  59 gdcidcescvkvcPtg 74 
                                     c  c  c ++cP +
  gi|91772586|ref|YP_565278.1| 203 DSCDYCTLCQDICPED 218
                                   5688899999999964 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0062
                       Fer4_18  55 ekgagdcidcescvkvcPtg.idirkGlqleci 86 
                                   + ++++c+ c+ c +vcP + +d+ k +  e +
  gi|91772586|ref|YP_565278.1| 238 TVDDAKCTRCGWCDAVCPYDaVDMLKPFEGELM 270
                                   567899************743788776665555 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.00015
                       Fer4_18  57 gagdcidcescvkvcPtgidi..rkGlqle.....ciscllcidac.dkvmeklgk 104
                                   ++ d   c++c ++cP ++     +G  +      c  c+ c++ac ++vm+ +++
  gi|91772586|ref|YP_565278.1| 277 QKCDAQGCHACFNICPSHLWYvpDDGKNIAavydlCTYCGACVNACpEDVMKVFRT 332
                                   5677889***********95422466665433445999********5579987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3137.46
//
Query:       gi|91772587|ref|YP_565279.1|  [L=107]
Description: hypothetical protein Mbur_0554 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0035   16.6   1.7     0.0039   16.4   1.7    1.0  1  Actin_micro     Putative actin-like family
  ------ inclusion threshold ------
       0.11   12.9   2.7       0.15   12.4   1.2    1.8  2  Ribosomal_L27e  Ribosomal L27e protein family


Domain annotation for each model (and alignments):
>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.7   4.3e-07    0.0039      11     102 ..      10     102 ..       8     107 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.3e-07
                   Actin_micro  11 itsffmrsdnSyfvkekeryaaYrkdedrvlivvvedkliisekevetddyfykselnk.eeeeglieegkiaknikkvsl 90 
                                   i sff  +d+     +     +Yr++ ++v+i+ +++  +i +k  +t++y y++ l+   ++e ++  +k+a +  ++s 
  gi|91772587|ref|YP_565279.1|  10 IISFFTSNDVYLDFISAVNVDTYRNSSHKVYIIKNQHFTMIPKKPEDTEEYVYETVLYGgGKVEYIKYPRKEAEEKWRKSF 90 
                                   78999999998878889999**************9999999*************998852467777778888888888888 PP

                   Actin_micro  91 dklfktikeivy 102
                                   d+ ++  k ++ 
  gi|91772587|ref|YP_565279.1|  91 DETYQKNKWLFD 102
                                   888876665555 PP

>> Ribosomal_L27e  Ribosomal L27e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   1.4e+03      40      62 ..      22      44 ..      14      65 .. 0.67
   2 ?   12.4   1.2   1.7e-05      0.15      56      83 ..      79     104 ..      71     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                Ribosomal_L27e 40 dlkelvkkealkdpakrkeakke 62
                                  d+ ++v+ ++ ++++++  + k+
  gi|91772587|ref|YP_565279.1| 22 DFISAVNVDTYRNSSHKVYIIKN 44
                                  55666777777777766665554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.7e-05
                Ribosomal_L27e  56 rkeakkevkkkfeeryksgknkwffkkL 83 
                                   rkea ++ +k f e y+++  kw+f +L
  gi|91772587|ref|YP_565279.1|  79 RKEAEEKWRKSFDETYQKN--KWLFDEL 104
                                   99**************866..9***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 750.10
//
Query:       gi|91772588|ref|YP_565280.1|  [L=257]
Description: hypothetical protein Mbur_0555 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0069   15.5   1.6     0.0088   15.2   1.6    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.017   15.2   0.1        5.3    7.2   0.0    2.5  2  DUF2023          Protein of unknown function (DUF2023)
       0.18   11.8   0.0        0.3   11.0   0.0    1.4  1  PsbI             Photosystem II reaction centre I protein (PS


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 !   15.2   1.6   1.5e-06    0.0088      12     123 ..       8     128 ..       6     207 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-06
               ABC2_membrane_3  12 iilvlllglifs...nsved........dentpiavvdedn............sslsqqlvealeaspsvelvyevdseee 69 
                                   ii+++ll ++f+    ++++        +        d+++               ++   ++ e++++++  +  ++e+e
  gi|91772588|ref|YP_565280.1|   8 IIIIVLLSFAFGcvsEDTSTnhggtiqdT--------DDTDvpepssltedeeVVETPATSNDTENTNDID--IVQKTEQE 78 
                                   44444455555422133332222333222........2222333333444446677777779999999999..99999999 PP

               ABC2_membrane_3  70 akkalkngdidgilvipkgfskdllkgesatvtvlinssnlnsskailnalns.l 123
                                     + +k++++++ + i++++ +  +     + t ++ +   +++++ ln++++ l
  gi|91772588|ref|YP_565280.1|  79 TDDFVKSTGYEADVNIDENNMNVYF-----DTTKFTKTDIHTMVSECLNTMTDyL 128
                                   9*******************97544.....3333333333333355555555433 PP

>> DUF2023  Protein of unknown function (DUF2023)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0029        17      45      77 ..      93     126 ..      67     151 .. 0.86
   2 ?    7.2   0.0   0.00089       5.3       7      43 ..     196     232 ..     193     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0029
                                   E-TSSEEEEEEE-HHHHHH.HHHHHTS-GGG--H CS
                       DUF2023  45 evseekvnlffGkkeciev.vrslvkkplneltp 77 
                                   +++e+++n++f ++++ ++ ++++v++ ln++t+
  gi|91772588|ref|YP_565280.1|  93 NIDENNMNVYFDTTKFTKTdIHTMVSECLNTMTD 126
                                   578999******9999886699999999998875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00089
                                   HHHHHCTS-SEEEEEEEGGGHHHHHHHHHHTT--EEE CS
                       DUF2023   7 iYeykkgvRklvlltlkkkeeelvvkrLekkeieylv 43 
                                   +Y ++kgv +  l+t+++k+ +++v++L ++  +  +
  gi|91772588|ref|YP_565280.1| 196 VYFHTKGVTDSDLHTMSEKCVKIMVRHLPDQMAKVAI 232
                                   8999************************988766555 PP

>> PsbI  Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.1e-05       0.3       8      31 ..       5      28 ..       1      31 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                          PsbI  8 VyivViffvslFvFGfLsnDPsRN 31
                                    i++i + + F FG  s D+s N
  gi|91772588|ref|YP_565280.1|  5 YKIIIIIVLLSFAFGCVSEDTSTN 28
                                  45788888888**********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1171  (0.0653132); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1669.39
//
Query:       gi|91772589|ref|YP_565281.1|  [L=165]
Description: hypothetical protein Mbur_0556 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0059   16.2   0.1      0.012   15.3   0.0    1.5  1  tRNA_anti-like  tRNA_anti-like
     0.0069   15.5   3.5       0.01   14.9   3.5    1.1  1  RapA_C          RNA polymerase recycling family C-terminal
  ------ inclusion threshold ------
      0.043   12.7   0.1      0.048   12.6   0.1    1.1  1  Serinc          Serine incorporator (Serinc)
      0.059   13.5   0.1        2.1    8.5   0.0    2.1  2  DUF3736         Protein of unknown function (DUF3736)
      0.065   12.3   2.1      0.088   11.8   2.1    1.2  1  DUF874          Helicobacter pylori protein of unknown functi


Domain annotation for each model (and alignments):
>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.3e-06     0.012       8      58 ..      33      96 ..      26     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-06
                                  XXXXXXXXXXXXXXXXXX..............XXXXXXXXXXXX---HHHHHTS-.......... CS
                tRNA_anti-like  8 ilviilivilllfvialv..............aqaaesardkekaekedadatlaeakakpeava 58
                                  +  +i++++l+ f+++ +              + a+e a+++ekaeke+ +a+++ +ka+ e+  
  gi|91772589|ref|YP_565281.1| 33 RTNWIVLLVLFSFIAY-GcvdlvtdsddeiaaREAQELAEQAEKAEKERIKAEEERIKAENERIQ 96
                                  4445555555555555.345667**9999999888999999999999999999998888777643 PP

>> RapA_C  RNA polymerase recycling family C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   3.5   2.8e-06      0.01     283     342 ..      55     111 ..      48     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-06
                                   TTTTTTSSSHHHHHHHHHHHHHHHHHHHHHTHHHHTHHHH--S--SSSHHHHTTTHHHHT CS
                        RapA_C 283 lkkaeklaeeqaeelieeakaraeqelsaEleRLeaLkavNpnirdeeiealeeqreell 342
                                    ++ +++a+++a+el e+a+++ +++++aE eR+   ka N+ i+ eei+ +e+++e +l
  gi|91772589|ref|YP_565281.1|  55 TDSDDEIAAREAQELAEQAEKAEKERIKAEEERI---KAENERIQAEEIDSFETEMEGIL 111
                                   56678999*************************8...57***************998765 PP

>> Serinc  Serine incorporator (Serinc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.3e-05     0.048     267     345 ..      18      93 ..       8     147 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                        Serinc 267 kecnpllssslegtetasvvigliltflcvlYstlraasssqveklralkaaeeegalpesaleeeeeeeeekekeeee 345
                                   ++ np  +++ +++++ +  i l+++f  ++Y ++   + s  +++ a +a+e ++++++ ++ e+ ++eee+ k+e+e
  gi|91772589|ref|YP_565281.1|  18 AKANPPSDEQ-RRKNKRTNWIVLLVLFSFIAYGCVDLVTDS-DDEIAAREAQELAEQAEKAEK-ERIKAEEERIKAENE 93 
                                   4578887776.46677788999999**********999983.455543322222222222111.111111111111111 PP

>> DUF3736  Protein of unknown function (DUF3736)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00057       2.1      11      43 ..      24      72 ..      23      74 .. 0.93
   2 ?    1.5   1.6     0.083     3e+02       3      32 ..      75     106 ..      73     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00057
                       DUF3736 11 leeqrrrearen................gsidesdeeeanaellkvmsg 43
                                  ++eqrr+ +r+n                + +++sd+e a +e +  +++
  gi|91772589|ref|YP_565281.1| 24 SDEQRRKNKRTNwivllvlfsfiaygcvDLVTDSDDEIAAREAQELAEQ 72
                                  69**************************************999887776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.083
                       DUF3736   3 qalaSrldleeqrrrearen..gsidesdeee 32 
                                   +a   r+  ee r+++  e+   + ++s+e e
  gi|91772589|ref|YP_565281.1|  75 KAEKERIKAEEERIKAENERiqAEEIDSFETE 106
                                   566789999*****999999777777777754 PP

>> DUF874  Helicobacter pylori protein of unknown function (DUF874)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.1   2.5e-05     0.088     159     194 ..      64      99 ..      49     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                        DUF874 159 ksnielansqikveqerqkteqekqkaekeaikleq 194
                                   + + ela++  k+e+er k+e+e+ kae+e+i+ e+
  gi|91772589|ref|YP_565281.1|  64 REAQELAEQAEKAEKERIKAEEERIKAENERIQAEE 99 
                                   556789999999999999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2425  (0.135256); expected 358.6 (0.02)
Passed bias filter:                     1222  (0.0681577); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); expected 17.9 (0.001)
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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1119.37
//
Query:       gi|91772590|ref|YP_565282.1|  [L=128]
Description: resolvase-like protein [Methanococcoides burtonii DSM 6242]
Scores for 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   84.1   0.0    1.2e-23   83.9   0.0    1.0  1  Resolvase  Resolvase, N terminal domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   6.6e-28   1.2e-23       1     115 [.       7     117 ..       7     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 6.6e-28
                                   EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-.TT.-HHHHHHHHHHTT-EE.EEEESSCCCC-S. CS
                     Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGak.le.RpglkrllaalregkgdvlvvekldRLaRs 79 
                                   a+gYaR St++q+  +e Q+ +l++ +     +i   f D+gvSG+  +e Rpg+k+ll+ ++++ +d+++  +++RL+R+
  gi|91772590|ref|YP_565282.1|   7 AVGYARTSTKDQN--IETQILQLKNKGIVA-EQI---FFDEGVSGSVpAEkRPGFKQLLKCIESNDIDTIYLFEISRLGRT 81 
                                   79***********..************777.448...**********6346****************************** PP

                                   ..S-HHHHHHHHHTT-EEEESS..SS----HHHHHH CS
                     Resolvase  80 vrdlltlleelrekgvslvsldegidtstpmgrlll 115
                                     d l+l+ ++++kg+++vsl+ +  +st +++  +
  gi|91772590|ref|YP_565282.1|  82 FVDTLNLVMDFEDKGIRVVSLSPSESWSTIEDSHYR 117
                                   *********************943444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 750.52
//
Query:       gi|91772591|ref|YP_565283.1|  [L=88]
Description: hypothetical protein Mbur_0558, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-06   26.7   0.2    6.6e-06   25.8   0.2    1.4  1  HTH_23           Homeodomain-like domain
    0.00043   20.4   0.1    0.00081   19.5   0.1    1.5  1  HTH_28           Helix-turn-helix domain
     0.0037   16.9   0.0     0.0054   16.4   0.0    1.3  1  Sigma70_r4_2     Sigma-70, region 4
     0.0056   16.7   0.1     0.0099   15.9   0.1    1.4  1  HTH_3            Helix-turn-helix
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.021   14.4   0.0    1.3  1  GerE             Bacterial regulatory proteins, luxR family
      0.021   14.3   0.1       0.13   11.8   0.0    2.1  2  Sigma70_r4       Sigma-70, region 4
      0.048   13.8   0.0      0.093   12.8   0.0    1.4  1  HTH_7            Helix-turn-helix domain of resolvase
      0.048   13.7   0.1      0.069   13.2   0.1    1.3  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
      0.059   13.2   0.0       0.13   12.0   0.0    1.6  1  HTH_38           Helix-turn-helix domain
      0.065   13.3   0.1       0.11   12.6   0.1    1.4  1  Resolvase        Resolvase, N terminal domain


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 !   25.8   0.2   3.7e-09   6.6e-06      13      44 ..      46      78 ..      41      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.7e-09
                        HTH_23 13 llaeGlsvreIAreLgvsrrTvyrwlkryre.e 44
                                    ++Gl+++eI+r L+++ +T+y+++  ++e +
  gi|91772591|ref|YP_565283.1| 46 YRKKGLTWAEISRVLNIPASTLYKYRDIWEErS 78
                                  3445*************************7644 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.5e-07   0.00081       3      41 ..      41      79 ..      39      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.5e-07
                        HTH_28  3 leiikllaaGhsvreaArelgisrrtvyrWikryeegGi 41
                                  +e++k+ ++G + +e++r l+i  +t+y+ +  +ee  +
  gi|91772591|ref|YP_565283.1| 41 KEVMKYRKKGLTWAEISRVLNIPASTLYKYRDIWEERSR 79
                                  58999******************************9655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     3e-06    0.0054      13      45 ..      38      69 ..      37      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                                  HHHHHHHHHHHTS---HHHHHHHHT--HHHHHH CS
                  Sigma70_r4_2 13 erqreifllryleglsykEIAellgisegtVks 45
                                  ++q+e++  r  +gl+ +EI+++l+i+ +t ++
  gi|91772591|ref|YP_565283.1| 38 PDQKEVMKYRK-KGLTWAEISRVLNIPASTLYK 69
                                  78888888865.*****************9876 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.5e-06    0.0099       2      29 ..      44      70 ..      41      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                                  HHHHHHTTHHHHHHHHHHTSSHHHHHHH CS
                         HTH_3  2 kelRkqlglsqeeLAeklGvsrstisri 29
                                  +++Rk +gl+ +e++++l+++ st++++
  gi|91772591|ref|YP_565283.1| 44 MKYRK-KGLTWAEISRVLNIPASTLYKY 70
                                  45666.********************98 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.021       7      33 ..      40      66 ..      38      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                  HHHHHHHHCTTS-HHHHHHHHTS-HHH CS
                          GerE  7 ErevLrllaeGksnkeIAeelniSekT 33
                                  ++ev+++  +G++  eI++ lni + T
  gi|91772591|ref|YP_565283.1| 40 QKEVMKYRKKGLTWAEISRVLNIPAST 66
                                  689********************9888 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.38   6.8e+02       7      16 ..       7      16 ..       5      25 .. 0.79
   2 ?   11.8   0.0   7.2e-05      0.13       7      36 ..      38      66 ..      37      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.38
                                  HHHHHHHHHH CS
                    Sigma70_r4  7 ererevlelr 16
                                  e+e+++l+ r
  gi|91772591|ref|YP_565283.1|  7 ENEKRILQER 16
                                  7899999987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.2e-05
                                  HHHHHHHHHHHTTT--HHHHHHHHTS-HHH CS
                    Sigma70_r4  7 ererevlelrfgeglTleEIgerlgiSrer 36
                                  ++++ev+++r  +glT +EI+++l+i+ ++
  gi|91772591|ref|YP_565283.1| 38 PDQKEVMKYRK-KGLTWAEISRVLNIPAST 66
                                  77888888886.899***********9876 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.2e-05     0.093       5      41 ..      36      70 ..      32      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                                  SS-HH.HHGGGGSSTTTT--STTTSSSS---SSSS--S CS
                         HTH_7  5 klskn.dinrvvkLleeGisiskIAkevnisRsTvYRy 41
                                  k   + d+ +v k +++G + ++I + +ni  sT+Y+y
  gi|91772591|ref|YP_565283.1| 36 K---EpDQKEVMKYRKKGLTWAEISRVLNIPASTLYKY 70
                                  3...3379*****************************9 PP

>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.9e-05     0.069      18      51 ..      24      57 ..      20      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                                  S-SS--TTS---HHHHHHHHHHHHHTT--HHHHH CS
               Ribosomal_S13_N 18 yrreapsWlklskeeveelivklakkGltpSqIG 51
                                  y++e+ +W + +ke  ++ ++k++kkGlt ++I 
  gi|91772591|ref|YP_565283.1| 24 YKKENDKWGRPTKEPDQKEVMKYRKKGLTWAEIS 57
                                  8999**************************9995 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.3e-05      0.13      12      39 ..      42      69 ..      37      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                        HTH_38 12 eIerllaeGlslreIArrLgrspsTIsR 39
                                  e  + +++Gl+ +eI r L+   sT ++
  gi|91772591|ref|YP_565283.1| 42 EVMKYRKKGLTWAEISRVLNIPASTLYK 69
                                  667889*******************985 PP

>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     6e-05      0.11     117     145 ..       1      29 [.       1      30 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                                   HHHHHHHHHHHHHHCT-TTHHHHHHHHHH CS
                     Resolvase 117 ilaalaeferelirertkeglaaakakGk 145
                                   +++++ae e++ ++er+k g+++ k++++
  gi|91772591|ref|YP_565283.1|   1 MFGWVAENEKRILQERIKVGIERYKKEND 29 
                                   899**********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 561.84
//
Query:       gi|91772592|ref|YP_565284.1|  [L=234]
Description: hypothetical protein Mbur_0559 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-05   23.0   0.0    0.00017   21.5   0.0    1.7  2  RadC      RadC-like JAB domain
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.38   10.5   0.0    1.7  1  Prok-JAB  Prokaryotic homologs of the JAB domain


Domain annotation for each model (and alignments):
>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.58   5.2e+03      68      78 ..      16      26 ..      15      43 .. 0.69
   2 !   21.5   0.0     2e-08   0.00017      25     105 ..      93     182 ..      75     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.58
                                  EEEEE-TTS-- CS
                          RadC 68 ilaHnhPsgdl 78
                                  +++H hP ++ 
  gi|91772592|ref|YP_565284.1| 16 VITHLHPLNEK 26
                                  67888886654 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2e-08
                                   EEEE-TTSBEEEEEEEEESTT-...GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--......S--HHHHHHHHHHHHHHH CS
                          RadC  25 vllLdsknrliadeelseGtln...stlvdprevfkealklnAaavilaHnhPsgdl......epSeeDieltkrlkealk 96 
                                   +++  +kn+ i+    ++G  +   s+ ++ +++++++ ++n + v+++HnhP+ d+      +pS++Di+  +  ++  +
  gi|91772592|ref|YP_565284.1|  93 AIIAFEKNKTIQLMWTNKGINKktvSIFLSTEQIIAKCKDNNYSTVLIFHNHPNSDPhtldcsRPSQQDINSAQIFSNDFN 173
                                   4444466666666666666555444678999***********************7663333337***********999999 PP

                                   HHT-EEEEE CS
                          RadC  97 llgiellDh 105
                                     gi+l++ 
  gi|91772592|ref|YP_565284.1| 174 KYGINLIEF 182
                                   999999875 PP

>> 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 ?   10.5   0.0   4.3e-05      0.38      61      93 ..     117     166 ..      80     168 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.3e-05
                      Prok-JAB  61 f...........earerglevvgiwHSHpggsa......rPSetDrrdaa 93 
                                   +           ++ +++ ++v i+H Hp++ +      rPS++D+++a+
  gi|91772592|ref|YP_565284.1| 117 VsiflsteqiiaKCKDNNYSTVLIFHNHPNSDPhtldcsRPSQQDINSAQ 166
                                   2333334444448899*************98765555569*****98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1410.36
//
Query:       gi|91772593|ref|YP_565285.1|  [L=402]
Description: CRISPR-associated Cas1 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-77  259.7   0.0    3.1e-77  259.5   0.0    1.1  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
       0.11   12.5   0.2       0.46   10.5   0.0    2.1  2  ER        Enhancer of rudimentary


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 !  259.5   0.0   3.5e-81   3.1e-77       7     282 ..      17     294 ..       4     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 259.5 bits;  conditional E-value: 3.5e-81
                                   EEEEEEETTEEEEEE.SSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSSTHHHHH CS
                      Cas_Cas1   7 gaylrkkgerlvvek.egeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlepeesgnvelrr 85 
                                    a+l++k++r+  ++  +e + + +  di+siv++g+  sls +a+r+l+++++++++l++ngk+l+++ p+es+nv+++ 
  gi|91772593|ref|YP_565285.1|  17 SAKLHIKDGRFSTTEdPEEYVFSPKRMDIDSIVVYGRsGSLSLEAIRWLIKHNVQITILDWNGKLLTTMLPSESTNVKTKF 97 
                                   4667888888877775556899999************9******************************************* PP

                                   HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHHHHHH CS
                      Cas_Cas1  86 aQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaYfeaf 166
                                   aQy+a++d+++r++lakk++++k++++++vl++lk ++      e   +++  + kle+a+s+ e++g+EG +a +Y++++
  gi|91772593|ref|YP_565285.1|  98 AQYHAYEDQDTRVKLAKKFIEAKFSKSEAVLDYLKLRY-----PEINYDISVDKGKLENAKSVREILGVEGGVAWKYWNEY 173
                                   **************************************.....445556667778************************** PP

                                   HHHCSCGGS-SS-SSSS-.....SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHHC CS
                      Cas_Cas1 167 dkllkeefefegRsrrpp.....kDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpllv 242
                                   +k ++ee++f+ R+ + +      D+vN++L++gY+ll+se+l+ai++vgLd ++GfLHe++p+++sLa+DL+E+fR  +v
  gi|91772593|ref|YP_565285.1| 174 AKAIPEEYDFRARTDNNArasnsGDKVNVMLNYGYALLESECLRAINSVGLDAHVGFLHEMNPSKNSLAYDLQEPFRF-IV 253
                                   *************99886455558*****************************************************9.9* PP

                                   HHHHHHHHHTTSS-GGGEEEETT.EEEE-HHHHHHHHHHHH CS
                      Cas_Cas1 243 DrlvlslinkrqlkekdFekeen.gvlLteegrkkfleafe 282
                                   D +v++li+k+++++kdF+++e+ +++L+++g +k++e+f+
  gi|91772593|ref|YP_565285.1| 254 DLTVMNLIEKGIMDSKDFIRTESfSLRLRPTGARKVTEEFN 294
                                   ***************************************97 PP

>> ER  Enhancer of rudimentary
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.33   2.9e+03      36      54 ..     125     143 ..      90     144 .. 0.60
   2 ?   10.5   0.0   5.1e-05      0.46      38      68 ..     230     260 ..     214     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.33
                            ER  36 eeaLkeanpskksitYdis 54 
                                   e+ L   + + ++i+Ydis
  gi|91772593|ref|YP_565285.1| 125 EAVLDYLKLRYPEINYDIS 143
                                   4444445555588888885 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.1e-05
                            ER  38 aLkeanpskksitYdisdLfefidsladlsa 68 
                                    L+e+npsk+s+ Yd+++ f+fi +l+ +++
  gi|91772593|ref|YP_565285.1| 230 FLHEMNPSKNSLAYDLQEPFRFIVDLTVMNL 260
                                   5899*******************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2286.31
//
Query:       gi|91772594|ref|YP_565286.1|  [L=372]
Description: hypothetical protein Mbur_0561 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.6   1.1       0.43   10.9   0.1    2.8  3  DUF1844   Domain of unknown function (DUF1844)
      0.071   13.5   0.0        1.7    9.0   0.0    2.8  3  HEAT_2    HEAT repeats


Domain annotation for each model (and alignments):
>> DUF1844  Domain of unknown function (DUF1844)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.4   1.2e+04      54      66 ..     150     162 ..     142     163 .. 0.70
   2 ?   -0.1   0.0      0.13   1.2e+03      38      51 ..     181     194 ..     172     202 .. 0.81
   3 ?   10.9   0.1   4.8e-05      0.43       4      36 ..     272     304 ..     269     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                       DUF1844  54 LdeeEerlLeeal 66 
                                   L+ ++++lL+++l
  gi|91772594|ref|YP_565286.1| 150 LKSDDTNLLDHVL 162
                                   6677777887776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                       DUF1844  38 qsIdlLamLkeKtk 51 
                                   ++Id+L+ L +K  
  gi|91772594|ref|YP_565286.1| 181 KTIDVLRSLLKKYP 194
                                   69*******99975 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 4.8e-05
                       DUF1844   4 stlvlslassAlvaLGelpdpetgkkekdlelA 36 
                                   ++++  + ++Al+ LG+  dp ++k +++le+ 
  gi|91772594|ref|YP_565286.1| 272 AQFIAEIRATALIDLGLKDDPFKNKDNNELEMD 304
                                   589**********************99999975 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0002       1.7       2      73 ..     108     192 ..     107     201 .. 0.71
   2 ?    1.3   0.0     0.052   4.7e+02      13      36 ..     200     223 ..     183     235 .. 0.74
   3 ?   -1.9   0.0       0.5   4.4e+03      15      30 ..     277     292 ..     273     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0002
                        HEAT_2   2 daLlqalendpdpevrraairaLg.....rignpealpaLvellededpavRraaaeaLg......aig...dpealpaLk 68 
                                   d+ ++ l ++ +p  +++a++++         np+ l++Lv++l+++d++   ++ +         +i+   + +++++L+
  gi|91772594|ref|YP_565286.1| 108 DVAINKL-QSNNPIKQKMALKEIEsyekhYALNPKQLDMLVSILKSDDTNLLDHVLRIVYnyieykKIDpsnETKTIDVLR 187
                                   6678889.799999999*******7776555689**********9999988777777664222122443322455777777 PP

                        HEAT_2  69 elldd 73 
                                    ll+ 
  gi|91772594|ref|YP_565286.1| 188 SLLKK 192
                                   77765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.052
                        HEAT_2  13 dpevrraairaLgrignpealpaL 36 
                                   ++++r + i  Lg +++  +++  
  gi|91772594|ref|YP_565286.1| 200 HTNLRSHLIFLLGYYNDSAVVERA 223
                                   567999999999999988776654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.5
                        HEAT_2  15 evrraairaLgrignp 30 
                                   e+r++a++ Lg +++p
  gi|91772594|ref|YP_565286.1| 277 EIRATALIDLGLKDDP 292
                                   6799999999976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2163.26
//
Query:       gi|91772595|ref|YP_565287.1|  [L=212]
Description: hypothetical protein Mbur_0562 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   13.8   0.0      0.036   13.6   0.0    1.1  1  GCHY-1    Type I GTP cyclohydrolase folE2


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 ?   13.6   0.0     2e-06     0.036     133     230 ..      71     197 ..      28     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-06
                                   EEEEEEEEEEEEEE-HHHHHHS.................................SS---EEEEEEEEEEEE......--H CS
                        GCHY-1 133 vkltvgvevpvttlCPCskeisrell.............................eagaHnQRsvvtvkvelaeeekevei 184
                                    +l++++  +v    P sk+i ++ +                             + +a n R +  +++ +++++++  i
  gi|91772595|ref|YP_565287.1|  71 RTLSLEILRNVRKGVPFSKAIEKTGAnkknvinnlgkylykskgkwrvtasdrieSEMAFNDRDKGLISIVTTRSKDRSLI 151
                                   55556666666666677777776666778888888888888888888888888888899************99999999** PP

                                   HHHHHHHHHHSSEE--S---HHHHHHHHHHHHTS---HHHHHHHHH CS
                        GCHY-1 185 edlielvessassevyellKReDEkavtekayenpkFvEDvvReva 230
                                    + +++v+++++s   + lK+ + ++v+ + +++  Fv D+ R   
  gi|91772595|ref|YP_565287.1| 152 AEYFNAVNQALKSGDSKFLKKFENAKVIDAEGNEHYFVTDLDRLYE 197
                                   ****************************************999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1348.18
//
Query:       gi|91772596|ref|YP_565288.1|  [L=110]
Description: hypothetical protein Mbur_0563 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0012   19.0   5.3      0.091   13.0   4.8    3.0  2  HNH            HNH endonuclease
  ------ inclusion threshold ------
      0.017   14.9   0.2      0.035   13.9   0.1    1.5  1  PRELI          PRELI-like family
      0.034   14.2   1.2      0.065   13.3   1.2    1.5  1  DZR            Double zinc ribbon
       0.07   13.3   0.2      0.089   12.9   0.2    1.2  1  RecA_dep_nuc   Recombination enhancement, RecA-dependent nucl
       0.29   10.9   1.5        5.6    6.8   0.2    2.2  2  zf-HYPF        HypF finger
       0.39   10.5   4.0        5.1    7.0   0.5    2.3  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   4.8     3e-05     0.091       1      46 [.      23      61 ..      23      62 .. 0.84
   2 ?    2.3   0.0     0.066     2e+02      19      35 ..      66      82 ..      65      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                           HNH  1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46
                                  C +Cg+    +  +e++H++     g+++ + + +lCk+CH k ++
  gi|91772596|ref|YP_565288.1| 23 CSVCGEDNSEV--IEMHHVD-----GRNTSDWVKPLCKNCHAKITA 61
                                  999**999888..9999996.....556777799*******99876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.066
                           HNH 19 iipisqggaddieNlql 35
                                  i p++++++++ eNl++
  gi|91772596|ref|YP_565288.1| 66 ISPKKRSKTTSSENLTA 82
                                  679999********986 PP

>> PRELI  PRELI-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.2e-05     0.035      49      91 ..      46      88 ..      31      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                  TTSTTTSSSEEEEEEEEEEEEETTTTEEEEEEEESSSTTTEEE CS
                         PRELI 49 rwlkkligvaktvyvleesvvdlkkrtlkletrNltfssllkv 91
                                   w+k l ++ +     e++ +++kkr+ ++ + Nlt  +++++
  gi|91772596|ref|YP_565288.1| 46 DWVKPLCKNCHAKITAEQNKISPKKRSKTTSSENLTAFNIISI 88
                                  7**********99**************************9987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.2   2.2e-05     0.065      13      43 ..      21      64 ..      12      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                           DZR 13 rfCseCgtklkavaa.............edrCpsCgekvdpear 43
                                  + Cs Cg++ ++v +             +  C +C++k+++e++
  gi|91772596|ref|YP_565288.1| 21 IACSVCGEDNSEVIEmhhvdgrntsdwvKPLCKNCHAKITAEQN 64
                                  579999999665555566********************998876 PP

>> RecA_dep_nuc  Recombination enhancement, RecA-dependent nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2     3e-05     0.089      16      62 ..      19      63 ..       7      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                                  --HHHHHTT-----.EEEEESS-SSSTTGGGSEEEEEHHHHT----HH CS
                  RecA_dep_nuc 16 gCiacrmdgvisse.velhhiagrtkpdahkktlpLcawhhqaaapae 62
                                  + iac + g  +se +e+hh++gr   d    + pLc+  h + +  +
  gi|91772596|ref|YP_565288.1| 19 PPIACSVCGEDNSEvIEMHHVDGRNTSD---WVKPLCKNCHAKITAEQ 63
                                  6799999999888659*******98765...56699999999887664 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0019       5.6      20      28 ..      19      27 ..      17      28 .. 0.93
   2 ?    3.2   0.1     0.025        76       1      14 [.      51      64 ..      51      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0019
                                  TT---TTTS CS
                       zf-HYPF 20 qfisCtnCG 28
                                  ++i+C  CG
  gi|91772596|ref|YP_565288.1| 19 PPIACSVCG 27
                                  8*******9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.025
                                  --HHHHHHHC-TTS CS
                       zf-HYPF  1 lCedClrEykdpld 14
                                  lC++C ++++  ++
  gi|91772596|ref|YP_565288.1| 51 LCKNCHAKITAEQN 64
                                  79999999887766 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   0.2    0.0078        23       2       9 ..      23      30 ..      13      33 .. 0.78
   2 ?    7.0   0.5    0.0017       5.1       2      12 ..      52      62 ..      51      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0078
                 zinc_ribbon_2  2 CpnCGael 9 
                                  C+ CG+ +
  gi|91772596|ref|YP_565288.1| 23 CSVCGEDN 30
                                  66666666 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0017
                 zinc_ribbon_2  2 CpnCGaelqdn 12
                                  C+nC+a++  +
  gi|91772596|ref|YP_565288.1| 52 CKNCHAKITAE 62
                                  *******9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 682.82
//
Query:       gi|91772597|ref|YP_565289.1|  [L=890]
Description: DNA-directed DNA polymerase B [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-10   40.0   1.5    5.2e-10   38.8   1.5    1.6  1  DNA_pol_B_2  DNA polymerase type B, organellar and viral
    2.9e-07   29.6   2.5       0.01   14.6   0.7    3.0  3  DNA_pol_B    DNA polymerase family B
  ------ inclusion threshold ------
      0.021   13.9   0.2       0.66    9.1   0.1    2.5  2  DNApol_Exo   DNA mitochondrial polymerase exonuclease domain


Domain annotation for each model (and alignments):
>> 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 !   38.8   1.5   8.8e-14   5.2e-10     121     245 ..     209     331 ..     156     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 8.8e-14
                   DNA_pol_B_2 121 enkelwkekeekkydivketleYckqDvlvlaklllklkesideffeasinifkrpTisslalaifkqilyrkkkk.ella 200
                                   ++++++k k  ++ ++++  ++Y+  Dv++++++ +kl ++++  +++si  +k+++ +s       q+  +++   ++  
  gi|91772597|ref|YP_565289.1| 209 LDTNVKKMKGIEHGKVTERYIDYLIDDVETTYQVYEKLIDELE-LYQISIPPTKIFSSASIGKYALGQLGIQSFLDlNPEF 288
                                   4445555555567889999***********************9.7889987777777666666666666533333346688 PP

                   DNA_pol_B_2 201 pskeldkyiRkayrGGrcypsvlgiyeeniyvyDvnSlYPsamth 245
                                    s+ + +++  +y+GGrc  +++g+   n+ v D+ S+YP++ ++
  gi|91772597|ref|YP_565289.1| 289 SSETIGTNM-TSYYGGRC-ECKIGKEPTNVTVLDFTSMYPTITME 331
                                   899999998.79******.8889*****************99877 PP

>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0     1e-05     0.061      54      79 ..     309     334 ..     276     373 .. 0.83
   2 !   14.6   0.7   1.7e-06      0.01     125     169 ..     464     510 ..     461     512 .. 0.89
   3 ?    0.5   0.0     0.032   1.9e+02     222     236 ..     572     586 ..     547     642 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                                   -EEESS-EEEEEETTHHHHHHHHTT- CS
                     DNA_pol_B  54 kglydkpvlvlDFaSLYPsiiqahNl 79 
                                    g   ++v+vlDF S+YP i ++  l
  gi|91772597|ref|YP_565289.1| 309 IGKEPTNVTVLDFTSMYPTITMEMDL 334
                                   5556689***************9876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHHHHHHHHHHH.CS--HHHHHHHHHHHHHHHHHHHHH.HHH CS
                     DNA_pol_B 125 lLkdllakRkaikkelk.eekdefekalldkqQlalKvtaNsv.YGf 169
                                   l++ l+++R+++k ++k  +kd+ e ++l+++ +a+K+++N++ YG+
  gi|91772597|ref|YP_565289.1| 464 LVQVLVEERQNLKIQMKsIDKDKSEYQQLESRAQAIKILVNAMsYGI 510
                                   67899************656777899****************97885 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.032
                                   T-EEEEEBSSEEEEE CS
                     DNA_pol_B 222 klkviYGDTDSvfie 236
                                   +    Y DTDS+f+ 
  gi|91772597|ref|YP_565289.1| 572 GSVHAYMDTDSIFVP 586
                                   5556799******95 PP

>> DNApol_Exo  DNA mitochondrial polymerase exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.018   1.1e+02      65      87 ..      25      47 ..      17     139 .. 0.57
   2 ?    9.1   0.1   0.00011      0.66     225     280 ..     190     248 ..     170     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.018
                    DNApol_Exo 65 esvdyPeeealvfDvevlvkesk 87
                                  + v+  ++++lvfD+e+ +++ +
  gi|91772597|ref|YP_565289.1| 25 KDVPLRHDRVLVFDTETTIDQYQ 47
                                  66777788999999998865543 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00011
                    DNApol_Exo 225 LadvaklycgieldKekrdlfvk.etleeir..enfqelleYcakDveathevfkkllp 280
                                   La+v     +i+ldK+ ++l ++ ++++ i+  +  +++++Y  +Dve+t++v++kl +
  gi|91772597|ref|YP_565289.1| 190 LAEVLLQSKRISLDKAGQKLDTNvKKMKGIEhgKVTERYIDYLIDDVETTYQVYEKLID 248
                                   66666555668888888877776567888875456789******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (890 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 5242.66
//
Query:       gi|91772598|ref|YP_565290.1|  [L=322]
Description: hypothetical protein Mbur_0565 [Methanococcoides burtonii DSM 6242]
Scores for 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-34  117.4  14.9      9e-34  117.4  14.9    2.3  2  PIN_12          PIN domain
    3.1e-19   69.7  14.0    1.1e-18   67.9  10.5    2.8  2  PIN_8           PIN like domain
     0.0057   17.2   0.4      0.013   16.0   0.1    1.9  2  PIN             PIN domain
  ------ inclusion threshold ------
      0.048   14.4   0.1        0.1   13.4   0.1    1.6  1  PIN_3           PIN domain
       0.26   10.2   2.2       0.41    9.6   2.2    1.2  1  AAA_6           Hydrolytic ATP binding site of dynein motor r
          1    9.4   6.0        1.2    9.1   0.8    2.9  3  Type2_restr_D3  Type-2 restriction enzyme D3 domain


Domain annotation for each model (and alignments):
>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4  14.9     3e-37     9e-34       1     171 []       4     183 ..       4     183 .. 0.92
   2 ?    0.4   4.9      0.28   8.4e+02      46     138 ..     227     318 ..     189     322 .] 0.71

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 3e-37
                        PIN_12   1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkiees......kkle.kalks........l 66 
                                   ifiDTnifl  +++++++ ++++++++i + k +li+p++v+dEfl+nr ++++++      +  + + +++        +
  gi|91772598|ref|YP_565290.1|   4 IFIDTNIFLG-LYESNNN-KVSQIFDDITKLKKRLIIPEQVYDEFLRNRDSVLQKQinssnkN--KvEIHTTalirhmeeY 80 
                                   9********8.****999.*******************************9999888878552..323333345677777* PP

                        PIN_12  67 sklksakkklnekkkllslkeikkkieekveeslkklleklea..ikvipetndevkkilerafkkkpPfskkkkkgfgDa 145
                                   ++lk+ k++++ek+kll++k ++ + ++  + +l+ +l+ +++  +k+i++t+++++k+ +r++ ++pP  +kkk ++gD+
  gi|91772598|ref|YP_565290.1|  81 DNLKTIKDDFDEKNKLLIQKLKDLQTHSDDDPILNGFLDIYNSkdVKKIKRTETIIQKAKDRMLMGNPPI-DKKKGTIGDQ 160
                                   *****************************9999*********99**************************.********** PP

                        PIN_12 146 liwesileyakknkekvifvsrDkDf 171
                                   +iwe++le+++   ++vifv++D+++
  gi|91772598|ref|YP_565290.1| 161 IIWETLLENLN---DDVIFVTEDNTY 183
                                   ***********...9********988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.28
                        PIN_12  46 lknr.ekkieeskklekalks.lsklksakkklnekkkllslkeikkkieekvees..lkkllekleaikvipetndevkk 122
                                   +k + +k++ e     +++k+ l +++++  +++ +     +k+ k++++  +ee+    ++ +++++ ++ +  +d+  +
  gi|91772598|ref|YP_565290.1| 227 EKTKkSKDFIEE----DEIKDlLAHFETEGIDISPNLLFFLFKYSKDNYNVFKEEIgiTSEIEKRYQK-PFHSIHSDY-IT 301
                                   333333333333....6777788888888888888888888888888887777777888888888888.887777755.88 PP

                        PIN_12 123 ilerafkkk.pPfskkk 138
                                   i++++f+ + +P+ kk+
  gi|91772598|ref|YP_565290.1| 302 IYRKYFNPEhSPYMKKE 318
                                   99999986425664444 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9  10.5   3.7e-22   1.1e-18       2     209 ..       4     181 ..       3     183 .. 0.79
   2 ?    0.9   0.1      0.11   3.4e+02      73     137 ..     219     248 ..     189     315 .. 0.57

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.7e-22
                         PIN_8   2 vvlDtNvLLnlYryseetrkdllkvlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaekkleealk 82 
                                   +++DtN++L lY+ +++  +++++ ++kl++rl++P qv  Ef rnr+sv++k+ ++ ++ + e+    ++      ++++
  gi|91772598|ref|YP_565290.1|   4 IFIDTNIFLGLYESNNNKVSQIFDDITKLKKRLIIPEQVYDEFLRNRDSVLQKQINSSNKNKVEI---HTT------ALIR 75 
                                   89**************************************************5555544443333...221......2344 PP

                         PIN_8  83 kwakkkaldteelrkelkkqleelkeelkaeleelkksskadkeedpilkkleellegkigealskeeleelvkegekRye 163
                                     +++++l+  +++++++++ + l ++l        k+ +++ ++dpil+   ++++ k  ++++  + e++++++++R+ 
  gi|91772598|ref|YP_565290.1|  76 HMEEYDNLK--TIKDDFDEKNKLLIQKL--------KDLQTHSDDDPILNGFLDIYNSKDVKKIK--RTETIIQKAKDRML 144
                                   444444444..55666666666666666........555566677**********9977666654..5589********** PP

                         PIN_8 164 nkiPPGykDekkdedeekagDlllWkqllekakkrekdvlfvtdDe 209
                                      PP   D+kk +    +gD ++W+ lle+    + dv+fvt+D+
  gi|91772598|ref|YP_565290.1| 145 MGNPP--IDKKKGT----IGDQIIWETLLENL---NDDVIFVTEDN 181
                                   *****..6888887....6**********998...899*******7 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                         PIN_8  73 aekkleealkkwakkkaldteelrkelkkqleelkeelkaeleelkksskadkeedpilkkleel 137
                                    +                                 e+l  e e ++k+sk+ +eed+i++ l+++
  gi|91772598|ref|YP_565290.1| 219 PS---------------------------------EAL-IEFE-KTKKSKDFIEEDEIKDLLAHF 248
                                   22.................................222.1112.222222222334444444433 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   4.4e-06     0.013       1      48 [.       4      62 ..       4     121 .. 0.70
   2 ?   -2.1   0.0       1.8   5.4e+03      49      68 ..     217     236 ..     188     254 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
                                  EEE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.........S CS
                           PIN  1 ivlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar.........r 48
                                  i++DT++++ l+ ++ +k     ++++++     +l++++ v+ E+l+   +         +
  gi|91772598|ref|YP_565290.1|  4 IFIDTNIFLGLYeSNNNKV---SQIFDDItklkKRLIIPEQVYDEFLRNRDSvlqkqinssN 62
                                  79**********5555555...5555555555***************998886666665442 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                   CHCHHHHHHHHHHHHHHHTS CS
                           PIN  49 kskrekaaelvelllllsal 68 
                                   ++ +e+++e+++++  ++ +
  gi|91772598|ref|YP_565290.1| 217 ETPSEALIEFEKTKKSKDFI 236
                                   44444444444444333333 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.4e-05       0.1       2      76 ..       4      86 ..       3     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                         PIN_3  2 vvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakva.ler........ 75
                                  +++Dtn++l    +++    +i+d + + + +l++ +++ dE+ r+ + +l +  + +++ +++  +++ a +++        
  gi|91772598|ref|YP_565290.1|  4 IFIDTNIFLGLYESNNNKVSQIFDDITKLKKRLIIPEQVYDEFLRNRDSVLQK--QINSSNKNKVEIHTTAlIRHmeeydnlk 84
                                  79***********9999***************************999777544..3555555555555554343345555554 PP

                         PIN_3 76 .k 76
                                    
  gi|91772598|ref|YP_565290.1| 85 tI 86
                                  41 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 ?    9.6   2.2   0.00014      0.41     184     302 ..      18     138 ..       6     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                         AAA_6 184 eakelakklvtlykllseqlskqdhydfglralksvlkaagelkreepeeseeelllralrdvnlpklvaeDvplfkglis 264
                                   +++++++ +  + kl ++ +  ++ yd  lr+  svl+   +   +++ e  ++ l+r +++    k +++D    ++l+ 
  gi|91772598|ref|YP_565290.1|  18 NNNKVSQIFDDITKLKKRLIIPEQVYDEFLRNRDSVLQKQINSSNKNKVEIHTTALIRHMEEYDNLKTIKDDFDEKNKLLI 98 
                                   556778888888999999999*******************9998888888899********************99999988 PP

                         AAA_6 265 dlFpgvelpesdyeeleeaieevlkekk...lqleekfvek 302
                                   +  +++++++ d+  l+  + +++++k+   ++ +e++++k
  gi|91772598|ref|YP_565290.1|  99 QKLKDLQTHSDDDPILNGFL-DIYNSKDvkkIKRTETIIQK 138
                                   88899887776666665544.33333330114444555554 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.8   5.4e+03      45      57 ..      20      32 ..      16      34 .. 0.77
   2 ?    9.1   0.8    0.0004       1.2       9      54 ..      45      90 ..      41      95 .. 0.85
   3 ?    1.8   0.1     0.078   2.3e+02      14      65 ..     207     256 ..     200     258 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                Type2_restr_D3 45 EdveTIkDDiqgl 57
                                   +v  I DDi+ l
  gi|91772598|ref|YP_565290.1| 20 NKVSQIFDDITKL 32
                                  5677899999977 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0004
                Type2_restr_D3  9 dYlRtRRtiilkylleskkrrsleeikayLklagleE..dveTIkDDi 54
                                  ++lR+R +++ k +  s+  +   ei++   +  +eE  +++TIkDD 
  gi|91772598|ref|YP_565290.1| 45 EFLRNRDSVLQKQINSSN--KNKVEIHTTALIRHMEEydNLKTIKDDF 90
                                  79******9999997777..7788999998889999855799*****6 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.078
                Type2_restr_D3  14 RRtiilkylleskkrrsleeikayLklag.leEdveTIkDDiqgliniGlnik 65 
                                   R ++ lk + e     +l e  +  k++  +eEd   IkD +  ++  G++i 
  gi|91772598|ref|YP_565290.1| 207 RVSVALKQVNETP-SEALIEFEKTKKSKDfIEED--EIKDLLAHFETEGIDIS 256
                                   5666677775555.44555555555555514444..49**9999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1975.19
//
Query:       gi|91772599|ref|YP_565291.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91772599|ref|YP_565291.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772599|ref|YP_565291.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772599|ref|YP_565291.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772599|ref|YP_565291.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772599|ref|YP_565291.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772599|ref|YP_565291.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772599|ref|YP_565291.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772599|ref|YP_565291.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2015.06
//
Query:       gi|91772600|ref|YP_565292.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91772600|ref|YP_565292.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772600|ref|YP_565292.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772600|ref|YP_565292.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772600|ref|YP_565292.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772600|ref|YP_565292.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772600|ref|YP_565292.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772600|ref|YP_565292.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772600|ref|YP_565292.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2029.18
//
Query:       gi|91772601|ref|YP_565293.1|  [L=889]
Description: DNA-directed DNA polymerase B [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-14   53.9   6.0    1.3e-14   53.9   6.0    1.6  2  DNA_pol_B_2  DNA polymerase type B, organellar and viral
    8.5e-07   28.0   0.6      0.012   14.4   0.1    3.1  3  DNA_pol_B    DNA polymerase family B
     0.0013   17.9   0.4      0.027   13.6   0.3    2.4  2  DNApol_Exo   DNA mitochondrial polymerase exonuclease domain


Domain annotation for each model (and alignments):
>> 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 !   53.9   6.0   2.2e-18   1.3e-14      71     276 ..     158     360 ..     153     413 .. 0.75
   2 ?   -3.9   0.0      0.76   4.6e+03     372     396 ..     497     523 ..     483     545 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.2e-18
                   DNA_pol_B_2  71 rklakafnl.....eikKgkfpykavn.elhliysyeqksdgfpvekywkekeeivenkelwkekeekkydivketleYck 145
                                   +k++ a+n+     +i+Kg+  +     + +++ +   +s+++  + ++ +k++++ +    k k+ ++ +++k+ ++Y+ 
  gi|91772601|ref|YP_565293.1| 158 KKMGDAYNFkftstKINKGNDHFTGYFlDAQKLAEVLLQSKKISLD-KAGQKLNTKTK----KMKNIEHGKVTKKYIDYLI 233
                                   7899999993333333333333222222333333333333333322.23333333333....33444489999******** PP

                   DNA_pol_B_2 146 qDvlvlaklllklkesideffeasinifkrpTisslalaifkqilyrkkkkellapskeldkyiRkayrGGrcypsvlgiy 226
                                   qDv++++++ +kl e++d+ ++++i  +k+++ +s      kq+  +++    +  s+e+  +i  +y+GGrc  +++++ 
  gi|91772601|ref|YP_565293.1| 234 QDVETTYQVYEKLIEELDH-YQIDIPPTKIFSSASIGKHSLKQLGIESFLSLNPEFSHEMLGNIMTSYYGGRC-ECKIRKE 312
                                   ******************6.559999999999999999999999966666688899*****************.7767777 PP

                   DNA_pol_B_2 227 eeniyvyDvnSlYPsamthypmPygkppfeeakavkeleekleekfgffd 276
                                     ++   D+ S+YP++ ++  m   k+   e++++k+ +++++e+++ ++
  gi|91772601|ref|YP_565293.1| 313 PVKVTTLDFTSMYPTITME--MDLWKFMIAESLEMKDITDEIKEMLSKVN 360
                                   789999*********9998..88899989999999999988888666555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.76
                   DNA_pol_B_2 372 siaKlllN.sLYGrFa.tnpdntkivi 396
                                   + +K+l N   YG F  +np+n+k +i
  gi|91772601|ref|YP_565293.1| 497 QAIKILVNaMSYGIFIeLNPENKKSDI 523
                                   678999994479999547888888776 PP

>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   8.6e-05      0.52      60      79 ..     315     334 ..     299     380 .. 0.83
   2 !   14.4   0.1   1.9e-06     0.012     125     169 ..     464     510 ..     461     515 .. 0.87
   3 ?    0.6   0.0      0.03   1.8e+02     219     235 ..     568     585 ..     538     595 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 8.6e-05
                                   -EEEEEETTHHHHHHHHTT- CS
                     DNA_pol_B  60 pvlvlDFaSLYPsiiqahNl 79 
                                   +v++lDF S+YP i ++  l
  gi|91772601|ref|YP_565293.1| 315 KVTTLDFTSMYPTITMEMDL 334
                                   6899************9877 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.9e-06
                                   HHHHHHHHHHHHHHHHH.CS--HHHHHHHHHHHHHHHHHHHHH.HHH CS
                     DNA_pol_B 125 lLkdllakRkaikkelk.eekdefekalldkqQlalKvtaNsv.YGf 169
                                   l++ l+++R++ik ++k  +kd+ e ++l ++ +a+K+++N++ YG+
  gi|91772601|ref|YP_565293.1| 464 LVQVLVEERQNIKLHMKdISKDDPEYQQLSSRAQAIKILVNAMsYGI 510
                                   67899************645566699****************97886 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.03
                                   ....T-EEEEEBSSEEEE CS
                     DNA_pol_B 219 eee.klkviYGDTDSvfi 235
                                   ++e +    Y DTDS+f+
  gi|91772601|ref|YP_565293.1| 568 TKElDSVHAYMDTDSIFV 585
                                   3344666789*******9 PP

>> DNApol_Exo  DNA mitochondrial polymerase exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.022   1.3e+02      72     149 ..      32     129 ..      20     147 .. 0.60
   2 !   13.6   0.3   4.5e-06     0.027     224     280 ..     189     248 ..     169     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.022
                    DNApol_Exo  72 eealvfDvevlvkesklpvlAvavsekaWYs.....WvSprlleeseee..eklelkeLiplessk.............ke 132
                                   +++lvfD+e+ +++ +   +     ++  Y          ++l+++e++  e +++k+ ipl + +              +
  gi|91772601|ref|YP_565293.1|  32 DRTLVFDTETTTDQYQNVKIGYFKICQDGYIqhkgmFYDAAMLNDNEKKvcEVYTSKYDIPLYTLNefidevfypevfgLK 112
                                   667777777765544433333333333333201111222233333333345667777778887776777888888888778 PP

                    DNApol_Exo 133 rvvvGhnvsyDRarike 149
                                    + vG+n  +D +ri  
  gi|91772601|ref|YP_565293.1| 113 TLCVGFNLPFDISRISK 129
                                   88899999999999876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.5e-06
                    DNApol_Exo 224 sLadvaklycgieldKekrdlfvk.etleeir..enfqelleYcakDveathevfkkllp 280
                                   +La+v     +i+ldK+ ++l +k +++++i+  +  +++++Y  +Dve+t++v++kl +
  gi|91772601|ref|YP_565293.1| 189 KLAEVLLQSKKISLDKAGQKLNTKtKKMKNIEhgKVTKKYIDYLIQDVETTYQVYEKLIE 248
                                   6777777777899****999988857799**96567889******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (889 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 4923.44
//
Query:       gi|91772602|ref|YP_565294.1|  [L=110]
Description: hypothetical protein Mbur_0570 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0058   17.0   0.1      0.008   16.5   0.1    1.2  1  DUF3268        zinc-finger-containing domain
     0.0058   16.8   5.6      0.032   14.4   5.6    2.0  1  HNH            HNH endonuclease
  ------ inclusion threshold ------
      0.024   15.1   0.9      0.037   14.5   0.9    1.3  1  zf-C4pol       C4-type zinc-finger of DNA polymerase delta
      0.089   12.8   1.8       0.22   11.6   1.8    1.6  1  DZR            Double zinc ribbon
        0.1   12.6   3.7       0.11   12.5   0.7    1.9  2  Cytochrome_C7  Cytochrome c7 and related cytochrome c
       0.17   11.9   2.4       0.63   10.1   2.4    1.9  1  Elf1           Transcription elongation factor Elf1 like
       0.39   10.5   2.0        5.5    6.8   0.3    2.3  2  zf-HYPF        HypF finger


Domain annotation for each model (and alignments):
>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.1e-06     0.008       3      63 ..      21      82 ..      19      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                       DUF3268  3 trCpyCGekvilvsaseiYkerskgklly.lCpkCdayvgvhkgtkiplGtlAnaelrklrk 63
                                  + C  CGe    v + +  ++r++ +++  lC++C + + +++++  p+ +  +a+l+++r+
  gi|91772602|ref|YP_565294.1| 21 IACAVCGEDNKNVIEMHHVEGRNNSDWIKpLCKNCHSKITAEQNKLSPKARSSEASLQNKRA 82
                                  68*****99887776666668888888877**************************999885 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   5.6   1.2e-05     0.032       1      46 [.      23      61 ..      23      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                           HNH  1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkhd 46
                                  C +Cg+  + +  +e++H+     +g+++ + + +lCk+CH+k ++
  gi|91772602|ref|YP_565294.1| 23 CAVCGEDNKNV--IEMHHV-----EGRNNSDWIKPLCKNCHSKITA 61
                                  99999998888..888888.....677799999*********9886 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9   1.5e-05     0.037       1      40 [.      23      79 ..      23      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                      zf-C4pol  1 ClvCk......eklk.............kalCkkCrsdkqesllkllsrlkelekklne 40
                                  C vC+         +             k+lCk+C+s+ +++  kl  + +++e  l++
  gi|91772602|ref|YP_565294.1| 23 CAVCGednknvI--EmhhvegrnnsdwiKPLCKNCHSKITAEQNKLSPKARSSEASLQN 79
                                  99***6655550..05556667777899*******988888899999999998887765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.8   8.4e-05      0.22      13      43 ..      21      64 ..      10      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                           DZR 13 rfCseCgtklkavaa.............edrCpsCgekvdpear 43
                                  + C  Cg++ k+v +             +  C +C++k+++e++
  gi|91772602|ref|YP_565294.1| 21 IACAVCGEDNKNVIEmhhvegrnnsdwiKPLCKNCHSKITAEQN 64
                                  568888888555555556********************998876 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.0   0.00046       1.2      15      60 ..      22      62 ..       2      70 .. 0.53
   2 ?   12.5   0.7   4.2e-05      0.11      15      36 ..      51      74 ..      33      98 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00046
                 Cytochrome_C7 15 kCtdCHsklfeskakkkmaemekgkskkaeveslt......CgaCHdgknaf 60
                                  +C+ C ++         ++ +e+++++ ++    +      C++CH + +a+
  gi|91772602|ref|YP_565294.1| 22 ACAVCGEDN--------KNVIEMHHVEGRNN---SdwikplCKNCHSKITAE 62
                                  555555554........11111122212222...022235588888776665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.2e-05
                 Cytochrome_C7 15 kCtdCHskl.feska.kkkmaeme 36
                                   C++CHsk+ +e+++ + k ++ e
  gi|91772602|ref|YP_565294.1| 51 LCKNCHSKItAEQNKlSPKARSSE 74
                                  599999999334433332222222 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.4   0.00025      0.63      16      63 ..      15      67 ..       2      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                          Elf1 16 kklptkFdCpfCnheksvevkldkkek.....iaevsCkvCgesfetkvnals 63
                                  k  +    C +C++++   +++++ e+       +  Ck+C+++++ + n+ls
  gi|91772602|ref|YP_565294.1| 15 KGKKPPIACAVCGEDNKNVIEMHHVEGrnnsdWIKPLCKNCHSKITAEQNKLS 67
                                  22344578****9999888888888776665555556********99999987 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0022       5.5      20      28 ..      19      27 ..      17      27 .. 0.93
   2 ?    2.9   0.1     0.037        95       1      14 [.      51      64 ..      51      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0022
                                  TT---TTTS CS
                       zf-HYPF 20 qfisCtnCG 28
                                  ++i+C  CG
  gi|91772602|ref|YP_565294.1| 19 PPIACAVCG 27
                                  8*******9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.037
                                  --HHHHHHHC-TTS CS
                       zf-HYPF  1 lCedClrEykdpld 14
                                  lC++C  +++  ++
  gi|91772602|ref|YP_565294.1| 51 LCKNCHSKITAEQN 64
                                  79999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 633.66
//
Query:       gi|91772603|ref|YP_565295.1|  [L=213]
Description: hypothetical protein Mbur_0571 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1351.23
//
Query:       gi|91772604|ref|YP_565296.1|  [L=299]
Description: hypothetical protein Mbur_0572 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.7   0.1        4.4    7.1   0.1    3.2  3  HTH_DeoR  DeoR-like helix-turn-helix domain
       0.11   12.6   1.1        2.3    8.4   0.2    3.1  2  Mrr_N     Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> 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 ?    6.6   0.1   0.00071       6.4       3      24 ..      10      31 ..       9      33 .. 0.92
   2 ?    7.1   0.1   0.00049       4.4       1      48 [.      23      72 ..      23      73 .. 0.82
   3 ?   -0.7   0.0      0.13   1.2e+03      20      33 ..     278     291 ..     275     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00071
                      HTH_DeoR  3 eqilellkqqgklsveelvell 24
                                  e+ +++l++ gk++ e+l+e l
  gi|91772604|ref|YP_565296.1| 10 EEVVQYLNKNGKMRREQLIEKL 31
                                  6899***************987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00049
                      HTH_DeoR  1 Rieqilellkqqgk..lsveelvellgvSeaTiRRDLneLeeqglltRth 48
                                  R+eq++e l+q+ +   ++ e     g+S+ Ti R L+e+  +g ++R +
  gi|91772604|ref|YP_565296.1| 23 RREQLIEKLRQKHTktYKTGEEFIDTGYSKPTINRKLKEMLVSGEIIRLY 72
                                  899999999997641155666666779****************9999987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.13
                      HTH_DeoR  20 lvellgvSeaTiRR 33 
                                    +++lg S+  iR+
  gi|91772604|ref|YP_565296.1| 278 CMAHLGMSDVPIRN 291
                                   699******99996 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00026       2.3      54      84 ..      69      99 ..       6     102 .. 0.69
   2 ?   -1.9   0.1      0.43   3.9e+03      18      45 ..     236     263 ..     230     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00026
                         Mrr_N 54 vgWartyLkkagllespkrgvwkiTekGrev 84
                                  ++ ++ +L++ g+le + r+++  Te+G +v
  gi|91772604|ref|YP_565296.1| 69 IRLYHYQLQNYGFLEDDGRATYLFTEEGLKV 99
                                  5667789999******************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.43
                         Mrr_N  18 hrlkeirervaerf.glseeeraellpsg 45 
                                   + ++ei e ++++  +l e er+ +  +g
  gi|91772604|ref|YP_565296.1| 236 YDISEIAELIINNPsKLFEVERQLMR-EG 263
                                   55688888888887788888888877.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2150.38
//
Query:       gi|91772605|ref|YP_565297.1|  [L=398]
Description: CRISPR-associated Cas1 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-78  262.8   0.1      4e-78  262.4   0.1    1.1  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
      0.083   12.9   0.0       0.24   11.4   0.0    1.8  1  ER        Enhancer of rudimentary


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 !  262.4   0.1   4.4e-82     4e-78       6     282 ..      16     294 ..       5     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 262.4 bits;  conditional E-value: 4.4e-82
                                   TEEEEEEETTEEEEEE.SSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSSTHHHH CS
                      Cas_Cas1   6 qgaylrkkgerlvvek.egeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlepeesgnvelr 84 
                                   +ga+l++k++r+  ++  +e + + +  di+siv++g+  sls +a+r+l++++++v++l++ngk+l+++ p+es+nv+++
  gi|91772605|ref|YP_565297.1|  16 DGAKLHIKDGRFSATEdPQEYVFSPKRIDIDSIVVYGRsGSLSFEAIRWLIKHNVQVTMLDWNGKFLTTMLPSESTNVKTK 96 
                                   688999999999988856678999999***********9****************************************** PP

                                   HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHHHHH CS
                      Cas_Cas1  85 raQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaYfea 165
                                    aQy+a++d+++r++la+k++++k++++++vl++lk+++   e+e+   + +  + kle+a+s+ e++giEG +a++Y+++
  gi|91772605|ref|YP_565297.1|  97 FAQYHAYEDQDARVKLARKFIEAKFYKSEAVLDYLKQRY--PEIEY---DFSVDKGKLENAKSVREILGIEGGVASKYWNE 172
                                   ***************************************..34444...34455679************************ PP

                                   HHHHCSCGGS-SS-SSSS-.....SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHH CS
                      Cas_Cas1 166 fdkllkeefefegRsrrpp.....kDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpll 241
                                   ++k +++e++f+ R+ + +      D+vN++L++gY+ll+se+l+ai++vgLd ++GfLHe++p+++sLa+DL+E+fR  +
  gi|91772605|ref|YP_565297.1| 173 YSKAIPDEYDFRARTDNNArasnsGDKVNVMLNYGYALLESECLRAINSVGLDAHVGFLHEMNPSKNSLAYDLQEPFRF-I 252
                                   **************99886455558*****************************************************9.9 PP

                                   CHHHHHHHHHTTSS-GGGEEEETT.EEEE-HHHHHHHHHHHH CS
                      Cas_Cas1 242 vDrlvlslinkrqlkekdFekeen.gvlLteegrkkfleafe 282
                                   vD +v++li+k+ +++kdF+++e+ +++L+++g +k++++f+
  gi|91772605|ref|YP_565297.1| 253 VDLAVMNLIEKEVMDSKDFIRTESfSLRLKPTGARKVTDKFN 294
                                   **************************************9997 PP

>> ER  Enhancer of rudimentary
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.24      38      69 ..     230     261 ..     214     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                            ER  38 aLkeanpskksitYdisdLfefidsladlsaL 69 
                                    L+e+npsk+s+ Yd+++ f+fi +la ++++
  gi|91772605|ref|YP_565297.1| 230 FLHEMNPSKNSLAYDLQEPFRFIVDLAVMNLI 261
                                   5899*********************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2615.68
//
Query:       gi|91772606|ref|YP_565298.1|  [L=167]
Description: hypothetical protein Mbur_0574 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1201.15
//
Query:       gi|91772607|ref|YP_565299.1|  [L=166]
Description: hypothetical protein Mbur_0575 [Methanococcoides burtonii DSM 6242]
Scores for 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-19   68.2   2.8    1.1e-18   67.9   2.8    1.1  1  DUF4263     Domain of unknown function (DUF4263)
  ------ inclusion threshold ------
      0.025   14.6   0.1      0.036   14.1   0.1    1.3  1  Pallilysin  Pallilysin beta barrel domain


Domain annotation for each model (and alignments):
>> DUF4263  Domain of unknown function (DUF4263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   2.8   1.3e-22   1.1e-18       2     158 .]       7     146 ..       6     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.3e-22
                       DUF4263   2 ssEkkwqkffeknpwll.........ypiisefpikevdfksDfllidslngnivlvEikkpdknlltkekkkgniapsee 73 
                                   ++E+++q+++ek+pw+l         ++++++++i       Df  ++  +++ +++Eik+p  nl++k+      ++s+e
  gi|91772607|ref|YP_565299.1|   7 ETEHRYQEWIEKYPWILglqyslvqrHTQFDNENI------PDFTAVRVHDNSRDIFEIKQPFLNLFRKNG-----VFSSE 76 
                                   689**************666544333333333333......3******99*****************9444.....56*** PP

                       DUF4263  74 lsgaisQikkylllldknkekgeeladlrntseleeglgikainpkgiliiGrreeleekekresfelfrreynn.ieiit 153
                                   +++  +Qi+ yl+++++nk   ++ +            g + +npk++l+iG +   ee   r++ +   +  n+ i i+t
  gi|91772607|ref|YP_565299.1|  77 FNDSWNQIERYLDFARENKDYLRRSK------------GLNIENPKCYLLIGYNLTHEE---RDKIRRKEKL-NSsIIILT 141
                                   ****************6666655555............889*************88888...6666666333.555***** PP

                       DUF4263 154 yDeLl 158
                                   y++L+
  gi|91772607|ref|YP_565299.1| 142 YNDLI 146
                                   ***96 PP

>> Pallilysin  Pallilysin beta barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     4e-06     0.036      46      94 ..      47      98 ..       8     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-06
                    Pallilysin 46 ifllddteevyewen...sslrrnGiylstknksitnlkrrldielesldei 94
                                  +  +d++++++e+++      r+nG++ s  n s ++++r ld + e+ d +
  gi|91772607|ref|YP_565299.1| 47 VRVHDNSRDIFEIKQpflNLFRKNGVFSSEFNDSWNQIERYLDFARENKDYL 98
                                  5678999******993334579*********************999888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1187.05
//
Query:       gi|91772608|ref|YP_565300.1|  [L=429]
Description: hypothetical protein Mbur_0576 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-14   53.0   0.6    3.7e-14   53.0   0.6    2.6  2  HEPN_Apea  Apea-like HEPN


Domain annotation for each model (and alignments):
>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       0.1   1.9e+03      64      74 ..      61      74 ..      10     121 .. 0.60
   2 !   53.0   0.6   2.1e-18   3.7e-14       6      98 ..     280     382 ..     276     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.1
                     HEPN_Apea 64 e...dkeerkelkk 74
                                  +   ++++rk +k 
  gi|91772608|ref|YP_565300.1| 61 KhinNNYSRKIIKR 74
                                  12222222333322 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 2.1e-18
                     HEPN_Apea   6 fekrlkralewfgeaireeddedaildlvialEaldll..ldkkeeitekis.......lrsn..aylkedkeerkelkkk 75 
                                   +e+rl+ra++ fg+ +++ ++ ++i++l++ lE+l+l+  ++k+ ++ e+++         sn  ++l+e k++r ++k+k
  gi|91772608|ref|YP_565300.1| 280 LEERLIRAINTFGSVLTNPENPENIIKLFTVLEILLLTqkDSKSINLGERVAlvnyplfDISNrdKFLEE-KQKRVDIKTK 359
                                   789********************************77764333334888887777777644445344455.********** PP

                     HEPN_Apea  76 ikklYdlRSkivHggkikkkdle 98 
                                   i  lY+ R+++vH+g+++ ++++
  gi|91772608|ref|YP_565300.1| 360 IATLYKHRNSLVHEGQSEVNKHD 382
                                   ***************98855544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2867.19
//
Query:       gi|91772609|ref|YP_565301.1|  [L=824]
Description: DNA-directed DNA polymerase B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-11   42.0   7.0    5.7e-11   42.0   7.0    1.6  2  DNA_pol_B_2  DNA polymerase type B, organellar and viral
    7.7e-09   34.8   1.5     0.0028   16.4   0.3    3.0  3  DNA_pol_B    DNA polymerase family B
  ------ inclusion threshold ------
      0.076   12.1   0.1       0.82    8.8   0.1    2.2  2  DNApol_Exo   DNA mitochondrial polymerase exonuclease domain


Domain annotation for each model (and alignments):
>> 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 !   42.0   7.0   9.5e-15   5.7e-11      71     297 ..      92     325 ..      87     353 .. 0.68
   2 ?   -3.3   0.0      0.49     3e+03     368     396 ..     427     457 ..     418     468 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 9.5e-15
                   DNA_pol_B_2  71 rklakafnl.....eikKgkfpykavn.elhliysyeqksdgfpvekywkekeeivenkelwkekeekkydivketleYck 145
                                   +k++ a+n+     +i+Kgk +++    + +++ +   +s+ +  +k + +    ++n++++k k  ++ ++++  ++Y+ 
  gi|91772609|ref|YP_565301.1|  92 KKMGDAYNFkftstKINKGKDKFSGYFlDAQKLAEVLLQSKHLSLDK-AGQ----KLNTNVKKMKGIEHGKVTERYIDYLI 167
                                   67888888855555555555555444434444444444444444333.333....34444444455558999********* PP

                   DNA_pol_B_2 146 qDvlvlaklllklkesideffeasinifkrpTisslalaifkqilyrkkkk.ellapskeldkyiRkayrGGrcypsvlgi 225
                                    Dv++++++ +kl +++d  ++++i  +k+++ +s      kq+  +++   ++   s+ + +++  +y+GGrc  +++++
  gi|91772609|ref|YP_565301.1| 168 ADVETTYQVYEKLIDELD-LYQINIPPTKIYSSASIGKYSLKQLGIQSFLDlNPEYSSETIGNNM-TSYYGGRC-ECKIRK 245
                                   ******************.7878888888888888888888888855444457788888888888.79******.666777 PP

                   DNA_pol_B_2 226 yeeniyvyDvnSlYPsamthypmPygkppfeeakavkeleeklee.....kfgffdakikppilked.....alpplpirl 296
                                      ++ v D+ S+YP++ ++  m   k+   e+++ k++++++++     ++ +++ k   +++ +       + +lp+r+
  gi|91772609|ref|YP_565301.1| 246 DPTKVTVLDFTSMYPTVTME--MNLWKFMIAESLESKDVTDEIKNmltnlNLNYLQNKDNWKEFVVMvklqpDYDILPVRM 324
                                   789*************9988..99999977777777777777777555676666655433333322222333677777777 PP

                   DNA_pol_B_2 297 d 297
                                   d
  gi|91772609|ref|YP_565301.1| 325 D 325
                                   7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.49
                   DNA_pol_B_2 368 evkrsiaKlllN.sLYGrFa.tnpdntkivi 396
                                   +   + +K+l N   YG F  +np+++k++i
  gi|91772609|ref|YP_565301.1| 427 DSRAQAIKILVNaMSYGIFIeLNPEDKKTDI 457
                                   5567889999**4489999547888888876 PP

>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.2e-06    0.0073      59      98 ..     248     286 ..     223     314 .. 0.78
   2 !   16.4   0.3   4.7e-07    0.0028     125     169 ..     398     444 ..     395     446 .. 0.86
   3 ?   -0.1   0.0     0.048   2.9e+02     222     235 ..     506     519 ..     482     529 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-06
                                   S-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT CS
                     DNA_pol_B  59 kpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaed 98 
                                   ++v+vlDF S+YP + ++ Nl ++ ++a+  e+k++++e+
  gi|91772609|ref|YP_565301.1| 248 TKVTVLDFTSMYPTVTMEMNL-WKFMIAESLESKDVTDEI 286
                                   579*****************9.555566555556555554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.7e-07
                                   HHHHHHHHHHHHHHHHHCS--HH.HHHHHHHHHHHHHHHHHHH.HHH CS
                     DNA_pol_B 125 lLkdllakRkaikkelkeekdef.ekalldkqQlalKvtaNsv.YGf 169
                                   l++ l+++R+++k ++k   +e+ e ++ld++ +a+K+++N++ YG+
  gi|91772609|ref|YP_565301.1| 398 LVQVLVEERQNLKIQMKGIDKEKpEYQQLDSRAQAIKILVNAMsYGI 444
                                   67899************665554499****************97885 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.048
                                   T-EEEEEBSSEEEE CS
                     DNA_pol_B 222 klkviYGDTDSvfi 235
                                   +    Y DTDS+f+
  gi|91772609|ref|YP_565301.1| 506 GSVHAYMDTDSIFV 519
                                   5556799******9 PP

>> DNApol_Exo  DNA mitochondrial polymerase exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.038   2.3e+02     132     149 ..      46      63 ..      14      81 .. 0.83
   2 ?    8.8   0.1   0.00014      0.82     225     280 ..     124     182 ..     104     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.038
                    DNApol_Exo 132 ervvvGhnvsyDRarike 149
                                   + + vG+n s+D +ri  
  gi|91772609|ref|YP_565301.1|  46 KALCVGFNLSFDISRISK 63 
                                   6789***********976 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00014
                    DNApol_Exo 225 LadvaklycgieldKekrdlfvk.etleeir..enfqelleYcakDveathevfkkllp 280
                                   La+v     + +ldK+ ++l ++ ++++ i+  +  +++++Y   Dve+t++v++kl +
  gi|91772609|ref|YP_565301.1| 124 LAEVLLQSKHLSLDKAGQKLNTNvKKMKGIEhgKVTERYIDYLIADVETTYQVYEKLID 182
                                   55555555556788888888777567888885456789******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (824 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:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 4914.46
//
Query:       gi|91772610|ref|YP_565302.1|  [L=60]
Description: hypothetical protein Mbur_0578 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 353.43
//
Query:       gi|91772611|ref|YP_565303.1|  [L=75]
Description: hypothetical protein Mbur_0579 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.7   1.9       0.66   10.7   1.9    1.8  1  zf-RVT    zinc-binding in reverse transcriptase


Domain annotation for each model (and alignments):
>> zf-RVT  zinc-binding in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.9   3.7e-05      0.66      43      71 ..      33      62 ..       1      67 [. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                        zf-RVT 43 rlptadnllkrgiesss.rCqlCgqeeEti 71
                                  r + ++  +k+++++ +  C++Cg+++E++
  gi|91772611|ref|YP_565303.1| 33 RNEQENTRNKKKWKKPPiACSVCGEDDENV 62
                                  4455666778999986559********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2331  (0.130013); expected 358.6 (0.02)
Passed bias filter:                      795  (0.0443416); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 487.61
//
Query:       gi|91772612|ref|YP_565304.1|  [L=212]
Description: hypothetical protein Mbur_0580 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.7   0.1      0.022   14.4   0.1    1.3  1  NS3       Non-structural protein NS3


Domain annotation for each model (and alignments):
>> NS3  Non-structural protein NS3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.2e-06     0.022     129     183 ..     150     202 ..      53     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-06
                           NS3 129 ldteefndsnlnGkpktmwkickfcfdngivinedsddyrytcdfsdnvtlldae 183
                                   l +e fn+ n     k+    c   fdn+ivi+ d +++++++d ++   +lda+
  gi|91772612|ref|YP_565304.1| 150 LIAEYFNAVNKAL--KSGDTKCLKKFDNAIVIDADGKEHYFVTDLERLYEILDAQ 202
                                   4566777766443..5555679999********************9999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1289.33
//
Query:       gi|91772613|ref|YP_565305.1|  [L=401]
Description: CRISPR-associated Cas1 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-76  257.6   0.0    1.6e-76  257.2   0.0    1.1  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
      0.057   13.5   0.1       0.22   11.5   0.0    2.0  2  ER        Enhancer of rudimentary


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 !  257.2   0.0   1.8e-80   1.6e-76       6     282 ..      16     294 ..       7     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 257.2 bits;  conditional E-value: 1.8e-80
                                   TEEEEEEETTEEEEEE.SSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSSTHHHH CS
                      Cas_Cas1   6 qgaylrkkgerlvvek.egeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlepeesgnvelr 84 
                                   +ga+l++k++r+  ++  +e + + +  di+siv++g+  sls +a+r+l+++++++++l++ngk+l+++ p+es+nv+++
  gi|91772613|ref|YP_565305.1|  16 DGAKLHIKDGRFSTTEdPQEYVFSPKRMDIDSIVVYGRsGSLSLEAIRWLIKHNVQITMLDWNGKLLTTMLPSESTNVKTK 96 
                                   79999*******999956678999**************9****************************************** PP

                                   HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHHHHH CS
                      Cas_Cas1  85 raQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaYfea 165
                                    aQy+a++d++ rl+lakk++++k++++++vl++lk+++   e+e+   + ++ ++kleka+s+  ++g+EG +a +Y+++
  gi|91772613|ref|YP_565305.1|  97 FAQYHAYEDSDVRLKLAKKFIEAKFSKSEAVLDYLKQRD--PEIEY---DFSDDKAKLEKANSIRDILGVEGGVAWKYWNE 172
                                   ***************************************..44554...455567799*********************** PP

                                   HHHHCSCGGS-SS-SSSS-.....SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHH CS
                      Cas_Cas1 166 fdkllkeefefegRsrrpp.....kDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpll 241
                                   ++k ++ee++f+ R+ + +      D++N++ ++gY+ll+se+++ai++vgLd ++GfLHe++p+++sLa+DL+E+fR  +
  gi|91772613|ref|YP_565305.1| 173 YAKAIPEEYDFRARTDNNArasnsGDKINVMFNYGYALLESECMRAINSVGLDAHVGFLHEMNPSKNSLAYDLQEPFRF-I 252
                                   **************99886455558*****************************************************9.9 PP

                                   CHHHHHHHHHTTSS-GGGEEEETT.EEEE-HHHHHHHHHHHH CS
                      Cas_Cas1 242 vDrlvlslinkrqlkekdFekeen.gvlLteegrkkfleafe 282
                                   vD +v++li+k+ +++kdF+++e+ +++L+++g +k++e+f+
  gi|91772613|ref|YP_565305.1| 253 VDLAVMNLIEKGVMNNKDFIRTESfSLRLRPTGARKVTEEFN 294
                                   ****************************************97 PP

>> ER  Enhancer of rudimentary
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.78     7e+03      36      54 ..     125     143 ..      93     144 .. 0.64
   2 ?   11.5   0.0   2.5e-05      0.22      38      69 ..     230     261 ..     211     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.78
                            ER  36 eeaLkeanpskksitYdis 54 
                                   e+ L   +++ ++i+Yd s
  gi|91772613|ref|YP_565305.1| 125 EAVLDYLKQRDPEIEYDFS 143
                                   4445555555677777766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.5e-05
                            ER  38 aLkeanpskksitYdisdLfefidsladlsaL 69 
                                    L+e+npsk+s+ Yd+++ f+fi +la ++++
  gi|91772613|ref|YP_565305.1| 230 FLHEMNPSKNSLAYDLQEPFRFIVDLAVMNLI 261
                                   699*********************99988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2262.07
//
Query:       gi|91772614|ref|YP_565306.1|  [L=259]
Description: hypothetical protein Mbur_0583 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   30.2   3.0    1.1e-06   29.5   3.0    1.4  1  Fer4_16     4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.012   16.2   4.5      0.045   14.3   4.6    1.9  1  Fer4_7      4Fe-4S dicluster domain
       0.12   12.5  10.2       0.12   12.5   0.8    2.7  2  Fer4_6      4Fe-4S binding domain
       0.13   12.4   5.4        6.1    7.1   5.6    2.3  2  Fer4_9      4Fe-4S dicluster domain
       0.32   11.1   6.1         19    5.5   0.4    2.3  2  Fer4_10     4Fe-4S dicluster domain
       0.38   10.9   5.7         10    6.3   0.5    2.3  2  Fer4_21     4Fe-4S dicluster domain
       0.42   11.6   9.2        1.9    9.6   2.8    2.5  2  Fer4_3      4Fe-4S binding domain
        0.5   10.3   0.1        0.5   10.3   0.1    3.2  3  Fer4        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> 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 !   29.5   3.0   4.9e-10   1.1e-06       2      66 ..     171     243 ..     170     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.9e-10
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy......ntaekkdlaedeekckkqeai..tgCdiCqdvCPa 66 
                                   C++   C+++CP +ai    ++ +e+ +++ y      ++ +k+  +++e++  + ++   + C iC+ +CP+
  gi|91772614|ref|YP_565306.1| 171 CQEHSLCVKSCPYQAIIPGPSQGVEPGKKVIYdkcvvsHEFDKDVSPQNEKHIRRITERgfMECTICNLICPY 243
                                   9999*************99999999999888888888566665555555555553333346***********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 ?   14.3   4.6     2e-05     0.045       6      51 ..     175     244 ..     165     245 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                        Fer4_7   6 gaCvaaCpvkaieldeeenekgtekv........................eidpekClgCgaCvavCPtg 51 
                                     Cv+ Cp++ai   +++  ++ +kv                        +i ++  + C+ C   CP+g
  gi|91772614|ref|YP_565306.1| 175 SLCVKSCPYQAIIPGPSQGVEPGKKViydkcvvshefdkdvspqnekhirRITERGFMECTICNLICPYG 244
                                   58**********99887666533333233334444444444444444444667777789*********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 ?   12.5   0.8   5.3e-05      0.12       4      24 .]     160     186 ..     160     186 .. 0.82
   2 ?    3.8   2.8      0.03        67      12      22 ..     234     244 ..     199     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                        Fer4_6   4 idpdkCi...gCgd...CvrvCPegai 24 
                                   + +d+C     C +   Cv+ CP++ai
  gi|91772614|ref|YP_565306.1| 160 FERDLCAeqpLCQEhslCVKSCPYQAI 186
                                   56899987777955599*********8 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.03
                        Fer4_6  12 CgdCvrvCPeg 22 
                                   C  C  +CP+g
  gi|91772614|ref|YP_565306.1| 234 CTICNLICPYG 244
                                   *********96 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.6    0.0027       6.1       5      48 ..     171     243 ..     164     247 .. 0.76
   2 ?    4.3   0.6     0.021        47       4      15 ..     233     244 ..     232     252 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0027
                        Fer4_9   5 Cga...CveaCpagvvvedaaerkarlraase..........................eaCigCgaCveaCpk 48 
                                   C++   Cv++Cp++++++  +++    ++  +                             ++C  C  +Cp 
  gi|91772614|ref|YP_565306.1| 171 CQEhslCVKSCPYQAIIPGPSQGVEPGKKVIYdkcvvshefdkdvspqnekhirriteRGFMECTICNLICPY 243
                                   554455*****99999999999998887766677888888888888888888888885223667778888886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.021
                        Fer4_9   4 gCgaCveaCpag 15 
                                   +C+ C   Cp+g
  gi|91772614|ref|YP_565306.1| 233 ECTICNLICPYG 244
                                   566666666665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.5     0.021        46       8      52 ..     170     238 ..     163     242 .. 0.58
   2 ?    5.5   0.4    0.0083        19      10      28 ..     232     247 ..     222     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.021
                       Fer4_10   8 tCirCgkCvkaCPadl...........................tsvgakgeaseeeavrkkvekCtgcgaCv 52 
                                    C +   Cvk+CP+++                           + v+ ++e+ +    + +  +   c+ C 
  gi|91772614|ref|YP_565306.1| 170 LCQEHSLCVKSCPYQAiipgpsqgvepgkkviydkcvvshefdKDVSPQNEKHIRRITERGFME---CTICN 238
                                   5777789*******77777777777777777777555555544333333333333333334444...44444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0083
                       Fer4_10  10 irCgkCvkaCPadltsvga 28 
                                   ++C+ C+  CP+   ++ +
  gi|91772614|ref|YP_565306.1| 232 MECTICNLICPY---GKTV 247
                                   68*********9...4333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5    0.0046        10       8      42 ..     171     206 ..     166     210 .. 0.61
   2 ?    6.1   1.6    0.0055        12      31      53 ..     220     243 ..     203     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0046
                       Fer4_21   8 CigCgkCliaCedtshqaieidaktvl....kvvedeCv 42 
                                   C +  +C+++C+   +qai   +++ +    kv+ d+Cv
  gi|91772614|ref|YP_565306.1| 171 CQEHSLCVKSCP---YQAIIPGPSQGVepgkKVIYDKCV 206
                                   556667888888...788754444433233367777776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0055
                       Fer4_21  31 ktvlkvv.edeCvGCnlCssvCPv 53 
                                   +++++ + e   + C++C  +CP 
  gi|91772614|ref|YP_565306.1| 220 EKHIRRItERGFMECTICNLICPY 243
                                   44444441556678999999**96 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.8   0.00086       1.9       4      15 .]     171     185 ..     164     185 .. 0.77
   2 ?    5.4   0.5     0.019        43       4      14 ..     234     244 ..     232     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00086
                        Fer4_3   4 Cg...aCvevCPvgA 15 
                                   C+   +Cv++CP+ A
  gi|91772614|ref|YP_565306.1| 171 CQehsLCVKSCPYQA 185
                                   434449******976 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                        Fer4_3   4 CgaCvevCPvg 14 
                                   C  C   CP+g
  gi|91772614|ref|YP_565306.1| 234 CTICNLICPYG 244
                                   888******98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00022       0.5      13      23 ..     176     186 ..     175     187 .. 0.92
   2 ?    0.1   0.2      0.36     8e+02       2       9 ..     199     206 ..     198     207 .. 0.85
   3 ?    3.0   1.3     0.044        99      10      21 ..     233     244 ..     232     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                   HHHHHSTTTEE CS
                          Fer4  13 aCvevCPvgAI 23 
                                   +Cv+ CP+ AI
  gi|91772614|ref|YP_565306.1| 176 LCVKSCPYQAI 186
                                   6*********9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                                   EEETTTSS CS
                          Fer4   2 videekCi 9  
                                   +++++kC+
  gi|91772614|ref|YP_565306.1| 199 KVIYDKCV 206
                                   5899***8 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.044
                                   S-THHHHHSTTT CS
                          Fer4  10 gCGaCvevCPvg 21 
                                    C +C  +CP+g
  gi|91772614|ref|YP_565306.1| 233 ECTICNLICPYG 244
                                   599*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1622.83
//
Query:       gi|91772615|ref|YP_565307.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91772615|ref|YP_565307.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772615|ref|YP_565307.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772615|ref|YP_565307.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772615|ref|YP_565307.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772615|ref|YP_565307.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772615|ref|YP_565307.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772615|ref|YP_565307.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772615|ref|YP_565307.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1993.08
//
Query:       gi|91772616|ref|YP_565308.1|  [L=369]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.044   13.8   0.0    2.1  2  DUF772    Transposase domain (DUF772)
      0.066   12.7   0.1       0.14   11.7   0.1    1.5  1  DUF4283   Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     5e-06     0.044       5      70 ..      58     126 ..      57     129 .. 0.81
   2 ?   -3.3   0.0       1.1   9.5e+03      21      37 ..     306     322 ..     305     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-06
                        DUF772   5 yppelmlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70 
                                   y +  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f k rl +  l++++
  gi|91772616|ref|YP_565308.1|  58 YKVSSMIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVKyRLVKtgLDEVM 126
                                   67889*************9999998772566667777664433.89****************99977776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                        DUF772  21 glSdreleealrenlsf 37 
                                   ++S r  +e++++++ +
  gi|91772616|ref|YP_565308.1| 306 DYSHRGECERVHNHIKW 322
                                   568888999***99988 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.6e-05      0.14      24      59 ..     252     287 ..     231     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                       DUF4283  24 lsalrrvlakaWklkggvkikelgdglflfrfssee 59 
                                   ++++ ++++k+Wkl+g +++k+ ++ +fl++   e+
  gi|91772616|ref|YP_565308.1| 252 MERIDHWVNKMWKLGGSIHMKYEEKLHFLYENGREK 287
                                   678999***********************9866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 00:00:00.40
# Mc/sec: 2743.67
//
Query:       gi|91772617|ref|YP_565309.1|  [L=134]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-13   50.3   0.0    2.4e-13   50.1   0.0    1.1  1  Putative_PNPOx  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 !   50.1   0.0   1.3e-17   2.4e-13       1      86 [.       4      89 ..       4      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.3e-17
                                  HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEEE CS
                Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtael 83
                                  l++ ++e++++ k++  AT+++ G Pnv p++ +++ ++++i++  n+  ++ +nl enp +++ ++ +e g  ++i+G +e+
  gi|91772617|ref|YP_565309.1|  4 LTKDMKEAFSKVKIFPFATASKAGVPNVIPIGMCKLVDDETIWVTDNYFLKTRQNLDENPVASIFVWGPEVGGCFQIKGDVEV 86
                                  68899*******************************9999******************************************9 PP

                                  ESC CS
                Putative_PNPOx 84 vsd 86
                                   + 
  gi|91772617|ref|YP_565309.1| 87 KTS 89
                                  775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 889.49
//
Query:       gi|91772618|ref|YP_565310.1|  [L=86]
Description: hypothetical protein Mbur_0587 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-24   83.6   0.1    9.6e-24   83.4   0.1    1.0  1  Cdd1      Pathogenicity locus
     0.0069   16.6   0.0      0.014   15.7   0.0    1.5  1  IMS_HHH   IMS family HHH motif
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.037   14.1   0.0    1.2  1  TfoX_C    TfoX C-terminal domain


Domain annotation for each model (and alignments):
>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.1   1.6e-27   9.6e-24      11      84 ..       1      77 [.       1      81 [. 0.97

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 1.6e-27
                          Cdd1 11 iPniGkalaedlvelGirsveelkgedpeelyeklekltgarhDpCvldvfrsvvkfaeg...deeakkWwsftder 84
                                  +P+ Gk+ ae+l++lGi+s+++lkgedpe +y kl +l g+++D+Cvl+ fr +v++a++   d+e +kWw+++d++
  gi|91772618|ref|YP_565310.1|  1 MPGFGKKSAEQLRDLGIYSISQLKGEDPELMYLKLIDLRGMHMDRCVLYGFREAVYYASHknhDPELLKWWNWSDKN 77
                                  699*******************************************************9999899*********986 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-06     0.014      16      32 .]       1      17 [.       1      17 [. 0.97

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                       IMS_HHH 16 ipGiGgklgekLeklGi 32
                                  +pG+G+k +e+L++lGi
  gi|91772618|ref|YP_565310.1|  1 MPGFGKKSAEQLRDLGI 17
                                  8***************9 PP

>> TfoX_C  TfoX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.2e-06     0.037      11      61 ..       4      55 ..       1      66 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-06
                        TfoX_C 11 lglklerlLkkaGIktveeLrelGaveaylkiket.gtsvslelLyaLegAl 61
                                   g+k++++L+  GI ++++L+    +  ylk+ +  g++++  +Ly +  A+
  gi|91772618|ref|YP_565310.1|  4 FGKKSAEQLRDLGIYSISQLKGEDPELMYLKLIDLrGMHMDRCVLYGFREAV 55
                                  6899****************************9988**********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 580.60
//
Query:       gi|91772619|ref|YP_565311.1|  [L=193]
Description: DNA-3-methyladenine glycosylase I [Methanococcoides burtonii DSM 6242]
Scores for complete 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-81  272.4   0.0    1.7e-81  272.2   0.0    1.0  1  Adenine_glyco  Methyladenine glycosylase


Domain annotation for each model (and alignments):
>> Adenine_glyco  Methyladenine glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.2   0.0   9.6e-86   1.7e-81       1     177 []       7     184 ..       7     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 272.2 bits;  conditional E-value: 9.6e-86
                 Adenine_glyco   1 wankdplyvaYhDeeWGvpvtddkklFelLvLegfqaglswetilkkreafreafdgFdlekvakydeekveelladegii 81 
                                   wan ++l ++YhD++WGvpv+dd++lFe+L+Leg+qaglsw tilk+r+++r+afd+Fd++ va+yd+ k+e+l++d+gii
  gi|91772619|ref|YP_565311.1|   7 WANVNELEIEYHDKQWGVPVHDDRNLFEFLILEGAQAGLSWGTILKRRDGYRKAFDDFDYNLVASYDDLKIEKLMQDSGII 87 
                                   9999***************************************************************************** PP

                 Adenine_glyco  82 rnrlKieavisnAravlalqeefgsfseylwsfv.dgkpiveelksaeevpattelsealskdLkkrGfkfvGptivysfl 161
                                   rnr+Ki ++i+nAr ++++++efgsfs+y+w+f+ dgkpi+++++s +++pa+telse +skdLkkrGf+fvGpti+y+f+
  gi|91772619|ref|YP_565311.1|  88 RNRRKILSSIKNARSFIEIRDEFGSFSKYIWKFLeDGKPIQNSFRSINDMPANTELSEMMSKDLKKRGFSFVGPTIIYAFM 168
                                   *********************************9677******************************************** PP

                 Adenine_glyco 162 qavGlvndhleeCfrk 177
                                   qavG+vndh+++Cfr+
  gi|91772619|ref|YP_565311.1| 169 QAVGMVNDHEVGCFRH 184
                                   *************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1318.42
//
Query:       gi|91772620|ref|YP_565312.1|  [L=45]
Description: hypothetical protein Mbur_0591 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-05   22.5   0.0    8.1e-05   22.4   0.0    1.0  1  DNA_alkylation  DNA alkylation repair enzyme


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 !   22.4   0.0   4.5e-09   8.1e-05     183     213 .]       4      34 ..       1      34 [. 0.93

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.5e-09
                DNA_alkylation 183 sktdpdlveeFlekhakrmprlslreAiekl 213
                                   sk  +++v+++l+k+++ mpr++lr+A+ek+
  gi|91772620|ref|YP_565312.1|   4 SKSFQKEVFDYLMKNKEVMPRITLRYASEKM 34 
                                   88899************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 332.03
//
Query:       gi|91772621|ref|YP_565313.1|  [L=241]
Description: hypothetical protein Mbur_0592 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  169.5   0.0    9.8e-50  169.3   0.0    1.0  1  DUF429    Protein of unknown function (DUF429)


Domain annotation for each model (and alignments):
>> DUF429  Protein of unknown function (DUF429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.0   5.5e-54   9.8e-50       1     207 [.       5     222 ..       5     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 5.5e-54
                        DUF429   1 GvDlagcrtgwaavale.dgrlrlvdveaeeivaalaallaaaeeaavvaiDaPiglperetggRaaDraarkll.arrga 79 
                                   GvD  gc++gw+a++l   ++ ++      e++a++++l+++++e  +++iD+Pigl e+  +gR +D +ark+l + r+ 
  gi|91772621|ref|YP_565313.1|   5 GVD--GCKSGWFAIELNeTNKFKI------ELFANISDLWQKYNENSIILIDIPIGLRENYPKGRSCDLEARKVLgSPRRN 77 
                                   9**..************999****......**********************************************666** PP

                        DUF429  80 svfpvparaalaag..............kglserafgllpklrevdelldarpelrgrvvEvhPeaafvalnggaplakkk 146
                                   svfpvp+r+a++++              +++s  a++++pk+revd++l +++++r  + E+hPe++f+ l +g+p+ ++k
  gi|91772621|ref|YP_565313.1|  78 SVFPVPCRQAIYEHtyesactvnekhfgNKISIFAWRIVPKIREVDAFLLKNESARSQILEIHPELCFCNL-AGKPMHYSK 157
                                   ********9999999********************************************************.********* PP

                        DUF429 147 ktaegraeRrellara...iaelllesea.kkeklvaadDvlDAvacaltArraarGraeslpgd 207
                                   k+++g aeR e+l+++     e++ +s   +k+k va+dD+lDA+ +a+tA+  ++   +s+p++
  gi|91772621|ref|YP_565313.1| 158 KKKDGIAERLEVLKQVcpsTNEIFSSSLSrYKRKEVARDDILDALSAAVTAKLGHKHGFTSIPEN 222
                                   ******************854555555558999******************98755555588776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1798.44
//
Query:       gi|91772622|ref|YP_565314.1|  [L=921]
Description: CRISPR-associated helicase Cas3 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  153.7   0.5    9.2e-45  153.2   0.5    1.3  1  HD_6        HD domain
    1.5e-05   25.0   0.0    4.5e-05   23.5   0.0    1.7  1  ResIII      Type III restriction enzyme, res subunit
    0.00043   20.6   0.0     0.0082   16.5   0.0    2.4  2  Helicase_C  Helicase conserved C-terminal domain
    0.00048   19.9   0.1      0.012   15.3   0.1    2.2  1  DEAD        DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.2   0.5   2.1e-48   9.2e-45       1     196 []       5     241 ..       5     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 153.2 bits;  conditional E-value: 2.1e-48
                                   EEEETTSTTS....EEEHHHHHHHHHHHHHHHHHHTS-HHHHHC...TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS--- CS
                          HD_6   1 WgKadkeeeeea..whpLvaHllDvaavaealldkwlsllarll.r.gleeealrrllaflaalHDlGKaspaFqakvpel 77 
                                   WgK+++ +e ++  +h+Lv+H lDvaa+++ +l+k++ ll++++   +l+ee++ +l+ f++a+HD+GK+s++Fq+++pel
  gi|91772622|ref|YP_565314.1|   5 WGKSKSATEYDNsnYHLLVYHGLDVAATGRTILQKDKLLLQKFTdIiSLDEEKTISLISFCLAVHDIGKFSERFQNLQPEL 85 
                                   *****988777779***********************9999999559********************************** PP

                                   -TTS-.....-GGGT----HHHHHHHHHH.........................HHHHHHHHHHHTTTS---HHHHHTSS- CS
                          HD_6  78 aekleeaglelekelekarHdslgaalle.........................evarslaaavggHHGkppkeeeekaek 133
                                   +++l++++++++   +++rHds+g++l +                         + + ++++ v+gHHGkpp+  ++    
  gi|91772622|ref|YP_565314.1|  86 LNDLRDHDSDKS---YTVRHDSMGLHLWKeiwstafdenwlgldkeiydkfdwnDLIGPWMNSVTGHHGKPPEYVHNGITI 163
                                   *******99999...9***********3355555555555666666666677778888***************99987654 PP

                                   HHHHTTHHHHHHH.HHHHHHHHHCT-TTS-S..........................---HHHHHHHHHHHHHHHHHCTSC CS
                          HD_6 134 kssaaedweeaqk.elleaaaeflgaaaalllelael....................elskaasvllaGlvvlADWigSne 193
                                   +ss      + ++ e++e+a +f+++aa+lll++a +                     + k++s+l+aGl++++DWigS+e
  gi|91772622|ref|YP_565314.1| 164 SSS------DLFTdEDIEMASSFVKEAASLLLSDALSdafeftscseeqaydiddmiLAFKRTSWLIAGLAIVSDWIGSSE 238
                                   443......44554******************998889*******************9*********************** PP

                                   CCC CS
                          HD_6 194 elf 196
                                   e+f
  gi|91772622|ref|YP_565314.1| 239 EHF 241
                                   *98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     1e-08   4.5e-05      24     143 ..     308     468 ..     254     477 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1e-08
                                   TSEEEEEESTTSTHHHHHHHHHHHH-S.........-EEEEESSHHHHHHHHHHG.................GGGTGG... CS
                        ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkee....kflflvprkslleqtleef.................kkflseayk 83 
                                    + ++++ aTG+GKT  a+ l+ rl+ kg  +        ++ +++++e++ + +                 +++ls+a+ 
  gi|91772622|ref|YP_565314.1| 308 PQLFILEDATGSGKTEAALCLAHRLMAKGLAQgafvGLPTMATSNAMYERLGNSYqrmyakgerpslvlahgQNYLSDAFR 388
                                   55678999********************99995333333467777888888888855555555555555555444444433 PP

                                   .......GEEE.......ESSS-B--................-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGG CS
                        ResIII  84 e......igkk.......vsgdkkka.........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaH 142
                                   +         k        sgd+ ++         ++k++  +++ v ti+++  ++ + + +s +ll  + +v+i+DE+H
  gi|91772622|ref|YP_565314.1| 389 SsigfqnS--KngyygdgSSGDETIQaqcsawiadNRKKALLADVGVGTIDQALMAILQSNHQSLRLLGLSRNVLIVDEVH 467
                                   34444320..134344446666666699999999999999999******988877776779999999************** PP

                                   G CS
                        ResIII 143 r 143
                                    
  gi|91772622|ref|YP_565314.1| 468 A 468
                                   6 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 ?    1.2   0.0       0.1   4.5e+02      39      66 ..     483     514 ..     448     525 .. 0.78
   2 !   16.5   0.0   1.8e-06    0.0082       9     109 ..     567     676 ..     560     678 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                                   T....TSTEEEESTTSTHHHHHHHHHHHHTTS CS
                    Helicase_C  39 k....gikvavlhgelpqnereeileqfnkge 66 
                                   +    g +++ l ++lpq++r+  ++ f kg 
  gi|91772622|ref|YP_565314.1| 483 FhvslGGSAILLSATLPQKHRQGLISHFCKGL 514
                                   23445778889999*************98875 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.8e-06
                                   HHHHTTTTSEEEEEESSHH.HHHH.HHHHHHHTTSTEEEESTTSTHHHHH....HHHHHHHTTS........SSEEEESGG CS
                    Helicase_C   9 llkleeeggkilifvntid.rlek.vklllekkgikvavlhgelpqnere....eileqfnkge........sdvLiatdv 75 
                                   l+k ++eg+ +  + nt+d  +e   k++ e  + +v+ +h++    +r+    ++le f   +         +vLiat+v
  gi|91772622|ref|YP_565314.1| 567 LIKCSKEGKCCCWIRNTVDdAIEAyEKIVSELGNDNVLLFHARFAMGDRLkienDVLETFG--KrsdrncrkGKVLIATQV 645
                                   5577788888888889999544436677777778999999999888888833334445553..12344444477******* PP

                                   GTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                    Helicase_C  76 aerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                   +e+++di + ++++   +p  ++ + qr+GR  R
  gi|91772622|ref|YP_565314.1| 646 VEQSLDI-DFDYMVSDLAP--MDLLFQRAGRLQR 676
                                   *******.57777766666..6789999999887 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.8e-06     0.012      17     171 ..     311     500 ..     294     504 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-06
                                   EEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT..TST...................S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx...................x RF
                          DEAD  17 vlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk..yid...................l 76 
                                   ++++ +TGsGKT+a+l  + + ++   +  +  a++  Pt +  + ++++l ++ +  y                      
  gi|91772622|ref|YP_565314.1| 311 FILEDATGSGKTEAALCLAHRLMA---KGLAQGAFVGLPTMATSNAMYERLGNSYQrmY-AkgerpslvlahgqnylsdaF 387
                                   567889********9999886664...34445899999999999999999998888552.134443333333333333331 PP

                                   EEEEEETT....................SSHHHHHHHH....HTT...CSEEEEEHHHHHH.HH..HCTSSHCTTE..EEE CS
                                   xxxxxxxx....................xxxxxxxxxx....xxx...xxxxxxxxxxxxx.xx..xxxxxxxxxx..xxx RF
                          DEAD  77 rvlliigg....................vaardqlskl....dng...vdivvgtpgrldd.ll..stgklnlsqv..rfl 125
                                                               ++ + q s+     +++   +d+ vgt ++ +  +l  + ++l+l  +  ++l
  gi|91772622|ref|YP_565314.1| 388 -------RssigfqnskngyygdgssgdETIQAQCSAWiadnRKKallADVGVGTIDQALMaILqsNHQSLRLLGLsrNVL 461
                                   .......03333333333344444443344455555557754233688999999997766636654444455544444679 PP

                                   EEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 126 VlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpk 171
                                   ++DE++ +    +   + ++l+       +  l    i+lSATlp+
  gi|91772622|ref|YP_565314.1| 462 IVDEVHAYDPY-MHTLLCSLLEFH----VS--LGGSAILLSATLPQ 500
                                   99999998876.333333323222....12..22238999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (921 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 6094.29
//
Query:       gi|91772623|ref|YP_565315.1|  [L=528]
Description: hypothetical protein Mbur_0594 [Methanococcoides burtonii DSM 6242]
Scores for 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-103  345.4   0.0   6.9e-103  345.2   0.0    1.0  1  CRISPR_Cse1  CRISPR-associated protein Cse1 (CRISPR_cse1)


Domain annotation for each model (and alignments):
>> CRISPR_Cse1  CRISPR-associated protein Cse1 (CRISPR_cse1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.2   0.0  3.8e-107  6.9e-103       1     453 [.       4     479 ..       4     480 .. 0.92

  Alignments for each domain:
  == domain 1  score: 345.2 bits;  conditional E-value: 3.8e-107
                                   BTTTSCEEEEEETTSSEEEEEHHHHHHTG..GGEEEEE-SSHHHHHHHHHHHHHHHHHHTT---SSHHHHHHHHHHSS--H CS
                   CRISPR_Cse1   1 NLldepWIpvrrrdgrreevsLrelllea..heirelagprpdqtvAllrlLlailqralqgppededeeWrelweegldp 79 
                                   NL++e+WI v+r+dg+r++++++++++e   ++i  l+ prpd++++++++L++++q++    p+++ + Wr+++ ++++p
  gi|91772623|ref|YP_565315.1|   4 NLIHEKWIWVQRQDGTRSMIAPWQITDEIgsNPIISLDEPRPDFNGSMIQFLIGLVQTT--MSPKSDGK-WRKRFISPPTP 81 
                                   9***************************999****************************..56698888.*********** PP

                                   HHHHHHHHHCGGGSBTT-SSS-TTSBTTCCCCTTSS.GGGSTTSSSSC....CCCHHSSSSTTSSSSBEHHHHHHHHHHHH CS
                   CRISPR_Cse1  80 ealeaylekwrdrFdLfhperPFlQvadleeeakkedakLlpelpgsg....nndalfdhrtdskealspaeaaraLvtlq 156
                                   e+l + +ek+++ FdL+++++ F+Q  +  e ak+ +++Ll+e+pg +    n+d++ +++t+   ++++++++ aL++lq
  gi|91772623|ref|YP_565315.1|  82 EELLETFEKVAHVFDLDGDDERFMQDHEHIEGAKNRVDALLMEMPGVQtlkhNADHFQKRDTV--TQMCLPCCVTALFNLQ 160
                                   *******************999***44443334666688******9999**9**********9..**************** PP

                                   HCS-TCEEEECE---TTSTSEEEEEE-SS..........HHHHHHHCS-.................T-S-GGG.S--SSSC CS
                   CRISPR_Cse1 157 afapsGiksgaagtGplgalgrvllrGgn..........LfetLlLNlvp................gdlPvWe.ptrtser 210
                                    +ap+           +g+++r++lrGg+          L++t++LN+++                +  P W+ ptrtse+
  gi|91772623|ref|YP_565315.1| 161 LNAPA-----------GGQGHRTSLRGGGplttlvlgsnLWQTIWLNVISdenfkglgdvdnceisDIYP-WMgPTRTSEK 229
                                   *****...........88888888888888888888888**********444455555455455544788.*********9 PP

                                   HHCCCCEEECCCSHHHHTTS--EEEEEEECSSET........EEEEEEEECEEEEC-SCCCCC..-TTS-EEEEEETTCEE CS
                   CRISPR_Cse1 211 kkaeeaatrapagpldlltwqsRrirLdpeeeeg........vrgvlvaagdrlpeganyega.pepmtayqrkkkkkkke 282
                                   k+a   +t+++++p +++++++RrirLd ++  +        +++ lv+++ ++++g ny+g  ++ ++++    +++k+ 
  gi|91772623|ref|YP_565315.1| 230 KNAM--TTPMDVNPKQMYWGMPRRIRLDLDDLIEgacdvcgcESDKLVSNYVTKNYGYNYDGGwCHVLSPH----NENKNG 304
                                   9887..8*********************9888888999**********************9888*******....899*** PP

                                   EEE-B-BTTSTGGGGHHHHHHCCCCSCEEC--HHHHHHHHHCCCCCCHHC.....EEEEEEEEEEETTEEEEEEEEEEEEE CS
                   CRISPR_Cse1 283 ylplkfdpgralWRdlaaLlaseesekgkrpakvvewlaelkrelgeree.....irlrvfGlaydqakvrdwveetlplp 358
                                    lp++++pg+ ++R++ +L++ ++ +kg  ++ ++e + + +++l++  +      +l++fG+  d++kvr+w+e+t+pl 
  gi|91772623|ref|YP_565315.1| 305 LLPRHPQPGGITYRHWLGLVQ-HDPDKGLYSSLAFERFVQKQKDLSDLGDvfkntPQLWAFGYDFDNMKVRCWYESTMPLF 384
                                   *********************.9999999999********9999988888*************778*************** PP

                                   CHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCSSHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCS..... CS
                   CRISPR_Cse1 359 aalledkealreaveeaveaaeevaralrsavkaaakellkkgkkkagdasaaraafwaalegpfrellaalgpddd.... 435
                                   ++++e ++ ++++v+++v++ae +a + rs+vk+a++  +++     gd s ++++fw+ +e++f+++l +l++  +    
  gi|91772623|ref|YP_565315.1| 385 NVADELRQSYEQIVSRLVKTAEIIAYNTRSCVKKALFGDNTPR----GDLSFIDSRFWHDTESEFYNILNQLTDVVNdeam 461
                                   ****************************************998....8********************9999987768889 PP

                                   HCTHHHHHHHHHHHHHHH CS
                   CRISPR_Cse1 436 aaealkawrktlrraalr 453
                                     e++ +w+k+l r+ ++
  gi|91772623|ref|YP_565315.1| 462 VLELKMKWHKELSRISEK 479
                                   8899*********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3654.01
//
Query:       gi|91772624|ref|YP_565316.1|  [L=143]
Description: hypothetical protein Mbur_0595 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   62.8   0.0    6.1e-17   62.5   0.0    1.1  1  CRISPR_Cse2  CRISPR-associated protein Cse2 (CRISPR_cse2)


Domain annotation for each model (and alignments):
>> CRISPR_Cse2  CRISPR-associated protein Cse2 (CRISPR_cse2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   3.4e-21   6.1e-17       1     141 []       7     135 ..       7     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.4e-21
                                   HHHHHHHHC.TSSTTTCGGHHHHHHHHTTTT.HHHHHHHHHHHHHHHHHCCHCS-SB-TT-CHHHHHHHHHHHTCTHHHHH CS
                   CRISPR_Cse2   1 alAaLRrga.gkepgespelwpyllrekeseeekepeeraayavaalyaahqqekehdsgkslgaalgrlreasessesie 80 
                                   ++A+LRr+    e+   p+ ++ l++e    ++    ++  +a +a ++ah++  ++++g+s++a+++ l   s+s + + 
  gi|91772624|ref|YP_565316.1|   7 DRADLRRCHnVVEVVFNPT-YHRLWSEL---NKIGFGNKDSVALIAGVLAHVK--NNQGGESFAAQMASLNGGSNS-QVSG 80 
                                   69*******6666655553.55666662...3566677777888888888899..469999*********999999.77** PP

                                   HHHHHHCT-SSCCCHHHHHHHHHHHHHCTT--B-HHHHHHHHHTTTTTCHHHHHHHHHHHH CS
                   CRISPR_Cse2  81 rRfqalltadtpeelarrLrrlvkllrskevpldyarLaddLlawqeerkrvrlrWardYY 141
                                   +Rf++ll+ ++ +el+  + r+vkl++++ v++    La++L++w+   + ++++Wa +YY
  gi|91772624|ref|YP_565316.1|  81 LRFKRLLKIEEKAELFSSIVRVVKLMDGN-VNIC--NLANSLYWWN---DITKKQWAFSYY 135
                                   ***************************98.****..**********...***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 993.27
//
Query:       gi|91772625|ref|YP_565317.1|  [L=367]
Description: CRISPR-associated Cse4 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-98  330.5   0.8    3.3e-98  329.5   0.8    1.4  1  Cas_CT1975  CT1975-like protein
    0.00037   20.1   0.0    0.00069   19.3   0.0    1.5  1  Cas_Cas7    CRISPR-associated protein Cas7
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.083   13.2   0.0    2.3  2  U3snoRNP10  U3 small nucleolar RNA-associated protein 10


Domain annotation for each model (and alignments):
>> Cas_CT1975  CT1975-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.5   0.8  5.5e-102   3.3e-98       1     329 [.       5     342 ..       5     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 329.5 bits;  conditional E-value: 5.5e-102
                                   EEEEEEEEECCETSSB-TTSSB-EEEETTEEEEEE-HHHHHHHHHCSH..HHTTT-CCHHS.EECHHHHHHHHHCCCTT.. CS
                    Cas_CT1975   1 idihilqsvppsnLNRDDtGspKtavfGgvrRaRvSSQslKraiResf..eelldesellgvRtkrlaelvaerlaeeg.. 77 
                                   i+ih+l s+ppsnLNRDD G pKtav+G+++R RvSSQslKra+R+s   +e+l ++   g Rtk +   + + l+e +  
  gi|91772625|ref|YP_565317.1|   5 IQIHTLVSYPPSNLNRDDLGRPKTAVMGDTQRLRVSSQSLKRAWRTSDvfKEALGDHI--GIRTKGMGVSIFKALTEGSrl 83 
                                   89********************************************765555444444..777776666666666666533 PP

                                   .................HHHHHHHHHHHHHCCSS-BS..B....TTSS-EECCEEEECHHHHHHHHHHHHHTHHHH..... CS
                    Cas_CT1975  78 ...............vdeeeaealaekllkaagiklekkk....ekkekktkallflsreeieelaelieelaeelakeak 139
                                                  v+e+ a+++a+ ++   g+++   k    + +  + ++l ++s+eei+++ el++++a++ ++   
  gi|91772625|ref|YP_565317.1|  84 kdvldnvtapvvnelVEEKIAKEWAKMIAGVFGKSK---KdtedSLTGLEIEQLTHFSPEEITAIDELVSKIAASGTAP-- 159
                                   333222222211111555555555555544444333...133357788999*****************66555554332.. PP

                                   .HCCCTT-HHCCHCCHHGHHHHHHHCB-TSSSTCT-BE-SEEEEEEEESC--S-EEEEEEECGTTS.CSSHCCCSEEEEEE CS
                    Cas_CT1975 140 kkkkakkkelkealdkeksvdiALFGRmvaddpelnvdAavqVAHaisthavenEfDYFtAvDDlk.eeeeaGagmigtve 219
                                        +k++l+   +++++vdiA+FGRm+a+++++n++AavqV+Hai++++v+ E D+FtAvDDl+  ee+ G+g++g++e
  gi|91772625|ref|YP_565317.1| 160 -----SKDDLDLLRKDHTAVDIAMFGRMLASNTKFNTEAAVQVSHAITVNKVAVEDDFFTAVDDLNrGEEDMGSGHLGETE 235
                                   .....3335554446669************************************************99************* PP

                                   EEEEEEEEEEEEEHHHHHHHCTS.HHHHHHHHHHHHHHHHH--SSTTCCCCTTT-SESEEEEEEESSS---GGGGGSS-B- CS
                    Cas_CT1975 220 fnsgtlYrYatvdldqLvenlegdreaaaeaveaflkafvtslPtgkqnsfAahtlpdlvlvevrddqpvslanAFeepvk 300
                                   f+sg++Y Y++vd + L++nl+gd+e+a + v+a+++a+++++PtgkqnsfA++++++++++e +++qp+sl+ A+ e+vk
  gi|91772625|ref|YP_565317.1| 236 FASGLFYTYICVDRELLESNLGGDKELADKSVRALVEAMAKVSPTGKQNSFASRAYASYMMIEKGKQQPRSLSVAYLEAVK 316
                                   ********************************************************************************* PP

                                   -SS..SCHHHHHHHHHHHHHHHHHHTT-- CS
                    Cas_CT1975 301 aeeegglleesikaLaeelekleeaygek 329
                                    +   ++l+++i+ L++  e++e++yg  
  gi|91772625|ref|YP_565317.1| 317 GK---SMLKDAIEGLKQTNENMEKVYGPC 342
                                   66...5********************975 PP

>> Cas_Cas7  CRISPR-associated protein Cas7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-07   0.00069      10     196 ..      12     281 ..       4     333 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-07
                      Cas_Cas7  10 dvkngNpNGDpdagnkPRi..dpetgeglvsDvclKrkiR..nyvekakeekeiyvkekkv.................... 66 
                                   +   +N N D d   +P++    +t++  vs  +lKr  R  +++++a +  +i +++k                      
  gi|91772625|ref|YP_565317.1|  12 SYPPSNLNRD-DL-GRPKTavMGDTQRLRVSSQSLKRAWRtsDVFKEALG-DHIGIRTKGMgvsifkaltegsrlkdvldn 89 
                                   5556899999.44.688883334788999999999999885556666665.455555544444444432222333333222 PP

                      Cas_Cas7  67 .....lnekkeeaykdeekkelreamcenf................................................... 91 
                                        +            ++ ++e++ +++                                                   
  gi|91772625|ref|YP_565317.1|  90 vtapvV------------NELVEEKIAKEWakmiagvfgkskkdtedsltgleieqlthfspeeitaidelvskiaasgta 158
                                   222221............112444444444444455556666666666666666777777888889999999999999999 PP

                      Cas_Cas7  92 ...............fDvRtFGavmstgvn.gqvrGpVqltfarslepvlpeeqsitrmaateekkekekkqrtmgrkhiv 156
                                                  +D+ +FG  ++ +++ + +  +Vq+++a  +++v +e+   t +   +   e++  +  +g+  + 
  gi|91772625|ref|YP_565317.1| 159 pskddldllrkdhtaVDIAMFGRMLASNTKfN-TEAAVQVSHAITVNKVAVEDDFFTAVDDLNR-GEEDMGSGHLGETEF- 236
                                   999999999999999***********765654.569*************888888777666555.333346777887665. PP

                      Cas_Cas7 157 pyglYrahgfinanla.....ektgfseeDlellkeallnmfehd 196
                                     gl+ +++ +  +l       ++++ ++ +  l ea+ ++    
  gi|91772625|ref|YP_565317.1| 237 ASGLFYTYICVDRELLesnlgGDKELADKSVRALVEAMAKVSPTG 281
                                   579999999999999933333245566666666666665554444 PP

>> U3snoRNP10  U3 small nucleolar RNA-associated protein 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.21   1.3e+03      78      99 ..      69      90 ..      61     123 .. 0.83
   2 ?   13.2   0.0   1.4e-05     0.083      37     109 ..     261     339 ..     254     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                                  --HHHHHHHTTSTTHHHHHHHH CS
                    U3snoRNP10 78 lpkkvlkallklpsladvLeel 99
                                  + ++++kal++ ++l dvL ++
  gi|91772625|ref|YP_565317.1| 69 MGVSIFKALTEGSRLKDVLDNV 90
                                  5678999999999999999875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                                   -S-HHHHHHHHHHHHHH--GGGHHHH...HHHHHHHH...HT-SS-S--HHHHHHHTTSTTHHHHHHHHTTTS--.HHHH CS
                    U3snoRNP10  37 pLsdkvleallesilknlskelaksa...llcllvla...qsqsakllpkkvlkallklpsladvLeelskeyrv.dkfl 109
                                    L+dk ++al+e+++k  s++ ++++   ++  + ++    +q+ ++l+++ l+a +  + l d +e l++++++ +k  
  gi|91772625|ref|YP_565317.1| 261 ELADKSVRALVEAMAKV-SPTGKQNSfasRAYASYMMiekGKQQPRSLSVAYLEAVKGKSMLKDAIEGLKQTNENmEKVY 339
                                   599*************8.54444444445666666666785555899***********888**********998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2554.68
//
Query:       gi|91772626|ref|YP_565318.1|  [L=244]
Description: CRISPR-associated Cas5e family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  178.6   0.0    1.7e-52  178.4   0.0    1.0  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 !  178.4   0.0   9.5e-57   1.7e-52       1     213 [.       4     234 ..       4     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 9.5e-57
                                   EEEEEEECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHHT--TTS-..-CCCCTTEEEEEEEEEEEEEEETEEEEECT. CS
                     Cas_Cas5d   1 tLllrlegplasfgrpsrkveretydvPtkSavlGllaaalGirrddd..leelkpalrwgvrvdrrgellrgdyhtvag. 78 
                                   +L++rl+gp+as+g+ ++ ++r+tyd P+kSa+ Gl+aaalGirrd++  + el++a+++g  ++++g+llr dyht ++ 
  gi|91772626|ref|YP_565318.1|   4 YLIFRLYGPMASWGDIAVGQHRPTYDHPSKSAIFGLIAAALGIRRDEEerHLELSNAYSYGTLINSAGKLLR-DYHTSQVp 83 
                                   699*********************************************99999*******************.******** PP

                                   .......-GGGS--BSSS----CCEEEEEEEEEEEECEEEEEECCSCCH..HHHHHHHHHHHHTTSSSSESSSTTSEEEEC CS
                     Cas_Cas5d  79 .......rtlperrkektadrkkraatvlseraYladahfevalegeee..gklleelaralrkpvwplyLGrkecivpve 150
                                          r++  +rk++ a  k++ +tvls r+Y +d++++v+l+++ +   + le l ++l++p ++lyLGrk+c + + 
  gi|91772626|ref|YP_565318.1|  84 sagtgrnRKTFATRKDELAVPKEELNTVLSTRDYYCDGVYTVILSCKTDtpPYSLELLGNSLKEPSFCLYLGRKSC-PLAL 163
                                   *******7777777777799********************************************************.**** PP

                                   ESETTT.CESSHHHCCHSSCEBSSSBS.........EEEEEEEE..--EESSCEEEEEEEEEEEEEEEECCEEE CS
                     Cas_Cas5d 151 pveaekvgeeegledalkelppkvegi.........lglmledf..dtdepdetslydvparffrakrkfgvrr 213
                                   p++ +k++++++ ++al++ +p +eg          ++l ++d   ++ ++++ s+yd  +  +r++++f++r+
  gi|91772626|ref|YP_565318.1| 164 PIN-PKIVSASNIKEALQSVDPGEEGLvkkiemkspYRLYWDDPkeSMTCEHTISRYDKLL--SRKRWQFSKRN 234
                                   ***.9****************999999*********999**98356889************..*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1715.35
//
Query:       gi|91772627|ref|YP_565319.1|  [L=224]
Description: CRISPR-associated Cse3 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-47  162.4   0.0    1.9e-47  162.2   0.0    1.0  1  CRISPR_assoc  CRISPR associated protein


Domain annotation for each model (and alignments):
>> CRISPR_assoc  CRISPR associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.2   0.0   1.1e-51   1.9e-47       4     227 .]       2     222 ..       1     222 [. 0.81

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 1.1e-51
                                   EEEEE-TTSCCH...HHHHHSHHHHHHHHHCCGCHCHHTTEE--EEEEEE-SSSS-EEEEEESS---GGTTC-..S-TTSE CS
                  CRISPR_assoc   4 srlrldprrraa...rkdladpyalHrallslfpddpeeeerrvLfRleeeaeaepvllvlSeekpdlshlveqadeaesa 81 
                                   sr +l p++ ++   r  + + +++Hr+++slfp ++ +++r++ +R+++  ++ p ++++Se++p  +         + +
  gi|91772627|ref|YP_565319.1|   2 SRAKLLPEAMSSkaiRGNMGNEHNVHRLVWSLFPVNE-DDKRKFIYRQDSM-GSLPSFYLVSENEPIDE--------LNVW 72 
                                   56666666555555688999**************865.66789******99.7888***********99........3445 PP

                                   EEEEEECC-----TT-EEEEEEEE---........................EEE.TTTSEEEEE-SCCHHHHHHHHHHCCT CS
                  CRISPR_assoc  82 eikdlkpllerlaegqrlaFrlranPv...........rsdvtedak.aeraekerergkrlahlteaaqleWLarraeka 150
                                   +i+  k++ + l++gq+laF+lranP+           r+dv++d+k + + e++ + +  ++ + +++  eWL+r+++ +
  gi|91772627|ref|YP_565319.1|  73 DIDV-KQYDPILKSGQKLAFSLRANPIvskrdendkqhRHDVVMDEKfRLKMENGGDIEPNMPDIVQRKGSEWLLRKGDMN 152
                                   5444.55555599*************97777777777777777777663333334444444445***************** PP

                                   CEE---EETTESEEEEEEEEEEEEEETTTTCCEEEEEEEEEEECEEEESSHHHHHHHHHH-CSS-GGGT-BEEEEE. CS
                  CRISPR_assoc 151 GfelleseeeeevevterqrlrfrkkakkkkkekvtlssvtfeGlltVtDpelfreaLleGiGraKAyGcGLLllap 227
                                   Gf++++    e+++v+++q++++ k ++k   ++v++s+v++ G+ltVtDp+ fr+aL++GiG+aK++GcG+Ll++p
  gi|91772627|ref|YP_565319.1| 153 GFSINA----EQIRVDAYQNHKLFKPKGK---HHVSFSTVDIVGTLTVTDPDIFRDALFKGIGPAKGFGCGMLLVRP 222
                                   **9966....79************95554...26*****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1617.79
//
Query:       gi|91772628|ref|YP_565320.1|  [L=303]
Description: CRISPR-associated Cas1 family protein [Methanococcoides burtonii DSM 6242]
Scores for 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   52.4   0.0    9.9e-08   31.4   0.0    2.1  2  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 !   19.3   0.0   2.8e-08    0.0005       6     107 ..      21     121 ..      16     125 .. 0.92
   2 !   31.4   0.0   5.5e-12   9.9e-08     146     254 ..     131     239 ..     121     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-08
                                   TEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSSTHHHHHH CS
                      Cas_Cas1   6 qgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlepeesgnvelrra 86 
                                   +g+ l + ++ +v  +++  + +ip+  i  +++   + +s++a++l+a+ g  ++++ e g  l++  ++    ++ ++ 
  gi|91772628|ref|YP_565320.1|  21 KGE-LDVIDGAFVLVDKNGIRSQIPVGGIACLMLEPGTRVSHAAISLAARVGCLLIWVGEAGVRLYSAGQPGGARADRLLY 100
                                   555.7777888999999999************************************************************* PP

                                   HHHHHHSHHHHHHHHHHHHHH CS
                      Cas_Cas1  87 Qyraaddeekrlelakkivag 107
                                   Q+++a dee rl++++++ + 
  gi|91772628|ref|YP_565320.1| 101 QAKLALDEELRLKVVRNMYEM 121
                                   ****************99765 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 5.5e-12
                                   HSHHHHHHHHHHHHHHHHHHHHHHCSCGGS-SS-SSSS....-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS-- CS
                      Cas_Cas1 146 esleeLrgiEGeaakaYfeafdkllkeefefegRsrrp....pkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHed 222
                                    s+e++rg+E++  k+ ++ f++     +e++gR+       + D  N +Ls + + +y    +ai a+g  P++Gf+H+ 
  gi|91772628|ref|YP_565320.1| 131 YSVEQMRGMEAARVKKMYKIFAQQY--GIEWKGRNYDVddwdAGDVQNRCLSSATSCIYGVAEAAILAAGYSPAVGFIHTG 209
                                   589*******************887..8******9998555579***********************************98 PP

                                   TTSS-HHHHHHHHHHHHHHCHHHHHHHHHTTS CS
                      Cas_Cas1 223 rpgrpsLalDLmEefRpllvDrlvlslinkrq 254
                                   +p+  s ++D++++f+   v  +++++ +++ 
  gi|91772628|ref|YP_565320.1| 210 KPR--SFVYDVADIFKFETVVPIAFRIASEKH 239
                                   886..89*********9888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2095.63
//
Query:       gi|91772629|ref|YP_565321.1|  [L=93]
Description: hypothetical protein Mbur_0600 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-33  113.3   0.1    4.5e-33  113.2   0.1    1.0  1  Cas_Cas2CT1978  CRISPR-associated protein (Cas_Cas2CT1978)


Domain annotation for each model (and alignments):
>> Cas_Cas2CT1978  CRISPR-associated protein (Cas_Cas2CT1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.1   2.5e-37   4.5e-33       1      86 []       1      86 [.       1      86 [. 0.99

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 2.5e-37
                                  EEEEEEES--HHHHHHHHHHSEEEETTEEEEEE-HHHHHHHHHHHHHH-TSSEEEEEEE-SSSSSEEEEEESTTSEEEEEETT CS
                Cas_Cas2CT1978  1 mvVivleavparlRGeLtrwllEvragVyvgrvsarVreklwerveekieegsavmvysanneqgfeirtlGetrrelvdldG 83
                                  m+Vivle++parlRG+L++wllEvragVyvg++s +Vre+++e++e+ +e+g+av+++s +neqg+++ t+Ge+rr + ++dG
  gi|91772629|ref|YP_565321.1|  1 MLVIVLENAPARLRGRLAVWLLEVRAGVYVGDYSVKVREMILENLEKGLEDGNAVVAWSCPNEQGYDFLTFGENRRIPKEMDG 83
                                  9********************************************************************************** PP

                                  EEE CS
                Cas_Cas2CT1978 84 ltL 86
                                  ++L
  gi|91772629|ref|YP_565321.1| 84 VKL 86
                                  *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 702.85
//
Query:       gi|91772630|ref|YP_565322.1|  [L=128]
Description: hypothetical protein Mbur_0601 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.26   11.7  11.9         16    6.0  11.9    2.3  1  DUF805    Protein of unknown function (DUF805)
        3.9    7.7  12.4        4.4    7.6   3.1    2.7  3  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D
          9    5.8  10.2        2.5    7.6   0.4    2.8  2  DUF4328   Domain of unknown function (DUF4328)


Domain annotation for each model (and alignments):
>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.9    0.0026        16      17     103 ..      11     123 ..       3     125 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0026
                        DUF805  17 vlfllllvivlallaavlaaaavasalsvvlallllvpslavtvR..RlHD..........................tgrs 69 
                                   +l+ +ll  +   ++ +l+++a+ ++++  ++ ++ ++++ +++R  Rl                            ++rs
  gi|91772630|ref|YP_565322.1|  11 ALIFVLLGYI--YTSFCLQKIAIKTSTANAWMAWIPLLNILLMFRvaRLSLwhaiiflipyvnflmgaylwgevagrLNRS 89 
                                   3333333332..2222333344555555555555555554444332254435556666666666666666666666679** PP

                        DUF805  70 gwllllllvplialllllvllllpgtpgenryGp 103
                                    wl +l+l+p+++l+l  ++++ + + + n y++
  gi|91772630|ref|YP_565322.1|  90 KWLGVLFLIPVLNLVLSGYFAFTDADVNRNGYDA 123
                                   *******************************987 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 ?    7.6   3.1   0.00073       4.4       7      50 ..      10      55 ..       5      62 .. 0.70
   2 ?    4.0   0.4    0.0095        57      23      60 ..      52      85 ..      48      90 .. 0.73
   3 ?    4.3   0.9    0.0079        47      16      54 ..      75     111 ..      67     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00073
                          DPM3  7 tlalallllalwlalllrlvslpl..skvqdevvpvlPlwalvlfG 50
                                  + ++++ll+ ++++++l+ + +++   + +  ++p+l +++++ ++
  gi|91772630|ref|YP_565322.1| 10 IALIFVLLGYIYTSFCLQKIAIKTstANAWMAWIPLLNILLMFRVA 55
                                  5688999*************98833455566666666665555555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0095
                          DPM3 23 lrlvslplskvqdevvpvlPlwalvlfGayslatlgyg 60
                                  +r+  l+    ++ +++++P+ + +l+Gay+  ++  +
  gi|91772630|ref|YP_565322.1| 52 FRVARLS---LWHAIIFLIPY-VNFLMGAYLWGEVAGR 85
                                  4555444...79999999995.56899***99988766 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0079
                          DPM3  16 alwlalllrlvslplskvqdevvpvlPlwalvlfGaysl 54 
                                   +++l+  +    l+  +++  v++++P++ lvl G ++ 
  gi|91772630|ref|YP_565322.1|  75 GAYLWGEVAGR-LN-RSKWLGVLFLIPVLNLVLSGYFAF 111
                                   55554432222.23.6689999************99875 PP

>> DUF4328  Domain of unknown function (DUF4328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   3.8     0.037   2.2e+02      58      75 ..      58      75 ..       3      88 .. 0.79
   2 ?    7.6   0.4   0.00042       2.5      57      76 ..      88     107 ..      80     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.037
                       DUF4328 58 pgwavggwlvPvvnLvlP 75
                                  + w  + +l+P vn+++ 
  gi|91772630|ref|YP_565322.1| 58 SLWHAIIFLIPYVNFLMG 75
                                  456667789999999875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00042
                       DUF4328  57 spgwavggwlvPvvnLvlPl 76 
                                   ++ w+ + +l+Pv+nLvl +
  gi|91772630|ref|YP_565322.1|  88 RSKWLGVLFLIPVLNLVLSG 107
                                   56899999*********866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1017.74
//
Query:       gi|91772631|ref|YP_565323.1|  [L=451]
Description: coenzyme F390 synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-16   57.8   0.0    1.1e-15   57.2   0.0    1.2  1  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.24   11.4   0.0    1.5  1  SIS_2        SIS 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 !   57.2   0.0   1.2e-19   1.1e-15     150     369 ..      81     287 ..      37     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.2e-19
                                   TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT- CS
                   AMP-binding 150 peeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGa 229
                                   + +  +++  d+++i  TSGT G PK   l+   ++  ++++  + + ++++++d++++++++   +g  + +l+a  +G+
  gi|91772631|ref|YP_565323.1|  81 DFQFMSADWTDIYTIHETSGTSGVPKSFFLTWHDWLRYAKKYGRSFCsQGFGPGDRMVMCASYGMNIGANTMTLAARDVGM 161
                                   3355568999****************************999763333566889***************9777777777777 PP

                                   EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC CS
                   AMP-binding 230 tvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfge 309
                                     v+++++ +++     + +e++++t i++    l +l++  +++    +  +  s+  +++gge+   +    ++++ g+
  gi|91772631|ref|YP_565323.1| 162 -AVIPEGKCTFP----TRIFETYRPTGIVASVFKLLRLARrLKNEG--IDP-KETSINKLIVGGESFADQSRSYLEEVWGC 234
                                   .55667666655....6899******66654444444444232222..222.4456888899******************* PP

                                   EEEEEEEEGGGSSEC.EECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEE CS
                   AMP-binding 310 evlegYGlTEttgvv.tvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellv 369
                                   +v+++YG TE t++  + +++++          p   v + + D+  +e ++dge G +++
  gi|91772631|ref|YP_565323.1| 235 PVYNTYGSTEGTMCGeC-VEQNG-------LHVPEDLVHLDVYDPYRKEFLEDGECGRIVL 287
                                   *************9854.44222.......2355668999999999999999999999986 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.24      85     134 ..     116     164 ..      83     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                                   HTT-TTHHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEE CS
                         SIS_2  85 lerdegyakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkvi 134
                                   l + + y++++ ++  + pgD ++   + G n  +  + +aa+++gm+vi
  gi|91772631|ref|YP_565323.1| 116 LRYAKKYGRSFCSQ-GFGPGDRMVMCASYGMNIGANTMTLAARDVGMAVI 164
                                   66678899999999.99********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3523.78
//
Query:       gi|91772632|ref|YP_565324.1|  [L=549]
Description: unusual protein kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-27   96.2   0.0    4.3e-27   94.6   0.0    1.9  1  ABC1      ABC1 family
      6e-08   32.5   0.2      3e-07   30.2   0.1    2.0  2  RIO1      RIO1 family
    5.7e-06   26.1   0.6    5.7e-06   26.1   0.6    2.4  3  WaaY      Lipopolysaccharide core biosynthesis protein (WaaY)
    4.6e-05   23.5   0.0     0.0014   18.6   0.2    2.2  2  APH       Phosphotransferase enzyme family
    0.00024   20.6   1.4    0.00088   18.7   0.6    2.0  2  Pkinase   Protein kinase domain


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.0   1.2e-30   4.3e-27       9     119 .]     136     246 ..     130     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.2e-30
                          ABC1   9 eiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkfl.kelrldleelvdefsksll 88 
                                   + F+ef+++PiA+ASiaqV++A+l +g++VavK+ rp++ + i+ Dl++++ l  ll ++   + + d++ ++def++ l 
  gi|91772632|ref|YP_565324.1| 136 SQFDEFNKKPIASASIAQVYEAVL-NGQKVAVKIARPNLIDLINVDLSIINDLKPLLVRMGgFGSNFDIDSFLDEFKELLN 215
                                   57********************99.6***************************998877761455589************* PP

                          ABC1  89 eEldferEAknaekfrenfaklkevkvPkvy 119
                                   +E+d+++EA+n  +f e f++ k++++P+v+
  gi|91772632|ref|YP_565324.1| 216 KEVDLRNEARNIMRFGEIFRSSKDIHIPNVH 246
                                   ****************************995 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.29     1e+03       1      21 [.     153     172 ..     153     185 .. 0.81
   2 !   30.2   0.1   8.5e-11     3e-07      67     152 ..     237     321 ..     210     335 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                                   EEEEEEETTTEEEEEEEE-S- CS
                          RIO1   1 nVyhavsedgkevaiKiykts 21 
                                   +Vy+av  +g++va+Ki + +
  gi|91772632|ref|YP_565324.1| 153 QVYEAVL-NGQKVAVKIARPN 172
                                   5999977.8999****98865 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 8.5e-11
                                   HTT--S--EEE..EETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHH..HHHHHHHTSTEEESS-STTSEEEETTE CS
                          RIO1  67 eagvpvPkpie..lkrhvlvmefigedgvaapklkdveeeeeaeelyeevle..emrklykeaglvHaDLSeyNvlvdedk 143
                                   ++++++P++ e  + + vlvm++++  gv +++l+d +  +++++ y+++++  +++++y  +g  HaD    N+l+ ed+
  gi|91772632|ref|YP_565324.1| 237 SKDIHIPNVHEalCTESVLVMDYME--GVLVKDLDDKN--QKLRSKYAHIISssYLEQVY-VHGFYHADPHSGNILLREDG 312
                                   3569999997633789*********..*******9999..899999***99988899999.9******************* PP

                                   EEE--GTTE CS
                          RIO1 144 vviIDvsQa 152
                                   + +ID++  
  gi|91772632|ref|YP_565324.1| 313 IAFIDFGEV 321
                                   *****9866 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.9      0.83     3e+03      12      44 ..       5      36 ..       2      44 .. 0.61
   2 !   26.1   0.6   1.6e-09   5.7e-06     118     210 ..     253     348 ..     217     359 .. 0.79
   3 ?   -1.9   0.1      0.56     2e+03      15      40 ..     454     479 ..     438     507 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.83
                          WaaY 12 vfvkendekyleilddllsynfkvikvlrnidd 44
                                  v + ++  +y  il+ ++ yn+  + ++r+i++
  gi|91772632|ref|YP_565324.1|  5 VLMFKKLRRYFSILKVFIRYNLFSL-LYREIQN 36
                                  4555556677777777777776443.4555555 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.6e-09
                          WaaY 118 yimiieyiegielvdmpeiddevkak....ikqs.ieklhqlgmvsgdphrgnfivkkdevriidlsgkrasaerkakdri 193
                                    +++++y+eg+ + d+ + ++++++k    i +s +e+++ +g+   dph gn+++++d++  id+           +   
  gi|91772632|ref|YP_565324.1| 253 SVLVMDYMEGVLVKDLDDKNQKLRSKyahiISSSyLEQVYVHGFYHADPHSGNILLREDGIAFIDFGEVGIIDSELKR--N 331
                                   58899*******************98333222223678999************************9655444443333..3 PP

                          WaaY 194 dlerhygikneirdlgy 210
                                    l+  ygi ++  d+ +
  gi|91772632|ref|YP_565324.1| 332 MLNLFYGIYKKNVDIAF 348
                                   45557777776667666 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.56
                          WaaY  15 kendekyleilddllsynfkvikvlr 40 
                                     ++++ylei+++l     +vi  +r
  gi|91772632|ref|YP_565324.1| 454 LLEGDRYLEIFKNLPQGINDVIETIR 479
                                   44567777777776555555555554 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.036   1.3e+02      28      89 ..     215     272 ..     144     281 .. 0.67
   2 !   18.6   0.2   3.8e-07    0.0014     167     200 ..     295     325 ..     292     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.036
                                   E-TTS-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHH CS
                           APH  28 npparaaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllrklsaa 89 
                                   n + ++ +e+r++ ++   ++ ++  ++P v+     ++e+ l++  +e+v  ++l++    +
  gi|91772632|ref|YP_565324.1| 215 NKEVDLRNEARNIMRFGEIFRSSKDiHIPNVHE--ALCTESVLVMDYMEGVLVKDLDD---KN 272
                                   55557888888889999999855445*****99..8***************9999999...33 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.8e-07
                                   EEE-SS-SGGGEEEC..TTEEEEE---TT-EEEE CS
                           APH 167 vllHgDlhpgNllvdpddgrvtGviDfedaglgp 200
                                   ++ H D+h+gN+l++  ++ + ++iDf+ +g+ +
  gi|91772632|ref|YP_565324.1| 295 GFYHADPHSGNILLR--EDGI-AFIDFGEVGIID 325
                                   678************..7887.9*****999876 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   5.5e+02      10      33 ..     149     170 ..     142     178 .. 0.82
   2 !   18.7   0.6   2.5e-07   0.00088      57     152 ..     224     328 ..     208     339 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                                   ESSEEEEEEEETTTTEEEEEEEEE CS
                       Pkinase  10 GsfGkVykaveketgkivAvKkik 33 
                                    s ++Vy+av   +g++vAvK+ +
  gi|91772632|ref|YP_565324.1| 149 ASIAQVYEAV--LNGQKVAVKIAR 170
                                   57899*****..79*******976 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.5e-07
                                   CTTB--EEEEEEE.............SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS- CS
                       Pkinase  57 hpnivrlyevfee.............kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDl 124
                                    +ni+r+ e+f++              +e +lv++y+eg  ++dl  ++++l ++ a  i ++    le ++ +g+ H D 
  gi|91772632|ref|YP_565324.1| 224 ARNIMRFGEIFRSskdihipnvhealCTESVLVMDYMEGVLVKDLDDKNQKLRSKYAHIISSSY---LEQVYVHGFYHADP 301
                                   345555555555555555555544444667899*****99999999887778877777777665...5677889******* PP

                                   SGGGEEEETTTEEEE-SGTTSEESSSSC CS
                       Pkinase 125 KpeNiLidekgelKitDFGlakelesss 152
                                    + NiL+  ++ +  +DFG +  ++s+ 
  gi|91772632|ref|YP_565324.1| 302 HSGNILLR-EDGIAFIDFGEVGIIDSEL 328
                                   ********.77799*****988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3299.77
//
Query:       gi|91772633|ref|YP_565325.1|  [L=67]
Description: hypothetical protein Mbur_0604 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.7    3.2e-17   62.3   0.7    1.0  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 !   62.3   0.7   1.8e-21   3.2e-17       3      62 .]      12      67 .]      10      67 .] 0.96

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.8e-21
                                  XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                          TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62
                                  + G+t++V++e+ + +eg+gi+r+  g+v+fvp ++   Gd+V++k+tkv +++++Gel+
  gi|91772633|ref|YP_565325.1| 12 EAGETYDVTIEDIA-REGDGIARVS-GFVIFVPEASV--GDEVTIKVTKVMSKFAFGELV 67
                                  67***********9.**********.********988..*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 469.64
//
Query:       gi|91772634|ref|YP_565326.1|  [L=477]
Description: ketoisovalerate ferredoxin oxidoreductase, gamma subunit / ketoisovalerate ferredoxin oxidoreductase, beta subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-38  132.5   0.0    2.8e-38  131.7   0.0    1.4  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    4.1e-22   78.6   0.1    6.2e-22   78.0   0.1    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
       0.26   11.0   0.5        0.5   10.1   0.5    1.4  1  TGBp3         Triple gene block 3


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 !  131.7   0.0   4.7e-42   2.8e-38       1     174 [.     305     467 ..     305     470 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 4.7e-42
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                   GGqGv+++g  la+a  r   y +++++yg+e+rGg s++ v is e ++ s+ v+e d+l+al++ +l++++ ++k+gg+
  gi|91772634|ref|YP_565326.1| 305 GGQGVLSMGLTLARAGCRDQRYTSWYPSYGPEQRGGTSNCSVVISGE-SIGSPVVYESDVLIALNQPSLEKFAGDVKKGGV 384
                                   9**********************************************.8999999************************** PP

                                   EEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT..S-HHHHHHHHHCCS-C CS
                           POR  82 iiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg..lplealeeaikkrfpk 160
                                   i+y+s+ ++  +++              vr ++v+at+iak++g   +aaNtvmlG+++ l++  lp++ ++eai+++f+ 
  gi|91772634|ref|YP_565326.1| 385 ILYDST-INAVDIPIPED----------VRAIAVPATQIAKDAGS-VKAANTVMLGVMMELGDtgLPEKVFREAIEDTFAS 453
                                   *****5.56666655332..........5789**********888.************9999888999************* PP

                                   H.HHHHHHHHHHHH CS
                           POR 161 kkeviekNlkafra 174
                                   k ++i +Nl++++a
  gi|91772634|ref|YP_565326.1| 454 KPKLIPMNLEVLEA 467
                                   ***********997 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 !   78.0   0.1     1e-25   6.2e-22       4     153 .]      63     220 ..      60     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1e-25
                                   HHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE- CS
                  TPP_enzyme_C   4 cltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnN 82 
                                   c  +           + y++  ++ +++G++ ++++G+++a+ ++ v+++ GDG+++ i l+e+++a++r+ ++ v+ +nN
  gi|91772634|ref|YP_565326.1|  63 CAVF----------AYYYFDcGNLQVAHGRAPAVGTGMSRAQDNAVVISYQGDGDLASIgLNETMQAANRGEKMAVFFVNN 133
                                   5555..........556777445899***************9999************************************ PP

                                   SBCCCHHHH...HHHHTCCTTTTSBB.....BS----HHHHHHHTTSEEE..EESSH.HHHH...HHHHHHHH....CSSS CS
                  TPP_enzyme_C  83 egygmtggq...qepfggkrksgpagk....dlkpvdfaklaealGakga..rvekadveel...eealkeal....ekkg 147
                                    ++gmtggq   ++  g+k+ ++p+g+     ++p++++++   l a+++  rv+ +d++++   ++a+++al    + kg
  gi|91772634|ref|YP_565326.1| 134 TVFGMTGGQmapTTLIGEKTVTCPDGRdprfAGYPLHMCEILDNLKAPVFieRVSISDISHIrkaRKAIRRALevqrDGKG 214
                                   *****************************988****************777*99988888874446778888899999999 PP

                                   EEEEEE CS
                  TPP_enzyme_C 148 paliev 153
                                    a++ev
  gi|91772634|ref|YP_565326.1| 215 YAFVEV 220
                                   999987 PP

>> TGBp3  Triple gene block 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   8.3e-05       0.5      22      36 ..     339     353 ..     334     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.3e-05
                         TGBp3  22 sssegCvivITGesv 36 
                                     +++C +vI+Ges+
  gi|91772634|ref|YP_565326.1| 339 GGTSNCSVVISGESI 353
                                   6799**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3448.28
//
Query:       gi|91772635|ref|YP_565327.1|  [L=353]
Description: 2-ketoisovalerate ferredoxin reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-53  182.2   0.0    1.6e-53  181.8   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.2e-25   89.8   0.0    2.5e-25   88.7   0.0    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0011   18.9   0.0     0.0024   17.7   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.15   12.2   0.1       0.28   11.3   0.1    1.4  1  DUF1968          Domain of unknown function (DUF1968)


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 !  181.8   0.0   3.6e-57   1.6e-53       2     230 ..      15     242 ..      14     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.8 bits;  conditional E-value: 3.6e-57
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   +a++ag+d +++YPITP+sei++e+++  +k +    ++vq+esE +ai++v GAa aG ra+Ta+Sg+G++L++e + + 
  gi|91772635|ref|YP_565327.1|  15 GALYAGCDCYFGYPITPASEILHEASQTFPKLGR---KFVQAESEEAAINMVYGAASAGHRAMTASSGPGMSLKQEGISYL 92 
                                   799******************************6...9******************************************* PP

                                   HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH......S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHH CS
                         POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaar......dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfl 157
                                   ag+elP viv+++Ra+p    +i ++q D  ++       ++  ivla+++vqe+ d +++Af lA k+r Pv+vl Dg+l
  gi|91772635|ref|YP_565327.1|  93 AGAELPSVIVDIMRAGPGL-GNIGPEQADYAQVVkggghgNYRNIVLAPNSVQEMCDHTIKAFELASKYRNPVVVLADGVL 172
                                   *******************.9************************************************************ PP

                                   H.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                         POR_N 158 lshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                                   +  ++e++++pd+  +  +i+e +    +ke + +    i+ +  + +d  ++ +ek +   +  e+v+ee++
  gi|91772635|ref|YP_565327.1| 173 G-QMIEPLHFPDKA-ITPVIDESWAVCGTKETKENLVTSIFLDFDKLEDFNYQLQEKYETIKK-NETVHEEYM 242
                                   *.*********999.9********999999998888888888888888888888887766555.677777776 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.0   5.7e-29   2.5e-25       1     102 []     246     341 ..     246     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 5.7e-29
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-S.EEEEEE-S--TT-G-HHHHHHHHHTGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvk.kvvvldrnisfgseGqlveevkaalkk 80 
                                   A +v+va+G++++ ++sav+ +R+eg+kvGl+r++tl+PFPe+elk ++++++  ++++++++     Gq++e+vk a+++
  gi|91772635|ref|YP_565327.1| 246 ASIVLVAYGISSRICHSAVEVARREGLKVGLFRPITLFPFPEKELKGIADSYDcTFISVEMSN-----GQMMEDVKLAIEC 321
                                   789************************************************9735899*****.....************* PP

                                   GTSEEEEEE--GGG----HHHH CS
                       PFOR_II  81 skvkvvnfvaglgGrditvedi 102
                                   s  k+v++v++lgG++it++++
  gi|91772635|ref|YP_565327.1| 322 S--KPVELVNRLGGNLITLDQV 341
                                   *..***************9986 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.4e-07    0.0024       9      64 ..     245     300 ..     239     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.4e-07
                                   TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEE CS
               Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrl 64 
                                      ++lvayG   + +  A+e +++eg+++ +  ++t+ p+ ++ ++ ++ +++  
  gi|91772635|ref|YP_565327.1| 245 DASIVLVAYGISSRICHSAVEVARREGLKVGLFRPITLFPFPEKELKGIADSYDCT 300
                                   5679****************************************999888877665 PP

>> DUF1968  Domain of unknown function (DUF1968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.2e-05      0.28      11      64 ..     203     258 ..     199     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.2e-05
                                   SSSSEEEEEESE-T..TSBCS-SSSTTEEEEEEEEEEETTTTEEEEEEEEEESSTT CS
                       DUF1968  11 ssnlsvCLfTDFds..qvnvsqskeseviktdstvldmksldskSngvvaWsnksd 64 
                                    +nl   +f DFd   + n + +++ e+ik+++tv ++  +d +S   va++ +s+
  gi|91772635|ref|YP_565327.1| 203 KENLVTSIFLDFDKleDFNYQLQEKYETIKKNETVHEEYMTDDASIVLVAYGISSR 258
                                   567777899****986788888888************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2532.18
//
Query:       gi|91772636|ref|YP_565328.1|  [L=73]
Description: ketoisovalerate ferredoxin oxidoreductase, delta subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-11   44.0   9.6    2.9e-11   43.8   9.6    1.1  1  Fer4_7    4Fe-4S dicluster domain
    6.6e-09   35.7  20.6    1.3e-06   28.4  10.9    1.7  2  Fer4_10   4Fe-4S dicluster domain
    4.3e-08   33.2   8.7    6.7e-08   32.6   8.7    1.3  1  Fer4_9    4Fe-4S dicluster domain
    8.5e-08   31.7  13.2    0.00021   21.0   1.4    2.2  2  Fer4      4Fe-4S binding domain
    1.5e-07   31.4   8.2    4.8e-07   29.8   8.2    1.7  1  Fer4_21   4Fe-4S dicluster domain
    6.5e-07   29.1  12.8    0.00062   19.7   2.1    2.2  2  Fer4_2    4Fe-4S binding domain
    2.2e-06   28.4   6.3      0.015   16.1   1.0    2.1  2  Fer4_22   4Fe-4S dicluster domain
    4.8e-06   26.4  14.0     0.0014   18.6   2.1    2.2  2  Fer4_6    4Fe-4S binding domain
      4e-05   24.1   6.0      0.003   18.1   0.7    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    5.3e-05   24.1  13.7     0.0049   17.8   2.4    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    5.4e-05   23.6  12.9     0.0016   18.9  12.9    2.0  1  Fer4_17   4Fe-4S dicluster domain
    0.00062   20.5  16.0       0.12   13.4   3.5    2.2  2  Fer4_3    4Fe-4S binding domain
    0.00065   20.0  18.2     0.0085   16.5   4.2    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00098   19.8   7.5       0.13   13.0   1.0    2.1  2  Fer4_15   4Fe-4S single cluster domain
     0.0019   18.6  13.2      0.024   15.1  13.5    2.0  2  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.041   14.1   6.6        1.3    9.3   1.0    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   9.6   2.6e-14   2.9e-11       2      50 ..      12      60 ..      11      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.6e-14
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50
                                  C gC++C +aCp +++ + e  ne+g ++ve++ e C+gCg+C  +CP 
  gi|91772636|ref|YP_565328.1| 12 CKGCERCIPACPKSVLFMSENINERGYRYVEYKGEGCTGCGNCYYTCPE 60
                                  ************************************************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4  10.9   1.1e-09   1.3e-06       5      56 .]       8      59 ..       5      59 .. 0.72
   2 !   18.3   2.1   1.6e-06    0.0018       4      22 ..      43      61 ..      40      72 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.1e-09
                       Fer4_10  5 dddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +   C +C++C  aCP ++  ++++++e+     v+ k e Ctgcg+C+  CP
  gi|91772636|ref|YP_565328.1|  8 NNLECKGCERCIPACPKSVlFMSENINERG-YRYVEYKGEGCTGCGNCYYTCP 59
                                  5668*************8863333333333.3334445778***********9 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.6e-06
                       Fer4_10  4 idddtCirCgkCvkaCPad 22
                                  +  + C++Cg+C   CP +
  gi|91772636|ref|YP_565328.1| 43 YKGEGCTGCGNCYYTCPET 61
                                  5556788888888888875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   8.7     6e-11   6.7e-08       1      49 [.      11      61 ..      11      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6e-11
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkg 49
                                  +C gC +C++aCp+ v  ++++ +++ +r  ++  e C+gCg C+  Cp++
  gi|91772636|ref|YP_565328.1| 11 ECKGCERCIPACPKSVLFMSENINERGYRYVEYkgEGCTGCGNCYYTCPET 61
                                  5*************9985555555444444444459*************85 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.4   1.8e-07   0.00021       3      21 ..       7      25 ..       5      28 .. 0.82
   2 !   16.2   4.5     6e-06    0.0067       7      19 ..      47      59 ..      42      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                                  EETTTSSS-THHHHHSTTT CS
                          Fer4  3 ideekCigCGaCvevCPvg 21
                                   +   C gC +C+ +CP  
  gi|91772636|ref|YP_565328.1|  7 LNNLECKGCERCIPACPKS 25
                                  56678************75 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6e-06
                                  TSSS-THHHHHST CS
                          Fer4  7 kCigCGaCvevCP 19
                                   C+gCG+C+  CP
  gi|91772636|ref|YP_565328.1| 47 GCTGCGNCYYTCP 59
                                  5************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   8.2   4.3e-10   4.8e-07       4      56 ..       8      63 ..       5      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.3e-10
                       Fer4_21  4 dedkCigCgkCliaCedts...hqaieidaktvlkvvedeCvGCnlCssvCPvedc 56
                                  ++ +C gC++C+ aC+++     + i+  + +++++  + C+GC  C+  CP + +
  gi|91772636|ref|YP_565328.1|  8 NNLECKGCERCIPACPKSVlfmSENINERGYRYVEYKGEGCTGCGNCYYTCPETLA 63
                                  6679************865222466677788899999***************6555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.2   1.7e-05     0.019       2      21 ..       4      23 ..       3      24 .. 0.84
   2 !   19.7   2.1   5.5e-07   0.00062       3      22 .]      41      60 ..      39      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                  +++ +   C gC+ C+ aCP
  gi|91772636|ref|YP_565328.1|  4 YPQLNNLECKGCERCIPACP 23
                                  56777667***********9 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.5e-07
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  v++  + C+gCg C+  CP+
  gi|91772636|ref|YP_565328.1| 41 VEYKGEGCTGCGNCYYTCPE 60
                                  6667778************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 !   15.6   0.4     2e-05     0.022      76      95 ..       6      25 ..       2      26 .. 0.86
   2 !   16.1   1.0   1.3e-05     0.015      75      95 ..      41      61 ..      29      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                       Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                  + ++  C GC RCi acp++
  gi|91772636|ref|YP_565328.1|  6 QLNNLECKGCERCIPACPKS 25
                                  678899************86 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.3e-05
                       Fer4_22 75 ekfgesgCvGCgRCieacpvk 95
                                   +++ +gC+GCg C  +cp++
  gi|91772636|ref|YP_565328.1| 41 VEYKGEGCTGCGNCYYTCPET 61
                                  4567899***********986 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   4.3   5.9e-05     0.066       9      23 ..      12      26 ..      12      27 .. 0.90
   2 !   18.6   2.1   1.2e-06    0.0014       9      21 ..      48      60 ..      41      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                        Fer4_6  9 CigCgdCvrvCPega 23
                                  C gC++C+ +CP  +
  gi|91772636|ref|YP_565328.1| 12 CKGCERCIPACPKSV 26
                                  ************776 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-06
                        Fer4_6  9 CigCgdCvrvCPe 21
                                  C+gCg+C+  CPe
  gi|91772636|ref|YP_565328.1| 48 CTGCGNCYYTCPE 60
                                  ************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 !    9.3   0.5    0.0015       1.6       4      18 ..      10      24 ..       7      36 .. 0.89
   2 !   18.1   0.7   2.7e-06     0.003       4      21 ..      46      63 ..      41      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                   +C +c+ C  ++P+
  gi|91772636|ref|YP_565328.1| 10 LECKGCERCIPACPK 24
                                  58************7 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.7e-06
                       Fer4_13  4 dtCiacgaCvelaPdvFe 21
                                  + C++cg+C+ ++P++ +
  gi|91772636|ref|YP_565328.1| 46 EGCTGCGNCYYTCPETLA 63
                                  79*************876 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.4   4.3e-06    0.0049       2      20 ..      12      30 ..      11      42 .. 0.82
   2 !   13.5   2.9   9.5e-05      0.11      48      65 ..      42      59 ..      29      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.3e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++C++C+ +CP +++ + 
  gi|91772636|ref|YP_565328.1| 12 CKGCERCIPACPKSVLFMS 30
                                  *************998766 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.5e-05
                       Fer4_16 48 ckkqeaitgCdiCqdvCP 65
                                  ++k+e +tgC++C  +CP
  gi|91772636|ref|YP_565328.1| 42 EYKGEGCTGCGNCYYTCP 59
                                  566788999999999998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9  12.9   1.5e-06    0.0016       1      60 [.      11      62 ..      11      63 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-06
                       Fer4_17  1 rCiqCgyClpeCpsyeaydn...epkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                  +C +C+ C+p+Cp      +   +++ +++            e k + C++Cg+C + CP+ l
  gi|91772636|ref|YP_565328.1| 11 ECKGCERCIPACPKSVLFMSeniNERGYRYV-----------EYKGEGCTGCGNCYYTCPETL 62
                                  6************876644400033333333...........456789************987 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   4.7   0.00012      0.13       1      13 [.      12      24 ..      12      26 .. 0.94
   2 !   13.4   3.5    0.0001      0.12       1      13 [.      48      60 ..      48      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C gC++C  +CP+
  gi|91772636|ref|YP_565328.1| 12 CKGCERCIPACPK 24
                                  9***********8 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.0001
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  CtgCg C   CP+
  gi|91772636|ref|YP_565328.1| 48 CTGCGNCYYTCPE 60
                                  ************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 !    9.8   6.2    0.0011       1.2       4      15 ..      12      23 ..       8      39 .. 0.90
   2 !   16.5   4.2   7.5e-06    0.0085       3      15 ..      47      59 ..      34      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                        Fer4_4  4 CigCgsCvaaCP 15
                                  C gC +C+ aCP
  gi|91772636|ref|YP_565328.1| 12 CKGCERCIPACP 23
                                  ************ PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.5e-06
                        Fer4_4  3 rCigCgsCvaaCP 15
                                   C+gCg C+++CP
  gi|91772636|ref|YP_565328.1| 47 GCTGCGNCYYTCP 59
                                  5************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.6   0.00037      0.41       7      24 ..      11      28 ..       6      46 .. 0.80
   2 !   13.0   1.0   0.00012      0.13       6      22 ..      46      62 ..      41      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                       Fer4_15  7 aCigcglCvaeapevfel 24
                                  +C gc++C+ ++p+ + +
  gi|91772636|ref|YP_565328.1| 11 ECKGCERCIPACPKSVLF 28
                                  7***********987654 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                       Fer4_15  6 daCigcglCvaeapevf 22
                                  + C+gcg+C+  +pe  
  gi|91772636|ref|YP_565328.1| 46 EGCTGCGNCYYTCPETL 62
                                  78************976 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  13.5   2.1e-05     0.024       4      63 ..      11      60 ..       8      62 .. 0.76
   2 !   12.9   3.2    0.0001      0.11       4      17 ..      47      60 ..      44      70 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                        Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                  +C +C++C  aCp    +  ++ + rg +     e ++       + Ct+cg+C   Cp+
  gi|91772636|ref|YP_565328.1| 11 ECKGCERCIPACPKSVLFMSENINERGYRYV---EYKG-------EGCTGCGNCYYTCPE 60
                                  7************666665566666666544...3444.......78************8 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0001
                        Fer4_8  4 kCieCgaCqsaCpv 17
                                   C++Cg C  +Cp 
  gi|91772636|ref|YP_565328.1| 47 GCTGCGNCYYTCPE 60
                                  47777777777764 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   1.0    0.0011       1.3      83      97 ..      10      24 ..       5      44 .. 0.67
   2 ?    9.1   0.3    0.0013       1.4      56      77 ..      42      64 ..      28      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                       Fer4_18 83 leciscllcidacdk 97
                                  lec  c +ci ac k
  gi|91772636|ref|YP_565328.1| 10 LECKGCERCIPACPK 24
                                  455555555555543 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                       Fer4_18 56 kgagd.cidcescvkvcPtgidi 77
                                  + +g+ c+ c+ c   cP  + i
  gi|91772636|ref|YP_565328.1| 42 EYKGEgCTGCGNCYYTCPETLAI 64
                                  444433************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 515.14
//
Query:       gi|91772637|ref|YP_565329.1|  [L=534]
Description: AMP-dependent synthetase and ligase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-74  250.6   0.0    5.3e-74  249.3   0.0    1.6  2  AMP-binding    AMP-binding enzyme
    8.5e-18   65.1   0.8    1.7e-17   64.2   0.8    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.3   0.0   5.9e-78   5.3e-74       3     422 ..      41     456 ..      39     457 .. 0.83
   2 ?   -1.7   0.0     0.094   8.4e+02     359     386 ..     484     511 ..     476     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: 249.3 bits;  conditional E-value: 5.9e-78
                                   HHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                   AMP-binding   3 eqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                   + a ++pdk+alv+   +g    +T+++l++ ++++A+ +++ G++kgd+V++ l+ ++e+ + +la+ k+Gav+ p    
  gi|91772637|ref|YP_565329.1|  41 RYAMEQPDKRALVWcddNGNELVYTFKDLKHYSDKAANLFKKYGIEKGDVVMLTLKGRYEFWICILALHKIGAVALPATHM 121
                                   67889*********9887777789********************************************************* PP

                                   S-HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-..HCCHCCCHCCCCSCTTS...-TSCCCS CS
                   AMP-binding  81 ltaeelayiledseakvliatvdsel.leklleaaakleavklvivldadel..lkeeelkeeeeseekae...kpeeeee 155
                                   lt +++ y +e s++k+++   d+e  +  ++e +    +  + i+l++++l   +e +l++++e ee++    +pe e++
  gi|91772637|ref|YP_565329.1| 122 LTTKDVTYRIELSNIKMVV-SADDEGlMGYIDEGH----KGYEDILLHKASLngGREGWLDFTKELEEASAdftRPEGEAA 197
                                   *******************.333333233332222....222333333222200233444444444433313444666778 PP

                                   -BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSC.CTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-T CS
                   AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfk.lkeddvvlsilplahifglilelllallsGatvvllp 235
                                   +k++++a++ ++SGTTG PK V++  ++ +  + ++k   +++ +++d   l++++  ++  +   l++  +sG +v +++
  gi|91772637|ref|YP_565329.1| 198 TKNEEIALLYFSSGTTGLPKMVQHDFAYPLGHIITAK---YWQnVRDDGLHLTVADSGWAKCVWGKLYGQWISGTAVFVYD 275
                                   999**************************99999975...54425444455999******999788999999998888888 PP

                                   TCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEE CS
                   AMP-binding 236 kdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegY 315
                                     +++d+k +le+ +k++vt+++++P++++ l++ +  l+    ++d+ssl++++++gepl+pe+ ++f + +g +++eg+
  gi|91772637|ref|YP_565329.1| 276 -YERFDAKNMLEFASKYGVTTFCAPPTIYRFLIKeD--LS----QYDFSSLEYCVVAGEPLNPEVYERFLEFTGLKLMEGF 349
                                   .5567989999*********************9944..33....45***************************99****** PP

                                   EEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET.....TS-SEBTT-HHHHHHHEEE CS
                   AMP-binding 316 GlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp.....gvmkgYlkkpeataeafds 391
                                   G+TE  + +++ p +e+  k+gs Gkp p+ ++++++ +  e +  geeGe+++        g++ gY  ++++t+e++  
  gi|91772637|ref|YP_565329.1| 350 GQTESIVSIATYPWMEP--KPGSMGKPSPEYDIELLNLD-DEVCDFGEEGEIVINTSkgktvGLFAGYRSDEKKTNEVWH- 426
                                   ********975444555..8*****************99.999**********9877666778***************97. PP

                                   TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 392 egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                    +++++TGD+++ dedGy+++vgR++d+ik+
  gi|91772637|ref|YP_565329.1| 427 -DGYYHTGDMAWKDEDGYFWFVGRSDDIIKS 456
                                   .57**************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.094
                                   EETTSEEEEEEEETTS-SEBTT-HHHHH CS
                   AMP-binding 359 vpdgeeGellvrgpgvmkgYlkkpeata 386
                                   vpd + G+++     ++kgY   +e+ +
  gi|91772637|ref|YP_565329.1| 484 VPDATRGQIVKATIVLAKGYVASEELKK 511
                                   788999**************99977765 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 !   64.2   0.8   1.8e-21   1.7e-17       1      67 [.     465     534 .]     465     534 .] 0.93

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.8e-21
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvd 67 
                                   evEsal++hpaV e+a+ Gvpd+++G++++a +vl++g    e+l+++L++hv+k+ +py+ p++v fvd
  gi|91772637|ref|YP_565329.1| 465 EVESALIEHPAVLECAITGVPDATRGQIVKATIVLAKGyvAsEELKKQLQDHVKKATAPYKYPRAVDFVD 534
                                   8**********************************889642345************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 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:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3439.87
//
Query:       gi|91772638|ref|YP_565330.1|  [L=184]
Description: cupin sensor transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-16   60.1   0.0    1.8e-16   59.6   0.0    1.3  1  Cupin_2          Cupin domain
    6.3e-06   26.1   0.0    1.9e-05   24.6   0.0    1.8  2  HTH_19           Helix-turn-helix domain
    8.6e-06   25.7   0.0    1.3e-05   25.2   0.0    1.3  1  HTH_3            Helix-turn-helix
    0.00024   21.0   0.0    0.00033   20.6   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0023   17.8   0.0     0.0038   17.1   0.0    1.3  1  AraC_binding     AraC-like ligand binding domain
     0.0031   17.8   0.0     0.0046   17.3   0.0    1.2  1  HTH_31           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.2   0.0      0.042   13.5   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
      0.067   13.0   0.0       0.12   12.2   0.0    1.4  1  EutQ             Ethanolamine utilisation protein EutQ
      0.075   12.6   0.0       0.13   11.9   0.0    1.4  1  Cupin_1          Cupin


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0     9e-20   1.8e-16      12      70 ..     124     182 ..     111     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 9e-20
                                   EEEC.SSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2  12 pshr.HpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                   ps + Hpg+ ef yV++G++++++ ++e++le+Gds+yf+++  H+++  gdepa++l +
  gi|91772638|ref|YP_565330.1| 124 PSMNsHPGQ-EFDYVISGTLKVWIHDNEIILEEGDSIYFDSNFAHAMEAVGDEPAKFLAM 182
                                   44444****.***********************************************975 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   9.6e-09   1.9e-05       2      64 ..      10      71 ..       9      72 .. 0.96
   2 ?   -2.0   0.0       1.9   3.8e+03      33      62 ..     155     182 ..     146     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9.6e-09
                        HTH_19  2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqged 64
                                   r+ e+Re   +++e +ae+lgis   + ++ +g++ +++a++l  i+++l++d   ll+ge+
  gi|91772638|ref|YP_565330.1| 10 SRISELRELSDIGLETMAEKLGISVDAYKQYDSGES-DIPASMLFEISQILNVDMGLLLTGEE 71
                                  5999********************************.999*******************9985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                        HTH_19  33 Engkkdvpsaelllkiaealgidleyllqg 62 
                                   E++++ ++  +++ ++ ea+g ++  +l +
  gi|91772638|ref|YP_565330.1| 155 EGDSI-YF-DSNFAHAMEAVGDEPAKFLAM 182
                                   33355.66.488888899999887777765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   6.3e-09   1.3e-05       1      54 [.      12      65 ..      12      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.3e-09
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                  + elR+  ++ +e +AeklG+s+ ++ ++ +Ge+ +  ++l+++++ L+v++  
  gi|91772638|ref|YP_565330.1| 12 ISELRELSDIGLETMAEKLGISVDAYKQYDSGESDIPASMLFEISQILNVDMGL 65
                                  568999999999***************************************976 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.6e-07   0.00033      83     131 ..     130     178 ..      92     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.6e-07
               MannoseP_isomer  83 hraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiple 131
                                      e   v++Gt kv ++d++++l+e +s+y   +  h++e  G  p +
  gi|91772638|ref|YP_565330.1| 130 PGQEFDYVISGTLKVWIHDNEIILEEGDSIYFDSNFAHAMEAVGDEPAK 178
                                   34577789***********************************998866 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.9e-06    0.0038      17      70 ..     125     178 ..     116     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-06
                                   EEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEE CS
                  AraC_binding  17 pphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgwe 70 
                                   + + h+  ++ yv++Gt ++++ +++  l++Gd + +  +  H +e+ ++++ +
  gi|91772638|ref|YP_565330.1| 125 SMNSHPGQEFDYVISGTLKVWIHDNEIILEEGDSIYFDSNFAHAMEAVGDEPAK 178
                                   55899*******************************************998876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06    0.0046       2      58 ..       8      63 ..       7      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                        HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldp 58
                                  ++ +  +lRe + + +e +Ae lg+s++ + ++ +G+ +  + + l  + ++l++d 
  gi|91772638|ref|YP_565330.1|  8 IASRISELRELSDIGLETMAEKLGISVDAYKQYDSGESD-IPASMLFEISQILNVDM 63
                                  5778889*******************************8.77************996 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 ?   13.5   0.0   2.1e-05     0.042      26      62 ..     132     167 ..     125     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                   EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEE CS
                       Cupin_3  26 dEfcyileGevkvtpeggetvelraGDlvvlpkglsg 62 
                                   +Ef y+++G  kv   + +++ l++GD++++  ++  
  gi|91772638|ref|YP_565330.1| 132 QEFDYVISGTLKVWI-HDNEIILEEGDSIYFDSNFAH 167
                                   8999***********.***************988765 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.8e-05      0.12      96     128 ..     132     164 ..     118     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                          EutQ  96 deidyvieGrldvlidGrkvvaeaGdviliPkg 128
                                    e dyvi G l+v i  ++++ e Gd i+   +
  gi|91772638|ref|YP_565330.1| 132 QEFDYVISGTLKVWIHDNEIILEEGDSIYFDSN 164
                                   699***********************9987655 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.3e-05      0.13      59     110 ..     136     180 ..     113     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                                   EEEESEEEEEEEETTSS.EEEEEE...EETTEEEEE-TT-EEEEEEESSSSEEEE CS
                       Cupin_1  59 yvlqGegrvgfvvpgngnrdfhkk...lreGdvfvvPaglvhfqynsgdepavai 110
                                   yv+ G++ v +            +   l+eGd +++ ++++h++ + gdepa  +
  gi|91772638|ref|YP_565330.1| 136 YVISGTLKVWIHD----------NeiiLEEGDSIYFDSNFAHAMEAVGDEPAKFL 180
                                   5555555533322..........22349**********************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1162.12
//
Query:       gi|91772639|ref|YP_565331.1|  [L=463]
Description: hypothetical protein Mbur_0610 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   33.0   0.7      0.035   14.3   0.1    4.0  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
    2.4e-05   24.4   1.1        2.4    8.2   0.0    4.4  4  DUF916       Bacterial protein of unknown function (DUF916)
    0.00068   20.3   2.7       0.64   10.7   0.4    4.2  3  fn3_5        Fn3-like domain
     0.0015   18.7   0.4       0.22   11.7   0.1    3.3  3  FixG_C       IG-like fold at C-terminal of FixG, putative oxi
     0.0059   17.2   3.2        2.6    8.6   0.0    2.8  3  DUF1735      Domain of unknown function (DUF1735)
  ------ inclusion threshold ------
      0.015   15.3   0.5        0.2   11.7   0.0    2.8  2  BACON        Putative binding domain, N-terminal
      0.018   15.2   0.1        2.1    8.5   0.0    2.6  2  fn3_6        Fibronectin type-III domain
       0.04   14.2   0.2        1.2    9.4   0.0    2.5  2  CBM_4_9      Carbohydrate binding domain
      0.048   14.0   0.0          3    8.2   0.1    3.4  2  DUF11        Domain of unknown function DUF11
      0.053   13.9   0.1       0.39   11.2   0.0    2.3  2  MG1          Macroglobulin domain MG1
      0.073   13.4   0.4       0.23   11.8   0.4    1.8  1  A2M_BRD      Alpha-2-macroglobulin bait region domain
      0.078   13.3   0.2        2.3    8.5   0.2    2.6  2  DUF4352      Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   6.6e-05     0.098       2      70 ..      92     164 ..      91     169 .. 0.76
   2 !   14.3   0.1   2.4e-05     0.035      45      67 ..     263     286 ..     255     295 .. 0.82
   3 ?   -1.7   0.0       2.5   3.7e+03      59      73 ..     445     458 ..     424     459 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                   NPCBM_assoc   2 epGetvtltltvtndgtaaat...nvslsls....lPeGWtvvevspasaaslapGetveatvkVtppagaaaGdy 70 
                                   +pGe+ ++t++++n+g++++t   +v  ++     l e+W   ++spa+a +l+ Ge++e+t+kV++p++a+   y
  gi|91772639|ref|YP_565331.1|  92 KPGESDEMTVVLFNHGKEPLTlepHVAPKVFsdnmLDEDWV--TISPAKA-ELRSGEKQEFTIKVSVPEDAELDSY 164
                                   68888888888888888888766666666542222578898..8889886.6*******************86555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.4e-05
                   NPCBM_assoc  45 a.slapGetveatvkVtppagaaa 67 
                                   +  +++Ge++++tvkV++pa+a+ 
  gi|91772639|ref|YP_565331.1| 263 PsVIKAGEKATVTVKVRVPADAEG 286
                                   3489******************83 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.5
                   NPCBM_assoc  59 VtppagaaaGdyevt 73 
                                   +  p ++++++y v 
  gi|91772639|ref|YP_565331.1| 445 I-MPHNTENFEYSVN 458
                                   3.5899999999986 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0016       2.4      17      50 ..      85     118 ..      82     129 .. 0.88
   2 ?    3.1   0.0     0.063        94      80     106 ..     131     158 ..     123     162 .. 0.85
   3 !    6.7   0.4    0.0048       7.2      82     118 ..     259     294 ..     192     295 .. 0.68
   4 ?   -3.5   0.0         7     1e+04      19      34 ..     441     456 ..     422     459 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                        DUF916  17 sYFdLkvkpgqeqelevkikNssdkeitveitvn 50 
                                   +Y  L++kpg+++e++v + N+ ++++t+e  v 
  gi|91772639|ref|YP_565331.1|  85 GYSYLRIKPGESDEMTVVLFNHGKEPLTLEPHVA 118
                                   67889***********************997765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.063
                        DUF916  80 lvkip.keitlpakesktvklkikmPke 106
                                    v+i+  + +l  +e++++++k+++P++
  gi|91772639|ref|YP_565331.1| 131 WVTISpAKAELRSGEKQEFTIKVSVPED 158
                                   5666668999****************97 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0048
                        DUF916  82 kipkeitlpakesktvklkikmPkeefdGvilGGiyv 118
                                   +i+    ++a+e+ tv++k+ +P+++ +G + G i++
  gi|91772639|ref|YP_565331.1| 259 TITAPSVIKAGEKATVTVKVRVPADA-EGNLNGRINL 294
                                   34444568999999999999999976.8888887765 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 7
                        DUF916  19 FdLkvkpgqeqelevk 34 
                                   + L++ p +++++e  
  gi|91772639|ref|YP_565331.1| 441 WTLEIMPHNTENFEYS 456
                                   4444445554444443 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.015        23      57      87 ..     130     160 ..      89     181 .. 0.65
   2 !   10.7   0.4   0.00043      0.64      14      98 ..     221     327 ..     212     336 .. 0.60
   3 ?   -3.2   0.0         9   1.3e+04       8      25 ..     353     370 ..     349     387 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                         fn3_5  57 aaltfetskvtvpAnssktvtvtldlpsdak 87 
                                     +t +++k  ++ ++++++t+++++p+da+
  gi|91772639|ref|YP_565331.1| 130 DWVTISPAKAELRSGEKQEFTIKVSVPEDAE 160
                                   3566677777777777777777777777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00043
                         fn3_5  14 ltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldlpsdakk...... 88 
                                   ++lkN+ +ka +++ + +      + ++e + + ++ s+  +e+ +t ++++v ++A++++tvtv++ +p da+       
  gi|91772639|ref|YP_565331.1| 221 IKLKNVADKAISINPEFE------VSENEWYGYSAQVSL--DEKDVTITAPSV-IKAGEKATVTVKVRVPADAEGnlngri 292
                                   566666666555554444......222333333333333..335677777775.899999999999999887776555555 PP

                         fn3_5  89 .........................kngyfveGfv 98 
                                                            ++++f  Gfv
  gi|91772639|ref|YP_565331.1| 293 nlniddrtmnewsqkvnmnldvwqqPEDPFTTGFV 327
                                   55555566666666666666666666666666666 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9
                         fn3_5   8 dkfsftltlkNtsnkalt 25 
                                   +  +f++ lkN + + ++
  gi|91772639|ref|YP_565331.1| 353 TAPTFDVVLKNADGQVKS 370
                                   456788888887665555 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0         1   1.5e+03      67      84 ..      87     104 ..      73     122 .. 0.81
   2 ?    2.7   0.0     0.096   1.4e+02      68      90 ..     138     160 ..     123     176 .. 0.68
   3 !   11.7   0.1   0.00015      0.22      50     104 ..     250     298 ..     211     313 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                                   -EEEE-TT-EEEEEEEEE CS
                        FixG_C  67 keitvapgekrkvpvfvr 84 
                                   + ++++pge+ +++v++ 
  gi|91772639|ref|YP_565331.1|  87 SYLRIKPGESDEMTVVLF 104
                                   668999******999986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.096
                                   EEEE-TT-EEEEEEEEEE-GGG- CS
                        FixG_C  68 eitvapgekrkvpvfvrvpaeal 90 
                                   + ++ +gek+++++ v+vp++a+
  gi|91772639|ref|YP_565331.1| 138 KAELRSGEKQEFTIKVSVPEDAE 160
                                   45667777777777777777663 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00015
                                   EEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEG CS
                        FixG_C  50 tlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvtdd 104
                                   ++s++ ++++++    +++  +++gek +v+v vrvpa+a+ + +  i++ + dd
  gi|91772639|ref|YP_565331.1| 250 QVSLD-EKDVTI----TAPSVIKAGEKATVTVKVRVPADAEGNLNGRINLNI-DD 298
                                   22222.123444....466779****************99554444666665.33 PP

>> DUF1735  Domain of unknown function (DUF1735)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0018       2.6      67     103 ..     126     162 ..      95     171 .. 0.85
   2 !    8.3   0.4    0.0023       3.5      31      98 ..     219     282 ..     199     298 .. 0.69
   3 ?   -3.3   0.0       8.7   1.3e+04      16      33 ..     416     431 ..     406     457 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                                   E--GGGEEE.GCGCEEECCGGTEEEEEEEEE--TT-- CS
                       DUF1735  67 llPeeyytlpsstvtikaGeessasveiklkplekld 103
                                   +l+e+ +t+++ +  + +Ge++  ++++++ ++ +ld
  gi|91772639|ref|YP_565331.1| 126 MLDEDWVTISPAKAELRSGEKQEFTIKVSVPEDAELD 162
                                   9*********************9******99955555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                                   EEEEECC--TT-EEEEEEE-CHHHCCHCCCCT--.EE--GGGEEE.GCGCEEECCGGTEEEEEEEEE- CS
                       DUF1735  31 ltvylsgsnpkdvtvtlevdeslldeyNaangtnykllPeeyytlpsstvtikaGeessasveiklkp 98 
                                   + ++l +  +k ++++ e + s  + y   + ++   l+e+ +t+ +   +ikaGe+++ +v++ + +
  gi|91772639|ref|YP_565331.1| 219 YVIKLKNVADKAISINPEFEVSENEWYG--YSAQ-VSLDEKDVTI-TAPSVIKAGEKATVTVKVRVPA 282
                                   5555555555555555555555555563..1222.499*******.699******9999999999887 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.7
                                   ECEEECEESSECEEEEEE CS
                       DUF1735  16 lsltlddlgeektieltv 33 
                                    +++++++g++  ++ +v
  gi|91772639|ref|YP_565331.1| 416 EQFNVYQQGST--TYMEV 431
                                   44444411221..22333 PP

>> BACON  Putative binding domain, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013       0.2       8      41 ..     128     172 ..     116     180 .. 0.85
   2 ?   -0.1   0.4      0.64   9.6e+02      38      50 ..     259     276 ..     236     280 .. 0.44

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                         BACON   8 dadWltvspas...........tltvtvaaNtsgeeRtatitvta 41 
                                   d+dW+t+spa+           t++v+v +  + +++ a++ ++ 
  gi|91772639|ref|YP_565331.1| 128 DEDWVTISPAKaelrsgekqefTIKVSVPEDAELDSYDANVFFSD 172
                                   889****998899999999*9999999999998888999998875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.64
                         BACON  38 tvta.....gsgegtvtV 50 
                                   t+ta     ++++ tvtV
  gi|91772639|ref|YP_565331.1| 259 TITApsvikAGEKATVTV 276
                                   333333332223333444 PP

>> fn3_6  Fibronectin type-III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0014       2.1      47      88 ..     132     172 ..      97     179 .. 0.86
   2 ?    4.0   0.0     0.038        57      33      78 ..     245     287 ..     210     307 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                         fn3_6  47 vtVePseLefsekgekksftvtvtakksaesevsfGsltWsd 88 
                                   vt++P++ e++ +gek++ft++v++ ++ae +   +++ +sd
  gi|91772639|ref|YP_565331.1| 132 VTISPAKAELR-SGEKQEFTIKVSVPEDAELDSYDANVFFSD 172
                                   99*********.*************99888776666666666 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.038
                         fn3_6  33 atYkakveapegvkvtVe.PseLefsekgekksftvtvtakksaese 78 
                                     Y+a+v+  e  +vt++ Ps++   ++gek+++tv+v++ ++ae++
  gi|91772639|ref|YP_565331.1| 245 YGYSAQVSLDE-KDVTITaPSVI---KAGEKATVTVKVRVPADAEGN 287
                                   56777776653.34444315544...467999999999999877655 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.016        25      51     132 ..     203     280 ..     174     283 .. 0.76
   2 ?    9.4   0.0   0.00081       1.2      57     132 ..     264     340 ..     257     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                                   EEEEEECCS-TT-EEEEEEEEEESSTSEEEEEEEEEESSTTSCTCEEEEEEEEEESTSEEEEEEEEE-SSCSCCEEEEEEE CS
                       CBM_4_9  51 qaiditirlekgktYtvsfwvkassgksrtikvkigdtdadganydevadekvelkgewktlegtFtipkstdenvelyve 131
                                   +   i++r+e g +Y+  ++ k +++  + i++  + + + +++++ + + +v l+ + +t+++  +i+ + + +v++ v 
  gi|91772639|ref|YP_565331.1| 203 FNSYINDRVEAGLEYEYVIKLKNVAD--KAISINPEFEVS-ENEWYGYSA-QVSLDEKDVTITAPSVIKAGEKATVTVKVR 279
                                   55557899********9999999999..777777777766.469999998.999999999999998888666666666655 PP

                                   E CS
                       CBM_4_9 132 l 132
                                   +
  gi|91772639|ref|YP_565331.1| 280 V 280
                                   5 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00081
                                   CCS-TT-EEEEEEEEEESSTSEEEEEEEEEESSTTSCTCEEEEEEEEEES.TSEEEEEEEEE-S..SCSCCEEEEEEEE CS
                       CBM_4_9  57 irlekgktYtvsfwvkassgksrtikvkigdtdadganydevadekvelk.gewktlegtFtip..kstdenvelyvel 132
                                   + ++ g++ tv ++v+  ++ + +++  i  + +d  ++ + + +kv++  + w++ e  Ft++    td+ v+l++ +
  gi|91772639|ref|YP_565331.1| 264 SVIKAGEKATVTVKVRVPADAEGNLNGRINLNIDD--RTMNEWSQKVNMNlDVWQQPEDPFTTGfvARTDDPVTLRIIS 340
                                   66777777777777777777779999999999996..66666666777777*************999999999998877 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.29   4.4e+02      61      61 ..     133     133 ..      82     166 .. 0.54
   2 ?    8.2   0.1     0.002         3      55      85 ..     256     287 ..     204     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.29
                         DUF11  61 v 61 
                                   +
  gi|91772639|ref|YP_565331.1| 133 T 133
                                   1 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.002
                         DUF11  55 asaltsvgsL.eagesatlsftvrvtrtaasg 85 
                                    +++ +++s+ +age+at++++vrv++ a+ +
  gi|91772639|ref|YP_565331.1| 256 KDVTITAPSViKAGEKATVTVKVRVPADAEGN 287
                                   344444444449***************99987 PP

>> MG1  Macroglobulin domain MG1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.3   1.9e+03      46      76 ..     133     163 ..     116     170 .. 0.77
   2 ?   11.2   0.0   0.00026      0.39       4      37 ..     258     294 ..     255     318 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.3
                                   EEEEEEEEESTTTTTEEEEEEEB-SGCSSSS CS
                           MG1  46 elasesvtLnsdnnfqalvkikippkdlkkd 76 
                                   +++ ++++L+s+++   ++k+ +p++  +++
  gi|91772639|ref|YP_565331.1| 133 TISPAKAELRSGEKQEFTIKVSVPEDAELDS 163
                                   5667788888999988999999998855544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00026
                                   EEEEEESSEETTSEEEEEEEEES...-SS-EEEEEEE CS
                           MG1   4 ylltaPnvlrvgseetivveahg...ltkeveVtitv 37 
                                    ++taP+v+++g + t++v++     ++++++ +i++
  gi|91772639|ref|YP_565331.1| 258 VTITAPSVIKAGEKATVTVKVRVpadAEGNLNGRINL 294
                                   68*****************997642244444433333 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00016      0.23       1     123 [.     132     279 ..     132     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                   -EEEESSSS--TTSEEEEEEE-SS-.EE-TT-.........BSS..-----.-S...S....-EEEEEE--TT-----EE. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.....xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       A2M_BRD   1 lqispdkeeykvGetakltvkstfa.tverdstl.....ylvls..rgnivssgekveeidsstsfsfpvtadmaPnarv. 72 
                                   ++isp k+e++ Ge++++t+k + +   e    l      +++s   g++  s  +    ++   ++++v+  + Pn+++ 
  gi|91772639|ref|YP_565331.1| 132 VTISPAKAELRSGEKQEFTIKVSVPeDAE----LdsydaNVFFSdlEGDV--SALY--PGYNG-ALELSVNVWLPPNIQIf 203
                                   589*******************9875233....22322334444333444..3322..23445.999999999999****6 PP

                                   EEEE..E-................................-CEEEEEEE----.-GGGB-EEEEEEE...-SSSEEEEEEE CS
                                   xxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       A2M_BRD  73 vvyyirrd................................gevvadsvqlpvekdfenklsvslesynetrPgeevtlkvk 121
                                    +y+  +d                                +e+   s+q++ +   e+ ++++    +  + ge++t++vk
  gi|91772639|ref|YP_565331.1| 204 NSYI--NDrveagleyeyviklknvadkaisinpefevseNEWYGYSAQVSLD---EKDVTITA--PSVIKAGEKATVTVK 277
                                   6666..4458999*************999999999999999999999999999...56677766..557899*99999998 PP

                                   .. CS
                                   xx RF
                       A2M_BRD 122 as 123
                                    +
  gi|91772639|ref|YP_565331.1| 278 VR 279
                                   54 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.2   3.1e+02      48     107 ..     105     159 ..      98     172 .. 0.54
   2 ?    8.5   0.2    0.0015       2.3      44     109 ..     221     286 ..     199     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.2
                                   E-SSS-EEEEGG.GEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEEEEEEEEESTT- CS
                       DUF4352  48 Nkgkealtvnss.qfkLkdgdgkeydadlsasskaddlflgtlnpGkkvtGklvFdvpkgk 107
                                   N+gke+lt+++    k+++++  + d d  + s a    + +l++G+k + ++   vp+++
  gi|91772639|ref|YP_565331.1| 105 NHGKEPLTLEPHvAPKVFSDN--MLDEDWVTISPA----KAELRSGEKQEFTIKVSVPEDA 159
                                   666666666555455555333..444444444444....2355555555555555555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                                   EEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB.--EEEE-TT-EEEEEEEEEESTT-CG CS
                       DUF4352  44 vtvkNkgkealtvnssqfkLkdgdgkeydadlsasskadd.lflgtlnpGkkvtGklvFdvpkgkkk 109
                                   +++kN  ++a+++n+  f++ +++ + y+a++s ++k+ +    + +++G+k t ++   vp ++++
  gi|91772639|ref|YP_565331.1| 221 IKLKNVADKAISINP-EFEVSENEWYGYSAQVSLDEKDVTiTAPSVIKAGEKATVTVKVRVPADAEG 286
                                   799**********98.7999999999999999998888878999*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3197.90
//
Query:       gi|91772640|ref|YP_565332.1|  [L=160]
Description: hypothetical protein Mbur_0611 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   57.4   0.2    1.3e-15   57.1   0.2    1.1  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 !   57.1   0.2   7.5e-20   1.3e-15      86     195 ..      40     147 ..      27     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 7.5e-20
                       S-layer  86 saetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dsty 165
                                   +++++ d++++ +e L++  +  +++++l++g++++L ++Y+l +kqiD++g ++wle++++g++vd++v++ s++  s +
  gi|91772640|ref|YP_565332.1|  40 DFSEHPDEEIIPHEVLREQTFSFSDSYVLSTGETFKLPDNYNLIPKQIDIEGRRAWLEVSRNGDFVDDQVLTISDDlGSGW 120
                                   334555788888888888888889*************************************************66665555 PP

                       S-layer 166 vyekdlgded.dvviiavhvdevfrgtedsl 195
                                       d+ +ed + +++ +++++v++++ ds+
  gi|91772640|ref|YP_565332.1| 121 ----DVYSEDgNQLMFRIYLHDVYQNKIDSV 147
                                   ....444444257899999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1143.43
//
Query:       gi|91772641|ref|YP_565333.1|  [L=942]
Description: copper-translocating P-type ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  182.9   5.2    3.9e-54  182.9   5.2    2.1  2  E1-E2_ATPase   E1-E2 ATPase
    2.7e-51  171.9   4.2    1.1e-16   61.0   0.4    3.9  3  HMA            Heavy-metal-associated domain
    7.9e-48  163.5   5.6    1.9e-47  162.3   5.6    1.7  1  Hydrolase      haloacid dehalogenase-like hydrolase
    9.2e-07   28.8   5.4    5.7e-05   23.0   1.4    2.7  3  Hydrolase_3    haloacid dehalogenase-like hydrolase
     0.0021   18.2   0.4        6.5    7.0   0.0    4.5  4  Poly_export    Polysaccharide biosynthesis/export protein
  ------ inclusion threshold ------
      0.014   15.5   0.1        6.6    6.9   0.0    3.1  3  Tox-PL-2       Papain fold toxin 2
      0.039   14.1   0.4        7.2    6.9   0.1    3.1  3  DUF3213        Protein of unknown function (DUF3213)
       0.06   13.4   0.3       0.23   11.6   0.3    2.1  1  DUF1206        Domain of Unknown Function (DUF1206)
      0.075   13.4   0.0       0.55   10.6   0.0    2.3  1  HAD            haloacid dehalogenase-like hydrolase
       0.16   12.0   2.6        7.4    6.7   0.1    3.8  3  Thioredoxin_3  Thioredoxin domain
        4.7    7.3   7.5         13    5.9   7.5    1.6  1  DUF997         Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       2.6   4.3e+03     122     160 ..     289     330 ..     269     331 .. 0.51
   2 !  182.9   5.2   2.4e-57   3.9e-54       2     180 ..     415     606 ..     414     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHHHHS- CS
                  E1-E2_ATPase 122 lvpvvlliallvflialllgksla...eallralallvaaiP 160
                                   l++ + l ++ + + ++l++ +++   +++l++l+++v+a P
  gi|91772641|ref|YP_565333.1| 289 LTIPIALGGMSAGFPQYLYFVPPIladRMVLFILTTIVMAFP 330
                                   222222223333333333444444577888888888888877 PP

  == domain 2  score: 182.9 bits;  conditional E-value: 2.4e-57
                                   SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEE CS
                  E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeak 82 
                                   l+++ta+vir+++e+e++++++v GDiv++++g++ p+Dg++veg++++des++ GEs pvek++gd+v++ tv+  g++k
  gi|91772641|ref|YP_565333.1| 415 LQARTARVIRNDEEVEVAVEDVVAGDIVVVRPGEKLPVDGIVVEGTSSIDESMISGESIPVEKNAGDTVIGATVNATGSFK 495
                                   7899***************************************************************************** PP

                                   EEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.............HHHHH CS
                  E1-E2_ATPase  83 avVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.............eallr 150
                                   +++t++g dt l++i++lve+a+ +k+p+q+ +d +++ ++++v++ia++ f++++++g +l              ++ll 
  gi|91772641|ref|YP_565333.1| 496 FKATKVGADTALAQIIKLVEDAQTSKAPIQRVADFVAGRFIVTVIAIAVISFMFWFFIGYGLYdvaqysvisspflFSLLI 576
                                   *********************************************************9999999999999*********** PP

                                   HHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                  E1-E2_ATPase 151 alallvaaiPcaLplavplalalgarrlak 180
                                   ++++lv+++Pca +la+p+a+++g+++ a+
  gi|91772641|ref|YP_565333.1| 577 GITVLVISCPCAVGLATPVAIMVGTGKGAE 606
                                   **************************9987 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.4   6.7e-20   1.1e-16       2      62 .]       5      65 ..       4      65 .. 0.96
   2 !   55.6   0.1   3.3e-18   5.4e-15       1      61 [.     126     186 ..     126     187 .. 0.96
   3 !   54.5   0.0     7e-18   1.1e-14       2      62 .]     195     255 ..     194     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 6.7e-20
                           HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                  ++v gm+C +C  +v+k++s+l+gVesv+v+l+++ +tV +d+e+++l++i +ai  +gy+
  gi|91772641|ref|YP_565333.1|  5 IDVLGMTCMHCHERVTKAISALKGVESVDVSLEENNATVIFDPEKVSLEEIEQAILGLGYE 65
                                  5788*******************************************************96 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 3.3e-18
                           HMA   1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaes.tklrkiieaiekagy 61 
                                   t++v gm+Ca+Ca ++e++L++ +gV sv+v+l   ++ V++d+   t+ +k+ +++e++gy
  gi|91772641|ref|YP_565333.1| 126 TLKVTGMTCAACAIRIEDALKKQSGVLSVTVNLPLEKASVTYDPQLfTT-EKLEKTVEDTGY 186
                                   6899******************************************666.***********9 PP

  == domain 3  score: 54.5 bits;  conditional E-value: 7e-18
                           HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                   ++v gm+Ca+Ca  +e++L++l+gV++++v++  +t+  ++d+++++  + ++aie++gy+
  gi|91772641|ref|YP_565333.1| 195 FDVGGMTCAACATNIERALKKLDGVSDASVNFPMSTARAKYDPDKVSAADMLKAIEEIGYT 255
                                   89*******************************************999***********95 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.3   5.6   1.2e-50   1.9e-47       2     210 .]     624     840 ..     623     840 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 1.2e-50
                                   SEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE...... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx...... RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakar...sgaltgfatfigrg...... 67 
                                    t+vfDk+GTLt+g+p+++dvi          l+laa  e gsehp+g+a+v+ a +      ++t f  ++g+g      
  gi|91772641|ref|YP_565333.1| 624 GTIVFDKTGTLTEGKPVLTDVITFGdhsrdeVLSLAATAEKGSEHPLGEAIVNGAVDSnvdILDTTAFDSIPGHGvtatid 704
                                   69***********************77777777777777777****************6655555**************** PP

                                   ..HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESS CS
                                   ..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  68 ..ayaigkpewltal.dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvlltgd 143
                                     +++ g +++++++    + + +a ++++ qg+t++l+  +++a +++++ad+  +k   ++av +Lk++gievv++tgd
  gi|91772641|ref|YP_565333.1| 705 grKVLLGTRKLMADNnVDVSGMTDALEELELQGKTAMLVsaDGNAIGIVAVADT--LKRNSVQAVSKLKSMGIEVVMMTGD 783
                                   ***************988899999***************8899***********..************************* PP

                                   EHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 144 npetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   n++ta ++a+++G           i+   ++++pe+k a +++Lq + + vamVGDg+nDa+al +A+
  gi|91772641|ref|YP_565333.1| 784 NSRTASAIASEAG-----------IDRvLSEVLPEDKAAEVKKLQKENKIVAMVGDGINDAPALTQAD 840
                                   *************...........6666*****************99999****************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 ?   -3.7   0.0       4.8   7.8e+03     204     215 ..     642     653 ..     641     655 .. 0.87
   2 !    6.8   0.0    0.0031         5      15      56 ..     758     799 ..     752     804 .. 0.89
   3 !   23.0   1.4   3.5e-08   5.7e-05     197     252 ..     814     870 ..     808     872 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.8
                                   GGEEEEESSGGG CS
                   Hydrolase_3 204 eeviafGDgeND 215
                                    +vi+fGD   D
  gi|91772641|ref|YP_565333.1| 642 TDVITFGDHSRD 653
                                   689*****9988 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0031
                                   ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                   Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                   +++ ++++a+ klk+ gi+vv  TG + r+++ ++ e g+d 
  gi|91772641|ref|YP_565333.1| 758 TLKRNSVQAVSKLKSMGIEVVMMTGDNSRTASAIASEAGIDR 799
                                   5678899***************************99999985 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 3.5e-08
                                   HHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG.THHH CS
                   Hydrolase_3 197 kelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne.dGVa 252
                                   k+l+ +++ v+ +GDg ND + L++a++g+Amg +++ + + A+ v   n+  d Va
  gi|91772641|ref|YP_565333.1| 814 KKLQKENKIVAMVGDGINDAPALTQADVGIAMGAGTDVAMESAQIVLIRNDLlDVVA 870
                                   566677777999*********************************999988777776 PP

>> Poly_export  Polysaccharide biosynthesis/export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.22   3.7e+02      49      80 ..       4      35 ..       3      37 .. 0.76
   2 !    7.0   0.0     0.004       6.5      48      81 ..     125     156 ..     120     158 .. 0.83
   3 ?    3.1   0.0     0.067   1.1e+02      50      70 ..     195     215 ..     165     226 .. 0.81
   4 ?   -0.8   0.0       1.1   1.8e+03      50      80 ..     399     432 ..     390     434 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.22
                   Poly_export 49 kikvaGltveelreeieeklskylkdp.qvtVr 80
                                  ki v G+t   + e++++++s  lk + +v+V+
  gi|91772641|ref|YP_565333.1|  4 KIDVLGMTCMHCHERVTKAISA-LKGVeSVDVS 35
                                  689*****************66.3443255554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.004
                   Poly_export  48 GkikvaGltveelreeieeklskylkdpqvtVrv 81 
                                    ++kv G+t + ++ +ie++l+k  ++  ++V+v
  gi|91772641|ref|YP_565333.1| 125 TTLKVTGMTCAACAIRIEDALKK--QSGVLSVTV 156
                                   689******************99..777666665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.067
                   Poly_export  50 ikvaGltveelreeieeklsk 70 
                                     v+G+t + ++  ie++l+k
  gi|91772641|ref|YP_565333.1| 195 FDVGGMTCAACATNIERALKK 215
                                   579****************87 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.1
                   Poly_export  50 ikvaGltveelreeieekl..skyl.kdpqvtVr 80 
                                    k+ G+t e +r++i  +   ++++ +d +v V 
  gi|91772641|ref|YP_565333.1| 399 AKARGRTSEAIRKLIGLQArtARVIrNDEEVEVA 432
                                   6899*********997766544444134566665 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 ?    6.9   0.0    0.0041       6.6      12      32 ..     128     148 ..     120     177 .. 0.87
   2 ?    4.8   0.0     0.018        29      14      31 ..     198     215 ..     190     254 .. 0.84
   3 ?   -3.4   0.0       6.7   1.1e+04      25      61 ..     726     762 ..     724     777 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                      Tox-PL-2  12 rfklleCveCAaalekyLkeq 32 
                                   +++ + C +CA  +e++Lk+q
  gi|91772641|ref|YP_565333.1| 128 KVTGMTCAACAIRIEDALKKQ 148
                                   677899************998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.018
                      Tox-PL-2  14 klleCveCAaalekyLke 31 
                                     + C +CA+++e++Lk+
  gi|91772641|ref|YP_565333.1| 198 GGMTCAACATNIERALKK 215
                                   5689************97 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.7
                      Tox-PL-2  25 lekyLkeqgisGkrlklktksaedaasfilserlekq 61 
                                   ++++L+e +++Gk+  l ++  ++     + + l+++
  gi|91772641|ref|YP_565333.1| 726 MTDALEELELQGKTAMLVSADGNAIGIVAVADTLKRN 762
                                   5677888888888888877777765444455555555 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0044       7.2      35      62 ..      39      66 ..      32      80 .. 0.87
   2 ?    3.7   0.0     0.043        70       5      57 ..     130     183 ..     126     195 .. 0.78
   3 ?   -3.2   0.0       6.3     1e+04      27      47 ..     410     430 ..     405     435 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0044
                                  S--EEE--B-S-SHHHHHHHT...TT-S CS
                       DUF3213 35 kvaevvideekvnieelkkkleelkgev 62
                                   +a v++d ekv+ ee+ +++  l  ev
  gi|91772641|ref|YP_565333.1| 39 NNATVIFDPEKVSLEEIEQAILGLGYEV 66
                                  589***************9997777666 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.043
                                   -S-TTTTTHHH.HHTTTTTTTB------TTSS--EEE--B-S-SHHHHHHHT.. CS
                       DUF3213   5 tdltpekakik.qyelekdervyrvflngyakvaevvideekvnieelkkklee 57 
                                   t +t     i+    l+k+  v  v +n     a v +d +++  e+l k +e+
  gi|91772641|ref|YP_565333.1| 130 TGMTCAACAIRiEDALKKQSGVLSVTVNLPLEKASVTYDPQLFTTEKLEKTVED 183
                                   55555555554134588999999999**9999******************9986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.3
                                   -----TTSS--EEE--B-S-S CS
                       DUF3213  27 rvflngyakvaevvideekvn 47 
                                   r ++   a++a v+ ++e v+
  gi|91772641|ref|YP_565333.1| 410 RKLIGLQARTARVIRNDEEVE 430
                                   556667799999999999876 PP

>> DUF1206  Domain of Unknown Function (DUF1206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00014      0.23      31      65 ..     519     553 ..     505     555 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                       DUF1206  31 gsdgalatlleqpfGrvllglvglgllgyglwqlv 65 
                                    s++ ++++++  +Gr+++ +++++++ + +w ++
  gi|91772641|ref|YP_565333.1| 519 TSKAPIQRVADFVAGRFIVTVIAIAVISFMFWFFI 553
                                   5566679999**********************997 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.55      91     187 ..     764     836 ..     749     837 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                           HAD  91 lellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidl 171
                                   ++++++ ++ G++vv+ +g +++ + +++ e g+d+vl++                     e+k+a++++   +++++i  
  gi|91772641|ref|YP_565333.1| 764 VQAVSKLKSMGIEVVMMTGDNSRTASAIASEAGIDRVLSE----------V--------LPEDKAAEVKK--LQKENKI-- 822
                                   6777888899***********************7777777..........3........33445555555..3334444.. PP

                           HAD 172 eevvayGDspsDlpll 187
                                     v  +GD+++D p+l
  gi|91772641|ref|YP_565333.1| 823 --VAMVGDGINDAPAL 836
                                   ..66669999999987 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0045       7.4       2      34 ..       4      37 ..       3      50 .. 0.77
   2 ?    1.8   0.1      0.15   2.5e+02       3      24 ..     127     149 ..     125     167 .. 0.81
   3 ?   -0.1   0.0      0.61   9.9e+02       3      22 ..     195     215 ..     193     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0045
                                  EEEEESSSSTTCH.HHHHHHHHHCHCCTCECEEE CS
                 Thioredoxin_3  2 eikvlgpgCakCp.klekavkeaaaekgikaeve 34
                                  +i vlg +C +C+ +++ka+ ++   + +++++e
  gi|91772641|ref|YP_565333.1|  4 KIDVLGMTCMHCHeRVTKAISALKGVESVDVSLE 37
                                  799**********888888776665555665555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                                   EEEESSSSTTCH.HHHHHHHHHC CS
                 Thioredoxin_3   3 ikvlgpgCakCp.klekavkeaa 24 
                                   +kv g +Ca C  ++e a+k+  
  gi|91772641|ref|YP_565333.1| 127 LKVTGMTCAACAiRIEDALKKQS 149
                                   7999********99999988765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.61
                                   EEEESSSSTTCH.HHHHHHHH CS
                 Thioredoxin_3   3 ikvlgpgCakCp.klekavke 22 
                                   + v g +Ca C  ++e+a+k+
  gi|91772641|ref|YP_565333.1| 195 FDVGGMTCAACAtNIERALKK 215
                                   566678888888555555554 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   7.5    0.0077        13       8      61 ..     538     587 ..     532     591 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0077
                        DUF997   8 ltllltllyflwwllfaYglgskeveeyyilglPlWfflscillpilfivlvil 61 
                                     ++++++ f++w++ +Ygl   +v +y+++  P  f++s ++++ ++++ +  
  gi|91772641|ref|YP_565333.1| 538 TVIAIAVISFMFWFFIGYGLY--DVAQYSVISSP--FLFSLLIGITVLVISCPC 587
                                   456778899************..788********..888999998888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (942 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 6211.97
//
Query:       gi|91772642|ref|YP_565334.1|  [L=67]
Description: heavy metal transport/detoxification protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-19   68.0   2.3      8e-19   67.8   2.3    1.0  1  HMA            Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.043   13.9   0.2    1.5  1  Thioredoxin_3  Thioredoxin domain
      0.078   13.4   0.3          2    8.8   0.1    2.1  2  Fer2_BFD       BFD-like [2Fe-2S] binding domain


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   2.3   1.3e-22     8e-19       2      62 .]       6      66 ..       5      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.3e-22
                           HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                  ++v+gm C++C+ +vek++s++ gV+sv+vdl+++++ V++d+ +t++ +i++a+ ++gyk
  gi|91772642|ref|YP_565334.1|  6 IKVDGMSCGHCKMHVEKAISGVAGVSSVDVDLDKGEAKVSYDENATDIDAIKKAVNDSGYK 66
                                  68**********************************************************7 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   7.2e-06     0.043       2      37 ..       5      41 ..       4      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.2e-06
                                  EEEEESSSSTTCH.HHHHHHHHHCHCCTCECEEECCT CS
                 Thioredoxin_3  2 eikvlgpgCakCp.klekavkeaaaekgikaevekvt 37
                                  +ikv g +C +C+ ++eka+  +a  + ++++++k +
  gi|91772642|ref|YP_565334.1|  5 KIKVDGMSCGHCKmHVEKAISGVAGVSSVDVDLDKGE 41
                                  79999********************999999777654 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00034         2      35      49 ..      10      24 ..       2      25 .. 0.81
   2 ?    2.8   0.0     0.025   1.5e+02      15      32 ..      44      60 ..      36      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00034
                      Fer2_BFD 35 gtgCggCrpaieeiL 49
                                  g+ Cg C+ ++e+ +
  gi|91772642|ref|YP_565334.1| 10 GMSCGHCKMHVEKAI 24
                                  677********9865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.025
                      Fer2_BFD 15 dairraglttveevkrrt 32
                                   +   +++t+++++k+++
  gi|91772642|ref|YP_565334.1| 44 VSY-DENATDIDAIKKAV 60
                                  555.57899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 486.28
//
Query:       gi|91772643|ref|YP_565335.1|  [L=306]
Description: quinolinate synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-117  389.7   1.1   8.6e-117  389.6   1.1    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 !  389.6   1.1  4.8e-121  8.6e-117       1     299 []       9     301 ..       9     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 389.6 bits;  conditional E-value: 4.8e-121
                                   HHHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT---HH CS
                          NadA   1 eeikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleagCsl 81 
                                   e+i+ lk+e +avilaHnYq++e+q+iadf+GDSl L++++ +++a+vivfcGV+FMae+a+iLspek vllp+++agC++
  gi|91772643|ref|YP_565335.1|   9 ERINILKTELDAVILAHNYQRPEVQDIADFTGDSLGLSQQVVNSDADVIVFCGVDFMAESAAILSPEKIVLLPEKDAGCPM 89 
                                   58999**************************************************************************** PP

                                   HCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH.SEEEEESS CS
                          NadA  82 admitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklgekkiilwk 162
                                   a+m++  ++++ k+++pdaavv+YvNssa +Ka sdi+cTS+na +vv++l+e++++f+PD+nLg+yva  + +k i  w+
  gi|91772643|ref|YP_565335.1|  90 AEMVDVISLDDEKKKHPDAAVVCYVNSSALIKAQSDICCTSANAIDVVNSLEEDEVIFVPDKNLGNYVAGFT-DKMIYSWD 169
                                   **********************************************************************98.668***** PP

                                   SS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TTSE CS
                          NadA 163 gaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglverlkkeapeke 243
                                   g+C++H++++ ++v ++keehpda +l+HPEc++ev+++ad v ST+++++++k+s+akefiigTe+gl++rl+ke+pek+
  gi|91772643|ref|YP_565335.1| 170 GFCPTHHQMRGHDVIKAKEEHPDALFLAHPECRTEVLDLADEVLSTTGMLNYAKKSDAKEFIIGTENGLLHRLSKENPEKK 250
                                   ********************************************************************************* PP

                                   EE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHHH CS
                          NadA 244 fialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalermle 299
                                   ++ +s+     ++C++Mk +tle++l+aLe++++  i+v+e+++ kAk+al+rml+
  gi|91772643|ref|YP_565335.1| 251 LYYVSE----FTICTNMKITTLESVLDALENMQY-VITVPEDTRLKAKEALDRMLA 301
                                   **5543....579********************9.9******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2431.16
//
Query:       gi|91772644|ref|YP_565336.1|  [L=290]
Description: cobyrinic acid a,c-diamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-14   54.3   0.0    1.8e-14   53.9   0.0    1.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    6.6e-14   51.0  13.4    1.8e-07   30.6   1.7    2.6  2  Fer4             4Fe-4S binding domain
    2.6e-09   36.9   1.0     0.0025   17.3   0.1    3.0  3  ParA             NUBPL iron-transfer P-loop NTPase
    3.8e-09   37.0   3.1    0.00077   20.0   0.3    2.5  2  Fer4_7           4Fe-4S dicluster domain
      2e-08   34.2  10.4      2e-08   34.2  10.4    2.0  1  Fer4_21          4Fe-4S dicluster domain
    3.3e-07   30.4   0.0      0.012   15.5   0.0    2.2  2  AAA_31           AAA domain
    5.7e-07   29.3  16.4    0.00014   21.8   2.3    2.5  2  Fer4_6           4Fe-4S binding domain
    1.1e-06   29.4   9.2      0.001   19.9   1.4    2.6  2  Fer4_16          4Fe-4S double cluster binding domain
    1.7e-06   28.5   1.5      0.059   13.9   0.1    2.4  2  Fer4_17          4Fe-4S dicluster domain
    3.3e-06   27.1  11.1    1.1e-05   25.4  11.5    1.7  2  Fer4_10          4Fe-4S dicluster domain
    7.6e-06   25.6   1.1       0.12   11.7   0.0    2.8  3  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    1.5e-05   25.0  11.5    0.00012   22.1  12.2    2.1  2  Fer4_9           4Fe-4S dicluster domain
    3.2e-05   23.9   0.0       0.03   14.2   0.0    2.6  3  RsgA_GTPase      RsgA GTPase
      8e-05   22.5  10.7      0.048   13.8   2.0    2.6  2  Fer4_2           4Fe-4S binding domain
     0.0001   21.9   0.5       0.23   10.9   0.7    2.3  2  PhoH             PhoH-like protein
    0.00013   22.4   0.0     0.0015   19.0   0.0    2.3  2  AAA_16           AAA ATPase domain
    0.00013   22.6   5.6      0.024   15.3   0.1    2.7  2  Fer4_15          4Fe-4S single cluster domain
    0.00056   18.2   0.0     0.0009   17.6   0.0    1.3  1  FTHFS            Formate--tetrahydrofolate ligase
    0.00097   18.9   0.1       0.73    9.5   0.1    2.3  2  IstB_IS21        IstB-like ATP binding protein
     0.0015   18.3   0.1      0.007   16.1   0.0    2.1  2  AAA_24           AAA domain
     0.0015   18.9   9.2       0.19   12.2   0.6    2.4  2  Fer4_8           4Fe-4S dicluster domain
     0.0023   18.3  11.3       0.18   12.4   1.5    2.6  2  Fer4_4           4Fe-4S binding domain
     0.0025   18.2   0.2       0.25   11.8   0.0    2.8  2  AAA              ATPase family associated with various cellul
     0.0029   16.9   2.0     0.0039   16.4   0.7    1.8  2  ArsA_ATPase      Anion-transporting ATPase
      0.003   17.8   0.0       0.22   11.8   0.0    2.3  2  AAA_22           AAA domain
     0.0031   16.8   0.2       0.68    9.1   0.0    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0044   16.8   0.9      0.091   12.5   0.2    2.5  3  AAA_30           AAA domain
     0.0054   17.2  11.1       0.13   12.8   1.9    2.6  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
     0.0089   15.8   0.0       0.51   10.1   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.019   15.0   0.2       0.28   11.2   0.2    2.1  2  DUF523           Protein of unknown function (DUF523)
       0.02   15.4   0.2       0.52   10.8   0.2    2.7  2  ABC_tran         ABC transporter
      0.029   15.3  17.0       0.28   12.2   2.6    2.6  2  Fer4_3           4Fe-4S binding domain
      0.032   13.8   2.0       0.57    9.7   1.1    2.2  2  AAA_25           AAA domain
      0.035   13.5   0.0        5.1    6.4   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.039   13.3   0.4       0.19   11.0   0.1    2.0  2  ATPase           KaiC
      0.046   14.3   0.6       0.89   10.1   0.0    2.4  2  AAA_18           AAA domain
      0.048   13.4   0.0      0.064   13.0   0.0    1.2  1  AAA_15           AAA ATPase domain
      0.059   12.5   0.1       0.88    8.7   0.1    2.2  2  NB-ARC           NB-ARC domain
      0.062   13.0   0.0        1.7    8.3   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      0.095   13.2   1.8       0.17   12.3   1.8    1.3  1  AAA_23           AAA domain
        0.1   11.9   0.1        4.1    6.7   0.1    2.2  2  DnaB_C           DnaB-like helicase C terminal domain
       0.11   12.4   0.0       0.35   10.8   0.0    1.8  2  NACHT            NACHT domain
       0.14   11.9   0.0         10    5.8   0.0    2.1  2  AAA_11           AAA domain
       0.21   10.6   0.1        1.8    7.6   0.1    2.0  2  T2SSE            Type II/IV secretion system protein
       0.22   10.8   0.1        1.2    8.4   0.1    2.0  2  Zeta_toxin       Zeta toxin
       0.27   11.0   1.6       0.71    9.7   0.3    2.3  2  AAA_29           P-loop containing region of AAA domain
       0.92   10.4  11.6        2.4    9.1   2.3    2.6  2  Fer4_22          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   4.7e-17   1.8e-14       1     115 [.       4     249 ..       4     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 4.7e-17
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   ++i+s+kGG+GKTt+aa++a +  +     +  D+D++a   +++   e+ +                             
  gi|91772644|ref|YP_565336.1|   4 LTIISGKGGTGKTTIAAAFASLAEN----AVIADCDVDAADMHLILNPEIIETIdfyglkeayiddslciqcglckeacrf 80 
                                   589*****************95555....9999********9975555544444888888888889*************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|91772644|ref|YP_565336.1|  81 daitdnikvdsfecegcgvcahicpegaitlverkageaylsetrfgpmahaklsvgeeasgklvafvrekardladrydk 161
                                   ********************************************************************************* PP

                                   .....................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHH CS
                                   .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkeale 98 
                                                                        dl+r+l ++ ++ ++       a v +nr+d ++e+t+ +e+++
  gi|91772644|ref|YP_565336.1| 162 eliiidgppgtgcsviasitgvdmvavvtepsvsgihDLERVLSVAGHFNIP-------AVVCINRYDINEENTRFIEDYC 235
                                   **********************************666666666666666666.......9**********99999999999 PP

                                   HHHHHCTS-EEEEEE-- CS
                                   xxxxxxxxxxxxxxxxx RF
                          CbiA  99 elkqrygvpvlgviprd 115
                                   + +   g+ v+g++p++
  gi|91772644|ref|YP_565336.1| 236 RDN---GIDVVGKLPFS 249
                                   999...********997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.7   4.8e-10   1.8e-07       2      24 .]      62      84 ..      61      84 .. 0.95
   2 !   25.3   4.4   2.4e-08   9.1e-06       1      24 []      87     110 ..      87     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.8e-10
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  +id ++Ci CG+C e+C ++AIt
  gi|91772644|ref|YP_565336.1| 62 YIDDSLCIQCGLCKEACRFDAIT 84
                                  8*********************7 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.4e-08
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   +++d   C gCG C+ +CP gAIt
  gi|91772644|ref|YP_565336.1|  87 IKVDSFECEGCGVCAHICPEGAIT 110
                                   5789999****************7 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 !   16.5   0.0   1.2e-05    0.0045       5      28 ..       3      26 ..       1      51 [. 0.73
   2 ?   -0.1   0.0       1.3   5.1e+02     175     222 ..      90     137 ..      75     161 .. 0.79
   3 !   17.3   0.1   6.6e-06    0.0025     113     172 ..     162     219 ..     156     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                          ParA  5 viavlSgKGGVGKStvavnlAlaL 28
                                   ++++SgKGG GK+t+a+ +A   
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFASLA 26
                                  5789***********998887533 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                          ParA 175 sgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdeg 222
                                     f c+ cg + +i  +g  + + ++ g  +l+e  + p  + +   g
  gi|91772644|ref|YP_565336.1|  90 DSFECEGCGVCAHICPEGAITLVERKAGEAYLSETRFGPMAHAKLSVG 137
                                   4699*************9999999999999999887777666655555 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 6.6e-06
                          ParA 113 DyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvve 172
                                   +++iiD PPGtg   ++ +  +  + + +Vt p    ++d ++ ++++ + +++ +  ++
  gi|91772644|ref|YP_565336.1| 162 ELIIIDGPPGTGCSVIASITGV--DMVAVVTEPSVSGIHDLERVLSVAGHFNIPAVVCIN 219
                                   579*********8877666665..67889***********************99876665 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   1.6e-05     0.006      29      52 .]      59      82 ..      31      91 .. 0.68
   2 !   20.0   0.3     2e-06   0.00077       2      23 ..      94     115 ..      93     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-05
                        Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                  ++++id + C++Cg C ++C ++a
  gi|91772644|ref|YP_565336.1| 59 KEAYIDDSLCIQCGLCKEACRFDA 82
                                  666777777777777777776654 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2e-06
                        Fer4_7   2 CigCgaCvaaCpvkaieldeee 23 
                                   C gCg C+  Cp +ai+l e++
  gi|91772644|ref|YP_565336.1|  94 CEGCGVCAHICPEGAITLVERK 115
                                   *****************99874 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2  10.4   5.3e-11     2e-08       1      58 [.      61     110 ..      61     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.3e-11
                       Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   A id++ Ci+Cg+C  aC+    +ai+      +kv + eC GC +C+++CP e++i+
  gi|91772644|ref|YP_565336.1|  61 AYIDDSLCIQCGLCKEACR---FDAITD----NIKVDSFECEGCGVCAHICP-EGAIT 110
                                   78*****************...899974....57999***************.89998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00022     0.085       1      26 [.       1      26 [.       1      53 [. 0.83
   2 !   15.5   0.0   3.2e-05     0.012     107     161 ..     148     204 ..     127     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                        AAA_31  1 gkvIaianqKGGvGKTTtsvnlaaal 26
                                  +k ++i+  KGG GKTT + ++a+  
  gi|91772644|ref|YP_565336.1|  1 MKQLTIISGKGGTGKTTIAAAFASLA 26
                                  678899***********999988643 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.2e-05
                        AAA_31 107 lkellekvkdeYD..yiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqll 161
                                   ++e+ +++ d+YD  +iiiD pP  g+ ++ +++  d+v ++++++   ++ le++l
  gi|91772644|ref|YP_565336.1| 148 VREKARDLADRYDkeLIIIDGPPGTGCSVIASITGVDMVAVVTEPSVSGIHDLERVL 204
                                   478889999***9778*****************************666666665555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.3   3.7e-07   0.00014       2      24 .]      61      83 ..      60      83 .. 0.93
   2 !   12.7   6.5   0.00028      0.11       9      24 .]      94     109 ..      93     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.7e-07
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  + id+++Ci+Cg C  +C ++ai
  gi|91772644|ref|YP_565336.1| 61 AYIDDSLCIQCGLCKEACRFDAI 83
                                  679***************99997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00028
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   C gCg C+ +CPegai
  gi|91772644|ref|YP_565336.1|  94 CEGCGVCAHICPEGAI 109
                                   99*************8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.5   0.00039      0.15       2      23 ..      68      87 ..      67      93 .. 0.86
   2 !   19.9   1.4   2.7e-06     0.001       2      23 ..      94     115 ..      93     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00039
                       Fer4_16  2 CgtCgkCaevCPtnaikekkek 23
                                  C++Cg C e+C  +ai+ +   
  gi|91772644|ref|YP_565336.1| 68 CIQCGLCKEACRFDAITDN--I 87
                                  ****************988..4 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.7e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                   C +Cg Ca +CP++ai+  ++k
  gi|91772644|ref|YP_565336.1|  94 CEGCGVCAHICPEGAITLVERK 115
                                   ****************988554 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   0.00025     0.097      45      57 ..      67      79 ..      49      88 .. 0.78
   2 !   13.9   0.1   0.00015     0.059       1      23 [.      93     115 ..      93     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00025
                       Fer4_17 45 lCieCgeCerkCP 57
                                  lCi+Cg+C+++C 
  gi|91772644|ref|YP_565336.1| 67 LCIQCGLCKEACR 79
                                  6777777777774 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00015
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepk 23 
                                   +C +Cg C+  Cp ++++  e+k
  gi|91772644|ref|YP_565336.1|  93 ECEGCGVCAHICPEGAITLVERK 115
                                   59***********9888766655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4  11.5   2.9e-08   1.1e-05       2      56 .]      61     105 ..      60     105 .. 0.95
   2 !   14.3   2.2   8.4e-05     0.032       2      23 ..      87     108 ..      86     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-08
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++idd+ Ci+Cg C++aC           ++ + + +++++ +C+gcg C+ +CP
  gi|91772644|ref|YP_565336.1|  61 AYIDDSLCIQCGLCKEAC----------RFDAITDNIKVDSFECEGCGVCAHICP 105
                                   689***************..........8999999999999*************9 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.4e-05
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                   +++d+  C +Cg C   CP  +
  gi|91772644|ref|YP_565336.1|  87 IKVDSFECEGCGVCAHICPEGA 108
                                   5678899999999999999944 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00043      0.16       4      55 ..       6      53 ..       3      71 .. 0.83
   2 ?   -0.5   0.1       1.7   6.5e+02      90     107 ..     169     186 ..     164     195 .. 0.88
   3 !   11.7   0.0   0.00033      0.12     176     236 ..     212     274 ..     176     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                     Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetv 55
                                   i GkGG Gk+t    ++aa+a+  +  +i  CD  a   +l+l+  ++et+
  gi|91772644|ref|YP_565336.1|  6 IISGKGGTGKTT----IAAAFASLAENAVIADCDVDAADMHLILNPEIIETI 53
                                  578*******77....5677777788899*******99999***99999886 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                     Fer4_NifH  90 epGvGCaGrgvitaiell 107
                                   +pG+GC+  + it+++++
  gi|91772644|ref|YP_565336.1| 169 PPGTGCSVIASITGVDMV 186
                                   48*************997 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00033
                     Fer4_NifH 176 lgGliinsr.kvd.dereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqake 236
                                   +  +++ +r +++ +++ +ie++ ++ g++v+ ++P + i ++a + +ktv+ey+ ++  +++
  gi|91772644|ref|YP_565336.1| 212 IPAVVCINRyDINeENTRFIEDYCRDNGIDVVGKLPFSRIPTEAMILEKTVMEYSGNELSGEF 274
                                   5556664451444144679***********************************987653333 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.0   0.00017     0.063      34      51 .]      66      83 ..      32      83 .. 0.74
   2 !   22.1  12.2   3.2e-07   0.00012       2      51 .]      68     109 ..      67     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00017
                        Fer4_9 34 eaCigCgaCveaCpkgai 51
                                  + Ci+Cg C eaC  +ai
  gi|91772644|ref|YP_565336.1| 66 SLCIQCGLCKEACRFDAI 83
                                  689999999999988776 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 3.2e-07
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C++Cg C eaC ++++++  +    +        C gCg C+++Cp+gai
  gi|91772644|ref|YP_565336.1|  68 CIQCGLCKEACRFDAITDNIKVDSFE--------CEGCGVCAHICPEGAI 109
                                   ****************9988777766........9************997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.025       9.5      99     123 ..       2      26 ..       1      37 [. 0.81
   2 ?    0.5   0.0       1.3   4.9e+02      88     115 ..     150     177 ..     139     198 .. 0.79
   3 !   14.2   0.0   7.8e-05      0.03      13      79 ..     177     242 ..     165     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.025
                                   TSEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                   ++++++ G+ G GK+t+  a+++ +
  gi|91772644|ref|YP_565336.1|   2 KQLTIISGKGGTGKTTIAAAFASLA 26 
                                   57899***********998877754 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.3
                                   TTHHHHHHHCTTSEEEEECSTTSSHHHH CS
                   RsgA_GTPase  88 egleelkellkdktsvlvGqSGvGKStL 115
                                   e++++l+++ +++++++ G+ G G S +
  gi|91772644|ref|YP_565336.1| 150 EKARDLADRYDKELIIIDGPPGTGCSVI 177
                                   67889999999************97754 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 7.8e-05
                                   EES--EEEEEEESTTTT--.HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEE CS
                   RsgA_GTPase  13 vaNvdqllivvslkepels.lnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyev 79 
                                   +a ++ + +v  ++ep++s  + l+r+L +a + +i+ v+++n+ D+ ee++  + +++  ++ g++v
  gi|91772644|ref|YP_565336.1| 177 IASITGVDMVAVVTEPSVSgIHDLERVLSVAGHFNIPAVVCINRYDINEENT--RFIEDYCRDNGIDV 242
                                   56666666677777787763688***********************998887..55666666666655 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.7    0.0002     0.077       3      20 ..      61      78 ..      59      79 .. 0.90
   2 !   13.8   2.0   0.00013     0.048       4      22 .]      88     106 ..      85     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                        Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                  +++d   Ci+Cg C  aC
  gi|91772644|ref|YP_565336.1| 61 AYIDDSLCIQCGLCKEAC 78
                                  5789999*********99 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00013
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   +vd+  C gCg C + CP+
  gi|91772644|ref|YP_565336.1|  88 KVDSFECEGCGVCAHICPE 106
                                   566556************5 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.7    0.0006      0.23      19      40 ..       2      23 ..       1      31 [. 0.88
   2 !    8.4   0.0    0.0034       1.3      18      44 ..     160     186 ..     149     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0006
                                  -SEEEEE--TTSSTTHHHHHHH CS
                          PhoH 19 ndivfaiGpaGtGKtylavala 40
                                  ++++++ G+ GtGKt +a a a
  gi|91772644|ref|YP_565336.1|  2 KQLTIISGKGGTGKTTIAAAFA 23
                                  5799**************9987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0034
                                   H-SEEEEE--TTSSTTHHHHHHHHHHH CS
                          PhoH  18 kndivfaiGpaGtGKtylavalaveal 44 
                                   +++++++ Gp GtG + +a  ++v+++
  gi|91772644|ref|YP_565336.1| 160 DKELIIIDGPPGTGCSVIASITGVDMV 186
                                   57899********************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.9e-06    0.0015      26      88 ..       4      65 ..       1     126 [. 0.80
   2 ?    1.0   0.0       1.3     5e+02      23      40 ..     160     177 ..     136     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.9e-06
                        AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy..sa.laqalareellrqllde 88
                                  l+++sG  G+GK++++ +++  +e +    + ++cd   +++++   + +++++++ +l ++  d+
  gi|91772644|ref|YP_565336.1|  4 LTIISGKGGTGKTTIAAAFASLAENA----VIADCDVDAADMHLilNPeIIETIDFYGLKEAYIDD 65
                                  689*****************555555....777777774454444477788888887777776666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.3
                        AAA_16  23 rpelvllsGesGvGKssl 40 
                                   + el+++ G++G+G s +
  gi|91772644|ref|YP_565336.1| 160 DKELIIIDGPPGTGCSVI 177
                                   448999********8876 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 ?    8.3   2.0      0.01       3.9       2      18 ..      62      78 ..      61      86 .. 0.87
   2 !   15.3   0.1   6.4e-05     0.024       1      20 [.      87     106 ..      87     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.01
                       Fer4_15  2 vvDrdaCigcglCvaea 18
                                  ++D ++Ci cglC +++
  gi|91772644|ref|YP_565336.1| 62 YIDDSLCIQCGLCKEAC 78
                                  69************999 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.4e-05
                       Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                   ++vD  +C+gcg+C+  +pe
  gi|91772644|ref|YP_565336.1|  87 IKVDSFECEGCGVCAHICPE 106
                                   789***************87 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.4e-06    0.0009     355     428 ..     195     267 ..     183     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                                   HHHHHHHHHHHHHCTTT--EEEEEE--TT--HHHHHHHHHHHHCTTSEEEEE-HHHHGGGGGHHHHHHHHHHCC CS
                         FTHFS 355 kGlanlekhienvkkfgvpvvvainkfktDteaelelvkelaeakavevalsevwakGgeGalelaeavveale 428
                                   +G+++le+ ++ + +f++p+vv+in+++   e++++++++++++++++v+    +++  + a+ l ++v+e   
  gi|91772644|ref|YP_565336.1| 195 SGIHDLERVLSVAGHFNIPAVVCINRYDIN-EENTRFIEDYCRDNGIDVVGKLPFSRIPTEAMILEKTVMEYSG 267
                                   79*************************886.56789*************9998888888888888888887665 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 !    9.5   0.1    0.0019      0.73      48      71 ..       3      26 ..       1      46 [. 0.78
   2 !    7.2   0.0    0.0099       3.8      46      86 ..     160     200 ..     151     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                     IstB_IS21 48 enivllGpsGvGKshlaialgvea 71
                                  +  ++ G  G+GK+ +a+a++  a
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFASLA 26
                                  557899************987644 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0099
                     IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedL 86 
                                   +ke i++ Gp+G+G s +a   gv+ v+  ++ +   ++dL
  gi|91772644|ref|YP_565336.1| 160 DKELIIIDGPPGTGCSVIASITGVDMVAVVTEPSVSGIHDL 200
                                   578899*************9999988775555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-05     0.007       5      51 ..       5      54 ..       1      89 [. 0.82
   2 ?   -0.9   0.0         3   1.2e+03       5      38 ..     164     197 ..     161     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-05
                        AAA_24  5 iliyGpsgiGKTtlakel...gpkplfidtekGlksldadkfpdieswed 51
                                   +i G+ g+GKTt+a+ +    +++++ d++  ++++  +  p+i   +d
  gi|91772644|ref|YP_565336.1|  5 TIISGKGGTGKTTIAAAFaslAENAVIADCDVDAADMHLILNPEIIETID 54
                                  6799***************************8777776666666554444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksl 38 
                                   i+i Gp+g+G + +a+  g + + + te ++  +
  gi|91772644|ref|YP_565336.1| 164 IIIDGPPGTGCSVIASITGVDMVAVVTEPSVSGI 197
                                   67889*****999999888888888888776655 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   2.4    0.0014      0.55       5      17 ..      68      80 ..      65      91 .. 0.80
   2 !   12.2   0.6   0.00049      0.19       3      17 ..      92     111 ..      90     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0014
                        Fer4_8  5 CieCgaCqsaCpv 17
                                  Ci+Cg+C++aC +
  gi|91772644|ref|YP_565336.1| 68 CIQCGLCKEACRF 80
                                  9999*99999965 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00049
                        Fer4_8   3 ekCieCgaCqsaCp.....v 17 
                                   ++C +Cg C + Cp     +
  gi|91772644|ref|YP_565336.1|  92 FECEGCGVCAHICPegaitL 111
                                   67999999999998555552 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   2.7    0.0026      0.98       4      15 ..      68      79 ..      65      81 .. 0.87
   2 !   12.4   1.5   0.00047      0.18       4      16 ..      94     106 ..      90     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0026
                        Fer4_4  4 CigCgsCvaaCP 15
                                  Ci+Cg C  aC 
  gi|91772644|ref|YP_565336.1| 68 CIQCGLCKEACR 79
                                  ***********6 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00047
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C gCg+C  +CP 
  gi|91772644|ref|YP_565336.1|  94 CEGCGVCAHICPE 106
                                   99**********5 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00066      0.25       2      23 ..       6      27 ..       5      61 .. 0.84
   2 ?    3.5   0.0      0.24        92       2      18 ..     165     181 ..     164     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00066
                                  EEESSTTSSHHHHHHHHHHHHT CS
                           AAA  2 llyGppGtGKTllakavakelg 23
                                  +++G  GtGKT++a a a+ ++
  gi|91772644|ref|YP_565336.1|  6 IISGKGGTGKTTIAAAFASLAE 27
                                  6799************998765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.24
                                   EEESSTTSSHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakav 18 
                                   ++ GppGtG + +a+  
  gi|91772644|ref|YP_565336.1| 165 IIDGPPGTGCSVIASIT 181
                                   567******99999865 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7     1e-05    0.0039       4      23 ..       5      24 ..       2      30 .. 0.85
   2 ?   -2.3   0.0       5.2     2e+03     209     250 ..     186     227 ..     179     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                                  EEEEESTTSSHHHHHHHHHH CS
                   ArsA_ATPase  4 ilvgGKGGVGKttvsaatav 23
                                   +++GKGG GKtt++aa+a 
  gi|91772644|ref|YP_565336.1|  5 TIISGKGGTGKTTIAAAFAS 24
                                  579**************994 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.2
                                   EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE.E-TTCS CS
                   ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNk.llpeee 250
                                   +++V+ p    +++ eR ++   +++i +  v +N+  ++ee+
  gi|91772644|ref|YP_565336.1| 186 VAVVTEPSVSGIHDLERVLSVAGHFNIPA-VVCINRyDINEEN 227
                                   67788899999999999999999999976.5677773354444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00057      0.22       5      31 ..       2      28 ..       1      61 [. 0.83
   2 ?    3.7   0.0      0.18        68       4      20 ..     160     176 ..     137     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00057
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqlde 31
                                  ++++++ G  GtGKTt ++ +++ +++
  gi|91772644|ref|YP_565336.1|  2 KQLTIISGKGGTGKTTIAAAFASLAEN 28
                                  5789*****************999865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.18
                        AAA_22   4 tagilvvtGesGtGKTt 20 
                                   ++ ++++ G++GtG ++
  gi|91772644|ref|YP_565336.1| 160 DKELIIIDGPPGTGCSV 176
                                   67889999999999776 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0018      0.68       1      23 [.       2      24 ..       2      53 .. 0.82
   2 ?    6.0   0.1     0.016         6       1      19 [.     161     179 ..     161     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0018
                       DUF2075  1 kavvlVtGvaGtGKtvvllnlla 23
                                  k++ +++G+ GtGKt ++ +++ 
  gi|91772644|ref|YP_565336.1|  2 KQLTIISGKGGTGKTTIAAAFAS 24
                                  6789*************987654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                       DUF2075   1 kavvlVtGvaGtGKtvvll 19 
                                   k+++++ G +GtG +v+++
  gi|91772644|ref|YP_565336.1| 161 KELIIIDGPPGTGCSVIAS 179
                                   6799*************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   0.00024     0.091      19      45 ..       3      29 ..       1      39 [. 0.89
   2 ?    1.7   0.0      0.49   1.9e+02      18      33 ..     161     176 ..     150     183 .. 0.81
   3 ?   -1.5   0.0       4.7   1.8e+03      91     113 ..     186     208 ..     177     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaa 45
                                  +++++ G  GtGKtt+ +a + ++e+a
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFASLAENA 29
                                  689****************99998875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.49
                        AAA_30  18 drvavltGpAGtGKtt 33 
                                   + + ++ Gp+GtG + 
  gi|91772644|ref|YP_565336.1| 161 KELIIIDGPPGTGCSV 176
                                   45889********776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.7
                        AAA_30  91 llivDEagmvdtkqlaallkaae 113
                                   + +v E ++ ++++l+++l+ a 
  gi|91772644|ref|YP_565336.1| 186 VAVVTEPSVSGIHDLERVLSVAG 208
                                   67999*************99886 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   2.1    0.0054       2.1       1      16 [.      63      78 ..      63      80 .. 0.92
   2 !   12.8   1.9   0.00035      0.13       1      18 [.      89     106 ..      89     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0054
                       Fer4_13  1 VDrdtCiacgaCvela 16
                                  +D + Ci cg+C e++
  gi|91772644|ref|YP_565336.1| 63 IDDSLCIQCGLCKEAC 78
                                  78899*********99 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00035
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   VD  +C +cg+C++++P+
  gi|91772644|ref|YP_565336.1|  89 VDSFECEGCGVCAHICPE 106
                                   8999*************8 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.13        50      37      55 ..       6      24 ..       2      38 .. 0.84
   2 !   10.1   0.0    0.0013      0.51      25      95 ..     151     220 ..     131     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                        RuvB_N 37 llyGpPGlGkttlakiiak 55
                                  +++G  G Gktt+a+  a+
  gi|91772644|ref|YP_565336.1|  6 IISGKGGTGKTTIAAAFAS 24
                                  789***********98876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                        RuvB_N  25 aakkreealdh..vllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihr 95 
                                    a+   +  d   +++ GpPG G + +a+i   ++ + +   + P ++   dl  +l+   + ++  +  i r
  gi|91772644|ref|YP_565336.1| 151 KARDLADRYDKelIIIDGPPGTGCSVIASITGVDMVAVV---TEPSVSGIHDLERVLSVAGHFNIPAVVCINR 220
                                   55555555554227789*************999997655...5566666666666666555555555555555 PP

>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00072      0.28       7     105 ..      73     177 ..      67     194 .. 0.82
   2 ?    1.5   0.0      0.72   2.7e+02      43      83 ..     242     285 ..     219     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00072
                        DUF523   7 LlgekvrydgkakksevleeelkelvkeelvpvCPEvaggLptPRepael..........akrvlkkegedvtealekgae 77 
                                   L+ e++r+d  + + +v + e++ +    + ++CPE a+ L + R++ e           a + + + ge+ + +l+++++
  gi|91772644|ref|YP_565336.1|  73 LCKEACRFDAITDNIKVDSFECEGCG--VCAHICPEGAITL-VERKAGEAylsetrfgpmA-HAKLSVGEEASGKLVAFVR 149
                                   8899******9999777777777777..889**********.99**999999999998642.4666777899999999999 PP

                        DUF523  78 ealeelkeeeikgailkekSPSCGveki 105
                                   e ++ l++   k  i+ ++ P  G++ i
  gi|91772644|ref|YP_565336.1| 150 EKARDLADRYDKELIIIDGPPGTGCSVI 177
                                   9999888888888888899998888765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.72
                        DUF523  43 vaggLptPRepael...akrvlkkegedvtealekgaeealeel 83 
                                   v g Lp  R p e    +k+v++ +g++++ ++ +  +++ e++
  gi|91772644|ref|YP_565336.1| 242 VVGKLPFSRIPTEAmilEKTVMEYSGNELSGEFSEKLKDMWEKV 285
                                   56778888888888887767999999999999999888877765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0014      0.52      12      36 ..       3      27 ..       1     152 [. 0.91
   2 ?    1.9   0.0      0.78     3e+02      11      30 ..     161     180 ..     157     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0014
                                  SEEEEEESTTSSHHHHHHHHTTSS- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 12 ekvaivGenGaGKStLlkllagllk 36
                                  +++ i G+ G+GK+t+++++a l +
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFASLAE 27
                                  67899**************999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.78
                                   TSEEEEEESTTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  11 gekvaivGenGaGKStLlkl 30 
                                    e++ i G+ G+G+S ++++
  gi|91772644|ref|YP_565336.1| 161 KELIIIDGPPGTGCSVIASI 180
                                   6789999********98764 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   2.6   0.00073      0.28       1      15 []      68      82 ..      68      82 .. 0.95
   2 ?    8.3   6.7     0.013       4.9       1      15 []      94     108 ..      94     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00073
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C++Cg+C e+C+ +A
  gi|91772644|ref|YP_565336.1| 68 CIQCGLCKEACRFDA 82
                                  ***********9987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.013
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C gCg C   CP+gA
  gi|91772644|ref|YP_565336.1|  94 CEGCGVCAHICPEGA 108
                                   99************9 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.1    0.0015      0.57      33      54 ..       2      23 ..       1      26 [. 0.88
   2 ?    2.8   0.0       0.2        78      25      57 ..     155     185 ..     131     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                        AAA_25 33 gelallaGapgtGKttlaldla 54
                                  + l+++ G +gtGKtt+a   a
  gi|91772644|ref|YP_565336.1|  2 KQLTIISGKGGTGKTTIAAAFA 23
                                  5799*************98776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                        AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalav 57 
                                   l +++   +el+++ G+pgtG +++a+  ++++
  gi|91772644|ref|YP_565336.1| 155 LADRY--DKELIIIDGPPGTGCSVIASITGVDM 185
                                   44444..56788888888888888877666666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.038        14      26      46 ..       6      26 ..       2      45 .. 0.86
   2 ?    6.4   0.0     0.013       5.1      25      65 ..     164     208 ..     151     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.038
                  Mg_chelatase 26 llvGppGsGKtmlakrlpsll 46
                                  ++ G  G+GKt +a++++sl 
  gi|91772644|ref|YP_565336.1|  6 IISGKGGTGKTTIAAAFASLA 26
                                  678************999875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                  Mg_chelatase  25 lllvGppGsGKtmlakr....lpsllpplseeealevakiasvag 65 
                                   +++ GppG+G +++a+     + +++++ s + +++ +++ svag
  gi|91772644|ref|YP_565336.1| 164 IIIDGPPGTGCSVIASItgvdMVAVVTEPSVSGIHDLERVLSVAG 208
                                   6778***********853333677778888888888888888887 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0005      0.19      20      40 ..       3      23 ..       1      35 [. 0.90
   2 ?   -0.4   0.0       1.6   5.9e+02      19      36 ..     161     178 ..     158     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                        ATPase 20 rvvlitGepGtGKtifalqFl 40
                                  + + i+G+ GtGKt++a+ F+
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFA 23
                                  6899***************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                        ATPase  19 grvvlitGepGtGKtifa 36 
                                   ++ + i G pGtG +++a
  gi|91772644|ref|YP_565336.1| 161 KELIIIDGPPGTGCSVIA 178
                                   67899********99887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0023      0.89       2      24 ..       6      28 ..       6      78 .. 0.77
   2 ?    1.7   0.4      0.94   3.6e+02       1      15 [.     164     178 ..     164     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0023
                        AAA_18  2 lltGtpGvGKttlakeLskrlgf 24
                                  +++G+ G+GKtt+a + +++ ++
  gi|91772644|ref|YP_565336.1|  6 IISGKGGTGKTTIAAAFASLAEN 28
                                  699***********999888755 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.94
                        AAA_18   1 IlltGtpGvGKttla 15 
                                   I++ G+pG+G + +a
  gi|91772644|ref|YP_565336.1| 164 IIIDGPPGTGCSVIA 178
                                   99********98877 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00017     0.064      24      53 ..       3      32 ..       1      98 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                        AAA_15 24 eltvliGkNnsGKSsilealdlFlnnkekk 53
                                  +lt++ Gk ++GK++i+ a+  + +n    
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFASLAENAVIA 32
                                  49******************9999987333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0023      0.88      24      39 ..       6      21 ..       2      29 .. 0.84
   2 ?    1.1   0.0      0.48   1.8e+02      18      38 ..     159     179 ..     147     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                                  EEEESTTSSHHHHHHH CS
                        NB-ARC 24 alvGmgGvGKttlakq 39
                                   ++G+gG GKtt+a+ 
  gi|91772644|ref|YP_565336.1|  6 IISGKGGTGKTTIAAA 21
                                  589**********985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.48
                                   SCSEEEEEEESTTSSHHHHHH CS
                        NB-ARC  18 lqslvvalvGmgGvGKttlak 38 
                                    ++ ++ + G +G G +++a+
  gi|91772644|ref|YP_565336.1| 159 YDKELIIIDGPPGTGCSVIAS 179
                                   3445999************96 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0045       1.7      25      61 ..       5      41 ..       1      78 [. 0.75
   2 ?    2.6   0.0      0.25        95      13      40 ..     150     179 ..     139     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0045
                                  EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
               Sigma54_activat 25 vlitGesGtGKellaraiheaskrkekpfvavncaai 61
                                  ++i G+ GtGK+++a a  +  +++      v+ a++
  gi|91772644|ref|YP_565336.1|  5 TIISGKGGTGKTTIAAAFASLAENAVIADCDVDAADM 41
                                  689*************998887776666666666654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.25
                                   HHHHHHCTSS..S-EEEECSTTSSHHHHHH CS
               Sigma54_activat  13 eqikkvaktd..lsvlitGesGtGKellar 40 
                                   e+++ +a+      ++i G  GtG +++a+
  gi|91772644|ref|YP_565336.1| 150 EKARDLADRYdkELIIIDGPPGTGCSVIAS 179
                                   555555543223557899**********97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   0.00046      0.17      20      39 ..       3      22 ..       2      25 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00046
                        AAA_23 20 gltlItGpNGaGKTTildAi 39
                                   lt+I+G+ G+GKTTi  A+
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAF 22
                                  79**************9997 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.011       4.1      20      44 ..       3      27 ..       1      44 [. 0.77
   2 ?    3.0   0.0      0.14        53     100     136 ..     130     167 ..     107     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                                  XEEEEEEXTTSSHHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 20 dliiiAarpsmGktalalniaenaa 44
                                  +l+ii ++ ++Gkt++a  +a+ a 
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFASLAE 27
                                  79**************998886543 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                                   HHSEEEEEEXSS.XCHHHHHHHHHHHHHHTTEEEEEEE CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 100 seaklfiddtpa.ltvseirskarrlkkekglgliviD 136
                                   ++akl + ++++   v+ +r+kar l+ + + +li+iD
  gi|91772644|ref|YP_565336.1| 130 AHAKLSVGEEASgKLVAFVREKARDLADRYDKELIIID 167
                                   56666666555414456689999999999999999999 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00092      0.35       2      26 ..       4      28 ..       3      47 .. 0.86
   2 ?   -1.6   0.0         6   2.3e+03       2      12 ..     163     173 ..     147     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00092
                                  CEEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                  l i+ G+ G GKTt ++ +a+++  
  gi|91772644|ref|YP_565336.1|  4 LTIISGKGGTGKTTIAAAFASLAEN 28
                                  679****************998766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6
                                   CEEEEC-TTTC CS
                         NACHT   2 lvilqGeaGsG 12 
                                   l+i+ G++G G
  gi|91772644|ref|YP_565336.1| 163 LIIIDGPPGTG 173
                                   56677777766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.027        10      18      39 ..       3      24 ..       1      46 [. 0.82
   2 ?    4.1   0.0     0.087        33      18      31 ..     162     175 ..     147     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                        AAA_11 18 eitliqGPPGtgKTktivells 39
                                  ++t+i+G+ GtgKT+  +++ s
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFAS 24
                                  579***********98777665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.087
                        AAA_11  18 eitliqGPPGtgKT 31 
                                   e+ +i GPPGtg +
  gi|91772644|ref|YP_565336.1| 162 ELIIIDGPPGTGCS 175
                                   3689*******976 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   0.1    0.0046       1.8     130     152 ..       3      25 ..       1      35 [. 0.80
   2 ?    0.7   0.0      0.58   2.2e+02     128     147 ..     160     179 ..     127     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0046
                         T2SSE 130 glilvsGgTgsGKttllyallke 152
                                   +l ++sG  g+GKtt++ a  + 
  gi|91772644|ref|YP_565336.1|   3 QLTIISGKGGTGKTTIAAAFASL 25 
                                   5679***********99776554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.58
                         T2SSE 128 erglilvsGgTgsGKttlly 147
                                    + li++ G+ g+G ++++ 
  gi|91772644|ref|YP_565336.1| 160 DKELIIIDGPPGTGCSVIAS 179
                                   5789**********999875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0031       1.2      17      50 ..       3      33 ..       1      37 [. 0.79
   2 ?   -0.4   0.0       1.6     6e+02      12      39 ..     157     184 ..     148     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0031
                    Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgnvvrld 50
                                   l +++G  G GK+++a++++     ++n+v  d
  gi|91772644|ref|YP_565336.1|  3 QLTIISGKGGTGKTTIAAAFASL---AENAVIAD 33
                                  5789*************999865...46666555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                    Zeta_toxin  12 sqerPklillgGqpGAGKselaellkde 39 
                                   ++  + li++ G pG G s +a+ +  +
  gi|91772644|ref|YP_565336.1| 157 DRYDKELIIIDGPPGTGCSVIASITGVD 184
                                   55678899*********99999877665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0019      0.71      24      45 ..       4      25 ..       1      30 [. 0.84
   2 ?   -1.5   0.0       5.8   2.2e+03      24      38 ..     163     177 ..     157     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                        AAA_29 24 atlltGpsGsGKSTllDAiqal 45
                                   t+++G+ G+GK+T+  A++ l
  gi|91772644|ref|YP_565336.1|  4 LTIISGKGGTGKTTIAAAFASL 25
                                  699************8887765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.8
                        AAA_29  24 atlltGpsGsGKSTl 38 
                                    +++ Gp G+G S +
  gi|91772644|ref|YP_565336.1| 163 LIIIDGPPGTGCSVI 177
                                   56789******9876 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.8     0.051        20      77      93 ..      63      79 ..      51      83 .. 0.79
   2 ?    9.1   2.3    0.0062       2.4      76      94 ..      88     106 ..      80     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.051
                       Fer4_22 77 fgesgCvGCgRCieacp 93
                                  ++ s C+ Cg C+eac 
  gi|91772644|ref|YP_565336.1| 63 IDDSLCIQCGLCKEACR 79
                                  47889999999999996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0062
                       Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                   k+++  C GCg C + cp+
  gi|91772644|ref|YP_565336.1|  88 KVDSFECEGCGVCAHICPE 106
                                   568889***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1891.83
//
Query:       gi|91772645|ref|YP_565337.1|  [L=110]
Description: hypothetical protein Mbur_0616 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-30  105.2   2.1    2.1e-30  105.0   2.1    1.0  1  CGGC      CGGC domain


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   2.1   1.2e-34   2.1e-30       1     106 []       3     110 .]       3     110 .] 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.2e-34
                          CGGC   1 kiaiirCekvedvCpgvkClkalkerkgaFeeye.eevelvgfvtCggCpgkkvveklkelkkegvdvihlssCiktk.ka 79 
                                   ki+++rCe ++++Cpg++C+ka+k+ +g+ ee++ ee++++g+vtCggCpg++ +++++e++++g++vi+l++C+ ++  +
  gi|91772645|ref|YP_565337.1|   3 KIGLVRCEIASRSCPGTSCFKAIKNGTGTLEEFKdEEIDIIGMVTCGGCPGRDSIRQIREMIRRGAEVIFLCTCMIKPiPN 83 
                                   89************************************************************************8567799 PP

                          CGGC  80 kkeCpeieeikeaieeklgievvegth 106
                                    ++Cp++ee++eai++ ++++v++gth
  gi|91772645|ref|YP_565337.1|  84 PPKCPYAEELAEAIRDICDVRVIMGTH 110
                                   99************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 766.63
//
Query:       gi|91772646|ref|YP_565338.1|  [L=284]
Description: cobyrinic acid a,c-diamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   71.1   0.0    1.1e-19   70.7   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.2e-15   57.7   0.1      1e-08   34.9   0.0    3.0  2  ParA         NUBPL iron-transfer P-loop NTPase
      1e-09   37.7  10.8    9.3e-06   25.3   1.2    3.4  4  Fer4         4Fe-4S binding domain
    1.4e-07   31.3  16.5    0.00017   21.5   1.6    3.2  3  Fer4_6       4Fe-4S binding domain
    3.8e-07   30.2   0.1    6.8e-05   22.8   0.0    2.1  2  AAA_31       AAA domain
    5.6e-06   26.4  13.6    0.00019   21.5   0.8    2.9  3  Fer4_10      4Fe-4S dicluster domain
    5.8e-06   26.4   9.6    3.4e-05   23.9   9.8    2.2  2  Fer4_9       4Fe-4S dicluster domain
      2e-05   25.4   8.9    0.00094   20.1   0.6    2.6  2  Fer4_16      4Fe-4S double cluster binding domain
    7.7e-05   23.2  20.1      0.001   19.6  10.5    2.5  3  Fer4_7       4Fe-4S dicluster domain
    0.00011   22.2   8.5    0.00011   22.2   8.5    1.9  2  Fer4_21      4Fe-4S dicluster domain
     0.0024   17.3   0.0        1.4    8.3   0.0    2.3  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0045   16.6   0.0      0.011   15.3   0.0    1.7  2  AAA_25       AAA domain
     0.0055   16.5   0.3      0.085   12.7   0.0    2.2  2  AAA_26       AAA domain
     0.0064   15.7   0.5      0.011   14.9   0.5    1.4  1  ArsA_ATPase  Anion-transporting ATPase
  ------ inclusion threshold ------
       0.01   15.9   1.8       0.01   15.9   1.8    3.2  3  Fer4_2       4Fe-4S binding domain
      0.036   14.9   5.9        1.2   10.0   1.0    2.4  2  Fer4_22      4Fe-4S dicluster domain
       0.04   13.4   0.2      0.083   12.3   0.2    1.5  2  PhoH         PhoH-like protein
      0.042   14.4  17.1      0.058   13.9   1.7    3.2  2  Fer4_4       4Fe-4S binding domain
      0.053   12.8   0.0      0.073   12.3   0.0    1.2  1  MipZ         ATPase MipZ
       0.07   13.6  11.1       0.26   11.8   1.8    2.7  2  Fer4_8       4Fe-4S dicluster domain
       0.19   11.4   0.0        0.8    9.3   0.0    2.0  2  Zot          Zonular occludens toxin (Zot)
       0.19   10.9   0.0       0.24   10.6   0.0    1.1  1  DUF2075      Uncharacterized conserved protein (DUF2075)
        0.5   11.1   6.5        5.3    7.9   1.5    2.8  2  Fer4_15      4Fe-4S single cluster domain
       0.76   10.9  21.3        1.4   10.1   6.6    3.1  2  Fer4_3       4Fe-4S binding domain
       0.85   10.2  13.5       0.66   10.6   3.1    2.6  3  Fer4_17      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   1.6e-22   1.1e-19       1     127 [.       3     253 ..       3     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.6e-22
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH........................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx........................ RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep........................ 54 
                                   iaias+kGG+GKTt+a+nLa +l++     +l+D+D++ +n ++   +  + ++ie                         
  gi|91772646|ref|YP_565338.1|   3 IAIASGKGGTGKTTVAVNLALSLKD----AQLFDCDVEEPNCNLflgY--DLEKIEDvnvktpvvdknkcdlcgkcsdfcq 77 
                                   89**********************9....9*************96442..33333336699******************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|91772646|ref|YP_565338.1|  78 fnalailpedvmifptlchgcggctivcpnkaisevdrkvgviegsvngelafcqgllkigepmtslvikalqehidknat 158
                                   ********************************************************************************* PP

                                   ...................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHH CS
                                   ...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeel 100
                                                                      dlk  l +++ lg++        gvv+nr d    +++ +e + e+
  gi|91772646|ref|YP_565338.1| 159 aiidappgtacpviasvknvdycilvtestpfgfhDLKLALDVMRILGIP-------FGVVINRCDIG--DNRVEEYCIEE 230
                                   ************************************************99.......9**********..89999999998 PP

                                   HHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA 101 kqrygvpvlgviprdeavaeapargep 127
                                       g+p+l +ip+d ++a+++++g p
  gi|91772646|ref|YP_565338.1| 231 ----GIPILMKIPYDREIARLYSKGIP 253
                                   ....********************987 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 !   34.9   0.0   1.4e-11     1e-08       5      68 ..       2      60 ..       1      69 [. 0.85
   2 !   18.0   0.0   2.2e-06    0.0016      99     231 ..     145     260 ..     136     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.4e-11
                          ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPv 68
                                  +ia++SgKGG GK+tvavnlAl+L++      l+D D+  p+   +lg + ek+e  +   +Pv
  gi|91772646|ref|YP_565338.1|  2 KIAIASGKGGTGKTTVAVNLALSLKDA----QLFDCDVEEPNCNLFLGYDLEKIEDVN-VKTPV 60
                                  69**********************866....58***************9998887776.34465 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.2e-06
                          ParA  99 aikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvc 179
                                   +ik l ++++ +     iiD PPGt+   ++ ++++  + +++Vt      ++d k a+++++ + ++  Gvv N     c
  gi|91772646|ref|YP_565338.1| 145 VIKALQEHIDKN--ATAIIDAPPGTACPVIASVKNV--DYCILVTESTPFGFHDLKLALDVMRILGIPF-GVVIN----RC 216
                                   555555544433..3569********9999988888..689**********************999995.77776....34 PP

                          ParA 180 pkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepe 231
                                   +         g++ +e+++ e g+p+l +ip d ei++   +g p+v + pe
  gi|91772646|ref|YP_565338.1| 217 D--------IGDNRVEEYCIEEGIPILMKIPYDREIARLYSKGIPFVNEMPE 260
                                   4........467789999***************************9998765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.2   1.3e-08   9.3e-06       1      23 [.      59      81 ..      59      82 .. 0.95
   2 !   24.7   2.7   1.9e-08   1.4e-05       2      24 .]      89     111 ..      88     111 .. 0.92
   3 ?   -2.3   0.3       6.6   4.7e+03      17      20 ..     168     171 ..     167     171 .. 0.82
   4 ?   -2.5   0.1       7.7   5.6e+03       3       9 ..     176     182 ..     175     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.3e-08
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  +v+d++kC  CG+C + C ++A+
  gi|91772646|ref|YP_565338.1| 59 PVVDKNKCDLCGKCSDFCQFNAL 81
                                  69*******************97 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.9e-08
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                    i + +C gCG C  vCP+ AI+
  gi|91772646|ref|YP_565338.1|  89 MIFPTLCHGCGGCTIVCPNKAIS 111
                                   58899****************96 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.6
                                   HSTT CS
                          Fer4  17 vCPv 20 
                                   +CPv
  gi|91772646|ref|YP_565338.1| 168 ACPV 171
                                   8**7 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.7
                                   EETTTSS CS
                          Fer4   3 ideekCi 9  
                                    + + Ci
  gi|91772646|ref|YP_565338.1| 176 KNVDYCI 182
                                   6789998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.6   2.4e-07   0.00017       2      24 .]      59      81 ..      58      81 .. 0.91
   2 !   18.5   2.3   2.1e-06    0.0015       5      24 .]      91     110 ..      90     110 .. 0.90
   3 ?   -2.2   0.2       7.2   5.2e+03      17      22 ..     167     172 ..     167     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.4e-07
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  +++d++kC+ Cg+C + C ++a+
  gi|91772646|ref|YP_565338.1| 59 PVVDKNKCDLCGKCSDFCQFNAL 81
                                  89**************9988875 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.1e-06
                        Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                    p +C gCg C++vCP +ai
  gi|91772646|ref|YP_565338.1|  91 FPTLCHGCGGCTIVCPNKAI 110
                                   6899************9887 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.2
                        Fer4_6  17 rvCPeg 22 
                                   ++CP  
  gi|91772646|ref|YP_565338.1| 167 TACPVI 172
                                   69*975 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   9.5e-08   6.8e-05       4      29 ..       3      28 ..       1      94 [. 0.79
   2 ?    5.7   0.0     0.017        12     107     159 ..     145     197 ..     101     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.5e-08
                        AAA_31  4 IaianqKGGvGKTTtsvnlaaalakl 29
                                  Iaia  KGG GKTT +vnla +l  +
  gi|91772646|ref|YP_565338.1|  3 IAIASGKGGTGKTTVAVNLALSLKDA 28
                                  9*******************999754 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                        AAA_31 107 lkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleq 159
                                   + ++l++  d+    iiD+pP   + ++ ++   d++i +++++++  + l+ 
  gi|91772646|ref|YP_565338.1| 145 VIKALQEHIDKNATAIIDAPPGTACPVIASVKNVDYCILVTESTPFGFHDLKL 197
                                   367788888888899****************************9998887765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   3.3    0.0005      0.36       3      19 ..      60      76 ..      58      89 .. 0.86
   2 !   21.5   0.8   2.7e-07   0.00019       5      47 ..      91     133 ..      87     139 .. 0.89
   3 ?   -1.4   0.0       3.7   2.7e+03      18      23 ..     168     173 ..     166     188 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                       Fer4_10  3 vidddtCirCgkCvkaC 19
                                  v+d+++C  CgkC ++C
  gi|91772646|ref|YP_565338.1| 60 VVDKNKCDLCGKCSDFC 76
                                  7899************* PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.7e-07
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg 47 
                                    +  C +Cg C+ +CP ++ s + ++   +e+ v++ +  C+g
  gi|91772646|ref|YP_565338.1|  91 FPTLCHGCGGCTIVCPNKAISEVDRKVGVIEGSVNGELAFCQG 133
                                   5788***************999999999999999999999986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.7
                       Fer4_10  18 aCPadl 23 
                                   aCP+ +
  gi|91772646|ref|YP_565338.1| 168 ACPVIA 173
                                   788732 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   1.6   0.00031      0.22      34      50 ..      64      80 ..      38      83 .. 0.71
   2 !   23.9   9.8   4.8e-08   3.4e-05       1      51 []      65     110 ..      65     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                        Fer4_9 34 eaCigCgaCveaCpkga 50
                                  ++C  Cg+C + C+ +a
  gi|91772646|ref|YP_565338.1| 64 NKCDLCGKCSDFCQFNA 80
                                  57999999999998664 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.8e-08
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kC  Cg+C + C++++        ++  +      C+gCg C+ +Cp++ai
  gi|91772646|ref|YP_565338.1|  65 KCDLCGKCSDFCQFNALAILPEDVMIFPT-----LCHGCGGCTIVCPNKAI 110
                                   7************9999777666666653.....6*************987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   2.3    0.0045       3.2      51      67 .]      63      79 ..      33      83 .. 0.74
   2 !   20.1   0.6   1.3e-06   0.00094       2      24 ..      95     117 ..      94     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0045
                       Fer4_16 51 qeaitgCdiCqdvCPan 67
                                  ++++  C++C d C +n
  gi|91772646|ref|YP_565338.1| 63 KNKCDLCGKCSDFCQFN 79
                                  56778888888888776 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.3e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                   C++Cg C+ vCP +ai+e  +k+
  gi|91772646|ref|YP_565338.1|  95 CHGCGGCTIVCPNKAISEVDRKV 117
                                   *****************986555 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   2.4    0.0015       1.1      29      52 .]      57      80 ..      37      80 .. 0.75
   2 !   19.6  10.5   1.4e-06     0.001       1      52 []      65     109 ..      65     109 .. 0.94
   3 !   16.5   2.0   1.4e-05    0.0098       2      24 ..      95     117 ..      94     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0015
                        Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                  +++++d +kC  Cg+C + C ++a
  gi|91772646|ref|YP_565338.1| 57 KTPVVDKNKCDLCGKCSDFCQFNA 80
                                  567788888888888888888776 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.4e-06
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C  Cg+C + C  +a+ + +e       +v i p+ C gCg C  vCP +a
  gi|91772646|ref|YP_565338.1|  65 KCDLCGKCSDFCQFNALAILPE-------DVMIFPTLCHGCGGCTIVCPNKA 109
                                   7******************997.......689*****************876 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.4e-05
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeen 24 
                                   C gCg C+ +Cp+kai+  ++++
  gi|91772646|ref|YP_565338.1|  95 CHGCGGCTIVCPNKAISEVDRKV 117
                                   ****************9776644 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   8.5   1.5e-07   0.00011       2      57 ..      60     110 ..      59     112 .. 0.88
   2 ?   -2.2   0.1       6.8   4.9e+03      50      55 ..     168     173 ..     151     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   ++d++kC  CgkC   C+    +a+ i ++ v  +    C GC  C++vCP +++i
  gi|91772646|ref|YP_565338.1|  60 VVDKNKCDLCGKCSDFCQ---FNALAILPEDV-MIFPTLCHGCGGCTIVCP-NKAI 110
                                   69****************...78999888877.577899************.5777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.8
                       Fer4_21  50 vCPved 55 
                                    CPv  
  gi|91772646|ref|YP_565338.1| 168 ACPVIA 173
                                   455543 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 !    8.3   0.0    0.0019       1.4       2      26 ..       2      27 ..       1      62 [. 0.84
   2 !    6.9   0.0    0.0053       3.8     178     245 ..     210     273 ..     201     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0019
                     Fer4_NifH  2 kiai.yGkGGiGksttsqnlsaalae 26
                                  kiai  GkGG Gk+t + nl+ +l++
  gi|91772646|ref|YP_565338.1|  2 KIAIaSGKGGTGKTTVAVNLALSLKD 27
                                  677735**************998865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0053
                     Fer4_NifH 178 GliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkil 245
                                   G++in r  d +++ +e++  e g+++l ++P d ++ +   +    ++  pe++  + +  l r+++
  gi|91772646|ref|YP_565338.1| 210 GVVIN-R-CDIGDNRVEEYCIEEGIPILMKIPYDREIARLYSKGIPFVNEMPEWK--DRFLRLFRDVT 273
                                   89999.5.89999************************998777776666667666..66666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.011      35      58 ..       3      26 ..       1      44 [. 0.83
   2 ?   -3.0   0.0       6.3   4.5e+03      26      44 ..     149     167 ..     147     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                        AAA_25 35 lallaGapgtGKttlaldlalava 58
                                  +a+  G +gtGKtt+a++lal++ 
  gi|91772646|ref|YP_565338.1|  3 IAIASGKGGTGKTTVAVNLALSLK 26
                                  68899****************975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.3
                        AAA_25  26 vkgllpagelallaGapgt 44 
                                   +++++ ++++a++ ++pgt
  gi|91772646|ref|YP_565338.1| 149 LQEHIDKNATAIIDAPPGT 167
                                   5789999999999999998 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.28     2e+02       3      26 ..       3      26 ..       1      32 [. 0.84
   2 !   12.7   0.0   0.00012     0.085     132     194 ..     182     244 ..     171     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.28
                        AAA_26  3 ifvtgtdtgvGKTvvslgLvralk 26
                                  i +++   g GKT+v+  L+ +lk
  gi|91772646|ref|YP_565338.1|  3 IAIASGKGGTGKTTVAVNLALSLK 26
                                  678888999**********98885 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                        AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNkv.rnpenvetlekksgipvlGvvPylpdl 194
                                   ilV+ ++   + +l l+++++r  +++ +Gv++N++   +++ve+++   gip+l  +Py++++
  gi|91772646|ref|YP_565338.1| 182 ILVTESTPFGFHDLKLALDVMRILGIP-FGVVINRCdIGDNRVEEYCIEEGIPILMKIPYDREI 244
                                   888888899999999999999987776.8******866779*******************9986 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   1.6e-05     0.011       1      27 [.       1      27 [.       1      30 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                  -EEEEEEESTTSSHHHHHHHHHHHHHH CS
                   ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklse 27
                                  +k+ + +GKGG GKttv+  +a+ l +
  gi|91772646|ref|YP_565338.1|  1 MKIAIASGKGGTGKTTVAVNLALSLKD 27
                                  788999***************998865 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   1.8   1.4e-05      0.01       3      20 ..      59      76 ..      57      78 .. 0.93
   2 ?    9.3   2.4    0.0018       1.3       9      22 .]      94     107 ..      86     107 .. 0.83
   3 ?   -2.4   0.4       9.2   6.6e+03      18      21 ..     167     170 ..     167     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                        Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                  +vvd ++C  Cg+C + C
  gi|91772646|ref|YP_565338.1| 59 PVVDKNKCDLCGKCSDFC 76
                                  799*************** PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                        Fer4_2   9 rCigCgaCvsaCPa 22 
                                    C gCg C+ +CP+
  gi|91772646|ref|YP_565338.1|  94 LCHGCGGCTIVCPN 107
                                   599**********5 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.2
                        Fer4_2  18 saCP 21 
                                   +aCP
  gi|91772646|ref|YP_565338.1| 167 TACP 170
                                   79*9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3     0.016        11      76      93 ..      60      77 ..      46      80 .. 0.73
   2 ?   10.0   1.0    0.0017       1.2       2      15 ..      95     108 ..      93     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.016
                       Fer4_22 76 kfgesgCvGCgRCieacp 93
                                   +++++C  Cg+C++ c+
  gi|91772646|ref|YP_565338.1| 60 VVDKNKCDLCGKCSDFCQ 77
                                  348999***********7 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                       Fer4_22   2 ClsCgaCtlvCptC 15 
                                   C +Cg Ct+vCp  
  gi|91772646|ref|YP_565338.1|  95 CHGCGGCTIVCPNK 108
                                   77888888888764 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00012     0.083      20      45 ..       2      27 ..       1      33 [. 0.86
   2 ?   -3.2   0.0       6.5   4.7e+03      78      95 ..     140     157 ..     119     177 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                  SEEEEE--TTSSTTHHHHHHHHHHHH CS
                          PhoH 20 divfaiGpaGtGKtylavalavealk 45
                                  +i +a G+ GtGKt +av la+++  
  gi|91772646|ref|YP_565338.1|  2 KIAIASGKGGTGKTTVAVNLALSLKD 27
                                  68899****************98755 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.5
                                   TTTHHHHHHHTTTS-TTC CS
                          PhoH  78 pylrplydaLkdllgaek 95 
                                   p+ + ++ aL++ +++++
  gi|91772646|ref|YP_565338.1| 140 PMTSLVIKALQEHIDKNA 157
                                   444445555555544443 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.7    0.0049       3.5       1      16 [.      63      78 ..      63      79 .. 0.88
   2 ?   13.9   1.7   8.1e-05     0.058       3      15 ..      94     106 ..      92     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0049
                        Fer4_4  1 qerCigCgsCvaaCPq 16
                                  +++C  Cg+C ++C +
  gi|91772646|ref|YP_565338.1| 63 KNKCDLCGKCSDFCQF 78
                                  689***********65 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.1e-05
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                    C gCg C+++CP
  gi|91772646|ref|YP_565338.1|  94 LCHGCGGCTIVCP 106
                                   5************ PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001     0.073       3      28 ..       3      28 ..       1      64 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                  EEE--SSTTSSHHHHHHHHHHHHHTT CS
                          MipZ  3 ivlgnekGGsGksttavhvavaLlkk 28
                                  i ++  kGG+Gk+t+av +a +L ++
  gi|91772646|ref|YP_565338.1|  3 IAIASGKGGTGKTTVAVNLALSLKDA 28
                                  788999**************999764 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.2     0.021        15      49      62 ..      64      77 ..      32      80 .. 0.82
   2 ?   11.8   1.8   0.00036      0.26      50      64 ..      94     108 ..      89     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                        Fer4_8 49 wsCttcgaCtevCp 62
                                  ++C  cg+C++ C 
  gi|91772646|ref|YP_565338.1| 64 NKCDLCGKCSDFCQ 77
                                  67999999999886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00036
                        Fer4_8  50 sCttcgaCtevCpvg 64 
                                    C++cg Ct vCp++
  gi|91772646|ref|YP_565338.1|  94 LCHGCGGCTIVCPNK 108
                                   7************87 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011       0.8       2      23 ..       3      24 ..       2      96 .. 0.72
   2 ?   -0.7   0.0       1.3   9.3e+02      88     112 ..     243     267 ..     240     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                           Zot  2 islvtGapGsgKtsgavkkdll 23
                                  i +  G++G+gKt +av+  l 
  gi|91772646|ref|YP_565338.1|  3 IAIASGKGGTGKTTVAVNLALS 24
                                  67899************98664 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                           Zot  88 Ecqeifpvrakegrkdpevinafte 112
                                   E  +++++  ++++++pe+ + f +
  gi|91772646|ref|YP_565338.1| 243 EIARLYSKGIPFVNEMPEWKDRFLR 267
                                   78899**************998876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.24       2      27 ..       2      27 ..       1      45 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                       DUF2075  2 avvlVtGvaGtGKtvvllnllaeled 27
                                  ++ + +G+ GtGKt v++nl+  l+d
  gi|91772646|ref|YP_565338.1|  2 KIAIASGKGGTGKTTVAVNLALSLKD 27
                                  577899***************99933 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.5    0.0073       5.3       2      18 ..      60      76 ..      60      83 .. 0.89
   2 ?    4.9   0.2     0.061        44       6      20 ..      93     107 ..      88     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0073
                       Fer4_15  2 vvDrdaCigcglCvaea 18
                                  vvD+++C+ cg C + +
  gi|91772646|ref|YP_565338.1| 60 VVDKNKCDLCGKCSDFC 76
                                  69***********9877 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.061
                       Fer4_15   6 daCigcglCvaeape 20 
                                   ++C gcg C  ++p+
  gi|91772646|ref|YP_565338.1|  93 TLCHGCGGCTIVCPN 107
                                   78*******999975 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.0    0.0021       1.5       1      15 []      66      80 ..      66      80 .. 0.95
   2 ?   10.1   6.6    0.0019       1.4       1      15 []      95     109 ..      95     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0021
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C + C  +A
  gi|91772646|ref|YP_565338.1| 66 CDLCGKCSDFCQFNA 80
                                  ***********9988 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0019
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gCg C  vCP++A
  gi|91772646|ref|YP_565338.1|  95 CHGCGGCTIVCPNKA 109
                                   ************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 ?    4.2   2.8     0.092        66      44      57 ..      64      77 ..      44      80 .. 0.73
   2 ?    3.8   2.6      0.12        84       1      15 [.      65      79 ..      65      90 .. 0.77
   3 ?   10.6   3.1   0.00092      0.66      44      58 ..      93     107 ..      86     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.092
                       Fer4_17 44 slCieCgeCerkCP 57
                                  ++C  Cg+C+  C 
  gi|91772646|ref|YP_565338.1| 64 NKCDLCGKCSDFCQ 77
                                  56666777766664 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                       Fer4_17  1 rCiqCgyClpeCpsy 15
                                  +C  Cg C + C ++
  gi|91772646|ref|YP_565338.1| 65 KCDLCGKCSDFCQFN 79
                                  588888888888765 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00092
                       Fer4_17  44 slCieCgeCerkCPq 58 
                                    lC++Cg+C+ +CP+
  gi|91772646|ref|YP_565338.1|  93 TLCHGCGGCTIVCPN 107
                                   58************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1957.84
//
Query:       gi|91772647|ref|YP_565339.1|  [L=411]
Description: cation diffusion facilitator family transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-42  145.1  17.2    2.8e-42  144.7  17.2    1.1  1  Cation_efflux  Cation efflux family
      2e-13   50.3   0.3      4e-13   49.3   0.3    1.5  1  ZT_dimer       Dimerisation domain of Zinc Transporter
    2.7e-13   50.0   0.0    5.9e-13   49.0   0.0    1.5  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
       0.13   12.6   3.9       0.49   10.7   3.9    2.0  1  DUF1056        Protein of unknown function (DUF1056)


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 !  144.7  17.2   6.3e-46   2.8e-42       5     199 .]      18     207 ..      15     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 6.3e-46
                 Cation_efflux   5 llanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllglavfl 85 
                                   +++ ++la+++++vg++++S++l+ada+h+  d++++l ++++lkls k++ e+f +Gy+++e+l+al++++l+l+ +v l
  gi|91772647|ref|YP_565339.1|  18 TIVLVFLAAIKGTVGFYSGSSSLIADAIHTSMDIFTSLAVWIGLKLSLKSSGEQFHYGYYKAENLVALFVSVLILLSGVEL 98 
                                   678899*************************************************************************** PP

                 Cation_efflux  86 lleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvillfnlk 166
                                   +   ++++   +++++h glal+ a++s++  +al  +  + gr+++s+al a+a h+ +D+++s++v+v++ +++++   
  gi|91772647|ref|YP_565339.1|  99 VRGVLKSIK-DPVELEHQGLALGAAVFSVITIYALSQYKFKIGRQIGSQALIADATHSYTDVFSSIVVVVAITGSMFG--- 175
                                   ***999988.*******************************************************************7... PP

                 Cation_efflux 167 sgplaDpvaslligliilysalkllkeslseLl 199
                                     +++D+v+ l+i+lii++ +  ++kes + L+
  gi|91772647|ref|YP_565339.1| 176 -IHWLDGVGVLVISLIIFKLGITTAKESALTLM 207
                                   .489*************************9997 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 !   49.3   0.3   8.9e-17     4e-13       2      78 ..     212     288 ..     211     289 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 8.9e-17
                                   ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                      ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                   d++ +e+ir+ ++++pgv +v+d+r r+sG  +f ++++e  g+  ++    ++ e+e+++k+e+p+++++ + v P
  gi|91772647|ref|YP_565339.1| 212 DSDSLERIRRSVNHIPGVNKVDDIRLRRSGLVVFGEMQVESAGEYDLQIVEMLSVEIEEAVKSEIPNLEHISVDVKP 288
                                   78899**********************************************************************99 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 !   49.0   0.0   1.3e-16   5.9e-13       2      89 ..     307     393 ..     306     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.3e-16
                                   TSCB-STCCC-SEEEEEEESSSCEE...EEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEE CS
                 Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevk...ivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievy 79 
                                   +s+++ h G+apy++++e+++++++   i    +++aad + ++g k+a+ l+e++v++viv+ iG+++++k+ +  i+ +
  gi|91772647|ref|YP_565339.1| 307 QSKLSRHIGKAPYYIFIELKDNKIMswdIG---ENPAADLDRKRGVKTAEYLEEQDVNIVIVKDIGGGPFHKFHDSFIKLL 384
                                   6899****************8877744444...555********************************************* PP

                                   ES-SSBHHHH CS
                 Nitro_FeMo-Co  80 kgaggtveea 89 
                                   +    +ve++
  gi|91772647|ref|YP_565339.1| 385 E-MPDDVEDV 393
                                   *.77777776 PP

>> DUF1056  Protein of unknown function (DUF1056)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.9   0.00011      0.49      13      51 ..     156     196 ..     148     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                       DUF1056  13 lfDVLlFiaamivltytaF..lfnataGvlvisvvlflvGl 51 
                                   + DV   i  ++++t ++F   +    Gvlvis+++f +G+
  gi|91772647|ref|YP_565339.1| 156 YTDVFSSIVVVVAITGSMFgiHWLDGVGVLVISLIIFKLGI 196
                                   89*****************3345578899********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2798.32
//
Query:       gi|91772648|ref|YP_565340.1|  [L=639]
Description: nitrite and sulphite reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-36  124.4   0.1    8.7e-36  123.1   0.1    1.7  1  FrhB_FdhB_C   Coenzyme F420 hydrogenase/dehydrogenase, beta s
    3.6e-26   91.6   0.1    7.7e-26   90.5   0.1    1.5  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
      4e-22   78.2   0.1    7.6e-22   77.3   0.1    1.5  1  FrhB_FdhB_N   Coenzyme F420 hydrogenase/dehydrogenase, beta s
      1e-17   63.1  37.9    7.6e-07   28.7   1.0    5.7  6  Fer4          4Fe-4S binding domain
    1.3e-11   44.1   0.0    3.3e-11   42.9   0.0    1.7  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    3.8e-09   36.1  37.1    0.00063   19.7   1.9    5.6  5  Fer4_2        4Fe-4S binding domain
    4.8e-09   36.7  34.2    2.5e-05   24.8  10.5    5.2  5  Fer4_7        4Fe-4S dicluster domain
    6.1e-09   35.9  30.8    0.00046   20.2   0.5    4.1  4  Fer4_10       4Fe-4S dicluster domain
    2.1e-08   34.2  29.2     0.0012   19.0   0.5    4.1  4  Fer4_21       4Fe-4S dicluster domain
    2.6e-08   33.6  22.8    2.9e-05   24.0   2.7    5.6  5  Fer4_6        4Fe-4S binding domain
    1.1e-07   31.9  35.1    4.3e-06   26.8  10.0    4.5  5  Fer4_9        4Fe-4S dicluster domain
    4.1e-06   27.4  23.1      0.011   16.5   0.8    4.7  4  Fer4_15       4Fe-4S single cluster domain
    7.5e-05   23.1  23.7      0.033   14.6   0.7    4.8  4  Fer4_8        4Fe-4S dicluster domain
    0.00011   23.1  30.1       0.14   13.1   0.4    5.2  5  Fer4_16       4Fe-4S double cluster binding domain
    0.00057   20.4  23.4      0.013   16.0   0.1    4.4  4  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    0.00094   19.7  26.4      0.071   13.7   0.5    4.9  5  Fer4_17       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.021   15.0   2.1      0.021   15.0   2.1    3.1  3  Fer4_18       4Fe-4S dicluster domain
       0.36   11.7  27.0      0.053   14.4   2.8    4.4  4  Fer4_22       4Fe-4S dicluster domain
        1.4    9.6  45.9       0.13   12.9   2.7    6.4  6  Fer4_4        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.1   9.3e-39   8.7e-36       2     151 ..     171     329 ..     170     332 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 9.3e-39
                   FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk................kklkekilltiglfCggnfspealrklleelgvdpedvkklefrg 66 
                                   k+va+vG+PCq ++ r+ q                 k +  +i +tiglfC++nf++e+l + ++++g+d ++++k+ +r 
  gi|91772648|ref|YP_565340.1| 171 KNVAMVGVPCQTYGTRRTQFftglnvhpmevgmngeKADIPNIPYTIGLFCMENFNYEKLSEHMKSIGIDLDKIRKYAIR- 250
                                   79*****************777888899999999999999***************************************8. PP

                   FrhB_FdhB_C  67 kgkfrvelkd.ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveage 146
                                      ++v++ d e eislk++ +++ ++C++C+d ++++ADis G v      g ++ g++t+++r++kg elle+a++ag+
  gi|91772648|ref|YP_565340.1| 251 LDVMIVTTDDgEIEISLKDIADCVWDGCRICRDAVSKVADISAGHV------G-SSTGWTTLIARNDKGLELLEAAEKAGY 324
                                   55555555559999********************************......8.*************************** PP

                   FrhB_FdhB_C 147 lelee 151
                                   +e+ +
  gi|91772648|ref|YP_565340.1| 325 IETVD 329
                                   **975 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.1   8.2e-29   7.7e-26       9     152 ..     450     637 ..     445     639 .] 0.97

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 8.2e-29
                                   CCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE.......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                       NIR_SIR   9 tlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei.......... 79 
                                   ++cpg   c+e l+ t++la++++     ++++   P+K+Ki v+gcpn cv++e+nDig+vg  +++             
  gi|91772648|ref|YP_565340.1| 450 NACPGMDYCPEGLVTTKDLANELT----MQFAQKLTPHKMKIGVAGCPNSCVRAESNDIGIVGQLRPKVDTekctgcgrcs 526
                                   79**********************....99************************************99999********** PP

                                   ..........................................EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHH CS
                                   ..........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  80 ..........................................gfnilvGGglgrthgakktsarlgfvpeeevlevveaiv 118
                                                                             g+++++GG+ gr++ ++  ++  +f+++ee+ ++v+++ 
  gi|91772648|ref|YP_565340.1| 527 elcklnaisvisgkavidrdlcincgwcvrgcpheaavedqkGYSVWIGGNDGRRPTNGVLLK--TFCTKEEIPSLVDKVG 605
                                   ***************************************************************..8*************** PP

                                   HHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR 119 evyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                   +++    +r++  keRl++++e +G  +F+++v 
  gi|91772648|ref|YP_565340.1| 606 KTFV--KYRTKPGKERLGNIIELVGEGQFISEVL 637
                                   ****..99***********************995 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 !   77.3   0.1     8e-25   7.6e-22       2      77 ..      91     163 ..      90     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 8e-25
                   FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlklL 77 
                                   v+Ar+td++i +k+q+GG+vtall+y++++g+idg++++a  +   +p   i+ +keell+++G kY+ +p++++L
  gi|91772648|ref|YP_565340.1|  91 VSARATDPSIAEKGQDGGAVTALLGYCFDNGLIDGAVTTAGFT---KPDSCIVASKEELLDTQGAKYSAVPVMAAL 163
                                   89*************************************9553...7***************************99 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   5.1   3.2e-09     3e-06       2      24 .]      13      35 ..      12      35 .. 0.94
   2 ?    0.8   0.3      0.51   4.8e+02      12      18 ..      53      59 ..      53      61 .. 0.90
   3 ?   -1.2   0.3       2.2   2.1e+03      10      17 ..     277     284 ..     276     284 .. 0.83
   4 ?   -2.8   0.0       7.4     7e+03      16      21 ..     456     461 ..     455     462 .. 0.79
   5 !   28.7   1.0   8.1e-10   7.6e-07       1      24 []     512     535 ..     512     535 .. 0.94
   6 !   26.6   3.6   3.8e-09   3.6e-06       2      22 ..     542     562 ..     541     564 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.2e-09
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  v+d+ +C+ CGaC+ vCP++ I+
  gi|91772648|ref|YP_565340.1| 13 VVDTGMCTLCGACAAVCPYEIIE 35
                                  89******************996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                                  THHHHHS CS
                          Fer4 12 GaCvevC 18
                                  GaC +vC
  gi|91772648|ref|YP_565340.1| 53 GACKDVC 59
                                  9****** PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.2
                                   S-THHHHH CS
                          Fer4  10 gCGaCvev 17 
                                   gC +C ++
  gi|91772648|ref|YP_565340.1| 277 GCRICRDA 284
                                   9****875 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 7.4
                                   HHSTTT CS
                          Fer4  16 evCPvg 21 
                                   + CP g
  gi|91772648|ref|YP_565340.1| 456 DYCPEG 461
                                   78**86 PP

  == domain 5  score: 28.7 bits;  conditional E-value: 8.1e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   +++d+ekC+gCG+C e C  +AI+
  gi|91772648|ref|YP_565340.1| 512 PKVDTEKCTGCGRCSELCKLNAIS 535
                                   589*******************95 PP

  == domain 6  score: 26.6 bits;  conditional E-value: 3.8e-09
                                   EEETTTSSS-THHHHHSTTTE CS
                          Fer4   2 videekCigCGaCvevCPvgA 22 
                                   vid ++Ci+CG Cv  CP++A
  gi|91772648|ref|YP_565340.1| 542 VIDRDLCINCGWCVRGCPHEA 562
                                   8******************98 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 !   42.9   0.0   3.5e-14   3.3e-11       3      65 ..     375     435 ..     373     437 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.5e-14
                  NIR_SIR_ferr   3 qkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeilee 65 
                                     +g+  ++v +++ +G++  +   ++a++aekyg+g + lT+r ++++ gv+ ++++ ++++
  gi|91772648|ref|YP_565340.1| 375 EANGT--NFVKIKTNSGIVQHDYIARVAELAEKYGDGSLELTSRKSVEIQGVKGKNVDSLMAD 435
                                   45665..89**************************************************9986 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   3.5   1.5e-06    0.0014       3      22 .]      12      31 ..      10      31 .. 0.92
   2 ?   -2.2   0.7       6.2   5.8e+03      14      20 ..      53      59 ..      46      60 .. 0.76
   3 ?    1.7   0.7      0.35   3.3e+02      12      19 ..     277     284 ..     270     284 .. 0.84
   4 !   19.7   1.9   6.7e-07   0.00063       2      20 ..     511     529 ..     510     530 .. 0.92
   5 !   17.2   2.0   4.2e-06    0.0039       2      22 .]     540     560 ..     539     560 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +vvdt +C+ CgaC  +CP+
  gi|91772648|ref|YP_565340.1| 12 AVVDTGMCTLCGACAAVCPY 31
                                  689****************5 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                        Fer4_2 14 gaCvsaC 20
                                  gaC ++C
  gi|91772648|ref|YP_565340.1| 53 GACKDVC 59
                                  6999999 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.35
                        Fer4_2  12 gCgaCvsa 19 
                                   gC++C++a
  gi|91772648|ref|YP_565340.1| 277 GCRICRDA 284
                                   7****987 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 6.7e-07
                        Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                   +++vdt++C+gCg C   C
  gi|91772648|ref|YP_565340.1| 511 RPKVDTEKCTGCGRCSELC 529
                                   689************9999 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 4.2e-06
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                   ++v+d+d Ci+Cg Cv  CP+
  gi|91772648|ref|YP_565340.1| 540 KAVIDRDLCINCGWCVRGCPH 560
                                   579*****************7 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   6.1   2.9e-06    0.0027       2      48 ..      19      59 ..      18      79 .. 0.75
   2 ?   -2.0   0.3       5.9   5.6e+03       4      11 ..     277     284 ..     272     295 .. 0.82
   3 !   16.4   5.9   1.1e-05      0.01       9      52 .]     489     533 ..     450     533 .. 0.78
   4 !   24.8  10.5   2.7e-08   2.5e-05       1      52 []     518     562 ..     518     562 .. 0.93
   5 !   12.4   2.5   0.00019      0.18       2      18 ..     548     564 ..     547     572 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekCl..gCgaCvavC 48
                                  C+ CgaC+a+Cp++ ie+de   +k         e+C+  g gaC +vC
  gi|91772648|ref|YP_565340.1| 19 CTLCGACAAVCPYEIIEFDEN-GPKL-------KEECYrnGEGACKDVC 59
                                  ******************986.2332.......3445411233355555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.9
                        Fer4_7   4 gCgaCvaa 11 
                                   gC+ C +a
  gi|91772648|ref|YP_565340.1| 277 GCRICRDA 284
                                   89999876 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.1e-05
                        Fer4_7   9 vaaCpvkaieldee.enekgtekveidpekClgCgaCvavCPtga 52 
                                   va Cp+++++ +       g+ ++++d ekC+gCg+C + C  +a
  gi|91772648|ref|YP_565340.1| 489 VAGCPNSCVRAESNdIGIVGQLRPKVDTEKCTGCGRCSELCKLNA 533
                                   466888888776431333477888*****************8765 PP

  == domain 4  score: 24.8 bits;  conditional E-value: 2.7e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C+gCg+C + C+ +ai++          k++id + C++Cg Cv+ CP++a
  gi|91772648|ref|YP_565340.1| 518 KCTGCGRCSELCKLNAISVIS-------GKAVIDRDLCINCGWCVRGCPHEA 562
                                   7*****************965.......379******************986 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00019
                        Fer4_7   2 CigCgaCvaaCpvkaie 18 
                                   Ci+Cg Cv+ Cp++a  
  gi|91772648|ref|YP_565340.1| 548 CINCGWCVRGCPHEAAV 564
                                   ************98865 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   7.5   4.2e-06     0.004       3      55 ..      13      59 ..      11      60 .. 0.88
   2 !    7.3   8.7    0.0052       4.9      24      55 ..     498     529 ..     449     530 .. 0.76
   3 !   11.3   3.3   0.00031      0.29       3      19 ..     513     529 ..     511     536 .. 0.83
   4 !   20.2   0.5   4.9e-07   0.00046       1      24 [.     540     566 ..     540     593 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.2e-06
                       Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaC 55
                                  v+d+  C+ Cg+C ++CP+        ++++ +e   k  e+C + g  aC ++C
  gi|91772648|ref|YP_565340.1| 13 VVDTGMCTLCGACAAVCPY--------EIIEFDENGPKLKEECYRNGegACKDVC 59
                                  788899*************........99999999999999999975559*9999 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0052
                       Fer4_10  24 tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   ++ ++   + ++ + +++ ekCtgcg C e C
  gi|91772648|ref|YP_565340.1| 498 RAESNDIGIVGQLRPKVDTEKCTGCGRCSELC 529
                                   55555566666666677778888888888777 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00031
                       Fer4_10   3 vidddtCirCgkCvkaC 19 
                                   ++d+++C++Cg+C + C
  gi|91772648|ref|YP_565340.1| 513 KVDTEKCTGCGRCSELC 529
                                   57899999999999999 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 4.9e-07
                       Fer4_10   1 kvvidddtCirCgkCvkaCPadl...t 24 
                                   k+vid+d Ci+Cg Cv+ CP  +   +
  gi|91772648|ref|YP_565340.1| 540 KAVIDRDLCINCGWCVRGCPHEAaveD 566
                                   579*****************9544331 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   5.9   0.00063      0.59       1      51 [.      12      59 ..      12      66 .. 0.81
   2 ?   -1.6   0.2       3.2   3.1e+03      40      48 ..     272     282 ..     255     286 .. 0.73
   3 !   18.4   3.7   1.8e-06    0.0017       9      58 ..     487     535 ..     483     536 .. 0.87
   4 !   19.0   0.5   1.2e-06    0.0012       1      26 [.     541     563 ..     541     574 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00063
                       Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCv..GCnlCssvC 51
                                  A++d  +C  Cg C+ +C+   ++ ie+d++   + +++eC   G   C +vC
  gi|91772648|ref|YP_565340.1| 12 AVVDTGMCTLCGACAAVCP---YEIIEFDENG--PKLKEECYrnGEGACKDVC 59
                                  7899999999999999999...8999998654..5778888544777888888 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                       Fer4_21  40 eCv..GCnlCs 48 
                                   +Cv  GC +C 
  gi|91772648|ref|YP_565340.1| 272 DCVwdGCRICR 282
                                   67666899986 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.8e-06
                       Fer4_21   9 igCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   ig   C  +C  +  + i i ++ + kv +++C+GC  Cs+ C + ++i+
  gi|91772648|ref|YP_565340.1| 487 IGVAGCPNSCVRAESNDIGIVGQLRPKVDTEKCTGCGRCSELCKL-NAIS 535
                                   6667799999999999999999*9*******************86.7775 PP

  == domain 4  score: 19.0 bits;  conditional E-value: 1.2e-06
                       Fer4_21   1 AridedkCigCgkCliaCedtshqai 26 
                                   A+id+d Ci+Cg C+  C+    +a 
  gi|91772648|ref|YP_565340.1| 541 AVIDRDLCINCGWCVRGCPH---EAA 563
                                   89****************94...443 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   3.8   2.6e-07   0.00025       2      24 .]      12      34 ..      12      34 .. 0.93
   2 ?   -2.6   2.1       7.6   7.1e+03       9      15 ..     273     281 ..     269     283 .. 0.82
   3 ?   -2.1   0.2       5.1   4.8e+03      16      22 ..     455     461 ..     450     462 .. 0.64
   4 !   16.5   1.4   7.1e-06    0.0067       2      19 ..     512     529 ..     511     534 .. 0.87
   5 !   24.0   2.7   3.1e-08   2.9e-05       1      23 [.     540     562 ..     540     563 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.6e-07
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  +++d   C+ Cg+C++vCP+ +i
  gi|91772648|ref|YP_565340.1| 12 AVVDTGMCTLCGACAAVCPYEII 34
                                  5899***************9987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.6
                        Fer4_6   9 Ci..gCgdC 15 
                                   C+  gC+ C
  gi|91772648|ref|YP_565340.1| 273 CVwdGCRIC 281
                                   77769**99 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.1
                        Fer4_6  16 vrvCPeg 22 
                                   ++ CPeg
  gi|91772648|ref|YP_565340.1| 455 MDYCPEG 461
                                   5678887 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 7.1e-06
                        Fer4_6   2 veidpdkCigCgdCvrvC 19 
                                   + +d +kC+gCg+C   C
  gi|91772648|ref|YP_565340.1| 512 PKVDTEKCTGCGRCSELC 529
                                   789***********9888 PP

  == domain 5  score: 24.0 bits;  conditional E-value: 3.1e-08
                        Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                   +++id+d+Ci Cg Cvr CP+ a
  gi|91772648|ref|YP_565340.1| 540 KAVIDRDLCINCGWCVRGCPHEA 562
                                   689*****************976 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   7.8     6e-05     0.057       2      48 ..      19      61 ..      18      63 .. 0.81
   2 ?   -0.6   0.2       1.6   1.5e+03      18      44 ..     257     283 ..     252     284 .. 0.59
   3 !   13.8   6.4   5.2e-05     0.049      11      51 .]     457     534 ..     450     534 .. 0.71
   4 !   26.8  10.0   4.6e-09   4.3e-06       1      50 [.     518     562 ..     518     564 .. 0.91
   5 !   15.1   2.1     2e-05     0.019       2      24 ..     548     570 ..     547     575 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48
                                  Ct CgaC ++Cp+++++ d+++ k + +++++    g gaC ++C++
  gi|91772648|ref|YP_565340.1| 19 CTLCGACAAVCPYEIIEFDENGPKLKEECYRN----GEGACKDVCQR 61
                                  ***********************999876655....33557777765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                        Fer4_9  18 vedaaerkarlraaseeaC..igCgaCve 44 
                                   + d++e +++l+     +C   gC+ C +
  gi|91772648|ref|YP_565340.1| 257 TTDDGEIEISLKDIA--DCvwDGCRICRD 283
                                   455555555655554..486446888875 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 5.2e-05
                        Fer4_9  11 aCpagvvvedaaerkarlraase.....................................eaCigCgaCveaCpkgai 51 
                                    Cp g+v+ ++ +++  ++ a++                                     e+C+gCg+C e C+ +ai
  gi|91772648|ref|YP_565340.1| 457 YCPEGLVTTKDLANELTMQFAQKltphkmkigvagcpnscvraesndigivgqlrpkvdtEKCTGCGRCSELCKLNAI 534
                                   5666666666666666666655566666666666666666666777777777777779999************99876 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 4.6e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   kCtgCg+C e C+ ++++  +++  +  +      Ci Cg Cv  Cp++a
  gi|91772648|ref|YP_565340.1| 518 KCTGCGRCSELCKLNAISVISGKAVIDRD-----LCINCGWCVRGCPHEA 562
                                   7****************999999998874.....6************975 PP

  == domain 5  score: 15.1 bits;  conditional E-value: 2e-05
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaer 24 
                                   C++Cg Cv+ Cp++++ved++++
  gi|91772648|ref|YP_565340.1| 548 CINCGWCVRGCPHEAAVEDQKGY 570
                                   9**************99998775 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   3.2   0.00067      0.63       2      29 ..      13      41 ..      13      68 .. 0.82
   2 ?   -1.5   0.0       4.7   4.4e+03      18      30 ..     302     314 ..     275     340 .. 0.47
   3 !   11.0   2.1   0.00057      0.54       2      19 ..     513     530 ..     513     543 .. 0.82
   4 !   16.5   0.8   1.1e-05     0.011       2      33 ..     542     574 ..     541     590 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00067
                       Fer4_15  2 vvDrdaCigcglCvaeap.evfeldedgl 29
                                  vvD   C+ cg+C+a++p e++e+de+g 
  gi|91772648|ref|YP_565340.1| 13 VVDTGMCTLCGACAAVCPyEIIEFDENGP 41
                                  589999***********658999999985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.7
                       Fer4_15  18 apevfeldedgla 30 
                                   +++++  +++gl 
  gi|91772648|ref|YP_565340.1| 302 WTTLIARNDKGLE 314
                                   3444444444444 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00057
                       Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                   +vD ++C+gcg+C ++++
  gi|91772648|ref|YP_565340.1| 513 KVDTEKCTGCGRCSELCK 530
                                   59*************996 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 1.1e-05
                       Fer4_15   2 vvDrdaCigcglCvaea.pevfeldedglasvl 33 
                                   v+Drd+Ci cg Cv+ +  e  ++d++g+++ +
  gi|91772648|ref|YP_565340.1| 542 VIDRDLCINCGWCVRGCpHEAAVEDQKGYSVWI 574
                                   79***************5578888889998665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.7   3.5e-05     0.033      49      65 .]      17      33 ..       6      33 .. 0.87
   2 ?    2.7   0.1      0.19   1.8e+02       4      17 ..      46      62 ..      44     119 .. 0.69
   3 ?    5.1   7.5     0.034        32      45      62 ..     513     530 ..     449     533 .. 0.65
   4 !    9.4   0.3    0.0015       1.4       5      63 ..     548     560 ..     544     584 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                        Fer4_8 49 wsCttcgaCtevCpvgi 65
                                  + Ct cgaC+ vCp +i
  gi|91772648|ref|YP_565340.1| 17 GMCTLCGACAAVCPYEI 33
                                  57***********9876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                        Fer4_8  4 kCieCg..aCqsaCp.v 17
                                  +C ++g  aC++ C  v
  gi|91772648|ref|YP_565340.1| 46 ECYRNGegACKDVCQrV 62
                                  68888555999999632 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.034
                        Fer4_8  45 eealwsCttcgaCtevCp 62 
                                   +   ++Ct+cg+C+e C+
  gi|91772648|ref|YP_565340.1| 513 KVDTEKCTGCGRCSELCK 530
                                   555677888888888886 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0015
                        Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                   Ci+Cg C   C                                              p 
  gi|91772648|ref|YP_565340.1| 548 CINCGWCVRGC----------------------------------------------PH 560
                                   55555555555..............................................54 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 !   10.8   8.3    0.0008      0.75       2      30 ..      19      47 ..      18      69 .. 0.73
   2 ?   -0.1   0.1       1.9   1.8e+03      53      62 ..     272     283 ..     239     284 .. 0.72
   3 ?   -2.1   0.1         8   7.6e+03      11      20 ..     457     466 ..     451     502 .. 0.58
   4 !   11.6   0.8   0.00043       0.4       1      18 [.     518     535 ..     511     545 .. 0.83
   5 !   13.1   0.4   0.00015      0.14       2      21 ..     548     567 ..     547     575 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0008
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearec 30
                                  C+ Cg+Ca vCP + i+ +++    ++ec
  gi|91772648|ref|YP_565340.1| 19 CTLCGACAAVCPYEIIEFDENGPKLKEEC 47
                                  *****************995444334444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                       Fer4_16  53 ai..tgCdiCqd 62 
                                   ++   gC+iC d
  gi|91772648|ref|YP_565340.1| 272 DCvwDGCRICRD 283
                                   444589999986 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 8
                       Fer4_16  11 vCPtnaikek 20 
                                    CP++ +++k
  gi|91772648|ref|YP_565340.1| 457 YCPEGLVTTK 466
                                   5666665555 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00043
                       Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                   +C++Cg+C e C  nai+
  gi|91772648|ref|YP_565340.1| 518 KCTGCGRCSELCKLNAIS 535
                                   599999999999999987 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 0.00015
                       Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                   C++Cg C+  CP++a  e++
  gi|91772648|ref|YP_565340.1| 548 CINCGWCVRGCPHEAAVEDQ 567
                                   **************988873 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 ?    6.1   4.2     0.017        16       1      17 [.      14      30 ..      14      62 .. 0.85
   2 ?   -2.4   0.0       7.9   7.5e+03      44      56 ..     485     497 ..     474     498 .. 0.79
   3 !    9.9   1.7    0.0011         1       1      16 [.     514     529 ..     514     531 .. 0.95
   4 !   16.0   0.1   1.4e-05     0.013       1      34 [.     543     576 ..     543     590 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  VD   C+ cgaC++++P
  gi|91772648|ref|YP_565340.1| 14 VDTGMCTLCGACAAVCP 30
                                  88999************ PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.9
                       Fer4_13  44 aeeAadaCPvesI 56 
                                   ++  +++CP +++
  gi|91772648|ref|YP_565340.1| 485 MKIGVAGCPNSCV 497
                                   5566789**9986 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0011
                       Fer4_13   1 VDrdtCiacgaCvela 16 
                                   VD ++C++cg C el+
  gi|91772648|ref|YP_565340.1| 514 VDTEKCTGCGRCSELC 529
                                   9*************99 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.4e-05
                       Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeq 34 
                                   +Drd Ci+cg Cv  +P+  + +d++g+sv   +
  gi|91772648|ref|YP_565340.1| 543 IDRDLCINCGWCVRGCPHEAAVEDQKGYSVWIGG 576
                                   8****************99888888888876655 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.5   7.5e-05     0.071      45      60 ..      18      33 ..      10      42 .. 0.83
   2 ?   -1.0   0.1       2.8   2.7e+03       6      17 ..      53      64 ..      46      91 .. 0.78
   3 ?   -2.1   0.0       6.4   6.1e+03       4       9 ..     277     282 ..     246     284 .. 0.67
   4 ?    5.8   6.3     0.022        20      33      57 ..     506     530 ..     450     533 .. 0.70
   5 !   12.1   0.4   0.00023      0.21      44      59 ..     546     561 ..     536     566 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-05
                       Fer4_17 45 lCieCgeCerkCPqgl 60
                                   C+ Cg C+++CP+++
  gi|91772648|ref|YP_565340.1| 18 MCTLCGACAAVCPYEI 33
                                  6888888888888875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.8
                       Fer4_17  6 gyClpeCpsyea 17
                                  g+C ++C + + 
  gi|91772648|ref|YP_565340.1| 53 GACKDVCQRVMT 64
                                  569999988665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.4
                       Fer4_17   4 qCgyCl 9  
                                   +C+ C+
  gi|91772648|ref|YP_565340.1| 277 GCRICR 282
                                   344443 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.022
                       Fer4_17  33 lleeaekeekaslCieCgeCerkCP 57 
                                   ++++   +   ++C++Cg+C++ C 
  gi|91772648|ref|YP_565340.1| 506 IVGQLRPKVDTEKCTGCGRCSELCK 530
                                   4444444457899999999999995 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00023
                       Fer4_17  44 slCieCgeCerkCPqg 59 
                                   +lCi+Cg C+r CP++
  gi|91772648|ref|YP_565340.1| 546 DLCINCGWCVRGCPHE 561
                                   6899999999999986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.1   2.2e-05     0.021      57     102 ..      15      66 ..       6      78 .. 0.74
   2 ?   -2.1   0.4       4.6   4.3e+03      87     100 ..     277     290 ..     257     296 .. 0.60
   3 ?    5.2   8.8     0.024        23      53      96 ..     511     559 ..     494     571 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                       Fer4_18  57 gagdcidcescvkvcPtgi.di.rkG..lqleciscll..cidacdkvmekl 102
                                   ++g c+ c++c +vcP +i +   +G  l+ ec   ++  c d c++vm   
  gi|91772648|ref|YP_565340.1|  15 DTGMCTLCGACAAVCPYEIiEFdENGpkLKEECYRNGEgaCKDVCQRVMTDA 66 
                                   6789************997333234533677899875434*********764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
                       Fer4_18  87 scllcidacdkvme 100
                                    c  c da +kv +
  gi|91772648|ref|YP_565340.1| 277 GCRICRDAVSKVAD 290
                                   36666666665543 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.024
                       Fer4_18  53 rkekgagdcidcescvkvcPt.gidirkGlql.e...ciscllcidacd 96 
                                   r + ++ +c+ c+ c ++c    i +  G  + +   ci+c+ c+  c 
  gi|91772648|ref|YP_565340.1| 511 RPKVDTEKCTGCGRCSELCKLnAISVISGKAViDrdlCINCGWCVRGCP 559
                                   55667889***********973599999976532445********9995 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4    0.0062       5.9      78      95 ..      15      32 ..       4      33 .. 0.74
   2 ?   -1.8   0.0       6.3   5.9e+03      58      87 ..     468     498 ..     452     507 .. 0.69
   3 ?   14.4   2.8   5.6e-05     0.053      74      94 ..     511     531 ..     504     533 .. 0.85
   4 ?    6.0   1.2     0.023        22      77      94 ..     543     560 ..     535     562 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0062
                       Fer4_22 78 gesgCvGCgRCieacpvk 95
                                  ++ +C+ Cg C ++cp +
  gi|91772648|ref|YP_565340.1| 15 DTGMCTLCGACAAVCPYE 32
                                  667888888888888876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.3
                       Fer4_22  58 kkerlrqrllhklsefkekfgesgC.vGCgR 87 
                                    ++ l  ++ +kl+ +k k+g  gC   C R
  gi|91772648|ref|YP_565340.1| 468 LANELTMQFAQKLTPHKMKIGVAGCpNSCVR 498
                                   4556666777777777777777777224555 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5.6e-05
                       Fer4_22  74 kekfgesgCvGCgRCieacpv 94 
                                   + k+++++C+GCgRC+e c+ 
  gi|91772648|ref|YP_565340.1| 511 RPKVDTEKCTGCGRCSELCKL 531
                                   567899*************85 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.023
                       Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                   +++  C+ Cg C++ cp+
  gi|91772648|ref|YP_565340.1| 543 IDRDLCINCGWCVRGCPH 560
                                   578899999999999997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.7   0.00014      0.13       3      16 ..      18      31 ..      15      32 .. 0.91
   2 ?    4.5   0.7     0.063        60       2      14 ..      45      59 ..      44      65 .. 0.88
   3 ?   -0.7   1.1       2.9   2.8e+03       4      13 ..     273     284 ..     271     284 .. 0.80
   4 ?   -1.3   0.2       4.5   4.3e+03       6      12 ..     491     498 ..     490     499 .. 0.73
   5 ?    7.4   3.6    0.0075       7.1       2      15 ..     517     530 ..     516     532 .. 0.83
   6 ?   12.0   1.3   0.00025      0.23       2      15 ..     546     559 ..     544     571 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                   C+ Cg+C a+CP+
  gi|91772648|ref|YP_565340.1| 18 MCTLCGACAAVCPY 31
                                  5************8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.063
                        Fer4_4  2 erC..igCgsCvaaC 14
                                  e C  +g g+C ++C
  gi|91772648|ref|YP_565340.1| 45 EECyrNGEGACKDVC 59
                                  778889********* PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.9
                        Fer4_4   4 Ci..gCgsCvaa 13 
                                   C+  gC+ C++a
  gi|91772648|ref|YP_565340.1| 273 CVwdGCRICRDA 284
                                   76669****985 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.5
                        Fer4_4   6 gCg.sCva 12 
                                   gC+ sCv+
  gi|91772648|ref|YP_565340.1| 491 GCPnSCVR 498
                                   78877987 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0075
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   e+C+gCg+C   C+
  gi|91772648|ref|YP_565340.1| 517 EKCTGCGRCSELCK 530
                                   89*******77775 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00025
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   + Ci+Cg Cv+ CP
  gi|91772648|ref|YP_565340.1| 546 DLCINCGWCVRGCP 559
                                   67***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4471.70
//
Query:       gi|91772649|ref|YP_565341.1|  [L=123]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Methanococcoides burtonii DSM 6242]
Scores for complete 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   73.0   0.0    2.8e-20   72.5   0.0    1.3  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 !   72.5   0.0   1.5e-24   2.8e-20       2      94 ..      14     101 ..      13     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.5e-24
                                   TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES- CS
                 Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykga 82 
                                   ++ v qhFGr p+++i ++e++e++ +en+     +++ gg g +++ll++eg+dv+++g+ G +a++++e+ g+evy+ga
  gi|91772649|ref|YP_565341.1|  14 DDLVGQHFGRVPTYTIKDTETNEIRTIENK-----SEHMGGVGLPPELLSQEGIDVMLCGGLGDKAVQQFEQFGMEVYVGA 89 
                                   67899*************************.....889999**************************************** PP

                                   SSBHHHHHHHHH CS
                 Nitro_FeMo-Co  83 ggtveealkevl 94 
                                   +gtveea++++ 
  gi|91772649|ref|YP_565341.1|  90 KGTVEEAIMAWE 101
                                   *********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 00:00:00.47
# Mc/sec: 790.64
//
Query:       gi|91772650|ref|YP_565342.1|  [L=153]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   87.9   0.0    5.7e-25   87.5   0.0    1.2  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   3.2e-29   5.7e-25       4      94 ..      15     102 ..      12     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 3.2e-29
                                   CB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SS CS
                 Nitro_FeMo-Co   4 rvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykgagg 84 
                                    +d +FGr+pyF+i++ e+ e+k v+n    aa+a+gg+g+++aq ++++g+dv+++g+iGp+a+  l+aagi+v++ga+g
  gi|91772650|ref|YP_565342.1|  15 ALDLRFGRCPYFIIVDSETMEFKAVDNS---AASAAGGAGIQAAQNISDKGIDVLLTGSIGPNAFPILSAAGIQVMTGASG 92 
                                   67899***********************...************************************************** PP

                                   BHHHHHHHHH CS
                 Nitro_FeMo-Co  85 tveealkevl 94 
                                   +v +a+ +++
  gi|91772650|ref|YP_565342.1|  93 SVTDAISQYK 102
                                   *******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1184.66
//
Query:       gi|91772651|ref|YP_565343.1|  [L=233]
Description: hypothetical protein Mbur_0622 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-54  184.7   0.0    2.4e-54  184.4   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 !  184.4   0.0   1.3e-58   2.4e-54       2     204 ..      10     217 ..       9     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 1.3e-58
                        DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklksg... 79 
                                   L e+l+lk +PVa+ +++++ ++pe+ +kie + r+Cqm + ar +++  ++t  +++C+gGaaa+G+++ p+k+ksg   
  gi|91772651|ref|YP_565343.1|  10 LIETLKLKGKPVAISLLKREIDIPEDLQKIEIPRRYCQMLQDARFNDTVTFATMGEHACKGGAAAIGLQDYPDKIKSGely 90 
                                   899*****************************************99999999**************************888 PP

                        DUF169  80 ...egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvsfpgngaa 157
                                      +g+  s+ +ak++v+++pr  +g++ +++vapL++++  Pdv+++++n+  ++r+++++ y+rgg r++++f+g++++
  gi|91772651|ref|YP_565343.1|  91 fdkLGKEISLSVAKRVVDNMPRPAPGSTVATIVAPLDNTPTRPDVIIVIGNTLVARRIAHSVIYRRGG-RMTANFAGIQST 170
                                   8766666699***********99*******************************************99.************ PP

                        DUF169 158 CadivaypykegepniglgdpgarkfaklkddelafgiPyelleemv 204
                                   Cad++  py +ge ni++g+ ga k+a+lkdde+++giP e+le++ 
  gi|91772651|ref|YP_565343.1| 171 CADATGSPYITGEVNISIGCDGAAKNAGLKDDEMVIGIPEEQLEDIT 217
                                   *******************************************9985 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:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1705.27
//
Query:       gi|91772652|ref|YP_565344.1|  [L=135]
Description: JAMM-like protein. metallo peptidase. MEROPS family M67B [Methanococcoides burtonii DSM 6242]
Scores for complete 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   34.0   0.0    3.1e-08   33.4   0.0    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain
     0.0027   17.6   0.0     0.0037   17.2   0.0    1.3  1  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   3.5e-12   3.1e-08       8     117 ..      14     108 ..       7     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.5e-12
                      Prok-JAB   8 lvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpggsarPSetD 88 
                                   +++  ++++p+E +Gll  k  +  ev + p           + + ++ a++k   +  + + vg +HSHpg+  rPS +D
  gi|91772652|ref|YP_565344.1|  14 ILKVSESTSPNEFAGLLQEKDGIITEVLILPG----------TESSEINAVIK-LFMMPNVSSVGSVHSHPGPNIRPSNAD 83 
                                   66667788999999999887733334444443..........58888899999.999************************ PP

                      Prok-JAB  89 rrdaaalarvkalliivgdkaeelrawrl 117
                                   +r + +++     +iivg+ +++   w++
  gi|91772652|ref|YP_565344.1|  84 LRLFGKTG---NCHIIVGQ-PYDESNWQC 108
                                   ******95...55555554.566557765 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.2e-07    0.0037      28      90 ..      30      89 ..       9     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.2e-07
                                  E-TTSBEEEEEEEEESTT-GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHHH CS
                          RadC 28 LdsknrliadeelseGtlnstlvdprevfkealklnAaavilaHnhPsgdlepSeeDieltkr 90
                                  L +k  +i++  +  Gt +    +++ v+k  +  n ++v  +H hP  +++pS++D++l  +
  gi|91772652|ref|YP_565344.1| 30 LQEKDGIITEVLILPGTES---SEINAVIKLFMMPNVSSVGSVHSHPGPNIRPSNADLRLFGK 89
                                  5666667777777777754...5678899999999**********************998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 872.65
//
Query:       gi|91772653|ref|YP_565345.1|  [L=134]
Description: hypothetical protein Mbur_0624 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 892.69
//
Query:       gi|91772654|ref|YP_565346.1|  [L=382]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0054   17.0   1.6      0.014   15.6   1.6    1.7  1  DDE_Tnp_IS240    DDE domain
     0.0073   16.3   1.5      0.025   14.5   1.5    1.9  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0091   16.1   0.4        3.9    7.7   0.0    2.6  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
       0.01   16.5   4.7       0.01   16.5   4.7    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
      0.034   14.5   0.2      0.074   13.4   0.2    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.063   13.1   0.6       0.27   11.1   0.0    2.4  3  DUF4817          Helix-turn-helix domain (DUF4817)
       0.08   13.2   0.0       0.17   12.1   0.0    1.5  1  UPF0489          UPF0489 domain
       0.47   11.0   4.8        2.5    8.7   1.9    2.6  2  zf-H2C2_2        Zinc-finger double domain
        1.9    9.6   6.0        2.5    9.2   0.3    3.3  3  zf-C2H2_4        C2H2-type zinc finger
        1.9    9.1   5.9        2.7    8.6   1.8    3.2  2  zf-C2H2          Zinc finger, C2H2 type
        2.2    8.0   4.7        3.1    7.6   0.0    2.5  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI


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 !   15.6   1.6   8.5e-06     0.014       6     124 ..     189     307 ..     186     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.5e-06
                 DDE_Tnp_IS240   6 vDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkregelf. 84 
                                    DE y+k +G+  Y   ++D+  +  ++ ++  + + + +k f++ka+++      +i tD    y+s +++l  + +l  
  gi|91772654|ref|YP_565346.1| 189 YDEQYLKLNGRRFYRLSLIDSIFNkPVEEMIVTNLEYDTVKDFIEKATSNR--LIYAISTDHRIKYKSIMDKLEIKHQLCi 267
                                   6********************9999***********************999..7889****************98765544 PP

                 DDE_Tnp_IS240  85 ............devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                               +             + s++  ++++++    f ++k++ +
  gi|91772654|ref|YP_565346.1| 268 fylykligndvfK------------KLKSKFVSYREKINMCLTFTEIKEIFR 307
                                   4444333333331............444555555555555555555544444 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.5   1.5e-05     0.025      19      45 ..      67     109 ..      59     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                 Zn_Tnp_IS1595  19 fvCPhCgsr....kayrikt................rglfqCkeCrk 45 
                                   + CP Cgs     +    +                  +++ Ck+C+k
  gi|91772654|ref|YP_565346.1|  67 PQCPVCGSNkinkQ----EYytrklklaefgsqiihVRRYYCKKCSK 109
                                   89*****9955532....3344469********************97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0024       3.9      26      38 ..      66      79 ..      52      80 .. 0.77
   2 !    5.8   0.1    0.0091        15       6      17 ..     102     114 ..     101     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                   Zn-ribbon_8 26 ltaCPeCgs.evrr 38
                                   ++CP Cgs +  +
  gi|91772654|ref|YP_565346.1| 66 HPQCPVCGSnKINK 79
                                  567******88766 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0091
                   Zn-ribbon_8   6 YrCeeCghefe.v 17 
                                   Y C++C ++f+ +
  gi|91772654|ref|YP_565346.1| 102 YYCKKCSKRFTtP 114
                                   99********853 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 ?   16.5   4.7   6.4e-06      0.01       3      47 .]      67     107 ..      66     107 .. 0.94
   2 ?   -2.7   0.1         6   9.8e+03      32      42 ..     191     201 ..     186     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.4e-06
                       zf-ISL3   3 hrCPnCgsktvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47 
                                   ++CP Cgs +  k  +++r+ +   +g +     + +rRy+Ck+C
  gi|91772654|ref|YP_565346.1|  67 PQCPVCGSNKINKQEYYTRKLKLAEFGSQI----IHVRRYYCKKC 107
                                   68************************9985....6789******9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6
                       zf-ISL3  32 rvyLrlrkrRy 42 
                                   + yL+l+ rR+
  gi|91772654|ref|YP_565346.1| 191 EQYLKLNGRRF 201
                                   55788887877 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.5e-05     0.074       5      37 ..      68     115 ..      66     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
               Lar_restr_allev   5 pCPfCggravlersqrvvaeigq..........cvyCadCga.....s 37 
                                    CP Cg+ ++ ++++++++ +              yC++C        
  gi|91772654|ref|YP_565346.1|  68 QCPVCGSNKINKQEYYTRKLKLAefgsqiihvrRYYCKKCSKrfttpL 115
                                   7*****************987779****************98664443 PP

>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.4     1e+04      44      52 ..      36      44 ..      34      45 .. 0.82
   2 ?   -2.9   0.1       3.9   6.4e+03       9      18 ..      99     108 ..      96     110 .. 0.82
   3 ?   11.1   0.0   0.00017      0.27      23      47 ..     144     170 ..     137     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.4
                       DUF4817 44 lvkkfeetG 52
                                  ++ +f +tG
  gi|91772654|ref|YP_565346.1| 36 IISHFSSTG 44
                                  6899**999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.9
                       DUF4817   9 VkaYyknges 18 
                                   V+ Yy+ ++s
  gi|91772654|ref|YP_565346.1|  99 VRRYYCKKCS 108
                                   8899999876 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00017
                       DUF4817  23 qrafrrrFp..nrsvPsrstirrlvkk 47 
                                   +r++ + F    +  Ps++ti+++++k
  gi|91772654|ref|YP_565346.1| 144 FRHLQKIFSslYDCSPSHQTIYNWIRK 170
                                   566667777666788***********9 PP

>> UPF0489  UPF0489 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.17      18      57 ..      43      90 ..      33     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                       UPF0489 18 igskklp.sdlslvHlDaHpDllipk.......kmsaddvfnallkil 57
                                   g++ +  ++  ++H D H+Dll p+       k+++++ ++++lk+ 
  gi|91772654|ref|YP_565346.1| 43 TGKRNIRnEKELVLHADNHFDLLHPQcpvcgsnKINKQEYYTRKLKLA 90
                                  4667777788899*************9999999999999999977765 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 ?    2.1   0.1      0.18     3e+02      16      21 ..      68      73 ..      49      75 .. 0.76
   2 ?    8.7   1.9    0.0015       2.5      13      26 .]     100     113 ..      98     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                     zf-H2C2_2 16 eCplCd 21
                                  +Cp+C+
  gi|91772654|ref|YP_565346.1| 68 QCPVCG 73
                                  9****8 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                     zf-H2C2_2  13 kpyeCplCdkaFkt 26 
                                   ++y C++C+k+F+t
  gi|91772654|ref|YP_565346.1| 100 RRYYCKKCSKRFTT 113
                                   579*********97 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 ?    2.0   0.1      0.31   5.1e+02       2       9 ..      68      75 ..      67      85 .. 0.75
   2 ?    9.2   0.3    0.0015       2.5       1      15 [.     102     116 ..     102     126 .. 0.81
   3 ?   -2.4   0.1       8.1   1.3e+04       4      11 ..     140     145 ..     137     152 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                     zf-C2H2_4  2 kCpiCgks 9 
                                  +Cp+Cg +
  gi|91772654|ref|YP_565346.1| 68 QCPVCGSN 75
                                  7****755 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                     zf-C2H2_4   1 fkCpiCgksFsskka 15 
                                   ++C+ C+k+F+++ +
  gi|91772654|ref|YP_565346.1| 102 YYCKKCSKRFTTPLD 116
                                   89********99865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.1
                     zf-C2H2_4   4 piCgksFs 11 
                                    +C  sF+
  gi|91772654|ref|YP_565346.1| 140 GYC--SFR 145
                                   577..664 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.75   1.2e+03       2       7 ..      68      73 ..      68      85 .. 0.84
   2 ?    8.6   1.8    0.0016       2.7       1      13 [.     102     114 ..     102     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.75
                                  EETTTT CS
                       zf-C2H2  2 kCpdCg 7 
                                  +Cp+Cg
  gi|91772654|ref|YP_565346.1| 68 QCPVCG 73
                                  7****9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                                   EEETTTTEEESSH CS
                       zf-C2H2   1 ykCpdCgksFkrk 13 
                                   y+C++C+k+F+++
  gi|91772654|ref|YP_565346.1| 102 YYCKKCSKRFTTP 114
                                   99*********97 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 ?    7.6   0.0    0.0019       3.1       4      12 ..      66      74 ..      63      83 .. 0.84
   2 ?    0.3   2.2      0.36   5.9e+02      21      27 ..     101     107 ..     101     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                       zf-RRN7  4 gppCgvCgc 12
                                  +p+C+vCg+
  gi|91772654|ref|YP_565346.1| 66 HPQCPVCGS 74
                                  699*****9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                       zf-RRN7  21 fyyCrrC 27 
                                   +yyC+ C
  gi|91772654|ref|YP_565346.1| 101 RYYCKKC 107
                                   7*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2694.13
//
Query:       gi|91772655|ref|YP_565347.1|  [L=470]
Description: hypothetical protein Mbur_0626 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-56  190.7  17.0    2.7e-56  190.7  17.0    2.7  3  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 ?   -3.6   0.5      0.34   6.1e+03     154     164 ..      77      89 ..      70     117 .. 0.43
   2 ?   -2.2   2.8      0.13   2.3e+03     147     183 ..     159     195 ..     152     203 .. 0.51
   3 !  190.7  17.0   1.5e-60   2.7e-56       2     235 ..     240     458 ..     239     459 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.34
                         DUF92 154 lGalliall..av 164
                                   ++++li +l  +v
  gi|91772655|ref|YP_565347.1|  77 VASILILFLvsFV 89 
                                   3333333221111 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.13
                         DUF92 147 lGllasllGalliallavlllllellillltlaGllG 183
                                   +G+l++ +++l i+ +  + + ++ +++++++  +++
  gi|91772655|ref|YP_565347.1| 159 IGILFASIAGLWIVYWQGANISYNMIFFVAVIGSITA 195
                                   4555555555555555444443333344444444444 PP

  == domain 3  score: 190.7 bits;  conditional E-value: 1.5e-60
                         DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdavqVla 80 
                                   ++++l+++a+  k  + s+ l+a+l+gvli++  +++ +f+lll+Ff+lg ++tk+k+k K+  +++e k+g R++++V++
  gi|91772655|ref|YP_565347.1| 240 FSMFLGYLAYCAKIADISASLSATLIGVLIIAF-SNIYWFILLLTFFILGGMFTKYKYKLKEsmGIAEGKDGVRTYENVFS 319
                                   6799************************99999.8889************************9999*************** PP

                         DUF92  81 nslvalllally.....lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGllasllGa 156
                                   ns++al+la++y     + ++l+++++++++A++a+DTlaSE+G++ ++ +pr+it+lk+v++G++GgV+llG l s+ G+
  gi|91772655|ref|YP_565347.1| 320 NSTAALILAIAYgiypqY-GELIIFAYLGTVATAAGDTLASEIGTTAQQ-QPRMITSLKPVKTGVDGGVTLLGELSSIGGS 398
                                   ************887643.999**********************66655.******************************* PP

                         DUF92 157 lliallavlllllel...lillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvsGldlLdNnaVNllsall 234
                                   ++ia++a+++ ++++   +++++++ G+lG+++DSlLGatlq++                       lL+N++VN++++++
  gi|91772655|ref|YP_565347.1| 399 AIIAIFAIMFAMVDSlyaALVITVAGGFLGTNIDSLLGATLQNR----------------------GLLTNSGVNFVATFA 457
                                   ****9988888888788455555556******************......................789999999999887 PP

                         DUF92 235 t 235
                                   +
  gi|91772655|ref|YP_565347.1| 458 G 458
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2782.65
//
Query:       gi|91772656|ref|YP_565348.1|  [L=245]
Description: silent information regulator protein Sir2 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-52  176.9   0.0    4.2e-52  176.6   0.0    1.0  1  SIR2         Sir2 family
  ------ inclusion threshold ------
      0.017   14.5   0.6        3.1    7.2   0.0    2.4  2  Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger do
       0.05   13.6   0.6        0.1   12.6   0.6    1.6  1  ADK_lid      Adenylate kinase, active site lid
       0.07   13.2   0.0       0.12   12.5   0.0    1.3  1  HypA         Hydrogenase/urease nickel incorporation, metallo


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.0   9.5e-56   4.2e-52       1     177 []      19     194 ..      19     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 9.5e-56
                                   -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEEEEES CS
                          SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllrliTQ 81 
                                   GAG+St sGipdfR+++G+y+k++ + + s +++++++    + +++++   l+ + +p+++H++l+kle+kg  +++iTQ
  gi|91772656|ref|YP_565348.1|  19 GAGVSTFSGIPDFRGRSGVYNKFDADLIFSIDHFNKDPAYFYA-HSKSFIYDLE-HRQPSIVHSVLSKLEEKGIIKAIITQ 97 
                                   9*******************************99999988777.5666655555.79************************ PP

                                   -SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGGHCHHHCCTT.B-TTTCCBEEEEE--CTSB-S.HHHHHHHHHHH CS
                          SIR2  82 NiDgLekkaGskkvvelHGslakakcvkcekkldkeelqeeieaekvpecekcgkllkpdvvfFGealp.dklkkliekve 161
                                   NiD+L++kaGsk+v+e+HGs ++  c +c+kk+++e++ e ++ae  p c++cg+l+kpd+vf+Ge+l  d+++k+i++ +
  gi|91772656|ref|YP_565348.1|  98 NIDMLHQKAGSKNVIEVHGSPQEHVCLACGKKYSYEYIAELLKAEGFPLCNECGGLVKPDIVFYGEMLRqDTIEKAIQESS 178
                                   *********************************************************************9*********** PP

                                   H-SEEEEES--STSTT CS
                          SIR2 162 eadlllviGtSlkVap 177
                                   +adl+lv+G+ l V+p
  gi|91772656|ref|YP_565348.1| 179 KADLMLVLGSTLVVQP 194
                                   **************98 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0007       3.1      35      54 ..     122     141 ..     108     143 .. 0.85
   2 ?    5.8   0.2    0.0019       8.6      31      47 ..     142     160 ..     140     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0007
                   Vps36-NZF-N  35 pClaCGvkpdlelikksika 54 
                                   +ClaCG k ++e i + +ka
  gi|91772656|ref|YP_565348.1| 122 VCLACGKKYSYEYIAELLKA 141
                                   8*************998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0019
                   Vps36-NZF-N  31 tplPpClaCG..vkpdlel 47 
                                   + +P C+ CG  vkpd+  
  gi|91772656|ref|YP_565348.1| 142 EGFPLCNECGglVKPDIVF 160
                                   569*******999999865 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 ?   12.6   0.6   2.3e-05       0.1       3      32 ..     122     154 ..     121     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                                   E-TTT--EEETTT..B--SSTT..B-TTT--.-B CS
                       ADK_lid   3 vCpkCGrsYhvvf..npPkveg..lCDkCGepLv 32 
                                   vC +CG+ Y++++     k+eg  lC +CG+ Lv
  gi|91772656|ref|YP_565348.1| 122 VCLACGKKYSYEYiaELLKAEGfpLCNECGG-LV 154
                                   9*********997755578887447*****9.65 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   0.0   2.6e-05      0.12      38      94 ..      89     152 ..      71     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                   T--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHH.HHH.......S-TTTSS CS
                          HypA  38 gvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkefelee.kal.......rCpkCgs 94 
                                   g+ + ++++  ++l+++    + ++e++  p +  C  Cgk+++ e  ++l        C++Cg+
  gi|91772656|ref|YP_565348.1|  89 GIIKAIITQNIDMLHQKAGS-KNVIEVHGSPQEHVCLACGKKYSYEYiAELlkaegfpLCNECGG 152
                                   56666777777777776444.4899*******************886323377889999****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1624.85
//
Query:       gi|91772657|ref|YP_565349.1|  [L=420]
Description: diaminopimelate decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-29  103.0   0.0      2e-29  102.7   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    2.7e-20   72.4   0.0    2.9e-20   72.3   0.0    1.3  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.0   2.3e-33     2e-29       4     246 ..      32     278 ..      29     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 2.3e-33
                                   HHHHHHHHHHHCT...CCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHHHH CS
                 Orn_Arg_deC_N   4 ierklkrwkkalp...rikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelryale 81 
                                   i+ ++++ k+a+      + f+avKa +++ +l++l+++G g dc+S  El l+ ++g+  e+i+f+++   +ee  +a+e
  gi|91772657|ref|YP_565349.1|  32 IRTNARKLKDAFSiveGFQEFFAVKALPNPYILKILKSEGFGADCSSLPELLLAEKTGIVGENIMFSSNDTPAEEFVKAKE 112
                                   66677777777776668899************************************************************* PP

                                   CTHTEEEESSHHHHHHHHHHHCC.EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTEEEEEEE--- CS
                 Orn_Arg_deC_N  82 kgvkvvtvdnveeleklaklape.akvllRiktdvsaatcelistggessKFGaaleeavealleaakeenlqlvGvsfHv 161
                                    g   +++d  + +e l+k+a+  + v+ R++++  ++   +     e+ K+G++ ++ +e ++ + ke++++  G++  v
  gi|91772657|ref|YP_565349.1| 113 LGAI-INLDDISHIEFLEKEAELpELVCFRFNPGPLKEGNAI-IGNPEEAKYGFTKKQLFEGYR-MLKEKGVKRFGLHTMV 190
                                   *986.*****************9556789****876666665.778899*******89999886.67999*********** PP

                                   BSSC-SCHHHHHHHHHHHHHHHHHH.HHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHHH..TSSS-EEEE CS
                 Orn_Arg_deC_N 162 GSgvsdleafvkavekalklfdela.elGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeeafp..gdkevtiia 239
                                    S   + + fv+ ++ ++++++e+  el +  +++++GGG g+ y+ ++e+++ + iae +r+  e+ ++  g + ++i +
  gi|91772657|ref|YP_565349.1| 191 ASNELEPSYFVETAKLLFEVIVEISnELDIRFDFVNLGGGIGIPYRLDQEAVPYDVIAEGVRDEYEKSIKanGLDPLKIYL 271
                                   ************************99*****************************************999999999***** PP

                                   --SHHHH CS
                 Orn_Arg_deC_N 240 EpGRalv 246
                                   E GR ++
  gi|91772657|ref|YP_565349.1| 272 ECGRTIT 278
                                   ****997 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 !   72.3   0.0   3.2e-24   2.9e-20       6      98 .]     280     368 ..      24     368 .. 0.73

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 3.2e-24
                                   GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC   6 eagvLvtrViavkesekkkfvivdaGmndllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCesgDvlakdrelpe 85 
                                     g+Lvt+V + k+  k ++v +da m++l+rp lyg++h+i ++     ++++ e + +dv G++Ce +D +a dr+lpe
  gi|91772657|ref|YP_565349.1| 280 PYGYLVTEVRHLKHIYK-DYVGTDACMANLMRPGLYGAYHHItVLG----KENKPEDHLYDVTGSLCENNDKFAIDRMLPE 355
                                   679**********9976.9***********************5554....233445688********************** PP

                                   --TT-EEEESS-S CS
                                   xxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC  86 levGdllafedaG 98 
                                   +e+Gd+la++d G
  gi|91772657|ref|YP_565349.1| 356 VERGDILAIHDSG 368
                                   **********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2760.96
//
Query:       gi|91772658|ref|YP_565350.1|  [L=1049]
Description: TPR repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-137  441.3  57.4    2.2e-08   33.5   0.2   24.3 24  TPR_1            Tetratricopeptide repeat
   1.6e-131  418.1  45.2    3.6e-08   32.9   0.0   24.2 24  TPR_2            Tetratricopeptide repeat
   3.4e-112  365.9  77.2    6.9e-07   28.9   0.0   24.2 24  TPR_11           TPR repeat
   1.4e-105  336.9  63.3    8.9e-07   28.6   0.1   23.3 23  TPR_8            Tetratricopeptide repeat
    4.3e-89  292.9   2.6      1e-09   38.9   0.0   16.0 17  TPR_16           Tetratricopeptide repeat
    2.6e-65  212.2  54.8    5.8e-05   23.2   0.0   23.9 25  TPR_17           Tetratricopeptide repeat
    4.9e-63  204.4  13.1     0.0011   19.6   0.0   21.0 22  TPR_14           Tetratricopeptide repeat
    2.4e-53  178.3  35.0    1.1e-05   25.7   0.1   16.2 15  TPR_12           Tetratricopeptide repeat
    2.5e-46  156.1  24.9    1.3e-05   25.6   0.0   14.2 15  TPR_19           Tetratricopeptide repeat
    1.9e-45  152.8   0.0    0.00039   20.5   0.0   13.2 13  TPR_9            Tetratricopeptide repeat
    5.4e-42  138.8  35.2     0.0098   15.9   0.0   19.5 20  TPR_7            Tetratricopeptide repeat
    4.3e-39  130.6  33.7        0.1   13.3   0.0   20.3 20  TPR_6            Tetratricopeptide repeat
    6.7e-32  109.6  39.0    0.00015   22.0   0.3   11.9 14  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.3e-18   65.9  18.7        0.2   10.5   0.4    9.8 11  NARP1            NMDA receptor-regulated protein 1
      2e-16   60.3   6.0       0.32   11.0   0.1   12.4 12  DUF3856          Domain of Unknown Function (DUF3856)
      4e-16   58.8  23.8      0.084   13.0   0.0   13.2 13  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
      3e-13   49.6  44.1     0.0072   16.4   0.1   15.4 15  MIT              MIT (microtubule interacting and transport) 
    6.8e-12   44.9  25.3        2.1    8.3   0.0   15.7 18  TPR_10           Tetratricopeptide repeat
    1.7e-08   34.0   7.8       0.64    9.2   0.1    9.0 10  TPR_15           Tetratricopeptide repeat
    4.3e-06   27.2   1.6          3    8.3   0.1    6.8  7  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    1.6e-05   25.3   7.0        2.5    8.5   0.0    8.2  9  BTAD             Bacterial transcriptional activator domain
    6.5e-05   23.2   5.8         43    4.4   0.0    8.9 10  TPR_5            Tetratrico peptide repeat
    9.1e-05   22.4  43.2       0.36   10.9   2.0   13.4 13  TPR_3            Tetratricopeptide repeat
     0.0012   18.9   1.8         60    4.2   0.0    7.5  6  PPR              PPR repeat
     0.0017   18.6   4.3          9    6.6   0.0    6.6  6  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
     0.0036   17.0  18.2        9.3    5.9   0.0    9.6 11  RPN7             26S proteasome subunit RPN7
  ------ inclusion threshold ------
      0.013   14.3   7.5        2.5    6.7   0.4    5.7  6  PknG_TPR         Protein kinase G tetratricopeptide repeat
      0.046   13.5   5.3         13    5.5   0.0    5.7  6  TOM20_plant      Plant specific mitochondrial import receptor
       0.13   13.0   0.1       0.55   11.0   0.1    2.1  1  TraD_N           F sex factor protein N terminal
       0.15   11.8   3.6         39    4.2   0.0    5.2  5  PPTA             Protein prenyltransferase alpha subunit repe
       0.26   11.4   1.5         30    4.8   0.0    4.4  3  Exonuc_VII_S     Exonuclease VII small subunit
       0.63    9.8   5.2       0.38   10.5   0.2    2.8  3  DUF764           Borrelia burgdorferi protein of unknown func
        1.3    8.4   7.5         26    4.1   0.0    5.0  5  Coatomer_E       Coatomer epsilon subunit
        4.9    6.8  16.6         18    5.0   0.2    7.0  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 !   12.2   0.0   0.00024      0.13       1      34 []      29      62 ..      29      62 .. 0.94
   2 !   19.0   0.7   1.7e-06   0.00087       3      33 ..      65      95 ..      64      96 .. 0.93
   3 !   19.6   0.0   1.1e-06   0.00058       4      28 ..     100     124 ..      97     125 .. 0.91
   4 !   11.4   0.2   0.00043      0.23       3      30 ..     162     189 ..     160     191 .. 0.91
   5 !   22.5   0.0   1.4e-07   7.1e-05       3      34 .]     196     227 ..     194     227 .. 0.96
   6 !   31.8   0.0   1.5e-10     8e-08       3      33 ..     230     260 ..     229     261 .. 0.94
   7 !    9.6   0.1    0.0016      0.84       3      31 ..     264     292 ..     262     294 .. 0.90
   8 !   26.2   0.0   8.8e-09   4.6e-06       1      34 []     296     329 ..     296     329 .. 0.98
   9 !   30.7   0.0   3.4e-10   1.8e-07       2      34 .]     331     363 ..     330     363 .. 0.97
  10 !   28.5   0.0   1.6e-09   8.7e-07       1      33 [.     397     429 ..     397     430 .. 0.96
  11 !   33.5   0.2   4.2e-11   2.2e-08       1      34 []     431     464 ..     431     464 .. 0.96
  12 !   23.7   0.0   5.3e-08   2.8e-05       2      34 .]     466     498 ..     465     498 .. 0.95
  13 !   21.4   0.0   2.9e-07   0.00015       3      34 .]     501     532 ..     499     532 .. 0.95
  14 !   23.2   0.0   7.7e-08     4e-05       2      34 .]     534     566 ..     533     566 .. 0.95
  15 !   17.4   0.0   5.5e-06    0.0029       2      33 ..     634     665 ..     633     666 .. 0.95
  16 !   21.8   0.0   2.2e-07   0.00011       3      34 .]     669     700 ..     667     700 .. 0.94
  17 ?    2.0   1.4      0.39   2.1e+02       2      33 ..     702     733 ..     702     734 .. 0.84
  18 !    9.2   0.1    0.0022       1.1       3      31 ..     737     765 ..     736     768 .. 0.92
  19 !   24.8   0.0   2.5e-08   1.3e-05       2      34 .]     770     802 ..     769     802 .. 0.97
  20 ?    4.6   0.0      0.06        31      10      30 ..     812     832 ..     811     836 .. 0.88
  21 !   10.5   0.0   0.00082      0.43       3      27 ..     839     863 ..     837     870 .. 0.84
  22 ?    6.3   0.1     0.017         9       3      33 ..     873     903 ..     871     904 .. 0.93
  23 !   17.5   0.1     5e-06    0.0026       1      33 [.     905     937 ..     905     938 .. 0.96
  24 !   33.5   0.1   4.2e-11   2.2e-08       3      33 ..     941     971 ..     939     972 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                                  HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                  a++++  G+a++ +g yd+A+e y+ AL  +Pn+
  gi|91772658|ref|YP_565350.1| 29 ARSFNEEGVALMLNGTYDKAIEKYDLALVSDPNY 62
                                  6788999*************************97 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.7e-06
                                  HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  3 alynlGnayfklgkydeAleyyekALelnPn 33
                                  al n+++a +  g+ydeA++ y+  L+l+P 
  gi|91772658|ref|YP_565350.1| 65 ALENKAAAQYLYGDYDEAIATYDHILKLQPG 95
                                  6779*************************95 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.1e-06
                                   HHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekAL 28 
                                   +  +G+++ k+g+y+ A++ y+kAL
  gi|91772658|ref|YP_565350.1| 100 FTKKGMVLAKKGDYENAIKTYDKAL 124
                                   5679********************9 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00043
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                   +ly ++  +  lg+ +eA++ yek Le+
  gi|91772658|ref|YP_565350.1| 162 ILYHKAKSLEGLGRNEEAIQLYEKFLEI 189
                                   69*********************97776 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 1.4e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +ly +G+ + + gk + A+e y++AL+++P+n
  gi|91772658|ref|YP_565350.1| 196 TLYEKGLDHARDGKSERAIELYDEALQIDPDN 227
                                   699***************************98 PP

  == domain 6  score: 31.8 bits;  conditional E-value: 1.5e-10
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                   ++y +G+a+ +lg y+eA+e y+kA+e + +
  gi|91772658|ref|YP_565350.1| 230 IWYSKGQAFDSLGLYEEAIESYNKAIEFDST 260
                                   6**************************9986 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                   ++ n+++ y kl k ++A+  y+++L l+
  gi|91772658|ref|YP_565350.1| 264 VWWNKALDYDKLDKKEDAIISYREVLVLD 292
                                   5669**********************887 PP

  == domain 8  score: 26.2 bits;  conditional E-value: 8.8e-09
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a+a++nlG+a+   g+y eA+  +e++L l+P+n
  gi|91772658|ref|YP_565350.1| 296 AEAWFNLGVALEGTGNYFEAINSFEQVLLLDPDN 329
                                   89******************************98 PP

  == domain 9  score: 30.7 bits;  conditional E-value: 3.4e-10
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +a+  +G+++ k g++deAl  y+ AL++nP+n
  gi|91772658|ref|YP_565350.1| 331 DAWHKKGLVLNKIGRFDEALVSYDSALKINPDN 363
                                   89*****************************98 PP

  == domain 10  score: 28.5 bits;  conditional E-value: 1.6e-09
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                   ak++y +G +y+ l +y+eA+  +ek+Lel+ +
  gi|91772658|ref|YP_565350.1| 397 AKIWYDKGTLYLGLSDYEEAVLSFEKVLELDSK 429
                                   89*****************************87 PP

  == domain 11  score: 33.5 bits;  conditional E-value: 4.2e-11
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a ++y +++a+ klg+y+eA+ +y +AL+ +P++
  gi|91772658|ref|YP_565350.1| 431 AVVWYKKALALDKLGNYNEAIICYTEALRRDPSC 464
                                   679*****************************86 PP

  == domain 12  score: 23.7 bits;  conditional E-value: 5.3e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +++y +G+ +   g+y+eA+ +y+k +el+P++
  gi|91772658|ref|YP_565350.1| 466 NVWYLKGYDLDTTGRYKEAVSCYRKTVELDPQF 498
                                   78*****************************86 PP

  == domain 13  score: 21.4 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a+y lG+ + ++ ++ eA+++y++++e n ++
  gi|91772658|ref|YP_565350.1| 501 AWYALGLDLAHMDEHSEAIAAYDQVIEQNSDF 532
                                   9***************************9986 PP

  == domain 14  score: 23.2 bits;  conditional E-value: 7.7e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +a+y++G ++ klg y++A+e y+ A++l+ +n
  gi|91772658|ref|YP_565350.1| 534 DAYYRKGRTLDKLGLYQDAIESYRVAISLDSSN 566
                                   8****************************9886 PP

  == domain 15  score: 17.4 bits;  conditional E-value: 5.5e-06
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                   +a+  +G  +f +g y+ Al  y+kA+ + Pn
  gi|91772658|ref|YP_565350.1| 634 DAWVAKGGSLFVKGSYENALLSYNKAIMIKPN 665
                                   899****************************9 PP

  == domain 16  score: 21.8 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++y +G++y  lg+   A+  yekA+ l+ ++
  gi|91772658|ref|YP_565350.1| 669 TWYMRGQTYEMLGDRSSAINNYEKAVDLDSSY 700
                                   7***************************9875 PP

  == domain 17  score: 2.0 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                   +a++ l++  +k  +y  A+++y+  L l+P+
  gi|91772658|ref|YP_565350.1| 702 DAWFALAQNVYKSSNYYYAIQAYDGLLNLDPE 733
                                   6999999999*************866666665 PP

  == domain 18  score: 9.2 bits;  conditional E-value: 0.0022
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                   al ++G+ay k g y   l+ y+k L+++
  gi|91772658|ref|YP_565350.1| 737 ALLQKGQAYDKIGIYRSSLASYNKLLKVD 765
                                   7899********************99998 PP

  == domain 19  score: 24.8 bits;  conditional E-value: 2.5e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +a+y +G+a ++lg++++A+  y+k+L+ +P+n
  gi|91772658|ref|YP_565350.1| 770 EAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQN 802
                                   79*****************************97 PP

  == domain 20  score: 4.6 bits;  conditional E-value: 0.06
                                   HHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1  10 ayfklgkydeAleyyekALel 30 
                                   ++  lg +++ +  y+k+Le 
  gi|91772658|ref|YP_565350.1| 812 VLEDLGLFEDSINNYDKVLEM 832
                                   57899**************97 PP

  == domain 21  score: 10.5 bits;  conditional E-value: 0.00082
                                   HHHHHHHHHHHTT-HHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                   +l  +Gn+y klg y++A ++y+ +
  gi|91772658|ref|YP_565350.1| 839 VLMKKGNVYEKLGLYKDANDCYDIV 863
                                   67889*************9999755 PP

  == domain 22  score: 6.3 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                   al ++G  ++ lg+y  A + y+ ++  nP 
  gi|91772658|ref|YP_565350.1| 873 ALSRKGFNLYMLGDYIGAMDQYDLVIAKNPY 903
                                   899************************9996 PP

  == domain 23  score: 17.5 bits;  conditional E-value: 5e-06
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                   a a+yn+Gn+ +    y    ++y kA+el+P+
  gi|91772658|ref|YP_565350.1| 905 AAAWYNKGNVAYLTSSYAGSTQFYLKAVELQPK 937
                                   78******************************7 PP

  == domain 24  score: 33.5 bits;  conditional E-value: 4.2e-11
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                   a+ynlG++    g+ d A+ yyekAL ++Pn
  gi|91772658|ref|YP_565350.1| 941 AWYNLGYIANIRGDVDTAITYYEKALAIDPN 971
                                   9*****************************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   9.2e-05     0.049       2      34 .]      30      62 ..      29      62 .. 0.92
   2 !   16.2   0.5   1.6e-05    0.0084       3      33 ..      65      95 ..      64      96 .. 0.94
   3 !   15.7   0.0   2.2e-05     0.011       6      28 ..     102     124 ..      97     126 .. 0.90
   4 !   14.8   0.2   4.4e-05     0.023       3      31 ..     162     190 ..     160     193 .. 0.92
   5 !   22.9   0.0   1.1e-07   5.8e-05       4      34 .]     197     227 ..     194     227 .. 0.96
   6 !   20.5   0.0   6.4e-07   0.00034       3      33 ..     230     260 ..     229     261 .. 0.93
   7 !   13.1   0.0   0.00015     0.077       2      31 ..     263     292 ..     262     295 .. 0.94
   8 !   32.9   0.0   6.8e-11   3.6e-08       1      34 []     296     329 ..     296     329 .. 0.98
   9 !   18.1   0.0   3.7e-06     0.002       2      34 .]     331     363 ..     330     363 .. 0.96
  10 !   21.9   0.0   2.3e-07   0.00012       1      33 [.     397     429 ..     397     430 .. 0.95
  11 !   29.3   0.1   9.8e-10   5.2e-07       2      33 ..     432     463 ..     431     464 .. 0.94
  12 !   22.5   0.0   1.4e-07   7.5e-05       2      33 ..     466     497 ..     465     498 .. 0.95
  13 !   18.6   0.1   2.6e-06    0.0013       3      33 ..     501     531 ..     499     532 .. 0.93
  14 !   19.8   0.0   1.1e-06   0.00058       2      33 ..     534     565 ..     533     566 .. 0.94
  15 !   13.5   0.0   0.00011      0.06       2      33 ..     634     665 ..     633     666 .. 0.95
  16 !   20.8   0.0   5.3e-07   0.00028       3      32 ..     669     698 ..     667     700 .. 0.94
  17 !   11.0   1.2   0.00072      0.38       2      34 .]     702     734 ..     701     734 .. 0.97
  18 !    8.2   0.0    0.0057         3       3      34 .]     737     768 ..     736     768 .. 0.91
  19 !   26.1   0.0     1e-08   5.3e-06       2      34 .]     770     802 ..     769     802 .. 0.97
  20 ?    4.1   0.0      0.12        62       3      29 ..     805     831 ..     803     833 .. 0.89
  21 !   10.7   0.0   0.00091      0.48       3      32 ..     839     868 ..     837     870 .. 0.85
  22 !   12.4   0.0   0.00025      0.13       2      33 ..     872     903 ..     871     904 .. 0.93
  23 !   14.9   0.1   4.2e-05     0.022       1      33 [.     905     937 ..     905     938 .. 0.96
  24 !   24.4   0.0   3.7e-08   1.9e-05       3      33 ..     941     971 ..     939     972 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.2e-05
                         TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                  +  ++ G a++ +g y++A+e ++ Al  dPn+
  gi|91772658|ref|YP_565350.1| 30 RSFNEEGVALMLNGTYDKAIEKYDLALVSDPNY 62
                                  567899*************************96 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-05
                         TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                  al n + a y  gdy+eA++ ++  l+l P+
  gi|91772658|ref|YP_565350.1| 65 ALENKAAAQYLYGDYDEAIATYDHILKLQPG 95
                                  78899************************96 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.2e-05
                         TPR_2   6 nlGlayyklgdyeeAleafekAl 28 
                                     G++++k+gdye A++ ++kAl
  gi|91772658|ref|YP_565350.1| 102 KKGMVLAKKGDYENAIKTYDKAL 124
                                   679*******************9 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 4.4e-05
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                   +ly  +++++ lg+ eeA++++ek le+ 
  gi|91772658|ref|YP_565350.1| 162 ILYHKAKSLEGLGRNEEAIQLYEKFLEIQ 190
                                   699***********************985 PP

  == domain 5  score: 22.9 bits;  conditional E-value: 1.1e-07
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ly+ Gl +++ g+ e+A+e++++Al++dP+n
  gi|91772658|ref|YP_565350.1| 197 LYEKGLDHARDGKSERAIELYDEALQIDPDN 227
                                   89***************************98 PP

  == domain 6  score: 20.5 bits;  conditional E-value: 6.4e-07
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   ++y  G+a   lg yeeA+e ++kA+e d +
  gi|91772658|ref|YP_565350.1| 230 IWYSKGQAFDSLGLYEEAIESYNKAIEFDST 260
                                   69*************************9876 PP

  == domain 7  score: 13.1 bits;  conditional E-value: 0.00015
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                   ++++n +l y kl++ e+A+  ++++l ld
  gi|91772658|ref|YP_565350.1| 263 KVWWNKALDYDKLDKKEDAIISYREVLVLD 292
                                   79*************************987 PP

  == domain 8  score: 32.9 bits;  conditional E-value: 6.8e-11
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   aea++nlG a++  g+y eA++ fe++l ldP+n
  gi|91772658|ref|YP_565350.1| 296 AEAWFNLGVALEGTGNYFEAINSFEQVLLLDPDN 329
                                   89******************************98 PP

  == domain 9  score: 18.1 bits;  conditional E-value: 3.7e-06
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +a++  Gl++ k g+++eAl  ++ Al+++P+n
  gi|91772658|ref|YP_565350.1| 331 DAWHKKGLVLNKIGRFDEALVSYDSALKINPDN 363
                                   69*****************************98 PP

  == domain 10  score: 21.9 bits;  conditional E-value: 2.3e-07
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                   a+++y  G +y+ l dyeeA+  fek+leld +
  gi|91772658|ref|YP_565350.1| 397 AKIWYDKGTLYLGLSDYEEAVLSFEKVLELDSK 429
                                   789***************************976 PP

  == domain 11  score: 29.3 bits;  conditional E-value: 9.8e-10
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    ++y  +la+ klg+y+eA+ ++ +Al+ dP 
  gi|91772658|ref|YP_565350.1| 432 VVWYKKALALDKLGNYNEAIICYTEALRRDPS 463
                                   58*****************************6 PP

  == domain 12  score: 22.5 bits;  conditional E-value: 1.4e-07
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    ++y  G+ +   g+y+eA+ +++k +eldP+
  gi|91772658|ref|YP_565350.1| 466 NVWYLKGYDLDTTGRYKEAVSCYRKTVELDPQ 497
                                   68*****************************7 PP

  == domain 13  score: 18.6 bits;  conditional E-value: 2.6e-06
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   a+y+lGl +++++++ eA++a+++++e + +
  gi|91772658|ref|YP_565350.1| 501 AWYALGLDLAHMDEHSEAIAAYDQVIEQNSD 531
                                   9**************************9865 PP

  == domain 14  score: 19.8 bits;  conditional E-value: 1.1e-06
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                   +a+y+ G+ + klg y++A+e ++ A++ld  
  gi|91772658|ref|YP_565350.1| 534 DAYYRKGRTLDKLGLYQDAIESYRVAISLDSS 565
                                   79***************************976 PP

  == domain 15  score: 13.5 bits;  conditional E-value: 0.00011
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                   +a+ + G +++ +g ye Al  ++kA+ + Pn
  gi|91772658|ref|YP_565350.1| 634 DAWVAKGGSLFVKGSYENALLSYNKAIMIKPN 665
                                   6999***************************8 PP

  == domain 16  score: 20.8 bits;  conditional E-value: 5.3e-07
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                    +y++G+ y+ lgd   A++ +ekA+ ld 
  gi|91772658|ref|YP_565350.1| 669 TWYMRGQTYEMLGDRSSAINNYEKAVDLDS 698
                                   5**************************995 PP

  == domain 17  score: 11.0 bits;  conditional E-value: 0.00072
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +a+++l++  yk+ +y  A++a++  l ldP+n
  gi|91772658|ref|YP_565350.1| 702 DAWFALAQNVYKSSNYYYAIQAYDGLLNLDPEN 734
                                   69*****************************97 PP

  == domain 18  score: 8.2 bits;  conditional E-value: 0.0057
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   al + G+ay k g y   l+ ++k l+ d +n
  gi|91772658|ref|YP_565350.1| 737 ALLQKGQAYDKIGIYRSSLASYNKLLKVDTDN 768
                                   68899**********************98765 PP

  == domain 19  score: 26.1 bits;  conditional E-value: 1e-08
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ea+y +Gla y+lg++e+A+  ++k+l+ dP+n
  gi|91772658|ref|YP_565350.1| 770 EAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQN 802
                                   89*****************************97 PP

  == domain 20  score: 4.1 bits;  conditional E-value: 0.12
                         TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                   +l ++ l+++ lg +e+ ++ ++k+le
  gi|91772658|ref|YP_565350.1| 805 VLLAQSLVLEDLGLFEDSINNYDKVLE 831
                                   67788999*****************98 PP

  == domain 21  score: 10.7 bits;  conditional E-value: 0.00091
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                   +l+  G++y+klg y++A ++++ +l  +P
  gi|91772658|ref|YP_565350.1| 839 VLMKKGNVYEKLGLYKDANDCYDIVLINEP 868
                                   68899*****************98776666 PP

  == domain 22  score: 12.4 bits;  conditional E-value: 0.00025
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    al + G  +y lgdy  A + ++ +++ +P 
  gi|91772658|ref|YP_565350.1| 872 LALSRKGFNLYMLGDYIGAMDQYDLVIAKNPY 903
                                   5899**************************96 PP

  == domain 23  score: 14.9 bits;  conditional E-value: 4.2e-05
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                   a a+yn G+++y    y+   +++ kA+el P+
  gi|91772658|ref|YP_565350.1| 905 AAAWYNKGNVAYLTSSYAGSTQFYLKAVELQPK 937
                                   789*****************************7 PP

  == domain 24  score: 24.4 bits;  conditional E-value: 3.7e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   a+ynlG+++  +gd + A+ ++ekAl++dPn
  gi|91772658|ref|YP_565350.1| 941 AWYNLGYIANIRGDVDTAITYYEKALAIDPN 971
                                   9*****************************9 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   1.5   5.6e-05      0.03       3      39 ..      38      74 ..      36      77 .. 0.91
   2 !   15.6   0.0   1.8e-05    0.0095       8      42 .]      77     111 ..      74     111 .. 0.96
   3 !   14.3   0.1   4.5e-05     0.024       3      21 ..     106     124 ..     104     125 .. 0.91
   4 ?    5.1   0.1     0.033        18       7      22 ..     173     188 ..     173     190 .. 0.84
   5 !   28.4   0.0   1.8e-09   9.5e-07       8      41 ..     208     241 ..     201     242 .. 0.90
   6 !   28.9   0.0   1.3e-09   6.9e-07       1      36 [.     235     270 ..     235     276 .. 0.91
   7 !   17.8   0.1   3.8e-06     0.002      11      42 .]     279     310 ..     272     310 .. 0.92
   8 !   23.1   0.0   8.1e-08   4.3e-05       8      42 .]     310     344 ..     308     344 .. 0.94
   9 !   20.9   0.0   3.9e-07   0.00021       1      28 [.     337     364 ..     337     368 .. 0.92
  10 ?    0.0   0.0       1.3   7.1e+02      23      39 ..     392     408 ..     391     411 .. 0.87
  11 !   16.2   0.1   1.1e-05     0.006       4      42 .]     407     445 ..     404     445 .. 0.90
  12 !   18.7   0.0     2e-06     0.001       6      35 ..     443     472 ..     441     473 .. 0.94
  13 !   22.4   0.0   1.3e-07     7e-05       8      36 ..     479     507 ..     477     510 .. 0.97
  14 !   17.9   0.2   3.5e-06    0.0019      10      42 .]     515     547 ..     511     547 .. 0.90
  15 !   11.9   0.0   0.00025      0.13       6      30 ..     545     569 ..     540     573 .. 0.84
  16 !   24.0   0.0   4.1e-08   2.2e-05       4      42 .]     643     681 ..     640     681 .. 0.94
  17 !   20.1   0.4   7.1e-07   0.00037      10      39 ..     683     712 ..     680     715 .. 0.86
  18 !   11.0   2.9   0.00049      0.26       7      42 .]     714     749 ..     709     749 .. 0.88
  19 !   19.3   0.1   1.3e-06   0.00068      10      42 .]     751     783 ..     747     783 .. 0.92
  20 !   15.0   0.1   2.9e-05     0.015       5      33 ..     780     808 ..     778     817 .. 0.86
  21 !   19.0   0.0   1.5e-06   0.00081       6      42 .]     815     851 ..     811     851 .. 0.95
  22 !   13.7   1.4   7.1e-05     0.038       5      39 ..     882     916 ..     880     919 .. 0.93
  23 !   18.9   0.1   1.6e-06   0.00087       1      36 [.     912     947 ..     912     950 .. 0.88
  24 !   28.5   0.5   1.6e-09   8.7e-07       2      42 .]     947     987 ..     946     987 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                        TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39
                                  a++  G y++Aie+Y  Al  dP++  a+ n ++a+y
  gi|91772658|ref|YP_565350.1| 38 ALMLNGTYDKAIEKYDLALVSDPNYRIALENKAAAQY 74
                                  677889****************************999 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                        TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G+y+eAi+ Y   lkl P ++ ++ + G +++k+G
  gi|91772658|ref|YP_565350.1|  77 GDYDEAIATYDHILKLQPGSPLIFTKKGMVLAKKG 111
                                   9*******************************998 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 4.5e-05
                        TPR_11   3 ayyeqGkyeeAieaYkkAl 21 
                                   ++ ++G+ye+Ai+ Y kAl
  gi|91772658|ref|YP_565350.1| 106 VLAKKGDYENAIKTYDKAL 124
                                   6889**************8 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.033
                        TPR_11   7 qGkyeeAieaYkkAlk 22 
                                   +G++eeAi+ Y+k l+
  gi|91772658|ref|YP_565350.1| 173 LGRNEEAIQLYEKFLE 188
                                   69*********98555 PP

  == domain 5  score: 28.4 bits;  conditional E-value: 1.8e-09
                        TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   Gk e Aie Y +Al++dPdn +++y  G+a+  +
  gi|91772658|ref|YP_565350.1| 208 GKSERAIELYDEALQIDPDNRTIWYSKGQAFDSL 241
                                   8999**************************8655 PP

  == domain 6  score: 28.9 bits;  conditional E-value: 1.3e-09
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                   G+a+ ++G yeeAie+Y+kA+++d++++ +++n +l
  gi|91772658|ref|YP_565350.1| 235 GQAFDSLGLYEEAIESYNKAIEFDSTDVKVWWNKAL 270
                                   7788899*************************9775 PP

  == domain 7  score: 17.8 bits;  conditional E-value: 3.8e-06
                        TPR_11  11 eeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   e+Ai +Y++ l ld  naea++nLG+a+   G
  gi|91772658|ref|YP_565350.1| 279 EDAIISYREVLVLDLYNAEAWFNLGVALEGTG 310
                                   89*************************98766 PP

  == domain 8  score: 23.1 bits;  conditional E-value: 8.1e-08
                        TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G+y eAi+++++ l ldPdn +a+++ Gl++ k G
  gi|91772658|ref|YP_565350.1| 310 GNYFEAINSFEQVLLLDPDNIDAWHKKGLVLNKIG 344
                                   9999**************************97766 PP

  == domain 9  score: 20.9 bits;  conditional E-value: 3.9e-07
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                   G ++ + G+++eA+ +Y  Alk++Pdn 
  gi|91772658|ref|YP_565350.1| 337 GLVLNKIGRFDEALVSYDSALKINPDNI 364
                                   7788999*******************96 PP

  == domain 10  score: 0.0 bits;  conditional E-value: 1.3
                        TPR_11  23 ldPdnaeayynLGlayy 39 
                                   +++d+a ++y  G +y+
  gi|91772658|ref|YP_565350.1| 392 FNSDSAKIWYDKGTLYL 408
                                   689**********9997 PP

  == domain 11  score: 16.2 bits;  conditional E-value: 1.1e-05
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   y  + +yeeA+ +++k l+ld++ a ++y+ +la+ k+G
  gi|91772658|ref|YP_565350.1| 407 YLGLSDYEEAVLSFEKVLELDSKHAVVWYKKALALDKLG 445
                                   556779****************************98887 PP

  == domain 12  score: 18.7 bits;  conditional E-value: 2e-06
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                   ++G+y+eAi +Y +Al+ dP+ ++++y  G
  gi|91772658|ref|YP_565350.1| 443 KLGNYNEAIICYTEALRRDPSCPNVWYLKG 472
                                   58*************************988 PP

  == domain 13  score: 22.4 bits;  conditional E-value: 1.3e-07
                        TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                   G+y+eA+ +Y+k ++ldP++  a+y+LGl
  gi|91772658|ref|YP_565350.1| 479 GRYKEAVSCYRKTVELDPQFTLAWYALGL 507
                                   9***************************6 PP

  == domain 14  score: 17.9 bits;  conditional E-value: 3.5e-06
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                     eAi+aY + ++ ++d+ +ayy  G ++ k+G
  gi|91772658|ref|YP_565350.1| 515 HSEAIAAYDQVIEQNSDFSDAYYRKGRTLDKLG 547
                                   68*********************9998877766 PP

  == domain 15  score: 11.9 bits;  conditional E-value: 0.00025
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaea 30 
                                   ++G y +Aie+Y+ A+ ld++n  a
  gi|91772658|ref|YP_565350.1| 545 KLGLYQDAIESYRVAISLDSSNSAA 569
                                   6788****************99655 PP

  == domain 16  score: 24.0 bits;  conditional E-value: 4.1e-08
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++ +G ye+A+ +Y+kA+ ++P++   +y +G++y ++G
  gi|91772658|ref|YP_565350.1| 643 LFVKGSYENALLSYNKAIMIKPNSSVTWYMRGQTYEMLG 681
                                   6779********************************998 PP

  == domain 17  score: 20.1 bits;  conditional E-value: 7.1e-07
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                      Ai++Y+kA++ld+++ +a+++L++  y
  gi|91772658|ref|YP_565350.1| 683 RSSAINNYEKAVDLDSSYKDAWFALAQNVY 712
                                   567**********************98666 PP

  == domain 18  score: 11.0 bits;  conditional E-value: 0.00049
                        TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                     +y  Ai+aY   l+ldP+n +a++  G+ay k G
  gi|91772658|ref|YP_565350.1| 714 SSNYYYAIQAYDGLLNLDPENKTALLQKGQAYDKIG 749
                                   556777**************************8776 PP

  == domain 19  score: 19.3 bits;  conditional E-value: 1.3e-06
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   y  ++++Y+k lk d dn ea+y +Gla y++G
  gi|91772658|ref|YP_565350.1| 751 YRSSLASYNKLLKVDTDNTEAWYLRGLASYNLG 783
                                   66789*************************998 PP

  == domain 20  score: 15.0 bits;  conditional E-value: 2.9e-05
                        TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayyn 33 
                                   y +G++e+A+ +Y k l  dP+n +++++
  gi|91772658|ref|YP_565350.1| 780 YNLGNLEDAVYSYDKVLSSDPQNIDVLLA 808
                                   779*********************99875 PP

  == domain 21  score: 19.0 bits;  conditional E-value: 1.5e-06
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++G +e++i++Y k l+ + d+++++ + G++y k+G
  gi|91772658|ref|YP_565350.1| 815 DLGLFEDSINNYDKVLEMKVDDPSVLMKKGNVYEKLG 851
                                   57889******************************99 PP

  == domain 22  score: 13.7 bits;  conditional E-value: 7.1e-05
                        TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                   y +G+y +A+ +Y   ++ +P +a a+yn G++ y
  gi|91772658|ref|YP_565350.1| 882 YMLGDYIGAMDQYDLVIAKNPYDAAAWYNKGNVAY 916
                                   779*****************************976 PP

  == domain 23  score: 18.9 bits;  conditional E-value: 1.6e-06
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                   G++ y    y ++ + Y kA++l P++ +a+ynLG+
  gi|91772658|ref|YP_565350.1| 912 GNVAYLTSSYAGSTQFYLKAVELQPKSITAWYNLGY 947
                                   6777777788899999*******************7 PP

  == domain 24  score: 28.5 bits;  conditional E-value: 1.6e-09
                        TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++   +G+ + Ai+ Y+kAl++dP+ a+a+yn  +a+y+ G
  gi|91772658|ref|YP_565350.1| 947 YIANIRGDVDTAITYYEKALAIDPNAASALYNKRFAHYRVG 987
                                   556679**************************999999876 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.46   2.4e+02       2      33 ..      30      61 ..      29      62 .. 0.83
   2 !    9.0   0.1    0.0035       1.8      15      32 ..      77      94 ..      66      96 .. 0.93
   3 !   18.9   0.2   2.3e-06    0.0012       5      28 ..     101     124 ..      99     130 .. 0.90
   4 !   17.1   0.3   8.6e-06    0.0045       4      32 ..     163     191 ..     162     193 .. 0.92
   5 !   12.0   0.0   0.00037      0.19      13      34 .]     206     227 ..     196     227 .. 0.85
   6 !   27.8   0.1   3.1e-09   1.6e-06       3      33 ..     230     260 ..     229     261 .. 0.94
   7 !    9.7   0.0    0.0019         1       2      28 ..     263     289 ..     262     293 .. 0.92
   8 !   24.7   0.0   3.2e-08   1.7e-05       1      34 []     296     329 ..     296     329 .. 0.97
   9 !   21.2   0.0   4.2e-07   0.00022       2      34 .]     331     363 ..     330     363 .. 0.96
  10 !   27.5   0.1   3.8e-09     2e-06       1      34 []     397     430 ..     397     430 .. 0.96
  11 !   28.6   0.1   1.7e-09   8.9e-07       3      34 .]     433     464 ..     431     464 .. 0.95
  12 !   20.5   0.0     7e-07   0.00037       3      33 ..     467     497 ..     465     498 .. 0.95
  13 ?    7.4   0.1     0.011       5.6       3      32 ..     501     530 ..     500     532 .. 0.92
  14 !   22.2   0.1     2e-07   0.00011       2      33 ..     534     565 ..     533     566 .. 0.94
  15 !   13.6   0.0   0.00011     0.058       2      33 ..     634     665 ..     633     666 .. 0.94
  16 !   20.8   0.0   5.6e-07   0.00029       3      33 ..     669     699 ..     668     700 .. 0.94
  17 ?    0.7   0.4       1.5   7.8e+02       3      34 .]     703     734 ..     702     734 .. 0.70
  18 !   10.5   0.1    0.0011       0.6       3      33 ..     737     767 ..     736     768 .. 0.93
  19 !   18.2   0.0   3.8e-06     0.002       2      34 .]     770     802 ..     769     802 .. 0.96
  20 ?    5.9   0.0     0.033        18       3      31 ..     805     833 ..     803     835 .. 0.89
  21 ?    5.5   0.0     0.043        23       3      24 ..     839     860 ..     837     861 .. 0.87
  22 !   11.2   0.1   0.00068      0.36       1      33 [.     905     937 ..     905     938 .. 0.95
  23 !   28.3   0.0   2.1e-09   1.1e-06       2      33 ..     940     971 ..     939     972 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.46
                                  CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                  ++ +  g +++  g y++A+e y  al  dp+
  gi|91772658|ref|YP_565350.1| 30 RSFNEEGVALMLNGTYDKAIEKYDLALVSDPN 61
                                  677778999999*********99999877776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0035
                                  T-HHHHHHHHHHHHHHHH CS
                         TPR_8 15 gdyeeAkeyyekaleldp 32
                                  gdy+eA+++y + l+l+p
  gi|91772658|ref|YP_565350.1| 77 GDYDEAIATYDHILKLQP 94
                                  9***************99 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekal 28 
                                    ++g+++ k+gdye+A+++y kal
  gi|91772658|ref|YP_565350.1| 101 TKKGMVLAKKGDYENAIKTYDKAL 124
                                   589********************9 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 8.6e-06
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldp 32 
                                   +y++++ ++ lg+ eeA++ yek le++ 
  gi|91772658|ref|YP_565350.1| 163 LYHKAKSLEGLGRNEEAIQLYEKFLEIQL 191
                                   89************************975 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00037
                                   HTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8  13 klgdyeeAkeyyekaleldpdn 34 
                                     g+ e A+e y +al++dpdn
  gi|91772658|ref|YP_565350.1| 206 RDGKSERAIELYDEALQIDPDN 227
                                   6699****************97 PP

  == domain 6  score: 27.8 bits;  conditional E-value: 3.1e-09
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++y +g++ ++lg yeeA+e+y+ka+e d +
  gi|91772658|ref|YP_565350.1| 230 IWYSKGQAFDSLGLYEEAIESYNKAIEFDST 260
                                   7**************************9975 PP

  == domain 7  score: 9.7 bits;  conditional E-value: 0.0019
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                   ++++n+++ y+kl ++e A+ +y+++l
  gi|91772658|ref|YP_565350.1| 263 KVWWNKALDYDKLDKKEDAIISYREVL 289
                                   79**********************997 PP

  == domain 8  score: 24.7 bits;  conditional E-value: 3.2e-08
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   aea++nlg +++ +g+y eA+ ++e++l ldpdn
  gi|91772658|ref|YP_565350.1| 296 AEAWFNLGVALEGTGNYFEAINSFEQVLLLDPDN 329
                                   79******************************97 PP

  == domain 9  score: 21.2 bits;  conditional E-value: 4.2e-07
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +a++++g+++ k g+++eA  +y  al+++pdn
  gi|91772658|ref|YP_565350.1| 331 DAWHKKGLVLNKIGRFDEALVSYDSALKINPDN 363
                                   79*****************************97 PP

  == domain 10  score: 27.5 bits;  conditional E-value: 3.8e-09
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   a+++y +g +yl l dyeeA+ ++ek+leld ++
  gi|91772658|ref|YP_565350.1| 397 AKIWYDKGTLYLGLSDYEEAVLSFEKVLELDSKH 430
                                   789****************************986 PP

  == domain 11  score: 28.6 bits;  conditional E-value: 1.7e-09
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   ++y+++++++klg+y+eA+ +y +al+ dp++
  gi|91772658|ref|YP_565350.1| 433 VWYKKALALDKLGNYNEAIICYTEALRRDPSC 464
                                   8*****************************86 PP

  == domain 12  score: 20.5 bits;  conditional E-value: 7e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++y++g+ ++++g+y+eA+++y+k +eldp+
  gi|91772658|ref|YP_565350.1| 467 VWYLKGYDLDTTGRYKEAVSCYRKTVELDPQ 497
                                   8*****************************7 PP

  == domain 13  score: 7.4 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                   a+y lg+ +  + ++ eA+++y +++e + 
  gi|91772658|ref|YP_565350.1| 501 AWYALGLDLAHMDEHSEAIAAYDQVIEQNS 530
                                   79999999******************9876 PP

  == domain 14  score: 22.2 bits;  conditional E-value: 2e-07
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +ayy++g++++klg y+ A+e+y+ a++ld +
  gi|91772658|ref|YP_565350.1| 534 DAYYRKGRTLDKLGLYQDAIESYRVAISLDSS 565
                                   79***************************986 PP

  == domain 15  score: 13.6 bits;  conditional E-value: 0.00011
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +a++ +g  ++ +g ye+A  +y+ka+ ++p+
  gi|91772658|ref|YP_565350.1| 634 DAWVAKGGSLFVKGSYENALLSYNKAIMIKPN 665
                                   799999999999*******************8 PP

  == domain 16  score: 20.8 bits;  conditional E-value: 5.6e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    +y+ g++y+ lgd  +A+  yeka++ld +
  gi|91772658|ref|YP_565350.1| 669 TWYMRGQTYEMLGDRSSAINNYEKAVDLDSS 699
                                   5***************************975 PP

  == domain 17  score: 0.7 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   a++ l++   k  +y  A+++y   l ldp+n
  gi|91772658|ref|YP_565350.1| 703 AWFALAQNVYKSSNYYYAIQAYDGLLNLDPEN 734
                                   78888855455555555899999999999875 PP

  == domain 18  score: 10.5 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   a++++g++y+k g y ++ ++y+k l+ d d
  gi|91772658|ref|YP_565350.1| 737 ALLQKGQAYDKIGIYRSSLASYNKLLKVDTD 767
                                   7899***********************9976 PP

  == domain 19  score: 18.2 bits;  conditional E-value: 3.8e-06
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   ea+y+ g++  +lg++e A+ +y k+l+ dp+n
  gi|91772658|ref|YP_565350.1| 770 EAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQN 802
                                   89*****************************96 PP

  == domain 20  score: 5.9 bits;  conditional E-value: 0.033
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                   +++  ++++++lg +e ++  y k+le++
  gi|91772658|ref|YP_565350.1| 805 VLLAQSLVLEDLGLFEDSINNYDKVLEMK 833
                                   667778999*****************985 PP

  == domain 21  score: 5.5 bits;  conditional E-value: 0.043
                                   HHHHHHHHHHHTT-HHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyy 24 
                                   +++++g++y+klg y+ A  +y
  gi|91772658|ref|YP_565350.1| 839 VLMKKGNVYEKLGLYKDANDCY 860
                                   7899***********9997776 PP

  == domain 22  score: 11.2 bits;  conditional E-value: 0.00068
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   a a+yn+g++   +  y  + ++y ka+el+p+
  gi|91772658|ref|YP_565350.1| 905 AAAWYNKGNVAYLTSSYAGSTQFYLKAVELQPK 937
                                   579*****************************8 PP

  == domain 23  score: 28.3 bits;  conditional E-value: 2.1e-09
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    a+ynlg+i    gd + A+ yyekal +dp+
  gi|91772658|ref|YP_565350.1| 940 TAWYNLGYIANIRGDVDTAITYYEKALAIDPN 971
                                   69*****************************7 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0039       2.1      33      66 ..      28      61 ..      13      63 .. 0.87
   2 !   21.0   0.0   7.3e-07   0.00038      11      61 ..      77     124 ..      69     129 .. 0.92
   3 ?    5.6   0.0     0.048        25      36      61 ..     162     187 ..     155     194 .. 0.76
   4 !   38.9   0.0   1.9e-12     1e-09       1      65 [.     198     259 ..     198     262 .. 0.95
   5 !   11.0   0.1     0.001      0.53       3      54 ..     268     316 ..     267     316 .. 0.89
   6 !   19.6   0.0   2.1e-06    0.0011      11      67 ..     310     363 ..     308     364 .. 0.96
   7 !   29.4   0.0   1.8e-09   9.6e-07       1      66 [.     401     463 ..     401     465 .. 0.96
   8 !   28.0   0.0   4.9e-09   2.6e-06       1      66 [.     435     497 ..     435     498 .. 0.96
   9 !   11.5   0.0   0.00071      0.37       1      42 [.     469     507 ..     469     511 .. 0.93
  10 !   28.8   0.3   2.7e-09   1.4e-06       1      65 [.     503     564 ..     503     567 .. 0.91
  11 !   11.4   0.0   0.00076       0.4      31      66 ..     630     665 ..     624     667 .. 0.86
  12 !   16.9   0.1   1.5e-05    0.0077       1      65 [.     671     732 ..     671     735 .. 0.91
  13 !   25.6   0.0   2.7e-08   1.4e-05       2      67 ..     740     802 ..     739     803 .. 0.94
  14 !   11.7   0.0    0.0006      0.32       1      53 [.     807     856 ..     807     856 .. 0.92
  15 !   16.3   0.0   2.1e-05     0.011       2      68 .]     842     905 ..     841     905 .. 0.95
  16 !   17.4   0.1     1e-05    0.0053      11      66 ..     885     937 ..     880     939 .. 0.90
  17 !   20.7   0.1   9.3e-07   0.00049      23      68 .]     931     973 ..     928     973 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0039
                        TPR_16 33 aaeAllllgdaalrqgrlaeAaalyraalraapd 66
                                  +a++ ++ g+a+  +g +++A++ y+ al  +p+
  gi|91772658|ref|YP_565350.1| 28 DARSFNEEGVALMLNGTYDKAIEKYDLALVSDPN 61
                                  67888999*********************99997 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 7.3e-07
                        TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                   gdyd+A+a ++  lk++p+sP+       +g +++++g+++ A+  y++al
  gi|91772658|ref|YP_565350.1|  77 GDYDEAIATYDHILKLQPGSPL---IFTKKGMVLAKKGDYENAIKTYDKAL 124
                                   8****************55555...*******************9999986 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.048
                        TPR_16  36 AllllgdaalrqgrlaeAaalyraal 61 
                                    l++++ ++  +gr +eA++ly++ l
  gi|91772658|ref|YP_565350.1| 162 ILYHKAKSLEGLGRNEEAIQLYEKFL 187
                                   67788888888888888888887755 PP

  == domain 4  score: 38.9 bits;  conditional E-value: 1.9e-12
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                   ++++++++r g+ ++A++++++al  d   Pd++  ++ +g+a+  +g ++eA++ y++a++ ++
  gi|91772658|ref|YP_565350.1| 198 YEKGLDHARDGKSERAIELYDEALQID---PDNRTIWYSKGQAFDSLGLYEEAIESYNKAIEFDS 259
                                   6789***********************...*****************************998776 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.001
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                   +a+++ ++ + +dA+  ++++l +d     +aeA+++lg+a+   g++ eA+
  gi|91772658|ref|YP_565350.1| 268 KALDYDKLDKKEDAIISYREVLVLD---LYNAEAWFNLGVALEGTGNYFEAI 316
                                   6888888999999999999999999...88****************997775 PP

  == domain 6  score: 19.6 bits;  conditional E-value: 2.1e-06
                        TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   g+y +A++ +e++l +d   Pd+ +A+  +g+++ + gr++eA+  y++al+  pd+
  gi|91772658|ref|YP_565350.1| 310 GNYFEAINSFEQVLLLD---PDNIDAWHKKGLVLNKIGRFDEALVSYDSALKINPDN 363
                                   8899*************...*********************************9997 PP

  == domain 7  score: 29.4 bits;  conditional E-value: 1.8e-09
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   +++++++l + dy++A+  +e +l++d   + +a  ++ +++a+ ++g++ eA+  y +alr +p+
  gi|91772658|ref|YP_565350.1| 401 YDKGTLYLGLSDYEEAVLSFEKVLELD---SKHAVVWYKKALALDKLGNYNEAIICYTEALRRDPS 463
                                   799************************...88888***************************9995 PP

  == domain 8  score: 28.0 bits;  conditional E-value: 4.9e-09
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   +++a+a+ ++g+y +A+  +++al+rd   P ++  ++l+g  +   gr++eA+  yr+ ++ +p+
  gi|91772658|ref|YP_565350.1| 435 YKKALALDKLGNYNEAIICYTEALRRD---PSCPNVWYLKGYDLDTTGRYKEAVSCYRKTVELDPQ 497
                                   789************************...*************************99999999886 PP

  == domain 9  score: 11.5 bits;  conditional E-value: 0.00071
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgd 42 
                                   + +++++   g+y +A+  ++ ++++d   P+   A+++lg+
  gi|91772658|ref|YP_565350.1| 469 YLKGYDLDTTGRYKEAVSCYRKTVELD---PQFTLAWYALGL 507
                                   5678999999*****************...**********96 PP

  == domain 10  score: 28.8 bits;  conditional E-value: 2.7e-09
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                   +al+++++   +  +A+aa++++++++   +d  +A++ +g+ + ++g +++A++ yr a+  ++
  gi|91772658|ref|YP_565350.1| 503 YALGLDLAHMDEHSEAIAAYDQVIEQN---SDFSDAYYRKGRTLDKLGLYQDAIESYRVAISLDS 564
                                   78899999999999*************...99999***********************9986665 PP

  == domain 11  score: 11.4 bits;  conditional E-value: 0.00076
                        TPR_16  31 PdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   Pd ++A+ ++g +++++g ++ A+  y++a+   p+
  gi|91772658|ref|YP_565350.1| 630 PDGYDAWVAKGGSLFVKGSYENALLSYNKAIMIKPN 665
                                   999*********************999998755555 PP

  == domain 12  score: 16.9 bits;  conditional E-value: 1.5e-05
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                   +++++ +  +gd   A++ +e a+++d   +   +A+++l++  ++ +++  A+++y+ +l  +p
  gi|91772658|ref|YP_565350.1| 671 YMRGQTYEMLGDRSSAINNYEKAVDLD---SSYKDAWFALAQNVYKSSNYYYAIQAYDGLLNLDP 732
                                   7889999999*****************...************************99998886666 PP

  == domain 13  score: 25.6 bits;  conditional E-value: 2.7e-08
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   ++++a+ + g y+  +a ++ +lk d    d+ eA++l+g+a + +g+l++A+  y++ l  +p++
  gi|91772658|ref|YP_565350.1| 740 QKGQAYDKIGIYRSSLASYNKLLKVD---TDNTEAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQN 802
                                   67899999999***************...9****************************99999986 PP

  == domain 14  score: 11.7 bits;  conditional E-value: 0.0006
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                   la+ + + ++g ++d ++ ++ +l++     d++  l+ +g+++ ++g +++A
  gi|91772658|ref|YP_565350.1| 807 LAQSLVLEDLGLFEDSINNYDKVLEMK---VDDPSVLMKKGNVYEKLGLYKDA 856
                                   577788999******************...77777****************98 PP

  == domain 15  score: 16.3 bits;  conditional E-value: 2.1e-05
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                   ++++ + ++g y dA   ++++l +    P++  Al  +g  ++ +g++ +A ++y+  ++  p+++
  gi|91772658|ref|YP_565350.1| 842 KKGNVYEKLGLYKDANDCYDIVLINE---PANSLALSRKGFNLYMLGDYIGAMDQYDLVIAKNPYDA 905
                                   68999*********************...*****************************999999885 PP

  == domain 16  score: 17.4 bits;  conditional E-value: 1e-05
                        TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   gdy  A  +++ +++++   P +a+A++++g++a+  + +a+  ++y++a++  p+
  gi|91772658|ref|YP_565350.1| 885 GDYIGAMDQYDLVIAKN---PYDAAAWYNKGNVAYLTSSYAGSTQFYLKAVELQPK 937
                                   777788888999999**...999****************************99997 PP

  == domain 17  score: 20.7 bits;  conditional E-value: 9.3e-07
                        TPR_16  23 alkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                   a++++   P    A+++lg +a  +g+++ A+ +y++al+ +p+a+
  gi|91772658|ref|YP_565350.1| 931 AVELQ---PKSITAWYNLGYIANIRGDVDTAITYYEKALAIDPNAA 973
                                   66677...99999******************************985 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       5.7     3e+03      12      34 .]      28      50 ..      27      50 .. 0.83
   2 ?    4.0   1.1      0.15        79       4      33 ..      54      83 ..      44      84 .. 0.78
   3 !    9.8   0.0     0.002       1.1       2      34 .]      86     118 ..      85     118 .. 0.94
   4 ?   -1.5   0.0       8.4   4.4e+03      15      34 .]     162     181 ..     159     181 .. 0.88
   5 ?    0.9   0.0       1.4   7.3e+02       1      34 []     182     215 ..     182     215 .. 0.87
   6 !   13.8   0.0   0.00011     0.056       1      34 []     216     249 ..     216     249 .. 0.96
   7 ?    7.4   0.0     0.012       6.2       2      32 ..     251     281 ..     250     282 .. 0.81
   8 !   10.6   0.1    0.0011       0.6      11      33 ..     294     316 ..     285     317 .. 0.84
   9 !   18.0   0.0     5e-06    0.0026       2      32 ..     319     349 ..     318     350 .. 0.95
  10 ?    0.8   0.1       1.6   8.2e+02       2      16 ..     353     368 ..     352     370 .. 0.81
  11 ?    7.6   0.0      0.01       5.4       9      32 ..     393     416 ..     391     417 .. 0.92
  12 !   21.7   0.0   3.4e-07   0.00018       2      33 ..     420     451 ..     419     452 .. 0.96
  13 !    8.7   0.0    0.0046       2.4       1      32 [.     453     484 ..     453     486 .. 0.91
  14 !    7.9   0.0    0.0086       4.5       1      21 [.     487     507 ..     487     520 .. 0.86
  15 !   20.2   0.1   9.9e-07   0.00052       1      34 []     521     554 ..     521     554 .. 0.96
  16 !   15.6   0.0   2.8e-05     0.015       2      28 ..     656     682 ..     655     687 .. 0.93
  17 !    8.1   0.2    0.0072       3.8       2      23 ..     690     712 ..     689     716 .. 0.88
  18 ?    5.2   0.1      0.06        32       2      27 ..     724     749 ..     723     755 .. 0.87
  19 !   16.3   0.3   1.8e-05    0.0094       2      33 ..     758     789 ..     757     790 .. 0.96
  20 ?    2.8   0.0      0.36   1.9e+02       2      27 ..     792     817 ..     791     823 .. 0.83
  21 ?    2.9   0.0      0.34   1.8e+02       2      32 ..     826     856 ..     825     856 .. 0.91
  22 ?    0.8   0.0       1.6   8.3e+02       5      32 ..     863     890 ..     859     891 .. 0.85
  23 !    8.6   0.7    0.0051       2.7       5      23 ..     897     915 ..     894     922 .. 0.85
  24 !   23.2   0.0   1.1e-07   5.8e-05       1      33 [.     927     959 ..     927     960 .. 0.96
  25 !   11.5   0.1   0.00062      0.32       1      32 [.     961     992 ..     961     994 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 5.7
                        TPR_17 12 nadaynnLAelllknGdlmtArq 34
                                  +a ++n+ +++l  nG +++A++
  gi|91772658|ref|YP_565350.1| 28 DARSFNEEGVALMLNGTYDKAIE 50
                                  67788888999999999999985 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.15
                        TPR_17  4 kaleldPnnadaynnLAelllknGdlmtAr 33
                                   al  dPn+  a+ n+A +++  Gd+++A+
  gi|91772658|ref|YP_565350.1| 54 LALVSDPNYRIALENKAAAQYLYGDYDEAI 83
                                  344458***********************8 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.002
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   y   l+l P ++  ++ ++ +l+k+Gd++ A++
  gi|91772658|ref|YP_565350.1|  86 YDHILKLQPGSPLIFTKKGMVLAKKGDYENAIK 118
                                   8999*************************9985 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 8.4
                        TPR_17  15 aynnLAelllknGdlmtArq 34 
                                    ++ +A+ l+ +G+ ++A+q
  gi|91772658|ref|YP_565350.1| 162 ILYHKAKSLEGLGRNEEAIQ 181
                                   68999999**********97 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.4
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   ly+k+le+   ++  +++++  +++ G++++A++
  gi|91772658|ref|YP_565350.1| 182 LYEKFLEIQLEHSMTLYEKGLDHARDGKSERAIE 215
                                   7999999999999999999998889999998875 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 0.00011
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   ly +al++dP+n   ++ +++++ ++G +++A++
  gi|91772658|ref|YP_565350.1| 216 LYDEALQIDPDNRTIWYSKGQAFDSLGLYEEAIE 249
                                   7******************************986 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.012
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   y ka+e d ++++++ n+A  + k+ ++++A
  gi|91772658|ref|YP_565350.1| 251 YNKAIEFDSTDVKVWWNKALDYDKLDKKEDA 281
                                   99*************9888766666666655 PP

  == domain 8  score: 10.6 bits;  conditional E-value: 0.0011
                        TPR_17  11 nnadaynnLAelllknGdlmtAr 33 
                                    na+a++nL+++l+  G++ +A+
  gi|91772658|ref|YP_565350.1| 294 YNAEAWFNLGVALEGTGNYFEAI 316
                                   59***************999886 PP

  == domain 9  score: 18.0 bits;  conditional E-value: 5e-06
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   ++++l ldP+n da++ ++ +l k+G++++A
  gi|91772658|ref|YP_565350.1| 319 FEQVLLLDPDNIDAWHKKGLVLNKIGRFDEA 349
                                   7999*************************99 PP

  == domain 10  score: 0.8 bits;  conditional E-value: 1.6
                        TPR_17   2 ylkaleldPnn.aday 16 
                                   y  al+++P+n a+ y
  gi|91772658|ref|YP_565350.1| 353 YDSALKINPDNiAKIY 368
                                   7789******967666 PP

  == domain 11  score: 7.6 bits;  conditional E-value: 0.01
                        TPR_17   9 dPnnadaynnLAelllknGdlmtA 32 
                                   + ++a+ ++ +++l+l + d+++A
  gi|91772658|ref|YP_565350.1| 393 NSDSAKIWYDKGTLYLGLSDYEEA 416
                                   8899*****************999 PP

  == domain 12  score: 21.7 bits;  conditional E-value: 3.4e-07
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   ++k+leld ++a++++ +A +l k+G++ +A+
  gi|91772658|ref|YP_565350.1| 420 FEKVLELDSKHAVVWYKKALALDKLGNYNEAI 451
                                   89***************************996 PP

  == domain 13  score: 8.7 bits;  conditional E-value: 0.0046
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   +y++al++dP+ +++++++++ l   G++++A
  gi|91772658|ref|YP_565350.1| 453 CYTEALRRDPSCPNVWYLKGYDLDTTGRYKEA 484
                                   8*******************988888888888 PP

  == domain 14  score: 7.9 bits;  conditional E-value: 0.0086
                        TPR_17   1 lylkaleldPnnadaynnLAe 21 
                                   +y+k +eldP    a++ L+ 
  gi|91772658|ref|YP_565350.1| 487 CYRKTVELDPQFTLAWYALGL 507
                                   8******************96 PP

  == domain 15  score: 20.2 bits;  conditional E-value: 9.9e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y +++e++ + +day+ ++++l k+G +++A++
  gi|91772658|ref|YP_565350.1| 521 AYDQVIEQNSDFSDAYYRKGRTLDKLGLYQDAIE 554
                                   599****************************986 PP

  == domain 16  score: 15.6 bits;  conditional E-value: 2.8e-05
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                   y ka+ + Pn+++ +++++++++++Gd
  gi|91772658|ref|YP_565350.1| 656 YNKAIMIKPNSSVTWYMRGQTYEMLGD 682
                                   899999*******************98 PP

  == domain 17  score: 8.1 bits;  conditional E-value: 0.0072
                        TPR_17   2 ylkaleldPnnadaynnLAe.ll 23 
                                   y+ka++ld ++ da++ LA+ ++
  gi|91772658|ref|YP_565350.1| 690 YEKAVDLDSSYKDAWFALAQnVY 712
                                   9******************8555 PP

  == domain 18  score: 5.2 bits;  conditional E-value: 0.06
                        TPR_17   2 ylkaleldPnnadaynnLAelllknG 27 
                                   y   l ldP n  a+ ++++++ k+G
  gi|91772658|ref|YP_565350.1| 724 YDGLLNLDPENKTALLQKGQAYDKIG 749
                                   5567899***************9998 PP

  == domain 19  score: 16.3 bits;  conditional E-value: 1.8e-05
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   y k l+ d +n +a+++++ + +++G+l++A+
  gi|91772658|ref|YP_565350.1| 758 YNKLLKVDTDNTEAWYLRGLASYNLGNLEDAV 789
                                   99***************************996 PP

  == domain 20  score: 2.8 bits;  conditional E-value: 0.36
                        TPR_17   2 ylkaleldPnnadaynnLAelllknG 27 
                                   y k+l  dP n d++     +l+ +G
  gi|91772658|ref|YP_565350.1| 792 YDKVLSSDPQNIDVLLAQSLVLEDLG 817
                                   99************987777776665 PP

  == domain 21  score: 2.9 bits;  conditional E-value: 0.34
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   y k+le   +++ ++  ++++++k+G +++A
  gi|91772658|ref|YP_565350.1| 826 YDKVLEMKVDDPSVLMKKGNVYEKLGLYKDA 856
                                   8899999999****************98877 PP

  == domain 22  score: 0.8 bits;  conditional E-value: 1.6
                        TPR_17   5 aleldPnnadaynnLAelllknGdlmtA 32 
                                   +l ++P n+ a+  ++  l+++Gd+  A
  gi|91772658|ref|YP_565350.1| 863 VLINEPANSLALSRKGFNLYMLGDYIGA 890
                                   56789*******************9765 PP

  == domain 23  score: 8.6 bits;  conditional E-value: 0.0051
                        TPR_17   5 aleldPnnadaynnLAell 23 
                                   +++++P +a a++n++++ 
  gi|91772658|ref|YP_565350.1| 897 VIAKNPYDAAAWYNKGNVA 915
                                   799*************964 PP

  == domain 24  score: 23.2 bits;  conditional E-value: 1.1e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +ylka+el P++  a++nL+++   +Gd +tA+
  gi|91772658|ref|YP_565350.1| 927 FYLKAVELQPKSITAWYNLGYIANIRGDVDTAI 959
                                   6******************************97 PP

  == domain 25  score: 11.5 bits;  conditional E-value: 0.00062
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   +y+kal++dPn a a++n+  ++++ G++  A
  gi|91772658|ref|YP_565350.1| 961 YYEKALAIDPNAASALYNKRFAHYRVGQSVSA 992
                                   6*****************86666666666655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.21   1.1e+02      10      42 ..      38      70 ..      35      72 .. 0.87
   2 !    8.9   0.0    0.0059       3.1       9      37 ..      71      99 ..      69     104 .. 0.84
   3 ?    2.3   0.0      0.73   3.8e+02      10      28 ..     106     124 ..     102     125 .. 0.89
   4 ?    7.4   0.0     0.017       9.1       5      36 ..     164     195 ..     161     202 .. 0.81
   5 !   19.0   0.1   3.2e-06    0.0017       8      43 ..     201     236 ..     194     237 .. 0.86
   6 !   11.0   0.0    0.0012      0.63       4      38 ..     231     265 ..     229     271 .. 0.89
   7 ?    5.6   0.0     0.067        35      14      42 ..     275     303 ..     264     306 .. 0.86
   8 !   15.3   0.0   4.9e-05     0.026       2      40 ..     297     335 ..     296     339 .. 0.93
   9 !   11.9   0.0   0.00063      0.33       3      35 ..     332     364 ..     331     368 .. 0.92
  10 !   11.4   0.0   0.00093      0.49       2      42 ..     398     438 ..     397     441 .. 0.92
  11 !   14.8   0.0   7.3e-05     0.039       3      42 ..     433     472 ..     431     474 .. 0.93
  12 !   13.6   0.0   0.00018     0.094       1      42 [.     465     506 ..     465     507 .. 0.94
  13 !   17.6   0.2   9.2e-06    0.0049       3      43 ..     501     541 ..     499     542 .. 0.96
  14 ?    7.1   0.0     0.021        11       2      37 ..     534     569 ..     533     575 .. 0.89
  15 !   17.6   0.0   8.8e-06    0.0047       3      43 ..     669     709 ..     667     710 .. 0.97
  16 ?    1.7   0.0       1.2   6.3e+02      20      43 ..     720     743 ..     716     744 .. 0.94
  17 !   13.1   0.0   0.00025      0.13       2      39 ..     770     807 ..     769     811 .. 0.93
  18 ?    3.2   0.0      0.39   2.1e+02       3      39 ..     805     841 ..     803     845 .. 0.85
  19 ?    2.4   0.0      0.67   3.5e+02       4      39 ..     840     875 ..     837     880 .. 0.85
  20 !   11.3   0.0   0.00098      0.52      12      41 ..     882     911 ..     873     914 .. 0.89
  21 ?    3.8   0.0      0.24   1.3e+02      21      43 ..     925     947 ..     920     948 .. 0.84
  22 !   19.6   0.0   2.2e-06    0.0011       3      39 ..     941     977 ..     939     979 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.21
                        TPR_14 10 allalGdpdeAiallrralalaPddaeawllla 42
                                  al+ +G +d+Ai+ ++ al  +P+ + a+   a
  gi|91772658|ref|YP_565350.1| 38 ALMLNGTYDKAIEKYDLALVSDPNYRIALENKA 70
                                  78999******************9988877665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0059
                        TPR_14  9 eallalGdpdeAiallrralalaPddaea 37
                                  +a +  Gd+deAia ++ +l+l+P+++ +
  gi|91772658|ref|YP_565350.1| 71 AAQYLYGDYDEAIATYDHILKLQPGSPLI 99
                                  555667******************99876 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.73
                        TPR_14  10 allalGdpdeAiallrral 28 
                                   +l+  Gd++ Ai+ +++al
  gi|91772658|ref|YP_565350.1| 106 VLAKKGDYENAIKTYDKAL 124
                                   78999***********997 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.017
                        TPR_14   5 lalaeallalGdpdeAiallrralalaPddae 36 
                                   +  a+ l+ lG+ +eAi+l+++ l+ + ++  
  gi|91772658|ref|YP_565350.1| 164 YHKAKSLEGLGRNEEAIQLYEKFLEIQLEHSM 195
                                   667889999*************9998766655 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 3.2e-06
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   +  +++ G+ ++Ai+l+++al+ +Pd++++w+  +q
  gi|91772658|ref|YP_565350.1| 201 GLDHARDGKSERAIELYDEALQIDPDNRTIWYSKGQ 236
                                   5568999************************97776 PP

  == domain 6  score: 11.0 bits;  conditional E-value: 0.0012
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeaw 38 
                                   ++  ++a+  lG ++eAi+ +++a++ + +d  +w
  gi|91772658|ref|YP_565350.1| 231 WYSKGQAFDSLGLYEEAIESYNKAIEFDSTDVKVW 265
                                   88889*********************999999888 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.067
                        TPR_14  14 lGdpdeAiallrralalaPddaeawllla 42 
                                   l++ ++Ai  +r++l l+  +aeaw+ l+
  gi|91772658|ref|YP_565350.1| 275 LDKKEDAIISYREVLVLDLYNAEAWFNLG 303
                                   556689********************998 PP

  == domain 8  score: 15.3 bits;  conditional E-value: 4.9e-05
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                   ea+  l+ al+  G++ eAi+ ++++l l+Pd+ +aw  
  gi|91772658|ref|YP_565350.1| 297 EAWFNLGVALEGTGNYFEAINSFEQVLLLDPDNIDAWHK 335
                                   89***********************************76 PP

  == domain 9  score: 11.9 bits;  conditional E-value: 0.00063
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPdda 35 
                                   a+ + + +l   G++deA+  ++ al+ +Pd+ 
  gi|91772658|ref|YP_565350.1| 332 AWHKKGLVLNKIGRFDEALVSYDSALKINPDNI 364
                                   89999999***********************85 PP

  == domain 10  score: 11.4 bits;  conditional E-value: 0.00093
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   + +++ + ++l l d++eA+  ++++l+l+ ++a++w+  a
  gi|91772658|ref|YP_565350.1| 398 KIWYDKGTLYLGLSDYEEAVLSFEKVLELDSKHAVVWYKKA 438
                                   579**********************************8766 PP

  == domain 11  score: 14.8 bits;  conditional E-value: 7.3e-05
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   ++++ a al  lG++ eAi ++ +al+++P+ + +w+l +
  gi|91772658|ref|YP_565350.1| 433 VWYKKALALDKLGNYNEAIICYTEALRRDPSCPNVWYLKG 472
                                   6999********************************9876 PP

  == domain 12  score: 13.6 bits;  conditional E-value: 0.00018
                        TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   p+++++ +  l + G+++eA+ ++r+ ++l+P++  aw++l+
  gi|91772658|ref|YP_565350.1| 465 PNVWYLKGYDLDTTGRYKEAVSCYRKTVELDPQFTLAWYALG 506
                                   678999999999***************************997 PP

  == domain 13  score: 17.6 bits;  conditional E-value: 9.2e-06
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   a++al+  l++ +++ eAia+++++++++ d+ +a+++ ++
  gi|91772658|ref|YP_565350.1| 501 AWYALGLDLAHMDEHSEAIAAYDQVIEQNSDFSDAYYRKGR 541
                                   8***********************************99987 PP

  == domain 14  score: 7.1 bits;  conditional E-value: 0.021
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaea 37 
                                   +a+++ ++ l  lG +++Ai+ +r a++l+ ++ +a
  gi|91772658|ref|YP_565350.1| 534 DAYYRKGRTLDKLGLYQDAIESYRVAISLDSSNSAA 569
                                   6999************************99888776 PP

  == domain 15  score: 17.6 bits;  conditional E-value: 8.8e-06
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                    ++++++ ++ lGd   Ai+ +++a++l+ +  +aw++laq
  gi|91772658|ref|YP_565350.1| 669 TWYMRGQTYEMLGDRSSAINNYEKAVDLDSSYKDAWFALAQ 709
                                   59**************************************8 PP

  == domain 16  score: 1.7 bits;  conditional E-value: 1.2
                        TPR_14  20 AiallrralalaPddaeawlllaq 43 
                                   Ai++++ +l l+P++ +a+l+ +q
  gi|91772658|ref|YP_565350.1| 720 AIQAYDGLLNLDPENKTALLQKGQ 743
                                   899*****************9998 PP

  == domain 17  score: 13.1 bits;  conditional E-value: 0.00025
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                   ea+++++ a ++lG++++A+  ++++l+ +P++ +++l
  gi|91772658|ref|YP_565350.1| 770 EAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQNIDVLL 807
                                   89******************************988876 PP

  == domain 18  score: 3.2 bits;  conditional E-value: 0.39
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                   +lla   +l+ lG ++++i+ ++++l+   dd+ +++
  gi|91772658|ref|YP_565350.1| 805 VLLAQSLVLEDLGLFEDSINNYDKVLEMKVDDPSVLM 841
                                   57888899******************98888887765 PP

  == domain 19  score: 2.4 bits;  conditional E-value: 0.67
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                   l++ + +++ lG +++A ++++ +l   P++  a+ 
  gi|91772658|ref|YP_565350.1| 840 LMKKGNVYEKLGLYKDANDCYDIVLINEPANSLALS 875
                                   677899******************999999988875 PP

  == domain 20  score: 11.3 bits;  conditional E-value: 0.00098
                        TPR_14  12 lalGdpdeAiallrralalaPddaeawlll 41 
                                   + lGd+ +A++ ++ ++a++P da+aw+  
  gi|91772658|ref|YP_565350.1| 882 YMLGDYIGAMDQYDLVIAKNPYDAAAWYNK 911
                                   568************************876 PP

  == domain 21  score: 3.8 bits;  conditional E-value: 0.24
                        TPR_14  21 iallrralalaPddaeawlllaq 43 
                                    + + +a++l+P++ +aw+ l+ 
  gi|91772658|ref|YP_565350.1| 925 TQFYLKAVELQPKSITAWYNLGY 947
                                   5778899************9986 PP

  == domain 22  score: 19.6 bits;  conditional E-value: 2.2e-06
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                   a++ l+ +   +Gd d+Ai+++++ala +P+ a a++
  gi|91772658|ref|YP_565350.1| 941 AWYNLGYIANIRGDVDTAITYYEKALAIDPNAASALY 977
                                   89*****************************998875 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.5   5.3e-05     0.028       5      74 ..      31      92 ..      27      94 .. 0.83
   2 !   12.0   0.0   0.00038       0.2       8      30 ..     102     124 ..      97     141 .. 0.84
   3 !   25.0   1.3   3.3e-08   1.7e-05       4      76 ..     161     225 ..     158     226 .. 0.92
   4 !   22.1   0.3   2.6e-07   0.00014       5      74 ..     196     257 ..     193     260 .. 0.92
   5 !    9.9   0.0    0.0016      0.87       6      70 ..     231     287 ..     226     291 .. 0.54
   6 !   10.5   0.0    0.0011      0.55      45      72 ..     296     323 ..     279     328 .. 0.66
   7 !   21.3   0.0   4.8e-07   0.00025       3      74 ..     296     359 ..     294     362 .. 0.94
   8 !   25.7   0.1     2e-08   1.1e-05       2      76 ..     396     462 ..     395     463 .. 0.91
   9 !   19.2   0.1   2.2e-06    0.0011       3      76 ..     431     496 ..     429     497 .. 0.89
  10 !   18.0   0.8   4.8e-06    0.0025       5      66 ..     501     561 ..     498     564 .. 0.80
  11 !   14.9   0.0   4.6e-05     0.024       8      75 ..     638     697 ..     634     699 .. 0.79
  12 !    7.5   0.2    0.0095         5       8      73 ..     740     797 ..     735     801 .. 0.71
  13 ?    4.2   0.0       0.1        53       9      33 ..     809     833 ..     801     861 .. 0.62
  14 ?    4.2   0.1     0.099        52       3      32 ..     905     934 ..     869     937 .. 0.67
  15 !   22.5   0.2     2e-07   0.00011       3      76 ..     905     970 ..     903     971 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.3e-05
                        TPR_12  5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                  + n+ +++l+  g yd+A+e ++ al           p++ ++l n + ++++ g+y+eA++ + + l++
  gi|91772658|ref|YP_565350.1| 31 SFNEEGVALMLNGTYDKAIEKYDLALVS--------DPNYRIALENKAAAQYLYGDYDEAIATYDHILKL 92
                                  5556688899999999999999999333........45689***********************999876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00038
                        TPR_12   8 nlaavlrrlgrydeAlellekal 30 
                                   + ++vl++ g+y+ A++ ++kal
  gi|91772658|ref|YP_565350.1| 102 KKGMVLAKKGDYENAIKTYDKAL 124
                                   679*******************9 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 3.3e-08
                        TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    +l++ a  l  lgr +eA++l+ek lei+      +h   + tl+  g  + + g+ e A+el+ eal+i++
  gi|91772658|ref|YP_565350.1| 161 MILYHKAKSLEGLGRNEEAIQLYEKFLEIQ-----LEH---SMTLYEKGLDHARDGKSERAIELYDEALQIDP 225
                                   567799************************.....457...89***************************975 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 2.6e-07
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   +l++ ++ ++r g+ + A+el+++al+i      pd+    t+ +  g++++ lg yeeA+e +++a++ 
  gi|91772658|ref|YP_565350.1| 196 TLYEKGLDHARDGKSERAIELYDEALQID-----PDN---RTIWYSKGQAFDSLGLYEEAIESYNKAIEF 257
                                   56699************************.....998...789999*********************985 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0016
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                   ++  +++   lg y+eA+e ++ka+e        +    + +  n +  y++l++ e+A+  ++e
  gi|91772658|ref|YP_565350.1| 231 WYSKGQAFDSLGLYEEAIESYNKAIEFD-----ST---DVKVWWNKALDYDKLDKKEDAIISYRE 287
                                   4455555555666666666666665554.....21...245555555555555555555555555 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.0011
                        TPR_12  45 attlrnLgrlyralgryeeAlelleeal 72 
                                   a++ +nLg +++ +g+y eA++ +e++l
  gi|91772658|ref|YP_565350.1| 296 AEAWFNLGVALEGTGNYFEAINSFEQVL 323
                                   5555555555555555555555555554 PP

  == domain 7  score: 21.3 bits;  conditional E-value: 4.8e-07
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   a a+ nl+++l   g+y eA+  +e++l +      pd+   + + +  g ++ + gr++eAl  +  al+i
  gi|91772658|ref|YP_565350.1| 296 AEAWFNLGVALEGTGNYFEAINSFEQVLLLD-----PDN---IDAWHKKGLVLNKIGRFDEALVSYDSALKI 359
                                   67888*************************9.....*98...89**************************98 PP

  == domain 8  score: 25.7 bits;  conditional E-value: 2e-08
                        TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    a++++  +++++ l +y+eA   +ek+le+       +h   a + +  + ++++lg+y eA+  ++eal++++
  gi|91772658|ref|YP_565350.1| 396 SAKIWYDKGTLYLGLSDYEEAVLSFEKVLELD-----SKH---AVVWYKKALALDKLGNYNEAIICYTEALRRDP 462
                                   6889999*************************.....788...888888888888****************9875 PP

  == domain 9  score: 19.2 bits;  conditional E-value: 2.2e-06
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                   a ++++ a++l +lg+y eA+ ++ +al++      p  p+   + +  g  ++ +gry+eA++ +++++++++
  gi|91772658|ref|YP_565350.1| 431 AVVWYKKALALDKLGNYNEAIICYTEALRRD-----PSCPN---VWYLKGYDLDTTGRYKEAVSCYRKTVELDP 496
                                   5678899********************9999.....76555...7999*********************99876 PP

  == domain 10  score: 18.0 bits;  conditional E-value: 4.8e-06
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                   a++ l++ l+++ ++ eA++ +++++e+ +    + ++   +tl  Lg +++a + y+ A++
  gi|91772658|ref|YP_565350.1| 501 AWYALGLDLAHMDEHSEAIAAYDQVIEQNSDF-SDAYYRKGRTLDKLGLYQDAIESYRVAIS 561
                                   5679*************************665.45566778888888888777777777765 PP

  == domain 11  score: 14.9 bits;  conditional E-value: 4.6e-05
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                     +  l+  g y+ Al  ++ka+ i      p+    + t +  g++y++lg+   A++ +e+a++++
  gi|91772658|ref|YP_565350.1| 638 AKGGSLFVKGSYENALLSYNKAIMIK-----PN---SSVTWYMRGQTYEMLGDRSSAINNYEKAVDLD 697
                                   56666777777777777777774444.....54...699*************************9986 PP

  == domain 12  score: 7.5 bits;  conditional E-value: 0.0095
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   + ++++ + g y  +l+ ++k l +   +  ++   +a++lr+L+ +   lg++e+A++ + ++l 
  gi|91772658|ref|YP_565350.1| 740 QKGQAYDKIGIYRSSLASYNKLLKVD--T--DN--TEAWYLRGLASYN--LGNLEDAVYSYDKVLS 797
                                   45555555555666666666666666..2..33..599********98..99********999986 PP

  == domain 13  score: 4.2 bits;  conditional E-value: 0.1
                        TPR_12   9 laavlrrlgrydeAlellekaleia 33 
                                     +vl  lg +++++ +++k+le+ 
  gi|91772658|ref|YP_565350.1| 809 QSLVLEDLGLFEDSINNYDKVLEMK 833
                                   5678888888889999998888876 PP

  == domain 14  score: 4.2 bits;  conditional E-value: 0.099
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                   a+a++n ++v +    y+ + +++ ka+e+
  gi|91772658|ref|YP_565350.1| 905 AAAWYNKGNVAYLTSSYAGSTQFYLKAVEL 934
                                   445556666666666666666666666655 PP

  == domain 15  score: 22.5 bits;  conditional E-value: 2e-07
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                   a+a++n ++v +    y+ + +++ ka+e++     p++   +t+ +nLg +   +g+ + A+ ++e+alai++
  gi|91772658|ref|YP_565350.1| 905 AAAWYNKGNVAYLTSSYAGSTQFYLKAVELQ-----PKS---ITAWYNLGYIANIRGDVDTAITYYEKALAIDP 970
                                   77889**************************.....875...9****************************975 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   5.7e-06     0.003       1      62 [.      39     100 ..      39     106 .. 0.91
   2 ?    3.2   0.0      0.23   1.2e+02       2      18 ..     108     124 ..     107     131 .. 0.83
   3 ?   -1.2   0.0       5.5   2.9e+03      37      49 ..     172     184 ..     160     192 .. 0.60
   4 !   22.1   0.0     3e-07   0.00016       4      55 ..     207     258 ..     205     268 .. 0.90
   5 !   10.4   0.0    0.0013       0.7      24      62 ..     295     334 ..     285     339 .. 0.86
   6 !   18.7   0.0   3.4e-06    0.0018       5      58 ..     310     363 ..     306     370 .. 0.93
   7 !   25.6   0.0   2.5e-08   1.3e-05       5      65 ..     411     471 ..     406     472 .. 0.95
   8 ?    4.7   0.0     0.082        43       5      31 ..     479     505 ..     478     510 .. 0.94
   9 !   17.3   0.3   9.4e-06     0.005       4      51 ..     512     559 ..     509     572 .. 0.87
  10 ?    3.7   0.0      0.17        87       5      44 ..     647     686 ..     643     687 .. 0.92
  11 !   13.0   0.9   0.00022      0.11       5      58 ..     681     734 ..     679     744 .. 0.91
  12 !   13.1   0.1    0.0002       0.1      11      62 ..     755     806 ..     743     812 .. 0.87
  13 ?    4.6   0.0     0.089        47       7      56 ..     819     868 ..     813     875 .. 0.85
  14 ?    1.9   0.1      0.63   3.3e+02       2      37 ..     882     917 ..     881     945 .. 0.80
  15 !   13.8   0.0   0.00012     0.061       4      45 ..     952     993 ..     949    1004 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.7e-06
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   l+ +g y+ A++ +  al  dp++  a+ + A a++  g++deA+a+ d +++ +p ++ + 
  gi|91772658|ref|YP_565350.1|  39 LMLNGTYDKAIEKYDLALVSDPNYRIALENKAAAQYLYGDYDEAIATYDHILKLQPGSPLIF 100
                                   6789******************988888899************************9988765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.23
                        TPR_19   2 laegdyaeAlalleqal 18 
                                    + gdy++A++ + +al
  gi|91772658|ref|YP_565350.1| 108 AKKGDYENAIKTYDKAL 124
                                   5789**********997 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.5
                        TPR_19  37 algqldeAealLd 49 
                                    lg+ +eA++l +
  gi|91772658|ref|YP_565350.1| 172 GLGRNEEAIQLYE 184
                                   5555555555543 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 3e-07
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                   +g+ ++A++l+ +alq dp+n  +++   +a  +lg ++eA++  +++ e d
  gi|91772658|ref|YP_565350.1| 207 DGKSERAIELYDEALQIDPDNRTIWYSKGQAFDSLGLYEEAIESYNKAIEFD 258
                                   68999**************************************999887765 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.0013
                        TPR_19  24 naearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                   naea+ +L  al  +g++ eA++  +++++ dpd+  +++
  gi|91772658|ref|YP_565350.1| 295 NAEAWFNLGVALEGTGNYFEAINSFEQVLLLDPDNiDAWH 334
                                   8999******************************844444 PP

  == domain 6  score: 18.7 bits;  conditional E-value: 3.4e-06
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                   g+y eA++ +eq+l  dp+n +a+     +l + g++deA    d +++ +pd+
  gi|91772658|ref|YP_565350.1| 310 GNYFEAINSFEQVLLLDPDNIDAWHKKGLVLNKIGRFDEALVSYDSALKINPDN 363
                                   7899************************************************95 PP

  == domain 7  score: 25.6 bits;  conditional E-value: 2.5e-08
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                    dy+eA+  +e++l+ d k+a +++  A al +lg+++eA+ +  ++++ dp +++++ L+
  gi|91772658|ref|YP_565350.1| 411 SDYEEAVLSFEKVLELDSKHAVVWYKKALALDKLGNYNEAIICYTEALRRDPSCPNVWYLK 471
                                   59*******************************************************9987 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.082
                        TPR_19   5 gdyaeAlalleqalqedpknaearllL 31 
                                   g+y eA++ +++  + dp+   a+++L
  gi|91772658|ref|YP_565350.1| 479 GRYKEAVSCYRKTVELDPQFTLAWYAL 505
                                   89**********************987 PP

  == domain 9  score: 17.3 bits;  conditional E-value: 9.4e-06
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                   +  + eA+a++ q+++++ + ++a ++  + l +lg +++A++    +
  gi|91772658|ref|YP_565350.1| 512 MDEHSEAIAAYDQVIEQNSDFSDAYYRKGRTLDKLGLYQDAIESYRVA 559
                                   56789************************************9987665 PP

  == domain 10  score: 3.7 bits;  conditional E-value: 0.17
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                   g y++Al  + +a+  +p+++  ++   + +  lg+   A
  gi|91772658|ref|YP_565350.1| 647 GSYENALLSYNKAIMIKPNSSVTWYMRGQTYEMLGDRSSA 686
                                   99******************************99998777 PP

  == domain 11  score: 13.0 bits;  conditional E-value: 0.00022
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                   gd  +A++ +e+a + d  + +a+ +LA+  +++ ++  A+++ d l++ dp +
  gi|91772658|ref|YP_565350.1| 681 GDRSSAINNYEKAVDLDSSYKDAWFALAQNVYKSSNYYYAIQAYDGLLNLDPEN 734
                                   78889********************************************99984 PP

  == domain 12  score: 13.1 bits;  conditional E-value: 0.0002
                        TPR_19  11 lalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   la + ++l+ d +n ea++l   a ++lg+l++A    d+++ +dp++ ++ 
  gi|91772658|ref|YP_565350.1| 755 LASYNKLLKVDTDNTEAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQNIDVL 806
                                   67788999**************************************955544 PP

  == domain 13  score: 4.6 bits;  conditional E-value: 0.089
                        TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                   +++ ++ + ++l+ + +++ +++   +++ +lg +++A ++ d ++  +p
  gi|91772658|ref|YP_565350.1| 819 FEDSINNYDKVLEMKVDDPSVLMKKGNVYEKLGLYKDANDCYDIVLINEP 868
                                   566688999*****************************998876666555 PP

  == domain 14  score: 1.9 bits;  conditional E-value: 0.63
                        TPR_19   2 laegdyaeAlalleqalqedpknaearllLAealla 37 
                                   ++ gdy  A++ +  +++++p +a+a+++  ++ + 
  gi|91772658|ref|YP_565350.1| 882 YMLGDYIGAMDQYDLVIAKNPYDAAAWYNKGNVAYL 917
                                   567999*********************987777665 PP

  == domain 15  score: 13.8 bits;  conditional E-value: 0.00012
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                   +gd + A+ ++e+al+ dp+ a a+++   a++  gq   Ae
  gi|91772658|ref|YP_565350.1| 952 RGDVDTAITYYEKALAIDPNAASALYNKRFAHYRVGQSVSAE 993
                                   79************************9999999888877776 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-05    0.0092       9      56 ..      77     124 ..      69     155 .. 0.88
   2 !   14.8   0.0   4.4e-05     0.023       5      60 ..     204     259 ..     203     264 .. 0.93
   3 ?    5.0   0.0      0.05        26      15      54 ..     282     321 ..     275     323 .. 0.84
   4 !   17.9   0.0     5e-06    0.0026      13      62 ..     314     363 ..     306     366 .. 0.93
   5 !   10.9   0.0   0.00074      0.39      17      59 ..     385     427 ..     373     428 .. 0.87
   6 !   15.8   0.0   2.1e-05     0.011       5      62 ..     407     464 ..     406     471 .. 0.92
   7 !   10.6   0.1   0.00091      0.48      10      65 ..     480     535 ..     477     569 .. 0.93
   8 !   14.8   0.0   4.4e-05     0.023      10      65 ..     648     703 ..     642     709 .. 0.89
   9 ?    2.8   0.0      0.25   1.3e+02      14      56 ..     720     762 ..     714     767 .. 0.88
  10 !   20.5   0.0   7.3e-07   0.00039      15      71 ..     755     811 ..     751     812 .. 0.93
  11 ?    4.4   0.0      0.08        42      16      63 ..     824     871 ..     817     875 .. 0.87
  12 ?    3.3   0.0      0.17        89      11      65 ..     853     907 ..     845     917 .. 0.86
  13 !   10.9   0.0   0.00071      0.38      22      65 ..     932     975 ..     927     980 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                         TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                    d+++a+a+++ +l l+P +p      G++la+ G+++ A++  + +l
  gi|91772658|ref|YP_565350.1|  77 GDYDEAIATYDHILKLQPGSPLIFTKKGMVLAKKGDYENAIKTYDKAL 124
                                   599*************************************99887766 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.4e-05
                         TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                   ++r  ++era++ ++  l+++Pd    ++  G++   lG +++A++  + +++ + 
  gi|91772658|ref|YP_565350.1| 204 HARDGKSERAIELYDEALQIDPDNRTIWYSKGQAFDSLGLYEEAIESYNKAIEFDS 259
                                   678899*****************************************999998765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.05
                         TPR_9  15 lavverllllaPddpeerrdRGlllaqlGclsaAladLea 54 
                                   +  +  +l+l+   +e ++  G++l+  G++ +A++ +e+
  gi|91772658|ref|YP_565350.1| 282 IISYREVLVLDLYNAEAWFNLGVALEGTGNYFEAINSFEQ 321
                                   555566788888899**********************997 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 5e-06
                         TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                   +a+   e +lll+Pd ++ +   Gl+l + G++ +Al   + +l ++pd+
  gi|91772658|ref|YP_565350.1| 314 EAINSFEQVLLLDPDNIDAWHKKGLVLNKIGRFDEALVSYDSALKINPDN 363
                                   5788889****************************************986 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00074
                         TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   ++  +  +++d++  ++d G l+  l ++++A+  +e  l+l+
  gi|91772658|ref|YP_565350.1| 385 CYAAIPSFNSDSAKIWYDKGTLYLGLSDYEEAVLSFEKVLELD 427
                                   6666667899**************************9999875 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 2.1e-05
                         TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                   ++   d+e+a    e +l l+++++  ++  +l+l +lG++++A+ +   +l+ +p+ 
  gi|91772658|ref|YP_565350.1| 407 YLGLSDYEEAVLSFEKVLELDSKHAVVWYKKALALDKLGNYNEAIICYTEALRRDPSC 464
                                   666789999*******************************************999975 PP

  == domain 7  score: 10.6 bits;  conditional E-value: 0.00091
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                   ++ +a  ++   + l+P+    ++  Gl la+++  s+A+a+ ++ ++++ d  da
  gi|91772658|ref|YP_565350.1| 480 RYKEAVSCYRKTVELDPQFTLAWYALGLDLAHMDEHSEAIAAYDQVIEQNSDFSDA 535
                                   678899999999***********************************999887776 PP

  == domain 8  score: 14.8 bits;  conditional E-value: 4.4e-05
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                    +e al  ++  ++++P++   ++ RG+ ++ lG+ s A++  e +++l+ +  da
  gi|91772658|ref|YP_565350.1| 648 SYENALLSYNKAIMIKPNSSVTWYMRGQTYEMLGDRSSAINNYEKAVDLDSSYKDA 703
                                   67899999999*************************************99866665 PP

  == domain 9  score: 2.8 bits;  conditional E-value: 0.25
                         TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                   a+++++ ll l+P+    ++  G+++ + G ++  la  +  l
  gi|91772658|ref|YP_565350.1| 720 AIQAYDGLLNLDPENKTALLQKGQAYDKIGIYRSSLASYNKLL 762
                                   88999**************************999998877666 PP

  == domain 10  score: 20.5 bits;  conditional E-value: 7.3e-07
                         TPR_9  15 lavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                                   la ++ ll ++ d  e ++ RGl+ + lG+l+ A+   +  l+ +p++ d+ +++++
  gi|91772658|ref|YP_565350.1| 755 LASYNKLLKVDTDNTEAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQNIDVLLAQSL 811
                                   788999********************************************9998765 PP

  == domain 11  score: 4.4 bits;  conditional E-value: 0.08
                         TPR_9  16 avverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                     ++ +l ++ ddp+ ++  G ++++lG ++ A ++ +  l ++p++ 
  gi|91772658|ref|YP_565350.1| 824 NNYDKVLEMKVDDPSVLMKKGNVYEKLGLYKDANDCYDIVLINEPANS 871
                                   5678899999*************************9999999888765 PP

  == domain 12  score: 3.3 bits;  conditional E-value: 0.17
                         TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                   +  a  +++ +l+  P     +   G+ l+ lG++ +A++  +  +a++p +++a
  gi|91772658|ref|YP_565350.1| 853 YKDANDCYDIVLINEPANSLALSRKGFNLYMLGDYIGAMDQYDLVIAKNPYDAAA 907
                                   55677899999999999999999999*********************99977765 PP

  == domain 13  score: 10.9 bits;  conditional E-value: 0.00071
                         TPR_9  22 lllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                   + l+P+++  ++  G +   +G++ +A+   e +la++p+a+ a
  gi|91772658|ref|YP_565350.1| 932 VELQPKSITAWYNLGYIANIRGDVDTAITYYEKALAIDPNAASA 975
                                   6799***********************************99876 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.088        47      13      33 ..      43      61 ..      36      61 .. 0.81
   2 ?    4.7   0.1      0.07        37      13      26 ..      77      90 ..      65      97 .. 0.76
   3 !    8.7   0.0    0.0036       1.9      10      26 ..     108     124 ..     104     137 .. 0.85
   4 !    7.6   0.1    0.0078       4.1       9      28 ..     170     189 ..     163     195 .. 0.80
   5 !   11.0   0.1   0.00064      0.34       7      31 ..     202     226 ..     196     229 .. 0.80
   6 !   11.1   0.0   0.00061      0.32       4      29 ..     233     258 ..     230     263 .. 0.82
   7 ?    1.4   0.1      0.77   4.1e+02       6      34 ..     269     295 ..     264     297 .. 0.76
   8 !   13.5   0.0    0.0001     0.055       1      33 [.     298     328 ..     298     331 .. 0.87
   9 ?   -0.9   0.0       4.3   2.3e+03      10      27 ..     341     358 ..     332     365 .. 0.74
  10 !    9.3   0.1    0.0023       1.2       6      29 ..     404     427 ..     400     431 .. 0.88
  11 !   15.9   0.0   1.9e-05    0.0098       6      35 ..     438     465 ..     433     466 .. 0.88
  12 !    8.9   0.0    0.0032       1.7      12      32 ..     478     496 ..     474     498 .. 0.88
  13 ?    2.4   0.2      0.37     2e+02       1      32 [.     501     532 ..     501     536 .. 0.78
  14 !   11.3   0.1   0.00052      0.28       1      30 [.     535     564 ..     535     569 .. 0.84
  15 !    8.5   0.0    0.0042       2.2       2      31 ..     670     697 ..     669     703 .. 0.82
  16 ?   -0.7   0.0       3.7     2e+03       1      31 [.     737     767 ..     737     771 .. 0.81
  17 ?    0.4   0.0       1.6   8.5e+02      10      34 ..     780     802 ..     771     804 .. 0.81
  18 ?    4.6   0.0     0.072        38       8      33 ..     812     837 ..     805     840 .. 0.83
  19 ?    2.9   0.0      0.25   1.3e+02       6      24 ..     844     862 ..     839     876 .. 0.84
  20 !   15.4   0.1   2.6e-05     0.013       1      29 [.     941     969 ..     941     980 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.088
                         TPR_7 13 GdyeeAielyeqsLaltkdpe 33
                                  G y++Aie y    al +dp+
  gi|91772658|ref|YP_565350.1| 43 GTYDKAIEKYDL--ALVSDPN 61
                                  66**********..9998885 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.07
                         TPR_7 13 GdyeeAielyeqsL 26
                                  Gdy+eAi  y   L
  gi|91772658|ref|YP_565350.1| 77 GDYDEAIATYDHIL 90
                                  9*********9844 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0036
                         TPR_7  10 srlGdyeeAielyeqsL 26 
                                    + Gdye+Ai+ y ++L
  gi|91772658|ref|YP_565350.1| 108 AKKGDYENAIKTYDKAL 124
                                   678************55 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0078
                         TPR_7   9 ysrlGdyeeAielyeqsLal 28 
                                    + lG+ eeAi+lye+ L++
  gi|91772658|ref|YP_565350.1| 170 LEGLGRNEEAIQLYEKFLEI 189
                                   5669************7765 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00064
                         TPR_7   7 rlysrlGdyeeAielyeqsLaltkd 31 
                                     + r+G+ e+Aiely ++L+++ d
  gi|91772658|ref|YP_565350.1| 202 LDHARDGKSERAIELYDEALQIDPD 226
                                   55899*************8877765 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00061
                         TPR_7   4 nLarlysrlGdyeeAielyeqsLalt 29 
                                     ++++ +lG yeeAie y ++++++
  gi|91772658|ref|YP_565350.1| 233 SKGQAFDSLGLYEEAIESYNKAIEFD 258
                                   5699*****************66655 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.77
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                   a  y +l + e+Ai  y++  +l  d ++
  gi|91772658|ref|YP_565350.1| 269 ALDYDKLDKKEDAIISYRE--VLVLDLYN 295
                                   5558899999*********..66666665 PP

  == domain 8  score: 13.5 bits;  conditional E-value: 0.0001
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                   a++nL+++ +  G+y eAi  +eq  +l  dp+
  gi|91772658|ref|YP_565350.1| 298 AWFNLGVALEGTGNYFEAINSFEQ--VLLLDPD 328
                                   799*********************..6666665 PP

  == domain 9  score: -0.9 bits;  conditional E-value: 4.3
                         TPR_7  10 srlGdyeeAielyeqsLa 27 
                                    + G+++eA+  y  +L 
  gi|91772658|ref|YP_565350.1| 341 NKIGRFDEALVSYDSALK 358
                                   5789*****999988554 PP

  == domain 10  score: 9.3 bits;  conditional E-value: 0.0023
                         TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                   + ly  l dyeeA+  +e++L+l+
  gi|91772658|ref|YP_565350.1| 404 GTLYLGLSDYEEAVLSFEKVLELD 427
                                   678999*************99887 PP

  == domain 11  score: 15.9 bits;  conditional E-value: 1.9e-05
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpeda 35 
                                   a +  +lG+y eAi +y++  al++dp+ +
  gi|91772658|ref|YP_565350.1| 438 ALALDKLGNYNEAIICYTE--ALRRDPSCP 465
                                   668899*************..*****9865 PP

  == domain 12  score: 8.9 bits;  conditional E-value: 0.0032
                         TPR_7  12 lGdyeeAielyeqsLaltkdp 32 
                                    G+y+eA+++y++   ++ dp
  gi|91772658|ref|YP_565350.1| 478 TGRYKEAVSCYRK--TVELDP 496
                                   69***********..888887 PP

  == domain 13  score: 2.4 bits;  conditional E-value: 0.37
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                   a+++L+     + +++eAi  y q+++  +d 
  gi|91772658|ref|YP_565350.1| 501 AWYALGLDLAHMDEHSEAIAAYDQVIEQNSDF 532
                                   6778888888999***********66655555 PP

  == domain 14  score: 11.3 bits;  conditional E-value: 0.00052
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                   a+++ +r+  +lG y++Aie y+ ++ l++
  gi|91772658|ref|YP_565350.1| 535 AYYRKGRTLDKLGLYQDAIESYRVAISLDS 564
                                   68899******************9555544 PP

  == domain 15  score: 8.5 bits;  conditional E-value: 0.0042
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   ++  +++y+ lGd++ Ai  ye+  a++ d
  gi|91772658|ref|YP_565350.1| 670 WYMRGQTYEMLGDRSSAINNYEK--AVDLD 697
                                   566799*****************..66544 PP

  == domain 16  score: -0.7 bits;  conditional E-value: 3.7
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   aLl+ +++y + G y+  +  y ++L ++ d
  gi|91772658|ref|YP_565350.1| 737 ALLQKGQAYDKIGIYRSSLASYNKLLKVDTD 767
                                   789999*****99999999999887766655 PP

  == domain 17  score: 0.4 bits;  conditional E-value: 1.6
                         TPR_7  10 srlGdyeeAielyeqsLaltkdped 34 
                                    +lG+ e+A+  y +  +l +dp++
  gi|91772658|ref|YP_565350.1| 780 YNLGNLEDAVYSYDK--VLSSDPQN 802
                                   579************..99999986 PP

  == domain 18  score: 4.6 bits;  conditional E-value: 0.072
                         TPR_7   8 lysrlGdyeeAielyeqsLaltkdpe 33 
                                   + ++lG +e+ i  y ++L++  d+ 
  gi|91772658|ref|YP_565350.1| 812 VLEDLGLFEDSINNYDKVLEMKVDDP 837
                                   5789***************9998875 PP

  == domain 19  score: 2.9 bits;  conditional E-value: 0.25
                         TPR_7   6 arlysrlGdyeeAielyeq 24 
                                   +++y++lG y++A ++y  
  gi|91772658|ref|YP_565350.1| 844 GNVYEKLGLYKDANDCYDI 862
                                   89***********999976 PP

  == domain 20  score: 15.4 bits;  conditional E-value: 2.6e-05
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                   a++nL+ +   +Gd ++Ai++ye++La++
  gi|91772658|ref|YP_565350.1| 941 AWYNLGYIANIRGDVDTAITYYEKALAID 969
                                   577888886669************77776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       4.2   2.2e+03      11      32 ..      40      61 ..      30      62 .. 0.75
   2 !    9.5   0.2    0.0031       1.6       6      33 .]      69      96 ..      64      96 .. 0.85
   3 ?    5.9   0.1     0.045        24       7      26 ..     104     123 ..     102     124 .. 0.86
   4 !   10.6   0.1    0.0014      0.72       3      28 ..     163     188 ..     162     190 .. 0.94
   5 ?    7.7   0.0     0.011       5.9       3      33 .]     197     227 ..     194     227 .. 0.82
   6 ?    5.0   0.0     0.086        45       6      28 ..     234     256 ..     231     256 .. 0.87
   7 ?    0.4   0.0       2.4   1.3e+03       4      27 ..     266     289 ..     263     290 .. 0.86
   8 !   11.8   0.0   0.00057       0.3       1      32 [.     297     328 ..     297     329 .. 0.94
   9 ?    5.8   0.0     0.045        24       1      33 []     331     363 ..     331     363 .. 0.92
  10 ?    3.9   0.0       0.2     1e+02       6      28 ..     403     425 ..     400     430 .. 0.85
  11 !   10.6   0.0    0.0013      0.71       3      31 ..     434     462 ..     432     463 .. 0.93
  12 ?    2.0   0.0      0.78   4.1e+02      13      31 ..     478     496 ..     467     497 .. 0.74
  13 !    8.4   0.0    0.0067       3.5       2      30 ..     501     529 ..     500     531 .. 0.89
  14 !   10.5   0.1    0.0015      0.78       1      28 [.     534     561 ..     534     564 .. 0.94
  15 ?    6.3   0.0     0.031        17       4      28 ..     671     695 ..     669     698 .. 0.92
  16 ?    4.9   0.1     0.091        48       2      28 ..     737     763 ..     736     764 .. 0.94
  17 !   13.3   0.0   0.00019       0.1       1      32 [.     770     801 ..     770     802 .. 0.95
  18 ?    2.4   0.0      0.57     3e+02       2      29 ..     839     866 ..     838     870 .. 0.86
  19 ?    2.0   0.0      0.78   4.1e+02       6      31 ..     877     902 ..     873     902 .. 0.84
  20 !    9.8   0.0    0.0025       1.3       2      32 ..     941     971 ..     940     972 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 4.2
                                  HHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6 11 rklgdtdkAlealerlikeYPd 32
                                     g +dkA+e ++  + + P+
  gi|91772658|ref|YP_565350.1| 40 MLNGTYDKAIEKYDLALVSDPN 61
                                  4446899999999877777776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0031
                                  HHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                         TPR_6  6 lalsyrklgdtdkAlealerlikeYPdS 33
                                   a +++  gd+d+A+++++ ++k  P+S
  gi|91772658|ref|YP_565350.1| 69 KAAAQYLYGDYDEAIATYDHILKLQPGS 96
                                  577889877**************99987 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.045
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerl 26 
                                   ++ + k gd+++A++++++ 
  gi|91772658|ref|YP_565350.1| 104 GMVLAKKGDYENAIKTYDKA 123
                                   88999988*********986 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlik 28 
                                   ly+ a+s++ lg+ ++A++++e++++
  gi|91772658|ref|YP_565350.1| 163 LYHKAKSLEGLGRNEEAIQLYEKFLE 188
                                   8999******99************97 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPdS 33 
                                   ly  +l + + g++++A+e++++ ++  Pd+
  gi|91772658|ref|YP_565350.1| 197 LYEKGLDHARDGKSERAIELYDEALQIDPDN 227
                                   566666666658***************9995 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.086
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                    ++++ +lg +++A+e +++ i+
  gi|91772658|ref|YP_565350.1| 234 KGQAFDSLGLYEEAIESYNKAIE 256
                                   589999999**********9985 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   4 yklalsyrklgdtdkAlealerli 27 
                                   ++ al y kl+++++A+  +++++
  gi|91772658|ref|YP_565350.1| 266 WNKALDYDKLDKKEDAIISYREVL 289
                                   67788899999*********9986 PP

  == domain 8  score: 11.8 bits;  conditional E-value: 0.00057
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                   +A ++l+ +++ +g++ +A+  +e+++   Pd
  gi|91772658|ref|YP_565350.1| 297 EAWFNLGVALEGTGNYFEAINSFEQVLLLDPD 328
                                   799*********99************999888 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.045
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                   dA  k +l + k g+ d+Al  +++ +k  Pd+
  gi|91772658|ref|YP_565350.1| 331 DAWHKKGLVLNKIGRFDEALVSYDSALKINPDN 363
                                   68889999999*88*****************95 PP

  == domain 10  score: 3.9 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                    + +y+ l d+++A+  +e++++
  gi|91772658|ref|YP_565350.1| 403 KGTLYLGLSDYEEAVLSFEKVLE 425
                                   588999989************97 PP

  == domain 11  score: 10.6 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYP 31 
                                    yk al++ klg++ +A+  + + +++ P
  gi|91772658|ref|YP_565350.1| 434 WYKKALALDKLGNYNEAIICYTEALRRDP 462
                                   79************************998 PP

  == domain 12  score: 2.0 bits;  conditional E-value: 0.78
                                   HHHHHHHHHHHHHHHHH-T CS
                         TPR_6  13 lgdtdkAlealerlikeYP 31 
                                   +g++ +A+  +++ ++  P
  gi|91772658|ref|YP_565350.1| 478 TGRYKEAVSCYRKTVELDP 496
                                   48***********999887 PP

  == domain 13  score: 8.4 bits;  conditional E-value: 0.0067
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlikeY 30 
                                   A y l+l +  ++++++A++a++++i++ 
  gi|91772658|ref|YP_565350.1| 501 AWYALGLDLAHMDEHSEAIAAYDQVIEQN 529
                                   7899999999999*************986 PP

  == domain 14  score: 10.5 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                   dA+y+ ++ + klg +++A+e ++  i+
  gi|91772658|ref|YP_565350.1| 534 DAYYRKGRTLDKLGLYQDAIESYRVAIS 561
                                   8**********************99885 PP

  == domain 15  score: 6.3 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   4 yklalsyrklgdtdkAlealerlik 28 
                                   y++++ y++lgd + A+  +e+ ++
  gi|91772658|ref|YP_565350.1| 671 YMRGQTYEMLGDRSSAINNYEKAVD 695
                                   99*******99**********9986 PP

  == domain 16  score: 4.9 bits;  conditional E-value: 0.091
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                   Al++ +++y k g ++ +l+ +++l+k
  gi|91772658|ref|YP_565350.1| 737 ALLQKGQAYDKIGIYRSSLASYNKLLK 763
                                   9**********88************97 PP

  == domain 17  score: 13.3 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                   +A y+++l+ ++lg+ ++A+  +++++++ P+
  gi|91772658|ref|YP_565350.1| 770 EAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQ 801
                                   79**********99**************9997 PP

  == domain 18  score: 2.4 bits;  conditional E-value: 0.57
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlike 29 
                                   +l+k +  y+klg + +A + ++ ++ +
  gi|91772658|ref|YP_565350.1| 839 VLMKKGNVYEKLGLYKDANDCYDIVLIN 866
                                   68999******99********9988755 PP

  == domain 19  score: 2.0 bits;  conditional E-value: 0.78
                                   HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                    +  +++lgd+  A++ ++ +i + P
  gi|91772658|ref|YP_565350.1| 877 KGFNLYMLGDYIGAMDQYDLVIAKNP 902
                                   566778889*************9988 PP

  == domain 20  score: 9.8 bits;  conditional E-value: 0.0025
                                   HHHHHH.HHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   2 Alykla.lsyrklgdtdkAlealerlikeYPd 32 
                                   A y+l+  + +++ d d+A++++e+ +   P+
  gi|91772658|ref|YP_565350.1| 941 AWYNLGyIANIRG-DVDTAITYYEKALAIDPN 971
                                   7899996666688.*************99998 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6    0.0006      0.32       3      81 ..      43     122 ..      41     123 .. 0.85
   2 !   11.0   0.1   0.00074      0.39       2      81 ..     110     185 ..     109     186 .. 0.85
   3 !   21.3   0.1   4.3e-07   0.00023       7      81 ..     178     253 ..     177     254 .. 0.94
   4 ?    7.2   0.0     0.011       5.8       7      79 ..     280     353 ..     276     356 .. 0.89
   5 !    9.0   0.0     0.003       1.6      32      81 ..     375     422 ..     358     423 .. 0.89
   6 !   20.4   0.7   8.3e-07   0.00044      21      79 ..     393     454 ..     385     457 .. 0.89
   7 !   22.0   0.3   2.8e-07   0.00015       3      79 ..     479     556 ..     477     559 .. 0.95
   8 ?    5.1   0.0     0.049        26      29      81 ..     639     692 ..     629     693 .. 0.78
   9 !   14.7   1.3     5e-05     0.026       2      80 ..     646     725 ..     645     727 .. 0.91
  10 !   14.8   2.4   4.6e-05     0.024       6      78 ..     684     757 ..     679     761 .. 0.87
  11 !   16.6   0.0   1.3e-05    0.0067       9      81 ..     755     828 ..     750     829 .. 0.88
  12 ?    2.2   0.0       0.4   2.1e+02      14      77 ..     794     858 ..     792     862 .. 0.61
  13 ?    2.7   0.2      0.28   1.5e+02      12      61 ..     894     944 ..     883     949 .. 0.83
  14 ?    6.0   0.1     0.027        14       4      42 ..     954     992 ..     952    1000 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0006
                                   T-HHHHHHHHHHHH.HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayll...AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   + y++Ai  ++++l     +p+ + +l   A + yl g+y++A+  ++   kl++ s+ +   ++ +l k + ye Ai+++
  gi|91772658|ref|YP_565350.1|  43 GTYDKAIEKYDLAL---VSDPNYRIALenkAAAQYLYGDYDEAIATYDHIlKLQPGSPLIFTKKGMVLAKKGDYENAIKTY 120
                                   66999999999999...4555554444445******************************99999*************999 PP

                                   -S CS
                        ANAPC3  80 ek 81 
                                   +k
  gi|91772658|ref|YP_565350.1| 121 DK 122
                                   87 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00074
                                   TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-...HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngq...ykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   +++y+nAi  ++++l     ++ + y l+ +l  +++    ++  ++++++        ++y +A++l  L++ eeAi+++
  gi|91772658|ref|YP_565350.1| 110 KGDYENAIKTYDKAL-----MSISKYILGNTLNDTSElngSTSTAYIIEEL--GVDESMILYHKAKSLEGLGRNEEAIQLY 183
                                   678999999999999.....7778899999999888866677888999999..5566678********************9 PP

                                   -S CS
                        ANAPC3  80 ek 81 
                                   ek
  gi|91772658|ref|YP_565350.1| 184 EK 185
                                   98 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 4.3e-07
                                   HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +Ai l+e+ l+ + e++  +y ++l + ++g+ +rA+el+++a ++++ +  ++y ++q+   L+ yeeAi  + k
  gi|91772658|ref|YP_565350.1| 178 EAIQLYEKFLEIQLEHSMTLYEKGLDHARDGKSERAIELYDEAlQIDPDNRTIWYSKGQAFDSLGLYEEAIESYNK 253
                                   7999******8888889999999************************************************98876 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.011
                                   HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   +Ai+ +  +l  + +++e+ + l+ +l  +g+y +A++ +++   l++ ++ ++  ++ +l k+++++eA+  +
  gi|91772658|ref|YP_565350.1| 280 DAIISYREVLVLDLYNAEAWFNLGVALEGTGNYFEAINSFEQVlLLDPDNIDAWHKKGLVLNKIGRFDEALVSY 353
                                   6666666777688899999999************************************************9766 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.003
                                   HHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  32 clylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   + ++++q+ ++y  + ++  ns s +++y ++  +l L+ yeeA+  +ek
  gi|91772658|ref|YP_565350.1| 375 ASLNTSQFSECYAAIPSF--NSDSAKIWYDKGTLYLGLSDYEEAVLSFEK 422
                                   568999************..99**********************988887 PP

  == domain 6  score: 20.4 bits;  conditional E-value: 8.3e-07
                                   --HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3  21 espedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   +s+++  ++  +  ++ +++y++A   ++k  +l+sk+  ++y +A +l kL++y+eAi ++
  gi|91772658|ref|YP_565350.1| 393 NSDSAKIWYdkGTLYLGLSDYEEAVLSFEKVlELDSKHAVVWYKKALALDKLGNYNEAIICY 454
                                   56666777777999********************************************9876 PP

  == domain 7  score: 22.0 bits;  conditional E-value: 2.8e-07
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   ++yk+A+ ++ + ++ +++   + y+l+l l ++ ++ +A+  +++  ++ns    + y ++++l kL+ y++Ai  +
  gi|91772658|ref|YP_565350.1| 479 GRYKEAVSCYRKTVELDPQFTLAWYALGLDLAHMDEHSEAIAAYDQViEQNSDFSDAYYRKGRTLDKLGLYQDAIESY 556
                                   79*********************************************99999999********************865 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.049
                                   HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   ++ +l+  g y+ A+  ++ka  ++++s   +y  +q++  L+    Ai+ +ek
  gi|91772658|ref|YP_565350.1| 639 KGGSLFVKGSYENALLSYNKAiMIKPNSSVTWYMRGQTYEMLGDRSSAINNYEK 692
                                   566788888888888888888888888888888888888888888888887776 PP

  == domain 9  score: 14.7 bits;  conditional E-value: 5e-05
                                   TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   ++ y+nA++ ++++   +++s+   y+ ++++  +g+  +A++ ++ka +l+s+ + +++ +Aq  +k ++y  Ai+a++
  gi|91772658|ref|YP_565350.1| 646 KGSYENALLSYNKAIMIKPNSSVTWYMRGQTYEMLGDRSSAINNYEKAvDLDSSYKDAWFALAQNVYKSSNYYYAIQAYD 725
                                   578************7777777777777************************************************9986 PP

  == domain 10  score: 14.8 bits;  conditional E-value: 4.6e-05
                                   HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                        ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                    +Ai  +e+++  ++   ++ ++lA+  y++++y+ A++ ++ + +l+++++ +++ ++q++ k++ y   +a 
  gi|91772658|ref|YP_565350.1| 684 SSAINNYEKAVDLDSSYKDAWFALAQNVYKSSNYYYAIQAYDGLlNLDPENKTALLQKGQAYDKIGIYRSSLAS 757
                                   579999*****666666666888***************************************999999876665 PP

  == domain 11  score: 16.6 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHH..HTT-HHHHHHHH-S CS
                        ANAPC3   9 iflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcll..kLkkyeeAiaaLek 81 
                                   +  +++ll+ +t++ e+ yl +l+ y++g+ + A + ++k  l s  +++ +l+Aq+l+  +L+ +e+ i+ ++k
  gi|91772658|ref|YP_565350.1| 755 LASYNKLLKVDTDNTEAWYLRGLASYNLGNLEDAVYSYDKV-LSSDPQNIDVLLAQSLVleDLGLFEDSINNYDK 828
                                   5568999**********************************.7777778999***99955799999999998876 PP

  == domain 12  score: 2.2 bits;  conditional E-value: 0.4
                                   HHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                        ANAPC3  14 rllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                   ++l++++++ + +++ +l+l  +g ++  ++ ++k  + +  ++ +++ ++ ++ kL+ y++A +
  gi|91772658|ref|YP_565350.1| 794 KVLSSDPQNIDVLLAQSLVLEDLGLFEDSINNYDKVlEMKVDDPSVLMKKGNVYEKLGLYKDAND 858
                                   55556666666666666666666666666666666666666666666666677777777777655 PP

  == domain 13  score: 2.7 bits;  conditional E-value: 0.28
                                   HHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHH CS
                        ANAPC3  12 aerllaaetespedayllAlclylngqykrAyellrka.klnskslgcryl 61 
                                   ++++ a++++++ + y ++ + yl++ y    +++ ka +l++ks+ ++y 
  gi|91772658|ref|YP_565350.1| 894 YDLVIAKNPYDAAAWYNKGNVAYLTSSYAGSTQFYLKAvELQPKSITAWYN 944
                                   677777888888888888*********999888888888*******99996 PP

  == domain 14  score: 6.0 bits;  conditional E-value: 0.027
                                   -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHH CS
                        ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrA 42 
                                   + ++Ai ++e++la +++ ++++y +  ++y+ gq  +A
  gi|91772658|ref|YP_565350.1| 954 DVDTAITYYEKALAIDPNAASALYNKRFAHYRVGQSVSA 992
                                   689**********99999999999999999998887766 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0013      0.67     205     252 ..      76     123 ..      62     127 .. 0.93
   2 !   10.5   0.4   0.00038       0.2      35     100 ..     157     221 ..     147     229 .. 0.83
   3 !    7.6   0.1    0.0029       1.6     205     259 ..     207     261 ..     195     272 .. 0.89
   4 ?    2.4   0.0      0.11        60     199     234 ..     235     270 ..     224     292 .. 0.87
   5 !    8.4   0.0    0.0016      0.86      15      74 ..     307     366 ..     295     400 .. 0.77
   6 !    9.8   0.0   0.00063      0.33     185     257 ..     426     496 ..     404     498 .. 0.87
   7 !    9.8   0.2   0.00063      0.33     195     257 ..     502     564 ..     496     567 .. 0.89
   8 !    6.6   0.0    0.0059       3.1     206     257 ..     647     698 ..     644     713 .. 0.93
   9 ?   -0.7   0.0      0.97   5.1e+02      44      79 ..     741     778 ..     733     803 .. 0.43
  10 !    7.2   0.0    0.0038         2       5      70 ..     804     869 ..     800     874 .. 0.91
  11 ?    3.9   0.0     0.037        20     210     256 ..     923     969 ..     900     994 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                   +g++++A+ + d+ ++ +p +  +++ K+ +l ++Gd ++A+++ ++a
  gi|91772658|ref|YP_565350.1|  76 YGDYDEAIATYDHILKLQPGSPLIFTKKGMVLAKKGDYENAIKTYDKA 123
                                   589*****************************************9998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00038
                                   --HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH..HHHHHHHHT..SSS-HHHHHHHHHHTT CS
                         NARP1  35 vDklavketkaelllkLgrkeeAeatyeaLlernpensk..Yyeglekakklskedeeallalydela 100
                                   vD+  ++  ka+ l  Lgr+eeA ++ye+ le   e+s   Y +gl +a++   +++e+  +lyde+ 
  gi|91772658|ref|YP_565350.1| 157 VDESMILYHKAKSLEGLGRNEEAIQLYEKFLEIQLEHSMtlYEKGLDHARD---GKSERAIELYDEAL 221
                                   788888899*************************99975448999999998...34468888888865 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0029
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                    g+ e+A+e+ d+a++ +p    +++ K++ +   G  ++A+e  ++a ++D  D
  gi|91772658|ref|YP_565350.1| 207 DGKSERAIELYDEALQIDPDNRTIWYSKGQAFDSLGLYEEAIESYNKAIEFDSTD 261
                                   456789**********************************************988 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.11
                                   HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                         NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKar 234
                                    q +d lg +e+A+e  +kaie + t v ++ +Ka 
  gi|91772658|ref|YP_565350.1| 235 GQAFDSLGLYEEAIESYNKAIEFDSTDVKVWWNKAL 270
                                   6889***************************99995 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0016
                                   HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHH CS
                         NARP1  15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskY 74 
                                   e +g++ eA++ +e++     D++    +k+ +l k+gr++eA   y + l+ np+n + 
  gi|91772658|ref|YP_565350.1| 307 EGTGNYFEAINSFEQVLLLDPDNIDAWHKKGLVLNKIGRFDEALVSYDSALKINPDNIAK 366
                                   5677888888888888888889999999****************************9853 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00063
                                   ---SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                         NARP1 185 kepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                    ++++a++w    lA   dklg++++A+ +  +a++++p++ ++++ K+  l  +G  k+A+++  ++ +lD 
  gi|91772658|ref|YP_565350.1| 426 LDSKHAVVWYKKALA--LDKLGNYNEAIICYTEALRRDPSCPNVWYLKGYDLDTTGRYKEAVSCYRKTVELDP 496
                                   556777778666555..7**********************************************999999995 PP

  == domain 7  score: 9.8 bits;  conditional E-value: 0.00063
                                   HHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                         NARP1 195 lyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                    y l     ++ + ++A+   d+ ie++  + + y++K+r l + G  ++A+e    a +lD 
  gi|91772658|ref|YP_565350.1| 502 WYALGLDLAHMDEHSEAIAAYDQVIEQNSDFSDAYYRKGRTLDKLGLYQDAIESYRVAISLDS 564
                                   466777788999999***************************************999999996 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.0059
                                   T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                         NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                   gs+e+Al   +kai+ +p++   ++++++ ++  Gd + A++  e+a  lD 
  gi|91772658|ref|YP_565350.1| 647 GSYENALLSYNKAIMIKPNSSVTWYMRGQTYEMLGDRSSAINNYEKAVDLDS 698
                                   68999**************9999999**********************9996 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 0.97
                                   HHHHHHHTT-HHHHHHHHHHHHHH-TT-CH..HHHHHH CS
                         NARP1  44 kaelllkLgrkeeAeatyeaLlernpensk..Yyegle 79 
                                   k++ + k+g +  + a y++Ll+  ++n++  Y +gl 
  gi|91772658|ref|YP_565350.1| 741 KGQAYDKIGIYRSSLASYNKLLKVDTDNTEawYLRGLA 778
                                   45555555555555555555555555554322223322 PP

  == domain 10  score: 7.2 bits;  conditional E-value: 0.0038
                                   HHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                         NARP1   5 ellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpe 70 
                                   ++lL +  ++e+ g  e+++++ +++ +  vD  +v+ +k++++ kLg +++A+  y   l   p 
  gi|91772658|ref|YP_565350.1| 804 DVLLAQSLVLEDLGLFEDSINNYDKVLEMKVDDPSVLMKKGNVYEKLGLYKDANDCYDIVLINEPA 869
                                   57899999*************************************************987766655 PP

  == domain 11  score: 3.9 bits;  conditional E-value: 0.037
                                   HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                         NARP1 210 kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                    ++++  ka+e +p+++  +++ + i    Gd+++A++  e+a ++D
  gi|91772658|ref|YP_565350.1| 923 GSTQFYLKAVELQPKSITAWYNLGYIANIRGDVDTAITYYEKALAID 969
                                   566666789999999999999999999999*9999999999998888 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.2   6.1e+02      52      83 ..      26      57 ..      19      87 .. 0.75
   2 !   11.0   0.1   0.00061      0.32     101     133 ..     161     193 ..      96     202 .. 0.67
   3 !    8.7   0.0    0.0033       1.7     104     128 ..     232     256 ..     209     263 .. 0.87
   4 ?   -1.8   0.0       5.7     3e+03     101     126 ..     263     288 ..     258     291 .. 0.85
   5 ?    2.5   0.0      0.26   1.4e+02     102     126 ..     298     322 ..     292     326 .. 0.87
   6 ?    3.9   0.0     0.097        51      61      83 ..     338     358 ..     324     361 .. 0.65
   7 ?    5.8   0.0     0.025        13      81     126 ..     416     457 ..     397     460 .. 0.65
   8 ?    3.0   0.0      0.18        96     104     129 ..     469     494 ..     465     496 .. 0.88
   9 ?    4.8   0.0      0.05        26     102     127 ..     535     560 ..     525     567 .. 0.88
  10 ?    1.2   0.0      0.66   3.5e+02     104     127 ..     671     694 ..     630     701 .. 0.61
  11 ?   -2.3   0.0       8.3   4.4e+03     102     125 ..     737     760 ..     735     771 .. 0.72
  12 ?    3.4   0.0      0.14        73      99     130 ..     802     833 ..     771     852 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                                  HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 52 Gfdalchaglsealaklgrydealesadkalr 83
                                  G+da  +     al+  g yd+a+e  d al 
  gi|91772658|ref|YP_565350.1| 26 GYDARSFNEEGVALMLNGTYDKAIEKYDLALV 57
                                  88999999999999999999999999998885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00061
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                       DUF3856 101 aavfsravaleelGrkdealkafrmagemiaer 133
                                    +++++a++le+lGr++ea++ +++  e+  e+
  gi|91772658|ref|YP_565350.1| 161 MILYHKAKSLEGLGRNEEAIQLYEKFLEIQLEH 193
                                   46799******************9999886665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0033
                                   HHHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 104 fsravaleelGrkdealkafrmage 128
                                   +s+++a+++lG ++ea++++++a e
  gi|91772658|ref|YP_565350.1| 232 YSKGQAFDSLGLYEEAIESYNKAIE 256
                                   89********************998 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.7
                                   HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                       DUF3856 101 aavfsravaleelGrkdealkafrma 126
                                   ++ +++a  +++l +k++a+ ++r +
  gi|91772658|ref|YP_565350.1| 263 KVWWNKALDYDKLDKKEDAIISYREV 288
                                   566899999***********999975 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHTT-HHHHHHHHHHH CS
                       DUF3856 102 avfsravaleelGrkdealkafrma 126
                                   a f+ +vale++G++ ea+++f+++
  gi|91772658|ref|YP_565350.1| 298 AWFNLGVALEGTGNYFEAINSFEQV 322
                                   568899**************99865 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.097
                                   HHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856  61 lsealaklgrydealesadkalr 83 
                                   l   l k+gr+deal s d+al+
  gi|91772658|ref|YP_565350.1| 338 L--VLNKIGRFDEALVSYDSALK 358
                                   3..35677788888888777775 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.025
                                   HHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                       DUF3856  81 alryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                   a+  f++  el++     W    +++a al++lG+++ea+  +  a
  gi|91772658|ref|YP_565350.1| 416 AVLSFEKVLELDSKHAVVW----YKKALALDKLGNYNEAIICYTEA 457
                                   4444444446666555555....67888888888888888776554 PP

  == domain 8  score: 3.0 bits;  conditional E-value: 0.18
                                   HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                   + ++  l+ +Gr++ea+  +r+++e+
  gi|91772658|ref|YP_565350.1| 469 YLKGYDLDTTGRYKEAVSCYRKTVEL 494
                                   568899***************99985 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.05
                                   HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                   a ++++++l++lG +++a++++r+a 
  gi|91772658|ref|YP_565350.1| 535 AYYRKGRTLDKLGLYQDAIESYRVAI 560
                                   7799*******************986 PP

  == domain 10  score: 1.2 bits;  conditional E-value: 0.66
                                   HHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856 104 fsravaleelGrkdealkafrmag 127
                                   + r++++e lG ++ a++++++a+
  gi|91772658|ref|YP_565350.1| 671 YMRGQTYEMLGDRSSAINNYEKAV 694
                                   457777777777777777777776 PP

  == domain 11  score: -2.3 bits;  conditional E-value: 8.3
                                   HHHHHHHHHHHTT-HHHHHHHHHH CS
                       DUF3856 102 avfsravaleelGrkdealkafrm 125
                                   a++++++a++++G +  +l ++++
  gi|91772658|ref|YP_565350.1| 737 ALLQKGQAYDKIGIYRSSLASYNK 760
                                   566777777777777777777765 PP

  == domain 12  score: 3.4 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                       DUF3856  99 WiaavfsravaleelGrkdealkafrmagemi 130
                                    i +++ ++  le+lG  +++++++ ++ em 
  gi|91772658|ref|YP_565350.1| 802 NIDVLLAQSLVLEDLGLFEDSINNYDKVLEMK 833
                                   58899999**********************94 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.3   1.2e+03      14      35 ..      42      63 ..      36      67 .. 0.83
   2 ?    5.4   0.1     0.037        19       8      33 ..      70      95 ..      68      96 .. 0.93
   3 ?   -0.6   0.1       2.8   1.5e+03      12      28 ..     108     124 ..     107     127 .. 0.81
   4 ?    4.9   0.0     0.053        28      11      35 ..     204     228 ..     196     230 .. 0.86
   5 ?    5.6   0.0     0.033        17       3      37 ..     298     332 ..     296     334 .. 0.90
   6 ?    4.8   0.0     0.058        30      13      34 ..     342     363 ..     340     364 .. 0.96
   7 !    7.8   0.1    0.0065       3.4       6      41 ..     436     471 ..     433     473 .. 0.86
   8 ?   -1.1   0.0       3.9   2.1e+03      15      34 ..     479     498 ..     478     500 .. 0.91
   9 !   11.2   0.6   0.00058       0.3       4      38 ..     704     738 ..     701     743 .. 0.87
  10 ?    3.7   0.0      0.13        67      10      40 ..     744     774 ..     740     775 .. 0.89
  11 !   13.0   0.0   0.00016     0.084       2      37 ..     770     805 ..     769     813 .. 0.90
  12 ?    5.1   0.0     0.046        24      13      37 ..     849     873 ..     847     875 .. 0.90
  13 ?   -0.6   0.0       2.8   1.5e+03      18      37 ..     956     975 ..     948     987 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.3
                                  HT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C 14 lgeYseArryvdalLeiEPenr 35
                                   g Y++A +  d  L  +P+ r
  gi|91772658|ref|YP_565350.1| 42 NGTYDKAIEKYDLALVSDPNYR 63
                                  689************9999987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.037
                                  HHHHHHHT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  8 AlGhyklgeYseArryvdalLeiEPe 33
                                  A ++y  g+Y+eA    d +L+++P+
  gi|91772658|ref|YP_565350.1| 70 AAAQYLYGDYDEAIATYDHILKLQPG 95
                                  7799999*****************96 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.8
                                   HHHT-HHHHHHHHHHHH CS
                    Fis1_TPR_C  12 yklgeYseArryvdalL 28 
                                   +k g+Y++A +  d  L
  gi|91772658|ref|YP_565350.1| 108 AKKGDYENAIKTYDKAL 124
                                   6889*****99887765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.053
                                   HHHHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenr 35 
                                   h++ g+ ++A ++ d  L+i+P+nr
  gi|91772658|ref|YP_565350.1| 204 HARDGKSERAIELYDEALQIDPDNR 228
                                   777788899***************8 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.033
                                   HHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C   3 clYylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                     + l ++    g+Y eA +  +++L ++P+n  a
  gi|91772658|ref|YP_565350.1| 298 AWFNLGVALEGTGNYFEAINSFEQVLLLDPDNIDA 332
                                   6689999999**********************765 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.058
                                   HHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPen 34 
                                   k+g+++eA+   d  L+i P+n
  gi|91772658|ref|YP_565350.1| 342 KIGRFDEALVSYDSALKINPDN 363
                                   99*******************9 PP

  == domain 7  score: 7.8 bits;  conditional E-value: 0.0065
                                   HHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHH CS
                    Fis1_TPR_C   6 ylAlGhyklgeYseArryvdalLeiEPenrQaqsLk 41 
                                     Al+  klg+Y+eA  +    L+ +P++ ++  Lk
  gi|91772658|ref|YP_565350.1| 436 KKALALDKLGNYNEAIICYTEALRRDPSCPNVWYLK 471
                                   5699999********************998776665 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 3.9
                                   T-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                   g+Y+eA  + +   e++P++
  gi|91772658|ref|YP_565350.1| 479 GRYKEAVSCYRKTVELDPQF 498
                                   89*************99986 PP

  == domain 9  score: 11.2 bits;  conditional E-value: 0.00058
                                   HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHH CS
                    Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPenrQaq 38 
                                    + lA   yk  +Y  A +  d lL+++Pen+ a+
  gi|91772658|ref|YP_565350.1| 704 WFALAQNVYKSSNYYYAIQAYDGLLNLDPENKTAL 738
                                   56677778***********************9775 PP

  == domain 10  score: 3.7 bits;  conditional E-value: 0.13
                                   HHHHHT-HHHHHHHHHHHHHHTTS-HHHHHH CS
                    Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQaqsL 40 
                                   ++ k+g Y+ ++   + lL+++ +n  a  L
  gi|91772658|ref|YP_565350.1| 744 AYDKIGIYRSSLASYNKLLKVDTDNTEAWYL 774
                                   67799********************998655 PP

  == domain 11  score: 13.0 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                   e  Y+  l++y lg+ ++A    d +L+ +P+n  +
  gi|91772658|ref|YP_565350.1| 770 EAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQNIDV 805
                                   678******************************765 PP

  == domain 12  score: 5.1 bits;  conditional E-value: 0.046
                                   HHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                                   klg Y++A  + d +L  EP n+ a
  gi|91772658|ref|YP_565350.1| 849 KLGLYKDANDCYDIVLINEPANSLA 873
                                   99********************755 PP

  == domain 13  score: -0.6 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  18 seArryvdalLeiEPenrQa 37 
                                   ++A  y +  L+i+P+   a
  gi|91772658|ref|YP_565350.1| 956 DTAITYYEKALAIDPNAASA 975
                                   78899999999999987666 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.46   2.4e+02      17      31 ..      42      56 ..      31      57 .. 0.87
   2 ?   -0.9   0.8       3.3   1.8e+03      16      29 ..      75      88 ..      64      92 .. 0.74
   3 !    9.0   0.0    0.0027       1.4       9      37 ..     102     130 ..      98     144 .. 0.83
   4 ?    4.3   0.0     0.081        43       7      29 ..     163     185 ..     157     189 .. 0.86
   5 ?    6.1   0.1     0.022        12       8      32 ..     198     222 ..     191     223 .. 0.80
   6 !   10.3   0.2    0.0011      0.56      11      32 ..     235     256 ..     232     257 .. 0.88
   7 ?    1.7   0.0       0.5   2.7e+02       9      29 ..     267     287 ..     266     290 .. 0.93
   8 ?   -0.5   0.0       2.5   1.3e+03       8      29 ..     300     321 ..     293     325 .. 0.79
   9 ?    0.4   0.0       1.3   6.8e+02      15      32 ..     341     358 ..     333     359 .. 0.81
  10 !   16.4   0.1   1.4e-05    0.0072       8      32 ..     435     459 ..     429     460 .. 0.90
  11 ?    6.8   0.0     0.013       6.8      13      32 ..     474     493 ..     471     494 .. 0.87
  12 ?    5.7   0.1     0.029        15      13      32 ..     542     561 ..     535     562 .. 0.86
  13 ?    0.1   0.0       1.6   8.6e+02      17      31 ..     646     660 ..     645     662 .. 0.90
  14 ?    1.5   0.0      0.59   3.1e+02      17      33 ..     680     696 ..     673     699 .. 0.82
  15 ?    0.7   0.0         1   5.5e+02      18      31 ..     953     966 ..     951     968 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.46
                           MIT 17 agnyeeAlelYkeal 31
                                  +g y++A+e+Y  al
  gi|91772658|ref|YP_565350.1| 42 NGTYDKAIEKYDLAL 56
                                  789********9886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.3
                           MIT 16 nagnyeeAlelYke 29
                                    g+y+eA+  Y +
  gi|91772658|ref|YP_565350.1| 75 LYGDYDEAIATYDH 88
                                  4599******9986 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0027
                           MIT   9 kkAveeDnagnyeeAlelYkealelLlqa 37 
                                   kk + + ++g+ye A++ Y +al  +++ 
  gi|91772658|ref|YP_565350.1| 102 KKGMVLAKKGDYENAIKTYDKALMSISKY 130
                                   7888999***************9776665 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.081
                           MIT   7 lvkkAveeDnagnyeeAlelYke 29 
                                   l +kA  ++  g  eeA++lY++
  gi|91772658|ref|YP_565350.1| 163 LYHKAKSLEGLGRNEEAIQLYEK 185
                                   7799*****************97 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.022
                           MIT   8 vkkAveeDnagnyeeAlelYkeale 32 
                                    +k  +  + g+ e A+elY eal+
  gi|91772658|ref|YP_565350.1| 198 YEKGLDHARDGKSERAIELYDEALQ 222
                                   56666777899************97 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.0011
                           MIT  11 AveeDnagnyeeAlelYkeale 32 
                                       D+ g yeeA+e Y +a+e
  gi|91772658|ref|YP_565350.1| 235 GQAFDSLGLYEEAIESYNKAIE 256
                                   5678999*************98 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.5
                           MIT   9 kkAveeDnagnyeeAlelYke 29 
                                   +kA ++D+  + e+A+  Y+e
  gi|91772658|ref|YP_565350.1| 267 NKALDYDKLDKKEDAIISYRE 287
                                   79*****************86 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 2.5
                           MIT   8 vkkAveeDnagnyeeAlelYke 29 
                                   ++  v ++  gny eA++ +++
  gi|91772658|ref|YP_565350.1| 300 FNLGVALEGTGNYFEAINSFEQ 321
                                   66778899999****9998765 PP

  == domain 9  score: 0.4 bits;  conditional E-value: 1.3
                           MIT  15 DnagnyeeAlelYkeale 32 
                                    + g ++eAl  Y +al+
  gi|91772658|ref|YP_565350.1| 341 NKIGRFDEALVSYDSALK 358
                                   566899**********96 PP

  == domain 10  score: 16.4 bits;  conditional E-value: 1.4e-05
                           MIT   8 vkkAveeDnagnyeeAlelYkeale 32 
                                    kkA  +D+ gny eA+ +Y+eal+
  gi|91772658|ref|YP_565350.1| 435 YKKALALDKLGNYNEAIICYTEALR 459
                                   59*********************85 PP

  == domain 11  score: 6.8 bits;  conditional E-value: 0.013
                           MIT  13 eeDnagnyeeAlelYkeale 32 
                                   ++D  g y+eA+++Y++ +e
  gi|91772658|ref|YP_565350.1| 474 DLDTTGRYKEAVSCYRKTVE 493
                                   689*************9887 PP

  == domain 12  score: 5.7 bits;  conditional E-value: 0.029
                           MIT  13 eeDnagnyeeAlelYkeale 32 
                                    +D+ g y++A+e Y+ a+ 
  gi|91772658|ref|YP_565350.1| 542 TLDKLGLYQDAIESYRVAIS 561
                                   689*************9985 PP

  == domain 13  score: 0.1 bits;  conditional E-value: 1.6
                           MIT  17 agnyeeAlelYkeal 31 
                                   +g ye Al  Y +a+
  gi|91772658|ref|YP_565350.1| 646 KGSYENALLSYNKAI 660
                                   689**********98 PP

  == domain 14  score: 1.5 bits;  conditional E-value: 0.59
                           MIT  17 agnyeeAlelYkealel 33 
                                    g+ + A+++Y++a++l
  gi|91772658|ref|YP_565350.1| 680 LGDRSSAINNYEKAVDL 696
                                   6778899******9986 PP

  == domain 15  score: 0.7 bits;  conditional E-value: 1
                           MIT  18 gnyeeAlelYkeal 31 
                                   g+ ++A+ +Y++al
  gi|91772658|ref|YP_565350.1| 953 GDVDTAITYYEKAL 966
                                   7899*********8 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       6.7   3.5e+03      16      31 ..      77      85 ..      65      93 .. 0.60
   2 ?   -0.7   0.0       2.7   1.4e+03       9      29 ..     104     124 ..     103     124 .. 0.82
   3 ?    3.4   0.1      0.14        74      14      32 ..     172     190 ..     161     193 .. 0.83
   4 ?    3.6   0.1      0.12        65       8      31 ..     200     223 ..     194     223 .. 0.84
   5 ?    4.0   0.0     0.094        50      13      41 ..     232     260 ..     229     261 .. 0.80
   6 ?   -2.1   0.0       7.4   3.9e+03      26      37 ..     279     290 ..     279     292 .. 0.87
   7 ?    6.6   0.0     0.014       7.2       7      29 ..     301     323 ..     301     325 .. 0.96
   8 ?    2.0   0.0      0.39   2.1e+02       9      31 ..     337     359 ..     335     360 .. 0.87
   9 ?    0.2   0.0       1.5   7.7e+02      11      31 ..     406     426 ..     404     432 .. 0.75
  10 ?    2.3   0.1      0.32   1.7e+02       9      30 ..     438     459 ..     437     460 .. 0.89
  11 ?    4.2   0.0     0.078        41      14      30 ..     477     493 ..     472     495 .. 0.79
  12 ?    2.0   0.2      0.38     2e+02       8      30 ..     505     527 ..     503     527 .. 0.93
  13 ?    3.8   0.0      0.11        57      11      34 ..     535     558 ..     530     564 .. 0.87
  14 ?    0.8   0.0      0.94     5e+02       9      30 ..     674     695 ..     673     696 .. 0.80
  15 ?   -1.6   0.0       5.4   2.8e+03      12      38 ..     738     764 ..     736     768 .. 0.77
  16 ?    0.6   0.0       1.1   5.6e+02       9      30 ..     776     797 ..     776     798 .. 0.85
  17 ?   -1.7   0.0       5.5   2.9e+03      10      30 ..     879     899 ..     873     900 .. 0.80
  18 !    8.3   0.0    0.0041       2.1       7      31 ..     944     968 ..     940     968 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.7
                        TPR_10 16 grydeAealleealai 31
                                  g+ydeA a       +
  gi|91772658|ref|YP_565350.1| 77 GDYDEAIA-------T 85
                                  66666654.......3 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.7
                        TPR_10   9 analrqrgrydeAealleeal 29 
                                   +++l + g+y+ A + +++al
  gi|91772658|ref|YP_565350.1| 104 GMVLAKKGDYENAIKTYDKAL 124
                                   789999999999988777776 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.14
                        TPR_10  14 qrgrydeAealleealair 32 
                                    +gr +eA +l+e+ l+i+
  gi|91772658|ref|YP_565350.1| 172 GLGRNEEAIQLYEKFLEIQ 190
                                   589**********988775 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.12
                        TPR_10   8 LanalrqrgrydeAealleealai 31 
                                    +  + + g+ ++A +l++eal+i
  gi|91772658|ref|YP_565350.1| 200 KGLDHARDGKSERAIELYDEALQI 223
                                   5778899999************97 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.094
                        TPR_10  13 rqrgrydeAealleealairrrllGpdHP 41 
                                   ++ g+  +++ l+eea++ + ++ + d+ 
  gi|91772658|ref|YP_565350.1| 232 YSKGQAFDSLGLYEEAIESYNKAIEFDST 260
                                   56677778999*********999887766 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 7.4
                        TPR_10  26 eealairrrllG 37 
                                   e+a+  +r++l 
  gi|91772658|ref|YP_565350.1| 279 EDAIISYREVLV 290
                                   799*******96 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.014
                        TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                   NL++al  +g+y eA + +e++l
  gi|91772658|ref|YP_565350.1| 301 NLGVALEGTGNYFEAINSFEQVL 323
                                   9********************98 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.39
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   + +l + gr+deA+  ++ al i
  gi|91772658|ref|YP_565350.1| 337 GLVLNKIGRFDEALVSYDSALKI 359
                                   6788899*******999999876 PP

  == domain 9  score: 0.2 bits;  conditional E-value: 1.5
                        TPR_10  11 alrqrgrydeAealleealai 31 
                                   ++  + +y+eA+  +e++l++
  gi|91772658|ref|YP_565350.1| 406 LYLGLSDYEEAVLSFEKVLEL 426
                                   566677888888888888875 PP

  == domain 10  score: 2.3 bits;  conditional E-value: 0.32
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   a al ++g+y+eA   + eal+
  gi|91772658|ref|YP_565350.1| 438 ALALDKLGNYNEAIICYTEALR 459
                                   678999********99999997 PP

  == domain 11  score: 4.2 bits;  conditional E-value: 0.078
                        TPR_10  14 qrgrydeAealleeala 30 
                                    +gry+eA+  ++++++
  gi|91772658|ref|YP_565350.1| 477 TTGRYKEAVSCYRKTVE 493
                                   67999999999999887 PP

  == domain 12  score: 2.0 bits;  conditional E-value: 0.38
                        TPR_10   8 LanalrqrgrydeAealleeala 30 
                                   L+  l ++ ++ eA a ++++++
  gi|91772658|ref|YP_565350.1| 505 LGLDLAHMDEHSEAIAAYDQVIE 527
                                   8999****************986 PP

  == domain 13  score: 3.8 bits;  conditional E-value: 0.11
                        TPR_10  11 alrqrgrydeAealleealairrr 34 
                                   a+++ gr  + + l+++a++ +r 
  gi|91772658|ref|YP_565350.1| 535 AYYRKGRTLDKLGLYQDAIESYRV 558
                                   899999999***********9985 PP

  == domain 14  score: 0.8 bits;  conditional E-value: 0.94
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   + ++  +g++  A + +e+a++
  gi|91772658|ref|YP_565350.1| 674 GQTYEMLGDRSSAINNYEKAVD 695
                                   5677788999999999999986 PP

  == domain 15  score: -1.6 bits;  conditional E-value: 5.4
                        TPR_10  12 lrqrgrydeAealleealairrrllGp 38 
                                   l q g+  +   +++ +la + +ll  
  gi|91772658|ref|YP_565350.1| 738 LLQKGQAYDKIGIYRSSLASYNKLLKV 764
                                   5566666677789999*****999974 PP

  == domain 16  score: 0.6 bits;  conditional E-value: 1.1
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   + a +++g++++A+  ++++l+
  gi|91772658|ref|YP_565350.1| 776 GLASYNLGNLEDAVYSYDKVLS 797
                                   567799********99999885 PP

  == domain 17  score: -1.7 bits;  conditional E-value: 5.5
                        TPR_10  10 nalrqrgrydeAealleeala 30 
                                     l+ +g+y +A++ ++ ++a
  gi|91772658|ref|YP_565350.1| 879 FNLYMLGDYIGAMDQYDLVIA 899
                                   568999******999887765 PP

  == domain 18  score: 8.3 bits;  conditional E-value: 0.0041
                        TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                   NL+ +   rg+ d A  ++e+alai
  gi|91772658|ref|YP_565350.1| 944 NLGYIANIRGDVDTAITYYEKALAI 968
                                   9**********************97 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         3   1.6e+03     222     268 ..      71     117 ..      47     129 .. 0.56
   2 ?   -0.1   0.0      0.83   4.4e+02     144     175 ..     158     189 ..     132     202 .. 0.82
   3 ?    3.6   0.0     0.062        33     156     182 ..     204     230 ..     184     233 .. 0.84
   4 ?   -0.5   0.0       1.1   5.5e+02     147     182 ..     297     332 ..     293     358 .. 0.82
   5 !    9.2   0.1    0.0012      0.64     123     238 ..     410     523 ..     394     531 .. 0.69
   6 ?    6.2   0.1      0.01       5.3     147     220 ..     466     536 ..     463     567 .. 0.81
   7 !    7.6   0.0    0.0037       1.9     144     178 ..     665     699 ..     650     708 .. 0.86
   8 ?    1.4   0.0      0.29   1.5e+02     120     182 ..     739     805 ..     733     817 .. 0.77
   9 ?   -0.6   0.0       1.2   6.2e+02     143     184 ..     833     875 ..     811     887 .. 0.80
  10 ?    1.5   0.0      0.26   1.4e+02     144     180 ..     937     973 ..     913     978 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                        TPR_15 222 aAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAw 268
                                   aA+ l g++++A + +   +k ++ +pl+  +   +l ++g+ ++A 
  gi|91772658|ref|YP_565350.1|  71 AAQYLYGDYDEAIATYDHILKLQPGSPLIFTKKGMVLAKKGDYENAI 117
                                   44445555555555555555555555544444433444444433333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.83
                        TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlal 175
                                   +++++l+  a++ +  g++++A+++y++ l+ 
  gi|91772658|ref|YP_565350.1| 158 DESMILYHKAKSLEGLGRNEEAIQLYEKFLEI 189
                                   789999999999***********999998765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.062
                        TPR_15 156 yrqegqtdaAlrdyreAlalapdssel 182
                                   + + g++++A+++y eAl+ +pd+ ++
  gi|91772658|ref|YP_565350.1| 204 HARDGKSERAIELYDEALQIDPDNRTI 230
                                   6789*******************9775 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.1
                        TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                     ++ ++ + + +g+  +A++ ++++l l+pd+ ++
  gi|91772658|ref|YP_565350.1| 297 EAWFNLGVALEGTGNYFEAINSFEQVLLLDPDNIDA 332
                                   5678888888999*******************8765 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0012
                        TPR_15 123 akdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWll..iDlgrraeLre 201
                                   + dy++ +  ++++ e++  ++ a +++  a +  + g+ ++A+ +y eAl+++p         +W+l   Dl+++   +e
  gi|91772658|ref|YP_565350.1| 410 LSDYEEAVLSFEKVLELD--SKHAVVWYKKALALDKLGNYNEAIICYTEALRRDPS-----CPNVWYLkgYDLDTTGRYKE 483
                                   555666555666644443..478999*****************************9.....44567774457788888999 PP

                        TPR_15 202 llkawkaraesdasLwgplaaAll...lLgrpkkALeylr 238
                                   +++ +++  e d++  ++  a  l    + + ++A + + 
  gi|91772658|ref|YP_565350.1| 484 AVSCYRKTVELDPQFTLAWYALGLdlaHMDEHSEAIAAYD 523
                                   9999999987777765555555440004455555655555 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.01
                        TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgpl 220
                                    ++++ +     +g+ ++A+ +yr+ ++l+p+   +  a+  l +Dl   +e  e+++a+ +  e++++   ++
  gi|91772658|ref|YP_565350.1| 466 NVWYLKGYDLDTTGRYKEAVSCYRKTVELDPQ---FTLAWYALGLDLAHMDEHSEAIAAYDQVIEQNSDFSDAY 536
                                   5777888788899******************9...44444445678889999999*****99999999998887 PP

  == domain 7  score: 7.6 bits;  conditional E-value: 0.0037
                        TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                   +s+  +++r++ y+  g+   A++ y++A++l+  
  gi|91772658|ref|YP_565350.1| 665 NSSVTWYMRGQTYEMLGDRSSAINNYEKAVDLDSS 699
                                   78999**************************9865 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 0.29
                        TPR_15 120 lerakdydriaellksleeeeaae....qsaafllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                   l++ ++yd+i+    sl +++++     ++   +++r+ +  + g+ ++A+  y ++l+ +p++ ++
  gi|91772658|ref|YP_565350.1| 739 LQKGQAYDKIGIYRSSLASYNKLLkvdtDNTEAWYLRGLASYNLGNLEDAVYSYDKVLSSDPQNIDV 805
                                   56667777777666665555553225567888999***9999******************9998665 PP

  == domain 9  score: -0.6 bits;  conditional E-value: 1.2
                        TPR_15 143 e.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselra 184
                                   + +++ +l+  +++y++ g  ++A  +y  +l  +p++s + +
  gi|91772658|ref|YP_565350.1| 833 KvDDPSVLMKKGNVYEKLGLYKDANDCYDIVLINEPANSLALS 875
                                   35899*****************************999987765 PP

  == domain 10  score: 1.5 bits;  conditional E-value: 0.26
                        TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                   +s + ++ ++ ++  +g+ d A++ y++Ala +p+ +
  gi|91772658|ref|YP_565350.1| 937 KSITAWYNLGYIANIRGDVDTAITYYEKALAIDPNAA 973
                                   6677899999999999****************99865 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       9.1   4.8e+03      78     112 ..      38      72 ..      22      96 .. 0.59
   2 ?    6.6   0.0     0.019       9.9      72     123 ..     197     248 ..     166     254 .. 0.88
   3 ?   -0.2   0.0       2.4   1.3e+03      83     123 ..     310     350 ..     304     357 .. 0.88
   4 ?   -0.3   0.0       2.6   1.3e+03      75     122 ..     403     450 ..     368     453 .. 0.78
   5 ?    1.6   0.0      0.66   3.5e+02      66     123 ..     626     687 ..     611     693 .. 0.85
   6 !    8.3   0.1    0.0057         3      69     127 ..     701     759 ..     688     770 .. 0.88
   7 ?   -0.5   0.0         3   1.6e+03      79     124 ..     779     824 ..     768     829 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9.1
                                   HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHH CS
               Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkada 112
                                   + + +g y  a+e  + ++ +dp+ + a e ka+a
  gi|91772658|ref|YP_565350.1|  38 ALMLNGTYDKAIEKYDLALVSDPNYRIALENKAAA 72 
                                   55566666667777777777766654444443332 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
               Alkyl_sulf_dimr  72 vlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                   + ek  +++++g+ + a+el + +++ dp+n++    k +a+++lg  +e+ 
  gi|91772658|ref|YP_565350.1| 197 LYEKGLDHARDGKSERAIELYDEALQIDPDNRTIWYSKGQAFDSLGLYEEAI 248
                                   67788889999*********************************99887765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.4
                                   T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
               Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                   g+y  a++  ++++  dp+n +a + k  +l+++g++ e+ 
  gi|91772658|ref|YP_565350.1| 310 GNYFEAINSFEQVLLLDPDNIDAWHKKGLVLNKIGRFDEAL 350
                                   667778888999***********************999875 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.6
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
               Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                   k + +l   dy+ a+   +++++ d+++a     ka al++lg+ +e+
  gi|91772658|ref|YP_565350.1| 403 KGTLYLGLSDYEEAVLSFEKVLELDSKHAVVWYKKALALDKLGNYNEA 450
                                   555555667899999999************************998775 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.66
                                   TT....SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
               Alkyl_sulf_dimr  66 mG....gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                   +G    g ++ ++k  + + +g y+ a+   n++++ +p+ + +  ++ +++e lg ++++ 
  gi|91772658|ref|YP_565350.1| 626 IGvvpdGYDAWVAKGGSLFVKGSYENALLSYNKAIMIKPNSSVTWYMRGQTYEMLGDRSSAI 687
                                   55555577888899999999************************************988765 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0057
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
               Alkyl_sulf_dimr  69 aekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                                   +++  + a++ +k+ +y  a++  + l+  dpen++a   k +a++++g   +s ++ n
  gi|91772658|ref|YP_565350.1| 701 KDAWFALAQNVYKSSNYYYAIQAYDGLLNLDPENKTALLQKGQAYDKIGIYRSSLASYN 759
                                   5677889*****************************************98888877666 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 3
                                   HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
               Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                   +++ g+++ a+   ++++ +dp+n +   ++  +le lg ++ s +
  gi|91772658|ref|YP_565350.1| 779 SYNLGNLEDAVYSYDKVLSSDPQNIDVLLAQSLVLEDLGLFEDSIN 824
                                   67778899999999***********999999999999999888865 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.43   2.3e+02      64     121 ..      65     122 ..      39     133 .. 0.80
   2 ?   -0.9   0.0       3.8     2e+03     106     122 ..     170     186 ..     163     197 .. 0.83
   3 ?    2.1   0.1      0.44   2.3e+02       9      34 ..     197     222 ..     189     223 .. 0.89
   4 ?    1.0   0.0         1   5.4e+02      74     122 ..     308     356 ..     274     363 .. 0.80
   5 ?   -1.4   0.0       5.4   2.8e+03      76     123 ..     411     458 ..     399     460 .. 0.79
   6 !    8.5   0.0    0.0047       2.5      75     124 ..     478     527 ..     474     531 .. 0.94
   7 ?    1.0   0.0         1   5.3e+02     105     135 ..     535     565 ..     532     576 .. 0.83
   8 ?   -0.4   0.0       2.7   1.4e+03      74     122 ..     679     727 ..     670     742 .. 0.72
   9 ?    0.7   0.0       1.2   6.3e+02      74     122 ..     747     795 ..     729     811 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.43
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                          BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                   ale  a+a+  +G+++ea+a+++ +++++P       +    la+ G+ + A+++Y++
  gi|91772658|ref|YP_565350.1|  65 ALENKAAAQYLYGDYDEAIATYDHILKLQPGSPLIFTKKGMVLAKKGDYENAIKTYDK 122
                                   6777888888888888888888888888887777777777777777777777777765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.8
                                   HHHTT-HHHHHHHHHHH CS
                          BTAD 106 larsGrqaeALevYerl 122
                                   l  +Gr++eA++ Ye++
  gi|91772658|ref|YP_565350.1| 170 LEGLGRNEEAIQLYEKF 186
                                   556899*******9987 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHTT-HHHHHHHHHHHHT CS
                          BTAD   9 lvaagraalaagdpeeaaelleaAla 34 
                                   l+++g + +++g+ e+a+el+++Al+
  gi|91772658|ref|YP_565350.1| 197 LYEKGLDHARDGKSERAIELYDEALQ 222
                                   57889999****************98 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1
                                   HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                     G + ea+   e+ + ++P + +++ +  + l + Gr  eAL  Y+++
  gi|91772658|ref|YP_565350.1| 308 GTGNYFEAINSFEQVLLLDPDNIDAWHKKGLVLNKIGRFDEALVSYDSA 356
                                   4567778888899999999999999999999999999999999999876 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 5.4
                                   T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                    ++eea+   e+ ++++  +   + +  +Al ++G+ +eA+  Y ++ 
  gi|91772658|ref|YP_565350.1| 411 SDYEEAVLSFEKVLELDSKHAVVWYKKALALDKLGNYNEAIICYTEAL 458
                                   477788888888888888888888999999999999999999998765 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0047
                                   TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                    Gr++ea++ +++ v+++P    ++ +l + la++++ +eA+++Y+++ +
  gi|91772658|ref|YP_565350.1| 478 TGRYKEAVSCYRKTVELDPQFTLAWYALGLDLAHMDEHSEAIAAYDQVIE 527
                                   69*******************************************99865 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 1
                                   HHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                          BTAD 105 AlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                   A++r Gr+ + L+ Y+++ ++ +  ++++ +
  gi|91772658|ref|YP_565350.1| 535 AYYRKGRTLDKLGLYQDAIESYRVAISLDSS 565
                                   9****************99988877777665 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 2.7
                                   HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                    lG+++ a+  +e++v+++    +++ +l +  ++s +   A+++Y+ l
  gi|91772658|ref|YP_565350.1| 679 MLGDRSSAINNYEKAVDLDSSYKDAWFALAQNVYKSSNYYYAIQAYDGL 727
                                   4677777777777777777777777777777777777777777777665 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 1.2
                                   HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                   ++G ++  la +++l++ +  + +++ +  +A + +G+ ++A   Y+++
  gi|91772658|ref|YP_565350.1| 747 KIGIYRSSLASYNKLLKVDTDNTEAWYLRGLASYNLGNLEDAVYSYDKV 795
                                   5677777888888888888889999999999999999999999999877 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.081        43       3      33 ..     162     192 ..     160     196 .. 0.83
   2 ?    2.5   0.0      0.31   1.6e+02       5      29 ..     198     222 ..     194     225 .. 0.80
   3 ?    3.8   0.0      0.13        67       5      29 ..     232     256 ..     228     265 .. 0.85
   4 ?   -1.1   0.0       4.1   2.2e+03      11      71 ..     272     329 ..     262     359 .. 0.51
   5 ?    1.8   0.0       0.5   2.6e+02       5      28 ..     435     458 ..     409     461 .. 0.79
   6 ?    1.0   0.0      0.89   4.7e+02      10      28 ..     474     492 ..     465     498 .. 0.84
   7 ?   -2.1   0.0       8.1   4.3e+03       3      28 ..     535     560 ..     533     570 .. 0.79
   8 ?   -1.2   0.0       4.3   2.2e+03       5      29 ..     671     695 ..     667     701 .. 0.85
   9 ?   -1.5   0.0       5.3   2.8e+03      50      88 ..     781     817 ..     736     830 .. 0.57
  10 ?   -0.9   0.0       3.5   1.8e+03      12      29 ..     950     967 ..     941     971 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.081
                         TPR_5   3 aaFeragarDstGhedkavplYrraLaeGLa 33 
                                   +++ +a + +  G++++a++lY++ L+  L+
  gi|91772658|ref|YP_565350.1| 162 ILYHKAKSLEGLGRNEEAIQLYEKFLEIQLE 192
                                   678889999999***********99987765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.31
                         TPR_5   5 FeragarDstGhedkavplYrraLa 29 
                                   +e++  +   G++++a++lY +aL+
  gi|91772658|ref|YP_565350.1| 198 YEKGLDHARDGKSERAIELYDEALQ 222
                                   56666666679************96 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.13
                         TPR_5   5 FeragarDstGhedkavplYrraLa 29 
                                   + ++ a+Ds G  ++a++ Y++a++
  gi|91772658|ref|YP_565350.1| 232 YSKGQAFDSLGLYEEAIESYNKAIE 256
                                   678899*****************97 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.1
                         TPR_5  11 rDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsde 71 
                                    D   +++ a+  Yr+ L   L +a    a   L  +L   G+  ea++  ++ l   +d+
  gi|91772658|ref|YP_565350.1| 272 YDKLDKKEDAIISYREVLVLDLYNA---EAWFNLGVALEGTGNYFEAINSFEQVLLLDPDN 329
                                   5666666777777777665444433...344444444444444444444444444444444 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.5
                         TPR_5   5 FeragarDstGhedkavplYrraL 28 
                                   +++a a D  G+ ++a+  Y +aL
  gi|91772658|ref|YP_565350.1| 435 YKKALALDKLGNYNEAIICYTEAL 458
                                   567777788888888888888777 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.89
                         TPR_5  10 arDstGhedkavplYrraL 28 
                                     D tG+ ++av  Yr+ +
  gi|91772658|ref|YP_565350.1| 474 DLDTTGRYKEAVSCYRKTV 492
                                   5799************976 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 8.1
                         TPR_5   3 aaFeragarDstGhedkavplYrraL 28 
                                   a + ++ + D  G  + a++ Yr a+
  gi|91772658|ref|YP_565350.1| 535 AYYRKGRTLDKLGLYQDAIESYRVAI 560
                                   55667778899999999999999886 PP

  == domain 8  score: -1.2 bits;  conditional E-value: 4.3
                         TPR_5   5 FeragarDstGhedkavplYrraLa 29 
                                   + r+ + +  G+   a++ Y++a++
  gi|91772658|ref|YP_565350.1| 671 YMRGQTYEMLGDRSSAINNYEKAVD 695
                                   6688889999************986 PP

  == domain 9  score: -1.5 bits;  conditional E-value: 5.3
                         TPR_5  50 nlGeaeealaLLraeleapsdelddalaaflaLvLsdlg 88 
                                   nlG++e+a+   ++ l++ ++++d  l    +LvL dlg
  gi|91772658|ref|YP_565350.1| 781 NLGNLEDAVYSYDKVLSSDPQNIDVLL--AQSLVLEDLG 817
                                   555555555555555554444444222..2344444444 PP

  == domain 10  score: -0.9 bits;  conditional E-value: 3.5
                         TPR_5  12 DstGhedkavplYrraLa 29 
                                   +  G+ d a+  Y++aLa
  gi|91772658|ref|YP_565350.1| 950 NIRGDVDTAITYYEKALA 967
                                   567999**********98 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.29   1.5e+02      15      31 ..      43      57 ..      38      61 .. 0.83
   2 !    8.9   1.5    0.0028       1.5       8      25 ..      70      87 ..      65      92 .. 0.92
   3 ?    3.0   0.0      0.19     1e+02      10      25 ..     106     121 ..     104     125 .. 0.87
   4 ?   -0.5   0.1       2.5   1.3e+03      17      25 ..     251     259 ..     244     259 .. 0.86
   5 ?   -2.1   0.0       7.9   4.2e+03      14      35 ..     309     328 ..     299     329 .. 0.77
   6 ?   -1.4   0.1       4.6   2.4e+03      14      26 ..     444     454 ..     434     455 .. 0.76
   7 ?    2.4   0.5       0.3   1.6e+02       4      25 ..     502     523 ..     501     524 .. 0.94
   8 ?    4.3   0.0      0.08        42      17      36 .]     549     566 ..     546     566 .. 0.90
   9 ?   -0.1   0.0       1.8   9.7e+02      16      25 ..     689     698 ..     688     700 .. 0.92
  10 !   10.9   2.0   0.00069      0.36       2      36 .]     702     734 ..     702     734 .. 0.94
  11 ?   -1.2   0.0       4.2   2.2e+03      10      25 ..     778     793 ..     772     797 .. 0.78
  12 ?    3.5   0.0      0.14        72       9      25 ..     879     895 ..     873     901 .. 0.85
  13 ?    2.6   0.0      0.27   1.4e+02       4      34 ..     942     970 ..     941     971 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.29
                                  T-HHHHHHH..HHHHHH CS
                         TPR_3 15 kkyqeArelfsYallai 31
                                  + y++A+e ++  l+ +
  gi|91772658|ref|YP_565350.1| 43 GTYDKAIEKYD--LALV 57
                                  77*******77..9975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
                                  HHHHHHTT-HHHHHHH.. CS
                         TPR_3  8 AaefynkkkyqeArelfs 25
                                  Aa++y+ ++y+eA+ +++
  gi|91772658|ref|YP_565350.1| 70 AAAQYLYGDYDEAIATYD 87
                                  9**************987 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.19
                                   HHHHTT-HHHHHHH.. CS
                         TPR_3  10 efynkkkyqeArelfs 25 
                                   ++  k++y+ A+ +++
  gi|91772658|ref|YP_565350.1| 106 VLAKKGDYENAIKTYD 121
                                   6788**********77 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.5
                                   HHHHHHH.. CS
                         TPR_3  17 yqeArelfs 25 
                                   y++A+e++s
  gi|91772658|ref|YP_565350.1| 251 YNKAIEFDS 259
                                   999999988 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 7.9
                                   TT-HHHHHHH..HHHHHHH-TT CS
                         TPR_3  14 kkkyqeArelfsYallaildke 35 
                                    ++y eA++   +++   ld++
  gi|91772658|ref|YP_565350.1| 309 TGNYFEAINS--FEQVLLLDPD 328
                                   58999****9..6576666665 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 4.6
                                   TT-HHHHHHH..H CS
                         TPR_3  14 kkkyqeArelfsY 26 
                                    ++y+eA+    Y
  gi|91772658|ref|YP_565350.1| 444 LGNYNEAIIC--Y 454
                                   699****987..4 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHTT-HHHHHHH.. CS
                         TPR_3   4 lysyAaefynkkkyqeArelfs 25 
                                   +y+++ ++  +++ +eA+ +++
  gi|91772658|ref|YP_565350.1| 502 WYALGLDLAHMDEHSEAIAAYD 523
                                   9*****************9976 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.08
                                   HHHHHHH..HHHHHHH-TT- CS
                         TPR_3  17 yqeArelfsYallaildken 36 
                                   yq+A+e   Y+++  ld+ n
  gi|91772658|ref|YP_565350.1| 549 YQDAIES--YRVAISLDSSN 566
                                   9******..****9999877 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 1.8
                                   -HHHHHHH.. CS
                         TPR_3  16 kyqeArelfs 25 
                                   +y++A++l+s
  gi|91772658|ref|YP_565350.1| 689 NYEKAVDLDS 698
                                   7*******98 PP

  == domain 10  score: 10.9 bits;  conditional E-value: 0.00069
                                   HHHHHHHHHHHHTT-HHHHHHH..HHHHHHH-TT- CS
                         TPR_3   2 dylysyAaefynkkkyqeArelfsYallaildken 36 
                                   d ++++A  +y + +y+ A+++++   l +ld+en
  gi|91772658|ref|YP_565350.1| 702 DAWFALAQNVYKSSNYYYAIQAYD--GLLNLDPEN 734
                                   569*******************77..*******99 PP

  == domain 11  score: -1.2 bits;  conditional E-value: 4.2
                                   HHHHTT-HHHHHHH.. CS
                         TPR_3  10 efynkkkyqeArelfs 25 
                                   + yn +++++A+  ++
  gi|91772658|ref|YP_565350.1| 778 ASYNLGNLEDAVYSYD 793
                                   569********97766 PP

  == domain 12  score: 3.5 bits;  conditional E-value: 0.14
                                   HHHHHTT-HHHHHHH.. CS
                         TPR_3   9 aefynkkkyqeArelfs 25 
                                   + +y+ ++y  A + ++
  gi|91772658|ref|YP_565350.1| 879 FNLYMLGDYIGAMDQYD 895
                                   679**********9977 PP

  == domain 13  score: 2.6 bits;  conditional E-value: 0.27
                                   HHHHHHHHHHTT-HHHHHHH..HHHHHHH-T CS
                         TPR_3   4 lysyAaefynkkkyqeArelfsYallaildk 34 
                                   +y +++     ++ ++A+ +  Y+ + ++d+
  gi|91772658|ref|YP_565350.1| 942 WYNLGYIANIRGDVDTAITY--YEKALAIDP 970
                                   77777777788999******..889999987 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.35   1.9e+02       9      25 ..     106     122 ..     105     125 .. 0.89
   2 ?    0.7   0.0       1.5   8.1e+02      14      28 ..     174     188 ..     169     191 .. 0.86
   3 ?    4.2   0.0      0.11        60      11      25 ..     205     219 ..     204     223 .. 0.89
   4 ?   -1.0   0.0       5.2   2.7e+03      13      26 ..     241     254 ..     240     258 .. 0.79
   5 ?   -0.3   0.0       3.1   1.6e+03      14      25 ..     479     490 ..     478     495 .. 0.85
   6 ?   -1.0   0.0       5.4   2.8e+03       8      24 ..     845     861 ..     845     862 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.35
                           PPR   9 gycknGkleeAlelfke 25 
                                   +++k+G++e A++ +++
  gi|91772658|ref|YP_565350.1| 106 VLAKKGDYENAIKTYDK 122
                                   589**********9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.5
                           PPR  14 GkleeAlelfkeMke 28 
                                   G+ eeA++l+++ +e
  gi|91772658|ref|YP_565350.1| 174 GRNEEAIQLYEKFLE 188
                                   899*******99765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                           PPR  11 cknGkleeAlelfke 25 
                                   ++ Gk e A+el++e
  gi|91772658|ref|YP_565350.1| 205 ARDGKSERAIELYDE 219
                                   899**********99 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 5.2
                           PPR  13 nGkleeAlelfkeM 26 
                                    G++eeA+e +++ 
  gi|91772658|ref|YP_565350.1| 241 LGLYEEAIESYNKA 254
                                   699****9988775 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 3.1
                           PPR  14 GkleeAlelfke 25 
                                   G+++eA++++++
  gi|91772658|ref|YP_565350.1| 479 GRYKEAVSCYRK 490
                                   99*******997 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 5.4
                           PPR   8 sgycknGkleeAlelfk 24 
                                   ++y k G++++A ++++
  gi|91772658|ref|YP_565350.1| 845 NVYEKLGLYKDANDCYD 861
                                   5799********99886 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.5   7.9e+02      18      39 ..     107     128 ..     101     136 .. 0.79
   2 ?   -1.4   0.0       5.6   2.9e+03      14      42 ..     166     195 ..     164     201 .. 0.74
   3 ?    2.4   0.0      0.36   1.9e+02      21      43 ..     241     263 ..     233     270 .. 0.83
   4 ?    2.3   0.0      0.38     2e+02      14      34 ..     437     457 ..     424     460 .. 0.83
   5 ?    6.6   0.0     0.017         9      20      36 ..     477     493 ..     471     498 .. 0.86
   6 ?   -2.2   0.0       9.5     5e+03       6      38 ..     944     976 ..     941     989 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                     NRBF2_MIT  18 llaaGkyeeaischkkaaayls 39 
                                   l   G ye+ai  + ka   +s
  gi|91772658|ref|YP_565350.1| 107 LAKKGDYENAIKTYDKALMSIS 128
                                   44579***********976665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.6
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaaay.lseam 42 
                                   ka+ l   G+ eeai  ++k  ++ l ++m
  gi|91772658|ref|YP_565350.1| 166 KAKSLEGLGRNEEAIQLYEKFLEIqLEHSM 195
                                   788888899******999987654245555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.36
                     NRBF2_MIT  21 aGkyeeaischkkaaaylseamk 43 
                                    G yeeai  ++ka ++ s  +k
  gi|91772658|ref|YP_565350.1| 241 LGLYEEAIESYNKAIEFDSTDVK 263
                                   589***********998776655 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.38
                     NRBF2_MIT  14 kadrllaaGkyeeaischkka 34 
                                   ka  l   G y+eai c++ a
  gi|91772658|ref|YP_565350.1| 437 KALALDKLGNYNEAIICYTEA 457
                                   566666789********9987 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.017
                     NRBF2_MIT  20 aaGkyeeaischkkaaa 36 
                                   ++G+y+ea+sc++k+ +
  gi|91772658|ref|YP_565350.1| 477 TTGRYKEAVSCYRKTVE 493
                                   68************865 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 9.5
                     NRBF2_MIT   6 nlahqqsrkadrllaaGkyeeaischkkaaayl 38 
                                   nl +  + + d   a   ye+a++    aa+ l
  gi|91772658|ref|YP_565350.1| 944 NLGYIANIRGDVDTAITYYEKALAIDPNAASAL 976
                                   666666777777788889999999998888776 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       1.5   8.1e+02      35      63 ..      62      90 ..      44      93 .. 0.79
   2 ?    2.6   0.1      0.18        96      41      63 ..     102     124 ..      99     130 .. 0.84
   3 ?   -0.5   0.1       1.6   8.6e+02      30      63 ..     188     221 ..     177     224 .. 0.85
   4 ?    5.1   0.0     0.031        16      30      64 ..     222     256 ..     209     264 .. 0.86
   5 ?    2.0   0.0      0.28   1.5e+02      33      64 ..     394     425 ..     390     433 .. 0.86
   6 ?    0.2   0.1         1   5.3e+02      93     129 ..     516     556 ..     469     573 .. 0.46
   7 ?   -0.5   0.0       1.7   8.8e+02      34      79 ..     531     577 ..     522     595 .. 0.79
   8 ?    5.9   0.0     0.018       9.3      38      69 ..     669     700 ..     647     710 .. 0.85
   9 ?    0.5   0.0       0.8   4.2e+02      34      64 ..     733     763 ..     729     769 .. 0.87
  10 ?   -0.1   0.0       1.2   6.6e+02      38      62 ..     839     863 ..     816     871 .. 0.81
  11 ?   -2.4   0.0       6.5   3.4e+03      47      63 ..     950     966 ..     940     972 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                                  HHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                          RPN7 35 irrakldlaehYlkigdleeAlkaysrir 63
                                   r a +++a   +  gd++eA+++y  i+
  gi|91772658|ref|YP_565350.1| 62 YRIALENKAAAQYLYGDYDEAIATYDHIL 90
                                  566777788888889**********9886 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                                   HHHHHHHHCT-HHHHHHHHHTCC CS
                          RPN7  41 dlaehYlkigdleeAlkaysrir 63 
                                   +++   +k gd+e+A+k+y +++
  gi|91772658|ref|YP_565350.1| 102 KKGMVLAKKGDYENAIKTYDKAL 124
                                   677888999**********9986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.6
                                   T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                          RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrir 63 
                                   +++ e  ++ ++++  +++ g+ e A+++y +++
  gi|91772658|ref|YP_565350.1| 188 EIQLEHSMTLYEKGLDHARDGKSERAIELYDEAL 221
                                   567788899999999999************9986 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.031
                                   T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                   +++ + r  ++ +++ + + g +eeA++ y++++e
  gi|91772658|ref|YP_565350.1| 222 QIDPDNRTIWYSKGQAFDSLGLYEEAIESYNKAIE 256
                                   68889999************************876 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  33 eeirrakldlaehYlkigdleeAlkaysrire 64 
                                   ++ ++ ++d++  Yl   d+eeA+  +++++e
  gi|91772658|ref|YP_565350.1| 394 SDSAKIWYDKGTLYLGLSDYEEAVLSFEKVLE 425
                                   56788999****************99999887 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 1
                                   HHHHHHHHCSSS---.....HHHHHHHHHHHHHHHHHTT-H CS
                          RPN7  93 skylekakellekggd....werknrlkvyeGlallairkf 129
                                   s+ ++   +++e+  d      rk r     Gl+++ai  +
  gi|91772658|ref|YP_565350.1| 516 SEAIAAYDQVIEQNSDfsdaYYRKGRTLDKLGLYQDAIESY 556
                                   33333333333333333333444444444444444444444 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHHCT-HHHHHHHHHT.CCCC--SHHHHHHHHHHH CS
                          RPN7  34 eirrakldlaehYlkigdleeAlkaysr.ireyctslkhkidmllnl 79 
                                   +  +a++++++   k g ++ A++ y+  i  +++++ ++++m   +
  gi|91772658|ref|YP_565350.1| 531 DFSDAYYRKGRTLDKLGLYQDAIESYRVaISLDSSNSAASFQMEADI 577
                                   667888999999999999********995556666777777775555 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHCT-HHHHHHHHHTCCCC--SH CS
                          RPN7  38 akldlaehYlkigdleeAlkaysrireyctsl 69 
                                   +++ +++ Y + gd+++A+++y+++++  +s 
  gi|91772658|ref|YP_565350.1| 669 TWYMRGQTYEMLGDRSSAINNYEKAVDLDSSY 700
                                   56678999*****************9977765 PP

  == domain 9  score: 0.5 bits;  conditional E-value: 0.8
                                   HHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  34 eirrakldlaehYlkigdleeAlkaysrire 64 
                                   e + a l++++ Y kig ++++l+ y+++++
  gi|91772658|ref|YP_565350.1| 733 ENKTALLQKGQAYDKIGIYRSSLASYNKLLK 763
                                   667899*********************9765 PP

  == domain 10  score: -0.1 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHCT-HHHHHHHHHTC CS
                          RPN7  38 akldlaehYlkigdleeAlkaysri 62 
                                      ++++ Y k g ++ A  +y  +
  gi|91772658|ref|YP_565350.1| 839 VLMKKGNVYEKLGLYKDANDCYDIV 863
                                   56899****************9865 PP

  == domain 11  score: -2.4 bits;  conditional E-value: 6.5
                                   HHCT-HHHHHHHHHTCC CS
                          RPN7  47 lkigdleeAlkaysrir 63 
                                      gd++ A+ +y++++
  gi|91772658|ref|YP_565350.1| 950 NIRGDVDTAITYYEKAL 966
                                   55799********9975 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 ?    1.6   0.0      0.17        91     134     160 ..      69      95 ..      39      99 .. 0.89
   2 ?    1.0   0.1      0.27   1.4e+02      91     221 ..     188     322 ..     160     325 .. 0.63
   3 ?    6.7   0.4    0.0047       2.5     110     231 ..     413     535 ..     389     543 .. 0.72
   4 ?   -0.6   0.0      0.81   4.3e+02     170     219 ..     675     725 ..     640     739 .. 0.80
   5 ?    2.0   0.0      0.14        71     131     175 ..     771     816 ..     748     835 .. 0.76
   6 ?   -1.9   0.1         2   1.1e+03     142     218 ..     885     962 ..     878     978 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.17
                                   HHHHHHHHT-HHHHHHHHHHHHHHSTT CS
                      PknG_TPR 134 rglaeLlegdyeeAaaeFdevlaalpG 160
                                   ++ a+ l gdy+eA+a++d++l++ pG
  gi|91772658|ref|YP_565350.1|  69 KAAAQYLYGDYDEAIATYDHILKLQPG 95 
                                   57789999****************999 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                                   CC-SHHHHHHHHHHHHC...T-HHHHHHHHHHHHHHH---HHHHHHH.HHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHH CS
                      PknG_TPR  91 seslevpLaevrahldl...GdveearelLdeleeeveedWrldWyr.glaeLlegdyeeAaaeFdevlaalpGEiaPkla 167
                                   + +le ++++    ld    G++e+a el de   ++  d r+ Wy+ g+a  + g yeeA++++++ +++ + ++     
  gi|91772658|ref|YP_565350.1| 188 EIQLEHSMTLYEKGLDHardGKSERAIELYDEA-LQIDPDNRTIWYSkGQAFDSLGLYEEAIESYNKAIEFDSTDVKVWWN 267
                                   445555555555555542226677777766665.45777889999954888889999999999999888776666666666 PP

                                   HHHHHHHHT---.TT-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHTS CS
                      PknG_TPR 168 LAataElagetd.eekyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLdeV 221
                                    A   +   +++ +   Yr V   d     A F l  +l  +g+  +A++  ++V
  gi|91772658|ref|YP_565350.1| 268 KALDYDKLDKKEdAIISYREVLVLDLYNAEAWFNLGVALEGTGNYFEAINSFEQV 322
                                   6665555543330445677777777777777777777777777777777766666 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0047
                                   HHHHHHHHHHHHHHH---HHHHHHHHHHHH.HHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHH..T-.--TT-HHHH CS
                      PknG_TPR 110 veearelLdeleeeveedWrldWyrglaeL.legdyeeAaaeFdevlaalpGEiaPklaLAataEla..ge.tdeekyYrt 186
                                    eea+  ++++ e   ++  + Wy+   +L   g+y+eA+ +++e l+  p  + P +      +l   g+ +++ + Yr 
  gi|91772658|ref|YP_565350.1| 413 YEEAVLSFEKVLE-LDSKHAVVWYKKALALdKLGNYNEAIICYTEALRRDP--SCPNVWYLKGYDLDttGRyKEAVSCYRK 490
                                   4455544444432.4455567777655555145677777777777777766..4677766666666522331334578999 PP

                                   HHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHTS-TTSTTHHHH CS
                      PknG_TPR 187 VwrtdrgvvsAaFGlaRqlaaagdraaAvaaLdeVpatSrhyttA 231
                                       d     A + l   la+ ++ ++A+aa d+V ++ + ++ A
  gi|91772658|ref|YP_565350.1| 491 TVELDPQFTLAWYALGLDLAHMDEHSEAIAAYDQVIEQNSDFSDA 535
                                   9999*******************************9999999887 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.81
                                   HHHHHHT---TT.-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                      PknG_TPR 170 ataElagetdee.kyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLd 219
                                    t E+ g++ ++ + Y+     d ++  A F la +  ++ +   A++a d
  gi|91772658|ref|YP_565350.1| 675 QTYEMLGDRSSAiNNYEKAVDLDSSYKDAWFALAQNVYKSSNYYYAIQAYD 725
                                   67888887775438899999999***********99999999999999887 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.14
                                   HHH.HHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHH CS
                      PknG_TPR 131 dWy.rglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataEla 175
                                    Wy rgla+   g++e A+ ++d+vl+  p  i   la + + E  
  gi|91772658|ref|YP_565350.1| 771 AWYlRGLASYNLGNLEDAVYSYDKVLSSDPQNIDVLLAQSLVLEDL 816
                                   46658*********************99888888777777776655 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 2
                                   T-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---.TT-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                      PknG_TPR 142 gdyeeAaaeFdevlaalpGEiaPklaLAataElagetd.eekyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaL 218
                                   gdy  A++++d v+a  p ++a       +a l+ +   ++++Y      +   ++A + l      +gd+++A++  
  gi|91772658|ref|YP_565350.1| 885 GDYIGAMDQYDLVIAKNPYDAAAWYNKGNVAYLTSSYAgSTQFYLKAVELQPKSITAWYNLGYIANIRGDVDTAITYY 962
                                   566667777777777777777777777777777654332567777777777777778888877777788887777654 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 ?   -2.7   0.0       8.1   4.3e+03      53      74 ..      47      68 ..      43      88 .. 0.61
   2 ?    3.7   0.0     0.086        45      53     102 ..     212     257 ..     204     271 .. 0.82
   3 ?   -1.6   0.0       3.8     2e+03      53      71 ..     314     332 ..     310     337 .. 0.88
   4 ?   -1.4   0.0       3.2   1.7e+03      53      74 ..     348     369 ..     323     459 .. 0.59
   5 ?   -0.3   0.1       1.4   7.4e+02      53      85 ..     685     718 ..     670     767 .. 0.68
   6 ?    5.5   0.0     0.024        13      50      93 ..     954     997 ..     943    1014 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.1
                                  HHHHHHHHHHHH-TT-HHHHHH CS
                   TOM20_plant 53 daiskleeallidPkkhdalWc 74
                                  +ai k++ al+ dP+   al  
  gi|91772658|ref|YP_565350.1| 47 KAIEKYDLALVSDPNYRIALEN 68
                                  5677777777777766555543 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.086
                                   HHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                   TOM20_plant  53 daiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqf 102
                                    ai  ++eal idP      +  g a+ s + +    eea e ++ka +f
  gi|91772658|ref|YP_565350.1| 212 RAIELYDEALQIDPDNRTIWYSKGQAFDSLGLY----EEAIESYNKAIEF 257
                                   5888999*******99888888999*9999998....5666777777665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.8
                                   HHHHHHHHHHHH-TT-HHH CS
                   TOM20_plant  53 daiskleeallidPkkhda 71 
                                   +ai  +e+ ll+dP   da
  gi|91772658|ref|YP_565350.1| 314 EAINSFEQVLLLDPDNIDA 332
                                   899***********99887 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHHH-TT-HHHHHH CS
                   TOM20_plant  53 daiskleeallidPkkhdalWc 74 
                                   +a+  ++ al i+P     ++ 
  gi|91772658|ref|YP_565350.1| 348 EALVSYDSALKINPDNIAKIYT 369
                                   4555555555555544333332 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHH-TT-HHHHHHHH.HHHHHHHHH CS
                   TOM20_plant  53 daiskleeallidPkkhdalWcig.naytsfafl 85 
                                    ai  +e+a+ +d + +da + ++ n y s  ++
  gi|91772658|ref|YP_565350.1| 685 SAINNYEKAVDLDSSYKDAWFALAqNVYKSSNYY 718
                                   4777777777777777777776654666665544 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHH CS
                   TOM20_plant  50 miqdaiskleeallidPkkhdalWcignaytsfafltpdeeeak 93 
                                    ++ ai+ +e+al idP+   al+    a+   +  ++ e+e k
  gi|91772658|ref|YP_565350.1| 954 DVDTAITYYEKALAIDPNAASALYNKRFAHYRVGQSVSAETERK 997
                                   5778********************99999988888887777755 PP

>> 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 ?   11.0   0.1     0.001      0.55      16      46 ..     704     736 ..     703     763 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.001
                        TraD_N  16 wlrlsqevflnglyYwaieeyvslknligs..a 46 
                                   w+ l q+v +++ yY+ai+ y +l+nl  +  +
  gi|91772658|ref|YP_565350.1| 704 WFALAQNVYKSSNYYYAIQAYDGLLNLDPEnkT 736
                                   999***********************9888543 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.073        39       7      20 ..     219     232 ..     215     232 .. 0.92
   2 ?   -1.3   0.0         4   2.1e+03       6      20 ..     320     334 ..     320     334 .. 0.85
   3 ?    2.6   0.0      0.23   1.2e+02       6      20 ..     455     469 ..     455     469 .. 0.91
   4 ?   -2.3   0.2       8.2   4.3e+03       9      20 ..     898     909 ..     896     910 .. 0.87
   5 ?    0.1   0.0       1.4   7.5e+02      10      21 ..     933     944 ..     929     945 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.073
                                   HHHHH-TT-CHHHH CS
                          PPTA   7 kliekdpkNYsaWn 20 
                                   ++++ dp+N ++W+
  gi|91772658|ref|YP_565350.1| 219 EALQIDPDNRTIWY 232
                                   7999*********7 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4
                                   HHHHHH-TT-CHHHH CS
                          PPTA   6 ekliekdpkNYsaWn 20 
                                   e+++ +dp+N  aW+
  gi|91772658|ref|YP_565350.1| 320 EQVLLLDPDNIDAWH 334
                                   578999****98888 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.23
                                   HHHHHH-TT-CHHHH CS
                          PPTA   6 ekliekdpkNYsaWn 20 
                                   ++++++dp++  +W+
  gi|91772658|ref|YP_565350.1| 455 TEALRRDPSCPNVWY 469
                                   589***********6 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 8.2
                                   HHH-TT-CHHHH CS
                          PPTA   9 iekdpkNYsaWn 20 
                                   i k+p +  aW+
  gi|91772658|ref|YP_565350.1| 898 IAKNPYDAAAWY 909
                                   889********8 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.4
                                   HH-TT-CHHHHH CS
                          PPTA  10 ekdpkNYsaWny 21 
                                   e+ pk+ +aW+ 
  gi|91772658|ref|YP_565350.1| 933 ELQPKSITAWYN 944
                                   778*******85 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1         2     1e+03      19      35 ..     154     170 ..     153     170 .. 0.86
   2 ?    4.8   0.0     0.056        30      19      37 ..     188     206 ..     187     211 .. 0.86
   3 ?    1.1   0.0      0.81   4.3e+02      24      38 ..     239     253 ..     239     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2
                  Exonuc_VII_S  19 elsLeeslklyeeGvkL 35 
                                   el ++es+ ly ++  L
  gi|91772658|ref|YP_565350.1| 154 ELGVDESMILYHKAKSL 170
                                   899********999765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.056
                  Exonuc_VII_S  19 elsLeeslklyeeGvkLlk 37 
                                   e+ Le s+ lye+G   ++
  gi|91772658|ref|YP_565350.1| 188 EIQLEHSMTLYEKGLDHAR 206
                                   789***********87766 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.81
                  Exonuc_VII_S  24 eslklyeeGvkLlke 38 
                                   +sl lyee+++ +++
  gi|91772658|ref|YP_565350.1| 239 DSLGLYEEAIESYNK 253
                                   689999999998775 PP

>> DUF764  Borrelia burgdorferi protein of unknown function (DUF764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00072      0.38      41     118 ..     152     228 ..     114     252 .. 0.83
   2 ?    0.3   0.0         1   5.5e+02      63     112 ..     478     527 ..     427     571 .. 0.77
   3 ?   -2.4   0.3       6.6   3.5e+03      47     121 ..     665     738 ..     652     769 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00072
                        DUF764  41 lekiaaassnllvlksestenltdrnlrarasykealefrlrfslyilaivlfkadkdayerilklyemlleflheka 118
                                   +e +  + s +l  k +s+e+l  rn  a + y+++le +l+ s+ +    l +a     er + ly+  l+   +++
  gi|91772658|ref|YP_565350.1| 152 IEELGVDESMILYHKAKSLEGL-GRNEEAIQLYEKFLEIQLEHSMTLYEKGLDHARDGKSERAIELYDEALQIDPDNR 228
                                   578889999************9.69****************************99999999******99888776666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1
                        DUF764  63 tdrnlrarasykealefrlrfslyilaivlfkadkdayerilklyemlle 112
                                   t r   a + y++  e+  +f l   a+ l  a++d +++ +  y+++ e
  gi|91772658|ref|YP_565350.1| 478 TGRYKEAVSCYRKTVELDPQFTLAWYALGLDLAHMDEHSEAIAAYDQVIE 527
                                   5677778899999***************************9999998876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.6
                        DUF764  47 assnllvlksestenltdrnlrarasykealefrlrfslyilaivlfkadkdayerilklyemlleflhekafky 121
                                   +ss    ++ +++e l dr + a + y++a ++   ++   +a+  +  +   y   ++ y+ ll++  e++   
  gi|91772658|ref|YP_565350.1| 665 NSSVTWYMRGQTYEMLGDRSS-AINNYEKAVDLDSSYKDAWFALAQNVYKSSNYYYAIQAYDGLLNLDPENKTAL 738
                                   666666677777777777755.66777788877777777777777776666667777777888877766666544 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.049        26     205     258 ..      33      86 ..      25     126 .. 0.85
   2 ?   -1.0   0.0       1.8   9.3e+02     178     231 ..     171     224 ..     155     231 .. 0.64
   3 ?   -0.6   0.0       1.4   7.2e+02     214     255 ..     241     282 ..     227     307 .. 0.82
   4 ?    3.2   0.0     0.093        49     179     235 ..     409     465 ..     404     469 .. 0.88
   5 ?   -1.6   0.8       2.7   1.4e+03       5      56 ..     711     765 ..     707     839 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.049
                                   HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHH CS
                    Coatomer_E 205 ngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsern 258
                                   n + v+ +l g y++A +    aL +d+++  +L N   a  + g  +e+++ +
  gi|91772658|ref|YP_565350.1|  33 NEEGVALMLNGTYDKAIEKYDLALVSDPNYRIALENKAAAQYLYGDYDEAIATY 86 
                                   6678999*******************************9999999999988766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                                   H-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH- CS
                    Coatomer_E 178 vggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkd 231
                                    g ++ ++A  +++ + e   + +++l  k   +   g+ e A +l  eaL+ d
  gi|91772658|ref|YP_565350.1| 171 EGLGRNEEAIQLYEKFLEIQLEHSMTLYEKGLDHARDGKSERAIELYDEALQID 224
                                   344555666666676666666666777777777777777777777777776665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.4
                                   TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                    Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                   lg yeeA ++ ++a++ d+ d  +  N      +l+k ++++
  gi|91772658|ref|YP_565350.1| 241 LGLYEEAIESYNKAIEFDSTDVKVWWNKALDYDKLDKKEDAI 282
                                   4569********************999999999999988875 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.093
                                   -TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-H CS
                    Coatomer_E 179 ggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakde 235
                                   g + +++A + f+ + e  ++  ++   kA +  +lg+y+eA     eaL +d+  +
  gi|91772658|ref|YP_565350.1| 409 GLSDYEEAVLSFEKVLELDSKHAVVWYKKALALDKLGNYNEAIICYTEALRRDPSCP 465
                                   66889999999**999998888999999999999******************98766 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.7
                                   THHHHHHHH.TT-HHHHHHHHH...S---SHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                    Coatomer_E   5 LfdvrnefY.lGaYqkainead...vaslseeekeerdvylyrsylAlgsaqivis 56 
                                    ++  n++Y + aY  ++n  d    + l +++++  ++ +yrs lA  + ++ ++
  gi|91772658|ref|YP_565350.1| 711 VYKSSNYYYaIQAYDGLLN-LDpenKTALLQKGQAYDKIGIYRSSLASYNKLLKVD 765
                                   5666677775567777776.221123334455666666777787777666655543 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 ?   -1.2   0.1       2.9   1.5e+03       2      14 ..     113     125 ..     112     130 .. 0.81
   2 ?    0.6   0.1      0.83   4.4e+02      30      47 ..     164     181 ..     159     183 .. 0.89
   3 ?    2.7   0.1      0.17        91       2      14 ..     244     256 ..     243     259 .. 0.93
   4 ?   -0.6   0.0       1.9     1e+03      29      46 ..     434     451 ..     433     453 .. 0.89
   5 ?    5.0   0.2     0.034        18      29      48 ..     536     555 ..     534     556 .. 0.93
   6 ?    3.1   0.2      0.14        72       2      15 ..     649     662 ..     648     690 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHHH CS
                      HTH_Bact   2 YeeaLeqvnkAie 14 
                                   Ye+a++  +kA++
  gi|91772658|ref|YP_565350.1| 113 YENAIKTYDKALM 125
                                   9999999999986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.83
                                   HHHHHHHHHTT--HHHHH CS
                      HTH_Bact  30 YqkgecleklgfseeeIk 47 
                                   Y k++ le lg +ee I+
  gi|91772658|ref|YP_565350.1| 164 YHKAKSLEGLGRNEEAIQ 181
                                   9**************997 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHHH CS
                      HTH_Bact   2 YeeaLeqvnkAie 14 
                                   Yeea+e  nkAie
  gi|91772658|ref|YP_565350.1| 244 YEEAIESYNKAIE 256
                                   9***********8 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHTT--HHHH CS
                      HTH_Bact  29 yYqkgecleklgfseeeI 46 
                                   +Y k+  l klg+ +e I
  gi|91772658|ref|YP_565350.1| 434 WYKKALALDKLGNYNEAI 451
                                   7***********999877 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.034
                                   HHHHHHHHHHTT--HHHHHH CS
                      HTH_Bact  29 yYqkgecleklgfseeeIke 48 
                                   yY kg  l klg  ++ I++
  gi|91772658|ref|YP_565350.1| 536 YYRKGRTLDKLGLYQDAIES 555
                                   9**************99987 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHH CS
                      HTH_Bact   2 YeeaLeqvnkAiei 15 
                                   Ye+aL   nkAi+i
  gi|91772658|ref|YP_565350.1| 649 YENALLSYNKAIMI 662
                                   9***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1049 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 1.03u 0.30s 00:00:01.33 Elapsed: 00:00:00.59
# Mc/sec: 5325.92
//
Query:       gi|91772659|ref|YP_565351.1|  [L=98]
Description: alkylhydroperoxidase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   72.4   0.7    2.8e-20   72.1   0.7    1.1  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.7   1.6e-24   2.8e-20       1      75 [.       9      82 ..       9      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.6e-24
                                  HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHH CS
                           CMD  1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpa 75
                                  pe+++a+ +lr a++   ++Ld k++eLia+a +++++ce Cv+ H ++A+++G+teeeiae +a+a + a++ +
  gi|91772659|ref|YP_565351.1|  9 PEAAKAFGDLRSAIFR-ANALDIKTKELIAVASAVLMRCEKCVKIHSERAKQNGATEEEIAESIAIATFIAAGSQ 82
                                  99*************7.999*************************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 714.58
//
Query:       gi|91772660|ref|YP_565352.1|  [L=93]
Description: hypothetical protein Mbur_0631 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   70.1   0.7    1.3e-19   69.9   0.7    1.0  1  HTH_45          Winged helix-turn-helix
    4.5e-08   32.5   0.1    6.3e-08   32.1   0.1    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.1e-05   25.7   0.1    1.3e-05   25.4   0.1    1.1  1  DUF2513         Hypothetical protein (DUF2513)
    1.4e-05   24.8   0.0    1.6e-05   24.7   0.0    1.2  1  HxlR            HxlR-like helix-turn-helix
      2e-05   24.4   0.3    3.5e-05   23.7   0.3    1.4  1  PadR            Transcriptional regulator PadR-like family
    2.3e-05   24.2   0.1    2.9e-05   23.9   0.1    1.3  1  DUF4364         Domain of unknown function (DUF4364)
    2.8e-05   24.5   0.0    3.4e-05   24.3   0.0    1.1  1  HTH_27          Winged helix DNA-binding domain
    0.00017   21.4   0.0    0.00025   20.9   0.0    1.2  1  MarR            MarR family
    0.00037   19.0   0.3    0.00048   18.6   0.3    1.2  1  DUF505          Protein of unknown function (DUF505)
     0.0039   17.0   1.4      0.031   14.1   1.4    2.0  1  DUF3116         Protein of unknown function (DUF3116)
     0.0055   16.9   0.1     0.0071   16.5   0.1    1.3  1  HTH_34          Winged helix DNA-binding domain
     0.0075   16.0   0.1       0.01   15.6   0.1    1.2  1  FtsK_gamma      Ftsk gamma domain
     0.0086   16.2   0.1      0.022   14.9   0.1    1.8  1  Mrr_N           Mrr N-terminal domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.016   14.9   0.0    1.3  1  Ribosomal_S19e  Ribosomal protein S19e
      0.017   15.4   0.1       0.02   15.1   0.1    1.1  1  STN1_2          CST, Suppressor of cdc thirteen homolog, comp
      0.038   13.8   0.1       0.07   13.0   0.0    1.5  2  DUF1495         Winged helix DNA-binding domain (DUF1495)
      0.044   13.7   0.1      0.062   13.3   0.1    1.3  1  HTH_11          HTH domain
      0.065   13.0   0.1       0.14   12.0   0.1    1.7  1  LexA_DNA_bind   LexA DNA binding domain
      0.079   12.8   0.1       0.11   12.4   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.099   12.9   0.0       0.11   12.7   0.0    1.2  1  Rio2_N          Rio2, N-terminal


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 !   69.9   0.7   1.5e-22   1.3e-19       1      75 [.       6      87 ..       6      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.5e-22
                        HTH_45  1 rRskleIiadILeais..egeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklkeleel 75
                                  +Rs+leIi dIL++i+  +++ ++Tk+   +nLs++++++Y++ L +kgli     k++ + Y+lT+kG+ +l+k++++ ++
  gi|91772660|ref|YP_565352.1|  6 KRSRLEIIRDILKVIResNNSISPTKLQRFSNLSFQMFEEYVKDLEKKGLIeakpyKEKRKIYSLTDKGRTFLDKYQDFVNF 87
                                  8**************944555679******************************9999*******************99765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1     7e-11   6.3e-08       3      48 .]      11      57 ..       9      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 7e-11
                        HTH_24  3 etdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  e+ r+IL+++++ n +is + L + ++lS +   +++k Le++GlI+
  gi|91772660|ref|YP_565352.1| 11 EIIRDILKVIREsNNSISPTKLQRFSNLSFQMFEEYVKDLEKKGLIE 57
                                  799*******************************************7 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   1.5e-08   1.3e-05       5      87 ..      11      83 ..       7      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.5e-08
                       DUF2513  5 dlvRdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiRd 87
                                  +++RdiL  ++e +++ ++ + +     ++ + s + + + +k l+++gLiea+  k+k +     +++Lt +G  FLd+ +d
  gi|91772660|ref|YP_565352.1| 11 EIIRDILKVIRESNNSISPTKLQ-----RFSNLSFQMFEEYVKDLEKKGLIEAKPYKEKRK-----IYSLTDKGRTFLDKYQD 83
                                  89**************9998886.....899**************************9999.....9************9987 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.8e-08   1.6e-05      28      80 ..      35      85 ..      12      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.8e-08
                                  STTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                          HxlR 28 lpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80
                                  + ++s +m  +  + Le++glie+++y+e   +  Yslt+kGr+  +  q + 
  gi|91772660|ref|YP_565352.1| 35 FSNLSFQMFEEYVKDLEKKGLIEAKPYKEK--RKIYSLTDKGRTFLDKYQDFV 85
                                  5689999********************996..56*********9877666655 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   3.9e-08   3.5e-05      39      74 ..      48      79 ..      45      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.9e-08
                                  HHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 39 krLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  k+Lek+gl+e++  ++    +rk+Y lTd+Gr+ l 
  gi|91772660|ref|YP_565352.1| 48 KDLEKKGLIEAKPYKE----KRKIYSLTDKGRTFLD 79
                                  89**********8875....9***********9886 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   3.2e-08   2.9e-05      29      75 ..      36      83 ..      12      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.2e-08
                       DUF4364 29 eytnYfdlqqalseLvesglieee.ekenktlykiTekGketlelfen 75
                                    +++  +++++++L+++glie++  ke++++y++T+kG+  l+  ++
  gi|91772660|ref|YP_565352.1| 36 SNLSFQMFEEYVKDLEKKGLIEAKpYKEKRKIYSLTDKGRTFLDKYQD 83
                                  4678899*****************999**************9987765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.8e-08   3.4e-05       8      68 .]      16      74 ..       8      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.8e-08
                        HTH_27  8 vLhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  +L +ir + + ++  + l ++ n++ + + + +k L++kGL+e ++++   ++k ++lTdkG
  gi|91772660|ref|YP_565352.1| 16 ILKVIR-ESNNSISpTKLQRFSNLSFQMFEEYVKDLEKKGLIEAKPYK--EKRKIYSLTDKG 74
                                  577777.6666666699999999*******************888888..999********9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.7e-07   0.00025       8      53 ..      16      62 ..      15      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.7e-07
                                  HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                          MarR  8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                  iL  ++e+++ +s ++L++++++s  +  + ++ LekkGlie ++ +
  gi|91772660|ref|YP_565352.1| 16 ILKVIRESNNsISPTKLQRFSNLSFQMFEEYVKDLEKKGLIEAKPYK 62
                                  88899999888******************************977655 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   5.3e-07   0.00048     358     404 ..      34      81 ..       9      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.3e-07
                        DUF505 358 kWyednfdl.reaLysLesfeLieseveekgkevyvlTeyGekvledq 404
                                   ++ +  f++ +e+ + Le ++Lie++  ++ +++y+lT++G+  l++ 
  gi|91772660|ref|YP_565352.1|  34 RFSNLSFQMfEEYVKDLEKKGLIEAKPYKEKRKIYSLTDKGRTFLDKY 81 
                                   555667888899***************99**************99975 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.4   3.5e-05     0.031      10      82 ..      14      80 ..       5      83 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                       DUF3116 10 levLelvkdpnftiknlqleeldeksvkkltkneLLytvYWLElkgyilRkeekannkkrYelTekGellyke 82
                                  + +L+++++ n+ i   +l+++ + s +      +   v  LE kg i  k +k +++k Y+lT+kG  ++++
  gi|91772660|ref|YP_565352.1| 14 RDILKVIRESNNSISPTKLQRFSNLSFQ-----MFEEYVKDLEKKGLIEAKPYK-EKRKIYSLTDKGRTFLDK 80
                                  5566666666655555555555333322.....222234459****99999997.9************99987 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   0.1   7.9e-06    0.0071      12      74 ..      24      83 ..       9      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.9e-06
                        HTH_34 12 vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvk 74
                                  ++++++++l+   +++       +k Lek+g ie +  +++   r ++++T++Gr+  +ky +
  gi|91772660|ref|YP_565352.1| 24 NNSISPTKLQRFSNLSFQMFEEYVKDLEKKGLIEAKPYKEK---RKIYSLTDKGRTFLDKYQD 83
                                  66667777777777777777777899*******98655555...58*********99999876 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-05      0.01       6      61 ..      12      68 ..       8      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                    FtsK_gamma  6 lfeeavelvveegka.StSllQRrlriGYnRAarlidqLeeeGiVgpaegskpReVl 61
                                  +++++++++ e+++  S   lQR  ++ ++   + + +Le++G+++++  + +R+++
  gi|91772660|ref|YP_565352.1| 12 IIRDILKVIRESNNSiSPTKLQRFSNLSFQMFEEYVKDLEKKGLIEAKPYKEKRKIY 68
                                  5667788888776533888***********************************996 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.5e-05     0.022      58      86 ..      47      79 ..       9      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                         Mrr_N 58 rtyLkkagllespk....rgvwkiTekGrevlk 86
                                   ++L k gl+e       r ++++T+kGr++l 
  gi|91772660|ref|YP_565352.1| 47 VKDLEKKGLIEAKPykekRKIYSLTDKGRTFLD 79
                                  578999999996533444************995 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.7e-05     0.016      84     130 ..      31      81 ..      20      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                   -THHHHHHHHHTTSSS--SSS---SS.-HHHHHTHH...HHH--SS--S-- CS
                Ribosomal_S19e  84 rpshfvkasgsvirkilqqLeklglv.kkekkkgrr...ltkkGqrlldri 130
                                   + ++f++ s ++  + +++Lek gl+  k+ k++r+   lt+kG+++ld+ 
  gi|91772660|ref|YP_565352.1|  31 KLQRFSNLSFQMFEEYVKDLEKKGLIeAKPYKEKRKiysLTDKGRTFLDKY 81 
                                   456777788899999***********76666666652227*********96 PP

>> STN1_2  CST, Suppressor of cdc thirteen homolog, complex subunit STN1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.2e-05      0.02      72     149 ..      10      83 ..       2      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                                   HHT-HHHHHHHSSHHCH-SS---SS----SCHHHHHHHHHHHHHHHHHCTSEE-SS.SSSTTEEEEGCCSHHHHHHHHH CS
                        STN1_2  72 letveslvslaskpvkessaaeevevagesaskqirslfkealqllqeeGlvfqkk.ksqdelyqvteqdkdLlkaild 149
                                   le ++++++++++     s+++  +++ + +s+   ++f+e ++ l+++Gl+  k  k+++++y  t++ ++ l + +d
  gi|91772660|ref|YP_565352.1|  10 LEIIRDILKVIRE-----SNNSISPTKLQRFSNLSFQMFEEYVKDLEKKGLIEAKPyKEKRKIYSLTDKGRTFLDKYQD 83 
                                   5555555555555.....333334456677999999****************9996367889******99988877666 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 ?   -2.8   0.0       6.6   5.9e+03      15      23 ..      13      21 ..       6      30 .. 0.49
   2 ?   13.0   0.0   7.8e-05      0.07      59      88 ..      50      79 ..      43      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.6
                       DUF1495 15 llyLysiyp 23
                                  + +++++++
  gi|91772660|ref|YP_565352.1| 13 IRDILKVIR 21
                                  333333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.8e-05
                       DUF1495 59 LielGLveeeeeseglklYklteeGieive 88
                                  L ++GL+e++  +e  k+Y+lt++G+++ +
  gi|91772660|ref|YP_565352.1| 50 LEKKGLIEAKPYKEKRKIYSLTDKGRTFLD 79
                                  5579***99999**************9876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.9e-05     0.062       3      51 ..      14      61 ..      13      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                  ++il+ ++e+++ is  +L +  n+S +    ++k+Le++g  Ie++p 
  gi|91772660|ref|YP_565352.1| 14 RDILKVIRESNNSISPTKLQRFSNLSFQMFEEYVKDLEKKG-LIEAKPY 61
                                  79*****999999****************************.9999985 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015      0.14      10      62 ..      15      62 ..       1      65 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                  HHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                 LexA_DNA_bind 10 evldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpgk 62
                                  ++l++i++s  ++   P+  +   +l ++     ee  k Le+KG+ie +p k
  gi|91772660|ref|YP_565352.1| 15 DILKVIRES--NNSISPTKLQRFSNLSFQ---MFEEYVKDLEKKGLIEAKPYK 62
                                  555566554..445666666555555555...88999************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012      0.11      27      66 ..      31      72 ..      18      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                  HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE-- CS
                          TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr..pklYravd 66
                                  ++ + ++++ +   e+++ Le+kGl+e ++ +  +k+Y+ +d
  gi|91772660|ref|YP_565352.1| 31 KLQRFSNLSFQMFEEYVKDLEKKGLIEAKPYKekRKIYSLTD 72
                                  5666677777888899************99554588998765 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.11      23      70 ..      25      74 ..       6      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                        Rio2_N 23 evVptelieeisrlkeeevkkrlsrllkaklisr..ktakydGYkLtyeG 70
                                  + ++ ++++++s+l+ + +++ +++l k++li+    + k + Y Lt +G
  gi|91772660|ref|YP_565352.1| 25 NSISPTKLQRFSNLSFQMFEEYVKDLEKKGLIEAkpYKEKRKIYSLTDKG 74
                                  56788899************************985555666677777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 685.01
//
Query:       gi|91772661|ref|YP_565353.1|  [L=258]
Description: hypothetical protein Mbur_0632 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); 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:                         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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1781.14
//
Query:       gi|91772662|ref|YP_565354.1|  [L=252]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-32  112.5   0.0    3.4e-32  111.8   0.0    1.3  1  ABC_tran      ABC transporter
    8.6e-06   25.3   0.1    6.7e-05   22.4   0.1    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.5e-05   24.6   0.0    3.1e-05   23.6   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      5e-05   23.3   0.1       0.07   12.9   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00067   20.1   0.1     0.0041   17.5   0.1    1.9  1  AAA_16        AAA ATPase domain
     0.0015   18.5   0.1     0.0032   17.4   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
     0.0036   17.6   0.0      0.014   15.6   0.0    1.9  2  AAA_22        AAA domain
     0.0037   17.0   0.0      0.046   13.4   0.0    2.1  2  AAA_30        AAA domain
     0.0062   17.1   0.1      0.018   15.5   0.0    1.8  2  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.046   13.4   0.3      0.077   12.7   0.1    1.5  2  AAA_15        AAA ATPase domain
      0.081   12.8   0.1       0.13   12.1   0.1    1.3  1  5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like do
       0.12   11.7   0.1        7.8    5.8   0.0    2.2  2  ATPase        KaiC
       0.14   11.1   0.0       0.21   10.6   0.0    1.2  1  DUF3987       Protein of unknown function (DUF3987)


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 !  111.8   0.0   2.4e-35   3.4e-32       1     136 [.      28     176 ..      28     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 2.4e-35
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                   lknv +++++ge +ai+G++G+GKSt+++l+  l  p +G+i l+++++ +    +  +   k ig+++q+ +l p++t+ 
  gi|91772662|ref|YP_565354.1|  28 LKNVCIEIEHGEFTAIIGPSGSGKSTMMNLVGCLDVPSKGDIFLKSRNIADmtesDLSTLRGKTIGFVFQQYNLIPGMTAL 108
                                   799********************************************99999885556667789***************** PP

                                   HH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   en          e+d  +eka + l+l++l d+  +++ps+LSgGq+qrv++ar+l+++p+l+l+DEpt
  gi|91772662|ref|YP_565354.1| 109 ENvllpleiqevEDDIALEKATEALELVGLSDKL-SNRPSQLSGGQQQRVSIARSLACDPELILADEPT 176
                                   ********99887777799999999999955555.6999*****************************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 !   22.4   0.1   4.9e-08   6.7e-05      23     205 ..      37     215 ..      20     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.9e-08
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TT..TTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersa..kklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsis 100
                                   + +ftai+Gp GSGKs +++ +  +L   s+    l+s+++ d+  +  + + +   ++  +f++ +     +  e+v + 
  gi|91772662|ref|YP_565354.1|  37 HGEFTAIIGPSGSGKSTMMNLV-GCLDVPSKgdIFLKSRNIADMTES--DLSTLRGKTIGFVFQQYNLIpGMTALENVLLP 114
                                   457****************988.677654431147999999999886..67777788899999888887445556667777 PP

                                   EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181
                                    ++++ ++ ++++++   +  e+  l  +    +++LSgG+++ v++a  +A    +p+ l l De   aLD k  + v  
  gi|91772662|ref|YP_565354.1| 115 LEIQEVED-DIALEK-ATEALELVGLSDKLSNRPSQLSGGQQQRVSIARSLAC---DPE-LILADEPTGALDSKTGRDVMG 189
                                   76666666.666654.34457888999999999**************999875...555.7889********999999999 PP

                                   HHHHHCTT..SEEEEE-SSHHHCCC- CS
                                   xxxxxxxx..xxxxxxxxxxxxxxxx RF
                         SMC_N 182 llkekskn..aQfivislreemleka 205
                                   +l +  k+    +++++++ ++ + a
  gi|91772662|ref|YP_565354.1| 190 ILYRLWKEkgKTIVMVTHDMDLAQYA 215
                                   99876555324455566666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.3e-08   3.1e-05      14      41 ..      30      57 ..      25      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.3e-08
                        AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDA 41
                                  +  iei+  ++t ++GpsGsGKST++  
  gi|91772662|ref|YP_565354.1| 30 NVCIEIEHGEFTAIIGPSGSGKSTMMNL 57
                                  5678888666***************965 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   5.1e-05      0.07       1      60 [.      40      96 ..      40     111 .. 0.71
   2 !    8.7   0.0     0.001       1.4     194     301 ..     121     211 ..     107     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfef 60
                                  ++++iGp gsGKS+ + +  +l   d  ++g+   +s++      + l++l+ ++i f+f
  gi|91772662|ref|YP_565354.1| 40 FTAIIGPSGSGKSTMMNLVGCL---DVPSKGDIFLKSRNIADMTESDLSTLRGKTIGFVF 96
                                  89************99888888...66666665555565555555566666665555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.001
                        AAA_21 194 lveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                   +++i l++ +e+ el  ++d ++++               +++lS G+++   ++ +l+ ++    l+l DEp   L+ k 
  gi|91772662|ref|YP_565354.1| 121 EDDIALEKATEALELVGLSDKLSNR---------------PSQLSGGQQQRVSIARSLACDP---ELILADEPTGALDSKT 183
                                   5666667777777777777777777...............8999999999999999999999...9*************** PP

                        AAA_21 275 lrrllellkelsr.ngaQviltTHSpll 301
                                    r ++++l +l + +g  ++++TH+  l
  gi|91772662|ref|YP_565354.1| 184 GRDVMGILYRLWKeKGKTIVMVTHDMDL 211
                                   ********99999999999*****9755 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.9e-06    0.0041       8     154 ..      24     219 ..      20     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-06
                        AAA_16   8 eleqLlsalervrsgrpelvllsGesGvGKsslvrellr.alekd.....................ggiflrgkcdqlesa 66 
                                   ++++L+++   +  g  e + ++G+sG+GKs++++ +    +  +                     +g ++   ++q+   
  gi|91772662|ref|YP_565354.1|  24 QVDALKNVCIEIEHG--EFTAIIGPSGSGKSTMMNLVGClDVPSKgdiflksrniadmtesdlstlRGKTIGFVFQQY--- 99 
                                   666666655556666..7899***********9977763222222335555555555555544444222222222322... PP

                        AAA_16  67 ipysalaqalareellrqlldeaesaeleawrekleeala.....................................avpe 110
                                     +++  +al ++ ll  + +e e++ + + +++ +e ++                                     ++++
  gi|91772662|ref|YP_565354.1| 100 -NLIPGMTAL-ENVLLPLEIQEVEDDIALEKATEALELVGlsdklsnrpsqlsggqqqrvsiarslacdpeliladePTGA 178
                                   .224456666.3366666666644444444444444444477777777777777777777766666666665544444444 PP

                        AAA_16 111 lagaeasrllellkrllallsrderplvlvlDdlqwadeaslql 154
                                   l+++  +++   l    +l +++++++v+v  d++ a+ a +++
  gi|91772662|ref|YP_565354.1| 179 LDSKTGRDVMGILY---RLWKEKGKTIVMVTHDMDLAQYAARHI 219
                                   44443344444444...555777888999999999999988887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.3e-06    0.0032      84     119 ..      22      58 ..       2      74 .. 0.77
   2 ?   -3.7   0.0       6.9   9.5e+03      35      56 ..     108     129 ..     105     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                   TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                   RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                   + + ++l+++  ++++ ++++++G+SG GKSt++n +
  gi|91772662|ref|YP_565354.1|  22 EVQVDALKNVCIEIEHgEFTAIIGPSGSGKSTMMNLV 58 
                                   445556666666777669*****************75 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.9
                                   HHHHHHHHHHTT-EEEEEEE-G CS
                   RsgA_GTPase  35 ldrfLvlaeekgiepvivlnKi 56 
                                   l+ +L+ +e +++e  i+l K+
  gi|91772662|ref|YP_565354.1| 108 LENVLLPLEIQEVEDDIALEKA 129
                                   6677777777777777777775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.014       4      25 ..      37      58 ..      33      88 .. 0.90
   2 ?   -0.7   0.0       1.2   1.6e+03      84     127 ..     156     204 ..     120     214 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                  +  +++++G+sG+GK+t ++ +
  gi|91772662|ref|YP_565354.1| 37 HGEFTAIIGPSGSGKSTMMNLV 58
                                  7889*************99865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                        AAA_22  84 qalrarav...ielliiDEaqh.lr.s..eealeeLrsllnlsrkgvqliL 127
                                   + + ar+    +el++ DE    l+ +   +++  L +l++  +kg ++++
  gi|91772662|ref|YP_565354.1| 156 RVSIARSLacdPELILADEPTGaLDsKtgRDVMGILYRLWK--EKGKTIVM 204
                                   33333333567788888886655554134555656655566..55555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.4e-05     0.046       5      38 ..      23      58 ..      19      73 .. 0.78
   2 ?    1.5   0.0      0.15   2.1e+02      34      62 ..     187     215 ..     150     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                        AAA_30  5 eQaaaveallts..gdrvavltGpAGtGKttalkal 38
                                   Q +a+++++ +  +  ++++ Gp G+GK+t+++ +
  gi|91772662|ref|YP_565354.1| 23 VQVDALKNVCIEieHGEFTAIIGPSGSGKSTMMNLV 58
                                  5777777776431144699**************976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                        AAA_30  34 alkalreaweaaggrviglAptgkaAkvL 62 
                                   +++ l ++w+++g++++++++    A+  
  gi|91772662|ref|YP_565354.1| 187 VMGILYRLWKEKGKTIVMVTHDMDLAQYA 215
                                   67888899999999999999988887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-05     0.018      15      37 ..      33      56 ..      23      59 .. 0.80
   2 ?   -3.3   0.0       7.8   1.1e+04      93      97 ..     230     234 ..     192     248 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                        AAA_23 15 idFsk.gltlItGpNGaGKTTild 37
                                  i+ ++  +t+I+Gp G+GK+T ++
  gi|91772662|ref|YP_565354.1| 33 IEIEHgEFTAIIGPSGSGKSTMMN 56
                                  67755359*************997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                        AAA_23  93 erels 97 
                                   e++ +
  gi|91772662|ref|YP_565354.1| 230 EINDN 234
                                   22222 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.6e-05     0.077      14      42 ..      28      57 ..      27      99 .. 0.85
   2 ?   -2.9   0.0       3.1   4.2e+03     145     145 ..     231     231 ..     185     249 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilea 42
                                  lk+v i+++   +t +iG+ +sGKS+ +++
  gi|91772662|ref|YP_565354.1| 28 LKNVCIEIEHGeFTAIIGPSGSGKSTMMNL 57
                                  677667776666**************9976 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                        AAA_15 145 k 145
                                    
  gi|91772662|ref|YP_565354.1| 231 I 231
                                   1 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.7e-05      0.13     107     143 ..     186     226 ..     179     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.7e-05
                  5_3_exonuc_N 107 Dvigtlakraeeeg..vvivsgDkDllQlvednvrvld..v 143
                                   Dv+g l +  +e+g  +v+v++D Dl+Q    ++ + d  v
  gi|91772662|ref|YP_565354.1| 186 DVMGILYRLWKEKGktIVMVTHDMDLAQYAARHIVLKDgmV 226
                                   9********76543469*************87888777541 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0056       7.8      16      35 ..      35      54 ..      23      57 .. 0.89
   2 ?    3.8   0.0     0.023        31     137     186 ..     181     227 ..     169     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0056
                        ATPase 16 ipegrvvlitGepGtGKtif 35
                                  i +g+ + i G +G+GK+++
  gi|91772662|ref|YP_565354.1| 35 IEHGEFTAIIGPSGSGKSTM 54
                                  678999************98 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.023
                        ATPase 137 eavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgviv 186
                                   +++ R+ +  l+r  k++g T ++v+   + ++ a ++ v +   dg++v
  gi|91772662|ref|YP_565354.1| 181 SKTGRDVMGILYRLWKEKGKTIVMVTHDMDLAQYAARHIVLK---DGMVV 227
                                   566777777777777***********9888888888888877...77765 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.21      38      56 ..      40      58 ..      29      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                       DUF3987 38 ytlvvapsGerKSpvdklv 56
                                  +t++++psG++KS++++lv
  gi|91772662|ref|YP_565354.1| 40 FTAIIGPSGSGKSTMMNLV 58
                                  89**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1719.85
//
Query:       gi|91772663|ref|YP_565355.1|  [L=419]
Description: hypothetical protein Mbur_0634 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-06   26.2   9.8        1.2    9.4   0.0    5.0  5  CARDB            CARDB
     0.0031   17.7   0.0        1.2    9.4   0.0    4.2  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
  ------ inclusion threshold ------
      0.015   15.2   0.9      0.032   14.2   0.9    1.5  1  Gram_pos_anchor  LPXTG cell wall anchor motif
       0.24   11.2   2.8       0.78    9.5   0.1    2.4  2  Peptidase_M73    Camelysin metallo-endopeptidase


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 !    9.4   0.0   0.00027       1.2       9      42 ..      40      73 ..      34      81 .. 0.89
   2 !    9.0   0.1   0.00037       1.7      12      67 ..     112     172 ..     105     173 .. 0.80
   3 !    8.3   0.2   0.00059       2.7      11      83 ..     158     238 ..     153     249 .. 0.81
   4 !    4.7   0.1    0.0078        35      23      76 ..     291     348 ..     280     362 .. 0.70
   5 ?    1.6   0.1     0.073   3.3e+02      30      64 ..     363     397 ..     344     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00027
                                  EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEE CS
                         CARDB  9 tlnpseafvgeentitvtvkNqGtaasgatkval 42
                                  +++p+++ +g+ ++++++++N+G+ + g+  v++
  gi|91772663|ref|YP_565355.1| 40 NQKPDPVKPGDILEVRYSIQNTGSSETGNLVVEV 73
                                  57889999******************99998887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00037
                                   -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.....SEE-CTEEEEEEE CS
                         CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.....psLaagesttvsf 67 
                                   +++ ++  ++ ++v v+ qG+++   ++ ++y+d ++ +++++     ++L +g++t+ sf
  gi|91772663|ref|YP_565355.1| 112 VDNNVNAGQYPLEVLVYEQGNKDNVCITREFYIDVDSESNAEIesislEKLVPGKKTNLSF 172
                                   55666777889999**********************9966666555559999999998887 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00059
                                   C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE......EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEE CS
                         CARDB  11 npseafvgeentitvtvkNqGtaasgatkvalyldgelv......gtvtvpsLaagesttvsftwtte..ategevtltvv 83 
                                   + +++++g++ ++++ +kN G+   ++   +     +lv      +  +++ ++ ++++tv+f++ t+  +++g ++l ++
  gi|91772663|ref|YP_565355.1| 158 SLEKLVPGKKTNLSFVIKNVGNSPLKNAMFSWESTSDLVlpvgssNVKYINFIDIDGNATVDFQVLTNvnTKPGLYKLDMT 238
                                   5678899*****************999999999999988899665556669999999999999999997777788877655 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.0078
                                   EEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S-S-C CS
                         CARDB  23 itvtvkNqGtaasgatkvalyldgelv.....gtvtvpsLaagesttvsftwtteateg 76 
                                    +++++N G+ ++ +++v++   +        ++v + sL+ +++t  +f  ++  + g
  gi|91772663|ref|YP_565355.1| 291 YSFSISNIGNNQASSVTVSIPEQERWSlsdgsNSVVLGSLQKSDYTLADFGLVPG-SYG 348
                                   6789***********9999866655555565445555777777777777766665.555 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.073
                                   -SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEE CS
                         CARDB  30 qGtaasgatkvalyldgelvgtvtvpsLaagestt 64 
                                    G+ + ++ ++++y++++ ++++ v+s ++g++ +
  gi|91772663|ref|YP_565355.1| 363 DGEREIQDKELSVYASRTDTSQSAVKSNSSGSNNN 397
                                   47788888899***********9999888887765 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 ?    0.8   0.0      0.13   5.9e+02       1      28 [.      46      73 ..      46      76 .. 0.85
   2 ?   -0.5   0.0      0.35   1.5e+03      52      74 ..     103     125 ..      96     128 .. 0.83
   3 !    9.4   0.0   0.00027       1.2       3      78 ..     164     241 ..     162     242 .. 0.87
   4 ?   -0.0   0.0      0.24   1.1e+03       9      35 ..     291     317 ..     283     358 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                   NPCBM_assoc  1 vepGetvtltltvtndgtaaatnvslsl 28
                                  v+pG+  +++ ++ n+g++ + n+ +++
  gi|91772663|ref|YP_565355.1| 46 VKPGDILEVRYSIQNTGSSETGNLVVEV 73
                                  5789999999999999999998888876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                   NPCBM_assoc  52 tveatvkVtppagaaaGdyevta 74 
                                   +  +++++ + ++  aG+y++++
  gi|91772663|ref|YP_565355.1| 103 SKVVKIELLVDNNVNAGQYPLEV 125
                                   66788899999999*****9987 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00027
                   NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWt..vvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                   pG++++l ++++n g+++++n  +s +  ++    v ++ ++ +  ++ +  ++++++V  + ++++G y++ +++++
  gi|91772663|ref|YP_565355.1| 164 PGKKTNLSFVIKNVGNSPLKNAMFSWESTSDLVlpVGSSNVKYINFIDIDGNATVDFQVLTNVNTKPGLYKLDMTLTY 241
                                   899999999999999999999999987766666666677888888999999*********************999986 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.24
                   NPCBM_assoc   9 ltltvtndgtaaatnvslslslPeGWt 35 
                                   + ++++n g+  a++v +s+   e W+
  gi|91772663|ref|YP_565355.1| 291 YSFSISNIGNNQASSVTVSIPEQERWS 317
                                   566778888888888888776666677 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   7.2e-06     0.032      12      40 ..     392     418 ..     391     418 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Gram_pos_anchor  12 TGengnifltaaGllallggllLlvkrRK 40 
                                    G+n+n++l+ ++  +l+g++++l+k++K
  gi|91772663|ref|YP_565355.1| 392 SGSNNNLVLLTFA--LLVGAGFVLYKKKK 418
                                   69999********..88888888888887 PP

>> Peptidase_M73  Camelysin metallo-endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00017      0.78      40     103 ..      27      93 ..      19     116 .. 0.74
   2 ?    1.4   0.5     0.056   2.5e+02      53      84 ..     157     188 ..     135     286 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                 Peptidase_M73  40 aGtldlsvdptviidv.knlkPGDtvtrefklenkGtLdikk..vlleteyevkdvkkdnegeDfgk 103
                                     tld ++  +++ +  + +kPGD ++  ++++n+G+ +  +  v++  +y  ++v ++n  e++gk
  gi|91772663|ref|YP_565355.1|  27 INTLDKGIMVDMLNQKpDPVKPGDILEVRYSIQNTGSSETGNlvVEVVPKYPFRKVSGSNLIENIGK 93 
                                   55555555544443331459*****************999872244556888888888887776665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.056
                 Peptidase_M73  53 idvknlkPGDtvtrefklenkGtLdikkvlle 84 
                                   i+++ l PG +   +f ++n G   +k+ +++
  gi|91772663|ref|YP_565355.1| 157 ISLEKLVPGKKTNLSFVIKNVGNSPLKNAMFS 188
                                   77889999999999999999998777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2723.99
//
Query:       gi|91772664|ref|YP_565356.1|  [L=435]
Description: ABC transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for 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   91.3   0.3      1e-25   91.3   0.3    3.0  3  MacB_PCD    MacB-like periplasmic core domain
    8.2e-13   48.7   8.6    8.2e-13   48.7   8.6    3.0  3  FtsX        FtsX-like permease family
  ------ inclusion threshold ------
      0.028   14.2   1.4        4.4    7.1   0.7    2.8  2  Collectrin  Renal amino acid transporter


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 !   91.3   0.3   1.7e-29     1e-25       1     194 [.      21     269 ..      21     270 .. 0.69
   2 ?    1.8   1.0     0.043   2.6e+02       4      34 ..     305     335 ..     302     350 .. 0.86
   3 ?   -1.1   2.1      0.36   2.1e+03       5      25 ..     367     387 ..     366     429 .. 0.79

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 1.7e-29
                      MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdl.gnlvtvtpgk................gsges............. 51 
                                   s+lt++G++iG+a+v+++v+ ge +q++v+++++d  g+ +t+  +                 +                 
  gi|91772664|ref|YP_565356.1|  21 SWLTIIGVVIGIASVMTVVTTGEYFQDQVTKTLEDFgGDGITIVASVpfmmneeesvgepvteN---Ketnqfiddpgses 98 
                                   79********************************997555555444357777777666555550...04555555555555 PP

                      MacB_PCD  52 ...lsdpdvealrrevp.veavapvv.....tvrgggsgeeevtvvgvdpdyfkvfgl.klaeGrffteadlrggpnvvvi 122
                                      l+  dv++l+r ++ +e++   v     + + g++ e++v v+gvdp+  +     ++ eGr++ +    g++nvvvi
  gi|91772664|ref|YP_565356.1|  99 qaqLTKKDVQTLER-ISaIEHINVKVesfpmL-SMGNE-ETSVHVSGVDPKVWSKMTTeDIGEGRLLKA----GDKNVVVI 172
                                   55578888876644.22233333322333322.55553.44599*****98888444435588**9977....5789**** PP

                      MacB_PCD 123 geelaerlf.....pvGdtirl..kpftVvGvledpp...gsgsalgddavylp............lttlqrrs....... 174
                                   +++la++ f     ++++ i l  k+++VvG+l + +   g++++l  ++v++p            ++     +       
  gi|91772664|ref|YP_565356.1| 173 SDNLANEAFkdkkiRLNQLILLngKSYRVVGILAKGDgllGGMGGLFGSSVFMPfedmyvmdqdneYS-----Tlqkgvyd 248
                                   *********8777778888888**********955224675555555899****44444444444433.....14444445 PP

                      MacB_PCD 175 .itvrlkdgadleaaaaelek 194
                                    i v+l ++a l+ a +e++k
  gi|91772664|ref|YP_565356.1| 249 sIEVKLYKNAELQPALDEMDK 269
                                   5**************999986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.043
                      MacB_PCD   4 tvLGiaiGvaaviaivslgeglqasvlsqis 34 
                                   + L+ + G+  +++ v++ +++  svl+  +
  gi|91772664|ref|YP_565356.1| 305 AFLAFIAGISLLVGSVGIANTMFTSVLEKTK 335
                                   679999******************9998766 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.36
                      MacB_PCD   5 vLGiaiGvaaviaivslgegl 25 
                                   ++Gi +G+a+v +iv l++  
  gi|91772664|ref|YP_565356.1| 367 IIGILFGTAFVQVIVYLISMQ 387
                                   7899******99999877654 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.19   1.1e+03      28      83 ..      23      36 ..      15      70 .. 0.63
   2 ?    1.8   0.3     0.056   3.4e+02      17      45 ..     299     324 ..     291     333 .. 0.54
   3 !   48.7   8.6   1.4e-16   8.2e-13       2      96 .]     335     428 ..     334     428 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.19
                          FtsX 28 itlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllalla 83
                                  +t+++ viG                                          +a+++
  gi|91772664|ref|YP_565356.1| 23 LTIIGVVIG------------------------------------------IASVM 36
                                  345555555..........................................22222 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.056
                          FtsX  17 vlllllteillitlvalviGlglgllaaq 45 
                                   ++ +l+  +++i+ ++l++G   ++ +a+
  gi|91772664|ref|YP_565356.1| 299 LISGLTAFLAFIAGISLLVG---SVGIAN 324
                                   44444444555555555555...444444 PP

  == domain 3  score: 48.7 bits;  conditional E-value: 1.4e-16
                          FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllall 82 
                                   +eigi++a+G+++ +vll++l  ++li+lv+ +iG+++g+++ q++  +++ ++  +   +++++ + +++ ++++ + l+
  gi|91772664|ref|YP_565356.1| 335 KEIGIMKAIGARNEDVLLIFLCNAALIGLVGGIIGILFGTAFVQVIVYLISMQLK-IPFVFTLSVKATVVATLVSIGVGLI 414
                                   8********************************************9999988877.************************* PP

                          FtsX  83 agllsiskilkkep 96 
                                   ag+ ++  ++k +p
  gi|91772664|ref|YP_565356.1| 415 AGFMPAKSAAKLNP 428
                                   *********99987 PP

>> Collectrin  Renal amino acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.7   0.00073       4.4     116     143 ..      12      39 ..       6      45 .. 0.84
   2 ?    4.6   0.0    0.0041        24      68     112 ..     161     205 ..     118     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00073
                    Collectrin 116 appveppvtiWlivfgvvmgvvvvgivl 143
                                   +    ++   Wl + gvv+g+  v +v+
  gi|91772664|ref|YP_565356.1|  12 NMVKANKLRSWLTIIGVVIGIASVMTVV 39 
                                   5556778899***********9999886 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0041
                    Collectrin  68 vvtspknesklvpkeeveeairksrnrineaflLddktLeflgil 112
                                   ++++ +++  +++ +  +ea ++++ r+n+  lL+ k+   +gil
  gi|91772664|ref|YP_565356.1| 161 LLKAGDKNVVVISDNLANEAFKDKKIRLNQLILLNGKSYRVVGIL 205
                                   5566677778999999*********************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3123.61
//
Query:       gi|91772665|ref|YP_565357.1|  [L=137]
Description: hypothetical protein Mbur_0636 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   56.2   9.5    4.6e-15   56.0   9.5    1.0  1  EamA      EamA-like transporter family
  ------ inclusion threshold ------
        1.2    8.9   4.3       0.57   10.0   0.3    2.2  3  DUF4668   Domain of unknown function (DUF4668)


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 !   56.0   9.5   5.2e-19   4.6e-15       8     134 ..       2     133 ..       1     135 [. 0.89

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 5.2e-19
                          EamA   8 llaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkd....wllllllgllgtvlafllf 82 
                                   + ++++w +y+++++++ r+ + + l+   +++++i+l+++all+++ +  +  s++d    + +l++l++lg++l+fll+
  gi|91772665|ref|YP_565357.1|   2 FGSVFSWVFYTTIIDKF-RSKDMVILSRDITMFGTIFLFPFALLEARDMrvDIVSQSDlvvaIVILMYLAILGSALGFLLW 81 
                                   6799**********885.666666666655669****************98555555577679999*************** PP

                          EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                   ++a+   ++s+ +  ++++P ++++  +++lg  ++l+ l+++vl+++Gv+l
  gi|91772665|ref|YP_565357.1|  82 NKAIDLAGSSTTTNGLYFVPPIAIFGDSIILGNLPNLYVLVSAVLVFVGVYL 133
                                   **************************************************98 PP

>> DUF4668  Domain of unknown function (DUF4668)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.32   2.9e+03     100     119 ..       2      21 ..       1      29 [. 0.67
   2 ?   10.0   0.3   6.4e-05      0.57      10      59 ..      30      83 ..      21      86 .. 0.75
   3 ?   -0.1   0.1     0.083   7.5e+02      17      55 ..      99     133 ..      92     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.32
                       DUF4668 100 lllyvslvyslviiqlffkt 119
                                   ++  +s v+  +ii+ f  +
  gi|91772665|ref|YP_565357.1|   2 FGSVFSWVFYTTIIDKFRSK 21 
                                   55567778888888877644 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.4e-05
                       DUF4668 10 lkivqttlvPplelLkekyp...kvlkiksvqlildlvylaiv.sivgflllke 59
                                  + ++ t ++ p+ lL+ +     +v +   v  i+ l+ylai+ s+ gfll+++
  gi|91772665|ref|YP_565357.1| 30 ITMFGTIFLFPFALLEARDMrvdIVSQSDLVVAIVILMYLAILgSALGFLLWNK 83
                                  57888899999****987651115566666677777889888768999****87 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.083
                       DUF4668  17 lvPplelLkekypkvlkiksvqlildlvylaivsivgfl 55 
                                   +vPp+ ++    +++l +  +  +l  v++++v++ ++l
  gi|91772665|ref|YP_565357.1|  99 FVPPIAIFG--DSIILGNLPNLYVL--VSAVLVFVGVYL 133
                                   778888875..56666655555555..777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 941.06
//
Query:       gi|91772666|ref|YP_565358.1|  [L=374]
Description: transposase, mutator type [Methanococcoides burtonii DSM 6242]
Scores for complete 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-111  371.8   4.0   4.3e-111  371.4   4.0    1.0  1  Transposase_mut  Transposase, Mutator family
      3e-10   40.4   0.0    8.5e-10   38.9   0.0    1.8  1  MULE             MULE transposase domain
    0.00011   21.8   0.2    0.00017   21.2   0.2    1.3  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.029   14.1   0.3       0.11   12.2   0.1    2.0  2  DUF4423          Domain of unknown function (DUF4423)
      0.036   13.2   0.1      0.067   12.4   0.1    1.4  1  SpvB             Salmonella virulence plasmid 65kDa B protein
       0.72   10.1   5.6         48    4.2   4.0    2.9  2  DDE_Tnp_IS240    DDE domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.4   4.0  1.4e-114  4.3e-111      22     380 ..      14     365 ..       4     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 371.4 bits;  conditional E-value: 1.4e-114
               Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykRreka 102
                                   ++  lk l++ +l+e++e+e+ e+ ga ++ers +r+ +RnG+r+r+l+Tr g+l+l+ P++R+  F ++++ery R+eka
  gi|91772666|ref|YP_565358.1|  14 SNVSLKPLITYFLNEVMEQEAIEQSGAGKHERSITRTAHRNGYRDRSLTTRHGELTLKKPQLRDFPFTTQVFERYSRTEKA 94 
                                   55678999************************************************************************* PP

               Transposase_mut 103 leavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrvvsk 183
                                   +e++++e yv+Gvstrkvek++ +l++ +s+S+s vS+i+++ld++v+ f ++++e++   +l++Da+ylkvR+  r v+k
  gi|91772666|ref|YP_565358.1|  95 IENAIVESYVQGVSTRKVEKIISQLGV-ESISRSRVSRIAQDLDKTVHGFMNKPIEHE-IKYLYVDATYLKVRDRVRYVNK 173
                                   ***************************.77***************************9.********************** PP

               Transposase_mut 184 avliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrvHllrnll 264
                                   av+i  gv+ dG+reiLg+++adsE++ fW++++++Lk+rGl+gvelv+sD+hkG+++a+++ f +a++Q C+vHl r +l
  gi|91772666|ref|YP_565358.1| 174 AVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKKRGLRGVELVISDGHKGIQRAVERQFLGASWQMCMVHLERLIL 254
                                   ********************************************************************************* PP

               Transposase_mut 265 akvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafpeqirrkikstNllErLN 344
                                   +k+p+k+ ++ +e++k + +       + +l  ++ ++ +  + k+ae++++ +  ++++ afp++++++ik+tN++E LN
  gi|91772666|ref|YP_565358.1| 255 KKLPRKHHKEAMESFKEVQDD------QTKLLGLMVEWDRpGFEKAAETIERFQHGLTNYQAFPKEHWKRIKTTNMVEILN 329
                                   **************9987543......345555666677789*************************************** PP

               Transposase_mut 345 keirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                   ke++Rr++vvg FPn+es++rlv+avl +++++w++
  gi|91772666|ref|YP_565358.1| 330 KEVKRRSKVVGAFPNDESLMRLVVAVLIDQNENWIT 365
                                   **********************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.8e-13   8.5e-10       2      94 ..     155     250 ..     154     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.8e-13
                          MULE   2 vvlDgTyktnkykl.....plltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnal 77 
                                   + +D+Ty++ + ++       ++v gv++ g   +l++ + +se+   +e ++++l+++ +  r  + +i+D +k++++a+
  gi|91772666|ref|YP_565358.1| 155 LYVDATYLKVRDRVryvnkAVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKKR-GL-RGVELVISDGHKGIQRAV 233
                                   679****99865441122167889*********************************95.44.79**************** PP

                          MULE  78 eevfpeakhrlClfHia 94 
                                   e++f +a  ++C+ H++
  gi|91772666|ref|YP_565358.1| 234 ERQFLGASWQMCMVHLE 250
                                   ***************97 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   5.6e-08   0.00017      11     215 ..      97     313 ..      88     348 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.6e-08
                  DDE_Tnp_IS66  11 eilvlkyadhlPlyRqeeilarlGv.elsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkks 90 
                                   +++v+ y+++++ +++e+i+++lGv  +sr+ +++  ++  +++  ++++  ++  + +++ +D T l+v +  r +  ++
  gi|91772666|ref|YP_565358.1|  97 NAIVESYVQGVSTRKVEKIISQLGVeSISRSRVSRIAQDLDKTVHGFMNKPIEH--EIKYLYVDATYLKVRD--RVRYVNK 173
                                   6799*********************569***99999988888888888776654..55799********877..6888888 PP

                  DDE_Tnp_IS66  91 ylWvyvtdkr...kpavlfeyspsRggevaealLag.....fkG..vlvsDgyagYnklae...eqvthalCwaHlrRkfv 158
                                    +++++  k+   +++   ++++s  +   e+++++      +G   ++sDg++g ++  e    ++  ++C++Hl R + 
  gi|91772666|ref|YP_565358.1| 174 AVFIVAGVKNdgyREILGVKIADSEEAMFWEEMFTDlkkrgLRGveLVISDGHKGIQRAVErqfLGASWQMCMVHLERLIL 254
                                   88888887777899*************999999777665665566679*********976657778888*********876 PP

                  DDE_Tnp_IS66 159 daeeakkk...sqaaaealar.igklyaiereareaeaeerlalrqeesrpllaeleawle 215
                                   +   +k +    +  +e +++   kl  +  e+  ++  e++a   e+ +  l++++a  +
  gi|91772666|ref|YP_565358.1| 255 KKLPRKHHkeaMESFKE-VQDdQTKLLGLMVEWD-RPGFEKAAETIERFQHGLTNYQAFPK 313
                                   66554432122222222.2222444444444442.24455555555555555555555555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.58   1.7e+03     106     130 ..     121     128 ..      86     148 .. 0.55
   2 ?   12.2   0.1   3.8e-05      0.11      92     145 ..     252     305 ..     244     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.58
                       DUF4423 106 iealervpkeeRdissltlaisked 130
                                   +e                 +is++ 
  gi|91772666|ref|YP_565358.1| 121 VE-----------------SISRSR 128
                                   33.................344444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.8e-05
                       DUF4423  92 eavrsyhkqmlelAiealervpkeeRdissltlaiskedyekikkeirefrkki 145
                                   + ++++ ++  ++A+e++++v+ ++ ++ +l++  ++  +ek+++ i++f++ +
  gi|91772666|ref|YP_565358.1| 252 LILKKLPRKHHKEAMESFKEVQDDQTKLLGLMVEWDRPGFEKAAETIERFQHGL 305
                                   667888889999**************************************9865 PP

>> SpvB  Salmonella virulence plasmid 65kDa B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.2e-05     0.067      79     151 ..     259     335 ..     231     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                          SpvB  79 vlkkdgekeveeeeekleeteleytvrrYrprvegkfarierwtkkad....eeevfWrviskdnvttlyGkteesr 151
                                    +++++++e+ +e+++++++ l   v+  rp  e++ + ier+++  +      +++W+ i++ n+++++ k+ + r
  gi|91772666|ref|YP_565358.1| 259 RKHHKEAMESFKEVQDDQTKLLGLMVEWDRPGFEKAAETIERFQHGLTnyqaFPKEHWKRIKTTNMVEILNKEVKRR 335
                                   233333344444444444444459*******************9976644446789*************99987766 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.8   5.4e+03      64      96 ..      82      97 ..      48     124 .. 0.58
   2 ?    4.2   4.0     0.016        48       6      84 ..     157     243 ..     153     360 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                 DDE_Tnp_IS240 64 tDkasayasalkelkregelfdevshvqvkyln 96
                                  t                    ++ s+ ++  +n
  gi|91772666|ref|YP_565358.1| 82 TQVF-----------------ERYSRTEKAIEN 97
                                  3222.................222333333333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                 DDE_Tnp_IS240   6 vDETyvkikGkwaYlyrav........DkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelk 78 
                                   vD Ty+k++ + +Y+  av        D   +il++ + +  ++     +++ + k+  +  e ++ D+++  ++a+++ +
  gi|91772666|ref|YP_565358.1| 157 VDATYLKVRDRVRYVNKAVfivagvknDGYREILGVKIADSEEAMFWEEMFTDLKKRGLRGVELVISDGHKGIQRAVERQF 237
                                   677777777777777666533344433333335555555554444444444444444422223333455555555554444 PP

                 DDE_Tnp_IS240  79 regelf 84 
                                      +++
  gi|91772666|ref|YP_565358.1| 238 LGASWQ 243
                                   433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2788.26
//
Query:       gi|91772667|ref|YP_565359.1|  [L=374]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-06   27.3   0.5      4e-06   26.6   0.5    1.3  1  DDE_Tnp_1     Transposase DDE domain
     0.0098   16.0   0.1      0.026   14.6   0.1    1.7  1  Hit1_C        Hit1 C-terminal
  ------ inclusion threshold ------
      0.046   13.8   1.8        2.2    8.4   0.1    2.6  2  TetR_C_8      Transcriptional regulator C-terminal region
       0.34   10.5   1.6        3.2    7.4   0.1    2.4  2  Fur_reg_FbpB  Fur-regulated basic protein B


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.5   8.9e-10     4e-06       7     182 ..     103     293 ..      97     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.9e-10
                     DDE_Tnp_1   7 livDattvrvpgtk.....edarwgykggk..ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgk 78 
                                   l++D t+ +  g+       +  +g+ +++  ++y y   ++++  +++ +s+  + + +  +++lk ++d ++++  k+ 
  gi|91772667|ref|YP_565359.1| 103 LAIDYTNDPYYGEVdainkNYVIRGQAKKStnSFYSYISLCIINKYTRFTISMLPVEKGRTKTDYLKYFIDLVDKInlKTN 183
                                   55666666666666333332222233322245899999***********99999988888888888776666666666*** PP

                     DDE_Tnp_1  79 lvlaDaGYasaelldtleekgvdyiirl...........kkntklyrk..............gaeskrrgrlrkhdrnkil 134
                                   ++  D+ + s++++ +l+e+ + +i ++            +n+k y+k               ++ k+ +  r+++ ++ l
  gi|91772667|ref|YP_565359.1| 184 VLCLDREFYSRDVFAFLQENEIPHITPVvrmgkrikdllDGNKKRYEKyvmknkkgdveldiAIDVKYLKGKRGKNGCENL 264
                                   ****************************98877777777444444444555666677666666888888888888888888 PP

                     DDE_Tnp_1 135 tksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFk 182
                                     +    +                    ++ ++  +yr+R +iE++ +
  gi|91772667|ref|YP_565359.1| 265 GFVVYGIDW-------------------EPGKISTIYRKRFTIESSYR 293
                                   888888888...................****************9876 PP

>> Hit1_C  Hit1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   5.9e-06     0.026      20      65 ..      67     116 ..      62     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                        Hit1_C  20 vkfhlakv.yrilttsegn...ggssdtlsseakkqlavdylntlryGGv 65 
                                   +++hl+k+ +  l  ++++   ++s++tl s+ k +la+dy n   yG v
  gi|91772667|ref|YP_565359.1|  67 MRYHLHKIdFDQLIENNAKillQSSHETLDSNKKYDLAIDYTNDPYYGEV 116
                                   689****965666655554232466677***************9999976 PP

>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2      0.01        47      39      80 ..     106     147 ..      78     151 .. 0.86
   2 ?    8.4   0.1   0.00049       2.2      28      87 ..     303     365 ..     291     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHHHH-TT--S-HHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_8  39 elikelilkvieelsegkelseedkefiadfysygfvgvild 80 
                                   +++++ +++ ++ +++++ ++ + k+   +fysy  + +i +
  gi|91772667|ref|YP_565359.1| 106 DYTNDPYYGEVDAINKNYVIRGQAKKSTNSFYSYISLCIINK 147
                                   5778889999************************99999865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00049
                                   -.THHHHHHHHHHHHHHHHHHHHHH-TT-..-S-HHHHHHHHHHH.HHHHHHHHHHHHHTTS- CS
                      TetR_C_8  28 ngresfekylkelikelilkvieelsegk..elseedkefiadfy.sygfvgvildWlengmk 87 
                                    +r+ + +y++ li+ ++++ + ++++ +  +++  +k +  d +    fv+ i++W++++ k
  gi|91772667|ref|YP_565359.1| 303 SSRNPMLRYFYALISFMLKNAWLSIQRMHfmKVKRGPKTIEEDVFrFDLFVHFIEEWVRKKLK 365
                                   5789999***************777744456**************5569**********9877 PP

>> Fur_reg_FbpB  Fur-regulated basic protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00071       3.2       4      22 ..      72      90 ..      70      94 .. 0.89
   2 ?    1.7   0.2     0.042   1.9e+02       5      17 ..     226     238 ..     216     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00071
                  Fur_reg_FbpB  4 kklsFeeLVeeNKkeLlnD 22
                                  +k+ F++L+e N k Ll++
  gi|91772667|ref|YP_565359.1| 72 HKIDFDQLIENNAKILLQS 90
                                  7899********9999987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.042
                  Fur_reg_FbpB   5 klsFeeLVeeNKk 17 
                                   k+++e  V++NKk
  gi|91772667|ref|YP_565359.1| 226 KKRYEKYVMKNKK 238
                                   6999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3239.87
//
Query:       gi|91772668|ref|YP_565360.1|  [L=456]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-33  113.2   0.3    4.3e-32  110.9   0.1    2.0  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.1e-18   67.1   0.0    2.2e-18   66.1   0.0    1.6  1  HisKA         His Kinase A (phospho-acceptor) domain
    1.3e-08   34.9   0.0    2.9e-08   33.7   0.0    1.7  1  PAS           PAS fold
    2.1e-08   34.0   0.0    4.5e-08   32.9   0.0    1.6  1  PAS_8         PAS domain
    2.7e-06   27.6   0.0    8.5e-06   26.0   0.0    1.9  1  PAS_9         PAS domain
    0.00065   19.9   0.0     0.0028   17.9   0.0    1.9  1  PAS_4         PAS fold
      0.001   18.9   0.3      0.039   13.8   0.0    2.3  2  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
     0.0043   17.0   0.0      0.011   15.7   0.0    1.6  1  HATPase_c_2   Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.047   13.6   0.0       0.15   12.0   0.0    1.9  1  HATPase_c_5   GHKL domain
       0.12   12.0   0.2       0.12   12.0   0.2    1.7  2  DUF4464       Domain of unknown function (DUF4464)
       0.19   10.5   2.4        0.3    9.8   2.4    1.3  1  GPDPase_memb  Membrane domain of glycerophosphoryl diester ph


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 ?   -0.4   0.0         1   1.6e+03      63      93 ..     181     218 ..     149     235 .. 0.72
   2 !  110.9   0.1   2.7e-35   4.3e-32       2     110 ..     340     449 ..     339     451 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                                   HHCSTCHTSTSSSHHHHHHHHHHHH.......TTTEEE CS
                     HATPase_c  63 qddstkrggggtGlGlsivkklvel.......mgGeiw 93 
                                   q +s+ +++gg    lsi++ ++e+       ++ +i+
  gi|91772668|ref|YP_565360.1| 181 QMRSQIIQYGGKTAILSIARDITERkkaeeaiLEAKIE 218
                                   45577888999999999999998852333333333444 PP

  == domain 2  score: 110.9 bits;  conditional E-value: 2.7e-35
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d ++++qi+ nlv Na+kf+ ++g++++  k s+d ++isv+D+GiG+++ed++klf +f q d+s++r++ggtGlGl++v
  gi|91772668|ref|YP_565360.1| 340 DMIKFKQILYNLVHNAIKFTDQGGSVTIGGKISDDLVHISVKDSGIGVSPEDQDKLFNPFFQlDSSNARKYGGTGLGLALV 420
                                   66789**************7799999997776689********************************************** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                   kk+ve++gGeiwvese g+G+tftf +p 
  gi|91772668|ref|YP_565360.1| 421 KKFVEMHGGEIWVESEVGKGSTFTFIIPT 449
                                   *************************9986 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 !   66.1   0.0   1.3e-21   2.2e-18       1      67 []     225     293 ..     225     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.3e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   ++++fla+++HELrtPL++i+g++++L +e  g+l+e +k+y   + +++++l+++++d+L +s ie+g
  gi|91772668|ref|YP_565360.1| 225 AKSEFLANMSHELRTPLNSIIGFSDVLYNEshGPLNEYQKKYTSNVLRNGKHLLDIINDILSISNIETG 293
                                   589************************44457**********************************987 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   1.8e-11   2.9e-08       2      74 ..      97     171 ..      96     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.8e-11
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..HHHHHHHHHHHHTT-ECC CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..elaelleqlleqgeesra 74 
                                   ++r+i++ + d+i ++D  gr++ vNa a++++G+sr+e+l   + d  ++e d+  +++el+++ + + e++++
  gi|91772668|ref|YP_565360.1|  97 KFRTIFDKANDGIYLIDLHGRFIDVNAMACKQTGYSRDEMLQMAYKDMGFPEIDYkkQVKELYKKGYTSFESASI 171
                                   799********************************************9999988766666666666666665554 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   2.8e-11   4.5e-08       1      43 [.      96     139 ..      96     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.8e-11
                         PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkge 43 
                                   e++r++f+ ++dgi ++dl +r++dvN  a++ +Gys ++++ +
  gi|91772668|ref|YP_565360.1|  96 EKFRTIFDKANDGIYLIDLHGRFIDVNAMACKQTGYSrDEMLQM 139
                                   79****************6667***************7666654 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.2e-09   8.5e-06       2     104 .]     107     204 ..     106     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.2e-09
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                   dgi +++ +gr +++N +a++ +Gys++e+l+  ++d+  ++ + ++ ++++++ g     ++e   i k+++t + +++ 
  gi|91772668|ref|YP_565360.1| 107 DGIYLIDLHGRFIDVNAMACKQTGYSRDEMLQMAYKDMGFPEIDYKKQVKELYKKGY---TSFESASILKDDSTAYGQMRS 184
                                   8999999***************************99999566777777777777777...8999999999999******** PP

                         PAS_9  83 spvkdddgelvgiivilrDite 104
                                     ++ ++++ ++  +i rDite
  gi|91772668|ref|YP_565360.1| 185 QIIQYGGKTAIL--SIARDITE 204
                                   ***988888888..*******8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.7e-06    0.0028       1     109 [.     102     206 ..     102     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlael.lpeedaarleralrrvlegeepiefleelllpgeerh 80 
                                   +d+ +d+++ +d +gr++++Na a++  g++++e+l + + ++ +pe    ++  +++++ + + + ++    l ++++ +
  gi|91772668|ref|YP_565360.1| 102 FDKANDGIYLIDLHGRFIDVNAMACKQTGYSRDEMLQMAYKDMgFPE---IDYKKQVKELYKKGYTSFESASILKDDSTAY 179
                                   7899*************************************972555...4555556665555555555555555677777 PP

                         PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                    ++r   +    G+  ++l i+rDiTer+
  gi|91772668|ref|YP_565360.1| 180 GQMRSQII--QYGGKTAILSIARDITERK 206
                                   77777655..2355588888888888887 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 ?    2.9   0.1     0.054        88      71     119 ..     187     233 ..     164     248 .. 0.75
   2 !   13.8   0.0   2.4e-05     0.039       3      80 ..     344     418 ..     342     434 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.054
                   HATPase_c_3  71 GkkGiGlklAslslgkkltvitkkegesstltldvdkidkenekvleel 119
                                    ++G G k+A+ls+++++t   k+e+   +++++ +  ++ +++ l+++
  gi|91772668|ref|YP_565360.1| 187 IQYG-G-KTAILSIARDITERKKAEEAILEAKIEAESANRAKSEFLANM 233
                                   5677.8.**********99998888888888888777666666666555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.4e-05
                   HATPase_c_3   3 lekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlklA 80 
                                   +++ l  lv N++    +  +v+i  +  + +   i+++D G G+s+e+ ++ +++  +  +  ++++++G  G+Gl  A
  gi|91772668|ref|YP_565360.1| 344 FKQILYNLVHNAIKftDQGGSVTIGGKISD-DLVHISVKDSGIGVSPEDQDKLFNPFFQLDS--SNARKYGGTGLGL--A 418
                                   566678888888873223334555544433.4589*******************98888877..48999*****994..4 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.7e-06     0.011      43     110 ..     351     425 ..     345     445 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.7e-06
                   HATPase_c_2  43 avehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGlalikglvD 110
                                    v+ a +     g+v++  +++++ ++++v+DsG g  pe++++     p        + +    G+Glal+k++v+
  gi|91772668|ref|YP_565360.1| 351 LVHNAIKFTDqGGSVTIGGKISDDLVHISVKDSGIGVSPEDQDKLFN--PffqldssnARKYGGTGLGLALVKKFVE 425
                                   55555554444789**********************99998665543..3568999777788888999*****9997 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.3e-05      0.15       6      90 ..     344     436 ..     339     447 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-05
                   HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ekkkle........sskskkeehGiGlks 73 
                                   +  il nl  NAi   ++      ++++  + +++ + is++ s  g     + +kl+        s+ +k +  G+Gl  
  gi|91772668|ref|YP_565360.1| 344 FKQILYNLVHNAIKFTDQGG----SVTIGGKISDDLVHISVKDSGIGvspedQ-DKLFnpffqldsSNARKYGGTGLGLAL 419
                                   56788999999997766644....78888888889999999998555444431.22222333343355778888999**** PP

                   HATPase_c_5  74 ireivkkykgnlsieae 90 
                                   +++ v+ ++g++++e e
  gi|91772668|ref|YP_565360.1| 420 VKKFVEMHGGEIWVESE 436
                                   *************9987 PP

>> DUF4464  Domain of unknown function (DUF4464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.2e-05      0.12     106     137 ..      71     104 ..      66     107 .. 0.87
   2 ?   -2.7   0.1       2.2   3.5e+03      34      71 ..     186     224 ..     173     239 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                       DUF4464 106 irdrnkkgqeiSgYIDyeqrLk..sedwkaiFeg 137
                                   +r +n++ qei +Y D++++L+  +e ++ iF++
  gi|91772668|ref|YP_565360.1|  71 LRSYNETDQEIGSYRDFKHSLQesEEKFRTIFDK 104
                                   7899******************65588*****87 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                       DUF4464  34 lvelgyrgtgevls.reeFearkkaleealepk..kkkkkk 71 
                                   +++ g ++   +ls   +  +rkka e+ le+k  +++ ++
  gi|91772668|ref|YP_565360.1| 186 IIQYGGKTA--ILSiARDITERKKAEEAILEAKieAESANR 224
                                   555554443..333134455566665666666643222222 PP

>> GPDPase_memb  Membrane domain of glycerophosphoryl diester phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.4   0.00019       0.3     200     264 ..       1      63 [.       1      72 [. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                  GPDPase_memb 200 lkeSwqltkknflrlllklllliliivivltvilsllllllqllldklpkkvslilaiinltllq 264
                                   +k+Sw++ k ++ r ++  +++++++viv +++++ +++  q +++ +  +  + + i+ + +l+
  gi|91772668|ref|YP_565360.1|   1 MKKSWKINKFKTNRAFFEVVVIVVATVIVTILAIISGGI--QMFCEWFQAHEVVHAPIFGFLFLM 63 
                                   79*******999999777777777777777777777777..557777666655555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3148.92
//
Query:       gi|91772669|ref|YP_565361.1|  [L=100]
Description: hypothetical protein Mbur_0640 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.036   14.0   0.4      0.042   13.7   0.4    1.1  1  LepB_GAP_N  LepB GAP domain N-terminal subdomain


Domain annotation for each model (and alignments):
>> LepB_GAP_N  LepB GAP domain N-terminal subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   2.4e-06     0.042     132     187 ..      17      72 ..       7      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-06
                                   HHHHHHHHHHHHHHHHHHHHCHHHCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    LepB_GAP_N 132 kkvetlltagfniivtlrvlqetqakedkemaeaikllkkaLqeflkafeevyklL 187
                                   + ++t+l  ++ ii+++ v+  ++ ++d++++ ++ + +k+L++f    +e+yk L
  gi|91772669|ref|YP_565361.1|  17 NFISTVLDSALVIITLVYVIITAEILKDSQQTRKVSIVQKQLDDFYIPMKEIYKEL 72 
                                   5699************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 687.22
//
Query:       gi|91772670|ref|YP_565362.1|  [L=85]
Description: hypothetical protein Mbur_0641 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0057   16.5   2.0     0.0062   16.4   2.0    1.1  1  Rep_2            Plasmid replication protein
  ------ inclusion threshold ------
      0.014   13.8   0.8      0.016   13.7   0.8    1.0  1  Adeno_terminal   Adenoviral DNA terminal protein
       0.02   15.3   0.0      0.062   13.7   0.0    1.8  2  ATP-gua_PtransN  ATP:guanido phosphotransferase, N-terminal d
      0.047   13.7   0.3      0.051   13.5   0.3    1.1  1  Lipase_GDSL      GDSL-like Lipase/Acylhydrolase
      0.047   13.5   0.1      0.048   13.5   0.1    1.1  1  AUX_IAA          AUX/IAA family


Domain annotation for each model (and alignments):
>> Rep_2  Plasmid replication protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.0   1.7e-06    0.0062     121     166 ..      24      74 ..       4      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                         Rep_2 121 dkv.....lasedkeklleeiedlieendiielaelvdylreeesellivv 166
                                   d++     l++++ +k+ +e++d i ++++i  +el+d+ ++ e  + + +
  gi|91772670|ref|YP_565362.1|  24 DDIkrkvyLSNKNSYKFFSELLDNIAKKNMITVCELLDVSQNLENIIENDI 74 
                                   44333457*****************************96655443344444 PP

>> Adeno_terminal  Adenoviral DNA terminal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   4.4e-06     0.016     434     494 ..      10      77 ..       6      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-06
                Adeno_terminal 434 dlvqvilrgrdengeqvfkRvWserelsa..feqlyeril.rdllaiveraer....edleeeeqeql 494
                                   +++q+ ++ r+ + +++ ++v+  +++s   f++l + i+ +++++++e  +     e++ e+++e+l
  gi|91772670|ref|YP_565362.1|  10 KIIQITVVNRNREVDDIKRKVYLSNKNSYkfFSELLDNIAkKNMITVCELLDVsqnlENIIENDIENL 77 
                                   789******************9776665556********7368999**98775433556666666666 PP

>> ATP-gua_PtransN  ATP:guanido phosphotransferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.7e-05     0.062      31      65 ..       9      48 ..       2      50 .. 0.86
   2 ?   -1.1   0.0      0.72   2.6e+03      28      42 ..      64      78 ..      61      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                  HHHHHHHHHSTT-......-S---SSTTHHHHTHHHHHHH CS
               ATP-gua_PtransN 31 ddvIqsgvdnpdsg.....vGvvAgDeesYevFaelFdpv 65
                                  +++Iq  v+n +++       v+  +++sY+ F+el+d +
  gi|91772670|ref|YP_565362.1|  9 AKIIQITVVNRNREvddikRKVYLSNKNSYKFFSELLDNI 48
                                  578999998888887777789*****************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.72
                                  --HHHHHHHHHHSTT CS
               ATP-gua_PtransN 28 ftLddvIqsgvdnpd 42
                                   +L+++I+  ++n  
  gi|91772670|ref|YP_565362.1| 64 QNLENIIENDIENLT 78
                                  689999999888875 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.4e-05     0.051     135     178 ..      26      69 ..       5      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                                   CCHCCHHHHHHHHHHHHHHHHHHHHHCTEEEECHHHHHHHTHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Lipase_GDSL 135 dakklgekgnefvgeynqrlndlaekdgfavvDlydelqglsgi 178
                                    ++k++   ++  ++++++l ++a+k++++v++l d +q l++i
  gi|91772670|ref|YP_565362.1|  26 IKRKVYLSNKNSYKFFSELLDNIAKKNMITVCELLDVSQNLENI 69 
                                   455555566667789*************************9776 PP

>> AUX_IAA  AUX/IAA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.3e-05     0.048     137     189 ..      25      78 ..       2      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                       AUX_IAA 137 pilRKvdLkayksYeeLssalekmFssftigqcgs.agtsekdklsesklldll 189
                                    i RKv L + +sY+ +s+ l+++ ++ +i+ c+     ++ +++ e+ + +l 
  gi|91772670|ref|YP_565362.1|  25 DIKRKVYLSNKNSYKFFSELLDNIAKKNMITVCELlDVSQNLENIIENDIENLT 78 
                                   589***************************999965666677777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 666.95
//
Query:       gi|91772671|ref|YP_565363.1|  [L=79]
Description: hypothetical protein Mbur_0642 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   7.2     0.0014   18.6   7.2    1.0  1  7TMR-DISM_7TM    7TM diverse intracellular signalling
     0.0027   17.2   3.2      0.003   17.0   3.2    1.0  1  DUF373           Domain of unknown function (DUF373)
     0.0031   17.5   2.6     0.0037   17.3   2.6    1.1  1  MARVEL           Membrane-associating domain
     0.0039   16.8   5.0     0.0046   16.6   4.6    1.3  1  DUF2208          Predicted membrane protein (DUF2208)
  ------ inclusion threshold ------
      0.016   14.3   3.4      0.018   14.1   3.4    1.1  1  DUF973           Protein of unknown function (DUF973)
      0.018   15.0   1.4        4.8    7.3   0.0    2.2  2  DUF3185          Protein of unknown function (DUF3185)
      0.019   15.2   7.6      0.022   14.9   7.6    1.1  1  DUF3784          Domain of unknown function (DUF3784)
       0.03   14.3   3.5      0.036   14.1   3.5    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.038   12.7   4.0       0.04   12.7   4.0    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
      0.054   13.9   1.3      0.061   13.8   1.3    1.1  1  DUF2583          Protein of unknown function (DUF2583)
      0.086   12.9   1.6      0.095   12.7   1.6    1.0  1  CoA_binding_3    CoA-binding domain
      0.095   12.4   5.2      0.093   12.4   5.2    1.0  1  Tetraspanin      Tetraspanin family
       0.17   12.0   5.3       0.21   11.8   5.3    1.2  1  SdpI             SdpI/YhfL protein family
       0.17   11.5   4.1        0.2   11.3   4.1    1.1  1  Wzy_C            O-Antigen ligase
        0.5   10.1   5.4       0.55   10.0   5.4    1.1  1  DUF5381          Family of unknown function (DUF5381)
        0.9    9.2   3.1          1    9.0   3.1    1.1  1  DUF4131          Domain of unknown function (DUF4131)
        1.1    8.9   6.5        0.3   10.8   0.8    2.0  2  Neurensin        Neurensin
        2.2    8.3   8.4        2.8    8.0   8.4    1.2  1  Ac76             Orf76 (Ac76)
        2.6    6.5   5.9        2.8    6.3   5.9    1.0  1  FUSC             Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   7.2   1.5e-06    0.0014      97     153 ..      11      67 ..       2      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                 7TMR-DISM_7TM  97 lklllllavllsllllllpllpyteslslaqllallvillllligikawrkgnkpar 153
                                    ++l+ + ++l+++ +ll++++ t  +s + l+++++i+++++ig+++++kg+ + r
  gi|91772671|ref|YP_565363.1|  11 TRFLMSMGLVLCITGALLFAFLLTIPSSTMVLFLFIFIVVFIFIGFILLYKGFNDLR 67 
                                   4666666667667777777889999999999*********************98877 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.2   3.2e-06     0.003     153     198 ..       9      64 ..       5      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.2e-06
                        DUF373 153 lrktiLvplGlllliyallll..........lglpelalaiillllGlylllrGfg 198
                                     + +L+ +Gl+l i ++ll+          + l  ++++++++++G++ll++Gf+
  gi|91772671|ref|YP_565363.1|   9 STTRFLMSMGLVLCITGALLFaflltipsstMVLFLFIFIVVFIFIGFILLYKGFN 64 
                                   567899999999999999998999999999877788999****************8 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.6   3.9e-06    0.0037      37     103 ..       6      65 ..       2      77 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
                        MARVEL  37 spssalnfavfvavfsflyalfllvlylfknsaftsilwplidlivdalaallwlvafialaaglrd 103
                                   +++s++ f + ++ +  ++ ++l++  l    +   i    ++l++   ++++ +++fi+l +g++d
  gi|91772671|ref|YP_565363.1|   6 DYQSTTRFLMSMGLVLCITGALLFAFLL----T---IPSSTMVLFLFIFIVVFIFIGFILLYKGFND 65 
                                   7899999999999665555333333322....3...3344444444445678899*********999 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   4.6   4.9e-06    0.0046      10      63 ..      26      78 ..      15      79 .] 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                       DUF2208 10 iilfalvlaflpqylflviilYiivimvimsvltsrsllrerkkleevesgktL 63
                                   +lfa++l++   +++l+++++i+v+++i ++l ++   ++ +  e  e+g++L
  gi|91772671|ref|YP_565363.1| 26 ALLFAFLLTIPSSTMVLFLFIFIVVFIFIGFILLYKG-FNDLRLSEVQEKGNVL 78
                                  578999999999************************9.6677777777777776 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.4   1.9e-05     0.018      94     156 ..       5      64 ..       1      74 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                        DUF973  94 vgiGitgltliligaiiiiigvilaivsllslilslillgviilligiilaliGqillglsfy 156
                                   +   +t  +l+ +g+++ i g++ + ++ll + +s ++l  ++ ++ +++++iG+ill  +f 
  gi|91772671|ref|YP_565363.1|   5 IDYQSTTRFLMSMGLVLCITGAL-LFAFLLTIPSSTMVL--FLFIFIVVFIFIGFILLYKGFN 64 
                                   55567778899999999888877.344555555555444..33444467889*****987775 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0051       4.8      37      58 ..       7      28 ..       5      39 .. 0.77
   2 ?    7.0   0.3     0.006       5.7       5      21 ..      49      65 ..      46      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0051
                       DUF3185 37 ttdktlllligGgvaaivGlvl 58
                                  ++ +t  l+ +G v+ i+G +l
  gi|91772671|ref|YP_565363.1|  7 YQSTTRFLMSMGLVLCITGALL 28
                                  5677778888888888888554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.006
                       DUF3185  5 iiLlvaGivLlvfGyna 21
                                  ++++++G +Ll+ G+n 
  gi|91772671|ref|YP_565363.1| 49 VVFIFIGFILLYKGFND 65
                                  689***********986 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   7.6   2.4e-05     0.022      45      89 ..      16      60 ..       3      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                       DUF3784 45 fmgivllligilflllgllsaiesealliialiviiiiviylivy 89
                                   mg vl+++g+l++++ l ++  +++l+++++iv++i++ ++++y
  gi|91772671|ref|YP_565363.1| 16 SMGLVLCITGALLFAFLLTIPSSTMVLFLFIFIVVFIFIGFILLY 60
                                  6999******88888888877777778888888888888877776 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 ?   14.1   3.5   3.9e-05     0.036      41      93 ..      16      68 ..       8      74 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-05
               Phage_holin_3_6 41 gaagvlallalllllvalalala.alwlaali.vaavllvlagvlalvglkklkk 93
                                   +++vl ++++ll+ ++l   +    ++ +l    +v++ ++ +l++ g + l+ 
  gi|91772671|ref|YP_565363.1| 16 SMGLVLCITGALLFAFLLT--IPsSTMVLFLFiFIVVFIFIGFILLYKGFNDLRL 68
                                  3444444444444444442..22122233444167999999******99998775 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.0   4.2e-05      0.04     381     430 ..       9      58 ..       2      76 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                       DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivlllf 430
                                    + ++l  ++++l++ ++ll+++ll++ ++ ++++l+i+++++i++ +++
  gi|91772671|ref|YP_565363.1|   9 STTRFLMSMGLVLCITGALLFAFLLTIPSSTMVLFLFIFIVVFIFIGFIL 58 
                                   45566666667777777777666666555555555555555555555443 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.3   6.4e-05     0.061      11      60 ..      12      62 ..       4      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-05
                       DUF2583 11 nvlmglGlllmvas.laysvlnqlpelelpellaeaallgifiGallWlaG 60
                                    lm++Gl+l +++ l ++ l  +p+  +  +l    ++ ifiG +l   G
  gi|91772671|ref|YP_565363.1| 12 RFLMSMGLVLCITGaLLFAFLLTIPSSTMVLFLFIFIVVFIFIGFILLYKG 62
                                  579*****998765389***************************9997766 PP

>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.6    0.0001     0.095      15      64 ..       7      56 ..       3      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                 CoA_binding_3 15 lrlllrvlsawllvllllallsfslk.da.fSRlwlaywavvglvllivsrl 64
                                  +++++r+l+++ lvl ++++l+f++  ++  S ++l  ++++ +++ i   +
  gi|91772671|ref|YP_565363.1|  7 YQSTTRFLMSMGLVLCITGALLFAFLlTIpSSTMVLFLFIFIVVFIFI--GF 56
                                  6889***********999988886652332444555544444443333..22 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.2   9.8e-05     0.093      45      95 ..       6      58 ..       1      75 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.8e-05
                                  ........XXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin 45 dpailaillivvGvllfllg..flGcigalkenkcllltfsllllvlfllela 95
                                  d ++ + +l+ +G +l+++g  ++ ++ ++  ++++l++f+++++++f+ ++ 
  gi|91772671|ref|YP_565363.1|  6 DYQSTTRFLMSMGLVLCITGalLFAFLLTIPSSTMVLFLFIFIVVFIFIGFIL 58
                                  55666789************4446789999****************9999886 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.3   0.00022      0.21      30      62 ..      18      56 ..       2      61 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                          SdpI 30 gklwiiaGlilllla......lgavvlvllvlvlllviv 62
                                  g +++i+G +l+++       +  ++l+++++v++++ +
  gi|91772671|ref|YP_565363.1| 18 GLVLCITGALLFAFLltipssTMVLFLFIFIVVFIFIGF 56
                                  345556665444444887644323333333333333333 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.1   0.00021       0.2      17      65 ..      18      65 ..      11      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                         Wzy_C 17 sgiigllvalivlliifykrripfllllgilvgvilliilfvlstnlet 65
                                  + ++ + +al++++++++      +l+l+i+++v ++i +++l + ++ 
  gi|91772671|ref|YP_565363.1| 18 GLVLCITGALLFAFLLTIPSST-MVLFLFIFIVVFIFIGFILLYKGFND 65
                                  55677899*************9.44444466667777777776666655 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.4   0.00058      0.55       5      61 ..       5      60 ..       2      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00058
                       DUF5381  5 vksrkflrvllflatvglglaglfllfeglkfeskysllyiiigiigtifgliillm 61
                                  + ++   r+l+ ++ ++l ++g  l+   l++ s+  +l ++i i++ if+  ill 
  gi|91772671|ref|YP_565363.1|  5 IDYQSTTRFLMSMG-LVLCITGALLFAFLLTIPSSTMVLFLFIFIVVFIFIGFILLY 60
                                  56667777777776.4578999999*99****9999999999888888888877774 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.1    0.0011         1       7      50 ..      19      59 ..      10      77 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                       DUF4131  7 lvllalllllllllllllrrrprrrv.llllllllllallgfalr 50
                                  lvl ++++ll+++ll +    p+ ++ l+l++++ +++++gf l 
  gi|91772671|ref|YP_565363.1| 19 LVLCITGALLFAFLLTI----PSSTMvLFLFIFIVVFIFIGFILL 59
                                  23333333333333333....222222333333333444444333 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.8   0.00032       0.3      84     118 ..       3      37 ..       2      42 .. 0.89
   2 ?    1.7   0.8       0.2   1.9e+02      45      63 ..      45      63 ..      37      78 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                     Neurensin  84 qaiefnnaLdtlklaGavllclGglllalsllvpa 118
                                   + i+++   + l  +G+vl+  G+ll+a+ l +p+
  gi|91772671|ref|YP_565363.1|   3 SKIDYQSTTRFLMSMGLVLCITGALLFAFLLTIPS 37 
                                   5789999999*******************999986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                     Neurensin 45 lvvgtlvlllGvtallvGy 63
                                  +++ ++++ +G + l  G+
  gi|91772671|ref|YP_565363.1| 45 FIFIVVFIFIGFILLYKGF 63
                                  4444556666666666665 PP

>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   8.4    0.0029       2.8       1      40 [.      17      54 ..      15      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                          Ac76  1 mliilllialivlafildkneklsellltllllfvlFiil 40
                                  m ++l + + +++af+l     +s+++l+l++++v+Fi++
  gi|91772671|ref|YP_565363.1| 17 MGLVLCITGALLFAFLLTIP--SSTMVLFLFIFIVVFIFI 54
                                  55667778888999999877..577888888888888775 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.9     0.003       2.8     397     442 ..      13      58 ..       3      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.003
                          FUSC 397 lqfligtllavlaallllfvvlPhvdgfplLvlvlapplllgglll 442
                                   + + +g +l++  all+ f++   ++++ l++ ++ ++++++g++l
  gi|91772671|ref|YP_565363.1|  13 FLMSMGLVLCITGALLFAFLLTIPSSTMVLFLFIFIVVFIFIGFIL 58 
                                   56889****************9999999999999988888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1427  (0.0795917); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 591.00
//
Query:       gi|91772672|ref|YP_565364.1|  [L=128]
Description: hypothetical protein Mbur_0643 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0082   15.0   0.8       0.01   14.7   0.8    1.1  1  WAPL      Wings apart-like protein regulation of heterochroma
  ------ inclusion threshold ------
      0.017   14.0   0.2       0.02   13.8   0.2    1.1  1  TruD      tRNA pseudouridine synthase D (TruD)
      0.034   14.3   0.2      0.064   13.4   0.2    1.5  1  PYRIN     PAAD/DAPIN/Pyrin domain


Domain annotation for each model (and alignments):
>> WAPL  Wings apart-like protein regulation of heterochromatin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.8   1.7e-06      0.01      49     122 ..      39     107 ..      38     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                          WAPL  49 aspqfrrqlrahgiakrlfkalvdapdddspsLalaaaalfyvlssdshdadldrssgllrlllkLLesdtdiv 122
                                   a+ ++++++++ g +k l+k  +++ +d      l +a l++ l++ ++ +d++ +   + +l   L++ + ++
  gi|91772672|ref|YP_565364.1|  39 ADTAQVKFVLETGDVKELLKIAQAKLTDA---KRLQVARLMFNLQQNRLALDHLNWR--ISILQLHLRMWEALS 107
                                   6899****************999999998...47999*******************9..777665566555555 PP

>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.3e-06      0.02     172     260 ..       7      94 ..       1     101 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-06
                          TruD 172 rrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslry.ErallkrLaekpkdykkA 251
                                    + + h+++ a v++d+++ +++++ ++f ++ ++  ++ ++v etgd++e l+  + +l+   r  + rL+ + ++ + A
  gi|91772672|ref|YP_565364.1|   7 HKANFHIMAYAGVQRDYQSVADALIREKFGDKADT-AQV-KFVLETGDVKELLKIAQAKLTDaKRLQVARLMFNLQQNRLA 85 
                                   67899************************766655.455.5566***********99998752677789999988888888 PP

                          TruD 252 lealpknLq 260
                                   l  l+ +++
  gi|91772672|ref|YP_565364.1|  86 LDHLNWRIS 94 
                                   888876665 PP

>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.1e-05     0.064      16      52 ..      43      80 ..      37      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                  HHHHHHHH..--SSSHTTHCCHCT-SHHHHHHHHHHHH CS
                         PYRIN 16 kFKslLkee.eeglksiprgelekadrvdladlLvehy 52
                                  ++K+ L++   ++l +i +++l +a+r+++a+l+ +  
  gi|91772672|ref|YP_565364.1| 43 QVKFVLETGdVKELLKIAQAKLTDAKRLQVARLMFNLQ 80
                                  679999776788899*******************8755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 934.13
//
Query:       gi|91772673|ref|YP_565365.1|  [L=206]
Description: hypothetical protein Mbur_0644 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   34.3   6.0    2.7e-08   34.3   6.0    1.9  2  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
       0.15   12.0   0.0       0.15   12.0   0.0    2.4  3  DUF5345      Family of unknown function (DUF5345)
        1.9    8.2   8.0       0.26   11.0   2.6    1.9  2  Claudin_2    PMP-22/EMP/MP20/Claudin tight junction


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.6      0.29   1.7e+03      21      31 ..      64      74 ..      27      86 .. 0.56
   2 !   34.3   6.0   4.5e-12   2.7e-08       7     115 ..      89     196 ..      78     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.29
                   SNARE_assoc 21 lvtslgallGa 31
                                  l++++ a++G+
  gi|91772673|ref|YP_565365.1| 64 LLVFMLAIIGG 74
                                  22222222222 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 4.5e-12
                   SNARE_assoc   7 lvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygf.lallllrllpivPrdlvn 86 
                                   ++ +G + +++   l +slg + G+++ y+lg +  + + +r + s  r+ ++ + ++ + + +++++  l+p +P+d+++
  gi|91772673|ref|YP_565365.1|  89 VISLGGV-SPIGIALFASLGLTFGDLVFYYLGMKSKQCIKGRYANSVFRLTKWMEQIDDRLTmVLIFFYSLTP-LPSDIIA 167
                                   3444444.4777999********************99888888888888888555555555516666666666.89***** PP

                   SNARE_assoc  87 yvaGltrvsfkrFflatfiGsipwalvya 115
                                   +++++ +++f++ ++  f+G +  +l+++
  gi|91772673|ref|YP_565365.1| 168 IALAIVGFPFRKMIIPLFVGNFTLILILV 196
                                   *********************99999987 PP

>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.15      38      63 ..      25      50 ..      22      53 .. 0.91
   2 ?   -2.5   1.9      0.87   5.2e+03      52      70 ..      75      93 ..      62     100 .. 0.51
   3 ?   -3.5   0.2       1.8   1.1e+04      46      54 ..     167     175 ..     166     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                       DUF5345 38 rrElllFlliAllilsllllalvqap 63
                                  +r +l++ liAl+i++ ++l++++ p
  gi|91772673|ref|YP_565365.1| 25 KRNILILSLIALFIVTWTILLFYHPP 50
                                  6889******************9977 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.87
                       DUF5345 52 lsllllalvqapalfiviQ 70
                                  +s+++++ +    + i + 
  gi|91772673|ref|YP_565365.1| 75 ISAFTSTTFYTALIVISLG 93
                                  4444444444444444444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.8
                       DUF5345  46 liAllilsl 54 
                                    iAl i+++
  gi|91772673|ref|YP_565365.1| 167 AIALAIVGF 175
                                   689999986 PP

>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6   4.3e-05      0.26      95     144 ..      28      85 ..      23      91 .. 0.87
   2 ?   -0.4   0.3      0.13     8e+02     104     126 ..     165     187 ..     132     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                     Claudin_2  95 lliLslvlivlavvlgllallkqsv........lllkaagilfllagvlgllavvvfi 144
                                   +liLsl++++++++++ll+               +++++++l +++g+  + ++  + 
  gi|91772673|ref|YP_565365.1|  28 ILILSLIALFIVTWTILLFYHPPGElverlgvrNVYLLVFMLAIIGGISAFTSTTFYT 85 
                                   689**************8765444448999**99*****************9998875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                     Claudin_2 104 vlavvlgllallkqsvlllkaag 126
                                   ++a+ l+++++++++ ++ +++g
  gi|91772673|ref|YP_565365.1| 165 IIAIALAIVGFPFRKMIIPLFVG 187
                                   77888888888888885555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1330.42
//
Query:       gi|91772674|ref|YP_565366.1|  [L=156]
Description: hypothetical protein Mbur_0645 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-35  121.5   8.4    3.6e-33  114.8   8.4    2.0  1  DUF2227          Uncharacterized metal-binding protein (DUF22
    0.00073   18.9   1.4    0.00073   18.9   1.4    1.6  1  YdjM             LexA-binding, inner membrane-associated puta
      0.004   16.6   2.0     0.0048   16.3   2.0    1.0  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
  ------ inclusion threshold ------
       0.11   12.3   1.8       0.55   10.1   0.2    2.2  2  DUF2631          Protein of unknown function (DUF2631)


Domain annotation for each model (and alignments):
>> DUF2227  Uncharacterized metal-binding protein (DUF2227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   8.4   8.1e-37   3.6e-33       1     168 [.       2     154 ..       2     156 .] 0.89

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 8.1e-37
                       DUF2227   1 psGrtHdritlvalpllavlall...........ltrslelallvalaylfgglllsPDlDiaskqykrWgilrwlWlPYq 70 
                                   p G+tHd i++++l+++ +++++              +  ++ +++l+y+f++++lsPDlDi+sk+ykrW+++r+lW+PY+
  gi|91772674|ref|YP_565366.1|   2 PGGKTHDTINIAVLIIILAGIFYlimgnlsemaaRYLDIYTISVLSLSYIFATFFLSPDLDIESKPYKRWKMFRILWWPYK 82 
                                   78**************999999999****9998777788888999************************************ PP

                       DUF2227  71 kllrHRsllSHglivGtllRllYllllllllllllallllavlelnwqalvaelkkelkllasllekkekellalllGlel 151
                                    +++HR+ lSH +i+G+l  ++ l+l+++llll++++                         +l + +++ ++a++ G++l
  gi|91772674|ref|YP_565366.1|  83 VIFKHRG-LSHNPIIGPLSIVINLALIVALLLLFMGV-------------------------ELHQGHSRYIIAATTGMIL 137
                                   *******.*******************4333333333.........................3456788999********* PP

                       DUF2227 152 gamlHllsDwvvsalkr 168
                                   +  +H++sD+++s++k+
  gi|91772674|ref|YP_565366.1| 138 SMEIHIISDFLISKMKN 154
                                   *************9986 PP

>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.4   1.6e-07   0.00073      38     116 ..      57     150 ..      25     156 .] 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-07
                          YdjM  38 llPDiDhpsstlgr..klgllskklaklvgHRgftHSllf.....lallalvlllllrlfgrsa........lrlglllll 103
                                   l PD+D+ s  ++r   ++ l +    +++HRg++H  +      ++ lal+++lll ++g +         + ++++++l
  gi|91772674|ref|YP_565366.1|  57 LSPDLDIESKPYKRwkMFRILWWPYKVIFKHRGLSHNPIIgplsiVINLALIVALLLLFMGVELhqghsryiIAATTGMIL 137
                                   78****877777752258888888889*********765411111444555555555555555478887765555555777 PP

                          YdjM 104 gvlsHlllDlltk 116
                                   ++ +H++ D l +
  gi|91772674|ref|YP_565366.1| 138 SMEIHIISDFLIS 150
                                   7888*****9865 PP

>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.0   1.1e-06    0.0048     164     249 ..      13     139 ..       9     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
               Cyt_bd_oxida_II 164 lvalflllGalylalktegelqerarrlalvlalvllvllvvvl....................lwtll............ 212
                                   +v++++l G  yl++   +e+++r+  + ++ +l l  +++ ++                    lw+++            
  gi|91772674|ref|YP_565366.1|  13 AVLIIILAGIFYLIMGNLSEMAARYLDIYTISVLSLSYIFATFFlspdldieskpykrwkmfriLWWPYkvifkhrglshn 93 
                                   789999***********99*******9999999888888888888999999999999999998877777999999999999 PP

               Cyt_bd_oxida_II 213 .........lvllllavlalllavlllrkkreglaflasaltvllv 249
                                            + l+l+++l+ll++ + l+++++ + ++a+++++l +
  gi|91772674|ref|YP_565366.1|  94 piigplsivINLALIVALLLLFMGVELHQGHSRYIIAATTGMILSM 139
                                   9999988643333333333333334455667777888888887765 PP

>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.06   2.7e+02      28      51 ..       5      29 ..       3      44 .. 0.74
   2 ?   10.1   0.2   0.00012      0.55      37      57 ..     106     126 ..      98     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.06
                       DUF2631 28 espkttriaGlisvlallam.liGn 51
                                   ++ t++ia li++la +++ ++Gn
  gi|91772674|ref|YP_565366.1|  5 KTHDTINIAVLIIILAGIFYlIMGN 29
                                  5678999999999988555405566 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00012
                       DUF2631  37 GlisvlallamliGnhqGhve 57 
                                   +li++l+ll+m ++ hqGh+ 
  gi|91772674|ref|YP_565366.1| 106 ALIVALLLLFMGVELHQGHSR 126
                                   79*****************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1139.99
//
Query:       gi|91772675|ref|YP_565367.1|  [L=353]
Description: magnesium and cobalt transport protein CorA [Methanococcoides burtonii DSM 6242]
Scores for complete 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-75  252.6   6.6    6.2e-75  252.2   6.6    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 !  252.2   6.6   3.4e-79   6.2e-75       2     288 ..      59     347 ..      58     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 252.2 bits;  conditional E-value: 3.4e-79
                          CorA   2 agfvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdnfli 81 
                                   ++++W++++  ++   +e++  ++gl++l+led+l++++rp++ed+++y+++v++ +  d++ +e +  ++s++l +n++i
  gi|91772675|ref|YP_565367.1|  59 KTVTWINIDGIHQVdVIEKIGLNFGLTSLVLEDILNTNQRPKLEDFENYIYVVMKMISFDEKVNELTTEQVSFILAPNLVI 139
                                   6799*******99879*************************************************9999************ PP

                          CorA  82 tvrreplealdevikrlk..deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrl 160
                                   +++++  + +d v+ rl+  + + ++ ++  l y+l+d+ivd++f +lek+ e++d +e+el ++ + + l ++ +l+r++
  gi|91772675|ref|YP_565367.1| 140 SFQERIGDTFDPVRGRLRapKGRIRKMDADYLAYALIDSIVDNYFIILEKIGEKIDFIEEELVTDPTPDTLTTIHELKREM 220
                                   *******************99999********************************************************* PP

                          CorA 161 vklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserlNrvmkvLTvlt 241
                                   + l+r+++p+re+l++l    + +l+ d  + yl+d++d++ ++++++e+++e+l+ + d+y s ls+++N+vmkvLT+++
  gi|91772675|ref|YP_565367.1| 221 ISLKRSIWPLREILNSLRM-MESSLIMDSTHVYLKDVHDHIIQIIDTIETYKEMLSGMLDIYLSSLSNKMNEVMKVLTLVA 300
                                   **************66665.77888888888************************************************** PP

                          CorA 242 aiflPlTlitGiyGmNfkglPelewsygypfvlllglmallailllf 288
                                   +if+PlT+i+G+yGmNf+++Pel+w++ yp v+l+++++ ++++l+f
  gi|91772675|ref|YP_565367.1| 301 TIFIPLTFIAGVYGMNFQHMPELGWKWSYPVVWLIMISVGMSMVLYF 347
                                   ********************************777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2389.73
//
Query:       gi|91772676|ref|YP_565368.1|  [L=306]
Description: MscS mechanosensitive ion channel [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-21   75.3   0.4    4.5e-21   75.3   0.4    1.9  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
        8.3    6.0  17.2         12    5.5  17.2    1.2  1  CbiQ        Cobalt transport protein


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.4   1.8         2   1.8e+04       2      23 ..      67      88 ..      66      91 .. 0.69
   2 !   75.3   0.4     5e-25   4.5e-21       7     110 ..     113     217 ..     107     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 2
                                  .HHHHHHHHHHHHHHHHTTT-- CS
                    MS_channel  2 kilkiliivvgilivlsllgvn 23
                                  k+++ +ii+ ++ +++  + vn
  gi|91772676|ref|YP_565368.1| 67 KLVYTIIITYTFATIFLKFTVN 88
                                  5667777777777777777666 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 5e-25
                                   HHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEE CS
                    MS_channel   7 liivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttkir 87 
                                    +++++  ++++++g+++++++  lG+++ + ++a +++i++++ ++ill++kpfkiGD++ ig+ eG V++igl+ + + 
  gi|91772676|ref|YP_565368.1| 113 FVYAFTSAVMFWQIGIDTQNIVIFLGLAATGFAFAIREIILSYFIWFILLTKKPFKIGDYICIGEEEGLVKHIGLFYVVVS 193
                                   67899999*******************************************************************998887 PP

                                   .ETTSEEEEEEHHHHHTS-EEESS CS
                    MS_channel  88 .tfdgrivtiPnsslvtsnieNls 110
                                    t+ ++   iPn+ ++++ i+N+ 
  gi|91772676|ref|YP_565368.1| 194 pTRHKEFYKIPNKVFLEKPIKNYG 217
                                   477788889*************95 PP

>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  17.2    0.0013        12      13     126 ..      37     169 ..      31     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE.................... CS
                          CbiQ  13 kliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillf..................ql 75 
                                   +l++++ ++ +l++  + + ++ +i++ +l l+  i+   +++a i  +l +++++++ +f                  ++
  gi|91772676|ref|YP_565368.1|  37 FLFFILPISAILFVDHQSWIIIPVIIINFLKLVYTIII-TYTFATI--FLKFTVNIILKMFesvskkeekillskiyigFV 114
                                   78999999*************99999988888888877.6777777..8888888888888999***************99 PP

                                   .....EECTTEEE.......E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHH CS
                          CbiQ  76 ittegefvfaggg....qisitseGllrglllalRiltllslllllalTTppeel 126
                                   + ++++++f+++g    +i i+     +g  +a+R ++l+ +  +++lT +p ++
  gi|91772676|ref|YP_565368.1| 115 YAFTSAVMFWQIGidtqNIVIFLGLAATGFAFAIREIILSYFIWFILLTKKPFKI 169
                                   9************77766666666699*********************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2230.91
//
Query:       gi|91772677|ref|YP_565369.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.7   0.4    6.3e-67  226.0   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
      9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.2e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00011   22.5   0.3       0.17   12.1   0.2    2.8  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.067   13.8   1.4        0.3   11.7   1.4    2.2  1  BST2             Bone marrow stromal antigen 2
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.7   2.6       0.55   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.36   11.2   6.9       0.52   10.7   4.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
          1   10.1   8.9        7.1    7.4   1.5    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.1    9.0   6.0       0.65   10.7   1.1    2.7  2  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.44   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  226.0   0.0   3.5e-70   6.3e-67       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772677|ref|YP_565369.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 226.0 bits;  conditional E-value: 3.5e-70
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91772677|ref|YP_565369.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91772677|ref|YP_565369.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierear..ea..eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++r  +   ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91772677|ref|YP_565369.1| 329 SENDN--QLWSKAMNIlLIDVKKSVDQIRgmSGcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **976..*********************964338888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91772677|ref|YP_565369.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.5e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91772677|ref|YP_565369.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7     8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772677|ref|YP_565369.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.6     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.5   0.0    0.0025       4.5       5      45 ..     249     287 ..     245     290 .. 0.84
   3 !   12.1   0.2   9.3e-05      0.17      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91772677|ref|YP_565369.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91772677|ref|YP_565369.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91772677|ref|YP_565369.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91772677|ref|YP_565369.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00046      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91772677|ref|YP_565369.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91772677|ref|YP_565369.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00031      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    0.9   0.1      0.34   6.2e+02      11      58 ..     392     446 ..     383     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772677|ref|YP_565369.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91772677|ref|YP_565369.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999888854444440......55555555555555555553 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?   10.7   4.5   0.00029      0.52       2      36 ..     156     213 ..     155     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91772677|ref|YP_565369.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91772677|ref|YP_565369.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCellADvCGC 213
                                   79***************99987555588888888888888887775555444446666 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 ?    3.3   0.1     0.074   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.4   1.5     0.004       7.1       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.0   0.1      0.19   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91772677|ref|YP_565369.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91772677|ref|YP_565369.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91772677|ref|YP_565369.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00036      0.65      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.6   0.3        10   1.8e+04      55      66 ..     154     165 ..     144     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772677|ref|YP_565369.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                         PLATZ  55 kssseaCetCar 66 
                                   +++ ++C +C++
  gi|91772677|ref|YP_565369.1| 154 RAEIKSCPHCGC 165
                                   334478999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 3399.36
//
Query:       gi|91772678|ref|YP_565370.1|  [L=193]
Description: hypothetical protein Mbur_0649 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1483.98
//
Query:       gi|91772679|ref|YP_565371.1|  [L=237]
Description: oxidoreductase, molybdopterin binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  123.9   0.0    8.5e-36  123.2   0.0    1.3  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain
  ------ inclusion threshold ------
      0.031   13.8   0.9      0.055   13.0   0.9    1.3  1  4HB_MCP_1       Four helix bundle sensory module for signal t


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   0.0   9.5e-40   8.5e-36       8     172 .]      81     220 ..      73     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 9.5e-40
                                   GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHHHTTB- CS
                Oxidored_molyb   8 dpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLekagvk 88 
                                    ++++ l+vdg v++pl+l+++++ ++p+v+  ++l+C++              +w     ++ +WtGv+++++L++agv+
  gi|91772679|ref|YP_565371.1|  81 IEDTYLLKVDGIVDEPLDLTYEQITSYPNVSKLIDLNCVE--------------GW----DFTGKWTGVPVSTLLNEAGVQ 143
                                   4689************************************..............79....79******************7 PP

                                   ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEEESS--- CS
                Oxidored_molyb  89 kpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkrievsdeese 169
                                    + a+ v+f++ad      +y++s++l++++e+d++LAy++n   Lp+d+G+Pl lv +  +g++++Kw++ iev +e+ e
  gi|91772679|ref|YP_565371.1| 144 -EGATTVIFYSAD------GYSTSLNLDYLIENDIILAYRLNAVTLPQDRGFPLQLVAESKYGYKWAKWITGIEVINEPYE 217
                                   .9**********9......5************************************************************* PP

                                   SHH CS
                Oxidored_molyb 170 gyw 172
                                   gyw
  gi|91772679|ref|YP_565371.1| 218 GYW 220
                                   **9 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   6.1e-06     0.055       4      29 ..      16      41 ..      14      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-06
                     4HB_MCP_1  4 irkKLillflllallliivGvvGlys 29
                                  i  K+i++f++l++++ i+G +++y+
  gi|91772679|ref|YP_565371.1| 16 IAMKMISVFIILCFFMSISGCTSYYQ 41
                                  789*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1644.43
//
Query:       gi|91772680|ref|YP_565372.1|  [L=131]
Description: methyltransferase, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-12   47.7   0.0    2.6e-12   47.2   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    4.1e-10   39.4   0.0    4.7e-10   39.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.1e-08   32.7   0.0    1.4e-07   32.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    4.6e-07   29.8   0.0    4.6e-07   29.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    3.1e-06   27.1   0.0    3.3e-06   27.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    0.00018   22.2   0.0    0.00029   21.5   0.0    1.3  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   8.8e-16   2.6e-12      31      95 ..       2      64 ..       1      65 [. 0.92

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 8.8e-16
                                  HHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11 31 lklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllv 95
                                  +  ak +a +++  ve+v +da++l f+dn fD vv+ +vl+ v+dp k ++e +Rv+kp+G+++
  gi|91772680|ref|YP_565372.1|  2 IGKAKIRAAKSD--VEMVIMDAQHLAFKDNVFDSVVMIFVLCSVPDPVKGVEEYVRVCKPEGKII 64
                                  666777777777..99**********************************************986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   1.6e-13   4.7e-10      88     164 ..       3      78 ..       1      92 [. 0.90

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.6e-13
                                   HHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHH CS
               Ubie_methyltran  88 gekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsq 164
                                   g++k++  +k+++e++  +a++L f+d+ fD+v + f l  v+D  k+++e  rv kp G+++ le  + + +++s+
  gi|91772680|ref|YP_565372.1|   3 GKAKIR-AAKSDVEMVIMDAQHLAFKDNVFDSVVMIFVLCSVPDPVKGVEEYVRVCKPEGKIINLEHVRSKYQIISF 78 
                                   566664.6899*******************************************************99998888765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   4.7e-11   1.4e-07      34      97 .]       2      61 ..       1      61 [. 0.84

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.7e-11
                                  HHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25 34 leaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97
                                  + +a+ ra  ++ +ve+v +da++l f+d+ fD vv++++l+ +  +d  k ++e  rv+kp+G
  gi|91772680|ref|YP_565372.1|  2 IGKAKIRA--AKSDVEMVIMDAQHLAFKDNVFDSVVMIFVLCSV--PDPVKGVEEYVRVCKPEG 61
                                  55555555..5569***********************9776665..5778************99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.5e-10   4.6e-07      69     132 ..      17      80 ..       1     120 [. 0.83

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.5e-10
               Methyltransf_23  69 dqfdeqeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllld 132
                                   + +d+q  a++++ fd +v+++vl++vpdp + +    + +kp+G ++ +e+ +s ++  ++++
  gi|91772680|ref|YP_565372.1|  17 VIMDAQHLAFKDNVFDSVVMIFVLCSVPDPVKGVEEYVRVCKPEGKIINLEHVRSKYQIISFME 80 
                                   4567889999******************************************999988777765 PP

>> Methyltransf_31  Methyltransferase 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   3.3e-06      41     120 ..       2      84 ..       1     115 [. 0.84

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-09
               Methyltransf_31  41 ielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileeiervlkpggilliedpr........ 113
                                   i +A+ +a+k     ve+ + d+++l   ++d+ fD ++   vl+ ++dp k  ee  rv kp+g ++  ++         
  gi|91772680|ref|YP_565372.1|   2 IGKAKIRAAKSD---VEMVIMDAQHLA--FKDNVFDSVVMIFVLCSVPDPVKGVEEYVRVCKPEGKIINLEHVrskyqiis 77 
                                   667888887544...67**********..**************************************98888755555555 PP

               Methyltransf_31 114 llaelpa 120
                                    ++el+ 
  gi|91772680|ref|YP_565372.1|  78 FMEELIN 84 
                                   5555554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   9.6e-08   0.00029      58      99 .]      21      63 ..       2      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.6e-08
               Methyltransf_12 58 lldldgg.ssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99
                                  +  l+ + + fD vv+++vl+ ++d+ + +++  +++kp+G++
  gi|91772680|ref|YP_565372.1| 21 AQHLAFKdNVFDSVVMIFVLCSVPDPVKGVEEYVRVCKPEGKI 63
                                  3323333469*******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 942.05
//
Query:       gi|91772681|ref|YP_565373.1|  [L=104]
Description: hypothetical protein Mbur_0652 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0063   16.5   0.0      0.008   16.1   0.0    1.3  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.096   12.8   0.0        0.5   10.5   0.0    2.0  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     9e-07     0.008      34      72 ..      64     102 ..      38     104 .] 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9e-07
                        HTH_45  34 kllnkYLdmLvekglikkskekYvlTekGlelleklkel 72 
                                   ++l+  +d+L + +++  +++ ++lT+ G ++l ++k  
  gi|91772681|ref|YP_565373.1|  64 NTLKYHMDFLKNANIVVIKEDLFRLTDSGVDMLASIKSH 102
                                   5677779***************************99875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.6e-05       0.5       6      54 ..      32      79 ..      28      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.6e-05
                                  HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                        HTH_20  6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                  A +hP Rr i   + +  g   + +++++++++ntl yH++ L  a +v
  gi|91772681|ref|YP_565373.1| 32 AASHPIRRQIVISI-GVFGKAEAGIKAEVETDDNTLKYHMDFLKNANIV 79
                                  55667777776666.666666777999999***********99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 665.15
//
Query:       gi|91772682|ref|YP_565374.1|  [L=320]
Description: N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-133  444.7   0.0     2e-133  444.5   0.0    1.0  1  MCH       Cyclohydrolase (MCH)
  ------ inclusion threshold ------
      0.078   13.0   0.0        1.3    9.1   0.0    2.3  2  HTH_54    ParA helix turn helix domain


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 !  444.5   0.0  2.2e-137    2e-133       1     311 []       3     315 ..       3     315 .. 1.00

  Alignments for each domain:
  == domain 1  score: 444.5 bits;  conditional E-value: 2.2e-137
                                   -HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEEEEES CS
                           MCH   1 SvnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpavevstd 81 
                                   Svne++l +++e+l+ +e+++ie++ lengat+iD+Gv++eGg++AG++l+++cl++Lae+s+++ + +g+++pa++++td
  gi|91772682|ref|YP_565374.1|   3 SVNEKGLAIIDEMLDWEEDVKIESKVLENGATIIDCGVNVEGGYDAGMYLSRLCLADLAEISYTKVDLEGLAVPAIQIATD 83 
                                   8******************************************************************************** PP

                                   SHHHHHTTTTS--EEEEETTEEEEEESTTHHHHTS.HHHHHHHT-----S-EEEEEESSS---HHHHHHHHHHHTS-GGGE CS
                           MCH  82 hPvlacLasqkAgWelsaekffalgsGPaRalaak.eelfeelgyedeadaavlvlesdklPdeevvekvaeecgvepenv 161
                                   hP++ac+asq+AgW+++++++f++gsGPaR l  k +el+ee+gy+deadaavlv+esdklP+ee+ve++a++c+vep+nv
  gi|91772682|ref|YP_565374.1|  84 HPTIACMASQYAGWRIAVGDYFGMGSGPARGLGLKpKELYEEIGYKDEADAAVLVMESDKLPTEEIVEYIAKHCSVEPQNV 164
                                   ********************************************************************************* PP

                                   EEEEE-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH-EEEEEES....T CS
                           MCH 162 tllvaptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYggrvhltve.aede 241
                                   +++vapt+S+aGsvq++aRvve+++hkle++g+d++ki+s++g+aPiap+ +d++k+mg+tnd+i+Y+g++++tve +++e
  gi|91772682|ref|YP_565374.1| 165 FIAVAPTSSIAGSVQISARVVETGIHKLESIGYDINKIKSGFGVAPIAPIVGDDTKCMGSTNDCIIYCGETYYTVEdGNAE 245
                                   ****************************************************************************88999 PP

                                   THHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHHHHHT CS
                           MCH 242 eaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneellaesf 311
                                   e+ed++kk pss+s+d+gkpF+++fkea++df+k+d+ +F+pA++t+ndl+++k+f+ G++n+ +l esf
  gi|91772682|ref|YP_565374.1| 246 ELEDFVKKAPSSTSRDFGKPFYTTFKEAGFDFFKVDAGMFAPAKITINDLKSKKSFTSGRINPGILLESF 315
                                   *********************************************************************9 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00015       1.3      29      64 ..     170     205 ..     147     208 .. 0.84
   2 ?    1.3   0.0     0.041   3.7e+02      51      76 ..     270     295 ..     251     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00015
                        HTH_54  29 skaalaklpklsrrkvdkavsemeaeGyefekkeag 64 
                                     +++a   ++s r v++ ++++e+ Gy+++k ++g
  gi|91772682|ref|YP_565374.1| 170 PTSSIAGSVQISARVVETGIHKLESIGYDINKIKSG 205
                                   5567888899*********************98876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.041
                        HTH_54  51 meaeGyefekkeagstekYaltiqnv 76 
                                    +++G++f k +ag     ++ti++ 
  gi|91772682|ref|YP_565374.1| 270 FKEAGFDFFKVDAGMFAPAKITINDL 295
                                   5799******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2312.56
//
Query:       gi|91772683|ref|YP_565375.1|  [L=157]
Description: hypothetical protein Mbur_0654 [Methanococcoides burtonii DSM 6242]
Scores for 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-53  177.9   0.2      1e-52  177.7   0.2    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 !  177.7   0.2   5.9e-57     1e-52       2     140 ..       9     150 ..       8     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.7 bits;  conditional E-value: 5.9e-57
                                   HHHHHHHHHHHHTTT-SEEEEEE-TTTTHHHHHHHHHHTTT..SEEEEEETT-GGG-EEEEEETTEEEEEEE-.-S-EEEE CS
                       DUF2124   2 glsgllrefkelvkesekivfvGspgvCtpfaellayaiRdlekelvfvpdldlekarklevtdvGmqleeeaeeekadvv 82 
                                   g++gll++f++lvk+s+ki+f+G++g+Ctpfael+ay iR+++ e+ f+p+++ e+ar++++t++Gmq+++++ + +ad++
  gi|91772683|ref|YP_565375.1|   9 GVGGLLTSFRKLVKDSNKIMFIGTAGFCTPFAELMAYGIRNTNIEIGFIPETSPEEAREIVKTSFGMQIGDNI-DYHADTI 88 
                                   99***********************************************************************.******* PP

                                   EEEGGGGSTTTS--HHHHHHHHHHH....EEEEEEEEEETTHHHHTTHHHHS--SEEEEEEE CS
                       DUF2124  83 vllGGlampkikveaedvkelieki....ekkkviGvcfmsifekagWldkidFdliidakl 140
                                   vllGGl+mpk++++ ++vke++ek+    +++++iGvcf+s fe+++W + i+Fd+iid+++
  gi|91772683|ref|YP_565375.1|  89 VLLGGLSMPKMGINLNAVKETMEKVfentDEGMTIGVCFQSAFENQCWIGPIEFDHIIDSDI 150
                                   ************************99988899****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1181.41
//
Query:       gi|91772684|ref|YP_565376.1|  [L=337]
Description: methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-64  215.4   0.0      9e-64  214.9   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.044   13.7   0.0    1.7  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
      0.041   13.5   0.0      0.073   12.6   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.12   12.3   0.0       0.23   11.4   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
       0.19   11.4   0.0        0.9    9.2   0.0    1.9  2  Cons_hypoth95    Conserved hypothetical protein 95


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 !  214.9   0.0   2.5e-67     9e-64       2     199 .]      88     284 ..      87     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.9 bits;  conditional E-value: 2.5e-67
                                   EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS CS
                        Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskv 81 
                                   +++ iGdv+i+++++e+++y+++++e +l ++ ++++v+r+ +  +g fR++e e++ G++ tet++kEngc fk+Dv k 
  gi|91772684|ref|YP_565376.1|  88 GWHLIGDVIIIHIPAEIQNYRTEVAEKLLLMNpRCNCVVRDLGI-KGPFREPEREIIIGNK-TETMEKENGCLFKIDVMKL 166
                                   699*****************************9********997.****************.******************* PP

                                   ---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG CS
                        Met_10  82 yfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgre 162
                                   +fs+++ aE++r+ kl  +g+vVvd+fAGiG+f+ip+a+++++k+v++i+lnP s+ yl eni+lN+ e+v+++i++ +++
  gi|91772684|ref|YP_565376.1| 167 MFSKGNLAEKKRMSKL-GKGDVVVDMFAGIGYFSIPLAVHGNPKKVYSIELNPVSYGYLLENIRLNHQEDVIEAINGNCKD 246
                                   ************9876.78************************************************************** PP

                                   ---TT-EEEEEE--TTTGGGGHHH.HHHHEEEEEEEEE CS
                        Met_10 163 vireqladrvvmnlpksaieFldk.vlaalkdggvihy 199
                                   v++  +adrv+m+++ +++e+l + + a+ k+gg  hy
  gi|91772684|ref|YP_565376.1| 247 VTPVGIADRVIMGYVGTTHEYLRQgISAIRKEGGTLHY 284
                                   ************************78888888999998 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 ?   13.7   0.0   1.2e-05     0.044       1      43 [.       3      49 ..       3      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                  EEEEEGGGHHHHHHHHHHTT-B-TTS--EEE....TTEEEEEB-S-- CS
                        Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksd....ddylyIPvkeep 43
                                  ++ Vp   +E +  kL+e ++Ld+ +KI       +   +IP+  ++
  gi|91772684|ref|YP_565376.1|  3 AVVVPIGSVEAIMAKLAESNVLDKARKIVVVdsleGRMAEIPILCDV 49
                                  68899999********************9985666666666666555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05     0.073       3      61 ..     187     247 ..     185     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
               Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfel 61 
                                   v++D+f+G G  +i +a +   +kv++ie n+       +N ++   +d i  + g+++++
  gi|91772684|ref|YP_565376.1| 187 VVVDMFAGIGYFSIPLAVHgnPKKVYSIELNPVSYGYLLENIRLNHQEDVIEAINGNCKDV 247
                                   79***************9955579**********************************984 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.3e-05      0.23      12      90 ..     182     259 ..     176     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
               Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaG 90 
                                   + kg++v+D  +  gy +i l+ +g+ kkv+ +++n+ ++    eni+ ++ ed ie++ ++  ++   + +d v++ G
  gi|91772684|ref|YP_565376.1| 182 LGKGDVVVDMFAGIGYFSIPLAVHGNPKKVYSIELNPVSYGYLLENIRLNHQEDVIEAINGNCKDVTPVGIADRVIM-G 259
                                   5578999999999**********************************************999877665454555554.3 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.27   9.5e+02     130     160 ..      12      42 ..       8      59 .. 0.76
   2 ?    9.2   0.0   0.00025       0.9      40      97 ..     183     241 ..     171     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.27
                                   HHHHHHHHHTT-EEEEEEEEEEEECCSSS-- CS
                 Cons_hypoth95 130 eevlelleekkllkenalvvvetekekelpe 160
                                   e+++++l+e+++l +   +vv  + e  + e
  gi|91772684|ref|YP_565376.1|  12 EAIMAKLAESNVLDKARKIVVVDSLEGRMAE 42 
                                   7889999999999998887776656555554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00025
                                   HCC-EEEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEE CS
                 Cons_hypoth95  40 iegarvLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelkleeetaelk 97 
                                   ++g  v+D+faG G  ++  A+  + kk++ +e ++  +  l en++  + e+ +++++
  gi|91772684|ref|YP_565376.1| 183 GKGDVVVDMFAGIGYFSIPlAVHGNPKKVYSIELNPVSYGYLLENIRLNHQEDVIEAIN 241
                                   678899***********9757888899*******************9988776555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2456.49
//
Query:       gi|91772685|ref|YP_565377.1|  [L=244]
Description: 4-vinyl reductase, 4VR [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-14   51.3   0.7    1.8e-13   50.3   0.6    1.6  2  V4R       V4R domain
    4.5e-10   39.2   0.0    7.5e-10   38.5   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00034   20.5   0.0    0.00052   19.8   0.0    1.3  1  MarR_2    MarR family
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.028   14.3   0.1    1.5  1  MarR      MarR family
      0.017   15.1   0.0      0.029   14.4   0.0    1.3  1  HTH_20    Helix-turn-helix domain
       0.02   14.7   0.0      0.033   14.0   0.0    1.3  1  HTH_IclR  IclR helix-turn-helix domain
      0.049   13.3   0.2        6.4    6.5   0.1    2.2  2  TRAPP     Transport protein particle (TRAPP) component
      0.051   13.8   0.0      0.077   13.2   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
      0.051   14.0   0.1      0.098   13.1   0.1    1.5  1  HTH_40    Helix-turn-helix domain
       0.14   12.6   0.1       0.28   11.7   0.1    1.5  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.3   1.1e+04      28      36 ..     156     164 ..     154     166 .. 0.60
   2 !   50.3   0.6     1e-16   1.8e-13       3      60 ..     186     243 ..     184     244 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.3
                                   HHHHHHHHH CS
                           V4R  28 llagalsel 36 
                                   +++g+++e 
  gi|91772685|ref|YP_565377.1| 156 YIEGLFEEV 164
                                   566666654 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 1e-16
                                   EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEE CS
                           V4R   3 lsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFev 60 
                                   ++i++s+ ++g +++++ +C + +G+l g+  ++++  +++ E+eC+++Gh+hC+F+ 
  gi|91772685|ref|YP_565377.1| 186 INIKDSFICEGTKNIGQTLCSFNEGILQGIILNKMNLQCNIVETECCGTGHGHCLFVM 243
                                   789*****************************************************85 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 !   38.5   0.0   4.2e-13   7.5e-10       2      46 ..      22      66 ..      21      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.2e-13
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  p +l+I+ lL e  +++ ++++++g+ +st+S HLk L+ ++L+e
  gi|91772685|ref|YP_565377.1| 22 PVKLQIMELLYETAQSFDDIVKHTGKAKSTISVHLKDLKASNLLE 66
                                  889***************************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.9e-07   0.00052      11      61 ..      28      75 ..      19      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.9e-07
                                  HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  +  L+       +  ++++++g  ks++s +lk+L a  L+e+  +p+D+R
  gi|91772685|ref|YP_565377.1| 28 MELLYETA---QSFDDIVKHTGKAKSTISVHLKDLKASNLLEEHVDPDDRR 75
                                  44455555...4899***********************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.6e-05     0.028       9      58 ..      28      76 ..      22      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                  HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                  +++ly + ++s  ++ k+ g  kst++  l+ L   +l+e   +p+DrR+
  gi|91772685|ref|YP_565377.1| 28 MELLY-ETAQSFDDIVKHTGKAKSTISVHLKDLKASNLLEEHVDPDDRRK 76
                                  44444.4589999************************************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 ?   14.4   0.0   1.6e-05     0.029      10      56 ..      22      67 ..      17      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  Pv + i+ +L  + ++++ ++ +  + +k+t+s HL+ L    L+e 
  gi|91772685|ref|YP_565377.1| 22 PVKLQIMELL-YETAQSFDDIVKHTGKAKSTISVHLKDLKASNLLEE 67
                                  999*******.****************************99999985 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 ?   14.0   0.0   1.8e-05     0.033       6      49 ..      25      66 ..      24      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  l+i+++l e++q   + ++ ++tg +kSt + +L+ L    ++e
  gi|91772685|ref|YP_565377.1| 25 LQIMELLYETAQS--FDDIVKHTGKAKSTISVHLKDLKASNLLE 66
                                  89**********6..********************999988887 PP

>> TRAPP  Transport protein particle (TRAPP) component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.016        28      26      42 ..     137     153 ..     112     157 .. 0.82
   2 ?    6.5   0.1    0.0036       6.4      67     128 ..     160     229 ..     156     244 .] 0.71

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                         TRAPP  26 LekmGyrvGlrllelll 42 
                                   +e++G ++G++++e ++
  gi|91772685|ref|YP_565377.1| 137 MENIGQDIGMKIAETFT 153
                                   79************775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0036
                         TRAPP  67 lfgkqidnlktnhrgeyvltdnefpltrf....velpke..ls....ylaflcGiirGa.LenlgfpakVtah 128
                                   lf+   d  ++n+ g++++   ++++ ++    +    e   +     ++f  Gi++G+ L+++++++++  +
  gi|91772685|ref|YP_565377.1| 160 LFEEVTDYWQKNEMGKLTVRSYDPLIINIkdsfI--C-EgtKNigqtLCSFNEGILQGIiLNKMNLQCNIVET 229
                                   7889999999999999999999996666644332..2.123113445999********648999999987653 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 ?   13.2   0.0   4.3e-05     0.077       1      59 [.      23      80 ..      23     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                        HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtll 59
                                  v+l+++ +L+++ + +f ++ + ++  ++ +svhlk L++ + +e + + ++++++t +
  gi|91772685|ref|YP_565377.1| 23 VKLQIMELLYETAQ-SFDDIVKHTGKAKSTISVHLKDLKASNLLEEHVDPDDRRKKTYV 80
                                  7899***9998765.79*************************99999999999888865 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.4e-05     0.098       8      79 ..      31     100 ..      24     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-05
                        HTH_40   8 lleeglsieeIAkerglkesTIegHLaelieegeeidlerlvse.eeekeIeeaiekvgseklkpikealpee 79 
                                   l+e  +s+++I k  g ++sTI  HL +l  ++    le+ v++ +++k+    + ++   + kp++++  ++
  gi|91772685|ref|YP_565377.1|  31 LYETAQSFDDIVKHTGKAKSTISVHLKDLKASNL---LEEHVDPdDRRKKTYVMCSQYTACSQKPVFDHYRKN 100
                                   56999***********************999965...677775548888888888888888888888887655 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 ?   11.7   0.1   0.00016      0.28      21      62 ..      38      79 ..      22      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                        HTH_27 21 ladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                                    d+++ +   +s+is  lk L +  L+e+  d+ drr k++
  gi|91772685|ref|YP_565377.1| 38 FDDIVKHTGKAKSTISVHLKDLKASNLLEEHVDPDDRRKKTY 79
                                  478888889999***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1822.24
//
Query:       gi|91772686|ref|YP_565378.1|  [L=229]
Description: hypothetical protein Mbur_0657 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  283.5   0.0    1.3e-84  283.3   0.0    1.0  1  DUF2110   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2110  Uncharacterized protein conserved in archaea (DUF2110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.3   0.0     7e-89   1.3e-84       1     223 []       6     225 ..       6     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 283.3 bits;  conditional E-value: 7e-89
                       DUF2110   1 latkvYdareralesleslvenelkdLdveleisvreddfvkvtleGedeevaanllreefgeitkeveegevyvGtlesl 81 
                                   l++k+Y++ er+l+s++ ++enelkdLd+++e+s+  d++++v  +G+d e+a n+l+e+fg++++ v+++ vy+G+++s+
  gi|91772686|ref|YP_565378.1|   6 LTIKIYGNVERSLSSASFMLENELKDLDAKAEVSLGPDGWLQVAATGDDGEFAINFLKEKFGTPVTYVDDKAVYRGFISSI 86 
                                   578****************************************************************************** PP

                       DUF2110  82 dedgfvldigvevripkdelkpLgegspeqiaerFGlvqhlpleveveeveeeekeiearltdeqvdrlyewkkgkedrli 162
                                   +edg+++dig++++i+++el+ Lg g+  qia+rFGl++hlp+ ++v   ++e++++ a++t++qvd +++wkk ++drl+
  gi|91772686|ref|YP_565378.1|  87 NEDGITVDIGITLKIKSSELSVLGAGTSPQIASRFGLIPHLPVYIRV--LKQEDGTF-ASFTKKQVDLFWSWKKFPTDRLV 164
                                   ***********************************************..66777888.*********************** PP

                       DUF2110 163 vnsatrsevkaalnraGhardivtverlglleqsvvcredtdapGlvaeiGpylpaelkvv 223
                                   vns+trse+k+a++++Gh+rdi+++erlglle+ vvcre+td+pG+vaeiGp+l+ae++v+
  gi|91772686|ref|YP_565378.1| 165 VNSVTRSELKSAIKKKGHGRDIYGIERLGLLENLVVCREKTDGPGIVAEIGPLLNAEIGVI 225
                                   **********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 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:                        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 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1736.51
//
Query:       gi|91772687|ref|YP_565379.1|  [L=184]
Description: MarR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00012   22.4   0.0    0.00047   20.6   0.0    2.0  2  HTH_27    Winged helix DNA-binding domain
    0.00095   19.0   0.4     0.0026   17.6   0.1    1.7  2  DUF4364   Domain of unknown function (DUF4364)
     0.0049   16.8   0.0      0.012   15.5   0.0    1.6  1  MarR      MarR family
     0.0061   16.5   0.1      0.011   15.6   0.1    1.4  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
       0.11   12.6   0.0        0.3   11.2   0.0    1.7  2  DUF2250   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.3e-07   0.00047      18      68 .]      19      66 ..       6      66 .. 0.85
   2 ?   -1.8   0.0       1.2   4.5e+03      22      39 ..     163     180 ..     148     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-07
                        HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  r  ++ + +  n + +h+ ++l++++e GLv+      ++r k v+lT+kG
  gi|91772687|ref|YP_565379.1| 19 RTYASVITKEINSTFAHTTKVLSRMEEDGLVQ-FS--FEGRIKYVELTEKG 66
                                  5566889999999******************3.33..569**********9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                        HTH_27  22 adlcgrlnvedshisysl 39 
                                   ++++++++++   +s+ l
  gi|91772687|ref|YP_565379.1| 163 TEVIRAYDTTRDVFSSLL 180
                                   678888887766666655 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   7.1e-07    0.0026      26      77 ..      26      77 ..      20      91 .. 0.88
   2 ?   -1.7   0.0      0.58   2.1e+03     142     160 ..     110     128 ..     103     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.1e-07
                       DUF4364 26 leneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfenri 77
                                  +++   ++ + +++ls ++e+gl++ + +   ++ ++TekG ++++++++ i
  gi|91772687|ref|YP_565379.1| 26 TKEINSTFAHTTKVLSRMEEDGLVQFSFEGRIKYVELTEKGTNVVSILKDLI 77
                                  555566788999***************99*******************9987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.58
                       DUF4364 142 aicknwkknseeiYskile 160
                                   +i k+ + + e+iY+++++
  gi|91772687|ref|YP_565379.1| 110 DIVKKLRFKIESIYKELID 128
                                   5778888888999998886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.4e-06     0.012       7      49 ..       9      51 ..       5      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-06
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  ++L  ++  g  + s + k ++ + +++t+vl r+e++Gl++ 
  gi|91772687|ref|YP_565379.1|  9 LVLLAIWFYGRTYASVITKEINSTFAHTTKVLSRMEEDGLVQF 51
                                  588899999999*****************************86 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.2e-06     0.011      21      72 ..      21      76 ..      10      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-06
                        HTH_45 21 kkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkel 72
                                    + i ++ n ++  + k L+ + e gl+    + + +  +lTekG ++++ lk+l
  gi|91772687|ref|YP_565379.1| 21 YASVITKEINSTFAHTTKVLSRMEEDGLVqfsfEGRIKYVELTEKGTNVVSILKDL 76
                                  567799999********************776444444557********9999876 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.3e-05       0.3      21      69 ..      18      66 ..       4      71 .. 0.87
   2 ?   -2.5   0.0       1.6   5.8e+03      35      45 ..     115     125 ..     100     131 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.3e-05
                       DUF2250 21 nvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKk 69
                                  +  Ya  i+ke++  + + +++l ++ee GL++   +  ik+ e   K 
  gi|91772687|ref|YP_565379.1| 18 GRTYASVITKEINSTFAHTTKVLSRMEEDGLVQFSFEGRIKYVELTEKG 66
                                  5679*****************************9999999999877775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                       DUF2250  35 pleevrellkk 45 
                                    + ++++++k+
  gi|91772687|ref|YP_565379.1| 115 LRFKIESIYKE 125
                                   23344455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1444.44
//
Query:       gi|91772688|ref|YP_565380.1|  [L=388]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-105  351.8   0.0   5.6e-105  351.6   0.0    1.0  1  TRM             N2,N2-dimethylguanosine tRNA methyltransferas
  ------ inclusion threshold ------
        2.7    7.5   5.3         14    5.2   0.1    3.0  3  zf-ribbon_3     zinc-ribbon 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 !  351.6   0.0  6.3e-109  5.6e-105      15     376 .]      28     386 ..      10     386 .. 0.93

  Alignments for each domain:
  == domain 1  score: 351.6 bits;  conditional E-value: 6.3e-109
                                   -TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-.......EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHH CS
                           TRM  15 skkeeVFYNPvqefnRDlsvlvirqlellkkklgek.......ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAve 88 
                                   +++++VFYNP +e nRD+sv++    ++  k++  k       i++lda+sasG+R++R a E  g  ++l ND s+ A+ 
  gi|91772688|ref|YP_565380.1|  28 PSEAPVFYNPHMELNRDISVAAT---SACAKRILLKkdmelkdITYLDAMSASGIRGLRIANE-VGITSIL-NDWSDDAYG 103
                                   5789*****************94...33333333223445555********************.5777887.********* PP

                                   HHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHH CS
                           TRM  89 likeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclr 169
                                   li eN+ l  v++i ++  ++Anvl+  +++rf+++DlDPfGsp+p+ld+a +s+ +  +L vTaTDta+L+Ga+ ++++r
  gi|91772688|ref|YP_565380.1| 104 LILENIGLTGVSDIAEATCKNANVLM--HERRFNIVDLDPFGSPTPYLDAATRSAVH--FLEVTATDTAPLCGAHFNSGMR 180
                                   **************************..899************************99..********************** PP

                                   HHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--EEE CS
                           TRM 170 kYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClseek 250
                                   kY av+l++e+  E+++Rill+++are ak +k ++plls+++ +Yvr +++vk+ga+ ++k ++ lg++ hC +C ++e 
  gi|91772688|ref|YP_565380.1| 181 KYAAVPLNNEFHSEMGVRILLGKIARELAKHDKGMTPLLSHATRHYVRTYLQVKKGAKLADKAFKDLGFLSHCEHCGHREI 261
                                   ******************************************************************************999 PP

                                   E--GGG.--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHH CS
                           TRM 251 vkglak.fkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyydlsqlasv 330
                                    +g+a  ++ +c+ cg+ + +aGPlwlg+l++ ++ +evl e+e+ ++  +k++ kkl+ ++++E ld p++yd + ++++
  gi|91772688|ref|YP_565380.1| 262 FHGMAIsISDHCSSCGNDVYIAGPLWLGQLHEPQYCDEVLLELED-RSLGTKEQAKKLILACRDE-LDIPFFYDQHVICKM 340
                                   9999852579**********************************9.577789*************.*************** PP

                                   HT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHHH CS
                           TRM 331 lklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevlr 376
                                   + +s+p ++ +++al+e g +vsrtH+++ ++kT+a+++++ +vlr
  gi|91772688|ref|YP_565380.1| 341 IGVSAPAMDMFIAALRETGANVSRTHFTGISFKTDAKIDTIKDVLR 386
                                   *******************************************996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.58   5.2e+03       8      11 ..     171     174 ..     169     180 .. 0.63
   2 ?    3.3   0.6    0.0064        57      18      25 ..     252     259 ..     251     259 .. 0.81
   3 ?    5.2   0.1    0.0016        14       4      11 ..     272     280 ..     270     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.58
                   zf-ribbon_3   8 CGap 11 
                                   CGa+
  gi|91772688|ref|YP_565380.1| 171 CGAH 174
                                   8883 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0064
                   zf-ribbon_3  18 vCpyCGtk 25 
                                   +C +CG++
  gi|91772688|ref|YP_565380.1| 252 HCEHCGHR 259
                                   79999985 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0016
                   zf-ribbon_3   4 rCPnCGa.p 11 
                                   +C++CG+ +
  gi|91772688|ref|YP_565380.1| 272 HCSSCGNdV 280
                                   899999855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2332.17
//
Query:       gi|91772689|ref|YP_565381.1|  [L=154]
Description: hypothetical protein Mbur_0660 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0034   17.5   0.0     0.0046   17.1   0.0    1.2  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 !   17.1   0.0   2.5e-07    0.0046      32     104 .]      80     153 ..      60     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-07
                  Cupredoxin_1  32 fePskievkagekvklkik.nkdktp.eefesed.lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                                     P+ +e+++g  v  + + n +++   +++sed l+e+  +++g  ++ t+   ++G+Y++    ++ + G++iV
  gi|91772689|ref|YP_565381.1|  80 SRPALLEINKGDAVFWNNRqNSGDRKrFTLVSEDgLWEDRSINYGVPFNYTF--TEEGTYNYSILGQPRMSGTVIV 153
                                   569999*****988765440444443455566668*****************..999*****999999999***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1056.44
//
Query:       gi|91772690|ref|YP_565382.1|  [L=192]
Description: MerR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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-14   51.0   0.1    1.5e-13   50.2   0.1    1.4  1  Cupin_2       Cupin domain
    3.9e-08   33.2   0.1    5.2e-08   32.8   0.1    1.2  1  HTH_3         Helix-turn-helix
    1.5e-07   31.4   0.1    2.3e-07   30.7   0.1    1.3  1  HTH_19        Helix-turn-helix domain
    3.9e-07   30.3   0.0    5.6e-07   29.8   0.0    1.2  1  HTH_31        Helix-turn-helix domain
      9e-07   29.2   0.0    1.3e-06   28.7   0.0    1.3  1  HTH_26        Cro/C1-type HTH DNA-binding domain
    0.00096   19.0   0.5     0.0017   18.2   0.5    1.4  1  HTH_25        Helix-turn-helix domain
     0.0013   18.4   0.0     0.0024   17.5   0.0    1.4  1  Cupin_3       Protein of unknown function (DUF861)
     0.0037   17.2   0.1     0.0058   16.5   0.1    1.2  1  AraC_binding  AraC-like ligand binding domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.1   6.8e-17   1.5e-13      14      64 ..     133     182 ..     122     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 6.8e-17
                                   ECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS- CS
                       Cupin_2  14 hrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdep 64 
                                    +H+ge ef+yVleG +el ++  +++l++Gds+y ++ +pH+++ +g+e 
  gi|91772690|ref|YP_565382.1| 133 SSHEGE-EFIYVLEGDIELSYGKDKHTLTKGDSIYYDSIVPHDLHAAGKES 182
                                   46****.*****************************************774 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   2.3e-11   5.2e-08       1      53 [.      11      63 ..      11      65 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.3e-11
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53
                                  +++ R+ + ++ eeLA ++   +  i ++E+Ge +Psl+ l+k+a+aLgv l 
  gi|91772690|ref|YP_565382.1| 11 IRQFREDRSMTVEELANESQSNVELIEKLEKGELIPSLTPLLKIARALGVRLG 63
                                  89************************************************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 !   30.7   0.1     1e-10   2.3e-07       1      63 [.       8      69 ..       8      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1e-10
                        HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqge 63
                                  Ge+++++Re + +t eela++ + +   i ++E+g+   ps   llkia+alg+ l  +l+ +
  gi|91772690|ref|YP_565382.1|  8 GENIRQFREDRSMTVEELANESQSNVELIEKLEKGEL-IPSLTPLLKIARALGVRLGTFLDDT 69
                                  9**********************************87.8888889*********999998865 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.5e-10   5.6e-07       3      57 ..       8      61 ..       6      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.5e-10
                        HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                  G+  r++Re + ++ ee+A  ++  +  + +lE G+  +ps+  l ++aralg+ 
  gi|91772690|ref|YP_565382.1|  8 GENIRQFREDRSMTVEELANESQSNVELIEKLEKGEL-IPSLTPLLKIARALGVR 61
                                  7789*********************************.7**************95 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 !   28.7   0.0   5.9e-10   1.3e-06       1      62 [.      10      70 ..      10      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.9e-10
                        HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleyep 62
                                  ++r+   dr +t+ eLa  +  +   +++l kg+   +sl+ L ki++aLg+++g  l+ +p
  gi|91772690|ref|YP_565382.1| 10 NIRQFREDRSMTVEELANESQSNVELIEKLEKGEL-IPSLTPLLKIARALGVRLGTFLDDTP 70
                                  799999****************************8.********************999887 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.5   7.5e-07    0.0017       2      38 ..      11      45 ..      10      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.5e-07
                                  HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TTS CS
                        HTH_25  2 LraaRearglsleevaketkIrkdylealEeddfdal 38
                                   r+ Re r++++ee+a+e +  ++++e+lE++  +++
  gi|91772690|ref|YP_565382.1| 11 IRQFREDRSMTVEELANESQSNVELIEKLEKG--ELI 45
                                  5999***************************9..455 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06    0.0024      24      56 ..     136     167 ..     123     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                   SSEEEEEEEECEEEEEETTTEEEEEETTEEEEE CS
                       Cupin_3  24 eedEfcyileGevkvtpeggetvelraGDlvvl 56 
                                   e +Ef+y+leG +++   g  +++l +GD++++
  gi|91772690|ref|YP_565382.1| 136 EGEEFIYVLEGDIELSY-GKDKHTLTKGDSIYY 167
                                   559**************.7778********997 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.6e-06    0.0058      21      66 ..     135     180 ..     131     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
                                   T-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TT CS
                  AraC_binding  21 hdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdse 66 
                                   h+  +++yv+eG   l+++   + l++Gd +     +pHd+++++ 
  gi|91772690|ref|YP_565382.1| 135 HEGEEFIYVLEGDIELSYGKDKHTLTKGDSIYYDSIVPHDLHAAGK 180
                                   8899**************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1364.87
//
Query:       gi|91772691|ref|YP_565383.1|  [L=137]
Description: thioesterase superfamily protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-08   33.4   0.0    7.1e-08   32.7   0.0    1.4  1  4HBT         Thioesterase superfamily
    2.3e-07   31.3   0.0    2.8e-07   31.1   0.0    1.1  1  4HBT_2       Thioesterase-like superfamily
    0.00047   19.5   0.0     0.0083   15.4   0.0    2.0  2  Acyl-ACP_TE  Acyl-ACP thioesterase


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 !   32.7   0.0   1.2e-11   7.1e-08       2      75 ..      17      96 ..      16     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.2e-11
                                  SSB-HHHHHHHHHHHHHHHHHHTTST......TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                          4HBT  2 GvvhgGvylallDeaagaalrslggr......gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75
                                  G+v++ v+  +++ a+  ++r    +      + ++  +++  dfl  + ++ ++++++ v rlg++s+++++e ++ ++
  gi|91772691|ref|YP_565383.1| 17 GHVNNTVLPGWFELARNPIFRMFEPDldlspeKWGLIMARIDFDFLGEIFFDGDVEIRTYVKRLGNKSFTLHHEAWQRGE 96
                                  9*****************************99888889999999********************************9876 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   4.7e-11   2.8e-07       2     117 ..       9     120 ..       8     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.7e-11
                        4HBT_2   2 rpndvDlnghlnnarylryleearvkflertglksrsiarrgiglilssahvryrrplkfpdrltvefrvididaktliie 82 
                                   r++d+D +gh+nn     ++e ar   +   + + ++ + +++gli++++  ++  +++f   +++++ v +   k++ + 
  gi|91772691|ref|YP_565383.1|   9 RFGDIDGLGHVNNTVLPGWFELARNPIFRMFEPDLDLSP-EKWGLIMARIDFDFLGEIFFDGDVEIRTYVKRLGNKSFTLH 88 
                                   689**********************99864455555666.78*************************************** PP

                        4HBT_2  83 hrflsnadgkkaarveerivvmdygkrskkapvPp 117
                                   h+  +   g +   ++ ++v +d  ++ +++++ +
  gi|91772691|ref|YP_565383.1|  89 HEAWQ--RGELKTKGDAVLVGYDFVNK-RSKTLAD 120
                                   **999..78888888888888887665.5665555 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-06    0.0083     157     181 ..       4      28 ..       1      42 [. 0.87
   2 ?    2.6   0.0     0.012        70      71     131 ..      67     126 ..      45     137 .] 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                   Acyl-ACP_TE 157 kelkvrysDlDlnqHvNNvkYlewi 181
                                   +  ++r+ D+D  +HvNN++  +w 
  gi|91772691|ref|YP_565383.1|   4 TTVTPRFGDIDGLGHVNNTVLPGWF 28 
                                   5789***************999885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.012
                   Acyl-ACP_TE  71 fgdkveietwaesenklfcyrdfkvrd...ekgekiieaksvfvlmdqetrrlsrvtdeilaey 131
                                   f   vei+t+++  ++      f+++    + ge   +  +v v  d  ++r + ++d+i + +
  gi|91772691|ref|YP_565383.1|  67 FDGDVEIRTYVKRLGNK----SFTLHHeawQRGELKTKGDAVLVGYDFVNKRSKTLADDIKETL 126
                                   44455555555443333....3333321223566666666666666777777777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1013.19
//
Query:       gi|91772692|ref|YP_565384.1|  [L=547]
Description: AMP-binding domain protein [Methanococcoides burtonii DSM 6242]
Scores for 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-112  376.9   0.0   1.2e-112  376.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.7e-18   65.9   0.0    9.1e-18   65.0   0.0    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.058   13.4   0.0         15    5.6   0.0    2.5  2  Nup35_RRM      Nup53/35/40-type RNA recognition motif


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 !  376.6   0.0  2.1e-116  1.2e-112       1     422 [.      14     446 ..      14     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: 376.6 bits;  conditional E-value: 2.1e-116
                                   HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                   AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                   +eeqa+k p++ ++v+ +++ +++Y+e+++rv+ lA+gL s+G++kgd+V+i+++n p+w+  l+a++++Gav+v++n+++
  gi|91772692|ref|YP_565384.1|  14 FEEQARKDPNRDFIVYPDRNLRFSYSEFNDRVDDLANGLISIGITKGDHVGIWARNVPDWLTFLFATARIGAVLVTVNTAY 94 
                                   89**************999************************************************************** PP

                                   -HHHHHHHHHHHTESEEE...................ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCC CS
                   AMP-binding  82 taeelayiledseakvli...................atvdselleklleaaakleavklvivldadellkeeelkeeees 143
                                   +++elay++++s++k++                    +              +   + k   + +++ ++ e+   + +e+
  gi|91772692|ref|YP_565384.1|  95 KSHELAYVMKQSDMKAIAivdrfrdvdyvetiyelvpE-------------LK---TCKRGNLNSKGYPKLESVIFIGQEK 159
                                   ****************9988877665555444433321.............21...1122221111111111111111111 PP

                                   SCTTS....................-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-E CS
                   AMP-binding 144 eekae....................kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddv 204
                                       +                    +   + +l+ +d+++++YTSGTTG PKGVml+h+n+++n + +   +r+k++edd+
  gi|91772692|ref|YP_565384.1| 160 H---RgmyntaemlllgkhseseelDS-LKGTLDCKDVINMQYTSGTTGFPKGVMLTHENILNNGYYI--GERQKFTEDDR 234
                                   1...02223344455555565666523.3446889*****************************7775..7789999**** PP

                                   EEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT CS
                   AMP-binding 205 vlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalk.aakkakdlss 284
                                   ++  +pl+h+fg++l++l++l++G+t+v+++ +++    l+l++++k+k+t ++gvP+++ a ++++ +k +     d+ss
  gi|91772692|ref|YP_565384.1| 235 LCLPVPLFHCFGIVLGVLATLTHGGTLVMIELFDP---LLVLAAVQKEKCTALYGVPTMFIAEFSHPMFKmF-----DMSS 307
                                   *******************************7766...5579************************999944.....9*** PP

                                   -SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTS CS
                   AMP-binding 285 lrlvllggeplspellrffralfge.evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdge 363
                                   lr+ +++g+p++ e+++++ + + +  +  +YGlTE+++v+t   +++  ++++++vG+ l +++vkivD etge v+++e
  gi|91772692|ref|YP_565384.1| 308 LRTGIMAGSPCPIEAMKKVIDEMNCkDITIAYGLTEASPVFTQtSTNDPIERRVSTVGTSLEHIDVKIVDSETGEIVGPNE 388
                                   *************************99**************55533344456899************************** PP

                                   EEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 364 eGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                   +Ge++ rg +vmkgY+k pe t++a+d +++wl++GDl+++dedGy++i+gR+kd+i++
  gi|91772692|ref|YP_565384.1| 389 QGEICCRGYNVMKGYYKMPEMTNRAID-KDGWLHSGDLATVDEDGYYRITGRIKDMIIR 446
                                   **************************9.767**************************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   1.5e-21   9.1e-18       1      76 []     455     530 ..     455     530 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.5e-21
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   e+E+ l + +++++a V+G+pde+ Ge++ afVvlk+gs++++e+++++  ++++ y+vpk++ +vde p+t+sGK
  gi|91772692|ref|YP_565384.1| 455 EIEEFLYTIEGIKDAQVIGIPDEKYGEIVGAFVVLKEGSKLTPEDIRDFSITKIARYKVPKHIFIVDEYPLTASGK 530
                                   8***********************************9988899********************************9 PP

>> Nup35_RRM  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0041        25      26      83 ..     360     425 ..     347     428 .. 0.66
   2 ?    5.6   0.0    0.0025        15      28      51 ..     477     500 ..     469     528 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0041
                                   HHHTTS-BSS--CCC---------............---EETTEEEEEBS-HHHHHHHHTTTTEEETTEE CS
                     Nup35_RRM  26 hFskfGeiledvqvlklgkglnpk............piptgenwvkltYksessaskAlqengtilngsl 83 
                                   + s  G+ le++ v    k ++++               +g n +k  Yk +   ++A+ ++g +  g+l
  gi|91772692|ref|YP_565384.1| 360 RVSTVGTSLEHIDV----KIVDSEtgeivgpneqgeICCRGYNVMKGYYKMPEMTNRAIDKDGWLHSGDL 425
                                   45667777776633....2222223333444466655678889********************9988876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0025
                                   HTTS-BSS--CCC----------- CS
                     Nup35_RRM  28 skfGeiledvqvlklgkglnpkpi 51 
                                   +k+Gei+  + vlk+g +l+p+ i
  gi|91772692|ref|YP_565384.1| 477 EKYGEIVGAFVVLKEGSKLTPEDI 500
                                   58*******************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3737.38
//
Query:       gi|91772693|ref|YP_565385.1|  [L=402]
Description: transposase, IS204/IS1001/IS1096/IS1165 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-70  237.8   4.3    2.3e-70  237.0   4.3    1.3  1  DDE_Tnp_ISL3  Transposase
    2.4e-14   52.5   0.1    4.1e-14   51.7   0.1    1.4  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
    5.6e-11   42.9   1.3    1.5e-10   41.6   1.3    1.8  1  zf-ISL3       zinc-finger of transposase IS204/IS1001/IS1096/
     0.0011   17.7   0.3     0.0026   16.5   0.2    1.6  1  UPF0236       Uncharacterised protein family (UPF0236)
     0.0042   16.8   0.0      0.024   14.4   0.0    2.2  2  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.056   13.5   0.0       0.13   12.3   0.0    1.6  1  HTH_29        Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.0   4.3   7.8e-74   2.3e-70       1     234 [.     156     382 ..     156     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 237.0 bits;  conditional E-value: 7.8e-74
                  DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkafleslsek.erekveavvmDmsaayksavkealPnAkiv 80 
                                   +g+DEis+kkgh+yvt ++dl  +++r+++i +g+k++++k+f e ls+k +++++++++mDm++a+k  ++e++PnAkiv
  gi|91772693|ref|YP_565385.1| 156 IGVDEISVKKGHSYVTLFYDL--NKSRIIHIENGKKRSVFKKFREYLSKKiDPDNIKYISMDMYPAFKGGAREYFPNAKIV 234
                                   8********************..**********************997778****************************** PP

                  DDE_Tnp_ISL3  81 vDrFHvvklanealdevRrreqkelreekrkklkrsrrlllknpenlteeqkqrldelleaspelekaYelkeelrevfrk 161
                                   +D+FH+vk++n+a+d+vRr e ++ ++     l ++r+++lknpenl++++ ++++++ +++++++kaY++k +l+++++ 
  gi|91772693|ref|YP_565385.1| 235 YDKFHIVKMMNDAIDKVRRSEYQSNKD-----LGKTRFMWLKNPENLSDREIAKIQSIKDLDTKTAKAYKFKLALQRLWEI 310
                                   ***********************8765.....************************************************* PP

                  DDE_Tnp_ISL3 162 kdkeearkalkewiekaersglkefkklaktlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayGfrnfe 234
                                   k+ + ar+++++w+ + ++s++ke+ +lak++k++ ++Il++++ ++sng+vEg+Nnkik++ +r+yG ++ e
  gi|91772693|ref|YP_565385.1| 311 KNMDVAREYIEKWHYWGTHSNIKEVITLAKMIKRNSHGILESIKGNISNGVVEGLNNKIKTAFKRSYGLKT-E 382
                                   ********************************************99**********************964.4 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 !   51.7   0.1   1.4e-17   4.1e-14       2      52 .]      92     141 ..      91     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.4e-17
                  HTH_Tnp_ISL3   2 elPwarrrsriTlrleayilelllesrsvkavArqlgvSwtTVwrildryv 52 
                                   ++Pw+r + ++Tl +ea i++ ++e+ +v+a+A++ ++++++Vwril +yv
  gi|91772693|ref|YP_565385.1|  92 NVPWTRQNTGFTLFFEALIVAISKEM-TVSAIAEMINIHEDSVWRILTHYV 141
                                   79************************.**********************97 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   1.3   4.9e-14   1.5e-10       4      47 .]      44      86 ..      41      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.9e-14
                       zf-ISL3  4 rCPnCgsktvvkhgkkerrvrhlpiggkrvyLrlrkrRyrCkeC 47
                                   CP C++ +   h++k+  +rhl+++++++yL++r++R +C+e+
  gi|91772693|ref|YP_565385.1| 44 SCPVCNKLS-ELHDTKKKVWRHLDFFHYETYLHARVPRTKCNEH 86
                                  7*******8.889999*************************987 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   8.7e-07    0.0026     232     306 ..     186     259 ..     161     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.7e-07
                       UPF0236 232 aekeeDvWedleeyleeeYklekiekviinGDaasWikegle.wikkalfqlDRfhlkkelrkvlskePryrekvr 306
                                   + k++ v++++ eyl ++ + ++i   +i+ D  +  k g   +++ a  + D+fh+ k ++ ++ k  r   + +
  gi|91772693|ref|YP_565385.1| 186 NGKKRSVFKKFREYLSKKIDPDNI--KYISMDMYPAFKGGAReYFPNAKIVYDKFHIVKMMNDAIDKVRRSEYQSN 259
                                   367899******************..59999**9999998655********************9988766555555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   8.1e-06     0.024      17      45 ..     116     144 ..     108     151 .. 0.83
   2 ?   -1.9   0.0       1.1   3.2e+03      17      25 ..     275     283 ..     267     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.1e-06
                        HTH_23  17 GlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                    ++v++IA++ ++++  v+r+l  y+++ 
  gi|91772693|ref|YP_565385.1| 116 EMTVSAIAEMINIHEDSVWRILTHYVNKA 144
                                   589*******************9997665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                        HTH_23  17 GlsvreIAr 25 
                                    ls reIA+
  gi|91772693|ref|YP_565385.1| 275 NLSDREIAK 283
                                   6899****8 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.2e-05      0.13       6      38 ..     111     142 ..     108     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                        HTH_29   6 lllaeGvstvsqiAkllglsrrtvyrwlkrfee 38 
                                    ++++++ tvs iA++ ++++++v r+l  +++
  gi|91772693|ref|YP_565385.1| 111 VAISKEM-TVSAIAEMINIHEDSVWRILTHYVN 142
                                   4567778.9*****************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3044.14
//
Query:       gi|91772694|ref|YP_565386.1|  [L=783]
Description: hypothetical protein Mbur_0667 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-245  816.7   0.1   1.5e-245  816.5   0.1    1.0  1  DUF3160   Protein of unknown function (DUF3160)
  ------ inclusion threshold ------
       0.06   13.5   0.3        6.9    6.8   0.4    2.6  2  Med9      RNA polymerase II transcription mediator complex su


Domain annotation for each model (and alignments):
>> DUF3160  Protein of unknown function (DUF3160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  816.5   0.1  1.7e-249  1.5e-245       2     631 .]      99     778 ..      98     778 .. 0.98

  Alignments for each domain:
  == domain 1  score: 816.5 bits;  conditional E-value: 1.7e-249
                       DUF3160   2 eeelalLkkngfvvieseke...eelvelYeslkekelPlfittDsvlhayHlfFdeiLkevEeeelapelkellkallee 79 
                                   +++ ++L+++gfvvi+++ +   e++ ++Y sl++k +P+fit+Ds+lh+yH++Fde+L+++Ee++++++++++++all++
  gi|91772694|ref|YP_565386.1|  99 DSAVEQLSEHGFVVISNPFNpveESISDVYGSLEDKAIPNFITSDSILHIYHIQFDETLRQIEEDVFYDAIWSIDSALLDR 179
                                   67899***********9988999********************************************************** PP

                       DUF3160  80 lekqyesekseelkeaakrnvayfavArsLldekak................................evpeevkeeveee 128
                                   ++++y +++s+++keaak+nvayf+vA+sLl++ ++                                e+pe v+eeve+e
  gi|91772694|ref|YP_565386.1| 180 SMEDY-NSSSGDMKEAAKNNVAYFSVALSLLKPVPEqlqikeydqfewggseshdgyftkeegdkfqfEIPEIVREEVEAE 259
                                   *****.9999*********************************************************************** PP

                       DUF3160 129 lelieaaeglaespifgyeekeDYSqYkpRGHYtksekLkrYFrammWlGrisfll......aesseeearrqteaallit 203
                                   leli++++g++ sp+f+y  +eDYSqY+pRGHYt+sekLk+YFr++mW+Gr+s+ll      + + e++ar+qt +a li+
  gi|91772694|ref|YP_565386.1| 260 LELINKHSGFSISPVFNY--QEDYSQYVPRGHYTHSEKLKNYFRTFMWHGRMSMLLkgdlieSADPEKDARIQTMSASLIA 338
                                   ******************..*****************************************97899*************** PP

                       DUF3160 204 ellkedeellkkwkriyevtaflvGesDdlslyeyaellkkvkgkdaeelkldeeklkalkkelaklkppqiigst..svp 282
                                   +++ +d+e+++kw+r+y +taf+vG sDdl++yey+e+l++v g+d + ++l++e++ +lk++la++++p+i+g+t  +v+
  gi|91772694|ref|YP_565386.1| 339 SHM-TDKEIMEKWDRVYGITAFYVGLSDDLGPYEYQEALNSVLGNDPDPVNLNNETIGELKAKLAECRSPEIYGGTgnCVI 418
                                   ***.*************************************************************************999* PP

                       DUF3160 283 ispleeeeeek.lketkgfrllGQRfvlDsyifqnlvsprvkentek................RalPkgLDvmaaLGserA 346
                                   ++p+++e++++ lk+tkgfrl+GQRf++Dsy+f+nlv ++++++ ++                R +P+gLD+ma+LGserA
  gi|91772694|ref|YP_565386.1| 419 LPPYTPEQADQcLKDTKGFRLMGQRFIPDSYMFSNLVGTHTGDYLGNrkpepftyidsaagpvRGFPQGLDMMALLGSERA 499
                                   ********************************************99999******************************** PP

                       DUF3160 347 eelLkkeleeteyenYkenleklkkevkaldeeawnknlYnswLyalrpllkekeegyPtfmkteaWedkeLntalaSWte 427
                                   + lL+++ ++++yenY+ +++kl+ke++++++++wn+nlY+s+Ly+l+pllke+++gyPtfm+t++W+dkeLntalaSWte
  gi|91772694|ref|YP_565386.1| 500 KVLLDES-DDSNYENYDLQYRKLEKEFDSFSDADWNQNLYWSQLYTLKPLLKEYDSGYPTFMQTQNWQDKELNTALASWTE 579
                                   ******9.************************************************************************* PP

                       DUF3160 428 LrHDtiLYakqsya..emggggepeeekedrgYVEPnpefykrlaalteltaeglkerelldeeskeklekleellerLke 506
                                   LrHDtiLY+k s++   ++ g++pe+  +  gYVEP+pefy+rl+alt++t++gl+e +++d++ +++lekle++l+rL++
  gi|91772694|ref|YP_565386.1| 580 LRHDTILYSKPSFTgfLYNMGSTPETPDPIMGYVEPVPEFYNRLLALTRMTRNGLNEIDAIDKSAEQRLEKLETILQRLTN 660
                                   **************8767777778888899*************************************************** PP

                       DUF3160 507 isekelaneelteeeyefirsigeeleseleevderseeedekkkdaivADvhTdpetgsvleegtGkvdlivvavpdadg 587
                                   is++el+n+eltee+yefir++g+el+  +++vders      +k++i+ADvhTdp+tg+vleeg+G+vdlivva+  +dg
  gi|91772694|ref|YP_565386.1| 661 ISRNELENKELTEEDYEFIRTFGDELDVVVAGVDERS------QKTTIIADVHTDPNTGNVLEEGVGYVDLIVVAYMAPDG 735
                                   ***********************************99......99************************************ PP

                       DUF3160 588 klrlaaGpvfsyYefkqplseRLtdeeWremlkegkaperpeWt 631
                                   ++ l aGp++s+Yefk+p+++RLtde+Wreml+ +++per+ Wt
  gi|91772694|ref|YP_565386.1| 736 RILLGAGPAMSQYEFKHPMNDRLTDEKWREMLR-TDPPERSGWT 778
                                   *********************************.8********7 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0081        73      23      40 ..     389     406 ..     373     407 .. 0.75
   2 ?    6.8   0.4   0.00076       6.9      39      67 ..     631     659 ..     628     663 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0081
                          Med9  23 dletktgelrhkLkkare 40 
                                        +gel+ kL ++r+
  gi|91772694|ref|YP_565386.1| 389 LNNETIGELKAKLAECRS 406
                                   445678***********7 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00076
                          Med9  39 relirelpgidrsveeqeaeieeleeqla 67 
                                   r+ ++e++ id+s e++++++e+  ++l+
  gi|91772694|ref|YP_565386.1| 631 RNGLNEIDAIDKSAEQRLEKLETILQRLT 659
                                   66789999***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (783 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.41
# Mc/sec: 5763.90
//
Query:       gi|91772695|ref|YP_565387.1|  [L=308]
Description: hypothetical protein Mbur_0668 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2029.52
//
Query:       gi|91772696|ref|YP_565388.1|  [L=570]
Description: cell surfacr protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-45  154.0  79.7    2.2e-19   69.7  30.9    3.1  3  NosD             Periplasmic copper-binding protein (NosD)
    9.7e-41  139.2 112.0    4.3e-19   68.9  36.4    3.1  3  Beta_helix       Right handed beta helix region
    1.2e-05   25.3  48.2     0.0087   15.9   9.1    3.2  3  Pectate_lyase_3  Pectate lyase superfamily protein
     0.0035   17.3   0.5     0.0089   16.0   0.5    1.6  1  DUF1160          Protein of unknown function (DUF1160)


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8  22.0   8.4e-19   3.8e-15       2     144 ..      49     208 ..      48     212 .. 0.85
   2 !   69.7  30.9   4.8e-23   2.2e-19      36     167 ..     189     319 ..     189     320 .. 0.94
   3 !   54.3  30.8   2.5e-18   1.1e-14      47     148 ..     289     391 ..     288     401 .. 0.72

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 8.4e-19
                          NosD   2 nnaisgdevlvsa..rgngiqlens.........egseisnneisnsrdgilldnssnntitgntienl........ryGi 63 
                                   +na  gd+++v    +++ i++++s         +g+  s  + ++s+d++++ ++++++i g +++++          Gi
  gi|91772696|ref|YP_565388.1|  49 DNATAGDTIIVNFgtYTEKIHVNKSltiisksgnPGN--SIVQAIDSSDSVFHITADEVKINGFHVKDSverywedsVPGI 127
                                   6777778877665665555555555666655444444..446778899999999999999999999888888899999*** PP

                          NosD  64 hlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgN 143
                                   +l+++++++i++n++s+ ++Gi+l+ss nntl+nN+++ n + Gi l ds+nn + nNt + n+++Gif+e s +n + +N
  gi|91772696|ref|YP_565388.1| 128 YLDGAHNSVISNNQFSNIYYGIVLESSGNNTLSNNIATYNIG-GIHLIDSNNNILDNNTLLnNSENGIFFEHSIYNHLINN 207
                                   ****************************************99.******************999*************9999 PP

                          NosD 144 r 144
                                   +
  gi|91772696|ref|YP_565388.1| 208 T 208
                                   7 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 4.8e-23
                          NosD  36 nsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnn 116
                                   ns++gi++++s  n + +nt  n+  Gi+l++s++n +++n++s+n++Gi+l+ s +ntl++N++ nn   Gi l +ss++
  gi|91772696|ref|YP_565388.1| 189 NSENGIFFEHSIYNHLINNTAFNSVDGIRLTKSQNNFLNNNIVSNNSCGIYLETSDENTLDDNIALNNFC-GIRLIGSSYC 268
                                   6899****************************************************************99.********** PP

                          NosD 117 tisnNtisnnnkGiflens.ssntitgNriesnqkiGilllsssegntiynN 167
                                    ++nNt+snnn+Gi+l++s s+nt+ +N+ ++n   Gi l   +++nt+  N
  gi|91772696|ref|YP_565388.1| 269 ILKNNTASNNNDGIYLQDScSNNTLINNNASNN-HAGISLRVFNKNNTLSYN 319
                                   *******************9*************.*****9888999988777 PP

  == domain 3  score: 54.3 bits;  conditional E-value: 2.5e-18
                          NosD  47 snntitgntienlryGihle.nsesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnntisnNtisn 125
                                   snnt+ +n  +n+++Gi l   +++nt++ n+++sn+  Gi+l ss+nn+l++Nt+snn++ Gi+l++s+ n ++nNt sn
  gi|91772696|ref|YP_565388.1| 289 SNNTLINNNASNNHAGISLRvFNKNNTLSYNKANSNNeHGILLFSSNNNILRGNTASNNDI-GIFLKYSNRNLLENNTGSN 368
                                   6777777777777777777514455777777777777777777777777777777777777.7777777777777777777 PP

                          NosD 126 nnkGiflensssntitgNriesn 148
                                   +++Gi+ ++s++nt+++N+i++n
  gi|91772696|ref|YP_565388.1| 369 KKYGIYHSDSKYNTLSNNKINGN 391
                                   77777777777777777777776 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 !   68.9  36.4   9.7e-23   4.3e-19       2     145 ..     126     263 ..      95     264 .. 0.87
   2 !   57.7  36.4   2.6e-19   1.2e-15      14     138 ..     227     348 ..     226     348 .. 0.94
   3 !   41.2  23.3   3.3e-14   1.5e-10      21     114 ..     300     392 ..     299     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 9.7e-23
                                   SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EE CS
                    Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnli 82 
                                   gi+++g +n  i+nn++sn+ +yGi l++s+n++++nn  ++ +  Gi++  s+nn+++nnt  +n + gi ++ + +n +
  gi|91772696|ref|YP_565388.1| 126 GIYLDGAHNSVISNNQFSNI-YYGIVLESSGNNTLSNNIATY-NIGGIHLIDSNNNILDNNTLLNNSENGIFFEHSIYNHL 204
                                   89999999999999999996.999999999999999777777.99999999999999999999999999999999999999 PP

                                   ES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-T CS
                    Beta_helix  83 enneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavv 145
                                    nn+ ++  + Gi+l+ s+nn ++nNi++nn+ +Gi+++ s+ ++t  +N++ nn  +Gi ++
  gi|91772696|ref|YP_565388.1| 205 INNTAFNSVD-GIRLTKSQNNFLNNNIVSNNS-CGIYLETSD-ENTLDDNIALNNF-CGIRLI 263
                                   9999999988.999998888888888888888.999999999.8889999999998.999775 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 2.6e-19
                                   ESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S--EEES-EEES-SS- CS
                    Beta_helix  14 knntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.gasnnlienneitdnggs 93 
                                   +nn++sn +++Giyl++s+ +++++n   n ++ Gi++ gss+++++nnt s+nn +gi+l+   snn++ nn+ ++n   
  gi|91772696|ref|YP_565388.1| 227 NNNIVSN-NSCGIYLETSDENTLDDNIALN-NFCGIRLIGSSYCILKNNTASNNN-DGIYLQdSCSNNTLINNNASNNHA- 303
                                   5777777.7***************999888.************************.******999*************87. PP

                                   SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-S CS
                    Beta_helix  94 Giyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnk 138
                                   Gi+l   ++nnt+++N +++n+++Gi + +s+ n+  ++Nt++nn+
  gi|91772696|ref|YP_565388.1| 304 GISLRvFNKNNTLSYNKANSNNEHGILLFSSN-NNILRGNTASNND 348
                                   **99955*************************.999********95 PP

  == domain 3  score: 41.2 bits;  conditional E-value: 3.3e-14
                                   -SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT- CS
                    Beta_helix  21 sggyGiylrgssn.vvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnys 100
                                   ++++Gi lr  ++ ++++ n+ ++n+++Gi + +s+nn++++nt s+n   gi l+++++nl+enn+ ++ +  Giy ++s
  gi|91772696|ref|YP_565388.1| 300 NNHAGISLRVFNKnNTLSYNKANSNNEHGILLFSSNNNILRGNTASNND-IGIFLKYSNRNLLENNTGSNKKY-GIYHSDS 378
                                   468888888877768999999999**********************999.*****************999976.******* PP

                                   S--EEES-EEESTT CS
                    Beta_helix 101 snntienNiidnna 114
                                   + nt++nN i++n 
  gi|91772696|ref|YP_565388.1| 379 KYNTLSNNKINGNV 392
                                   **********9996 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 !   13.1  18.7   1.4e-05     0.064      20     213 ..      43     237 ..      33     239 .. 0.79
   2 !   15.9   9.1   1.9e-06    0.0087     120     214 ..     216     305 ..     213     306 .. 0.80
   3 !   10.7   9.3   7.6e-05      0.34     132     209 ..     313     390 ..     309     392 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                   HHHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEE..ES-TTTEEEEE-TT-SS--SEEES-TT.T-......... CS
               Pectate_lyase_3  20 aiqkaiscasatttgavVYfPaGtYlvsspiilksgvqLv..Gdgngrpvlkaaaafvgaglidgdpyv.sg..gs..... 90 
                                    iq+ai   ++ t g+++ +  GtY  +  + +ks + +   G++ g+++++a ++++  + i++d+++ +g  ++     
  gi|91772696|ref|YP_565388.1|  43 TIQQAI---DNATAGDTIIVNFGTYTEKIHV-NKSLTIISksGNP-GNSIVQAIDSSDSVFHITADEVKiNGfhVKdsver 118
                                   69****...88888999999*****987776.7888777455999.9********************99855542256777 PP

                                   -EEEEEEEEEEE.GGGG-SS---SSEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS- CS
               Pectate_lyase_3  91 ealiatnnfyrq.irnlkiditavapgatgihwqtaqatslenvefemseasgtkhqgifiengsggfl.ndlvfsglgdi 169
                                    +  ++  +y + + n +i+ +++++ ++gi  +++ + +l+n++ +++ +      gi + ++++++l n+   ++ ++ 
  gi|91772696|ref|YP_565388.1| 119 YWEDSVPGIYLDgAHNSVISNNQFSNIYYGIVLESSGNNTLSNNIATYNIG------GIHLIDSNNNILdNNTLLNN-SEN 192
                                   7888899999999******************************84444433......78888889999955555555.999 PP

                                   SEEE.S.-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEE CS
               Pectate_lyase_3 170 giav.g.nqqftvrnitfnnattgievlwgwgwtlknvkinncegG 213
                                   gi + +  ++  ++n +fn+   gi++ ++ +  l+n+ ++n   G
  gi|91772696|ref|YP_565388.1| 193 GIFFeHsIYNHLINNTAFNS-VDGIRLTKSQNNFLNNNIVSNNSCG 237
                                   99996545555666666666.9999999988877766666555445 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.9e-06
                                   -EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E CS
               Pectate_lyase_3 120 ihwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg 199
                                   i+ + +q+  l n+++ ++++      gi++e + +++l+d ++ +    gi++ g+ + +++n+t +n++ gi+++++ +
  gi|91772696|ref|YP_565388.1| 216 IRLTKSQNNFLNNNIVSNNSC------GIYLETSDENTLDDNIALN-NFCGIRLiGSSYCILKNNTASNNNDGIYLQDSCS 289
                                   555566666666655544444......6***********7666666.699999999**********************555 PP

                                   .EEEEEEEEESSSEEE CS
               Pectate_lyase_3 200 .wtlknvkinncegGi 214
                                     tl n++ +n   Gi
  gi|91772696|ref|YP_565388.1| 290 nNTLINNNASNNHAGI 305
                                   5999999999998887 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 7.6e-05
                                   S-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEES CS
               Pectate_lyase_3 132 nvefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinn 209
                                   n+++ +++a+ +++ gi++ ++++++l+  ++s+  digi +  ++   ++n+t +n + gi+ ++++  tl+n+kin+
  gi|91772696|ref|YP_565388.1| 313 NNTLSYNKANSNNEHGILLFSSNNNILRGNTASN-NDIGIFLkYSNRNLLENNTGSNKKYGIYHSDSKYNTLSNNKING 390
                                   778888888889999************9999999.9******5599999****************8888********97 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.5     2e-06    0.0089      45      86 ..     194     236 ..     177     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-06
                       DUF1160  45 mFiereievediye.iveavdgikLtkkQidylvkqvyeneki 86 
                                   +F e+ i ++ i +   ++vdgi+Ltk+Q ++l +++++n++ 
  gi|91772696|ref|YP_565388.1| 194 IFFEHSIYNHLINNtAFNSVDGIRLTKSQNNFLNNNIVSNNSC 236
                                   58888888888876258***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3794.50
//
Query:       gi|91772697|ref|YP_565389.1|  [L=90]
Description: hypothetical protein Mbur_0670 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.002   17.9   0.9       0.11   12.2   0.2    2.1  2  Gly-zipper_YMGG  YMGG-like Gly-zipper
     0.0025   17.8   1.6      0.046   13.7   0.1    2.1  2  Gly-zipper_Omp   Glycine zipper
  ------ inclusion threshold ------
      0.082   13.2   0.9       0.26   11.6   0.1    1.9  2  DUF1269          Protein of unknown function (DUF1269)
       0.65    9.8   5.1        1.6    8.6   0.9    2.1  2  Gly-zipper_OmpA  Glycine-zipper domain


Domain annotation for each model (and alignments):
>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0077        34      36      44 ..      15      23 ..      10      27 .. 0.48
   2 !   12.2   0.2   2.5e-05      0.11      30      44 ..      70      84 ..      64      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0077
                                  XXXXXXXXX CS
               Gly-zipper_YMGG 36 GalaGgaiG 44
                                  Gal+G + G
  gi|91772697|ref|YP_565389.1| 15 GALVGIVWG 23
                                  222222222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.5e-05
                                  XXXXXXXXXXXXXXX CS
               Gly-zipper_YMGG 30 aiGAaaGalaGgaiG 44
                                  aiGA +Ga +G++i 
  gi|91772697|ref|YP_565389.1| 70 AIGALIGAGFGYLID 84
                                  799999999999886 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.018        81       6      14 ..      15      23 ..      12      29 .. 0.55
   2 !   13.7   0.1     1e-05     0.046      25      40 ..      70      85 ..      66      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.018
                Gly-zipper_Omp  6 GAaaGaliG 14
                                  GA++G + G
  gi|91772697|ref|YP_565389.1| 15 GALVGIVWG 23
                                  444444433 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1e-05
                Gly-zipper_Omp 25 liGAavGaavGgliGa 40
                                  +iGA +Ga  G+li +
  gi|91772697|ref|YP_565389.1| 70 AIGALIGAGFGYLIDR 85
                                  8999999999999875 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       0.2   9.2e+02       2       8 ..      17      23 ..      12      45 .. 0.60
   2 ?   11.6   0.1   5.8e-05      0.26       7      34 ..      58      85 ..      56      90 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.2
                       DUF1269  2 lsGalwG 8 
                                  l G +wG
  gi|91772697|ref|YP_565389.1| 17 LVGIVWG 23
                                  2222222 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.8e-05
                       DUF1269  7 wGllvGllflnPllGaavGAaaGAlvga 34
                                  w + v l +l P +Ga++GA++G l  +
  gi|91772697|ref|YP_565389.1| 58 WDSHVVLFLLAPAIGALIGAGFGYLIDR 85
                                  6667788999*************88765 PP

>> Gly-zipper_OmpA  Glycine-zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.018        82      32      41 ..      15      24 ..      13      26 .. 0.39
   2 ?    8.6   0.9   0.00035       1.6      25      38 ..      69      82 ..      67      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.018
               Gly-zipper_OmpA 32 GAasGavaGl 41
                                  GA +G+v G+
  gi|91772697|ref|YP_565389.1| 15 GALVGIVWGA 24
                                  3333333333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00035
               Gly-zipper_OmpA 25 aGtGAaiGAasGav 38
                                  ++ GA iGA+ G +
  gi|91772697|ref|YP_565389.1| 69 PAIGALIGAGFGYL 82
                                  6779*****99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 626.33
//
Query:       gi|91772698|ref|YP_565390.1|  [L=401]
Description: hypothetical protein Mbur_0671 [Methanococcoides burtonii DSM 6242]
Scores for 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   0.8      1e-09   38.2   0.8    3.5  4  PLDc_N           Phospholipase_D-nuclease N-terminal
  ------ inclusion threshold ------
      0.015   15.6  15.6       0.12   12.6  13.0    3.2  2  DUF2516          Protein of unknown function (DUF2516)
       0.11   12.4   4.8      0.054   13.5   1.9    2.0  2  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
          6    7.2   6.5         13    6.1   0.6    2.7  2  Chordopox_A13L   Chordopoxvirus A13L protein
        7.5    6.8   5.4         47    4.2   0.1    3.1  3  DUF4381          Domain of unknown function (DUF4381)
        9.4    6.4  12.2        3.7    7.7   0.3    3.8  4  ETRAMP           Malarial early transcribed membrane protein 


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   1.3       4.1   1.2e+04      20      27 ..      29      36 ..      14      38 .. 0.57
   2 !   38.2   0.8   3.4e-13     1e-09       1      39 [.      39      84 ..      39      87 .. 0.90
   3 ?   -2.8   0.2       2.1   6.3e+03      23      30 ..     110     117 ..     100     124 .. 0.61
   4 ?   -4.5   3.5         6   1.8e+04      23      29 ..     131     137 ..     128     148 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.1
                        PLDc_N 20 laWllvil 27
                                  ++W +v +
  gi|91772698|ref|YP_565390.1| 29 FLWGIVAV 36
                                  34555555 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 3.4e-13
                        PLDc_N  1 ilwiialidiird.rnpss......klaWllvilflPvlGailYll 39
                                  ++w+++l d++++ +++ +      kl+W+lvi++++++Ga+lY+ 
  gi|91772698|ref|YP_565390.1| 39 VFWLWMLSDCLQRpTEHFPnageyeKLIWCLVIIVVNFIGAVLYYY 84
                                  69**********87666668999*********************96 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.1
                        PLDc_N  23 llvilflP 30 
                                    ++i+fl 
  gi|91772698|ref|YP_565390.1| 110 SVLIFFLS 117
                                   45666665 PP

  == domain 4  score: -4.5 bits;  conditional E-value: 6
                        PLDc_N  23 llvilfl 29 
                                   ++++ +l
  gi|91772698|ref|YP_565390.1| 131 MIAVALL 137
                                   4444443 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  13.0   4.2e-05      0.12       7      59 ..      29     119 ..      23     154 .. 0.77
   2 ?   -0.9   3.0       0.7   2.1e+03       8      43 ..     131     166 ..     123     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                       DUF2516   7 vllllalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlll............................. 58 
                                   +l+ ++ vv+v+ l+ l d+l r+ + F+ ag   K +W ++++v  +++ +                             
  gi|91772698|ref|YP_565390.1|  29 FLWGIVAVVFVFWLWMLSDCLQRPTEHFPNAGEYEKLIWCLVIIVVNFIGAVlyyylvkrkdqdekesidlnnisqkkvii 109
                                   78999***********************************99999999988877888888888888777777766544444 PP

                       DUF2516  59 .........g 59 
                                            +
  gi|91772698|ref|YP_565390.1| 110 svlifflslA 119
                                   4443333331 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.7
                       DUF2516   8 llllalvvlvlslvAlvdalrrradaFeaagkrtKp 43 
                                   ++++al+++++ +v ++ + + ++   +++gkr K+
  gi|91772698|ref|YP_565390.1| 131 MIAVALLLIIFLIVSMLAVYLIKESSMTQTGKRMKQ 166
                                   344444555556666666666666666666666665 PP

>> Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.9   1.8e-05     0.054      10     119 ..       8     134 ..       6     151 .. 0.72
   2 ?   -2.5   0.1       1.4   4.3e+03      92     106 ..     298     312 ..     267     345 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
               Abhydrolase_9_N  10 wlfqgvvsGls.aaiGYglGvllawlvrrllr.........lpepsrrvrr.......rlrlalavvalvvllvalvlaar 73 
                                   w ++g+v+++   a+ + +G +l  +v+++ +         l++p++++++       ++ l+++vv  +++++ ++l +r
  gi|91772698|ref|YP_565390.1|   8 WTITGLVMAFViLALSFYVGQFLWGIVAVVFVfwlwmlsdcLQRPTEHFPNageyeklIWCLVIIVVNFIGAVLYYYLVKR 88 
                                   666666666431466666776666666655556666777774444444444555565344455555556888899999999 PP

               Abhydrolase_9_N  74 wQrelralmgaeplgaaeyllvllvallvfalllllgrllralvrl 119
                                   + ++ ++ ++++++++ +++  +l+ +l +a+++ lg+++ +++ +
  gi|91772698|ref|YP_565390.1|  89 KDQDEKESIDLNNISQKKVIISVLIFFLSLAIFVYLGQFFLWMIAV 134
                                   999999**********************************999875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
               Abhydrolase_9_N  92 yllvllvallvfall 106
                                   +l +  va+l+ +ll
  gi|91772698|ref|YP_565390.1| 298 ALSISSVAMLIGGLL 312
                                   222222222222222 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.8     0.033        99       6      33 ..      68      95 ..      65     111 .. 0.68
   2 ?    6.1   0.6    0.0045        13       1      26 [.     131     156 ..     131     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.033
                Chordopox_A13L  6 llliiCvaivglivYgiYnrkketqttn 33
                                   l+ii v  +g+++Y    ++k++ +++
  gi|91772698|ref|YP_565390.1| 68 CLVIIVVNFIGAVLYYYLVKRKDQDEKE 95
                                  58999999******96555555544443 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0045
                Chordopox_A13L   1 MiadlllliiCvaivglivYgiYnrk 26 
                                   Mia +lllii  ++  l vY i +  
  gi|91772698|ref|YP_565390.1| 131 MIAVALLLIIFLIVSMLAVYLIKESS 156
                                   9*******************885443 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.0       1.3     4e+03      30      41 ..      32      43 ..       8      55 .. 0.61
   2 ?    4.0   0.0     0.018        54      22      50 ..      67      95 ..      45     111 .. 0.66
   3 ?    4.2   0.1     0.016        47      22      43 ..     130     156 ..     123     182 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                       DUF4381 30 lllllvlalwll 41
                                   ++ +v+++wl+
  gi|91772698|ref|YP_565390.1| 32 GIVAVVFVFWLW 43
                                  244444444444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.018
                       DUF4381 22 wlllaalllllllvlalwllrrrkrnrre 50
                                  w+l+++++ ++ +vl ++l++r+++  +e
  gi|91772698|ref|YP_565390.1| 67 WCLVIIVVNFIGAVLYYYLVKRKDQDEKE 95
                                  55552444466666666666666664444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.016
                       DUF4381  22 wlllaalll...llllvlalwllr..r 43 
                                   w++++alll   l++ +la++l++   
  gi|91772698|ref|YP_565390.1| 130 WMIAVALLLiifLIVSMLAVYLIKesS 156
                                   666666666533444555555555332 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0012       3.7      13      74 ..      71     125 ..      65     129 .. 0.67
   2 ?    5.2   0.3    0.0076        23       5      43 ..     133     168 ..     130     204 .. 0.68
   3 ?   -1.9   0.4       1.2   3.5e+03      61      75 ..     300     314 ..     295     318 .. 0.75
   4 ?   -2.3   0.0       1.6   4.8e+03      56      72 ..     323     339 ..     312     347 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                        ETRAMP  13 LlavnlltpeslcdevnkkkekakkaikkiddkiekkkkkkKliiistiatalallvasalG 74 
                                   +++vn++   ++ + v+    k++++ ++id +    + ++K++iis+++  l l++ + lG
  gi|91772698|ref|YP_565390.1|  71 IIVVNFIGAVLYYYLVKR---KDQDEKESIDLN----NISQKKVIISVLIFFLSLAIFVYLG 125
                                   566677777777776663...334444444432....334466**************99988 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0076
                        ETRAMP   5 kvllffafLlavnlltpeslcdevnkkkekakkaikkid 43 
                                   +v+l+++++l+v++l++ + ++ + ++    +k +k+  
  gi|91772698|ref|YP_565390.1| 133 AVALLLIIFLIVSMLAVYLIKESSMTQ---TGKRMKQSL 168
                                   689999***********9999998854...444444433 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                        ETRAMP  61 iatalallvasalGl 75 
                                    ++++a+l++++l++
  gi|91772698|ref|YP_565390.1| 300 SISSVAMLIGGLLAF 314
                                   567888999998875 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.6
                        ETRAMP  56 iiistiatalallvasa 72 
                                    ++st+  ++ ll++s+
  gi|91772698|ref|YP_565390.1| 323 FLLSTTFDSVSLLLGSV 339
                                   67888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1676  (0.0934798); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.91u 0.32s 00:00:01.23 Elapsed: 00:00:00.54
# Mc/sec: 2217.29
//
Query:       gi|91772699|ref|YP_565391.1|  [L=194]
Description: hypothetical protein Mbur_0672 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1171.68
//
Query:       gi|91772700|ref|YP_565392.1|  [L=431]
Description: hypothetical protein Mbur_0673 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-06   28.8   2.7       0.12   12.4   0.1    4.5  5  DUF916        Bacterial protein of unknown function (DUF916)
    1.7e-06   28.1   1.0      0.079   13.2   0.2    3.9  3  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
    3.8e-05   24.4   1.4       0.55   10.9   0.3    3.7  3  fn3_5         Fn3-like domain
    0.00077   19.3   0.6       0.12   12.2   0.0    2.9  2  Motile_Sperm  MSP (Major sperm protein) domain
    0.00083   19.6   0.7      0.016   15.4   0.1    2.7  2  DUF4625       Domain of unknown function (DUF4625)
  ------ inclusion threshold ------
       0.12   12.3   0.6       0.74    9.7   0.5    2.1  2  PapD_N        Pili and flagellar-assembly chaperone, PapD N-t
       0.12   12.6   0.9        0.5   10.6   0.2    2.1  2  DUF1775       Domain of unkown function (DUF1775)
       0.17   11.9   0.1       0.42   10.6   0.1    1.6  1  CtaG_Cox11    Cytochrome c oxidase assembly protein CtaG/Cox1
       0.27   10.5   2.0        4.4    6.6   0.1    2.5  2  DUF4097       Putative adhesin


Domain annotation for each model (and alignments):
>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   6.1e-05      0.12      22      49 ..      70      97 ..      63     107 .. 0.90
   2 ?    0.6   0.0      0.28   5.5e+02      86     111 ..     118     143 ..     101     152 .. 0.75
   3 ?    3.7   0.0     0.032        63      22      50 ..     192     220 ..     179     225 .. 0.84
   4 !    7.8   0.0    0.0016       3.3      79     118 ..     241     279 ..     236     280 .. 0.85
   5 ?   -2.5   0.0       2.5     5e+03      11      25 ..     339     353 ..     336     372 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                        DUF916 22 kvkpgqeqelevkikNssdkeitveitv 49
                                  ++kpg++++++v+++N+ +k+itve  v
  gi|91772700|ref|YP_565392.1| 70 QLKPGSSDKITVTVTNKDNKTITVEPRV 97
                                  79**********************9776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                        DUF916  86 eitlpakesktvklkikmPkeefdGv 111
                                   + ++++  ++++++k+++P+++  G 
  gi|91772700|ref|YP_565392.1| 118 SKNIEPDAKQEFTIKMNIPQDADIGN 143
                                   55688888999999999999876665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.032
                        DUF916  22 kvkpgqeqelevkikNssdkeitveitvn 50 
                                   +v+ g e   e+k+kN  dk+i ++ ++ 
  gi|91772700|ref|YP_565392.1| 192 RVEAGDEYDYEIKLKNVADKDIAIDPKIS 220
                                   689999****************9998775 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0016
                        DUF916  79 elvkipkeitlpakesktvklkikmPkeefdGvilGGiyv 118
                                   + ++i+   t++a+e+  vkl++++P+++ +G + G+i++
  gi|91772700|ref|YP_565392.1| 241 DAITITAPSTVKAGETAVVKLHLEVPDDA-KGGYNGAINL 279
                                   5667777789*****************88.8888898886 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 2.5
                        DUF916  11 qidkkksYFdLkvkp 25 
                                   q +k++  FdL ++ 
  gi|91772700|ref|YP_565392.1| 339 QNEKSEASFDLALEG 353
                                   667777777777653 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2     4e-05     0.079       2      70 ..      72     144 ..      71     151 .. 0.71
   2 !    9.4   0.1    0.0006       1.2      44      68 ..     247     272 ..     241     281 .. 0.84
   3 ?   -1.2   0.0       1.3   2.6e+03      61      74 ..     414     427 ..     408     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                   NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslsl.PeGWtvvevspasaa....slapGetveatvkVtppagaaaGdy 70 
                                   +pG++ ++t+tvtn+ ++++t v+ ++ + P + ++ e s  +++     ++p++++e+t+k+ +p++a+ G y
  gi|91772700|ref|YP_565392.1|  72 KPGSSDKITVTVTNKDNKTIT-VEPRVVAsPYEENIFEESWITVTpaskNIEPDAKQEFTIKMNIPQDADIGNY 144
                                   678888888888888877776.5555555576655333332222222369**********************99 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0006
                   NPCBM_assoc  44 aa.slapGetveatvkVtppagaaaG 68 
                                   a+ ++++Get+ +++ + +p++a+ G
  gi|91772700|ref|YP_565392.1| 247 APsTVKAGETAVVKLHLEVPDDAKGG 272
                                   4459*******************966 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                   NPCBM_assoc  61 ppagaaaGdyevta 74 
                                    p++++ +dy +t+
  gi|91772700|ref|YP_565392.1| 414 LPTNTERFDYSITI 427
                                   599*******9985 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.3   0.00028      0.55      58     103 ..      61     117 ..      33     120 .. 0.84
   2 !    6.5   0.1    0.0064        13      57      88 ..     110     141 ..      90     154 .. 0.78
   3 !    6.2   0.0    0.0079        16       7      88 ..     196     271 ..     193     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                         fn3_5  58 altfetskvtvpAnssktvtvtldlpsdakk............kngyfveGfvtlkds 103
                                   +++  +s+ +++++ss ++tvt++  +d k             +++ f e+ +t++ +
  gi|91772700|ref|YP_565392.1|  61 KINPRHSSTQLKPGSSDKITVTVTN-KDNKTitveprvvaspyEENIFEESWITVTPA 117
                                   5566789999***************.77777899999999999999999999999865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0064
                         fn3_5  57 aaltfetskvtvpAnssktvtvtldlpsdakk 88 
                                   + +t+++++  +++++++++t+++++p+da+ 
  gi|91772700|ref|YP_565392.1| 110 SWITVTPASKNIEPDAKQEFTIKMNIPQDADI 141
                                   57899999999*****************9886 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0079
                         fn3_5   7 gdkfsftltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldlpsdak 87 
                                   gd+ + +++lkN+ +k+  ++ + +d ++   +  +g       + e    a+t ++++ tv+A++++ v++ l +p+dak
  gi|91772700|ref|YP_565392.1| 196 GDEYDYEIKLKNVADKDIAIDPKISDNNRWNHYGPYGMIG---PAFED--DAITITAPS-TVKAGETAVVKLHLEVPDDAK 270
                                   6777888888888888888877766555555544444443...22233..366666666.9***************99877 PP

                         fn3_5  88 k 88 
                                    
  gi|91772700|ref|YP_565392.1| 271 G 271
                                   5 PP

>> Motile_Sperm  MSP (Major sperm protein) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.9     0.032        64       2      35 ..      60      92 ..      59     140 .. 0.74
   2 !   12.2   0.0   6.1e-05      0.12      17      58 ..     196     237 ..     180     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.032
                                  SEEESSSEEEEESSTSSHEEEEEEEEE-SSSSEE CS
                  Motile_Sperm  2 lkidPsdllvfaaelnkqgtsklklkNtskkrva 35
                                  lki+P +  ++ +++ ++ + +++++N+ +k++ 
  gi|91772700|ref|YP_565392.1| 60 LKINPRHSSTQLKPG-SSDKITVTVTNKDNKTIT 92
                                  566666666666655.334555566666666554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.1e-05
                                   SSHEEEEEEEEE-SSSSEEEEEEES-TTTEEEESSEEEETTT CS
                  Motile_Sperm  17 nkqgtsklklkNtskkrvaFkvkttapkkyrvrPnvGiikpg 58 
                                   +++  +++klkN+ +k++a   k +++++   + ++G+i p 
  gi|91772700|ref|YP_565392.1| 196 GDEYDYEIKLKNVADKDIAIDPKISDNNRWNHYGPYGMIGPA 237
                                   5567899********************************996 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   8.2e-06     0.016      56     117 ..      82     152 ..      64     154 .. 0.77
   2 ?    1.7   0.0      0.15   2.9e+02      90     107 ..     255     272 ..     174     285 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-06
                       DUF4625  56 dihnnfDhhshsseakeg...ekewsfeksy.dlsgskk......eyelheeieiPadaeaGdYhlvirvtD 117
                                    +  n D+ + + e +      +e  fe+s+ +++  +k      ++e++ +++iP+da+ G+Y   i  tD
  gi|91772700|ref|YP_565392.1|  82 TV-TNKDNKTITVEPRVVaspYEENIFEESWiTVTPASKniepdaKQEFTIKMNIPQDADIGNYGTEIAFTD 152
                                   55.55666666665544456666677888887666655567777799**********************999 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                       DUF4625  90 keyelheeieiPadaeaG 107
                                   +++ ++ ++e+P+da+ G
  gi|91772700|ref|YP_565392.1| 255 ETAVVKLHLEVPDDAKGG 272
                                   367788888888888755 PP

>> PapD_N  Pili and flagellar-assembly chaperone, PapD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5   0.00037      0.74      13      73 ..      74     133 ..      67     141 .. 0.79
   2 ?   -0.4   0.0      0.52     1e+03      15      41 ..     198     224 ..     193     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                                   TTSSEEEEEEEE-SSS-EEEEEEEECTTSSSTCCSSCS.SEEEESSEEEE-TTEEEEEEE.E CS
                        PapD_N  13 adekeasvtvkNtgkepylvqswvddgdeeaedekakaspfvvtPPlfrlepgeeqvlRi.v 73 
                                   +++ +++vtv+N++++ + v+ +v ++   +e+   ++s ++vtP    +ep+++q   i +
  gi|91772700|ref|YP_565392.1|  74 GSSDKITVTVTNKDNKTITVEPRVVASPY-EENIF-EESWITVTPASKNIEPDAKQEFTIkM 133
                                   677899********************333.33333.34479**************9988844 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.52
                                   SSEEEEEEEE-SSS-EEEEEEEECTTS CS
                        PapD_N  15 ekeasvtvkNtgkepylvqswvddgde 41 
                                   e +  +++kN +++ + +  +++d+++
  gi|91772700|ref|YP_565392.1| 198 EYDYEIKLKNVADKDIAIDPKISDNNR 224
                                   556778999999999999999988655 PP

>> DUF1775  Domain of unkown function (DUF1775)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00025       0.5      42     106 ..      79     139 ..      69     151 .. 0.89
   2 ?   -0.1   0.0       0.5     1e+03       8      54 ..     250     299 ..     243     348 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                       DUF1775  42 asvkpqpkpgWtvevekeklakpvesehgkevteavkevtWtagealkdgqfdefelsaklpdka 106
                                   + v++++k + t++ve + +a+p+e+   +  +e+  +vt   ++ ++++  +ef++++++p++a
  gi|91772700|ref|YP_565392.1|  79 ITVTVTNKDNKTITVEPRVVASPYEE---NIFEESWITVTPASKN-IEPDAKQEFTIKMNIPQDA 139
                                   578999999****************9...5689999999999997.****************965 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.5
                       DUF1775   8 eaaagsy..akltfrVphgcdgaaTtkvevtlPeg.vasvkpqpkpgWtv 54 
                                   + +ag++  +kl ++Vp++ +g    ++++++ +  +++   q  ++ +v
  gi|91772700|ref|YP_565392.1| 250 TVKAGETavVKLHLEVPDDAKGGYNGAINLNINDPsIREWDGQVEMNFEV 299
                                   44444442267778888888887766666666654455555555555554 PP

>> CtaG_Cox11  Cytochrome c oxidase assembly protein CtaG/Cox11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00021      0.42      41      94 ..      33     102 ..      16     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                    CtaG_Cox11  41 eFdadvsekl................pwefkpeqrslevkpGetalafytaknksdkpiigqavysvaPe 94 
                                   e+ a+ ++++                +++++p ++s+++kpG + +++ t++nk +k+i+       +P 
  gi|91772700|ref|YP_565392.1|  33 EMYATSEQDMimvddvamldpymdfaKLKINPRHSSTQLKPGSSDKITVTVTNKDNKTITVEPRVVASPY 102
                                   44444444444444444444444666789******************************98766666665 PP

>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0022       4.4       1      36 [.      57      92 ..      57      99 .. 0.90
   2 ?    3.0   0.2     0.027        53      99     143 ..     317     367 ..     218     378 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0022
                       DUF4097  1 ikeldissesadvtikesddekitveystakklkkq 36
                                  + +l+i+   ++ + k+++++kitv+++ +++++ +
  gi|91772700|ref|YP_565392.1| 57 FAKLKINPRHSSTQLKPGSSDKITVTVTNKDNKTIT 92
                                  56899*************************999765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.027
                       DUF4097  99 tklkaetlelksssGdltlsnvs......aktltvksesGdvtiegseakk 143
                                   + ++ e  + ++++G    +  +        +l + +esG+v++++++++ 
  gi|91772700|ref|YP_565392.1| 317 DPITIEVSSNDHNYGRWMGAGSQnekseaSFDLALEGESGKVELNQVKTTY 367
                                   333333333333333333333333333333355566666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2820.70
//
Query:       gi|91772701|ref|YP_565393.1|  [L=323]
Description: HEAT repeat-containing PBS lyase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-54  180.7  11.5    9.5e-17   61.2   0.1    4.1  4  HEAT_2          HEAT repeats
    1.4e-49  161.7   4.4      2e-07   31.0   0.1    8.4  8  HEAT_PBS        PBS lyase HEAT-like repeat
    1.8e-23   80.6   3.0       0.44   10.9   0.0    8.9  9  HEAT            HEAT repeat
    5.2e-15   55.6   9.1       0.36   11.4   0.2    8.0  8  HEAT_EZ         HEAT-like repeat
    1.3e-11   44.1   0.0      0.012   15.6   0.0    7.2  8  Arm             Armadillo/beta-catenin-like repeat
    1.1e-05   24.1   0.1      0.091   11.1   0.0    3.0  3  Vitellogenin_N  Lipoprotein amino terminal region
    2.6e-05   24.3   1.8       0.43   10.6   0.0    4.8  5  Cnd1            non-SMC mitotic condensation complex subunit 
    0.00011   22.3   0.1      0.055   13.5   0.0    3.5  5  Aconitase_B_N   Aconitate B N-terminal domain
      0.001   18.7   0.1      0.053   13.1   0.0    2.5  3  ERAP1_C         ERAP1-like C-terminal domain
  ------ inclusion threshold ------
      0.011   15.9   0.0         16    5.9   0.0    4.3  4  RICTOR_V        Rapamycin-insensitive companion of mTOR, doma
      0.013   14.1   0.2        1.3    7.5   0.0    3.4  4  Adaptin_N       Adaptin N terminal region
      0.018   15.1   2.7         16    5.7   0.0    4.1  4  UPF0147         Uncharacterised protein family (UPF0147)
      0.034   14.4   1.8         55    4.1   0.0    5.3  6  UPF0253         Uncharacterised protein family (UPF0253)


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 !   47.8   0.3     1e-15   1.4e-12       4      83 ..      37     118 ..      35     118 .. 0.87
   2 !   48.1   0.1   8.2e-16   1.1e-12      15      76 ..     113     174 ..     110     176 .. 0.95
   3 !   61.2   0.1   6.9e-20   9.5e-17       1      88 []     162     252 ..     162     252 .. 0.90
   4 !   50.7   0.4   1.3e-16   1.8e-13       2      84 ..     229     314 ..     228     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1e-15
                        HEAT_2   4 Llqalen.dpdpevrraairaLgrignpealpaLvellededpa..vRraaaeaLgaigdpealpaLkellddddd.dvvR 80 
                                   L+ ++e+   +p vr +a+++L+  g+++a++ L+++++d ++a  vRr aa aLg+igd++a+++L + ++d+++ ++vR
  gi|91772701|ref|YP_565393.1|  37 LIHVIEDkNGNPFVRERAAWTLA--GTEDAMDPLIRVVSDGNEAaiVRRSAAYALGEIGDERAVDILIQVVTDENEeRIVR 115
                                   5666644478899*********9..7889**********9886556****************************9747888 PP

                        HEAT_2  81 eaA 83 
                                   ++A
  gi|91772701|ref|YP_565393.1| 116 RSA 118
                                   875 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 8.2e-16
                        HEAT_2  15 evrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddd 76 
                                    vrr a+ aLg+ig+ +a++ L+++++ded   R aa+ +Lg++g+++a++ L +l +d+++
  gi|91772701|ref|YP_565393.1| 113 IVRRSAAYALGKIGDGKAVDPLIQAISDEDQFLRDAAVCSLGRCGNKRAVDPLIQLINDENE 174
                                   59******************************************************999987 PP

  == domain 3  score: 61.2 bits;  conditional E-value: 6.9e-20
                        HEAT_2   1 ldaLlqalen.dpdpevrraairaLgrignpealpaLvell..ededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                   +d+L+q++ +  ++++vr++a+ +Lg+i+++ a++ L++l+  e+ed +vR+ a  aLg igd+e++++L   +++d++  
  gi|91772701|ref|YP_565393.1| 162 VDPLIQLINDeNESTNVRWHAAYSLGKIKDEIAVDPLIQLMcdENEDLEVRKGATVALGMIGDDETVDSLILVMREDEEIM 242
                                   689*****43466668*************************44446678******************************** PP

                        HEAT_2  79 vReaAaeaLa 88 
                                   +R  Aa aL+
  gi|91772701|ref|YP_565393.1| 243 IRKTAAYALG 252
                                   ******9996 PP

  == domain 4  score: 50.7 bits;  conditional E-value: 1.3e-16
                        HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpa..vRraaaeaLgaigdpealpaLkellddddd.dvv 79 
                                   d L+ ++++d++  +r++a+ aLg+ g++++ + L+++++d d++  vRr aa +L++ig++ea ++L++ +dd+++  + 
  gi|91772701|ref|YP_565393.1| 229 DSLILVMREDEEIMIRKTAAYALGTTGDDRVAEPLIQVMKDRDERdiVRRFAALSLSKIGSEEAMESLTQVMDDENEsGYM 309
                                   788999999******************************88776556****************************975788 PP

                        HEAT_2  80 ReaAa 84 
                                   R +Aa
  gi|91772701|ref|YP_565393.1| 310 RDSAA 314
                                   88887 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 !    7.4   0.0    0.0059       8.1       1      27 []      50      74 ..      50      74 .. 0.90
   2 !   31.0   0.1   1.5e-10     2e-07       1      25 [.      81     105 ..      81     107 .. 0.94
   3 !   28.9   0.0   6.9e-10   9.5e-07       1      27 []     114     140 ..     114     140 .. 0.96
   4 !   20.1   0.0   4.9e-07   0.00068       2      27 .]     146     171 ..     145     171 .. 0.94
   5 !   20.5   0.0   3.5e-07   0.00049       1      24 [.     178     201 ..     178     202 .. 0.96
   6 !   12.2   0.0   0.00018      0.24       1      24 [.     211     234 ..     211     237 .. 0.91
   7 !   18.7   0.0   1.4e-06    0.0019       2      27 .]     244     269 ..     243     269 .. 0.94
   8 !   16.0   0.0     1e-05     0.014       1      27 []     276     302 ..     276     302 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0059
                                  HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                  vR +Aa+ L+   d  a ++L+++  d
  gi|91772701|ref|YP_565393.1| 50 VRERAAWTLAGTED--AMDPLIRVVSD 74
                                  8*********9999..99999998765 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.5e-10
                                   HHHHHHHHHHHCTSGGGHHHHHHHC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                   vRr+Aa+aLg++gde+a+++L+++ 
  gi|91772701|ref|YP_565393.1|  81 VRRSAAYALGEIGDERAVDILIQVV 105
                                   9*********************986 PP

  == domain 3  score: 28.9 bits;  conditional E-value: 6.9e-10
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   vRr+Aa+aLg++gd  a+++L++a  d
  gi|91772701|ref|YP_565393.1| 114 VRRSAAYALGKIGDGKAVDPLIQAISD 140
                                   9***********************876 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 4.9e-07
                                   HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                   R aA+ +Lg++g ++a+++L+++ +d
  gi|91772701|ref|YP_565393.1| 146 RDAAVCSLGRCGNKRAVDPLIQLIND 171
                                   99********************9887 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 3.5e-07
                                   HHHHHHHHHHHCTSGGGHHHHHHH CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLlea 24 
                                   vR+ Aa++Lg+++de a+++L+++
  gi|91772701|ref|YP_565393.1| 178 VRWHAAYSLGKIKDEIAVDPLIQL 201
                                   8*********************97 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHHHCTSGGGHHHHHHH CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLlea 24 
                                   vR  A+ aLg +gd+e ++ L+ +
  gi|91772701|ref|YP_565393.1| 211 VRKGATVALGMIGDDETVDSLILV 234
                                   8999****************9965 PP

  == domain 7  score: 18.7 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                   R  Aa+aLg+ gd++++++L+++ +d
  gi|91772701|ref|YP_565393.1| 244 RKTAAYALGTTGDDRVAEPLIQVMKD 269
                                   888*******************9987 PP

  == domain 8  score: 16.0 bits;  conditional E-value: 1e-05
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   vRr Aa +L ++g+eea + L ++ +d
  gi|91772701|ref|YP_565393.1| 276 VRRFAALSLSKIGSEEAMESLTQVMDD 302
                                   9**********************9987 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       8.4   1.2e+04      24      30 ..      21      27 ..       5      32 .. 0.63
   2 !    6.9   0.0    0.0065       8.9      12      25 ..      46      59 ..      36      60 .. 0.85
   3 !   10.9   0.0   0.00032      0.44       3      28 ..      66      93 ..      64      95 .. 0.81
   4 !    9.8   0.0   0.00072         1       4      28 ..     100     126 ..      97     128 .. 0.73
   5 !    7.5   0.0    0.0041       5.6       3      21 ..     132     150 ..     130     158 .. 0.83
   6 !    8.8   0.0    0.0016       2.2       3      27 ..     163     189 ..     161     191 .. 0.91
   7 !    8.7   0.0    0.0017       2.4       4      27 ..     197     222 ..     194     225 .. 0.85
   8 !   10.9   0.0   0.00034      0.46       4      26 ..     231     253 ..     230     254 .. 0.89
   9 !    7.5   0.0    0.0041       5.6       3      28 ..     262     288 ..     262     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.4
                                  HHHHHHC CS
                          HEAT 24 Lgalaev 30
                                  L  l+ +
  gi|91772701|ref|YP_565393.1| 21 LISLCAG 27
                                  3333333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0065
                                  SSHHHHHHHHHHHH CS
                          HEAT 12 pspeVReaAakaLg 25
                                   +p+VRe Aa++L+
  gi|91772701|ref|YP_565393.1| 46 GNPFVRERAAWTLA 59
                                  69**********96 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00032
                                  HHHHHHHT-..SSHHHHHHHHHHHHHHH CS
                          HEAT  3 PlllkllsD..pspeVReaAakaLgala 28
                                  ++l++  sD  +++ VR++Aa+aLg++ 
  gi|91772701|ref|YP_565393.1| 66 DPLIRVVSDgnEAAIVRRSAAYALGEIG 93
                                  567777788878888***********95 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00072
                                   HHHHHHT-SSHH..HHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspe..VReaAakaLgala 28 
                                   +l++  +D++ e  VR++Aa+aLg++ 
  gi|91772701|ref|YP_565393.1| 100 ILIQVVTDENEEriVRRSAAYALGKIG 126
                                   667777785544448*********996 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0041
                                   HHHHHHHT-SSHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAa 21 
                                   ++l++++sD++ + R+aA+
  gi|91772701|ref|YP_565393.1| 132 DPLIQAISDEDQFLRDAAV 150
                                   578999************8 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.0016
                                   HHHHHHHT-..SSHHHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsD..pspeVReaAakaLgal 27 
                                   ++l++l++D  +s +VR  Aa++Lg++
  gi|91772701|ref|YP_565393.1| 163 DPLIQLINDenESTNVRWHAAYSLGKI 189
                                   6799999**99999***********98 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0017
                                   HHHHHHT-..SSHHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsD..pspeVReaAakaLgal 27 
                                   +l++l++D  ++ eVR+ A  aLg +
  gi|91772701|ref|YP_565393.1| 197 PLIQLMCDenEDLEVRKGATVALGMI 222
                                   6788888888*************988 PP

  == domain 8  score: 10.9 bits;  conditional E-value: 0.00034
                                   HHHHHHT-SSHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaLga 26 
                                   l+l + +D++  +R++Aa+aLg+
  gi|91772701|ref|YP_565393.1| 231 LILVMREDEEIMIRKTAAYALGT 253
                                   5777789**************95 PP

  == domain 9  score: 7.5 bits;  conditional E-value: 0.0041
                                   HHHHHHH.T-SSHHHHHHHHHHHHHHH CS
                          HEAT   3 Plllkll.sDpspeVReaAakaLgala 28 
                                   Pl++ +  +D+   VR+ Aa++L ++ 
  gi|91772701|ref|YP_565393.1| 262 PLIQVMKdRDERDIVRRFAALSLSKIG 288
                                   7888886689*************9986 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.6   0.00038      0.52       1      55 []      48      92 ..      48      92 .. 0.72
   2 !   11.4   0.2   0.00026      0.36       3      55 .]      81     125 ..      79     125 .. 0.73
   3 !    9.6   0.2   0.00094       1.3       3      54 ..     114     155 ..     112     155 .. 0.79
   4 !   10.7   0.0   0.00042      0.58      28      55 .]     160     189 ..     159     189 .. 0.90
   5 !    9.2   0.0    0.0013       1.8      30      53 ..     195     220 ..     193     222 .. 0.88
   6 ?    5.8   0.0     0.015        20      36      53 ..     234     252 ..     225     253 .. 0.68
   7 ?    0.5   0.0      0.66   9.1e+02      42      54 ..     274     286 ..     257     287 .. 0.57
   8 ?    0.5   0.0      0.66   9.1e+02       3      17 ..     276     287 ..     274     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                       HEAT_EZ  1 wrvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd..eVRaaAagaLgnl 55
                                  ++vR+ Aaw+L+    g          +++++L++  +d +    VR  Aa+aLg +
  gi|91772701|ref|YP_565393.1| 48 PFVRERAAWTLA----GTE--------DAMDPLIRVVSDGNEaaIVRRSAAYALGEI 92
                                  689999999994....333........666677777777666644499999999976 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                       HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                   vRr+Aa aLG   + ++e   + + +++         ++  VR  Aa+aLg++
  gi|91772701|ref|YP_565393.1|  81 VRRSAAYALG---EIGDERAVDILIQVVTDEN-----EERIVRRSAAYALGKI 125
                                   9********9...7777766654444444444.....55577*********97 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00094
                       HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLgn 54 
                                   vRr+Aa aLG +       +     +++++L+++ +d+++  R aA+  Lg+
  gi|91772701|ref|YP_565393.1| 114 VRRSAAYALGKIG------DG----KAVDPLIQAISDEDQFLRDAAVCSLGR 155
                                   8999999999555......33....47788888888888899****999997 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00042
                       HEAT_EZ  28 eilpaLlalLnddsd..eVRaaAagaLgnl 55 
                                   +++++L++l nd++   +VR+ Aa+ Lg++
  gi|91772701|ref|YP_565393.1| 160 RAVDPLIQLINDENEstNVRWHAAYSLGKI 189
                                   6799********9997788*********97 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0013
                       HEAT_EZ  30 lpaLlalLnddsd..eVRaaAagaLg 53 
                                   +++L++l++d++   eVR+ A  aLg
  gi|91772701|ref|YP_565393.1| 195 VDPLIQLMCDENEdlEVRKGATVALG 220
                                   789*******7777999********9 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.015
                       HEAT_EZ  36 lL.nddsdeVRaaAagaLg 53 
                                    + +d++ ++R++Aa+aLg
  gi|91772701|ref|YP_565393.1| 234 VMrEDEEIMIRKTAAYALG 252
                                   3424555588********9 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 0.66
                       HEAT_EZ  42 deVRaaAagaLgn 54 
                                   d VR  Aa  L++
  gi|91772701|ref|YP_565393.1| 274 DIVRRFAALSLSK 286
                                   3557777777776 PP

  == domain 8  score: 0.5 bits;  conditional E-value: 0.66
                       HEAT_EZ   3 vRraAawaLGrlagg 17 
                                   vRr Aa+ L+     
  gi|91772701|ref|YP_565393.1| 276 VRRFAALSLS---KI 287
                                   8999999997...33 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.11   1.5e+02      23      36 ..      45      58 ..      36      59 .. 0.73
   2 ?    2.8   0.0     0.094   1.3e+02      13      39 ..      64      92 ..      62      94 .. 0.90
   3 ?    2.5   0.0      0.12   1.7e+02       8      33 ..      92     119 ..      91     126 .. 0.67
   4 ?    2.5   0.0      0.12   1.6e+02      13      36 ..     130     153 ..     129     155 .. 0.78
   5 !    6.9   0.0    0.0048       6.7      13      28 ..     161     176 ..     158     182 .. 0.87
   6 !   15.6   0.0   8.7e-06     0.012      12      37 ..     193     220 ..     188     224 .. 0.92
   7 ?    0.0   0.0      0.72   9.9e+02      15      37 ..     229     252 ..     221     252 .. 0.77
   8 ?   -2.8   0.0       5.5   7.6e+03      15      26 ..     261     272 ..     260     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                                  TSSHHHHHHHHHHH CS
                           Arm 23 sedeevqeeAawAL 36
                                  ++++ v+e Aaw+L
  gi|91772701|ref|YP_565393.1| 45 NGNPFVRERAAWTL 58
                                  6666699******9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.094
                                  HHHHHHHHTT..TSSHHHHHHHHHHHHHH CS
                           Arm 13 avppLvrLLs..sedeevqeeAawALsNL 39
                                  a++pL+r  s  +e   v++ Aa AL+ +
  gi|91772701|ref|YP_565393.1| 64 AMDPLIRVVSdgNEAAIVRRSAAYALGEI 92
                                  799*******9999999999999999976 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.12
                                   HHHTTHHHHHHHHTT..TSSHHHHHHHH CS
                           Arm   8 vieaGavppLvrLLs..sedeevqeeAa 33 
                                   + +  av++L++  +  +e   v++ Aa
  gi|91772701|ref|YP_565393.1|  92 IGDERAVDILIQVVTdeNEERIVRRSAA 119
                                   567889*********7444444444455 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.12
                                   HHHHHHHHTTTSSHHHHHHHHHHH CS
                           Arm  13 avppLvrLLssedeevqeeAawAL 36 
                                   av+pL++ +s+ed+ ++ +A++ L
  gi|91772701|ref|YP_565393.1| 130 AVDPLIQAISDEDQFLRDAAVCSL 153
                                   89********99876666666665 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0048
                                   HHHHHHHHTTTSSHHH CS
                           Arm  13 avppLvrLLssedeev 28 
                                   av+pL++L+++e+e++
  gi|91772701|ref|YP_565393.1| 161 AVDPLIQLINDENEST 176
                                   8*********888875 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 8.7e-06
                                   THHHHHHHHTT..TSSHHHHHHHHHHHH CS
                           Arm  12 GavppLvrLLs..sedeevqeeAawALs 37 
                                    av+pL++L+   +ed ev++ A+ AL+
  gi|91772701|ref|YP_565393.1| 193 IAVDPLIQLMCdeNEDLEVRKGATVALG 220
                                   58************************97 PP

  == domain 7  score: 0.0 bits;  conditional E-value: 0.72
                                   HHHHHHTT.TSSHHHHHHHHHHHH CS
                           Arm  15 ppLvrLLs.sedeevqeeAawALs 37 
                                   + L+  ++ +e  ++++ Aa AL+
  gi|91772701|ref|YP_565393.1| 229 DSLILVMReDEEIMIRKTAAYALG 252
                                   55666666788999******9996 PP

  == domain 8  score: -2.8 bits;  conditional E-value: 5.5
                                   HHHHHHTTTSSH CS
                           Arm  15 ppLvrLLssede 26 
                                   +pL++ +++ de
  gi|91772701|ref|YP_565393.1| 261 EPLIQVMKDRDE 272
                                   599999999887 PP

>> Vitellogenin_N  Lipoprotein amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.054        74     558     588 ..      92     122 ..      59     131 .. 0.81
   2 !   10.7   0.0   9.1e-05      0.13     499     588 ..     134     219 ..     128     220 .. 0.88
   3 !   11.1   0.0   6.6e-05     0.091     505     608 ..     206     303 ..     190     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.054
                                   T-HHHHHHHHHHHHH-TTS-HHHHHHHHHHH CS
                Vitellogenin_N 558 kaprkvrsvllriyentaekpevRvaAvlal 588
                                     ++ + ++l++++ +++e+  vR  A++al
  gi|91772701|ref|YP_565393.1|  92 IGDERAVDILIQVVTDENEERIVRRSAAYAL 122
                                   445668899***************9999998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.1e-05
                                   HHHHHHTT-HHHHHHHHHHHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HH CS
                Vitellogenin_N 499 lkeavekgdsekiqvylkaLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllriyentaekpe 579
                                   l +a++++d+  +  ++ +Lg  G++  ++ l +++  +e+ st vR +a  +L    k +++ + + l++++ +++e+ e
  gi|91772701|ref|YP_565393.1| 134 LIQAISDEDQFLRDAAVCSLGRCGNKRAVDPLIQLI-NDENESTNVRWHAAYSLG---KIKDEIAVDPLIQLMCDENEDLE 210
                                   6678888888889999999*****************.9999*************9...77778899*************** PP

                                   HHHHHHHHH CS
                Vitellogenin_N 580 vRvaAvlal 588
                                   vR  A +al
  gi|91772701|ref|YP_565393.1| 211 VRKGATVAL 219
                                   **8887765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 6.6e-05
                                   TT-HHHHHHHHHHHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HHHHHHHH CS
                Vitellogenin_N 505 kgdsekiqvylkaLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllriyentaekpevRvaAv 585
                                   ++d e +  +  aLg +G +e++++l   +   e  + ++R +a  aL    ++ ++ v + l+++++++ e   vR  A+
  gi|91772701|ref|YP_565393.1| 206 NEDLEVRKGATVALGMIGDDETVDSLILVM--REDEEIMIRKTAAYALG---TTGDDRVAEPLIQVMKDRDERDIVRRFAA 281
                                   455556666889**************8888..888889***********...888888*********************** PP

                                   HHHHHT---HHHHHHHHHHHTT- CS
                Vitellogenin_N 586 lalmetkPsaallqriaestnkd 608
                                   l l +   s + ++ + +++ ++
  gi|91772701|ref|YP_565393.1| 282 LSLSKI-GSEEAMESLTQVMDDE 303
                                   ***999.5555577777777666 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 ?    1.6   0.0      0.18   2.5e+02      23      49 ..      65      93 ..      59     127 .. 0.51
   2 ?    3.6   0.1     0.044        60      22      46 ..     130     154 ..      80     171 .. 0.68
   3 !    5.8   0.0    0.0094        13      23      88 ..     131     192 ..     128     204 .. 0.75
   4 ?    4.8   0.0     0.019        27       2      44 ..     211     250 ..     177     254 .. 0.52
   5 !   10.6   0.0   0.00032      0.43       1      57 [.     242     296 ..     242     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                          Cnd1 23 vepLrkrLkDed..pyVRktaaivvakLi 49
                                  ++pL + ++D +  + VR+ aa+++ ++ 
  gi|91772701|ref|YP_565393.1| 65 MDPLIRVVSDGNeaAIVRRSAAYALGEIG 93
                                  55555555554411356666666655432 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.044
                          Cnd1  22 lvepLrkrLkDedpyVRktaaivva 46 
                                    v+pL ++++Ded+  R  a+  + 
  gi|91772701|ref|YP_565393.1| 130 AVDPLIQAISDEDQFLRDAAVCSLG 154
                                   3455555666666666666655544 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0094
                          Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDen..prVvanalaalteisek 88 
                                   v+pL ++++Ded+  R  a+  + +      + +k  ++ l +l++Den  ++V+  a ++l +i+++
  gi|91772701|ref|YP_565393.1| 131 VDPLIQAISDEDQFLRDAAVCSLGR------CGNKRAVDPLIQLINDENesTNVRWHAAYSLGKIKDE 192
                                   7899999999999999999988866......6677777888888888884456777777777777765 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.019
                          Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaiv 44 
                                   +R  a ++lg+i  +++v+ l+  +r   +De+ ++Rktaa++
  gi|91772701|ref|YP_565393.1| 211 VRKGATVALGMIGDDETVDSLILVMR---EDEEIMIRKTAAYA 250
                                   34444444444444444444444444...35555555555544 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00032
                          Cnd1   1 liRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkek 57 
                                   +iR  a  +lg+   + + e+l++ ++   +De   VR+ aa+ ++k+ +++ +++ 
  gi|91772701|ref|YP_565393.1| 242 MIRKTAAYALGTTGDDRVAEPLIQVMKD--RDERDIVRRFAALSLSKIGSEEAMESL 296
                                   79999*********************99..5****************9888877654 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 ?   -1.8   0.0       2.1   2.9e+03      63     104 ..      35      73 ..      11      92 .. 0.67
   2 !   13.5   0.0     4e-05     0.055      65     118 ..     101     153 ..      95     156 .. 0.83
   3 ?    3.6   0.0     0.046        63      65     111 ..     165     210 ..     160     222 .. 0.77
   4 ?   -1.4   0.0       1.6   2.2e+03      83     119 ..     215     252 ..     209     255 .. 0.67
   5 ?   -0.4   0.0       0.8   1.1e+03      80     118 ..     244     284 ..     229     315 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                 Aconitase_B_N  63 efLaaiakgeaesplispeeAvelLgtMlGGynvksLidllk 104
                                   + L ++++++  +p + ++ A +l gt     ++++Li +++
  gi|91772701|ref|YP_565393.1|  35 GSLIHVIEDKNGNPFVRERAAWTLAGTE---DAMDPLIRVVS 73 
                                   5566777777777777777777776663...34555555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4e-05
                 Aconitase_B_N  65 LaaiakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                   L +++++e e +++  ++A   Lg++  G +v++Li++++++d+ l+++a+  L
  gi|91772701|ref|YP_565393.1| 101 LIQVVTDENEERIVR-RSAAYALGKIGDGKAVDPLIQAISDEDQFLRDAAVCSL 153
                                   778888888777665.5666789********************99999998776 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.046
                 Aconitase_B_N  65 LaaiakgeaesplispeeAvelLgtMlGGynvksLidllkekdeela 111
                                   L +++++e es+ +  +     Lg+++   +v++Li+l+ +++e+l+
  gi|91772701|ref|YP_565393.1| 165 LIQLINDENESTNVRWHA-AYSLGKIKDEIAVDPLIQLMCDENEDLE 210
                                   567888899999987655.5679***************987766553 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.6
                 Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekdee.laeeaaeaLk 119
                                   A+  Lg +     v+sLi +++e++e  ++++aa aL 
  gi|91772701|ref|YP_565393.1| 215 ATVALGMIGDDETVDSLILVMREDEEImIRKTAAYALG 252
                                   66667755556789999999996655414666777765 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.8
                 Aconitase_B_N  80 peeAvelLgtMlGGynvksLidllkekdee..laeeaaeaL 118
                                   +++A   Lgt       ++Li+++k++de+  +++ aa  L
  gi|91772701|ref|YP_565393.1| 244 RKTAAYALGTTGDDRVAEPLIQVMKDRDERdiVRRFAALSL 284
                                   55566666666555566677777775444311333333333 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 ?    2.7   0.0     0.055        76     166     221 ..      83     138 ..      54     144 .. 0.68
   2 !   13.1   0.0   3.8e-05     0.053     121     222 ..     108     203 ..      95     226 .. 0.79
   3 ?    2.8   0.0     0.051        71     176     254 ..     222     297 ..     204     317 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.055
                                   HHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHH...HHHHHHHHCC-S-HHHHHHHHHHC CS
                       ERAP1_C 166 rwavycalaanggeaewdallerykdtsapse...keaalralaatpdpellerllnfv 221
                                   r+a+y+ +   g+e  +d l++ + d++   e   ++ a++al+ + d +++  l++ +
  gi|91772701|ref|YP_565393.1|  83 RSAAYALG-EIGDERAVDILIQVVTDENE--ErivRRSAAYALGKIGDGKAVDPLIQAI 138
                                   33344444.44688888888888755554..2245888888888888777777666666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.8e-05
                                   S-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-S.SHHHHHH CS
                       ERAP1_C 121 shldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallerykdts.apsekea 200
                                   ++ ++ +r+++  a+++ gd+++v+ + +   +        ++ lr a++c+l + g++  +d l+++ +d++ + + + +
  gi|91772701|ref|YP_565393.1| 108 ENEERIVRRSAAYALGKIGDGKAVDPLIQAISDE-------DQFLRDAAVCSLGRCGNKRAVDPLIQLINDENeSTNVRWH 181
                                   4578889999999999999997777666554444.......789*********999*************98873457799* PP

                                   HHHHHCC-S-HHHHHHHHHHCT CS
                       ERAP1_C 201 alralaatpdpellerllnfvl 222
                                   a+++l+ ++d+ ++  l++++ 
  gi|91772701|ref|YP_565393.1| 182 AAYSLGKIKDEIAVDPLIQLMC 203
                                   **********999998888876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.051
                                   HS-HHHHHHHHHHH.HC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHHH.HSTTHHHHHHHHHH CS
                       ERAP1_C 176 nggeaewdallery.kdtsapsekeaalralaatpdpellerllnfvlesdevrnqdlrallaglannpegrellwefvk 254
                                    g+++ +d+l+    +d+ +   +++a++al+ t d  + e l++ +  +      d+   +a+l+ ++ g+e++ e ++
  gi|91772701|ref|YP_565393.1| 222 IGDDETVDSLILVMrEDEEI-MIRKTAAYALGTTGDDRVAEPLIQVMK-DR--DERDIVRRFAALSLSKIGSEEAMESLT 297
                                   46788888888665223334.668888888888888777777666663.43..344444444444336777777766554 PP

>> RICTOR_V  Rapamycin-insensitive companion of mTOR, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.87   1.2e+03      44      56 ..      81      93 ..      56     105 .. 0.73
   2 ?    1.2   0.0      0.32   4.4e+02      43      55 ..     113     125 ..      80     138 .. 0.57
   3 ?    3.4   0.0     0.064        88      30      55 ..     197     222 ..     113     227 .. 0.64
   4 ?    5.9   0.0     0.011        16      27      54 ..     226     253 ..     221     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.87
                      RICTOR_V 44 lRGtafyvLglis 56
                                  +R  a y+Lg i+
  gi|91772701|ref|YP_565393.1| 81 VRRSAAYALGEIG 93
                                  5555556665554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                      RICTOR_V  43 slRGtafyvLgli 55 
                                    +R  a y+Lg i
  gi|91772701|ref|YP_565393.1| 113 IVRRSAAYALGKI 125
                                   3455555555555 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.064
                      RICTOR_V  30 edivelaeespvlslRGtafyvLgli 55 
                                   + i  ++ e + l +R  a ++Lg+i
  gi|91772701|ref|YP_565393.1| 197 PLIQLMCDENEDLEVRKGATVALGMI 222
                                   33444556666666666666666666 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.011
                      RICTOR_V  27 divedivelaeespvlslRGtafyvLgl 54 
                                   + v++++ +++e + + +R ta y+Lg 
  gi|91772701|ref|YP_565393.1| 226 ETVDSLILVMREDEEIMIRKTAAYALGT 253
                                   678999999*****************97 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.28   3.9e+02     114     140 ..      63      91 ..      58     111 .. 0.64
   2 ?    7.5   0.0   0.00094       1.3     323     370 ..      96     159 ..      94     194 .. 0.71
   3 ?    4.4   0.0    0.0082        11      84     141 ..     134     189 ..     130     236 .. 0.68
   4 ?    0.9   0.0     0.094   1.3e+02      94     143 ..     242     289 ..     235     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHT-SSH..HHHHHHHHHHHH CS
                     Adaptin_N 114 dlapaikkllkdrsp..yvrkkAalailk 140
                                   d ++ + ++++d +    vr++Aa+a+  
  gi|91772701|ref|YP_565393.1|  63 DAMDPLIRVVSDGNEaaIVRRSAAYALGE 91 
                                   56666666666665555666666666543 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00094
                                   HHHHHHCCCXXTTTHHHHHHHHHHH..............TTSSXXHH..HHHHHHHHHHHHHHH CS
                     Adaptin_N 323 kaldlllklvdesNvkeivkeLkky..............vkevaded..fksklvkaIgrlaek 370
                                   +a+d+l++ v+++N ++iv+    y              ++ ++ded  +++++v ++gr++ k
  gi|91772701|ref|YP_565393.1|  96 RAVDILIQVVTDENEERIVRRSAAYalgkigdgkavdplIQAISDEDqfLRDAAVCSLGRCGNK 159
                                   8999999999999999999999999555555555544444556666666666666666666655 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0082
                                   HHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHC CS
                     Adaptin_N  84 lqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailkl 141
                                   l ++ +d +q++r  A+++L++ + ++ ++ l + i +  + +s+ vr  Aa+++ k+
  gi|91772701|ref|YP_565393.1| 134 LIQAISDEDQFLRDAAVCSLGRCGNKRAVDPLIQLIND--ENESTNVRWHAAYSLGKI 189
                                   56678888999999999999999888877766655555..344447888777776655 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.094
                                   HHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCC CS
                     Adaptin_N  94 lirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklyk 143
                                   +ir  A  +L++ +++++ae l + +k+  +d++  vr+ Aal++ k+ +
  gi|91772701|ref|YP_565393.1| 242 MIRKTAAYALGTTGDDRVAEPLIQVMKD--RDERDIVRRFAALSLSKIGS 289
                                   5666666666666666666666655555..46666999999998888754 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.011        16       7      40 ..      96     129 ..      91     139 .. 0.87
   2 ?    5.4   0.0     0.014        19      26      65 ..     159     201 ..     157     205 .. 0.71
   3 ?    0.4   0.1      0.49   6.7e+02      15      39 ..     266     290 ..     257     310 .. 0.50
   4 ?   -0.4   0.0       0.9   1.2e+03       6      20 ..     290     304 ..     285     318 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TT CS
                       UPF0147   7 evielLeeiiedtsvPrniRraakeakekLkdek 40 
                                   +++++L ++++d++  r +Rr+a  a+ k+ d k
  gi|91772701|ref|YP_565393.1|  96 RAVDILIQVVTDENEERIVRRSAAYALGKIGDGK 129
                                   7899*******************99998887765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHT-TTS-HHHH..HHHHHH.HHHHHHT-TTS-H CS
                       UPF0147  26 RraakeakekLkdekeslavr..aatais.iLdeisnDpnmPl 65 
                                   +ra++  ++ ++de+es +vr  aa ++  i dei+ Dp ++l
  gi|91772701|ref|YP_565393.1| 159 KRAVDPLIQLINDENESTNVRwhAAYSLGkIKDEIAVDPLIQL 201
                                   5777888889999999999984344444324588988887765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.49
                                   HHT-TTS-HHHHHHHHHHHHHHT-T CS
                       UPF0147  15 iiedtsvPrniRraakeakekLkde 39 
                                   +++d++    +Rr a  +++k+ +e
  gi|91772701|ref|YP_565393.1| 266 VMKDRDERDIVRRFAALSLSKIGSE 290
                                   4444444444444444444443333 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.9
                                   HHHHHHHHHHHT-TT CS
                       UPF0147   6 kevielLeeiiedts 20 
                                   +e++e L+++++d++
  gi|91772701|ref|YP_565393.1| 290 EEAMESLTQVMDDEN 304
                                   567778888887765 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.88   1.2e+03      37      55 ..      40      58 ..      36      61 .. 0.76
   2 ?    0.6   0.0       0.5   6.9e+02      34      54 ..      68      88 ..      62      92 .. 0.79
   3 ?    4.1   0.0      0.04        55      30      54 ..      97     121 ..      95     125 .. 0.89
   4 ?    1.2   0.0      0.34   4.7e+02      33      54 ..     164     185 ..     158     188 .. 0.84
   5 ?   -1.1   0.0       1.8   2.4e+03      46      54 ..     242     250 ..     233     252 .. 0.81
   6 ?   -0.0   0.0      0.81   1.1e+03      30      52 ..     292     314 ..     287     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.88
                       UPF0253 37 vaanealpeevrekAAyAA 55
                                  v ++++ +  vre+AA+  
  gi|91772701|ref|YP_565393.1| 40 VIEDKNGNPFVRERAAWTL 58
                                  6666777778******975 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.5
                       UPF0253 34 LdevaanealpeevrekAAyA 54
                                  L +v+++ +  + vr +AAyA
  gi|91772701|ref|YP_565393.1| 68 LIRVVSDGNEAAIVRRSAAYA 88
                                  55677777888889******9 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.04
                       UPF0253  30 alktLdevaanealpeevrekAAyA 54 
                                   a+  L +v+ +e+ ++ vr +AAyA
  gi|91772701|ref|YP_565393.1|  97 AVDILIQVVTDENEERIVRRSAAYA 121
                                   6778889*****************9 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.34
                       UPF0253  33 tLdevaanealpeevrekAAyA 54 
                                    L ++ ++e+ + +vr +AAy 
  gi|91772701|ref|YP_565393.1| 164 PLIQLINDENESTNVRWHAAYS 185
                                   56688999999**********5 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 1.8
                       UPF0253  46 evrekAAyA 54 
                                    +r  AAyA
  gi|91772701|ref|YP_565393.1| 242 MIRKTAAYA 250
                                   5899****9 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 0.81
                       UPF0253  30 alktLdevaanealpeevrekAA 52 
                                   a++ L +v ++e+ +  +r++AA
  gi|91772701|ref|YP_565393.1| 292 AMESLTQVMDDENESGYMRDSAA 314
                                   78899999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1860.53
//
Query:       gi|91772702|ref|YP_565394.1|  [L=399]
Description: hypothetical protein Mbur_0676 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-47  158.9   0.5    4.5e-47  158.9   0.5    1.6  2  UPF0228        Uncharacterised protein family (UPF0228)
  ------ inclusion threshold ------
      0.083   13.0   3.7       0.16   12.0   3.7    1.3  1  Herpes_capsid  Gammaherpesvirus capsid protein


Domain annotation for each model (and alignments):
>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.5   4.5e+03      14      43 ..     168     195 ..     155     215 .. 0.60
   2 !  158.9   0.5   5.1e-51   4.5e-47       4     121 ..     267     395 ..     264     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.5
                       UPF0228  14 veekyYivvdkdnitdvrkelekeknwtss 43 
                                   + +  Y+    d+ + v++e+e ++ w+ +
  gi|91772702|ref|YP_565394.1| 168 TMN--YTDCRMDEPVLVYYEIEGHEAWMLN 195
                                   433..5555555555566666666666655 PP

  == domain 2  score: 158.9 bits;  conditional E-value: 5.1e-51
                       UPF0228   4 nYtieydsniveekyYivvdkdnitdvrkelekeknwtssipaikkgdeyiievseqaied............eevlaiLe 72 
                                    Y+++yd++++++ +Y++vd++n+t+v+++l++++nw++++pai+kgd+y+ie+se++ied            eev++iL+
  gi|91772702|ref|YP_565394.1| 267 GYELQYDVDYFGPGSYVCVDENNFTSVKQRLQQTENWIDAGPAIRKGDRYYIEISEHVIEDydfedegdyegrEEVREILN 347
                                   59******************************************************************************* PP

                       UPF0228  73 kydlqvkkfvwCyiefgdgsekywineedairikneLeknekilsvsld 121
                                   +ydl+vk+fvwCy+e+g+g+ek+ +ne++a+rik+eLe +e+il+v+ld
  gi|91772702|ref|YP_565394.1| 348 IYDLPVKRFVWCYLEYGSGTEKQ-FNEANASRIKKELEGHEMILKVYLD 395
                                   *********************99.***********************99 PP

>> Herpes_capsid  Gammaherpesvirus capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.7   1.8e-05      0.16     119     154 ..      28      63 ..      20      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                 Herpes_capsid 119 asGasGgsastlsSgpsssaaasglssgasStsdta 154
                                   + G +Ggs st++ ++++sa+a gl ++ +S  d+ 
  gi|91772702|ref|YP_565394.1|  28 GEGETGGSLSTKATANTTSASATGLDTSFPSSDDAF 63 
                                   7899***************************99883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2311.84
//
Query:       gi|91772703|ref|YP_565395.1|  [L=150]
Description: hypothetical protein Mbur_0678 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0086   16.2   0.3      0.013   15.6   0.3    1.3  1  Hit1_C    Hit1 C-terminal
  ------ inclusion threshold ------
      0.058   13.5   0.9      0.091   12.9   0.8    1.4  1  Mg296     Mg296 protein


Domain annotation for each model (and alignments):
>> Hit1_C  Hit1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.5e-06     0.013      20      64 ..      67     115 ..      56     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                        Hit1_C  20 vkfhlakv.yrilttsegn...ggssdtlsseakkqlavdylntlryGG 64 
                                   +++hl+k+ +  l  ++++   ++s++tl s  k +la+dy n   yG 
  gi|91772703|ref|YP_565395.1|  67 MRYHLHKIdFDQLIENNAKillQSSHKTLDSSKKYDLAIDYTNDPYYGE 115
                                   78*****9656666655542324566779**************999985 PP

>> Mg296  Mg296 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8     1e-05     0.091       8      68 ..      64     124 ..      57     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                                   HHHHHHHHHTS-HHHHHHHHHHHHHHHHT-SSGGGSS---.S-HHHHHHHHHHHHHHHHHHH CS
                         Mg296   8 ktflkeilekvdlekliqnynlileretstlliyedddye.eidffeksieselfyvksklv 68 
                                   kt ++  l+k+d+++li+n  +il ++ +  l      y+  id+ + +  +e++ v+++ v
  gi|91772703|ref|YP_565395.1|  64 KTSMRYHLHKIDFDQLIENNAKILLQSSHKTL-DSSKKYDlAIDYTNDPYYGEANSVNENYV 124
                                   7889999*****************99988766.45566764789999999999998876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 971.61
//
Query:       gi|91772704|ref|YP_565396.1|  [L=574]
Description: thiamine pyrophosphate requiring enzyme [Methanococcoides burtonii DSM 6242]
Scores for complete 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-49  166.9   0.0    8.7e-49  165.4   0.0    1.7  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    6.5e-38  129.9   0.1    9.4e-37  126.2   0.1    2.3  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      9e-28   96.7   0.0    2.4e-27   95.3   0.0    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


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 !  165.4   0.0   1.5e-52   8.7e-49       1     167 [.       4     168 ..       4     171 .. 0.98
   2 ?   -3.3   0.0         1   6.1e+03     115     159 ..     500     540 ..     488     543 .. 0.63

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 1.5e-52
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   m++ae+lv++L++lgv+h+fg+ G  ilp++ al++++ i++v+ ++Eq++af A gy+r+++++gv++vtsgp++tn+lt
  gi|91772704|ref|YP_565396.1|   4 MNGAEVLVKCLEDLGVKHIFGYTGAAILPVFHALEKSD-IKIVVNSNEQSCAFSAAGYSRSSNEVGVAIVTSGPAITNTLT 83 
                                   89***********************************6.****************************************** PP

                                   HHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                   ++a+A+ d+iPllv++g++p++++g++ +q  ++ +++f + +k + ++++ +++++++++A+  a sg+pgPv++++p+d
  gi|91772704|ref|YP_565396.1|  84 SVADAYGDSIPLLVFAGQVPEHKIGTDSFQ-HINVKGIFGDAAKKVIQLSNGDDIESIVKDAYYFARSGKPGPVVIDVPLD 163
                                   ******************************.************************************************** PP

                                   HCC-E CS
                  TPP_enzyme_N 163 vllee 167
                                    +++ 
  gi|91772704|ref|YP_565396.1| 164 KQQKL 168
                                   98875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                                   -CCHHHCCCS.SEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEE CS
                  TPP_enzyme_N 115 dqlalfrpvt.kyaervtspeelpealrrAirtalsgrpgPvylel 159
                                   + +++++++  +ya r+++ ++l++ l++ +        gP +le+
  gi|91772704|ref|YP_565396.1| 500 HFADIANSFGfNYAKRISDRNDLKQGLEDFLNSE-----GPCFLEV 540
                                   4555555554477888888888877777665544.....6666665 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 ?    1.2   0.0     0.048   2.9e+02     122     153 .]     125     160 ..     101     160 .. 0.77
   2 !  126.2   0.1   1.6e-40   9.4e-37       1     153 []     391     540 ..     391     540 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.048
                                   SE.EEEESSH.HHHHHHHHHHHH.....CSSSEEEEEE CS
                  TPP_enzyme_C 122 ak.garvekadveeleealkeal.....ekkgpaliev 153
                                   ak ++++++   +++e ++k+a       k gp++i+v
  gi|91772704|ref|YP_565396.1| 125 AKkVIQLSNG--DDIESIVKDAYyfarsGKPGPVVIDV 160
                                   3436676777..**********999999999*****97 PP

  == domain 2  score: 126.2 bits;  conditional E-value: 1.6e-40
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvln 81 
                                   ++G+ ++ aa++l++++ +s+++sg +gtmG+++paAiG+  a+p+++v++i GDG++ m+l el t++  + p+++++ln
  gi|91772704|ref|YP_565396.1| 391 GVGNQQMLAAQHLSMQKEKSFMSSGSFGTMGFSMPAAIGVHYANPNARVISIDGDGSLKMNLGELHTIASLDMPVKILLLN 471
                                   69******************************************************************************* PP

                                   -SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEE.EESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  82 NegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakga.rvekadveeleealkealekkgpaliev 153
                                   N++ gm+++ q+ ++++ ++++++  +k+v+fa +a ++G + a r++++  ++l++ l++ l+++gp+++ev
  gi|91772704|ref|YP_565396.1| 472 NQSDGMVQNLQDANYDGIRTATQR--QKDVHFADIANSFGFNYAkRISDR--NDLKQGLEDFLNSEGPCFLEV 540
                                   ********************9997..99**************555*9999..*******************97 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 !   95.3   0.0   4.1e-31   2.4e-27       2     137 .]     195     331 ..     194     331 .. 0.90
   2 ?   -3.9   0.0       1.8   1.1e+04     101     112 ..     434     445 ..     430     447 .. 0.79

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 4.1e-31
                                   HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEE CS
                  TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvl 82 
                                   e+  +ll ++++p++++Ggg +++  s ++rel e+lgiP v+tlm+kgv++e+++ ++gmlg++g+++an++++e D+ +
  gi|91772704|ref|YP_565396.1| 195 EEFFQLLTKSSKPLLYLGGGLNSEAGSYAIRELNEQLGIPSVNTLMAKGVVDERDDINMGMLGMFGTPYANMLIQENDFFF 275
                                   57789**************************************************************************** PP

                                   EES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC...--SEEEECTHHHHHHHH CS
                  TPP_enzyme_M  83 alGarfddirttgsepefapeakiihididpaeigkny...qvdlaivgdvketleaL 137
                                   a+G+r+dd r++++   fa  + +  idi+p+++++ +    ++ + +gd+ ++++ L
  gi|91772704|ref|YP_565396.1| 276 AIGVRWDD-RVAEKV-GFAIGTDVAYIDINPEKMHQIKierAPKFTFIGDAPTAIRDL 331
                                   ********.887655.5666668999****9888877644468899999999888765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.8
                                   TTT-EEEEEESS CS
                  TPP_enzyme_M 101 apeakiihidid 112
                                   +p+a++i id d
  gi|91772704|ref|YP_565396.1| 434 NPNARVISIDGD 445
                                   6788*****988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3884.14
//
Query:       gi|91772705|ref|YP_565397.1|  [L=250]
Description: beta-lactamase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-22   78.7   0.0      5e-22   78.4   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    2.9e-11   43.7   0.6    8.8e-11   42.2   0.3    2.0  2  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0033   17.3   0.1       0.01   15.8   0.1    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   8.3e-26     5e-22       2     200 ..      32     215 ..      31     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 8.3e-26
                                   EEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE.EEEEEEHHHHHHCCTTC.GH CS
                 Lactamase_B_2   2 riLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk.lplyapkgvlavleanf.vy 76 
                                    +L+D+g +++   +++       +++  +id ++l+h H DH+a++++l +   l++k  + +y+p g+++ l + + +y
  gi|91772705|ref|YP_565397.1|  32 KVLFDCGGGILNRiFESG-----VLHT--EIDTIVLSHLHLDHVADVMCLLKanwLCEKLdAVIYGPVGTQEWLGRLMaIY 105
                                   69*******987743333.....4788..9**********************9996665457799*******998886256 PP

                                   HHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT- CS
                 Lactamase_B_2  77 laleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgga 157
                                     ++++ +v+v+e+ +ge+fel   g+++++t   h+ +          lG+r+e +g+ v+y+gDt+ ++ +i ++ +ga
  gi|91772705|ref|YP_565397.1| 106 PYMKVKVNVEVREVVAGEEFELS-QGCNVRCTDGIHSVPS---------LGYRVEHDGEVVVYSGDTEPCD-SIMKLAQGA 175
                                   66666689**************8.589************9.........*******************999.8888***** PP

                                   SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                 Lactamase_B_2 158 dllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                   d+l++++ +  d  m     H+tp+     ++  ++++++l+H
  gi|91772705|ref|YP_565397.1| 176 DMLIHECSFPLDFPMT---NHATPDMLRPYLENSDISKVYLTH 215
                                   ********99998865...699999888888888888888888 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.3   1.5e-14   8.8e-11       9     153 ..      24     164 ..      17     198 .. 0.81
   2 ?   -2.1   0.0      0.53   3.1e+03      39      53 ..     202     216 ..     190     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.5e-14
                                   EEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHH CS
                   Lactamase_B   9 yliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeadd 89 
                                   +lie ++  +L+D+G++  +  +       g+   ++d+++l+HlHlDH+++++ l +a + +    a ++    + e  +
  gi|91772705|ref|YP_565397.1|  24 VLIEYGENKVLFDCGGGILNRIFE-----SGVLHTEIDTIVLSHLHLDHVADVMCLLKANWLCEKLDAVIYGPVGTQEWLG 99 
                                   89*********************9.....6**********************87666666655555555555555555544 PP

                                   HHHHCCHH.TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                   Lactamase_B  90 aasrkgll.lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall 153
                                     ++   + +  v++   +v+  e+ +   g+    + g++   +++++ve +g+ v+++GD+ +
  gi|91772705|ref|YP_565397.1| 100 RLMAIYPYmKVKVNVEVREVVAGEEFELSQGCNVRCTDGIHSVPSLGYRVEHDGEVVVYSGDTEP 164
                                   444333224445888888888888888888899999999***********************975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.53
                                   TSGGGGEEEEE-SBS CS
                   Lactamase_B  39 glkpkdvdavilTHl 53 
                                   +l+  d++ v lTHl
  gi|91772705|ref|YP_565397.1| 202 YLENSDISKVYLTHL 216
                                   678899********6 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 !   15.8   0.1   1.7e-06      0.01       9     131 ..      23     177 ..      20     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                 Lactamase_B_3   9 sflletagarilvDPfka....nlgyeppaeeaDlvlisqaledHahletlkql........................... 58 
                                    +l+e ++ ++l D + +      + +    e+D +++s+ + dH +      l                           
  gi|91772705|ref|YP_565397.1|  23 GVLIEYGENKVLFDCGGGilnrIFESGVLHTEIDTIVLSHLHLDHVADVMCL-Lkanwlcekldaviygpvgtqewlgrlm 102
                                   5788888999999988543211334444459**************8765332.1236888877777777777777777775 PP

                 Lactamase_B_3  59 ..........aenvkvleegeslevg.gleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgr 128
                                             + +v+ +  ge++e+  g+++r + + h         +  g+++e dg  +++ G++     ++  k  + 
  gi|91772705|ref|YP_565397.1| 103 aiypymkvkvNVEVREVVAGEEFELSqGCNVRCTDGIH-------SVPSLGYRVEHDGEVVVYSGDTEP--CDSIMKLAQG 174
                                   55554444333333333334555543245555554444.......78899****************986..4444444445 PP

                 Lactamase_B_3 129 vDv 131
                                   +D 
  gi|91772705|ref|YP_565397.1| 175 ADM 177
                                   555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1662.24
//
Query:       gi|91772706|ref|YP_565398.1|  [L=217]
Description: metallophosphoesterase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-16   60.7   0.0    3.3e-16   59.9   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    7.8e-16   59.2   0.0    1.3e-15   58.5   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
      1e-12   47.9   0.7    7.6e-08   32.0   0.0    2.7  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 !   59.9   0.0   5.5e-20   3.3e-16       1     149 [.       1     198 [.       1     208 [. 0.70

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 5.5e-20
                 Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeep...evleellela..pvlaVrGNnD.............. 62 
                                   Mk+++i+D+H+n++ le + +++ e   d ++ +GD+  +++   + +++l+ ++  pv aV+GN+D              
  gi|91772706|ref|YP_565398.1|   1 MKILAIADIHGNFSHLEDIKDKAGEI--DVVVISGDI--TNFgpsSQVDNLKGIFdvPVFAVPGNCDkrdilevldnseiv 77 
                                   *********************98888..*********..333222488888888899**************9999998888 PP

                 Metallophos_2  63 .....................eevveedvlreaaelgtdl.peeaelelagek......vlliHgdpl.......gvkdal 108
                                                        ++ +   +  e++e++++l p    +e ++ k      vl+ H  p+       g++ + 
  gi|91772706|ref|YP_565398.1|  78 nlhkntekigeftfvgiggssPTPFNTPFELEEQEIEDALePMFNACE-GDCKdckstiVLVSHAPPKglldsisGDNVGS 157
                                   888888777555555555443222444444444444444421222222.22224557779999999889999886444444 PP

                 Metallophos_2 109 aellkeaeegsdvvvcGHtHvp.evekeggvlvvnPGsvgep 149
                                    +++k   ++s++v+c H+H++ +  + g++ +vnPG ++e+
  gi|91772706|ref|YP_565398.1| 158 VSVAKF-IDRSKLVICAHIHEArGFARSGDTFLVNPGMAAEG 198
                                   443333.66788**********455555899999***99987 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   2.1e-19   1.3e-15       1     203 [.       1     177 [.       1     178 [. 0.70

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 2.1e-19
                                   EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH.H CS
                   Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee.e 80 
                                   ++il i+D+H     g+++ l+++ d++    ++d+v++ GD+++ g+ ++  +++l+  ++  +pv++++GN++   + +
  gi|91772706|ref|YP_565398.1|   1 MKILAIADIH-----GNFSHLEDIKDKA---GEIDVVVISGDITNFGPSSQ--VDNLKGIFD--VPVFAVPGNCD---KrD 66 
                                   89********.....**********999...677*************8888..555577777..9**********...335 PP

                                   HHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE...EEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.....HHHHHH CS
                   Metallophos  81 llnkygylgifsepwrsdaevfnnlplaslgsgs...lkvlllhGgspellvsldklgslnleleapepg.....dewlkd 153
                                   +l+  ++++i                   l++++    ++ ++  g        ++ + +n ++e +e++     + +++ 
  gi|91772706|ref|YP_565398.1|  67 ILEVLDNSEIV-----------------NLHKNTekiGEFTFVGIG-------GSSPTPFNTPFELEEQEiedalEPMFNA 123
                                   55555554444.................222222223223333333.......2333345555555555563344333333 PP

                                   ..HHHHTTCSEEEEEESSESS....CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                   Metallophos 154 ..lekrekadwvivlgHsply....rgsgylfgdealedllkkygvdlvisGHtHv 203
                                      + ++ + ++++++H p+     + sg+  g+ +++  +++ + +lvi++H+H+
  gi|91772706|ref|YP_565398.1| 124 ceGDCKDCKSTIVLVSHAPPKglldSISGDNVGSVSVA--KFIDRSKLVICAHIHE 177
                                   77777777788**********88888888888888888..6666667********7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   5.3e-06     0.032       7      44 ..       2      37 ..       1      48 [. 0.88
   2 !   32.0   0.0   1.3e-11   7.6e-08      87     254 ..      50     212 ..      41     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-06
                                  EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES---- CS
                 Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvk 44
                                  k+lai+d++g++  le +++++ +   D++v+ Gd+ +
  gi|91772706|ref|YP_565398.1|  2 KILAIADIHGNFSHLEDIKDKAGE--IDVVVISGDITN 37
                                  9***************99998876..79*******964 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.3e-11
                                   TT-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTEEEEEE-SEEESS--BSSSS-EEEHHHHHHHGGG CS
                 Metallophos_3  87 eldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGevliaGmGGeivdgekeeefrLkYPaweveyrLkv 167
                                     dvp+f vPG+ D      l  + + e+       +h++  ek Ge+ ++G+GG      ++  f L    +e+e +L  
  gi|91772706|ref|YP_565398.1|  50 IFDVPVFAVPGNCDK--RDILEVLDNSEI-----VNLHKN-TEKIGEFTFVGIGGSS-PTPFNTPFEL--EEQEIEDALEP 119
                                   569*********995..455666666444.....445555.4677**********74.3444445555..46777777764 PP

                                   G.G....GS---EE..EEEESS--S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEEE--BGGG CS
                 Metallophos_3 168 l.k....elkdrrk..vlllatpPigelvadkglkekgsevvaelvktlnPevvvvghavkeh..eelgktlvvnPGalee 239
                                   + +    + kd +   vl+ + pP g l+   g  + gs  va+++     ++v+++h + ++     g+t+ vnPG  +e
  gi|91772706|ref|YP_565398.1| 120 MfNacegDCKDCKStiVLVSHAPPKGLLDSISG-DNVGSVSVAKFIDR--SKLVICAHIHEARgfARSGDTFLVNPGMAAE 197
                                   4131112457776522556689*******9999.99**********86..579******999988999************* PP

                                   TEEEEEETTTTEEEE CS
                 Metallophos_3 240 Gdfavvdleekkvel 254
                                   G  a+++le+ +v +
  gi|91772706|ref|YP_565398.1| 198 GYAALIELEQDNVSV 212
                                   **********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1604.26
//
Query:       gi|91772707|ref|YP_565399.1|  [L=259]
Description: hypothetical protein Mbur_0683 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-70  234.7   0.7    9.6e-70  234.5   0.7    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 !  234.5   0.7   5.4e-74   9.6e-70       1     200 [.       7     214 ..       7     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 5.4e-74
                                   EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE....--------------EEEEEEES.SS-.EEEEE--SSSE CS
                         AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet....gllkalkrlltgeslfllkftakiss.gtvllapklpg 76 
                                   ++++g++++l++++L++ge++ ae+Ga+++m ++++m+t    gllk+lkr+++ges+f+++ft++ ++ gtv++++++pg
  gi|91772707|ref|YP_565399.1|   7 YKIHGNEMQLVEIELDQGETVRAEAGAMMFMGDGIKMDTstggGLLKGLKRAFSGESFFITSFTQNGKGkGTVAFGAPYPG 87 
                                   799*************************************************************765557*********** PP

                                   EEEEEEG.GTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEE CS
                         AIM24  77 tivtlel.gggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielkageelvvd 155
                                   +i++++l ++g ++++qkdafL+a+++v++ ++f+k++ +glfggeg++lq+l+G+Gl++++++G+i+++el++ge+l++d
  gi|91772707|ref|YP_565399.1|  88 KIIPIDLaSEGGSFLCQKDAFLCAANGVDITVAFSKKIgAGLFGGEGFILQRLKGNGLAFVHAGGTIIKKELAPGETLRID 168
                                   ******988888************************999****************************************** PP

                                   GGGEEEEETTEEEEEEEETT---STTTTS-E.EEEEEEEEEEEEES CS
                         AIM24 156 pghlvafsgslkfdiervgglkrrligGegl.flkltGpgtvllqs 200
                                   +g+lvafs+s+++die vgg+k++l+gGeg+ +++++Gpgtv+lqs
  gi|91772707|ref|YP_565399.1| 169 TGCLVAFSESVNYDIEFVGGFKNALFGGEGIvLATVSGPGTVYLQS 214
                                   *********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1830.33
//
Query:       gi|91772708|ref|YP_565400.1|  [L=110]
Description: hypothetical protein Mbur_0684 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-16   57.9   0.0    9.6e-16   57.7   0.0    1.0  1  META      META domain


Domain annotation for each model (and alignments):
>> META  META domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   5.4e-20   9.6e-16      16     108 ..      12     102 ..       6     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 5.4e-20
                                   SSCS-BTT---EEEECCCEEEEE-SSSEEEEEEEECTTEEEESSEEE-----SCHHHHCHHHHHHCCCH-CEEEE-SSEEE CS
                          META  16 gkavaasapatltfaedgrvsgsagCNrfsGsytleggrltlgalasTrmaCspalmelEqallkaLqavtsyriegdrLt 96 
                                   ++ v+ +++++ltf+ dg++s ++ CN+  G+ tl+g++ltl +  +T  +   + +++++++l++L++vt++++e+d+L+
  gi|91772708|ref|YP_565400.1|  12 KSVVPGPENYKLTFNLDGTYSIKTDCNHGVGGHTLDGSELTLASGPMTLAYF--SPDSQDSQYLSLLSNVTTVSMENDQLV 90 
                                   567899999*****************************************99..9999*********************** PP

                                   EE-TTS.-EEEE CS
                          META  97 Ltdadgeelltf 108
                                   L  +++ e + f
  gi|91772708|ref|YP_565400.1|  91 LGIRENGEKMLF 102
                                   *96655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.64
# Mc/sec: 519.62
//
Query:       gi|91772709|ref|YP_565401.1|  [L=160]
Description: hypothetical protein Mbur_0685 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-35  120.3   0.0    5.9e-35  120.1   0.0    1.0  1  Zn_protease  Putative ATP-dependant zinc protease


Domain annotation for each model (and alignments):
>> Zn_protease  Putative ATP-dependant zinc protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.0   3.3e-39   5.9e-35       1     137 [.       9     145 ..       9     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 3.3e-39
                   Zn_protease   1 vvGekEelsLpelkiq.lkakidtgaltsSLsagdiesferdgekwVrfkevrldekkaegvvlEakvlrivkirqsagda 80 
                                   ++G++E++ Lpel i+ +k k+dtga+ts+L+a+++e ++++g + Vrf ++ +++++  + ++ a++ +++++ +s+g++
  gi|91772709|ref|YP_565401.1|   9 ILGWREWVALPELGIHaIKVKVDTGAKTSALHAFNVELYRENGVEMVRFLVHPIQRDQDFQIECIAPLKDRRQVTDSGGHK 89 
                                   68**************9********************************999***************************** PP

                   Zn_protease  81 ekRpViklqlllgpeiekievtLtdRsavkypvllgvralikakaaVDpsrkyirkk 137
                                   e+R+Vi+++ ++ +e  +ie tLtdR  +++++llg r+++k +a VDp+ ++i  k
  gi|91772709|ref|YP_565401.1|  90 ETRYVIETDAVIASERYTIELTLTDRDTMRFRMLLG-RSAMKNIAIVDPGASFINGK 145
                                   ************************************.****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1126.31
//
Query:       gi|91772710|ref|YP_565402.1|  [L=301]
Description: SSU ribosomal protein S6P modification protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-68  229.1   0.1    4.2e-68  228.7   0.1    1.1  1  RimK             RimK-like ATP-grasp domain
    7.3e-44  148.1   0.1    1.3e-43  147.3   0.1    1.4  1  Rimk_N           RimK PreATP-grasp domain
    4.1e-18   65.4   0.4    6.7e-18   64.7   0.4    1.3  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    2.7e-09   37.3   0.1    4.4e-09   36.6   0.1    1.3  1  ATP-grasp_3      ATP-grasp domain
    2.9e-07   30.0   0.2     0.0043   16.3   0.0    2.6  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    0.00023   20.8   0.4     0.0019   17.8   0.4    2.0  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0011   18.3   0.0      0.052   12.8   0.0    2.8  3  ATPgrasp_YheCD   YheC/D like ATP-grasp
  ------ inclusion threshold ------
      0.035   13.6   0.2      0.065   12.8   0.2    1.4  1  ATP-grasp_2      ATP-grasp domain
       0.06   13.1   0.1        0.1   12.4   0.1    1.3  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
       0.11   12.5   0.0       0.18   11.8   0.0    1.3  1  R2K_3            ATP-grasp domain, R2K clade family 3
       0.16   11.1   0.0        3.5    6.7   0.0    2.3  2  TTL              Tubulin-tyrosine ligase family


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 !  228.7   0.1   2.6e-71   4.2e-68       2     188 .]      98     286 ..      97     286 .. 0.99

  Alignments for each domain:
  == domain 1  score: 228.7 bits;  conditional E-value: 2.6e-71
                                   H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...GGG--EEE CS
                          RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...lkeailvq 79 
                                   rdKl+sl+lL +++i++p+t  a +++d++++i++++ ++P+vvK +eg+qGi+vvla++++++++v+e+   +k++ilvq
  gi|91772710|ref|YP_565402.1|  98 RDKLRSLQLLSRKGIGMPVTGYASKPDDIKDVIKMVG-GAPLVVKLLEGTQGIGVVLAETQKAAESVIEGfmgVKANILVQ 177
                                   8***********************************9.********************************999******** PP

                                   EE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEETTEEEE CS
                          RimK  80 eyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllrakrgllv 160
                                   eyi+ea+++diR++v++++vva+++r++ +G+FRsnlhrGg ae++ +++ee+  A+ aak+m+l vaGvDllr+++g++v
  gi|91772710|ref|YP_565402.1| 178 EYIKEANGADIRCFVIGGKVVASMKRQAPNGEFRSNLHRGGSAEVIRITPEERSTAVSAAKIMGLNVAGVDLLRSNHGPVV 258
                                   ********************************************************************************* PP

                                   EEEESS--SHHHHHHHT--HHHHHHHHH CS
                          RimK 161 lEvnsspglekiektlgidiakklieai 188
                                   +Evnsspgl++ie  +g dia  +ie+i
  gi|91772710|ref|YP_565402.1| 259 MEVNSSPGLRGIETATGKDIAGMIIEYI 286
                                   **************************98 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   0.1   7.9e-47   1.3e-43       1      94 []       1      94 [.       1      94 [. 1.00

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 7.9e-47
                        Rimk_N  1 mkiaiLsrnpelystrrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipRigasitfygtavlrqFemm 83
                                  mkia+Lsr+++lys+rrL+eaae+rghe++v+d+lr y++i+++kp+++ykge+le fd+vipRigas+tfyg++vlrqFemm
  gi|91772710|ref|YP_565402.1|  1 MKIALLSRSRKLYSSRRLIEAAEERGHEIQVIDVLRAYMNITSHKPSIHYKGEELEGFDVVIPRIGASVTFYGASVLRQFEMM 83
                                  9********************************************************************************** PP

                        Rimk_N 84 gvfvlneseAi 94
                                  gv+ lnes Ai
  gi|91772710|ref|YP_565402.1| 84 GVYPLNESVAI 94
                                  **********9 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 !   64.7   0.4   4.1e-21   6.7e-18      12     172 ..     114     272 ..     100     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 4.1e-21
                                   S--EEEES-HHHHHHHHHHHSS..EEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEEEE CS
                     GSH-S_ATP  12 ipktlvskdkeeirafleeqgd..vilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeikeGDkRill 90 
                                   +p t  +++ ++i+++++  g   +++K l+g+ G gv+  ++ ++  +s++e ++  +   +++q+y++e++  D R ++
  gi|91772710|ref|YP_565402.1| 114 MPVTGYASKPDDIKDVIKMVGGapLVVKLLEGTQGIGVVLAET-QKAAESVIEGFMGVKA-NILVQEYIKEANGADIRCFV 192
                                   6788888999999999999887679*************98877.5567788888877655.799***************** PP

                                   ETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETTE....EEEEE-SS---H CS
                     GSH-S_ATP  91 vdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigdk....ltEinvtsPtgi 167
                                   + G+ +  +++R + +ge+Rsnl+ gg+ae  ++t ++r+ a + a+     Gl ++G+D++ ++    ++E+n  s  g+
  gi|91772710|ref|YP_565402.1| 193 IGGKVVA-SMKRQAPNGEFRSNLHRGGSAEVIRITPEERSTAVSAAKI---MGLNVAGVDLLRSNhgpvVMEVN--SSPGL 267
                                   ******9.*******************************998876655...6*********9654222156665..55577 PP

                                   HHHHH CS
                     GSH-S_ATP 168 reiee 172
                                   r ie+
  gi|91772710|ref|YP_565402.1| 268 RGIET 272
                                   77766 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   2.7e-12   4.4e-09       3     156 ..      99     263 ..      97     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.7e-12
                                   SHHHHHHHHTTT.S---............-EESS--SSSEEEEESS-------B--SS--TTE.............EEEE- CS
                   ATP-grasp_3   3 dKlktykkLkeagvkvP........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......lvqef 69 
                                   dKl++ + L+++g+ +P        + +++    +   +lvvK  +G  g +v+++e +++ae+ ie         lvqe+
  gi|91772710|ref|YP_565402.1|  99 DKLRSLQLLSRKGIGMPvtgyaskpDDIKDVIKMVGGAPLVVKLLEGTQGIGVVLAETQKAAESVIEGFMgvkaniLVQEY 179
                                   9****************8666655555555555555***************************9999888889999***** PP

                                   --.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SE CS
                   ATP-grasp_3  70 ie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeep 149
                                   i+  + + + + + g   +v ++ rq  + + +++  +G+++++  + + e +++a ++ + + gl+ ++GvDl+ ++++p
  gi|91772710|ref|YP_565402.1| 180 IKeANGADIRCFVIG-GKVVASMKRQAPNGEFRSNLHRGGSAEVI-RITPEERSTAVSAAKIM-GLN-VAGVDLLRSNHGP 256
                                   *63334556555544.45678999999998888899999999998.45555667777777777.776.79*********** PP

                                   EEEEEES CS
                   ATP-grasp_3 150 yviEvNP 156
                                   +v+EvN+
  gi|91772710|ref|YP_565402.1| 257 VVMEVNS 263
                                   ******7 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1    0.0001      0.17      11      85 ..      89     160 ..      82     226 .. 0.88
   2 !   16.3   0.0   2.7e-06    0.0043     231     280 ..     232     279 ..     226     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                   ATPgrasp_ST  11 NpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredq 85 
                                   N+  ++    dKl   +l++r+g+ +p   g  ++ ++i+++ ++v +  + +v+K  +g  G G++ +  ++ +
  gi|91772710|ref|YP_565402.1|  89 NESVAITRSRDKLRSLQLLSRKGIGMPV-TGYASKPDDIKDVIKMVGGA-P-LVVKLLEGTQGIGVVLAETQKAA 160
                                   66666666789****************9.8999999************9.7.9*************998665443 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.7e-06
                   ATPgrasp_ST 231 laakaaeklpglgylGwDivldeekgplllElNarpglaivqiangegll 280
                                   +a++aa+ ++gl + G+D+ l  + gp+++E+N  pgl  ++ a g+ + 
  gi|91772710|ref|YP_565402.1| 232 TAVSAAK-IMGLNVAGVDL-LRSNHGPVVMEVNSSPGLRGIETATGKDIA 279
                                   6788888.**********9.666777*************99999988665 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 !   17.8   0.4   1.2e-06    0.0019      22     178 ..     121     267 ..     112     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                                   H-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--...ESEEEEEEEEETSSCEEE CS
               Dala_Dala_lig_C  22 eekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeai...egreievavlgneklevs 99 
                                   ++++++ + ++   g p++VK  +    +Gv  +e+++  ++ ie  +   +++lv e+i   +g +i + v+g     v+
  gi|91772710|ref|YP_565402.1| 121 SKPDDIKDVIKMVGGAPLVVKLLEGTQGIGVVLAETQKAAESVIEGFMGVKANILVQEYIkeaNGADIRCFVIG--GKVVA 199
                                   5666777888888899*******9999********************************9866689********..44555 PP

                                   EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS--- CS
               Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlPGf 178
                                   ++++ +++++f   +    + +a++   +++++e++     +a+ a k+++l  +a vD++ + +  +v+ EvN  PG+
  gi|91772710|ref|YP_565402.1| 200 SMKRQAPNGEFRS-NLH-RGGSAEV---IRITPEER----STAVSAAKIMGL-NVAGVDLLRS-NHGPVVMEVNSSPGL 267
                                   6666666666533.322.2334433...34444443....345555566655.5788998766.66678889***9997 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 ?    0.9   0.0      0.13   2.2e+02      29      69 ..     114     156 ..      95     164 .. 0.70
   2 !   12.8   0.0   3.2e-05     0.052      91     168 ..     156     225 ..     144     242 .. 0.81
   3 ?    1.8   0.0     0.073   1.2e+02     208     251 ..     246     284 ..     230     288 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.13
                ATPgrasp_YheCD  29 LPetellesledleemlekyks..vylKpanGskGkgilriek 69 
                                   +P t   ++++d++++++  +   +++K  +G++G g++  e 
  gi|91772710|ref|YP_565402.1| 114 MPVTGYASKPDDIKDVIKMVGGapLVVKLLEGTQGIGVVLAET 156
                                   567777777888888888776545899***********98776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.2e-05
                ATPgrasp_YheCD  91 slselesllkkllkkkr.ylvQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalplee 168
                                   ++++ es+++ +++ k+ +lvQ++i+ a+      D+R +v        +v++ + R+a++g++ +nl+rGG+a  ++ 
  gi|91772710|ref|YP_565402.1| 156 TQKAAESVIEGFMGVKAnILVQEYIKEAN----GADIRCFVIGG-----KVVASMKRQAPNGEFRSNLHRGGSAEVIRI 225
                                   56778889999998877799999998665....68999999933.....589999******************987665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.073
                ATPgrasp_YheCD 208 GlDlgidkegkvWllEvNskpgrsifkeagdkeaarksvkrple 251
                                   G+Dl   +++   ++EvNs pg +  + a      ++++ +++e
  gi|91772710|ref|YP_565402.1| 246 GVDLLR-SNHGPVVMEVNSSPGLRGIETATG----KDIAGMIIE 284
                                   556544.44556688*******988776544....444444444 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     4e-05     0.065       7      79 ..     103     171 ..     100     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                                   HHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSE CS
                   ATP-grasp_2   7 akeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgke 79 
                                   + ++l++ g+ +p +  a++++++++++k +g+  lvvK   l G  G   Gv l+++++ a+++++ ++g +
  gi|91772710|ref|YP_565402.1| 103 SLQLLSRKGIGMPVTGYASKPDDIKDVIKMVGGAPLVVK--LLEGTQG--IGVVLAETQKAAESVIEGFMGVK 171
                                   779***********************************9..6899887..69***********9999999865 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.2e-05       0.1       7     104 ..     104     196 ..      98     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                                   HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE CS
                        GARS_A   7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEe 87 
                                    +ll++ gi  +     ++p+++k++i+ ++   lVvK    + g gv++a++++ a ++++ ++        ++++++ e
  gi|91772710|ref|YP_565402.1| 104 LQLLSRKGIGMPVTGYASKPDDIKDVIKMVGGAPLVVKLLEGTQGIGVVLAETQKAAESVIEGFMG------VKANILVQE 178
                                   578999999999999999************99999***99999********999999999999994......567788888 PP

                                   ---.SEEEEEEEEECTTE CS
                        GARS_A  88 lle.GeEvsllalvdgkt 104
                                   +++  +   + ++v g +
  gi|91772710|ref|YP_565402.1| 179 YIKeANGADIRCFVIGGK 196
                                   775133344556655544 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 ?   11.8   0.0   0.00011      0.18     105     183 ..     172     263 ..     115     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                         R2K_3 105 tevlvsevv..rfsaEwRvFvvdGevvaasrYrkanddpdl...........epdlaafaeavralv.gappfyvlDvavt 171
                                     +lv e++    +a  R+Fv++G+vva    +  n+++               ++++  +av+a++   +++  +D+ ++
  gi|91772710|ref|YP_565402.1| 172 ANILVQEYIkeANGADIRCFVIGGKVVASMKRQAPNGEFRSnlhrggsaeviRITPEERSTAVSAAKiMGLNVAGVDLLRS 252
                                   55666666642237899***********998885555555555556655557556666777777777867*********** PP

                         R2K_3 172 adGrwkVVEvnd 183
                                   + G   V Evn 
  gi|91772710|ref|YP_565402.1| 253 NHG-PVVMEVNS 263
                                   ***.99***995 PP

>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.062     1e+02      69     110 ..     138     181 ..     120     193 .. 0.82
   2 ?    6.7   0.0    0.0022       3.5     238     264 ..     243     269 ..     201     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.062
                                   ---SS---XX------BSSTHHHHHH..HH..SSS-EEEEB--S CS
                           TTL  69 wIvKpsasarGkgirvfnkledikki..vsqsqkeplvvqkYie 110
                                   ++vK   + +G+g+++ ++ +    +    +  k +++vq+Yi+
  gi|91772710|ref|YP_565402.1| 138 LVVKLLEGTQGIGVVLAETQKAAESVieGFMGVKANILVQEYIK 181
                                   578888899999999999999988777655667899*******8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0022
                                   XXXXXXXXXXXXXXXXXXXXXXXX...X CS
                           TTL 238 elyGvDilidenlkpwLlEvNasPdl.k 264
                                   ++ GvD+ +++n  p ++EvN+sP l  
  gi|91772710|ref|YP_565402.1| 243 NVAGVDL-LRSNHGPVVMEVNSSPGLrG 269
                                   5667885.68999***********9843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2080.92
//
Query:       gi|91772711|ref|YP_565403.1|  [L=348]
Description: succinylglutamate desuccinylase/aspartoacylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-50  171.7   0.0      2e-50  171.5   0.0    1.0  1  AstE_AspA      Succinylglutamate desuccinylase / Aspartoacyla
  ------ inclusion threshold ------
      0.013   14.9   0.0          3    7.1   0.0    2.1  2  DUF2817        Protein of unknown function (DUF2817)
      0.015   14.7   0.0      0.022   14.2   0.0    1.2  1  Peptidase_M99  Carboxypeptidase controlling helical cell shap


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.5   0.0   3.4e-54     2e-50       1     290 [.      45     315 ..      45     316 .. 0.97

  Alignments for each domain:
  == domain 1  score: 171.5 bits;  conditional E-value: 3.4e-54
                                   SS-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTCHHHH CS
                     AstE_AspA   1 sgpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrsldealr 81 
                                   +gp +li+A++HG+E++Gve++r++l      +++g+ +++pl+N++++  +sRy+p dr+dLNR+Fpg+  g        
  gi|91772711|ref|YP_565403.1|  45 PGPCLLICAAIHGDEINGVEIIRRVLAHKTINNLKGTLIAIPLVNVFGFVSQSRYLP-DRRDLNRSFPGSKTG-------- 116
                                   6999*****************************************************.***************........ PP

                                   HHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHHHHHHHHTTTSEEEEEESS--SSHHHHHHHHCT CS
                     AstE_AspA  82 ateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqslallkalglpavllldekesagfletaaeelg 162
                                      a+rla+ l ++ + ++ +v+DLHtg  ++ +l++++a  + + +++ a+++a+ +p+++  +++ ++g+l+ a+++ +
  gi|91772711|ref|YP_565403.1| 117 -PMASRLANILMTEIISHCTHVIDLHTGAVARENLPQIRACLKGD-TETEAMARAFRVPVII--NSELRDGSLREAVRKNN 193
                                   .*************************************9999777.5579************..***************** PP

                                   SEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEGGSCCCSSCSEEECCCCSTTTTETCT CS
                     AstE_AspA 163 alaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlreldeprdiraeeaGlvefkvklgddveag 243
                                   ++ + +E G+a r+++ +i+  ++g+l v++h+g+  ++    + k+ + +   ++ ++ira+e+G+    v+lg  v+ g
  gi|91772711|ref|YP_565403.1| 194 VPVLLYEAGEALRFNEVAIRAGVRGILGVMSHLGMRPKS----RKKKESDTLISRSTQWIRAPESGMLRSIVPLGTLVKVG 270
                                   *************************************99....57888888999999************************ PP

                                   EEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEEEE CS
                     AstE_AspA 244 ellakalvldslggekvelrapqdgvivfineaalvekgaalvkvak 290
                                   ++l  a++ d+lg+ +  +     g++++  + +l+++g+a++++ak
  gi|91772711|ref|YP_565403.1| 271 DIL--AYINDPLGECEMKVLSSAFGIVIGKTNLPLAHEGEAIFHIAK 315
                                   ***..***************************************987 PP

>> DUF2817  Protein of unknown function (DUF2817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00051         3      42     119 ..      37     111 ..      28     124 .. 0.82
   2 ?    5.3   0.0    0.0018        11     210     247 ..     135     172 ..     116     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00051
                       DUF2817  42 varlgpadakklLvltsGthGveGfaGSavqvalLrealakllaegvavLlvhalNPyGfahlrrvnedNVDLnRNfl 119
                                   v ++ +++   +L++ +++hG e   G  +  ++L ++  ++++ +  ++ +  +N +Gf  + r+  d  DLnR f 
  gi|91772711|ref|YP_565403.1|  37 VHVVHGSKPGPCLLICAAIHGDE-INGVEIIRRVLAHK--TINNLKGTLIAIPLVNVFGFVSQSRYLPDRRDLNRSFP 111
                                   566677778889999999**977.78999999999986..666666678999999********************996 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0018
                       DUF2817 210 vaviDlHTGlGprgkgeiivsseedkealerarkwwgk 247
                                     viDlHTG   r +   i ++ +  ++ e ++++++ 
  gi|91772711|ref|YP_565403.1| 135 THVIDLHTGAVARENLPQIRACLKGDTETEAMARAFRV 172
                                   568**********9998888775555555555555443 PP

>> Peptidase_M99  Carboxypeptidase controlling helical cell shape catalytic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.6e-06     0.022      33      98 ..      43     112 ..      29     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-06
                                   GGSS-EEEEE--SSTT-HHHHHHHHHHHHHEEE..-SSEEEEES-STHHHHHTT-S-TTS..-GGG-SSS CS
                 Peptidase_M99  33 rdkaphllllagiqgdepggfnaanlflmhyev..kkglvevvpvlnkpsilrnhrglyd..dmnrkfaa 98 
                                       p ll+ a i gde  g +     l h  +  +kg +  +p +n   ++ + r l d  d+nr f  
  gi|91772711|ref|YP_565403.1|  43 SKPGPCLLICAAIHGDEINGVEIIRRVLAHKTInnLKGTLIAIPLVNVFGFVSQSRYLPDrrDLNRSFPG 112
                                   445799999*********************9985569*******************99765599999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2194.16
//
Query:       gi|91772712|ref|YP_565404.1|  [L=341]
Description: hypothetical protein Mbur_0688 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-37  126.6   1.0    1.1e-36  126.2   1.0    1.1  1  DUF21     Cyclin M transmembrane N-terminal domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   1.0   6.1e-41   1.1e-36       1     169 [.       8     167 ..       8     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 6.1e-41
                         DUF21   1 liivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellae 81 
                                   ++i l+l+ s++fsg++++l+ lsrlrle  ae+++ +a+++lkl+++p+ lLstll gn  vn+l+++l+++++v   a 
  gi|91772712|ref|YP_565404.1|   8 ILIALCLIQSGIFSGLTIGLFGLSRLRLEIEAEANNIHAQKVLKLRHDPHLLLSTLLWGNVCVNVLITLLTDSVMVGSAA- 87 
                                   6789999*******************************************************************888765. PP

                         DUF21  82 galavviatviv.tllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlilesesepavseeelkk 161
                                            +i+ t++i  fgEi+P+++++++a+k+ + l p++++++ llyP++++  ++l+  l++e+ ++++e  l+ 
  gi|91772712|ref|YP_565404.1|  88 ---------FIFsTVFITCFGEIMPQAYFTRNALKMGASLTPLVKLYILLLYPFTKPSAMILDRWLGKEKLEYFKETSLRI 159
                                   .........8888******************************************************************** PP

                         DUF21 162 lveeseee 169
                                   +++ + ++
  gi|91772712|ref|YP_565404.1| 160 MLQKHMKS 167
                                   **999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2299.29
//
Query:       gi|91772713|ref|YP_565405.1|  [L=76]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.7   4.1      0.019   14.6   4.1    1.0  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   4.1   1.1e-06     0.019     122     214 .]       2      68 ..       1      68 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-06
                     DDE_Tnp_1 122 rgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrve 202
                                   r+r+rk+++++ ++k  ++++                           +y+ R   E+ F+ lkrk+g ++lr+r+++  +
  gi|91772713|ref|YP_565405.1|   2 RQRERKRIKGRYRKKMLQEFDS-------------------------KIYSMRNLSETMFSVLKRKYG-ENLRARKYRNQV 56 
                                   6788888888888888888888.........................******************999.************ PP

                     DDE_Tnp_1 203 aqllllllalnl 214
                                    ++ ++ + +nl
  gi|91772713|ref|YP_565405.1|  57 KEVKFKVILHNL 68 
                                   **9999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 579.57
//
Query:       gi|91772714|ref|YP_565406.1|  [L=576]
Description: RNA-directed DNA polymerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-42  145.7   0.1    3.1e-42  144.6   0.0    1.5  2  RVT_1            Reverse transcriptase (RNA-dependent DNA pol
    7.4e-28   96.6   2.2    7.4e-28   96.6   2.2    1.9  2  RVT_N            N-terminal domain of reverse transcriptase
    3.4e-24   84.7   6.4    8.9e-24   83.4   6.4    1.8  1  GIIM             Group II intron, maturase-specific domain
  ------ inclusion threshold ------
      0.011   15.7   3.7       0.13   12.2   0.5    3.8  3  Intron_maturas2  Type II intron maturase
       0.12   12.6   3.4       0.25   11.6   3.4    1.6  1  HNH              HNH endonuclease


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   0.0   8.7e-46   3.1e-42       1     222 []     129     350 ..     129     350 .. 0.95
   2 ?   -3.3   0.0       1.4     5e+03      94     136 ..     453     497 ..     444     498 .. 0.63

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 8.7e-46
                                   EE-TT.S-EEE......-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEBCCGCC CS
                         RVT_1   1 ipKkgpgsyRpisllsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaFd 81 
                                   i K g ++ Rp++++++ ++a+++l+a +L +++e + +++++gfr+ rst+da  ++  +++kk +a+++l+ D+k++Fd
  gi|91772714|ref|YP_565406.1| 129 IEKYGSDKKRPLGIPTMYDRAMQALYALALDPIAEVTADKRSFGFRKFRSTHDACSQIFGTISKKDSAQCILEGDIKGCFD 209
                                   56777899************************************************************************* PP

                                   CSBB-GGGGGGG-EEET..........................TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T...... CS
                         RVT_1  82 svpleellrkltafkvptklinliksflstrsfsvrv.ngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra... 158
                                   ++++++l+  +     +++   ++k+fl    +++ v ++   + +++k+g+pqG+++SP+l+n++++ ++  l+ ++   
  gi|91772714|ref|YP_565406.1| 210 NISHQWLIDNIPM---DKS---ILKQFL----KAGFVyEN---SLFPTKAGTPQGGIISPILANMTLDGIEGVLADKYhrg 277
                                   ********99888...534...899999....56666355...89*******************************99*** PP

                                   ...............TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE.....ESSEEETTEEE CS
                         RVT_1 159 ............kgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlftvkseevkyLGvtl 222
                                                +v+++rYaDD+++++k+ke ++e+ e ++++l + gl++++eKt +++     + +++LG ++
  gi|91772714|ref|YP_565406.1| 278 vsgkittrqrakHKVNFVRYADDFIVTAKTKEIAEEAKELIKNFLTDRGLELSDEKTLITH---IDDGFDFLGWNV 350
                                   ************************************************************9...89*******875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                   -EEET...........................TEEEEESB--ST- CS
                         RVT_1  94 afkvptklinliksflstrsfsvrvnge..eskgryekkglpqGs 136
                                    f++ +++++l+++ +  r   ++++++  + +++++++ l qGs
  gi|91772714|ref|YP_565406.1| 453 VFSTMKNQLKLMSDKMIVRNPQIKLDKNpyTDTEYFVERKLNQGS 497
                                   456666667777666666666666633335777888888888887 PP

>> RVT_N  N-terminal domain of reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   2.2   2.1e-31   7.4e-28       1      83 []      33     114 ..      33     114 .. 0.99
   2 ?   -3.3   0.0       3.2   1.1e+04      49      58 ..     365     372 ..     360     388 .. 0.53

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 2.1e-31
                         RVT_N   1 WkeidWkkvekkVfkLqkrIykAsqegdikkvkkLqklLtkSlsakllAvrrVtqdnkgkktagvDgvksltpkerlelve 81 
                                   W+ i+W++ve++V+++q rI+kA+ +++++ vk+L +lLt+S++akllAvr+V   nkg++tag+Dg+ ++tp +++++++
  gi|91772714|ref|YP_565406.1|  33 WNFINWSSVESHVNRIQVRITKAVINKNWNLVKRLSYLLTHSHYAKLLAVRKVIR-NKGRRTAGIDGEFWSTPVSKVNAAR 112
                                   *******************************************************.**********************998 PP

                         RVT_N  82 eL 83 
                                   +L
  gi|91772714|ref|YP_565406.1| 113 SL 114
                                   76 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                         RVT_N  49 AvrrVtqdnk 58 
                                   ++++Vt+  k
  gi|91772714|ref|YP_565406.1| 365 SIKKVTE--K 372
                                   4555555..2 PP

>> GIIM  Group II intron, maturase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   6.4   2.5e-27   8.9e-24       1      80 []     366     444 ..     366     444 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2.5e-27
                          GIIM   1 vkrlkrkireltkrsskgvsleelirklnpilrGWanYyrlgvakrvfskldhyirrrLrrwllrkhkkkkrrralrkyw 80 
                                   +k++++ki++++ ++ k++++e+li klnpi++GW nY++ + +k++fs +d  i++ L++w++r+h+ k+r ++++kyw
  gi|91772714|ref|YP_565406.1| 366 IKKVTEKISNTI-KDGKTWTQEDLISKLNPIITGWSNYHQGVASKETFSLIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 444
                                   6999********.7779**************************************************************9 PP

>> Intron_maturas2  Type II intron maturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.19   6.7e+02      68     103 ..      61      90 ..      49     125 .. 0.68
   2 ?   -0.4   0.0      0.29     1e+03       4      32 ..     216     249 ..     213     261 .. 0.76
   3 ?   12.2   0.5   3.8e-05      0.13      38     103 ..     383     444 ..     356     475 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.19
               Intron_maturas2  68 krlrerikyilrkscvkTLArKlklktvrkvikkfG 103
                                    +l++r+ y+l +s         kl  vrkvi+  G
  gi|91772714|ref|YP_565406.1|  61 WNLVKRLSYLLTHSH------YAKLLAVRKVIRNKG 90 
                                   466677777777664......344445555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.29
               Intron_maturas2   4 lvlnaPir.kiikkLakagfvktkk....ekgkP 32 
                                   l+ n+P++ +i k+  kagfv +++    + g P
  gi|91772714|ref|YP_565406.1| 216 LIDNIPMDkSILKQFLKAGFVYENSlfptKAGTP 249
                                   566899973588999******9986665555555 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 3.8e-05
               Intron_maturas2  38 widledrdIllrykaiirgllnYYsfadnkkrlrerikyilrkscvkTLArKlklktvrkvikkfG 103
                                   w+   + d++ + + ii g +nY++++  k+++  +i + + + + k   r++ +k +  + +k+ 
  gi|91772714|ref|YP_565406.1| 383 WT---QEDLISKLNPIITGWSNYHQGVASKETFS-LIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 444
                                   44...457899**********************9.**99988888877777777777766666665 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.4   6.9e-05      0.25      23      46 ..     534     561 ..     515     562 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.9e-05
                           HNH  23 sq..ggadd..ieNlqllCksCHnkkhd 46 
                                   ++  g++dd  i Nl+ ++  CH++ h+
  gi|91772714|ref|YP_565406.1| 534 HHknGNHDDngITNLVYAHVYCHRQYHA 561
                                   44437777799**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3873.37
//
Query:       gi|91772715|ref|YP_565407.1|  [L=217]
Description: hypothetical protein Mbur_0692 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.3   0.4       0.18   12.3   0.4    3.2  3  AtpR          N-ATPase, AtpR subunit
       0.23   11.3  10.9        1.2    8.9  10.5    2.3  1  DUF2238       Predicted membrane protein (DUF2238)


Domain annotation for each model (and alignments):
>> AtpR  N-ATPase, AtpR subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4     2e-05      0.18      36      70 ..      12      41 ..       3      59 .. 0.83
   2 ?    2.1   1.4      0.03   2.7e+02      61      79 ..      95     113 ..      70     122 .. 0.69
   3 ?   -1.2   0.0      0.33   2.9e+03      59      75 ..     176     192 ..     166     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                          AtpR 36 lllvsslllRlgivlagfyllaagglarlLaallG 70
                                  l +++s ++Rl++v++g++ +  g++ +l     G
  gi|91772715|ref|YP_565407.1| 12 LEFWISSIFRLLVVIGGVVAILTGNWIHL-----G 41
                                  679******************99999876.....4 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.03
                          AtpR  61 larlLaallGFllaRllll 79 
                                   +  +L ++lG+++a l ++
  gi|91772715|ref|YP_565407.1|  95 WDVFLHTFLGIIIASLGFI 113
                                   5666666666666655444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.33
                          AtpR  59 gglarlLaallGFllaR 75 
                                   + l +lL+++lG l ++
  gi|91772715|ref|YP_565407.1| 176 ETLSALLVSTLGYLYLK 192
                                   56778888888877654 PP

>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  10.5   0.00013       1.2      59     131 ..      95     171 ..      23     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00013
                       DUF2238  59 YDrlvHfaqGllla...lvvrelllrkkkl..rk.wllllavlvvlaisalYEliEwlvalllggeaaeaflGtqGdiW 131
                                   +D + H + G+++a   ++++ +l +++k+  +  +++l+++++++a++a++E++E+++ +++g +   +  G    +W
  gi|91772715|ref|YP_565407.1|  95 WDVFLHTFLGIIIAslgFILVYVLNSEHKVnlSPfFVALFSFSIAVAFGAIWEIFEYAMDVVFGLNM--QTSGLVDTMW 171
                                   688999999999882223445556666666776646999***********************99433..3344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1480.65
//
Query:       gi|91772716|ref|YP_565408.1|  [L=155]
Description: hypothetical protein Mbur_0693 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-10   42.1   0.3    1.5e-10   41.7   0.3    1.1  1  DUF3887       Protein of unknown function (DUF3887)
     0.0049   17.2   0.0      0.011   16.2   0.0    1.6  1  DUF4019       Protein of unknown function (DUF4019)
  ------ inclusion threshold ------
      0.016   15.3   0.1      0.023   14.9   0.1    1.1  1  DUF1510       Domain of unknown function (DUF1510)
      0.025   14.6   0.1      0.031   14.3   0.1    1.1  1  YpjP          YpjP-like protein
       0.12   12.7   0.0       0.18   12.1   0.0    1.3  1  DUF2745       Protein of unknown function (DUF2745)
       0.15   12.4   0.9       0.25   11.7   0.2    1.7  2  DUF4969       Domain of unknown function (DUF4969)
       0.15   12.7   0.1       0.15   12.7   0.1    1.4  2  Chordopox_G3  Chordopoxvirus G3 protein


Domain annotation for each model (and alignments):
>> DUF3887  Protein of unknown function (DUF3887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.3   5.8e-14   1.5e-10       1      85 [.      45     130 ..      45     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.8e-14
                       DUF3887   1 AeeiiellnsgdyeeaqdlfsedlkealseetleeawkalkeelGefesieeyeveetseeyavvtveakfek..gsadle 79 
                                   Ae+ ++ ln+++y+++ ++f++++k+a++e+ ++e    + ee+G++ s e  e++ t+     v++++ fek  + a ++
  gi|91772716|ref|YP_565408.1|  45 AENTLQGLNENNYTKFSANFNPTMKKAITEDLFLELTAIVHEEVGNYTSKELAEITVTDR-HSAVVYNVAFEKepEGAIFR 124
                                   7899999************************************************99999.77888888887622468888 PP

                       DUF3887  80 faFded 85 
                                   ++F ed
  gi|91772716|ref|YP_565408.1| 125 LIFIED 130
                                   888554 PP

>> DUF4019  Protein of unknown function (DUF4019)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.2e-06     0.011       2      73 ..      45     108 ..      44     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                       DUF4019   2 AkawlelvDagkyeesWeeasalfkkavteeewekalkavraplGavksRklasaeearslpgaPdGeYvvi 73 
                                   A++ l+ + +++y++  ++  +++kka+te+ + + ++ v++++G+ +s +la+ + + + +        ++
  gi|91772716|ref|YP_565408.1|  45 AENTLQGLNENNYTKFSANFNPTMKKAITEDLFLELTAIVHEEVGNYTSKELAEITVTDRHS--------AV 108
                                   788999999********************************************999877433........34 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   8.8e-06     0.023      14      77 ..      50     114 ..      38     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.8e-06
                       DUF1510  14 tgehtssydkgsvDwn.EmekavskatglsednmivwwlgnggspqkaigtvsskdktekYrVyl 77 
                                   +g ++++y+k s ++n  m+ka+++   l+   ++   +gn  s++ a  tv+++++   Y+V  
  gi|91772716|ref|YP_565408.1|  50 QGLNENNYTKFSANFNpTMKKAITEDLFLELTAIVHEEVGNYTSKELAEITVTDRHSAVVYNVAF 114
                                   47789**********95699******************************************986 PP

>> YpjP  YpjP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.2e-05     0.031       6      69 ..      44     107 ..      39     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                          YpjP   6 llellleeaeeqsllKlGkkiaekiedefeeeilpkieevieellekveeekleeleisekpas 69 
                                   ++e++l+  +e+ ++K+  + ++ +++ ++e+++ ++ ++++e + ++++++l+e++++++ ++
  gi|91772716|ref|YP_565408.1|  44 IAENTLQGLNENNYTKFSANFNPTMKKAITEDLFLELTAIVHEEVGNYTSKELAEITVTDRHSA 107
                                   56778899999************************************************98775 PP

>> DUF2745  Protein of unknown function (DUF2745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     7e-05      0.18      11      69 ..      68     125 ..      58     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                                   HHHHHHHHHHHTT-EEEEE-S--SSS----EEEEEE-SSS-EEEEEEE--S-HHHHHHH CS
                       DUF2745  11 afkaatnklfqldlaviyddwydaytrkdcirlriedrsgnlidtstfyhhdedvlfnm 69 
                                     ka t+ lf l+l+ i  +    yt k+   + + dr   ++   +f +  e  +f +
  gi|91772716|ref|YP_565408.1|  68 MKKAITEDLF-LELTAIVHEEVGNYTSKELAEITVTDRHSAVVYNVAFEKEPEGAIFRL 125
                                   4578888888.89999999999***********************99999999988875 PP

>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   9.9e-05      0.25       1      68 [.       1      70 [.       1      75 [. 0.86
   2 ?   -2.0   0.0       1.9   4.9e+03      32      45 ..      89     103 ..      77     111 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.9e-05
                       DUF4969  1 mkkRgllLvsvLvlFillavaCsdsedneesvei..ilkeielsvddpiklvdengeatvevdvdPkskl 68
                                  mk R  lL+s +vl +++   C++ +    sve    ++  e   ++ ++  +en+ +  +++ +P  k 
  gi|91772716|ref|YP_565408.1|  1 MKVRTALLMSLVVLVVIICSGCASIKLEGSSVEDdgLTEYAEPIAENTLQGLNENNYTKFSANFNPTMKK 70
                                  899*********************998889998532577788888999999***********99997664 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                       DUF4969  32 veiilkei.elsvdd 45 
                                   ++   ke+ e++v d
  gi|91772716|ref|YP_565408.1|  89 GNYTSKELaEITVTD 103
                                   333333322445445 PP

>> Chordopox_G3  Chordopoxvirus G3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       5.3   1.4e+04       2      13 ..       8      19 ..       7      28 .. 0.69
   2 ?   12.7   0.1     6e-05      0.15      35      96 ..      53     117 ..      31     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.3
                  Chordopox_G3  2 llnliffilfll 13
                                  l+ l+++++ ++
  gi|91772716|ref|YP_565408.1|  8 LMSLVVLVVIIC 19
                                  556666666664 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6e-05
                  Chordopox_G3  35 senaiikkrddelpe...lletvlflskekiisdqvilsydadtatvtvavkskkyvfrlddeed 96 
                                   +en+ +k  ++++p+   +    lfl+  +i++++v  +  ++ a +tv+ +++  v+++ +e++
  gi|91772716|ref|YP_565408.1|  53 NENNYTKFSANFNPTmkkAITEDLFLELTAIVHEEVGNYTSKELAEITVTDRHSAVVYNVAFEKE 117
                                   45667777777777732244556**************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 972.30
//
Query:       gi|91772717|ref|YP_565409.1|  [L=592]
Description: external sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-28   99.5   0.4    1.5e-28   99.5   0.4    2.1  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.7e-21   77.1   6.1    3.7e-21   76.0   5.9    1.6  2  dCache_1     Cache domain
    8.5e-18   64.2   2.1    2.5e-17   62.7   0.2    2.6  3  HisKA        His Kinase A (phospho-acceptor) domain
    1.6e-05   24.9   0.0    2.7e-05   24.2   0.0    1.3  1  CHASE        CHASE domain
    0.00035   20.4   0.2     0.0016   18.3   0.1    2.3  2  HATPase_c_5  GHKL domain
     0.0041   17.0   0.1      0.011   15.6   0.1    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
       0.03   14.3   0.0       0.06   13.3   0.0    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain
       0.11   12.0   1.8       0.18   11.3   0.3    2.1  2  SieB         Super-infection exclusion protein B
       0.24   11.7   3.8        1.8    8.9   1.3    2.3  2  Rx_N         Rx N-terminal domain


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 ?   -1.9   0.2       2.4   4.8e+03       6      32 ..     434     459 ..     431     464 .. 0.78
   2 !   99.5   0.4   7.8e-32   1.5e-28       1     111 [.     469     580 ..     469     581 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHHSTTTEEEEEEE CS
                     HATPase_c   6 LrqiisnlvdNavkfatkageieveik 32 
                                   +++ii   + N  k+ +k+++i++ ++
  gi|91772717|ref|YP_565409.1| 434 IKEIIEISLHNVTKH-AKDKSIKIMVN 459
                                   578888889999999.88888888776 PP

  == domain 2  score: 99.5 bits;  conditional E-value: 7.8e-32
                                   EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHH CS
                     HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsi 80 
                                   +d+++L +i+ nl++Na+kf++++ge++v ++ +ed+l+ s++DnGiGi +e+++k+f+kf+q d++++r+ ggtGlGl+i
  gi|91772717|ref|YP_565409.1| 469 TDKDKLIRIFVNLLTNAIKFTPEEGEVTVIVEDHEDYLQTSIKDNGIGILEEKRDKIFDKFYQvDSTATRKAGGTGLGLAI 549
                                   58999***************88**********888****************************999999999********* PP

                                   HHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                     HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlple 111
                                    k +++  gG+i++ese g+G+tftf+lp+e
  gi|91772717|ref|YP_565409.1| 550 IKGIIDGQGGKIYLESETGKGSTFTFRLPKE 580
                                   ******99********************986 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   5.9   1.9e-24   3.7e-21       5     249 .]      41     280 ..      38     280 .. 0.82
   2 ?   -3.5   0.0       3.5   7.1e+03     108     131 ..     504     535 ..     490     560 .. 0.55

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.9e-24
                      dCache_1   5 eqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvdadGq 85 
                                   e ++++++++a+q++  i ++l++  + +e +++n +               +++++ ++  +++  ++++++ ++++ G 
  gi|91772717|ref|YP_565409.1|  41 EMFTREQTSQAQQISTGITTFLNEKITMLEIISRNHN------------SIPDDNFNTIFSIVYNESEGFHAIEYINSTGI 109
                                   567899****************************976............23589999************************ PP

                      dCache_1  86 viassdpssppnleg....tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiyddsgkfiGvlaadldldn 162
                                   +++ +++++          +++  +   + +++++g  +++i++p +  + gk+ i + +p y ++g f+G+++a + +d+
  gi|91772717|ref|YP_565409.1| 110 IVSGYPEENV----PfgydLYEKDKAAVFEQIKETG--ETHITNPLTTLE-GKLAIFVWIPFYLENGSFEGAIVAVIEIDE 183
                                   *985544443....1343455555555599999999..********8888.****************************** PP

                      dCache_1 163 lqd.llsniklgetgyvfivdsdGniiahpd.kdllgknlrdelkaq..........ealekalakiesgvssvklng..e 229
                                   +++ ++++   +e+gy++++d++ +++++++   l+g+n ++  ++           +++        ++ s+   ng  e
  gi|91772717|ref|YP_565409.1| 184 ITKqTIKTE--YESGYIYLIDDNAKLLYDSSdDHLVGQNYFNIINEPdhrrldiigmQTEGLS---GSGQFSERNTNGflE 259
                                   ***788865..999**************7653777*999999999999*99965554333333...334444444555777 PP

                      dCache_1 230 eylvayapip.tglgWylvvv 249
                                   e+++ y+p++  ++ W++ vv
  gi|91772717|ref|YP_565409.1| 260 EKIISYVPVNwYNQQWSVGVV 280
                                   99999******88*****986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.5
                      dCache_1 108 dwykealaggg.......gkpvisdpy.vdqt 131
                                   d++++ ++++g       ++ ++ ++y vd+t
  gi|91772717|ref|YP_565409.1| 504 DYLQTSIKDNGigileekRDKIFDKFYqVDST 535
                                   55555555555555555544445555553333 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.12   2.3e+02      30      57 ..     322     360 ..     308     361 .. 0.63
   2 !   62.7   0.2   1.3e-20   2.5e-17       2      67 .]     358     423 ..     357     423 .. 0.96
   3 ?   -2.9   0.0       3.6   7.2e+03      20      57 ..     475     512 ..     474     512 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.12
                                   .............T-HSSCHHHHHHHHHHHHHHHHHHHH CS
                         HisKA  30 e...........gklteelkeyletiesearrldhlved 57 
                                   +            +  e+  +yl+ + +  + ld+l +d
  gi|91772717|ref|YP_565409.1| 322 WnktledevkskTSELERSNDYLQNANKKLKELDRLKND 360
                                   344444447555444466666999999999999999887 PP

  == domain 2  score: 62.7 bits;  conditional E-value: 1.3e-20
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   +++f+++v+HEL+tPL+a++  +e L++++  +e  +e+l+ i+++++r  ++v+dlLd+srie+g
  gi|91772717|ref|YP_565409.1| 358 KNDFVSMVSHELKTPLTAMKTSSEFLRESECSREIKEEMLDLIIRNIDRQARMVDDLLDISRIESG 423
                                   789***********************9997888*******************************97 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.6
                                   HHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHH CS
                         HisKA  20 ilgnaeaLkregklteelkeyletiesearrldhlved 57 
                                   i+ ++ +L + +k t+e  e   ++e++++ l+  ++d
  gi|91772717|ref|YP_565409.1| 475 IRIFVNLLTNAIKFTPEEGEVTVIVEDHEDYLQTSIKD 512
                                   67777888777777888888888888888877776665 PP

>> CHASE  CHASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.4e-08   2.7e-05      75     164 ..     117     192 ..      82     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.4e-08
                         CHASE  75 nnaalGlDllseperrealerardtgrpvlsgpvrLvqededgqagfllylPvyrkegpetveerraallGfvyavfridd 155
                                   +n  +G+Dl+  +  ++++e+  +tg+++++ p++ ++    g+ ++ +  P y +         + ++ G ++av++id+
  gi|91772717|ref|YP_565409.1| 117 ENVPFGYDLYE-KDKAAVFEQIKETGETHITNPLTTLE----GKLAIFVWIPFYLE---------NGSFEGAIVAVIEIDE 183
                                   3459*****75.78899******************887....9***********99.........446************* PP

                         CHASE 156 lleklllql 164
                                   + ++ ++ +
  gi|91772717|ref|YP_565409.1| 184 ITKQTIKTE 192
                                   ***999743 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.9   9.8e+03      14      39 ..     344     370 ..     342     380 .. 0.78
   2 !   18.3   0.1   8.1e-07    0.0016       4      92 ..     472     568 ..     469     577 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.9
                   HATPase_c_5  14 LdNAieacskiee.ekrfIrltvrekk 39 
                                   L NA    +++++ ++ f+++  +e k
  gi|91772717|ref|YP_565409.1| 344 LQNANKKLKELDRlKNDFVSMVSHELK 370
                                   788888888888888888888777655 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 8.1e-07
                   HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ek........kklesskskkeehGiGlk 72 
                                     l++i+ nlL NAi    +    + ++++ v+ +++ l  si+ +  g    +         +   + ++k +  G+Gl 
  gi|91772717|ref|YP_565409.1| 472 DKLIRIFVNLLTNAIKFTPE----EGEVTVIVEDHEDYLQTSIKDNGIGileeKRdkifdkfyQVDSTATRKAGGTGLGLA 548
                                   5799***********86555....66899999999999999998774444544223335323233336689999******* PP

                   HATPase_c_5  73 sireivkkykgnlsieaedg 92 
                                    i+ i++  +g++ +e e g
  gi|91772717|ref|YP_565409.1| 549 IIKGIIDGQGGKIYLESETG 568
                                   ***********999888765 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 !   15.6   0.1   5.4e-06     0.011       9      80 ..     480     548 ..     476     587 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-06
                   HATPase_c_3   9 elvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklA 80 
                                    l+ N++    +  +v++ v++ + +  + +i+D+G G+ ee+ ++ + ++ + + +a    ++ G  G+G  lA
  gi|91772717|ref|YP_565409.1| 480 NLLTNAIKftPEEGEVTVIVEDHE-DYLQTSIKDNGIGILEEKRDKIFdKFYQVDSTA---TRKAGGTGLG--LA 548
                                   677788773344556999999976.799******************996688888884...6777878888..44 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05      0.06      40     111 ..     482     556 ..     475     576 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                   HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikglvDe 111
                                   +tNa++   +   eg+v+v +e+ e+ l+ +++D+G g   e++++   + +      + ++   G+Gla+ikg+ D 
  gi|91772717|ref|YP_565409.1| 482 LTNAIKFTPE---EGEVTVIVEDHEDYLQTSIKDNGIGILEEKRDKIFDKFYqvdstaTRKAGGTGLGLAIIKGIIDG 556
                                   4555555554...688**********************777765554443338889888999999**********995 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.8   1.6e+03      36      53 ..      10      27 ..       3      50 .. 0.71
   2 ?   11.3   0.3   9.1e-05      0.18      17      77 ..     288     346 ..     275     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.8
                          SieB 36 glvflisiayllaqvvsk 53
                                  ++++++++ ++++++++ 
  gi|91772717|ref|YP_565409.1| 10 VIIVVMVTMLFISSILFL 27
                                  556666666666665554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.1e-05
                          SieB  17 slleklnlgkfleeyglwiglvflisiayllaqvvskllaeikekikkkreqkk.vekklkn 77 
                                   sl+++++++   +  + +i ++f+++i+ ++a ++ +  +++ +++k+k+++ +  +++l+n
  gi|91772717|ref|YP_565409.1| 288 SLIQSVYVK---QGLFAMISIAFILFISAFIALILLSWNKTLEDEVKSKTSELErSNDYLQN 346
                                   667777655...667889*****************************666553303444444 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4      0.05        99      21      49 ..     324     352 ..     319     371 .. 0.77
   2 ?    8.9   1.3   0.00089       1.8      22      87 ..     364     430 ..     349     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.05
                          Rx_N  21 kgvkeeleklkdeLesiqavLedaeerqi 49 
                                   k +++e+++  +eLe+ + +L+ a ++  
  gi|91772717|ref|YP_565409.1| 324 KTLEDEVKSKTSELERSNDYLQNANKKLK 352
                                   5689********************99544 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00089
                          Rx_N  22 gvkeeleklkdeLesiqavLedaee.rqikdeavkeWlkelrdlaydaeDvlDefetealrrksspk 87 
                                    v +el+   + +++   +L++ e  r+ik+e ++  ++++   a  ++D+lD  ++e+++ k +p+
  gi|91772717|ref|YP_565409.1| 364 MVSHELKTPLTAMKTSSEFLRESECsREIKEEMLDLIIRNIDRQARMVDDLLDISRIESGKMKFTPE 430
                                   56777777777888888899999986888********************************996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1411  (0.0786993); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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 0.36s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 3583.95
//
Query:       gi|91772718|ref|YP_565410.1|  [L=170]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-33  113.1   0.6    9.5e-33  112.7   0.6    1.2  1  Response_reg   Response regulator receiver domain
    2.4e-07   30.6   0.2    6.6e-07   29.2   0.2    1.8  2  HTH_11         HTH domain
    0.00037   20.4   0.1    0.00075   19.4   0.1    1.5  1  MarR           MarR family
     0.0014   18.2   0.6     0.0029   17.1   0.3    1.8  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0094   15.8   1.3      0.012   15.4   0.1    1.8  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.044   13.5   0.0      0.058   13.2   0.0    1.2  1  NIF            NLI interacting factor-like phosphatase
      0.053   13.4   0.0        0.1   12.5   0.0    1.4  1  MarR_2         MarR family


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 !  112.7   0.6   3.7e-36   9.5e-33       1     112 []      50     162 ..      50     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 3.7e-36
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   vlivdD+p+++ +++++le +gy +v ea++g+ a++ lk++ +d+illD++mp+mdG+e++++++ee+  +++pvi+lta
  gi|91772718|ref|YP_565410.1|  50 VLIVDDEPDAVIATKRALEADGY-NVIEANNGTMAFDALKSDIPDVILLDVMMPDMDGFEVCRRLKEEPlyENIPVIMLTA 129
                                   8**********************.999*******************************************999******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkale 112
                                   ++e +d+ve+l++gadd+++Kpf+ +eL+++++
  gi|91772718|ref|YP_565410.1| 130 KGEINDKVEGLDIGADDYMTKPFNLKELKARIK 162
                                   *****************************9985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.2   2.6e-10   6.6e-07       3      45 ..       8      49 ..       6      72 .. 0.86
   2 ?   -2.2   0.0       1.7   4.3e+03      38      47 ..      66      75 ..      59      80 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.6e-10
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                  ++i++lL e+++ is++ +A++L+vS+  v r I++L+++  +
  gi|91772718|ref|YP_565410.1|  8 KDIMRLL-EQQPEISAKGIADRLSVSEDIVTRTIESLSDTRHK 49
                                  6788888.88888************************998844 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                        HTH_11 38 aLeelgvpIe 47
                                  aLe+ g+ ++
  gi|91772718|ref|YP_565410.1| 66 ALEADGYNVI 75
                                  6888895443 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.9e-07   0.00075       7      41 ..       9      43 ..       6      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.9e-07
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHH CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrL 41
                                  +i+r+l++q+++s + +a++l+vs   vtr++  L
  gi|91772718|ref|YP_565410.1|  9 DIMRLLEQQPEISAKGIADRLSVSEDIVTRTIESL 43
                                  69*****************************9887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   1.2e-06    0.0029       2      36 ..       4      38 ..       3      46 .. 0.84
   2 ?   -2.9   0.0       2.1   5.3e+03      39      46 ..      65      72 ..      65      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnr 36
                                   +++++I++lL+++p is + +A+rl +S   v+r
  gi|91772718|ref|YP_565410.1|  4 EKLEKDIMRLLEQQPEISAKGIADRLSVSEDIVTR 38
                                  57899**********************99765555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                        HTH_24 39 krLeeeGl 46
                                  + Le +G+
  gi|91772718|ref|YP_565410.1| 65 RALEADGY 72
                                  67999998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   4.6e-06     0.012       6      40 ..       8      42 ..       5      44 .. 0.89
   2 ?   -3.1   0.1       2.8   7.2e+03      33      38 ..     163     168 ..     162     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-06
                 HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrr 40
                                  + I+++L++++ is + +A+r+ +Se+ v r ++ 
  gi|91772718|ref|YP_565410.1|  8 KDIMRLLEQQPEISAKGIADRLSVSEDIVTRTIES 42
                                  569***********************999887765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                 HTH_AsnC-type  33 tvlrRv 38 
                                   tvlrR 
  gi|91772718|ref|YP_565410.1| 163 TVLRRT 168
                                   899*97 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.3e-05     0.058      60     120 ..       4      63 ..       1      88 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                           NIF  60 eeyaeavidildpekkllshrlyrescvkkkgeyvKdLsllgrdlsrvvivDdspdsfelq 120
                                   e+  +++++ l+++ + +s++   ++    +  +++ ++ l    ++v+ivDd+pd++ + 
  gi|91772718|ref|YP_565410.1|   4 EKLEKDIMRLLEQQPE-ISAKGIADRLSVSEDIVTRTIESLSDTRHKVLIVDDEPDAVIAT 63 
                                   566789999****999.999999999954588999*********************98864 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.9e-05       0.1       9      47 ..       9      45 ..       6      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                  HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLva 47
                                  +++  L   p+  ++++ +a+rl +s   v+r+++ L++
  gi|91772718|ref|YP_565410.1|  9 DIMRLLEQQPE--ISAKGIADRLSVSEDIVTRTIESLSD 45
                                  67888999999..**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1039.12
//
Query:       gi|91772719|ref|YP_565411.1|  [L=93]
Description: hypothetical protein Mbur_0696 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00028   20.7   0.0    0.00037   20.3   0.0    1.2  1  MarR_2    MarR family
     0.0031   17.4   0.1     0.0042   16.9   0.1    1.2  1  RuvB_C    RuvB C-terminal winged helix domain
     0.0068   16.5   0.1      0.013   15.6   0.1    1.4  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
     0.0078   15.7   0.1      0.017   14.7   0.1    1.7  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.017   15.5   0.1      0.023   15.0   0.1    1.2  1  Rrf2      Transcriptional regulator
      0.018   15.0   0.2      0.027   14.4   0.2    1.3  1  HTH_11    HTH domain
      0.021   14.6   0.0       0.03   14.1   0.0    1.3  1  HTH_IclR  IclR helix-turn-helix domain
      0.031   14.1   0.0      0.042   13.7   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.044   13.7   0.1       0.61   10.1   0.0    2.1  2  TBPIP     TBPIP/Hop2 winged helix domain
      0.045   13.7   0.1      0.072   13.0   0.1    1.3  1  MarR      MarR family
      0.064   13.3   0.1       0.11   12.6   0.1    1.5  1  HTH_46    Winged helix-turn-helix DNA binding
       0.16   12.0   0.0       0.21   11.6   0.0    1.2  1  HTH_35    Winged helix-turn-helix DNA-binding


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 !   20.3   0.0   2.5e-07   0.00037       6      53 ..      12      59 ..       8      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                                  HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  aq  vL +L  + g+    + +a+++gls+s+v r+++ L +   v +
  gi|91772719|ref|YP_565411.1| 12 AQITVLKNLIQHKGESTYLSGIAEETGLSHSSVARVIEPLLKSNIVIE 59
                                  8999***********99*********************9999888755 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 !   16.9   0.1   2.8e-06    0.0042       8      56 ..      13      60 ..      10      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.8e-06
                                  HHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEE CS
                        RuvB_C  8 dikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIer 56
                                   i++Lk l+++ kg+ + l+ +a+ +g++ + +  viEP+L  +  Ie+
  gi|91772719|ref|YP_565411.1| 13 QITVLKNLIQH-KGESTYLSGIAEETGLSHSSVARVIEPLLKSNIVIEK 60
                                  67899999965.***************************9877777776 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 !   15.6   0.1   8.4e-06     0.013       7      57 ..       4      57 ..       3      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.4e-06
                                  HHHCSTTHHH.HHHHHHHHHSSBE..HHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9  7 ieehFGevva.kVvetLlrkgrlt..lrelvkktkLsldqVkksLvvLiqhrlV 57
                                  +e++FG++++ +V + L+++   +  l+ ++++t+Ls+++V ++   L++ ++V
  gi|91772719|ref|YP_565411.1|  4 LEKIFGKTAQiTVLKNLIQHKGEStyLSGIAEETGLSHSSVARVIEPLLKSNIV 57
                                  689******96799****98777646789***************9999999998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.1e-05     0.017      23      47 ..      33      57 ..      16      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                        HTH_24 23 LAerlglSpstvnrrlkrLeeeGlI 47
                                  +Ae++glS s v r ++ L ++ ++
  gi|91772719|ref|YP_565411.1| 33 IAEETGLSHSSVARVIEPLLKSNIV 57
                                  9********************9998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.5e-05     0.023      11      58 ..      14      60 ..       9      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  +++l  L ++++e+   ++ iae++++s+s ++++++ L k+++v  +
  gi|91772719|ref|YP_565411.1| 14 ITVLKNLIQHKGES-TYLSGIAEETGLSHSSVARVIEPLLKSNIVIEK 60
                                  57788899999987.99************************9998654 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.8e-05     0.027       3      49 ..      14      61 ..      12      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                        HTH_11  3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIese 49
                                   ++l+ L++++g     + +Aee+++S + v r I+ L ++ + Ie++
  gi|91772719|ref|YP_565411.1| 14 ITVLKNLIQHKGEsTYLSGIAEETGLSHSSVARVIEPLLKSNIVIEKR 61
                                  578999*******999***********************999999986 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 ?   14.1   0.0     2e-05      0.03      12      40 ..      21      49 ..      14      57 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                  -CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                      HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLq 40
                                  + + ++   ls +A++tgl+ S+v R + 
  gi|91772719|ref|YP_565411.1| 21 IQHKGESTYLSGIAEETGLSHSSVARVIE 49
                                  34444445899**************9876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.8e-05     0.042      11      55 ..      14      60 ..       7      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                  CCHCHHHH.HHCCCH.HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 11 akvYlaLl.klgpat.adeiaeelgvprskvYevLrsLedkGlVere 55
                                  + v + L+  +g++t  + iaee+g+++s+v +v++ L++  +V  +
  gi|91772719|ref|YP_565411.1| 14 ITVLKNLIqHKGESTyLSGIAEETGLSHSSVARVIEPLLKSNIVIEK 60
                                  5677777754444442478*********************9999765 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.15   2.3e+02      25      44 ..       3      22 ..       1      25 [. 0.65
   2 ?   10.1   0.0   0.00041      0.61      29      56 ..      38      65 ..      28      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.15
                         TBPIP 25 nlqkklgKtavqkaLdeLvd 44
                                  +l+k +gKta   +L +L +
  gi|91772719|ref|YP_565411.1|  3 ALEKIFGKTAQITVLKNLIQ 22
                                  56667777777766666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00041
                         TBPIP 29 klgKtavqkaLdeLvdegkiieKeyGKq 56
                                  +l+  +v ++++ L +++ +ieK  GKq
  gi|91772719|ref|YP_565411.1| 38 GLSHSSVARVIEPLLKSNIVIEKRLGKQ 65
                                  688999*********************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.8e-05     0.072       5      47 ..      13      57 ..      11      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                                  HHHHHHHHHHSTT..EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  5 qfviLrilyeqgp..lsvseLakklgvskstvtrvldrLekkGli 47
                                  q+ +L +l ++ +   ++s +a+  g+s s+v rv+  L k + +
  gi|91772719|ref|YP_565411.1| 13 QITVLKNLIQHKGesTYLSGIAEETGLSHSSVARVIEPLLKSNIV 57
                                  7888888888877557888*********************99877 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 ?   12.6   0.1   7.1e-05      0.11      29      53 ..      33      57 ..      12      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                        HTH_46 29 IqkrtnLSrSsimkvLseLkkggyI 53
                                  I + t LS Ss+++v+  L k + +
  gi|91772719|ref|YP_565411.1| 33 IAEETGLSHSSVARVIEPLLKSNIV 57
                                  899**************98776533 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.21      16      54 ..      28      65 ..      17      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                        HTH_35 16 ttLaalsreaglssstlsnaltrpwpkgEalIAeaLgvp 54
                                  t L+++++e gls+s+++++++ p  k+  +I + Lg +
  gi|91772719|ref|YP_565411.1| 28 TYLSGIAEETGLSHSSVARVIE-PLLKSNIVIEKRLGKQ 65
                                  569****************985.8999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 562.69
//
Query:       gi|91772720|ref|YP_565412.1|  [L=251]
Description: hypothetical protein Mbur_0697 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-41  141.7  12.9    2.5e-41  141.4  12.9    1.1  1  Sensor    Putative sensor
  ------ inclusion threshold ------
        1.2    9.1   8.4        0.1   12.6   1.9    2.0  2  PgpA      Phosphatidylglycerophosphatase A
        4.8    7.3   6.7       0.75    9.9   1.0    2.3  2  DUF5392   Family of unknown function (DUF5392)


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4  12.9   4.2e-45   2.5e-41       1     162 []      28     208 ..      28     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 4.2e-45
                        Sensor   1 YlllglplgvaafvllvtglslglgllvllvGlplLalalllarglaaveRrrarlllglpvprphrapep....pgllar 77 
                                   Yll ++plg+a+f++lvtgls+glgl+++l+Glp+L+l+l++++ laa+eR++a +llg++vp  ++        +  +++
  gi|91772720|ref|YP_565412.1|  28 YLLFTFPLGTAYFIFLVTGLSMGLGLSITLIGLPILILMLVAWWELAAFERQLAIWLLGVDVPPMEN---RgikyQKNFEK 105
                                   9**************************************************************4432...234578889** PP

                        Sensor  78 lrallrdpatwrdllylllhfplglvlfvvavvllalalalltaPlw..................tlpeallvavlGllll 140
                                   ++ ++ +p+tw+ l++l+++fplg+++++v+++l+ ++l+++++P++                  +l++al+++++G+++ 
  gi|91772720|ref|YP_565412.1| 106 IKGYILNPVTWKGLVFLFIKFPLGIFTLIVSFTLIGITLVFIATPFVyklteigyssgtstfvidSLAGALMMMFFGMIFG 186
                                   **********************************************6477777766666555544499************* PP

                        Sensor 141 lvllwvvrglarlqallaraLL 162
                                   +++l++++++a+l++ la+ LL
  gi|91772720|ref|YP_565412.1| 187 VFSLHIMNWMAKLSGILAKNLL 208
                                   *********************9 PP

>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.6      0.13   7.9e+02      41      62 ..      57      79 ..      24      87 .. 0.62
   2 ?   12.6   1.9   1.7e-05       0.1      16      88 ..     112     184 ..     102     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.13
                                  HH.HHHHHHHHHHHHHHHHHHT- CS
                          PgpA 41 ll.llilllflvGiwackkteke 62
                                  l+ l il+l+lv++w  +++e++
  gi|91772720|ref|YP_565412.1| 57 LIgLPILILMLVAWWELAAFERQ 79
                                  22355666667777766666655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.7e-05
                                   ..--HHHHHHHHHHHTT.HHHHH.HHHHHHHHHHHHHHHHHHHHHT-S-HHT-TT--HHHHTTHHHHH..... CS
                          PgpA  16 aPgtvgslaalllalllllleslslllllilllflvGiwackktekelgekDpgeiviDEvvgqwiallllpa 88 
                                    P+t++ l+ l + + l +++ + ++ l+ ++l+++++ ++ k ++   ++  + +viD ++g ++++++ ++
  gi|91772720|ref|YP_565412.1| 112 NPVTWKGLVFLFIKFPLGIFTLIVSFTLIGITLVFIATPFVYKLTEIGYSSGTSTFVIDSLAGALMMMFFGMI 184
                                   69***************99998877776777777777777777777666799*************99965543 PP

>> DUF5392  Family of unknown function (DUF5392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.5      0.14   8.1e+02      28      46 ..      26      44 ..      13      76 .. 0.66
   2 ?    9.9   1.0   0.00012      0.75      10      49 ..     100     140 ..      92     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.14
                       DUF5392 28 skysfislPLllvslinli 46
                                  ++y ++++PL ++ +i l+
  gi|91772720|ref|YP_565412.1| 26 LTYLLFTFPLGTAYFIFLV 44
                                  3455555555444444433 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00012
                       DUF5392  10 kkEldklqevi.aPllkKsskysfislPLllvslinlilll 49 
                                   +k ++k++  i +P+  K + + fi +PL +++li  ++l+
  gi|91772720|ref|YP_565412.1| 100 QKNFEKIKGYIlNPVTWKGLVFLFIKFPLGIFTLIVSFTLI 140
                                   6889999987648****************999998777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); 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:                         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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1370.99
//
Query:       gi|91772721|ref|YP_565413.1|  [L=74]
Description: hypothetical protein Mbur_0698 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-13   49.8   2.9    2.4e-13   49.8   2.9    1.7  2  PLDc_N    Phospholipase_D-nuclease N-terminal
  ------ inclusion threshold ------
       0.04   13.5   0.1      0.053   13.1   0.1    1.1  1  DUF1496   Protein of unknown function (DUF1496)


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3      0.42   3.8e+03      24      28 ..      14      18 ..      12      22 .. 0.49
   2 !   49.8   2.9   2.7e-17   2.4e-13       1      42 []      27      70 ..      27      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.42
                        PLDc_N 24 lvilf 28
                                  l++lf
  gi|91772721|ref|YP_565413.1| 14 LFLLF 18
                                  44444 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 2.7e-17
                        PLDc_N  1 ilwiialidiirdrnpss...klaWllvilflPvlGailYllfGr 42
                                  i+w ++lid+++ ++ps+   kl+W+++i+f  +lGa+ Y++f+r
  gi|91772721|ref|YP_565413.1| 27 IFWTWMLIDCVM-NEPSYgndKLIWIIIIVFAQLLGALTYFIFRR 70
                                  79**********.******************************98 PP

>> DUF1496  Protein of unknown function (DUF1496)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.9e-06     0.053      22      52 ..      23      53 ..      22      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-06
                       DUF1496 22 eGAvikvegvlLqCsrdekfegngeLiWkel 52
                                  +G+ i    +l+ C+ +e ++gn +LiW ++
  gi|91772721|ref|YP_565413.1| 23 IGSTIFWTWMLIDCVMNEPSYGNDKLIWIII 53
                                  67778888899*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 416.07
//
Query:       gi|91772722|ref|YP_565414.1|  [L=404]
Description: hypothetical protein Mbur_0699 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-25   89.9   3.0    2.7e-25   89.9   3.0    1.8  2  MacB_PCD  MacB-like periplasmic core domain
    3.5e-13   49.8   4.2    3.5e-13   49.8   4.2    3.0  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 !   89.9   3.0     3e-29   2.7e-25       1     194 [.      22     238 ..      22     239 .. 0.78
   2 ?   -2.1   0.7      0.46   4.2e+03      13      37 ..     289     313 ..     282     360 .. 0.68

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 3e-29
                      MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv....tvr 76 
                                   s lt LGi+iGvaavia vslg++++++++++i   g  + +++++++++++ d+++e +r + p v +++p+     +v+
  gi|91772722|ref|YP_565414.1|  22 STLTTLGIVIGVAAVIANVSLGASFNQYFDEEIGTIGS-NFIYVSANEPNTFFDNELEVVR-KTPgVLRASPINeqvaEVT 100
                                   68********************************9996.6688888999999999996654.5688999999877666334 PP

                      MacB_PCD  77 gggsgeeevtvvgvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf..........pvGdtirl........ 139
                                   + ++ ++ v+++gv+ dy +v ++ l+eG f+ ++    +++v+vig+++ e+ f                 +        
  gi|91772722|ref|YP_565414.1| 101 YMSD-SRRVSITGVTGDYDEVANIGLSEGNFIKDN----DQYVAVIGYDVSEDTFdrklsnknsiE------Infrtrdge 170
                                   4432.5669***************88999998664....689***********9999886655441......344445566 PP

                      MacB_PCD 140 ...kpftVvGvled.pp..gsgsalgddavylplttl.......qrrsitvrlkdgadleaaaaelek 194
                                      ++f+V G++++ +p   sg++  d ++++p+ t+       ++++i+++ ++ +++++++ e++k
  gi|91772722|ref|YP_565414.1| 171 eitQTFQVKGIVQKsEPsfISGGMVPDKRIFIPIPTMneilsvsDYSTIFAEGESIETVTETSGEIDK 238
                                   656********966444553334556*******77775555544566799988888888888888875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.46
                      MacB_PCD  13 aaviaivslgeglqasvlsqisdlg 37 
                                     v++ +++++ ++ +v+++ s+ g
  gi|91772722|ref|YP_565414.1| 289 SLVVGSIGIMNIMLVTVTERTSEIG 313
                                   5567777777777777777666554 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.021   1.9e+02      28      51 ..      24      45 ..      11      77 .. 0.50
   2 ?   -1.1   1.2       0.3   2.7e+03      26      38 ..     283     296 ..     271     306 .. 0.56
   3 !   49.8   4.2   3.9e-17   3.5e-13       2      96 .]     310     397 ..     309     397 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.021
                          FtsX 28 itlvalviGlglgllaaqllsdvl 51
                                  +t +++viG  +++++a+++    
  gi|91772722|ref|YP_565414.1| 24 LTTLGIVIG--VAAVIANVSLGAS 45
                                  233344444..4444443322222 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                          FtsX  26 llitlvalviG.lg 38 
                                    ++++++lv+G +g
  gi|91772722|ref|YP_565414.1| 283 TAVAFISLVVGsIG 296
                                   34455555555222 PP

  == domain 3  score: 49.8 bits;  conditional E-value: 3.9e-17
                          FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllall 82 
                                   +eig+++++G+++ +vl ++++e+++++ ++ ++G++lg++ a+   ++       ++l++ ++ + +++++v+++++ l+
  gi|91772722|ref|YP_565414.1| 310 SEIGLMKSIGYSNFDVLTMFIVESAVVGTIGGILGVILGCAGAYGAATF-------MNLPVVLPASKIFAGFVVSIFVGLI 383
                                   7*****************************************9984444.......89*********************** PP

                          FtsX  83 agllsiskilkkep 96 
                                   ag++++ k++k++p
  gi|91772722|ref|YP_565414.1| 384 AGAYPANKAAKMKP 397
                                   ***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2979.74
//
Query:       gi|91772723|ref|YP_565415.1|  [L=411]
Description: hypothetical protein Mbur_0700 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   17.8   0.2       0.07   13.4   0.0    3.0  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
     0.0045   17.3   1.5      0.022   15.0   1.3    2.2  2  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.015   15.3   0.4       0.38   10.8   0.0    2.5  2  Wzt_C        Wzt C-terminal domain
      0.085   12.9   0.0       0.48   10.5   0.0    2.0  2  ETRAMP       Malarial early transcribed membrane protein (ETR
       0.81    9.7   2.7        3.1    7.8   0.1    2.3  2  NVEALA       NVEALA protein


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 ?    0.4   0.0      0.21   7.7e+02       2      21 ..     169     188 ..     168     192 .. 0.83
   2 !   13.4   0.0   1.9e-05      0.07      39      74 ..     217     252 ..     214     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                   NPCBM_assoc   2 epGetvtltltvtndgtaaa 21 
                                   +pG++ t+ + +tn+ ++ +
  gi|91772723|ref|YP_565415.1| 169 SPGDKGTISFKLTNTASENT 188
                                   79************998765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.9e-05
                   NPCBM_assoc  39 vspasaaslapGetveatvkVtppagaaaGdyevta 74 
                                   + +++a  + pG +v+ t++V +p++ + G+y + +
  gi|91772723|ref|YP_565415.1| 217 SGVQEAGIVGPGNSVTLTFNVEVPEDVQEGTYYLDL 252
                                   556777789***********************8865 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.78   2.8e+03       9      34 ..      50      75 ..      34      82 .. 0.79
   2 !   15.0   1.3   6.2e-06     0.022       4      86 ..     162     247 ..     158     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.78
                         DUF11  9 evrpGdtvtytltvtNtgpasangvv 34
                                  ++  G+ v++ + v N    ++ +v+
  gi|91772723|ref|YP_565415.1| 50 PAEIGQYVDVWVKVENFRSGQSDDVT 75
                                  67889999999999997766666665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.2e-06
                         DUF11   4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.qgtasaltsv...gsLeagesatlsftvrvtr 80 
                                   t+++  + pGd+ t    +tNt   +  ++  +D   ++ +++s+s +   +++++++v   g + +g+s tl+f v+v+ 
  gi|91772723|ref|YP_565415.1| 162 TSTPNMFSPGDKGTISFKLTNTASENTINIDGED-YDTNARIQSASLTgADSIKVTSGVqeaGIVGPGNSVTLTFNVEVPE 241
                                   45566889**************************.7899999****99444555666669999****************99 PP

                         DUF11  81 taasga 86 
                                     ++g+
  gi|91772723|ref|YP_565415.1| 242 DVQEGT 247
                                   988775 PP

>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.033   1.2e+02      72     109 ..     154     204 ..     121     226 .. 0.62
   2 ?   10.8   0.0   0.00011      0.38      76     113 ..     221     260 ..     203     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.033
                         Wzt_C  72 k....ks.feleel.kagervevefef.......klpLapGeYlltvaled 109
                                   +    ++  +++++ ++g++++++f++       ++++ + +Y  ++ +++
  gi|91772723|ref|YP_565415.1| 154 GtlelTEtTSTPNMfSPGDKGTISFKLtntasenTINIDGEDYDTNARIQS 204
                                   233332223355555**********99744443323566666666666544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                         Wzt_C  76 eleelkagervevefef...klpLapGeYlltvaledrdge 113
                                   e + + +g++v+ +f++   + + ++G+Y+l++a+ +++++
  gi|91772723|ref|YP_565415.1| 221 EAGIVGPGNSVTLTFNVevpE-DVQEGTYYLDLAIIGNSYS 260
                                   56677999*********8644.9************888775 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.24   8.6e+02       8      29 ..      13      34 ..       8     167 .. 0.74
   2 ?   10.5   0.0   0.00014      0.48      61      82 ..     388     409 ..     335     410 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                        ETRAMP  8 lffafLlavnlltpeslcdevn 29
                                   +fa+++++ +++ ++++ ++n
  gi|91772723|ref|YP_565415.1| 13 TVFAVMIVLLIMVMPTVSAQEN 34
                                  4444444444444444444443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                        ETRAMP  61 iatalallvasalGlgiykkkk 82 
                                     +a +ll+++a G+ iykk+k
  gi|91772723|ref|YP_565415.1| 388 STIAFVLLIVAAAGIFIYKKRK 409
                                   34455678889**********8 PP

>> NVEALA  NVEALA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3     0.083     3e+02       4      33 ..      12      41 ..       9      44 .. 0.62
   2 ?    7.8   0.1   0.00087       3.1       5      26 ..     389     410 ..     387     411 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.083
                        NVEALA  4 fkilfvlvfavlagtgiyksnkkevslsdL 33
                                  +++ +v+++  +  + +++ ++++v++ d+
  gi|91772723|ref|YP_565415.1| 12 ITVFAVMIVLLIMVMPTVSAQENSVTSLDI 41
                                  445555555555666667788888877766 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00087
                        NVEALA   5 kilfvlvfavlagtgiyksnkk 26 
                                   +i+fvl+++++ag+ iyk  k+
  gi|91772723|ref|YP_565415.1| 389 TIAFVLLIVAAAGIFIYKKRKQ 410
                                   89************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:01.51
# Mc/sec: 824.65
//
Query:       gi|91772724|ref|YP_565416.1|  [L=241]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-33  115.4   0.1    3.8e-33  114.9   0.1    1.2  1  ABC_tran        ABC transporter
    6.8e-09   35.9   0.6    0.00011   22.2   0.2    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.4e-07   31.2   0.1    4.2e-07   29.6   0.1    1.6  1  SMC_N           RecF/RecN/SMC N terminal domain
    6.9e-05   22.5   0.3    0.00032   20.4   0.1    2.1  2  AAA_29          P-loop containing region of AAA domain
    0.00011   22.2   0.1    0.00018   21.5   0.1    1.4  1  RsgA_GTPase     RsgA GTPase
     0.0021   18.4   0.1     0.0033   17.7   0.1    1.7  1  AAA_22          AAA domain
     0.0023   18.3   0.0     0.0034   17.8   0.0    1.4  1  AAA_16          AAA ATPase domain
     0.0033   18.0   0.1      0.007   16.9   0.1    1.6  1  AAA_18          AAA domain
     0.0084   15.9   0.0      0.067   12.9   0.0    2.1  2  IstB_IS21       IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.045   13.8   0.0    1.9  2  MMR_HSR1        50S ribosome-binding GTPase
      0.015   15.8   0.1      0.031   14.8   0.1    1.5  1  AAA_23          AAA domain
      0.018   15.2   0.0      0.046   13.8   0.0    1.6  1  DUF87           Helicase HerA, central domain
      0.019   14.7   0.1       0.06   13.1   0.0    1.9  2  AAA_24          AAA domain
      0.048   13.4   0.0       0.53    9.9   0.0    2.1  2  AAA_15          AAA ATPase domain
      0.059   13.1   0.0        0.1   12.3   0.0    1.3  1  AAA_30          AAA domain
      0.069   12.3   0.0      0.085   12.0   0.0    1.1  1  G-alpha         G-protein alpha subunit
      0.071   12.2   0.1       0.19   10.7   0.0    1.7  2  T2SSE           Type II/IV secretion system protein
      0.076   12.6   0.0       0.14   11.7   0.0    1.3  1  AAA_25          AAA domain
      0.095   12.4   0.1       0.16   11.7   0.1    1.3  1  Cytidylate_kin  Cytidylate kinase
      0.096   12.9   0.0       0.15   12.3   0.0    1.3  1  AAA_28          AAA domain
      0.099   12.0   0.1          9    5.6   0.0    2.2  2  ATPase          KaiC
       0.13   12.7   0.0       0.29   11.5   0.0    1.7  1  RNA_helicase    RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.1   4.7e-36   3.8e-33       1     136 [.      41     189 ..      41     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 4.7e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                   l+++++++k+ge +ai+G++G+GKStL++ll  l +p eG++l+ gkd+++    +  +    eig+++q+ +l ++lt+ 
  gi|91772724|ref|YP_565416.1|  41 LHDINITVKKGEFIAIMGPSGSGKSTLMNLLGCLDRPSEGQVLVMGKDINSisetELAKLRGLEIGFVFQNFNLVSRLTAL 121
                                   789************************************************8774444555569***************99 PP

                                   HH..........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx..........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en..........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   +n          +   +    e+a + lgl +  d++++++p++LSgGq qrva+aral+++p ++l+DEpt
  gi|91772724|ref|YP_565416.1| 122 QNvllpthanrrT---DidvNERAKQLLGLMG-LDDRMEHKPTELSGGQSQRVAIARALINEPAIILADEPT 189
                                   99****9766542...1444566666677777.556778899*****************************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 !   12.6   0.1   0.00011     0.087       1      23 [.      53      75 ..      53     109 .. 0.79
   2 !   22.2   0.2   1.3e-07   0.00011     180     300 ..     129     222 ..      86     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                        AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                  + ++ Gp gsGKS+L+ +l +l 
  gi|91772724|ref|YP_565416.1| 53 FIAIMGPSGSGKSTLMNLLGCLD 75
                                  57899**************9993 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.3e-07
                        AAA_21 180 kekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsl 260
                                   + +r+++  v+++ ++ + l+ l+++                         e  ++elS G+ +  a++ al+  +   ++
  gi|91772724|ref|YP_565416.1| 129 HANRRTDIDVNERAKQLLGLMGLDDRM------------------------EHKPTELSGGQSQRVAIARALINEP---AI 182
                                   444455555555555555555554333........................3346788999999989999999888...** PP

                        AAA_21 261 lliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                   +l DEp  +L+ k   +++el++ l++ng+ +i+ TH+p+
  gi|91772724|ref|YP_565416.1| 183 ILADEPTGNLDSKTSVEIMELFSGLHKNGSTIIMITHDPE 222
                                   **********************99999************7 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   5.1e-10   4.2e-07      24     212 ..      51     234 ..      41     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.1e-10
                                   SSEEEEEESTTSSHHHHHHHHHHHCTT.TT.TTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersa.kklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                    +f ai+Gp GSGKs l++ +  +L   s  + l   k  + i++  e a++   e+  +f+n +   +  +   ++    
  gi|91772724|ref|YP_565416.1|  51 GEFIAIMGPSGSGKSTLMNLL-GCLDRPSEgQVLVMGKDINSISE-TELAKLRGLEIGFVFQNFNLV-SRLTALQNVLLPT 128
                                   4699**************987.78875443033444444444555.677888888999999998876.4444445677777 PP

                                   ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 104 krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                     + ++++ +n++  +   ++ l  +++ ++++LSgG+ + va+a       ++  ++ l De   +LD k   ++ el+ 
  gi|91772724|ref|YP_565416.1| 129 HANRRTDIDVNERAKQLLGLMGLDDRMEHKPTELSGGQSQRVAIARA----LINEPAIILADEPTGNLDSKTSVEIMELFS 205
                                   7888889********************************99988754....4677789999******************** PP

                                   HHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 185 ekskn.aQfivislreemlekadklvgvt 212
                                     +kn + +i+i+++ e+ + ad+++ v+
  gi|91772724|ref|YP_565416.1| 206 GLHKNgSTIIMITHDPETSAYADRTIHVK 234
                                   888887999***************99986 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 !   20.4   0.1   3.9e-07   0.00032      16      39 ..      45      68 ..      40      75 .. 0.79
   2 ?   -1.3   0.0       2.4   1.9e+03      41      50 ..     120     129 ..     118     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.9e-07
                        AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                   i+++  g ++ ++GpsGsGKSTl+
  gi|91772724|ref|YP_565416.1| 45 NITVKK-GeFIAIMGPSGSGKSTLM 68
                                  455554.4599*************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                        AAA_29  41 AiqalLvpak 50 
                                   A+q +L+p++
  gi|91772724|ref|YP_565416.1| 120 ALQNVLLPTH 129
                                   8999***998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.2e-07   0.00018      72     120 ..      22      72 ..       7      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-07
                                   HHHTTSE.EEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  72 lealgye.vllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                   +e++g++  +++s ++   l++++  +k+ ++++++G+SG GKStL+n l 
  gi|91772724|ref|YP_565416.1|  22 METIGLKkSYYLSDTEVPILHDINITVKKgEFIAIMGPSGSGKSTLMNLLG 72 
                                   556665414456666667788899888888******************985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.1e-06    0.0033       4      25 ..      50      71 ..      46     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.1e-06
                        AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                  +  +++++G+sG+GK+tl++ l
  gi|91772724|ref|YP_565416.1| 50 KGEFIAIMGPSGSGKSTLMNLL 71
                                  6789***************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.2e-06    0.0034      18     107 ..      47     158 ..      34     215 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-06
                        AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd..........................ggiflrgkcdqlesaipysal 72 
                                   +v++g  e + + G+sG+GKs+l++ l   l +                           ++ f+ +++            
  gi|91772724|ref|YP_565416.1|  47 TVKKG--EFIAIMGPSGSGKSTLMNLLG-CLDRPsegqvlvmgkdinsisetelaklrglEIGFVFQNFNLV-------SR 117
                                   45555..789*************97665.2333322225555554544444444444444333333333333.......23 PP

                        AAA_16  73 aqalareellrqlldeaesaeleawrekleeala.......a 107
                                   ++al ++ ll   +++ ++ ++++ +++l++ ++        
  gi|91772724|ref|YP_565416.1| 118 LTAL-QNVLLPTHANRRTDIDVNERAKQLLGLMGlddrmehK 158
                                   4445.4466666666666666666666666666655555553 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   8.6e-06     0.007       1      61 [.      54     143 ..      54     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.6e-06
                        AAA_18   1 IlltGtpGvGKttlakeL......skrlgf......................gvnlrdvakenglllevdpe.....alde 48 
                                   I+++G++G+GK+tl + L      s                           g ++++v+++ +l+   ++       ++ 
  gi|91772724|ref|YP_565416.1|  54 IAIMGPSGSGKSTLMNLLgcldrpS----EgqvlvmgkdinsisetelaklrGLEIGFVFQNFNLVSRLTALqnvllPTHA 130
                                   89****************6666442....0223556666665666666667777777777777777776666666675555 PP

                        AAA_18  49 skrldedkldkll 61 
                                   ++r d+d+ +++ 
  gi|91772724|ref|YP_565416.1| 131 NRRTDIDVNERAK 143
                                   5555555544444 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   8.2e-05     0.067      15      68 ..      18      72 ..       6      82 .. 0.80
   2 ?    0.6   0.0      0.51   4.2e+02     102     146 ..     172     216 ..     152     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                     IstB_IS21 15 aqktledidfraarsldkrkvkeLatlsf.iekkenivllGpsGvGKshlaialg 68
                                  + k++e+i  +++  l+ ++v  L   +  ++k e i+++GpsG GKs l   lg
  gi|91772724|ref|YP_565416.1| 18 PDKVMETIGLKKSYYLSDTEVPILHDINItVKKGEFIAIMGPSGSGKSTLMNLLG 72
                                  567888888888888888888888777752688899************9987766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.51
                     IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiit 146
                                   ++++l++   +il d  + +ld++ + +++e+ +   ++ s+ii 
  gi|91772724|ref|YP_565416.1| 172 IARALINEPAIILADEPTGNLDSKTSVEIMELFSGLHKNGSTIIM 216
                                   455666667788888889999999999999999999999998763 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-05     0.045       2      19 ..      54      71 ..      53      98 .. 0.87
   2 ?   -2.2   0.0         5   4.1e+03      80      80 ..     214     214 ..     168     239 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                                  EEEEESTTSSHHHHHHHH CS
                      MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                  +ai+G + +GKStL+n l
  gi|91772724|ref|YP_565416.1| 54 IAIMGPSGSGKSTLMNLL 71
                                  89**************88 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5
                                   E CS
                      MMR_HSR1  80 l 80 
                                   +
  gi|91772724|ref|YP_565416.1| 214 I 214
                                   0 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.8e-05     0.031      15      39 ..      46      71 ..      32      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-05
                        AAA_23 15 idFsk.gltlItGpNGaGKTTildAi 39
                                  i  +k  + +I Gp G+GK+T+++ +
  gi|91772724|ref|YP_565416.1| 46 ITVKKgEFIAIMGPSGSGKSTLMNLL 71
                                  4554425789************9865 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-05     0.046       8      43 ..      34      71 ..      29      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                         DUF87  8 sgsevpvyldlnklvtrH..lAilgsTGsGKSntvavL 43
                                  s++evp+  d+n  v++   +Ai+g +GsGKS+++ +L
  gi|91772724|ref|YP_565416.1| 34 SDTEVPILHDINITVKKGefIAIMGPSGSGKSTLMNLL 71
                                  788899998998888764339**************998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.3e-05      0.06       5      23 ..      54      79 ..      50     112 .. 0.80
   2 ?   -2.0   0.0       3.1   2.5e+03     120     142 ..     117     141 ..     104     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                        AAA_24  5 iliyGpsgiGKTtlakel.......g 23
                                  i+i+Gpsg+GK+tl++ l       +
  gi|91772724|ref|YP_565416.1| 54 IAIMGPSGSGKSTLMNLLgcldrpsE 79
                                  89*************99877555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                        AAA_24 120 elrk..nvifiahektrkdedpege 142
                                    l    nv +  h+  r+d d +++
  gi|91772724|ref|YP_565416.1| 117 RLTAlqNVLLPTHANRRTDIDVNER 141
                                   4444448999999999999998777 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00065      0.53      16      83 ..      43     109 ..      33     168 .. 0.68
   2 ?    1.4   0.0      0.25   2.1e+02     322     366 ..     178     221 ..     167     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00065
                        AAA_15  16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83 
                                   d+ i +++  +  + G+ +sGKS+++++l  +   + + ++ v+ ++ ++++++ + ++ + ++I + f
  gi|91772724|ref|YP_565416.1|  43 DINITVKKGeFIAIMGPSGSGKSTLMNLLGCLDRPS-EGQVLVMGKDINSISET-ELAKLRGLEIGFVF 109
                                   566666666799*****************8888877.33333333333333333.33344444444444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.25
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                   ++++i+l +EP  +L  +   ++++l+  l ++++  +i+ TH p
  gi|91772724|ref|YP_565416.1| 178 NEPAIILADEPTGNLDSKTSVEIMELFSGLHKNGS-TIIMITHDP 221
                                   67899999***999999999**************9.9******98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012       0.1      16      51 ..      49      84 ..      44     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                        AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                  ++  + ++ Gp G+GK+t+++ l  + + ++g+v++
  gi|91772724|ref|YP_565416.1| 49 KKGEFIAIMGPSGSGKSTLMNLLGCLDRPSEGQVLV 84
                                  4556899**************998877777666665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001     0.085      26     150 ..      54     230 ..      36     239 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                   EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHH......HHHHHHTT..... CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsikti......lealesleselse 87 
                                   + ++G s+SGKsT+++ l +l +++             +se ela++r + +  + ++++++       + l  ++ +   
  gi|91772724|ref|YP_565416.1|  54 IAIMGPSGSGKSTLMNLLGCLDRPSegqvlvmgkdinsISETELAKLRGLEIGFVFQNFNLVsrltalQNVLLPTHANRRT 134
                                   7899******************99999999999999998888999999965555555555441100003333333333333 PP

                                   ..HHHC-SS-SCCCS-HCHHHH..................................HHCCHHC-HCHHH............ CS
                       G-alpha  88 sfelqelkerldplkkveasliaklssateee........................qeiefnpraevge............ 132
                                   +++ +e+ ++l  l+ +++++ +k ++    +                                    +            
  gi|91772724|ref|YP_565416.1| 135 DIDVNERAKQLLGLMGLDDRMEHKPTEL---SggqsqrvaiaralinepaiiladeP-----------Tgnldsktsveim 201
                                   4455666666666666666654433333...33435445554444444333333331...........0333333333344 PP

                                   ...........HHHHHCCSHHHHHHHCCG CS
                       G-alpha 133 ...........dikaLwndpgiqelyerr 150
                                               i+++ +dp  +++ +r 
  gi|91772724|ref|YP_565416.1| 202 elfsglhkngsTIIMITHDPETSAYADRT 230
                                   45555555555888888887666655554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00023      0.19     117     148 ..      39      70 ..       9      88 .. 0.78
   2 ?   -1.1   0.0      0.95   7.8e+02      78     139 ..     119     190 ..     106     236 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                         T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllya 148
                                    i + ++  v++   i + G+ gsGK+tl++ 
  gi|91772724|ref|YP_565416.1|  39 PILHDINITVKKGEFIAIMGPSGSGKSTLMNL 70 
                                   55666778888999999************985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.95
                         T2SSE  78 vrlrvvllPvvagealviR..kksakeltlddlgaeealk.......ekiaevlrkav.rerglilvsGgTg 139
                                   + l+ vllP++a+ +  i   +++++ l l  l  + + k       + ++ ++++a+ +e  +il   +Tg
  gi|91772724|ref|YP_565416.1| 119 TALQNVLLPTHANRRTDIDvnERAKQLLGLMGLDDRMEHKptelsggQSQRVAIARALiNEPAIILADEPTG 190
                                   566667777777644444322333333333333333222244455553333334333303334444444555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.14      30      50 ..      48      68 ..      39      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                        AAA_25 30 lpagelallaGapgtGKttla 50
                                  + +ge+++++G++g+GK+tl 
  gi|91772724|ref|YP_565416.1| 48 VKKGEFIAIMGPSGSGKSTLM 68
                                  579****************96 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0002      0.16       1      18 [.      54      71 ..      54      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                  EEEE-STTSSHHHHHHHH CS
                Cytidylate_kin  1 iaiDGPagsGKssvaral 18
                                  iai GP+gsGKs++  +l
  gi|91772724|ref|YP_565416.1| 54 IAIMGPSGSGKSTLMNLL 71
                                  89***********99877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019      0.15       2      20 ..      54      72 ..      53     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  i+i+G++++GK+tl++ L 
  gi|91772724|ref|YP_565416.1| 54 IAIMGPSGSGKSTLMNLLG 72
                                  89*************9996 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.011         9      16      35 ..      48      67 ..      35      70 .. 0.83
   2 ?    4.3   0.0     0.027        22     142     171 ..     198     227 ..     189     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                        ATPase 16 ipegrvvlitGepGtGKtif 35
                                  + +g+ + i+G +G+GK+++
  gi|91772724|ref|YP_565416.1| 48 VKKGEFIAIMGPSGSGKSTL 67
                                  568999***********987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.027
                        ATPase 142 eilrqlvrvlkklgvTailvsekssseeaa 171
                                    ++++l++ l+k+g T i+++  ++++  a
  gi|91772724|ref|YP_565416.1| 198 VEIMELFSGLHKNGSTIIMITHDPETSAYA 227
                                   6899****************9988755444 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   0.00036      0.29       1      18 [.      54      71 ..      54      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                  RNA_helicase  1 iwlyGpsgeGKStlakeL 18
                                  i + Gpsg GKStl++ L
  gi|91772724|ref|YP_565416.1| 54 IAIMGPSGSGKSTLMNLL 71
                                  5689***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1579.82
//
Query:       gi|91772725|ref|YP_565417.1|  [L=420]
Description: proteinase inhibitor I4, serpin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-118  394.6   5.0   5.7e-118  394.4   5.0    1.0  1  Serpin    Serpin (serine protease inhibitor)
  ------ inclusion threshold ------
      0.036   13.8   0.0       0.14   11.8   0.0    2.1  1  DUF956    Domain of unknown function (DUF956)


Domain annotation for each model (and alignments):
>> Serpin  Serpin (serine protease inhibitor)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.4   5.0  6.3e-122  5.7e-118       2     371 .]      47     414 ..      46     414 .. 0.94

  Alignments for each domain:
  == domain 1  score: 394.4 bits;  conditional E-value: 6.3e-122
                                   HHHHHHHHHHHHHHHHSTTSSEEE-HHHHHHHHHHHHHTB-HHHHHHHHHHHTGCCHCHHHHHHHHHHHHHHHCSSGGTSE CS
                        Serpin   2 antkfaldlfkalskekpskNiifSPlsistaLallllGakgetaeellevLglnesdeeelhealekllsrlneseekdk 82 
                                   an++fa+d++ ++++e+  +Ni+fSP+si+ta+a+++ Ga+g+t++++++v+ ++  +++ l+e+ +++++++n+  ++++
  gi|91772725|ref|YP_565417.1|  47 ANNAFAFDMYSMIESED--ENIFFSPYSIFTAMAICYDGAEGSTKKQISNVFYYP-LSKPVLEESSKEMIDTINS-ANDEY 123
                                   79**************9..*********************************996.889999*************.9**** PP

                                   EEEEEEEEEEETTSEB-HHHHHHHHHHHS-EEEEE-TTTHHH.HHHHHHHHHHHHTTTSSSSSSSTTSS-T.TECEEEEEE CS
                        Serpin  83 elkianglfvekglklkeeflklakklykaevesvdfkddee.arkkINswvekqTngkIkdllsegsids.dtrlvlvNa 161
                                   +lk+an+l+++k+++l+e+f +++k +y+ +v++vdf++++e +++ IN+wv+++TngkIkd++s+++id+ +t ++++Na
  gi|91772725|ref|YP_565417.1| 124 DLKTANALWIRKNYPLNEQFAHNLKIYYDGNVTNVDFRNEPEkSKDIINEWVSTNTNGKIKDIISDEMIDPyNTAIIITNA 204
                                   ***********************************************************************99******** PP

                                   EEEEEEBSS--BGGGEEEEEEE..SSSSEEEEEEEEEEEEEEEEEEETTTTEEEEEEEBGG.SEEEEEEEESSTTTHHHHH CS
                        Serpin 162 iyFkGkWeepFqpeatreekFy..vnegekvkvpmMsqegkfkyaedeelnakvlelpYkg.nlsmlillPdeekgleele 239
                                   iyFkGkW ++F+ e+t++e Fy   ++ e + ++mM+++++f+y+e+e  +ak++elpYkg +l m+i+lP+ e++++++e
  gi|91772725|ref|YP_565417.1| 205 IYFKGKWINEFDIENTQKELFYnsSSNDEGTLIDMMYTRQYFNYGESE--DAKIVELPYKGnDLCMYIVLPE-ENNIDDFE 282
                                   **********************7555556669************9988..*********99999*******6.567***** PP

                                   HHHSHHHHHHHHHHGEEEEEEE.EEEEE-EEEEEEEEHHHHHHHTTHCGGGSTTTB.BTTTBSSSSEEEEEEEEEEEEEES CS
                        Serpin 240 kkltaerleewlsklkmkkeke.evslPkfkieesidlkevLqklGlkdlFseneadlsgiskkeplfvsevlhkafievn 319
                                   +++t + +++++s+++++  k+ ++ lPkfk++++ +l ++L+++G+ ++F+ ++a++s is++ +l +sev+h+a+i+vn
  gi|91772725|ref|YP_565417.1| 283 NRFTLSYYNKLKSSMESE--KDvRIWLPKFKFNTKNELSNTLRNMGIVEAFT-SNANFSSISTRGDLSISEVIHQAYIDVN 360
                                   ***************954..33489***************************.*********99***************** PP

                                   SSEEEEEEEEEE..CCTTCS-SSCEEEEECSEEEEEEEETTTTEEEEEEEESSC CS
                        Serpin 320 EeGteaaaatav..atllskksspvefkvdrPFlflireektgliLFlGkvvnP 371
                                   EeGteaaaata+  +  + ++ + +efk+d+PF+f+i++++tg+iLF+Gkv +P
  gi|91772725|ref|YP_565417.1| 361 EEGTEAAAATAIeaTDSAPMPGQIMEFKADHPFMFFIEDKRTGSILFMGKVGSP 414
                                   ***********55345566677789*************************9876 PP

>> DUF956  Domain of unknown function (DUF956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.6e-05      0.14      49      91 ..     194     237 ..     184     251 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                        DUF956  49 pWeevdsvvasvlfkgklirrfaivtkkngkf.sFsskdskkvL 91 
                                   p++    ++  ++fkgk+i++f i   +++ f + ss d+++++
  gi|91772725|ref|YP_565417.1| 194 PYNTAIIITNAIYFKGKWINEFDIENTQKELFyNSSSNDEGTLI 237
                                   66777778899*************86665555055555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3105.91
//
Query:       gi|91772726|ref|YP_565418.1|  [L=429]
Description: thiamine biosynthesis protein ThiC [Methanococcoides burtonii DSM 6242]
Scores for complete 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-186  620.2   0.6   1.8e-186  620.0   0.6    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family
  ------ inclusion threshold ------
      0.055   12.9   0.0        0.1   12.0   0.0    1.4  1  PALP          Pyridoxal-phosphate dependent enzyme


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 !  620.0   0.6    2e-190  1.8e-186       1     417 [.       2     418 ..       2     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 620.0 bits;  conditional E-value: 2e-190
                  ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEveKl 81 
                                   t +e+arkg it+e+++vae e++++e vr+ va+G + ip+n++ k+++++iGk +++kvnaniGts+d ++i+eEv+K+
  gi|91772726|ref|YP_565418.1|   2 TLMEDARKGLITPEIRSVAELEGIDVELVRSCVAKGLVTIPKNIKGKSRAFGIGKYMSVKVNANIGTSRDFVNIDEEVDKA 82 
                                   789****************************************************************************** PP

                  ThiC_Rad_SAM  82 kvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdfltiHagvt 162
                                   k+a+k+gadt+mdLstggd+d ir++i+++++vp+gtvpiYqa++ ++k+v+++t+++++++++++aedGvdf+tiH+gv+
  gi|91772726|ref|YP_565418.1|  83 KAAVKYGADTIMDLSTGGDLDLIRSRIMDAVDVPIGTVPIYQAAA-SHKTVVDMTSDDMFNAVRKHAEDGVDFVTIHSGVN 162
                                   ********************************************8.789******************************** PP

                  ThiC_Rad_SAM 163 lellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlaelivl 243
                                    ++le+lkk +R+t++vSrgGs+++awm++ne+enp+y+e+d+l+ei+keyd+t+Slgdg+RpG+i+Da+d+ +++e+i+l
  gi|91772726|ref|YP_565418.1| 163 YNALERLKKGDRITNVVSRGGSFTIAWMIHNEQENPFYSEYDYLVEIAKEYDLTISLGDGMRPGCIHDASDAPKFMEFITL 243
                                   ********************************************************************************* PP

                  ThiC_Rad_SAM 244 gelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGadllCyvt 324
                                   gelv++are++vq++veGPGHvpl+e+e +vk++k+lc++aP+y+lGplvtDiapgYDhit+aiG++la+++Gad+lC+ t
  gi|91772726|ref|YP_565418.1| 244 GELVSKARESDVQTFVEGPGHVPLNEVELSVKAMKELCHGAPLYLLGPLVTDIAPGYDHITGAIGGTLAGMYGADFLCMTT 324
                                   ********************************************************************************* PP

                  ThiC_Rad_SAM 325 paEHlglPdeedvkeGviaakiaahaadlakg..lkkarerdkalskaRkeldwekqfelaldpekareireeklpeeeea 403
                                   paEHl+lP+++d++eG i++ iaahaadl+++  ++kare d+++++aR+eldwe+qfe+a+d+ekar+ire++++  ++a
  gi|91772726|ref|YP_565418.1| 325 PAEHLALPTVDDIREGAIVTNIAAHAADLTREgqKEKARELDDRMAHARAELDWETQFEVAIDSEKARKIRESRNT-GTDA 404
                                   ******************************98556789999*******************************9985.99** PP

                  ThiC_Rad_SAM 404 CsmCgekCavkive 417
                                   CsmCge Ca+kiv+
  gi|91772726|ref|YP_565418.1| 405 CSMCGELCAMKIVK 418
                                   ***********986 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.1e-05       0.1     211     288 ..      95     175 ..      49     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.1e-05
                                   .B..........SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB.-B-HHHHHHHHHHHHHHHHC CS
                          PALP 211 pvs.........dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregi.vvepssaaalaalklreage 281
                                   + s         + i+d+++v+  ++   ++++ + +++v  ++++++ a+r+ a ++g+ +v  +s++++ al     ++
  gi|91772726|ref|YP_565418.1|  95 DLStggdldlirSRIMDAVDVPIGTVPIYQAAASH-KTVVDMTSDDMFNAVRKHA-EDGVdFVTIHSGVNYNAL-----ER 168
                                   444566666666899*******6566666665555.559****************.666626666*********.....55 PP

                                   CTTCEEE CS
                          PALP 282 lkegdrv 288
                                   lk+gdr+
  gi|91772726|ref|YP_565418.1| 169 LKKGDRI 175
                                   5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2658.92
//
Query:       gi|91772727|ref|YP_565419.1|  [L=148]
Description: hypothetical protein Mbur_0704 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-33  115.5   0.0      3e-33  115.3   0.0    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   1.7e-37     3e-33       2     141 .]       6     148 .]       5     148 .] 0.97

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 1.7e-37
                                   -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHHHCTT CS
                           Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...akaaaeagg 79 
                                   yk+Il+a+Dgs+++k+A+  +++la   ga+++++ v+++++ ++ + + + ++ e   +  +e+  +a     + a++ g
  gi|91772727|ref|YP_565419.1|   6 YKKILIATDGSDNAKNAIFSGINLAGLLGAKIYAVCVLPTHPASSMPIGSRMMRWEIPFDVMREEGTKAvneVVEHAKING 86 
                                   9**********************************************99999999999999988887778999******** PP

                                   CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                   v+ e v++eg+p+eeil++a+++d+dliV+G+ g++gl rlllGSv+e+vlrh+p+ VlvVr
  gi|91772727|ref|YP_565419.1|  87 VDAEPVLLEGHPSEEILRYAQDNDIDLIVLGTLGKTGLTRLLLGSVAENVLRHSPVEVLVVR 148
                                   *************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 965.63
//
Query:       gi|91772728|ref|YP_565420.1|  [L=780]
Description: DNA topoisomerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-106  354.5   0.0   9.9e-106  354.2   0.0    1.1  1  Topoisom_bac     DNA topoisomerase
    1.8e-11   43.6  19.1    1.2e-09   37.8   2.2    3.5  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    2.3e-09   37.4   0.1    2.8e-08   33.9   0.0    2.7  3  Toprim           Toprim domain
  ------ inclusion threshold ------
      0.094   12.9   1.7       0.33   11.1   0.1    2.5  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1


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 !  354.2   0.0  2.2e-109  9.9e-106       2     408 ..     154     562 ..     153     567 .. 0.91

  Alignments for each domain:
  == domain 1  score: 354.2 bits;  conditional E-value: 2.2e-109
                  Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg....kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekk 78 
                                   ++en++ +aeaR++lD+ +G++++r++t+++++    k+vls+G++qtpt ++++eRe +i++F ++++w++e+ ++ +++
  gi|91772728|ref|YP_565420.1| 154 PDENMAMSAEARQILDLKMGASFTRFVTLSVRErartKGVLSIGPCQTPTCGFVYERELAIRKFDSRDFWKIEGVFTGKGA 234
                                   799**************************444444559************************************9944444 PP

                  Topoisom_bac  79 ekekkkkkkkerikdkeeaeaileklkk.keakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYeka 158
                                          ++ ++i dke+a+ai++klk  k+a++++ + ke +++pp p++t++++k+as++lg+s++++l+ia++LY + 
  gi|91772728|ref|YP_565420.1| 235 DI--IGVHRGGHIYDKEKAAAIFKKLKGcKTAVISKKTVKEMNTNPPFPLNTNEFLKRASKYLGVSPDQALEIAEQLYLS- 312
                                   44..489*******************88769************************************************7. PP

                  Topoisom_bac 159 glitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkv..eaHeAIrPteelp..klkels.. 233
                                   g+ +YpRT+++ + ++ ++++il+ ++k    +y++fa  ll++++   v++n k+   +H++I+P++  +  + +  +  
  gi|91772728|ref|YP_565420.1| 313 GFTSYPRTETNMYADDMDFASILKGFTKG---DYQDFALLLLSQKA--IVPRNGKKdgHDHPPIHPIKAGSrmEVE--Rai 386
                                   ****************88*********95...69999999998554..33333333369********999853223..245 PP

                  Topoisom_bac 234 ..ddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvke 312
                                        +++Y+lIvr+f+a l+++a++e+t+ +++ e+e f+++g++ +++G+++vy+ ek +++   lp+l  ge ++vk+
  gi|91772728|ref|YP_565420.1| 387 kmPRAWDVYDLIVRHFIANLLPPAVFEKTRFEITMEDELFDSTGSIQKNAGWLAVYPFEKPQDK--ILPALDLGEVLDVKK 465
                                   778999*******************************************************998..6************** PP

                  Topoisom_bac 313 veleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvell.ekfkdlvspelTa 392
                                   ++  + +T+ppkr+tea+L+++m+k+giGt+aT  ++ie+ ++rgY e+k+k +   ++G++l+++l + ++ lv+p++++
  gi|91772728|ref|YP_565420.1| 466 ITNIKSQTTPPKRLTEAELLTLMDKHGIGTKATAPSHIETNKKRGYFEVKGKTIAILDTGFTLMDALnSSVPILVKPDIRS 546
                                   *************************************************98****************5555********** PP

                  Topoisom_bac 393 eleekLdeIaegkada 408
                                   ++e+ ++++++g+++ 
  gi|91772728|ref|YP_565420.1| 547 SIESLIQDVEDGNKKF 562
                                   ************9876 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 !   37.8   2.2   2.7e-13   1.2e-09       2      38 ..     609     645 ..     608     646 .. 0.95
   2 !   16.6   1.0   1.1e-06    0.0049       1      39 []     695     731 ..     695     731 .. 0.93
   3 ?   -1.2   1.7       0.4   1.8e+03       3      15 ..     740     753 ..     738     768 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.7e-13
                                   EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-G CS
                zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkk 38 
                                   +kC +C   L + ++ kG+FvGC+ YP Ck+t +l+k
  gi|91772728|ref|YP_565420.1| 609 GKCNECERVLRIVSTDKGRFVGCTGYPQCKNTFPLPK 645
                                   79******************************99987 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.1e-06
                                   -EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-GG CS
                zf-C4_Topoisom   1 vekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkkn 39 
                                   v++CP+C g+  l ++k  +F+GC+   +C +t + +kn
  gi|91772728|ref|YP_565420.1| 695 VGECPACDGQTFLITTKDSRFLGCTK--RCGHTQSVPKN 731
                                   589***********************..9**99999886 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.4
                                   E-SSS-.-EEEEEE CS
                zf-C4_Topoisom   3 kCPkCg.gdLvlkr 15 
                                    C+ Cg   L +k+
  gi|91772728|ref|YP_565420.1| 740 VCEGCGwRLLRVKE 753
                                   7*****77777665 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   6.2e-12   2.8e-08       2     102 ..       4     138 ..       3     139 .. 0.79
   2 ?   -0.6   0.0      0.34   1.5e+03      27      45 ..     240     265 ..     218     302 .. 0.64
   3 ?   -2.2   0.0       1.1     5e+03      14      37 ..     577     600 ..     564     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6.2e-12
                                   EEEESSHHHHHHHHHTHT....................STEEEEEEESSSSEEEHS......TTEEEEE............ CS
                        Toprim   2 lvivEgpsdaktiakalg....................sgfqavtaslGhildlet......efkpvye............ 44 
                                   +v  E++++a++i+ +l+                    ++  +++ + Ghi+  +                          
  gi|91772728|ref|YP_565420.1|   4 VVFTEKNKAAAQISTILSggsakrsivdgvsvyefqrdGSLWKIMGLAGHIMGYDYpeefhnW-----Rdvdpaalldtdp 79 
                                   56789***********99999999999999999999888888999999999999987555540.....2455555575554 PP

                                   ECTTTHHHHHH.....HHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                        Toprim  45 eiedkkkvlka.....lkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                   +++ +k    a     + +++k ad ++la+D DreGe+i++e+ + +++  +++++r++fs+
  gi|91772728|ref|YP_565420.1|  80 VKQINK----AsfgsaILKISKGADLLVLACDFDREGENIGFEAKSIAEKVSDATVKRARFSS 138
                                   222222....23444699999************************999988888*******97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.34
                                   EESSSSEEEHS..TTEEEEE.....E CS
                        Toprim  27 aslGhildlet..efkpvye.....e 45 
                                   +  Ghi+d e+   ++++++     +
  gi|91772728|ref|YP_565420.1| 240 HRGGHIYDKEKaaAIFKKLKgcktaV 265
                                   55788888888442222222343331 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                                   HHHTHTSTEEEEEEESSSSEEEHS CS
                        Toprim  14 iakalgsgfqavtaslGhildlet 37 
                                    +++l++ +++vt   G+i+d + 
  gi|91772728|ref|YP_565420.1| 577 YSQLLSNRDLMVTRIAGTITDEAV 600
                                   467788999999999999999876 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.31   1.4e+03      18      29 ..     698     711 ..     695     720 .. 0.72
   2 ?   11.1   0.1   7.4e-05      0.33      12      37 ..     735     763 ..     733     766 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.31
                 Auto_anti-p27  18 CpvC..gvPLmrdr 29 
                                   Cp C  ++ L  ++
  gi|91772728|ref|YP_565420.1| 698 CPACdgQTFLITTK 711
                                   99997777777665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.4e-05
                 Auto_anti-p27  12 tMLaetCpvCgvPLmrdr...kggkvyCv 37 
                                   t ++++C+ Cg  L+r +   k+ k yC+
  gi|91772728|ref|YP_565420.1| 735 TITDKVCEGCGWRLLRVKeqgKDAKEYCA 763
                                   789***************98878888997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (780 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 4616.80
//
Query:       gi|91772729|ref|YP_565421.1|  [L=212]
Description: hypothetical protein Mbur_0706 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   67.0   0.2    3.2e-18   66.2   0.2    1.5  1  NERD         Nuclease-related domain
  ------ inclusion threshold ------
       0.18   11.8   1.5       0.38   10.7   1.5    1.6  1  Blo-t-5      Mite allergen Blo t 5
       0.23   11.4   0.2        0.3   11.0   0.2    1.2  1  CAF1-p150_N  CAF1 complex subunit p150, region binding to PCN


Domain annotation for each model (and alignments):
>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.2   5.3e-22   3.2e-18       1      93 [.      41     145 ..      41     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 5.3e-22
                          NERD   1 kgaegEravakeLkelkedeylvlhdvrlrpg..........tg.eiDhlvispkgifviEvKnwsGwifgdkegrwtqki 70 
                                   kga gE av k L el +d+y+ ++dv+l+ +          ++ +iDhlv++p+g+fviE+Knws     +    +tq+ 
  gi|91772729|ref|YP_565421.1|  41 KGALGEIAVIKKLTEL-SDDYFQFNDVYLELNeyikfngsslKSaQIDHLVVGPTGVFVIETKNWSK----N----YTQTV 112
                                   7999**********88.555777******9889999876655227*********************5....2....44444 PP

                          NERD  71 .kkgfknpleqakrhakalkksl.........l 93 
                                    ++g + p++q++r   +++++l         +
  gi|91772729|ref|YP_565421.1| 113 fNEGSYTPYDQIQRSSYIVYRYLndnkygnaiQ 145
                                   455557*************99996554444441 PP

>> Blo-t-5  Mite allergen Blo t 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.5   6.4e-05      0.38      30      91 ..      16      77 ..       2      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.4e-05
                                  HHHHHHHHHHHHHHHHHHH--SSHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS---HHHHHH CS
                       Blo-t-5 30 klekallklseqvkelektkskelkeqilreltialnfiegakgflerelkRtDLnllekfn 91
                                  + e  l +l  q++ le+ k+ ++ +  l e+ + +++ e +  +++ +    +Ln   kfn
  gi|91772729|ref|YP_565421.1| 16 EAESRLSHLVSQLNKLEDLKNSNEYKGALGEIAVIKKLTELSDDYFQFNDVYLELNEYIKFN 77
                                  68999******************************************998888888888888 PP

>> CAF1-p150_N  CAF1 complex subunit p150, region binding to PCNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2     5e-05       0.3      73     131 ..       3      61 ..       1      83 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                   CAF1-p150_N  73 easldtlennchvgsdidfrpklvnGkgPldnfl.rsrvktsigqsvviidltedsseqp 131
                                   +  ld lenn+ v+++  ++  lv     l+++  +++ k ++g+ +vi  lte s++  
  gi|91772729|ref|YP_565421.1|   3 KHKLDRLENNIDVEAESRLS-HLVSQLNKLEDLKnSNEYKGALGEIAVIKKLTELSDDYF 61 
                                   6689***********99886.699999999887625689*****************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1136.28
//
Query:       gi|91772730|ref|YP_565422.1|  [L=177]
Description: nitroreductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  117.9   0.5    2.5e-19   70.0   0.0    2.1  2  Nitroreductase  Nitroreductase family
    1.6e-20   73.6   0.7    5.7e-08   32.6   0.0    3.0  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.035   13.4   0.1      0.045   13.1   0.1    1.1  1  Urate_ox_N      Urate oxidase N-terminal


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   4.2e-23   2.5e-19       1      58 [.       8      65 ..       8      79 .. 0.92
   2 !   47.2   0.2   4.1e-16   2.4e-12      88     170 .]      71     147 ..      62     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 4.2e-23
                                  HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHH CS
                Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaal 58
                                  i++RrS+R+++depv++ ++ +il++ar+aPs+ n qpw+f+v+qd++++++la+  +
  gi|91772730|ref|YP_565422.1|  8 ILSRRSVREYTDEPVSEKDINTILDCARWAPSGLNNQPWKFIVIQDENTIKDLAQCTH 65
                                  789*************************************************998766 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 4.1e-16
                                   HHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEE CS
                Nitroreductase  88 agapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvliav 168
                                    g+ +li +      + ++++  + + +++ +ga +qn+lLa+ +lGlgs+++g + ++ae+v+ +l++p+ +e++++ia+
  gi|91772730|ref|YP_565422.1|  71 LGSKLLIAV------YLDNSEMYHHDKDVMAIGASIQNMLLACVELGLGSVWLGEILKQAEKVNSILEVPEIYELMAVIAI 145
                                   556667777......78888888889999*****************************************99********* PP

                                   E- CS
                Nitroreductase 169 Gy 170
                                   G+
  gi|91772730|ref|YP_565422.1| 146 GK 147
                                   96 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.9e-06     0.029       2      27 ..       4      29 ..       3      30 .. 0.89
   2 !   27.1   0.0   4.6e-10   2.7e-06     158     205 ..      25      72 ..      23      76 .. 0.76
   3 !   32.6   0.0   9.6e-12   5.7e-08      80     153 ..      92     167 ..      77     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-06
                                  HHHHHHH--B---B--S---HHHHHH CS
                TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeellee 27
                                  ++e+i  R+svR+Y+de+++e+ +++
  gi|91772730|ref|YP_565422.1|  4 TIETILSRRSVREYTDEPVSEKDINT 29
                                  6899*****************98775 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 4.6e-10
                                   HHHHHHHHHHHTS--GGG----EEE..E-SSEE.....EEE-S-HHHHH CS
                TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfel.kdddeikikasvlgklskiDlG 205
                                   +++++il++ar APs lN+qpw+f + +d+++ik +a++  ++s i lG
  gi|91772730|ref|YP_565422.1|  25 KDINTILDCARWAPSGLNNQPWKFIViQDENTIKDLAQC-THYSTIVLG 72 
                                   57899*******************851444455555555.778888776 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 9.6e-12
                                   HHHHHHHHHHHHHHHHHHTT-EEEEES--SST..............T-S-EEEEE-BS----.-----HHHHBSS-G CS
                TM1586_NiRdase  80 leekaGYygeqlvLkltalGlgtcWvggtykk...kkakvelkkgeklvivIalGyaktklveakrkpleelcevke 153
                                     + +G   ++++L +++lGlg+ W+g   k+   +++ +e+++  +l++vIa+G++ +k  +  rk+++el+ +k+
  gi|91772730|ref|YP_565422.1|  92 DVMAIGASIQNMLLACVELGLGSVWLGEILKQaekVNSILEVPEIYELMAVIAIGKPVKKERTSSRKSVSELT-FKN 167
                                   4567888999*****************876654336677899999**************************98.444 PP

>> Urate_ox_N  Urate oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.6e-06     0.045      84     140 ..      65     122 ..      58     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-06
                    Urate_ox_N  84 aYttwlsGfaLlvvvyylnaelylidksvlkl.splaavaialaflvlgwlvYdllcr 140
                                    Y+t + G  Ll+ vy+ n+e+y  dk+v+++ ++++ +++a   l lg +    + +
  gi|91772730|ref|YP_565422.1|  65 HYSTIVLGSKLLIAVYLDNSEMYHHDKDVMAIgASIQNMLLACVELGLGSVWLGEILK 122
                                   69****************************9944567777787777777665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1303.93
//
Query:       gi|91772731|ref|YP_565423.1|  [L=335]
Description: ketol-acid reductoisomerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-76  255.3   0.7    2.5e-76  254.9   0.7    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    5.4e-61  205.1   0.4    7.8e-61  204.6   0.4    1.2  1  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    6.2e-06   26.7   0.1    1.3e-05   25.6   0.1    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    7.1e-05   23.0   0.0    0.00013   22.2   0.0    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    8.1e-05   22.0   0.0    0.00014   21.3   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00022   21.3   0.1    0.00042   20.4   0.1    1.3  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
  ------ inclusion threshold ------
      0.026   14.2   0.0      0.049   13.3   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.043   14.1   0.3        0.3   11.4   0.3    2.3  1  Mur_ligase      Mur ligase family, catalytic domain
      0.063   12.0   0.0       0.13   11.0   0.0    1.4  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
      0.067   12.8   0.0       0.12   12.0   0.0    1.4  1  YfaZ            YfaZ precursor


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 !  254.9   0.7   1.4e-79   2.5e-76       2     165 .]      15     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 254.9 bits;  conditional E-value: 1.4e-79
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeie 82 
                                   lkgk iav+GyGsqGhaqa+nl+dsgldvv+glregs+ +k+A+++g++v+tva+a+k+advv il+PDe+q++vy +eie
  gi|91772731|ref|YP_565423.1|  15 LKGKIIAVMGYGSQGHAQAQNLHDSGLDVVIGLREGSRRWKQAEDDGLKVMTVADAAKAADVVQILLPDEIQSKVYYSEIE 95 
                                   89******************************************************************************* PP

                                   GG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHHHHHTTHHH CS
                          IlvN  83 pnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalayakgiGatr 163
                                   p l++g+ l+f+hGfnih+++i+p kd+dv++vAPk+pGhlvr++y+eg Gvp liav+qdasg+a e+ala+akg+G+tr
  gi|91772731|ref|YP_565423.1|  96 PGLEAGNSLVFSHGFNIHYNQIVPSKDLDVYMVAPKSPGHLVRRTYKEGAGVPGLIAVYQDASGNALEMALAHAKGVGCTR 176
                                   ********************************************************************************* PP

                                   H- CS
                          IlvN 164 aG 165
                                   aG
  gi|91772731|ref|YP_565423.1| 177 AG 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 !  204.6   0.4   4.4e-64   7.8e-61       1     144 []     184     327 ..     184     327 .. 1.00

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 4.4e-64
                                   HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHH CS
                          IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltagp 81 
                                   F+eEtetDlfgEq+ LcGgv++l+++ Fe+lveaGy+pe+Ayfe+lhelklivdli+egG++km++s+S+taeyg+lt+gp
  gi|91772731|ref|YP_565423.1| 184 FREETETDLFGEQVDLCGGVASLIKTSFEVLVEAGYQPEMAYFETLHELKLIVDLIHEGGLEKMWYSVSNTAEYGGLTVGP 264
                                   99******************************************************************************* PP

                                   HHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                          IlvC  82 rviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                   ++i+ee++e+m+  le+iq+Gefa+e+++e +++++ l+++++ e+eh++e vgkklra+mpw
  gi|91772731|ref|YP_565423.1| 265 QIINEESREAMYVALERIQNGEFAREFVLEGQTNHAVLTSMERLEKEHPVEVVGKKLRAMMPW 327
                                   *************************************************************98 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   7.5e-09   1.3e-05       2      78 ..      20      90 ..      19     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.5e-09
                                  EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                 F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevl 78
                                  i++ G+G++g+a a++l  +g    ++v++  r+ +++ + ae+ g kv++   ++aa+ advv + ++ e  ++v 
  gi|91772731|ref|YP_565423.1| 20 IAVMGYGSQGHAQAQNLHDSG---LDVVIG-LREGSRRWKQAEDDGLKVMT--VADAAKAADVVQILLPDEIQSKVY 90
                                  99*******************...****88.88888888999999978877..***********9988877766665 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 !   22.2   0.0   7.1e-08   0.00013       2      87 ..      20     105 ..      19     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.1e-08
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--T CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkk 82 
                                   i+++G G  G+  a+nl ++g +v++  r+ ++  + +++    + +++++++++dvv ++++++ + +  ++++ + l++
  gi|91772731|ref|YP_565423.1|  20 IAVMGYGSQGHAQAQNLHDSGLDVVIGLREGSRRWKQAEDDGLKVMTVADAAKAADVVQILLPDEIQSKVYYSEIEPGLEA 100
                                   89************************99998877777777766788999******************************** PP

                                   T-EEE CS
                 NAD_binding_2  83 gdili 87 
                                   g+ l+
  gi|91772731|ref|YP_565423.1| 101 GNSLV 105
                                   99887 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 !   21.3   0.0   7.9e-08   0.00014      33     102 ..      14      84 ..       4      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.9e-08
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlplt 102
                                    l+gk ++++G+G+ G+a a+ l+  g++v++  r  +++  ++e+ g++++++ ++ + +D+v + lp +
  gi|91772731|ref|YP_565423.1|  14 ALKGKIIAVMGYGSQGHAQAQNLHDSGLDVVIGLREGSRRWkQAEDDGLKVMTVADAAKAADVVQILLPDE 84 
                                   699*************************8877766666444489999*******************99965 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 !   20.4   0.1   2.3e-07   0.00042      21      82 ..      15      77 ..       8      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                                  -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HH.HHHHHHCTT-EE--HHHCTTT-SEE CS
                 AdoHcyase_NAD 21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPi.calqaameGfevvtleevvkkadiv 82
                                  l Gk++ v+GyG  G   a+ l+  G  v++   +      qa  +G++v+t+ +++k ad+v
  gi|91772731|ref|YP_565423.1| 15 LKGKIIAVMGYGSQGHAQAQNLHDSGLDVVIGLREGSrRWKQAEDDGLKVMTVADAAKAADVV 77
                                  78****************************987776515679*******************97 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.7e-05     0.049       1      44 [.      20      65 ..      20      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH..HHHHHHHHCEEEE CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr..rlealkknGlrlt 44
                                  ia++G G++G   a +L+  g dv++ lr+   r ++ +++Gl++ 
  gi|91772731|ref|YP_565423.1| 20 IAVMGYGSQGHAQAQNLHDSGLDVVIGLREGsrRWKQAEDDGLKVM 65
                                  89*********************99999988445555666777665 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00017       0.3      18      79 ..      19      70 ..      13     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                  HHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHHH CS
                    Mur_ligase 18 flalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpeleaakepgipvesraea 79
                                  ++a +Gy  +G+  +++l ++G  +v+g +++              ++a + g++v+ +a+a
  gi|91772731|ref|YP_565423.1| 19 IIAVMGYGSQGHAQAQNLHDSGLDVVIGLREG----------SRRWKQAEDDGLKVMTVADA 70
                                  899*************************9999..........77777777777777777665 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     7e-05      0.13     269     343 ..      14      82 ..       5     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7e-05
                                   HHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHHHHHHHHT- CS
                Oxidored_nitro 269 ylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepeviddadleeleelikelkp 343
                                    l+gk +a++g++++ +a a+ l++ G +vv +g ++++r+++ +++++   g  +v+  ad  + ++ ++ l p
  gi|91772731|ref|YP_565423.1|  14 ALKGKIIAVMGYGSQGHAQAQNLHDSGLDVV-IGLREGSRRWK-QAEDD---G-LKVMTVADAAKAADVVQILLP 82 
                                   589**************************87.68888888888.45552...3.345555555555555555555 PP

>> YfaZ  YfaZ precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.8e-05      0.12      53     123 ..     153     223 ..     136     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                          YfaZ  53 irsDddGdvagvglglnlpvGpltatvGakgvylsadegdeGsavavGgglalaigksfslfgeayyaPee 123
                                   +++D +G+ ++++l     vG   a v        ++    G  v + gg+a  i  sf +  ea y Pe 
  gi|91772731|ref|YP_565423.1| 153 VYQDASGNALEMALAHAKGVGCTRAGVIETTFREETETDLFGEQVDLCGGVASLIKTSFEVLVEAGYQPEM 223
                                   699**************************99999999999*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2392.89
//
Query:       gi|91772732|ref|YP_565424.1|  [L=161]
Description: acetolactate synthase 3 regulatory subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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   3.5    9.6e-30  102.6   1.2    2.0  2  ALS_ss_C        Small subunit of acetolactate synthase
    9.3e-19   67.0   0.7    3.6e-18   65.2   0.1    2.1  2  ACT_5           ACT domain
    8.1e-18   63.9   0.7    1.5e-17   63.1   0.1    1.7  2  ACT             ACT domain
    7.7e-07   29.6   0.3    7.7e-07   29.6   0.3    2.0  2  ACT_4           ACT domain
  ------ inclusion threshold ------
      0.014   15.8   0.1      0.026   14.9   0.1    1.5  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
      0.025   14.4   3.5      0.081   12.7   0.6    1.9  2  SLS             Mitochondrial inner-membrane-bound regulator
      0.032   14.1   0.4        1.1    9.1   0.0    2.7  3  NIL             NIL domain


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 ?    0.9   0.0      0.21   5.4e+02      37      58 ..      46      67 ..      36      81 .. 0.62
   2 !  102.6   1.2   3.7e-33   9.6e-30       1      74 []      84     157 ..      84     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                                  EEEEEEE-HHHHHHHHHHS-GG CS
                      ALS_ss_C 37 liieltgteekidaliellkpf 58
                                  ++i ++g+ + ++++++ l+++
  gi|91772732|ref|YP_565424.1| 46 MTIIVSGDDHVLEQVMKQLNKL 67
                                  5566666666666666666532 PP

  == domain 2  score: 102.6 bits;  conditional E-value: 3.7e-33
                                   EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                      ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                   RElaLiKV++++++r+ei++i++ifra+++dv+++sl+ie+tg+ eki+a+  llkpfgi+e++RtG+vAl+RG
  gi|91772732|ref|YP_565424.1|  84 RELALIKVNTDASNRAEIIQIVNIFRARTIDVASKSLTIEVTGDVEKIKAIQTLLKPFGIKELARTGIVALNRG 157
                                   9************************************************************************8 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.1   1.4e-21   3.6e-18       4      62 .]      14      73 ..      11      73 .. 0.97
   2 ?   -0.2   0.1      0.36   9.3e+02      11      22 ..     106     117 ..     101     136 .. 0.56

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.4e-21
                         ACT_5  4 gvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                  gvL Rv ++++rrgF+++sl + tted + +r+++ V++ +  +e++++Ql+KLidV++V
  gi|91772732|ref|YP_565424.1| 14 GVLARVAGLFSRRGFNIDSLAVGTTEDPTLSRMTIIVSGdDHVLEQVMKQLNKLIDVIRV 73
                                  9**************************************99****************998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
                         ACT_5  11 rvvrrrgFevks 22 
                                   +++r r  +v+s
  gi|91772732|ref|YP_565424.1| 106 NIFRARTIDVAS 117
                                   556666655543 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.1   5.8e-21   1.5e-17       1      66 [.       3      68 ..       3      69 .. 0.97
   2 ?   -1.8   0.1       1.1   2.7e+03      26      30 ..     113     117 ..     101     139 .. 0.53

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 5.8e-21
                                  EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                  ++l v+v+++ G+Larv+g++++rg+Nids+ ++++ed   +++++++ +d+ +le+v+++l+kl+
  gi|91772732|ref|YP_565424.1|  3 HTLAVLVENKYGVLARVAGLFSRRGFNIDSLAVGTTEDPTLSRMTIIVSGDDHVLEQVMKQLNKLI 68
                                  67889***********************************************************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                   SEEEE CS
                           ACT  26 iNids 30 
                                   i ++s
  gi|91772732|ref|YP_565424.1| 113 IDVAS 117
                                   33332 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.3     3e-10   7.7e-07       8      78 ..       4      73 ..       2      74 .. 0.93
   2 ?   -1.0   0.2       1.1   2.7e+03      48      49 ..     116     117 ..      89     139 .. 0.53

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3e-10
                         ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdveh.LsrviakLraipgVisV 78
                                  +l v +e++ g+La+++ ++s  + ni s+ + t++ d  +  ++t+ V+  +h L++v+++L+++ +Vi+V
  gi|91772732|ref|YP_565424.1|  4 TLAVLVENKYGVLARVAGLFSRRGFNIDSLAVGTTE-D-PTLSRMTIIVSGDDHvLEQVMKQLNKLIDVIRV 73
                                  6899******************************64.5.89999*****9988879**************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                         ACT_4  48 ae 49 
                                   a+
  gi|91772732|ref|YP_565424.1| 116 AS 117
                                   22 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 ?   14.9   0.1     1e-05     0.026      30      71 ..      28      69 ..      14     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                  EEEEEEEXXSSTTSX.EEEEEEEEESSHHHHHHHHHHHHHHHH CS
                Saccharop_dh_N 30 fevlefevGkkkkdt.SyaelevsaedeevLeeileeltelga 71
                                  f++ ++ vG++++ t S  ++ vs++d +vLe+++++l++l +
  gi|91772732|ref|YP_565424.1| 28 FNIDSLAVGTTEDPTlSRMTIIVSGDD-HVLEQVMKQLNKLID 69
                                  99*******988754377777777766.89********99833 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   3.2e-05     0.081      56     117 ..      36      96 ..       6     110 .. 0.77
   2 ?    3.1   0.6     0.029        74      54      84 ..     107     138 ..      93     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                           SLS  56 gakielnrsenklritAtkstaeyieasineilknittetvdlsellkl....skvdklkdl.lsee 117
                                   g + + ++s+ +++++++ ++ e++++++n+++  i++ +++++e+++            ++  ++ 
  gi|91772732|ref|YP_565424.1|  36 GTTEDPTLSRMTIIVSGDDHVLEQVMKQLNKLIDVIRVIDLSSEEFVERelalI------KVnTDAS 96 
                                   56677789999*******************************999985433221......3333444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.029
                           SLS  54 i.hgakielnrsenklritAtkstaeyieasi 84 
                                   i + ++i++  ++ ++ +t++ +++++i+  +
  gi|91772732|ref|YP_565424.1| 107 IfRARTIDVASKSLTIEVTGDVEKIKAIQTLL 138
                                   357899*********************98765 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00044       1.1      34      66 ..      34      66 ..      15      73 .. 0.87
   2 ?   -0.8   0.0      0.54   1.4e+03      53      71 ..      97     115 ..      87     117 .. 0.79
   3 ?    2.1   0.0     0.067   1.7e+02      45      64 ..     119     138 ..     105     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                                  EEEEETTEEEEEEEEEEES-HHHHHHHHHHHHH CS
                           NIL 34 sveriqgtpfGqlvielsgsqesiaaalqylrk 66
                                   v++  + ++ +++i +sg+++ ++++++ l+k
  gi|91772732|ref|YP_565424.1| 34 AVGTTEDPTLSRMTIIVSGDDHVLEQVMKQLNK 66
                                  5788889999*******************9998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.54
                                   -HHHHHHHHHHHHHTT-EE CS
                           NIL  53 sqesiaaalqylrkrnvdv 71 
                                   ++++i ++++ +r r +dv
  gi|91772732|ref|YP_565424.1|  97 NRAEIIQIVNIFRARTIDV 115
                                   4568899999999999998 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.067
                                   EEEEEEES-HHHHHHHHHHH CS
                           NIL  45 qlvielsgsqesiaaalqyl 64 
                                   +l+ie++g+ e+i+a+   l
  gi|91772732|ref|YP_565424.1| 119 SLTIEVTGDVEKIKAIQTLL 138
                                   68999**9999999877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1304.32
//
Query:       gi|91772733|ref|YP_565425.1|  [L=563]
Description: acetolactate synthase 3 catalytic subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-58  196.3   0.3    4.6e-56  189.1   0.1    2.4  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    2.7e-55  186.4   0.3    5.9e-54  182.0   0.4    2.4  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    5.6e-51  171.9   0.1    9.9e-51  171.1   0.1    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
     0.0044   16.8   0.3      0.011   15.5   0.3    1.7  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 !  189.1   0.1     1e-59   4.6e-56       1     169 [.       8     174 ..       8     175 .. 0.99
   2 !    5.0   0.0    0.0039        17     104     146 ..     485     527 ..     438     535 .. 0.82

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 1e-59
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   mt+a+a+v++L +++ve++fg+pG+ +l+++d+l +++ ++++l+rhEq+a++aA+gyaratgk+gv+l+tsgpGatn++t
  gi|91772733|ref|YP_565425.1|   8 MTGARAFVECLYRENVEVIFGYPGGVLLHIYDELYDAH-LHHLLVRHEQAAVHAAEGYARATGKVGVCLATSGPGATNLVT 87 
                                   89***********************************6.****************************************** PP

                                   HHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                   ++a+A+ d++P+++++g++p+s++g +++q e +++++  p+tk+++ v+++++lp+++++A+ +a +grpgPv+++lpkd
  gi|91772733|ref|YP_565425.1|  88 GIANAYMDSVPMVAFTGQVPSSMIGNDAFQ-EANITGITMPITKHNYLVQDVKDLPRIIKEAFHIASTGRPGPVLIDLPKD 167
                                   ******************************.************************************************** PP

                                   HCC-EEE CS
                  TPP_enzyme_N 163 vlleevd 169
                                   + ++e+d
  gi|91772733|ref|YP_565425.1| 168 ITTDEID 174
                                   ***9987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0039
                                   CHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHH CS
                  TPP_enzyme_N 104 lrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirt 146
                                   + ++ ++++ +d ++l++ +     rvt+p+e++ a+++A+++
  gi|91772733|ref|YP_565425.1| 485 RYSHTTIENSVDFVKLAEAYGAMGIRVTKPSEVKAAIEKAVEA 527
                                   33367778888*****************************986 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 ?    1.8   0.0     0.042   1.9e+02     129     152 ..     135     163 ..      92     164 .. 0.85
   2 !  182.0   0.4   1.3e-57   5.9e-54       2     153 .]     388     535 ..     387     535 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.042
                                   SH.HHHHHHHHHHHH.....CSSSEEEEE CS
                  TPP_enzyme_C 129 kadveeleealkeal.....ekkgpalie 152
                                   ++dv++l +++kea+      + gp+li+
  gi|91772733|ref|YP_565425.1| 135 VQDVKDLPRIIKEAFhiastGRPGPVLID 163
                                   5677**********999999999999998 PP

  == domain 2  score: 182.0 bits;  conditional E-value: 1.3e-57
                                   SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE- CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnN 82 
                                   +G++++waa+++++++pr++++sgglgtmGyg+paAiGak+ +pd+ v+ ++GDG+f+m+ qe+at+v++n+pi++ ++nN
  gi|91772733|ref|YP_565425.1| 388 VGQHQMWAAQYFNYTEPRTFISSGGLGTMGYGFPAAIGAKIGRPDKVVFDVSGDGSFQMNSQEMATIVQNNIPIIIAIFNN 468
                                   9******************************************************************************** PP

                                   SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  83 egygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                   +++gm++++q  f++ r+s+++  ++++vdf+klaea+Ga g+rv+k+  +e+++a+++a+e + p+li++
  gi|91772733|ref|YP_565425.1| 469 GYLGMVRQWQALFFEHRYSHTT--IENSVDFVKLAEAYGAMGIRVTKP--SEVKAAIEKAVEANAPVLIDF 535
                                   ********************99..7*******************9999..*******************95 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 !  171.1   0.1   2.2e-54   9.9e-51       1     137 []     197     332 ..     197     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 2.2e-54
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEE CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlv 81 
                                   i++aa+ lk akrpvi++Gggv+ s+ s+el ++aekl++Pv+ttl g g +p+d++lylgm g+hg+k+an a++e+D++
  gi|91772733|ref|YP_565425.1| 197 IKRAAAVLKDAKRPVIYAGGGVIGSEGSKELLAFAEKLKAPVTTTLTGIGGFPNDNELYLGMPGMHGTKYANYAIQESDVL 277
                                   79******************************************************************************* PP

                                   EEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                  TPP_enzyme_M  82 lalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                   +a+G+rfdd r+tg+ + fap+a++ihididpaei+k  +vd++ivgd+k++l aL
  gi|91772733|ref|YP_565425.1| 278 IAVGVRFDD-RVTGKTTSFAPNATVIHIDIDPAEISKIIKVDVPIVGDAKQILGAL 332
                                   *********.9***999***********************************9887 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 !   15.5   0.3   2.5e-06     0.011      21     171 ..      33     182 ..      16     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                                   CHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHH.HHCTT-EEE.EEEECCHHHHCCCCHHHHHHTT--EEEEEEEEE-S CS
                         POR_N  21 eiaeelaellakgevgdvevvqmesEigaisaviG.AaaaGaraa.TaTSgqGllLmienlglaageelPvvivvvaRalp 99 
                                    +++ ++el++ +     + + +  E +a+ a+ G A a+G  ++  aTSg+G    +  +  a ++ +P+v +  +   +
  gi|91772733|ref|YP_565425.1|  33 VLLHIYDELYDAHL----HHLLVRHEQAAVHAAEGyARATGKVGVcLATSGPGATNLVTGIANAYMDSVPMVAFTGQVPSS 109
                                   55555566664444....6788899**********7778898765169************************999886666 PP

                                   TTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH.CTSEEEEEEEHHHH.HEEEEEEC-SGG CS
                         POR_N 100 stglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek.vrvPvivlfDgfllshevekvelpdee 171
                                   + g   +++ +              +++v++  +++ +Af +A +    Pv++ + + ++++e++ v+  ++e
  gi|91772733|ref|YP_565425.1| 110 MIGNDAFQEANITGITMPITKHNYLVQDVKDLPRIIKEAFHIASTgRPGPVLIDLPKDITTDEIDFVYPDTVE 182
                                   6655555555444444455555666777777777777777777774445666666677777777666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3642.37
//
Query:       gi|91772734|ref|YP_565426.1|  [L=485]
Description: (R)-citramalate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-78  261.8   1.2    1.3e-77  261.0   1.2    1.5  1  HMGL-like   HMGL-like
      6e-37  126.5   2.6    1.1e-36  125.6   2.6    1.5  1  LeuA_dimer  LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
       0.17   11.7   1.6       0.52   10.1   0.2    2.4  3  DRTGG       DRTGG 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 !  261.0   1.2   2.1e-81   1.3e-77       5     264 .]       1     255 [.       1     255 [. 0.99

  Alignments for each domain:
  == domain 1  score: 261.0 bits;  conditional E-value: 2.1e-81
                                   EE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH.. CS
                     HMGL-like   5 vdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaaveal 85 
                                   +dttLRDGeq++++al++eek+ ia++Lde+gvd iE+g +  se+++e++ra+a+++ +a+i++++r  ++d++ a e  
  gi|91772734|ref|YP_565426.1|   1 MDTTLRDGEQTPGVALKTEEKVWIARKLDELGVDIIEAGSAITSEGEREAIRAVAAEGLDAEICSYCRIMQQDVDFALE-- 79 
                                   69*****************************************************************************.. PP

                                   ..TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEE CS
                     HMGL-like  86 kgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatrinia 166
                                     + ++++h++ ++s+lh+++klkkdre  +++a  av++a+++g  vels edasr+dl+fl ++++  +e+Ga+r+ + 
  gi|91772734|ref|YP_565426.1|  80 --CDVDSIHLVAPVSDLHISVKLKKDREALKEMALSAVEYAKDHGLIVELSGEDASRADLDFLKDLYKSGVEVGADRVCFC 158
                                   ..******************************************************************************* PP

                                   ETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT CS
                     HMGL-like 167 DtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaalealg 247
                                   DtvG+l P+   e+++ l++ ++  v+++vHcHnd+GlAv nt+aA++aGa++   t+nG+GeraGnaalee+++ le l 
  gi|91772734|ref|YP_565426.1| 159 DTVGLLVPERTTEIFKDLSSSID--VPVAVHCHNDFGLAVSNTVAALNAGAREAHMTINGIGERAGNAALEEVAMILEWLY 237
                                   ***********************..*****************************************************987 PP

                                   .-B----HHHHHHHHHHH CS
                     HMGL-like 248 .vdtgldlqklrsiaalv 264
                                     +t +++++l+++++lv
  gi|91772734|ref|YP_565426.1| 238 kRETSIKTNELYKVSRLV 255
                                   7**************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 !  125.6   2.6   1.9e-40   1.1e-36       2     132 ..     351     482 ..     350     483 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 1.9e-40
                                   XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T-EEE CS
                    LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..dikLl 79 
                                   vtd+dl+++++++l   + +++kle+l+v+sg++ ++ta+v+l v dg+e +++a+G+GpvdA+++ +rka++   di+L+
  gi|91772734|ref|YP_565426.1| 351 VTDADLQTIAETVLDIYReSKVKLEDLTVVSGNRATPTASVRLIV-DGKEIVEAATGDGPVDAAFEGIRKAVSGvaDIHLE 430
                                   9**************9888**************************.**************************9989***** PP

                                   EEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                    LeuA_dimer  80 dYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                   +Y+v+ait+gtda++ev V+l+ +dgk v+ +G+++di++AS++A+i+++n+l
  gi|91772734|ref|YP_565426.1| 431 EYHVDAITGGTDALVEVLVKLS-KDGKMVTSRGARTDIIMASVEAVINGINQL 482
                                   **********************.99999***********************97 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.38   2.3e+03      23      58 ..      21      56 ..      14      61 .. 0.70
   2 ?   -2.2   0.0      0.61   3.7e+03      39      51 ..     373     385 ..     357     388 .. 0.77
   3 ?   10.1   0.2   8.7e-05      0.52      27      65 ..     440     479 ..     424     483 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.38
                                  EEEE-SS-HHHHHHHHHTSEEEEEETT-HHHHHHHT CS
                         DRTGG 23 kvvvgamsvenmlerlkegdlvivpGDRediqlaal 58
                                  kv ++    e  ++ ++ g+++   G+Re i   a+
  gi|91772734|ref|YP_565426.1| 21 KVWIARKLDELGVDIIEAGSAITSEGEREAIRAVAA 56
                                  555544444555788888999999999998876665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.61
                                   HTSEEEEEETT-H CS
                         DRTGG  39 kegdlvivpGDRe 51 
                                   k +dl +v+G+R+
  gi|91772734|ref|YP_565426.1| 373 KLEDLTVVSGNRA 385
                                   4478999999996 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 8.7e-05
                                   -SS-HHHHHHHHHT.SEEEEEETT-HHHHHHHTT-TEEEE CS
                         DRTGG  27 gamsvenmlerlke.gdlvivpGDRediqlaaleagiaal 65 
                                   g++++ ++l +l + g++v   G R+di++a +ea i+++
  gi|91772734|ref|YP_565426.1| 440 GTDALVEVLVKLSKdGKMVTSRGARTDIIMASVEAVINGI 479
                                   5566666666666669999999*************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3177.28
//
Query:       gi|91772735|ref|YP_565427.1|  [L=350]
Description: cellulase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-113  377.9   2.8   3.1e-113  377.7   2.8    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    3.5e-12   46.5   0.1    5.8e-12   45.8   0.1    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
     0.0002   21.1   0.1      0.034   13.8   0.0    2.5  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.7   2.8  5.1e-117  3.1e-113       1     292 []      44     338 ..      44     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: 377.7 bits;  conditional E-value: 5.1e-117
                                   S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGCHHHH CS
                 Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHllkeee 81 
                                   Gnlia+kkg  ++p vm+aAHmDeiG+mV+ I+++Gfl+f  +GG+ +++l +qrv +++++ +++GvigskppH++kee+
  gi|91772735|ref|YP_565427.1|  44 GNLIATKKG--DGPTVMLAAHMDEIGLMVQYIDDKGFLHFVMIGGWFDQTLHSQRVIVHGSNAQLTGVIGSKPPHVMKEED 122
                                   9********..********************************************************************** PP

                                   HHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEEEE CS
                 Peptidase_M42  82 rkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeeleatvylva 162
                                   r+k+++ +++fiDigak+ke+a ++G++vG+ +++d++f++lang +++ka+D+ragva+l++++k+++e++++at+y+v+
  gi|91772735|ref|YP_565427.1| 123 RNKPVKAEDMFIDIGAKDKEDAMKMGVDVGTAISMDRDFATLANGLVTCKAFDNRAGVAMLIDAMKQISETKVNATIYAVG 203
                                   ********************************************************************************* PP

                                   ESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT...CCSHHHHHHHHHHHHHHTT- CS
                 Peptidase_M42 163 tvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas...giyhpklrkkllelAkknni 238
                                   tvqEEvGl+Ga+tsa+ ++pd+aiavDvt+ gd+pg ++++++  +gkG+vi+v+Das   +i++++++k+l+e+A++n+i
  gi|91772735|ref|YP_565427.1| 204 TVQEEVGLKGARTSAFGLNPDVAIAVDVTFPGDHPGISKNDSAleMGKGAVITVVDASgrgLIADKNVVKWLKETAEENDI 284
                                   ***************************************998899************99989******************* PP

                                   -EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                 Peptidase_M42 239 pyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                   pyql+v  gg+tDA+aihlt+eg+p+ +is+ptryiHspvev++l+dl ++++L
  gi|91772735|ref|YP_565427.1| 285 PYQLNVGCGGTTDATAIHLTREGIPSSTISVPTRYIHSPVEVLSLEDLRSCADL 338
                                   ***************************************************987 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   9.7e-16   5.8e-12      30     207 .]     168     345 ..     157     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 9.7e-16
                                   EESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20  30 lyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgileagkl 110
                                   l  + a d+ +gv++++ a++++ ++++  + ti  + ++ EE+g +Ga+  + g     ++d ++++ +  pg       
  gi|91772735|ref|YP_565427.1| 168 LVTCKAFDNRAGVAMLIDAMKQISETKV--NATIYAVGTVQEEVGLKGARTSAFG----LNPDVAIAVDVTFPGDHP---- 238
                                   556999********************86..78***********888999999985....556665555544333333.... PP

                                   TEEEE.........E.EEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH....TTTEEEEEEE CS
                                   xxxxx.........x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xxxxxxxxxx RF
                 Peptidase_M20 111 aigvv.........k.vevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarff....agiptvmifg 176
                                     g++         k + ++ + ++    + d+ +vk+l+e+aee     ++l   +g g+tda  +    +gip+  i +
  gi|91772735|ref|YP_565427.1| 239 --GISkndsalemgKgAVITVVDASGRGLIADKNVVKWLKETAEEN-DIPYQLNvGCG-GTTDATAIhltrEGIPSSTISV 315
                                   ..344444455555557777776666666777*************5.44444443566.*********9999999887888 PP

                                   SSGGCTTSTTTEEEHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 177 pgsglaHspnEyvdledlekgikvlarllee 207
                                   p    +Hsp E ++ledl+ +++++a+++++
  gi|91772735|ref|YP_565427.1| 316 PT-RYIHSPVEVLSLEDLRSCADLIAKAVQN 345
                                   99.9**********************99975 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0033        20       1      26 [.      45      68 ..      45      84 .. 0.79
   2 !   13.8   0.0   5.7e-06     0.034      35     110 ..     173     256 ..     163     343 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0033
                                  EEEEEESTTCESEEEEEEEE--B-TT CS
                 Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgv 26
                                  N+iat +g+    +++l+AH+D +g 
  gi|91772735|ref|YP_565427.1| 45 NLIATKKGDG--PTVMLAAHMDEIGL 68
                                  7888888888..58********9986 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.7e-06
                                   TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH.HHC.CCTTEEEEEEECS-SSSS--EEE.... CS
                 Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak.akp.elkkiaavlnlDmvgsggkellf.... 109
                                   A Dn +gva+l+  ++++ +  ++ + ++  + +  EE gl G++  a   +p  + ++++ +  D  g +++        
  gi|91772735|ref|YP_565427.1| 173 AFDNRAGVAMLIDAMKQISE--TKVNATIYAVGTVQEEVGLKGARTSAFgLNPdVAIAVDVTFPGDHPGISKNDSALemgk 251
                                   78*****************9..689********************988553333333444444444444333333334555 PP

                                   ....H CS
                 Peptidase_M28 110 ....e 110
                                       +
  gi|91772735|ref|YP_565427.1| 252 gaviT 256
                                   55441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2187.52
//
Query:       gi|91772736|ref|YP_565428.1|  [L=178]
Description: hypothetical protein Mbur_0713 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       912  (0.0508673); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1223.24
//
Query:       gi|91772737|ref|YP_565429.1|  [L=167]
Description: hypothetical protein Mbur_0714 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0052   17.1   0.4       0.01   16.2   0.4    1.5  1  Aim19            Altered inheritance of mitochondria protein 
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.032   14.3   0.0    1.3  1  MDH              Methanol dehydrogenase beta subunit
       0.12   12.3   1.1        1.6    8.7   0.0    2.3  2  Gram_pos_anchor  LPXTG cell wall anchor motif
       0.22   10.7   0.0       0.26   10.4   0.0    1.1  1  DUF2920          Protein of unknown function (DUF2920)
       0.25   11.6   1.7       0.34   11.1   0.2    2.0  2  DUF2749          Protein of unknown function (DUF2749)


Domain annotation for each model (and alignments):
>> Aim19  Altered inheritance of mitochondria protein 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   2.8e-06      0.01      42      72 ..       6      36 ..       1      38 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                         Aim19 42 lsvllfgaafalggymiydgDlenGsGfltA 72
                                  l  ll +++ ++g+ m ydg+l+n++G+++A
  gi|91772737|ref|YP_565429.1|  6 LIYLLVAIIATAGTAMAYDGNLYNAAGTAAA 36
                                  5678999*********************998 PP

>> MDH  Methanol dehydrogenase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     9e-06     0.032       9      59 ..      11      64 ..       4      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9e-06
                                  XXX...XXXXXX--S---SBTTB-----TTS..-.S--TTSTT-----HHHHTH CS
                           MDH  9 allaavaasalaydGtkCkapGnCWepkPgy..P.ekvaGskydPkhdpkelnk 59
                                  +++ a+a +a+aydG+  +a+G    p+P    P e v  s y  + +p++lnk
  gi|91772737|ref|YP_565429.1| 11 VAIIATAGTAMAYDGNLYNAAGTAAAPNPMIiqPgETVTLSYYMENMNPADLNK 64
                                  44567999********************97533336788888888888888888 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.0      0.11   3.8e+02      18      33 ..       6      21 ..       3      23 .. 0.83
   2 ?    8.7   0.0   0.00045       1.6      21      42 ..     146     167 .]     144     167 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                                  XXXXXXXXXXXXXXXX CS
               Gram_pos_anchor 18 ifltaaGllallggll 33
                                  +++++++++a++g+++
  gi|91772737|ref|YP_565429.1|  6 LIYLLVAIIATAGTAM 21
                                  579999*999999986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00045
                                   XXXXXXXXXXXXXXXXXXXXXX CS
               Gram_pos_anchor  21 taaGllallggllLlvkrRKke 42 
                                   t+a   a++ gl++++ rRK+e
  gi|91772737|ref|YP_565429.1| 146 TIALPVAAIIGLAFFLQRRKEE 167
                                   5666678999999999999997 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.3e-05      0.26     111     179 ..      60     126 ..      40     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.3e-05
                       DUF2920 111 kalvellefvsdkieelkalnlvdenaklrlsatliPpkgeYqnfGimaAlDiinalkdlvkrfpkead 179
                                     l +++++    +  +k     +++  + + a++iP+ + Y   Gi+     ina  d v      a+
  gi|91772737|ref|YP_565429.1|  60 ADLNKTFPYSYSVV--VKSGTGSPSDIAVTVPASVIPTTNPYTDVGIITVTKDINAPMDTVYTIKVVAG 126
                                   56677777666555..45666778889999**************************9998877766665 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   9.5e-05      0.34       1      23 [.       1      23 [.       1      40 [. 0.79
   2 ?   -2.1   0.1       1.3   4.7e+03      22      33 ..      71      82 ..      69      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                       DUF2749  1 msprilIvlviavaagagtilwl 23
                                  m+ +ilI l +a+ a+agt+++ 
  gi|91772737|ref|YP_565429.1|  1 MKSKILIYLLVAIIATAGTAMAY 23
                                  999*********99999999875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                       DUF2749 22 wlvvqpragtsg 33
                                   +vv++ +g+++
  gi|91772737|ref|YP_565429.1| 71 SVVVKSGTGSPS 82
                                  588999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1293.86
//
Query:       gi|91772738|ref|YP_565430.1|  [L=774]
Description: hypothetical protein Mbur_0715 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-89  300.7   0.4    1.6e-89  300.2   0.4    1.3  1  DUF1616   Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
      0.077   12.6   0.2       0.31   10.6   0.2    2.1  1  Saf_2TM   SAVED-fused 2TM effector domain
      0.091   12.6   8.4       0.15   11.9   6.0    2.0  2  Bax1-I    Inhibitor of apoptosis-promoting Bax1
       0.22   11.1   1.9         15    5.2   0.1    2.5  2  DUF4131   Domain of unknown function (DUF4131)


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 !  300.2   0.4   3.6e-93   1.6e-89       2     293 .]      17     293 ..      16     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 300.2 bits;  conditional E-value: 3.6e-93
                       DUF1616   2 lvlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtpwgir 82 
                                   +v+a+l++++ilvp+lnetplRi+++lpl++f+PGY++ia++FP+k+di++ieR++LS+g+Siai+++ g+++++t+w +r
  gi|91772738|ref|YP_565430.1|  17 VVFAMLAVIFILVPPLNETPLRIFFALPLIFFIPGYTFIAMMFPKKGDISNIERFTLSVGFSIAITVFDGFAVSLTQWLFR 97 
                                   799****************************************************************************** PP

                       DUF1616  83 lepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleek.sesr....ldkalnvlLvvsivlavaalgy 158
                                   +++i +sl l+t ++al+A++ R+r pee++f+++++ +ies++++ e+  +++r    ++kal ++Lv si++a ++l+y
  gi|91772738|ref|YP_565430.1|  98 PNSISISLLLLTAIFALLAYIARRRHPEEDQFTFSVHGFIESIRSDDENIpKKDRippeIEKALIIALVGSIIIASGMLVY 178
                                   ***********************************************9996666699999********************* PP

                       DUF1616 159 avvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrr 239
                                   a+v+ +e+e+fT+ly+lg++g   +aenypt+ + +++ +v+vgieN+E+++v+Y+++++l+             ++l++ 
  gi|91772738|ref|YP_565430.1| 179 AKVT-QEKEQFTALYILGPEG---MAENYPTNASIENPLKVTVGIENYEKQDVDYILQMRLDG------------KVLQTL 243
                                   ****.****************...*************************************95............799*** PP

                       DUF1616 240 evtladnetweqelevepea.tgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                   ++tl+d+e+we+el+++pe+ + ++ +le+ L+k+     + + ++yrs+hlw++
  gi|91772738|ref|YP_565430.1| 244 NITLSDEEKWEDELTYKPEQiRVGRSKLEYALFKE-----EISFNPYRSVHLWIT 293
                                   ********************9999***********.....999**********96 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   6.8e-05      0.31       4     138 ..      84     234 ..      81     242 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.8e-05
                       Saf_2TM   4 ldyvirklidwlfRkrsaell.lftigvalllailgt.......dwalkialkla.ggslevsfssse..ipeivl.aiil 72 
                                   +d +  +l +wlfR+ s+    l+ ++++ lla  +        ++ +++   ++  +s +++  +++  +pei   +ii 
  gi|91772738|ref|YP_565430.1|  84 FDGFAVSLTQWLFRPNSISISlLLLTAIFALLAYIARrrhpeedQFTFSVHGFIEsIRSDDENIPKKDriPPEIEKaLIIA 164
                                   7889999***********8877999********999999999876777776666645666666777777444555514455 PP

                       Saf_2TM  73 vigvllivvGavllilryvneakrqskkkvivIEgrgLrdts....gsplesavpk.eikgrrvdllldlr 138
                                   ++g+++i+ G +l ++   +e+++     ++  Eg +  +++     +pl+ +v+  + +++ vd+ l +r
  gi|91772738|ref|YP_565430.1| 165 LVGSIIIASG-MLVYAKVTQEKEQFTALYILGPEGMAENYPTnasiENPLKVTVGIeNYEKQDVDYILQMR 234
                                   5666666666.888888877766666666665555555444311115677777777666666666666554 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.0   3.3e-05      0.15      14     114 ..      15     119 ..       8     136 .. 0.70
   2 ?    0.4   0.0      0.11   4.7e+02      95     119 ..     160     184 ..     154     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                        Bax1-I  14 gllltalvaavvlsspa..qlflslhivlflvvilaplalvflslsaarlkkkssa....lalallllftlleGlslspil 88 
                                   + ++ a++a++++ +p+  ++ l+ +++l l+ +++p + ++ ++++ ++ + s+     l++++ +++t++ G+ +s++ 
  gi|91772738|ref|YP_565430.1|  15 ATVVFAMLAVIFILVPPlnETPLRIFFALPLI-FFIPGYTFI-AMMFPKKGDISNIerftLSVGFSIAITVFDGFAVSLTQ 93 
                                   44566666666666666755555555554444.444555544.44666777666655663448888889999999999988 PP

                        Bax1-I  89 lvytgaiilqaflltaaifgglslya 114
                                    ++ +++i   +ll +aif+ l+ +a
  gi|91772738|ref|YP_565430.1|  94 WLFRPNSISISLLLLTAIFALLAYIA 119
                                   8888****************998887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                        Bax1-I  95 iilqaflltaaifgglslyalttkr 119
                                    ++ a+++  +i  g+ +ya +t++
  gi|91772738|ref|YP_565430.1| 160 ALIIALVGSIIIASGMLVYAKVTQE 184
                                   5677888888888888888877743 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2    0.0045        20      10      48 ..      14      55 ..      10      69 .. 0.73
   2 ?    5.2   0.1    0.0035        15      14      62 ..      87     129 ..      71     147 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0045
                       DUF4131 10 lalllllllllllllrr...rprrrvllllllllllallgfa 48
                                  +a++++++l+ +++l      +  r++++l l++++ ++ f 
  gi|91772738|ref|YP_565430.1| 14 IATVVFAMLAVIFILVPplnETPLRIFFALPLIFFIPGYTFI 55
                                  455555555555554445659999999999999999877665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0035
                       DUF4131  14 lllllllllllrrrprrrvllllllllllallgfalrapqpnandlsql 62 
                                   +++ l+ +l+   rp+   + llll +++all + +r ++p+++   q+
  gi|91772738|ref|YP_565430.1|  87 FAVSLTQWLF---RPNSISISLLLLTAIFALLAYIARRRHPEED---QF 129
                                   3333333333...6666666666666666666666666666654...44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (774 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 5214.46
//
Query:       gi|91772739|ref|YP_565431.1|  [L=263]
Description: protease HtpX-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-12   45.9   0.0    8.1e-12   45.3   0.0    1.2  1  Peptidase_M48  Peptidase family M48


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 !   45.3   0.0   4.5e-16   8.1e-12      12     193 ..      54     259 ..      48     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 4.5e-16
                                   HHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                 Peptidase_M48  12 eelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivslla.. 90 
                                   e+la +ag+   ++++y++++     F+ g   +  i++++g +  l + +el+  l+ E+GHi ++++  +++v+l a  
  gi|91772739|ref|YP_565431.1|  54 ENLAVKAGV--VTPDMYMFDHHLPMIFTAGTRGKFDIAVSSGAM-GLFDASELEVMLAREIGHILNNDVPMNTMVALFAgs 131
                                   678888888..888888888887777777766444*********.***********************9999777765510 PP

                                   ..HHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT.........HHHHHHHHHHHHHHHHTTT.HHHHHHHHHH CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48  91 ..sillllglallisraeedaagafldalavliglliillfl.........alSRkrEyqADeagvellkrakdlvralik 160
                                     s+  + +  +l++  ++      +d ++  i +l++ l++         alS +rE + D+++vel+k++k l+++l  
  gi|91772739|ref|YP_565431.1| 132 laSVSTFALWGALLGGFGQ-----DYDPAPRFIRFLGMGLVAvpsaliaqlALSPSREIMVDAVSVELTKEPKLLADTLEY 207
                                   0044444333333333222.....223333332222222222234445556**********************99999999 PP

                                   HHHHTT--S---HHHH...................HHS-SS--HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 161 lakdlerqdvsaslrs...................ellstHPplleRiqalk 193
                                   ++k    ++ s  +                      l+ tHP+   R++++ 
  gi|91772739|ref|YP_565431.1| 208 MQKYVGHYPMSLNPGHahlfplnllsmeefydmhlSLFNTHPDVDIRVKQIM 259
                                   99999888888877777888899999999999999*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1674.03
//
Query:       gi|91772740|ref|YP_565432.1|  [L=277]
Description: hypothetical protein Mbur_0717 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-27   94.3  23.3    1.1e-26   93.9  23.3    1.1  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9  23.3   6.3e-31   1.1e-26      14     253 ..      14     271 ..       7     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 6.3e-31
               Exosortase_EpsH  14 alvshWlasedyshgllvpllalyllwdrwrr.....al.aasasllgllllllglfl..lallgelsrvlllsalslvli 86 
                                   +l+   +a+ ++s+g   ++++l+l +    +     ++   +as + +l+ +l++f+  ++ + + s++++l+++    +
  gi|91772740|ref|YP_565432.1|  14 TLALFIGATIELSEGSTTIGVILLLAAVAAITqirmsERkDIRASKFYILIGALIVFAdlFYNFRAGSDLGTLDSMT---F 91 
                                   22333455555555555555555555433333444553335555555222223333335367777777888888885...5 PP

               Exosortase_EpsH  87 llglvllllG...........lralrlllfpllllllalPlpavlvaqlslpLqllvaavagfllsllgipvereG...nv 153
                                   ++g+ l+++G           + a+ +  f +l+l+++  +++  +  l+++ + lv   ++ +++l+gipv + G   ++
  gi|91772740|ref|YP_565432.1|  92 FFGASLVAYGtdrpqlrhlgeFGAYISGVFTVLYLIFYSLFGMLDIGFLHVFDHYLVLIPTVTIIQLFGIPVDVVGietVY 172
                                   599999999999999999999999999999*****************************************9999986533 PP

               Exosortase_EpsH 154 iql.ptgqveVaeaCsGlrsllallalglllallfrrrlwkrklllllaavpiaflaNlvRilllvllayhygpeaaegll 233
                                   +   ++ ++ +   CsGl s++ l+ + + +  + +++l +  l ll +a++++++aNlvR+++l+l+ay+yg ea+  ++
  gi|91772740|ref|YP_565432.1| 173 LAGvEDLTIIIGGPCSGLYSMFLLIGIVAGYSRMEKMKLGQT-LNLLGFAIIVSYIANLVRVTILYLAAYYYGLEAM-RVV 251
                                   33337779********************************77.**********************************.8** PP

               Exosortase_EpsH 234 HeiaGwllfgvalllllgll 253
                                   H+++Gw++f++++ ++++++
  gi|91772740|ref|YP_565432.1| 252 HTHLGWIIFAIVAGAIMYIM 271
                                   ************87777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2091.52
//
Query:       gi|91772741|ref|YP_565433.1|  [L=266]
Description: hypothetical protein Mbur_0718 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1848.86
//
Query:       gi|91772742|ref|YP_565434.1|  [L=333]
Description: hypothetical protein Mbur_0719 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   42.5   1.5    1.4e-05   24.2   0.1    3.1  3  FemAB           FemAB family
    4.5e-05   23.6   0.0    6.8e-05   23.0   0.0    1.3  1  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   8.2e-05      0.73       4      32 ..      11      39 ..       8      90 .. 0.82
   2 !   24.2   0.1   1.5e-09   1.4e-05     152     236 ..     141     227 ..     129     232 .. 0.88
   3 !    7.1   0.6   0.00025       2.2     347     382 ..     273     305 ..     228     333 .] 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 8.2e-05
                         FemAB  4 eefdkFtkehsqesflqssewaklkekrg 32
                                  e +d+F+ eh++++ +q+s++a++ ++ +
  gi|91772742|ref|YP_565434.1| 11 EVWDEFVYEHPHGNIFQTSSMANVYRQAK 39
                                  6789*******************975433 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.5e-09
                         FemAB 152 wqlvldleeiteedllksfskktrknikkakkkGvkvrrltr.eeldvFkeltqkTeerkgialrsldYYeklldtf..gd 229
                                     +++dl+  +e ++++  sk++rk +++a+k+G+ +++++   el+  ++l+++T    ++ + + + ++ ++d f  +d
  gi|91772742|ref|YP_565434.1| 141 LDFLIDLDR-DEAEIWSDISKSRRKGVNRAEKSGIIIQKVKNdAELQASYDLIHQTYLNVKMPVADFSLFKAIYDEFvpKD 220
                                   568999999.8888**************************77489********************************9555 PP

                         FemAB 230 kaelmlA 236
                                    a + +A
  gi|91772742|ref|YP_565434.1| 221 MADFFIA 227
                                   5999998 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00025
                         FemAB 347 AlergieryNfyGiegkfdgsdGvlrFKtgFngfve 382
                                   A   +++ ++f+G  g+ d+  Gv +FK++F+g+ +
  gi|91772742|ref|YP_565434.1| 273 A--GKYKVFDFGG-AGHPDKPYGVREFKRRFGGEQV 305
                                   3..4578899999.79999999**********9855 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   7.6e-09   6.8e-05       7     139 ..     162     287 ..     156     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7.6e-09
                Acetyltransf_6   7 lrrkrrkleelgevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAval 87 
                                    r++ +++e++g   ++   ++++l+a ++l  +++      + + +  ++++++++++ +++ + ++ +  ++ pv++ +
  gi|91772742|ref|YP_565434.1| 162 RRKGVNRAEKSGI-IIQKVKNDAELQASYDLIHQTYLNV---KMPVADFSLFKAIYDEFVPKDMADFFIALQNDIPVGARI 238
                                   4788888999885.4556689**********98776655...66788889******************************* PP

                Acetyltransf_6  88 glrsgdrlyywlggydpelaklspgllllweliedaaeeGlrrfdlgggdee 139
                                   +l ++d +y w++g  ++ + +   + l+w+++ + a   +++fd+gg+  +
  gi|91772742|ref|YP_565434.1| 239 TLNYKDLVYDWYAGSLADVPYVD--EALVWKILSENA-GKYKVFDFGGAGHP 287
                                   ****************9999965..9*******9988.6699*****96543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2386.65
//
Query:       gi|91772743|ref|YP_565435.1|  [L=344]
Description: hypothetical protein Mbur_0720 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-13   50.6   0.1    1.8e-13   50.3   0.1    1.1  1  DUF354           Protein of unknown function (DUF354)
     0.0025   17.8   0.0      0.004   17.2   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0034   17.4   0.1      0.011   15.7   0.0    1.9  2  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.1   3.1e-17   1.8e-13       2     333 ..       2     334 ..       1     340 [. 0.80

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.1e-17
                        DUF354   2 dvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvtlkekliesakrvinlskliaev 82 
                                   ++ +d+      + f+++i  +e+ G  v + +r     +++++  +f++     + +++  k +      + l k+  + 
  gi|91772743|ref|YP_565435.1|   2 KILLDIGHPKDFNVFKNVIISLEEMGHTVKIFVRAKESTKRMLDDAGFEYDVCPYY-KSMAGKALGIFANDLRLYKIARKF 81 
                                   788999999999*************************************9977655.556666666666678999****** PP

                        DUF354  83 kpdvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeGtsevinvq 163
                                   kpdv ++  s     v+  +  p +   d e a     ltlp++d+i            ++G +    +r++G  e++ ++
  gi|91772743|ref|YP_565435.1|  82 KPDVFISPGSPYSAHVSTLMRRPHLAFSDTEIAGLVTMLTLPFTDKIYTSTSF----YLDLGPK---QERFKGYYELAYLH 155
                                   **********************************************9876654....4567877...46799*****9887 PP

                        DUF354 164 s..yeideeilkdlnlkledektilmrpepslasyldadc......hkdvltkiveklkdridilviprdeeqkeiyeevd 236
                                      ++ +++il++ +l   +e  il+r    las+ d  +       +d l + +  l+++ ++ +i  ++ + +  ++++
  gi|91772743|ref|YP_565435.1| 156 PkyFKPNKNILDKYGL---EEGYILLRLSA-LASHHDLHAsgfnfeTEDDLKDYISSLEKYGKV-IISSEKSDWNTIKDYQ 231
                                   6669***********4...57789999887.888776522111111355666667777777665.5666666667778888 PP

                        DUF354 237 nviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkyliekdlmirstdvdeivntalrllvdkl 317
                                      +  ++ d   l+  + + +  G tm  eaa+lGip +     +   ++   +e +l+++  d ++ +  a+ ll++  
  gi|91772743|ref|YP_565435.1| 232 ---LEFDPDDLHDLIDCASICLSEGATMASEAAVLGIPSIYVSNTERGYLNELEMEYGLVYNIPDREKALKKAISLLNEVS 309
                                   ...8889999999*********************************************************99999997654 PP

                        DUF354 318 ekkk........lie.edltdlive 333
                                    k          l + +d++++i+e
  gi|91772743|ref|YP_565435.1| 310 TKDIwrlkkenmLENtDDIVEFIIE 334
                                   4332110000113223555555555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.6e-07     0.004      10      92 ..      18     100 ..      14     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.6e-07
                Glyco_transf_4  10 eLaraLarrGheVtvvtpgddgpleeevelvvrvprvpl..pllkrllrslaflrrlrrllkrekpDvvHahspaalgaal 88 
                                   +++  L ++Gh V +++++ +   +  ++ + +    p+     +++l ++a+ +rl ++++++kpDv  + ++++   a+
  gi|91772743|ref|YP_565435.1|  18 NVIISLEEMGHTVKIFVRAKESTKRMLDDAGFEYDVCPYykSMAGKALGIFANDLRLYKIARKFKPDVFISPGSPYS--AH 96 
                                   5666799*********7776665555553444444444411556788899*******************88875554..33 PP

                Glyco_transf_4  89 lalr 92 
                                   +  +
  gi|91772743|ref|YP_565435.1|  97 VSTL 100
                                   3333 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 !   15.7   0.0   1.9e-06     0.011      14      78 ..      17      86 ..       2     105 .. 0.75
   2 ?   -1.8   0.0      0.49   2.9e+03      28      72 ..     269     319 ..     267     321 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
               Glyco_trans_4_2 14 lrlakeLakrgyeVhvitpkkga.kdeleaegihvhrl..kvdrkg.pleylk.afklkklikkikPDvv 78
                                  ++++ +L + g++V+++ + k++ k+ l ++g++       ++ +g +l+ ++  ++l+k+ +k+kPDv 
  gi|91772743|ref|YP_565435.1| 17 KNVIISLEEMGHTVKIFVRAKEStKRMLDDAGFEYDVCpyYKSMAGkALGIFAnDLRLYKIARKFKPDVF 86
                                  5678899************55555**9*9999965555113344445555555357************95 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.49
               Glyco_trans_4_2  28 hvitpkkgakdeleaegihvhrlkvdrkg......pleylkafklkklikk 72 
                                   +v+  + g+ +ele+e   v++++++ k        l++++ + +++l k+
  gi|91772743|ref|YP_565435.1| 269 YVSNTERGYLNELEMEYGLVYNIPDREKAlkkaisLLNEVSTKDIWRLKKE 319
                                   566666677666666666788887553332221223333344677777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2149.82
//
Query:       gi|91772744|ref|YP_565436.1|  [L=149]
Description: galactoside-O-acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-12   46.0   6.9    5.6e-09   35.4   3.5    4.0  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    5.5e-07   29.2   8.5    2.9e-06   26.9   3.0    3.0  3  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 ?    2.6   0.0     0.014   1.3e+02      22      34 ..      35      47 ..      32      49 .. 0.71
   2 !    4.9   0.1    0.0025        22      22      33 ..      59      70 ..      55      73 .. 0.43
   3 ?    1.1   0.0     0.041   3.7e+02      12      24 ..      78      90 ..      74      91 .. 0.82
   4 !   35.4   3.5   6.2e-13   5.6e-09       2      36 .]      93     127 ..      92     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.014
                                  E-TTEEEETTEEE CS
                       Hexapep 22 IGdnvkIgagvvi 34
                                  IG+ v+I++g +i
  gi|91772744|ref|YP_565436.1| 35 IGKQVYIAEGLTI 47
                                  7777777777666 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0025
                                  E-TTEEEETTEE CS
                       Hexapep 22 IGdnvkIgagvv 33
                                  I d+v Ig++v 
  gi|91772744|ref|YP_565436.1| 59 IDDRVAIGPNVI 70
                                  333333333332 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.041
                                  TTEEEETTEEE-T CS
                       Hexapep 12 pfaviggnVkIGd 24
                                  +f++i + VkI +
  gi|91772744|ref|YP_565436.1| 78 NFSKIWDSVKIQR 90
                                  7999999999976 PP

  == domain 4  score: 35.4 bits;  conditional E-value: 6.2e-13
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   ++I s+++Ig++a+i+++++IG+++++gag+v+++
  gi|91772744|ref|YP_565436.1|  93 IIINSDAWIGAGAIILPDITIGEGAIVGAGAVVTK 127
                                   5899*****************************86 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.061   5.4e+02      17      32 ..      32      47 ..      30      49 .. 0.77
   2 !    3.4   0.1    0.0074        67       2      15 ..      57      70 ..      56      73 .. 0.67
   3 !   26.9   3.0   3.3e-10   2.9e-06       2      34 .]      93     127 ..      92     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.061
                                  SEEE-TT-EE-TT-EE CS
                     Hexapep_2 17 GvslGdncvvgaGvvi 32
                                  G s+G+ + ++ G++i
  gi|91772744|ref|YP_565436.1| 32 GYSIGKQVYIAEGLTI 47
                                  5578998999888877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0074
                                  EEE-TT-EE-TT-E CS
                     Hexapep_2  2 viIGdnCliGanag 15
                                  ++I d++ iG+n +
  gi|91772744|ref|YP_565436.1| 57 LRIDDRVAIGPNVI 70
                                  56677777777754 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 3.3e-10
                                   EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                     Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                   +iI  +  iGa a+i   +++G++++vgaG v+t+
  gi|91772744|ref|YP_565436.1|  93 IIINSDAWIGAGAIIlpDITIGEGAIVGAGAVVTK 127
                                   67888999********99****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1049.62
//
Query:       gi|91772745|ref|YP_565437.1|  [L=294]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-11   43.0   0.1    2.3e-10   40.6   0.1    2.2  2  Glycos_transf_2  Glycosyl transferase family 2
    4.5e-06   26.7   0.0    2.4e-05   24.3   0.0    1.9  2  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   2.5e-14   2.3e-10       2     121 ..       7     139 ..       6     171 .. 0.83
   2 ?   -1.9   0.0      0.28   2.5e+03     108     132 ..     195     218 ..     183     254 .. 0.59

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.5e-14
                                   EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.....C-TTEEEEEESSS-HHHHHHHHHHHH CS
               Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.....edprvrvirreenvGkagalnaglra 77 
                                   vv+p+ Nee++l+ +  s++++ +   +  ++ +DgStD+t +++ +l       ++    + +r+ ++ ++  +  ++r+
  gi|91772745|ref|YP_565437.1|   7 VVTPCKNEEANLPHLAQSIIKN-TIHPVLWVIYNDGSTDSTGDVISNLEGshawiKGLEGAISKRDLGFHYSDIVEYAIRY 86 
                                   9*********************.999999999****************99***9944444444444455555555555555 PP

                                   --SS.........EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEEC CS
               Glycos_transf_2  78 atgd.........yilflDaDdepdpdwleklvealekdgadvvlgqrprifg 121
                                   a  +         yi ++DaD + d d++ek++ ++e++++ +++ +++++  
  gi|91772745|ref|YP_565437.1|  87 AINKcdnnnidfeYIGLIDADMILDLDFFEKMLIRFENNPKIGICSGTVAYLN 139
                                   5555555599999***************************9999998887755 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.28
                                   TTCEEEEEEEEEECCCCCCCHC-SS CS
               Glycos_transf_2 108 gadvvlgqrprifgetdeiernkrv 132
                                    +dvv +q++r+++ ++ ++   +v
  gi|91772745|ref|YP_565437.1| 195 YDDVVGVQTRRTSSAEGLWKGY-GV 218
                                   4566666666666666555543.33 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 !   24.3   0.0   2.7e-09   2.4e-05       4     129 ..       5     141 ..       2     190 .. 0.84
   2 ?    0.9   0.0      0.04   3.6e+02     169     218 ..     162     210 ..     144     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.7e-09
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalp..dvrvrvvvnarnlgstgksralnea 82 
                                   ++v+ p+ nee+ l  +  s+++++ ++v  v+  d+s+++t +v+  l+  +   + ++  ++ +r+lg+  +s+ ++ a
  gi|91772745|ref|YP_565437.1|   5 YIVVTPCKNEEANLPHLAQSIIKNTIHPVLWVIYNDGSTDSTGDVISNLEGSHAwiK-GLEGAISKRDLGF-HYSDIVEYA 83 
                                   67999********************9***********************99999855.79999999****9.999999999 PP

               Glyco_tranf_2_3  83 lra.........vksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpv.fllnr 129
                                   +r          ++++++ l+D+D +++ d+++++l  f + pk+g+  + v +l+n+
  gi|91772745|ref|YP_565437.1|  84 IRYainkcdnnnIDFEYIGLIDADMILDLDFFEKMLIRFeNNPKIGICSGTVaYLNNG 141
                                   9954555555555599***********************9999*99998555266665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.04
               Glyco_tranf_2_3 169 revlkelegldplflltdDyelglrlrragfrtayvpgaa.vrevfpsslk 218
                                    +++ +++g+ +  +   D  + ++++ +g+ t+ + +++ v++ ++ss +
  gi|91772745|ref|YP_565437.1| 162 KKCYYDTGGFPK--SYSADSVSNVSAMLHGWETKKYDDVVgVQTRRTSSAE 210
                                   555555545544..7778888999*********987777655555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1741.07
//
Query:       gi|91772746|ref|YP_565438.1|  [L=517]
Description: hypothetical protein Mbur_0723 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-05   23.2  19.0    6.4e-05   23.2  19.0    3.2  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 !   23.2  19.0   3.6e-09   6.4e-05       6     154 ..      83     235 ..      79     242 .. 0.83
   2 ?    1.5   4.0     0.017   3.1e+02     109     150 ..     259     301 ..     232     309 .. 0.72
   3 ?   -2.5   8.8       0.3   5.4e+03      32     112 ..     272     355 ..     256     361 .. 0.40

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.6e-09
                         PMT_2   6 iawllalftklfgf.selairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsa.lftpdaplvllwa 83 
                                   ++++l+ +++ +g   e ai + +++ag+l+++  ylla ++++  +  ++ +l+ ++ p +++ ++ ++ +  ++++l  
  gi|91772746|ref|YP_565438.1|  83 VPFMLSEIAQMTGLeMEKAILVYCIIAGLLGMFTSYLLAGQIYNdFKFKYIMSLFFSLAPGVMVFTTwEVSTRGLFIVLFP 163
                                   6788888899999779999*************************99**************99999999************* PP

                         PMT_2  84 lalylllraleknklkywllagvlfGlgflsKytaallliaallyllis..arrilke.kkpylalllalllfs 154
                                   +++ylllr  ++  +k ++l+ + f+l f ++ +a +l++ +++y+ ++  ++  + + kk +l +++ +++++
  gi|91772746|ref|YP_565438.1| 164 FFIYLLLRIDKT--IKKYILLTICFVLLFATHHYAYFLIPVIVVYFSLNilKKVNIPHfKKNHLNYIFSFAIIA 235
                                   *****9997555..579***********************8888999997533355444444555555555444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.017
                         PMT_2 109 GlgflsKytaalllia..allyllisarrilkekkpylalllal 150
                                   +l+++++yt   l++a   l+yll + ++ ++e +++  l+l+l
  gi|91772746|ref|YP_565438.1| 259 ALITNIRYTGPALILAfgGLVYLLQK-KKSFNEIIFLSLLILFL 301
                                   78899999977666663266699999.88888877766555544 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.3
                         PMT_2  32 gvltilllyllarrlfgkraallaalllavvplfvalsa...lftpdaplvllwalalylllraleknk.lkywllagvlf 108
                                   ++    l+yll ++   +++ +l+ l+l ++p ++ l++    + + +++++ +++   l   a++knk +  ++++ ++f
  gi|91772746|ref|YP_565438.1| 272 ILAFGGLVYLLQKKKSFNEIIFLSLLIL-FLPTIYSLTYgpyFLVLFIVFLASISFGNILNSLAIHKNKlFALFVISIIVF 351
                                   3333334444444332222323332222.2222222222212222234444444444444455555555444445566666 PP

                         PMT_2 109 Glgf 112
                                    ++f
  gi|91772746|ref|YP_565438.1| 352 SVAF 355
                                   6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.25s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3652.38
//
Query:       gi|91772747|ref|YP_565439.1|  [L=371]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-24   86.3   0.1    3.4e-24   85.3   0.1    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
      8e-15   55.4   0.0      2e-14   54.2   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00092   19.3   0.0     0.0017   18.4   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4


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 !   85.3   0.1   5.7e-28   3.4e-24       6     171 ..     178     346 ..     175     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 5.7e-28
                                   HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCC..HCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
               Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkq..lnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                   ++  +k ++   i++ grl++eKgvdllik ++l+  +     ++ l iaG+g++ ++lk+l+ +l + dnviflg+++++
  gi|91772747|ref|YP_565439.1| 178 HEFIKKSDNSIKIFYHGRLSPEKGVDLLIKGLKLFLSTksGSTKIYLYIAGDGPQMQYLKALSIQLDIVDNVIFLGNLNQK 258
                                   56667889999***********************9988777899************************************* PP

                                   SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT.--EEEET.TTTHCHHCHTTTSEEEE-TT.-HHHHHHHHHHHHHSHHHH CS
               Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaag.lpviasn.aggpaevvkdgetGllvkpn.naealaeairklledeelr 162
                                    ++++l++ d++++psi + f++++lEA+a+  +pv  s+ ag +  ++ dg   +l + + n+e +++ + ++ e+++++
  gi|91772747|ref|YP_565439.1| 259 MIIKYLQKVDAAIYPSILDTFALAILEAFACAeCPVYFSKkAGIYDFIIDDGY--VLGAFEpNVENISNIVSSIFEKSNKN 337
                                   ******************************96266667775555555555555..566655799***************** PP

                                   HHHHHHHHH CS
               Glycos_transf_1 163 erlgenark 171
                                   ++++e  +k
  gi|91772747|ref|YP_565439.1| 338 DNIIEHQKK 346
                                   ***998876 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 ?   -2.6   0.0       1.2     7e+03      18      39 ..      85     106 ..      82     123 .. 0.73
   2 !   54.2   0.0   3.3e-18     2e-14       3     115 ..     189     312 ..     187     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHH.HHEEEEEES- CS
               Glyco_trans_1_4  18 dllleavpllrkkdvrlvivGd 39 
                                   ++ll+ +++++k+++ l   Gd
  gi|91772747|ref|YP_565439.1|  85 KFLLHVFAKIKKNKLILNYHGD 106
                                   7899999999977666766664 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 3.3e-18
                                   EEEEES---GG.GTHHHHHHHHHHHH.HH.....EEEEEES---...HHHHHHH.T.T-T.TEEEE---.TH.HHHHHHH- CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkd.....vrlvivGdgp.rpeeleela.a.gleerveftGfv.ed.laellaaa 73 
                                   +i + Grl+ ++kgvdll++ ++l ++ +     + l+i+Gdgp + + l++l  + ++ ++v+f+G + ++ + ++l+++
  gi|91772747|ref|YP_565439.1| 189 KIFYHGRLS-PEKGVDLLIKGLKLFLSTKsgstkIYLYIAGDGPqM-QYLKALSiQlDIVDNVIFLGNLnQKmIIKYLQKV 267
                                   6999****5.56**********99995523456799*******965.58886553466669********7336******** PP

                                   SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--TTSSEE CS
               Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvg.giaevvgengll 115
                                   d ++ Ps   +f l++lEa+a++ + V ++ + gi +++ ++g++
  gi|91772747|ref|YP_565439.1| 268 DAAIYPSilDTFALAILEAFACAECPVYFSKKaGIYDFIIDDGYV 312
                                   ********99***********987777776544888887445654 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.8e-07    0.0017      90     167 ..      92     170 ..      61     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.8e-07
                Glyco_transf_4  90 alrrrlgiplVltvHglye.....krllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnG 165
                                   a    ++ +l+l +Hg        ++ +  +l + ++    l+  ll ++++ i++S ++a+ +++ryg+ +  i+V+pn+
  gi|91772747|ref|YP_565439.1|  92 AKI--KKNKLILNYHGDICkelvlRYKYDHKLELSKIPTCILLPILLFSSNKNIVNSYSLANIFKHRYGLGN--IEVVPNA 168
                                   333..57799999***99999998777777777778888888888899*********************876..******* PP

                Glyco_transf_4 166 vD 167
                                   +D
  gi|91772747|ref|YP_565439.1| 169 ID 170
                                   *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2604.13
//
Query:       gi|91772748|ref|YP_565440.1|  [L=377]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-25   87.9   0.2      9e-25   87.2   0.2    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
      6e-20   72.0   0.1    9.8e-20   71.3   0.1    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-15   57.2   0.0    2.7e-15   56.8   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
    4.3e-06   26.8   0.5    8.6e-06   25.8   0.5    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
        0.1   13.0   0.0       0.15   12.5   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.2   2.5e-28     9e-25       4     163 ..     193     347 ..     190     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 2.5e-28
                                   HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
               Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                   + + k+++n k+++++s   l+  Kgv+ lika++ + k   pn+k++++G+ge + +l++++++l+l++ v f+g++   
  gi|91772748|ref|YP_565440.1| 193 TTKLKEKLNIKDEFVVSTVGLRADKGVNCLIKAIPNIIKS-MPNTKFILVGEGECRSYLERMVDNLKLNNYVVFTGNMV-- 270
                                   44555666669999999999*****************765.*************************************9.. PP

                                   SHHHHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHH CS
               Glycos_transf_1  85 dleellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelre 163
                                   d+  ++++++++v++s   E+f+ v++EAmaag+ via ++g ++ev+ d +   l+++n    l+++i+k l+ ++ ++
  gi|91772748|ref|YP_565440.1| 271 DISGIYQISSCVVVSSLVeEAFCFVAVEAMAAGTQVIAFDSGALREVLYDLD--QLIPKN-YTLLSQKIIKCLKTNNINN 347
                                   ****************************************************..466555.8999999999999885544 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 !   71.3   0.1   2.7e-23   9.8e-20       7     132 ..     211     340 ..     205     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2.7e-23
                                   ES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH-SEEEE--.. CS
               Glyco_trans_1_4   7 vGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaadvfvaPs.. 80 
                                   vG l +  kgv  l++a+p + k+  + ++++vG+g+ r+  le++++  +l++ v+ftG + d++ +++ ++++v+ s  
  gi|91772748|ref|YP_565440.1| 211 VG-L-RADKGVNCLIKAIPNIIKSmpNTKFILVGEGEcRS-YLERMVDnlKLNNYVVFTGNMVDISGIYQISSCVVVSSlv 288
                                   44.4.345**********999978744*********9776.99999965888888*****999****************** PP

                                   .---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  81 .egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLl 132
                                    e f  +++Eamaag+ v+a+d g+++ev+   +  l+p ++   l ++i+++l
  gi|91772748|ref|YP_565440.1| 289 eEAFCFVAVEAMAAGTQVIAFDSGALREVLyDLD-QLIP-KNYTLLSQKIIKCL 340
                                   88*********************999**997665.4775.57888999998887 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   7.6e-19   2.7e-15      11     169 ..      31     185 ..      22     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 7.6e-19
                Glyco_transf_4  11 LaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallal 91 
                                   ++ +L ++G++ +++ ++++ +  e   ++ +  +    l++ + +++ f   l ++lk+ +p +vH h++ +++ +l +l
  gi|91772748|ref|YP_565440.1|  31 MTDELNKKGFKHVIIFRDRPIKCVED--TLLASNAEIKILKPTRSNIYIF-MELYQILKEIRPNIVHFHFY-PIYSSLNYL 107
                                   56788899998888888877777777..3333333333334444444444.479***************94.444454555 PP

                Glyco_transf_4  92 rrrlgiplVltvHglyekrllkarlkplsrllralerrl.....lrradrviavSeatadelrerygvppekitVipnGvD 167
                                   +    i++V+t H        +  + p++++lr+l++++         d++++vS++++  + + y+++++k+ Vi+nGv+
  gi|91772748|ref|YP_565440.1| 108 KFFFSIKIVYTDHMGS-----RELKTPFKKALRKLYYKThsilfNCGIDKIVCVSNYIKLKYSKEYNIHSSKLLVIYNGVN 183
                                   5569************.....466677777777777777677645599********************************9 PP

                Glyco_transf_4 168 le 169
                                   l 
  gi|91772748|ref|YP_565440.1| 184 LR 185
                                   86 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 !   25.8   0.5   2.4e-09   8.6e-06      12     136 ..      27     154 ..      22     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.4e-09
               Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg.pleylkaf.klkklikkikPDvvhahyakpygllg 90 
                                   +++ + +eL k+g++ ++i ++ + k ++    +   ++k  +   + +++ +f +l++++k+i P +vh h  + y  l 
  gi|91772748|ref|YP_565440.1|  27 FLVVMTDELNKKGFKHVIIFRDRPIKCVEDTLLASNAEIK--ILKpTRSNIYIFmELYQILKEIRPNIVHFHFYPIYSSLN 105
                                   6666778999999998888888886555544444444444..4444778889877*****************986666666 PP

               Glyco_trans_4_2  91 slaarlsgvipvv.lsvwGldvlkfpkksk...lkklllklalk.katkvi 136
                                   +l  ++   i++v +++ G+  lk+p+k++   l+++++ ++++  ++k+ 
  gi|91772748|ref|YP_565440.1| 106 YL--KFFFSIKIVyTDHMGSRELKTPFKKAlrkLYYKTHSILFNcGIDKIV 154
                                   55..433349***455667766*******9444444455556666666665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05      0.15      63     160 .]      81     181 ..      65     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
               Glyco_trans_4_4  63 lrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg...sgavrrlyraler.rllrradavlvvsea 139
                                   l ++l  ++ rp +vh h +++ +    ++   +i++v+t h   ++     + a+r ly   ++ +  ++ d +++vs++
  gi|91772748|ref|YP_565440.1|  81 LYQIL--KEIRPNIVHFHFYPIYSSLNYLKFFFSIKIVYTDHMGSRELKtpfKKALRKLYYKTHSiLFNCGIDKIVCVSNY 159
                                   56777..899********977555556666589*********64444342256666666655554488888********** PP

               Glyco_trans_4_4 140 eaeelra.lgvpadrvvvvpng 160
                                   +  ++   +++  +++ v+ ng
  gi|91772748|ref|YP_565440.1| 160 IKLKYSKeYNIHSSKLLVIYNG 181
                                   **88888799*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2687.02
//
Query:       gi|91772749|ref|YP_565441.1|  [L=373]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-42  144.3   0.0    5.1e-42  143.3   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-31  109.4   0.0    3.7e-31  108.3   0.0    1.5  2  Glyco_trans_1_4  Glycosyl transferases group 1
    8.3e-21   74.7   0.0    5.1e-20   72.2   0.0    2.0  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.2e-12   48.0   0.0    2.6e-12   46.9   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    9.8e-08   32.6   0.0    4.9e-07   30.3   0.0    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.5e-07   31.5   2.4    1.8e-06   28.0   0.3    2.7  3  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 !  143.3   0.0   1.7e-45   5.1e-42      16     172 .]     197     352 ..     189     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 1.7e-45
                                   EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEE CS
               Glycos_transf_1  16 kiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadif 96 
                                   + i++ gr+ k+Kg+d+lika++ +k    p+++l iaG+g++ k+l++l  +l l++n++fl ++ ++++++++ + d++
  gi|91772749|ref|YP_565441.1| 197 PSIFCAGRFIKMKGIDVLIKALPIIKLS-IPDIHLYIAGDGDQYKYLQSLTFKLDLQKNITFLNFIAKSKMIQMFASTDLV 276
                                   6799*********************875.**************************************************** PP

                                   EEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHHH CS
               Glycos_transf_1  97 vlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenarkr 172
                                   v+ps++E+fG+v+lEA+++g pv+as +gg++e++ +g  G lvkpn++++la++i+ + ++++ r+++++++++r
  gi|91772749|ref|YP_565441.1| 277 VVPSRYESFGMVALEALSSGSPVVASSVGGIPEMLDNGRYGMLVKPNDPKELAQQIIYIFNNSNIRKKMSYAGKQR 352
                                   *************************************************************************986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.1   1.5e+04      23      41 ..      25      46 ..       6      64 .. 0.56
   2 !  108.3   0.0   1.2e-34   3.7e-31       2     134 .]     197     338 ..     196     338 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.1
                                  HH.HHHH.HH..EEEEEES--- CS
               Glyco_trans_1_4 23 av.pllrkkd..vrlvivGdgp 41
                                  ++   ++k +  +++++v  g+
  gi|91772749|ref|YP_565441.1| 25 NLiNTILKYKypIEIHVVSFGN 46
                                  4444455332345666665553 PP

  == domain 2  score: 108.3 bits;  conditional E-value: 1.2e-34
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHH.T.T-T.TEEEE---..THHHHHHHH-SE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleela.a.gleerveftGfv..edlaellaaadv 75 
                                   p i + Gr+  + kg+d+l++a+p ++ +  d++l+i+Gdg+   + l++l+ + +l+++++f+ f+  +++ +++a+ d+
  gi|91772749|ref|YP_565441.1| 197 PSIFCAGRF-IKMKGIDVLIKALPIIKLSipDIHLYIAGDGDqY-KYLQSLTfKlDLQKNITFLNFIakSKMIQMFASTDL 275
                                   7899*****.567**************77745*********855.5888766448999*********8667********** PP

                                   EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                   +v+Ps  e+fg+++lEa+++g pvVa++vggi+e++  g+ g+lv+p+dp++la++i+ ++++
  gi|91772749|ref|YP_565441.1| 276 VVVPSryESFGMVALEALSSGSPVVASSVGGIPEMLdnGRYGMLVKPNDPKELAQQIIYIFNN 338
                                   *****999*****************************99*******************99875 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   1.7e-23   5.1e-20       2     169 ..      17     183 ..      16     184 .. 0.84
   2 ?   -0.0   0.0      0.26   7.7e+02     125     144 ..     264     283 ..     244     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.7e-23
                Glyco_transf_4   2 GGverhvleLaraLarrGh..eVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                   GG+ +++ +L++   +  +  e++vv++g + ++  +   ++ ++ v  ++++   +++ +++ l + + + +pD++H h+
  gi|91772749|ref|YP_565441.1|  17 GGAFTVLDNLINTILKYKYpiEIHVVSFGNKNETKHQ--KGYTIHLVKNCIFPTS-QYWYSPKLLEKKIVEINPDLIHLHF 94 
                                   7888888888888888654228889998888888888..8888999988888876.678888899999999********** PP

                Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglye.....krllkarlkplsrllralerrllrradrviavSeatadelrerygvpp 156
                                    ++ +     +r  l ip+V+t Hgl        +  ++ l+p+ +l  ++e+++l+++ +viavS ++++e++++ g p+
  gi|91772749|ref|YP_565441.1|  95 TYPPYSF--ICR--LPIPTVVTTHGLVSlrikgAHSKRSQLSPFFILGPYFEKKALKKVGKVIAVSTYMKNEVEKLIG-PN 170
                                   9999766..455..89***********99987655556677788899999*************************999.99 PP

                Glyco_transf_4 157 ekitVipnGvDle 169
                                   +k + ipnG++ e
  gi|91772749|ref|YP_565441.1| 171 QKTVYIPNGINYE 183
                                   **********966 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.26
                Glyco_transf_4 125 alerrllrradrviavSeat 144
                                     + +++ ++d v+++S+++
  gi|91772749|ref|YP_565441.1| 264 SKMIQMFASTDLVVVPSRYE 283
                                   44556678888888888875 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 !   46.9   0.0   8.8e-16   2.6e-12       2      89 ..     276     364 ..     275     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 8.8e-16
               Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                   v+ psr+es+ ++ +Ea+ +G+++++++  g++e++++g+ ++l++  d++ela++i y  +n   r++++ a+++r  ++
  gi|91772749|ref|YP_565441.1| 276 VVVPSRYESFGMVALEALSSGSPVVASSVGGIPEMLDNGRYGMLVKpnDPKELAQQIIYIFNNSNIRKKMSYAGKQR-SQD 355
                                   5679***********************99************************************************.99* PP

               Glyco_trans_1_2  81 htydhraeq 89 
                                   + +d  a++
  gi|91772749|ref|YP_565441.1| 356 YLWDDIAKR 364
                                   ***998876 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 !   30.3   0.0   1.6e-10   4.9e-07      73     160 .]      86     179 ..      48     179 .. 0.78
   2 ?   -0.5   0.0      0.48   1.4e+03     129     140 ..     272     283 ..     257     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.6e-10
               Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhgll.......lrrgsgavrrly..ralerrllrradavlvvseaeaeel 144
                                   +pd++h+h  + + +  ++  r  ip vvt hgl        + ++s  ++ ++    +e+ +l+ +  v++vs+++  e+
  gi|91772749|ref|YP_565441.1|  86 NPDLIHLHFTYPP-YS-FIC-RLPIPTVVTTHGLVslrikgaHSKRSQLSPFFIlgPYFEKKALKKVGKVIAVSTYMKNEV 163
                                   7*******95333.33.444.5669*******854333332133334444444465666********************** PP

               Glyco_trans_4_4 145 ralgvpadrvvvvpng 160
                                   + l +p +++v++png
  gi|91772749|ref|YP_565441.1| 164 EKLIGPNQKTVYIPNG 179
                                   ***************8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
               Glyco_trans_4_4 129 radavlvvseae 140
                                   + d+v+v+s++e
  gi|91772749|ref|YP_565441.1| 272 STDLVVVPSRYE 283
                                   556666666654 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.3   6.2e-10   1.8e-06      25     138 ..      37     155 ..       5     156 .. 0.76
   2 ?    2.7   0.1     0.039   1.2e+02      74     104 ..     187     215 ..     184     258 .. 0.83
   3 ?   -2.1   0.0       1.2   3.6e+03      84     106 ..     283     303 ..     226     306 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.2e-10
               Glyco_trans_4_2  25 yeVhvitpkkgakdeleaegihvhrlkvdrkgpleyl.kafkl.kklikkikPDvvhahyakpygllgslaarlsgvipvv 103
                                   +e+hv++ +++  + + ++g+++h +k ++ +p +      kl  k i +i+PD++h+h + p+    s+++rl   ip+v
  gi|91772749|ref|YP_565441.1|  37 IEIHVVSFGNK-NETKHQKGYTIHLVK-NCIFPTSQYwYSPKLlEKKIVEINPDLIHLHFTYPPY---SFICRLP--IPTV 110
                                   69999999888.566668899999999.888855554154455599999**********997762...4667887..9*** PP

               Glyco_trans_4_2 104 lsvwGldv..lkfpkksk.....lkkl...llklalkkatkvist 138
                                   ++ +Gl    +k+++ ++     ++ l    +k alkk+ kvi+ 
  gi|91772749|ref|YP_565441.1| 111 VTTHGLVSlrIKGAHSKRsqlspFFILgpyFEKKALKKVGKVIAV 155
                                   ******66776666666665666333366699999*999999986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.039
               Glyco_trans_4_2  74 kPDvvhahyakpygllgslaarlsgvipvvl 104
                                   +PDv++ ++ ++++ +g+++ +++g i v++
  gi|91772749|ref|YP_565441.1| 187 NPDVINDITHPSIFCAGRFI-KMKG-IDVLI 215
                                   8********99999999887.8887.66665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
               Glyco_trans_4_2  84 kpygllgslaarlsgvipvvlsv 106
                                    + g+++ l a+ sg +pvv+s 
  gi|91772749|ref|YP_565441.1| 283 ESFGMVA-LEALSSG-SPVVASS 303
                                   3445555.5556666.7777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2791.28
//
Query:       gi|91772750|ref|YP_565442.1|  [L=478]
Description: polysaccharide biosynthesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  119.1  34.9    2.3e-34  119.1  34.9    2.6  2  Polysacc_synt    Polysaccharide biosynthesis protein
    5.8e-15   55.6  23.9    5.8e-15   55.6  23.9    4.9  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    9.1e-12   44.8  26.4    9.1e-12   44.8  26.4    2.0  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.07   11.7  49.5       0.16   10.5  49.4    1.5  1  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1  34.9     5e-38   2.3e-34       1     274 []       7     275 ..       7     275 .. 0.94
   2 ?  -14.9  25.7         4   1.8e+04      82     216 ..     295     432 ..     283     457 .. 0.54

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 5e-38
                 Polysacc_synt   1 llkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnv 81 
                                   ++k++++ll+++l tk+++f +l y+ar+lgp +fG++++++a+v ++  + dlG+ ++lvre ak+ +      +++ n+
  gi|91772750|ref|YP_565442.1|   7 IVKNTSFLLVGRLSTKIISFFILLYIARYLGPDDFGKFSFVFAFVYFFAFIPDLGIHNILVREAAKEPA---NAGILIGNA 84 
                                   58******************************************************************8...899****** PP

                 Polysacc_synt  82 llvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavfl 162
                                   + +++vl+l++++l ++  +l++   ++ + ++ +++ ll+++ s ++ ++  + rm+y a+ +v +++++++lvl  v+ 
  gi|91772750|ref|YP_565442.1|  85 TAIKIVLSLIAIFLAFFTINLMDYPISTKNALYLASIGLLITNLSAFGIIYEIKLRMEYSALFSVTSRIIFLMLVLYGVLQ 165
                                   ****************97777777777778888888888******************************999999999999 PP

                 Polysacc_synt 163 fldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsillglllgaeavGi 243
                                    + ++  v++  +a +v  i+  ++++++ +++f++   kl++++l +++p+ + s+++ +y+++d ++l++l ++++vG 
  gi|91772750|ref|YP_565442.1| 166 NSTLLFFVFASISADFVHNILMVVFSKRFVNVQFNFD-YKLIKQILHEALPIALASVFVMIYFRVDILMLSFLKNDVDVGL 245
                                   999*******99*****99999888886669999999.******************************************* PP

                 Polysacc_synt 244 YnaayqllvaisgllapivtaalfPvfselq 274
                                   Y+aay+++ a  +++ +i+++++fP++s+++
  gi|91772750|ref|YP_565442.1| 246 YSAAYRFTEAF-IFVPSILMTSMFPLMSKYF 275
                                   *******9987.788888999*******985 PP

  == domain 2  score: -14.9 bits;  conditional E-value: 4
                 Polysacc_synt  82 llvllvlvllfllllliaa.....flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvl 157
                                    ++l++++++ +l+++i        +++++ a+ +li a +++ ++ + + ++ +  g   +   a  +     + ++l +
  gi|91772750|ref|YP_565442.1| 295 ASGLILAIIVSFLADVIILkvyglEYSGSISALQILIWATSIM-FINILLSFTYISSGN--QGVMAKLTAFAAFFNIALNF 372
                                   3455666666666666644545667777777777777777777.334444444444443..33444444445556666888 PP

                 Polysacc_synt 158 iavflfldivaavlgavlaalvggivslavlrkkf.r.........prfvilslklvrellsfsaplti 216
                                   i++  f+ + +a++++++  lv  +++++ + k+  +         p        l+  l+   +++++
  gi|91772750|ref|YP_565442.1| 373 IFIPSFS-YNGAAISTMITELVVMVFGIYWINKNIcHkslfnegvyP--------LIGVLIILLFYTMF 432
                                   8888888.888888888888888888887777666543333222221........22222222222222 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 ?   -4.7   6.2         4   1.8e+04     122     132 ..      84      94 ..      14     106 .. 0.45
   2 ?   -4.8  13.1         4   1.8e+04      39     115 ..      85     171 ..      69     179 .. 0.60
   3 !    7.1   2.1    0.0012       5.5      60     116 ..     174     237 ..     172     266 .. 0.73
   4 ?    0.7   2.2      0.11   4.8e+02      68     114 ..     266     309 ..     257     319 .. 0.59
   5 !   55.6  23.9   1.3e-18   5.8e-15       1     141 [.     326     456 ..     326     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 4
               Polysacc_synt_C 122 alllavlvgal 132
                                   a+++++++  +
  gi|91772750|ref|YP_565442.1|  84 ATAIKIVLSLI 94 
                                   22222222222 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 4
               Polysacc_synt_C  39 alvklilnllli..plfgi.............vGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgiv 104
                                    ++k++l+l+ i   +f i             + a+i+ +++ l ++ + +y ++ ++ ++  l+  + ++++++lv+++v
  gi|91772750|ref|YP_565442.1|  85 TAIKIVLSLIAIflAFFTInlmdypistknalYLASIGLLITNLSAFGI-IYEIKLRMEYSA-LFSVTSRIIFLMLVLYGV 163
                                   4566666666665444444555556666555455566666665555544.477777777777.777778999999999998 PP

               Polysacc_synt_C 105 vylllllllgl 115
                                      l++ +l +
  gi|91772750|ref|YP_565442.1| 164 ---LQNSTLLF 171
                                   ...44444333 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0012
               Polysacc_synt_C  60 iatvlallvvavlnlyalrrllgikl....ellrrll....kpllaalvmgivvylllllllgll 116
                                   +a++ a +v  +l++++ +r +++++    +l++++l     ++la+++++i  + +  l+l++l
  gi|91772750|ref|YP_565442.1| 174 FASISADFVHNILMVVFSKRFVNVQFnfdyKLIKQILhealPIALASVFVMIY-FRVDILMLSFL 237
                                   7899999*******************999977777766653555555555554.33555555544 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.11
               Polysacc_synt_C  68 vvavlnlyalrrllgikl.ellrrllkpllaalvmgivvylllllllg 114
                                    ++ l+  + +  +++ + + ++++ k+l+a+ ++ ++   ++++l  
  gi|91772750|ref|YP_565442.1| 266 SMFPLMSKYFKESFNLFVySYVKSF-KYLFASGLILAI---IVSFLAD 309
                                   5555666666666666665434444.666666666666...4444443 PP

  == domain 5  score: 55.6 bits;  conditional E-value: 1.3e-18
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrll 81 
                                   +L+il++++ +++++++ls   ++ g q  ++k ++++a+++++ln+++ip+f+++Gaai+t++++lvv+v+ +y++++ +
  gi|91772750|ref|YP_565442.1| 326 ALQILIWATSIMFINILLSFTYISSGNQGVMAKLTAFAAFFNIALNFIFIPSFSYNGAAISTMITELVVMVFGIYWINKNI 406
                                   69******************************************************************************* PP

               Polysacc_synt_C  82 giklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                    +k  l++  + pl+ +l++ +  y++++l ++       +++l++ v +l+Y+++l+ +
  gi|91772750|ref|YP_565442.1| 407 CHKS-LFNEGVYPLIGVLIILLF-YTMFKLYVN-------NFILCA-VSILIYIGVLYGT 456
                                   ***9.788887888888888777.445555543.......566677.8999999888755 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8  26.4     2e-15   9.1e-12       2     291 ..      32     323 ..      31     325 .. 0.86
   2 ?   -2.8   1.8      0.65   2.9e+03     105     105 ..     374     374 ..     330     440 .. 0.61

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2e-15
               Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlgllialvlfllapliasfynqpel. 81 
                                   +AR L p+dFG  +++++++ ++  + d+G+ ++l+++   + +++  +     ++ ++++l+ ++la +  ++ + p+  
  gi|91772750|ref|YP_565442.1|  32 IARYLGPDDFGKFSFVFAFVYFFAFIPDLGIHNILVREAAKEPANAGILIGNATAIKIVLSLIAIFLAFFTINLMDYPISt 112
                                   69************************************9888886665555555555555555555555555666777641 PP

               Polysacc_synt_3  82 vtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlask 162
                                   ++ l ++++ l+++ ls+    +++++l+ +  + ++++s ++ +++ ++ +l   ++  +v+ ++ ++++  +l++++sk
  gi|91772750|ref|YP_565442.1| 113 KNALYLASIGLLITNLSAFGI-IYEIKLRMEYSALFSVTSRIIFLMLVLYGVLQNSTLLFFVFASISADFVHNILMVVFSK 192
                                   678899999999999999876.678999999999999*************************************9999999 PP

               Polysacc_synt_3 163 wr..prlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsviakVlfPalS 241
                                       ++++f+ k +k++++  l + l+++  +++ ++d l+   + ++ ++GlYs a+r++++ +  + s++ + +fP +S
  gi|91772750|ref|YP_565442.1| 193 RFvnVQFNFDYKLIKQILHEALPIALASVFVMIYFRVDILMLSFLKNDVDVGLYSAAYRFTEAFI-FVPSILMTSMFPLMS 272
                                   7622556666788************************************************9987.789999999****** PP

               Polysacc_synt_3 242 rlqddkkkl.relylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                   +  +++ +l   +y k+++ +    l +a+++ ++a+ ++  ++G +++ +
  gi|91772750|ref|YP_565442.1| 273 KYFKESFNLfVYSYVKSFKYLFASGLILAIIVSFLADVIILKVYGLEYSGS 323
                                   *99998776267899999999999999999999************999876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.65
               Polysacc_synt_3 105 l 105
                                   +
  gi|91772750|ref|YP_565442.1| 374 F 374
                                   1 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  49.4   3.6e-05      0.16      36     437 ..      55     440 ..      54     453 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.6e-05
                          MurJ  36 aFvPvlaeak..kkdeekaaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvsls 114
                                   aF+P l  ++    ++ k+ + ++ +++ ++++ +++ li+i++a + i+l+++++     + a     +l+   ll++  
  gi|91772750|ref|YP_565442.1|  55 AFIPDLGIHNilVREAAKEPANAGILIGNATAIKIVLSLIAIFLAFFTINLMDYPI---STKNA----LYLASIGLLITNL 128
                                   6777776666433455555566778899999999999*****************99...22233....2334445555555 PP

                          MurJ 115 avfgavLnarkkFfapafsPvllNvsvIltl.lllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkprfafrd 194
                                   + fg +   +     + +s++++  s I++l l+l+ +l+   ++ L + v++   + ++ ++ +++  +  ++  f+f  
  gi|91772750|ref|YP_565442.1| 129 SAFGIIYEIKL---RMEYSALFSVTSRIIFLmLVLYGVLQ---NSTLLFFVFASISADFVHNILMVVFSKRFVNVQFNFDY 203
                                   55666777775...56777776666666665155666666...45555999****************************** PP

                          MurJ 195 eglkkflklllptllgvsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvs.istvlLPrlSrsakekdedev 274
                                   + +k++l  +lp  l++   ++ + vd+ + sfl+  +   l+ a   ++ +  +f+ s ++t ++P +S+ +ke  +  +
  gi|91772750|ref|YP_565442.1| 204 KLIKQILHEALPIALASVFVMIYFRVDILMLSFLKNDVDVGLYSAAYRFTEA-FIFVPSiLMTSMFPLMSKYFKESFNL-F 282
                                   ********************************99998887776665555444.45655526899******999988766.7 PP

                          MurJ 275 rdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPv 355
                                        ++ + +++  + +++++ +l++ i+  ++  G   e++  + a  + ++a +++++    ll+ ++ +++++   +
  gi|91772750|ref|YP_565442.1| 283 VYSYVKSFKYLFASGLILAIIVSFLADVIILKVY--G--LEYSGSISALQILIWATSIMFIN--ILLSFTYISSGNQGVMA 357
                                   77888999**************************..4..35555566666788999999875..589999*********** PP

                          MurJ 356 kislislvlnillsllllpplgvvglalatslsaliglvllyvllrkrlk..lteargiktflak...lvvllalaavvil 431
                                   k++ ++++ ni+l+++++p+++++g a++t +  l+ +v+ ++ ++k          ++   ++    ++++l++  +  l
  gi|91772750|ref|YP_565442.1| 358 KLTAFAAFFNIALNFIFIPSFSYNGAAISTMITELVVMVFGIYWINKNIChkS----LFNEGVYPligVLIILLFYTMFKL 434
                                   ***********************************************955321....222222221123555555555555 PP

                          MurJ 432 llsslt 437
                                   +++++ 
  gi|91772750|ref|YP_565442.1| 435 YVNNFI 440
                                   555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2721.96
//
Query:       gi|91772751|ref|YP_565443.1|  [L=1126]
Description: Ig [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   30.6   6.7    4.2e-07   30.6   6.7    6.3  7  Big_9       Bacterial Ig domain
    4.9e-07   29.8   1.2    4.9e-07   29.8   1.2    5.1  4  He_PIG      Putative Ig domain
    7.4e-07   29.3   1.3    3.6e-06   27.1   1.3    2.3  1  Dockerin_1  Dockerin type I domain
    6.7e-05   22.8   0.9    6.7e-05   22.8   0.9    6.2  6  Cadherin_5  Cadherin-like domain
     0.0028   17.5   1.0     0.0028   17.5   1.0    5.4  5  PKD         PKD domain
     0.0086   15.8   6.8       0.79    9.5   0.1    5.0  5  PKD_3       PKD-like domain
  ------ inclusion threshold ------
      0.011   15.7   0.2         47    4.1   0.0    4.1  4  BiPBP_C     Penicillin-Binding Protein C-terminus Family
      0.036   14.2   7.1      0.061   13.5   0.1    4.2  4  DUF5011     Domain of unknown function (DUF5011)


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 ?   -1.8   0.2       2.5   5.6e+03      33      71 ..     164     205 ..     132     227 .. 0.57
   2 ?   -2.5   0.2       4.1   9.2e+03      25      48 ..     351     381 ..     324     399 .. 0.49
   3 ?   -3.4   3.2       7.5   1.7e+04      76      76 ..     516     516 ..     431     559 .. 0.57
   4 ?    2.4   1.0      0.12   2.6e+02      61      90 .]     696     725 ..     634     725 .. 0.88
   5 !   10.6   5.5   0.00032      0.72      10      88 ..     747     823 ..     742     825 .. 0.76
   6 !   30.6   6.7   1.9e-10   4.2e-07       3      88 ..     971    1054 ..     969    1055 .. 0.88
   7 ?   -4.2   0.2         8   1.8e+04      52      66 ..    1094    1108 ..    1080    1117 .. 0.51

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.5
                         Big_9  33 dtdpdgdaltvtsltvtlvta...panGtvtinadgtltytp 71 
                                   dtd+++  ++ ts +++++++   + +  +  n++g +ty+ 
  gi|91772751|ref|YP_565443.1| 164 DTDINNIEMESTSGSLEIADGnnsTVHEIALYNTSGFYTYDL 205
                                   333333333333333332222333555555556666677765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                         Big_9  25 tedsv....la...ndtdpdgdaltvtsltv 48 
                                   ++++v    la   +  d dg  ++v+++t+
  gi|91772751|ref|YP_565443.1| 351 SQQNVsdiyLAniyQEGDRDGMGISVQNFTL 381
                                   3333344443311123344555555555544 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.5
                         Big_9  76 s 76 
                                   +
  gi|91772751|ref|YP_565443.1| 516 A 516
                                   2 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.12
                         Big_9  61 inadgtltytpnagfsgtdsftYtvsDgsg 90 
                                   + adg  + t + ++ gt+++ +t+s+++g
  gi|91772751|ref|YP_565443.1| 696 VIADGVMSTTVDWNEPGTYNIRFTASNDNG 725
                                   4469999999999*************9987 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00032
                         Big_9  10 pvndaPvavdds...vtv.tedsvla...ndtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftY 83 
                                   +vn aPv+++      tv +e++v++    ++d+dgd lt+         + ++ tv+ +    +++t +++  g  ++ +
  gi|91772751|ref|YP_565443.1| 747 SVNNAPVITTFGpanNTVfQEGNVINigvIASDADGDELTY-----L--LKVDGATVSTT--SGYVWTTDSSNIGAHTIGV 818
                                   499*****99555554443899995555699*******973.....2..24455566666..459**************** PP

                         Big_9  84 tvsDg 88 
                                    vsDg
  gi|91772751|ref|YP_565443.1| 819 VVSDG 823
                                   ****9 PP

  == domain 6  score: 30.6 bits;  conditional E-value: 1.9e-10
                         Big_9    3 tvtvtvtpvndaPvavdds.vtvtedsv...landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsg 77  
                                    tvt t+  +++aPv ++    tv+e ++   +++++d+dgd+l     t++++  p + ++    +g +++tp++g+ g
  gi|91772751|ref|YP_565443.1|  971 TVTDTMVVIDTAPVLNSIGdKTVDEENAltfVTSASDADGDSL-----TYSATGLPVGASFDTA-SGAFSWTPSEGQEG 1043
                                    788899999********8779999999967777*********9.....5778888888888776.99************ PP

                         Big_9   78 tdsftYtvsDg 88  
                                    t+ + + vsD+
  gi|91772751|ref|YP_565443.1| 1044 TYAIAFEVSDS 1054
                                    **********6 PP

  == domain 7  score: -4.2 bits;  conditional E-value: 8
                         Big_9   52 tapanGtvtinadgt 66  
                                    t +a+    +n+dg 
  gi|91772751|ref|YP_565443.1| 1094 TDGAGTDQDVNQDGV 1108
                                    333444444444443 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.032        73      21      47 ..     657     684 ..     653     686 .. 0.87
   2 !    7.6   0.1    0.0019       4.2      22      48 ..     699     724 ..     698     725 .. 0.88
   3 ?   -4.4   3.5         8   1.8e+04      20      47 ..     797     823 ..     793     824 .. 0.78
   4 !   29.8   1.2   2.2e-10   4.9e-07       1      47 [.    1014    1054 ..    1014    1056 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.032
                        He_PIG  21 stGtitGtpdqtvapG.sytftVtatdg 47 
                                    tG++ Gt + +++ G s +f Vta ++
  gi|91772751|ref|YP_565443.1| 657 ITGAFPGTSSRSQELGsSTDFSVTADQS 684
                                   58999999999999999********875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
                        He_PIG  22 tGtitGtpdqtvapGsytftVtatdgs 48 
                                   +G  + t+d + +pG+y+++ ta++ +
  gi|91772751|ref|YP_565443.1| 699 DGVMSTTVDWN-EPGTYNIRFTASNDN 724
                                   78889999999.***********9876 PP

  == domain 3  score: -4.4 bits;  conditional E-value: 8
                        He_PIG  20 sstGtitGtpdqtvapGsytftVtatdg 47 
                                   s+t  + +t d++ + G  t+ V ++dg
  gi|91772751|ref|YP_565443.1| 797 STTSGYVWTTDSS-NIGAHTIGVVVSDG 823
                                   4555677887877.88999999999997 PP

  == domain 4  score: 29.8 bits;  conditional E-value: 2.2e-10
                        He_PIG    1 tytlttpgsngLPsGLtLdsstGtitGtpdqtvapGsytftVtatdg 47  
                                    ty++t     gLP G ++d+++G++++tp+ + + G+y +   ++d+
  gi|91772751|ref|YP_565443.1| 1014 TYSAT-----GLPVGASFDTASGAFSWTPSEG-QEGTYAIAFEVSDS 1054
                                    899*5.....**********************.66*****9999997 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   1.3   1.6e-09   3.6e-06       3      56 ..    1073    1120 ..    1071    1122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.6e-09
                                    ETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHH CS
                    Dockerin_1    3 DVNgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallviny 56  
                                    D+N+D  Vn lD++l+ + +       ++  g+  DvN+DG vn  D++lv ++
  gi|91772751|ref|YP_565443.1| 1073 DINRDCAVNILDITLVSQKIG------TDGAGTDQDVNQDGVVNIQDLTLVAQH 1120
                                    9********************......89999999***************9876 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         3   6.7e+03      35      57 ..     164     181 ..     128     205 .. 0.57
   2 ?   -1.1   0.1      0.85   1.9e+03      29      58 ..     324     353 ..     317     362 .. 0.72
   3 ?    0.2   0.1      0.33   7.5e+02      53      89 ..     618     654 ..     577     659 .. 0.76
   4 ?    1.2   0.2      0.17   3.7e+02      53      86 ..     704     738 ..     668     749 .. 0.70
   5 ?    3.0   3.1     0.043        97      33      91 ..     777     830 ..     748     836 .. 0.66
   6 !   22.8   0.9     3e-08   6.7e-05       4      97 ..     982    1066 ..     979    1067 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3
                    Cadherin_5  35 DvdgdtLsvssltadaenGtvvd 57 
                                   D+d +     ++++++++G++  
  gi|91772751|ref|YP_565443.1| 164 DTDIN-----NIEMESTSGSLEI 181
                                   44433.....3333333444433 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.85
                    Cadherin_5  29 LLanasDvd.gdtLsvssltadaenGtvvdn 58 
                                   L a+ sD    ++++++++  ++++G v ++
  gi|91772751|ref|YP_565443.1| 324 LTAGLSDSPsTENITITNVY-SKNSGIVSQQ 353
                                   5588999885677******4.5557777654 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.33
                    Cadherin_5  53 GtvvdngdGtftftpeanynGevtlsYtvsDgeggtt 89 
                                   + +v +++G   +   +n nG +t +++++ g+g++ 
  gi|91772751|ref|YP_565443.1| 618 AWTVPDENGHTIIFEGTNANGIITKTWDINGGSGSVL 654
                                   3456778887777788899999999999999988765 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.17
                    Cadherin_5  53 GtvvdngdGtftftpe.anynGevtlsYtvsDgeg 86 
                                    tv  n+ Gt+ +  + +n nGev+ s++v  +eg
  gi|91772751|ref|YP_565443.1| 704 TTVDWNEPGTYNIRFTaSNDNGEVSRSWEVVSNEG 738
                                   35666888888887542688999998888876665 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.043
                    Cadherin_5  33 asDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggttta 91 
                                   asD+dgd+L+   l++   +G +v+   G +++t ++   G+ t+   vsDg  ++t++
  gi|91772751|ref|YP_565443.1| 777 ASDADGDELTYL-LKV---DGATVSTTSG-YVWTTDSSNIGAHTIGVVVSDGVEQVTDQ 830
                                   799****99853.322...3677776666.77788888889999*******97555443 PP

  == domain 6  score: 22.8 bits;  conditional E-value: 3e-08
                    Cadherin_5    4 aPvvssevtlaagseDtaltitaaqLLanasDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvs 82  
                                    aPv++s +  ++++e++alt+     ++ asD+dgd+L+ s+  +    G   d + G f++tp +  +G+  + ++vs
  gi|91772751|ref|YP_565443.1|  982 APVLNS-IGDKTVDEENALTF-----VTSASDADGDSLTYSATGLPV--GASFDTASGAFSWTPSEGQEGTYAIAFEVS 1052
                                    555553.33344555555554.....589*********999987777..****************************** PP

                    Cadherin_5   83 Dgeggtttatasltv 97  
                                    D    t ++t+s+ v
  gi|91772751|ref|YP_565443.1| 1053 DSY-LTDSETISIAV 1066
                                    *96.66777777666 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.78   1.8e+03       5      48 ..     455     527 ..     451     531 .. 0.67
   2 ?    0.4   0.1      0.27     6e+02      24      36 ..     613     628 ..     605     655 .. 0.73
   3 !   17.5   1.0   1.3e-06    0.0028       6      70 ..     667     728 ..     662     729 .. 0.83
   4 !   10.2   1.8   0.00023      0.51      18      70 ..     777     828 ..     760     829 .. 0.91
   5 ?    1.2   0.4      0.15   3.3e+02      18      65 ..    1005    1054 ..     995    1056 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.78
                                   -S--BSSEEEEEEEES.-........SS-SEEEEE--SS.....................--EEEEETTEEEE CS
                           PKD   5 ptvlvpgatvaftaavpd........ganvtysWdfgdg.....................svvqvlseptvth 48 
                                      +++gat+a +++v++        g++ +   ++ +g                     s+++++ ++t+t+
  gi|91772751|ref|YP_565443.1| 455 NDIPAAGATIAVENTVDSshsslngfGNDKSMFLTTSNGhtelpnenrsespampeyyksSAGTQTFSHTATI 527
                                   5567889999999999555556666666666666666667766666666666666666666666666666666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                                   S-SEEEEE--SS...- CS
                           PKD  24 anvtysWdfgdg...s 36 
                                   +++ y W++ d+   +
  gi|91772751|ref|YP_565443.1| 613 TSLEYAWTVPDEnghT 628
                                   5678999999964331 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.3e-06
                                   S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD   6 tvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                   ++ + g +  f+ +  d + ++  W+ +d  v ++++ + +t  +++pG+Y+++ tasn+ g ++
  gi|91772751|ref|YP_565443.1| 667 RSQELGSSTDFSVTA-DQSMTSMVWYKND-AVIADGVMS-TTVDWNEPGTYNIRFTASNDNGEVS 728
                                   556678888888888.99***********.666666665.699*****************99876 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00023
                                   EES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD  18 aavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                   a+ +dg+++ty+  ++   +v ++s+   t   ++ G +++ v++s+ v+ +t
  gi|91772751|ref|YP_565443.1| 777 ASDADGDELTYLLKVDG-ATVSTTSGYVWTTDSSNIGAHTIGVVVSDGVEQVT 828
                                   4559***********99.*******************************9887 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.15
                                    EES..-SS-SEEE...EE--SS--EEEEETTEEEEEE-S..SEEEEEEEEEE-S CS
                           PKD   18 aav.pdganvtys...WdfgdgsvvqvlseptvthtYls..pGeYeVtvtasna 65  
                                    a + +dg+++tys     +g     +++ +  ++ t+++  +G+Y +   +s++
  gi|91772751|ref|YP_565443.1| 1005 A-SdADGDSLTYSatgLPVGA---SFDTASGAFSWTPSEgqEGTYAIAFEVSDS 1054
                                    3.3589999999988888888...888889999999998889999999999997 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3      0.12   2.7e+02      34      68 .]     599     635 ..     589     635 .. 0.77
   2 !    9.5   0.1   0.00035      0.79      35      68 .]     688     722 ..     676     722 .. 0.84
   3 ?    1.7   0.0     0.097   2.2e+02      30      56 ..     780     808 ..     752     821 .. 0.81
   4 ?    1.9   0.0     0.085   1.9e+02      18      55 ..     967    1004 ..     965    1008 .. 0.90
   5 ?   -2.1   0.0       1.5   3.4e+03      51      67 ..    1036    1052 ..    1030    1053 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.12
                         PKD_3  34 a.faWtieGk.ivsteptytfteeelgsyevtleven 68 
                                   +  +W+++G+ + st  +y  t      +++++e +n
  gi|91772751|ref|YP_565443.1| 599 TsMKWIVDGEtKQSTSLEYAWTVPDENGHTIIFEGTN 635
                                   3589*****9779999999999888888888887665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00035
                         PKD_3  35 faWtieGkivste.ptytfteeelgsyevtleven 68 
                                     W+ +++++ +  ++ t  ++e g+y+++++++n
  gi|91772751|ref|YP_565443.1| 688 MVWYKNDAVIADGvMSTTVDWNEPGTYNIRFTASN 722
                                   78******999874789999*************98 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.097
                         PKD_3  30 aenaa..faWtieGkivsteptytfteee 56 
                                   a++++  ++ +++G+ vst   y+ t ++
  gi|91772751|ref|YP_565443.1| 780 ADGDEltYLLKVDGATVSTTSGYVWTTDS 808
                                   555555688899*********99998765 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.085
                         PKD_3   18 greltiaPtvenaenaafaWtieGkivsteptytftee 55  
                                    g+++t++ t+  ++ a  + +i +k v +e+ +tf+ +
  gi|91772751|ref|YP_565443.1|  967 GTPYTVTDTMVVIDTAPVLNSIGDKTVDEENALTFVTS 1004
                                    88999999999999999999***************976 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 1.5
                         PKD_3   51 tfteeelgsyevtleve 67  
                                    t +e + g+y + +ev+
  gi|91772751|ref|YP_565443.1| 1036 TPSEGQEGTYAIAFEVS 1052
                                    55678899****99997 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.057   1.3e+02      40      72 ..     595     627 ..     581     631 .. 0.70
   2 ?    3.3   0.0     0.038        85      31      86 ..     673     729 ..     654     733 .. 0.74
   3 ?    4.1   0.0     0.021        47      15      82 ..     757     823 ..     745     827 .. 0.80
   4 ?   -3.0   0.0       3.4   7.6e+03      45      71 ..    1012    1040 ..     988    1047 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.057
                       BiPBP_C  40 rggeaplrWlldgeplaetkrgrelawqpepGr 72 
                                   +    +++W++dge  ++t+ + +++++ e+G+
  gi|91772751|ref|YP_565443.1| 595 DEDMTSMKWIVDGETKQSTSLEYAWTVPDENGH 627
                                   4444589********977766666665557775 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.038
                       BiPBP_C  31 krqrlqlkarggeaplrWlldgeplaetkrgrelawqpepGrhrL..tvvDaaGrvdd 86 
                                   +   + ++a+++  ++ W+ +++++a +  + ++ w  epG++ +  t+ +++G+v++
  gi|91772751|ref|YP_565443.1| 673 SSTDFSVTADQSMTSMVWYKNDAVIADGVMSTTVDWN-EPGTYNIrfTASNDNGEVSR 729
                                   566778889999889**********998888888887.56655541166788887765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.021
                       BiPBP_C  15 afPadGailaldpdipkrqrlqlkarggeaplrWlldgeplaetkrgrelawqp.epGrhrLtvvDaaG 82 
                                    +Pa++++++  + i + + ++  a+g e ++ + +dg+ + +t++g  ++ ++ + G h++ vv  +G
  gi|91772751|ref|YP_565443.1| 757 FGPANNTVFQEGNVI-NIGVIASDADGDELTYLLKVDGATV-STTSGYVWTTDSsNIGAHTIGVVVSDG 823
                                   479999999999888.67777777777777888889*****.8888888888889*******9987666 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3.4
                       BiPBP_C   45 plrWlldgepl.aet.krgrelawqpepG 71  
                                    +l+    g p+ a+  +++ +++w+p++G
  gi|91772751|ref|YP_565443.1| 1012 SLTYSATGLPVgASFdTASGAFSWTPSEG 1040
                                    66666666666433313456788999665 PP

>> DUF5011  Domain of unknown function (DUF5011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.6   3.6e+03      13      44 ..     433     473 ..     428     475 .. 0.52
   2 ?   13.5   0.1   2.7e-05     0.061      37      62 ..     702     727 ..     684     733 .. 0.83
   3 ?   -2.2   0.1         2   4.6e+03      20      44 ..     773     799 ..     757     801 .. 0.74
   4 ?    1.6   0.1      0.14   3.1e+02      46      61 ..    1042    1057 ..    1039    1063 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                                   TT-------EEEEETT......EE-G...GG-EEES---TT CS
                       DUF5011  13 vgetYkepGatatddd......gdit...skvkvtgsVdts 44 
                                   + +tY+ + +t ++ d      +di    +++ v+++Vd s
  gi|91772751|ref|YP_565443.1| 433 YQTTYHKNHVTHYYSDlfvtysNDIPaagATIAVENTVDSS 473
                                   55555555555554431111113333333688888888876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.7e-05
                                   EES---TTS-EEEEEEEEEE-TTSEE CS
                       DUF5011  37 vtgsVdtskvGtYtitYtvtdssgne 62 
                                   ++ +Vd +++GtY+i  t+++ +g+ 
  gi|91772751|ref|YP_565443.1| 702 MSTTVDWNEPGTYNIRFTASNDNGEV 727
                                   5779****************998864 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                   --EEEEETTE.E-GGG-EEES.---TT CS
                       DUF5011  20 pGatatdddg.ditskvkvtg.sVdts 44 
                                    G+ a+d dg ++t  +kv+g +V t+
  gi|91772751|ref|YP_565443.1| 773 IGVIASDADGdELTYLLKVDGaTVSTT 799
                                   589999986526999999999777665 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.14
                                    -EEEEEEEEEE-TTSE CS
                       DUF5011   46 vGtYtitYtvtdssgn 61  
                                     GtY i  +v+ds+ +
  gi|91772751|ref|YP_565443.1| 1042 EGTYAIAFEVSDSYLT 1057
                                    7***********9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 6968.45
//
Query:       gi|91772752|ref|YP_565444.1|  [L=226]
Description: cellulosome anchoring protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   52.0   1.7    1.4e-13   51.3   1.4    1.5  1  Cohesin   Cohesin domain


Domain annotation for each model (and alignments):
>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   1.4   7.9e-18   1.4e-13       6     128 ..      58     178 ..      53     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 7.9e-18
                                   SEEEE.-TTSEEEEEEEEESECTTEEEEEEEEEE.TTTEEEEEEEE-TTSSSGG.HCEEEEEECGTTEEEEEEE.TTSSST CS
                       Cohesin   6 dkvsa.kvGdtvtvpvtvsnvskkvaaaqftikYDpavlevvsvkaGsivknss.vnfgsnlleepgkikflfldlaslgs 84 
                                   ++v + ++G+t++v v vs   + +a++qf++ +D++++++ sv++G+++k s    f  +  ++pg +  +  + + lg+
  gi|91772752|ref|YP_565444.1|  58 GEVLNvAPGETFNVDVFVSPDVD-IAGMQFDLLFDSSKFQIDSVTEGNLFKQSGmGTFFVAASVTPGLLDNT--YGCILGN 135
                                   5666669****************.**************************55541456677788********..88899** PP

                                   TCBEESSEEEEEEEEEESTTS-TCEEEEEEEEEEEEEETTSEBE CS
                       Cohesin  85 sgiaekdgvlatitfkvkskaaegttaikisdtlsfgdgeekei 128
                                    ++  + +++atit ++++ a   ++ i+ +  +s++ g+ +++
  gi|91772752|ref|YP_565444.1| 136 AAVL-TPANFATITITANEHASGRSAFILKDVIVSDPKGNAVNV 178
                                   ****.****************65588888888888888866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1538.10
//
Query:       gi|91772753|ref|YP_565445.1|  [L=132]
Description: hypothetical protein Mbur_0730 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   18.9   0.0     0.0024   17.9   0.0    1.5  1  PspB            Phage shock protein B
     0.0097   15.6   1.4      0.015   15.0   1.4    1.3  1  Tetraspanin     Tetraspanin family
  ------ inclusion threshold ------
      0.011   14.4   0.9      0.013   14.2   0.9    1.1  1  Ndc1_Nup        Nucleoporin protein Ndc1-Nup
      0.063   12.8   0.2       0.11   12.0   0.2    1.4  1  Trimer_CC       Trimerisation motif
      0.067   13.2   1.0      0.086   12.9   1.0    1.1  1  G3P_acyltransf  Glycerol-3-phosphate acyltransferase
      0.096   13.0   1.2       0.13   12.5   1.2    1.2  1  Tup_N           Tup N-terminal
       0.17   11.5   1.6       0.23   11.1   1.6    1.2  1  DUF2968         Protein of unknown function (DUF2968)


Domain annotation for each model (and alignments):
>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.5e-07    0.0024       9      60 ..      61     121 ..      55     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.5e-07
                          PspB   9 liifvlfVapiWLiLHYrskkkrskglsae.........dekrLeellekAekleeRietL 60 
                                     + +++Va+i+++L Y+    +++++s+e           ++L +++e+ +++++ i+ L
  gi|91772753|ref|YP_565445.1|  61 FLVGMIVVAFIGMWLTYVYIFPSKQKFSQEqaikdgrspMYDKLVQMHEEMHQMQSTIDDL 121
                                   5799**************9888888888887888778777789999999999999988776 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.4   5.9e-06     0.015      50     142 ..      17     124 ..       4     126 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.9e-06
                                   ...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXX....XXXXXXXXXXXXXXX.XXX--HHH........HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxx....xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  50 aillivvGvllfllgflGcigalkenk.........cllltfs....llllvlfllelaagi.lgfvfsdkargkvseiin 116
                                     lli+vG ++fl+++l ++++ + ++         +   +f     +l+ +++++++++ + ++++f +k++   ++ i+
  gi|91772753|ref|YP_565445.1|  17 GGLLILVGETMFLFSLLNFLMITRIQYyssndtlfrT---LFPeytfFLVGMIVVAFIGMWLtYVYIFPSKQKFSQEQAIK 94 
                                   4569**************9999998888888874442...33333323333444444444444667777774333344577 PP

                                   HHHHHHHHHHHHHHHH.T...HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx.x...xxxxxxxxx RF
                   Tetraspanin 117 naievkyrddldlkkc.q...nlldslqkk 142
                                   +  +  y++  +  +      +++d lq++
  gi|91772753|ref|YP_565445.1|  95 DGRSPMYDKLVQMHEEmHqmqSTIDDLQEQ 124
                                   766555555555433222455777777776 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   5.2e-06     0.013      47     114 ..      19      90 ..       5     106 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-06
                      Ndc1_Nup  47 llflsl.lpilvlrkaqlhvgprttssrlstllaslfslqtletllvyllSal..lfaevyiw.slpedarl 114
                                   ll l++  + l+   ++l++++  + s   tl+++lf+  t+ +++ ++++++  +++ vyi+ s ++ ++ 
  gi|91772753|ref|YP_565445.1|  19 LLILVGeTMFLFSLLNFLMITRIQYYSSNDTLFRTLFPEYTFFLVGMIVVAFIgmWLTYVYIFpSKQKFSQE 90 
                                   4444445444444444444443333344589999*******************9999999998644433333 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   4.4e-05      0.11      15      42 ..      98     125 ..      88     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                                   XXXXXX--HHHHHHHHHHHHHHHHHHHH CS
                     Trimer_CC  15 tpssdavSRLEEelrkLqatVQelQkRL 42 
                                    p  d +  + Ee+ ++q t+ +lQ+ +
  gi|91772753|ref|YP_565445.1|  98 SPMYDKLVQMHEEMHQMQSTIDDLQEQV 125
                                   5778888899***************976 PP

>> G3P_acyltransf  Glycerol-3-phosphate acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.0   3.3e-05     0.086      88     150 ..      10      73 ..       7      88 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                                   -SHHHHHHHHHHHH....HHHHHHHHHHHHHHH--HHHHHHHHHHHHHH.HH.......HH..HHHHHH CS
                G3P_acyltransf  88 KGvatalGvllaldl.lllllallvfllvllltryvslaslvaalllpllllll.....llllllllal 150
                                   K+ +t lG ll+l    ++l+ ll fl+++ +  y+s  +l+  +l+p ++++l     +    +++++
  gi|91772753|ref|YP_565445.1|  10 KATSTRLGGLLILVGeTMFLFSLLNFLMITRIQYYSSNDTLFR-TLFPEYTFFLvgmivV----AFIGM 73 
                                   899999**99999552555556889999989888888888865.5565444433343211....11111 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.2   5.2e-05      0.13      21      55 ..      91     125 ..      84     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                         Tup_N  21 sslkaqkdeyelkiqsqiqElqqirqtlyeLeeah 55 
                                   + +k  +  +  k+ +  +E++q+++t+ +L+e+ 
  gi|91772753|ref|YP_565445.1|  91 QAIKDGRSPMYDKLVQMHEEMHQMQSTIDDLQEQV 125
                                   45666666677789999***************985 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.6     9e-05      0.23     134     177 ..      88     131 ..      83     132 .] 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9e-05
                       DUF2968 134 qQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaq 177
                                   +Qeqa+++  + + ++  +++++ +++q+ +++lq+q+ +L ++
  gi|91772753|ref|YP_565445.1|  88 SQEQAIKDGRSPMYDKLVQMHEEMHQMQSTIDDLQEQVGTLTRD 131
                                   79*************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1749  (0.0975515); expected 358.6 (0.02)
Passed bias filter:                     1039  (0.0579508); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 924.42
//
Query:       gi|91772754|ref|YP_565446.1|  [L=287]
Description: phosphoesterase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-06   27.0   0.6    7.5e-06   26.6   0.6    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    0.00037   20.7   0.0    0.00056   20.1   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
        0.1   12.6   0.2        1.3    9.0   0.1    2.2  2  RadC           RadC-like JAB domain
       0.17   11.1   0.0       0.31   10.3   0.0    1.3  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.6   1.7e-09   7.5e-06       3     173 ..      22     198 ..      20     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.7e-09
                                   EEEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS...HHHHHHHHH..HHHHHHH...T CS
                   Metallophos   3 ilvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg...dlekellel..laalvky...p 64 
                                    lv++D+Hl           +  + q+++ l+ +  l ++  pd ++l+GD+ +     +    ++e   + ++++    +
  gi|91772754|ref|YP_565446.1|  22 SLVLADIHLgiewdlyqsgfS-IPSQIEQRLERIMGLVEQTSPDHIILLGDIKHNVpqvS----WQERdeIPYFISTlaeR 97 
                                   699*************88852.3333333333333445666**********777764332....33331344444446667 PP

                                   SEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE...CEEE..THHHHHHHHHHHS CS
                   Metallophos  65 ipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg...spel..lvsldklgslnle 140
                                     v + +GNH+    +  ++   +          ++v+ + p  ++++g   v   hG+   s+e+   +++  +++ +  
  gi|91772754|ref|YP_565446.1|  98 ATVDIFPGNHD----GGIEFLLPK---------GCDVKLHSPRGAIIDG---VGYFHGHtwpSIEIlsAEQVIVAHNHPTV 162
                                   778999*****....333332222.........2677778888887777...77777774444444553333333333444 PP

                                   CHHHHCC.....HHHHHHHHHHTTCSEEEEEESSESS...C CS
                   Metallophos 141 leapepg.....dewlkdlekrekadwvivlgHsply...r 173
                                   + ++  g     + wlk      + +  +++ H  ++   +
  gi|91772754|ref|YP_565446.1| 163 RFTDAMGysvveQVWLKT-----HFKKEVFVDHFKNSfldE 198
                                   444444455666666666.....555555555555555544 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 !   20.1   0.0   1.3e-07   0.00056       4     103 ..      23     163 ..      21     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-07
                 Metallophos_2   4 aiiSDlH................snldaleavlealkevgvdaiihaGDleeeep...........evleellelapvlaV 57 
                                   ++++D+H                +  ++le+++  ++++++d+ii++GD++   p            ++ +l e+a v + 
  gi|91772754|ref|YP_565446.1|  23 LVLADIHlgiewdlyqsgfsipsQIEQRLERIMGLVEQTSPDHIILLGDIKHNVPqvswqerdeipYFISTLAERATVDIF 103
                                   6788888888888888888888655678899999***************722222456666654434888888888***** PP

                 Metallophos_2  58 rGNnD...........eevveedvlreaaelgtdl....peeaelelagekvlliHgdpl.g 103
                                   +GN+D           +  + + +++   ++g  +    p+ + l    e+v + H +p  +
  gi|91772754|ref|YP_565446.1| 104 PGNHDggiefllpkgcDVKLHSPRGAIIDGVGYFHghtwPSIEIL--SAEQVIVAHNHPTvR 163
                                   *****8887777776433355555666555555553222333333..344577777775554 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.089     4e+02      86     109 ..      46      69 ..      42      85 .. 0.83
   2 ?    9.0   0.1   0.00029       1.3      63      75 ..     149     161 ..     146     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.089
                                   HHHHHHHHHHHHHT-EEEEEEEEE CS
                          RadC  86 eltkrlkealkllgiellDhiIig 109
                                   ++ +rl++++ l++ +  DhiI+ 
  gi|91772754|ref|YP_565446.1|  46 QIEQRLERIMGLVEQTSPDHIILL 69 
                                   5679999***************86 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00029
                                   T-SEEEEEEE-TT CS
                          RadC  63 nAaavilaHnhPs 75 
                                   +A++vi+aHnhP 
  gi|91772754|ref|YP_565446.1| 149 SAEQVIVAHNHPT 161
                                   799*********7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.9e-05      0.31      19      46 ..      49      75 ..      43      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.9e-05
                                  GGHHHHHHHHHHH--SEEEEES-----H CS
                 Metallophos_3 19 ellerlveviedkdpDllvlvGdlvkae 46
                                  ++ler+++++e+ +pD ++l+Gd+ + +
  gi|91772754|ref|YP_565446.1| 49 QRLERIMGLVEQTSPDHIILLGDIKH-N 75
                                  589*********************44.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2105.83
//
Query:       gi|91772755|ref|YP_565447.1|  [L=944]
Description: DEAD/DEAH box helicase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-33  115.2   0.0    7.2e-33  114.0   0.0    1.7  2  DEAD_assoc       DEAD/H associated
    2.2e-30  105.7   0.0    5.2e-30  104.5   0.0    1.6  1  DEAD             DEAD/DEAH box helicase
    1.3e-20   73.8   0.1      1e-19   70.9   0.0    2.5  3  Helicase_C       Helicase conserved C-terminal domain
    8.1e-08   32.4   0.0    1.5e-07   31.6   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.012   14.4   0.0      0.021   13.6   0.0    1.3  1  SNF2_N           SNF2 family N-terminal domain
      0.025   15.1   0.0      0.078   13.5   0.0    1.8  1  ANAPC2           Anaphase promoting complex (APC) subunit 2
      0.051   12.4   0.0      0.098   11.4   0.0    1.3  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
       0.17   11.4   0.2       0.69    9.5   0.0    2.2  3  AAA_25           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 ?   -3.7   0.0       3.8   8.5e+03     159     182 ..     433     456 ..     432     462 .. 0.77
   2 !  114.0   0.0   3.2e-36   7.2e-33       1     190 [.     613     784 ..     613     785 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.8
                    DEAD_assoc 159 qlDlerlaellrriaageirvvev 182
                                   +l le+l++++++i + ++ ++e 
  gi|91772755|ref|YP_565447.1| 433 DLSLEQLKRVIEQITEYRMVWREE 456
                                   577899999999999999888875 PP

  == domain 2  score: 114.0 bits;  conditional E-value: 3.2e-36
                    DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellell 81 
                                   lP+++t++vE   +      ++++s+fG++vne+l+ ++++ l++rfg +v+  +++++i l+lp + ++ l+++e++  l
  gi|91772755|ref|YP_565447.1| 613 LPDNDTIVVEDEGE-----AVIINSCFGHNVNETLGKVITSLLAARFGGSVGQEVDPYRIRLQLPRRMKA-LHIQEMIYDL 687
                                   8*********9977.....79*****************************************99554444.67999***** PP

                    DEAD_assoc  82 spdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDl 162
                                   +p+++e ++e  l++++++k+++ +vA+++++l+r+ +         r+++++Ll++++   ++ +++e +re+++++lD+
  gi|91772755|ref|YP_565447.1| 688 QPEHIEPIIEMTLKNTSVMKWKMVHVARKFGALSREIDY-------DRISMKKLLEIYK---GTAMYDEVIREIFHNMLDV 758
                                   *************************************99.......***********99...******************* PP

                    DEAD_assoc 163 erlaellrriaageirvvevetprpSpf 190
                                   +++ e+l  ia++e+ +    +p p+p+
  gi|91772755|ref|YP_565447.1| 759 DKASEVLGLIASEEMVILS--SPVPTPI 784
                                   ******************9..9999996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   2.3e-33   5.2e-30       1     171 [.      27     198 ..      27     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 2.3e-33
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                   t+ Q+ ++p+il g++ ++ a+TGsGKT+ +++p++++++++  +++ g  al+++P+r+L +++l++++ ++++++l v+
  gi|91772755|ref|YP_565447.1|  27 TQPQEMSFPHILAGEHTFLIAPTGSGKTESAVLPMFDHILRKseEDRVGMSALYITPLRALNRDMLTRIQWWGQELGLDVQ 107
                                   5679************************************999889999****************************9999 PP

                                   EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  80 liiggvaardqlskldngvdivvgtpgrlddll..stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgkl 158
                                   +  g+++  + +++ +n +d++++tp+ l+ ++  s+ + nl+ v+++V+DE+++l +++++ +++  l++l +i+ +   
  gi|91772755|ref|YP_565447.1| 108 VRHGDTTPYQRQKQSKNPPDLLITTPETLQAMFtgSRLRKNLECVSYVVVDEIHELASSKRGAQLSVGLERLVEISGEF-- 186
                                   777766666666666566*************9977555568*******************************7776654.. PP

                                   TSEEEEEESSBS.H CS
                                   xxxxxxxxxxxx.x RF
                          DEAD 159 qrqvivlSATlp.k 171
                                     q + lSAT+   
  gi|91772755|ref|YP_565447.1| 187 --QRVGLSATVGnP 198
                                   ..4*******9755 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 ?   -1.7   0.0       1.7   3.8e+03      32      59 ..      95     122 ..      62     132 .. 0.69
   2 !   70.9   0.0   4.6e-23     1e-19      14     108 ..     261     355 ..     249     357 .. 0.88
   3 ?   -2.3   0.0       2.5   5.7e+03      50      50 ..     850     850 ..     803     916 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                                   HHHHHHHTTSTEEEESTTSTHHHHHHHH CS
                    Helicase_C  32 vklllekkgikvavlhgelpqnereeil 59 
                                   +++  ++ g+ v v hg+++  +r++  
  gi|91772755|ref|YP_565447.1|  95 IQWWGQELGLDVQVRHGDTTPYQRQKQS 122
                                   444444559999999***9999999865 PP

  == domain 2  score: 70.9 bits;  conditional E-value: 4.6e-23
                                   TTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
                    Helicase_C  14 eeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                                   e +  +lifvnt++++e     +kll    g +v v+hg+l+ + r+e+ e+f++g+ + Li+t+ +e Gidi kv++V++
  gi|91772755|ref|YP_565447.1| 261 ETHISTLIFVNTRQSAEAlasgFKLL----GASVGVHHGSLSVDARIEAEESFKAGDLRGLICTSSMELGIDIGKVDHVVQ 337
                                   667789********997553344444....9************************************************** PP

                                   SSSSSSHHHHHHHHTTSS CS
                    Helicase_C  91 fdlprnvtsyiqriGRtg 108
                                   ++ pr+v+++ qr+GR+g
  gi|91772755|ref|YP_565447.1| 338 YGSPRQVSRLLQRVGRAG 355
                                   *****************8 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                                   S CS
                    Helicase_C  50 l 50 
                                   +
  gi|91772755|ref|YP_565447.1| 850 M 850
                                   1 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 !   31.6   0.0   6.6e-11   1.5e-07      25     169 ..      41     195 ..      12     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.6e-11
                                   SEEEEEESTTSTHHHHH.HHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--. CS
                        ResIII  25 krglikmaTGtGKTlva.aklierllkkgkee....kflflvprkslleqtleefkkflseayke...igkkvsgdkkka. 96 
                                   ++ ++ ++TG+GKT  a + + +++l+k +e+     +l + p ++l   +l++++ + +e   +        +gd+    
  gi|91772755|ref|YP_565447.1|  41 EHTFLIAPTGSGKTESAvLPMFDHILRKSEEDrvgmSALYITPLRALNRDMLTRIQWWGQELGLDvqvR----HGDTTPYq 117
                                   5778999**********788888888888877999999**************99998888876654332....33332223 PP

                                   ........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS- CS
                        ResIII  97 .kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllglTATp 169
                                    ++++++  ++l+tt ++l+a     +  + ++  +   ++++DE H l+++k         ++++e   e+ ++gl+AT 
  gi|91772755|ref|YP_565447.1| 118 rQKQSKNPPDLLITTPETLQAMF---TGSRLRKNLECVSYVVVDEIHELASSKrgaqlsvGLERLVEISGEFQRVGLSATV 195
                                   345788999**************...7788888888888************86677777888888999999*********6 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.3e-06     0.021      91     198 ..      70     172 ..      20     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-06
                                   ......S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT...... CS
                                   xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N  91 rkdtlagptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkr 170
                                   ++d++   +L + P  +l +   + i+ + ++  l+v v +g+++  ++    +++  +  d +itt ++l+     +  r
  gi|91772755|ref|YP_565447.1|  70 EEDRVGMSALYITPLrALNRDMLTRIQWWGQELGLDVQVRHGDTTPYQR----QKQSKNPPDLLITTPETLQAMFTGSRLR 146
                                   445555668888999888889999******************9854444....67778899***********777666666 PP

                                   TTS-S-S-SEEEES-GGGT--TTSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 171 svlkqvewkrvvlDEghtlknstskaae 198
                                   + l+ v   +vv+DE h l +s++ a+ 
  gi|91772755|ref|YP_565447.1| 147 KNLECV--SYVVVDEIHELASSKRGAQL 172
                                   666655..79************877665 PP

>> ANAPC2  Anaphase promoting complex (APC) subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05     0.078       2      45 ..     406     446 ..     406     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                        ANAPC2   2 IvgMLtNlgslpleRIhsmLkmfvpkdegyd.isdeeLkefLdel 45 
                                   I gM   +g +++e+Ihs+L+ +      +   s e+Lk++ ++ 
  gi|91772755|ref|YP_565447.1| 406 ISGMVIDFGDVEIEKIHSILNRTY----PFRdLSLEQLKRVIEQI 446
                                   88**********************....3444*******998876 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.4e-05     0.098      44      64 ..      34      60 ..      10      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
               T4SS-DNA_transf 44 f......ehvlvvAptrsgKgvgvviP 64
                                  f      eh +++Apt+sgK+ + v+P
  gi|91772755|ref|YP_565447.1| 34 FphilagEHTFLIAPTGSGKTESAVLP 60
                                  46666669*****************99 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00031      0.69      13      52 ..      21      59 ..      11     181 .. 0.75
   2 ?   -3.9   0.0       3.9   8.8e+03     128     146 ..     434     452 ..     427     453 .. 0.83
   3 ?   -3.7   0.0       3.3   7.5e+03     109     138 ..     857     885 ..     849     890 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00031
                        AAA_25 13 adlaapppprrwlvkgllpagelallaGapgtGKttlald 52
                                   +++ap +p++  ++ +l age + l++++g+GKt  a+ 
  gi|91772755|ref|YP_565447.1| 21 QGFKAPTQPQEMSFPHIL-AGEHTFLIAPTGSGKTESAVL 59
                                  567888888888887776.8***************87764 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.9
                        AAA_25 128 advdaleaaieevegvrlv 146
                                     +++l ++ie++ ++r+v
  gi|91772755|ref|YP_565447.1| 434 LSLEQLKRVIEQITEYRMV 452
                                   5678999999999999998 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.3
                        AAA_25 109 agveslpLfakdrggtlltadvdaleaaie 138
                                   ++++++ L++k+++  ++++dv++++++ +
  gi|91772755|ref|YP_565447.1| 857 WEEDEIKLVKKQDKV-TAKEDVKRIQRVYR 885
                                   555788898865444.45899999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (944 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.53
# Mc/sec: 5392.78
//
Query:       gi|91772756|ref|YP_565448.1|  [L=584]
Description: adenine deaminase [Methanococcoides burtonii DSM 6242]
Scores for 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-63  212.8   0.1    3.3e-63  212.0   0.1    1.4  1  Adenine_deam_C  Adenine deaminase C-terminal domain
    2.1e-25   89.8   0.2    7.4e-24   84.7   0.2    2.3  1  Amidohydro_1    Amidohydrolase family
    3.4e-09   36.7   0.7    0.00014   21.5   0.0    2.2  2  Amidohydro_3    Amidohydrolase family
     0.0037   17.5   0.2        2.4    8.4   0.0    2.8  3  MR_MLE_N        Mandelate racemase / muconate lactonizing enz


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 !  212.0   0.1   7.3e-67   3.3e-63       3     168 ..     407     573 ..     405     574 .. 0.95

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 7.3e-67
                                   S-EEEEEEE.EEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHHHHHHH CS
                Adenine_deam_C   3 iTkelevel.pvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedmalAvn 82 
                                   +T++++  l + ++g + +d+e+d+l +av+eRhgk+gn+g+gf+kg+gl++gAi +s++hDshn++v G++++dmal +n
  gi|91772756|ref|YP_565448.1| 407 VTENETFVLhSDRHGILMPDVENDVLSVAVIERHGKNGNIGTGFIKGMGLRNGAIGQSIGHDSHNVVVTGVDHSDMALCAN 487
                                   67777777624556699**************************************************************** PP

                                   HHHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-TTTBSGGGGGSTT-TTSSSEEEETTSEE CS
                Adenine_deam_C  83 rvielgGGivvvedgkvlaelpLpiaGlmSdepaeevaekleeleaalkelgvkledpfmtlsflalpviPelkltdkGlv 163
                                   ++++++GGi+vv++gkv+++l+Lp aGl+S+ paeev +kl++l++a+ke+g+ l +pf+t sf+alpviP+l+ltd+Gl+
  gi|91772756|ref|YP_565448.1| 488 TIRSMNGGICVVSNGKVVEQLELPFAGLLSTLPAEEVEKKLTDLHKAVKEIGCALPAPFITHSFIALPVIPSLRLTDMGLF 568
                                   ********************************************************************************* PP

                                   ETTTT CS
                Adenine_deam_C 164 dvkkf 168
                                   dv+kf
  gi|91772756|ref|YP_565448.1| 569 DVDKF 573
                                   ***98 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.2   1.7e-27   7.4e-24       2     344 .]      73     357 ..      72     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.7e-27
                                   EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEE CS
                  Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilgg 82 
                                   ++PGl D HvH+e+s++         +  ++a  al++g++  + +++++++  g     gie++l++a  lpl+  + ++
  gi|91772756|ref|YP_565448.1|  73 LCPGLMDGHVHFESSMV---------TLSQFAVPALAHGTTSVVIDPHEIANVLGRG---GIELVLDEAATLPLNAFVAVS 141
                                   68***********9987.........999***************************7...********************* PP

                                   SSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TSSCHHHH CS
                  Amidohydro_1  83 kvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa..letkgeve 160
                                   +++++  s+et  as+       +++ ++ ++ vv   ++++++ + f de+   +++ a k+ l v+ H+  l+ +    
  gi|91772756|ref|YP_565448.1| 142 SCVPA-TSFETAGASIDVD----DIVSLIANENVVGlGEMMDYPGVVFCDETKLSMIRTALKERLVVDGHCpaLSREQLFG 217
                                   *****.7888778777777....45567889999999**************9999999999************66666666 PP

                                   HHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSC CS
                  Amidohydro_1 161 daeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvk 241
                                   ++ a++  ++e+  + e +e+          l  g+ l+  e    +++               l++ +    +++ +Gv 
  gi|91772756|ref|YP_565448.1| 218 YMCAGISTDHESIEYEEALEK----------LRLGMKLMIREGSA-AKA---------------LDKFL---PRLIGDGVS 269
                                   ************999999999..........********662112.122...............44444...455555776 PP

                                   ...EEEEEECT.......TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB- CS
                  Amidohydro_1 242 ...vglgtDga.......asgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdA 312
                                      v+++tD+        + ++++     +r a+           e gls+++a++m+Tin+Ak++++d+ vGs+  G++A
  gi|91772756|ref|YP_565448.1| 270 lenVFFVTDDKhpsdllkGYMDVI-----VRRAI-----------ELGLSPLDAISMCTINAAKHYRVDHIVGSLSMGRKA 334
                                   677******555555555555555.....88888...........99********************************** PP

                                   -EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                  Amidohydro_1 313 DlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                   D++v+         ++ +++ +++v+ +G+ v
  gi|91772756|ref|YP_565448.1| 335 DIIVL---------EDLEKFIIDSVYASGRPV 357
                                   *****.........99999*********9865 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.5     1e-05     0.046       1      40 [.      64      98 ..      64     120 .. 0.74
   2 !   21.5   0.0   3.1e-08   0.00014     402     447 ..     296     341 ..     278     358 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                  Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvts 40
                                  e iD +G+++ PG+ D H H  +       + l++  v++
  gi|91772756|ref|YP_565448.1| 64 EMIDVTGKHLCPGLMDGHVHFESSM-----VTLSQFAVPA 98
                                  579*****************55544.....4444444444 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.1e-08
                  Amidohydro_3 402 lrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvlda 447
                                   + ++  ls  +a+ ++T ++Ak ++ ++  G+L  G +AD++vl++
  gi|91772756|ref|YP_565448.1| 296 RAIELGLSPLDAISMCTINAAKHYRVDHIVGSLSMGRKADIIVLED 341
                                   457788999*******************99**************83 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0029        13      32      78 ..      41      88 ..      29     109 .. 0.76
   2 !    8.4   0.0   0.00053       2.4      30      68 ..     161     202 ..     138     231 .. 0.85
   3 ?   -2.8   0.0       1.6   7.3e+03      54      92 ..     503     541 ..     492     544 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0029
                                  EEEECTT.EEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHH CS
                      MR_MLE_N 32 kietseG.vvGigeatsvggraetikaelddhlapllvgkdaanisdl 78
                                  +i+ +eG +vGig+ +s  g + ++     +hl+p l+    + +s +
  gi|91772756|ref|YP_565448.1| 41 DIAVKEGyIVGIGDVSSLKGDETEMIDVTGKHLCPGLMDGHVHFESSM 88
                                  566667769**********999999999999******98777655544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00053
                                   EEEEEECTTEEEEEEEE-STT...GHHHHHHHHHHHHHHHHT CS
                      MR_MLE_N  30 lvkietseGvvGigeatsvgg...raetikaelddhlapllv 68 
                                   +v + ++e vvG+ge++ ++g   ++et  + +++ l + lv
  gi|91772756|ref|YP_565448.1| 161 IVSLIANENVVGLGEMMDYPGvvfCDETKLSMIRTALKERLV 202
                                   56667799***************************9999887 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSSCHHH CS
                      MR_MLE_N  54 tikaelddhlapllvgkdaanisdlaqllkravlgnmsA 92 
                                   ++  +l+   a ll   +a+++++    l++av+ +  A
  gi|91772756|ref|YP_565448.1| 503 KVVEQLELPFAGLLSTLPAEEVEKKLTDLHKAVKEIGCA 541
                                   566666666777777888889999888888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3711.66
//
Query:       gi|91772757|ref|YP_565449.1|  [L=407]
Description: glucoamylase and related glycosyl hydrolases [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.3   0.4      0.037   13.3   0.1    1.7  2  Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin gly
       0.11   11.3   0.1       0.39    9.4   0.1    2.1  2  Glyco_hydro_15   Glycosyl hydrolases family 15


Domain annotation for each model (and alignments):
>> Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.1e-06     0.037     109     217 ..     115     215 ..     111     272 .. 0.82
   2 ?   -2.7   0.0      0.31   2.7e+03      67      72 ..     326     331 ..     286     387 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-06
                                   HHHHHH--HHHHHHHHHHHHHHHHHHHHTSBT.TB..--S-S--STT.....-SS----HHHHHHHHHHHHHHHHHHHHHH CS
               Bac_rhamnosid6H 109 elyetygDkeilkkqYesmkryldylkqrsddgle.elskfqlgDWldpeardgaaktekalvataylvrslklvakiael 188
                                   + +e+  Dk++++k++ ++++ ++ ++ +++++ +   + + +  +        a +   ++ a++      + + k++++
  gi|91772757|ref|YP_565449.1| 115 MFFEKLADKKFVEKHWDTISKAVEFILMNKNEEVDlVHTINSIHEYP-------AYEHGFEIYANCACCAGIQAAVKMGAA 188
                                   6789999*******************999999333234444444444.......555667788****************** PP

                                   TTS..--HHHHHHHHHHHHHHHHHHB.-T CS
               Bac_rhamnosid6H 189 lgkeedakkyaalaeelkaafnkkyldse 217
                                   lgk  d+ +++++ae++k+a+ ++ + + 
  gi|91772757|ref|YP_565449.1| 189 LGK--DVTTWEMEAEKIKEAILTRMYSPR 215
                                   **6..9***************99988444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.31
                                   HHHHHH CS
               Bac_rhamnosid6H  67 kwlrdl 72 
                                    w+ d+
  gi|91772757|ref|YP_565449.1| 326 GWVVDM 331
                                   222222 PP

>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   4.4e-05      0.39     109     165 ..      78     136 ..       7     235 .. 0.78
   2 ?   -1.6   0.0     0.095   8.5e+02     426     447 ..     378     399 ..     354     400 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 4.4e-05
                                   TTS-B--S-...-S--BTTHHHHHHHHHHHH.HCTTHCHCCCCHHHHTHHHHHHHHHHH CS
                Glyco_hydro_15 109 ktgstvvGdde.wghlQlDatslyllalaqm.tasglqiistldevafvqnlvdYieaa 165
                                   ++   v+G+d+ ++ lQ+D+ +l+l+ + ++  a+g ++ ++l   +fv++  d i +a
  gi|91772757|ref|YP_565449.1|  78 SQRYDVDGNDAsYKDLQIDGNGLVLYSMGKYfEATGGMFFEKLADKKFVEKHWDTISKA 136
                                   445567787753899****************8777755555555555665555544443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.095
                                   TT--EESSTT-HHHHHHHHHHH CS
                Glyco_hydro_15 426 ylgeliraqpllfsealllrig 447
                                   ++g+   + pl++ +a+++r+ 
  gi|91772757|ref|YP_565449.1| 378 KDGMAYVTIPLIWPHAEYIRAY 399
                                   578888999**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2575.23
//
Query:       gi|91772758|ref|YP_565450.1|  [L=176]
Description: hypothetical protein Mbur_0735 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1216.45
//
Query:       gi|91772759|ref|YP_565451.1|  [L=272]
Description: mannosyl-3-phosphoglycerate phosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   71.1   0.0      4e-19   69.4   0.0    1.7  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
    1.3e-06   28.2   0.0     0.0045   16.6   0.0    2.2  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
    4.7e-06   27.1   2.0     0.0057   17.1   0.0    2.8  3  HAD          haloacid dehalogenase-like hydrolase
      1e-05   25.6   0.0    1.7e-05   24.8   0.0    1.5  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
     0.0007   19.9   1.5       0.31   11.3   1.5    3.0  1  Hydrolase    haloacid dehalogenase-like hydrolase
     0.0071   16.5   1.0          2    8.4   0.5    3.0  3  HAD_2        Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   1.3e-22     4e-19       1     228 [.       5     231 ..       5     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.3e-22
                                   EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEEEEE--B- CS
                   Hydrolase_3   1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgkilykstis 80 
                                   i++DlDGTL+++d    + ++ a+  lkek+i ++++T     +++ +++el+   p+i+ NG+ i   +++      +i+
  gi|91772759|ref|YP_565451.1|   5 IFTDLDGTLIDHDTYSYDAARPALDLLKEKEIPLIFCTSKTRAELEVYVDELECHHPFISENGGAIfIPKDHF-----SIE 80 
                                   89************999*************************************************5333333.....455 PP

                                   HHHHHHHHHHHHHTT......CEEEEEESSEEEESTT.THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEE.EES-HHHH CS
                   Hydrolase_3  81 kedvkeiikllkenn......veillytedkvyvlnkeksekkkkeeektkkkkeeidseeeledeeiakil.ilkdkekl 154
                                    +dv+ei ++   +       ++ +l++ +k ++ +      + + e  +k +  +i+s +  + +e    + + +d++ +
  gi|91772759|ref|YP_565451.1|  81 LKDVHEIGNYKVIEFgtsytrIRGVLEDIRKKTGFKI-TGFGDLDAEGVSKDTGLDIRSAKLAKLREYDEAFrLEEDENAT 160
                                   5555555554333222222266666776666666666.5566777777777777777777777777887777777777777 PP

                                   HHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGE..EEEESSGGGHHHHHHSSEEEEE CS
                   Hydrolase_3 155 delekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleev..iafGDgeNDieMLeaaglgvAm 228
                                    ++++ + +       +++ ++ y+ im  + +Kg+a+++l + ++ +  ev  ia GD+ ND++ML+a+++ + +
  gi|91772759|ref|YP_565451.1| 161 AKVIELIHAAG----LNYTKGGRYWHIMGDN-DKGKAVRALTEIYRQQFTEVvtIALGDSLNDLPMLKAVDIPFLV 231
                                   77777777775....67899999*****765.9*********999888877522788*************998766 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.5e-06    0.0045       2      57 ..       2      57 ..       1      70 [. 0.87
   2 !    9.8   0.0   0.00018      0.53     164     199 ..     187     224 ..     145     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                                  SEEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT CS
                          S6PP  2 klllvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRsldsakellkekn 57
                                  k ++ +dLD+tl+d+d  + ++ +  l+  ++k++ l+f+T ++ ++ +  + e +
  gi|91772759|ref|YP_565451.1|  2 KHIIFTDLDGTLIDHDTYSYDAARPALDLLKEKEIPLIFCTSKTRAELEVYVDELE 57
                                  5799*************************************998777666666655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                                   -SHHHHHHHHHHHHT--..GGGEEEEE-SGGGHHHHTS CS
                          S6PP 164 askgeAlryLakklele..leqilvcGdsgnDeellig 199
                                    +kg+A+r L + ++ +     ++  Gds nD  +l++
  gi|91772759|ref|YP_565451.1| 187 NDKGKAVRALTEIYRQQftEVVTIALGDSLNDLPMLKA 224
                                   69*********999988334455678********9975 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.8    0.0011       3.2       1      20 [.       5      24 ..       5      54 .. 0.79
   2 ?   -1.8   0.0       1.2   3.5e+03     143     167 ..     129     151 ..     105     162 .. 0.67
   3 !   17.1   0.0   1.9e-06    0.0057     137     188 .]     173     223 ..     156     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                           HAD  1 alfDfDgTLldgdslelllr 20
                                  ++ D+DgTL+d d++ + + 
  gi|91772759|ref|YP_565451.1|  5 IFTDLDGTLIDHDTYSYDAA 24
                                  699**********9986444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                           HAD 143 glegkpvrgegkvaalrewlaaege 167
                                     + ++  +++k+a+lre  ++e  
  gi|91772759|ref|YP_565451.1| 129 SKDTGLDIRSAKLAKLRE--YDEAF 151
                                   455666777888888888..44333 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.9e-06
                           HAD 137 rltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                    +t++ g ++++  +++k +a+r+  +   +  ++  ++a GDs +Dlp+l+
  gi|91772759|ref|YP_565451.1| 173 NYTKG-GRYWHIMGDNDKGKAVRALTEIYRQQFTEVVTIALGDSLNDLPMLK 223
                                   34444.48888888888889999977777777777779999*********97 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.7e-09   1.7e-05       1      54 [.       5      59 ..       5     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.7e-09
                                  EEEESTTTSEETTE.E-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHT CS
                   Hydrolase_6  1 flfDidGvLwrgdk.aipgaaealnalraagkpvvllTNnsskseeeyakklekl 54
                                  +++D+dG+L++ d+  ++ a  al+ l+++++p++++T +++   e y+++le  
  gi|91772759|ref|YP_565451.1|  5 IFTDLDGTLIDHDTySYDAARPALDLLKEKEIPLIFCTSKTRAELEVYVDELECH 59
                                  589*******8665279******************************99999865 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.5   0.00011      0.31     181     210 .]     202     226 ..       2     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                   HHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 181 aaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   +     q     +++ GD++nD+++l+a++
  gi|91772759|ref|YP_565451.1| 202 Q-----QFTEVVTIALGDSLNDLPMLKAVD 226
                                   2.....2334458899***********987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.5   0.00068         2       1      23 [.       4      27 ..       4      29 .. 0.84
   2 !    8.3   0.0   0.00077       2.3      78     122 ..      18      62 ..      16      66 .. 0.92
   3 ?   -0.0   0.0      0.28   8.2e+02     148     175 ..     202     229 ..     184     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00068
                         HAD_2  1 iiF.DlDgTlldteeliiqafnel 23
                                  iiF DlDgTl+d  +++++a++ +
  gi|91772759|ref|YP_565451.1|  4 IIFtDLDGTLIDHDTYSYDAARPA 27
                                  5666**************998765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00077
                         HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyF 122
                                   +  yd ++ +L+ Lke+++ l   Tsk+r+++e  +++l+ ++ F
  gi|91772759|ref|YP_565451.1|  18 TYSYDAARPALDLLKEKEIPLIFCTSKTRAELEVYVDELECHHPF 62 
                                   67899999*****************************99998877 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.28
                         HAD_2 148 lklkkeeviyvGDsptDieaakkagikv 175
                                   +++++  +i  GDs +D+   k++ i +
  gi|91772759|ref|YP_565451.1| 202 QQFTEVVTIALGDSLNDLPMLKAVDIPF 229
                                   46667778999******98888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1936.64
//
Query:       gi|91772760|ref|YP_565452.1|  [L=404]
Description: hypothetical protein Mbur_0737 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.51   10.2   0.0    2.1  2  SufE      Fe-S metabolism associated domain


Domain annotation for each model (and alignments):
>> SufE  Fe-S metabolism associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.19   3.4e+03      44      67 ..     125     148 ..     120     154 .. 0.86
   2 ?   10.2   0.0   2.8e-05      0.51      71     119 ..     245     290 ..     242     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.19
                                   EEEEEEEEETTSEEEEEEESSHHH CS
                          SufE  44 qvwlaaeledgklkfeadsdariv 67 
                                   +vw+a+ +   + +  a+ da iv
  gi|91772760|ref|YP_565452.1| 125 DVWIATGIATLESYAIAYHDADIV 148
                                   699999998877899999999998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHCTTEECCCCTCC-TCHHHHHTTSHHHHCHHHHHHHHHHHHHH CS
                          SufE  71 lalllevlsgktpeeilavdledfleelglsehlspsRsnGlaamlkri 119
                                   + ll ev+ ++t ++i ++dl  ++++   ++ l  +Rs+Gl +m+  i
  gi|91772760|ref|YP_565452.1| 245 VGLLAEVYRNATTKKICQIDL-GYYDHK--HQELGVNRSEGLCKMVSDI 290
                                   5799*****************.888876..799************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2726.30
//
Query:       gi|91772761|ref|YP_565453.1|  [L=307]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-06   26.5   1.3    6.7e-06   25.9   1.3    1.3  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
       0.05   13.1   0.1       0.11   12.0   0.1    1.5  1  DUF4283    Domain of unknown function (DUF4283)
      0.062   13.3   0.0       0.22   11.6   0.0    2.0  2  DUF772     Transposase domain (DUF772)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.3   1.1e-09   6.7e-06      10     185 ..      83     259 ..      75     287 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-09
                     DDE_Tnp_1  10 Dattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYas 88 
                                   D+t++++ + +  ++  y+ +  ++  k+hi +   + l++ +  t g +hds+ lk  +d+l ++  + +++  D+GY+s
  gi|91772761|ref|YP_565453.1|  83 DSTPLEASRYD--KYADYNPHYNCKMDKAHITM--IGPLPIYMTHTKGASHDSPELKKHIDALVEMgvDIDTYALDGGYDS 159
                                   88888888888..44444444445555888888..4457***********************9999*************** PP

                     DDE_Tnp_1  89 aelldtle.ekgvdyiirlkkntklyrk.....................gaeskrrgrlrkhdrnkiltksqkrrnkskke 147
                                    +++ ++  + +++++i++++++k++                        + +++ ++l  ++r+k++    + +n     
  gi|91772761|ref|YP_565453.1| 160 FRNHADIWyKLNAKPVIAYSSDSKVQYEgmmeridhwvnkmwklggsihMKYEEKLHFLYENGREKQVGMHLRNKNI---- 236
                                   888888888**********9999999888887777777666666555541333344444444444444444444444.... PP

                     DDE_Tnp_1 148 kgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlk 185
                                                  +   + e y++R ++Erv+  +k
  gi|91772761|ref|YP_565453.1| 237 ---------------KDDGFDEDYSHRGECERVHNHIK 259
                                   ...............556669************99888 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.8e-05      0.11      24      59 ..     190     225 ..     169     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                       DUF4283  24 lsalrrvlakaWklkggvkikelgdglflfrfssee 59 
                                   ++++ ++++k+Wkl+g +++k+ ++ +fl++   e+
  gi|91772761|ref|YP_565453.1| 190 MERIDHWVNKMWKLGGSIHMKYEEKLHFLYENGREK 225
                                   678999***********************9866655 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.6e-05      0.22      10      70 ..       1      64 [.       1      67 [. 0.79
   2 ?   -2.8   0.0       1.1   6.8e+03      21      37 ..     244     260 ..     243     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                        DUF772 10 mlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70
                                  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f k rl++  l++++
  gi|91772761|ref|YP_565453.1|  1 MIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVKyRLGKtgLDEVM 64
                                  89999999999999998888762566666666664333.89*****************9977776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                        DUF772  21 glSdreleealrenlsf 37 
                                   ++S r  +e++++++ +
  gi|91772761|ref|YP_565453.1| 244 DYSHRGECERVHNHIKW 260
                                   56888899****99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2208.58
//
Query:       gi|91772762|ref|YP_565454.1|  [L=129]
Description: hypothetical protein Mbur_0741 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.1   0.2       0.19   12.2   0.1    2.0  2  FDX-ACB   Ferredoxin-fold anticodon binding domain


Domain annotation for each model (and alignments):
>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.1e-05      0.19      56      90 ..      48      82 ..      10      85 .. 0.91
   2 ?   -0.4   0.0     0.091   1.6e+03      40      64 ..      96     120 ..      91     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                                  EEEEEEE--SSS---HHHHHHHHHHHHHHHHTT.T CS
                       FDX-ACB 56 lalrltlqskertLtdeevnaaiekvvealekklg 90
                                   +++  ++++++ +td+ev ++ + + ++l kk++
  gi|91772762|ref|YP_565454.1| 48 FTIAHYYHDNDKKITDKEVVNLLKDIKANLDKKMN 82
                                  5677889*************************998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.091
                                   EEEEEESTTS-SSEEEEEEEEEE-- CS
                       FDX-ACB  40 lfDvYrgkklaegkkSlalrltlqs 64 
                                   l++++ +++++ ++ +l +  +l+s
  gi|91772762|ref|YP_565454.1|  96 LIEIFDEENITVHEFNLVIDYVLES 120
                                   6788888888888877777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1227  (0.0684366); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 839.53
//
Query:       gi|91772763|ref|YP_565455.1|  [L=153]
Description: hypothetical protein Mbur_0742 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.9   0.0      0.082   13.8   0.0    2.1  3  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.41   7.4e+03      24      33 ..       9      18 ..       7      21 .. 0.81
   2 ?   13.8   0.0   4.6e-06     0.082       2      36 ..      55      89 ..      54      96 .. 0.86
   3 ?   -3.3   0.0         1   1.8e+04      23      29 ..     109     115 ..     106     121 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.41
                        TPR_14 24 lrralalaPd 33
                                   +++l+++Pd
  gi|91772763|ref|YP_565455.1|  9 IDDLLEKFPD 18
                                  6789999998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.6e-06
                        TPR_14  2 eallalaeallalGdpdeAiallrralalaPddae 36
                                  ++ la+++ l+ +G+ d Ai+l++ra +++ +   
  gi|91772763|ref|YP_565455.1| 55 NLFLAYLSELESNGNIDIAIKLAKRASKRFGEMFS 89
                                  67899*********************999987655 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1
                        TPR_14  23 llrrala 29 
                                   +++ra++
  gi|91772763|ref|YP_565455.1| 109 YYNRAIS 115
                                   5566654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1072.42
//
Query:       gi|91772764|ref|YP_565456.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.7   0.4    6.3e-67  226.0   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
      9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.2e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00011   22.5   0.3       0.17   12.1   0.2    2.8  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.067   13.8   1.4        0.3   11.7   1.4    2.2  1  BST2             Bone marrow stromal antigen 2
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.7   2.6       0.55   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.36   11.2   6.9       0.52   10.7   4.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
          1   10.1   8.9        7.1    7.4   1.5    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.1    9.0   6.0       0.65   10.7   1.1    2.7  2  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.44   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  226.0   0.0   3.5e-70   6.3e-67       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772764|ref|YP_565456.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 226.0 bits;  conditional E-value: 3.5e-70
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91772764|ref|YP_565456.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91772764|ref|YP_565456.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierear..ea..eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++r  +   ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91772764|ref|YP_565456.1| 329 SENDN--QLWSKAMNIlLIDVKKSVDQIRgmSGcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **976..*********************964338888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91772764|ref|YP_565456.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.5e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91772764|ref|YP_565456.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7     8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772764|ref|YP_565456.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.6     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.5   0.0    0.0025       4.5       5      45 ..     249     287 ..     245     290 .. 0.84
   3 !   12.1   0.2   9.3e-05      0.17      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91772764|ref|YP_565456.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91772764|ref|YP_565456.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91772764|ref|YP_565456.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91772764|ref|YP_565456.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00046      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91772764|ref|YP_565456.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91772764|ref|YP_565456.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00031      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    0.9   0.1      0.34   6.2e+02      11      58 ..     392     446 ..     383     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772764|ref|YP_565456.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91772764|ref|YP_565456.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999888854444440......55555555555555555553 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?   10.7   4.5   0.00029      0.52       2      36 ..     156     213 ..     155     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91772764|ref|YP_565456.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91772764|ref|YP_565456.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCellADvCGC 213
                                   79***************99987555588888888888888887775555444446666 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 ?    3.3   0.1     0.074   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.4   1.5     0.004       7.1       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.0   0.1      0.19   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91772764|ref|YP_565456.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91772764|ref|YP_565456.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91772764|ref|YP_565456.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00036      0.65      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.6   0.3        10   1.8e+04      55      66 ..     154     165 ..     144     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772764|ref|YP_565456.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                         PLATZ  55 kssseaCetCar 66 
                                   +++ ++C +C++
  gi|91772764|ref|YP_565456.1| 154 RAEIKSCPHCGC 165
                                   334478999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 3535.65
//
Query:       gi|91772765|ref|YP_565457.1|  [L=102]
Description: hypothetical protein Mbur_0745, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.045   12.7   1.4      0.057   12.4   1.4    1.1  1  Asp2       Accessory Sec system GspB-transporter
       0.13   12.0   0.6       0.15   11.7   0.6    1.0  1  Maelstrom  piRNA pathway germ-plasm component


Domain annotation for each model (and alignments):
>> Asp2  Accessory Sec system GspB-transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.4   6.3e-06     0.057     424     475 ..       4      56 ..       2      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-06
                          Asp2 424 ikelnekfwekf.dkadfsktkfaiaymenDdYDdtaykellevlkkqnakvi 475
                                   +++ n+ + +kf +k+d++k k++  y ++ + D++++ ++ e l+k+  k++
  gi|91772765|ref|YP_565457.1|   4 VEKTNQTLLRKFaEKQDYEKRKIVFWYEKDETADEDSFAQIEEELAKHDIKIK 56 
                                   67889999*9994579********************************88774 PP

>> Maelstrom  piRNA pathway germ-plasm component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   1.6e-05      0.15      79     139 ..      13      73 ..       3      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                                   HHHH-SS...S-EEEEE-GGGHHHHHHHHHHH----HHHH-EEEEEHHHHHHHHHHHHHHHT CS
                     Maelstrom  79 essseks.neksliiltkeeeisvvksclknlaedvkfeeevsvydiqelfldlkkevldva 139
                                   ++  ek+  ek +i++  e++ +  ++++ +++e+   ++ +++  + + f+++kk ++   
  gi|91772765|ref|YP_565457.1|  13 RKFAEKQdYEKRKIVFWYEKDETADEDSFAQIEEELAKHD-IKIKVLADNFYEVKKFLEVED 73 
                                   3333333467****************************98.*************99776444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1338  (0.0746277); 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:                         2  (0.000111551); expected 0.2 (1e-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: 749.75
//
Query:       gi|91772766|ref|YP_565458.1|  [L=208]
Description: hypothetical protein Mbur_0747 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-09   36.9   2.5    9.4e-09   35.8   2.5    1.5  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.062   12.6   0.1        1.5    8.1   0.1    2.0  2  DUF4866   Domain of unknown function (DUF4866)
       0.15   11.7   2.1       0.28   10.9   2.1    1.4  1  DUF2650   Protein of unknown function (DUF2650)


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 !   35.8   2.5   1.6e-12   9.4e-09       2      72 ..      25     101 ..      24     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.6e-12
                      CxxCxxCC   2 Cke.C.gaCCkelkvklteedlerlkaaevaeeeeeskkiak.....adgrCvfldeetklCkiYeeRpkicrlfpas 72 
                                   C + C ++CC++ +v + e++++ lk+ +  + ++ +++i       ++ +C fl++++ +C+iYe+R ++c ++p+ 
  gi|91772766|ref|YP_565458.1|  25 CPDtCkAECCRNGRVHIFEDEFNFLKENHPEKAKDIKSDILVpslyvMTSPCSFLNPTN-RCEIYEKRLTVCGMYPFK 101
                                   7666*99******************9998855555555555599999**********96.****************96 PP

>> DUF4866  Domain of unknown function (DUF4866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.012        71     160     188 ..      12      40 ..       2      57 .. 0.70
   2 ?    8.1   0.1   0.00025       1.5     191     237 ..     147     196 ..     119     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.012
                       DUF4866 160 klekkrGilllyelPdtvklklteaeaYa 188
                                   + +  + il  ye+Pdt+k +   +    
  gi|91772766|ref|YP_565458.1|  12 HYNAIQNILQYYECPDTCKAECCRNGRVH 40 
                                   56777889***********9876665555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00025
                       DUF4866 191 wdlllklqkelpralvyYGqetlekkekkfdel...gilLpisefekkle 237
                                   ++  ++l++ +++a  +Y +e+l++ +  +del    i+L+ ++  kk++
  gi|91772766|ref|YP_565458.1| 147 LQWEISLESYAMEASDFYSRESLQEMQIPYDELemlSIFLRSKNALKKIN 196
                                   5556789999*********************9722256666666555543 PP

>> DUF2650  Protein of unknown function (DUF2650)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.1   4.7e-05      0.28       5      23 ..      18      36 ..      16      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                       DUF2650  5 sifhyYkCCgdlnkeCCfe 23
                                  +i+ yY+C ++ + eCC +
  gi|91772766|ref|YP_565458.1| 18 NILQYYECPDTCKAECCRN 36
                                  8999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1345.76
//
Query:       gi|91772767|ref|YP_565459.1|  [L=216]
Description: phosphate uptake regulator, PhoU [Methanococcoides burtonii DSM 6242]
Scores for complete 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-40  135.7  14.5    5.7e-22   78.0   4.9    2.1  2  PhoU      PhoU domain
  ------ inclusion threshold ------
       0.06   13.2   0.1       0.47   10.3   0.1    2.2  2  HxlR      HxlR-like helix-turn-helix


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 !   78.0   4.9   6.3e-26   5.7e-22       1      88 [.      17     104 ..      17     105 .. 0.98
   2 !   63.5   2.0     2e-21   1.8e-17       2      87 ..     120     202 ..     119     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 6.3e-26
                                   HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                   +++m++i+++ml ++++ale  d ela+ vie+d  +d+le+++e++ + +la +qp+a+dlr ++++ +ia dlER++D 
  gi|91772767|ref|YP_565459.1|  17 IQEMGDISQKMLVNSIQALEYLDLELAKNVIEMDSIVDDLEYDVEKATVHLLALQQPMAKDLRLITASYKIAIDLERMSDF 97 
                                   689****************************************************************************** PP

                                   HHHHHHH CS
                          PhoU  82 avniaer 88 
                                   avniae 
  gi|91772767|ref|YP_565459.1|  98 AVNIAEL 104
                                   *****97 PP

  == domain 2  score: 63.5 bits;  conditional E-value: 2e-21
                                   HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82 
                                   + +a+i++ m++++++a++e+d elar+  e+d ++drl++    +l++++ ++  l   +  +++l+ + r+lERi+Dha
  gi|91772767|ref|YP_565459.1| 120 NTIASITQMMMENSMKAYAENDAELARATAEEDSQVDRLFYSTWQKLVNLMIEDAAL---IPNAVDLIFVLRYLERIADHA 197
                                   67899**************************************99999999766655...7789***************** PP

                                   HHHHH CS
                          PhoU  83 vniae 87 
                                   +ni+e
  gi|91772767|ref|YP_565459.1| 198 CNICE 202
                                   ***98 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   5.3e-05      0.47      19      46 ..       8      38 ..       3      76 .. 0.76
   2 ?    0.2   0.0     0.075   6.7e+02      27      45 ..     121     139 ..     113     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.3e-05
                                  EEHHHHH...HHSTTS-HHHHHHHHHHHHHT CS
                          HxlR 19 kRfselk...ralpkisqkmLaqrLreLeqd 46
                                  +R ++l+   +++++isqkmL++++++Le  
  gi|91772767|ref|YP_565459.1|  8 QRLEDLRseiQEMGDISQKMLVNSIQALEYL 38
                                  666666622235799*************964 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.075
                                   HSTTS-HHHHHHHHHHHHH CS
                          HxlR  27 alpkisqkmLaqrLreLeq 45 
                                   ++ +i+q m+ +++++  +
  gi|91772767|ref|YP_565459.1| 121 TIASITQMMMENSMKAYAE 139
                                   5679999999999997644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1410.40
//
Query:       gi|91772768|ref|YP_565460.1|  [L=255]
Description: ABC phosphate transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  116.1   0.0    2.4e-33  115.6   0.0    1.2  1  ABC_tran     ABC transporter
    4.8e-12   46.3   0.1    3.7e-05   23.7   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.7e-08   33.1   0.2    3.9e-06   26.5   0.2    2.2  1  SMC_N        RecF/RecN/SMC N terminal domain
    8.9e-06   25.6   0.0    3.6e-05   23.6   0.0    1.7  2  AAA_15       AAA ATPase domain
    0.00032   20.7   0.0    0.00063   19.7   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
     0.0008   19.1   0.0     0.0017   18.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00087   19.8   0.0     0.0018   18.8   0.0    1.5  1  AAA_23       AAA domain
      0.001   19.4   0.0     0.0016   18.7   0.0    1.6  1  AAA_22       AAA domain
     0.0011   18.9   0.0     0.0024   17.8   0.0    1.5  2  Rad17        Rad17 P-loop domain
     0.0032   17.9   0.0      0.005   17.3   0.0    1.6  1  AAA_16       AAA ATPase domain
     0.0043   16.7   0.0      0.012   15.2   0.0    1.7  2  AAA_25       AAA domain
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.045   13.5   0.0    1.6  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.023   15.2   0.0      0.047   14.2   0.0    1.6  1  AAA_18       AAA domain
      0.033   14.4   0.0      0.067   13.4   0.0    1.8  1  AAA_33       AAA domain
      0.068   13.6   0.0       0.58   10.6   0.0    2.3  1  AAA          ATPase family associated with various cellular a
       0.11   12.2   0.0        0.3   10.8   0.0    1.7  2  AAA_24       AAA domain
        0.2   10.4   0.0       0.35    9.6   0.0    1.3  1  PPV_E1_C     Papillomavirus 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 !  115.6   0.0   2.2e-36   2.4e-33       1     136 [.      25     179 ..      25     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 2.2e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepqlfpel 74 
                                   lk++sl++ e +++a++G++G+GKSt+l++l ++ +       eGe+l+dg+++ +   +   lrk++g+++q+p+ fp +
  gi|91772768|ref|YP_565460.1|  25 LKDISLDIPEKSVTALIGPSGCGKSTFLRCLNRMNDLvkscsIEGEVLVDGENIYDkdVDVVDLRKNVGMVFQKPNPFPMS 105
                                   79********************************99899999************9977788899***************** PP

                                   BHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  75 tvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +++n             e +e+++kal+   l +  ++++++++ sLSgGq+qr+++ar+l+ kp++ll+DEp+
  gi|91772768|ref|YP_565460.1| 106 -IYDNiaygpkihgcsksETEERVHKALDDAALMGEVQDRLGDQAFSLSGGQQQRLCIARTLAVKPEILLFDEPC 179
                                   .9**************9999999***************************************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.9e-07   0.00031       1      30 [.      37      68 ..      37      95 .. 0.77
   2 !   23.7   0.0   3.5e-08   3.7e-05     232     298 ..     147     209 ..     117     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.9e-07
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..drdve 30
                                  +++liGp g+GKS++L++l  + +l   +++e
  gi|91772768|ref|YP_565460.1| 37 VTALIGPSGCGKSTFLRCLNRMNDLvkSCSIE 68
                                  69*****************9998877644443 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.5e-08
                        AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    +a++lS G+++ l+++  l+  +    +ll+DEp + L+P  ++++ +l+ el++ +  ++++TH+
  gi|91772768|ref|YP_565460.1| 147 DQAFSLSGGQQQRLCIARTLAVKP---EILLFDEPCSALDPISTSKIEDLILELKK-DYTIVIVTHN 209
                                   37899999*999977777777666...9*************999999999988888.9********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   3.7e-09   3.9e-06      23     205 ..      34     216 ..      22     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.7e-09
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCC..CC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsd..lihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                   +ks+ta++Gp G+GKs +l  +  +    ++ ++  e l d   i+ ++      + +v ++f++++       +++    
  gi|91772768|ref|YP_565460.1|  34 EKSVTALIGPSGCGKSTFLRCLNRMNDLVKSCSIEGEVLVDgeNIYDKDVDVVDLRKNVGMVFQKPNPFPMSIYDNIAYGP 114
                                   6889***************99944433334434444433221123333333444456777777777776222233322222 PP

                                   EE.....ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                   xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 102 rv.....krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                   ++     ++++e  +k  +  +   ev++ l ++ +   +LSgG+++ + +a  +A+   kp+ + l+De  +aLD   ++
  gi|91772768|ref|YP_565460.1| 115 KIhgcskSETEERVHKALDDAALMGEVQDRLGDQAF---SLSGGQQQRLCIARTLAV---KPE-ILLFDEPCSALDPISTS 188
                                   220000022222222223334445677777777776...69******9999998886...455.789************** PP

                                   HHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 178 kvaellkeksknaQfivislreemleka 205
                                   k+ +l+ e +k+  +++++++ ++ ++ 
  gi|91772768|ref|YP_565460.1| 189 KIEDLILELKKDYTIVIVTHNMQQAARI 216
                                   ********************98877665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.4e-08   3.6e-05      13      55 ..      24      77 ..      23     130 .. 0.77
   2 ?   -0.8   0.0      0.93   9.8e+02     323     365 ..     169     209 ..     155     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.4e-08
                        AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn..........k 55
                                  +lkd+++d+ e+ +t liG+ ++GKS++l+ l+ + +  ++ +          +
  gi|91772768|ref|YP_565460.1| 24 ALKDISLDIPEKsVTALIGPSGCGKSTFLRCLNRMNDLVKSCSiegevlvdgeN 77
                                  689******9999*********************99976555574444433330 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.93
                        AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   k+ ill++EP   L p   + + +l++el +d    ++i TH+
  gi|91772768|ref|YP_565460.1| 169 KPEILLFDEPCSALDPISTSKIEDLILELKKDYT--IVIVTHN 209
                                   6778999999888888888888888888888885..8888887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     6e-07   0.00063      74     122 ..       9      58 ..       2      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6e-07
                                   HTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  74 algyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                   +++++ l +   +k++l++++  + + ++++l+G+SG GKSt++  l+  
  gi|91772768|ref|YP_565460.1|   9 NINIKDLNLWYGEKHALKDISLDIPEkSVTALIGPSGCGKSTFLRCLNRM 58 
                                   56666666667788899999999888699***************999875 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 !   18.1   0.0   1.6e-06    0.0017      15      39 ..      28      52 ..      16      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                        AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                   +++i +k++t l+GpsG GKST+l
  gi|91772768|ref|YP_565460.1| 28 ISLDIPEKSVTALIGPSGCGKSTFL 52
                                  456677677**************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-06    0.0018      12      40 ..      27      56 ..      10      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                        AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAik 40
                                  d ++d  +k +t+++Gp G+GK+T+l+++ 
  gi|91772768|ref|YP_565460.1| 27 DISLDIpEKSVTALIGPSGCGKSTFLRCLN 56
                                  4444558999******************85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06    0.0016       5      34 ..      35      64 ..      32     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeak 34
                                  +++++++G+sG+GK+t lr l + +d +++
  gi|91772768|ref|YP_565460.1| 35 KSVTALIGPSGCGKSTFLRCLNRMNDLVKS 64
                                  7899******************99987654 PP

>> Rad17  Rad17 P-loop 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    0.0024      33      68 ..      23      58 ..      17      89 .. 0.86
   2 ?   -3.6   0.0       8.7   9.1e+03      54      62 ..     117     125 ..     113     132 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                         Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLske 68
                                  ++lk  +L+  +k +  + GPsGCgkst ++ L + 
  gi|91772768|ref|YP_565460.1| 23 HALKDISLDIPEKSVTALIGPSGCGKSTFLRCLNRM 58
                                  67888899999999999**************99875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.7
                         Rad17  54 sGCgkstvv 62 
                                    GC+ks + 
  gi|91772768|ref|YP_565460.1| 117 HGCSKSETE 125
                                   499999765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.7e-06     0.005      24      47 ..      33      60 ..      22     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-06
                        AAA_16 24 p..elvllsGesGvGKsslvrellr..a 47
                                  p  +++ l+G+sG+GKs+ +r+l r   
  gi|91772768|ref|YP_565460.1| 33 PekSVTALIGPSGCGKSTFLRCLNRmnD 60
                                  4448999***************986443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.012      30      50 ..      32      52 ..      21      57 .. 0.89
   2 ?   -1.9   0.0       1.9     2e+03      87     103 ..     125     160 ..     120     214 .. 0.45

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                        AAA_25 30 lpagelallaGapgtGKttla 50
                                  +p++++++l+G++g+GK+t++
  gi|91772768|ref|YP_565460.1| 32 IPEKSVTALIGPSGCGKSTFL 52
                                  79*****************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                        AAA_25  87 rrRlravgeal...................rddarl 103
                                   ++R+++++ ++                    +++rl
  gi|91772768|ref|YP_565460.1| 125 EERVHKALDDAalmgevqdrlgdqafslsgGQQQRL 160
                                   555555555544444444333333333333333333 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   4.3e-05     0.045       3      47 ..      39      81 ..      37     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                           PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekd 47
                                  ++ g+SG+Gk+t+ r l+ +     vk+ +ieg +++  ++++++
  gi|91772768|ref|YP_565460.1| 39 ALIGPSGCGKSTFLRCLNRMND--LVKSCSIEGEVLVDGENIYDK 81
                                  788************9987655..888899999998887776654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.4e-05     0.047       3      25 ..      40      79 ..      39     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                        AAA_18  3 ltGtpGvGKttlakeLskrlgf.................g 25
                                  l G++G+GK+t+ + L++++ +                  
  gi|91772768|ref|YP_565460.1| 40 LIGPSGCGKSTFLRCLNRMNDLvkscsiegevlvdgeniY 79
                                  89**************999755566655655555533332 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   6.3e-05     0.067       1      22 [.      37      58 ..      37     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                        AAA_33  1 lvllvGlpGsGKstlaerllkk 22
                                  ++ l+G++G+GKst+++ l + 
  gi|91772768|ref|YP_565460.1| 37 VTALIGPSGCGKSTFLRCLNRM 58
                                  5679***********9987554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00055      0.58       3      35 ..      40      73 ..      38     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                                  EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCS CS
                           AAA  3 lyGppGtGKTllakavakelg.vefleisgsell 35
                                  l+Gp G+GK+++ + + +  + v+ ++i+g  l+
  gi|91772768|ref|YP_565460.1| 40 LIGPSGCGKSTFLRCLNRMNDlVKSCSIEGEVLV 73
                                  89**********9998776445566666666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029       0.3       4      22 ..      37      55 ..      34      86 .. 0.87
   2 ?   -1.6   0.1       1.7   1.8e+03     116     135 ..     192     213 ..     186     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                        AAA_24  4 kiliyGpsgiGKTtlakel 22
                                    +++Gpsg GK+t+++ l
  gi|91772768|ref|YP_565460.1| 37 VTALIGPSGCGKSTFLRCL 55
                                  5789***********9988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                        AAA_24 116 kklqelrk..nvifiahektrk 135
                                   + + el+k  +++++ h  ++ 
  gi|91772768|ref|YP_565460.1| 192 DLILELKKdyTIVIVTHNMQQA 213
                                   5677888888888888877665 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00034      0.35     251     285 ..      24      58 ..      20      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                      PPV_E1_C 251 alkefLkgvPkknclvllGppntGkslfamslikf 285
                                   alk+   ++P k++  l+Gp+  Gks+f   l+++
  gi|91772768|ref|YP_565460.1|  24 ALKDISLDIPEKSVTALIGPSGCGKSTFLRCLNRM 58 
                                   678888899*******************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1607.54
//
Query:       gi|91772769|ref|YP_565461.1|  [L=286]
Description: ABC phosphate transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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   82.6  18.8    2.9e-23   82.6  18.8    2.7  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.24   11.4   0.2       0.24   11.4   0.2    2.7  3  FtsL          Cell division protein FtsL


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   5.2     0.028   2.6e+02     102     166 ..      16      77 ..       8      81 .. 0.64
   2 !   82.6  18.8   3.2e-27   2.9e-23       1     183 [.      79     284 ..      79     286 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.028
                  BPD_transp_1 102 vlPnalppiitglilafggl.lggavlleflgswpGlgtllleailgydyseisnggvlalviavl 166
                                   +l++++  +++++ + ++++ ++g+++l++ +     ++++ + ++g  y++i+ g++  ++++++
  gi|91772769|ref|YP_565461.1|  16 TLRLSMALVLAFVSIIVIYItVNGYSALSLDF---ITQMPMKRMTQGGIYPAIM-GSLMLIGLSMA 77 
                                   46666666666665555555577777777666...2577788888888888888.55555554443 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 3.2e-27
                  BPD_transp_1   1 gillGilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                   +i+lGil+a     ++  ++ ++++   i+ l ++Ps+v++++ +++fv   ++g + l++ ++l+l ++p++++  ++al
  gi|91772769|ref|YP_565461.1|  79 AIPLGILSAiylneYSTPGRASWAIEMAINNLAGTPSVVFGLFGLALFVKYFGFGASLLSASLTLALLIVPVIIRASKEAL 159
                                   589*******999*9*********************************9999***************************** PP

                  BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis... 154
                                    ++p++++ea++alG+++wq+ rkv+lP+a+p ++tg+il++g++ g+++ ++++g      ++l ++  +   ++++   
  gi|91772769|ref|YP_565461.1| 160 MTVPQEYREASLALGVTKWQTTRKVILPAAIPGMMTGIILSVGRVAGETAPILLTG----AAYFLPRIPDSVFSQFMAlpy 236
                                   ********************************************************....445444444444444444668 PP

                  BPD_transp_1 155 ...................nggvlalviavlllnlvadilqrlldprv 183
                                                      +g++l+l+++v+ +n +a ++ r+   ++
  gi|91772769|ref|YP_565461.1| 237 hlfvlatsgtsitqtrpiqYGTALILLLIVVMMNSIAVVIRRHYRNKL 284
                                   999999999999999999999999999999999999999999877665 PP

>> FtsL  Cell division protein FtsL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2     0.025   2.2e+02      12      34 ..      14      36 ..       4      43 .. 0.78
   2 ?   -2.8   0.0      0.74   6.6e+03      14      27 ..     141     154 ..     134     170 .. 0.54
   3 ?   11.4   0.2   2.7e-05      0.24      10      36 ..     254     280 ..     246     286 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.025
                          FtsL 12 vgkvlllllllvlvsavavvlit 34
                                  ++++ l ++l++ + ++ v++it
  gi|91772769|ref|YP_565461.1| 14 FATLRLSMALVLAFVSIIVIYIT 36
                                  44677888999999999999998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.74
                          FtsL  14 kvlllllllvlvsa 27 
                                    +l ll++ v++ a
  gi|91772769|ref|YP_565461.1| 141 LTLALLIVPVIIRA 154
                                   34444444444443 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 2.7e-05
                          FtsL  10 lsvgkvlllllllvlvsavavvlithq 36 
                                   +++g+ l+lll++v+++++avv+  h 
  gi|91772769|ref|YP_565461.1| 254 IQYGTALILLLIVVMMNSIAVVIRRHY 280
                                   4789999***************98863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1976.34
//
Query:       gi|91772770|ref|YP_565462.1|  [L=297]
Description: phosphate ABC transporter inner membrane protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-22   79.6  14.5    2.4e-22   79.6  14.5    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.2   11.2   1.2       0.34   10.4   0.0    1.9  2  DUF1295       Protein of unknown function (DUF1295)


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 ?    0.1   2.6     0.062   5.6e+02      13      66 ..       4      79 ..       1      85 [. 0.66
   2 !   79.6  14.5   2.7e-26   2.4e-22       2     181 ..      85     289 ..      84     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.062
                  BPD_transp_1 13 nkkldkllrpliivllslPsfvlaillvlvf......................vilsilghlilpviillllsaap 66
                                  +kk  k++     +++++ +++l++l +++f                        +s ++++ lp+++ +l+ +a+
  gi|91772770|ref|YP_565462.1|  4 RKKKEKAIESTLLMVSGITVVALFLLCFFLFregyllfgdysiisfltetswyPSSSPAKFGLLPLLTGSLIVTAG 79
                                  5666666677777777777777777777777888888888888888888887766677777777755555544444 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 2.7e-26
                  BPD_transp_1   2 illGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrlir 72 
                                   ++lGi +a         k+ +l+ p++++l ++Ps+v +++ + v+       ++   g+++l++ i+l ++a+p+++ + 
  gi|91772770|ref|YP_565462.1|  85 VPLGIASAiyisELADPKIAQLIKPFVEILAGIPSVVYGFFGLIVVvpllqdLLDLPTGQTALAGSIMLGMMALPTIISVS 165
                                   789999998888888999*******************7777555556679988888999********************** PP

                  BPD_transp_1  73 raalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.............lgtl 140
                                   ++a++s+p+ l+e ++alG ++wq++++vvlP+al+ i + ++l +g+++g+++ + +++++++              +++
  gi|91772770|ref|YP_565462.1| 166 EDAINSVPTALKEGSLALGSTKWQTIYRVVLPAALSGISAAVMLGIGRAIGETMTVMMVTGNTAiipgipeglfdpvRTMT 246
                                   ************************************************************887777777755333322223 PP

                  BPD_transp_1 141 lleailgydyseis.........nggvlalviavlllnlvadilqrlldp 181
                                    + a++       +         + +++a++++++l++++++++++ + +
  gi|91772770|ref|YP_565462.1| 247 ATIALE-------MgevpqgsehFHALFAVGAVLFLITFIINLIADSVKK 289
                                   333333.......15566777**555555555555555555555555554 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3       0.4   3.6e+03      99     135 ..     192     227 ..     188     229 .. 0.70
   2 ?   10.4   0.0   3.7e-05      0.34      99     146 ..     245     292 ..     238     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.4
                       DUF1295  99 ylvalpvllaaaskeeqalkaldviglalwlvgivle 135
                                   y v+lp  l+   + +  l++   ig ++++++++++
  gi|91772770|ref|YP_565462.1| 192 YRVVLPAALSGI-SAAVMLGIGRAIGETMTVMMVTGN 227
                                   566677766654.456678888899999998888765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.7e-05
                       DUF1295  99 ylvalpvllaaaskeeqalkaldviglalwlvgivlealaDqQlsafk 146
                                   ++ ++++ + ++++ +++++al  +g++l+l+ ++++ +aD  +++++
  gi|91772770|ref|YP_565462.1| 245 MTATIALEMGEVPQGSEHFHALFAVGAVLFLITFIINLIADSVKKKYR 292
                                   55667778888999999***************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2215.02
//
Query:       gi|91772771|ref|YP_565463.1|  [L=285]
Description: phosphate ABC transporter phosphate-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-45  153.9   0.9    1.1e-44  153.2   0.9    1.3  1  PBP_like_2      PBP superfamily domain
    7.4e-19   67.6   0.2    9.7e-19   67.2   0.2    1.1  1  PBP_like        PBP superfamily domain
  ------ inclusion threshold ------
       0.23   10.8   0.0       0.54    9.6   0.0    1.6  1  LysR_substrate  LysR substrate binding domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.2   0.9   1.8e-48   1.1e-44       4     281 ..      30     271 ..      27     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 153.2 bits;  conditional E-value: 1.8e-48
                    PBP_like_2   4 aeatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangagg 84 
                                   +++++ ++i++ Gs+t+ p+ ++ a+ f+ ++p+++v + ++GSg gi+al +g++d+a+++r +++sei + ++ang ++
  gi|91772771|ref|YP_565463.1|  30 GSEAEMQSIMIKGSDTVLPLAQAEAEVFMMEYPDTSVSIIGGGSGVGIAALIDGEIDIAMTSREMKGSEI-ENAQANG-ID 108
                                   56677788**************************************************************.7889999.** PP

                    PBP_like_2  85 liqvpvaigaialvvnkdnpln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpwtasg 164
                                   +++  +a ++i +vvn++np+  ++ e++++I+ g ++nWn+  +++ d  I v +r  +sgt ++f++ ++e     a +
  gi|91772771|ref|YP_565463.1| 109 PVEQTIAWDGISVVVNPENPVSeMTFEQIKAIYVGDVSNWNE--VGGEDREIVVLSRDSSSGTYEYFKDEVLEGNEYRADA 187
                                   ******************************************..5668**************************6555555 PP

                    PBP_like_2 165 igasgsegvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpveeniad 244
                                   + +  ++++ ++v +n++aigyv vay                      t    ++al v     +++++ ++p+ eni +
  gi|91772771|ref|YP_565463.1| 188 LITPSTGAIIQTVsQNQNAIGYVGVAYLD-------------------GT----TKALAV-----DNGSGAEEPTSENILA 240
                                   55555666666665889999999998554...................34....899999.....999************* PP

                    PBP_like_2 245 gayPlsrftyiivyqpyayhgnnaalakaFldyllsd 281
                                   g+yPl r++y++++ ++       +la +F++++ s+
  gi|91772771|ref|YP_565463.1| 241 GTYPLARPLYFYTNGEP------TGLALEFIEFISSE 271
                                   ***************99......9*********9876 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.2   1.6e-22   9.7e-19       2     156 ..      55     217 ..      54     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.6e-22
                                   HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS CS
                      PBP_like   2 eelaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkk 82 
                                   e ++ + p+++v++++ Gsg G++al +ge+dia++++  k +e  na+      +gi+ v+ + a + +++vv+++np  
  gi|91772771|ref|YP_565463.1|  55 EVFMMEYPDTSVSIIGGGSGVGIAALIDGEIDIAMTSREMKGSEIENAQ-----ANGIDPVEQTIAWDGISVVVNPENPVS 130
                                   6678889*******************************88867666666.....368889*******************95 PP

                                   ..............--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCC CS
                      PBP_like  83 ..............itnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradv 147
                                                 ++nw+++   d+++++  R+ +SGt  +f +++    +++++++  a    s +a+ ++V++++ ++
  gi|91772771|ref|YP_565463.1| 131 emtfeqikaiyvgdVSNWNEVggEDREIVVLSRDSSSGTYEYFKDEV----LEGNEYRADALITPSTGAIIQTVSQNQNAI 207
                                   56666677777777******************************999....556778888999****************** PP

                                   EC.CCGG-HC CS
                      PBP_like 148 gv.gieavae 156
                                   g+ g++  + 
  gi|91772771|ref|YP_565463.1| 208 GYvGVAYLDG 217
                                   *878877665 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0     9e-05      0.54      28      69 ..      57      98 ..      54     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 9e-05
                                  HHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSSCCTT CS
                LysR_substrate 28 fraryPevelelvegdseelldllaegelDlairagppedsg 69
                                  f+ +yP+ ++++  g s   +++l +ge+D+a ++++   s+
  gi|91772771|ref|YP_565463.1| 57 FMMEYPDTSVSIIGGGSGVGIAALIDGEIDIAMTSREMKGSE 98
                                  8899****************************9987765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2182.36
//
Query:       gi|91772772|ref|YP_565464.1|  [L=594]
Description: ATP-dependent OLD family endonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-26   91.7  16.8    7.4e-26   91.7  16.8    3.1  2  AAA_15     AAA ATPase domain
      3e-22   79.4   0.1    1.6e-11   44.1   0.0    2.4  2  DUF2813    Protein of unknown function (DUF2813)
    1.9e-16   60.8   4.0    1.9e-16   60.8   4.0    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    1.4e-08   35.5   3.9    1.4e-08   35.5   3.9    2.7  2  AAA_23     AAA domain
    6.3e-05   22.5   0.1     0.0011   18.4   0.0    2.5  2  SMC_N      RecF/RecN/SMC N terminal domain
     0.0026   17.4   0.0     0.0059   16.3   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.075   13.2   3.6        4.5    7.4   0.9    2.6  2  p25-alpha  p25-alpha


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7  16.8   2.9e-29   7.4e-26       3     368 ..       5     357 ..       4     358 .. 0.59
   2 ?   -2.4   6.7       1.1   2.9e+03      96     184 ..     487     560 ..     403     594 .] 0.47

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 2.9e-29
                        AAA_15   3 IkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83 
                                   Ik+++i  FR l+++e++l+  +t+l G Nn+GK+s+l+al+l l n         ++ ++d+ i+  +  sk+i +d+  
  gi|91772772|ref|YP_565464.1|   5 IKTVRIAGFRGLENIEVELEQ-TTILTGMNNTGKTSFLKALQLALGNR-------QFVSQDDFFIK-GDFVSKEIIVDLLI 76 
                                   99*******************.************************88.......23333333333.55777778888777 PP

                        AAA_15  84 ...........aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekee 153
                                              ++++++++ + +++ ++++          ++++ + ++ +++  +n+++++ +      + +   ++k +
  gi|91772772|ref|YP_565464.1|  77 vpingdgderdDFSPDWETLFTIERVRNDDAG--------RSFVPLRTVITFDEVNNNYKTQQFI----LKFWPELIKKFD 145
                                   66555544433222333333333333333322........2333333333344333333333333....334444444444 PP

                        AAA_15 154 klekekeelkid.kedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqek 233
                                      +e++++  +  +d+ + +k   +++  +e          i + +  a+R++ ++ +    s+lgk ++ki+ +   + 
  gi|91772772|ref|YP_565464.1| 146 VPGSEQKDINWYeVKDIGDSSK---SNFHFDE----------IPFFYMDAQRDILEDIKLR-FSNLGKMLSKIKYSD--DD 210
                                   4444444444443444444444...5555555..........6677777777777766665.445556655554431..11 PP

                        AAA_15 234 l.............eeelteklkeiqeklkeidkklaeelk....kilkkkidkikkfnykgkkneeieik.........d 288
                                                   ++  +l+ ++++lke+d  ++++ +      ++kki ++               +          
  gi|91772772|ref|YP_565464.1| 211 IneiesqiktlnekAVSSSPILSILKTNLKELDTAMDSHGEgieiTPFTKKIRDL---------------NkgltiyyndQ 276
                                   1111111111122222223333333333333333333333354444444444444...............25555555666 PP

                        AAA_15 289 deelplnknGsGvqrllllillileaekk.....dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   +e++p+++ G G+++  +l+ l+++         ++  +   il iEEPEahLHp+aqk l++++ +++ ++    ii+TH
  gi|91772772|ref|YP_565464.1| 277 NESFPMENHGMGTRSWSSLLALKAFVFLLsnnamEKGTKFFPILTIEEPEAHLHPNAQKKLYEQIDSIVGQK----IISTH 353
                                   79***********987666666666666555598899999*****************************998....9**** PP

                        AAA_15 365 Sphi 368
                                   Sp i
  gi|91772772|ref|YP_565464.1| 354 SPSI 357
                                   **88 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                        AAA_15  96 lkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkl 176
                                   +k++++++  +l +  ++++              +l+ +++sve k ++ +  ++  + ++k+ +e +i+k d kkl+  +
  gi|91772772|ref|YP_565464.1| 487 SKKSDINCVVFLDDGNDFEK--------------QLIADNFSVEIKSAISSSCNY-MNGQHKKAKEKEIEKYDDKKLYTII 552
                                   22222222222222222222..............223333333333333333322.2223333444444444444444444 PP

                        AAA_15 177 eeslkkee 184
                                     s++++ 
  gi|91772772|ref|YP_565464.1| 553 MGSKTQYG 560
                                   45555554 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   1.6e-11   4.1e-08       3      63 ..       5      62 ..       3      97 .. 0.85
   2 !   44.1   0.0   6.3e-15   1.6e-11     269     369 ..     302     401 ..     273     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.6e-11
                       DUF2813  3 LerieisGFRGinrLSlsleentvLiGENaWGKSSLldALslilnvekelyqFtlkDFhvd 63
                                  ++ + i+GFRG++ + ++le++t+L G N  GK S l+AL l+l + + +   +++DF+++
  gi|91772772|ref|YP_565464.1|  5 IKTVRIAGFRGLENIEVELEQTTILTGMNNTGKTSFLKALQLALGNRQFV---SQDDFFIK 62
                                  67899***************************************988644...45677765 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 6.3e-15
                       DUF2813 269 tllqakgkvelkriarPilllEdpearLHPtmlaiaWellellPlQkiltTNSveLlsqvplesirrLvResdrtqaysle 349
                                    +l +++ +e      Pil +E+pea+LHP   + ++e ++++  Qki++T S  + s+  l++ir    +++++++ ++e
  gi|91772772|ref|YP_565464.1| 302 VFLLSNNAMEKGTKFFPILTIEEPEAHLHPNAQKKLYEQIDSIVGQKIISTHSPSITSAARLSQIRNFY-KNEKVTCGKIE 381
                                   3444444455455567*************************************************9986.578999***** PP

                       DUF2813 350 rkslskedlRriaFHirlnR 369
                                    ++l  ed+R+i   +  +R
  gi|91772772|ref|YP_565464.1| 382 TDKLEPEDIRQINRQVTNTR 401
                                   ************98887777 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 !   60.8   4.0   7.3e-20   1.9e-16       2     301 ..      27     357 ..      26     359 .. 0.56
   2 ?   -3.8   0.0       3.3   8.5e+03      58     109 ..     490     540 ..     474     547 .. 0.59

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 7.3e-20
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie.......eflsqgvryryg 75 
                                   ++l+G N++GK+++L+al+l+ +           ++ +++ ++   + d+ ++ei + + i        e ++ +++++  
  gi|91772772|ref|YP_565464.1|  27 TILTGMNNTGKTSFLKALQLALG-----------NRQFVSQDDFFIKGDFVSKEIIVDLLIVpingdgdERDDFSPDWETL 96 
                                   89*****************9965...........44444444444444444444444444440000000444444555555 PP

                        AAA_21  76 lrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawslll 156
                                   +++er +        + +++  +l+     +e ++ + + + i + + +   k+  + +++++++     di+    s  +
  gi|91772772|ref|YP_565464.1|  97 FTIERVRN------DDAGRSFVPLRTVITFDEVNNNYKTQQFILKFWPELIKKFDVPGSEQKDINWYEVKDIGDSSKSNFH 171
                                   55555555......3333333333333333333333333333333333333333322222222222222222222222222 PP

                        AAA_21 157 lldglrke....rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.............. 219
                                    ++  + +    r  l +i  ++ +  k +  ++   + ++++e+ + +l+e+ ++          +              
  gi|91772772|ref|YP_565464.1| 172 FDEIPFFYmdaqRDILEDIKLRFSNLGKMLSKIKYSDDDINEIESQIKTLNEKAVS----------Sspilsilktnlkel 242
                                   22111111222344444444444444444444444444444444444444444444..........144444455559999 PP

                        AAA_21 220 .........................gvvflengdgqelparelSdGtkrll......alltallralkkg..........s 259
                                                            g++++ n++   +p+ + ++Gt+++       a    +  +l ++          +
  gi|91772772|ref|YP_565464.1| 243 dtamdshgegieitpftkkirdlnkGLTIYYNDQNESFPMENHGMGTRSWSsllalkA----FVFLL-SNnamekgtkffP 318
                                   999999999999999999*****88888888888888999999*******76533322....33333.3336777****** PP

                        AAA_21 260 llliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                   +l i+EpE++LHP ++++l+e +++      Q i++THSp++
  gi|91772772|ref|YP_565464.1| 319 ILTIEEPEAHLHPNAQKKLYEQIDSIVG---QKIISTHSPSI 357
                                   ***********************99999...*********98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.3
                        AAA_21  58 fefeieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeed 109
                                   + + +  fl++g++++  l  +++ v e +s+  +    +  + k+++e+e 
  gi|91772772|ref|YP_565464.1| 490 SDINCVVFLDDGNDFEKQLIADNFSV-EIKSAISSSCNYMNGQHKKAKEKEI 540
                                   44444457778888888888888877.5555555555555555555555444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   3.9   5.5e-12   1.4e-08       2     184 ..       8     238 ..       7     270 .. 0.61
   2 ?   -0.1   3.0      0.43   1.1e+03      90     154 ..     363     468 ..     321     550 .. 0.56

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 5.5e-12
                        AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks....grgfeksdveiese.......... 68 
                                   ++i +fr +++ e++++   t++tG+N +GKT++l A++laL+++   + +++    +++f++ ++ +             
  gi|91772772|ref|YP_565464.1|   8 VRIAGFRGLENIEVELE-QTTILTGMNNTGKTSFLKALQLALGNRQ--FVSQDdffiKGDFVSKEIIVDLLivpingdgde 85 
                                   789*************9.899**********************953..344334455666666666644445555655665 PP

                        AAA_23  69 .......gkvkayveltfenkdgry......trsiererelskkkgkttkkaklellei............deleqfisel 124
                                           ++   +e+  +++ gr+         i  ++ +  ++ kt+++  +++ e             d ++ +++++
  gi|91772772|ref|YP_565464.1|  86 rddfspdWETLFTIERVRNDDAGRSfvplrtV--I--TFDEVNNNYKTQQFILKFWPELikkfdvpgseqkDINWYEVKDI 162
                                   55555433444447777777777667765321..2..22222233333333333333334445666666677788888887 PP

                        AAA_23 125 lgskki.....ilnlilflgqerfeefelkdkkerleelekeleeledekkllekleqekekek............e 184
                                    +s+k+     +++++ + +q +   ++ k +++ l ++  +++   d+++++e +++ +++++            +
  gi|91772772|ref|YP_565464.1| 163 GDSSKSnfhfdEIPFFYMDAQRD-ILEDIKLRFSNLGKMLSKIKYSDDDINEIESQIKTLNEKAvssspilsilktN 238
                                   77777766554556555555544.34444556667777777777777777777777666665555445533322222 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.43
                        AAA_23  90 iererelskkkgkttkkaklelleideleqfisellgskkiil.nlilflgqerfeefel....kdkke............ 153
                                   +++ r+ +k++++t  k ++++le+++ +q+ ++  + + +i+ + +l + ++++ee++l    ++ ++            
  gi|91772772|ref|YP_565464.1| 363 LSQIRNFYKNEKVTCGKIETDKLEPEDIRQINRQVTNTRGEIFfSKVLVFVEGETEEQALpifaEKYFKkspveigldfig 443
                                   556677777778888888888888888888888888877775555555555555444444333322222233334555555 PP

                        AAA_23 154 ........................r 154
                                                            
  gi|91772772|ref|YP_565464.1| 444 vgghpkylpflrfaealnipwlilS 468
                                   5555555555554444444444441 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.3e-07    0.0011       2      52 ..       5      52 ..       4      59 .. 0.90
   2 ?    0.9   0.0     0.098   2.5e+02     156     205 ..     314     361 ..     292     376 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.3e-07
                                  EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.T CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGers 52
                                  +k+++i +F+ +  +++++++++  t+++G N  GK+++l A++  LG+r+
  gi|91772772|ref|YP_565464.1|  5 IKTVRIAGFRGL--ENIEVELEQ-TTILTGMNNTGKTSFLKALQLALGNRQ 52
                                  899*********..688888887.99**********************765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.098
                                   CS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 156 vkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                    k  p+  + e +a+L  +  kk+ e +++     Q i+ +++  +++ a
  gi|91772772|ref|YP_565464.1| 314 TKFFPILTIEEPEAHLHPNAQKKLYEQIDSIV--GQKIISTHSPSITSAA 361
                                   455799999*******************9998..99**999998887776 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 !   16.3   0.0   2.3e-06    0.0059      11      47 ..      12      49 ..       5      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-06
                        AAA_29 11 tfdg.htieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                   f+g + ie++l+++t+ltG + +GK+++l A+q  L 
  gi|91772772|ref|YP_565464.1| 12 GFRGlENIEVELEQTTILTGMNNTGKTSFLKALQLALG 49
                                  58899999***99********************98875 PP

>> p25-alpha  p25-alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.007        18      31      81 ..     389     434 ..     367     450 .. 0.81
   2 ?    7.4   0.9    0.0018       4.5      42     121 ..     476     550 ..     467     557 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.007
                     p25-alpha  31 DckiidkkvtstdvDiiFsKvkaksarkitfeqfkealeelaekkfkkkkk 81 
                                   D   i+++vt+t+ +i+FsKv       ++ e  ++al  +aek f kk++
  gi|91772772|ref|YP_565464.1| 389 DIRQINRQVTNTRGEIFFSKVL----VFVEGETEEQALPIFAEKYF-KKSP 434
                                   6777999**************9....56677788888888888855.5544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                     p25-alpha  42 tdvDiiFsKvkaksarkitfeqfkealeelaekkfkkkkkeeeleliekliegkgPklqgvtkatkagavdrltDtskYT 121
                                   ++v   FsK+  +++++i++  f +  +++ ++ +++++++e +      i+++   ++g  k  k++++++++D++ YT
  gi|91772772|ref|YP_565464.1| 476 ESVLSQFSKCS-SKKSDINCVVFLDDGNDFEKQLIADNFSVEIK----SAISSSCNYMNGQHKKAKEKEIEKYDDKKLYT 550
                                   55666788887.45577888888777777777766556655555....33344446779999*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3900.66
//
Query:       gi|91772773|ref|YP_565465.1|  [L=587]
Description: ATP-dependent DNA helicase Rep [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-55  188.8   3.5    1.7e-55  188.8   3.5    2.2  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
      2e-33  116.2  10.4      3e-21   76.2   1.0    2.5  3  UvrD_C           UvrD-like helicase C-terminal domain
    2.1e-27   96.3   0.0    5.6e-27   94.9   0.0    1.8  1  AAA_19           AAA domain
    2.3e-09   37.0   0.0    4.6e-09   36.0   0.0    1.6  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    2.9e-09   37.0   0.2     0.0019   18.0   0.0    3.4  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    2.9e-08   33.6   0.0    0.00029   20.6   0.0    2.3  2  AAA_30           AAA domain
      1e-06   28.5   1.6     0.0001   22.0   1.7    3.2  2  AAA_12           AAA domain
     0.0003   20.3   0.1       0.29   10.5   0.0    3.2  3  PhoH             PhoH-like protein
      0.002   18.0   0.4      0.017   14.9   0.0    2.5  2  AAA_11           AAA domain
     0.0042   17.4   1.5        3.6    7.9   1.5    2.9  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.054   13.5   2.4        1.3    9.1   0.1    3.4  3  P2               P2 response regulator binding domain
      0.089   12.8   9.6      0.018   15.0   2.3    3.3  3  ResIII           Type III restriction enzyme, res subunit
       0.11   12.8   0.3        1.7    9.0   0.3    2.5  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   3.5   1.2e-58   1.7e-55       1     308 [.       7     268 ..       7     276 .. 0.92
   2 ?   -2.9   3.5       2.7   3.7e+03     168     236 ..     366     488 ..     278     514 .. 0.41

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 1.2e-58
                                   SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HH CS
                 UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdder 81 
                                   l+++q+e++   +g i v AsAGsGKT+vl+er+ +l++++   ++++l++TFTnkA eE+keR+  + + +         
  gi|91772773|ref|YP_565465.1|   7 LSKKQEEIVFAENGAIYVKASAGSGKTRVLTERVRYLLDKT---NKKVLALTFTNKAGEEIKERLSDISEID--------- 75 
                                   57899***********************************9...99*********************98876......... PP

                                   HHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHH CS
                 UvrD-helicase  82 lrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldkkkleklikels 162
                                           +++ ++T+Hsfcq il+++ n ig+ +  +i+++e+    +++el+++ +  ++ ++ ++ k+k +++ +   
  gi|91772773|ref|YP_565465.1|  76 --------NRVFVGTFHSFCQSILENHGNLIGRAQMPHIFEDES----DRLELVEQAIM-QTPSYAEIYKNKSKQNQI--- 140
                                   ........79**********************************....79999999997.666778888888776644... PP

                                   CCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHH CS
                 UvrD-helicase 163 ksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkkeenalDfsdllhallell 243
                                                     ++  ++sk+k +++s  el +        ++ +  ++++y e ++++na+Df+dll  + +ll
  gi|91772773|ref|YP_565465.1| 141 --------------DYRYSVLSFISKVKRELISDSELGQ-----HTTDDNLVLIYHNYREILDNQNAIDFDDLLFLAHNLL 202
                                   ..............34568999****************9.....56889999***************************** PP

                                   HHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT.EEEEE-GGG--GGGGTB-THHHH CS
                 UvrD-helicase 244 eeneelaealrerykeiliDEyQDTnkiQyrilkllasghee.lfmvGDpkQsIYgFRgAdielfl 308
                                    + ++ a+ +r+ +  i iDE+QD+n++Qy++l  l++g+ + ++mvGD +QsIY F g+ ++ + 
  gi|91772773|ref|YP_565465.1| 203 VNYPKTAALYRRSFFAICIDEAQDLNNAQYQLLLALVNGEFNnIIMVGDSNQSIYNFNGSSPKYMD 268
                                   ************************************9999777*****************999875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                                   H....................................................HHHCCCHHHHHCHHHHHHHHHHHTTCCT CS
                 UvrD-helicase 168 k....................................................keelslskskaeelrelvskakekqlsp 196
                                                                                          +l+ ++s   +l+ ++          
  gi|91772773|ref|YP_565465.1| 366 FnqlenlltennlpfyykmtpgmirfesdlmkifdlslrvrlnplddlhkqrlLNYLNIKNSENMNLESMIPL-------- 438
                                   0222222222222333335555555555555555555543333333333333311111111111111111111........ PP

                                   THHCHSS................TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHH CS
                 UvrD-helicase 197 kelkkaf................ekasdlqkkiaeflkeyqeqkkeenalDfsdll 236
                                                             s+ ++k++ f  ++  ++++e+++ f+d+ 
  gi|91772773|ref|YP_565465.1| 439 ------VpdelvqnlillvtelhDDGSNIKQKLESFRDTLTVNDENEKNMIFNDIT 488
                                   ......12222222222222233444444445555555555555555554444444 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.3   3.1e+03      86      95 ..      62      71 ..      26     159 .. 0.63
   2 !   45.4   3.0   5.1e-15   7.1e-12       1     140 [.     281     423 ..     281     435 .. 0.85
   3 !   76.2   1.0   2.1e-24     3e-21     177     345 ..     421     587 .]     395     587 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                                  xxxxxxxxxx RF
                        UvrD_C 86 dkiskaLkke 95
                                  ++i++ L+ +
  gi|91772773|ref|YP_565465.1| 62 EEIKERLSDI 71
                                  4444444332 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 5.1e-15
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxx RF
                        UvrD_C   1 ivLekNyRStksLlkaankflenilnrralekekktvekgekivvleaeteeeEaekiaatikall........eknekle 73 
                                   i+L++NyRS+k++l aa+k++    +       ++tv++g   +++  ++e +Ea++++++i++ll        e ++ le
  gi|91772773|ref|YP_565465.1| 281 IKLNENYRSSKEVLLAAKKIIPDESDI------SETVKEGI-FKIHCLKNEHDEAQWVVDKINELLtakthddiEGEITLE 354
                                   78*******************444333......58999998.888888999*********************999999*** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C  74 diavLvRsnkdadkiskaLkkegipfnvvd..eekfFkreeikdilaylkllankqdkialkrilkrlv 140
                                   +iavL R+++  +++++ L ++++pf      ++  F+   +k +   l++ +n+ d++  +r+l+ l 
  gi|91772773|ref|YP_565465.1| 355 KIAVLARNKYIFNQLENLLTENNLPFYYKMtpGMIRFESDLMKIFDLSLRVRLNPLDDLHKQRLLNYLN 423
                                   ***********************9986333236666888899988899999999999999999888664 PP

  == domain 3  score: 76.2 bits;  conditional E-value: 2.1e-24
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                        UvrD_C 177 Fieliraleeknlelllkk.iektaeerqalvskyadlfkelaeklaelkekseskrkkee..klenlreLysllkelekk 254
                                   ++ +i++ e+ nle ++    ++  ++   lv++  d+ +++++kl++++++   ++++e+    + + e+++   ++ k 
  gi|91772773|ref|YP_565465.1| 421 YL-NIKNSENMNLESMIPLvPDELVQNLILLVTELHDDGSNIKQKLESFRDTLTVNDENEKnmIFNDITEILNHWHNYAK- 499
                                   44.7777888888877877666666667788888999999999******9999988855555455566666666666666. PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                        UvrD_C 255 eeeeeveeklneileiatLseseleeskkkekipiiTiHqAKGlEFdvVflagleegtfPsyrskk..ekrleEEkRlfYV 333
                                     +++++ +l ++ +  +L ++ +  +++++ i+++T+H  KG EFd+Vf++g++++tfP yr+ +    +l  Ek+ +YV
  gi|91772773|ref|YP_565465.1| 500 --KTDNK-SLHQFKNAMALGKTHP--LTQHSGITLSTVHTMKGQEFDIVFIIGMDDETFPDYRAVRsgGIELIQEKNNLYV 575
                                   ..44544.5********9*99999..55559***********************************66335679******* PP

                                   xxxxxxxxxxxx RF
                        UvrD_C 334 aiTRAkkrLfis 345
                                   a TRAk+ L+++
  gi|91772773|ref|YP_565465.1| 576 AFTRAKRFLYVT 587
                                   **********96 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0     4e-30   5.6e-27       1     146 []      11     260 ..      11     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 4e-30
                        AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.....atTiHrla 76 
                                   q+e+v  ++++ + v a +G+GKTrvl+++v++l++ ++   +++l+++ft++A +e++erl+ + +        T+H++ 
  gi|91772773|ref|YP_565465.1|  11 QEEIV-FAENGAIYVKASAGSGKTRVLTERVRYLLDKTN---KKVLALTFTNKAGEEIKERLSDISEIdnrvfVGTFHSFC 87 
                                   78999.8999*************************9994...79******************77666589999*******8 PP

                        AAA_19  77 l................................................................................ 77 
                                                                                                                    
  gi|91772773|ref|YP_565465.1|  88 Qsilenhgnligraqmphifedesdrlelveqaimqtpsyaeiyknkskqnqidyrysvlsfiskvkrelisdselgqhtt 168
                                   8******************************************************************************** PP

                        AAA_19  78 ....................ldfddlltealelleeaeeekkl.qeee.llivDEfqdvdelqyrLlkallgek.kklllv 135
                                                       +dfddll  a +ll +  ++  l ++ + ++ +DE+qd++  qy+Ll al++ + +++++v
  gi|91772773|ref|YP_565465.1| 169 ddnlvliyhnyreildnqnaIDFDDLLFLAHNLLVNYPKTAALyRRSFfAICIDEAQDLNNAQYQLLLALVNGEfNNIIMV 249
                                   ***************************9999999854555555155669**********************888999**** PP

                        AAA_19 136 GDpdQliyvfr 146
                                   GD +Q+iy f+
  gi|91772773|ref|YP_565465.1| 250 GDSNQSIYNFN 260
                                   ********995 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   3.4e-12   4.6e-09       3      51 ..     528     586 ..     526     587 .] 0.90

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.4e-12
                      UvrD_C_2   3 yaltihkaQGsefpaVivfdpd.laaarmgel.........rrrlLYtavTRAreklil 51 
                                   + +t+h  +G+ef++V+++ +d ++ ++  ++          ++ LY+a+TRA++ l++
  gi|91772773|ref|YP_565465.1| 528 TLSTVHTMKGQEFDIVFIIGMDdETFPDYRAVrsggieliqEKNNLYVAFTRAKRFLYV 586
                                   689******************98887775555***********************9998 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0016       2.3       1      37 [.      22      56 ..      22      93 .. 0.68
   2 !    7.5   0.0    0.0022         3      66     134 ..     219     288 ..     198     349 .. 0.71
   3 !   18.0   0.0   1.4e-06    0.0019     158     230 ..     501     584 ..     464     587 .] 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0016
               Viral_helicase1  1 ivvhGvpGcGKStlirkllrtsliltvnrptaellte 37
                                  i+v++ +G+GK++++ + +r    l + ++ + +lt 
  gi|91772773|ref|YP_565465.1| 22 IYVKASAGSGKTRVLTERVRY--LLDKTNKKVLALTF 56
                                  579999************998..43333333444333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0022
               Viral_helicase1  66 lilDEylllhaGyilllaalskakl..vilfGDplQipfhsrnasfllahlpssl..shrvgrrttyllpsdv 134
                                   + +DE++ l+ ++ +ll+al + ++  +i++GD++Q+ ++  n+  + +++  +   +++ +    +l+ +++
  gi|91772773|ref|YP_565465.1| 219 ICIDEAQDLNNAQYQLLLALVNGEFnnIIMVGDSNQSIYNF-NG--SSPKYMDEQfvHDFDPVAVIKLNENYR 288
                                   679*********9999777766554228********99885.44..333332222234555555555555555 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.4e-06
               Viral_helicase1 158 tepkgq.e.kvlvyltftqalkealgvrevttvhevqGltfdkVtlvllketdlelis..........esrenllvAlTRh 226
                                   t+ k+  + k++  l  t+ l+++ g +  +tvh   G++fd V ++  ++ +   ++          ++++nl+vA+TR+
  gi|91772773|ref|YP_565465.1| 501 TDNKSLhQfKNAMALGKTHPLTQHSGIT-LSTVHTMKGQEFDIVFIIGMDDETFPDYRavrsggieliQEKNNLYVAFTRA 580
                                   3333332347888888899999999999.*****************987555443344899*******88*********** PP

               Viral_helicase1 227 rksl 230
                                   ++ l
  gi|91772773|ref|YP_565465.1| 581 KRFL 584
                                   9755 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00029       2      67 ..       7      69 ..       6     105 .. 0.82
   2 !   10.8   0.0   0.00022       0.3      91     129 ..     218     256 ..     164     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                        AAA_30  2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLaeelg 67
                                  l+++Q+++v  ++++g     +++ AG+GKt +l++  r ++++ +++v++l+ t+ka ++++e l 
  gi|91772773|ref|YP_565465.1|  7 LSKKQEEIV--FAENG--AIYVKASAGSGKTRVLTERvRYLLDKTNKKVLALTFTNKAGEEIKERLS 69
                                  677888887..66666..6999************98736666666*****************99775 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00022
                        AAA_30  91 llivDEagmvdtkqlaallkaaekagakvilvGDerQla 129
                                    + +DEa  ++++q + ll+ ++ +   +i+vGD +Q  
  gi|91772773|ref|YP_565465.1| 218 AICIDEAQDLNNAQYQLLLALVNGEFNNIIMVGDSNQSI 256
                                   578*********************99**********964 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   1.6e+03      14      31 ..     277     294 ..     265     304 .. 0.78
   2 !   22.0   1.7   7.2e-08    0.0001     101     194 ..     489     586 ..     284     587 .] 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                        AAA_12  14 kekvvlLdtqYRmhpeIs 31 
                                   + +v+ L+++YR+ +e++
  gi|91772773|ref|YP_565465.1| 277 PVAVIKLNENYRSSKEVL 294
                                   667899******999986 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 7.2e-08
                        AAA_12 101 kllkkgseeerkkigvitpYraqvellkkklkekeeekseke............................ievntvdgfQG 153
                                   ++l+++++                                 +                            i+ +tv  + G
  gi|91772773|ref|YP_565465.1| 489 EILNHWHNY--------------------------------AkktdnkslhqfknamalgkthpltqhsgITLSTVHTMKG 537
                                   333333222................................02222233334444455555555555566*********** PP

                        AAA_12 154 rekdviilslVRsn........ekkeigflkderrlNValTRAksklii 194
                                   +e d++++     +        +++ i ++++++ l Va+TRAk+ l++
  gi|91772773|ref|YP_565465.1| 538 QEFDIVFIIGMDDEtfpdyravRSGGIELIQEKNNLYVAFTRAKRFLYV 586
                                   ******99888886777777778889*******************9987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.024        33      17      66 ..      17      65 ..       5     104 .. 0.80
   2 !   10.5   0.0   0.00021      0.29     123     186 ..     219     283 ..     213     295 .. 0.76
   3 ?    1.8   0.0       0.1   1.4e+02      87     124 ..     509     546 ..     485     551 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.024
                                  HH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT---- CS
                          PhoH 17 kkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelG 66
                                   +n  + + ++aG+GKt + ++  v++l +k+ k+++ +  + +agee+ 
  gi|91772773|ref|YP_565465.1| 17 AENGAIYVKASAGSGKTRV-LTERVRYLLDKTNKKVLALTFTNKAGEEIK 65
                                  4677888999*******87.566788999999899888888888888875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00021
                                   EEE-SGGG--HHHHHHHHTTB.-TT-EEEEEE--------------THHHHHHTTT-TTEEEEE- CS
                          PhoH 123 vilDEAQnttkeqmkmfltRl.GenskvvvtGdvtqidlpkgkksGlaealevlknvegieivel 186
                                   + +DEAQ+++++q + +l  + Ge   ++++Gd +q   + + +s      + +++ + +++++l
  gi|91772773|ref|YP_565465.1| 219 ICIDEAQDLNNAQYQLLLALVnGEFNNIIMVGDSNQSIYNFNGSSPKYMDEQFVHDFDPVAVIKL 283
                                   789**************9987578889999****9987665545555555555566666666666 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.1
                                   HTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEE CS
                          PhoH  87 LkdllgaekvekllekgkievaplaymRGrTlndafvi 124
                                    k+ +   k++ l++++ i +  ++ m+G+ ++  f+i
  gi|91772773|ref|YP_565465.1| 509 FKNAMALGKTHPLTQHSGITLSTVHTMKGQEFDIVFII 546
                                   566677788999999*********************99 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.2e-05     0.017      19     253 ..      21     254 ..       7     254 .. 0.74
   2 ?   -1.0   0.1       0.9   1.2e+03     132     191 ..     457     519 ..     410     545 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                        AAA_11  19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr.glldsegekykpkivRvgnee. 97 
                                      ++   G+gKT++++e +++l          ++++++L+ + +N+A  e+ erl++ + +d        + v vg    
  gi|91772773|ref|YP_565465.1|  21 AIYVKASAGSGKTRVLTERVRYL--------LDKTNKKVLALTFTNKAGEEIKERLSDiSEID--------NRVFVGTFHs 85 
                                   55677888***************........36899**********************32222........3333333333 PP

                        AAA_11  98 ......eriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkk 172
                                         e+ ++ + + ++ +++e++++     +l+++   ++ ++a+  ++++++++ + +    ++ ++ +++  ++++ 
  gi|91772773|ref|YP_565465.1|  86 fcqsilENHGNLIGRAQMPHIFEDESDR---LELVEQAIMQTPSYAEIYKNKSKQNQIDYRYSVLSFISKVKRELISDSEL 163
                                   4533444456666777777777777755...67777777777778887777777777777777777777777777788888 PP

                        AAA_11 173 erkelskeleeaeesleeevldeaeiv.ltTlsgagsklleklak.......kfdvviIDEAaqavE..pstliPlrlga. 242
                                    +++ +++l  +  ++ +e+ld+ + + +  l + +++ll ++ k        f ++ IDEA        + l +l +g  
  gi|91772773|ref|YP_565465.1| 164 GQHTTDDNLVLIYHNY-REILDNQNAIdFDDLLFLAHNLLVNYPKtaalyrrSFFAICIDEAQDLNNaqYQLLLALVNGEf 243
                                   8888899999999998.556655554449999999999999998899999999999999**98765511568999988877 PP

                        AAA_11 243 kkvvLvGDpkQ 253
                                   +++++vGD +Q
  gi|91772773|ref|YP_565465.1| 244 NNIIMVGDSNQ 254
                                   99999999998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.9
                        AAA_11 132 eleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskeleeaeesle...ee 191
                                      +++++l++f ++ + + ++++ + +++  e  ++ ++ ++k+ +k+l ++++++    ++
  gi|91772773|ref|YP_565465.1| 457 DGSNIKQKLESFRDTLTVNDENEKNMIFNDITEILNHWHNYAKKTDNKSLHQFKNAMAlgkTH 519
                                   334444444444444444444444444444444444444444444555555555555455444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   1.5    0.0026       3.6      93     117 ..     217     240 ..      17     254 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0026
                        AAA_22  93 elliiDEaqhlrseealeeLrslln 117
                                    ++ iDEaq l ++++++ L  l+n
  gi|91772773|ref|YP_565465.1| 217 FAICIDEAQDL-NNAQYQLLLALVN 240
                                   35667777777.6777777777777 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00098       1.3      51      76 ..      52      76 ..      40      79 .. 0.78
   2 ?   -1.9   0.0       2.6   3.5e+03      27      55 ..     115     148 ..     112     160 .. 0.60
   3 ?    2.2   0.1      0.14   1.9e+02      34      72 ..     299     336 ..     293     345 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00098
                                  EEEEEEESS-HHHHHHHHHTSSS-SE CS
                            P2 51 fevvlltkeskeeikealasiseies 76
                                  + +++ t++  eeike+l++isei++
  gi|91772773|ref|YP_565465.1| 52 LALTF-TNKAGEEIKERLSDISEIDN 76
                                  34444.******************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                                   HHTTEEEEEES-HHHHHT.....T-SSSEEEEEE CS
                            P2  27 eelgeiiksiPsvediee.....ekfdegfevvl 55 
                                   e + + i  +Ps  +i +     +++d +++v+ 
  gi|91772773|ref|YP_565465.1| 115 ELVEQAIMQTPSYAEIYKnkskqNQIDYRYSVLS 148
                                   5555667777888888885555555555555554 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.14
                                   EEES-HHHHHTT-S.SSEEEEEEEESS-HHHHHHHHHTSS CS
                            P2  34 ksiPsvedieeekf.degfevvlltkeskeeikealasis 72 
                                   k iP++ di e  + ++ f++ +l k++ +e + ++ +i 
  gi|91772773|ref|YP_565465.1| 299 KIIPDESDISET-VkEGIFKIHCL-KNEHDEAQWVVDKIN 336
                                   789********5.54888999985.455555555555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.3   1.3e-05     0.018      23      75 ..      18     104 ..       5     250 .. 0.65
   2 ?   -1.5   0.0       1.5   2.1e+03     103     118 ..     327     342 ..     266     388 .. 0.54
   3 ?   -0.5   0.1       0.8   1.1e+03      97     130 ..     473     507 ..     410     544 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                   TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG............................. CS
                        ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef............................. 74 
                                   ++  +++k+  G+GKT+v+++ +++ll k + +k+l l  +++  e  +e++                             
  gi|91772773|ref|YP_565465.1|  18 ENGAIYVKASAGSGKTRVLTERVRYLLDKTN-KKVLALTFTNKAGEEIKERLsdiseidnrvfvgtfhsfcqsilenhgnl 97 
                                   556789**********************955.7*********999999998844444444444444444444444444444 PP

                                   ......G CS
                        ResIII  75 ......k 75 
                                          
  gi|91772773|ref|YP_565465.1|  98 igraqmP 104
                                   4444440 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                   .-SEEEEEHHHHHHTH CS
                        ResIII 103 nkkilvttiqsldads 118
                                   +++ +v +i++l  ++
  gi|91772773|ref|YP_565465.1| 327 EAQWVVDKINELLTAK 342
                                   3333333333333333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.8
                                   .......-SEEEEEHHHHHHTH.........HHHT CS
                        ResIII  97 kekdstnkkilvttiqsldadseee.eeeseellr 130
                                   + +d+++k++++  i ++ ++ ++  ++++++ l+
  gi|91772773|ref|YP_565465.1| 473 TVNDENEKNMIFNDITEILNHWHNYaKKTDNKSLH 507
                                   44555555555555555555554443333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3    0.0012       1.7      26     160 ..      21     240 ..      13     249 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                        AAA_16  26 lvllsGesGvGKsslvrellralekd............................ggiflrgkcdqlesaipysalaqalar 78 
                                   ++++   +G+GK+++++e  r+l ++                            +                  +++ ++  
  gi|91772773|ref|YP_565465.1|  21 AIYVKASAGSGKTRVLTERVRYLLDKtnkkvlaltftnkageeikerlsdiseiD----------------NRVFVGTF-H 84 
                                   67788889********777778887767644433333332222222222222221................23344444.2 PP

                        AAA_16  79 eellrqllde...............aesaeleawrekleeala...................................... 106
                                    ++++ +l++               +                +                                      
  gi|91772773|ref|YP_565465.1|  85 -SFCQSILENhgnligraqmphifeD----------------Esdrlelveqaimqtpsyaeiyknkskqnqidyrysvls 148
                                   .4444444444333333322222211................022233333344455556666677777777777777777 PP

                        AAA_16 107 .................................avpelagaea........srllellkrllallsrder.....plvlvl 141
                                                                    +                  +ll l  +ll+ +++++       + +++
  gi|91772773|ref|YP_565465.1| 149 fiskvkrelisdselgqhttddnlvliyhnyreI--------LdnqnaidfDDLLFLAHNLLVNYPKTAAlyrrsFFAICI 221
                                   7777777776555555555555555544444431........032223334444444444443333323355555799999 PP

                        AAA_16 142 DdlqwadeaslqllaaLlr 160
                                   D++q++  a+ qll aL+ 
  gi|91772773|ref|YP_565465.1| 222 DEAQDLNNAQYQLLLALVN 240
                                   9999999999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 3426.56
//
Query:       gi|91772774|ref|YP_565466.1|  [L=190]
Description: GPR1/FUN34/yaaH [Methanococcoides burtonii DSM 6242]
Scores for 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  143.6  19.6    8.2e-42  143.2  19.6    1.1  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2  19.6   4.6e-46   8.2e-42      12     194 ..       5     180 ..       2     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 4.6e-46
               Gpr1_Fun34_YaaH  12 vpkrkfaNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsy 92 
                                   v+k + aNPaPlgl++f++tt +l+l+n+g  g+ +   ++++ lfyGG++q++aG++e+  gntFg+ta++sYG+Fwl++
  gi|91772774|ref|YP_565466.1|   5 VTKITTANPAPLGLMGFGMTTVLLNLHNAGFFGLGV--TILAMGLFYGGIAQIIAGLMEWKNGNTFGTTAFTSYGAFWLTL 83 
                                   567789****************************99..699999************************************* PP

               Gpr1_Fun34_YaaH  93 aaili.pgfgilaaYeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvlkAgg 172
                                    +ili p++g+ ++        +  ++ yl++w +ftf +++ t++++ al ++f  l+l flllai++ltg+a +++ +g
  gi|91772774|ref|YP_565466.1|  84 VFILIaPKLGMGDTPG------AIEMSAYLFMWGLFTFGMFIGTFKANRALQVVFGSLTLLFLLLAISDLTGNAALKQFAG 158
                                   *999957999988873......445788***************************************************** PP

               Gpr1_Fun34_YaaH 173 vfgiiaaflawYnalaglatke 194
                                   + gi++++ a Y ala++++++
  gi|91772774|ref|YP_565466.1| 159 YEGIFCGLSAIYLALAEIINEK 180
                                   ******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1256.89
//
Query:       gi|91772775|ref|YP_565467.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-22   76.9   0.0    1.8e-21   75.9   0.0    1.5  1  DUF772       Transposase domain (DUF772)
    1.8e-16   60.4   2.1    5.5e-16   58.9   2.1    1.8  1  DDE_Tnp_1    Transposase DDE domain
     0.0038   17.4   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.037   13.7   0.0      0.067   12.9   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   5.1e-25   1.8e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.1e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+++    +++++e
  gi|91772775|ref|YP_565467.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERIAQsgkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   2.1   1.5e-19   5.5e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.5e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772775|ref|YP_565467.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772775|ref|YP_565467.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772775|ref|YP_565467.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772775|ref|YP_565467.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772775|ref|YP_565467.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772775|ref|YP_565467.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.067      72     132 ..     213     276 ..     160     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772775|ref|YP_565467.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2027.08
//
Query:       gi|91772776|ref|YP_565468.1|  [L=455]
Description: dihydroorotase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-21   76.7   0.2    4.2e-21   75.6   0.2    1.7  1  Amidohydro_1  Amidohydrolase family
    1.1e-14   54.8   0.2    1.4e-06   28.1   0.0    2.2  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.2   4.7e-25   4.2e-21       3     341 ..      53     428 ..      51     431 .. 0.70

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4.7e-25
                                   EE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT.SSSEE CS
                  Amidohydro_1   3 lPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee.lplgl 77 
                                   +PG+ID+HvH++             +p+++ +e   +g   a  +Gtttv ++++t ++     +++  l+ a +  ++++
  gi|91772776|ref|YP_565468.1|  53 IPGGIDVHVHFR-------------EPGMIKKEDWYTGSCSAAAGGTTTVVEHPNTIPPtidksSFKEKLKLANRkSIIDF 120
                                   8**********9.............******************************76669999988888886666688999 PP

                                   EEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHH CS
                  Amidohydro_1  78 rilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkge 158
                                   +i gg   ++ ++ e+   ++e  ++ + e+  ++++g+++          + +   +eal   k+ d+  +iHa +++  
  gi|91772776|ref|YP_565468.1| 121 GINGG---VT-KNLESLSLLWELGVTSFGEIFMAESTGGLN----------IDEKDFSEALGIIKELDAVACIHAEDENIR 187
                                   99988...44.999999999999999997777777666666..........4444566777788999********444433 PP

                                   HHHHHHHHTTTEEEETTTTSTCC.....HHTTTHCCEEEHCTCEEE...HH..HHHHHHHHHHHHCEEHHHHHHHH..... CS
                  Amidohydro_1 159 vedaeaafgetiehgthlevaes.....lglldeiklilahgvhlt...pt..eaellkerlkeagvahcpfsnsi..... 224
                                     + e+  +++   ++h + + s     +++ + + +i+++g+  +    +  +a  l+++  ea va+    +s+     
  gi|91772776|ref|YP_565468.1| 188 L-ENEKLLKHDLSPNSHSRIR-SnlcegIAVQNALETIAEKGTRSHfchIStlDALGLIRK--EAYVAQNEGRESKvtcet 264
                                   3.3444444344333333332.235555555666666655555444443222455555555..666664444444444555 PP

                                   ..........................SEHHHHHHHHHHHHTSCEEEEEECT..............TSSCCG..GHHHHHHH CS
                  Amidohydro_1 225 ..........................lrsgrealrkaldeGvkvglgtDga..............asgnsl..nlleelrl 263
                                                              r ++ al +a+++G+  ++++D+a               sg  +  +l   + l
  gi|91772776|ref|YP_565468.1| 265 aphhlflstrdwdrlgtfgkmnpplrDRRNVKALMNAINDGTVNAIASDHAphsefdkdldirsaPSGVPGveTL---MPL 342
                                   5555777777899999999999999999*****************************996555543333333222...444 PP

                                   HHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-T..TTSSSS-TTSB--EEEECC...CT...........CGGGTT CS
                  Amidohydro_1 264 alklqrgllye.deegglslkealrmaTingAkalgld..dkvGsievGkdADlvvvdl...di...........laafvg 327
                                   +l          +++  l++ + +++++ n+A+++gld  + +G +++G+dADl++vd+   ++            ++f++
  gi|91772776|ref|YP_565468.1| 343 ML--------MaVKKNLLPIGRMIEVTSRNPARIFGLDtkHSKGVFAEGYDADLIIVDThtaTPikadklhskagWTPFEN 415
                                   44........2256888********************86678*****************6552256666666665444444 PP

                                   TCTSEEEEEEEETT CS
                  Amidohydro_1 328 lkkdgnvkkvivkG 341
                                   +     +k++i kG
  gi|91772776|ref|YP_565468.1| 416 MDA-IFPKMTISKG 428
                                   433.3355555555 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.4e-09   1.3e-05       2      54 ..      44      95 ..      43     101 .. 0.86
   2 !   28.1   0.0   1.5e-10   1.4e-06     354     472 ..     292     431 ..     209     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.4e-09
                  Amidohydro_3  2 viDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagt 54
                                   iDakG+l +PG++D+H H  + g  +    ++   ++++++g +t+v ++ +t
  gi|91772776|ref|YP_565468.1| 44 LIDAKGALTIPGGIDVHVHFREPG--MiKKEDWYTGSCSAAAGGTTTVVEHPNT 95
                                  59*****************99999..5588888888999999999999887666 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.5e-10
                  Amidohydro_3 354 argstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg.....evlrpdeelsleealalyTrgpAkalgle 428
                                   +r++ +++  +n+g   a +sD ap + fd+   i++a  + ++ +        +  ++ l++  ++  ++r+pA+++gl+
  gi|91772776|ref|YP_565468.1| 292 RRNVKALMNAINDGTVNAIASDhAPHSEFDKDLDIRSAPSGVPGVETlmplmLMAVKKNLLPIGRMIEVTSRNPARIFGLD 372
                                   566777788888888888888888888888888888887777765557777656667889********************9 PP

                  Amidohydro_3 429 d..rkGtLevGadADlvvld.adpldvdppelaear............vrltvvdGrvv 472
                                   +   kG  ++G+dADl++ d   +  +++++l+++             +++t+ +G+v+
  gi|91772776|ref|YP_565468.1| 373 TkhSKGVFAEGYDADLIIVDtHTATPIKADKLHSKAgwtpfenmdaifPKMTISKGEVI 431
                                   95567***************845555666677887789999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2949.68
//
Query:       gi|91772777|ref|YP_565469.1|  [L=301]
Description: KaiC [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-44  152.1   0.2    1.4e-43  148.9   0.2    2.0  1  ATPase           KaiC
    4.8e-07   29.5   0.0    7.2e-07   28.9   0.0    1.4  1  RecA             recA bacterial DNA recombination protein
    1.2e-06   28.0   0.0    2.6e-06   27.0   0.0    1.6  2  DnaB_C           DnaB-like helicase C terminal domain
    1.6e-06   27.5   0.1    3.1e-06   26.6   0.1    1.4  1  Rad51            Rad51
    2.9e-06   27.0   0.0    1.6e-05   24.6   0.0    2.0  1  AAA_25           AAA domain
    1.5e-05   23.8   0.2      0.032   12.9   0.0    2.2  2  GvpD             GvpD gas vesicle protein
    3.2e-05   23.7   0.0    7.3e-05   22.6   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
    8.3e-05   23.0   0.0    0.00017   22.0   0.0    1.5  1  AAA_16           AAA ATPase domain
    0.00015   21.8   0.0    0.00042   20.4   0.0    1.8  2  AAA_14           AAA domain
    0.00019   21.2   0.3    0.00086   19.1   0.1    2.1  2  AAA_24           AAA domain
    0.00046   20.5   0.0     0.0012   19.2   0.0    1.6  1  AAA_22           AAA domain
    0.00051   19.2   0.0    0.00082   18.5   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
    0.00071   18.8   0.0     0.0012   18.1   0.0    1.2  1  PAXNEB           PAXNEB protein
     0.0011   18.5   0.0     0.0024   17.4   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0011   19.5   0.0     0.0041   17.7   0.0    2.0  2  AAA_18           AAA domain
     0.0016   18.3   0.0      0.004   17.1   0.0    1.6  1  NACHT            NACHT domain
     0.0017   18.8   0.1     0.0042   17.5   0.1    1.8  1  AAA              ATPase family associated with various cellul
     0.0048   16.8   0.1       0.01   15.7   0.1    1.6  1  NTPase_1         NTPase
     0.0051   17.1   0.0      0.012   15.9   0.0    1.5  1  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.016   14.4   0.0       0.24   10.5   0.0    2.2  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.019   15.0   0.0      0.053   13.5   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
      0.026   13.8   0.0      0.053   12.8   0.0    1.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.028   14.2   0.0      0.062   13.1   0.0    1.5  1  AAA_11           AAA domain
      0.033   14.7   0.2      0.078   13.5   0.2    1.8  1  ABC_tran         ABC transporter
      0.033   14.4   0.1      0.061   13.6   0.1    1.4  1  AAA_28           AAA domain
      0.038   14.1   0.0       0.11   12.6   0.0    1.7  2  AAA_33           AAA domain
      0.044   13.5   0.0      0.083   12.6   0.0    1.4  1  AAA_30           AAA domain
      0.048   12.5   0.0      0.088   11.6   0.0    1.3  1  PPV_E1_C         Papillomavirus helicase
      0.057   13.8   0.0       0.23   11.8   0.0    2.0  1  RNA_helicase     RNA helicase
      0.064   12.8   0.0       0.15   11.6   0.0    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.069   12.9   0.0       0.18   11.5   0.0    1.7  2  Sigma54_activat  Sigma-54 interaction domain
       0.14   11.9   0.2       0.28   10.9   0.2    1.4  1  AAA_29           P-loop containing region of AAA domain
       0.59   10.5   3.6         14    6.2   0.1    3.4  4  Ca_bind_SSO6904  Calcium binding protein SSO6904


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 !  148.9   0.2   2.6e-46   1.4e-43       1     225 [.      62     271 ..      62     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 2.6e-46
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   v+tg+ glD++l+gG+p+g++v +tG pGtGKt++++qFl++g++  +e+++f ++ee+  +l++++ ++Gwdl    + g
  gi|91772777|ref|YP_565469.1|  62 VSTGVAGLDDMLEGGVPKGSSVIVTGPPGTGKTTLCMQFLMEGVKA-DEKCLFFSFEERIPQLIQHFMRFGWDLGSHIDDG 141
                                   78*****************************************888.********************************** PP

                        ATPase  82 klaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReil..rqlvrvlkklgvTail 160
                                    l i  +s+ +                ee+ e+i+++k +r+v Ds++++   ++++++R+ +  r l + lkkl++T+ l
  gi|91772777|ref|YP_565469.1| 142 YLEIFGMSMLT---------------FEEIGEIIETYKPQRIVFDSLNVF---TDPEEFRKSIswRSLHKLLKKLNITTFL 204
                                   99999999886...............5699********************...89999999875589************** PP

                        ATPase 161 vsekssseeaaggygveefivdgvivLdlkeiee...elvRtleivkmRgtkhskkehpfeIteegik 225
                                   v+ek+++  +++ y+   f+ dg+i Ld+++i+e   +l+ +l + kmR tk+++   pf  t++gi+
  gi|91772777|ref|YP_565469.1| 205 VTEKENG-MEKKVYDKYDFVGDGIIFLDKMQINEvepTLTPVLAVQKMRATKVDTTPQPFRFTDKGIS 271
                                   ***8887.55667788899*************9999999***************************97 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.3e-09   7.2e-07      26      93 ..      54     120 ..      33     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.3e-09
                                   -.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS--- CS
                          RecA  26 keklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehal 93 
                                   + ++ ++ +s+G  +ld  l  GG+pkG  + + Gp  +Gkttl+++ + e  k++  + f   e  +
  gi|91772777|ref|YP_565469.1|  54 NIDKVIKRVSTGVAGLDDMLE-GGVPKGSSVIVTGPPGTGKTTLCMQFLMEGVKADEKCLFFSFEERI 120
                                   44567999**********998.***************************************9888765 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 !   27.0   0.0   4.8e-09   2.6e-06       2      69 ..      62     129 ..      61     199 .. 0.81
   2 ?   -2.2   0.0       3.9   2.1e+03     133     184 ..     168     214 ..     157     220 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.8e-09
                                   BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHH CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRlls 69 
                                   +stg + LD++++ G+ kg  +i+ + p++Gkt+l++++  + ++ ++ ++++fs+e    ql+q ++ 
  gi|91772777|ref|YP_565469.1|  62 VSTGVAGLDDMLEgGVPKGSSVIVTGPPGTGKTTLCMQFLMEGVK-ADEKCLFFSFEERIPQLIQHFMR 129
                                   78999****988627999*********************988764.5669*************998775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                   EEEEEGGGTBTSCSSSCCCHHHHHHHHHHHHHHHHCTSXEEEEEEXSGGGCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 133 iviDyLqlmegseekenreqevseisrsLkalakelnvpvialsqLsraves 184
                                   iv D L++ +++e  e r + +s   rsL +l k ln+    +   +  +e+
  gi|91772777|ref|YP_565469.1| 168 IVFDSLNVFTDPE--EFR-KSIS--WRSLHKLLKKLNITTFLVTEKENGMEK 214
                                   6666666666322..222.3343..388888888888877666665555555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   5.7e-09   3.1e-06       3      57 ..      46     100 ..      44     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.7e-09
                                   -EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                         Rad51   3 fvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57 
                                   f s  ++++  + + +++tG   lD++L+GG++ gs   + G  ++Gkt lc+++
  gi|91772777|ref|YP_565469.1|  46 FKSKIDINNIDKVIKRVSTGVAGLDDMLEGGVPKGSSVIVTGPPGTGKTTLCMQF 100
                                   6667778888888999*************************************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.9e-08   1.6e-05      23      82 ..      70     119 ..      55     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.9e-08
                        AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds 82 
                                   ++ ++g +p+g+ ++++G+pgtGKttl+++   + ++ +           k+l+ s+E++
  gi|91772777|ref|YP_565469.1|  70 DDMLEGGVPKGSSVIVTGPPGTGKTTLCMQFLMEGVKAD----------EKCLFFSFEER 119
                                   66788888**********************988776433..........15566666555 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   5.9e-05     0.032       9      44 ..      79     115 ..      39     128 .. 0.90
   2 !    9.2   0.0   0.00074       0.4     117     219 ..     168     279 ..     151     296 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.9e-05
                          GvpD   9 aGktllikGaPGtGktlftlrgl.dvlrresdvlyvs 44 
                                    G ++++ G PGtGkt++ +++l + ++ +++ l+ s
  gi|91772777|ref|YP_565469.1|  79 KGSSVIVTGPPGTGKTTLCMQFLmEGVKADEKCLFFS 115
                                   599*******************835677777777765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00074
                          GvpD 117 lvyeylaerydsPedikt.v.kndlvvlaresgvrlvlvlet......aansrleyivdGvvtl...nvkeddrgrlrrdl 186
                                   +v++ l + + +Pe+++  +    l  l ++ ++   lv+e       +  ++ +++ dG++ l   +++e     l   l
  gi|91772777|ref|YP_565469.1| 168 IVFDSLNV-FTDPEEFRKsIsWRSLHKLLKKLNITTFLVTEKengmekKVYDKYDFVGDGIIFLdkmQINEV-EPTLTPVL 246
                                   55555544.55666654312135677777888888888876511111155678999*******995555555.4567789* PP

                          GvpD 187 rleklrGvrignrlqPftladGkfksitrvelv 219
                                    ++k+r  +++   qPf ++d        v+l+
  gi|91772777|ref|YP_565469.1| 247 AVQKMRATKVDTTPQPFRFTDKGISKYRTVNLM 279
                                   *****************9999766665555555 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 !   22.6   0.0   1.3e-07   7.3e-05      45      90 ..      78     123 ..      35     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-07
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveel 90 
                                    k  +++++Gp+G+GK+ l + + +e+v+a+ + lf++ e+ + +l
  gi|91772777|ref|YP_565469.1|  78 PKGSSVIVTGPPGTGKTTLCMQFLMEGVKADEKCLFFSFEERIPQL 123
                                   567899*******************************988765555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.2e-07   0.00017      12      47 ..      69     103 ..      65     131 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-07
                        AAA_16  12 Llsale.rvrsgrpelvllsGesGvGKsslvrellra 47 
                                   L ++le  v +g  ++v+++G++G+GK++l  ++l +
  gi|91772777|ref|YP_565469.1|  69 LDDMLEgGVPKG--SSVIVTGPPGTGKTTLCMQFLME 103
                                   556666334344..89***************888743 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.6e-07   0.00042       4      78 ..      82     161 ..      79     210 .. 0.71
   2 ?   -2.1   0.0       6.8   3.7e+03      55      74 ..     215     234 ..     176     243 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.6e-07
                        AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe........kllelileklkeekktylflDEiqev 76 
                                    +++tG+  +GKTtl+ q++ e    +e++l++++++   + ++++         ++++ +le +   ++++l + Ei e+
  gi|91772777|ref|YP_565469.1|  82 SVIVTGPPGTGKTTLCMQFLMEGVKADEKCLFFSFEERIPQLIQHFMrfgwdlgsHIDDGYLEIF---GMSMLTFEEIGEI 159
                                   689*****************9999999*********97666555554444544445566666653...5677777777777 PP

                        AAA_14  77 pe 78 
                                    e
  gi|91772777|ref|YP_565469.1| 160 IE 161
                                   44 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.8
                        AAA_14  55 lileklke...ekktylflDEiq 74 
                                    + +   +    ++ ++flD +q
  gi|91772777|ref|YP_565469.1| 215 KVYD---KydfVGDGIIFLDKMQ 234
                                   2222...0222355667777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.6e-06   0.00086       3      35 ..      81     120 ..      79     181 .. 0.75
   2 ?   -0.5   0.0       1.6   8.5e+02      24      59 ..     201     236 ..     193     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                        AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGl 35 
                                    +++++Gp+g+GKTtl+ ++        +k lf+ +e+  
  gi|91772777|ref|YP_565469.1|  81 SSVIVTGPPGTGKTTLCMQFlmegvkaDEKCLFFSFEERI 120
                                   5799**********************99******999855 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                        AAA_24  24 pkplfidtekGlksldadkfpdieswedfldevvel 59 
                                    ++l+   e+G+ +   dk++ +   + fld+++ +
  gi|91772777|ref|YP_565469.1| 201 TTFLVTEKENGMEKKVYDKYDFVGDGIIFLDKMQIN 236
                                   456777888888888888888777777777766655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.1e-06    0.0012       6      28 ..      81     103 ..      78     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.1e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleq 28 
                                   ++++vtG++GtGKTtl+ ++l++
  gi|91772777|ref|YP_565469.1|  81 SSVIVTGPPGTGKTTLCMQFLME 103
                                   789**************999887 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.5e-06   0.00082      97     158 ..      21     110 ..       4     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                         T2SSE  97 kksakeltlddlgaeealk...........................ekiaevlrkavrerglilvsGgTgsGKttllyall 150
                                   ++ +kel  ++l+ e+al                            + ++++l+  v +  +++v+G+ g+GKttl    l
  gi|91772777|ref|YP_565469.1|  21 ERYEKELGAKNLVLEKALLsldstkfkskidinnidkvikrvstgvAGLDDMLEGGVPKGSSVIVTGPPGTGKTTLCMQFL 101
                                   555555666666666555556666666666677777777777777789999*************************97666 PP

                         T2SSE 151 ke.inksde 158
                                    e ++++++
  gi|91772777|ref|YP_565469.1| 102 MEgVKADEK 110
                                   551444444 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.2e-06    0.0012      19      79 ..      62     121 ..      59     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                        PAXNEB  19 tStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpe 79 
                                   +StG+  LD++L GG+p Gs++++      + +++L+  Fl eGv  + + l+ s+++   
  gi|91772777|ref|YP_565469.1|  62 VSTGVAGLDDMLEGGVPKGSSVIVTGP-PGTGKTTLCMQFLMEGVKADEKCLFFSFEERIP 121
                                   8***********************977.5566899****************9999966544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.3e-06    0.0024      30      71 ..      77     118 ..      66     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.3e-06
                         AAA_7  30 lknkkpvllvGptGtGKtviikd.llkkldkekylsltinfsa 71 
                                   + ++ +v+++Gp GtGKt+++++ l++ ++  + ++l+++f  
  gi|91772777|ref|YP_565469.1|  77 VPKGSSVIVTGPPGTGKTTLCMQfLMEGVK-ADEKCLFFSFEE 118
                                   678899*****************5666655.777777777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.2   3.9e+03      37      62 ..      39      60 ..      10      65 .. 0.52
   2 !   17.7   0.0   7.6e-06    0.0041       1      16 [.      83      98 ..      83     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.2
                        AAA_18 37 lllevdpealdeskrldedkldklld 62
                                  l+l+     ++ + ++d+++ dk+++
  gi|91772777|ref|YP_565469.1| 39 LSLD----STKFKSKIDINNIDKVIK 60
                                  2222....234577888888877776 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 7.6e-06
                        AAA_18  1 IlltGtpGvGKttlak 16
                                  +++tG+pG+GKttl+ 
  gi|91772777|ref|YP_565469.1| 83 VIVTGPPGTGKTTLCM 98
                                  79************95 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.3e-06     0.004       3     132 ..      83     212 ..      81     223 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.3e-06
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.......-HCHHHCCCCTS--SSS-C...CHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna....rsladllfsqlpepaapvse...vwavl 76 
                                   vi++G++G GKTtL  ++ ++  + + +    +l+F ++ r  + ++ +      l  ++ + ++e+ + +      + ++
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQFLMEGVKADEK----CLFFSFEERIPQLIQHFmrfgWDLGSHIDDGYLEIFGMSMLtfeEIGEI 159
                                   89************99988776555522....3444444443333333344444444444444444444333333345555 PP

                                   CCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCH CS
                         NACHT  77 lelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpral 132
                                   +e  +   +++D+l+ + +  ++ +k  + + L++l++k  l  +++l+t + ++ 
  gi|91772777|ref|YP_565469.1| 160 IETYKPQRIVFDSLNVFTDPEEF-RKSISWRSLHKLLKK--LNITTFLVTEKENGM 212
                                   55555555999999988876666.777777888899998..888888888766655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.8e-06    0.0042       1      21 [.      83     103 ..      83     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.8e-06
                                   EEEESSTTSSHHHHHHHHHHH CS
                           AAA   1 vllyGppGtGKTllakavake 21 
                                   v+++GppGtGKT+l+ +   e
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQFLME 103
                                   6899**********9887766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.9e-05      0.01       2      19 ..      83     100 ..      82     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                                   EEEE--TTSSHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkv 19 
                                   v++TGppG+GKtTl+ + 
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQF 100
                                   89************9764 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.2e-05     0.012      11      53 ..      81     119 ..      76     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
                        AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgr 53 
                                   + ++vt++pGtGKT++ ++ + + v++     e++l  +f +r
  gi|91772777|ref|YP_565469.1|  81 SSVIVTGPPGTGKTTLCMQFLMEGVKAD----EKCLFFSFEER 119
                                   6799***********9988877777666....66777666655 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00045      0.24      23      50 ..      80     107 ..      74     115 .. 0.87
   2 ?    1.4   0.0      0.27   1.5e+02     256     298 ..     139     186 ..     115     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                                   --EEEEE-SSSSSTTTTHHHHHHHGGGS CS
                          DAP3  23 vkrlvltGekgsGKSvlLlqalayAlek 50 
                                      +++tG +g+GK++l +q l  ++++
  gi|91772777|ref|YP_565469.1|  80 GSSVIVTGPPGTGKTTLCMQFLMEGVKA 107
                                   5679****************99887765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.27
                                   ......EEE-----GGGTHHHHHHHHHTT---ST....TSSHHHHHHH CS
                          DAP3 256 k.gkvepieveglskeEarslleyyadsgvlqek....vneelveekl 298
                                   + g +e++ ++ l+ eE+ +++e y+ ++++ +     ++ e +++++
  gi|91772777|ref|YP_565469.1| 139 DdGYLEIFGMSMLTFEEIGEIIETYKPQRIVFDSlnvfTDPEEFRKSI 186
                                   3588999*******************9999987766666666666665 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 ?   13.5   0.0   9.7e-05     0.053       2      19 ..      83     100 ..      82     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-05
                                   EEEE--SSSSHHHHHHHG CS
                         AAA_5   2 vlLvGppGtgKselaerl 19 
                                   v++ GppGtgK++l +++
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQF 100
                                   89*************997 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.8e-05     0.053       4      25 ..      83     104 ..      80     126 .. 0.83
   2 ?   -3.6   0.0       9.2     5e+03     202     218 ..     173     189 ..     171     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.8e-05
                       DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                   v+VtG +GtGKt + +++l e 
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQFLMEG 104
                                   89***************99886 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.2
                       DUF2075 202 irvfddleelkkalkek 218
                                   ++vf+d+ee++k +  +
  gi|91772777|ref|YP_565469.1| 173 LNVFTDPEEFRKSISWR 189
                                   67899999998887655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.062      19      40 ..      82     103 ..      70     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                        AAA_11  19 itliqGPPGtgKTktivellsq 40 
                                    +++ GPPGtgKT+  +++l++
  gi|91772777|ref|YP_565469.1|  82 SVIVTGPPGTGKTTLCMQFLME 103
                                   5799**********99998875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   0.00014     0.078       6      32 ..      75     101 ..      71     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                                   EEEETTSEEEEEESTTSSHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlklla 32 
                                     + +g+ v ++G+ G+GK+tL++ ++
  gi|91772777|ref|YP_565469.1|  75 GGVPKGSSVIVTGPPGTGKTTLCMQFL 101
                                   57899*****************97655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   0.00011     0.061       2      18 ..      83      99 ..      82     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                        AAA_28  2 ivitGgestGKTtllea 18
                                  +++tG+++tGKTtl+ +
  gi|91772777|ref|YP_565469.1| 83 VIVTGPPGTGKTTLCMQ 99
                                  89************865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021      0.11       2      20 ..      83     101 ..      83     125 .. 0.89
   2 ?   -1.7   0.0       5.3   2.9e+03      33      55 ..     247     271 ..     180     292 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                        AAA_33   2 vllvGlpGsGKstlaerll 20 
                                   v++ G+pG+GK+tl  + l
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQFL 101
                                   7899**********98865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.3
                        AAA_33  33 lrrrlfgtdqqsktdytrvldr..l 55 
                                   + +++++t+++++ ++ r++d+   
  gi|91772777|ref|YP_565469.1| 247 AVQKMRATKVDTTPQPFRFTDKgiS 271
                                   5556666666666666666655553 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   0.00015     0.083      20      35 ..      82      97 ..      74     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                        AAA_30 20 vavltGpAGtGKttal 35
                                   +++tGp+GtGKtt+ 
  gi|91772777|ref|YP_565469.1| 82 SVIVTGPPGTGKTTLC 97
                                  579***********84 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016     0.088     255     283 ..      72     101 ..      59     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                      PPV_E1_C 255 fLk.gvPkknclvllGppntGkslfamsli 283
                                   +L+ gvPk ++++++Gpp tGk++++m ++
  gi|91772777|ref|YP_565469.1|  72 MLEgGVPKGSSVIVTGPPGTGKTTLCMQFL 101
                                   555269********************9865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00043      0.23       1      20 [.      83     102 ..      83     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00043
                  RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                                   ++++Gp+g+GK+tl+ ++  
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQFLM 102
                                   6799***********99654 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   0.00028      0.15       3      21 ..      83     101 ..      81     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                   EEEEESTTCCHHHHHHHHH CS
                          cobW   3 tvltGflGsGKTtLlnhll 21 
                                   +++tG++G+GKTtL  + l
  gi|91772777|ref|YP_565469.1|  83 VIVTGPPGTGKTTLCMQFL 101
                                   79************98877 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.18      20     105 ..      78     159 ..      62     174 .. 0.80
   2 ?   -2.7   0.0       7.6   4.1e+03      94     103 ..     225     234 ..     217     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                                   TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHH.HEBSSSSSTTTSS-BEHHHHHTTTSEEEE CS
               Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseL.FGhekGaFtGAekekkGlfekadgGtlfL 99 
                                   ++ +sv++tG  GtGK++l  +   +  +++++ + +   +  ++l++  + FG   G++ +      G++e    ++l +
  gi|91772777|ref|YP_565469.1|  78 PKGSSVIVTGPPGTGKTTLCMQFLMEGVKADEKCLFFSFEERIPQLIQHFMrFGWDLGSHID-----DGYLEIFGMSMLTF 153
                                   56789***************999999999999999999998888888876669999988754.....57777777777777 PP

                                   ETGGGS CS
               Sigma54_activat 100 Deigel 105
                                   +eige+
  gi|91772777|ref|YP_565469.1| 154 EEIGEI 159
                                   777766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.6
                                   TSEEEEETGG CS
               Sigma54_activat  94 gGtlfLDeig 103
                                   +G++fLD ++
  gi|91772777|ref|YP_565469.1| 225 DGIIFLDKMQ 234
                                   7999999743 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00052      0.28      22      46 ..      79     102 ..      75     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                        AAA_29  22 kg.atlltGpsGsGKSTllDAiqalL 46 
                                   kg ++++tGp G+GK+Tl   +q+l+
  gi|91772777|ref|YP_565469.1|  79 KGsSVIVTGPPGTGKTTLC--MQFLM 102
                                   566899***********97..66665 PP

>> Ca_bind_SSO6904  Calcium binding protein SSO6904
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.18        97      68      82 ..      18      32 ..      12      41 .. 0.86
   2 ?    6.2   0.1     0.025        14      13      36 ..      44      67 ..      33      75 .. 0.84
   3 ?   -2.1   0.0       9.6   5.2e+03      62      75 ..     152     165 ..     142     175 .. 0.76
   4 ?   -0.9   0.0       3.9   2.1e+03      13      32 ..     180     199 ..     169     239 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                                  HHHHHHHTTT-HHHH CS
               Ca_bind_SSO6904 68 kilekyakkiGvenv 82
                                  kile+y k +G+ n+
  gi|91772777|ref|YP_565469.1| 18 KILERYEKELGAKNL 32
                                  8**********9985 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.025
                                  HHHT--S-HHHHHHHHHHHHHHHH CS
               Ca_bind_SSO6904 13 rkfkgkvdveevekileeieedlr 36
                                   kfk+k+d++ ++k+++ + + ++
  gi|91772777|ref|YP_565469.1| 44 TKFKSKIDINNIDKVIKRVSTGVA 67
                                  59**************99987665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.6
                                   HHHHHHHHHHHHHT CS
               Ca_bind_SSO6904  62 fydliskilekyak 75 
                                   +++ i++i+e y++
  gi|91772777|ref|YP_565469.1| 152 TFEEIGEIIETYKP 165
                                   57778888888876 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.9
                                   HHHT--S-HHHHHHHHHHHH CS
               Ca_bind_SSO6904  13 rkfkgkvdveevekileeie 32 
                                   ++f+  ++ + ++k+l++++
  gi|91772777|ref|YP_565469.1| 180 EEFRKSISWRSLHKLLKKLN 199
                                   55666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1856.82
//
Query:       gi|91772778|ref|YP_565470.1|  [L=230]
Description: hypothetical protein Mbur_0759 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  10.8    1.1e-33  116.7  10.8    1.4  1  DUF1614   Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7  10.8     6e-38   1.1e-33       1     169 [.      50     225 ..      50     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 6e-38
                       DUF1614   1 llgslinipvaelkske.elve..vkvlgisykvpvleeeekk......tvvavNvGGaviPlllslylllrlavsllaal 72 
                                   l++ +i+ipv+++k+k+ +  +  + +l+  ++vp ++e + +      tvv++N+GG++iP+++ ++l++ +a   +  +
  gi|91772778|ref|YP_565470.1|  50 LVTANIDIPVSSIKTKKvQSLDrdALILEELFSVPLVKELSYSskqafnTVVSLNLGGFIIPFFVLIFLIVFQA--DFVGI 128
                                   68899**********775553346999*******988887766778899*********************9998..78999 PP

                       DUF1614  73 lavlivaavvyllarpvpgvGivvpllipplvaalaalllaeeeaaavaYisgvlGtLiGadllnl.kkieklgapvvsIG 152
                                     +li++++v++l+++ +g+G+vvp +i++l++ +a l++++++ a+v++isg+ G+L+G+ ++ l  + ek g+ ++++G
  gi|91772778|ref|YP_565470.1| 129 ELMLIMMLAVIFLSDFRNGIGVVVPDFIGILAIPFA-LIFSPDNLASVIFISGIGGILLGSMVTLLmVDREKKGSALIDVG 208
                                   999**************************9999988.9*************************9997677778888***** PP

                       DUF1614 153 GaGtFdGifltgilavl 169
                                   G+GtF++i++t+ila l
  gi|91772778|ref|YP_565470.1| 209 GVGTFKAIYVTAILASL 225
                                   ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); 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:                         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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1509.11
//
Query:       gi|91772779|ref|YP_565471.1|  [L=438]
Description: phenylacetate-CoA ligase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-25   89.8   0.1    3.5e-25   88.1   0.0    1.9  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    5.5e-09   35.1   0.0    8.3e-09   34.5   0.0    1.2  1  AMP-binding      AMP-binding enzyme
    0.00023   20.2   0.0     0.0019   17.2   0.0    2.0  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 ?   -2.1   0.0      0.83   4.9e+03      54      71 ..     221     238 ..     193     240 .. 0.74
   2 !   88.1   0.0   5.9e-29   3.5e-25       1      96 []     343     436 ..     343     436 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.83
                                   HHHHHHHHHHHHHHHSS- CS
               AMP-binding_C_2  54 ealekkiakklksklgvs 71 
                                   e+ + k++k+++++lg++
  gi|91772779|ref|YP_565471.1| 221 ERWSPKMRKRIEQELGIE 238
                                   556667788888888875 PP

  == domain 2  score: 88.1 bits;  conditional E-value: 5.9e-29
                                   TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE-TT- CS
               AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelvepgt 81 
                                   Gvnv+P qie+v++++e+v++eYqiv++r++++D++  +vE++ +  d+l + ++ +  ++k++++ +g+sv+ve+v++g 
  gi|91772779|ref|YP_565471.1| 343 GVNVYPGQIEDVIQKVEGVSSEYQIVLERKQGRDSMLFRVEIDGA--DDLGNNRNRAGLLKKAFRDFIGISVDVECVKMGG 421
                                   9*****************************************996..78999***************************** PP

                                   S---------EEE-S CS
               AMP-binding_C_2  82 lprsegKakrviDkR 96 
                                   lprse+K+krv+D+R
  gi|91772779|ref|YP_565471.1| 422 LPRSEKKSKRVLDNR 436
                                   **************9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.4e-12   8.3e-09     153     370 ..      86     294 ..      25     297 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.4e-12
                                   CCS-BTTSEEEEEEE--SSSS-EEEEEEHHHH...HHHHHHHHHHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT- CS
                   AMP-binding 153 eeelkpddlayiiYTSGTTGkPKGVmlshrnl...vanvaslkletrfklkeddvv.lsilplahifglilelllallsGa 229
                                    +++  +d++ i  +SGTTG P  + +++r +   ++++    +++  +l+++d++ ++     + +g+  +  +a l Ga
  gi|91772779|ref|YP_565471.1|  86 LQAVPDEDIIRIHSSSGTTGSPVIIPYTQRDVdiwANMMMR--CYQMAGLTKNDRIqITPGYGLWTAGI-GFQAGAELLGA 163
                                   44567899**********************99754333333..56667788888883444445578885.99999999999 PP

                                   EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTC CS
                   AMP-binding 230 tvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlss.lrlvllggeplspellrffralfge 309
                                     +   + ++ + k+ l+++ +l+ t +a++ + +  l+e+ +++      + +  l++ ++g e+ sp++ +++++ +g 
  gi|91772779|ref|YP_565471.1| 164 MAIPTGPGNT-E-KQ-LQMLLDLRSTALASTSSYALLLAEEINKRGL----KKNIdLKIGIIGSERWSPKMRKRIEQELGI 237
                                   5555555544.3.33.689999********99999999775333312....2334499999******************** PP

                                   EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                   AMP-binding 310 evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                   e ++++GlTE  g  + +++  +    g       +   +i+D+ t+e +pdg+ Gel++ 
  gi|91772779|ref|YP_565471.1| 238 ETFDIFGLTEIYGPGIGIDCYIH---DG-LHYWSDHLLFEIIDPVTEEKLPDGTLGELVIT 294
                                   **************974333333...22.3344569999*******************996 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.1e-07    0.0019      71     112 ..      89     128 ..      26     152 .. 0.72
   2 ?    0.7   0.0      0.03   1.8e+02     361     419 ..     290     357 ..     273     399 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-07
                                   TSSSS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHH CS
                           GH3  71 LtsepiklfalsSGTtsgksKliPvteeslkelallvlalla 112
                                     +e i+++  sSGTt g + +iP+t++ ++ +a+++++  +
  gi|91772779|ref|YP_565471.1|  89 VPDEDIIRIHSSSGTT-GSPVIIPYTQRDVDIWANMMMRC-Y 128
                                   457899**********.***************99985443.3 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.03
                                   EEEEES..TTS..-SSEEECEEEEEEEEETT....EEEE.EEEECCTEEE-SSSS-CCHHHHHHHHH. CS
                           GH3 361 elvvTt..faG..LyRYrigDvvrvtgfynk....aPrl.eFvgRknvvlsidgeklteeelqkavee 419
                                   elv+Tt    G  L RYr+ D+ r+     k    +Pr+ +++gR++  ++i+g  +   ++++++++
  gi|91772779|ref|YP_565471.1| 290 ELVITTltKEGapLIRYRTRDLTRIIPEPCKcgclFPRIdRLLGRTDDRIKIKGVNVYPGQIEDVIQK 357
                                   88999844345559*******99986443331122576645777777777777777777777777773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3139.09
//
Query:       gi|91772780|ref|YP_565472.1|  [L=199]
Description: indolepyruvate oxidoreductase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-36  126.1   0.1    1.7e-36  125.9   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 !  125.9   0.1   9.7e-41   1.7e-36       1     177 []      11     189 ..      11     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 9.7e-41
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                   GGqGvv+a+++la+aa++a ++v+++++ g+++r g+++shvri+de+  + i+ g+adl+++l++++ +++l+ l +gg 
  gi|91772780|ref|YP_565472.1|  11 GGQGVVLASRLLATAAMNASFHVTTAETIGMAQREGSVTSHVRIGDEVCGSLIPSGNADLIIGLEPAETARNLHFLGNGGS 91 
                                   9**********************************************999****************9999*********** PP

                                   EEEECTCGTT-CCHHHCTS-HHHHHHH...T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H..HHHHHHHHCC CS
                           POR  82 iiynseelkpdelkkakeeerelkerl...gvrvygvdatkiakeiggneraaNtvmlGalaallglpl..ealeeaikkr 157
                                   ii+n++ + p++    k++  ++ e l     +++ +d+t++ak++g   raaN++ml+a+a+   lp+  ++l  +++k+
  gi|91772780|ref|YP_565472.1|  92 IIVNEHAVMPSVNGSVKYDPEQVLEFLkanCQEIISFDFTQLAKQAGT-YRAANVAMLAAVAGTDLLPFtpDDLWNVLEKM 171
                                   ************9999997655555559977789*********99777.***********88776699999********** PP

                                   S-CH.HHHHHHHHHHHHHHH CS
                           POR 158 fpkkkeviekNlkafragye 177
                                   +p+k    + N +af+ ++e
  gi|91772780|ref|YP_565472.1| 172 VPEK--YRDVNRRAFDMAFE 189
                                   **96..89********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1388.09
//
Query:       gi|91772781|ref|YP_565473.1|  [L=628]
Description: thiamine pyrophosphate enzyme-like TPP-binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   96.4   0.5    2.3e-27   95.6   0.5    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    5.3e-18   65.6   0.1      8e-18   65.0   0.1    1.2  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    4.8e-08   32.5  17.4    7.3e-06   25.6   3.8    3.4  4  Fer4          4Fe-4S binding domain
    3.9e-07   30.1  12.4    1.1e-06   28.7  10.4    2.5  2  Fer4_21       4Fe-4S dicluster domain
    1.6e-05   24.7  17.3     0.0018   18.2   2.4    3.2  3  Fer4_2        4Fe-4S binding domain
    3.1e-05   24.5  10.3     0.0042   17.7   0.7    2.8  2  Fer4_7        4Fe-4S dicluster domain
    0.00011   22.1  19.2     0.0056   16.7   3.6    3.5  3  Fer4_6        4Fe-4S binding domain
    0.00028   20.9  13.7    0.00028   20.9  13.7    2.4  2  Fer4_10       4Fe-4S dicluster domain
     0.0004   20.5  12.4    0.00079   19.6  11.2    2.2  2  Fer4_9        4Fe-4S dicluster domain
     0.0018   17.9   0.1      0.016   14.8   0.1    2.1  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
     0.0061   16.3   0.2      0.041   13.6   0.1    2.4  2  Transket_pyr  Transketolase, pyrimidine binding domain
     0.0092   16.9   1.6     0.0092   16.9   1.6    2.6  2  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.028   14.7   0.0    1.7  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 
      0.014   16.2   4.0      0.014   16.2   4.0    3.0  2  Fer4_3        4Fe-4S binding domain
       0.03   15.1   7.5       0.89   10.3   1.2    2.7  2  Fer4_15       4Fe-4S single cluster domain
      0.076   13.6  11.4        3.4    8.3   3.3    3.2  3  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
       0.29   11.7  19.0       0.54   10.9   3.8    3.1  3  Fer4_4        4Fe-4S binding domain
        0.5   10.7   2.2        1.7    9.0   0.1    2.6  3  Tim17         Tim17/Tim22/Tim23/Pmp24 family
        8.6    6.9  14.6        3.8    8.0   3.8    2.7  2  Fer4_8        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.5   2.5e-30   2.3e-27       1     152 [.     408     555 ..     408     556 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 2.5e-30
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHH.....HSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakl.....akpdrevvaivGDGgflmi.lqelatavrrnlpi 75 
                                   diGc++l      + ++p ++++  ++ +mG g+++A G++       +++++ va++GD++f+++ + +++ av++n++i
  gi|91772781|ref|YP_565473.1| 408 DIGCYSL------GNAKPLNMVD--TCLCMGAGISIAAGLSHthhyqEDKKAKQVAFIGDSTFFHSgVAAVISAVYNNADI 480
                                   89*****......9999******..****************96654223468***************************** PP

                                   EEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                  TPP_enzyme_C  76 tvvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                   t+ vl+N++++mtg+q++p  g + +g++   +k +d+a++ +++G++ + +++++d+ e  ++ k+a++ +gp+ ++
  gi|91772781|ref|YP_565473.1| 481 TIAVLDNRTTAMTGHQPHPGIGLTATGVS---TKIIDIAEVLKSCGVDlVETIDVNDLGECIDTAKRAMDFEGPSAVV 555
                                   *************************9999...99**************999***********************9885 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 !   65.0   0.1   8.5e-21     8e-18       2     174 ..      18     186 ..      17     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 8.5e-21
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   +a++agv+++++YP TPs+e++e++ ++++k ++   +   + +E  a ++++GAa++Ga ++++    Gl  +++ l+  
  gi|91772781|ref|YP_565473.1|  18 GAMKAGVQITSGYPGTPSTEVMETIISHAKKYGI---YAEWATNEKVALETAVGAAYSGANTMVTMKQVGLNVASDPLMSL 95 
                                   799**************************99996...8999**********************************998865 PP

                                   ..HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HE CS
                         POR_N  83 ..ageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshe 161
                                     +g + ++vi v    +p +    +t+q    +    ++ vl +++ qea+d++  Af+l+ ++++Pvi+ +  ++lsh 
  gi|91772781|ref|YP_565473.1|  96 syIGIKGSLVILVSDDPGPHS---SQTEQDTRSFGHFANIPVLDPSTPQEAYDMTKLAFKLSHEMEIPVILRT-TTRLSHG 172
                                   226889999999999999988...67777777888889999****************************9987.57888** PP

                                   EEEEEC-SGG..GS CS
                         POR_N 162 vekvelpdee.del 174
                                     +v ++d + +++
  gi|91772781|ref|YP_565473.1| 173 CADVMIEDIDpVSR 186
                                   *******9994443 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.7   4.5e+03       5      11 ..     374     380 ..     371     381 .. 0.81
   2 ?   -2.3   0.0       4.9   4.6e+03       2      10 ..     554     562 ..     553     562 .. 0.77
   3 !   15.2   1.3   1.5e-05     0.014       1      16 [.     570     585 ..     570     586 .. 0.92
   4 !   25.6   3.8   7.7e-09   7.3e-06       2      23 ..     600     621 ..     599     622 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.7
                                   TTTSSS- CS
                          Fer4   5 eekCigC 11 
                                   + +C gC
  gi|91772781|ref|YP_565473.1| 374 PTLCAGC 380
                                   6789999 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.9
                                   EEETTTSSS CS
                          Fer4   2 videekCig 10 
                                   v+ + kC+g
  gi|91772781|ref|YP_565473.1| 554 VVFKGKCVG 562
                                   677889997 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.5e-05
                                   EEEETTTSSS-THHHH CS
                          Fer4   1 vvideekCigCGaCve 16 
                                   +vide+kC++C  Cv 
  gi|91772781|ref|YP_565473.1| 570 YVIDENKCTRCRVCVT 585
                                   69************95 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 7.7e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    ++++ C+gC +C+++CP +AI
  gi|91772781|ref|YP_565473.1| 600 PVIQDNCTGCSLCAQICPSDAI 621
                                   6899*****************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.1     1e+03      18      43 ..     538     562 ..     535     566 .. 0.78
   2 !   28.7  10.4   1.2e-09   1.1e-06       2      57 ..     571     621 ..     570     623 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                       Fer4_21  18 CedtshqaieidaktvlkvvedeCvG 43 
                                   C dt+  a+++++ +   v + +CvG
  gi|91772781|ref|YP_565473.1| 538 CIDTAKRAMDFEGPSA-VVFKGKCVG 562
                                   8899999999876554.678999999 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.2e-09
                       Fer4_21   2 ridedkCigCgkClia..CedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   +ide+kC  C  C++   C+     ai ++++++ +v++d+C+GC lC+++CP +d+i
  gi|91772781|ref|YP_565473.1| 571 VIDENKCTRCRVCVTQlgCP-----AI-FSPSNKPPVIQDNCTGCSLCAQICP-SDAI 621
                                   69***********9752266.....77.5688888******************.5887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       7.6   7.2e+03       7      13 ..     374     380 ..     370     381 .. 0.74
   2 !   18.2   2.4   1.9e-06    0.0018       3      22 .]     570     591 ..     568     591 .. 0.88
   3 !   13.9   3.6   4.5e-05     0.042       5      21 ..     601     617 ..     598     618 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.6
                        Fer4_2   7 tdrCigC 13 
                                   +  C gC
  gi|91772781|ref|YP_565473.1| 374 PTLCAGC 380
                                   5679999 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.9e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsa..CPa 22 
                                   +v+d+++C++C+ Cv+   CPa
  gi|91772781|ref|YP_565473.1| 570 YVIDENKCTRCRVCVTQlgCPA 591
                                   689***********96668997 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 4.5e-05
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                   v  d+C+gC+ C + CP
  gi|91772781|ref|YP_565473.1| 601 VIQDNCTGCSLCAQICP 617
                                   6789************* PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.2   0.00024      0.23      26      49 ..     565     590 ..     530     592 .. 0.79
   2 !   17.7   0.7   4.4e-06    0.0042      37      52 .]     605     620 ..     596     627 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                        Fer4_7  26 kgtekveidpekClgCgaCva..vCP 49 
                                   kg  +++id++kC+ C++Cv+   CP
  gi|91772781|ref|YP_565473.1| 565 KGAGQYVIDENKCTRCRVCVTqlGCP 590
                                   577899**************955677 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4.4e-06
                        Fer4_7  37 kClgCgaCvavCPtga 52 
                                   +C+gC  C++ CP++a
  gi|91772781|ref|YP_565473.1| 605 NCTGCSLCAQICPSDA 620
                                   5555555555555554 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.3   1.2e+03       7      13 ..     375     381 ..     374     382 .. 0.81
   2 !   13.1   3.0   8.3e-05     0.078       3      21 ..     571     591 ..     571     592 .. 0.90
   3 !   16.7   3.6   5.9e-06    0.0056       4      24 .]     601     621 ..     598     621 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                        Fer4_6   7 dkCigCg 13 
                                    +C gC+
  gi|91772781|ref|YP_565473.1| 375 TLCAGCM 381
                                   69****9 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.3e-05
                        Fer4_6   3 eidpdkCigCgdCvrv..CPe 21 
                                   +id++kC+ C+ Cv+   CP+
  gi|91772781|ref|YP_565473.1| 571 VIDENKCTRCRVCVTQlgCPA 591
                                   69************9888886 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 5.9e-06
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   + +d+C+gC  C+ +CP +ai
  gi|91772781|ref|YP_565473.1| 601 VIQDNCTGCSLCAQICPSDAI 621
                                   679***************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  13.7   2.9e-07   0.00028       3      56 .]     571     617 ..     569     617 .. 0.92
   2 !   11.4   3.7   0.00029      0.27       6      21 ..     603     618 ..     598     625 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.9e-07
                       Fer4_10   3 vidddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   vid+++C+rC+ Cv+   CPa         + s++++  +  ++Ctgc  C+++CP
  gi|91772781|ref|YP_565473.1| 571 VIDENKCTRCRVCVTQlgCPA---------IFSPSNKPPVIQDNCTGCSLCAQICP 617
                                   89*************777***.........88888888999**************9 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00029
                       Fer4_10   6 ddtCirCgkCvkaCPa 21 
                                   +d C++C  C + CP+
  gi|91772781|ref|YP_565473.1| 603 QDNCTGCSLCAQICPS 618
                                   5899999999999999 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.2   3.9e+03      34      40 ..     375     381 ..     356     382 .. 0.67
   2 !   19.6  11.2   8.3e-07   0.00079       1      51 []     576     621 ..     575     621 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.2
                        Fer4_9  34 eaCigCg 40 
                                   + C gC+
  gi|91772781|ref|YP_565473.1| 375 TLCAGCM 381
                                   4677776 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 8.3e-07
                        Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kCt+C+ Cv++  Cpa  +++++++  ++       +C+gC  C+++Cp++ai
  gi|91772781|ref|YP_565473.1| 576 KCTRCRVCVTQlgCPAI-FSPSNKPPVIQD------NCTGCSLCAQICPSDAI 621
                                   7*******87777**96.566666666664......6*************997 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.7e-05     0.016      11     141 ..      19     164 ..      10     172 .. 0.74
   2 ?    0.4   0.0      0.47   4.4e+02      97     151 ..     493     551 ..     464     557 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                   HHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH.HCHHHHHHHH CS
                  TPP_enzyme_N  11 LkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat.naltalaeAk 87 
                                     ++gv+   g+pG+ ++++++ +  +    gi    a +E +a   A+g a +  + +v + ++g +++   l++l    
  gi|91772781|ref|YP_565473.1|  19 AMKAGVQITSGYPGTPSTEVMETIISHAkkyGIYAEWATNEKVALETAVGAAYSGANTMVTMKQVGLNVAsDPLMSLSYIG 99 
                                   4577***********************9999999999*****************************976625999999999 PP

                                   HHT--EEEEEEE--CCCHH.............S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHH CS
                  TPP_enzyme_N  88 vdriPllvlsgdrptslrg.............qgvlqqeldqlalfrpvtkyaervtspeelpealr 141
                                     ++ ++++s d++ ++ +              +vl + + q+a   ++tk a+++++  e+p++lr
  gi|91772781|ref|YP_565473.1| 100 IKGSLVILVSDDPGPHSSQteqdtrsfghfanIPVLDPSTPQEAY--DMTKLAFKLSHEMEIPVILR 164
                                   999999999998887777744444444444443333333333333..55555555555555555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.47
                                   EEE--CCCHH...S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH.HSSS CS
                  TPP_enzyme_N  97 sgdrptslrg...qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirta.lsgr 151
                                   +g++p+  +g   +gv  + +d++++++++  + ++  ++++l e ++ A r++  +g+
  gi|91772781|ref|YP_565473.1| 493 TGHQPHPGIGltaTGVSTKIIDIAEVLKSCGVDLVETIDVNDLGECIDTAKRAMdFEGP 551
                                   55556666667777888877799999999999999999999999999999888833333 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   4.4e-05     0.041     124     174 ..     117     169 ..      45     171 .. 0.85
   2 ?   -1.1   0.0       1.3   1.3e+03      89     169 ..     473     555 ..     440     558 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                                   TSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE-SSE CS
                  Transket_pyr 124 hqsaeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlpksl 174
                                    q  ++++++ + +++ v+ Ps+p+e++ + + a +   e + Pv+lr++ +l
  gi|91772781|ref|YP_565473.1| 117 SQTEQDTRSFGHFANIPVLDPSTPQEAYDMTKLAFKLshEMEIPVILRTTTRL 169
                                   344579***************************99887688899999998765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                   HHGGHHHHHCHHHHHT--EEEEESBSG...GGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS.SS.SE CS
                  Transket_pyr  89 qiyadqairsgeakgklkvgvvtrlpi...gvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairr.edrkP 165
                                    +y+++ i+  + + ++++ ++ + p+   g+   G + + + +  +l+++ g+  v   d +++ +++ +a r  ++++P
  gi|91772781|ref|YP_565473.1| 473 AVYNNADIT-IAVLDNRTTAMTGHQPHpgiGLTATGVSTKIIDIAEVLKSC-GVDLVETIDVNDLGECIDTAKRAmDFEGP 551
                                   677777777.77777777777777765322666666666666666677776.66777777777777777666666667777 PP

                                   EEEE CS
                  Transket_pyr 166 vvlr 169
                                   ++++
  gi|91772781|ref|YP_565473.1| 552 SAVV 555
                                   7776 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.2      0.51   4.8e+02       1      10 [.     576     585 ..     564     593 .. 0.67
   2 !   16.9   1.6   9.8e-06    0.0092       1      20 [.     605     624 ..     605     628 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.51
                       Fer4_16   1 rCgtCgkCae 10 
                                   +C++C+ C+ 
  gi|91772781|ref|YP_565473.1| 576 KCTRCRVCVT 585
                                   3555655554 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 9.8e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C++C  Ca++CP++ai  k
  gi|91772781|ref|YP_565473.1| 605 NCTGCSLCAQICPSDAIVLK 624
                                   6****************988 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 ?   14.7   0.0     3e-05     0.028      14      60 ..     252     295 ..     239     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE- CS
                       PFOR_II  14 taksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldr 60 
                                       a ++ ++++    l+++ t++PFPe++  ++l ++k ++v++ 
  gi|91772781|ref|YP_565473.1| 252 Y---AKEATKDSSATFSLFKIGTVYPFPEKAALDFLTHIKDLIVIEE 295
                                   4...4455677788899***************************995 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   2.8       5.8   5.5e+03       1       9 [.     577     585 ..     577     586 .. 0.89
   2 ?   16.2   4.0   1.5e-05     0.014       1      15 []     606     620 ..     606     620 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.8
                        Fer4_3   1 CtgCgaCve 9  
                                   Ct C+ Cv 
  gi|91772781|ref|YP_565473.1| 577 CTRCRVCVT 585
                                   9***99*95 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.5e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   CtgC++C + CP++A
  gi|91772781|ref|YP_565473.1| 606 CTGCSLCAQICPSDA 620
                                   *************98 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.6    0.0078       7.3       2      18 ..     571     587 ..     571     597 .. 0.82
   2 ?   10.3   1.2   0.00095      0.89       5      19 ..     603     617 ..     601     626 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0078
                       Fer4_15   2 vvDrdaCigcglCvaea 18 
                                   v+D+++C+ c +Cv+ +
  gi|91772781|ref|YP_565473.1| 571 VIDENKCTRCRVCVTQL 587
                                   69************975 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00095
                       Fer4_15   5 rdaCigcglCvaeap 19 
                                   +d+C+gc lC++ +p
  gi|91772781|ref|YP_565473.1| 603 QDNCTGCSLCAQICP 617
                                   69************6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.6   3.4e+03      37      55 ..     499     526 ..     475     529 .. 0.69
   2 ?    8.3   1.1    0.0036       3.4       1      21 [.     572     594 ..     572     598 .. 0.82
   3 ?    8.3   3.3    0.0036       3.4       3      17 ..     603     617 ..     601     618 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.6
                       Fer4_13  37 s.........eeekadaeeAadaCPves 55 
                                   +          +++ d+ e +++C v+ 
  gi|91772781|ref|YP_565473.1| 499 PgigltatgvSTKIIDIAEVLKSCGVDL 526
                                   355555555566788999999***9986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0036
                       Fer4_13   1 VDrdtCiacgaCvel..aPdvFe 21 
                                   +D+++C+ c +Cv    +P +F 
  gi|91772781|ref|YP_565473.1| 572 IDENKCTRCRVCVTQlgCPAIFS 594
                                   89**********97444898886 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0036
                       Fer4_13   3 rdtCiacgaCvelaP 17 
                                   +d+C++c +C++++P
  gi|91772781|ref|YP_565473.1| 603 QDNCTGCSLCAQICP 617
                                   599************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2         9   8.5e+03       3       8 ..     376     381 ..     374     381 .. 0.78
   2 ?    9.7   2.7    0.0014       1.3       2      15 ..     575     590 ..     574     594 .. 0.88
   3 ?   10.9   3.8   0.00058      0.54       1      16 [.     603     618 ..     603     619 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9
                        Fer4_4   3 rCigCg 8  
                                    C gC+
  gi|91772781|ref|YP_565473.1| 376 LCAGCM 381
                                   599996 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                        Fer4_4   2 erCigCgsCvaa..CP 15 
                                   ++C++C++Cv    CP
  gi|91772781|ref|YP_565473.1| 575 NKCTRCRVCVTQlgCP 590
                                   79********887777 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00058
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   q++C+gC  C  +CP+
  gi|91772781|ref|YP_565473.1| 603 QDNCTGCSLCAQICPS 618
                                   79*************7 PP

>> Tim17  Tim17/Tim22/Tim23/Pmp24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       3.9   3.7e+03      58      68 ..      66      76 ..      10      82 .. 0.51
   2 ?    1.7   0.1      0.34   3.2e+02      63     109 ..     386     431 ..     377     433 .. 0.75
   3 ?    9.0   0.1    0.0018       1.7      14      73 ..     428     485 ..     425     495 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                         Tim17 58 vvgglysgiec 68
                                  +vg+ ysg+++
  gi|91772781|ref|YP_565473.1| 66 AVGAAYSGANT 76
                                  22555555554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                         Tim17  63 ysgiecaleklRgkediwnsvaAGaltGall.ragpqaaavgaiggaa 109
                                   + +++ +  kl  k+  +n++++G ++ + l +a p +++ ++++++a
  gi|91772781|ref|YP_565473.1| 386 FYAFKKVAGKL--KTEKINTIFSGDIGCYSLgNAKPLNMVDTCLCMGA 431
                                   33344444444..78889************97799*****99999887 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0018
                         Tim17  14 llGavfglvkgsrradtpapskerlreglrsvgkrgpslGknfgvvgglysgiecalekl 73 
                                    +Ga +++  g+ ++ +      + +++++ +g +++++++ ++v+ ++y+ ++ ++  l
  gi|91772781|ref|YP_565473.1| 428 CMGAGISIAAGLSHTHH--YQEDKKAKQVAFIGDSTFFHSGVAAVISAVYNNADITIAVL 485
                                   56777777777777774..555667888999********************999998765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   3.0     0.096        90       3      18 ..     575     592 ..     573     602 .. 0.76
   2 ?    8.0   3.8    0.0041       3.8       3      17 ..     604     618 ..     602     626 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.096
                        Fer4_8   3 ekCieCgaCqsa..Cpvl 18 
                                   +kC++C  C ++  Cp++
  gi|91772781|ref|YP_565473.1| 575 NKCTRCRVCVTQlgCPAI 592
                                   589999999976668865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0041
                        Fer4_8   3 ekCieCgaCqsaCpv 17 
                                   ++C++C++C + Cp+
  gi|91772781|ref|YP_565473.1| 604 DNCTGCSLCAQICPS 618
                                   578888888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4460.63
//
Query:       gi|91772782|ref|YP_565474.1|  [L=118]
Description: hypothetical protein Mbur_0763 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.5   0.0      0.051   13.9   0.0    1.2  1  mCpol     minimal CRISPR polymerase domain


Domain annotation for each model (and alignments):
>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.8e-06     0.051      23      74 ..      51     101 ..      46     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-06
                         mCpol  23 eeleklskevkeaikklkkllkdelgasvifaaGDsilakssleedllvels 74 
                                    e +++ +e++++ ++ ++l+ ++++++vif+  D+++  ++  +   ve++
  gi|91772782|ref|YP_565474.1|  51 AETKRMIHEITKKCDSFRSLMPENINCEVIFKDLDDLTYVADEGN-FQVEYN 101
                                   56788999******************************9995433.333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 848.28
//
Query:       gi|91772783|ref|YP_565475.1|  [L=576]
Description: RNA-directed DNA polymerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-42  145.7   0.1    3.1e-42  144.6   0.0    1.6  2  RVT_1            Reverse transcriptase (RNA-dependent DNA pol
    7.4e-28   96.6   2.2    7.4e-28   96.6   2.2    1.9  2  RVT_N            N-terminal domain of reverse transcriptase
    3.4e-24   84.7   6.4    8.9e-24   83.4   6.4    1.8  1  GIIM             Group II intron, maturase-specific domain
  ------ inclusion threshold ------
      0.012   15.6   3.5       0.12   12.3   0.5    3.7  3  Intron_maturas2  Type II intron maturase
       0.73   10.1   6.0        1.5    9.0   6.0    1.6  1  HNH              HNH endonuclease


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   0.0   8.7e-46   3.1e-42       1     222 []     129     350 ..     129     350 .. 0.95
   2 ?   -3.3   0.0       1.4     5e+03      94     136 ..     453     497 ..     444     498 .. 0.63

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 8.7e-46
                                   EE-TT.S-EEE......-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEBCCGCC CS
                         RVT_1   1 ipKkgpgsyRpisllsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaFd 81 
                                   i K g ++ Rp++++++ ++a+++l+a +L +++e + +++++gfr+ rst+da  ++  +++kk +a+++l+ D+k++Fd
  gi|91772783|ref|YP_565475.1| 129 IEKYGSDKKRPLGIPTMYDRAMQALYALALDPIAEVTADKRSFGFRKFRSTHDACSQIFGTISKKDSAQCILEGDIKGCFD 209
                                   56777899************************************************************************* PP

                                   CSBB-GGGGGGG-EEET..........................TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T...... CS
                         RVT_1  82 svpleellrkltafkvptklinliksflstrsfsvrv.ngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra... 158
                                   ++++++l+  +     +++   ++k+fl    +++ v ++   + +++k+g+pqG+++SP+l+n++++ ++  l+ ++   
  gi|91772783|ref|YP_565475.1| 210 NISHQWLIDNIPM---DKS---ILKQFL----KAGFVyEN---SLFPTKAGTPQGGIISPILANMTLDGIEGVLADKYhrg 277
                                   ********99888...534...899999....56666355...89*******************************99*** PP

                                   ...............TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE.....ESSEEETTEEE CS
                         RVT_1 159 ............kgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlftvkseevkyLGvtl 222
                                                +v+++rYaDD+++++k+ke ++e+ e ++++l + gl++++eKt +++     + +++LG ++
  gi|91772783|ref|YP_565475.1| 278 vsgkittrqrakHKVNFVRYADDFIVTAKTKEIAEEAKELIKNFLTDRGLELSDEKTLITH---IDDGFDFLGWNV 350
                                   ************************************************************9...89*******875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                   -EEET...........................TEEEEESB--ST- CS
                         RVT_1  94 afkvptklinliksflstrsfsvrvnge..eskgryekkglpqGs 136
                                    f++ +++++l+++ +  r   ++++++  + +++++++ l qGs
  gi|91772783|ref|YP_565475.1| 453 VFSTMKNQLKLMSDKMIVRNPQIKLDKNpyTDTEYFVERKLNQGS 497
                                   456666667777666666666666633335777888888888887 PP

>> RVT_N  N-terminal domain of reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   2.2   2.1e-31   7.4e-28       1      83 []      33     114 ..      33     114 .. 0.99
   2 ?   -3.3   0.0       3.2   1.1e+04      49      58 ..     365     372 ..     360     388 .. 0.53

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 2.1e-31
                         RVT_N   1 WkeidWkkvekkVfkLqkrIykAsqegdikkvkkLqklLtkSlsakllAvrrVtqdnkgkktagvDgvksltpkerlelve 81 
                                   W+ i+W++ve++V+++q rI+kA+ +++++ vk+L +lLt+S++akllAvr+V   nkg++tag+Dg+ ++tp +++++++
  gi|91772783|ref|YP_565475.1|  33 WNFINWSSVESHVNRIQVRITKAVINKNWNLVKRLSYLLTHSHYAKLLAVRKVIR-NKGRRTAGIDGEFWSTPVSKVNAAR 112
                                   *******************************************************.**********************998 PP

                         RVT_N  82 eL 83 
                                   +L
  gi|91772783|ref|YP_565475.1| 113 SL 114
                                   76 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                         RVT_N  49 AvrrVtqdnk 58 
                                   ++++Vt+  k
  gi|91772783|ref|YP_565475.1| 365 SIKKVTE--K 372
                                   4555555..2 PP

>> GIIM  Group II intron, maturase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   6.4   2.5e-27   8.9e-24       1      80 []     366     444 ..     366     444 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2.5e-27
                          GIIM   1 vkrlkrkireltkrsskgvsleelirklnpilrGWanYyrlgvakrvfskldhyirrrLrrwllrkhkkkkrrralrkyw 80 
                                   +k++++ki++++ ++ k++++e+li klnpi++GW nY++ + +k++fs +d  i++ L++w++r+h+ k+r ++++kyw
  gi|91772783|ref|YP_565475.1| 366 IKKVTEKISNTI-KDGKTWTQEDLISKLNPIITGWSNYHQGVASKETFSLIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 444
                                   6999********.7779**************************************************************9 PP

>> Intron_maturas2  Type II intron maturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.19   6.7e+02      68     103 ..      61      90 ..      49     125 .. 0.68
   2 ?   -0.4   0.0      0.29     1e+03       4      32 ..     216     249 ..     213     261 .. 0.76
   3 ?   12.3   0.5   3.4e-05      0.12      38     103 ..     383     444 ..     356     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.19
               Intron_maturas2  68 krlrerikyilrkscvkTLArKlklktvrkvikkfG 103
                                    +l++r+ y+l +s         kl  vrkvi+  G
  gi|91772783|ref|YP_565475.1|  61 WNLVKRLSYLLTHSH------YAKLLAVRKVIRNKG 90 
                                   466677777777664......344445555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.29
               Intron_maturas2   4 lvlnaPir.kiikkLakagfvktkk....ekgkP 32 
                                   l+ n+P++ +i k+  kagfv +++    + g P
  gi|91772783|ref|YP_565475.1| 216 LIDNIPMDkSILKQFLKAGFVYENSlfptKAGTP 249
                                   566899973588999******9986665555555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.4e-05
               Intron_maturas2  38 widledrdIllrykaiirgllnYYsfadnkkrlrerikyilrkscvkTLArKlklktvrkvikkfG 103
                                   w+   + d++ + + ii g +nY++++  k+++  +i + + + + k   r++ +k +  + +k+ 
  gi|91772783|ref|YP_565475.1| 383 WT---QEDLISKLNPIITGWSNYHQGVASKETFS-LIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 444
                                   44...457899**********************9.***9998888887777777777776666665 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.0   0.00043       1.5      17      46 ..     534     561 ..     515     562 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00043
                           HNH  17 dHiipisqggadd..ieNlqllCksCHnkkhd 46 
                                   +H    ++g++dd  i Nl+ ++  CH++ h+
  gi|91772783|ref|YP_565475.1| 534 HH----KNGNHDDngITNLVYAHVYCHRQYHA 561
                                   33....346667688**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3856.14
//
Query:       gi|91772784|ref|YP_565476.1|  [L=496]
Description: hypothetical protein Mbur_0767 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   28.5   0.0    1.5e-06   27.7   0.0    1.3  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
    5.9e-06   26.2   0.0    1.1e-05   25.3   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    8.3e-06   25.7   0.0    1.7e-05   24.6   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    5.3e-05   22.6   0.5    0.00029   20.2   0.5    2.0  1  Methyltransf_2   O-methyltransferase domain
    0.00075   20.2   0.2     0.0083   16.8   0.1    2.4  2  Methyltransf_12  Methyltransferase domain
     0.0017   17.9   0.0     0.0051   16.4   0.0    1.8  1  MTS              Methyltransferase small domain
     0.0042   17.7   0.0     0.0082   16.8   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      0.005   17.5   0.0      0.011   16.4   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.087   12.3   0.1       0.15   11.6   0.1    1.5  1  TRM13            Methyltransferase TRM13
       0.23   11.4   0.5         27    4.8   0.1    2.8  3  Levi_coat        Levivirus coat protein


Domain annotation for each model (and alignments):
>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   8.2e-10   1.5e-06       6     227 ..     149     400 ..     145     430 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 8.2e-10
                         Rsm22   6 aYalarlpatyavlrrvLdelaervpdflPkslldvgegpgtalwaaselweelee....vlvidas....eelleiskel 78 
                                    Y+++++p  +   + +L +++      +  +++d+g gpgt+  a+ + + +le+    + +++      e+ ++i  e 
  gi|91772784|ref|YP_565476.1| 149 GYLAYQFPVYFIQFQHILYSMELDGLLKTRMKIVDFGTGPGTVPAAIADHYMRLENaevdIHSVELYdeniEAYKHIVPEY 229
                                   68888888888888888888877777777789*****************99987761111445654411113444455555 PP

                         Rsm22  79 aadapelkeaalrrsvirealeleea......dLviisyvLleled...esreklvknlWakask..ilvivEeGtpaGfr 148
                                   a+d  ++k ++  +  i+   +l+ +      d+++ s vL+e+ +   +++++l+k+l +k+ +   +v++E+  +a ++
  gi|91772784|ref|YP_565476.1| 230 AKDDLNVKIEEIIKANIK---DLTADdlpdkvDMMVFSNVLNEISElslDEKAALLKELSKKLVDdgNIVLIEPADKANST 307
                                   555555555544444443...33333555569**********99987778999******999977789************* PP

                         Rsm22 149 rvleaRealkaagfhivAPCPHeaaCPlvatedwC.hFsqrvaRlslhrlak..sasvpv....edekfsy..vakerqpr 220
                                    +  +  alk +g  +  PC     C   ++ d C  F q+       ++ k  + + p+     d k+sy  ++k rq r
  gi|91772784|ref|YP_565476.1| 308 ELRRLMFALKGSGLNVYSPCSF-IWCAGCKP-DECwSFEQKNDINPPVLMKKlaDCDEPFrylnTDIKYSYviLRKDRQTR 386
                                   ********************97.56776666.4442688887743333333333334443223358899998778888877 PP

                         Rsm22 221 asa.......aaRv 227
                                    +         aR+
  gi|91772784|ref|YP_565476.1| 387 IKFkvplkskFARL 400
                                   66655555555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   6.3e-09   1.1e-05      20     130 ..     175     310 ..     161     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.3e-09
               Methyltransf_23  20 lraggrvLdiGcGtGillevl.....rengf..svtgvDlspeaveiae.................kakkaqkdqfdeqea 76 
                                   l+++++++d+G+G G++   +     r + +  ++  v+l++e++e ++                  +k ++kd +    a
  gi|91772784|ref|YP_565476.1| 175 LKTRMKIVDFGTGPGTVPAAIadhymRLENAevDIHSVELYDENIEAYKhivpeyakddlnvkieeIIKANIKDLT----A 251
                                   6899************966662222333444458888888888888888999999988888877654455555555....8 PP

               Methyltransf_23  77 aepqgkfdlIvlrevlehvp....d.ppellrqiatllkpgGylllseplaslkedrll 130
                                   ++  +k d +v ++vl+ +     d  ++ll+ + + l ++G+++l ep+ ++ +++l 
  gi|91772784|ref|YP_565476.1| 252 DDLPDKVDMMVFSNVLNEISelslDeKAALLKELSKKLVDDGNIVLIEPADKANSTELR 310
                                   88899************99954442466*********************7665444443 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   9.7e-09   1.7e-05       3     116 ..     177     303 ..     175     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9.7e-09
               Methyltransf_31   3 kglrvlDlGCGtGeltfelae....elgpkaevvGiDiseeaielArenaqklgldnveFeq.....gdieelekl.lede 73 
                                     ++++D G+G G+   ++a+    + + + ++++++   e ie  + +  +   d +++++     ++i +l  + l  +
  gi|91772784|ref|YP_565476.1| 177 TRMKIVDFGTGPGTVPAAIADhymrLENAEVDIHSVELYDENIEAYKHIVPEYAKDDLNVKIeeiikANIKDLTADdLP-D 256
                                   6799*****************99876677888****************6665555544444400333666666655444.9 PP

               Methyltransf_31  74 kfDlilsnevl.....naladpdkileeiervlkpggilliedprlla 116
                                   k+D+++  +vl       l ++++ l+e+++ l ++g +++ +p   +
  gi|91772784|ref|YP_565476.1| 257 KVDMMVFSNVLneiseLSLDEKAALLKELSKKLVDDGNIVLIEPA-DK 303
                                   ***********999888899999******************9999.22 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.5   1.6e-07   0.00029      60     178 ..     175     310 ..     156     319 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.6e-07
                                   GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHH.............H.HHHHHHS-----TTEEEEES-TTTS--- CS
                Methyltransf_2  60 leglkslvDvGGGtGalakaivsayPtikvivfDlpeV.............v.eaAkehlsageeervefvgGdffkdslP 126
                                   l++  ++vD G G G + +ai+ +y  ++    D+ +V             v e Ak+ l+++ ee ++    d+  d lP
  gi|91772784|ref|YP_565476.1| 175 LKTRMKIVDFGTGPGTVPAAIADHYMRLENAEVDIHSVelydenieaykhiVpEYAKDDLNVKIEEIIKANIKDLTADDLP 255
                                   3344689*******************99999999876643333311111112245777777788888999999******** PP

                                   .--SEEEEESSGGGS-H...HHHHHHHHHHHHH--TT-EEEEEE----TTS---HH CS
                Methyltransf_2 127 .eaDaillkrvlhDwsd...ekcvklLkrvkkalpagGkvivveavlgadpsgele 178
                                    + D++++++vl + s+   ++ + lLk++ k l ++G+++++e   + ++s+el+
  gi|91772784|ref|YP_565476.1| 256 dKVDMMVFSNVLNEISElslDEKAALLKELSKKLVDDGNIVLIEPADK-ANSTELR 310
                                   99**********9988733366788*******************7644.4444555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   4.6e-06    0.0083       1      98 [.     182     294 ..     182     295 .. 0.76
   2 ?    0.2   0.0      0.69   1.2e+03      13      57 ..     357     404 ..     353     419 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
               Methyltransf_12   1 LeiGcGtGsllrallekl.....pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg........ssfD 68 
                                   +++G+G G++ +a++++       +++++ v++  + ie+ k    ++ + +  nv++e++   +   +        +++D
  gi|91772784|ref|YP_565476.1| 182 VDFGTGPGTVPAAIADHYmrlenAEVDIHSVELYDENIEAYKHIVPEYAK-DDLNVKIEEII--KANIKdltaddlpDKVD 259
                                   59****************88877778888888888888555555555544.33334333332..2222234577889**** PP

               Methyltransf_12  69 lvvasnvlhhl.....kdirevldnirklLkpgGr 98 
                                   + v snvl+ +     ++++++l+++ k L+++G 
  gi|91772784|ref|YP_565476.1| 260 MMVFSNVLNEIselslDEKAALLKELSKKLVDDGN 294
                                   ***************9****************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.69
               Methyltransf_12  13 alleklpdieytgvDispsai...edakeklakrennnnnnveleald 57 
                                    l++  ++ +y+ +Di  s +   +d++++++++ +++ ++ +l ++d
  gi|91772784|ref|YP_565476.1| 357 KLADCDEPFRYLNTDIKYSYVilrKDRQTRIKFKVPLKSKFARLSTID 404
                                   5555558899*******9999566666666666655555555554444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.9e-06    0.0051      31     136 ..     177     296 ..     166     315 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.9e-06
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC................EEEEE-STTTTSTT CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle................vevvasdvleevee 95 
                                   ++ k++D+G+G G + aa+a+++ +  ++  +vd +++e+  en+ea k+                 +++  +d++++  +
  gi|91772784|ref|YP_565476.1| 177 TRMKIVDFGTGPGTVPAAIADHYMR--LENAEVDIHSVELYDENIEAYKHIvpeyakddlnvkieeiIKANIKDLTADDLP 255
                                   4668***************998766..555566666666666666555443211111111144444445555555555555 PP

                                   S-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                           MTS  96 kkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                   +k+d++v    + + ++ +l+   +l++e  + L ++G+++
  gi|91772784|ref|YP_565476.1| 256 DKVDMMVFSNVLNEISELSLDEKAALLKELSKKLVDDGNIV 296
                                   56666555555555555555555555555555555555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.6e-06    0.0082       1      95 [.     182     296 ..     182     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
                                   EEET-TTSHHHHHHHHTT.......SEEEEEES-HHHHHHHHHHCCHHT-......EEEETTEECCCTSS-T..T-EEEEE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg.......arvvgvDlskemlklakekaseegl......kvefvvadaeklpfed..nsfDlvv 66 
                                   +d+G+G G + +a+a+++        ++  v+l +e +++ k+ ++e           e+++a++++l   d  +++D+ v
  gi|91772784|ref|YP_565476.1| 182 VDFGTGPGTVPAAIADHYmrlenaeVDIHSVELYDENIEAYKHIVPEYAKddlnvkIEEIIKANIKDLTADDlpDKVDMMV 262
                                   599************8876655667777777777777755544444433377744322459*****997555445****** PP

                                   EES-CCC-.....CCHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  67 ssevlhhv.....edpekalkeiaRvLkpgGllv 95 
                                    s+vl+ +     ++ +++lke+ + L  +G +v
  gi|91772784|ref|YP_565476.1| 263 FSNVLNEIselslDEKAALLKELSKKLVDDGNIV 296
                                   ********988888*************9999887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.4e-06     0.011       1      97 []     181     293 ..     181     293 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
                                   EEEET-TTSHHHHHHHCTS....T.SSEEEEEESSHHHHHHHHHHHHH...TTTTEEE...EESBCCGBSS..STTTEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrl....g.kakvtgvDiseemleaareraee...eglnvef...vqgdaedlpf..edgsfDlv 68 
                                   ++d+G+G+G++ +a+a+++    + + +++ v++ +e +ea ++ + e   ++lnv++   ++++++dl      +++D++
  gi|91772784|ref|YP_565476.1| 181 IVDFGTGPGTVPAAIADHYmrleNaEVDIHSVELYDENIEAYKHIVPEyakDDLNVKIeeiIKANIKDLTAddLPDKVDMM 261
                                   89****************98775367888889999999998885554433355666654448899999975224469***9 PP

                                   EEESTGGG...SSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  69 vssgalhh...lsdedlekalkeiarvLkpgG 97 
                                   v s++l+    ls ++ +++lke+++ L ++G
  gi|91772784|ref|YP_565476.1| 262 VFSNVLNEiseLSLDEKAALLKELSKKLVDDG 293
                                   99888775122556677888999888777666 PP

>> TRM13  Methyltransferase TRM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.1e-05      0.15       4      92 ..     163     256 ..     160     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                         TRM13   4 sslignleelkllekssayvEfGaGkgelsryvnqaleed...kkenskyvLidrasnrlka..Drklrkdeselai.kRl 78 
                                   + ++  +e  +ll+++ ++v+fG+G g +   +++ + +    + +++++ L d + + +k+   +  ++d  +++i + +
  gi|91772784|ref|YP_565476.1| 163 QHILYSMELDGLLKTRMKIVDFGTGPGTVPAAIADHYMRLenaEVDIHSVELYDENIEAYKHivPEYAKDDL-NVKIeEII 242
                                   6688899999***********************996654423377777788888877666641134444444.45551568 PP

                         TRM13  79 kidIkdLnlsalee 92 
                                   k++IkdL+ + l+ 
  gi|91772784|ref|YP_565476.1| 243 KANIKDLTADDLPD 256
                                   *******9999987 PP

>> Levi_coat  Levivirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.031        56      91     128 ..       4      41 ..       2      45 .. 0.88
   2 ?   -2.1   0.0         2   3.6e+03      94     122 ..     153     181 ..     149     183 .. 0.84
   3 ?    4.8   0.1     0.015        27      86     130 ..     260     306 ..     229     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.031
                                   EEEEEEETTS-HHHHHHHHHHHHHHTSTTSHHHHHHHT CS
                     Levi_coat  91 dvelsitiyatdeerelvvkelkallkdgnlidaiial 128
                                   +  ls+ +y    ++e++  elk  ++d + i++i + 
  gi|91772784|ref|YP_565476.1|   4 NKVLSVLKYVSRMKKEFMLSELKNHVEDEMSIQSIYNE 41 
                                   5568999999999*********************9885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                                   EEEETTS-HHHHHHHHHHHHHHTSTTSHH CS
                     Levi_coat  94 lsitiyatdeerelvvkelkallkdgnli 122
                                   + +++y  + +  l   el +llk  + i
  gi|91772784|ref|YP_565476.1| 153 YQFPVYFIQFQHILYSMELDGLLKTRMKI 181
                                   67888888889999999*******99887 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.015
                                   EEEEEEEEEEEETTS-HHHHHHHHHHHHHHTSTTS..HHHHHHHTT- CS
                     Levi_coat  86 rrayldvelsitiyatdeerelvvkelkallkdgn..lidaiialns 130
                                      + +v   i+  + de+ +l+++  k l+ dgn  li+ ++ +ns
  gi|91772784|ref|YP_565476.1| 260 MMVFSNVLNEISELSLDEKAALLKELSKKLVDDGNivLIEPADKANS 306
                                   55677888899999**********999*******8446899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3253.21
//
Query:       gi|91772785|ref|YP_565477.1|  [L=383]
Description: signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-22   80.4   0.0    2.2e-22   79.7   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.5e-15   56.9   0.0      3e-15   56.0   0.0    1.5  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0099   15.7   0.0      0.019   14.8   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


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 !   79.7   0.0   3.7e-26   2.2e-22       2     110 ..     271     380 ..     270     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3.7e-26
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d  +++ ++  l+ Na++f +++++i+   +++e dl +++  +G Gip+e+lk++f++f +  +   ++++gtGl l iv
  gi|91772785|ref|YP_565477.1| 271 DRAKFKDVLYDLINNAINFVSDDETIRCYATVHESDLYVTIHYTGVGIPEEELKNVFQPFINvRNFHVQKYQGTGLRLPIV 351
                                   56778999***********6677777666665688***************************98999999*********** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                   kk+vel+gG iw+es+p+ G+tftft+p 
  gi|91772785|ref|YP_565477.1| 352 KKIVELHGGAIWIESKPENGSTFTFTIPY 380
                                   **************************996 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 !   56.0   0.0     5e-19     3e-15       2      67 .]     157     224 ..     156     224 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 5e-19
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   +++fla+++ ELrtPL++i+g++++L+ e  g+l+e++ +yl+ +  +++ l++l++ lL+l +ie+g
  gi|91772785|ref|YP_565477.1| 157 KSDFLASMSYELRTPLNSIIGFSDVLRTEeiGPLNEKQLKYLKNVSTSGKELLELINGLLELLKIESG 224
                                   79************************8888***********************************997 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 !   14.8   0.0   3.1e-06     0.019       3      57 ..     275     330 ..     273     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-06
                   HATPase_c_3   3 lekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrla 57 
                                   ++++l +l++N++   +d e++  ++   + ++  ++i   G G++eeelkn++++ 
  gi|91772785|ref|YP_565477.1| 275 FKDVLYDLINNAINfvSDDETIRCYATVHE-SDLYVTIHYTGVGIPEEELKNVFQPF 330
                                   6889*********99999999999998875.799*******************9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2192.17
//
Query:       gi|91772786|ref|YP_565478.1|  [L=201]
Description: hypothetical protein Mbur_0769 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.27   11.4   0.0    1.2  1  DUF4080   Protein of unknown function (DUF4080)


Domain annotation for each model (and alignments):
>> DUF4080  Protein of unknown function (DUF4080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.5e-05      0.27       7      45 ..      98     136 ..      96     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.5e-05
                       DUF4080   7 ysdkpPYevLstkwlsyeeilrLkriEelvekYYNSgqf 45 
                                   y+d+p Y vL + ++ yee l+ k+  + ++   N++ f
  gi|91772786|ref|YP_565478.1|  98 YQDDPKYCVLGNIVILYEEFLKVKSSTDPIDMVINAHPF 136
                                   99**********************998888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1232.82
//
Query:       gi|91772787|ref|YP_565479.1|  [L=443]
Description: aspartyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-89  299.6   0.1    2.8e-89  299.3   0.1    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    8.9e-15   54.4   0.8    1.6e-14   53.6   0.8    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00073   19.1   0.0      0.065   12.7   0.0    2.4  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.3   0.1   4.7e-93   2.8e-89       3     313 ..     123     437 ..     121     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: 299.3 bits;  conditional E-value: 4.7e-93
                                   CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                   tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqsp 79 
                                   ++rl+ r++dlr+e++ +++++r++v++avr++l+++g+ie   P ++ ++te+g  lF +       ++f    +L+qsp
  gi|91772787|ref|YP_565479.1| 123 DTRLDSRFMDLRRERTTAIFKIRHEVLRAVRDFLSKDGYIETCSPKVVATATEGGTSLFPI-------TYFdreaFLNQSP 196
                                   799**********************************************************.......56666667***** PP

                                   HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrn 160
                                   ql++++l+++g+d+vf+i++ FRaE+++t+rhl+E t+i++e sf+++ d+m+vle+++ ++ ++v+e++a  ++    + 
  gi|91772787|ref|YP_565479.1| 197 QLFKQILMSGGLDKVFEIGPIFRAEEHDTRRHLNEATSIDIEASFLDHFDVMEVLEDMVAYVYEQVIENEAASLKALDIEL 277
                                   ******************************************************************999988888777776 PP

                                   SEE-SSS-EEEEHHHHHHHHHTS...........-SS--HHHHHHHHH....HS--SEEEEEEEBGGGSTTCBBBSTTSTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 161 skdlkkpfkrltykeaieklnei...........gkdldkaderalvk....keknepvfvtdfPaelkpFyarkeeddkk 226
                                   s  +k+pf +++y++ai+++n +           g    +  e    +    +++ + +f+td+P e+kpFya   ed++ 
  gi|91772787|ref|YP_565479.1| 278 S-VPKTPFMKVPYSQAIDIVNAEseetvewggdlG----TVAEHTIGEhvfkETGESHYFITDWPTEIKPFYAMPYEDNPL 353
                                   5.77999************9988777777744331....3333333225555899************************** PP

                                   BBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 227 ltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdv 307
                                   +++s+D++ + +El +G++Ri+ +++l+++++s+gld   ++ f++yl+a++yG+pph+G+g+G++Rlvm++l  e+Ird+
  gi|91772787|ref|YP_565479.1| 354 ISKSFDMMHRTMELSSGAQRIHIHDMLKARIESQGLD---SDGFDFYLRAFKYGMPPHSGWGIGCERLVMTMLSVENIRDT 431
                                   *************************************...***************************************** PP

                                   SSS-XX CS
                                   xxxxxx RF
                   tRNA-synt_2 308 iaFPkl 313
                                   ++FP+ 
  gi|91772787|ref|YP_565479.1| 432 VLFPRD 437
                                   ****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 !   53.6   0.8   2.7e-18   1.6e-14       1      76 []      24     103 ..      24     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.7e-18
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEE CS
               tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeie 74 
                                   Vtv+G+v+ +  r+ g+++f+++rD++gr q++l +    +e ++ a +l ++++v vtG+ k+    p+g +e++ e+i 
  gi|91772787|ref|YP_565479.1|  24 VTVCGWVHEV--RDLGGICFVVVRDREGRAQITLVKkkidKEIFDAARKLVRESIVAVTGTAKAEgkaPNG-YEIIPESIV 101
                                   9*********..***********************************************************.*****9998 PP

                                   EE CS
               tRNA_anti-codon  75 ll 76 
                                   +l
  gi|91772787|ref|YP_565479.1| 102 VL 103
                                   75 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0061        36     103     154 ..     210     264 ..     195     315 .. 0.70
   2 !   12.7   0.0   1.1e-05     0.065     213     234 ..     410     431 ..     402     440 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0061
                                   EEEEEEEEEBSST-SS.SB-SEEEE..EEEEEEETT--HHHHHHHHHHHHHHHCT CS
                  tRNA-synt_2d 103 kiisigrvfRrdavDa.thlaeFhq..veglvvdenvsladlkgvleellkklfg 154
                                   k++ ig +fR ++ D  +hl e ++  +e  ++d+   ++ l  ++  +++++ +
  gi|91772787|ref|YP_565479.1| 210 KVFEIGPIFRAEEHDTrRHLNEATSidIEASFLDHFDVMEVLEDMVAYVYEQVIE 264
                                   899**********775156655544114555556555555555555555555544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.1e-05
                                   EEEEEHHHHHHHHHT-SSGHHH CS
                  tRNA-synt_2d 213 afGlGveRlamlkygieDiRel 234
                                   ++G+G eRl m ++++e+iR+ 
  gi|91772787|ref|YP_565479.1| 410 GWGIGCERLVMTMLSVENIRDT 431
                                   7*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2821.98
//
Query:       gi|91772788|ref|YP_565480.1|  [L=231]
Description: ribose-5-phosphate isomerase A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-60  203.0   0.7    3.4e-60  202.6   0.7    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    2.3e-08   34.1   2.0    2.9e-05   24.1   0.1    2.3  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.012   14.7   0.1      0.022   13.9   0.1    1.4  1  Sugar-bind      Putative sugar-binding domain
      0.039   14.1   0.2      0.094   12.9   0.1    1.7  2  Dppa2_A         Dppa2/4 conserved region in higher vertebrate


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 !  202.6   0.7   7.6e-64   3.4e-60       2     173 .]      58     225 ..      57     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.6 bits;  conditional E-value: 7.6e-64
                                   EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTTSS CS
                Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlveklgkf 82 
                                   +v tS+q+e+la e+g+pl+sl e++ +dlaiDGaD+vd +ln+iKGgG+a+++EK+va++ak+fiv++desK++e+l+ +
  gi|91772788|ref|YP_565480.1|  58 AVVTSYQAEMLAIEAGVPLTSLAEHPVLDLAIDGADQVDAKLNVIKGGGAAHTHEKVVAHSAKRFIVVVDESKISEELD-H 137
                                   799***************************************************************************7.9 PP

                                   -EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S-- CS
                Rib_5-P_isom_A  83 pvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlgla 163
                                    vP+eVlp+a+e  ++++ +l ggkp++R a++kdgpv++dngn+i+Dv+f + ied++el+++l++++GVve+G+Fl++ 
  gi|91772788|ref|YP_565480.1| 138 FVPIEVLPYARELAKKQFIEL-GGKPQIRLASRKDGPVISDNGNVIIDVEF-GVIEDAAELSQKLSTCVGVVEHGIFLNT- 215
                                   9****************9975.*****************************.6899**********************97. PP

                                   SEEEEEETTC CS
                Rib_5-P_isom_A 164 dkvlvgkedg 173
                                   d+v+vg +dg
  gi|91772788|ref|YP_565480.1| 216 DEVYVGMKDG 225
                                   9*****9997 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   6.4e-09   2.9e-05       3      40 ..      10      47 ..       8      70 .. 0.83
   2 !    9.4   0.2   0.00021      0.95      93     141 ..      85     133 ..      76     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.4e-09
                         DeoRC  3 aeeKrrIAkaAaeliedgdtifldaGtTtlelaraLae 40
                                  ++eK++ ++aAa+l+edg++i l++G+Tt++ + ++ +
  gi|91772788|ref|YP_565480.1| 10 SSEKEAAGNAAASLVEDGMIIGLGTGSTTAFAIAEVGR 47
                                  679*************************9987777655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00021
                         DeoRC  93 vdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgk 141
                                   +d+a+ ga+ +da+ ++++   +    ++ ++++a+r i+++D+sK+ +
  gi|91772788|ref|YP_565480.1|  85 LDLAIDGADQVDAKLNVIKGGGAAHTHEKVVAHSAKRFIVVVDESKISE 133
                                   577777888888888888888888888999999*************986 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.9e-06     0.022      40      90 ..      14      65 ..       2      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-06
                                  HHHHHHHHHH--TTEEEEE-SSHHHHHHHHHTHH.CCHTCEEEEESBSECSS CS
                    Sugar-bind 40 raaaqllesllkdgdvvgvgwGrtlsavaealtp.kslrdvkvvqliGglse 90
                                  +aa++   sl++dg+++g+g+G t++ +++++ +  + +++ v +++ ++++
  gi|91772788|ref|YP_565480.1| 14 EAAGNAAASLVEDGMIIGLGTGSTTAFAIAEVGRrVREEGLNVLAVVTSYQA 65
                                  5777888899***************999999988677777777766666655 PP

>> Dppa2_A  Dppa2/4 conserved region in higher vertebrates
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.1e-05     0.094      33      58 ..      45      70 ..      37      78 .. 0.89
   2 ?   -3.1   0.0       2.1   9.2e+03      31      53 ..     127     149 ..     113     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                       Dppa2_A 33 ckksereeetnvvEvvtsaqeamLAa 58
                                  + ++ ree+ nv+ vvts q  mLA 
  gi|91772788|ref|YP_565480.1| 45 VGRRVREEGLNVLAVVTSYQAEMLAI 70
                                  57899*******************95 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                       Dppa2_A  31 ksckksereeetnvvEvvtsaqe 53 
                                   +++k se  ++   +Ev+  a+e
  gi|91772788|ref|YP_565480.1| 127 DESKISEELDHFVPIEVLPYARE 149
                                   44566666666667788777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1443.03
//
Query:       gi|91772789|ref|YP_565481.1|  [L=62]
Description: hypothetical protein Mbur_0775, partial [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.6   0.0    2.9e-05   24.2   0.0    1.2  1  FeoA      FeoA domain
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.17   11.9   0.0    1.2  1  UBA       UBA/TS-N 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 !   24.2   0.0   3.3e-09   2.9e-05      29      70 ..       2      41 ..       1      42 [. 0.92

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.3e-09
                                  HHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTE CS
                          FeoA 29 remGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaI 70
                                  +e+G++++++i+  +    gg l++ ++++r aLg+++A++I
  gi|91772789|ref|YP_565481.1|  2 LEIGFTENSVIKANR--VCGGSLIIYLNGNRYALGKGMAKKI 41
                                  699*********995..469*********************9 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.17       9      29 ..       1      21 [.       1      23 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                                  HHHTTS-HHHHHHHHHHTTTS CS
                           UBA  9 LveMGFdreevveALratgnN 29
                                  ++e GF+++ v++A r +g++
  gi|91772789|ref|YP_565481.1|  1 MLEIGFTENSVIKANRVCGGS 21
                                  689*************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 393.24
//
Query:       gi|91772790|ref|YP_565482.1|  [L=163]
Description: iron dependent repressor [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-17   61.8   0.3    8.4e-17   61.1   0.3    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    4.5e-15   55.5   0.1    7.2e-15   54.8   0.1    1.3  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    5.4e-05   22.7   0.0    8.2e-05   22.1   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00014   21.5   0.0    0.00034   20.3   0.0    1.6  1  LexA_DNA_bind   LexA DNA binding domain
     0.0003   20.7   0.0    0.00052   19.9   0.0    1.3  1  MarR            MarR family
    0.00031   19.7   0.1    0.00033   19.6   0.1    1.2  1  HTH_micro       HTH-like
    0.00032   20.4   0.0    0.00073   19.3   0.0    1.6  2  HTH_IclR        IclR helix-turn-helix domain
     0.0011   18.8   0.0      0.002   18.0   0.0    1.4  1  MarR_2          MarR family
     0.0024   17.7   0.0     0.0041   17.0   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0037   17.2   0.0      0.011   15.7   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0083   16.0   0.1      0.016   15.1   0.1    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.02   15.3   0.0       0.03   14.7   0.0    1.4  1  Rrf2            Transcriptional regulator
      0.063   13.1   0.0       0.11   12.3   0.0    1.4  1  RQC             RQC domain
      0.076   12.9   0.0        3.3    7.7   0.0    2.2  2  LcrG            LcrG protein
       0.11   10.8   0.0       0.15   10.4   0.0    1.1  1  DUF505          Protein of unknown function (DUF505)
       0.13   12.5   0.1       0.57   10.4   0.0    2.2  2  HTH_34          Winged helix DNA-binding domain
       0.17   12.0   0.0       0.31   11.1   0.0    1.5  1  FeoC            FeoC like transcriptional regulator
       0.17   12.0   0.0       0.84    9.8   0.0    2.2  3  HTH_28          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.3   8.4e-20   8.4e-17       2      60 .]       2      60 ..       1      60 [. 0.96

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 8.4e-20
                                  --HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                Fe_dep_repress  2 LvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                   +e+tEdYL+ + ++ ++k+++++kd++e+++  pssV+ m kkL+++Gy++yeky+++
  gi|91772790|ref|YP_565482.1|  2 ATERTEDYLKILDSIIKKKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYINYEKYGAV 60
                                  699*****************************************************986 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 !   54.8   0.1   7.2e-18   7.2e-15       1      62 [.      63     123 ..      63     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 7.2e-18
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB- CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeec 62 
                                   T+kG+e+A+ + +++ +l++fL ++lgvd + a+e+A+r+Eh l+ e+++ + ++++f+++ 
  gi|91772790|ref|YP_565482.1|  63 TPKGEEIARATEEKYDVLQEFL-QILGVDTKTADEDACRIEHGLTHETLDVFTKFIEFINKK 123
                                   9*********************.***********************************9876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.3e-08   8.2e-05       6      47 ..      10      52 ..      10      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.3e-08
                        HTH_24  6 rkIL.elLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +kIL ++++k++    ++++e  gl ps v+   k+L +eG+I
  gi|91772790|ref|YP_565482.1| 10 LKILdSIIKKKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYI 52
                                  6999888888999*****************************9 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.4e-07   0.00034       5      58 ..       3      54 ..       2      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.4e-07
                                  -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                 LexA_DNA_bind  5 TerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                                  Ter ++ l+++ + i+++gy+  ++++++ +gl+ ps+v    k+L+r Gyi+ 
  gi|91772790|ref|YP_565482.1|  3 TERTEDYLKILDSIIKKKGYA-RVKDVSEIMGLN-PSSVTGMFKKLNREGYINY 54
                                  8999999*************9.79**********.*****************86 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.2e-07   0.00052      11      48 ..      16      53 ..       7      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.2e-07
                                  HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  i++ +g ++v++  + +g+++s+vt + ++L ++G+i+
  gi|91772790|ref|YP_565482.1| 16 IIKKKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYIN 53
                                  6788888*****************************97 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.3e-07   0.00033      89     141 ..       6      57 ..       2     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                     HTH_micro  89 tskeyykivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktk 141
                                   t+  y ki+d ++k+k y+ ++++ + + ++p  +  + kkL+++g+i++++ 
  gi|91772790|ref|YP_565482.1|   6 TE-DYLKILDSIIKKKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYINYEKY 57 
                                   44.499*******************************************7754 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.4e-07   0.00073       6      49 ..      10      53 ..       9      56 .. 0.94
   2 ?   -3.4   0.1       9.2   9.2e+03      23      28 ..      68      73 ..      67      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.4e-07
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  l iLd + +  +  +++++++  gl++S+v ++ + L ++Gy+ 
  gi|91772790|ref|YP_565482.1| 10 LKILDSIIKKKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYIN 53
                                  789*********9*****************************86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.2
                                  HHHHHH CS
                      HTH_IclR 23 elArrt 28
                                  e+Ar+t
  gi|91772790|ref|YP_565482.1| 68 EIARAT 73
                                  899988 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     2e-06     0.002      10      54 ..      12      55 ..       8      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  +L  +    g+  +v+++ + +gl +s+v+ + k+L + G++ ++
  gi|91772790|ref|YP_565482.1| 12 ILDSIIKKKGY-ARVKDVSEIMGLNPSSVTGMFKKLNREGYINYE 55
                                  67777778887.69****************************776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.1e-06    0.0041       5      47 .]      10      54 ..       7      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-06
                                  HHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  5 lkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  lkIL +  +  g + v + +e++gl++s v   +kkL  +G++++
  gi|91772790|ref|YP_565482.1| 10 LKILDSIIKkkGYARVKDVSEIMGLNPSSVTGMFKKLNREGYINY 54
                                  79******98888******************************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 !   15.7   0.0   1.1e-05     0.011      25      57 ..      26      60 ..      22      65 .. 0.83
   2 ?   -2.0   0.0       3.7   3.7e+03      15      27 ..      97     110 ..      82     110 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.E CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.i 57
                                  ++ ++++Gl++++v+ ++++L reg+i   +++ +
  gi|91772790|ref|YP_565482.1| 26 KDVSEIMGLNPSSVTGMFKKLNREGYINyEKYGaV 60
                                  68899**********************95444335 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                                   TC.EEEEEHHHHHH CS
                     HTH_Crp_2  15 gg.eielpltqeel 27 
                                   ++ +ie  lt+e l
  gi|91772790|ref|YP_565482.1|  97 DAcRIEHGLTHETL 110
                                   23678888888865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.6e-05     0.016      19      56 ..      19      56 ..       6      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  k+g a++++++e+ g+  s+v  + ++L + G+++ ek
  gi|91772790|ref|YP_565482.1| 19 KKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYINYEK 56
                                  8899******************************9886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     3e-05      0.03       4      59 ..       3      56 ..       1      73 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                                  -HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2  4 sskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                  +++te  l++l  + k+++   +++++++e ++++ps +  +++kL+++g+++ ++
  gi|91772790|ref|YP_565482.1|  3 TERTEDYLKILDSIIKKKGY--ARVKDVSEIMGLNPSSVTGMFKKLNREGYINYEK 56
                                  56677777777777777774..79****************************9764 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.11      57     101 ..      32      74 ..      11      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                   TTS-HHHHHHHHHHHHHTTSEEEE..SSSBEEE-CCGHHHHTSSS CS
                           RQC  57 kdlskkewrrlirqLiaegyLeedveeygvlkltekarevlkgee 101
                                    +l+ + ++ ++++L  egy+ ++  +yg+++lt+k++e+ + +e
  gi|91772790|ref|YP_565482.1|  32 MGLNPSSVTGMFKKLNREGYINYE--KYGAVTLTPKGEEIARATE 74 
                                   56677888999**********999..9*************99655 PP

>> LcrG  LcrG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.082        82      28      51 ..      27      50 ..      14      58 .. 0.84
   2 ?    7.7   0.0    0.0033       3.3      15      39 ..      69      93 ..      56     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.082
                          LcrG 28 elleglGlapeageklfggleael 51
                                  ++ e +Gl+p  ++ +f++l++e 
  gi|91772790|ref|YP_565482.1| 27 DVSEIMGLNPSSVTGMFKKLNREG 50
                                  566779*************99984 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0033
                          LcrG 15 airdsdeRakllqelleglGlapea 39
                                    r ++e+ ++lqe+l+ lG+ +++
  gi|91772790|ref|YP_565482.1| 69 IARATEEKYDVLQEFLQILGVDTKT 93
                                  457899***************8876 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.15     471     537 ..       8      75 ..       5      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                        DUF505 471 yelkvlkkiP.krgvsveelveevdeleeeevrealeklearglvevlpdgnvvlTeaGelikrAlsg 537
                                     lk+l +i  k+g+++ + v+e+ +l+   v+   +kl+  g+++  + g+v+lT  Ge+i rA ++
  gi|91772790|ref|YP_565482.1|   8 DYLKILDSIIkKKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYINYEKYGAVTLTPKGEEIARATEE 75 
                                   557889887767777665555888899999*********************************99775 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 ?   10.4   0.0   0.00057      0.57       5      49 ..      12      57 ..       9      84 .. 0.77
   2 ?   -3.2   0.0       9.8   9.7e+03      42      52 ..     141     151 ..     137     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00057
                        HTH_34  5 vlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                  +l + ++ +  a  ++++e ++++ +      kkL+  gYi+++k 
  gi|91772790|ref|YP_565482.1| 12 ILDSIIKkKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYINYEKY 57
                                  5555555467789999***************************995 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.8
                        HTH_34  42 gYievdkefkg 52 
                                   +Y+e++ + ++
  gi|91772790|ref|YP_565482.1| 141 EYVECTPATQD 151
                                   79999877665 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00031      0.31       2      48 ..      10      56 ..       9      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                          FeoC  2 LtelkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekva 48
                                  L+ l + ++++g + +k+ s  +  +p+ + +m   + r G ++ ++
  gi|91772790|ref|YP_565482.1| 10 LKILDSIIKKKGYARVKDVSEIMGLNPSSVTGMFKKLNREGYINYEK 56
                                  7889999********************************99887665 PP

>> HTH_28  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   0.00084      0.84      10      40 ..      19      50 ..      10      56 .. 0.83
   2 ?   -2.4   0.0       5.3   5.3e+03      36      47 ..      54      65 ..      51      65 .. 0.84
   3 ?   -1.3   0.0       2.6   2.5e+03      20      29 ..     101     110 ..      75     113 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00084
                        HTH_28 10 aaGh.svreaArelgisrrtvyrWikryeegG 40
                                  ++G  +v+++++++g+++++v +  k+++ +G
  gi|91772790|ref|YP_565482.1| 19 KKGYaRVKDVSEIMGLNPSSVTGMFKKLNREG 50
                                  368899***************99888888887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.3
                        HTH_28 36 yeegGiagLvpr 47
                                  ye++G   L p+
  gi|91772790|ref|YP_565482.1| 54 YEKYGAVTLTPK 65
                                  999999888885 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.6
                        HTH_28  20 relgisrrtv 29 
                                    e+g++++t+
  gi|91772790|ref|YP_565482.1| 101 IEHGLTHETL 110
                                   3567777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1040.06
//
Query:       gi|91772791|ref|YP_565483.1|  [L=82]
Description: hypothetical protein Mbur_0777 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   63.8   0.1    1.4e-17   63.7   0.1    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.1     8e-22   1.4e-17       1      73 [.       7      78 ..       7      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 8e-22
                                  EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                          FeoA  1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                  ++L+ l++G ++++ +i  + +  +rr ++mG+vpGa+iev+++ap+g+pl   v++ +++L++ eA+ I V+
  gi|91772791|ref|YP_565483.1|  7 TTLNLLEPGSKAKVIQITGR-GSARRRILDMGMVPGAEIEVIRKAPMGDPLEFLVKGYNLSLRKAEAELIVVQ 78
                                  69***************988.99************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 594.95
//
Query:       gi|91772792|ref|YP_565484.1|  [L=75]
Description: hypothetical protein Mbur_0778 [Methanococcoides burtonii DSM 6242]
Scores for 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-19   67.4   0.1    1.1e-18   67.3   0.1    1.0  1  FeoA      FeoA domain
  ------ inclusion threshold ------
      0.061   13.4   0.1      0.074   13.1   0.1    1.2  1  Cpn10     Chaperonin 10 Kd subunit
          1    9.4   4.5        2.1    8.4   0.4    2.3  2  KOW       KOW motif


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 !   67.3   0.1   1.8e-22   1.1e-18       2      73 ..       6      74 ..       5      75 .] 0.93

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.8e-22
                                  EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                          FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                  pL++++eG++g++++i++  + l+rrL emG++ G+ ++v + +  +g lvv v++t+ aLg+++A +I+V 
  gi|91772792|ref|YP_565484.1|  6 PLTMMPEGKEGKVVSINAG-QGLKRRLVEMGFCDGSLVTVHR-SE-RGALVVVVNGTKYALGKGMATKIMVS 74
                                  9***************876.99*******************5.44.699*********************96 PP

>> Cpn10  Chaperonin 10 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.2e-05     0.074      26      83 ..       5      63 ..       4      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                  --HHHHHSEEEEEEEEE-T........TS-TTS--T-EEEEEGGG..TSS-GG---.EEE CS
                         Cpn10 26 lpdsakekpeqGvVvaVGegarnekgedvplevkvgdkVlfpkya..gtkvkvdgkeyli 83
                                  lp +   + ++G+Vv++ +g+  +    v+++++ g  V ++  +  +  v v+g++y +
  gi|91772792|ref|YP_565484.1|  5 LPLTMMPEGKEGKVVSINAGQGLK-RRLVEMGFCDGSLVTVHRSErgALVVVVNGTKYAL 63
                                  56666667799********99996.566**********9988776433444447777765 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.4   0.00036       2.1      13      25 ..      12      24 ..      12      45 .. 0.75
   2 ?    2.8   0.4      0.02   1.2e+02       1      11 [.      49      59 ..      49      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00036
                                  TTCEEEEEEEETT CS
                           KOW 13 kGktGkVvkvdqh 25
                                  +Gk+GkVv+++  
  gi|91772792|ref|YP_565484.1| 12 EGKEGKVVSINAG 24
                                  7*********965 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.02
                                  TTSEEEESSST CS
                           KOW  1 pGdhVkVvsGp 11
                                  +G  V Vv G+
  gi|91772792|ref|YP_565484.1| 49 RGALVVVVNGT 59
                                  5999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 559.85
//
Query:       gi|91772793|ref|YP_565485.1|  [L=688]
Description: ferrous iron transport protein B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-71  236.7   0.6    1.2e-70  236.0   0.6    1.3  1  FeoB_N       Ferrous iron transport protein B
      7e-47  158.3  12.2    1.7e-30  105.5   2.6    2.8  2  Gate         Nucleoside recognition
    5.9e-22   77.1   1.3    5.9e-22   77.1   1.3    3.6  4  FeoB_C       Ferrous iron transport protein B C terminus
    2.3e-19   69.5   0.2    4.6e-19   68.6   0.2    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    4.9e-17   62.3   0.7    1.2e-16   61.1   0.7    1.7  1  FeoB_Cyto    FeoB cytosolic helical domain
    3.5e-05   23.3   0.0    6.8e-05   22.4   0.0    1.5  1  SRPRB        Signal recognition particle receptor beta subuni
    5.1e-05   22.7   0.2    0.00043   19.7   0.0    2.1  2  AIG1         AIG1 family
    0.00013   21.9   0.6      0.049   13.5   0.0    2.5  2  RsgA_GTPase  RsgA GTPase
    0.00093   18.8   1.5      0.063   12.8   1.5    2.6  1  GTP_EFTU     Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.021   14.3   0.3      0.042   13.3   0.3    1.5  1  Arf          ADP-ribosylation factor family
      0.099   12.2   0.0       0.21   11.1   0.0    1.5  1  AAA_25       AAA domain
        0.1   11.6   0.3        1.9    7.4   0.0    2.2  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.15   11.2   0.1       0.24   10.4   0.1    1.3  1  Parvo_NS1    Parvovirus non-structural protein NS1


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 !  236.0   0.6   8.9e-74   1.2e-70       1     155 [.      19     173 ..      19     174 .. 0.99

  Alignments for each domain:
  == domain 1  score: 236.0 bits;  conditional E-value: 8.9e-74
                                   EEEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSE CS
                        FeoB_N   1 itvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdv 81 
                                   it+al+GnpnvGkttlfna+tga+q+vgNwpGvtvekk+gk ++k++e+e+vDlPG+Ysl+ays++e vard+++ee+pdv
  gi|91772793|ref|YP_565485.1|  19 ITIALAGNPNVGKTTLFNAITGARQHVGNWPGVTVEKKTGKRTYKDTEIEVVDLPGTYSLTAYSIDEVVARDYVVEEKPDV 99 
                                   689****************************************************************************** PP

                                   EEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                        FeoB_N  82 vvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                   vv++vdatnlernLyLt+ql+elg +vv+alnm+d ae++g +id++k+++ L++pvvkt+ak+ egi++ll++
  gi|91772793|ref|YP_565485.1| 100 VVQIVDATNLERNLYLTTQLMELGSKVVIALNMWDLAESRGDKIDTRKMEDFLEIPVVKTVAKRAEGIDALLEE 173
                                   ***********************************************************************987 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   2.2   1.1e-18   1.6e-15       4     111 ..     363     455 ..     360     456 .. 0.96
   2 !  105.5   2.6   1.3e-33   1.7e-30       1     112 []     522     656 ..     522     656 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.1e-18
                          Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpks 84 
                                   ++p ill++++i++l++s++++r+++++++++ ++g  l+++++++ll+gf+   ++v++++ ++         +++++k+
  gi|91772793|ref|YP_565485.1| 363 FLPNILLLFLMISLLEDSGYMARAAFVMDKLMYKIG--LNGRSFIPLLMGFG---CNVPAIMATR---------TIEDEKD 429
                                   6899********************************..**************...*********9.........******* PP

                          Gate  85 alafllfvllytpcvatlavivrelgs 111
                                   +l+++l++ + + c+a+l+v+   +g+
  gi|91772793|ref|YP_565485.1| 430 RLVTILVNPFIS-CGARLPVYLMLAGA 455
                                   **********87.********999886 PP

  == domain 2  score: 105.5 bits;  conditional E-value: 1.3e-33
                          Gate   1 llkagpiillasiliwflss...................ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvg 62 
                                   l+kag+iil +++++w+ls+                   +sl+g +g ++ep++aplg  +dwk++v+l++gf+ake+v+g
  gi|91772793|ref|YP_565485.1| 522 LKKAGTIILTGVVFVWLLSAipapgvdaafaseeilgteDSLVGVLGHIIEPLVAPLG--FDWKVAVALVFGFIAKEIVIG 600
                                   79********************************************************..********************* PP

                          Gate  63 tlgtly......tsalgellqgfdtpksalafllfvllytpcvatlavivrelgsk 112
                                   ++g+ly         +  l +g+ +p +al +++f+lly+pc+a ++v+++e+gs+
  gi|91772793|ref|YP_565485.1| 601 SMGVLYgtgedeDALAEILTAGAMSPLTALGLMVFTLLYVPCIACVGVVKKETGSW 656
                                   **********9666667778999*******************************98 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 !   77.1   1.3   4.3e-25   5.9e-22       1      53 []     465     517 ..     465     517 .. 0.98
   2 ?   -0.7   0.1      0.83   1.1e+03       8      21 ..     528     541 ..     519     554 .. 0.54
   3 ?   -1.6   0.3       1.6   2.2e+03       9      22 ..     584     597 ..     583     602 .. 0.83
   4 ?   -3.7   1.0       7.6     1e+04       3      21 ..     661     679 ..     660     682 .. 0.74

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 4.3e-25
                        FeoB_C   1 lfslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvliktweR 53 
                                   +f++Y+lgi+va+l+a+l++  t lkg+pspf+mELPpYrlP++k  +i++we+
  gi|91772793|ref|YP_565485.1| 465 IFGIYILGIIVAILSAKLIRG-TvLKGKPSPFIMELPPYRLPTPKASAIHMWEK 517
                                   69*******************.99****************************98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.83
                        FeoB_C   8 gilvallvalllkk 21 
                                    il  ++  +ll+ 
  gi|91772793|ref|YP_565485.1| 528 IILTGVVFVWLLSA 541
                                   34444555555554 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.6
                        FeoB_C   9 ilvallvalllkkt 22 
                                   ++val+ ++++k +
  gi|91772793|ref|YP_565485.1| 584 VAVALVFGFIAKEI 597
                                   6899******9985 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 7.6
                        FeoB_C   3 slYllgilvallvalllkk 21 
                                   ++ + g  +a ++a+l+ +
  gi|91772793|ref|YP_565485.1| 661 FMMAYGTTLAWIAAFLIYR 679
                                   5777788888888888755 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.2   3.4e-22   4.6e-19       2     111 ..      21     129 ..      20     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 3.4e-22
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCTSEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleeadlil 80 
                                   +a++G+pNvGK+tL+na+tg++ +v+++pg+T + ++g+ ++k++eie+vD+pG ++    s ++ +++++   e+ d+++
  gi|91772793|ref|YP_565485.1|  21 IALAGNPNVGKTTLFNAITGARQHVGNWPGVTVEKKTGKRTYKDTEIEVVDLPGTYSltAYSIDEVVARDYVVEEKPDVVV 101
                                   89*************************************9999***********87655667788999999988889**** PP

                                   EEEETTTTCSHHHHHHHHHHHHHTTSEEEEE CS
                      MMR_HSR1  81 lvvdaseeklkpldeeleelleeakkplilv 111
                                    +vda+ + l+++   l   l e + +++++
  gi|91772793|ref|YP_565485.1| 102 QIVDAT-N-LERN-LYLTTQLMELGSKVVIA 129
                                   ****77.3.4333.33333333444555555 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.7   8.4e-20   1.2e-16       1      90 [.     190     276 ..     190     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 8.4e-20
                     FeoB_Cyto   1 YgeeiEkaiekleellkes.nlkaklppRwlAlklLegDeelleelkedpelraeveearkeleaelgedledvIvdaryk 80 
                                   Yg++iEk+i +le++++++  l  k+p Rwl++klL+gDe++l++++    ++a+v+ + + +++   ed e +++++ry+
  gi|91772793|ref|YP_565485.1| 190 YGNDIEKKIIELEKIVSKDsALSGKYPVRWLSVKLLDGDENILKKIEG-SSVAAQVNSILSAIKK---EDYEAAMAEKRYE 266
                                   9******************999*************************9.9999999999999997...8************ PP

                     FeoB_Cyto  81 fiegilrevv 90 
                                    i+ +l +v+
  gi|91772793|ref|YP_565485.1| 267 TINTVLPQVC 276
                                   ******9998 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 !   22.4   0.0     5e-08   6.8e-05       3      97 ..      18     118 ..      16     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5e-08
                                   --EEEEE-STTSSHHHHHHHHHHS..S---.B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG.E... CS
                         SRPRB   3 kpavllvGlsdsGKTslftrLttd..svkk.tvtSqessaalkvksekgskltliDfPGheklrqklleklkakss.l... 76 
                                   k ++ l+G  + GKT+lf+ +t    +v +   + +e+++ +++   k+++++++D+PG  +l    +++++a++  +   
  gi|91772793|ref|YP_565485.1|  18 KITIALAGNPNVGKTTLFNAITGArqHVGNwPGVTVEKKTGKRT--YKDTEIEVVDLPGTYSLTAYSIDEVVARDYvVeek 96 
                                   66899****************98743222212344455555555..7****************998888877776522211 PP

                                   .EEEEEEEETTS-HHHHHHHHH CS
                         SRPRB  77 .kglvfvvDStidpkevkevAE 97 
                                      +v +vD+t  ++++  +  
  gi|91772793|ref|YP_565485.1|  97 pDVVVQIVDATNLERNLYLTTQ 118
                                   1357788888887777755544 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.1e-07   0.00043       2      97 ..      20     110 ..      19     154 .. 0.78
   2 ?   -0.4   0.0      0.44     6e+02     167     198 ..     160     189 ..     156     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-07
                                   EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT CS
                          AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllsee 82 
                                   ti l G   +Gk +  N+i g ++   +    +vt + ++ +rt ++++i+V+D Pg  +l +   +i + + r + + ee
  gi|91772793|ref|YP_565485.1|  20 TIALAGNPNVGKTTLFNAITGARQHVGNW--PGVTVEKKTGKRTYKDTEIEVVDLPGTYSLTAY--SIDEVVARDYVV-EE 95 
                                   78999******************999885..99************************9998753..333444454555.55 PP

                                   -ESEEEEEEETTB-S CS
                          AIG1  83 gihalllvlslgrft 97 
                                    +++++ ++++++++
  gi|91772793|ref|YP_565485.1|  96 KPDVVVQIVDATNLE 110
                                   599988777766655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHHHHHHHHHHHHTTTT--B-HHH CS
                          AIG1 167 keekeeQvkellelveaivkenggkpytnely 198
                                    ++++e  + lle  e ++++n+g+++ +e++
  gi|91772793|ref|YP_565485.1| 160 VAKRAEGIDALLE--EVVREANKGEHHEHEVS 189
                                   5677777888888..88999999999999986 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   3.5e-05     0.049      98     146 ..      17      67 ..       4      78 .. 0.75
   2 !    6.0   0.1    0.0071       9.8      34      97 ..     108     174 ..      98     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                                   TTSEEEEECSTTSSHHHHHHHHCTT-----S-...-------------SEEE CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktge...vseklgrGkhTTtavel 146
                                   k+ t++l+G+  vGK+tL na+++  ++++g+   v  ++++Gk T + +e+
  gi|91772793|ref|YP_565485.1|  17 KKITIALAGNPNVGKTTLFNAITGA-RQHVGNwpgVTVEKKTGKRTYKDTEI 67 
                                   456789*****************97.55555323388999999999776654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0071
                                   HHHHHHH...HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                   RsgA_GTPase  34 lldrfLv...laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                    l+r L    ++ e g ++vi+ln  Dl+e++ +  ++++    l+++v+++ ak+ eg+++l e++
  gi|91772793|ref|YP_565485.1| 108 NLERNLYlttQLMELGSKVVIALNMWDLAESRGDKIDTRKMEDFLEIPVVKTVAKRAEGIDALLEEV 174
                                   455555411145667889*************9966677777788999**************998765 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 !   12.8   1.5   4.6e-05     0.063      53     191 ..      50     177 ..      16     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                                   TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEE.....EEEETTTBST.HHHHHHHHHHHHTTTEEEE CS
                      GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgav.....lvvdaveGve.pqteevlrlalkegvpiiv 127
                                   g+T++ ++ +    +k+++i ++D PG  + +   i  + + D++v     +vv++v+  + ++   +  ++ ++g ++++
  gi|91772793|ref|YP_565485.1|  50 GVTVEKKTGKRT--YKDTEIEVVDLPGTYSLTAYSIDEVVARDYVVeekpdVVVQIVDATNlERNLYLTTQLMELGSKVVI 128
                                   778888877777..9************998666555554444444444444444444443303445567789999****** PP

                                   EEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                      GTP_EFTU 128 fiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                   ++N  D ++++ ++i +   +++                e+pvv + a+++eg+++lle +v+ 
  gi|91772793|ref|YP_565485.1| 129 ALNMWDLAESRGDKIDTRKMEDF---------------LEIPVVKTVAKRAEGIDALLEEVVRE 177
                                   **************999988899...............379*******************9986 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   3.1e-05     0.042      11     107 ..      15     122 ..       9     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                                   .TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSS..SSSEEEEEEEETTEEEEEEEE-SSGGGGGG......GGGGC..T CS
                           Arf  11 kkkelrilllGLDnaGKtTilkklkleelvt.tvP..TigfnveeleiknlkftvwDvGGqeklRpl......WknYf..e 80 
                                   +kk++ i l G  n GKtT+ + ++  +++    P  T+  ++ + ++k+ +++v D+ G  +l  +       ++Y   e
  gi|91772793|ref|YP_565485.1|  15 EKKKITIALAGNPNVGKTTLFNAITGARQHVgNWPgvTVEKKTGKRTYKDTEIEVVDLPGTYSLTAYsidevvARDYVveE 95 
                                   589999******************98776554777446677777899**************99987522222268898334 PP

                                   TESEEEEEEETT-CTTHHHHHHHHHHH CS
                           Arf  81 ktdavifvvDsadreRleeakeeLkal 107
                                   k d+v+ +vD+++ eR     ++L +l
  gi|91772793|ref|YP_565485.1|  96 KPDVVVQIVDATNLERNLYLTTQLMEL 122
                                   678999999999999987777777766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.21      32      91 ..      17      77 ..       8     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                        AAA_25 32 agelallaGapgtGKttlaldlalavatGkpwlg.pvapeqgkVlyvsaEdsedelrrRlr 91
                                  ++ +++laG p +GKttl   +  a     +w+g  v+ + gk  y ++E    +l+  ++
  gi|91772793|ref|YP_565485.1| 17 KKITIALAGNPNVGKTTLFNAITGARQHVGNWPGvTVEKKTGKRTYKDTEIEVVDLPGTYS 77
                                  567899**************99999998888***98888********99999888876666 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 ?    1.9   0.0     0.064        88      31      52 ..      20      41 ..      13      53 .. 0.82
   2 ?    7.4   0.0    0.0014       1.9     199     229 ..     147     178 ..      90     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.064
                                  EEEEEE-TTSSHHHHHHHHHHH CS
                          MeaB 31 vvGltGvPGaGkstlvealgle 52
                                   + l G P +Gk tl +a++  
  gi|91772793|ref|YP_565485.1| 20 TIALAGNPNVGKTTLFNAITGA 41
                                  68899***********999865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                                   T.BTTB--EEEEEBCCCTBSHHHHHHHHHHHH CS
                          MeaB 199 k.ekeWrpkvlktsavegeGidelvdaieehr 229
                                   k e+  + +v+kt+a++ eGid l++++ + +
  gi|91772793|ref|YP_565485.1| 147 KmEDFLEIPVVKTVAKRAEGIDALLEEVVREA 178
                                   325666789****************9997654 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 ?   10.4   0.1   0.00018      0.24     107     141 ..      12      45 ..       5      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                     Parvo_NS1 107 lskqlgkrntvwfyGpantGktnlaeaIakavply 141
                                   ++ +  k+ t+ + G +n Gkt l++aI+ a + +
  gi|91772793|ref|YP_565485.1|  12 IDME-KKKITIALAGNPNVGKTTLFNAITGARQHV 45 
                                   5555.7899********************887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 4676.70
//
Query:       gi|91772794|ref|YP_565486.1|  [L=146]
Description: hypothetical protein Mbur_0780 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.12   12.2   0.6       0.23   11.3   0.6    1.5  1  ATP-synt_S1  Vacuolar ATP synthase subunit S1 (ATP6S1)
        6.7    6.2  12.4         10    5.6  12.4    1.4  1  DUF1700      Protein of unknown function (DUF1700)


Domain annotation for each model (and alignments):
>> ATP-synt_S1  Vacuolar ATP synthase subunit S1 (ATP6S1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   2.6e-05      0.23      96     132 ..      72     108 ..      57     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                   ATP-synt_S1  96 CvgFfsigiwmgLvvslillliltyglhmimdlktmd 132
                                    v+++ +gi+m+Lv +++ ll++   l m   +k+ d
  gi|91772794|ref|YP_565486.1|  72 GVSYVYVGILMSLVFMAVYLLVMGADLLMFYVVKSED 108
                                   5899*************************99998876 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  12.4    0.0012        10     104     171 ..      33     102 ..       1     106 [. 0.60

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0012
                       DUF1700 104 islvlsllvvalallvsplvllvksllkgfeelslnvfvsigllglGllllivayylvk..ilykltvky 171
                                     l  sll+ +  +    +v++++++l ++ els+ v+++++ + +G+l+++v +++    +  +l++ y
  gi|91772794|ref|YP_565486.1|  33 TGLAESLLIPGDFFGGFCFVVIGAVFLYAVKELSAGVYMGVSYVYVGILMSLVFMAVYLlvMGADLLMFY 102
                                   3334444555555555568899999************************998876654300444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1158.86
//
Query:       gi|91772795|ref|YP_565487.1|  [L=110]
Description: hypothetical protein Mbur_0781 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-08   34.6   0.5    2.6e-08   33.8   0.1    1.6  2  FeoC           FeoC like transcriptional regulator
  ------ inclusion threshold ------
      0.042   13.4   0.1      0.064   12.8   0.1    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.054   13.3   0.0      0.088   12.6   0.0    1.3  1  LexA_DNA_bind  LexA DNA binding domain
       0.13   12.5   0.0          2    8.7   0.0    2.0  2  HTH_34         Winged helix DNA-binding domain
       0.13   12.1   0.0        0.2   11.6   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   7.3e-12   2.6e-08       4      64 ..      11      71 ..       8      76 .. 0.84
   2 ?   -1.9   0.1         1   3.6e+03      47      58 ..      86      96 ..      78     101 .. 0.53

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 7.3e-12
                          FeoC  4 elkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaatacc.sgsCkkCggke 64
                                  e+      +  + ++eLsr+++  p+ l+ +Le+++rkG +e   ++ +   +sC +Cg  +
  gi|91772795|ref|YP_565487.1| 11 EVATI-LSQDNITFGELSRRLNLGPKELKELLETMERKGDIEISCMSPPPdTTSCAGCGMGH 71
                                  55554.4567899*****************************998877656*******9766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                          FeoC 47 vaataccsgsCk 58
                                  +++++  + +C+
  gi|91772795|ref|YP_565487.1| 86 LTENGR-KVCCE 96
                                  444333.34443 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.8e-05     0.064      12      45 ..      15      48 ..      12      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                        HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                  +  + +i+  eL++rl+l p  +++ l+ +e++G
  gi|91772795|ref|YP_565487.1| 15 ILSQDNITFGELSRRLNLGPKELKELLETMERKG 48
                                  677899*************************999 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.5e-05     0.088      29      59 ..      24      53 ..      21      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                                  HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                 LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierd 59
                                   e++r+l+l  p+  +e L+++erKG ie+ 
  gi|91772795|ref|YP_565487.1| 24 GELSRRLNLG-PKELKELLETMERKGDIEIS 53
                                  699******9.*****************985 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00056         2       7      47 ..      13      53 ..       9      61 .. 0.91
   2 ?    1.7   0.0     0.082   2.9e+02      58      67 ..      83      92 ..      81      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00056
                        HTH_34  7 syLasvdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                                  ++ +s+d+++f el+  l++   +L   l+++e +g ie++
  gi|91772795|ref|YP_565487.1| 13 ATILSQDNITFGELSRRLNLGPKELKELLETMERKGDIEIS 53
                                  667789*******************************9985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.082
                        HTH_34 58 llriTpeGre 67
                                  ++r+T++Gr+
  gi|91772795|ref|YP_565487.1| 83 TYRLTENGRK 92
                                  79*******8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.6e-05       0.2      16      57 ..      14      55 ..      12      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                  ++l++++ t  e++++l++      e L+ +e+kG +e++  
  gi|91772795|ref|YP_565487.1| 14 TILSQDNITFGELSRRLNLGPKELKELLETMERKGDIEISCM 55
                                  78999********************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 785.03
//
Query:       gi|91772796|ref|YP_565488.1|  [L=113]
Description: hypothetical protein Mbur_0782 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.0     0.0093   15.9   0.0    2.0  1  HTH_45          Winged helix-turn-helix
     0.0003   20.8   0.1    0.00046   20.2   0.1    1.3  1  FeoC            FeoC like transcriptional regulator
  ------ inclusion threshold ------
      0.029   14.9   0.0      0.054   14.0   0.0    1.4  2  PCI             PCI domain
      0.063   13.3   0.1      0.097   12.7   0.1    1.2  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
       0.13   12.4   0.0       0.25   11.5   0.0    1.4  1  DUF2802         Protein of unknown function (DUF2802)


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 !   15.9   0.0   2.6e-06    0.0093       7      71 ..       8      96 ..       6     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-06
                        HTH_45  7 IiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli........................kkskekYvlTekGlel 65
                                  I   IL+ +s+g+++  +i  k  ++ k l+  L+ +v++g+i                           + +Y lTekG e+
  gi|91772796|ref|YP_565488.1|  8 ISRRILDLVSQGNTTFDRIACKLGITHKELEFLLELMVHRGYIrsvcdpknssccsmvskpldsnsvYSCGVTYLLTEKGVEV 90
                                  56679*************************************9999***999999999999998775557899*********9 PP

                        HTH_45 66 leklke 71
                                   +++ e
  gi|91772796|ref|YP_565488.1| 91 CRNITE 96
                                  999877 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.3e-07   0.00046      11      58 ..      17      63 ..      14      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                          FeoC 11 ergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaataccsgsCk 58
                                   +g   ++ +++++ ++ + le +Le++v +G ++ v      s++C+
  gi|91772796|ref|YP_565488.1| 17 SQGNTTFDRIACKLGITHKELEFLLELMVHRGYIRSVCDPKN-SSCCS 63
                                  57788899***************************9988555.55553 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.5e-05     0.054      60     100 ..      20      60 ..       6      64 .. 0.87
   2 ?   -3.6   0.0       4.5   1.6e+04      44      54 ..      92     102 ..      88     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                   EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSSEEEETTTTE CS
                           PCI  60 sislerlaklldlsvdevEkilvklIrdgeirakidqesgi 100
                                   + +++r+a +l+++ +e+E +l  ++  g+ir  +d+++  
  gi|91772796|ref|YP_565488.1|  20 NTTFDRIACKLGITHKELEFLLELMVHRGYIRSVCDPKNSS 60 
                                   5589********************************99864 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.5
                                   HHHHHHHHHHH CS
                           PCI  44 kkvrerllrqv 54 
                                   ++++e+ +++v
  gi|91772796|ref|YP_565488.1|  92 RNITEHHVQRV 102
                                   56667766665 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   2.7e-05     0.097       6      48 ..       8      50 ..       5      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                Sulfolobus_pRN  6 lsekillilsrrcatleeleektGiekeellvyltrlykrGli 48
                                   s +il  +s++  t++++  k Gi ++el   l  + +rG i
  gi|91772796|ref|YP_565488.1|  8 ISRRILDLVSQGNTTFDRIACKLGITHKELEFLLELMVHRGYI 50
                                  67899999*********************************98 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.9e-05      0.25      36      66 ..      12      43 ..      10      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-05
                       DUF2802 36 AiklvrqG.asveelaeecgLsraEAeLllrL 66
                                   + lv qG  + + +a + g+++ E e+ll L
  gi|91772796|ref|YP_565488.1| 12 ILDLVSQGnTTFDRIACKLGITHKELEFLLEL 43
                                  56799***9999*****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 765.87
//
Query:       gi|91772797|ref|YP_565489.1|  [L=72]
Description: iron dependent repressor [Methanococcoides burtonii DSM 6242]
Scores for complete 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-18   65.2   0.0      5e-18   65.1   0.0    1.0  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00013   21.7   0.0    0.00016   21.5   0.0    1.1  1  MarR_2          MarR family
     0.0025   17.4   0.0      0.003   17.1   0.0    1.1  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.017   15.5   0.0    1.1  1  Rrf2            Transcriptional regulator
      0.052   13.4   0.0       0.07   12.9   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
      0.059   13.0   0.0      0.065   12.8   0.0    1.0  1  DDRGK           DDRGK domain
       0.08   12.9   0.0       0.11   12.5   0.0    1.2  1  MarR            MarR family
       0.11   12.2   0.0       0.13   11.9   0.0    1.1  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   2.2e-21     5e-18       1      60 []       1      60 [.       1      60 [. 0.98

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.2e-21
                                  X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                  +L++++EdYLe+I+ + ++k++++ kd+a  L+ +p+ V+em++kL++ Gyv+   y g+
  gi|91772797|ref|YP_565489.1|  1 MLSRKAEDYLEAILNITNDKGYARIKDVAVSLDLRPPNVTEMVQKLDSLGYVVCRRYEGV 60
                                  89*******************************************************997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.1e-08   0.00016      11      52 ..      13      53 ..       9      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.1e-08
                                  HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  ++++ +  g+  +++++a  l+l +++v+ ++++L + G+v+
  gi|91772797|ref|YP_565489.1| 13 ILNITNDKGY-ARIKDVAVSLDLRPPNVTEMVQKLDSLGYVV 53
                                  6778888888.6*****************************4 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 !   17.1   0.0   1.3e-06     0.003       7      47 ..      12      52 ..       7      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                        HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +IL++  +++   ++++A  l+l p++v++ +++L + G++
  gi|91772797|ref|YP_565489.1| 12 AILNITNDKGYARIKDVAVSLDLRPPNVTEMVQKLDSLGYV 52
                                  7***************************************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   7.4e-06     0.017       1      59 [.       1      56 [.       1      67 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.4e-06
                                  X---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2  1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                  M ls+k e  l a+l +++ ++   ++++++a + ++ p+ +  +++kL   g+v  +r
  gi|91772797|ref|YP_565489.1|  1 M-LSRKAEDYLEAILNITNDKGY--ARIKDVAVSLDLRPPNVTEMVQKLDSLGYVVCRR 56
                                  5.789999999999999998885..7*****************************8877 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   3.1e-05      0.07      19      48 ..      23      52 ..       6      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                  -BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyv 48
                                   +++++A  ++l +++v  ++q L  lGyv
  gi|91772797|ref|YP_565489.1| 23 ARIKDVAVSLDLRPPNVTEMVQKLDSLGYV 52
                                  4899*************************9 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.9e-05     0.065      97     142 ..       6      51 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                                   XXXHHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSS CS
                         DDRGK  97 eeklleefinyikekKvvlleelavkfklktqevierikeLeeqgs 142
                                   +e  le ++n  ++k +  ++++av ++l+  +v e +++L++ g 
  gi|91772797|ref|YP_565489.1|   6 AEDYLEAILNITNDKGYARIKDVAVSLDLRPPNVTEMVQKLDSLGY 51 
                                   345899***********************************98875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.7e-05      0.11       9      47 ..      14      52 ..      12      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                                  HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                  L i  ++g +++++ a  l + +++vt+++ +L   G++
  gi|91772797|ref|YP_565489.1| 14 LNITNDKGYARIKDVAVSLDLRPPNVTEMVQKLDSLGYV 52
                                  5555677889999********************888876 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.9e-05      0.13       1      54 [.       1      53 [.       1      57 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                  HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                  +L+   ++ l+a++++ + k+   + +++A  l+  +  v  ++q L +lg v 
  gi|91772797|ref|YP_565489.1|  1 MLSRKAEDYLEAILNITNDKGY-ARIKDVAVSLDLRPPNVTEMVQKLDSLGYVV 53
                                  588889999******9998854.46679***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); 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:                         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 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 535.21
//
Query:       gi|91772798|ref|YP_565490.1|  [L=420]
Description: hypothetical protein Mbur_0784 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00078   19.5   0.1     0.0016   18.5   0.1    1.6  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
      0.036   13.4   0.3       0.11   11.7   0.1    1.8  3  Baculo_E56   Baculoviral E56 protein, specific to ODV envelop


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 !   18.5   0.1   1.8e-07    0.0016      83     161 .]     251     330 ..     216     330 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-07
                                   SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTST..T--EEEEEEEEESS.SEEEEEEESS-- CS
                   ATP-grasp_3  83 gekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekle..glaGyvGvDlvlkdeepyviEvNPRlt 159
                                   + ++  l + +q+ e+   ++v  G +   +++   ++ + ++  ++v ++   g +G+vG+D +++d+++  +E N+R+ 
  gi|91772798|ref|YP_565490.1| 251 EGNINSLGMRDQICER---GMVHIGTLKGDDHSPeiSNYIAKTSAKIVTNMAkfGYRGVVGIDYIVSDDGIFPVENNARFN 328
                                   5555556666666544...45555555444444333455555555555555556**************************9 PP

                                   GG CS
                   ATP-grasp_3 160 ts 161
                                   +s
  gi|91772798|ref|YP_565490.1| 329 GS 330
                                   97 PP

>> Baculo_E56  Baculoviral E56 protein, specific to ODV envelope
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.3e-05      0.11     168     225 ..     162     221 ..     135     256 .. 0.73
   2 ?   -2.0   0.0      0.19   1.7e+03      35      77 ..     258     299 ..     223     326 .. 0.72
   3 ?   -1.9   0.0      0.18   1.6e+03     241     276 ..     305     340 ..     282     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                    Baculo_E56 168 sdvfvceldPllpnnvdelrnlcdGynleveksvcrgsdpsadPds..eqyvdisdleen 225
                                   ++    e++P + +n  +++n+ +Gy   +e+ + rg+  +ad +   ++  dis++ ++
  gi|91772798|ref|YP_565490.1| 162 VEGSSFEMNPEDNENCTDMKNIINGYLSTCETVIIRGTLGEADMSLykTKGNDISEIYHE 221
                                   222334789**********************************98511445688887665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.19
                    Baculo_E56  35 alfqdasdtqlnglsqlrradniPdatlhikqtrknavktsfP 77 
                                   ++ +++ +  +  +++l+  d  P+ + +i++t  + v t+  
  gi|91772798|ref|YP_565490.1| 258 GMRDQICERGMVHIGTLKGDDHSPEISNYIAKTSAKIV-TNMA 299
                                   45566777778888888888888888888887755433.4444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.18
                    Baculo_E56 241 gdlGldwllGenGlvtkssnslssvssklttillli 276
                                   g +G+d+++ ++G+     n+    ss++ +i+  i
  gi|91772798|ref|YP_565490.1| 305 GVVGIDYIVSDDGIFPVENNARFNGSSYVSMIVDNI 340
                                   557999999999998888888877777777776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2885.30
//
Query:       gi|91772799|ref|YP_565491.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91772799|ref|YP_565491.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772799|ref|YP_565491.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772799|ref|YP_565491.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772799|ref|YP_565491.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772799|ref|YP_565491.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772799|ref|YP_565491.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772799|ref|YP_565491.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772799|ref|YP_565491.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2168.88
//
Query:       gi|91772800|ref|YP_565492.1|  [L=216]
Description: CDP-alcohol phosphatidyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-10   41.7   0.5    1.5e-10   41.7   0.5    3.0  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 !   41.7   0.5   8.4e-15   1.5e-10       2      66 .]      21      88 ..      21      88 .. 0.84
   2 ?   -3.2   6.7      0.84   1.5e+04      33      35 ..     173     175 ..      92     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 8.4e-15
                                  -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---...H.HHHHHHHHHH CS
               CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvs...t.lGkllDslaD 66
                                  lPn+ +l++ll++vl+i+ + ++  + lai+ ++ a+++D+ DG +ARr++  +   + +G +lDsl+D
  gi|91772800|ref|YP_565492.1| 21 LPNICSLAGLLCAVLSIY-YGILGNFPLAIIGMIWAVVFDWGDGLIARRMKGRTdeyRaFGGQLDSLID 88
                                  6***********888884.4344449************************874444555********99 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.84
                                   HHH CS
               CDP-OH_P_transf  33 lll 35 
                                   l++
  gi|91772800|ref|YP_565492.1| 173 LFI 175
                                   111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1210.75
//
Query:       gi|91772801|ref|YP_565493.1|  [L=371]
Description: L-threonine O-3-phosphate decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for 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-31  107.3   0.0    1.2e-30  107.0   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.0   6.5e-35   1.2e-30      50     363 .]      62     359 ..      43     359 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 6.5e-35
                                   HHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE CS
                 Aminotran_1_2  50 eealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhl 130
                                   + ala ++g    + +++  ++vvg+Ga +li ++   ++     + +vp p++ +y n++ + +  v+++pl+  ++f+l
  gi|91772801|ref|YP_565493.1|  62 QDALAGLIG---DVIHQPAERIVVGNGAAELIKIISGHIS----NKLIVPVPSFNEYANAAPADR--VFEFPLE-FPSFQL 132
                                   678888999...56666666*************9999995....789*********999988776..4555533.569*** PP

                                   -HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTST CS
                 Aminotran_1_2 131 dlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeep 211
                                   d++++ +   +     +k  v +v +p+NPt  + ++ +l  l++   k+ ++l++De + +fv + +d +++  ++e++p
  gi|91772801|ref|YP_565493.1| 133 DVDKFAAEAIR-----IKADVAVVVTPNNPTSMLVPKSDLISLAQKLAKHDCMLIIDESFLDFVHD-PDQTTLENELERYP 207
                                   ****9984444.....377888999****************************************9.777777******** PP

                                   TEEEEEESSSTTSSGGG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 212 nllivgslsKafGlaGeRvGyilg.naavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrde 291
                                   n++i+ s+sKa+G+ G+R+Gy l  n a+++ +r  +  +++   + +++  +l d  +   e+ e+ +++   r+ l+++
  gi|91772801|ref|YP_565493.1| 208 NIAILKSMSKAYGICGIRIGYMLTaNLAFAESVREGVHIWNINGFAEEFL-RILPDYRQ---EFVESCKQVRIDRDNLYKK 284
                                   ***********************9999***************99998886.67777775...999**************** PP

                                   HHHS.TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHHHH CS
                 Aminotran_1_2 292 Lael.glkvlasqsgmflltdlsae.takelskkLleevgvyvtpgtsftvpgrlRitv.Aglteeeleelveal 363
                                   L ++ g +v++++++++  ++ +++ +  el + L  e++ y+ +++  t+p + R    A+ te e+ +lveal
  gi|91772801|ref|YP_565493.1| 285 LCAIpGMTVYKPDANFIFCRLPDHAqSGPELTRRLFIEHNMYIKHCQDKTLPDSSRYVRiASRTETENCKLVEAL 359
                                   *999********************9999*****************999999555554444669999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2032.14
//
Query:       gi|91772802|ref|YP_565494.1|  [L=249]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-10   40.0   0.1    1.1e-09   38.3   0.1    1.9  1  NTP_transferase  Nucleotidyl transferase
    1.5e-08   35.1   0.0    1.9e-08   34.8   0.0    1.3  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 !   38.3   0.1   1.2e-13   1.1e-09       2     118 ..      16     126 ..      15     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.2e-13
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   a++La G+G+RL+PLt++++k l  v +  ++++  + +l ++g+++ +vv+t +++  +++ l++ +  g+e+++++ p 
  gi|91772802|ref|YP_565494.1|  16 ALLLAAGKGSRLYPLTQNSPKCLTMVHEA-SILERLVINLKKQGFKR-LVVVTGFQEKCIRDFLETRA-CGMEIEFIISPL 93 
                                   789**************999988888888.*****************.99999999999998888776.899999999998 PP

                                   --..BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTT CS
               NTP_transferase  83 gk..gtAdAvalaaelledeksdelvlvLggDhlikda 118
                                       +   ++  a++++++      +l + +D ++++ 
  gi|91772802|ref|YP_565494.1|  94 YAttNNIYSLWMARDIINE-----PFLLIESDLVFDES 126
                                   8745555666666666663.....45788888888764 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   2.1e-12   1.9e-08       1      54 [.      16      75 ..      16     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.1e-12
                                  EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHHH CS
                  NTP_transf_3  1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd.eevlaa 54
                                  a++LA+G++sR+     +++K+l  +++ ++ler++ +l+++g++++vvv+g  e++ ++
  gi|91772802|ref|YP_565494.1| 16 ALLLAAGKGSRLypltqNSPKCLTMVHEASILERLVINLKKQGFKRLVVVTGFqEKCIRD 75
                                  689*********8877667********************************994333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1538.92
//
Query:       gi|91772803|ref|YP_565495.1|  [L=145]
Description: hypothetical protein Mbur_0789 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1003.19
//
Query:       gi|91772804|ref|YP_565496.1|  [L=410]
Description: TrkA-C [Methanococcoides burtonii DSM 6242]
Scores for complete 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   85.4   0.3    2.7e-13   49.5   0.1    2.7  2  TrkA_C    TrkA-C domain
    2.4e-20   72.8  15.3    4.1e-10   40.0   1.4    2.4  2  PhoU      PhoU domain
     0.0056   16.0   7.1       0.13   11.6   0.3    2.2  2  PhoU_div  Protein of unknown function DUF47


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.1   4.5e-17   2.7e-13       2      68 ..     132     200 ..     131     202 .. 0.95
   2 !   33.1   0.0     6e-12   3.6e-08      10      54 ..     341     387 ..     332     391 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.5e-17
                                   EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                        TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                   ++vt++++s +vG tl++l l+ + g  ++airR+ ++++ p  dt+++++Dv++  g+++++  l el
  gi|91772804|ref|YP_565496.1| 132 IRVTINENSDMVGSTLGDLELEVEtGMWIIAIRRHtDWVYDPHHDTRIRADDVIFARGHDEGVPLLVEL 200
                                   79********************99**************************************9988765 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 6e-12
                                   GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEE CS
                        TrkA_C  10 splvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvll 54 
                                   sp++Gk+ +el+l ++ gv ++a++R   ++++ps  t+ +eGD+l+
  gi|91772804|ref|YP_565496.1| 341 SPIIGKSYRELKLGTEtGVHIMAVKRAeRWVYSPSAKTTVQEGDILI 387
                                   9**************************9*****************96 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   6.6   3.2e-13   1.9e-09       1      89 []      26     110 ..      26     110 .. 0.88
   2 !   40.0   1.4   6.9e-14   4.1e-10       2      87 ..     228     309 ..     227     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.2e-13
                                   HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                   l +m++++e m+d+a++a + +d+++  ev+++++++d l++ ++ +++     r   +e  ++++++l++a + E i+  
  gi|91772804|ref|YP_565496.1|  26 LIEMKDTSELMVDLAYSAMVYDDEDISGEVLDLEEKMDTLHYHMKMAAMLSTR-R--IEE-AEDMVGVLQVAASAENIANA 102
                                   679********************9999*****************777554442.2..233.6789**************** PP

                                   HHHHHHHH CS
                          PhoU  82 avniaerv 89 
                                   a +ia+++
  gi|91772804|ref|YP_565496.1| 103 AGDIAKII 110
                                   *****986 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 6.9e-14
                                   HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82 
                                    +m++++e ++ +a++al  ++t++a+ev ++++e+d++ ++++  +le +++       ++el +ll++a+  E i+D a
  gi|91772804|ref|YP_565496.1| 228 VDMKNTAELAVGLAYSALLFDNTDIAEEVKALEREMDEMKYDLQHWVLETAKHVAD----VNELRGLLHLANASESISDAA 304
                                   68********************************************9999977665....5556679************** PP

                                   HHHHH CS
                          PhoU  83 vniae 87 
                                     ia+
  gi|91772804|ref|YP_565496.1| 305 YGIAD 309
                                   *9997 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   1.8   0.00046       2.7     144     210 ..      43     112 ..       8     114 .. 0.73
   2 !   11.6   0.3   2.2e-05      0.13     142     208 ..     244     311 ..     203     313 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00046
                      PhoU_div 144 alskk..diveeieslEdeiDqlqrkl.ikklfsredasnplevlllveiieklenvsdraedvadrisi 210
                                   a+     di  e+ +lE+++D l+ ++ +  ++s    +   +++ + +     en++++a d+a+ i++
  gi|91772804|ref|YP_565496.1|  43 AMVYDdeDISGEVLDLEEKMDTLHYHMkMAAMLSTRRIEEAEDMVGVLQVAASAENIANAAGDIAKIIEM 112
                                   33322448889************8764256667777888899999999****************998876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.2e-05
                      PhoU_div 142 etalskkdiveeieslEdeiDqlqrklikklfs.redasnplevlllveiieklenvsdraedvadri 208
                                   +  +++ di+ee++ lE e+D+++  l    ++  + +  + e   l ++ +  e +sd+a  +ad++
  gi|91772804|ref|YP_565496.1| 244 ALLFDNTDIAEEVKALEREMDEMKYDLQHWVLEtAKHVADVNELRGLLHLANASESISDAAYGIADTV 311
                                   33355569****************99876555427777777788888888888888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2804.96
//
Query:       gi|91772805|ref|YP_565497.1|  [L=186]
Description: MgtE, divalent cation transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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   66.9   9.3    2.1e-18   66.9   9.3    1.4  2  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.65   1.2e+04      47      47 ..      24      24 ..       9      44 .. 0.58
   2 !   66.9   9.3   1.2e-22   2.1e-18       1     123 [.      48     177 ..      48     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.65
                                  H CS
                          MgtE 47 g 47
                                  g
  gi|91772805|ref|YP_565497.1| 24 G 24
                                  1 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 1.2e-22
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-........CTSHHH.. CS
                          MgtE   1 iPvilglgGnlgaqlasristalhlgelekk..lkkvllkelrvvlllgvilgllifllalllgw.......slllalv.. 70 
                                   +P+++ +gG +g++l +r+s+ +h+g  +++   + v+ +++++++++g++ +++++++a+++++             +  
  gi|91772805|ref|YP_565497.1|  48 VPALIKIGGDTGSILGARLSSTFHMGIGTTHihKNPVVKNSVIAAFIVGITASVALSVIAWMMSGfgdsplgF-----Ftl 123
                                   69***********************94444444689***********************99988887555431.....312 PP

                                   ...HHHHHHHHHHHHHHH.....HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                          MgtE  71 ...vglalvlvllaaall...ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                      ++++ +l l     l    ++++++++++++g+DPd  +iP++++lgDl+g+   +
  gi|91772805|ref|YP_565497.1| 124 fkiCTISGTLEL-----LavfSATIAIAFASHRFGIDPDDTVIPVIATLGDLVGITAIF 177
                                   222333333223.....233345888****************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1233.08
//
Query:       gi|91772806|ref|YP_565498.1|  [L=206]
Description: MgtE integral membrane region [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-21   76.3  15.9    3.2e-21   76.0  11.4    2.0  2  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   0.1    0.0068   1.2e+02      33      62 ..      26      53 ..      13      68 .. 0.68
   2 !   76.0  11.4   1.8e-25   3.2e-21       2     124 .]      69     198 ..      68     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0068
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          MgtE 33 kkvllkelrvvlllgvilgllifllalllg 62
                                   + ++ke++ +++l++i g++++++    g
  gi|91772806|ref|YP_565498.1| 26 VRSIVKEALPFQILATIGGAVAGFIFA--G 53
                                  6889999**********9999998822..2 PP

  == domain 2  score: 76.0 bits;  conditional E-value: 1.8e-25
                                   HHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-......CTSHHHHHHHHH CS
                          MgtE   2 PvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgw.....slllalvvglalv 76 
                                   P++lg++Gn+  +l sr+ +a+h+g+++k   +  l++++   lllg+i++++++++ ++++      s+ ++++ ++a++
  gi|91772806|ref|YP_565498.1|  69 PAVLGMRGNISCTLGSRLGSAIHMGLITKIeNNPELTNNIYGSLLLGLIMSIALGIIGHTMTVllgfeSAGILALTSIAVL 149
                                   9************************99666778999999999999999999999999776555667778888889****** PP

                                   HHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHHH CS
                          MgtE  77 lvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllvl 124
                                   + + + ++l +++vll+l ++++g+DPdn+++P ++++gD++++l+l+l
  gi|91772806|ref|YP_565498.1| 150 AGVSSGIILsVIAVLLALGMFRFGFDPDNVVTPSIATIGDIVSMLMLFL 198
                                   ***********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1444.67
//
Query:       gi|91772807|ref|YP_565499.1|  [L=361]
Description: hypothetical protein Mbur_0793 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-09   38.0   1.3    3.8e-09   37.0   1.3    1.5  1  PDDEXK_4  PD-(D/E)XK nuclease superfamily
     0.0053   16.7   2.9     0.0053   16.7   2.9    2.4  2  DUF2972   Protein of unknown function (DUF2972)
     0.0082   16.1   0.1      0.087   12.8   0.0    2.4  2  HSDR_N_2  Type I restriction enzyme R protein N terminus (HSD
  ------ inclusion threshold ------
      0.063   12.9   1.2       0.12   12.1   0.1    2.1  2  VraX      Family of unknown function


Domain annotation for each model (and alignments):
>> PDDEXK_4  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   1.3   8.4e-13   3.8e-09      35     163 ..      20     166 ..       4     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 8.4e-13
                      PDDEXK_4  35 sflkafldllrerlf.ssdeisas...vadlesaevere......nasekngriDlll....qenkivvlIEnKvaAkdqk 101
                                    f + f +ll+  ++ +s+ i++      ++++ +v ++         ++++r D+++    + +k +++IE K+++ + +
  gi|91772807|ref|YP_565499.1|  20 FFTEIFTHLLKSDSDlFSKLIQDFnisNINFNDSFVSTQesfdalDNHFSGSRPDIFIelsnDTEKELIFIECKIGSEEGQ 100
                                   45555556666555544444444455544555555555578877766777778888888888999**************** PP

                      PDDEXK_4 102 eQlarYeefakkkakkkdivvvyLtldgeapsedslee....dekeayktisyeqilewleecvkk 163
                                   +Ql+rY+e++++ ++ ++  ++y t+d +a+ ++ +      ++  ++k++ + qi+++l+   k 
  gi|91772807|ref|YP_565499.1| 101 DQLQRYAEHLDNIENINKKSLIYITRDFDAKNQKYIFMncknKSSLTFKQFRWYQIYQFLSLFNKD 166
                                   ************998889999999877654444433334766888899***********9988877 PP

>> DUF2972  Protein of unknown function (DUF2972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.9      0.27   1.2e+03      84     136 ..      74     113 ..      36     136 .. 0.45
   2 !   16.7   2.9   1.2e-06    0.0053      25     142 ..     235     356 ..     222     360 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.27
                       DUF2972  84 ditkelfnkqkcfyeriiiyikkkdfeilkeneklleqvkeyllelieeLkkq 136
                                   di++el+n  ++ +e i i +           +   e+ +++l++ +e+L ++
  gi|91772807|ref|YP_565499.1|  74 DIFIELSN--DTEKELIFIEC-----------KIGSEEGQDQLQRYAEHLDNI 113
                                   33333332..11222232222...........222223333333333333333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-06
                       DUF2972  25 fpkpkeedkelfakkas.elevllPltlkln..kdlnkk.ikitlldrvyikkqaleedinltditkelfnkqkcfyerii 101
                                   ++  k +++ ++ ++++ +++ +l   ++    +++ k+ i i+l+ +++ ++q++e   +++  + +  + + +  ++  
  gi|91772807|ref|YP_565499.1| 235 LNDLKDHNRYVYLQEQNdKFQLILGYFMNNLtiESYPKVgISINLSPKASERIQIMEVMKKIVSSSDKWKGYDLNEANNWA 315
                                   6778899999998877669**999987753325666553389*****************************999******* PP

                       DUF2972 102 iyikkkdfeilkeneklleqvkeyllelieeLkkqkeiekk 142
                                   ++ ++k ++++ ++e  ++  ++y+lel++eL+ +k+  ++
  gi|91772807|ref|YP_565499.1| 316 VISQTKSLDYFLNQEDHITALQNYFLELLNELETIKKNYNN 356
                                   *********************************99987665 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   1.9e-05     0.087      37     105 ..      71     137 ..      45     140 .. 0.73
   2 ?    1.7   0.1     0.057   2.5e+02      45      79 ..     129     164 ..     121     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                      HSDR_N_2  37 kraDivv..ykkdkkpllivecKapsvkiseevleqlksYlealkaeylvvtNglehivykvdkkkkkfee 105
                                   +r+Di +   ++++k l+++ecK  s+    e+ +ql++Y+e+l     +   +l  i  + d k++k+ +
  gi|91772807|ref|YP_565499.1|  71 SRPDIFIelSNDTEKELIFIECKIGSE----EGQDQLQRYAEHLDNIENINKKSLIYITRDFDAKNQKYIF 137
                                   689999984555588********8877....5668********9665555455555555555555556655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.057
                      HSDR_N_2  45 kkdkkpllivecKapsvki.seevleqlksYlealk 79 
                                   + +++ +++  cK++s  + ++   +q+ ++l+ ++
  gi|91772807|ref|YP_565499.1| 129 DAKNQKYIFMNCKNKSSLTfKQFRWYQIYQFLSLFN 164
                                   455789*******98766658888999998888765 PP

>> VraX  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.4   6.3e+03      22      35 ..      43      56 ..      39      63 .. 0.70
   2 ?   12.1   0.1   2.6e-05      0.12      33      55 .]     151     173 ..     139     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                          VraX 22 FktitikcDetFnk 35
                                  F+   i ++++F  
  gi|91772807|ref|YP_565499.1| 43 FNISNINFNDSFVS 56
                                  55556889999854 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.6e-05
                          VraX  33 FnktEiykLLsLLenDvDnmkvs 55 
                                   F  + iy+ LsL + D++n+ +s
  gi|91772807|ref|YP_565499.1| 151 FRWYQIYQFLSLFNKDINNILIS 173
                                   77899*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2431.00
//
Query:       gi|91772808|ref|YP_565500.1|  [L=87]
Description: hypothetical protein Mbur_0794 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 608.21
//
Query:       gi|91772809|ref|YP_565501.1|  [L=374]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-06   27.3   0.5      4e-06   26.6   0.5    1.3  1  DDE_Tnp_1     Transposase DDE domain
     0.0098   16.0   0.1      0.026   14.6   0.1    1.7  1  Hit1_C        Hit1 C-terminal
  ------ inclusion threshold ------
      0.046   13.8   1.8        2.2    8.4   0.1    2.6  2  TetR_C_8      Transcriptional regulator C-terminal region
       0.34   10.5   1.6        3.2    7.4   0.1    2.4  2  Fur_reg_FbpB  Fur-regulated basic protein B


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.5   8.9e-10     4e-06       7     182 ..     103     293 ..      97     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.9e-10
                     DDE_Tnp_1   7 livDattvrvpgtk.....edarwgykggk..ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgk 78 
                                   l++D t+ +  g+       +  +g+ +++  ++y y   ++++  +++ +s+  + + +  +++lk ++d ++++  k+ 
  gi|91772809|ref|YP_565501.1| 103 LAIDYTNDPYYGEVdainkNYVIRGQAKKStnSFYSYISLCIINKYTRFTISMLPVEKGRTKTDYLKYFIDLVDKInlKTN 183
                                   55666666666666333332222233322245899999***********99999988888888888776666666666*** PP

                     DDE_Tnp_1  79 lvlaDaGYasaelldtleekgvdyiirl...........kkntklyrk..............gaeskrrgrlrkhdrnkil 134
                                   ++  D+ + s++++ +l+e+ + +i ++            +n+k y+k               ++ k+ +  r+++ ++ l
  gi|91772809|ref|YP_565501.1| 184 VLCLDREFYSRDVFAFLQENEIPHITPVvrmgkrikdllDGNKKRYEKyvmknkkgdveldiAIDVKYLKGKRGKNGCENL 264
                                   ****************************98877777777444444444555666677666666888888888888888888 PP

                     DDE_Tnp_1 135 tksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFk 182
                                     +    +                    ++ ++  +yr+R +iE++ +
  gi|91772809|ref|YP_565501.1| 265 GFVVYGIDW-------------------EPGKISTIYRKRFTIESSYR 293
                                   888888888...................****************9876 PP

>> Hit1_C  Hit1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   5.9e-06     0.026      20      65 ..      67     116 ..      62     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                        Hit1_C  20 vkfhlakv.yrilttsegn...ggssdtlsseakkqlavdylntlryGGv 65 
                                   +++hl+k+ +  l  ++++   ++s++tl s+ k +la+dy n   yG v
  gi|91772809|ref|YP_565501.1|  67 MRYHLHKIdFDQLIENNAKillQSSHETLDSNKKYDLAIDYTNDPYYGEV 116
                                   689****965666655554232466677***************9999976 PP

>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2      0.01        47      39      80 ..     106     147 ..      78     151 .. 0.86
   2 ?    8.4   0.1   0.00049       2.2      28      87 ..     303     365 ..     291     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHHHH-TT--S-HHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_8  39 elikelilkvieelsegkelseedkefiadfysygfvgvild 80 
                                   +++++ +++ ++ +++++ ++ + k+   +fysy  + +i +
  gi|91772809|ref|YP_565501.1| 106 DYTNDPYYGEVDAINKNYVIRGQAKKSTNSFYSYISLCIINK 147
                                   5778889999************************99999865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00049
                                   -.THHHHHHHHHHHHHHHHHHHHHH-TT-..-S-HHHHHHHHHHH.HHHHHHHHHHHHHTTS- CS
                      TetR_C_8  28 ngresfekylkelikelilkvieelsegk..elseedkefiadfy.sygfvgvildWlengmk 87 
                                    +r+ + +y++ li+ ++++ + ++++ +  +++  +k +  d +    fv+ i++W++++ k
  gi|91772809|ref|YP_565501.1| 303 SSRNPMLRYFYALISFMLKNAWLSIQRMHfmKVKRGPKTIEEDVFrFDLFVHFIEEWVRKKLK 365
                                   5789999***************777744456**************5569**********9877 PP

>> Fur_reg_FbpB  Fur-regulated basic protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00071       3.2       4      22 ..      72      90 ..      70      94 .. 0.89
   2 ?    1.7   0.2     0.042   1.9e+02       5      17 ..     226     238 ..     216     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00071
                  Fur_reg_FbpB  4 kklsFeeLVeeNKkeLlnD 22
                                  +k+ F++L+e N k Ll++
  gi|91772809|ref|YP_565501.1| 72 HKIDFDQLIENNAKILLQS 90
                                  7899********9999987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.042
                  Fur_reg_FbpB   5 klsFeeLVeeNKk 17 
                                   k+++e  V++NKk
  gi|91772809|ref|YP_565501.1| 226 KKRYEKYVMKNKK 238
                                   6999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 2178.75
//
Query:       gi|91772810|ref|YP_565502.1|  [L=459]
Description: Sep-tRNA:Cys-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-19   68.9   0.0    4.8e-19   68.3   0.0    1.2  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    1.1e-13   50.9   0.0    1.4e-13   50.5   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
      0.003   16.1   0.0      0.005   15.4   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
       0.09   12.8   0.0       0.19   11.7   0.0    1.5  1  HemeBinding_Shp  Cell surface heme-binding protein Shp


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 !   68.3   0.0   1.1e-22   4.8e-19     100     364 ..     166     443 ..     132     455 .. 0.77

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.1e-22
                                   C--CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTCCC...EEEEEECSSTTTTB----HHHH CS
                       SepSecS 100 kakkviwvridekSslkavelaGleialvekvlegDelitdvedveeiiekkreev...ilavlstlsffaprspDdvkei 177
                                   k+++v+    ++   + ave aG   ++ e   ++ ++ t ++ +++i e kre      l+++   +    +  D +  i
  gi|91772810|ref|YP_565502.1| 166 KGDTVVVSTFAHYTEFLAVEGAGG--IVREAPVNEHNILTAESVAHKIDEVKRETGklpALIMIDHFDYLFCNEHD-IYGI 243
                                   666777777777777888877773..34455555556666666666555433333211134555666777789999.**** PP

                                   HHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCCCCCHCCCHCHCTSCHC CS
                       SepSecS 178 akiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfikeiskeypgrasaaps 258
                                    k+ +ey++P+l NgAY++               G ++v  ++++++++v++G++++a+  +s++    +e+++++ ++ +
  gi|91772810|ref|YP_565502.1| 244 GKVAQEYGIPFLYNGAYTV---------------GIMPVNGQKIGADFVVGSGHKSMASAAPSGVLATTEEWADKIFRTTQ 309
                                   *******************...............9****************************************998765 PP

                                   ........CCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC...............EEESSSTT-SSEEEEE- CS
                       SepSecS 259 ........kdvlisllllGskaykkllkeqkesfkllreklkklaeeve...............ekllevpeNpissaltl 316
                                           k  +++++ lG++  +++l   ++sf++++e+ k+++eev+               e+l e p  + +s + +
  gi|91772810|ref|YP_565502.1| 310 mvgdvtgrKFGIKEVEFLGCTLMGAPLLSMMASFPHVKERTKHWDEEVKksnyfineflriegnEVLSEFPRKHALSKVDT 390
                                   22221111345799***********************************9*************999999999999999876 PP

                                   CC.CHCCCC...THHHHHHHHHHHTTECSS.E.EE-SSTCECTTSSS-SSSEE CS
                       SepSecS 317 et.ldeikk...karldlaseLfsrkvtGa.rgvrasdsklTshlkeyhsrYl 364
                                    + +d++ k   ++  ++  eL++r + G   g ++s ++ T  l   + +Yl
  gi|91772810|ref|YP_565502.1| 391 TGsFDKVAKthkRKGYFFSDELKKRGIAGEfPGATRSWKMSTYGLSWDQIHYL 443
                                   5414444434435678999*********9624677777777755555555555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   3.2e-17   1.4e-13      48     228 ..     133     312 ..     114     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.2e-17
                                   HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE CS
                   Aminotran_5  48 arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld 128
                                    ++++ae+++ ++  +  ++ G+ +++++va s+   +++gd++vv++  h  ++++ + +    g  v+ +p++e+  l+
  gi|91772810|ref|YP_565502.1| 133 FHTDLAEFVGMDQ-AR--VVPGARRGFQAVASSI---IEKGDTVVVSTFAHYTEFLAVEGA----GGIVREAPVNEHNILT 203
                                   5677888888886.44..4689999*********...******************554444....789************* PP

                                   GGGHHHH-.......-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT. CS
                   Aminotran_5 129 ldelekll.......nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK. 201
                                    + +++++        + ++l++i h      + +++  igk+a+++g+ +l  +a +vg +p++ +k+g+Df++ sghK 
  gi|91772810|ref|YP_565502.1| 204 AESVAHKIdevkretGKLPALIMIDHFDYLFCNEHDIYGIGKVAQEYGIPFLYNGAYTVGIMPVNGQKIGADFVVGSGHKs 284
                                   99999999777666457789************************************************************8 PP

                                   TTSSTT-EEEEEEHHHHHTS...SS.ST CS
                   Aminotran_5 202 llgPtGiGvlyvrkellekl.eplllgg 228
                                   +  ++  Gvl   +e   k+ +++++ g
  gi|91772810|ref|YP_565502.1| 285 MASAAPSGVLATTEEWADKIfRTTQMVG 312
                                   8888888889888877777633333333 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 !   15.4   0.0   1.1e-06     0.005      47     233 ..     123     314 ..     103     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-06
                                   TTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSS.......HHHHHHH.HHTHHHTTCEE CS
               Cys_Met_Meta_PP  47 sRsgnptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlY.......ggtqrll.kkvlkklgiev 119
                                    +++ p  s++   +a+  g ++a +v+      +a+  +++++Gd +vvs+ ++       +g+  ++ +  +++++i +
  gi|91772810|ref|YP_565502.1| 123 DKIEKPSISTFHTDLAEFVGMDQARVVPGARRGFQAVASSIIEKGDTVVVSTFAHyteflavEGAGGIVrEAPVNEHNILT 203
                                   56788999999999************99999999999999*******9988755312223333333334134456677777 PP

                                   EEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTT CS
               Cys_Met_Meta_PP 120 kfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKy 199
                                        ++++e+++   +   l+ ++     +++ +Di  i k+a++ g++ +   +++ + + ++  k gaD vv S+ K 
  gi|91772810|ref|YP_565502.1| 204 AESVAHKIDEVKRETGKLPALIMIDHFDYLFCNEHDIYGIGKVAQEYGIPFLYNGAYTVGiMPVNGQKIGADFVVGSGHKS 284
                                   66667899999999999999****************************************7779****************9 PP

                                   TTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B CS
               Cys_Met_Meta_PP 200 lgGhsdvvaGvivvkgkeelkkelkflqnalGav 233
                                   ++  s +  Gv+++ +  e+++++ ++++ +G v
  gi|91772810|ref|YP_565502.1| 285 MA--SAAPSGVLATTE--EWADKIFRTTQMVGDV 314
                                   87..667789998554..8888888888888766 PP

>> HemeBinding_Shp  Cell surface heme-binding protein Shp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.2e-05      0.19      58      99 ..     130     171 ..     123     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
               HemeBinding_Shp  58 vltfrmsladysgnyqfwiqpggtgsfqavdynitqkgtdtn 99 
                                   + tf+  la++ g  q  + pg    fqav   i +kg    
  gi|91772810|ref|YP_565502.1| 130 ISTFHTDLAEFVGMDQARVVPGARRGFQAVASSIIEKGDTVV 171
                                   569**********************************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2690.88
//
Query:       gi|91772811|ref|YP_565503.1|  [L=431]
Description: O-acetylhomoserine/O-acetylserine sulfhydrylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-141  469.8   0.0   5.3e-141  469.6   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.2e-11   44.5   0.1      2e-11   43.8   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      8e-08   31.6   0.4    1.4e-07   30.9   0.4    1.3  1  Aminotran_5      Aminotransferase class-V
    8.5e-06   25.2   0.0    1.2e-05   24.7   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-05   24.3   0.0      3e-05   23.4   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.016   14.0   0.0      0.027   13.3   0.0    1.2  1  GDC-P            Glycine cleavage system P-protein
       0.11   11.2   0.0       0.17   10.6   0.0    1.2  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
       0.12   10.8   2.0       0.31    9.5   2.0    1.7  1  Met_gamma_lyase  Methionine gamma-lyase


Domain annotation for each model (and alignments):
>> 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 !  469.6   0.0  2.4e-144  5.3e-141       1     382 []       9     428 ..       9     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.6 bits;  conditional E-value: 2.4e-144
                                   HHHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHH CS
               Cys_Met_Meta_PP   1 eTllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavssGma 78 
                                   +T+++h g+e+d +tg++avpiy+t++y+f+d+++a   fa ++ g++Y+R++npt++vle+r+aa+egg+ al v+sGm+
  gi|91772811|ref|YP_565503.1|   9 DTIALHGGHEPD-ATGSRAVPIYQTAAYVFNDAEHAanlFALKAFGNIYTRLMNPTTDVLEKRVAAIEGGTGALGVASGMS 88 
                                   799*******99.8*********************9999****************************************** PP

                                   HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHH CS
               Cys_Met_Meta_PP  79 AiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDieki 159
                                   Ai++a la+ + Gdeiv+ ++lYggt++l++++++klg +v+fvd ++++++ekai+e+t+++y+E ++np+l+++D+eki
  gi|91772811|ref|YP_565503.1|  89 AITLAALAVTQLGDEIVSANNLYGGTYQLFNHTFPKLGRKVNFVDSTKPDDFEKAITEKTRAIYVEIIGNPKLDIPDLEKI 169
                                   ********************************************************************************* PP

                                   HHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH............. CS
               Cys_Met_Meta_PP 160 aklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq............. 227
                                   a++a++ag++++vDnt+  ++ ++p+++gaDivv SaTK+lgGh++ ++G+iv++g++++++  kf +             
  gi|91772811|ref|YP_565503.1| 170 AEIAHNAGIPLIVDNTVGVGI-VKPIDYGADIVVLSATKFLGGHGTSIGGIIVDSGNFSWDNG-KFPEftdpdpsyhglkf 248
                                   *****************9996.79************************************996.6555889********** PP

                                   ........................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTS CS
               Cys_Met_Meta_PP 228 ........................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpsh 284
                                                           ++lG+++spf+a+++++G++TLslR++rh enAl+vA++L++hp ve+v+Ypgl++h
  gi|91772811|ref|YP_565503.1| 249 wesfgnipgmgnlafilrvrtqllRDLGPAMSPFNAFQFIQGVETLSLRVKRHGENALAVARHLNSHPLVEWVNYPGLEDH 329
                                   ********************************************************************************* PP

                                   TTHHHHHHHSSSG-S.EEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE CS
               Cys_Met_Meta_PP 285 pqhelakkqlkgagg.vlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkeereaagvtddliRls 364
                                   p+hela+k+l+g+ g +l+F +k+++e+ kkf++n++l+s+++++G++++l+++pas+th++++keere++gvtdd+iR+s
  gi|91772811|ref|YP_565503.1| 330 PSHELAQKYLNGSYGaILGFGVKGGLEAGKKFIENVELLSHLANIGDAKTLVIHPASTTHQQLTKEEREQTGVTDDFIRMS 410
                                   ***********98767***************************************************************** PP

                                   --SS-HHHHHHHHHHHHH CS
               Cys_Met_Meta_PP 365 vGiEdvdDliaDlkqale 382
                                   vG+Ed+dD+iaD++qale
  gi|91772811|ref|YP_565503.1| 411 VGLEDIDDIIADIDQALE 428
                                   ****************96 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 !   43.8   0.1   8.8e-15     2e-11      20     150 ..      57     189 ..      39     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 8.8e-15
                                   SS..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHH....TT-EEEEE-B-T CS
               DegT_DnrJ_EryC1  20 ts..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavle....lgakpvfvDvdp 94 
                                   t+  +p+++ +Ek++aa  g   a++v+sG +A+ la  a+    gde++ + + + +t +   +    lg k+ fvD + 
  gi|91772811|ref|YP_565503.1|  57 TRlmNPTTDVLEKRVAAIEGGTGALGVASGMSAITLAALAVTQ-LGDEIVSANNLYGGTYQLFNHtfpkLGRKVNFVDST- 135
                                   445599***************************9887555333.37*************98765422228********99. PP

                                   TTSSB-GGGCGGG--TTEEEEEEB-GGGB--....-HHHHHHHHHHCT-EEEEE-TT-TT CS
               DegT_DnrJ_EryC1  95 dtynidpaaieaaitertkaIlpVhlyGqva....dmdalkaiaakhglkvieDaAhAlG 150
                                        +p++ e+aite+t+aI  V++ G++     d++++ +ia++ g+++i D   ++G
  gi|91772811|ref|YP_565503.1| 136 -----KPDDFEKAITEKTRAI-YVEIIGNPKldipDLEKIAEIAHNAGIPLIVDNTVGVG 189
                                   .....8**************9.69****986655588999999***********877666 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.4   6.1e-11   1.4e-07      73     210 ..      89     216 ..      70     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 6.1e-11
                                   HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                   Aminotran_5  73 ainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                   ai+l+al++    + gdeiv  ++ + ++    ++   + g kv+++        ++d++ek+++ekt+++++  + n   
  gi|91772811|ref|YP_565503.1|  89 AITLAALAV---TQLGDEIVSANNLYGGTYQLFNHTFPKLGRKVNFVDS-----TKPDDFEKAITEKTRAIYVEIIGNPKL 161
                                   555555555...6667777777777777766666666666777766665.....7899*********************** PP

                                   EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EE CS
                   Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGv 210
                                    i ++e+i+++a+++g+ ++vD + +vg   ++  ++g+D++++s+ K+lg  G+++
  gi|91772811|ref|YP_565503.1| 162 DIPDLEKIAEIAHNAGIPLIVDNTVGVG--IVKPIDYGADIVVLSATKFLGGHGTSI 216
                                   **********************876665..5677889*****************875 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.3e-09   1.2e-05      69     237 ..      79     223 ..      32     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.3e-09
                                   EGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHT....TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCT CS
                 Aminotran_1_2  69 aavvvgsGagaliealifllklnpgdeilvpdptyasyknilrls....ggevvryplyseedfhldlealeealkeapeg 145
                                   +a+ v sG +a+  a+ ++++   gdei++ +  y+   + +++     g +v  +        +   +++e+a++e    
  gi|91772811|ref|YP_565503.1|  79 GALGVASGMSAITLAALAVTQ--LGDEIVSANNLYGGTYQLFNHTfpklGRKVNFVD-------STKPDDFEKAITE---- 146
                                   4777899***99999999998..9******998888777777776222266666666.......8899*********.... PP

                                   TETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSG CS
                 Aminotran_1_2 146 nkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGla 226
                                     kt+ i+ve + NP  ++++le++ ++   a+  ++ l+vD + +++  ++           ++ ++++v s  K +G  
  gi|91772811|ref|YP_565503.1| 147 --KTRAIYVEIIGNPKLDIPDLEKIAEI---AHNAGIPLIVDNTVGVGIVKP----------IDYGADIVVLSATKFLGGH 212
                                   ..*************9777777777777...9999*******9988887773..........4455568888999999988 PP

                                   GG-EEEEEEEH CS
                 Aminotran_1_2 227 GeRvGyilgna 237
                                   G  +G i++++
  gi|91772811|ref|YP_565503.1| 213 GTSIGGIIVDS 223
                                   88888888865 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.3e-08     3e-05      31     273 ..      61     315 ..      54     323 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-08
                                   -HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-EBTTTBE- CS
               Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiael.agvklrdlknkeaGkmd 110
                                   ++t+ +Le++va++ g  +al v++G  A  ++  +++q g+e++  ++  + ++   ++ +   g k++ +++      +
  gi|91772811|ref|YP_565503.1|  61 NPTTDVLEKRVAAIEGGTGALGVASGMSAITLAALAVTQLGDEIVSANNLYGGTYQLFNHTFPkLGRKVNFVDST-----K 136
                                   7899*****************************************999988889999999888445544444444.....5 PP

                                   HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSE CS
               Beta_elim_lyase 111 lekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDs 191
                                   ++++e+ai+e      k+++i++++  n      + +  l+++a+ia++ gipl++D        + +  ivk +  ++D+
  gi|91772811|ref|YP_565503.1| 137 PDDFEKAITE------KTRAIYVEIIGN----PKLDIPDLEKIAEIAHNAGIPLIVDN------TVGV-GIVKPIDYGADI 200
                                   **********......699*****9988....489********************994......4333.3677777889** PP

                                   EEEESSS...TT--SS-EEEEE-HH......................................HHHHHHHHHHHHT---SS CS
               Beta_elim_lyase 192 vtmslkK...dllanvGgvlafrddel..................................edylaerveqrkylggglrq 235
                                   v++s++K   + ++ +Gg+++ + +                                       l+ r+++ + lg  ++ 
  gi|91772811|ref|YP_565503.1| 201 VVLSATKflgGHGTSIGGIIVDSGNFSwdngkfpeftdpdpsyhglkfwesfgnipgmgnlAFILRVRTQLLRDLGPAMS- 280
                                   *****996655678999999877664466667777777777777777777777777766643334445555666666666. PP

                                   THHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHC CS
               Beta_elim_lyase 236 agvlaaleagiraleeglaslerdhktaeqlaeklelv 273
                                     + a     i  +e  + +++r+ ++a   a++l+ +
  gi|91772811|ref|YP_565503.1| 281 -PFNAF--QFIQGVETLSLRVKRHGENALAVARHLNSH 315
                                   .34444..445555555555555555666666655555 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.027     142     260 ..      89     208 ..      79     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHH-SSS--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-.....S-EEEEEEEES.-TTSB----HHH CS
                         GDC-P 142 Avllaaraskkkakkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd..kekevagvlvqyp.nteGriedlkel 219
                                   A++laa a  +  +++v +++++  t +  +    +lg ++  vd+t+ +  +   ++++ ++ v    n +  i dl+++
  gi|91772811|ref|YP_565503.1|  89 AITLAALAVTQLGDEIVSANNLYGGTYQLFNHTFPKLGRKVNFVDSTKPDDFEkaITEKTRAIYVEIIgNPKLDIPDLEKI 169
                                   77787777777788999999999999999998889999999988877655544345677888888764255778******* PP

                                   HHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTT CS
                         GDC-P 220 vekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrf 260
                                   +e a++  + ++v  + + ++++k P ++gaDivv sa +f
  gi|91772811|ref|YP_565503.1| 170 AEIAHNAGIPLIVD-NTVGVGIVK-PIDYGADIVVLSATKF 208
                                   **********9875.789999998.78********999988 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.5e-05      0.17     144     197 ..     140     189 ..     130     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.5e-05
                                   HHHHHHCCTCCCEEEEEECSSTTTTB----HHHHHHHHHCCT--EEEEGCCCCT CS
                       SepSecS 144 veeiiekkreevilavlstlsffaprspDdvkeiakiCaeydvPhlvNgAYaiq 197
                                    e++i++k     + ++  ++      pD +++ia+i ++ ++P++v +  ++ 
  gi|91772811|ref|YP_565503.1| 140 FEKAITEKTRAIYVEIIGNPKL---DIPD-LEKIAEIAHNAGIPLIVDNTVGVG 189
                                   5555555444444444444433...4678.*******************99983 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.0   0.00014      0.31     147     238 ..     139     222 ..      63     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00014
               Met_gamma_lyase 147 avkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefveekePtevGadliaGsliknpGG 227
                                     ++ai+ekt+ i +         + l i ++e+i ++ +  n  + + vdn  G  v    P++ Gad++  s  k  GG
  gi|91772811|ref|YP_565503.1| 139 DFEKAITEKTRAIYVEI----IGNPKLDIPDLEKIAEIAH--NAGIPLIVDNTVG--VGIVKPIDYGADIVVLSATKFLGG 211
                                   56677777777777653....2357788999988888765..45667779****9..77899******************* PP

               Met_gamma_lyase 228 giaktGGyiaG 238
                                     +++GG i+ 
  gi|91772811|ref|YP_565503.1| 212 HGTSIGGIIVD 222
                                   *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2613.65
//
Query:       gi|91772812|ref|YP_565504.1|  [L=488]
Description: homoserine O-acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  123.9   0.1      1e-35  123.6   0.1    1.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    6.5e-28   97.0   1.5    1.1e-13   51.4   0.3    2.6  2  CBS            CBS domain
    0.00029   20.2   0.1     0.0017   17.7   0.1    1.9  2  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.019   15.6   0.0      0.023   15.3   0.0    1.3  1  Abhydrolase_6  Alpha/beta hydrolase family
       0.14   11.8   0.0       0.21   11.2   0.0    1.3  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   0.1   2.9e-39     1e-35       1     256 [.      47     355 ..      47     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 2.9e-39
                                   SEEEEE-STTTCGGG............GTTGHHHHHHHHT..TSEEEEEEETTSTTSSSTTTGB.........CHHSHHHH CS
                 Abhydrolase_1   1 pvlvilhGlpgssdv............waerglapaLakd..gfdvillDlrGvgySspapacin........ddygtasv 59 
                                   ++++++h+l+g ++             w+   ++p+ a d  +++v++ +++G ++++++pa+ +         +++ +++
  gi|91772812|ref|YP_565504.1|  47 NAILVCHALTGDAHAagrhsdddkkpgWWDDIIGPGKALDtdRYFVLCSNVLGGCKGTTGPASLDpdtgrqygITFPVITI 127
                                   689********66666777788999**********9999999***********************99998888668***** PP

                                   HHHHH...HHHHHCTTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE....CSSCCHHHHHHHHHHHHHHCHHCHHH CS
                 Abhydrolase_1  60 addld...rildalgddklt.lvGhSmGGmialayaaeyperVkalvllga....idpaaslieaqrqqaksfpdffdgya 132
                                   +d+++   r+ d+ g+  l  +vG+SmGGm+ l+++  ype Vk+ v +++    ++  ++++e  r+++ s+pd++ g++
  gi|91772812|ref|YP_565504.1| 128 RDMVNvqkRLIDHMGITTLFaVVGGSMGGMQTLQWCVAYPELVKKAVVIAStavsSPQQIAFNEVGRNAIISDPDWNGGDY 208
                                   *****99899********************************************9999*********************** PP

                                   HHHHHHHHHHHHHCCSCHHHHHHHHHHHHHH...........HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHH CS
                 Abhydrolase_1 133 adcarnpagplladelaaleqrhrlvdalkf...........pdkskrfpssgsdnasslatgalksieqwpttdsaklll 202
                                   +++++++ g++ a++ a++++ ++++   kf            d+s +f  +++   +++++++ ++ +++ +  +a  + 
  gi|91772812|ref|YP_565504.1| 209 YEGEPPVNGLSTARMIAHITYLSDASMHEKFgrrlqqgesykFDMSNDFQVGSYLKYQGDTFTGRFDANSYLYATKAVDYF 289
                                   ************************998877799999988888888888888888888888888888888888888888888 PP

                                   HHHC.......THHHHSEEEEEEETTCSSSCH.HHHHHHHHC..HTS..EEEEEEETCSSSHHHHS CS
                 Abhydrolase_1 203 rlre.......lknvlaptlvisgtsDplvpp.kaledlaql..lpk..krlvvisdagHlafleg 256
                                   +l +       lk v a+ lvis+tsD+l +p +++   ++l    +  ++++++s +gH+afl++
  gi|91772812|ref|YP_565504.1| 290 DLSMngslaegLKYVQAKMLVISITSDWLYSPyHSKKIVEGLtvKEHdvSYREIESSYGHDAFLLE 355
                                   8888*******999******************666666677786666****************986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   5.6e-15     2e-11       1      55 [.     372     426 ..     372     428 .. 0.93
   2 !   51.4   0.3   2.9e-17   1.1e-13       3      54 ..     435     486 ..     433     488 .] 0.93

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5.6e-15
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+d+mt++v t+++ +++  a++ m e+++++lPVV+e+g lvGivt  D+ +a+
  gi|91772812|ref|YP_565504.1| 372 VADVMTEKVATIREGASIDTAAKVMFEEALTHLPVVNENGCLVGIVTSWDISKAV 426
                                   89**********************6588899*********999********8886 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 2.9e-17
                                   HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                    imtrdv+t+ pd+++  a+++m+++ +s+lPVVde ++l+Gi+  +D+ r+
  gi|91772812|ref|YP_565504.1| 435 NIMTRDVLTAFPDEPIVAAAKRMERHSISALPVVDEKNRLIGIIDSEDINRL 486
                                   69*********************9999*********************9776 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.6e-07    0.0017      77     117 ..     146     187 ..     119     199 .. 0.77
   2 ?   -0.3   0.0      0.15   5.3e+02     188     224 ..     302     340 ..     290     352 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.6e-07
                   Hydrolase_4  77 plfllGhSmGGliallyllrypdkva.glilsaPalkikakl 117
                                    + ++G SmGG+ +l+++  yp+ v+ +++++++a++ ++++
  gi|91772812|ref|YP_565504.1| 146 LFAVVGGSMGGMQTLQWCVAYPELVKkAVVIASTAVSSPQQI 187
                                   45699********************98999999999887765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.15
                   Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerlgsk..dktl 224
                                   + +++ +l+++ ++D++ +p  s++++e l+ k  d+++
  gi|91772812|ref|YP_565504.1| 302 KYVQAKMLVISITSDWLYSPYHSKKIVEGLTVKehDVSY 340
                                   5678899********************999887444444 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   6.5e-06     0.023      49     122 ..     122     207 ..      49     354 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.5e-06
                                   H....CHHHHHHHCCTT....TTSE.EEEEETCHHHHHHHHHHCC.......EE.EEES-..----TTTS----TTHHHHH CS
                 Abhydrolase_6  49 d....ladlaalldelaa..gggpv.vlvGHSlGGalalaaapla.....lvvg.vlldppptalpagllaaalelllall 116
                                        ++d +++  +l++  g      +vG S+GG+  l+    +     lv + v++++  ta+  + + a+ e+ + ++
  gi|91772812|ref|YP_565504.1| 122 FpvitIRDMVNVQKRLIDhmGITTLfAVVGGSMGGMQTLQ---WCvaypeLVKKaVVIAS--TAVSSPQQIAFNEVGRNAI 197
                                   23222355555444444444455558**************...44444764344799999..6666666666666666555 PP

                                   HTT-C....C CS
                 Abhydrolase_6 117 allrl....l 122
                                    + ++    +
  gi|91772812|ref|YP_565504.1| 198 ISDPDwnggD 207
                                   5444333321 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     6e-05      0.21     117     171 ..     147     209 ..     131     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6e-05
                                   EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC...........HCHHHCTTCCHHHCC-CC CS
                      Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvssfSpivnps...........namWgqeekeawqendpv 171
                                    av+G SmGG+  L   + +p++ + + + +  +  s           na++   +++ w+ +d +
  gi|91772812|ref|YP_565504.1| 147 FAVVGGSMGGMQTLQWCVAYPELVKKAVVIASTAVSSpqqiafnevgrNAII---SDPDWNGGDYY 209
                                   59***********************999888554444555555555553333...44555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 3123.84
//
Query:       gi|91772813|ref|YP_565505.1|  [L=801]
Description: phosphoenolpyruvate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-114  381.0   0.0   7.8e-114  380.3   0.0    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
      1e-60  205.4   0.0    1.6e-60  204.7   0.0    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    1.2e-25   89.0   0.5    1.1e-24   85.9   0.4    2.5  2  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.067   13.5   0.3       0.84   10.0   0.2    2.8  2  PPR              PPR repeat
      0.091   13.0   0.1       0.43   10.8   0.0    2.0  2  PPR_2            PPR repeat family


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 !  380.3   0.0  2.2e-117  7.8e-114       2     318 ..      19     350 ..      18     358 .. 0.97

  Alignments for each domain:
  == domain 1  score: 380.3 bits;  conditional E-value: 2.2e-117
                        PPDK_N   2 elvGGKganLael...lneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPe 79 
                                   ++vGGK+a+L+e+   l+ ++i++P+gfa+tada++++le++g+ +k++++l+ ld++dv++l++++k++r+++l+a +P+
  gi|91772813|ref|YP_565505.1|  19 PSVGGKNASLGEMyreLTGKDIKIPNGFAVTADAYWHVLESAGVLQKLKDSLEGLDTNDVTDLAERGKKARSIVLDAGIPD 99 
                                   68***********87777788************************************************************ PP

                        PPDK_N  80 eleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrkekgl 160
                                   +l e+ikeay++l++++g+e ++vaVRSSataEDlp asfaGqq+tyLnv+g +++ +a++++ aSlf++rAi+Yr ++++
  gi|91772813|ref|YP_565505.1| 100 DLWEEIKEAYDKLSEEYGSE-TDVAVRSSATAEDLPHASFAGQQETYLNVHGYHSLKDACNRCLASLFTDRAISYRVHHKF 179
                                   *******************9.9*********************************************************** PP

                        PPDK_N 161 dheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrk.....ilekkige 236
                                   dh++v+l+++v+kmv+sdl++sGV f++d+e+Gf+d+v+i+ +yGlGe++V+G v+pdef+v+k+t k     i++k +g+
  gi|91772813|ref|YP_565505.1| 180 DHFKVGLSIGVMKMVRSDLASSGVIFTIDTESGFEDVVFITGAYGLGENIVQGLVNPDEFYVFKPTLKegyipIIKKMMGS 260
                                   ********************************************************************************* PP

                        PPDK_N 237 keikivydekeeg..tkevevpeeereklaLsdeeveeLaeiakkiekhyg......tpmdiEfaideeegklyllQaRpe 309
                                   keik++y + +++  t++vevp ++++k++++d+e+  La++a +ie+hy+       pmdiE+a+d+++++l+++QaRpe
  gi|91772813|ref|YP_565505.1| 261 KEIKMIYGRGDSRilTRNVEVPLADQRKFCINDDEILLLAKYAATIEDHYSkkkgqaVPMDIEWAKDGNTDELFIVQARPE 341
                                   **********99999************************************9999999*********************** PP

                        PPDK_N 310 trtsekkek 318
                                   t++s+k ++
  gi|91772813|ref|YP_565505.1| 342 TVQSRKRKD 350
                                   ***998764 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 !  204.7   0.0   4.4e-64   1.6e-60      17     290 ..     486     794 ..     477     798 .. 0.88

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 4.4e-64
                                   CXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCC..HHHHHH..............................HH CS
               PEP-utilizers_C  17 gkkikvlaNidtpedaekalengaeGiGLlRtEflfmaree..lpteee..............................qa 65 
                                   ++k+++++N+++pe+a +    + +GiGL R Ef++ +  +  + +++                               + 
  gi|91772813|ref|YP_565505.1| 486 KTKTEMMMNLGNPEEAFSLSMIPNDGIGLARLEFIISSYIKvhPMALIHpekvedesvleeiekltdgykskedyfvekLS 566
                                   5799*******************************9988442244444478899*************************** PP

                                   HHHHHHHHHTTTSEEEEEXXXSSCC..GGSGGCHHHH..XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCCCC...EE CS
               PEP-utilizers_C  66 eaykkvleamngrpvvvRtlDiggd..kelpelkeep.eevNPmlGfRgirlglse..pelfetqlrAllrasaag...kl 138
                                   +  ++++++++++pvvvR+ D++++    l  +k+++ ee NPm+GfRg +++ +e  +e f  + +A+++++ ++   +l
  gi|91772813|ref|YP_565505.1| 567 QGVATIVASFYPKPVVVRMSDFKSNeyASLIGGKYFEfEESNPMIGFRGASRYYDEryREGFALECKAMKKVRDEMgltNL 647
                                   ************************94445555555442799***********9998779***************7755588 PP

                                   EEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCC CS
               PEP-utilizers_C 139 eimlPmvasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdn 219
                                    +m+P+ + vee     k+i+e+k++  ++    +++++v +M E+ps +ll+d++ k+ d+fSiG+NDLtQ+tl+vdRd+
  gi|91772813|ref|YP_565505.1| 648 ILMIPFCRRVEEA---EKVIAEMKKNGLER---GENGLQVYVMCEIPSNVLLIDEFSKYFDGFSIGSNDLTQLTLGVDRDS 722
                                   8888888887765...55666664443333...4789******************************************** PP

                                   HCHHHHSXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCCS.CCCHHHHHHCTXSEEEEXGGGHHHHHHHHH CS
               PEP-utilizers_C 220 eevaklydplepavlrlikevikaaeekglkvgiCGelagd.psavellvglGldelSmsaasvpaaraala 290
                                   e +a  +d+ + av++++++ i+ a+++g++ giCG++++d p+ +e+lv+ G++++S++++sv+++  ++ 
  gi|91772813|ref|YP_565505.1| 723 EILASSFDERDEAVKKMVSMAIQGAKRNGKHSGICGQAPSDfPEFAEFLVREGIESISLNPDSVMKISLKVL 794
                                   ****************************************769**********************9987765 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 !   85.9   0.4   3.2e-28   1.1e-24       2      73 .]     391     462 ..     390     462 .. 0.97
   2 ?   -0.1   0.0      0.22     8e+02      38      57 ..     570     589 ..     567     599 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 3.2e-28
                                   --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                 PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                   +++g+ILva+ t+p++ + +++aa+i+t++GG+t+HaAiv+relg+PaVvg+++at++l++g  +tv +++G
  gi|91772813|ref|YP_565505.1| 391 FKHGEILVADTTTPDWEPIMKRAAAIITNKGGRTCHAAIVSRELGVPAVVGAQDATEKLNNGMDVTVSCAEG 462
                                   6789****************************************************************9998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                                   HHHHHHHTT--EEE--SSHH CS
                 PEP-utilizers  38 aAivArelgiPaVvgvgeat 57 
                                   a ivA  + +P+Vv +++ +
  gi|91772813|ref|YP_565505.1| 570 ATIVASFYPKPVVVRMSDFK 589
                                   679***********999875 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.51   1.8e+03      13      22 ..     495     504 ..     492     504 .. 0.87
   2 ?   10.0   0.2   0.00023      0.84      14      31 .]     655     672 ..     654     672 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.51
                           PPR  13 nGkleeAlel 22 
                                    G++eeA++l
  gi|91772813|ref|YP_565505.1| 495 LGNPEEAFSL 504
                                   79*****997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00023
                           PPR  14 GkleeAlelfkeMkekGi 31 
                                   +++eeA++++ eMk++G+
  gi|91772813|ref|YP_565505.1| 655 RRVEEAEKVIAEMKKNGL 672
                                   689*************96 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         1   3.6e+03      13      25 ..     492     504 ..     490     506 .. 0.84
   2 ?   10.8   0.0   0.00012      0.43      17      35 ..     655     673 ..     643     675 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                         PPR_2  13 lckkgkveeAfkl 25 
                                   +++ g++eeAf+l
  gi|91772813|ref|YP_565505.1| 492 MMNLGNPEEAFSL 504
                                   68899******98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                         PPR_2  17 gkveeAfklfneMkkrgle 35 
                                   ++veeA k+  eMkk+gle
  gi|91772813|ref|YP_565505.1| 655 RRVEEAEKVIAEMKKNGLE 673
                                   78***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 4828.21
//
Query:       gi|91772814|ref|YP_565506.1|  [L=373]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   83.9   0.7    1.3e-23   82.7   0.7    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.1e-12   46.8   0.1    5.8e-12   45.9   0.1    1.4  1  OrfB_IS605      Probable transposase
    0.00025   21.3   1.8    0.00051   20.3   1.8    1.5  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.011   15.6   1.2      0.023   14.6   1.2    1.5  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.031   14.3   0.1      0.056   13.5   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.041   13.9   1.1      0.081   13.0   1.1    1.4  1  DZR             Double zinc ribbon
       0.14   11.8   3.5       0.37   10.5   3.5    1.7  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.15   11.6   0.1       0.26   10.8   0.1    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.21   11.3   3.5        0.8    9.4   3.7    1.9  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.42   10.6   2.4        3.6    7.6   0.3    2.7  2  zinc_ribbon_4   zinc-ribbon domain
       0.48   10.2   7.0        1.3    8.8   1.0    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.51   10.1   7.7        2.3    8.0   0.3    3.0  3  zf-C2H2_11      zinc-finger C2H2-type
        1.5    8.8   4.3        8.1    6.4   0.2    2.4  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        2.8    8.7   6.7        2.5    8.8   0.1    3.1  4  zinc-ribbon_6   zinc-ribbon domain
        3.6    7.4   5.8         88    3.0   5.9    2.5  2  zinc_ribbon_2   zinc-ribbon domain
        7.7    6.7   5.9         18    5.6   0.6    2.4  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.7   1.1e-26   1.3e-23       1      68 [.     280     347 ..     280     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 1.1e-26
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                   f++l+++++yka+  G++v+ v+p+++S++Cs+Cg++ k +++g  ++C++Cgf++++D+nAa+Ni++
  gi|91772814|ref|YP_565506.1| 280 FYQLEQFIRYKAEALGKQVVSVDPRFSSQKCSKCGHTYKGNRDGSSYRCRSCGFQIHADLNAARNIAQ 347
                                   899***************************************************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.1   5.2e-15   5.8e-12       3     102 ..     158     248 ..     156     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 5.2e-15
                    OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrk 83 
                                    v++++e+pkp gn+++giD Gi n a+++++    f++++ ++k++  ++a  ++elqsk  ks     a+r l++++rk
  gi|91772814|ref|YP_565506.1| 158 HVTLRTESPKPSGNTVLGIDRGIVNVAVCSNNV---FFNDS-KVKNARAKYAYLRKELQSKGTKS-----AKRLLKKMSRK 229
                                   5788999**************************...77777.9******************6666.....8********** PP

                    OrfB_IS605  84 rsrrrkhllhklathlikt 102
                                    +r+++++ h +a+++++ 
  gi|91772814|ref|YP_565506.1| 230 ERRFVTDVNHCIAKDIVNM 248
                                   ****************985 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.8   4.5e-07   0.00051      14      44 ..     303     337 ..     296     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.5e-07
                          C1_2  14 dssesfnCsaCgrkidgff....YsCseCdfslhv 44 
                                   ++ +s +Cs Cg++ +g++    Y+C  C f++h 
  gi|91772814|ref|YP_565506.1| 303 PRFSSQKCSKCGHTYKGNRdgssYRCRSCGFQIHA 337
                                   566789********666666678***********7 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.2   2.1e-05     0.023      10      40 ..     306     337 ..     302     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                   S--B-TTT-SB--S.SSS-EEEETTT--EE-C CS
                          C1_1  10 qptfCkhCgeflwg.kekqglkCswCkllvHk 40 
                                   ++++C++Cg   +g      ++C+ C++ +H 
  gi|91772814|ref|YP_565506.1| 306 SSQKCSKCGHTYKGnRDGSSYRCRSCGFQIHA 337
                                   6799***************************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 ?   13.5   0.1     5e-05     0.056      56      94 ..     293     333 ..     236     346 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                   TTTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSS CS
                          HypA  56 vlegaeLeieevpvkvrCreCgkefeleek..alrCpkCgs 94 
                                   +l + +++++    + +C++Cg++++ +++  ++rC +Cg 
  gi|91772814|ref|YP_565506.1| 293 ALGKQVVSVDPRFSSQKCSKCGHTYKGNRDgsSYRCRSCGF 333
                                   45556666777778899*********77645699*****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.1   7.3e-05     0.081      12      43 ..     307     340 ..     302     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                           DZR  12 arfCseCgtklkavaa..edrCpsCgekvdpear 43 
                                   ++ Cs+Cg++ k   +  ++rC sCg +++++ +
  gi|91772814|ref|YP_565506.1| 307 SQKCSKCGHTYKGNRDgsSYRCRSCGFQIHADLN 340
                                   678*******99777699********99888765 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.5   0.00033      0.37       2      27 ..     309     335 ..     308     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                   B-SSS--B--.--SSS----SSS---- CS
                DNA_RNApol_7kD   2 iCgeCgaevs.lkkgdpiRCkeCGhRi 27 
                                   +C +Cg+  +  + g + RC+ CG+ i
  gi|91772814|ref|YP_565506.1| 309 KCSKCGHTYKgNRDGSSYRCRSCGFQI 335
                                   6*********9999***********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 ?   10.8   0.1   0.00023      0.26       2      29 ..     309     335 ..     308     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                   EETTTTCEECHEETSTTCEEESSSSBEE CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVl 29 
                                   kC +Cg+t+   + +   ++C +CG  +
  gi|91772814|ref|YP_565506.1| 309 KCSKCGHTY-KGNRDGSSYRCRSCGFQI 335
                                   9******98.8999999********665 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         3   3.4e+03      16      24 ..     118     126 ..     114     130 .. 0.81
   2 ?    9.4   3.7   0.00071       0.8       6      28 ..     310     332 ..     306     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3
                 zf-NADH-PPase  16 aeggwarvC 24 
                                   + +g+ +vC
  gi|91772814|ref|YP_565506.1| 118 SVNGRVKVC 126
                                   5689***** PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00071
                 zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCg 28 
                                   C++CG+  + +++g + +C +Cg
  gi|91772814|ref|YP_565506.1| 310 CSKCGHTYKGNRDGSSYRCRSCG 332
                                   **********************8 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0032       3.6      27      35 ..     309     317 ..     301     318 .. 0.84
   2 ?    2.1   0.1      0.17   1.9e+02      23      33 ..     323     333 ..     320     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0032
                 zinc_ribbon_4  27 rCskCghvF 35 
                                   +CskCgh+ 
  gi|91772814|ref|YP_565506.1| 309 KCSKCGHTY 317
                                   9******85 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.17
                 zinc_ribbon_4  23 gvkvrCskCgh 33 
                                   g++ rC  Cg 
  gi|91772814|ref|YP_565506.1| 323 GSSYRCRSCGF 333
                                   67779999985 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6     0.027        30       3      10 ..     310     317 ..     309     319 .. 0.87
   2 ?    8.8   1.0    0.0012       1.3       1      10 [.     326     335 ..     326     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.027
                  Rubredoxin_2   3 CsqCGfes 10 
                                   Cs+CG+++
  gi|91772814|ref|YP_565506.1| 310 CSKCGHTY 317
                                   ******97 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                  Rubredoxin_2   1 YvCsqCGfes 10 
                                   Y+C++CGf+ 
  gi|91772814|ref|YP_565506.1| 326 YRCRSCGFQI 335
                                   9*******96 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 ?   -1.3   0.0       1.7   1.9e+03      11      16 ..     124     129 ..     124     130 .. 0.85
   2 ?    4.4   1.3     0.028        31       3      14 ..     306     317 ..     305     318 .. 0.89
   3 ?    8.0   0.3    0.0021       2.3       1      11 [.     322     332 ..     322     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.7
                    zf-C2H2_11  11 GlcftS 16 
                                   ++cft+
  gi|91772814|ref|YP_565506.1| 124 KVCFTI 129
                                   79***7 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.028
                    zf-C2H2_11   3 stcqCleCGlcf 14 
                                   s+++C +CG  +
  gi|91772814|ref|YP_565506.1| 306 SSQKCSKCGHTY 317
                                   89*******876 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0021
                    zf-C2H2_11   1 destcqCleCG 11 
                                   d s+++C+ CG
  gi|91772814|ref|YP_565506.1| 322 DGSSYRCRSCG 332
                                   78********9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0072       8.1      12      21 ..     308     317 ..     302     317 .. 0.82
   2 ?    3.4   0.6     0.063        70      13      21 ..     327     335 ..     326     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0072
                       DUF35_N  12 qrCpdCGtvq 21 
                                   q+C++CG+ +
  gi|91772814|ref|YP_565506.1| 308 QKCSKCGHTY 317
                                   9******975 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.063
                       DUF35_N  13 rCpdCGtvq 21 
                                   rC++CG  +
  gi|91772814|ref|YP_565506.1| 327 RCRSCGFQI 335
                                   9*****866 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0022       2.5       6      56 ..     185     234 ..     181     250 .. 0.80
   2 ?    1.1   0.3      0.57   6.4e+02      13      24 ..     305     316 ..     302     321 .. 0.87
   3 ?   -1.5   2.4       3.6   4.1e+03       4      24 ..     310     334 ..     307     346 .. 0.53
   4 ?   -0.7   0.1       2.2   2.4e+03       2      12 ..     326     336 ..     325     370 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0022
                 zinc-ribbon_6   6 qCgqllffenssClkCgaalgfapeelellaleeaeeeewrslaekeskyk 56 
                                    C++++ff++s+ ++  a+ ++  +el+ +  ++a++   +++++ke+++ 
  gi|91772814|ref|YP_565506.1| 185 VCSNNVFFNDSKVKNARAKYAYLRKELQSKGTKSAKR-LLKKMSRKERRFV 234
                                   7*************************99999888887.6677777766554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.57
                 zinc-ribbon_6  13 fenssClkCgaa 24 
                                   f +++C kCg++
  gi|91772814|ref|YP_565506.1| 305 FSSQKCSKCGHT 316
                                   89999****986 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.6
                 zinc-ribbon_6   4 CeqCgqllffe....nssClkCgaa 24 
                                   C++Cg++   +    + +C +Cg +
  gi|91772814|ref|YP_565506.1| 310 CSKCGHTYKGNrdgsSYRCRSCGFQ 334
                                   5555555432211113455555544 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.2
                 zinc-ribbon_6   2 feCeqCgqllf 12 
                                   ++C++Cg +++
  gi|91772814|ref|YP_565506.1| 326 YRCRSCGFQIH 336
                                   67777776665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   5.9     0.078        88       1      21 [.     309     333 ..     309     335 .. 0.65
   2 ?    2.6   0.2       0.1   1.2e+02       1       9 [.     327     335 ..     327     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.078
                 zinc_ribbon_2   1 fCpnCGae...lqdnakF.CpyCGt 21 
                                   +C++CG++   + d++ + C  CG+
  gi|91772814|ref|YP_565506.1| 309 KCSKCGHTykgNRDGSSYrCRSCGF 333
                                   7999998822244555558888886 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                 zinc_ribbon_2   1 fCpnCGael 9  
                                   +C +CG ++
  gi|91772814|ref|YP_565506.1| 327 RCRSCGFQI 335
                                   699999887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   6.0      0.33   3.7e+02       7      33 ..     309     332 ..     308     332 .. 0.72
   2 ?    5.6   0.6     0.016        18       6      14 ..     326     334 ..     325     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.33
                   Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCg 33 
                                   +C +Cgh++   +   d +   C +Cg
  gi|91772814|ref|YP_565506.1| 309 KCSKCGHTYKGNR---DGSSYRCRSCG 332
                                   6999999998555...44456688887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
                   Zn-ribbon_8   6 YrCeeCghe 14 
                                   YrC++Cg +
  gi|91772814|ref|YP_565506.1| 326 YRCRSCGFQ 334
                                   *******65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2261.31
//
Query:       gi|91772815|ref|YP_565507.1|  [L=813]
Description: hypothetical protein Mbur_0801 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-13   49.6   0.7    1.4e-07   32.0   0.0    2.6  2  VWA           von Willebrand factor type A domain
    1.6e-09   37.6   0.0    0.00049   19.6   0.0    2.4  2  GATase1_like  Putative glutamine amidotransferase
    3.2e-07   31.0   0.0    3.1e-06   27.8   0.0    2.5  2  VWA_2         von Willebrand factor type A domain
    0.00016   21.1   0.0     0.0015   17.9   0.0    2.4  3  VWA_CoxE      VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
       0.17   12.4   0.3        1.9    9.0   0.0    2.9  3  DUF4350       Domain of unknown function (DUF4350)
        9.9    6.6  10.5        3.5    8.1   0.5    2.7  3  BatA          Aerotolerance regulator N-terminal


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 !   15.3   0.1     6e-06     0.018     105     141 ..     121     161 ..     100     188 .. 0.80
   2 !   32.0   0.0   4.6e-11   1.4e-07       2     150 ..     366     513 ..     365     532 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                                   EEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEE...SS CS
                           VWA 105 kviilltdGksndg.dpkeaaneakeqgikvfavGv...gn 141
                                   + i+l++dG++n g d++e ++ ake g +v++v+    +n
  gi|91772815|ref|YP_565507.1| 121 NQIVLVSDGNNNFGkDIDESLQYAKEMGTTVYSVAPdleKN 161
                                   559**********77*******************9855332 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 4.6e-11
                                   EEEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS....EEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                           VWA   2 ivfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse....vktefslndysskeellsalnnlkysggg 77 
                                   iv++lD+S+s    e++  ++ ++ +l+++ e   ++++ g++ f+se        + l ++s+ e+l +++++l    ++
  gi|91772815|ref|YP_565507.1| 366 IVLILDVSQSTaAHETLSDILGYATNLLRSDE--LKDASAGVIAFGSEgedvSGGLVYLGTHSNLEKLEESISSLAPGATS 444
                                   9**********6667777**************..788899******99888556669******************888888 PP

                                   SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS..HTHHHHHHHHGCTEEEEEEEESSSHHHHHHHH CS
                           VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksndg..dpkeaaneakeqgikvfavGvgnadekelLnk 150
                                   +t+++++l  a e  ++ ++g     +  ii+++dG   ++  + +++++e+ ++gi+++ + v++    +++ +
  gi|91772815|ref|YP_565507.1| 445 ETSLDQGLLIAQE-WLETESG-----ELDIIIISDGGFAQSydESLKVVEEIHDEGIDFYFIHVHEQGAPSQYDQ 513
                                   888******9977.7777777.....789999***87744335*******************9966555444555 PP

>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.6e-07   0.00049      91     147 ..     309     361 ..     291     427 .. 0.79
   2 !   15.4   0.0   3.2e-06    0.0096     160     221 ..     568     627 ..     557     653 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.6e-07
                  GATase1_like  91 ksvPnrlkllkdyvaeGggllmvGGylsfqGidgkarykktpvedvlPvtcldvddr 147
                                   ++  n ++ lk+yv++G gl++vGG  sf     + +y ++++e+ lPv   ++d +
  gi|91772815|ref|YP_565507.1| 309 EISENNINKLKEYVSQGNGLVLVGGEASFD----RGNYLDSSLEELLPVASRPTDWK 361
                                   456789999********************6....789************99998865 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.2e-06
                  GATase1_like 160 asehpvlkglssewPkllGyneveakdnaevlatvsedshPllvvGeygkGrtaaftsdisp 221
                                   +++h +++ +  e  ++ Gyn+v++k++a+ +  ++++++P++ + +yg Gr+aa t+d + 
  gi|91772815|ref|YP_565507.1| 568 NPNHFITRNIEIE-GNITGYNDVTPKPGADRII-ITATGKPVVTTWRYGLGRVAAITTDNGR 627
                                   5788888888866.5799***********9885.677789******************9874 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 ?   -0.6   0.0      0.67     2e+03      53     106 ..     100     129 ..      85     148 .. 0.58
   2 !   27.8   0.0     1e-09   3.1e-06       1     106 [.     366     474 ..     366     475 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.67
                         VWA_2  53 ipltkdkakilnalrnleakgggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                   i lt   +++ +a+++  +                          ++ivl++Dg
  gi|91772815|ref|YP_565507.1| 100 IRLTGESTSLGDAIEQYSTG------------------------DNQIVLVSDG 129
                                   55555555555555444433........................3444444444 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1e-09
                         VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk..slpgdrvglvtfsdgpevlipl......tkdkakilnalrnleak. 72 
                                   +v++lD+S+S ++ +     l+ +   +++ll   +l++   g+++f+++ e +++       +++ +k+++ + +l +  
  gi|91772815|ref|YP_565507.1| 366 IVLILDVSQSTAAHE----TLSDILGYATNLLRsdELKDASAGVIAFGSEGEDVSGGlvylgtHSNLEKLEESISSLAPGa 442
                                   79*********9984....788888888888884455777*********7655554325555359***************9 PP

                         VWA_2  73 gggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                   + +t+l+++L  a+++l+ ++   +  i++i+Dg
  gi|91772815|ref|YP_565507.1| 443 TSETSLDQGLLIAQEWLETES--GELDIIIISDG 474
                                   ******************986..9999******8 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 ?   -1.2   0.0      0.35   1.1e+03      54      73 ..      61      79 ..      49      98 .. 0.82
   2 ?   -1.5   0.0      0.44   1.3e+03     151     189 ..     120     157 ..     105     168 .. 0.68
   3 !   17.9   0.0   5.2e-07    0.0015      58     191 ..     364     505 ..     347     526 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.35
                      VWA_CoxE 54 erkprelvllvDvSgSmaay 73
                                  +++p +lv+++D  +Sm+ +
  gi|91772815|ref|YP_565507.1| 61 DENP-NLVVISDETASMSLF 79
                                  4567.9***********986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.44
                      VWA_CoxE 151 ravvvlvsDglergdreellaelarlvrrarrlvwlnpl 189
                                   +  +vlvsDg + +  + +++ l+  ++ +  +  ++p 
  gi|91772815|ref|YP_565507.1| 120 DNQIVLVSDG-NNNFGKDIDESLQYAKEMGTTVYSVAPD 157
                                   567999***9.5666666666666666666666666665 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 5.2e-07
                      VWA_CoxE  58 relvllvDvSgSmaaysai..flallhAllqqlp....rtevfaFdtrlvdlTralrerDpaeaLarv....saavedlgG 128
                                   r +vl++DvS S aa+ ++  +l ++  ll++ +    ++ v+aF+++  d++  l      + L+++    s+ + +  +
  gi|91772815|ref|YP_565507.1| 364 RSIVLILDVSQSTAAHETLsdILGYATNLLRSDElkdaSAGVIAFGSEGEDVSGGLVYLGTHSNLEKLeesiSSLAPGATS 444
                                   479************87761244445555555548899999*************997777777777774334666667778 PP

                      VWA_CoxE 129 gTrigaalaeflelvtrpaLsrravvvlvsDglergdreellaelarlvrrarrlvwlnplsd 191
                                    T + ++l  ++e+ + ++   +  ++++sDg   ++ +e+l+ +++++  ++ +  +   ++
  gi|91772815|ref|YP_565507.1| 445 ETSLDQGLLIAQEWLETES--GELDIIIISDGGFAQSYDESLKVVEEIHDEGIDFYFIHVHEQ 505
                                   8999999999999999777..8889*************************9998887766644 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.79   2.4e+03      30      60 ..     112     145 ..      86     153 .. 0.51
   2 ?    9.0   0.0   0.00062       1.9      31      68 ..     294     331 ..     275     332 .. 0.68
   3 ?   -3.6   0.0       5.4   1.6e+04       9      26 ..     760     778 ..     759     782 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.79
                       DUF4350  30 aleg...edgtllvvapdlrlte...eelaallewva 60 
                                   a e+   +d+ +++v+++   ++   +++++ l++++
  gi|91772815|ref|YP_565507.1| 112 AIEQystGDNQIVLVSDG---NNnfgKDIDESLQYAK 145
                                   333344434444444444...2224456666665555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00062
                       DUF4350  31 legedgtllvvapdlr.lteeelaallewvarGntlvla 68 
                                   l+ ++ t+++ + ++r ++e+ +++l e+v++Gn lvl+
  gi|91772815|ref|YP_565507.1| 294 LDNKK-TVVLDNVNMReISENNINKLKEYVSQGNGLVLV 331
                                   33333.5555555555478899***************98 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.4
                       DUF4350   9 alaelLeaq.Gvevrrvrk 26 
                                   ala lL+++ G +++ v++
  gi|91772815|ref|YP_565507.1| 760 ALALLLKDArGNSLKSVER 778
                                   8999999965888776665 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5    0.0012       3.5       2      33 ..       3      32 ..       1      36 [. 0.79
   2 ?    5.3   1.7    0.0084        25      57      77 .]      31      51 ..      29      51 .. 0.89
   3 ?   -2.9   0.1       3.2   9.5e+03       9      17 ..     786     794 ..     773     804 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                          BatA  2 lpFlnPllLlallllplpiillyllkrrpqev 33
                                  ++F +Pl  +++l+lp++i  l++l++  +++
  gi|91772815|ref|YP_565507.1|  3 FTFEQPL--MFALILPVIIGGLFFLREGARRP 32
                                  5688888..779*****999999999988876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0084
                          BatA 57 nllllLrllalallvlalArP 77
                                  + +++ r+++l llv+alA P
  gi|91772815|ref|YP_565507.1| 31 RPIIISRMIVLSLLVIALASP 51
                                  567889*************98 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.2
                          BatA   9 lLlallllp 17 
                                   +L+a+lll 
  gi|91772815|ref|YP_565507.1| 786 FLIAALLLF 794
                                   232333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.76u 0.35s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 4678.58
//
Query:       gi|91772816|ref|YP_565508.1|  [L=623]
Description: hypothetical protein Mbur_0802 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   55.5   9.6    5.3e-15   55.5   9.6    1.6  2  BatA             Aerotolerance regulator N-terminal
    6.8e-06   26.7   1.1    3.9e-05   24.3   0.4    2.7  2  VWA_2            von Willebrand factor type A domain
    6.2e-05   23.3   2.5     0.0053   17.0   0.5    3.1  2  VWA              von Willebrand factor type A domain
    9.8e-05   21.9   0.0    0.00031   20.3   0.0    1.7  1  ABC_transp_aux   ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.014   15.8   0.1        1.3    9.6   0.0    3.4  3  DUF4350          Domain of unknown function (DUF4350)
      0.019   14.5   0.1      0.043   13.3   0.1    1.5  1  Glyco_hydro_42M  Beta-galactosidase trimerisation domain


Domain annotation for each model (and alignments):
>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   9.6   1.8e-18   5.3e-15       1      77 []       1      78 [.       1      78 [. 0.98
   2 ?   -5.0   1.2         6   1.8e+04      13      18 ..     607     612 ..     601     618 .. 0.42

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.8e-18
                          BatA  1 MlpFlnPllLlallllplpiillyllkrrpqevvfsslrlleevekdeea...lqrlkknllllLrllalallvlalArP 77
                                  M pF+n l L+al+ +++ +i+lyll+++p e +++sl++l+ +ek++++   l+rl k+ ++l +ll+l+l+ +a+A+P
  gi|91772816|ref|YP_565508.1|  1 M-PFANILGLAALASIIP-LIILYLLRPKPLELKIPSLMFLMLAEKKKKRfasLRRLIKDPIFLAQLLILILISVAIAGP 78
                                  9.9*************99.9*****************************9999**************************9 PP

  == domain 2  score: -5.0 bits;  conditional E-value: 6
                          BatA  13 llllpl 18 
                                   +ll++l
  gi|91772816|ref|YP_565508.1| 607 MLLVVL 612
                                   222222 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 !   24.3   0.4   1.3e-08   3.9e-05       1     106 [.      91     183 ..      91     185 .. 0.83
   2 ?   -2.2   0.0       2.1   6.3e+03      26      56 ..     432     463 ..     403     471 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.3e-08
                         VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaaa 81 
                                   ++fv+D S+Sm+++     r++ a d++++++++    + +++  ++ p v +  + + ++ +n l++l++kg   +l +a
  gi|91772816|ref|YP_565508.1|  91 TIFVIDASASMNTDG----RFDSATDIAKTYISK----KNSIILAENIP-VNVLESGGSSATKNSLDSLTPKGSVADLSSA 162
                                   69*********9997....**************9....44666666644.444445556788999*******999****** PP

                         VWA_2  82 LqlarkalkkrrkgekrvivlitDg 106
                                   +  a+ +l+++      +iv+++D 
  gi|91772816|ref|YP_565508.1| 163 ITNAMRTLSNE----GGRIVVVSDF 183
                                   *********66....6999*99995 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                         VWA_2  26 daveallksl.pgdrvglvtfsdgpevliplt 56 
                                    av ++l+s  + d v+lv   +++  l+ ++
  gi|91772816|ref|YP_565508.1| 432 IAVYTYLNSTiRSDAVSLVDTPSNVPMLAYWN 463
                                   35556666444788999999888888877776 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 !   17.0   0.5   1.8e-06    0.0053       3     144 ..      92     215 ..      91     248 .. 0.69
   2 ?    1.4   0.1      0.11   3.3e+02      58     133 ..     256     342 ..     224     375 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                                   EEEEE-STTS.CHHHHHHHHHHHHHHHHHHT..BTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC- CS
                           VWA   3 vfvlDgSgsm.geenfekvkefikklvekle..vgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttn 80 
                                   +fv+D+S sm ++++f+++ +++k+ ++k +  +  e++ v+++  +++             ++ +++l++l+ +g+  + 
  gi|91772816|ref|YP_565508.1|  92 IFVIDASASMnTDGRFDSATDIAKTYISKKNsiILAENIPVNVLESGGS-------------SATKNSLDSLTPKGSVAD- 158
                                   69********999****************99333555555555555554.............555566666644444444. PP

                                   HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSHH CS
                           VWA  81 tgkalkyaleklfkssagaRenakkviilltdGksndg.dpkeaaneakeqgikvfavGvgnade 144
                                   + +a+ +a+++l ++  +        i++++d ++ +g dp  a + a ++g+kv  v vg+ ++
  gi|91772816|ref|YP_565508.1| 159 LSSAITNAMRTLSNEGGR--------IVVVSDFTNWQGeDPVSAMRLAESYGLKVTFVRVGSPTD 215
                                   777777777744444333........677777666554477777777777777777777766655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                                   HCHHHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGT....SST....TSEEEEEEEES.S--CSS...HTHHHHHH CS
                           VWA  58 ysskeellsalnnlkysgggttntgkalkyaleklfkssag....aRe....nakkviilltd.Gksndg...dpkeaane 126
                                    ++k++++ ++  ++++  + t++g+++ +++    ++ a     +      n+++ ++l+td  +s ++   +++++++ 
  gi|91772816|ref|YP_565508.1| 256 SQNKKKFQLDIGPFSTKQFKLTDLGTGITEVTIDREDKLAVdnvaY-IsipaNVQNELLLVTDvKRSPSStalSLLPNIKA 335
                                   4577777888888888888888888888888775555555544431.1345699999999999633334347899999999 PP

                                   HHGCTEE CS
                           VWA 127 akeqgik 133
                                   ++++++ 
  gi|91772816|ref|YP_565508.1| 336 IQSNNVP 342
                                   9988875 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     1e-07   0.00031     107     231 ..     131     385 ..      91     402 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-07
                ABC_transp_aux 107 mglvieygdkeetipllkn....tsesnlEyeltsairkltdkk..................................... 146
                                   +  v+e+g+++ t + l++     s+  l  ++t+a+r+l+++                                      
  gi|91772816|ref|YP_565508.1| 131 PVNVLESGGSSATKNSLDSltpkGSVADLSSAITNAMRTLSNEGgrivvvsdftnwqgedpvsamrlaesyglkvtfvrvg 211
                                   556666666655555555566677778888888888888888888888888888888888888888888888888888888 PP

                ABC_transp_aux 147 ................................................................................. 146
                                                                                                                    
  gi|91772816|ref|YP_565508.1| 212 sptdnvgiiqgwidadeegytyncvlknymettqnvemiidtpgsqnkkkfqldigpfstkqfkltdlgtgitevtidred 292
                                   886666666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                ABC_transp_aux 147 ...kpkvgflt....ghgelslssp...........seadfleeleenYnveevdldsedilpedidvlviakptkdlsee 209
                                       ++v++++             +           s+    + l+   n+++++ +++    +d++v+v+  ++++++ e
  gi|91772816|ref|YP_565508.1| 293 klaVDNVAYISipanV--------QnelllvtdvkrSP--SSTALSLLPNIKAIQSNNVPADLSDYKVIVVDTQQRAITSE 363
                                   6665555555422211........01222223332322..335555555999999999888779***************** PP

                ABC_transp_aux 210 elykldqflmnGgkllvfldpv 231
                                   e  +l+ f+++Gg++lv ++p 
  gi|91772816|ref|YP_565508.1| 364 EAARLSTFIKSGGNVLVIASPT 385
                                   *****************99986 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.34     1e+03      27      49 ..      78     103 ..      63     116 .. 0.70
   2 ?    0.8   0.0      0.22   6.6e+02      47      69 .]     159     181 ..     151     181 .. 0.82
   3 ?    9.6   0.0   0.00042       1.3      37      68 ..     350     381 ..     315     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.34
                       DUF4350  27 pfdaleg...edgtllvvapdlrlte 49 
                                   pf+  e+   +++t++v++   + ++
  gi|91772816|ref|YP_565508.1|  78 PFYSTEEelsGEHTIFVIDASASMNT 103
                                   55533333447889999998877665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                       DUF4350  47 lteeelaallewvarGntlvlaa 69 
                                   l+++ ++a++ +   G+++v+++
  gi|91772816|ref|YP_565508.1| 159 LSSAITNAMRTLSNEGGRIVVVS 181
                                   55566789999999*******95 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00042
                       DUF4350  37 tllvvapdlrlteeelaallewvarGntlvla 68 
                                   +++v +++  +t+ee+a+l  + ++G++++++
  gi|91772816|ref|YP_565508.1| 350 VIVVDTQQRAITSEEAARLSTFIKSGGNVLVI 381
                                   5677778888**************99888776 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 ?   13.3   0.1   1.4e-05     0.043      52     186 ..     342     474 ..     337     487 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
               Glyco_hydro_42M  52 eadlsgYklvvaPtly.lvseelvkkleafvenGGtlvltylsGvvdendrihlggvpgpLrellGikveeldtlpeeeev 131
                                    adls Yk++v+ t +  +++e + +l+ f+++GG++++ ++s   d ++   +     p + ++  ++++  +l  e+e+
  gi|91772816|ref|YP_565508.1| 342 PADLSDYKVIVVDTQQrAITSEEAARLSTFIKSGGNVLV-IASPTLDPKNANIDLMQLLPVKIITTSESSKGVALKVEQET 421
                                   589******999876537899999************877.56777777776666666678888888888888889888888 PP

               Glyco_hydro_42M 132 evsaegktyearlwseilepetaevlatyatdfyagtpAvtrnnygkGkaiYvgs 186
                                   +++ +  + e   + ++l+++  +   +   d+ ++ p +   n+g+G+++Y+g 
  gi|91772816|ref|YP_565508.1| 422 RLTKK-VKFEDIAVYTYLNSTIRSDAVSLV-DTPSNVPMLAYWNVGDGTVMYLGL 474
                                   88832.222333333444444333322222.356788999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 3786.29
//
Query:       gi|91772817|ref|YP_565509.1|  [L=293]
Description: hypothetical protein Mbur_0803 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-19   70.6   0.0      2e-19   69.6   0.0    1.5  1  DUF58     Protein of unknown function DUF58
    3.2e-06   27.7   0.2    7.8e-06   26.5   0.1    1.7  2  VWA_2     von Willebrand factor type A domain
    4.7e-05   23.7   0.3    7.3e-05   23.1   0.3    1.4  1  VWA       von Willebrand factor type A domain
     0.0011   18.3   0.2     0.0025   17.2   0.2    1.6  1  VWA_CoxE  VWA domain containing CoxE-like protein


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 !   69.6   0.0   4.5e-23     2e-19       1      85 [.      43     127 ..      43     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 4.5e-23
                         DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqlldeg 81 
                                   gld  g  eY+pgD+l++IdW+++AR  +lyvrefe+ ++ t+ ++ld s++m+   ++ +k+e+ + +aa  a+ + + +
  gi|91772817|ref|YP_565509.1|  43 GLDTMGYTEYHPGDDLKSIDWNVYARSEKLYVREFEEDKSVTTHILLDSSNSMDYTLNTITKFEYGAMLAAGFAYLVTKDN 123
                                   57888999***********************************************************************99 PP

                         DUF58  82 drvg 85 
                                   d++g
  gi|91772817|ref|YP_565509.1| 124 DKFG 127
                                   9987 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 !   26.5   0.1   1.7e-09   7.8e-06       3     106 ..      87     188 ..      85     190 .. 0.82
   2 ?   -2.2   0.0       1.5   6.8e+03      14      14 ..     246     246 ..     209     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.7e-09
                         VWA_2   3 fvlDtSgSmrngdygptrleaakdaveallk..slpgdrvglvtfsdgpevlipltkdkakilnalrnleak..gggtnla 79 
                                   ++lD+S+Sm  +  + t++e+ + ++  +    + ++d++g+ t+s++  +  + +++++++l+ +++l +   +g+t l 
  gi|91772817|ref|YP_565509.1|  87 ILLDSSNSMDYTLNTITKFEYGAMLAAGFAYlvTKDNDKFGISTYSEDIAISQT-HRGRRHLLRDIDRLAEVelKGQTALS 166
                                   89*******99855677777666666555552155799**********997655.56699**********9899******* PP

                         VWA_2  80 aaLqlarkalkkrrkgekrvivlitDg 106
                                     +ql +k++k+r+      +++i+D 
  gi|91772817|ref|YP_565509.1| 167 HCVQLYEKMIKSRS-----LVIIISDF 188
                                   ***********885.....99999995 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                         VWA_2  14 g 14 
                                   +
  gi|91772817|ref|YP_565509.1| 246 K 246
                                   1 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 !   23.1   0.3   1.6e-08   7.3e-05       4     137 ..      87     210 ..      86     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-08
                                   EEEE-STTSCHHHHHHHHHHHHHHHHHHT....BTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTG.SGGGGSSC CS
                           VWA   4 fvlDgSgsmgeenfekvkefikklvekle....vgpegtrvglvqfssevktefslndysskeellsalnnl.kysgggtt 79 
                                   ++lD+S+sm + +++++ +f    +        v ++++++g+ ++s+++ +    ++++ + +ll+++++l +++ +g+t
  gi|91772817|ref|YP_565509.1|  87 ILLDSSNSM-DYTLNTITKFEYGAMLAAGfaylVTKDNDKFGISTYSEDIAIS---QTHRGRRHLLRDIDRLaEVELKGQT 163
                                   79*******.999999999987766666644555***************9998...6778889********9777777777 PP

                                   -HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.SHTHHHHHHHHGCTEEEEEE CS
                           VWA  80 ntgkalkyaleklfkssagaRenakkviilltdGksnd.gdpkeaaneakeqgikvfav 137
                                       al++ ++ l++++ +     ++++i+++d   +d ++++ a+ ++ +   +++ +
  gi|91772817|ref|YP_565509.1| 164 ----ALSHCVQ-LYEKMIK----SRSLVIIISD-FMEDlKSIESAIYRLSN--HDLILI 210
                                   ....*******.7777777....2456666665.55564677777777764..344444 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 !   17.2   0.2   5.7e-07    0.0025      61     172 ..      86     198 ..      59     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.7e-07
                      VWA_CoxE  61 vllvDvSgSmaaysaiflallhAllqqlp.......rtevfaFdtrlvdlTralrerDpaeaLarvsaaved.lgGgTrig 133
                                    +l+D S+Sm+   + + ++ ++++  +        +   f  +t   d+     +r +  +L+++ + +e  l+G T   
  gi|91772817|ref|YP_565509.1|  86 HILLDSSNSMDYTLNTITKFEYGAMLAAGfaylvtkDNDKFGISTYSEDIAISQTHRGRRHLLRDIDRLAEVeLKGQT--- 163
                                   468899999988777777776665544433355566777788888888999888999999******888887799988... PP

                      VWA_CoxE 134 aalaeflelvtrpaLsrravvvlvsDglergdreellae 172
                                    al ++ +l + + +++r++v+++sD++e  d + ++++
  gi|91772817|ref|YP_565509.1| 164 -ALSHCVQLYE-KMIKSRSLVIIISDFME--DLKSIESA 198
                                   .5666666666.4556799********66..44445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1713.79
//
Query:       gi|91772818|ref|YP_565510.1|  [L=324]
Description: ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-61  204.8   0.1    5.7e-61  204.1   0.1    1.3  1  AAA_3            ATPase family associated with various cellul
    2.8e-18   65.5   0.1    5.6e-18   64.6   0.1    1.5  1  AAA_lid_2        AAA lid domain
    3.6e-12   46.5   0.0    7.7e-12   45.4   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    2.2e-05   24.9   0.0    6.8e-05   23.3   0.0    1.9  2  AAA              ATPase family associated with various cellul
    0.00021   20.5   0.0    0.00049   19.3   0.0    1.7  1  MCM              MCM P-loop domain
    0.00083   19.1   0.0      0.003   17.3   0.0    1.8  1  Sigma54_activat  Sigma-54 interaction domain
     0.0048   16.7   0.0       0.55   10.0   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0086   15.5   0.1       0.11   11.9   0.0    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.091   13.1   0.0        4.7    7.5   0.0    2.3  2  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.1   0.1   2.9e-64   5.7e-61       1     131 []      52     184 ..      52     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 2.9e-64
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrappktq 79 
                                   h l+e+ PGl+ktl+v++++k+ldl+f+r+q+tpdl+P+di+Gt+++ee+   kef+f++Gpvfan++ladeinra+pktq
  gi|91772818|ref|YP_565510.1|  52 HALMESNPGLGKTLTVSTISKTLDLSFSRVQCTPDLMPADITGTHFIEETGgkKEFKFEPGPVFANIVLADEINRASPKTQ 132
                                   99*********************************************99866699************************** PP

                         AAA_3  80 salleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                   salleam+e+qvtv+++t+ l++pf++latqnPie+eGt+plpeaqldrfll
  gi|91772818|ref|YP_565510.1| 133 SALLEAMQEKQVTVGNDTFILDKPFFLLATQNPIEMEGTFPLPEAQLDRFLL 184
                                   **************************************************96 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.1   2.8e-21   5.6e-18       6      73 .]     251     319 ..     246     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2.8e-21
                     AAA_lid_2   6 hlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiveei 73 
                                   +++ie+g+s+r a++ l+ aA+A+A+++gr++V+ eDv ++a +VL+HR++   e e+ g +++ +++ei
  gi|91772818|ref|YP_565510.1| 251 KEYIEFGASPR-ASIGLILAAKARALVRGRNFVSVEDVDAMAYPVLRHRIIltFESERRGISQDHVIKEI 319
                                   689********.***************************************8777777778888888775 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 !   45.4   0.0   3.8e-15   7.7e-12       7     138 .]      58     182 ..      52     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 3.8e-15
                                   -SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHH CS
                         AAA_5   7 ppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevln 83 
                                   +pG gK+  +  +++ l  ++  vq+t d+ ++d++g   i+    +++ +++++p+      + i++ DE++ra++++++
  gi|91772818|ref|YP_565510.1|  58 NPGLGKTLTVSTISKTLDLSFSRVQCTPDLMPADITGTHFIEetggKKEFKFEPGPVF-----ANIVLADEINRASPKTQS 133
                                   7****************************************9**9999999*******.....9***************** PP

                                   HHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                         AAA_5  84 sLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                   +Ll  + e+++ + + ++  +++       f ++at np +  +  +l +a ++Rf
  gi|91772818|ref|YP_565510.1| 134 ALLEAMQEKQVTVGNDTFILDKP-------FFLLATQNPIEmEGTFPLPEAQLDRF 182
                                   ************99999999775.......99********9999999999999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.4e-08   6.8e-05       3     112 ..      55     165 ..      53     190 .. 0.78
   2 ?   -1.8   0.0         2     4e+03     101     110 ..     239     248 ..     197     291 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.4e-08
                                   EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                           AAA   3 lyGppGtGKTllakavakelgvefleisgsellsk.......yvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                   +  +pG GKTl+++ + k+l+ +f +++++  l         +++e+  k +  f+     a   i++ DEi +  ++   
  gi|91772818|ref|YP_565510.1|  55 MESNPGLGKTLTVSTISKTLDLSFSRVQCTPDLMPaditgthFIEETGGKKEFKFEPGPVFA--NIVLADEINRASPKT-- 131
                                   5678********************99999655522478999899999999999999988887..9***********999.. PP

                                   CCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESSG CS
                           AAA  77 seseeeervvnqLlteldgvkkk........eskvivigatnrp 112
                                            +++Ll+++++ +          ++  ++++at++p
  gi|91772818|ref|YP_565510.1| 132 ---------QSALLEAMQEKQVTvgndtfilDK-PFFLLATQNP 165
                                   .........**********99999888888544.4555555553 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                                   STEEEEEEES CS
                           AAA 101 skvivigatn 110
                                   + + +i+at 
  gi|91772818|ref|YP_565510.1| 239 RAIKIIMATR 248
                                   2333344333 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.5e-07   0.00049      52     175 ..      45     167 ..      27     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                                   SBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEE..EEESSSSSSSHSSSE..EEEESSSSSEEEEETHHHHTTTSEEEEE CS
                           MCM  52 tklrgdinvllvgdpgtaKsqlLkyveklaprav..ytsgkgssaagLtaa..vvrdeetgefvleaGalvladkGvcciD 128
                                   + + ++ + l+ ++pg++K+  + +++k+++ +     +      a++t +  +     ++ef +e G +      +++ D
  gi|91772818|ref|YP_565510.1|  45 IAILSNGHALMESNPGLGKTLTVSTISKTLDLSFsrVQCTPDLMPADITGThfIEETGGKKEFKFEPGPVFAN---IVLAD 122
                                   457788999**********9999999998776541145555667788866511555556778******98754...9**** PP

                                   SGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                           MCM 129 efdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                   e+++ + +++sal+Eam ++++++       +L+    +la  np++
  gi|91772818|ref|YP_565510.1| 123 EINRASPKTQSALLEAMQEKQVTVGNDT--FILDKPFFLLATQNPIE 167
                                   **********************998766..67777777788888875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-06     0.003       9     142 ..      37     163 ..      33     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHH CS
               Sigma54_activat   9 kelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlf 89 
                                   k+++eqi  ++ ++ + l++ + G GK+l  ++i +     + +f +v+c+   ++l+ +++ G++    tG +ke k   
  gi|91772818|ref|YP_565510.1|  37 KDTVEQIIIAILSNGHALMESNPGLGKTLTVSTISK---TLDLSFSRVQCT---PDLMPADITGTHFIEETGGKKEFKFEP 111
                                   567888888999999999999999999999988855...456789999985...788888888888878888877766555 PP

                                   HHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
               Sigma54_activat  90 ekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                         +++ Dei++ ++++Q+ Ll+++qe++v+ vG+++ i  +  ++ at+
  gi|91772818|ref|YP_565510.1| 112 GPVFANIVLADEINRASPKTQSALLEAMQEKQVT-VGNDTFILDKPFFLLATQ 163
                                   5566789999*********************996.787766655555555555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00028      0.55      33      62 ..      50      79 ..      28      98 .. 0.75
   2 ?    4.1   0.0     0.017        34      86     114 ..     117     145 ..     113     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                        RuvB_N 33 ldhvllyGpPGlGkttlakiiakelgvklk 62
                                    h l+   PGlGkt   + i+k l+ ++ 
  gi|91772818|ref|YP_565510.1| 50 NGHALMESNPGLGKTLTVSTISKTLDLSFS 79
                                  469************999999999998764 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                        RuvB_N  86 dvlfideihrlsraveevlysamedfrld 114
                                   ++++ dei r s++++  l  am++ ++ 
  gi|91772818|ref|YP_565510.1| 117 NIVLADEINRASPKTQSALLEAMQEKQVT 145
                                   68899******************998875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   5.3e-05      0.11       4      45 ..      32      73 ..      29      82 .. 0.90
   2 ?    1.1   0.0      0.11   2.1e+02     109     158 ..     118     165 ..     101     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                  Mg_chelatase  4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                   ++Gq+++ + + ia+  + + l+  +pG GKt+  + +++ 
  gi|91772818|ref|YP_565510.1| 32 VIVGQKDTVEQIIIAILSNGHALMESNPGLGKTLTVSTISKT 73
                                  589*******************************99988765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                  Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                   +++ DE+   + k+  +L e +++++vt+   +     +  f l+a+ Np
  gi|91772818|ref|YP_565510.1| 118 IVLADEINRASPKTQSALLEAMQEKQVTVGNDTFI--LDKPFFLLATQNP 165
                                   6778***********************99765544..4455777777777 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0024       4.7       6      34 ..      46      74 ..      41      85 .. 0.82
   2 ?    3.0   0.0     0.057   1.1e+02     104     135 ..     117     146 ..      92     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                        AAA_19  6 ealkekvllvtaGpGtGKTrvlkhivall 34
                                  + l++++ l+   pG GKT ++ +i + l
  gi|91772818|ref|YP_565510.1| 46 AILSNGHALMESNPGLGKTLTVSTISKTL 74
                                  37889999999***********9998876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.057
                        AAA_19 104 ellivDEfqdvd.elqyrLlkallgekkklllv 135
                                   ++++ DE+   + ++q +Ll+a+  ek+  + v
  gi|91772818|ref|YP_565510.1| 117 NIVLADEINRASpKTQSALLEAMQ-EKQ--VTV 146
                                   58999*******9**********9.444..345 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1859.30
//
Query:       gi|91772819|ref|YP_565511.1|  [L=298]
Description: hypothetical protein Mbur_0805 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1771.64
//
Query:       gi|91772820|ref|YP_565512.1|  [L=284]
Description: prephenate dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-58  196.2   0.0    5.9e-58  195.7   0.0    1.1  1  PDT       Prephenate dehydratase
    1.4e-09   37.6   0.0    2.6e-09   36.7   0.0    1.4  1  ACT       ACT domain


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.7   0.0   6.6e-62   5.9e-58       1     180 [.       3     181 ..       3     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.7 bits;  conditional E-value: 6.6e-62
                                   EEEES-TTSHHHHHHCCCS.........EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEE CS
                           PDT   1 vaylGpegtyshqAalkvf....kaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgE 77 
                                   v++lGp g+ys++Aa+  +    k+e++ l+ ++ i++ f++v +g++d+++vPiENs+eGsV  tlDlLl+ s++ i+gE
  gi|91772820|ref|YP_565512.1|   3 VGVLGPAGSYSEKAAKGWIskesKSEGTSLVYYDDINDTFTSVINGDSDIGIVPIENSIEGSVGITLDLLLE-SEITIIGE 82 
                                   789*************88877778999*********************************************.99****** PP

                                   EEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHTT- CS
                           PDT  78 vvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaelygl 158
                                   +v+pi hcLl+k +   ++ik ++ShpqalgQc+kf++eh++++e++++ st++Aak   a++  ++aaias++ a+ ygl
  gi|91772820|ref|YP_565512.1|  83 IVVPIGHCLLSKGEI--KDIKIIMSHPQALGQCSKFIREHFKNAEIRTTGSTSHAAKL--ANEFCEMAAIASKESAREYGL 159
                                   *********987665..*****************************************..9999***************** PP

                                   EEEECS-SS-S--EEEEEEEEE CS
                           PDT 159 kvleeniedkknntTRFlvlak 180
                                   k+l  ni+d ++n+TRF+++++
  gi|91772820|ref|YP_565512.1| 160 KILVPNIQDWEKNHTRFIIIKQ 181
                                   ********************87 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   2.9e-13   2.6e-09       8      62 ..     207     261 ..     199     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.9e-13
                                   ESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHH CS
                           ACT   8 pDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevleal 62 
                                   +D+PG L ++ g +a+r+iN+++ie+r+s++++++++f +++++  +++++++al
  gi|91772820|ref|YP_565512.1| 207 EDKPGSLYEIIGEFAKRDINLTRIESRPSKRSLGDYMFYIDIEGSTGDADIKDAL 261
                                   5************************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1805.27
//
Query:       gi|91772821|ref|YP_565513.1|  [L=484]
Description: metalloenzyme [Methanococcoides burtonii DSM 6242]
Scores for complete 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   43.3   0.0    8.9e-11   41.6   0.0    1.9  2  Metalloenzyme  Metalloenzyme superfamily
    1.6e-08   34.3   0.0    4.2e-08   33.0   0.0    1.6  2  Sulfatase      Sulfatase
      0.001   18.7   0.2       0.01   15.5   0.0    2.5  3  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


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 ?   -3.4   0.0      0.82   4.9e+03       4      16 ..      49      61 ..      47      87 .. 0.79
   2 !   41.6   0.0   1.5e-14   8.9e-11     123     245 ..     231     354 ..     199     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.82
                                  EEEEETTBB---- CS
                                  xxxxxxxxxxxxx RF
                 Metalloenzyme  4 vlvvlDGlGeapa 16
                                  v++++DGlG    
  gi|91772821|ref|YP_565513.1| 49 VILITDGLGANYI 61
                                  7899999997655 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 1.5e-14
                                   HHHHH.CC.-S...EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS....... CS
                                   xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                 Metalloenzyme 123 aldailsgkfd...lvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk.... 196
                                   +++ +++   d   ++ +ni   D++G  +  e++++ iea+D +v+ ++++ e++d  +++t+DHg a + ++       
  gi|91772821|ref|YP_565513.1| 231 VIEMMEQY-PDqkyILTTNIGAIDAAGIYRRNEGYVECIEALDIMVQPLIERTEDNDLAFILTSDHGMAFQSTDGRGgsks 310
                                   45555222.223447899***************************************************999985558889 PP

                                   ......-----EEEEEESTT----S--SSHHHHTT-TTEEEEGGGHHHHH CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme 197 .qplTsHtlepVPilivgkglapdkvkegakfrekggLanvaatllnllg 245
                                    +  Ts  + ++P++ ++ ++++         re+ g  ++a+t+l++l 
  gi|91772821|ref|YP_565513.1| 311 gKYATSPEVLQIPFIATSSNIER------KFIREQIGQEDIAPTILSILD 354
                                   999****************9886......578889999999999998876 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.32   1.9e+03      49      94 ..     103     138 ..      49     143 .. 0.61
   2 !   33.0   0.0     7e-12   4.2e-08     208     308 ..     221     354 ..     198     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHSS-HHHHTHSSCCSTTTHHCTTTS-HHHHHHHHTT- CS
                     Sulfatase  49 cspsraalltgryphnsgvasntevgggglpqteatLpellkeaGY 94 
                                     +  + + tg + ++          +  ++ + at+ ++ +++GY
  gi|91772821|ref|YP_565513.1| 103 GENGHSVIVTGNPGAT----------TAMIAYNDATIYDIARDNGY 138
                                   4444444444444333..........45677888888888888888 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 7e-12
                                   H.....................................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS CS
                     Sulfatase 208 r.....................................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhga 251
                                   +                                     +  e y  ++e  D +++ ++++     ++++  ++ tSDhg 
  gi|91772821|ref|YP_565513.1| 221 NlwgietslkviemmeqypdqkyilttnigaidaagiyRRNEGYVECIEALDIMVQPLIERT----EDNDLAFILTSDHGM 297
                                   3444455555555555555555556666666666777778889*****************99....*************** PP

                                   CCCG..HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTT CS
                     Sulfatase 252 slee..sngplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlag 308
                                   + +   ++g  + gk+ +++++ +++P++  ++++ ++    e + + D++ptil+ ++
  gi|91772821|ref|YP_565513.1| 298 AFQStdGRGGSKSGKY-ATSPEVLQIPFIATSSNIERK-FIREQIGQEDIAPTILSILD 354
                                   9988999999******.*********************.89999999********9886 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.072   4.3e+02       2      22 ..      49      67 ..      48     131 .. 0.78
   2 !   15.5   0.0   1.7e-06      0.01     195     237 ..     262     300 ..     167     315 .. 0.82
   3 ?   -2.6   0.0      0.54   3.2e+03     262     294 ..     398     435 ..     365     459 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.072
                                  EEEEETT-BTTHHHHHGSTSH CS
                  Phosphodiest  2 lvislDGlradlldrlaellp 22
                                  ++++ DGl a+++++  e+ p
  gi|91772821|ref|YP_565513.1| 49 VILITDGLGANYINP--EKIP 67
                                  788899999999987..5544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEE CS
                  Phosphodiest 195 pevedalrrvDkaigdLlealderglsaetniilvSDHGmadv 237
                                   +   + ++ +D +++ L+e  +++    ++++il+SDHGma  
  gi|91772821|ref|YP_565513.1| 262 EGYVECIEALDIMVQPLIERTEDN----DLAFILTSDHGMAFQ 300
                                   555667899**************9....************965 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.54
                                   HHS.SSEEEEEESTEE.E.CCCTTHHHHHHHHH....H CS
                  Phosphodiest 262 kggakaliainpkare.lnrvaeaeaeevyael....k 294
                                     +++ ++++ p++ + + ++  ++ e+vy++     +
  gi|91772821|ref|YP_565513.1| 398 DDSEYIFYGLEPDKEYsITAELSGNDEQVYERTvfadS 435
                                   24566778888888888888899999999887543332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3060.03
//
Query:       gi|91772822|ref|YP_565514.1|  [L=338]
Description: methylcobalamin:coenzyme M methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-92  309.4   0.2    3.5e-92  309.2   0.2    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
       0.16   12.0   0.0       0.35   10.9   0.0    1.5  1  DUF2375   Protein of unknown function (DUF2375)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.2   0.2   3.9e-96   3.5e-92       2     346 .]       6     336 ..       5     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.2 bits;  conditional E-value: 3.9e-96
                                   ---HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGGT CS
                         URO-D   2 knerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaealG 82 
                                   ++erll+al++e+vd+vPv+    +++++    +  +g+ ++e+++++e++a ++++ ++ +gl+a+ ++++++v aea+G
  gi|91772822|ref|YP_565514.1|   6 PKERLLNALNREPVDKVPVVS---VTQTAIVDLMDQTGAEWPEAHSDAEKMATLAVASHEIAGLEAVRYPYCLTVLAEAMG 83 
                                   79*******************...999****************************************************** PP

                                   -EEEEETTTE.EEEE--S-....GGGS----GGG..G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT-SS- CS
                         URO-D  83 levefeegeg.Pvvekpvrtaedveklevpddvee.grlpyvleaikllkkelggevpligfvgaPftlasylveGgskgf 161
                                   +ev++++++  P+v++++   +dv++l  pdd+   gr+p vlea+k++ +++g+++pl++++ +P+tlas lv      +
  gi|91772822|ref|YP_565514.1|  84 CEVNMGTKNRqPSVTDHPY--KDVDNLVMPDDLLSnGRIPAVLEATKIIIDKVGDKIPLVAGMEGPVTLASDLV-----SV 157
                                   *******6666******99..9**********85589*************************************.....** PP

                                   HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-E CS
                         URO-D 162 ekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkrivdevkaegpkvpv 240
                                   +k++k+ +k+p++++++ld++td++i y++a+++agAd+i++ D  ++++ll+pe f+++  p l+r +++vk      p+
  gi|91772822|ref|YP_565514.1| 158 KKFMKWSIKKPDDLETILDFATDACIVYANALADAGADVICVPDpvASPDLLNPETFDKMLKPRLARFAEGVKC-----PM 233
                                   *************************************************************************9.....** PP

                                   EEEESSHH.HHHHHHTTS--SEEE--TTS.-HHHHHHSS....EEE--B-G.GGGG.S-HHHHHHHHHHHHT.T---SSSE CS
                         URO-D 241 ilfikgagaeiledlaelgadvlsldwtv.dlkeaarevgdkvalqGnldPialLl.gspeeiekevkeilekgaggkkgy 319
                                   +l+i+g+ ++il+ +a++++++ls++++v dlk a+++vgd+++++Gn++ + +Ll g+ e++++e k++le+g++     
  gi|91772822|ref|YP_565514.1| 234 VLHICGNVTPILDMMADCKFEGLSIEEKVaDLKGAIKTVGDRAVIVGNVSSPFTLLsGDVEKVKAESKDALEGGVA----- 309
                                   *****************************999*****************99999999***************9999..... PP

                                   EB-BSS---TTS-HHHHHHHHHHHHT- CS
                         URO-D 320 ilnlGhgippetppenvkalveavkey 346
                                   +l++G+gi+p+tp+envkalvea++ey
  gi|91772822|ref|YP_565514.1| 310 VLSPGCGIAPNTPVENVKALVEARDEY 336
                                   ***********************9987 PP

>> DUF2375  Protein of unknown function (DUF2375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.9e-05      0.35      12      66 ..      84     138 ..      76     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.9e-05
                       DUF2375  12 yeapallllhnavlkslpvsesGrviiPqeFkrGKsiiaVlEGeikilNslGerv 66 
                                   +e++ +   ++  +++ p  +  ++++P++      i aVlE    i+ ++G+++
  gi|91772822|ref|YP_565514.1|  84 CEVNMGTKNRQPSVTDHPYKDVDNLVMPDDLLSNGRIPAVLEATKIIIDKVGDKI 138
                                   88999999999999****************998889*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2125.10
//
Query:       gi|91772823|ref|YP_565515.1|  [L=535]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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-68  230.5   3.8      3e-68  229.7   3.8    1.4  1  RACo_C_ter   C-terminal domain of RACo the ASKHA domain
      3e-09   36.8   0.3    1.8e-08   34.2   0.0    2.4  2  Raco_middle  RACo middle region
    2.7e-07   30.4  11.8    0.00052   20.0   3.4    2.6  2  Fer4_6       4Fe-4S binding domain
    3.5e-07   29.8  12.7    1.2e-06   28.1   4.3    2.7  2  Fer4         4Fe-4S binding domain
    1.7e-06   28.5  10.1    6.6e-06   26.6  10.5    1.8  1  Fer4_7       4Fe-4S dicluster domain
    2.2e-06   28.5   9.3    0.00018   22.4   1.6    2.7  2  Fer4_16      4Fe-4S double cluster binding domain
    1.2e-05   25.3  11.1    4.3e-05   23.6  11.3    1.8  1  Fer4_9       4Fe-4S dicluster domain
      2e-05   24.6  12.8    6.1e-05   23.0  12.9    1.8  1  Fer4_10      4Fe-4S dicluster domain
    2.4e-05   24.1  10.5    0.00078   19.4   1.7    2.5  2  Fer4_2       4Fe-4S binding domain
    4.5e-05   23.5  11.6    9.9e-05   22.4  11.6    1.6  1  Fer4_21      4Fe-4S dicluster domain
    0.00024   21.4  12.3     0.0011   19.3   2.1    2.5  2  Fer4_4       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.032   15.1  15.8       0.18   12.8   3.6    2.5  2  Fer4_3       4Fe-4S binding domain
      0.047   14.2   1.0      0.047   14.2   1.0    2.4  2  Fer4_8       4Fe-4S dicluster domain
       0.38   11.3  14.0       0.15   12.7   2.8    2.5  2  Fer4_17      4Fe-4S dicluster domain
       0.52   10.9  12.8          3    8.5  12.8    2.2  1  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
        2.1    8.5  13.4         26    5.0  13.4    2.3  1  Fer4_18      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.7   3.8   2.7e-71     3e-68       2     259 ..     169     427 ..     168     428 .. 0.92

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 2.7e-71
                                   -EEEEEESSSEEEEEE-SS-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGG.....SSEEEEECTSS-....... CS
                    RACo_C_ter   2 lslliDiGTNaEivlgnkdellaasaaaGPAlEGaeikcGmrAapgAIedveidpet.....levelkvigdek....... 70 
                                   +++ +D+GTNaE++l++++ ++++saaaGPAlEG+ei  G  A p  I+dve+++ +     l+ e++++ ++        
  gi|91772823|ref|YP_565515.1| 169 IAIATDYGTNAEMALKVGNVIFTGSAAAGPALEGQEIGDGSIARPFVISDVEFNNGDvlnyvLDKEMNTVSGSLvnykngd 249
                                   7899**************************************************999777777788888844445666666 PP

                                   ........-SEEEHHHHHHHHHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSSS-EEEEHHHHHHHHHHH CS
                    RACo_C_ter  71 ........akGicGsGiidliaelleagiidkkgklnkelkserireeeetleyvlakaeetetkdivitekDieelikak 143
                                           a Gi+G+G+i+li e++++g i+  +++             +t++  l  ++     ++ +tekD+ e+++a+
  gi|91772823|ref|YP_565515.1| 250 vlkngdvhAIGITGTGVIALIDEAIKNGTIQ-LPNI-------------NTPDKKLYLQD-----GLHFTEKDLAEAGRAI 311
                                   77777777**********************5.5677.............56777777776.....9*************** PP

                                   HHHHHHHHHHHHHTT--GGG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHHHHHCBHHHHHHHHHHH CS
                    RACo_C_ter 144 aAiyagiktLleevglevediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAreallseealeeleeia 224
                                   +Ai+ag+ tL++++++++ed+e +y+AGa G+y+da kA++iG++P  +++k++q+GNtsl +Are+llsee+l++l+eia
  gi|91772823|ref|YP_565515.1| 312 GAIRAGHVTLCNAANVAMEDVEVAYMAGAAGTYMDAIKAHRIGMIPY-NVSKICQIGNTSLIVAREILLSEERLWDLQEIA 391
                                   ***********************************************.********************************* PP

                                   HHE..EE--TTSSSHHHHHHHHHSSSS-SSGGG-ST- CS
                    RACo_C_ter 225 rki..tyielateeeFqeeyvaalflphtdlelfpsv 259
                                    +i  t++++a++e+F++ y+ +l+++++++ +f+++
  gi|91772823|ref|YP_565515.1| 392 VEIvgTHVMFAMDEAFKDSYILELSYWNEGM-PFKTL 427
                                   *******************************.99987 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.6e-11   1.8e-08       2     161 ..       4     164 ..       3     166 .. 0.83
   2 ?   -0.9   0.1         1   1.2e+03      70     112 ..     318     358 ..     305     374 .. 0.62

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.6e-11
                   Raco_middle   2 GlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleeagieke 82 
                                   G+a+D+Gt+   a+ +dl +g++  +  ++ +    G++v+  + +a++   g +k +++v++++ ++++el  e g+   
  gi|91772823|ref|YP_565515.1|   4 GIAIDLGTSGFRAQKIDLGSGEIQRTVITM-RNPLPGANVMDHLDFAMT--YGQDKAHDLVINAFIHILNELEPEGGL--- 78 
                                   9********************987766555.34457*************..999***********9999999888865... PP

                   Raco_middle  83 eiyevvvagNttMlhlllgldpkslaka........pyvpvvseavelkakelglkinpeakvyvlpnvssyvGgDivagi 155
                                    +++++v+gN + l l+ g+    la a        +   + ++a ++++++++     ++kv++ p++ + vG+D++a i
  gi|91772823|ref|YP_565515.1|  79 -VERIAVCGNPIQLSLFQGIPIDDLAYAgerkkklmNIEEQKRNACIIDSTQVKGLEFLNCKVVIPPAIKHEVGADALALI 158
                                   .999*********************87622222222344555666777777776666689********************* PP

                   Raco_middle 156 lasglh 161
                                   + sg+ 
  gi|91772823|ref|YP_565515.1| 159 VKSGML 164
                                   ****96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                   Raco_middle  70 ieelleeagiekeeiyevvvag..NttMlhlllgldpkslakapy 112
                                     +l++ a+++ e+++ + +ag   t M      +++++++  py
  gi|91772823|ref|YP_565515.1| 318 HVTLCNAANVAMEDVEVAYMAGaaGTYMD----AIKAHRIGMIPY 358
                                   55678888888777766655551144454....345555555555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   3.4   4.6e-07   0.00052       3      24 .]     475     496 ..     473     496 .. 0.89
   2 !   14.9   1.3   1.8e-05      0.02       2      24 .]     503     527 ..     502     527 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.6e-07
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   eid + Ci+C +Cv+vCP +a+
  gi|91772823|ref|YP_565515.1| 475 EIDMEGCIDCKKCVDVCPNDAL 496
                                   799999************8875 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.8e-05
                        Fer4_6   2 veidpdkCi..gCgdCvrvCPegai 24 
                                   v+i  d+C+  +C +C+  CPe+++
  gi|91772823|ref|YP_565515.1| 503 VRIRTDLCDgaHCQKCIHSCPENVL 527
                                   77889****666**********986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   4.3     1e-09   1.2e-06       2      24 .]     475     497 ..     474     497 .. 0.94
   2 !    6.1   1.2    0.0092        10      10      23 ..     514     527 ..     503     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1e-09
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   +id+e Ci C++Cv+vCP++A++
  gi|91772823|ref|YP_565515.1| 475 EIDMEGCIDCKKCVDVCPNDALE 497
                                   79*******************85 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0092
                                   S-THHHHHSTTTEE CS
                          Fer4  10 gCGaCvevCPvgAI 23 
                                   +C +C+  CP +++
  gi|91772823|ref|YP_565515.1| 514 HCQKCIHSCPENVL 527
                                   5**********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 !   26.6  10.5   5.9e-09   6.6e-06       2      52 .]     481     526 ..     480     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.9e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekC..lgCgaCvavCPtga 52 
                                   Ci C++Cv++Cp++a+e +++       +v+i+ + C   +C++C+  CP ++
  gi|91772823|ref|YP_565515.1| 481 CIDCKKCVDVCPNDALEQEDR-------SVRIRTDLCdgAHCQKCIHSCPENV 526
                                   *****************9887.......5888888886679*********875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.6   1.6e-07   0.00018       2      28 ..     481     506 ..     480     513 .. 0.85
   2 !    9.3   1.7    0.0019       2.2       4      17 ..     514     527 ..     510     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-07
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                   C++C+kC++vCP +a++++ ++++++r
  gi|91772823|ref|YP_565515.1| 481 CIDCKKCVDVCPNDALEQE-DRSVRIR 506
                                   *****************99.5666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                       Fer4_16   4 tCgkCaevCPtnai 17 
                                    C+kC+ +CP+n++
  gi|91772823|ref|YP_565515.1| 514 HCQKCIHSCPENVL 527
                                   6**********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 !   23.6  11.3   3.8e-08   4.3e-05       2      49 ..     481     525 ..     480     527 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.8e-08
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaC..igCgaCveaCpkg 49 
                                   C++C++Cv++Cp+++ ++++    +r +      C   +C++C++ Cp++
  gi|91772823|ref|YP_565515.1| 481 CIDCKKCVDVCPNDALEQEDRSVRIRTD-----LCdgAHCQKCIHSCPEN 525
                                   ****************888888777774.....585567*********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 !   23.0  12.9   5.5e-08   6.1e-05       3      56 .]     475     523 ..     473     523 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.5e-08
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                   +id + Ci C+kCv++CP         + + e+  vr+  + C+g  c +C+ +CP
  gi|91772823|ref|YP_565515.1| 475 EIDMEGCIDCKKCVDVCPN-------DALEQEDRSVRIRTDLCDGahCQKCIHSCP 523
                                   799****************.......78888888888888999988899******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 !   19.4   1.7     7e-07   0.00078       4      22 .]     475     493 ..     473     493 .. 0.91
   2 !    9.2   1.9    0.0012       1.3       7      22 .]     507     524 ..     501     524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7e-07
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   ++d + Ci C++Cv++CP+
  gi|91772823|ref|YP_565515.1| 475 EIDMEGCIDCKKCVDVCPN 493
                                   689999************5 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                        Fer4_2   7 tdrCig..CgaCvsaCPa 22 
                                   td C g  C +C+++CP+
  gi|91772823|ref|YP_565515.1| 507 TDLCDGahCQKCIHSCPE 524
                                   89999989*********5 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4  11.6   8.9e-08   9.9e-05       3      54 ..     476     524 ..     474     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.9e-08
                       Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvG..CnlCssvCPve 54 
                                   id + Ci+C+kC+ +C++   +a+e  +++ +++++d C G  C+ C++ CP e
  gi|91772823|ref|YP_565515.1| 476 IDMEGCIDCKKCVDVCPN---DALEQ-EDRSVRIRTDLCDGahCQKCIHSCP-E 524
                                   999**************5...99996.577789******9888*********.4 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.1   9.8e-07    0.0011       2      15 ..     479     492 ..     478     500 .. 0.89
   2 !    6.8   2.7    0.0098        11       4      16 ..     510     524 ..     507     525 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.8e-07
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   e Ci+C++Cv++CP
  gi|91772823|ref|YP_565515.1| 479 EGCIDCKKCVDVCP 492
                                   67************ PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0098
                        Fer4_4   4 C..igCgsCvaaCPq 16 
                                   C   +C +C+ +CP 
  gi|91772823|ref|YP_565515.1| 510 CdgAHCQKCIHSCPE 524
                                   64459*********6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.6   0.00016      0.18       1      15 []     481     495 ..     481     495 .. 0.96
   2 ?    7.7   4.5    0.0067       7.6       1      14 [.     510     525 ..     510     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C  Cv+vCP++A
  gi|91772823|ref|YP_565515.1| 481 CIDCKKCVDVCPNDA 495
                                   99**********998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0067
                        Fer4_3   1 Ct..gCgaCvevCPvg 14 
                                   C+  +C+ C  +CP++
  gi|91772823|ref|YP_565515.1| 510 CDgaHCQKCIHSCPEN 525
                                   88668*********87 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   4.2e-05     0.047      44      64 ..     469     494 ..     426     495 .. 0.74
   2 ?    2.8   3.3      0.15   1.6e+02      51      65 .]     510     526 ..     494     526 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                        Fer4_8  44 e.....eealwsCttcgaCtevCpvg 64 
                                   +     e  ++ C  c++C++vCp++
  gi|91772823|ref|YP_565515.1| 469 QigtflEIDMEGCIDCKKCVDVCPND 494
                                   144555677999***********975 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                        Fer4_8  51 C..ttcgaCtevCpvgi 65 
                                   C   +c++C   Cp+++
  gi|91772823|ref|YP_565515.1| 510 CdgAHCQKCIHSCPENV 526
                                   54468999******986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.8   0.00013      0.15      42      59 ..     477     494 ..     465     496 .. 0.88
   2 ?    3.7   3.5     0.082        92      47      60 ..     513     526 ..     496     527 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                       Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                    ++ Ci C++C+ +CP++
  gi|91772823|ref|YP_565515.1| 477 DMEGCIDCKKCVDVCPND 494
                                   6899************97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.082
                       Fer4_17  47 ieCgeCerkCPqgl 60 
                                   ++C++C ++CP+++
  gi|91772823|ref|YP_565515.1| 513 AHCQKCIHSCPENV 526
                                   68999999999876 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 ?    8.5  12.8    0.0026         3       1      55 [.     476     526 ..     476     529 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                       Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPves 55 
                                   +D + Ci+c++Cv+++P+   e+++   +++   +t+  + a++++ +++CP + 
  gi|91772823|ref|YP_565515.1| 476 IDMEGCIDCKKCVDVCPNDALEQED-RSVRI---RTDLCDGAHCQKCIHSCPENV 526
                                   899**************86444443.45555...344445678999999999876 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  13.4     0.023        26      59      96 ..     479     523 ..     472     529 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.023
                       Fer4_18  59 gdcidcescvkvcPtg........idirkGlqleciscllcidacd 96 
                                     cidc++cv+vcP +        + ir  l  +   c++ci +c 
  gi|91772823|ref|YP_565515.1| 479 EGCIDCKKCVDVCPNDaleqedrsVRIRTDL-CDGAHCQKCIHSCP 523
                                   67************75222222225666665.47789999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3365.21
//
Query:       gi|91772824|ref|YP_565516.1|  [L=1116]
Description: multi-PAS sensor [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  169.5   0.0    1.7e-08   34.5   0.0    6.4  6  PAS       PAS fold
    2.4e-46  156.3  10.0    4.7e-12   46.1   0.0    6.5  6  PAS_9     PAS domain
    1.7e-37  128.0   0.0    4.1e-07   30.2   0.0    6.3  6  PAS_4     PAS fold
    2.1e-32  111.2   0.0    2.8e-16   59.6   0.1    5.5  5  PAS_3     PAS fold
    8.4e-26   89.5   0.1    1.6e-06   28.0   0.0    6.2  6  PAS_8     PAS domain
    2.5e-11   44.0   0.0    6.5e-05   23.3   0.0    2.6  2  GAF_2     GAF domain
    3.7e-08   33.5   0.1       0.13   12.4   0.0    6.0  5  PAS_7     PAS fold
     0.0011   19.3   0.0      0.017   15.5   0.0    2.4  2  GAF_3     GAF domain


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   5.6e-10   1.2e-06       3     107 ..      47     150 ..      45     156 .. 0.94
   2 !   30.4   0.0   1.4e-10   3.1e-07       2     113 .]     172     281 ..     171     281 .. 0.88
   3 !   19.2   0.1     4e-07   0.00089       4     111 ..     299     401 ..     296     403 .. 0.79
   4 !   34.5   0.0   7.5e-12   1.7e-08       2     113 .]     588     697 ..     587     697 .. 0.89
   5 !   26.8   0.0   1.9e-09   4.2e-06       3     113 .]     717     830 ..     715     830 .. 0.92
   6 !   21.9   0.0   5.9e-08   0.00013       2      53 ..    1006    1057 ..    1005    1078 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.6e-10
                                   HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECT CS
                           PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklr 82 
                                   ++ai+ sl ++ +++D d + +y+N+++ ++++ ++++vlg    +++  ++++ el ++l++++++g   +++  + ++ 
  gi|91772824|ref|YP_565516.1|  47 FEAIVASLKEALMILDPDLNLIYANDSFYKMFNVKPDDVLGNDADIFVDFKKNSpELFDRLSRVCKEGFLLEDFGLTYPFI 127
                                   89******************************************************************************* PP

                                   TSSEEEEEEEEEEEEETTEEEEEEE CS
                           PAS  83 dgrpihlevraspvrdaggeilgfl 107
                                   + +++ ++++ +p+r  gg    +l
  gi|91772824|ref|YP_565516.1| 128 NAGTRSVLINGRPIRYDGGC--VAL 150
                                   ***************99994..444 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 1.4e-10
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT.-ECCCCEEEEC CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqge.esrageisfkl 81 
                                   ++++++e   ++i+vv  d +i y+N++++el+G s ++++g+++ld i+ e+++ + +++ ++l++++ +s+++e ++  
  gi|91772824|ref|YP_565516.1| 172 QYSTLIEKGNEGIIVV-LDNEIRYTNKKFCELTGSSKDDIIGSPFLDHISLEYRRMVSKKYNKCLSSKKnDSNIYEANIVS 251
                                   7899999999******.**************************************99999999998865156667777777 PP

                                   TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                      ++i++e+++s +  +g+    +++ l+di
  gi|91772824|ref|YP_565516.1| 252 LIEGEIPVEMTNSYIEYEGQS--AVMLNLNDI 281
                                   889999999999999999887..888888886 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 4e-07
                                   HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTS CS
                           PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdg 84 
                                   r i+e +p +i+  D++g+i+  N+ ++e++   r+ + g ++ldl++ +d   +++ ++ + + + ++  g++ + + d+
  gi|91772824|ref|YP_565516.1| 299 RIIFEKSPIGIVRFDRKGIITNSNEVFNEIFDHLRDVITGYNVLDLFSDTD---FRSDISDVVSGKIRNYEGDVHLIVNDN 376
                                   6689999****************************************9998...888888888887777777777777666 PP

                                   SEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           PAS  85 rpihlevraspvrdaggeilgflgvlr 111
                                     i  ++  s ++d++ +  g +g++ 
  gi|91772824|ref|YP_565516.1| 377 NSILHVTFSSLIVDGSLQ--GGMGIFE 401
                                   666666666666666544..5555555 PP

  == domain 4  score: 34.5 bits;  conditional E-value: 7.5e-12
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81 
                                   ++++++ +  d+i+++ +d +  +vN+ ++e+ G+s++ v ++s++ ++++e+++  +++  + l++q+++s+ +e+++  
  gi|91772824|ref|YP_565516.1| 588 KYSNLVKNGNDGIIII-RDDVLEFVNSMFCEIIGFSPQKVHNSSFSSYLSPEYRRmVTKQFSKILEKQKSSSNKFEVDLLD 667
                                   6889999999******.899999********************************55555555566788888889999999 PP

                                   TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                   r+g+++++e+  s ++d g+    ++ ++rdi
  gi|91772824|ref|YP_565516.1| 668 RKGETVPVEISPSRIYDQGKP--AVMAIIRDI 697
                                   ******************987..9******98 PP

  == domain 5  score: 26.8 bits;  conditional E-value: 1.9e-09
                                   HHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEE CS
                           PAS   3 lraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfk 80 
                                   l++++ s+p+ +f ++  +g+ +++ ++  + +G+s+ + ++gk  +++i++++da  +++ + +  +++ ++   e ++ 
  gi|91772824|ref|YP_565516.1| 717 LQTVIKSSPAIVFFWNaQSGWPVEFVSENIDTFGYSPsDFLSGKLQYGDIIHPSDAeRVHSYFARKFAENASEYRLEYRII 797
                                   578999**********99*******************999**************997777778777888888888888888 PP

                                   CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                   +r   +++++ r +p +d++g + ++ g+++di
  gi|91772824|ref|YP_565516.1| 798 TRSDDVRWVVERSTPQYDEEGDLVHIQGIIMDI 830
                                   89******************************8 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 5.9e-08
                                    HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTT CS
                           PAS    2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldlihee 53  
                                    dl+++++ ++d i+v+D  g++ly N+a  + l  s ee+ g +++   +++
  gi|91772824|ref|YP_565516.1| 1006 DLKSLVDGIDDLILVLDSEGCVLYSNEAVSKKLAHSKEEITGMNFIKMHPHN 1057
                                    7899****************************************99766665 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.2e-12   2.7e-09       3     100 ..      57     154 ..      55     158 .. 0.89
   2 !   24.3   0.1   1.3e-08   2.8e-05       2     104 .]     182     283 ..     181     283 .. 0.72
   3 !   19.0   0.6   5.4e-07    0.0012       8     103 ..     313     404 ..     306     405 .. 0.87
   4 !   46.1   0.0   2.1e-15   4.7e-12       2     104 .]     598     699 ..     597     699 .. 0.91
   5 !   22.2   0.0   5.7e-08   0.00013       6     104 .]     730     832 ..     725     832 .. 0.87
   6 !    8.1   0.0    0.0013         3       2      36 ..    1016    1050 ..    1015    1109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.2e-12
                         PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                   + +i +pd +++yaN+++ +++  +p++vlg + + ++   +++pe  +rl+++ ++g    +++ +++   n +t  vl+
  gi|91772824|ref|YP_565516.1|  57 ALMILDPDLNLIYANDSFYKMFNVKPDDVLGNDADIFVdfkKNSPELFDRLSRVCKEGF-LLEDFGLTYPFINAGTRSVLI 136
                                   677888***************************99999889999999999999999999.99******************* PP

                         PAS_9  81 taspvkdddgelvgiivilr 100
                                   + +p++ d+g + +  v+++
  gi|91772824|ref|YP_565516.1| 137 NGRPIRYDGGCVAL--VTFE 154
                                   ******99877666..5554 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.3e-08
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk..kerevevvlirkngetfwv 78 
                                   +gi+++  d++i y N+++++l+G+s+++++g ++ d +  +      ++ +++l ++++  + +e ++v   +  ++++v
  gi|91772824|ref|YP_565516.1| 182 EGIIVV-LDNEIRYTNKKFCELTGSSKDDIIGSPFLDHIslEYRRMVSKKYNKCLSSKKNdsNIYEANIVSLIE--GEIPV 259
                                   789988.788799**************************66333333333333333333344355555555555..67999 PP

                         PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                   ++t s +  +++  v+  + l+Di e
  gi|91772824|ref|YP_565516.1| 260 EMTNSYIEYEGQSAVM--LNLNDIRE 283
                                   9999999888888888..88888865 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 5.4e-07
                         PAS_9   8 npdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkd 87 
                                   + +g i+   Ne +++++   ++ + g ++ dlf +d + ++++++++  +    +e++v+li ++++ ++ ++t+s ++ 
  gi|91772824|ref|YP_565516.1| 313 DRKG-IItNSNEVFNEIFDHLRDVITGYNVLDLF-SDTDFRSDISDVVSGKI-RNYEGDVHLIVNDNNSIL-HVTFSSLIV 389
                                   4788.666**********999*************.**************999.89************9999.666666654 PP

                         PAS_9  88 ddgelvgiivilrDit 103
                                    dg l+g  +i++Dit
  gi|91772824|ref|YP_565516.1| 390 -DGSLQGGMGIFEDIT 404
                                   .57899999******9 PP

  == domain 4  score: 46.1 bits;  conditional E-value: 2.1e-15
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvl 79 
                                   dgi+i+ +d  ++++N ++++++G+sp+ v + s++  + ++++++   +++ + ++k   +   +ev+l +++get++v+
  gi|91772824|ref|YP_565516.1| 598 DGIIIIRDDV-LEFVNSMFCEIIGFSPQKVHNSSFSSYL-SPEYRRMVTKQFSKILEKqksSSNKFEVDLLDRKGETVPVE 676
                                   8999984554.55**************************.888888888888888888999******************** PP

                         PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                   ++ s+++d+++  v+  +i+rDite
  gi|91772824|ref|YP_565516.1| 677 ISPSRIYDQGKPAVM--AIIRDITE 699
                                   ***************..*******8 PP

  == domain 5  score: 22.2 bits;  conditional E-value: 5.7e-08
                         PAS_9   6 i.dnpdgril.yaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvl 79 
                                   + +  +g  + +++e   + +Gysp ++l  +  + d++  +p+++er++ ++ ++     +e++ e+ +i++++   wv 
  gi|91772824|ref|YP_565516.1| 730 FwNAQSGWPVeFVSENIDT-FGYSPSDFLSGKlqYGDII--HPSDAERVHSYFARKFAenaSEYRLEYRIITRSDDVRWVV 807
                                   4566777444477777665.5******999998899999..99999999999999999999******************** PP

                         PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                    + +p +d++g lv+i +i+ Dite
  gi|91772824|ref|YP_565516.1| 808 ERSTPQYDEEGDLVHIQGIIMDITE 832
                                   ************************8 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0013
                         PAS_9    2 dgilidnpdgrilyaNeaalrllGyspeevlgksi 36  
                                    d il+ +++g +ly Nea+ + l  s+ee+ g ++
  gi|91772824|ref|YP_565516.1| 1016 DLILVLDSEGCVLYSNEAVSKKLAHSKEEITGMNF 1050
                                    6688888************************9775 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.2e-08   0.00014       2     100 ..      52     153 ..      51     157 .. 0.81
   2 !   10.1   0.0   0.00033      0.73      14      64 ..     189     239 ..     178     262 .. 0.89
   3 !   15.6   0.0   6.4e-06     0.014       1     109 [.     302     407 ..     302     408 .. 0.94
   4 !   30.2   0.0   1.8e-10   4.1e-07       8     109 ..     600     701 ..     593     702 .. 0.92
   5 !   25.6   0.0   4.8e-09   1.1e-05       3     109 ..     723     834 ..     721     835 .. 0.89
   6 !   16.1   0.0   4.6e-06      0.01       2      74 ..    1012    1084 ..    1011    1114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.2e-08
                         PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee..daarleralrrvlegeepiefleelll..pgee 78 
                                    sl +al +ldpd++ +yaN ++ ++f + p+++lG     ++ +     ++l + l rv +++  +e+   + +  + ++
  gi|91772824|ref|YP_565516.1|  52 ASLKEALMILDPDLNLIYANDSFYKMFNVKPDDVLGNDAD-IFVDFkkNSPELFDRLSRVCKEGFLLEDFGLTYPfiNAGT 131
                                   578899******************************8665.66666677777777778888887777766665556***** PP

                         PAS_4  79 rhyelrllPlrdesGevigvlv 100
                                   r ++++ +P+r + G+v  v +
  gi|91772824|ref|YP_565516.1| 132 RSVLINGRPIRYDGGCVALVTF 153
                                   **********987777666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
                         PAS_4  14 dgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegee 64 
                                   d  ++y+N+ ++el g + ++++G+++ +  + e ++ ++  ++++l++++
  gi|91772824|ref|YP_565516.1| 189 DNEIRYTNKKFCELTGSSKDDIIGSPFLDHISLEYRRMVSKKYNKCLSSKK 239
                                   557999***********************9999999999999999998876 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 6.4e-06
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerh 80 
                                   ++++p +++ +d+ g ++  N+ + e+f + ++ ++G  + +l+++   +++++++  v++g+ + ++ +++l  ++   +
  gi|91772824|ref|YP_565516.1| 302 FEKSPIGIVRFDRKGIITNSNEVFNEIFDHLRDVITGYNVLDLFSD---TDFRSDISDVVSGKIRNYEGDVHLIvNDNNSI 379
                                   799****************************************998...9************9999999999999888888 PP

                         PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                   + ++++ l   +G  +g ++i+ DiT r+
  gi|91772824|ref|YP_565516.1| 380 LHVTFSSL-IVDGSLQGGMGIFEDITLRK 407
                                   88888888.689**************886 PP

  == domain 4  score: 30.2 bits;  conditional E-value: 1.8e-10
                         PAS_4   8 lavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...pgeerhyelrl 85 
                                   ++++ +d + +++N  ++e++g++p+ + ++++ ++l++e ++ +  +  + le +++ +   e++l    ge++++e++ 
  gi|91772824|ref|YP_565516.1| 600 IIII-RDDVLEFVNSMFCEIIGFSPQKVHNSSFSSYLSPEYRRMVTKQFSKILEKQKSSSNKFEVDLldrKGETVPVEISP 679
                                   5553.677999**************************************************99999999999999999999 PP

                         PAS_4  86 lPlrdesGevigvlvisrDiTerr 109
                                   +++ d +G+  +v++i+rDiTe++
  gi|91772824|ref|YP_565516.1| 680 SRIYD-QGK-PAVMAIIRDITEQK 701
                                   99987.999.9***********97 PP

  == domain 5  score: 25.6 bits;  conditional E-value: 4.8e-09
                         PAS_4   3 slpdalavldpdgr..vlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll..pge 77 
                                   s+p++++++++++   v+++++++   fg++p ++l  +l+  ++  ++da+r++++ +r  +++++ ++le++    +++
  gi|91772824|ref|YP_565516.1| 723 SSPAIVFFWNAQSGwpVEFVSENIDT-FGYSPSDFLSGKLQygDIIHPSDAERVHSYFARKFAENASEYRLEYRIItrSDD 802
                                   78888999988875227999999888.888888888777777**99999***********************998899*** PP

                         PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                    r++  r +P  de+G+ +++ +i+ DiTer+
  gi|91772824|ref|YP_565516.1| 803 VRWVVERSTPQYDEEGDLVHIQGIIMDITERK 834
                                   *******************************8 PP

  == domain 6  score: 16.1 bits;  conditional E-value: 4.6e-06
                         PAS_4    2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll 74  
                                    d + d+++vld++g vly N+a  + ++++ ee++G+ +  ++p+    + +     +l+g+++ ++l  ++ 
  gi|91772824|ref|YP_565516.1| 1012 DGIDDLILVLDSEGCVLYSNEAVSKKLAHSKEEITGMNFIKMHPHNKVLEAAKLFGDALAGNKVEFRLPLVTG 1084
                                    7899*****************************************9999999999999999988777665554 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.015        35       2      22 ..      68      88 ..      67      96 .. 0.89
   2 !   14.1   0.0   1.9e-05     0.043       3      50 ..     194     239 ..     192     249 .. 0.90
   3 !   24.9   0.0   7.9e-09   1.8e-05       3      85 ..     610     691 ..     608     695 .. 0.90
   4 !   59.6   0.1   1.3e-19   2.8e-16       4      89 .]     742     827 ..     739     827 .. 0.93
   5 ?   -0.4   0.0      0.64   1.4e+03       2      50 ..    1028    1074 ..    1027    1105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                         PAS_3  2 iyvserveeilGyspeellgk 22
                                  iy+++++++++ + p+++lg+
  gi|91772824|ref|YP_565516.1| 68 IYANDSFYKMFNVKPDDVLGN 88
                                  8*****************998 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.9e-05
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge 50 
                                   y +++++e++G s+++++g+   +ld++  e r  v ++++++l++++
  gi|91772824|ref|YP_565516.1| 194 YTNKKFCELTGSSKDDIIGS--PFLDHISLEYRRMVSKKYNKCLSSKK 239
                                   7899****************..**********************7665 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 7.9e-09
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..pyegeyRirrkdGeyrwveararvirdengk 81 
                                   +v+  ++ei+G+sp+ + ++  s+ +++ pe r  v +++ ++l+k++  + ++e+ ++ + Ge++ ve + + i +++gk
  gi|91772824|ref|YP_565516.1| 610 FVNSMFCEIIGFSPQKVHNS--SFSSYLSPEYRRMVTKQFSKILEKQKssSNKFEVDLLDRKGETVPVEISPSRI-YDQGK 687
                                   79999***************..**********************77775455999**************999999.88888 PP

                         PAS_3  82 pvrv 85 
                                   p  +
  gi|91772824|ref|YP_565516.1| 688 PAVM 691
                                   8755 PP

  == domain 4  score: 59.6 bits;  conditional E-value: 1.3e-19
                         PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkpv 83 
                                   vse++ +++Gysp+++l+ + ++ d++hp D erv + +++ +++++ +y  eyRi++++ ++rwv +r ++ +de+g  v
  gi|91772824|ref|YP_565516.1| 742 VSENI-DTFGYSPSDFLSGKLQYGDIIHPSDAERVHSYFARKFAENAsEYRLEYRIITRSDDVRWVVERSTPQYDEEGDLV 821
                                   56666.789*******************************99988887********************************* PP

                         PAS_3  84 rvigva 89 
                                   +++g++
  gi|91772824|ref|YP_565516.1| 822 HIQGII 827
                                   ****96 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.64
                         PAS_3    2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge 50  
                                    +y +e+v++ l +s+ee++g  ++++++ h     ++ + + +al++++
  gi|91772824|ref|YP_565516.1| 1028 LYSNEAVSKKLAHSKEEITGM-NFIKMHPHNKV-LEAAKLFGDALAGNK 1074
                                    6889999999999********.55555555544.555566666665555 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   6.9e-10   1.6e-06       2      48 ..      46      95 ..      45     113 .. 0.82
   2 !   22.5   0.0   3.7e-08   8.2e-05       2      46 ..     172     216 ..     171     230 .. 0.80
   3 !    8.3   0.0     0.001       2.3       3      49 ..     298     342 ..     296     357 .. 0.76
   4 !   16.8   0.0   2.3e-06     0.005       1      41 [.     587     627 ..     587     648 .. 0.77
   5 ?   -1.2   0.0      0.98   2.2e+03      32      57 ..     747     775 ..     746     787 .. 0.67
   6 ?    4.9   0.0     0.012        27       3      34 ..    1007    1038 ..    1006    1071 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.9e-10
                         PAS_8  2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg..ql 48
                                  +++a++ s+ ++++++d + +++++N+++++++ ++ +d++g + +  ++
  gi|91772824|ref|YP_565516.1| 46 YFEAIVASLKEALMILDPDLNLIYANDSFYKMFNVKpDDVLGNDADifVD 95
                                  89***************7778***************99999999853333 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.7e-08
                         PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46 
                                   ++ +l+e  ++gi+vv +++ i++ N++++el+G s +d++g+++ 
  gi|91772824|ref|YP_565516.1| 172 QYSTLIEKGNEGIIVVLDNE-IRYTNKKFCELTGSSkDDIIGSPFL 216
                                   5899**********976445.*************668888887765 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.001
                         PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkgell.g.qll 49 
                                   +r +fe sp gi+ +d+ + i+  N+ + e++     ++++++ g ++l
  gi|91772824|ref|YP_565516.1| 298 FRIIFEKSPIGIVRFDRKGIITNSNEVFNEIFD----HLRDVItGyNVL 342
                                   7889************5566999*********7....665555234444 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 2.3e-06
                         PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlk 41 
                                   e++ +l+ + +dgi+++ ++  + +vN  ++e+ G+s + + 
  gi|91772824|ref|YP_565516.1| 587 EKYSNLVKNGNDGIIIIRDDV-LEFVNSMFCEIIGFSpQKVH 627
                                   78999***********98666.*************6544443 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.98
                         PAS_8  32 ellGys.adlkgellg..qllpvlrplle 57 
                                   + +Gys  d++  +l+  ++++ ++ +++
  gi|91772824|ref|YP_565516.1| 747 DTFGYSpSDFLSGKLQygDIIHPSDAERV 775
                                   579*******9999954455555555544 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.012
                         PAS_8    3 lralfesspdgiavvd.lgdrivdvNqaalell 34  
                                    l++l++ ++d i+v+d +g  +++ N+a  + l
  gi|91772824|ref|YP_565516.1| 1007 LKSLVDGIDDLILVLDsEGC-VLYSNEAVSKKL 1038
                                    789*************9999.999999986666 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     1e-06    0.0023       2     133 ..     432     569 ..     431     574 .. 0.76
   2 !   23.3   0.0   2.9e-08   6.5e-05       3     137 ..     855     991 ..     853     992 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                                   HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHH......HHHHHTS-EEES-GG CS
                         GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrlaawgeaeeefgaaldrplgeglvg......ealrtgrpvilndle 75 
                                    ++e++l+++l+++++l+ + +gy++ v +d+++++      +e    +l+++lge ++       ++  +g+ ++ n + 
  gi|91772824|ref|YP_565516.1| 432 ESIEDILNFTLEAAARLTlSNIGYLVSVREDNSFDMIFLLLKDEIGQYKLSKDLGEYPLDissraiKVNSSGKYLLSNYPN 512
                                   589**************9899************888855555555555554444444333112111666668766666677 PP

                                   G-S-HHHHHHHHHTT--EEEEEE-T.TS---EEEEES......--HHHHHHHHHHHHHH CS
                         GAF_2  76 edpdkkglpaghaglrsflavPlis.egrvvGvlnlyankppafdeedlelLeelaeqi 133
                                   +     +       ++++  +P+   eg    vl++ +nk++++d+ d + L++l + +
  gi|91772824|ref|YP_565516.1| 513 DLFEIENNYDVNGTIKRHFDIPISNeEG-ERFVLGV-GNKDSPYDDLDTRNLTLLIQEM 569
                                   78888888899************99678.8889**8.899999**********998766 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2.9e-08
                                   HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EE.ES-GGG.-S- CS
                         GAF_2   3 dleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvi.lndlee.dpd 79 
                                   dl+e++d++l+ ++ ++ ++ g ++l+d ++g l l +  +    f    ++  +++   + +++g p++    + +  p 
  gi|91772824|ref|YP_565516.1| 855 DLQETFDQLLEFALHIDsIDSGSLYLIDKNNGgLNLISHKGLSQDFVKNNSHYAADSMQSRFFMMGYPLYkM--YSDiYPV 933
                                   89**************8799******9966555888877777777777776677888899**********41..4443667 PP

                                   HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                         GAF_2  80 kkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                    k+ +  ++gl +++++P+ ++++ v+vl+l++  +++     ++ +e++aeq++ +i
  gi|91772824|ref|YP_565516.1| 934 TKRDNRVDEGLLATAVIPVKYQEEEVAVLFLASRTEYEMLYNIRTSVETVAEQMGSII 991
                                   77778899***********99889************999999999*********9987 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   5.7e-05      0.13       3      38 ..      53      87 ..      51     152 .. 0.83
   2 ?    1.2   0.0      0.17   3.9e+02       5      45 ..     181     219 ..     177     235 .. 0.77
   3 !    5.5   0.0    0.0083        19       4      48 ..     305     348 ..     302     411 .. 0.69
   4 ?    4.5   0.0     0.017        38       5     115 .]     597     705 ..     593     705 .. 0.59
   5 ?    1.4   0.0      0.15   3.3e+02       4      49 ..    1014    1058 ..    1011    1093 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                         PAS_7  3 nmsqGisvfDadlrLvawNrrylelldlpeelvqvg 38
                                  +++++++++D dl+L+  N+ + +++++ ++ v  g
  gi|91772824|ref|YP_565516.1| 53 SLKEALMILDPDLNLIYANDSFYKMFNVKPDDV-LG 87
                                  78899**********************988776.45 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                         PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                   ++Gi+v+  d++++  N++++el + +++ + +g p+ + +
  gi|91772824|ref|YP_565516.1| 181 NEGIIVV-LDNEIRYTNKKFCELTGSSKDDI-IGSPFLDHI 219
                                   5676655.35678899*********999998.888876655 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0083
                         PAS_7   4 msqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn 48 
                                    + Gi+ fD+++ ++ +N+ + e++d  ++++ +g ++ +l+  +
  gi|91772824|ref|YP_565516.1| 305 SPIGIVRFDRKGIITNSNEVFNEIFDHLRDVI-TGYNVLDLFSDT 348
                                   567************************99999.787777766554 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.017
                         PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaara.gkphsfererpd 84 
                                   ++Gi+++ +d+ L ++N+ ++e+ +++++ v    ++++ l    +r       v +++ ++l++ ++  ++  ++   ++
  gi|91772824|ref|YP_565516.1| 597 NDGIIII-RDDVLEFVNSMFCEIIGFSPQKV-HNSSFSSYLSPEYRR------MVTKQFSKILEKQKSsSNKFEVDLLDRK 669
                                   5677666.67789999999999999999998.555666666544333......3444555555443331222223334455 PP

                         PAS_7  85 grvi..evrgnplpdgG...fVttytDiTerrraee 115
                                   g+++  e+  +++ d G   ++++  DiTe++++e+
  gi|91772824|ref|YP_565516.1| 670 GETVpvEISPSRIYDQGkpaVMAIIRDITEQKKKEQ 705
                                   666511555555556554447889999999999886 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.15
                         PAS_7    4 msqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryna 49  
                                    +++ i+v+D+++ ++ +N+ + + l  ++e + +g+++ ++  +n+
  gi|91772824|ref|YP_565516.1| 1014 IDDLILVLDSEGCVLYSNEAVSKKLAHSKEEI-TGMNFIKMHPHNK 1058
                                    566699***************99999998888.8998888877774 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.21   4.7e+02       1      32 [.     433     463 ..     433     469 .. 0.89
   2 !   15.5   0.0   7.7e-06     0.017       1     126 [.     855     990 ..     855     993 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.21
                         GAF_3   1 sldellekllkllvkllgaevgalllldedgn 32 
                                   s++++l+ +l+++++l+ +++g l+ ++ed n
  gi|91772824|ref|YP_565516.1| 433 SIEDILNFTLEAAARLTLSNIGYLVSVRED-N 463
                                   689*********************999977.4 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.7e-06
                         GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesld..edsalarralssgevvse........ps 71 
                                   +l+e++++ll+++ ++ + ++g+l+l d+    l+ +++++ +++++++    +++++ +r +++g ++++        ++
  gi|91772824|ref|YP_565516.1| 855 DLQETFDQLLEFALHIDSIDSGSLYLIDKNNGGLNLISHKGLSQDFVKNNShyAADSMQSRFFMMGYPLYKmysdiypvTK 935
                                   79**************************998899999999888888885545688888889*****999997766665422 PP

                         GAF_3  72 faeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiata 126
                                    + +    + a  ++P++ +++ + vl+las+ + +++   +  +e++A q+++ 
  gi|91772824|ref|YP_565516.1| 936 RDNRVDEGLLATAVIPVKYQEEEVAVLFLASRTEYEMLYNIRTSVETVAEQMGSI 990
                                   23344466788899******************99999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.87u 0.31s 00:00:01.18 Elapsed: 00:00:00.50
# Mc/sec: 6676.35
//
Query:       gi|91772825|ref|YP_565517.1|  [L=254]
Description: methanol corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-16   58.9   0.1    8.3e-16   58.1   0.1    1.4  1  B12-binding      B12 binding domain
    7.8e-16   58.3   0.3    3.1e-15   56.4   0.0    2.0  2  B12-binding_2    B12 binding domain
  ------ inclusion threshold ------
      0.029   14.5   0.5       0.15   12.3   0.0    2.4  3  UPF0180          Uncharacterised protein family (UPF0180)
      0.031   13.8   0.2      0.054   13.0   0.2    1.4  1  DUF2192          Uncharacterized protein conserved in archaea
       0.04   13.8   0.0      0.074   13.0   0.0    1.4  1  DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau do
      0.046   12.4   0.2      0.057   12.1   0.2    1.2  1  SpoVAD           Stage V sporulation protein AD (SpoVAD)
       0.15   12.5   0.1        9.7    6.7   0.0    2.5  2  Rep_fac_C        Replication factor C C-terminal domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.1   3.3e-19   8.3e-16       2     104 ..     122     222 ..     121     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 3.3e-19
                   B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprv 82 
                                   k++  +v+gd+h++G++++   lr++g+eV++lg +v +e+++aa+++ekp ++  ++l+t+++ +++++  +l + + +v
  gi|91772825|ref|YP_565517.1| 122 KIVSYVVEGDIHDIGKKIVTVLLRAKGYEVVDLGKDVCVEEVIAAVKREKPIMLTGTSLMTTTMVGFQDVNSRLLESDINV 202
                                   788899***********************************************777777**************999999** PP

                   B12-binding  83 kvvvGGahpsldpeetleaklg 104
                                   ++v+GG ++  +++++ +++lg
  gi|91772825|ref|YP_565517.1| 203 PIVCGGGAV--TQDFVSQYELG 222
                                   ******985..55554444455 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   1.2e-18   3.1e-15       3      74 ..      38     109 ..      37     110 .. 0.96
   2 ?   -1.1   0.1       1.1   2.7e+03       8      39 ..     126     159 ..     122     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.2e-18
                 B12-binding_2   3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74 
                                   +++++a+ +gd+++++e i+ a+++g +++ ++n++ll +m++V  l++ g l+lp+v+ sa++m ++++++
  gi|91772825|ref|YP_565517.1|  38 REVAKAVFEGDEDEVVESIQNAINNGLDPLNLINNALLVGMEIVSTLYDDGVLYLPDVIISAQAMIEGIEYC 109
                                   6799**************************************************************999987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                 B12-binding_2   8 aivhgdkegieelideal..aqgsaavdvlndvl 39 
                                    +v+gd  +i + i ++l  a+g+++vd+  dv+
  gi|91772825|ref|YP_565517.1| 126 YVVEGDIHDIGKKIVTVLlrAKGYEVVDLGKDVC 159
                                   6788888888888888774456677777766665 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.6   4.1e+03      64      74 ..      20      30 ..      18      32 .. 0.84
   2 ?   -2.0   0.1       1.6   4.2e+03      37      42 ..      42      47 ..      22      64 .. 0.56
   3 ?   12.3   0.0   5.8e-05      0.15      13      52 ..     141     190 ..     137     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.6
                       UPF0180 64 gktaeeIlqev 74
                                   +t+ee+ +++
  gi|91772825|ref|YP_565517.1| 20 EMTPEEVAEKL 30
                                  69*****9875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                       UPF0180 37 aiVvtG 42
                                    V +G
  gi|91772825|ref|YP_565517.1| 42 KAVFEG 47
                                  334444 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 5.8e-05
                       UPF0180  13 keaLrekGYeVvdleteedaqsvdaiVvtG..........qdtnvmgied 52 
                                      Lr+kGYeVvdl+++   ++v a V             ++t ++g++d
  gi|91772825|ref|YP_565517.1| 141 TVLLRAKGYEVVDLGKDVCVEEVIAAVKREkpimltgtslMTTTMVGFQD 190
                                   5679***********96667788777773333333336666666666666 PP

>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.1e-05     0.054      65     113 ..      10      60 ..       8      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                       DUF2192  65 vgkyGlgleeel..kelfdkifsvEekleealeiilskkkeeavekvkevl 113
                                   + +y + +e+e+  +e+ +k+f vEe++ e+++++ +++++e ve +++ +
  gi|91772825|ref|YP_565517.1|  10 LTRYNVKVEKEMtpEEVAEKLFPVEENIREVAKAVFEGDEDEVVESIQNAI 60 
                                   567788888887656899**************************9999866 PP

>> DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.9e-05     0.074      16      53 ..      35      72 ..      33      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
               DNA_pol3_gamma3 16 arlldlleallegdaaaalaelreqyaaGadpvvvlrd 53
                                  +++ ++ +a++egd +++++++++++++G+dp  ++++
  gi|91772825|ref|YP_565517.1| 35 ENIREVAKAVFEGDEDEVVESIQNAINNGLDPLNLINN 72
                                  578899**************************988876 PP

>> SpoVAD  Stage V sporulation protein AD (SpoVAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.2e-05     0.057     223     310 ..     124     214 ..      97     239 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                                   -SEEEESS-HHHHHHHHHHHHHHTT---GGGEEE.HHHHSS-..TT.S--TT-EESHHHHHHHHHHHHHHHHHTTS-SEEE CS
                        SpoVAD 223 yDlivtGDlgkvGkeileellkekgldiseeykD.CGlliyd..eekqdvlaGgsGcgcsavvlagyllkklkkgelkrvl 300
                                      +v GD+  +Gk+i++ ll+ kg+++ +  kD C  ++    + +++++  g    ++ +v    + ++l + +++  +
  gi|91772825|ref|YP_565517.1| 124 VSYVVEGDIHDIGKKIVTVLLRAKGYEVVDLGKDvCVEEVIAavKREKPIMLTGTSLMTTTMVGFQDVNSRLLESDINVPI 204
                                   346899*********************999877746555544112334555555555556666666677777777777777 PP

                                   EEEEEE---H CS
                        SpoVAD 301 lvatGallsp 310
                                   + + Ga+   
  gi|91772825|ref|YP_565517.1| 205 VCGGGAVTQD 214
                                   7777776555 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 ?    6.7   0.0    0.0038       9.7       3      43 ..      34      73 ..      32     111 .. 0.86
   2 ?    3.4   0.0     0.039     1e+02       8      40 ..     122     155 ..     120     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0038
                                  HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHH CS
                     Rep_fac_C  3 pteieeileaclngdfeeaykklrellvekGysaediltql 43
                                  ++ i+e+++a+ +gd +e+ ++++ + +++G+ +  ++++ 
  gi|91772825|ref|YP_565517.1| 34 EENIREVAKAVFEGDEDEVVESIQ-NAINNGLDPLNLINNA 73
                                  789********************7.********99999875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.039
                                   HHHHHHHHT-HHHHHHH.HHHHHHHC---HHHHH CS
                     Rep_fac_C   8 eileaclngdfeeaykk.lrellvekGysaedil 40 
                                   +i++ + +gd+ +++kk +++ll +kGy + d+ 
  gi|91772825|ref|YP_565517.1| 122 KIVSYVVEGDIHDIGKKiVTVLLRAKGYEVVDLG 155
                                   58888878999999998577889999**999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1573.31
//
Query:       gi|91772826|ref|YP_565518.1|  [L=462]
Description: methanol:corrinoid methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-223  741.2   0.5   4.7e-223  741.1   0.5    1.0  1  MtaB      Methanol-cobalamin methyltransferase B subunit


Domain annotation for each model (and alignments):
>> MtaB  Methanol-cobalamin methyltransferase B subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  741.1   0.5  2.6e-227  4.7e-223       2     460 .]       6     461 ..       5     461 .. 1.00

  Alignments for each domain:
  == domain 1  score: 741.1 bits;  conditional E-value: 2.6e-227
                          MtaB   2 kkftklayksaddlvfGkakkPvkaklgleiGaGtvvpeinvapreeseeskeklvkeyekittdileravelglPavvlE 82 
                                   k+++k+ay++++d+vfG++ +P+k++++leiGaG++ +e+n+apr++++eskekl++ey+kittd+l+r+v++g+P+vvlE
  gi|91772826|ref|YP_565518.1|   6 KRYNKMAYDDFEDMVFGHSIYPIKTGFDLEIGAGYTSAEVNYAPRPAAGESKEKLIAEYQKITTDVLQRMVQVGFPSVVLE 86 
                                   8******************************************************************************** PP

                          MtaB  83 tEhvqqmtenpewgaevakaqkeileeyedkyglksalratiaDiReeeealelrgdkllekllesfeevaenGadllsiE 163
                                   tEhvqqmt np+wgae+a+ qk+i+ee++d+yg+k+alr+t+aDiR  +eal+lrgd++   llesfeeva+nGad+lsiE
  gi|91772826|ref|YP_565518.1|  87 TEHVQQMTVNPSWGAEIAHEQKTIMEEFYDEYGIKCALRHTPADIRGGKEALDLRGDSY-GILLESFEEVASNGADMLSIE 166
                                   ***********************************************************.********************* PP

                          MtaB 164 svGGKevsDeaivrndirgvlfaigvlGsiDmeylWkeivkiakkkgvvaaGDtdCaqantamflagglldkdvpktlaav 244
                                   s+GGK+v+D++i+rnd++gvlf+ig+lG++D+e++W++i+kiakk++vvaaGDtdC+qantamf+agglld+++++tla+v
  gi|91772826|ref|YP_565518.1| 167 SLGGKSVFDSSIIRNDLSGVLFSIGILGTLDVEFIWEDISKIAKKHDVVAAGDTDCSQANTAMFIAGGLLDRKLAHTLAVV 247
                                   ********************************************************************************* PP

                          MtaB 245 aRaiaaarsLvayEaGavGPdKDCgYEnpiiKaiagvPisqEGktaacAHsdlvGnlaaavcDlWsnEsveyhkelggttv 325
                                   aRa++a+rsL+ayEaGavGP+KDCgYEn+iiKaiagvPisqEGk ++cAHsd++Gnla+++cDlWsnEsvey+ e+ggt+v
  gi|91772826|ref|YP_565518.1| 248 ARAVSAPRSLAAYEAGAVGPGKDCGYENTIIKAIAGVPISQEGKGSTCAHSDVMGNLAMQCCDLWSNESVEYRGEFGGTSV 328
                                   ********************************************************************************* PP

                          MtaB 326 qvwleqlgydcalmntalekgqekelrdllvesDkyrdpqayiLaydnaykigeaivkegddlylrakaaalkaielleea 406
                                   q+w e+l+ydc++mnta+e+g++k++rd+++ sD+yrdpqa+iLa+dnay+igeaivk+g+d+ylrak+aa++a+++++e+
  gi|91772826|ref|YP_565518.1| 329 QCWGETLSYDCSMMNTAIEAGYAKVFRDVFMVSDRYRDPQAFILAFDNAYRIGEAIVKDGNDIYLRAKNAAIEACNIVDEG 409
                                   ********************************************************************************9 PP

                          MtaB 407 veekklklskfekkaLdkakkelealpddedkFikeclkkykkevkkfkpenYg 460
                                   + +++l+ls+fek +L+ka k+l++l+d++d Fi+e l+k++ ++++f++enYg
  gi|91772826|ref|YP_565518.1| 410 S-RGQLELSRFEKASLAKAIKSLHSLTDEKDVFIEENLNKLS-TMESFRSENYG 461
                                   8.9***************************************.5*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 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:                        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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:01.05
# Mc/sec: 1331.05
//
Query:       gi|91772827|ref|YP_565519.1|  [L=256]
Description: methanol corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   67.1   0.3    2.7e-18   66.1   0.3    1.4  1  B12-binding    B12 binding domain
      4e-16   59.2   0.2    1.2e-15   57.7   0.2    1.8  1  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.3   3.1e-22   2.7e-18       2     114 ..     124     228 ..     123     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 3.1e-22
                   B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprv 82 
                                   kv+ ++++gd+h++G+ ++aa lr++g+eV++lg +v+++++++a++aekp ++  +al+t+++ a+k++ ++l +++ +v
  gi|91772827|ref|YP_565519.1| 124 KVVCHVAEGDVHDIGKSIVAALLRANGYEVVDLGRDVPVDEVIDAVKAEKPILLTGTALMTTTMYAFKAVNDRLLEAGLNV 204
                                   899**********************************************************************9999**** PP

                   B12-binding  83 kvvvGGahpsldpeetleaklgiddvvvgege 114
                                   + ++GG +++ d   t e  lg  +     ge
  gi|91772827|ref|YP_565519.1| 205 PFACGGGAVNQDFVSTYE--LG-IY-----GE 228
                                   ******996655555444..77.33.....33 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.2   1.4e-19   1.2e-15       3      72 ..      40     109 ..      38     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.4e-19
                 B12-binding_2   3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkava 72 
                                   ++++ ai +g+++++ e +++a+++g+ + ++++d+l+ +mk+V dl+++g++flp v++sa++m  +++
  gi|91772827|ref|YP_565519.1|  40 REIAVAIFDGEEDDVIEGLEKAIKAGKNPIALIDDALMVGMKVVTDLYDQGTIFLPNVMMSADAMLDGIE 109
                                   67899************************************************************88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1510.00
//
Query:       gi|91772828|ref|YP_565520.1|  [L=461]
Description: methanol:corrinoid methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-235  780.5   3.8   5.8e-235  780.3   3.8    1.0  1  MtaB             Methanol-cobalamin methyltransferase B subun
  ------ inclusion threshold ------
      0.036   13.5   0.0      0.097   12.1   0.0    1.7  2  Rhamnogal_lyase  Rhamnogalacturonate lyase family


Domain annotation for each model (and alignments):
>> MtaB  Methanol-cobalamin methyltransferase B subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  780.3   3.8  6.4e-239  5.8e-235       2     460 .]       4     460 ..       3     460 .. 1.00

  Alignments for each domain:
  == domain 1  score: 780.3 bits;  conditional E-value: 6.4e-239
                          MtaB   2 kkftklayksaddlvfGkakkPvkaklgleiGaGtvvpeinvapreeseeskeklvkeyekittdileravelglPavvlE 82 
                                   +++tk+ay+sadd++fGk+k+Pvka+lgleiGaG+++pe+n+apr+e+++skeklvkey+kittdi++r+v++g+PavvlE
  gi|91772828|ref|YP_565520.1|   4 NRYTKMAYDSADDMIFGKCKHPVKAGLGLEIGAGYTIPEVNYAPRPEAGASKEKLVKEYQKITTDIMNRMVQVGFPAVVLE 84 
                                   79******************************************************************************* PP

                          MtaB  83 tEhvqqmtenpewgaevakaqkeileeyedkyglksalratiaDiReeeealelrgdkllekllesfeevaenGadllsiE 163
                                   tEhv+qmt+np+wg+eva+aqk+i+ee++d+yg+k+alr+t++DiRe+++ l+lrgdk+ + ++esfee+a+nGad+ls+E
  gi|91772828|ref|YP_565520.1|  85 TEHVEQMTNNPTWGGEVAHAQKTIMEEFHDEYGIKCALRHTPGDIRENRDFLDLRGDKF-NVMMESFEEIASNGADMLSVE 164
                                   ***********************************************************.********************* PP

                          MtaB 164 svGGKevsDeaivrndirgvlfaigvlGsiDmeylWkeivkiakkkgvvaaGDtdCaqantamflagglldkdvpktlaav 244
                                   s+GGKev+D+ai+rnd+ g+l+aig+lG+iDm+++W+ei+++akk+gvv+aGDtdC++antamf++gglldk++++tla++
  gi|91772828|ref|YP_565520.1| 165 SMGGKEVFDYAILRNDVPGMLYAIGCLGTIDMDFIWQEISSVAKKHGVVSAGDTDCSEANTAMFIGGGLLDKNLAHTLAII 245
                                   ********************************************************************************* PP

                          MtaB 245 aRaiaaarsLvayEaGavGPdKDCgYEnpiiKaiagvPisqEGktaacAHsdlvGnlaaavcDlWsnEsveyhkelggttv 325
                                   aRai+a+rsL+ayEaGavGP+KDCgYEn+iiKai+gvPi+qEGk+++cAHsd++Gnl++++cDlWsnEsveyh e+ggt+v
  gi|91772828|ref|YP_565520.1| 246 ARAISAPRSLAAYEAGAVGPGKDCGYENTIIKAISGVPIAQEGKSSTCAHSDVMGNLVMQCCDLWSNESVEYHAEFGGTSV 326
                                   ********************************************************************************* PP

                          MtaB 326 qvwleqlgydcalmntalekgqekelrdllvesDkyrdpqayiLaydnaykigeaivkegddlylrakaaalkaielleea 406
                                   q+w e+l+ydcalmnta+++gqek+lrdl++ sDkyrdpq+y+Laydnay++geaivk+g+d+ylrak+aalk++e++ee+
  gi|91772828|ref|YP_565520.1| 327 QCWGESLAYDCALMNTATATGQEKTLRDLFMLSDKYRDPQGYVLAYDNAYRVGEAIVKDGNDIYLRAKNAALKSVEIMEEG 407
                                   ********************************************************************************* PP

                          MtaB 407 veekklklskfekkaLdkakkelealpddedkFikeclkkykkevkkfkpenYg 460
                                   + ++kl+l+kfek aL++ak++l al+dd+d+F+++c++kyk+evk f penYg
  gi|91772828|ref|YP_565520.1| 408 I-AGKLELTKFEKGALADAKAALMALTDDQDTFMSDCMTKYKEEVKVFLPENYG 460
                                   9.9**************************************************7 PP

>> Rhamnogal_lyase  Rhamnogalacturonate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.29   2.6e+03      85      99 ..     137     151 ..     106     187 .. 0.70
   2 ?   12.1   0.0   1.1e-05     0.097     149     206 ..     400     458 ..     382     461 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.29
               Rhamnogal_lyase  85 klkGtkfeivvqnee 99 
                                    l+G kf++++++ e
  gi|91772828|ref|YP_565520.1| 137 DLRGDKFNVMMESFE 151
                                   345555555555544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.1e-05
               Rhamnogal_lyase 149 dvdldqirivfklrkdkfdfmaiaddrqrimpldedreikkg.rplaykeavllvnpvn 206
                                   +v++ +  i+ kl+ +kf+  a+ad +   m l++d+++  +     yke v++  p n
  gi|91772828|ref|YP_565520.1| 400 SVEIMEEGIAGKLELTKFEKGALADAKAALMALTDDQDTFMSdCMTKYKEEVKVFLPEN 458
                                   67888889999***************************999934557*****9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3625.03
//
Query:       gi|91772829|ref|YP_565521.1|  [L=205]
Description: GPR1/FUN34/YaaH family protein [Methanococcoides burtonii DSM 6242]
Scores for 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-24   85.1  28.3    6.4e-24   84.7  28.3    1.0  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7  28.3   3.6e-28   6.4e-24      15     193 ..      24     196 ..      15     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 3.6e-28
               Gpr1_Fun34_YaaH  15 rkfaNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsyaai 95 
                                    k a+ aPlg+++ ++ +++l+++  g    t   +vv++ +f+GG++q++aGi  +  g+ Fgata+s +G Fw+s+a+i
  gi|91772829|ref|YP_565521.1|  24 DKTADHAPLGFAGLGFAAIMLGMMGSGF--FTDATMVVSMSIFLGGFAQVFAGIEGWKKGDVFGATAFSAFGLFWFSFAFI 102
                                   5889*******************98877..57888********************************************** PP

               Gpr1_Fun34_YaaH  96 lipgfgilaaYeedeeelnnalglyllgwfiftfllllatlrstv.alfllfffldltflllaigeltgsakvlkAggvfg 175
                                   l+ + gi++      +  +  +g yl++w +++++ll++tl+  v a++++f++l+ltf+l a++++    +v   +g+++
  gi|91772829|ref|YP_565521.1| 103 LM-SSGIASGVL--GAASAISVGYYLFIWGLVSLVLLFVTLKIGVkAITIVFITLTLTFFLNAAANF--GMGVGSLAGYMA 178
                                   99.589999884..4566788*********************998468899****************..466778899*** PP

               Gpr1_Fun34_YaaH 176 iiaaflawYnalaglatk 193
                                   ++ ++ a Y+ la ++++
  gi|91772829|ref|YP_565521.1| 179 LLLGISALYTSLALVTNS 196
                                   ***********9988864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); 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):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1177.76
//
Query:       gi|91772830|ref|YP_565522.1|  [L=638]
Description: hydantoinase/oxoprolinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-32  111.1   0.8    4.7e-27   94.8   0.1    3.3  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
      5e-31  108.0   0.4    3.2e-29  102.1   0.0    2.4  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    4.9e-08   32.0   1.1      0.002   16.8   0.2    2.4  2  MutL            MutL protein
  ------ inclusion threshold ------
       0.01   15.3   0.3       0.83    9.1   0.1    2.6  3  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
      0.018   15.2   0.0       0.32   11.2   0.0    2.5  2  DprA_WH         DprA winged helix domain
      0.031   13.5   0.1      0.074   12.3   0.1    1.6  1  StbA            StbA protein
      0.046   13.5   0.0       0.11   12.2   0.0    1.6  1  Sda             Sporulation inhibitor A
       0.15   11.5   0.1       0.28   10.6   0.1    1.4  1  ROK             ROK family


Domain annotation for each model (and alignments):
>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.1   2.1e-30   4.7e-27       2     176 ..       5     158 ..       4     160 .. 0.91
   2 !   10.2   0.1    0.0002      0.45       2      19 ..     257     274 ..     256     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2.1e-30
                    Hydant_A_N   2 igIDvGGTfTDavaldeke.eevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaL 81 
                                   +gID+GGT+TDa+++++ +  +v + K+l+t  + +egir+a++   e+     +++dv+ ++TT+atN++le +g +v+L
  gi|91772830|ref|YP_565522.1|   5 LGIDAGGTYTDAILISDSDrSVVMSNKALTTYPDHIEGIRNAIDGIDEKYL---KNVDVISVSTTLATNTVLEDTGYPVGL 82 
                                   79*************98887888999*******************988865...6************************** PP

                    Hydant_A_N  82 ittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhSyl 162
                                   i + ++                        +++++++v +++++ g++lkpld +++++ +   k + v+++av++ +S +
  gi|91772830|ref|YP_565522.1|  83 ILIGDHSLNK------------------NFPTSDIIFVAGGHDHMGDELKPLDVDAIKNFVLGSKGR-VSAFAVSSHFSIR 144
                                   *998765332..................2356788******************************98.************* PP

                    Hydant_A_N 163 npehElrvaeiare 176
                                   npehEl+ ++++++
  gi|91772830|ref|YP_565522.1| 145 NPEHELKTKQLISK 158
                                   **********9987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0002
                    Hydant_A_N   2 igIDvGGTfTDavaldek 19 
                                   + IDvGGT TD+ +l+e+
  gi|91772830|ref|YP_565522.1| 257 VVIDVGGTSTDVSMLSEG 274
                                   78**********999976 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.015        33      82     105 ..       5      28 ..       2      46 .. 0.81
   2 !  102.1   0.0   1.4e-32   3.2e-29       1     145 [.     179     320 ..     179     333 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.015
                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsl 105
                                   +++D GGT tD++li+d    v++
  gi|91772830|ref|YP_565522.1|   5 LGIDAGGTYTDAILISDSDRSVVM 28 
                                   578*************88766655 PP

  == domain 2  score: 102.1 bits;  conditional E-value: 1.4e-32
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   r++ta++nA l p+ ++++e + ++++ r++ arl+++++dG++v +++a ++p+eti SGPaa+++ga+    l g +++
  gi|91772830|ref|YP_565522.1| 179 RAVTAYLNAQLLPVGENFIEAMISEIKRRDMDARLLMLKCDGSVVGIRDALERPIETIFSGPAASLIGASF---LSGLESC 256
                                   899*******************************************************************9...99***** PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpe 145
                                   +++D+GGTstDvs +++g + +s +  + ++ ++r++a++++t ++gG+s +++++ + l +gp+
  gi|91772830|ref|YP_565522.1| 257 VVIDVGGTSTDVSMLSEGVPDISEAGAViGKWQTRVKAIHMETSAMGGDSHIWTKD-NDLFIGPR 320
                                   **********************999877699*********************8888.55557776 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2     9e-07     0.002       2      57 ..       5      56 ..       4      72 .. 0.82
   2 !   13.7   0.0     8e-06     0.018     222     274 ..     234     281 ..     221     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9e-07
                          MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgk 57
                                  l iD G t+T ++l+++++   +++ + +a+Tt    d  eG+++a++ + ek  k
  gi|91772830|ref|YP_565522.1|  5 LGIDAGGTYTDAILISDSD--RSVVMSNKALTTYP--DHIEGIRNAIDGIDEKYLK 56
                                  569**************66..*************6..889**********999653 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8e-06
                          MutL 222 aeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekekv 274
                                   ++i   PaA l ++++l+      l+ ++v+DvGG++Tdv   +eg p++++ 
  gi|91772830|ref|YP_565522.1| 234 ETIFSGPAASLIGASFLSG-----LESCVVIDVGGTSTDVSMLSEGVPDISEA 281
                                   5678889999999999998.....5689*************999999988765 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 ?    9.1   0.1   0.00037      0.83       1      29 [.       5      34 ..       5     101 .. 0.80
   2 ?    3.6   0.0     0.017        38       3      30 ..     259     304 ..     257     358 .. 0.68
   3 ?   -2.4   0.0       1.2   2.6e+03     220     264 ..     503     540 ..     489     541 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00037
                                  EEEEE-SSEEEEEEEETTTE.EEEEEEE-- CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmdekge.vlgrgitns 29
                                  +GiD G+T t a+l+ ++   v+   ++ +
  gi|91772830|ref|YP_565522.1|  5 LGIDAGGTYTDAILISDSDRsVVMSNKALT 34
                                  8*************9988776666655554 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
                                   EEE-SSEEEEEEEE.......TTTEEEEEEEE--...........T CS
                   BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitns...........a 30 
                                   iD+G+T+t +  +        e g v+g+++t              
  gi|91772830|ref|YP_565522.1| 259 IDVGGTSTDVSMLSegvpdisEAGAVIGKWQTRVkaihmetsamgG 304
                                   9********9999889999999999999999988555555555550 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                   EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHH CS
                   BcrAD_BadFG 220 vtltGGvakneaavkelrklvkenygevkininpdsiytgalGAa 264
                                   v++ GG  ++      +r+ v++ +   +i ++++s++  a GA+
  gi|91772830|ref|YP_565522.1| 503 VVFIGGPVSA------YRDEVSSFIKA-DIIVPKYSDVGNAAGAL 540
                                   6677776666......88888877766.89999999999999996 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.32       4      32 ..     364     392 ..     361     400 .. 0.85
   2 ?    1.1   0.0      0.19   4.3e+02      11      28 ..     406     423 ..     395     427 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                       DprA_WH   4 ppaepplddlerrvLaaLgpePvhvDqLv 32 
                                   ++ + +l ++e  +L+ +g +P+++D+++
  gi|91772830|ref|YP_565522.1| 364 RQEPMELNEDENMILSVIGDDPLSFDDIS 392
                                   56677899*******************97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                       DprA_WH  11 ddlerrvLaaLgpePvhv 28 
                                   +   +r+++a+g++P+ v
  gi|91772830|ref|YP_565522.1| 406 SLISKRLVQAIGFTPTDV 423
                                   56789999******9975 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.3e-05     0.074     150     189 ..     240     280 ..     233     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                          StbA 150 Pagfealke.ldeleslLiiDlGGttLDvakvrgklegisk 189
                                   Pa+    ++ l+ les ++iD+GGt  Dv+ +   + +is+
  gi|91772830|ref|YP_565522.1| 240 PAASLIGASfLSGLESCVVIDVGGTSTDVSMLSEGVPDISE 280
                                   5555555556999*****************99988888886 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     5e-05      0.11      12      38 ..     183     209 ..     178     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                           Sda  12 aYekAlelnLdpDFIeLieeEierRsL 38 
                                   aY +A+ l + + FIe +  Ei+rR +
  gi|91772830|ref|YP_565522.1| 183 AYLNAQLLPVGENFIEAMISEIKRRDM 209
                                   899**********************86 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00012      0.28       2      61 ..       5      64 ..       4      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                  EEEEE-SSEEEEEEE.ETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEE CS
                           ROK  2 igidiGgtkialalv.deegeilarekvetptetteetlvdaiaelvdeaerkadeliavg 61
                                  +gid+Ggt++ ++l+ d+++ ++ ++k  t+ ++  e++++ai+ + +++ +++d +i+v+
  gi|91772830|ref|YP_565522.1|  5 LGIDAGGTYTDAILIsDSDRSVVMSNKALTTYPDHIEGIRNAIDGIDEKYLKNVD-VISVS 64
                                  69********999873667888888888899999999999999998888877775.66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 3625.42
//
Query:       gi|91772831|ref|YP_565523.1|  [L=381]
Description: cobalamin synthesis protein, P47K [Methanococcoides burtonii DSM 6242]
Scores for complete 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  126.1   0.6    1.9e-36  125.3   0.6    1.4  1  cobW      CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.012   15.7   3.7      0.075   13.1   3.7    2.6  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
      0.016   14.9   0.5      0.044   13.4   0.5    1.8  1  SRP54     SRP54-type protein, GTPase domain
      0.028   13.4   2.4       0.05   12.6   0.3    2.3  2  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.11   12.5   0.7       0.35   10.8   0.2    2.1  2  MobB      Molybdopterin guanine dinucleotide synthesis protei


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 !  125.3   0.6   5.2e-40   1.9e-36       2     176 ..       3     179 ..       2     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 5.2e-40
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeere 80 
                                   +++++GflGsGKTt + ++      +g+k+a+ivNe+ge++iD++++++ g  + e++nGciCc+l+  l  ++  l + +
  gi|91772831|ref|YP_565523.1|   3 TLIVGGFLGSGKTTTIINTGkyLVDKGYKVAIIVNEIGEIGIDGDIIKKFGFDTKEITNGCICCSLKMGLRSTVITLFNSY 83 
                                   579**********9999988777889******************************************************* PP

                                   TT-SEEEEEECTTTTHHHH..HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..H CS
                          cobW  81 erldviliEttGlaePapv..afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeall 159
                                    ++dv++iE tG+a P+ +   ++  +l + +++  +v+++D++++++  ++ ++   +q++ a++l +nK+Dl+d+ + +
  gi|91772831|ref|YP_565523.1|  84 -NPDVLIIEPTGIAFPNLIkrEIELMDLGEGAEIAPLVTLIDGSRFKHILKEMKNFSTRQIEDAEILAINKIDLMDKIQ-I 162
                                   .9*****************54444889999****************99999999999*********************6.5 PP

                                   HHHHHHHHHHHTTS-EE CS
                          cobW 160 ekleerlrqlnpeakvl 176
                                     +ee ++qln++akv+
  gi|91772831|ref|YP_565523.1| 163 PIIEESVQQLNRKAKVI 179
                                   **************997 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 ?   13.1   3.7   2.1e-05     0.075       4      33 ..       6      35 ..       3     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                  EESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  4 astkGGvGKTtlaanLaralarrglrVllv 33
                                  +++  G+GKTt+ +n +++l ++g++V+ +
  gi|91772831|ref|YP_565523.1|  6 VGGFLGSGKTTTIINTGKYLVDKGYKVAII 35
                                  555669*********************987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   1.2e-05     0.044       4      35 ..       4      35 ..       1      39 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                  +++ G+ G+GKTtt+    ++l ++g+kv+++
  gi|91772831|ref|YP_565523.1|  4 LIVGGFLGSGKTTTIINTGKYLVDKGYKVAII 35
                                  4556899**********************998 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 ?   12.6   0.3   1.4e-05      0.05      34      64 ..       6      36 ..       2      49 .. 0.91
   2 ?   -0.0   0.1     0.099   3.5e+02     165     178 ..     142     155 ..      68     187 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEEE CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavla 64
                                  + G+ G+Gk t++ + g  l+++G++va++ 
  gi|91772831|ref|YP_565523.1|  6 VGGFLGSGKTTTIINTGKYLVDKGYKVAIIV 36
                                  67999************************95 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.099
                                   CHHH-SEEEEE--- CS
                          MeaB 165 ileiaDiivvnkaD 178
                                    +e a+i+++nk D
  gi|91772831|ref|YP_565523.1| 142 QIEDAEILAINKID 155
                                   34555666666666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   9.8e-05      0.35       3      39 ..       5      41 ..       2      55 .. 0.85
   2 ?   -2.2   0.0      0.97   3.5e+03      55      81 ..     225     251 ..     213     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.8e-05
                          MobB  3 givgksgsGKTtLleklipelkarglrvgtiKhahhg 39
                                   + g+ gsGKTt + +  + l ++g++v++i  +  +
  gi|91772831|ref|YP_565523.1|  5 IVGGFLGSGKTTTIINTGKYLVDKGYKVAIIVNEIGE 41
                                  455889***********************99766555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.97
                          MobB  55 AGAkevlvaskerlalikeleeaelsl 81 
                                   A A+    +sk+ + li++ +e+e s+
  gi|91772831|ref|YP_565523.1| 225 APANGLSFVSKKDMELIRDEQETESSI 251
                                   556667778888888888877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2105.00
//
Query:       gi|91772832|ref|YP_565524.1|  [L=55]
Description: hypothetical protein Mbur_0819 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.35s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 312.12
//
Query:       gi|91772833|ref|YP_565525.1|  [L=519]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-34  117.6   0.2    1.8e-33  115.4   0.0    2.2  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    9.5e-29  100.5   0.0    5.9e-28   97.9   0.0    2.0  2  GAF_2          GAF domain
    1.1e-15   57.4   0.1    1.1e-15   57.4   0.1    2.5  3  HisKA          His Kinase A (phospho-acceptor) domain
    2.6e-07   30.9   0.3    8.3e-07   29.2   0.0    2.0  2  PAS_9          PAS domain
    3.4e-05   23.7   0.0    0.00011   22.0   0.0    1.8  1  HATPase_c_5    GHKL domain
    0.00021   21.3   0.0    0.00078   19.4   0.0    2.1  2  PAS            PAS fold
    0.00044   20.6   0.0     0.0012   19.2   0.0    1.7  1  GAF_3          GAF domain
    0.00052   19.8   0.0     0.0032   17.3   0.0    2.2  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
     0.0015   18.7   0.0     0.0035   17.6   0.0    1.7  1  PAS_4          PAS fold
     0.0048   16.9   0.1      0.023   14.7   0.0    2.1  2  HATPase_c_2    Histidine kinase-like ATPase domain
     0.0052   15.5   0.4     0.0076   15.0   0.4    1.2  1  WEMBL          Weak chloroplast movement under blue light
     0.0075   16.9   0.0      0.014   16.1   0.0    1.4  1  GAF            GAF domain
  ------ inclusion threshold ------
       0.11   11.6   0.6       0.21   10.7   0.6    1.5  1  Phyto_Pns9_10  Phytoreovirus nonstructural protein Pns9/Pns10
       0.13   11.9   2.5       0.28   10.8   2.5    1.5  1  DUF4795        Domain of unknown function (DUF4795)


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 ?   -1.0   0.1       1.9   2.4e+03      28      46 ..     371     393 ..     343     401 .. 0.65
   2 !  115.4   0.0   1.4e-36   1.8e-33       1     109 [.     409     518 ..     409     519 .] 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                                   EEEEEEEE......TEEEEEEEESS CS
                     HATPase_c  28 eveikase......ddlvisveDnG 46 
                                   +v+i   e      +d+ +++eD G
  gi|91772833|ref|YP_565525.1| 371 KVRIA--EiidnvvNDVNLQIEDKG 393
                                   34444..222335678888888887 PP

  == domain 2  score: 115.4 bits;  conditional E-value: 1.4e-36
                                   EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHH CS
                     HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsi 80 
                                   gd+ rL  ++ nlvdNa+kf++++g+i ++   +eddl+i+v+D+GiGipke +++lf++f+q d+s kr++ggtG+Gl+i
  gi|91772833|ref|YP_565525.1| 409 GDKARLSDMLTNLVDNAIKFTPSEGRIILNAYEEEDDLHIEVKDTGIGIPKELIPNLFQRFYQvDASIKRRYGGTGVGLYI 489
                                   7999***************95555555555553669********************************************* PP

                                   HHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlp 109
                                   +k++ve ++G+iw+ese+++Gtt++++lp
  gi|91772833|ref|YP_565525.1| 490 CKNIVEAHKGNIWIESEEEKGTTVHIRLP 518
                                   **************************998 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   4.6e-31   5.9e-28       2     138 .]     117     260 ..     116     260 .. 0.94
   2 ?    0.0   0.0      0.74   9.5e+02       3      36 ..     413     448 ..     411     479 .. 0.74

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 4.6e-31
                                   HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEES-GG CS
                         GAF_2   2 adleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrpl.....geglvgealrtgrpvilndle 75 
                                   ++++ ++d++ +e+v+l+ +++gyi++v++d++ l++++w++a +  +   d+p+       gl+gealr+++p+i nd+ 
  gi|91772833|ref|YP_565525.1| 117 RSMQKIVDFAREEAVRLTqSQVGYIAFVNEDESvLTMHSWSQAAMLECKIRDKPIvytlkTTGLWGEALRQRKPIITNDYN 197
                                   78999***********955**********998889999*********9999997788998888****************55 PP

                                   G.-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                         GAF_2  76 e.dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                     +p kkg+p +h +l +++ +P+++++rvv+v ++ +nk++++de+d+++L++l+e ++++i+
  gi|91772833|ref|YP_565525.1| 198 VpNPLKKGYPKDHMKLTRHMNIPVFDGERVVAVAGV-GNKDEEYDESDVRQLTLLMEGMWRIIQ 260
                                   55************************99*******8.89999*******************996 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.74
                                   HHHHHHHHHHHHHHHSS....EEEEEEE-TTS-EEE CS
                         GAF_2   3 dleelldlvldelvelg.aa.lgyillvdddgglrl 36 
                                    l+++l +++d +++++ ++   ++  ++++++l++
  gi|91772833|ref|YP_565525.1| 413 RLSDMLTNLVDNAIKFTpSEgRIILNAYEEEDDLHI 448
                                   6899***********965883334444777777444 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   0.1       6.9   8.9e+03      42      65 ..     106     129 ..     101     131 .. 0.59
   2 ?   -2.5   0.1       4.2   5.4e+03      35      54 ..     266     285 ..     250     293 .. 0.52
   3 !   57.4   0.1   8.8e-19   1.1e-15       1      66 [.     295     362 ..     295     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.9
                                   HHHHHHHHHHHHHHHHHHHHCCHH CS
                         HisKA  42 etiesearrldhlvedlLdlsrie 65 
                                   et+ +  +  d+  + + d++r+e
  gi|91772833|ref|YP_565525.1| 106 ETLLQLNQMTDRSMQKIVDFAREE 129
                                   445555555555566666666666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                   SSCHHHHHHHHHHHHHHHHH CS
                         HisKA  35 eelkeyletiesearrldhl 54 
                                   e l++y + + +  + l+++
  gi|91772833|ref|YP_565525.1| 266 EALQKYANELSEVNKELEKV 285
                                   44444444444444444444 PP

  == domain 3  score: 57.4 bits;  conditional E-value: 8.8e-19
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                   ++++fl++++HEL+tPL +i+g++e+  +   g l+e++k++++++ ++++rl++l+e lL +s +e+
  gi|91772833|ref|YP_565525.1| 295 MKNEFLSNISHELKTPLVSIKGYVELVFDGslGTLNEQQKKAVNIVLRNSERLRRLIESLLFISGLES 362
                                   689************************888999****************************9997775 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   6.5e-10   8.3e-07      13     103 ..       2      89 ..       1      90 [. 0.94
   2 ?   -2.7   0.0       5.4   6.9e+03      43      70 ..     261     286 ..     252     297 .. 0.52

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.5e-10
                         PAS_9  13 ilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelv 93 
                                   i+++N+++l+++  s+++v+g ++ + +  d++ ++ ++a+l ++    + +   ++  +g+ +++++   p ++++g+l 
  gi|91772833|ref|YP_565525.1|   2 ITHCNDKFLEIISASRKDVIGFNMATSI-RDEKMRDAVKAVLSRKP--GHYEGKYCTVISGKVIFIKADYNPNISEEGTLL 79 
                                   78**************************.88888888888898888..999999*************************** PP

                         PAS_9  94 giivilrDit 103
                                   g i+i++Dit
  gi|91772833|ref|YP_565525.1|  80 GGIGIFEDIT 89 
                                   *********9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                         PAS_9  43 dpeanerlraaleqgrkkerevevvlir 70 
                                    ++++e l+++ ++++  e ++e++ ++
  gi|91772833|ref|YP_565525.1| 261 RKQSEEALQKYANELS--EVNKELEKVN 286
                                   3344444444444444..5555544444 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.7e-08   0.00011       6      92 ..     414     508 ..     410     517 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.7e-08
                   HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..........ek..kklesskskkeehGiGlksi 74 
                                   l+ +l nl dNAi         +  I l++ e++++l i+++ +  g          +   +   s k++ +  G+Gl   
  gi|91772833|ref|YP_565525.1| 414 LSDMLTNLVDNAIKFTPS----EGRIILNAYEEEDDLHIEVKDTGIGipkelipnlfQRfyQVDASIKRRYGGTGVGLYIC 490
                                   777899*****9976544....66899*****************777666555544321445555889999********** PP

                   HATPase_c_5  75 reivkkykgnlsieaedg 92 
                                   ++iv+ +kgn++ie e++
  gi|91772833|ref|YP_565525.1| 491 KNIVEAHKGNIWIESEEE 508
                                   *************99875 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.1e-07   0.00078      23     113 .]       2      88 ..       1      88 [. 0.96
   2 ?   -3.8   0.0       9.9   1.3e+04      28      43 ..     117     132 ..     115     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.1e-07
                                   EEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEE CS
                           PAS  23 ilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggei 103
                                   i+++N+++ e+   sr++v+g ++  +i  e+   ++++++ +l+ +     g+ +     g++i +    +p ++++g++
  gi|91772833|ref|YP_565525.1|   2 ITHCNDKFLEIISASRKDVIGFNMATSIRDEK---MRDAVKAVLSRKPGHYEGKYCTVI-SGKVIFIKADYNPNISEEGTL 78 
                                   89**************************9885...9********999999999999999.********************* PP

                                   EEEEEEEEES CS
                           PAS 104 lgflgvlrdi 113
                                   lg +g++ di
  gi|91772833|ref|YP_565525.1|  79 LGGIGIFEDI 88 
                                   *******998 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.9
                                   HHHHHHHSSTHHHCTT CS
                           PAS  28 aaaeellGlsreevlg 43 
                                   ++++++  ++ree+++
  gi|91772833|ref|YP_565525.1| 117 RSMQKIVDFAREEAVR 132
                                   7899999999999875 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.1e-07    0.0012       1     120 [.     118     252 ..     118     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.1e-07
                         GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse........sld.edsalarralssgevvsepsf 72 
                                   s++++++ + +++v+l++++vg +  ++ed +++ ++++w +++ l e        + + + + l+ +al ++ +++++++
  gi|91772833|ref|YP_565525.1| 118 SMQKIVDFAREEAVRLTQSQVGYIAFVNED-ESVLTMHSWSQAAML-EckirdkpiVYTlKTTGLWGEALRQRKPIITNDY 196
                                   6899********************999977.7777*****444444.4577777443336777778888888888888666 PP

                         GAF_3  73 ae.........edglpdraalavPLvagrqviGvlalastkprafdaedlelleslA 120
                                              +d + ++  + +P+ +g++v+ v +++ ++ +++d++d++ l  l+
  gi|91772833|ref|YP_565525.1| 197 NVpnplkkgypKDHMKLTRHMNIPVFDGERVVAVAGVGNKD-EEYDESDVRQLTLLM 252
                                   33222222222355777888*****************9977.55*******999987 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 !   17.3   0.0   2.5e-06    0.0032       7      77 ..     418     487 ..     413     494 .. 0.83
   2 ?   -0.8   0.0      0.98   1.3e+03      10      34 ..     489     513 ..     487     517 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-06
                   HATPase_c_3   7 laelvdNsldAdaenvkievnknr.gktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGl 77 
                                   l+ lvdN++     +  i +n  + +++  i ++D G G+++e + n + r+ + + +    ++ +G  G+Gl
  gi|91772833|ref|YP_565525.1| 418 LTNLVDNAIKFTPSEGRIILNAYEeEDDLHIEVKDTGIGIPKELIPNLFqRFYQVDAS---IKRRYGGTGVGL 487
                                   889*******8888888888866646789******************88358888877...578899999995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.98
                   HATPase_c_3  10 lvdNsldAdaenvkievnknrgktg 34 
                                   +++N ++A+  n+ ie ++++g t 
  gi|91772833|ref|YP_565525.1| 489 ICKNIVEAHKGNIWIESEEEKGTTV 513
                                   799**************99986544 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.8e-06    0.0035      17     110 .]       2      93 ..       1      93 [. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-06
                         PAS_4  17 vlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevi 96 
                                   ++++N  + e++ a++++++G  +a        +  ++a+++vl+ +  +++  + +  +g+  ++   ++P   e+G+ +
  gi|91772833|ref|YP_565525.1|   2 ITHCNDKFLEIISASRKDVIGFNMATSI---RDEKMRDAVKAVLSRKPGHYEGKYCTViSGKVIFIKADYNPNISEEGTLL 79 
                                   689*********************9533...56899999999**999999998888889********************** PP

                         PAS_4  97 gvlvisrDiTerrr 110
                                   g ++i+ DiT+r++
  gi|91772833|ref|YP_565525.1|  80 GGIGIFEDITRRKE 93 
                                   ***********985 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.5     2e+03       7      52 ..     343     390 ..     341     404 .. 0.67
   2 !   14.7   0.0   1.8e-05     0.023      39     124 ..     417     516 ..     411     517 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                   HATPase_c_2   7 hvrtvrevaeavlrraglseelld....eirlaveEactNavehayleap 52 
                                   +++ +r+ +e++l  +gl++++++    +  + ++E++ N+v+  +l+ +
  gi|91772833|ref|YP_565525.1| 343 NSERLRRLIESLLFISGLESRAIQyhieK--VRIAEIIDNVVNDVNLQIE 390
                                   56667888888888888888887765333..4456888887776555555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.8e-05
                   HATPase_c_2  39 actNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikglvDev 112
                                   ++tN v  a +  p eg++ + +  +e+ l++ev+D G g + e +p+  +  +      k      G+Gl++ k++v+  
  gi|91772833|ref|YP_565525.1| 417 MLTNLVDNAIKFTPsEGRIILNAYEEEDDLHIEVKDTGIGIPKELIPNLFQRFYqvdasiKRRYGGTGVGLYICKNIVEAH 497
                                   8999999999999*99************************999988877664449999999999999************99 PP

                   HATPase_c_2 113 ..ey.....dgegnvvtms 124
                                     ++     +++g++v+++
  gi|91772833|ref|YP_565525.1| 498 kgNIwieseEEKGTTVHIR 516
                                   6633678788889999886 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   5.9e-06    0.0076     288     341 ..     261     315 ..     233     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.9e-06
                         WEMBL 288 etsikealasarkELeevkaniekakdevklLkvaaasLrseLeke.kaeLaslr 341
                                   +++ +eal++  +EL ev++++ek++d++k+L v+ + + s++++e k+ L+s++
  gi|91772833|ref|YP_565525.1| 261 RKQSEEALQKYANELSEVNKELEKVNDDLKSLDVMKNEFLSNISHElKTPLVSIK 315
                                   5678899*****************************9999999998677777776 PP

>> GAF  GAF 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     0.014       2     123 ..     119     249 ..     118     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHHHHHHTESEEEE.EE.EEETTEEECEEEEECC..........EEEETTSHHHHHHHHHSSSEEESTGG.T CS
                           GAF   2 leelldtvveelrellgadrval.yl.pdydGlhydipqasrw..........lfmkngrgicgqvlatgqplvipdst.p 69 
                                   +++++d + ee+ +l++ + + + +  +d++ l+ +   +++           +++   +g+ g++l++++p++ +d+  p
  gi|91772833|ref|YP_565525.1| 119 MQKIVDFAREEAVRLTQSQVGYIaFVnEDESVLTMHSWSQAAMleckirdkpiVYTLKTTGLWGEALRQRKPIITNDYNvP 199
                                   6788888899999999999988844432222232233333333355543333333333666777************97657 PP

                                   STTHHTT.HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHH CS
                           GAF  70 dprfaqy.nrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreelellq 123
                                    p    y +     ++m     + +P++++++++++  + n+++++++++++ l+
  gi|91772833|ref|YP_565525.1| 200 NPLKKGYpK-----DHMKLTRHMNIPVFDGERVVAVAGVGNKDEEYDESDVRQLT 249
                                   777666553.....68999999999****************88899999988775 PP

>> Phyto_Pns9_10  Phytoreovirus nonstructural protein Pns9/Pns10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00017      0.21     153     292 ..     293     431 ..     260     454 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                 Phyto_Pns9_10 153 yvlrtkrlskilkeyytaleeveayleklpddskdsllnqkskevlrvifsnakvliatkinkyvtlyedsyley.vreva 232
                                    v++ + ls+i +e  t l  ++ y+e + d s ++l +q+ k v  v+ ++ + +   +  ++++  e    +y + +v 
  gi|91772833|ref|YP_565525.1| 293 DVMKNEFLSNISHELKTPLVSIKGYVELVFDGSLGTLNEQQKKAVNIVLRNSERLRRLIESLLFISGLESRAIQYhIEKVR 373
                                   58889999****************************988877777666555555555555557888777666555155554 PP

                 Phyto_Pns9_10 233 .eyvadlwdvqtttntqghenelaaedfGvlaalsqmdttddelgdsviksdGvevklepa 292
                                      + d  +v   +n q  ++ l  e+  v+  l+ +++ +  l+d ++    + +k+ p+
  gi|91772833|ref|YP_565525.1| 374 iAEIID--NVVNDVNLQIEDKGLLIEN-NVPENLPLINGDKARLSDMLTNLVDNAIKFTPS 431
                                   555666..888999***9999999986.6*****************999988888888874 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.5   0.00022      0.28      37     130 ..     258     373 ..     240     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                       DUF4795  37 ledkekklealkkqieelekvkadkeeveeel.aekadkeaLatkvsrdq..............fDeakkeLekmleelle 102
                                   + +++++ eal+k+++el +v+++ e+v++ l ++ + k+   + +s++               fD ++  L+++ +++++
  gi|91772833|ref|YP_565525.1| 258 IIQRKQSEEALQKYANELSEVNKELEKVNDDLkSLDVMKNEFLSNISHELktplvsikgyvelvFDGSLGTLNEQQKKAVN 338
                                   4456666788888888888888888888887755778888888888888888888888888888***************** PP

                       DUF4795 103 kleeqeealkkaldtLq.......eelkekldrle 130
                                    +  ++e+l+++++ L        ++++  ++++ 
  gi|91772833|ref|YP_565525.1| 339 IVLRNSERLRRLIESLLfisglesRAIQYHIEKVR 373
                                   **************998775555544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1505  (0.0839422); expected 358.6 (0.02)
Passed bias filter:                      937  (0.0522617); 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):              14  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 3299.45
//
Query:       gi|91772834|ref|YP_565526.1|  [L=232]
Description: signal transduction ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  116.2   0.0      2e-33  115.7   0.0    1.1  1  ATPase    KaiC
      3e-05   23.7   0.0    4.2e-05   23.2   0.0    1.2  1  AAA_25    AAA domain
    0.00042   19.1   0.2    0.00056   18.6   0.2    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 !  115.7   0.0   3.3e-37     2e-33       5     228 ..       7     228 ..       5     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 3.3e-37
                        ATPase   5 IeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklai 85 
                                   I glD+i++  ip+g+v+litG+pG+ K+ +    l k +e++ge g ++t+e+++ +   n+ks+G +l    ++  l i
  gi|91772834|ref|YP_565526.1|   7 IDGLDDIFSTDIPKGSVILITGVPGSLKSGITFSILSKYLENVGEFGTYITLEQSKDNHLANMKSMGLELS---DN--LSI 82 
                                   99*****************************************************************9875...45..899 PP

                        ATPase  86 idasesaeesaeekdkedleelieelaeaikeika..krvviDsitgl..ayeekeavaReilrqlvrvlkklgvTailvs 162
                                    d s  + ++ e  + + l  + +++ ++ ++++   ++v +Ds+++l    + ++  +R+ l +l++ l+  ++T+ ++ 
  gi|91772834|ref|YP_565526.1|  83 SDFSDYRLQYDE-FSGDLLTLIETNILQYKQKMGDkfTCVALDSLGALysLLDVEPRDMRKRLYHLFEPLRRENLTTFMIL 162
                                   999999866443.4444444555678888888877678999*******6444567888*********************** PP

                        ATPase 163 ekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvle 228
                                   e s+s + +  ++ e++++dg+i L l+ +++++ R++++ kmR ++hs++ +++++++eg kv+ 
  gi|91772834|ref|YP_565526.1| 163 ETSESLGLNHANNFENYLADGIIELGLHMKDNTTNRYIQVKKMRASEHSMDPFILTVSDEGLKVYR 228
                                   ****************************************************************96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     7e-09   4.2e-05      21     178 ..       9     154 ..       2     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7e-09
                        AAA_25  21 prrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrdda 101
                                    +++++   +p+g+++l++G pg+ K+ ++ ++  ++++    +g          y+ +E+s d+    ++ +g +l   +
  gi|91772834|ref|YP_565526.1|   9 GLDDIFSTDIPKGSVILITGVPGSLKSGITFSILSKYLENVGEFG---------TYITLEQSKDNHLANMKSMGLEL--SD 78 
                                   5677778889****************************9997788.........6*********************9..79 PP

                        AAA_25 102 rllvldlagveslpLfakdrggtlltadvdaleaaieeveg.vrlvviDplsralgg.densnsdv.galvealeriarr 178
                                   +l + d     + +L ++++ g llt    ++ +  +++ +    v +D+l ++++  d +  +d+ ++l+  +e ++r+
  gi|91772834|ref|YP_565526.1|  79 NLSISDF---SDYRLQYDEFSGDLLTLIETNILQYKQKMGDkFTCVALDSLGALYSLlDVE-PRDMrKRLYHLFEPLRRE 154
                                   9999987...568******99999766555666666666667************9996665.555547777777777544 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   9.4e-08   0.00056       9     205 ..      20     217 ..      10     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.4e-08
                          GvpD   9 aGktllikGaPGtGktlftlrgldv.lrresdv.lyvs.trvddetvseayfsgeaeldktalldllkdpleldldvdvPi 86 
                                    G  +li G PG+ k   t   l   l++ ++   y++  +++d+ + ++   g    d+  + d++   l+ d      +
  gi|91772834|ref|YP_565526.1|  20 KGSVILITGVPGSLKSGITFSILSKyLENVGEFgTYITlEQSKDNHLANMKSMGLELSDNLSISDFSDYRLQYDEFSG-DL 99 
                                   588999*********999999997625554443256652678889999998666555556666677766666554332.23 PP

                          GvpD  87 ekldlesllefvdeiaaiatkli.ialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaansrl.... 162
                                    +l    +l++ +   ++++k + +alds   +y  l ++   P d++    +l    r +++   ++let +   l    
  gi|91772834|ref|YP_565526.1| 100 LTLIETNILQYKQ---KMGDKFTcVALDSLGALYSLLDVE---PRDMRKRLYHLFEPLRRENLTTFMILETSESLGLnhan 174
                                   3455567888888...667765439****99999999885...88988888888888899999999999997644332222 PP

                          GvpD 163 ...eyivdGvvtl..nvkeddrgrlrrdlrleklrGvrignrlqPftl 205
                                      +y++dG++ l  ++k++    + r ++++k+r       + Pf l
  gi|91772834|ref|YP_565526.1| 175 nfeNYLADGIIELglHMKDN---TTNRYIQVKKMRASE--HSMDPFIL 217
                                   2226*******998899999...99**********754..44577655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1615.11
//
Query:       gi|91772835|ref|YP_565527.1|  [L=375]
Description: hypothetical protein Mbur_0823 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0044   17.1   0.3       0.33   11.1   0.0    3.0  3  DUF3976   Domain of unknown function (DUF3976)
  ------ inclusion threshold ------
      0.021   12.8   1.4       0.03   12.3   1.4    1.1  1  Med16     Mediator complex subunit 16
       0.15   11.1   3.1        1.2    8.2   0.0    2.3  2  DUF5081   Domain of unknown function (DUF5081)


Domain annotation for each model (and alignments):
>> DUF3976  Domain of unknown function (DUF3976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.9   1.1e+04       6      11 ..     143     148 ..     143     150 .. 0.85
   2 ?    2.5   0.0     0.028   1.7e+02       4      23 ..     168     187 ..     166     188 .. 0.88
   3 !   11.1   0.0   5.5e-05      0.33       7      19 ..     341     353 ..     338     357 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                       DUF3976   6 RKDvtk 11 
                                   RKD++k
  gi|91772835|ref|YP_565527.1| 143 RKDISK 148
                                   9***77 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.028
                       DUF3976   4 FvRKDvtkdnTLTKRGFYKl 23 
                                    +RK v  +  LT+ G Y l
  gi|91772835|ref|YP_565527.1| 168 KIRKLVDANAQLTQQGHYYL 187
                                   69****9999*******965 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 5.5e-05
                       DUF3976   7 KDvtkdnTLTKRG 19 
                                   KD+t +nTLT RG
  gi|91772835|ref|YP_565527.1| 341 KDITAENTLTERG 353
                                   9***********9 PP

>> Med16  Mediator complex subunit 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.4     5e-06      0.03     622     699 ..     281     357 ..     257     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-06
                         Med16 622 dierEkelLvkgeippeleelakvlldrtsisllsevklsalyfydtswLgigedkrfenyvrtllvdii....kktadds 698
                                   + e    lL  ++i++  e+l + +l++  + +++e ++++l   d ++L+i+  + +en  +t++++++    +      
  gi|91772835|ref|YP_565527.1| 281 ESEDNVLLLALSRILNMNENLHTRILNCLYVGIKEEKDMANLLYIDPHELEISMREMMENKDITAENTLTergiE-----T 356
                                   334445567778*******************************************************99922220.....2 PP

                         Med16 699 i 699
                                   +
  gi|91772835|ref|YP_565527.1| 357 V 357
                                   2 PP

>> DUF5081  Domain of unknown function (DUF5081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0002       1.2      34      73 ..     153     192 ..     132     197 .. 0.88
   2 ?    2.6   1.0      0.01        61      95     174 ..     283     370 ..     272     374 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0002
                       DUF5081  34 lLldeevleeakeaLkeKgllteeekltdagfkviellke 73 
                                   +  d ev++ a+ +Lk + l+  + +lt+ g++ +e++ke
  gi|91772835|ref|YP_565527.1| 153 ISNDMEVIKRAFGTLKIRKLVDANAQLTQQGHYYLETIKE 192
                                   5568899****************************99998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.01
                       DUF5081  95 kdelvll..vei.epnkkyqleiinKlva.lkslldeiPlllRepkeneteF...l.kkkltneerktaeeldlkknvlei 167
                                   +d+++ll  ++i + n++ + +i+n l++  k+ +d   ll  +p+e e      + +k +t e+  t   +++ k  l+i
  gi|91772835|ref|YP_565527.1| 283 EDNVLLLalSRIlNMNENLHTRILNCLYVgIKEEKDMANLLYIDPHELEISMremMeNKDITAENTLTERGIETVKHTLKI 363
                                   555554311555255777778888877763566677788888888888866511021344555566667778888888888 PP

                       DUF5081 168 Eiykree 174
                                   E   r+e
  gi|91772835|ref|YP_565527.1| 364 EKISRQE 370
                                   8777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2662.80
//
Query:       gi|91772836|ref|YP_565528.1|  [L=333]
Description: hypothetical protein Mbur_0824 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   1.6      2e-46  157.1   0.3    1.7  2  DUF835    Protein of unknown function (DUF835)
    3.2e-12   46.6   2.6    4.5e-09   36.5   0.6    2.6  2  PAS_9     PAS domain
    1.7e-08   34.7   0.0      0.003   17.8   0.0    3.2  4  PAS_4     PAS fold
    9.8e-08   32.0   0.1    3.8e-06   26.9   0.1    3.1  2  PAS       PAS fold
    2.2e-06   27.5   0.9    4.1e-05   23.5   0.1    2.9  3  PAS_8     PAS domain
    9.8e-06   25.7   0.6      0.031   14.4   0.0    4.0  3  PAS_7     PAS fold
    0.00049   20.7   0.6      0.015   15.9   0.3    3.0  2  PAS_10    PAS domain
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.027   14.5   0.2    1.6  1  SpoVT_C   Stage V sporulation protein T C-terminal, transcrip
       0.24   11.5   0.0        0.4   10.8   0.0    1.3  1  MLTR_LBD  MmyB-like transcription regulator ligand binding do


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 ?   -2.7   0.0       2.2   4.4e+03      95     111 ..      79      95 ..      57     113 .. 0.64
   2 !  157.1   0.3     1e-49     2e-46       6     136 .]     190     322 ..     186     322 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.2
                        DUF835  95 esvlkflltlkDavllk 111
                                   e+ +++l + +D ++ +
  gi|91772836|ref|YP_565528.1|  79 EKAMDLLGYANDEIIGN 95 
                                   34555555555655555 PP

  == domain 2  score: 157.1 bits;  conditional E-value: 1e-49
                        DUF835   6 ekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkvee..entvsPtnlekltetivkflkeaekgvvliDg 84 
                                   + +++i+s++vk+g+++l+itRenp kir+k++i+++++iwltk+++  + +++Pt+l kl+ ti++f+k+ ++g+vliDg
  gi|91772836|ref|YP_565528.1| 190 NASYDIFSTMVKQGRPGLCITRENPAKIRSKYNITKTPIIWLTKTKTseYPSIDPTELFKLHPTIENFIKKVNDGIVLIDG 270
                                   56789***************************************9963477****************************** PP

                        DUF835  85 leyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136
                                   leyL+len+ +sv+kf+++++D++++++++lil+id+ ++++k+++lLkr++
  gi|91772836|ref|YP_565528.1| 271 LEYLILENDLKSVIKFMEQTNDTIMVSDSRLILQIDPLIFDTKDHHLLKRWM 322
                                   **************************************************98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00054       1.1      68     103 ..       3      38 ..       1      39 [. 0.90
   2 !   36.5   0.6   2.3e-12   4.5e-09       4     104 .]      65     154 ..      62     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00054
                         PAS_9  68 lirkngetfwvlltaspvkdddgelvgiivilrDit 103
                                   +i+k+g++     +++ +kd++g+ +gii+  +Dit
  gi|91772836|ref|YP_565528.1|   3 IITKSGQKKVLSWNVIKLKDNNGKTTGIICSGEDIT 38 
                                   67889988888999*********************9 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2.3e-12
                         PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltasp 84 
                                   +++ + + +i+ aNe+a++llGy  +e++g +i++++     +n++l ++ +  +       ++l +k+ge + +++  s+
  gi|91772836|ref|YP_565528.1|  65 TIVLDREQNIVTANEKAMDLLGYANDEIIGNPISTII-----SNNELLEFTDKND-----LSIELLKKDGECIDANIATSA 135
                                   445557778****************************.....6666666666666.....99***************9999 PP

                         PAS_9  85 vkdddgelvgiivilrDite 104
                                   ++d+ ++ +g+iv+l+Di+e
  gi|91772836|ref|YP_565528.1| 136 IMDN-NNHKGLIVTLQDISE 154
                                   9765.688999*******98 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   6.7e-05      0.13      75     109 ..       7      41 ..       2      42 .. 0.92
   2 !   17.8   0.0   1.5e-06     0.003       5      40 ..      62      97 ..      60     108 .. 0.91
   3 ?   -2.1   0.0       2.2   4.5e+03      13      26 ..     122     135 ..     116     150 .. 0.81
   4 ?   -0.9   0.0      0.96   1.9e+03      96     109 ..     143     156 ..     133     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                         PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                   +g+ ++++++++ l+d +G++ g+++ + DiT r+
  gi|91772836|ref|YP_565528.1|   7 SGQKKVLSWNVIKLKDNNGKTTGIICSGEDITPRK 41 
                                   68999***************************986 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.5e-06
                         PAS_4  5 pdalavldpdgrvlyaNaaaaelfgappeellGktl 40
                                  p a++vld++++++ aN+ a++l+g++ +e++G + 
  gi|91772836|ref|YP_565528.1| 62 PIATIVLDREQNIVTANEKAMDLLGYANDEIIGNPI 97
                                  7899*****************************886 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.2
                         PAS_4  13 pdgrvlyaNaaaae 26 
                                   +dg +++aN a  +
  gi|91772836|ref|YP_565528.1| 122 KDGECIDANIATSA 135
                                   79999999998665 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.96
                         PAS_4  96 igvlvisrDiTerr 109
                                    g++v+++Di+e+r
  gi|91772836|ref|YP_565528.1| 143 KGLIVTLQDISELR 156
                                   599********987 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.31   6.3e+02      83     113 .]       7      37 ..       1      37 [. 0.79
   2 !   26.9   0.1   1.9e-09   3.8e-06       7     113 .]      58     152 ..      52     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.31
                                   TSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  83 dgrpihlevraspvrdaggeilgflgvlrdi 113
                                    g ++ l  ++ ++ d  g+ +g+++ + di
  gi|91772836|ref|YP_565528.1|   7 SGQKKVLSWNVIKLKDNNGKTTGIICSGEDI 37 
                                   566666677888889999*********9998 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.9e-09
                                   HHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEE CS
                           PAS   7 leslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpi 87 
                                   +  +p +++v+D+  +i+ +N++a +llG++ +e++g +++  i++           + l++ +++++  i + ++dg+ i
  gi|91772836|ref|YP_565528.1|  58 IRIAPIATIVLDREQNIVTANEKAMDLLGYANDEIIGNPISTIISN-----------NELLEFTDKNDLSIELLKKDGECI 127
                                   5558999**********************************77765...........5688888888888888889***** PP

                                   EEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  88 hlevraspvrdaggeilgflgvlrdi 113
                                    + + +s ++d   +++g++++l+di
  gi|91772836|ref|YP_565528.1| 128 DANIATSAIMDNN-NHKGLIVTLQDI 152
                                   ************5.578*******98 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.1e-08   4.1e-05       2      49 ..      53     101 ..      52     114 .. 0.83
   2 ?    0.7   0.0      0.29   5.8e+02       4      21 ..     255     270 ..     253     277 .. 0.74
   3 ?   -1.8   0.0       1.8   3.5e+03       6      22 ..     286     300 ..     280     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.1e-08
                         PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqll 49 
                                   +l  l+  +p + +v+d+ ++iv +N++a +llGy  ++++g ++ +++
  gi|91772836|ref|YP_565528.1|  53 YLNLLIRIAPIATIVLDREQNIVTANEKAMDLLGYAnDEIIGNPISTII 101
                                   5667889999999****6667*********************9997554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                         PAS_8   4 ralfesspdgiavvdlgd 21 
                                   ++++  ++dgi+++d  +
  gi|91772836|ref|YP_565528.1| 255 ENFIKKVNDGIVLID--G 270
                                   56777899******9..4 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.8
                         PAS_8   6 lfesspdgiavvdlgdr 22 
                                   ++e+ +d i+v d   r
  gi|91772836|ref|YP_565528.1| 286 FMEQTNDTIMVSD--SR 300
                                   689999****988..43 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.018        36      86     115 .]      16      45 ..       8      45 .. 0.91
   2 !   14.4   0.0   1.6e-05     0.031       9      48 ..      66     104 ..      62     158 .. 0.89
   3 ?   -0.1   0.1      0.49   9.7e+02       2      21 ..     259     278 ..     258     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                         PAS_7  86 rvievrgnplpdgGfVttytDiTerrraee 115
                                   +vi+++ n     G++ + +DiT r+ aee
  gi|91772836|ref|YP_565528.1|  16 NVIKLKDNNGKTTGIICSGEDITPRKIAEE 45 
                                   68999999999**************99986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.6e-05
                         PAS_7   9 svfDadlrLvawNrrylelldlpeelvqvgvpleellryn 48 
                                   +v+D+++++v+ N++ ++ll++ ++ + +g p+++++  n
  gi|91772836|ref|YP_565528.1|  66 IVLDREQNIVTANEKAMDLLGYANDEI-IGNPISTIISNN 104
                                   79***********************99.9*******9877 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.49
                         PAS_7   2 enmsqGisvfDadlrLvawN 21 
                                   +++++Gi+++D  + L++ N
  gi|91772836|ref|YP_565528.1| 259 KKVNDGIVLIDGLEYLILEN 278
                                   6899*******999998887 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.63   1.3e+03      77     106 .]       9      38 ..       3      38 .. 0.84
   2 !   15.9   0.3   7.3e-06     0.015       1     105 [.      54     152 ..      54     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.63
                        PAS_10  77 ngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                   ++k+   ++  ++d++g++ G++    Dit
  gi|91772836|ref|YP_565528.1|   9 QKKVLSWNVIKLKDNNGKTTGIICSGEDIT 38 
                                   5677788899999*********99999986 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 7.3e-06
                        PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfkl.ipadvGrpladihpkkavknveeviealrtgekdevevvvpkngkw 80 
                                   ln l++ +pi+++ lD++ +i   +++a  l+ + +++ +G+p+++i +++++ ++        ++++   e   +k+g++
  gi|91772836|ref|YP_565528.1|  54 LNLLIRIAPIATIVLDREQNIVTANEKAMDLLGYaNDEIIGNPISTIISNNELLEF-------TDKNDLSIE-LLKKDGEC 126
                                   7999*********************998877766156678*******766554443.......333433333.33567888 PP

                        PAS_10  81 vlvrylp.yrdedgeiaGvvetfvDi 105
                                   +  ++      ++++ +G+++t++Di
  gi|91772836|ref|YP_565528.1| 127 IDANIATsAIMDNNNHKGLIVTLQDI 152
                                   77776431344677789999999998 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.4e-05     0.027       5      99 ..      49     150 ..      45     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                       SpoVT_C   5 fakeyaeslaetlghivlitDrdqiiavagaskkel....lekeiskeleklmeerktvlakkeekklv...veeekeeys 78 
                                    a++y + l +    ++++ Dr+q i +a  +  +l     +  i + + +++++++ + ++++++  +   +++++    
  gi|91772836|ref|YP_565528.1|  49 HANDYLNLLIRIAPIATIVLDREQNIVTANEKAMDLlgyaNDEIIGNPISTIISNNELLEFTDKNDLSIellKKDGECIDA 129
                                   6899*************************9999888555556789999**********99999777777764466665555 PP

                       SpoVT_C  79 aqviaPIiaeGdviGaVills 99 
                                   +++ + I+ + +  G ++ l+
  gi|91772836|ref|YP_565528.1| 130 NIATSAIMDNNNHKGLIVTLQ 150
                                   588889999999999999885 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 ?   10.8   0.0    0.0002       0.4       7      39 ..      55      87 ..      51      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                      MLTR_LBD  7 rlLdalepvPAlVldrrwdvlaaNraaraLlgd 39
                                  +lL ++ p + +Vldr  +++ aN+ a  Llg 
  gi|91772836|ref|YP_565528.1| 55 NLLIRIAPIATIVLDREQNIVTANEKAMDLLGY 87
                                  689999***********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2108.16
//
Query:       gi|91772837|ref|YP_565529.1|  [L=204]
Description: response regulator receiver, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-30  104.1   0.5      8e-30  103.3   0.2    1.5  2  Response_reg  Response regulator receiver domain
    7.1e-08   32.6   0.2      2e-07   31.2   0.1    1.8  3  PAS_9         PAS domain
    7.5e-08   32.4   0.0    1.8e-07   31.1   0.0    1.6  1  PAS           PAS fold
    0.00021   21.5   0.0    0.00038   20.7   0.0    1.4  1  PAS_4         PAS fold
     0.0029   17.9   0.0     0.0076   16.5   0.0    1.7  1  PAS_3         PAS fold
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.025   14.6   0.0    1.5  1  PAS_8         PAS domain
      0.025   14.7   0.0      0.059   13.5   0.0    1.6  1  PAS_11        PAS domain
      0.026   14.7   0.9      0.047   13.9   0.9    1.4  1  DUF4030       Protein of unknown function (DUF4030)


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 !  103.3   0.2   3.6e-33     8e-30       1     111 [.       8     118 ..       8     119 .. 0.96
   2 ?   -2.9   0.0       3.2   7.3e+03       1      15 [.     149     163 ..     149     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 3.6e-33
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +l+vdD+p ++el++ +l   +y e+a a+dg eale++k  ++d+illD++mp+mdG+++++++++++  + +pv+++ta
  gi|91772837|ref|YP_565529.1|   8 ILVVDDEPWNLELMEAYLS-GDY-EIALASDGVEALEKVKDFDPDIILLDVRMPKMDGYQTCEKLKNDErtKFIPVVLVTA 86 
                                   8*****************9.889.9****************************************99995566******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    se+ed+++++ agad+flsKp+d+ eL++++
  gi|91772837|ref|YP_565529.1|  87 LSEKEDRIKGIAAGADEFLSKPVDMLELKTRV 118
                                   ****************************9987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                                   EEEESSSHHHHHHHH CS
                  Response_reg   1 vlivdDdplvrellr 15 
                                   ++i+d+++ ++++ +
  gi|91772837|ref|YP_565529.1| 149 IVIIDNEHNIVNINK 163
                                   689999988887765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.4   7.5e+03      71      94 ..      73      96 ..      54     103 .. 0.59
   2 ?   -2.5   0.0       2.8   6.3e+03      29      40 ..     102     113 ..      85     138 .. 0.60
   3 !   31.2   0.1   9.1e-11     2e-07       4      58 ..     149     202 ..     145     204 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                         PAS_9 71 kngetfwvlltaspvkdddgelvg 94
                                  +++++f   + ++++ +++++++g
  gi|91772837|ref|YP_565529.1| 73 DERTKFIPVVLVTALSEKEDRIKG 96
                                  344444444555555555666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                         PAS_9  29 eevlgksitdlf 40 
                                   +e+l k++++l 
  gi|91772837|ref|YP_565529.1| 102 DEFLSKPVDMLE 113
                                   555555555554 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 9.1e-11
                         PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgr 58 
                                   i+i++++++i+ +N++  ++lGys+ee++gk++ d f  + e++e+l+a ++ ++
  gi|91772837|ref|YP_565529.1| 149 IVIIDNEHNIVNINKKGGEILGYSKEELIGKNYYDNF-VPVEERETLKAHYKKLQ 202
                                   455668888***********************99999.89999999888888766 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   8.1e-11   1.8e-07      13      57 ..     148     192 ..     139     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 8.1e-11
                                   EEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHH CS
                           PAS  13 pifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddae 57 
                                   +i+++D  ++i+ +N++  e+lG+s ee++gk+++d +++ +++e
  gi|91772837|ref|YP_565529.1| 148 MIVIIDNEHNIVNINKKGGEILGYSKEELIGKNYYDNFVPVEERE 192
                                   799**********************************99876553 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.7e-07   0.00038       2      57 ..     143     199 ..     142     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-07
                         PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralr 57 
                                   d    +++++d + +++ +N+ + e++g++ eel+Gk +++++ +   ++ l ++++
  gi|91772837|ref|YP_565529.1| 143 DVAGIMIVIIDNEHNIVNINKKGGEILGYSKEELIGKNYYDNFVPVeERETLKAHYK 199
                                   5566789999******************************97776547777776665 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.4e-06    0.0076       2      43 ..     159     199 ..     158     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.4e-06
                         PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealq 43 
                                   + ++++  eilGys+eel+gk  +++d   p + re ++++++
  gi|91772837|ref|YP_565529.1| 159 VNINKKGGEILGYSKEELIGK--NYYDNFVPVEeRETLKAHYK 199
                                   67889999*************..66666666551665555554 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.025      12      56 ..     147     189 ..     140     200 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                         PAS_8  12 dgiavvdlgdrivdvNqaalellGys.adlkgellg.qllpvlrpll 56 
                                     i+++d+  +iv +N++  e+lGys +    el+g ++ + + p +
  gi|91772837|ref|YP_565529.1| 147 IMIVIIDNEHNIVNINKKGGEILGYSkE----ELIGkNYYDNFVPVE 189
                                   34555785558*************9955....555545555444444 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-05     0.059       5      60 ..     149     202 ..     147     204 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                        PAS_11   5 ttrldidgkIisvDtsaLrasfslglekeelvgrsiyd.Lchpqdlstlkshlrevi 60 
                                   ++++d + +I+++++   ++   lg++keel+g+ +yd ++  ++++tlk h+++ +
  gi|91772837|ref|YP_565529.1| 149 IVIIDNEHNIVNINK---KGGEILGYSKEELIGKNYYDnFVPVEERETLKAHYKKLQ 202
                                   67889999*******...****************99974777777999***999765 PP

>> DUF4030  Protein of unknown function (DUF4030)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   2.1e-05     0.047      17      74 ..     128     185 ..     113     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                       DUF4030  17 ssklkkeinkrlknqdirpytinisqrdmevvkkekrwnkvlssileevftkngykGf 74 
                                    + ++ke ++  k  d+    i i + + ++v+++k+  ++l++  ee+  kn y+ f
  gi|91772837|ref|YP_565529.1| 128 HDTIRKERDTAHKYFDVAGIMIVIIDNEHNIVNINKKGGEILGYSKEELIGKNYYDNF 185
                                   456899999999*******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1459.88
//
Query:       gi|91772838|ref|YP_565530.1|  [L=379]
Description: major facilitator transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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  110.9  49.9    1.5e-19   70.2  20.8    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2  20.8   8.2e-24   1.5e-19       4     219 ..      22     229 ..      18     230 .. 0.80
   2 !   45.7  25.4   2.3e-16     4e-12       1     166 [.     221     375 ..     221     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 8.2e-24
                         MFS_1   4 aaflsalarsilgpalpl.al.aedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   +a++++  +++++p+lp+    ++ +     + +l+++ ++lga+ ++lp+G lsdr    +++ lglll+++++l+++f 
  gi|91772838|ref|YP_565530.1|  22 SALVIMGLSNAVIPILPElSAtGQIY--GINSSSLVYSSFFLGALSTMLPFGILSDRTDNLKLVSLGLLLSFISGLCMIF- 99 
                                   55666666777889999643313334..5777889***************************999999999999899999. PP

                         MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                   + ++ +++ +r++ G+++ga+fpa+++ +a++++   r+r++g +s  +++G + g ++ g+l+ + +     +++ i+++
  gi|91772838|ref|YP_565530.1| 100 TDSFiIFVSARFIEGAACGAFFPAAYSRLARYTK---RARYMGEFSFLINAGLAAGVAVTGYLV-HSNIKNGIILFSILTF 176
                                   78888****************************5...7**************************.7789************ PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvp...awkallkdpvlw.illialllf 219
                                   l ++   + ++++ +++ + ++++      ++++++   + +++++++    i++i+++l+
  gi|91772838|ref|YP_565530.1| 177 LTII---FAIYRSIVSSNTIATITS-----QKKIIErehPSSHIFTSKDTRgIWIISFILA 229
                                   *999...566566555555555555.....2223333555677777776654677777665 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 2.3e-16
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                   ++++ f+ a ++++l++++p  +++d ++s++e+g+ ++l ++ ++++sl+++++  ++G  +++ +g+ +  +g +l ++
  gi|91772838|ref|YP_565530.1| 221 IWIISFILAGSSGVLISLYP-EYGTD-TLSKTELGISISLLYVSTMISSLVTSYV--NIGYAKLIKIGIMIATIG-ILVTI 296
                                   6899****************.67777.58**************************..99****************.55553 PP

                         MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                    +s    +++ ++ G+g+ +l+ +g+ ++ +  +  e+g+a+g++++++ +G +l pl++g+la sl    +f+i ai++ 
  gi|91772838|ref|YP_565530.1| 297 -NS---SMAGFFIIGIGS-GLMLVGLPIAIASMNI-EKGMAMGIYNTCIYAGLALMPLIAGVLANSLEVKTIFFITAILFG 371
                                   .66...8**********5.6666666666666777.9******************************************99 PP

                         MFS_1 163 lafv 166
                                   l + 
  gi|91772838|ref|YP_565530.1| 372 LTIF 375
                                   9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2547.78
//
Query:       gi|91772839|ref|YP_565531.1|  [L=173]
Description: shikimate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-32  111.8   0.0    3.8e-32  111.6   0.0    1.0  1  SKI              Shikimate kinase
    4.5e-07   30.1   0.0    7.5e-07   29.4   0.0    1.5  1  AAA_33           AAA domain
    2.1e-06   27.6   0.0    2.8e-06   27.2   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
    2.4e-06   28.0   0.7    8.4e-06   26.2   0.4    2.1  1  AAA_17           AAA domain
      3e-06   27.5   0.5    3.8e-06   27.2   0.5    1.6  1  Cytidylate_kin2  Cytidylate kinase-like family
    7.9e-06   26.4   0.2    2.2e-05   25.0   0.2    1.9  1  AAA_18           AAA domain
    0.00027   20.8   1.1      0.093   12.6   0.1    2.1  2  dNK              Deoxynucleoside kinase
    0.00081   19.5   0.7      0.015   15.4   0.1    2.1  2  ADK              Adenylate kinase
     0.0042   17.0   0.2      0.031   14.2   0.1    2.0  2  APS_kinase       Adenylylsulphate kinase
     0.0058   17.1   0.0     0.0095   16.4   0.0    1.4  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.014   15.1   0.2      0.024   14.3   0.2    1.4  1  CoaE             Dephospho-CoA kinase
      0.034   14.6   0.1      0.073   13.6   0.1    1.5  1  ABC_tran         ABC transporter
      0.041   14.3   0.0      0.069   13.5   0.0    1.4  1  RNA_helicase     RNA helicase
      0.044   13.7   0.0      0.071   13.0   0.0    1.2  1  Rad17            Rad17 P-loop domain
      0.051   13.8   0.0      0.076   13.2   0.0    1.3  1  AAA_28           AAA domain
      0.054   13.8   0.0       0.12   12.6   0.0    1.7  2  AAA_22           AAA domain
      0.056   13.2   0.4      0.082   12.6   0.1    1.6  2  AAA_24           AAA domain
      0.064   13.2   0.1       0.12   12.3   0.1    1.4  1  RsgA_GTPase      RsgA GTPase
      0.065   12.4   0.2       0.11   11.6   0.1    1.4  2  NB-ARC           NB-ARC domain
       0.14   11.9   1.7       0.95    9.2   0.1    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.16   12.3   0.0       0.22   11.9   0.0    1.3  1  AAA_16           AAA ATPase domain
       0.16   11.9   0.1       0.33   11.0   0.1    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.34   10.7   2.1       0.44   10.3   0.8    1.8  2  AAA_29           P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   4.9e-35   3.8e-32       1     155 [.       9     161 ..       9     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 4.9e-35
                                   TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHHHHHH CS
                           SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlseenrel 81 
                                   +GaGKst+Gk+lAkklg++fiD+D+li  ++g+  +++++ +g ++F  lE++++  l ++++++iatGG++v se + ++
  gi|91772839|ref|YP_565531.1|   9 SGAGKSTIGKQLAKKLGYKFIDIDDLIRAKIGTGLQTFIDTYGDDEFIGLEEQIVIGLHSMDDHIIATGGSIVYSETAIRH 89 
                                   59******************************************************************************* PP

                                   HHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEE.CTSSHHHHHHHHHHH CS
                           SKI  82 lkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvd.eseeskeevaeeile 155
                                   lk+  +++yLdv++  +++r++  ++  l+  k+k   l++ +  r++lye++ d+ ++ ++ e+k+ ++e+i++
  gi|91772839|ref|YP_565531.1|  90 LKDISTIVYLDVPFIRIAQRISPSQR-GLVGFKDK--GLRDLYNDRKKLYEHYMDIRIKiKKGETKRDIVERIIA 161
                                   *********************98887.67777777..6666666********86665551667778999999986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   9.6e-10   7.5e-07       3      44 ..       4      45 ..       3     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.6e-10
                        AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqs 44
                                   l+G++G+GKst  ++l+kklg+ +++ d+l+r+  gt+ q+
  gi|91772839|ref|YP_565531.1|  4 TLIGMSGAGKSTIGKQLAKKLGYKFIDIDDLIRAKIGTGLQT 45
                                  689******************************998877664 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   3.6e-09   2.8e-06       1      66 [.       3      68 ..       3     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.6e-09
                                  EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEE CS
                Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalvelakevelsfea 66
                                  i++ G +g+GKs+++++la+klg+k++d   l Ra     l++ +d+   ++++ l +++ + +++
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGYKFIDIDDLIRAKIGTGLQTFIDTYGDDEFIGLEEQIVIGLHS 68
                                  788899*****************************9999999999999999888888887776554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.4   1.1e-08   8.4e-06       1      39 [.       6      43 ..       6     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.1e-08
                                  EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS CS
                        AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl 39
                                  +G+ G+GK+t+ ++l++k+g++++   dl+r+ +   gl
  gi|91772839|ref|YP_565531.1|  6 IGMSGAGKSTIGKQLAKKLGYKFIDIDDLIRAKI-GTGL 43
                                  69******************************98.4455 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.5   4.9e-09   3.8e-06       2      33 ..       3      35 ..       2     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.9e-09
               Cytidylate_kin2  2 ITIsreyGsgGetigeaLAekLglpfydr.eii 33
                                  IT+ +  G+g++tig++LA+kLg++f+d  ++i
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGYKFIDIdDLI 35
                                  9***************************74444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.2   2.8e-08   2.2e-05       1      31 [.       3      31 ..       3     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.8e-08
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdv 31
                                  I l G++G+GK+t++k L+k+lg+  + +d+
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGY--KFIDI 31
                                  899*******************55..44443 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00012     0.093       1      27 [.       3      29 ..       3      46 .. 0.90
   2 !    7.5   0.1    0.0044       3.4     114     181 ..      84     150 ..      67     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                  EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                  i++ G  gaGKst+ k+L+kklg+k++
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGYKFI 29
                                  5667899****************9976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0044
                                   HHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETS CS
                           dNK 114 dnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidve 181
                                   + ++++l+ ++ ++YL+++   + +ri   +r    + + + l+ L ++ ++ +++++ + + +  +e
  gi|91772839|ref|YP_565531.1|  84 ETAIRHLKDISTIVYLDVPFIRIAQRISPSQRGL-VGFKDKGLRDLYNDRKKLYEHYMDIRIKIKKGE 150
                                   44568889999****************9777665.677777788888888888888777766666555 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.9e-05     0.015       1      38 [.       5      42 ..       5      51 .. 0.92
   2 ?    2.7   0.1      0.16   1.3e+02     100     123 ..      90     131 ..      81     161 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                                  EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg 38
                                  l+G  gaGK t  ++l+kk+g++ +   dl+Ra++ +g
  gi|91772839|ref|YP_565531.1|  5 LIGMSGAGKSTIGKQLAKKLGYKFIDIDDLIRAKIGTG 42
                                  689******************************99765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                                   TSEESEEEEEE--HHHHHHHHHT..................G CS
                                   xxxxxxxxxxxxxxxxxxxxxxx..................x RF
                           ADK 100 kvkldlvleldvpeevlveRltg..................D 123
                                    +++ ++++ldvp   + +R++                   D
  gi|91772839|ref|YP_565531.1|  90 LKDISTIVYLDVPFIRIAQRISPsqrglvgfkdkglrdlynD 131
                                   568999***************985555555555555433331 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1     4e-05     0.031       5      35 ..       3      33 ..       1      49 [. 0.77
   2 ?    0.8   0.0      0.51     4e+02      72     114 ..     100     147 ..      83     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                                  EEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                    APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvyl 35
                                  + l G+sg+GKsti ++l+kkL  k i +  
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGYKFIDIDD 33
                                  6789****************99776655554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                                   HTT-EEEEE----SHH.....HHHHHHHHHHCHTEEEEEEEE--HHHH CS
                    APS_kinase  72 daglivlvafisPyre.....eReaarelleealkfievfvdtplevc 114
                                   d   i ++  isP ++     + +  r+l ++ +k++e ++d+ +++ 
  gi|91772839|ref|YP_565531.1| 100 DVPFIRIAQRISPSQRglvgfKDKGLRDLYNDRKKLYEHYMDIRIKIK 147
                                   566777888888877633322345677888887888888888777665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0095       2      30 ..       4      32 ..       3      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                  EEESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                           AAA  2 llyGppGtGKTllakavakelgvefleis 30
                                   l+G  G GK+++ k++ak+lg +f+ i+
  gi|91772839|ref|YP_565531.1|  4 TLIGMSGAGKSTIGKQLAKKLGYKFIDID 32
                                  699**********************9986 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   3.1e-05     0.024       3      41 ..       3      42 ..       1      57 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                  EEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCT CS
                          CoaE  3 vgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepg 41
                                  + l G  ++GKst+ + +a+ lg++ +D D + r  +  g
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKkLGYKFIDIDDLIRAKIGTG 42
                                  77889999**********999*********9988655544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.4e-05     0.073      14      34 ..       3      23 ..       1      33 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-05
                                  EEEEESTTSSHHHHHHHHTTS CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 14 vaivGenGaGKStLlkllagl 34
                                  + ++G +GaGKSt+ k la++
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKK 23
                                  689***********9999876 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   8.9e-05     0.069       1      48 [.       3      51 ..       3      65 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl.klkkkdsvysrnpeddfwdgYt 48
                                  i l G sg GKSt+ k+Lak+l  k+ + +   +  +++  ++f d Y 
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGYKFiDIDDLIRAKIGTGLQTFIDTYG 51
                                  5689******************977633333333333555666666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.1e-05     0.071      50      75 ..       5      30 ..       2      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-05
                         Rad17 50 isGPsGCgkstvvkvLskelgiklre 75
                                  + G sG gkst+ k L+k+lg+k+++
  gi|91772839|ref|YP_565531.1|  5 LIGMSGAGKSTIGKQLAKKLGYKFID 30
                                  5699*******************986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.8e-05     0.076       2      27 ..       3      29 ..       2      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.8e-05
                        AAA_28  2 ivitGgestGKTtlleaLaar.gypvv 27
                                  i ++G +++GK+t+ ++La++ gy+ +
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKlGYKFI 29
                                  899****************98899977 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00016      0.12       8      29 ..       3      24 ..       1      55 [. 0.87
   2 ?   -2.6   0.0       7.9   6.2e+03      44      60 ..     143     159 ..     123     165 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                        AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                  ++++G sG+GK+t  ++l+++l
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKL 24
                                  789****************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.9
                        AAA_22  44 fvtlpsstsskdllrel 60 
                                   +++++++++ +d+ +++
  gi|91772839|ref|YP_565531.1| 143 RIKIKKGETKRDIVERI 159
                                   45555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011     0.082       4      33 ..       2      33 ..       1      98 [. 0.66
   2 ?   -3.3   0.0       8.1   6.3e+03      32      55 ..     122     145 ..     120     159 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                        AAA_24  4 kiliyGpsgiGKTtlakel..gpkplfidtek 33
                                  +i ++G sg+GK+t+ k+l  +    fid+++
  gi|91772839|ref|YP_565531.1|  2 NITLIGMSGAGKSTIGKQLakKLGYKFIDIDD 33
                                  799****************5433334677776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.1
                        AAA_24  32 ekGlksldadkfpdieswedflde 55 
                                   +kGl++l++d+ +  e + d++ +
  gi|91772839|ref|YP_565531.1| 122 DKGLRDLYNDRKKLYEHYMDIRIK 145
                                   566666666665544444444443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00015      0.12     103     127 ..       4      28 ..       2      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                   EEECSTTSSHHHHHHHHCTT----- CS
                   RsgA_GTPase 103 vlvGqSGvGKStLinallpelelkt 127
                                   +l+G SG+GKSt+ ++l+ +l  k 
  gi|91772839|ref|YP_565531.1|   4 TLIGMSGAGKSTIGKQLAKKLGYKF 28 
                                   69**************999876555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00014      0.11      23      43 ..       3      23 ..       1      34 [. 0.90
   2 ?   -3.5   0.0       6.1   4.8e+03      58      72 ..     145     159 ..     127     165 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                  EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 23 valvGmgGvGKttlakqilnk 43
                                  ++l Gm G GK+t+ kq  +k
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKK 23
                                  799**************9988 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.1
                                   EEESXXHHHHHHHXX CS
                        NB-ARC  58 vvsktdkseeileti 72 
                                    + k  ++++i+e+i
  gi|91772839|ref|YP_565531.1| 145 KIKKGETKRDIVERI 159
                                   333333334444433 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0012      0.95       2      25 ..       3      26 ..       2      46 .. 0.86
   2 ?    2.2   0.2      0.16   1.3e+02     123     178 ..      84     141 ..      63     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                           PRK  2 IgvagsSGaGkttvarklekifgr 25
                                  I + g SGaGk+t+ ++l k +g 
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGY 26
                                  7889**************999984 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.16
                           PRK 123 dervaelldlkiyvdisi.dlelarklqRDiaeR...Grsleavldsilrrkpdyvnyik 178
                                    + +++l d++  v  ++  +++a++++   ++R   G + ++  d ++ rk+ y++y++
  gi|91772839|ref|YP_565531.1|  84 ETAIRHLKDISTIVYLDVpFIRIAQRISP--SQRglvGFKDKGLRDLYNDRKKLYEHYMD 141
                                   44599999988555443314788888874..44411267889999999999999999976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.22      27      51 ..       3      27 ..       1      77 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                        AAA_16 27 vllsGesGvGKsslvrellralekd 51
                                  + l+G+sG GKs++ ++l++ l  +
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGYK 27
                                  679****************998876 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   0.00042      0.33       2      26 ..       3      27 ..       2      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                                  EEEE--SSSSHHHHHHHGGGGBS-- CS
                         AAA_5  2 vlLvGppGtgKselaerlaaalnre 26
                                  + L+G +G gKs++ ++la+ l+ +
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTIGKQLAKKLGYK 27
                                  679*****************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 ?   10.3   0.8   0.00057      0.44      25      38 ..       3      16 ..       1      17 [. 0.89
   2 ?   -1.8   0.0       3.5   2.8e+03      26      41 ..      34      49 ..      28      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00057
                        AAA_29 25 tlltGpsGsGKSTl 38
                                  + l+G sG+GKST+
  gi|91772839|ref|YP_565531.1|  3 ITLIGMSGAGKSTI 16
                                  5699*********8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.5
                        AAA_29 26 lltGpsGsGKSTllDA 41
                                  l+  ++G+G  T++D 
  gi|91772839|ref|YP_565531.1| 34 LIRAKIGTGLQTFIDT 49
                                  6666889999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1144.23
//
Query:       gi|91772840|ref|YP_565532.1|  [L=453]
Description: hypothetical protein Mbur_0828 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-184  612.1   9.8   5.4e-184  611.8   9.8    1.0  1  DUF711    Uncharacterised ACR (DUF711)
  ------ inclusion threshold ------
      0.083   12.8   1.2       0.25   11.3   0.1    2.3  2  DUF5402   Family of unknown function (DUF5402)


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.8   9.8    6e-188  5.4e-184       1     405 [.      14     417 ..      14     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 611.8 bits;  conditional E-value: 6e-188
                        DUF711   1 mieeekldiRtvTlgislldcasedleklaekiyekiikkaaklvktveeieeeyGievvtkRisvtpisellaeasaeea 81 
                                   mi+ e++diRtvT+gi+l+ c+++d++ ++++iy+ki+ +a++lv+t+ee+++ yGi++ +kRi+vtpi+ ++ae++++e+
  gi|91772840|ref|YP_565532.1|  14 MIKAENFDIRTVTMGINLRGCCHSDIDVFNKNIYNKITGYAKELVRTTEEVQNLYGIPITNKRIAVTPIA-IVAESCNTED 93 
                                   9*********************************************************************.9999886666 PP

                        DUF711  82 .velaktldelakevgvdfiggfsalvekgltkgdkeliesipealaetervcssvnvastkaginmdavraaaevikeia 161
                                    v++aktld++a++vg+dfiggfsalv+kg+t gd +li+sip+ala+t++vc+s+nva+tkaginmdav+++++++k++a
  gi|91772840|ref|YP_565532.1|  94 yVSIAKTLDRAAEDVGIDFIGGFSALVHKGITPGDMKLINSIPQALASTKKVCASINVATTKAGINMDAVAMMGHIVKKTA 174
                                   8******************************************************************************** PP

                        DUF711 162 eltkdkdglgnaklvvfanvpednPFfpgAfhgvgeaeavinvGvsgpgvvkkaleeakkeasleelaeaikktafkitrl 242
                                   e+tkd dg+g+aklv+fan+pednPF++gAfhg+ge+++vinvGvsgpgvv++a++e+ k+ +l e++eaikktafkitr+
  gi|91772840|ref|YP_565532.1| 175 EATKDADGIGCAKLVIFANAPEDNPFMAGAFHGIGEPDCVINVGVSGPGVVNSAVREL-KDPDLGEISEAIKKTAFKITRM 254
                                   **********************************************************.6699****************** PP

                        DUF711 243 gelvarevakrlgvefggiDlSlaPtpavgdSvaeileelglesfGapGtlaalalltdavkkGGvmasskvgGlsGlflp 323
                                   ge+v+rev++rl+v+fg++DlSlaPtp++gdSva+ile++gle++G++Gt+aalall+davkkGG mass+vgGlsG+f+p
  gi|91772840|ref|YP_565532.1| 255 GEMVGREVSRRLNVDFGVLDLSLAPTPEIGDSVAAILEAMGLETCGTHGTTAALALLNDAVKKGGSMASSYVGGLSGAFIP 335
                                   ********************************************************************************* PP

                        DUF711 324 vsEDaglaeaaeegaltiekLlamsaVCsvGLDmvpipgdtsaetiaaliaDeaalavrlnKtlavRliPvpgkkaGdkve 404
                                   vsEDag+++a+e gal++ekL+am++VCsvGLDm++ipgdtsa+ti+a+iaDe+a++++++Kt+avRliP+pgkk+Gd+ve
  gi|91772840|ref|YP_565532.1| 336 VSEDAGMIRAVELGALSLEKLEAMTSVCSVGLDMIAIPGDTSAATISAIIADEMAIGMINKKTTAVRLIPAPGKKVGDSVE 416
                                   ********************************************************************************* PP

                        DUF711 405 F 405
                                   F
  gi|91772840|ref|YP_565532.1| 417 F 417
                                   9 PP

>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.8e-05      0.25      29      74 ..      17      60 ..       6     100 .. 0.71
   2 ?   -0.8   0.1      0.16   1.4e+03      35      71 ..     145     180 ..     139     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                       DUF5402 29 vdifalrcGcvGilievrGlevddveifkekileklkelakdleik 74
                                   + f +r   +   i++rG    d+++f+++i +k+   ak+l   
  gi|91772840|ref|YP_565532.1| 17 AENFDIRTVTM--GINLRGCCHSDIDVFNKNIYNKITGYAKELVRT 60
                                  55555555444..4799*******************9999987544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.16
                       DUF5402  35 rcGcvGilievrGlevddveifkekileklkelakdl 71 
                                    c  + +  +  G+++d v  +  +i++k  e++kd 
  gi|91772840|ref|YP_565532.1| 145 VCASINVATTKAGINMDAVA-MMGHIVKKTAEATKDA 180
                                   57777777888899999998.5678888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3179.03
//
Query:       gi|91772841|ref|YP_565533.1|  [L=92]
Description: hypothetical protein Mbur_0829 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.6    2.6e-16   59.4   0.6    1.0  1  ACT_6     ACT domain
    1.4e-07   31.1   1.2      2e-07   30.7   1.2    1.3  1  ACT       ACT domain
    0.00014   22.4   1.0    0.00023   21.7   1.0    1.4  1  ACT_4     ACT domain
  ------ inclusion threshold ------
      0.011   15.4   0.7      0.018   14.8   0.7    1.3  1  ACT_7     ACT domain
       0.15   12.2   0.0       0.19   11.8   0.0    1.2  1  Fn3-like  Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.6   7.1e-20   2.6e-16       2      76 .]       5      81 ..       4      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.1e-20
                         ACT_6  2 illitvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped..alarlekaLlflakelgltvefk 76
                                   ++itv+G d+ G++as+t+v a+f+vni+Di q + ++ ++ ++l  ++++  +la  +ka+ +  +elg++v+++
  gi|91772841|ref|YP_565533.1|  5 RFIITVIGIDKIGIVASITKVMADFNVNIVDISQTIMEDLFTMIMLAGVDSEnfDLASFQKAMVEEGEELGVEVRVQ 81
                                  68************************************************77699*******************986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   1.2   5.5e-11     2e-07       2      54 ..       7      57 ..       6      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.5e-11
                                  EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHH CS
                           ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeed 54
                                  ++ v   D+ G+ a ++ ++ad ++Ni+ i+q+ +ed     +++   vd e+
  gi|91772841|ref|YP_565533.1|  7 IITVIGIDKIGIVASITKVMADFNVNIVDISQTIMED--LFTMIMLAGVDSEN 57
                                  5778888******************************..77777777666665 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   1.0   6.4e-08   0.00023       9      52 ..       8      49 ..       3      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.4e-08
                         ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeiki 52
                                  ++v+++d+ g++a+it+v ++ ++niv+++ +  + d l+++ +
  gi|91772841|ref|YP_565533.1|  8 ITVIGIDKIGIVASITKVMADFNVNIVDISQTIME-D-LFTMIM 49
                                  89***************************988853.5.565544 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.7   4.9e-06     0.018      17      44 ..      12      40 ..       5      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-06
                                  --SS--HHHHHHHHHHTTT---EEEE.-S CS
                         ACT_7 17 pfdvtGivaklaspLaeagIsifqiS.ty 44
                                   +d +Giva+++++ a+ +++i  iS t 
  gi|91772841|ref|YP_565533.1| 12 GIDKIGIVASITKVMADFNVNIVDISqTI 40
                                  4499*******************999764 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.4e-05      0.19      13      45 ..      52      84 ..      43      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                                  STTSBS-EEEEEEEEEE-TT-EEEEEEEEECGG CS
                      Fn3-like 13 sverpvkeLkgFekveLapGesktvtftldrkd 45
                                  +v+  +  L+ F+k  ++ Ge+  v+++++ +d
  gi|91772841|ref|YP_565533.1| 52 GVDSENFDLASFQKAMVEEGEELGVEVRVQHED 84
                                  67788889*********************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 707.08
//
Query:       gi|91772842|ref|YP_565534.1|  [L=138]
Description: hypothetical protein Mbur_0830 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1038.36
//
Query:       gi|91772843|ref|YP_565535.1|  [L=314]
Description: K+-dependent Na+/Ca+ exchanger related-protein [Methanococcoides burtonii DSM 6242]
Scores for 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-52  175.6  33.3    1.6e-29  102.9  10.3    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1  14.9   1.9e-26   3.3e-22       3     150 ..       5     144 ..       4     145 .. 0.90
   2 !  102.9  10.3   8.7e-34   1.6e-29       4     148 ..     171     308 ..     168     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.9e-26
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHH CS
                      Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllvi 83 
                                   +++f+lsl+li  +ad+++++a +i+ + g+++ ++G t++++++++pE+++s +aa  +++dl ign++Gs+i n++l +
  gi|91772843|ref|YP_565535.1|   5 LLYFLLSLVLITKGADWFIEAAVAISAKSGLPKMIIGATIVSFATTAPEFTVSAMAAYMDHTDLTIGNAVGSAICNIGLAL 85 
                                   578***********************99***************************************************** PP

                                   HHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  84 GlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                   G+++ +++++v++ s+  +  +++l+a+l l+ +l+l       g l+ ++g++ll++++ +l++++
  gi|91772843|ref|YP_565535.1|  86 GVVIAVKAIPVEGDSFLHKS-AIMLIAALTLV-ALTLD------GILSSFDGIILLIIFVGFLYYNY 144
                                   ******99999999975555.55555555544.34446......99******************986 PP

  == domain 2  score: 102.9 bits;  conditional E-value: 8.7e-34
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHH CS
                      Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviG 84 
                                   ++f+l+  l+++++++lv++  +ia+++gi++ ++Gltl+Alg+slpE+i++i+a l+g+ dl+ign+lG+n++++ l++G
  gi|91772843|ref|YP_565535.1| 171 FYFLLGATLVVIGSQILVKTGIAIAEWIGIPEMIIGLTLVALGTSLPEIITAISATLKGHQDLSIGNILGANTMDIALILG 251
                                   789****************************************************************************** PP

                                   HHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  85 lialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvl 148
                                   ++  i  +k++++sl++d++++++++lll+++ ++        +rl+++eg+v +l+Y+ y++ 
  gi|91772843|ref|YP_565535.1| 252 FSSQIREIKIQPQSLMYDFPFMIVIMLLLVIFGIT-R------KRLDRWEGVVIILVYFSYIAG 308
                                   *****99************8877777777554444.4......******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2191.62
//
Query:       gi|91772844|ref|YP_565536.1|  [L=151]
Description: hypothetical protein Mbur_0832 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-11   43.3   0.4      8e-11   42.6   0.4    1.3  1  Usp           Universal stress protein family
  ------ inclusion threshold ------
      0.039   14.0   0.0      0.049   13.6   0.0    1.2  1  Ncstrn_small  Nicastrin small lobe
      0.061   13.3   0.2      0.076   13.0   0.2    1.2  1  DAP_B         D-aminopeptidase, domain B


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 !   42.6   0.4   1.3e-14     8e-11       2     116 ..       6     121 ..       5     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.3e-14
                                   -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHCTTCE CS
                           Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaaeaggvk 81 
                                   yk+IlV++D+ + sk+++++Al+ a +  ++li+++v   ++ +     + + +    ++e  e+  +  ++ a+  g+++
  gi|91772844|ref|YP_565536.1|   6 YKNILVPIDEKQLSKRVIDHALHVADKESGKLIIVYVERKKTLECIFPKELAKKMMVIVKENIESNMEYaLENAKISGIAV 86 
                                   9**************************************999988877777777777777777766666567788888888 PP

                                   EEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSST CS
                           Usp  82 vevvveegdpaeeilevaeeedadliVvGsrgrsg 116
                                   + +++ + + a  ++++ ee++++l V+Gs  +++
  gi|91772844|ref|YP_565536.1|  87 ENIILDNDEIAKDLIRISEEKSVNLTVMGSESLKA 121
                                   88999999999999****************98765 PP

>> Ncstrn_small  Nicastrin small lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.3e-06     0.049      21      89 ..      35     108 ..      29     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-06
                                   EEEEEEEE-SHHHHHTTTT--S-SEEEEEE-GGG-SHHHHHT---SS.EEEEEEE--.........--SS----S-S CS
                  Ncstrn_small  21 nvgvlhliesekdlddllssgpsspyvvvlpldlftrevlerlksesekvaGvlvls.e.......eklegfSpdsk 89 
                                    + +++++e++k l+ ++ ++ +++++v+++ + + ++++e   + + k++G+ v++         ++l ++S++++
  gi|91772844|ref|YP_565536.1|  35 GKLIIVYVERKKTLECIFPKELAKKMMVIVK-ENI-ESNMEYALE-NAKISGIAVENiIldndeiaKDLIRISEEKS 108
                                   45689999******99999777766555555.667.588888888.67*******9952445555555555666655 PP

>> DAP_B  D-aminopeptidase, domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.3e-05     0.076      20      82 ..      26      88 ..      20     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                         DAP_B 20 lvtvekgekgkvkvtYaksaeelkltseteaesksvvaeiegdelrierlkenrtlkarrvke 82
                                  +++v ++e+gk+ + Y + +++l+++ ++e   k++v+  e+ e ++e   en +++   v++
  gi|91772844|ref|YP_565536.1| 26 ALHVADKESGKLIIVYVERKKTLECIFPKELAKKMMVIVKENIESNMEYALENAKISGIAVEN 88
                                  67899************************************************9998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 00:00:00.41
# Mc/sec: 1103.84
//
Query:       gi|91772845|ref|YP_565537.1|  [L=174]
Description: hypothetical protein Mbur_0833 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   54.6  12.2    7.8e-09   35.7   0.7    2.0  2  VIT1      VIT family
  ------ inclusion threshold ------
      0.067   12.9   2.6       0.15   11.8   2.6    1.5  1  DUF3159   Protein of unknown function (DUF3159)


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 !   24.4   4.4   2.6e-09   2.3e-05       2      58 ..       9      64 ..       8      76 .. 0.91
   2 !   35.7   0.7   8.7e-13   7.8e-09     128     209 ..      88     167 ..      69     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.6e-09
                          VIT1  2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvks 58
                                  r ++lG  DG++ ++++v+G s +  +++++++ a+l +++A a+  giG Yl+ ++
  gi|91772845|ref|YP_565537.1|  9 RYIILGSIDGILAVLGVVIGTSHVV-DDPSIIINAALGGAVALALTNGIGSYLAESA 64
                                  668*******************766.69*************************9876 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 8.7e-13
                          VIT1 128 seelasplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaa 208
                                   ++++++ ++  ++ + s +iG+l+P++p+++++  +  l ++i++++ +l+++G+ ++++ ++s ++ a+rm+ +G+l  +
  gi|91772845|ref|YP_565537.1|  88 RDTKKKIWNDSITHGGSSFIGSLVPIMPFVLFD--SFSLEIAIILSISVLAILGIYSGKIAKQSLIKHAVRMVGLGILIVL 166
                                   33347789**********************999..68888999999******************************98655 PP

                          VIT1 209 a 209
                                   a
  gi|91772845|ref|YP_565537.1| 167 A 167
                                   5 PP

>> DUF3159  Protein of unknown function (DUF3159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.6   1.6e-05      0.15       3      71 ..     102     169 ..     101     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                       DUF3159   3 GvrGlvesavPvvvFvvlflitkeLrlaiiaavavavlllvv..Rlvqresvqqalsgllgvaisavialr 71 
                                   G + ++ s vP++ Fv+  +   +L++aii+++ v ++l +   ++++++ +++a+  ++g++i +v+a++
  gi|91772845|ref|YP_565537.1| 102 GGSSFIGSLVPIMPFVLFDS--FSLEIAIILSISVLAILGIYsgKIAKQSLIKHAVR-MVGLGILIVLAVT 169
                                   5567999********99888..89999999999987776554337888888888875.8999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1187.20
//
Query:       gi|91772846|ref|YP_565538.1|  [L=134]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-19   69.4   0.3    3.3e-19   69.1   0.3    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.3   1.8e-23   3.3e-19       1     111 [.       6     116 ..       6     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.8e-23
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEEEESS CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpg.mdGlellkeireedpelpviiltah 80 
                                   +liv+D+ +v++ ++  l e gy+  + a +g++al +++++ +dl+++Di + g +dG+e+++e++ +  ++p+i+lt+ 
  gi|91772846|ref|YP_565538.1|   6 ILIVEDEMIVAMMIKLKLLEMGYKIAEYAVSGEQALIMVNKKVPDLVIMDIHLKGkLDGIETATEMESRY-SIPIIFLTGD 85 
                                   8**********************7777999************************999**********988.********** PP

                                   TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                   s +e + +   a+  ++l+Kpf ++eL  a+
  gi|91772846|ref|YP_565538.1|  86 SFNEKTARSSFANRAGYLQKPFMEKELEYAI 116
                                   **************************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1105.41
//
Query:       gi|91772847|ref|YP_565539.1|  [L=181]
Description: neelarodoxin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  133.9   4.0    5.7e-33  113.4   0.9    2.1  2  Desulfoferrodox  Desulfoferrodoxin
  ------ inclusion threshold ------
      0.066   13.6   0.0      0.066   13.6   0.0    1.1  1  DUF737           Protein of unknown function (DUF737)


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.9   6.3e-37   5.7e-33       2      92 ..      39     131 ..      38     134 .. 0.96
   2 !   21.8   0.1   2.4e-08   0.00021      79      96 .]     144     161 ..     132     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 6.3e-37
                                   SHTTTHTTSEEEEEESEEEETTEEEEEEEESSSS--BSSSS-EEEEEEEEEETTSSEEEE-TBSE.SEEEEEEEESSS.EE CS
               Desulfoferrodox   2 adekeekHvPvieadevvkagelfevkvkvgkipHpneeeHyIewielyleeegekrvelsaede.pevtftvklkke.kk 80 
                                   ++e+e+kHvPvieadev++a+++fev+vkvg++pH++++eHyIewiel+l+++++ rvels++de +e+tftv++++e   
  gi|91772847|ref|YP_565539.1|  39 ITETEQKHVPVIEADEVMTAEGSFEVTVKVGELPHVMQDEHYIEWIELSLGDMKIGRVELSPSDEkAEATFTVEPTEEiVG 119
                                   7899************************************************************77***********9667 PP

                                   EEEEEEETTTEE CS
               Desulfoferrodox  81 lvalsyCnlHGl 92 
                                   ++a++ Cn+HG+
  gi|91772847|ref|YP_565539.1| 120 IHAYQVCNIHGV 131
                                   ***********7 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.4e-08
                                   EEEEEEEEETTTEEEEEE CS
               Desulfoferrodox  79 kklvalsyCnlHGlWese 96 
                                   +kl+al++Cn+HGlWes+
  gi|91772847|ref|YP_565539.1| 144 MKLDALISCNVHGLWESK 161
                                   89**************85 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.4e-06     0.066      15      40 ..      25      67 ..      20     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-06
                        DUF737 15 LsedVinRmkesskaakkkqakepl.................p 40
                                  +se+VinR k++++  +++q++ p+                 +
  gi|91772847|ref|YP_565539.1| 25 MSEQVINRLKDPENITETEQKHVPVieadevmtaegsfevtvK 67
                                  7***************989988888433333333332222220 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1300.01
//
Query:       gi|91772848|ref|YP_565540.1|  [L=82]
Description: hypothetical protein Mbur_0836 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.4   4.1      0.028   14.9   4.1    1.2  1  FtsX      FtsX-like permease family
      0.092   11.7   5.3        0.1   11.6   5.3    1.1  1  PalH      PalH/RIM21


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   4.1   3.1e-06     0.028      18      89 ..      11      78 ..       3      81 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-06
                          FtsX 18 lllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsis 89
                                  + + +  il+i+++a +  +++  +++q    v+ +    + +++ +d+ +++ +++++l+++ ++++ s+ 
  gi|91772848|ref|YP_565540.1| 11 MFMTIFDILFIFILAGI--CIVVPVIIQGTVLVGWEGT--GTMQFVWDPVQYFGLLAVILVFFFVVLYHSVK 78
                                  44444445555554444..7778888887666665553..8********************99999665554 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.3   1.1e-05       0.1     181     239 ..      20      82 .]       9      82 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                          PalH 181 iiilvGlaliildtilsalllf....skkfldalpalsylfelalvtlyaalviyYliskrky 239
                                   +i++++ ++i++ +i+++  l+    + + + ++ +++y   la+++++ ++v+y+++++ ++
  gi|91772848|ref|YP_565540.1|  20 FIFILAGICIVVPVIIQGTVLVgwegTGTMQFVWDPVQYFGLLAVILVFFFVVLYHSVKNYRF 82 
                                   79*****************9997654449999**************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 504.91
//
Query:       gi|91772849|ref|YP_565541.1|  [L=89]
Description: monomethylamine transporter [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 565.34
//
Query:       gi|91772850|ref|YP_565542.1|  [L=456]
Description: amino acid transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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  130.1  42.2    1.2e-37  129.6  42.2    1.1  1  AA_permease    Amino acid permease
    3.3e-22   78.9  45.3    4.6e-22   78.4  45.3    1.1  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6  42.2   1.4e-41   1.2e-37       9     434 ..      25     413 ..      18     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 1.4e-41
                   AA_permease   9 gviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitv 89 
                                   g++ +g ++g  ++++++G+lg l a+l+ag+++++v l+ +e+ +  + +gg y +a+ f+gp ++  +Gl   + +i+ 
  gi|91772850|ref|YP_565542.1|  25 GIVLVGEYMGWNFTVAKGGILGSLFALLVAGTMYVMVSLCASELGSSTKLAGGPYDWARLFVGPGAAAIVGLAVYMEYIAL 105
                                   444577889999*************************************************************77777788 PP

                   AA_permease  90 laleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkga 170
                                    a++ ++++++ q +  ++++  ++ + ++++++l+++n+ gv +     f l++ ++iaiiaf+ + i + +gg   ++ 
  gi|91772850|ref|YP_565542.1| 106 EAADAIVVASIAQSI--FPEIQ-TFPVTLLVIAALTFMNYRGVVAALNLNFALTFTALIAIIAFFFMNI-SGIGGTWHPE- 181
                                   888999999999999..*****.999999***************************************5.4444444444. PP

                   AA_permease 171 gfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsl 251
                                             + +  +p+g        f ++++++++    + Gie  a+ a+E+k P ++iP +    +i++++   + l
  gi|91772850|ref|YP_565542.1| 182 ---------YLISGAIPNG--------FIGIFAALQFGPWFYLGIEGAAMCAEECKHPTRAIPLGQQAGMITLLLGSGMTL 245
                                   .........2334458999........**************************************9988887777666777 PP

                   AA_permease 252 lligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP.kvlkkv 331
                                   ++++ l+p+  lg+       + p+  + + sgv++l  ++++++l ++l san+ +  +sR  ++l++d  +  ++++++
  gi|91772850|ref|YP_565542.1| 246 YVCSGLIPTAELGVSV-----Y-PLFEAANRSGVKFLIAFLAVGTLFTCLASANGTVCDSSRSWFALSRDHFLTnWFAAVH 320
                                   8888899999977766.....4.56667899************************************************** PP

                   AA_permease 332 skrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallp 412
                                   +k+  P+ra++++m i++++    ++ +      + ++++s  +gl+++++i +s++rfRk + +++ ++   +f  +l+p
  gi|91772850|ref|YP_565542.1| 321 TKYSTPYRAVIFTMPIAVAFA---YSGFL-----DQVITFSITSGLVCYVMIPFSLIRFRKMFPEHTQKV--RPFVGPLQP 391
                                   *******************99...55554.....5578889999******************99999955..89******* PP

                   AA_permease 413 lgvilvlaaliiillilalyay 434
                                   +++++++++ i i+ +l++ ++
  gi|91772850|ref|YP_565542.1| 392 YLAYFTILLAIVIMSTLNWGYS 413
                                   ****999999999888887665 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4  45.3   5.1e-26   4.6e-22      10     406 ..      23     413 ..      16     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 5.1e-26
                 AA_permease_2  10 vigsvigsgifvkn.......laasggpa.lilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsaw 82 
                                    +g+v+       +        +a+gg++ +++ +++a  ++ ++v+l+  El+s  +  gG y +++ + g+ +a +++ 
  gi|91772850|ref|YP_565542.1|  23 GVGIVLV------GeymgwnfTVAKGGILgSLFALLVAGTMY-VMVSLCASELGSSTKLAGGPYDWARLFVGPGAAAIVGL 96 
                                   4444433......33333347688888885777777777777.8*********766************************* PP

                 AA_permease_2  83 fnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilg 163
                                   +  + y++  a+ ++v+as  ++ ++p++     +t+ +  ++++ ++++n+rg+    ++++ l+ + + + +i ++   
  gi|91772850|ref|YP_565542.1|  97 AVYMEYIALEAADAIVVASIAQS-IFPEI-----QTFPVTLLVIAALTFMNYRGVVAALNLNFALTFTAL-IAIIAFFFMN 170
                                   ********887777777777777.56876.....56777889******************9999998888.5555555566 PP

                 AA_permease_2 164 litvdgggfsslstetdt....ffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifigllivlvlyllvn 238
                                   +  ++g+++++      +      png  g++++l    w + G+e+aa  +ee  ++++ +p++   g+++ l+    + 
  gi|91772850|ref|YP_565542.1| 171 ISGIGGTWHPE------YlisgAIPNGFIGIFAALQFGPWFYLGIEGAAMCAEEckHPTRAIPLGQQAGMITLLLGSGMTL 245
                                   66667788884......22223577777788999999*****************5555699***99888877766666666 PP

                 AA_permease_2 239 iaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.kf 318
                                    +  g +p  e+ +   +++++   ++++g k++ +++++++ + +l ++n+ v  ssr  +al+rd +l ++fa v+ k+
  gi|91772850|ref|YP_565542.1| 246 YVCSGLIPTAELGV---SVYPLFEAANRSGVKFLIAFLAVGTLFTCLASANGTVCDSSRSWFALSRDHFLTNWFAAVHtKY 323
                                   66777888888875...334555566666789************************************************* PP

                 AA_permease_2 319 gspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl.kr...pgk.....ilvaii 390
                                    +p+ra+i+t+ +++++    ++  s  ++ + + s  + +++y ++ ++++  rk  p+  ++   +       +l +++
  gi|91772850|ref|YP_565542.1| 324 STPYRAVIFTMPIAVAF----AY--SGFLDQVITFSITSGLVCYVMIPFSLIRFRKMFPEHtQKvrpF-VgplqpYLAYFT 397
                                   *************9554....33..4567888888888888888888889999999888663335541.244444566666 PP

                 AA_permease_2 391 galfllfllvalffpp 406
                                   ++l ++++  +++ ++
  gi|91772850|ref|YP_565542.1| 398 ILLAIVIMSTLNWGYS 413
                                   6666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2536.94
//
Query:       gi|91772851|ref|YP_565543.1|  [L=217]
Description: monomethylamine corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-22   78.4   0.5    8.5e-22   77.4   0.1    1.7  2  B12-binding_2  B12 binding domain
    1.7e-16   60.4   0.3    3.2e-16   59.5   0.3    1.4  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.1   9.4e-26   8.5e-22       3      75 .]       8      80 ..       6      80 .. 0.98
   2 ?   -2.5   0.0      0.83   7.5e+03      19      29 ..     134     144 ..     133     174 .. 0.53

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 9.4e-26
                 B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75
                                  ++l++aiv+ d +g+  +++eal++g  a+d++n++l+p+mk+VGd f+a +++lpq ++sa++mk+a+++Le
  gi|91772851|ref|YP_565543.1|  8 DKLKNAIVNQDINGCPVITQEALDAGITALDIINEALAPGMKIVGDNFEAATIYLPQIMMSAKAMKAAMEILE 80
                                  789********************************************************************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.83
                 B12-binding_2  19 elidealaqgs 29 
                                   e++ ea+a+++
  gi|91772851|ref|YP_565543.1| 134 EDVVEAIAKNK 144
                                   56666666443 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.3   3.5e-20   3.2e-16       7     120 ..     100     209 ..      94     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.5e-20
                   B12-binding   7 tvggdlhplGlavlaaalrdagfeVqllganvenedivaairae.kpdv.vglSalltsqleavkelvel..lkrirprvk 83 
                                   + +gd+h++G +++  +l ++gfe+ +lg +++ned+v+ai+++    + ++ Sal+t+++ + k++v+l  ++  r+ vk
  gi|91772851|ref|YP_565543.1| 100 VQEGDIHDIGHRLVTTMLGANGFEIMDLGTDIPNEDVVEAIAKNkGKKMlLVGSALMTTSMLGQKDVVRLleEENLRDSVK 180
                                   5689**************************************99544443444999**************99899999*** PP

                   B12-binding  84 vvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   +++GGa+++ ++     +  g +d   g++e+a+ea+
  gi|91772851|ref|YP_565543.1| 181 IMFGGAPVTDAWIA---E-CG-AD---GTAENAAEAA 209
                                   *****996555555...4.99.99...9999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1370.10
//
Query:       gi|91772852|ref|YP_565544.1|  [L=135]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-23   82.5   0.1    2.7e-23   82.3   0.1    1.1  1  Response_reg  Response regulator receiver domain
     0.0098   15.9   0.0       0.18   11.8   0.0    2.1  2  MRP-S24       Mitochondrial ribosome subunit S24


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 !   82.3   0.1     3e-27   2.7e-23       1     111 [.       6     116 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 3e-27
                                   EEEESSSHHHHHHHHHHHHHTTEEEEE.EESSHHHHHHHHHHHHESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeeva.eaedgkealellkeekvdlillDinmpg.mdGlellkeireedpelpviilta 79 
                                   +l+v+D+ +v++++++ l   gy +v  +a++g++a+++++   +dl+l+Di++ g mdG+e+++eir++  ++pvi lta
  gi|91772852|ref|YP_565544.1|   6 ILVVEDEAIVAMVIKKRLMGLGY-VVSgVAATGTDAINKVEGTFPDLVLMDIMLKGeMDGIEVADEIRKRF-SIPVIYLTA 84 
                                   8**********************.6666***************************99*************9.********* PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                   hs+e+++++a   + ++++ Kpf++++L + +
  gi|91772852|ref|YP_565544.1|  85 HSDEKTLERAKLTEPYGYILKPFTENNLSTNI 116
                                   ***************************99876 PP

>> MRP-S24  Mitochondrial ribosome subunit S24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0     2e-05      0.18      62     102 ..      44      83 ..      36      93 .. 0.86
   2 ?    1.9   0.0     0.023     2e+02      98     126 ..     101     129 ..      90     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                       MRP-S24  62 itGtfhkllaseiiikRranviriaalllrklsarkiyfli 102
                                   ++Gtf++l++ +i++k +++ i++a  + +++s+  iy+ +
  gi|91772852|ref|YP_565544.1|  44 VEGTFPDLVLMDIMLKGEMDGIEVADEIRKRFSIPVIYL-T 83 
                                   79**************************99999877664.4 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.023
                       MRP-S24  98 iyfligytEelLsallkcpvklelqtves 126
                                    y l  +tE+ Ls+ +   ++ +l+ +e+
  gi|91772852|ref|YP_565544.1| 101 GYILKPFTENNLSTNIEMAIHKHLREMEK 129
                                   58999**********99999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.53
# Mc/sec: 770.61
//
Query:       gi|91772853|ref|YP_565545.1|  [L=727]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-28   96.7   1.8    1.9e-27   95.1   1.8    1.9  1  HisKA_2          Histidine kinase
    5.2e-22   78.8   4.7    5.3e-22   78.8   1.6    2.3  2  dCache_1         Cache domain
    1.1e-15   57.6   0.6    2.5e-15   56.5   0.6    1.6  1  PAS_3            PAS fold
    1.9e-05   25.2   0.4    5.5e-05   23.6   0.4    1.8  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    0.00042   19.7   1.4    0.00052   19.4   0.0    1.8  2  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
    0.00049   20.0   0.0     0.0012   18.8   0.0    1.6  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0049   17.5   0.1      0.013   16.2   0.1    1.7  1  HWE_HK           HWE histidine kinase
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.057   13.7   0.1    2.1  1  PAS_9            PAS domain
      0.017   15.0   0.0      0.055   13.3   0.0    1.8  1  sCache_2         Single Cache domain 2
      0.017   15.1   0.0      0.056   13.5   0.0    2.0  1  PAS              PAS fold


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   1.8   1.1e-30   1.9e-27       1      76 []     534     609 ..     534     609 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 1.1e-30
                       HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                   EihHR+kNnLqv+s++L l++ +++ +ev +a+r+s+nRv+sialihe+Ly+s+dl ++d+++y+++L+++lf+sy
  gi|91772853|ref|YP_565545.1| 534 EIHHRIKNNLQVVSGMLYLESLNFRYQEVIDAFRDSENRVRSIALIHEKLYQSKDLVSLDLADYIKDLTDHLFHSY 609
                                   9*************************************************************************98 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   1.6   2.9e-25   5.3e-22      14     247 ..      46     295 ..      31     297 .. 0.71
   2 ?    0.1   0.1      0.31   5.6e+02      52      90 ..     446     491 ..     420     581 .. 0.74

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.9e-25
                      dCache_1  14 laeqlanniedvlds.lenlaetlasnpslqdlleepnraneasreslqallksilksn....................pd 73 
                                    + q a+++ ++ +  +++++      ++l+ ll  ++   +a+r++++++l+++l  n                    ++
  gi|91772853|ref|YP_565545.1|  46 DSIQNAKSFANYYNAdMKANMAVA---QTLAALLVRYD---NADRDEINSMLEELLLENpdllasyvafepnafdgkdaEF 120
                                   444444444444322133222111...22444444444...79*************9994444444444444444444444 PP

                      dCache_1  74 isgvylvdadGqviassdpssppnleg.......tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiydds 147
                                   i++ +  d+ G++i   +++++    g       + d+   d+y+ +++ +  ++ i++py +   g +++++ +pi  d 
  gi|91772853|ref|YP_565545.1| 121 INADTAHDETGRFI---PYWNK---IGgemfvepLVDYDTLDYYQLTKQLEQ-DI-ITEPYLY-Q-GALIVSYDAPIVRD- 190
                                   44455555899987...44443...3345799*******************4.66.*****85.5.78**********86. PP

                      dCache_1 148 gkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd.kdllgknlrdelkaq.....ealekalakiesgvs 222
                                   g+fiG+ ++d+ l+++++++s++k  +tgy+f+v+++G +++hp  kd++g +     +++     e+   ++++  +g  
  gi|91772853|ref|YP_565545.1| 191 GEFIGIGGVDVELNYVDETVSSVKAFDTGYLFMVSNTGVLLSHPTrKDWIGMKSM---TEFeipmiEIVTEDINNGIGGHI 268
                                   *******************************************998999875333...33356799999999999999999 PP

                      dCache_1 223 svk..lngeeylvayapiptglgWylv 247
                                   +++  l+g+e  + y pi+tg+  +++
  gi|91772853|ref|YP_565545.1| 269 DTIdpLTGKEVVMFYEPIETGKFAIVL 295
                                   88878999999666*****85554444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                      dCache_1  52 a.....neasreslqallksil.ksnpdi.sgvylvdadGqviass 90 
                                         + ++r+++++ lk  + ++++++ ++  +++++G++ ++ 
  gi|91772853|ref|YP_565545.1| 446 LygniiYKDDRDEVWSELKRSAdEGHDHFhKDYRIITKSGEMRWVH 491
                                   2455667788888888888866466688866888888888887753 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.6   1.4e-18   2.5e-15       3      89 .]     425     511 ..     423     511 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.4e-18
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +vs++v +  Gys e +++    + ++++ +Dr++v+++l++++++g+ +++ +yRi++k+Ge+rwv++ +++ r+e+ k+
  gi|91772853|ref|YP_565545.1| 425 FVSDNVAQF-GYSLENFMSGNLLYGNIIYKDDRDEVWSELKRSADEGHdHFHKDYRIITKSGEMRWVHEDTFIQRNEEEKV 504
                                   788888776.**********88899***********************9******************************** PP

                         PAS_3  83 vrvigva 89 
                                    +++g++
  gi|91772853|ref|YP_565545.1| 505 EYFQGTI 511
                                   *****96 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 !   23.6   0.4   3.1e-08   5.5e-05       6     111 ..     635     726 ..     631     727 .] 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.1e-08
                                   HHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHH CS
                     HATPase_c   6 LrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkk 83 
                                   L  ii++l +Na+++   ++ +geie+   ++++ ++++++++G+  p+ d++     f +          + lGl +v +
  gi|91772853|ref|YP_565545.1| 635 LGIIINELTSNALQHafgNGIGGEIEIDFFKRDEIFELTISNTGKHFPE-DID-----FKN---------TESLGLQLVTN 700
                                   6679***********333334445555555455799***********98.777.....666.........677******** PP

                                   HHHHTTTEEEEEEETTTEEEEEEEEESS CS
                     HATPase_c  84 lvelmgGeiwvesepgrGttftftlple 111
                                   lv++++Gei +++++   ttft+t++ +
  gi|91772853|ref|YP_565545.1| 701 LVSQIEGEIGLDTTD--KTTFTITFRDD 726
                                   9999*******9999..9****998765 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       1.9   3.4e+03      15      62 ..      39      86 ..      31      94 .. 0.60
   2 !   19.4   0.0   2.9e-07   0.00052     158     291 ..     185     311 ..     174     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
               Cache_3-Cache_2 15 elekevedlaetletqdellrekverdlnvfakllsnewrvdnqetvk 62
                                  e +   +d  + ++++ +  ++ ++ ++ v+++l +  +r dn+++ +
  gi|91772853|ref|YP_565545.1| 39 EEQLAYHDSIQNAKSFANYYNADMKANMAVAQTLAALLVRYDNADRDE 86
                                  444445555666666777777777777777776666655555555555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.9e-07
               Cache_3-Cache_2 158 ePikdadgkViGilyVgvdqsealkslrkelkklkvGktGylyvldgkgdkkgkliihptlk....gknvldlkdadgesv 234
                                   +Pi  +dg+ iGi   gvd   +l+ + ++ +++k  +tGyl++++++    g l+ hpt+k     k++++      e  
  gi|91772853|ref|YP_565545.1| 185 APIV-RDGEFIGIG--GVDV--ELNYVDETVSSVKAFDTGYLFMVSNT----GVLLSHPTRKdwigMKSMTEF-----EIP 251
                                   6777.9********..7777..7788**********************....*********965533444444.....333 PP

               Cache_3-Cache_2 235 vkkllkk..ksgsleyelk..kdekgreklavftyfepwdWvivasvyedefqeevnrvrn 291
                                   + +++ +  ++g   + +   +  +g+e +++++  e    +iv  v+ +e++++v+++r+
  gi|91772853|ref|YP_565545.1| 252 MIEIVTEdiNNGIGGH-IDtiDPLTGKEVVMFYEPIETGKFAIVLVVPTEEMLAGVESLRS 311
                                   3444444465555444.22358999*******************************99986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   6.5e-07    0.0012      28     123 ..     631     721 ..     614     723 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.5e-07
                   HATPase_c_2  28 lldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikgl 108
                                   ++  + + ++E+ +Na +ha  ++  g++e+ +  ++e +++++++ G++f+               + ++ +Gl l+++l
  gi|91772853|ref|YP_565545.1| 631 TAVPLGIIINELTSNALQHAFGNGIGGEIEIDFFKRDEIFELTISNTGKHFPEDIDF----------KNTESLGLQLVTNL 701
                                   55567899*******************************************997544..........44567899999999 PP

                   HATPase_c_2 109 vDev..ey...dgegnvvtm 123
                                   v ++  e+   + ++++ t+
  gi|91772853|ref|YP_565545.1| 702 VSQIegEIgldTTDKTTFTI 721
                                   98884444665555666655 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.1e-06     0.013       1      52 [.     534     587 ..     534     616 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                                   HHHHHHHHHHHHHHHHHHHHSS..SXS-HHHHHHHHHHHHHHHHHHHHHHHHCT CS
                        HWE_HK   1 ElnHRvKNlLavvqsiarqtlr..saesleefaeklsgRLqALsaahdllsree 52 
                                   E++HR+KN L vv+++    +   + +++ ++ ++ ++R+++++  h+ l +++
  gi|91772853|ref|YP_565545.1| 534 EIHHRIKNNLQVVSGMLYLESLnfRYQEVIDAFRDSENRVRSIALIHEKLYQSK 587
                                   89**************8654330134455566677799********99887765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.2e-05     0.057       8     104 .]     418     516 ..     410     516 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                         PAS_9   8 npdgrilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltas 83 
                                   ++d +++++++ ++++ Gys e ++  +  + +++   ++++++++  l++  +     +++++ +i+k+ge  wv+   +
  gi|91772853|ref|YP_565545.1| 418 DHDYPVEFVSDNVAQF-GYSLENFMSGNllYGNII--YKDDRDEVWSELKRSADeghDHFHKDYRIITKSGEMRWVHEDTF 495
                                   5889999********9.***999999998888999..5555555555555555567789****************997777 PP

                         PAS_9  84 pvkdddgelvgiivilrDite 104
                                     +++++++  + +++ Dite
  gi|91772853|ref|YP_565545.1| 496 IQRNEEEKVEYFQGTILDITE 516
                                   7788899999999*******8 PP

>> sCache_2  Single Cache domain 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     0.055      41      80 ..     206     244 ..     203     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                      sCache_2  41 vkelvnglkfgdGkgYffvldedgtllvhPfnpqleGkna 80 
                                   v e+v++ k  d  gY+f++ ++g ll hP++++++G + 
  gi|91772853|ref|YP_565545.1| 206 VDETVSSVKAFD-TGYLFMVSNTGVLLSHPTRKDWIGMKS 244
                                   678899999999.************************775 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.1e-05     0.056      33     113 .]     432     514 ..     399     514 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                                   HHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           PAS  33 llGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlr 111
                                   ++G+s  + ++g  l++ i+ +dd+ e+ ++l++ + +g++  +++ ++ ++ g+ ++++  +   r++++++ +f g++ 
  gi|91772853|ref|YP_565545.1| 432 QFGYSLeNFMSGNLLYGNIIYKDDRdEVWSELKRSADEGHDHFHKDYRIITKSGEMRWVHEDTFIQRNEEEKVEYFQGTIL 512
                                   699999788999********************************************************************9 PP

                                   ES CS
                           PAS 112 di 113
                                   di
  gi|91772853|ref|YP_565545.1| 513 DI 514
                                   98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (727 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 4138.36
//
Query:       gi|91772854|ref|YP_565546.1|  [L=260]
Description: hypothetical protein Mbur_0843 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-25   89.6   0.1    2.4e-25   88.4   0.1    1.7  1  DUF1724   Domain of unknown function (DUF1724)
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.018   14.5   0.0    1.1  1  DUF5581   Family of unknown function (DUF5581)
      0.017   15.1   0.2      0.065   13.2   0.0    2.1  2  HTH_45    Winged helix-turn-helix
      0.028   14.1   0.0      0.075   12.7   0.0    1.6  2  DUF4423   Domain of unknown function (DUF4423)
      0.042   14.0   0.0       0.08   13.1   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
      0.054   13.4   0.0       0.12   12.3   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
       0.06   11.8   0.0      0.075   11.5   0.0    1.1  1  FHIPEP    FHIPEP family
      0.086   12.7   0.0       0.15   11.9   0.0    1.5  1  HTH_5     Bacterial regulatory protein, arsR family


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 !   88.4   0.1   1.1e-28   2.4e-25       2      61 ..     198     257 ..     197     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 1.1e-28
                       DUF1724   2 klyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSe 61 
                                    + v+++ ikp+s+ vtD+fl++slfd +g+ydh+d++sf++sAl+WGe+LFeyY + S 
  gi|91772854|ref|YP_565546.1| 198 TILVCEDTIKPPSFSVTDTFLYMSLFDINGRYDHHDIMSFEDSALEWGERLFEYYQNLSS 257
                                   589******************************************************997 PP

>> DUF5581  Family of unknown function (DUF5581)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.8e-06     0.018      94     157 ..     144     207 ..     129     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.8e-06
                       DUF5581  94 ttvfqlidpwkfqrmkkvgtaqtkiqllllsdlleq.ldrgreelvallessdvltflakwdlvk 157
                                   ++v+ l  p  ++ +  +  a tkiq++l + +le+ l+ + +e+++ll ssd +t l + d++k
  gi|91772854|ref|YP_565546.1| 144 SSVLSLYHPDNLELLNNMEAAGTKIQIILTESVLERmLNDSEKEMETLL-SSDNTTILVCEDTIK 207
                                   67889999999999*********************83566667777766.678889998888876 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.9e-05     0.065      40      75 ..      47      83 ..      21      85 .. 0.88
   2 ?   -1.6   0.1       1.3   2.8e+03      12      26 ..     155     169 ..     153     186 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                        HTH_45 40 LdmLvekgli.kkskekYvlTekGlelleklkeleel 75
                                  +++L + g+i k+++++YvlT  G+ ++e+lk l  +
  gi|91772854|ref|YP_565546.1| 47 IKKLRNVGFIdKNESGSYVLTSIGRLVVENLKPLSGM 83
                                  899*******7779***************99977655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                        HTH_45  12 LeaisegeakkTkim 26 
                                   Le ++++ea  Tki 
  gi|91772854|ref|YP_565546.1| 155 LELLNNMEAAGTKIQ 169
                                   677777788777773 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.3e-05     0.075      31      80 ..      22      68 ..      16      80 .. 0.88
   2 ?   -2.4   0.0       1.5   3.3e+03      64     103 ..     115     156 ..     107     161 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                       DUF4423 31 plkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqte 80
                                   l+d  ad++++   l+  ++ + +   ++ L ++g+++k+e+g y+ t+
  gi|91772854|ref|YP_565546.1| 22 LLNDP-ADIKTINSTLT--VTSSSILPQIKKLRNVGFIDKNESGSYVLTS 68
                                  45556.9**********..***************************9997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                       DUF4423  64 klgllkkdedgkyrqtekslt..tssevkseavrsyhkqmle 103
                                   +++l+  d d  y+  +++l+    s+  s +++ yh ++le
  gi|91772854|ref|YP_565546.1| 115 NIQLIIPDLDHMYELQDEFLKnmRASSKVSSVLSLYHPDNLE 156
                                   555666666666666666666422334445556666666555 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 ?   13.1   0.0   3.6e-05      0.08       9      45 ..      20      57 ..      17      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                        HTH_34  9 Las.vdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                  L+  +d ad +++ ++l +t++ +  ++kkL + g+i 
  gi|91772854|ref|YP_565546.1| 20 LMLlNDPADIKTINSTLTVTSSSILPQIKKLRNVGFID 57
                                  444599*****************************996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05      0.12      16      60 ..      20      64 ..      12      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                   +l ++pa++++i + l v  s++   +++L + G+++++++  +
  gi|91772854|ref|YP_565546.1| 20 LMLLNDPADIKTINSTLTVTSSSILPQIKKLRNVGFIDKNESGSY 64
                                  45689**********************************997655 PP

>> FHIPEP  FHIPEP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.4e-05     0.075     522     636 ..      97     212 ..      73     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.4e-05
                                   XXHHHHHHHHHHHTTTXXSHHHHHHHHHH..HTHHHHHHHHH.TTSXEEEEEEXHHHHHHHHHHEEESSSE..EEXXXHHH CS
                        FHIPEP 522 rdlrtIletlaeaakktkdvellteavRq..aLkrqivqklaeedgelkvitldpeleqalaeslkqsegegsalalepel 600
                                   rdl+tI + l ++  +  +++l++    +  +L+ +  +++ +++++ +v+ l +  + +l ++++ +  ++ ++ l++++
  gi|91772854|ref|YP_565546.1|  97 RDLTTIPDNLLDNIGSLGNIQLIIPDLDHmyELQDEFLKNMRASSKVSSVLSLYHPDNLELLNNMEAAG-TKIQIILTESV 176
                                   899999999999999999999998876542389999*****************9999999****99865.56799****** PP

                                   HHHHHHHHHHHH.CXXSXGGGXEEEEXCCCHHHHHH CS
                        FHIPEP 601 aeklleklkeavekleekgekpvllvspevRrllrk 636
                                   +e++l++ ++++e+l +++++++l+++ ++++   +
  gi|91772854|ref|YP_565546.1| 177 LERMLNDSEKEMETLLSSDNTTILVCEDTIKPPSFS 212
                                   ***************************999876655 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   6.9e-05      0.15       2      47 .]      13      58 ..      12      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  ++R  +L +L + ++ +  +   l ++ s +  + kkLr+ G+++k
  gi|91772854|ref|YP_565546.1| 13 EKRENLLLMLLNDPADIKTINSTLTVTSSSILPQIKKLRNVGFIDK 58
                                  78999**************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1569.65
//
Query:       gi|91772855|ref|YP_565547.1|  [L=261]
Description: hypothetical protein Mbur_0844 [Methanococcoides burtonii DSM 6242]
Scores for 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   83.4   0.2    1.9e-23   82.3   0.2    1.6  1  DUF1724      Domain of unknown function (DUF1724)
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.21   11.3   0.0    1.3  1  Herpes_UL92  UL92 family


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 !   82.3   0.2   2.1e-27   1.9e-23       1      62 []     196     257 ..     196     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 2.1e-27
                       DUF1724   1 tklyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSep 62 
                                   t+ly+y+++ +p+++ v+D+f+++s+f+++g+ydh+d++sfd+ Al+WG+eLF+yY+++S++
  gi|91772855|ref|YP_565547.1| 196 TRLYLYKGKGRPPAIDVSDWFMYVSFFNEQGRYDHRDIMSFDNTALNWGKELFQYYCDQSTE 257
                                   589*********************************************************96 PP

>> Herpes_UL92  UL92 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.21      33      97 ..      50     116 ..      35     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                   Herpes_UL92  33 ggeeCilvntgeglvCaltGncvvnniq..esellepieeakldeqedlealeniveavkkdvysyl 97 
                                   ++e+C +v+  e ++   tG+ +v n++   ++l   +e+++  eq+d + l   +   ++++ +yl
  gi|91772855|ref|YP_565547.1|  50 LKEKCLIVEEDETYILSNTGRHIVRNMLplINTLRMINENRSYWEQHDINILPPHLFKRLHELGNYL 116
                                   5789**********************99533333333334444455566665554444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1645.23
//
Query:       gi|91772856|ref|YP_565548.1|  [L=217]
Description: monomethylamine corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-22   77.3   0.4    2.1e-21   76.1   0.1    1.7  2  B12-binding_2  B12 binding domain
    1.5e-16   60.5   0.3    2.8e-16   59.7   0.3    1.4  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.1   2.4e-25   2.1e-21       3      75 .]       8      80 ..       6      80 .. 0.98
   2 ?   -2.3   0.0      0.73   6.5e+03      19      29 ..     134     144 ..     132     175 .. 0.53

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 2.4e-25
                 B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75
                                  ++l++aiv+ d +g+  +++eal++g  a d++n++l+p+mk+VGd f+a +++lpq ++sa++mk+a+++Le
  gi|91772856|ref|YP_565548.1|  8 DKLKNAIVNQDINGCPVITQEALDAGITAFDIINEALAPGMKIVGDNFEAATIYLPQIMMSAKAMKAAMEILE 80
                                  789********************************************************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.73
                 B12-binding_2  19 elidealaqgs 29 
                                   e++ ea+a+++
  gi|91772856|ref|YP_565548.1| 134 EDVVEAIAKNK 144
                                   56666776443 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.3   3.1e-20   2.8e-16       7     120 ..     100     209 ..      94     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.1e-20
                   B12-binding   7 tvggdlhplGlavlaaalrdagfeVqllganvenedivaairae.kpdv.vglSalltsqleavkelvel..lkrirprvk 83 
                                   + +gd+h++G +++  +l ++gfe+ +lg +++ned+v+ai+++    + ++ Sal+t+++ + k++v+l  ++  r+ vk
  gi|91772856|ref|YP_565548.1| 100 VQEGDIHDIGHRLVTTMLGANGFEILDLGTDIPNEDVVEAIAKNkGKKMlLVGSALMTTSMLGQKDVVRLleEENLRDSVK 180
                                   5689**************************************99544443444999**************99899999*** PP

                   B12-binding  84 vvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   +++GGa+++ ++     +  g +d   g++e+a+ea+
  gi|91772856|ref|YP_565548.1| 181 IMFGGAPVTDAWIA---E-CG-AD---GTAENAAEAA 209
                                   *****996555555...4.99.99...9999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1349.19
//
Query:       gi|91772857|ref|YP_565549.1|  [L=136]
Description: transposase ISA1083-3, ISORF2 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-13   49.7   0.1    7.2e-13   48.9   0.1    1.4  1  HTH_32        Homeodomain-like domain
    7.6e-11   41.9   0.1    1.1e-10   41.4   0.1    1.3  1  HTH_29        Winged helix-turn helix
    5.2e-09   35.6   0.3    1.3e-08   34.3   0.0    1.8  2  HTH_33        Winged helix-turn helix
    8.2e-09   35.5   1.5    1.3e-08   34.8   1.0    1.6  2  HTH_28        Helix-turn-helix domain
    2.8e-07   30.1   0.3    5.5e-07   29.2   0.3    1.5  1  HTH_23        Homeodomain-like domain
      6e-05   23.5   0.6    0.00014   22.3   0.2    1.7  2  LZ_Tnp_IS481  leucine-zipper of insertion element IS481
  ------ inclusion threshold ------
      0.035   14.7   0.2      0.094   13.3   0.0    1.7  2  DUF2407       DUF2407 ubiquitin-like 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 !   48.9   0.1   2.8e-16   7.2e-13       3      72 ..      62     131 ..      60     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.8e-16
                        HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                   + w kR+n++G++gL +r  +grp+kl+d+++  ++  lr +  W++ ++++ +++++gv++S  +v+ i
  gi|91772857|ref|YP_565549.1|  62 YVWQKRWNRDGYAGLLPRYAGGRPSKLTDDQKSDLKFYLRMQENWTTARVRELIRDKFGVDYSLKQVRVI 131
                                   78*************************************8788************************987 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   4.3e-14   1.1e-10      10      62 ..      43      93 ..      34      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.3e-14
                        HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeqe 62
                                   G s v ++A+ +g+++r  y w+kr++ +G a+ll+r+++grp++ l+++q+
  gi|91772857|ref|YP_565549.1| 43 MGDS-VEEAARKVGVTKRVAYVWQKRWNRDGYAGLLPRYAGGRPSK-LTDDQK 93
                                  5776.***************************************96.999885 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         1   2.7e+03      25      34 ..      59      68 ..      52      70 .. 0.53
   2 !   34.3   0.0   5.1e-12   1.3e-08       2      34 ..     103     135 ..     102     136 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                        HTH_33 25 sgvyrlLkrl 34
                                  +  y + kr+
  gi|91772857|ref|YP_565549.1| 59 RVAYVWQKRW 68
                                  3334444444 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 5.1e-12
                        HTH_33   2 fgrWtlarlaqlieerfgvsysvsgvyrlLkrl 34 
                                   ++ Wt+ar+++li+++fgv+ys ++v+ ++k +
  gi|91772857|ref|YP_565549.1| 103 QENWTTARVRELIRDKFGVDYSLKQVRVIMKGM 135
                                   578***************************987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   1.0   5.1e-12   1.3e-08      11      51 ..      43      83 ..      33      86 .. 0.87
   2 ?   -2.5   0.0       2.3   5.8e+03      21      30 ..     118     129 ..     108     133 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 5.1e-12
                        HTH_28 11 aGhsvreaArelgisrrtvyrWikryeegGiagLvprrrrp 51
                                   G+sv eaAr++g++ r  y+W kr++  G agL+pr  ++
  gi|91772857|ref|YP_565549.1| 43 MGDSVEEAARKVGVTKRVAYVWQKRWNRDGYAGLLPRYAGG 83
                                  699**********************************6433 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                        HTH_28  21 elgi..srrtvy 30 
                                   ++g+  s  +v+
  gi|91772857|ref|YP_565549.1| 118 KFGVdySLKQVR 129
                                   566643445555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.3   2.1e-10   5.5e-07      16      50 .]      41      77 ..      25      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.1e-10
                        HTH_23 16 e..GlsvreIAreLgvsrrTvyrwlkryreeGlegll 50
                                  +  G+sv+e+Ar+ gv++r  y w kr++++G +gll
  gi|91772857|ref|YP_565549.1| 41 RymGDSVEEAARKVGVTKRVAYVWQKRWNRDGYAGLL 77
                                  1449*******************************96 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 !   22.3   0.2   5.5e-08   0.00014      27      62 ..      46      81 ..      29      95 .. 0.82
   2 ?   -1.1   0.0       1.1   2.8e+03      22      31 ..     102     111 ..      85     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.5e-08
                  LZ_Tnp_IS481 27 tvaqvarelGvslrtaykwlarfraeGldGlldrss 62
                                  +v ++ar++Gv++r+ay w  r+  +G  Gll r +
  gi|91772857|ref|YP_565549.1| 46 SVEEAARKVGVTKRVAYVWQKRWNRDGYAGLLPRYA 81
                                  6899****************************9965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                  LZ_Tnp_IS481  22 vedrrtvaqv 31 
                                   +++++t a+v
  gi|91772857|ref|YP_565549.1| 102 MQENWTTARV 111
                                   8899998877 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   5.7e+03      35      48 ..      11      24 ..       8      28 .. 0.53
   2 ?   13.3   0.0   3.7e-05     0.094      12      52 ..      94     134 ..      88     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                       DUF2407 35 erlpaelasrrLrL 48
                                  ++l+ e  ++r+r 
  gi|91772857|ref|YP_565549.1| 11 KKLTYEELNKRIRY 24
                                  44444444555554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.7e-05
                       DUF2407  12 pDleLdipdpntttvagLkqliRerlpaelasrrLrLIyaG 52 
                                    Dl+      ++ t+a +++liR++   +++ +++r I++G
  gi|91772857|ref|YP_565549.1|  94 SDLKFYLRMQENWTTARVRELIRDKFGVDYSLKQVRVIMKG 134
                                   588888888999***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 872.21
//
Query:       gi|91772858|ref|YP_565550.1|  [L=291]
Description: hypothetical protein Mbur_0849 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-53  180.1   0.0    6.7e-53  179.9   0.0    1.0  1  DUF89     Protein of unknown function DUF89


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.9   0.0   3.8e-57   6.7e-53       3     346 ..       5     278 ..       3     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 3.8e-57
                                   HTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHHHHTHS CS
                         DUF89   3 eerlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrllelfgls 83 
                                   ++++ c+l++v+ +++ ++++       +i + +    ++ +d+ ++ +            p  ++ + ++r+ +e+++  
  gi|91772858|ref|YP_565550.1|   5 ARCTYCLLSRVHYEAKLSTND-----DDLIHKTMLAGIDVLKDTYIPGV------------PAGVVSTAIHRKAYEVLN-- 66 
                                   689**************9888.....44444444444455556666666............66679*************.. PP

                                   GGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSH.HHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHHHHHHHHCT CS
                         DUF89  84 kelknyDpFkeqKeesnksalkaveelakrleelede.kelfkellkislwGNaiDlsllateediqkdqeeearkalekn 163
                                       ++Dp+ ++K  sn+ a+k+++   + ++e e +  e+f++++ +s++GN +D+++ +  ++ ++   +++ + ++k 
  gi|91772858|ref|YP_565550.1|  67 ----DNDPYLDLKILSNEIAEKVYPYAHSLVHEGEPSdLEMFRRAVLASVIGNFFDFGIMG-FDVGEDVFDKTFADIFRKG 142
                                   ....**************************988877769**********************.99***************** PP

                                   ESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHHHHHHHHHHH-TT CS
                         DUF89 164 ilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeDfewlleqladsk 244
                                   + vdd++++++ l      +v++v+DN+G E+++D l+++ +++   + k++l+v++ P +++Dvt++D++          
  gi|91772858|ref|YP_565550.1| 143 LDVDDTPEMFDLL-----DNVVYVVDNCG-EIILDTLVLDIIRK--VGGKITLVVRGAP-MLTDVTMDDVR---------- 204
                                   *************.....***********.**************..*************.***********.......... PP

                                   TSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEEEHHHHHHHHTTSCTTTTTSEHHHHTG CS
                         DUF89 245 sfelsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvifKGdlNyrkLtgdrkwppttpfttalg 325
                                            +ld+  k+++++++g +   +g+s++e+  +pe++e+le+a+L+i+KG++Ny++++ +r   p         
  gi|91772858|ref|YP_565550.1| 205 -------KYELDK--KVDRVLTTGCN--AVGVSFDEA--PPEFLEALEDASLIISKGMANYETMS-ERSFGP--------- 262
                                   .......9*****..***********..*********..*************************5.566664......... PP

                                   TSS--EEEEEE--SHHHHHHH CS
                         DUF89 326 fspvpvlaLrtvKadvvagll 346
                                        +++L+++K++ va+++
  gi|91772858|ref|YP_565550.1| 263 -----IAYLLRTKCEAVAEDM 278
                                   .....*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1932.30
//
Query:       gi|91772859|ref|YP_565551.1|  [L=62]
Description: hypothetical protein Mbur_0850 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-20   71.9   4.6    4.2e-20   71.8   4.6    1.0  1  CooT      CO dehydrogenase accessory protein CooT
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.39   10.8   0.0    1.6  2  bPH_6     Bacterial PH domain


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 !   71.8   4.6   4.7e-24   4.2e-20       1      60 [.       1      59 [.       1      60 [. 0.96

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 4.7e-24
                          CooT  1 MCeanvyllkngkeeelvmedVdkiepeedgvvltdifGeekevegkIkeidLvehkiil 60
                                  MCe+nv+++k++ e+elvme+V+k+ +++d+++lt+ifGe++++ g+Ikeid+++++ i+
  gi|91772859|ref|YP_565551.1|  1 MCELNVIVVKGD-EKELVMESVTKMLVDGDSIELTGIFGEKTIIFGTIKEIDFSKGETII 59
                                  ********9877.55******************************************998 PP

>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.23     2e+03      56      68 ..      10      22 ..       8      24 .. 0.80
   2 ?   10.8   0.0   4.3e-05      0.39       6      37 ..      26      57 ..      22      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.23
                         bPH_6 56 lgddpelvadalr 68
                                  +gd  elv+++++
  gi|91772859|ref|YP_565551.1| 10 KGDEKELVMESVT 22
                                  6888899999986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.3e-05
                         bPH_6  6 vdpdGvevrnlfrtrrlpWsaiagvrfpegrr 37
                                  vd d +e+ ++f+++++    i++++f +g +
  gi|91772859|ref|YP_565551.1| 26 VDGDSIELTGIFGEKTIIFGTIKEIDFSKGET 57
                                  899************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.29s 00:00:00.69 Elapsed: 00:00:00.50
# Mc/sec: 375.68
//
Query:       gi|91772860|ref|YP_565552.1|  [L=335]
Description: glyceraldehyde-3-phosphate dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-29  102.1   0.0    3.6e-29  101.4   0.0    1.4  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    1.7e-10   41.1   0.7      3e-10   40.3   0.7    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    1.4e-06   28.6   1.2    8.8e-06   26.0   1.2    2.3  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
      6e-05   23.3   0.3    0.00015   22.0   0.1    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    6.2e-05   22.6   0.3      0.027   14.0   0.1    2.3  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    0.00029   20.2   0.3      0.017   14.5   0.2    2.4  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.022   15.4   0.2      0.068   13.8   0.2    1.9  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
      0.026   15.3   0.1      0.054   14.3   0.1    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.063   14.0   2.1       0.32   11.7   2.1    2.1  1  CoA_binding      CoA binding domain
      0.072   13.5   0.1       0.17   12.3   0.1    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.092   13.0   0.7       0.19   12.0   0.4    1.8  2  TrkA_N           TrkA-N domain
       0.14   12.7   0.4       0.48   11.1   0.4    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.0   2.4e-32   3.6e-29       1     157 [.     146     297 ..     146     298 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 2.4e-32
                                   HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEEEEEE CS
                       Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldglAvrV 79 
                                   L++++  l+++fg+kk+++t++++++++          d+++++++a  +n+i+ +++++++v++V+p  ++++ ++Av++
  gi|91772860|ref|YP_565552.1| 146 LCRVLSPLDKEFGVKKARVTLLRRAADP---------GDIKTGPINAivPNPIKLPSHHGPDVKTVIP--NIDIATTAVKL 215
                                   89**************************.........9******************************..79********* PP

                                   SSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH..TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEETTTEEEEEE CS
                       Gp_dh_C  80 Ptpnvsvvdlvvelekevtveevnaalkeaae..galkgilsyteeelvssDlvgdph..ssifdaketivveenlvkvva 156
                                   Pt+ ++++ + +eleke t+e+v ++l e+++     +gi+s++e ++ ++Dl +++    ++  ++e+i++ e +++ ++
  gi|91772860|ref|YP_565552.1| 216 PTTLMHLHTINLELEKECTAEDVESVLAEQSRvrFVGQGITSTAEIMELAKDLGRSRGdmWENCIWNESITMYEGELYFFQ 296
                                   ********************************766679*****************9988899**********999888777 PP

                                   E CS
                       Gp_dh_C 157 w 157
                                   +
  gi|91772860|ref|YP_565552.1| 297 A 297
                                   6 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.7     2e-13     3e-10       1      95 [.       4     107 ..       4     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2e-13
                                   EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHH........HHSSSS--S-BEBSSHHHHHHH-SEE CS
                        DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdag........ellglgklgvavtddleevlekadvl 71 
                                   +kva++G+ G++Gk+v++av  ++d+e+ +  ++++  +++ +kd g        ++  ++k g++v+ ++ee++++adv+
  gi|91772860|ref|YP_565552.1|   4 VKVAINGY-GTIGKRVADAVALQDDMEIIGIAKTRPnfETVMAKDKGfnvytladRVGAMEKEGIEVSGTVEEMIKAADVV 83 
                                   69******.**********************9999978888999999****9996666777******************** PP

                                   EE-S-HHHHHHHHHHHHHT.T-EEE CS
                        DapB_N  72 iDFTtpeavlenlklalek.gvklV 95 
                                   +D T p  v ++ k ++ek g+k++
  gi|91772860|ref|YP_565552.1|  84 VDCT-PGKVGATNKDLYEKaGIKAI 107
                                   ****.66666665555555477766 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.2   5.9e-09   8.8e-06       1      39 [.       4      43 ..       4      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.9e-09
                                  CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-T.S-HHHH CS
                       Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindl.tdletl 39
                                  vkvainG+G IG+ v+ a++ ++++e++ i ++  + et+
  gi|91772860|ref|YP_565552.1|  4 VKVAINGYGTIGKRVADAVALQDDMEIIGIAKTrPNFETV 43
                                  69****************************9941333333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1     1e-07   0.00015       2      80 ..       7      90 ..       6     130 .. 0.87
   2 ?   -2.7   0.0       4.3   6.4e+03      53      65 ..     232     244 ..     222     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1e-07
                                  EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
               Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......lgvrfeaialdaenyeavLaallkegdlvvnls 77
                                   i G+G +G+ va+ +a ++d+  ei+ + +++ + e + ak        l  r+ a++    +++ ++++++k +d+vv+++
  gi|91772860|ref|YP_565552.1|  7 AINGYGTIGKRVADAVALQDDM--EIIGIAKTRPNFETVMAKDkgfnvytLADRVGAMEKEGIEVSGTVEEMIKAADVVVDCT 87
                                  567*******************..999999999999999988889999999999999999999******************** PP

                                  SGG CS
               Sacchrp_dh_NADP 78 ppi 80
                                  p  
  gi|91772860|ref|YP_565552.1| 88 PGK 90
                                  976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                                   E--TTTHHHHHHH CS
               Sacchrp_dh_NADP  53 aldaenyeavLaa 65 
                                   +++ae++e+vLa+
  gi|91772860|ref|YP_565552.1| 232 ECTAEDVESVLAE 244
                                   6777777777765 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 !   14.0   0.1   1.8e-05     0.027       4      58 ..       3      59 ..       1      64 [. 0.82
   2 !    6.9   0.0    0.0028       4.3      45      80 ..      63     102 ..      58     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                  TS-EEEES-SHHHH..HHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHH CS
                          IlvN  4 gkkiaviGyGsqGh..aqalnlrdsgldvvvglregsksvkkAkeegfevltvaeav 58
                                  + k+a+ GyG+ G+  a a  l+d    + ++  + +  +  Ak++gf+v+t+a+ v
  gi|91772860|ref|YP_565552.1|  3 KVKVAINGYGTIGKrvADAVALQDDMEIIGIAKTRPNFETVMAKDKGFNVYTLADRV 59
                                  679*********984467788999877677777777778999**********99865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                   HHTT-EEE.EHHHHHHT-SEEEE-S-HHH...HHHHHHHH CS
                          IlvN  45 keegfevl.tvaeavkkadvvmiliPDel...qkevyeee 80 
                                   ++eg+ev  tv+e++k+advv+  +P ++   +k++ye++
  gi|91772860|ref|YP_565552.1|  63 EKEGIEVSgTVEEMIKAADVVVDCTPGKVgatNKDLYEKA 102
                                   68899996489***************98622256777764 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   1.1e-05     0.017      36      85 ..       3      55 ..       1      62 [. 0.79
   2 ?    4.7   0.0     0.012        17      59     102 ..      49      90 ..      42     110 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                  TSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH..CHHHHTCEECSH CS
                  2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlk.afgmkviaydrskkkee..eeeelgvelvsl 85
                                  + +v+i G+G IG++va+ ++ + +m++i++ +++ + e   ++++g+++ +l
  gi|91772860|ref|YP_565552.1|  3 KVKVAINGYGTIGKRVADAVAlQDDMEIIGIAKTRPNFEtvMAKDKGFNVYTL 55
                                  5689**************9998999******9998765545556666655555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.012
                                   T-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--S CS
                  2-Hacid_dh_C  59 gmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlplt 102
                                   g++v+    +     ++e++g+e+  ++ee+++ +D+v+ ++p +
  gi|91772860|ref|YP_565552.1|  49 GFNVYTLADRVG---AMEKEGIEVSgTVEEMIKAADVVVDCTPGK 90 
                                   555555544433...356778887779***********9998843 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.6e-05     0.068       1      69 [.      10      89 ..      10     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                                  --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT...............HHHHHT--CB---HHHHHHHHS-EEEEE-S CS
                 NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd...............rkallasealtldlddliahldpdvvVEca 67
                                  G+G+iG++v+++++ q +   +e+ ++a+ +   +                   + + +  ++   ++++i+  ++dvvV+c+
  gi|91772860|ref|YP_565552.1| 10 GYGTIGKRVADAVALQDD---MEIIGIAKTRpNFETVMakdkgfnvytladrvGAMEKEGIEVSGTVEEMIK--AADVVVDCT 87
                                  99************9996...789999988855544446667777776665544445555566667777777..9*******9 PP

                                  -- CS
                 NAD_binding_3 68 ss 69
                                  + 
  gi|91772860|ref|YP_565552.1| 88 PG 89
                                  75 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.6e-05     0.054       1      78 [.       4      98 ..       4     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-05
                                  EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.................HHHHHTCTTESEE CS
                  GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.................leelladpeidav 66
                                  ++vai G+G ig++ +    + q++ e++++ +++++    +a+  g+++y+                  +ee+ +  ++d+v
  gi|91772860|ref|YP_565552.1|  4 VKVAINGYGTIGKRVA-DAVALQDDMEIIGIAKTRPNFETVMAKDKGFNVYTLadrvgamekegievsgtVEEMIK--AADVV 83
                                  589*************.555566***********997777779999999888877888888888888888888888..88998 PP

                                  EE-S-G...GGHHHH CS
                  GFO_IDH_MocA 67 ivatpn...gtheel 78
                                  + +tp     t ++l
  gi|91772860|ref|YP_565552.1| 84 VDCTPGkvgATNKDL 98
                                  888888665555555 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.1   0.00021      0.32      32      91 ..      51     108 ..       1     110 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                   EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEE CS
                   CoA_binding  32 avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiv 91 
                                    v+   +r ++ e +g++v  +v+e+++   +dv v ++P +  +   d   +agik i+
  gi|91772860|ref|YP_565552.1|  51 NVYTLADRVGAMEKEGIEVSGTVEEMIKA--ADVVVDCTPGKVGATNKDLYEKAGIKAIW 108
                                   355566677778888**************..**********999999999999****998 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 ?   12.3   0.1   0.00012      0.17       9      94 ..      12     107 ..       5     110 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                   SHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG..........GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
                Semialdhyde_dh   9 GyvGqellrlLeehpevelvvllsssrsaGkklaeavk..........aleegkdlkvedvdeeelkevdivflalpagvs 79 
                                   G +G++++  ++ + ++e++ ++ ++ +  + +a+ ++             e++ ++v+ + ee +k++d+v+ ++p++v 
  gi|91772860|ref|YP_565552.1|  12 GTIGKRVADAVALQDDMEIIGIAKTRPNFETVMAKDKGfnvytladrvGAMEKEGIEVSGTVEEMIKAADVVVDCTPGKVG 92 
                                   556666666666666666666555555333333333335555555566567778888888899999*************** PP

                                   HHHHHHHHHTTSEEE CS
                Semialdhyde_dh  80 kelapklaeagvkvi 94 
                                   +   + + +ag+k i
  gi|91772860|ref|YP_565552.1|  93 ATNKDLYEKAGIKAI 107
                                   **9999999999876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   0.00013      0.19       1      59 [.       6      66 ..       6      85 .. 0.78
   2 ?   -2.9   0.0       5.4   8.1e+03      49      61 ..      93     105 ..      90     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                  EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHH..HHTTSEEEES-TTSHHHHHHTT CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveel..reeglevvvgdatdeevLeeag 59
                                  ++i G+G++G+++a+ +   + +++++i k + ++e++  +++g++v+   a +  ++e+ g
  gi|91772860|ref|YP_565552.1|  6 VAINGYGTIGKRVADAVALqDDMEIIGIAKTRPNFETVmaKDKGFNVYT-LADRVGAMEKEG 66
                                  6799************99966678**********999943455577654.344555555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.4
                                   TTSHHHHHHTTGG CS
                        TrkA_N  49 atdeevLeeagie 61 
                                   at++++ e+agi+
  gi|91772860|ref|YP_565552.1|  93 ATNKDLYEKAGIK 105
                                   7889999999986 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   0.4   0.00032      0.48       1      70 [.       5      88 ..       5     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.................-EEECECHHHHHHH-SEEE CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.................vkvtavdneeaaeeadvvv 66
                                  k++i G+G +g+ +a  ++ ++  + ei+ +++  p+  + +a++ g                 ++v++ + ee+++ advvv
  gi|91772860|ref|YP_565552.1|  5 KVAINGYGTIGKRVADAVALQD--DMEIIGIAKTRPNFETVMAKDKGfnvytladrvgamekegIEVSG-TVEEMIKAADVVV 84
                                  68888***********999999..6666655577777777777777789**************999999.***********99 PP

                                  E-S- CS
                 F420_oxidored 67 lavk 70
                                   + +
  gi|91772860|ref|YP_565552.1| 85 DCTP 88
                                  7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2117.54
//
Query:       gi|91772861|ref|YP_565553.1|  [L=266]
Description: bifunctional inositol-1 monophosphatase/fructose-1,6-bisphosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  110.3   0.0    1.4e-31  110.0   0.0    1.0  1  Inositol_P   Inositol monophosphatase family
    6.1e-05   22.6   0.1    8.8e-05   22.1   0.1    1.2  1  FBPase       Fructose-1-6-bisphosphatase, N-terminal domain
  ------ inclusion threshold ------
       0.12   11.3   0.0       0.17   10.7   0.0    1.3  1  FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-enco


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 !  110.0   0.0   2.4e-35   1.4e-31      44     249 ..      45     242 ..       5     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 2.4e-35
                                   HHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEE..TTEEEEEE CS
                    Inositol_P  44 taadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllv..egkpvlGv 122
                                   + +d ++e++i+e l++   s ++l+ee ++      +++ ++t+i+DPiDGT+n ++ ip +++si++         +G 
  gi|91772861|ref|YP_565553.1|  45 KLIDDVSEKAIIEILKADGRSIRLLSEELGEVVF---GDDPEFTIILDPIDGTYNVANDIPFYGISIAIGTpdLSSTYFGY 122
                                   4689*************************99999...78888*************************998866788999** PP

                                   EEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHH CS
                    Inositol_P 123 iaqPllgqlysaakgkGaflngeklplsrappiseallvtlfavssrkdtseasllekvesavsaegvrsvgssalklaav 203
                                   + + ++g ++ a  gkGa++n+++++ s++++++++++ +l  ++++ +++  +l+++v    +  ++r +gs  l+l++v
  gi|91772861|ref|YP_565553.1| 123 VRNLANGDTFYAESGKGAYFNDKRISHSKCSSLNDFCV-SLYGYRKNVERTV-DLCKNV----R--RIRIFGSVSLELCYV 195
                                   *******************************9999887.5555544444444.244444....3..35899********** PP

                                   HHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC....SSSTTSS CS
                    Inositol_P 204 aeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge....grlllar 249
                                   a+G++da+++ + ++   D+AAG +i+ee GG+vtd +g+    +    ++
  gi|91772861|ref|YP_565553.1| 196 ASGRLDAFVDVRgSLRLVDVAAGKLIIEESGGIVTDGDGNtlklK----DS 242
                                   ***********999**************************55542....32 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 !   22.1   0.1   1.5e-08   8.8e-05      55     119 ..      38      99 ..       7     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.5e-08
                        FBPase  55 NvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnidt 119
                                     +G + k +D ++++ +ie lka ++   l SEE  e+++     + ++++++DP+DG  n+  
  gi|91772861|ref|YP_565553.1|  38 GADGTDTKLIDDVSEKAIIEILKADGRSIRLLSEELGEVVFG---DDPEFTIILDPIDGTYNVAN 99 
                                   568999999****************************98655...7889***********99965 PP

>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.8e-05      0.17      66      96 ..      69     102 ..       7     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.8e-05
                   FBPase_glpX  66 iGekvGs...gegpevdiavdpleGttlvAkglp 96 
                                     e++G+   g++pe+ i +dp++Gt  vA++ p
  gi|91772861|ref|YP_565553.1|  69 LSEELGEvvfGDDPEFTIILDPIDGTYNVANDIP 102
                                   5688888777788*****************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.65
# Mc/sec: 1238.26
//
Query:       gi|91772862|ref|YP_565554.1|  [L=278]
Description: NAD(+) kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-53  181.7   1.4      2e-53  181.5   1.4    1.1  1  NAD_kinase  ATP-NAD kinase
  ------ inclusion threshold ------
      0.026   14.1   0.1      0.055   13.1   0.1    1.6  1  DAGK_cat    Diacylglycerol kinase catalytic domain
      0.055   13.7   0.1        2.6    8.3   0.0    2.9  3  PK_C        Pyruvate kinase, alpha/beta 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 !  181.5   1.4   3.4e-57     2e-53      71     291 ..      54     263 ..       5     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 3.4e-57
                                   C-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEET CS
                    NAD_kinase  71 leafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrs 151
                                   +e + ++gv+l+i vGGDGT+l+    +++   P+lg+n+G++gfl e++p++a++++ek+le +++ ++r++l + ++ +
  gi|91772862|ref|YP_565554.1|  54 VELMREHGVELLISVGGDGTVLRNIARMED-PLPILGINMGTVGFLVEVNPSEAISTIEKVLE-GFKYSERSRLAIDLNGE 132
                                   566889****************98888886.9*******************************.9**********766555 PP

                                   TE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEE CS
                    NAD_kinase 152 kgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpi 232
                                   +           +++ nevv+ ++++++++++ + +d++ +e++++dg++++tPtGstay++saGgpli+P+v+a livp+
  gi|91772862|ref|YP_565554.1| 133 SI----------PAATNEVVLTTARPAKILTFRITIDDQKAEEMRADGVVIATPTGSTAYAMSAGGPLIDPAVNATLIVPL 203
                                   55..........789****************************************************************** PP

                                   SESSS----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                    NAD_kinase 233 cPhslssrpiVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfklir 291
                                    P++ls+rp Vv+ ss +++++   ++ea l++dG+++  ++++d+v++t+s  ++++++
  gi|91772862|ref|YP_565554.1| 204 APFKLSARPWVVPASSIIKVEMIvPEKEAALVVDGQYTHTIQKSDVVTLTMSGMPARFVE 263
                                   *********************999********************************9997 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.1e-06     0.055      49      93 ..      55      95 ..      22     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-06
                                  HHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS- CS
                      DAGK_cat 49 keakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtg 93
                                  + ++e+gv+l++ +GGDGtv   +  + +    ++p+  i +Gt+
  gi|91772862|ref|YP_565554.1| 55 ELMREHGVELLISVGGDGTVLRNIARMED----PLPILGINMGTV 95
                                  55677899***********8666665555....777777777775 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.078   4.6e+02       8      44 ..      54      90 ..      52     145 .. 0.86
   2 ?    8.3   0.0   0.00043       2.6      11      34 ..     163     186 ..     160     198 .. 0.90
   3 ?   -0.1   0.0      0.18   1.1e+03      12      30 ..     242     260 ..     222     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.078
                                  HHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEE CS
                          PK_C  8 veaaeelgakaIvvltesGetArliskyrpkvpiiav 44
                                  ve+ +e g+++ + +   G+  r i+++   +pi+ +
  gi|91772862|ref|YP_565554.1| 54 VELMREHGVELLISVGGDGTVLRNIARMEDPLPILGI 90
                                  677788899999999999999999***9999999976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00043
                                   HHHHT-SEEEEE-SSSHHHHHHHH CS
                          PK_C  11 aeelgakaIvvltesGetArlisk 34 
                                   aee+ a+ +v++t +G+tA  +s 
  gi|91772862|ref|YP_565554.1| 163 AEEMRADGVVIATPTGSTAYAMSA 186
                                   99*****************99986 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.18
                                   HHHT-SEEEEE-SSSHHHH CS
                          PK_C  12 eelgakaIvvltesGetAr 30 
                                   ++++ + +v+lt sG  Ar
  gi|91772862|ref|YP_565554.1| 242 HTIQKSDVVTLTMSGMPAR 260
                                   5566678999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1614.11
//
Query:       gi|91772863|ref|YP_565555.1|  [L=389]
Description: trans-homoaconitate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-79  266.0   4.3    5.1e-79  265.6   4.3    1.2  1  HMGL-like   HMGL-like
  ------ inclusion threshold ------
        0.2   12.1   0.1        0.7   10.3   0.1    2.0  1  Spore_SspJ  Small spore protein J (Spore_SspJ)


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 !  265.6   4.3   5.6e-83   5.1e-79       2     262 ..      22     276 ..      21     278 .. 0.99

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 5.6e-83
                                   -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHH CS
                     HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaav 82 
                                   ++i+d+tLRDGeq++++a++ +ek+ +a +Ld +gv++iE+gfp+ s  + + v++i + + +a+i++l+r++++d++aa+
  gi|91772863|ref|YP_565555.1|  22 IEICDVTLRDGEQTPGVAFTRDEKIDLALELDSIGVEVIEAGFPVVSTSEKDIVKEISNLGLDASICCLARSVIDDVDAAI 102
                                   79******************************************************************************* PP

                                   H....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEE CS
                     HMGL-like  83 ealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatri 163
                                   +    + +++v +fia+s+lhlk k++k+ ++v++ a  a++ a+++g +v++ +eda+rt++e+l +   aae++ ++++
  gi|91772863|ref|YP_565555.1| 103 D----CDVDIVSIFIAMSDLHLKFKYHKSCADVFSCAMGAIEHAKDHGLKVRFAAEDATRTNIETLKRAFLAAEDYHVDYV 179
                                   *....**************************************************************************** PP

                                   EEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHH CS
                     HMGL-like 164 niaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaale 244
                                   +iaDt+G+l+P   + l+s++k++v   +++ +HcHndlG+A+antl+A+eaGa+++ +t+nG+GeraGna+leel +al+
  gi|91772863|ref|YP_565555.1| 180 SIADTIGILSPATTHYLVSEIKKVVH--TPICIHCHNDLGMATANTLVAAEAGAKQLHTTINGIGERAGNASLEELLVALR 258
                                   **************************..***************************************************** PP

                                   HTT-B----HHHHHHHHH CS
                     HMGL-like 245 algvdtgldlqklrsiaa 262
                                   +++    +d++kl si++
  gi|91772863|ref|YP_565555.1| 259 VQHGIETYDTTKLNSISR 276
                                   ***9999******99986 PP

>> Spore_SspJ  Small spore protein J (Spore_SspJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   7.8e-05       0.7      16      44 ..     338     366 ..     333     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.8e-05
                    Spore_SspJ  16 knavdgaLEdAgkaLkgDPLQEAVqKKKN 44 
                                   k+a++g+  d g +L +D L E ++K KN
  gi|91772863|ref|YP_565555.1| 338 KKALKGIVNDLGYELDNDELCELINKVKN 366
                                   899*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2330.65
//
Query:       gi|91772864|ref|YP_565556.1|  [L=183]
Description: hypothetical protein Mbur_0855 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   89.6   0.0    3.5e-25   89.2   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 !   89.2   0.0     2e-29   3.5e-25       2     146 ..      26     156 ..      25     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 2e-29
                           NYN   2 vavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgkkavDv 81 
                                   +++++Dg n+    k+ +v+++++++ ++++g++++ r+++n++++   k+ +a++++g+ ++              +vDv
  gi|91772864|ref|YP_565556.1|  26 IGLLVDGPNVLR--KEFNVNLEEIRDVLKEYGNVKIGRVFLNQYAS--DKLVEAIENNGFePIICS----------SDVDV 92 
                                   7899*******9..6568************************5444..7999********888433..........67*** PP

                           NYN  82 elavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                   +lav+ +el+y++++dti Lv++D+DF pl++k++e+gk+++++++e +  s++L+++ad++i l
  gi|91772864|ref|YP_565556.1|  93 RLAVEGMELVYNPTIDTIALVTRDADFKPLLNKANEHGKETILFGVE-PGFSTALRNSADYVIIL 156
                                   *********************************************66.9*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1173.44
//
Query:       gi|91772865|ref|YP_565557.1|  [L=110]
Description: hypothetical protein Mbur_0856 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 714.13
//
Query:       gi|91772866|ref|YP_565558.1|  [L=279]
Description: rhomboid-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  124.7  17.4    4.3e-36  124.2  14.3    1.9  2  Rhomboid   Rhomboid family
    1.1e-10   41.5   3.0    1.8e-10   40.8   3.0    1.3  1  zf-AN1     AN1-like Zinc finger
    5.7e-05   23.6   2.2    5.7e-05   23.6   2.2    2.8  3  DUF1751    Eukaryotic integral membrane protein (DUF1751)
  ------ inclusion threshold ------
       0.14   12.4   2.0       0.29   11.3   2.0    1.5  1  C5HCH      NSD Cys-His rich domain
        3.9    8.6   6.8          2    9.5   2.8    2.3  2  zf-C2H2_4  C2H2-type zinc finger


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 ?    1.3   0.0     0.085     3e+02      90     126 ..      81     113 ..      69     117 .. 0.69
   2 !  124.2  14.3   1.2e-39   4.3e-36       7     147 ..     127     265 ..     125     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.085
                                   HHCCCCGS----HC...CCCCCCCCCCHHHCTSSSTT CS
                      Rhomboid  90 vprnrkllrkliiallllllfillnlvlgllpraggv 126
                                     r+r ++++ +   ++++++ +++++l ++p++  v
  gi|91772866|ref|YP_565558.1|  81 ARRTRSSIKTSP--SMAIIFICIVSFFLKIIPGY--V 113
                                   444444444444..55999999999999999988..4 PP

  == domain 2  score: 124.2 bits;  conditional E-value: 1.2e-39
                                   TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHHHHHH CS
                      Rhomboid   7 lwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgllgall 87 
                                    w+l+t+mflHa++ Hl+fNml+l++fG +le+r+G+  fl++y++sg++++l+++++sa++  p++GaSGai+g+++al+
  gi|91772866|ref|YP_565558.1| 127 PWTLITHMFLHASFGHLFFNMLVLFFFGRELEKRIGKDLFLYVYFISGIIAALGYSITSANN-VPIIGASGAIMGVFAALT 206
                                   7***********************************************************96.8***************** PP

                                   HHHHCCCCGS----HC....CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHCC CS
                      Rhomboid  88 vlvprnrkllrkliia.llllllfillnlvlgllpraggvsnlAHlgGllaGlllgllllr 147
                                   +l p+   ++ +++++   +lllf+ll+++l   +    v++ AHl+G+l+G+++g+ + +
  gi|91772866|ref|YP_565558.1| 207 ILAPNMEVYVYFIPMKiKYALLLFVLLDFMLLNAND--MVAHTAHLSGVLVGVIMGYKIKK 265
                                   ***********9999956666777777766666555..5*****************98766 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   3.0   4.9e-14   1.8e-10      13      39 ..       2      28 ..       1      29 [. 0.93

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 4.9e-14
                        zf-AN1 13 pfkCryCgkvFClkHrlpedHdCkkla 39
                                  +f+Cr+Cgk++C++Hrlpe H+C++l+
  gi|91772866|ref|YP_565558.1|  2 MFTCRFCGKSYCSDHRLPERHACTGLD 28
                                  69*********************9986 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4       2.7   9.8e+03      48      61 ..      96     109 ..      93     116 .. 0.72
   2 !   23.6   2.2   1.6e-08   5.7e-05       1      60 [.     120     179 ..     120     207 .. 0.72
   3 ?    1.0   0.6      0.18   6.3e+02      58      98 ..     223     262 ..     209     263 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                       DUF1751  48 lkFilvvnvitnll 61 
                                   ++Fi++v+++ +++
  gi|91772866|ref|YP_565558.1|  96 IIFICIVSFFLKII 109
                                   57888888877776 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.6e-08
                       DUF1751   1 PgallpypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFil.vvnvitnl 60 
                                   P+ ++  pwtl+t++f  +++ ++ +++l l+++g+ lE+  g+  l+ ++  + ++i++l
  gi|91772866|ref|YP_565558.1| 120 PSLMFLKPWTLITHMFLHASFGHLFFNMLVLFFFGRELEKRIGKD-LFLYVYfISGIIAAL 179
                                   8889999*********************************99965.555544033333333 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.18
                       DUF1751  58 tnllvvlltlllylvtkseelllvpisGlagilagflvalk 98 
                                    +   +l+ ll +++ + ++ ++++ + l g+l+g++  +k
  gi|91772866|ref|YP_565558.1| 223 IKYALLLFVLLDFMLLNAND-MVAHTAHLSGVLVGVIMGYK 262
                                   33444556666677777777.66777777788888888776 PP

>> C5HCH  NSD Cys-His rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.0     8e-05      0.29      14      27 ..       4      17 ..       2      30 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8e-05
                         C5HCH 14 fCefCPssFCkeHe 27
                                   C fC +s+C +H+
  gi|91772866|ref|YP_565558.1|  4 TCRFCGKSYCSDHR 17
                                  6************6 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.8   0.00056         2       1      19 [.       3      22 ..       3      23 .. 0.88
   2 ?    0.3   0.1      0.48   1.7e+03      10      23 ..     124     137 ..     121     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00056
                     zf-C2H2_4  1 fkCpiCgksFsskkaL.lrH 19
                                  f+C++Cgks++s ++L  rH
  gi|91772866|ref|YP_565558.1|  3 FTCRFCGKSYCSDHRLpERH 22
                                  89********9998897777 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                     zf-C2H2_4  10 FsskkaLlrHlkth 23 
                                   F  + +L +H+  h
  gi|91772866|ref|YP_565558.1| 124 FLKPWTLITHMFLH 137
                                   6677889****988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1785.57
//
Query:       gi|91772867|ref|YP_565559.1|  [L=802]
Description: acetyl-CoA decarbonylase/synthase complex subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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-121  405.7   0.4   3.2e-102  342.9   0.0    2.1  2  Prismane  Prismane/CO dehydrogenase family
    1.9e-07   31.5   5.0    1.9e-07   31.5   5.0    2.4  1  Fer4_7    4Fe-4S dicluster domain
    2.5e-07   30.8   4.4    2.5e-07   30.8   4.4    2.6  2  Fer4_9    4Fe-4S dicluster domain
    3.8e-06   27.3  17.4     0.0015   19.1   0.4    3.5  3  Fer4_17   4Fe-4S dicluster domain
    1.5e-05   25.0  21.8    0.00013   22.0  12.3    3.1  2  Fer4_10   4Fe-4S dicluster domain
    2.7e-05   23.8  22.9    5.3e-05   22.8   2.3    3.5  3  Fer4      4Fe-4S binding domain
    3.5e-05   23.8  20.2    0.00011   22.3  10.3    2.6  2  Fer4_21   4Fe-4S dicluster domain
    4.6e-05   23.8   0.6      0.014   15.8   0.1    2.8  2  Fer4_8    4Fe-4S dicluster domain
    0.00044   20.2  23.0     0.0019   18.2   1.0    3.8  3  Fer4_2    4Fe-4S binding domain
     0.0017   19.2   7.3       0.34   11.9   0.4    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
     0.0018   18.1   6.5       0.12   12.1   0.2    2.6  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
     0.0018   18.3   0.0      0.012   15.6   0.0    2.4  2  CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-termi
      0.002   18.5   1.5      0.002   18.5   1.5    3.2  2  Fer4_4    4Fe-4S binding domain
     0.0054   16.8   3.5     0.0054   16.8   3.5    3.1  2  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.061   13.5   8.9       0.74   10.0   2.0    2.6  2  Fer4_18   4Fe-4S dicluster domain
       0.69   10.5  10.2       0.99   10.0   1.8    2.9  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   2.0   2.6e-19   2.9e-16       2      56 ..      71     125 ..      70     132 .. 0.96
   2 !  342.9   0.0  2.8e-105  3.2e-102     109     510 ..     144     688 ..     130     689 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.6e-19
                                   EE-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane   2 fCrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladtli 56 
                                   +C++C++gpC++++nk+G+CG++ ++++ar+++++v++gaaah+ h+r+l+++li
  gi|91772867|ref|YP_565559.1|  71 QCCYCTFGPCDLSGNKEGACGINLEGHNAREFMLRVITGAAAHSGHGRHLLHHLI 125
                                   7*************************************************99986 PP

  == domain 2  score: 342.9 bits;  conditional E-value: 2.8e-105
                                   -SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 109 eenedirslkellpkglkglyaehaivlgyadeevveflaktlaglesdpldllskalrlGlldlkgmelldeantslfGt 189
                                   +   ++++++++ pk+l +l    ++vl+y++e+++++la++++g+e++++d++skal+ G++d++gme++d+a++s++++
  gi|91772867|ref|YP_565559.1| 144 P---NVQLVTGVQPKTLGDL----DSVLSYVEEQITQLLAAIHVGQEGAAIDFESKALHGGMIDHVGMEISDIAQISCLDF 217
                                   3...7999************....********************************************************* PP

                                   -....--EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHH.HHHCC......EEEEE CS
                                   x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx......xxxxx RF
                      Prismane 190 P....eppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalk.lkyrh......lvgnv 259
                                   P    e+pl+++++g+ld++k++++v+GH++a+++++++++e+kgln++++   L g+cctal+ ++y++       +++v
  gi|91772867|ref|YP_565559.1| 218 PksdeEAPLADIGMGCLDASKPTLIVIGHNVAAVTDIIDYMEDKGLNDKIE---LGGLCCTALDmTRYKTgdrtlpRAKVV 295
                                   *****999*******************************************...**********999999*********** PP

                                   CSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE-..-CTTCH.................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.................. RF
                      Prismane 260 GnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhie..eeekad.................. 320
                                   G+++++ k++++g++d+i+vd++Ci++++ ++a+k+++++itt++++++g+k+ +  +   +d                  
  gi|91772867|ref|YP_565559.1| 296 GTLAKELKTIRSGIPDVIIVDEQCIRADVLKEASKLMIPVITTNDKVMYGLKDRSndS--IEDiledlttgkekgalmfdy 374
                                   ******************************************************9332..222333444455555666666 PP

                                   .......HHHHHHHHHHHCCHCCTTCGG.-................................................... CS
                                   .......xxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                      Prismane 321 .......kdaseiiekAielakareekkve................................................... 343
                                           + ++++++  +++++      +                                                   
  gi|91772867|ref|YP_565559.1| 375 vklgelaPRLTMMMSEIRKQKGI------Kalptdeelkeladscvhclkcevacpnslpiseamtalsegdlskfellhd 449
                                   64444444444444444444444......2444555677888888888888888888888777777777777777666666 PP

                                   ................HHH.....................................HHTTSS-EEEEE-B---TTCGCCHH CS
                                   ................xxx.....................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 344 ................ida.....................................iksGtIkgvvlvvGCdnakkgrdyy 371
                                                                                           ++ Gt++g+v++vGC+n+++g+++ 
  gi|91772867|ref|YP_565559.1| 450 kciacgrceyacpkdiD-IvnviekssqrviseevgkvrvgrgpisdpeireegvnLVLGTTPGIVALVGCSNYPDGTKDL 529
                                   66666666666666650.1555666777777777777777888888888888888899*********************** PP

                                   HHHHHHCHHTTEEEEEECHHHHHC...CCTTTTEC...GHHHHSTHCEESEEEEESCCCHHHHHHHHHHHHHHT....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                      Prismane 372 telakelikrdvlvltaGCakyal...nklglgti...eaaelagegiPrvLdvGsCvdnyrivvialklaeal....... 439
                                   +++a+e+++r ++v+++GC++++l   + ++++t+   ++++++++g   +L++GsCv+n++i+++++k+a+++       
  gi|91772867|ref|YP_565559.1| 530 FTIADEMLRRSYIVVVSGCSAMDLgmyKGEDGLTLyekYPSRFKSGG---LLNTGSCVSNAHITGAVIKVASIFaqknisg 607
                                   ***********************9999888888888999******99...******************************7 PP

                                   TS.SGGGSSE...EEEECC-..-SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHHCH....HHHHHCEEEECHCHH CS
                                   xx.xxxxxxx...xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                      Prismane 440 gv.dindLpl...aalalew..yeqKAvailltllalGinihlgptlpafgspnvlkvlved....fedriggivtveedp 510
                                   ++ +i+d++l   +a+ ++w  y+qKA++i++++ +lGi+++lgp++++++++ ++k ++e+    +++r g++++++++p
  gi|91772867|ref|YP_565559.1| 608 NYeEIADYTLnrvGAVGVAWgaYSQKAASIGTGCSRLGIPVILGPHGSKYRRALIAKPYEEEkwkvYDARNGSEMQIPAAP 688
                                   799*********99****************************************************9********999887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   5.0   1.7e-10   1.9e-07       1      52 []     412     465 ..     402     465 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.7e-10
                        Fer4_7   1 rCigCgaCvaaCpvkaielde..eenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C++C +C++aCp++    +   + +e    k e+ ++kC+ Cg+C+ +CP+++
  gi|91772867|ref|YP_565559.1| 412 SCVHCLKCEVACPNSLPISEAmtALSEGDLSKFELLHDKCIACGRCEYACPKDI 465
                                   5************55443332112222344899******************985 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   2.4       2.3   2.6e+03       2       9 ..      69      76 ..      51      98 .. 0.80
   2 !   30.8   4.4   2.2e-10   2.5e-07       2      49 ..     413     464 ..     399     467 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.3
                        Fer4_9  2 CtgCgaCv 9 
                                  C +C +C+
  gi|91772867|ref|YP_565559.1| 69 CDQCCYCT 76
                                  66666665 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.2e-10
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkg 49 
                                   C+ C +C+ aCp+ + + +a +   + +  +     ++Ci Cg+C+ aCpk+
  gi|91772867|ref|YP_565559.1| 413 CVHCLKCEVACPNSLPISEAMTALSEGDLSKFellhDKCIACGRCEYACPKD 464
                                   *****************99999999998777799**9*************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 ?   -2.5   4.0       7.3   8.2e+03       2       9 ..      69      76 ..      68     106 .. 0.81
   2 !   19.1   0.4   1.3e-06    0.0015      35      60 ..     402     427 ..     378     428 .. 0.74
   3 !   18.6   0.6   1.8e-06     0.002      43      61 .]     448     466 ..     431     466 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.3
                       Fer4_17  2 CiqCgyCl 9 
                                  C qC yC+
  gi|91772867|ref|YP_565559.1| 69 CDQCCYCT 76
                                  99999997 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.3e-06
                       Fer4_17  35 eeaekeekaslCieCgeCerkCPqgl 60 
                                   +++e +e a++C++C +Ce +CP++l
  gi|91772867|ref|YP_565559.1| 402 TDEELKELADSCVHCLKCEVACPNSL 427
                                   33445689****************98 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.8e-06
                       Fer4_17  43 aslCieCgeCerkCPqgld 61 
                                    ++Ci Cg+Ce++CP+++d
  gi|91772867|ref|YP_565559.1| 448 HDKCIACGRCEYACPKDID 466
                                   589**************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0  12.3   1.1e-07   0.00013       6      56 .]     410     462 ..     406     462 .. 0.78
   2 !   17.3   1.9   3.5e-06    0.0039       6      34 ..     448     476 ..     443     488 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                       Fer4_10   6 ddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +d+C++C kC  aCP +l  ++  +   + + ++ +   +kC++cg C  aCP
  gi|91772867|ref|YP_565559.1| 410 ADSCVHCLKCEVACPNSLpiSEAMTALSEGDLSKFELLHDKCIACGRCEYACP 462
                                   699*************99954444444444444555599*************9 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.5e-06
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgease 34 
                                    d+Ci Cg+C  aCP d++ v+++++ s+
  gi|91772867|ref|YP_565559.1| 448 HDKCIACGRCEYACPKDIDIVNVIEKSSQ 476
                                   589*************9977776666554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   3.0       7.6   8.5e+03       7      14 ..      68      75 ..      64      76 .. 0.86
   2 !   13.9   2.4   3.1e-05     0.035       6      20 ..     411     425 ..     409     426 .. 0.93
   3 !   22.8   2.3   4.8e-08   5.3e-05       6      21 ..     449     464 ..     445     465 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.6
                                  TSSS-THH CS
                          Fer4  7 kCigCGaC 14
                                  +C  C +C
  gi|91772867|ref|YP_565559.1| 68 MCDQCCYC 75
                                  69999999 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.1e-05
                                   TTSSS-THHHHHSTT CS
                          Fer4   6 ekCigCGaCvevCPv 20 
                                   + C++C +C+ +CP+
  gi|91772867|ref|YP_565559.1| 411 DSCVHCLKCEVACPN 425
                                   89************7 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 4.8e-08
                                   TTSSS-THHHHHSTTT CS
                          Fer4   6 ekCigCGaCvevCPvg 21 
                                   +kCi+CG+C+ +CP +
  gi|91772867|ref|YP_565559.1| 449 DKCIACGRCEYACPKD 464
                                   9*************87 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  10.3   9.5e-08   0.00011       6      53 ..     411     463 ..     407     473 .. 0.79
   2 !   16.0   2.2   9.1e-06      0.01       5      39 ..     448     481 ..     445     483 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.5e-08
                       Fer4_21   6 dkCigCgkCliaCedt.....shqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                   d+C++C kC +aC+++     +++a++  + +++++++d+C++C  C   CP 
  gi|91772867|ref|YP_565559.1| 411 DSCVHCLKCEVACPNSlpiseAMTALSEGDLSKFELLHDKCIACGRCEYACPK 463
                                   79************75332224555555556788999***************4 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.1e-06
                       Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvved 39 
                                   +dkCi Cg+C  aC+ + ++ +++ +k+  +v+++
  gi|91772867|ref|YP_565559.1| 448 HDKCIACGRCEYACP-KDIDIVNVIEKSSQRVISE 481
                                   699************.5789998888888888766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.3e-05     0.014      44      64 ..     398     426 ..     357     427 .. 0.75
   2 !   15.2   0.1     2e-05     0.022       3      64 ..     449     464 ..     434     500 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                        Fer4_8  44 e........eealwsCttcgaCtevCpvg 64 
                                   +        +e ++sC++c +C+++Cp++
  gi|91772867|ref|YP_565559.1| 398 KalptdeelKELADSCVHCLKCEVACPNS 426
                                   1344445557999**************87 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-05
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +kCi Cg+C+ aCp                                              ++
  gi|91772867|ref|YP_565559.1| 449 DKCIACGRCEYACP----------------------------------------------KD 464
                                   46777777777776..............................................33 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   5.3       4.2   4.7e+03       7      18 ..      66      77 ..      62      80 .. 0.79
   2 !   13.8   2.0   4.3e-05     0.048       7      22 .]     410     425 ..     406     425 .. 0.91
   3 !   18.2   1.0   1.7e-06    0.0019       8      21 ..     449     462 ..     443     463 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.2
                        Fer4_2  7 tdrCigCgaCvs 18
                                  t +C +C  C+ 
  gi|91772867|ref|YP_565559.1| 66 TPMCDQCCYCTF 77
                                  679****99985 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.3e-05
                        Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                   +d+C++C +C  aCP+
  gi|91772867|ref|YP_565559.1| 410 ADSCVHCLKCEVACPN 425
                                   689************5 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.7e-06
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                   d+Ci+Cg C  aCP
  gi|91772867|ref|YP_565559.1| 449 DKCIACGRCEYACP 462
                                   8************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1         3   3.4e+03      36      60 ..      48      72 ..      25      77 .. 0.55
   2 !    9.7   0.2    0.0014       1.6      36      66 ..     395     425 ..     380     433 .. 0.67
   3 !   11.9   0.4   0.00031      0.34       1      16 [.     450     465 ..     450     496 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3
                       Fer4_16 36 aekkdlaedeekckkqeaitgCdiC 60
                                     +d+ +++  +++   +  Cd C
  gi|91772867|ref|YP_565559.1| 48 SSLRDWDHNILDRYNPVYTPMCDQC 72
                                  5556666666666644444556666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                       Fer4_16  36 aekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                   ++ k l++dee ++ +  +  C +C+ +CP+
  gi|91772867|ref|YP_565559.1| 395 KGIKALPTDEELKELADSCVHCLKCEVACPN 425
                                   5556666666666666666666666666664 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00031
                       Fer4_16   1 rCgtCgkCaevCPtna 16 
                                   +C+ Cg+C  +CP + 
  gi|91772867|ref|YP_565559.1| 450 KCIACGRCEYACPKDI 465
                                   5************865 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2   0.00011      0.12       9      55 ..     398     442 ..     390     449 .. 0.85
   2 !    8.0   1.6    0.0021       2.4      22      55 ..     449     480 ..     445     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                   B----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HH CS
                       Fer4_20   9 alglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnle 55 
                                   +   t+ee +e A+ C++C   +c+ +CP ++ i e +++++eg+l+
  gi|91772867|ref|YP_565559.1| 398 KALPTDEELKELADSCVHC--LKCEVACPNSLPISEAMTALSEGDLS 442
                                   555677888999*******..88*******************99986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                                   TT----TT-HHHHCSTT---HHHHHHHHHTT-HH CS
                       Fer4_20  22 sRClqCkkapcvkgCPveidipefikkiaegnle 55 
                                   ++C+ C    c+ +CP +idi + i+k +++ ++
  gi|91772867|ref|YP_565559.1| 449 DKCIAC--GRCEYACPKDIDIVNVIEKSSQRVIS 480
                                   58****..78***************998877665 PP

>> CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.012       4      67 ..     121     184 ..     118     207 .. 0.85
   2 ?   -1.5   0.0       2.3   2.6e+03      39      59 ..     376     396 ..     370     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                      CODH_A_N   4 lekaikkygkdkkvefPdTAYylPviyaltGekvktlgdleevLerarsllkeeetLedaldaG 67 
                                   l++ i  ygkd+++    T    P +  +tG + ktlgdl +vL  +++++++  +  ++ + G
  gi|91772867|ref|YP_565559.1| 121 LHHLIGLYGKDHPLDVGATNIIAPNVQLVTGVQPKTLGDLDSVLSYVEEQITQLLAAIHVGQEG 184
                                   6677889********************************************9987744444444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                      CODH_A_N  39 tlgdleevLerarsllkeeet 59 
                                   +lg+l++ L+++ s +++++ 
  gi|91772867|ref|YP_565559.1| 376 KLGELAPRLTMMMSEIRKQKG 396
                                   799999999999999998876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   1.4   5.7e-05     0.063       2      15 ..     411     424 ..     410     434 .. 0.92
   2 !   18.5   1.5   1.8e-06     0.002       2      16 ..     449     463 ..     448     474 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   ++C++C +C+ aCP
  gi|91772867|ref|YP_565559.1| 411 DSCVHCLKCEVACP 424
                                   89************ PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.8e-06
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++Ci Cg+C++aCP 
  gi|91772867|ref|YP_565559.1| 449 DKCIACGRCEYACPK 463
                                   89************5 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.7   2.3e-05     0.026       7      20 ..     411     424 ..     410     432 .. 0.91
   2 !   16.8   3.5   4.8e-06    0.0054       7      21 ..     449     463 ..     448     471 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                        Fer4_6   7 dkCigCgdCvrvCP 20 
                                   d+C++C +C+++CP
  gi|91772867|ref|YP_565559.1| 411 DSCVHCLKCEVACP 424
                                   99************ PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.8e-06
                        Fer4_6   7 dkCigCgdCvrvCPe 21 
                                   dkCi Cg+C+ +CP 
  gi|91772867|ref|YP_565559.1| 449 DKCIACGRCEYACPK 463
                                   8*************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.7    0.0064       7.1      49      80 ..     401     432 ..     385     436 .. 0.71
   2 ?   10.0   2.0   0.00066      0.74      58      79 ..     448     469 ..     431     475 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0064
                       Fer4_18  49 ekeerkekgagdcidcescvkvcPtgidirkG 80 
                                    ++e+ ++ a  c++c +c   cP  + i + 
  gi|91772867|ref|YP_565559.1| 401 PTDEELKELADSCVHCLKCEVACPNSLPISEA 432
                                   345555677888************99988765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00066
                       Fer4_18  58 agdcidcescvkvcPtgidirk 79 
                                   + +ci+c+ c   cP +idi +
  gi|91772867|ref|YP_565559.1| 448 HDKCIACGRCEYACPKDIDIVN 469
                                   678****************976 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 ?    4.0   1.5     0.065        73       4      19 ..     411     426 ..     410     436 .. 0.86
   2 ?   10.0   1.8   0.00088      0.99       4      18 ..     449     463 ..     448     472 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.065
                       Fer4_13   4 dtCiacgaCvelaPdv 19 
                                   d+C+ c +C  ++P+ 
  gi|91772867|ref|YP_565559.1| 411 DSCVHCLKCEVACPNS 426
                                   79************86 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00088
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                   d+Ciacg C  ++P+
  gi|91772867|ref|YP_565559.1| 449 DKCIACGRCEYACPK 463
                                   89************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (802 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 4637.34
//
Query:       gi|91772868|ref|YP_565560.1|  [L=171]
Description: acetyl-CoA decarbonylase/synthase complex subunit epsilon [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-31  107.5   0.0    6.9e-31  107.3   0.0    1.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
    4.9e-05   23.1   0.1     0.0001   22.0   0.1    1.7  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.079   12.4   0.0       0.12   11.8   0.0    1.2  1  ComA          (2R)-phospho-3-sulfolactate synthase (ComA)


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 !  107.3   0.0   1.2e-34   6.9e-31      16     156 ..      16     158 ..       8     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 1.2e-34
                                   XX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTS.SSEEEEET.....HHHTT-G..GGSE.-HHHHH CS
                         CO_dh  16 skkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilek.klkvvata.....lkeaglkdyekkn.klvelt 89 
                                    k  +++++  v+ kmi+kakrPl ivG q+lk+e++ +++  i++k +l+v+at+     l ++g++    k+  ++ l 
  gi|91772868|ref|YP_565560.1|  16 CKSSKAVQP-DVAGKMISKAKRPLFIVGSQILKDEELLKRSIEIAKKaDLPVAATGhsmsgLVDQGVN---AKYiNVHALA 92 
                                   567788999.9************************98888888776658*******666666666666...55559999** PP

                                   HHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEEE---GGG CS
                         CO_dh  90 kllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvslanlske 156
                                     l dp++ g dg+g+yd+++ +G   Yy +q ls lk f+ k++ iai + y ++A +s++n++  
  gi|91772868|ref|YP_565560.1|  93 TYLCDPNWTGLDGKGQYDTIIVLGHFKYYIDQVLSGLKSFS-KLKSIAIEREYIQNATMSFGNITPA 158
                                   *****************************************.*********************9865 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.7e-08    0.0001       6      54 ..      29      79 ..      25     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-08
                                  HHHHH-SSEEEEE-CHHCHT.TGHHHHHHHHHHHT-EEEEEGGG.TTSS-T CS
                  TPP_enzyme_M  6 ellkaakrpvilvGggvars.gaseelrelaeklgiPvvttlmg.kgvipe 54
                                  +++++akrp+++vG+++  + +  +   e a+k ++Pv+ t +   g++++
  gi|91772868|ref|YP_565560.1| 29 KMISKAKRPLFIVGSQILKDeELLKRSIEIAKKADLPVAATGHSmSGLVDQ 79
                                  79***************98878999999**********9999885666664 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05      0.12      33      89 ..      28      87 ..      17      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                                  GGG-SEEE...E-TTGGGGSTCHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT-HHHHHH CS
                          ComA 33 geyiDglK...lgggtsallpeeilrekielahehgvyvstGgtlfEaalaqgkvdeyle 89
                                  g++i  +K   + +g+++l +ee+l++ ie+a++++ +v   g  +  ++ qg   +y++
  gi|91772868|ref|YP_565560.1| 28 GKMISKAKrplFIVGSQILKDEELLKRSIEIAKKADLPVAATGHSMSGLVDQGVNAKYIN 87
                                  55555555555889*************************987778888898888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1139.52
//
Query:       gi|91772869|ref|YP_565561.1|  [L=470]
Description: acetyl-CoA decarbonylase/synthase complex subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete 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-63  211.0   0.1    1.1e-62  210.6   0.1    1.2  1  CdhC      CO dehydrogenase/acetyl-CoA synthase complex beta s
  ------ inclusion threshold ------
        0.5   11.3   3.2       0.85   10.6   1.2    2.0  2  PE_PPE_C  Polymorphic PE/PPE proteins C terminal


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 !  210.6   0.1   1.2e-66   1.1e-62       2     154 ..       6     158 ..       5     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 1.2e-66
                          CdhC   2 pvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkleedlEp 82 
                                   p+e+sp+feGeriRk+ ++vel+g k+k++Elv+++++de+edgk+++iGpdi+e+eegsr+p+a+++++aG+ +eedlE+
  gi|91772869|ref|YP_565561.1|   6 PFEISPMFEGERIRKDGMHVELSGPKSKGYELVRATSMDEIEDGKFTLIGPDISEMEEGSRHPFAMIYKIAGELVEEDLES 86 
                                   899*********************99******************************************************* PP

                          CdhC  83 vlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdeek 154
                                   ++ERr+H+f+nyi+G+mHl+qR+++w+R+sk+av+kGl +++ i++++++++k+e+ ++++kve  +itd ++
  gi|91772869|ref|YP_565561.1|  87 IVERRNHDFQNYIQGLMHLNQRYDVWIRVSKDAVAKGLtSFEPIAQAVMMLFKNEL-PFIEKVEAVYITDLAE 158
                                   **************************************99****************.************9876 PP

>> PE_PPE_C  Polymorphic PE/PPE proteins C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.21   1.9e+03      47      64 ..     306     323 ..     298     330 .. 0.71
   2 ?   10.6   1.2   9.4e-05      0.85      17      62 ..     400     447 ..     398     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                      PE_PPE_C  47 aalggmPlaaagaggaag 64 
                                   +a  g+P+  +++++++g
  gi|91772869|ref|YP_565561.1| 306 VAPNGLPFSTMAGQTGGG 323
                                   444599999999999833 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9.4e-05
                      PE_PPE_C  17 psWaaaapaasaaaaalsgttaaaaaaaagaalg..gmPlaaagagga 62 
                                   + W++ a +   a + ++ +t+ aa+ ++++ ++  gmP+++ +++g+
  gi|91772869|ref|YP_565561.1| 400 QRWEEEAEEEPEAEEEVQEATMFAAPPTMQNTMPmqGMPMMMPSSSGT 447
                                   579999999999*******************99999****88777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2803.58
//
Query:       gi|91772870|ref|YP_565562.1|  [L=250]
Description: cobyrinic acid a,c-diamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-17   64.3   0.1    2.3e-17   63.3   0.1    1.5  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    3.5e-16   59.6   0.2    6.3e-16   58.8   0.2    1.4  1  AAA_31        AAA domain
    2.1e-10   40.5   1.2    5.8e-10   39.1   1.2    1.6  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    1.6e-09   37.6   2.1    9.6e-09   35.0   2.1    2.1  1  ParA          NUBPL iron-transfer P-loop NTPase
    8.6e-09   35.2   0.1    9.2e-08   31.8   0.1    2.5  1  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
      6e-07   28.9   6.1    1.5e-05   24.4   6.1    2.7  2  ArsA_ATPase   Anion-transporting ATPase
    2.2e-05   24.6   0.3     0.0021   18.3   0.1    2.4  2  Toprim        Toprim domain
    0.00014   22.3   0.3     0.0032   17.9   0.1    2.4  2  Toprim_4      Toprim domain
    0.00019   21.2   0.3    0.00039   20.2   0.3    1.6  1  AAA_24        AAA domain
    0.00025   21.0   4.7       0.13   12.2   0.4    2.3  2  NTPase_1      NTPase
    0.00046   19.9   2.6       0.44   10.1   0.1    2.3  2  SRP54         SRP54-type protein, GTPase domain
     0.0017   18.8   0.0     0.0028   18.1   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0021   17.9   1.3      0.053   13.4   0.1    2.2  2  APS_kinase    Adenylylsulphate kinase
     0.0057   17.0   0.3        5.2    7.6   0.0    2.3  2  Toprim_2      Toprim-like
      0.006   17.1   0.1     0.0087   16.6   0.1    1.7  1  ABC_tran      ABC transporter
  ------ inclusion threshold ------
      0.013   14.8   2.5        3.4    6.9   2.5    2.5  1  MipZ          ATPase MipZ
      0.019   15.2   2.0        8.7    6.6   0.1    3.1  3  TrkA_N        TrkA-N domain
      0.022   14.4   0.0      0.063   12.9   0.0    1.7  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
      0.027   13.8   0.1      0.065   12.5   0.1    1.6  1  Zeta_toxin    Zeta toxin
      0.028   13.9   0.1      0.069   12.6   0.1    1.7  1  AAA_7         P-loop containing dynein motor region
       0.03   13.5   0.3      0.049   12.8   0.3    1.3  1  PIF1          PIF1-like helicase
      0.031   13.7   0.0      0.069   12.6   0.0    1.7  1  PhoH          PhoH-like protein
      0.037   13.8   0.0      0.054   13.2   0.0    1.5  1  AAA_30        AAA domain
      0.037   13.5   0.0      0.067   12.7   0.0    1.4  1  DUF3372       Domain of unknown function (DUF3372)
      0.038   14.3   3.1      0.052   13.9   0.3    2.4  3  AAA_19        AAA domain
       0.04   12.9   1.1        0.1   11.6   0.1    1.9  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.045   13.6   0.0      0.092   12.6   0.0    1.4  1  Rop-like      Rop-like
      0.054   13.1   4.1      0.097   12.2   0.8    2.6  2  AAA_25        AAA domain
      0.074   13.1   0.2       0.21   11.6   0.2    2.0  1  AAA_14        AAA domain
      0.085   13.4   0.2       0.17   12.5   0.2    1.8  1  AAA_18        AAA domain
       0.09   12.2   0.0        7.4    5.9   0.0    2.4  2  Pox_A32       Poxvirus A32 protein
      0.092   13.0   0.0       0.17   12.1   0.0    1.4  1  DUF4276       Domain of unknown function (DUF4276)
       0.11   12.4   0.3       0.39   10.6   0.1    2.0  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.15   12.5   0.0        1.1    9.7   0.0    2.2  2  RNA_helicase  RNA helicase
       0.18   11.5   0.8       0.53   10.0   0.8    1.9  1  PRK           Phosphoribulokinase / Uridine kinase family
        0.2   11.4   0.4        1.5    8.5   0.0    2.2  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
       0.23   11.3   5.4        1.1    9.0   0.4    2.5  2  AAA_26        AAA domain
       0.25   11.3   2.4        1.2    9.2   0.5    2.8  2  PDDEXK_10     PD-(D/E)XK nuclease superfamily
        0.3   11.1   1.1        0.6   10.1   1.1    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.72    9.9   4.6       0.35   10.9   0.8    2.1  2  DUF87         Helicase HerA, central 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 !   63.3   0.1   5.1e-20   2.3e-17       2     127 ..       5     227 ..       4     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 5.1e-20
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH........................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx........................ RF
                          CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep........................ 54 
                                   ++  +kGG+GKT ++  L+r l + ++ Vl++DaDp++n+ ++    + ++++d ++                        
  gi|91772870|ref|YP_565562.1|   5 IALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTNLPETlgceVSKTVGDMKQfmqderdnlppdvnkqsifeskly 85 
                                   6789**************************************8777766666666669999999***************** PP

                                   ..............................................................................CCH CS
                                   ..............................................................................xxx RF
                          CbiA  55 ..............................................................................dlk 57 
                                                                                                                 +++
  gi|91772870|ref|YP_565562.1|  86 evleempkydlivmgrpegsgcycyvnnllrgimdklvknydvviidteaglehfsrkmirdvdelivvtdgsrrglrTAE 166
                                   ***********************************************************************8887777777 PP

                                   CCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  58 rllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                   r+  l e+l+++    +k + vv+n+v     +++++++ +e +   +++++g +p d+ +ae + +g p
  gi|91772870|ref|YP_565562.1| 167 RIRDLTEELDTN----IKNIVVVANKVTDA--NRAEIKSTAEGL---NLELIGTVPMDSIIAERDLKGIP 227
                                   777777777777....99*********998..777777777777...9****************999987 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.2   1.4e-18   6.3e-16       1     172 [.       2     180 ..       2     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.4e-18
                        AAA_31   1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktkven 80 
                                   +kvIa++  KGG GKT+ +  l   l+k++k vL +D+Dp +n+  +lg+e +++  ++ + +  e+ n+   ++k+++ +
  gi|91772870|ref|YP_565562.1|   2 TKVIALT-GKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTNLPETLGCEVSKTVGDMKQFMQdERDNLPPDVNKQSIFE 81 
                                   5888876.6****************************************98888888888888767777777777777777 PP

                        AAA_31  81 ldlipssidLaeaeielvelekk.......eeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayal 154
                                    +l     ++ +++  +++  +        ++ l+ +++k+ ++YD++iiD+   L+ + ++ +   d++i++++ + + l
  gi|91772870|ref|YP_565562.1|  82 SKLYEVLEEMPKYDLIVMGRPEGsgcycyvNNLLRGIMDKLVKNYDVVIIDTEAGLEHFSRKMIRDVDELIVVTDGSRRGL 162
                                   7888777888888888777766678888878889******************************************99999 PP

                        AAA_31 155 eGleqllktieevkkkln 172
                                   +++e++ +  ee++++++
  gi|91772870|ref|YP_565562.1| 163 RTAERIRDLTEELDTNIK 180
                                   999998888888877765 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 !   39.1   1.2   1.3e-12   5.8e-10       2     243 ..       4     247 ..       3     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.3e-12
                     Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlr....ekgav.edvkvedvvkkG 77 
                                    ia+ GkGG Gk+  ++ l   l++++k vl +  DP ++    +lg  + +tv d+ +    e++    dv+ +++  + 
  gi|91772870|ref|YP_565562.1|   4 VIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTNLP-ETLGCEVSKTVGDMKQfmqdERDNLpPDVNKQSIFESK 83 
                                   599**********************************99887.689999*****988652222344445778888876554 PP

                     Fer4_NifH  78 yggv.......kcvesGGPepGvGCaGrgvitaielleelgayddlDfvlyDvLGDvvCGGfalPiredkaqevyivtsge 151
                                     +v       + +  G P  G GC  ++      ++++l   +++D+v+ D         f+  +  +  +e+++vt+g 
  gi|91772870|ref|YP_565562.1|  84 LYEVleempkyDLIVMGRP-EGSGCYCYVNNLLRGIMDKL--VKNYDVVIIDTEAG--LEHFSRKMI-RDVDELIVVTDGS 158
                                   3333222122134445555.599**999877777788876..5789*****98554..567988877.46799******** PP

                     Fer4_NifH 152 lmalyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapese 232
                                      l +a +i    e+     +++   ++ n + +d +r  i+  ae l+++++ +vP+d i+ + +l+   +++  ++s 
  gi|91772870|ref|YP_565562.1| 159 RRGLRTAERIRDLTEELDT--NIKNIVVVAN-KVTDANRAEIKSTAEGLNLELIGTVPMDSIIAERDLKGIPLFDLPDDSV 236
                                   *********9887776654..4555557778.7789999************************************999999 PP

                     Fer4_NifH 233 qakeyrelark 243
                                     +e  ++a+k
  gi|91772870|ref|YP_565562.1| 237 AVQEVDKIAKK 247
                                   99999999988 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 !   35.0   2.1   2.1e-11   9.6e-09       6     245 ..       4     248 ..       1     249 [. 0.75

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.1e-11
                          ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee.......ekpeqsekkliPvea..kgi.kvm 76 
                                   ++ l gKGG GK+ +++ l  +L+k+++ v  +DaD    ++p+ lg+e        ++ +q+e+  +P ++  ++i +  
  gi|91772870|ref|YP_565562.1|   4 VIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADP-DTNLPETLGCEVsktvgdmKQFMQDERDNLPPDVnkQSIfESK 83 
                                   56689*******************************5.5788888888775566665455666666677666333331333 PP

                          ParA  77 Sigfllesedeavvwr....Gpmkskaikqllkdve...wgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqeval 150
                                     ++l e  +  ++      G+     +++ll+ +     ++ D++iiD+  G   e+ +     ++++ ++Vt   +  l
  gi|91772870|ref|YP_565562.1|  84 LYEVLEEMPKYDLIVMgrpeGSGCYCYVNNLLRGIMdklVKNYDVVIIDTEAGL--EHFSRKMIRDVDELIVVTDGSRRGL 162
                                   3456666555555554012234444567777664431116899*******8776..566655555678************* PP

                          ParA 151 advkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepe 231
                                     +++  ++++++++++  +v   + ++           ++ + +++ae l+++l+g++p+d+ i+e   +g pl+   ++
  gi|91772870|ref|YP_565562.1| 163 RTAERIRDLTEELDTNIKNIVVVANKVTDA---------NRAEIKSTAEGLNLELIGTVPMDSIIAERDLKGIPLFDLPDD 234
                                   ***************998887544333333.........4667899******************************99999 PP

                          ParA 232 seaakaleeiaekv 245
                                   s a +++++ia+k+
  gi|91772870|ref|YP_565562.1| 235 SVAVQEVDKIAKKL 248
                                   ***********986 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1     2e-10   9.2e-08       2     146 ..       3     156 ..       1     248 [. 0.76

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2e-10
                      CBP_BcsQ   2 kvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqreg....waraeldgap...wrqaale. 74 
                                   kv+al+G +GG+G+t++++ L + l + ++ vl+iD+ pd  L      +++++ g    +++ e d+ p    +q+++e 
  gi|91772870|ref|YP_565562.1|   3 KVIALTG-KGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTNLPETLGCEVSKTVGdmkqFMQDERDNLPpdvNKQSIFEs 82 
                                   6899999.9*******************************87776666666665552111666666665433234555542 PP

                      CBP_BcsQ  75 .yapgldllPfGelnveeken.lqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvve 146
                                    + + l+ +P   l v  + +   +++  ++ l   +++l ++y+ +++D  ag ++  r++++  d  + v+ 
  gi|91772870|ref|YP_565562.1|  83 kLYEVLEEMPKYDLIVMGRPEgSGCYCYVNNLLRGIMDKLVKNYDVVIIDTEAGLEHFSRKMIRDVDELIVVTD 156
                                   256777777855555555554145588889999999****************************9999888875 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   6.1   3.3e-08   1.5e-05       1      61 [.       2      62 ..       2     207 .. 0.77
   2 ?    1.8   1.3      0.24   1.1e+02     123     132 ..     124     133 ..     110     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.3e-08
                                  -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSS CS
                   ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeN 61
                                  +kvi ++GKGG GKt++ + +  +l++++k vl i  DP  +l   +  +++k++  +k+ 
  gi|91772870|ref|YP_565562.1|  2 TKVIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTNLPETLGCEVSKTVGDMKQF 62
                                  699**********************************************999998877743 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.24
                                   SSSSEEEEES CS
                   ArsA_ATPase 123 eeydvvvlDt 132
                                   ++ydvv++Dt
  gi|91772870|ref|YP_565562.1| 124 KNYDVVIIDT 133
                                   5666666666 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.096        43      55      75 ..      21      41 ..       3      44 .. 0.77
   2 !   18.3   0.1   4.7e-06    0.0021      38     100 ..     121     184 ..      50     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.096
                                  HHHHHHHHHSEEEEECSSSHH CS
                        Toprim 55 alkelakradeiilatDpDre 75
                                   l + + + ++++la+D+D +
  gi|91772870|ref|YP_565562.1| 21 LLIRHLTKTNKVVLAIDADPD 41
                                  4445557999*********75 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.7e-06
                                   TTEEEEE.ECTTTHHHHHHHHHHH.HHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEE CS
                        Toprim  38 efkpvye.eiedkkkvlkalkela.kradeiilatDpDreGeaiawellevlkellenkigrvef 100
                                   ++ ++y+ +i d++  l+ + +   +++de+i+ tD+ r G  +a +++++ +el+ n i+++++
  gi|91772870|ref|YP_565562.1| 121 KLVKNYDvVIIDTEAGLEHFSRKMiRDVDELIVVTDGSRRGLRTAERIRDLTEELDTN-IKNIVV 184
                                   4556777877777777777666656************************999988888.888876 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.68     3e+02      47      64 ..      22      39 ..       6      43 .. 0.77
   2 !   17.9   0.1   7.2e-06    0.0032      35      86 ..     138     180 ..     118     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.68
                      Toprim_4 47 lveaekkvkevilaldgD 64
                                  l++++ k+++v+la d+D
  gi|91772870|ref|YP_565562.1| 22 LIRHLTKTNKVVLAIDAD 39
                                  44467889********99 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 7.2e-06
                      Toprim_4  35 dgirpeklktenlveaekkvkevilaldgDaeGeataerlaellleegvkvt 86 
                                   ++ +++ ++          v+e+i+++dg+ +G +taer+ +l +e +++++
  gi|91772870|ref|YP_565562.1| 138 EHFSRKMIR---------DVDELIVVTDGSRRGLRTAERIRDLTEELDTNIK 180
                                   444433333.........49********************995556566655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   8.7e-07   0.00039       2     134 ..       2     191 ..       1     207 [. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.7e-07
                        AAA_24   2 klkiliyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdie.........swedfldevvel......... 59 
                                    + i+++G+ g+GKT + + l     + + +++ +++       d   +++         ++ d++++++           
  gi|91772870|ref|YP_565562.1|   2 TKVIALTGKGGTGKTAITSLLirhltKTNKVVLAIDA-------DPDTNLPetlgcevskTVGDMKQFMQDErdnlppdvn 75 
                                   5789*************99997777744444444444.......33333333334445578888888888878999***** PP

                        AAA_24  60 ............................................aaeladyktlviDtideleelclaevirqnekaeske 96 
                                                                               ++  ++y++++iDt   le + ++++++ +e      
  gi|91772870|ref|YP_565562.1|  76 kqsifesklyevleempkydlivmgrpegsgcycyvnnllrgimDKLVKNYDVVIIDTEAGLEHFSRKMIRDVDELIVVT- 155
                                   **********************************************************9999999999999999984443. PP

                        AAA_24  97 dkgdgkGygelaeefrrllkklqelrknvifiahektr 134
                                   d g+ +G  + ae++r+l + l+   kn++++a   t+
  gi|91772870|ref|YP_565562.1| 156 D-GSRRG-LRTAERIRDLTEELDTNIKNIVVVANKVTD 191
                                   3.33356.456778888888888888899999877665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.4   0.00084      0.37       2      31 ..       5      34 ..       4     100 .. 0.71
   2 !   12.2   0.4   0.00029      0.13      86     164 ..     116     198 ..     107     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00084
                                  EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                  +++TG+ G+GKt + + +++ l + +  v 
  gi|91772870|ref|YP_565562.1|  5 IALTGKGGTGKTAITSLLIRHLTKTNKVVL 34
                                  79********************99987775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00029
                                   HHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT...TTSEEEEE--SS--SHHHHHHHT-TT...-EEEE--TTTT CS
                      NTPase_1  86 lealrkalseadviviDEiGkmElkskkfkeaveevLk...sekpvlavihrrkdlalveeirerkd...vkvfevteenr 160
                                     +++k +++ dv++iD    +E +s+k+++ v+e++     ++  l +  r +  +l+ee+  + +   v+  +vt +nr
  gi|91772870|ref|YP_565562.1| 116 RGIMDKLVKNYDVVIIDTEAGLEHFSRKMIRDVDELIVvtdGSRRGLRTAERIR--DLTEELDTNIKnivVVANKVTDANR 194
                                   4566777799*******7777*************98743236778888888874..5666666554432133445999999 PP

                                   TTHH CS
                      NTPase_1 161 dall 164
                                    ++ 
  gi|91772870|ref|YP_565562.1| 195 AEIK 198
                                   9876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.6    0.0015      0.65       2      38 ..       3      39 ..       2      41 .. 0.88
   2 !   10.1   0.1   0.00098      0.44      77     112 ..     119     155 ..     105     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  +vi+l G  G+GKT  ++ L ++l+k +k vl + aD
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDAD 39
                                  799*****************99999999988877666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00098
                                   HHHHHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHH CS
                         SRP54  77 ekakeekidvvlvDT.aGrlqndkelmeelkkikkvv 112
                                     +  +++dvv++DT aG  +  ++++++++++  v+
  gi|91772870|ref|YP_565562.1| 119 MDKLVKNYDVVIIDTeAGLEHFSRKMIRDVDELIVVT 155
                                   5556689********99**********9999988777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.1e-06    0.0028      26      76 ..       4      48 ..       1     133 [. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.1e-06
                        AAA_16 26 lvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqal 76
                                  ++ l+G  G+GK+++   l r+l+k++ ++  + ++ d +        l ++l
  gi|91772870|ref|YP_565562.1|  4 VIALTGKGGTGKTAITSLLIRHLTKTNKVVlaIDADPDTN--------LPETL 48
                                  689***********************75551466666666........44444 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   0.00012     0.053       3      39 ..       3      39 ..       1      61 [. 0.87
   2 ?    3.5   0.1      0.13        60      53      80 ..     172     199 ..     140     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                  EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                    APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                   v+ ltG  g+GK++i+  l ++L+++++ v  +d d
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDAD 39
                                  6899************************999999988 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                    APS_kinase  53 eedRkenirrvaevaklladaglivlva 80 
                                   +e+ ++ni+ ++ va++++da+   + +
  gi|91772870|ref|YP_565562.1| 172 TEELDTNIKNIVVVANKVTDANRAEIKS 199
                                   577889**************99887765 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.012       5.2      25      55 ..       6      40 ..       1      44 [. 0.65
   2 ?    7.5   0.1     0.012       5.4      39      87 ..     145     193 ..     120     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.012
                      Toprim_2 25 algGt......alteaalkllerypekkvvlalDnDk 55
                                  al G       a+t  +++ l ++  +kvvla D+D 
  gi|91772870|ref|YP_565562.1|  6 ALTGKggtgktAITSLLIRHLTKT--NKVVLAIDADP 40
                                  554444324445555666666666..89********7 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.012
                      Toprim_2  39 lerypekkvvlalDnDkaGrkaakrlaellreag..vrekirelpegkDwn 87 
                                   +++   +++++ +D  + G + a+r+++l +e    ++++++  ++  D+n
  gi|91772870|ref|YP_565562.1| 145 IRD--VDELIVVTDGSRRGLRTAERIRDLTEELDtnIKNIVVVANKVTDAN 193
                                   223..3789*******************99977744545555445556777 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.9e-05    0.0087      12      94 ..       3      93 ..       1     248 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.9e-05
                                  SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.......B-HHHCCHCEEEE-SS.....--S-TTSBHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx RF
                      ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.......qeleslrkeigvlpqe.....pqlfpeltvrenesd 82
                                  +++a++G+ G+GK+ + +ll+++l++t+  +l  ++d ++           +++k +g ++q      ++l p++ ++++  +
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTnlpetlgC---EVSKTVGDMKQFmqderDNLPPDV-NKQSIFE 81
                                  689**********************99988865566666644443332...223333333322111344444444.4444666 PP

                                  TCHHHHHHHSTT CS
                                  xxxxxxxxxxxx RF
                      ABC_tran 83 eeiekalsklgl 94
                                  ++++++l+++  
  gi|91772870|ref|YP_565562.1| 82 SKLYEVLEEMPK 93
                                  666666666654 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.5    0.0075       3.4       9      39 ..      10      40 ..       3     202 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0075
                                  STTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                          MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldl 39
                                  kGG+Gk++++  ++  L+k+ + v aid d 
  gi|91772870|ref|YP_565562.1| 10 KGGTGKTAITSLLIRHLTKTNKVVLAIDADP 40
                                  6666666666666666666666666666553 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     0.074        33       8      33 ..      17      42 ..       5      56 .. 0.78
   2 ?    6.6   0.1     0.019       8.7       4      41 ..     109     144 ..     109     170 .. 0.70
   3 ?    1.4   0.2       0.8   3.6e+02       8      38 ..     159     196 ..     152     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.074
                                  HHHHHHHHHHHHTTEEEEEEESSHHH CS
                        TrkA_N  8 rvGrslaeeLseggkdvvvidkdeer 33
                                   +++ l++ L++ +k v++id d+++
  gi|91772870|ref|YP_565562.1| 17 AITSLLIRHLTKTNKVVLAIDADPDT 42
                                  46677888888855679999999975 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                   ES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT CS
                        TrkA_N   4 iGlGrvGrslaeeLseggkdvvvidkdeerveelreeg 41 
                                   + ++++ r ++++L +++ dvv+id++ + +e+++++ 
  gi|91772870|ref|YP_565562.1| 109 CYVNNLLRGIMDKLVKNY-DVVIIDTE-AGLEHFSRKM 144
                                   567788899*********.6*****95.4555555544 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.8
                                   HHHHHHHHHHHH.TT......EEEEEEESSHHHHHHHH CS
                        TrkA_N   8 rvGrslaeeLse.gg......kdvvvidkdeerveelr 38 
                                   r G + ae++++  +      k++vv+ ++   +++++
  gi|91772870|ref|YP_565562.1| 159 RRGLRTAERIRDlTEeldtniKNIVVVANKVTDANRAE 196
                                   55666666666544455666677999988877777766 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 ?   12.9   0.0   0.00014     0.063      18      94 ..       6     204 ..       2     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                   EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.................................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                   ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg.................................................. 48 
                                   ++ g+ g+Gkt+i + l+++ ++++ ++++                                                   
  gi|91772870|ref|YP_565562.1|   6 ALTGKGGTGKTAITSLLIRHLTKTNKVVLAIdadpdtnlpetlgcevsktvgdmkqfmqderdnlppdvnkqsifesklye 86 
                                   6789999*******99999988887777777999*********************************************** PP

                                   ......................................................................ESEEHHHHHHH CS
                                   ......................................................................xxxxxxxxxxx RF
                   ATP-synt_ab  49 ......................................................................iGergnevaev 59 
                                                                                                            rg   ae 
  gi|91772870|ref|YP_565562.1|  87 vleempkydlivmgrpegsgcycyvnnllrgimdklvknydvviidteaglehfsrkmirdvdelivvtdGSRRGLRTAER 167
                                   *****************************************************************9999877788888999 PP

                                   HHHCHH..SSGGGGEEEEEEETTS-HHHHHHHHHHHH CS
                                   xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  60 leefpe..gtimkrtvlvantsnepvaareasiytgi 94 
                                   +++++e  +t +k+ v+van+  ++  a ++s   g+
  gi|91772870|ref|YP_565562.1| 168 IRDLTEelDTNIKNIVVVANKVTDANRAEIKSTAEGL 204
                                   99998866779***********999999998887776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00014     0.065      17      52 ..       3      39 ..       2      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                    Zeta_toxin 17 klillgGqpGAGKselaellkdele.rqgnvvrldpD 52
                                  k+i l G  G GK+++ +ll + l+ +++ v+ +d+D
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTkTNKVVLAIDAD 39
                                  68999*******************9455555567766 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 ?   12.6   0.1   0.00015     0.069      35      70 ..       4      39 ..       1      50 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                         AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                   + l+G+ GtGKt+i++ l+++l k++ ++l i   
  gi|91772870|ref|YP_565562.1|  4 VIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDAD 39
                                  5789********************999988888765 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00011     0.049      23      56 ..       3      36 ..       1      38 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                  S-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEE CS
                          PIF1 23 klfFvtGsgGtgKtflwkallkklrsegkivlav 56
                                  k++ +tG gGtgKt +   l+  l +++k+vla+
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKTNKVVLAI 36
                                  68889**************************987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.069      20      93 ..       3      76 ..       1     106 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                  SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS-T CS
                          PhoH 20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpylrplydaLkdllga 93
                                  +++  +G+ GtGKt ++  l  +++k +kv   i + p  +  e lG    ++   ++ +++   d+L   +++
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTNLPETLGCEVSKTVGDMKQFMQDERDNLPPDVNK 76
                                  688999**************9999999***999999*****999999999988888888888888887665555 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   0.00012     0.054      19      77 ..       3      60 ..       1     154 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi.eastiakll 77
                                  +v +ltG  GtGKt + + l +++++ +   ++lA  +    +L e lg   ++t+  + 
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKTN--KVVLAIDADPDTNLPETLGCeVSKTVGDMK 60
                                  47899***************99888775..377888888888888888873345555444 PP

>> DUF3372  Domain of unknown function (DUF3372)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.067      89     163 ..     168     238 ..     153     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                       DUF3372  89 iddgtgladldpkldalvvvfNaspeeqsitvpelagkkleLhpvqaesadevvkqasfeeatgtftvPartvaV 163
                                   i d   +++ld +++++vvv N  +++++ +++++a+ +l+L+ + +   d+++++  ++     f +P  +vaV
  gi|91772870|ref|YP_565562.1| 168 IRD--LTEELDTNIKNIVVVANKVTDANRAEIKSTAE-GLNLELIGTVPMDSIIAERDLKG-IPLFDLPDDSVAV 238
                                   556..5689***********************88665.79999999889999999988888.4788888888887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   0.00012     0.052      11      40 ..       3      32 ..       1      41 [. 0.90
   2 ?   -1.5   0.0       6.3   2.8e+03      98     135 ..     121     154 ..     112     161 .. 0.64
   3 ?   -0.6   0.1       3.3   1.5e+03      54      72 ..     164     182 ..     133     219 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                        AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggv 40
                                  kv+++t+  GtGKT ++   +++l ++++v
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKTNKV 32
                                  899**********************99876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.3
                        AAA_19  98 kklqeee.llivDEfqdvdelqyrLlkallgekkklllv 135
                                   k + +++ ++i+D    ++    ++++ +     +l++v
  gi|91772870|ref|YP_565562.1| 121 KLV-KNYdVVIIDTEAGLEHFSRKMIRDVD----ELIVV 154
                                   444.44448888877777666666666655....35555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.3
                        AAA_19  54 AakelrerlaalgaeatTi 72 
                                    a+++r+ +++l+ +++ i
  gi|91772870|ref|YP_565562.1| 164 TAERIRDLTEELDTNIKNI 182
                                   3344444443333333333 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00022       0.1      29      68 ..       2      41 ..       1      53 [. 0.85
   2 ?   -0.2   0.1       0.9     4e+02     122     150 ..     126     155 ..     118     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                  SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                          MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                  ++v+ ltG  G+Gk  +++ l+ +l++  k v  +  DP 
  gi|91772870|ref|YP_565562.1|  2 TKVIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADPD 41
                                  6899*********************998877666666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.9
                                   -SEEEEEE.ESSTTHHHHHHTT-SEEEEEE CS
                          MeaB 122 fDvvliet.vGvGqsevdvaevvdtfvvll 150
                                   +Dvv+i+t  G      ++++ vd  +v++
  gi|91772870|ref|YP_565562.1| 126 YDVVIIDTeAGLEHFSRKMIRDVDELIVVT 155
                                   899999884577776777777777777665 PP

>> Rop-like  Rop-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0002     0.092      19      49 ..     163     193 ..     156     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHTTTTGGGHHHHHHHHHHHH CS
                      Rop-like  19 qakmdLHDLaEdLPtnyeeipevAqktyeaf 49 
                                    ++  ++DL E+L tn ++i+ vA+k  +a 
  gi|91772870|ref|YP_565562.1| 163 RTAERIRDLTEELDTNIKNIVVVANKVTDAN 193
                                   678899********************99885 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   0.00022     0.097      34      59 ..       3      29 ..       1     101 [. 0.81
   2 ?    2.0   0.2       0.3   1.3e+02     142     152 ..     125     135 ..      75     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                        AAA_25 34 elallaGapgtGKttlaldlalava.t 59
                                  ++++l+G +gtGKt++++ l  +++ t
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTkT 29
                                  689*****************9999943 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.3
                        AAA_25 142 gvrlvviDpls 152
                                   ++++v+iD+ +
  gi|91772870|ref|YP_565562.1| 125 NYDVVIIDTEA 135
                                   35555555533 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00048      0.21       3      47 ..       3      45 ..       1     180 [. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00048
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                                  k++++tG   +GKT +   li++l   k + + +++d ++d++l 
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLT--KTNKVVLAIDADPDTNLP 45
                                  899******************9999..555555555555553322 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00037      0.17       1      25 [.       5      32 ..       5     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00037
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf..g 25
                                  I+ltG+ G+GKt ++  L ++l +   +
  gi|91772870|ref|YP_565562.1|  5 IALTGKGGTGKTAITSLLIRHLtKTnkV 32
                                  89****************9987444552 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.017       7.4      16      45 ..       5      34 ..       2      41 .. 0.86
   2 ?    3.8   0.0     0.073        33      13      41 ..      93     122 ..      82     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                       Pox_A32 16 lalvGgsGsGktvyLlsLlrtlvkkykhif 45
                                  +al+G+ G Gkt+    L+r l k  k ++
  gi|91772870|ref|YP_565562.1|  5 IALTGKGGTGKTAITSLLIRHLTKTNKVVL 34
                                  79***********99999999988877765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.073
                       Pox_A32  13 pFrlalvGg.sGsGktvyLlsLlrtlvkky 41 
                                   ++ l+++G   GsG   y+ +Llr +++k 
  gi|91772870|ref|YP_565562.1|  93 KYDLIVMGRpEGSGCYCYVNNLLRGIMDKL 122
                                   47788888746************9988875 PP

>> DUF4276  Domain of unknown function (DUF4276)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00038      0.17       3      79 ..      11     180 ..      11     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00038
                       DUF4276   3 Gqteeeflkellrrlleskgiylsar.............vsysklkkdikkllkqekd....................... 47 
                                   G+t ++++ +ll r+l + + ++ a+             +++sk  +d+k+++++e+d                       
  gi|91772870|ref|YP_565562.1|  11 GGTGKTAITSLLIRHLTKTNKVVLAIdadpdtnlpetlgCEVSKTVGDMKQFMQDERDnlppdvnkqsifesklyevleem 91 
                                   8999***************99988889*****************************99********999999999999999 PP

                       DUF4276  48 ...............................edtavttliDlyal..........................dafkrveele 71 
                                                                   + + +++iD +a                           + ++r++ l+
  gi|91772870|ref|YP_565562.1|  92 pkydlivmgrpegsgcycyvnnllrgimdklVKNYDVVIIDTEAGlehfsrkmirdvdelivvtdgsrrglRTAERIRDLT 172
                                   999999999999999999999999999999955555555555555444444444444444555555554766666677777 PP

                       DUF4276  72 ralkedid 79 
                                   ++l  +i+
  gi|91772870|ref|YP_565562.1| 173 EELDTNIK 180
                                   77776664 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00088      0.39       1      31 [.       4      34 ..       4      46 .. 0.87
   2 ?   -2.2   0.0       7.8   3.5e+03      78      95 ..      81      98 ..      73     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00088
                          MobB  1 vlgivgksgsGKTtLleklipelkarglrvg 31
                                  v++++gk g+GKT++ + li++l++ +  v 
  gi|91772870|ref|YP_565562.1|  4 VIALTGKGGTGKTAITSLLIRHLTKTNKVVL 34
                                  6899*******************99886665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.8
                          MobB 78 elsleellarlsevDlvl 95
                                  e +l e+l+ + ++Dl++
  gi|91772870|ref|YP_565562.1| 81 ESKLYEVLEEMPKYDLIV 98
                                  568899999999999997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0024       1.1       1      26 [.       5      30 ..       5      49 .. 0.87
   2 ?   -0.1   0.0       2.8   1.2e+03       2      34 ..      97     129 ..      96     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0024
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                  i l+G+ g+GK+ ++  L+++l+k+ 
  gi|91772870|ref|YP_565562.1|  5 IALTGKGGTGKTAITSLLIRHLTKTN 30
                                  5689******************9765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.8
                  RNA_helicase   2 wlyGps.geGKStlakeLakallkklklkkkdsv 34 
                                   ++ G++ g G   ++++L + +++kl ++  d v
  gi|91772870|ref|YP_565562.1|  97 IVMGRPeGSGCYCYVNNLLRGIMDKLVKNY-DVV 129
                                   577888888888899999999998884433.333 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8    0.0012      0.53       1      40 [.       4      43 ..       4     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                           PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflr 40
                                  vI+++g+ G Gkt+++  l   + ++++    i+ d +++
  gi|91772870|ref|YP_565562.1|  4 VIALTGKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTN 43
                                  8******************999998888867775544433 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 ?    8.5   0.0    0.0035       1.5       1      44 [.       9      49 ..       9      68 .. 0.79
   2 ?    0.9   0.1      0.78   3.5e+02     103     125 ..     126     148 ..     107     215 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtis 44
                                  G+  +GK++++ lL+  +++ ++ ++ +D+D+  +    P t++
  gi|91772870|ref|YP_565562.1|  9 GKGGTGKTAITSLLIRHLTKTNKVVLAIDADPDTNL---PETLG 49
                                  66789************999999999*****97653...55555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.78
                        CLP1_P 103 asgliIntpGwvkglgaelllel 125
                                    +++iI+t    + + ++++ ++
  gi|91772870|ref|YP_565562.1| 126 YDVVIIDTEAGLEHFSRKMIRDV 148
                                   45555555544444444444333 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.6     0.077        34      11      30 ..      12      30 ..       4      34 .. 0.80
   2 ?    9.0   0.4    0.0025       1.1     134     193 ..     153     217 ..     112     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.077
                        AAA_26 11 gvGKTvvslgLvralkrkgv 30
                                  g GKT+++ +L+r l++ + 
  gi|91772870|ref|YP_565562.1| 12 GTGKTAITSLLIRHLTK-TN 30
                                  68************954.43 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0025
                        AAA_26 134 Vargglgtinqllltiealr...qknvrvlGvilNkvrnp..envetlekksgipvlGvvPylpd 193
                                   V++ g++   +++ +i  l    ++n++ + v++Nkv+++  +++++  +  +++++G+vP+++ 
  gi|91772870|ref|YP_565562.1| 153 VVTDGSRRGLRTAERIRDLTeelDTNIKNIVVVANKVTDAnrAEIKSTAEGLNLELIGTVPMDSI 217
                                   4444444444555555555433346888899*****877733366666677779*******9976 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.92   4.1e+02      36      53 ..     138     155 ..     119     157 .. 0.55
   2 ?    9.2   0.5    0.0026       1.2      25      74 .]     159     207 ..     144     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.92
                     PDDEXK_10  36 elYekakgvkvdrlivvt 53 
                                   e + ++  + vd+livvt
  gi|91772870|ref|YP_565562.1| 138 EHFSRKMIRDVDELIVVT 155
                                   345566666677777776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0026
                     PDDEXK_10  25 rgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgie 74 
                                   r  l + +r++ l e +    +++++vv+  + d n + +k +Ae l++e
  gi|91772870|ref|YP_565562.1| 159 RRGLRTAERIRDLTEELDT-NIKNIVVVANKVTDANRAEIKSTAEGLNLE 207
                                   4458889999999998865.569**********************99875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1    0.0013       0.6      20      46 ..       3      29 ..       1      34 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                                  EEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE 20 dvilLeGdLGaGKTtlvrglakalgve 46
                                  +vi+L+G+ G+GKT+++  l+++l  +
  gi|91772870|ref|YP_565562.1|  3 KVIALTGKGGTGKTAITSLLIRHLTKT 29
                                  689*******************99765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00078      0.35      25      61 ..       4      39 ..       1      41 [. 0.89
   2 ?   -0.4   0.2       2.3     1e+03      40      60 ..     115     133 ..     110     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00078
                         DUF87 25 HlAilgsTGsGKSntvavLleellekkgatililDpH 61
                                   +A  g+ G+GK+  +++L++ l  k +  +l +D++
  gi|91772870|ref|YP_565562.1|  4 VIALTGKGGTGKTAITSLLIRHLT-KTNKVVLAIDAD 39
                                  57999*******************.999999999975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.3
                         DUF87  40 vavLleellekkgatililDp 60 
                                    + ++++l+  k++ ++i+D 
  gi|91772870|ref|YP_565562.1| 115 LRGIMDKLV--KNYDVVIIDT 133
                                   444555555..7888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); 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):              40  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 1471.59
//
Query:       gi|91772871|ref|YP_565563.1|  [L=439]
Description: acetyl-CoA decarbonylase/synthase complex subunit delta [Methanococcoides burtonii DSM 6242]
Scores for complete 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-87  293.2   2.6      9e-80  268.2   0.1    3.1  3  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit
  ------ inclusion threshold ------
      0.066   12.9   0.1        0.1   12.3   0.1    1.2  1  GDPD      Glycerophosphoryl diester phosphodiesterase family


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 !  268.2   0.1     1e-83     9e-80       1     226 [.     116     365 ..     116     368 .. 0.97
   2 !   12.9   0.0   3.8e-06     0.034     263     292 ..     368     393 ..     366     401 .. 0.90
   3 !   11.9   0.1   7.3e-06     0.066     347     384 ..     399     437 ..     393     439 .] 0.90

  Alignments for each domain:
  == domain 1  score: 268.2 bits;  conditional E-value: 1e-83
                                   EEEESS.......GCG-EEEE----S.STTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE.......ETTEEEE- CS
                          CdhD   1 evvlGa.......eekavkiGgeevL.yrfeltffnptaiaidvsDelseellkalaerieevvdd...wakkrvgekltl 70 
                                   ev+lGa       ++ +v++Gge++L y f++++++++ +++dv+D++ +  +k+++e++ +v +d   wakk v+  +++
  gi|91772871|ref|YP_565563.1| 116 EVTLGAtsadggsRKSTVTLGGENALpYYFDAEMPHRNYVTMDVFDMPIS-MAKSVKENYGDVINDpaeWAKKVVKD-FNA 194
                                   6777777777777999**********888*****************9998.5*************************.*** PP

                                   -EEEEE--SSST.......HHHHHHHHHHHCC--SEEEEE-S.....SHHHHHHHHTTTCCC--EEEEE-TT.THHHHHHH CS
                          CdhD  71 daiairlistdP......akkfakavekvakavkvplvlggs.....dpevlkaalevvederpllyaAtkd.dykeiael 139
                                   d+++i+listdP      a+++ak+ve+v++avkvp+v+ggs     dpevl++a+ev+e+er+ll++A+++ dy+++a++
  gi|91772871|ref|YP_565563.1| 195 DMVTIHLISTDPlindtpAREAAKVVEDVLQAVKVPIVIGGSgnpkkDPEVLERAAEVAEGERVLLASASLNlDYERVAKA 275
                                   ********************************************************************************* PP

                                   HHHTT--EEEE-.SSHHHHHHHHHHHHC.TT-..--EEEE---SH.....HHHHHHHHHHHHHHHHS-TTS-S-BEEE--- CS
                          CdhD 140 aleykvpvvllsindleelkelarkllk.agv..kdivldPttaalGegleetidnvvriRraaikgdkdlafPilslttn 217
                                   a +++++v+++++ +++++kel+rkl+k ++v  ++iv+dPttaalG+gl+++++n++riR+a+++gd++l+fP++s+ttn
  gi|91772871|ref|YP_565563.1| 276 ATDHGHAVLSWTQLEINAQKELNRKLMKqCNVprDSIVMDPTTAALGYGLDYAYTNMERIRLAGLMGDDELTFPMSSGTTN 356
                                   ***************************98999*9*********************************************** PP

                                   SSHHHHHHH CS
                          CdhD 218 awlaresde 226
                                   aw+ares++
  gi|91772871|ref|YP_565563.1| 357 AWGARESWM 365
                                   ********8 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.8e-06
                                   S--B--SSEEEESS--TTS-EEEEESBHHH CS
                          CdhD 263 kPvavdpglyeigdrdensPvflttnfsLt 292
                                   +P+++d ++   g+r++++P++++++  Lt
  gi|91772871|ref|YP_565563.1| 368 SPLKQDSDW---GPREYRGPIWEIIT-GLT 393
                                   7********...*************9.887 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 7.3e-06
                                   SS-EEEE.-GGGGGGHHHHHHHHTSEEEE--SSGGGHHH CS
                          CdhD 347 khrflil.Pglvavlkgkiedltgwkvlvgprdsseiva 384
                                   ++ f+++ P++v+vlk+++++l g+  +++++ +++i+a
  gi|91772871|ref|YP_565563.1| 399 NDMFMMMhPTSVQVLKEITQTLYGSIEAEEIDITKWIGA 437
                                   6889***********************999999999876 PP

>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.1e-05       0.1      97     238 ..     158     296 ..     139     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTHHHHHHHHHTCT..CTEEEE CS
                          GDPD  97 evlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnpdilkllrekqp..klpllf 175
                                   +v+++p ++ +++  +++   ++ +e+ +++vk++++ + +i+         + +i  +   ++ k +   ++  k+p++ 
  gi|91772871|ref|YP_565563.1| 158 DVFDMPISMAKSVKENYGDVINDPAEWAKKVVKDFNADMVTIH-----LISTDPLINDTPAREAAKVVEDVLQavKVPIVI 233
                                   6888888999999999999999999999999999999999999.....457888888888888888888888855666666 PP

                                   EEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THS...H CS
                          GDPD 176 lteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnned...e 238
                                     +g+  +     leraa++a  + +l  ++ ++    + ++ k+a ++g +v+ +t  + +   e
  gi|91772871|ref|YP_565563.1| 234 GGSGNPKKDP-EVLERAAEVAEGERVLLASASLNLD--YERVAKAATDHGHAVLSWTQLEINaqkE 296
                                   6654444444.6***************999999888..79*****************988743333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.25s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2827.18
//
Query:       gi|91772872|ref|YP_565564.1|  [L=468]
Description: acetyl-CoA decarbonylase/synthase complex subunit gamma [Methanococcoides burtonii DSM 6242]
Scores for complete 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-148  493.2   0.5     5e-148  492.9   0.5    1.0  1  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit
    3.1e-13   49.1   1.0    5.5e-13   48.3   1.0    1.4  1  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.9   0.5  5.5e-152    5e-148       1     385 [.      69     459 ..      69     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 492.9 bits;  conditional E-value: 5.5e-152
                                   EEEESSGCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE....ETTEEEE--EEEEE--SSS CS
                          CdhD   1 evvlGaeekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvddwakkrvgekltldaiairlistd 81 
                                   evv+G++++a+ iGg++vL+r++ltffn+ta+a+dv+D+++e     l+er+++++d ++k++vg  ltld+ia+r  s+d
  gi|91772872|ref|YP_565564.1|  69 EVVIGVGDNAISIGGDDVLHRHKLTFFNKTALAYDVWDTMEET---DLVERVNKIQD-FKKFYVGDYLTLDMIAVRSVSND 145
                                   8*************************************99985...999******99.*********************** PP

                                   T.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE-.SSHHHHHHHH CS
                          CdhD  82 PakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvllsindleelkela 162
                                   P +kfa++v+kv++ +++p++l++++p+vl+a+lev++++rpllyaA+kd+++e+a+la e++vpv++++ ndl+ lk++a
  gi|91772872|ref|YP_565564.1| 146 P-EKFAATVKKVMETTEFPMILCSFEPAVLRAGLEVAAEKRPLLYAANKDNWQEVAALAQEFNVPVTVFAPNDLDLLKSMA 225
                                   *.******************************************************************************* PP

                                   HHHHCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS-TTS-S-BEEE---SSHHHHHHHHH...........HHHT CS
                          CdhD 163 rkllkagvkdivldPttaalGegleetidnvvriRraaikgdkdlafPilslttnawlaresdeve...........lvvr 232
                                   ++++++ ++d+vldP+t++ G+gl++t++n+++iRra+i+gd+d+afPi++++ +aw+a+ +dev+           ++++
  gi|91772872|ref|YP_565564.1| 226 KTFADNAIEDVVLDPGTFPTGKGLKTTLNNFLKIRRASINGDRDIAFPIMAVPFTAWMAH-DDEVSasywetvvasiFTIK 305
                                   ***********************************************************6.9999999999********** PP

                                   T-SEEEES---HHHHHHHHHHHHHHTS-SSS--B--SSEEEESS--TTS-EEEEESBHHHHHHHHHHHHHTTS-EEEEEE- CS
                          CdhD 233 YadililrslekeellPvltlrqniYtDPrkPvavdpglyeigdrdensPvflttnfsLtyYtvegdlesdkitayLLvld 313
                                   Y+di+i++s+e ++l+P+l++r+++YtDPrkPv+vdp +yeig +  +sP+ +ttnf+LtyYtve+dl+s+++ +yL ++d
  gi|91772872|ref|YP_565564.1| 306 YGDIMIMHSIEPYALMPQLHIRDTMYTDPRKPVTVDPAVYEIGSPTADSPLLVTTNFALTYYTVESDLSSNGVDCYLTAID 386
                                   ********************************************************************************* PP

                                   SSS--HHHHHHTTSSSHHHHHHHHHHTTHH.HHSSS-EEEE-GGGGGGHHHHHHHHTSEEEE--SSGGGHHHH CS
                          CdhD 314 teGlgvevslaggqleaekvkdlieetgie.ekvkhrflilPglvavlkgkiedltgwkvlvgprdsseivav 385
                                   t+G+gve+++aggql+a+k+k+ ++++g++ ek  h++++lPgl+a+l+g++ed+tg+ v+ gp+ds++++++
  gi|91772872|ref|YP_565564.1| 387 TDGIGVEAAVAGGQLTAAKIKKGLDDAGFDmEKLTHKVIVLPGLAARLQGDVEDETGAGVMIGPADSGRLPGW 459
                                   *****************************9678***********************************99887 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   1.0   6.1e-17   5.5e-13       1      33 []      13      45 ..      13      45 .. 0.99

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 6.1e-17
                           FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                  LPgtNCg+CG+ +CmafA+ l+  + + +dC+p
  gi|91772872|ref|YP_565564.1| 13 LPGTNCGECGETSCMAFASHLIDRSLKATDCTP 45
                                  9******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3038.19
//
Query:       gi|91772873|ref|YP_565565.1|  [L=314]
Description: hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-07   28.1   0.0    2.2e-06   26.6   0.0    1.6  1  AXE1             Acetyl xylan esterase (AXE1)
    5.8e-05   22.5   0.0      0.033   13.5   0.0    2.1  2  Hydrolase_4      Serine aminopeptidase, S33
    0.00055   19.5   0.0    0.00084   19.0   0.0    1.3  1  DLH              Dienelactone hydrolase family
     0.0012   18.8   0.0     0.0021   18.0   0.0    1.4  1  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
     0.0023   17.4   0.0       0.01   15.3   0.0    2.1  1  Peptidase_S9     Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.037   13.3   0.0    1.8  2  Abhydrolase_7    Abhydrolase family
      0.062   12.3   0.1       0.18   10.8   0.1    1.6  1  Chlorophyllase   Chlorophyllase
      0.083   11.8   0.0         10    4.9   0.0    2.1  2  Chlorophyllase2  Chlorophyllase enzyme


Domain annotation for each model (and alignments):
>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   9.6e-10   2.2e-06      69     204 ..      91     217 ..      61     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.6e-10
                                   EEEEEEEES..SSSSEEEEEEEE-TT--GGGHHH.HHHHHHTT-EEEEEE-TTTS..SSB-SSCCSS-SSSSTTTTTTSTT CS
                          AXE1  69 ikaklvlPke.keeklPavvefhGYegsrgeihd.llnyaaaGyavvvmdvRGqggesedkvgskgnkakGfiirGlldke 147
                                   + + l+ P++ ++ ++Pa+v   G   ++ + h   +  a +Gya + +d R  g    d+   +          G+ +  
  gi|91772873|ref|YP_565565.1|  91 VPSLLTIPRTtTDSQIPAIVVLPGAGVTKENEHGlSVILADMGYASIIIDQRDLGAIDLDSDIEM-------FKTGV-ESV 163
                                   45566777751456889999999998886666652688899999999999998884444433332.......22344.333 PP

                                   T-HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEE CS
                          AXE1 148 klyyrrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavvad 204
                                   +++   +  Da ++ +++++ pe+D ++va+lG+s GG  a+ ++al++ +  v+a 
  gi|91772873|ref|YP_565565.1| 164 QYL---IIYDALKASDVLRDQPEIDASKVAMLGSSNGGRPAIIATALDDSLSGVIAI 217
                                   443...455******************************************999885 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.5e-05     0.033       6     136 ..     108     243 ..     104     256 .. 0.77
   2 !    7.5   0.0   0.00095       2.1     192     233 ..     256     296 ..     231     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                   Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.......gkrghvpsfdd.yvdDlaafvekvkeehpel.. 76 
                                   ++v+++G + + +  + l   La+ G+a +++D+r  G  +        k+  v+s++  ++ D+ ++ + ++++ +    
  gi|91772873|ref|YP_565565.1| 108 AIVVLPGAGVTKENEHGLSVILADMGYASIIIDQRDLGAIDldsdiemFKT-GVESVQYlIIYDALKASDVLRDQPEIDas 187
                                   68999999999999999999*******************988888884444.46666651568999998999955554469 PP

                   Hydrolase_4  77 plfllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpk 136
                                   ++ +lG S GG  a+ +++   + ++g+i +++     +   a   ++++ kl+ +++++
  gi|91772873|ref|YP_565565.1| 188 KVAMLGSSNGGRPAIIATALDDS-LSGVIAISTCGYDSS---AIDPAQVTDKLAYEFFRS 243
                                   ***********999999988888.999999998754443...445555555555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00095
                   Hydrolase_4 192 lPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                                    P+ +lh+ +D v++++ ++ +++++    k++ +++   H 
  gi|91772873|ref|YP_565565.1| 256 RPFVMLHSINDSVISYGSAQLTFKKAEE-PKSFVTIDSTSHG 296
                                   69************************96.9999999999985 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.7e-07   0.00084       9     128 ..     102     217 ..      92     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.7e-07
                           DLH   9 knakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavayl 89 
                                   ++++ p++vv++ +   ++n +  s  la+ GY+ ++ d  +r+   + d + + ++++  v+ v +  +  d+  a + l
  gi|91772873|ref|YP_565565.1| 102 TDSQIPAIVVLPGAGVTKENEHGLSVILADMGYASIIID--QRDL-GAIDLDSDIEMFKTGVESV-QYLIIYDALKASDVL 178
                                   34489*******97555599999**************88..6666.5678888888888888888.555555555999*** PP

                           DLH  90 ksvpevstkkvgvvGfCmGGalalllaaevpevdaavaf 128
                                   + +pe + +kv++ G   GG+ a+   a ++ + +++a 
  gi|91772873|ref|YP_565565.1| 179 RDQPEIDASKVAMLGSSNGGRPAIIATALDDSLSGVIAI 217
                                   *************************99999999999875 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 !   18.0   0.0   9.5e-07    0.0021       8      61 ..     173     226 ..     172     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.5e-07
                                   HHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SS CS
                        BAAT_C   8 eainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvveg 61 
                                   +a + l+++p++  +k+++lG S Gg  a++ ++  ++ s v++i+ + + +++
  gi|91772873|ref|YP_565565.1| 173 KASDVLRDQPEIDASKVAMLGSSNGGRPAIIATALDDSLSGVIAISTCGYDSSA 226
                                   67889************************99999999********999876654 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.6e-06      0.01      44      83 ..     167     206 ..     125     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-06
                                   HHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHH CS
                  Peptidase_S9  44 efdDfiaaaealakegyvdserlaitGgSyGGyltgaaln 83 
                                    + D ++a + l ++  +d++++a+ G S+GG  +  a +
  gi|91772873|ref|YP_565565.1| 167 IIYDALKASDVLRDQPEIDASKVAMLGSSNGGRPAIIATA 206
                                   5789****************************76665555 PP

>> Abhydrolase_7  Abhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.6e-05     0.037      60     133 ..      52     125 ..      42     149 .. 0.85
   2 ?   -1.9   0.0      0.66   1.5e+03     212     250 ..     174     212 ..     162     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                                   HHHH-----------EEEEEEEETTEEEEEEEE--STTB-EEEEEEEETT-.-S-EEEEEEE--TT--HHHHCT- CS
                 Abhydrolase_7  60 eelmkfPelkklpapvcvkteqrdgyrlekwefyPlpkavstflvliPdnv.kkpvpavlciPGsgktkeelaGe 133
                                   e l+ +Pe  +++  ++       +y++   e y   + +++ l+ iP +   ++ pa++ +PG g tke+  G 
  gi|91772873|ref|YP_565565.1|  52 EGLLSYPERDAIQYSIIDIDDSNSNYTVSTIE-YTSRSRIVPSLLTIPRTTtDSQIPAIVVLPGAGVTKENEHGL 125
                                   5689999999999999888899999***9998.67777888888889988758899**************98775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                                   HHHHHCT-TTEEEEEEEEEEEGGGHHHHHHHHHH-TT-- CS
                 Abhydrolase_7 212 vldwmktqslirkdriivsGfslGteplmvlGaldesiy 250
                                     d ++ q+ i   ++ + G s G  p ++  ald+s+ 
  gi|91772873|ref|YP_565565.1| 174 ASDVLRDQPEIDASKVAMLGSSNGGRPAIIATALDDSLS 212
                                   5567889999999999999*********99999999875 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1     8e-05      0.18      31     148 ..      91     212 ..      71     237 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8e-05
                Chlorophyllase  31 pPkpliivtPaeaGtypvvlflhGtllsnkfyskllnhiashGf..ivvaPqlykllp.PsaqdeidsaaevieWl....s 104
                                    P  l i   + + + p +++l G  ++ ++   l   +a  G+  i++  +    +   s ++  ++  e +++l    +
  gi|91772873|ref|YP_565565.1|  91 VPSLLTIPRTTTDSQIPAIVVLPGAGVTKENEHGLSVILADMGYasIIIDQRDLGAIDlDSDIEMFKTGVESVQYLiiydA 171
                                   455555555566777888888877766666655555556666654366666656666634444444555555555511114 PP

                Chlorophyllase 105 eglkavlptsveanlsklalvGhsrGGktaf.alalgysseltfs 148
                                    +   vl+++ e + sk+a+ G s GG+ a  a al  s    +s
  gi|91772873|ref|YP_565565.1| 172 LKASDVLRDQPEIDASKVAMLGSSNGGRPAIiATALDDS----LS 212
                                   45567899********************98537888666....22 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0047        10     130     181 ..      85     135 ..      72     144 .. 0.74
   2 ?    4.6   0.0    0.0056        13      79     111 ..     176     209 ..     152     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0047
               Chlorophyllase2 130 askskqtepkiLtyepesfnlkmpvlviGtgLgeekknallppcapkgvnha 181
                                   + + +++ p++Lt   ++ + ++p++v+  g g  k+n    + + +++++a
  gi|91772873|ref|YP_565565.1|  85 T-SRSRIVPSLLTIPRTTTDSQIPAIVVLPGAGVTKENEHGLSVILADMGYA 135
                                   3.478999*****************999555555555555555566666665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0056
               Chlorophyllase2  79 svlpeevepdlsklalsgHSrGgktaf.alalgk 111
                                    vl ++ e d sk+a+ g S+Gg++a+ a al+ 
  gi|91772873|ref|YP_565565.1| 176 DVLRDQPEIDASKVAMLGSSNGGRPAIiATALDD 209
                                   5788888999*************98752555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 1824.77
//
Query:       gi|91772874|ref|YP_565566.1|  [L=2065]
Description: hydrogenobyrinic acid a,c-diamide cobaltochelatase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
          0 1085.5   0.0          0 1084.0   0.0    1.7  2  CobN-Mg_chel     CobN/Magnesium Chelatase
    3.3e-20   72.1  11.5    1.4e-05   25.3   0.1    6.0  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    6.1e-17   61.9  14.0    0.00015   22.0   0.2    6.1  5  SdrD_B           SdrD B-like domain
    2.5e-11   43.4  11.7      0.012   15.6   0.2    5.6  5  CarbopepD_reg_2  CarboxypepD_reg-like domain
    4.7e-11   42.9   0.4      0.095   12.8   0.0    4.8  4  DUF2012          Protein of unknown function (DUF2012)
    3.3e-09   36.5   0.2    1.3e-08   34.5   0.2    2.1  1  PKD              PKD domain
    4.7e-08   33.2  13.0       0.23   11.8   0.2    5.4  4  SpaA             Prealbumin-like fold domain
    4.4e-07   29.9   0.0       0.22   11.6   0.0    3.6  3  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    6.1e-05   22.7  14.5       0.16   11.8   2.8    5.6  5  fn3_3            Polysaccharide lyase family 4, domain II
     0.0024   17.7   0.0        1.2    9.0   0.0    3.3  3  DUF1416          Protein of unknown function (DUF1416)


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 ?   -3.3   0.0      0.76   1.4e+03     120     186 ..     119     193 ..      88     200 .. 0.74
   2 ! 1084.0   0.0         0         0       2    1088 ..     571    1908 ..     570    1909 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.76
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel 120 eelftkegeekvdalinttsfalvkgpaeeeeeeaeeea.........lkelnvPvlqa.ilssqsreeWeessqGl 186
                                    + f keg  k +alin ts  l + + e+ ++++++++           + n+  l+   +s+++++ W ++++ l
  gi|91772874|ref|YP_565566.1| 119 GTTF-KEG-RKSNALINATSLVLISDTGEYIANTTSDQNgsfcftdipNGNYNIAALNYlYSSMSKKDIWYTNTTSL 193
                                   3344.566.8999********99999988888777666699999999888999999999667777778898887776 PP

  == domain 2  score: 1084.0 bits;  conditional E-value: 0
                                    xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx......xxxxx RF
                  CobN-Mg_chel    2 aYlkeggveNlknllryladkllg......kkeeeveppvelpeegiyhpdake.lfesleeylewyk......kakke 67  
                                    +Y++e+ ++N+ +l++yl+   l+      +   ++e+p+ +p++gi+hpda   +f++l +ylewy+      + +++
  gi|91772874|ref|YP_565566.1|  571 DYWMEQYDNNIIRLITYLSVVDLSapfteyNGMIRIEEPSITPTNGIVHPDAGYeIFDDLVSYLEWYCeddgkhHIYNP 649 
                                    7****************665555555555988999*****************988************************ PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel   68 kaptvgilfyrahllagntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgp 146 
                                    ++ tvgi+f + h  +    v++ali++le+rg+nv+p+f  +    + +++e +f++++e k+da i + ++  ++++
  gi|91772874|ref|YP_565566.1|  650 ENYTVGITFFEGHDGDLCDGVTEALINELESRGINVIPTFRPA-VIYELDDAEIYFKADNEWKADAFIDVGMGVSSMSS 727 
                                    **************99999***********************9.5566778899****************998888777 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  147 aeeeeeeaeeealkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetevekye 225 
                                       ++     eal+e++vPv+++i +++++eeWe+s +G +  ++++++ + E+ G ie++vi++ke + e+ e+ +++
  gi|91772874|ref|YP_565566.1|  728 FVWQN-----EALQEMGVPVINGIQYQGTIEEWENSVSGQD-GRFQYQIPIMEIGGEIESIVIGGKEYD-EDMEAWTFQ 799 
                                    65554.....468**************************95.8899*******************9865.78889**** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  226 pipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeL 304 
                                    pi+ ++++++d++  w++L++ +n++k+vaii++n+  ++g++ +a +Ldv +S+ n+L+a+k +GYd++ +  +++e+
  gi|91772874|ref|YP_565566.1|  800 PIDYQMKWMVDRTVGWIDLQHIKNKDKRVAIIYYNHG-KQGAMVAA-NLDVAPSIPNMLTAMKGDGYDLDGKDINRSEF 876 
                                    *************************************.77777756.9*********************765679**** PP

                                    xxxxxxxxxxxxxx.....xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                  CobN-Mg_chel  305 iellleggtndpew.....eelkv....gaaallpaeeYeewfeeLpeelreeveerWgeppge.mveeeksgekklvi 373 
                                    iel+l++g+n   w     +   +     +++llp+e+Y ewfe++++++r++v+ +Wge+pg+ mv+e ++++k++v+
  gi|91772874|ref|YP_565566.1|  877 IELVLQQGRNVGVWapgelN---YmvenYDVELLPVETYLEWFEDIEPAARQSVIGTWGEAPGKgMVYE-NESGKYFVF 951 
                                    *********99999885541...2444599**********************************88886.6666***** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                  CobN-Mg_chel  374 pglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlree.....fgadavvHvGkHGtlEwlPGKqvgls. 446 
                                    p++++Gnv++++QP+rg++ +++ lyhd+++pP+h+Y+AfYlWl++e     f++davvH+G+HG+ Ewl GK+vgls 
  gi|91772874|ref|YP_565566.1|  952 PKIEVGNVLIAPQPPRGLTINDTMLYHDQSVPPSHNYIAFYLWLNKEqneggFDTDAVVHFGRHGSEEWLQGKGVGLSv 1030
                                    *********************************************9666677*************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  447 eecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkalr 525 
                                    +ec+P++l++d+P++Y+Y v  +gEG++AKRR++Av++dHlt+p+ +++lyg+l++L++++++Yeeae +    +++ +
  gi|91772874|ref|YP_565566.1| 1031 KECWPALLIQDMPVIYLYDVGGIGEGITAKRRGNAVMVDHLTAPVINSGLYGNLTQLHDAMHNYEEAEGS---LKQEYK 1106
                                    ******************************************************************9877...566777 PP

                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  526 eqilelveelnldkdlg..leeakeeeeeefeelle..kldgyleelkeaqirdglhilGeapegeqlvdlvvailrle 600 
                                    ++i++ +e+lnl+++lg  +++ +++e+e+fe+++    +++yl+e++++ +++glhilGe +++e l+++v+++l   
  gi|91772874|ref|YP_565566.1| 1107 RSIINYYEDLNLEHELGnsSDDLSAMENETFENFVLhgPVHDYLHEIASSYMPYGLHILGEDMSEEGLTAMVKSML--- 1182
                                    7***************9765556899********65358*************************************... PP

                                    xxxxxxxxxxxxxxxxxxxxx.......................................................xxx RF
                  CobN-Mg_chel  601 neegesltealaealgldlde.......................................................lee 624 
                                       g++++++++++ gl  d+                                                          
  gi|91772874|ref|YP_565566.1| 1183 ---GNDFRKHVNAT-GLCEDPdmlspahspnvldeiltkvlingtepmdvvidqfnidytyghyystvlsntsgsyD-- 1255
                                    ...99*****9999.77777755555555555555555555555555555555555554444444444444444440.. PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                  CobN-Mg_chel  625 ksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee............................ 675 
                                                                                      +                            
  gi|91772874|ref|YP_565566.1| 1256 --------------------------------------------------Aefvkdgkytiyafkevsdgwitgkdytt 1284
                                    ..................................................04455555555555555555555555555 PP

                                    ............................................................................... RF
                  CobN-Mg_chel  676 ............................................................................... 675 
                                                                                                                   
  gi|91772874|ref|YP_565566.1| 1285 iqngetignigitlsknatgttdseleyvlnmlndvpsigsgagvisgqtrypgmdgsikarinstvvlqrdgkaidmc 1363
                                    5555555555556666666666666666666666666666666666666667777777777777777777777777777 PP

                                    ............................................................................... RF
                  CobN-Mg_chel  676 ............................................................................... 675 
                                                                                                                   
  gi|91772874|ref|YP_565566.1| 1364 vtgddanytftdipngeyviasiyqsmisgswyfdsenieitengssnvilemekdntnaqaiisllgevsgttimngs 1442
                                    777777777777777777777777777777777777777777777777777888888888888888888888888899* PP

                                    .....................................xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  676 .....................................ete.eEitallraLdGeyippgpsGdptrgraevLPTGrNfy 716 
                                                                         e++ +Ei+ +++aL+G+yipp+ ++dptr+++evLPTG+Nfy
  gi|91772874|ref|YP_565566.1| 1443 lvaedgcnvviitrltdvqltvandlyaaldysnalkECKdAEINGMIDALNGKYIPPALGDDPTRSPDEVLPTGKNFY 1521
                                    *************************************8877************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  717 svDpraiPteaAwevGkklaeellerylqeh.geyPekvglslwgtetmrteGediAqiLallGvrPvwdaagrvvdle 794 
                                    +++p+ +Pt+++wevGk+l++++l+++++ h g+yPekvg++lw++e mr++G ++A++++llGv+P ++++g+v++++
  gi|91772874|ref|YP_565566.1| 1522 AFNPNIVPTKESWEVGKQLVDDFLNEWKDGHdGQYPEKVGFVLWSSESMRHKGVMEAEVMYLLGVEPDYSSSGKVEGVK 1600
                                    ******************************************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx RF
                  CobN-Mg_chel  795 lipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleeke.....eaeerat 868 
                                    lip +eLgRPRiDV+v+++G++RD+++++++l+d+av+l+a+++ +++ N+v++h+++ +++l+e+e     ea+  ++
  gi|91772874|ref|YP_565566.1| 1601 LIPEDELGRPRIDVLVTMTGVYRDNWKWQVQLMDRAVRLAADAESNAYPNYVNEHSEAIYDALMETEnytpsEARGLSM 1679
                                    *****************************************************************4445544777**** PP

                                    xxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                  CobN-Mg_chel  869 yRvFgskpGaYga.gvqelies.snWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsre...h 942 
                                    +R+Fg+ +G++g  g+++ +++ ++W++ee+La++Y+n++syaYg +  + +++e+f+++L+++d+v+ +++ +     
  gi|91772874|ref|YP_565566.1| 1680 CRLFGPDDGSWGIgGLTNSVDAsGTWTEEEKLANLYINSMSYAYGDKIWAFKDTEVFKKALADTDAVLFSRSGNSgrgS 1758
                                    ************989*******9************************************************98875557 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  943 dlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaa 1021
                                    + +  d+ y+f+GG+ +avr++sg++p+++++++++p+++ ++tl  +++r+lrs+++NP+Wiegmm+hGy Ga+e+++
  gi|91772874|ref|YP_565566.1| 1759 SSVIFDHTYEFFGGFGMAVRHVSGDTPDMFIVNLKDPAQAMTETLGAFLSRDLRSTYWNPTWIEGMMEHGYVGASEIDR 1837
                                    88889************************************************************************** PP

                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel 1022 tvdnlfgwdata.dvvddwvyeevaetYvlDee...vrefleekNpwAlreiaerLlEaarrglWeaseet 1088
                                    +++ ++g +++  d +++++++e+++ Y +D++   ++e+++++N wA +++ +r++Ea+r+g+W+a++e 
  gi|91772874|ref|YP_565566.1| 1838 MLEDFWGLNVMLpDEINNDMWNEFYNIYENDKYelgLDEWFQSENSWAKQSMEARMIEAIRKGYWDAPDEV 1908
                                    ********************************************************************986 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   3.3e-06    0.0059      27      52 ..      35      60 ..      29      69 .. 0.88
   2 !   19.4   0.1   5.2e-07   0.00093      10      55 ..     128     173 ..     116     197 .. 0.77
   3 !   25.3   0.1   7.8e-09   1.4e-05       9      64 ..     237     292 ..     226     307 .. 0.79
   4 ?    5.4   0.3     0.012        22      29      54 ..    1243    1268 ..    1228    1299 .. 0.81
   5 !    7.8   0.0    0.0021       3.8      17      56 ..    1349    1387 ..    1330    1417 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-06
               CarboxypepD_reg 27 gtvastttdadGafrlrglppgtysv 52
                                  + va+tt+d++G+f ++g+p g+ys+
  gi|91772874|ref|YP_565566.1| 35 ELVANTTSDENGNFVFEGVPNGDYSI 60
                                  5689********************98 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 5.2e-07
               CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvs 55 
                                   s+a i   ++++ ++ ++  a+tt+d++G+f ++++p g+y++ + 
  gi|91772874|ref|YP_565566.1| 128 SNALINATSLVLISDTGEYIANTTSDQNGSFCFTDIPNGNYNIAAL 173
                                   56677778888887777789**********************9884 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 7.8e-09
               CarboxypepD_reg   9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                   +s++pi   t+++ ++ ++ va+tt+d++G+f ++++p g+y++ + +  y + ++
  gi|91772874|ref|YP_565566.1| 237 KSNTPINDTTLVLISDTGEYVANTTSDQNGSFCFTDIPNGNYNIAALSYLYSSMSK 292
                                   3899**********988889************************996665655555 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.012
               CarboxypepD_reg   29 vastttdadGafrlrglppgtysvtv 54  
                                     +++ ++++G++  ++++ g+y++ +
  gi|91772874|ref|YP_565566.1| 1243 YSTVLSNTSGSYDAEFVKDGKYTIYA 1268
                                    57899******************987 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0021
               CarboxypepD_reg   17 atVtvtnadtgtvastttdadGafrlrglppgtysvtvsa 56  
                                     tV+++  d+++    +t++d +++++++p g+y +   +
  gi|91772874|ref|YP_565566.1| 1349 STVVLQ-RDGKAIDMCVTGDDANYTFTDIPNGEYVIASIY 1387
                                    578888.588999*********************997744 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0    0.0001      0.18      35      64 ..      33      62 ..      23      87 .. 0.87
   2 !   17.6   0.1   1.9e-06    0.0035      24      66 ..     132     174 ..     125     217 .. 0.82
   3 !   22.0   0.2   8.3e-08   0.00015      20      65 ..     238     283 ..     234     326 .. 0.86
   4 ?    3.2   1.3     0.055        98      34      65 ..    1238    1269 ..    1226    1306 .. 0.81
   5 !   10.7   0.0   0.00026      0.46      28      68 ..    1350    1389 ..    1340    1427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                        SdrD_B 35 kgevvatttTdasGkYkFtnltpGeYkVef 64
                                  + e+va+tt+d++G++ F+++ +G+Y+++ 
  gi|91772874|ref|YP_565566.1| 33 SYELVANTTSDENGNFVFEGVPNGDYSIAS 62
                                  456779*********************976 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.9e-06
                        SdrD_B  24 isgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVefta 66 
                                   i+   + L++++ge +a+tt+d++G++ Ft++ +G+Y+++  +
  gi|91772874|ref|YP_565566.1| 132 INATSLVLISDTGEYIANTTSDQNGSFCFTDIPNGNYNIAALN 174
                                   6777788999****************************98755 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 8.3e-08
                        SdrD_B  20 gekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeft 65 
                                    ++ i++ t+ L++++ge va+tt+d++G++ Ft++ +G+Y+++  
  gi|91772874|ref|YP_565566.1| 238 SNTPINDTTLVLISDTGEYVANTTSDQNGSFCFTDIPNGNYNIAAL 283
                                   5689**************************************9875 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.055
                        SdrD_B   34 akgevvatttTdasGkYkFtnltpGeYkVeft 65  
                                    + g+  +t+++++sG+Y  + +++G+Y++   
  gi|91772874|ref|YP_565566.1| 1238 TYGHYYSTVLSNTSGSYDAEFVKDGKYTIYAF 1269
                                    556777999******************99653 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00026
                        SdrD_B   28 tVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapa 68  
                                    tV L +++g++++  +T  + +Y+Ft++ +GeY ++ ++ +
  gi|91772874|ref|YP_565566.1| 1350 TVVL-QRDGKAIDMCVTGDDANYTFTDIPNGEYVIASIYQS 1389
                                    5666.78999999*********************9876654 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00012      0.21      26      50 ..      38      62 ..      29      88 .. 0.85
   2 !   15.5   0.1   6.9e-06     0.012       1      61 [.     117     183 ..     117     206 .. 0.72
   3 !   15.6   0.2   6.4e-06     0.012      13      61 ..     241     293 ..     227     315 .. 0.69
   4 ?   -0.4   0.3      0.65   1.2e+03      28      49 ..    1246    1267 ..    1239    1306 .. 0.85
   5 ?    3.5   0.1     0.041        74      28      82 ..    1363    1422 ..    1347    1427 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
               CarbopepD_reg_2 26 kgtvTdenGnFelknlpagkytLvv 50
                                  ++t++denGnF ++ +p+g+y +  
  gi|91772874|ref|YP_565566.1| 38 ANTTSDENGNFVFEGVPNGDYSIAS 62
                                  689******************8864 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.9e-06
               CarbopepD_reg_2   1 isGtVvdketk.eplpgat..Vyvkgtk...kgtvTdenGnFelknlpagkytLvvsyvGyktqekk 61 
                                   isGt ++++ k ++l+ at  V++ +t+   ++t++d+nG+F ++++p+g+y + +  + y +++kk
  gi|91772874|ref|YP_565566.1| 117 ISGTTFKEGRKsNALINATslVLISDTGeyiANTTSDQNGSFCFTDIPNGNYNIAALNYLYSSMSKK 183
                                   567777666554788888544777777655689********************99988888887765 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 6.4e-06
               CarbopepD_reg_2  13 plpgat.Vyvkgtk...kgtvTdenGnFelknlpagkytLvvsyvGyktqekk 61 
                                   p+   t V++ +t+   ++t++d+nG+F ++++p+g+y + + ++ y +++kk
  gi|91772874|ref|YP_565566.1| 241 PINDTTlVLISDTGeyvANTTSDQNGSFCFTDIPNGNYNIAALSYLYSSMSKK 293
                                   5544431444555444589*********************9999999998765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.65
               CarbopepD_reg_2   28 tvTdenGnFelknlpagkytLv 49  
                                    + ++ +G++  + +++gkyt+ 
  gi|91772874|ref|YP_565566.1| 1246 VLSNTSGSYDAEFVKDGKYTIY 1267
                                    45999**************985 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.041
               CarbopepD_reg_2   28 tvTdenGnFelknlpagkytLvvsyvGykt.....qekkvtvskektldvnillkeeale 82  
                                    +vT ++ n++++++p+g+y +   y ++ +     ++++++++++ + +v +++++++++
  gi|91772874|ref|YP_565566.1| 1363 CVTGDDANYTFTDIPNGEYVIASIYQSMISgswyfDSENIEITENGSSNVILEMEKDNTN 1422
                                    6899999************87655544433222223455666666666666666666665 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.011        20      24      51 ..      40      65 ..      18      71 .. 0.80
   2 !   12.4   0.0   7.1e-05      0.13       3      46 ..     128     172 ..     126     180 .. 0.81
   3 !   12.8   0.0   5.3e-05     0.095       4      48 ..     239     284 ..     236     289 .. 0.80
   4 !    6.1   0.0    0.0066        12       9      47 ..    1348    1386 ..    1343    1425 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                       DUF2012 24 alvrrDGsFifrdlpegsYlLevespey 51
                                  +   ++G+F+f+ +p+g Y +   s +y
  gi|91772874|ref|YP_565566.1| 40 TTSDENGNFVFEGVPNGDYSI--ASMNY 65
                                  556789*************75..45555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.1e-05
                       DUF2012   3 plnllantrvlL..dsgqqrkfkalvrrDGsFifrdlpegsYlLev 46 
                                   ++ l++ t+ +L  d+g++   ++   ++GsF f+d+p+g Y++ +
  gi|91772874|ref|YP_565566.1| 128 SNALINATSLVLisDTGEY-IANTTSDQNGSFCFTDIPNGNYNIAA 172
                                   5667777777777888999.8999999***************9865 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 5.3e-05
                       DUF2012   4 lnllantrvlL..dsgqqrkfkalvrrDGsFifrdlpegsYlLeves 48 
                                   ++ +++t+ +L  d+g++   ++   ++GsF f+d+p+g Y++ + s
  gi|91772874|ref|YP_565566.1| 239 NTPINDTTLVLisDTGEY-VANTTSDQNGSFCFTDIPNGNYNIAALS 284
                                   555667777777888888.788899999*************997765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0066
                       DUF2012    9 ntrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLeve 47  
                                    n++v+L+ + ++    ++  D++++f+d+p+g+Y++   
  gi|91772874|ref|YP_565566.1| 1348 NSTVVLQRDGKAIDMCVTGDDANYTFTDIPNGEYVIASI 1386
                                    778888777776666777899*************98654 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.2   7.3e-12   1.3e-08      10      68 ..     382     435 ..     373     436 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 7.3e-12
                                   SSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                           PKD  10 pgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68 
                                   +  tv+ft  +   + ++++Wdfgd   +  ++ +++ h+Y s G++ V++tasna +s
  gi|91772874|ref|YP_565566.1| 382 CPLTVEFTDLS--ENATSWHWDFGD---GSNSTDQKPIHVYDSVGSFCVKLTASNAQNS 435
                                   66799999999..999*********...***************************9775 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00018      0.32      33      57 ..      35      59 ..       5      61 .. 0.87
   2 !   10.2   0.1   0.00042      0.76       5      57 ..     116     169 ..     112     171 .. 0.74
   3 !   11.8   0.2   0.00013      0.23       4      57 ..     225     279 ..     222     281 .. 0.79
   4 ?    2.6   2.2     0.095   1.7e+02      28      58 ..    1345    1383 ..    1254    1384 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                  CEESEEE-BTTSEEEEEEEESEEEE CS
                          SpaA 33 tevttlttdenGkatfegLplGtYl 57
                                  + v++ t+denG++ feg+p G+Y 
  gi|91772874|ref|YP_565566.1| 35 ELVANTTSDENGNFVFEGVPNGDYS 59
                                  5678899*****************6 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00042
                                   B-TS-EEEEEETTTSCCCHCHHTT...........TTCCEESEEE-BTTSEEEEEEEESEEEE CS
                          SpaA   5 pLaGaeFtlykvdtttdgkdalea..........kktgtevttlttdenGkatfegLplGtYl 57 
                                    ++G +F+  +++   +      a           +tg+ +++ t+d+nG + f+++p G+Y 
  gi|91772874|ref|YP_565566.1| 116 EISGTTFKEGRKS---N------AlinatslvliSDTGEYIANTTSDQNGSFCFTDIPNGNYN 169
                                   5566666666665...2......12223557888889999**********************6 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00013
                                   CB-TS-EEEEEETTTSCCCHCHHTT.......TTCCEESEEE-BTTSEEEEEEEESEEEE CS
                          SpaA   4 kpLaGaeFtlykvdtttdgkdalea......kktgtevttlttdenGkatfegLplGtYl 57 
                                   ++++G +F+  +++     ++ +++       +tg+ v++ t+d+nG + f+++p G+Y 
  gi|91772874|ref|YP_565566.1| 225 NAISGTTFKKGRKS-----NTPINDttlvliSDTGEYVANTTSDQNGSFCFTDIPNGNYN 279
                                   57788888888887.....233333455678899*************************6 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.095
                                    T.........TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                          SpaA   28 a........kktgtevttlttdenGkatfegLplGtYll 58  
                                    a        + +g+ ++  +t+++ + tf+++p G+Y++
  gi|91772874|ref|YP_565566.1| 1345 ArinstvvlQRDGKAIDMCVTGDDANYTFTDIPNGEYVI 1383
                                    13333444455666679999*****************86 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 !    7.8   0.0    0.0019       3.4      39      95 ..      33      89 ..      29      93 .. 0.86
   2 !    5.9   0.0    0.0071        13      32      96 ..     136     198 ..     127     204 .. 0.72
   3 !   11.6   0.0   0.00012      0.22      23      94 ..     237     308 ..     231     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0019
                          bMG3 39 kgevlaegtTDaqGvarfaallar.gkegaapylvsArkdedlaflkldwergldlsr 95
                                  + e++a++t+D++G   f++  +  ++ ++  yl sA  +ed+ f +++ + ++++s+
  gi|91772874|ref|YP_565566.1| 33 SYELVANTTSDENGNFVFEGVPNGdYSIASMNYLYSAMAKEDMWFCNTS-NINIESSD 89
                                  66899**************9966567778889999999**********5.99999987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0071
                          bMG3  32 eVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsAr.kdedlaflkldwergldlsrf 96 
                                   ++ l++++ge +a++t+D++G   f++  + + + aa  ++    +++d+ +++++ + +l  + +
  gi|91772874|ref|YP_565566.1| 136 SLVLISDTGEYIANTTSDQNGSFCFTDIPNGNYNIAALNYLYSSmSKKDIWYTNTT-SLEL--TSS 198
                                   57799********************9986664444444444444489999998885.4444..433 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00012
                          bMG3  23 dsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsAr.kdedlaflkldwergldls 94 
                                   +s+ P+ + ++ l++++ge +a++t+D++G   f++  + + + aa  ++    +++d+ +++++ + +l +s
  gi|91772874|ref|YP_565566.1| 237 KSNTPINDTTLVLISDTGEYVANTTSDQNGSFCFTDIPNGNYNIAALSYLYSSmSKKDIWYTNTT-SLELTSS 308
                                   5889******************************9986664444444444444489999998885.4444443 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 ?    3.0   0.0     0.049        87      29      49 ..      40      60 ..      31      69 .. 0.88
   2 !    5.4   0.0    0.0085        15      26      50 ..     145     171 ..     123     176 .. 0.70
   3 ?    4.9   0.0     0.013        23      27      50 ..     256     281 ..     234     287 .. 0.81
   4 !   11.8   2.8     9e-05      0.16      15      73 ..    1228    1291 ..    1217    1293 .. 0.84
   5 ?    0.6   0.1      0.28   5.1e+02      34      72 ..    1368    1409 ..    1348    1412 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.049
                         fn3_3 29 teadssgsftipnVkpGtYrl 49
                                  t+ d++g+f ++ V  G+Y+ 
  gi|91772874|ref|YP_565566.1| 40 TTSDENGNFVFEGVPNGDYSI 60
                                  566899*************85 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0085
                         fn3_3  26 QYwtea..dssgsftipnVkpGtYrlt 50 
                                    Y +++  d++gsf ++++  G+Y+  
  gi|91772874|ref|YP_565566.1| 145 EYIANTtsDQNGSFCFTDIPNGNYNIA 171
                                   56666633666*************976 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.013
                         fn3_3  27 Ywtea..dssgsftipnVkpGtYrlt 50 
                                   Y +++  d++gsf ++++  G+Y+  
  gi|91772874|ref|YP_565566.1| 256 YVANTtsDQNGSFCFTDIPNGNYNIA 281
                                   5555533667*************976 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 9e-05
                         fn3_3   15 vvsfqne...tkayQYwteadss.gsftipnVkpGtYrltvYadglfgdyk.qdsvtVtagktt 73  
                                    vv  q +   t + +Y t ++++ gs+  + Vk G+Y+ +++++   g+ + +d  t++ g+t+
  gi|91772874|ref|YP_565566.1| 1228 VVIDQFNidyTYGHYYSTVLSNTsGSYDAEFVKDGKYTIYAFKEVSDGWITgKDYTTIQNGETI 1291
                                    555555556778999*****7777*******************999999989999999999986 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.28
                         fn3_3   34 sgsftipnVkpGtYrlt.vYadglfgdyk..qdsvtVtagkt 72  
                                    + ++t++++  G+Y    +Y++ + g      +++++t++ +
  gi|91772874|ref|YP_565566.1| 1368 DANYTFTDIPNGEYVIAsIYQSMISGSWYfdSENIEITENGS 1409
                                    5799**********98779****9998755799999997655 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.016        30      33      73 ..     132     173 ..     102     188 .. 0.79
   2 !    9.0   0.0   0.00069       1.2      19      74 ..     224     284 ..     207     301 .. 0.76
   3 ?   -3.7   0.0       6.5   1.2e+04      50      74 ..    1245    1270 ..    1239    1275 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.016
                       DUF1416  33 vggayvRLLdssgeFtaevvtsaeGefrFfaap.GeWtvRal 73 
                                   ++++   L+ ++ge+ a+ ++ ++G+f F   p G++++ al
  gi|91772874|ref|YP_565566.1| 132 INATSLVLISDTGEYIANTTSDQNGSFCFTDIPnGNYNIAAL 173
                                   5555667999*******************8754488888777 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00069
                       DUF1416  19 eaviqGkvtr....dgepvggayvRLLdssgeFtaevvtsaeGefrFfaap.GeWtvRala 74 
                                      i+G+  +    +++p++ +   L+ ++ge++a+ ++ ++G+f F   p G++++ al+
  gi|91772874|ref|YP_565566.1| 224 RNAISGTTFKkgrkSNTPINDTTLVLISDTGEYVANTTSDQNGSFCFTDIPnGNYNIAALS 284
                                   55566655441112678999999************************87644888888886 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.5
                       DUF1416   50 evvtsaeGefrF.faapGeWtvRala 74  
                                     v ++++G++   f  +G++t+ a++
  gi|91772874|ref|YP_565566.1| 1245 TVLSNTSGSYDAeFVKDGKYTIYAFK 1270
                                    56666666664336777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.28u 0.32s 00:00:01.60 Elapsed: 00:00:00.52
# Mc/sec: 11918.73
//
Query:       gi|91772875|ref|YP_565567.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-66  224.1   0.6    6.9e-66  222.6   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
    8.9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.1e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00016   21.9   0.5       0.16   12.2   0.2    2.7  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
       0.06   13.9   1.4        0.3   11.7   1.4    2.3  1  BST2             Bone marrow stromal antigen 2
        0.1   12.7   0.2        3.3    7.9   0.0    2.6  2  GutM             Glucitol operon activator protein (GutM)
       0.12   12.9   2.7       0.55   10.7   0.3    2.6  2  DUF16            Protein of unknown function DUF16
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.51   10.7   7.5        1.1    9.7   5.6    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.54   11.0   8.1          5    7.9   1.0    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        1.9    9.2   6.0       0.65   10.7   1.1    2.8  1  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.49   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  222.6   0.0   4.2e-69   6.9e-66       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.49
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772875|ref|YP_565567.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 222.6 bits;  conditional E-value: 4.2e-69
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+ a++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91772875|ref|YP_565567.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELRADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+e+++ +  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91772875|ref|YP_565567.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSEAMNVMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************87744666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierearea....eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++re+    ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91772875|ref|YP_565567.1| 329 SENDD--QLWSKAMNIlLIDVKKSVDQIREMsgcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **977..*********************955678888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91772875|ref|YP_565567.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.7e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.7e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91772875|ref|YP_565567.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7   8.8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772875|ref|YP_565567.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.2     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.0   0.0    0.0038       6.3       5      44 ..     249     286 ..     245     289 .. 0.83
   3 !   12.2   0.2    0.0001      0.16      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.2
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91772875|ref|YP_565567.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0038
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaa 44 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a 
  gi|91772875|ref|YP_565567.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSEAM 286
                                   68************99866..7777899999999998876 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.0001
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91772875|ref|YP_565567.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00018       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91772875|ref|YP_565567.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.002       3.3      42      90 ..     331     379 ..     322     397 .. 0.79
   2 ?    1.8   0.1      0.15   2.4e+02      64      82 ..     448     466 ..     430     481 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                          GutM  42 kkgrfragvivllavdedgiivearvmkGvTvfarfkeleelegkslee 90 
                                   +  ++ ++++ +l +d ++ + ++r+m+G     r+ke+e+  g+ ++ 
  gi|91772875|ref|YP_565567.1| 331 NDDQLWSKAMNILLIDVKKSVDQIREMSGCMKPERIKEFEDWYGQIIHI 379
                                   56677889999*******************9999999999999988764 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                          GutM  64 earvmkGvTvfarfkelee 82 
                                    +r m+G  +f+r+++  +
  gi|91772875|ref|YP_565567.1| 448 TFRSMQGALIFSRVRSYIS 466
                                   5689**********98654 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00034      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    1.1   0.1      0.35   5.7e+02      11      58 ..     392     446 ..     383     477 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772875|ref|YP_565567.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.35
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91772875|ref|YP_565567.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999988854444440......55555555555555555543 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.34   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00051      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.34
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91772875|ref|YP_565567.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00051
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91772875|ref|YP_565567.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.5   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?    9.7   5.6   0.00067       1.1       2      36 ..     156     213 ..     155     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91772875|ref|YP_565567.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00067
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91772875|ref|YP_565567.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCelrADvCGC 213
                                   79***************99987555588888888888888888875555444445666 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 ?    3.3   0.1     0.081   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.9   1.0    0.0031         5       4      13 ..     159     168 ..     158     183 .. 0.69
   3 ?    2.0   0.1       0.2   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.081
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91772875|ref|YP_565567.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0031
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91772875|ref|YP_565567.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.2
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91772875|ref|YP_565567.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1    0.0004      0.65      34      71 ..      73     130 ..      19     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772875|ref|YP_565567.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1648  (0.0919181); expected 358.6 (0.02)
Passed bias filter:                      869  (0.048469); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 2959.48
//
Query:       gi|91772876|ref|YP_565568.1|  [L=185]
Description: pentapeptide repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   73.2  27.7    1.7e-08   33.9   0.8    3.8  3  Pentapeptide    Pentapeptide repeats (8 copies)
    1.9e-19   69.6  22.1    4.6e-10   39.5   6.5    2.3  2  Pentapeptide_4  Pentapeptide repeats (9 copies)
    2.3e-14   53.3  13.7      2e-08   34.2   1.5    3.2  2  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
      0.062   13.3   6.6        1.7    8.7   1.9    2.1  2  CfAFP           Choristoneura fumiferana antifreeze protein (
        2.7    7.0   6.8        9.1    5.2   0.1    2.8  3  Glyco_hydro_28  Glycosyl hydrolases family 28


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 !   33.9   0.8   4.9e-12   1.7e-08       2      40 .]      30      68 ..      29      68 .. 0.97
   2 !   30.4   5.6     6e-11   2.1e-07       7      40 .]      97     130 ..      94     130 .. 0.95
   3 !   33.0   6.6   9.5e-12   3.4e-08       1      37 [.     116     152 ..     116     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.9e-12
                                  B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                  Pentapeptide  2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40
                                  +Lsg  + ++++ ++ ++++nL++++l +++++++++++
  gi|91772876|ref|YP_565568.1| 30 DLSGISFKNSKFIDCVFEECNLSNVDLDNTRFQDTKFKN 68
                                  89***********************************86 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 6e-11
                                   B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                  Pentapeptide   7 nLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    +s+ nL+++n+s++  ++++l +++L++an+++
  gi|91772876|ref|YP_565568.1|  97 VFSHLNLENTNFSNCQIYDCDLVNTNLTNANFEN 130
                                   69******************************97 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 9.5e-12
                                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEE CS
                  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsgan 37 
                                   ++L ++nL++an+++++l+++ ++++nls+A +++a+
  gi|91772876|ref|YP_565568.1| 116 CDLVNTNLTNANFENSDLKNSLFQKTNLSFASFKNAK 152
                                   9**********************************95 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   6.5   1.3e-13   4.6e-10       2      62 ..      20      80 ..      19      97 .. 0.90
   2 !   35.7   7.5     2e-12     7e-09       8      60 ..      98     150 ..      93     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.3e-13
                Pentapeptide_4  2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcn 62
                                  ef++ +f++ +ls+++F++++++dc F+ec+lsnv +d++ ++d++f + ++    ++ cn
  gi|91772876|ref|YP_565568.1| 20 EFESQTFKDIDLSGISFKNSKFIDCVFEECNLSNVDLDNTRFQDTKFKNSKILGFDLTKCN 80
                                  69999***************************99999999999999999999888888887 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 2e-12
                Pentapeptide_4   8 fnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsg 60 
                                   f   +l+n+nFs++++ dc++++++l+n+nF++++l+++ f++++l  asF++
  gi|91772876|ref|YP_565568.1|  98 FSHLNLENTNFSNCQIYDCDLVNTNLTNANFENSDLKNSLFQKTNLSFASFKN 150
                                   55668999999999999999999999999999999999999999999999987 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   1.5   5.6e-12     2e-08       1      47 [.      26      69 ..      26      70 .. 0.92
   2 !   22.6   4.6   2.4e-08   8.6e-05       2      45 ..     104     144 ..      94     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.6e-12
                Pentapeptide_3  1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47
                                  F++  +sg  +F ++ F++++ F++++++++d++++rF  d+ F+++
  gi|91772876|ref|YP_565568.1| 26 FKDIDLSGI-SFKNSKFIDCV-FEECNLSNVDLDNTRFQ-DTKFKNS 69
                                  566678999.**********6.****************8.*****98 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.4e-08
                Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFs 45 
                                   +++nFs++ +  ++   ++ + +na+F+++d+ ++ F   +++s
  gi|91772876|ref|YP_565568.1| 104 ENTNFSNC-QIYDCDLVNT-NLTNANFENSDLKNSLFQ-KTNLS 144
                                   57777777.7777777777.788888888888888886.66655 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0013       4.7      30      73 ..      37      80 ..       8      88 .. 0.85
   2 ?    8.7   1.9   0.00046       1.7      15      78 ..      97     162 ..      91     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                         CfAFP 30 anskcvkstltncyidnselessictrsqysdayvkksvttdcn 73
                                  +nsk +  +   c++ n +l+++    ++++++++     t+cn
  gi|91772876|ref|YP_565568.1| 37 KNSKFIDCVFEECNLSNVDLDNTRFQDTKFKNSKILGFDLTKCN 80
                                  69999999999999999999999999999999999888888887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00046
                         CfAFP  15 vssdGscvntn...sqisanskcvkstltncyidnselessictrsqysdayvkksvttdcnidksq 78 
                                   v+s     ntn    qi  +   v++ ltn + +ns+l++s+  +++ s a  k+++  d++ +++ 
  gi|91772876|ref|YP_565568.1|  97 VFSHLNLENTNfsnCQIY-DCDLVNTNLTNANFENSDLKNSLFQKTNLSFASFKNAKNYDIDPNNNF 162
                                   555555566652115555.566689999999999999999999999999999988887777666655 PP

>> Glyco_hydro_28  Glycosyl hydrolases family 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1    0.0074        26      93     124 ..      19      50 ..       8      60 .. 0.75
   2 ?    5.2   0.1    0.0025       9.1      99     128 ..      55      84 ..      50      86 .. 0.89
   3 ?    0.9   0.8     0.054   1.9e+02      86     114 ..     109     137 ..      94     161 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0074
                Glyco_hydro_28  93 kflvikkvknskiknlniknspvfhfsvesgk 124
                                   k ++ ++ k+ ++++++ kns+++  ++e+++
  gi|91772876|ref|YP_565568.1|  19 KEFESQTFKDIDLSGISFKNSKFIDCVFEECN 50 
                                   55666778888999999999999999999875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0025
                Glyco_hydro_28  99 kvknskiknlniknspvfhfsvesgkdlti 128
                                   +++n+++++ + kns+   f++++++d+ +
  gi|91772876|ref|YP_565568.1|  55 DLDNTRFQDTKFKNSKILGFDLTKCNDFIL 84 
                                   578999*********************986 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.054
                Glyco_hydro_28  86 kegkkkpkflvikkvknskiknlniknsp 114
                                   ++++  +  lv  +++n++++n  +kns 
  gi|91772876|ref|YP_565568.1| 109 SNCQIYDCDLVNTNLTNANFENSDLKNSL 137
                                   33333333344444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); 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:                         5  (0.000278878); expected 0.2 (1e-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: 1385.93
//
Query:       gi|91772877|ref|YP_565569.1|  [L=76]
Description: hypothetical protein Mbur_0868 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00073   17.5   1.1    0.00088   17.3   1.1    1.0  1  PolC_DP2       DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.066   13.4   0.8      0.077   13.2   0.8    1.1  1  HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
       0.15   11.6   6.6       0.46   10.0   6.3    1.9  2  TF_Zn_Ribbon   TFIIB zinc-binding
       0.22   11.2   4.4       0.55    9.9   4.4    1.7  1  Zn_ribbon_17   Zinc-ribbon, C4HC2 type


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 !   17.3   1.1     2e-07   0.00088     615     680 ..       5      70 ..       2      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-07
                      PolC_DP2 615 eiarrkCkkCgketlearCeeCgekteeklvCkkcee..eveeekcekcekeakavkkkkidlkelle 680
                                   e ++++C+ Cg et ++ C++C+e +e+ +  ++++e   +  ++c++    +k++ k +++++++++
  gi|91772877|ref|YP_565569.1|   5 EGNTMQCNVCGVETNKTYCTDCEEVMEQII--RQVGEkrWAAIDDCSHIYPMVKRAVKGELNINDIVN 70 
                                   567899********************9944..455441144477899999999999999999998875 PP

>> HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.8   1.7e-05     0.077       4      64 ..       7      70 ..       5      76 .] 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                 HEPN_RES_NTD1  4 eeeeCdYCgkskk...vvsleellefilegi.ekeYedaane.lpydsreggylvgetydtedlle 64
                                  +  +C+ Cg +++   +++ ee++e+i++++ ek+++  ++    y       + + + + +d+++
  gi|91772877|ref|YP_565569.1|  7 NTMQCNVCGVETNktyCTDCEEVMEQIIRQVgEKRWAAIDDCsHIYPM-VKRAV-KGELNINDIVN 70
                                  5679*****555546555************944678888877444443.23333.33336666665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.8     0.041   1.8e+02       1       8 [.       9      16 ..       5      18 .. 0.60
   2 ?   10.0   6.3    0.0001      0.46       1      31 [.       9      32 ..       9      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.041
                                  EEETTTTC CS
                  TF_Zn_Ribbon  1 ykCPnCgs 8 
                                  ++C +Cg 
  gi|91772877|ref|YP_565569.1|  9 MQCNVCGV 16
                                  45555654 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0001
                                  EEETTTTCEECHEETSTTCEEESSSSBEEEE CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVled 31
                                  ++C +Cg        e++ ++CtdC++V+e 
  gi|91772877|ref|YP_565569.1|  9 MQCNVCGV-------ETNKTYCTDCEEVMEQ 32
                                  68888997.......589***********95 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.4   0.00012      0.55       3      28 ..       7      30 ..       5      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                  Zn_ribbon_17  3 llksCayCelavkgrvvlcgvCeHvl 28
                                  ++++C++C ++ ++  ++c+ Ce v+
  gi|91772877|ref|YP_565569.1|  7 NTMQCNVCGVETNK--TYCTDCEEVM 30
                                  689*****988776..68*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); 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: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 488.31
//
Query:       gi|91772878|ref|YP_565570.1|  [L=373]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   30.1   2.0    5.8e-07   29.4   2.0    1.4  1  DDE_Tnp_1  Transposase DDE domain
     0.0077   16.2   0.0      0.035   14.1   0.0    2.2  2  DUF772     Transposase domain (DUF772)
  ------ inclusion threshold ------
      0.065   12.7   0.1       0.14   11.6   0.1    1.6  1  DUF4283    Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   2.0   9.8e-11   5.8e-07      10     197 ..     149     337 ..     141     353 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.8e-11
                     DDE_Tnp_1  10 Dattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYas 88 
                                   D+t++++ + +  ++  y+ +  ++  k+hi + +   l++ +  t g +hds+ lk  +d+l ++  + +++  D+GY+s
  gi|91772878|ref|YP_565570.1| 149 DSTPLEASRYD--KYADYNPHYNCKMDKAHITMIGT--LPICMTHTKGASHDSPELKKHIDALVEMgvDIDTYALDGGYDS 225
                                   89999998888..44455555555555999999666..5***********************9999*************** PP

                     DDE_Tnp_1  89 aelldtle.ekgvdyiirlkkntklyrk.....................gaeskrrgrlrkhdrnkiltksqkrrnkskke 147
                                    +++ ++  + +++++i++++++k++                        + +++ ++l  ++r+k++    + +n     
  gi|91772878|ref|YP_565570.1| 226 FRNHADIWyKLNAKPVIAYSSDSKVQYEgmmeridhwvnkmwklggsihMKYEEKLHFLYENGREKQVGMHLRNKNI---- 302
                                   888888888**********9999999888888777777666666555551333344444555555555555554444.... PP

                     DDE_Tnp_1 148 kgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrg 197
                                                  +   + e y++R ++Erv+  +k + ++d +r+++
  gi|91772878|ref|YP_565570.1| 303 ---------------KDDGFDEDYSHRGECERVHNHIKWTVKFDIRRMKN 337
                                   ...............556669***************99887777777755 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.9e-06     0.035       5      70 ..      62     130 ..      61     133 .. 0.81
   2 ?   -3.1   0.0       1.4   8.6e+03      21      37 ..     310     326 ..     309     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-06
                        DUF772   5 yppelmlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70 
                                   y +  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f k rl++  l++++
  gi|91772878|ref|YP_565570.1|  62 YKVSSMIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVKyRLGKtgLDEVM 130
                                   67889*************9999998772566667777664433.89*****************9977776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                        DUF772  21 glSdreleealrenlsf 37 
                                   ++S r  +e++++++ +
  gi|91772878|ref|YP_565570.1| 310 DYSHRGECERVHNHIKW 326
                                   568888999***99998 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.4e-05      0.14      24      59 ..     256     291 ..     235     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                       DUF4283  24 lsalrrvlakaWklkggvkikelgdglflfrfssee 59 
                                   ++++ ++++k+Wkl+g +++k+ ++ +fl++   e+
  gi|91772878|ref|YP_565570.1| 256 MERIDHWVNKMWKLGGSIHMKYEEKLHFLYENGREK 291
                                   678999***********************9866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2209.44
//
Query:       gi|91772879|ref|YP_565571.1|  [L=365]
Description: carbamoyl phosphate synthase small subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  157.7   0.1    1.8e-46  157.1   0.1    1.3  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    9.4e-42  142.9   0.0    1.4e-41  142.4   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    1.9e-06   27.8   0.5     0.0011   18.7   0.5    2.3  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 !  157.1   0.1   3.1e-50   1.8e-46       2     127 ..       4     130 ..       3     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 3.1e-50
               CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvvrel 81 
                                   av+ LedGt+++G++fg ++ ++GE+vf+T  tGY+e+ltDpsY+gqil++typliGnyGvn+e+++s+ +kv+glvvre+
  gi|91772879|ref|YP_565571.1|   4 AVIGLEDGTFLKGTGFGaEGIVCGELVFTTQYTGYEESLTDPSYSGQILMFTYPLIGNYGVNDETFQSDGVKVEGLVVREA 84 
                                   6889*************77999*********************************************************** PP

               CPSase_sm_chain  82 seepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                   +++ps++++ +++ +++++e+ pgisgvDTR+Lt   re+g+m+++
  gi|91772879|ref|YP_565571.1|  85 CRSPSHHQSMRNIYKLMEDEGKPGISGVDTRMLTIGTREHGTMRAA 130
                                   *******************************************997 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.0   2.3e-45   1.4e-41       2     185 ..     182     354 ..     181     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 2.3e-45
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGm 81 
                                   liD +  +++n+  +l+++g++v+vvp +++a+ i+  + +pd +++s+Gpg+p+ +  +i+a+ke+++  +Pi GICLG+
  gi|91772879|ref|YP_565571.1| 182 LIDLG--MKKNISTSLLNRGIDVTVVPATTPASVIQ--EFDPDLLFLSNGPGDPQnANAAIDAVKEMAG-TVPIAGICLGH 257
                                   78999..****************************5..69*****************************.*********** PP

                                   HHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETT CS
                        GATase  82 QllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekkn 162
                                   Q++a ++g++++k k ++h+g++++++d       +++ ++i++++H+++v+ +++ +++++vt  +++d ++++i +k+ 
  gi|91772879|ref|YP_565571.1| 258 QIIARALGADTYKLK-FGHRGANQPVKD------LETGIVHITSQNHGFAVEGDSFDDTDVIVTQINTNDRTVEGIEQKDL 331
                                   ***************.************......78889*******************************99999999999 PP

                                   TEEEESSBTTSTTSTTHHHHHHH CS
                        GATase 163 pfvgvQFHPEststpegpellfn 185
                                    +++vQ+HPE++ +p+++e +f 
  gi|91772879|ref|YP_565571.1| 332 DIFSVQYHPEAHAGPRDTEKIFF 354
                                   ******************99985 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   1.9e-07    0.0011     101     216 .]     243     341 ..     236     341 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-07
                 Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike. 180
                                   +++  vPi giC+G+q+++ alG ++y+          hr +     ++ vk  + ++++   +         H +a++  
  gi|91772879|ref|YP_565571.1| 243 EMAGTVPIAGICLGHQIIARALGADTYKLKF------GHRGA-----NQPVKDLETGIVHITSQ--------NHGFAVEGd 304
                                   677899*****************99996433......34333.....34554444444333333........466666654 PP

                 Peptidase_C26 181 ..laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                      ++++ v+ + + D ++E ie ++ +  +++vQ+HPE
  gi|91772879|ref|YP_565571.1| 305 sfDDTDVIVTQINTnDRTVEGIEQKDLD--IFSVQYHPE 341
                                   4446677777777779999999999977..999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2379.91
//
Query:       gi|91772880|ref|YP_565572.1|  [L=1075]
Description: carbamoyl phosphate synthase large subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-106  352.3   1.3    2.1e-70  236.5   0.1    2.4  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.1e-39  134.6   0.0    5.4e-39  133.3   0.0    1.8  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    3.8e-21   75.1   1.4    9.1e-20   70.7   0.0    3.7  5  MGS              MGS-like domain
    1.3e-17   63.9   0.1    1.2e-09   37.9   0.0    2.5  2  ATP-grasp        ATP-grasp domain
    2.9e-15   56.2   0.0    2.5e-06   27.3   0.0    2.8  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    8.8e-15   54.8   0.1    4.9e-06   26.2   0.1    2.5  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.9e-13   50.2   0.6    9.2e-06   25.8   0.0    2.5  2  ATP-grasp_3      ATP-grasp domain
     0.0024   17.5   0.1        6.6    6.2   0.0    3.8  3  ATP-grasp_2      ATP-grasp domain
     0.0043   16.5   0.0       0.26   10.7   0.0    3.0  3  ATP-grasp_5      ATP-grasp domain
  ------ inclusion threshold ------
      0.012   16.2   0.5        3.8    8.1   0.0    4.0  4  MerR-DNA-bind    MerR, DNA binding
      0.079   12.4   0.0       0.17   11.3   0.0    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family


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 !  236.5   0.1   1.3e-73   2.1e-70       1     210 [.     128     331 ..     128     332 .. 0.99
   2 !  114.8   0.1   2.3e-36   3.8e-33       2     210 ..     672     873 ..     671     874 .. 0.94

  Alignments for each domain:
  == domain 1  score: 236.5 bits;  conditional E-value: 1.3e-73
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                   CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                   D+e +k+++++i+++v +s+a+  +tl+ea ai +e+g P ii++a++lGG G+++a+++e+l e+ +++l+ ++     +
  gi|91772880|ref|YP_565572.1| 128 DRELFKNKMEDIGEKVPRSVAV--STLKEAEAIIDELGLPLIIRPAYTLGGAGGGIAYTKEQLLEISERGLRRSR----IN 202
                                   9********************9..**************************************************7....9* PP

                                   -EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                   CPSase_L_D2  82 qvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                   qvl+e+s+ g+ke E+ev+rD+++++i++c++en++++  +t+++i+v PsqtL+d e+q+lr+aa+k++r++g++g++++
  gi|91772880|ref|YP_565572.1| 203 QVLIEESVLGWKEFEYEVMRDSNDTCIVICNMENLDPMgvHTGESIVVTPSQTLNDIEHQMLRTAAIKIIRALGIEGGCNI 283
                                   ********************************************************************************* PP

                                   EEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                   CPSase_L_D2 161 eflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                   +f+ +  ++ey ++EvN+R+s++sala+kaTG++++ ++akia g++L+e
  gi|91772880|ref|YP_565572.1| 284 QFAAK--DGEYRIVEVNPRISRSSALASKATGYPIARVTAKIAIGMTLDE 331
                                   ***99..6****************************************97 PP

  == domain 2  score: 114.8 bits;  conditional E-value: 2.3e-36
                                   HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS- CS
                   CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkq 82 
                                   +e+++ +++k++v   ++  a  +++e+a++ia +igyPv++++++ lGG+ m +++++++l+  +++a++ ++    ++ 
  gi|91772880|ref|YP_565572.1| 672 REKFNLMMSKLGVAQPEAGYA--TSQEDAIEIATRIGYPVLVRPSYVLGGRAMEIVYEQNDLERYMREAVRVSP----EQP 746
                                   789999999999988887777..9*************************************************7....99* PP

                                   EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                   CPSase_L_D2  83 vlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtve 161
                                   vl++ +l+   ei+v+ + D k+  i    +e + +   + +++  v P + L++e+ +++r  + k++ +++v+g  +++
  gi|91772880|ref|YP_565572.1| 747 VLIDDFLEAAVEIDVDAVCDGKDVLIGA-IMEHIEEAgvHSGDSACVIPPRYLSEETLNTVRDYTRKIALSLNVIGLINIQ 826
                                   **********************987765.4777776667****************************************** PP

                                   EEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                   CPSase_L_D2 162 flldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                    + +  +++ yv+E N+R s+  +  +ka Gl+l+k+aa++  g++Lee
  gi|91772880|ref|YP_565572.1| 827 MAEQ--DGKVYVLEANPRSSRTIPFVSKAVGLPLAKIAAQVIIGHSLEE 873
                                   9877..7****************************************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 !  133.3   0.0   3.3e-42   5.4e-39       3     122 .]     418     538 ..     416     538 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 3.3e-42
                   CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkk..eldeellreakklGfsDkqiaelle 81 
                                   lk+pt+eR+f+i++al+ g+s+ee++el+ id +F+ek+ ++v++ek+l+++    e d +ll+eak+lGf+D++i e+++
  gi|91772880|ref|YP_565572.1| 418 LKTPTSERLFVIFHALNTGMSIEEVSELSGIDVFFIEKIDNIVKMEKKLAAELFagEPDIALLTEAKRLGFTDERIGEMTG 498
                                   89***********************************************9997778888999*****************77 PP

                   CPSase_L_D3  82 eeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                    +++ee+++lr++ ++  +yk+vDtcAaeF+aetpY+Ys+Y
  gi|91772880|ref|YP_565572.1| 499 -KSREEINDLRRNNDVISTYKMVDTCAAEFAAETPYYYSCY 538
                                   .67778**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.4   3.9e+03      45      72 ..      18      53 ..       5      64 .. 0.70
   2 ?   -1.1   0.0       1.3   2.2e+03      48      93 ..     279     327 ..     253     329 .. 0.72
   3 ?   -0.5   0.0      0.88   1.4e+03      51      72 ..     574     595 ..     552     605 .. 0.79
   4 ?   -3.4   0.0       7.3   1.2e+04      50      76 ..     770     804 ..     753     821 .. 0.63
   5 !   70.7   0.0   5.6e-23   9.1e-20       2      95 .]     956    1041 ..     955    1041 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.4
                                  GGTHCH........HHHHHHHTTSCCEEEEE--THH CS
                           MGS 45 rlggrv........eildaikngeidlvintlypfk 72
                                  ++ g+         +    +k++++++v ++ +p +
  gi|91772880|ref|YP_565572.1| 18 IMIGQAaefdfsgtQACRSLKEEGYKVVLVNSNPAT 53
                                  555555566666667777888999999988888866 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                   HCHHHHHHHHTTSCCEEEEE--THHHHHH...CHHHHHHHHHHHTTSHE CS
                           MGS  48 grveildaikngeidlvintlypfkatva...kdgykirraaenidIpl 93 
                                   g ++i+ a k+ge+ +v +++   ++        gy i+r+  +i I++
  gi|91772880|ref|YP_565572.1| 279 GGCNIQFAAKDGEYRIVEVNPRISRSSALaskATGYPIARVTAKIAIGM 327
                                   4457788888888888888887766665556678999999999999997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.88
                                   HHHHHHHTTSCCEEEEE--THH CS
                           MGS  51 eildaikngeidlvintlypfk 72 
                                   + + ai++ +i++ i++ +p++
  gi|91772880|ref|YP_565572.1| 574 HAVTAIREDGIEAHIVNNNPET 595
                                   67899*******8888877765 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 7.3
                                   H...HHHHHHHTTSCC.....EEEEE--THHHHHH CS
                           MGS  50 v...eildaikngeid.....lvintlypfkatva 76 
                                   v    i+++i++ +++     +vi   y  ++t +
  gi|91772880|ref|YP_565572.1| 770 VligAIMEHIEEAGVHsgdsaCVIPPRYLSEETLN 804
                                   45557888888888877777666655555555554 PP

  == domain 5  score: 70.7 bits;  conditional E-value: 5.6e-23
                                    HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHCHHH CS
                           MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvakdgy 80  
                                    +ve+akk++++g +l+ T+GTa++l+e+gi+  e v k++eg +++    + d+++  e+ l++nt+++ ++++  dgy
  gi|91772880|ref|YP_565572.1|  956 FVEIAKKMQDAGLKLIGTKGTANYLAEKGIN-MEAVMKLHEG-SPN----VIDMLRRDEVGLIVNTPTGSQSRK--DGY 1026
                                    79*****************************.**********.9*9....*********************996..*** PP

                                    HHHHHHHHTTSHEES CS
                           MGS   81 kirraaenidIplpt 95  
                                    +irraa+++++p++t
  gi|91772880|ref|YP_565572.1| 1027 QIRRAAVDFKVPYIT 1041
                                    *************98 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.2e-08   3.6e-05       4     160 ..     139     301 ..     136     309 .. 0.88
   2 !   37.9   0.0   7.6e-13   1.2e-09       2     160 ..     680     843 ..     679     846 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.2e-08
                                   TT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEE CS
                     ATP-grasp   4 lglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsv 80 
                                    g +vpr +av++ +e+e++++elglp++++ +     G G  +   +e+l ++ e      + ++v++Ee v   kE   
  gi|91772880|ref|YP_565572.1| 139 IGEKVPRSVAVSTLKEAEAIIDELGLPLIIR-PAYTLGGAGGGIAYTKEQLLEISERGlrrsRINQVLIEESVLGWKEFEY 218
                                   67789**************************.8888889999999999998888877667778899*******99999999 PP

                                   EEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCHHHHHHHHHHH.HHHHHHTSSEEEEEEEEEETTCTEEEEEEE CS
                     ATP-grasp  81 lvvrsaeGetafypvvetvqedgilr...lsvapaevsekaqkkaeeiak.kiveeLggvGvfavElFvledgellvnEla 157
                                    v+r+ + +  ++  +e++   g+     ++v p++  ++++++  ++a+ ki+++Lg+ G   +  F  +dge  + E+ 
  gi|91772880|ref|YP_565572.1| 219 EVMRDSNDTCIVICNMENLDPMGVHTgesIVVTPSQTLNDIEHQMLRTAAiKIIRALGIEGGCNIQ-FAAKDGEYRIVEVN 298
                                   99*****999999999****9999853338999***999999998888777*************98.5556********** PP

                                   SS- CS
                     ATP-grasp 158 pRp 160
                                   pR 
  gi|91772880|ref|YP_565572.1| 299 PRI 301
                                   *96 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 7.6e-13
                                   HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEE CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekEl 78 
                                   +klg++ p+  +++s+e++ e+a+++g+pv+v+ +     G+   +v +++dle+ ++++     e++v++ +f +  +E+
  gi|91772880|ref|YP_565572.1| 680 SKLGVAQPEAGYATSQEDAIEIATRIGYPVLVR-PSYVLGGRAMEIVYEQNDLERYMREAvrvsPEQPVLIDDFLEAAVEI 759
                                   68999999*9***********************.99999***************9999999998999************** PP

                                   EEEEEEETTC-EEE--EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEE CS
                     ATP-grasp  79 svlvvrsaeGetafypvvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnE 155
                                    v +v + +  + + +++e+++e g+       ++ p  +se+ +++++++++ki+ +L+++G++ + + ++ dg+++v E
  gi|91772880|ref|YP_565572.1| 760 DVDAVCDGKD-VLIGAIMEHIEEAGVHsgdsACVIPPRYLSEETLNTVRDYTRKIALSLNVIGLINIQMAEQ-DGKVYVLE 838
                                   ***9998776.88888889988876642221678889999999**************************999.******** PP

                                   EESS- CS
                     ATP-grasp 156 lapRp 160
                                     pR 
  gi|91772880|ref|YP_565572.1| 839 ANPRS 843
                                   ***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 !   25.6   0.0   4.8e-09   7.9e-06      46     116 ..     261     332 ..     252     347 .. 0.80
   2 !   27.3   0.0   1.5e-09   2.5e-06       5     118 ..     747     876 ..     744     890 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.8e-09
                  ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteev 116
                                   ++ l  +a ++++++g++g  n+Q+  +++++++ E+NpR+s      s ++G  ++++ +k + g+  +e+
  gi|91772880|ref|YP_565572.1| 261 HQMLRTAAIKIIRALGIEGGCNIQFAAKDGEYRIVEVNPRISRSSAlASKATGYPIARVTAKIAIGMTLDEI 332
                                   56677899*********************************9655515667799999999999999744443 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.5e-09
                  ATPgrasp_Ter   5 llvmeyLegp.EySvDvlae.kgevlaavpRrKekgglq.............elekdeelielaerlaeefgldglvnvQv 70 
                                   +l+ ++Le + E+ vD +++ k  ++ a+    e+ g++             + e+ + + ++++++a ++++ gl+n+Q+
  gi|91772880|ref|YP_565572.1| 747 VLIDDFLEAAvEIDVDAVCDgKDVLIGAIMEHIEEAGVHsgdsacvipprylSEETLNTVRDYTRKIALSLNVIGLINIQM 827
                                   5666666543377777777755444445554444333333444455555522234446778999***************** PP

                  ATPgrasp_Ter  71 rededgpkLLEiNpRasGGlgy.salaGvnlpylalklllgleteevee 118
                                    e++++ ++LE NpR s ++   s + G+ l+++a++ + g++ ee   
  gi|91772880|ref|YP_565572.1| 828 AEQDGKVYVLEANPRSSRTIPFvSKAVGLPLAKIAAQVIIGHSLEELGY 876
                                   ********************9625566************9985555543 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 !   25.8   0.0   4.1e-09   6.7e-06      27     174 ..     154     299 ..     143     306 .. 0.82
   2 !   26.2   0.1     3e-09   4.9e-06      23     174 ..     693     841 ..     673     865 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.1e-09
                                   HHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEE CS
               Dala_Dala_lig_C  27 llekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgneklevsevgei 104
                                     e++++elg+p++++pa +    G   + ++e+l e  e+ +++   ++vl+Ee +   +e+e  v+ + + ++ ++ ++
  gi|91772880|ref|YP_565572.1| 154 EAEAIIDELGLPLIIRPAYTLGGAGGGIAYTKEQLLEISERGLRRSriNQVLIEESVlGWKEFEYEVMRDSNDTCIVICNM 234
                                   56899*************98777788889999*******99988763379*****99899*********776666655544 PP

                                   E-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
               Dala_Dala_lig_C 105 vvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                          d    ++++++ ++   +l++ +++ ++++a+k+ +al+++G + + f  + +ge  + EvN+
  gi|91772880|ref|YP_565572.1| 235 EN----LDPMGVHTGESIVVTPSQTLNDIEHQMLRTAAIKIIRALGIEGGCNIQFAAK-DGEYRIVEVNP 299
                                   33....4444455666777777777888888899********************9876.**********6 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 3e-09
                                   -H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEE.EEEETSSCEEE CS
               Dala_Dala_lig_C  23 ekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreiev.avlgneklevs 99 
                                   +++e   ++ +++gypv+V+p+       ++ v  +++l+++++ea++   ++ vl++ ++ ++ ei+v av +  ++ + 
  gi|91772880|ref|YP_565572.1| 693 TSQEDAIEIATRIGYPVLVRPSYVLGGRAMEIVYEQNDLERYMREAVRVspEQPVLIDDFLeAAVEIDVdAVCDGKDVLIG 773
                                   4556677899************9888889*****************98733577*******8889****678888889999 PP

                                   EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
               Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                    + e++ + g+       s+d+a +  p  l++e+ ++++++  k+   l++ Gl  + +  +++g++++ E N+
  gi|91772880|ref|YP_565572.1| 774 AIMEHIEEAGVH------SGDSACVIPPRYLSEETLNTVRDYTRKIALSLNVIGLINIQM-AEQDGKVYVLEANP 841
                                   99***9999986......678999999****************************99985.577**********6 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   6.1e-08   9.9e-05       6     159 ..     131     302 ..     126     304 .. 0.75
   2 !   25.8   0.0   5.7e-09   9.2e-06      10     157 ..     678     842 ..     669     846 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.1e-08
                                   HHHHHHTTT.S---.........-EE..SS--SSSEEEEESS-------B--SS--TTE...............EEEE--- CS
                   ATP-grasp_3   6 ktykkLkeagvkvP.....tkleaee..leeeekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefie 71 
                                    + +k+++ g kvP     ++l+++e  ++e   +l++ p++  gg +  ++  ke++ ++ e           l+ e + 
  gi|91772880|ref|YP_565572.1| 131 LFKNKMEDIGEKVPrsvavSTLKEAEaiIDELGLPLIIRPAYTLGGAGGGIAYTKEQLLEISERGLrrsrinqvLIEESVL 211
                                   56678888888999777663333333114455899*******999999999999988776555444777866666666666 PP

                                   S.EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEE...EES----H...HHHHHHHHHHHHTTSTT--EEEEEEEEES CS
                   ATP-grasp_3  72 G.kplSvsllsdgekvlvlavnrqliekaekefvyaGn...vtpietel...keevvelaeevvekleglaGyvGvDlvlk 145
                                   G k++  +++ d ++  ++ +n + ++      v +G+   vtp++t +   ++ ++++a +++++l g+ G   + +  k
  gi|91772880|ref|YP_565572.1| 212 GwKEFEYEVMRDSNDTCIVICNMENLDPM---GVHTGEsivVTPSQTLNdieHQMLRTAAIKIIRAL-GIEGGCNIQFAAK 288
                                   65789999999999999999999999874...5666652226788876656577789999*******.************* PP

                                   S.SEEEEEEESS-- CS
                   ATP-grasp_3 146 deepyviEvNPRlt 159
                                   d+e  ++EvNPR+ 
  gi|91772880|ref|YP_565572.1| 289 DGEYRIVEVNPRIS 302
                                   ************96 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.7e-09
                                   HHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE...............EEEE---S.EE CS
                   ATP-grasp_3  10 kLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefieG.kp 74 
                                    +++ gv  P       ++   e +++  +++ v p++  gg ++ +v e++++e+ + e          l+ +f+e   +
  gi|91772880|ref|YP_565572.1| 678 MMSKLGVAQPeagyatsQEDAIEIATRIGYPVLVRPSYVLGGRAMEIVYEQNDLERYMREAVrvspeqpvLIDDFLEAaVE 758
                                   5566677777777666566667788888******************************998899*************7369 PP

                                   EEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTST...T--EEEEEEEEESS.SEE CS
                   ATP-grasp_3  75 lSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekle...glaGyvGvDlvlkdeepy 150
                                   + v++++dg++vl+ a+ + + e      v +G ++ +   +  +ee+ +++++ ++k+    ++ G+  + +  +d++ y
  gi|91772880|ref|YP_565572.1| 759 IDVDAVCDGKDVLIGAIMEHIEEA----GVHSGDSACVIPPRylSEETLNTVRDYTRKIAlslNVIGLINIQMAEQDGKVY 835
                                   **********99999988776655....6666665544433333888888888888888776688899999999999**** PP

                                   EEEEESS CS
                   ATP-grasp_3 151 viEvNPR 157
                                   v+E NPR
  gi|91772880|ref|YP_565572.1| 836 VLEANPR 842
                                   ******* PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0091        15      11      67 ..     136     187 ..     129     288 .. 0.82
   2 ?    0.8   0.0      0.19   3.1e+02     119     162 ..     426     470 ..     418     475 .. 0.75
   3 !    6.2   0.0     0.004       6.6      10      53 ..     678     720 ..     674     738 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0091
                                   HHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHH CS
                   ATP-grasp_2  11 lakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskee 67 
                                   +++ g kvp++  +++ +eae+++++lg    +++     GG G  gG+ ++k+  +
  gi|91772880|ref|YP_565572.1| 136 MEDIGEKVPRSVAVSTLKEAEAIIDELGLPL-IIRPAYTLGGAG--GGIAYTKE--Q 187
                                   6677889*********************998.899999999765..88877654..3 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                                   EEEEEEESSTTS-HHHHHHH-G.GGEEEEEEBTTTB--HHHHHHH CS
                   ATP-grasp_2 119 kvvviaSseGGvdiEevaakkP.ekiikvaidpakglkeeqarei 162
                                    +v+    + G+ iEev + +  +  +  +id+ + ++++ a e+
  gi|91772880|ref|YP_565572.1| 426 LFVIFHALNTGMSIEEVSELSGiDVFFIEKIDNIVKMEKKLAAEL 470
                                   4566677899********987624455678888888888887776 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.004
                                   HHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTC CS
                   ATP-grasp_2  10 ilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGR 53 
                                   +++k gv+ pe+  a+s+e+a e+a+++g  +  v+     GGR
  gi|91772880|ref|YP_565572.1| 678 MMSKLGVAQPEAGYATSQEDAIEIATRIGYPV-LVRPSYVLGGR 720
                                   68999*************************99.66666667887 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.095   1.5e+02      19      51 ..     136     168 ..     123     171 .. 0.89
   2 ?   -1.9   0.0       1.1   1.8e+03     146     178 ..     608     640 ..     598     649 .. 0.85
   3 !   10.7   0.0   0.00016      0.26      19      51 ..     679     711 ..     667     714 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.095
                   ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvl 51 
                                   +e++g +v+++  +s+ +ea ++++e+g p  +
  gi|91772880|ref|YP_565572.1| 136 MEDIGEKVPRSVAVSTLKEAEAIIDELGLPLII 168
                                   5789999**********************9877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                   ATP-grasp_5 146 lpplnstlareliertkaskllkgvrgekkadl 178
                                   + pl+ ++++++ier k + +l ++ g++ ++l
  gi|91772880|ref|YP_565572.1| 608 FEPLTLEDVMNIIEREKPYGVLVQFGGQTSVNL 640
                                   5699999**********9999999999977776 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00016
                   ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvl 51 
                                   ++ +g+  +e  +a+s+e+a+e+a +igypv +
  gi|91772880|ref|YP_565572.1| 679 MSKLGVAQPEAGYATSQEDAIEIATRIGYPVLV 711
                                   67899*************************976 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.9   3.1e+03      12      20 ..     324     332 ..     324     333 .. 0.90
   2 ?    8.1   0.0    0.0023       3.8       2      23 ..     424     445 ..     423     449 .. 0.93
   3 ?    2.7   0.0      0.11   1.8e+02       6      24 ..     479     497 ..     476     510 .. 0.82
   4 ?   -1.6   0.0       2.5     4e+03      11      22 ..     852     863 ..     850     866 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                                   HTT--HHHH CS
                 MerR-DNA-bind  12 rlGFsLdeI 20 
                                   ++G++LdeI
  gi|91772880|ref|YP_565572.1| 324 AIGMTLDEI 332
                                   58******9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0023
                                   HHHHHHHHHHHTT--HHHHHHH CS
                 MerR-DNA-bind   2 eRLkfIrrarrlGFsLdeIrel 23 
                                   eRL +I +a ++G+s++e++el
  gi|91772880|ref|YP_565572.1| 424 ERLFVIFHALNTGMSIEEVSEL 445
                                   7999***************998 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.11
                                   HHHHHHHTT--HHHHHHHH CS
                 MerR-DNA-bind   6 fIrrarrlGFsLdeIrelL 24 
                                   +   a+rlGF+ + I e+ 
  gi|91772880|ref|YP_565572.1| 479 LLTEAKRLGFTDERIGEMT 497
                                   56789******99999985 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.5
                                   HHTT--HHHHHH CS
                 MerR-DNA-bind  11 rrlGFsLdeIre 22 
                                   +++G++L+ I++
  gi|91772880|ref|YP_565572.1| 852 KAVGLPLAKIAA 863
                                   99*******986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.17       9      71 ..      28      89 ..      27     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                  HHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                     Epimerase  9 fiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihl 71
                                  f G++ ++ l+e+gy+v+ +++++ +  t   e   + v+++ ++++ +++++++e+pda+i  
  gi|91772880|ref|YP_565572.1| 28 FSGTQACRSLKEEGYKVVLVNSNPATIMTDP-E-MaDAVYIEPLEAKIIAKIIEKERPDAIIAG 89
                                  6799****************99955555432.2.259************************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1075 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.93u 0.31s 00:00:01.24 Elapsed: 00:00:00.54
# Mc/sec: 5947.11
//
Query:       gi|91772881|ref|YP_565573.1|  [L=394]
Description: argininosuccinate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-175  582.1   0.1   7.2e-175  581.9   0.1    1.0  1  Arginosuc_synth  Arginosuccinate synthase
     0.0042   16.6   0.0      0.013   15.0   0.0    1.7  2  QueC             Queuosine biosynthesis protein QueC
     0.0046   16.1   0.0     0.0081   15.3   0.0    1.4  1  NAD_synthase     NAD synthase
  ------ inclusion threshold ------
      0.036   13.7   0.0      0.054   13.2   0.0    1.2  1  Asn_synthase     Asparagine synthase
       0.05   12.4   0.0      0.081   11.7   0.0    1.3  1  tRNA_Me_trans    tRNA methyl transferase
      0.059   13.2   0.5        1.3    9.0   0.0    2.7  3  ROQ_II           Roquin II domain


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 !  581.9   0.1  2.4e-178  7.2e-175       2     387 ..       7     387 ..       6     388 .. 0.99

  Alignments for each domain:
  == domain 1  score: 581.9 bits;  conditional E-value: 2.4e-178
               Arginosuc_synth   2 LaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYedr 81 
                                   LaysGGlDts++i+llke++g +evi+vavdvGq++ed+ +++eka+k+++ k+++ D++eefv+dyifp i+an+ Ye+ 
  gi|91772881|ref|YP_565573.1|   7 LAYSGGLDTSICIPLLKEEYGyDEVITVAVDVGQPKEDVAQAEEKAKKISD-KHFTLDVREEFVNDYIFPLIRANGDYEG- 85 
                                   9********************899**************************9.9***************************. PP

               Arginosuc_synth  82 YllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgipve 162
                                   Y++gt++aRPliakk+ve+a++ega a+ahGctGkGnDq+Rfe+++r ++  ++viaP+Re++ltRe+eieyake+gipv 
  gi|91772881|ref|YP_565573.1|  86 YVMGTSIARPLIAKKVVEIAEQEGAVALAHGCTGKGNDQLRFEAVFRLTD--MDVIAPMREMNLTREWEIEYAKEHGIPVG 164
                                   **********************************************9988..***************************** PP

               Arginosuc_synth 163 vtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsvlelieklneia 243
                                   vt++kp+s+Den+++rsie+g+Ledp   ppe+iy++t++p++ap +++++ei+fe+GvPv+ldg+++  +eliek+n ia
  gi|91772881|ref|YP_565573.1| 165 VTTAKPWSVDENIWSRSIEGGKLEDPGYIPPEEIYKWTTAPEDAP-DAQIIEIGFENGVPVSLDGQKMGGVELIEKMNIIA 244
                                   *********************************************.789******************************** PP

               Arginosuc_synth 244 gkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkGlwfsPlkealdafie 324
                                   g hGvGR+D++edR++glk+Re+Ye+paa+vL++ahkdlekl+l+r ++kfk +v+++++el Y+Gl+ +Pl+++l+afi+
  gi|91772881|ref|YP_565573.1| 245 GTHGVGRTDMIEDRVLGLKARENYEHPAATVLLAAHKDLEKLVLTRAELKFKATVDAQWSELAYYGLVDEPLYDDLNAFID 325
                                   ********************************************************************************* PP

               Arginosuc_synth 325 ktqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqakly 387
                                   ktqerv Gtv +kl+kGsv vl+R+s+++lY+eel+s+d  +++dqk+aeGf+k+hg+qa+ly
  gi|91772881|ref|YP_565573.1| 326 KTQERVAGTVTMKLYKGSVLVLARTSPYALYSEELVSFD-GTSIDQKDAEGFAKYHGFQARLY 387
                                   ***************************************.9*******************998 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.3e-06     0.013       5      61 ..       8      64 ..       4      73 .. 0.73
   2 ?   -2.4   0.0      0.91   2.7e+03     150     180 ..     134     166 ..     125     168 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                                  E--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE- CS
                          QueC  5 llSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildl 61
                                    SGGlD ++++ l k+e+  +ev+++ +d gq ++  +  a++ ak++   +h +ld+
  gi|91772881|ref|YP_565573.1|  8 AYSGGLDTSICIPLLKEEYgyDEVITVAVDVGQPKED-VAQAEEKAKKISD-KHFTLDV 64
                                  57**************997669***********8554.4444444444443.4555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                                   S--EEE-TT..TT--HHHHHHHHHHTTHHHHH- CS
                          QueC 150 kkieieaPl..idlsKaeivklgkelgvpleet 180
                                   +++ + aP+  ++l+++  ++ +ke g+p+  t
  gi|91772881|ref|YP_565573.1| 134 TDMDVIAPMreMNLTREWEIEYAKEHGIPVGVT 166
                                   567888898334445555556677777776555 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.7e-06    0.0081      19      83 ..       3      66 ..       1      74 [. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                                  SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                  NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                  k+v l  SGG+D s+   l ++  g ++v+++ + ++ +++edv +a + a++++++  t+d+++
  gi|91772881|ref|YP_565573.1|  3 KKVALAYSGGLDTSICIPLLKEEYGYDEVITVAV-DVGQPKEDVAQAEEKAKKISDKHFTLDVRE 66
                                  8999******************************.9999******************99999976 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.054      20      94 ..       5      79 ..       2     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                  Asn_synthase 20 vGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyh 94
                                  v++  SGGlD S+   l++++    ++ t++++   +  ++++ a+e a+++  +h +l + ee + d++  +i++
  gi|91772881|ref|YP_565573.1|  5 VALAYSGGLDTSICIPLLKEEYGyDEVITVAVDV-GQPKEDVAQAEEKAKKISDKHFTLDVREEFVNDYIFPLIRA 79
                                  66677**************999888999999999.899************************99888887776664 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.7e-05     0.081       1      83 [.       3      77 ..       3      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                 tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfee 81
                                  kkv+ a SgG D s+   llke++   evi v + +             +ed+++ae+ a+k++ ++ ++d+++e+ ++ + +
  gi|91772881|ref|YP_565573.1|  3 KKVALAYSGGLDTSICIPLLKEEYgyDEVITVAVDVG----------QPKEDVAQAEEKAKKISDKHFTLDVREEFVNDYIFP 75
                                  589******************9973233444433322..........235788888888888888888888888888887766 PP

                 tRNA_Me_trans 82 fl 83
                                  ++
  gi|91772881|ref|YP_565573.1| 76 LI 77
                                  65 PP

>> ROQ_II  Roquin II domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       3.7   1.1e+04      16      25 ..      30      39 ..      29      39 .. 0.83
   2 ?    9.0   0.0   0.00042       1.3      14      31 ..     210     227 ..     207     229 .. 0.92
   3 ?    1.4   0.0     0.094   2.8e+02      32      55 ..     302     328 ..     291     329 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.7
                        ROQ_II 16 qivqvAfeag 25
                                  +++ vA++ g
  gi|91772881|ref|YP_565573.1| 30 EVITVAVDVG 39
                                  799***9976 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00042
                        ROQ_II  14 DaqivqvAfeaglrlspe 31 
                                   Daqi+++ fe+g+ +s++
  gi|91772881|ref|YP_565573.1| 210 DAQIIEIGFENGVPVSLD 227
                                   9************99987 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.094
                        ROQ_II  32 qWSalLY.g..dqdhrshmqSiidklq 55 
                                   qWS l Y g  d+     ++  idk q
  gi|91772881|ref|YP_565573.1| 302 QWSELAYyGlvDEPLYDDLNAFIDKTQ 328
                                   9**997635335555667888888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2442.49
//
Query:       gi|91772882|ref|YP_565574.1|  [L=287]
Description: shikimate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-13   48.6   1.6    2.2e-12   47.0   1.2    2.0  2  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.023   15.0   0.1      0.078   13.3   0.0    1.9  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.3   2.7e+03      20      47 ..      15      45 ..      12      57 .. 0.64
   2 !   47.0   1.2   2.5e-16   2.2e-12       2      66 .]      80     148 ..      79     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.3
                                  HHHHHHHHHHHHTTEHHHH...HHHHHHHHH CS
                GHMP_kinases_N 20 lavalvaAllallglslee...aklaleaer 47
                                  ++ a+++   a++g++l++   ++l+ e+  
  gi|91772882|ref|YP_565574.1| 15 VINAIATWKGAAFGVDLKTfadVELTKESSS 45
                                  5666777777788888866666777776664 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 2.5e-16
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDv.aasvyGg 66 
                                   +v++se+P+++GL SS+A+a a+++A l++lg  le    +k++++a + a+++ ++ +D+ +as++Gg
  gi|91772882|ref|YP_565574.1|  80 VVTRSEVPLASGLKSSSAAANATILATLDALGETLEPldaVKMGVRAAKDAGVTITGAFDDaCASFFGG 148
                                   789****************************988733467*********************77788876 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 ?   -2.5   0.0      0.74   6.7e+03      42      56 ..     126     137 ..     103     145 .. 0.69
   2 ?   13.3   0.0   8.8e-06     0.078      15      69 ..     209     256 ..     204     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.74
                GHMP_kinases_C  42 alselGalgaklsGa 56 
                                   a++++G   + ++Ga
  gi|91772882|ref|YP_565574.1| 126 AAKDAG---VTITGA 137
                                   444455...777777 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.8e-06
                GHMP_kinases_C  15 ellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdk 69 
                                   ++++l+    l  ++g l  + + + eal ++G+ g++lsG+  Gp+  al++ k
  gi|91772882|ref|YP_565574.1| 209 KAMTLNGF--L--YCGALGFSTDVMMEAL-KCGVKGVSLSGT--GPAYSALVDRK 256
                                   56777777..6..7777888888888887.************..*******9443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1733.70
//
Query:       gi|91772883|ref|YP_565575.1|  [L=95]
Description: chorismate mutase [Methanococcoides burtonii DSM 6242]
Scores for 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   2.5    1.2e-15   57.6   2.5    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 !   57.6   2.5   6.7e-20   1.2e-15       1      75 []       8      86 ..       8      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 6.7e-20
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHHH CS
                          CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralqk 75
                                  R++I++iD ei++L++eR ++a +v ++Kk+e++++ d  +   vl+r ++ a    ld+ a+++if+ +i++s+++q+
  gi|91772883|ref|YP_565575.1|  8 RNRIEQIDYEIIKLIEERIDCATDVLAVKKKEHMSINDGTQNHVVLDRATNSAtersLDSGAVKEIFEILIRMSIERQH 86
                                  99*************************************************445567********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 646.68
//
Query:       gi|91772884|ref|YP_565576.1|  [L=129]
Description: phosphoribosylaminoimidazole carboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-46  155.2   1.9    9.3e-46  155.1   1.9    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 !  155.1   1.9   5.2e-50   9.3e-46       2     128 ..       4     126 ..       3     129 .] 0.96

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 5.2e-50
                                   EEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEE CS
                          AIRC   2 VgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVig 82 
                                   + i+mGS+sD  ++ +++++l++ + ++ev+v+Sahr p++l ey+++ +    +v+Ia+AG +a+Lpgv+as+t  PVig
  gi|91772884|ref|YP_565576.1|   4 ISILMGSESDHAIATRVTSVLEDTDYSFEVKVISAHRDPKKLDEYIAKSD---ANVFIAIAGLSAALPGVIASKTIKPVIG 81 
                                   89********************************************9776...57************************** PP

                                   EEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHT CS
                          AIRC  83 vPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqila 128
                                   vPv++ +l gld+llSivqmP+gvpva v+i++++nAa lA++il 
  gi|91772884|ref|YP_565576.1|  82 VPVSA-KLGGLDALLSIVQMPPGVPVASVGIDNGANAAKLAIRILD 126
                                   *****.9*************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 800.70
//
Query:       gi|91772885|ref|YP_565577.1|  [L=302]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  168.7   1.2    1.3e-49  168.2   1.2    1.2  1  MetOD1         Metanogen output domain 1
      2e-28   98.8   1.4    3.7e-28   97.9   0.5    1.9  2  Response_reg   Response regulator receiver domain
     0.0047   16.3   0.1     0.0074   15.6   0.1    1.4  1  Baculo_E56     Baculoviral E56 protein, specific to ODV envel
  ------ inclusion threshold ------
      0.014   16.1   0.2      0.033   15.0   0.2    1.8  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   1.2   2.8e-53   1.3e-49       1     154 [.     150     298 ..     150     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 2.8e-53
                        MetOD1   1 elkkkkvkaelrsfllsaiPtlaskippeekkilikqfadrveknlkpkfkeelkeaekeeedaekvlkayiewlnqlfan 81 
                                   e++++++++e+rs++++++Ptl+++ip+e+kki+++q++d+ve+++k + +     +  e ++ +++++++++++nql+++
  gi|91772885|ref|YP_565577.1| 150 ERDQLEMQNEVRSIMTNIVPTLLANIPMEQKKIIVHQMVDMVETIIKGTKQ----GYVAELNSISDAAQLCCDTMNQLGGS 226
                                   7899***********************************************....8999********************** PP

                        MetOD1  82 fgiktekkedeknvlleftnCpWge.earknPifCllcraivsrsftwtglkgsveqkktlgngdekCvFeikv 154
                                   ++i+++  +de+++l+++++C+Wg+ ea+ nPi+C+l++++++r++++++ + +v+++ktlgngd++C+Fei +
  gi|91772885|ref|YP_565577.1| 227 YYIDRT--DDEDICLIKARKCLWGKvEAHLNPIMCNLTTGVFMRIINQFFPNSNVKVQKTLGNGDQYCHFEILK 298
                                   ******..9**************************************************************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 !   97.9   0.5   8.4e-32   3.7e-28       1     111 [.      24     134 ..      24     135 .. 0.95
   2 ?   -1.7   0.0      0.74   3.3e+03      10      39 ..     187     216 ..     184     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 8.4e-32
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +livdD+p ++ell+ ll   +y e+++a+ g+eal+++++e+ dl+llD++mp+++G+e++++i+     + lpvi++ta
  gi|91772885|ref|YP_565577.1|  24 ILIVDDEPNNVELLEALLF-VDY-EIMTASGGQEALDIINKENLDLVLLDVMMPEITGYEVCEHIKSSIktQFLPVIMVTA 102
                                   8*****************9.999.9****************************************99884455******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    +e ed++++++agaddflsKp+d+ eL +++
  gi|91772885|ref|YP_565577.1| 103 LTEREDRIKGIEAGADDFLSKPVDRLELNTRV 134
                                   ****************************9987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.74
                                   HHHHHHHHHH..HTTEEEEEEESSHHHHHHHH CS
                  Response_reg  10 vrellrqlle..eegyeevaeaedgkealell 39 
                                   +++ ++++++  ++gy  vae ++ ++a +l+
  gi|91772885|ref|YP_565577.1| 187 MVDMVETIIKgtKQGY--VAELNSISDAAQLC 216
                                   6677888999656666..88888888887765 PP

>> Baculo_E56  Baculoviral E56 protein, specific to ODV envelope
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.7e-06    0.0074     120     175 ..     209     261 ..     177     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                    Baculo_E56 120 aadlvqdivealnrtGGsyyvrGkngGdnvdacllkyrscgvdqsladsdvfvcel 175
                                     d  q   +++n+ GGsyy+      d+ d cl+k r c   +  a+ + ++c+l
  gi|91772885|ref|YP_565577.1| 209 ISDAAQLCCDTMNQLGGSYYIDRT---DDEDICLIKARKCLWGKVEAHLNPIMCNL 261
                                   4566777889**********9887...999**********9988888888888887 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   7.4e-06     0.033      78     144 ..     229     295 ..     150     296 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                 ATC_hydrolase  78 vlee.dkdeleidvtrCpyceawkkeGl.pelgkllCeiDkavaeginpkvklertktlaeGgdcCdfr 144
                                   ++++ d+d + i+ ++C + ++    +l p  + l   + + +++ ++p+ + + +ktl+ G+++C+f 
  gi|91772885|ref|YP_565577.1| 229 IDRTdDEDICLIKARKCLWGKVE--AHLnPIMCNLTTGVFMRIINQFFPNSNVKVQKTLGNGDQYCHFE 295
                                   3344368888899****999974..444355555556678899999999999999************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1910.66
//
Query:       gi|91772886|ref|YP_565578.1|  [L=239]
Description: KaiC [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-47  161.6   0.4    2.1e-47  161.4   0.4    1.0  1  ATPase    KaiC
    2.5e-06   27.1   0.0    3.6e-06   26.7   0.0    1.2  1  RecA      recA bacterial DNA recombination protein
    9.7e-06   25.1   0.0    1.8e-05   24.2   0.0    1.4  1  DnaB_C    DnaB-like helicase C terminal domain
    9.3e-05   21.2   0.3     0.0004   19.1   0.3    1.8  1  GvpD      GvpD gas vesicle protein
    0.00081   19.0   0.0     0.0011   18.6   0.0    1.3  1  AAA_25    AAA domain
     0.0055   16.0   0.0     0.0088   15.3   0.0    1.4  2  DUF2075   Uncharacterized conserved protein (DUF2075)
     0.0056   16.0   0.1     0.0092   15.3   0.1    1.4  1  Rad51     Rad51
     0.0097   15.6   0.1       0.02   14.6   0.1    1.7  1  AAA_24    AAA domain
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.16   12.5   0.0    1.4  1  AAA_18    AAA domain
       0.14   12.5   0.6       0.63   10.3   0.6    2.0  1  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.4   1.2e-50   2.1e-47       1     227 [.       4     232 ..       4     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.2e-50
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   ++tgI++lD+ l+gG+p+g+ +litG+pG+GKtif+l+ l +g+ + g+++v+v++ee++ed+  +a++lG dl+   ++g
  gi|91772886|ref|YP_565578.1|   4 ISTGIKYLDDKLDGGYPKGKGILITGVPGSGKTIFGLHALDQGCID-GKKCVMVATEESPEDILVQAEMLGLDLKSHMDNG 83 
                                   68********************************************.********************************** PP

                        ATPase  82 klaiidasesaeesaee..kdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkklgvTa 158
                                   +l i+ + e++++++++  +  +  +    ++  +i+ i    + vviD+i+++a  ++++++R+ ++ l   +++++ T+
  gi|91772886|ref|YP_565578.1|  84 NLEILRVLEQRTRDIAQasEMIKGFSIREINMIGIIDLIPDdtEFVVIDNIGVFAIGMEPKEFRDKFDVLNLLISQKNFTT 164
                                   ***********9988876544444444455778888888877799*********999************************ PP

                        ATPase 159 ilvsekssseeaaggygveefivdgvivLdlkeiee..elvRtleivkmRgtkhskkehpfeIteegikvl 227
                                   +lv++   +++ + +++++ ++ +g +++  ke+ +  +++R+l i kmR+t++s +   ++It++gi+ +
  gi|91772886|ref|YP_565578.1| 165 LLVMD---EASYNLTHRIADYSTYGCLKISIKENPYtgNMERYLLITKMRSTNISLDANRYDITSQGIEFH 232
                                   *****...8999**********************9999******************************976 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0     2e-09   3.6e-06      32     107 ..       2      78 ..       1      99 [. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2e-09
                                   -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----H..HHHHHTT--GGG CS
                          RecA  32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldp..kyakklGvdide 107
                                   e is+G   ld  l  GG+pkG+ i i G+  sGkt + lha+ +    g+ ++++ +e + +   + a+ lG+d+++
  gi|91772886|ref|YP_565578.1|   2 ERISTGIKYLDDKLD-GGYPKGKGILITGVPGSGKTIFGLHALDQGCIDGKKCVMVATEESPEDilVQAEMLGLDLKS 78 
                                   679***********9.******************************************99876512467889999764 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   9.9e-09   1.8e-05       2     101 ..       4     107 ..       3     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.9e-09
                                   BXSSTHHHH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH.HHH..HHHTXXHHH CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxxx RF
                        DnaB_C   2 lstgfkdLD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR.lls..seaeidskk 78 
                                   +stg k LD kl +G+ kg+ i+i + p+ Gkt + l+   + +++ k+ v+v   e +++ lvq  +l    ++++d+ +
  gi|91772886|ref|YP_565578.1|   4 ISTGIKYLDdKLDGGYPKGKGILITGVPGSGKTIFGLHALDQGCIDGKKCVMVATEESPEDILVQAeMLGldLKSHMDNGN 84 
                                   78999***946668899*************************999999999999999999988875244322556666666 PP

                                   HHHTTSXHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  79 lrtgklkeedweklteaieelse 101
                                   l+  ++ e+ ++++++a e+++ 
  gi|91772886|ref|YP_565578.1|  85 LEILRVLEQRTRDIAQASEMIKG 107
                                   66666666677777777766654 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   2.2e-07    0.0004       9     196 ..      21     215 ..      18     231 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.2e-07
                          GvpD   9 aGktllikGaPGtGktlftlrgldv..lrresdvlyvstrvddetvs..eay.fsgeaeld..ktalldllkd...pleld 79 
                                    Gk +li G PG+Gkt+f l+ ld   ++ ++ v+  +  + ++ +   e+  ++ ++++d  + ++l +l+     +   
  gi|91772886|ref|YP_565578.1|  21 KGKGILITGVPGSGKTIFGLHALDQgcIDGKKCVMVATEESPEDILVqaEMLgLDLKSHMDngNLEILRVLEQrtrDIAQA 101
                                   599********************9532666666655555555554431244464444444422333333222200022222 PP

                          GvpD  80 ldvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaery..dsPediktvkndlvvlaresgvrlvlvl.eta 157
                                    +++  +           + ei+ i+   +i  d+  +v++ + +     +P++++   + l  l  +++   +lv+ e+ 
  gi|91772886|ref|YP_565578.1| 102 SEMIKGF----------SIREINMIGIIDLIPDDTEFVVIDNIGVFAigMEPKEFRDKFDVLNLLISQKNFTTLLVMdEAS 172
                                   2222222..........1344555555555555554455555443221135666666555555555666665555550444 PP

                          GvpD 158 an...srleyivdGvvtlnvkedd.rgrlrrdlrleklrGvri 196
                                    n      +y   G + + +ke+   g + r l + k+r  +i
  gi|91772886|ref|YP_565578.1| 173 YNlthRIADYSTYGCLKISIKENPyTGNMERYLLITKMRSTNI 215
                                   3311133466667888888888853688888888899887766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     6e-07    0.0011      23     155 ..      12     138 ..       1     168 [. 0.74

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6e-07
                        AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...rd 99 
                                   ++ ++g  p+g+ +l++G pg+GKt + l+     +  Gk           k+++v++E+s +++   ++ +g +l    d
  gi|91772886|ref|YP_565578.1|  12 DDKLDGGYPKGKGILITGVPGSGKTIFGLHALDQGCiDGK-----------KCVMVATEESPEDILVQAEMLGLDLkshMD 81 
                                   55566677**********************9999997877...........89*****************99999988867 PP

                        AAA_25 100 darllvldlagveslpLf...akdrggtlltadvdaleaaieevegvrlvviDplsral 155
                                   +++l +l + ++  ++++   ++++g ++++  +  +++ i +  + ++vviD++  + 
  gi|91772886|ref|YP_565578.1|  82 NGNLEILRVLEQRTRDIAqasEMIKGFSIREINMIGIIDLIPD--DTEFVVIDNIGVFA 138
                                   7888888865553333331113456666655554455555444..49999999986655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.9e-06    0.0088       4      25 ..      25      46 ..      22     115 .. 0.72
   2 ?   -3.7   0.0       2.9   5.2e+03      88     102 ..     162     176 ..     148     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                       DUF2075  4 vlVtGvaGtGKtvvllnllael 25
                                  +l+tGv+G+GKt+ +l++l + 
  gi|91772886|ref|YP_565578.1| 25 ILITGVPGSGKTIFGLHALDQG 46
                                  89***************99876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.9
                       DUF2075  88 kedvvivDEAhrllt 102
                                     +++++DEA   lt
  gi|91772886|ref|YP_565578.1| 162 FTTLLVMDEASYNLT 176
                                   456788899865555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.1e-06    0.0092      18     129 ..       3     106 ..       1     132 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.1e-06
                                   EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--S.SEEEEEESSS---GGGGHHHHHHTT- CS
                         Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGge.gkavyidtegtfrperlveiaerykl 97 
                                   +++tG k lD+ L+GG + g+   i G  +sGkt +           l++g  + +k+v + te +  pe ++  ae  +l
  gi|91772886|ref|YP_565578.1|   3 RISTGIKYLDDKLDGGYPKGKGILITGVPGSGKTIFGLH-------ALDQGCIDgKKCVMVATEES--PEDILVQAEMLGL 74 
                                   69********************************99754.......34555554167999999985..9999999****** PP

                                   -HHHHGGGEEEEE--STTHHHHHHHHTHHHHH CS
                         Rad51  98 dkeevlenvayaRaytiehqeellqqaaalla 129
                                   d ++ ++n   +     e++++ ++qa+++++
  gi|91772886|ref|YP_565578.1|  75 DLKSHMDNGNLEILRVLEQRTRDIAQASEMIK 106
                                   ***99999988888888888888888888765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.1e-05      0.02       3      38 ..      23      65 ..      21     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                        AAA_24  3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksl 38
                                  + ili+G +g+GKT + +++       g+k +++ te++  ++
  gi|91772886|ref|YP_565578.1| 23 KGILITGVPGSGKTIFGLHAldqgcidGKKCVMVATEESPEDI 65
                                  679*******************************999986655 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   9.1e-05      0.16       1      33 [.      25      58 ..      25     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf..gvnlrdvak 33
                                  Il+tG+pG+GKt ++ +  +  g+  g ++  va+
  gi|91772886|ref|YP_565578.1| 25 ILITGVPGSGKTIFGLHALDQ-GCidGKKCVMVAT 58
                                  99**********887666444.4555444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00035      0.63       8     104 ..      25     138 ..      21     181 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.................. 70 
                                   +++tG +G+GKT      l+q +++      +++   v ++ ++s++d+l + ++ lgl+lk+                  
  gi|91772886|ref|YP_565578.1|  25 ILITGVPGSGKTIFGLHALDQGCID------GKK--CVMVATEESPEDILVQ-AEMLGLDLKShmdngnleilrvleqrtr 96 
                                   89**********9999999998644......222..3333333334444222.2223333333333333322222211111 PP

                        AAA_22  71 erlsseellealeqalrarav.....................ielliiDEaqhlr 104
                                     ++ +e             +                     +e+++iD++  + 
  gi|91772886|ref|YP_565578.1|  97 DIAQASE-------------MikgfsireinmigiidlipddTEFVVIDNIGVFA 138
                                   1122222.............12223333334444466666666777777766664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1642.83
//
Query:       gi|91772887|ref|YP_565579.1|  [L=637]
Description: ATP-dependent protease Lon [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-32  110.6   4.7    1.2e-31  109.8   4.7    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    5.8e-29  101.3   0.1    1.6e-20   73.4   0.0    2.2  2  AAA_32           AAA domain
    1.1e-17   64.2   0.1    6.1e-11   42.1   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.4e-15   56.6   0.1    2.5e-08   33.8   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    2.7e-12   46.8   0.0    7.4e-05   22.8   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
    2.5e-10   40.3   0.5    5.9e-10   39.0   0.5    1.6  1  ChlI             Subunit ChlI of Mg-chelatase
    4.3e-08   33.7   0.0      0.007   16.8   0.0    2.7  2  AAA              ATPase family associated with various cellul
    1.8e-07   30.5   1.7      0.054   12.6   0.0    3.6  4  MCM              MCM P-loop domain
    1.7e-05   24.6   0.0      0.014   15.1   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.4e-05   23.8   0.0     0.0016   18.7   0.0    2.5  2  AAA_22           AAA domain
    5.7e-05   23.0   0.0       0.33   10.8   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    7.3e-05   22.3   0.0    0.00054   19.5   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
    7.5e-05   23.1   0.8     0.0022   18.3   0.8    2.9  1  AAA_19           AAA domain
    0.00023   21.3   0.0       0.85    9.7   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0018   18.0   0.0     0.0098   15.6   0.0    2.1  2  AAA_30           AAA domain
     0.0045   17.4   0.0       0.18   12.2   0.0    2.5  2  AAA_16           AAA ATPase domain
     0.0048   16.4   0.0      0.012   15.0   0.0    1.6  1  PhoH             PhoH-like protein
     0.0052   15.9   0.0     0.0092   15.1   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
  ------ inclusion threshold ------
      0.012   14.7   0.0      0.054   12.5   0.0    2.0  2  T2SSE            Type II/IV secretion system protein
      0.017   15.3   0.0      0.037   14.2   0.0    1.6  1  AAA_33           AAA domain
       0.02   14.6   0.0      0.082   12.6   0.0    2.0  2  IstB_IS21        IstB-like ATP binding protein
      0.022   15.3   0.0      0.054   14.0   0.0    1.7  1  AAA_18           AAA domain
       0.03   14.9   0.0      0.088   13.3   0.0    1.8  1  ABC_tran         ABC transporter
       0.04   13.1   0.0      0.079   12.1   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.047   13.8   0.2         11    6.1   0.0    2.8  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.049   13.0   0.0       0.14   11.5   0.0    1.7  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.053   12.4   0.0       0.11   11.4   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.055   13.7   0.0       0.15   12.3   0.0    1.8  1  AAA_28           AAA domain
      0.057   13.8   0.0        0.3   11.5   0.0    2.2  1  Styelin          Styelin
      0.069   13.1   0.0       0.18   11.7   0.0    1.7  1  NACHT            NACHT domain
       0.14   12.2   1.0       0.34   10.9   1.0    1.7  1  DUF1676          Protein of unknown function (DUF1676)


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 !  109.8   4.7   2.1e-34   1.2e-31      25     204 ..     426     603 ..     402     604 .. 0.86

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 2.1e-34
                                   -BSSEEEEEEEET.TEEEEEEEEEEEESS-....S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-TTT-EEEEEE CS
                         Lon_C  25 dqvGvvtGlawte.vGGdlltieavllpgk....gklkltGklgdvmkesaqaalsyvrsraeelgidkevfekkdihihv 100
                                     vG v Gla      G +l i a ++p +    g+++ tG l+d+ ke++q   +++++ +          +++dihi +
  gi|91772887|ref|YP_565579.1| 426 AAVGRVNGLAVMGgDSGIVLPIVAEVTPTQssagGHVIATGMLKDIAKEAVQNVSAVIKKVTG---E---DISNHDIHIQF 500
                                   679******974313456899988887754223379****************98888875432...2...35678****** PP

                                   -S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGGTTTS-H CS
                         Lon_C 101 PeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekdlediPe 181
                                          +G sa +++ata++s+l ++++++ vamtG +++rG vlpiGG   k+ aa +agikkvi+Pk+ne d+  i +
  gi|91772887|ref|YP_565579.1| 501 IGTYEGVEGDSASISIATAVISALENIPIDQTVAMTGSLSVRGDVLPIGGATYKIEAAVQAGIKKVIIPKSNEADVL-IED 580
                                   9999999********************************************************************95.99* PP

                                   HHHTS-B--EESBHHHHHHHHB- CS
                         Lon_C 182 evreeleiilveevdevlkaalv 204
                                   + ++++eii+v+++ ev+++ lv
  gi|91772887|ref|YP_565579.1| 581 YYKDKVEIIPVTTIAEVIEHSLV 603
                                   ********************996 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   9.2e-09   5.3e-06       7      89 ..      31     108 ..      26     127 .. 0.85
   2 !   73.4   0.0   2.8e-23   1.6e-20     281     507 ..     171     396 ..     167     401 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.2e-09
                        AAA_32   7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpaGkGk 87 
                                   ++++igqe Ave ++ + + +    ++ ++G +gtG+++l+k + e   k  +  +D++   n +++++Pk+ ++paGkG+
  gi|91772887|ref|YP_565579.1|  31 IDQVIGQEHAVEVVKKAASQR---RHVMMIGTPGTGKSMLAKAMAELLPK--EELEDIMTYPNLEDNNNPKIREVPAGKGR 106
                                   5899**********9987765...59***************999988754..4568999999******************9 PP

                        AAA_32  88 el 89 
                                   e 
  gi|91772887|ref|YP_565579.1| 107 EI 108
                                   84 PP

  == domain 2  score: 73.4 bits;  conditional E-value: 2.8e-23
                        AAA_32 281 nvlvdnsetegaPVvvednptyanLfGkieyesemg.alvt.dftlIkaGaLhkAnGGyLildaedlLeeplaWeaLkraL 359
                                   +++v+n ++e+aP +  +  +   L+G + ++  +   l t  + ++++G +hk + G+L +d  + L+ + + ++L  aL
  gi|91772887|ref|YP_565579.1| 171 KLIVSNYQKEHAPYIDATGTHAGALLGDVRHDPFQSgGLETpAHDRVESGDIHKSHKGVLFIDEINTLRLE-SQQSLLTAL 250
                                   79****************************997544355553899*********************99865.6799***** PP

                        AAA_32 360 rskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteenekkyarfia 440
                                   ++ke  i       + +s    k ep+p+d   +  G+ +  + ++ +     k +  ++ + d+me t en k+++rf+a
  gi|91772887|ref|YP_565579.1| 251 QEKEYAITGQ---SERSSGALVKTEPVPCDFIMVAAGNLDAVEKMHPALRSRIKGYGYEVFMRDSMEDTLENRKSLVRFVA 328
                                   ********53...446788999************99*99999999999888899999***********************8 PP

                        AAA_32 441 s.ivkkekllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekA 507
                                   + +v++ +++pfd+ av+++i++s r a+++ +l+++f+++  l+r A  +a++e+ae+ +a+hV +A
  gi|91772887|ref|YP_565579.1| 329 QeVVRDGHIPPFDKGAVKEVIRESRRRAGRKGHLTLKFRDLGGLVRVAGDIAHSENAEITTATHVLAA 396
                                   63788899*********************************************************988 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   1.1e-13   6.1e-11       3      56 ..      32      85 ..      30     110 .. 0.91
   2 !   19.7   0.0   7.7e-07   0.00045      96     158 ..     216     286 ..     207     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.1e-13
                  Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeale 56
                                   +v+Gqe+a ++++ aa+ + +++++G+pG+GK+mlak++++llp+ + e+++ 
  gi|91772887|ref|YP_565579.1| 32 DQVIGQEHAVEVVKKAASQRRHVMMIGTPGTGKSMLAKAMAELLPKEELEDIMT 85
                                  68*******************************************998888765 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7.7e-07
                  Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakak....v....efparfqlvaamNp 158
                                   +++ G+i ++h+GvLf+DE+  ++ +  ++L + l+++e +i+ ++++    +      p++f +vaa N+
  gi|91772887|ref|YP_565579.1| 216 RVESGDIHKSHKGVLFIDEINTLRLESQQSLLTALQEKEYAITGQSERssgaLvktePVPCDFIMVAAGNL 286
                                   6789**********************************999975443211112111146778888887775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.9e-07    0.0004       9      48 ..      38      77 ..      30      91 .. 0.87
   2 !   33.8   0.0   4.4e-11   2.5e-08      83     130 ..     215     263 ..     205     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.9e-07
                                  HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTT CS
               Sigma54_activat  9 kelleqikkvaktdlsvlitGesGtGKellaraiheaskr 48
                                  ++++e +kk+a+++ +v++ G  GtGK++la+a+ e  ++
  gi|91772887|ref|YP_565579.1| 38 EHAVEVVKKAASQRRHVMMIGTPGTGKSMLAKAMAELLPK 77
                                  578999****************************986655 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 4.4e-11
                                   S-BE.HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
               Sigma54_activat  83 kekk.GlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                   ++ + G ++k+++G+lf+Dei++l le Q+ Ll++lqe+e+   G+s+ 
  gi|91772887|ref|YP_565579.1| 215 DRVEsGDIHKSHKGVLFIDEINTLRLESQQSLLTALQEKEYAITGQSER 263
                                   44334*************************************9998765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     3e-07   0.00018       1      37 [.      53      90 ..      53     120 .. 0.86
   2 !   22.8   0.0   1.3e-07   7.4e-05      64     137 ..     221     299 ..     153     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3e-07
                                  EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                         AAA_5  1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtt 37
                                  +v+++G pGtgKs+la+ +a++l + e+e ++ + +++
  gi|91772887|ref|YP_565579.1| 53 HVMMIGTPGTGKSMLAKAMAELLpKEELEDIMTYPNLE 90
                                  79*********************888888888777665 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.3e-07
                                   -....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEESS--.-TT-TTHHH CS
                         AAA_5  64 r....egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller......frviatanpldrslnelspal 134
                                        ++ +l++DE+++++ e ++sLl+ l e+++ +    e+ + +     ++      f  +a++n     ++++ pal
  gi|91772887|ref|YP_565579.1| 221 DihksHKGVLFIDEINTLRLESQQSLLTALQEKEYAITGQSERSSGALV---KTepvpcdFIMVAAGNLDA--VEKMHPAL 296
                                   15555789****************************8777777777663...3345899999999999888..9999**** PP

                                   HTT CS
                         AAA_5 135 rsR 137
                                   rsR
  gi|91772887|ref|YP_565579.1| 297 RSR 299
                                   **9 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.5     1e-12   5.9e-10      14     121 .]     464     572 ..     451     572 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1e-12
                          ChlI  14 ivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGeLsldGs 93 
                                    +G+++   ke+ + v + +k+ +g ++ ++ i +         eG + +++iA ++++ale+i+ ++++ + G Ls  G+
  gi|91772887|ref|YP_565579.1| 464 ATGMLKDIAKEAVQNVSAVIKKvTGEDISNHDIHIQFIGTYEGVEGDSASISIATAVISALENIPIDQTVAMTGSLSVRGD 544
                                   479999999***********99899******************************************************** PP

                          ChlI  94 lrpvkgvlpialaakkegikkvivpken 121
                                   + p+ g++  + aa ++gikkvi+pk+n
  gi|91772887|ref|YP_565579.1| 545 VLPIGGATYKIEAAVQAGIKKVIIPKSN 572
                                   *************************998 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   1.2e-05     0.007       1      22 [.      54      75 ..      54     128 .. 0.78
   2 !   13.9   0.0   9.5e-05     0.055      56     125 ..     225     301 ..     212     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                                  EEEESSTTSSHHHHHHHHHHHH CS
                           AAA  1 vllyGppGtGKTllakavakel 22
                                  v+++G+pGtGK++laka+a+ l
  gi|91772887|ref|YP_565579.1| 54 VMMIGTPGTGKSMLAKAMAELL 75
                                  6899***************976 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.5e-05
                                   TSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GGGST CS
                           AAA  56 kakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pdkld 116
                                   + ++ +lfiDEi  l  ++           ++ Llt+l++ +                      ++i+++a+n   ++k+ 
  gi|91772887|ref|YP_565579.1| 225 S-HKGVLFIDEINTLRLES-----------QQSLLTALQEKEYAitgqserssgalvktepvPCDFIMVAAGNLdaVEKMH 293
                                   2.359**********8888...........999999999999999999*************9667*********99***** PP

                                   HHHHSTTSS CS
                           AAA 117 pallrgRfd 125
                                   pal+ +R++
  gi|91772887|ref|YP_565579.1| 294 PALR-SRIK 301
                                   ****.9975 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00011     0.065      51      84 ..      45      78 ..      26      85 .. 0.76
   2 !   12.6   0.0   9.4e-05     0.054      82     150 ..     180     255 ..     145     261 .. 0.72
   3 ?   -3.1   0.0       5.7   3.3e+03      19      47 ..     479     507 ..     468     519 .. 0.64
   4 ?    2.4   0.1      0.12        69     132     162 ..     585     615 ..     575     619 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                  SSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                           MCM 51 ktklrgdinvllvgdpgtaKsqlLkyveklapra 84
                                  k+    + +v+++g pgt+Ks l k++++l+p+ 
  gi|91772887|ref|YP_565579.1| 45 KKAASQRRHVMMIGTPGTGKSMLAKAMAELLPKE 78
                                  34456678********************999975 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.4e-05
                                   SSEEEEESSSSSSSHSSSEEEEESSSSS.......EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEE CS
                           MCM  82 pravytsgkgssaagLtaavvrdeetge.......fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqti 150
                                   ++a y+ ++g+ a  L   v++d+ ++          +e+G +  ++kGv+ iDe++  + e +++l+ a+ +++ 
  gi|91772887|ref|YP_565579.1| 180 EHAPYIDATGTHAGALLGDVRHDPFQSGgletpahDRVESGDIHKSHKGVLFIDEINTLRLESQQSLLTALQEKEY 255
                                   45678888888888888888888866654444444569******************************99987765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.7
                                   HHHSSTTSSS-HHHHHHHHHHHH---EBB CS
                           MCM  19 vksiapsiyghedvkkaillqlfggvkkk 47 
                                   v++++++++g++   + i +q +g+++  
  gi|91772887|ref|YP_565579.1| 479 VSAVIKKVTGEDISNHDIHIQFIGTYEGV 507
                                   34456667777777777777777766655 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.12
                                   GSTCHHHHHHHHHHHHSEEEEESSSCEEEEE CS
                           MCM 132 kmkeedrsalhEamEqqtisiaKaGivatLn 162
                                   k++    +++ E++E+  +   KaGiv +L+
  gi|91772887|ref|YP_565579.1| 585 KVEIIPVTTIAEVIEHSLVGEDKAGIVEKLK 615
                                   555556789******************9987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.5e-05     0.014       7      57 ..      32      75 ..      27      93 .. 0.78
   2 !    6.7   0.0    0.0095       5.5      84     116 ..     226     258 ..     221     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                        RuvB_N  7 eeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                  ++ igqe+    ++++ +aa +r+    hv+++G PG Gk+ lak +a+ l
  gi|91772887|ref|YP_565579.1| 32 DQVIGQEHA---VEVVKKAASQRR----HVMMIGTPGTGKSMLAKAMAELL 75
                                  566677654...456667777775....*****************999755 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0095
                        RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldiv 116
                                   +k vlfidei  l+ + ++ l +a+++ +  i+
  gi|91772887|ref|YP_565579.1| 226 HKGVLFIDEINTLRLESQQSLLTALQEKEYAIT 258
                                   578*********************998776664 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.8e-06    0.0016       3      38 ..      49      90 ..      45     130 .. 0.76
   2 ?    2.1   0.0      0.38   2.2e+02      86     109 ..     222     247 ..     213     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.8e-06
                        AAA_22  3 ktagilvvtGesGtGKTtllrrlleqldeeakaee......e 38
                                  +++++++ +G +GtGK++l++ ++e l++e+  +       e
  gi|91772887|ref|YP_565579.1| 49 SQRRHVMMIGTPGTGKSMLAKAMAELLPKEELEDImtypnlE 90
                                  47999**********************987665545555551 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.38
                        AAA_22  86 lraravielliiDEaqhlr..s.eeal 109
                                   +++ ++ ++l iDE+  lr  s + +l
  gi|91772887|ref|YP_565579.1| 222 IHKSHK-GVLFIDEINTLRleSqQSLL 247
                                   466667.9**********765323333 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0015      0.89       1      24 [.      53      76 ..      53      89 .. 0.88
   2 !   10.8   0.0   0.00056      0.33      64      98 ..     228     262 ..     213     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                         AAA_3  1 hvllegvPGlaktllvkalakald 24
                                  hv++ g+PG++k +l+ka+a+ l 
  gi|91772887|ref|YP_565579.1| 53 HVMMIGTPGTGKSMLAKAMAELLP 76
                                  9*******************9885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00056
                         AAA_3  64 nllladeinrappktqsalleameerqvtvegeth 98 
                                    +l+ dein     +q +ll a++e++ +++g++ 
  gi|91772887|ref|YP_565579.1| 228 GVLFIDEINTLRLESQQSLLTALQEKEYAITGQSE 262
                                   5899***********************99998875 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 !   19.5   0.0   9.3e-07   0.00054      25      63 ..      43      81 ..      19      88 .. 0.88
   2 ?   -0.5   0.0       1.3   7.5e+02     100     115 ..     226     241 ..     223     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.3e-07
                         AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkekyl 63
                                  ++++  +++++v+++G+ GtGK++++k + + l+ke++ 
  gi|91772887|ref|YP_565579.1| 43 VVKKAASQRRHVMMIGTPGTGKSMLAKAMAELLPKEELE 81
                                  6788999************************99999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                         AAA_7 100 kklvvFvDDlnmpake 115
                                   +k v+F+D++n  + e
  gi|91772887|ref|YP_565579.1| 226 HKGVLFIDEINTLRLE 241
                                   6889*******98777 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.8   3.8e-06    0.0022       6     129 ..      46     254 ..      37     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-06
                        AAA_19   6 e.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal........ 77 
                                   + a++++++++++ pGtGK+ + k++ +ll +++ ++   ++   +      ++re  a+ g+e+   H++          
  gi|91772887|ref|YP_565579.1|  46 KaASQRRHVMMIGTPGTGKSMLAKAMAELLPKEELEDI--MTYPNLEDNNNPKIREVPAGKGREIVLAHKMEArkkaqsrn 124
                                   3468999*************999999999988886543..33334455555666666666666666666654456666666 PP

                        AAA_19  78 ...............................................................................ld 79 
                                                                                                                    
  gi|91772887|ref|YP_565579.1| 125 mmmmflvlgivmysfyvgqllwgiiaaimilmltrqfmpkeelmipklivsnyqkehapyidatgthagallgdvrhdpF- 204
                                   66666666666666677777777777777777777777777777777777777777776655555555555555444332. PP

                        AAA_19  80 fddlltealelle.....eaeeekklqeee.llivDEfqdvd.elqyrLlkallgek 129
                                          + + le     + e+ +  ++++ +l++DE+  +  e q++Ll al +++
  gi|91772887|ref|YP_565579.1| 205 -------QSGGLEtpahdRVESGDIHKSHKgVLFIDEINTLRlESQQSLLTALQEKE 254
                                   .......233333555542223333344557*********************99554 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    0.0026       1.5      14      44 ..      44      74 ..      39      95 .. 0.84
   2 !    9.7   0.0    0.0015      0.85      66      97 ..     223     254 ..     200     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0026
                                  HHHHHT-SS-EEEEEETT--HHHHHHCC--T CS
               Sigma54_activ_2 14 LeqaaqsklpvfltGekGsgkelvArlLhkn 44
                                  +++aa++   v ++G +G+gk++ A+++++ 
  gi|91772887|ref|YP_565579.1| 44 VKKAASQRRHVMMIGTPGTGKSMLAKAMAEL 74
                                  789999********************99875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                                   HHTTTSEEEEEE-TT--HHHHHHHHHHHHHHT CS
               Sigma54_activ_2  66 eqakggtLylkdiadlskaeqkeLlellakae 97 
                                    +++ g+L++ +i+ l  + q+ Ll +l+++e
  gi|91772887|ref|YP_565579.1| 223 HKSHKGVLFIDEINTLRLESQQSLLTALQEKE 254
                                   45789************************964 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05    0.0098       9      46 ..      43      79 ..      35     121 .. 0.81
   2 ?   -1.0   0.0       2.1   1.2e+03      88     116 ..     226     254 ..     194     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                        AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaag 46
                                  +v++ ++s++r +++ G +GtGK+++ ka++e++ +++
  gi|91772887|ref|YP_565579.1| 43 VVKK-AASQRRHVMMIGTPGTGKSMLAKAMAELLPKEE 79
                                  3344.556667999******************998775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                        AAA_30  88 pgtllivDEagmvdtkqlaallkaaekag 116
                                   ++ +l +DE+  +  ++ ++ll+a+++++
  gi|91772887|ref|YP_565579.1| 226 HKGVLFIDEINTLRLESQQSLLTALQEKE 254
                                   457999*******9999999999998865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00031      0.18      16      51 ..      44      78 ..      34      99 .. 0.82
   2 ?    2.2   0.0      0.37   2.1e+02     134     161 ..     225     252 ..     219     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                        AAA_16 16 lervrsgrpelvllsGesGvGKsslvrellralekd 51
                                  +++++s+r + v+ +G +G+GKs l+++ ++ l k+
  gi|91772887|ref|YP_565579.1| 44 VKKAASQR-RHVMMIGTPGTGKSMLAKAMAELLPKE 78
                                  44555555.9******************99877776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.37
                        AAA_16 134 erplvlvlDdlqwadeaslqllaaLlrl 161
                                   +++ vl++D++  ++ +s+q l + l++
  gi|91772887|ref|YP_565579.1| 225 SHKGVLFIDEINTLRLESQQSLLTALQE 252
                                   5668**************9995555544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.012       8      53 ..      36      84 ..      32      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                  HHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEE CS
                          PhoH  8 eQkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvkrii 53
                                  +Q++++e++k    +   v++iG  GtGK++la a+a e+l k++++ i+
  gi|91772887|ref|YP_565579.1| 36 GQEHAVEVVKkaasQRRHVMMIGTPGTGKSMLAKAMA-ELLPKEELEDIM 84
                                  688888888866556779*****************98.666666666654 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 !   15.1   0.0   1.6e-05    0.0092     104     139 ..      41      76 ..      32      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                     Parvo_NS1 104 lawlskqlgkrntvwfyGpantGktnlaeaIakavp 139
                                   + +++k  ++r  v+++G++ tGk++la+a+a+ +p
  gi|91772887|ref|YP_565579.1|  41 VEVVKKAASQRRHVMMIGTPGTGKSMLAKAMAELLP 76 
                                   67889999*************************988 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.4e-05     0.054     107     162 ..      28      85 ..      16     102 .. 0.78
   2 ?   -2.1   0.0       2.7   1.6e+03      39      67 ..     468     496 ..     459     499 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-05
                         T2SSE 107 dlgaeeal.kekiaevlrkavrerglilvsGgTgsGKttllyallkeinks.derivt 162
                                   +l++++   +e+  ev++ka ++r  +++ G+ g+GK+ l+ a+ + ++k+  e i+t
  gi|91772887|ref|YP_565579.1|  28 ELMIDQVIgQEHAVEVVKKAASQRRHVMMIGTPGTGKSMLAKAMAELLPKEeLEDIMT 85 
                                   55555544146777999***9***************************9994566766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                         T2SSE  39 veelekaalerlisriaalakldiseerp 67 
                                   ++++ k+a++ + + i+ ++++dis++ +
  gi|91772887|ref|YP_565579.1| 468 LKDIAKEAVQNVSAVIKKVTGEDISNHDI 496
                                   56788999999999999999999999865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.3e-05     0.037       2      24 ..      54      76 ..      54     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                  v+++G pG+GKs la+ +++ l+
  gi|91772887|ref|YP_565579.1| 54 VMMIGTPGTGKSMLAKAMAELLP 76
                                  89**************9997665 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 ?   12.6   0.0   0.00014     0.082      46      69 ..      50      73 ..      29      83 .. 0.88
   2 ?   -2.8   0.0       7.6   4.4e+03     110     127 ..     228     245 ..     218     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                     IstB_IS21 46 kkenivllGpsGvGKshlaialgv 69
                                  ++  ++++G +G+GKs la a++ 
  gi|91772887|ref|YP_565579.1| 50 QRRHVMMIGTPGTGKSMLAKAMAE 73
                                  567899****************86 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.6
                     IstB_IS21 110 dllilDdlgllpldqaea 127
                                    +l +D++ +l l+++++
  gi|91772887|ref|YP_565579.1| 228 GVLFIDEINTLRLESQQS 245
                                   689999999999987753 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.4e-05     0.054       2      44 ..      55      96 ..      54     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.4e-05
                        AAA_18  2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                  +  GtpG+GK+ lak+ +++l   ++l d+ +  +l++ ++p+
  gi|91772887|ref|YP_565579.1| 55 MMIGTPGTGKSMLAKAMAELL-PKEELEDIMTYPNLEDNNNPK 96
                                  678**************9995.266677777776666666666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00015     0.088       9      39 ..      49      79 ..      42     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                                  ETTSEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  9 kegekvaivGenGaGKStLlkllagllkpte 39
                                  ++ + v ++G  G+GKS L+k++a+ll ++e
  gi|91772887|ref|YP_565579.1| 49 SQRRHVMMIGTPGTGKSMLAKAMAELLPKEE 79
                                  5667899*****************9987754 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014     0.079      53      82 ..      51      80 ..      25      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                        DUF815 53 annvLLwGarGtGKSslvkallneyaeegL 82
                                   ++v+++G+ GtGKS l ka+ + + +e+L
  gi|91772887|ref|YP_565579.1| 51 RRHVMMIGTPGTGKSMLAKAMAELLPKEEL 80
                                  479******************998877776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.019        11       5      28 ..      53      76 ..      49      96 .. 0.86
   2 ?    4.6   0.0     0.055        32      61      82 ..     219     240 ..     215     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                                  -EEEE--TTSSHHHHHHHHHHHTT CS
                         AAA_2  5 silllgptgvGktelakalaellf 28
                                   ++++g+ g+Gk++laka+aell 
  gi|91772887|ref|YP_565579.1| 53 HVMMIGTPGTGKSMLAKAMAELLP 76
                                  57899****************997 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.055
                                   TT-HHHHTTSEEEEETGGG--- CS
                         AAA_2  61 pgyvgaeegGivllDEidKihp 82 
                                    g++ +  +G++++DEi     
  gi|91772887|ref|YP_565579.1| 219 SGDIHKSHKGVLFIDEINTLRL 240
                                   578889999********86655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.14      21      59 ..      29      71 ..      13      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                  EEEEETTS-EEEEEGGGS-.....SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE 21 algkeisgnplvldlkkma....shllvaGatgsGKStalntL 59
                                  ++  +++g+ + ++ +k a     h++ +G++g+GKS   +++
  gi|91772887|ref|YP_565579.1| 29 LMIDQVIGQEHAVEVVKKAasqrRHVMMIGTPGTGKSMLAKAM 71
                                  444455888888888888889999*************987776 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.11      12      35 ..      48      71 ..      40      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                 TrwB_AAD_bind 12 eretqhilivGttGsGKtqalekl 35
                                   + ++h++++Gt G+GK+  ++++
  gi|91772887|ref|YP_565579.1| 48 ASQRRHVMMIGTPGTGKSMLAKAM 71
                                  57899*************877766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00027      0.15       2      22 ..      54      74 ..      53     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00027
                        AAA_28  2 ivitGgestGKTtlleaLaar 22
                                  ++++G+++tGK+ l++a+a+ 
  gi|91772887|ref|YP_565579.1| 54 VMMIGTPGTGKSMLAKAMAEL 74
                                  789***************974 PP

>> Styelin  Styelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00052       0.3      10      41 ..     174     205 ..     171     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00052
                       Styelin  10 vskfYkkhktYikaalsiakhlLGDmtDeefq 41 
                                   vs++ k h  Yi a+   a  lLGD+  + fq
  gi|91772887|ref|YP_565579.1| 174 VSNYQKEHAPYIDATGTHAGALLGDVRHDPFQ 205
                                   99************8877777******99999 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    0.0003      0.18       2      30 ..      53      81 ..      52      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegklp 30
                                   v++ G +G GK++L++ +a+++ +++l+
  gi|91772887|ref|YP_565579.1| 53 HVMMIGTPGTGKSMLAKAMAELLPKEELE 81
                                  6899****************999888765 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.0   0.00059      0.34     109     151 ..      94     153 ..      23     159 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                       DUF1676 109 e....................egRkkkkkkkklkkmllplllalklklklLlplalgllalla 151
                                   +                    e+Rkk+   + + +m++ l+l++++    ++ l+ g++a + 
  gi|91772887|ref|YP_565579.1|  94 NpkirevpagkgreivlahkmEARKKA---QSRNMMMMFLVLGIVMYSFYVGQLLWGIIAAIM 153
                                   233333444544445555555777333...333455555555555888889999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); 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: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 4285.09
//
Query:       gi|91772888|ref|YP_565580.1|  [L=443]
Description: peptidase U62, modulator of DNA gyrase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-68  230.7   0.2    4.1e-68  230.2   0.2    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 !  230.2   0.2   2.3e-72   4.1e-68       1     279 []       6     299 ..       6     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 230.2 bits;  conditional E-value: 2.3e-72
                                   EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-...... CS
                     PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea...... 75 
                                   +++vr+ +++sts+ ++ng++e++s + ++g g r+++gg++gf+++  +   +l+++++ a e+a   ++   +      
  gi|91772888|ref|YP_565580.1|   6 FYDVRMIDGTSTSIILDNGNIEEISVNYSKGCGARALCGGSWGFTTAEGEF--DLKATIDSASELAAQMNSISPKdevklk 84 
                                   589*****************************************9966555..67777777666663333333336666** PP

                                   .................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEE CS
                     PmbA_TldD  76 .................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtr 139
                                                    ++v++eek++ll+++e+   ++ +        ++s++sa +s+   ++++++SeG+d+e++  r
  gi|91772888|ref|YP_565580.1|  85 pvekpviknipiakidpADVPIEEKVQLLKDIEDH--AKMD--------GVSSTSAVYSEASVKVHYISSEGIDCEYSLIR 155
                                   *********************************65..2222........899***************************** PP

                                   EEEEEEEEE..STCS..ET.EEEEEEEESSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHH CS
                     PmbA_TldD 140 vslslsvia.ddggs..gd.gmgggsgyedleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavgha 216
                                   +++ +s++a ++g +  g+ ++ g  g+e +e++d+ ++a+ a e+a+++lea++++ g+ pV+l+pe +g++ heavgha
  gi|91772888|ref|YP_565580.1| 156 TGFAISAVAtENGSYqvGReSRFGVCGFELFEKNDALALARSAGETAVELLEAEQAKGGTLPVILDPELAGVFAHEAVGHA 236
                                   *********666444455545555555588999************************************************ PP

                                   TBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE--- CS
                     PmbA_TldD 217 leadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkny 279
                                    ead vleg+S+l+d+lGe++as+l++i+ddpt +++g+ypfD+EGv +++t++I++GvL++y
  gi|91772888|ref|YP_565580.1| 237 SEADLVLEGSSILADRLGEQIASPLVNIIDDPTLHEYGYYPFDSEGVMSSKTTIIKEGVLNSY 299
                                   *************99*****************99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2808.47
//
Query:       gi|91772889|ref|YP_565581.1|  [L=436]
Description: peptidase U62, modulator of DNA gyrase [Methanococcoides burtonii DSM 6242]
Scores for 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-50  170.0   2.4    1.2e-49  169.7   2.4    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 !  169.7   2.4   6.6e-54   1.2e-49       1     279 []      19     305 ..      19     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 6.6e-54
                                   EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-...... CS
                     PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea...... 75 
                                   eaev+++ + s s  ++++++e+++++ ++g+g+r i +g++gfast++ s   +e+ v+ +v++ak+ ++dpe+      
  gi|91772889|ref|YP_565581.1|  19 EAEVYISYNHSISADIRKNTIESAKENVSQGIGIRSIINGAVGFASTNNVS--RIEDIVNISVSSAKVRESDPEWtslpsn 97 
                                   69*********************************7779*******99999..**********************755554 PP

                                   ..............GGS-HHHHHHHHHHHHHH.CHCST.........TEEEEE.EEEEE......EEE.EEEEEEETTSEE CS
                     PmbA_TldD  76 ..............eevsaeekielleelekalrsadp.........kiensk.garisgvsaslsaskeeklianSeGld 132
                                                 +e+                              +ie +    +++ +s+s s+s+ + li+n++G++
  gi|91772889|ref|YP_565581.1|  98 akypavsgtydkkiSEIG-------------------LddcigltgkMIEGALsVPDVNTTSGSFSTSYNKHLIMNTNGVE 159
                                   444443333222222222...................1333344333222222333899********************** PP

                                   EEEEEEEEEEEEEEEE...STCSETEEEEEEEE.......SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHH CS
                     PmbA_TldD 133 veqtrtrvslslsvia.d.dggsgdgmgggsgy.......edleeedleeiaeeaaekalasleakplppgkypVvlspea 204
                                   + ++ t vs ++ vi+ + d      +++ +++        d+++     i++ a   a++s +  +++p k++V+l+p a
  gi|91772889|ref|YP_565581.1| 160 IVDEGTGVSGFVDVITtKgD------LSTAYDFevsrsldIDVFG-----IGASASSLAIRSQNGISIEPKKTNVILHPFA 229
                                   ****************6644......4445555555444555555.....******************************* PP

                                   HHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                     PmbA_TldD 205 vgsllheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                   + +++++++ ++++ad++++ rS l +k Ge +a + l+i+dd++  gg+ ++  D EG+p+qrt++IenG++k++
  gi|91772889|ref|YP_565581.1| 230 FSDIFENTFEPSIDADNMQKERSSLIGKKGETIATSDLNIIDDGLLeGGIETSISDEEGTPSQRTPIIENGIFKSF 305
                                   *************************88******************99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3065.92
//
Query:       gi|91772890|ref|YP_565582.1|  [L=273]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for 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-21   74.1   0.1    1.6e-20   73.3   0.1    1.4  1  Response_reg  Response regulator receiver domain
    8.8e-13   48.4   0.1    1.6e-12   47.6   0.1    1.5  1  PAS_9         PAS domain
    2.6e-11   43.5   0.0    4.1e-11   42.9   0.0    1.2  1  PAS           PAS fold
    2.4e-07   31.0   0.0    3.3e-07   30.5   0.0    1.2  1  PAS_4         PAS fold
    0.00015   21.7   0.0    0.00041   20.3   0.0    1.8  1  PAS_8         PAS domain
  ------ inclusion threshold ------
      0.013   16.1   0.0      0.026   15.1   0.0    1.5  1  PAS_10        PAS 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 !   73.3   0.1   5.3e-24   1.6e-20       1     111 [.       9     120 ..       9     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 5.3e-24
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH...ESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEEE CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeek...vdlillDinmpg.mdGlellkeireedpelpviil 77 
                                   +l+vdD+p+++ell+ +l   +y ++    +g+eal++l++++   +dl+l+Di++ + mdG+e++++i+ +  ++pv+ +
  gi|91772890|ref|YP_565582.1|   9 ILVVDDEPDNVELLTAYLS-YDY-DIVPSYSGNEALQILENSDqvyPDLVLMDIMLKDgMDGVEAANQIHLKY-DIPVVYI 86 
                                   8*****************9.899.89999**********9999999**********999**********9977.******* PP

                                   ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                   ta+++++ +++a   + ++++ Kpf+++eL++ +
  gi|91772890|ref|YP_565582.1|  87 TAYADDNIMQRAKLTEPFGYILKPFEESELRTNI 120
                                   ******************************9987 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   5.4e-16   1.6e-12       2     104 .]     149     256 ..     148     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 5.4e-16
                         PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlf.....vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                   d+++ +++dg ++ ++N+ a+ llG +  +vlgk++ d+f     +t +  ++ +++++++g     + ++ l++k+++++
  gi|91772890|ref|YP_565582.1| 149 DAMIATDKDG-LIkFINPFAEALLGRNLIDVLGKPLNDVFcvesgETGAIVDDPVKKVIREGMFYGLANQTLLVTKDNTKV 228
                                   5667689***.999****************************999999999999999999999999999************ PP

                         PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                   +v++  sp+k ++++++gi++++ Di++
  gi|91772890|ref|YP_565582.1| 229 PVDIIGSPIKGENENVMGILITFCDISD 256
                                   **************************95 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.4e-14   4.1e-11       5     113 .]     142     254 ..     140     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.4e-14
                                   HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECCCCEEEEC. CS
                           PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda...elaelleqlleqgeesrageisfkl. 81 
                                   ail+++ d+++++D+dg i ++N+ ae llG +  +vlgk+l+d++  e+ +   ++ + +++++++g      + ++ + 
  gi|91772890|ref|YP_565582.1| 142 AILNNTGDAMIATDKDGLIKFINPFAEALLGRNLIDVLGKPLNDVFCVESGEtgaIVDDPVKKVIREGMFYGLANQTLLVt 222
                                   89********************************************998887999***********************999 PP

                                   TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                   +d++++++++  sp+  + +++ g+l ++ di
  gi|91772890|ref|YP_565582.1| 223 KDNTKVPVDIIGSPIKGENENVMGILITFCDI 254
                                   ****************************9887 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.1e-10   3.3e-07       1     110 []     144     259 ..     144     259 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.1e-10
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...daarleralrrvlegeepiefleelll...p 75 
                                   l+++ da ++ d+dg + ++N+ a++l+g+   ++lGk+l +++  e    +a +++++++v++++ ++  +  +ll   +
  gi|91772890|ref|YP_565582.1| 144 LNNTGDAMIATDKDGLIKFINPFAEALLGRNLIDVLGKPLNDVFCVEsgeTGAIVDDPVKKVIREGMFYGLANQTLLvtkD 224
                                   68999*****************9999****************88776688******************999999999999* PP

                         PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                      +++++  +P++ e+  v+g+l+++ Di++r+r
  gi|91772890|ref|YP_565582.1| 225 NTKVPVDIIGSPIKGENENVMGILITFCDISDRKR 259
                                   ***************9999**************97 PP

>> PAS_8  PAS 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   0.00041       3      52 ..     140     190 ..     138     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-07
                         PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvl 52 
                                   l a++++  d+++ +d +++i ++N+ a+ llG +  d++g++l ++++v 
  gi|91772890|ref|YP_565582.1| 140 LTAILNNTGDAMIATDKDGLIKFINPFAEALLGRNlIDVLGKPLNDVFCVE 190
                                   5789************6667*************777778888876665554 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   8.6e-06     0.026       1     105 [.     140     254 ..     140     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                        PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipadv.Grpladi......hpk.kavknveeviealrtgekdevevv 73 
                                   l  +Ln+t  +++  D++  i++ +p a+ l+ ++  dv G pl+d+       +     + v++vi +       +++  
  gi|91772890|ref|YP_565582.1| 140 LTAILNNTGDAMIATDKDGLIKFINPFAEALLGRNLIDVlGKPLNDVfcvesgETGaIVDDPVKKVIREGMFYGLANQTLL 220
                                   5689**********************99999999987755******97755432223556678999988888888888888 PP

                        PAS_10  74 vpkngkwvlvry..lpyrdedgeiaGvvetfvDi 105
                                   v+k+++ v v +  +p++ e++++ G+++tf Di
  gi|91772890|ref|YP_565582.1| 221 VTKDNTKVPVDIigSPIKGENENVMGILITFCDI 254
                                   886666555555338******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1770.66
//
Query:       gi|91772891|ref|YP_565583.1|  [L=2552]
Description: KP-43 peptidase [Methanococcoides burtonii DSM 6242]
Scores for 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-41  141.2   5.7      4e-41  141.2   5.7    2.9  1  Peptidase_S8  Subtilase family
      3e-33  114.7  50.6    0.00074   19.2   0.4   13.0 13  Big_3_3       Bacterial Ig-like domain (group 3)
    4.4e-22   77.7  50.3    5.4e-09   35.8   1.6   10.2 10  PKD           PKD domain
    1.9e-19   69.8  10.8      0.063   13.7   0.0    9.1 10  LIFR_N        Leukemia inhibitory factor receptor N-terminal 
    2.4e-19   70.3  11.0       0.18   11.9   0.0   10.3 10  DUF2057       Uncharacterized protein conserved in bacteria (
    6.8e-14   51.5   8.5        6.8    6.5   0.0   10.6 10  Big_3_4       Domain of unknown function
    3.3e-07   30.6  26.6      0.054   13.8   1.5    6.5  5  fn3           Fibronectin type III domain
    3.4e-07   30.5  49.3        6.5    7.2   0.0   12.9 13  HYR           HYR domain
  ------ inclusion threshold ------
      0.056   13.4  26.6         11    6.1   0.2    8.9  8  Y_Y_Y         Y_Y_Y domain
      0.078   12.6   6.2    1.7e+02    1.8   0.0    6.8  8  DUF2271       Predicted periplasmic protein (DUF2271)
        1.3    8.8   6.5        4.3    7.1   0.2    4.9  4  PKD_3         PKD-like domain
        3.2    7.8  10.8         49    4.0   0.1    5.0  5  YebF          YebF-like protein


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 !  141.2   5.7   2.7e-44     4e-41       1     298 []     248     548 ..     248     548 .. 0.79

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 2.7e-44
                                   -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B...SSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                  Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan.apeeg 80 
                                   g+g +vav+DtG+d++    s ++d e  ++           +a     ++  a+d+ng    HGthvAG +++n   ++g
  gi|91772891|ref|YP_565583.1| 248 GSGQIVAVADTGLDTGFNNASMHDDLEGRID---------GLYAWWGYLNDTGAEDNNG----HGTHVAGSVLGNgNLSSG 315
                                   799**********998888775555555553.........4556666667777777778....************777788 PP

                                   SSB-SSTTSEEE..EEE-SSTTSB-HH...HHHHHH.HHHHHHCT-SEEEE-EE..SCETTCHHCHHHHHHHHHHHH.CC. CS
                                   xxxxxxxxxxxx..xxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx. RF
                  Peptidase_S8  81 ekngvapgakil..svkvldtsggsmetg.telira.ieeaaedkvdvinmslg..estslpktgrsiealainravnkk. 154
                                      g ap+a++   +++  ++ ++s     ++ ++  +++a   +++++++s+g  ++++ +++ ++++   i+ +++++ 
  gi|91772891|ref|YP_565583.1| 316 LYAGMAPEARLVfqALQYDGPTLTSGGLYtPTNLDTlFQQAYDTNARIHSNSWGskDPSQYGNYTDRSQ--NIDSFMWDNp 394
                                   899********96533333333333322223444442555555999********444444444444444..9********* PP

                                   T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES...........TTSSB-TT--B-TT.......-EEEE-S-C CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt...........tegkiapfSsrGpssdgklkpdivapGgni 224
                                   + l+v++aGN+g    +++++ +  +  t+kn++tvga +           + ++ia+fSs+Gp+ d ++kpd+vapG+ i
  gi|91772891|ref|YP_565583.1| 395 DLLIVFAAGNEG----GINNTLTPAA--TAKNALTVGASEnyrpdkgipsdNIDDIAYFSSKGPTDDNRIKPDVVAPGTYI 469
                                   ************....4455555444..448*******************9999*************************** PP

                                   CCCCCCCCHHHTTTHH....EEEE-SHHHCHHHHHHHHHHHHH.HHTT....--HHHHHHHHHCCS-EE......SSSSSS CS
                                   xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 225 vstwsrqsnnsaglss....yqsmsGTSmAsPnaagaaAllls.alpk....ltpetvraallntAqdlgkadniesfaqG 296
                                   vst s+ +n s++       y + sGTSmA+P+ ag aAl+++ + ++     t++ ++a+l+n A dlgk     s aqG
  gi|91772891|ref|YP_565583.1| 470 VSTRSKMPNVSYSWGTvddfYAYNSGTSMATPLTAGTAALVRQyYVDNesinPTAALLKATLINGAADLGKS----SDAQG 546
                                   ********8887766699*************************55555996666666*********999555....99*** PP

                                   TT CS
                                   xx RF
                  Peptidase_S8 297 aG 298
                                   +G
  gi|91772891|ref|YP_565583.1| 547 WG 548
                                   *9 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 ?   -3.1   0.1       3.7   5.5e+03     118     137 ..     735     754 ..     734     758 .. 0.87
   2 ?    1.0   0.1       0.2   2.9e+02      36      76 ..     947     983 ..     913     992 .. 0.73
   3 !   17.8   0.4   1.4e-06     0.002       8      58 ..    1005    1054 ..     998    1069 .. 0.80
   4 !   19.2   0.4   4.9e-07   0.00074       8      76 ..    1090    1153 ..    1083    1162 .. 0.83
   5 !   17.9   0.5   1.2e-06    0.0018       8      58 ..    1175    1224 ..    1168    1239 .. 0.80
   6 !   16.9   0.6   2.5e-06    0.0038       8      58 ..    1260    1309 ..    1253    1324 .. 0.80
   7 !   15.0   0.1   9.9e-06     0.015       8      63 ..    1345    1396 ..    1338    1416 .. 0.75
   8 !   12.8   0.0   4.8e-05     0.071      11      63 ..    1431    1479 ..    1424    1499 .. 0.77
   9 !   12.8   0.0   4.8e-05     0.071      11      63 ..    1514    1562 ..    1507    1582 .. 0.77
  10 !   12.1   0.0   7.6e-05      0.11      11      63 ..    1597    1645 ..    1590    1665 .. 0.77
  11 !   11.9   0.0   8.6e-05      0.13      11      63 ..    1680    1728 ..    1673    1749 .. 0.77
  12 ?    5.0   0.1     0.012        18      11      50 ..    1763    1801 ..    1756    1813 .. 0.71
  13 ?   -3.6   0.3       5.1   7.7e+03      23      50 ..    1951    1978 ..    1933    1992 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.7
                       Big_3_3 118 leegesYtltvkaeDeagNa 137
                                   l+++ +Y l+ k+ D +gN 
  gi|91772891|ref|YP_565583.1| 735 LTANTTYELSTKTVDLTGNI 754
                                   67899*************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.2
                       Big_3_3  36 lstilvdntpPtvsisegkkisdgavvkglenlritladal 76 
                                   ++ +++d t+P++++     + ++ ++++ +++  +++ + 
  gi|91772891|ref|YP_565583.1| 947 TTLVALDITAPVITV----DQPENNAIYTTDKVPLNVTGDE 983
                                   334689*********....7777888888888888887665 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 1.4e-06
                       Big_3_3    8 dlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisd 58  
                                     l +lp+G +n++++a+d  +n+     l ++ +d+t+P++++ + +++++
  gi|91772891|ref|YP_565583.1| 1005 TLPALPDGDHNITIYANDSLGNENSSM-LINFNIDTTAPVITVDQPENNAN 1054
                                    5778****************9986655.55*************44444444 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 4.9e-07
                       Big_3_3    8 dlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladal 76  
                                     l ++p+G +n++++a+d  +n+     l ++ +d+t+P++++    ++ ++ ++++ +++  +++ + 
  gi|91772891|ref|YP_565583.1| 1090 TLPAMPDGDHNITIYANDSLGNENSSM-LINFNIDTTAPVITV----NQPENNAIYTTDKVPLNVTGDE 1153
                                    56789***************9986655.55*************....7888888999999888887665 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 1.2e-06
                       Big_3_3    8 dlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisd 58  
                                     l +lp+G +n++++a+d  +n+     l ++ +d+t+P++++ + +++++
  gi|91772891|ref|YP_565583.1| 1175 TLPALPDGDHNITIYANDSLGNENSSM-LINFNIDTTAPVITVNQPENNAN 1224
                                    5778****************9986655.55*************55555554 PP

  == domain 6  score: 16.9 bits;  conditional E-value: 2.5e-06
                       Big_3_3    8 dlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisd 58  
                                     l ++p+G +n++++a+d  +n+     l ++ +d+t+P++++ + +++++
  gi|91772891|ref|YP_565583.1| 1260 TLPAMPDGDHNITIYANDSLGNENSSM-LINFNIDTTAPVITVNQPENNAN 1309
                                    56789***************9986655.55*************55555554 PP

  == domain 7  score: 15.0 bits;  conditional E-value: 9.9e-06
                       Big_3_3    8 dlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvk 63  
                                     l +lp+G +n++++a+d  +n+     + ++++d+ +Pt++i  + + ++   + 
  gi|91772891|ref|YP_565583.1| 1345 TLPALPDGDHNITIYANDSLGNKNSS--MVNFTIDTITPTITI--DIPEENHNYIS 1396
                                    5778*****************98654..4579***********..44444444444 PP

  == domain 8  score: 12.8 bits;  conditional E-value: 4.8e-05
                       Big_3_3   11 elpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvk 63  
                                    +lp+G++++++ a+d  +n++      ++++d+ +Pt++i  + + ++   + 
  gi|91772891|ref|YP_565583.1| 1431 TLPDGNHSITIIAQDLAGNNASAM--VNFTIDTIAPTITI--DIPEENHNYIS 1479
                                    69****************987655..5699**********..44444444444 PP

  == domain 9  score: 12.8 bits;  conditional E-value: 4.8e-05
                       Big_3_3   11 elpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvk 63  
                                    +lp+G++++++ a+d  +n++      ++++d+ +Pt++i  + + ++   + 
  gi|91772891|ref|YP_565583.1| 1514 TLPDGNHSITIIAQDLAGNNASAM--VNFTIDTIAPTITI--DIPEENHNYIS 1562
                                    69****************987655..5699**********..44444444444 PP

  == domain 10  score: 12.1 bits;  conditional E-value: 7.6e-05
                       Big_3_3   11 elpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvk 63  
                                    +lp+G++++++ a+d  +n+       ++++d+ +Pt++i  + + ++   + 
  gi|91772891|ref|YP_565583.1| 1597 TLPDGNHSITIIAQDLAGNNGSSM--VNFTIDTITPTITI--DIPEENHNYIS 1645
                                    69***************9987654..4699*********9..44444444444 PP

  == domain 11  score: 11.9 bits;  conditional E-value: 8.6e-05
                       Big_3_3   11 elpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvk 63  
                                    +lp+G++++++ a+d  +n+       ++++d+ +Pt++i  + + ++   + 
  gi|91772891|ref|YP_565583.1| 1680 TLPDGNHSITVIAQDLAGNNGSSM--VNFTIDTIAPTITI--DIPEENHNYIS 1728
                                    69**************99987654..4699**********..44444444444 PP

  == domain 12  score: 5.0 bits;  conditional E-value: 0.012
                       Big_3_3   11 elpeGkynlvlaakdtfnnqvtksllstilvdn.tpPtvsi 50  
                                    +lp+G++++++ a+d  +n+    ++  +++d+ +pP+v+ 
  gi|91772891|ref|YP_565583.1| 1763 TLPDGNHSITVIAQDLAGNNGSAMVN--FTIDTiAPPSVTN 1801
                                    68999999999999999998776665..5556526667664 PP

  == domain 13  score: -3.6 bits;  conditional E-value: 5.1
                       Big_3_3   23 akdtfnnqvtksllstilvdntpPtvsi 50  
                                    +++   +++++s +++ ++ + pPtv+ 
  gi|91772891|ref|YP_565583.1| 1951 KTVDIVGNINLSWTNDTATTRNPPTVNF 1978
                                    3333344455555556666666666655 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       4.7   7.1e+03      24      35 ..     477     488 ..     470     504 .. 0.72
   2 ?    0.5   0.1      0.37   5.6e+02      51      64 ..     644     657 ..     630     658 .. 0.87
   3 ?    0.9   0.2      0.28   4.1e+02      39      70 ..     997    1028 ..     967    1029 .. 0.73
   4 ?   -0.0   0.2      0.53     8e+02      53      70 ..    1096    1113 ..    1056    1114 .. 0.69
   5 ?    0.9   0.2      0.28   4.1e+02      38      70 ..    1166    1198 ..    1136    1199 .. 0.73
   6 ?   -0.0   0.2      0.53     8e+02      53      70 ..    1266    1283 ..    1226    1284 .. 0.69
   7 ?    0.8   0.3       0.3   4.5e+02      38      70 ..    1336    1368 ..    1310    1369 .. 0.71
   8 !   31.5   0.6     8e-11   1.2e-07      12      68 ..    1989    2040 ..    1972    2042 .. 0.81
   9 !   35.8   1.6   3.6e-12   5.4e-09      15      68 ..    2075    2123 ..    2067    2125 .. 0.89
  10 !   34.9   0.9   6.8e-12     1e-08      14      65 ..    2157    2203 ..    2146    2205 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.7
                                   S-SEEEEE--SS CS
                           PKD  24 anvtysWdfgdg 35 
                                    nv+ysW + d+
  gi|91772891|ref|YP_565583.1| 477 PNVSYSWGTVDD 488
                                   589999977665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.37
                                   -SSEEEEEEEEEE- CS
                           PKD  51 lspGeYeVtvtasn 64 
                                   +s+G Y+Vtvt sn
  gi|91772891|ref|YP_565583.1| 644 PSTGWYTVTVTGSN 657
                                   68999*******99 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.28
                                    EEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD   39 qvlseptvthtYlspGeYeVtvtasnavgsat 70  
                                      +   ++t+  l  G++++t  a++++g+ +
  gi|91772891|ref|YP_565583.1|  997 IRSFTTNTTLPALPDGDHNITIYANDSLGNEN 1028
                                    445555667777778**************987 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.53
                                    SEEEEEEEEEE-SS-EEE CS
                           PKD   53 pGeYeVtvtasnavgsat 70  
                                     G++++t  a++++g+ +
  gi|91772891|ref|YP_565583.1| 1096 DGDHNITIYANDSLGNEN 1113
                                    69*************987 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.28
                                    EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD   38 vqvlseptvthtYlspGeYeVtvtasnavgsat 70  
                                       +   ++t+  l  G++++t  a++++g+ +
  gi|91772891|ref|YP_565583.1| 1166 EIRSFTTNTTLPALPDGDHNITIYANDSLGNEN 1198
                                    4445556667777778**************987 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 0.53
                                    SEEEEEEEEEE-SS-EEE CS
                           PKD   53 pGeYeVtvtasnavgsat 70  
                                     G++++t  a++++g+ +
  gi|91772891|ref|YP_565583.1| 1266 DGDHNITIYANDSLGNEN 1283
                                    69*************987 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 0.3
                                    EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD   38 vqvlseptvthtYlspGeYeVtvtasnavgsat 70  
                                       +   ++t+  l  G++++t  a++++g+ +
  gi|91772891|ref|YP_565583.1| 1336 EIRSFTTNTTLPALPDGDHNITIYANDSLGNKN 1368
                                    4445556667777778**************976 PP

  == domain 8  score: 31.5 bits;  conditional E-value: 8e-11
                                    EEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                           PKD   12 atvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68  
                                      v+f  ++   a  ++ W fgd   + ++  +++ htY++pG+Y V++ta n++g 
  gi|91772891|ref|YP_565583.1| 1989 LDVQFIDTS--TAAGSWVWIFGD---GNDSNAQNPLHTYAEPGKYSVSLTAINSDGF 2040
                                    445555555..7777999*****...***************************9986 PP

  == domain 9  score: 35.8 bits;  conditional E-value: 3.6e-12
                                    EEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                           PKD   15 aftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68  
                                     f+  +   + +t++Wdfg    + +++e  + htY+ pG+Y+V++++sn++gs
  gi|91772891|ref|YP_565583.1| 2075 KFEDLS--SNALTWEWDFGE---GNTSTEIDPVHTYTVPGTYNVSLNVSNYDGS 2123
                                    555555..7889********...*****************************98 PP

  == domain 10  score: 34.9 bits;  conditional E-value: 6.8e-12
                                    EEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-S CS
                           PKD   14 vaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasna 65  
                                    v ft ++   + +   W+fgd   + ++s ++++htY ++G+Y+V++++sna
  gi|91772891|ref|YP_565583.1| 2157 VSFTDRS--INATERVWNFGD---GNTSSDRHPSHTYVAAGTYTVSLNVSNA 2203
                                    4455555..5667778*****...***************************8 PP

>> LIFR_N  Leukemia inhibitory factor receptor N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.2e-05     0.063      41      77 ..     998    1034 ..     994    1035 .. 0.89
   2 !   12.2   0.0   0.00012      0.18      41      77 ..    1083    1119 ..    1078    1120 .. 0.89
   3 !   13.7   0.0   4.2e-05     0.063      41      77 ..    1168    1204 ..    1164    1205 .. 0.89
   4 !   12.2   0.0   0.00012      0.18      41      77 ..    1253    1289 ..    1248    1290 .. 0.89
   5 !   13.3   0.0   5.5e-05     0.082      41      73 ..    1338    1370 ..    1333    1377 .. 0.81
   6 ?   -0.7   0.0       1.3     2e+03      51      73 ..    1431    1453 ..    1426    1458 .. 0.86
   7 ?   -0.7   0.0       1.3     2e+03      51      73 ..    1514    1536 ..    1509    1541 .. 0.86
   8 ?   -0.7   0.0       1.2   1.9e+03      51      72 ..    1597    1618 ..    1592    1626 .. 0.72
   9 ?   -2.0   0.0       3.2   4.8e+03      51      72 ..    1680    1701 ..    1677    1709 .. 0.70
  10 ?   -2.9   0.0       6.2   9.3e+03      51      72 ..    1763    1784 ..    1761    1790 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                        LIFR_N   41 rlektnikipalspgdheitinslhdfgssiskFiln 77  
                                    r+ +tn+ +pal+ gdh+iti +  + g+  s   +n
  gi|91772891|ref|YP_565583.1|  998 RSFTTNTTLPALPDGDHNITIYANDSLGNENSSMLIN 1034
                                    56689********************999999887766 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                        LIFR_N   41 rlektnikipalspgdheitinslhdfgssiskFiln 77  
                                    r+ +tn+ +pa++ gdh+iti +  + g+  s   +n
  gi|91772891|ref|YP_565583.1| 1083 RSFTTNTTLPAMPDGDHNITIYANDSLGNENSSMLIN 1119
                                    56689********************999999887766 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 4.2e-05
                        LIFR_N   41 rlektnikipalspgdheitinslhdfgssiskFiln 77  
                                    r+ +tn+ +pal+ gdh+iti +  + g+  s   +n
  gi|91772891|ref|YP_565583.1| 1168 RSFTTNTTLPALPDGDHNITIYANDSLGNENSSMLIN 1204
                                    56689********************999999887766 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00012
                        LIFR_N   41 rlektnikipalspgdheitinslhdfgssiskFiln 77  
                                    r+ +tn+ +pa++ gdh+iti +  + g+  s   +n
  gi|91772891|ref|YP_565583.1| 1253 RSFTTNTTLPAMPDGDHNITIYANDSLGNENSSMLIN 1289
                                    56689********************999999887766 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 5.5e-05
                        LIFR_N   41 rlektnikipalspgdheitinslhdfgssisk 73  
                                    r+ +tn+ +pal+ gdh+iti +  + g+  s 
  gi|91772891|ref|YP_565583.1| 1338 RSFTTNTTLPALPDGDHNITIYANDSLGNKNSS 1370
                                    56689****************988888776554 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 1.3
                        LIFR_N   51 alspgdheitinslhdfgssisk 73  
                                    +l+ g+h iti ++  +g+  s 
  gi|91772891|ref|YP_565583.1| 1431 TLPDGNHSITIIAQDLAGNNASA 1453
                                    6889*********9999998775 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 1.3
                        LIFR_N   51 alspgdheitinslhdfgssisk 73  
                                    +l+ g+h iti ++  +g+  s 
  gi|91772891|ref|YP_565583.1| 1514 TLPDGNHSITIIAQDLAGNNASA 1536
                                    6889*********9999998775 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 1.2
                        LIFR_N   51 alspgdheitinslhdfgssis 72  
                                    +l+ g+h iti ++  +g+  s
  gi|91772891|ref|YP_565583.1| 1597 TLPDGNHSITIIAQDLAGNNGS 1618
                                    6889*******99887665433 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 3.2
                        LIFR_N   51 alspgdheitinslhdfgssis 72  
                                    +l+ g+h it+ ++  +g+  s
  gi|91772891|ref|YP_565583.1| 1680 TLPDGNHSITVIAQDLAGNNGS 1701
                                    5889******998876665433 PP

  == domain 10  score: -2.9 bits;  conditional E-value: 6.2
                        LIFR_N   51 alspgdheitinslhdfgssis 72  
                                    +l+ g+h it+ ++  +g+  s
  gi|91772891|ref|YP_565583.1| 1763 TLPDGNHSITVIAQDLAGNNGS 1784
                                    5789*******99988877655 PP

>> DUF2057  Uncharacterized protein conserved in bacteria (DUF2057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.099   1.5e+02      13      54 ..     992    1030 ..     990    1059 .. 0.68
   2 ?    0.7   0.0      0.35   5.2e+02      13      54 ..    1077    1115 ..    1075    1141 .. 0.66
   3 ?    2.7   0.1     0.083   1.2e+02      13      54 ..    1162    1200 ..    1160    1230 .. 0.66
   4 ?    1.1   0.1      0.25   3.8e+02      13      54 ..    1247    1285 ..    1245    1315 .. 0.61
   5 ?    2.8   0.0     0.079   1.2e+02      13      54 ..    1332    1370 ..    1330    1394 .. 0.72
   6 !   10.3   0.0   0.00039      0.58      17      60 ..    1418    1452 ..    1404    1477 .. 0.75
   7 !   10.3   0.0   0.00039      0.58      17      60 ..    1501    1535 ..    1487    1560 .. 0.75
   8 !   11.1   0.0   0.00021      0.32      17      54 ..    1584    1619 ..    1570    1643 .. 0.78
   9 !   11.9   0.0   0.00012      0.18      17      54 ..    1667    1702 ..    1653    1726 .. 0.78
  10 !   10.5   0.0   0.00034      0.51      17      50 ..    1750    1783 ..    1736    1793 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.099
                       DUF2057   13 vdgqkvksslfkgaksltLtpGkhqivvrykdlfkddsdsds 54  
                                    ++g ++  s++ +++   L++G h i++  +d + +++  +s
  gi|91772891|ref|YP_565583.1|  992 INGTEIR-SFTTNTTLPALPDGDHNITIYANDSLGNEN--SS 1030
                                    7999999.555555666789**************3332..22 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.35
                       DUF2057   13 vdgqkvksslfkgaksltLt...pGkhqivvrykdlfkddsdsds 54  
                                    ++g ++  s+   +++ tL+   +G h i++  +d +  ++ ++s
  gi|91772891|ref|YP_565583.1| 1077 INGTEIR-SF---TTNTTLPampDGDHNITIYANDSL--GNENSS 1115
                                    7899999.33...3444443344**************..333222 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.083
                       DUF2057   13 vdgqkvksslfkgaksltLtpGkhqivvrykdlfkddsdsds 54  
                                    ++g ++  s++ +++   L++G h i++  +d +  ++ ++s
  gi|91772891|ref|YP_565583.1| 1162 INGTEIR-SFTTNTTLPALPDGDHNITIYANDSL--GNENSS 1200
                                    7999999.555555666789**************..333222 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.25
                       DUF2057   13 vdgqkvksslfkgaksltLt...pGkhqivvrykdlfkddsdsds 54  
                                    ++g ++  s+   +++ tL+   +G h i++  +d +  ++ ++s
  gi|91772891|ref|YP_565583.1| 1247 INGTEIR-SF---TTNTTLPampDGDHNITIYANDSL--GNENSS 1285
                                    7899999.33...3444443344**************..333222 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.079
                       DUF2057   13 vdgqkvksslfkgaksltLtpGkhqivvrykdlfkddsdsds 54  
                                    ++g ++  s++ +++   L++G h i++  +d +  +++++s
  gi|91772891|ref|YP_565583.1| 1332 INGTEIR-SFTTNTTLPALPDGDHNITIYANDSL--GNKNSS 1370
                                    7999999.555555666789**************..444333 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00039
                       DUF2057   17 kvksslfkgaksltLtpGkhqivvrykdlfkddsdsdsqdlvkS 60  
                                       +s+f+g++sltL++G+h i++  +dl   ++++       S
  gi|91772891|ref|YP_565583.1| 1418 NTGNSIFSGNRSLTLPDGNHSITIIAQDLA--GNNA-------S 1452
                                    5679********************999999..4442.......3 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.00039
                       DUF2057   17 kvksslfkgaksltLtpGkhqivvrykdlfkddsdsdsqdlvkS 60  
                                       +s+f+g++sltL++G+h i++  +dl   ++++       S
  gi|91772891|ref|YP_565583.1| 1501 NTGNSIFSGNRSLTLPDGNHSITIIAQDLA--GNNA-------S 1535
                                    5679********************999999..4442.......3 PP

  == domain 8  score: 11.1 bits;  conditional E-value: 0.00021
                       DUF2057   17 kvksslfkgaksltLtpGkhqivvrykdlfkddsdsds 54  
                                       +s+f+g++sltL++G+h i++  +dl   +++++s
  gi|91772891|ref|YP_565583.1| 1584 NTGNSIFSGNRSLTLPDGNHSITIIAQDLA--GNNGSS 1619
                                    5679************************99..444344 PP

  == domain 9  score: 11.9 bits;  conditional E-value: 0.00012
                       DUF2057   17 kvksslfkgaksltLtpGkhqivvrykdlfkddsdsds 54  
                                       +s+f+g++sltL++G+h i+v  +dl  ++++  s
  gi|91772891|ref|YP_565583.1| 1667 NTGNSIFSGNRSLTLPDGNHSITVIAQDLAGNNGS--S 1702
                                    5679*************************944443..3 PP

  == domain 10  score: 10.5 bits;  conditional E-value: 0.00034
                       DUF2057   17 kvksslfkgaksltLtpGkhqivvrykdlfkdds 50  
                                       +s+f+g++sltL++G+h i+v  +dl  +++
  gi|91772891|ref|YP_565583.1| 1750 NTGNSIFSGNQSLTLPDGNHSITVIAQDLAGNNG 1783
                                    5679********************9999994443 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0094        14      25      62 ..    1003    1040 ..     985    1084 .. 0.77
   2 ?    4.6   0.0     0.017        26      25      62 ..    1088    1125 ..    1070    1168 .. 0.78
   3 !    5.5   0.0     0.009        14      25      63 ..    1173    1211 ..    1154    1252 .. 0.77
   4 ?    4.9   0.0     0.014        21      25      63 ..    1258    1296 ..    1240    1339 .. 0.76
   5 !    6.5   0.0    0.0045       6.8      25     101 ..    1343    1422 ..    1324    1426 .. 0.71
   6 !    5.4   0.0    0.0098        15      33     101 ..    1434    1505 ..    1429    1509 .. 0.73
   7 ?    5.4   0.0      0.01        15      33     101 ..    1517    1588 ..    1513    1592 .. 0.72
   8 ?    2.7   0.0     0.068     1e+02      33     101 ..    1600    1671 ..    1596    1675 .. 0.66
   9 ?    2.5   0.0     0.077   1.2e+02      33     101 ..    1683    1754 ..    1678    1758 .. 0.66
  10 ?    0.6   0.0      0.31   4.6e+02      33      50 ..    1766    1783 ..    1761    1795 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0094
                       Big_3_4   25 nvpvPldedGeyvvellaedeaGnqayiakllyvvdie 62  
                                    n ++P + dG++ + ++a+d  Gn      + + +d+ 
  gi|91772891|ref|YP_565583.1| 1003 NTTLPALPDGDHNITIYANDSLGNENSSMLINFNIDTT 1040
                                    7899********************98777777777765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                       Big_3_4   25 nvpvPldedGeyvvellaedeaGnqayiakllyvvdie 62  
                                    n ++P   dG++ + ++a+d  Gn      + + +d+ 
  gi|91772891|ref|YP_565583.1| 1088 NTTLPAMPDGDHNITIYANDSLGNENSSMLINFNIDTT 1125
                                    779999******************98777777777665 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.009
                       Big_3_4   25 nvpvPldedGeyvvellaedeaGnqayiakllyvvdien 63  
                                    n ++P + dG++ + ++a+d  Gn      + + +d+  
  gi|91772891|ref|YP_565583.1| 1173 NTTLPALPDGDHNITIYANDSLGNENSSMLINFNIDTTA 1211
                                    7899********************987777777777654 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.014
                       Big_3_4   25 nvpvPldedGeyvvellaedeaGnqayiakllyvvdien 63  
                                    n ++P   dG++ + ++a+d  Gn      + + +d+  
  gi|91772891|ref|YP_565583.1| 1258 NTTLPAMPDGDHNITIYANDSLGNENSSMLINFNIDTTA 1296
                                    779999******************987777777777654 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.0045
                       Big_3_4   25 nvpvPldedGeyvvellaedeaGnqayiakllyvvdie....nicvevrpldylsekleteftieavapkitiellvtg 99  
                                    n ++P + dG++ + ++a+d  Gn+   + + +++d+      i +  +  +y+s+++  + t++  ++k   ++  tg
  gi|91772891|ref|YP_565583.1| 1343 NTTLPALPDGDHNITIYANDSLGNKNS-SMVNFTIDTItptiTIDIPEENHNYISKMIWLNATVDEDIAKWWYNINNTG 1420
                                    7899*******************9863.445566664311013444445666888888888888888877777777777 PP

                       Big_3_4  100 kr 101 
                                      
  gi|91772891|ref|YP_565583.1| 1421 NS 1422
                                    65 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.0098
                       Big_3_4   33 dGeyvvellaedeaGnqayiakllyvvdie..nicvev..rpldylsekleteftieavapkitiellvtgkr 101 
                                    dG++ + ++a+d aGn a  a + +++d+    i++++  +  +y+s+++  + t++  ++k   ++  tg  
  gi|91772891|ref|YP_565583.1| 1434 DGNHSITIIAQDLAGNNAS-AMVNFTIDTIapTITIDIpeENHNYISKMIWLNATVDEDIAKWWYNINNTGNS 1505
                                    8999************995.67788888641234444321566688888888888888888887777777765 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.01
                       Big_3_4   33 dGeyvvellaedeaGnqayiakllyvvdie..nicvev..rpldylsekleteftieavapkitiellvtgkr 101 
                                    dG++ + ++a+d aGn a  a + +++d+    i++++  +  +y+s+++  + t++  ++k   ++  tg  
  gi|91772891|ref|YP_565583.1| 1517 DGNHSITIIAQDLAGNNAS-AMVNFTIDTIapTITIDIpeENHNYISKMIWLNATVDEDIAKWWYNINNTGNS 1588
                                    8999************995.67788888641234444321566688888888888888888887777777765 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.068
                       Big_3_4   33 dGeyvvellaedeaGnqayiakllyvvdie....nicvevrpldylsekleteftieavapkitiellvtgkr 101 
                                    dG++ + ++a+d aGn    + + +++d+      i +  +  +y+s+++  + t++  ++k   ++  tg  
  gi|91772891|ref|YP_565583.1| 1600 DGNHSITIIAQDLAGNNGS-SMVNFTIDTItptiTIDIPEENHNYISKMIWLNATVDEDIAKWWYNINNTGNS 1671
                                    89999**********9863.34455555431101344444556688888777777777777777777777665 PP

  == domain 9  score: 2.5 bits;  conditional E-value: 0.077
                       Big_3_4   33 dGeyvvellaedeaGnqayiakllyvvdie....nicvevrpldylsekleteftieavapkitiellvtgkr 101 
                                    dG++ + ++a+d aGn    + + +++d+      i +  +  +y+s+++  + t++  ++k   ++  tg  
  gi|91772891|ref|YP_565583.1| 1683 DGNHSITVIAQDLAGNNGS-SMVNFTIDTIaptiTIDIPEENHNYISKMIWLNATVDEDIAKWWYNINNTGNS 1754
                                    89999**********9863.34455655431101344444556677777777777777777777777766665 PP

  == domain 10  score: 0.6 bits;  conditional E-value: 0.31
                       Big_3_4   33 dGeyvvellaedeaGnqa 50  
                                    dG++ + ++a+d aGn  
  gi|91772891|ref|YP_565583.1| 1766 DGNHSITVIAQDLAGNNG 1783
                                    8999************75 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.6   8.3e-05      0.12       5      76 ..     685     748 ..     681     757 .. 0.76
   2 !   13.3   1.9   5.5e-05     0.083       3      80 ..     866     935 ..     864     940 .. 0.83
   3 ?    3.8   0.2     0.048        71       2      36 ..    1798    1829 ..    1797    1866 .. 0.84
   4 !   13.8   1.5   3.6e-05     0.054       3      79 ..    1888    1956 ..    1886    1962 .. 0.78
   5 ?   -1.6   0.1       2.5   3.7e+03       3      23 ..    2071    2091 ..    2069    2102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                                   EEEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEE CS
                           fn3   5 nlsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqav 76 
                                   +l  s++++t ++  W+ p    +p+ + +  y +        + +v++tt+ +++tgL+++t+Ye++ ++v
  gi|91772891|ref|YP_565583.1| 685 DLATSDRGTTWINWAWNNP---IDPDFNHTMLYLDN-----VFRTNVSNTTKFYNVTGLTANTTYELSTKTV 748
                                   5555666666666666666...66666666666655.....67899********************987776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.5e-05
                                   ECEEEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSE CS
                           fn3   3 PsnlsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavnggg 80 
                                   ++nl+ s+++ t ++++W+ p    + + + +  y +        e + ++tt+ +++tgL+++t+Y ++ ++v  +g
  gi|91772891|ref|YP_565583.1| 866 VTNLTTSDRGVTWINMTWNNP---IDLDFNHTMLYIDG-----VFEKNTSNTTNFYNVTGLTANTTYGFSTKTVDIAG 935
                                   788999999999999999999...67777777777666.....7899**********************998887665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.048
                                    CECEEEEEEESSSEEEEEEE-CSSSSSTEEEEEEE CS
                           fn3    2 aPsnlsvsevtstsltvsWeppkdgggpitgYeve 36  
                                    +++nls s+++st +t +W +p   +++ ++Y+  
  gi|91772891|ref|YP_565583.1| 1798 SVTNLSESNNGSTWITWTWIKP---HDDESYYTMV 1829
                                    689*******************...6666666555 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 3.6e-05
                                    ECEEEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETS CS
                           fn3    3 PsnlsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngg 79  
                                    ++nls s++++t ++ +W+ p   + ++ + ++ y + g        +v+++tt +++tgL+ +t Ye++ ++v  +
  gi|91772891|ref|YP_565583.1| 1888 VTNLSESARGPTWISWTWTNP--IDNDFNHTTI-YVNNG-----FLANVSKDTTFYNVTGLTTNTAYEFSTKTVDIV 1956
                                    788999999999999999999..3555555555.55553.....3469*********************98888655 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.5
                                    ECEEEEEEESSSEEEEEEE-C CS
                           fn3    3 PsnlsvsevtstsltvsWepp 23  
                                    P  +++++ +s+ lt +W+  
  gi|91772891|ref|YP_565583.1| 2071 PLSVKFEDLSSNALTWEWDFG 2091
                                    778999999999999999855 PP

>> HYR  HYR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2      0.03        45       2      74 ..     953    1029 ..     952    1034 .. 0.77
   2 ?    3.5   0.5     0.061        91       2      74 ..    1038    1114 ..    1037    1118 .. 0.72
   3 !    6.4   0.4    0.0076        11       2      74 ..    1123    1199 ..    1122    1204 .. 0.81
   4 ?    4.0   0.5     0.041        62       2      74 ..    1208    1284 ..    1207    1288 .. 0.73
   5 ?    5.9   0.9     0.011        17       2      79 ..    1293    1374 ..    1292    1377 .. 0.73
   6 !    7.2   0.0    0.0043       6.5      53      80 ..    1431    1458 ..    1401    1460 .. 0.87
   7 !    7.2   0.0    0.0044       6.5      53      80 ..    1514    1541 ..    1485    1543 .. 0.87
   8 ?    5.8   0.0     0.012        18      53      79 ..    1597    1623 ..    1568    1626 .. 0.86
   9 ?    5.9   0.0     0.011        16      53      79 ..    1680    1706 ..    1650    1709 .. 0.86
  10 !    6.5   0.0    0.0071        11      53      79 ..    1763    1789 ..    1729    1792 .. 0.82
  11 ?   -2.7   0.0       5.2   7.8e+03      24      45 ..    1900    1921 ..    1893    1924 .. 0.82
  12 ?   -2.2   0.1       3.6   5.4e+03       4      29 ..    1972    1993 ..    1970    2000 .. 0.70
  13 ?   -1.3   0.2       1.9   2.8e+03       8      50 ..    2257    2299 ..    2255    2304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.03
                           HYR    2 DttpPtvkcpnn.ivrtvelgkstvevffteptakdnsg...qaalvsrtaqpGdsFpvGsttVtyvaeDesgneas 74  
                                    D+t P++++ +     + + +k   +v  +e++a+       + ++  +t+     +p G++++t  a+D  gne+s
  gi|91772891|ref|YP_565583.1|  953 DITAPVITVDQPeNNAIYTTDKVPLNVTGDETVANWWYKingTEIRSFTTNTTLPALPDGDHNITIYANDSLGNENS 1029
                                    8888888776653466678889999999999999854443236677777777778999*****************97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.061
                           HYR    2 DttpPtvkcpnn.ivrtvelgkstvevffteptakdnsg...qaalvsrtaqpGdsFpvGsttVtyvaeDesgneas 74  
                                    Dtt P++++ +       +  k   +v  +e++a+       + ++  +t+     +p G++++t  a+D  gne+s
  gi|91772891|ref|YP_565583.1| 1038 DTTAPVITVDQPeNNANYTTHKVPLNVTGDETVANWWYKingTEIRSFTTNTTLPAMPDGDHNITIYANDSLGNENS 1114
                                    89999887755433455556677778888888887544432266666677777778999****************97 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0076
                           HYR    2 DttpPtvkcpnn.ivrtvelgkstvevffteptakdnsg...qaalvsrtaqpGdsFpvGsttVtyvaeDesgneas 74  
                                    Dtt P++++ +     + + +k   +v  +e++a+       + ++  +t+     +p G++++t  a+D  gne+s
  gi|91772891|ref|YP_565583.1| 1123 DTTAPVITVNQPeNNAIYTTDKVPLNVTGDETVANWWYKingTEIRSFTTNTTLPALPDGDHNITIYANDSLGNENS 1199
                                    99***998876644677789999*********9986544333777777777788899******************97 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.041
                           HYR    2 DttpPtvkcpnn.ivrtvelgkstvevffteptakdnsg...qaalvsrtaqpGdsFpvGsttVtyvaeDesgneas 74  
                                    Dtt P++++ +       +  k   +v  +e++a+       + ++  +t+     +p G++++t  a+D  gne+s
  gi|91772891|ref|YP_565583.1| 1208 DTTAPVITVNQPeNNANYTTHKVPLNVTGDETVANWWYKingTEIRSFTTNTTLPAMPDGDHNITIYANDSLGNENS 1284
                                    99999987755433555566677788888899988554432366666677777778999****************97 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.011
                           HYR    2 DttpPtvkcpnn.ivrtvelgkstvevffteptakdnsg...qaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCk 76  
                                    Dtt P++++ +       +  k   +v  +e++a+       + ++  +t+     +p G++++t  a+D  gn++s  
  gi|91772891|ref|YP_565583.1| 1293 DTTAPVITVNQPeNNANYTTHKVPLNVTGDETVANWWYKingTEIRSFTTNTTLPALPDGDHNITIYANDSLGNKNSSM 1371
                                    999999977554335555666777888889999885444323677777777777899*******************876 PP

                           HYR   77 FtV 79  
                                    ++ 
  gi|91772891|ref|YP_565583.1| 1372 VNF 1374
                                    554 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.0043
                           HYR   53 sFpvGsttVtyvaeDesgneasCkFtVt 80  
                                    ++p G++++t +a+D +gn+as  ++ t
  gi|91772891|ref|YP_565583.1| 1431 TLPDGNHSITIIAQDLAGNNASAMVNFT 1458
                                    6899*****************8766544 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.0044
                           HYR   53 sFpvGsttVtyvaeDesgneasCkFtVt 80  
                                    ++p G++++t +a+D +gn+as  ++ t
  gi|91772891|ref|YP_565583.1| 1514 TLPDGNHSITIIAQDLAGNNASAMVNFT 1541
                                    6899*****************8766544 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.012
                           HYR   53 sFpvGsttVtyvaeDesgneasCkFtV 79  
                                    ++p G++++t +a+D +gn++s  ++ 
  gi|91772891|ref|YP_565583.1| 1597 TLPDGNHSITIIAQDLAGNNGSSMVNF 1623
                                    6899****************9766554 PP

  == domain 9  score: 5.9 bits;  conditional E-value: 0.011
                           HYR   53 sFpvGsttVtyvaeDesgneasCkFtV 79  
                                    ++p G++++t +a+D +gn++s  ++ 
  gi|91772891|ref|YP_565583.1| 1680 TLPDGNHSITVIAQDLAGNNGSSMVNF 1706
                                    6899****************9766554 PP

  == domain 10  score: 6.5 bits;  conditional E-value: 0.0071
                           HYR   53 sFpvGsttVtyvaeDesgneasCkFtV 79  
                                    ++p G++++t +a+D +gn++s  ++ 
  gi|91772891|ref|YP_565583.1| 1763 TLPDGNHSITVIAQDLAGNNGSAMVNF 1789
                                    6899****************9876554 PP

  == domain 11  score: -2.7 bits;  conditional E-value: 5.2
                           HYR   24 tvevffteptakdnsgqaalvs 45  
                                      ++ +t+p  +d  ++++ v 
  gi|91772891|ref|YP_565583.1| 1900 WISWTWTNPIDNDFNHTTIYVN 1921
                                    56899*********99887765 PP

  == domain 12  score: -2.2 bits;  conditional E-value: 3.6
                           HYR    4 tpPtvkcpnnivrtvelgkstvevff 29  
                                    +pPtv+ ++n    v+ gk+   v f
  gi|91772891|ref|YP_565583.1| 1972 NPPTVNFTSN----VTSGKQPLDVQF 1993
                                    79***99999....566666555555 PP

  == domain 13  score: -1.3 bits;  conditional E-value: 1.9
                           HYR    8 vkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqp 50  
                                    +++++ ++++ ++ +    + + ++ta+ n+g+++ ++++++ 
  gi|91772891|ref|YP_565583.1| 2257 MHIIKDVEKSFTFTNEMIDITYINVTADLNVGNVKAIVESLNT 2299
                                    5677889999999999****************99988877665 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0072        11      30      65 ..    1003    1037 ..     987    1038 .. 0.79
   2 ?    3.8   0.1     0.037        56      30      65 ..    1088    1122 ..    1072    1123 .. 0.79
   3 ?    6.1   0.2    0.0072        11      30      65 ..    1173    1207 ..    1157    1208 .. 0.79
   4 ?    3.8   0.1     0.037        56      30      65 ..    1258    1292 ..    1242    1293 .. 0.79
   5 ?    5.6   0.2      0.01        16      30      65 ..    1343    1376 ..    1327    1377 .. 0.77
   6 ?   -0.9   0.1       1.1   1.6e+03      17      37 ..    1868    1892 ..    1867    1893 .. 0.89
   7 ?   -2.0   0.0       2.4   3.6e+03      36      52 ..    2023    2039 ..    2012    2050 .. 0.82
   8 ?   -2.0   0.1       2.4   3.6e+03      30      51 ..    2183    2204 ..    2171    2214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0072
                                    EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                         Y_Y_Y   30 easytnlppGdYtlkVkakdndgqwnyditslsfti 65  
                                    + +   lp Gd  ++++a d++g++n+    ++f+i
  gi|91772891|ref|YP_565583.1| 1003 NTTLPALPDGDHNITIYANDSLGNENSS-MLINFNI 1037
                                    677789********************98.8888877 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.037
                                    EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                         Y_Y_Y   30 easytnlppGdYtlkVkakdndgqwnyditslsfti 65  
                                    + +    p Gd  ++++a d++g++n+    ++f+i
  gi|91772891|ref|YP_565583.1| 1088 NTTLPAMPDGDHNITIYANDSLGNENSS-MLINFNI 1122
                                    56667789******************98.8888877 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0072
                                    EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                         Y_Y_Y   30 easytnlppGdYtlkVkakdndgqwnyditslsfti 65  
                                    + +   lp Gd  ++++a d++g++n+    ++f+i
  gi|91772891|ref|YP_565583.1| 1173 NTTLPALPDGDHNITIYANDSLGNENSS-MLINFNI 1207
                                    677789********************98.8888877 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.037
                                    EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                         Y_Y_Y   30 easytnlppGdYtlkVkakdndgqwnyditslsfti 65  
                                    + +    p Gd  ++++a d++g++n+    ++f+i
  gi|91772891|ref|YP_565583.1| 1258 NTTLPAMPDGDHNITIYANDSLGNENSS-MLINFNI 1292
                                    56667789******************98.8888877 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.01
                                    EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                         Y_Y_Y   30 easytnlppGdYtlkVkakdndgqwnyditslsfti 65  
                                    + +   lp Gd  ++++a d++g++n+    ++fti
  gi|91772891|ref|YP_565583.1| 1343 NTTLPALPDGDHNITIYANDSLGNKNSS--MVNFTI 1376
                                    677789*******************985..777776 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 1.1
                                    TESSEEEESSTS.....EEEEES-- CS
                         Y_Y_Y   17 idkeWveasdysq....easytnlp 37  
                                    i+  W+++s++++     as tnl+
  gi|91772891|ref|YP_565583.1| 1868 INSAWINSSASTMntlpPASVTNLS 1892
                                    7889*******99999999999996 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 2.4
                                    --SEEEEEEEEEEETTS CS
                         Y_Y_Y   36 lppGdYtlkVkakdndg 52  
                                     +pG+Y + + a+++dg
  gi|91772891|ref|YP_565583.1| 2023 AEPGKYSVSLTAINSDG 2039
                                    58******999999775 PP

  == domain 8  score: -2.0 bits;  conditional E-value: 2.4
                                    EEEEES--SEEEEEEEEEEETT CS
                         Y_Y_Y   30 easytnlppGdYtlkVkakdnd 51  
                                    + s t   +G+Yt+ + +++ +
  gi|91772891|ref|YP_565583.1| 2183 HPSHTYVAAGTYTVSLNVSNAK 2204
                                    556788999****999988754 PP

>> DUF2271  Predicted periplasmic protein (DUF2271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       6.5   9.7e+03      51      85 ..    1072    1107 ..    1069    1111 .. 0.77
   2 ?   -3.9   0.0       6.5   9.7e+03      51      85 ..    1242    1277 ..    1239    1281 .. 0.77
   3 ?   -3.6   0.0       5.4   8.1e+03      52      86 ..    1328    1363 ..    1325    1376 .. 0.70
   4 ?    1.5   0.0      0.14   2.1e+02      47      90 ..    1407    1450 ..    1381    1457 .. 0.87
   5 ?    1.5   0.0      0.15   2.2e+02      47      90 ..    1490    1533 ..    1466    1540 .. 0.88
   6 ?    0.9   0.0      0.22   3.3e+02      47      88 ..    1573    1614 ..    1550    1618 .. 0.88
   7 ?    1.2   0.0      0.17   2.6e+02      47      88 ..    1656    1697 ..    1632    1701 .. 0.88
   8 ?    1.8   0.0      0.12   1.7e+02      47      89 ..    1739    1781 ..    1715    1785 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6.5
                       DUF2271   51 qWwrksg.rklkeeidgvsgaTrapGkyklkvdekd 85  
                                    +Ww k + ++ ++ +   + +  + G++++++  +d
  gi|91772891|ref|YP_565583.1| 1072 NWWYKINgTEIRSFTTNTTLPAMPDGDHNITIYAND 1107
                                    566665559988899999999999999999887665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.5
                       DUF2271   51 qWwrksg.rklkeeidgvsgaTrapGkyklkvdekd 85  
                                    +Ww k + ++ ++ +   + +  + G++++++  +d
  gi|91772891|ref|YP_565583.1| 1242 NWWYKINgTEIRSFTTNTTLPAMPDGDHNITIYAND 1277
                                    566665559988899999999999999999887665 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.4
                       DUF2271   52 Wwrksg.rklkeeidgvsgaTrapGkyklkvdekdd 86  
                                    Ww k + ++ ++ +   + +  + G++++++  +d+
  gi|91772891|ref|YP_565583.1| 1328 WWYKINgTEIRSFTTNTTLPALPDGDHNITIYANDS 1363
                                    555444477777777888888888888888766665 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.14
                       DUF2271   47 kdlrqWwrksgrklkeeidgvsgaTrapGkyklkvdekddklkk 90  
                                    +d+ +Ww + +++ ++  +g  + T + G++++++  +d ++++
  gi|91772891|ref|YP_565583.1| 1407 EDIAKWWYNINNTGNSIFSGNRSLTLPDGNHSITIIAQDLAGNN 1450
                                    689********99889*******************999987765 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.15
                       DUF2271   47 kdlrqWwrksgrklkeeidgvsgaTrapGkyklkvdekddklkk 90  
                                    +d+ +Ww + +++ ++  +g  + T + G++++++  +d ++++
  gi|91772891|ref|YP_565583.1| 1490 EDIAKWWYNINNTGNSIFSGNRSLTLPDGNHSITIIAQDLAGNN 1533
                                    689********99889*******************999987765 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.22
                       DUF2271   47 kdlrqWwrksgrklkeeidgvsgaTrapGkyklkvdekddkl 88  
                                    +d+ +Ww + +++ ++  +g  + T + G++++++  +d ++
  gi|91772891|ref|YP_565583.1| 1573 EDIAKWWYNINNTGNSIFSGNRSLTLPDGNHSITIIAQDLAG 1614
                                    689********99889******************99988765 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.17
                       DUF2271   47 kdlrqWwrksgrklkeeidgvsgaTrapGkyklkvdekddkl 88  
                                    +d+ +Ww + +++ ++  +g  + T + G+++++v  +d ++
  gi|91772891|ref|YP_565583.1| 1656 EDIAKWWYNINNTGNSIFSGNRSLTLPDGNHSITVIAQDLAG 1697
                                    689********99889******************99988765 PP

  == domain 8  score: 1.8 bits;  conditional E-value: 0.12
                       DUF2271   47 kdlrqWwrksgrklkeeidgvsgaTrapGkyklkvdekddklk 89  
                                    +d+ +Ww + +++ ++  +g  + T + G+++++v  +d +++
  gi|91772891|ref|YP_565583.1| 1739 EDIAKWWYNINNTGNSIFSGNQSLTLPDGNHSITVIAQDLAGN 1781
                                    689********99889******************999887765 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       4.9   7.3e+03      18      54 ..    1943    1980 ..    1937    1983 .. 0.71
   2 ?   -1.1   0.0       1.1   1.7e+03      35      68 .]    2003    2036 ..    1990    2036 .. 0.72
   3 ?    7.1   0.2    0.0029       4.3      33      68 .]    2083    2119 ..    2073    2119 .. 0.82
   4 ?    0.6   0.0      0.31   4.7e+02      37      68 .]    2171    2202 ..    2162    2202 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.9
                         PKD_3   18 grelti.aPtvenaenaafaWtieGkivsteptytfte 54  
                                    ++ +++ + tv+++ n + +Wt + +   + pt  ft+
  gi|91772891|ref|YP_565583.1| 1943 NTAYEFsTKTVDIVGNINLSWTNDTATTRNPPTVNFTS 1980
                                    66777733478899999999998877766666666666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                         PKD_3   35 faWtieGkivsteptytfteeelgsyevtleven 68  
                                    + W+  +   s+ ++   t  e g+y v l+++n
  gi|91772891|ref|YP_565583.1| 2003 WVWIFGDGNDSNAQNPLHTYAEPGKYSVSLTAIN 2036
                                    7777776666777777778899*********998 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0029
                         PKD_3   33 aa.faWtieGkivsteptytfteeelgsyevtleven 68  
                                    a  ++W       ste + + t ++ g+y+v l+v+n
  gi|91772891|ref|YP_565583.1| 2083 ALtWEWDFGEGNTSTEIDPVHTYTVPGTYNVSLNVSN 2119
                                    334777776669***********************98 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.31
                         PKD_3   37 WtieGkivsteptytfteeelgsyevtleven 68  
                                    W   +   s++     t   +g+y+v l+v+n
  gi|91772891|ref|YP_565583.1| 2171 WNFGDGNTSSDRHPSHTYVAAGTYTVSLNVSN 2202
                                    777777777787778888899*********98 PP

>> YebF  YebF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.6   3.8e+03      54      79 ..     964     992 ..     951     996 .. 0.62
   2 ?    2.0   0.1      0.14   2.1e+02      41      80 ..    1039    1078 ..    1035    1082 .. 0.82
   3 ?   -0.3   0.1      0.74   1.1e+03      41      80 ..    1124    1163 ..    1120    1167 .. 0.79
   4 ?    4.0   0.1     0.033        49      41      80 ..    1209    1248 ..    1205    1253 .. 0.86
   5 ?    4.0   0.1     0.033        49      41      80 ..    1294    1333 ..    1290    1338 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.6
                          YebF  54 tgkddky...kvplkvrGkkkdlsYkvtv 79 
                                    ++++ y   kvpl+v G+++  ++  ++
  gi|91772891|ref|YP_565583.1| 964 PENNAIYttdKVPLNVTGDETVANWWYKI 992
                                   444444422279*******9977766555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                          YebF   41 tskpvawvnaedvtgkddkykvplkvrGkkkdlsYkvtvd 80  
                                    t+ pv+ v + + + +  ++kvpl+v G+++  ++  +++
  gi|91772891|ref|YP_565583.1| 1039 TTAPVITVDQPENNANYTTHKVPLNVTGDETVANWWYKIN 1078
                                    67899999999999999999*********99877666655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.74
                          YebF   41 tskpvawvnaedvtgkddkykvplkvrGkkkdlsYkvtvd 80  
                                    t+ pv+ vn+ + +    + kvpl+v G+++  ++  +++
  gi|91772891|ref|YP_565583.1| 1124 TTAPVITVNQPENNAIYTTDKVPLNVTGDETVANWWYKIN 1163
                                    677888888888888888889********99877666655 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.033
                          YebF   41 tskpvawvnaedvtgkddkykvplkvrGkkkdlsYkvtvd 80  
                                    t+ pv+ vn+ + + +  ++kvpl+v G+++  ++  +++
  gi|91772891|ref|YP_565583.1| 1209 TTAPVITVNQPENNANYTTHKVPLNVTGDETVANWWYKIN 1248
                                    7889*************************99887766665 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.033
                          YebF   41 tskpvawvnaedvtgkddkykvplkvrGkkkdlsYkvtvd 80  
                                    t+ pv+ vn+ + + +  ++kvpl+v G+++  ++  +++
  gi|91772891|ref|YP_565583.1| 1294 TTAPVITVNQPENNANYTTHKVPLNVTGDETVANWWYKIN 1333
                                    7889*************************99887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        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: 1.10u 0.29s 00:00:01.39 Elapsed: 00:00:00.48
# Mc/sec: 15984.37
//
Query:       gi|91772892|ref|YP_565584.1|  [L=887]
Description: cation transporting P-type ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  170.6   4.4    2.4e-50  170.6   4.4    3.7  4  E1-E2_ATPase     E1-E2 ATPase
    6.4e-37  127.0  13.1    6.4e-37  127.0  13.1    2.3  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.5e-22   81.0   0.2    3.4e-22   79.8   0.2    1.7  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.5e-18   65.5   0.0    7.3e-18   64.0   0.0    1.9  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    2.6e-10   40.2   0.0    9.4e-10   38.5   0.0    1.9  1  Cation_ATPase    Cation transport ATPase (P-type)
    4.9e-08   33.0   2.4    2.3e-05   24.3   1.1    2.6  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.058   13.8   0.0       0.17   12.3   0.0    1.8  1  HAD              haloacid dehalogenase-like hydrolase
        1.1   10.0   5.0       0.37   11.5   1.0    2.4  2  DUF2809          Protein of unknown function (DUF2809)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4     0.028        62     107     141 ..      48      78 ..      41      99 .. 0.52
   2 !  170.6   4.4   1.1e-53   2.4e-50       2     180 ..     114     306 ..     113     307 .. 0.98
   3 ?   -2.7   0.0       1.6   3.7e+03      92     128 ..     658     694 ..     652     722 .. 0.68
   4 ?    1.8   0.1     0.066   1.5e+02     119     152 ..     755     789 ..     739     799 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.028
                                   ---HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTT CS
                  E1-E2_ATPase 107 kktplqkkldklgkvlvpvvlliallvflialllg 141
                                   k++++ ++++++++ l+ v l++a+++fl+    +
  gi|91772892|ref|YP_565584.1|  48 KESSIHRFVRQFASPLIYVLLIAAFVTFLL----R 78 
                                   455555555555555555555555555544....3 PP

  == domain 2  score: 170.6 bits;  conditional E-value: 1.1e-53
                                   SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-.............G-TT CS
                  E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek.............ekgd 68 
                                   +l p++ ++rdg+   ++++elv+GDivll++g rvpaD r++  ++ ++des+LTGEs +vek             e+++
  gi|91772892|ref|YP_565584.1| 114 MLVPETSILRDGQRLIVASRELVVGDIVLLETGGRVPADLRLIYKKNlRIDESMLTGESIAVEKntdviearnvpiaEQKN 194
                                   66789999************************************************************************* PP

                                   EE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHH CS
                  E1-E2_ATPase  69 mvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeall 149
                                    +f+Gt v++g+ ++vV+at+ ++e+gki +l++++k+  tpl++ +d +gk+l++v++l+a+l+f+i  l+g +  + ++
  gi|91772892|ref|YP_565584.1| 195 IAFAGTLVTKGNGIGVVVATAANSEIGKISELIKKTKKLSTPLVRTIDHMGKTLAFVIVLVAMLTFAIGKLRGLDDLDLFF 275
                                   ****************************************************************************9**** PP

                                   HHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                  E1-E2_ATPase 150 ralallvaaiPcaLplavplalalgarrlak 180
                                    +++l+vaaiP++Lp++++++la+g++++a 
  gi|91772892|ref|YP_565584.1| 276 ASVSLAVAAIPEGLPALITITLAIGIKKMAS 306
                                   *****************************96 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.6
                                   STTTTTSTTS--------HHHHHHHHHHHHHHHHHHH CS
                  E1-E2_ATPase  92 telgkiarlveeakskktplqkkldklgkvlvpvvll 128
                                     ++ i+++vee +   +++qk +     + ++ +l+
  gi|91772892|ref|YP_565584.1| 658 DNFSSIVNAVEEGRDVYSKIQKVILWTLPTNAAEGLA 694
                                   5678889999999888888888775544444444444 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.066
                                   HHHHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHH CS
                  E1-E2_ATPase 119 gkvlvpvvlliallvflialllgksla...eallral 152
                                    + +++v+ll++ ++fl+ l++ ++     ++   ++
  gi|91772892|ref|YP_565584.1| 755 KRRIITVALLMVTATFLLYLFNINNGMdvsTSQ--TI 789
                                   455999999999999999999877776443222..33 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.99   2.2e+03     105     140 ..      41      75 ..      40      94 .. 0.59
   2 ?   -1.6   0.1      0.85   1.9e+03      93     148 ..     248     262 ..     210     297 .. 0.61
   3 !  127.0  13.1   2.8e-40   6.4e-37       2     182 .]     706     876 ..     705     876 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.99
               Cation_ATPase_C 105 nalnlrsrreslfkfsglfsnkllllaillslllqv 140
                                   n + l++++ s+ +f+  f ++l+++ ++++++  +
  gi|91772892|ref|YP_565584.1|  41 NEVELKKKESSIHRFVRQFASPLIYVLLIAAFVT-F 75 
                                   5566677777777777777664433333333322.2 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.85
               Cation_ATPase_C  93 maFit.lvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpgl 148
                                   +aF++ lv + +f                                           +
  gi|91772892|ref|YP_565584.1| 248 LAFVIvLVAMLTFA------------------------------------------I 262
                                   22221011111121..........................................2 PP

  == domain 3  score: 127.0 bits;  conditional E-value: 2.8e-40
               Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgiseke 82 
                                   lpl +++iLwin vt l +++ + +ep ek++++rpPr+++epl+ + + rri++++ll++ +t+l++++++  +g++ ++
  gi|91772892|ref|YP_565584.1| 706 LPLLPLHILWINTVTALGLGVPMTVEPMEKGLLNRPPRPQNEPLLLPVIKRRIITVALLMVTATFLLYLFNIN-NGMDVST 785
                                   7*******************************************************************99997.8888887 PP

               Cation_ATPase_C  83 nklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsleewl 163
                                           qt+a++t+v+++if+++n++s +e+++   +lfsnk++ll+i + ++lq++i+y p +n +++t+p+ l +w+
  gi|91772892|ref|YP_565584.1| 786 -------SQTIALNTIVFFEIFYLFNCKSINENVIG--QLFSNKYMLLGISVVIGLQMFITYNPAMNVIMRTSPIRLVDWV 857
                                   .......9*********************8887776..999**************************************** PP

               Cation_ATPase_C 164 ialllalvvllvdelvKll 182
                                   +++l  + ++++ e  K++
  gi|91772892|ref|YP_565584.1| 858 VIILTTSSIFVLIEFEKFI 876
                                   ****************986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.2   1.5e-25   3.4e-22       3     210 .]     325     634 ..     323     634 .. 0.80

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.5e-25
                                   EEEEESBTTTBCHHHHHHHHHHHH.................................CHHHHHHHHHH............. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxx............. RF
                     Hydrolase   3 tvvfDkdGTLttgepsvedvivsa.................................alalaaaletg............. 37 
                                   +++ Dk+GTLt+ e+ v++++                                    +      l  g             
  gi|91772892|ref|YP_565584.1| 325 VICSDKTGTLTQNEMTVRKIYTDEgmftvtgqgydpkgdielngkkidpfdhralleT------LKAGalcndaylreegg 399
                                   7999***************999999***********************8874444443......444466666699999** PP

                                   .HHCHHHHHH.HHHHHHHHHHHHHHHHETTTE.................HHHHTHHHHHHHH............HCHHHHH CS
                                   .xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxx............xxxxxxx RF
                     Hydrolase  38 .sehpigkal.vaaakarsgaltgfatfigrg.................ayaigkpewltal............dippdlg 87 
                                       p   al v aaka  + +t++ +++ +                  +ya+g+pe + +l                   
  gi|91772892|ref|YP_565584.1| 400 iDGDPTEGALlVSAAKAGNFYITRVDEVPFESekrfmatlhqddagnswVYAKGSPEIISKLssmqfngkdfsrM------ 474
                                   *99999999999999999888888888544445566777777788888999999999888883222222222222...... PP

                                   HHHHHHHHHCHHHHHH.................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE CS
                                   xxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  88 aaigsaqsqgrtvall.................................qaralavftiadplkvkpeaaeavasLkaagi 135
                                              + +ll                                 +   l++  + dp  +++++++ + + + agi
  gi|91772892|ref|YP_565584.1| 475 ---------EPEKVLLvaedmaseglrviatayrklergkteieetdvdELIFLGLQGMIDP--PREDVKKSIFKCNNAGI 544
                                   .........222222246667777777777799999999999998877766778888888**..***************** PP

                                   EEEEEESSEHHHHHHHHHHTT.........GGGESEEEEHHCES......STTTSHHHHHHHHHHHTSTGGGEEEEESSHH CS
                                   xxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 136 evvlltgdnpetaeraanqlG.........ddyfdaviasdiet......vakpspegkvaaireLqgkpeevamVGDgvn 201
                                   +v+++tgd+ +ta+ +a+qlG          d+ + +++  ie+      +a  spe+k +++  L+ ++e va+ GDg+n
  gi|91772892|ref|YP_565584.1| 545 RVIMITGDHIKTAHTIARQLGirtegalagSDIGSMTDEELIEAlrsvsvFARTSPEDKSRIVGLLKQEGEVVAVTGDGIN 625
                                   *********************999665553333355555555559999999999*************************** PP

                                   HHHHHHHTT CS
                                   xxxxxxxxx RF
                     Hydrolase 202 DaaalaaAg 210
                                   Da+al++A+
  gi|91772892|ref|YP_565584.1| 626 DAPALENAD 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 !   64.0   0.0   3.3e-21   7.3e-18       1      68 [.       7      73 ..       7      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 3.3e-21
               Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                  +++ s++e+l+ Le ++ +GL+ +ea+ rl+k+G Ne++ kkk+s ++++++qf +pl+++Ll+aa v
  gi|91772892|ref|YP_565584.1|  7 WQHISVDEALALLE-TDRDGLSAEEAQLRLSKFGFNEVELKKKESSIHRFVRQFASPLIYVLLIAAFV 73
                                  7899*********9.89*************************************************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   4.2e-13   9.4e-10       2      87 ..     388     461 ..     387     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.2e-13
                 Cation_ATPase   2 lcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApe 82 
                                   lcN+a +      +e  + G++tE ALlv a+k+g      +   ++v e+pF+s++++m+++++  + ++  +y KG+pe
  gi|91772892|ref|YP_565584.1| 388 LCNDAYL-----REEGGIDGDPTEGALLVSAAKAG------NFYITRVDEVPFESEKRFMATLHQD-DAGNSWVYAKGSPE 456
                                   7888888.....6777889***************4......455689******************8.7************* PP

                 Cation_ATPase  83 iilkr 87 
                                   ii k 
  gi|91772892|ref|YP_565584.1| 457 IISKL 461
                                   **986 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0017       3.8      18      66 ..     530     577 ..     526     591 .. 0.79
   2 !   24.3   1.1     1e-08   2.3e-05     201     254 ..     612     666 ..     604     667 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE CS
                   Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali 66 
                                   e  k+ i k+ ++gi v+  TG ++++++ ++++lg+ +   al G+ i
  gi|91772892|ref|YP_565584.1| 530 EDVKKSIFKCNNAGIRVIMITGDHIKTAHTIARQLGIRT-EGALAGSDI 577
                                   56789999****************************983.333445555 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1e-08
                                   --GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGGTHHHHH CS
                   Hydrolase_3 201 isleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnnedGVaka 254
                                    + e v++ GDg ND + Le a++g+Amg  ++e +k aAd+v ++ n +++++a
  gi|91772892|ref|YP_565584.1| 612 QEGEVVAVTGDGINDAPALENADIGIAMGRsGTEVAKDAADMVLADDNFSSIVNA 666
                                   566778999*******************9626777899*******9999999876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.4e-05      0.17      88     188 .]     530     631 ..     468     631 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
                           HAD  88 pgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrg.egkvaalre....... 160
                                   +++++ + ++  aG+rv++++g +   ++ ++++lg    + te        g l +++  +   e+ + alr+       
  gi|91772892|ref|YP_565584.1| 530 EDVKKSIFKCNNAGIRVIMITGDHIKTAHTIARQLG----IRTE--------GALAGSDIGSMTdEELIEALRSvsvfart 598
                                   466777777889************************....8883........33333333333313333444444322233 PP

                           HAD 161 ....wlaaegegidleevvay.GDspsDlpllr 188
                                       +    g   ++ evva+ GD+++D p+l+
  gi|91772892|ref|YP_565584.1| 599 spedKSRIVGLLKQEGEVVAVtGDGINDAPALE 631
                                   3333223333333333488888********996 PP

>> DUF2809  Protein of unknown function (DUF2809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   0.00017      0.37       4      56 ..      54     106 ..      52     116 .. 0.89
   2 ?   -3.3   0.2       6.5   1.5e+04      38      50 ..     764     776 ..     753     810 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                       DUF2809   4 gfirkylGdvlvvillyllvrllvpkksplllalavllfavliEllQltqlpa 56 
                                    f+r+++   ++v+l+ ++v +l+++   ++++++v+l+  +i ++Q  ++ +
  gi|91772892|ref|YP_565584.1|  54 RFVRQFASPLIYVLLIAAFVTFLLREYADMTVIIGVVLANAIIGFIQERKAEN 106
                                   79*******************************************99766655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.5
                       DUF2809  38 avllfavliEllQ 50 
                                   +++ +++l+ l+ 
  gi|91772892|ref|YP_565584.1| 764 LMVTATFLLYLFN 776
                                   3333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (887 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.40
# Mc/sec: 6586.32
//
Query:       gi|91772893|ref|YP_565585.1|  [L=208]
Description: hypothetical protein Mbur_0886 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 1368.93
//
Query:       gi|91772894|ref|YP_565586.1|  [L=298]
Description: hypothetical protein Mbur_0887 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1987.76
//
Query:       gi|91772895|ref|YP_565587.1|  [L=215]
Description: lysine exporter protein LysE/YggA [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   87.3  16.6      1e-24   87.1  16.6    1.0  1  LysE      LysE type translocator
  ------ inclusion threshold ------
      0.014   15.2   2.9      0.014   15.2   2.9    2.4  2  DUF5362   Family of unknown function (DUF5362)


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 !   87.1  16.6   1.1e-28     1e-24       1     191 [.      16     206 ..      16     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.1e-28
                          LysE   1 lslllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrda 81 
                                   +s +l pGp ++++   ++++g+++g +v lg+ ++++  ill++ G + +++        +++lGg++ + +g+  l++a
  gi|91772895|ref|YP_565587.1|  16 ISAALIPGPMMFATAGISLNKGWRTGPFVFLGHSMVELTVILLVIAGASSFIS--DSTIGYVSILGGIVMIIFGLVLLKSA 94 
                                   57899************************************************..777899*******************9 PP

                          LysE  82 kekkveaeksve...aslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaflaa 159
                                   k+ ++ + +++    +  v p+++g+l++ +NP +il+wl  +sa++ + +  g+ +++++ +g+++a+++++  +a ++ 
  gi|91772895|ref|YP_565587.1|  95 KSVSNINIAESAkkfKGSVGPVSAGILTTALNPAFILWWLTAGSAIILQEYLLGMFAIVAFLIGHWLADFTFLLTVASSTV 175
                                   98766555444445899*******************************99****************************999 PP

                          LysE 160 rlsrrlsskkvlriinvvvgvlligfavklll 191
                                        ls+k ++  i ++++v+l++f+v ++ 
  gi|91772895|ref|YP_565587.1| 176 KGKDLLSEKTHR-KILYFCSVFLMIFGVWFVS 206
                                   999999999866.78899**********9875 PP

>> DUF5362  Family of unknown function (DUF5362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.9   1.6e-06     0.014       9      64 ..      52     112 ..      46     125 .. 0.81
   2 ?   -0.9   0.1      0.17   1.5e+03       7      21 ..     189     203 ..     183     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                       DUF5362   9 kilGvlliilGaltcLs.....IigiiigvllIivglklfkaakaikealrskseeklkea 64 
                                    +  +ll+i Ga   +s      + i+ g+++Ii gl l k+ak + +    +s++k k+ 
  gi|91772895|ref|YP_565587.1|  52 ELTVILLVIAGASSFISdstigYVSILGGIVMIIFGLVLLKSAKSVSNINIAESAKKFKGS 112
                                   56678889999876553222117899**********************9999999998875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                       DUF5362   7 wmkilGvlliilGal 21 
                                   +  ++ v+l+i+G+ 
  gi|91772895|ref|YP_565587.1| 189 ILYFCSVFLMIFGVW 203
                                   556778888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1368.31
//
Query:       gi|91772896|ref|YP_565588.1|  [L=284]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete 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  103.9   0.0      1e-29  103.3   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.6e-28   98.6   0.0    2.6e-28   97.9   0.0    1.4  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit
  ------ inclusion threshold ------
       0.14   11.5   0.0       0.22   10.9   0.0    1.3  1  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   1.7e-33     1e-29       6     153 .]      51     194 ..      44     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 1.7e-33
                                   HHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SB CS
                  TPP_enzyme_C   6 tlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNeg 84 
                                   +            ++yl+ + + g +G++lp AiGak+a+ + +v a++GDG+++   ++++++ +rrn +it++v++N++
  gi|91772896|ref|YP_565588.1|  51 SK----------LPHYLKcNVFNGLHGRSLPPAIGAKVANHELTVLAVTGDGDCYGEgGNHFVHNIRRNPDITLIVHDNQI 121
                                   43..........78999956699****************9999************************************** PP

                                   CCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  85 ygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   yg+t+gq   ++  g+k+k +++g   +p+++  la +l ++ + r    dve+l e +k+a+++kg++l++v
  gi|91772896|ref|YP_565588.1| 122 YGLTKGQaspTSELGMKTKIQNHGVFNTPLNPLSLAISLDCSfVSRGFAGDVEHLTELIKKAIQHKGFSLVDV 194
                                   *******9999999*********999****************666889***********************98 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   4.4e-32   2.6e-28       1      64 [.     198     261 ..     198     263 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 4.4e-32
                                   XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT-----EEEEEEEETTS--HHHHHHT. CS
                    PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgdkiplGifYkeekptyeerleel 64 
                                   Cv+FNk+nTf+wY ervy++ee+++ p+d+ kA+ek+lewg++iplG+fY +ekpt+e++l++l
  gi|91772896|ref|YP_565588.1| 198 CVSFNKLNTFKWYSERVYRMEEKDHSPKDRVKAFEKSLEWGERIPLGVFYVNEKPTFEDHLDVL 261
                                   **********************99*************************************987 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 ?   10.9   0.0   3.7e-05      0.22      42     123 ..     110     195 ..     100     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                                   TT-EEEEEGGGEET--SSHHHHHH...HHH.TT-SEEEES-HHHHHHHHHTT--EEEEEE--SHHHHHHHHH.HHHHHT-S CS
                  G3P_antiterm  42 agkkvfvhiDlieGlskdeaavef...lkkeikvdGiistksslikkakklglltiqrlfliDssalekalk.qiekskpd 118
                                    + +++vh + i Gl+k +a+ +    +k++i+ +G+  t  + ++ a +l+   + r f  D + l++ +k +i++    
  gi|91772896|ref|YP_565588.1| 110 PDITLIVHDNQIYGLTKGQASPTSelgMKTKIQNHGVFNTPLNPLSLAISLDCSFVSRGFAGDVEHLTELIKkAIQHKGFS 190
                                   35678999999****7776654322248999999*******************************9998876266777788 PP

                                   EEEEE CS
                  G3P_antiterm 119 avevl 123
                                   +v+vl
  gi|91772896|ref|YP_565588.1| 191 LVDVL 195
                                   88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1575.95
//
Query:       gi|91772897|ref|YP_565589.1|  [L=574]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-60  205.0   0.3    1.9e-60  204.5   0.3    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.9e-38  132.3   0.9    7.5e-38  130.4   0.4    2.1  2  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.7e-06   27.9   0.0    4.3e-06   26.6   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
    8.3e-06   26.1   0.0    2.1e-05   24.8   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0029   17.2   1.0     0.0053   16.4   1.0    1.3  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.5   0.3   5.3e-64   1.9e-60       2     226 ..     208     442 ..     207     447 .. 0.88

  Alignments for each domain:
  == domain 1  score: 204.5 bits;  conditional E-value: 5.3e-64
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   +a+aagv+++aaYP+TPs+ ++  +a+ +++++v   +v q+e+Ei+a ++++GA++aG+ra+T+TSg G+ Lm e+lgla
  gi|91772897|ref|YP_565589.1| 208 GALAAGVQFLAAYPMTPSTGVMTYIAAKADEFNV---VVEQAEDEIAALNMILGASYAGVRAMTTTSGGGFCLMAEALGLA 285
                                   799******************************8...******************************************** PP

                                   HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH CS
                         POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfll 158
                                   +++e+P+vi++ +R +p+tgl+++t+q+Dl +++     +++ ++la+++  ++f l+++Afn+Aek+++Pv+v++D++l+
  gi|91772897|ref|YP_565589.1| 286 GMTETPAVIFLSQRPGPATGLPTMTEQGDLQFVLtaaqgEFPRCILAPGTPDDCFYLTAKAFNIAEKFQIPVFVMSDQYLA 366
                                   ********************************************************************************* PP

                                   .HEEEEEEC-SGG....GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHH CS
                         POR_N 159 shevekvelpdee...delklikekleeyerkey........aldpekpiargtaanpdtglehrekgneaedaaekvv 226
                                    ++  + +  d      e++++ +++ + +++ y        +++p+  + + + ++ + ++eh+e+g+ +   +++++
  gi|91772897|ref|YP_565589.1| 367 -DSLFTCKKFDTSkieIERHMMADDELKGKNE-YnryeltptGISPRAIPGQAGFTVVVDSDEHNETGHLDQT-IDNRI 442
                                   .7665555554442213333333333333332.236889999*************************998776.66655 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.4   2.1e-41   7.5e-38       1     177 []      13     173 ..      11     173 .. 0.95
   2 ?   -1.1   0.0      0.47   1.7e+03      51     105 ..     411     465 ..     390     522 .. 0.67

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 2.1e-41
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                   +GqG++t+g +lak++ ++G++v+++++y s+ rGgh +++vris+e ++++   +++d+l+ald+++++ehl+++  +g+
  gi|91772897|ref|YP_565589.1|  13 AGQGLQTIGVVLAKTFKKSGFNVFTTQFYLSRVRGGHNTYQVRISNE-PIRAMT-EKVDILIALDEASINEHLKEIS-DGV 90 
                                   4**********************************************.778888.8********************9.9** PP

                                   EEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH. CS
                           POR  82 iiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeaikkrfpkkk 162
                                   +i++++ +k ++++++              ++ v++ kiak+ +gn+++ N v++Ga+++l+ + +e+le ++ ++f+kk+
  gi|91772897|ref|YP_565589.1|  91 VIVDTDVIKIEQMNES--------------IFHVPMLKIAKDVCGNKIYFNSVAIGAALGLMCFNFEYLESVLTATFQKKG 157
                                   *****87777666664..............679**********************************************99 PP

                                   .HHHHHHHHHHHHHHH CS
                           POR 163 .eviekNlkafragye 177
                                    e+ie N+ka+ragy+
  gi|91772897|ref|YP_565589.1| 158 dEIIENNIKAARAGYD 173
                                   ***************7 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
                                   SS--TTSEEEEEESSHHHHH..HHGGGEEEEEEEEEECTCGTT-CCHHHCTS-HHHH CS
                           POR  51 psievgeadllvaldaetls..ehldglkpggiiiynseelkpdelkkakeeerelk 105
                                   ++i+ g+a + v+ d ++ +   hld+   +  i++n++++k+  + ++ +e+++l 
  gi|91772897|ref|YP_565589.1| 411 RAIP-GQAGFTVVVDSDEHNetGHLDQTI-DNRILMNEKRMKKLKFLEKEMEAPQLY 465
                                   4555.788888888777665544554444.556667776666666666666665554 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.2e-09   4.3e-06       8      72 ..     468     532 ..     464     568 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-09
                                   TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEES CS
               Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavk 72 
                                   ++ d+tl+++Gs+    +e+++ L +eg s++ +    v pl  + i++++   g++v+ve++++
  gi|91772897|ref|YP_565589.1| 468 KKADITLIGWGSTYGPLMEVVDILTSEGHSVDHLHFTHVYPLPVDAIKDMMTDAGKIVCVENNAT 532
                                   678**********************************************************9875 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 !   24.8   0.0   5.9e-09   2.1e-05       1      70 [.     470     535 ..     470     564 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.9e-09
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HH CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGql 70 
                                   A++ +++ Gs+ g + ++vd l  eg +v  l  + ++P P +++k+++ ++ k+v ++ n++    Gq 
  gi|91772897|ref|YP_565589.1| 470 ADITLIGWGSTYGPLMEVVDILTSEGHSVDHLHFTHVYPLPVDAIKDMMTDAGKIVCVENNAT----GQF 535
                                   89***********************************************************94....444 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 !   16.4   1.0   1.5e-06    0.0053      11     157 ..     209     359 ..     200     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                                   HHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT CS
                  TPP_enzyme_N  11 LkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdr 90 
                                     a+gv+ + ++p + ++ ++ ++++   +++vv+   E   a+    +  +   + +  +tsg G+  +  al  A  + 
  gi|91772897|ref|YP_565589.1| 209 ALAAGVQFLAAYPMTPSTGVMTYIAAKAdEFNVVVEQAEDEIAALNMILGASYAGVRAMTTTSGGGFCLMAEALGLAGMTE 289
                                   4456***************9998888888888887666666666666666666679999999******************* PP

                                   --EEEEEEE--CCCHH......S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                  TPP_enzyme_N  91 iPllvlsgdrptslrg......qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvyl 157
                                   +P +++  +rp   +g      qg lq +   +a   ++ ++   + +p++   + ++A+ +a ++ + Pv++
  gi|91772897|ref|YP_565589.1| 290 TPAVIFLSQRPGPATGlptmteQGDLQFV--LTAAQGEFPRCILAPGTPDDCFYLTAKAFNIA-EKFQIPVFV 359
                                   ****************6644444444422..2333448899999999*************999.888999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3770.75
//
Query:       gi|91772898|ref|YP_565590.1|  [L=123]
Description: glyoxalase/bleomycin resistance protein/dioxygenase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-06   29.0   0.0    1.8e-06   28.7   0.0    1.1  1  Glyoxalase_6  Glyoxalase-like domain
     0.0001   22.5   0.0    0.00022   21.4   0.0    1.7  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   2.1e-10   1.8e-06       6     105 ..      11     114 ..       5     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.1e-10
                  Glyoxalase_6   6 aadpaalaaFwaaalgweveree..........aaledpegvgpaaedaatllfqrvpepaknrvHldlavedldaevarl 76 
                                   a+d +++ +F+ ++++w+ e+ +          ++l+ ++      + a  + ++r pe   +r+   ++v++++  + r+
  gi|91772898|ref|YP_565590.1|  11 ANDIDRAKEFYTELFDWKFEKVPgpmdyyfietESLDGEK------GVAGGMGLRRSPE---QRITNFIEVASVEDYCTRV 82 
                                   89******************99999**9665543344444......44559999****9...5899999************ PP

                  Glyoxalase_6  77 valGArvlreprdgthgr...vlaDPeGneFc 105
                                   ++lG+ v++++    +++   v+ D e n F 
  gi|91772898|ref|YP_565590.1|  83 EKLGGIVQQPKMPVPGWGylaVCMDTEENTFG 114
                                   ********99998888889**********996 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 !   21.4   0.0   2.4e-08   0.00022       2      53 ..       4      54 ..       3     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.4e-08
                                  EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEE CS
                    Glyoxalase  2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghie 53
                                  i+h+ l+++d++++ +FYt+ +++k  k+ +    + +     ++ ++g+++
  gi|91772898|ref|YP_565590.1|  4 IAHLDLPANDIDRAKEFYTELFDWKFEKVPG-PMDYYFIETESLDGEKGVAG 54
                                  89************************99988.33335555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 830.80
//
Query:       gi|91772899|ref|YP_565591.1|  [L=332]
Description: hypothetical protein Mbur_0893 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0001   22.0   0.0    0.00018   21.2   0.0    1.4  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     1e-08   0.00018      29     182 ..     130     251 ..      97     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1e-08
                     DDE_Tnp_1  29 ggk..ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleekgvdyiir 105
                                   +++  ++  y   ++++  +++ +s+  + + +  +++lk ++d+++++  k  ++  D+ + s++++ +l+e+ + +i +
  gi|91772899|ref|YP_565591.1| 130 KKStnSFCSYISLCIINKYTRFTISMLPVEKGKTKTDYLKYFIDQVDKInlKINILCLDREFYSRDVFTFLQENDIPHITP 210
                                   22235889999999999***********99999999**********99999****************************** PP

                     DDE_Tnp_1 106 lkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFk 182
                                   +                  +r+++ ++ l  +    +                    ++ ++  +yr+R  iE++ +
  gi|91772899|ref|YP_565591.1| 211 V-----------------VRRGKNGCENLGFVVYGIDW-------------------EPGKISTIYRKRFAIESSYR 251
                                   *.................99******************...................****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2659.67
//
Query:       gi|91772900|ref|YP_565592.1|  [L=389]
Description: hypothetical protein Mbur_0894 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-14   53.2   6.1    0.00049   20.3   0.0    3.3  3  CARDB            CARDB
    0.00014   21.1   0.0    0.00032   20.0   0.0    1.5  1  TRAP_alpha       Translocon-associated protein (TRAP), alpha 
    0.00038   20.5   1.0          1    9.4   0.2    2.6  3  DUF4366          Domain of unknown function (DUF4366)
     0.0048   16.9  12.8        1.3    9.0   0.0    4.7  5  DUF2393          Protein of unknown function (DUF2393)
  ------ inclusion threshold ------
      0.038   14.4   3.7        0.4   11.1   0.4    3.2  3  Arrestin_C       Arrestin (or S-antigen), C-terminal domain
      0.039   14.2   0.0        3.5    8.0   0.0    2.8  3  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
       0.11   12.6   0.3         21    5.2   0.0    3.5  3  DUF1573          Protein of unknown function (DUF1573)
       0.16   12.4   0.0       0.63   10.5   0.0    2.1  1  Acylphosphatase  Acylphosphatase
       0.17   12.2   0.9         21    5.5   0.2    3.2  3  DUF11            Domain of unknown function DUF11
       0.17   11.2   0.7        4.9    6.5   0.1    2.4  2  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 !   17.8   1.5   1.7e-06    0.0031       6      97 ..      33     133 ..      29     137 .. 0.84
   2 !   16.0   0.0   6.2e-06     0.011       1      72 [.     141     214 ..     141     230 .. 0.80
   3 !   20.3   0.0   2.7e-07   0.00049       2      84 ..     252     333 ..     251     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                   E..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEE......SEE-CTEEEEEEEEEE-S..-S CS
                         CARDB   6 v.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtv......psLaagesttvsftwtte..at 74 
                                   v t +++p+ +++g+++t+++ ++N+G ++  ++ v+l ++       +            L+ g+s++ ++   ++  a+
  gi|91772900|ref|YP_565592.1|  33 VtTLETTPQLVEPGNDVTVKIRISNEGVQTIDDFVVKLDANYPFYlksE---SnnfnqkRTLSVGSSIDNTYYLIVDtdAK 110
                                   357789999****************************999998875542...233566799************99999999 PP

                                   -CEEEEEEEESTT-SS--SSCCC CS
                         CARDB  75 egevtltvvvDpdnevaEsnEtN 97 
                                   +g ++l++ +  d+ +    ++N
  gi|91772900|ref|YP_565592.1| 111 SGIYQLEFEIHVDDVILKPSDNN 133
                                   9********99999887665544 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.2e-06
                                   S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEE.SEE-CTEEEEEEEEEE-S CS
                         CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtv.psLaagesttvsftwtte 72 
                                   +pDLt+ +t   s++++ge++ ++++v+N Gt+ ++++k+    d+ l   ++ +v ++++++++++++ ++ ++
  gi|91772900|ref|YP_565592.1| 141 KPDLTL-KTNINSTLSPGETFPLQIEVQNVGTGIAKNIKIIPRSDDILMlgSNLKViKNVEPNDNSSIECNFIVK 214
                                   69****.889999**************************999888888877555555788888877777777666 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 2.7e-07
                                   --EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEE CS
                         CARDB   2 pDLtv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtlt 81 
                                   +D  + + +++ps+ ++ +e+ i+  v+N+G+++++++ v+l+ ++e+  ++ + +L++++ +   f   +e ++g+ +++
  gi|91772900|ref|YP_565592.1| 252 ADIGIqNIKIEPSQITPLDEIHIQGMVENTGKGDAKNVIVELISEDEN-HKSFIGQLKSDDDAPFYFDLSPE-SAGSKEFN 330
                                   577776678899*******************************99999.78999*****9999999999999.77777766 PP

                                   EEE CS
                         CARDB  82 vvv 84 
                                   +++
  gi|91772900|ref|YP_565592.1| 331 INI 333
                                   555 PP

>> TRAP_alpha  Translocon-associated protein (TRAP), alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-07   0.00032     136     187 ..     192     243 ..     190     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                    TRAP_alpha 136 alaynkvvkPkkqatleYsFipaeafagRPfGlvinlaYkdaeGnqfqeavf 187
                                    l+  k v+P+ ++++e +Fi+++++    + + i+l+Y d++Gn ++++ +
  gi|91772900|ref|YP_565592.1| 192 NLKVIKNVEPNDNSSIECNFIVKDSLDPDSYKFPIDLEYLDEQGNYYSDSYY 243
                                   6777899*****************************************9987 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2   0.00057         1      15      48 ..      83     116 ..      75     127 .. 0.77
   2 ?   -3.1   0.0       4.1   7.3e+03      10      34 ..     290     316 ..     284     319 .. 0.72
   3 !    9.0   0.0   0.00076       1.4     117     145 ..     356     384 ..     330     385 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00057
                       DUF4366  15 eeesnkqfitvttksgntFYivIDrdeegeeenv 48 
                                   ++ ++k  ++v ++ +nt+Y+++D d+++  ++ 
  gi|91772900|ref|YP_565592.1|  83 NNFNQKRTLSVGSSIDNTYYLIVDTDAKSGIYQL 116
                                   5567888999****************76655544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.1
                       DUF4366  10 lvddl.eeesnkqfit.vttksgntFY 34 
                                   +v+ + e+e++k fi  +++ ++  FY
  gi|91772900|ref|YP_565592.1| 290 IVELIsEDENHKSFIGqLKSDDDAPFY 316
                                   567777788888998537777777777 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00076
                       DUF4366 117 nnglllvvlavaligggaayyfkvlkpkk 145
                                   ++ ++l++  +ali++ ++yyf ++k+k+
  gi|91772900|ref|YP_565592.1| 356 KTNIALILGFLALIAVSIVYYFGYMKKKE 384
                                   46789999999****************97 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.015        27      23      86 ..      11      72 ..       2     107 .. 0.62
   2 ?   -1.4   0.1       1.2   2.1e+03      54      74 ..     151     171 ..     134     180 .. 0.71
   3 !    9.0   0.0   0.00072       1.3      42      83 ..     221     262 ..     217     268 .. 0.93
   4 !    7.1   0.0    0.0028         5      61     103 ..     270     308 ..     263     349 .. 0.70
   5 ?    1.3   0.4      0.18   3.2e+02      12      38 ..     354     380 ..     348     384 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                       DUF2393 23 flsllilflapfvvhliidkylkkaeltilsqkrlly..teafvvdgtitNeGkftikeCkleikl 86
                                  +  +l+l+  p ++   ++     + +t l+ ++ l+   +++ v+++i NeG  ti   +++++ 
  gi|91772900|ref|YP_565592.1| 11 LSVILVLTTIPLASSSSVN----GIVVTTLETTPQLVepGNDVTVKIRISNEGVQTIDDFVVKLDA 72
                                  3334444444444444444....44444444444444116899**************999998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                       DUF2393  54 qkrllyteafvvdgtitNeGk 74 
                                   ++ l+  e+f ++++++N G 
  gi|91772900|ref|YP_565592.1| 151 NSTLSPGETFPLQIEVQNVGT 171
                                   455666778888888888875 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00072
                       DUF2393  42 kylkkaeltilsqkrllyteafvvdgtitNeGkftikeCkle 83 
                                    y ++++l+ l+ + + y+++++v +++ N+ +  i++ k+e
  gi|91772900|ref|YP_565592.1| 221 SYKFPIDLEYLDEQGNYYSDSYYVGINVLNKADIGIQNIKIE 262
                                   67799*******************************999987 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0028
                       DUF2393  61 eafvvdgtitNeGkftikeCkleiklvnkshnkkskellkklk 103
                                   + + ++g + N+Gk + k++++e+   +++h++ +  +   lk
  gi|91772900|ref|YP_565592.1| 270 DEIHIQGMVENTGKGDAKNVIVELISEDENHKS-FIGQ---LK 308
                                   56789******************9999999999.3322...23 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.18
                       DUF2393  12 kkrsavalfliflsllilflapfvvhl 38 
                                   + ++ +al+l fl+l+ ++++++++++
  gi|91772900|ref|YP_565592.1| 354 RPKTNIALILGFLALIAVSIVYYFGYM 380
                                   556667999999999999999999987 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 ?   11.1   0.4   0.00022       0.4      11      88 ..      38     123 ..      29     154 .. 0.73
   2 ?    1.5   0.1      0.21   3.8e+02      17      41 ..     155     179 ..     140     183 .. 0.82
   3 ?    0.9   0.0      0.33     6e+02       9      45 ..     259     295 ..     253     356 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                   ES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEEEESS.....SEEEEEEEEEE.EEE---......B-TTEE.EEE CS
                    Arrestin_C  11 lpkkgyvpGetipvtvkidndskkkvkkikvslvqhvdvcafnr...snkkeknvvak.sdsvkv......tsaakdklet 81 
                                   +  + + pG +++v++ i n+  +++    v+l  ++ +  +++      ++k++++  s  +++      t a+++ +++
  gi|91772900|ref|YP_565592.1|  38 TTPQLVEPGNDVTVKIRISNEGVQTIDDFVVKLDANYPFYLKSEsnnF--NQKRTLSVgSSIDNTyylivdTDAKSGIYQL 116
                                   55567789**********************************886443..4444444333333335888887777777887 PP

                                   EEEE.-- CS
                    Arrestin_C  82 evelqiP 88 
                                   e+e+++ 
  gi|91772900|ref|YP_565592.1| 117 EFEIHVD 123
                                   7777665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                                   ETT--EEEEEEEEE-SSSEEEEEEE CS
                    Arrestin_C  17 vpGetipvtvkidndskkkvkkikv 41 
                                    pGet p++++++n      k+ik+
  gi|91772900|ref|YP_565592.1| 155 SPGETFPLQIEVQNVGTGIAKNIKI 179
                                   69***********988888888876 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.33
                                   EEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEE CS
                    Arrestin_C   9 aslpkkgyvpGetipvtvkidndskkkvkkikvslvq 45 
                                   ++++ + ++p ++i ++  ++n  k + k++ v+l+ 
  gi|91772900|ref|YP_565592.1| 259 IKIEPSQITPLDEIHIQGMVENTGKGDAKNVIVELIS 295
                                   5667778899999999999999999999999999985 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 ?    8.0   0.0    0.0019       3.5       1      77 [.      43     121 ..      43     123 .. 0.82
   2 ?    3.0   0.0     0.069   1.2e+02       2      26 ..     155     179 ..     154     182 .. 0.92
   3 ?   -3.4   0.0       6.9   1.2e+04      13      27 ..     278     292 ..     273     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                   NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                   vepG +vt+++ ++n+g +++ +  ++l++  P   + ++   ++ ++l  G +   t  + + ++a+ G y++++++ 
  gi|91772900|ref|YP_565592.1|  43 VEPGNDVTVKIRISNEGVQTIDDFVVKLDAnyPFYLKSESNNFNQKRTLSVGSSIDNTYYLIVDTDAKSGIYQLEFEIH 121
                                   689******************9977777665588888455555555599999999999999999999999999998875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.069
                   NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsl 26 
                                   +pGet  l+++v n gt  a+n+++
  gi|91772900|ref|YP_565592.1| 155 SPGETFPLQIEVQNVGTGIAKNIKI 179
                                   79******************99987 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.9
                   NPCBM_assoc  13 vtndgtaaatnvsls 27 
                                   v n+g+  a+nv ++
  gi|91772900|ref|YP_565592.1| 278 VENTGKGDAKNVIVE 292
                                   789999999999776 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.11   1.9e+02      45      70 ..      34      59 ..      29      75 .. 0.78
   2 ?   -0.0   0.0       0.5     9e+02      52      81 ..     152     179 ..     135     186 .. 0.80
   3 ?    5.2   0.0     0.012        21      58      92 ..     327     361 ..     320     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                       DUF1573 45 ttpeypkepiapGesgkikvtfnakg 70
                                  tt e + + ++pG+  ++k++ +++g
  gi|91772900|ref|YP_565592.1| 34 TTLETTPQLVEPGNDVTVKIRISNEG 59
                                  67788888899999999999888877 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.5
                       DUF1573  52 epiapGesgkikvtfnakgrpgefnktvtv 81 
                                   +++ pGe++ ++++ ++ g  g + k++++
  gi|91772900|ref|YP_565592.1| 152 STLSPGETFPLQIEVQNVG-TG-IAKNIKI 179
                                   5789999999999999999.55.6788877 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.012
                       DUF1573  58 esgkikvtfnakgrpgefnktvtvyantekepttl 92 
                                   ++++i++t+n +  p +++ t+++ +n  k+++ l
  gi|91772900|ref|YP_565592.1| 327 KEFNINITYNDDFGPHRIDNTIEIEVNRPKTNIAL 361
                                   7899********99*************99888776 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.63      23      60 ..     270     310 ..     256     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
               Acylphosphatase  23 kelglkGyvrNlsdg...sVeivaegeeekvekfleelksg 60 
                                   +e++++G+v+N+ +g   +V +++  e+e+ ++f+ +lks+
  gi|91772900|ref|YP_565592.1| 270 DEIHIQGMVENTGKGdakNVIVELISEDENHKSFIGQLKSD 310
                                   6889***********999999*****************996 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.012        21       6      36 ..      39      69 ..      32     117 .. 0.77
   2 ?    2.6   0.0     0.096   1.7e+02       3      34 ..     147     178 ..     144     182 .. 0.87
   3 ?    0.0   0.0       0.6   1.1e+03      21      35 ..     277     291 ..     262     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                         DUF11  6 dksevrpGdtvtytltvtNtgpasangvvvt 36
                                  +++ v pG  vt+ +  +N g ++  + vv+
  gi|91772900|ref|YP_565592.1| 39 TPQLVEPGNDVTVKIRISNEGVQTIDDFVVK 69
                                  45689******************99988885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.096
                         DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvv 34 
                                   Kt  +s++ pG+t    + v+N g+  a++++
  gi|91772900|ref|YP_565592.1| 147 KTNINSTLSPGETFPLQIEVQNVGTGIAKNIK 178
                                   677788999***************99998876 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.6
                         DUF11  21 tvtNtgpasangvvv 35 
                                    v Ntg  +a++v v
  gi|91772900|ref|YP_565592.1| 277 MVENTGKGDAKNVIV 291
                                   589*********988 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 ?    6.5   0.1    0.0027       4.9       5      52 ..      17      64 ..      11     115 .. 0.79
   2 ?    2.6   0.0     0.043        77      24      57 ..     147     180 ..     144     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0027
                     TRAP_beta  5 llalaalaqedasarvlvkKkilnrllvegedltveytiyNvGssaAl 52
                                  l   + +++++ + +v+   ++  +l+  g+d+tv++ i N G ++  
  gi|91772900|ref|YP_565592.1| 17 LTTIPLASSSSVNGIVVTTLETTPQLVEPGNDVTVKIRISNEGVQTID 64
                                  444556667777888999999999*******************88765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.043
                     TRAP_beta  24 KkilnrllvegedltveytiyNvGssaAldVslv 57 
                                   K+ +n  l+ ge   +++++ NvG+  A ++++ 
  gi|91772900|ref|YP_565592.1| 147 KTNINSTLSPGETFPLQIEVQNVGTGIAKNIKII 180
                                   7888999999******************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3006.56
//
Query:       gi|91772901|ref|YP_565593.1|  [L=400]
Description: hypothetical protein Mbur_0895 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-07   30.0   2.5    5.2e-07   30.0   2.5    2.8  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
        1.3    9.4   5.0       0.78   10.1   0.6    2.7  2  DUF5438   Family of unknown function (DUF5438)


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.078     7e+02      69      82 ..      27      40 ..      11      61 .. 0.57
   2 ?   -1.0   0.2      0.28   2.5e+03      63      77 ..     277     291 ..     247     297 .. 0.51
   3 !   30.0   2.5   5.9e-11   5.2e-07       1      92 [.     299     389 ..     299     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.078
                          FtsX 69 vliiivlllllall 82
                                  +++++++++l +++
  gi|91772901|ref|YP_565593.1| 27 IVAVLAMSFLSITF 40
                                  22222222222222 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.28
                          FtsX  63 sidlitvliiivlll 77 
                                   +i l+t +++i +++
  gi|91772901|ref|YP_565593.1| 277 TIGLLTAFATIYIII 291
                                   233333333333333 PP

  == domain 3  score: 30.0 bits;  conditional E-value: 5.9e-11
                          FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs...selkisidlitvliiivllll 78 
                                   +++igil+a+G kk  +l+ +++++l +++ + +iG    +l+ q+l + l+    s   + + + +    ++++ + l+l
  gi|91772901|ref|YP_565593.1| 299 RKQIGILKAVGIKKEIILGSYVLQSLTYGVTGVIIG----NLLMQVLLSILSIHPLSmpiGDVVPILTKDRIITTTFTLIL 375
                                   79**********************************....55555554444444333344777777777888888888888 PP

                          FtsX  79 lallagllsiskil 92 
                                     l+ag++++ k++
  gi|91772901|ref|YP_565593.1| 376 ASLVAGIFPSKKAA 389
                                   88888999999986 PP

>> DUF5438  Family of unknown function (DUF5438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.15   1.4e+03      23      40 ..      21      38 ..       4      47 .. 0.67
   2 ?   10.1   0.6   8.7e-05      0.78      18      49 ..     322     353 ..     314     376 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                       DUF5438 23 sttnsvisallmynllti 40
                                   tt  vi a+l   +l+i
  gi|91772901|ref|YP_565593.1| 21 KTTFMVIVAVLAMSFLSI 38
                                  356666777666666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 8.7e-05
                       DUF5438  18 rsiiysttnsvisallmynlltiisttylsvs 49 
                                   +s+ y  t  +i  llm  ll+i+s   ls+ 
  gi|91772901|ref|YP_565593.1| 322 QSLTYGVTGVIIGNLLMQVLLSILSIHPLSMP 353
                                   6999*********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2907.49
//
Query:       gi|91772902|ref|YP_565594.1|  [L=229]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-37  127.3   0.0    7.8e-37  126.8   0.0    1.2  1  ABC_tran     ABC transporter
    1.1e-08   34.8   0.1    6.1e-08   32.4   0.1    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
    3.6e-07   30.3   0.2     0.0032   17.3   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      8e-06   25.8   0.3     0.0055   16.5   0.1    2.1  2  AAA_15       AAA ATPase domain
    0.00012   21.8   0.1    0.00023   20.8   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00015   21.4   0.0      0.015   14.9   0.0    2.2  2  AAA_25       AAA domain
    0.00015   20.6   0.0    0.00021   20.2   0.0    1.1  1  RNA12        RNA12 protein
    0.00051   20.0   0.1     0.0013   18.6   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
     0.0014   18.9   0.1     0.0046   17.2   0.1    2.0  1  AAA_22       AAA domain
      0.002   18.6   0.5      0.068   13.7   0.1    2.2  2  AAA_18       AAA domain
     0.0021   18.6   0.5     0.0041   17.7   0.5    1.4  1  AAA_23       AAA domain
     0.0039   17.6   0.1     0.0051   17.2   0.1    1.5  1  AAA_16       AAA ATPase domain
     0.0094   15.7   0.2       0.12   12.1   0.0    2.1  2  AAA_24       AAA domain
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.046   13.7   0.0    1.9  2  AAA_14       AAA domain
      0.016   14.3   0.0      0.023   13.8   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
      0.018   15.2   0.1      0.023   14.8   0.1    1.5  1  AAA_33       AAA domain
      0.024   14.9   0.1       0.18   12.1   0.1    2.1  2  AAA_28       AAA domain
      0.037   13.2   0.1      0.079   12.1   0.1    1.7  1  G-alpha      G-protein alpha subunit
      0.045   13.8   0.7       0.18   11.9   0.7    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
       0.06   13.3   0.0        0.1   12.5   0.0    1.4  1  NACHT        NACHT domain
      0.061   12.7   0.1          2    7.7   0.0    2.2  2  ATPase       KaiC
      0.079   13.2   0.5       0.56   10.5   0.5    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.088   12.4   0.1       0.22   11.1   0.1    1.6  1  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.0     1e-39   7.8e-37       1     137 []      25     174 ..      25     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 1e-39
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                   lk++s++++ege vai+G++G+GKStLl  l  l +pt+G+i++d++d+ +    +++++   ++g+++q  +l pelt+ 
  gi|91772902|ref|YP_565594.1|  25 LKDISVEIYEGEFVAIMGPSGSGKSTLLHQLGLLDTPTNGKITIDDNDIINlsdaKKTQFRLDKLGYVFQSYNLIPELTAL 105
                                   79*******************************************99999999999999999******************* PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   en             +++++++++l+ +gl +    ++++ ps+LSgGq+qrv++aral+++pk+l++DEpta
  gi|91772902|ref|YP_565594.1| 106 ENvyitdmarglgkeKYEKKAKDILEAVGLGN----RIDHYPSELSGGQQQRVSIARALVNEPKILFADEPTA 174
                                   *************9999999*********998....667778*****************************97 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 !   32.4   0.1   7.8e-11   6.1e-08       3     211 ..      12     218 ..      10     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 7.8e-11
                                   EEEEEES.ETTEECEEEEEET.TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEE CS
                                   xxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                         SMC_N   3 krleien.Fksyagktvilpf.sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeve 80 
                                   +r+ i++ +k+ya k +++++ + +f ai+Gp GSGKs ll  +  +L + ++ k+  ++ +d+i+   ++k +    ++ 
  gi|91772902|ref|YP_565594.1|  12 ERVYITGpVKTYALKDISVEIyEGEFVAIMGPSGSGKSTLLHQL-GLLDTPTNGKITIDD-NDIINLsDAKKTQFRLDKLG 90 
                                   5666665489999999999872557****************999.667766666776554.78888744455556666777 PP

                                   EEEEETTEE.SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--S CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  81 itfdnedkk.lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpap 160
                                    +f+  +   + +  e+v+i+  +   g+ +y+  +k     e   l ++ + ++++LSgG+++ v++a  +    v+   
  gi|91772902|ref|YP_565594.1|  91 YVFQSYNLIpELTALENVYITDMARGLGKEKYE--KKAKDILEAVGLGNRIDHYPSELSGGQQQRVSIARAL----VNEPK 165
                                   888777776445667778888888888887775..4445556778899999999**********99987653....34444 PP

                                   EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEE.E-SSHHHCCC-SCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxx RF
                         SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn.aQfiv.islreemlekadklvgv 211
                                   + + De  a+LD    k+v +l+++ +k+  Q iv ++++ee   kad+++ v
  gi|91772902|ref|YP_565594.1| 166 ILFADEPTANLDTDSSKEVIDLFRKFNKEiGQTIVmVTHEEEEGLKADRIIWV 218
                                   5567*********************9999789988479999999999998876 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 !   17.3   0.1   4.1e-06    0.0032       1      65 [.      37      89 ..      37     131 .. 0.89
   2 !   11.4   0.0   0.00026       0.2     211     297 ..     138     204 ..     114     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieef 65
                                  + ++ Gp gsGKS+LL  l ll            + + +g+i+++++ + + ++ ++++f+++++
  gi|91772902|ref|YP_565594.1| 37 FVAIMGPSGSGKSTLLHQLGLL------------DTPTNGKITIDDNDIINLSDAKKTQFRLDKL 89
                                  57899**************999............9999**********************99965 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                        AAA_21 211 svderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQ 291
                                   ++d+                   ++elS G+++   ++ al   +   ++l+ DEp ++L+    +++++l+++ +++ +Q
  gi|91772902|ref|YP_565594.1| 138 RIDHY------------------PSELSGGQQQRVSIARALVNEP---KILFADEPTANLDTDSSKEVIDLFRKFNKEIGQ 197
                                   44444..................5679999999878888888777...9***********************888887888 PP

                        AAA_21 292 v.iltTH 297
                                     +++TH
  gi|91772902|ref|YP_565594.1| 198 TiVMVTH 204
                                   8799999 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.1e-06    0.0055      14      81 ..      25      88 ..      24     146 .. 0.73
   2 !    7.7   0.0    0.0032       2.5     322     364 ..     162     204 ..     144     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.1e-06
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdv 81
                                  lkd+++++ e  +  + G+ +sGKS++l+ l l+ + +    + +i+i+++d+ +  +++++ ++++d+
  gi|91772902|ref|YP_565594.1| 25 LKDISVEIYEGeFVAIMGPSGSGKSTLLHQLGLLDTPT----NGKITIDDNDIINL-SDAKKTQFRLDK 88
                                  899999999888*******************9999988....78899999998877.566666666654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0032
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   ++++il+ +EP a+L ++  k++i+l+++  ++  + +++ TH
  gi|91772902|ref|YP_565594.1| 162 NEPKILFADEPTANLDTDSSKEVIDLFRKFNKEIGQTIVMVTH 204
                                   4689**************************9999966667899 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1     3e-07   0.00023      17      40 ..      30      53 ..      22      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-07
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllD 40
                                  +ei + +++ ++GpsGsGKSTll 
  gi|91772902|ref|YP_565594.1| 30 VEIYEGEFVAIMGPSGSGKSTLLH 53
                                  566544599*************95 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   1.9e-05     0.015      31      55 ..      33      57 ..      25      64 .. 0.91
   2 ?    4.3   0.0     0.034        26     160     189 ..     175     205 ..     166     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                        AAA_25 31 pagelallaGapgtGKttlaldlal 55
                                   +ge+++++G++g+GK+tl+ +l+l
  gi|91772902|ref|YP_565594.1| 33 YEGEFVAIMGPSGSGKSTLLHQLGL 57
                                  489*****************99975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.034
                        AAA_25 160 nsnsdv.galvealeriarrtgaavllvhHv 189
                                   n ++d  +++++ ++++ ++ g ++++v H 
  gi|91772902|ref|YP_565594.1| 175 NLDTDSsKEVIDLFRKFNKEIGQTIVMVTHE 205
                                   445565699*********************6 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.7e-07   0.00021      17     115 ..      35     133 ..      22     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                         RNA12  17 ntFivvkGPrGSGkkeLvldrvlkdrkk..vlvidCdelvkarndaelisaaAsqlGYfPvFswlnsissliDlavqgliG 95 
                                     F+ + GP GSGk+ L+ +  l d  +  +++id +++++  +da++ +   ++lGY  vF   n i +l  l  + ++ 
  gi|91772902|ref|YP_565594.1|  35 GEFVAIMGPSGSGKSTLLHQLGLLDTPTngKITIDDNDIINL-SDAKKTQFRLDKLGY--VFQSYNLIPELTALENVYITD 112
                                   56****************999998888789*********985.78888999999****..8***********999999999 PP

                         RNA12  96 qkagls.etkeaqlknileia 115
                                   +  gl  e+ e++ k+ile +
  gi|91772902|ref|YP_565594.1| 113 MARGLGkEKYEKKAKDILEAV 133
                                   999997256688999998865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.7e-06    0.0013      87     119 ..      22      55 ..       3      95 .. 0.81
   2 ?   -2.0   0.0       3.8     3e+03      58      91 ..     178     211 ..     174     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.7e-06
                                   HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                   RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                   + +l++++ ++ + ++++++G+SG GKStL+ +l
  gi|91772902|ref|YP_565594.1|  22 TYALKDISVEIYEgEFVAIMGPSGSGKSTLLHQL 55 
                                   556677766665559****************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                                   G--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHH CS
                   RsgA_GTPase  58 lleeeeeleelkeelealgyevllvsaktkegle 91 
                                     +++e ++ +++  +++g ++++v  +++egl+
  gi|91772902|ref|YP_565594.1| 178 TDSSKEVIDLFRKFNKEIGQTIVMVTHEEEEGLK 211
                                   5555566677777788889889988888888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.8e-06    0.0046       5      29 ..      35      59 ..      30     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.8e-06
                        AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                    +++++G+sG+GK+tll +l   +
  gi|91772902|ref|YP_565594.1| 35 GEFVAIMGPSGSGKSTLLHQLGLLD 59
                                  57899*************9998766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   8.8e-05     0.068       1      19 [.      38      56 ..      38     132 .. 0.68
   2 ?    3.3   0.0      0.15   1.2e+02      47      91 ..     171     213 ..     144     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.8e-05
                        AAA_18  1 IlltGtpGvGKttlakeLs 19
                                  ++++G++G+GK+tl + L 
  gi|91772902|ref|YP_565594.1| 38 VAIMGPSGSGKSTLLHQLG 56
                                  689************9993 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                        AAA_18  47 deskrldedkldklldaleenssaleegknlvidghlaeleseaa 91 
                                   +++  ld+d  ++++d++++ ++  e g+++v+  h +e    a+
  gi|91772902|ref|YP_565594.1| 171 EPTANLDTDSSKEVIDLFRKFNK--EIGQTIVMVTHEEEEGLKAD 213
                                   366889999999*********97..99*****9999888776555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   5.2e-06    0.0041      19     164 ..      35     193 ..      20     214 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.2e-06
                        AAA_23  19 kgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvelt.....fenkdgry........ 86 
                                     +++I Gp G+GK+T+l  + l  +       ++ +  + ++d+  + ++ +k++++l+     f  ++           
  gi|91772902|ref|YP_565594.1|  35 GEFVAIMGPSGSGKSTLLHQLGLLDTP------TNGKITIDDNDII-NLSDAKKTQFRLDklgyvF--QSYNLipeltale 106
                                   46789*************977665443......3335667788875.4555778888888777553..2222255666655 PP

                        AAA_23  87 trsierere.lskkkgkttkkaklellei.deleqfisellgskkiilnlilflgqerfeefel.......kdkkerleel 158
                                   ++ i+++   l k+k +++ k++le ++  +  + + sel g ++++ ++   l  e +  f++        d ++++ +l
  gi|91772902|ref|YP_565594.1| 107 NVYITDMARgLGKEKYEKKAKDILEAVGLgNRIDHYPSELSGGQQQRVSIARALVNEPKILFADeptanldTDSSKEVIDL 187
                                   444555444144444444444455555446666677777888877755554444444433333322222223333333333 PP

                        AAA_23 159 ekelee 164
                                    +++++
  gi|91772902|ref|YP_565594.1| 188 FRKFNK 193
                                   333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   6.5e-06    0.0051      23      45 ..      34      56 ..      24     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                  ++e v + G+sG+GKs+l+ +l 
  gi|91772902|ref|YP_565594.1| 34 EGEFVAIMGPSGSGKSTLLHQLG 56
                                  6689***************9875 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   0.00015      0.12       5      22 ..      38      55 ..      35      85 .. 0.85
   2 ?    1.3   0.1      0.31   2.4e+02     109     135 ..     182     209 ..     178     218 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                        AAA_24  5 iliyGpsgiGKTtlakel 22
                                  ++i+Gpsg+GK+tl+ +l
  gi|91772902|ref|YP_565594.1| 38 VAIMGPSGSGKSTLLHQL 55
                                  78*************998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.31
                        AAA_24 109 eefrrllkk.lqelrknvifiahektrk 135
                                   +e+++l +k  +e +++++++ he+++ 
  gi|91772902|ref|YP_565594.1| 182 KEVIDLFRKfNKEIGQTIVMVTHEEEEG 209
                                   4566666663344555********9986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.4   5.8e+03      94     110 ..      13      29 ..       3      32 .. 0.68
   2 ?   13.7   0.0     6e-05     0.046       3      49 ..      36      79 ..      34     112 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.4
                        AAA_14  94 dvivtGSnskllskeia 110
                                   +v++tG  +   +k+i+
  gi|91772902|ref|YP_565594.1|  13 RVYITGPVKTYALKDIS 29 
                                   78888877777777665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6e-05
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                  + ++i+G+  +GK+tll+ql   ll +      i++dd++  +l+d 
  gi|91772902|ref|YP_565594.1| 36 EFVAIMGPSGSGKSTLLHQLG--LL-DTPTNGKITIDDNDIINLSDA 79
                                  6799****************7..44.334444455555444444333 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.9e-05     0.023     126     182 ..      32      87 ..       8      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                         T2SSE 126 vrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak 182
                                   + e   + + G+ gsGK+tll   l  +++ ++  +t+ D   i+l++a+++q + +
  gi|91772902|ref|YP_565594.1|  32 IYEGEFVAIMGPSGSGKSTLLH-QLGLLDTPTNGKITIDDNDIINLSDAKKTQFRLD 87 
                                   5555677899**********97.5788899888899*****9999999998887655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1     3e-05     0.023       2      20 ..      38      58 ..      37     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                        AAA_33  2 vllvGlpGsGKstlaerl..l 20
                                  v + G++GsGKstl+++l  l
  gi|91772902|ref|YP_565594.1| 38 VAIMGPSGSGKSTLLHQLglL 58
                                  5678************98432 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00023      0.18       2      20 ..      38      56 ..      37      68 .. 0.87
   2 ?    0.3   0.0      0.96   7.5e+02      17      79 ..     100     170 ..      97     177 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  ++i+G++++GK+tll +L 
  gi|91772902|ref|YP_565594.1| 38 VAIMGPSGSGKSTLLHQLG 56
                                  89**************996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.96
                        AAA_28  17 eaLaargypvvpEaareileekl.akgedalpwv...edllafaervleeqleee..aaa..aankvlfcD 79 
                                    +L+a + ++++++ar + +ek+ +k +d+l++v   +++ ++ +++   q ++   a+a  +++k+lf D
  gi|91772902|ref|YP_565594.1| 100 PELTALENVYITDMARGLGKEKYeKKAKDILEAVglgNRIDHYPSELSGGQQQRVsiARAlvNEPKILFAD 170
                                   56777777888999999999999555556666654333555555444444443332244456777777777 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0001     0.079      27      51 ..      39      68 ..      34     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                  EEEESTTSSHHHHHHHHHHHCS--.....- CS
                       G-alpha 27 lllGqseSGKsTilkqlkllykkg.....f 51
                                   ++G s+SGKsT+l ql ll +++     +
  gi|91772902|ref|YP_565594.1| 39 AIMGPSGSGKSTLLHQLGLLDTPTngkitI 68
                                  579****************99988555551 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   0.7   0.00023      0.18       2      19 ..      38      55 ..      37     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                                  EEEEESTTSSHHHHHHHH CS
                      MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                  vai+G + +GKStL+ +l
  gi|91772902|ref|YP_565594.1| 38 VAIMGPSGSGKSTLLHQL 55
                                  89*************988 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013       0.1       3      20 ..      38      55 ..      36      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                  EEEEC-TTTCHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkl 20
                                  v++ G++GsGK+tLl++l
  gi|91772902|ref|YP_565594.1| 38 VAIMGPSGSGKSTLLHQL 55
                                  899************997 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0026         2      16      38 ..      32      54 ..      23      60 .. 0.89
   2 ?    2.6   0.0     0.093        73     142     167 ..     182     208 ..     173     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0026
                        ATPase 16 ipegrvvlitGepGtGKtifalq 38
                                  i+eg+ v i+G +G+GK+++  q
  gi|91772902|ref|YP_565594.1| 32 IYEGEFVAIMGPSGSGKSTLLHQ 54
                                  7899**************98665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.093
                        ATPase 142 eilrqlvrvl.kklgvTailvseksss 167
                                   +++  l+r + k++g+T ++v+  +++
  gi|91772902|ref|YP_565594.1| 182 KEVIDLFRKFnKEIGQTIVMVTHEEEE 208
                                   567788888889999999999985443 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 ?   10.5   0.5   0.00072      0.56      62      89 ..     162     189 ..     129     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00072
                       SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                   + ++++f DE  ++lD +s++++++l++
  gi|91772902|ref|YP_565594.1| 162 NEPKILFADEPTANLDTDSSKEVIDLFR 189
                                   56899*********************98 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 ?   11.1   0.1   0.00028      0.22       3      37 ..      38      74 ..      36      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                  EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-S CS
                          cobW  3 tvltGflGsGKTtLlnhll..enraglklavivNefg 37
                                  + + G+ GsGK+tLl +l   +   + k+ +  N++ 
  gi|91772902|ref|YP_565594.1| 38 VAIMGPSGSGKSTLLHQLGllDTPTNGKITIDDNDII 74
                                  5799***********9985557777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1448.62
//
Query:       gi|91772903|ref|YP_565595.1|  [L=76]
Description: hypothetical protein Mbur_0898 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 560.47
//
Query:       gi|91772904|ref|YP_565596.1|  [L=643]
Description: hydantoinase/oxoprolinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-33  114.7   6.0    1.6e-28   99.6   3.0    3.3  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    2.2e-32  112.5   2.6    1.4e-30  106.6   0.0    2.8  3  Hydantoinase_A  Hydantoinase/oxoprolinase
    9.3e-09   34.4   3.2    0.00053   18.7   0.5    2.2  2  MutL            MutL protein
     0.0032   17.0   1.6      0.066   12.7   0.1    2.8  3  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
     0.0032   17.7   0.0     0.0076   16.4   0.0    1.6  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.056   12.7   0.3       0.16   11.2   0.1    1.8  2  StbA            StbA protein
       0.13   11.4   0.1       0.35   10.0   0.0    1.6  2  TGT             Queuine tRNA-ribosyltransferase
       0.14   11.7   0.5        2.4    7.7   0.5    2.5  1  FGGY_N          FGGY family of carbohydrate kinases, N-termin


Domain annotation for each model (and alignments):
>> 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 !   99.6   3.0   7.2e-32   1.6e-28       2     177 ..       5     159 ..       4     160 .. 0.90
   2 !   11.6   0.0   7.3e-05      0.16       2      83 ..     257     362 ..     256     382 .. 0.73

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 7.2e-32
                    Hydant_A_N   2 igIDvGGTfTDavaldeke.eevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaL 81 
                                   +gID+GGT+TDav++++++  +v ++K+ +t  +   gi +al+ v +e     ++++ v ++TT+atN++le++g +v+L
  gi|91772904|ref|YP_565596.1|   5 LGIDAGGTYTDAVLINDGDgSVVGATKARTTYPDLLVGIQNALDGVDQEI---LQQVKLVSVSTTLATNTILEKTGYPVGL 82 
                                   79*************9888788999*********************7764...57************************** PP

                    Hydant_A_N  82 ittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhSyl 162
                                   i     +    i ++  + +            +  + vd++++  g++  pld ++v+e ++++ka+ v+++av++++S++
  gi|91772904|ref|YP_565596.1|  83 ILVGNAE----IPKN--SAI------------KYSISVDGGHSSGGNETAPLDIDSVKEFVESVKAK-VSAFAVSSYFSVR 144
                                   9976654....3322..122............44699****************************98.************* PP

                    Hydant_A_N 163 npehElrvaeiarei 177
                                   npehEl+v+e++ e+
  gi|91772904|ref|YP_565596.1| 145 NPEHELKVKEVITEL 159
                                   ***********9985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.3e-05
                    Hydant_A_N   2 igIDvGGTfTDavaldeke..............eevavlKllst...........pdavaegirealeevleesiprtski 57 
                                   + IDvGGT TD+ ++ ++               ++v ++K+ ++           ++ ++ g r+++     +s+  +  i
  gi|91772904|ref|YP_565596.1| 257 VVIDVGGTSTDVSLIVDGLpqisdtgavvggwqTKVEAIKMETSamggdshvwvrNHVISIGPRRVVPLCVAASKY-PMII 336
                                   78**********9998554889999999999988899999998877777776665555555666666666666555.7777 PP

                    Hydant_A_N  58 dvvrmGTTvatNallerkgervaLit 83 
                                   + +++G  v  N l e+ +++  +i 
  gi|91772904|ref|YP_565596.1| 337 KKLKHGQSVTRNQLGENLQPTKFFIR 362
                                   77777777777777776665555555 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.2     0.008        18      82     108 ..       5      31 ..       2      42 .. 0.82
   2 !  106.6   0.0   6.1e-34   1.4e-30       1     145 [.     179     320 ..     179     398 .. 0.92
   3 ?   -0.5   0.0      0.25   5.7e+02     208     284 ..     462     541 ..     401     546 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.008
                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevslete 108
                                   +++D GGT tD+ li+dg   v+ +t+
  gi|91772904|ref|YP_565596.1|   5 LGIDAGGTYTDAVLINDGDGSVVGATK 31 
                                   578***************987776665 PP

  == domain 2  score: 106.6 bits;  conditional E-value: 6.1e-34
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   r+ ta +nA l pi +++++ v +++e rg+ a+lm++++dG++v + ea k+p+e i  GPaa++ gaa+   l +e  +
  gi|91772904|ref|YP_565596.1| 179 RGITAFLNAQLLPIANQFMNTVVSEIERRGIDAKLMMLKCDGSIVGITEALKHPIESIFTGPAASLLGAAY---LSKEPTC 256
                                   789********************************************************************...7778889 PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpe 145
                                   +++D+GGTstDvsli dg +++s    + +g +++++a++++t ++gG+s ++v +  ++++gp+
  gi|91772904|ref|YP_565596.1| 257 VVIDVGGTSTDVSLIVDGLPQISDTGAVvGGWQTKVEAIKMETSAMGGDSHVWVRN-HVISIGPR 320
                                   **********************98877669**********************6655.89999997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.25
                Hydantoinase_A 208 lk.veevAegilsvavenmana.vrkl.svergld.pkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmal 284
                                   +k ++++A ++ls + en+a a ++k    ++++  ++++ +v  GG+    ++a+ +++   +++ p+ya+v +a+G+++
  gi|91772904|ref|YP_565596.1| 462 KKvAKNMALNLLSYLMENVAPAeIEKGlDGDYRAGfKTDVPVVLLGGPVRAYTEAI-KKFVDANILLPEYAEVGNAVGALA 541
                                   22256666666666666666432444312333333134555677788888888888.444456788888889999998765 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   2.3e-07   0.00053       2      57 ..       5      56 ..       4      71 .. 0.83
   2 !   16.1   0.1   1.5e-06    0.0033     222     274 ..     234     281 ..     221     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-07
                          MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgk 57
                                  l iD G t+T ++l+++ +  ++++g ++a Tt    d+l G+++al+ + +++ +
  gi|91772904|ref|YP_565596.1|  5 LGIDAGGTYTDAVLINDGD--GSVVGATKARTTYP--DLLVGIQNALDGVDQEILQ 56
                                  569**************76..*************5..***********99998653 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-06
                          MutL 222 aeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekekv 274
                                   + i + PaA l ++  l++  e     ++v+DvGG++Tdv  +++g p+++++
  gi|91772904|ref|YP_565596.1| 234 ESIFTGPAASLLGAAYLSK--EP---TCVVIDVGGTSTDVSLIVDGLPQISDT 281
                                   678899*************..45...68*******************999876 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1     3e-05     0.066       1      30 [.       5      48 ..       5     162 .. 0.65
   2 ?    2.0   0.0     0.054   1.2e+02       3      29 ..     259     292 ..     244     354 .. 0.84
   3 ?   -0.5   0.0      0.32   7.1e+02     212     263 ..     494     539 ..     423     541 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                  EEEEE-SSEEEEEEEET.TTEEEEEEEE--.............T CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmde.kgevlgrgitns.............a 30
                                  +GiD G+T t avl+++ +g+v+g +++ +             +
  gi|91772904|ref|YP_565596.1|  5 LGIDAGGTYTDAVLINDgDGSVVGATKARTtypdllvgiqnalD 48
                                  8*************998256699998887744555544444440 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.054
                                   EEE-SSEEEEEEEE.......TTTEEEEEEEE-- CS
                   BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitns 29 
                                   iD+G+T+t + l+        + g v+g ++t+ 
  gi|91772904|ref|YP_565596.1| 259 IDVGGTSTDVSLIVdglpqisDTGAVVGGWQTKV 292
                                   8899999887765546666666677777766665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.32
                                   TT---SS..EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHH CS
                   BcrAD_BadFG 212 rsggvtde.vtltGGvakneaavkelrklvkenygevkininpdsiytgalGA 263
                                   r g+ td  v+l GG  ++  + ++++k v+ n++      + ++++  a+GA
  gi|91772904|ref|YP_565596.1| 494 RAGFKTDVpVVLLGGPVRA--YTEAIKKFVDANILL-----PEYAEVGNAVGA 539
                                   3344444489999999988..788887777777654.....566666666666 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.4e-06    0.0076      54     136 ..     534     617 ..     530     632 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-06
                                   EEEEEEEE-SSSSSEEEEEEE--TTS--EEGGG-EEEEEESS.--EE--E.....................T-EE-TT-EE CS
                Arch_flagellin  54 tgdvgdsatngtineitiyvklnaGsspidlnkttisvtddg.qetlltadefgivvisdtdgsltng...devlekgekv 130
                                    ++vg+ a +g ++ i+i ++++ G s+ +l+ t+isv+ +  + +++++ e  i   ++  + l+ +   d  l++g+ +
  gi|91772904|ref|YP_565596.1| 534 GNAVGALAGKG-VKRIEILIRVTFGESKYNLKPTSISVFSPQgKHEMVNYGE-AIQFAEKLGNDLVMQymkDAQLDDGD-I 611
                                   56677666665.999***************************9*******64.44444444444444445455555544.4 PP

                                   EEEEE- CS
                Arch_flagellin 131 elevnv 136
                                   ++ev  
  gi|91772904|ref|YP_565596.1| 612 KIEVSK 617
                                   566554 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.5   3.4e+03     203     235 ..     119     151 ..     116     158 .. 0.80
   2 ?   11.2   0.1   6.9e-05      0.16     158     190 ..     249     281 ..     232     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                          StbA 203 davkealetaktrtssfladeliknrkdeeyLk 235
                                   d+vke +e++k ++s f + +  + r+ e+ Lk
  gi|91772904|ref|YP_565596.1| 119 DSVKEFVESVKAKVSAFAVSSYFSVRNPEHELK 151
                                   678889999999999999998888888887776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.9e-05
                          StbA 158 eldeleslLiiDlGGttLDvakvrgklegiskv 190
                                    l++    ++iD+GGt  Dv+ +   l +is++
  gi|91772904|ref|YP_565596.1| 249 YLSKEPTCVVIDVGGTSTDVSLIVDGLPQISDT 281
                                   477788899*********************986 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1   2.5e+03     201     235 ..     451     485 ..     446     488 .. 0.87
   2 ?   10.0   0.0   0.00016      0.35      92     135 ..     562     604 ..     545     619 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                                   SSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHH CS
                           TGT 201 geekeellevveavtellpedkprylmGvgtPedl 235
                                   +e k+  l++ ++v++++  +   ylm    P ++
  gi|91772904|ref|YP_565596.1| 451 MEVKDLCLDIKKKVAKNMALNLLSYLMENVAPAEI 485
                                   677888999999****************9999987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00016
                                   EEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE------ CS
                           TGT  92 kiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvv 135
                                   +++ +++s++s+ +G++ +++  e i++ eklg D++m+  +  
  gi|91772904|ref|YP_565596.1| 562 NLKPTSISVFSP-QGKHEMVNYGEAIQFAEKLGNDLVMQYMKDA 604
                                   457889******.5*************************54434 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 ?    7.7   0.5    0.0011       2.4       1      31 [.       3      34 ..       3      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                                  EEEEEEEESSEEEEEEEE.TTS-EEEEEEEE- CS
                        FGGY_N  1 lilglDcGttstkaivld.ekgkvvasaqael 31
                                  + lg+D G+t t a++++  +g vv++ +a  
  gi|91772904|ref|YP_565596.1|  3 YSLGIDAGGTYTDAVLINdGDGSVVGATKART 34
                                  679***************99****99877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4351.08
//
Query:       gi|91772905|ref|YP_565597.1|  [L=641]
Description: hydantoinase/oxoprolinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-31  108.2   0.9    4.2e-30  105.0   0.1    2.6  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.9e-29  102.6   0.2    8.5e-25   87.5   0.0    3.4  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    2.5e-06   26.4   0.3      0.043   12.4   0.0    2.2  2  MutL            MutL protein
  ------ inclusion threshold ------
       0.04   13.7   0.1      0.094   12.5   0.1    1.6  1  Sda             Sporulation inhibitor A
      0.063   12.7   0.1       0.16   11.4   0.0    1.7  2  ROK             ROK family
      0.097   11.9   0.0       0.19   10.9   0.0    1.4  1  StbA            StbA protein
       0.13   12.2   0.0        1.9    8.4   0.0    2.5  2  GCV_H           Glycine cleavage H-protein
       0.13   12.2   0.0       0.41   10.6   0.0    1.8  2  Endopep_inhib   IseA DL-endopeptidase inhibitor
       0.52    9.8   1.8        6.8    6.1   1.7    2.4  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family


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 ?    0.5   0.1      0.15     3e+02      83     105 ..       6      28 ..       3      48 .. 0.80
   2 !  105.0   0.1   2.1e-33   4.2e-30       1     146 [.     179     321 ..     179     545 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                Hydantoinase_A  83 tfDmGGTstDvslikdgevevsl 105
                                   ++D GGT tD   i+d   e++ 
  gi|91772905|ref|YP_565597.1|   6 GIDAGGTYTDSVIIRDSDGEIVD 28 
                                   689*******9999988777654 PP

  == domain 2  score: 105.0 bits;  conditional E-value: 2.1e-33
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   r+ ta++nA l pi   ++e + ++l  r+++ar++++++dG++v +dea++kp+e i SGPaa++vgaa+   l +++ +
  gi|91772905|ref|YP_565597.1| 179 RGITAYLNAQLIPITDHFIETIINELGRRQIEARVLMLKCDGSVVGIDEAKEKPIESIFSGPAASLVGAAY---LSKSDTC 256
                                   789********************************************************************...899999* PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpes 146
                                    ++D+GGTstDvs i++  +e   e  i +g +++++a++++t ++gG+s ++  ++++ ++gp+ 
  gi|91772905|ref|YP_565597.1| 257 AVIDVGGTSTDVSMINNELPELCDEGAIvGGWQTKVKAIRMETSAMGGDSHIW-IKNQRPNIGPRR 321
                                   *********************999987769**********************5.555888888874 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 !   87.5   0.0   4.3e-28   8.5e-25       2     176 ..       5     158 ..       4     160 .. 0.88
   2 !    8.6   0.1    0.0007       1.4       3      19 ..     258     274 ..     257     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 4.3e-28
                    Hydant_A_N   2 igIDvGGTfTDavaldeke.eevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaL 81 
                                   +gID+GGT+TD v++++ + e v + K+l+t  +  egi+++l+ + ++      +++ v ++TT+ tN++le +g +vaL
  gi|91772905|ref|YP_565597.1|   5 MGIDAGGTYTDSVIIRDSDgEIVDSNKALTTYPNLLEGIKNSLDGLDQSYLV---NVKLVSVSTTLSTNTILESTGYPVAL 82 
                                   79************99888788999*********************887766...9************************* PP

                    Hydant_A_N  82 ittkgf..rdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhS 160
                                   i+  ++  +d+++i      +                + +++++  +ge+ +pld + ++  +   k++ v+++av++++S
  gi|91772905|ref|YP_565597.1|  83 IMAGDYliPDTHSIT-----N---------------YFVAEGGHGPNGEETSPLDINGIKDYVLLNKDK-VSAFAVSSYFS 142
                                   *98764223444333.....3...............35699*******************999877776.*********** PP

                    Hydant_A_N 161 ylnpehElrvaeiare 176
                                    +np+hEl+v+e++++
  gi|91772905|ref|YP_565597.1| 143 IRNPDHELQVKELIKD 158
                                   *************987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0007
                    Hydant_A_N   3 gIDvGGTfTDavaldek 19 
                                    IDvGGT TD+ +++++
  gi|91772905|ref|YP_565597.1| 258 VIDVGGTSTDVSMINNE 274
                                   69*********999844 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   3.1e-05     0.062       4      55 ..       7      54 ..       5      73 .. 0.85
   2 !   12.4   0.0   2.2e-05     0.043     212     269 ..     224     276 ..     206     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.1e-05
                          MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleekl 55
                                  iD G t+T  +++++++  ++++ + +a+Tt    ++leG++++l+ l ++ 
  gi|91772905|ref|YP_565597.1|  7 IDAGGTYTDSVIIRDSD--GEIVDSNKALTTYP--NLLEGIKNSLDGLDQSY 54
                                  89*************66..*************5..9**********999874 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.2e-05
                          MutL 212 glskleelvsaeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegsp 269
                                   g+++++e   + i   PaA l ++  l++  +   + + v+DvGG++Tdv  + ++ p
  gi|91772905|ref|YP_565597.1| 224 GIDEAKEKPIESIFSGPAASLVGAAYLSK--S---DTCAVIDVGGTSTDVSMINNELP 276
                                   677777777889999**************..3...3689***********98865555 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.7e-05     0.094      10      39 ..     181     210 ..     181     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                           Sda  10 ieaYekAlelnLdpDFIeLieeEierRsLs 39 
                                   i aY +A+   + + FIe i +E+ rR+++
  gi|91772905|ref|YP_565597.1| 181 ITAYLNAQLIPITDHFIETIINELGRRQIE 210
                                   6799************************97 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.1e-05      0.16       2      52 ..       5      56 ..       4      72 .. 0.80
   2 ?   -3.2   0.0       2.3   4.5e+03       3      19 ..     258     274 ..     256     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.1e-05
                                  EEEEE-SSEEE.EEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHC CS
                           ROK  2 igidiGgtkia.lalvdeegeilarekvetptetteetlvdaiaelvdeaer 52
                                  +gid+Ggt++  ++++d++gei++++k  t+ +++ e++ ++++ l +++  
  gi|91772905|ref|YP_565597.1|  5 MGIDAGGTYTDsVIIRDSDGEIVDSNKALTTYPNLLEGIKNSLDGLDQSYLV 56
                                  69*******96378899***********899999999988888777666644 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.3
                                   EEEE-SSEEEEEEEETT CS
                           ROK   3 gidiGgtkialalvdee 19 
                                    id+Ggt + + ++++e
  gi|91772905|ref|YP_565597.1| 258 VIDVGGTSTDVSMINNE 274
                                   69******999999876 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.5e-05      0.19     150     187 ..     240     278 ..     232     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.5e-05
                          StbA 150 Pagfealke.ldeleslLiiDlGGttLDvakvrgklegi 187
                                   Pa+  + +  l++ +   +iD+GGt  Dv+ ++ +l ++
  gi|91772905|ref|YP_565597.1| 240 PAASLVGAAyLSKSDTCAVIDVGGTSTDVSMINNELPEL 278
                                   77766666669*********************9998665 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00094       1.9      63     105 ..      18      65 ..      11      76 .. 0.78
   2 ?    0.4   0.0      0.29   5.7e+02      67     104 ..     261     298 ..     250     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00094
                                   EE-SSSEEEEEE-GGGTT-TTHH....HH.-TTTTT--EEEEES-GGG CS
                         GCV_H  63 vyapvsGevvevNekleeepeli....Nk.dpyeegWliklklsnlee 105
                                   +  + +Ge+v+ N++l+  p+l+    N+ d +++++l+ +kl ++++
  gi|91772905|ref|YP_565597.1|  18 IIRDSDGEIVDSNKALTTYPNLLegikNSlDGLDQSYLVNVKLVSVST 65 
                                   667889***************983333324778899999999877765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.29
                                   SSEEEEEE-GGGTT-TTHHHH-TTTTT--EEEEES-GG CS
                         GCV_H  67 vsGevvevNekleeepeliNkdpyeegWliklklsnle 104
                                   v G+ ++v    +e pel  +     gW  k+k+  +e
  gi|91772905|ref|YP_565597.1| 261 VGGTSTDVSMINNELPELCDEGAIVGGWQTKVKAIRME 298
                                   5566666666667889****************986655 PP

>> Endopep_inhib  IseA DL-endopeptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         3     6e+03      28      62 ..     106     141 ..      95     143 .. 0.71
   2 ?   10.6   0.0    0.0002      0.41      49     107 ..     171     232 ..     168     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3
                                   S-TT-S---EEEETT.EEEEE--TTSSSHHHHHHHH CS
                 Endopep_inhib  28 kspkkkeiksievkg.keYaklkddintkeklfnYL 62 
                                   + p+ +e   ++++g k+Y+ l++d  +   +++Y+
  gi|91772905|ref|YP_565597.1| 106 HGPNGEETSPLDINGiKDYVLLNKDKVSAFAVSSYF 141
                                   555666778888888557999999966666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                                   -TTSSSHHH.HHHHHTT...TB-HHHHHHHHHTTT-EEETTEEEEE-------B-GGG-EEEE CS
                 Endopep_inhib  49 kddintkek.lfnYLne...yfTkeaiekiikdlkfkeidgklavpvgdggslldikkakikl 107
                                   ++d++ +++ +++YLn      T+ +ie ii++l+ ++i+ ++ ++ +dg s ++i++ak k 
  gi|91772905|ref|YP_565597.1| 171 SQDLGAYNRgITAYLNAqliPITDHFIETIINELGRRQIEARVLMLKCDG-SVVGIDEAKEKP 232
                                   667777764499****988889***************************7.678899998765 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 ?    6.1   1.7    0.0034       6.8       2      30 ..       6     179 ..       5     274 .. 0.54
   2 ?    2.5   0.1     0.042        83       3      33 ..     259     296 ..     257     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0034
                                   EEEE-SSEEEEEEE.ETTTEEEEEEEE--.................................................... CS
                   BcrAD_BadFG   2 GiDgGsTttkavlm.dekgevlgrgitns.................................................... 29 
                                   GiD G+T t  v++ d +ge++   ++ +                                                    
  gi|91772905|ref|YP_565597.1|   6 GIDAGGTYTDSVIIrDSDGEIVDSNKALTtypnllegiknsldgldqsylvnvklvsvsttlstntilestgypvalimag 86 
                                   9*******9877661567889988888776666666666666666666666666666666666666666666666666666 PP

                                   ................................................................................. CS
                   BcrAD_BadFG  30 ................................................................................. 29 
                                                                                                                    
  gi|91772905|ref|YP_565597.1|  87 dylipdthsitnyfvaegghgpngeetspldingikdyvllnkdkvsafavssyfsirnpdhelqvkelikdltglpvvcg 167
                                   666666666666666666666666666666666666666666666666666666555555555555555555555555555 PP

                                   ...........T CS
                   BcrAD_BadFG  30 ...........a 30 
                                              +
  gi|91772905|ref|YP_565597.1| 168 helsqdlgaynR 179
                                   555555555542 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.042
                                   EEE-SSEEEEEEEE.......TTTEEEEEEEE--TTS- CS
                   BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitnsanle 33 
                                   iD+G+T+t +  ++       ++g ++g ++t+ + ++
  gi|91772905|ref|YP_565597.1| 259 IDVGGTSTDVSMINnelpelcDEGAIVGGWQTKVKAIR 296
                                   9********99999899999999999999998876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 4305.35
//
Query:       gi|91772906|ref|YP_565598.1|  [L=202]
Description: methylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-07   31.3   0.0    1.1e-06   28.3   0.0    2.0  2  MTS              Methyltransferase small domain
    4.5e-06   26.5   0.0    6.3e-06   26.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    6.1e-06   26.9   0.0    1.4e-05   25.7   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00048   19.9   0.0    0.00077   19.3   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00084   19.2   0.0     0.0022   17.9   0.0    1.6  2  Methyltransf_23  Methyltransferase domain
    0.00097   19.7   0.0      0.003   18.2   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
     0.0071   17.1   0.0      0.015   16.1   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.7   0.2      0.017   15.0   0.2    1.3  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.014   15.1   0.0      0.021   14.6   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
      0.019   14.6   0.0      0.037   13.6   0.0    1.4  2  MetW             Methionine biosynthesis protein MetW
      0.027   13.8   0.0       0.16   11.2   0.0    1.9  2  CMAS             Mycolic acid cyclopropane synthetase
       0.06   12.4   0.0      0.085   11.9   0.0    1.1  1  DREV             DREV methyltransferase
      0.088   13.8   0.0       0.64   11.1   0.0    2.0  1  Methyltransf_24  Methyltransferase domain
       0.12   11.4   0.0       0.16   11.0   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase


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 !   28.3   0.0   8.7e-10   1.1e-06      31     108 ..      37     108 ..      21     119 .. 0.81
   2 ?    0.6   0.0      0.28   3.6e+02     115     147 ..     131     163 ..     124     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.7e-10
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEEEEE---ST CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdlivsNPPfh 108
                                      +vl +G+G+G+++a+l+  + ++++++++++  A e+ak+n       vev+  d++  +  + kfdli+ NPP+ 
  gi|91772906|ref|YP_565598.1|  37 DGMHVLEVGAGTGFVSAVLQT-NVDVDLVATEISPFAAECAKRNS------VEVIRADMFGCFGsDTKFDLILFNPPYL 108
                                   4567************99877.66779*************99874......67888888887765899*********85 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHH CS
                           MTS 115 lavaeeliaeAkeaLkegGeLliVanrklgyes 147
                                    ++++++++e + +L++gG +l+ +++  g+++
  gi|91772906|ref|YP_565598.1| 131 REAVDRFLEEFPPYLSDGGIILVLISSLTGIDK 163
                                   5688999************99999988777665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   4.9e-09   6.3e-06       2     111 ..      36     155 ..      35     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.9e-09
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                   ++g++vl++G+GtG+ + +l    + + ++v  +is++a e A+ n        ve+ ++d++  +    +d kfDlil n
  gi|91772906|ref|YP_565598.1|  36 QDGMHVLEVGAGTGFVSAVLQ--TNVDVDLVATEISPFAAECAKRN-------SVEVIRADMFGcFG---SDTKFDLILFN 104
                                   579*****************9..45588899999999999999997.......8**********777...579******** PP

               Methyltransf_31  82 .................evl.....naladpdkileeiervlkpggillied 111
                                                            +   + d +lee + +l++ggi+l+  
  gi|91772906|ref|YP_565598.1| 105 ppylptaedekipgwlnY-AfdggiDGREAVDRFLEEFPPYLSDGGIILVLI 155
                                   888888888777755552.04666699999999999**********998754 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.1e-08   1.4e-05       1      72 [.      41     105 ..      41     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.1e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEES CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssg 72 
                                   vL++G+GtG +++ l++++ + ++++++is+ + e a+++       ve++++d+  +   d +fDl++ + 
  gi|91772906|ref|YP_565598.1|  41 VLEVGAGTGFVSAVLQTNV-DVDLVATEISPFAAECAKRNS------VEVIRADMFGCFGSDTKFDLILFNP 105
                                   9*****************9.7**************999998......9*******999999*******9864 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     6e-07   0.00077      71     115 ..      35      77 ..       3      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6e-07
                                   --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHH CS
                          PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeak 115
                                    ++g++vLevG+G+G+ +avl + v  +   v+ e ++  +e ak
  gi|91772906|ref|YP_565598.1|  35 AQDGMHVLEVGAGTGFVSAVLQTNVDVDL--VATEISPFAAECAK 77 
                                   478*******************9998776..66665555555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.7e-06    0.0022      20      88 ..      35     103 ..      20     105 .. 0.83
   2 ?   -1.8   0.0       1.9   2.5e+03     108     118 ..     144     154 ..     129     183 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvl 88 
                                    + g+ vL++G+GtG ++ vl++n+  ++++ ++sp a e a+      ++   + +f       ++ kfdlI  
  gi|91772906|ref|YP_565598.1|  35 AQDGMHVLEVGAGTGFVSAVLQTNVDvDLVATEISPFAAECAKrnsveVIRADMFGCF------GSDTKFDLILF 103
                                   577899******************877*********9999888887766677777777......78889999976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
               Methyltransf_23 108 llkpgGyllls 118
                                   +l++gG +l++
  gi|91772906|ref|YP_565598.1| 144 YLSDGGIILVL 154
                                   45555555554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.3e-06     0.003       1      67 [.      42     103 ..      42     116 .. 0.90
   2 ?   -1.9   0.0       4.2   5.4e+03      76      95 ..     133     152 ..     118     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                                   EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvs 67 
                                   L+vG+GtG +++ l+ ++  ++v++++s+ + ++ak++++e      +++ad+      d +fDl++ 
  gi|91772906|ref|YP_565598.1|  42 LEVGAGTGFVSAVLQTNVdVDLVATEISPFAAECAKRNSVE------VIRADMFGCFGSDTKFDLILF 103
                                   89*************8889*************999988866......489999998888899999976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.2
                                   CHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                    ++++l+e+   L  gG+++
  gi|91772906|ref|YP_565598.1| 133 AVDRFLEEFPPYLSDGGIIL 152
                                   57899999999999999986 PP

>> Methyltransf_12  Methyltransferase 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     0.015       1      39 [.      42      79 ..      42     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
               Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakek 39
                                  Le+G+GtG ++++l  +  d+++++++isp a e ak+ 
  gi|91772906|ref|YP_565598.1| 42 LEVGAGTGFVSAVLQTN-VDVDLVATEISPFAAECAKRN 79
                                  8*******888887666.*************99555544 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   1.4e-05     0.017       5      61 ..      28      89 ..      25      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                  HHHHHHHS-SS.EEEEET-TT--HHHHHHHHHS.-EEEEE-SS-S........STTEE---SS CS
                       UPF0146  5 akkiaeenarg.kvvEvGiGrkldvaealakrg.vdlvatDikek...kak.egvrivrDDvt 61
                                  a++++ +++ g +v EvG+G+ + v++ l+    vdlvat+i +     ak ++v+++r D++
  gi|91772906|ref|YP_565598.1| 28 ADVAIDVAQDGmHVLEVGAGTGF-VSAVLQTNVdVDLVATEISPFaaeCAKrNSVEVIRADMF 89
                                  6778888888889*******998.5556655545********987333334467777777765 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.021      44      88 ..      35      79 ..      14      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
               Methyltransf_16 44 elsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkkn 88
                                  ++ +++vlE+G+GtG v  ++++   +++++ t ++  + e+ k+n
  gi|91772906|ref|YP_565598.1| 35 AQDGMHVLEVGAGTGFVSAVLQTN-VDVDLVATEISPfAAECAKRN 79
                                  56789*************999998.789999999988677888776 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.9e-05     0.037       9      81 ..      33     103 ..      27     115 .. 0.82
   2 ?   -3.1   0.0       3.9     5e+03      37      67 ..     168     183 ..     161     196 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                          MetW   9 elikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvl 81 
                                   ++ ++g +vl++G+G G +  +l+ + +vd    e++  +   +    ++vi+ d+   +   +d +fd++++
  gi|91772906|ref|YP_565598.1|  33 DVAQDGMHVLEVGAGTGFVSAVLQTNVDVDLVATEISPFAAECAKRNSVEVIRADMFGCF--GSDTKFDLILF 103
                                   5668999*****************************988766566668999999885543..35777887765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                          MetW  37 vdgrGleldeegvaecvakGlsviqgdldkd 67 
                                   ++grGl+++  ++               d+d
  gi|91772906|ref|YP_565598.1| 168 MQGRGLDVEVCNI---------------DRD 183
                                   4445554444444...............433 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.16      60     102 ..      35      77 ..       3      87 .. 0.77
   2 ?    0.3   0.0      0.26   3.4e+02     141     180 ..     130     171 ..     126     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                   --TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHH CS
                          CMAS  60 lkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklak 102
                                    ++Gm++L++G+G G +      + dv+ v+  +S   a+ ak
  gi|91772906|ref|YP_565598.1|  35 AQDGMHVLEVGAGTGFVSAVLQTNVDVDLVATEISPFAAECAK 77 
                                   379***************9999999**9999999876666555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.26
                                   SGGGHHHHHHHHHHHS-TT-EE..EEEEEEE--HHHHHCTTC CS
                          CMAS 141 gkenydtffkklkkllkedGll..llhtitslhkkelaergl 180
                                   g e  d+f +++   l ++G++  l+ ++t  +k +++ +g 
  gi|91772906|ref|YP_565598.1| 130 GREAVDRFLEEFPPYLSDGGIIlvLISSLTGIDKVKMHMQGR 171
                                   667889999999999999997611568888888888887765 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.6e-05     0.085      91     156 ..      34     102 ..      22     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
                          DREV  91 sdqedkklldlGaGdGeitkrvaptfe.evyatelsetmrdrlkkkkynvlsale..lqetdvkldlil 156
                                     q+  ++l++GaG G ++  ++  ++ ++ ate+s    +  k+   +v+ a       +d k+dlil
  gi|91772906|ref|YP_565598.1|  34 VAQDGMHVLEVGAGTGFVSAVLQTNVDvDLVATEISPFAAECAKRNSVEVIRADMfgCFGSDTKFDLIL 102
                                   4577889***************99998359******999999999999999876523446788888885 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005      0.64       2     102 ..      43     152 ..      42     153 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
               Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikads................eealasla 66 
                                   E+G  +G    ++ + l+ n +  lva +  p    aa+ a++    + v++i+ad+                + +l++ +
  gi|91772906|ref|YP_565598.1|  43 EVG--AGT--GFVSAVLQTNVDVDLVATEISP---FAAECAKR----NSVEVIRADMfgcfgsdtkfdlilfnPPYLPTAE 112
                                   677..333..3344457788888899999999...77777765....8999999999666666666666665544444444 PP

               Methyltransf_24  67 agsiD...llfiDgghaa.eavledleallprlapggvvl 102
                                   +++i     + +Dgg ++ eav ++le + p+l++gg++l
  gi|91772906|ref|YP_565598.1| 113 DEKIPgwlNYAFDGGIDGrEAVDRFLEEFPPYLSDGGIIL 152
                                   3333233344567777763567777899999999999887 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.16      30      84 ..      37      87 ..      10      91 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                  TTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S- CS
                        RrnaAD 30 ekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkklskdeklkvvhqD 84
                                  + + vle+g+G+G+ ++ L   +   +v+ E+ + +a++  k     + ++v+ +D
  gi|91772906|ref|YP_565598.1| 37 DGMHVLEVGAGTGFVSAVLQTNVdVDLVATEISP-FAAECAK----RNSVEVIRAD 87
                                  789****************777768999999865.4444444....2445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1405.79
//
Query:       gi|91772907|ref|YP_565599.1|  [L=270]
Description: dimethyladenosine transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-57  192.2   0.1    1.1e-56  191.9   0.1    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      6e-07   30.1   0.0    2.1e-06   28.3   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    4.2e-05   24.2   0.0    0.00023   21.8   0.0    2.2  2  Methyltransf_12  Methyltransferase domain
    8.6e-05   23.1   0.0    0.00027   21.5   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
     0.0049   16.3   0.1     0.0084   15.5   0.1    1.3  1  Spermine_synth   Spermine/spermidine synthase domain
      0.009   15.6   0.0      0.014   15.1   0.0    1.2  1  NodS             Nodulation protein S (NodS)
     0.0094   15.7   0.0      0.016   14.9   0.0    1.4  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.021   14.1   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
      0.021   14.7   0.0      0.025   14.4   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.027   14.0   0.0      0.051   13.1   0.0    1.4  1  MTS              Methyltransferase small domain
      0.029   13.9   0.0      0.046   13.2   0.0    1.3  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas


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 !  191.9   0.1   6.7e-60   1.1e-56      10     227 ..      18     222 ..      15     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 6.7e-60
                                   --EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHH CS
                        RrnaAD  10 qnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfet 90 
                                   q+fl+++  +++I+d+++l+ek+ vleig G G+lTe+L++ a +v v+Eld++L+ +l++++s++ekl+++  D+lk ++
  gi|91772907|ref|YP_565599.1|  18 QHFLIDERSLDSIVDQAELSEKDVVLEIGGGIGNLTERLLEKAGKVYVIELDPALVHVLKDRFSDNEKLEIIPGDVLKLDL 98 
                                   9******************************************************************************** PP

                                   HHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEE CS
                        RrnaAD  91 peevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdvklva 171
                                   p++           +vvanlPy is+++ ++l++ + f  +  +l+ q efa+r++a+ +  ++srlsv++++f+d+ +++
  gi|91772907|ref|YP_565599.1|  99 PKFN----------KVVANLPYSISSPITFKLFK-HEF--ELGILMYQYEFAQRMVAKANTENYSRLSVNTHYFADADIIM 166
                                   **55..........9******************6.777..89*************************************** PP

                                   EC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCC CS
                        RrnaAD 172 kveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslks 227
                                   k+++s+fsPpp+v sa+v+  +++ ++  +d + +  +v++++ ++rk+l++++ +
  gi|91772907|ref|YP_565599.1| 167 KIPPSAFSPPPEVWSAVVKVVPRPSSFHTEDPQFFLDLVTAVFLQRRKKLRNAIVK 222
                                   *****************************************************873 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.3e-09   2.1e-06       1      71 [.      42     107 ..      42     127 .. 0.87
   2 ?   -1.5   0.0       2.6   4.2e+03      28      41 ..     135     148 ..     113     172 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-09
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71 
                                   vL++G G G+lt++l+++   +kv+ ++++++++   + r+++++ ++e++ gd+ +l++++  f+ vv++
  gi|91772907|ref|YP_565599.1|  42 VLEIGGGIGNLTERLLEKA--GKVYVIELDPALVHVLKDRFSDNE-KLEIIPGDVLKLDLPK--FNKVVAN 107
                                   9*****************6..9*******************8776.************9986..9999985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                                   ESSHHHHHHHHHHH CS
               Methyltransf_25  28 Diseemleaarera 41 
                                   +++++m+++a++++
  gi|91772907|ref|YP_565599.1| 135 EFAQRMVAKANTEN 148
                                   66778888877544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.4e-07   0.00023       1      72 [.      43     106 ..      43     120 .. 0.83
   2 ?   -0.7   0.0       1.6   2.5e+03      27      56 ..     203     232 ..     194     258 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                   LeiG+G G+l+++llek    ++++++++p+ ++  k +++++e     ++e+   d+l+ld + +f  vva
  gi|91772907|ref|YP_565599.1|  43 LEIGGGIGNLTERLLEK--AGKVYVIELDPALVHVLKDRFSDNE-----KLEIIPGDVLKLDLP-KFNKVVA 106
                                   8****************..**************88888888887.....566666666666665.6666655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
               Methyltransf_12  27 Dispsaiedakeklakrennnnnnveleal 56 
                                   D+ ++++ ++++kl+  + + n+ +++ ++
  gi|91772907|ref|YP_565599.1| 203 DLVTAVFLQRRKKLRNAIVKGNHLLNVPNI 232
                                   555555556667776666666666666554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.7e-07   0.00027       1      59 [.      43     100 ..      43     108 .. 0.92
   2 ?   -2.3   0.0       4.5   7.3e+03      21      38 ..     131     148 ..     120     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-T CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfed 59 
                                   L++G G G l+e l +++++v+ ++l+++++ + k++ s+++ k+e++ +d+ kl +++
  gi|91772907|ref|YP_565599.1|  43 LEIGGGIGNLTERLLEKAGKVYVIELDPALVHVLKDRFSDNE-KLEIIPGDVLKLDLPK 100
                                   89*************9999*********************99.59*********99986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.5
                                   EEEEES-HHHHHHHHHHC CS
               Methyltransf_11  21 vvgvDlskemlklakeka 38 
                                    +  +++++m++ a++++
  gi|91772907|ref|YP_565599.1| 131 MYQYEFAQRMVAKANTEN 148
                                   566778888887776554 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.1e-06    0.0084      19      62 ..      39      80 ..      26      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.1e-06
                                  T-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHS CS
                Spermine_synth 19 pkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkfl 62
                                  +  vL iGGg G+++ +++      k+ ++++D   + + k  +
  gi|91772907|ref|YP_565599.1| 39 KDVVLEIGGGIGNLTERLLEKA--GKVYVIELDPALVHVLKDRF 80
                                  45699*************9988..************99998755 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.3e-06     0.014      47     113 ..      42     106 ..      25     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.3e-06
                          NodS  47 alevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivva 113
                                   +le+G   G lterl   + ++ v+++ +  ++  + r  +  ++  i  dv ++++  kf+ + va
  gi|91772907|ref|YP_565599.1|  42 VLEIGGGIGNLTERLLEKAGKVYVIELDPALVHVLKDRFSDNEKLEIIPGDVLKLDLP-KFNKV-VA 106
                                   8******************************************************985.56654.34 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.9e-06     0.016      98     182 ..      36     114 ..      21     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.9e-06
                                   --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TT CS
                        Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpk 178
                                    +e +vV+++  GiG ++  +    ka +v+ i+l+P+ v+ lk+    N+  +++    +D+ ++    ++++vv nlp+
  gi|91772907|ref|YP_565599.1|  36 LSEKDVVLEIGGGIGNLTERLLE--KAGKVYVIELDPALVHVLKDRFSDNEKLEII---PGDVLKLD-LPKFNKVVANLPY 110
                                   56889************999987..9*******************99999765555...78888886.5678889999988 PP

                                   TGGG CS
                        Met_10 179 saie 182
                                   s  +
  gi|91772907|ref|YP_565599.1| 111 SISS 114
                                   7655 PP

>> Methyltransf_2  O-methyltransferase 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      52     128 ..      28     101 ..      15     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                   HHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS----- CS
                Methyltransf_2  52 kkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGdffkdslPea 128
                                   ++++ + +l++  +++++GGG+G l +   ++  ++ vi +D p  v+  k++  ++ +e++e + Gd+ k  lP+ 
  gi|91772907|ref|YP_565599.1|  28 DSIVDQAELSEKDVVLEIGGGIGNLTERLLEKAGKVYVIELD-PALVHVLKDR--FSDNEKLEIIPGDVLKLDLPKF 101
                                   578889999*********************************.8888999999..677899999******9999975 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-05     0.025      20      62 ..      36      83 ..      18     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
               Methyltransf_23 20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....k 62
                                  l ++  vL+iG G G+l+e l e+  +v++++l+p++v+ ++     +
  gi|91772907|ref|YP_565599.1| 36 LSEKDVVLEIGGGIGNLTERLLEKAGKVYVIELDPALVHVLKdrfsdN 83
                                  677889*************9999988**********999874333330 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.1e-05     0.051      31     110 ..      38     113 ..      25     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTT CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhag 110
                                   +++ vl +G G+G l+  l+++  +  v +++ d + +++ k  +++n+ ++e++  dvl+     kf+ +v N P+  +
  gi|91772907|ref|YP_565599.1|  38 EKDVVLEIGGGIGNLTERLLEKAGK--VYVIELDPALVHVLKDRFSDNE-KLEIIPGDVLKLDL-PKFNKVVANLPYSIS 113
                                   56679****************9998..99*******************9.7*********9766.7********998655 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05     0.046      51     100 ..      34      82 ..      12     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
               Methyltransf_PK  51 pgkrevkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelae 100
                                   ++ +e +v+l++G GiG +t++lL k ++kv ++e    +++ +k+++++
  gi|91772907|ref|YP_565599.1|  34 AELSEKDVVLEIGGGIGNLTERLLEK-AGKVYVIELDPALVHVLKDRFSD 82 
                                   4677899***************9976.68888888777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1912.68
//
Query:       gi|91772908|ref|YP_565600.1|  [L=198]
Description: hypothetical protein Mbur_0903 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-65  219.9   0.1    2.6e-65  219.7   0.1    1.0  1  DUF655    Protein of unknown function (DUF655)
    0.00013   22.1   0.0    0.00019   21.6   0.0    1.4  1  HHH_6     Helix-hairpin-helix motif
     0.0014   18.9   0.0     0.0029   17.8   0.0    1.5  1  HHH_3     Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.12   13.0   0.2        1.9    9.1   0.1    2.3  2  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7   0.1   5.9e-69   2.6e-65       2     180 ..      11     189 ..      10     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 5.9e-69
                                   --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS-HHH CS
                        DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLtdva 82 
                                   e++a+vLDylp+G  +dk+  +++kp+vqa+g +++ L+elvp++ v  +++++v+ig g +d i+++k +++++dL+++a
  gi|91772908|ref|YP_565600.1|  11 EDYAWVLDYLPYGSNTDKRPAYQKKPLVQAIGDKHFALVELVPKEGVSPEIQSKVYIGDGDRDVIDHVKHRVHFDDLSHGA 91 
                                   89******************************************************************************* PP

                                   HHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHHHH CS
                        DUF655  83 raeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaeilve 163
                                   + eLp v+e  vk++E++fv+ffn+a+pit+RlH LelLpg+gkkl+++i++eR++ +F+  +d+++rv g++ p++i+v+
  gi|91772908|ref|YP_565600.1|  92 QLELPFVLEICVKDREEKFVKFFNDAHPITTRLHMLELLPGIGKKLMWAIIDERKKGEFKDLQDLHDRVGGVHIPQKIIVN 172
                                   ********************************************************************************* PP

                                   HHHHHHH-TTSS--SS- CS
                        DUF655 164 rileEiedktekYylFv 180
                                   rileE++d++ kY+lF+
  gi|91772908|ref|YP_565600.1| 173 RILEELKDDNIKYRLFT 189
                                   ****************8 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.3e-08   0.00019      30      66 ..     128     165 ..      98     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.3e-08
                         HHH_6  30 aaikglgeaaaerivaeRekegpfksledlarrvds..l 66 
                                   + + g+g++ + +i++eR+ +g+fk+l+dl +rv+   +
  gi|91772908|ref|YP_565600.1| 128 ELLPGIGKKLMWAIIDERK-KGEFKDLQDLHDRVGGvhI 165
                                   56679*************9.8************997443 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.5e-07    0.0029      13      47 ..     124     157 ..     121     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.5e-07
                         HHH_3  13 aeeLqklpGlgpklAknIvayReknGpfksreeLl 47 
                                   +  L+ lpG+g+kl  +I++ R k+G fk++++L 
  gi|91772908|ref|YP_565600.1| 124 LHMLELLPGIGKKLMWAIIDER-KKGEFKDLQDLH 157
                                   567999****************.999********7 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00043       1.9      37      57 .]     127     147 ..     121     147 .. 0.87
   2 ?    1.3   0.0      0.12   5.4e+02      47      57 .]     170     180 ..     159     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                                   HHTSTTS-HHHHHHHHHHHHH CS
                         HHH_5  37 LakipGiGkktAeriilelkd 57 
                                   L  +pGiGkk+   ii+e k+
  gi|91772908|ref|YP_565600.1| 127 LELLPGIGKKLMWAIIDERKK 147
                                   6668*************9986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHH CS
                         HHH_5  47 tAeriilelkd 57 
                                    + ri++elkd
  gi|91772908|ref|YP_565600.1| 170 IVNRILEELKD 180
                                   688******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1568.87
//
Query:       gi|91772909|ref|YP_565601.1|  [L=129]
Description: DNA-directed RNA polymerase, subunit F [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-10   40.0   1.3      7e-10   39.3   1.3    1.3  1  RNA_pol_Rpb4  RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.058   13.8   1.3       0.28   11.7   0.1    2.2  2  CRR7          Protein CHLORORESPIRATORY REDUCTION 7
       0.12   12.2   0.3       0.34   10.8   0.0    1.9  2  EF-hand_8     EF-hand domain pair
       0.23   11.9   2.6       0.25   11.8   0.2    2.2  2  FumaraseC_C   Fumarase C C-terminus
       0.69   10.1   2.9        9.2    6.5   0.0    3.0  4  FANC_SAP      Fanconi anemia-associated nuclease SAP domain


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 !   39.3   1.3   1.9e-13     7e-10       1     120 [.      23     125 ..      23     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.9e-13
                                   EE-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.STHH CS
                  RNA_pol_Rpb4   1 lLsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfe.Ltka 80 
                                   lL+  Ev+++l++ +eer ++                +++l ++l+k++++ +  f++++ ++  +elv +l +++ +++ 
  gi|91772909|ref|YP_565601.1|  23 LLTVPEVKEILNKIMEERVAR----------------EEELGYELRKAINHADM-FAKMD-ASRSRELVGKLLEMGkMKPE 85 
                                   58999*******999999766................4689*************.****9.77777777777777769999 PP

                                   HHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHH CS
                  RNA_pol_Rpb4  81 EklqlvnlkPesavelktlieeleerfedeqleeiLdelk 120
                                    ++ + +++P +++el+tl ++++  +++e+l++iLd++ 
  gi|91772909|ref|YP_565601.1|  86 IAIHIADIAPLTRDELRTLYAKERFTLTEEELDAILDLVL 125
                                   99***********************************985 PP

>> CRR7  Protein CHLORORESPIRATORY REDUCTION 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.7e-05      0.28      14      50 ..      14      53 ..       4      75 .. 0.79
   2 ?    1.2   0.2      0.14   5.1e+02      21      39 ..     108     127 ..     101     129 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
                                  EEESSS-SEEE-HHHHHHHHHHHHHH...-TTTS-HHHHH CS
                          CRR7 14 vLepnqpEqfltaeellekLkelLek...eqdelprdlak 50
                                  + ++ q+E++lt  e++e L++++e+   +++el  +l+k
  gi|91772909|ref|YP_565601.1| 14 IVKHIQSEELLTVPEVKEILNKIMEErvaREEELGYELRK 53
                                  567789******************9944445566666655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                                   SEE.E-HHHHHHHHHHHHHH CS
                          CRR7  21 Eqf.ltaeellekLkelLek 39 
                                   E+f lt+eel + L  +Le+
  gi|91772909|ref|YP_565601.1| 108 ERFtLTEEELDAILDLVLEA 127
                                   55548999**9999999986 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 ?   -2.9   0.1       1.8   6.4e+03      30      38 ..      59      67 ..      58      69 .. 0.76
   2 ?   10.8   0.0   9.4e-05      0.34       5      34 ..      96     123 ..      95     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                     EF-hand_8 30 ilfrefDtd 38
                                  ++f ++D  
  gi|91772909|ref|YP_565601.1| 59 DMFAKMDAS 67
                                  599999975 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.4e-05
                     EF-hand_8   5 Itreelrrilrilglkk...glseeevdilfre 34 
                                   +tr+elr+ +     +k   +l+eee+d+++++
  gi|91772909|ref|YP_565601.1|  96 LTRDELRTLY-----AKerfTLTEEELDAILDL 123
                                   69******55.....444699*********986 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   3.8e+03      34      48 ..      20      34 ..      14      37 .. 0.71
   2 ?   11.8   0.2   6.9e-05      0.25      14      49 ..      87     123 ..      85     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                  HTT-.-HHHHHHHT- CS
                   FumaraseC_C 34 elgllteeeldelld 48
                                   ++llt  e++e+l+
  gi|91772909|ref|YP_565601.1| 20 SEELLTVPEVKEILN 34
                                  466777777777775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.9e-05
                                   HHHHHHHHHHHT--HHHHHHHTT-..-HHHHHHHT-H CS
                   FumaraseC_C  14 AakIAkeAlkegktlreavlelgl.lteeeldelldp 49 
                                   A  IA  A  ++  lr +  ++ + lteeeld++ld 
  gi|91772909|ref|YP_565601.1|  87 AIHIADIAPLTRDELRTLYAKERFtLTEEELDAILDL 123
                                   6679999999999999999987777**********95 PP

>> FANC_SAP  Fanconi anemia-associated nuclease SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0026       9.2      10      39 ..      23      52 ..      22      69 .. 0.81
   2 ?   -0.1   0.1       0.3   1.1e+03      11      16 ..      96     101 ..      82     102 .. 0.55
   3 ?    2.5   0.1     0.047   1.7e+02      11      21 ..      96     106 ..      93     109 .. 0.82
   4 ?   -1.4   0.2      0.77   2.7e+03      11      24 ..     112     125 ..     111     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0026
                      FANC_SAP 10 LltkpELlqaFaavlaaksarKaelleaLr 39
                                  Llt pE+ +++ + +  + ar  el   Lr
  gi|91772909|ref|YP_565601.1| 23 LLTVPEVKEILNKIMEERVAREEELGYELR 52
                                  9***********999888888777655555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.3
                      FANC_SAP  11 ltkpEL 16 
                                   lt++EL
  gi|91772909|ref|YP_565601.1|  96 LTRDEL 101
                                   455555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.047
                      FANC_SAP  11 ltkpELlqaFa 21 
                                   lt++EL+++ a
  gi|91772909|ref|YP_565601.1|  96 LTRDELRTLYA 106
                                   89999998866 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.77
                      FANC_SAP  11 ltkpELlqaFaavl 24 
                                   lt  EL +++ +vl
  gi|91772909|ref|YP_565601.1| 112 LTEEELDAILDLVL 125
                                   68889999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 967.47
//
Query:       gi|91772910|ref|YP_565602.1|  [L=97]
Description: 50S ribosomal protein L21e [Methanococcoides burtonii DSM 6242]
Scores for complete 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-35  118.9   0.4    7.5e-35  118.8   0.4    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.4   4.2e-39   7.5e-35       1     100 [.       1      96 [.       1      97 [] 0.99

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 4.2e-39
                                   X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEET CS
                Ribosomal_L21e   1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvg 81 
                                   m+ s+g+r+ tr++++k++r++g++p+s++++++++G++V+i+idpsvqkgmp   ++Gktg+v   +kr++++++++++g
  gi|91772910|ref|YP_565602.1|   1 MPTSHGERSCTRYKLKKTVRERGLSPISKAIQDFEEGQMVHIDIDPSVQKGMPNAKFQGKTGKV--LGKRGRAYLLQVTDG 79 
                                   899*************************************************************..*************** PP

                                   TE..EEEEEE-GGGEEE-- CS
                Ribosomal_L21e  82 gkileKriivriehlkksk 100
                                   +   +K++i   +hlk++k
  gi|91772910|ref|YP_565602.1|  80 NS--KKEVISLSQHLKPQK 96 
                                   **..*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 00:00:00.38
# Mc/sec: 760.08
//
Query:       gi|91772911|ref|YP_565603.1|  [L=428]
Description: pseudouridylate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-12   46.6   0.4    2.5e-11   43.9   0.0    2.2  2  THUMP     THUMP domain
  ------ inclusion threshold ------
      0.025   14.9   0.2       0.63   10.4   0.2    2.5  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 !   43.9   0.0   2.8e-15   2.5e-11      57     143 ..      86     184 ..      31     185 .. 0.87
   2 ?    0.2   0.1     0.081   7.2e+02      88     128 ..     324     363 ..     305     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.8e-15
                                   EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-S CS
                         THUMP  57 cevceadledileaakeivkkkfeeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdl 122
                                   c + +++l+   e a+ + k++ +    tF V++k  g                  e  + e+nrevGk+i e+tg++V+l
  gi|91772911|ref|YP_565603.1|  86 CLGLFEKLDTWAERAETALKDYEHS---TFLVGTKMSGLLSeneeiiwtesgttyaEQFKSEMNREVGKLIAERTGKEVEL 163
                                   5566677777778888888888888...********998779999***********88899******************** PP

                                   SS-SEEEEEEEETTEEEEEEE CS
                         THUMP 123 enPdivvrveiikdkayisid 143
                                   enPdi+v +++ ++++ ++++
  gi|91772911|ref|YP_565603.1| 164 ENPDILVTLDLAEETVHLQVR 184
                                   *******************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.081
                                   EEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEE CS
                         THUMP  88 VrvkrrgkhfeftsreinrevGkaivektglkVdlenPdiv 128
                                   V++k    + +  +  in  +G  i ++t  +V+  + d+v
  gi|91772911|ref|YP_565603.1| 324 VTFKEQIPE-DKLRSTINELIGVQIQQRTPQRVSHRRADLV 363
                                   444444444.77889999***********999998888865 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 ?   10.4   0.2     7e-05      0.63     119     149 .]     363     393 ..     310     393 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7e-05
                                   ---EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                        TruB_N 119 krkvtiyelelleveepevelevecskGtYi 149
                                    rk t+++++l e++++++ lev+c+ G Y+
  gi|91772911|ref|YP_565603.1| 363 VRKRTVHDMKLNELTDDYAMLEVHCEGGLYV 393
                                   5999**************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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 0.22s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3323.40
//
Query:       gi|91772912|ref|YP_565604.1|  [L=202]
Description: hypothetical protein Mbur_0907 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-65  218.1   0.0    1.1e-64  217.8   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
       0.01   15.2   0.0      0.014   14.7   0.0    1.1  1  Methyltrans_RNA  RNA methyltransferase
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.36   10.9   0.0    1.8  1  MurB_C           UDP-N-acetylenolpyruvoylglucosamine reductas


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 !  217.8   0.0   1.8e-68   1.1e-64       1     195 [.       1     195 [.       1     197 [. 0.98

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 1.8e-68
                                   -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSHH CS
               Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvspder 81 
                                   mr+fv++a+ka T++d++l+dlpG+agr+d+l+rc++  lf+sh+ R+dv+v+l+L+g+p+p ++i+++ + v++ +pder
  gi|91772912|ref|YP_565604.1|   1 MRNFVIIAHKALTTGDFSLNDLPGSAGRMDILCRCINSCLFLSHDLRRDVQVHLLLLGEPEPGKIIRFDSEHVRYLNPDER 81 
                                   9******************************************************************************** PP

                                   HHHHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCT.SEEEEESTTSEEGGGS---S.SEEEEEE-TT-SHHH CS
               Methyltrn_RNA_2  82 niailikkalkaveeikkqekkvrpgltVrkegfealleelsek.ksiillkekGedisnakiel.nPvFilgdHidlpee 160
                                   +   likkal++    ++ e +++pg+ +r   +  ll+e ++  + +i+l+e+Gedi++  +   n vFilgdH++++ee
  gi|91772912|ref|YP_565604.1|  82 SAGSLIKKALQKT--AGEYEVRSTPGVFIRSGNLGTLLNEFKDAgRRLIYLHEDGEDIRELSDLTnNAVFILGDHMGVTEE 160
                                   **********888..999999*********************9989**************9887779************** PP

                                   HHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHH CS
               Methyltrn_RNA_2 161 eekllerlkakrvslgPlsLhadhcvtlihneldk 195
                                   ee+l+++ +ak +slgP  Lhadhc++li ne+d+
  gi|91772912|ref|YP_565604.1| 161 EEQLIKEHEAKTISLGPIPLHADHCIILINNEIDR 195
                                   *********************************98 PP

>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.4e-06     0.014     139     208 ..     113     177 ..     107     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-06
                                   HHHHHHHCSCCEEEEEEETTSSEBGGGSSHCCHTHHCSEEEEEE--TT---HHHHHHHHHTTCEEEB-SS CS
               Methyltrans_RNA 139 lkelleelkeadlklildeeekksleelsekkkelkevkvlliiGPEGGfsekEiellkeagfkpvsLgp 208
                                   l +ll+e+k+a ++li   e+ +++ els+ ++     ++++i G   G +e+E +l+ke+++k++sLgp
  gi|91772912|ref|YP_565604.1| 113 LGTLLNEFKDAGRRLIYLHEDGEDIRELSDLTN-----NAVFILGDHMGVTEEEEQLIKEHEAKTISLGP 177
                                   667899999999977766666777777777666.....89*****************************9 PP

>> MurB_C  UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.1e-05      0.36      17      86 ..      76     191 ..      63     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.1e-05
                                   HSTTCTCEESESB---EESHHHHHHHH...................................................... CS
                        MurB_C  17 kqpldtpsaGSfFknPivegeeaeelk...................................................... 43 
                                   ++p d +saGS  k+ + +  +a e +                                                      
  gi|91772912|ref|YP_565604.1|  76 LNP-DERSAGSLIKKALQK--TAGEYEvrstpgvfirsgnlgtllnefkdagrrliylhedgedirelsdltnnavfilgd 153
                                   566.677777777776222..233333446667777777777777777777777777777777777777777777765544 PP

                                   EEEETTSSEEE-HHHHHHHTT-TTSEETTEEEESSSTTEEEES CS
                        MurB_C  44 eyeaeegevklsagwLIeqaglkGlrvggaqvsekhalflvNg 86 
                                   +  ++e        +LI++   k +++g++ ++  h+ +l+N+
  gi|91772912|ref|YP_565604.1| 154 HMGVTE-----EEEQLIKEHEAKTISLGPIPLHADHCIILINN 191
                                   333333.....4479***************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1379.59
//
Query:       gi|91772913|ref|YP_565605.1|  [L=170]
Description: deoxyuridine 5'-triphosphate nucleotidohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-11   42.2   0.0    7.7e-11   41.8   0.0    1.2  1  dUTPase   dUTPase
  ------ inclusion threshold ------
       0.13   11.0   0.0        0.2   10.4   0.0    1.4  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   8.6e-15   7.7e-11      34     110 ..      83     158 ..      66     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 8.6e-15
                                   EEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEEEBECGEEE CS
                       dUTPase  34 vptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifariltaele 110
                                   v ++  + +p++laa+  pRS l + g + ++ v+d+ y G  + ++++++k+ + +kk +Ri qL+f ++ t e+e
  gi|91772913|ref|YP_565605.1|  83 VLLNEIVNIPKDLAAIAKPRSTLIRCGATLETAVWDAGYSGRSECMIVVHNKDGFDLKKDARIMQLLFYHLHT-EVE 158
                                   556778999********************************6666666666777**************86666.444 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 ?   10.4   0.0   2.3e-05       0.2       6     110 ..       5     107 ..       1     120 [. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.3e-05
                           DCD   6 pdqeiealieegaikaeeple.eeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavlekgcvYi 85 
                                   +++e+++l+ ++    e+ ++ ++q+qP+ +++ L +   r   s  + + ++  ++l+e ++ e++      l+   vY 
  gi|91772913|ref|YP_565605.1|   5 SQNELRELVLANPPLVENMIDmDTQLQPNGVEMTLKEI--RTIKSPGAVDFDNSGRRLSEGDTIEFNEDGWIHLDP-GVYK 82 
                                   55555555544443344444314677777777777542..333332222334445566655555555444444544.5999 PP

                           DCD  86 vplleslaLpadlsaaanpksstGR 110
                                   v l+e +++p+dl+a+a p+s+  R
  gi|91772913|ref|YP_565605.1|  83 VLLNEIVNIPKDLAAIAKPRSTLIR 107
                                   ********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1293.68
//
Query:       gi|91772914|ref|YP_565606.1|  [L=400]
Description: hypothetical protein Mbur_0911 [Methanococcoides burtonii DSM 6242]
Scores for 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-29  100.6   0.1    2.5e-28   99.3   0.1    1.7  2  FIST      FIST N domain
    1.4e-15   57.4   0.1    5.3e-14   52.3   0.0    2.7  3  FIST_C    FIST C domain


Domain annotation for each model (and alignments):
>> FIST  FIST N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.1   2.7e-32   2.5e-28       1     172 []      35     228 ..      35     228 .. 0.83
   2 ?   -3.3   0.0      0.87   7.8e+03      27      42 ..     364     379 ..     361     392 .. 0.74

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 2.7e-32
                          FIST   1 dlvlvfas.aeasdleallealrealpgapliGcstageiase.gleledgvvalalasa.................da.. 60 
                                   dlv+++++    +dl++++++ +e +p+a+++Gc+ +g+i++e   e  +++ ++ +  +                 ++  
  gi|91772914|ref|YP_565606.1|  35 DLVVIYTTiG--HDLNDIISEAHELAPSAKVVGCTCSGIIGKEgPNEAMRSLAIMTV--KggndefsvvikdnitgpNSye 111
                                   6899998844..59**************************87745556666555555..3447788888887776653367 PP

                          FIST  61 ageelakal....pkl..lllladglssneeellegldealaspdvpivGGlagdgtlaf.ktyvlfnggvledgvvvvll 134
                                   + ++la++l    p +  +  la+g+ +  ++ leg+++++++ dvpi+G+ ++d+ ++  + +++ +g++le+g++++ +
  gi|91772914|ref|YP_565606.1| 112 VSAQLAQDLknknPNVnmIHFLASGIDIAADKALEGIESVFGT-DVPIFGATSSDN-MKAiNNFQFVDGQILEKGALAIGF 190
                                   777777777877744422223459999999***********98.*******99998.888789****************** PP

                          FIST 135 sgeslevgtavsqgyrpigkpfvVTkaegnvileLdgk 172
                                      +lev +  s+g++ i+ pf VT++e+n+++eLdg+
  gi|91772914|ref|YP_565606.1| 191 ADPTLEVISQASHGFEIIEMPFEVTRSESNRVFELDGQ 228
                                   9999********************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.87
                          FIST  27 gapliGcstageiase 42 
                                   ++p++G+ + ge+a  
  gi|91772914|ref|YP_565606.1| 364 DIPWLGMYGLGEFARL 379
                                   7899999999999753 PP

>> FIST_C  FIST C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.028   2.5e+02      99     128 ..      44      72 ..       9      74 .. 0.70
   2 ?   -1.0   0.0      0.18   1.6e+03     102     124 ..     141     163 ..     126     164 .. 0.84
   3 !   52.3   0.0     6e-18   5.3e-14      29     129 ..     257     377 ..     230     378 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.028
                        FIST_C  99 gedadeelqavrealgdgvplaGfftyGEi 128
                                   g d ++ +++++e   + ++++G+ + G i
  gi|91772914|ref|YP_565606.1|  44 GHDLNDIISEAHEL-APSAKVVGCTCSGII 72 
                                   55777877888888.6779*******9955 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
                        FIST_C 102 adeelqavrealgdgvplaGfft 124
                                   ad+ l+ +++++g +vp++G+ +
  gi|91772914|ref|YP_565606.1| 141 ADKALEGIESVFGTDVPIFGATS 163
                                   566788999999999*****876 PP

  == domain 3  score: 52.3 bits;  conditional E-value: 6e-18
                        FIST_C  29 l.........ggdflvrhllgvdpedgslaladdveeGqrlqlmlrdaealiedlerlleeaak.e......gallfsCig 93 
                                   +         +g++++ ++++    dgs+ +  d +eG++l l++rd +++ ++l ++++++ + +      +++  +C++
  gi|91772914|ref|YP_565606.1| 257 EelpeslqeeYGNTHILRVIAKKGPDGSIYMPVDCPEGTKLCLTKRDEDRIFDGLDQMVGQIVErCdgrrpvAVFHADCVA 337
                                   2344555445667777777776788*********************************9999666345566579999**** PP

                        FIST_C  94 Rglgl..gedadeelqavreal..gdgvplaGfftyGEig 129
                                   Rg g+     +de ++ ++  l  g+++p++G+++ GE++
  gi|91772914|ref|YP_565606.1| 338 RGRGMlnCILKDEIVARMQYPLcnGEDIPWLGMYGLGEFA 377
                                   *99998888888888999988778999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2771.40
//
Query:       gi|91772915|ref|YP_565607.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-22   76.9   0.0    1.8e-21   75.9   0.0    1.5  1  DUF772       Transposase domain (DUF772)
    1.8e-16   60.4   2.1    5.5e-16   58.9   2.1    1.8  1  DDE_Tnp_1    Transposase DDE domain
     0.0038   17.4   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.037   13.7   0.0      0.067   12.9   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   5.1e-25   1.8e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.1e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+++    +++++e
  gi|91772915|ref|YP_565607.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERIAQsgkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   2.1   1.5e-19   5.5e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.5e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772915|ref|YP_565607.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772915|ref|YP_565607.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772915|ref|YP_565607.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772915|ref|YP_565607.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772915|ref|YP_565607.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772915|ref|YP_565607.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.067      72     132 ..     213     276 ..     160     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772915|ref|YP_565607.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        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 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2071.48
//
Query:       gi|91772916|ref|YP_565608.1|  [L=991]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-31  106.7   6.4      1e-30  105.6   3.2    3.1  2  HisKA_2          Histidine kinase
    7.2e-17   61.5   4.1    2.6e-07   30.8   0.0    4.1  4  PAS_9            PAS domain
    1.1e-16   60.8   0.8    2.2e-10   40.5   0.0    3.1  3  PAS              PAS fold
    1.9e-14   53.3   0.0    9.6e-07   28.7   0.0    3.2  3  PAS_8            PAS domain
    1.2e-11   44.8   0.0    1.5e-06   28.4   0.0    2.8  2  PAS_4            PAS fold
    5.7e-10   39.7   0.5    1.6e-09   38.3   0.5    1.8  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    6.8e-10   39.7   0.0    1.4e-05   25.8   0.0    3.5  3  GAF              GAF domain
    5.4e-07   30.2   0.2    2.9e-06   27.9   0.2    2.3  1  HWE_HK           HWE histidine kinase
    8.7e-07   29.3   0.0      0.031   14.6   0.0    3.0  3  GAF_3            GAF domain
    1.4e-06   28.3   0.0    3.1e-06   27.2   0.0    1.5  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0004   20.5   0.6        2.3    8.4   0.0    4.5  3  PAS_7            PAS fold
     0.0058   15.9   2.1       0.08   12.2   0.0    2.9  3  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
     0.0068   16.3   0.7      0.025   14.5   0.7    2.0  1  HATPase_c_5      GHKL domain
  ------ inclusion threshold ------
      0.086   12.7   0.0       0.24   11.2   0.0    1.7  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
      0.087   13.2   0.6       0.48   10.9   0.1    2.5  2  Spa1_C           Lantibiotic immunity protein Spa1 C-terminal
       0.22   11.3   2.2        2.3    8.0   1.6    2.8  2  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.97   1.1e+03      24      43 ..     662     681 ..     659     689 .. 0.83
   2 !  105.6   3.2   9.4e-34     1e-30       1      76 []     800     875 ..     800     875 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.97
                       HisKA_2  24 akdeevkealresqnRvlsi 43 
                                   ++ ++++e+l+e +++v+si
  gi|91772916|ref|YP_565608.1| 662 IQRNRAEEVLQENEEKVKSI 681
                                   5678889***********98 PP

  == domain 2  score: 105.6 bits;  conditional E-value: 9.4e-34
                       HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                   EihHRvkNnLqvisslL+lq+r+++de+v +a+ esqnRv+s+a+ h++Ly+s+dl ++++++y+++L++ lf++y
  gi|91772916|ref|YP_565608.1| 800 EIHHRVKNNLQVISSLLNLQSRNFNDEKVIAAFMESQNRVRSMAIAHQKLYQSNDLASIEVGDYIKNLTTYLFQTY 875
                                   9************************************************************************987 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.7   4.1e+03      28      57 ..     181     210 ..     170     232 .. 0.62
   2 !   30.8   0.0   2.3e-10   2.6e-07       1     104 []     385     485 ..     385     485 .. 0.91
   3 !   29.3   0.1   7.2e-10   8.1e-07       3     104 .]     688     784 ..     686     784 .. 0.81
   4 ?   -1.3   0.0       2.3   2.5e+03      59      77 ..     966     986 ..     917     989 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                         PAS_9  28 peevlgksitdlfvtdpeanerlraaleqg 57 
                                   ++e++ ++i++l  ++++ ++++++  ++ 
  gi|91772916|ref|YP_565608.1| 181 SREIIRHNISELTISNEQLQREIKQRERTE 210
                                   788999999999944444444444433333 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.3e-10
                         PAS_9   1 pdgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                   p+gi+ ++ dg i+ ++N +++r++G  +e ++g +i d   t+++  e +++ l   +   +e+e++ + + g++  +++
  gi|91772916|ref|YP_565608.1| 385 PVGIFHYDQDG-IItHCNSSFARIIGPPAEKIIGVNILDSK-TNAHVSEVVKETLSKNT-GSFEGEYISVIS-GKKTQIKA 461
                                   68999999***.666*********************99999.99999999999999888.899999999988.889999** PP

                         PAS_9  81 taspvkdddgelvgiivilrDite 104
                                    a+ v++++g   g i++++Dit+
  gi|91772916|ref|YP_565608.1| 462 EARSVFSNNGSPLGGICVVEDITK 485
                                   **********************95 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 7.2e-10
                         PAS_9   3 gili.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                   g++i d + ++i++aN++a + +G  ++e++gk ++ ++ t++++++ ++++ ++++    + e vl + +ge++++l ++
  gi|91772916|ref|YP_565608.1| 688 GVVIiDAETHMIVDANPSAVQSIGAPKQEIVGKVCHKFICTAEKGECPISDLKQNID----RSERVLLNVKGEEIPILKNV 764
                                   6676599999999**************************677777777777777776....66777777779999999888 PP

                         PAS_9  83 spvkdddgelvgiivilrDite 104
                                   + v   +g+  ++i  ++Dite
  gi|91772916|ref|YP_565608.1| 765 ASVNL-NGR-LHLIESFIDITE 784
                                   88832.444.5589*******8 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.3
                         PAS_9  59 k..kerevevvlirkngetfw 77 
                                   +  k+ +++++l r+ng++f 
  gi|91772916|ref|YP_565608.1| 966 TlvKQIHGNIELDRSNGTKFV 986
                                   244588999999999999986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       4.4   4.9e+03      40      78 ..     183     219 ..     178     221 .. 0.71
   2 !   40.5   0.0     2e-13   2.2e-10       2     113 .]     376     483 ..     375     483 .. 0.90
   3 !   17.6   0.0   2.5e-06    0.0028       2      92 ..     677     763 ..     676     782 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.4
                                   HCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                           PAS  40 evlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                   e+++ ++++l + +++  l+++++q++++  + + ++++
  gi|91772916|ref|YP_565608.1| 183 EIIRHNISELTISNEQ--LQREIKQRERTEDRIKRMNKC 219
                                   7778888888877765..888888888887766666655 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 2e-13
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                   ++r i+e++p++if  D dg+i+++N++++++ G ++e ++g ++ld+  + +   + e +++ l+ ++ s  ge      
  gi|91772916|ref|YP_565608.1| 376 KYRMIFENSPVGIFHYDQDGIITHCNSSFARIIGPPAEKIIGVNILDSKTNAH---VSEVVKETLSKNTGSFEGEYISVI- 452
                                   6899*******************************************998875...777777777777777776666666. PP

                                   TSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  83 dgrpihlevraspvrdaggeilgflgvlrdi 113
                                    g+++++  +a++v++  g +lg ++v+ di
  gi|91772916|ref|YP_565608.1| 453 SGKKTQIKAEARSVFSNNGSPLGGICVVEDI 483
                                   7***************************998 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 2.5e-06
                                   HHHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC CS
                           PAS   2 dlraileslpdpifvvD.edgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl 81 
                                   ++++il s+ ++++++D e + i+ +N++a +  G + +e++gk    +i       +ae+ e+ +++ +++ +   ++ l
  gi|91772916|ref|YP_565608.1| 677 KVKSILASIQTGVVIIDaETHMIVDANPSAVQSIGAPKQEIVGKVCHKFIC------TAEKGECPISDLKQNIDRSERVLL 751
                                   6789***************************************98887774......666666666666655554444444 PP

                                   .TTSSEEEEEEE CS
                           PAS  82 .rdgrpihlevr 92 
                                    ++g++i+++ +
  gi|91772916|ref|YP_565608.1| 752 nVKGEEIPILKN 763
                                   556666666655 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   8.5e-10   9.6e-07       2      38 ..     376     413 ..     375     428 .. 0.81
   2 ?   -3.0   0.0       7.1     8e+03      29      40 ..     506     519 ..     476     530 .. 0.76
   3 !   20.9   0.0   2.5e-07   0.00027       1      61 [.     676     741 ..     676     748 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.5e-10
                         PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.a 38 
                                   ++r +fe+sp+gi+ +d ++ i+++N +++++ G + +
  gi|91772916|ref|YP_565608.1| 376 KYRMIFENSPVGIFHYDQDGIITHCNSSFARIIGPPaE 413
                                   8*************9997778*************3333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.1
                         PAS_8  29 aalellG.ys.adl 40 
                                   aa++llG y+ +d 
  gi|91772916|ref|YP_565608.1| 506 AAEKLLGpYPlEDA 519
                                   78999997775443 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.5e-07
                         PAS_8   1 erlralfesspdgiavvdlgd.rivdvNqaalellGys.adlkgellgqllpvlrplle...daeq 61 
                                   e+ ++++ s++ g++++d+ +  ivd+N++a +  G + +++ g++++++++  + +++   d++q
  gi|91772916|ref|YP_565608.1| 676 EKVKSILASIQTGVVIIDAEThMIVDANPSAVQSIGAPkQEIVGKVCHKFICTAEKGECpisDLKQ 741
                                   57799*************66657*************99*********9888888777775655555 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.3e-09   1.5e-06       1     109 [.     381     487 ..     381     488 .. 0.95
   2 !   13.6   0.0   5.3e-05     0.059       2     110 .]     683     787 ..     682     787 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.3e-09
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerh 80 
                                   ++++p++++  d dg ++++N ++a+++g p+e ++G    +       a +++ +++ l+ ++  ++ e+    +g+   
  gi|91772916|ref|YP_565608.1| 381 FENSPVGIFHYDQDGIITHCNSSFARIIGPPAEKIIGVNILD---SKTNAHVSEVVKETLSKNTGSFEGEYISViSGKKTQ 458
                                   79**************************************98...4589**************99999998888******* PP

                         PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                   +  +++ ++  +G ++g ++++ DiT ++
  gi|91772916|ref|YP_565608.1| 459 IKAEARSVFSNNGSPLGGICVVEDITKQK 487
                                   **************************986 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.3e-05
                         PAS_4   2 dslpdalavldpdgr.vlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeer 79 
                                    s++ +++++d++ + +++aN++a + +gap +e++Gk ++ +     a+  e+++  + +  ++ e++    l   gee 
  gi|91772916|ref|YP_565608.1| 683 ASIQTGVVIIDAETHmIVDANPSAVQSIGAPKQEIVGKVCHKFIC--TAEKGECPISDLKQNIDRSERVL---LnvKGEEI 758
                                   678889999988877368***********************9866..58999999998888854444444...4458**** PP

                         PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerrr 110
                                   +++ ++  + + +G+ +++++ ++DiTer++
  gi|91772916|ref|YP_565608.1| 759 PILKNVASV-NLNGR-LHLIESFIDITERKQ 787
                                   ********9.89999.*************85 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 !   38.3   0.5   1.4e-12   1.6e-09       4     108 ..     899     989 ..     896     991 .] 0.83

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.4e-12
                                   HHHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                     HATPase_c   4 krLrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                   + L  ii++lv+N++k+   + k+gei ++ + +++ +++ v+DnG Gip+  l+     + +          + lGl +v
  gi|91772916|ref|YP_565608.1| 899 IPLGLIINELVSNSLKHaykSEKKGEINIKFHLENNVITLIVSDNGEGIPE-YLD-----YKN---------THSLGLQLV 964
                                   67888************664448889999888666788889*********8.555.....444.........788****** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEE CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftl 108
                                     lv++++G+i+++ +   Gt+f++t+
  gi|91772916|ref|YP_565608.1| 965 TTLVKQIHGNIELDRSN--GTKFVITF 989
                                   *****9*******8888..***99986 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.019        22       1      95 [.      44     132 ..      44     153 .. 0.56
   2 ?    4.0   0.0     0.063        71      10     131 ..     235     359 ..     226     360 .. 0.66
   3 !   25.8   0.0   1.2e-08   1.4e-05       2     133 .]     516     662 ..     515     662 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                                   SHHHHHHHHHHHHHHHHTESEEEEEE..........EEETTEEE......CEEEEECCEEEETTSHHHH.HHHHHSSSEEE CS
                           GAF   1 dleelldtvveelrellgadrvalyl..........pdydGlhy......dipqasrwlfmkngrgicg.qvlatgqplvi 64 
                                   +l+el+ ++ve++ e+++++ +a+++                 +      + p   +w        i+   +++ ++ + i
  gi|91772916|ref|YP_565608.1|  44 SLDELASITVESIVEVFEVECGAIFTydatnnslaiV------EnygleeKHPLVMDW--------IVSeDIINAKEGVFI 110
                                   589*********************9833322222221......011222222222222........111334444555555 PP

                                   STGGTSTTHHTTHHHHHHHHTTESEEEEEEE CS
                           GAF  65 pdstpdprfaqynrrdllenmgirsslvvPl 95 
                                   ++s+p+  +            g + ++ +P 
  gi|91772916|ref|YP_565608.1| 111 EGSKPSKPWGS---------LGLCQVIYAPY 132
                                   55554444444.........55555555555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.063
                                   HHHHHHHHTESEEEEEEEEETTEEECEEEEECC........EEEETTSHHHHHHHHH..SSSEEESTGGTSTTHHTTHHHH CS
                           GAF  10 veelrellgadrvalylpdydGlhydipqasrw........lfmkngrgicgqvlat..gqplvipdstpdprfaqynrrd 80 
                                   ++  +el+ga  +aly    dG+ y      +w        l  ++g+  c  v++   +  +v+     +  +aq     
  gi|91772916|ref|YP_565608.1| 235 TALFGELMGA-TCALYNRLDDGILY---SWGQWktptdynpLDEPEGHI-CYDVIQRadNHLMVVR-NLSETAYAQ--TDP 307
                                   5566788886.89999867788544...444444433343244444444.7755553113333333.336666777..556 PP

                                   HHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHH CS
                           GAF  81 llenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvav 131
                                    + ++  +++++  ++ ++  +G l+++ +++   t+e+  ++ v+a+ +av
  gi|91772916|ref|YP_565608.1| 308 NVIPYALKTYIGTGVKLGESFVGSLCCVFQKDiVPTKEDKWMIGVIATAIAV 359
                                   677899**********************988853388888888888888887 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 1.2e-08
                                   HHHHHHHHHHHHHHHHTESEEEEEE..EEETTEEECEEEEECC..........EEEETTSHHHH..........HHHHHSS CS
                           GAF   2 leelldtvveelrellgadrvalyl..pdydGlhydipqasrw..........lfmkngrgicg..........qvlatgq 60 
                                   le++ +tv+e+l+++++ d + +++    +dG+  + +q  +w          +f +     +           ++l+ g 
  gi|91772916|ref|YP_565608.1| 516 LEDAIQTVLERLGQATNIDQAYIFKnvVGEDGIL-RAYQTNQWkitgindlndSFEPH--R-ISyteddyerwiKILKAGN 592
                                   7999*********************553345543.47888888755544433322222..1.1133444444434444333 PP

                                   SEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHHH CS
                           GAF  61 plvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvaval 133
                                   ++      p   f +  +  +l++    s ++vP+ ++++ wG +++ ++++  ++ + e + l++ ad ++ a+
  gi|91772916|ref|YP_565608.1| 593 VIAG----PIHEFPE-IEYPILKACKALSIAAVPIQVEENWWGFICFNDCTNerEWFTVEKDALKAAADAIGAAI 662
                                   3332....3333444.5678999**************************877889*9**************9997 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   2.6e-09   2.9e-06       1      52 [.     800     853 ..     800     878 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.6e-09
                                   HHHHHHHHHHHHHHHHHHHHSSSXS-HHHHHHHH..HHHHHHHHHHHHHHHHCT CS
                        HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesleefaekl..sgRLqALsaahdllsree 52 
                                   E++HRvKN L v++s+ +  +r+ ++ + +a+ +  ++R+++++ ah+ l +++
  gi|91772916|ref|YP_565608.1| 800 EIHHRVKNNLQVISSLLNLQSRNFNDEKVIAAFMesQNRVRSMAIAHQKLYQSN 853
                                   89********************9998887776552268*********9998876 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.8e-05     0.031       1      41 [.      44      86 ..      44     118 .. 0.87
   2 !   11.3   0.0    0.0003      0.33      82     129 .]     616     664 ..     583     664 .. 0.87
   3 ?   -3.1   0.0       8.6   9.6e+03      49      76 ..     820     848 ..     806     855 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                         GAF_3  1 sldellekllkllvkllgaevgalllldedgnklqvaagw..d 41
                                  sldel++++++ +v+++ +e ga++ +d+  n+l+++ ++  +
  gi|91772916|ref|YP_565608.1| 44 SLDELASITVESIVEVFEVECGAIFTYDATNNSLAIVENYglE 86
                                  69***********************************999433 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0003
                         GAF_3  82 aalavPLvagrqviGvlala.stkprafdaedlelleslArqiataier 129
                                   ++ avP++++++  G+++++  t++r++  ++++ l++ A+ i+ ai+r
  gi|91772916|ref|YP_565608.1| 616 SIAAVPIQVEENWWGFICFNdCTNEREWFTVEKDALKAAADAIGAAIQR 664
                                   6789*****99********72567888999*****************97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.6
                         GAF_3  49 sld.edsalarralssgevvsepsfaeed 76 
                                   s   +d++++++ ++s++ v   + a++ 
  gi|91772916|ref|YP_565608.1| 820 SRNfNDEKVIAAFMESQNRVRSMAIAHQK 848
                                   44447888888888888887766666554 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.7e-09   3.1e-06      32     112 ..     901     971 ..     891     989 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.7e-09
                   HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDe 111
                                   + l ++E+++N  +hay+++++g++++++  +++ +t+ v+D+G+g  ++ +            + ++ +Gl l+++lv +
  gi|91772916|ref|YP_565608.1| 901 LGLIINELVSNSLKHAYKSEKKGEINIKFHLENNVITLIVSDNGEGiPEYLD-----------YKNTHSLGLQLVTTLVKQ 970
                                   6799******************************************777764...........344677888888888887 PP

                   HATPase_c_2 112 v 112
                                   +
  gi|91772916|ref|YP_565608.1| 971 I 971
                                   7 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.56   6.2e+02      34      67 ..     174     207 ..     166     219 .. 0.79
   2 !    8.4   0.0     0.002       2.3       2     114 ..     382     490 ..     381     491 .. 0.65
   3 ?    5.0   0.0     0.023        26       1     114 [.     682     789 ..     682     790 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.56
                         PAS_7  34 lvqvgvpleellrynaergefgagdveaeverrl 67 
                                    ++  ++ +e++r+n ++  +++++ + e+++r 
  gi|91772916|ref|YP_565608.1| 174 ALRYNIESREIIRHNISELTISNEQLQREIKQRE 207
                                   5667788899******999999999888888875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.002
                         PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrl.aaaragkphsfere 81 
                                   en + Gi  +D+d+ ++ +N+ + ++ + p+e + +gv++ +    na+  e+ +++ ++    +  + ++  + ++++ +
  gi|91772916|ref|YP_565608.1| 382 ENSPVGIFHYDQDGIITHCNSSFARIIGPPAEKI-IGVNILDSKT-NAHVSEVVKETLSKNTGSFEgEYISVISGKKTQIK 460
                                   77889*********************99999998.8888766433.33333333233333322222133444555666666 PP

                         PAS_7  82 rpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                    ++  v + +g+pl +   + + +DiT++++ae
  gi|91772916|ref|YP_565608.1| 461 AEARSVFSNNGSPLGG---ICVVEDITKQKKAE 490
                                   6677777777777644...44558999999887 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.023
                         PAS_7   1 lenmsqGisvfDadlrLva.wNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfer 80 
                                   l +++ G++++Da++ +++  N   ++  + p++ + vg+  ++++  +ae+ge+  +d ++ ++r  + + + k + +  
  gi|91772916|ref|YP_565608.1| 682 LASIQTGVVIIDAETHMIVdANPSAVQSIGAPKQEI-VGKVCHKFIC-TAEKGECPISDLKQNIDRSERVLLNVKGEEIPI 760
                                   568899999999998876658999999999999888.8888888875.458888887777777776655555444444444 PP

                         PAS_7  81 erpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                     ++   ++++g+      ++ ++ DiTer++ae
  gi|91772916|ref|YP_565608.1| 761 L-KNVASVNLNGRL----HLIESFIDITERKQAE 789
                                   2.333333333332....3566666777777766 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   7.1e-05      0.08      25     105 ..     148     255 ..     142     258 .. 0.90
   2 ?    1.9   0.0     0.098   1.1e+02     210     251 ..     405     449 ..     392     469 .. 0.74
   3 ?   -2.2   0.6       1.8     2e+03       8      62 ..     779     840 ..     776     860 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
               Cache_3-Cache_2  25 etletqdellrekverdlnvfakllsn...........................ewrvdnqetvkvgevslPklklggewl 78 
                                   ++ + ++++++e+++ +++vf ++++                            e++ ++ ++ +++ ++   l+ g + l
  gi|91772916|ref|YP_565608.1| 148 TKKKDFYDTIDEEIKPSFRVFVQQMDAlryniesreiirhniseltisneqlqrEIKQRERTEDRIKRMNKCFLNFGADPL 228
                                   5667788999999999999999999999999999999999999999999999989************************** PP

               Cache_3-Cache_2  79 nknfelvdefteltgatatvFqrmndd 105
                                    + ++l   f el+gat++++ r +d 
  gi|91772916|ref|YP_565608.1| 229 ENINSLTALFGELMGATCALYNRLDDG 255
                                   ***********************9985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.098
               Cache_3-Cache_2 210 gkliihptlk..gknvldlkdadge.svvkkllkkksgsleyelk 251
                                    ++i  p  k  g n+ld k++    +vvk+ l+k++gs+e e+ 
  gi|91772916|ref|YP_565608.1| 405 ARIIGPPAEKiiGVNILDSKTNAHVsEVVKETLSKNTGSFEGEYI 449
                                   556667777799******966655589***********9987776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
               Cache_3-Cache_2   8 vnklieeelekevedlaetletqdellrekverdlnvfakllsn.......ewrvdnqetvk 62 
                                   + +++e+++++ev++   +l+  +  ++++++  +++++ + +n        + ++ q++v+
  gi|91772916|ref|YP_565608.1| 779 FIDITERKQAEEVQKKDILLKEIHHRVKNNLQVISSLLNLQSRNfndekviAAFMESQNRVR 840
                                   56677888888888888888777777777766555555444444444666644444444444 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.7   2.3e-05     0.025       6      93 ..     901     983 ..     897     988 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                   HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegekkklesskskkeehGiGlksireivkkykgnls 86 
                                   l +i+  l  N++  + k e+ k +I+++++ +++ ++++++ + eg  + l      k+ h +Gl+ ++ +vk+ +gn++
  gi|91772916|ref|YP_565608.1| 901 LGLIINELVSNSLKHAYKSEK-KGEINIKFHLENNVITLIVSDNGEGIPEYLDY----KNTHSLGLQLVTTLVKQIHGNIE 976
                                   567889999********9995.99****************99988887777665....56899****************** PP

                   HATPase_c_5  87 ieaedgl 93 
                                   ++ ++g+
  gi|91772916|ref|YP_565608.1| 977 LDRSNGT 983
                                   9998874 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 ?   11.2   0.0   0.00021      0.24       8      48 ..     906     950 ..     903     966 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                   HATPase_c_3   8 aelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmsee 48 
                                    elv Nsl    ++     ++i+++ + +++ ++ + D+G+G++e 
  gi|91772916|ref|YP_565608.1| 906 NELVSNSLKHAYKSekkgeINIKFHLE-NNVITLIVSDNGEGIPEY 950
                                   69******9666656788899999997.579************975 PP

>> Spa1_C  Lantibiotic immunity protein Spa1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00043      0.48      19      59 ..     337     376 ..     333     384 .. 0.86
   2 ?   -2.4   0.1         6   6.8e+03      22      54 ..     645     677 ..     644     700 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                        Spa1_C  19 ledtVseeelgeylgviaelivvdetgkilskeelkkievs 59 
                                   ++d V+ +e + ++gvia+ i+v+e ++ + +eel k + +
  gi|91772916|ref|YP_565608.1| 337 QKDIVPTKEDKWMIGVIATAIAVEE-KRKWVQEELVKSDNK 376
                                   7899******************965.678999999998765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                        Spa1_C  22 tVseeelgeylgviaelivvdetgkilskeelk 54 
                                   tV++++l+   ++i+  i  ++ +++l+++e k
  gi|91772916|ref|YP_565608.1| 645 TVEKDALKAAADAIGAAIQRNRAEEVLQENEEK 677
                                   688888888888888888888888888777644 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.53   5.9e+02      26      45 ..     772     791 ..     770     795 .. 0.90
   2 ?    8.0   1.6     0.002       2.3      15      37 ..     797     819 ..     783     840 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.53
                        SPOB_a  26 hLQvIsGylqLgkydkaeey 45 
                                   +L++I +++++ +  +aee+
  gi|91772916|ref|YP_565608.1| 772 RLHLIESFIDITERKQAEEV 791
                                   59*************99997 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.002
                        SPOB_a  15 lLrsqRHDflNhLQvIsGylqLg 37 
                                   lL+  +H   N+LQvIs++l L+
  gi|91772916|ref|YP_565608.1| 797 LLKEIHHRVKNNLQVISSLLNLQ 819
                                   678889999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (991 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 6100.63
//
Query:       gi|91772917|ref|YP_565609.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.7   0.4    6.3e-67  226.0   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
      9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.2e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00011   22.5   0.3       0.17   12.1   0.2    2.8  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.067   13.8   1.4        0.3   11.7   1.4    2.2  1  BST2             Bone marrow stromal antigen 2
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.7   2.6       0.55   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.36   11.2   6.9       0.52   10.7   4.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
          1   10.1   8.9        7.1    7.4   1.5    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.1    9.0   6.0       0.65   10.7   1.1    2.7  2  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.44   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  226.0   0.0   3.5e-70   6.3e-67       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91772917|ref|YP_565609.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 226.0 bits;  conditional E-value: 3.5e-70
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91772917|ref|YP_565609.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91772917|ref|YP_565609.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierear..ea..eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++r  +   ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91772917|ref|YP_565609.1| 329 SENDN--QLWSKAMNIlLIDVKKSVDQIRgmSGcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **976..*********************964338888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91772917|ref|YP_565609.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.5e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91772917|ref|YP_565609.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7     8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91772917|ref|YP_565609.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.6     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.5   0.0    0.0025       4.5       5      45 ..     249     287 ..     245     290 .. 0.84
   3 !   12.1   0.2   9.3e-05      0.17      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91772917|ref|YP_565609.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91772917|ref|YP_565609.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91772917|ref|YP_565609.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91772917|ref|YP_565609.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00046      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91772917|ref|YP_565609.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91772917|ref|YP_565609.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00031      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    0.9   0.1      0.34   6.2e+02      11      58 ..     392     446 ..     383     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91772917|ref|YP_565609.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91772917|ref|YP_565609.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999888854444440......55555555555555555553 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?   10.7   4.5   0.00029      0.52       2      36 ..     156     213 ..     155     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91772917|ref|YP_565609.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91772917|ref|YP_565609.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCellADvCGC 213
                                   79***************99987555588888888888888887775555444446666 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 ?    3.3   0.1     0.074   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.4   1.5     0.004       7.1       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.0   0.1      0.19   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91772917|ref|YP_565609.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91772917|ref|YP_565609.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91772917|ref|YP_565609.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00036      0.65      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.6   0.3        10   1.8e+04      55      66 ..     154     165 ..     144     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91772917|ref|YP_565609.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                         PLATZ  55 kssseaCetCar 66 
                                   +++ ++C +C++
  gi|91772917|ref|YP_565609.1| 154 RAEIKSCPHCGC 165
                                   334478999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.53
# Mc/sec: 2782.59
//
Query:       gi|91772918|ref|YP_565610.1|  [L=263]
Description: fructose-bisphosphate aldolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-60  203.4   0.1    4.4e-60  203.2   0.1    1.0  1  DeoC          DeoC/LacD family aldolase
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.64    9.4   0.0    1.9  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.2   0.1     5e-64   4.4e-60       2     234 ..      22     236 ..      21     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.2 bits;  conditional E-value: 5e-64
                                   EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEET CS
                          DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvde 82 
                                   +i+++D++v+ +++++       +d+ a+v++++++ga+avl + g++ +++++y++d++l+++l+ +t l ++++++v+ 
  gi|91772918|ref|YP_565610.1|  22 IIIPMDHGVSAGPIKGL------IDMPATVNKVAEGGANAVLGHMGLAKHGHRGYGRDVGLIIHLSGSTSLGPDPNHKVL- 95 
                                   699**************......9********************************************************. PP

                                   TCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTCC CS
                          DeoC  83 vasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsael 163
                                   v++ eea++ GAdav+v++++   g+e+e+++l++++ v+++c+e+g+pl++++y+r++++  e+ d + v++Aar++ael
  gi|91772918|ref|YP_565610.1|  96 VTTMEEAIKVGADAVSVHINV---GAEDEAEMLKDLGFVAKKCDEWGMPLLAMMYPRGAKVPSEH-DVEYVKHAARIGAEL 172
                                   *********************...*****************************************.*************** PP

                                   T-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHT CS
                          DeoC 164 GaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsGRaifq 234
                                   GaDi+K++++        +d e+fk+vi+++pvp vv++GG+   +e+++l++v+dA+   g  Gv++GR++fq
  gi|91772918|ref|YP_565610.1| 173 GADIVKTSYT--------GDPESFKEVIDGCPVP-VVIAGGPqmdTEREILQMVSDAL-SVGCKGVAMGRNVFQ 236
                                   **********........****************.***********************.9*************9 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0    0.0074        67      53     122 ..      73     137 ..      55     144 .. 0.63
   2 ?    9.4   0.0   7.1e-05      0.64      27      90 ..     125     180 ..      99     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0074
                                   HSTCTHC.......HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2  53 fgypded.......erearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaek 122
                                   + ++  +         +++     + l  ++e a ++Ga+ + +h+           +e+ + + ++l  +a+++++
  gi|91772918|ref|YP_565610.1|  73 DVGLIIHlsgstslGPDPN----HKVLVTTMEEAIKVGADAVSVHIN--------VGAEDEAEMLKDLGFVAKKCDE 137
                                   5554444444444444555....77788999**********999977........3345555566666666666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 7.1e-05
                                   HHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEE CS
                  AP_endonuc_2  27 deelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlh 90 
                                    ++l  ++k +de g+ + ++ ++ +   p e    ++    v+++k+a+++ a+LGa+++ + 
  gi|91772918|ref|YP_565610.1| 125 LKDLGFVAKKCDEWGMPLLAMMYPRGAKVPSE----HD----VEYVKHAARIGAELGADIVKTS 180
                                   45666678888888888666666666666655....58....*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.69
# Mc/sec: 1156.66
//
Query:       gi|91772919|ref|YP_565611.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-22   76.9   0.0    1.8e-21   75.9   0.0    1.5  1  DUF772       Transposase domain (DUF772)
    1.8e-16   60.4   2.1    5.5e-16   58.9   2.1    1.8  1  DDE_Tnp_1    Transposase DDE domain
     0.0038   17.4   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.037   13.7   0.0      0.067   12.9   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   5.1e-25   1.8e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.1e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+++    +++++e
  gi|91772919|ref|YP_565611.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERIAQsgkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   2.1   1.5e-19   5.5e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.5e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91772919|ref|YP_565611.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91772919|ref|YP_565611.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91772919|ref|YP_565611.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91772919|ref|YP_565611.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91772919|ref|YP_565611.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91772919|ref|YP_565611.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.067      72     132 ..     213     276 ..     160     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91772919|ref|YP_565611.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1939.42
//
Query:       gi|91772920|ref|YP_565612.1|  [L=581]
Description: glycyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-21   75.7   0.1    2.4e-21   75.7   0.1    2.8  4  HGTP_anticodon  Anticodon binding domain
    7.5e-11   42.3   0.0    1.9e-10   41.0   0.0    1.6  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.11   11.6   0.8        3.1    6.8   0.2    2.4  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)


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 ?   -1.4   0.1      0.45   2.7e+03      12      36 ..      98     122 ..      91     126 .. 0.80
   2 ?   -3.1   0.0       1.5   9.1e+03      22      35 ..     386     399 ..     371     405 .. 0.64
   3 ?   -3.4   0.1       1.9   1.2e+04      31      74 ..     453     469 ..     446     471 .. 0.50
   4 !   75.7   0.1   4.1e-25   2.4e-21       1      89 [.     476     562 ..     476     567 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.45
                                   HHHHHHHHHHHHHHHTTTSEEEEES CS
                HGTP_anticodon  12 eeleeyakklaeeLraagirveldd 36 
                                   + l +   ++a++L+++++++ +++
  gi|91772920|ref|YP_565612.1|  98 DHLVDKIVEVADALSNEELDRLIKE 122
                                   4577888999999999999988876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                                   HHHHHTTTSEEEEE CS
                HGTP_anticodon  22 aeeLraagirveld 35 
                                    +eL++++i+v ++
  gi|91772920|ref|YP_565612.1| 386 EDELSKDEIKVIVN 399
                                   35677777777665 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.9
                                   EEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET CS
                HGTP_anticodon  31 rvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr 74 
                                   +ve d+                            e++ + +r r
  gi|91772920|ref|YP_565612.1| 453 EVEGDE---------------------------EEEERMVLRFR 469
                                   344444...........................34445544444 PP

  == domain 4  score: 75.7 bits;  conditional E-value: 4.1e-25
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                   qv+++pl + ++el e ak +a++Lr+ g+ v +d +++ ig+++r+ d++g+p+ +++++++le+++vt+rdrdt++q+r
  gi|91772920|ref|YP_565612.1| 476 QVAILPLLT-RDELIEPAKAIAQKLRERGLLVAYD-DSRAIGRRYRRNDEIGTPYSITIDYDTLEDNSVTIRDRDTMKQVR 554
                                   8********.888****************977776.799****************************************** PP

                                   EETTHHHH CS
                HGTP_anticodon  82 vsldelve 89 
                                    s++ +++
  gi|91772920|ref|YP_565612.1| 555 ASVEGIEN 562
                                   **997766 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 !   41.0   0.0   3.2e-14   1.9e-10      11     178 ..     156     445 ..     151     446 .. 0.67

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.2e-14
                                   EEE-SSSHHHHHHHHHHHEEEBGG..SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  11 yiLkPtneetfvelirdevlrskr..LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdlikais 88 
                                    +++P+  +++   ++    r +r  LP+  +qi+  yR+E s  +G++R+reF+q ++++f + +++    ++   +++ 
  gi|91772920|ref|YP_565612.1| 156 GYMRPETAQGMFINFQRL-SRYYRdkLPFGATQIGKSYRNEISPRQGVIRLREFTQAEAEIFTHpKEKGHPNFERFAEVTL 235
                                   577887777766555533.4543335****************9566******************7799999********** PP

                                   HHHHHTT.SCEEEEEEGTTSC............................................................ CS
                                   xxxxxxxxxxxxxxxxxxxxx............................................................ RF
                  tRNA-synt_2b  89 riferlglefraiielmsaks............................................................ 109
                                   +++++   e+ ai++++ ++                                                             
  gi|91772920|ref|YP_565612.1| 236 NLYSDEAQEKGAIEQMTVREAvendiiaheflayhialtnhflqrvgiaadklrfrqhqkdemahyaidcwdaeiltdrfg 316
                                   ******999888888744443556777788889999999999999988888888777777777777777777777777777 PP

                                   .................BTTSEEEEEEEEETT................................................. CS
                                   .................xxxxxxxxxxxxxxx................................................. RF
                  tRNA-synt_2b 110 .................adykdkkefeavses................................................. 124
                                                                                                                    
  gi|91772920|ref|YP_565612.1| 317 wievvgiadrtdfdlkaH-------------Aktsgtkleihieydepkmveqfvvkpdmgklgplfkgkakavadalrel 384
                                   777744444444444440.............34444444444444555555555555555555555555555555555555 PP

                                   ....TSEEEEEEEEEEEETHHHHHTTE...EEECTTSSEEEEEEEEEEEEHHHHHHHHHHH CS
                                   ....xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 125 ....ltkgieigtiqklgtrlserlga...tvldennreksvimicaaigveRllsaileq 178
                                       l+k    + +++ ++  ++++     ++++  +++  +++i  + g+ R+l + +e+
  gi|91772920|ref|YP_565612.1| 385 sedeLSKDEIKVIVNGEKFTVPSEIISyaqETVKVSGEKIVPHVIEPSYGIDRILYCTMEH 445
                                   5555444332344444445666555443566667777777888888888888888877775 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0    0.0075        45      27      49 ..      43      66 ..      38      73 .. 0.72
   2 ?    6.8   0.2   0.00051       3.1      96     130 ..     187     223 ..     177     478 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0075
                                  HHHHHHHH.HHHHTT-EE----SE CS
                                  xxxxxxxx.xxxxxxxxxxxxxxx RF
                   tRNA-synt_2 27 tvtkavrk.yleengfieietPiL 49
                                  ++ ++ r+ y  ++gf+eietP++
  gi|91772920|ref|YP_565612.1| 43 RIEQIWRElYVIHEGFMEIETPTV 66
                                  55666666244567********97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00051
                                   EEEEEE--S--BTT..B-S-CEEEEEEEEET-SCHHH CS
                                   xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  96 qiaraFRaEdsrtd..rhlaEFtqieaemsfieeedi 130
                                   qi++++R+E s  +    l EFtq eae+    +e+ 
  gi|91772920|ref|YP_565612.1| 187 QIGKSYRNEISPRQgvIRLREFTQAEAEIFTHPKEKG 223
                                   89*******98655225799********955444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3617.54
//
Query:       gi|91772921|ref|YP_565613.1|  [L=769]
Description: Hef nuclease [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-29  102.9   0.3    1.6e-28   99.8   0.0    2.6  2  ERCC4          ERCC4 domain
    3.8e-25   88.4   0.6      2e-22   79.7   0.0    3.1  3  Helicase_C     Helicase conserved C-terminal domain
    6.6e-19   68.3   0.8    4.1e-18   65.7   0.0    2.5  3  DEAD           DEAD/DEAH box helicase
    1.3e-13   51.3   2.2      2e-13   50.7   0.0    2.4  3  ResIII         Type III restriction enzyme, res subunit
    4.6e-11   42.7   0.0    1.5e-10   41.0   0.0    1.9  1  HHH_2          Helix-hairpin-helix motif
    6.2e-11   42.7   0.0    2.5e-10   40.8   0.0    2.0  1  HHH_5          Helix-hairpin-helix domain
    0.00074   20.1   1.5      0.028   15.0   0.1    3.5  2  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
     0.0016   18.8   0.6       0.02   15.2   0.0    3.1  2  HHH_8          Helix-hairpin-helix domain
     0.0046   16.8   0.2      0.018   14.9   0.1    2.1  2  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.046   13.3   0.7        9.9    5.6   0.0    2.6  2  LPD37          Large polyvalent protein associated domain 37
      0.058   13.2   0.1        1.7    8.5   0.0    3.1  3  TusA           Sulfurtransferase TusA
      0.061   13.1   0.1       0.21   11.4   0.1    2.0  1  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin
      0.074   12.5   0.2        0.7    9.3   0.0    2.4  2  PhoH           PhoH-like protein
       0.13   12.5   0.0       0.41   10.9   0.0    1.9  1  HHH_3          Helix-hairpin-helix motif
        3.8    7.5   6.7          2    8.4   1.4    2.6  2  DUF1151        Protein of unknown function (DUF1151)


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.1   1.3e+03      87     120 ..     479     528 ..     468     543 .. 0.65
   2 !   99.8   0.0   1.4e-31   1.6e-28       1     153 [.     562     679 ..     562     682 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                   H-SE...EEEEE.ES......-GGGTT.......................T CS
                         ERCC4  87 gykk...pillv.eg......ldqykrknknsrnkqykakvrq.......i 120
                                   g k+   +++lv +g      ++++ +k k+++++  +++++         
  gi|91772921|ref|YP_565613.1| 479 GRKHegrVVVLVtKGtrdeayYWSCAHKEKRMQSN-MQQWQENmselnraN 528
                                   44445556777768899888888888888777666.466666666644432 PP

  == domain 2  score: 99.8 bits;  conditional E-value: 1.4e-31
                                   EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHHH CS
                         ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqvs 81 
                                   +D+re++s + +  le+lg+++v++tl++gdy ++   +++               v++erks +d+v+s+ d+++++q+s
  gi|91772921|ref|YP_565613.1| 562 LDQREIRSTVARS-LEKLGFNIVVKTLEVGDY-IV---SDR---------------VAIERKSTEDFVNSLLDRHIFRQIS 622
                                   69***********.******************.99...9**...............************************* PP

                                   HHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHH CS
                         ERCC4  82 rlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewl 153
                                   +l+  +y+kpil++eg+  +  +               +n+++i ++L++l ldfgvsil+t++a++ta ++
  gi|91772921|ref|YP_565613.1| 623 DLAG-AYEKPILIIEGEGLFTTRM--------------VNPNAIHGMLASLSLDFGVSILHTRDAEDTASLI 679
                                   ****.*****************98..............*******************************987 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.018        21       8      94 ..      58     153 ..      53     162 .. 0.73
   2 !   79.7   0.0   1.6e-25     2e-22       8     110 ..     371     481 ..     361     482 .. 0.83
   3 ?   -1.8   0.0       3.4     4e+03      50      70 ..     541     561 ..     495     575 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                                   HHH....HHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHH.TTSSSEEEESGGGTS CS
                    Helicase_C   8 ell....kleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfn.kgesdvLiatdvaer 78 
                                   +ll     l++ ggk+li ++t+  +e+ + +l++      + ++++++g    ++ree  ++ +   ++  +i  d++ +
  gi|91772921|ref|YP_565613.1|  58 ALLviasRLQKTGGKALILSPTKPLVEQhAAFLRS-TlnipEDEILTFTGAVAPDKREELWKKGKvIISTPQVIENDILTK 137
                                   4444556789**************99986555533.24667899999****999999999998874344447777777777 PP

                                   SSTSTTESEEEESSSS CS
                    Helicase_C  79 GidipkvnlVinfdlp 94 
                                    i +++v+++ + ++ 
  gi|91772921|ref|YP_565613.1| 138 RISLEDVTHITFDEAH 153
                                   7777777777665555 PP

  == domain 2  score: 79.7 bits;  conditional E-value: 1.6e-25
                                   HHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT........STHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                    Helicase_C   8 ellkleeeggkilifvntidrlek.vklllekkgikvavlhge........lpqnereeileqfnkgesdvLiatdvaerG 79 
                                   ++l + + ++++++f+n++d+ e+ ++ l e k+i+ +++ g+        l+q+++ ei+e+f++ge++vL+at+vae+G
  gi|91772921|ref|YP_565613.1| 371 KEL-NGKPDSRVIVFTNYRDTSEMvTNALSEIKDIRPVKFVGQsskfkdkgLTQKQQVEIIEKFKAGEYNVLVATSVAEEG 450
                                   445.678899**********8888766665555555555555445555555****************************** PP

                                   STSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   +dip  +lV+++++  +  + iqr+GRtgR 
  gi|91772921|ref|YP_565613.1| 451 LDIPATDLVVFYEPVPSEIRSIQRKGRTGRK 481
                                   ******************************5 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.4
                                   STHHHHHHHHHHHHTTSSSEE CS
                    Helicase_C  50 lpqnereeileqfnkgesdvL 70 
                                    + +e++  l++f ++e++v+
  gi|91772921|ref|YP_565613.1| 541 RSEEEQQTGLSDFSDEEVTVI 561
                                   455566666666666666655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.0   3.5e-21   4.1e-18      17     167 ..      44     182 ..      30     191 .. 0.84
   2 ?   -0.4   0.1      0.72   8.6e+02      35      87 ..     364     415 ..     357     448 .. 0.61
   3 ?   -3.9   0.0       8.3     1e+04      87     112 ..     567     594 ..     552     602 .. 0.58

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 3.5e-21
                                   EEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  17 vlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng 97 
                                    lv  +TG GKT ++l+ + +++    +ktg kali++Pt+ L+eq++  l++ ++  +  + l+++g  a d++++l ++
  gi|91772921|ref|YP_565613.1|  44 TLVVLPTGLGKTIVALLVIASRL----QKTGGKALILSPTKPLVEQHAAFLRSTLNIPE-DEILTFTGAVAPDKREELWKK 119
                                   58999***************999....89***************************644.6667778888889999999** PP

                                   CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTSTTTSEEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  98 vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqitcdgklqrqvivlSA 167
                                    +++++tp+ + + + t++++l++v+ + +DEa+r   +  +    +r ++  ++         ++++++A
  gi|91772921|ref|YP_565613.1| 120 GKVIISTPQVIENDILTKRISLEDVTHITFDEAHRAVGNyAYTYIAERYFEDAKKP--------HCLAITA 182
                                   *************8889******************999966666666666666322........2555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.72
                                   HHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSH CS
                                   xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  35 vlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaa 87 
                                   v++ ++++  +gk+  ++++ +  r   e + n l+++k+   +r + ++g++++
  gi|91772921|ref|YP_565613.1| 364 VVKDIVSKelNGKPDSRVIVFTNYRDTSEMVTNALSEIKD---IRPVKFVGQSSK 415
                                   4444444447899999999999999999999999999998...444444453333 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 8.3
                                   HHHHHHHH..HTTCSEEEEEHHHHHHHH CS
                                   xxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                          DEAD  87 ardqlskl..dngvdivvgtpgrlddll 112
                                    r+ +++   + g +ivv t +  d ++
  gi|91772921|ref|YP_565613.1| 567 IRSTVARSleKLGFNIVVKTLEVGDYIV 594
                                   4333333211235888888887766666 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 !   50.7   0.0   1.7e-16     2e-13      25     169 ..      42     184 ..      11     186 .. 0.83
   2 ?   -2.8   0.1       4.5   5.3e+03     100     118 ..     376     394 ..     342     439 .. 0.54
   3 ?   -2.1   0.3       2.9   3.4e+03     101     125 ..     514     546 ..     492     565 .. 0.50

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.7e-16
                                   SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--...... CS
                        ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkkakekdst 102
                                      l++++TG GKT+va+ +i++ l+k +  k+l+l p+k l+eq    ++++l+ + +e    ++ v  dk+++     +
  gi|91772921|ref|YP_565613.1|  42 APTLVVLPTGLGKTIVALLVIASRLQKTGG-KALILSPTKPLVEQHAAFLRSTLNIPEDEiltFTGAVAPDKREE---LWK 118
                                   57899************7777777776553.**************998888888888777666677788888888...899 PP

                                   .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH.HHT-...--SEEEEEESS- CS
                        ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei.lekf...keavllglTATp 169
                                   + k++++t q + +d+      +++ + +    i +DEaHr+ ++ +++ i  ++f   k+   l++TA p
  gi|91772921|ref|YP_565613.1| 119 KGKVIISTPQVIENDI-----LTKRISLEDVTHITFDEAHRAVGNYAYTYIaERYFedaKKPHCLAITASP 184
                                   ****************.....99999999999************989999864444444779999999988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                                   ....-SEEEEEHHHHHHTH CS
                        ResIII 100 dstnkkilvttiqsldads 118
                                   + +++ i++t++   ++  
  gi|91772921|ref|YP_565613.1| 376 KPDSRVIVFTNYRDTSEMV 394
                                   3455555666655554444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.9
                                   ...-SEEEEEHHHHHHTH............... CS
                        ResIII 101 stnkkilvttiqsldadseee........eees 125
                                    ++++  +++ ++++++++++        eee+
  gi|91772921|ref|YP_565613.1| 514 MQQWQENMSELNRANNENDKTdiasefrsEEEQ 546
                                   334444444444444444433555555542222 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.2e-13   1.5e-10       7      56 ..     715     764 ..     711     768 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.2e-13
                         HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFe 56 
                                   +I ++G ++Ak+L  +F+++++ +ka+l+eL ev++iG+++A + +e ++
  gi|91772921|ref|YP_565613.1| 715 SISNIGPNAAKNLLDHFGTVENVMKAELDELKEVKNIGPKTAGKMREILS 764
                                   699***************************************99988776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   2.1e-13   2.5e-10       5      55 ..     714     763 ..     711     765 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.1e-13
                                   HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                         HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                    s+s iGp  A++ll++ +++ve +++a+ +eL +++ iG+ktA ++ + l
  gi|91772921|ref|YP_565613.1| 714 SSISNIGPNAAKNLLDH-FGTVENVMKAELDELKEVKNIGPKTAGKMREIL 763
                                   69***************.****************************98765 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       1.4   1.6e+03      48      76 ..     323     355 ..     267     374 .. 0.53
   2 !   15.0   0.1   2.3e-05     0.028      22      53 ..     715     747 ..     711     764 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.4
                    5_3_exonuc  48 ldelke.......kklkekLeenkeearlskkLati 76 
                                   l+   +       +k+ ++L ++  + +l+k+L + 
  gi|91772921|ref|YP_565613.1| 323 LE---NeatsrtgSKASKRLSDDLYMRQLYKRLEEC 355
                                   11...1111122244445555555555555555444 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-05
                    5_3_exonuc  22 GvpgiGektAakLlkeygsleeilenl.delke 53 
                                    ++ iG+ +A++Ll ++g++e+++++  delke
  gi|91772921|ref|YP_565613.1| 715 SISNIGPNAAKNLLDHFGTVENVMKAElDELKE 747
                                   6899********************943256655 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       1.2   1.4e+03      34      66 ..     250     283 ..     233     285 .. 0.72
   2 !   15.2   0.0   1.7e-05      0.02      41      67 ..     733     763 ..     713     764 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                                   CCCC-SS-HHHHTTHCTTSTT--..HHHHHHHHHH CS
                         HHH_8  34 aiealpeeitsleeeltklpgiG..kkiaakieei 66 
                                    + +l++ i+ +++ ++k++ +G  kk+  +i+e+
  gi|91772921|ref|YP_565613.1| 250 KLTELGYSIQYGKK-ASKMDLLGlqKKLQGQIREM 283
                                   56677788888766.76666666668888888886 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-05
                                   -HHHH.TT...HCTTSTT--HHHHHHHHHHH CS
                         HHH_8  41 eitsl.ee...eltklpgiGkkiaakieeil 67 
                                    ++++ ++   el+++++iG+k+a k++eil
  gi|91772921|ref|YP_565613.1| 733 TVENVmKAeldELKEVKNIGPKTAGKMREIL 763
                                   5555552235569*****************8 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.8     7e+03       4      13 ..     107     116 ..     106     116 .. 0.86
   2 !   14.9   0.1   1.5e-05     0.018       2      26 ..     734     758 ..     733     762 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.8
                                   HHHTSSHHHH CS
                           HHH   4 glipasreeL 13 
                                   ++ p+ reeL
  gi|91772921|ref|YP_565613.1| 107 AVAPDKREEL 116
                                   578******9 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.5e-05
                                   HHHHHTSSHHHHHTSTT-SHHHHHH CS
                           HHH   2 leglipasreeLlalPGVGpktAea 26 
                                   +e+++ a ++eL++++ +GpktA++
  gi|91772921|ref|YP_565613.1| 734 VENVMKAELDELKEVKNIGPKTAGK 758
                                   799********************86 PP

>> LPD37  Large polyvalent protein associated domain 37
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0083       9.9     160     237 ..     117     194 ..     102     202 .. 0.88
   2 ?    4.9   0.6     0.014        17       8      58 ..     494     541 ..     488     577 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0083
                         LPD37 160 WkdGddahnleeLlktsyanvkklvpeikdvtydfakarfrerdgkpvtdetlkslveearkertarigsatlkRavl 237
                                   Wk+G     + ++++  + + + ++++++++t+d a++   +  ++ + +++++++ + +    ta  gs++ k + +
  gi|91772921|ref|YP_565613.1| 117 WKKGKVIISTPQVIENDILTKRISLEDVTHITFDEAHRAVGNYAYTYIAERYFEDAKKPHCLAITASPGSSDEKISEV 194
                                   99999999999999999999999999*************99****************988888999999999886655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                         LPD37   8 esdelFrlp.ksqkttlagiaaeidptlsvvadakaedele....reeaevdrawv 58 
                                   + de++  + + +++ +++ ++++++++s ++ a++e+++     +        + 
  gi|91772921|ref|YP_565613.1| 494 TRDEAYYWScAHKEKRMQSNMQQWQENMSELNRANNENDKTdiasE--------FR 541
                                   67899988889999***************88888888775534331........32 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.5     6e+02      19      60 ..     167     209 ..     164     219 .. 0.77
   2 ?   -2.8   0.0         5     6e+03      19      47 ..     371     398 ..     369     400 .. 0.78
   3 ?    8.5   0.0    0.0014       1.7      28      64 ..     556     592 ..     550     595 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.5
                                   HHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-.G CS
                          TusA  19 kalekleegevlevladdpaatediprfakklghelvevee.e 60 
                                   +  e ++    l ++a+  ++ e i++ + +l  + v+++  +
  gi|91772921|ref|YP_565613.1| 167 RYFEDAKKPHCLAITASPGSSDEKISEVCTNLYIRSVAIKTeT 209
                                   5566777777899999999999*********999888885534 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                                   HHHCCCGCT-EEEEEESSCHHHHHHHHHH CS
                          TusA  19 kalekleegevlevladdpaatediprfa 47 
                                   k+l+  ++  ++ v ++ +++ e + + +
  gi|91772921|ref|YP_565613.1| 371 KELNG-KPDSRVIVFTNYRDTSEMVTNAL 398
                                   66777.677778899*****999998876 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0014
                                   -EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-E CS
                          TusA  28 evlevladdpaatediprfakklghelveveeedgey 64 
                                   e++ v++d ++   ++ r+++klg+++v  + e g y
  gi|91772921|ref|YP_565613.1| 556 EEVTVILDQREIRSTVARSLEKLGFNIVVKTLEVGDY 592
                                   7789**********************77665566666 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.21      35      66 ..     733     764 ..     728     765 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                   BHHHHHHS-HHHHTTSSS-SSHHHHHHHHHHH CS
                 RNA_pol_A_CTD  35 tvgeLvklseeeLlkikNlGkKSleEIkekLe 66 
                                   tv++++k + +eL+++kN+G K+    +e L+
  gi|91772921|ref|YP_565613.1| 733 TVENVMKAELDELKEVKNIGPKTAGKMREILS 764
                                   899********************988888775 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00059       0.7       2      61 ..      21      85 ..      20     103 .. 0.80
   2 ?   -0.0   0.0      0.42     5e+02      68     109 ..     276     317 ..     270     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00059
                                  ----SHHHHHHHHHHHH-S...EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE..EE-S--T CS
                          PhoH  2 ikpktkeQkeylealkknd...ivfaiGpaGtGKtylavalavealkkkkvkriil..trpavea 61
                                  +kp+t eQ+ y   l  +     + ++ p+G GKt +a+ + ++ l+k   k +il  t+p ve 
  gi|91772921|ref|YP_565613.1| 21 VKPNTVEQRLYQLDLAGKAlsaPTLVVLPTGLGKTIVALLVIASRLQKTGGKALILspTKPLVEQ 85
                                  7899999999999999555222578899********************99999999445777764 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.42
                                   S---------TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEE CS
                          PhoH  68 lpgdleekvdpylrplydaLkdllgaekvekllekgkievap 109
                                   l+g+++e  +p +    + L ++++ ++  +++e++ ie ++
  gi|91772921|ref|YP_565613.1| 276 LQGQIREMAEPAVYSALSILAEVMKVSHAVEIVETQGIEALK 317
                                   6899999999**9999********************999876 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00034      0.41      18      62 ..     715     761 ..     712     764 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                         HHH_3  18 klpGlgpklAknIvayReknG..pfksreeLlkvkglgpktfeqlag 62 
                                    ++ +gp+ Akn++++         + ++eL++vk++gpkt  ++++
  gi|91772921|ref|YP_565613.1| 715 SISNIGPNAAKNLLDHFGTVEnvMKAELDELKEVKNIGPKTAGKMRE 761
                                   57778888888888886433311446689***********9888775 PP

>> DUF1151  Protein of unknown function (DUF1151)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.43   5.2e+02      67      89 ..     233     255 ..     218     284 .. 0.68
   2 ?    8.4   1.4    0.0017         2      26      76 ..     505     555 ..     502     570 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.43
                       DUF1151  67 akkkkseLeqelekraqrleele 89 
                                    ++ k  Le++le+r q+l el 
  gi|91772921|ref|YP_565613.1| 233 MRELKDLLEKVLEDRFQKLTELG 255
                                   44555667888888888887553 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                       DUF1151  26 hrELllnqkrglvleeKpELqrvlekrkeeqvlkqkkeeeeakkkkseLeq 76 
                                   h+E  ++  +++ +e+ +EL+r+ ++  +  ++++ ++eee+++  s++  
  gi|91772921|ref|YP_565613.1| 505 HKEKRMQSNMQQWQENMSELNRANNENDKTDIASEFRSEEEQQTGLSDFSD 555
                                   99**********************999999*************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.50
# Mc/sec: 4672.21
//
Query:       gi|91772922|ref|YP_565614.1|  [L=158]
Description: hypothetical protein Mbur_0921 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-13   48.8   2.3    9.1e-13   48.1   2.3    1.4  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
  ------ inclusion threshold ------
      0.012   15.6   1.7      0.021   14.9   1.7    1.3  1  DZR            Double zinc ribbon
      0.098   12.2   1.9        0.3   10.7   1.9    1.8  1  RecR           RecR protein
       0.17   11.6   4.9        0.5   10.1   4.9    1.8  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain


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 !   48.1   2.3     2e-16   9.1e-13       1      40 []       9      46 ..       9      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2e-16
                 Auto_anti-p27  1 kkmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                  k++++lL +G tMLa++C +Cg+P++r  ++g+v+C++C+
  gi|91772922|ref|YP_565614.1|  9 KQISRLLEMGGTMLAQHCATCGAPMFR--YQGEVLCPICQ 46
                                  789************************..679*******6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.7   4.6e-06     0.021      12      40 ..      23      51 ..      20      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-06
                           DZR 12 arfCseCgtklkavaaedrCpsCgekvdp 40
                                  a+ C +Cg+++ +++ e  Cp C+ ++ +
  gi|91772922|ref|YP_565614.1| 23 AQHCATCGAPMFRYQGEVLCPICQDSNAN 51
                                  789*********9***********99655 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.9   6.6e-05       0.3      17      37 ..      24      48 ..      23      49 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.6e-05
                                  EE-TTT--E....ESSSS-CCCCST CS
                          RecR 17 rhCsrCgnl....teedlCaICsdp 37
                                  +hC  Cg        e lC+IC+d+
  gi|91772922|ref|YP_565614.1| 24 QHCATCGAPmfryQGEVLCPICQDS 48
                                  699999987555466669******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 ?   10.1   4.9   0.00011       0.5       4      28 ..      24      46 ..      22      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                 zf-NADH-PPase  4 rFCgrCGaptepaeggwarvCpaCg 28
                                  + C++CGap+ + +g     Cp C+
  gi|91772922|ref|YP_565614.1| 24 QHCATCGAPMFRYQG--EVLCPICQ 46
                                  89*********9999..56777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 968.03
//
Query:       gi|91772923|ref|YP_565615.1|  [L=91]
Description: hypothetical protein Mbur_0922 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  120.9   1.5    1.9e-35  120.8   1.5    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
  ------ inclusion threshold ------
      0.019   15.2   0.1       0.23   11.8   0.1    2.0  2  UPF0253   Uncharacterised protein family (UPF0253)


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   1.5   2.1e-39   1.9e-35       2      81 .]       8      87 ..       7      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 2.1e-39
                                  HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                       UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                  e++ik+++++Le+i++d+svPrniRr+a++++++Lk+e e l +r++++isiL++isnDpn+Plh+Rtliw+v s+LEti
  gi|91772923|ref|YP_565615.1|  8 EDVIKQCTQVLEHIANDNSVPRNIRRSANDILATLKNEAEPLFLRTSSSISILEDISNDPNIPLHTRTLIWNVASQLETI 87
                                  689***************************************************************************98 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.5e-05      0.23      25      51 ..       9      35 ..       7      42 .. 0.88
   2 ?    1.4   0.0     0.045     4e+02      30      48 ..      56      74 ..      53      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                       UPF0253 25 dAiscalktLdevaanealpeevrekA 51
                                  d i+   ++L+++a+++++p+++r +A
  gi|91772923|ref|YP_565615.1|  9 DVIKQCTQVLEHIANDNSVPRNIRRSA 35
                                  56777889****************987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.045
                       UPF0253 30 alktLdevaanealpeevr 48
                                   +  L+++ ++ ++p ++r
  gi|91772923|ref|YP_565615.1| 56 SISILEDISNDPNIPLHTR 74
                                  6889*********998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 555.31
//
Query:       gi|91772924|ref|YP_565616.1|  [L=539]
Description: O-phosphoseryl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-53  179.8   0.0    3.2e-48  164.4   0.0    2.1  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    5.6e-13   48.7   0.0    1.4e-12   47.5   0.0    1.7  1  SepRS_C          O-phosphoseryl-tRNA synthetase C-terminal do
    1.2e-07   31.4   0.0     0.0001   21.8   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.19   11.8   0.0    1.6  1  Lambda_Bor       Bor protein


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 !   13.4   0.0   8.9e-06      0.04       3      48 ..      33      78 ..      31      87 .. 0.87
   2 !  164.4   0.0   7.1e-52   3.2e-48      19     239 ..     123     353 ..     104     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-06
                                  -TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHH CS
                  tRNA-synt_2d  3 dvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefy 48
                                  + ++p+++ + gk hp+ +++ +++e +l++gf e+ +p + +e  
  gi|91772924|ref|YP_565616.1| 33 NQQYPHTSFHFGKAHPVYDTIAKLREAYLRMGFDEMMNPLIVDEKE 78
                                  66778889999****************************9977755 PP

  == domain 2  score: 164.4 bits;  conditional E-value: 7.1e-52
                                   HHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH.... CS
                  tRNA-synt_2d  19 ltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl.... 95 
                                    ++ +e i+++++++++ eveg+++     ++  Lnv++   +  ++ +F+  k+ ++++++++LR+h+t+ ++++l    
  gi|91772924|ref|YP_565616.1| 123 DDEGIETIRKVLHSYKKGEVEGDDL--VPEIALKLNVSDALVVEMIDKVFPEFKELTPQATTKTLRSHMTSGWFISLsgil 201
                                   567799***************8888..4567889**********************************************9 PP

                                   TTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTST.EEEEEEECEETTEEEEEE CS
                  tRNA-synt_2d  96 ekkkppikiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkklfgae.vkvrfrpsyfpftePsae 174
                                   e+++pp+ ++si+r fRr++ +Da++l+++++++++++de+v++++ k+v++ ll ++ g+e + +r +++ ++++ P+++
  gi|91772924|ref|YP_565616.1| 202 ERSRPPFHLFSIDRSFRREQqEDASRLMTYYSASCVIMDEDVTVDHGKAVAQGLLAQF-GFEkFMFRPDEKRSKYYVPDTQ 281
                                   9******************999************************************.9998999*************** PP

                                   EEEEE.........CCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.H CS
                  tRNA-synt_2d 175 vdvyl.........vekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRelvendl 239
                                   ++v++         ++ +++w+E++++G+++p++l++++i    +++++GlGveRlam+ ++ +D+R + +++l
  gi|91772924|ref|YP_565616.1| 282 IEVFAyhpklvgsnTKYSDGWIEIATFGIYSPTALAEYNI--PCPVMNLGLGVERLAMILHDSTDLRGMTYPQL 353
                                   9999999*******99************************..***************************99876 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 !   47.5   0.0   3.1e-16   1.4e-12       1      31 []     436     467 ..     436     467 .. 0.98

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 3.1e-16
                                   EEEEEETTEEEEEES-TTTCCHHHH.SEEEEE CS
                       SepRS_C   1 NEvyVYdGnIlGvPdtekwkearen.GvsTGI 31 
                                   NEv V+++++lG+P+++kwk+a+en +++TG+
  gi|91772924|ref|YP_565616.1| 436 NEVLVHENDVLGLPNNKKWKKAFENhSARTGV 467
                                   *******************************6 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00063       2.8       3      50 ..      34      81 ..      32      91 .. 0.90
   2 !   21.8   0.0   2.3e-08    0.0001      71     208 ..     182     326 ..     178     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00063
               tRNA_synthFbeta  3 stlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldk 50
                                  ++ P+++   g+ ++  ++  klr++   +G+ E+++   v+eke+ k
  gi|91772924|ref|YP_565616.1| 34 QQYPHTSFHFGKAHPVYDTIAKLREAYLRMGFDEMMNPLIVDEKEVYK 81
                                  6789999999*******************************9999866 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.3e-08
               tRNA_synthFbeta  71 qsvlRtsLlpglLevlarNlargnedvrlFEigkvflkdseeel..peeerhlaivltgkreeeswsekaravdfydlkgi 149
                                   +++lR+ +++g    l+  l+r+ + + lF i + f+ +++e+          ++v++            ++v + + k++
  gi|91772924|ref|YP_565616.1| 182 TKTLRSHMTSGWFISLSGILERSRPPFHLFSIDRSFRREQQEDAsrLMTYYSASCVIMD-----------EDVTVDHGKAV 251
                                   6899***********************************33333113333334444444...........559******** PP

               tRNA_synthFbeta 150 vealleslgiekvefep..aehpalhpgrsAei....kvdgk.............evGvlGelhpevleafdlkqrvy 208
                                   ++ ll+++g+ek+ f+p  +  +++ p  + e+        k             e+  +G  +p  l++++++ +v+
  gi|91772924|ref|YP_565616.1| 252 AQGLLAQFGFEKFMFRPdeKRSKYYVPDTQIEVfayhP---KlvgsntkysdgwiEIATFGIYSPTALAEYNIPCPVM 326
                                   ****************9656699**********55550...24455555666669*******************9986 PP

>> Lambda_Bor  Bor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.2e-05      0.19      49      70 ..     294     315 ..     288     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                    Lambda_Bor  49 tqqtfvngLlgvvTlGIYtPrt 70 
                                   + +   +g +++ T+GIY+P+ 
  gi|91772924|ref|YP_565616.1| 294 SNTKYSDGWIEIATFGIYSPTA 315
                                   567778999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3459.77
//
Query:       gi|91772925|ref|YP_565617.1|  [L=205]
Description: hypothetical protein Mbur_0924 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-27   95.7   0.0      4e-27   95.5   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 !   95.5   0.0   2.2e-31     4e-27      15     205 ..      15     195 ..       5     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 2.2e-31
                        DUF169  15 vkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfk.elpeklksgegylkspeaakkfve 94 
                                   v  ++++ ++ e++e       +C m+++ar kg+++++   +++Cp G+++l    ++p+++    g + + e+a+k+v 
  gi|91772925|ref|YP_565617.1|  15 VCVTFQEGDIGEEYEL-----LYCEMITKAR-KGESFLA--ASQSCPPGKYVLSKSeDKPDRYYLASGRYIDAETAQKAVL 87 
                                   5555566667777665.....9*********.******9..77789********97466688888899999********** PP

                        DUF169  95 slprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvsfpgngaaCadivaypykegepnigl 175
                                   +lpr+ ++++ ++ ++pL+k + e dv++++ +pe +mr vq++ y++g+ r+++++ g +++C d++a +  e+   +++
  gi|91772925|ref|YP_565617.1|  88 ALPRI-KKKYGHIRIEPLSKNNGEFDVIILYLKPEIAMRVVQALAYNNGD-RVSIDTFGAASICGDCTALA-IENGIGLSY 165
                                   ***99.6788****************************************.*****************765.567799*** PP

                        DUF169 176 gdpgarkfaklkddelafgiPyelleemve 205
                                   g+ g+rk+++ +d+e+ +gi  + ++++++
  gi|91772925|ref|YP_565617.1| 166 GCKGSRKHSEYSDNEIPIGIDLDNAKKIEK 195
                                   **************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1557.84
//
Query:       gi|91772926|ref|YP_565618.1|  [L=129]
Description: hypothetical protein Mbur_0925 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  146.8   0.6    2.5e-43  146.7   0.6    1.0  1  DUF473    Protein of unknown function (DUF473)


Domain annotation for each model (and alignments):
>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   0.6   1.4e-47   2.5e-43       1     118 []       1     118 [.       1     118 [. 0.99

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 1.4e-47
                        DUF473   1 MkvvaLtGiseevieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvvesse 81 
                                   M+++aLtGis++vi+eLk + lrtie+rs++N++t l+++v+d++FlT++s++D+++Gt+G++a+v+++++st+++++ ++
  gi|91772926|ref|YP_565618.1|   1 MEYAALTGISDTVISELKGHLLRTIEIRSPQNFFTSLDFDVNDHIFLTRTSAQDIMRGTSGVVAQVVKHHVSTHKMITGND 81 
                                   9******************************************************************************** PP

                        DUF473  82 sfieErEttvarvqlkllglgrvrevkeeellkptkv 118
                                   +f+eE E++++r+qlk++g++r++++ ++el+k+t v
  gi|91772926|ref|YP_565618.1|  82 TFYEEYESMIIRLQLKPIGVARINNIISNELGKVTLV 118
                                   ********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 908.12
//
Query:       gi|91772927|ref|YP_565619.1|  [L=248]
Description: hypothetical protein Mbur_0926 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-53  180.4   0.3    5.1e-53  180.2   0.3    1.0  1  PAC2            PAC2 family
  ------ inclusion threshold ------
      0.062   13.8   2.4        4.6    7.8   0.2    2.9  3  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain


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 !  180.2   0.3   5.7e-57   5.1e-53       1     213 []      25     228 ..      25     228 .. 0.94

  Alignments for each domain:
  == domain 1  score: 180.2 bits;  conditional E-value: 5.7e-57
                                   EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT.SEEEEEEE...E-H CS
                          PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsgsrdllvlqg...rep 77 
                                   Li+GfpgiG+Vg +a + +ie+l++e++g+i+s+y +p     p++++ eg   +p+r+y + +   ++ + +++   + p
  gi|91772927|ref|YP_565619.1|  25 LIEGFPGIGLVGNIASQQIIEELNMEYIGSIESRY-FP-----PIAVLYEGLVNMPVRIYENvE---HNTIMVVSdipINP 96 
                                   8**********************************.**.....********99*******8874...4555555559999* PP

                                   SCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT....-CEEEEHHHHHHHHHH CS
                          PAC2  78 ilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees....eyggivgitglLlsaa 154
                                   ++ y+ ++kal+ wa+++gvkev+ ++g++++        ++ kv+gaat+ee+le+++++    ++g+i+gi+g+ + ++
  gi|91772927|ref|YP_565619.1|  97 SVSYD-VSKALVGWAKSIGVKEVISIAGIATMS-------DEYKVFGAATTEEMLEKIKDQveifQMGTISGISGSVMAEC 169
                                   ****9.************************764.......456***************8667889**************** PP

                                   HHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHHH CS
                          PAC2 155 kergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleela 213
                                    ++++pa++ll+ ++ + pdP+aaa+++++l+ ++++++dtedL+e+ae++e ++++la
  gi|91772927|ref|YP_565619.1| 170 FMQNVPAISLLGATKTQNPDPRAAAVVVDVLNSMYNFSIDTEDLIEQAEKIEIEMQKLA 228
                                   *******************************************************9985 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 ?    4.4   0.0    0.0056        50      30      79 ..      36      84 ..      32      90 .. 0.79
   2 ?    7.8   0.2   0.00052       4.6      19      45 ..     124     150 ..     110     155 .. 0.81
   3 ?   -1.4   0.1      0.37   3.3e+03      32      48 ..     208     223 ..     195     231 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0056
                                  S---HHHHHHHHHHHT-----GGGEE-TTT-SBSSEEEEEEESSSS-EEE CS
                Ribosomal_L9_C 30 GsVtakdIaealkkklgieidkkkieleepiktlGeyevtvkLhkevtak 79
                                  G + +++I+e+l+ ++  +i+++ +    ++   G  +++v+++++v+ +
  gi|91772927|ref|YP_565619.1| 36 GNIASQQIIEELNMEYIGSIESRYFPP-IAVLYEGLVNMPVRIYENVEHN 84
                                  999***********9877899998873.4577779999999999988866 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00052
                                   E--B-TT-BBSS---HHHHHHHHHHHT CS
                Ribosomal_L9_C  19 kakagedgklFGsVtakdIaealkkkl 45 
                                    a+++++ k+FG+ t+++  e++k+++
  gi|91772927|ref|YP_565619.1| 124 IATMSDEYKVFGAATTEEMLEKIKDQV 150
                                   46678999****************994 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.37
                                   --HHHHHHHHHHHT--- CS
                Ribosomal_L9_C  32 VtakdIaealkkklgie 48 
                                   + ++d++e+ +k  +ie
  gi|91772927|ref|YP_565619.1| 208 IDTEDLIEQAEKI-EIE 223
                                   4555555555443.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1641.93
//
Query:       gi|91772928|ref|YP_565620.1|  [L=197]
Description: hypothetical protein Mbur_0927 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-15   56.3   0.5    4.6e-15   55.9   0.5    1.2  1  PK_C      Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.5   2.6e-19   4.6e-15       1     117 []      17     170 ..      17     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 2.6e-19
                                   HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TS..SEEEEEES.................HHHH............ CS
                          PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpk..vpiiavtp.................nelt............ 50 
                                   + ++k a+++aeel++++Iv  ++ G+tA+++++  ++  v++ia+t+                 +  +            
  gi|91772928|ref|YP_565620.1|  17 DDVVKVAANRAEELEIEYIVLSSTEGYTALKMAEAVKGknVKVIAITHqyglredgkwemdeenlK--Klqemgvivttqs 95 
                                   57999*******************************9999********999998888887666551..0556666775555 PP

                                   ......HHHHH.HCTTEEHHH.HHHHH...TTSHHHHHHHHHHH.......TTSS..-STSEEEEEE-SSSS..SS--EEE CS
                          PK_C  51 ......arqla.lyrGvypvlvekaktaestdellreavkvake.......aglv..kkgdevvvtaGtpkgesgttNtlr 115
                                         +r+++  ++G +++ v+    ++++ +++ +++kva+e       +g++  +k+ ev++++Gt++g    ++++ 
  gi|91772928|ref|YP_565620.1|  96 hmfsgvERAISnRLGGASRADVI----SDTLRAVFGKGFKVALEvvmmaadSGYIpvSKDTEVIAIGGTRQG----ADVAL 168
                                   55556577777777888888766....5667778888899999999989999997436777***********....99999 PP

                                   EE CS
                          PK_C 116 Vv 117
                                   Vv
  gi|91772928|ref|YP_565620.1| 169 VV 170
                                   86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1282.60
//
Query:       gi|91772929|ref|YP_565621.1|  [L=74]
Description: hypothetical protein Mbur_0928 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.027   14.7   0.6      0.038   14.3   0.6    1.1  1  Sigma_reg_N  Sigma factor regulator N-terminal
      0.053   12.8   0.1      0.066   12.5   0.1    1.1  1  DUF4436      Domain of unknown function (DUF4436)


Domain annotation for each model (and alignments):
>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   4.3e-06     0.038      12      41 ..       3      35 ..       2      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-06
                   Sigma_reg_N 12 ilrivlislivlllifvil...vvtllylaeke 41
                                  +l++v i+++v+l+++v++   ++t++y+++++
  gi|91772929|ref|YP_565621.1|  3 TLTTVAIAIAVFLVLIVLTameLKTASYMHTEK 35
                                  799**********99999866778888884443 PP

>> DUF4436  Domain of unknown function (DUF4436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.3e-06     0.066     164     200 ..       5      41 ..       3      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.3e-06
                       DUF4436 164 stlifalvivlvlialpvlalivaiqvlrgrrklepp 200
                                    t++ a+ + lvli+l+++ l  a ++ +++  l pp
  gi|91772929|ref|YP_565621.1|   5 TTVAIAIAVFLVLIVLTAMELKTASYMHTEKNSLSPP 41 
                                   5899******************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 453.79
//
Query:       gi|91772930|ref|YP_565622.1|  [L=273]
Description: F420-dependent methylenetetrahydromethanopterin dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-129  428.7   3.2   9.8e-129  428.5   3.2    1.0  1  MTD       methylene-5,6,7,8-tetrahydromethanopterin dehydroge


Domain annotation for each model (and alignments):
>> MTD  methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.5   3.2  5.5e-133  9.8e-129       2     272 ..       3     271 ..       2     273 .] 0.99

  Alignments for each domain:
  == domain 1  score: 428.5 bits;  conditional E-value: 5.5e-133
                                   EEEEEEES--HHHHHTTGGGSTTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SEEEEE-S-TTSHHHHHHHHHHHH CS
                           MTD   2 kigiiklGnigtslvidlllDeradRedievrvvgsgaklkkeeveevveklkefdpdlvivisPnaaapgptkarellse 82 
                                   kig+iklGn+g+s+vidl++De+a+Re+i+vrv+g+g+k++k+e++  +++lke+d+d++++isPn++apgpt+are++  
  gi|91772930|ref|YP_565622.1|   3 KIGFIKLGNLGMSQVIDLVQDEIAAREGISVRVFGTGPKMGKDEAA-ETAALKEWDADFYVMISPNSSAPGPTAAREIY-- 80 
                                   9********************************************9.6899****************************.. PP

                                   SSS-EEEEEEGGGGGGH.HHHHHTT-EEEEETTS------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHT CS
                           MTD  83 kdvpaivisDapgkkek.deleeeglGYiivkaDpliGarrefLDptemalfnadvlkvLaatGavRlvqeeldkviekvk 162
                                   kdvp+ivisD+p+kk++ ++le+ g+GYii+++DpliGa+refLD++ema+fn+d++kvL+++G+vRl+qeeld v+++v+
  gi|91772930|ref|YP_565622.1|  81 KDVPCIVISDGPTKKDDrQALEDAGFGYIIMTVDPLIGAKREFLDSVEMASFNSDAMKVLSTCGVVRLIQEELDIVTAQVD 161
                                   9**************998*************************************************************** PP

                                   TT-GGGS-EEEESGGGGGGSS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           MTD 163 agkeielPkividaekaveaaefsnPYakakalaayeiaekvadidvkaCfmekelekyilivasahellraaakLadeaR 243
                                   +gkei lP+i++++ek++e+a+fsnPYakakalaa+++a+kva+i++ aCfm+ke+e+++l++a+ahe++raaa+La +aR
  gi|91772930|ref|YP_565622.1| 162 EGKEIVLPHILAKPEKCIERAGFSNPYAKAKALAALHMADKVAQINFPACFMMKEIEQVTLTTATAHEMMRAAAQLAIDAR 242
                                   ********************************************************************************* PP

                                   HHHHHTT---B--B-TTSSB--BSSTTS- CS
                           MTD 244 eieksndtvlRkphakdGkvlsktkllek 272
                                   eieksndtvlR+phak+G++lskt+l+ek
  gi|91772930|ref|YP_565622.1| 243 EIEKSNDTVLRQPHAKKGNILSKTALYEK 271
                                   ***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1574.34
//
Query:       gi|91772931|ref|YP_565623.1|  [L=579]
Description: hypothetical protein Mbur_0930 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 3917.45
//
Query:       gi|91772932|ref|YP_565624.1|  [L=152]
Description: hypothetical protein Mbur_0931 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 904.50
//
Query:       gi|91772933|ref|YP_565625.1|  [L=210]
Description: Rh-like protein/ammonium transporter, partial [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  226.2  26.7    6.3e-67  226.0  26.7    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 !  226.0  26.7   3.5e-71   6.3e-67      86     307 ..       2     210 .]       1     210 [] 0.98

  Alignments for each domain:
  == domain 1  score: 226.0 bits;  conditional E-value: 3.5e-71
                                   HHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSSTTTTHHHHHHHHHH CS
               Ammonium_transp  86 lfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgstvVHlvggvagLa 166
                                   lf++fq++faa+a++i +++vaerik+s++++f++l++tlvy p+a+w+wg +gw+ ++g+l DfAg+tvVH+ +g+ +La
  gi|91772933|ref|YP_565625.1|   2 LFMAFQIVFAAIALAILTSGVAERIKLSSFIVFGLLWTTLVYDPLAYWAWG-DGWVGSMGAL-DFAGGTVVHISSGFGALA 80 
                                   68*************************************************.**********.****************** PP

                                   HHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCS CS
               Ammonium_transp 167 aalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaagaltallisrlkeg 247
                                   + +v+gkr+g +   ++++++ n++ ++lG +lLwfgWf+FNaG al+an      a+v+Tl++a+ galt++ +s++k g
  gi|91772933|ref|YP_565625.1|  81 LSFVIGKRIGFG---KYSMEPENITTTLLGGALLWFGWFAFNAGNALAAN------AFVVTLISASSGALTWMGASWIK-G 151
                                   **********99...9**************************99888764......89*********************.* PP

                                   S-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHH CS
               Ammonium_transp 248 kinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldv 307
                                   k + lg+ +G++AGlVAiT+ac++v p++A+iiG  Ag+l++ ++ ++    k+d+sld+
  gi|91772933|ref|YP_565625.1| 152 KSSSLGMNSGAIAGLVAITPACGFVGPLAAIIIGGSAGILCYGTL-LFCIYKKFDESLDA 210
                                   *********************************************.6***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1298.48
//
Query:       gi|91772934|ref|YP_565626.1|  [L=110]
Description: nitrogen regulatory protein P-II [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-31  107.7   3.7    4.2e-31  107.6   3.7    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 !  107.6   3.7   2.4e-35   4.2e-31       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.4e-35
                                   EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SS CS
                          P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaaktg 81 
                                   i+aiirp kle+vke+L +ag++++t+ +vkGrG+qkg    +rg++  ++++pk++++ivv++++v +v+++i +a++tg
  gi|91772934|ref|YP_565626.1|   4 ITAIIRPGKLETVKEELVTAGLNAMTIFDVKGRGEQKGICLQFRGKRNLIDMIPKIQIDIVVKNDEVVTVIQTIKHAVRTG 84 
                                   89******************************************************************************* PP

                                   STTSEEEEEEEESEEEETTTT CS
                          P-II  82 eiGDGkiFvlpveevirirtg 102
                                   +iGDGkiF  pve +i irtg
  gi|91772934|ref|YP_565626.1|  85 KIGDGKIFGPPVEMMIGIRTG 105
                                   ********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 748.79
//
Query:       gi|91772935|ref|YP_565627.1|  [L=224]
Description: phosphoserine phosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-20   73.8   0.1    3.2e-20   73.3   0.1    1.2  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.3e-20   73.3   0.0    4.3e-20   72.9   0.0    1.2  1  HAD              haloacid dehalogenase-like hydrolase
    3.6e-13   49.5   0.4    1.7e-11   44.0   0.4    2.0  1  Put_Phosphatase  Putative Phosphatase
    2.4e-11   43.9   0.0    1.8e-09   37.8   0.0    2.5  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
      1e-09   38.7   0.5    3.3e-08   33.8   0.5    2.8  1  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0017   17.9   0.0       0.24   10.9   0.0    2.2  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.061   13.4   0.0    2.1  2  Hydrolase_like   HAD-hyrolase-like
      0.052   13.4   0.0       0.43   10.4   0.0    2.2  1  Acid_PPase       Acid Phosphatase
      0.055   13.2   0.0       0.63    9.7   0.0    2.1  2  PNK3P            Polynucleotide kinase 3 phosphatase
      0.096   12.1   0.0       0.15   11.5   0.0    1.3  1  DUF705           Protein of unknown function (DUF705)


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 !   73.3   0.1   1.8e-23   3.2e-20       2     210 .]      14     187 ..      13     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.8e-23
                                   SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltaldi 82 
                                   k++vfD+d TL++ e      i+++                     a a ++  +++ +++     +++ g+ ++ +al  
  gi|91772935|ref|YP_565627.1|  14 KLIVFDMDSTLIDAE-----SIDEL---------------------ARAAGVMDKVSVVTE-----KAMNGEIDYNQAL-- 61 
                                   89*************.....*****.....................999999999******.....*************.. PP

                                   HHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                     Hydrolase  83 ppdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfda 162
                                                + r + l+  ++    ++ d+ +++p+a+e+v++ ++ g+++++l+g++    +r+a+ l  d  f++
  gi|91772935|ref|YP_565627.1|  62 -------------KERVALLKGLKLETAMEAMDSMPLMPGAEELVKHVRSLGFKTAILSGGFTLSTDRVAKLLEmDYVFSN 129
                                   .............9999999988999999999******************************************5444455 PP

                                   EEEHHCES....STTT......SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxx....xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 163 viasdiet....vakp......spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   ++++ +      v++p      + ++++++ +e + +pe++++VGDg+nD+  +++Ag
  gi|91772935|ref|YP_565627.1| 130 ILEIKDGCltgrVSGPmtqnlsKEQAFEQITEENGLNPENCIVVGDGANDICIFKRAG 187
                                   5555554487888888999999999999999999*****************9999997 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   2.4e-23   4.3e-20       1     187 [.      16     183 ..      16     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 2.4e-23
                           HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerfvaev 80 
                                   ++fD+D TL+d +s+++l+r  +++      + + + +++a+    ++ d++++ +   all+gl+ e   + ++ +    
  gi|91772935|ref|YP_565627.1|  16 IVFDMDSTLIDAESIDELAR-AAGV-----MDKVSVVTEKAM---NGEIDYNQALKERVALLKGLKlETAMEAMDSMP--- 84 
                                   79******************.5555.....677777777777...4445555999999********666666666666... PP

                           HAD  81 irpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkvaalre 160
                                       l+ pga el++++r+ G++++++Sgg+   + +++++l  d+v ++ le +d +ltg+  ++g+++    k +a ++
  gi|91772935|ref|YP_565627.1|  85 ----LM-PGAEELVKHVRSLGFKTAILSGGFTLSTDRVAKLLEMDYVFSNILEIKDgCLTGR--VSGPMTQNLSKEQAFEQ 158
                                   ....56.*******************************************************..88888888778899999 PP

                           HAD 161 wlaaegegidleevvayGDspsDlpll 187
                                       e++g+ +e+++++GD+ +D++ +
  gi|91772935|ref|YP_565627.1| 159 --ITEENGLNPENCIVVGDGANDICIF 183
                                   ..99999*****************976 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.4   9.4e-15   1.7e-11       2     187 ..      15     185 ..      14     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 9.4e-15
               Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkgl..wnelmdrvlkelheqgvseadikkvlrsiplspglveli 80 
                                   l+vfD D t+id +s + + ++++  ++ + + e+  +g   +n+ +++ ++ l+  g + +   +++ s+pl pg  el+
  gi|91772935|ref|YP_565627.1|  15 LIVFDMDSTLIDAESIDELARAAGVMDKVSVVTEKAMNGEidYNQALKERVALLK--GLKLETAMEAMDSMPLMPGAEELV 93 
                                   89*************************9999988877653349999999999995..6778888999************** PP

               Put_Phosphatase  81 kslakkkleldliiiSDaNsffieeileaagledlFseiftNPaavdasGeltvlpyhehsCklcpsNlCKgkvleelvae 161
                                   k++  ++l++   i+S   ++  + + + +++  +Fs+i+       ++G lt +           +Nl K++ +e++++e
  gi|91772935|ref|YP_565627.1|  94 KHV--RSLGFKTAILSGGFTLSTDRVAKLLEMDYVFSNILEI-----KDGCLTGR-----VSGPMTQNLSKEQAFEQITEE 162
                                   ***..689************************9999999753.....56777643.....3456789*************9 PP

               Put_Phosphatase 162 qaregveyerliYvGDganDlCpvlk 187
                                      +g + e  i vGDganD+C  ++
  gi|91772935|ref|YP_565627.1| 163 ---NGLNPENCIVVGDGANDICIFKR 185
                                   ...699****************8765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.037        66       1      13 [.      16      28 ..      16      38 .. 0.87
   2 ?   -2.3   0.0       1.6   2.9e+03      21      58 ..      90     126 ..      81     137 .. 0.79
   3 !   37.8   0.0   9.8e-13   1.8e-09     182     246 ..     146     209 ..     142     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.037
                                  EEEEIIIIIS-TT CS
                   Hydrolase_3  1 ialDlDGTLlnsd 13
                                  i++D+D TL++ +
  gi|91772935|ref|YP_565627.1| 16 IVFDMDSTLIDAE 28
                                  89*******9864 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                                   HHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                   Hydrolase_3  21 keaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                    e +k +++ g+k +i +G  + ++ +v++ l++d +v
  gi|91772935|ref|YP_565627.1|  90 EELVKHVRSLGFKTAILSGGFTLSTDRVAKLLEMD-YV 126
                                   57788888889999999988888888888888877.44 PP

  == domain 3  score: 37.8 bits;  conditional E-value: 9.8e-13
                                   EETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--G CS
                   Hydrolase_3 182 mpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksn 246
                                   m ++ sK +a +++ +e ++++e++i++GDg NDi  +++ag ++A  n ++ + ++Ad v++++
  gi|91772935|ref|YP_565627.1| 146 MTQNLSKEQAFEQITEENGLNPENCIVVGDGANDICIFKRAGCAIAF-NPKPILRQYADAVITQK 209
                                   6789*****************************************97.78999999999998765 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.5   1.8e-11   3.3e-08       1     175 [.      16     190 ..      16     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.8e-11
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpy 81 
                                   i+FD+D Tl+d e +  + ++ +    ++s ++e+ ++  i  +       l+e+     +++ l  +   e  + ++ ++
  gi|91772935|ref|YP_565627.1|  16 IVFDMDSTLIDAESID-ELARAAGVMDKVSVVTEKAMNGEIDYNQ-----ALKERVA---LLKGLKLETAMEAMD-SMPLM 86 
                                   89*********87543.3333333344444555555544443333.....3444322...566664444445555.6**** PP

                         HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsed..........vekk..KPdpeviekaleklkl 150
                                   +g++el++ +++ g+k +i + + + ++++  + l+++ +F+ i+  +d          ++++  K   + +e++ e+ +l
  gi|91772935|ref|YP_565627.1|  87 PGAEELVKHVRSLGFKTAILSGGFTLSTDRVAKLLEMDYVFSNILEIKDgcltgrvsgpMTQNlsK--EQAFEQITEENGL 165
                                   ********************************************8655533322111112232234..78899999999** PP

                         HAD_2 151 kkeeviyvGDsptDieaakkagikv 175
                                   ++e++i+vGD  +Di   k+ag+ +
  gi|91772935|ref|YP_565627.1| 166 NPENCIVVGDGANDICIFKRAGCAI 190
                                   **********************976 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0079        14       3      27 ..      14      36 ..      12      64 .. 0.85
   2 !   10.9   0.0   0.00013      0.24     163     200 ..     149     186 ..     146     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0079
                                  EEEEE-TBTTTB.S-HHHHHHHHHH CS
                          S6PP  3 lllvsdLDntlvdgdnealarlnel 27
                                  +l+v d+D+tl+  d+e++++l + 
  gi|91772935|ref|YP_565627.1| 14 KLIVFDMDSTLI--DAESIDELARA 36
                                  79**********..88888888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                   T-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSS CS
                          S6PP 163 raskgeAlryLakkleleleqilvcGdsgnDeellign 200
                                   + sk++A + + +  +l++e+ +v+Gd  nD+ +++  
  gi|91772935|ref|YP_565627.1| 149 NLSKEQAFEQITEENGLNPENCIVVGDGANDICIFKRA 186
                                   569*****************************999654 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    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      41      74 ..      99     132 ..      97     133 .. 0.76
   2 ?   13.4   0.0   3.4e-05     0.061       9      44 ..     155     189 ..     151     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                                   CT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                Hydrolase_like  41 aGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                    G k++    G t  +d+ ++  + +yv+ ++ e
  gi|91772935|ref|YP_565627.1|  99 LGFKTAILSGGFTLSTDRVAKLLEMDYVFSNILE 132
                                   5777888888888888877666899999999876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-E CS
                Hydrolase_like   9 mydfalevlgsdpeevlmiGDrlatDiagAnnaGwk 44 
                                   +++++ e++g++pe+++++GD  a Di   ++aG+ 
  gi|91772935|ref|YP_565627.1| 155 AFEQITEENGLNPENCIVVGDG-ANDICIFKRAGCA 189
                                   689999999*************.****888888875 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00024      0.43       2      23 ..      12      34 ..      11     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                                  --SEEEE-STTTSSSS-.TTTSS CS
                    Acid_PPase  2 lpklivFDLDyTLWpfe.vdtlv 23
                                  + klivFD+D TL + e +d l+
  gi|91772935|ref|YP_565627.1| 12 YSKLIVFDMDSTLIDAEsIDELA 34
                                  679**********8776245553 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00035      0.63       1      22 [.      14      35 ..      14      66 .. 0.85
   2 ?    1.3   0.0      0.14   2.5e+02     108     130 ..     157     179 ..     146     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                         PNK3P  1 kiaaFDlDstliktksgkefak 22
                                  k+++FD+Dstli ++s  e a+
  gi|91772935|ref|YP_565627.1| 14 KLIVFDMDSTLIDAESIDELAR 35
                                  6899**********99777665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                         PNK3P 108 kdleekleidkeksfyvGDaagr 130
                                   ++++e+  ++ e+++ vGD a+ 
  gi|91772935|ref|YP_565627.1| 157 EQITEENGLNPENCIVVGDGAND 179
                                   444556889999********986 PP

>> DUF705  Protein of unknown function (DUF705)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.2e-05      0.15     133     161 ..      12      41 ..       1      52 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.2e-05
                        DUF705 133 ikhvvvfDlDstLitdeeevel.Rdhavyd 161
                                      ++vfD+DstLi  e   el R   v+d
  gi|91772935|ref|YP_565627.1|  12 YSKLIVFDMDSTLIDAESIDELaRAAGVMD 41 
                                   3459**********8765554425555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1339.10
//
Query:       gi|91772936|ref|YP_565628.1|  [L=285]
Description: phosphoserine phosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0075   16.0  17.0     0.0075   16.0  17.0    3.2  3  YkyA          Putative cell-wall binding lipoprotein
  ------ inclusion threshold ------
      0.014   15.7   8.8      0.014   15.7   8.8    3.7  3  Syntaxin_2    Syntaxin-like protein
      0.015   15.8   2.7      0.015   15.8   2.7    2.6  3  DUF5600       Domain of unknown function (DUF5600)
        0.3   10.5  39.5        1.1    8.7  21.0    2.4  2  Golgin_A5     Golgin subfamily A member 5
       0.51   10.3  29.9        0.7    9.9   1.0    4.8  5  Laminin_II    Laminin Domain II
        1.6    9.1   6.9       0.28   11.5   1.5    2.4  2  mCpol         minimal CRISPR polymerase domain
        1.9    7.6  50.0        9.2    5.3  50.0    2.0  1  Taxilin       Myosin-like coiled-coil protein
        5.7    6.8  21.3       0.64    9.9   5.9    2.9  3  TarH          Tar ligand binding domain homologue
        6.5    7.0  46.2        1.3    9.3  17.2    4.3  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
        6.8    6.9  25.1       0.83    9.9   3.7    4.6  4  JIP_LZII      JNK-interacting protein  leucine zipper II
        6.9    5.2  38.6        3.7    6.1  10.4    2.0  2  AAA_13        AAA domain
        7.9    6.9  38.5        2.5    8.5  17.5    2.1  2  Fez1          Fez1
        8.8    6.7  21.7        8.2    6.8   5.0    3.7  3  DUF2935       Domain of unknown function (DUF2935)


Domain annotation for each model (and alignments):
>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  17.1     0.048        66      37     120 ..       7      89 ..       1      94 [. 0.76
   2 ?    1.5   7.3      0.15     2e+02      42     118 ..      65     146 ..      62     150 .. 0.82
   3 !   16.0  17.0   5.4e-06    0.0075       3     120 ..     148     265 ..     146     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.048
                          YkyA  37 lyeeiielgmde.fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieameeryea 116
                                   + ++ +++  +e ++k ++l +ea +++ +R++l ++ ke i+ea+e  +  +e+ e+++++  k + +e + + +e +++
  gi|91772936|ref|YP_565628.1|   7 TKKQDLKAASEEyKEKRNALNAEASTLAAKRNDLNKSTKELINEAQEYKKLRDENNEQVKEN--KAKRDEINAKANEVFAK 85 
                                   44455555556657889*****************************9999999999999877..55566666666666666 PP

                          YkyA 117 ydkl 120
                                    d+l
  gi|91772936|ref|YP_565628.1|  86 VDAL 89 
                                   6555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                          YkyA  42 ielgmdefdkikklsdealenveeReellekekesieeakeefekikee..ieei...edeelkkeaeelieameeryeay 117
                                   ++ ++ + d+i+++++e+++ v++ +   +    si++ ++e++ ++ +  +e +   ++++l ++++el++++  ++++ 
  gi|91772936|ref|YP_565628.1|  65 VKENKAKRDEINAKANEVFAKVDALRAASNLTGPSIKDIRKEIDRLEFTqqTEVLtpaKEKDLVSKITELQKQYVVKKDQL 145
                                   455666789*********************************99887542233337779999********99998888877 PP

                          YkyA 118 d 118
                                   +
  gi|91772936|ref|YP_565628.1| 146 E 146
                                   6 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 5.4e-06
                          YkyA   3 eekiyealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakee 83 
                                    +++ + l+ea+++ +e  e  + L+e+ +k qe+ +++i+ + +e dk+ ++sd a +   e +e+ +++ + + +a++e
  gi|91772936|ref|YP_565628.1| 148 NTELKNLLDEAQQIRDEASEFHNVLSEYAQKAQEYHDKMIS-TFKEADKMRAESDAAHKQFVEFQEKADEQHKLFISAQKE 227
                                   5788999*********************************8.88888********************************** PP

                          YkyA  84 fekikeeieei.edeelkkeaeelieameeryeaydkl 120
                                   + +i++e+ ++ + e+  k++ +++++ ++  e ++k+
  gi|91772936|ref|YP_565628.1| 228 IRDIDKEVRKMrKGETDGKKVASMEDVRKDAAELFEKF 265
                                   ***********878889999999999999999988887 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4  10.6      0.31   4.3e+02      19      85 ..       2      67 ..       1     115 [. 0.75
   2 ?   15.7   8.8     1e-05     0.014      11      99 ..     127     220 ..     123     222 .. 0.90
   3 ?    2.7   0.3      0.12   1.7e+02       5      57 ..     228     280 ..     224     283 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.31
                    Syntaxin_2 19 vkqLgtkkd.....teelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqe 85
                                  +k L+tkk+     +ee++ek + l  e+++l+ k n+l k+ ++l+n  + +       kL+++ +e ++e
  gi|91772936|ref|YP_565628.1|  2 MKELNTKKQdlkaaSEEYKEKRNALNAEASTLAAKRNDLNKSTKELINEAQEY------KKLRDENNEQVKE 67
                                  67888886448888888888888888888888888888888888888887643......3333333333333 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1e-05
                    Syntaxin_2  11 nvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqkl.....qkekLkkdfkealqeF 86 
                                   +vs++ +l+kq   kkd+ e + +l++l +e++++  + +e  + ls+++++ + ++ k+     +++k++ +  +a+++F
  gi|91772936|ref|YP_565628.1| 127 LVSKITELQKQYVVKKDQLESNTELKNLLDEAQQIRDEASEFHNVLSEYAQKAQEYHDKMistfkEADKMRAESDAAHKQF 207
                                   7999**********************************************9999885555566689*************** PP

                    Syntaxin_2  87 qkiqrqyaekekq 99 
                                    + q+++ e  k 
  gi|91772936|ref|YP_565628.1| 208 VEFQEKADEQHKL 220
                                   *******998875 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.12
                    Syntaxin_2   5 lqkinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkkls 57 
                                   +  i + v++++k  ++ ++    e++r+ + el e+ +   k t+e+l  l+
  gi|91772936|ref|YP_565628.1| 228 IRDIDKEVRKMRKGETDGKKVASMEDVRKDAAELFEKFKSGEKLTTENLMTLQ 280
                                   33333333333333333333344888888888888888888888888887776 PP

>> DUF5600  Domain of unknown function (DUF5600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   2.7   1.1e-05     0.015       6      97 ..      36     133 ..      31     141 .. 0.81
   2 ?    0.3   1.3      0.78   1.1e+03      23      86 ..     147     212 ..     125     237 .. 0.63
   3 ?   -2.2   0.0       4.6   6.3e+03      24      38 ..     251     265 ..     223     278 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                       DUF5600   6 klNdlvkRaRlvkvhalllaelrkempsvfgke.kkkkeLieelpeiyekvsrkhnlplgdFPdvekfkeklkaldftkfk 85 
                                   k Ndl k ++ +  +a   ++lr+e ++ + ++ +k++e+ ++ +e++ kv      +    P+++ +++++  l+ft+  
  gi|91772936|ref|YP_565628.1|  36 KRNDLNKSTKELINEAQEYKKLRDENNEQVKENkAKRDEINAKANEVFAKVDALRAASNLTGPSIKDIRKEIDRLEFTQQT 116
                                   679********************9987655555168999999***********************************8876 PP

                       DUF5600  86 kl.....kpkliealde 97 
                                   ++     ++ l+++++e
  gi|91772936|ref|YP_565628.1| 117 EVltpakEKDLVSKITE 133
                                   64444444445555554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.78
                       DUF5600  23 llaelrkempsvfgkekkkkeLieelpeiyekvsrkhnlplgdFPdvekfkeklka..ldftkfkk 86 
                                     +el++ + +    + + +e  + l+e  +k ++ h+  +  F + +k++ +  a   +f +f++
  gi|91772936|ref|YP_565628.1| 147 SNTELKNLLDEAQQIRDEASEFHNVLSEYAQKAQEYHDKMISTFKEADKMRAESDAahKQFVEFQE 212
                                   455666666665555666667777777777777888888888888888887654441146666655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.6
                       DUF5600  24 laelrkempsvfgke 38 
                                   ++++rk   ++f k 
  gi|91772936|ref|YP_565628.1| 251 MEDVRKDAAELFEKF 265
                                   344444444444444 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  21.0   0.00078       1.1      44     193 ..       7     152 ..       1     160 [. 0.82
   2 ?    6.8  10.5    0.0029         4       4     107 ..     167     270 ..     164     282 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00078
                     Golgin_A5  44 alsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelr 124
                                   +++++l ++++e +  r+ l++  +++   r++l++  ++  +ea+++++   e +eq++e+++++     e++ + +e+ 
  gi|91772936|ref|YP_565628.1|   7 TKKQDLKAASEEYKEKRNALNAEASTLAAKRNDLNKSTKELINEAQEYKKLRDENNEQVKENKAKRD----EINAKANEVF 83 
                                   5667788888888888999999999999999999999999999999999999999999987777777....5555556665 PP

                     Golgin_A5 125 yleeelvrskatlqsrikdrekeieklrnqlttkslsssseselesRlkqLtesLiqKQtvlEalstek 193
                                   +  + l+ + + +   ikd  kei++l+   +t+ l+ ++e++l s++ +L  + + K  +lE+ +  k
  gi|91772936|ref|YP_565628.1|  84 AKVDALRAASNLTGPSIKDIRKEIDRLEFTQQTEVLTPAKEKDLVSKITELQKQYVVKKDQLESNTELK 152
                                   5555666666677889************99999999999************************865555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0029
                     Golgin_A5   4 sakqeledYKqkAarILQsKekliasLkegs.geeglesstalsaeldelkqerdll....reelqklnqqieqlrtelqd 79 
                                   + ++ l++Y qkA+      +k+i++ ke+     ++++++++ +e++e  +e+  l    ++e+ +  ++++++r+   +
  gi|91772936|ref|YP_565628.1| 167 EFHNVLSEYAQKAQE---YHDKMISTFKEADkMRAESDAAHKQFVEFQEKADEQHKLfisaQKEIRDIDKEVRKMRKG--E 242
                                   567778999999996...689999999986513344444445555555554444432111145555555555555554..5 PP

                     Golgin_A5  80 leaqqqaeaeslreqlqeleeqleeerk 107
                                   ++ ++ a +e +r+  +el e++++ +k
  gi|91772936|ref|YP_565628.1| 243 TDGKKVASMEDVRKDAAELFEKFKSGEK 270
                                   5566666666666666666666665444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   4.0      0.33   4.6e+02      16      75 ..       6      51 ..       1      63 [. 0.45
   2 ?    8.4   5.7    0.0015         2      12      94 ..      51     133 ..      44     140 .. 0.76
   3 ?    4.2   3.1      0.03        42      15      61 ..     140     186 ..     124     199 .. 0.72
   4 ?    9.9   1.0   0.00051       0.7       4      66 ..     178     240 ..     176     244 .. 0.92
   5 ?    4.5   0.3     0.025        34      38      84 ..     226     274 ..     225     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.33
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGH CS
                    Laminin_II 16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldkl 75
                                    ++++l++  e+ kek + +n+++    +k +d+nk                 +L++  
  gi|91772936|ref|YP_565628.1|  6 NTKKQDLKAASEEYKEKRNALNAEASTLAAKRNDLNK--------------STKELINEA 51
                                  3444455555555555555555554444444444444..............444444444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....HHHH CS
                    Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.lsdn 91 
                                   a+e ++   + ++++++ k+k  ein++++e+ +kv+++  a ++ + s+k++ k++++L+   ++ + l +a++  l  +
  gi|91772936|ref|YP_565628.1|  51 AQEYKKLRDENNEQVKENKAKRDEINAKANEVFAKVDALRAASNLTGPSIKDIRKEIDRLEFT-QQTEVLTPAKEKdLVSK 130
                                   4555666677788999******************************************99754.45555555544334444 PP

                                   HHH CS
                    Laminin_II  92 ise 94 
                                   i e
  gi|91772936|ref|YP_565628.1| 131 ITE 133
                                   444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.03
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsv 61 
                                   v+++  + +++l+n+ +++++i++++ e +++++++ +  ++  +++
  gi|91772936|ref|YP_565628.1| 140 VKKDQLESNTELKNLLDEAQQIRDEASEFHNVLSEYAQKAQEYHDKM 186
                                   66777777888999999999999999999999998888777666665 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00051
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                    Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66 
                                   +a+e  +++ ++ +   ++ ++ +   ++  e++++++e +++  +a+k ird  ++v+k+ k
  gi|91772936|ref|YP_565628.1| 178 KAQEYHDKMISTFKEADKMRAESDAAHKQFVEFQEKADEQHKLFISAQKEIRDIDKEVRKMRK 240
                                   577888888899999999******************************************976 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.025
                                   XXXXXXXXXXXXXXXXXXXXXX..XXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II  38 rsveetnekvkdankairdArr..svkkLeklapqLldklkelkqleea 84 
                                   ++++ ++++v+++ k+  d ++  s+ ++ k a +L++k+k+ ++l  +
  gi|91772936|ref|YP_565628.1| 226 KEIRDIDKEVRKMRKGETDGKKvaSMEDVRKDAAELFEKFKSGEKLTTE 274
                                   56788899999999999998754489999************98887665 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.95   1.3e+03      39      39 ..      68      68 ..       8     120 .. 0.61
   2 ?   11.5   1.5    0.0002      0.28      12      87 ..     144     224 ..     142     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.95
                         mCpol 39 l 39
                                   
  gi|91772936|ref|YP_565628.1| 68 N 68
                                  1 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                         mCpol  12 kleall.lsndeeeleklskevkeaikklkkllkdel..gasvi..faaGDsilakssleedllvelsrvyqkitgltvSi 87 
                                   +le+   l+n + e+++++ e  e+ + l+++ ++ +  + ++i  f+++D++ a+s++ ++++ve+++  +++ +l +S+
  gi|91772936|ref|YP_565628.1| 144 QLESNTeLKNLLDEAQQIRDEASEFHNVLSEYAQKAQeyHDKMIstFKEADKMRAESDAAHKQFVEFQEKADEQHKLFISA 224
                                   56777767888889999999999999999999998886733443349**************************99998886 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  50.0    0.0067       9.2      34     265 ..       2     247 ..       1     282 [. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0067
                       Taxilin  34 rkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRel...qkqnkklkeeskqrareeeekrkelaekfqak 111
                                   +k+l+ + + lk   e+ ++++++l ae s  a+ ++ L+k  +el    ++ kkl++e++++++e+++kr+e+++k ++ 
  gi|91772936|ref|YP_565628.1|   2 MKELNTKKQDLKAASEEYKEKRNALNAEASTLAAKRNDLNKSTKELineAQEYKKLRDENNEQVKENKAKRDEINAKANEV 82 
                                   677777788888899999999999****************99999944445678999************************ PP

                       Taxilin 112 Lkdiqaqieekserneklreenae.....lteKlkslieqye......lreehfekllktkelelqlaeaK.lqqadallk 180
                                    ++++a  ++++ +  + ++  +e     +t+  + l    e      + e++ + ++k+ +le     +  l++a+   +
  gi|91772936|ref|YP_565628.1|  83 FAKVDALRAASNLTGPSIKDIRKEidrleFTQQTEVLTPAKEkdlvskITELQKQYVVKKDQLESNTELKNlLDEAQQIRD 163
                                   ******999999888877777776334556666666665555888887888888999999999998876552578888889 PP

                       Taxilin 181 eeqekkkrekeyllkeakeltkkvkalketekelkeqlnlYaeKfeefqdtLakSnelFatFkkEmekmtkktkklEketn 261
                                   e+ e ++   ey +++a+e+++k+ +  ++  ++++  +   ++f efq+      +lF + +kE+ ++ k+++k+ k  +
  gi|91772936|ref|YP_565628.1| 164 EASEFHNVLSEY-AQKAQEYHDKMISTFKEADKMRAESDAAHKQFVEFQEKADEQHKLFISAQKEIRDIDKEVRKMRKGET 243
                                   999999999999.***************************************************************99776 PP

                       Taxilin 262 lwks 265
                                     k+
  gi|91772936|ref|YP_565628.1| 244 DGKK 247
                                   6554 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   7.0      0.13   1.8e+02      50     109 ..       8      70 ..       2      96 .. 0.56
   2 ?    9.9   5.9   0.00046      0.64      55     161 ..     159     264 ..     136     268 .. 0.81
   3 ?    2.2   0.0      0.11   1.5e+02      74     114 ..     236     274 ..     225     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSS....SHHHHHHHHHHHHHHHHHHHHHTS-- CS
                          TarH  50 qqaaLaearvsllqaRltLnragiaaladeaeda....kellaraeeslaqseeawkaYlalpr 109
                                   ++++L  a+ +  + R++Ln   + +la++++d     kel+++a+e+ +  +e+ ++ ++  +
  gi|91772936|ref|YP_565628.1|   8 KKQDLKAASEEYKEKRNALNA-EASTLAAKRNDLnkstKELINEAQEYKKLRDENNEQVKENKA 70 
                                   445566666666666666663.555555555555555666666666665555555444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00046
                                   HHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHHHHHHHHHHTS---GGGHH.HHHHHHHHHHHHHHHHHHH CS
                          TarH  55 aearvsllqaRltLnragiaaladeaedakellaraeeslaqseeawkaYlalprtaeeeealaaelkakykalqdglapl 135
                                    ++r++  +  + L+   ++ ++  ++++ ++ ++a++++a+s++a k++ + +++a+e+ +l   +++  + +++ ++ +
  gi|91772936|ref|YP_565628.1| 159 QQIRDEASEFHNVLSE-YAQKAQEYHDKMISTFKEADKMRAESDAAHKQFVEFQEKADEQHKLFISAQKEIRDIDKEVRKM 238
                                   4556666666677777.455566667777999*************************9999********999999999999 PP

                                   HHHHHTT-HHHHHHS-HHHHHHHHHH CS
                          TarH 136 iaaleagnleaffdlptqkiqplfea 161
                                    +    g+  a ++ + + +  lfe+
  gi|91772936|ref|YP_565628.1| 239 RKGETDGKKVASMEDVRKDAAELFEK 264
                                   99999998888888888888888887 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.11
                                   HHTTTSSSSSSHHHHHHHHHHHHHHHHHHHHHTS---GGGH CS
                          TarH  74 aaladeaedakellaraeeslaqseeawkaYlalprtaeee 114
                                   + +++ ++d  + +a  e+ ++++ e ++++++ ++ +  e
  gi|91772936|ref|YP_565628.1| 236 RKMRKGETDG-KKVASMEDVRKDAAELFEKFKSGEKLT-TE 274
                                   5555555555.889999***************999988.33 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 ?    9.3  17.2   0.00092       1.3      29     100 ..      14      82 ..       1      89 [. 0.62
   2 ?    6.7   7.7     0.006       8.2      13     103 ..     189     278 ..     184     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00092
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                   ++  e  ekr +l++e+  l a+rN l+k+ ++++++    +e ++  +e++e++k+ +a+ +e++a+ +++
  gi|91772936|ref|YP_565628.1|  14 AASEEYKEKRNALNAEASTLAAKRNDLNKSTKELINEA---QEYKKLRDENNEQVKENKAKRDEINAKANEV 82 
                                   34456677888889999999999999999988888754...5555555555555555555555555555554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.006
                                   HHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  13 avkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                   ++ke+ k R e++a  ++++e +ek  e  + + ++q+e   + ke+ k ++k+e   + +a+++++ ++ ++l ++ k  
  gi|91772936|ref|YP_565628.1| 189 TFKEADKMRAESDAAHKQFVEFQEKADEQHKLFISAQKEIRDIDKEVRK-MRKGETDGKKVASMEDVRKDAAELFEKFKSG 268
                                   67888899999************************************76.5668999******************999998 PP

                                   HHHHHHHHCT CS
                  Seryl_tRNA_N  94 eaelekllla 103
                                   e+  ++ l++
  gi|91772936|ref|YP_565628.1| 269 EKLTTENLMT 278
                                   8877777766 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.7    0.0006      0.83      23      69 ..       4      50 ..       1      52 [. 0.93
   2 ?    1.7   1.5      0.21   2.9e+02      18      60 ..      69     111 ..      51     118 .. 0.69
   3 ?    5.4   2.7     0.015        21      29      60 ..     125     156 ..     113     164 .. 0.85
   4 ?    1.3   1.8      0.28   3.8e+02      36      68 ..     152     184 ..     139     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0006
                      JIP_LZII 23 aLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEee 69
                                   Ln+ k+dL a  +e ++ r++L+ E ++l + ++ l++++kel +e
  gi|91772936|ref|YP_565628.1|  4 ELNTKKQDLKAASEEYKEKRNALNAEASTLAAKRNDLNKSTKELINE 50
                                  79*****************************************9665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.21
                      JIP_LZII  18 letknaLnvvkddLIarvdeLtsereiLreEleslqkakerle 60 
                                   ++ +  +n   ++  a+vd L    +     ++ ++k+ +rle
  gi|91772936|ref|YP_565628.1|  69 KAKRDEINAKANEVFAKVDALRAASNLTGPSIKDIRKEIDRLE 111
                                   2445678999999999999998888877777777777777775 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.015
                      JIP_LZII  29 ddLIarvdeLtsereiLreEleslqkakerle 60 
                                   +dL+++++eL++++ + ++ les ++ k+ l 
  gi|91772936|ref|YP_565628.1| 125 KDLVSKITELQKQYVVKKDQLESNTELKNLLD 156
                                   8*****************99999998887665 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.28
                      JIP_LZII  36 deLtsereiLreEleslqkakerlesrikelEe 68 
                                    +L  e + +r+E ++ ++++++  ++ +e  +
  gi|91772936|ref|YP_565628.1| 152 KNLLDEAQQIRDEASEFHNVLSEYAQKAQEYHD 184
                                   445567778888888888888887777777655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  25.5     0.019        27     317     469 ..       6     174 ..       2     175 .. 0.77
   2 ?    6.1  10.4    0.0026       3.7     382     470 ..     148     238 ..     142     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.019
                        AAA_13 317 safeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakk 397
                                   +  ++d + +++e ++ +++L++  + l aKr+++ k  +++++ +++++ kkl +e ne+++++ +k ++++++++e+  
  gi|91772936|ref|YP_565628.1|   6 NTKKQDLKAASEEYKEKRNALNAEASTLAAKRNDLNK--STKELINEAQEYKKLRDENNEQVKENKAKRDEINAKANEVFA 84 
                                   45677888888899999999*****************..9999************************************** PP

                        AAA_13 398 klelhlv.........eeleseldeyk..........kkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpa 459
                                   k+ + ++         +++++e+d+++           k k+l  +i++l+k+   ++++l+  + e k+L  + ++++  
  gi|91772936|ref|YP_565628.1|  85 KVDALRAasnltgpsiKDIRKEIDRLEftqqtevltpAKEKDLVSKITELQKQYVVKKDQLE-SNTELKNLLDEAQQIRDE 164
                                   *9998877788888887777777766656666666665556666677777766555555554.455666666777777777 PP

                        AAA_13 460 aeeinkeLka 469
                                   a+e+ + L++
  gi|91772936|ref|YP_565628.1| 165 ASEFHNVLSE 174
                                   7776666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0026
                        AAA_13 382 Nekvanleeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaa 460
                                   N   +nl +e+++++++   +   ++e+ ++ +ey++k+ ++ k++ k+ +e +++ ++  + +e++ e  k   + ++ +
  gi|91772936|ref|YP_565628.1| 148 NTELKNLLDEAQQIRDEASEFHnvLSEYAQKAQEYHDKMISTFKEADKMRAESDAAHKQFVEFQEKADEQHKLFISAQKEI 228
                                   77888888888888888776543379******************************************************* PP

                        AAA_13 461 eeinkeLkaf 470
                                    +i ke++++
  gi|91772936|ref|YP_565628.1| 229 RDIDKEVRKM 238
                                   ******9987 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  17.5    0.0018       2.5      59     184 ..       3     139 ..       1     144 [. 0.80
   2 ?    4.0  14.0     0.045        62      16     140 ..     142     261 ..     139     282 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                          Fez1  59 esleektlelevcenelqrk....kseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqe.aeeleelk 134
                                   ++l++k+++l+   +e ++k    ++ea++l  k + l++ +kel +e++e ++ ++e++++ +e+ka+r+e + +++e  
  gi|91772936|ref|YP_565628.1|   3 KELNTKKQDLKAASEEYKEKrnalNAEASTLAAKRNDLNKSTKELINEAQEYKKLRDENNEQVKENKAKRDEiNAKANEVF 83 
                                   456666667666666666665565889999999999999999999999999999999999999999999998545667777 PP

                          Fez1 135 reverlra.......eLkeerqkkeeqassFeqERrtWqeeKekVirYqkqLQlnYv 184
                                   ++v+ lra       ++k  r++ ++ + + ++E  t ++eK+ V +   +LQ  Yv
  gi|91772936|ref|YP_565628.1|  84 AKVDALRAasnltgpSIKDIRKEIDRLEFTQQTEVLTPAKEKDLVSKI-TELQKQYV 139
                                   88888888888888899999999999999999999*******998775.57888887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.045
                          Fez1  16 KqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeel 96 
                                   K QL +s +e+ + l+e  +++ +  e ++ l+e  ++++e+++++ +  +e +++ +e + ++++   ++ek+++ ++ +
  gi|91772936|ref|YP_565628.1| 142 KDQL-ESNTELKNLLDEAQQIRDEASEFHNVLSEYAQKAQEYHDKMISTFKEADKMRAESDAAHKQFVEFQEKADEQHKLF 221
                                   5566.7889999999999999999999999999999999999999999999999999999998666666666666666666 PP

                          Fez1  97 kelreelselsleeeeaalesdeakaqrqeaeeleelkreverl 140
                                    + ++e+++  +e +++++      +  ++  ++e+ +++ ++l
  gi|91772936|ref|YP_565628.1| 222 ISAQKEIRDIDKEVRKMRKGE----TDGKKVASMEDVRKDAAEL 261
                                   666666666544433332111....1112222233333333333 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.6     0.038        52      24      98 ..       4      70 ..       1      83 [. 0.77
   2 ?    5.8   1.9     0.012        16      21      91 ..     116     188 ..     105     193 .. 0.74
   3 ?    6.8   5.0     0.006       8.2      21      93 ..     151     218 ..     141     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.038
                       DUF2935 24 lldpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekvlsckl 98
                                   l+ k +dl + ++e+k++ ++l aea  l          + ++++k ++e +++++e+ ++ +e  e+v+++k+
  gi|91772936|ref|YP_565628.1|  4 ELNTKKQDLKAASEEYKEKRNALNAEASTL--------AAKRNDLNKSTKELINEAQEYKKLRDENNEQVKENKA 70
                                  57889999999****************555........6666677777777777777777777777777777665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                       DUF2935  21 iealldpkekdlikeakefkkeF...ekllaeavelseglvrasseleeavakLneealkltreliqFkkelle 91 
                                    e l + kekdl+ +  e++k++   +++l+++ el++ l   +++  ++ +++++   +++++  ++ +++++
  gi|91772936|ref|YP_565628.1| 116 TEVLTPAKEKDLVSKITELQKQYvvkKDQLESNTELKNLL-DEAQQIRDEASEFHNVLSEYAQKAQEYHDKMIS 188
                                   5677788899999999999888755556777777888888.778888888888888888888887777776655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.006
                       DUF2935  21 iealldpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekv 93 
                                   +++lld+ + ++ +ea ef++ ++++ ++a+e+ + +     +++++  k+  e+ ++ +++++F+++  e++
  gi|91772936|ref|YP_565628.1| 151 LKNLLDEAQ-QIRDEASEFHNVLSEYAQKAQEYHDKM----ISTFKEADKMRAESDAAHKQFVEFQEKADEQH 218
                                   556666554.788999999999999999999988777....77888888888888888888888888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3230  (0.180155); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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):              13  [number of targets reported over threshold]
# CPU time: 1.19u 0.37s 00:00:01.56 Elapsed: 00:00:00.61
# Mc/sec: 1399.00
//
Query:       gi|91772937|ref|YP_565629.1|  [L=1351]
Description: KP-43 peptidase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  162.1   8.1    1.7e-47  162.1   8.1    2.5  2  Peptidase_S8  Subtilase family
      6e-09   36.2   3.8       0.17   12.2   0.0    5.5  5  DUF4959       Domain of unknown function (DUF4959)
    8.4e-08   32.1   3.1       0.16   12.0   0.1    4.6  4  DUF2846       Protein of unknown function (DUF2846)
    4.1e-05   23.9   8.6      0.066   13.6   0.0    4.0  4  DUF2369       Uncharacterised conserved protein (DUF2369)
  ------ inclusion threshold ------
      0.036   14.4  31.6       0.05   13.9   0.5    7.5  5  fn3           Fibronectin type III domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   8.1   4.7e-51   1.7e-47       1     298 []     244     546 ..     244     546 .. 0.87
   2 ?   -8.5  11.8         5   1.8e+04      82     223 ..     905    1059 ..     890    1138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 4.7e-51
                                   -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B...SSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                  Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan.apeeg 80 
                                   g+g +vav+DtG+d++  d  +t++ + + + v  + + + +++ s ++ ++ a+d ng    HGthvAG +++n  +++g
  gi|91772937|ref|YP_565629.1| 244 GSGQIVAVADTGLDTGLND--ETMHDDIEGRVVALHAWWTAAHNLSADYGDSGAEDLNG----HGTHVAGSVLGNgNRSSG 318
                                   799**************99..66777777777888888889999999999999999999....************888888 PP

                                   SSB-SSTTSEEE.......EEE-SSTTSB-HH...HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH..HHHHHH CS
                                   xxxxxxxxxxxx.......xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                  Peptidase_S8  81 ekngvapgakil.......svkvldtsggsmetg.teliraieeaaedkvdvinmslgestslpktgrsieal..ainrav 151
                                     +g apgak+        +++     ++    + ++l   ++e+  ++++++ +s+g s+s p++  +++    ai++++
  gi|91772937|ref|YP_565629.1| 319 LYSGTAPGAKLVfqalqyeGIQTA---NNGRLLTpSNLEILFQESYDNGARIHTNSWGTSDSYPEFFGNYSPKsvAIDTFM 396
                                   89**********777754433333...22222221444444899999*******************999988889****** PP

                                   .CC.T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES...........TTSSB-TT--B-TT.......-EEEE CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 152 nkk.gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt...........tegkiapfSsrGpssdgklkpdivap 220
                                   +++ ++l+ +SaGN+g      +   +v++ ++skn++tvga +           + ++ia+fSsrGp+ dg++kpd+vap
  gi|91772937|ref|YP_565629.1| 397 WDHpESLILFSAGNSG------SGATTVSDQASSKNILTVGASEnnrpykgtssdNINEIADFSSRGPTLDGRIKPDVVAP 471
                                   ****************......8999****************************999************************ PP

                                   -S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHH.....HHHHHHCCS-EE......SSSSSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 221 GgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpet.....vraallntAqdlgkadniesfaqG 296
                                   G+ i st+s       + ++y++msGTSmA+P+ ag +Al+++++ +++ +t     ++a+l+n A+dl     + s aqG
  gi|91772937|ref|YP_565629.1| 472 GTFINSTASSLV----YNTNYTYMSGTSMATPLTAGTVALVRQYYTDIKSTTpsgalLKATLINGATDL----GYASSAQG 544
                                   ***766666666....4456***************************7777778899*********999....46688999 PP

                                   TT CS
                                   xx RF
                  Peptidase_S8 297 aG 298
                                   +G
  gi|91772937|ref|YP_565629.1| 545 FG 546
                                   88 PP

  == domain 2  score: -8.5 bits;  conditional E-value: 5
                                    SB-SSTTSEEEEEE-SSTTSB-.HH...HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH.....HHHHHH.C CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxx RF
                  Peptidase_S8   82 kngvapgakilsvkvldtsggs.metg.teliraieeaaedkvdvinmslgestslpktgrsieal.....ainravnk 153 
                                    ++g+ p+a+ +sv+v++ ++ + ++t+ ++ +++++ ++ +   v n+s  +++++ + + +i+ +      i+  v  
  gi|91772937|ref|YP_565629.1|  905 ISGLDPSAS-YSVNVYSVDDFNnANTSsSAFLANTTPDITSPFSVTNLSAEAGDHWINLS-WINPNdidlsSIDVYV-- 979 
                                    566666665.45777765544304444688888888888888889999999999998888.6665567877666666.. PP

                                    CT-EEEEE--SS-T-HH......EEE-TTCEECTTTST..TCEEEEEES....TTSSB-TT--B-TT.......-EEEE CS
                                    xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx..xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8  154 kgvlvviSaGNngktgs......slqagspvgtpstsk..nvitvgayt....tegkiapfSsrGpssdgklkpdivap 220 
                                    +++l+   +GN    +          ++ +v t+++++  +v  ++++t    ++g++++ Ss++++s   + ++ + p
  gi|91772937|ref|YP_565629.1|  980 NNSLLGNTSGNFFFVNYldanasYNLSTHTVDTTGNTNstGVYVIMNTTvdntPPGSVSSLSSSSSESS--ITWSWLNP 1056
                                    377777777777633335454442223344555554444467777777799987777777777777764..55555555 PP

                                    -S- CS
                                    xxx RF
                  Peptidase_S8  221 Ggn 223 
                                       
  gi|91772937|ref|YP_565629.1| 1057 SDV 1059
                                    544 PP

>> DUF4959  Domain of unknown function (DUF4959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.54   1.9e+03      15      49 ..     674     708 ..     669     719 .. 0.76
   2 !   12.2   0.0   4.8e-05      0.17      13      96 ..     761     838 ..     754     849 .. 0.85
   3 !   11.8   0.0   6.3e-05      0.22      13      96 ..     850     927 ..     843     940 .. 0.83
   4 ?    3.0   0.0     0.035   1.3e+02      13      50 ..     939     976 ..     930     984 .. 0.87
   5 ?    4.6   0.4     0.011        40      12      96 ..    1027    1105 ..    1019    1114 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.54
                       DUF4959  15 dkaaPgkvtnvkvknlpGgavisytlPddedLlyv 49 
                                   d ++Pg+v+n++ +  +   + ++++P++ d+  +
  gi|91772937|ref|YP_565629.1| 674 DFTPPGNVSNLNATVGERWITWTWDNPSEGDFSHT 708
                                   67899***999887666666667778888888655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.8e-05
                       DUF4959  13 etdkaaPgkvtnvkvknlpGgavisytlPddedLlyvkaeYklknGkerevkaSvykdsltveGFgdtkeyevklyavsrs 93 
                                   + d+++P  v+n+ + + +    +s+t+Pdd+dL     +Y   nG   + ++ v  +s  v+G++ + +y++++y v++ 
  gi|91772937|ref|YP_565629.1| 761 TPDTTQPLDVSNLDYSAGERWINLSWTNPDDPDLSHSD-VYV--NG---SFRSNVTGNSHLVSGLDPSTNYSFNVYPVDVF 835
                                   56899************9999*************9755.677..45...678889999******************99987 PP

                       DUF4959  94 ene 96 
                                   +n 
  gi|91772937|ref|YP_565629.1| 836 NNT 838
                                   664 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 6.3e-05
                       DUF4959  13 etdkaaPgkvtnvkvknlpGgavisytlPddedLlyvkaeYklknGkerevkaSvykdsltveGFgdtkeyevklyavsrs 93 
                                   + d+++P  v+++++++ +  + + +t+Pdd+dL     +Y   nG   +  + v ++   ++G++ + +y+v++y+v+  
  gi|91772937|ref|YP_565629.1| 850 TFDTTPPLDVSDLSFTAGERWVNLIWTNPDDPDLSHAD-VYI--NG---SFLSNVTDNFYLISGLDPSASYSVNVYSVDDF 924
                                   568999****************************9866.577..45...46666777779******************976 PP

                       DUF4959  94 ene 96 
                                   +n+
  gi|91772937|ref|YP_565629.1| 925 NNA 927
                                   664 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.035
                       DUF4959  13 etdkaaPgkvtnvkvknlpGgavisytlPddedLlyvk 50 
                                   + d ++P +vtn++ ++      +s+ +P+d dL  + 
  gi|91772937|ref|YP_565629.1| 939 TPDITSPFSVTNLSAEAGDHWINLSWINPNDIDLSSID 976
                                   56789999*********9999*************9875 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.011
                       DUF4959   12 ietdkaaPgkvtnvkvknlpGgavisytlPddedLlyvkaeYklknGkerevkaSvykdsltveGFgdtkeyevklyav 90  
                                     + d+++Pg+v+ ++  + +   + s+ +P+d d   v+   +         ++S    s  v G+++++ y+++ ++v
  gi|91772937|ref|YP_565629.1| 1027 TTVDNTPPGSVSSLSSSSSESSITWSWLNPSDVDNSHVELYLN------AIFQSSSNGTSYSVVGLNSSSVYNLSTRTV 1099
                                    57899*****************************999986444......468889999999999999999999999999 PP

                       DUF4959   91 srsene 96  
                                    ++s+n 
  gi|91772937|ref|YP_565629.1| 1100 DTSGNV 1105
                                    998764 PP

>> DUF2846  Protein of unknown function (DUF2846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00089       3.2      14      57 ..     698     742 ..     692     763 .. 0.80
   2 ?    1.4   0.0     0.088   3.2e+02      21      50 ..     794     823 ..     785     840 .. 0.86
   3 !    7.1   0.0    0.0015       5.5      22      61 ..     884     926 ..     875     959 .. 0.78
   4 !   12.0   0.1   4.6e-05      0.16      21      57 ..     972    1009 ..     960    1029 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00089
                       DUF2846  14 sqwlkeeaeapdvfvngkkigelankeYfvaevepGe.ykister 57 
                                    ++  + +   +v++ng+   ++  ++++++++ p++ y +st+ 
  gi|91772937|ref|YP_565629.1| 698 DNPSEGDFSHTEVYLNGSFQENIFVNSFTALDLIPNTtYVLSTRT 742
                                   56778889999*************************966677776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.088
                       DUF2846  21 aeapdvfvngkkigelankeYfvaevepGe 50 
                                   +   dv+vng+   ++  ++ +v  ++p +
  gi|91772937|ref|YP_565629.1| 794 LSHSDVYVNGSFRSNVTGNSHLVSGLDPST 823
                                   56789*****************99999976 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0015
                       DUF2846  22 eapdvfvngkkigelankeYfvaevepGe.ykister..efes 61 
                                     +dv++ng+ + ++ ++ Y+   ++p   y++ + +   f +
  gi|91772937|ref|YP_565629.1| 884 SHADVYINGSFLSNVTDNFYLISGLDPSAsYSVNVYSvdDFNN 926
                                   6789***********************8768888887665555 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 4.6e-05
                       DUF2846   21 aeapdvfvngkkigelankeYfvaevepGe.ykister 57  
                                    + + dv+vn++ +g+++ + +fv +++++  y++st  
  gi|91772937|ref|YP_565629.1|  972 LSSIDVYVNNSLLGNTSGNFFFVNYLDANAsYNLSTHT 1009
                                    56779**********************98768888876 PP

>> DUF2369  Uncharacterised conserved protein (DUF2369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.67   2.4e+03       8      45 ..     724     761 ..     722     773 .. 0.78
   2 !   12.9   0.1     3e-05      0.11       7      35 ..     812     840 ..     808     864 .. 0.79
   3 !   13.6   0.0   1.8e-05     0.066       6      41 ..     900     938 ..     897     962 .. 0.84
   4 ?   -2.2   0.2       1.6   5.6e+03       9      41 ..     992    1026 ..     986    1043 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.67
                       DUF2369   8 kvtlseLkpdtqYyfdVFvvdqkrntssaytgttaqtr 45 
                                   ++t  +L p+t+Y ++   vd  +n    + ++ ++t 
  gi|91772937|ref|YP_565629.1| 724 SFTALDLIPNTTYVLSTRTVDIYNNINLSWSNSSINTT 761
                                   67778999*******99999999997777777766664 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3e-05
                       DUF2369   7 tkvtlseLkpdtqYyfdVFvvdqkrntss 35 
                                   +++++s+L+p+t+Y f+V+ vd  +nt +
  gi|91772937|ref|YP_565629.1| 812 NSHLVSGLDPSTNYSFNVYPVDVFNNTNT 840
                                   899*******************9888544 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.8e-05
                       DUF2369   6 ktkvtlseLkpdtqYyfdVFvvdqkrn...tssaytgtt 41 
                                    + +++s+L+p+ +Y ++V+ vd  +n   +ssa+  +t
  gi|91772937|ref|YP_565629.1| 900 DNFYLISGLDPSASYSVNVYSVDDFNNantSSSAFLANT 938
                                   5789*******************9999888888888777 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.6
                       DUF2369    9 vtlseLkpdtqYyfdVFvvdqkrn..tssaytgtt 41  
                                    + ++ L+ + +Y ++   vd++ n  ++ +y+ + 
  gi|91772937|ref|YP_565629.1|  992 FFVNYLDANASYNLSTHTVDTTGNtnSTGVYVIMN 1026
                                    56788999999999999999976632455665444 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.4      0.11   3.8e+02       3      72 ..     681     739 ..     676     748 .. 0.61
   2 ?   13.9   0.5   1.4e-05      0.05       9      74 ..     776     830 ..     766     837 .. 0.75
   3 ?    9.7   0.2    0.0003       1.1      51      77 ..     895     922 ..     858     928 .. 0.78
   4 ?    1.7   0.2     0.094   3.4e+02       3      35 ..     948     977 ..     947    1018 .. 0.72
   5 ?    0.0   5.5       0.3   1.1e+03       7      80 ..    1038    1103 ..    1032    1108 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                                   ECEEEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEE CS
                           fn3   3 PsnlsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevr 72 
                                   +snl+++  +++ +t +W+ p+  +g++++ ev +        + + ++  ++  +t  +L p+t+Y+++
  gi|91772937|ref|YP_565629.1| 681 VSNLNATV-GERWITWTWDNPS--EGDFSHTEVYLNG------SFQENIFVNS--FTALDLIPNTTYVLS 739
                                   34444444.8888888888885..8888887774322......2344455454..666667777777665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.4e-05
                                   EEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEE CS
                           fn3   9 sevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVq 74 
                                   s+ +++ +++sW+ p   ++p+ + +    ++  ++ + + +v++++  + ++gL p+t+Y+++V+
  gi|91772937|ref|YP_565629.1| 776 SA-GERWINLSWTNP---DDPDLSHS----DVYVNG-SFRSNVTGNS--HLVSGLDPSTNYSFNVY 830
                                   44.788888888888...56655444....444444.7888999999..****************8 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0003
                                   ECSTSS.EEEEESSSTTEEEEEEEEEEE CS
                           fn3  51 vprttt.svtltgLkpgteYevrVqavn 77 
                                   +++ t+  + ++gL p++ Y+v+V++v 
  gi|91772937|ref|YP_565629.1| 895 LSNVTDnFYLISGLDPSASYSVNVYSVD 922
                                   66666669*****************996 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.094
                                   ECEEEEEEESSSEEEEEEE-CSSSSSTEEEEEE CS
                           fn3   3 PsnlsvsevtstsltvsWeppkdgggpitgYev 35 
                                   ++nls+++ +++ +++sW  p+  + ++++  v
  gi|91772937|ref|YP_565629.1| 948 VTNLSAEA-GDHWINLSWINPN--DIDLSSIDV 977
                                   67888888.9999999999996..444444444 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.3
                                    EEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSE CS
                           fn3    7 svsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavnggg 80  
                                    s  + +s++ +++W++ +   +++++ +ve+         + ++ ++ t s+ + gL+ ++ Y+++ ++v + g
  gi|91772937|ref|YP_565629.1| 1038 SSLSSSSSESSITWSWLN--PSDVDNSHVELYLN-----AIFQSSSNGT-SYSVVGLNSSSVYNLSTRTVDTSG 1103
                                    444444444444444442..45555555555444.....2333444444.788889988888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.32s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 8038.48
//
Query:       gi|91772938|ref|YP_565630.1|  [L=381]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-19   68.6   0.0    1.1e-18   68.1   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    2.5e-07   31.1   0.1    5.3e-07   30.1   0.1    1.6  1  SPASM        Iron-sulfur cluster-binding domain
    7.8e-05   22.8   0.0    0.00014   22.0   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
    0.00019   21.7   0.0    0.00031   21.0   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 !   68.1   0.0   2.6e-22   1.1e-18       1     165 [.      98     252 ..      98     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.6e-22
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   +++t+ C+++C +Ca p     ++  ++l+ve +++ ++++  + g  ++++ ggepl y+ ++el+e   +       + 
  gi|91772938|ref|YP_565630.1|  98 ISITEECPNKCLHCALPD----TKNKATLPVETVKNVIDQV-LDLGSTFIVFDGGEPLTYDGLEELIEYVDRD---RALTG 170
                                   67999************5....8******************.8****************99887777777776...9**** PP

                                   EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeele 161
                                   + t+g+ ++ ek+  l+e+g+d +s++l++a++   ++ m+ r + f   +e++++  ++g+   v+++v++   n +el+
  gi|91772938|ref|YP_565630.1| 171 MFTSGVGLTLEKAMSLKEAGLDMISVSLDSANEA-GHDSMRgRLGVFNSAIEGIKNSLKSGLL--VNMYVVISPDNIDELD 248
                                   **********************************.999999999****************999..9*************** PP

                                   HHHH CS
                                   xxxx RF
                   Radical_SAM 162 elle 165
                                   +++ 
  gi|91772938|ref|YP_565630.1| 249 DFYT 252
                                   9986 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   1.2e-10   5.3e-07       1      46 [.     316     355 ..     316     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.2e-10
                         SPASM   1 CfapsrslfInsdGdVvpC.cvdkktyveelklGnireesleeIwns 46 
                                   Cfa+++ l I+++Gd++pC c+       +l++Gni +++++++w++
  gi|91772938|ref|YP_565630.1| 316 CFAGRKWLHITPEGDIFPCaCL-------PLSFGNIDQNKIADVWRK 355
                                   9******************444.......5***************75 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.2e-08   0.00014       5      73 ..     101     164 ..      98     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-08
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgk.pqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkr 73 
                                   +  C+ +C  C   +t+++   + + ++++++q+l      +    ++v+ GGePL y   +el++ v+r
  gi|91772938|ref|YP_565630.1| 101 TEECPNKCLHCALPDTKNKATLPvETVKNVIDQVL------DLGSTFIVFDGGEPLTYDGLEELIEYVDR 164
                                   578*********77766665554055566666666......4445789**********888888888776 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      13     116 ..     102     199 ..      93     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7e-08
                       Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp.ekdiwlyt 92 
                                   + C+ +C  C    + + k++   + e+ +++i+++ +   + +++ GGEPl    ++ l el+++v +    ++  ++  
  gi|91772938|ref|YP_565630.1| 102 EECPNKCLHCA---LPDTKNKATLPVETVKNVIDQVLDLGSTFIVFDGGEPLT---YDGLEELIEYVDRDRAlTGMFTSGV 176
                                   67888888877...55556677788899999999999999*************...8888888888888777455555556 PP

                       Fer4_12  93 gytleelskkekeellkeidvlvd 116
                                   g tle+ ++  ke  l++i v +d
  gi|91772938|ref|YP_565630.1| 177 GLTLEKAMS-LKEAGLDMISVSLD 199
                                   677777765.35555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 2451.68
//
Query:       gi|91772939|ref|YP_565631.1|  [L=385]
Description: FAD dependent oxidoreductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   43.2   0.2    9.4e-06   25.1   0.1    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.8e-11   42.0   0.4    8.7e-08   31.3   0.1    2.2  2  HI0933_like     HI0933-like protein
    6.9e-10   38.5   0.0    3.3e-09   36.3   0.0    1.8  1  Lycopene_cycl   Lycopene cyclase protein
    1.9e-09   37.3   0.1    4.6e-06   26.1   0.1    2.3  2  FAD_binding_3   FAD binding domain
    6.8e-08   32.1   0.0    2.5e-07   30.2   0.0    1.9  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.8e-07   30.5   0.1     0.0016   18.1   0.0    2.5  3  DAO             FAD dependent oxidoreductase
    5.2e-07   29.4   0.0    8.4e-07   28.7   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    3.2e-05   23.2   0.0    6.9e-05   22.1   0.0    1.5  1  FAD_binding_2   FAD binding domain
    3.7e-05   23.1   0.0    7.2e-05   22.1   0.0    1.5  1  Thi4            Thi4 family
    7.1e-05   23.0   0.0    0.00021   21.4   0.0    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0002   20.6   0.0    0.00033   19.8   0.0    1.4  1  GIDA            Glucose inhibited division protein A
    0.00079   18.4   0.2       0.25   10.2   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
     0.0097   15.2   0.2       0.02   14.2   0.2    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.56   10.8   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 !   25.1   0.1   7.4e-09   9.4e-06       2      44 ..       4      45 ..       3      72 .. 0.82
   2 !   15.9   0.0   4.4e-06    0.0056     184     240 ..      94     149 ..      62     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.4e-09
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllsk 44
                                  dv+viG+ pAGl aa++++++g+kv+l+ +++++ ++   +++
  gi|91772939|ref|YP_565631.1|  4 DVIVIGASPAGLMAARNASRKGVKVLLL-DKKEIIGHPTHPAN 45
                                  8***************************.77777666555554 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.4e-06
                                   HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrps 240
                                   ++ ++++++ +++Gve+++g  v++i +n++ +++ ++dg ++ +++v+v+ G+  +
  gi|91772939|ref|YP_565631.1|  94 KFDEFYAKQTQDSGVEMRMGVDVHNILRNSNGMSLSTDDG-VLTCKMVIVSDGINSK 149
                                   5899**************************9777666665.59*********98766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   6.8e-11   8.7e-08       2      36 ..       4      38 ..       3      40 .. 0.95
   2 !    8.7   0.0   0.00049      0.62     115     166 ..      99     148 ..      96     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.8e-11
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  dviviG+ +AGlmaA +a+++g +Vlll+k++ +g
  gi|91772939|ref|YP_565631.1|  4 DVIVIGASPAGLMAARNASRKGVKVLLLDKKEIIG 38
                                  8*****************************99887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00049
                                   HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                   HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                   + k+ +++gv++r+  +v+++ ++++g ++++t +++ l+++ ++++ G +S
  gi|91772939|ref|YP_565631.1|  99 YAKQTQDSGVEMRMGVDVHNILRNSNG-MSLST-DDGVLTCKMVIVSDGINS 148
                                   5678999**************999999.9****.9***********988665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   2.5e-12   3.3e-09       1     347 [.       4     349 ..       4     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.5e-12
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtivylddgkkil 76 
                                   Dv+viGa pAgl  A +   +++g+kv+l++  + + +p      +++   ++      ++ v +  +g+ + ++ g ++ 
  gi|91772939|ref|YP_565631.1|   4 DVIVIGASPAGLMAARNA--SRKGVKVLLLDKKEIIGHPTHPANTFFKGMFDRagetvDQSYVLKNMNGAYLIAPSGGRVA 82 
                                   9**********9877777..**********998866444433444444444442224445566666788899999****** PP

                 Lycopene_cycl  77 lgraYgrvsskrlkeellerlvengvkllea.kvesveeeeageslvvleggrkirarlvvdarglaslk......karrl 150
                                   ++ +   + + ++ e  +++  ++gv+++ +  v+++  +++g s     ++  + +++v+++ g+ s+       ++++ 
  gi|91772939|ref|YP_565631.1|  83 IEAPAYFLDRLKFDEFYAKQTQDSGVEMRMGvDVHNILRNSNGMS--LSTDDGVLTCKMVIVSDGINSKLagllglQPMKY 161
                                   **88889***************999987765389***99999433..4455568***********7776699999989999 PP

                 Lycopene_cycl 151 glQtfyGvevevdnppfdldkmvlMDfrveqklkgltFlYalPldsdrllvEeTelaskpeLpadalkkrlaaylra.lgl 230
                                   +  ++  +e+ v+++  +++++++  + v ++  g +  Y  P ++d + +    +++++      +  r + + ++ +g+
  gi|91772939|ref|YP_565631.1| 162 SNDIAWAMEAFVEAD--GIGEPDMFEYYVGNHCPGWKSTYS-PCGKDLATL--GVYVRRNGKDVTSFFDRWVDKFKKiKGI 237
                                   999999999999999..***************99******8.*****9988..5899999889999999999999988*** PP

                 Lycopene_cycl 231 kvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsarawatlwpr 310
                                     + + e   g  P+     +++++   v+ +G+aag      GYs+ + +   ++ a+aia+    s    ++ +++w  
  gi|91772939|ref|YP_565631.1| 238 DDLVIHERAVGGDPI--VTMPKQMHTDgVMLVGGAAGQ--SGIGYSMHAGQMCGDVAADAIAKGDV-SAKVLSEYRSKWNT 313
                                   ***************..55666666656********96..689*******************9888.46667777777777 PP

                 Lycopene_cycl 311 erkrqreffrllglalllkldiegrrrfldaFfrlpk 347
                                   e + +  +   +gl++l+k++  ++ r++++F + + 
  gi|91772939|ref|YP_565631.1| 314 EYRAEYILG-RIGLETLRKMEDREIDRLMKTFEDEDF 349
                                   776665555.68999*****************87655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   3.6e-09   4.6e-06       2      33 ..       3      34 ..       2      39 .. 0.95
   2 !    9.1   0.0   0.00055      0.71     113     194 ..     101     175 ..      90     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.6e-09
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                  +dV+++Ga+paGlm+a+  s++Gv+v+l++k 
  gi|91772939|ref|YP_565631.1|  3 ADVIVIGASPAGLMAARNASRKGVKVLLLDKK 34
                                  79****************************97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00055
                                   HHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEEEEEEEEE CS
                 FAD_binding_3 113 ehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgie.fegeetvyeagvldvlf 192
                                   ++ +  g+++r++ +v++++++ +g +    d        +++k ++  DG +S+ +  lg++ ++ ++++  a  +++ +
  gi|91772939|ref|YP_565631.1| 101 KQTQDSGVEMRMGVDVHNILRNSNGMSLSTDDG------VLTCKMVIVSDGINSKLAGLLGLQpMKYSNDI--AWAMEAFV 173
                                   566788999999999999999999965444433......48**********************88888777..55555555 PP

                                   EC CS
                 FAD_binding_3 193 da 194
                                   +a
  gi|91772939|ref|YP_565631.1| 174 EA 175
                                   55 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 !   30.2   0.0     2e-10   2.5e-07       1     134 [.       6     146 ..       6     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2e-10
                   Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtfispsftsekleipdlnaiseets...........pa 70 
                                   i+iGa PaGl aa ++ ++g+ ++l l+k++i    ++ p  +tf+   f   + e+ d   + ++ +            a
  gi|91772939|ref|YP_565631.1|   6 IVIGASPAGLMAARNASRKGV-KVLLLDKKEIIGHPTH-P-ANTFFKGMFDRAG-ETVDQSYVLKNMNgayliapsggrVA 82 
                                   89*******************.7*******88654443.3.3456665554443.44444455544443445554443334 PP

                   Pyr_redox_3  71 fslkeeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                   +      l r ++ e++++ ++   ++ ++  +V ++ ++++g +++t+ +++++k vi++ G 
  gi|91772939|ref|YP_565631.1|  83 IEAPAYFLDRLKFDEFYAKQTQDSGVEMRMGVDVHNILRNSNGMSLSTDDGVLTCKMVIVSDGI 146
                                   455566899999*************************************************997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.3e-06    0.0016       1      36 [.       4      41 ..       4      61 .. 0.89
   2 !    9.8   0.0   0.00042      0.54     141     210 ..      88     154 ..      54     166 .. 0.78
   3 ?   -3.6   0.1         5   6.3e+03     314     347 ..     248     284 ..     231     288 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                  dv++iG+  +Gl +A+ ++r+g  V+ll+k++i+g+ +
  gi|91772939|ref|YP_565631.1|  4 DVIVIGASPAGLMAARNASRKGvkVLLLDKKEIIGHPT 41
                                  8******************************9999443 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00042
                                   EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTT CS
                           DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgll 210
                                     +d  k+  ++a++ ++ Gve++ g  v ++ + +  ++ +   t+ g  + ++ v+++ G+ s+l+gll
  gi|91772939|ref|YP_565631.1|  88 YFLDRLKFDEFYAKQTQDSGVEMRMGVDVHNILR-NSNGMSL--STDdGVLT-CKMVIVSDGINSKLAGLL 154
                                   4568889999*********************844.3346788..67769754.488********9876333 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5
                                   TSSEEEEEEE...TEEEEEEEEEC.TTTHHHHHHHHHH CS
                           DAO 314 dglpligetp...gvkglylatGh.sghGltlapatGk 347
                                    g+p++   p   +++g+ l+ G+ + +G+  ++ +G+
  gi|91772939|ref|YP_565631.1| 248 GGDPIVTM-PkqmHTDGVMLVGGAaGQSGIGYSMHAGQ 284
                                   45666655.35666778888888766677777776666 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   6.6e-10   8.4e-07       1      35 [.       4      38 ..       4      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.6e-10
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                  Dv+V+G+ paG++AA  A r+G kvlL+++++ +G
  gi|91772939|ref|YP_565631.1|  4 DVIVIGASPAGLMAARNASRKGVKVLLLDKKEIIG 38
                                  9******************************9998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.4e-08   6.9e-05       1      39 [.       4      42 ..       4      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.4e-08
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                  DviViG+  AGL+AA +a+++G kv++++k++  g  t+
  gi|91772939|ref|YP_565631.1|  4 DVIVIGASPAGLMAARNASRKGVKVLLLDKKEIIGHPTH 42
                                  9*****************************997776555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.6e-08   7.2e-05      17      57 ..       2      41 ..       1      70 [. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.6e-08
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                  ++Dv+++Ga ++GL aa+  ++k ++kv++l+++  +G  +
  gi|91772939|ref|YP_565631.1|  2 DADVIVIGASPAGLMAARNASRK-GVKVLLLDKKEIIGHPT 41
                                  79*********************.********998777655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.7e-07   0.00021       1      32 [.       7      38 ..       7      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  ++Ga  +Gl aA+ ++++g++vlll+k + +G
  gi|91772939|ref|YP_565631.1|  7 VIGASPAGLMAARNASRKGVKVLLLDKKEIIG 38
                                  8***************************9998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.6e-07   0.00033       1      29 [.       4      37 ..       4      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.6e-07
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE.....E CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.....t 29
                                  dviViG+  AG+ AA +a+r+G+kvlL+      
  gi|91772939|ref|YP_565631.1|  4 DVIVIGASPAGLMAARNASRKGVKVLLLdkkeiI 37
                                  8**************************9544440 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0026       3.3       1      36 [.       4      36 ..       4      44 .. 0.91
   2 !   10.2   0.0   0.00019      0.25     136     214 ..      75     151 ..      43     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0026
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseei 36
                                  +++++G+ +aG +aA   ++ +   ++v+l++++ei
  gi|91772939|ref|YP_565631.1|  4 DVIVIGASPAGLMAARNASRKG---VKVLLLDKKEI 36
                                  699*************999999...99*****9998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                                   SB-TTS-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGGG-III CS
                Trp_halogenase 136 prekdglsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqlde.dgrveslrledgreveadlfiDcsGfrglli 214
                                    ++   ++  + Ay ld+ ++++f  +  ++ Gv+++ g  v+  l++ +g   sl ++dg  +   ++i   G +++l 
  gi|91772939|ref|YP_565631.1|  75 APSGGRVAIEAPAYFLDRLKFDEFYAKQTQDSGVEMRMGVDVHNILRNsNG--MSLSTDDGV-LTCKMVIVSDGINSKLA 151
                                   455555566678***************************888777777355..378887765.88888888888777775 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   1.6e-05      0.02      29      60 ..       3      34 ..       1      39 [. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                  -EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                   AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                  a v+viG+  aGl A+++a++ g kV +lD++
  gi|91772939|ref|YP_565631.1|  3 ADVIVIGASPAGLMAARNASRKGVKVLLLDKK 34
                                  89****************************86 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.56       2      35 ..       5      38 ..       4      53 .. 0.91
   2 ?    2.1   0.0      0.23   2.9e+02      44      72 ..      97     125 ..      89     133 .. 0.82
   3 ?   -2.1   0.0       4.5   5.7e+03      33      46 ..     328     341 ..     301     355 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  v+v+G++  gl++A ++++ g kV +++ ++ + 
  gi|91772939|ref|YP_565631.1|  5 VIVIGASPAGLMAARNASRKGVKVLLLDKKEIIG 38
                                  89***********************999887665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                                   HHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                     Pyr_redox  44 kilqeklekngievllntkveeiegsedg 72 
                                   +  +++ ++ g+e++++  v +i  +++g
  gi|91772939|ref|YP_565631.1|  97 EFYAKQTQDSGVEMRMGVDVHNILRNSNG 125
                                   5677899999*************999988 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.5
                                   SSSTTSSHHHHHHH CS
                     Pyr_redox  33 kllrllDeeaskil 46 
                                   +l++++D+e+ +++
  gi|91772939|ref|YP_565631.1| 328 TLRKMEDREIDRLM 341
                                   34455566655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 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:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2208.24
//
Query:       gi|91772940|ref|YP_565632.1|  [L=313]
Description: UbiA prenyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  140.2  17.9    8.2e-41  140.0  17.9    1.0  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 !  140.0  17.9   4.6e-45   8.2e-41       4     246 ..      32     281 ..      30     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 4.6e-45
                          UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllll 84 
                                   +al++  la+   p+l  ++++++g+++a+++++++Nd  D++iD++  + p+RPl+s  +s+k++l+++++l++++++ +
  gi|91772940|ref|YP_565632.1|  32 SALLASYLATSALPPLIPFIIAVIGGYAAITSSYVYNDCCDVDIDKI--NLPDRPLASETLSRKNGLTYSLILFFVAAVAA 110
                                   67888888889999999******************************..******************************** PP

                          UbiA  85 alllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl..........sllalllalavfll 155
                                    ++lnp +++++++a++   +Y+ ++ Kr+t+l  + +gia+gl+p++ w a+              +l+a+++++++ + 
  gi|91772940|ref|YP_565632.1| 111 -FYLNPESLFILVIAVVTISIYS-MFAKRMTFLSFIPVGIAYGLVPVGIWLAFDPAGilrgndgvilPLPAIFFFIMMCVA 189
                                   .**********************.5***************************76666779999****99999999999999 PP

                          UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraarlvr 235
                                    w++ l   +rd+egDr+ g +t+pv++G   +  + la++++++l+++++  +a l+++++  a+l+++++l +a+++v+
  gi|91772940|ref|YP_565632.1| 190 DWGFTLSGVCRDVEGDRAKGAPTFPVTFGVPLTSKFiLACWVIGILASMAIGITAKLGPVFFTGAILSGIWMLSKALYFVK 270
                                   99999999********************99999997777777777777899999*************************** PP

                          UbiA 236 rrdakkaakff 246
                                   +  ++++ k+f
  gi|91772940|ref|YP_565632.1| 271 NPLPERGGKLF 281
                                   99999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1910.41
//
Query:       gi|91772941|ref|YP_565633.1|  [L=483]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-85  286.6   0.0    3.8e-85  286.1   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 !  286.1   0.0   2.1e-89   3.8e-85       3     349 ..      14     335 ..      11     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 286.1 bits;  conditional E-value: 2.1e-89
                                   EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE-S CS
                           TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltdsg 83 
                                   +R+Gkl++phgt+etP++mpv  +++++ ++p e++ ++gaq++++n+y++  r + +  a   glh++l++d+pi+tdsg
  gi|91772941|ref|YP_565633.1|  14 GRIGKLRTPHGTVETPTVMPV-INPNLQVIKPSEMR-DFGAQMLITNSYIISRRDKLREKALKDGLHSLLDFDGPIMTDSG 92 
                                   8********************.999**********5.99*****************99999999***************** PP

                                   HHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH.. CS
                           TGT  84 gfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah.. 162
                                   +fq   l           s + G+ +++t+e++ie+q+++gsD+ ++ld ++p++  ++r+e ++e+T+++l ++      
  gi|91772941|ref|YP_565633.1|  93 SFQ---L-----------SVY-GD-IEVTNEQIIEFQKTIGSDVGVPLDIPTPPDVPRSRAESEMETTIERLIEARSMVnd 157
                                   ***...3...........336.**.***********************************************999976688 PP

                                   SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHH CS
                           TGT 163 qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylmGvgtPedlleav 239
                                   ++ l g+vqG++y+dlre++a  +++ +fd+y++g+ ++++e  +++el++v+ ++++ l+   p++l+G+g+P++++ av
  gi|91772941|ref|YP_565633.1| 158 EMlLAGPVQGSTYTDLREKCASTISEHKFDVYPLGAvVPLMEsyRYAELVDVIVSSKKGLDPTVPVHLFGAGHPMMFALAV 238
                                   666*********************************888***8999*********************************** PP

                                   HTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           TGT 240 alGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhy 320
                                   alG+D+fd+++++++a++ r++ts+g++++ n +y     p    CsC++C ++t +++++  ++       Ll+ HNl++
  gi|91772941|ref|YP_565633.1| 239 ALGCDLFDSAAYALYAKDRRYITSKGTYHIDNLSYL----P----CSCPICVSHTAEEVKKADNCSD-----LLARHNLYV 306
                                   *******************************99999....9....******99*******9999888.....********* PP

                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                           TGT 321 ylelfkriReaIkegtfeefveefarkye 349
                                   ++e+++ i+++Ikeg++ e+ve ++r+++
  gi|91772941|ref|YP_565633.1| 307 TFEEIRLIKQSIKEGNLLELVEMRCRSHP 335
                                   *************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2841.80
//
Query:       gi|91772942|ref|YP_565634.1|  [L=126]
Description: hypothetical protein Mbur_0942 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-32  112.0   0.8    1.8e-32  111.6   0.8    1.2  1  DGC       DGC domain
  ------ inclusion threshold ------
      0.043   12.8   0.1      0.053   12.5   0.1    1.0  1  PDH       Prephenate dehydrogenase


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 !  111.6   0.8     2e-36   1.8e-32       2     104 ..      16     118 ..      15     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 2e-36
                           DGC   2 vvsCsGasnvGqlaneaavklakegeakmiclagvgagveelvelaksarkiiaidGCpleCakkilekagvkpdehlvvt 82 
                                   ++sCsGasnvGql+n+++++l++++ +km+c  g+g++v++l+++a+  ++ii+idGCpleC+kk le  ++++d+h+++t
  gi|91772942|ref|YP_565634.1|  16 LFSCSGASNVGQLSNQVVIELNDREVGKMMCAVGIGGKVSGLIRSAEGCDRIIVIDGCPLECTKKSLELSNINIDRHIILT 96 
                                   79**********************99******************************************************* PP

                           DGC  83 dlgikkeekldlseeeiekvve 104
                                   dlgi k+++l++se ++ +++e
  gi|91772942|ref|YP_565634.1|  97 DLGIAKNKSLKVSESDVSEAFE 118
                                   *****************99887 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.9e-06     0.053      11     100 ..      31     120 ..      23     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-06
                                   -SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE..-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHH CS
                           PDH  11 kvtvigydideekaeaalelglvdeatddieavkeadivvl..avPvevilevlkelaphlkedalitDvgsvKekvvrel 89 
                                   +v + + d++ +k+  a  +g++ ++   i+ ++ +d +++    P e +++ l+     + ++ ++tD+g +K+k  +  
  gi|91772942|ref|YP_565634.1|  31 QVVIELNDREVGKMMCA--VGIGGKVSGLIRSAEGCDRIIVidGCPLECTKKSLELSNINIDRHIILTDLGIAKNKSLKVS 109
                                   56677788888887777..889999999999*****966663479**********9999*****************99999 PP

                                   HHHCC..GCEE CS
                           PDH  90 eellkegksfv 100
                                   e  ++e  ++v
  gi|91772942|ref|YP_565634.1| 110 ESDVSEAFEIV 120
                                   99888877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 780.50
//
Query:       gi|91772943|ref|YP_565635.1|  [L=77]
Description: redox-active disulfide protein 2 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-28   98.4   1.1    1.9e-28   98.3   1.1    1.0  1  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.023   15.1   0.0    1.2  1  ArsD           Arsenical resistance operon trans-acting repre
       0.11   12.8   0.2       0.23   11.7   0.2    1.7  1  Glutaredoxin   Glutaredoxin
       0.11   12.6   0.3       0.25   11.5   0.3    1.6  1  Thioredoxin_4  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 !   98.3   1.1   4.2e-32   1.9e-28       1      75 [.       1      75 [.       1      76 [. 0.99

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 4.2e-32
                                  EEEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                 Thioredoxin_3  1 meikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                  m+i++lg+gCakC+kl+++v+++++e+ i+ae++kv+d+++i +ygVm +P+lvidg v+++Gk+pse+++r++l
  gi|91772943|ref|YP_565635.1|  1 MKIEILGSGCAKCNKLKELVEKVVNENSINAEITKVEDINKILEYGVMITPGLVIDGDVKIAGKIPSEDKVREWL 75
                                  89************************************************************************9 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   5.1e-06     0.023      53      99 ..      31      76 ..      10      77 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.1e-06
                          ArsD 53 qaFvenkavkellekkgaeaLPlvlvdgeivktgrYptreelaewlg 99
                                  ++ ++ + ++++le  g+ + P +++dg++  +g+ p+++++ ewl+
  gi|91772943|ref|YP_565635.1| 31 AEITKVEDINKILE-YGVMITPGLVIDGDVKIAGKIPSEDKVREWLT 76
                                  56677889999998.8****************************985 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   5.2e-05      0.23       7      59 ..       8      59 ..       1      60 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                                  TSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHHTSSSSSEEEETTEE CS
                  Glutaredoxin  7 ptCpyCkkakrlLkelgvkfeeidvdkde.eireelkelsgvrtvPqvfidgkh 59
                                  ++C  C+k k+l ++  v+   i+ +  + e   ++ e+ gv+  P ++idg++
  gi|91772943|ref|YP_565635.1|  8 SGCAKCNKLKELVEKV-VNENSINAEITKvEDINKILEY-GVMITPGLVIDGDV 59
                                  79***********666.3333333333322334555566.99999999999986 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   5.5e-05      0.25     110     159 ..      17      69 ..       8      77 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                                   HHHHTS-------HHHH..HHHHHHHHHHT--SS-EEEETTEE.E-TT--HHH CS
                 Thioredoxin_4 110 dekfeacleeekldalv..eaeskeakkagiestPtfiingek.veepqtyee 159
                                   +e +e+ ++e ++ a++  +++ ++  + g+  tP ++i+g + ++++++ e+
  gi|91772943|ref|YP_565635.1|  17 KELVEKVVNENSINAEItkVEDINKILEYGVMITPGLVIDGDVkIAGKIPSED 69 
                                   44477888999999999333455666788**********99886666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      777  (0.0433376); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 487.65
//
Query:       gi|91772944|ref|YP_565636.1|  [L=347]
Description: transporter [Methanococcoides burtonii DSM 6242]
Scores for 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-85  284.7  25.6    8.8e-85  284.4  25.6    1.0  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 !  284.4  25.6   4.9e-89   8.8e-85       5     293 ..      14     343 ..      12     344 .. 0.94

  Alignments for each domain:
  == domain 1  score: 284.4 bits;  conditional E-value: 4.9e-89
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1   5 altlfasilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkGaplg 84 
                                   ++++  +++l++ll+L+++f+++gai++ +++e + +++g +++ ++s++vaa++G ll+vCsc+++Pl+++++k+Ga++g
  gi|91772944|ref|YP_565636.1|  14 VQSVQNYLALHVLLCLIPAFFLAGAIASLFSKESVLKYFGsDAPGYVSYTVAAVSGCLLAVCSCTVLPLFAGIYKRGAGIG 94 
                                   788999*************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                        ArsP_1  85 aavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek........... 154
                                   +a +Fl++aPaini+ai++t+ +lg++l++ar+v+a++++iv+g+++  +f+++++e ++  +   g  +           
  gi|91772944|ref|YP_565636.1|  95 PASTFLFSAPAINILAIVYTAKILGYDLGAARAVIAILLSIVVGISMAFIFERKQQEIKKGIKTF-GDDEhkksaylfill 174
                                   ****************************************************9998876653322.222235689****** PP

                                   ......................xxxxxxxxxxxxxxxxxxxxx.xxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1 155 ......................ltlkpklealkafaknevkew.lelg.......kyLiiGvaiagviqaflpesvllsll 205
                                                         l l+++  + k+f+k+e+kew +e++       ++L++Gv++ag+i ++lp++++++++
  gi|91772944|ref|YP_565636.1| 175 lailitpeiisngrflgvimfaLILITAHFSNKWFTKEELKEWmGETWflikqitPLLLVGVFFAGIIVEILPKEYVVEFV 255
                                   ********************995555555567************************************************* PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1 206 ggnsvsssllamligvvlyvcslgevpfiaalfesglalGsalAfLlagpllslpellillkvlkkklvavllglvvvsvv 286
                                   ggn++ss+++a++ ++++y+ +l+evp+i+al  +g+++G+ lA Llagp+lslp++++++ ++++k+++v++ l+v++++
  gi|91772944|ref|YP_565636.1| 256 GGNTLSSNFIAAISAALMYFSTLTEVPIISALTILGMGKGPSLAMLLAGPALSLPNMIVISRIMGAKKASVYISLIVIIST 336
                                   ********************************************************************************* PP

                                   xxxxxxx RF
                        ArsP_1 287 laglvin 293
                                   + g  ++
  gi|91772944|ref|YP_565636.1| 337 ISGFAYG 343
                                   ***9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2489.17
//
Query:       gi|91772945|ref|YP_565637.1|  [L=373]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.035   14.1   0.0    1.9  1  DUF772    Transposase domain (DUF772)
      0.074   12.6   0.1       0.14   11.6   0.1    1.5  1  DUF4283   Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.9e-06     0.035       5      70 ..      62     130 ..      61     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                        DUF772   5 yppelmlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70 
                                   y +  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f k rl++  l++++
  gi|91772945|ref|YP_565637.1|  62 YKVSSMIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVKyRLGKtgLDEVM 130
                                   67889*************9999998772566667777664433.89*****************9977776 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.6e-05      0.14      24      59 ..     256     291 ..     235     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                       DUF4283  24 lsalrrvlakaWklkggvkikelgdglflfrfssee 59 
                                   ++++ ++++k+Wkl+g +++k+ ++ +fl++   e+
  gi|91772945|ref|YP_565637.1| 256 MERIDHWVNKMWKLGGSIHMKYEEKLHFLYENGREK 291
                                   678999***********************9866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2745.18
//
Query:       gi|91772946|ref|YP_565638.1|  [L=171]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.1    1.9e-11   43.8   0.1    1.4  1  HTH_20    Helix-turn-helix domain
    6.2e-10   38.8   0.3    9.9e-10   38.1   0.3    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
    1.7e-06   27.5   0.2      3e-06   26.7   0.2    1.3  1  HTH_24    Winged helix-turn-helix DNA-binding
    4.5e-05   23.3   0.1    7.7e-05   22.5   0.1    1.4  1  MarR      MarR family
    0.00028   20.7   0.1    0.00041   20.2   0.1    1.2  1  MarR_2    MarR family
    0.00054   20.5   0.2     0.0023   18.5   0.2    2.0  1  DUF4430   Domain of unknown function (DUF4430)
     0.0024   18.0   0.0     0.0049   17.0   0.0    1.6  1  HTH_28    Helix-turn-helix domain
     0.0043   16.8   0.0     0.0063   16.2   0.0    1.3  1  DUF4423   Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.039   14.0   0.0    1.5  1  HTH_29    Winged helix-turn helix
      0.049   13.6   0.2      0.084   12.8   0.2    1.4  1  HTH_11    HTH domain
        0.1   12.4   0.1       0.69    9.8   0.1    2.0  2  HTH_IclR  IclR helix-turn-helix domain
       0.15   12.0   0.0        0.5   10.3   0.0    1.7  2  GATase_7  Glutamine amidotransferase 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 !   43.8   0.1   1.3e-14   1.9e-11       2      57 ..       7      61 ..       6      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.3e-14
                                  HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                        HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                  ++++AL++ +R +il +L +++++  sela++l++s   + +H+++Leea+L++++
  gi|91772946|ref|YP_565638.1|  7 KVFHALGSDTRIKILELL-DEGEHHISELARELRISVPVAAKHVNILEEADLIDRR 61
                                  589***************.**********************************987 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 !   38.1   0.3   6.6e-13   9.9e-10       2      46 ..      15      59 ..      14      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 6.6e-13
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   tR+kIL lL ege+ ++ela+el++s +    H ++L+ea+L++
  gi|91772946|ref|YP_565638.1| 15 DTRIKILELLDEGEHHISELARELRISVPVAAKHVNILEEADLID 59
                                  69*****************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2     2e-09     3e-06       3      47 ..      15      58 ..      14      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2e-09
                        HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +t++kILelL + +   ++eLA++l +S++   ++++ Lee+ lI
  gi|91772946|ref|YP_565638.1| 15 DTRIKILELLDE-GEHHISELARELRISVPVAAKHVNILEEADLI 58
                                  799*********.*****************************999 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   5.2e-08   7.7e-05       4      50 ..      16      61 ..      14      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.2e-08
                                  HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                  t+++iL++l+ +g++ +seLa+ l +s + + + +  Le+++li+R+
  gi|91772946|ref|YP_565638.1| 16 TRIKILELLD-EGEHHISELARELRISVPVAAKHVNILEEADLIDRR 61
                                  6777887775.699*******************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   2.7e-07   0.00041      13      54 ..      22      61 ..      11      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                                  HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  +L ++++    ++elar+l++s + + ++++ L++a L+ rr
  gi|91772946|ref|YP_565638.1| 22 ELLDEGE--HHISELARELRISVPVAAKHVNILEEADLIDRR 61
                                  4445555..79****************************998 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.5e-06    0.0023       2      71 ..      95     155 ..      79     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                       DUF4430   2 ttvfdvleaaakkkedkteaqsgehyitsIngleqdtakksyWmyevNGepsdvGagsyklkdgdkivfr 71 
                                   tt++d+l  +a  k  k   ++    i s +g           +ye+NGe+s++ ++++ l+++++i+++
  gi|91772946|ref|YP_565638.1|  95 TTLLDALRGVAAIKVQKKGDRE---VIVSTDGE------EGLYVYEINGEFSEKSVKNCVLEKDTTIEWK 155
                                   5566666555555555554433...45555554......3456899***********************7 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.3e-06    0.0049       2      48 ..      17      61 ..      16      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                        HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikryeegGiagLvprr 48
                                  R++i++ll +G+  ++e+Arel is     + ++ +ee   a+L +rr
  gi|91772946|ref|YP_565638.1| 17 RIKILELLDEGEhHISELARELRISVPVAAKHVNILEE---ADLIDRR 61
                                  99*********88************9999999999888...8888887 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.2e-06    0.0063       9      78 ..       3      68 ..       1      84 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                       DUF4423  9 kLdeeefeyfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78
                                  +L+ + f+ + s     i+ell+  ++++ ++ela+ lr  is+  ++k +++L++++l+++   gk ++
  gi|91772946|ref|YP_565638.1|  3 QLNNKVFHALGSDTRIKILELLD--EGEHHISELARELR--ISVPVAAKHVNILEEADLIDRRIFGKTHV 68
                                  56666666666666666777655..5567**********..********************987777665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.039       1      38 [.      17      54 ..      17      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                        HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfee 38
                                  R+++l ll+eG+  +s++A+ l++s +   ++++  ee
  gi|91772946|ref|YP_565638.1| 17 RIKILELLDEGEHHISELARELRISVPVAAKHVNILEE 54
                                  99***********************9988888775555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.6e-05     0.084       2      42 ..      17      55 ..      16      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                        HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                  + +ilelL ++ +   ++eLA+eL +S  +  +++ +Lee+
  gi|91772946|ref|YP_565638.1| 17 RIKILELL-DEGE-HHISELARELRISVPVAAKHVNILEEA 55
                                  56999999.4444.8999********************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00046      0.69       7      49 ..      19      59 ..      18      61 .. 0.88
   2 ?    0.2   0.0      0.44   6.6e+02       2      13 ..      91     102 ..      90     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00046
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   iL++l e+     +selAr++ ++ + +  +++ L+e  ++ 
  gi|91772946|ref|YP_565638.1| 19 KILELLDEGEHH--ISELARELRISVPVAAKHVNILEEADLID 59
                                  699999999997..************99999999999988775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.44
                                   HHHHHHHHCT-C CS
                      HTH_IclR   2 ldRalaiLdala 13 
                                   ++++  +Ldal+
  gi|91772946|ref|YP_565638.1|  91 VEKGTTLLDALR 102
                                   899*******96 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   1.7e+03      51      70 ..      12      34 ..       2      39 .. 0.68
   2 ?   10.3   0.0   0.00033       0.5      62     111 ..      89     135 ..      71     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                      GATase_7 51 tksDtev.llallea..ewgeea 70
                                    sDt + +l+ll++  +++ e+
  gi|91772946|ref|YP_565638.1| 12 LGSDTRIkILELLDEgeHHISEL 34
                                  47999999999998865555554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00033
                      GATase_7  62 leaewgeealerlnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgda 111
                                   +e e+g+ +l+ l+G  A+ + ++ ++++++  D  G+  Ly++e +g +
  gi|91772946|ref|YP_565638.1|  89 IEVEKGTTLLDALRGVAAIKVQKKGDREVIVSTD--GEEGLYVYEING-E 135
                                   444899****************************..*******99865.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1155.17
//
Query:       gi|91772947|ref|YP_565639.1|  [L=264]
Description: protein of unknown function RIO1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-59  199.7   0.1    4.7e-59  199.2   0.1    1.1  1  RIO1            RIO1 family
      8e-05   22.1   0.3    0.00011   21.7   0.3    1.3  1  Pkinase         Protein kinase domain
    0.00066   19.1   0.2      0.076   12.4   0.1    2.1  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00088   18.2   0.4     0.0014   17.4   0.4    1.4  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.038   13.9   0.0    1.6  2  APH             Phosphotransferase enzyme family
      0.071   12.4   0.0       0.17   11.2   0.0    1.6  2  Pkinase_Tyr     Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   0.1   1.6e-62   4.7e-59       2     183 ..      68     249 ..      67     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 1.6e-62
                                   EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTE CS
                          RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhv 82 
                                   V+ +   +++++aiKiy++s ++F++++ y+ g++rf++   ++n+r+++ +w++kEfrnL r++eag++vP pi  +r++
  gi|91772947|ref|YP_565639.1|  68 VFLGEG-EEHDIAIKIYRISSSTFRSMEDYILGDPRFTNI--RHNKRDIIFAWTKKEFRNLIRANEAGIRVPVPIITERNI 145
                                   555543.5567***************************88..8************************************** PP

                                   EEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT..EEEE--GTTEEETTSTTH CS
                          RIO1  83 lvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded..kvviIDvsQaveldhpna 160
                                   l+mef+g+++ + p lkd++ e e+ + ++e++++ m+kly++a+lvH+DLSeyN+l+d++   +++ID++Q+v+l+hp+a
  gi|91772947|ref|YP_565639.1| 146 LIMEFMGKNEKPFPALKDIKlELEDGQLIFETIIDDMHKLYTKANLVHGDLSEYNILIDTNdlTPIMIDMGQSVTLEHPRA 226
                                   ********************777888999*****************************99868899*************** PP

                                   HHHHHHHHHHHHHHHHTTC---- CS
                          RIO1 161 lefLerDveniikfFrrkgvekv 183
                                     fL+rD+eni ++F+r +++++
  gi|91772947|ref|YP_565639.1| 227 DIFLKRDIENILRYFKRFKIDET 249
                                   *****************999854 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   3.5e-08   0.00011      71     150 ..     142     223 ..      60     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.5e-08
                                   SEEEEEEE--TTEB.HHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEE.TTTEEEE-SGTTSEES CS
                       Pkinase  71 delylvleyvegge.ladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLid.ekgelKitDFGlakel 148
                                   ++ +l++e++ ++e  + +l+ + +l+ e+ + i+++i+  ++ l+ +++++H Dl   NiLid ++    ++D G +  l
  gi|91772947|ref|YP_565639.1| 142 ERNILIMEFMGKNEkPFPALK-DIKLELEDGQLIFETIIDDMHKLYtKANLVHGDLSEYNILIDtNDLTPIMIDMGQSVTL 221
                                   556799***988775677775.689*********************7788**************55555778899998877 PP

                                   SS CS
                       Pkinase 149 es 150
                                   e+
  gi|91772947|ref|YP_565639.1| 222 EH 223
                                   66 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0059        18      59      81 ..     119     141 ..     108     146 .. 0.90
   2 !   12.4   0.1   2.5e-05     0.076     130     195 ..     178     246 ..     172     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0059
                           Kdo  59 vrEfrllkrLeeagvavpkpvaa 81 
                                    +Efr+l r +eag++vp p+  
  gi|91772947|ref|YP_565639.1| 119 KKEFRNLIRANEAGIRVPVPIIT 141
                                   58*****************9976 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.5e-05
                           Kdo 130 liaklhr....agvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsfl..kiel 195
                                   +i ++h+    a++ H+dl   nil+++++   ++ ++iD+ ++ +     ad   ++d+++++r+f+  k  +
  gi|91772947|ref|YP_565639.1| 178 IIDDMHKlytkANLVHGDLSEYNILIDTND---LTPIMIDMGQSVTLEHprADIFLKRDIENILRYFKrfK--I 246
                                   577788533337999**************8...9*********9876652366667999999999998443..3 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   4.8e-07    0.0014     316     364 ..     179     223 ..     172     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.8e-07
                Pkinase_fungal 316 IkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsd 364
                                   I    +L++ka+++H D Se+Nili     +++ + ++iD+   ++l++
  gi|91772947|ref|YP_565639.1| 179 IDDMHKLYTKANLVHGDLSEYNILID----TNDLTPIMIDMGQSVTLEH 223
                                   666789*******************9....5677888888877777665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.9   2.7e+03      39      59 ..     120     140 ..     115     152 .. 0.74
   2 ?   13.9   0.0   1.3e-05     0.038     151     195 ..     169     217 ..     136     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.9
                                   HHHHHHHHHHHTT-B--B-CT CS
                           APH  39 revallrlLakagvpvPevla 59 
                                   +e++ l   ++ag++vP+++ 
  gi|91772947|ref|YP_565639.1| 120 KEFRNLIRANEAGIRVPVPII 140
                                   677777777999999999986 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                                   H....HHHHHHHH--S.SS-EEEE-SS-SGGGEEEC...TTEEEEE---TT CS
                           APH 151 q....vlaalaallpg.elptvllHgDlhpgNllvd.pddgrvtGviDfed 195
                                   +    + +++ + +++   ++ l+HgDl+  N+l+d  d +++  +iD + 
  gi|91772947|ref|YP_565639.1| 169 EdgqlIFETIIDDMHKlYTKANLVHGDLSEYNILIDtNDLTPI--MIDMGQ 217
                                   3334444555555555555789**************7777788..999854 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.61   1.8e+03       8      10 ..      61      63 ..      10      94 .. 0.61
   2 ?   11.2   0.0   5.6e-05      0.17      74     144 ..     142     211 ..     113     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.61
                                  EEE CS
                   Pkinase_Tyr  8 GeG 10
                                    G
  gi|91772947|ref|YP_565639.1| 61 STG 63
                                  222 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.6e-05
                                   SSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHT.TEEEST-SGGGEEEEETTEEEE CS
                   Pkinase_Tyr  74 epllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLesk.klvHrdlaarNvLlsenkvvki 144
                                   e+ ++++e++ +++  k   + ++ kl+l+d   +   + + m+ L +k +lvH dl+  N+L+++n++  i
  gi|91772947|ref|YP_565639.1| 142 ERNILIMEFMGKNE--KPFPALKDIKLELEDGQLIFETIIDDMHKLYTKaNLVHGDLSEYNILIDTNDLTPI 211
                                   45577777776554..33333346788999988889999999998865428**************9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1994.15
//
Query:       gi|91772948|ref|YP_565640.1|  [L=178]
Description: RNA-processing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   44.3   5.9    1.5e-07   31.1   0.6    2.2  2  KH_1      KH domain
    0.00085   19.1   5.0       0.12   12.2   1.0    2.5  2  KH_2      KH domain
  ------ inclusion threshold ------
          2    8.6   4.4         10    6.3   0.5    2.7  3  KH_5      NusA-like KH domain
        2.6    8.0   8.4        8.8    6.3   2.3    3.0  3  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.6   3.3e-11   1.5e-07       4      65 ..       4      61 ..       2      62 .. 0.82
   2 !   15.8   0.5     2e-06     0.009      11      56 ..     102     139 ..      95     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.3e-11
                                  EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEE.E.SHHHHHHHHHHHH CS
                          KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtis.G.speavekAkelie 65
                                  i+vP++ +g+iIG++Gs+ k I+e+t a  +++ se+      +v+++ G +p +  +A++ i+
  gi|91772948|ref|YP_565640.1|  4 IKVPQDRIGAIIGPQGSVKKIIEERTTATLDID-SEN-----GTVEVIaGdDPVGAMRAADVIQ 61
                                  89**********************9******87.655.....5777753877777777777665 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2e-06
                                   HHHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EEEEEESHHH CS
                          KH_1  11 vgriIGkgGsnIkeIreet.gakIkvpksedegsderevtisGspea 56 
                                    griIGkgG++   I++   g+k+ v  ++       +v  +G p++
  gi|91772948|ref|YP_565640.1| 102 KGRIIGKGGKTREIIES-LiGVKMSVY-GK-------TVSAIGHPDQ 139
                                   69********9777777.67****987.43.......4555554444 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.2   0.00039       1.8      32      58 ..       7      33 ..       2      46 .. 0.79
   2 !   12.2   1.0   2.8e-05      0.12      36      66 ..     102     131 ..      99     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00039
                                  EESCHHHHHTGGGHHHHHHHHHHHHHH CS
                          KH_2 32 resqpgivIGkgGsnikkigkelrkdi 58
                                     + g +IG +Gs  k i++     +
  gi|91772948|ref|YP_565640.1|  7 PQDRIGAIIGPQGSVKKIIEERTTATL 33
                                  56799**************98766555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.8e-05
                                   HHHHHTGGGHHHHHHHHHHHHHHHHHHTTCE CS
                          KH_2  36 pgivIGkgGsnikkigkelrkdieklegkkV 66 
                                   +g++IGkgG++ + i++ ++ ++  + gk V
  gi|91772948|ref|YP_565640.1| 102 KGRIIGKGGKTREIIESLIGVKMS-VYGKTV 131
                                   8*******************9995.777766 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5    0.0023        10      17      35 ..       9      26 ..       3      60 .. 0.85
   2 ?   -2.1   0.0      0.97   4.3e+03      17      34 ..      49      64 ..      37      74 .. 0.61
   3 ?    3.2   0.2     0.021        95      20      44 ..     103     126 ..      96     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0023
                          KH_5 17 dpvGaivgkkGsrikavss 35
                                  d +Gai+g +Gs  k++++
  gi|91772948|ref|YP_565640.1|  9 DRIGAIIGPQGSV-KKIIE 26
                                  78*********95.55544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.97
                          KH_5 17 dpvGaivgkkGsrikavs 34
                                  dpvGa+  +  + i+a+ 
  gi|91772948|ref|YP_565640.1| 49 DPVGAM--RAADVIQAIG 64
                                  566654..3344455554 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.021
                          KH_5  20 GaivgkkGsrikavsseLkgekidv 44 
                                   G i+gk+G+  + ++s + g k+ v
  gi|91772948|ref|YP_565640.1| 103 GRIIGKGGKTREIIESLI-GVKMSV 126
                                   899**9998766555555.777665 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1    0.0095        42      33      49 ..       4      20 ..       2      23 .. 0.89
   2 ?   -0.7   0.0      0.29   1.3e+03       9      33 ..      22      44 ..      20      52 .. 0.49
   3 ?    6.3   2.3     0.002       8.8      40      57 ..     102     119 ..     100     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0095
                          KH_4 33 lnvegedlGrvIGkrGr 49
                                  ++v ++ +G +IG +G 
  gi|91772948|ref|YP_565640.1|  4 IKVPQDRIGAIIGPQGS 20
                                  88999**********96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                          KH_4  9 kalvddpeevevteeeeeeeveiel 33
                                  k+++++  + + +++  +e+ ++e+
  gi|91772948|ref|YP_565640.1| 22 KKIIEERTTATLDID--SENGTVEV 44
                                  566654443333333..44444444 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.002
                          KH_4  40 lGrvIGkrGrtldAlqyl 57 
                                   +Gr+IGk G+t   +  l
  gi|91772948|ref|YP_565640.1| 102 KGRIIGKGGKTREIIESL 119
                                   6*********96555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1243.31
//
Query:       gi|91772949|ref|YP_565641.1|  [L=135]
Description: beta-Ig-H3/fasciclin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   95.9   0.0    2.4e-27   95.7   0.0    1.0  1  Fasciclin  Fasciclin domain


Domain annotation for each model (and alignments):
>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.0   1.3e-31   2.4e-27       2     128 .]      16     135 .]      15     135 .] 0.97

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.3e-31
                                   GGHHHHHHHHTTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHHEEEECC CS
                     Fasciclin   2 dlstfvsllekaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkasetlatl 82 
                                   d++t+vs+ +k gl++++ +k+g++T+FaP  +Af+ +p +  ++ ++d+ +l++i++yH++++++ + +lk+  + ++  
  gi|91772949|ref|YP_565641.1|  16 DFTTLVSAAKKLGLTNKF-SKEGPYTIFAPIEKAFEPIPDSVIDEAFDDQGYLMDIVNYHIIEGKYFTYDLKDI-QIITA- 93 
                                   89****************.888***************************************************9.77777. PP

                                   TTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                     Fasciclin  83 legaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                   l+g++l ++++   +++ +ng  ++ ++die++ng+ih i+++L+p
  gi|91772949|ref|YP_565641.1|  94 LNGKTLDISNN---EKLLING-IEIKKKDIECSNGIIHAIEEILIP 135
                                   **********9...69*****.**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1001.17
//
Query:       gi|91772950|ref|YP_565642.1|  [L=396]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-25   89.9   0.4    2.7e-25   89.1   0.1    1.6  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.2e-20   71.2   0.0    9.9e-20   70.4   0.0    1.5  1  HisKA        His Kinase A (phospho-acceptor) domain
    1.9e-15   57.0   0.0    4.8e-15   55.7   0.0    1.7  1  PAS_9        PAS domain
    2.4e-12   46.8   0.0    5.2e-12   45.8   0.0    1.5  1  PAS          PAS fold
    4.2e-07   30.2   0.0    8.4e-07   29.2   0.0    1.5  1  PAS_3        PAS fold
      1e-06   29.0   0.0    1.6e-06   28.3   0.0    1.3  1  PAS_4        PAS fold
    0.00014   21.8   0.0     0.0003   20.7   0.0    1.6  1  PAS_8        PAS domain
    0.00069   19.7   0.0     0.0015   18.6   0.0    1.5  1  PAS_11       PAS domain
     0.0081   16.0   0.0      0.016   15.0   0.0    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.045   13.9   0.1       0.14   12.3   0.0    1.8  2  PAS_7        PAS fold
      0.079   13.1   0.0       0.23   11.6   0.0    1.7  1  sCache_like  Single Cache-like


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 ?   -3.2   0.0       7.5   1.2e+04       5      18 ..     222     235 ..     218     256 .. 0.63
   2 !   89.1   0.1   1.6e-28   2.7e-25       2     110 ..     286     395 ..     285     396 .] 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.5
                                   HHHHHHHHHHHHHH CS
                     HATPase_c   5 rLrqiisnlvdNav 18 
                                   +L +ii+++++ + 
  gi|91772950|ref|YP_565642.1| 222 HLSEIINEILEISK 235
                                   66777777766443 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 1.6e-28
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGls 79 
                                   d++++++i+ +l+ Navkf  ++++++v i+as   d  +i + D+GiGip+e+l++l +kf+q d+stkr++ggtGlGl+
  gi|91772950|ref|YP_565642.1| 286 DKTKFKHILHHLLINAVKF--TSDHGSVGIHASAisDMMHIVIFDDGIGIPREQLPHLYDKFYQvDGSTKRKYGGTGLGLA 364
                                   77899*************9..5677777777644558******************************************** PP

                                   HHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                     HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlpl 110
                                   + kklv l  G++wvese + Gt++++ lpl
  gi|91772950|ref|YP_565642.1| 365 LTKKLVILNSGQMWVESEVNVGTKVHMMLPL 395
                                   ******9788*****************9997 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 !   70.4   0.0   6.1e-23   9.9e-20       1      67 []     171     239 ..     171     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 6.1e-23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   s+++fla+v+HELrtPL++i g++e+L +   g l++ +++y++ + +++++l+++++++L++s+ieag
  gi|91772950|ref|YP_565642.1| 171 SKSEFLANVSHELRTPLNSIVGFSEILLDGrcGGLNDVQRRYVQNVSNNGNHLSEIINEILEISKIEAG 239
                                   799************************9*9*************************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   2.9e-18   4.8e-15       2     103 ..      48     149 ..      47     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.9e-18
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                    gi + ++dg+i+yaNea+ +l Gys++e+l+ ++ +++   + p+ ++ l+++l +    +++++v ++rk+g+ f++ l
  gi|91772950|ref|YP_565642.1|  48 YGISVLDMDGNIIYANEAFSQLHGYSADELLNINFLMFYheGQVPHLKRLLDKLLSSDG--CENEDVWHMRKDGSIFPAIL 126
                                   5888989********************************66666666666666666666..******************** PP

                         PAS_9  81 taspvkdddgelvgiivilrDit 103
                                    +  + d+d+e   i v lrD+t
  gi|91772950|ref|YP_565642.1| 127 ECNLILDGDNEPSYIFVALRDLT 149
                                   ************9999*****99 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   3.2e-15   5.2e-12      11     112 ..      47     147 ..      38     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 3.2e-15
                                   SSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEE CS
                           PAS  11 pdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlev 91 
                                     +i v+D dg+i+y+N+a+ +l G+s++e+l+ ++l+++he +   + ++l+  l+++  +++++++  ++dg+++++ +
  gi|91772950|ref|YP_565642.1|  47 NYGISVLDMDGNIIYANEAFSQLHGYSADELLNINFLMFYHEGQ-VPHLKRLLDKLLSSDGCENEDVWHMRKDGSIFPAIL 126
                                   5699*************************************964.335555555555555555566666669********* PP

                                   EEEEEEETTEEEEEEEEEEEE CS
                           PAS  92 raspvrdaggeilgflgvlrd 112
                                   +++ ++d++ e+ ++++ lrd
  gi|91772950|ref|YP_565642.1| 127 ECNLILDGDNEPSYIFVALRD 147
                                   ********************9 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   5.2e-10   8.4e-07       1      85 [.      59     141 ..      59     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.2e-10
                         PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengk 81 
                                   iiy++e+++++ Gys++ell+   ++l++ h    +++++ l+++l+++++ ++++  +rkdG+++     ++ i d +++
  gi|91772950|ref|YP_565642.1|  59 IIYANEAFSQLHGYSADELLNI--NFLMFYHEGQVPHLKRLLDKLLSSDGCENEDVWHMRKDGSIFPAILECNLILDGDNE 137
                                   69********************..**************************99999************99999999999999 PP

                         PAS_3  82 pvrv 85 
                                   p ++
  gi|91772950|ref|YP_565642.1| 138 PSYI 141
                                   8765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   9.8e-10   1.6e-06       7     108 ..      49     151 ..      45     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.8e-10
                         PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeerhyelrl 85 
                                   ++ vld dg+++yaN+a+ +l g++++ell+  +  ++ e++ + l r l+++l++ + +e +++ +   +g+  +  l++
  gi|91772950|ref|YP_565642.1|  49 GISVLDMDGNIIYANEAFSQLHGYSADELLNINFLMFYHEGQVPHLKRLLDKLLSS-DGCENEDVWHMrkDGSIFPAILEC 128
                                   6789*******************************999999***************.68888888888899********** PP

                         PAS_4  86 lPlrdesGevigvlvisrDiTer 108
                                   + ++d + e+  ++v +rD+T +
  gi|91772950|ref|YP_565642.1| 129 NLILDGDNEPSYIFVALRDLTVT 151
                                   ********************976 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.9e-07    0.0003      12      41 ..      48      78 ..      45     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.9e-07
                         PAS_8 12 dgiavvd.lgdrivdvNqaalellGys.adlk 41
                                   gi v+d +g+ i+++N+a+ +l Gys ++l+
  gi|91772950|ref|YP_565642.1| 48 YGISVLDmDGN-IIYANEAFSQLHGYSaDELL 78
                                  6999***5555.***************55554 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   9.3e-07    0.0015       7      85 ..      52     126 ..      49     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.3e-07
                        PAS_11   7 rldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvkt 85 
                                    ld+dg+Ii  ++     s   g++ +el+++ +  + h+ ++ +lk+ l + +ss g   +++ ++r  ++ +  +  
  gi|91772950|ref|YP_565642.1|  52 VLDMDGNIIYANE---AFSQLHGYSADELLNINFLMFYHEGQVPHLKRLLDKLLSSDGCENEDVWHMRK-DGSIFPAIL 126
                                   69***********...999999********************************************998.666555555 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 !   15.0   0.0   9.7e-06     0.016       7      78 ..     294     364 ..     288     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                   HATPase_c_3   7 laelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelkn.alrlatsskeakrkstslGkkGiGlk 78 
                                   l  l+ N++   +d  +v i+++    +   ivi DdG G+++e+l   + ++ + + +   +++++G  G+Gl 
  gi|91772950|ref|YP_565642.1| 294 LHHLLINAVKftSDHGSVGIHASAIS-DMMHIVIFDDGIGIPREQLPHlYDKFYQVDGS---TKRKYGGTGLGLA 364
                                   56677888765589999999999985.799*****************955589998888...7899999999953 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.8e-05      0.14       5      33 ..      47      75 ..      45      82 .. 0.90
   2 ?   -2.8   0.0       4.3     7e+03      33      63 ..     215     245 ..     211     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
                         PAS_7  5 sqGisvfDadlrLvawNrrylelldlpee 33
                                  + Gisv+D d++++  N+ + +l++++++
  gi|91772950|ref|YP_565642.1| 47 NYGISVLDMDGNIIYANEAFSQLHGYSAD 75
                                  56***********************9876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.3
                         PAS_7  33 elvqvgvpleellrynaergefgagdveaev 63 
                                   ++ + g +l+e+++ + e  +++ag++e  +
  gi|91772950|ref|YP_565642.1| 215 NVSNNGNHLSEIINEILEISKIEAGKAEVNL 245
                                   5667788899999988888888887777655 PP

>> sCache_like  Single Cache-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.23      15      62 ..      20      65 ..      19      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                  HHHHHHHS-GGG-SSHHHHHHHHHHHHHHT-EEEEEETTS-EEEETTS CS
                   sCache_like 15 akllasllenenlkaaenkkvleeasekldaritivdadgkvlydtgq 62
                                  +++l+  +e + +++++n  +++ +s k +  i+++d dg+++y  ++
  gi|91772950|ref|YP_565642.1| 20 THYLSKFVEMKLVENDLN--IFKSISYKANYGISVLDMDGNIIYANEA 65
                                  678999999999999999..************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2798.46
//
Query:       gi|91772951|ref|YP_565643.1|  [L=233]
Description: hypothetical protein Mbur_0951 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   22.2   0.0    0.00023   21.4   0.0    1.4  1  PAS_4     PAS fold
    0.00083   19.6   0.1     0.0048   17.1   0.0    2.2  3  PAS_9     PAS domain
     0.0034   17.4   0.0     0.0082   16.1   0.0    1.6  2  PAS       PAS fold
     0.0051   16.8   0.0      0.015   15.4   0.0    1.8  1  PAS_8     PAS domain
  ------ inclusion threshold ------
      0.038   13.9   2.6      0.094   12.7   2.6    1.6  1  DUF4801   Domain of unknown function (DUF4801)


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.4e-08   0.00023      17     109 ..      68     152 ..      56     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.4e-08
                         PAS_4  17 vlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrdesGevig 97 
                                   +l +N+a+++++g+  ++++Gk++ +++p+ d   +e + + +l+ge ++++    l   ++r+ye++++         ig
  gi|91772951|ref|YP_565643.1|  68 FLNVNPAFERIVGLKKDDVIGKCVLDIFPHMDVSWVEKYGKVALTGESAYFDDY-SLM--GDRFYEVNAFSSS------IG 139
                                   6779**************************888888877777776665555555.555..5********9973......56 PP

                         PAS_4  98 vl.visrDiTerr 109
                                   v+ +++ DiTerr
  gi|91772951|ref|YP_565643.1| 140 VFaMTFFDITERR 152
                                   5515678999997 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0048       6      40 ..      56      95 ..      51     121 .. 0.84
   2 ?   -1.5   0.0      0.84     3e+03      93     104 .]     139     150 ..     128     150 .. 0.76
   3 ?   -2.3   0.0       1.5   5.5e+03      16      40 ..     188     212 ..     176     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                         PAS_9  6 idnpdg.....rilyaNeaalrllGyspeevlgksitdlf 40
                                  i+n+dg       l +N+a++r+ G ++++v+gk + d+f
  gi|91772951|ref|YP_565643.1| 56 ICNDDGvpinyCFLNVNPAFERIVGLKKDDVIGKCVLDIF 95
                                  577888777777889*******************999998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.84
                         PAS_9  93 vgiivilrDite 104
                                     ++ ++ Dite
  gi|91772951|ref|YP_565643.1| 139 GVFAMTFFDITE 150
                                   34679******8 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.5
                         PAS_9  16 aNeaalrllGyspeevlgksitdlf 40 
                                    Ne++ ++  + + ++  +s+t ++
  gi|91772951|ref|YP_565643.1| 188 LNEGFQKVVDSVFSDLKDRSVTGCC 212
                                   5666666665556666666655444 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-06    0.0082      22      54 ..      67      99 ..      62     115 .. 0.86
   2 ?   -3.5   0.0       2.9     1e+04      78      98 ..     164     183 ..     156     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                                  BEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTH CS
                           PAS 22 rilyvNaaaeellGlsreevlgkslldliheed 54
                                  ++l vN+a+e++ Gl+ ++v+gk +ld +++ d
  gi|91772951|ref|YP_565643.1| 67 CFLNVNPAFERIVGLKKDDVIGKCVLDIFPHMD 99
                                  6789*******************9999988865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.9
                                   EEECTTSSEEEEEEEEEEEEE CS
                           PAS  78 sfklrdgrpihlevraspvrd 98 
                                   ++++ + +  ++++++s+++d
  gi|91772951|ref|YP_565643.1| 164 DLNK-HVCDLECLLNVSSIVD 183
                                   4555.6677888888888876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.1e-06     0.015      23      52 ..      68      98 ..      41     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                         PAS_8 23 ivdvNqaalellGys.adlkgellgqllpvl 52
                                  ++ vN+a++++ G++ +d++g+ + +++p+ 
  gi|91772951|ref|YP_565643.1| 68 FLNVNPAFERIVGLKkDDVIGKCVLDIFPHM 98
                                  777******************9999888775 PP

>> DUF4801  Domain of unknown function (DUF4801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.6   2.6e-05     0.094      17      44 ..     153     179 ..     149     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                       DUF4801  17 CiCdslessekaarreHCgradCvlecv 44 
                                   C+Cd+le + +   ++H   ++C+l+++
  gi|91772951|ref|YP_565643.1| 153 CVCDVLEMQTHDL-NKHVCDLECLLNVS 179
                                   ********99996.999999****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1715.43
//
Query:       gi|91772952|ref|YP_565644.1|  [L=365]
Description: hypothetical protein Mbur_0952 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      8e-30  102.9   5.8    4.1e-16   59.0   0.0    2.7  3  CCG         Cysteine-rich domain
    1.1e-09   38.5   7.3    1.1e-09   38.5   7.3    2.1  2  Fer4_8      4Fe-4S dicluster domain
    2.8e-09   37.4   7.7    2.8e-09   37.4   7.7    2.6  2  Fer4_17     4Fe-4S dicluster domain
    3.8e-06   26.9  20.3    1.4e-05   25.1  10.7    3.0  4  Fer4_10     4Fe-4S dicluster domain
    1.3e-05   25.7   9.4    1.3e-05   25.7   9.4    2.5  3  Fer4_7      4Fe-4S dicluster domain
     0.0015   18.7   6.7       0.15   12.3   0.4    3.3  3  Fer4_18     4Fe-4S dicluster domain
     0.0033   16.8   0.0     0.0052   16.2   0.0    1.2  1  Thiolase_N  Thiolase, N-terminal domain
      0.006   16.7  10.4        0.1   12.8   0.4    3.4  3  Fer4_21     4Fe-4S dicluster domain
     0.0062   17.0   0.5     0.0062   17.0   0.5    3.8  3  Fer4_4      4Fe-4S binding domain
  ------ inclusion threshold ------
       0.02   14.7  11.9      0.026   14.3   3.6    3.0  2  Fer4        4Fe-4S binding domain
      0.022   14.9  14.9      0.022   14.9  14.9    3.2  4  Fer4_9      4Fe-4S dicluster domain
      0.051   13.7   1.5      0.051   13.7   1.5    3.4  3  Fer4_2      4Fe-4S binding domain
       0.28   11.0   7.4       0.32   10.8   0.6    2.7  2  Fer4_20     Dihydroprymidine dehydrogenase domain II, 4Fe-4S 
       0.45   11.4   8.1        8.4    7.3   0.2    3.4  3  Fer4_22     4Fe-4S dicluster domain
       0.46   11.5  18.4       0.24   12.4  14.1    2.7  2  Fer4_16     4Fe-4S double cluster binding domain
        1.3   10.2  15.0         12    7.1   3.7    3.4  2  Fer4_3      4Fe-4S binding domain
        8.4    7.0  10.7        8.7    7.0   1.3    2.8  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
        9.1    6.5  19.5       0.16   12.1   3.0    3.1  2  Fer4_6      4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       8.3   8.2e+03      72      81 ..      14      23 ..       2      23 .. 0.59
   2 !   46.3   0.6   3.8e-15   3.7e-12       1      85 []     137     220 ..     137     220 .. 0.96
   3 !   59.0   0.0   4.1e-19   4.1e-16       1      84 [.     254     339 ..     254     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.3
                           CCG 72 aivtacpgCl 81
                                  + +t+c++C+
  gi|91772952|ref|YP_565644.1| 14 INCTQCGFCK 23
                                  3368899985 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 3.8e-15
                           CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee.laealakrnvetaeetgadaivtacpgC 80 
                                   +ayf+gC  + ++++e  +a   +l++lgv++  l +e CCG+  gr g+ +   ++ a+ nv+++e t a++++  c+gC
  gi|91772952|ref|YP_565644.1| 137 IAYFTGC-SAAYRNKEIAEAGISILKKLGVDYTLL-DEVCCGSVLGRLGFSDdNIKRQAEVNVKAIEATCAEIVLFSCAGC 215
                                   69*****.9************************99.**************998999************************* PP

                           CCG  81 llqlk 85 
                                   l +++
  gi|91772952|ref|YP_565644.1| 216 LRMFR 220
                                   99985 PP

  == domain 3  score: 59.0 bits;  conditional E-value: 4.1e-19
                           CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadaivtac 77 
                                   v+y+d+Ch++r+   y+++r ++ +++  ++ve+ +  e + CCG ggg++ + + ++ ++a ++v++ae   ad+++t+c
  gi|91772952|ref|YP_565644.1| 254 VTYHDPCHIGRHLgiYDAPRDVINNIPDIEFVEMADSrESARCCGGGGGVRAQFPeISGNIASKRVDQAEF--ADVLLTTC 332
                                   89***********************************************99998889**************..8******* PP

                           CCG  78 pgCllql 84 
                                   p+C ++l
  gi|91772952|ref|YP_565644.1| 333 PFCVNNL 339
                                   ***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 !   38.5   7.3   1.2e-12   1.1e-09       2      64 ..      13      80 ..      12      81 .. 0.83
   2 ?   -1.2   0.2         3     3e+03      44      54 ..     203     215 ..     173     217 .. 0.59

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.2e-12
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.........dvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  l +C++Cg+C++ Cp++ +   ++  arg+ a          +  e+      e l++Cttc  Ct++Cp +
  gi|91772952|ref|YP_565644.1| 13 LINCTQCGFCKDVCPIFADVEWDSSVARGKMALcyglysgdiEPDESV----VERLYQCTTCADCTRRCPSS 80
                                  569*****************9999999999888888877655333333....578***************75 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3
                        Fer4_8  44 e..eealwsCttc 54 
                                   +  e  l+sC +c
  gi|91772952|ref|YP_565644.1| 203 TcaEIVLFSCAGC 215
                                   1436778888888 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   7.7   2.9e-12   2.8e-09       1      60 [.      15      81 ..      15      82 .. 0.78
   2 ?   -0.4   0.3       1.8   1.8e+03      26      49 ..     190     215 ..     174     217 .. 0.65

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.9e-12
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl......glleeaeke.ekaslCieCgeCerkCPqgl 60
                                  +C+qCg+C ++Cp +++ +++    + +++l      g++e  e   e+  +C++C  C+r+CP++ 
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCPIFADVEWDSSVARGKMALcyglysGDIEPDESVvERLYQCTTCADCTRRCPSST 81
                                  6****************9997665555555555444377777655469****************975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                       Fer4_17  26 lraakl..glleeaekeekaslCieC 49 
                                    r+a++  + +e++ +e +  +C++C
  gi|91772952|ref|YP_565644.1| 190 KRQAEVnvKAIEATCAEIVLFSCAGC 215
                                   45555522455555555688999998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1  10.7   1.4e-08   1.4e-05       2      56 .]       9      78 ..       8      78 .. 0.90
   2 !   15.1   2.0   1.9e-05     0.019       7      35 ..      65      93 ..      59     101 .. 0.70
   3 ?   -2.0   0.2       4.1   4.1e+03      41      48 ..     208     215 ..     190     217 .. 0.62
   4 ?   -1.6   0.0       3.2   3.2e+03      39      48 ..     326     335 ..     308     345 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.4e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl...............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  ++++   C++Cg C+++CP  +                   ++g ++++e v + +++Ct+c  C++ CP
  gi|91772952|ref|YP_565644.1|  9 WKKELINCTQCGFCKDVCPIFAdvewdssvargkmalCYGLYSGDIEPDESVVERLYQCTTCADCTRRCP 78
                                  5667778*************88***********999766677888999999999***************9 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.9e-05
                       Fer4_10  7 dtCirCgkCvkaCPadltsvgakgeasee 35
                                   +C+ C++C++ CP++ + vg+ +++ ++
  gi|91772952|ref|YP_565644.1| 65 YQCTTCADCTRRCPSSTDVVGVVEAIRKD 93
                                  5799*********9966655555555555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.1
                       Fer4_10  41 kvekCtgc 48 
                                   ++ +C gc
  gi|91772952|ref|YP_565644.1| 208 VLFSCAGC 215
                                   34444444 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.2
                       Fer4_10  39 rkkvekCtgc 48 
                                   ++ +  C++c
  gi|91772952|ref|YP_565644.1| 326 DVLLTTCPFC 335
                                   5566667777 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   9.4   1.3e-08   1.3e-05       2      50 ..      16      79 ..      15      81 .. 0.70
   2 ?   -1.9   0.1       5.2   5.2e+03      32      41 ..     206     215 ..     181     218 .. 0.56
   3 ?   -2.6   0.3       9.1     9e+03       4      10 ..     331     337 ..     330     338 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-08
                        Fer4_7  2 CigCgaCvaaCp.vkaieldeeenekgt...............ekveidpekClgCgaCvavCPt 50
                                  C++Cg+C ++Cp    +e+d  ++++g+               e+v+ +  +C++C  C ++CP+
  gi|91772952|ref|YP_565644.1| 16 CTQCGFCKDVCPiFADVEWDS-SVARGKmalcyglysgdiepdESVVERLYQCTTCADCTRRCPS 79
                                  ************666666665.467755344444444444433556677788************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.2
                        Fer4_7  32 eidpekClgC 41 
                                   ei+  +C gC
  gi|91772952|ref|YP_565644.1| 206 EIVLFSCAGC 215
                                   3444455555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.1
                        Fer4_7   4 gCgaCva 10 
                                    C +Cv+
  gi|91772952|ref|YP_565644.1| 331 TCPFCVN 337
                                   5888886 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.4   0.00015      0.15      55      77 ..      10      32 ..       2      48 .. 0.84
   2 !    7.2   0.6    0.0057       5.7      55      77 ..      61      83 ..      49      91 .. 0.82
   3 ?    0.4   0.0      0.74   7.4e+02      55      77 ..     321     345 ..     299     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                       Fer4_18 55 ekgagdcidcescvkvcPtgidi 77
                                  +k+  +c++c++c +vcP+  d+
  gi|91772952|ref|YP_565644.1| 10 KKELINCTQCGFCKDVCPIFADV 32
                                  667789************99987 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0057
                       Fer4_18 55 ekgagdcidcescvkvcPtgidi 77
                                   +   +c++c  c + cP   d+
  gi|91772952|ref|YP_565644.1| 61 VERLYQCTTCADCTRRCPSSTDV 83
                                  566679************99997 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.74
                       Fer4_18  55 ekgagdc..idcescvkvcPtgidi 77 
                                   +++ +d   ++c +cv+    gid 
  gi|91772952|ref|YP_565644.1| 321 QAEFADVllTTCPFCVNNLALGIDE 345
                                   44445532278999**999999985 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.3e-06    0.0052      22      86 ..     148     213 ..     134     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                                   -HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT..TSTSCHHHHHHHHTTS-TTSEEEEEEHGGG CS
                    Thiolase_N  22 saeeLlaealkallekagvdpeevdevivGnvlqa..gegqniarqaalkagipeevpavtvnkvcs 86 
                                   + +e+ aea+ ++l+k gvd+  +dev +G vl    +++ ni+rqa +++   e ++a+ v   c+
  gi|91772952|ref|YP_565644.1| 148 RNKEI-AEAGISILKKLGVDYTLLDEVCCGSVLGRlgFSDDNIKRQAEVNVKAIEATCAEIVLFSCA 213
                                   55554.5677889********************99889************99988888877766665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.4    0.0001       0.1      40      53 ..      15      28 ..       2      33 .. 0.83
   2 !    9.0   0.5    0.0015       1.5      40      53 ..      66      79 ..      52      97 .. 0.72
   3 ?   -1.3   0.2       2.6   2.6e+03      30      44 ..     201     215 ..     187     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                       Fer4_21 40 eCvGCnlCssvCPv 53
                                  +C+ C  C +vCP+
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCPI 28
                                  7************8 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                       Fer4_21 40 eCvGCnlCssvCPv 53
                                  +C+ C+ C+  CP 
  gi|91772952|ref|YP_565644.1| 66 QCTTCADCTRRCPS 79
                                  67777777777773 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.6
                       Fer4_21  30 aktvlkvvedeCvGC 44 
                                   ++t +++v  +C GC
  gi|91772952|ref|YP_565644.1| 201 EATCAEIVLFSCAGC 215
                                   445556666677777 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   6.2e-06    0.0062       3      15 ..      15      27 ..       9      43 .. 0.90
   2 ?    5.1   2.4     0.039        38       4      16 ..      67      79 ..      62      85 .. 0.90
   3 ?    0.4   0.1       1.2   1.2e+03       6      12 ..     331     337 ..     330     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.2e-06
                        Fer4_4  3 rCigCgsCvaaCP 15
                                  +C++Cg C ++CP
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCP 27
                                  6***********9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.039
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C+ C  C++ CP+
  gi|91772952|ref|YP_565644.1| 67 CTTCADCTRRCPS 79
                                  ************5 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.2
                        Fer4_4   6 gCgsCva 12 
                                    C+ Cv+
  gi|91772952|ref|YP_565644.1| 331 TCPFCVN 337
                                   6999996 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.6   2.7e-05     0.026       8      20 ..      16      28 ..      15      30 .. 0.90
   2 ?    3.9   1.3     0.053        53       8      19 ..      67      78 ..      64      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                  SSS-THHHHHSTT CS
                          Fer4  8 CigCGaCvevCPv 20
                                  C+ CG C +vCP 
  gi|91772952|ref|YP_565644.1| 16 CTQCGFCKDVCPI 28
                                  ************6 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.053
                                  SSS-THHHHHST CS
                          Fer4  8 CigCGaCvevCP 19
                                  C+ C  C   CP
  gi|91772952|ref|YP_565644.1| 67 CTTCADCTRRCP 78
                                  ************ PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.9   0.00063      0.63      33      47 ..      11      27 ..       1      30 [. 0.70
   2 ?   14.9  14.9   2.2e-05     0.022       1      48 [.      15      79 ..      15      81 .. 0.69
   3 ?   -1.8   0.1       3.6   3.6e+03      34      39 ..     210     215 ..     185     217 .. 0.60
   4 ?   -2.7   0.0       6.9   6.9e+03      35      39 ..     331     335 ..     313     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00063
                        Fer4_9 33 e..eaCigCgaCveaCp 47
                                  +   +C++Cg C ++Cp
  gi|91772952|ref|YP_565644.1| 11 KelINCTQCGFCKDVCP 27
                                  34567999999999998 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.2e-05
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..................eaCigCgaCveaCpk 48
                                  +Ct+Cg C ++Cp  + ve +    ar ++a                     +C++C +C+ +Cp+
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCPIFADVE-WDSSVARGKMALCyglysgdiepdesvverlYQCTTCADCTRRCPS 79
                                  6***********7544432.222222332222234477888888888888889************8 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.6
                        Fer4_9  34 eaCigC 39 
                                    +C gC
  gi|91772952|ref|YP_565644.1| 210 FSCAGC 215
                                   445555 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6.9
                        Fer4_9  35 aCigC 39 
                                    C +C
  gi|91772952|ref|YP_565644.1| 331 TCPFC 335
                                   34333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.5   5.1e-05     0.051       9      21 ..      15      27 ..       9      27 .. 0.93
   2 ?    3.0   3.9      0.13   1.3e+02      10      21 ..      67      78 ..      60      79 .. 0.89
   3 ?   -2.1   0.1       5.4   5.4e+03       9      13 ..     211     215 ..     205     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                        Fer4_2  9 rCigCgaCvsaCP 21
                                  +C++Cg C ++CP
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCP 27
                                  6***********9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                        Fer4_2 10 CigCgaCvsaCP 21
                                  C+ C  C+  CP
  gi|91772952|ref|YP_565644.1| 67 CTTCADCTRRCP 78
                                  ***********9 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.4
                        Fer4_2   9 rCigC 13 
                                   +C gC
  gi|91772952|ref|YP_565644.1| 211 SCAGC 215
                                   59999 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 ?    3.0   1.1     0.085        85      22      43 ..      14      33 ..       5      51 .. 0.76
   2 ?   10.8   0.6   0.00032      0.32      19      54 ..      62      95 ..      50     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.085
                                  TT----TT-HHHHCSTT---HH CS
                       Fer4_20 22 sRClqCkkapcvkgCPveidip 43
                                    C qC    c++ CP+  d++
  gi|91772952|ref|YP_565644.1| 14 INCTQC--GFCKDVCPIFADVE 33
                                  569999..79******998874 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00032
                                  HHHTT----TT-HHHHCSTT---HHHHHHHHHTT-H CS
                       Fer4_20 19 eeAsRClqCkkapcvkgCPveidipefikkiaegnl 54
                                  e    C +C  a c++ CP ++d+ + +++i+++ +
  gi|91772952|ref|YP_565644.1| 62 ERLYQCTTC--ADCTRRCPSSTDVVGVVEAIRKDLV 95
                                  444567777..88*****************998755 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0084       8.4       2      13 ..      16      27 ..       5      39 .. 0.72
   2 ?    6.5   0.6     0.015        15       1      14 [.      66      79 ..      63     105 .. 0.83
   3 ?   -0.4   0.1       2.1   2.1e+03      64      87 ..     194     217 ..     179     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0084
                       Fer4_22  2 ClsCgaCtlvCp 13
                                  C +Cg C+ vCp
  gi|91772952|ref|YP_565644.1| 16 CTQCGFCKDVCP 27
                                  555555555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                       Fer4_22  1 rClsCgaCtlvCpt 14
                                  +C +C+ Ct  Cp+
  gi|91772952|ref|YP_565644.1| 66 QCTTCADCTRRCPS 79
                                  58888888888886 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.1
                       Fer4_22  64 qrllhklsefkekfgesgCvGCgR 87 
                                   +  ++ ++ + +++   +C GC R
  gi|91772952|ref|YP_565644.1| 194 EVNVKAIEATCAEIVLFSCAGCLR 217
                                   444555566666777789999987 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 ?   12.4  14.1   0.00024      0.24       1      65 [.      15      78 ..      15      80 .. 0.82
   2 ?    6.1   4.7     0.022        22       1      15 [.      66      80 ..      66      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                  +C++Cg C +vCP  a  e  + +++ ++   y      d+++de   ++ +++t C+ C++ CP
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCPIFADVEWDSSVARGKMALCY-GLYSGDIEPDESVVERLYQCTTCADCTRRCP 78
                                  6*************9988885566666666666.66678888999888889************** PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                       Fer4_16  1 rCgtCgkCaevCPtn 15
                                  +C+tC  C+  CP++
  gi|91772952|ref|YP_565644.1| 66 QCTTCADCTRRCPSS 80
                                  599999999999985 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.6     0.013        13       1      12 [.      16      27 ..      16      30 .. 0.94
   2 ?    7.1   3.7     0.013        12       1      13 [.      67      79 ..      67      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                        Fer4_3  1 CtgCgaCvevCP 12
                                  Ct+Cg C +vCP
  gi|91772952|ref|YP_565644.1| 16 CTQCGFCKDVCP 27
                                  ************ PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  Ct C  C + CP+
  gi|91772952|ref|YP_565644.1| 67 CTTCADCTRRCPS 79
                                  ************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 ?    7.0   1.3    0.0087       8.7       5      17 ..      15      27 ..      12      39 .. 0.87
   2 ?    3.9   2.4     0.077        77       5      18 ..      66      79 ..      61      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0087
                       Fer4_13  5 tCiacgaCvelaP 17
                                  +C+ cg C +++P
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCP 27
                                  7************ PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.077
                       Fer4_13  5 tCiacgaCvelaPd 18
                                  +C+ c+ C   +P 
  gi|91772952|ref|YP_565644.1| 66 QCTTCADCTRRCPS 79
                                  8***********96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.0   0.00016      0.16       8      20 ..      15      27 ..      15      32 .. 0.90
   2 ?    4.7   2.6     0.034        34       9      21 ..      67      79 ..      66      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                        Fer4_6  8 kCigCgdCvrvCP 20
                                  +C++Cg C +vCP
  gi|91772952|ref|YP_565644.1| 15 NCTQCGFCKDVCP 27
                                  6************ PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.034
                        Fer4_6  9 CigCgdCvrvCPe 21
                                  C+ C dC+r CP 
  gi|91772952|ref|YP_565644.1| 67 CTTCADCTRRCPS 79
                                  999*********4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2585.64
//
Query:       gi|91772953|ref|YP_565645.1|  [L=474]
Description: FAD linked oxidase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-58  198.2   0.0    2.4e-58  197.7   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    3.1e-38  130.7   0.3    4.9e-38  130.0   0.3    1.3  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
      0.053   13.5   0.1        0.3   11.1   0.0    2.1  2  DUF4920        Domain of unknown function (DUF4920)


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 !  197.7   0.0     4e-62   2.4e-58       1     250 []     213     456 ..     213     456 .. 0.97

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 4e-62
                                   --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHH CS
                 FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeele 81 
                                   lpea+ava++ f+++e+a ++v+ i++  +ip+ lelm ++ +++v++         ++eea+ll+e++g++   ++ ++e
  gi|91772953|ref|YP_565645.1| 213 LPEATAVAVAVFETLEDAGRCVSNIIAYPVIPSGLELMSRVCIEAVNKAVCL---GLPDEEAILLIEVDGSS-HDVKGQIE 289
                                   59***********************************************999...7888999**********.67777888 PP

                                   HHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEEE CS
                 FAD-oxidase_C  82 alveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglevvl 162
                                    +v++ ++  g  +v ++ d++++e+lwk Rka++p l++   +  +++l  D++vP s+++++v++++a+ dky+++++ 
  gi|91772953|ref|YP_565645.1| 290 -KVTDVCKRSGSLSVDFTFDAERKEELWKGRKAMIPALSKYHDDLVTVMLADDMAVPMSKVPEAVKAFQAISDKYDIIIAS 369
                                   .8******************************************************************************* PP

                                   EEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH-TT- CS
                 FAD-oxidase_C 163 fgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPkg 243
                                   +gH gdgnlh  +l+d+  +  +++aek+v e+ +++++lgG+i+gEHGvG+ k+++  +e+ e  l +m+ iK+ lDP++
  gi|91772953|ref|YP_565645.1| 370 YGHSGDGNLHTKVLMDPTRQSHWDQAEKAVSEIYEKVMDLGGTITGEHGVGMTKAPFFLKER-ESSLGVMKVIKKGLDPNN 449
                                   *************************************************************9.66**************** PP

                                   -BSTT-- CS
                 FAD-oxidase_C 244 iLNPgkv 250
                                   i+NP+k+
  gi|91772953|ref|YP_565645.1| 450 IMNPYKI 456
                                   *****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 !  130.0   0.3   8.3e-42   4.9e-38       1     138 [.      39     176 ..      39     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 8.3e-42
                                   EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                 FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                   p+av+rp+ +eevaa+++lane   pv++rG+G+ l+g++v   ggvv+dl+r+n i e+  e+ +++ve+Gv+ +dl++ 
  gi|91772953|ref|YP_565645.1|  39 PDAVLRPKITEEVAAVVKLANELLFPVVPRGAGTALCGHCVpVAGGVVMDLQRMNVIKELHIEDLYVVVEPGVIHKDLNAK 119
                                   89***************************************99************************************** PP

                                   HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                 FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                   l+++g++++  p+sg+ + +GG++atna+G ++ kyG++rd+vlg+evvl++Ge+ r+
  gi|91772953|ref|YP_565645.1| 120 LKEYGFFIP-GPSSGNVANIGGMVATNASGGNAVKYGATRDYVLGMEVVLPTGEIARF 176
                                   ********9.********************************************9886 PP

>> DUF4920  Domain of unknown function (DUF4920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     5e-05       0.3      39      68 ..     115     144 ..     112     156 .. 0.85
   2 ?   -1.1   0.0      0.32   1.9e+03      18      27 ..     290     299 ..     277     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5e-05
                       DUF4920  39 evrVkfKdYgffvPkdikgkevvveGkafv 68 
                                   +++ k+K+Ygff+P  ++g+   + G++ +
  gi|91772953|ref|YP_565645.1| 115 DLNAKLKEYGFFIPGPSSGNVANIGGMVAT 144
                                   66789**************99999998766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                       DUF4920  18 kveevcqkkG 27 
                                   kv++vc+  G
  gi|91772953|ref|YP_565645.1| 290 KVTDVCKRSG 299
                                   6788999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3354.23
//
Query:       gi|91772954|ref|YP_565646.1|  [L=416]
Description: hypothetical protein Mbur_0954 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-62  209.0   0.0    9.1e-62  207.9   0.0    1.6  2  Lar_N         Lactate racemase N-terminal domain
    0.00089   19.5   0.1     0.0023   18.1   0.1    1.7  1  Mur_ligase_C  Mur ligase family, glutamate ligase domain


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 !  207.9   0.0     1e-65   9.1e-62       5     201 ..      13     201 ..       7     204 .. 0.93
   2 ?   -2.8   0.0      0.33     3e+03     114     140 ..     331     358 ..     328     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 1e-65
                         Lar_N   5 kleleipeenllgvlepkevkeekdeeeaieeaLenpigsekleelvkekekvvivvsDiTRptpskiilpllleelkeag 85 
                                   +++++ip+e    vl+p+e +e+ de ++i eaL+np+++e++ e++++++k++++v+D TRptp++++l+ + ++l++  
  gi|91772954|ref|YP_565646.1|  13 DIDVTIPHE----VLSPNE-PEVGDELSIILEALSNPVEKEPFVEFANNADKILVIVNDATRPTPTARVLEEVQDTLRS-- 86 
                                   345555555....79***9.99********************************************************9.. PP

                         Lar_N  86 vkdeditilvAtGlHrkqteeelkkilGeevvkri..kvvnhdaedksslvklGttskGtpveinklvaeadlviltGfie 164
                                     + d++++vAtG+Hr  te+e++ i+G ++++++  +++ hda++++++++lG +s+Gt++++nk+v ea +++++G++e
  gi|91772954|ref|YP_565646.1|  87 --HPDVKFIVATGAHRGPTEDEFRFIFG-NLYDEFkdSIYVHDARKDEDMEYLGVSSNGTEIYLNKMVREAGNILVIGSVE 164
                                   ..899***********************.9*****999******************************************* PP

                         Lar_N 165 pHyfaGfsGGrKsilpGvasretimanHkavlaepra 201
                                   pHyfaG++GGrK++lpGva+++ti++nHk++l+++++
  gi|91772954|ref|YP_565646.1| 165 PHYFAGYTGGRKAFLPGVAGFKTIEMNHKHALSNKAQ 201
                                   ******************************9977665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.33
                         Lar_N 114 eevvkri.kvvnhdaedksslvklGtts 140
                                   e+v+++  ++++   +++ +++++Gt  
  gi|91772954|ref|YP_565646.1| 331 EDVMEKTsQCYKLGFHKAARMAQIGTMA 358
                                   6777777689999999999999999876 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.6e-07    0.0023       7      81 ..      53     128 ..      51     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-07
                                   EEEETTTEEEEEET--SHHHHHHHHHHHHHHSS.SSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEESS CS
                  Mur_ligase_C   7 vvgeadgvtvidDyahnpdslsaalkalreiap.dkrlilvfgpggelgertrtfhdefgrlasaladslvvlgdy 81 
                                     + ad+++vi+  a+ p+ +  +l+ ++++   +  + +++  g+++g  + +f++ fg l  +++ds++v++  
  gi|91772954|ref|YP_565646.1|  53 FANNADKILVIVNDATRPTPTARVLEEVQDTLRsHPDVKFIVATGAHRGPTEDEFRFIFGNLYDEFKDSIYVHDAR 128
                                   5678899******************999988777455555555589**************************8763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2649.04
//
Query:       gi|91772955|ref|YP_565647.1|  [L=765]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-36  125.0   9.1    2.9e-14   53.2   0.0    4.7  4  PAS_9        PAS domain
    1.3e-30  105.7   2.7    2.4e-10   40.4   0.0    4.3  4  PAS          PAS fold
    2.4e-30  105.3   0.1      1e-29  103.3   0.1    2.1  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.2e-19   70.4   0.7    1.8e-05   24.9   0.1    3.7  3  PAS_3        PAS fold
    4.5e-18   65.5   0.0    6.3e-07   29.6   0.0    5.2  4  PAS_4        PAS fold
    6.3e-14   51.8   0.0    1.9e-13   50.2   0.0    1.8  1  HisKA        His Kinase A (phospho-acceptor) domain
    1.1e-13   50.8   0.1      2e-05   24.5   0.0    3.8  3  PAS_8        PAS domain
    2.4e-05   24.4   0.1      0.024   14.8   0.0    2.8  2  PAS_11       PAS domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.056   13.4   0.0    2.2  1  HATPase_c_5  GHKL domain
       0.08   12.8   0.0       0.21   11.4   0.0    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.11   12.5   0.0       0.27   11.2   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain


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 ?    4.9   0.0     0.019        31       2      25 ..      23      46 ..      22     132 .. 0.64
   2 !   37.6   1.8   1.3e-12   2.1e-09       7     104 .]     162     261 ..     157     261 .. 0.92
   3 !   53.2   0.0   1.8e-17   2.9e-14       3     103 ..     282     382 ..     280     383 .. 0.94
   4 !   30.7   0.1   1.8e-10   2.9e-07       2     104 .]     407     507 ..     406     507 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.019
                         PAS_9  2 dgilidnpdgrilyaNeaalrllG 25
                                  d i+i+npdg i+y N+ ++ +  
  gi|91772955|ref|YP_565647.1| 23 DNIVIINPDGFITYTNKNWESFAK 46
                                  5688889***788*****998854 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 1.3e-12
                         PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltasp 84 
                                    ++ g+++++Ne +l+++G ++ee+++k++++lf   + ++e n+ +r  +++ +  +  +e+++ +kn e+  +  + + 
  gi|91772955|ref|YP_565647.1| 162 LDTIGNLIFCNEYFLNITGWKKEEIIHKNWFELFvshDIKSEINDMFRTTIKNNS-YPTYYENEILTKNCEKKIIAWNNVV 241
                                   56889*****************************999999999999999999999.9***************9*99999** PP

                         PAS_9  85 vkdddgelvgiivilrDite 104
                                    kd+++++ +i +i +D+te
  gi|91772955|ref|YP_565647.1| 242 NKDQNDKILSISCIGEDVTE 261
                                   *******************8 PP

  == domain 3  score: 53.2 bits;  conditional E-value: 1.8e-17
                         PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                   g + ++ +g+++y+N+ ++ l Gysp+e++gk+++ +    + +e ++  ++++e+g+    + e+ +++kng+tf+ l++
  gi|91772955|ref|YP_565647.1| 282 GSATTDLHGNVTYINDYFAYLHGYSPDELIGKNLSIFHsdGQLEEVHRVNEELMENGS--YTNIEIWHTHKNGTTFPMLMS 360
                                   6677889*******************************98888888889999999999..********************* PP

                         PAS_9  82 aspvkdddgelvgiivilrDit 103
                                   a+ +kd++++ + + +  +Dit
  gi|91772955|ref|YP_565647.1| 361 AVVMKDEGRNPQYLSASAVDIT 382
                                   *********************9 PP

  == domain 4  score: 30.7 bits;  conditional E-value: 1.8e-10
                         PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwvl 79 
                                   dgi+i+  dg ++ yaN++++++  ys+ee++  ++ d++ ++++ +  ++++ +++    ++ ++e+++  ++++t++v+
  gi|91772955|ref|YP_565647.1| 407 DGIIII-QDG-LIkYANRKMIEMSEYSHEELIENPFIDFV-SPKYIEIVKDRYQKRLNGedIPSHYEIEIEANDDRTIPVD 484
                                   899999.9**.999**************************.66666666666666666688******************** PP

                         PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                   l++s +  ++  l +  +ilrDi++
  gi|91772955|ref|YP_565647.1| 485 LSVSIINYQG--LLATMAILRDISD 507
                                   ******5554..66667******95 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1    0.0097        16      12      33 ..      23      44 ..      15      51 .. 0.86
   2 !   25.3   0.1   7.3e-09   1.2e-05       2     112 ..     147     258 ..     146     259 .. 0.80
   3 !   31.7   0.0   7.4e-11   1.2e-07      13     105 ..     282     373 ..     270     381 .. 0.85
   4 !   40.4   0.0   1.5e-13   2.4e-10       2      96 ..     397     490 ..     396     505 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0097
                                  SEEEEEETTSBEEEECHHHHHH CS
                           PAS 12 dpifvvDedgrilyvNaaaeel 33
                                  d i++++ dg i+y+N+++e++
  gi|91772955|ref|YP_565647.1| 23 DNIVIINPDGFITYTNKNWESF 44
                                  5699**************9986 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 7.3e-09
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81 
                                   ++r++le+++   + +D  g+ +++N+ +  ++G++ ee+++k+ ++l++  d   e ++ +++ +++++ ++ +e  + +
  gi|91772955|ref|YP_565647.1| 147 QFRNVLENIRLISITLDTIGNLIFCNEYFLNITGWKKEEIIHKNWFELFVSHDIKsEINDMFRTTIKNNSYPTYYENEILT 227
                                   799********************************************988655446**********999999988888888 PP

                                   TTSSEEEEEEEEEEE.EETTEEEEEEEEEEEE CS
                           PAS  82 rdgrpihlevraspv.rdaggeilgflgvlrd 112
                                    +++++ +  +++ v  d  ++il + +++ d
  gi|91772955|ref|YP_565647.1| 228 -KNCEKKIIAWNNVVnKDQNDKILSISCIGED 258
                                   .5555555554444413444556677777776 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 7.4e-11
                                   EEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEE CS
                           PAS  13 pifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevr 92 
                                   +   +D  g+++y+N+ ++ l G+s++e++gk+l+  i++ d + e + ++ + l ++ + ++ ei+ + ++g+++++++ 
  gi|91772955|ref|YP_565647.1| 282 GSATTDLHGNVTYINDYFAYLHGYSPDELIGKNLS--IFHSDGQlEEVHRVNEELMENGSYTNIEIWHTHKNGTTFPMLMS 360
                                   66779******************************..666666668888888888888999999**9999*********** PP

                                   EEEEEETTEEEEE CS
                           PAS  93 aspvrdaggeilg 105
                                   a+ + d+g ++ +
  gi|91772955|ref|YP_565647.1| 361 AVVMKDEGRNPQY 373
                                   ******9988754 PP

  == domain 4  score: 40.4 bits;  conditional E-value: 1.5e-13
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                   ++++++e+  d+i+++  dg i y+N+++ e+  +s ee++  +++d++++++ ++++++++++l+    ++++ei ++  
  gi|91772955|ref|YP_565647.1| 397 KYSSLVENGNDGIIII-QDGLIKYANRKMIEMSEYSHEELIENPFIDFVSPKYIEIVKDRYQKRLNGEDIPSHYEIEIEAN 476
                                   6899************.**********************************9988************************** PP

                                   TSSEEEEEEEEEEE CS
                           PAS  83 dgrpihlevraspv 96 
                                   d r+i++++ +s +
  gi|91772955|ref|YP_565647.1| 477 DDRTIPVDLSVSII 490
                                   ********998865 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 !  103.3   0.1   6.3e-33     1e-29       2     110 ..     643     752 ..     642     753 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 6.3e-33
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d+++ r+i+ nl++Na+kf++++g+++++  +++d+++isv+D+GiGi  +d+  +f +f q d+st+r++ g+GlGl++v
  gi|91772955|ref|YP_565647.1| 643 DKTKTREILYNLIENAIKFTPSGGHVSIHAIQKDDYVQISVTDTGIGIAHSDIGIIFRPFLQvDSSTTRQYDGVGLGLMLV 723
                                   77889**************88*******9998779********************************************** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                   k++v+l gG+iwv+se g+G+tftftlp+
  gi|91772955|ref|YP_565647.1| 724 KEYVKLQGGDIWVDSELGKGSTFTFTLPM 752
                                   ***************************96 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.1e-08   1.8e-05       2      87 ..     169     254 ..     168     255 .. 0.95
   2 !   23.7   0.0   2.8e-08   4.5e-05       2      85 ..     293     374 ..     292     378 .. 0.91
   3 !   18.0   0.0   1.6e-06    0.0026       3      76 ..     419     491 ..     417     497 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                         PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.pyegeyRirrkdGeyrwveararvirdeng 80 
                                   i+++e + +i+G+ +ee+++k  +w +l    D  +++++ + + +k+++ p   e  i++k+ e   + +  +v +d+n 
  gi|91772955|ref|YP_565647.1| 169 IFCNEYFLNITGWKKEEIIHK--NWFELFVSHDiKSEINDMFRTTIKNNSyPTYYENEILTKNCEKKIIAWNNVVNKDQND 247
                                   89*******************..**********999**************999*******************9999***** PP

                         PAS_3  81 kpvrvig 87 
                                   k++ + +
  gi|91772955|ref|YP_565647.1| 248 KILSISC 254
                                   *998876 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.8e-08
                         PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvirdengk 81 
                                   +y+++ +  + Gysp+el+gk    l++ h +  +e+v +  +e++++g+  ++e+   +k+G+++ +  +a+v++de  +
  gi|91772955|ref|YP_565647.1| 293 TYINDYFAYLHGYSPDELIGK---NLSIFHSDGqLEEVHRVNEELMENGSYTNIEIWHTHKNGTTFPMLMSAVVMKDEGRN 370
                                   699999***************...7889999988999999999*******77***********************999888 PP

                         PAS_3  82 pvrv 85 
                                   p+++
  gi|91772955|ref|YP_565647.1| 371 PQYL 374
                                   8765 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.6e-06
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvir 76 
                                   y+++++ e+  ys eel+++   ++d+v p  +e v++ +q+ l++   p + e+ i   d  ++ v+ ++++i+
  gi|91772955|ref|YP_565647.1| 419 YANRKMIEMSEYSHEELIEN--PFIDFVSPKYIEIVKDRYQKRLNGEDiPSHYEIEIEANDDRTIPVDLSVSIIN 491
                                   899*****************..**********************9888888999999999999999999999994 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0006      0.97       6      89 ..      23     117 ..      18     136 .. 0.67
   2 !    9.0   0.0   0.00097       1.6       2     109 ..     153     263 ..     152     264 .. 0.79
   3 !   29.6   0.0   3.8e-10   6.3e-07       9     109 ..     284     385 ..     277     386 .. 0.92
   4 !    9.8   0.0   0.00058      0.94       5     106 ..     406     506 ..     402     510 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0006
                         PAS_4   6 dalavldpdgrvlyaNaa....aaelfgappeellGktla....ellpee......daarleralrrvlegeepiefleel 72 
                                   d++++++pdg ++y+N++    a +  g++p  +   t +    +   e        a   +  +  v+ g++ i+  e++
  gi|91772955|ref|YP_565647.1|  23 DNIVIINPDGFITYTNKNwesfAKD-NGLDPSKCSEGTNYlkicD---EAngehatGASIEAKGIIDVINGNKDIYKIEYP 99 
                                   8999**************6663333.4444444443333333442...224446766677777788888888888888888 PP

                         PAS_4  73 ll.pgeerhyelrllPlr 89 
                                    + p+e r+++l ++Pl 
  gi|91772955|ref|YP_565647.1| 100 CHsPDEKRWFLLKATPLS 117
                                   778888888888888885 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00097
                         PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegee..piefleelllpgeer 79 
                                   +++  + + ld+ g+ +++N+ +  + g+  ee++ k ++el+  +  + ++ +  r  ++ +   ++++ e+l+ + e +
  gi|91772955|ref|YP_565647.1| 153 ENIRLISITLDTIGNLIFCNEYFLNITGWKKEEIIHKNWFELFVSHdIKSEINDMFRTTIKNNSypTYYENEILTKNCEKK 233
                                   6666777889*******************************8877757888888888777766432555555555588888 PP

                         PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerr 109
                                   ++ ++ +  +d + +++ + +i+ D+Te r
  gi|91772955|ref|YP_565647.1| 234 IIAWNNVVNKDQNDKILSISCIGEDVTEKR 263
                                   888888888888888888888888888877 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 3.8e-10
                         PAS_4   9 avldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPl 88 
                                   a  d +g+v+y+N  +a+l g++p+el+Gk l  ++++++ ++++r  ++++e +     ++ +++ +g + +++++++ +
  gi|91772955|ref|YP_565647.1| 284 ATTDLHGNVTYINDYFAYLHGYSPDELIGKNLSIFHSDGQLEEVHRVNEELMENGSYTNIEIWHTHkNGTTFPMLMSAVVM 364
                                   67899**************************************************99888888888*************** PP

                         PAS_4  89 rdesGevigvlvisrDiTerr 109
                                   +de   ++ + + ++DiT ++
  gi|91772955|ref|YP_565647.1| 365 KDEGRNPQYLSASAVDITHLK 385
                                   985555************765 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00058
                         PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeerhyel 83 
                                   +d+++++  dg + yaN+ + e+  ++ eel+  ++ +++++   + + + +++ l ge+  +  e+     ++++ +++l
  gi|91772955|ref|YP_565647.1| 406 NDGIIII-QDGLIKYANRKMIEMSEYSHEELIENPFIDFVSPKYIEIVKDRYQKRLNGEDIPSHYEIEIEanDDRTIPVDL 485
                                   5666664.6899**********************************************97433322222245788888888 PP

                         PAS_4  84 rllPlrdesGevigvlvisrDiT 106
                                   +++ + + +G  +++++i+rDi+
  gi|91772955|ref|YP_565647.1| 486 SVSII-NYQGL-LATMAILRDIS 506
                                   88777.44454.88888888887 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 !   50.2   0.0   1.2e-16   1.9e-13       2      61 ..     529     590 ..     528     594 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.2e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdl 61 
                                   +++fla+v+HELrtPL+ i+g++++L     g+l+e++k+y   i++++  l+ +v+++ d+
  gi|91772955|ref|YP_565647.1| 529 KTEFLANVSHELRTPLNPIIGFSDILVSGvaGELNEKQKKYALNIKQNGSKLLTIVNRIIDM 590
                                   89************************8888999*************************9986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-05      0.03       1      41 [.     146     187 ..     146     211 .. 0.78
   2 !    7.4   0.0    0.0027       4.5      18      48 ..     287     317 ..     271     338 .. 0.77
   3 !   24.5   0.0   1.2e-08     2e-05       2      48 ..     397     443 ..     396     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                         PAS_8   1 erlralfesspd.giavvd.lgdrivdvNqaalellGys.adlk 41 
                                   +++r+++e+++  +i  +d  g+ ++++N+ +l ++G++ ++++
  gi|91772955|ref|YP_565647.1| 146 QQFRNVLENIRLiSIT-LDtIGN-LIFCNEYFLNITGWKkEEII 187
                                   68999*******8888.554888.*************8854443 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0027
                         PAS_8  18 d.lgdrivdvNqaalellGys.adlkgellgql 48 
                                   d  g+ ++++N+ ++ l Gys ++l+g+ l  +
  gi|91772955|ref|YP_565647.1| 287 DlHGN-VTYINDYFAYLHGYSpDELIGKNL-SI 317
                                   53444.***************999999888.33 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 1.2e-08
                         PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgql 48 
                                   ++ +l+e+ +dgi+++ +g  i ++N++++e+  ys ++l++ ++ ++
  gi|91772955|ref|YP_565647.1| 397 KYSSLVENGNDGIIIIQDGL-IKYANRKMIEMSEYShEELIENPFIDF 443
                                   899***********987666.***************999999998643 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.5e-05     0.024       5      63 ..     159     214 ..     156     222 .. 0.86
   2 !    6.4   0.0    0.0059       9.7       8      67 ..     286     341 ..     283     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                        PAS_11   5 ttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqd.lstlkshlrevissn 63 
                                   +++ld+ g+ i +++  L+    +g++kee++ + +++L+  +d  s++++ +r +i +n
  gi|91772955|ref|YP_565647.1| 159 SITLDTIGNLIFCNEYFLN---ITGWKKEEIIHKNWFELFVSHDiKSEINDMFRTTI-KN 214
                                   5789999********6666...579*******************999********99.33 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0059
                        PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeat 67 
                                    d++g+++ ++       +  g++ +el+g+ +  +++  +l+++++  +e + +ng  t
  gi|91772955|ref|YP_565647.1| 286 TDLHGNVTYIND---YFAYLHGYSPDELIGKNLSIFHSDGQLEEVHRVNEELM-ENGSYT 341
                                   6999********...99*****************9999999******999999.888765 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.4e-05     0.056       9      90 ..     650     739 ..     643     750 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                   HATPase_c_5   9 ilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg............ekkklesskskkeehGiGlksirei 77 
                                   il nl++NAi            +++++ +k++ + is++ +  g              +   s++++ +  G+Gl  ++e 
  gi|91772955|ref|YP_565647.1| 650 ILYNLIENAIKFTPS----GGHVSIHAIQKDDYVQISVTDTGIGiahsdigiifrpFLQVDSSTTRQYDGVGLGLMLVKEY 726
                                   899999999987665....4579999*************99655555555544433226666888999999********** PP

                   HATPase_c_5  78 vkkykgnlsieae 90 
                                   vk  +g+++++ e
  gi|91772955|ref|YP_565647.1| 727 VKLQGGDIWVDSE 739
                                   ********99876 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 ?   11.4   0.0   0.00013      0.21       6      62 ..     650     707 ..     645     722 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                   HATPase_c_3   6 AlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                    l  l++N++    +  +v+i++ +++ +  +i+++D G G+  +++   +r+  +  +
  gi|91772955|ref|YP_565647.1| 650 ILYNLIENAIKftPSGGHVSIHAIQKD-DYVQISVTDTGIGIAHSDIGIIFRPFLQVDS 707
                                   578899999985567788999999986.789***************9888875443333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.27      37     109 ..     648     727 ..     644     729 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                   HATPase_c_2  37 eEactNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetl...pdpteeep......keslkegGrGlalikg 107
                                    E+++N +e a +  p  g+v++++ ++++ ++++v+D G g   +++    +p    +      + + +  G+Gl+l+k+
  gi|91772955|ref|YP_565647.1| 648 REILYNLIENAIKFTPsGGHVSIHAIQKDDYVQISVTDTGIGIAHSDIgiiFRPF---LqvdsstTRQYDGVGLGLMLVKE 725
                                   69**************99******9999999999999998884443320112222...12335445666677777777777 PP

                   HATPase_c_2 108 lv 109
                                   +v
  gi|91772955|ref|YP_565647.1| 726 YV 727
                                   65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 5029.95
//
Query:       gi|91772956|ref|YP_565648.1|  [L=214]
Description: cobalamin B12-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-08   32.6   0.0    1.3e-07   31.6   0.0    1.5  1  B12-binding    B12 binding domain
    7.7e-08   32.7   0.0    1.6e-07   31.7   0.0    1.6  1  B12-binding_2  B12 binding domain
  ------ inclusion threshold ------
      0.052   13.7   0.2       0.11   12.6   0.2    1.6  1  DUF4304        Domain of unknown function (DUF4304)


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.2e-11   1.3e-07       5      95 ..      96     185 ..      93     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.2e-11
                   B12-binding   5 latvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvv 85 
                                   ++t   d h lG+++l   +   gf+ +++g     e+i ++i++ + +v+ +S+l+  q   +ke++e+++ ++ ++kv+
  gi|91772956|ref|YP_565648.1|  96 GITTLEDQHMLGKQILRSLINSTGFNLTDYGSIS-IENIKEKIKSDNIEVLFISTLMLNQALTIKEVTEFIELEKTNTKVI 175
                                   6777889***********************8655.8**********************************999999***** PP

                   B12-binding  86 vGGahpsldp 95 
                                   vGGa++ +d 
  gi|91772956|ref|YP_565648.1| 176 VGGAPFLFDD 185
                                   ****987765 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.7e-11   1.6e-07       4      71 ..      10      78 ..       7      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.7e-11
                 B12-binding_2  4 rlhwaivhgdkegieelideal.aqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkav 71
                                  ++ +a+++ dk  +e ++++ l +++ +   +++ ++ pa++ +G ++++g + l q+ +++++ ++ +
  gi|91772956|ref|YP_565648.1| 10 DFENALLKIDKITAENIVQKELlDAQVDIFNIIDYIISPALESIGHKWENGDIALSQEYMASKITEEII 78
                                  5679**************9888799999**********************************9988776 PP

>> DUF4304  Domain of unknown function (DUF4304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.9e-05      0.11      65     114 ..      33      84 ..       4      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                       DUF4304  65 e.....pkeydcdlrtrieplelgkdklwslyneqeqeelleevseeiekailpi 114
                                   +      +++d+++   +e++    +k+ + +   +qe+++++++eei++ ilp+
  gi|91772956|ref|YP_565648.1|  33 DaqvdiFNIIDYIISPALESIG---HKWENGDIALSQEYMASKITEEIINEILPL 84 
                                   1344457889999999999999...9***************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1488.25
//
Query:       gi|91772957|ref|YP_565649.1|  [L=348]
Description: uroporphyrinogen decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  228.4   0.0    1.4e-67  228.3   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
      0.088   12.6   0.0       0.18   11.6   0.0    1.4  1  DUF4817   Helix-turn-helix domain (DUF4817)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.3   0.0   1.6e-71   1.4e-67       1     346 []       8     341 ..       8     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: 228.3 bits;  conditional E-value: 1.6e-71
                                   ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGG CS
                         URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaeal 81 
                                   t++er+l++l +e++drvP+ l      +     a+  g+s++e++++ e+++e +l  ++++g+D+ + f++ ++e ea 
  gi|91772957|ref|YP_565649.1|   8 TSMERVLTTLGQEEPDRVPYFL------FPNMHGAKELGMSIKEYFSTSENVVEGQLRLREKYGHDCYTPFCYASLEIEAW 82 
                                   689*******************......7777777777******************************************* PP

                                   T-EEEEETTTEEEEE--S-.....GGGS----GGG.G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT-SS- CS
                         URO-D  82 GlevefeegegPvvekpvr.taedveklevpddveegrlpyvleaikllkkelggevpligfvgaPftlasylveGgskgf 161
                                   G +  f e+ + +   p++ ++ed+e le p++ + ++l  vl+++++lk++ g++vp+ig+v++Pf+   + +     gf
  gi|91772957|ref|YP_565649.1|  83 GGSTIFYEDGPANAGAPFIkNIEDIESLEAPSVWDSPQLLKVLKTTEMLKEHAGEDVPIIGVVISPFSAPPMQL-----GF 158
                                   *******************************9986689************************************.....** PP

                                   HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-E CS
                         URO-D 162 ekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkrivdevkaegpkvpv 240
                                   +k++  +y+++e+++kl+++ td++ie+ +aqieagA +i++fD  s++ l+++e ++e  ++  k +++++++     p 
  gi|91772957|ref|YP_565649.1| 159 SKYFDIMYENRELFDKLMEVNTDFCIEWSNAQIEAGATIICYFDpiSSPLLVPKELYKETGYKIEKNVISNLNG-----PT 234
                                   *************************************************************************9.....77 PP

                                   EEEESSHH.H.HHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S-HHHHHHHHHHHHT.T---SSSE CS
                         URO-D 241 ilfikgagae.iledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLl.gspeeiekevkeilekgaggkkgy 319
                                    ++    +a  i++d+a++ga v+      dl+e++++++ ++ ++Gnl+ i  +   + e+ e++vke+++k a++++g+
  gi|91772957|ref|YP_565649.1| 235 AVHLASGTALpIIDDIADAGAAVVCTSAMEDLAEVKAACKGRMSVLGNLNGI-EMRnWTAETAENKVKEAIDK-AAKGGGF 313
                                   77776665555*********************99999**************7.6666***************6.788**** PP

                                   EB-BSS-.--TTS-HHHHHHHHHHHHT- CS
                         URO-D 320 ilnlGhg.ippetppenvkalveavkey 346
                                   il+  hg ip+++p e + a+ +av++y
  gi|91772957|ref|YP_565649.1| 314 ILSDNHGeIPYQVPDEVLIAISNAVRKY 341
                                   ******99******************97 PP

>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.18       9      32 ..      43      66 ..      41      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                       DUF4817  9 VkaYykngesvtatqrafrrrFpn 32
                                  +k+Y+++ e+v++ q ++r+++++
  gi|91772957|ref|YP_565649.1| 43 IKEYFSTSENVVEGQLRLREKYGH 66
                                  89********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2623.85
//
Query:       gi|91772958|ref|YP_565650.1|  [L=563]
Description: ATP-binding region, ATPase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   64.3   0.2    2.9e-17   63.2   0.2    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0036   17.1   0.4       0.01   15.7   0.4    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0069   16.3   0.8      0.029   14.3   0.8    2.1  1  HATPase_c_5  GHKL domain
     0.0081   16.1   0.0      0.015   15.2   0.0    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain


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 !   63.2   0.2   6.5e-21   2.9e-17       9     109 ..     461     556 ..     455     559 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 6.5e-21
                                   HHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHT CS
                     HATPase_c   9 iisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsivkklvelm 88 
                                    i n+v Na  + +ka+++++ i+ ++ +  i ++DnG Gip+++  ++f+  f        ++g tGlGl+ivkk +e++
  gi|91772958|ref|YP_565650.1| 461 TIENIVRNAQIH-GKADNVQIIIEDNKANCIINIKDNGVGIPEKIKTQIFDeGFKY-----GDSGNTGLGLYIVKKTIERY 535
                                   699********9.***********8779**********************987777.....4489***********9999* PP

                                   TTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  89 gGeiwvesepgrGttftftlp 109
                                   +G+i+v++++ +G tf+++lp
  gi|91772958|ref|YP_565650.1| 536 QGTIYVKDNEPKGATFVIELP 556
                                   ******************998 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 !   15.7   0.4   2.3e-06      0.01       9      48 ..     464     503 ..     457     524 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                   HATPase_c_3   9 elvdNs.ldAdaenvkievnknrgktgeivieDdGkGmsee 48 
                                    +v+N+ + ++a nv+i +++n+ ++  i i+D+G G++e+
  gi|91772958|ref|YP_565650.1| 464 NIVRNAqIHGKADNVQIIIEDNK-ANCIINIKDNGVGIPEK 503
                                   689999668************97.7999**********987 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.8   6.4e-06     0.029      14      90 ..     462     544 ..     442     554 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                   HATPase_c_5  14 LdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kkle...sskskkeehGiGlksireivkkykgnlsi 87 
                                   ++N +  ++    +   +++ ++ +k + ii+i+ +  g   ++  +++    +  ++++ G+Gl  +++++++y+g++ +
  gi|91772958|ref|YP_565650.1| 462 IENIVRNAQIHG-KADNVQIIIEDNKANCIINIKDNGVGipeKIkTQIFdegFKYGDSGNTGLGLYIVKKTIERYQGTIYV 541
                                   566555555444.4778888888888889998887755534322222222222357899*******************998 PP

                   HATPase_c_5  88 eae 90 
                                   + +
  gi|91772958|ref|YP_565650.1| 542 KDN 544
                                   766 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.5e-06     0.015      42     112 ..     464     535 ..     461     553 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-06
                   HATPase_c_2  42 NavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDev 112
                                   N+v+ a+ +++ + v++ +e+++  + + ++D+G g  +  + +  +e  + ++  + G+Gl+++k+  + +
  gi|91772958|ref|YP_565650.1| 464 NIVRNAQIHGKADNVQIIIEDNKANCIINIKDNGVGiPEKIKTQIFDEGFKYGDSGNTGLGLYIVKKTIERY 535
                                   999999999999************************655445554555555799************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4204.12
//
Query:       gi|91772959|ref|YP_565651.1|  [L=228]
Description: peroxiredoxin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-31  106.6   0.0    9.7e-31  106.3   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    1.3e-14   53.7   0.3      2e-13   49.9   0.3    2.3  2  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
    4.7e-12   45.8   0.0    6.5e-12   45.4   0.0    1.2  1  Redoxin     Redoxin
     0.0038   17.3   0.1     0.0079   16.3   0.1    1.6  1  P_C10       Protein C10


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 !  106.3   0.0   2.2e-34   9.7e-31       1     123 [.      15     151 ..      15     152 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2.2e-34
                                   TTSB----EEESTTCEEEEC.HHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                      AhpC-TSA   1 vgdkapdfelknadgetvsl.sdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                   +gd ap f++ ++  +++s+ +dykgk+v+lf +p+d++pvCtte   +a + e+f+e++ e+ig+s+ds+++h ++ +++
  gi|91772959|ref|YP_565651.1|  15 IGDIAPTFKVDTTM-GEISFpEDYKGKWVILFSHPADFTPVCTTEFMTFASMQEDFRELNTELIGLSIDSKYAHIAWLRTI 94 
                                   89********9876.777877************************************************************ PP

                                   H.............SSEEEE-TTSHHHHHTT-EETT..TTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  81 s............lnfpllsDeegkvakaygvlkee..kglalratfvidkegkiry 123
                                   +            + fp+++D + +vak +g+++++   + a+ra+f+ d+e k+r+
  gi|91772959|ref|YP_565651.1|  95 KekieykgmknveVLFPVIADIKMEVAKMFGMVQPNasDNQAVRAVFIMDPEAKVRA 151
                                   ***********************************9*99****************97 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 ?    1.4   0.0     0.066     3e+02      23      35 ..     126     138 ..     125     141 .. 0.86
   2 !   49.9   0.3   4.5e-17     2e-13       1      38 [.     172     209 ..     172     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.066
                                   EE---SSHHHHHH CS
                    1-cysPrx_C  23 ivpPpateedavk 35 
                                   +v+P a++++av 
  gi|91772959|ref|YP_565651.1| 126 MVQPNASDNQAVR 138
                                   9********9985 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 4.5e-17
                                   HHHHHHHHT-BB-TTT.TBT-EEE---SSHHHHHHHHH CS
                    1-cysPrx_C   1 ALQladkhgvatPAnWkpGdkvivpPpateedavkryl 38 
                                   A+Q +dk+++atPAnW+pGd+vi+pPp ++  a++r++
  gi|91772959|ref|YP_565651.1| 172 AMQKSDKENIATPANWNPGDDVIIPPPGSCGAAKERVE 209
                                   89*****************************9999986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.5e-15   6.5e-12       3     136 ..      16     158 ..      14     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.5e-15
                                   TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH....HHH CS
                       Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf....vke 78 
                                   gd aP+f+    +t   ++s  e +kgk v++++ p+ f+P+C++e   ++  +e ++e + + +++++d+         +
  gi|91772959|ref|YP_565651.1|  16 GDIAPTFKV---DTTMGEISFPEdYKGKWVILFSHPADFTPVCTTEFMTFASMQEDFRELNTELIGLSIDSKYAhiawL-R 92 
                                   788999995...466666777666**********************************************998866641.2 PP

                                   HHHH............TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSSC CS
                       Redoxin  79 fwgk............eglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepep 136
                                                    ++ fpv++D + +++k++G  + +++++   + +++++ d + kv+++ + p +
  gi|91772959|ref|YP_565651.1|  93 ---TikekieykgmknVEVLFPVIADIKMEVAKMFG--MVQPNASDnQAVRAVFIMDPEAKVRAILYYPLS 158
                                   ...24446777888777888999*************..5566555558**************998766655 PP

>> P_C10  Protein C10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.8e-06    0.0079      24      62 ..      89     127 ..      79     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                         P_C10  24 akleeakesagndmlkvmqlvlPvvvqiqmevikkyGFa 62 
                                   a l  +ke+++   +k +++++Pv+++i+mev k +G  
  gi|91772959|ref|YP_565651.1|  89 AWLRTIKEKIEYKGMKNVEVLFPVIADIKMEVAKMFGMV 127
                                   56788999999999***********************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1678.54
//
Query:       gi|91772960|ref|YP_565652.1|  [L=331]
Description: methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-61  207.3   0.6    2.8e-61  206.7   0.6    1.2  1  Met_10           Met-10+ like-protein
    4.2e-13   48.9   0.6    4.2e-13   48.9   0.6    1.8  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    5.2e-07   29.2   0.1    7.9e-07   28.6   0.1    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.5e-06   27.8   0.1    2.5e-06   27.2   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.9e-06   27.5   0.1    3.4e-06   26.7   0.1    1.4  1  MTS              Methyltransferase small domain
    2.4e-05   24.9   0.0    6.3e-05   23.6   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
    6.8e-05   22.0   0.0    0.00011   21.4   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0006   19.5   0.0      0.001   18.7   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00091   19.0   0.1     0.0014   18.5   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
      0.001   18.2   0.0     0.0017   17.5   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0052   16.2   0.3     0.0095   15.4   0.3    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0057   16.6   0.0      0.011   15.8   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0086   15.7   0.0      0.015   14.9   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.036   14.1   0.4      0.062   13.3   0.4    1.3  1  DUF3867          Protein of unknown function (DUF3867)
      0.044   13.7   0.1       0.12   12.3   0.1    1.7  1  Methyltransf_18  Methyltransferase domain
      0.057   13.1   0.1      0.097   12.3   0.1    1.3  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
       0.11   12.3   2.3        0.2   11.4   2.3    1.4  1  PTP_N            Protein tyrosine phosphatase N terminal
       0.11   11.9   0.0       0.17   11.3   0.0    1.2  1  TehB             Tellurite resistance protein TehB
       0.16   11.3   0.0       0.25   10.6   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G


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 !  206.7   0.6     3e-64   2.8e-61       2     199 .]      84     278 ..      83     278 .. 0.97

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 3e-64
                                   EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS CS
                        Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskv 81 
                                   ++e++Gd+++++ +e + e    ig+++l+++ +vktvl   s vegefRt+++ v+aG+++t t+hk++gc++++D+s+ 
  gi|91772960|ref|YP_565652.1|  84 SYEVVGDIALIEADEPAAE---NIGKALLEVHhHVKTVLGAASAVEGEFRTRRFTVIAGDGRTDTVHKDHGCNYHVDLSRA 161
                                   69*********99876665...9*********9************************************************ PP

                                   ---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG CS
                        Met_10  82 yfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgre 162
                                   yf ++l++Er+r++++++  +vVvd+fAG+Gp++ipiak  k k+v+a+d+nP+++++lken+ lN v++ +++i++D++e
  gi|91772960|ref|YP_565652.1| 162 YFTPRLSTERQRIVSQINGEDVVVDMFAGVGPYSIPIAK--KCKMVIAMDKNPDAIHFLKENVILNSVDN-IEVIEGDANE 239
                                   ***************************************..9**************************87.67******** PP

                                   ---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                        Met_10 163 vir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                   ++r  e + d+v+mnlp+sa  Fld+++ +   ggvihy
  gi|91772960|ref|YP_565652.1| 240 IVRnyEGMGDHVIMNLPHSADAFLDAAVFVTASGGVIHY 278
                                   ***9999*******************************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 !   48.9   0.6   4.5e-16   4.2e-13       1      46 [.       5      50 ..       5      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 4.5e-16
                                  EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--HHH CS
                        Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepegy 46
                                  ci +pk++gE++Rk+ le++lLd+++KI s d  +++P+ ++ +++
  gi|91772960|ref|YP_565652.1|  5 CILIPKNKGEPARKVILELDLLDKGLKIVSVDTDIFLPLFRKLSSE 50
                                  ***************************************9998876 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   8.3e-10   7.9e-07      51     149 ..     182     276 ..     152     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 8.3e-10
                                   EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS- CS
                           TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGs 131
                                     v+d +++ G  +i  a+     k v+a D ++ A++ +keNv ln+v++i vi+  dAn ++++ +   d++ +    s
  gi|91772960|ref|YP_565652.1| 182 DVVVDMFAGVGPYSIPIAKK---CKMVIAMDKNPDAIHFLKENVILNSVDNIEVIEG-DANEIVRNYEGMGDHVIMNLPHS 258
                                   34889999999999999987...8899************************655555.*******9999999998987789 PP

                                   -GGGHHHHHHHEEEEEEE CS
                           TRM 132 papfldsavqsvkekglL 149
                                   +  fld+av   +++g++
  gi|91772960|ref|YP_565652.1| 259 ADAFLDAAVFVTASGGVI 276
                                   9*********99998876 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   2.7e-09   2.5e-06       3      80 ..     183     256 ..     181     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.7e-09
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                   v++D+f+G G  +i +a++ + via+++n++ +   ++N  +    d+i ++ gd +e++++ +      d v++  P
  gi|91772960|ref|YP_565652.1| 183 VVVDMFAGVGPYSIPIAKKCKMVIAMDKNPDAIHFLKENVILN-SVDNIEVIEGDANEIVRNYEGM---GDHVIMNLP 256
                                   79*************************************9776.7799***********9985432...345555555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   3.6e-09   3.4e-06      32     110 ..     181     260 ..     152     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.6e-09
                                   CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEEEE---STT CS
                           MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdlivsNPPfha 109
                                   ++ v+D+ +G+G+ ++ +ak+++   v ++d++  A+++ ken+  n ++ +ev++ d+ e v   e+  d++++N P  a
  gi|91772960|ref|YP_565652.1| 181 EDVVVDMFAGVGPYSIPIAKKCKM--VIAMDKNPDAIHFLKENVILNSVDnIEVIEGDANEIVRnyEGMGDHVIMNLPHSA 259
                                   4459****************9999..99***********************9**9999988877445889******99665 PP

                                   T CS
                           MTS 110 g 110
                                   +
  gi|91772960|ref|YP_565652.1| 260 D 260
                                   5 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   6.7e-08   6.3e-05       1      94 [.     184     271 ..     184     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.7e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS.SSTTTEEEEEEESTGGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp.fedgsfDlvvssgalhhlsd 79 
                                   v+d+ +G G +++ +ak++  + v+++D +++++   +e++  +++ n+e+++gda+++    +g  D v+++  l h   
  gi|91772960|ref|YP_565652.1| 184 VVDMFAGVGPYSIPIAKKC--KMVIAMDKNPDAIHFLKENVILNSVdNIEVIEGDANEIVrNYEGMGDHVIMN--LPHSA- 259
                                   899***************9..9*******************99999**********99651677789999995..55533. PP

                                   HHHHHHHHHHHHHEE CS
               Methyltransf_25  80 edlekalkeiarvLk 94 
                                      +++l+ +  v+ 
  gi|91772960|ref|YP_565652.1| 260 ---DAFLDAAVFVTA 271
                                   ...355555555555 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 !   21.4   0.0   1.1e-07   0.00011     203     267 ..     182     246 ..     171     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
               tRNA_U5-meth_tr 203 gdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeeltealkk 267
                                   + +++++ G G +s+++a++ + v+a +    ++++ + n+  n++dn+++i   a+e+ + +++
  gi|91772960|ref|YP_565652.1| 182 DVVVDMFAGVGPYSIPIAKKCKMVIAMDKNPDAIHFLKENVILNSVDNIEVIEGDANEIVRNYEG 246
                                   34679***************************************************999888776 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-06     0.001      42     125 ..     181     259 ..     171     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                                   C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--S CS
                 Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPP 122
                                   +  v+D+faG G  ++  +  ++k +++++k++ a++ lken+    +++ ++++  da e +++     +  d v ++ P
  gi|91772960|ref|YP_565652.1| 181 EDVVVDMFAGVGPYSI-PIAKKCKMVIAMDKNPDAIHFLKENVILNSVDN-IEVIEGDANEIVRNYE---GMGDHVIMNLP 256
                                   34589***********.599***********************9988776.8888888888776652...33355655555 PP

                                   SST CS
                 Cons_hypoth95 123 yak 125
                                     +
  gi|91772960|ref|YP_565652.1| 257 HSA 259
                                   555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.4e-06    0.0014       3      81 ..     180     254 ..     178     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                    + +v+D  +G G +++ +a++    ++ v+  D +++ai + +en   + +dn+e+ +gd++e+  ++e    D ++ n
  gi|91772960|ref|YP_565652.1| 180 GEDVVVDMFAGVGPYSIPIAKK----CKmVIAMDKNPDAIHFLKENVILNSVDNIEVIEGDANEIVRNYE-GMGDHVIMN 254
                                   56789***************54....333***********************************775566.455555555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0017      23      85 ..     175     237 ..     169     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                   HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                        RrnaAD  23 ldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                                   +++  ++ ++ v+++ +G+G  + ++ak +k v ++ + ++ + +l++++   +  +++v++ D+
  gi|91772960|ref|YP_565652.1| 175 VSQ--INGEDVVVDMFAGVGPYSIPIAKKCKMVIAMDKNPDAIHFLKENVIlnSVDNIEVIEGDA 237
                                   544..55789**************************************98877899******997 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3     1e-05    0.0095     158     255 ..     177     275 ..     169     286 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                          PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva.lseellk..eekadvivaNIL 235
                                   ++++++ v+D+ +G G  +i  ak   k v+a+D ++ A++  keN+ lN+v++   +   ++e+++  e+  d ++ N L
  gi|91772960|ref|YP_565652.1| 177 QINGEDVVVDMFAGVGPYSIPIAK-KCKMVIAMDKNPDAIHFLKENVILNSVDNIEVIEgDANEIVRnyEGMGDHVIMN-L 255
                                   567788999***********9999.6899***********************996644323344443455667888888.4 PP

                          PrmA 236 aevlielaedikklvkeggl 255
                                    +    +++ +  + ++gg+
  gi|91772960|ref|YP_565652.1| 256 PHSADAFLDAAVFVTASGGV 275
                                   45555555555555555555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05     0.011       1      96 [.     190     286 ..     190     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET....TTCHHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHH CS
                    ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny....keadlverikeltg.gegvdvvfecvGsgatleaal 76 
                                   gvG + + +Ak ++  via+d +++ + ++k++     +++    +  d +e ++   g g+ v   + +++  a l+aa+
  gi|91772960|ref|YP_565652.1| 190 GVGPYSIPIAKKCK-MVIAMDKNPDAIHFLKENVILNSVDNieviEG-DANEIVRNYEGmGDHVIMNLPHSA-DAFLDAAV 267
                                   56666666666544.69***************977777777776555.899999999854444555555666.9999**** PP

                                   HCEEEEEEEEECSCTSSEEE CS
                    ADH_zinc_N  77 kllkpgGrlvvvGggkgeee 96 
                                    +++ gG + ++G+ ++ ++
  gi|91772960|ref|YP_565652.1| 268 FVTASGGVIHYYGMTHE-DD 286
                                   *************7444.33 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.6e-05     0.015       8      95 ..     180     263 ..     174     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                   TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE- CS
               Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaP 88 
                                    e+ ++D+ a+ G        + k+ + v+A+d+n   ++ ++en+   +v n+ v+e+Da++i +   g + D++++  P
  gi|91772960|ref|YP_565652.1| 180 GEDVVVDMFAGVGPYSI---PIAKKCKMVIAMDKNPDAIHFLKENVILNSVDNIEVIEGDANEIVRNYEG-MGDHVIMNLP 256
                                   56778888888886554...45577899*******************99***************998887.89******** PP

                                   -CCGGGT CS
               Methyltr_RsmB-F  89 Csgtgvi 95 
                                    s+   +
  gi|91772960|ref|YP_565652.1| 257 HSADAFL 263
                                   9997655 PP

>> DUF3867  Protein of unknown function (DUF3867)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   6.6e-05     0.062     121     167 ..     202     248 ..     194     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-05
                       DUF3867 121 ieykikndkndlkilleeenvilisekkidlsDeelnefllsYkkvl 167
                                    ++ i  dkn   i + +envil s ++i++ + + ne++ +Y  + 
  gi|91772960|ref|YP_565652.1| 202 CKMVIAMDKNPDAIHFLKENVILNSVDNIEVIEGDANEIVRNYEGMG 248
                                   56789999***********************************9876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00013      0.12       6      91 ..     172     247 ..     166     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
               Methyltransf_18   6 kaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtv 86 
                                   ++i+s ++ +++v+D  +  g  +i ++  +k+k via+D n+ +++  ken+  +++ d+iev+ +d  e +++ e    
  gi|91772960|ref|YP_565652.1| 172 QRIVSQINGEDVVVDMFAGVGPYSIPIA--KKCKMVIAMDKNPDAIHFLKENVILNSV-DNIEVIEGDANEIVRNYE---- 245
                                   5677788877788888777776666666..79999******************99888.78******9988887665.... PP

               Methyltransf_18  87 viaGm 91 
                                      Gm
  gi|91772960|ref|YP_565652.1| 246 ---GM 247
                                   ...33 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1    0.0001     0.097      11      66 ..     173     227 ..     169     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                   HHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHH.HHCCHSH CS
               MethyltransfD12  11 eIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlyk.aliknnv 66 
                                    I+++i   +++++v+ FaG g  ++ + k+ k v++ D n+d i + k ++i n+v
  gi|91772960|ref|YP_565652.1| 173 RIVSQIN--GEDVVVDMFAGVGPYSIPIAKKCKMVIAMDKNPDAIHFLKeNVILNSV 227
                                   5778888..899**********************************99823555533 PP

>> PTP_N  Protein tyrosine phosphatase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.3   0.00021       0.2       9      18 ..     261     270 ..     259     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                         PTP_N   9 AFLDteVfVt 18 
                                   AFLD++VfVt
  gi|91772960|ref|YP_565652.1| 261 AFLDAAVFVT 270
                                   9********9 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.17      33      97 ..     183     245 ..     157     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                   EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EE CS
                          TehB  33 kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderyd 97 
                                    v+d+  g g  s+ ++ +   v a+dkn ++i fl+e    ++++ni+    d ne  + ++y+
  gi|91772960|ref|YP_565652.1| 183 VVVDMFAGVGPYSIPIAKKCKMVIAMDKNPDAIHFLKENVILNSVDNIEVIEGDANE--IVRNYE 245
                                   4789999********************************999999999887777775..556665 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00027      0.25      46     165 ..     179     296 ..     166     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                                   -CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC..TTTTT-EEEEEEC-S CS
                          GidB  46 kekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee..kqeeekydvvtsRAl 124
                                   + ++  v+D  +G G  +ip+a  ++ + ++ ++++   i+FL+e +    ++n+e++e +a+e  ++ e   d v++  l
  gi|91772960|ref|YP_565652.1| 179 NGED-VVVDMFAGVGPYSIPIA--KKCKMVIAMDKNPDAIHFLKENVILNSVDNIEVIEGDANEivRNYEGMGDHVIMN-L 255
                                   4444.49999999999999975..66677889********************************644444555555553.3 PP

                                   SSHHHHHHHHCCCEEEEEEEEEEESS--HHHHHCCHCCCCC CS
                          GidB 125 aslnelteillkllkegglilalKGksaedeleekekalql 165
                                    +  + +  +  ++   g ++++ G ++ed+l     +l++
  gi|91772960|ref|YP_565652.1| 256 PHSADAFLDAAVFVTASGGVIHYYGMTHEDDLYDGSIKLIS 296
                                   33333333334456666777777777777777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2452.92
//
Query:       gi|91772961|ref|YP_565653.1|  [L=205]
Description: lysine exporter protein LysE/YggA [Methanococcoides burtonii DSM 6242]
Scores for complete 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  108.9  15.5    2.4e-31  108.7  15.5    1.0  1  LysE             LysE type translocator
  ------ inclusion threshold ------
        2.9    8.0   8.7         14    5.7   0.0    3.4  4  Phage_holin_2_1  Bacteriophage P21 holin S


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 !  108.7  15.5   2.7e-35   2.4e-31       2     191 ..      19     204 ..      18     205 .] 0.95

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2.7e-35
                          LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrdak 82 
                                   +++l pGp ++++++  +k+g+++g  v lg++i + v ++l+l+Gl +L+ +++  +++++++Gg+ L+ +gv+++  a 
  gi|91772961|ref|YP_565653.1|  19 TGALVPGPMLFVTIDGTLKKGWRAGPEVFLGHAIIETVVLVLILFGLTALIGESE--MAFISVAGGLALVVFGVMTIMGAR 97 
                                   689*************************************************555..56799******************* PP

                          LysE  83 ekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaflaarlsr 163
                                   +++   + +++ + +++  +g+++s sNP++ ++wl+ +sal+ + ++ g+ ++l++ +g+++a+l wf+ ++++++r + 
  gi|91772961|ref|YP_565653.1|  98 KTSYDPKTQDK-VQSNSLVAGIVTSASNPYFWIWWLAAGSALVLESYKIGMVAVLFFIIGHWLADLGWFTAVSLSFSRGRG 177
                                   ***98888887.99******************************99*********************************** PP

                          LysE 164 rlsskkvlriinvvvgvlligfavklll 191
                                    +s++ ++  i v +g++li+f+  +++
  gi|91772961|ref|YP_565653.1| 178 MFSQRAYK-QILVACGIFLILFGGWFAI 204
                                   *****877.999***********98876 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.0    0.0023        20      23      48 ..      65      93 ..      57      95 .. 0.70
   2 ?    5.7   0.0    0.0016        14      40      56 ..     113     129 ..     111     136 .. 0.87
   3 ?   -3.1   0.1      0.92   8.2e+03      35      45 ..     145     155 ..     144     162 .. 0.70
   4 ?   -0.8   0.0      0.17   1.6e+03       5      19 ..     166     180 ..     164     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0023
               Phage_holin_2_1 23 lldklspeeWsaigvlggl...vigllTy 48
                                  l + +  +e ++i+v+ggl   v+g++T+
  gi|91772961|ref|YP_565653.1| 65 LTALIGESEMAFISVAGGLalvVFGVMTI 93
                                  55566778999******973225666665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0016
               Phage_holin_2_1  40 glvigllTyltnlYFKr 56 
                                   +lv g++T ++n YF +
  gi|91772961|ref|YP_565653.1| 113 SLVAGIVTSASNPYFWI 129
                                   89*************77 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.92
               Phage_holin_2_1  35 igvlgglvigl 45 
                                   ig+++ l++++
  gi|91772961|ref|YP_565653.1| 145 IGMVAVLFFII 155
                                   77788777765 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.17
               Phage_holin_2_1   5 tgvsYgaSggsigyw 19 
                                   t+vs+ +S g +++ 
  gi|91772961|ref|YP_565653.1| 166 TAVSLSFSRGRGMFS 180
                                   778888888877553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1548.31
//
Query:       gi|91772962|ref|YP_565654.1|  [L=337]
Description: transcription initiation factor IIB [Methanococcoides burtonii DSM 6242]
Scores for complete 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-45  150.8   1.1    2.2e-21   75.7   0.3    2.3  2  TFIIB            Transcription factor TFIIB repeat
    7.1e-17   60.6   1.8    7.1e-17   60.6   1.8    1.7  2  TF_Zn_Ribbon     TFIIB zinc-binding
    3.6e-05   23.2   0.5      0.019   14.4   0.1    3.2  2  Sigma70_r4       Sigma-70, region 4
     0.0005   19.9   0.4     0.0015   18.4   0.4    1.8  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.01   16.2   1.4      0.085   13.2   0.4    2.7  3  Lar_restr_allev  Restriction alleviation protein Lar
      0.016   15.0   0.9      0.057   13.3   0.2    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.024   15.2   0.1        1.8    9.2   0.0    2.4  2  RPA_interact_C   Replication protein A interacting C-terminal
      0.049   13.7   0.0        8.4    6.5   0.0    2.4  2  Cyclin_C         Cyclin, C-terminal domain
      0.071   13.1   1.0       0.77    9.8   0.7    2.5  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.077   13.0   1.0       0.41   10.7   0.3    2.2  2  DZR              Double zinc ribbon
      0.078   13.0   0.6      0.078   13.0   0.6    1.9  2  Elf1             Transcription elongation factor Elf1 like
      0.088   12.2   2.5       0.71    9.4   2.5    2.3  1  zf-ribbon_3      zinc-ribbon domain
       0.16   11.9   0.1        3.2    7.7   0.1    2.3  2  DUF3797          Domain of unknown function (DUF3797)
       0.19   12.1   4.0        7.7    6.9   0.1    3.3  3  HTH_31           Helix-turn-helix domain
       0.22   11.2   4.5        0.3   10.8   0.1    2.9  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.22   11.7   1.8        2.5    8.3   0.7    2.3  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.74   10.0   6.1       0.99    9.6   0.5    3.1  3  Zn-ribbon_8      Zinc ribbon domain
       0.99    9.6   3.5         25    5.0   2.0    3.3  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.2    9.1   5.6       0.53   10.2   1.2    2.7  2  Nudix_N_2        Nudix N-terminal
        2.5    8.4   6.8        3.1    8.1   0.1    2.8  2  Methyltransf_13  Putative zinc binding domain
        4.5    7.2   5.2         19    5.2   0.2    3.0  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


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 !   75.7   0.3   2.5e-24   2.2e-21       2      71 .]     157     226 ..     156     226 .. 0.98
   2 !   73.8   0.0   9.8e-24   8.4e-21       1      71 []     250     320 ..     250     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 2.5e-24
                                   HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    r+a+al+Lp +V++ A  ++++a++++++ Grs +g+aAA+ly Acr++ v rt+ ei +v++Vs k+i
  gi|91772962|ref|YP_565654.1| 157 DRMASALGLPRTVRETAAVVYRKAVDKNLIRGRSIEGVAAAALYAACRQCSVPRTLDEIGEVSRVSRKEI 226
                                   69*****************************************************************997 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 9.8e-24
                                   HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   ++rf++ l+L+ +V+++ +e++++a+e+++++Gr p+g+aAA++yiA+ +++++rtq+e+++v+ V+e+ti
  gi|91772962|ref|YP_565654.1| 250 VPRFCSGLNLKGEVQSRGVEILRQASEKELTSGRGPTGVAAAAIYIASILCGERRTQREVADVAGVTEVTI 320
                                   689******************************************************************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 !   60.6   1.8   8.3e-20   7.1e-17       3      43 .]      41      81 ..      39      81 .. 0.98
   2 ?   -3.5   0.1       9.4     8e+03       3      10 ..     203     210 ..     202     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 8.3e-20
                                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                  CP+Cgs++l+ D+er+elvC dCGlV++ + +degpewr+f
  gi|91772962|ref|YP_565654.1| 41 CPECGSRSLEQDYERAELVCADCGLVVDAEFVDEGPEWRAF 81
                                  ***************************************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.4
                                   ETTTTCEE CS
                  TF_Zn_Ribbon   3 CPnCgstn 10 
                                   C  C+ ++
  gi|91772962|ref|YP_565654.1| 203 CRQCSVPR 210
                                   89998875 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.014        12      20      36 ..     209     225 ..     204     237 .. 0.90
   2 !   14.4   0.1   2.3e-05     0.019      18      43 ..     301     326 ..     292     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                                   T--HHHHHHHHTS-HHH CS
                    Sigma70_r4  20 glTleEIgerlgiSrer 36 
                                   ++Tl EIge+  +Sr  
  gi|91772962|ref|YP_565654.1| 209 PRTLDEIGEVSRVSRKE 225
                                   79*********999965 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.3e-05
                                   TTT--HHHHHHHHTS-HHHHHHHHHH CS
                    Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekr 43 
                                   ge +T+ E++++ g+++ ++r + k+
  gi|91772962|ref|YP_565654.1| 301 GERRTQREVADVAGVTEVTIRNRYKE 326
                                   7899*******************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 !   18.4   0.4   1.7e-06    0.0015      29      60 ..      39      71 ..      17      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfeadrDv 60
                                   +C+eCgs++ e + ++ +++C +Cg++ d+ +
  gi|91772962|ref|YP_565654.1| 39 VECPECGSRSLEqDYERAELVCADCGLVVDAEF 71
                                  68*******999899***************975 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4    0.0001     0.085       4      45 ..      39      75 ..      25      86 .. 0.77
   2 ?    0.4   0.0       1.1     9e+02      27      36 ..     193     208 ..     166     226 .. 0.68
   3 ?   -2.4   0.0       7.6   6.5e+03       9      28 ..     254     292 ..     253     313 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
               Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga.stpwfkiae 45
                                    CP Cg+r   +  +r          CadCg  +  +f  ++
  gi|91772962|ref|YP_565654.1| 39 VECPECGSRSLEQDYERA------ELVCADCGLvVDAEFVDEG 75
                                  58*******876666555......58******96555555544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
               Lar_restr_allev  27 q......cvyCadCga 36 
                                          + +C +C +
  gi|91772962|ref|YP_565654.1| 193 GvaaaalYAACRQCSV 208
                                   1444555999**9*98 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.6
               Lar_restr_allev   9 Cggravlersqrvvaeigq...................c 28 
                                   C g + +++ q++  ei                      
  gi|91772962|ref|YP_565654.1| 254 CSGLNLKGEVQSRGVEILRqasekeltsgrgptgvaaaA 292
                                   555555555555554444333333333333444333341 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.9   3.3e+03      19      36 ..     211     228 ..     208     231 .. 0.63
   2 ?   13.3   0.2   6.7e-05     0.057      17      41 ..     303     327 ..     301     328 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.9
                 HTH_AsnC-type  19 syaeLAervGlSestvlr 36 
                                   +  e++e   +S+ ++ r
  gi|91772962|ref|YP_565654.1| 211 TLDEIGEVSRVSRKEIGR 228
                                   556777766666666655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.7e-05
                 HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                   R++ +e+A+  G++e t+++R++ L
  gi|91772962|ref|YP_565654.1| 303 RRTQREVADVAGVTEVTIRNRYKEL 327
                                   99********************988 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 ?    9.2   0.0    0.0021       1.8       2      27 ..      41      69 ..      40     116 .. 0.83
   2 ?    3.6   0.0      0.12     1e+02      65      78 ..     195     208 ..     180     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlet 27
                                  CP C +r+l+++     ++C+ Cgl ++ 
  gi|91772962|ref|YP_565654.1| 41 CPECGSRSLEQDYerAELVCAdCGLVVDA 69
                                  **********9653477***99**98877 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                RPA_interact_C  65 gveaLlaeCeeCdf 78 
                                     +aL+a C++C++
  gi|91772962|ref|YP_565654.1| 195 AAAALYAACRQCSV 208
                                   5689********97 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.042        36      47      87 ..     194     234 ..     191     244 .. 0.86
   2 ?    6.5   0.0    0.0099       8.4      47      88 ..     288     329 ..     283     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                                   HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHH CS
                      Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelil 87 
                                   +Aaaal++a+++ + p   +++ +++++s +++   ++ i 
  gi|91772962|ref|YP_565654.1| 194 VAAAALYAACRQCSVPRTLDEIGEVSRVSRKEIGRTYRFIS 234
                                   7***********99999999999999999988888777775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0099
                                   HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                      Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                   +Aaaa+++a+   ++   ++++  + g+++  +++ ++ ++e
  gi|91772962|ref|YP_565654.1| 288 VAAAAIYIASILCGERRTQREVADVAGVTEVTIRNRYKELAE 329
                                   8***********9**********************9999987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7    0.0009      0.77      63      93 ..      31      64 ..      12      76 .. 0.76
   2 ?    0.6   0.0      0.65   5.6e+02      47      78 ..     176     208 ..     144     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0009
                                  EEEEE--EEEETTTS-EEECHH..H.HHS-TTTS CS
                          HypA 63 eieevpvkvrCreCgkefelee..k.alrCpkCg 93
                                  + e ++ +v+C eCg++  +++  + +l C +Cg
  gi|91772962|ref|YP_565654.1| 31 TTEVENKVVECPECGSRSLEQDyeRaELVCADCG 64
                                  4677788899999998887555443678999998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.65
                                   HHHHHHCC.TTTT-EEE.EEEE--EEEETTTS- CS
                          HypA  47 afellaegtvlegaeLe.ieevpvkvrCreCgk 78 
                                   +++ + ++++++g ++e +    + + Cr+C+ 
  gi|91772962|ref|YP_565654.1| 176 VYRKAVDKNLIRGRSIEgVAAAALYAACRQCSV 208
                                   555555555666666554556667778888864 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00048      0.41      10      41 ..      36      70 ..      31      72 .. 0.74
   2 ?   -0.2   0.0       1.2     1e+03      30      35 ..     202     207 ..     188     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                           DZR 10 pdarfCseCgtk.lkavaa..edrCpsCgekvdpe 41
                                  ++   C+eCg++ l++  +  e +C  Cg  vd+e
  gi|91772962|ref|YP_565654.1| 36 NKVVECPECGSRsLEQDYEraELVCADCGLVVDAE 70
                                  55567*****9965543337899*****9988876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                           DZR  30 rCpsCg 35 
                                   +C +C+
  gi|91772962|ref|YP_565654.1| 202 ACRQCS 207
                                   566665 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   9.1e-05     0.078       6      56 ..      23      68 ..      14      75 .. 0.79
   2 ?   -2.4   0.1       6.1   5.2e+03      46      53 ..     201     208 ..     196     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-05
                          Elf1  6 kakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                  ka k+k+k+++  +++ +Cp C++      +l++  ++ae+ C  Cg+ ++
  gi|91772962|ref|YP_565654.1| 23 KARKEKEKTTEVENKVVECPECGSR-----SLEQDYERAELVCADCGLVVD 68
                                  5555666767768999*********.....89999999********98665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.1
                          Elf1  46 vsCkvCge 53 
                                   + C++C+ 
  gi|91772962|ref|YP_565654.1| 201 AACRQCSV 208
                                   67888875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5   0.00084      0.71       3      24 ..      39      65 ..      37      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00084
                   zf-ribbon_3  3 vrCPnCGa.plssd....dnvCpyCGt 24
                                  v+CP+CG+  l+ d      vC+ CG 
  gi|91772962|ref|YP_565654.1| 39 VECPECGSrSLEQDyeraELVCADCGL 65
                                  89******9998775555678999987 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   0.1    0.0037       3.2       6      21 ..      31      46 ..      28      52 .. 0.84
   2 ?    1.3   0.0      0.37   3.1e+02      13      34 ..     200     222 ..     190     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0037
                       DUF3797  6 ivkLdekYvqCPeCgN 21
                                  + + ++k v CPeCg 
  gi|91772962|ref|YP_565654.1| 31 TTEVENKVVECPECGS 46
                                  6788999*******96 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.37
                       DUF3797  13 YvqCPeCgNnkvlNsegkv.iie 34 
                                   Y++C +C   + l   g+v +++
  gi|91772962|ref|YP_565654.1| 200 YAACRQCSVPRTLDEIGEVsRVS 222
                                   *******9988888888887776 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     0.053        45      44      62 ..     153     171 ..     131     174 .. 0.82
   2 ?   -0.6   0.1         2   1.7e+03      16      33 ..     211     228 ..     187     234 .. 0.77
   3 ?    6.9   0.1     0.009       7.7      14      32 ..     303     321 ..     269     322 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.053
                        HTH_31  44 pavlealaralgldpaera 62 
                                   ++ l+++a algl++  r+
  gi|91772962|ref|YP_565654.1| 153 LSELDRMASALGLPRTVRE 171
                                   5799**********88776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                        HTH_31  16 sqeevAerlgvsestlsr 33 
                                   +++e +e ++vs+  ++r
  gi|91772962|ref|YP_565654.1| 211 TLDEIGEVSRVSRKEIGR 228
                                   667777777788777766 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.009
                        HTH_31  14 GLsqeevAerlgvsestls 32 
                                   + +q+evA+ +gv+e t++
  gi|91772962|ref|YP_565654.1| 303 RRTQREVADVAGVTEVTIR 321
                                   78************99986 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00036       0.3      15      28 ..      36      49 ..      28      49 .. 0.80
   2 ?    0.6   0.1      0.52   4.5e+02       3       7 ..      60      64 ..      58      69 .. 0.78
   3 ?   -2.2   0.1         4   3.4e+03      20      23 ..     203     206 ..     202     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                                  SS----SSS----- CS
                DNA_RNApol_7kD 15 gdpiRCkeCGhRil 28
                                  + ++ C eCG+R+l
  gi|91772962|ref|YP_565654.1| 36 NKVVECPECGSRSL 49
                                  569*********97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.52
                                  -SSS- CS
                DNA_RNApol_7kD  3 CgeCg 7 
                                  C++Cg
  gi|91772962|ref|YP_565654.1| 60 CADCG 64
                                  89997 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4
                                   -SSS CS
                DNA_RNApol_7kD  20 CkeC 23 
                                   C++C
  gi|91772962|ref|YP_565654.1| 203 CRQC 206
                                   6777 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 ?    8.3   0.7     0.003       2.5      17      40 .]      40      64 ..      39      64 .. 0.91
   2 ?    2.0   0.0      0.29   2.5e+02      16      25 ..     201     210 ..     197     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
                 Auto_anti-p27 17 tCpvCgvPLmrdr.kggkvyCvaCd 40
                                   Cp+Cg+  +++  ++ +++C+ C+
  gi|91772962|ref|YP_565654.1| 40 ECPECGSRSLEQDyERAELVCADCG 64
                                  5**********988899*******6 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.29
                 Auto_anti-p27  16 etCpvCgvPL 25 
                                   + C +C+vP 
  gi|91772962|ref|YP_565654.1| 201 AACRQCSVPR 210
                                   46*******7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5    0.0012      0.99      23      37 ..      35      50 ..      23      53 .. 0.68
   2 ?    2.0   0.1      0.27   2.3e+02       5      16 ..      57      68 ..      52      78 .. 0.71
   3 ?   -1.8   0.1       4.1   3.5e+03      28      32 ..     201     206 ..     192     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                   Zn-ribbon_8 23 dapltaCPeCgs.evr 37
                                  +++ ++CPeCgs  ++
  gi|91772962|ref|YP_565654.1| 35 ENKVVECPECGSrSLE 50
                                  344455******7776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.27
                   Zn-ribbon_8  5 eYrCeeCghefe 16
                                  e  C +Cg + +
  gi|91772962|ref|YP_565654.1| 57 ELVCADCGLVVD 68
                                  345888886665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.1
                   Zn-ribbon_8  28 a.CPeC 32 
                                   a C +C
  gi|91772962|ref|YP_565654.1| 201 AaCRQC 206
                                   447777 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 ?    5.0   2.0      0.03        25       2      26 ..      41      67 ..      22      71 .. 0.71
   2 ?   -0.5   0.0       1.7   1.4e+03      17      26 ..     201     210 ..     182     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.03
                      zf-Mss51  2 CPvpkhkqt..apkhvdfeCpdCGipt 26
                                  CP + ++    + ++ ++ C dCG+++
  gi|91772962|ref|YP_565654.1| 41 CPECGSRSLeqDYERAELVCADCGLVV 67
                                  666655443335667777788888765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                      zf-Mss51  17 feCpdCGipt 26 
                                     C +C +p 
  gi|91772962|ref|YP_565654.1| 201 AACRQCSVPR 210
                                   57*****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 ?   10.2   1.2   0.00062      0.53       3      31 ..      41      66 ..      41      67 .. 0.86
   2 ?   -1.6   0.2       3.2   2.7e+03       3       7 ..     203     207 ..     202     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00062
                                  -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                     Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                  C++CG++    ++++ +r  lvC++Cg +
  gi|91772962|ref|YP_565654.1| 41 CPECGSR---SLEQDYERAELVCADCGLV 66
                                  *****99...6666779999*******87 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                                   -TTT- CS
                     Nudix_N_2   3 CsqCG 7  
                                   C+qC 
  gi|91772962|ref|YP_565654.1| 203 CRQCS 207
                                   77875 PP

>> Methyltransf_13  Putative zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0036       3.1      25      60 ..      22      57 ..      19      58 .. 0.85
   2 ?    4.6   0.2     0.045        38      42      57 ..      58      73 ..      48      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0036
               Methyltransf_13 25 lkpeqldepepfyplrlvvCedCglvQleevvdpee 60
                                  +k+++++e+++ ++ ++v C++Cg   le+ +++ e
  gi|91772962|ref|YP_565654.1| 22 IKARKEKEKTTEVENKVVECPECGSRSLEQDYERAE 57
                                  5778888899**************999998887766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
               Methyltransf_13 42 vvCedCglvQleevvd 57
                                  +vC dCglv   e+vd
  gi|91772962|ref|YP_565654.1| 58 LVCADCGLVVDAEFVD 73
                                  79******98777776 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 ?    5.2   0.2     0.022        19      14      29 ..      31      46 ..      29      48 .. 0.81
   2 ?   -0.6   0.1       1.5   1.3e+03      16      28 ..      56      64 ..      49      70 .. 0.72
   3 ?    2.7   0.1      0.14   1.2e+02      23      28 ..     202     207 ..     194     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
                                  EECSCCCEEEESSSS- CS
                RNA_POL_M_15KD 14 kedkegknfeCrqCgY 29
                                  ++ +e+k++eC  Cg+
  gi|91772962|ref|YP_565654.1| 31 TTEVENKVVECPECGS 46
                                  6778898999999997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                                  CSCCCEEEESSSS CS
                RNA_POL_M_15KD 16 dkegknfeCrqCg 28
                                  ++++    C+ Cg
  gi|91772962|ref|YP_565654.1| 56 AELV----CADCG 64
                                  5555....88887 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.14
                                   EESSSS CS
                RNA_POL_M_15KD  23 eCrqCg 28 
                                   +CrqC+
  gi|91772962|ref|YP_565654.1| 202 ACRQCS 207
                                   8****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      861  (0.0480228); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2125.36
//
Query:       gi|91772963|ref|YP_565655.1|  [L=102]
Description: RNA-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.5   0.1    2.2e-05   24.3   0.1    1.1  1  Gar1             Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.28   11.5   0.0    1.5  2  Phage_int_SAM_3  Phage integrase, N-terminal SAM-like 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 !   24.3   0.1   2.5e-09   2.2e-05      17      98 ..      14     100 ..       7     102 .] 0.74

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.5e-09
                                   TS-EEEEEEEEEEETT.EEEEEE---S--B-....-BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTT CS
                          Gar1  17 peevleiGtvssiven.evviksttsgekkv....ldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfk 92 
                                   +++++ +Gtv ++v +  ++++  + g+       + +n  + ++  + iGkV  ++G vn+py s+k+    +i+ + + 
  gi|91772963|ref|YP_565655.1|  14 KKHMKRLGTVVQTVAHnGLLVRGENIGPDTPlnnlPRINLFVVDKSVRRIGKVNGVIGSVNSPYISIKVM--GDISPSDLR 92 
                                   55677888877776553677777766664445555999*******************************9..777666554 PP

                                   T..TSEEE CS
                          Gar1  93 v..gdkvy 98 
                                   +  ++kvy
  gi|91772963|ref|YP_565655.1|  93 KylNEKVY 100
                                   33367776 PP

>> Phage_int_SAM_3  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.93   8.3e+03       9      40 ..      10      15 ..       3      23 .. 0.53
   2 ?   11.5   0.0   3.1e-05      0.28      35      57 ..      76      98 ..      69      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.93
                                  HHHHHHHHH-HHHHHHHHHHHTTTHHHHTTSS CS
               Phage_int_SAM_3  9 WleeykprvkesTyatyksiiknhIlPyFgni 40
                                  +++                          g++
  gi|91772963|ref|YP_565655.1| 10 YIN--------------------------GKK 15
                                  333..........................333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.1e-05
                                  HHTTSSBGGG--HHHHHHHHHHH CS
               Phage_int_SAM_3 35 PyFgniklkkItpadiqkfqnel 57
                                  Py+  + + +I+p+d++k+ ne+
  gi|91772963|ref|YP_565655.1| 76 PYISIKVMGDISPSDLRKYLNEK 98
                                  9999999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); 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:                         2  (0.000111551); expected 0.2 (1e-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: 715.49
//
Query:       gi|91772964|ref|YP_565656.1|  [L=374]
Description: transposase, mutator type [Methanococcoides burtonii DSM 6242]
Scores for 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-113  376.9   3.9   1.2e-112  376.6   3.9    1.0  1  Transposase_mut  Transposase, Mutator family
    3.1e-10   40.4   0.0    8.9e-10   38.9   0.0    1.8  1  MULE             MULE transposase domain
    0.00019   21.0   0.7    0.00039   20.0   0.7    1.5  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.033   13.9   0.3       0.12   12.1   0.1    2.1  2  DUF4423          Domain of unknown function (DUF4423)
      0.041   14.1   5.7        5.7    7.2   4.1    2.9  2  DDE_Tnp_IS240    DDE domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.6   3.9  3.3e-116  1.2e-112      22     380 ..      14     365 ..       4     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 376.6 bits;  conditional E-value: 3.3e-116
               Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykRreka 102
                                   ++  lk l++ +l+e++e+e+ e+ ga ++ers +r+ +RnG+r+r+l+Tr g+l+l+ P++R+  F ++++ery R+eka
  gi|91772964|ref|YP_565656.1|  14 SNVSLKPLITYFLNEVMEQEAIEQSGAGKHERSITRTAHRNGYRDRSLTTRHGELTLKKPQLRDFPFTTQVFERYSRTEKA 94 
                                   55678999************************************************************************* PP

               Transposase_mut 103 leavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrvvsk 183
                                   +e++++e yv+Gvstrkvek++ +l++ +s+S+s vS+i+++ld++v+ f ++++e++   +l++Da+ylkvR+  r v+k
  gi|91772964|ref|YP_565656.1|  95 IENAIVESYVQGVSTRKVEKIISQLGV-ESISRSRVSRIAQDLDKTVHGFMNKPIEHE-IKYLYVDATYLKVRDRVRYVNK 173
                                   ***************************.77***************************9.********************** PP

               Transposase_mut 184 avliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrvHllrnll 264
                                   av+i  gv+ dG+reiLg+++adsE++ fW++++++Lk+rGl+gvelv+sD+hkG+++a+++ f +a++Q C+vHl r +l
  gi|91772964|ref|YP_565656.1| 174 AVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKERGLRGVELVISDGHKGIQRAVERQFLGASWQMCIVHLERLIL 254
                                   ********************************************************************************* PP

               Transposase_mut 265 akvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafpeqirrkikstNllErLN 344
                                   +k+p+k+ ++ +e++k + +       + +l  ++ ++ +  + k+ae++++ +  ++++ afp++++++ik+tN++ErLN
  gi|91772964|ref|YP_565656.1| 255 KKLPRKHHKEAMESFKEVQDD------QTKLLGLMVEWDRpGFEKAAETIERFQHGLTNYQAFPKEHWKRIKTTNMIERLN 329
                                   **************9987543......345555666677789*************************************** PP

               Transposase_mut 345 keirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                   ke++Rr++vvg FPn+es++rlv avl +++++w++
  gi|91772964|ref|YP_565656.1| 330 KEVKRRSKVVGAFPNDESLMRLVIAVLIDQNENWIT 365
                                   **********************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.5e-13   8.9e-10       2      94 ..     155     250 ..     154     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.5e-13
                          MULE   2 vvlDgTyktnkykl.....plltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnal 77 
                                   + +D+Ty++ + ++       ++v gv++ g   +l++ + +se+   +e ++++l+e+ +  r  + +i+D +k++++a+
  gi|91772964|ref|YP_565656.1| 155 LYVDATYLKVRDRVryvnkAVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKER-GL-RGVELVISDGHKGIQRAV 233
                                   679****99865441122167889**********************************5.44.7***************** PP

                          MULE  78 eevfpeakhrlClfHia 94 
                                   e++f +a  ++C+ H++
  gi|91772964|ref|YP_565656.1| 234 ERQFLGASWQMCIVHLE 250
                                   ***************97 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.7   1.1e-07   0.00039      11     238 ..      97     336 ..      88     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                  DDE_Tnp_IS66  11 eilvlkyadhlPlyRqeeilarlGv.elsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkks 90 
                                   +++v+ y+++++ +++e+i+++lGv  +sr+ +++  ++  +++  ++++  ++  + +++ +D T l+v +  r +  ++
  gi|91772964|ref|YP_565656.1|  97 NAIVESYVQGVSTRKVEKIISQLGVeSISRSRVSRIAQDLDKTVHGFMNKPIEH--EIKYLYVDATYLKVRD--RVRYVNK 173
                                   6799*********************569***99999988888888888776654..55799********877..6888888 PP

                  DDE_Tnp_IS66  91 ylWvyvtdkr...kpavlfeyspsRggevaealLag.....fkG..vlvsDgyagYnklae...eqvthalCwaHlrRkfv 158
                                    +++++  k+   +++   ++++s  +   e+++++      +G   ++sDg++g ++  e    ++  ++C +Hl R + 
  gi|91772964|ref|YP_565656.1| 174 AVFIVAGVKNdgyREILGVKIADSEEAMFWEEMFTDlkergLRGveLVISDGHKGIQRAVErqfLGASWQMCIVHLERLIL 254
                                   88888887777899*************999999777664665556679*********976657778888*********887 PP

                  DDE_Tnp_IS66 159 daeeakkk...sqaaaealar.igklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgkairyll 235
                                   +   +k +    +  +e +++   kl  +  e+  ++  e++a   e+ +  l++++a  +e+ k+++  + ++++ ++++
  gi|91772964|ref|YP_565656.1| 255 KKLPRKHHkeaMESFKE-VQDdQTKLLGLMVEWD-RPGFEKAAETIERFQHGLTNYQAFPKEHWKRIKTTNMIERLNKEVK 333
                                   66655432232222222.2222555555555553.2456677777777777777777766666566655555555555555 PP

                  DDE_Tnp_IS66 236 krw 238
                                   +r 
  gi|91772964|ref|YP_565656.1| 334 RRS 336
                                   555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.48   1.7e+03     106     130 ..     121     128 ..      86     148 .. 0.55
   2 ?   12.1   0.1   3.3e-05      0.12      92     145 ..     252     305 ..     247     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.48
                       DUF4423 106 iealervpkeeRdissltlaisked 130
                                   +e                 +is++ 
  gi|91772964|ref|YP_565656.1| 121 VE-----------------SISRSR 128
                                   33.................344444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.3e-05
                       DUF4423  92 eavrsyhkqmlelAiealervpkeeRdissltlaiskedyekikkeirefrkki 145
                                   + ++++ ++  ++A+e++++v+ ++ ++ +l++  ++  +ek+++ i++f++ +
  gi|91772964|ref|YP_565656.1| 252 LILKKLPRKHHKEAMESFKEVQDDQTKLLGLMVEWDRPGFEKAAETIERFQHGL 305
                                   567788888999**************************************9866 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.4e+03      64      96 ..      82      97 ..      48     124 .. 0.58
   2 ?    7.2   4.1    0.0016       5.7      84     124 ..     292     350 ..     153     360 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                 DDE_Tnp_IS240 64 tDkasayasalkelkregelfdevshvqvkyln 96
                                  t                    ++ s+ ++  +n
  gi|91772964|ref|YP_565656.1| 82 TQVF-----------------ERYSRTEKAIEN 97
                                  3222.................222333333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0016
                 DDE_Tnp_IS240  84 f...................devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                                        + +h+++    n+iE+ ++++K+r ++++ f + +s+ +
  gi|91772964|ref|YP_565656.1| 292 EkaaetierfqhgltnyqafPK-EHWKRIKTTNMIERLNKEVKRRSKVVGAFPNDESLMR 350
                                   0333333333344444444333.7888888999999999999999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2797.78
//
Query:       gi|91772965|ref|YP_565657.1|  [L=884]
Description: pyruvate phosphate dikinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-94  314.6   0.0    9.5e-94  313.8   0.0    1.3  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    3.6e-63  213.8   0.1    1.4e-37  129.7   0.0    3.3  3  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
      2e-29  101.1   1.2    6.9e-29   99.4   1.2    2.0  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
       0.53   10.3   2.4       0.87    9.6   0.0    2.4  3  RNA_pol_Rpb1_4   RNA polymerase Rpb1, domain 4


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.8   0.0   2.1e-97   9.5e-94       6     292 ..     522     878 ..     519     880 .. 0.97

  Alignments for each domain:
  == domain 1  score: 313.8 bits;  conditional E-value: 2.1e-97
                                   SCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH....................HHH CS
               PEP-utilizers_C   6 klktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee....................qae 66 
                                   +l+t+l+++++++ +kv  N+dtp+dae a+++gaeGiGL+RtE++f+  +++p+++e                    q+e
  gi|91772965|ref|YP_565657.1| 522 ELETILTWADEVRTLKVRTNADTPHDAEVARDFGAEGIGLCRTEHMFFGEDRIPAVREmimaediesrklalkkllpmQRE 602
                                   67899**************************************************************************** PP

                                   HHHHHHHHTTTSEEEEEXXXSSCCGGSGGC.............................HHHH.XSXGGGSSXTHHHHCCS CS
               PEP-utilizers_C  67 aykkvleamngrpvvvRtlDiggdkelpel.............................keepeevNPmlGfRgirlglse 118
                                   ++ ++++am+g pv++R+lD++ +++lp+                              +e ++e NPmlG+Rg+rlg+++
  gi|91772965|ref|YP_565657.1| 603 DFIGIFKAMEGFPVTIRLLDPPLHEFLPNHeevmeklwelessdasqeemdrvkkigerIEYLKEINPMLGHRGCRLGITY 683
                                   *****************************99****************************99******************** PP

                                   HHHHHHHHHHHHHHCCCC.......EEEEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHH CS
               PEP-utilizers_C 119 pelfetqlrAllrasaag.......kleimlPmvasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaallad 192
                                   pe++e+q++A+++a+ +          eim+P+v++v+ele  kk i ++ e + +e +++k +++vG+MiE p+a+l+ad
  gi|91772965|ref|YP_565657.1| 684 PEIYEMQAQAIIEAACELskdgmkiVPEIMIPLVSHVKELEFVKKHITSIFESVMEE-MGIKLDYMVGTMIELPRAVLTAD 763
                                   **************9966677888889****************************99.*********************** PP

                                   HHCTTSSEEEEXHHHHHHHHHTXXCCCHC...HHHH......SXTTTCHHCCCHHHHHHHHHHCC......XEEEEESCCC CS
               PEP-utilizers_C 193 klakevdFfSiGtNDLtQytlavdRdnee...vakl......ydplepavlrlikevikaaeekg......lkvgiCGela 258
                                   ++ake++FfS+GtNDLtQ t++ +Rd++    + +l       dp+ ++++ ++++++k+  ekg      +k+giCGe++
  gi|91772965|ref|YP_565657.1| 764 QIAKEAEFFSFGTNDLTQTTFGFSRDDAGkflPFYLesgileDDPFAVLDQDGVGQLVKIGIEKGratrpdIKIGICGEHG 844
                                   ****************************988866668889999******************9999999999********** PP

                                   CSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
               PEP-utilizers_C 259 gdpsavellvglGldelSmsaasvpaaraalaqv 292
                                   g+p++v++ +++Gld++S+s+++vp+ar a+a++
  gi|91772965|ref|YP_565657.1| 845 GEPKSVKFGHNVGLDYVSCSPFRVPIARLAAAHA 878
                                   *****************************99986 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.8e-13   8.2e-10       2      40 ..      23      60 ..      22      64 .. 0.92
   2 !  129.7   0.0   3.1e-41   1.4e-37      77     226 ..      66     301 ..      60     306 .. 0.95
   3 !   41.7   0.2   1.9e-14   8.7e-11     271     326 ..     307     360 ..     304     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.8e-13
                        PPDK_N  2 elvGGKganLaellneagipvPpgfaitadafrefleen 40
                                  +l+GGKganLae+ +++gipvP gf+it+++++ +l+++
  gi|91772965|ref|YP_565657.1| 23 DLLGGKGANLAEM-SNLGIPVPVGFTITTEVCTLYLKNG 60
                                  79***********.66*******************9976 PP

  == domain 2  score: 129.7 bits;  conditional E-value: 3.1e-41
                        PPDK_N  77 lPeeleeaikeayeelgkkfgde..elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle.................. 137
                                   + e +++aik++++ ++k+fgd   +l+++VRS+      ++ s++G++dt+Ln+g +++ +                   
  gi|91772965|ref|YP_565657.1|  66 FEEHIDNAIKQLESTTKKNFGDLknPLLLSVRSG------ARVSMPGMMDTVLNLGLNDDSVVglaaktgnerfaydsyrr 140
                                   45678888888888899999987889********......9******************99999***************** PP

                        PPDK_N 138 ......................................................................aikavfaSlfn 148
                                                                                                         ai avf S++n
  gi|91772965|ref|YP_565657.1| 141 fltmfanvvldidhekfestlsamkkdknvkqdndlevedlkelvekfktiikdeagkefpqnareqlqmAIDAVFGSWNN 221
                                   ********************************************************************************* PP

                        PPDK_N 149 erAilYrkekgldheevalavvvqkmvnsdlg...asGVafsldpetG...fkdevlinasyGlGeaVVaGrvtpdefvve 223
                                   +rA +Yrk +g++  e+++av+vq+mv +++g    +GVaf++dp+tG   f +e+lina   +Ge+VVaG++tp+ +   
  gi|91772965|ref|YP_565657.1| 222 QRAKTYRKLNGIP-GEWGTAVNVQSMVYGNMGetsGTGVAFTRDPATGekrFFGEYLINA---QGEDVVAGIRTPQPIKAL 298
                                   *************.*******************999**************99********...*************99877 PP

                        PPDK_N 224 kst 226
                                   k+t
  gi|91772965|ref|YP_565657.1| 299 KNT 301
                                   765 PP

  == domain 3  score: 41.7 bits;  conditional E-value: 1.9e-14
                        PPDK_N 271 eeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetlee 326
                                   ++L +i  k+e+h+++++diEf+i+  +gkl++lQ+R ++rt +++ k+a+e+ ee
  gi|91772965|ref|YP_565657.1| 307 DQLVDIYMKLEDHFKDMQDIEFTIE--KGKLFMLQTRTGKRTAAAAIKIATEMVEE 360
                                   6899*********************..************************99987 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 !   99.4   1.2   1.5e-32   6.9e-29       4      73 .]     424     505 ..     421     505 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 1.5e-32
                                   S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.............HH--TEEEEEETTT CS
                 PEP-utilizers   4 egvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati............elkegdlitvDgst 72 
                                   e++ILv+ etsp+di g+++ +Gi+t rGGmtSHaA+vAr++g+P+V+g+ge+ti            ++kegd+i++Dgst
  gi|91772965|ref|YP_565657.1| 424 EKTILVRAETSPEDIGGMNASEGILTVRGGMTSHAAVVARGMGKPCVAGCGEITIdikekvfnvgdyTVKEGDIISIDGST 504
                                   569****************************************************************************** PP

                                   T CS
                 PEP-utilizers  73 G 73 
                                   G
  gi|91772965|ref|YP_565657.1| 505 G 505
                                   9 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00019      0.87      24      76 ..      68     117 ..      63     134 .. 0.74
   2 ?   -1.3   0.3      0.47   2.1e+03       5      43 ..     168     206 ..     163     221 .. 0.57
   3 ?   -3.6   0.1       2.4   1.1e+04      10      31 ..     636     657 ..     632     670 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHHHHHHHHHHHCST.TTSHHHHHHHCTSSS-HHHHHHHHTB-EEE CS
                RNA_pol_Rpb1_4  24 akinkilnkardkagkiasksla.asNsiliMvksGaKGsiinisqiagclGqq 76 
                                   + i++++++ +++     +k+    +N++l  v+sGa+ s+  ++  +  lG+ 
  gi|91772965|ref|YP_565657.1|  68 EHIDNAIKQLEST----TKKNFGdLKNPLLLSVRSGARVSMPGMMDTVLNLGLN 117
                                   4444555544444....333333346***************9999999888885 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.47
                                   CTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                RNA_pol_Rpb1_4   5 erygkledlpgksleelfeakinkilnkardkagkiask 43 
                                   ++ ++ +dl+ + l+el e+  + i+++a +++ + a++
  gi|91772965|ref|YP_565657.1| 168 KNVKQDNDLEVEDLKELVEKFKTIIKDEAGKEFPQNARE 206
                                   444555566666666666654555555555554444444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.4
                                   CHHHTTHCHHHHHHHHHHHHHH CS
                RNA_pol_Rpb1_4  10 ledlpgksleelfeakinkiln 31 
                                   +e+l++ ++++  +++++ +++
  gi|91772965|ref|YP_565657.1| 636 MEKLWELESSDASQEEMDRVKK 657
                                   6778888888888777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (884 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.26s 00:00:01.02 Elapsed: 00:00:00.41
# Mc/sec: 6406.99
//
Query:       gi|91772966|ref|YP_565658.1|  [L=300]
Description: cytidine kinase / inosine-guanosine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-47  160.7   0.0    5.7e-47  160.5   0.0    1.1  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.5   0.0   3.2e-51   5.7e-47       3     301 ..       4     280 ..       2     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 3.2e-51
                                   EEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETT CS
                          PfkB   3 kvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdy 81 
                                   ++ v+G+a id+  ++e++  ++e++   ++++ +GG +aN++ a++ lg+++++i+avGdD+  + ++++l++ gvd + 
  gi|91772966|ref|YP_565658.1|   4 SISVVGHAAIDFLFDVEGIsgPNESNPIVDYQRFYGGGAANIVAAISILGGRSQLISAVGDDFSTSGYESYLESLGVDLSL 84 
                                   789*****************99999999999999*********************************************** PP

                                   EEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE.. CS
                          PfkB  82 vkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt.. 160
                                   + + ++++ + a++++d  ++++ +f++ga+a+l++        +  e+d++++++      +e++++  a++ak++++  
  gi|91772966|ref|YP_565658.1|  85 LFRLKGEKGTAAYVFTDPFHNQSTYFYWGASAKLKE-------LEPPEVDFVHLAT------SESNFN--AKIAKKAKFvs 150
                                   *****************88****************9.......4789********9......344443..34555555556 PP

                                   EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEE CS
                          PfkB 161 fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgel 241
                                   fdp +   +   ++e l+ +l+ +d+l++n +E++++++++  + e++ a+        +++vvvt  ++G+ +++ d+e+
  gi|91772966|ref|YP_565658.1| 151 FDPGQDLVTY--TRENLEIVLENTDILFTNKYEIKRVCEMTESTFEDIRAQ--------IDVVVVTYDADGSKIFTADAEH 221
                                   9*********..69***************************9999999988........579******************* PP

                                   EEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSCC CS
                          PfkB 242 kvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslpt 301
                                   ++p vp v++ D+tGAGD++ +gfl+++ +g +l  + r + +vA+++v + g++++lpt
  gi|91772966|ref|YP_565658.1| 222 EIPIVP-VNALDPTGAGDAYRAGFLVSYRRGYPLDSCGRVGATVASFAVGSVGCQTDLPT 280
                                   ****98.**************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2126.44
//
Query:       gi|91772967|ref|YP_565659.1|  [L=114]
Description: hypothetical protein Mbur_0968 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  162.7   0.1    2.7e-48  162.4   0.1    1.0  1  DUF555    Protein of unknown function (DUF555)


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 !  162.4   0.1   1.5e-52   2.7e-48       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 1.5e-52
                        DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkvfnae 80 
                                   +y+v+leaaw+vrdv+++ddAig+Aiseagkrlnp+ ldfve++vg+t cP+c e++ s++++a+talvgl+lemkvf+ae
  gi|91772967|ref|YP_565659.1|   3 NYHVTLEAAWLVRDVETADDAIGVAISEAGKRLNPKkLDFVEVDVGTTYCPACSEPFGSVFIAANTALVGLVLEMKVFDAE 83 
                                   8**********************************99******************************************** PP

                        DUF555  81 seEhaeriakseigkaledvP 101
                                   s+Eha+riaks+igkal+dvP
  gi|91772967|ref|YP_565659.1|  84 SDEHASRIAKSVIGKALTDVP 104
                                   ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 672.71
//
Query:       gi|91772968|ref|YP_565660.1|  [L=93]
Description: hypothetical protein Mbur_0969 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-31  107.1   0.1    3.9e-31  106.9   0.1    1.1  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.1   2.2e-35   3.9e-31       1      73 []      11      83 ..      11      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 2.2e-35
                                  HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                        DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                  rY+rll eal+k++i+p e+s+++++ae++ +ma+sY+eD+ +f++ +d+vnAl +fsY+++wLDagarlg++
  gi|91772968|ref|YP_565660.1| 11 RYERLLSEALAKADISPIENSHMRTVAEDYKNMARSYYEDGIHFIRSEDPVNALICFSYGHAWLDAGARLGVF 83
                                  8**********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 598.96
//
Query:       gi|91772969|ref|YP_565661.1|  [L=557]
Description: hypothetical protein Mbur_0970 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-40  139.4   0.2    3.8e-40  138.4   0.0    1.6  2  DUF87          Helicase HerA, central domain
    1.8e-09   37.6   0.0    5.4e-09   36.1   0.0    1.9  2  HAS-barrel     HAS barrel domain
    0.00073   18.6   0.0       0.03   13.2   0.0    2.2  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
     0.0014   17.6   0.0      0.011   14.7   0.0    2.2  2  AAA_10         AAA-like domain
     0.0015   18.4   0.0     0.0037   17.1   0.0    1.6  1  SBP_bac_8      Bacterial extracellular solute-binding protein
     0.0018   16.9   0.0       0.55    8.8   0.0    2.2  2  DUF853         Bacterial protein of unknown function (DUF853)
     0.0025   18.1   0.0        2.1    8.6   0.0    2.7  2  AAA_22         AAA domain
     0.0033   17.2   0.0        1.6    8.5   0.0    3.1  3  DEAD           DEAD/DEAH box helicase
     0.0078   16.2   0.0      0.022   14.8   0.0    1.7  2  ResIII         Type III restriction enzyme, res subunit


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 ?   -3.0   0.0       3.2   6.4e+03     137     157 ..      61      79 ..      31      91 .. 0.55
   2 !  138.4   0.0   1.9e-43   3.8e-40       2     226 ..     135     354 ..     134     355 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                         DUF87 137 lssdepveklleelkkekeel 157
                                    s+de  +k+++elkke+ + 
  gi|91772969|ref|YP_565661.1|  61 HSFDE-AKKVFDELKKES-KT 79 
                                   33333.233444444111.22 PP

  == domain 2  score: 138.4 bits;  conditional E-value: 1.9e-43
                         DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal.............. 68 
                                   +iG l +g+++pv l +n+lv++H+ il++TGsGKS+t+avLleell ++++++li+DpH+EY++++              
  gi|91772969|ref|YP_565661.1| 135 YIGML-DGTDIPVHLSVNSLVQKHVSILAKTGSGKSYTAAVLLEELL-DRKVPLLIIDPHSEYASMKdaspkndgfkkfgi 213
                                   69999.*****************************************.********************************* PP

                         DUF87  69 .ekllsekvkvitpspsa....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepve 144
                                    +k++ ++v ++tp+++      d+ +++n ++l+ ++l  +++    + +a++  +l+ea+++++   e e ++ d+++ 
  gi|91772969|ref|YP_565661.1| 214 sPKGYGSNVTIYTPANKVinpnADELFRLNGNNLTAKDLTAIFPD---NFTATHIGILYEAIQKLR--AEMETYTLDDIIF 289
                                   **************9998***9999********************...88889************9..9*********999 PP

                         DUF87 145 klleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilr 225
                                              e+ ++ ++a++++   led+ ++ ++  +s+t+l++l+     ++gk ++id++gv+ + q ++v+ ++ 
  gi|91772969|ref|YP_565661.1| 290 -----------EVGNNESKARWNVMGVLEDIRDSDILS-SSPTELTELM-----HNGKASVIDFKGVPPELQSMIVARLCS 353
                                   ...........5667888********************.**********.....************************997 PP

                         DUF87 226 r 226
                                    
  gi|91772969|ref|YP_565661.1| 354 A 354
                                   5 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   2.7e-12   5.4e-09       1      68 [.       5      68 ..       5      98 .. 0.80
   2 ?   -2.8   0.0       3.6   7.1e+03      39      62 ..     302     325 ..     301     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.7e-12
                    HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleelee 68
                                  +G++ ge++s ++ f +  s+ v  GeyV+++++ +++vl++v++i+r     s++ ++ +s++e++ 
  gi|91772969|ref|YP_565661.1|  5 VGIISGETGSFGFNFLISDSTAVNRGEYVKAWHESDGWVLCQVLSIKR----SSDVANNKHSFDEAKK 68
                                  79999*******************************************....5666666666655543 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                    HAS-barrel  39 vlGmvtdirrgnselsndlalvls 62 
                                   v G+ +dir  ++  s+ ++l + 
  gi|91772969|ref|YP_565661.1| 302 VMGVLEDIRDSDILSSSPTELTEL 325
                                   678888888865555555555554 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 !   13.2   0.0   1.5e-05      0.03      12      56 ..     152     196 ..     143     203 .. 0.90
   2 ?    2.8   0.0     0.022        44     261     322 ..     392     445 ..     388     455 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                 TrwB_AAD_bind  12 eretqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                   +  ++h+ i+  tGsGK+ ++  ll+++  r+   +++D++ ++ 
  gi|91772969|ref|YP_565661.1| 152 SLVQKHVSILAKTGSGKSYTAAVLLEELLDRKVPLLIIDPHSEYA 196
                                   46789***********************************99886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.022
                 TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeelsell 322
                                   l +++ egRkfG  + +  q  a++ +        ++ls ++t++i++v++ +  + +s+ l
  gi|91772969|ref|YP_565661.1| 392 LRTIASEGRKFGLGMMVISQRPARIDK--------NVLSQCGTQIIMKVTNPNDLKSISKGL 445
                                   677888999999988888888888864........677888888888888777777777655 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.5e-06     0.011      23     172 ..     157     314 ..     150     320 .. 0.58
   2 ?   -0.2   0.0      0.18   3.6e+02     259     302 ..     389     431 ..     369     456 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                        AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe........iakk..invvtLdseeenegvLdPl 93 
                                   ++ i+ ++G GKS++a +l   ++ ++  +liiDp  e   +k + p+        i  k     vt+   + ++ v++P 
  gi|91772969|ref|YP_565661.1| 157 HVSILAKTGSGKSYTAAVLLEELLDRKVPLLIIDPHSEYASMKDASPKndgfkkfgISPKgyGSNVTIY--TPANKVINPN 235
                                   6788999*******************************7777777666333222221111222333333..2222344443 PP

                        AAA_10  94 v..llkeekeaeslaedilelllgvkkkesekkaalseaveavl.egkqrgllavieelrkedekvareiarhlesvvkks 171
                                      l+  +   + +a+d++ +  +   ++++   +l ea+++   e ++  l ++i e+ ++++k+  ++   le +++ +
  gi|91772969|ref|YP_565661.1| 236 AdeLFRLN-GNNLTAKDLTAIFPDN-FTATHIG-ILYEAIQKLRaEMETYTLDDIIFEVGNNESKARWNVMGVLEDIRDSD 313
                                   22133333.3344444443333332.2333333.46666665442455566666666666666666666666666666666 PP

                        AAA_10 172 l 172
                                   +
  gi|91772969|ref|YP_565661.1| 314 I 314
                                   5 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                        AAA_10 259 kkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFr 302
                                    ++l+ +   GR++   ++ ++q +  ++k+ l++  g++++ +
  gi|91772969|ref|YP_565661.1| 389 SEVLRTIASEGRKFGLGMMVISQRPARIDKNVLSQ-CGTQIIMK 431
                                   4678888899***************9999987653.34444444 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 !   17.1   0.0   1.8e-06    0.0037      23      95 ..     270     346 ..     265     363 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                                   SHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HHHHHTT--TS......----EEEEEEE- CS
                     SBP_bac_8  23 dleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltdalaavgydgk.....lygvPyasetpy 95 
                                   +++qkl+a++++ t++di+ +++n++  a+++++g+l+d+ d+d l + ++ l+  + +gk     ++gvP+  ++ +
  gi|91772969|ref|YP_565661.1| 270 EAIQKLRAEMETYTLDDIIFEVGNNESKARWNVMGVLEDIRDSDILSSSPTELTELMHNGKasvidFKGVPPELQS-M 346
                                   689**************999************************************99999999999****99887.4 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 !    6.0   0.0    0.0019       3.8      18      71 ..     152     205 ..     139     212 .. 0.82
   2 !    8.8   0.0   0.00028      0.55     289     334 ..     400     443 ..     343     458 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0019
                        DUF853  18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGevk 71 
                                   +l+ +h  i   tG Gk  t  vl e+l +  vp ++ d   + +++  a   +
  gi|91772969|ref|YP_565661.1| 152 SLVQKHVSILAKTGSGKSYTAAVLLEELLDRKVPLLIIDPHSEYASMKDASPKN 205
                                   4678999999****************************9887777776665555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00028
                        DUF853 289 rskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavka 334
                                   r  G G+  ++q P+ + ++vL+q G+++   ++   p+d k++ +
  gi|91772969|ref|YP_565661.1| 400 RKFGLGMMVISQRPARIDKNVLSQCGTQI--IMKVTNPNDLKSISK 443
                                   44589*********************977..466677777777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.001       2.1       5      50 ..     155     194 ..     153     211 .. 0.79
   2 !    6.5   0.0    0.0048       9.5      72     112 ..     342     395 ..     308     435 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpss 50 
                                   ++++ + + +G+GK+++++ lle+l  +      +++++ +++ s+
  gi|91772969|ref|YP_565661.1| 155 QKHVSILAKTGSGKSYTAAVLLEELLDR------KVPLLIIDPHSE 194
                                   67889999***************99755......666666666555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0048
                        AAA_22  72 rlsseellealeqalrarav....ielliiDEaqhlr.....s....eealeeL 112
                                   +l+s  + +++   ++ar++    +++l+++Ea+++      s     e+l+++
  gi|91772969|ref|YP_565661.1| 342 ELQSMIVARLCSALFEARKMnaipPGMLVVEEAHNFApergfSktasSEVLRTI 395
                                   4444444455555556666689999***********877555243335555444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00081       1.6      12      58 ..     154     194 ..     144     200 .. 0.73
   2 !    5.0   0.0    0.0092        18     106     144 ..     349     389 ..     291     410 .. 0.79
   3 ?   -1.3   0.0       0.8   1.6e+03      78     129 ..     406     455 ..     389     459 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00081
                                   HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtre 58 
                                   + +++v + a+TGsGK+  +++ + + +     +++   li+ P  e
  gi|91772969|ref|YP_565661.1| 154 V-QKHVSILAKTGSGKSYTAAVLLEELL-----DRKVPLLIIDPHSE 194
                                   3.67999**********99777655444.....56666777777665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0092
                                   HHHHH.HHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHH CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          DEAD 106 grldd.llstgklnlsqvrflVlDEadrlldq.gfsdfinr 144
                                    rl + l++ +k+n     +lV+ Ea+++  + gfs++ ++
  gi|91772969|ref|YP_565661.1| 349 ARLCSaLFEARKMNAIPPGMLVVEEAHNFAPErGFSKTASS 389
                                   456664558999999999***********998899887654 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.8
                                   EEEEETTSSHHHHHHHHH.TTCSEE..EEEHHHHHHHHHCTSSHCTTEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  78 vlliiggvaardqlskld.ngvdiv..vgtpgrlddllstgklnlsqvrflVlDE 129
                                   + ++i++ +ar ++++l+ +g++i+  v++p  l ++ +     l+ v+ +V DE
  gi|91772969|ref|YP_565661.1| 406 M-MVISQRPARIDKNVLSqCGTQIImkVTNPNDLKSISK--G--LEGVNSFVEDE 455
                                   3.3678888888888885455555522677777776442..3..78888888888 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.022      24     119 ..     155     280 ..     144     335 .. 0.69
   2 ?   -3.2   0.0       3.7   7.4e+03     135     146 ..     368     379 ..     341     398 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                   TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH......HHGGGGTGG.............GEEEE CS
                        ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl......eefkkflseayke.........igkkv 89 
                                   +k++ i + TG+GK+++aa l e+ll     +  l++++  s +  ++      + fkkf  +++           +    
  gi|91772969|ref|YP_565661.1| 155 QKHVSILAKTGSGKSYTAAVLLEELLDR---KVPLLIIDPHSEYASMKdaspknDGFKKFGISPKGYgsnvtiytpA---- 228
                                   7899999*******************96...3468888888888888855555555555554443324433333332.... PP

                                   SSS-B--................................-SEEEEEHHHHHHTH. CS
                        ResIII  90 sgdkkka.........................kekdstnkkilvttiqsldadse 119
                                      +k +                          +  +t++ il + iq+l a++e
  gi|91772969|ref|YP_565661.1| 229 ---NKVInpnadelfrlngnnltakdltaifpDNFTATHIGILYEAIQKLRAEME 280
                                   ...2222222222244444444446666677767777777777777777777774 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.7
                                   EEEEETGGGTTS CS
                        ResIII 135 viiiDEaHrlga 146
                                   ++++ EaH+++ 
  gi|91772969|ref|YP_565661.1| 368 MLVVEEAHNFAP 379
                                   788888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 3141.39
//
Query:       gi|91772970|ref|YP_565662.1|  [L=267]
Description: diphthine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-16   59.6   0.0      5e-16   59.3   0.0    1.1  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 !   59.3   0.0   2.8e-20     5e-16       4     188 ..       4     195 ..       1     213 [. 0.77

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.8e-20
                  TP_methylase   4 lVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvl 84 
                                   +VG+G+ d +++++++l+ + +ad v+ +   +++il   + e++e  ++++ ++ ++e + + ++++l++a ++   Vv+
  gi|91772970|ref|YP_565662.1|   4 FVGLGLFDEKDISLKGLEKIHNADKVYVEF--YTSILMGTDLEKMEMLYKKKITVLSREDVEQHAEDWLVDAKDSN--VVF 80 
                                   8*************************8555..88888766655555556666665666666666666667777665..*** PP

                  TP_methylase  85 lvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl............lpglakeeere 153
                                   l++GD +v++t+  l   lra++ gi++  i G s+++a++  +g+  + +g+++++                     ++ 
  gi|91772970|ref|YP_565662.1|  81 LTGGDTMVSTTHVDLR--LRAADMGIKTTLIHGASIASAICGLSGLQNYRFGKSVTIPhpyvsnrgvrvvS-------QTP 152
                                   ***************6..99999***********************************9999966654442.......333 PP

                  TP_methylase 154 leallan....gdtlvllkapr.k....laelaelLkealyddt 188
                                   ++ + +n     +t v+l+  + k    +++++e+L+e   +++
  gi|91772970|ref|YP_565662.1| 153 YDTIKNNieagLHTAVFLDIDKdKgymtVNQAMEILLEV-EGKL 195
                                   333333333347899999666643777799999999887.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1716.94
//
Query:       gi|91772971|ref|YP_565663.1|  [L=537]
Description: chaperonin Cpn60/TCP-1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-158  528.3  24.7   1.9e-158  528.1  24.7    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.1  24.7  1.1e-162  1.9e-158       1     490 [.      33     518 ..      33     519 .. 0.97

  Alignments for each domain:
  == domain 1  score: 528.1 bits;  conditional E-value: 1.1e-162
                                   HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                   +a+ivkttlGPkGmdKmlvn  g++v+TnDGa ilk +eiehP+ak++ve+a++q++ +GDGTt++v+Lag+Lle+ae+l+
  gi|91772971|ref|YP_565663.1|  33 VANIVKTTLGPKGMDKMLVNGVGDIVLTNDGAMILKGMEIEHPTAKMIVEVAKTQENIAGDGTTSAVVLAGALLEKAEELL 113
                                   689****************************************************************************** PP

                                   HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCSEECSC CS
                    Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieenekeldl 162
                                   ++g+hpt+ii+g+ +a +ka+e L+++  +++++++dr+ L+++a+t++ +k +++ a+++s+++vdA + +e +++++dl
  gi|91772971|ref|YP_565663.1| 114 DTGIHPTVIIKGFLEASSKAMELLDNY--AVQVTKEDRDVLVNIAKTAIAGKSSEAFADHISNICVDAALEVE-EDGKVDL 191
                                   ***************************..7777778*********************************5554.4489*** PP

                                   CCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1 163 grikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqlee 243
                                   ++i + +  g++++d+e++eG+v++k  l++ mp+k+en+k+++l   ++ +kt++k+++++++a++++++ ++e++ +e 
  gi|91772971|ref|YP_565663.1| 192 NNIMLTQDPGQQIDDTEFLEGIVVNKARLHSAMPEKVENPKIAILASDISVKKTKNKASLQIDSADKMKEFIEQEKADFEA 272
                                   ********************************************************************************* PP

                                   HHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETTCC CS
                    Cpn60_TCP1 244 llekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigsek 324
                                   +l+ki ++g++ ++ +k id++a ++++k+g+ a+rrv ++d++ +++atGa++v++++d+++++lGta+ ve+    +  
  gi|91772971|ref|YP_565663.1| 273 MLDKILDTGATAIIGTKNIDQVAMDYFQKKGVYAIRRVNEDDIKAISRATGAHIVKNIMDISEKDLGTADLVEQIGAFDLG 353
                                   ************************************************************************665555667 PP

                                   EEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHH CS
                    Cpn60_TCP1 325 ttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaieaf 405
                                    t+i+++k+ ++ tillrg+t+++ d +er+ +dAlnv+kn+ied+ +v+GGGa+e+e+a+ lk+ya+sv g+eqla+ af
  gi|91772971|ref|YP_565663.1| 354 KTYIRGCKNTNTITILLRGSTEHITDNLERTMDDALNVIKNTIEDGMIVAGGGASEIEIAQGLKSYATSVGGREQLAVSAF 434
                                   79******************************************************************************* PP

                                   HHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEE CS
                    Cpn60_TCP1 406 akALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLridei 486
                                   a+ALe+ip+ +a NaG+d+i+++  lra+h + + ++g+dv s ei+d +e+g+vD+l+vk+qa+ksA+e+a+++Lr+d++
  gi|91772971|ref|YP_565663.1| 435 AEALESIPREIAINAGMDGIDTILALRAKHTEIK-NAGLDVYSTEIVDTFEKGIVDSLRVKKQAIKSASEVANMVLRVDDM 514
                                   ******************************9999.********************************************** PP

                                   EXXX CS
                    Cpn60_TCP1 487 ikak 490
                                   +ka+
  gi|91772971|ref|YP_565663.1| 515 LKAR 518
                                   *987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3552.87
//
Query:       gi|91772972|ref|YP_565664.1|  [L=193]
Description: hypothetical protein Mbur_0973 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-72  241.4   0.0    5.2e-72  241.2   0.0    1.0  1  DUF2119   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2119  Uncharacterized protein conserved in archaea (DUF2119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.2   0.0   2.9e-76   5.2e-72       2     188 .]       9     192 ..       8     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 2.9e-76
                       DUF2119   2 egpvrlfvgGlHGdEgkdtskileklkeedlsegllvipnlekskYiSTldkeyyeseegkklidlveklkpeiYvElHsY 82 
                                   ++p rlfv+GlHG+E++dts++l +++ ++ s++l+++p+++++kYiSTld ++y+  +gk ++d+ve+++p+iYvElHsY
  gi|91772972|ref|YP_565664.1|   9 GRPFRLFVAGLHGQEWQDTSDVLLNIE-RPSSGTLAILPVVSRGKYISTLDGDFYKG-MGKLIVDVVEECQPDIYVELHSY 87 
                                   689************************.9****************************.*********************** PP

                       DUF2119  83 skenykkLtdedRlkktgvPplvdlengvLigSvsplirkkyfkkealcltlEipklkskesleevlkileliaesksree 163
                                   s+en++kL++++R+++ gvP+++ len+vL+gSvsp+ir+++f+ ealclt+Ei++l+ ++s+e+++k+l++++e++sr+ 
  gi|91772972|ref|YP_565664.1|  88 SSENFHKLVSSTRINEIGVPGFSVLENNVLMGSVSPHIRRDHFPVEALCLTFEIERLD-QSSKEFAAKMLRVVKECRSRDG 167
                                   *********************************************************9.9********************* PP

                       DUF2119 164 lieklkkkYpeqvekakeyakkfyg 188
                                   +ie+++++Yp+ ++ka+e++kkfyg
  gi|91772972|ref|YP_565664.1| 168 FIEYMMERYPNVAKKAIEDYKKFYG 192
                                   ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 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:                        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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1290.36
//
Query:       gi|91772973|ref|YP_565665.1|  [L=104]
Description: Sec-independent protein translocase TatA [Methanococcoides burtonii DSM 6242]
Scores for complete 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   53.0   0.4    1.9e-14   52.7   0.4    1.3  1  MttA_Hcf106  mttA/Hcf106 family
     0.0015   18.5   0.0       0.66    9.9   0.0    2.1  2  DUF1804      Protein of unknown function (DUF1804)


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.4   2.1e-18   1.9e-14       1      44 [.       2      45 ..       2      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 2.1e-18
                                  S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHH CS
                   MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkele 44
                                  +g  e+++  +ValllFGp+k PE ar+LGk+  eFk++++ +e
  gi|91772973|ref|YP_565665.1|  2 IGSMEIIVSSLVALLLFGPDKFPEFARSLGKAVGEFKNELRKAE 45
                                  688999**********************************9876 PP

>> DUF1804  Protein of unknown function (DUF1804)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00052       4.6     124     163 ..       4      43 ..       1      44 [. 0.91
   2 !    9.9   0.0   7.4e-05      0.66      79     114 ..      63     100 ..      44     104 .] 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00052
                       DUF1804 124 klavalevlellaefvrekfpehaealleiLepfgeelak 163
                                    +++++  l  l+ f  +kfpe+a  l  ++ +f++el+k
  gi|91772973|ref|YP_565665.1|   4 SMEIIVSSLVALLLFGPDKFPEFARSLGKAVGEFKNELRK 43 
                                   57899999999999************************98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 7.4e-05
                       DUF1804  79 vqetleelrentelsaedkv..eiLasLsdsfsktvaa 114
                                   + + + +l e+  ++++ k+  e+L sLsd f+k+ ++
  gi|91772973|ref|YP_565665.1|  63 IDSHIRKLAEEGGIETKGKTtnEVLESLSDVFNKMNEI 100
                                   55667788888866665554338************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 665.62
//
Query:       gi|91772974|ref|YP_565666.1|  [L=262]
Description: hypothetical protein Mbur_0976 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       506  (0.0282224); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1859.36
//
Query:       gi|91772975|ref|YP_565667.1|  [L=316]
Description: hypothetical protein Mbur_0977 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2484.72
//
Query:       gi|91772976|ref|YP_565668.1|  [L=366]
Description: hypothetical protein Mbur_0978 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.5   0.1        0.1   12.3   0.1    1.6  1  DUF5053   Domain of unknown function (DUF5053)


Domain annotation for each model (and alignments):
>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.7e-06       0.1       3      50 ..     160     208 ..     159     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-06
                       DUF5053   3 ildivslsyiAkkYFgKsksWlyq.rlnGidvngkvatFteeeletLke 50 
                                   i+ ++s++++A  +   s+ Wly+ r++G +  + + +++ +  +t++ 
  gi|91772976|ref|YP_565668.1| 160 INSLLSMKSFAAPFLSVSQEWLYHfRIEGEESIKSKSGLSANKRDTFNY 208
                                   67899******************99***********9999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2742.23
//
Query:       gi|91772977|ref|YP_565669.1|  [L=225]
Description: RNA-binding S4 [Methanococcoides burtonii DSM 6242]
Scores for 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-13   49.3   0.1    5.7e-13   48.4   0.1    1.5  1  S4               S4 domain
    2.3e-08   34.3   0.0    3.7e-08   33.7   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    3.1e-07   29.8   0.0    4.5e-07   29.2   0.0    1.1  1  Fibrillarin      Fibrillarin
    8.9e-05   23.1   0.0    0.00013   22.6   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    0.00035   20.4   0.0    0.00047   20.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0087   16.7   0.0      0.015   15.9   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.031   14.1   0.1      0.071   12.9   0.1    1.6  1  S4_2             S4 domain
      0.038   13.6   0.1        1.9    8.0   0.0    2.2  2  MetW             Methionine biosynthesis protein MetW
       0.15   13.1   0.0       0.25   12.4   0.0    1.3  1  Methyltransf_24  Methyltransferase 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 !   48.4   0.1   2.9e-16   5.7e-13       1      48 []       1      48 [.       1      48 [. 0.97

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.9e-16
                                  EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                            S4  1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                  +RLd +l+++g  +sr   +++I +G+V+++G vv++ps  V+  D +
  gi|91772977|ref|YP_565669.1|  1 MRLDAYLVEMGSFKSRGRSKKAIVDGHVKIDGSVVTKPSKDVSIDDDV 48
                                  8******************************************99976 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   1.9e-11   3.7e-08       5      96 ..      59     151 ..      56     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.9e-11
                                   HHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T..-SEEEEEESSSS.....HHHTTEEEECS-CCCSSHHHHH CS
                          FtsJ   5 sayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlga.kgkvvavDlqpm.....aplpgvttiqgditdpetieki 79 
                                   + +KL  i+++ +l+k+g+ v+Dlg++ Gg++ ++++     +g  ++ D ++      + +++v+++ gd+++   + + 
  gi|91772977|ref|YP_565669.1|  59 GYFKLKGIQDETGLIKEGDSVLDLGSSAGGFIVFASEIAADvRGLEFSRDFREElgqiaHERSNVSVMFGDVFTFPLETMA 139
                                   789********************************999543557777888766688776666**********998766655 PP

                                   CHCHHHSSEEEEEE--S CS
                          FtsJ  80 kealserkvdlvvsDga 96 
                                         ++vd+++sD+ 
  gi|91772977|ref|YP_565669.1| 140 P-----EPVDVILSDMT 151
                                   5.....48********7 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.3e-10   4.5e-07      67     177 ..      72     180 ..      63     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.3e-10
                                   S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEE CS
                   Fibrillarin  67 pikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaD 147
                                    ik+g++vL lG+++G  +   s+i      v ++efs     el ++a++R+n+  + +D  +     +  e vDvi +D
  gi|91772977|ref|YP_565669.1|  72 LIKEGDSVLDLGSSAGGFIVFASEIAA---DVRGLEFSRDFREELGQIAHERSNVSVMFGDVFTFPLETMAPEPVDVILSD 149
                                   69***********************98...899****************************865445578899******** PP

                                   SS.STTHHHHHHHHHHHHEEEEEEEEEEEEH CS
                   Fibrillarin 148 va.qpdqarilaknaklflkeggyllisika 177
                                   ++ +p+    + k +   lk +g+ll +ik 
  gi|91772977|ref|YP_565669.1| 150 MTlEPEDSLAALKRVLPLLKLDGQLLQVIKM 180
                                   9846788878888888999999999999985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.3e-08   0.00013       1      97 []      79     172 ..      79     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.3e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSS...STTTEEEEEEESTGGGSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpf...edgsfDlvvssgalhhls 78 
                                   vLdlG   G ++  +++    a+v g+++s ++ e+  + a+e + nv+++ gd+ ++p+   + + +D+++s ++   l+
  gi|91772977|ref|YP_565669.1|  79 VLDLGSSAGGFIVFASEIA--ADVRGLEFSRDFREELGQIAHE-RSNVSVMFGDVFTFPLetmAPEPVDVILSDMT---LE 153
                                   9**********99999875..***************9998855.56***********995344888*******544...67 PP

                                   HHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                   +ed  +alk++  +Lk +G
  gi|91772977|ref|YP_565669.1| 154 PEDSLAALKRVLPLLKLDG 172
                                   899999*****99999877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.3e-07   0.00047       2     108 ..      74     175 ..      73     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsn 81 
                                   ++g +vlDlG+ +G ++  +  e+   a+v G+++s +  e   ++   ++ +nv++  gd+++++   +++e++D+ils+
  gi|91772977|ref|YP_565669.1|  74 KEGDSVLDLGSSAGGFIVFAS-EI--AADVRGLEFSRDFREELGQI--AHERSNVSVMFGDVFTFPLEtMAPEPVDVILSD 149
                                   67899**********999999.55..47899999999998888887..45778***********99888999********* PP

               Methyltransf_31  82 evlnaladpdkileeiervlkpggill 108
                                    +l    d+ ++l+++  +lk +g ll
  gi|91772977|ref|YP_565669.1| 150 MTL-EPEDSLAALKRVLPLLKLDGQLL 175
                                   999.55666666666666666666654 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.5e-06     0.015       1      94 [.      80     174 ..      80     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.5e-06
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-T...T-EEEEEEES-CCC-CCHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfed...nsfDlvvssevlhhvedpe 78 
                                   Ld+G+ +G +     + +a+v g+++s  +++   + a+e+  +v+++ +d+ ++p+e    + +D+++s ++l+   d  
  gi|91772977|ref|YP_565669.1|  80 LDLGSSAGGFIVFASEIAADVRGLEFSRDFREELGQIAHERS-NVSVMFGDVFTFPLETmapEPVDVILSDMTLEPE-DSL 158
                                   8**************999*************88877777777.599999*****996553338*********99987.577 PP

                                   HHHHHHHHHEEEEEEE CS
               Methyltransf_11  79 kalkeiaRvLkpgGll 94 
                                   +alk +  +Lk +G l
  gi|91772977|ref|YP_565669.1| 159 AALKRVLPLLKLDGQL 174
                                   7888888888888876 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.6e-05     0.071       9      59 ..       2      52 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                          S4_2  9 tLgqlLKlaglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVeidg 59
                                  +L+  L ++g  +s g  K  i +g+Vk++G v t+  k +  +d V++d+
  gi|91772977|ref|YP_565669.1|  2 RLDAYLVEMGSFKSRGRSKKAIVDGHVKIDGSVVTKPSKDVSIDDDVKVDE 52
                                  57777777788888899******************************9986 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00096       1.9      10      47 ..      72     108 ..      66     153 .. 0.85
   2 ?    3.8   0.0     0.019        38      15      61 ..     162     215 ..     149     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00096
                          MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldee 47 
                                   lik+g  vldlG+  G ++ +   e   d rGle +++
  gi|91772977|ref|YP_565669.1|  72 LIKEGDSVLDLGSSAGGFIVFA-SEIAADVRGLEFSRD 108
                                   89***************99776.55889999**99876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.019
                          MetW  15 srvldlGcGdGellellkeekqvdg.......rGleldeegvaecvakGlsviq 61 
                                    rvl l   dG+ll+++k +k ++        +Gl l+ ++v e+ ++ ++v+ 
  gi|91772977|ref|YP_565669.1| 162 KRVLPLLKLDGQLLQVIKMSKRIKRepllsimEGLSLEIQNVLESEKQEIYVVA 215
                                   689999999************998622222224666666666666666666665 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.25      31     101 ..     109     174 ..      80     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
               Methyltransf_24  31 hdpgaeeaaalareaglddrvrlikadseea.laslaagsiDllfiDgghaaeavledleallprlapggvv 101
                                     +   e +++a e   +++v ++ +d +   l+++a +++D+++ D+  + e+ l++l+ +lp+l+ +g +
  gi|91772977|ref|YP_565669.1| 109 FRE---ELGQIAHE---RSNVSVMFGDVFTFpLETMAPEPVDVILSDMTLEPEDSLAALKRVLPLLKLDGQL 174
                                   333...55555555...88999999999995488999*****************************988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); 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:                         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: 00:00:00.39
# Mc/sec: 1716.89
//
Query:       gi|91772978|ref|YP_565670.1|  [L=360]
Description: NADH peroxidase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-70  238.4   0.0    1.6e-70  238.1   0.0    1.0  1  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
    0.00091   18.7   0.0     0.0028   17.1   0.0    1.8  2  His_biosynth  Histidine biosynthesis protein
     0.0013   17.9   0.0      0.055   12.6   0.0    2.2  2  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.1   0.0   2.6e-74   1.6e-70       2     338 ..       2     335 ..       1     338 [. 0.84

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 2.6e-74
                                   CCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGGGHHHH CS
                  Oxidored_FMN   2 LFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksggfdnapgiwdeeqieew 82 
                                   LF+Pi++   t+knR+v ++     a+ +g+v++    + y+  a+ +v+liit+++ v+ k++  + + gi+d+  i  +
  gi|91772978|ref|YP_565670.1|   2 LFEPITMAGLTVKNRFVRSATNEGMAELDGTVTK-GIGDMYEDLAREDVGLIITGYSYVDVKGQSDERQQGIYDDRFIGPY 81 
                                   9********************9999999998888.67778888************************************** PP

                                   HHHHHHHHHTT-EEEEEEE--GGGS...SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHHHHHHHHHH CS
                  Oxidored_FMN  83 rklteavhengskvvvqlwhlGreak.seyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqefveAAkrai 162
                                   r+++  vh+++sk+++q+ h+Gr++  +e +a      ps  v+ +a+    +++v   e+t+e+i ++i++f+eAA+r++
  gi|91772978|ref|YP_565670.1|  82 REIVSRVHKYDSKIFLQIVHGGRQSIvKEGVALLA---PS-AVEDPAS---GKVPV---EMTEEDIFDTIENFAEAARRSK 152
                                   *************************8455555555...66.3344444...45677...********************** PP

                                   HTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSS.EEEEEECE--ST..TS--HHHH CS
                  Oxidored_FMN 163 eAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeer.vgyRlSpedvve..kgldfaet 240
                                   eAgfDgV+ih a+G+Ll  F+sp++n+rtD++gGs+enRar + e+v+ ++e+vg+++ v++++ + d ++  +g+++ ++
  gi|91772978|ref|YP_565670.1| 153 EAGFDGVQIHCAHGFLLSSFISPYTNHRTDKWGGSVENRARIVTEIVKRIQEKVGKDFpVMVKMNATDGFDvfSGKIGLDA 233
                                   ********************************************************************9882245555555 PP

                                   HHHHHHHCHCCEEEEEEE...TT-SSSSS...TTS-TTTTHHHCCTTHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS CS
                  Oxidored_FMN 241 aqkivllkelekrlkdgk...klalvhaa...eprkrgagsvrteqekntefvkevwkkplitvgriadeekaaeivaege 315
                                     ++v+++ l +++ ++    ++ + +a    ++   ++  ++ + ++  +++   +k p+i vg+i  + +++ i+ +g+
  gi|91772978|ref|YP_565670.1| 234 -PECVEIASLLEKAGICAievSGGIFEAGpvmSQNGIDSEDKEAYFRRYSKMILDTVKIPVILVGGIRTKAVMESIL-RGY 312
                                   .66666666666666554111344445440003333344444444556679999*****************887775.8** PP

                                   -SEEEESTHHHH-TTHHHHHHCC CS
                  Oxidored_FMN 316 adLvamgRefladpdlveklkkg 338
                                   ad++++ R+f+a+pdlv klk+g
  gi|91772978|ref|YP_565670.1| 313 ADMISLSRPFIAEPDLVVKLKEG 335
                                   *********************98 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.34     2e+03     110     161 ..     197     248 ..     189     254 .. 0.60
   2 !   17.1   0.0   4.7e-07    0.0028      66     117 ..     283     334 ..     269     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHCGG.GEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT- CS
                  His_biosynth 110 elikelaekfgsq.kivvaiDarrgykvaikgwreetgldavelakkleelga 161
                                   e++k++ ek+g++  ++v   a +g++v+  +   + + + ve+a+ le++g+
  gi|91772978|ref|YP_565670.1| 197 EIVKRIQEKVGKDfPVMVKMNATDGFDVFSGKIGLD-APECVEIASLLEKAGI 248
                                   667777777777534566677777755554333333.4555666666666555 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.7e-07
                                   HHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHH CS
                  His_biosynth  66 eeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelae 117
                                   + i+++v+ipv + GGIr+   +e++l+  ad ++++   + +p+l+ +l e
  gi|91772978|ref|YP_565670.1| 283 KMILDTVKIPVILVGGIRTKAVMESILRGYADMISLSRPFIAEPDLVVKLKE 334
                                   568999****************************************999877 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.1   0.0    0.0069        41     119     159 ..     118     163 ..     106     166 .. 0.81
   2 !   12.6   0.0   9.2e-06     0.055     101     223 ..     186     329 ..     175     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0069
                                   CCSSS-EEEEEESESS.....TTTC.HHHHHHHHHHCT-SEEEEES CS
                           Dus 119 kaveiPvtvkirigid.....deeenalelakiveaaGaqaltvHg 159
                                   +ave P + k+ + +      d+ en  e+a++ ++aG + + +H+
  gi|91772978|ref|YP_565670.1| 118 SAVEDPASGKVPVEMTeedifDTIENFAEAARRSKEAGFDGVQIHC 163
                                   56777777666666554456799999*******************8 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.2e-06
                                   GGGGGSHHHHHHHHHHHHCCSS..S-EEEEEESESS..........TTTC.HHHHHHHHHHCT-SEEEEESS........E CS
                           Dus 101 aaLlrkpdlvaqivkavvkave..iPvtvkirigid..........deeenalelakiveaaGaqaltvHgR........t 161
                                    +  + ++ v +ivk ++++v+  +Pv vk+               d   +++e+a  +e+aG+ a+ v g         +
  gi|91772978|ref|YP_565670.1| 186 GSVENRARIVTEIVKRIQEKVGkdFPVMVKMNATDGfdvfsgkiglD-APECVEIASLLEKAGICAIEVSGGifeagpvmS 265
                                   5555678899***********999*******8744333776666534.556********************99**999663 PP

                                   CCCTT-C..G--CHHHHH.HHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHH CS
                           Dus 162 raqnyeg..tadweaIke.vkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlf 223
                                   ++   ++  +a++++ ++ + + v+ipvi  G+I++   ++ il+   ad +  +r    +P l+
  gi|91772978|ref|YP_565670.1| 266 QNGIDSEdkEAYFRRYSKmILDTVKIPVILVGGIRTKAVMESILRG-YADMISLSRPFIAEPDLV 329
                                   3322222468999887662567778**********99999999876.466666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2311.27
//
Query:       gi|91772979|ref|YP_565671.1|  [L=235]
Description: ABC heme exporter, inner membrane subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete 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-26   91.6  15.0    5.9e-26   91.6  15.0    2.0  2  Cytochrom_C_asm  Cytochrome C assembly protein
  ------ inclusion threshold ------
          6    6.9   0.0          6    6.9   0.0    4.2  5  FixQ             Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6  15.0   6.6e-30   5.9e-26      29     210 ..       6     172 ..       1     175 [. 0.92
   2 ?   -1.0   0.1      0.14   1.3e+03     188     203 ..     198     213 ..     192     224 .. 0.54

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 6.6e-30
               Cytochrom_C_asm  29 lnlsllaavaliaalillgfalflllaelqesadlnpalqspilmiHvplallsYatliigallsialliierqlkkkkkl 109
                                   l +++l  ++++++l+++g+++f  l +++ ++  +   + +i+++H p+a++sY ++++ ++ si++l            
  gi|91772979|ref|YP_565671.1|   6 LRDKFLPVLSATTMLLAIGMIIF-YLPDMKGASGETLDMSFRIFYFHMPIAITSYLAFTVIFFSSILFL------------ 73 
                                   45689999***************.7777888888888899*****************************............ PP

               Cytochrom_C_asm 110 klsanlkllkqldrlsyriiliGfvlltigiilGsvWaeeaWGsywsWDpketaslitWlvfaallhsri..ek.gwrgkk 187
                                         +    +d ls+++  +G+++ ++ + +Gs+Wa+ +WG yw+W p++t sl ++lv+ a++++r       +r++ 
  gi|91772979|ref|YP_565671.1|  74 -----RTGKYGYDILSRSASEVGVIFAFLVLATGSIWARATWGWYWVWEPRLTTSLALFLVYVAYIVLRQavDGvDKRARL 149
                                   .....3445567999******************************************************997668999*** PP

               Cytochrom_C_asm 188 aailailgflllllayfgvrllg 210
                                   a+++ ilgf+ ++l ++++rl++
  gi|91772979|ref|YP_565671.1| 150 ASVFGILGFISVPLSFLSIRLWR 172
                                   *********************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.14
               Cytochrom_C_asm 188 aailailgflllllay 203
                                   ++++++++f+ll +  
  gi|91772979|ref|YP_565671.1| 198 TLLVNVIAFTLLFITL 213
                                   4445555555544443 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.4         1   9.2e+03      20      28 ..      20      28 ..      17      30 .. 0.53
   2 ?   -2.5   1.3      0.58   5.2e+03      16      25 ..      60      69 ..      56      73 .. 0.57
   3 ?    2.4   0.1     0.017   1.5e+02       3      29 ..      80     106 ..      79     107 .. 0.91
   4 ?    1.9   0.1     0.025   2.3e+02      20      30 ..     125     135 ..     122     150 .. 0.63
   5 ?    6.9   0.0   0.00067         6      16      40 ..     204     229 ..     201     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1
                          FixQ 20 llfygvviy 28
                                  ll +g++i+
  gi|91772979|ref|YP_565671.1| 20 LLAIGMIIF 28
                                  445555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.58
                          FixQ 16 lflvllfygv 25
                                  l+++++f   
  gi|91772979|ref|YP_565671.1| 60 LAFTVIFFSS 69
                                  4566666544 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.017
                          FixQ   3 yealrgfadswgllflvllfygvviya 29 
                                   y++l+  a  +g +f +l+++   i+a
  gi|91772979|ref|YP_565671.1|  80 YDILSRSASEVGVIFAFLVLATGSIWA 106
                                   88999999999**********999998 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.025
                          FixQ  20 llfygvviyaf 30 
                                   +lf+ +v+y+ 
  gi|91772979|ref|YP_565671.1| 125 ALFLVYVAYIV 135
                                   45666666654 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.00067
                          FixQ  16 lflvllfygvviyafrpgn.rkdfed 40 
                                   ++++llf+ +v+y +r +  +++ ++
  gi|91772979|ref|YP_565671.1| 204 IAFTLLFITLVVYKMRNEQmEERADE 229
                                   89**************9997777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1596.82
//
Query:       gi|91772980|ref|YP_565672.1|  [L=224]
Description: ABC heme exporter, inner membrane subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-37  129.5  18.8    1.4e-37  129.3  18.8    1.0  1  CcmB             CcmB protein
    9.5e-16   57.8  17.0    9.5e-16   57.8  17.0    1.5  1  ABC2_membrane    ABC-2 type transporter
    3.3e-09   36.3  22.7    3.3e-09   36.3  22.7    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
    1.3e-05   24.6  22.8    3.4e-05   23.3  15.3    2.4  2  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.24   11.3   0.0       0.24   11.3   0.0    3.5  4  Deltameth_res    Deltamethrin resistance


Domain annotation for each model (and alignments):
>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3  18.8   3.9e-41   1.4e-37       4     207 ..       7     216 ..       4     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 3.9e-41
                          CcmB   4 lllrdlrlalRakgelllgllFfllvvtllplavGP...dtallsriapgilWvaallaslLsldrlfaadfedGsLelll 81 
                                   + ++dl+ ++R+k+ l   +lF llv++++ +++ P    ++ ++ +apg+lW+a ++a  ++l r f a+ e+G Le l 
  gi|91772980|ref|YP_565672.1|   7 IAAKDLKEEFRTKQMLNSMVLFSLLVIVVFSITFAPilgSSQDVAMVAPGVLWIAFIFAGSIGLSRSFVAELENGCLEGLK 87 
                                   7789********************************55556889999********************************** PP

                          CcmB  82 lapvplellvlaKalAhwlltglplvllapllalllnleaaalgllaltLllGtpalsllgavgaAltvgLkrgglLlslL 162
                                   l p++ ++++++K++A+ ll++l  +++ pl+a+++n  ++++ +la+ + lGt ++ ++g++ +Altv+ +  ++Ll++L
  gi|91772980|ref|YP_565672.1|  88 LCPISRSAIYTGKMVANLLLMLLVEIITVPLFAIMFNYSITGYFWLAIIIFLGTVGFVCVGTLLSALTVNTRTREILLPVL 168
                                   ********************************************************************************* PP

                          CcmB 163 vlPliiPvlifaveaveaaaeg...ldveaalalllaltvvtlvlapf 207
                                    lPl +P li av a+     g    d++  l+lll  ++v+ ++a +
  gi|91772980|ref|YP_565672.1| 169 LLPLLLPALIPAVMATGSILIGasyGDITQELRLLLVYDIVFFLVAQL 216
                                   *************99999988855567788899999999888888765 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8  17.0   2.7e-19   9.5e-16       4     174 ..       5     174 ..       3     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2.7e-19
                 ABC2_membrane   4 kallkreflqrwrdpslgllwrliqplllalvfgtvfgn.lgnsedgl.nrpgllffsvlflafsaltsvapvferergvl 82 
                                   + +  ++++  +r+++++  +++++ ll+++vf   f   lg+s+d++   pg+l ++++f + s+  s ++v e e+g l
  gi|91772980|ref|YP_565672.1|   5 LYIAAKDLKEEFRTKQML-NSMVLFSLLVIVVFSITFAPiLGSSQDVAmVAPGVLWIAFIFAG-SIGLSRSFVAELENGCL 83 
                                   66788999999****888.9******************7444777777355************.6666666********** PP

                 ABC2_membrane  83 erelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf.flflllllltalaasslgllisalapsfedas 162
                                   e +   p+ s+sa++++k++++l+++ll+ +i + ++ +++++ ++ + f++ ++++l ++ ++++g l+sal+++ ++  
  gi|91772980|ref|YP_565672.1|  84 EGLKLCPI-SRSAIYTGKMVANLLLMLLVEIITVPLFAIMFNYSIT-GyFWLAIIIFLGTVGFVCVGTLLSALTVNTRTRE 162
                                   ********.************************************9.55******************************** PP

                 ABC2_membrane 163 qlaslvllplll 174
                                   +l +++llplll
  gi|91772980|ref|YP_565672.1| 163 ILLPVLLLPLLL 174
                                   *********986 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3  22.7   9.2e-13   3.3e-09     146     281 ..      37     174 ..       4     190 .. 0.80
   2 ?   -0.2   0.7      0.12   4.2e+02     306     343 ..     176     214 ..     167     215 .. 0.64

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 9.2e-13
               ABC2_membrane_3 146 nvestqleeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllil. 225
                                   +++  +   ++++va  + g++ i +if +++ +++s+v E e++ +e+++++++s+++++++k+++ +l++ll+ ++++ 
  gi|91772980|ref|YP_565672.1|  37 SITFAPILGSSQDVAMVAPGVLWIAFIFAGSIGLSRSFVAELENGCLEGLKLCPISRSAIYTGKMVANLLLMLLVEIITVp 117
                                   44445556677888888888999****************************************************999875 PP

               ABC2_membrane_3 226 ..llafglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivil.lls 281
                                     +++f+  ++++++++l + ++l+   ++++g+lls+l+ n++t  il+++++l ll+
  gi|91772980|ref|YP_565672.1| 118 lfAIMFN--YSITGYFWLAIIIFLGTVGFVCVGTLLSALTVNTRTREILLPVLLLpLLL 174
                                   3347***..******************************99998877777666663233 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
               ABC2_membrane_3 306 ffapglgllrli.tgdplweillsliilalfavvyllla 343
                                      p+++ +  i  g+++ +i + l +l++  +v++l+a
  gi|91772980|ref|YP_565672.1| 176 ALIPAVMATGSIlIGASYGDITQELRLLLVYDIVFFLVA 214
                                   444444443332477777778888888888888888765 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 !    4.6   3.2    0.0047        17     154     211 ..      14      68 ..       5      80 .. 0.55
   2 !   23.3  15.3   9.4e-09   3.4e-05      94     225 ..      71     193 ..      57     217 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0047
               ABC2_membrane_2 154 ivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpi 211
                                    +++++++l+ +v++ ll+++v  ++++++  ++  s+ +a+ +  +l++++ ++ +i
  gi|91772980|ref|YP_565672.1|  14 EEFRTKQMLNSMVLFSLLVIVV--FSITFA-PILGSSQDVAMVAPGVLWIAFIFAGSI 68 
                                   4556666666666666666633..444443.344445556666666666665555444 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 9.4e-09
               ABC2_membrane_2  94 adaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllll 174
                                   + +++ E e+g l+ l   P+sR++i++gK++++l++   +++  ++tv l +ai+  ++i   +  +l ++++  ++++ 
  gi|91772980|ref|YP_565672.1|  71 SRSFVAELENGCLEGLKLCPISRSAIYTGKMVANLLL---MLLVEIITVPL-FAIMFNYSITGYF--WLAIIIFLGTVGF- 144
                                   578999*******************************...********666.6666555555544..4555555554566. PP

               ABC2_membrane_2 175 vvflalglllSsvarssrea...aalalglfvvlailvpivlygvaellagpav 225
                                      + +g+llS+++ ++r+    + + l  +++ a++  +++   +++l g+++
  gi|91772980|ref|YP_565672.1| 145 ---VCVGTLLSALTVNTRTReilLPVLLLPLLLPALIPAVMA--TGSILIGASY 193
                                   ...445666666665444330003334444444444444444..3444444444 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.8e-05      0.24      10      40 ..      12      42 ..       9      48 .. 0.90
   2 ?   -0.8   0.0      0.41   1.5e+03      31      42 ..      63      74 ..      60      80 .. 0.82
   3 ?    1.9   1.1     0.057     2e+02      25      40 ..     131     146 ..     123     154 .. 0.83
   4 ?   -3.3   0.1       2.5   8.8e+03      30      42 ..     181     193 ..     180     197 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-05
                 Deltameth_res 10 wkeqysakqrkYNavLaaGiviligTialak 40
                                   ke++++kq+   +vL++ +vi++++i++a 
  gi|91772980|ref|YP_565672.1| 12 LKEEFRTKQMLNSMVLFSLLVIVVFSITFAP 42
                                  599*************************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.41
                 Deltameth_res 31 iligTialakes 42
                                  i++g+i+l +++
  gi|91772980|ref|YP_565672.1| 63 IFAGSIGLSRSF 74
                                  899***998875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.057
                 Deltameth_res  25 LaaGiviligTialak 40 
                                   + ++i+i+ gT++++ 
  gi|91772980|ref|YP_565672.1| 131 FWLAIIIFLGTVGFVC 146
                                   5679********9986 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2.5
                 Deltameth_res  30 viligTialakes 42 
                                   v+  g+i ++ + 
  gi|91772980|ref|YP_565672.1| 181 VMATGSILIGASY 193
                                   4555666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1271.18
//
Query:       gi|91772981|ref|YP_565673.1|  [L=266]
Description: ABC heme exporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-34  119.6   0.0    1.8e-34  119.2   0.0    1.2  1  ABC_tran    ABC transporter
    2.2e-08   34.3   4.6     0.0015   18.4   0.4    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0004   20.2   0.2     0.0009   19.1   0.1    1.5  2  AAA_15      AAA ATPase domain
    0.00057   19.6   0.3     0.0015   18.2   0.1    1.8  2  AAA_29      P-loop containing region of AAA domain
     0.0017   18.8   0.0      0.007   16.8   0.0    1.9  1  AAA         ATPase family associated with various cellular ac
      0.003   17.9   0.0     0.0047   17.3   0.0    1.3  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.011   16.0   0.4        2.4    8.5   0.0    2.3  2  AAA_22      AAA domain
      0.013   16.0   0.1      0.026   15.0   0.1    1.4  1  AAA_23      AAA domain
      0.018   15.3   0.1      0.052   13.8   0.0    1.7  2  AAA_28      AAA domain
      0.031   13.0   0.0      0.038   12.6   0.0    1.1  1  AAA_13      AAA domain
      0.036   14.1   0.0      0.084   12.9   0.0    1.8  1  AAA_5       AAA domain (dynein-related subfamily)
      0.044   13.4   0.2       0.12   11.9   0.0    1.8  2  AAA_25      AAA domain
      0.046   13.3   0.1        0.5    9.9   0.0    2.1  2  AAA_27      AAA domain
      0.056   13.4   0.0       0.11   12.5   0.0    1.5  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
      0.093   13.3   0.3       0.29   11.7   0.3    2.0  1  AAA_18      AAA domain
      0.097   12.1   0.2        0.9    8.9   0.0    2.0  2  SMC_N       RecF/RecN/SMC N terminal domain
        0.1   12.6   0.0        0.3   11.1   0.0    2.0  1  AAA_14      AAA domain
       0.13   12.6   0.8        9.1    6.6   0.1    2.1  2  AAA_19      AAA domain
       0.13   11.8   0.1       0.29   10.7   0.1    1.5  1  SRP54       SRP54-type protein, GTPase domain
       0.15   12.0   0.1       0.32   10.9   0.1    1.5  1  NACHT       NACHT domain
       0.15   11.8   0.2       0.61    9.8   0.1    1.8  2  AAA_30      AAA domain
       0.27   10.5   0.7       0.57    9.4   0.1    1.8  3  Zeta_toxin  Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0   2.3e-37   1.8e-34       1     136 [.      44     187 ..      44     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 2.3e-37
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   lk+++l++k+ge va++G nGaGK+tL+k+++ l++p eG++ ++g+d+++ +  slr  igv+++e+ l ++lt+ en  
  gi|91772981|ref|YP_565673.1|  44 LKDIDLDIKKGEFVALLGANGAGKTTLVKIMSALSSPSEGTVMVNGNDISN-DQGSLRGIIGVISHETYLYNDLTAVENlh 123
                                   799************************************************.99*************************** PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              + +++i+ +l++++l++ +d++v    s++S G+kqr+++arall +p++l+lDEp 
  gi|91772981|ref|YP_565673.1| 124 ffgqmysiaseNLEARINGLLEEVELVKRADDRV----STFSRGMKQRLSIARALLHEPSILFLDEPY 187
                                   ********99999999******************....*****************************5 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4   1.8e-06    0.0015       1      26 [.      56      86 ..      56     114 .. 0.70
   2 !   17.8   0.4   2.9e-06    0.0023     210     298 ..     151     218 ..     122     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl.....d 26
                                  + +l G+Ng+GK++L ++++ l++      +
  gi|91772981|ref|YP_565673.1| 56 FVALLGANGAGKTTLVKIMSALSSPsegtvM 86
                                  679*****************99875655332 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.9e-06
                        AAA_21 210 asvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrnga 290
                                   +++d+r                  ++ +S G+k+ l ++ all  +   s+l++DEp +gL+ ++ +++ ++l el  +++
  gi|91772981|ref|YP_565673.1| 151 KRADDR------------------VSTFSRGMKQRLSIARALLHEP---SILFLDEPYTGLDQHAAHTFEKVLLELDPKDT 210
                                   444444..................4558*******99999999988...********************999977777777 PP

                        AAA_21 291 QviltTHS 298
                                     ++ TH+
  gi|91772981|ref|YP_565673.1| 211 TRLMITHD 218
                                   77999997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.1e-06    0.0009      14      67 ..      44      94 ..      40     142 .. 0.84
   2 ?   -2.6   0.0       4.1   3.4e+03     323     361 ..     177     215 ..     160     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedlei 67
                                  lkd+++d+++  +  l G+N++GK+++++++  + + +    + ++ ++ +d+++
  gi|91772981|ref|YP_565673.1| 44 LKDIDLDIKKGeFVALLGANGAGKTTLVKIMSALSSPS----EGTVMVNGNDISN 94
                                  799999999989***********************999....6666666666654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                        AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                   ++ il+++EP + L   a   + k l+el  ++ t ++i
  gi|91772981|ref|YP_565673.1| 177 EPSILFLDEPYTGLDQHAAHTFEKVLLELDPKDTTRLMI 215
                                   457999999988887777777777777776555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.8e-06    0.0015      16      51 ..      48      84 ..      40      96 .. 0.76
   2 ?   -2.7   0.0       6.3   5.1e+03      10      25 ..     196     211 ..     196     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak.k 51
                                  +++i+  +++ l G++G+GK+Tl+  ++al  p++ +
  gi|91772981|ref|YP_565673.1| 48 DLDIKKGEFVALLGANGAGKTTLVKIMSALSSPSEgT 84
                                  4566644599**************9999998888763 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                        AAA_29  10 gtfdghtieidlkgat 25 
                                   +tf++  +e+d+k++t
  gi|91772981|ref|YP_565673.1| 196 HTFEKVLLELDPKDTT 211
                                   7999999999999954 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   8.6e-06     0.007       2      74 ..      58     193 ..      57     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.6e-06
                                   EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................... CS
                           AAA   2 llyGppGtGKTllakavakelg..vefleisgsellsk........................................... 37 
                                    l G  G GKT+l+k +   ++     + ++g ++ ++                                           
  gi|91772981|ref|YP_565673.1|  58 ALLGANGAGKTTLVKIMSALSSpsEGTVMVNGNDISNDqgslrgiigvishetylyndltavenlhffgqmysiasenlea 138
                                   689************988887543558999999999778999999999999999999999999999999999999999999 PP

                                   .................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                           AAA  38 .................yvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                                     v+  ++ +++ ++ a++   +psilf+DE +    + 
  gi|91772981|ref|YP_565673.1| 139 ringlleevelvkraddRVSTFSRGMKQRLSIARALLhEPSILFLDEPYTGLDQH 193
                                   9999999999888888888888888888888887777999*******77665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.8e-06    0.0047      24     143 ..      54     185 ..      46     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.8e-06
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa...........ipysalaqalareellrqllde.... 88 
                                   +e v l G+ G GK++lv+      + ++g + ++g+  +++++                        ++l   l++    
  gi|91772981|ref|YP_565673.1|  54 GEFVALLGANGAGKTTLVKIMSALSSPSEGTVmVNGNDISNDQGslrgiigvishE------------TYLYNDLTAvenl 122
                                   4789**************76665444445555599998888666444444443331............2222222222333 PP

                        AAA_16  89 ........aesaeleawrekleealaavpelagaeasrllellkrllallsrd.erplvlvlDd 143
                                            +s +lea    l+e+++   + a++  s + + +k+ l+ ++   ++p +l+lD+
  gi|91772981|ref|YP_565673.1| 123 hffgqmysIASENLEARINGLLEEVE-LVKRADDRVSTFSRGMKQRLSIARALlHEPSILFLDE 185
                                   33333332222255555555555555.4444444457777777777733333304479999995 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0029       2.4       4      24 ..      53      73 ..      49      91 .. 0.87
   2 ?    5.7   0.1      0.02        16      37     115 ..     172     255 ..     135     262 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0029
                        AAA_22  4 tagilvvtGesGtGKTtllrr 24
                                  +  ++++ G  G+GKTtl++ 
  gi|91772981|ref|YP_565673.1| 53 KGEFVALLGANGAGKTTLVKI 73
                                  667999************985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                        AAA_22  37 e...erpevvfvtlpsst...sskdllrellralglelkaerlsseell.ealeqalraravielliiDEaqhlr.....s 105
                                   +   ++p+++f + p  +     +  ++++l +l+       ++++ ++ + +++a + +++  ++i+D    ++     +
  gi|91772981|ref|YP_565673.1| 172 RallHEPSILFLDEPYTGldqHAAHTFEKVLLELD----P-KDTTRLMItHDINRAYHMCDR--VIILDKGSIVFdslmsQ 245
                                   25567788888888888865555555666666666....2.34566666799********99..****9754433333333 PP

                        AAA_22 106 eealeeLrsl 115
                                       eeLr++
  gi|91772981|ref|YP_565673.1| 246 VVSAEELRDI 255
                                   5555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   3.2e-05     0.026      11      37 ..      45      72 ..      29      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-05
                        AAA_23 11 rdqeidF.skgltlItGpNGaGKTTild 37
                                  +d ++d  +  ++++ G NGaGKTT++ 
  gi|91772981|ref|YP_565673.1| 45 KDIDLDIkKGEFVALLGANGAGKTTLVK 72
                                  44444444446889***********986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.4e-05     0.052       2      22 ..      57      77 ..      56     101 .. 0.78
   2 ?   -1.2   0.0       2.7   2.2e+03      71      79 ..     176     184 ..     117     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-05
                        AAA_28  2 ivitGgestGKTtlleaLaar 22
                                  ++++G+ ++GKTtl++ ++a 
  gi|91772981|ref|YP_565673.1| 57 VALLGANGAGKTTLVKIMSAL 77
                                  89*************988865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                        AAA_28  71 aankvlfcD 79 
                                   +++ +lf+D
  gi|91772981|ref|YP_565673.1| 176 HEPSILFLD 184
                                   344444444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.7e-05     0.038      22      68 ..      60     115 ..      54     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                        AAA_13  22 YGwNGaGKTtLSrllrslelgetepkfangsieitnge..........eldirVfNr 68 
                                    G+NGaGKTtL ++++ l++ +  + + ng+  i+n++          ++++  +N+
  gi|91772981|ref|YP_565673.1|  60 LGANGAGKTTLVKIMSALSSPSEGTVMVNGN-DISNDQgslrgiigviSHETYLYND 115
                                   59***************97655443333332.3333333345555555555666655 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    0.0001     0.084       3      40 ..      58      96 ..      57     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                  EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHH CS
                         AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvqltrdtteed 40
                                   L+G+ G gK++l++ ++a+   +e +++ +  d++ ++
  gi|91772981|ref|YP_565673.1| 58 ALLGANGAGKTTLVKIMSALSsPSEGTVMVNGNDISNDQ 96
                                  69******************9988888888888888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.12      30      50 ..      51      71 ..      35      94 .. 0.88
   2 ?   -1.4   0.0       1.8   1.4e+03     131     151 ..     188     208 ..     132     246 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                        AAA_25 30 lpagelallaGapgtGKttla 50
                                  + +ge+++l Ga g+GKttl+
  gi|91772981|ref|YP_565673.1| 51 IKKGEFVALLGANGAGKTTLV 71
                                  689****************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                        AAA_25 131 daleaaieevegvrlvviDpl 151
                                     l++++ ++ + +l+ +Dp 
  gi|91772981|ref|YP_565673.1| 188 TGLDQHAAHTFEKVLLELDPK 208
                                   444444444433444444433 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00062       0.5      18      49 ..      46      77 ..      35      79 .. 0.78
   2 ?    1.1   0.0      0.32   2.6e+02     115     139 ..     121     145 ..      93     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00062
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   +d++ ++ ++  ++G+N AGK+t+++ +s+l
  gi|91772981|ref|YP_565673.1| 46 DIDLDIKKGEFVALLGANGAGKTTLVKIMSAL 77
                                  4556666899**************99888766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.32
                        AAA_27 115 dretFealFgLdherLreGGealle 139
                                   + ++F +++++ +e+L++  + lle
  gi|91772981|ref|YP_565673.1| 121 NLHFFGQMYSIASENLEARINGLLE 145
                                   45789***********987777776 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   0.00014      0.11      19      40 ..      54      75 ..      30      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                  TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                  g++++L G  GaGKTtlv+ + 
  gi|91772981|ref|YP_565673.1| 54 GEFVALLGANGAGKTTLVKIMS 75
                                  677***************9764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00036      0.29       1      42 [.      57      95 ..      57     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevd 42
                                  ++l G+ G+GKttl k  s +   +  +  ++  ng  +++d
  gi|91772981|ref|YP_565673.1| 57 VALLGANGAGKTTLVKIMSAL---SSPSEGTVMVNGNDISND 95
                                  6899*************9887...333333333333333333 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 ?    8.9   0.0    0.0011       0.9      24      43 ..      54      73 ..      37      86 .. 0.81
   2 ?    1.2   0.0      0.25   2.1e+02     136     198 ..     159     218 ..     110     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                  SSEEEEEESTTSSHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 24 ksftaivGpNGSGKsnlldA 43
                                   +f a++G+NG+GK+ l+  
  gi|91772981|ref|YP_565673.1| 54 GEFVALLGANGAGKTTLVKI 73
                                  3699***********99864 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.25
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC.TTSEEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks.knaQfivislr 198
                                   ++S+G k+ +++    A    +  ++ +lDe    LD++  + + ++l e   k++  ++i+++
  gi|91772981|ref|YP_565673.1| 159 TFSRGMKQRLSI----ARALLHEPSILFLDEPYTGLDQHAAHTFEKVLLELDpKDTTRLMITHD 218
                                   556666554443....3334455677889999999**999999999877654155666667765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00037       0.3       3      45 ..      55      96 ..      53     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                  + +++ Ga  +GKTtl+k +   l  ++e ++ +n +d ++++
  gi|91772981|ref|YP_565673.1| 55 EFVALLGANGAGKTTLVKIMS-ALSSPSEGTVMVNGNDISNDQ 96
                                  67899***********96665.555699999999999988855 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.011       9.1      10      32 ..      54      76 ..      48      87 .. 0.81
   2 ?    4.6   0.1     0.047        38      67     138 ..     166     263 ..     132     265 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                        AAA_19 10 ekvllvtaGpGtGKTrvlkhiva 32
                                   + +++++  G GKT+++k + a
  gi|91772981|ref|YP_565673.1| 54 GEFVALLGANGAGKTTLVKIMSA 76
                                  67899**********99886654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.047
                        AAA_19  67 ae...........................atTiHrlalldfddlltealelleeaeeekklqeee.llivDEfqdvd.elq 118
                                   ++                           a+T+ ++ ll++d++ t+ l +   ++ ++  + ++ ++i D  + v   l+
  gi|91772981|ref|YP_565673.1| 166 QRlsiarallhepsilfldepytgldqhaAHTFEKV-LLELDPKDTTRLMI--THDINRAYHMCDrVIILDKGSIVFdSLM 243
                                   3344444455556777777777777777899**988.89999999777766..55566666667779999*9999877999 PP

                        AAA_19 119 yrLlkallgekkklllvGDp 138
                                    ++++a   ++ +   vGD 
  gi|91772981|ref|YP_565673.1| 244 SQVVSAEELRDIYSSHVGDY 263
                                   99988877666556667775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00036      0.29       4      38 ..      57      91 ..      55      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  ++l+G +GaGKTt +  ++al + ++ +v++   D
  gi|91772981|ref|YP_565673.1| 57 VALLGANGAGKTTLVKIMSALSSPSEGTVMVNGND 91
                                  789**********9998888888777777776655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00039      0.32       3      25 ..      57      78 ..      55      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                                  EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                  v+l G++G GKTtL++ +++a+ 
  gi|91772981|ref|YP_565673.1| 57 VALLGANGAGKTTLVK-IMSALS 78
                                  899***********95.666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00075      0.61      19      50 ..      55      86 ..      49      94 .. 0.82
   2 ?   -0.7   0.0       1.2   9.9e+02      70     124 ..     195     262 ..     183     264 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00075
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                   +++l G+ G+GKtt++k + ++   ++g+v+
  gi|91772981|ref|YP_565673.1| 55 EFVALLGANGAGKTTLVKIMSALSSPSEGTVM 86
                                  488999************99988877766665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                        AAA_30  70 astiakllkrlk.............grarlepgtllivDEagmvdtkqlaallkaaekagakvilvGD 124
                                   a+t +k+l +l+             +ra    ++++i D  + v  + + ++++a e +++    vGD
  gi|91772981|ref|YP_565673.1| 195 AHTFEKVLLELDpkdttrlmithdiNRAYHMCDRVIILDKGSIVFDSLMSQVVSAEELRDIYSSHVGD 262
                                   55666666555566666666666575555566689999999999999999999888877777777777 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0007      0.57      19      54 ..      57      92 ..      44     105 .. 0.87
   2 ?   -2.9   0.0       4.3   3.5e+03     157     188 ..     134     163 ..     131     168 .. 0.65
   3 ?   -3.2   0.0       5.3   4.3e+03     178     189 ..     225     236 ..     210     250 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0007
                    Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                  + l G+ GAGK++l + + +   + ++ v +++ d+
  gi|91772981|ref|YP_565673.1| 57 VALLGANGAGKTTLVKIMSALSSPSEGTVMVNGNDI 92
                                  66789************9999999999999998775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                    Zeta_toxin 157 eehdeafeglresvealeeekqldrvkikdrd 188
                                   e+ ++  +gl e+ve ++++   drv+ + r+
  gi|91772981|ref|YP_565673.1| 134 ENLEARINGLLEEVELVKRAD--DRVSTFSRG 163
                                   556677788888888887765..666655555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.3
                    Zeta_toxin 178 qldrvkikdrdg 189
                                    +drv+i d+++
  gi|91772981|ref|YP_565673.1| 225 MCDRVIILDKGS 236
                                   667777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1514.42
//
Query:       gi|91772982|ref|YP_565674.1|  [L=408]
Description: hypothetical protein Mbur_0984 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-09   37.5   0.1     0.0024   18.1   0.0    3.0  3  CARDB         CARDB
     0.0037   17.5   0.0         13    6.2   0.0    3.7  4  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
     0.0038   17.3   0.3      0.089   12.9   0.0    2.8  3  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.055   14.3   0.0        0.2   12.5   0.0    2.1  1  Filamin       Filamin/ABP280 repeat
       0.11   12.9   0.5        2.7    8.5   0.0    3.1  4  Arrestin_C    Arrestin (or S-antigen), C-terminal domain


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 ?   -1.0   0.0       0.6   2.1e+03       9      43 ..      41      75 ..      32     123 .. 0.62
   2 !   18.1   0.0   6.6e-07    0.0024       8      89 ..     155     235 ..     149     242 .. 0.93
   3 !   15.8   0.0   3.5e-06     0.013       9      91 ..     262     343 ..     255     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.6
                                  EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEE CS
                         CARDB  9 tlnpseafvgeentitvtvkNqGtaasgatkvaly 43
                                  +++ps+    ee+t+ ++++  G++a ++++ +++
  gi|91772982|ref|YP_565674.1| 41 EISPSSIGIDEEFTLGINIESCGSKAPEDITFEII 75
                                  55666777777888888888888887777766654 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.6e-07
                                   EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT- CS
                         CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvDpdn 88 
                                   +++np+  ++g+++ +++ ++N G+a +++++v+l  + +  +++t+  +  +++ t  f+++++  +ge ++ v ++ ++
  gi|91772982|ref|YP_565674.1| 155 VKTNPEYIYEGDTVDLRLGIENFGEAIAKSVSVSLEHEFKGIKNSTIGTIGMNGTQTALFKFKAN-RSGEFEIPVIIEYED 234
                                   6789999*********************************************************9.*******99999887 PP

                                   S CS
                         CARDB  89 e 89 
                                   +
  gi|91772982|ref|YP_565674.1| 235 D 235
                                   5 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 3.5e-06
                                   EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT CS
                         CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLaagesttvsftwtteategevtltvvvDpd 87 
                                   ++ p  ++ g+++++t+ ++N+G+ +  +++v  y+d   +  +++ +  L+++e   v +t+ ++ ++ge+++ v++  +
  gi|91772982|ref|YP_565674.1| 262 KVDPVLPYMGDTVELTMRIENSGERTINSIRV--YVDHPFKglKESFIGTLDPNEDGPVVITFIAD-QAGEYEIPVTITYS 339
                                   5667778999***************9998765..6666665559**********************.*******9999777 PP

                                   -SS- CS
                         CARDB  88 neva 91 
                                   ++  
  gi|91772982|ref|YP_565674.1| 340 DDFG 343
                                   6655 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.11   3.9e+02       5      78 ..      51     126 ..      48     127 .. 0.76
   2 !    4.9   0.0     0.009        32       3      29 ..     164     190 ..     162     191 .. 0.94
   3 !    6.2   0.0    0.0035        13       4      31 ..     271     298 ..     269     300 .. 0.94
   4 ?   -2.2   0.0       1.4   5.2e+03      67      78 ..     327     338 ..     324     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.11
                   NPCBM_assoc   5 etvtltltvtndgtaaatnvslsl.slPeGWtvvevspasaaslapGet.veatvkVtppagaaaGdyevtakarl 78 
                                   e+ tl + + + g++a +++ +++ s P++  ++e  ++++++l +  +    t  ++  ++a +G + +++++++
  gi|91772982|ref|YP_565674.1|  51 EEFTLGINIESCGSKAPEDITFEIiSIPSDIIITEDLVTKIPKLSYSTSeRHLTYHMRTTTDANPGPHIIKMRLTY 126
                                   5667777788888888888888862458888888888888888888765145788999999999999999998875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.009
                   NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslsls 29 
                                    G+tv l+l + n g+a a++vs+sl+
  gi|91772982|ref|YP_565674.1| 164 EGDTVDLRLGIENFGEAIAKSVSVSLE 190
                                   69***********************96 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0035
                   NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslP 31 
                                   G+tv+lt+ + n+g++++ ++++ ++ P
  gi|91772982|ref|YP_565674.1| 271 GDTVELTMRIENSGERTINSIRVYVDHP 298
                                   99*********************99988 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.4
                   NPCBM_assoc  67 aGdyevtakarl 78 
                                   aG+ye+ +++++
  gi|91772982|ref|YP_565674.1| 327 AGEYEIPVTITY 338
                                   89****999997 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   2.5e-05     0.089       2      96 ..      12     107 ..      10     111 .. 0.84
   2 ?   -3.1   0.0       2.4   8.8e+03      73      90 ..     209     226 ..     206     227 .. 0.76
   3 ?    1.2   0.0      0.11   3.9e+02      76      90 ..     318     332 ..     232     344 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                  Cupredoxin_1   2 laalavllllsskaaaaaektveitvkdggfePskievkagekvklkiknkdktp.eefesedlgeekvlapgktttitia 81 
                                   l++ +v+l+  s+a a+ + ++ + v+ ++++Ps+i + ++  + ++i+  ++++ e +++e +++  ++   +  + +i+
  gi|91772982|ref|YP_565674.1|  12 LLVFVVILTGISTAGAQTSGEICVNVEVQEISPSSIGIDEEFTLGINIESCGSKApEDITFEIISIPSDIIITEDLVTKIP 92 
                                   567788999999999***********************************9999779999999998888888888888888 PP

                  Cupredoxin_1  82 plkpGeYeftcdmhm 96 
                                   +l+  + e +  +hm
  gi|91772982|ref|YP_565674.1|  93 KLSYSTSERHLTYHM 107
                                   887666666666666 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                  Cupredoxin_1  73 gktttitiaplkpGeYef 90 
                                    +t+ +++++   Ge+e+
  gi|91772982|ref|YP_565674.1| 209 TQTALFKFKANRSGEFEI 226
                                   567778889999999875 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.11
                  Cupredoxin_1  76 ttitiaplkpGeYef 90 
                                    +it+ ++++GeYe+
  gi|91772982|ref|YP_565674.1| 318 VVITFIADQAGEYEI 332
                                   567788888888886 PP

>> Filamin  Filamin/ABP280 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05       0.2      17      92 ..     212     336 ..     132     340 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                                   E....ETTS-EEEEEEESSSTSCCCSTTS..EEEEE..ESSTS...................................... CS
                       Filamin  17 s....vagesltFtvytkdakgeksevggdelqvrivtgsphgaatk.................................. 59 
                                   +    +a++s +F++ +  ++++++ +++de  ++i++ +++g+ +                                   
  gi|91772982|ref|YP_565674.1| 212 AlfkfKANRSGEFEIPVIIEYEDDFGKQKDEYAITITVLDKKGSLNLasvkvdpvlpymgdtveltmriensgertinsir 292
                                   255556778889999999999999999999999999855665554446666666666666666666666655555555555 PP

                                   ............EEEEEEEE-SSSEEEEEE--SSSCEEEEEEEE CS
                       Filamin  60 s...........svkievvdnedgtytvsYtpeepgtyrvsvkl 92 
                                   +           s+    + nedg  ++++ + ++g+y++ v++
  gi|91772982|ref|YP_565674.1| 293 VyvdhpfkglkeSFIGTLDPNEDGPVVITFIADQAGEYEIPVTI 336
                                   05555566666655667***********************9985 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 ?   -1.2   0.0      0.72   2.6e+03      15      44 ..      46      75 ..      35     142 .. 0.75
   2 ?    0.5   0.0      0.22   7.8e+02       9      49 ..     155     195 ..     148     250 .. 0.67
   3 ?    8.5   0.0   0.00074       2.7      17      43 ..     269     295 ..     252     302 .. 0.89
   4 ?   -2.3   0.0       1.6   5.8e+03     105     129 ..     329     355 ..     318     359 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.72
                                  EEETT--EEEEEEEEE-SSSEEEEEEEEEE CS
                    Arrestin_C 15 gyvpGetipvtvkidndskkkvkkikvslv 44
                                  ++ + e+ ++ ++i++  +k  + i+++++
  gi|91772982|ref|YP_565674.1| 46 SIGIDEEFTLGINIESCGSKAPEDITFEII 75
                                  556666667777777777777777766655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                                   EEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEEE CS
                    Arrestin_C   9 aslpkkgyvpGetipvtvkidndskkkvkkikvslvqhvdv 49 
                                   ++++ + ++ G+t+++ + i+n      k+++vsl+   + 
  gi|91772982|ref|YP_565674.1| 155 VKTNPEYIYEGDTVDLRLGIENFGEAIAKSVSVSLEHEFKG 195
                                   55666667778888888888888888888888888766554 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00074
                                   ETT--EEEEEEEEE-SSSEEEEEEEEE CS
                    Arrestin_C  17 vpGetipvtvkidndskkkvkkikvsl 43 
                                   + G+t+++t+ i+n   +++++i+v +
  gi|91772982|ref|YP_565674.1| 269 YMGDTVELTMRIENSGERTINSIRVYV 295
                                   68**********************987 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.6
                                   EEEEEEEEEEE..SSEEEEEEEEEEEE CS
                    Arrestin_C 105 sYklkvkltls..gsggelslelPivl 129
                                   +Y++ v++t s  +   +++ ++  ++
  gi|91772982|ref|YP_565674.1| 329 EYEIPVTITYSddFGEDQIETKINLIV 355
                                   567777777774324445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2516.90
//
Query:       gi|91772983|ref|YP_565675.1|  [L=402]
Description: hypothetical protein Mbur_0985 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   35.5   6.7    1.1e-08   35.5   6.7    3.1  3  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2     0.066   1.2e+03      70      83 ..      26      39 ..       7      59 .. 0.55
   2 ?    0.5   0.5     0.048   8.5e+02      65      78 ..     277     290 ..     245     298 .. 0.47
   3 !   35.5   6.7   5.9e-13   1.1e-08       1      95 [.     300     394 ..     300     395 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.066
                          FtsX 70 liiivlllllalla 83
                                  +i++vl+l+++ l+
  gi|91772983|ref|YP_565675.1| 26 FIVFVLSLIFMNLV 39
                                  22222222222222 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.048
                          FtsX  65 dlitvliiivllll 78 
                                   ++ +++++++l+l+
  gi|91772983|ref|YP_565675.1| 277 KFVSLVVAAALILI 290
                                   22222222222222 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 5.9e-13
                          FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllal 81 
                                   k+eigil+a+G + ++++l +   + +++ +++++Gl+l + +  ++++    ++  + +++ id++ ++  iv +l l +
  gi|91772983|ref|YP_565675.1| 300 KKEIGILKAVGITPRSIVLSYAFLSTFYVSLGILAGLVLYFSLMLYFQANPVVFYETMKISPLIDPMLLIQSIVTMLTLSV 380
                                   79**********************************999888888888888888888************************ PP

                          FtsX  82 lagllsiskilkke 95 
                                   +ag l+++ ++k +
  gi|91772983|ref|YP_565675.1| 381 IAGTLPAWSVSKES 394
                                   **********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.50
# Mc/sec: 2432.89
//
Query:       gi|91772984|ref|YP_565676.1|  [L=232]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-33  116.0   0.0    2.4e-33  115.5   0.0    1.2  1  ABC_tran      ABC transporter
    1.1e-08   34.8   0.1    2.2e-08   33.8   0.1    1.4  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.7e-08   33.5   0.0     0.0012   18.7   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.2e-05   23.8   0.0       0.16   11.6   0.0    2.2  2  AAA_15        AAA ATPase domain
    0.00027   21.2   0.0    0.00073   19.8   0.0    1.8  2  AAA_28        AAA domain
    0.00027   20.6   0.2      0.047   13.3   0.1    2.3  2  AAA_25        AAA domain
    0.00028   21.5   0.2    0.00058   20.4   0.2    1.5  1  AAA_23        AAA domain
     0.0003   20.5   0.1    0.00052   19.7   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0003   21.3   0.3     0.0042   17.6   0.3    2.1  1  AAA_18        AAA domain
    0.00038   20.7   0.1     0.0008   19.7   0.1    1.7  1  AAA_22        AAA domain
      0.002   18.5   0.1     0.0028   18.1   0.1    1.5  1  AAA_16        AAA ATPase domain
     0.0024   17.6   0.0      0.057   13.2   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
     0.0048   16.8   0.3      0.015   15.2   0.0    1.9  2  RsgA_GTPase   RsgA GTPase
     0.0091   16.2   0.1       0.24   11.7   0.1    2.5  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.021   14.2   0.0    1.5  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.017   14.8   0.0      0.036   13.8   0.0    1.5  1  AAA_30        AAA domain
      0.018   15.0   0.0      0.032   14.2   0.0    1.4  1  NACHT         NACHT domain
      0.029   14.6   0.1      0.082   13.1   0.1    1.8  1  AAA_33        AAA domain
       0.05   11.1   0.1      0.071   10.6   0.1    1.1  1  DUF3584       Protein of unknown function (DUF3584)
      0.057   12.6   0.0      0.076   12.2   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.062   13.2   0.0       0.13   12.2   0.0    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.08   12.3   0.3       0.22   10.8   0.2    1.7  2  ATPase        KaiC
      0.081   12.1   0.2       0.16   11.2   0.2    1.4  1  NB-ARC        NB-ARC domain
      0.082   12.5   0.2       0.36   10.4   0.1    2.0  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.084   11.5   0.1        2.4    6.7   0.0    2.1  2  AAA_13        AAA domain
      0.092   12.5   0.2       0.18   11.5   0.1    1.7  2  AAA_24        AAA domain
       0.15   12.1   0.9        1.3    9.1   0.2    2.1  2  DUF87         Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   3.6e-36   2.4e-33       1     137 []      21     170 ..      21     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 3.6e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                   l+ vs+++k+ge vai+G +G+GK+tLl++la l + t+Ge +++g ++++    ++      ++g+++q+  l +e++++
  gi|91772984|ref|YP_565676.1|  21 LNGVSFEIKKGEFVAIMGASGSGKTTLLRILALLDDATAGEYTIRGLKVSSlpeaERSYYRLTQVGYVFQDYALINEMSAA 101
                                   789******************************************9999999885555556689***************** PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   en             es + + +al+k+glk+++d++      +LSgG+kqrva+ara++kkp+++++DEp+a
  gi|91772984|ref|YP_565676.1| 102 ENvyvlsmmegnskkESYKTALEALEKVGLKGKQDRIP----DELSGGEKQRVAIARAIAKKPNIMFADEPCA 170
                                   **********9877666666999999999999888887....*****************************85 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   3.3e-11   2.2e-08      24     209 ..      31     212 ..      16     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.3e-11
                                   SSEEEEEESTTSSHHHHHHHHHHHCTT...TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSC.EEE.E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.x RF
                         SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGer..sakklrseklsdlihkskekasvkkaeveitfdnedkklkiekee.vsi.s 100
                                    +f ai+G+ GSGK+ ll  +  +L ++     ++r  k+s+l  +  e++     +v  +f++     ++++ e v++ s
  gi|91772984|ref|YP_565676.1|  31 GEFVAIMGASGSGKTTLLRIL-ALLDDAtaGEYTIRGLKVSSLPEA--ERSYYRLTQVGYVFQDYALINEMSAAEnVYVlS 108
                                   3699**************977.5666551233589999**999887..888889999999998877663333333133302 PP

                                   EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181
                                       ++++ +yk   +  +k  ++    +++  +++LSgGek+ va+a  +A    kp  +++ De  a+LD +n k+v +
  gi|91772984|ref|YP_565676.1| 109 MMEGNSKKESYKTALEALEKVGLK---GKQDRIPDELSGGEKQRVAIARAIA---KKP-NIMFADEPCANLDTNNSKQVLD 182
                                   333333334444333333333332...334444669*******999987654...344.46667***************** PP

                                   HHHHHCTT.SEEEE.E-SSHHHCCC-SCEE CS
                                   xxxxxxxx.xxxxx.xxxxxxxxxxxxxxx RF
                         SMC_N 182 llkekskn.aQfiv.islreemlekadklv 209
                                   ++k  ++n  Q iv ++++  ++e +d+++
  gi|91772984|ref|YP_565676.1| 183 VFKDLNDNyGQTIVmVTHEPWHTEYVDRVI 212
                                   ***999997899983466666666667666 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   0.1   1.8e-06    0.0012       1      24 [.      33      56 ..      33      98 .. 0.79
   2 !   12.9   0.0   0.00011      0.07     228     299 ..     133     202 ..     103     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.8e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                  + ++ G+ gsGK++LL++l ll +
  gi|91772984|ref|YP_565676.1| 33 FVAIMGASGSGKTTLLRILALLDD 56
                                  57899****************933 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                        AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSp 299
                                   + q++ ++elS G k+  a++ a++    k+ + + DEp ++L+    + +l+++k+l++n +Q  +++TH p
  gi|91772984|ref|YP_565676.1| 133 GKQDRIPDELSGGEKQRVAIARAIAK---KPNIMFADEPCANLDTNNSKQVLDVFKDLNDNYGQTiVMVTHEP 202
                                   55666778889999998566656655...5599***************************999988*****77 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0006       0.4      19      47 ..      26      55 ..      19     128 .. 0.78
   2 !   11.6   0.0   0.00025      0.16     319     367 ..     155     203 ..     145     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0006
                        AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFl 47
                                   ++++  +  + G+ +sGK+++l++l l+ 
  gi|91772984|ref|YP_565676.1| 26 FEIKKGeFVAIMGASGSGKTTLLRILALLD 55
                                  344444499*****************7764 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00025
                        AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                    + +k++i + +EP a+L +++ k++ + +k+l ++  + +++ TH p+
  gi|91772984|ref|YP_565676.1| 155 AIAKKPNIMFADEPCANLDTNNSKQVLDVFKDLNDNYGQTIVMVTHEPW 203
                                   46789****************************99999667789**986 PP

>> AAA_28  AAA 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   0.00073       2      35 ..      34      80 ..      33     110 .. 0.68
   2 ?   -2.6   0.0       8.6   5.7e+03      63      80 ..     148     167 ..     116     171 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                        AAA_28  2 ivitGgestGKTtlleaLa........ar...gypvv..pEaareil 35
                                  ++i+G++++GKTtll+ La        +    g +v   pEa r ++
  gi|91772984|ref|YP_565676.1| 34 VAIMGASGSGKTTLLRILAllddatagEYtirGLKVSslPEAERSYY 80
                                  89*****************7665433311444333333366666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.6
                        AAA_28  63 qleeeaaa..aankvlfcDr 80 
                                   q+ + a+a  ++++++f D 
  gi|91772984|ref|YP_565676.1| 148 QRVAIARAiaKKPNIMFADE 167
                                   22223333346777777775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   7.1e-05     0.047      30      54 ..      28      52 ..      25      63 .. 0.89
   2 ?    5.0   0.0     0.024        16     165     191 ..     177     203 ..     162     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-05
                        AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                  + +ge+++++Ga+g+GKttl+  la
  gi|91772984|ref|YP_565676.1| 28 IKKGEFVAIMGASGSGKTTLLRILA 52
                                  5689****************86665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.024
                        AAA_25 165 vgalvealeriarrtgaavllvhHvgK 191
                                    +++++ ++++ +++g ++++v H  +
  gi|91772984|ref|YP_565676.1| 177 SKQVLDVFKDLNDNYGQTIVMVTHEPW 203
                                   3789999999999***********865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   8.7e-07   0.00058      12     146 ..      23     164 ..      16     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.7e-07
                        AAA_23  12 dqeidFsk.gltlItGpNGaGKTTildAikl...aLyget..prlsrksgrgfeksdveiesegkvkayveltfenkdgry 86 
                                   +++++ +k  +++I G  G+GKTT+l+ + l   a+ ge   ++l+ +s   +e+s +++++ g v + + l  e    ++
  gi|91772984|ref|YP_565676.1|  23 GVSFEIKKgEFVAIMGASGSGKTTLLRILALlddATAGEYtiRGLKVSSLPEAERSYYRLTQVGYVFQDYALINEMSAAEN 103
                                   5566665525789*************9887544466665544455554444566666666665444222333333333332 PP

                        AAA_23  87 trsiererelskkkgkttkkaklelleideleqfisellgskki.ilnlilflgqerfeef 146
                                    + ++ +  +skk++ +t  ++le+++ + ++++i+++l+  ++ +  +   ++++ + +f
  gi|91772984|ref|YP_565676.1| 104 VYVLSMMEGNSKKESYKTALEALEKVGLKGKQDRIPDELSGGEKqRVAIARAIAKKPNIMF 164
                                   4667667777778888889999999999999999988777544423333334444433333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   7.9e-07   0.00052      13      39 ..      22      48 ..      19      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.9e-07
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                  +g ++ei+  +++ ++G+sGsGK+Tll
  gi|91772984|ref|YP_565676.1| 22 NGVSFEIKKGEFVAIMGASGSGKTTLL 48
                                  67889999666***************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   6.4e-06    0.0042       1      68 [.      34     114 ..      34     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.4e-06
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpe.....aldeskrldedkldklldaleens 68 
                                   ++++G++G+GKttl + L+ +           g +++++   +++++  ++      ++   +++      ++l+ +e+ns
  gi|91772984|ref|YP_565676.1|  34 VAIMGASGSGKTTLLRILALLDDAtageytirGLKVSSLPEAERSYYRLTQVgyvfqDYALINEMSAAENVYVLSMMEGNS 114
                                   689***************554322344457785555554444444444444444555555555555555555555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.2e-06    0.0008       4      38 ..      30      99 ..      27     207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-06
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.....................................e 38
                                  +  +++++G sG+GKTtllr l+  +d+ a   e                                      
  gi|91772984|ref|YP_565676.1| 30 KGEFVAIMGASGSGKTTLLRILALLDDATA--GEytirglkvsslpeaersyyrltqvgyvfqdyalinemS 99
                                  67799*****************99986433..2245777777777554444444444444444444444441 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   4.2e-06    0.0028      24      69 ..      31      79 ..      15     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.2e-06
                        AAA_16 24 pelvllsGesGvGKsslvrellralekd..ggiflrgkcdql..esaipy 69
                                  +e v + G+sG+GK++l+r l+  l ++  g +++rg  +++  e++++y
  gi|91772984|ref|YP_565676.1| 31 GEFVAIMGASGSGKTTLLRILA-LLDDAtaGEYTIRGLKVSSlpEAERSY 79
                                  378***************8777.455543333445544444444444444 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   8.5e-05     0.057      30      67 ..      13      51 ..       5      84 .. 0.80
   2 ?    2.3   0.0      0.19   1.3e+02     108     149 ..     159     202 ..     138     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                     IstB_IS21 30 ldkrkvkeLatlsf.iekkenivllGpsGvGKshlaial 67
                                  + +++vk+L + sf i+k e ++++G sG GK+ l   l
  gi|91772984|ref|YP_565676.1| 13 SGETAVKALNGVSFeIKKGEFVAIMGASGSGKTTLLRIL 51
                                  5678999*******99999**************986443 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                     IstB_IS21 108 kvdllilDdlgllpldqaeae...llfeviekryerrsiiitsnl 149
                                   k++++  D+    +ld ++++   ++f+ +++ y+++ +++t + 
  gi|91772984|ref|YP_565676.1| 159 KPNIMFADEPC-ANLDTNNSKqvlDVFKDLNDNYGQTIVMVTHEP 202
                                   55666666643.344444444001566668899***999999764 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.2e-05     0.015      89     124 ..      20      56 ..       9      66 .. 0.78
   2 ?   -2.2   0.0       5.2   3.5e+03      45      77 ..      99     131 ..      91     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                                   THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                   +l+ ++ ++k+ ++++++G SG GK+tL+  l+  ++
  gi|91772984|ref|YP_565676.1|  20 ALNGVSFEIKKgEFVAIMGASGSGKTTLLRILALLDD 56 
                                   5566667777779****************99876555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.2
                                   TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTS CS
                   RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkeelealgy 77 
                                   + +e v vl+ ++  +++e++++  e+le++g+
  gi|91772984|ref|YP_565676.1|  99 SAAENVYVLSMMEGNSKKESYKTALEALEKVGL 131
                                   455666777777777788878888888887775 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00036      0.24      23      89 ..     132     185 ..     115     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                       SbcCD_C  23 ekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   +++ +r   +lSGGekq    +    a+a ++ +      ++ ++f DE  ++lD ++++++l++++
  gi|91772984|ref|YP_565676.1| 132 KGKQDRIPDELSGGEKQR---V----AIARAIAK------KPNIMFADEPCANLDTNNSKQVLDVFK 185
                                   555666677888888843...2....33344444......5899*******************9997 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.2e-05     0.021      32      59 ..      25      51 ..      14     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                                  EEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE 32 vldlkkmashllvaGatgsGKStalntL 59
                                   +++kk +  + ++Ga+gsGK+t l+ L
  gi|91772984|ref|YP_565676.1| 25 SFEIKKGE-FVAIMGASGSGKTTLLRIL 51
                                  56777778.99**************955 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   5.5e-05     0.036      19      52 ..      32      67 ..      25      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g.grvigl 52
                                   ++++ G+ G+GKtt+l+ l+ + +a  g +++ gl
  gi|91772984|ref|YP_565676.1| 32 EFVAIMGASGSGKTTLLRILALLDDATaGeYTIRGL 67
                                  4899****************9998887545666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.8e-05     0.032       3      22 ..      34      53 ..      32      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-05
                                  EEEEC-TTTCHHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqklal 22
                                  v++ G++GsGKTtLl+ lal
  gi|91772984|ref|YP_565676.1| 34 VAIMGASGSGKTTLLRILAL 53
                                  899************98875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.082       2      28 ..      34      59 ..      33     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavll 28
                                  v + G++GsGK+tl++ l+  l+  + 
  gi|91772984|ref|YP_565676.1| 34 VAIMGASGSGKTTLLRILA-LLDDATA 59
                                  5678***********9876.3444444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00011     0.071       8      37 ..      22      51 ..      19      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                       DUF3584  8 kGrvaeldldghtnieGtNaaGKTtLlrLi 37
                                   G+  e++  + + i G+ ++GKTtLlr++
  gi|91772984|ref|YP_565676.1| 22 NGVSFEIKKGEFVAIMGASGSGKTTLLRIL 51
                                  577778899999****************98 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011     0.076      26     147 ..      34     208 ..      22     221 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                   EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT........... CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsiktilealesleselsesf.... 89 
                                   + ++G+s+SGK+T+l+ l ll + +               e e+ ++r      + ++  +i e    ++    +++    
  gi|91772984|ref|YP_565676.1|  34 VAIMGASGSGKTTLLRILALLDDATageytirglkvssLPEAERSYYRLTQVGYVFQDYALINEMSAAENVYVLSMMegns 114
                                   5689***************99988878888888888654445555588888888888888777777776666666664444 PP

                                   ............................HHHC-SS-SCCCS-HCHHHH................................. CS
                       G-alpha  90 ............................elqelkerldplkkveasliaklssateee....................... 119
                                                               +                                                    
  gi|91772984|ref|YP_565676.1| 115 kkesyktalealekvglkgkqdripdelS----------------------------Ggekqrvaiaraiakkpnimfade 167
                                   33333333333333333333333333330............................033333444433333333333333 PP

                                   ............HHCCHHC.-HCHHHHHHHHCCSHHHHHHH CS
                       G-alpha 120 ............qeiefnp.raevgedikaLwndpgiqely 147
                                                 ++f++ + ++g+ i+++ ++p   e++
  gi|91772984|ref|YP_565676.1| 168 pcanldtnnskqVLDVFKDlNDNYGQTIVMVTHEPWHTEYV 208
                                   33222222111122222224445555666666666555555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.13       2      19 ..      34      51 ..      33      79 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                          MobB  2 lgivgksgsGKTtLlekl 19
                                  ++i+g sgsGKTtLl  l
  gi|91772984|ref|YP_565676.1| 34 VAIMGASGSGKTTLLRIL 51
                                  789***********9743 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00034      0.22      16     111 ..      28     126 ..      15     159 .. 0.65
   2 ?   -1.1   0.0       1.5     1e+03     143     169 ..     179     206 ..     168     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                        ATPase  16 ipegrvvlitGepGtGKtifalqFli...kgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesae 93 
                                   i +g+ v i+G +G+GKt++    ++     a +y  +g+ v+   +ae  + + +++G  ++++   +++   + +   +
  gi|91772984|ref|YP_565676.1|  28 IKKGEFVAIMGASGSGKTTLLRILALlddATAGEYTIRGLKVSSLPEAERSYYRLTQVGYVFQDYALINEMSAAENVYVLS 108
                                   78999*************987666552222344555577778877777888888888888888776555555544444433 PP

                        ATPase  94 esaeekdkedleelieel 111
                                     + +++ke+ +  +e l
  gi|91772984|ref|YP_565676.1| 109 MMEGNSKKESYKTALEAL 126
                                   333334444444444444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                        ATPase 143 ilrqlvrvl.kklgvTailvseksssee 169
                                   ++  +++ l  ++g+T ++v+  + + e
  gi|91772984|ref|YP_565676.1| 179 QVLDVFKDLnDNYGQTIVMVTHEPWHTE 206
                                   4555566665778888888887665544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00024      0.16      19      38 ..      32      49 ..      15      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                  CSEEEEEEESTTSSHHHHHH CS
                        NB-ARC 19 qslvvalvGmgGvGKttlak 38
                                  +  +va++G  G+GKttl++
  gi|91772984|ref|YP_565676.1| 32 E--FVAIMGASGSGKTTLLR 49
                                  4..9**************87 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 ?   10.4   0.1   0.00054      0.36       3      21 ..      34      52 ..      32      63 .. 0.81
   2 ?   -0.7   0.0       1.4   9.2e+02     101     155 ..      89     140 ..      83     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00054
                                  EEEEESTTCCHHHHHHHHH CS
                          cobW  3 tvltGflGsGKTtLlnhll 21
                                  + + G  GsGKTtLl+ l 
  gi|91772984|ref|YP_565676.1| 34 VAIMGASGSGKTTLLRILA 52
                                  568999*********9765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                   TTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEE.EEE-HHHHCH CS
                          cobW 101 fteeelksdltldavvavvDaknleaeeekieekaedqlaaadll.vlnKtDllde 155
                                   f++  l +++ +   v+v++      e+++++e ++  l+a + + +  K D +++
  gi|91772984|ref|YP_565676.1|  89 FQDYALINEMSAAENVYVLSM----MEGNSKKESYKTALEALEKVgLKGKQDRIPD 140
                                   566677777777788888888....6667777777766666554423345555555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0037       2.4      21      41 ..      36      56 ..      30      76 .. 0.82
   2 ?    2.4   0.0     0.071        47     498     570 ..     140     201 ..     128     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0037
                        AAA_13 21 iYGwNGaGKTtLSrllrslel 41
                                  i G+ G+GKTtL r+l+ l  
  gi|91772984|ref|YP_565676.1| 36 IMGASGSGKTTLLRILALLDD 56
                                  78999***********99854 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.071
                        AAA_13 498 etLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfi.LTHn 570
                                   ++LS GEk  +a+        ++++  +k  i + D P   LD+n +  v    k+     +++ Q ++  TH 
  gi|91772984|ref|YP_565676.1| 140 DELSGGEKQRVAIA-------RAIA--KKPNIMFADEPCANLDTNNSKQVLDVFKDLN---DNYGQTIVmVTHE 201
                                   56777777777654.......2333..389999*****************99999996...9999977625885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00026      0.18       5      31 ..      34      57 ..      30     123 .. 0.75
   2 ?   -2.5   0.0       5.5   3.6e+03     124     131 ..     194     201 ..     175     227 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                        AAA_24  5 iliyGpsgiGKTtlakelgpkplfidt 31
                                  ++i+G sg+GKTtl++ l   +l+ d 
  gi|91772984|ref|YP_565676.1| 34 VAIMGASGSGKTTLLRIL---ALLDDA 57
                                  79************9987...444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.5
                        AAA_24 124 nvifiahe 131
                                   +++++ he
  gi|91772984|ref|YP_565676.1| 194 TIVMVTHE 201
                                   44444443 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0019       1.3      26      43 ..      34      51 ..      24      53 .. 0.92
   2 ?    1.5   0.0       0.4   2.6e+02     108     181 ..     112     193 ..      79     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                         DUF87 26 lAilgsTGsGKSntvavL 43
                                  +Ai+g +GsGK+++ ++L
  gi|91772984|ref|YP_565676.1| 34 VAIMGASGSGKTTLLRIL 51
                                  7*************9987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.4
                         DUF87 108 e.ddkpaaavqrsvleealdqaka........keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkg 179
                                   + ++k+++++  ++le++  + k+        + ek+++ +++ ++k  + +   +e+  +l+++  +++ld ++dl +++
  gi|91772984|ref|YP_565676.1| 112 GnSKKESYKTALEALEKVGLKGKQdripdelsGGEKQRVAIARAIAKKPNIMF-ADEPCANLDTNNSKQVLDVFKDLNDNY 191
                                   25555566666666666666665566666655555555555555555555555.555666666666666666666666666 PP

                         DUF87 180 gs 181
                                   g+
  gi|91772984|ref|YP_565676.1| 192 GQ 193
                                   55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 1332.60
//
Query:       gi|91772985|ref|YP_565677.1|  [L=97]
Description: hypothetical protein Mbur_0987 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 648.24
//
Query:       gi|91772986|ref|YP_565678.1|  [L=201]
Description: hypothetical protein Mbur_0988 [Methanococcoides burtonii DSM 6242]
Scores for 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   24.9   0.2     0.0049   17.1   0.2    2.2  2  DUF4352   Domain of unknown function (DUF4352)
     0.0077   16.1   0.4      0.027   14.4   0.2    2.0  2  DUF5067   Domain of unknown function (DUF5067)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   5.5e-07    0.0049       4      59 ..      39      95 ..      38     123 .. 0.82
   2 !    5.8   0.0    0.0018        16      87     108 ..     165     186 ..     134     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-07
                                  CEEECCTTEEEE.EEEEEEEEEETTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGG CS
                       DUF4352  4 getvkvgdlevt.VnsveytksvgkneylqpdaggeflivdvtvkNkgkealtvnss 59
                                  g++ +++ + ++ V+s+e+++   k+ y  p +g +fl+v + v+N g ++++ +++
  gi|91772986|ref|YP_565678.1| 39 GDSLEINVVDYKlVDSFETMNVPNKPVYYYPPEGAQFLLVYLEVTNVGTDKTSSDTI 95
                                  66677777777636677*********************************9998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0018
                                   EEE-TT-EEEEEEEEEESTT-C CS
                       DUF4352  87 gtlnpGkkvtGklvFdvpkgkk 108
                                   +++ p  + +G+++F vp + +
  gi|91772986|ref|YP_565678.1| 165 ENVYPEVTKEGWIAFLVPHNID 186
                                   4568999***********9977 PP

>> DUF5067  Domain of unknown function (DUF5067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   3.1e-06     0.027      10      63 ..      31      94 ..      23     158 .. 0.84
   2 ?   -1.0   0.0      0.18   1.6e+03      95     114 ..     164     183 ..     153     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                                  GGS-EEEETTEEEESSEEEEE---EEE..........EECCCTCEEEEEEEEEE-SS-TTBCHH CS
                       DUF5067 10 eekasskkkeeaeiddftvkitkaevi..........kdyegkpvlvvyyeftNnsdeeispss 63
                                  + +++ ++++++ei+ +++k+ ++  +           + eg ++l+vy e+tN + +++s ++
  gi|91772986|ref|YP_565678.1| 31 SISDTGFTGDSLEINVVDYKLVDSFETmnvpnkpvyyYPPEGAQFLLVYLEVTNVGTDKTSSDT 94
                                  7789999*************988877779999999988999*************9999988544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
                                   CSEE-TTSEEEEEEEEE-TT CS
                       DUF5067  95 dkeikpgktvevviaYeLqd 114
                                   ++++ p+ t+e+ ia+ ++ 
  gi|91772986|ref|YP_565678.1| 164 YENVYPEVTKEGWIAFLVPH 183
                                   67899999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1261.75
//
Query:       gi|91772987|ref|YP_565679.1|  [L=160]
Description: hypothetical protein Mbur_0989 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   30.9   0.0    3.1e-07   30.5   0.0    1.0  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.7e-11   3.1e-07       4     146 ..      13     151 ..      11     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.7e-11
                                   -CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHH.CCCCCCCHHG.........CTEEEEESSS....SECGCTTC CS
                           UDG   4 gppdakvvivGeaPgaeedatglpFsgragnllrkllne.aglkrdlese.........qgvyitnvvkcrppgnrdtpts 74 
                                   ++++++++i G  P++++  + +++ + ++n++++l++  +g++ + +++         +++++++++ +   g    +++
  gi|91772987|ref|YP_565679.1|  13 VNEETEILITGTFPSEKSRNQKQYY-ADSRNQFWNLMSFvLGIDLKKIEYnnrvsilkkHKIGLWDTIESCEIG---GSSD 89 
                                   6899*********************.99*****************888889******************55444...4455 PP

                                   CCCTCCHHHHHHHHHHHHSSEEEEESHHHHHH..HHHHSCESCCCSCT.SEEEEES-SSTTTTTTTTSHHHH CS
                           UDG  75 aeikacaplleeeiellkprlivllGktaakallgeklgklrgklleakirvlplphPsplnrnffksnpel 146
                                   +  ++c p  ++   l + + iv+ G +  +++      + ++ +l+  ++v+ +++ s +n   +  +pe+
  gi|91772987|ref|YP_565679.1|  90 K--NICNPQYNDFSHLTQIKKIVCNGGKVEETC------NKHCNVLDG-VQVVRVLSSSSANNG-AIGRPEE 151
                                   5..57***8888888888999***********8......778999999.999999999999988.3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1047.05
//
Query:       gi|91772988|ref|YP_565680.1|  [L=262]
Description: metal-dependent phosphohydrolase [Methanococcoides burtonii DSM 6242]
Scores for 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   1.2    1.8e-10   41.1   1.2    1.4  1  HD        HD domain
  ------ inclusion threshold ------
      0.051   13.9   1.4       0.35   11.2   0.0    2.7  3  DUF4894   Domain of unknown function (DUF4894)


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 !   41.1   1.2     2e-14   1.8e-10       3     120 ..      36     150 ..      35     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2e-14
                                   HHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH..HHHCTCCHHHHHHHHHHHHHHHHHHHHH... CS
                            HD   3 eHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk..eeefekflaHekvgaeilrevekrlgld... 77 
                                    Hs++V   a  + + +++ ++d  l++++aL+HDiG      ++ k+  ++  +  ++H+  g+ il+ +e  +gl+   
  gi|91772988|ref|YP_565680.1|  36 GHSVRVCDNASLITKAEKLaDDDLYLAKTIALFHDIGRFE---QINKYrtFR-DTDSENHALLGVNILKTEEVISGLKdee 112
                                   5**************99999********************...555665422.455579********************** PP

                                   HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                            HD  78 ledvaklirehheswegkkrprglaerqlslearivklaDrla 120
                                    ++++ +ir+h+  +       +l+ r   l  +i+++aD+l+
  gi|91772988|ref|YP_565680.1| 113 QKIILTAIRNHNVHILP-----SLPDRRTLLHCKIIRDADKLD 150
                                   ***************94.....6******************97 PP

>> DUF4894  Domain of unknown function (DUF4894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.9e-05      0.35      60     118 ..      18      75 ..      13      81 .. 0.86
   2 ?   -0.7   0.0       0.2   1.8e+03      51      76 ..      92     118 ..      77     129 .. 0.69
   3 ?    0.0   0.1      0.11     1e+03      47      55 ..     210     222 ..     138     256 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
                       DUF4894  60 ssyvseidfeekkvvLkkgirvkfnewedleekkekleelienaedrseYllssdGkll 118
                                   ss+ ++ df +++v+Lk g  v + +  +l++k ekl    +   +++  l+ + G++ 
  gi|91772988|ref|YP_565680.1|  18 SSFYTDDDFIQQNVMLKEGHSVRVCDNASLITKAEKLADD-DLYLAKTIALFHDIGRFE 75 
                                   6677777999***************************998.777788888888888775 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.2
                       DUF4894  51 ilkkl.pvlkssyvseidfeekkvvLk 76 
                                    l  + +++ ++++s ++ ee+k++L 
  gi|91772988|ref|YP_565680.1|  92 ALLGVnILKTEEVISGLKDEEQKIILT 118
                                   455563445567888888888888885 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.11
                       DUF4894  47 v....dreilkkl 55 
                                   +    d ++++ +
  gi|91772988|ref|YP_565680.1| 210 LswifDMNFIETI 222
                                   1122233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1686.51
//
Query:       gi|91772989|ref|YP_565681.1|  [L=302]
Description: hypothetical protein Mbur_0991 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   56.8   0.0    3.5e-15   56.2   0.0    1.3  1  ATP_bind_3       PP-loop family
    1.9e-07   30.2   0.0      3e-07   29.6   0.0    1.3  1  tRNA_Me_trans    tRNA methyl transferase
    4.8e-05   23.5   0.0    8.6e-05   22.6   0.0    1.4  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
    7.3e-05   22.0   0.1     0.0001   21.5   0.1    1.1  1  NAD_synthase     NAD synthase
    0.00094   18.8   0.0     0.0016   18.1   0.0    1.3  1  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0038   16.7   0.1      0.044   13.3   0.0    2.5  3  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.021   14.3   7.5      0.021   14.3   7.5    2.6  3  zn-ribbon_14     Zinc-ribbon
      0.075   12.5   0.1       0.14   11.6   0.1    1.4  1  Diphthami_syn_2  Diphthamide synthase
       0.17   11.5   5.9        1.5    8.4   3.4    2.6  2  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 !   56.2   0.0   1.8e-18   3.5e-15       2     168 ..      52     229 ..      51     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.8e-18
                                   EEEE--SCHHHHHHHHHHHHHCT.TTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.HHCTTSTCCCHH CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkk.klgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.akkkgknleeaA 80 
                                   ++vA+SgG DS++Ll+ll+k    +  i++va+++d g+    +e  +  ++l ++l+i++++ +++    k+ ++l ++ 
  gi|91772989|ref|YP_565681.1|  52 IAVALSGGKDSVVLLYLLHKIFGvRRDIEIVALTIDEGIAGYREETLAKARKLTSELGIRHIVRSFKDeYDKTLDELTAQE 132
                                   579****************987514566**************************************998444466666666 PP

                                   HH.........HHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT.CCEE-CCCT--HHH CS
                    ATP_bind_3  81 Re.........lRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias.irlvRPlLkvskee 151
                                   R+         lR  ++++++++ g++ l+++h+ dD a t+++++  g     ++ +++ +ei++ +    Pl kv  +e
  gi|91772989|ref|YP_565681.1| 133 RKlgacsycgvLRKSLMNKIANEIGANKLATGHNLDDEAQTIMMNHLGGDVD-RMIRLSPPREIEGlVLRAKPLRKVPEKE 212
                                   65333333333799********************************998775.5666777777888455578999999999 PP

                                   HHHHHHHTT---B--CG CS
                    ATP_bind_3 152 leeylkekkikwveDes 168
                                   +  y+  +++++   e 
  gi|91772989|ref|YP_565681.1| 213 VALYAIVNELPFDMSEC 229
                                   99999888888766555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.5e-10     3e-07       3     125 ..      52     166 ..      50     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.5e-10
                 tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeefl 83 
                                   ++valSgG DS v ++ll++ +   + + +   +  de   +   ee l++a++  ++lgi++ v +f++ey +++ e + 
  gi|91772989|ref|YP_565681.1|  52 IAVALSGGKDSVVLLYLLHKIFGVRRDIEIVALTI-DEGI-AGYREETLAKARKLTSELGIRHIVRSFKDEYDKTLDELTA 130
                                   89****************99886666665555444.3333.678999********************************** PP

                 tRNA_Me_trans  84 eeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                   +e + G     +  C      + l++k+ +e ga++latGH 
  gi|91772989|ref|YP_565681.1| 131 QERKLGA----CSYCGVL--RKSLMNKIANEIGANKLATGHN 166
                                   **99997....9999754..55788888889**********6 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.3e-08   8.6e-05       2     154 ..      52     223 ..      51     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.3e-08
                                   EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S- CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinaekhgs 75 
                                   ++v+ sgGkds+Vll L+ k+f  +       + +d g     +et++   +l++++g+r +v + ++e ++ + + +  +
  gi|91772989|ref|YP_565681.1|  52 IAVALSGGKDSVVLLYLLHKIFGVRrdieiVALTIDEGIAgyREETLAKARKLTSELGIRHIVRSFKDEYDKTLDELTAQE 132
                                   7899*****************988667776789999998633799***************999999999999999999877 PP

                                   THHHC.HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S.............CEEE-CCCT--HH CS
                   PAPS_reduct  76 slyee.aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek.............slrvfPllnWtee 142
                                   ++     ++ + +   ++k  ++++++ l tG   d++++   ++ +  d d  +             +lr  Pl +  e+
  gi|91772989|ref|YP_565681.1| 133 RKLGAcSYCGVLRKSLMNKIANEIGANKLATGHNLDDEAQTIMMNHLGGDVD--RmirlsppreieglVLRAKPLRKVPEK 211
                                   777779999999999999999999*9******99999987666665555555..445788889999999999999999999 PP

                                   HHHHHHHHCT-- CS
                   PAPS_reduct 143 dvwqyilrenip 154
                                   +v  y+  +++p
  gi|91772989|ref|YP_565681.1| 212 EVALYAIVNELP 223
                                   999998887776 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   5.3e-08    0.0001       6     130 ..      37     166 ..      32     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.3e-08
                                   HHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGE...EEEEE--SSST..THHHHHHHHHHHHHHTSEEEE--- CS
                  NAD_synthase   6 vdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgken...vlalllPssvs..seedvedalalaenlgievktidi 81 
                                   +  ++++ k ++ + + + lSGG DS +  +l  k++g  +   ++al + +  +   ee + +a++l  +lgi+  + + 
  gi|91772989|ref|YP_565681.1|  37 KLTIRKQYKIEKGDIIAVALSGGKDSVVLLYLLHKIFGVRRdieIVALTIDEGIAgyREETLAKARKLTSELGIRHIVRSF 117
                                   5566666666667778899******************76552226788887444322788899****************** PP

                                   HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BH CS
                  NAD_synthase  82 kpivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnk 130
                                   k+ +    +el+ ++ +l +   +  +R  +  +ian+ +   l+Tg++
  gi|91772989|ref|YP_565681.1| 118 KDEYDKTLDELTAQERKLGACSYCGVLRKSLMNKIANEIGANKLATGHN 166
                                   ****999999999999**********************99999999886 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     8e-07    0.0016       9     122 ..      55     171 ..      47     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8e-07
                          ThiI   9 LlSgGiDSpVaayll.....lkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv. 83 
                                    lSgG DS V  yll     ++R +++v+++++   g +   +e + k+ +l +e +  + v+ +  +++++l+e++ +  
  gi|91772989|ref|YP_565681.1|  55 ALSGGKDSVVLLYLLhkifgVRRDIEIVALTID--EGIAGYREETLAKARKLTSELGIRHIVRSFKDEYDKTLDELTAQEr 133
                                   48***********98555556899999999996..566666677777778888888888899999999*****99987773 PP

                          ThiI  84 ...kekltivllkrkmlriAekvaeeegakalvtGesLgqVa 122
                                         +  vl k  m +iA+    e ga+ l tG +L   a
  gi|91772989|ref|YP_565681.1| 134 klgACSYCGVLRKSLMNKIAN----EIGANKLATGHNLDDEA 171
                                   344445666777777777777....88999999999997655 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.25   4.9e+02     126     155 ..      18      47 ..      12      49 .. 0.83
   2 !   13.3   0.0   2.2e-05     0.044       4      58 ..      54     114 ..      51     141 .. 0.81
   3 ?   -2.1   0.0       1.1   2.3e+03     104     125 ..     148     169 ..     143     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.25
                                   TT--GGGSHHHHHHHHHHHHHHHTS--EEE CS
                          QueC 126 fsgYPDcrdefvkalnkalnlgedkkieie 155
                                   +sg   c+++f++ +++ ++l   k+ +ie
  gi|91772989|ref|YP_565681.1|  18 YSGMHICKRHFIEDVERKVKLTIRKQYKIE 47 
                                   667777**************9988887775 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.2e-05
                                   EE--SSHHHHHHHHHHHHH-.....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEE CS
                          QueC   4 vllSGGlDSttvlalakkeg.....kevealtfdYgqr..hkkeleaakkiakelgveehki 58 
                                   v lSGG DS ++l+l +k +      e+ alt+d g    ++++l +a+k+++elg+ +h +
  gi|91772989|ref|YP_565681.1|  54 VALSGGKDSVVLLYLLHKIFgvrrdIEIVALTIDEGIAgyREETLAKARKLTSELGI-RHIV 114
                                   789************99977565557999*****998865677789999*******9.6665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.1
                                   HHHHHHHHHT-SEEEE---S-S CS
                          QueC 104 laasyaealgaeaiiiGvneed 125
                                   l    a+++ga+++++G n  d
  gi|91772989|ref|YP_565681.1| 148 LMNKIANEIGANKLATGHNLDD 169
                                   5567899999999999999877 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   1.3       2.7   5.4e+03       2       7 ..       4       9 ..       4      10 .. 0.81
   2 ?   -0.6   0.3      0.47   9.4e+02       1       8 [.     136     143 ..     136     144 .. 0.81
   3 ?   14.3   7.5     1e-05     0.021       2      22 ..     280     300 ..     279     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                  zn-ribbon_14 2 kCerCG 7
                                 kC +C+
  gi|91772989|ref|YP_565681.1| 4 KCMKCN 9
                                 699996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.47
                  zn-ribbon_14   1 gkCerCGy 8  
                                   g C+ CG 
  gi|91772989|ref|YP_565681.1| 136 GACSYCGV 143
                                   57*****7 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1e-05
                  zn-ribbon_14   2 kCerCGylSSqkiCkACvLLe 22 
                                   kC+ CG  +   +C+AC LL 
  gi|91772989|ref|YP_565681.1| 280 KCRICGETCTATLCQACKLLG 300
                                   8******************95 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.2e-05      0.14       4     116 ..      53     162 ..      51     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-05
               Diphthami_syn_2   4 avlysGGkDsilaLykalkeseves....LvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgt 80 
                                   av  sGGkDs++ Ly   k + v+     +   i+e+ + y+  ++ ++  +l++  +Gi  i+   + e +k  ++L  +
  gi|91772989|ref|YP_565681.1|  53 AVALSGGKDSVVLLYLLHKIFGVRRdieiVALTIDEGIAGYREETL-AKARKLTS-ELGIRHIVRSFKDEYDKTLDELTAQ 131
                                   6789*******99998888776654111044445677776665544.34455555.5999999999999999999999999 PP

               Diphthami_syn_2  81 lkkldveavviGaieseyqksriervCrelGlksva 116
                                    +kl++ + ++G +    +ks ++++ +e+G  ++a
  gi|91772989|ref|YP_565681.1| 132 ERKLGACS-YCGVL----RKSLMNKIANEIGANKLA 162
                                   88888654.33443....577777777777776665 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.051     1e+02       8      25 ..     127     144 ..     125     147 .. 0.80
   2 ?    8.4   3.4   0.00077       1.5      15      35 ..     277     297 ..     275     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.051
                                   HHHHHHHH-EE-TTT--E CS
                          RecR   8 aLqeakekvrhCsrCgnl 25 
                                   +L++  +k++ Cs Cg l
  gi|91772989|ref|YP_565681.1| 127 ELTAQERKLGACSYCGVL 144
                                   67777789999****977 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00077
                                   H-EE-TTT--EESSSS-CCCC CS
                          RecR  15 kvrhCsrCgnlteedlCaICs 35 
                                   +++ C++Cg  ++ +lC+ C+
  gi|91772989|ref|YP_565681.1| 277 ELSKCRICGETCTATLCQACK 297
                                   5789****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1874.54
//
Query:       gi|91772990|ref|YP_565682.1|  [L=301]
Description: hypothetical protein Mbur_0992 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 1940.08
//
Query:       gi|91772991|ref|YP_565683.1|  [L=153]
Description: hypothetical protein Mbur_0993 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-06   27.4   0.0    3.5e-06   27.1   0.0    1.1  1  DUF523    Protein of unknown function (DUF523)


Domain annotation for each model (and alignments):
>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0     2e-10   3.5e-06       2     129 ..      11     139 ..      10     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2e-10
                        DUF523   2 lvSaCLlgekvrydgkakksevleeelkelvkeelvpv.CPEvaggLptPRepaelakrvlkkegedvtealekgaeeale 81 
                                   ++ +CL++ + r +g + +  +++++ k     ++v++ CPE    L+  R+++  + ++ + + + + ++l +  ++++e
  gi|91772991|ref|YP_565683.1|  11 VIGHCLANVSSRLKGIKGP-PLVDTKGK-----NIVQLpCPELI-YLGEARREITRD-QLENPNYRRFCHSLFEPFADMIE 83 
                                   6889999999999999988.45555444.....445656***86.599999999995.45555554444444444444444 PP

                        DUF523  82 elkeeeikgail.kekSPSCGvekiY.......dgtfskklvegeGvfaallkeeg 129
                                   +  +e+ ++ +l   kSPSCG +++           f++++v+g+G+f + ++ee 
  gi|91772991|ref|YP_565683.1|  84 QFYQEGYSIKVLgVPKSPSCGAQTTTvggpagrVEVFTHDNVPGTGIFYEEIAEEL 139
                                   444444444433259********995577766646899999*******99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 1088.04
//
Query:       gi|91772992|ref|YP_565684.1|  [L=672]
Description: membrane-bound proton-translocating pyrophosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-267  889.9  54.2   1.3e-267  889.8  54.2    1.0  1  H_PPase       Inorganic H+ pyrophosphatase


Domain annotation for each model (and alignments):
>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  889.8  54.2  7.1e-272  1.3e-267       1     650 []      13     662 ..      13     662 .. 0.97

  Alignments for each domain:
  == domain 1  score: 889.8 bits;  conditional E-value: 7.1e-272
                                   HHHHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT....HHHHHHHHHHHHHHH CS
                       H_PPase   1 vlallfalvllkkvlkedegtekmkeiaeaikegaeaflkrqykviailvvvlavlllllal.lsvltaiaflvGallSal 80 
                                   +++l+fa+++++ vlke +gt++m++i+ ai+ega+a+l+rqyk++a+++++la+l+++l+   s  ++i f+vGa++Sal
  gi|91772992|ref|YP_565684.1|  13 IVSLAFAAFFASGVLKEGTGTKEMQDISLAIQEGAMAYLNRQYKTVAVVAIILAALMFFLLGdDSGKIVIGFIVGAAASAL 93 
                                   6899*****************************************************998765567899************ PP

                                   HHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-EE-HHHHHHHHHHHHHHHH CS
                       H_PPase  81 agyigmkvavranvrtakaarkslkkalkvafrsGavmgllvvglallgvsllllllkaaalelekllellvgfglGaslv 161
                                   agy+gm+v++ranvrta+aa+ksl++a++vafr+Gav+gl+vvglallg s +++l+ +        ++l++gfg+Gasl+
  gi|91772992|ref|YP_565684.1|  94 AGYVGMNVSIRANVRTAHAASKSLQEAMSVAFRGGAVTGLAVVGLALLGTSGFYILFGD--------VDLVIGFGFGASLI 166
                                   ***********************************************************........99************ PP

                                   HHHHHHCHHHHHHHHHHHHTCHHHHTS---TT-TT-TTHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH......SHH CS
                       H_PPase 162 alfarvgGGiytKaADvGaDLvGKveagipEDdprnpaviADnvGDnvGDvaGmgADlfesyvasivaamvlg.....aav 237
                                   +lfarvgGGi+tKaADvGaDLvGKveagipEDdprn+aviADnvGDnvGD+aGmgADlfe+yv++++a+m+lg     +  
  gi|91772992|ref|YP_565684.1| 167 SLFARVGGGIFTKAADVGADLVGKVEAGIPEDDPRNAAVIADNVGDNVGDCAGMGADLFETYVVTVLASMLLGslileQFP 247
                                   *************************************************************************87765378 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHH.......HHSS--HHHHHHHHHHHHHHHHHHHHHHHHH-S-TTTTSHHHHHHHHHHH CS
                       H_PPase 238 klvllpllvaavgilasiigillvktkedasskkkeellkaLkkgllvsavlsvvlvallslllkeaaalklflavlvGlv 318
                                   +++l+pl++ av i+asii++++vk+ +d       +++kaL+kg+ vsa+ls++++++++  l+    ++l++a lvG++
  gi|91772992|ref|YP_565684.1| 248 NAILYPLILGAVAIFASIISMFFVKVGKD------GKIMKALYKGVAVSAILSMIAFYFVTDSLM--GDVRLYYASLVGII 320
                                   9***********************87766......4599******************99999986..789*********** PP

                                   HHHHHHHHHHHHH-TTSHHHHHHHHHGGG-HHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH........HHHHHHHHH CS
                       H_PPase 319 agllivllteyytsteykpvkeiaeasetGaatniisGlavgmestvlpvlviavaillsylla........glygialaa 391
                                   + +l+v++teyytst+ +pvk+ia+asetGa+tn+isGla+g+est+lp+++i+++il+s+ +         g+ygia+aa
  gi|91772992|ref|YP_565684.1| 321 IMVLMVIFTEYYTSTSFRPVKTIAKASETGAGTNVISGLAIGFESTALPLIIIIAGILASFFVVggatdpsmGVYGIAIAA 401
                                   **************************************************************98667777778******** PP

                                   HHHTTTHHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..HHC CS
                       H_PPase 392 vgmLstlgitlavdayGPiaDNAggiaemseleeevreitdklDavGNttkAitKgfaigsAalaalaLfaaylee..akl 470
                                    +mLst+g+++a+d+yGPi+DNAggiaem++++ evr+itd+lDavGNttkA+tKg+ai+sAal+alaLfa y ++   ++
  gi|91772992|ref|YP_565684.1| 402 AAMLSTTGMIVALDSYGPITDNAGGIAEMAKMPAEVRKITDALDAVGNTTKAVTKGYAIASAALGALALFADYRHKvnLEA 482
                                   ***************************************************************************955345 PP

                                   S--BTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTTSS---HHHHHHHHHHHHHHTTHHHH CS
                       H_PPase 471 ekvdllnpevlvglliGamlvflfsaltmkaVgkaAeevveevrrqfkeipgilegkekpdykkcveistkaalkemilpg 551
                                    +++l np vlvglliGa+l+flf+a+tmkaVgkaA ++v+evrrqf+eipgi+eg++kp+y kcv+i+t aa++em++pg
  gi|91772992|ref|YP_565684.1| 483 GSLSLENPIVLVGLLIGALLPFLFTAVTMKAVGKAAFAIVNEVRRQFREIPGIMEGTAKPEYGKCVDIVTAAAIREMVIPG 563
                                   679****************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTT.SSSHHHHHHHHHHHHHHHHHCTH CS
                       H_PPase 552 llavlapivvglllgaealagllagalvsgvllAifmanaGgawDNAKkyiEegelggkgseahkaaVvGDtVGDPfKDta 632
                                   +la+++p++vg++lg+eal+gll+g++vsg+llA++m+n+GgawDNAKk+iE+g++ggkgs+ahkaa+vGDtVGDPfKDt+
  gi|91772992|ref|YP_565684.1| 564 ILAIFVPLLVGIVLGPEALGGLLIGIIVSGLLLALTMNNGGGAWDNAKKLIEDGQYGGKGSDAHKAAIVGDTVGDPFKDTS 644
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHH CS
                       H_PPase 633 gpslniliklmsivslvi 650
                                   gp+ln lik+++++++++
  gi|91772992|ref|YP_565684.1| 645 GPALNALIKVVNMIAILF 662
                                   ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1171  (0.0653132); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.53
# Mc/sec: 3845.90
//
Query:       gi|91772993|ref|YP_565685.1|  [L=160]
Description: hypothetical protein Mbur_0996 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-06   26.1   0.0    1.1e-05   25.2   0.0    1.3  1  MarR_2          MarR family
    0.00059   19.7   0.0    0.00099   19.0   0.0    1.3  1  HTH_11          HTH domain
    0.00083   19.9   0.1     0.0026   18.3   0.0    1.8  2  Mga             Mga helix-turn-helix domain
     0.0027   18.0   0.0     0.0037   17.6   0.0    1.4  1  Rrf2            Transcriptional regulator
     0.0028   17.7   0.0     0.0048   16.9   0.0    1.4  1  HTH_29          Winged helix-turn helix
     0.0042   16.7   0.0     0.0075   15.9   0.0    1.4  1  GntR            Bacterial regulatory proteins, gntR family
     0.0046   16.9   0.0     0.0085   16.0   0.0    1.5  1  MarR            MarR family
       0.01   15.8   0.0      0.016   15.1   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.025   14.2   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.02   14.8   0.0      0.032   14.1   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.021   14.6   0.0      0.045   13.5   0.0    1.6  1  HTH_8           Bacterial regulatory protein, Fis family
      0.025   14.7   0.0      0.043   13.9   0.0    1.3  1  HTH_28          Helix-turn-helix domain
      0.028   14.4   0.0      0.054   13.5   0.0    1.4  1  HTH_6           Helix-turn-helix domain, rpiR family
       0.03   14.5   0.0      0.077   13.2   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.036   13.9   0.0      0.063   13.1   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.059   13.3   0.0      0.071   13.1   0.0    1.2  1  SLM4            Protein SLM4
      0.075   13.1   0.0       0.17   12.0   0.0    1.5  1  HTH_7           Helix-turn-helix domain of resolvase
       0.14   12.0   0.0       0.25   11.2   0.0    1.3  1  HTH_10          HTH DNA binding domain
       0.14   12.0   0.0       0.23   11.3   0.0    1.3  1  HTH_23          Homeodomain-like domain
       0.14   12.0   0.0       0.21   11.4   0.0    1.3  1  DUF746          Domain of Unknown Function (DUF746)


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.2e-08   1.1e-05       7      56 ..      13      62 ..      12      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  ++r+L +L   +g +++++ela++ ++s+++++++++ +++ GL+  +++
  gi|91772993|ref|YP_565685.1| 13 ELRLLEFLLPLEGLEFNISELAEEVNISRPTLTKVVQMFSEWGLLLSSKN 62
                                  689*********9888****************************977765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.1e-06   0.00099       3      51 ..      14      63 ..      13      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                        HTH_11  3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                  l +le+Ll  +g  ++++eLAee n+Sr t  + ++  +e+g+ + s++g
  gi|91772993|ref|YP_565685.1| 14 LRLLEFLLPLEGLeFNISELAEEVNISRPTLTKVVQMFSEWGLLLSSKNG 63
                                  57899999999999****************************99999988 PP

>> Mga  Mga 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   2.9e-06    0.0026      13      55 ..       8      52 ..       4      72 .. 0.86
   2 ?   -1.2   0.0       3.6   3.2e+03       8      20 ..      87      99 ..      70     112 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-06
                                  HHHSHHHHHHHHHH..HHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                           Mga 13 lkeslkyqllkflf..eeeevsieelaqelyiSestlkrkikeln 55
                                  l +s +++ll+fl+  e  e++i ela+e+ iS+ tl ++++ + 
  gi|91772993|ref|YP_565685.1|  8 LGNSCELRLLEFLLplEGLEFNISELAEEVNISRPTLTKVVQMFS 52
                                  667999********99999******************99887655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.6
                                  HHHHHHHHSHHHH CS
                           Mga  8 llqellkeslkyq 20
                                  l++ +l e   ++
  gi|91772993|ref|YP_565685.1| 87 LIETMLGEEALFE 99
                                  3333333444444 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.2e-06    0.0037      23      61 ..      26      64 ..      11      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-06
                                  CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE.EEETTT CS
                          Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglv.ksvrGk 61
                                   e ++++e+ae++nis++ l k++++ ++ gl+  s+ G+
  gi|91772993|ref|YP_565685.1| 26 LE-FNISELAEEVNISRPTLTKVVQMFSEWGLLlSSKNGN 64
                                  44.89**************************861455565 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.4e-06    0.0048      10      51 ..      24      63 ..      19      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.4e-06
                        HTH_29 10 eGvs.tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51
                                  eG+  ++s++A+ +++sr+t  +++  f e+Gl  ll++++ g
  gi|91772993|ref|YP_565685.1| 24 EGLEfNISELAEEVNISRPTLTKVVQMFSEWGL--LLSSKN-G 63
                                  566679**************************7..877664.5 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.4e-06    0.0075      28      58 ..      31      61 ..      27      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.4e-06
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 28 reLaaefgVsrttvReALrrLeaeglverrq 58
                                  +eLa+e ++sr+t+ ++ ++ +++gl+ + +
  gi|91772993|ref|YP_565685.1| 31 SELAEEVNISRPTLTKVVQMFSEWGLLLSSK 61
                                  79************************98755 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.5e-06    0.0085      19      52 ..      29      62 ..      16      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.5e-06
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR 19 svseLakklgvskstvtrvldrLekkGlieRsks 52
                                  ++seLa+ +++s++t+t+v+    + Gl+ +sk+
  gi|91772993|ref|YP_565685.1| 29 NISELAEEVNISRPTLTKVVQMFSEWGLLLSSKN 62
                                  89******************99888888887776 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 !   15.1   0.0   1.8e-05     0.016       2      53 ..      15      61 ..      14      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                  HHHHHHHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E CS
                     HTH_Crp_2  2 RlArfLlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglis..r 53
                                  Rl  fLl l    +g   l ++  elA+ ++++r t++++ + +++ gl+   +
  gi|91772993|ref|YP_565685.1| 15 RLLEFLLPL----EG---LEFNISELAEEVNISRPTLTKVVQMFSEWGLLLssK 61
                                  677777766....23...777889************************987433 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.025      20      41 ..      30      51 ..      29      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                        HTH_24 20 qreLAerlglSpstvnrrlkrL 41
                                  ++eLAe++++S++t+++ ++ +
  gi|91772993|ref|YP_565685.1| 30 ISELAEEVNISRPTLTKVVQMF 51
                                  68*************9988765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.5e-05     0.032      17      56 ..      20      61 ..      10      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                                  HH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 17 Ll..klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  Ll  +  + +++e+aee++++r++  +v++  ++ Gl   +k
  gi|91772993|ref|YP_565685.1| 20 LLplEGLEFNISELAEEVNISRPTLTKVVQMFSEWGLLLSSK 61
                                  55435557899*******************999999876655 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-05     0.045      18      36 ..      27      45 ..      23      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                  TT-HHHHHHHHTS-HHHHH CS
                         HTH_8 18 gGnkskAArlLGisRrtLy 36
                                  ++n+s+ A++ +isR tL+
  gi|91772993|ref|YP_565685.1| 27 EFNISELAEEVNISRPTLT 45
                                  58****************8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.8e-05     0.043       9      40 ..      23      55 ..      17      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                        HTH_28  9 laaGh.svreaArelgisrrtvyrWikryeegG 40
                                  l   + +++e+A+e++isr t+ + ++ + e+G
  gi|91772993|ref|YP_565685.1| 23 LEGLEfNISELAEEVNISRPTLTKVVQMFSEWG 55
                                  4444579***************99999777777 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 ?   13.5   0.0     6e-05     0.054      20      58 ..      15      51 ..       9      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                                  HHHHHHHH-S---TT--HHHHHHHTT--HHHHHHHH--- CS
                         HTH_6 20 kiaeyilaspdkaielsikalAkaaavSeativrfakkL 58
                                  +++e++l  p +  e+ i++lA++ ++S++t++++ + +
  gi|91772993|ref|YP_565685.1| 15 RLLEFLL--PLEGLEFNISELAEEVNISRPTLTKVVQMF 51
                                  5666665..44567899*****************99865 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.6e-05     0.077      26      55 ..      31      60 ..      27      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-05
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyveye 55
                                  ++lae+ n+s ++ ++ ++  ++ G++  +
  gi|91772993|ref|YP_565685.1| 31 SELAEEVNISRPTLTKVVQMFSEWGLLLSS 60
                                  79*********************9998655 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.1e-05     0.063       8      48 ..      16      57 ..      14      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-05
                                  HHCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR  8 iLdalaeapqel.tlselArrtglpkStvhRlLqtLvelGyv 48
                                  +L++l    +   ++selA++  ++++t    +q + e+G++
  gi|91772993|ref|YP_565685.1| 16 LLEFLLPLEGLEfNISELAEEVNISRPTLTKVVQMFSEWGLL 57
                                  555555555532489*************************98 PP

>> SLM4  Protein SLM4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.9e-05     0.071      34      86 ..      56     107 ..      31     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                                   EEEETTT--EEEEEE--S-S-HHHHHHHHHHHHHHHHHHHHHHHHHHT-SS-- CS
                          SLM4  34 lLlsaengsilsyanssdkssleeestslnnLkmmsLlikdkwsedekeeeeq 86 
                                   lLls++ng i++y+  + +ss   + +  nn+ + ++l +++++e +   ee+
  gi|91772993|ref|YP_565685.1|  56 LLLSSKNGNITTYSI-NMNSSIVASIQEFNNMLIETMLGEEALFEIHDYLEEK 107
                                   79*************.55799999***********999999999977766666 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 ?   12.0   0.0   0.00018      0.17      24      41 ..      30      47 ..      26      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                  STTTSSSS---SSSS--S CS
                         HTH_7 24 iskIAkevnisRsTvYRy 41
                                  is++A+evnisR T+ ++
  gi|91772993|ref|YP_565685.1| 30 ISELAEEVNISRPTLTKV 47
                                  99************9665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00027      0.25      25      44 ..      29      48 ..      27      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                        HTH_10 25 tlkeLAkelGIskstlsehL 44
                                  +++eLA+e +Is++tl++ +
  gi|91772993|ref|YP_565685.1| 29 NISELAEEVNISRPTLTKVV 48
                                  789*************9876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.23      18      42 ..      28      52 ..      14      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                        HTH_23 18 lsvreIAreLgvsrrTvyrwlkryr 42
                                   +++e A+e ++sr T+ ++++ + 
  gi|91772993|ref|YP_565685.1| 28 FNISELAEEVNISRPTLTKVVQMFS 52
                                  6789***************999885 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.21      10      43 ..      25      58 ..      13      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                        DUF746 10 sqplslaeaadllgtdegiiakwvreFrewllqL 43
                                  +++  + e+a+ +  +  +  k v++F ew l L
  gi|91772993|ref|YP_565685.1| 25 GLEFNISELAEEVNISRPTLTKVVQMFSEWGLLL 58
                                  57899*************************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1015.36
//
Query:       gi|91772994|ref|YP_565686.1|  [L=166]
Description: hypothetical protein Mbur_0997 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.002   18.0   0.0     0.0043   17.0   0.0    1.5  1  UnbV_ASPIC  ASPIC and UnbV
  ------ inclusion threshold ------
      0.078   13.2   0.3       0.14   12.4   0.3    1.3  1  YiaAB       yiaA/B two helix domain
       0.08   12.8   0.0       0.13   12.1   0.0    1.3  1  MerR_2      MerR HTH family regulatory protein


Domain annotation for each model (and alignments):
>> UnbV_ASPIC  ASPIC and UnbV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.2e-07    0.0043      28      63 ..     122     157 ..     119     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.2e-07
                    UnbV_ASPIC  28 ssdprlhFGLGkatkidsvevrWpdGkvqtlenvka 63 
                                   s ++ lh G + +t+++s+ev++p+G+++t+++v a
  gi|91772994|ref|YP_565686.1| 122 SDSYYLHDGRDLDTNVQSIEVIYPNGQTKTITDVRA 157
                                   56677888889999*******************987 PP

>> YiaAB  yiaA/B two helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.4e-05      0.14      23      45 ..      12      34 ..       8      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                         YiaAB 23 lpldlseKgfyamgllfllfsaf 45
                                  ++++l+++ f +++ll++lf++f
  gi|91772994|ref|YP_565686.1| 12 NTIQLNMRLFSFIVLLLVLFTTF 34
                                  799*******************9 PP

>> MerR_2  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.2e-05      0.13      11      66 ..      86     144 ..      82     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                        MerR_2  11 gieeeflieLvelgliepeiee.eewyfdesqlarlekavRLq..rDLeinleGiavil 66 
                                   ++e++f+    +++ i++e+++ ++  ++ +++ r+     L+  rDL+ n++ i+vi+
  gi|91772994|ref|YP_565686.1|  86 HLESSFIDIFSKYENIQIEEVGyDTVKLSIKDVSRASDSYYLHdgRDLDTNVQSIEVIY 144
                                   899*******************77888**********999998668***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1088.85
//
Query:       gi|91772995|ref|YP_565687.1|  [L=113]
Description: ABC transporter, ATPase subunit, partial [Methanococcoides burtonii DSM 6242]
Scores for complete 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   31.5   0.0    3.3e-07   30.9   0.0    1.3  1  ABC_tran  ABC transporter
     0.0016   17.9   0.1     0.0018   17.8   0.1    1.1  1  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.051   13.4   0.0        0.3   10.9   0.0    2.2  2  Qua1      Qua1 domain
       0.12   12.2   0.2       0.14   12.0   0.2    1.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
       0.13   12.1   0.0       0.14   12.0   0.0    1.2  1  DEAD      DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   9.2e-11   3.3e-07      85     137 .]       5      57 ..       1      57 [. 0.91

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.2e-11
                                   HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  85 iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   ie++ + ++l++l+ +++++ p +LSgG+ qr++lar++  +p+++++DE t+
  gi|91772995|ref|YP_565687.1|   5 IENVDDLIELVGLRREHLTRYPGQLSGGEIQRIVLARIISIDPSFIVADEVTS 57 
                                   677778889999999***********************************985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1     5e-07    0.0018     135     205 ..      20      95 ..       2     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-07
                                   T.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC- CS
                                   x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemleka 205
                                   e       +LSgGe + + la +++i      ++ + De+ + LD +  +++ +l++  ++++n+ ++ is++ ++l+++
  gi|91772995|ref|YP_565687.1|  20 EhltrypgQLSGGEIQRIVLARIISID----PSFIVADEVTSMLDVSVQAQILRLMEriQEETNVSYLLISHDIDLLKNV 95 
                                   444444449*****9999999998875....4699**********9988888777774444457889999*999988876 PP

>> Qua1  Qua1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.5e-05       0.3       7      21 ..      39      53 ..      37      58 .. 0.87
   2 ?   -0.9   0.0      0.43   1.5e+03      18      31 ..      86      99 ..      84     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                          Qua1  7 mAekdSLdPsftham 21
                                  +A+++S+dPsf++a 
  gi|91772995|ref|YP_565687.1| 39 LARIISIDPSFIVAD 53
                                  8***********995 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.43
                          Qua1 18 thamqLlsaEIeki 31
                                  +h + Ll+++ ++i
  gi|91772995|ref|YP_565687.1| 86 SHDIDLLKNVCDRI 99
                                  68889999988887 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.8e-05      0.14     236     302 ..      28      92 ..      16      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                        AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                   +lS G  +   +l+ +++ ++  s+++ DE+ + L+ ++++ +l+l+ ++ +++++  +l +H+  ll
  gi|91772995|ref|YP_565687.1|  28 QLSGGEIQR-IVLARIISIDP--SFIVADEVTSMLDVSVQAQILRLMeRIQEETNVSYLLISHDIDLL 92 
                                   555565555.55566666665..99999*******************64444488********98776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.8e-05      0.14     123     154 ..      48      79 ..       6      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                                   EEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 123 rflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                   +f+V DE+  +ld + + +i r+++++++ t+
  gi|91772995|ref|YP_565687.1|  48 SFIVADEVTSMLDVSVQAQILRLMERIQEETN 79 
                                   89*************************76654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 761.71
//
Query:       gi|91772996|ref|YP_565688.1|  [L=649]
Description: acetyl-coenzyme A synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-99  332.7   0.0    3.2e-99  332.4   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      3e-27   95.4   0.2    9.3e-27   93.8   0.2    1.9  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    1.4e-19   69.7   2.6    4.2e-19   68.2   2.6    1.9  1  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 !  332.4   0.0  5.3e-103   3.2e-99       2     423 .]      84     522 ..      83     522 .. 0.88

  Alignments for each domain:
  == domain 1  score: 332.4 bits;  conditional E-value: 5.3e-103
                                   HHHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                   AMP-binding   2 eeqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                   +++++k+ dk+al++    +  +t+TY+el++++ r+AagL++lGvkkgd+V i+lp+ pe v+++la+ ++Ga ++++ +
  gi|91772996|ref|YP_565688.1|  84 DRHVQKHGDKPALIWegeMENSETYTYKELRDATARFAAGLKELGVKKGDVVTIYLPMVPEAVISMLACSRIGAPHSVVFA 164
                                   7899*************98889*********************************************************** PP

                                   TS-HHHHHHHHHHHTESEEE.......E..TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS... CS
                   AMP-binding  80 tltaeelayiledseakvli.......a..tvdselleklleaaakleavklvivldadellkeeelkeeeeseekae... 148
                                   ++++e+la+ +ed+ ++++i       +   +++   e++++  ++ +av++viv+d+++     +++ +  ++   +   
  gi|91772996|ref|YP_565688.1| 165 GFSSEALAQRVEDAHSRFVItcngyfhKgnLIQQ--KERADKGLENAPAVEKVIVVDHAANIIPMKEERDIWWN---Dlih 240
                                   ********************99998852444344..45566666666788999999977654443333333333...1455 PP

                                   ...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHH CS
                   AMP-binding 149 ...kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsilplahifglilellla 224
                                       ++e+e  +++d+++i+YTSGTTG+PKGV++++ +++v +  +    +  f+lk+dd +++++++ +i+g+++ ++++
  gi|91772996|ref|YP_565688.1| 241 nvdSECEPEHMDSEDTLFIMYTSGTTGRPKGVVHTTgGYMVGTNVTS---NWiFDLKDDDIFWCTADVGWITGHSYLVYGP 318
                                   6777889999**************************55554443332...23478999*********************** PP

                                   HHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHH CS
                   AMP-binding 225 llsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrff 303
                                   l++Gat+v+ ++ ++ +d++++++ +ek++vt+++++P++++ +++  +++    +++dlsslrl+ ++gep++p+++ ++
  gi|91772996|ref|YP_565688.1| 319 LSNGATIVMHEGAPDyPDKGRFWDIVEKYGVTIFYTAPTAIRTFMKwGDEIP---AKYDLSSLRLLGSVGEPINPKAWLWY 396
                                   ***************88899**************************988888...556*********************** PP

                                   HHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBT CS
                   AMP-binding 304 ralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYl 379
                                   +++ g+   ++++++++TEt+++++ + +   + ++g++ +p+pg+++ i+D+e g++vp g  G l ++ p  ++ +   
  gi|91772996|ref|YP_565688.1| 397 YETIGKskcPIVDTWWQTETGMIMISPLPGITTMRPGTATRPFPGIKANILDDE-GNEVPMGSGGYLALQNPwpSMIRTIN 476
                                   ****99******************764446666789*****************9.****************9777****** PP

                                   T-HHHHHHHEEET..CCEEEEEEEEEEETTSEEEEEEECCCEEEET CS
                   AMP-binding 380 kkpeataeafdse..grwlrTGDlgrldedGyleivgRkkdliklr 423
                                   +++++  ++++s+   + + TGD +r dedG+++i+gR++d+ik++
  gi|91772996|ref|YP_565688.1| 477 GDEQRFIDTYWSKwgADTYLTGDGARKDEDGNFWILGRLDDVIKVS 522
                                   ***********856345***************************85 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 !   93.8   0.2   1.6e-30   9.3e-27       1      76 []     530     609 ..     530     609 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.6e-30
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---....HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea....leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   e+Esalvshp VaeaaV G+ de+kGe+++a+V+l++    +    le+eLk+hv +e+gp+a+pk ++f++elpktrsGK
  gi|91772996|ref|YP_565688.1| 530 EIESALVSHPSVAEAAVDGKVDEIKGEVICAYVILESScD-DqcsiLEDELKQHVVDEIGPIARPKMIIFTEELPKTRSGK 609
                                   8**********************************64442.23578**********************************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 !   68.2   2.6   7.1e-23   4.2e-19       4      55 .]      32      82 ..      30      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 7.1e-23
                                  HHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                        ACAS_N  4 lykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                  +y+++ +d e+FW+  a ++dW+k++d+vld+ ++p++kWF+GGklN++yNc
  gi|91772996|ref|YP_565688.1| 32 IYEKAEADIEGFWEGLAGNIDWFKKWDTVLDW-QPPHAKWFSGGKLNASYNC 82
                                  699*****************************.999**************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4116.78
//
Query:       gi|91772997|ref|YP_565689.1|  [L=215]
Description: orotidine 5'-phosphate decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  135.1   0.1    3.3e-39  134.8   0.1    1.1  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    0.00071   19.0   0.0    0.00088   18.7   0.0    1.2  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
     0.0015   18.1   0.4       0.02   14.4   0.1    2.4  3  PcrB            PcrB family
  ------ inclusion threshold ------
      0.072   12.3   0.1        0.1   11.8   0.1    1.3  1  DHO_dh          Dihydroorotate dehydrogenase
      0.077   12.2   0.7        5.4    6.2   0.2    2.7  2  NanE            Putative N-acetylmannosamine-6-phosphate epim


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 !  134.8   0.1   9.2e-43   3.3e-39       2     225 .]       6     209 ..       5     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 9.2e-43
                                   EEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTCHH CS
                     OMPdecase   2 nLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatagsar 82 
                                   +L+lalDv++++++l++a++v ++++ +K++y+lv g+g      ++++++ +  +++++D+K+aDI+nt +++++   + 
  gi|91772997|ref|YP_565689.1|   6 RLILALDVTDRENALRIANEVSDYVDSIKVGYPLVLGEG-----LSIVKELVEI-APVIADFKVADIPNTDRLICE---HV 77 
                                   79*************************************.....9******999.6*******************9...67 PP

                                   HHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTH. CS
                     OMPdecase  83 ikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetln. 162
                                   + ++a  ++ h++ G +s+ +++++a+++g   ++++++ms++g+ ++ +  ++++++  a e+       G+va +t++ 
  gi|91772997|ref|YP_565689.1|  78 FNAGAAGIITHGFTGRDSLDSCVKVANEFG-TDVYVVTEMSHPGGVEFFR-PVAEDIASMAVEAG----ASGVVAPATRPe 152
                                   9****************************8.9******************.55555655555555....56*********6 PP

                                   ...HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                     OMPdecase 163 ...ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                      +++++ ++++ ++ pg+g+ qgg + ++ +         agad +ivGR+I++++ p+e+a+++
  gi|91772997|ref|YP_565689.1| 153 rvkDIRKIiGEELSIISPGVGA-QGGSAADVIR---------AGADWVIVGRSIYNSDSPAEAAKKI 209
                                   5544444488888888888887.7666666553.........68********************986 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 !   18.7   0.0   2.5e-07   0.00088      45     198 .]      44     197 ..      11     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                                   -HHHHHHHGGGE-S-EEEEEE.SSSHHHCH.HHHHHCT-SEEEEE-S.T-TTHHHHHHHHHHTTSEEEEEE-TT--..GGG CS
                Ribul_P_3_epim  45 gplvvealrkltelpldvHLm.veevdriv.pefaeagasiisvHaE.alehlkrtiqeikeaGakaglvlnpatp..lea 120
                                   g  +v++l ++  +  d+ +  + + dr++ ++  +aga+ i  H     + l+ +++   e G+ + +v + + p  +e+
  gi|91772997|ref|YP_565689.1|  44 GLSIVKELVEIAPVIADFKVAdIPNTDRLIcEHVFNAGAAGIITHGFtGRDSLDSCVKVANEFGTDVYVVTEMSHPggVEF 124
                                   56678888888888888877547888887636667899997777755388999******************9999855677 PP

                                   GTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEES.S--TTTCHHHHHHT--EEEESHHHH CS
                Ribul_P_3_epim 121 leyllekldlvllmsvePgfgGQkFipevlekikkvrklidekeldlkievDG.GvkldnieqiaeagadvlVagsavf 198
                                   ++ ++e+   +  m+ve g +G     +  e++k++rk+i e   +l i   G G +  +++ +++agad +++g+ ++
  gi|91772997|ref|YP_565689.1| 125 FRPVAED---IASMAVEAGASGVVAPATRPERVKDIRKIIGE---ELSIISPGvGAQGGSAADVIRAGADWVIVGRSIY 197
                                   7777776...567**********9999999***********9...444443333666678999*************997 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.71   2.5e+03      15      36 ..      15      35 ..       3      41 .. 0.46
   2 ?    1.2   0.0     0.061   2.2e+02      22      71 ..      73     122 ..      66     137 .. 0.86
   3 !   14.4   0.1   5.5e-06      0.02     162     218 ..     142     205 ..     128     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.71
                                  TSS-CHHHHHHHHCTT-SEEEE CS
                          PcrB 15 eeenpdEiveiviesgtDavmi 36
                                  ++en   i++ v +++ D++ +
  gi|91772997|ref|YP_565689.1| 15 DRENALRIANEV-SDYVDSIKV 35
                                  233333333333.555555544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.061
                                   HHHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHCTSSS-EEEEESSGGG- CS
                          PcrB  22 iveiviesgtDavmigGsq.svtldntvrllkkvsriklPivlepsnvegv 71 
                                   i e v + g+ +++  G +    ld  v++ ++   +++ +v e s + gv
  gi|91772997|ref|YP_565689.1|  73 ICEHVFNAGAAGIITHGFTgRDSLDSCVKVANEF-GTDVYVVTEMSHPGGV 122
                                   56889999*******9999788899999999999.9999999999988877 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5.5e-06
                                   TTSSS-H...HHHHHHHHHHSSSEEEEESS-.-SHHHHHHHHCC.SSEEEE-CHHHHHH..HCH CS
                          PcrB 162 sGaledv...eevialkkklekarlivGGGi.rsaEkAkevvea.ADvivvGnvveekd..erk 218
                                   sG+  +    e v++++k + ++  i+  G+  ++ +A++v++a AD ++vG  ++++d   ++
  gi|91772997|ref|YP_565689.1| 142 SGVVAPAtrpERVKDIRKIIGEELSIISPGVgAQGGSAADVIRAgADWVIVGRSIYNSDspAEA 205
                                   777654333499*****999776555555552678899*******************9855334 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.8e-05       0.1     221     292 ..     141     214 ..     100     215 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                                   EEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGT..CHHHHHHHHHH CS
                        DHO_dh 221 lsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegp..kiakkikkele 292
                                    sG     +  + + +++k + +e+ iI+ G    g  a + i+aGA  v v+  ++ ++    +akki++e++
  gi|91772997|ref|YP_565689.1| 141 ASGVVAPATRPERVKDIRKIIGEELSIISPGVGAQGGSAADVIRAGADWVIVGRSIYNSDSpaEAAKKICDEMN 214
                                   44544444445667788888999*******9778888999*************999666642257899999875 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 ?    3.6   0.0    0.0093        33      66      95 ..       7      40 ..       2      61 .. 0.73
   2 ?    6.2   0.2    0.0015       5.4     136     177 ..     156     197 ..     135     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0093
                                  SEEEEE--SS--T....--HHHHHHHHHHH--EE CS
                          NanE 66 diialDatdrerp....vtieelikkikekyqll 95
                                   i+alD tdre       ++ + + +ik  y l+
  gi|91772997|ref|YP_565689.1|  7 LILALDVTDRENAlriaNEVSDYVDSIKVGYPLV 40
                                  589*******988444455666777787777554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0015
                                   HHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                          NanE 136 lvkalseaglkviaeGrintPekakkaieiGvdavvvGsait 177
                                    ++++  ++l +i  G       a+++i+ G+d v+vG +i 
  gi|91772997|ref|YP_565689.1| 156 DIRKIIGEELSIISPGVGAQGGSAADVIRAGADWVIVGRSIY 197
                                   5788889999999999999999****************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 1597.69
//
Query:       gi|91772998|ref|YP_565690.1|  [L=369]
Description: hypothetical protein Mbur_1001 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-64  217.9   1.0    1.6e-64  217.5   1.0    1.1  1  CbiZ      Adenosylcobinamide amidohydrolase


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.5   1.0   9.1e-69   1.6e-64       2     192 .]      31     236 ..      30     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 217.5 bits;  conditional E-value: 9.1e-69
                          CbiZ   2 feeprrvlssavlngGlre.lravlnhqvpegyered......peeyleeyleelglppektvgllTaadmenaaiaeeef 75 
                                   +++ r++ls+++lngG+++ +++vlnh++++  + ++       +eyl+ ++++lgl+p++++g+lT a+mena+++++++
  gi|91772998|ref|YP_565690.1|  31 LPKGRKTLSTSWLNGGYHNnIEYVLNHTIDNRSHGTSdleggnVKEYLKIVAKRLGLEPDSSTGMLTTASMENAVVVSDSY 111
                                   67899**************************999999887666688888888888************************** PP

                          CbiZ  76 edlevtavvTaGvesnavragd.......edeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsryse 149
                                   ++levta+vT+Gve n++ragd       +++ ++  GTIN i+lina+L+d a++ra+itatEAK+aalq+l+++srys+
  gi|91772998|ref|YP_565690.1| 112 RGLEVTAIVTGGVEINGGRAGDeasyyqeDEHFEPVGGTINAILLINADLPDYAMARAMITATEAKSAALQQLMAPSRYSS 192
                                   ***************************96444556678******************************************* PP

                          CbiZ 150 g.atGTgTDaiavaadkegeeeltyaGkhtklGeliaraVyeAv 192
                                   g atGTgTD ++++ad+++  +lt+aGkh+klGeli++++ eA+
  gi|91772998|ref|YP_565690.1| 193 GiATGTGTDMMIIVADSTSHIRLTDAGKHSKLGELIGKCMMEAI 236
                                   ****************99999********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2356.92
//
Query:       gi|91772999|ref|YP_565691.1|  [L=284]
Description: metal-dependent phosphohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-19   68.8   0.0    6.1e-19   68.3   0.0    1.2  1  HD_4             HD domain
     0.0014   18.8   0.2     0.0063   16.7   0.0    2.1  2  HD               HD domain
  ------ inclusion threshold ------
      0.083   13.2   0.0        4.4    7.7   0.0    2.3  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0     1e-22   6.1e-19       3     142 ..     107     241 ..     105     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1e-22
                          HD_4   3 elaaelhagqrkltgepllahalevAailaelgldaetviAalLhdvveda.lsleeirerfGeevarLvegvsklkrlqk 82 
                                   +++ ++h+ +++++g+p ++h++ vA+il + +  ++ + A++Lhdvveda l+ ++ir+r G++va+ v +v++ ++l++
  gi|91772999|ref|YP_565691.1| 107 AFVNHAHRMNKRKSGTPFITHPMDVASILIKENATSDLIFAGFLHDVVEDAgLTNADIRRRYGPTVADYVSAVTEPEELKQ 187
                                   789999********************************************98888************************** PP

                          HD_4  83 vaaadeaeekaeqvenlRkmLlAmveDirvvliklAdrlqtlrslaaakeekrrdvaret 142
                                   +   d ++ ka++   +R +  A++   +v +++ Ad+l +lr l  +  ek  + a+e+
  gi|91772999|ref|YP_565691.1| 188 G--DDVESWKARKEYIIRSISKAIS---EVKILSCADKLANLRDL-IQYLEKEGESAWEM 241
                                   *..3444444444446677777997...9***************9.44455555666665 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.35   2.1e+03      59      93 ..      88     117 ..      65     120 .. 0.65
   2 !   16.7   0.0   1.1e-06    0.0063       2     121 ..     125     223 ..     124     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHH CS
                            HD  59 Hekvgaeilrevekrlgldledvaklirehheswe 93 
                                    e +g++i +++ ++      dv + +++ h++  
  gi|91772999|ref|YP_565691.1|  88 DEMYGEKIEKDLTELG-----DVFAFVNHAHRMNK 117
                                   4556666666666666.....77777777777655 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.1e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.HHHH CS
                            HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.ledv 81 
                                   ++H++ Va ++ +     +       l +a+ lHD++++       ++    ++ +      a  +++v ++++l+  +dv
  gi|91772999|ref|YP_565691.1| 125 ITHPMDVASILIKENATSD-------LIFAGFLHDVVEDAGLT---NA----DIRRRYGPTVADYVSAVTEPEELKqGDDV 191
                                   79*********99999988.......99************332...33....34445677888899999999988899999 PP

                                   HHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                            HD  82 aklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                     + +++   ++         +   ++e++i++ aD+la+
  gi|91772999|ref|YP_565691.1| 192 ESWKARKEYIIR--------SISKAISEVKILSCADKLAN 223
                                   999999999997........7899*************997 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.02   1.2e+02      19      65 ..      77     120 ..      71     127 .. 0.78
   2 ?    7.7   0.0   0.00074       4.4      18      84 .]     171     235 ..     164     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.02
                                   HHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS---------- CS
               Phage_int_SAM_1  19 lraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsats 65 
                                   ++ Yr +L ++ ++  e  k   +  +  dv af+++ ++ + +++s
  gi|91772999|ref|YP_565691.1|  77 MSGYRIQLLELDEMYGE--KIEKDLTELGDVFAFVNHAHRMN-KRKS 120
                                   67899999999999999..44455556679********9964.6666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00074
                                   HHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHHHTT CS
               Phage_int_SAM_1  18 TlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflvreg 84 
                                   T+++Y+ ++ + ++  + +  es+ + ++  +r++ ++  e  ++  s a +l+ lr++ q+l +eg
  gi|91772999|ref|YP_565691.1| 171 TVADYVSAVTEPEELKQGDDVESWKARKEYIIRSISKAISE--VKILSCADKLANLRDLIQYLEKEG 235
                                   88888888888888888888888888777777777777777..99******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2056.24
//
Query:       gi|91773000|ref|YP_565692.1|  [L=169]
Description: hypothetical protein Mbur_1003 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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:                         0  (0); expected 0.2 (1e-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: 1277.65
//
Query:       gi|91773001|ref|YP_565693.1|  [L=438]
Description: hypothetical protein Mbur_1004 [Methanococcoides burtonii DSM 6242]
Scores for 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-77  260.1  34.4    3.5e-77  259.9  34.4    1.0  1  TctA      Tripartite tricarboxylate transporter TctA family
  ------ inclusion threshold ------
          5    7.8   6.9       0.77   10.4   2.1    2.3  2  DUF3139   Protein of unknown function (DUF3139)


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 !  259.9  34.4   3.9e-81   3.5e-77       1     408 [.       3     426 ..       3     427 .. 0.92

  Alignments for each domain:
  == domain 1  score: 259.9 bits;  conditional E-value: 3.9e-81
                          TctA   1 LllvllGvllGtliGllPGlhatlavalllpltf.....gldpeaalilllgiyvgaifggsipaillgvPGtpssvatvl 76 
                                   Ll+vl G++lG+++Gl+PG+h+++++ +l++l++     g++p ++++++++ +++++f+++ipai+lg+P + +++++vl
  gi|91773001|ref|YP_565693.1|   3 LLSVLTGYTLGIFSGLVPGIHTNNFALMLVALSPifmdwGIPPAYIAVAIVANSLSHSFHDIIPAIYLGAP-NDDMALAVL 82 
                                   899********************************************************************.********* PP

                          TctA  77 dgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse............. 144
                                   +g++l+++G+++eA+rl+a+gS+ +++vs+ll+++la +++   l+  ++ y+ ++ll +++++i++e             
  gi|91773001|ref|YP_565693.1|  83 PGHRLLLEGHGSEAIRLSALGSAGSVVVSLLLAVPLAFAFS--ILYPVLQSYLGWLLLLISIALIMTEkgeqvinqgslvk 161
                                   *****************************************..************************************** PP

                          TctA 145 .ksllkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip.....lslkdlkk 219
                                    k  + +l+++ll ++lgt+++ ++s+++      i++ +   l+p+l+GlFg+s+l+ sl s+s+ip     +    +k+
  gi|91773001|ref|YP_565693.1| 162 yKYKAYALVLFLLTGILGTFAFRMESNMN----PLIDIGSSSILLPLLSGLFGASQLIISLFSGSSIPpqkysKMELPVKR 238
                                   **************************777....799***************************999986544312223336 PP

                          TctA 220 slptilrgsliGtivGilPgvGasiaaflayavakr.lskk....pekf...gkgaiegvaapeaannaaaggaliplltl 292
                                   ++  +++gs++G++v++lPg+++siaa+la  + ++ ++k+     e f    +g++e+++a++++n+a+a++ l++l ++
  gi|91773001|ref|YP_565693.1| 239 IIRGVITGSAAGSVVAWLPGISSSIAAVLARLFIRSdFEKEtvaeDEDFdeqMEGSKEFIIAVSGVNTANAIFGLFALAVI 319
                                   67778888**********************999877544532322455754246*************************** PP

                          TctA 293 gipgsgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvllvi 372
                                   g ++sg+++++++++       + +    + ++++++l+++ ++++l+++ ++++++ ++++l k++++ +++++l+ l++
  gi|91773001|ref|YP_565693.1| 320 GKTRSGAMVAINEII-----DAASL----DQQFIILFLIVISLTAFLSYFSTIKIGNNIHRFLaKLDYSKICITVLAGLTL 391
                                   *************75.....44555....678*****************************666***************** PP

                          TctA 373 gayalnnslfdvlvmlifgvlGlllrrlgvplaplv 408
                                   ++ ++++  f++++++i++ lG+  + +++++++++
  gi|91773001|ref|YP_565693.1| 392 MSLLFTGL-FGLMIFMISIPLGMSASFMKIRRSHAM 426
                                   ********.*************************99 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.78     7e+03      10      10 ..     138     138 ..     108     178 .. 0.64
   2 ?   10.4   2.1   8.6e-05      0.77       3      36 ..     342     375 ..     340     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.78
                       DUF3139  10 l 10 
                                   l
  gi|91773001|ref|YP_565693.1| 138 L 138
                                   2 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.6e-05
                       DUF3139   3 kiiiililliillvivkvflglvgskpikkylan 36 
                                    +ii+++++i+l++++  f ++ + ++i+++la+
  gi|91773001|ref|YP_565693.1| 342 QFIILFLIVISLTAFLSYFSTIKIGNNIHRFLAK 375
                                   689************99999********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); 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:                         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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3166.00
//
Query:       gi|91773002|ref|YP_565694.1|  [L=345]
Description: methylcobalamin:coenzyme M methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-87  291.9   0.0    7.4e-87  291.7   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.7   0.0   4.1e-91   7.4e-87       1     346 []       5     338 ..       5     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 291.7 bits;  conditional E-value: 4.1e-91
                                   ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGG CS
                         URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaeal 81 
                                   t+++r++r l+g++vd+vPv+    ++++ + + ++ +++ ++++++++e++a+++++  + +gl+a+ ++++++v+a+al
  gi|91773002|ref|YP_565694.1|   5 TPKKRFIRSLKGKTVDKVPVCS---VTQTGTTELMKSSKAYWPQAHYDAEKMADLAIAGNEVAGLEAVRYPFCVTVIAQAL 82 
                                   6899******************...888***************************************************** PP

                                   T-EEEEET.TTEEEEE--S-.....GGGS----GGG..G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT-S CS
                         URO-D  82 Glevefee.gegPvvekpvr.taedveklevpddvee.grlpyvleaikllkkelggevpligfvgaPftlasylveGgsk 159
                                   G+++  ++ +++P+ e  +  + edv++++vp+d+ e +r+++vl+a++++kk++++++p+i+++++P  +a +l      
  gi|91773002|ref|YP_565694.1|  83 GCTIMEGTsDAQPHQEGVPCaRKEDVKDISVPSDLLErERIATVLKATDIVKKRVDDDIPIIAGMIGPAGIAFHLA----- 158
                                   ****99994555********9*************86688*************************************..... PP

                                   S-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S CS
                         URO-D 160 gfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkrivdevkaegpkv 238
                                   g ++++ +l+k+p+++++l+ + t+v+iey +a++e+g+da++i D    + l+sp++fe fvlp +k+i ++v++     
  gi|91773002|ref|YP_565694.1| 159 GEKNYFIWLIKKPDLIKDLIGIGTEVCIEYSNALFEHGVDAVTISDpeGGPALISPQMFESFVLPEYKKINKKVNG----- 234
                                   ***********************************************9999*************************..... PP

                                   -EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S-HHHHHHHHHHHHT.T---SSS CS
                         URO-D 239 pvilfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLl.gspeeiekevkeilekgaggkkg 318
                                     il+++g++++ile l ++g+d++s++++v++k a++ +gd+++l+Gn++P+++Ll ++pe++++e+ +++++g+g    
  gi|91773002|ref|YP_565694.1| 235 LKILHMCGDSTSILEPLLKSGFDGISIEEKVEVKRAKEIIGDRACLIGNVSPSSTLLsKTPEDVKREAMQCIRDGVG---- 311
                                   78*******************************88888999********************************99**.... PP

                                   EEB-BSS---TTS-HHHHHHHHHHHHT- CS
                         URO-D 319 yilnlGhgippetppenvkalveavkey 346
                                    il++G+gi+p+tp++n+ka+v a++ey
  gi|91773002|ref|YP_565694.1| 312 -ILAPGCGIAPHTPLKNMKAFVAARDEY 338
                                   .***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2183.42
//
Query:       gi|91773003|ref|YP_565695.1|  [L=120]
Description: desulfoferrodoxin [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-27   93.4   0.4    1.1e-26   93.2   0.4    1.0  1  Desulfoferrodox  Desulfoferrodoxin


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.4   6.4e-31   1.1e-26       3      95 ..      16     116 ..      14     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 6.4e-31
                                   HTTTHTTSEEEEEESEEEETTEEEEEEEESS.SS--BSSSS-EEEEEEEEEETTSS.....EEEE-TBS.ESEEEEEEEES CS
               Desulfoferrodox   3 dekeekHvPvieadevvkagelfevkvkvgk.ipHpneeeHyIewielyleeegek.....rvelsaed.epevtftvklk 76 
                                   ++++ekHvP+ie+ +++  +e+  ++v vgk ++Hpn+ eH+I+w+ely +++g +     rv++s+++ +p+++f++++ 
  gi|91773003|ref|YP_565695.1|  16 SAMKEKHVPTIEILKKHGGTEADLIRVIVGKeTAHPNTVEHHIAWVELYGKKTGGEvvnlgRVNFSPGNtKPDCWFKLENI 96 
                                   5789*************************************************99999999******9955*******998 PP

                                   SS.EEEEEEEEETTTEEEEE CS
               Desulfoferrodox  77 ke.kklvalsyCnlHGlWes 95 
                                   +e k+++al yCn+HGlWe+
  gi|91773003|ref|YP_565695.1|  97 SEyKAFCALGYCNIHGLWEN 116
                                   876899************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 756.19
//
Query:       gi|91773004|ref|YP_565696.1|  [L=181]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-12   46.6   9.4    6.1e-10   38.9   1.2    3.2  3  Fer4_5      4Fe-4S binding domain
    1.9e-08   33.8  21.3    1.1e-05   25.1   2.3    3.7  4  Fer4        4Fe-4S binding domain
      5e-07   29.8  25.3    2.2e-06   27.7  13.0    2.8  3  Fer4_9      4Fe-4S dicluster domain
      1e-06   28.7  15.3    3.5e-06   27.0  14.2    2.4  2  Fer4_10     4Fe-4S dicluster domain
      1e-06   28.7  15.5     0.0019   18.3   3.1    2.9  3  Fer4_21     4Fe-4S dicluster domain
    1.3e-06   28.8  12.4     0.0035   17.9   1.4    3.0  3  Fer4_7      4Fe-4S dicluster domain
      3e-05   23.9  21.0     0.0037   17.3   3.5    3.6  4  Fer4_6      4Fe-4S binding domain
    6.6e-05   23.1  11.7    0.00028   21.0   9.7    2.3  2  Fer4_18     4Fe-4S dicluster domain
    0.00012   22.5  14.9      0.085   13.4   4.5    3.2  3  Fer4_17     4Fe-4S dicluster domain
    0.00071   19.5  22.3     0.0044   17.0   2.0    3.7  4  Fer4_2      4Fe-4S binding domain
     0.0014   19.5  17.5      0.018   16.0   3.3    3.0  3  Fer4_16     4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.061   14.3   5.0      0.061   14.3   5.0    3.9  4  Fer4_3      4Fe-4S binding domain
      0.097   12.0   0.9       0.12   11.7   0.9    1.1  1  Bestrophin  Bestrophin, RFP-TM, chloride channel
       0.11   13.0  20.8       0.13   12.7   1.7    2.8  4  Fer4_8      4Fe-4S dicluster domain
       0.21   11.7   0.2       0.39   10.8   0.2    1.4  1  YebO        YebO-like protein
       0.58   10.8  23.0       0.32   11.6   4.0    3.6  4  Fer4_4      4Fe-4S binding domain
        9.1    7.2  15.1        4.6    8.2   1.7    2.6  2  Fer4_22     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   1.2   5.8e-13   6.1e-10      11      47 ..       3      39 ..       1      40 [. 0.88
   2 ?   -0.6   0.3       1.3   1.4e+03       4      16 ..      59      71 ..      56      73 .. 0.72
   3 !   11.7   0.1   0.00019       0.2       5      38 ..      89     122 ..      88     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.8e-13
                        Fer4_5 11 aivlvtllfGRafCgWiCPfGalqellakllrrklgk 47
                                  + v v+llfG ++CgW+CP+G++q +++  ++r lgk
  gi|91773004|ref|YP_565696.1|  3 LSVPVALLFGPVYCGWVCPRGMFQNIIGSMGKRVLGK 39
                                  5666899**********************99998887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                        Fer4_5  4 lllilflaivlvt 16
                                   +l+++l++++++
  gi|91773004|ref|YP_565696.1| 59 GVLLFLLTALVMY 71
                                  5677888888776 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00019
                        Fer4_5   5 llilflaivlvtllfGRafCgWiCPfGalqella 38 
                                   ll+++++ +l+++++ Ra C ++C  Ga   l++
  gi|91773004|ref|YP_565696.1|  89 LLLIMVVSILLSFFVDRAACKYFCKEGAAASLTN 122
                                   699*********************8887777777 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.066        69      14      22 ..      16      24 ..      15      26 .. 0.82
   2 ?   -2.3   0.3       4.3   4.6e+03      13      22 ..     107     116 ..     106     116 .. 0.75
   3 !   16.8   2.9     4e-06    0.0042       2      19 ..     130     147 ..     129     148 .. 0.90
   4 !   25.1   2.3     1e-08   1.1e-05       5      24 .]     160     179 ..     157     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.066
                                  HHHHSTTTE CS
                          Fer4 14 CvevCPvgA 22
                                  C  vCP g 
  gi|91773004|ref|YP_565696.1| 16 CGWVCPRGM 24
                                  999***985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                                   HHHHHSTTTE CS
                          Fer4  13 aCvevCPvgA 22 
                                   aC   C  gA
  gi|91773004|ref|YP_565696.1| 107 ACKYFCKEGA 116
                                   6888887776 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 4e-06
                                   EEETTTSSS-THHHHHST CS
                          Fer4   2 videekCigCGaCvevCP 19 
                                   + d ++C  CG+C  vCP
  gi|91773004|ref|YP_565696.1| 130 KRDDSLCNSCGICDRVCP 147
                                   5699************** PP

  == domain 4  score: 25.1 bits;  conditional E-value: 1e-08
                                   TTTSSS-THHHHHSTTTEEE CS
                          Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                      Ci C++Cv+ CPv+A++
  gi|91773004|ref|YP_565696.1| 160 DTACISCMKCVQKCPVDALR 179
                                   568***************85 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.1   1.1e+03       8      17 ..      16      25 ..      14      37 .. 0.70
   2 !   14.6   4.3   2.6e-05     0.027       7      48 ..     107     148 ..     105     150 .. 0.73
   3 !   27.7  13.0   2.1e-09   2.2e-06       2      50 ..     136     177 ..     135     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                        Fer4_9  8 CveaCpagvv 17
                                  C  +Cp g++
  gi|91773004|ref|YP_565696.1| 16 CGWVCPRGMF 25
                                  5556666655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.6e-05
                        Fer4_9   7 aCveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpk 48 
                                   aC + C+ g++ +  +  ++++++ ++++ C +Cg C  +Cp 
  gi|91773004|ref|YP_565696.1| 107 ACKYFCKEGAAaSLTNLVKIRKIK-RDDSLCNSCGICDRVCPM 148
                                   699999888883555555555554.45569***********96 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 2.1e-09
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   C++Cg C ++Cp+++ v ++    +        aCi+C++Cv++Cp +a
  gi|91773004|ref|YP_565696.1| 136 CNSCGICDRVCPMWIDVSKKDVVRDT-------ACISCMKCVQKCPVDA 177
                                   **************998887776666.......5************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 ?   -1.3   0.0       2.3   2.5e+03      15      21 ..      16      22 ..      14      46 .. 0.69
   2 !   27.0  14.2   3.4e-09   3.5e-06       2      56 .]     129     174 ..     128     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.3
                       Fer4_10 15 CvkaCPa 21
                                  C  +CP 
  gi|91773004|ref|YP_565696.1| 16 CGWVCPR 22
                                  7778887 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 3.4e-09
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +++dd+ C  Cg C ++CP+          ++ ++++ +   +C+ c +Cv++CP
  gi|91773004|ref|YP_565696.1| 129 IKRDDSLCNSCGICDRVCPM---------WIDVSKKDVVRDTACISCMKCVQKCP 174
                                   7899****************.........*************************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.1   1.1e+03      14      23 ..      16      25 ..      12      42 .. 0.65
   2 !   18.3   3.1   1.8e-06    0.0019      13      53 ..     107     148 ..     103     154 .. 0.86
   3 !   15.6   3.8   1.2e-05     0.013      34      57 ..     156     178 ..     148     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                       Fer4_21 14 CliaCedtsh 23
                                  C  +C+ +  
  gi|91773004|ref|YP_565696.1| 16 CGWVCPRGMF 25
                                  4444554444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.8e-06
                       Fer4_21  13 kCliaCedtshqai.eidaktvlkvvedeCvGCnlCssvCPv 53 
                                    C   C++++   + ++ + +++k  ++ C  C +C  vCP+
  gi|91773004|ref|YP_565696.1| 107 ACKYFCKEGAAASLtNLVKIRKIKRDDSLCNSCGICDRVCPM 148
                                   699*****9999884567778899999**************7 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.2e-05
                       Fer4_21  34 lkvvedeCvGCnlCssvCPvedci 57 
                                     v++  C+ C  C++ CPv d++
  gi|91773004|ref|YP_565696.1| 156 DVVRDTACISCMKCVQKCPV-DAL 178
                                   34678899999999999999.655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0         1   1.1e+03       7      15 ..      15      23 ..      14      39 .. 0.78
   2 !   15.3   2.3   2.2e-05     0.023       7      49 ..     107     147 ..     105     150 .. 0.75
   3 !   17.9   1.4   3.4e-06    0.0035      37      52 .]     162     177 ..     151     181 .] 0.67

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1
                        Fer4_7  7 aCvaaCpvk 15
                                  +C  +Cp +
  gi|91773004|ref|YP_565696.1| 15 YCGWVCPRG 23
                                  566677755 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.2e-05
                        Fer4_7   7 aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                   aC   C+ +a          +++k++ d + C +Cg C +vCP
  gi|91773004|ref|YP_565696.1| 107 ACKYFCKEGAAASLTN--LVKIRKIKRDDSLCNSCGICDRVCP 147
                                   6777887665554332..345789999***************9 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 3.4e-06
                        Fer4_7  37 kClgCgaCvavCPtga 52 
                                    C++C +Cv+ CP++a
  gi|91773004|ref|YP_565696.1| 162 ACISCMKCVQKCPVDA 177
                                   5666666666666654 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.5   1.6e+03      17      23 ..      18      24 ..      15      27 .. 0.78
   2 ?   -0.8   0.1       1.8   1.9e+03       4       9 ..     103     108 ..     101     116 .. 0.70
   3 !   15.9   3.0   9.6e-06      0.01       2      21 ..     129     148 ..     128     151 .. 0.91
   4 !   17.3   3.5   3.5e-06    0.0037       6      24 .]     160     178 ..     157     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                        Fer4_6 17 rvCPega 23
                                   vCP g+
  gi|91773004|ref|YP_565696.1| 18 WVCPRGM 24
                                  69**776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                        Fer4_6   4 idpdkC 9  
                                   +d+ +C
  gi|91773004|ref|YP_565696.1| 103 VDRAAC 108
                                   677777 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 9.6e-06
                        Fer4_6   2 veidpdkCigCgdCvrvCPe 21 
                                   +  d+++C++Cg C rvCP+
  gi|91773004|ref|YP_565696.1| 129 IKRDDSLCNSCGICDRVCPM 148
                                   778****************5 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 3.5e-06
                        Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                   + +Ci+C++Cv  CP +a+
  gi|91773004|ref|YP_565696.1| 160 DTACISCMKCVQKCPVDAL 178
                                   679************9996 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.31   3.2e+02       5      19 ..      15      29 ..      13      44 .. 0.84
   2 !   21.0   9.7   2.7e-07   0.00028      54      95 ..     129     173 ..     102     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.31
                       Fer4_18  5 vcvyvcPyarvqsvl 19
                                  +c  vcP + +q ++
  gi|91773004|ref|YP_565696.1| 15 YCGWVCPRGMFQNII 29
                                  699999999999886 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.7e-07
                       Fer4_18  54 kekgagdcidcescvkvcPtgidirkG...lqleciscllcidac 95 
                                    +++++ c +c+ c +vcP+ id+ k        cisc++c+  c
  gi|91773004|ref|YP_565696.1| 129 IKRDDSLCNSCGICDRVCPMWIDVSKKdvvRDTACISCMKCVQKC 173
                                   3456677*****************8752224678*********99 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.7   7.4e+02       7      17 ..      15      25 ..      13      54 .. 0.62
   2 !   13.4   4.5     8e-05     0.085      40      61 .]     130     151 ..     105     151 .. 0.77
   3 !   12.5   2.0   0.00015      0.16      45      58 ..     162     175 ..     154     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.7
                       Fer4_17  7 yClpeCpsyea 17
                                  yC  +Cp+++ 
  gi|91773004|ref|YP_565696.1| 15 YCGWVCPRGMF 25
                                  67777887665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8e-05
                       Fer4_17  40 eekaslCieCgeCerkCPqgld 61 
                                   ++  slC++Cg C+r+CP+ +d
  gi|91773004|ref|YP_565696.1| 130 KRDDSLCNSCGICDRVCPMWID 151
                                   455689************9776 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00015
                       Fer4_17  45 lCieCgeCerkCPq 58 
                                    Ci+C +C++kCP 
  gi|91773004|ref|YP_565696.1| 162 ACISCMKCVQKCPV 175
                                   69**********96 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3       1.2   1.2e+03      16      21 ..      16      21 ..      15      22 .. 0.83
   2 ?   -0.9   0.1       2.1   2.2e+03       4      10 ..     102     108 ..     100     113 .. 0.74
   3 !   17.0   2.0   4.2e-06    0.0044       3      21 ..     129     147 ..     127     148 .. 0.86
   4 !   14.0   3.0   3.8e-05      0.04       6      21 ..     160     174 ..     155     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                        Fer4_2 16 CvsaCP 21
                                  C ++CP
  gi|91773004|ref|YP_565696.1| 16 CGWVCP 21
                                  7799*9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                        Fer4_2   4 vvdtdrC 10 
                                   +vd+++C
  gi|91773004|ref|YP_565696.1| 102 FVDRAAC 108
                                   7888888 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 4.2e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   ++ d   C++Cg+C  +CP
  gi|91773004|ref|YP_565696.1| 129 IKRDDSLCNSCGICDRVCP 147
                                   6678889************ PP

  == domain 4  score: 14.0 bits;  conditional E-value: 3.8e-05
                        Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                   dt+ Ci+C +Cv+ CP
  gi|91773004|ref|YP_565696.1| 160 DTA-CISCMKCVQKCP 174
                                   555.************ PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.4   2.5e+03       8      16 ..      16      24 ..      14      34 .. 0.74
   2 !    9.3   4.5     0.002       2.1      48      66 ..     131     148 ..     104     149 .. 0.73
   3 !   16.0   3.3   1.7e-05     0.018       2      19 ..     163     180 ..     162     181 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.4
                       Fer4_16  8 CaevCPtna 16
                                  C  vCP + 
  gi|91773004|ref|YP_565696.1| 16 CGWVCPRGM 24
                                  666777765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.002
                       Fer4_16  48 ckkqeaitgCdiCqdvCPa 66 
                                   ++    +  C+iC +vCP+
  gi|91773004|ref|YP_565696.1| 131 RD-DSLCNSCGICDRVCPM 148
                                   33.5668899999999996 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.7e-05
                       Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                   C++C kC++ CP++a++ 
  gi|91773004|ref|YP_565696.1| 163 CISCMKCVQKCPVDALRV 180
                                   ***************975 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.7      0.32   3.3e+02       7      14 ..      16      23 ..      12      23 .. 0.88
   2 ?   -0.3   0.2       2.6   2.8e+03       6      15 .]     107     116 ..     105     116 .. 0.83
   3 ?    5.6   4.0     0.035        37       1      12 [.     136     147 ..     136     149 .. 0.96
   4 ?   14.3   5.0   5.7e-05     0.061       1      15 []     163     177 ..     163     177 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.32
                        Fer4_3  7 CvevCPvg 14
                                  C  vCP g
  gi|91773004|ref|YP_565696.1| 16 CGWVCPRG 23
                                  899***87 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.6
                        Fer4_3   6 aCvevCPvgA 15 
                                   aC   C +gA
  gi|91773004|ref|YP_565696.1| 107 ACKYFCKEGA 116
                                   6888999887 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.035
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+ Cg C +vCP
  gi|91773004|ref|YP_565696.1| 136 CNSCGICDRVCP 147
                                   99*********9 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 5.7e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C+ Cv+ CPv+A
  gi|91773004|ref|YP_565696.1| 163 CISCMKCVQKCPVDA 177
                                   *************98 PP

>> Bestrophin  Bestrophin, RFP-TM, chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.9   0.00012      0.12      29      72 ..      58     106 ..      41     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                    Bestrophin  29 lllflllyalvvllyr..l.eerlfellsice....lipLsfvLgFrvnav 72 
                                     + ll+ ++  ++y+  l +++++e+++i +    ++++s++L+F+v  +
  gi|91773004|ref|YP_565696.1|  58 YGV-LLFLLTALVMYEfqLiDDTIMESVVI-DglllIMVVSILLSFFVDRA 106
                                   333.33333333444447778899******.44678999********9865 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       6.9   7.3e+03      57      64 ..      16      23 ..      15      24 .. 0.78
   2 ?   12.3   1.8   0.00016      0.17      50      63 ..     135     148 ..     113     151 .. 0.76
   3 ?   12.7   1.7   0.00012      0.13       5      19 ..     136     150 ..     132     162 .. 0.69
   4 ?   11.5   4.4    0.0003      0.32      50      64 ..     162     176 ..     151     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.9
                        Fer4_8 57 CtevCpvg 64
                                  C  vCp g
  gi|91773004|ref|YP_565696.1| 16 CGWVCPRG 23
                                  78899976 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                        Fer4_8  50 sCttcgaCtevCpv 63 
                                    C++cg C++vCp+
  gi|91773004|ref|YP_565696.1| 135 LCNSCGICDRVCPM 148
                                   67777777777775 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00012
                        Fer4_8   5 CieCgaCqsaCpvlr 19 
                                   C+ Cg C   Cp++ 
  gi|91773004|ref|YP_565696.1| 136 CNSCGICDRVCPMWI 150
                                   777777777777655 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.0003
                        Fer4_8  50 sCttcgaCtevCpvg 64 
                                   +C +c++C+++Cpv+
  gi|91773004|ref|YP_565696.1| 162 ACISCMKCVQKCPVD 176
                                   688899999999875 PP

>> YebO  YebO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00037      0.39       4      23 ..      90     109 ..      88     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                          YebO   4 vivvlvgllvwFFvnRasvr 23 
                                   +++++v +l++FFv Ra+ +
  gi|91773004|ref|YP_565696.1|  90 LLIMVVSILLSFFVDRAACK 109
                                   678899***********976 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       9.3   9.8e+03      13      16 ..      19      22 ..      16      23 .. 0.65
   2 ?    2.4   0.2      0.27   2.8e+02       9      15 ..     107     113 ..     105     118 .. 0.85
   3 ?    9.3   1.5    0.0017       1.8       4      16 ..     136     148 ..     130     152 .. 0.91
   4 ?   11.6   4.0    0.0003      0.32       3      16 ..     162     175 ..     159     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.3
                        Fer4_4 13 aCPq 16
                                  +CP 
  gi|91773004|ref|YP_565696.1| 19 VCPR 22
                                  6885 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                        Fer4_4   9 sCvaaCP 15 
                                   +C ++C+
  gi|91773004|ref|YP_565696.1| 107 ACKYFCK 113
                                   6*****8 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0017
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C+ Cg C ++CP+
  gi|91773004|ref|YP_565696.1| 136 CNSCGICDRVCPM 148
                                   ************7 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.0003
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                    Ci C++Cv  CP+
  gi|91773004|ref|YP_565696.1| 162 ACISCMKCVQKCPV 175
                                   5************7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.7    0.0044       4.6      76      94 ..     130     148 ..     113     150 .. 0.74
   2 ?    6.8   2.8     0.012        13      78      94 ..     159     175 ..     151     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                       Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                   k + s C  Cg C+++cp+
  gi|91773004|ref|YP_565696.1| 130 KRDDSLCNSCGICDRVCPM 148
                                   4577888888888888886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                     ++C+ C +C+++cpv
  gi|91773004|ref|YP_565696.1| 159 RDTACISCMKCVQKCPV 175
                                   66789999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1175.29
//
Query:       gi|91773005|ref|YP_565697.1|  [L=191]
Description: PBP family phospholipid-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-30  103.7   0.0    1.1e-29  103.4   0.0    1.1  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.0   6.4e-34   1.1e-29       2     132 .]      62     188 ..      61     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 6.4e-34
                                   --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSE.E-TTC...EE-B-TTSSCCCCS CS
                           PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvts.lpega...vqgknslgeesesg 76 
                                   +p++y  +g+n++P+l   ++pe+t s++l+v DpDap  ++ f+Hw+v+ni   + s ++e++   +qg n ++    + 
  gi|91773005|ref|YP_565697.1|  62 IPSRYtcDGDNINPELVPGSLPEDTVSLVLIVDDPDAP-IGT-FTHWIVWNIA--PGSiIEENTvpgIQGLNGAKG---TD 135
                                   89999999******************************.777.*********8..555255555999999999999...** PP

                                   ---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                           PBP  77 YlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                   YlgpcPp g+  HrY+f  yald+  ld+ +g tr  l++a+++h++a+ +l+g+Y
  gi|91773005|ref|YP_565697.1| 136 YLGPCPPSGT--HRYFFRFYALDTM-LDIGSGSTRTTLEEAMQEHIIAEGELMGTY 188
                                   **********..************9.58999999*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1373.74
//
Query:       gi|91773006|ref|YP_565698.1|  [L=119]
Description: cupin family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   58.8   0.0    4.7e-16   58.3   0.0    1.3  1  Cupin_2          Cupin domain
    3.2e-07   30.3   0.0    4.3e-07   29.9   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
    3.5e-05   23.8   0.0    4.2e-05   23.5   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    3.8e-05   23.3   0.0    4.6e-05   23.1   0.0    1.2  1  Cupin_1          Cupin
     0.0041   16.8   0.0     0.0051   16.5   0.0    1.2  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.099   12.4   0.0       0.11   12.2   0.0    1.2  1  Cupin_6          Cupin


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.6e-19   4.7e-16       4      69 ..      39     104 ..      36     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.6e-19
                                   EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                       Cupin_2   4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69 
                                    +p G s+ +hrHp ++e++++  G g++t+d+ ++e++aGd+v++++g+ H+++Ntg+e++++l+
  gi|91773006|ref|YP_565698.1|  39 IVPMGSSTLAHRHPVAEEIYHITTGSGRMTLDSDVFEVNAGDTVLINSGVSHKIENTGSEDLKILC 104
                                   466777999*******************************************************98 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.4e-10   4.3e-07      18      70 ..      48     101 ..      37     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.4e-10
                                   EETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEE CS
                  AraC_binding  18 phvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgwe 70 
                                    h+h+   +i  +t G+gr +l+   +++++Gd +L++ g+ H +e  ++++++
  gi|91773006|ref|YP_565698.1|  48 AHRHPvAEEIYHITTGSGRMTLDSDVFEVNAGDTVLINSGVSHKIENTGSEDLK 101
                                   699**999**************************************99988776 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.4e-08   4.2e-05      70     144 ..      40     114 ..      28     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.4e-08
               MannoseP_isomer  70 vkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylged 144
                                   v  g+    ++h    e + + +G  ++t d++v+++++ +++ i  g+ h++en G  +l+++   s +y   d
  gi|91773006|ref|YP_565698.1|  40 VPMGSSTLAHRHPVAEEIYHITTGSGRMTLDSDVFEVNAGDTVLINSGVSHKIENTGSEDLKILCCCSPAYSHKD 114
                                   5455555566777778889999*****************************************998888887665 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.5e-08   4.6e-05      34     115 ..      34     108 ..       6     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                                   EEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEEE CS
                       Cupin_1  34 saarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivvfd 114
                                   s+a   +  g+  l h hp a+ei  ++ G+gr +++ ++        ++++Gd++ + +g+ h + n+g e++ ++ + +
  gi|91773006|ref|YP_565698.1|  34 SVAEAIVPMGSSTLAHRHPVAEEIYHITTGSGR-MTLDSD------VFEVNAGDTVLINSGVSHKIENTGSEDLKILCCCS 107
                                   5666666889999********************.666666......578*********************66666665554 PP

                                   S CS
                       Cupin_1 115 t 115
                                    
  gi|91773006|ref|YP_565698.1| 108 P 108
                                   4 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.7e-06    0.0051      21      63 ..      50      91 ..      30     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-06
                                  ECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEEC CS
                       Cupin_3 21 ltyeedEfcyileGevkvtpeggetvelraGDlvvlpkglsgt 63
                                   +  ++E+ +i  G  + t  ++  +e+ aGD v +  g s +
  gi|91773006|ref|YP_565698.1| 50 RHPVAEEIYHITTGSGRMTL-DSDVFEVNAGDTVLINSGVSHK 91
                                  455669**************.**************99998655 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.8e-05      0.11      36      82 ..      57     100 ..      34     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                       Cupin_6  36 lhvvlrGscwlidpasgepvrLsagdvvllpggephvladspgtapl 82 
                                   ++ +++Gs ++++++     +++agd vl+++g +h + +++g+++l
  gi|91773006|ref|YP_565698.1|  57 IYHITTGSGRMTLDS--DVFEVNAGDTVLINSGVSHKI-ENTGSEDL 100
                                   566889999999777..579*****************9.66665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 926.94
//
Query:       gi|91773007|ref|YP_565699.1|  [L=261]
Description: cobyrinic acid a,c-diamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-18   67.2   0.1    1.8e-18   66.8   0.1    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    9.1e-11   42.0   0.0    3.7e-10   40.0   0.0    1.9  2  AAA_31       AAA domain
    4.4e-09   36.1   0.2    1.3e-05   24.7   0.1    2.9  2  ParA         NUBPL iron-transfer P-loop NTPase
    2.9e-08   33.3   0.3    7.1e-08   32.0   0.1    1.6  2  ArsA_ATPase  Anion-transporting ATPase
    3.8e-05   23.3   0.0      0.001   18.6   0.3    2.0  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    0.00021   20.8   0.1     0.0016   17.9   0.1    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00091   19.2   0.1     0.0016   18.4   0.1    1.3  1  NTPase_1     NTPase
     0.0026   17.6   1.0       0.02   14.7   0.0    2.1  2  AAA_26       AAA domain
     0.0042   16.8   0.1     0.0098   15.6   0.1    1.7  2  AAA_24       AAA domain
     0.0058   17.2   0.0     0.0088   16.6   0.0    1.3  1  AAA_18       AAA domain
  ------ inclusion threshold ------
      0.012   14.6   0.3      0.019   13.9   0.3    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.014   15.5   0.5      0.028   14.5   0.1    1.7  2  DUF87        Helicase HerA, central domain
      0.017   15.5   0.0       0.03   14.7   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.019   14.9   0.2      0.058   13.3   0.1    1.7  2  NACHT        NACHT domain
      0.019   14.6   0.4      0.031   13.9   0.4    1.3  1  SRP54        SRP54-type protein, GTPase domain
      0.021   14.6   0.2      0.055   13.2   0.1    1.7  2  AAA_30       AAA domain
      0.037   13.9   0.1      0.057   13.3   0.1    1.3  1  APS_kinase   Adenylylsulphate kinase
       0.04   13.7   0.1       0.47   10.2   0.1    2.1  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.046   13.5   0.0       0.07   12.9   0.0    1.2  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.053   13.4   0.1       0.45   10.4   0.0    2.1  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.054   12.7   0.3       0.09   11.9   0.3    1.3  1  NB-ARC       NB-ARC domain
       0.12   11.7   0.4       0.23   10.7   0.4    1.4  1  MipZ         ATPase MipZ
       0.16   11.7   0.1       0.31   10.8   0.1    1.4  1  IstB_IS21    IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.1   2.3e-21   1.8e-18       3     127 ..       5     227 ..       3     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 2.3e-21
                                   EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                          CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                   ++ +kGGvGKTtl+ ++ar+lar+g++Vl++DaD ++n++++  g  +   p                             
  gi|91773007|ref|YP_565699.1|   5 AVTGKGGVGKTTLSGTIARLLARDGYDVLAIDADSDMNLASS-LGIAEPPLPltnykemiderageaggmfkynpkvddit 84 
                                   6889***********************************994.3333333336888888888******************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|91773007|ref|YP_565699.1|  85 dkygvtgpdgvkmlvmgtverggsgcmcpassflrallrhvvlkdssalimdmeagiehlgrgttrgidlmiivvepgmrs 165
                                   *************************************************************************99998888 PP

                                   ..CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS.- CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                          CbiA  55 ..dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge.p 127
                                     +++r++ l++ +g++       +  v+n+  +      +k  l+el    g+ vlg+ip++ +++ a+ +g+ p
  gi|91773007|ref|YP_565699.1| 166 ieTASRIKDLASGIGIE------HLAAVVNKGTS----SDIKPKLAEL----GITVLGEIPFSAELMNADFEGKaP 227
                                   88888888888888866......68999999554....5788888887....******************999866 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   4.7e-13   3.7e-10       8      53 ..       7      52 ..       1      83 [. 0.85
   2 ?   -0.6   0.0       1.4   1.1e+03     141     160 ..     153     172 ..     118     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 4.7e-13
                        AAA_31  8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekn 53
                                    KGGvGKTT s  +a  la+ g+ vL +D+D+  n++++lgi + 
  gi|91773007|ref|YP_565699.1|  7 TGKGGVGKTTLSGTIARLLARDGYDVLAIDADSDMNLASSLGIAEP 52
                                  56***************************************99765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                        AAA_31 141 dsviipvqaeayaleGleql 160
                                   d +ii+v++  +++e+++++
  gi|91773007|ref|YP_565699.1| 153 DLMIIVVEPGMRSIETASRI 172
                                   88999999999999998765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   1.7e-08   1.3e-05       9      41 ..       6      38 ..       1      59 [. 0.91
   2 !    7.4   0.0    0.0035       2.7      97     212 ..     115     229 ..     108     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                          ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                  + gKGGVGK+t++ ++A  La+ g++v  +DaD
  gi|91773007|ref|YP_565699.1|  6 VTGKGGVGKTTLSGTIARLLARDGYDVLAIDAD 38
                                  57******************************9 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0035
                          ParA  97 skaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgf 177
                                   s++++ ll++v  ++   Li+D+  G   e+l    +  ++ ++iV  p   +++ +++  ++++ + ++ l+ v N  + 
  gi|91773007|ref|YP_565699.1| 115 SSFLRALLRHVVLKDSSALIMDMEAGI--EHLGRGTTRGIDLMIIVVEPGMRSIETASRIKDLASGIGIEHLAAVVNKGTS 193
                                   578899999999999999999997655..8898888888999999999999999999999999999999988888775333 PP

                          ParA 178 vcpk.cgekteifgkgggeklaeelgvpllgeipld 212
                                      k    +  i   g+    ae +++++ g+ pld
  gi|91773007|ref|YP_565699.1| 194 SDIKpKLAELGITVLGEIPFSAELMNADFEGKAPLD 229
                                   222201233344444555555555555555555555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   9.1e-11   7.1e-08       4      48 ..       4      48 ..       1      57 [. 0.92
   2 ?   -2.1   0.0       2.2   1.7e+03     210     244 ..     156     190 ..     151     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 9.1e-11
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHT CS
                   ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfd 48
                                  i v+GKGGVGKtt+s ++a  l++ g++vl i  D   +l+ s+ 
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGYDVLAIDADSDMNLASSLG 48
                                  889********************************9999998775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                   EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                   ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                   ++Vv p   s++   R     + +gi+  a +vNk
  gi|91773007|ref|YP_565699.1| 156 IIVVEPGMRSIETASRIKDLASGIGIEHLAAVVNK 190
                                   68999999999888887776677999999999998 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   1.3e-06     0.001       1      44 [.       1      43 [.       1      51 [. 0.88
   2 ?    2.4   0.0      0.12        94      97     149 ..     110     163 ..      84     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                      CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlL 44
                                  m  +a++G +GGvG+t+l++++a+ l + g+ vl+iD+ +d  L
  gi|91773007|ref|YP_565699.1|  1 MVKIAVTG-KGGVGKTTLSGTIARLLARDGYDVLAIDADSDMNL 43
                                  66788888.8***************************9988666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                      CBP_BcsQ  97 qlaekaeallaalkelk.eqyrwillDlpagasaltrellaladlvllvvepda 149
                                   +++++++ l a l+++  ++ + +++D+ ag ++l r +++  dl++ vvep +
  gi|91773007|ref|YP_565699.1| 110 CMCPASSFLRALLRHVVlKDSSALIMDMEAGIEHLGRGTTRGIDLMIIVVEPGM 163
                                   45666677777777766677888999***************9*******99976 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   0.1   2.1e-06    0.0016       2      38 ..       3      39 ..       2      52 .. 0.91
   2 ?    0.4   0.0      0.44   3.5e+02     146     222 ..     157     225 ..     139     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                     Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDP 38
                                  kia+ GkGG+Gk+t s  ++  la++g  vl +  D 
  gi|91773007|ref|YP_565699.1|  3 KIAVTGKGGVGKTTLSGTIARLLARDGYDVLAIDADS 39
                                  89*****************************998885 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.44
                     Fer4_NifH 146 ivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkk 222
                                   iv++ ++ ++ +a +i    +  a   g++    ++n +   + ++ i+   +elg+ vl  +P + ++ +a+++ k
  gi|91773007|ref|YP_565699.1| 157 IVVEPGMRSIETASRI----KDLASGIGIEHLAAVVN-K--GTSSD-IKPKLAELGITVLGEIPFSAELMNADFEGK 225
                                   5555555555555444....33444444443344455.3..22334.444445799999999999999988887765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1     2e-06    0.0016       1      30 [.       3      32 ..       3      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                                  EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                                  k+++TG+ GvGKtTl   +++ll+++g+ v
  gi|91773007|ref|YP_565699.1|  3 KIAVTGKGGVGKTTLSGTIARLLARDGYDV 32
                                  689************************987 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.29   2.2e+02      11      31 ..      11      31 ..       3      33 .. 0.82
   2 !   14.7   0.0   2.6e-05      0.02     131     197 ..     155     220 ..     152     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.29
                        AAA_26 11 gvGKTvvslgLvralkrkgvk 31
                                  gvGKT++s  ++r l r g+ 
  gi|91773007|ref|YP_565699.1| 11 GVGKTTLSGTIARLLARDGYD 31
                                  8************99887765 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.6e-05
                        AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetlekksgipvlGvvPylpdleap 197
                                   +i+V+ +g ++i+ +    +++   +++ l+ ++Nk     +++   +  gi+vlG++P +++l+++
  gi|91773007|ref|YP_565699.1| 155 MIIVVEPGMRSIETASRIKDLASGIGIEHLAAVVNKG-TSSDIKPKLAELGITVLGEIPFSAELMNA 220
                                   699*********************************5.556699999999**************985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.3e-05    0.0098       3      48 ..       2      55 ..       1     111 [. 0.72
   2 ?   -2.1   0.0       3.3   2.6e+03      24      39 ..     130     145 ..     117     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                        AAA_24  3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.s 48
                                  +ki+++G+ g+GKTtl  ++       g+++l id +  ++      + +++  
  gi|91773007|ref|YP_565699.1|  2 VKIAVTGKGGVGKTTLSGTIarllardGYDVLAIDADSDMNLASSLGIAEPPlP 55
                                  69***************9999999999999999999985554444444444453 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                        AAA_24  24 pkplfidtekGlksld 39 
                                    ++l++d+e+G  +l 
  gi|91773007|ref|YP_565699.1| 130 SSALIMDMEAGIEHLG 145
                                   688999***9998775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0088       1      36 [.       4      40 ..       4      95 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakeng 36
                                  I++tG+ GvGKttl+  ++++l+  g+ +  + ++++
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARdGYDVLAIDADSD 40
                                  89****************9998667333333333333 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   0.3   2.5e-05     0.019      31      78 ..       3      48 ..       1      50 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                  EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------- CS
                          MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilG 78
                                  ++ +tG  G+Gk tl   ++  l+r G+   vla+D  s ++  s lG
  gi|91773007|ref|YP_565699.1|  3 KIAVTGKGGVGKTTLSGTIARLLARDGYD--VLAIDADSDMNLASSLG 48
                                  689************************96..699**999887666665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.6e-05     0.028      26      63 ..       4      40 ..       2      63 .. 0.94
   2 ?   -1.9   0.1       3.9     3e+03      37      60 ..     115     137 ..     115     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                         DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDpHGE 63
                                  +A+ g+ G+GK+++ + + + l+ ++g+ +l +D++++
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLA-RDGYDVLAIDADSD 40
                                  79********************9.**********9876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                         DUF87  37 SntvavLleellekkgatililDp 60 
                                   S + + Ll+ ++  k+++ li D+
  gi|91773007|ref|YP_565699.1| 115 SSFLRALLRHVV-LKDSSALIMDM 137
                                   677888999999.99999999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.8e-05      0.03      27      63 ..       4      40 ..       3      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                        AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  + ++G  GvGK++l  +++r l +dg  +l+ ++d+ 
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGYDVLAIDADSD 40
                                  579****************999999655555555554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.4e-05     0.058       3      29 ..       4      30 ..       3      36 .. 0.90
   2 ?   -2.1   0.0       3.9   3.1e+03     104     134 ..     113     143 ..     109     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                                  EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                  ++++G+ G+GKTtL   +a+++a++ +
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGY 30
                                  689********************9875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                                   .....HHHHHCTTTTT--EEEEEEECCCHHH CS
                         NACHT 104 pvrtlLselirkkllpeasllltvrpralrd 134
                                   p+   L+ l+r  +l+ +s l+     + ++
  gi|91773007|ref|YP_565699.1| 113 PASSFLRALLRHVVLKDSSALIMDMEAGIEH 143
                                   6677899999999999888887655555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   3.9e-05     0.031       4      38 ..       4      38 ..       1      41 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.9e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  i++ G  G+GKTt  + +a+ll ++g++vl + aD
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGYDVLAIDAD 38
                                  7899*************************998888 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     7e-05     0.055      22      64 ..       5      45 ..       2      71 .. 0.82
   2 ?   -1.4   0.0       2.1   1.7e+03      90     112 ..     154     176 ..     113     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                        AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae 64
                                  ++tG  G GKtt+ ++++++++++g++v++    +    +La 
  gi|91773007|ref|YP_565699.1|  5 AVTGKGGVGKTTLSGTIARLLARDGYDVLA--IDADSDMNLAS 45
                                  689**********************99864..44444445555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                        AAA_30  90 tllivDEagmvdtkqlaallkaa 112
                                    ++iv E gm +++++ ++ + a
  gi|91773007|ref|YP_565699.1| 154 LMIIVVEPGMRSIETASRIKDLA 176
                                   47888899999998888877666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.3e-05     0.057       5      50 ..       4      48 ..       1      52 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-05
                                  EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
                    APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50
                                  + +tG  g GK+t++ ++++ L ++g+ v  +d d+  ++L + Lg
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGYDVLAIDADS-DMNLASSLG 48
                                  779******************************997.456666665 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 ?   10.2   0.1    0.0006      0.47       1      32 [.       8      39 ..       8      49 .. 0.91
   2 ?    1.0   0.0       0.4   3.1e+02       8      38 ..     115     145 ..     114     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0006
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                  G+  +GK+Tl+ +++  ++r g+ ++ +D+D 
  gi|91773007|ref|YP_565699.1|  8 GKGGVGKTTLSGTIARLLARDGYDVLAIDADS 39
                                  66789*************************95 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.4
                        CLP1_P   8 STlarlLlNyalrkgrkpvyvDlDvGqseis 38 
                                   S++ r Ll  ++ k  + +++D+  G  +++
  gi|91773007|ref|YP_565699.1| 115 SSFLRALLRHVVLKDSSALIMDMEAGIEHLG 145
                                   89*********************99977765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-05      0.07       2      43 ..       4      45 ..       3      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldr 43
                                  I+v+g+ G Gktt++ ++  +++r +     i+ ds+++l +
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGYDVLAIDADSDMNLAS 45
                                  9*************************9999999999988765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00058      0.45       2      34 ..       4      36 ..       3      43 .. 0.89
   2 ?    0.4   0.0      0.73   5.7e+02      93     104 ..     246     257 ..     216     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiK 34
                                  ++++gk g GKTtL   + + l++ g+ v +i 
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGYDVLAID 36
                                  6799************************98875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.73
                          MobB  93 lvlvEGfkkeal 104
                                   l ++EGfk+e++
  gi|91773007|ref|YP_565699.1| 246 LGMIEGFKDEET 257
                                   4479****9975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00012      0.09      23      43 ..       4      24 ..       1      35 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                  EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 23 valvGmgGvGKttlakqilnk 43
                                  +a+ G+gGvGKttl+  i + 
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARL 24
                                  899***********9999876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00029      0.23       8      39 ..       8      39 ..       2      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                  SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                          MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldl 39
                                   kGG Gk+t +  +a  L++ G  v aid d 
  gi|91773007|ref|YP_565699.1|  8 GKGGVGKTTLSGTIARLLARDGYDVLAIDADS 39
                                  69***************************996 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0004      0.31      50      81 ..       4      35 ..       2      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                     IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfv 81
                                  i+++G  GvGK+ l+ ++++  +r+g+ vl +
  gi|91773007|ref|YP_565699.1|  4 IAVTGKGGVGKTTLSGTIARLLARDGYDVLAI 35
                                  899************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1566.31
//
Query:       gi|91773008|ref|YP_565700.1|  [L=289]
Description: cation diffusion facilitator family transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-44  150.6  14.4    5.1e-44  150.4  14.4    1.1  1  Cation_efflux    Cation efflux family
    4.7e-21   74.7   2.6    1.1e-20   73.5   2.6    1.6  1  ZT_dimer         Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.49   10.8   2.5        1.1    9.6   0.1    2.3  2  DUF2663          Protein of unknown function (DUF2663)
        1.6    8.2   4.6        1.4    8.4   0.2    2.7  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
        7.8    6.7  11.0       0.11   12.8   0.7    2.7  3  ABC_trans_CmpB   Putative ABC-transporter type IV


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 !  150.4  14.4   1.4e-47   5.1e-44       2     198 ..      13     204 ..      12     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 1.4e-47
                 Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgla 82 
                                    + l++n+++a+v++++g ltn l++ +d++hsl+d +s++++++a+ ++ kppd+++p+G++++e+l++++ ++l+++++
  gi|91773008|ref|YP_565700.1|  13 AVILVLNFLVAFVKIVYGTLTNTLSMKSDGYHSLFDGISNIVGIIAIFVAAKPPDKTHPYGHQKFETLASIIIAILIIFVG 93 
                                   5789***************************************************************************** PP

                 Cation_efflux  83 vfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvillf 163
                                   + ++ ++i+++  ++   + + l ++v+++ +++n+++  + rr+g++l+s +l a+++h+++D++ sl vlv+++ i+ +
  gi|91773008|ref|YP_565700.1|  94 FEIFHNSIDRFT-SNISPNVTNLSFLVMIGTMAINMMVTEYERRKGEQLSSDILLADSIHTRSDIFVSLSVLVALVAIKAG 173
                                   ************.*******************************************************************7 PP

                 Cation_efflux 164 nlksgplaDpvaslligliilysalkllkeslseL 198
                                        p++Dp++sl+i+++i++++++++ +s++ L
  gi|91773008|ref|YP_565700.1| 174 ----YPIIDPLISLIIAAVIVKAGVSIILSSSKTL 204
                                   ....367************************9988 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 !   73.5   2.6     3e-24   1.1e-20       5      78 ..     211     284 ..     208     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 3e-24
                                   HHHHHHHHHTT-SS-EEEEEEEEE.-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                      ZT_dimer   5 eeeeireiiksvpgvkgvhdlrtr.ksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                   ee+ i +++ +++gv+++h++rtr  +G +i++dlhi v +d+++++aH+i+++v +++k++++gv++v++Hv+P
  gi|91773008|ref|YP_565700.1| 211 EEDMICSLVYEIEGVENCHNVRTRgCIG-EIHIDLHIMVRPDMPLYDAHAISHKVMEHLKSKIKGVSEVMVHVDP 284
                                   5788999*****************7777.********************************************** PP

>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.18   6.4e+02      21      59 ..       8      47 ..       1      70 [. 0.53
   2 ?    9.6   0.1   0.00031       1.1      23      83 ..      78     140 ..      68     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                       DUF2663 21 llsllallvlllfliyvlik.ssslssllsallessvlll 59
                                    ++la++++l fl+  +    ++l++ ls+ ++   +l+
  gi|91773008|ref|YP_565700.1|  8 IQQILAVILVLNFLVAFVKIvYGTLTNTLSMKSDGYHSLF 47
                                  3344455544444443332245666666666655555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00031
                       DUF2663  23 sllallvlllfliyvlik..ssslssllsallessvlllllllvallyvavkllkkKaeKaEk 83 
                                   ++la +++++++i+v +   ++s+ ++ s ++ + ++l +l+++ ++ + + + +  + K E+
  gi|91773008|ref|YP_565700.1|  78 ETLASIIIAILIIFVGFEifHNSIDRFTSNISPNVTNLSFLVMIGTMAINMMVTEYERRKGEQ 140
                                   444455555555565444779*************************99999999888888876 PP

>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.7      0.15   5.3e+02      20      33 ..      47      60 ..      45      62 .. 0.87
   2 ?    8.4   0.2   0.00039       1.4      18      43 ..     183     209 ..     180     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.15
                                  HHHHHHHHHHHHHH CS
               ATP1G1_PLM_MAT8 20 fAglLfivGiliil 33
                                  f+g+  ivGi+ i+
  gi|91773008|ref|YP_565700.1| 47 FDGISNIVGIIAIF 60
                                  899999*****985 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00039
                                   HHHHHHHHHHHHHHHHCC.HHHCCCS- CS
               ATP1G1_PLM_MAT8  18 LifAglLfivGiliilSk.kckCkfkq 43 
                                   Li+A++   +G+ iilS  k  C + q
  gi|91773008|ref|YP_565700.1| 183 LIIAAVIVKAGVSIILSSsKTLCDAAQ 209
                                   9***********999986145666655 PP

>> ABC_trans_CmpB  Putative ABC-transporter type IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       0.3   1.1e+03     105     114 ..      20      29 ..       3      63 .. 0.51
   2 ?   12.8   0.7   2.9e-05      0.11      95     147 ..      79     131 ..      68     132 .. 0.85
   3 ?   -0.8   0.3      0.45   1.6e+03     103     127 ..     163     187 ..     151     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.3
                ABC_trans_CmpB 105 lglllvklih 114
                                   + +++vk+++
  gi|91773008|ref|YP_565700.1|  20 FLVAFVKIVY 29 
                                   2222333333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.9e-05
                ABC_trans_CmpB  95 clefsllwgllglllvklihpllekllskipkkvlkilliillvlflvdlvvs 147
                                   +l ++++  l++++ ++++h+ +++++s+i+++v+++ ++++++ ++++++v+
  gi|91773008|ref|YP_565700.1|  79 TLASIIIAILIIFVGFEIFHNSIDRFTSNISPNVTNLSFLVMIGTMAINMMVT 131
                                   566667777777788889********************************987 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.45
                ABC_trans_CmpB 103 gllglllvklihpllekllskipkk 127
                                    l++l+ +k  +p+++ l+s+i   
  gi|91773008|ref|YP_565700.1| 163 VLVALVAIKAGYPIIDPLISLIIAA 187
                                   4667777788888887776664333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1828.43
//
Query:       gi|91773009|ref|YP_565701.1|  [L=366]
Description: chorismate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-144  478.3   1.1   9.5e-144  478.1   1.1    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.1   1.1  5.3e-148  9.5e-144       1     327 []      10     353 ..      10     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: 478.1 bits;  conditional E-value: 5.3e-148
                                   SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TTS CS
               Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkdq 81 
                                   +r+tt+GeShg+alg+vidgvpagl+ld+e +qkeLdrRrpgqs+++t+r+E+D+vei+sG+fegkt+Gtpi+++++Nkd+
  gi|91773009|ref|YP_565701.1|  10 FRITTWGESHGRALGVVIDGVPAGLPLDTEIVQKELDRRRPGQSAVSTPRSETDKVEIISGIFEGKTTGTPISMMVWNKDA 90 
                                   89******************************************************************************* PP

                                   -..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE......... CS
               Chorismate_synt  82 rskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei......... 153
                                   +s++y++ik+ pRpgHAD+ y++kYgird+rgggrsSaReT++rvaaGavak++L+ +gi+i+a+v+++g+i         
  gi|91773009|ref|YP_565701.1|  91 DSSSYDNIKDLPRPGHADYPYMEKYGIRDHRGGGRSSARETIGRVAAGAVAKEILSIFGIDIIAHVTELGGIrakempfdt 171
                                   **********************************************************************77777888887 PP

                                   ..CHH.HHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTSTTEEEEEETTG CS
               Chorismate_synt 154 ..eke.aenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsipAvkgveiGsG 231
                                     e + +++pvrc+d eaa+ m e++ +a++e++s+Ggvve+++ g+p+G+Gepvfdklda++aka+msi+AvkgveiG G
  gi|91773009|ref|YP_565701.1| 172 ikE-HlEKTPVRCADLEAAQLMLEKVGKAREEHESIGGVVEIIAIGLPPGIGEPVFDKLDADIAKAIMSIGAVKGVEIGIG 251
                                   743.43777************************************************************************ PP

                                   GGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E-EEEE--S-S-S-T CS
               Chorismate_synt 232 feaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletkeevelevkgrhDpcv 306
                                    eaa++kGs++nD+++      + +tnnaGGi+GG+s+G+pi++r+ vKp+psi+k q+tv+++++++ ++ +kgrhDp++
  gi|91773009|ref|YP_565701.1| 252 NEAAQMKGSQMNDPFIledgkiIAQTNNAGGILGGLSTGMPIICRASVKPTPSISKVQHTVNTKEMKNSDIIIKGRHDPTI 332
                                   ****************66665444********************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHH CS
               Chorismate_synt 307 vpravvvveamvalvladall 327
                                    pr+v+v+eam+alvl+d+++
  gi|91773009|ref|YP_565701.1| 333 PPRMVPVAEAMMALVLVDHMI 353
                                   ******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2131.11
//
Query:       gi|91773010|ref|YP_565702.1|  [L=385]
Description: LL-diaminopimelate aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-60  205.3   0.0    1.7e-60  205.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.016   13.7   0.1      0.025   13.1   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.1   0.0   1.9e-64   1.7e-60       2     362 ..      30     379 ..      29     380 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.1 bits;  conditional E-value: 1.9e-64
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   dvi+Lg+++++      t++++++ + e a   + +++y+ ++g  e++ea+a + ++  +l+l++ ++ +++ G++++ +
  gi|91773010|ref|YP_565702.1|  30 DVIDLGVGDPDMP----TPEHIVESMCE-AVRDPATHRYPSYTGMIEFREAVANWCKDTRGLELDAATETLTLIGSKEGVA 105
                                   89********999....***********.**************************************************** PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    ++ ++ +npgd+ l+pdp y+ yk + + +gge + +pl +e++f  d++a+ ++         k k+++++ p+NPt +
  gi|91773010|ref|YP_565702.1| 106 HIPLAF-VNPGDVALIPDPGYPVYKIGTQFAGGEPHVMPLLEENGFLPDFDAIPADKLA------KAKLMFLNYPNNPTSA 179
                                   ******.9*********************************************997666......89************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsql 243
                                    a+ +  ++++++ak + + ++ D aY+++v+++  a +  + v+ + +  + ++s+sK ++++G+R+++++gn++++   
  gi|91773010|ref|YP_565702.1| 180 TADVKFFKEVVEFAKNNDITVVHDNAYSEMVYDDYTAPS-FLSVDGAMDvGMELYSMSKTYNMTGWRLAFAVGNKDLIAGF 259
                                   *********************************776655.8888888888899**************************** PP

                                   HHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH.CHHHHH CS
                 Aminotran_1_2 244 rklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae.takels 321
                                    k+++++ s    ++q+a  +a+s +++    +++m + +qkrr+ l ++L+ +gl+  a+++++++++ ++   + + +s
  gi|91773010|ref|YP_565702.1| 260 GKVKSNIDSgaFDAVQRAGITAVSSSQQ---CVTDMNSIYQKRRDALLKGLRGIGLDAKAPKATFYMWVPTPDGyDSMGFS 337
                                   ***************************8...9************************************9988767999*** PP

                                   HHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                 Aminotran_1_2 322 kkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                   k Llee g++ tpg  f+   +g +R+ + + + e +ee+v +
  gi|91773010|ref|YP_565702.1| 338 KLLLEESGIVATPGVGFGEygEGYIRFAL-TQSVERIEEAVAR 379
                                   ******************9**********.*********9987 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.8e-06     0.025     135     177 ..     162     207 ..     150     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-06
                                   CTTEEEEEEESS-TTTT----H...HHHHHHHHHTT-EEEEEGTTT CS
               Cys_Met_Meta_PP 135 kentklvylEtptnpllkvvDi...ekiaklakkagvlvvvDntfa 177
                                     + kl++l  p np+  ++D+   ++++++ak+++++vv Dn+++
  gi|91773010|ref|YP_565702.1| 162 LAKAKLMFLNYPNNPTSATADVkffKEVVEFAKNNDITVVHDNAYS 207
                                   5689*****************733369****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2356.65
//
Query:       gi|91773011|ref|YP_565703.1|  [L=275]
Description: acetolactate decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-84  280.2   0.0      1e-83  280.0   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 !  280.0   0.0   5.8e-88     1e-83       1     217 [.      43     260 ..      43     262 .. 0.99

  Alignments for each domain:
  == domain 1  score: 280.0 bits;  conditional E-value: 5.8e-88
                 AAL_decarboxy   1 lyqvstlsaLmegvyegtltvsellkhGdfGlGTfeeldGEliildgkvYqlksdgsvrevddeektPFavvtkfepektv 81 
                                   lyqvst++aL+eg+y+g++t++el+++Gd+GlGTf++ldGE+i++dg+vYq+k+dg ++ +dd+ +tPFa+vt+fe+++++
  gi|91773011|ref|YP_565703.1|  43 LYQVSTIDALLEGLYDGEVTIKELKEKGDTGLGTFNTLDGEMIMIDGEVYQIKTDGLAYLADDTMRTPFAAVTTFEADEAI 123
                                   7******************************************************************************** PP

                 AAL_decarboxy  82 klkealskeeleealeellpskNlfyairidGtfksvkvRsvpkqekpyeplaevakk.qsefefenveGtlvGfrtPeyl 161
                                    ++++++ +e++ +le++lpskNl+yairidG+f+s+kvRsvp+qe+py+ l++v+++ q++fe+e+veG++vGf++P y+
  gi|91773011|ref|YP_565703.1| 124 VMQDTVNSSEVAFMLEQVLPSKNLMYAIRIDGNFSSMKVRSVPAQERPYPLLVDVVANeQAVFEHEDVEGSIVGFWLPYYV 204
                                   ******************************************************99877********************** PP

                 AAL_decarboxy 162 qginvaGlHlHFisddrkfGGHvldfeleeveveiakisklelelpedeeFeeadl 217
                                   +++nv+G+H+HFi+++r+ GGHvld++l +++v+i++++ +el lp d++F +adl
  gi|91773011|ref|YP_565703.1| 205 ESMNVPGYHFHFIDSERTEGGHVLDYTLIDGTVSIDRTTGFELLLPGDDDFLSADL 260
                                   *****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1835.91
//
Query:       gi|91773012|ref|YP_565704.1|  [L=310]
Description: solute binding protein [Methanococcoides burtonii DSM 6242]
Scores for 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  198.8   0.0    1.2e-58  198.5   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 !  198.5   0.0   6.7e-63   1.2e-58       1     242 [.      36     293 ..      36     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 6.7e-63
                                   EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTT...SGTHHHHHHHHTTCCCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF
                          ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglel...Etwldkllasssqatrvevi 78 
                                   V +++ p +++v+++aGd+ve  +++ppga+p +yep+p ++r+l++A  ++ +g +l   E wl+k+ + ++  +++ ++
  gi|91773012|ref|YP_565704.1|  36 VAVSILPQQEFVEKIAGDNVETILMIPPGASPATYEPSPGQLRELTKARAFFIVGSGLpfeEVWLGKI-EGIN--KDMLIV 113
                                   789****************************************************9984444889988.6776..455677 PP

                                   ETTTTC.....CSEBCSS...................ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHH CS
                                   xxxxxx.....xxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ZnuA  79 dlsegv.....eeeeeee...................DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekL 135
                                   d s+g+     e+ee+++                   DpHiW+sp na++mven++ +L+e+dp+n+d y +n ++y ++L
  gi|91773012|ref|YP_565704.1| 114 DCSKGIniigtETEENTHlknidenfqedgdhahegsDPHIWTSPINAKMMVENTYLGLIEIDPENKDIYLNNKENYLKEL 194
                                   7776554455433333334455555666666666788******************************************** PP

                                   HHHHHHHHHHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS.....HHHHHHHHHHHHHTT-SEEEEETTS-TH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ZnuA 136 eeldaeireelaeipeekrklvtthdafgylarayglevagiagiste.....aaqiaalieeikeagvkaifveplaspk 211
                                   ++ da ire+l e   e+r ++t+h+++gy+a +ygl++++i    +e     +++++++i+++ke+++++ifv+ ++s++
  gi|91773012|ref|YP_565704.1| 195 DDADAMIREKLMEG--EERSFMTYHPSWGYFAAEYGLDMITIE---NEgkepsPQDMQRVIDKAKEKNIRTIFVQAQFSKQ 270
                                   ************55..5667********************766...3333456**************************** PP

                                   HHHHHHHHHT-EEEEE-STSSSTSTTSTTSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ZnuA 212 laetlaeeagvkvatlysldslgdegsaetY 242
                                   +aet+a+++  kv+++++l +        +Y
  gi|91773012|ref|YP_565704.1| 271 SAETIASAIDGKVVVVDPLAK--------DY 293
                                   *********99*999999443........44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2170.83
//
Query:       gi|91773013|ref|YP_565705.1|  [L=249]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-32  110.4   0.0    1.3e-31  109.9   0.0    1.2  1  ABC_tran       ABC transporter
    2.6e-12   47.2   1.0    3.3e-05   23.9   0.0    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.8e-07   30.8   0.0    2.7e-07   30.2   0.0    1.2  1  SMC_N          RecF/RecN/SMC N terminal domain
     0.0011   18.7   0.0     0.0023   17.7   0.0    1.5  1  AAA_30         AAA domain
     0.0019   17.9   0.1     0.0043   16.7   0.1    1.6  1  AAA_29         P-loop containing region of AAA domain
     0.0065   16.2   0.3      0.047   13.4   0.1    2.0  2  AAA_15         AAA ATPase domain
  ------ inclusion threshold ------
      0.023   15.2   0.2       0.04   14.4   0.2    1.3  1  AAA_23         AAA domain
      0.027   14.7   0.5       0.14   12.4   0.5    2.0  1  AAA_22         AAA domain
      0.062   13.3   0.8       0.33   10.9   0.6    2.3  2  AAA_5          AAA domain (dynein-related subfamily)
      0.078   13.1   0.5       0.35   11.0   0.5    2.1  1  MMR_HSR1       50S ribosome-binding GTPase
      0.084   12.8   0.2       0.37   10.7   0.0    2.1  3  RsgA_GTPase    RsgA GTPase
      0.098   11.4   0.0       0.16   10.7   0.0    1.3  1  Adeno_IVa2     Adenovirus IVa2 protein
       0.11   12.9   0.0       0.18   12.2   0.0    1.4  1  AAA_16         AAA ATPase domain
       0.11   12.1   0.3       0.19   11.3   0.3    1.3  1  Phage_fiber_2  Phage tail fibre repeat
       0.12   12.0   0.0       0.21   11.2   0.0    1.3  1  AAA_27         AAA domain
       0.16   11.5   0.0       0.33   10.5   0.0    1.5  1  HTH_47         winged helix-turn-helix
        0.4   11.1   1.4        3.9    7.9   1.4    2.2  1  AAA            ATPase family associated with various cellular


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.0   1.3e-34   1.3e-31       1     136 [.      20     165 ..      20     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 1.3e-34
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren 79 
                                   l+ v+l+++eg  ++i+G+nG GKStLlk+++gl kp+ G++++ g+       e++r+ ig++pq   ++l+  ++vre 
  gi|91773013|ref|YP_565705.1|  20 LESVNLSIEEGDFLGIIGPNGGGKSTLLKVILGLIKPQRGTVEVLGTTP-----EKARHLIGYVPQYnpSSLDFPINVREV 95 
                                   6789**************************************7776655.....56***********98777777879999 PP

                                   .................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    e+ +  +kal+++++ e  d+ +     +LSgGq+qrv +aral+++pk+l+lDEp 
  gi|91773013|ref|YP_565705.1|  96 vlmgrmgkkglfqkyteEDHAATKKALKTVEMLEYSDRQI----GELSGGQRQRVFIARALVSEPKVLILDEPV 165
                                   *************988777777******************....*****************************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 !   21.8   0.6   1.3e-07   0.00014       2      24 ..      33      55 ..      32      96 .. 0.80
   2 !   23.9   0.0   3.1e-08   3.3e-05     225     299 ..     126     196 ..     102     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.3e-07
                        AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                   ++iGpNg GKS+LL+ + +l  
  gi|91773013|ref|YP_565705.1| 33 LGIIGPNGGGKSTLLKVILGLIK 55
                                  68****************99943 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.1e-08
                        AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                   e+  + ++++ elS G+++  +++ al + +   ++l++DEp +g++  ++ +++ellk+l++ ++ +++++H+ 
  gi|91773013|ref|YP_565705.1| 126 EMLEYSDRQIGELSGGQRQRVFIARALVSEP---KVLILDEPVTGIDTMMQMEFYELLKKLRS-RVTIVMVSHDI 196
                                   555555678999********88888888877...9**************************99.*********96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.6e-10   2.7e-07      25     202 ..      31     199 ..      17     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.6e-10
                                   SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                    f  i+GpNG GKs ll  i   LG  +    ++ +++ l + + eka+   ++v   ++ ++ +++i+  ev+++ r+ +
  gi|91773013|ref|YP_565705.1|  31 DFLGIIGPNGGGKSTLLKVI---LGLIKP---QRGTVEVLGT-TPEKARHLIGYVPQ-YNPSSLDFPINVREVVLMGRMGK 103
                                   5889***************9...995443...4455555555.59999999****99.6888889**************** PP

                                   TSE.EEEEETTEEE-HHHHH..HHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                   xxx.xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 106 kge.seykingkevtkkevs..ellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                   kg  ++y+ +++ +tkk ++  e+le ++ ++ +LSgG+++ v +a       v+   + +lDe    +D +   ++ ell
  gi|91773013|ref|YP_565705.1| 104 KGLfQKYTEEDHAATKKALKtvEMLEYSDRQIGELSGGQRQRVFIAR----ALVSEPKVLILDEPVTGIDTMMQMEFYELL 180
                                   **978899999999998876337899999**********98665543....34455557799******************* PP

                                   HHHCTTSEEEEE-SSHHHC CS
                                   xxxxxxxxxxxxxxxxxxx RF
                         SMC_N 184 keksknaQfivislreeml 202
                                   k+ ++++ ++++s++   +
  gi|91773013|ref|YP_565705.1| 181 KKLRSRVTIVMVSHDISAV 199
                                   ****999999999976655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.2e-06    0.0023      16      97 ..      29     164 ..      21     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.2e-06
                        AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa................................. 63 
                                   +gd +  + Gp G GK+t+lk++  +++ + g+v +l  t + A+ L                                  
  gi|91773013|ref|YP_565705.1|  29 EGD-FLGIIGPNGGGKSTLLKVILGLIKPQRGTVEVLGTTPEKARHLIgyvpqynpssldfpinvrevvlmgrmgkkglfq 108
                                   444.77899*********************99********99999987566666666666666666555555555555544 PP

                        AAA_30  64 .......eelgieastiakllkrlk...............grarlepgtllivDEa 97 
                                          +++  + +t++ l ++ +               +ra +++ ++li DE 
  gi|91773013|ref|YP_565705.1| 109 kyteedhAATKKALKTVEMLEYSDRqigelsggqrqrvfiARALVSEPKVLILDEP 164
                                   44332211222233333333333337777777777777775556666677777774 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.1e-06    0.0043      17      49 ..      25      57 ..      18      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  ++i++ ++  ++Gp+G GKSTll  i  l+ p+
  gi|91773013|ref|YP_565705.1| 25 LSIEEGDFLGIIGPNGGGKSTLLKVILGLIKPQ 57
                                  5666555888*************8887777776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   4.4e-05     0.047      19      49 ..      25      56 ..      15     132 .. 0.81
   2 ?    1.0   0.0      0.26   2.7e+02     323     355 ..     155     187 ..     137     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                        AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFlnn 49
                                  ++++e  +  +iG+N+ GKS++l+++  +++ 
  gi|91773013|ref|YP_565705.1| 25 LSIEEGdFLGIIGPNGGGKSTLLKVILGLIKP 56
                                  4444446899***************9877765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                        AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandn 355
                                   ++++l+++EP + + + +q+++++llk+l +  
  gi|91773013|ref|YP_565705.1| 155 EPKVLILDEPVTGIDTMMQMEFYELLKKLRSRV 187
                                   5789999********************997665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   3.8e-05      0.04      22      39 ..      33      50 ..      14      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                        AAA_23 22 tlItGpNGaGKTTildAi 39
                                    I+GpNG GK+T+l  i
  gi|91773013|ref|YP_565705.1| 33 LGIIGPNGGGKSTLLKVI 50
                                  57************9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   0.00013      0.14       6     116 ..      31     184 ..      27     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...........................erpevvfvtlpsstsskdllre 59 
                                    +l ++G+ G GK+tll+ +l   + +    +                            +  v +v l + ++ k l+++
  gi|91773013|ref|YP_565705.1|  31 DFLGIIGPNGGGKSTLLKVILGLIKPQRG--TvevlgttpekarhligyvpqynpssldFPINVREVVLMGRMGKKGLFQK 109
                                   67889*************99998754333..14478888877777777777754444433333337777777777777777 PP

                        AAA_22  60 llralglelka..........erlsseellealeqalrarav...............ielliiDEaqh.lr...seealee 111
                                     ++ +  +k+          +            +++ + +                +++li+DE    ++   ++e +e 
  gi|91773013|ref|YP_565705.1| 110 YTEEDHAATKKalktvemleyS-----------DRQIGELSGgqrqrvfiaralvsePKVLILDEPVTgIDtmmQMEFYEL 179
                                   7777776666655445554442...........222222222333344444444666668888884444443336777777 PP

                        AAA_22 112 Lrsll 116
                                   L++l 
  gi|91773013|ref|YP_565705.1| 180 LKKLR 184
                                   66554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00032      0.33       4      43 ..      35      76 ..      33     184 .. 0.93
   2 ?   -0.6   0.0       1.2   1.2e+03      20      38 ..     177     198 ..     169     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                  EE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH- CS
                         AAA_5  4 LvGppGtgKselaerlaaal..nreveyvqltrdtteedlkg 43
                                  ++Gp G gKs+l + ++ ++  +r +++v++t   ++++l+g
  gi|91773013|ref|YP_565705.1| 35 IIGPNGGGKSTLLKVILGLIkpQRGTVEVLGTTPEKARHLIG 76
                                  69*******************999999999998777777776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                                   GGGB...S--EEEEE--TT--H CS
                         AAA_5  20 aaal...nreveyvqltrdtte 38 
                                    ++l   +++v++v+ + d+++
  gi|91773013|ref|YP_565705.1| 177 YELLkklRSRVTIVMVSHDISA 198
                                   4444444999999999988876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   0.00033      0.35       3      39 ..      34      73 ..      32     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                                  EEEESTTSSHHHHHHHHHT..S.TEEESSSTTSSSSEEEE CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltg..e.kaivsdkpgtTrdineg 39
                                  +i+G    GKStL++ ++g  + +  + +  gtT +  ++
  gi|91773013|ref|YP_565705.1| 34 GIIGPNGGGKSTLLKVILGliKpQRGTVEVLGTTPEKARH 73
                                  89****************9542444555666777655544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00035      0.37      89     124 ..      19      55 ..       4      73 .. 0.75
   2 ?   -1.9   0.0       2.6   2.8e+03     100     129 ..      93     120 ..      82     126 .. 0.75
   3 ?   -2.1   0.0       3.1   3.2e+03      88     105 ..     174     191 ..     156     213 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                                   THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                    le+++  +++ ++  ++G+ G GKStL++++l+  +
  gi|91773013|ref|YP_565705.1|  19 VLESVNLSIEEgDFLGIIGPNGGGKSTLLKVILGLIK 55 
                                   55666666666688889*************9998554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                                   SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktge 129
                                   + +vl+G   +GK  L  + ++e++++t++
  gi|91773013|ref|YP_565705.1|  93 REVVLMGR--MGKKGLFQKYTEEDHAATKK 120
                                   56788887..78999999999888888875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.1
                                   TTHHHHHHHCTTSEEEEE CS
                   RsgA_GTPase  88 egleelkellkdktsvlv 105
                                    ++ el ++l++++++++
  gi|91773013|ref|YP_565705.1| 174 MEFYELLKKLRSRVTIVM 191
                                   334444444444444333 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.16      78     122 ..      20      63 ..       3      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                    Adeno_IVa2  78 lsslnyglq..PviGviyGPtGsGksqllrnlissklisPiPetvif 122
                                   l s+n+  +   ++G+i GP G Gks ll+ ++   li+P   tv  
  gi|91773013|ref|YP_565705.1|  20 LESVNLSIEegDFLGII-GPNGGGKSTLLKVILG--LIKPQRGTVEV 63 
                                   56666654422799987.************9985..89999988744 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.18      26     122 ..      32     149 ..      17     191 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                        AAA_16  26 lvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa.....ipy..salaqalareellrqlldeaesaeleawr 98 
                                    + ++G+ G GKs+l++ +l  ++ ++g + + g++ +  +        y  s  ++   + + +  ++++ ++ +++ + 
  gi|91773013|ref|YP_565705.1|  32 FLGIIGPNGGGKSTLLKVILGLIKPQRGTVeVLGTTPEKARHligyvPQYnpS-SLDFPINVREVVLMGRMGKKGLFQKYT 111
                                   56689****************99999887777776666633332222222221.111111222233333333333333333 PP

                        AAA_16  99 ekleeala..............avpelagaeasrllel 122
                                   e+ ++a++              +++el+g +++r++ +
  gi|91773013|ref|YP_565705.1| 112 EEDHAATKkalktvemleysdrQIGELSGGQRQRVFIA 149
                                   33333333444444556666666666666666655544 PP

>> Phage_fiber_2  Phage tail fibre repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00018      0.19      17      31 ..     111     125 ..     110     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                 Phage_fiber_2  17 tsetlAATpkAVKta 31 
                                   t e++AAT kA+Kt+
  gi|91773013|ref|YP_565705.1| 111 TEEDHAATKKALKTV 125
                                   679**********97 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.21      18      49 ..      22      53 ..      13      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                  s+++s ee d+  i+GpN  GKst+l+ i  l
  gi|91773013|ref|YP_565705.1| 22 SVNLSIEEGDFLGIIGPNGGGKSTLLKVILGL 53
                                  677888899999**************988765 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031      0.33      13      44 ..     100     132 ..      99     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                   -TTS-----------.-----HHHHHHHHHH-E CS
                        HTH_47  13 qLGrrGLYrtiggkn.takqaemallwvLnlaD 44 
                                   ++G++GL+++  +++  a++++ +++++L ++D
  gi|91773013|ref|YP_565705.1| 100 RMGKKGLFQKYTEEDhAATKKALKTVEMLEYSD 132
                                   69*******9999994577789999*******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 ?    7.9   1.4    0.0037       3.9       3      66 ..      35     163 ..      33     204 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0037
                                   EESSTTSSHHHHHHHHHHHHTHE.......................................EEEEETTTCSSS....... CS
                           AAA   3 lyGppGtGKTllakavakelgve.......................................fleisgsellsk....... 37 
                                   ++Gp G GK++l k +   ++ +                                       +          +       
  gi|91773013|ref|YP_565705.1|  35 IIGPNGGGKSTLLKVILGLIKPQrgtvevlgttpekarhligyvpqynpssldfpinvrevvL----------Mgrmgkkg 105
                                   68**************99986442333333333444444444444444444444444333330..........03444444 PP

                                   ............................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                           AAA  38 ............................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                                +ge +   r+ +  a++   +p++l++DE
  gi|91773013|ref|YP_565705.1| 106 lfqkyteedhaatkkalktvemleysdrQIGELSGGQRQRVFIARALVsEPKVLILDE 163
                                   4444555555555555555555555555666666665555555555555677777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 1835.56
//
Query:       gi|91773014|ref|YP_565706.1|  [L=275]
Description: ABC transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-81  272.6  32.8    3.8e-81  272.4  32.8    1.0  1  ABC-3     ABC 3 transport family
    3.7e-12   45.9  28.6    6.1e-12   45.2  28.5    1.4  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 !  272.4  32.8   4.2e-85   3.8e-81       1     257 [.       6     262 ..       6     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 272.4 bits;  conditional E-value: 4.2e-85
                         ABC-3   1 qyeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrktklk 81 
                                   qyef+++a+ a+il s+ac+++g++vv++r++l++++++Ha+++G+++ y+lg+n+++g++ ++l+ a++++  +++t ++
  gi|91773014|ref|YP_565706.1|   6 QYEFMINAITAGILASIACGMIGVYVVVKRIALISGGIAHASFGGIGISYFLGINPIMGVLPFSLLSALTIGTFSKRTDVA 86 
                                   79******************************************************************************* PP

                         ABC-3  82 edtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveg 162
                                   edt+igi++s+++a+g++++ l+++++ dl+ yLfGnilt+ q d+ ++++++a+++l++  ++ke++++++dee+++v g
  gi|91773014|ref|YP_565706.1|  87 EDTIIGILWSMGMAIGIIFIGLTPGYAPDLMTYLFGNILTVPQSDITMMLALDAIIILVVYALYKEFMALCYDEEFSTVVG 167
                                   ********************************************************************************* PP

                         ABC-3 163 lsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldlatGavi 243
                                   ++v+ l+llll+lial+vvv++++vG+iLviall+iPaa+ r++t+++++++ ++i +g+ ++++Gl+lSyy+d+a+Ga+i
  gi|91773014|ref|YP_565706.1| 168 IPVEKLYLLLLCLIALTVVVMIRVVGLILVIALLTIPAALSREFTNDMRKMMFLSIFFGAAFTIIGLMLSYYFDIASGATI 248
                                   ********************************************************************************* PP

                         ABC-3 244 vlvatllfllallv 257
                                   +lv+++++ll +++
  gi|91773014|ref|YP_565706.1| 249 ILVMSSFYLLNIII 262
                                   *********99875 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2  28.5   6.8e-16   6.1e-12      94     286 ..      41     240 ..      14     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6.8e-16
                         FecCD  94 l......lgslslfalplaaflgallalllvllla..rkrkgasplkliLaGiavsallsaltsllllllneealesilfw 166
                                   +      +g++++ + + +  ++++l ++l+ +l+  + +k+++ +   ++Gi  s+ ++  + ++ l  ++  + +++++
  gi|91773014|ref|YP_565706.1|  41 GgiahasFGGIGISYFLGINPIMGVLPFSLLSALTigTFSKRTDVAEDTIIGILWSMGMAIGIIFIGL--TPGYAPDLMTY 119
                                   155544445555555556666666665555444444477899999999*******9988666666654..699******** PP

                         FecCD 167 llGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGL 247
                                   l+G++ ++  s++ ++l+l ++++l++++l++++ +l +++e ++ +G++ve++ llll+l+al + v++ +vG i  ++L
  gi|91773014|ref|YP_565706.1| 120 LFGNILTVPQSDITMMLALDAIIILVVYALYKEFMALCYDEEFSTVVGIPVEKLYLLLLCLIALTVVVMIRVVGLILVIAL 200
                                   ********************************************************************************8 PP

                         FecCD 248 i.vPhiarllvgadhrkllplsallGallllladllarll 286
                                   + +P  +++ + +d+rk+++ls+++Ga++ ++  +l+ ++
  gi|91773014|ref|YP_565706.1| 201 LtIPAALSREFTNDMRKMMFLSIFFGAAFTIIGLMLSYYF 240
                                   647999999***********************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1836.92
//
Query:       gi|91773015|ref|YP_565707.1|  [L=479]
Description: sodium--dicarboxylate symporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-120  401.5  44.6   4.4e-120  401.3  44.6    1.0  1  SDF       Sodium:dicarboxylate symporter family


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.3  44.6  2.5e-124  4.4e-120       1     390 []      34     444 ..      34     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: 401.3 bits;  conditional E-value: 2.5e-124
                           SDF   1 LllqiliglvlGlviGll..........elvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklglkt 71 
                                   L+l+i+ig++lG+++Gl+          +++ +++++++++g +f+ ll+m++vPlvfasii+gias +d+++l+ +gl+t
  gi|91773015|ref|YP_565707.1|  34 LWLKIMIGMFLGIIVGLVlgpstglvdqTVSYTIGEWLALPGYIFLALLQMIVVPLVFASIIRGIASGEDMEQLKLIGLRT 114
                                   799**************9*********999*************************************************** PP

                           SDF  72 llyfllttliAaiiglilalllkpg...........selaleassakeaekketdslldlilslipsnifealaegnvlav 141
                                   ++yfl+tt+iA++igl+lal+++pg           ++++ ++ ++ ++++    +++ ++++++p+n++ +la g++l+v
  gi|91773015|ref|YP_565707.1| 115 VAYFLATTAIAILIGLTLALIINPGsyisselvqstMGSEITQVNEISTTTPGIADVPGMVTNILPTNPLGSLATGQMLQV 195
                                   *****************************999988767777777777888888889999********************** PP

                           SDF 142 ivfailfGialaalgekg.epllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakflltvylglaih 221
                                   +vf++++G+al++++  + +pll+++ sl+ev m vv++ m laP++vf+li + +++ g+ al+ ++++++tv+lgl++ 
  gi|91773015|ref|YP_565707.1| 196 VVFSVIIGLALVSISPAQsKPLLDLMGSLQEVSMTVVRWSMLLAPFAVFGLISKFTLNLGVAALMGMLVYVGTVLLGLLL- 275
                                   *************998666*************************************************************. PP

                           SDF 222 llivlpllllvltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtalyeava 302
                                   ll +++l++++++++ p++f++ i+++ll+AfsT+SSa ++P+++++ae++lgv+ si++fv+PlGatinm+Gtaly+++a
  gi|91773015|ref|YP_565707.1| 276 LLAFYLLVVFIVSRRGPIDFMRSIRDVLLLAFSTSSSAVVMPLSIKTAEDKLGVRPSISQFVIPLGATINMNGTALYQSIA 356
                                   78889999999********************************************************************** PP

                           SDF 303 aifiaqlfgvelslgqllllvlvatlasiGaagvPgaglvalllvlsalglpvegialilaidrllDmfrTavNvtGdava 383
                                   a+f+aq+fgvel++g llll+++ + asiG+++ Pg g+v+l+l+ls +g+p++giali+++dr+lDm+rT+vNvtGd+v 
  gi|91773015|ref|YP_565707.1| 357 AVFLAQVFGVELGFGALLLLMVTVVGASIGTPSTPGVGIVILALILSNVGIPTAGIALIIGVDRILDMCRTSVNVTGDLVT 437
                                   ********************************************************************************* PP

                           SDF 384 alivakl 390
                                   ++i++k+
  gi|91773015|ref|YP_565707.1| 438 CVIMDKW 444
                                   *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2714.54
//
Query:       gi|91773016|ref|YP_565708.1|  [L=723]
Description: Cache sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-23   82.3   3.4    4.7e-23   82.3   3.4    2.3  2  dCache_1         Cache domain
    2.5e-19   69.8   1.4    4.2e-19   69.1   0.5    1.9  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    1.4e-05   25.0   2.3    0.00018   21.5   0.0    3.5  4  HisKA            His Kinase A (phospho-acceptor) domain
    2.3e-05   24.7   1.9     0.0013   19.1   0.0    3.2  3  HAMP             HAMP domain
    0.00089   19.1   3.4     0.0011   18.9   0.7    2.4  2  HATPase_c_5      GHKL domain
     0.0027   17.7   0.1       0.01   15.8   0.0    2.0  2  HATPase_c_2      Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.013   15.3   0.1    2.4  3  sCache_2         Single Cache domain 2
      0.039   14.4   0.9      0.039   14.4   0.9    2.4  2  Snapin_Pallidin  Snapin/Pallidin
      0.046   13.5   1.5       0.42   10.4   1.5    2.6  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
      0.054   13.2   0.4       0.23   11.2   0.1    2.3  2  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
       0.31   10.6   3.9       0.11   12.1   0.4    2.1  2  DUF3053          Protein of unknown function (DUF3053)
        1.9    8.4   6.2       0.55   10.2   0.7    2.5  2  LpoB             Peptidoglycan-synthase activator LpoB


Domain annotation for each model (and alignments):
>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   3.4   3.1e-26   4.7e-23       4     247 ..      40     295 ..      37     296 .. 0.78
   2 ?   -0.4   0.6      0.55   8.2e+02       9      71 ..     467     546 ..     462     594 .. 0.75

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 3.1e-26
                      dCache_1   4 eeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvd... 81 
                                   ee a++q+ ++ +++an+++ +++s  +l++ ++s+      ++e+n    ++r++++++l  il+ np+i g y+ +   
  gi|91773016|ref|YP_565708.1|  40 EELAYQQSIEITKGYANQFDGDMRSNMALVRAISSS------MSEYN---SSDRDEVNRMLHRILEDNPHIIGTYVGYepn 111
                                   67799********************88888888775......66666...69********************999999899 PP

                      dCache_1  82 ................adGqv..iassdpssppnleg......tddpadrdwykealaggggkpvisdpyvdqtggkpvit 138
                                                   a+G++  +   + +     eg      + d+   ++y  ++ ++  +++i+dpy +++ +  +++
  gi|91773016|ref|YP_565708.1| 112 afdgrdsefinaeghdASGRFmpF---WNK----IEGeielkpLMDYDTLEYYVYPKVFK--DSFITDPY-YYE-DIFMVS 181
                                   988877777777777677776222...222....22255668888888889998888899..99******.666.99**** PP

                      dCache_1 139 iavpiyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd.kdl.lgknlrdelkaq..ealekala 215
                                   +++pi + + +f+G++++d++l +++d +s+ik  +tgy+ + +s+G+i++ p  kd+   k+++d ++++   a+e++  
  gi|91773016|ref|YP_565708.1| 182 YVAPIIK-NDEFLGMAGVDVSLKYVDDVVSQIKAFDTGYAIMTGSSGTILSQPYnKDWiGYKTIYDYDNKElsKAAEDIHH 261
                                   ******9.69******************************************99777762355556555555522333333 PP

                      dCache_1 216 kiesgvssvk.lngeeylvayapip.tglgWylv 247
                                   k+ + v++++  +g+e  v y pi+  + g  lv
  gi|91773016|ref|YP_565708.1| 262 KKSGHVNTIDpVTGKEVVVFYEPIRsKNYGFFLV 295
                                   34444444443577888777****9655666555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.55
                      dCache_1   9 eqllglaeqlanniedvldslenlaetlasnpslqdlleepnra.................neasreslqallksilksn 71 
                                   eq+  ++++++ n +++ ++l+  a+ l ++ +l+d+++ + r                  + + +e+++++lk+i ksn
  gi|91773016|ref|YP_565708.1| 467 EQTRHSLQRASVNQQRTEQELKEYAKKLEQSNELKDMFTDIMRHdllnpagvvkgftevllMTERDEKTERYLKKIWKSN 546
                                   66777777777777788888888888888888888888887777788888888888888887777788888888777766 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 ?   -2.9   0.0       6.5   9.7e+03      11      32 ..     576     600 ..     575     611 .. 0.58
   2 !   69.1   0.5   2.8e-22   4.2e-19       7     109 ..     614     715 ..     609     718 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.5
                                   HHHHHHHHHH...HSTTTEEEEEEE CS
                     HATPase_c  11 snlvdNavkf...atkageieveik 32 
                                    +++ N++++   ++  ++ie+e  
  gi|91773016|ref|YP_565708.1| 576 VEVINNSIEIlatQSAIKDIEIEFI 600
                                   5788899998532224445566555 PP

  == domain 2  score: 69.1 bits;  conditional E-value: 2.8e-22
                                   HHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHH CS
                     HATPase_c   7 rqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklv 85 
                                   + ++ n+++Na+k++++ +++ veik  e  ++ +i+++D G G++ +  k +f++f +   +k+g +g+GlGl+ivk+ +
  gi|91773016|ref|YP_565708.1| 614 ETVFTNIISNAIKYSPERSKVIVEIK--EnvEHTEITISDLGEGVDNAYKKTIFDRFER--VNKSGVKGSGLGLAIVKRTI 690
                                   6799**********99**********..4459***************************..889999************** PP

                                   HHTTTEEEEEEET.TTEEEEEEEEE CS
                     HATPase_c  86 elmgGeiwvesep.grGttftftlp 109
                                   el++Ge++v+++p g+Gt f+++l 
  gi|91773016|ref|YP_565708.1| 691 ELHKGEVEVRDNPeGHGTVFWVRLN 715
                                   *********9999899*****9985 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 ?   -3.3   0.0       6.4   9.6e+03      21      44 ..      70      94 ..      62      97 .. 0.52
   2 ?    0.6   0.0      0.41   6.1e+02      49      63 ..     336     350 ..     328     354 .. 0.81
   3 ?   -1.2   0.2       1.4   2.1e+03      25      47 ..     471     497 ..     464     499 .. 0.76
   4 !   21.5   0.0   1.2e-07   0.00018       4      65 ..     503     563 ..     500     565 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.4
                                  HHHHHHHHC...T-HSSCHHHHHHH CS
                         HisKA 21 lgnaeaLkre.gklteelkeyleti 44
                                  ++ ++ ++++  + ++e+ ++l++i
  gi|91773016|ref|YP_565708.1| 70 RAISSSMSEYnSSDRDEVNRMLHRI 94
                                  4444455554544455555555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.41
                                   HHHHHHHHHHHHHCC CS
                         HisKA  49 rrldhlvedlLdlsr 63 
                                     +d++v+d+ d++ 
  gi|91773016|ref|YP_565708.1| 336 SSIDDIVNDFKDMAD 350
                                   589*******99986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                                   HHHHC......T-HSSCHHHHHHHHHH CS
                         HisKA  25 eaLkre....gklteelkeyletiese 47 
                                   + L+r     +++ +elkey +++e++
  gi|91773016|ref|YP_565708.1| 471 HSLQRAsvnqQRTEQELKEYAKKLEQS 497
                                   667776777767789999999999887 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                         HisKA   4 rflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                    f+  + H+L +P  +++g++e+L  + + +e+ ++yl++i ++  +l ++++   +++++e
  gi|91773016|ref|YP_565708.1| 503 MFTDIMRHDLLNPAGVVKGFTEVLLMT-ERDEKTERYLKKIWKSNYQLIEMIQSASQFAKLE 563
                                   678889*****************9664.578************************9999998 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.5   8.2e+03      43      50 ..     344     351 ..     332     367 .. 0.62
   2 !   19.1   0.0   8.8e-07    0.0013       7      49 ..     384     426 ..     382     429 .. 0.92
   3 ?    3.6   0.1     0.059        88      16      53 .]     438     475 ..     436     475 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.5
                                   HHHHHHHH CS
                          HAMP  43 afNaMldr 50 
                                    f +M+d+
  gi|91773016|ref|YP_565708.1| 344 DFKDMADA 351
                                   44455444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 8.8e-07
                                   HHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHH CS
                          HAMP   7 lrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMld 49 
                                   + P ++  r+a+++++Gdl+tr + +   E++ La ++N++++
  gi|91773016|ref|YP_565708.1| 384 MVPFEETIRVAEHLSKGDLKTRFEGEYAGEFRKLADSMNVFAK 426
                                   67889999********************************986 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.059
                                   HHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                          HAMP  16 aarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                   +  ++ + d++  l v+g   +  L   +++ +++L++
  gi|91773016|ref|YP_565708.1| 438 VLSAMKEEDFTRNLRVHGHGDLKLLTDGIEQTRHSLQR 475
                                   66788899***************************986 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.92   1.4e+03      13      44 ..     578     608 ..     573     614 .. 0.83
   2 !   18.9   0.7   7.1e-07    0.0011       6      89 ..     613     701 ..     608     707 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.92
                   HATPase_c_5  13 lLdNAieacskieeekrfIrltvrekkkslii 44 
                                   +++N+ie   ++++  + I++++ e+ +++++
  gi|91773016|ref|YP_565708.1| 578 VINNSIEILATQSA-IKDIEIEFIEDREHFVL 608
                                   689****9999885.99999999999888776 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7.1e-07
                   HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliis.....ieNsyegek.kkle.sskskkeehGiGlksireivk 79 
                                   + +++ n++ NAi  + + +  k +++++ + ++  ++is     ++N y++++ +++e  +ks  +  G+Gl  ++++++
  gi|91773016|ref|YP_565708.1| 613 IETVFTNIISNAIKYSPERS--KVIVEIKENVEHTEITISdlgegVDNAYKKTIfDRFErVNKSGVKGSGLGLAIVKRTIE 691
                                   5689*********9998877..6777777777777777755555588999999986666356889999************* PP

                   HATPase_c_5  80 kykgnlsiea 89 
                                    +kg+++++ 
  gi|91773016|ref|YP_565708.1| 692 LHKGEVEVRD 701
                                   *****99865 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   3.2e+03      34      68 ..     573     607 ..     548     610 .. 0.74
   2 !   15.8   0.0   6.7e-06      0.01      40     110 ..     617     691 ..     609     714 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                   HATPase_c_2  34 laveEactNavehayleapegpvevrlesdeealt 68 
                                   l + E+++N +e    +   +++e+++  d e ++
  gi|91773016|ref|YP_565708.1| 573 LEIVEVINNSIEILATQSAIKDIEIEFIEDREHFV 607
                                   55779999999988888888999999888877776 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 6.7e-06
                   HATPase_c_2  40 ctNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpe..tlpdpteeepkeslkegGrGlalikglvD 110
                                   +tN++  a +  p   +v v+++ + e  +++++D G+g +++   t+ d+ e  +k   k +G+Gla++k+  +
  gi|91773016|ref|YP_565708.1| 617 FTNIISNAIKYSPeRSKVIVEIKENVEHTEITISDLGEGvDNAYkkTIFDRFERVNKSGVKGSGLGLAIVKRTIE 691
                                   566666666666656899*********************777653355666666669999**********99776 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   8.9e-06     0.013      41      81 ..     205     244 ..     201     270 .. 0.84
   2 ?   -3.6   0.3       5.8   8.7e+03      22      44 ..     472     494 ..     458     502 .. 0.53
   3 ?   -1.0   0.2      0.93   1.4e+03       5      36 ..     535     566 ..     532     581 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.9e-06
                      sCache_2  41 vkelvnglkfgdGkgYffvldedgtllvhPfnpqleGknas 81 
                                   v + v+++k  d  gY +++ + gt+l +P+n++++G + +
  gi|91773016|ref|YP_565708.1| 205 VDDVVSQIKAFD-TGYAIMTGSSGTILSQPYNKDWIGYKTI 244
                                   677899******.************************7754 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.8
                      sCache_2  22 avykqvesgkiteeeaqeevkel 44 
                                    +++   +++ te+e +e +k+l
  gi|91773016|ref|YP_565708.1| 472 SLQRASVNQQRTEQELKEYAKKL 494
                                   34444445555555555555544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.93
                      sCache_2   5 keaelknqvetaislieavykqvesgkiteee 36 
                                    e+ lk++ ++ ++lie++++  +  k+ + e
  gi|91773016|ref|YP_565708.1| 535 TERYLKKIWKSNYQLIEMIQSASQFAKLERSE 566
                                   5677899999999*******999999998866 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.9   2.6e-05     0.039       8      61 ..     459     510 ..     455     512 .. 0.93
   2 ?   -1.0   0.3       1.6   2.4e+03      17      51 ..     534     567 ..     532     582 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
               Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkey 61 
                                   l+ll   +++++++l+    +Q+   ++l++ ++kL++ +e+++  +++d++++
  gi|91773016|ref|YP_565708.1| 459 LKLLTDGIEQTRHSLQRASVNQQRTEQELKEYAKKLEQSNELKD--MFTDIMRH 510
                                   7889999*************************************..****9876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
               Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                   +++  lk++ +s  +L e++++  +++++le+ ++
  gi|91773016|ref|YP_565708.1| 534 KTERYLKKIWKSNYQLIEMIQSA-SQFAKLERSED 567
                                   56778888888999999988774.45555665555 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 ?   10.4   1.5   0.00028      0.42       4      81 ..     614     685 ..     572     693 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                   HATPase_c_3   4 ekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklAs 81 
                                   e++ + ++ N++    +  +v +e+++n  +++ei+i D G+G++++  k  + r+ + +k+        G kG Gl lA+
  gi|91773016|ref|YP_565708.1| 614 ETVFTNIISNAIKysPERSKVIVEIKENV-EHTEITISDLGEGVDNAYKKTIFdRFERVNKS--------GVKGSGLGLAI 685
                                   55677899999883344555666666664.78*************99888877567777766........77777766666 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.9   8.9e+03      43      54 ..     202     213 ..     195     214 .. 0.72
   2 ?   11.2   0.1   0.00016      0.23       9      51 ..     497     544 ..     489     558 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.9
                        SPOB_a  43 eeyieevvkelk 54 
                                    +y+++vv ++k
  gi|91773016|ref|YP_565708.1| 202 LKYVDDVVSQIK 213
                                   578888887776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00016
                        SPOB_a   9 lkeliklL.rsqRHDflNhLQvIsGylq....Lgkydkaeeyieevvk 51 
                                    +el +++    RHD lN   v++G+++    +++ +k e y++++ k
  gi|91773016|ref|YP_565708.1| 497 SNELKDMFtDIMRHDLLNPAGVVKGFTEvllmTERDEKTERYLKKIWK 544
                                   444444444557*************97733336888999999988876 PP

>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       4.2   6.3e+03      54      81 ..      44      71 ..      43      91 .. 0.66
   2 ?   12.1   0.4   7.4e-05      0.11      77     152 ..     445     519 ..     397     531 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.2
                       DUF3053 54 YasdYailtafsqqlnqavetslepvvd 81
                                  Y +  +i +++ +q++  ++++++ v +
  gi|91773016|ref|YP_565708.1| 44 YQQSIEITKGYANQFDGDMRSNMALVRA 71
                                  6677778888988998888888765443 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.4e-05
                       DUF3053  77 epvvdalqsirspqdyltrrdelrqaagalneleqqlqnakaqadkaraaLkqpddlkavydkayektVtqpanal 152
                                   e+  ++l +++   d+    d ++q + +l++++ + q+++++ ++   +L+q+++lk ++  +  +   +pa ++
  gi|91773016|ref|YP_565708.1| 445 EDFTRNL-RVHGHGDLKLLTDGIEQTRHSLQRASVNQQRTEQELKEYAKKLEQSNELKDMFTDIMRHDLLNPAGVV 519
                                   2333333.899999999999*****************************************999988888887766 PP

>> LpoB  Peptidoglycan-synthase activator LpoB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.5      0.67     1e+03      36      85 ..     430     488 ..     424     500 .. 0.48
   2 ?   10.2   0.7   0.00037      0.55       8      61 ..     551     602 ..     545     621 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.67
                          LpoB  36 svkNkTsehidt...esltkkirraLlksgkvrf..........vsgaqrerareelreqqes 85 
                                    ++N++++ + +   e +t+++r      g  ++          ++  qr+++++++ eq+ +
  gi|91773016|ref|YP_565708.1| 430 LIINDSNQVLSAmkeEDFTRNLR----VHGHGDLklltdgieqtRHSLQRASVNQQRTEQELK 488
                                   57788887776633344444444....333333333423211114444455555555554433 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00037
                          LpoB   8 emvqsllssplveqllkkdgkr.pvlvvssvkNkTsehidtesltkkirraLlks 61 
                                   em+qs+ +   +    ++++ +   l + +v+N++ e + t+s++k+i+ + +++
  gi|91773016|ref|YP_565708.1| 551 EMIQSASQFAKL---ERSEDLKlESLEIVEVINNSIEILATQSAIKDIEIEFIED 602
                                   677777664444...4455555699**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (723 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 4357.71
//
Query:       gi|91773017|ref|YP_565709.1|  [L=631]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-30  104.5   0.0    8.2e-30  103.6   0.0    1.5  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    2.2e-25   88.9   0.0    1.3e-07   31.6   0.0    3.5  3  PAS            PAS fold
    3.1e-23   82.0   0.2    2.4e-07   30.9   0.0    3.6  3  PAS_9          PAS domain
    1.4e-20   73.4   0.0    2.9e-15   56.3   0.0    3.7  3  PAS_3          PAS fold
      4e-18   65.2   0.1    9.7e-18   64.0   0.1    1.7  1  HisKA          His Kinase A (phospho-acceptor) domain
    8.1e-16   58.2   0.0    4.5e-07   30.1   0.0    3.6  3  PAS_4          PAS fold
    1.3e-10   41.0   0.0    1.5e-06   28.0   0.0    2.7  2  PAS_8          PAS domain
     0.0017   18.9   0.0        0.3   11.7   0.0    3.5  3  PAS_10         PAS domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.076   12.9   0.0    1.9  1  HATPase_c_5    GHKL domain
       0.03   13.5   0.6      0.047   12.9   0.6    1.2  1  Phyto_Pns9_10  Phytoreovirus nonstructural protein Pns9/Pns10
      0.032   14.4   0.1         14    5.8   0.0    3.4  3  PAS_7          PAS fold
      0.036   13.9   0.0      0.083   12.7   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


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 !  103.6   0.0   5.5e-33   8.2e-30       1     109 [.     520     630 ..     520     631 .] 0.95

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 5.5e-33
                                   EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHH CS
                     HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsi 80 
                                   gd ++L+ ++ n+vdN++kf++++g+++ +ik +++ ++i  +DnGiGip++++++lf++f+q d+s++r++ggtGlGl+i
  gi|91773017|ref|YP_565709.1| 520 GDRDKLTDMLTNMVDNSIKFTPEGGSLKFTIKEEDEFIHIVLKDNGIGIPPDMIPMLFQRFYQiDASRTRKYGGTGLGLYI 600
                                   7999****************88**********76689******************************************** PP

                                   HHHHHHHTTTEEEEEEET.TTEEEEEEEEE CS
                     HATPase_c  81 vkklvelmgGeiwvesep.grGttftftlp 109
                                   +k++v+ ++G+iwves+  ++Gt+++++lp
  gi|91773017|ref|YP_565709.1| 601 CKEIVTAHKGKIWVESKGeNKGTEMHIQLP 630
                                   ***9999*******8888799*****9998 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   5.7e-10   8.5e-07       3     111 ..       5     118 ..       3     120 .. 0.89
   2 !   24.5   0.0   1.4e-08   2.1e-05       2     113 .]     139     253 ..     138     253 .. 0.92
   3 !   31.6   0.0   8.4e-11   1.3e-07       2     113 .]     269     376 ..     268     376 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.7e-10
                                   HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.....HHHHHHHHHHHHTT-ECCCCEE CS
                           PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.....elaelleqlleqgeesrageis 78 
                                   l+ +l++l  + ++vD++ +++y+++ +e+++G+s+e ++gk + d++   +        + el +q+    ++ r    s
  gi|91773017|ref|YP_565709.1|   5 LDKMLSNLYKGLWAVDANNKFIYFSKGMEDITGISEERIIGKDIKDFMEVAQLCvgdetHFTELSLQAKDKLKPTRYHSLS 85 
                                   67899******************************************9887554877778888888888899999999999 PP

                                   EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlr 111
                                   f ++ g    l  +  p+++++++ +g+++++ 
  gi|91773017|ref|YP_565709.1|  86 FLTPEGNLNLLSGHIIPMLNGSDKYTGLICTVE 118
                                   999999999999999999999999999999875 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.4e-08
                                   HHHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEE CS
                           PAS   2 dlraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisf 79 
                                   +l++i  ++p+  f++  e+ + +++ +   +++G+++ +  +g +++++i+++dd   ++  +++l+ +g+++ ++e ++
  gi|91773017|ref|YP_565709.1| 139 ELEEIYKNSPVVAFLWTaEKDWPVEFVSDNITQFGYTPeDFTSGNMIYGDIVHPDDLdFVRNDITRLEIEGRQFFSKEYRI 219
                                   678888899999999998777778888888899*****77899**************99999******************* PP

                                   ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                    +r  +p+++  r   v d++g++ ++ g++ d+
  gi|91773017|ref|YP_565709.1| 220 LTRAEEPRWVAERSLMVPDEDGRPSYYQGIIIDV 253
                                   *******************************997 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 8.4e-11
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                   ++r i+e++p +if  D+dg+i+++N++++ + G s + ++g ++l++i  +++  + +     ++ + + +++++s    
  gi|91773017|ref|YP_565709.1| 269 RFRLIFENSPLGIFTFDKDGIITHCNTNFAMIMGASMDKIIGLNILRSIKDKKM--TDAVKPVFARKTGHYEGKCVSALS- 346
                                   799**********************************************87765..444444445566666676676666. PP

                                   TSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  83 dgrpihlevraspvrdaggeilgflgvlrdi 113
                                    g+++++    sp + ++g ilg +g++ di
  gi|91773017|ref|YP_565709.1| 347 -GKVTPIKADYSPNIAEDGSILGGIGIIEDI 376
                                   .***************************998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.6e-10   2.4e-07       7     104 .]      19     122 ..      14     122 .. 0.92
   2 !   19.7   0.0   5.1e-07   0.00076      10     104 .]     159     255 ..     148     255 .. 0.88
   3 !   27.5   0.0   1.8e-09   2.8e-06       2     104 .]     279     378 ..     278     378 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.6e-10
                         PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf......vtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                   ++ +++ +y+++++++++G s+e ++gk+i+d++      v+d+ +  +l+ + +++ k+ r   + + +++g+  +   +
  gi|91773017|ref|YP_565709.1|  19 VDANNKFIYFSKGMEDITGISEERIIGKDIKDFMevaqlcVGDETHFTELSLQAKDKLKPTRYHSLSFLTPEGNLNLLSGH 99 
                                   668999******************************998888888888888888888889********************* PP

                         PAS_9  82 aspvkdddgelvgiivilrDite 104
                                   ++p+ +++++++g+i++++ ++e
  gi|91773017|ref|YP_565709.1| 100 IIPMLNGSDKYTGLICTVESVSE 122
                                   ******************99987 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.1e-07
                         PAS_9  10 dgrilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltaspv 85 
                                   d +++++++   ++ Gy+pe++   +  + d++  +p++ +++r+ + +++    +++++e+ + ++ +e+ wv  +   v
  gi|91773017|ref|YP_565709.1| 159 DWPVEFVSDNITQF-GYTPEDFTSGNmiYGDIV--HPDDLDFVRNDITRLEIegrQFFSKEYRILTRAEEPRWVAERSLMV 236
                                   44666999999998.*********999888888..999999999999999999999************************* PP

                         PAS_9  86 kdddgelvgiivilrDite 104
                                    d+dg+   + +i++D+t+
  gi|91773017|ref|YP_565709.1| 237 PDEDGRPSYYQGIIIDVTD 255
                                   *****************96 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 1.8e-09
                         PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                    gi+  ++dg i+ ++N+ ++ ++G s + ++g +i   + +d++  + ++ ++ +++   + +       +g+  ++++ 
  gi|91773017|ref|YP_565709.1| 279 LGIFTFDKDG-IItHCNTNFAMIMGASMDKIIGLNILRSI-KDKKMTDAVKPVFARKT--GHYEGKCVSALSGKVTPIKAD 355
                                   6899877***.666**************************.99999999999999999..666666666678899****** PP

                         PAS_9  82 aspvkdddgelvgiivilrDite 104
                                    sp + +dg + g i+i++Dit+
  gi|91773017|ref|YP_565709.1| 356 YSPNIAEDGSILGGIGIIEDITT 378
                                   *********************95 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0014       2.1       2      30 ..      26      52 ..      25      64 .. 0.89
   2 !   56.3   0.0     2e-18   2.9e-15       3      89 .]     164     250 ..     162     250 .. 0.91
   3 ?    4.1   0.0     0.038        57       2      88 ..     291     372 ..     290     373 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                         PAS_3  2 iyvserveeilGyspeellgkveswldlv 30
                                  iy s+ +e+i+G+s+e ++gk  +++d++
  gi|91773017|ref|YP_565709.1| 26 IYFSKGMEDITGISEERIIGK--DIKDFM 52
                                  99*******************..777665 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 2e-18
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqeal.kkgepyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +vs+++ +  Gy+pe++++    + d+vhp+D++ vr+++ ++  ++++ ++ eyRi+++  e rwv +r   + de+g+p
  gi|91773017|ref|YP_565709.1| 164 FVSDNITQF-GYTPEDFTSGNMIYGDIVHPDDLDFVRNDITRLEiEGRQFFSKEYRILTRAEEPRWVAERSLMVPDEDGRP 243
                                   677788776.**********9999*****************9973666688****************************** PP

                         PAS_3  83 vrvigva 89 
                                    +++g++
  gi|91773017|ref|YP_565709.1| 244 SYYQGII 250
                                   *****86 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.038
                         PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.pyegeyRirrk.dGeyrwveararvirden 79 
                                   ++++ ++  i+G s + ++g   ++l  +      + v+  ++    +++ +yeg  +++ + +G+++ ++a +++   e+
  gi|91773017|ref|YP_565709.1| 291 THCNTNFAMIMGASMDKIIGL--NILRSIKDKKmTDAVKPVFA----RKTgHYEG--KCVSAlSGKVTPIKADYSPNIAED 363
                                   6899****************9..66666655443444444444....44435644..456666999999999999999999 PP

                         PAS_3  80 gkpvrvigv 88 
                                   g ++  ig+
  gi|91773017|ref|YP_565709.1| 364 GSILGGIGI 372
                                   998888887 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 !   64.0   0.1   6.5e-21   9.7e-18       1      67 []     406     474 ..     406     474 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 6.5e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   ++ rfl++v+HEL+tPL++i+g++e++ +e  g l+e++ke  +t+ ++a+rl +lv+ lL +sr ++g
  gi|91773017|ref|YP_565709.1| 406 MKDRFLSNVSHELKTPLTSIKGYTELIYDEslGTLSEQQKEVEKTVLRNANRLKRLVDSLLYISRAQSG 474
                                   689************************77789*********************************9987 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00055      0.82       7     108 ..      15     123 ..       9     125 .. 0.70
   2 !   14.3   0.0   2.4e-05     0.036       3     109 ..     146     257 ..     144     258 .. 0.76
   3 !   30.1   0.0     3e-10   4.5e-07       1     108 [.     274     379 ..     274     381 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00055
                         PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktla...ellpeedaarleralrrvlegeepiefleelll.....pgeer 79 
                                   +l ++d++ +++y ++ ++++ g++ e+++Gk      e++   + ++  +  +  l+ ++ ++ + ++ l     +g   
  gi|91773017|ref|YP_565709.1|  15 GLWAVDANNKFIYFSKGMEDITGISEERIIGKDIKdfmEVAQL-CVGDETHFTELSLQAKDKLKPTRYHSLsfltpEGNLN 94 
                                   67788******************************44445554.4444444444444444444444444444444488888 PP

                         PAS_4  80 hyelrllPlrdesGevigvlvisrDiTer 108
                                    ++ +++P+++ s +  g+++++  ++e+
  gi|91773017|ref|YP_565709.1|  95 LLSGHIIPMLNGSDKYTGLICTVESVSEQ 123
                                   88888888888888888888888888876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.4e-05
                         PAS_4   3 slpdalavl..dpdgrvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrv.legeepiefleelll.pge 77 
                                   ++p++ + +   +d  v++++ ++ + fg++pe+++   +   +++ ++d + ++++++r+ +eg+++ + +   l+   e
  gi|91773017|ref|YP_565709.1| 146 NSPVVAFLWtaEKDWPVEFVSDNITQ-FGYTPEDFTSGNMIygDIVHPDDLDFVRNDITRLeIEGRQFFSKEYRILTrAEE 225
                                   56666666666777778888888887.777777776443333788888888888888888845666666666666669*** PP

                         PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                   +r++  r l + de+G++  + +i++D+T+r+
  gi|91773017|ref|YP_565709.1| 226 PRWVAERSLMVPDEDGRPSYYQGIIIDVTDRK 257
                                   ******************************97 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 3e-10
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerh 80 
                                   ++++p +++ +d+dg ++++N+++a ++ga+ + ++G                +a++ v + ++ +++  ++   +g+  +
  gi|91773017|ref|YP_565709.1| 274 FENSPLGIFTFDKDGIITHCNTNFAMIMGASMDKIIGLNILRS---IKDKKMTDAVKPVFARKTGHYEGKCVSAlSGKVTP 351
                                   79***********************************999854...35699****************************** PP

                         PAS_4  81 yelrllPlrdesGevigvlvisrDiTer 108
                                   +   ++P  +e+G ++g ++i+ DiT r
  gi|91773017|ref|YP_565709.1| 352 IKADYSPNIAEDGSILGGIGIIEDITTR 379
                                   **************************98 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00046      0.68      13      50 ..      15      53 ..       6      67 .. 0.76
   2 !   28.0   0.0     1e-09   1.5e-06       2      52 ..     269     317 ..     268     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                         PAS_8 13 giavvdlgdrivdvNqaalellGys.adlkgellgqllp 50
                                  g++ vd+++++++  + +++++G s + ++g+++ ++++
  gi|91773017|ref|YP_565709.1| 15 GLWAVDANNKFIYFSKGMEDITGISeERIIGKDIKDFME 53
                                  99****6666*************7666666655544444 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1e-09
                         PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvl 52 
                                   r+r +fe+sp gi+ +d ++ i+++N  ++++ G s + ++g    ++l+ +
  gi|91773017|ref|YP_565709.1| 269 RFRLIFENSPLGIFTFDKDGIITHCNTNFAMIMGASmDKIIGL---NILRSI 317
                                   9****************7777*************776555552...555544 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0002       0.3       1      49 [.       5      54 ..       5     121 .. 0.62
   2 ?   -1.0   0.0       1.8   2.7e+03      45     104 ..     188     255 ..     178     256 .. 0.72
   3 ?    2.7   0.0      0.13   1.9e+02       4     106 .]     273     377 ..     271     377 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                        PAS_10  1 lnnlLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpk 49
                                  l+ +L+++  +l  +D n+++++F++  + +  + ++  +G +++d+ + 
  gi|91773017|ref|YP_565709.1|  5 LDKMLSNLYKGLWAVDANNKFIYFSKGMEDITGISEERiIGKDIKDFMEV 54
                                  6889999999******************999999876527***9999533 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                        PAS_10  45 dihpkkavknveeviealrtgekdevevvvp.....kngkwvlvrylpyrdedge...iaGvvetfvD 104
                                   di++++ ++ v+++i +l  + ++  +++       ++ +wv  r l + dedg+   ++G+++ ++D
  gi|91773017|ref|YP_565709.1| 188 DIVHPDDLDFVRNDITRLEIEGRQFFSKEYRiltraEEPRWVAERSLMVPDEDGRpsyYQGIIIDVTD 255
                                   67788888888888888876666655554444445577899999999999999875557788777766 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.13
                        PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfkl.ipadvGrp.ladihpkkavknveeviealrtgekdevevvvpkngkwvl 82 
                                   ++++ p+++  +D++  i+  +++ ++++    ++ +G + l +i+ kk  + v+ v+ +   + + +     + + + + 
  gi|91773017|ref|YP_565709.1| 273 IFENSPLGIFTFDKDGIITHCNTNFAMIMGAsMDKIIGLNiLRSIKDKKMTDAVKPVFARKTGHYEGKCVSALSGKVTPIK 353
                                   567788888888888888888888777765415566785514666666666666666665555555544444456677799 PP

                        PAS_10  83 vrylpyrdedgeiaGvvetfvDit 106
                                     y+p   edg+i G + ++ Dit
  gi|91773017|ref|YP_565709.1| 354 ADYSPNIAEDGSILGGIGIIEDIT 377
                                   99*************999999996 PP

>> HATPase_c_5  GHKL 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     0.076       6      91 ..     525     618 ..     521     628 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                   HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..............ekkkle.sskskkeehGiGl 71 
                                   l+ +l n+ dN+i    +      ++++t++e+++++ i ++ +  g              ++     s+++k +  G+Gl
  gi|91773017|ref|YP_565709.1| 525 LTDMLTNMVDNSIKFTPE----GGSLKFTIKEEDEFIHIVLKDNGIGippdmipmlfqrfyQI---DaSRTRKYGGTGLGL 598
                                   677888999998876665....55799999999999888887665555777776665433222...2366677899***** PP

                   HATPase_c_5  72 ksireivkkykgnlsieaed 91 
                                      +eiv  +kg++++e + 
  gi|91773017|ref|YP_565709.1| 599 YICKEIVTAHKGKIWVESKG 618
                                   ***************99875 PP

>> Phyto_Pns9_10  Phytoreovirus nonstructural protein Pns9/Pns10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   3.1e-05     0.047     156     301 ..     407     555 ..     376     565 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                 Phyto_Pns9_10 156 rtkrlskilkeyytaleeveayleklpddskdsllnqkskevlrvifsnak..vliatkinkyvtlyedsyleyvrevaey 234
                                   + + ls++ +e  t l  ++ y e + d+s ++l +q+ kev + ++ na+   ++ ++  +y++  +  + +y+ e  + 
  gi|91773017|ref|YP_565709.1| 407 KDRFLSNVSHELKTPLTSIKGYTELIYDESLGTLSEQQ-KEVEKTVLRNANrlKRLVDS-LLYISRAQSGNVQYLFEPVSI 485
                                   334588999************************99875.55555556665311344444.59**************99998 PP

                 Phyto_Pns9_10 235 vadlwdvqtttntqghenelaaedfGvlaalsqmdttddelgdsviksdGvevklepa....mftrnedee 301
                                   v+ +       + q  e++la+e   ++   + +++  d+l d ++    + +k+ p      ft +e++e
  gi|91773017|ref|YP_565709.1| 486 VEIVEMTLQDLKIQIEEKKLAVE-KDIPNDIPTINGDRDKLTDMLTNMVDNSIKFTPEggslKFTIKEEDE 555
                                   87643333456788889999887.579********************999999998842222466555555 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.029        43       1      48 [.       9      55 ..       9     128 .. 0.84
   2 ?    5.8   0.0    0.0097        14       2      33 ..     275     306 ..     274     326 .. 0.85
   3 ?   -1.0   0.0       1.2   1.9e+03     101     115 .]     370     384 ..     365     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.029
                         PAS_7  1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn 48
                                  l+n+ +G+  +Da+++ + + + + ++ +++ee + +g+ +++++++ 
  gi|91773017|ref|YP_565709.1|  9 LSNLYKGLWAVDANNKFIYFSKGMEDITGISEERI-IGKDIKDFMEVA 55
                                  68999*****************************9.999999999875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0097
                         PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpee 33 
                                   en + Gi  fD+d+ ++ +N ++  +++ + +
  gi|91773017|ref|YP_565709.1| 275 ENSPLGIFTFDKDGIITHCNTNFAMIMGASMD 306
                                   78889******************999887665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.2
                         PAS_7 101 VttytDiTerrraee 115
                                   + + +DiT r+++ee
  gi|91773017|ref|YP_565709.1| 370 IGIIEDITTRIESEE 384
                                   55789*******986 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 ?   12.7   0.0   5.5e-05     0.083       6      80 ..     528     601 ..     524     630 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                   HATPase_c_3   6 AlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklA 80 
                                    l+ +vdNs+    +  + k ++++++ +   iv +D+G G++++ +   + r+ + + +     +++G  G+Gl   
  gi|91773017|ref|YP_565709.1| 528 MLTNMVDNSIKftPEGGSLKFTIKEED-EFIHIVLKDNGIGIPPDMIPMLFqRFYQIDAS---RTRKYGGTGLGLYIC 601
                                   578899999984433334555555543.4689*************999977357666666...578899999996443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3783.66
//
Query:       gi|91773018|ref|YP_565710.1|  [L=491]
Description: argininosuccinate lyase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-62  209.5   0.0    1.2e-61  208.8   0.0    1.3  1  Lyase_1   Lyase
    4.6e-13   49.7   0.1    2.3e-12   47.5   0.0    2.3  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 !  208.8   0.0   1.4e-65   1.2e-61      10     312 .]      17     300 ..       8     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 1.4e-65
                                   HHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSST..HHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHH CS
                       Lyase_1  10 lmgiftersrenfrlseedikalaalkkaaakanvdl..keeaaaiikaldevleegklddqfvlkviqegsgtavnmnln 88 
                                    + +ft ++  ++++ ++di  l+ l+  +  ++ +   +e  ++i+++l  + eeg +    +l+   e+++ +++ +l 
  gi|91773018|ref|YP_565710.1|  17 EIINFTSSMNADKWIFKADI--LVDLAHTIMLKERKIikAEDCKKILEGLLTIKEEGIE----KLDHTYEDIHISLESRLI 91 
                                   55679999999999997777..6666666666666553466667777777777775555....5***************** PP

                                   HHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHH CS
                       Lyase_1  89 evigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlg 169
                                   +++g       ++ +  h g+S+nD v+T +rl l++ l   L+++l  L+++l++++ e+ +++++G+Thlq+A+P+tl+
  gi|91773018|ref|YP_565710.1|  92 DMVG------EDTGGRMHSGRSRNDEVATCIRLTLRNDL-LLLMEELIALRNTLNDTSSENLNTLMPGFTHLQHAQPTTLA 165
                                   ****......6999*************************.67*************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHH CS
                       Lyase_1 170 qelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvellg 250
                                   + l a+a+a+ rd+er ++ +kr+++++lg+++ + tg++ d+e   + +k l+ ++g     +ns++avs+rD+++e ++
  gi|91773018|ref|YP_565710.1| 166 HHLTAHANAIGRDLERTMDCYKRVNLSPLGAAAFASTGFDLDRE---RTCKLLG-FDG---LIENSMDAVSSRDFLIESAS 239
                                   ********************************************...*******.***...******************** PP

                                   HHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
                       Lyase_1 251 alkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                                   + ++l+++Lsk+ae++ + s++e+ ++el++++ +  SSiMP+K+NP+++Ell+g++g  +G
  gi|91773018|ref|YP_565710.1| 240 VFANLMINLSKVAEEIVIWSTSEFAFIELDDRYAS-TSSIMPQKKNPDTAELLRGKSGVTIG 300
                                   **********************************9.9*******************998766 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.9     8e+03      21      30 ..     165     174 ..     163     192 .. 0.78
   2 !   47.5   0.0   2.5e-16   2.3e-12       1      65 [.     363     432 ..     363     436 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.9
                                   HHHHHHHHHH CS
                        ASL_C2  21 AHeivgravr 30 
                                   AH+++++a +
  gi|91773018|ref|YP_565710.1| 165 AHHLTAHANA 174
                                   8999998754 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 2.5e-16
                                   STTHHHHHHHHHHC.TS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-.........TT.--.GGGGGGSSHH CS
                        ASL_C2   1 FstATdlADyLvrk.GlpFReAHeivgravrlaeekgkeleeltleelkeis.........pl.le.edveeaLdpe 65 
                                   F+tAT+lAD +vr  ++pFR+AH+ivg ++r +        e tl e+++++         ++ l+ + v+eaLdp 
  gi|91773018|ref|YP_565710.1| 363 FTTATELADTMVRVcDIPFRTAHQIVGVLARGS-------GEPTLGEIDAVAhnvigeslsSRgLTeKMVKEALDPI 432
                                   99*****************************94.......4566666665533444444433367768899999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3049.06
//
Query:       gi|91773019|ref|YP_565711.1|  [L=415]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete 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-60  201.6   1.8    1.3e-59  201.0   1.5    1.5  2  Asparaginase    Asparaginase, N-terminal
      9e-35  119.3   0.0    2.8e-33  114.5   0.0    2.4  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    6.5e-18   63.8   0.1    1.4e-17   62.8   0.1    1.6  1  GatD_N          GatD N-terminal domain
     0.0011   18.9   0.1     0.0029   17.5   0.1    1.6  1  Asp_Glu_race    Asp/Glu/Hydantoin racemase
     0.0041   16.7   0.1       0.59    9.6   0.0    2.3  2  Peripla_BP_4    Periplasmic binding protein domain
  ------ inclusion threshold ------
      0.073   12.9   0.0       0.16   11.9   0.0    1.5  1  DUF2642         Protein of unknown function (DUF2642)


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 !  201.0   1.5   4.3e-63   1.3e-59       1     185 [.      76     265 ..      76     270 .. 0.97
   2 ?   -4.0   0.0         3   8.8e+03     140     156 ..     338     354 ..     334     367 .. 0.59

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 4.3e-63
                                   EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-SEEE CS
                  Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.ydgfV 80 
                                   kv +l+tGGTias++d+++ga++ ++sa+++++a+pel++ia+++ ++l ni S+nm+ + w +la a+++++e+ +dg++
  gi|91773019|ref|YP_565711.1|  76 KVTILSTGGTIASKVDYRTGAVTAQFSADDIVDAIPELTEIADINGRVLYNILSENMKAEYWTELAGAVAQEIENgADGII 156
                                   799**********************************************************************777***** PP

                                   EE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEETT CS
                  Asparaginase  81 vlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llran 154
                                   ++hGTDT+ y+A+aLs+mlk+ ++pvv++Gsqr++++++sD ++N + A +va s+  ia+v+vv++++       ++ ++
  gi|91773019|ref|YP_565711.1| 157 IAHGTDTMMYSAAALSFMLKT-PVPVVFVGSQRSADRPSSDNAMNAICATKVAVSD--IAEVCVVMHDTtsddrcaIHFGT 234
                                   *********************.********************************87..*********************** PP

                                   TEEE-BSSSSS-EEETTT--SEEEETTEEEE CS
                  Asparaginase 155 rvtKvhtssldaFespnlgplaevegskvkv 185
                                   +v+K+hts++daF+s+n  p++++++s+ k+
  gi|91773019|ref|YP_565711.1| 235 KVRKMHTSRRDAFQSINSDPIGYIDHSTHKI 265
                                   ************************7776665 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3
                                   SECEEEETTEEEETTTE CS
                  Asparaginase 140 agvlvvfngkllranrv 156
                                   +g+ v++  ++++++ +
  gi|91773019|ref|YP_565711.1| 338 NGIPVIMTSQCISGRVC 354
                                   45555555555555555 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.06   1.8e+02      17      56 ..     145     182 ..     112     224 .. 0.67
   2 !  114.5   0.0   9.4e-37   2.8e-33       4     114 .]     291     401 ..     288     401 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.06
                                   HHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEE CS
                Asparaginase_C  17 kallkkgakGvvlegtGvGnlpsallealkeakargivvv 56 
                                    + +++ga+G++++ +  + + sa   al+ + ++ ++vv
  gi|91773019|ref|YP_565711.1| 145 AQEIENGADGIIIAHGTDTMMYSAA--ALSFMLKTPVPVV 182
                                   3334999******999888887732..3333333444444 PP

  == domain 2  score: 114.5 bits;  conditional E-value: 9.4e-37
                                   EEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHTEEE CS
                Asparaginase_C   4 vlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlgvis 84 
                                   ++k++pg++++vl +++++g+kG+v+egtG G++++++++ +k+a+++gi+v++tsqc+sg+v + +y++g+++ ++g+i+
  gi|91773019|ref|YP_565711.1| 291 LVKFVPGANPDVLSYYIDSGYKGLVIEGTGLGHVSTDWIPNIKRATENGIPVIMTSQCISGRVCDRVYDTGRDILKAGAIE 371
                                   899****************************************************************************** PP

                                   -TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                Asparaginase_C  85 addmtpeaarikLmlllgkgldpaevrklf 114
                                   ++dm pe a +kLm++lg+ +d +e+++++
  gi|91773019|ref|YP_565711.1| 372 GEDMLPEVALVKLMWALGQSNDVDEIKEIM 401
                                   ****************************98 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   4.6e-21   1.4e-17       1      55 []       3      52 ..       3      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 4.6e-21
                                  --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                        GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                  +e GD+i++ek+g +yeGi+mP++    +d+iv+K+ +GYN+G++ e++ +i+ll
  gi|91773019|ref|YP_565711.1|  3 FELGDRIRIEKDGNTYEGIVMPSN----TDHIVVKMVSGYNAGVDPEGA-SITLL 52
                                  589*********************....*********************.99986 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   9.6e-07    0.0029      72     190 ..      20     158 ..      16     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.6e-07
                                   EEEE--CHHHHHHHHHH........HH-SSEEEECHHHH........HHHHHH.HSS-EEEEEE-HHHHHCTH......HH CS
                  Asp_Glu_race  72 aiviaCnTahavadelq........kkikiPvlgiveat........aealka.tgvkkvglLgTrgtlksgl......yq 129
                                    iv++ nT h+v++ ++        + ++i +l   +a+         +++k  +++ kv +L T gt++s++        
  gi|91773019|ref|YP_565711.1|  20 GIVMPSNTDHIVVKMVSgynagvdpEGASITLLE--KAGpknapkakPDKAKGqKKLPKVTILSTGGTIASKVdyrtgaVT 98 
                                   79***************97765555555555555..44466777755445555799999**********987642222266 PP

                                   HHHHHHGT.EEE....T-CCCHH.CCHCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE- CS
                  Asp_Glu_race 130 keleanqgievvvpseelqssvn.qaiyeelkaGevteearrailkllerlaergadaviLG 190
                                   ++++a ++i   +p+  ++ ++n ++ y  + +++++ e   +++ ++++ +e+gad++i++
  gi|91773019|ref|YP_565711.1|  99 AQFSA-DDIVDAIPELTEIADINgRVLY-NILSENMKAEYWTELAGAVAQEIENGADGIIIA 158
                                   77888.5765567776666666515555.666899999966666666665669*******97 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.1    0.0064        19      47      90 ..     143     191 ..     133     298 .. 0.73
   2 !    9.6   0.0    0.0002      0.59      48     115 ..     303     375 ..     297     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0064
                                   HHHHHHHTT-SEEEE--SSHHHHH..HHHHHHHHTT-EEEEESTT...G CS
                  Peripla_BP_4  47 qiedaiakgvdgiivapvdstala..palkkakaaGIpVvafdsd...d 90 
                                   ++ + i++g+dgii+a    t ++  +al    +  +pVv++ s+   d
  gi|91773019|ref|YP_565711.1| 143 AVAQEIENGADGIIIAHGTDTMMYsaAALSFMLKTPVPVVFVGSQrsaD 191
                                   567899*********9998877763355556777788888887774443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0002
                                   HHHHHHTT-SEEEE--SSH....HHHHHHHHHHHHTT-EEEEESTT.GCTTT-CEEEEEC-HHHHHHHHHHHH CS
                  Peripla_BP_4  48 iedaiakgvdgiivapvds....talapalkkakaaGIpVvafdsd.dapsgerlayvgfdneaaGelqaeyl 115
                                   ++  i++g++g+++  +      t   p +k+a+++GIpV+   +       +r++  g d  +aG++ +e +
  gi|91773019|ref|YP_565711.1| 303 LSYYIDSGYKGLVIEGTGLghvsTDWIPNIKRATENGIPVIMTSQCiSGRVCDRVYDTGRDILKAGAIEGEDM 375
                                   56678999999998877654455778899************98777444445666677777777777777766 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.3e-05      0.16      18      47 ..       5      34 ..       3      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                       DUF2642 18 lgqevvvqttrgsvrGiLkdvkPDHivvei 47
                                  lg+++ ++   ++ +Gi++    DHivv++
  gi|91773019|ref|YP_565711.1|  5 LGDRIRIEKDGNTYEGIVMPSNTDHIVVKM 34
                                  7999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2429.57
//
Query:       gi|91773020|ref|YP_565712.1|  [L=158]
Description: hypothetical protein Mbur_1027 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-25   89.4   2.7      4e-25   88.5   2.7    1.5  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   2.7   2.2e-29     4e-25       1      79 [.       9      86 ..       9      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 2.2e-29
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgkna.vslehkgGdsidt..kdlkivlnse 79
                                  +AVSpViGviLmvaitvIlaAviaafv+g+ + +e+apqas+       a+ g+n+ ++leh+gGd+++   +++++++n++
  gi|91773020|ref|YP_565712.1|  9 DAVSPVIGVILMVAITVILAAVIAAFVFGM-GAPETAPQASVRGA---PAELGGNNvLKLEHQGGDMVTFtdANTRVTVNGN 86
                                  69****************************.9**********544...444444444**********998556667777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1028.04
//
Query:       gi|91773021|ref|YP_565713.1|  [L=81]
Description: hypothetical protein Mbur_1028 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  134.1   6.5    1.6e-39  133.9   6.5    1.1  1  DUF5371   Family of unknown function (DUF5371)


Domain annotation for each model (and alignments):
>> DUF5371  Family of unknown function (DUF5371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   6.5     9e-44   1.6e-39       1      65 []      13      77 ..      13      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 9e-44
                       DUF5371  1 mvKivHAqtvLaeeeLeeLKkKtnesstkdAlsiAveHYleCeYtdlneemwtkKlEkvvqKKkk 65
                                  ++KivHAqtvL+e++LeeLKkKtne+stk+Als+Av+HYleCeYt++n+emwt+KlEkvvqKK++
  gi|91773021|ref|YP_565713.1| 13 LMKIVHAQTVLTEDQLEELKKKTNEPSTKEALSVAVQHYLECEYTEMNDEMWTRKLEKVVQKKQQ 77
                                  59*************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1850  (0.103185); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 505.74
//
Query:       gi|91773022|ref|YP_565714.1|  [L=385]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein [Methanococcoides burtonii DSM 6242]
Scores for 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  256.7   0.0    1.4e-76  256.2   0.0    1.2  1  DUF1297   Domain of unknown function (DUF1297)
    3.8e-43  146.3   0.0    7.2e-43  145.4   0.0    1.5  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 !  256.2   0.0   1.6e-80   1.4e-76       1     188 []     191     385 .]     191     385 .] 0.98

  Alignments for each domain:
  == domain 1  score: 256.2 bits;  conditional E-value: 1.6e-80
                                   HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTT...TEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-.. CS
                       DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplk...eevellgidrRyesnldglvrlpakeqlelev.. 76 
                                   e+ ek+e+l+++g+i++e+l++a+ie+y++G  fn+++f+sp++   +++e+lg+d+R+e++ldg+vrlpa +q++l +  
  gi|91773022|ref|YP_565714.1| 191 EYVEKSESLIKQGVITREALAEARIERYIIGPVFNFDMFHSPIEeemNKTEILGVDWRFETSLDGYVRLPAPQQMNLAEhq 271
                                   799*****************************************888899*************************998877 PP

                                   .---EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT.--CC CS
                       DUF1297  77 .epeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme.gspy 155
                                    +pey+v+G+++++lREslle+vf+l+e +++a+k+ ++pG+iGpFcLq++++kdl+++++dv++R++ggtnv+m+ g+py
  gi|91773022|ref|YP_565714.1| 272 lTPEYTVCGHNSATLRESLLEEVFKLSEMYIKASKEFYDPGVIGPFCLQTCIDKDLNFHIYDVAPRVGGGTNVHMSvGHPY 352
                                   89******************************************************************************* PP

                                   HHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                       DUF1297 156 skllfgeplsmGrrialEikeaiekdrleeivt 188
                                   +++l+++p+s+Grr+a+E+++aie+++l++i+t
  gi|91773022|ref|YP_565714.1| 353 ANTLWRKPMSTGRRVAFEVRRAIESGQLDKIIT 385
                                   ********************************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 !  145.4   0.0   8.1e-47   7.2e-43       1     122 []      21     158 ..      21     158 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 8.1e-47
                                   EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.............TT-SEEEE.S.S..TTSS--HHHHHHTTCE CS
                       DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.............kvidevivldkfkdilkeevqeklreenai 68 
                                   i+t+aSHs l++++gA +e+f+t+a+c+ grek+Y+++             +++d+ +v+dkf++++  e+q+kl+++n++
  gi|91773022|ref|YP_565714.1|  21 IGTVASHSGLDVFDGAIEENFETFAICQAGREKTYTEYfkskrdangnvvrGIVDDHVVYDKFNELMLPENQQKLVDDNVL 101
                                   89************************************************99***************************** PP

                                   E--BTTHHHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--BE CS
                       DUF1246  69 lvPhgsfveYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkki 122
                                   ++P++sf++Y+ i+++e +++vp++G+r++lr+Eer  ++++y  LekAg+++P++i
  gi|91773022|ref|YP_565714.1| 102 FIPNRSFTSYCDIDEVEnDFRVPMVGSRNMLRSEERGMDQDYYwlLEKAGLPFPERI 158
                                   ******************************************99**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 2485.44
//
Query:       gi|91773023|ref|YP_565715.1|  [L=215]
Description: hypothetical protein Mbur_1030 [Methanococcoides burtonii DSM 6242]
Scores for 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-32  111.4  18.3    5.3e-32  111.0  18.3    1.1  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0  18.3     3e-36   5.3e-32       2     156 .]      38     205 ..      37     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 3e-36
                        SpoIIM   2 lllflvgillgallaa....snfaeqis........seskensalslflaifanNlrvalllfllGllllgiptilvllin 70 
                                   +llf++++++g++ +a    s   +++s        +  k+ + ++++l+if+nN++ +l++f++Gl  +gi+++++++ n
  gi|91773023|ref|YP_565715.1|  38 VLLFIISVIVGYAHTAfdpsS---STLSlegleelvEFIKSLNVFEIMLFIFFNNAIKSLIAFVFGL-GFGIIPLVFVVSN 114
                                   79**************55430...33335566678788899999**********************6.************* PP

                        SpoIIM  71 GfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal.....rsrrkalkeakrellklllllvpllli 146
                                   G+vlG+v++l +  +gl ++ ++ilPhg++elp+i+i++a+glr+g+ +      + ++ +ke+ + l  ++ +++plll+
  gi|91773023|ref|YP_565715.1| 115 GYVLGVVTYLESMDNGLVYVGIAILPHGVIELPMILISAAMGLRMGLLVfntltGKDVDLKKELLQGLNIFFRFVAPLLLV 195
                                   *******888888888*****************************99999999866777888888888888888889**** PP

                        SpoIIM 147 AaliEafvtp 156
                                   Aa iE+f+tp
  gi|91773023|ref|YP_565715.1| 196 AAAIETFITP 205
                                   *********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1397.11
//
Query:       gi|91773024|ref|YP_565716.1|  [L=283]
Description: hypothetical protein Mbur_1031 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-106  355.9  16.9   2.6e-106  355.8  16.9    1.0  1  DUF63            Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
       0.02   15.1   4.1       0.02   15.1   4.1    2.6  3  VKOR             Vitamin K epoxide reductase family
        1.6    9.1   7.1        0.7   10.3   1.1    3.1  4  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
        2.7    8.2   5.7         11    6.2   1.7    2.5  2  Tr-sialidase_C   Trans-sialidase of Trypanosoma hydrophobic C


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 !  355.8  16.9  5.9e-110  2.6e-106       1     272 []       8     283 .]       8     283 .] 0.98

  Alignments for each domain:
  == domain 1  score: 355.8 bits;  conditional E-value: 5.9e-110
                         DUF63   1 iseFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllkppls 81 
                                   i eF+++yY++pi++++gYn+vntlt+a+iL+++v+++ +ll+k+++++d+kfv+++ip++++gsslRv+eDag++++pls
  gi|91773024|ref|YP_565716.1|   8 ILEFVNRYYLEPIFQDSGYNVVNTLTWALILGICVFAVAWLLEKWNVEVDDKFVFSIIPFILAGSSLRVIEDAGVFDAPLS 88 
                                   789****************************************************************************** PP

                         DUF63  82 yllitPliyflvflitlavlliskklekk.lkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaavltalvl 161
                                   yl+itP+iyf+vf++t+++ll+s+ + ++  ++d+k  +a++G++++++++++Ll++e+++++++l++++ll +vl+  ++
  gi|91773024|ref|YP_565716.1|  89 YLFITPNIYFFVFVVTVFCLLLSRSIASSeKVSDWKVPFALLGLCWFAINIITLLVVEDITRPFILVAIVLLGTVLAGSIY 169
                                   **************************9999*************************************************** PP

                         DUF63 162 lllrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipvlyildkevkee 242
                                   l ++ + +++++d+ln++++++hllDas+tf+g+d+lgY+E+Hvvp++LidltGtalvm+plkl++++pv+yi+d+++  +
  gi|91773024|ref|YP_565716.1| 170 LAFNRAGVSFVKDPLNMMIIWSHLLDASSTFIGVDILGYYEKHVVPAYLIDLTGTALVMFPLKLAIFLPVIYIIDTQFVAD 250
                                   ****************************************************************************98766 PP

                         DUF63 243 ee...lrnlvklailvlGlaPgiRnllrmvlgv 272
                                   ee   lr++vk++i++lGl+P++Rn++rm +g+
  gi|91773024|ref|YP_565716.1| 251 EEskrLRTFVKMVIIILGLSPACRNTIRMAFGI 283
                                   66679*************************997 PP

>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.9      0.47   2.1e+03      43      43 ..      82      82 ..      23     113 .. 0.48
   2 ?   15.1   4.1   4.5e-06      0.02      42      96 ..     113     172 ..     104     178 .. 0.79
   3 ?   -2.9   0.1       1.6   7.2e+03      79      79 ..     227     227 ..     195     250 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.47
                                  H CS
                          VKOR 43 v 43
                                  v
  gi|91773024|ref|YP_565716.1| 82 V 82
                                  1 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.5e-06
                                   HHHCSTTSEETTEEHHHHHHHHHHHHHHHHHS-......HHHHHHHHHHHHHHHHHHHHH CS
                          VKOR  42 kvlnSpyasilgvplsllGllayalvlllalapl.....lwlllllgslagvvfslyLiy 96 
                                   ++++S+  s ++vp +llGl+++a+ ++++l+       + l++++++ + +++s+yL++
  gi|91773024|ref|YP_565716.1| 113 SIASSEKVSDWKVPFALLGLCWFAINIITLLVVEditrpFILVAIVLLGTVLAGSIYLAF 172
                                   556677667799****************9998889*886555555555588999999986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.6
                                   H CS
                          VKOR  79 l 79 
                                   +
  gi|91773024|ref|YP_565716.1| 227 V 227
                                   1 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 ?   -0.9   0.1      0.47   2.1e+03      53      65 ..      30      46 ..      14      52 .. 0.66
   2 ?   -1.6   0.0      0.78   3.5e+03      21      31 ..      63      73 ..      54      76 .. 0.73
   3 ?   10.3   1.1   0.00016       0.7       1      63 [.     103     166 ..     103     172 .. 0.72
   4 ?    0.6   1.7      0.17   7.5e+02      19      43 ..     149     178 ..     132     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.47
               Phage_holin_5_2 53 g....aiiqGilsggas 65
                                  +    a+i Gi + +++
  gi|91773024|ref|YP_565716.1| 30 NtltwALILGICVFAVA 46
                                  23446888888888777 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.78
               Phage_holin_5_2 21 kyIPlilgiiG 31
                                    IP+il+  +
  gi|91773024|ref|YP_565716.1| 63 SIIPFILAGSS 73
                                  68999998765 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00016
               Phage_holin_5_2   1 ivvilyiiGeilKktekvkdkyIPlilgiiGii.lgvvivfta.dfqaedilifgaiiqGilsgg 63 
                                   ++v+++++   +  +ekv+d+ +P+ l+ +  + ++++ +++  d+    il+ ++++ G + +g
  gi|91773024|ref|YP_565716.1| 103 VTVFCLLLSRSIASSEKVSDWKVPFALLGLCWFaINIITLLVVeDITRPFILV-AIVLLGTVLAG 166
                                   789**********************9998886615544444445555555554.45666766665 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.17
               Phage_holin_5_2  19 kdkyIPlilgiiGiilgvvivft.a....d 43 
                                      +I + ++++G +l+  i+++ +    +
  gi|91773024|ref|YP_565716.1| 149 TRPFILVAIVLLGTVLAGSIYLAfNragvS 178
                                   446899999999999998888775555443 PP

>> Tr-sialidase_C  Trans-sialidase of Trypanosoma hydrophobic C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.024   1.1e+02      14      23 ..      36      45 ..      36      46 .. 0.88
   2 ?    6.2   1.7    0.0025        11      15      22 ..     129     136 ..     125     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.024
                Tr-sialidase_C 14 LLLGLWGfAA 23
                                  L LG + fA 
  gi|91773024|ref|YP_565716.1| 36 LILGICVFAV 45
                                  77*******7 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0025
                Tr-sialidase_C  15 LLGLWGfA 22 
                                   LLGL++fA
  gi|91773024|ref|YP_565716.1| 129 LLGLCWFA 136
                                   9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); 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:                         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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1831.90
//
Query:       gi|91773025|ref|YP_565717.1|  [L=357]
Description: NAD(P)-dependent glycerol-1-phosphate dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-74  248.5   6.3    1.1e-73  248.0   6.3    1.2  1  Fe-ADH_2         Iron-containing alcohol dehydrogenase
      3e-27   95.4   6.2    1.5e-26   93.1   6.2    1.8  1  Fe-ADH           Iron-containing alcohol dehydrogenase
    7.7e-07   28.5   0.4    1.6e-06   27.5   0.4    1.6  1  DHQ_synthase     3-dehydroquinate synthase
     0.0088   16.0   0.0      0.019   14.9   0.0    1.5  1  Methyltransf_18  Methyltransferase domain


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 !  248.0   6.3   2.5e-77   1.1e-73       1     250 []      21     279 ..      21     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 248.0 bits;  conditional E-value: 2.5e-77
                      Fe-ADH_2   1 vigegaleklgellkelel.kkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvv 80 
                                   vig+g+++++++++++l+l +++l+v+++ tk +age v++sl++ag +ve+v   +e+a+++eve++ + + e++t+ ++
  gi|91773025|ref|YP_565717.1|  21 VIGNGVINEVRDVCTDLKLiDNALVVTGKSTKGIAGEIVQDSLQDAGQNVELV--ISESASMKEVERIRKHAIESGTKYFL 99 
                                   699**************9638******************************77..589*********************** PP

                      Fe-ADH_2  81 avGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDl 161
                                   +vG+G+ iD+ak++++ l+vp++svpTaaS+DG+ s+ as++  + +++v +a+aP+aviaD++++a+AP rlla+G+GD+
  gi|91773025|ref|YP_565717.1| 100 GVGSGKTIDVAKLAATDLEVPFISVPTAASHDGIVSSRASIKDGKTTTSV-QANAPMAVIADTEIIANAPYRLLAAGCGDI 179
                                   *****************************************988877777.****************************** PP

                      Fe-ADH_2 162 lgkytaladwklan........evseplaklsaamvqeaaeklvedkke.teal.eellea.lalsgigisrpaSGsEHli 231
                                   ++++ta+ dw+la+        e+++ la ++a+++ ++a+++  + ++ ++++ ++l+++ +a+s++g+srpaSGsEH++
  gi|91773025|ref|YP_565717.1| 180 ISNCTAVLDWQLASrlqnvqfsEYAAALASMTAQILIDSADSIKPELESsVRMVvKALVSSgVAMSIAGSSRPASGSEHMF 260
                                   **************9999988888999************999987544223333144444426****************** PP

                      Fe-ADH_2 232 SHaldmlalkqalHGeqVG 250
                                   SHald++a ++alHGeq+G
  gi|91773025|ref|YP_565717.1| 261 SHALDRVADEPALHGEQCG 279
                                   ******************9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   6.2   3.4e-30   1.5e-26       1     276 [.      17     280 ..      17     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 3.4e-30
                                   -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT CS
                        Fe-ADH   1 Ptrivfgkgaleelgellkklg.akralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalaree 80 
                                   P+++v+g+g+++e+ + + +l+ +++al+vt+k++  k  + + v++sl++ag +v++   +++  + +eve++ + a e+
  gi|91773025|ref|YP_565717.1|  17 PRNVVIGNGVINEVRDVCTDLKlIDNALVVTGKST--KGIAGEIVQDSLQDAGQNVEL--VISESASMKEVERIRKHAIES 93 
                                   899******************9789*********4..555777889999********4..57888**************** PP

                                   .--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS CS
                        Fe-ADH  81 gadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpel 161
                                   g  ++++vG G++iD+AK++a  l+                  +p+i +PT a+ +  v++ a i d ++   +s+     
  gi|91773025|ref|YP_565717.1|  94 GTKYFLGVGSGKTIDVAKLAATDLE------------------VPFISVPTAASHDGIVSSRASIKDGKT--TTSVQ--AN 152
                                   *************************..................***********************4444..55555..88 PP

                                   --SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSS.B--HHHHHHHHHHHHHHHHHH....HHHHHHHHH CS
                        Fe-ADH 162 lPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsda.laleairliaknleravadge....dleareqml 237
                                    P ++i D+e+++++P r++aa+ +D+++ +   +  + a+ l+++ ++++a+ l+    + +++ ++     le   +m+
  gi|91773025|ref|YP_565717.1| 153 APMAVIADTEIIANAPYRLLAAGCGDIISNCTAVLDWQLASRLQNVqFSEYAAALASMTAQILIDSADsikpELESSVRMV 233
                                   ********************************9988899999888757777777777777777766653434559999999 PP

                                   HHHHH.HHHHHHSS---.....HHHHHHHHHHC.CGGG..GGS-HHH CS
                        Fe-ADH 238 lastl.aglafsnaglg.....avHalahalgalfgip..hglanai 276
                                     +++ +g+a+s ag +       H+++hal    + p  hg+ +++
  gi|91773025|ref|YP_565717.1| 234 VKALVsSGVAMSIAGSSrpasgSEHMFSHALDRVADEPalHGEQCGV 280
                                   999998***99999999888889********9977888889999987 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.4   3.6e-10   1.6e-06      13     244 ..      80     311 ..      72     329 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.6e-10
                                   HHHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE- CS
                  DHQ_synthase  13 letlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafa 93 
                                   ++++e+i + ++e++   +++ + +G G   D+a ++A  +   v f+ vPt+  a  D  v  + +i   +    + a  
  gi|91773025|ref|YP_565717.1|  80 MKEVERIRKHAIESG---TKYFLGVGSGKTIDVAKLAATDLE--VPFISVPTA--ASHDGIVSSRASIKDGKTTTSVQA-N 152
                                   555566666666655...46899*************999886..********7..999**********99888888866.6 PP

                                   --SEEEEEGGGGGGS-HHHHHHHHHHHHH.HHHHT-HHHHHHHHHHHHHHHC...............TTTHHHHHHHHHHH CS
                  DHQ_synthase  94 qPkavlidlevLktLperelraGlaEviK.yalikdeelfelleenaeallk...............eeeeealeeliars 158
                                    P av++d+e+++  p r l+aG++++i  ++++ d +l ++l++ + +  +                + + +le+ ++  
  gi|91773025|ref|YP_565717.1| 153 APMAVIADTEIIANAPYRLLAAGCGDIISnCTAVLDWQLASRLQNVQFSEYAaalasmtaqilidsaDSIKPELESSVRMV 233
                                   8**************************9626889***********999888877888887777554433344444444444 PP

                                   HHHHHHHHHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT-- CS
                  DHQ_synthase 159 ievkaevveeDekekglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglp 239
                                   +++  +   +     + r +    H ++Ha++++++    lHGe   +G +l ++l          + +++ + lk +g p
  gi|91773025|ref|YP_565717.1| 234 VKALVSSGVAMSIAGSSRPASGSEHMFSHALDRVADE-PALHGEQCGVGTILMMYLH-------GGDWKKISDALKLIGAP 306
                                   444333333335557788889999***********99.9***********9998876.......23345666666666666 PP

                                   -STTT CS
                  DHQ_synthase 240 vslke 244
                                   ++ ke
  gi|91773025|ref|YP_565717.1| 307 TTAKE 311
                                   66655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.2e-06     0.019      17      60 ..      29      72 ..      22     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.2e-06
               Methyltransf_18 17 rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniek 60
                                   v D++tD  +++ +lv +gk +k ia +i + +l+ a +n+e 
  gi|91773025|ref|YP_565717.1| 29 EVRDVCTDLKLIDNALVVTGKSTKGIAGEIVQDSLQDAGQNVEL 72
                                  688**************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2291.35
//
Query:       gi|91773026|ref|YP_565718.1|  [L=150]
Description: hypothetical protein Mbur_1033 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-51  171.7   2.4    8.3e-51  171.6   2.4    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 !  171.6   2.4   4.6e-55   8.3e-51       1     140 []       7     148 ..       7     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.6 bits;  conditional E-value: 4.6e-55
                       UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheegvvaveveeapiealieskk 81 
                                   +itLig++lAkeG+eF + g+++eCe+Cklk++C++Lekg+kYr+v+vr++t heC+vh++g+++v+v++api al++skk
  gi|91773026|ref|YP_565718.1|   7 TITLIGTRLAKEGVEFFFDGDTPECEQCKLKNTCMSLEKGKKYRVVKVRNNTLHECFVHDKGAMVVDVVKAPIFALLDSKK 87 
                                   59******************************************************************************* PP

                       UPF0179  82 avegskitleseeCde.vecesyelcepeglkegekvkivevlgeiee.ckkgrslkkvel 140
                                   a+egski++++++Cde ++ e+yelc p+gl++ge++++ +v+g++e  ++ + +lkkvel
  gi|91773026|ref|YP_565718.1|  88 AIEGSKIRYQAPKCDEkLDAETYELCYPKGLRNGERCTVLKVMGTVEMeADPSITLKKVEL 148
                                   ***************989****************************988888899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 971.76
//
Query:       gi|91773027|ref|YP_565719.1|  [L=207]
Description: hypothetical protein Mbur_1034 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-70  235.8   5.8    4.1e-70  235.6   5.8    1.0  1  DUF2150   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.6   5.8   2.3e-74   4.1e-70       1     188 []      11     200 ..      11     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 235.6 bits;  conditional E-value: 2.3e-74
                       DUF2150   1 eFYteeRwqNWlnrvkeedldleedseele..aavllnlqdDvilavlkiikaveeeelskeeAleeleevreivleevee 79 
                                   eFYt+eRw+NWl +vke+ ++++e++++ +  +a++++++dD+ila+lk+i+++e+++l  ++A++ ++++r+i leeve+
  gi|91773027|ref|YP_565719.1|  11 EFYTTERWSNWLGQVKESGFEFKEEEDNSGkeGAIFVTMEDDIILACLKVIAKYENKTLPLDDAIAIIKDIRDITLEEVET 91 
                                   7**********************888888789************************************************* PP

                       DUF2150  80 ddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklpekvledl 160
                                    +e++++++esvqt+l+  faa+e+yi+g+++ke++ie+l+  a+e e++ed+++a++++aq+Ga ++dg++lpe+++edl
  gi|91773027|ref|YP_565719.1|  92 VSEDIDMMLESVQTALAGSFAACECYIAGDFDKESSIEDLIAVAIEYEEAEDIDSAITCIAQVGALILDGKSLPEAAMEDL 172
                                   ********************************************************************************* PP

                       DUF2150 161 eyglvaewldgidslaaamsssesveee 188
                                   +yglvaewldgids++aam +++ ++++
  gi|91773027|ref|YP_565719.1| 173 PYGLVAEWLDGIDSVEAAMIGADGYKQD 200
                                   ***********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1418.92
//
Query:       gi|91773028|ref|YP_565720.1|  [L=131]
Description: sirohydrochlorin cobaltochelatase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-27   96.4   0.0    1.3e-27   96.2   0.0    1.0  1  CbiX            CbiX
    0.00054   19.4   0.1    0.00063   19.1   0.1    1.1  1  CbiK            Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
      0.041   13.0   0.0      0.048   12.7   0.0    1.1  1  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   2.2e-31   1.3e-27       1     106 [.      12     124 ..      12     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 2.2e-31
                                   -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SS CS
                          CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaee 81 
                                   HGSr+p+ +e v ++a+++ +k+p + ++ gf+e + p++ eal+ ++  gv++i++vP+fl++Gvh++eDIpe+l++++e
  gi|91773028|ref|YP_565720.1|  12 HGSRLPYNKEVVSEIAATIAKKHPDYVIKAGFMENTLPTVMEALADFDGTGVTKIIAVPVFLASGVHITEDIPEILKLDPE 92 
                                   ********************************************************************************* PP

                                   SS-.......TTEEEEE---CCCSCCHHHHHH CS
                          CbiX  82 ahp.......kdveieytepLGthplvaevlk 106
                                   +++       +++ +++++pLG h+l+a+++ 
  gi|91773028|ref|YP_565720.1|  93 TNEgkitvdgNEIPVTFGKPLGHHELLADLVF 124
                                   *****************************986 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.1e-07   0.00063     144     256 ..       7     126 ..       2     131 .] 0.73

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-07
                                   EEEEE---SCHHH.HHHHHHHHHHHH.CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCS.. CS
                          CbiK 144 lvfvgHGtehesn.avyaeldkvlke.kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknDmas.. 219
                                   ++ +gHG++ + n +v +e+   + + ++   +  g +e + P+v e ++   ++g++++  +P++l  G H ++D+ +  
  gi|91773028|ref|YP_565720.1|   7 ILAIGHGSRLPYNkEVVSEIAATIAKkHPDYVIKAGFMEnTLPTVMEALADFDGTGVTKIIAVPVFLASGVHITEDIPEil 87 
                                   5669****9987625788898888772544456677777257**********************************96422 PP

                                   .SSTTSHHHHHHHTT--EEE--.--GGGSHHHHHHHHHH CS
                          CbiK 220 .deedswkealeaaGikveiil.kgLGeieeirsifikh 256
                                     + ++   +++ +G ++ +++ k LG  e ++++  ++
  gi|91773028|ref|YP_565720.1|  88 kLDPETNEGKITVDGNEIPVTFgKPLGHHELLADLVFER 126
                                   246666666777777777554326788877777776665 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.1e-06     0.048      68     123 ..      16      72 ..       6      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-06
                                   HHHHHHHHHHHHHHHHHH---EEEEEE.ESSSSSBHHHHHHHHHCTT-SEEEEEES- CS
                Ferrochelatase  68 neitrkqaealekelaergidvkvyla.mrywePsiedaleelkadgvervvvlply 123
                                   + ++++   ++++++a+++ d+ ++ + m+++ P + +al+++  +gv++++++p +
  gi|91773028|ref|YP_565720.1|  16 LPYNKEVVSEIAATIAKKHPDYVIKAGfMENTLPTVMEALADFDGTGVTKIIAVPVF 72 
                                   46899999**********9999999996799***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 893.31
//
Query:       gi|91773029|ref|YP_565721.1|  [L=454]
Description: hypothetical protein Mbur_1036 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-06   26.6   2.0    1.3e-05   25.3   2.0    1.7  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 !   25.3   2.0   7.4e-10   1.3e-05       1     163 [.     117     282 ..     117     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.4e-10
                                   EESSS-HHHHHHHHHHHHHCT..EEEEETTC.................SS-THHHHHHHHHHHHHTT-SEEEEE--HCHHH CS
                  Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvg.................ttnneiglpktlaemekkeaeyavlEvsshglg 62 
                                   +TGt+ KT+t++l+a i++++  + ++++ g                   + +i +   + e e+ + +++++E+s     
  gi|91773029|ref|YP_565721.1| 117 ITGTKAKTSTASLLADIISRKqtVLLHTSRGleywkegiatvihkglsIAPGSILMAIEIMEKERLRPDVIIFETSIG--- 194
                                   8*****************9987444555556***************99667888888888888889************... PP

                                   CTTTCCHCBESEEEE---TSTTHHHHSSHHH.HHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSST CS
                  Mur_ligase_M  63 ekrlegllkpdvavitnispdHldfhgtlen.yaeaKaelferlkeegiavinaddpyakelikklkkakvkvvtfgleke 142
                                    +  +     d++vit+++ d   ++ +  +   +aK +++e+ k+++i++i    +   + i  ++k++++++tf+ e++
  gi|91773029|ref|YP_565721.1| 195 -GTGC----ADIGVITSLELDY--RIASGTAwASDAKLQMVENAKADSILLISSNAE---KAIGSTRKKNIDTITFSDEAD 265
                                   .3334....59*******9654..33444441579*************999998888...999999************999 PP

                                   SECEEEEEEEEETTEEEEEEE CS
                  Mur_ligase_M 143 aedlraknieeksegteiell 163
                                   +  ++  n+    +g e++++
  gi|91773029|ref|YP_565721.1| 266 N--VADVNVMI--KGHEVSIH 282
                                   8..23223333..33333223 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2957.07
//
Query:       gi|91773030|ref|YP_565722.1|  [L=370]
Description: hypothetical protein Mbur_1037 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   65.9   0.1    4.4e-18   65.2   0.1    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.054   13.3   0.4      0.097   12.5   0.1    1.5  2  Tipalpha        TNF-alpha-Inducing protein of Helicobacter
      0.084   12.6   0.1       0.16   11.7   0.1    1.5  1  SHOCT           Short C-terminal domain
       0.14   12.1   0.0       0.27   11.3   0.0    1.4  1  GvpG            Gas vesicle protein G


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 !   65.2   0.1   9.9e-22   4.4e-18      17     138 ..      29     144 ..      14     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 9.9e-22
                                   EEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSEEEEEE-HHHHHTTTTHHHHH CS
                Oxidored_nitro  17 lplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpkaIgVittClteliGdDieava 97 
                                   + ++hGp GC++ + +ll     + i +++t+l+e+  vfGg ++L++ ++++ +++kpk+IgV+ tC++ +iG+ ++  +
  gi|91773030|ref|YP_565722.1|  29 VAVLHGPPGCSFKHARLLEE---DGIHVVTTALDETGFVFGGHDALVNVLHKVNEMFKPKLIGVVGTCASMIIGEEMHEPV 106
                                   789*********99999954...4569****************************************************** PP

                                   HHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT CS
                Oxidored_nitro  98 reaeeelgeipvipvstpgfggsqseGydaalealvrklvg 138
                                    ea+ +    pvi v++     + ++G  +ale+ ++  v 
  gi|91773030|ref|YP_565722.1| 107 MEADLDV---PVIEVEVHAGYRNNTKGVIIALESALDVGVI 144
                                   ***9876...9*******999999********999876555 PP

>> Tipalpha  TNF-alpha-Inducing protein of Helicobacter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.2     1e+04     136     147 ..      72      83 ..      68      85 .. 0.61
   2 ?   12.5   0.1   2.2e-05     0.097      45     114 ..     180     250 ..     164     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHH CS
                      Tipalpha 136 klilakvkeifk 147
                                     +l kv+e+fk
  gi|91773030|ref|YP_565722.1|  72 VNVLHKVNEMFK 83 
                                   456666776665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHHHHHHHHHHSTT----S---HHHHHHTHHHHHHHEEEEEEEEEEEETTT.TEEEEEEEEEE CS
                      Tipalpha  45 rarirvaihiankikeiykssqnaekkkiddeifkqitqaiaasldkevrlGeyinpnn.eevfalvrvdG 114
                                     +++va++i++ +ke  +     + kk +  +f +it ai +  ++  +  + in  n +e + l rv+ 
  gi|91773030|ref|YP_565722.1| 180 DVKYKVAQRIIELLKEGKRGLVIMNAKKETGYMFADITVAINEVAEQLGKADNIINMANiDEKLGLPRVRH 250
                                   35789**************99999999******************99999999999765378888888875 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.6e-05      0.16       6      27 ..     135     156 ..     132     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                         SHOCT   6 LkeLyarGeIteEEFeakKakL 27 
                                   L + ++ G+I++ EFe+++a L
  gi|91773030|ref|YP_565722.1| 135 LESALDVGVIDKTEFERQRALL 156
                                   6777899************988 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     6e-05      0.27      37      58 ..     132     153 ..     117     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6e-05
                          GvpG  37 LaaLqqeLdaGeIdeeeFdrrE 58 
                                   + aL+ +Ld G Id++eF+r+ 
  gi|91773030|ref|YP_565722.1| 132 IIALESALDVGVIDKTEFERQR 153
                                   679*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2107.38
//
Query:       gi|91773031|ref|YP_565723.1|  [L=264]
Description: nitrogenase iron protein subunit NifH [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-92  307.5   1.9    9.1e-92  307.3   1.9    1.0  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    3.4e-12   46.3   0.2    7.4e-12   45.2   0.2    1.6  1  ParA         NUBPL iron-transfer P-loop NTPase
    2.6e-09   37.2   0.0    7.3e-09   35.8   0.0    1.7  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-07   32.0   0.6    5.1e-07   29.8   0.1    2.1  2  AAA_31       AAA domain
      2e-06   27.3   0.3    6.7e-06   25.5   0.3    1.9  2  ArsA_ATPase  Anion-transporting ATPase
    9.6e-05   22.2   0.2     0.0002   21.1   0.1    1.7  2  AAA_24       AAA domain
     0.0009   18.3   0.1     0.0013   17.8   0.1    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0038   16.6   0.2      0.046   13.0   0.0    2.1  2  MipZ         ATPase MipZ
      0.007   16.8   0.0      0.022   15.2   0.0    1.7  2  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.015   14.9   0.4      0.036   13.7   0.0    1.9  3  SRP54        SRP54-type protein, GTPase domain
      0.022   14.5   0.2       0.18   11.5   0.2    2.2  1  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.054   13.1   0.1       0.16   11.5   0.0    1.7  2  AAA_25       AAA domain
      0.095   12.2   0.0       0.14   11.6   0.0    1.2  1  AAA_7        P-loop containing dynein motor region
       0.15   12.1   0.0       0.29   11.2   0.0    1.4  1  DUF87        Helicase HerA, central domain


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 !  307.3   1.9   7.1e-95   9.1e-92       2     265 ..       6     263 ..       5     264 .] 0.97

  Alignments for each domain:
  == domain 1  score: 307.3 bits;  conditional E-value: 7.1e-95
                     Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggvk 82 
                                   +iaiyGkGGiGks t++n++aa a+ g  v+i+GCDPk+Ds  +llggk ++t+ld+lr+++   dvk edvv++Gy+gvk
  gi|91773031|ref|YP_565723.1|   6 RIAIYGKGGIGKSSTASNVAAACADEGYTVMIIGCDPKSDSSITLLGGKRIPTILDLLRKEK---DVKEEDVVFTGYNGVK 83 
                                   89*********************************************************998...7*************** PP

                     Fer4_NifH  83 cvesGGPepGvGCaGrgvitaielleelgayd.dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaannia 162
                                   cve GGPepG+GCaGrg+i ai+ l++ +    ++D+++yDv GD+vCGGf +Pir++  +e y++tsge m lyaanni+
  gi|91773031|ref|YP_565723.1|  84 CVEVGGPEPGIGCAGRGIIVAIQTLKKISKTLnEMDLIIYDVPGDIVCGGFVAPIRKGLVKEAYVLTSGEYMPLYAANNIC 164
                                   ***************************8765537*********************************************** PP

                     Fer4_NifH 163 kgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelark 243
                                   +g+ k +      l+G+i+nsr+v++e+e+++kfa+e+gt++++++P+++iv+  e     v+e ap+s++a+ yr+la++
  gi|91773031|ref|YP_565723.1| 165 RGLAKIN----TPLSGIICNSRSVSREKEIVTKFASEIGTDLMAFIPKEQIVQDCERDGFSVMEKAPDSSIAQVYRDLAKA 241
                                   ***9876....479******************************************************************* PP

                     Fer4_NifH 244 ilenkklviPkplsedeLeell 265
                                   i++ +  v+P  l +++L el+
  gi|91773031|ref|YP_565723.1| 242 IMQRDTSVMPVALDDERLRELT 263
                                   ******************9996 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.2   5.8e-15   7.4e-12       2     245 ..       3     242 ..       2     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 5.8e-15
                          ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaD.........iyGpsiprllgveeekpeqsekkliPveakgi 73 
                                   v+k ia+  gKGG+GKS++a+n+A+a a++g++v ++  D         + G  ip++l++ +++  ++e+ ++ +  +g+
  gi|91773031|ref|YP_565723.1|   3 VQKRIAIY-GKGGIGKSSTASNVAAACADEGYTVMIIGCDpksdssitlLGGKRIPTILDLLRKEKDVKEEDVVFTGYNGV 82 
                                   56666665.9***************************88866666655445888999999888888888888999999*** PP

                          ParA  74 kvmSigfllesedeavvwrGpmks.kaikqllkdvewgelDyLiiDlPPG..tgDeqltvaqklplagaviVttpqevala 151
                                   k++ +g            rG +++ +++k++ k  + +e+D++i D+P     g     + +   +++a + t+ + + l 
  gi|91773031|ref|YP_565723.1|  83 KCVEVGGPE--PGIGCAGRGIIVAiQTLKKISK--TLNEMDLIIYDVPGDivCGGFVAPIRKG-LVKEAYVLTSGEYMPLY 158
                                   ***999754..5777778887664244555444..4589********9542224444444444.489999*********** PP

                          ParA 152 dvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepes 232
                                    ++  ++ + k+++++ G++ N   +  +          k+ ++k+a+e+g++l++ ip ++ ++++  +g ++++k+p+s
  gi|91773031|ref|YP_565723.1| 159 AANNICRGLAKINTPLSGIICNSRSVSRE----------KEIVTKFASEIGTDLMAFIPKEQIVQDCERDGFSVMEKAPDS 229
                                   ********************997666554..........4557899*************99999999999*********** PP

                          ParA 233 eaakaleeiaekv 245
                                   ++a++++++a+++
  gi|91773031|ref|YP_565723.1| 230 SIAQVYRDLAKAI 242
                                   *********9988 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 !   35.8   0.0   5.7e-12   7.3e-09       4     121 ..       9     215 ..       7     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.7e-12
                                   EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                          CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................. 54 
                                   + +kGG GK+++a n a+a a++g+ V  + +Dp + ++ +   l +++ p                              
  gi|91773031|ref|YP_565723.1|   9 IYGKGGIGKSSTASNVAAACADEGYTVMIIGCDPKSDSSIT--LLGGKRIPtildllrkekdvkeedvvftgyngvkcvev 87 
                                   679********************************766653..33333333456888888888999*************** PP

                                   .......................................................................CCHCCCHHHH CS
                                   .......................................................................xxxxxxxxxx RF
                          CbiA  55 .......................................................................dlkrllelle 64 
                                                                                                           +  + + l+
  gi|91773031|ref|YP_565723.1|  88 ggpepgigcagrgiivaiqtlkkisktlnemdliiydvpgdivcggfvapirkglvkeayvltsgeymplyAANNICRGLA 168
                                   ************999999999999999999999999999999999999999999999999999888888887778788888 PP

                                   HHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  65 algkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaea 121
                                   ++ ++      + g++ n    ++e++   ++  e+    g  ++++ip+ + v ++
  gi|91773031|ref|YP_565723.1| 169 KINTP------LSGIICNSRSVSREKEIVTKFASEI----GTDLMAFIPKEQIVQDC 215
                                   88876......7888888866665555555555444....88888888888777665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1     4e-10   5.1e-07       4      71 ..       7      71 ..       4      82 .. 0.81
   2 ?   -0.2   0.1      0.65   8.4e+02     109     126 ..     109     126 ..      99     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4e-10
                        AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknike 71
                                  Iai+  KGG+GK+ t+ n+aaa a +g+ v+++ +Dp + ++++l     ++  t++++l +ek++ke
  gi|91773031|ref|YP_565723.1|  7 IAIY-GKGGIGKSSTASNVAAACADEGYTVMIIGCDPKSDSSITLL--GGKRIPTILDLLRKEKDVKE 71
                                  5655.5**********************************999664..34445678888777766665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.65
                        AAA_31 109 ellekvkdeYDyiiiDcp 126
                                   ++++k  +e D+ii D+p
  gi|91773031|ref|YP_565723.1| 109 KKISKTLNEMDLIIYDVP 126
                                   456777788999999998 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.3   5.2e-09   6.7e-06       3      40 ..       6      43 ..       4      49 .. 0.92
   2 ?   -1.9   0.0       1.1   1.4e+03     213     244 ..     150     181 ..     146     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.2e-09
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                   i + GKGG+GK++ ++ +a+ ++++g+ v++i  DP 
  gi|91773031|ref|YP_565723.1|  6 RIAIYGKGGIGKSSTASNVAAACADEGYTVMIIGCDPK 43
                                  68899********************************5 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                   EESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                   ArsA_ATPase 213 vipEklslkEteRaikeLkkygikvdavivNk 244
                                   +  E ++l+  +  ++ L+k++     +i N 
  gi|91773031|ref|YP_565723.1| 150 TSGEYMPLYAANNICRGLAKINTPLSGIICNS 181
                                   55799999999999999999999999999997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.6e-07    0.0002       3      55 ..       5      65 ..       3     125 .. 0.82
   2 ?   -1.9   0.0       1.8   2.3e+03      22      47 ..     198     232 ..     192     249 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                        AAA_24  3 lkiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdieswedflde 55
                                  ++i+iyG+ giGK+++a++        g+++ +i ++  +  s+    +++i+++ d+l +
  gi|91773031|ref|YP_565723.1|  5 KRIAIYGKGGIGKSSTASNVaaacadeGYTVMIIGCDPkSDSSITLLGGKRIPTILDLLRK 65
                                  79************************999999**999877777777777777766555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                        AAA_24  22 l........gpkplfidtek.Glksldadkfpdie 47 
                                   +        +++ ++ d+e+ G+  ++ +   +i 
  gi|91773031|ref|YP_565723.1| 198 IgtdlmafiPKEQIVQDCERdGFSVMEKAPDSSIA 232
                                   44333344567777779998899888888877775 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 !   17.8   0.1     1e-06    0.0013      30      73 ..       5      48 ..       2      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                                  EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-------- CS
                          MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftG 73
                                  +++ + G  G Gks + +++++  +++G+ v ++  DP s  + 
  gi|91773031|ref|YP_565723.1|  5 KRIAIYGKGGIGKSSTASNVAAACADEGYTVMIIGCDPKSDSSI 48
                                  68999**********************************98764 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.6e-05     0.046       9      44 ..      12      47 ..       7      60 .. 0.87
   2 ?    1.2   0.0      0.14   1.8e+02      91     110 ..     110     128 ..     101     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                                  STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HH CS
                          MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrqrtl 44
                                  kGG Gks ta  va a +++G  v  i  d +  ++
  gi|91773031|ref|YP_565723.1| 12 KGGIGKSSTASNVAAACADEGYTVMIIGCDPKSDSS 47
                                  9*************************9999877665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                                   HHHHHHHHH-SEEEEE--SS CS
                          MipZ  91 elvadleaeldfividtPGs 110
                                   + ++++ +e+d+i+ d+PG 
  gi|91773031|ref|YP_565723.1| 110 K-ISKTLNEMDLIIYDVPGD 128
                                   3.45666899********95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-05     0.022      27      76 ..       7      63 ..       2      92 .. 0.68
   2 ?   -1.4   0.0         2   2.6e+03      52      92 ..     219     249 ..     189     263 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                        AAA_16 27 vllsGesGvGKsslvrellralekdggif.lrgkcdql.esaipy.....sa.laqal 76
                                  + ++G  G+GKss +  ++ a+++d+g++ +   cd   +s+i++     ++ ++++l
  gi|91773031|ref|YP_565723.1|  7 IAIYGKGGIGKSSTASNVA-AACADEGYTvMIIGCDPKsDSSITLlggkrIPtILDLL 63
                                  689****************.56666566654445554424555444433322233333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                        AAA_16  52 ggiflrgkcdqlesaipysalaqalareellrqlldeaesa 92 
                                   g+ +++   d++        +aq+  r +l +++ ++++s 
  gi|91773031|ref|YP_565723.1| 219 GFSVMEKAPDSS--------IAQVY-R-DLAKAIMQRDTSV 249
                                   333333333333........66666.5.6666666664444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.8e-05     0.036       3      38 ..       6      41 ..       4      78 .. 0.94
   2 ?   -3.6   0.0       5.7   7.2e+03      81      91 ..     115     125 ..     103     127 .. 0.53
   3 ?   -2.3   0.0       2.3     3e+03      20      39 ..     237     256 ..     209     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                   i++ G  G+GK +t++ +aa + +eg++v+++ +D
  gi|91773031|ref|YP_565723.1|  6 RIAIYGKGGIGKSSTASNVAAACADEGYTVMIIGCD 41
                                  68899******************************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.7
                                   HTTSSEEEEEE CS
                         SRP54  81 eekidvvlvDT 91 
                                    +++d+++ D 
  gi|91773031|ref|YP_565723.1| 115 LNEMDLIIYDV 125
                                   24567777775 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                                   HHHHHHHHTTS-EEEEEEST CS
                         SRP54  20 KLaallkkegkkvllvaaDt 39 
                                    La+ ++++ ++v+ va+D 
  gi|91773031|ref|YP_565723.1| 237 DLAKAIMQRDTSVMPVALDD 256
                                   47777777777777777775 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 ?   11.5   0.2   0.00014      0.18       1     101 [.       9     128 ..       9     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaee....lpYeaavdireli.tledvmed..lglgpngalvvale. 73 
                                   + G  G GK++  ++++  + ++g++v ++  DP +++    l  +    i +l+ +++dv+e+    +g ng  v ++e 
  gi|91773031|ref|YP_565723.1|   9 IYGKGGIGKSSTASNVAAACADEGYTVMIIGCDPKSDSsitlLGGKRIPTILDLLrKEKDVKEEdvVFTGYNG--VKCVEv 87 
                                   57999*****************************887522112334444677777345567777555555665..788888 PP

                    ATP_bind_1  74 ...............flresldwldeelekeeddyllfDtPGQ 101
                                                  +  ++l +++++l  +e d++++D+PG 
  gi|91773031|ref|YP_565723.1|  88 ggpepgigcagrgiiVAIQTLKKISKTL--NEMDLIIYDVPGD 128
                                   8999999999998877777777777777..5569999999996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.16      35      60 ..       6      32 ..       2      45 .. 0.86
   2 ?   -1.6   0.0       1.3   1.7e+03     117     142 ..     222     246 ..     199     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                        AAA_25 35 lallaGapgtGKttlaldlalava.tG 60
                                   ++++G +g GK+  a+++a+a+a +G
  gi|91773031|ref|YP_565723.1|  6 RIAIYGKGGIGKSSTASNVAAACAdEG 32
                                  6899*******************9554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                        AAA_25 117 fakdrggtlltadvdaleaaieeveg 142
                                   +++++ ++ +++++++l++ai ++ +
  gi|91773031|ref|YP_565723.1| 222 VMEKAPDSSIAQVYRDLAKAIMQR-D 246
                                   556777788999999999999884.4 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 ?   11.6   0.0   0.00011      0.14      31      75 ..       2      46 ..       1      50 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                         AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsa 75
                                  + +k + ++G+ G GK+++++++  ++ +e y++++i +  + ++
  gi|91773031|ref|YP_565723.1|  2 SVQKRIAIYGKGGIGKSSTASNVAAACADEGYTVMIIGCDPKSDS 46
                                  5689999****************************9998877766 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   0.00023      0.29      22      58 ..       3      38 ..       2      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                         DUF87 22 vtrHlAilgsTGsGKSntvavLleellekkgatilil 58
                                  v++++Ai g+ G GKS t++   +  + + g+t+ i+
  gi|91773031|ref|YP_565723.1|  3 VQKRIAIYGKGGIGKSSTASNVAAACA-DEGYTVMII 38
                                  789****************98777777.777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1463.36
//
Query:       gi|91773032|ref|YP_565724.1|  [L=489]
Description: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) / cobyrinate a,c-diamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-41  142.0   0.3    2.6e-41  141.4   0.3    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    8.4e-18   64.9   0.5    5.6e-12   45.9   0.1    2.5  2  AAA_26         AAA domain
    2.5e-17   63.1   0.0    5.2e-17   62.1   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.025   14.5   0.0    1.5  1  MobB           Molybdopterin guanine dinucleotide synthesis p
      0.016   15.1   0.0      0.048   13.5   0.0    1.8  2  SNO            SNO glutamine amidotransferase family
      0.029   14.1   0.1       0.22   11.3   0.0    2.2  2  GATase         Glutamine amidotransferase class-I
       0.03   14.0   0.0      0.049   13.3   0.0    1.3  1  Peptidase_S51  Peptidase family S51


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 !  141.4   0.3     1e-44   2.6e-41       2     191 ..     268     467 ..     267     471 .. 0.87

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1e-44
                      GATase_3   2 iavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlg 80 
                                   i+++ ++a+++y+  +l++Le ++++  +f+p++de+l++ +d ++l+Gg++++ +++l+++++++e+i++a+e+g p++g
  gi|91773032|ref|YP_565724.1| 268 IGIALDEAFNFYYhnNLELLELAGAKLEYFSPIHDERLPN-IDGLYLGGGYPELYAAELEANESMREDIRKASENGLPIYG 347
                                   899***********************************76.**************************************** PP

                      GATase_3  81 iCGGlqmLGeei.edpegveg.......eageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGrt 149
                                   +CGGl++L e+i +  +g+ g        + ++e++g L+ +  ++++++++   g+++      ++g+ + G+E+H++++
  gi|91773032|ref|YP_565724.1| 348 ECGGLMYLTERItTGVKGK-GtyhmaemPEATHEMVGALPGHSLMGHKRVVSYNIGQLDEdtviGSKGNSFIGHEFHHSEV 427
                                   ************4444555.35889885556**************************88899998899***********65 PP

                      GATase_3 150 i.lkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglf 191
                                   + l e+a+ ++k+++g++++ + dG+vk+    n+lG Y H+ +
  gi|91773032|ref|YP_565724.1| 428 TeLPEDAEFAIKLSRGTGIRdGWDGLVKN----NTLGAYAHLEA 467
                                   50445555555554466655799****88....********865 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.6e-06     0.004       3      53 ..      14      64 ..      13      86 .. 0.78
   2 !   45.9   0.1   2.2e-15   5.6e-12      94     192 ..      88     194 ..      65     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.6e-06
                        AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselike 53
                                  +++++ + ++GKT++++gL++alk +g++v+ fK    +i   + se + +
  gi|91773032|ref|YP_565724.1| 14 VLLAADRSSSGKTTITAGLLAALKTRGYNVQPFKVALDYIDPSYHSEITGR 64
                                  577788899*********************999977666665555555555 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 2.2e-15
                        AAA_26  94 elekdadivvVEGagglgvp..itee.llnadiaknlgapvilVargglgt..inqllltiealrqknvrvlGvilNkvrn 169
                                   e+  +a+i v+EG+ gl ++  ++ +  ++a+iak+l++pvil++++++ t   ++l+  ++ +   +v+++GvilN++  
  gi|91773032|ref|YP_565724.1|  88 EVDGRAEIAVIEGVRGLFEGleSIGDmGSTAQIAKMLKCPVILIINARSITrsAAALVNGYKDFDP-DVNIVGVILNNIGG 167
                                   5566899**********988553444599******************9965215555555555555.8**********644 PP

                        AAA_26 170 p....envetlekksgipvlGvvPylp 192
                                        ++ e++e+++++pvlG++P + 
  gi|91773032|ref|YP_565724.1| 168 IrhakKAKEAVEHFTKLPVLGIIPRDN 194
                                   43334699****************875 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 !   62.1   0.0     2e-20   5.2e-17       2     124 ..      15     201 ..      14     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2e-20
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                          CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                   ++a+  + +GKTt++a+L++al+ rg++V+++++  +    ++     +++++                            
  gi|91773032|ref|YP_565724.1|  15 LLAADRSSSGKTTITAGLLAALKTRGYNVQPFKVALDYIDPSYHSEITGRRARnldgylmgedgvldvfahacevdgraei 95 
                                   56788899*************************9999777776344444444468899999999***************** PP

                                   .....................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHH CS
                                   .....................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....................................dlkrllellealgkkkall...lkiagvvlnrvdgeneetllke 95 
                                                                        ++ ++ ++++al+++++++   ++i+gv+ln ++g ++ ++ ke
  gi|91773032|ref|YP_565724.1|  96 aviegvrglfeglesigdmgstaqiakmlkcpviliiNARSITRSAAALVNGYKDFdpdVNIVGVILNNIGGIRHAKKAKE 176
                                   ********************************************************************************* PP

                                   HHHHHHHHCTS-EEEEEE--CCHCCCCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  96 aleelkqrygvpvlgviprdeavaeapar 124
                                   a+e      ++pvlg+iprd a  ++ +r
  gi|91773032|ref|YP_565724.1| 177 AVEHFT---KLPVLGIIPRDNAM-QISMR 201
                                   ****98...**********9986.55555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.6e-06     0.025       4      38 ..      17      51 ..      14      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.6e-06
                          MobB  4 ivgksgsGKTtLleklipelkarglrvgtiKhahh 38
                                   + +s sGKTt+   l+++lk rg++v   K a +
  gi|91773032|ref|YP_565724.1| 17 AADRSSSGKTTITAGLLAALKTRGYNVQPFKVALD 51
                                  45689**********************98887655 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.9e-05     0.048      28      86 ..     302     360 ..     284     368 .. 0.81
   2 ?   -3.0   0.0       2.2   5.6e+03     152     172 ..     407     428 ..     396     434 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                   GGGGCC-SEEEE-SS-HHHH.HHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEET CS
                           SNO  28 kedlaevdaliiPGGestam.skliertglyedllefvknsekvvlGtCaGlillskele 86 
                                    e l ++d+l + GG      + l  +  + ed+++  +n+ ++++G C Gl++l+++++
  gi|91773032|ref|YP_565724.1| 302 DERLPNIDGLYLGGGYPELYaAELEANESMREDIRKASENG-LPIYGECGGLMYLTERIT 360
                                   68899**********77654145566666778888877777.*************99886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                                   TEEEEEEETTEEEESS-.GGGS CS
                           SNO 152 geivvakqkkilatsfh.Pela 172
                                     +++ k + +++  fh  e++
  gi|91773032|ref|YP_565724.1| 407 DTVIGSKGNSFIGHEFHhSEVT 428
                                   3789999999999999724554 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.29   7.4e+02      42      77 ..     156     189 ..     130     190 .. 0.78
   2 ?   11.3   0.0   8.4e-05      0.22      39     144 ..     304     436 ..     279     447 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.29
                                   STSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEE CS
                        GATase  42 npdgilvsgGpgspgvegkieaikearenkiPiLGI 77 
                                   n+ g+++ +  g + ++++ ea++++ +  +P+LGI
  gi|91773032|ref|YP_565724.1| 156 NIVGVILNNIGGIRHAKKAKEAVEHFTK--LPVLGI 189
                                   6667777777788888888888888766..*****9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.4e-05
                                   THHSTSEEEEEEESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE................EEEC CS
                        GATase  39 llknpdgilvsgGpgspg......vegkieaikearenkiPiLGICLGmQllaiefgrkvv................keke 97 
                                    l n+dg+ + gG  + +       e + e i++a en++Pi G C G+  l++ ++  v                     
  gi|91773032|ref|YP_565724.1| 304 RLPNIDGLYLGGGYPELYaaeleaNESMREDIRKASENGLPIYGECGGLMYLTERITTGVKgkgtyhmaempeatheM--- 381
                                   36799********988888998888999999************************99977744444444443332210... PP

                                   EEEEEEEEEEEETTT...........CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEE CS
                        GATase  98 kehhggtmrlgddet...........allyglknevierhrHryevnpkelepaglev 144
                                    + + g + +g+++             ++  ++n++i    H  ev++   +p++ e+
  gi|91773032|ref|YP_565724.1| 382 VGALPGHSLMGHKRVvsynigqldedTVIGSKGNSFIGHEFHHSEVTE---LPEDAEF 436
                                   222222222222222444455555555555566666666666666666...6666665 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.049      77     136 ..     302     362 ..     273     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                   HHHHHHSSEEEE--S-HHHHHHHHHHTT.HHHHHHHHHHTT-EEEEETHHHHTTSSB-GGG CS
                 Peptidase_S51  77 eeklleadviyvgGGntfrLlkllketg.ldkllreavqqglvyiGvSAGaivagesiett 136
                                   +e+l + d++y+gGG     +++l+ ++ + + +r+a ++gl++ G   G +  +e i+t 
  gi|91773032|ref|YP_565724.1| 302 DERLPNIDGLYLGGGYPELYAAELEANEsMREDIRKASENGLPIYGECGGLMYLTERITTG 362
                                   458899*********998888888776527899*******************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2865.66
//
Query:       gi|91773033|ref|YP_565725.1|  [L=351]
Description: tRNA splicing endonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-50  169.0   0.1    5.2e-25   87.3   0.0    2.3  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    4.5e-44  148.0   2.0    3.5e-22   77.8   0.0    2.4  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
    0.00045   20.3   0.0       0.37   11.0   0.0    2.4  2  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t
  ------ inclusion threshold ------
      0.024   14.9   0.0       0.14   12.4   0.0    2.2  2  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 !   79.5   0.0   3.2e-26   1.5e-22       1      85 []      75     158 ..      75     158 .. 0.98
   2 !   87.3   0.0   1.2e-28   5.2e-25       1      83 [.     257     341 ..     257     343 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 3.2e-26
                                   HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETT CS
                 tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY..qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivda 79 
                                   f+lky+vy+dLre+G++v++G    +dFrvY  +++p+++ ++ +++v se+++++++dl++++  a++v+K+++laivd+
  gi|91773033|ref|YP_565725.1|  75 FELKYIVYKDLRERGFYVQPG---VTDFRVYprGSHPGKGAAKQFIYVRSERAPMPLRDLLRSLAAAENVRKQMVLAIVDE 152
                                   89*******************...78******************************************************* PP

                                   TSCEEE CS
                 tRNA_int_endo  80 egdvty 85 
                                   e d+t+
  gi|91773033|ref|YP_565725.1| 153 ESDITF 158
                                   ****96 PP

  == domain 2  score: 87.3 bits;  conditional E-value: 1.2e-28
                                   HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEET CS
                 tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivd 78 
                                   f lk  vy+dLr+kG+v+++G+kFG++FrvY   ++  +  hseyl++ ++ d+e+++p +s+a+rla+sv+K++++ai  
  gi|91773033|ref|YP_565725.1| 257 FNLKSSVYTDLRDKGVVPKTGFKFGSHFRVYsqvESPTKIPHSEYLIHSIPMDHEFTLPVMSRAIRLANSVRKRMLYAILT 337
                                   78999***************************9999999****************************************97 PP

                                   TTSCE CS
                 tRNA_int_endo  79 aegdv 83 
                                   ++g v
  gi|91773033|ref|YP_565725.1| 338 DDG-V 341
                                   766.5 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 !   69.3   0.5   3.6e-23   1.6e-19       1      67 []       1      65 [.       1      65 [. 0.97
   2 !   77.8   0.0   7.8e-26   3.5e-22       2      66 ..     181     246 ..     180     247 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 3.6e-23
                                  EEEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
               tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                                  +++e+++drvlve+ +a++++y++g+YG+  + + L+L+l+EA+YL+ +Gk+ev+++g++l+f +l+
  gi|91773033|ref|YP_565725.1|  1 MRAEIVKDRVLVEK-KAINEFYNNGYYGR-PKSSGLELTLIEAVYLAFRGKIEVEHEGKVLEFSDLF 65
                                  899**********6.**************.8********************************9996 PP

  == domain 2  score: 77.8 bits;  conditional E-value: 7.8e-26
                                   EEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHH CS
               tRNA_int_endo_N   2 egeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kggeplsfeel 66 
                                   ++++++drv+v+deea+k+l+e+gfYGkpl+ ++LqLslvE+ YLlekG+l++  +++e+++++ +
  gi|91773033|ref|YP_565725.1| 181 DATFLEDRVVVWDEEASKTLFENGFYGKPLDSQRLQLSLVESRYLLEKGVLNINnRQDESMDVDAF 246
                                   6899**********************************************************9987 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 !   11.0   0.0   8.2e-05      0.37      26      70 ..       9      52 ..       5      54 .. 0.85
   2 !    7.0   0.0    0.0014       6.5      22      70 ..     185     233 ..     135     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.2e-05
               tRNA_int_end_N2 26 vvvvespkarGkhfktmGvsra.rrgrlwLlpeEaLYLvErGsldi 70
                                  +v ve  k+  + f + G+  + +++ l+L+  Ea+YL+ rG++++
  gi|91773033|ref|YP_565725.1|  9 RVLVE--KKAINEFYNNGYYGRpKSSGLELTLIEAVYLAFRGKIEV 52
                                  67777..4477788888988888*******************9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0014
               tRNA_int_end_N2  22 prdrvvvvespkarGkhfktmGvs.ra.rrgrlwLlpeEaLYLvErGsldi 70 
                                    +drvvv +++ a+ ++f++ G   +   ++rl L   E  YL+E G l i
  gi|91773033|ref|YP_565725.1| 185 LEDRVVVWDEE-ASKTLFEN-GFYgKPlDSQRLQLSLVESRYLLEKGVLNI 233
                                   56777777755.55555555.433244699*****************9987 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.2e-05      0.14      56      91 ..     128     162 ..      97     168 .. 0.83
   2 ?   -1.1   0.0      0.52   2.3e+03      48      83 ..     309     340 ..     285     341 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                         Sen15  56 ldkvfkelkeekserkkrivLaivddDsTvvYYkvt 91 
                                   l++++++l   + +  k++vLaivd++s + +Y v+
  gi|91773033|ref|YP_565725.1| 128 LRDLLRSLAAAE-NVRKQMVLAIVDEESDITFYDVK 162
                                   666777776655.4699****************986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.52
                         Sen15  48 teklslekldkvfkelkeekserkkrivLaivddDs 83 
                                   +++++l  ++  ++      ++  kr++ ai+ dD+
  gi|91773033|ref|YP_565725.1| 309 DHEFTLPVMSRAIRLA----NSVRKRMLYAILTDDG 340
                                   4444444444444432....3357999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2183.24
//
Query:       gi|91773034|ref|YP_565726.1|  [L=234]
Description: Ala-tRNA(Pro) hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-15   55.5   0.0    4.9e-15   55.1   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)
    5.2e-14   52.1   0.9      8e-14   51.5   0.2    1.7  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   5.5e-19   4.9e-15     470     552 .]       9      90 ..       2      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 5.5e-19
                                   XXXSEEEEEEEEE.ETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEX CS
                  tRNA-synt_2c 470 lkdkefveeveeg.eevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevd 549
                                    ++kef+++v  + ++ +vvL+rT+fY+ sGGq  D+G++ ++ +e  v+ v k++g + h+++   + lk gdkvk+++d
  gi|91773034|ref|YP_565726.1|   9 SQMKEFEANVLDVtDDRFVVLNRTAFYPSSGGQPHDTGKLVCDRKEYPVTFVGKFDGKISHEVSE--AGLKAGDKVKGTID 87 
                                   567899999988615678*******************************************9987..59************ PP

                                   HHH CS
                  tRNA-synt_2c 550 eer 552
                                   ++r
  gi|91773034|ref|YP_565726.1|  88 WDR 90 
                                   986 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.81   7.3e+03      32      43 ..     117     128 ..     108     128 .. 0.83
   2 !   51.5   0.2   8.9e-18     8e-14       1      44 []     187     230 ..     187     230 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.81
                                   CCECCCTCEEEE CS
                      tRNA_SAD  32 seesiakglrRI 43 
                                   s+++ia+  +R+
  gi|91773034|ref|YP_565726.1| 117 SGNQIAEEKTRV 128
                                   799999988886 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 8.9e-18
                                   EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                      tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                   +rv++i d++ ++CgGtHv nTgeI ++ i + e+++k++rRIy
  gi|91773034|ref|YP_565726.1| 187 IRVIRIPDVDDQACGGTHVANTGEIPHIEIFKAENKGKNNRRIY 230
                                   7******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1557.87
//
Query:       gi|91773035|ref|YP_565727.1|  [L=365]
Description: cytochrome c assembly protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-32  110.5  23.5    9.2e-32  110.5  23.5    2.5  3  Cytochrom_C_asm  Cytochrome C assembly protein


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3     0.051   9.1e+02     115     138 ..      34      57 ..       7      64 .. 0.59
   2 !  110.5  23.5   5.1e-36   9.2e-32       1     208 [.      87     311 ..      87     315 .. 0.87
   3 ?   -3.5   0.0       0.4   7.1e+03      89      96 ..     331     338 ..     321     353 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.051
               Cytochrom_C_asm 115 lkllkqldrlsyriiliGfvllti 138
                                   + + kq++ ++  +++++++llt+
  gi|91773035|ref|YP_565727.1|  34 ISRSKQFELWCSVLTTFAIMLLTY 57 
                                   444455555555555555555554 PP

  == domain 2  score: 110.5 bits;  conditional E-value: 5.1e-36
               Cytochrom_C_asm   1 lsnleesllllawilsllgllley..larklnlsllaavaliaalillgfalf...........................l 52 
                                   +   e+s+ll+ w  +++ l++ y  +++++ + +l +++  + l++++f+l+                           +
  gi|91773035|ref|YP_565727.1|  87 WAGQEGSFLLWTWFTLMILLFIRYtgNTKEIADTKLMNITRAVCLTIVAFFLLllvlknpfetyyavfggaietsnwnpfV 167
                                   667799*******99999999966114555556666666665555555555556*************************99 PP

               Cytochrom_C_asm  53 llaelqesadlnpalqspilmiHvplallsYatliigallsialliierqlkkkkklklsanlkllkqldrlsyriiliGf 133
                                    +  l++++ +np+l++p++++H+p+++l+Ya+++i +++++a l                 l   +++ +l++ ++ +++
  gi|91773035|ref|YP_565727.1| 168 TVYHLIDGQGMNPLLRNPWMAVHPPILFLGYAAFTIPFATAFASL-----------------LIDDERWIKLTRNWMRLAW 231
                                   9999*****************************************.................6667889999********* PP

               Cytochrom_C_asm 134 vlltigiilGsvWa..eeaWGsy.wsWDpketaslitWlvfaallhsri..ekgwrgkkaailailgflllllayfgvrl 208
                                   ++lt+gi lG +Wa   ++WG + wsWDp+et+sli+W++++a lhs     +g     a +lai+ f+l+++a+f+ r+
  gi|91773035|ref|YP_565727.1| 232 LFLTAGIGLGGFWAyeVLGWGAWyWSWDPVETSSLIPWITATAFLHSATrvRDGEYRFLAPMLAIVSFILVIFATFVTRS 311
                                   **************8778999866***********************987444666667788***************998 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.4
               Cytochrom_C_asm  89 gallsial 96 
                                   +++l+i+ 
  gi|91773035|ref|YP_565727.1| 331 AFFLAILV 338
                                   33333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2039.03
//
Query:       gi|91773036|ref|YP_565728.1|  [L=163]
Description: rubrerythrin [Methanococcoides burtonii DSM 6242]
Scores for 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-25   87.6   7.1    9.7e-24   84.3   7.1    2.0  1  Rubrerythrin     Rubrerythrin
    1.9e-05   24.6   3.9    5.8e-05   23.1   3.2    2.1  2  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.019   15.0   0.5      0.028   14.4   0.5    1.3  1  DZR              Double zinc ribbon
       0.12   12.2   0.0       0.15   11.9   0.0    1.2  1  RB_A             Retinoblastoma-associated protein A domain
       0.13   11.8   1.6        0.3   10.7   1.6    1.5  1  RecR             RecR protein
        1.4    9.0   3.4        6.7    6.8   0.3    2.3  2  zf-C2H2_6        C2H2-type zinc finger
        2.9    7.6   7.2       0.14   11.8   1.4    1.8  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal 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 !   84.3   7.1   3.8e-27   9.7e-24       1     136 [.       5     119 ..       5     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 3.8e-27
                                   HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGG CS
                  Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflt 80 
                                   e+L++A+agEs+a r Y ++a+ a+ eg++q+a+lF++ A++E  Ha+ + ++l+ ++ ++e                   
  gi|91773036|ref|YP_565728.1|   5 ENLNEAFAGESMANRKYLAFAKMADkEGFGQVAKLFRAAAAAETVHAHAHLRVLGGVKSTEE------------------- 66 
                                   89******************************************************999999................... PP

                                   HHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  81 taknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                      nL+eai g++ e  emy+ + e+aekegn++a ++f+ + + E+ H+ ++ k+
  gi|91773036|ref|YP_565728.1|  67 ---NLQEAISGETLEFNEMYPAFIEEAEKEGNKQAVRSFDMANQVEQIHAGLYTKA 119
                                   ...***********************************************999886 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   3.2   2.3e-08   5.8e-05       1      50 [.       4      53 ..       4     111 .. 0.88
   2 ?   -1.5   0.0      0.82   2.1e+03       5      28 ..      95     118 ..      91     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.3e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  1 ikaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadk 50
                                  i+ Lne++a e  a  +yla+a +++ +g+ ++a++f+  a  e+ ha++
  gi|91773036|ref|YP_565728.1|  4 IENLNEAFAGESMANRKYLAFAKMADKEGFGQVAKLFRAAAAAETVHAHA 53
                                  689*********************************************86 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.82
                                   HHHHHHHHHHHHHHHHHHHHHHST CS
                      Ferritin   5 neqladeltaayqylamawyvkgp 28 
                                   n+q  + ++ a+q  ++++ +   
  gi|91773036|ref|YP_565728.1|  95 NKQAVRSFDMANQVEQIHAGLYTK 118
                                   778888888888888888755555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   1.1e-05     0.028      11      39 ..     130     157 ..     124     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                           DZR  11 darfCseCgtklkavaaedrCpsCgekvd 39 
                                   d  +C+ Cg++++  +a++rCp C++  +
  gi|91773036|ref|YP_565728.1| 130 DYYVCDICGNTVE-GEAPERCPICEAVHS 157
                                   6679********7.688*******98755 PP

>> RB_A  Retinoblastoma-associated protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.7e-05      0.15      32      98 ..      61     128 ..      33     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                          RB_A  32 fksctedpteeiekrvkelsekflkkyaesseee.essslaeelakkrlklaekLYykvLesilksEk 98 
                                   +ks +e+ +e i  +  e++e+  +  +e+++e  +++  + ++a++  +    LY k Le+i ++E+
  gi|91773036|ref|YP_565728.1|  61 VKSTEENLQEAISGETLEFNEMYPAFIEEAEKEGnKQAVRSFDMANQVEQIHAGLYTKALENIGSNEE 128
                                   789999999999999999999988833333332236889999*********************99887 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   0.00012       0.3      19      35 ..     134     153 ..     130     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                   -TTT--EESSS...S-CCCC CS
                          RecR  19 CsrCgnlteed...lCaICs 35 
                                   C +Cgn  e +    C+IC 
  gi|91773036|ref|YP_565728.1| 134 CDICGNTVEGEapeRCPICE 153
                                   *******99986557****6 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 ?    6.8   0.3    0.0026       6.7       1      10 [.     131     140 ..     131     140 .. 0.88
   2 ?    2.8   0.2     0.047   1.2e+02       3      15 ..     148     160 ..     148     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0026
                     zf-C2H2_6   1 vheCsvCsks 10 
                                   +++C++C+++
  gi|91773036|ref|YP_565728.1| 131 YYVCDICGNT 140
                                   79*****985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.047
                     zf-C2H2_6   3 eCsvCsksFpslq 15 
                                   +C++C ++ +++q
  gi|91773036|ref|YP_565728.1| 148 RCPICEAVHSKFQ 160
                                   7*****9977766 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4   5.4e-05      0.14       2      17 ..     127     142 ..     126     143 .. 0.89
   2 ?   -3.3   0.4       2.9   7.5e+03       8      12 ..     148     152 ..     148     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                                   -TT-EEE-TTT--EEE CS
               Desulfoferrod_N   2 eklevYkCevCGniVe 17 
                                   e+ + Y C +CGn Ve
  gi|91773036|ref|YP_565728.1| 127 EEVDYYVCDICGNTVE 142
                                   57899*********97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                                   E-TTT CS
               Desulfoferrod_N   8 kCevC 12 
                                   +C +C
  gi|91773036|ref|YP_565728.1| 148 RCPIC 152
                                   89999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 968.90
//
Query:       gi|91773037|ref|YP_565729.1|  [L=255]
Description: hypothetical protein Mbur_1046 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.57    9.9  12.0       0.71    9.6   2.2    3.6  3  DUF3188   Protein of unknown function (DUF3188)
        1.1    7.9  11.7       0.24   10.0   8.3    1.7  1  EMP70     Endomembrane protein 70


Domain annotation for each model (and alignments):
>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.2   7.9e-05      0.71       6      38 ..      30      61 ..      28      65 .. 0.93
   2 ?    6.7   0.3   0.00067         6       3      41 ..      60     100 ..      60     105 .. 0.81
   3 ?   -0.8   0.4      0.14   1.2e+03      26      37 ..     201     209 ..     189     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 7.9e-05
                       DUF3188  6 illgllillysqrqgsdrlqslPallvGlgLiv 38
                                  ill + ++++ ++q+  r+++l +++ Gl++++
  gi|91773037|ref|YP_565729.1| 30 ILLTMFVMIVTKSQSDLRIYAL-VMTLGLFILF 61
                                  899999****************.*******986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00067
                       DUF3188   3 plLillglli.llysqrqgsdr.lqslPallvGlgLivsga 41 
                                   ++L+ ++ ++ +++ +r +  + l+++P+l  G++ +++ +
  gi|91773037|ref|YP_565729.1|  60 LFLVPIATIGqNIVKNRRDIRKvLYYIPLLICGMFHTIIVI 100
                                   7999999998456999999999***********99666555 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.14
                       DUF3188  26 slPallvGlgLi 37 
                                   +   + +GlgLi
  gi|91773037|ref|YP_565729.1| 201 A---VQMGLGLI 209
                                   3...37888887 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   8.3   2.7e-05      0.24     338     397 ..      20      79 ..       5     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.7e-05
                         EMP70 338 lllpgllflvffllnlilwakessgalpfgtlvlllllwflisvPlvliGsllgfkkkai 397
                                   +++  + ++v++l  +++++ +s++ l +  lv+ l l++l  vP+  iG  + ++++ i
  gi|91773037|ref|YP_565729.1|  20 FFMAHIWVTVILLTMFVMIVTKSQSDLRIYALVMTLGLFILFLVPIATIGQNIVKNRRDI 79 
                                   333445566666677788899******************************999995433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); 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:                         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: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1445.61
//
Query:       gi|91773038|ref|YP_565730.1|  [L=370]
Description: Fe3+-hydroxamate binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   89.5   0.0    3.2e-25   89.1   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.19   11.3   0.0    1.2  1  MCD           Malonyl-CoA decarboxylase 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 !   89.1   0.0   3.6e-29   3.2e-25      39     234 ..      92     299 ..      54     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 3.6e-29
                                   ........TS-BS.BESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS...HHHHHHHHHHHHHT CS
                  Peripla_BP_2  39 e.......aivev.gadgeidvEklaalkPDlvilskglgltdedeellksgiptvivessntg...eslkeqiralgell 108
                                   +       + + +  ++g+ d Ek++ ++PD+++  + ++  d+de + k  ip+v+ +++n g   ++ + ++r  g + 
  gi|91773038|ref|YP_565730.1|  92 AianpqfqNLPLIgEHRGNTDPEKIVGVDPDVIFWTYVQSAKDADELQAKTEIPVVALNYGNLGvyrDDMYQSLRIMGNVM 172
                                   3444445433443045666777****************************************99***************** PP

                                   T-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-H CS
                  Peripla_BP_2 109 gledeaeklvaeidsklaaaksaidse...kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisa 186
                                   +++++ae+++ +++  + +++++++     +pk v v g a++g++ + ++ +   + ++ + ++n+a++  +   +++s 
  gi|91773038|ref|YP_565730.1| 173 DKNKRAEEVIGFFEMNIGNLENRTKDTandDPKNVYVGGIAYSGPHGFQSTEPTYPP-FEFISANNVASSL-GTTHADVSK 251
                                   ***********************9988855555555556566655555555555555.5559********9.********* PP

                                   HHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                  Peripla_BP_2 187 EqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyal 234
                                   E+i ++d+d++fv+ +  + +    ++lk++p++ +l Avkng+Vy++
  gi|91773038|ref|YP_565730.1| 252 EAIIEWDADILFVDLSTLMTTPSAIDELKSDPAYTSLSAVKNGNVYGI 299
                                   **********************************************97 PP

>> MCD  Malonyl-CoA decarboxylase C-terminal domain
   #    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      17      59 ..      62     104 ..      53     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                                   HHHHHHH--TT--SSHHHHHHCCSTTEEEEEEEBTTCTTSESE CS
                           MCD  17 leklikyEavHeirdwedlkrRldsdRrcfaffHpalpdePli 59 
                                   l  +   Ea  +i ++ed+  R++++Rr +a   p++++ Pli
  gi|91773038|ref|YP_565730.1|  62 LRYICYLEAQDAIVGVEDVELRINENRRPYAIANPQFQNLPLI 104
                                   5667778999********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 2130.08
//
Query:       gi|91773039|ref|YP_565731.1|  [L=336]
Description: ABC Fe3+-siderophore transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-92  307.4  29.6    1.1e-91  307.1  29.6    1.0  1  FecCD            FecCD transport family
    1.4e-06   28.0  13.6    3.4e-06   26.7  13.2    1.8  1  ABC-3            ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.1  29.6   1.2e-95   1.1e-91       1     312 []      10     332 ..      10     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 307.1 bits;  conditional E-value: 1.2e-95
                         FecCD   1 llllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGiss 81 
                                   ll+lll++s+++ga++i +++v+ +l+g ++ ++++i++++rlpr+l+a+++G++L+v+G+ lQ+++rNpL +P++lGis+
  gi|91773039|ref|YP_565731.1|  10 LLFLLLIYSIAVGATNIAFTDVILSLFGYGQGSASTIIWNIRLPRALVAIVAGVGLSVSGVALQSILRNPLGSPYTLGISH 90 
                                   68899**************************************************************************** PP

                         FecCD  82 gaalgavlallll............lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsl 150
                                   ++a+ga++++++l            +   + + +++++f ++l+a++ ++++a k +++sp+ +iL+G+a+++l++a t++
  gi|91773039|ref|YP_565731.1|  91 ACAFGAAFSVIVLgsgtmrstgadaIMLNNPYMTTAVSFCFSLIATFTLIAIA-KYRNSSPEVMILTGVALASLFTAGTMF 170
                                   ***********99*********999888899999*******************.*************************** PP

                         FecCD 151 lllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvall 231
                                   l++++++ +l++++fw++G++++a+w+++ +l++l++ +++++++++ +++++  gdetAk lGvnve+vrl+ +l+++l+
  gi|91773039|ref|YP_565731.1| 171 LQYFADDVQLAAVVFWTFGDVGRADWNDLTILFILTVPAVFYFFMNRWNYNAIDAGDETAKGLGVNVEKVRLWGMLVASLV 251
                                   ********************************************************************************* PP

                         FecCD 232 tavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                   ta +v++ G+igFvGL+ Ph+ar++vg++ r llp+s+l+Gallll ad++arl+l+p elpv i+ta++Gap+f+yll+r
  gi|91773039|ref|YP_565731.1| 252 TAFIVSFLGVIGFVGLVCPHMARRFVGDEQRFLLPASCLTGALLLLGADTAARLMLAPHELPVAILTAFMGAPLFLYLLIR 332
                                   *******************************************************************************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 !   26.7  13.2   3.8e-10   3.4e-06      49     248 ..     115     318 ..      58     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.8e-10
                         ABC-3  49 ayllgvn..lllgailvgliaavalellkrktklkedtai..givlsvflalglvlvslikk..skvdldsyLfGniltis 123
                                   a++l+ +   ++ +++++lia+++l ++++    + +++i  g+ l++ +  g +++++  +    + +  + fG++   +
  gi|91773039|ref|YP_565731.1| 115 AIMLNNPymTTAVSFCFSLIATFTLIAIAKYRNSSPEVMIltGVALASLFTAGTMFLQYFADdvQLAAVVFWTFGDVGRAD 195
                                   56677774344556899***********99888888875444*****************996644455666779******* PP

                         ABC-3 124 qedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatAr 204
                                    +dl +++i+++  + ++++ + +  +i    e+Ak  g++v+ ++l  +++ +l  + ++ + Gvi  + l + P  +Ar
  gi|91773039|ref|YP_565731.1| 196 WNDLTILFILTVPAVFYFFMNRWNYNAIDAGDETAKGLGVNVEKVRLWGMLVASLVTAFIVSFLGVIGFVGL-VCP-HMAR 274
                                   *******************************************************************99886.567.5799 PP

                         ABC-3 205 rltrslesllivAillglvsvvaGlllSyyldlatGavivlvat 248
                                   r++ + ++ l+ A+ l    +++G+ + + l la+  + v+++t
  gi|91773039|ref|YP_565731.1| 275 RFVGDEQRFLLPASCLTGALLLLGADTAARLMLAPHELPVAILT 318
                                   99999999999999999999999999988888887777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2157.51
//
Query:       gi|91773040|ref|YP_565732.1|  [L=250]
Description: ABC cobalamin/Fe3+-siderophores transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-34  119.5   0.0      2e-34  119.0   0.0    1.2  1  ABC_tran      ABC transporter
    8.3e-10   39.0   0.0    0.00056   19.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.5e-05   25.6   0.2      4e-05   24.2   0.0    1.7  2  AAA_23        AAA domain
    3.3e-05   23.9   0.0    6.1e-05   23.0   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
    6.8e-05   22.4   0.1       0.19   11.2   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00018   21.2   0.0    0.00043   20.0   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
    0.00021   21.6   1.3      0.005   17.1   1.3    2.1  1  AAA_22        AAA domain
     0.0004   19.3   0.1        1.1    8.0   0.0    3.0  2  ABC_ATPase    Predicted ATPase of the ABC class
    0.00054   19.2   0.4     0.0057   15.9   0.4    2.0  1  NB-ARC        NB-ARC domain
    0.00077   19.9   0.1     0.0012   19.3   0.1    1.5  1  AAA_16        AAA ATPase domain
      0.006   16.3   0.1        0.1   12.3   0.0    2.0  2  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.8   0.0        0.2   11.7   0.0    2.2  2  AAA_14        AAA domain
      0.011   15.5   0.1      0.028   14.2   0.1    1.7  1  AAA_30        AAA domain
      0.012   15.1   0.4        4.1    6.8   0.7    2.2  2  TniB          Bacterial TniB protein
      0.016   14.6   0.4       0.03   13.8   0.4    1.4  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
      0.016   14.6   0.1      0.053   12.9   0.0    1.8  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.018   14.9   0.0      0.039   13.9   0.0    1.5  1  Rad17         Rad17 P-loop domain
      0.038   13.9   0.8        2.1    8.2   0.8    2.4  1  NTPase_1      NTPase
      0.062   13.2   0.0       0.11   12.4   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
      0.074   12.8   0.0       0.12   12.1   0.0    1.3  1  AAA_24        AAA domain
      0.088   12.7   0.4       0.49   10.3   0.0    2.0  2  NACHT         NACHT domain
       0.12   12.0   0.0       0.24   11.0   0.0    1.5  1  AAA_27        AAA domain
       0.12   12.1   0.1       0.27   11.1   0.1    1.5  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
       0.13   12.6   0.0       0.24   11.7   0.0    1.4  1  YozD          YozD-like protein
       0.18   12.1   0.0        1.7    8.9   0.0    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.19   12.1   0.7          3    8.2   0.7    2.2  1  AAA_19        AAA domain
       0.19   10.3   0.0        7.9    5.0   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 !  119.0   0.0     3e-37     2e-34       1     137 []      17     163 ..      17     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 3e-37
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l++++++lk+g+++ai+G+nG GKStLl+++   + p+ G+i +dg+++   e+++  k++g++pq  +   +lt+++   
  gi|91773040|ref|YP_565732.1|  17 LNQIHFELKPGKILAILGPNGVGKSTLLRCINAIHPPKTGTIIVDGEEVLALEKHEIAKRVGYVPQR-SEAGQLTAYDAil 96 
                                   789****************************************************************.5555666888899 PP

                                   .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                ++++ +e +++klgl+el+ +++    +++SgG+ qrva+aral+++pkllllDEpt+
  gi|91773040|ref|YP_565732.1|  97 lgrkphigwnvgeKDRRVVESVIKKLGLEELALRHI----NEMSGGELQRVAIARALVQEPKLLLLDEPTS 163
                                   ***********9555555******************....*****************************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 !   19.8   0.0   8.4e-07   0.00056       2      22 ..      30      50 ..      29      86 .. 0.77
   2 !   17.4   0.0   4.5e-06     0.003     234     299 ..     132     195 ..     104     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.4e-07
                        AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                   ++ GpNg+GKS+LL+++  +
  gi|91773040|ref|YP_565732.1| 30 LAILGPNGVGKSTLLRCINAI 50
                                  589***************655 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.5e-06
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                   ++e+S G ++  a++ al + +   +lll+DEp ++L+ k + ++l+ +++  + n++  ++t H+ 
  gi|91773040|ref|YP_565732.1| 132 INEMSGGELQRVAIARALVQEP---KLLLLDEPTSSLDLKKQLEILRTVRQVVEnNKVSAVITMHDL 195
                                   6788999999988888888888...9*************9998888887444443566667776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     6e-08     4e-05      13      41 ..      20      49 ..       9      54 .. 0.79
   2 ?   -1.5   0.1       4.4   2.9e+03     149     174 ..     158     183 ..     108     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6e-08
                        AAA_23 13 qeidFsk.gltlItGpNGaGKTTildAikl 41
                                   ++++++ ++ +I GpNG GK+T+l++i  
  gi|91773040|ref|YP_565732.1| 20 IHFELKPgKILAILGPNGVGKSTLLRCINA 49
                                  34555664799*****************86 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.4
                        AAA_23 149 kdkkerleelekeleeledekkllek 174
                                    d++    +l+k+le l ++++ +e+
  gi|91773040|ref|YP_565732.1| 158 LDEPTSSLDLKKQLEILRTVRQVVEN 183
                                   34444555677777777777766665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   9.2e-08   6.1e-05      82     123 ..       9      61 ..       2     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.2e-08
                                   --TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT..........- CS
                   RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe..........l 123
                                    s +++e l++++ +lk  k+ +++G+ GvGKStL+  ++            +
  gi|91773040|ref|YP_565732.1|   9 FSYNNREILNQIHFELKPgKILAILGPNGVGKSTLLRCINAIhppktgtiivD 61 
                                   567888999********99****************877766522244555550 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00028      0.19      25      44 ..      28      47 ..      10      51 .. 0.77
   2 !    9.5   0.0   0.00088      0.59     134     196 ..     132     191 ..      57     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                                  SEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                  ++ ai+GpNG GKs ll  i
  gi|91773040|ref|YP_565732.1| 28 KILAILGPNGVGKSTLLRCI 47
                                  4789***********99877 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00088
                                   TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEE.EEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                         SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQf.ivis 196
                                   ++++SgGe + va+a       v+   l llDe  + LD k+  ++ + +++  +n  +  vi+
  gi|91773040|ref|YP_565732.1| 132 INEMSGGELQRVAIARA----LVQEPKLLLLDEPTSSLDLKKQLEILRTVRQVVENNKVsAVIT 191
                                   459*****998887654....45667799**************999999998776644323444 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 !   20.0   0.0   6.5e-07   0.00043      13      48 ..      18      53 ..       9      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-07
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                  ++  +e+++  +  + Gp+G+GKSTll  i+a+  p
  gi|91773040|ref|YP_565732.1| 18 NQIHFELKPGKILAILGPNGVGKSTLLRCINAIHPP 53
                                  4545778877799**************888877555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.3   7.5e-06     0.005       5     126 ..      27     189 ..      23     201 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.5e-06
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..................................erpevv....fvtl 47 
                                    +il++ G+ G+GK+tllr +   ++      +                                   ++ ++    ++  
  gi|91773040|ref|YP_565732.1|  27 GKILAILGPNGVGKSTLLRCINAIHPPKTG--TiivdgeevlalekheiakrvgyvpqrseagqltaYDAILLgrkpHIGW 105
                                   689********************9974333..2558888888887777777777777776666665433333355555666 PP

                        AAA_22  48 psstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsr 120
                                   +++++ + + + + ++lgle  a      e+    l++ + ara    ++ll++DE    l+   + e+l+++r+ ++   
  gi|91773040|ref|YP_565732.1| 106 NVGEKDRRVVESVIKKLGLEELA-LRHINEMSgGELQRVAIARALvqePKLLLLDEPTSsLDlkkQLEILRTVRQVVE--N 183
                                   66666677777777777777777.444444444666666666666677779999998888865433555555555555..5 PP

                        AAA_22 121 kgvqli 126
                                    +v+ +
  gi|91773040|ref|YP_565732.1| 184 NKVSAV 189
                                   555554 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 !    8.0   0.0    0.0016       1.1     244     265 ..      26      48 ..      22      86 .. 0.86
   2 !    6.5   0.0    0.0046         3     323     412 ..     135     209 ..     130     221 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                   SS.EEEEEE-TTSSHHHHHHHHH CS
                    ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAle 265
                                    G + +I G++  GKsTLL+ ++
  gi|91773040|ref|YP_565732.1|  26 PGkILAILGPNGVGKSTLLRCIN 48 
                                   55599**************9886 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0046
                                   --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTT CS
                    ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyld 403
                                    SG   q ++i++al  + kllL+DE ts   l        +l          ++  vr++++++ vs ++ +  ++  l+
  gi|91773040|ref|YP_565732.1| 135 MSGGELQRVAIARALVQEPKLLLLDEPTSSLDLKK------QLE---------ILRTVRQVVENNKVSAVITMHDLNLALR 200
                                   58888888999999999999999999998765422......221.........4455666666666666666666666666 PP

                                   T-SEEEEEE CS
                    ABC_ATPase 404 vAdtvilme 412
                                    Ad+ i ++
  gi|91773040|ref|YP_565732.1| 201 FADNYIFLK 209
                                   666666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   8.6e-06    0.0057      17     115 ..      25     164 ..      11     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.6e-06
                                   TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC..CBTEEEEE...................................... CS
                        NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdeveg..rFdsvawv...................................... 57 
                                   +++  ++a+ G  GvGK+tl++ i+  +   +g    d+   +                                      
  gi|91773040|ref|YP_565732.1|  25 KPG-KILAILGPNGVGKSTLLRCINAIHPPKTGtiIVDGEEVLalekheiakrvgyvpqrseagqltaydaillgrkphig 104
                                   455.69******************998887777222343333377999999999999999999999999999999999776 PP

                                   .EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEEEE-SH CS
                        NB-ARC  58 .vvsktdkseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlDDVwee 115
                                     v+++   ++++e+++k+L+l+e  l + +e          + r+L +   ll+lD    +
  gi|91773040|ref|YP_565732.1| 105 wNVGEK--DRRVVESVIKKLGLEELALRHINEMSGgelQRVAIARALVQEPKLLLLDEPTSS 164
                                   666655..468999999999999988888887766776778999999999999999975554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.8e-06    0.0012      25      61 ..      28      65 ..      14     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-06
                        AAA_16 25 elvllsGesGvGKsslvrellralekd..ggiflrgkcd 61
                                   ++ + G+ GvGKs+l+r++   +     g i + g+ +
  gi|91773040|ref|YP_565732.1| 28 KILAILGPNGVGKSTLLRCINA-IHPPktGTIIVDGEEV 65
                                  799*****************95.5544122333444333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00015       0.1      19      47 ..      22      51 ..      11      78 .. 0.73
   2 ?    2.1   0.0      0.19   1.3e+02     323     365 ..     152     194 ..     142     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                        AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFl 47
                                   +l++  +  + G+N++GKS++l+ ++ + 
  gi|91773040|ref|YP_565732.1| 22 FELKPGkILAILGPNGVGKSTLLRCINAIH 51
                                  3444446999**************998765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.19
                        AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   ++++ll++EP  +L  + q ++ ++ + ++++nk   +it H 
  gi|91773040|ref|YP_565732.1| 152 EPKLLLLDEPTSSLDLKKQLEILRTVRQVVENNKVSAVITMHD 194
                                   6799*****************************9988888886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0003       0.2       2      23 ..      27      48 ..      26      86 .. 0.74
   2 ?    2.1   0.0      0.28   1.9e+02      56      87 ..     144     175 ..     110     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                        AAA_14  2 rkilvitGaRrvGKTtllkqli 23
                                  +kil+i G+  vGK+tll+ + 
  gi|91773040|ref|YP_565732.1| 27 GKILAILGPNGVGKSTLLRCIN 48
                                  589**************97654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.28
                        AAA_14  56 ilek.lkeekktylflDEiqevpewekalkslv 87 
                                     ++ l  ++ ++l+lDE   + +++k l  l 
  gi|91773040|ref|YP_565732.1| 144 AIARaLV-QEPKLLLLDEPTSSLDLKKQLEILR 175
                                   3333233.478999****999866666665444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.2e-05     0.028      18     114 ..      27     179 ..      19     189 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                        AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g...........grviglAptgkaAkvLa.....eelgieastiakllkrlk 81 
                                    ++ ++ Gp G GK+t+l+ +++++  + g                   +++ Ak+++      e+g  ++  a ll r  
  gi|91773040|ref|YP_565732.1|  27 GKILAILGPNGVGKSTLLRCINAIHPPKtGtiivdgeevlaL------EKHEIAKRVGyvpqrSEAGQLTAYDAILLGRKP 101
                                   568899*******************99944555543222220......233444445433333222222222222222222 PP

                        AAA_30  82 ............................................grarlepgtllivDE.agmvdtkqlaallkaaek 114
                                                                               +ra +++ +ll+ DE ++ +d k+  ++l+ +++
  gi|91773040|ref|YP_565732.1| 102 higwnvgekdrrvvesvikklgleelalrhinemsggelqrvaiARALVQEPKLLLLDEpTSSLDLKKQLEILRTVRQ 179
                                   333333333333333334444455666666666666777777765555666677777775566677777777776665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0093       6.2      37      64 ..      29      56 ..      15     125 .. 0.70
   2 ?    6.8   0.7    0.0061       4.1      91     159 ..     124     190 ..     107     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0093
                          TniB 37 nlllvGdsnnGKtmivekFarlhppekd 64
                                   l ++G+  +GK+++++   + hpp++ 
  gi|91773040|ref|YP_565732.1| 29 ILAILGPNGVGKSTLLRCINAIHPPKTG 56
                                  5789***************999999864 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0061
                          TniB  91 LealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                   Le+l  ++ ++ +  +l++ +++     ++++L++DE  + l    +kq e+l ++++  ++ k++ v+
  gi|91773040|ref|YP_565732.1| 124 LEELALRHINEMSGGELQRVAIARALVQEPKLLLLDEPTSSL--DLKKQLEILRTVRQVVENNKVSAVI 190
                                   566666666666777777777777777899**********99..899***************9999885 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   4.5e-05      0.03      41     111 ..     144     214 ..     119     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                        HSM3_N  41 dakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidslvvaackvi 111
                                    + r l++  +ll+ ++++++ld +  le+l  + +v++ + v +v +++dl  al+   + +     kv 
  gi|91773040|ref|YP_565732.1| 144 AIARALVQEPKLLLLDEPTSSLDLKKQLEILRTVRQVVENNKVSAVITMHDLNLALRFADNYIFLKDGKVF 214
                                   66788888889999999***************************************987777766666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-05     0.053      25      69 ..      30      74 ..      25     102 .. 0.82
   2 ?   -1.1   0.0       1.6     1e+03     119     136 ..     170     187 ..     135     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                  Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkee 69
                                  l ++Gp G GK+ l ++++++ pp + + +++ +++ ++ +++ +
  gi|91773040|ref|YP_565732.1| 30 LAILGPNGVGKSTLLRCINAIHPPKTGTIIVDGEEVLALEKHEIA 74
                                  6689*********************99999999998888875444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                  Mg_chelatase 119 krkvlevLRePledgevt 136
                                   + ++l ++R+ +e+++v+
  gi|91773040|ref|YP_565732.1| 170 QLEILRTVRQVVENNKVS 187
                                   234677778888888876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.9e-05     0.039      34      72 ..      16      54 ..      12      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-05
                         Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelgik 72
                                   l+    e ++ +iL i GP G gkst ++ +  ++ +k
  gi|91773040|ref|YP_565732.1| 16 ILNQIHFELKPGKILAILGPNGVGKSTLLRCINAIHPPK 54
                                  5666677889999*****************999888776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.8    0.0032       2.1       3      21 ..      31      49 ..      29     227 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0032
                                  EEE--TTSSHHHHHHHHHH CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvle 21
                                  +i Gp GvGK+Tl++ +  
  gi|91773040|ref|YP_565732.1| 31 AILGPNGVGKSTLLRCINA 49
                                  5779999999999875543 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.11      16      40 ..      23      47 ..      13      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                      ATPase_2 16 erepneiyfiYGpegsGKtaLlkei 40
                                  e +p +i+ i Gp g+GK++Ll+ i
  gi|91773040|ref|YP_565732.1| 23 ELKPGKILAILGPNGVGKSTLLRCI 47
                                  678999****************965 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   0.00018      0.12       5      33 ..      30      64 ..      27      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                        AAA_24  5 iliyGpsgiGKTtlakel......gpkplfidtek 33
                                  ++i Gp+g+GK+tl++ +      +  ++++d e+
  gi|91773040|ref|YP_565732.1| 30 LAILGPNGVGKSTLLRCInaihppKTGTIIVDGEE 64
                                  79**************9999997666678888877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00074      0.49       3      20 ..      30      47 ..      28      50 .. 0.88
   2 ?    0.3   0.1       0.9     6e+02     112     151 ..     144     181 ..     123     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00074
                                  EEEEC-TTTCHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkl 20
                                  +++ G++G+GK+tLl+ +
  gi|91773040|ref|YP_565732.1| 30 LAILGPNGVGKSTLLRCI 47
                                  789************976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.9
                                   HHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--T CS
                         NACHT 112 lirkkllpeasllltvrpralrdleeqleeaivlevegfs 151
                                    i ++l++e +lll   p+++ dl++qle      v+  +
  gi|91773040|ref|YP_565732.1| 144 AIARALVQEPKLLLLDEPTSSLDLKKQLEIL--RTVRQVV 181
                                   4677788888888888888888888888876..4444444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036      0.24      18      48 ..      19      49 ..      16      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisd 48
                                  +++f+ +  ++  i+GpN  GKst+lr i++
  gi|91773040|ref|YP_565732.1| 19 QIHFELKPGKILAILGPNGVGKSTLLRCINA 49
                                  5777778888999**************9975 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 ?   11.1   0.1    0.0004      0.27      26      55 ..     162     191 ..     157     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                          NOG1  26 ecgysleeQlsLleeikelfankpvivvln 55 
                                   ++  +l++Ql++l+++++ ++n++v  v++
  gi|91773040|ref|YP_565732.1| 162 TSSLDLKKQLEILRTVRQVVENNKVSAVIT 191
                                   67789******************9999986 PP

>> YozD  YozD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.24       6      36 ..      58      89 ..      54      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                          YozD  6 vviDtEEiAeFFykELvkR.GyvPaeeEleel 36
                                  +++D EE+ +   +E++kR GyvP+ +E  +l
  gi|91773040|ref|YP_565732.1| 58 IIVDGEEVLALEKHEIAKRvGYVPQRSEAGQL 89
                                  799***************99*******98776 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0026       1.7      28      89 ..     130     178 ..     112     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0026
                       SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   r+++++SGGe q    +a+a a   l++        ++l++LDE  s+lD +++ ++l++++
  gi|91773040|ref|YP_565732.1| 130 RHINEMSGGELQR---VAIARA---LVQ-------EPKLLLLDEPTSSLDLKKQLEILRTVR 178
                                   6677777777743...344422...233.......4899***********999888887765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.7    0.0045         3       9      34 ..      26      51 ..      18     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0045
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhivall 34
                                  + k+l+++++ G GK+++l++i a+ 
  gi|91773040|ref|YP_565732.1| 26 PGKILAILGPNGVGKSTLLRCINAIH 51
                                  578899999**********9998764 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.012       7.9      17      39 ..      28      50 ..      17      75 .. 0.83
   2 ?    3.3   0.0     0.038        25     524     564 ..     150     189 ..     139     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                        AAA_13 17 riNliYGwNGaGKTtLSrllrsl 39
                                  +i  i G NG GK+tL r ++ +
  gi|91773040|ref|YP_565732.1| 28 KILAILGPNGVGKSTLLRCINAI 50
                                  556799**********9999876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.038
                        AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQl 564
                                   +++ k   +D P SSLD + +  +   +++++ +++k++ +
  gi|91773040|ref|YP_565732.1| 150 VQEPKLLLLDEPTSSLDLKKQLEILRTVRQVV-ENNKVSAV 189
                                   56888999*************99999999998.66665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1503.32
//
Query:       gi|91773041|ref|YP_565733.1|  [L=191]
Description: hypothetical protein Mbur_1050 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-16   58.2   0.0    1.2e-15   57.8   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
       0.04   13.7   0.0      0.057   13.2   0.0    1.5  1  DUF447         Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   1.4e-19   1.2e-15       4     138 ..      12     146 ..       8     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.4e-19
                                   S-EE-EEEEE.EETTEEEEEEESSEEEEETTT.TEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCC CS
                 Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldP.plvafslrlpsstadalkeagefvinllsesqealadafsqksgprtd 83 
                                   ++ pva+++t  + +  + a+ s  t++ l P   v+++   +++t+d+++++gefvin+ + + ++ +   s++ +  ++
  gi|91773041|ref|YP_565733.1|  12 FPLPVALISTVSNNGVLNVAPWSNITPI-LRPlEEVVMASWIKRDTLDNIRDTGEFVINIPPVEMSEKVMISSKNFP-ADV 90 
                                   789*******777888889********9.89987777777789********************99999999999887.*** PP

                                   CCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTT CS
                 Flavin_Reduct  84 dksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgdd 138
                                   d+++ +gl++++s   ++p ++g+la+ eC  ++++ ++   l+ig+Vv+ +v+d 
  gi|91773041|ref|YP_565733.1|  91 DEFKEVGLSPRRSsMIAPPGVEGCLAWAECSFIEEIAMDRFSLIIGKVVNLEVDDR 146
                                   ************977788*********************************99985 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.4e-06     0.057       4      53 ..      18      72 ..      17     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-06
                                  EEEEE-TT.-EEEEEEEEEE....SSSEEEEEEETTSHHHHHHHHHSEEEEEE-- CS
                        DUF447  4 ivtTksek.rpnaaPiGviv....kgdkvvlrlfkgsrTleNllengelvinvtd 53
                                  +++T s++ + n+aP   i+      ++vv++ + +  Tl+N++ +ge+vin+  
  gi|91773041|ref|YP_565733.1| 18 LISTVSNNgVLNVAPWSNITpilrPLEEVVMASWIKRDTLDNIRDTGEFVINIPP 72
                                  6788898999999997655555558899************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1503.88
//
Query:       gi|91773042|ref|YP_565734.1|  [L=175]
Description: hypothetical protein Mbur_1051 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  169.2   2.4    9.5e-50  169.0   2.4    1.0  1  CarS-like     CDP-archaeol synthase
    4.7e-07   29.9   4.7    4.7e-07   29.9   4.7    2.0  2  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   2.4   1.1e-53   9.5e-50      12     175 .]       1     175 []       1     175 [] 0.89

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 1.1e-53
                     CarS-like  12 llpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqg.lleklsi...laldssgs.vlef 87 
                                   +lpay++n +a l+GGG+p+d Gkt+ dGrr++GdG+tyrG+ +G++ G l gl+q  llek+ +     l ++g+   ++
  gi|91773042|ref|YP_565734.1|   1 MLPAYLPNPFAALFGGGRPIDNGKTMSDGRRILGDGKTYRGFFVGLIFGALAGLMQMqLLEKYPVlfgVELPTFGTgGSNT 81 
                                   8*******************************************************7256776653224455555514678 PP

                     CarS-like  88 vilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp......vkllpieliilivlitlvlhlsan 162
                                    il + la+G+l+Gd+  sf krr++++rG p +++dqldfvlgal++ay          +++++i++i++it++lhl++n
  gi|91773042|ref|YP_565734.1|  82 TILIFALAVGSLFGDMFMSFFKRRMGLKRGAPLPVIDQLDFVLGALIFAYLaspvwfAEQFTFKVIAVILIITPLLHLATN 162
                                   8999*********************************************765556545789******************** PP

                     CarS-like 163 iiayklglkdvwy 175
                                   ++ y +g+k+ ++
  gi|91773042|ref|YP_565734.1| 163 VVGYFIGVKKEPW 175
                                   *********9887 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   4.7   5.2e-11   4.7e-07     170     233 ..      36     109 ..      33     133 .. 0.85
   2 ?    1.5   1.5     0.023   2.1e+02      59     150 ..     126     164 ..     109     173 .. 0.51

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.2e-11
                                   --BHHHHHHHHHHHHHHHHHHHHHHHCTS..........---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-S CS
                  CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal..........alsllhllllslllslvavfGDLveSglKRafgiK 233
                                   +KT  Gf+ Gl++ +++gl+ +++l+k+            +    + +l + l++ + fGD+++S +KR++g K
  gi|91773042|ref|YP_565734.1|  36 GKTYRGFFVGLIFGALAGLMQMQLLEKYPvlfgvelptfGTGGSNTTILIFALAVGSLFGDMFMSFFKRRMGLK 109
                                   6**************************99******99987777788888899999*****************99 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.023
                                   .HHHHHHHHHHTTTSSSHHHHHHHHHHHHHHHHHH---...HHHHHHHHHHHHHHHHHTHHHH.TTHHHHHHHHHHHHHHH CS
                  CTP_transf_1  59 slvlllllllflylesliallklvlllvlvllllvlkvlkskskklervilallallyvvlllqslllienikeglllvll 139
                                    l++++l+  ++++e+++ ++ +v+l++  ll l+++                                            
  gi|91773042|ref|YP_565734.1| 126 ALIFAYLASPVWFAEQFTFKVIAVILIITPLLHLATN-------------------------------------------- 162
                                   3444444444444444444444444444444444443............................................ PP

                                   HHHHHHHHHHH CS
                  CTP_transf_1 140 llalvvaaDig 150
                                            ++
  gi|91773042|ref|YP_565734.1| 163 ---------VV 164
                                   .........33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1351.08
//
Query:       gi|91773043|ref|YP_565735.1|  [L=182]
Description: orotate phosphoribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   51.5   1.6    9.8e-14   51.2   1.6    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0032   16.9   0.2     0.0063   16.0   0.2    1.4  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   1.6   1.1e-17   9.8e-14       6     133 ..      43     159 ..      38     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.1e-17
                                   TT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----T CS
                  Pribosyltran   6 lenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpa 86 
                                    +np +l+ +a+ aa+ +++    +d++ g+a gGvp+a++++ e ++pl  +rk  ++ ++++ ++            ++
  gi|91773043|ref|YP_565735.1|  43 SSNPSTLKLIAKQAASMIKK--IDIDLIGGVALGGVPIATAVSLETGLPLLLIRKATKDYGTGGRFV---------GDATK 112
                                   579999**************..********************************************5.........6889* PP

                                   TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHH CS
                  Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeev 133
                                   + ++++ +D+ ++Gg++++a+ +++e+g+ + +++++vd+ +++ e 
  gi|91773043|ref|YP_565735.1| 113 DDRIILLEDVTTSGGSVIEAIGAIREAGCIIEKVITVVDREDGATEN 159
                                   *****************************999999999999987765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2     7e-07    0.0063     120     161 ..     112     151 ..     105     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7e-07
                       UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvla 161
                                   ++++++ll+ v  +Ggs+++ai  ++e+g+  ek++  +v+ 
  gi|91773043|ref|YP_565735.1| 112 KDDRIILLEDVTTSGGSVIEAIGAIREAGCIIEKVI--TVVD 151
                                   7899*************************9999876..4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1316.12
//
Query:       gi|91773044|ref|YP_565736.1|  [L=539]
Description: hydroxylamine reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-165  551.2   0.0   2.5e-165  551.1   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 !  551.1   0.0  1.4e-169  2.5e-165       1     511 []       1     535 [.       1     535 [. 0.96

  Alignments for each domain:
  == domain 1  score: 551.1 bits;  conditional E-value: 1.4e-169
                                   -EE-SST....CT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHC......HHHHHHHHHCHTSTTTB-SH CS
                                   xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                      Prismane   1 mfCrqCe....ngpCritknkrGvCGkdadtavardlliavlkgaaahaaharel......adtliakalfktltnvnfdd 71 
                                   mfC+qCe    +++C+ +    GvCGk+ ++a+++d li+vlk +a ++++ar++      +d+++++alf+t+tn++f+ 
  gi|91773044|ref|YP_565736.1|   1 MFCYQCEetmnGEGCTKN----GVCGKKGEVADLQDDLIYVLKSVAFYNQKARKAdiseesTDDFMLDALFSTITNTDFRA 77 
                                   9********9999*****....*********************************************************** PP

                                   HHHHHHHHHHHCHHHCC...............SSHHHHH.HHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHH..HHHHCH CS
                                   xxxxxxxxxxxxxxxxx...............xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                      Prismane  72 ekklkrlaealgieeel...............kdieela.akvaevaledlskeenedirslkellpkglkgl..yaehai 134
                                   + + +r+ + ++i+ e+                +i+++  +++++ + + l++e nedirsl+el+++g+kg+  y +ha+
  gi|91773044|ref|YP_565736.1|  78 TGIQDRIDRGFEIQGEIkqklldnnaldenelPEIATVSpENLKDRNTGILATE-NEDIRSLRELIIFGIKGIaaYGHHAM 157
                                   ***************99*********9997663333333255667777777755.9************************* PP

                                   HTT-HHHHHHHHHHHCCCCTTSTHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 135 vlgyadeevveflaktlaglesdpld...llskalrlGlldlkgmelldeantslfGtPeppltevnlgvldkdkvnIlvs 212
                                   vlg+++++v+ f+++ l+++++d+l+   l+s++l++G+  +++m+lld+ants+fG+Pep  t+vn+g++  + ++Ilvs
  gi|91773044|ref|YP_565736.1| 158 VLGHTNKKVNSFIEEGLVATTDDTLTdkkLISLVLKCGEKGFDVMALLDAANTSTFGNPEP--TQVNIGTR-GN-PGILVS 234
                                   ***********************9999**********************************..********.66.****** PP

                                   SS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 213 GHdladleelleqtegkglnvythgemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvae 293
                                   GHdl dl++ll+qt+g+g++vythgemLp++ ++++k ky+hlvgn+G +w+++k+ef++++++i+++ nCi+pp+++   
  gi|91773044|ref|YP_565736.1| 235 GHDLNDLKQLLDQTKGTGVDVYTHGEMLPANSYPEFK-KYEHLVGNYGGSWWHQKKEFESFNGPILMTSNCIIPPKDT--- 311
                                   *************************************.*************************************766... PP

                                   CHCCEEEEECTTB-TTSEEE--CTTCHHHHHHHHHHHHCCHCCTTCGG.-.................HHHHHTTSS-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxx RF
                      Prismane 294 kyktrlittsevakpgakhieeeekadkdaseiiekAielakareekkve.................idaiksGtIkgvvl 357
                                    y +r++tt++v++ g+ h+   ++ +kd+s+iie+A++++++ + ++ +                 +da+k+G+Ik++++
  gi|91773044|ref|YP_565736.1| 312 -YLDRIYTTGSVGFDGVVHLT-GNDGQKDFSAIIEQAKKCEPPVQLEEGTimggfaynsvlsvadkiVDAVKAGKIKKFIV 390
                                   .*******************9.78889*****************99666689***************************** PP

                                   E-B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHCEESEEEEESCCCHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 358 vvGCdnakkgrdyytelakelikrdvlvltaGCakyalnklglgtieaaelagegiPrvLdvGsCvdnyrivvialklaea 438
                                   ++GCd+++k r+yyt++a++l ++d+++ltaGCaky++nkl+lg+i       +giPrvLd+G+C+d+ ++v ia+ l   
  gi|91773044|ref|YP_565736.1| 391 MAGCDGRRKDRQYYTDFAEAL-PKDTVILTAGCAKYRYNKLNLGDI-------DGIPRVLDAGQCNDSFSLVIIAQGLMAR 463
                                   *********************.************************.......59************************** PP

                                   TTS.SGGGSSEEEEECC--SHHHHHHHHHHHHTT-.CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEECHCHHH CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 439 lgv.dindLplaalalewyeqKAvailltllalGi.nihlgptlpafgspnvlkvlvedfedriggivtveedpe 511
                                   lg  d+n+ p+ +++++wyeqKA+++ll+ll++Gi +i lgp+lpaf+spnvl+vlve+f  +i + +tveed+e
  gi|91773044|ref|YP_565736.1| 464 LGFtDVNEAPI-SYNIAWYEQKAIIVLLALLRMGIqDITLGPKLPAFVSPNVLNVLVEKF--NITPNTTVEEDME 535
                                   **66*******.************************************************..***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3454.46
//
Query:       gi|91773045|ref|YP_565737.1|  [L=104]
Description: cupin family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-13   49.4   0.0    3.4e-13   49.1   0.0    1.2  1  Cupin_2       Cupin domain
    0.00062   19.7   0.0    0.00076   19.4   0.0    1.1  1  AraC_binding  AraC-like ligand binding domain
     0.0063   16.9   0.0     0.0078   16.6   0.0    1.2  1  Pirin_C       Pirin C-terminal cupin domain
     0.0078   15.8   0.0     0.0098   15.5   0.0    1.2  1  Cupin_1       Cupin
  ------ inclusion threshold ------
       0.02   14.4   0.0       0.02   14.4   0.0    1.1  1  PCO_ADO       PCO_ADO
      0.055   13.4   0.0      0.067   13.1   0.0    1.2  1  Cupin_7       ChrR Cupin-like domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   1.1e-16   3.4e-13       3      70 ..      34     100 ..      32     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.1e-16
                                   EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                    el+pGe  + h  p +  +fyVleGeg + +++ee  ++++ ++  p+g pH +rN++++ +r+lvv
  gi|91773045|ref|YP_565737.1|  34 LELKPGEALKLHKTPMN-VLFYVLEGEGIVVIGDEEESVSRDMLIESPKGIPHLLRNESEGLFRFLVV 100
                                   789**************.***********************************************998 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.5e-07   0.00076      16      73 ..      42      99 ..      29     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.5e-07
                                  EEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEE CS
                  AraC_binding 16 fpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrw 73
                                   + h  +  v+ yv+eG+g++ +++++  ++ + l+  p+g pH ++ +se  +++ +
  gi|91773045|ref|YP_565737.1| 42 LKLHKTPMNVLFYVLEGEGIVVIGDEEESVSRDMLIESPKGIPHLLRNESEGLFRFLV 99
                                  566777788999**************************************96555555 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.6e-06    0.0078       2      59 ..      32      90 ..      31     101 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                                  EEEEE-TT-EEEEE--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-SSSEEEEE-- CS
                       Pirin_C  2 ldltleagaelelplpegleaavyvleGel..evggerseieeeqlavlgdgdslvvkae 59
                                  ++l+l++g+ l+l  +  ++++ yvleGe+   +g+e+++++ + l+   +g    ++ e
  gi|91773045|ref|YP_565737.1| 32 VHLELKPGEALKLH-KTPMNVLFYVLEGEGivVIGDEEESVSRDMLIESPKGIPHLLRNE 90
                                  899***********.99***********96335566665665554443335555555555 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.3e-06    0.0098      30     113 ..      26     100 ..       9     104 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.3e-06
                                   SSTEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEE CS
                       Cupin_1  30 tlgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavai 110
                                   t++  ++ + l+pg  l +h +   + ++yvl+Geg    vv g    d++  +++  ++  P+g++h   n   e ++ +
  gi|91773045|ref|YP_565737.1|  26 TEQTQVVHLELKPGEALKLHKT-PMNVLFYVLEGEGI---VVIG----DEEESVSRDMLIESPKGIPHLLRNES-EGLFRF 97 
                                   6667778888888888999999.8899*********9...4444....356789999***************96.777777 PP

                                   EEE CS
                       Cupin_1 111 vvf 113
                                    v+
  gi|91773045|ref|YP_565737.1|  98 LVV 100
                                   666 PP

>> PCO_ADO  PCO_ADO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.6e-06      0.02      23      82 ..       8      66 ..       1      93 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                       PCO_ADO 23 aaakskskppvtyltlyetdsfslgvFvlppgaviPLHdHPgMtvlskllyGslhiksyd 82
                                  +a +++++++v   +ly+t++ +++   l+pg+ + LH  P M+vl  +l G+  +   d
  gi|91773045|ref|YP_565737.1|  8 KAPEKENSHNVIAKELYDTEQTQVVHLELKPGEALKLHKTP-MNVLFYVLEGEGIVVIGD 66
                                  5667788999999*************************998.9****9*99986555555 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.2e-05     0.067      16      79 ..      24      88 ..       9     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                                  EEESSSS-EEEEEEEE-TTEE---EE-TT-EEEEEEEEE....EEETTEEEETTEEEEE-TT-EE--E CS
                       Cupin_7 16 erdgeekaratslvryapgsafsahkHpggeeilVLeGv....fsdeegdypaGsylrnppgsshapv 79
                                   ++  e ++++  ++++pg+a++ hk p  + ++VLeG+      dee+   +   + +p+g  h + 
  gi|91773045|ref|YP_565737.1| 24 YDT--E-QTQVVHLELKPGEALKLHKTPMNVLFYVLEGEgivvIGDEEESVSRDMLIESPKGIPHLLR 88
                                  322..2.3355556789*********************632225677777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 675.26
//
Query:       gi|91773046|ref|YP_565738.1|  [L=117]
Description: hypothetical protein Mbur_1055 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 925.65
//
Query:       gi|91773047|ref|YP_565739.1|  [L=432]
Description: phosphoribosylamine--glycine ligase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-56  189.1   0.0    1.3e-55  188.2   0.0    1.5  1  GARS_A         Phosphoribosylglycinamide synthetase, ATP-gras
    1.6e-24   86.5   0.4    3.2e-24   85.5   0.4    1.5  1  GARS_N         Phosphoribosylglycinamide synthetase, N domain
    1.5e-14   54.0   0.2    2.1e-13   50.3   0.1    2.3  2  GARS_C         Phosphoribosylglycinamide synthetase, C domain
      0.005   16.5   0.0      0.012   15.2   0.0    1.7  1  ATP-grasp_4    ATP-grasp domain
  ------ inclusion threshold ------
      0.024   14.7   0.0      0.053   13.6   0.0    1.7  1  ATP-grasp_3    ATP-grasp domain
      0.065   12.7   0.0       0.14   11.7   0.0    1.5  2  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind
      0.078   12.2   0.0          1    8.5   0.0    2.1  2  ATPgrasp_ST    Sugar-transfer associated ATP-grasp
       0.11   12.5   0.0       0.17   11.9   0.0    1.3  1  CoA_binding_3  CoA-binding domain
       0.12   11.8   0.0       0.25   10.7   0.0    1.5  1  GSH-S_ATP      Prokaryotic glutathione synthetase, ATP-grasp 


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 !  188.2   0.0   6.7e-59   1.3e-55       2     194 .]     105     296 ..     104     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 188.2 bits;  conditional E-value: 6.7e-59
                                   BHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCS CS
                        GARS_A   2 sKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeage 81 
                                   +K++a++++k+ +i+++  +++f+d e ++eyiee+++ a  +K++gl++gKgv+v+ ++   + a+ +  ++   G   +
  gi|91773047|ref|YP_565739.1| 105 DKAWARNFMKDNDIEGSpAFKVFSDKEGLQEYIEELGSVA--IKPAGLTGGKGVKVMGDQLPDTGAAYDYAVSLLDG---D 180
                                   79*************9989******************998..***************66655555555555544446...9 PP

                                   SEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHHHHHHTHHHHHHHH CS
                        GARS_A  82 kvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellekikeeileptvegl 158
                                   +vv+Ee l GeE++++a+vdgk+++ +p +qdhkr++e+D gpnTGGmG+ys     +p+vt ++l +++e i++ t+ +l
  gi|91773047|ref|YP_565739.1| 181 NVVVEENLVGEEFTVQAFVDGKNLAFTPCVQDHKRAFENDFGPNTGGMGSYSdsdgLLPFVTIDDLYHARE-IMKATITAL 260
                                   ****************************************************999889***********99.********* PP

                                   HCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                        GARS_A 159 kkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                    + ++pfkG+Ly++++l+++gpkv+efn+RfgDpe+
  gi|91773047|ref|YP_565739.1| 261 GATETPFKGMLYGQFILTKNGPKVIEFNARFGDPEA 296
                                   **********************************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 !   85.5   0.4   1.6e-27   3.2e-24       1      90 []       1     103 [.       1     103 [. 0.96

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 1.6e-27
                                   EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG............TTHHHHHHHHHHCTESEEEE-SHHHHHTTH CS
                        GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvap..gNagt............edlealvefakeekidlvvvGpeapLvaGv 67 
                                   m+vL++G+GGRe+a+a ++a+s++   +++++  +N+g+            +d+e++v +a+e++i++v++GpeapL+ G+
  gi|91773047|ref|YP_565739.1|   1 MNVLIIGGGGRENAIADAIARSERNPALFAVMakKNPGIaalcedfllakeTDVEKVVGYAREKGIEMVFIGPEAPLAVGL 81 
                                   9*************************999877669************99999999************************** PP

                                   HHHHHHHHT-EEES--CCCCHHH CS
                        GARS_N  68 adaleeekgikvfGpskeaAqlE 90 
                                   adale++ gi ++Gp+k+ A++E
  gi|91773047|ref|YP_565739.1|  82 ADALEDA-GIGAVGPRKNVARIE 103
                                   ****777.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.27   5.4e+02      46      75 ..      79     111 ..      59     112 .. 0.84
   2 !   50.3   0.1   1.1e-16   2.1e-13       1      79 [.     331     416 ..     331     417 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.27
                                   EEEESSHHHHHHHHH...HHHTTCB-TTEE--S CS
                        GARS_C  46 vavgetleeArakay...eavkkikfeglfyRk 75 
                                   v++++ le+A   a    ++v++i+f++++ R+
  gi|91773047|ref|YP_565739.1|  79 VGLADALEDAGIGAVgprKNVARIEFDKAWARN 111
                                   66777777777777677799********99995 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 1.1e-16
                                   EEEEEEEETTTTSS--ST-EEBS...TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE- CS
                        GARS_C   1 avgvvlaskGYPgsyekgkeitg...egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikfeglfy 73 
                                   +v+ +++++GYP++++k+ke+     +++ +f++++      ++t+++R +avv+v++++++A+  a +a+++i+  +l++
  gi|91773047|ref|YP_565739.1| 331 TVCKYAVPAGYPDEPSKDKEVVVgniGDALLFYSSVYekdgkVYTTSSRAVAVVGVANSITDAEVIAQNALENIT-GDLHF 410
                                   69***************9999558997788999987677788********************************5.58*** PP

                                   -STTTH CS
                        GARS_C  74 RkDIGa 79 
                                   R+DIG+
  gi|91773047|ref|YP_565739.1| 411 RRDIGT 416
                                   *****6 PP

>> ATP-grasp_4  ATP-grasp 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     0.012      43      89 ..     170     216 ..     144     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.2e-06
                   ATP-grasp_4  43 eeykeevveeesflvEeyieGeEfavdayfdeeGepvilnilkkefa 89 
                                    +y+ + +++++++vEe + GeEf v a++d +  +    + +++ a
  gi|91773047|ref|YP_565739.1| 170 YDYAVSLLDGDNVVVEENLVGEEFTVQAFVDGKNLAFTPCVQDHKRA 216
                                   568889999*********************87655555555555555 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-05     0.053      31     159 ..     140     292 ..     105     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                   SSSEEEEESS-------B--SS--TTE................EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET.... CS
                   ATP-grasp_3  31 ekklvvKprdGaggesvrvveekeeae.aaieeve........lvqefieGkplSvsllsdgekvlvlavnrqliekaeke 102
                                     ++ +Kp+   gg++v v+ ++  ++ aa ++          +v e + G++++v++ +dg k+l ++ + q  ++a ++
  gi|91773047|ref|YP_565739.1| 140 LGSVAIKPAGLTGGKGVKVMGDQLPDTgAAYDYAVslldgdnvVVEENLVGEEFTVQAFVDG-KNLAFTPCVQDHKRAFEN 219
                                   5567789999999999987766644430444444489999999*****************98.666677777777666666 PP

                                   ...........TEEEEEEES----H.HHHHHHHHHHHHTTST....T--EEEEEEEEESS.SEEEEEEESS-- CS
                   ATP-grasp_3 103 ...........fvyaGnvtpietel.keevvelaeevvekle....glaGyvGvDlvlkdeepyviEvNPRlt 159
                                              ++ + ++ p+ t +   +++e+++ ++ +l     + +G++   ++l++++p viE N+R+ 
  gi|91773047|ref|YP_565739.1| 220 dfgpntggmgsYSDSDGLLPFVTIDdLYHAREIMKATITALGatetPFKGMLYGQFILTKNGPKVIEFNARFG 292
                                   8999999996644455666766654366777777777777755557899*9999*****************95 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.8e-05      0.14       1      60 [.     105     162 ..     105     213 .. 0.80
   2 ?   -3.9   0.0       4.1   8.2e+03     161     180 ..     274     291 ..     256     293 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSH CS
                   CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarne 60 
                                   Dk  a++ +k+ +++  p++++  ++ e   +  +e+g  v ik+a   GGkG +v+ ++
  gi|91773047|ref|YP_565739.1| 105 DKAWARNFMKDNDIEGSPAFKV-FSDKEGLQEYIEELG-SVAIKPAGLTGGKGVKVMGDQ 162
                                   89999***************99.99999999******9.5***************98764 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.1
                                   EEEEETTTTEEEEEEEESS- CS
                   CPSase_L_D2 161 eflldpkskeyyviEvNtRl 180
                                   +f+l +  +   viE N+R 
  gi|91773047|ref|YP_565739.1| 274 QFILTK--NGPKVIEFNARF 291
                                   566663..555799999995 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 ?    8.5   0.0   0.00052         1      47      79 ..     128     159 ..      91     173 .. 0.78
   2 ?    1.2   0.0     0.088   1.7e+02     242     266 ..     268     291 ..     251     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00052
                   ATPgrasp_ST  47 aeiseleafvkeleegvviKpakgsgGkGilvi 79 
                                   ++ + l+++++el + v+iKpa   gGkG+ v+
  gi|91773047|ref|YP_565739.1| 128 SDKEGLQEYIEELGS-VAIKPAGLTGGKGVKVM 159
                                   55678999*****55.**************998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.088
                   ATPgrasp_ST 242 lgylGwDivldeekgplllElNarp 266
                                    g+l   + l++++ p ++E Nar 
  gi|91773047|ref|YP_565739.1| 268 KGMLYGQFILTKNG-PKVIEFNARF 291
                                   55666668899999.********95 PP

>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.7e-05      0.17      80     147 ..       2      71 ..       1      72 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-05
                 CoA_binding_3  80 errvvavgggeelakqiranpelgfrvvgvfddrddarseeva..gvpvlgnladlveyvretrvdevyl 147
                                   ++ ++++gg e++++   a+ e +    +v+ +++++    ++   + ++ +++++v y+re+ +++v++
  gi|91773047|ref|YP_565739.1|   2 NVLIIGGGGRENAIADAIARSERNPALFAVMAKKNPGIAALCEdfLLAKETDVEKVVGYAREKGIEMVFI 71 
                                   56666667777777666677888899999999999999999987899*********************97 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 ?   10.7   0.0   0.00012      0.25      13      63 ..     122     172 ..     112     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                   --EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHH CS
                     GSH-S_ATP  13 pktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilel 63 
                                   p   v +dke +++++ee g+v +KP + +gG+gv  + ++ p+ ++ ++ 
  gi|91773047|ref|YP_565739.1| 122 PAFKVFSDKEGLQEYIEELGSVAIKPAGLTGGKGVKVMGDQLPDTGAAYDY 172
                                   55678899***************************9998888777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2847.25
//
Query:       gi|91773048|ref|YP_565740.1|  [L=301]
Description: ornithine carbamoyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-60  201.6   0.0    1.2e-59  200.9   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    2.1e-55  186.8   0.5    3.1e-55  186.3   0.5    1.2  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 !  200.9   0.0   1.3e-63   1.2e-59       2     155 ..     149     297 ..     148     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 1.3e-63
                                   C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSE CS
                        OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvs 82 
                                   glk+a++Gd+ nnv+nsli ++a +gm++ +++P+g+ p++e++++ ++     gg+i it+d+eea+++aDv+y dvwvs
  gi|91773048|ref|YP_565740.1| 149 GLKFAWIGDG-NNVCNSLILGCALVGMQIAVACPEGYMPNPEIVAKGREL----GGDILITTDPEEAAADADVLYADVWVS 224
                                   99********.*********************************887776....9************************** PP

                                   TTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                        OTCace  83 mgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                   mg+e+ere+rl +l++yq++++l++lak+d+i++HcLPa+rgeEv++eV+d+p+svvf+qaeNrlh++kAll+
  gi|91773048|ref|YP_565740.1| 225 MGDEEEREKRLSDLENYQINSNLVELAKPDVIFMHCLPAHRGEEVSAEVMDGPHSVVFDQAENRLHAQKALLM 297
                                   ***********************************************************************97 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.3   0.5   3.4e-59   3.1e-55       1     148 []       2     142 ..       2     142 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 3.4e-59
                                   S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTT CS
                      OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlss 81 
                                   +hl+s++dl++eei e+ld a++lkek+ + k+++llk+k+la++Fe++StRTrvSfevA+++lGg+ ++l+ ++diq++ 
  gi|91773048|ref|YP_565740.1|   2 KHLISMTDLTQEEIIEILDMAEDLKEKRLRGKMTDLLKNKSLAMIFEKSSTRTRVSFEVAMSDLGGHSIYLN-SRDIQIG- 80 
                                   8***********************************************************************.88*****. PP

                                   GGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                      OTCace_N  82 vskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       r+E+++Dta+vlsryv +i +R+++++++e+lak+++vpviNa+ +d eHP+Q+LaD+ltire
  gi|91773048|ref|YP_565740.1|  81 ----RGETVSDTAQVLSRYVAGITARVNSHRTVEDLAKHSNVPVINAL-SDLEHPCQILADFLTIRE 142
                                   ....78******************************************.****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1982.40
//
Query:       gi|91773049|ref|YP_565741.1|  [L=231]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   33.3  12.2    1.5e-05   24.6   3.0    2.7  3  Fer4      4Fe-4S binding domain
    4.3e-07   29.7  11.3    0.00049   20.1   4.0    2.3  2  Fer4_6    4Fe-4S binding domain
    1.7e-06   28.0   6.2    0.00024   21.2   0.8    2.5  2  Fer4_21   4Fe-4S dicluster domain
    4.2e-06   26.8   3.0    0.00084   19.5   0.2    2.3  2  Fer4_9    4Fe-4S dicluster domain
    5.7e-06   26.8  18.7    7.2e-05   23.3   8.4    2.0  2  Fer4_7    4Fe-4S dicluster domain
    6.8e-06   26.9  10.4     0.0066   17.4  10.5    2.4  1  Fer4_16   4Fe-4S double cluster binding domain
    0.00044   21.0  10.5       0.23   12.5   0.7    2.6  2  Fer4_3    4Fe-4S binding domain
    0.00051   20.4   3.5      0.029   14.8   0.1    2.4  2  Fer4_8    4Fe-4S dicluster domain
    0.00059   19.9  11.8      0.014   15.5  12.6    2.2  1  Fer4_10   4Fe-4S dicluster domain
    0.00059   20.3   2.3       0.21   12.2   0.1    2.8  3  Fer4_17   4Fe-4S dicluster domain
     0.0014   19.0  10.3       0.15   12.6   3.3    2.5  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   15.6  12.1       0.24   11.6   1.9    2.5  2  Fer4_2    4Fe-4S binding domain
        1.9    8.7   9.9        2.1    8.6   2.2    2.4  2  Fer4_18   4Fe-4S dicluster domain
        4.1    8.0  10.1        3.2    8.4   4.5    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   3.0   1.2e-08   1.5e-05       3      24 .]     175     196 ..     173     196 .. 0.91
   2 ?   -2.1   0.0       3.2   4.1e+03       2       8 ..     200     206 ..     200     207 .. 0.85
   3 !   14.3   0.6   2.1e-05     0.027      10      20 ..     218     228 ..     217     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                                   EETTTSSS-THHHHHSTTTEEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                   ++ + C +C++C+e+CPv+A+t
  gi|91773049|ref|YP_565741.1| 175 FINDACSKCMKCIEICPVDALT 196
                                   6789****************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                                   EEETTTS CS
                          Fer4   2 videekC 8  
                                   vi+ ekC
  gi|91773049|ref|YP_565741.1| 200 VIHREKC 206
                                   6889999 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.1e-05
                                   S-THHHHHSTT CS
                          Fer4  10 gCGaCvevCPv 20 
                                   +CG+C++vCP 
  gi|91773049|ref|YP_565741.1| 218 RCGLCIKVCPL 228
                                   6*********5 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   4.0   3.8e-07   0.00049       4      24 .]     175     195 ..     175     195 .. 0.92
   2 !   14.0   0.7   3.2e-05      0.04       3      20 ..     200     227 ..     200     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.8e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   +  d+C  C++C+ +CP +a+
  gi|91773049|ref|YP_565741.1| 175 FINDACSKCMKCIEICPVDAL 195
                                   6689*************9996 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.2e-05
                        Fer4_6   3 eidpdkCi..........gCgdCvrvCP 20 
                                   +i ++kC            Cg C++vCP
  gi|91773049|ref|YP_565741.1| 200 VIHREKCAdymfnvlgglRCGLCIKVCP 227
                                   5789999867777776555********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 !   21.2   0.8   1.9e-07   0.00024      27      57 ..     166     195 ..     155     197 .. 0.84
   2 !    9.2   0.5   0.00099       1.3      44      54 ..     219     229 ..     214     231 .] 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.9e-07
                       Fer4_21  27 eidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   ++++kt ++ ++d C  C  C+++CPv d++
  gi|91773049|ref|YP_565741.1| 166 DTEEKTEMPFINDACSKCMKCIEICPV-DAL 195
                                   56788999******************9.665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00099
                       Fer4_21  44 CnlCssvCPve 54 
                                   C lC++vCP++
  gi|91773049|ref|YP_565741.1| 219 CGLCIKVCPLN 229
                                   9********85 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   6.5e-07   0.00084      33      50 ..     169     194 ..     142     195 .. 0.73
   2 !    7.7   0.3    0.0031         4      38      48 ..     218     228 ..     198     231 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.5e-07
                        Fer4_9  33 e........eaCigCgaCveaCpkga 50 
                                   e        +aC +C++C+e+Cp +a
  gi|91773049|ref|YP_565741.1| 169 EktempfinDACSKCMKCIEICPVDA 194
                                   03344555569************987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0031
                        Fer4_9  38 gCgaCveaCpk 48 
                                    Cg C+++Cp 
  gi|91773049|ref|YP_565741.1| 218 RCGLCIKVCPL 228
                                   58888888885 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   2.6   8.8e-06     0.011      23      52 .]     165     194 ..     152     194 .. 0.79
   2 !   23.3   8.4   5.7e-08   7.2e-05       1      50 [.     179     228 ..     179     230 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-06
                        Fer4_7  23 enekgtekveidpekClgCgaCvavCPtga 52 
                                    + +++ ++ +  + C+ C +C++ CP++a
  gi|91773049|ref|YP_565741.1| 165 LDTEEKTEMPFINDACSKCMKCIEICPVDA 194
                                   45556677888899*************997 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.7e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                   +C +C +C + Cpv+a++ + + + ++++++ ++    l Cg C++vCP 
  gi|91773049|ref|YP_565741.1| 179 ACSKCMKCIEICPVDALTSEGVIHREKCADYMFNVLGGLRCGLCIKVCPL 228
                                   5********************999999999*******************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 !   17.4  10.5   5.1e-06    0.0066       2      67 .]     180     229 ..     179     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.1e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPan 67 
                                   C +C kC+e+CP++a++++   +i  ++c +y            ++         C+ C +vCP n
  gi|91773049|ref|YP_565741.1| 180 CSKCMKCIEICPVDALTSE--GVIHREKCADY-----------MFNVL---GGLRCGLCIKVCPLN 229
                                   *******************..99999999777...........44444...345899999999877 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   3.4    0.0002      0.26       1      15 []     180     194 ..     180     194 .. 0.95
   2 !   12.5   0.7   0.00018      0.23       4      13 ..     219     228 ..     216     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C  C+ C e CPv+A
  gi|91773049|ref|YP_565741.1| 180 CSKCMKCIEICPVDA 194
                                   999**********98 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00018
                        Fer4_3   4 CgaCvevCPv 13 
                                   Cg+C +vCP 
  gi|91773049|ref|YP_565741.1| 219 CGLCIKVCPL 228
                                   *********4 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.3e-05     0.029      46      64 ..     175     193 ..     140     194 .. 0.79
   2 ?    6.1   0.5     0.012        15       7      17 ..     218     228 ..     216     230 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                        Fer4_8  46 ealwsCttcgaCtevCpvg 64 
                                    + ++C+ c++C e Cpv+
  gi|91773049|ref|YP_565741.1| 175 FINDACSKCMKCIEICPVD 193
                                   46689************86 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                        Fer4_8   7 eCgaCqsaCpv 17 
                                   +Cg+C + Cp+
  gi|91773049|ref|YP_565741.1| 218 RCGLCIKVCPL 228
                                   57777777764 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  12.6   1.1e-05     0.014       6      56 .]     177     227 ..     173     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..........cgaCveaCP 56 
                                    d C +C kC + CP+        ++ +   +  +  ekC +          cg C+++CP
  gi|91773049|ref|YP_565741.1| 177 NDACSKCMKCIEICPV--------DALTS--EGVIHREKCADymfnvlgglrCGLCIKVCP 227
                                   589*************........34443..344444788888888888888********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 ?   -1.6   0.0       3.3   4.2e+03      11      31 ..      28      49 ..      26      75 .. 0.72
   2 !   12.2   0.1   0.00016      0.21      34      58 ..     167     192 ..     144     195 .. 0.68
   3 !    6.7   0.3    0.0082        10       4      15 ..     218     229 ..     217     231 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.3
                       Fer4_17 11 eCpsyea.ydnepkkllraakl 31
                                  +C+   + ++n+p+ ++ ++++
  gi|91773049|ref|YP_565741.1| 28 SCFEDSDyTGNKPQDVMDDLQS 49
                                  5666666355788888887766 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                       Fer4_17  34 leeaekee.kaslCieCgeCerkCPq 58 
                                   +ee  +++   + C++C +C + CP 
  gi|91773049|ref|YP_565741.1| 167 TEEKTEMPfINDACSKCMKCIEICPV 192
                                   3333344425689***********96 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0082
                       Fer4_17   4 qCgyClpeCpsy 15 
                                   +Cg C+++Cp +
  gi|91773049|ref|YP_565741.1| 218 RCGLCIKVCPLN 229
                                   699999999975 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.3   0.00012      0.15       2      16 ..     178     192 ..     177     194 .. 0.91
   2 !   10.2   0.6    0.0007       0.9       5      16 ..     217     228 ..     203     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   + C  C++C+ +CP+
  gi|91773049|ref|YP_565741.1| 178 DACSKCMKCIEICPV 192
                                   78************7 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0007
                        Fer4_4   5 igCgsCvaaCPq 16 
                                   ++Cg C+ +CP 
  gi|91773049|ref|YP_565741.1| 217 LRCGLCIKVCPL 228
                                   69*********6 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9   0.00018      0.24       5      21 ..     176     191 ..     172     192 .. 0.82
   2 ?    9.0   2.8    0.0013       1.6      12      21 ..     218     227 ..     200     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                   ++ d+C  C +C+  CP
  gi|91773049|ref|YP_565741.1| 176 IN-DACSKCMKCIEICP 191
                                   44.78************ PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                        Fer4_2  12 gCgaCvsaCP 21 
                                   +Cg C+++CP
  gi|91773049|ref|YP_565741.1| 218 RCGLCIKVCP 227
                                   7********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 ?    8.6   2.2    0.0017       2.1      58      80 ..     177     199 ..     155     218 .. 0.74
   2 ?    4.9   0.6     0.022        28      62      73 ..     217     228 ..     209     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                       Fer4_18  58 agdcidcescvkvcPtgidirkG 80 
                                   +  c +c +c+++cP++    +G
  gi|91773049|ref|YP_565741.1| 177 NDACSKCMKCIEICPVDALTSEG 199
                                   457************98665555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                       Fer4_18  62 idcescvkvcPt 73 
                                   + c+ c+kvcP 
  gi|91773049|ref|YP_565741.1| 217 LRCGLCIKVCPL 228
                                   57********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 ?    8.4   4.5    0.0025       3.2       1      17 [.     176     191 ..     176     192 .. 0.92
   2 ?    2.3   0.3      0.19   2.5e+02       9      17 ..     219     227 ..     217     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   ++ d C+ c++C e++P
  gi|91773049|ref|YP_565741.1| 176 IN-DACSKCMKCIEICP 191
                                   56.99***********9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                       Fer4_13   9 cgaCvelaP 17 
                                   cg+C +++P
  gi|91773049|ref|YP_565741.1| 219 CGLCIKVCP 227
                                   ********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1776.59
//
Query:       gi|91773050|ref|YP_565742.1|  [L=121]
Description: hypothetical protein Mbur_1060 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00038   20.6   0.0     0.0073   16.5   0.0    2.0  1  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.1e-07    0.0073       5     124 ..       7     120 ..       4     121 .] 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.1e-07
                                   EEEEESHHHHHHHHHHHHHTSEEEEEEEEEEST...EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEE CS
                    Glyoxalase   5 vallvgdleksldFYtkvLGfklvkktdnteet...eglriaffhaggghielvlneapsgaakhvkkieetvhhvafial 82 
                                   v l+v+dl++s++F+tk LGf+   +  ++++t       + ++   +   +++      +a+k+          + + a+
  gi|91773050|ref|YP_565742.1|   7 VNLPVKDLDRSIEFFTK-LGFEFDPQLSDEKGTcmiVNKESFVMLLTESFFKMFTTKQICDAKKST------DVAISLPAQ 80 
                                   5699*************.999998888842222333555555566666666666666666666655......788999999 PP

                                   EHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSE CS
                    Glyoxalase  83 dvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGi 124
                                   +   v++ ++++keag+   +ep+++++  + s  f+D +G+
  gi|91773050|ref|YP_565742.1|  81 SRVKVDELVNKAKEAGGLEEGEPQDYGWMYGRS--FEDLNGH 120
                                   999999999999999999999999999977776..8988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 864.11
//
Query:       gi|91773051|ref|YP_565743.1|  [L=210]
Description: hypothetical protein Mbur_1061 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1729.76
//
Query:       gi|91773052|ref|YP_565744.1|  [L=216]
Description: hypothetical protein Mbur_1062 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   90.4   0.0    1.5e-25   90.1   0.0    1.0  1  Ala_racemase_N  Alanine racemase, N-terminal domain
     0.0015   17.7   0.0     0.0021   17.3   0.0    1.2  1  Mito_fiss_Elm1  Mitochondrial fission ELM1
  ------ inclusion threshold ------
      0.015   14.6   0.3      0.025   13.9   0.3    1.3  1  Orn_Arg_deC_N   Pyridoxal-dependent decarboxylase, pyridoxal 
        0.2   11.3   2.2          2    8.0   0.0    2.1  2  DUF4559         Domain of unknown function (DUF4559)
       0.37   11.2   7.1        0.4   11.1   0.1    3.3  3  NBD94           Nucleotide-Binding Domain 94 of RH


Domain annotation for each model (and alignments):
>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   4.2e-29   1.5e-25       6     218 ..       3     214 ..       2     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 4.2e-29
                                   HHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESCSTGGGHHHHH CS
                Ala_racemase_N   6 lrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvlegfspeelaala 86 
                                   +++N++r+ + + + +kl++v+K+     + +++ +  + +ga+ +g+++++E +   +  + ++  +++  + +++++++
  gi|91773052|ref|YP_565744.1|   3 VDENIKRIFNEL-GRTKLVCVTKT----IDTERINESIR-AGATIIGENRVQEFEDKCADILPCERHLIGNLQTNKVKKAV 77 
                                   579*********.8899*******....99999999777.66*************888887888888999999******** PP

                                   HT.TEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSS..SSSBSCHHHHHHHHHHHHTTTEEEEEEE-S-SSTTSTSH CS
                Ala_racemase_N  87 ey.dltvtvdsleqlealaaaareagkplrvhlkidtgmg..RlGftpeeleellealaalpglrleglmtHfasadepde 164
                                   +  d+ + vdsl+ ++ +++ a++ +k ++v+l++++g +  + Gf  +e+ +++ ++++l++++++glm ++++    + 
  gi|91773052|ref|YP_565744.1|  78 HLfDVIQSVDSLKLIQDIDKKAKAINKVQKVFLQVNIGNEpqKFGFGSDEIGQVITQIQSLKNVHVKGLMCIPPFVSP-E- 156
                                   *99***********************************88***********************************974.3. PP

                                   HHHHHHHHHHHHHHHH...HHTTGGGSEEEEESHHHHHHSGGG.TTEEEESGGGGT-S CS
                Ala_racemase_N 165 eteaqlarfeealeel...ekaglrppvvslanSaaillaaah.fdmvRpGialyGls 218
                                   +t+ ++++++++ +el   ++ +++++ +s+++S ++  a+ +  +mvR+G+a++G +
  gi|91773052|ref|YP_565744.1| 157 QTRSYFKKMKALFDELkqvDQDNIDIQELSMGMSNDYRVAIEEgATMVRVGSAIFGNR 214
                                   455566666666555533245669999*************7456***********975 PP

>> Mito_fiss_Elm1  Mitochondrial fission ELM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.8e-07    0.0021     113     204 ..      74     165 ..      63     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.8e-07
                Mito_fiss_Elm1 113 pnvvltlGalhrvtpaalaaaaaawkkelaelpkplvavliGGpskrfrfdedeakqlveelakllesegasllitfSrRT 193
                                   ++ v    ++  v++ +l +  ++ +k++++++k ++ v+iG + ++f f++de+ q+++++++l++ +   l+  +   +
  gi|91773052|ref|YP_565744.1|  74 KKAVHLFDVIQSVDSLKLIQDIDKKAKAINKVQKVFLQVNIGNEPQKFGFGSDEIGQVITQIQSLKNVHVKGLMCIPPFVS 154
                                   5566667788999999************************************************98776557777777777 PP

                Mito_fiss_Elm1 194 peeveailkke 204
                                   pe++++ +kk+
  gi|91773052|ref|YP_565744.1| 155 PEQTRSYFKKM 165
                                   77777666665 PP

>> 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 ?   13.9   0.3   7.1e-06     0.025      88     198 ..      82     188 ..      61     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.1e-06
                                   EESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTEEEEEEE-...--BSSC CS
                 Orn_Arg_deC_N  88 tvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaakeenlqlvGvsf...HvGSgv 165
                                   ++ +v+ l+ ++++ ++ak + +++        ++ + g+e +KFG+  +e  +++ ++ + +n+++ G+ +    v+   
  gi|91773052|ref|YP_565744.1|  82 VIQSVDSLKLIQDIDKKAKAINKVQK----VFLQV-NIGNEPQKFGFGSDEIGQVITQIQSLKNVHVKGLMCippFVSP-- 155
                                   67899999999999999999888777....33333.5699******************************993322332.. PP

                                   -SCHHHHHHHHHHHHHHHHHHHHT---SEEE-- CS
                 Orn_Arg_deC_N 166 sdleafvkavekalklfdelaelGvklkiLdvG 198
                                   ++++++ k ++ ++  ++++ +  ++++ L++G
  gi|91773052|ref|YP_565744.1| 156 EQTRSYFKKMKALFDELKQVDQDNIDIQELSMG 188
                                   345778888888888888888888888888887 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.1     0.021        77     203     297 ..      18     108 ..       1     121 [. 0.66
   2 ?    8.0   0.0   0.00055         2     161     210 ..     153     199 ..     124     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
                       DUF4559 203 efeislkeddevrvltdvllslqklkeleeellkedatkldelvlraeeqki..skeellkelqvlkeflnknkdLkenlk 281
                                   ++   +k +d  r++  +  +   + e + +++++   k  ++ l  e + i  ++ + +k+  +l ++++ +  Lk  l 
  gi|91773052|ref|YP_565744.1|  18 KLVCVTKTIDTERINESIRAGATIIGENRVQEFED---KCADI-LPCERHLIgnLQTNKVKKAVHLFDVIQSVDSLK--LI 92 
                                   44444555777778888888888888999999999...66666.555666662234556788888999999999999..66 PP

                       DUF4559 282 edvkklqeieekldkl 297
                                   +d+ k  +  +k++k+
  gi|91773052|ref|YP_565744.1|  93 QDIDKKAKAINKVQKV 108
                                   6665555555677765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00055
                       DUF4559 161 vssqdmkeymkkilrLledlktvpeleeaeeaieellkilkqefeislke 210
                                   vs ++ + y+kk++ L+++lk+v +++     i+el+  + +++ +  +e
  gi|91773052|ref|YP_565744.1| 153 VSPEQTRSYFKKMKALFDELKQVDQDN---IDIQELSMGMSNDYRVAIEE 199
                                   788999*************98877665...45566655566666555555 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   3.8e+03      19      29 ..       5      15 ..       2      36 .. 0.63
   2 ?    1.8   1.3     0.089   3.2e+02      25      45 ..      89     109 ..      66     144 .. 0.69
   3 ?   11.1   0.1   0.00011       0.4      13      41 ..     157     185 ..     153     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                         NBD94 19 eniekllnEle 29
                                  eni+ ++nEl 
  gi|91773052|ref|YP_565744.1|  5 ENIKRIFNELG 15
                                  55555555553 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.089
                         NBD94  25 lnEleeiekektsleevknie 45 
                                   l+ +++i+k   ++++v+++ 
  gi|91773052|ref|YP_565744.1|  89 LKLIQDIDKKAKAINKVQKVF 109
                                   455666666666666666554 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00011
                         NBD94  13 kkkkiyeniekllnEleeiekektsleev 41 
                                   ++++ +++++ l++El++++++++ ++e+
  gi|91773052|ref|YP_565744.1| 157 QTRSYFKKMKALFDELKQVDQDNIDIQEL 185
                                   567889******************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1524.11
//
Query:       gi|91773053|ref|YP_565745.1|  [L=478]
Description: K+ transporter Trk [Methanococcoides burtonii DSM 6242]
Scores for complete 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  228.0  19.3    2.3e-66  224.3  19.3    2.1  1  TrkH      Cation transport protein
  ------ inclusion threshold ------
      0.055   13.6   0.0       0.15   12.2   0.0    1.7  1  DUF5554   Family of unknown function (DUF5554)
       0.77    9.9   0.0       0.77    9.9   0.0    2.6  3  PufQ      PufQ cytochrome subunit


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 !  224.3  19.3   3.8e-70   2.3e-66       8     490 ..      41     471 ..      34     477 .. 0.92

  Alignments for each domain:
  == domain 1  score: 224.3 bits;  conditional E-value: 3.8e-70
                          TrkH   8 ggiitialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveesl 88 
                                    ++it+++ +   f +k ++ + +lk++f iv + +++  v  +++ +l  + ++ ++alfe++sg+t tg++  ++ es 
  gi|91773053|ref|YP_565745.1|  41 PLAITVLVASIFSFFFKRRDEEWDLKEGFFIVAMGWLIAAVFYSFPYML--EGVPPINALFESMSGVTATGATALTEIESH 119
                                   56788888888899999999**************************995..456679************************ PP

                          TrkH  89 prsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvvli 169
                                    +s l++r+++q++Gg+g++ l  ++lp lg+ + ++ ++e++  + ++   ++++e++kil+++y++l ++ + +l    
  gi|91773053|ref|YP_565745.1| 120 TKSLLFWRSMTQWLGGMGIIMLFIAILPKLGIAGRQMFRAEVP-GLQEEQLRPRIRETAKILWLVYIILSVVELTIL---- 195
                                   ******************************************5.577888899*****************9999999.... PP

                          TrkH 170 ytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrviiaikkkilr 250
                                          +++      + ++a+ h++++++  Gfs +++S+a f   ++++ ++++f++lG+ +F +++++i   kk+   
  gi|91773053|ref|YP_565745.1| 196 -----LIAGL------SFFDAITHTFTSISCSGFSPYSDSIAAFSD-PLVEGIIMVFMFLGGANFALHYKTIYSDKKSL-- 262
                                   .....45677......99****************************.************************99887776.. PP

                          TrkH 251 dlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfilldegslvvksipkgsrvlkalFqsvstrta.G 330
                                              ++d ++++  L + ++ + +l+  l                  + v s+p  ++++ + F ++s +t+ G
  gi|91773053|ref|YP_565745.1| 263 -----------IKDQEFKFY-LSIIVIGTLVLAYVLF----------------RTEVYSLP--DAFRYSSFHVISILTTtG 313
                                   ...........569999999.3333333334444434................57788888..889999************ PP

                          TrkH 331 FsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksidgkhlerqllvdlwslf 411
                                   +++vd+  ++++  ++l + m+igg++gSt gg++ ++++ + +  +  + +  +pka++++++  k++ +++++++ s++
  gi|91773053|ref|YP_565745.1| 314 YATVDFNIWPDSSRFILFILMFIGGCAGSTSGGLKVVRFLLLLKYTQKVLFKVIHPKAIVPIRFNNKTVPEDIIHSIVSFM 394
                                   ********************************************************************************* PP

                          TrkH 412 lvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlG.aknaslsaqlttisklvlialmirGrlrglpvlldr 490
                                   +++++i+++++  l  ++   ++f+++L ++++++g+vG++lG    ++ +  +++ +kl+lia+m++Grl++++v+++ 
  gi|91773053|ref|YP_565745.1| 395 IIYFLIFFASSTLLALMG---MDFVTSLSASIATLGNVGPGLGlVGPMANFDAIPDPGKLILIANMWIGRLEVFTVIVLL 471
                                   **********99999999...9*********************559*******************************975 PP

>> DUF5554  Family of unknown function (DUF5554)
   #    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      21      50 ..     112     140 ..     103     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                       DUF5554  21 rlgeveshacssllwnlltqyllpgvghil 50 
                                    l e+esh+ s l+w  +tq+l  g+g i+
  gi|91773053|ref|YP_565745.1| 112 ALTEIESHTKSLLFWRSMTQWL-GGMGIIM 140
                                   589*****************96.6888665 PP

>> PufQ  PufQ cytochrome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   0.5         3   1.8e+04      38      46 ..      73      81 ..      71      81 .. 0.80
   2 ?    9.9   0.0   0.00013      0.77      18      39 ..     264     285 ..     251     291 .. 0.84
   3 ?   -0.5   0.4      0.24   1.4e+03      22      40 ..     393     412 ..     388     428 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 3
                          PufQ 38 lltWvlaai 46
                                  +++W++aa+
  gi|91773053|ref|YP_565745.1| 73 AMGWLIAAV 81
                                  689*99987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00013
                          PufQ  18 pkaEFavYFaiilvaalPlAll 39 
                                      EF  Y +ii++++l lA +
  gi|91773053|ref|YP_565745.1| 264 KDQEFKFYLSIIVIGTLVLAYV 285
                                   568****************987 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.24
                          PufQ  22 Fa.vYFaiilvaalPlAllt 40 
                                   F+ +YF i + ++  lAl++
  gi|91773053|ref|YP_565745.1| 393 FMiIYFLIFFASSTLLALMG 412
                                   55167777777666677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3109.08
//
Query:       gi|91773054|ref|YP_565746.1|  [L=77]
Description: hypothetical protein Mbur_1064 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00047   20.6   0.4    0.00054   20.4   0.4    1.1  1  Rubrerythrin  Rubrerythrin
      0.002   18.5   0.3     0.0025   18.1   0.3    1.2  1  DUF2383       Domain of unknown function (DUF2383)
     0.0089   15.7   0.4     0.0097   15.6   0.4    1.1  1  DUF3231       Protein of unknown function (DUF3231)
  ------ inclusion threshold ------
      0.011   15.5   0.3      0.013   15.2   0.3    1.1  1  COQ7          Ubiquinone biosynthesis protein COQ7
      0.075   13.2   0.0      0.091   13.0   0.0    1.1  1  Ferritin_2    Ferritin-like domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   1.5e-07   0.00054      12      61 ..      15      62 ..      10      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                                  HHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH CS
                  Rubrerythrin 12 sarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele 61
                                  +a++lY+ +a  ++  +++++e+++++A++E+ H + +  ll   ++++ 
  gi|91773054|ref|YP_565746.1| 15 DAINLYEQMAALTD--NKEVKEVLLDIAKKEKTHVGEFQTLLLREDEQQV 62
                                  78899999999999..9999999999999999999999988866444433 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.3     7e-07    0.0025      14      60 ..      14      60 ..      10      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7e-07
                                  HHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-- CS
                       DUF2383 14 kdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralgge 60
                                   d+++ y+++a   +++++k++l +ia++ + ++ e+q  + ++ ++
  gi|91773054|ref|YP_565746.1| 14 LDAINLYEQMAALTDNKEVKEVLLDIAKKEKTHVGEFQTLLLREDEQ 60
                                  69*************************************99887765 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   2.7e-06    0.0097      31      75 ..      16      60 ..       7      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-06
                       DUF3231 31 gialitgFlqvaedkeikelleralelsnkhikelkelLkeenlp 75
                                  +i l+++++  +++ke+ke+l    +  + h+ e+++lL  e+ +
  gi|91773054|ref|YP_565746.1| 16 AINLYEQMAALTDNKEVKEVLLDIAKKEKTHVGEFQTLLLREDEQ 60
                                  578999*********************************999855 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   3.8e-06     0.013      16      60 ..      16      58 ..      13      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-06
                          COQ7 16 AvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellkerr 60
                                  A  +Y+  +a   ++++e+k++l +++++Ek H+  f++ll +++
  gi|91773054|ref|YP_565746.1| 16 AINLYEQMAAL--TDNKEVKEVLLDIAKKEKTHVGEFQTLLLRED 58
                                  67788755555..899999********************997765 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.5e-05     0.091      97     134 ..      17      54 ..      14      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                    Ferritin_2  97 vsAYlgaapllsnkelltaaasIlsvEArHaavirtll 134
                                   ++ Y + a+l +nke++++ + I+  E  H + ++tll
  gi|91773054|ref|YP_565746.1|  17 INLYEQMAALTDNKEVKEVLLDIAKKEKTHVGEFQTLL 54 
                                   56788999999999999999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 534.18
//
Query:       gi|91773055|ref|YP_565747.1|  [L=89]
Description: hypothetical protein Mbur_1065 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.2   0.0    4.1e-05   24.0   0.0    1.1  1  Rubrerythrin   Rubrerythrin
    0.00025   20.9   0.0    0.00029   20.7   0.0    1.0  1  COQ7           Ubiquinone biosynthesis protein COQ7
  ------ inclusion threshold ------
      0.021   14.7   0.1      0.021   14.7   0.1    1.2  1  Ferritin-like  Ferritin-like
      0.053   13.9   0.0       0.08   13.3   0.0    1.4  1  DUF2383        Domain of unknown function (DUF2383)
      0.064   13.5   0.0      0.072   13.3   0.0    1.1  1  Ferritin_2     Ferritin-like domain
      0.078   10.9   0.1      0.087   10.7   0.1    1.0  1  Med16          Mediator complex subunit 16


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 !   24.0   0.0   1.4e-08   4.1e-05       1      57 [.      20      74 ..      20      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
                                  HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCS CS
                  Rubrerythrin  1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllekle 57
                                  e++ + +++E +a ++Yk ++  +k   ++++++++e+A+eE  H ++++ +l +++
  gi|91773055|ref|YP_565747.1| 20 ELIRIGMIAELDAVNFYKQMTPLTK--DEDLKAVLLEVAREEMVHIAMFETVLMEVD 74
                                  56677889*****************..9**********************9998776 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.7e-08   0.00029       4      58 ..      20      72 ..      17      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.7e-08
                          COQ7  4 rllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellke 58
                                  +l+R+    El Av  Yk  +    +kd++lk++l e++++E  H+a+fe++l e
  gi|91773055|ref|YP_565747.1| 20 ELIRIGMIAELDAVNFYKQMTPL--TKDEDLKAVLLEVAREEMVHIAMFETVLME 72
                                  799**************987777..799999*******************99876 PP

>> Ferritin-like  Ferritin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     7e-06     0.021      28      55 ..      46      73 ..      10      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-06
                                  H.HHHHHHHHHHHHHHHHHHHHHHHHHT CS
                 Ferritin-like 28 eeaealilevvkeEMlHltlvaNllnal 55
                                  e+ +a++lev++eEM H+++   +l+ +
  gi|91773055|ref|YP_565747.1| 46 EDLKAVLLEVAREEMVHIAMFETVLMEV 73
                                  34899***************99999876 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.7e-05      0.08      13      53 ..      29      69 ..      19      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                                  HHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHH CS
                       DUF2383 13 lkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqse 53
                                  + d++++yk++    kd++lk++l ++a+e   +++ ++  
  gi|91773055|ref|YP_565747.1| 29 ELDAVNFYKQMTPLTKDEDLKAVLLEVAREEMVHIAMFETV 69
                                  56999999999999999999999999999988888766655 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.4e-05     0.072      84     135 ..      20      71 ..       6      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                    Ferritin_2  84 sflalaavlEdvgvsAYlgaapllsnkelltaaasIlsvEArHaavirtllg 135
                                   ++++  ++ E  +v+ Y++  pl ++++l+++ ++++  E  H a+++t+l 
  gi|91773055|ref|YP_565747.1|  20 ELIRIGMIAELDAVNFYKQMTPLTKDEDLKAVLLEVAREEMVHIAMFETVLM 71 
                                   5555566667778888888888888888888888888888888888888775 PP

>> Med16  Mediator complex subunit 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   2.9e-05     0.087     540     614 ..       6      80 ..       3      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.9e-05
                         Med16 540 iillskvprlfllkiisalgrihel.lkklhkdlakllg..eskeslnrvfsilnnspvtldlfekfLreldalvtke 614
                                   +i+   v   +l k +  +g i el ++++ k++++l++  ++k  l++v     + +v + +fe+ L+e+d+  +k 
  gi|91773055|ref|YP_565747.1|   6 PIIPENVNKEDLDKELIRIGMIAELdAVNFYKQMTPLTKdeDLKAVLLEVA---REEMVHIAMFETVLMEVDSVYLKV 80 
                                   66777788888999999999999987899*9*******9889*********...******************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 561.03
//
Query:       gi|91773056|ref|YP_565748.1|  [L=374]
Description: transposase, mutator type [Methanococcoides burtonii DSM 6242]
Scores for 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-113  376.9   3.9   1.2e-112  376.6   3.9    1.0  1  Transposase_mut  Transposase, Mutator family
    3.1e-10   40.4   0.0    8.9e-10   38.9   0.0    1.8  1  MULE             MULE transposase domain
    0.00019   21.0   0.7    0.00039   20.0   0.7    1.5  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.033   13.9   0.3       0.12   12.1   0.1    2.1  2  DUF4423          Domain of unknown function (DUF4423)
      0.041   14.1   5.7        5.7    7.2   4.1    2.9  2  DDE_Tnp_IS240    DDE domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.6   3.9  3.3e-116  1.2e-112      22     380 ..      14     365 ..       4     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 376.6 bits;  conditional E-value: 3.3e-116
               Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykRreka 102
                                   ++  lk l++ +l+e++e+e+ e+ ga ++ers +r+ +RnG+r+r+l+Tr g+l+l+ P++R+  F ++++ery R+eka
  gi|91773056|ref|YP_565748.1|  14 SNVSLKPLITYFLNEVMEQEAIEQSGAGKHERSITRTAHRNGYRDRSLTTRHGELTLKKPQLRDFPFTTQVFERYSRTEKA 94 
                                   55678999************************************************************************* PP

               Transposase_mut 103 leavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrvvsk 183
                                   +e++++e yv+Gvstrkvek++ +l++ +s+S+s vS+i+++ld++v+ f ++++e++   +l++Da+ylkvR+  r v+k
  gi|91773056|ref|YP_565748.1|  95 IENAIVESYVQGVSTRKVEKIISQLGV-ESISRSRVSRIAQDLDKTVHGFMNKPIEHE-IKYLYVDATYLKVRDRVRYVNK 173
                                   ***************************.77***************************9.********************** PP

               Transposase_mut 184 avliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrvHllrnll 264
                                   av+i  gv+ dG+reiLg+++adsE++ fW++++++Lk+rGl+gvelv+sD+hkG+++a+++ f +a++Q C+vHl r +l
  gi|91773056|ref|YP_565748.1| 174 AVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKERGLRGVELVISDGHKGIQRAVERQFLGASWQMCIVHLERLIL 254
                                   ********************************************************************************* PP

               Transposase_mut 265 akvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafpeqirrkikstNllErLN 344
                                   +k+p+k+ ++ +e++k + +       + +l  ++ ++ +  + k+ae++++ +  ++++ afp++++++ik+tN++ErLN
  gi|91773056|ref|YP_565748.1| 255 KKLPRKHHKEAMESFKEVQDD------QTKLLGLMVEWDRpGFEKAAETIERFQHGLTNYQAFPKEHWKRIKTTNMIERLN 329
                                   **************9987543......345555666677789*************************************** PP

               Transposase_mut 345 keirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                   ke++Rr++vvg FPn+es++rlv avl +++++w++
  gi|91773056|ref|YP_565748.1| 330 KEVKRRSKVVGAFPNDESLMRLVIAVLIDQNENWIT 365
                                   **********************************86 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.5e-13   8.9e-10       2      94 ..     155     250 ..     154     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.5e-13
                          MULE   2 vvlDgTyktnkykl.....plltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnal 77 
                                   + +D+Ty++ + ++       ++v gv++ g   +l++ + +se+   +e ++++l+e+ +  r  + +i+D +k++++a+
  gi|91773056|ref|YP_565748.1| 155 LYVDATYLKVRDRVryvnkAVFIVAGVKNDGYREILGVKIADSEEAMFWEEMFTDLKER-GL-RGVELVISDGHKGIQRAV 233
                                   679****99865441122167889**********************************5.44.7***************** PP

                          MULE  78 eevfpeakhrlClfHia 94 
                                   e++f +a  ++C+ H++
  gi|91773056|ref|YP_565748.1| 234 ERQFLGASWQMCIVHLE 250
                                   ***************97 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.7   1.1e-07   0.00039      11     238 ..      97     336 ..      88     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                  DDE_Tnp_IS66  11 eilvlkyadhlPlyRqeeilarlGv.elsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkks 90 
                                   +++v+ y+++++ +++e+i+++lGv  +sr+ +++  ++  +++  ++++  ++  + +++ +D T l+v +  r +  ++
  gi|91773056|ref|YP_565748.1|  97 NAIVESYVQGVSTRKVEKIISQLGVeSISRSRVSRIAQDLDKTVHGFMNKPIEH--EIKYLYVDATYLKVRD--RVRYVNK 173
                                   6799*********************569***99999988888888888776654..55799********877..6888888 PP

                  DDE_Tnp_IS66  91 ylWvyvtdkr...kpavlfeyspsRggevaealLag.....fkG..vlvsDgyagYnklae...eqvthalCwaHlrRkfv 158
                                    +++++  k+   +++   ++++s  +   e+++++      +G   ++sDg++g ++  e    ++  ++C +Hl R + 
  gi|91773056|ref|YP_565748.1| 174 AVFIVAGVKNdgyREILGVKIADSEEAMFWEEMFTDlkergLRGveLVISDGHKGIQRAVErqfLGASWQMCIVHLERLIL 254
                                   88888887777899*************999999777664665556679*********976657778888*********887 PP

                  DDE_Tnp_IS66 159 daeeakkk...sqaaaealar.igklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgkairyll 235
                                   +   +k +    +  +e +++   kl  +  e+  ++  e++a   e+ +  l++++a  +e+ k+++  + ++++ ++++
  gi|91773056|ref|YP_565748.1| 255 KKLPRKHHkeaMESFKE-VQDdQTKLLGLMVEWD-RPGFEKAAETIERFQHGLTNYQAFPKEHWKRIKTTNMIERLNKEVK 333
                                   66655432232222222.2222555555555553.2456677777777777777777766666566655555555555555 PP

                  DDE_Tnp_IS66 236 krw 238
                                   +r 
  gi|91773056|ref|YP_565748.1| 334 RRS 336
                                   555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.48   1.7e+03     106     130 ..     121     128 ..      86     148 .. 0.55
   2 ?   12.1   0.1   3.3e-05      0.12      92     145 ..     252     305 ..     247     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.48
                       DUF4423 106 iealervpkeeRdissltlaisked 130
                                   +e                 +is++ 
  gi|91773056|ref|YP_565748.1| 121 VE-----------------SISRSR 128
                                   33.................344444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.3e-05
                       DUF4423  92 eavrsyhkqmlelAiealervpkeeRdissltlaiskedyekikkeirefrkki 145
                                   + ++++ ++  ++A+e++++v+ ++ ++ +l++  ++  +ek+++ i++f++ +
  gi|91773056|ref|YP_565748.1| 252 LILKKLPRKHHKEAMESFKEVQDDQTKLLGLMVEWDRPGFEKAAETIERFQHGL 305
                                   567788888999**************************************9866 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.4e+03      64      96 ..      82      97 ..      48     124 .. 0.58
   2 ?    7.2   4.1    0.0016       5.7      84     124 ..     292     350 ..     153     360 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                 DDE_Tnp_IS240 64 tDkasayasalkelkregelfdevshvqvkyln 96
                                  t                    ++ s+ ++  +n
  gi|91773056|ref|YP_565748.1| 82 TQVF-----------------ERYSRTEKAIEN 97
                                  3222.................222333333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0016
                 DDE_Tnp_IS240  84 f...................devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                                        + +h+++    n+iE+ ++++K+r ++++ f + +s+ +
  gi|91773056|ref|YP_565748.1| 292 EkaaetierfqhgltnyqafPK-EHWKRIKTTNMIERLNKEVKRRSKVVGAFPNDESLMR 350
                                   0333333333344444444333.7888888999999999999999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2255.53
//
Query:       gi|91773057|ref|YP_565749.1|  [L=173]
Description: hypothetical protein Mbur_1069 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-19   66.8  16.6    8.7e-10   37.9   2.3    4.8  5  Hexapep     Bacterial transferase hexapeptide (six repeats)
    1.4e-08   34.4  18.0    1.5e-05   24.7   5.5    4.6  6  Hexapep_2   Hexapeptide repeat of succinyl-transferase
     0.0062   15.5   0.5        0.1   11.5   0.4    2.2  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 !   19.7   0.0   8.4e-08    0.0005       4      36 .]      12      44 ..       9      44 .. 0.87
   2 !    4.2   0.1    0.0065        39       3      17 ..      50      64 ..      48      66 .. 0.56
   3 !   12.8   0.3   1.2e-05     0.073      20      35 ..      71      86 ..      70      87 .. 0.79
   4 !   37.9   2.3   1.4e-13   8.7e-10       1      34 [.      87     120 ..      87     122 .. 0.95
   5 ?   -0.9   0.0      0.26   1.5e+03      28      36 .]     126     134 ..     125     134 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.4e-08
                                  EETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep  4 IGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                  I + +++   a i g+VkIG+++ ++ +++i+g
  gi|91773057|ref|YP_565749.1| 12 ISETSFVADSADIIGDVKIGEGSSVWFNATIRG 44
                                  556677888899*******************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0065
                                  EEETTEEE-TTEEEE CS
                       Hexapep  3 vIGsnvlIgpfavig 17
                                  ++G+++ I  ++v++
  gi|91773057|ref|YP_565749.1| 50 IVGKKSSIQDNCVVH 64
                                  456666666666654 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 1.2e-05
                                  EEE-TTEEEETTEEEE CS
                       Hexapep 20 VkIGdnvkIgagvvig 35
                                  V+IGdn+ Ig+g+ ++
  gi|91773057|ref|YP_565749.1| 71 VTIGDNASIGHGAILH 86
                                  8899999999988776 PP

  == domain 4  score: 37.9 bits;  conditional E-value: 1.4e-13
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   +++IG+nvl+g++++i++++++G+n++Iga++ +
  gi|91773057|ref|YP_565749.1|  87 GCTIGNNVLVGMNSTILDGAEVGENSIIGANALV 120
                                   699****************************987 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 0.26
                                   EETTEEEES CS
                       Hexapep  28 Igagvvigg 36 
                                   I +++v++g
  gi|91773057|ref|YP_565749.1| 126 IPPNSVVTG 134
                                   677787775 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.085   5.1e+02      16      25 ..      25      35 ..      20      42 .. 0.75
   2 !    4.0   1.5    0.0071        42       2      32 ..      28      63 ..      27      65 .. 0.63
   3 !   22.2   4.6   1.5e-08   8.7e-05       2      32 ..      71     102 ..      70     104 .. 0.95
   4 !   24.7   5.5   2.4e-09   1.5e-05       3      30 ..      89     118 ..      87     122 .. 0.94
   5 !   10.5   1.4   6.4e-05      0.38       4      16 ..     108     120 ..     105     134 .. 0.80
   6 ?   -1.1   0.1      0.27   1.6e+03      12      18 ..     128     135 ..     122     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.085
                                  ES.EEE-TT-E CS
                     Hexapep_2 16 iG.vslGdncv 25
                                  iG v++G+++ 
  gi|91773057|ref|YP_565749.1| 25 IGdVKIGEGSS 35
                                  55588888875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0071
                                  EEE-TT-EE-TT-EE.S....EEE-TT-EE-TT-EE CS
                     Hexapep_2  2 viIGdnCliGanagi.G....vslGdncvvgaGvvi 32
                                  v+IG+ + +  na+i G    +++G+++ ++ ++v+
  gi|91773057|ref|YP_565749.1| 28 VKIGEGSSVWFNATIrGdkdeIIVGKKSSIQDNCVV 63
                                  566666666667777755566777777776666665 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 1.5e-08
                                   EEE-TT-EE-TT-EE.SEEE-TT-EE-TT-EE CS
                     Hexapep_2   2 viIGdnCliGanagi.GvslGdncvvgaGvvi 32 
                                   v+IGdn  iG  a+  G ++G+n+ vg++++i
  gi|91773057|ref|YP_565749.1|  71 VTIGDNASIGHGAILhGCTIGNNVLVGMNSTI 102
                                   99************88*************998 PP

  == domain 4  score: 24.7 bits;  conditional E-value: 2.4e-09
                                   EE-TT-EE-TT-EE..SEEE-TT-EE-TT- CS
                     Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGv 30 
                                   +IG+n+l+G n++i  G ++G+n+++ga+ 
  gi|91773057|ref|YP_565749.1|  89 TIGNNVLVGMNSTIldGAEVGENSIIGANA 118
                                   7***************************96 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 6.4e-05
                                   E-TT-EE-TT-EE CS
                     Hexapep_2   4 IGdnCliGanagi 16 
                                   +G+n++iGana +
  gi|91773057|ref|YP_565749.1| 108 VGENSIIGANALV 120
                                   8999999999977 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 0.27
                                   TT-EE.SE CS
                     Hexapep_2  12 anagi.Gv 18 
                                   +n+++ Gv
  gi|91773057|ref|YP_565749.1| 128 PNSVVtGV 135
                                   46664465 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.6   0.1     0.009        54     286     332 ..      11      65 ..       5      73 .. 0.65
   2 !   11.5   0.4   1.7e-05       0.1     271     334 ..      74     136 ..      49     165 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.009
                    Fucokinase 286 svgegsviehs.slkgnvsigsnsiv.sglelessee......slelpddtilqt 332
                                   s++e+s + +s ++ g+v+ig++s v  +  ++ +++      + +++d+++++t
  gi|91773057|ref|YP_565749.1|  11 SISETSFVADSaDIIGDVKIGEGSSVwFNATIRGDKDeiivgkKSSIQDNCVVHT 65 
                                   5677777776625669999999988745777777777555555555555555554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.7e-05
                    Fucokinase 271 kesavvinSvlessvsvgegsvi.ehsslkgnvsigsnsivsglelesseeslelpddtilqtls 334
                                    ++a++ +  + +++++g++ ++ ++s++ ++ ++g+nsi+    l  s     +p ++++ +++
  gi|91773057|ref|YP_565749.1|  74 GDNASIGHGAILHGCTIGNNVLVgMNSTILDGAEVGENSIIGANALVPS--GKVIPPNSVVTGVP 136
                                   4455555555555555555554423555555555555555532222222..23455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1105.43
//
Query:       gi|91773058|ref|YP_565750.1|  [L=142]
Description: hypothetical protein Mbur_1070 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   39.9   0.4    4.2e-10   39.6   0.4    1.1  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.4   2.3e-14   4.2e-10      27     134 ..      40     135 ..      17     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.3e-14
                     DDE_Tnp_1  27 ykggkykygy.klhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgklvlaDaGYasaelldtle.ekgvdyii 104
                                   +  +k+++ y k  i vd    +i++++i+ + vhd+k++k+ll +++++ +++++++D++Y+s+++++  + + g   i+
  gi|91773058|ref|YP_565750.1|  40 WRIKKWRRSYvKTSISVDVSKFVITGYKISGKPVHDTKHAKTLLSQCHHNrRSRYYVMDKAYDSEKIHELTReKLGSIAIV 120
                                   45678888888**********9**************************************************555555566 PP

                     DDE_Tnp_1 105 rlkkntklyrkgaeskrrgrlrkhdrnkil 134
                                   +l               r+r+rk+++++ +
  gi|91773058|ref|YP_565750.1| 121 PL---------------RQRERKRIKGRYR 135
                                   55...............5555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 921.97
//
Query:       gi|91773059|ref|YP_565751.1|  [L=78]
Description: hypothetical protein Mbur_1071 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 523.30
//
Query:       gi|91773060|ref|YP_565752.1|  [L=157]
Description: hypothetical protein Mbur_1072 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 900.36
//
Query:       gi|91773061|ref|YP_565753.1|  [L=337]
Description: isocitrate dehydrogenase (NADP) [Methanococcoides burtonii DSM 6242]
Scores for complete 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-84  282.8   0.0    4.5e-84  282.6   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 !  282.6   0.0   2.5e-88   4.5e-84       3     348 .]       6     333 ..       4     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: 282.6 bits;  conditional E-value: 2.5e-88
                                   EEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS..SSS-HHHHHHHHHSSEEEEEE---CS.SSSSS CS
                        Iso_dh   3 allegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg..eplpeetleaikeadvvllgavgtpk.ekevr 80 
                                   a++egdg+Gpe v+a++kv +a+     +++ef ++++G +  ++ g  + +p+et + ++ead+  +g+++tp  +++ r
  gi|91773061|ref|YP_565753.1|   6 AVIEGDGVGPELVDAMVKVAEAVG----TNVEFVKCEAGVQWWEKNGgaTLIPDETWALLDEADACFKGPTTTPGgAGSPR 82 
                                   79*******************999....5688*************998899***********************9444455 PP

                                   HHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHH CS
                        Iso_dh  81 pengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseee 161
                                   +    +++r++ +l+an+rp+k f   + ++pl      +vd+v+vRe t+g+Y+gee + ++      v + + ++++ +
  gi|91773061|ref|YP_565753.1|  83 SVA--VSIRQKYNLYANVRPIKTF--PNTNNPLG-----DVDFVCVREGTEGMYIGEEVKLTDD-----VYIAIRKITRPA 149
                                   555..9******************..56667776.....59*****************999987.....89********** PP

                                   HHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGS..EEEE-H CS
                        Iso_dh 162 ieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspkqfd..VivtkN 239
                                    + ia+++fe A+krg ++v+ ++K+n+lk++  ++ ++ve+vae  yp+i + +  vD++a+ql+k+p+ f+  +++ +N
  gi|91773061|ref|YP_565753.1| 150 CKNIATYSFEEAKKRGYDTVVPIHKSNILKMTCgTFLEEVEKVAE-GYPGIDVWEYHVDNIAQQLIKNPQLFNnkILLSTN 229
                                   *********************************9***********.************************99889****** PP

                                   HHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHH CS
                        Iso_dh 240 lfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiekAvek 320
                                   lf D++S e++al+Gs+Gl+ Sa++g +++a+fE++HGsap++ag dk+Np+a+il+ a mL y lg++++ ++i kA e+
  gi|91773061|ref|YP_565753.1| 230 LFMDVISEECSALIGSIGLIYSANIG-DNFAMFEPAHGSAPKYAGLDKVNPVATILAGAWMLDY-LGESDKFAQIFKATED 308
                                   **************************.78***********************************.**************** PP

                                   HHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
                        Iso_dh 321 vlea.givTkDlageaakevstsefgdav 348
                                   v+ + + +T+Dl+g+a    s se++da+
  gi|91773061|ref|YP_565753.1| 309 VISEgKHLTYDLGGKA----SLSEMTDAI 333
                                   ****8889********....999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2212.42
//
Query:       gi|91773062|ref|YP_565754.1|  [L=395]
Description: MscS mechanosensitive ion channel [Methanococcoides burtonii DSM 6242]
Scores for 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-24   84.1   4.3    9.7e-24   84.1   4.3    1.7  2  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.15   12.0   5.2       0.11   12.4   3.3    1.8  2  Cauli_AT         Aphid transmission protein
       0.16   12.0   8.7       0.27   11.3   8.7    1.4  1  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
       0.23   11.8   3.3       0.83   10.0   3.3    2.0  1  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
       0.26   11.7   7.8       0.53   10.7   7.8    1.5  1  Caps_synth_CapC  Capsule biosynthesis CapC
        1.5    8.7   5.7        2.4    8.0   5.7    1.3  1  DUF2975          Protein of unknown function (DUF2975)
        8.3    5.2  10.3       0.55    9.1   4.6    1.7  2  LMBR1            LMBR1-like membrane 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 ?   -3.8   1.4       2.9   7.5e+03       5      22 ..      10      27 ..       7      34 .. 0.47
   2 !   84.1   4.3   3.8e-27   9.7e-24       6     206 .]      48     238 ..      40     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.9
                                  HHHHHHHHHHHHHHTTT- CS
                    MS_channel  5 kiliivvgilivlsllgv 22
                                   ++ii++++l++l ++  
  gi|91773062|ref|YP_565754.1| 10 IYTIIALFVLLTLLSYIL 27
                                  455555555555444433 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 3.8e-27
                                   HHHHHHHHHHHHHTTT--SCCHHHHHHH.HHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEE CS
                    MS_channel   6 iliivvgilivlsllgvnvsallavlGa.lglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttk 85 
                                    l+ +v il++l     + ++ll+ lG+ lg+ ++l + + ++n ++G++l + kpfk GD+++i+d  G+V +i+++ t+
  gi|91773062|ref|YP_565754.1|  48 TLLGIVLILLTLPITDNSKQTLLSFLGIlLGATIALSSTTFVANGMSGMMLNIIKPFKTGDYIRIEDKFGKVSSIKILHTQ 128
                                   4566677777777777779********846*************************************************** PP

                                   EEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SS CS
                    MS_channel  86 irtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefgds 166
                                   i++ d+ ++ iPn +lv++  +  s    ++ i  ++++ y+++   ++++ ++l +a++++  ++    ++v+++e+ d 
  gi|91773062|ref|YP_565754.1| 129 IQSIDRDLINIPNLKLVSNPLVTIST--SGTIISATVSLGYDTP---WKHIEKNLIRAAERTN-LE---SPFVHVTELNDH 200
                                   **************************..9999************...***********99887.44...59********** PP

                                   SEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                    MS_channel 167 slnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                   +++++v  ++++  ++     +s++n+ ++++l+e giei
  gi|91773062|ref|YP_565754.1| 201 AVTYKVGGLLRD--ISGLITKKSDLNKAVIDALHEDGIEI 238
                                   ************..9***********************97 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   7.6e+03     139     148 ..     124     133 ..      93     150 .. 0.58
   2 ?   12.4   3.3   4.2e-05      0.11      67     135 ..     324     391 ..     292     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                      Cauli_AT 139 llkeevkdld 148
                                    l+++++ +d
  gi|91773062|ref|YP_565754.1| 124 ILHTQIQSID 133
                                   2222222222 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                      Cauli_AT  67 ylGLekDesealsksksPfgsvfkklkkifkeggedkekktklletLkeaqnrikkleeetkklaekiv 135
                                    +  e+++ e + k+k  ++s fk +kk f++ ++dk+  + +l+tL+ +++r  ++++e++kl ek++
  gi|91773062|ref|YP_565754.1| 324 MFVTEQEKTEYIEKQKAELESSFKIMKKTFEK-EDDKTPDAIKLKTLQYVDSRLIEMDNEMEKLLEKLK 391
                                   56678899999******************976.67777888889********************99986 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 ?   11.3   8.7   0.00011      0.27      56     133 ..       6      81 ..       1      89 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
               Polysacc_synt_C  56 vGaaiatvlallvvavlnlyalrrllgikl.ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalv 133
                                   +   i t++al+v + l+ y+lr++  +   +++++++  + +a ++giv++ ll l ++ ++ ++l  +l++l+ga +
  gi|91773062|ref|YP_565754.1|   6 YQLTIYTIIALFVLLTLLSYILRKTAIFTRdKMIKQII--ISVATLLGIVLI-LLTLPITDNSKQTLLSFLGILLGATI 81 
                                   556788******************99999986677774..555555555533.44444444444567888999888876 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 ?   10.0   3.3   0.00033      0.83       3      66 ..      18      86 ..      16      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
               Phage_holin_5_2  3 vilyiiGeilKktekvkd.kyIPlilgiiGiilgvvivfta....dfqaedilifgaiiqGilsggast 66
                                  v l ++ +il+kt  +   k+I  i++ +  +lg+v +++     d  ++  l f  i+ G+ ++++st
  gi|91773062|ref|YP_565754.1| 18 VLLTLLSYILRKTAIFTRdKMIKQIIISVATLLGIVLILLTlpitDNSKQTLLSFLGILLGATIALSST 86
                                  667899999999986655677777777777777755555534654666666666669999999999998 PP

>> Caps_synth_CapC  Capsule biosynthesis CapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   7.8   0.00021      0.53      35     109 ..       8      84 ..       1      89 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
               Caps_synth_CapC  35 sllvtllialltylivrllsrflilyGrrrfvavlllgv..lvklllelllllllpaelveeleviGlivpgLiAnd 109
                                     ++t+++ ++++ ++ ++ r + ++ r++++  ++++v  l+ ++l ll+l+++++++++ l+++G+++ + iA +
  gi|91773062|ref|YP_565754.1|   8 LTIYTIIALFVLLTLLSYILRKTAIFTRDKMIKQIIISVatLLGIVLILLTLPITDNSKQTLLSFLGILLGATIALS 84 
                                   4456666666777777889999999******97666666115566666667777888888899******99999975 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.7   0.00094       2.4      27     108 ..       8      83 ..       1      93 [. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00094
                       DUF2975  27 allafvvalvqlwkLlrsirk.gevFspanvrrLrriglaliaaalllaagivalallaelelapgvvllllgvafaslvi 106
                                    ++  ++al+ l+ Ll++i +   +F++  +     i++a+++ ++l++++++++  +++       +ll+++ +++++ i
  gi|91773062|ref|YP_565754.1|   8 LTIYTIIALFVLLTLLSYILRkTAIFTRDKMIKQIIISVATLLGIVLILLTLPITDNSKQ-------TLLSFLGILLGATI 81 
                                   5688899**********98553899****999999999999999****************.......33333333333333 PP

                       DUF2975 107 gl 108
                                   +l
  gi|91773062|ref|YP_565754.1|  82 AL 83 
                                   33 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.6   0.00022      0.55     128     181 ..      10      61 ..       6      64 .. 0.69
   2 ?   -1.4   0.3      0.33   8.5e+02     196     218 ..     336     357 ..     239     391 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00022
                         LMBR1 128 iiyllllvivlglliyvliilqklsllsik.sllpilislantwGlvllilllGy 181
                                   i+ ++ l+++l ll y+l +     + + +  +++i+is+a+ +G+vl++l l++
  gi|91773062|ref|YP_565754.1|  10 IYTIIALFVLLTLLSYILRK---TAIFTRDkMIKQIIISVATLLGIVLILLTLPI 61 
                                   33344444444455555554...455555669********************997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.33
                         LMBR1 196 sdldeelkklyfeaaklntekee 218
                                   ++ + el++  f+++k + eke+
  gi|91773062|ref|YP_565754.1| 336 EKQKAELESS-FKIMKKTFEKED 357
                                   1222222222.333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1806  (0.100731); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2613.36
//
Query:       gi|91773063|ref|YP_565755.1|  [L=425]
Description: pyruvate carboxyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  136.5   0.0    1.6e-39  136.1   0.0    1.1  1  HMGL-like  HMGL-like
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.27   11.2   0.0    1.4  1  Mor        Mor transcription activator family


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 !  136.1   0.0   1.7e-43   1.6e-39       2     259 ..      21     284 ..      20     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 1.7e-43
                                   -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B...--EE-SSHHHHHHH CS
                     HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkar.ilalvrarekdikaa 81 
                                   v i+d+tLRDG q ++  l+v++k++i + L ++g++++E+ +      d++++    + + +   +++++ra+ +di+  
  gi|91773063|ref|YP_565755.1|  21 VSISDSTLRDGAQMPGIVLKVDHKVKIYEYLHNIGIEKLETFVYNDR--DRNAISMMLDRGYEFPeVTGWARAATSDIDLV 99 
                                   78**************************************9887766..99999999998866534*************** PP

                                   HH....TT-SEEEEEEES-HHHHHHHHSS.THHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--.HHHHHHHHHHHHHHT- CS
                     HMGL-like  82 vealkgagakrvhvfiatselhlkaklkk.dreevakkaeeavkaarslgkdvelsledasrtd.leflaevveaaeeaGa 160
                                    +     + ++  + +++s++h+  k++  +re + +k  +a+++a ++g +++  +ed +r+d  +f++ +++++ e+ +
  gi|91773063|ref|YP_565755.1| 100 LD---IGAIEETGILMSVSDVHIFDKMGLpSREAAEEKYLDALQYAVDHGLRTRAHIEDMTRADnTNFVYPMIKKILEIDP 177
                                   **...66778999**************974777788899***********************98357999*********99 PP

                                   SE.EEEEETTS--.......-HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB CS
                     HMGL-like 161 tr.iniaDtvGvl.......tPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGn 233
                                   ++ i++ Dt+G+        +P+ + e+++ +ke++k  v +++HcH+d+GlAvan++a++  Ga++ ++t +G+GeraGn
  gi|91773063|ref|YP_565755.1| 178 KCtIRLCDTIGFGipfvdveEPFGIPEMVRHVKEELK-AVNIETHCHDDFGLAVANSIAGYWHGANWSNVTFLGIGERAGN 257
                                   8559*****99762222222677899999******99.******************************************* PP

                                   -BHHHHHHHHHHTT.-B----HHHHHH CS
                     HMGL-like 234 aaleelvaalealg.vdtgldlqklrs 259
                                   a le+l + le++     ++dl++l +
  gi|91773063|ref|YP_565755.1| 258 AELEKLLLFLERRIeGFDKYDLKSLFE 284
                                   **********99864445566666655 PP

>> Mor  Mor transcription activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.27       9      48 ..     204     242 ..     198     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHHHHHTS.S-....TTSHHHHHHHHHHHH-SS- CS
                           Mor   9 dlakhvaaelkrlgeidealaeqigeevadalaahwGGqq 48 
                                   +++ hv++elk ++ i+++  + +g +va+++a +w G +
  gi|91773063|ref|YP_565755.1| 204 EMVRHVKEELKAVN-IETHCHDDFGLAVANSIAGYWHGAN 242
                                   7899**********.*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2688.48
//
Query:       gi|91773064|ref|YP_565756.1|  [L=167]
Description: amino acid-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.0   0.0    6.2e-05   22.7   0.0    1.7  1  ACT       ACT domain
  ------ inclusion threshold ------
       0.18   11.7   0.0        3.4    7.7   0.0    2.3  2  F-box     F-box domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.9e-09   6.2e-05      11      66 ..     106     159 ..     102     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.9e-09
                                   TTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT  11 PGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                   +G+L+ v++++++++i+i+ + +      +++ ++++i++d +++ ++++++ +l+
  gi|91773064|ref|YP_565756.1| 106 VGILFSVSQVISNHNISIRQAVSDDPY--FNSKAMLTIITDSKVPGDIVNEILQLP 159
                                   6*****************999988885..69*********************9998 PP

>> F-box  F-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00038       3.4       6      21 ..      66      79 ..      64      88 .. 0.79
   2 ?    1.5   0.0     0.032   2.9e+02       4      16 ..     145     157 ..     143     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00038
                                  S-HHHHHHHHHTS-HH CS
                         F-box  6 LPsevlrhILerLpls 21
                                  L++e+l++I++++  +
  gi|91773064|ref|YP_565756.1| 66 LSDELLKNIFQNV--T 79
                                  9**********95..4 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.032
                                   HHS-HHHHHHHHH CS
                         F-box   4 srLPsevlrhILe 16 
                                   s +P +++++IL+
  gi|91773064|ref|YP_565756.1| 145 SKVPGDIVNEILQ 157
                                   789*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.51
# Mc/sec: 990.56
//
Query:       gi|91773065|ref|YP_565757.1|  [L=399]
Description: geranylgeranyl reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-15   56.4   2.0    4.4e-09   36.1   0.1    2.6  2  FAD_binding_3   FAD binding domain
    9.1e-09   35.2   0.4    1.5e-08   34.5   0.4    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    1.7e-07   30.8   1.4    2.7e-07   30.1   1.4    1.4  1  Thi4            Thi4 family
    3.4e-07   29.6   0.9    4.1e-06   26.1   0.9    2.0  1  Lycopene_cycl   Lycopene cyclase protein
    6.4e-06   25.6   3.2    9.2e-06   25.1   0.2    2.4  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.3e-06   25.1   0.4     0.0066   15.3   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    1.5e-05   24.7   2.8    0.00012   21.8   1.2    2.3  2  DAO             FAD dependent oxidoreductase
    4.8e-05   22.3   1.0    7.4e-05   21.6   0.1    1.6  2  HI0933_like     HI0933-like protein
    0.00012   22.2   0.7    0.00058   20.0   0.1    2.4  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0018   17.5   0.3     0.0031   16.6   0.3    1.4  1  FAD_binding_2   FAD binding domain
     0.0024   17.0   0.7     0.0058   15.7   0.3    1.8  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
       0.11   11.7   0.0       0.11   11.7   0.0    2.3  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.13   11.4   0.2       0.29   10.3   0.2    1.5  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3     6e-07   0.00083       2      33 ..       3      34 ..       2      38 .. 0.95
   2 !   36.1   0.1   3.2e-12   4.4e-09      92     336 ..      83     318 ..      50     324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6e-07
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                  +dV++VGaGp+G ++a+  ++ G +v+++e +
  gi|91773065|ref|YP_565757.1|  3 YDVVVVGAGPTGSTAARYATMGGAKVLIIEEH 34
                                  59****************************87 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 3.2e-12
                                   CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHH CS
                 FAD_binding_3  92 lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktl 172
                                   ++ + ++ +v++ + ++r Lv+ a+ +g+++  k +v++++q  +g++     +  g+  tvr+k ++GaDG++S v++  
  gi|91773065|ref|YP_565757.1|  83 IDGKRTKAYVVSRKIFDRHLVSLAVDTGAELMLKGRVTGIQQK-DGIQLLSVIH-MGKMITVRSKVVIGADGVKSNVARYT 161
                                   5667777888888999**********************87665.5655544444.68888********************* PP

                                   TGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEE.EEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHH CS
                 FAD_binding_3 173 giefegeetvyeagvldvlfdadlsdiveplvlilsaesrgv.mviPlentlerfyvqvearaekeersekfteeevkarl 252
                                   g+     +++     ++++ +++ +d+ve   +++s+ ++++   +P+++     +  + +  e +++ ++++   +++++
  gi|91773065|ref|YP_565757.1| 162 GLG--KVDRILSGVQIEAVYSSNDTDFVEL--FVGSQAPGFFaWTVPVNER----ISRIGLAVEPGNEHNAIN--YLRKIV 232
                                   *87..5556666666777777766657766..8888888888567899993....333444444444444443..344444 PP

                                   HHHHTTS.SCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS.-GGGG CS
                 FAD_binding_3 253 reivgek.tldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeA.keelL 331
                                   ++  + +   + ++ +  + ++     ++  ++ +++aGDAa  + Pt G G+ t++  a   +   a+++++e  + ++L
  gi|91773065|ref|YP_565757.1| 233 NKNKHLAgNCTNNMLDLVVGGIPIGPLKRTYSDGILIAGDAAGQVKPTSGGGVYTGAVCAKMAGQVAAEAVSEENfSANRL 313
                                   4333333034457777777777777788888999*********************99888888887776665543266777 PP

                                   HHHHH CS
                 FAD_binding_3 332 dtYee 336
                                   + Ye+
  gi|91773065|ref|YP_565757.1| 314 KEYES 318
                                   77776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.4   1.1e-11   1.5e-08       1     142 [.       4     150 ..       4     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.1e-11
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG......Glltsglvatdignkaeeqvvtgiareflerlrqrgga.r 74 
                                   DvvVvG+gp G +AA  A   Gakvl++ee+  +G      Gll+  +v+  +     ++v + + + f++    +g++ +
  gi|91773065|ref|YP_565757.1|   4 DVVVVGAGPTGSTAARYATMGGAKVLIIEEHFSIGspvectGLLSTRAVSECDVRPEDDFVLNSVRGAFVNSP--NGTClP 82 
                                   9**********************************999999999999998888877688*************9..455664 PP

                  FAD_oxidored  75 lk.krskwntfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDA 142
                                   +  kr+k  ++  +++ + l  +  + g +++l+ r++++++++  i+ + v +  +++t+r+kv+i A
  gi|91773065|ref|YP_565757.1|  83 IDgKRTKAYVVSRKIFDRHLVSLAVDTGAELMLKGRVTGIQQKD-GIQLLSVIHMGKMITVRSKVVIGA 150
                                   443555556789999999999999999***************97.899999977668*********976 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   1.4   1.9e-10   2.7e-07      18     170 ..       3     155 ..       1     179 [. 0.68

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.9e-10
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEE....EETTTHHHHHHTT---EEESSEEEE. CS
                          Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaiv....vrkpakelLdelgikyedegdyvvv. 93 
                                    Dvv+vGaG++G taa+y +   + kv+i+e++ s+G  +   G l ++ v    vr + + +L+ +  ++ ++ ++    
  gi|91773065|ref|YP_565757.1|   3 YDVVVVGAGPTGSTAARYATMG-GAKVLIIEEHFSIGSPVECTGLLSTRAVsecdVRPEDDFVLNSVRGAFVNSPNGTCLp 82 
                                   6*****************8887.***************9999999877766344466667777888877766666655442 PP

                                   SEHHHHHHHHHHHHH.TSTTEEEEESEEEEEEEEETBTEEEEEEEE..EHHHHTCTTTSS.-B-EEEEEEEEEE--GSSS CS
                          Thi4  94 kdaalftstllskvl.qlanvkllnavaveDlivregegvaGvvin..wtlvelahdtqscvDPlvirakvvvdatGhdg 170
                                    d     + ++s+ + ++  v l   + + +l+++   +v+G+  +   +l+++ h         ++r+kvv+ a G  +
  gi|91773065|ref|YP_565757.1|  83 IDGKRTKAYVVSRKIfDRHLVSLAVDTGA-ELMLKG--RVTGIQQKdgIQLLSVIH----MGKMITVRSKVVIGADGVKS 155
                                   46666666666654315444444444444.467777..777766541134444446....22235677777777766655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.9     3e-09   4.1e-06       1     304 [.       4     320 ..       4     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3e-09
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtivylddgkkil 76 
                                   Dvvv+GaGp g   A        g kv++ie   s+  p + +     +++++      +++v  s +g+ v  ++g    
  gi|91773065|ref|YP_565757.1|   4 DVVVVGAGPTGSTAARYA--TMGGAKVLIIEEHFSIGSPVECTGLLSTRAVSEcdvrpEDDFVLNSVRGAFVNSPNGTCLP 82 
                                   9**********7755555..88999******999998888889888888888878777899***************99888 PP

                 Lycopene_cycl  77 lg....raYgrvsskrlkeellerlv.engvklleakvesveeeeageslvvleggr..kirarlvvdarglaslk...ka 147
                                   ++    +aY  vs+k + ++l    v +++  +l+++v+ +++++  + l v++ g+  ++r+++v+ a g+ s+     +
  gi|91773065|ref|YP_565757.1|  83 IDgkrtKAY-VVSRKIFDRHLVSLAVdTGAELMLKGRVTGIQQKDGIQLLSVIHMGKmiTVRSKVVIGADGVKSNVaryTG 162
                                   887764455.689999999999999945555678************999999999998999**********6665533333 PP

                 Lycopene_cycl 148 rrlglQtfyGvevevdnppfdldkmvlMDfrveqklkgltFlYalPldsdrllvEeTelaskpeLpadalkkrlaaylra. 227
                                   +     +  Gv +e   +  d d ++l    v  +     F +++P++++   +      +++e  a ++ ++++++ ++ 
  gi|91773065|ref|YP_565757.1| 163 LGKVDRILSGVQIEAVYSSNDTDFVEL---FVGSQ-APGFFAWTVPVNERISRIG-LAVEPGNEHNAINYLRKIVNKNKHl 238
                                   333345667888887777666666666...44444.234699*****98754443.3344555566777889999999997 PP

                 Lycopene_cycl 228 lglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres........sl 299
                                    g   +++     g iP+   g+l+r+ +   l +G aag v+P+ G  v      a+ +a  +aa + ++        + 
  gi|91773065|ref|YP_565757.1| 239 AGNCTNNMLDLVVGGIPI---GPLKRTYSDgILIAGDAAGQVKPTSGGGVYTGAVCAK-MAGQVAAEAVSEenfsanrlKE 315
                                   78889999999*******...77777777758999************77777666666.4444444443222333333333 PP

                 Lycopene_cycl 300 saraw 304
                                   +++ w
  gi|91773065|ref|YP_565757.1| 316 YESRW 320
                                   33333 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 !   25.1   0.2   6.6e-09   9.2e-06       1     112 [.       3     156 ..       3     185 .. 0.64
   2 ?   -1.7   0.2      0.94   1.3e+03     256     279 ..     252     281 ..     247     296 .. 0.69
   3 ?    0.3   0.1      0.23   3.2e+02     149     194 ..     283     329 ..     281     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.6e-09
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........................ 57 
                                   +dvvv+G+Gp G +aa+++   gakv+++  e+++  g ++  + ll++++  e                           
  gi|91773065|ref|YP_565757.1|   3 YDVVVVGAGPTGSTAARYATMGGAKVLII--EEHFSIGSPVECTGLLSTRAVSECDVrpeddfvlnsvrgafvnspngtcl 81 
                                   69***************************..88899999988777777777766555667777777777777777777777 PP

                                   ....HHHHCHHHHCCCCHCCTCEEEEESC.EEEEETEEEC................TCEEEEEESEEEE---EEE- CS
                                   ....xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx................xxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ....evvkklnqgielllgeevvkidpgk.kkvklekkke................gdeekiaydklvlAtGsspr 112
                                       + +k +  + + + + + v++  +  +++ l+ +++                g+  ++  + ++ A G +++
  gi|91773065|ref|YP_565757.1|  82 pidgKRTKAYVVSRKIFDR-HLVSLAVDTgAELMLKGRVTgiqqkdgiqllsvihmGKMITVRSKVVIGADGVKSN 156
                                   7777434444444332222.32222222222444444444343333444444444455555555555555555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.94
                                   TEEE--TTSBESSTTEEE-GGGC......T CS
                                   xxxxxxxxxxxxxxxxxxxxxxx......x RF
                   Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva......g 279
                                   ggi + +  rt  +gi  +GD a      +
  gi|91773065|ref|YP_565757.1| 252 GGIPIGPLKRTYSDGILIAGDAAgqvkptS 281
                                   566666667888999999999994443332 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.23
                                   S-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 149 GgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleeale 194
                                   Gg y+G ++A ++ ++++e++  e  +    ++++++++ al ++l+
  gi|91773065|ref|YP_565757.1| 283 GGVYTGAVCAKMAGQVAAEAVSEENFSANRlKEYESRWKSALGRELR 329
                                   7779************9997777776665557888888877777776 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.4     0.001       1.4       1      33 [.       4      33 ..       4      39 .. 0.87
   2 !   15.3   0.0   4.8e-06    0.0066     147     372 ..      89     325 ..      68     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.001
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                  ++v+vG+G+ G++aA +  + +   ++v+++e 
  gi|91773065|ref|YP_565757.1|  4 DVVVVGAGPTGSTAARYATMGG---AKVLIIEE 33
                                  69**************998887...77888875 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.8e-06
                                   -EEEE-HHHHHHHHHHHHHHCT-EE.EE--EEEEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE- CS
                Trp_halogenase 147 yAyhldaalyakfLrrvaearGvtr.vegkvvevqlde.dgrveslrledgreveadlfiDcsGfrgllieqaLktgfedw 225
                                    Ay + ++ ++++L   a + G +  ++g+v+ +q+++     + +++ +  +v    +i + G ++ +   +   g  ++
  gi|91773065|ref|YP_565757.1|  89 KAYVVSRKIFDRHLVSLAVDTGAELmLKGRVTGIQQKDgIQLLSVIHMGKMITVRSKVVIGADGVKSNVARYT---GLGKV 166
                                   599********************9626899999999994455555566567788899**********999986...88888 PP

                                   TTT----EEEEEE.EE--H...---SSEEEEE-SSE.EEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--TT... CS
                Trp_halogenase 226 sdvLltdrAlavq.vesee...lvepytrataekaG.WtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkle... 297
                                    ++L   +++ ++ v+s++    ve + ++ a   G   W +P ++r++  G+++     ++ +A++ l++ ++++++   
  gi|91773065|ref|YP_565757.1| 167 DRIL---SGVQIEaVYSSNdtdFVELFVGSQAP--GfFAWTVPVNERISRiGLAVE--PGNEHNAINYLRKIVNKNKHlag 240
                                   8888...44433312222223477888777775..5167***********888775..55678888888877766654111 PP

                                   .TS-EEEE---EE.....ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHHHHH CS
                Trp_halogenase 298 .aeprkirfttGr.....rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnreva 368
                                     +++++ + +G       k++++ +++  G+a+g v P  + ++++  +    a +  ++   ++ ++   ++e++++ +
  gi|91773065|ref|YP_565757.1| 241 nCTNNMLDLVVGGipigpLKRTYSDGILIAGDAAGQVKPTSGGGVYTGAVcakmAGQVAAEAVSEENFSANRLKEYESRWK 321
                                   1456999999999899999***********************999986653333556667777788888888999998888 PP

                                   HHHH CS
                Trp_halogenase 369 rele 372
                                   ++l+
  gi|91773065|ref|YP_565757.1| 322 SALG 325
                                   7765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.2   8.9e-08   0.00012       1      33 [.       4      38 ..       4      51 .. 0.86
   2 ?    1.5   0.0      0.13   1.8e+02     150     207 ..     100     158 ..      88     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.9e-08
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  dvv++G+G +G+++A++++  g  V+++e +  +g
  gi|91773065|ref|YP_565757.1|  4 DVVVVGAGPTGSTAARYATMGGakVLIIEEHFSIG 38
                                  9*****************88779********7666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                                   HHHHHHHHHTT-EEEESECEEEEEEEE.TCEEEEE.EECTEEE...EEEEEEEE--GGGHHHH CS
                           DAO 150 aalaraaealGveilegtevtgleeed.gkvwgve.rttpgen...daadavVnaaGawsdll 207
                                   + l + a + G+e+ ++ +vtg++++d +++  v      g     ++ + v+ a G+ s+ +
  gi|91773065|ref|YP_565757.1| 100 RHLVSLAVDTGAELMLKGRVTGIQQKDgIQLLSVIhM---GKMitvRS-KVVIGADGVKSNVA 158
                                   5688899999*****999*****87664333333121...22211122.44777777777644 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   5.3e-08   7.4e-05       1      43 [.       3      45 ..       3      46 .. 0.95
   2 ?   -2.2   0.1      0.93   1.3e+03     115     160 ..     102     148 ..      94     159 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.3e-08
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                  +dv+v+G+G+ G  aA  a   g++Vl++e+  ++g+ +  +G
  gi|91773065|ref|YP_565757.1|  3 YDVVVVGAGPTGSTAARYATMGGAKVLIIEEHFSIGSPVECTG 45
                                  59**********************************9999888 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.93
                                   HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEES.EEEE CS
                   HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvkt.kseeelead.klvl 160
                                   l++ + ++g +l+l+ +v++++++++ ++ +++ + ++ ++ + k+v+
  gi|91773065|ref|YP_565757.1| 102 LVSLAVDTGAELMLKGRVTGIQQKDGIQL-LSViHMGKMITVRsKVVI 148
                                   56666788999999999999977655543.333344444433303333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   4.2e-07   0.00058       1      32 [.       7      38 ..       7      57 .. 0.93
   2 ?   -2.7   0.0       5.4   7.5e+03      25      38 ..     232     245 ..     230     253 .. 0.79
   3 ?   -1.7   0.0       2.6   3.5e+03       6      20 ..     294     308 ..     283     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.2e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  +vGaG +G++aA++++  g++vl++e + ++G
  gi|91773065|ref|YP_565757.1|  7 VVGAGPTGSTAARYATMGGAKVLIIEEHFSIG 38
                                  8**************************98888 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                                   E-SSSSSSGGG-EE CS
                 NAD_binding_8  25 lekrdrlGGraasy 38 
                                   + k+ +l G+++ +
  gi|91773065|ref|YP_565757.1| 232 VNKNKHLAGNCTNN 245
                                   56889999999976 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHCCTE CS
                 NAD_binding_8   6 lsGlvaAylLakagf 20 
                                   ++G vaA + ++++f
  gi|91773065|ref|YP_565757.1| 294 MAGQVAAEAVSEENF 308
                                   678888888877766 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   0.3   2.3e-06    0.0031       1      36 [.       4      39 ..       4      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  Dv+V+G+G  G +AA  a+  G+kv+++e  ++ g+
  gi|91773065|ref|YP_565757.1|  4 DVVVVGAGPTGSTAARYATMGGAKVLIIEEHFSIGS 39
                                  9****************************9998766 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   4.2e-06    0.0058       1      33 [.       4      36 ..       4      56 .. 0.86
   2 ?   -2.1   0.0       1.1   1.6e+03      95     139 ..      86     130 ..      63     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.2e-06
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkld 33
                                  dv+V+G+G  G+ AA  a   Gakvl+i ++++
  gi|91773065|ref|YP_565757.1|  4 DVVVVGAGPTGSTAARYATMGGAKVLIIEEHFS 36
                                  79*************************977765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                   HHHHHH.HHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EE CS
                          GIDA  95 elyske.vteklenepnleiieeeveeliveekkvkgvvtedgeti 139
                                   ++ +++ v +k+ + + +++  ++ +el++ +++v+g+ ++dg ++
  gi|91773065|ref|YP_565757.1|  86 KRTKAYvVSRKIFDRHLVSLAVDTGAELML-KGRVTGIQQKDGIQL 130
                                   444444146677888888888888888866.888888888888655 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 ?   11.7   0.0   8.2e-05      0.11      31      60 ..       5      34 ..       3      68 .. 0.91
   2 ?   -2.4   0.1       1.7   2.4e+03     175     195 ..     222     243 ..     221     251 .. 0.71
   3 ?   -2.7   0.1       2.2     3e+03      35      69 ..     282     318 ..     271     335 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.2e-05
                                  EEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvr 60
                                  v+v+G+G  G  A++ a+  gakV +++  
  gi|91773065|ref|YP_565757.1|  5 VVVVGAGPTGSTAARYATMGGAKVLIIEEH 34
                                  9***********************999865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHC.HHHTCCHHHC CS
                   AlaDh_PNT_C 175 nntlpyleell.adkglkkalk 195
                                   +n ++yl++++ ++k+l+  ++
  gi|91773065|ref|YP_565757.1| 222 HNAINYLRKIVnKNKHLAGNCT 243
                                   6889999999988888844443 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.2
                                   STSH.HHHHHHHHHHHTT-E.EEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C  35 GgGv.aGlqAiatakglgak.VtvlDvrparleqles 69 
                                   GgGv  G   +++a ++ a+ V   + +++rl++ es
  gi|91773065|ref|YP_565757.1| 282 GGGVyTGAVCAKMAGQVAAEaVSEENFSANRLKEYES 318
                                   6666457777777777776523444455555555555 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 ?   10.3   0.2   0.00021      0.29       1      33 [.       6      38 ..       6      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                  +++GaGP G +aa  +   g  ++li+E + +ig
  gi|91773065|ref|YP_565757.1|  6 VVVGAGPTGSTAARYATMGGA-KVLIIEEHfSIG 38
                                  79************9999999.7*****986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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 0.26s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2656.88
//
Query:       gi|91773066|ref|YP_565758.1|  [L=427]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-113  380.0   0.4   1.4e-113  379.8   0.4    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.61   10.1   0.1    2.4  1  Cadherin_5     Cadherin-like domain


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.8   0.4  1.6e-117  1.4e-113       5     417 .]       8     415 ..       5     415 .. 0.94

  Alignments for each domain:
  == domain 1  score: 379.8 bits;  conditional E-value: 1.6e-117
                                   S--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHHH CS
                 EPSP_synthase   5 krlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeelv 85 
                                   + + ge+ +p+sks+++ra+ +AaL++ es i  +L s+D++s+++a+ +Lga i   +++++ + ++g  g+ ++p ++v
  gi|91773066|ref|YP_565758.1|   8 SGVHGEIFAPASKSYTHRAITVAALSK-ESIIHRPLISADTQSTIKACEMLGAYI---EKDGDKLLISGVDGEPQTP-DNV 83 
                                   5689********************986.699*********************654...4569999999999*****9.8** PP

                                   TT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEEEEETSSTT CS
                 EPSP_synthase  86 ldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgveikaevsS 165
                                   +d+gnsgt+lr++ta++al +g +vLtGd+sir+RP  +ll+ L+ lG++  + +g+++ap+ v g lk+  ++i++++sS
  gi|91773066|ref|YP_565758.1|  84 IDVGNSGTTLRFMTAIAALGQGTTVLTGDNSIRSRPNGPLLQVLNDLGVQSISTRGDGCAPIVVTGgLKGAIAKIDGSISS 164
                                   *******************99*****************************999************99************** PP

                                   HHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEET.TSSEEEEEE--SSB--EEEE--B-HHHHHHHH CS
                 EPSP_synthase 166 qqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikiets.gteesitvkGkeklpgteyvvegDassAayfl 243
                                   q++++lll+ +l+++  t+ +++ l+s+p++d tl++l+k+g++i  + +++ ++ + G++k    ey+v+gD ssA+y+l
  gi|91773066|ref|YP_565758.1| 165 QFISALLLACPLTKNStTLSIKGeLKSRPYVDVTLDILEKAGAEIYLEdNQNLKFIIPGNQKYRLKEYTVPGDFSSASYLL 245
                                   ***********888889999999**********************865155559********55558************** PP

                                   HHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEET.TS--BEEEEEBGSTTSBHGGGHHHHHHHH CS
                 EPSP_synthase 244 vaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgps.glklkdvdietlpdeaptlavlaafaegt 323
                                   +aAa+t+++++v+n+ + s+qGd++++d il++mga+i +++++ +v+ +  +l+++ +d    pd++pt+avl a+aeg+
  gi|91773066|ref|YP_565758.1| 246 AAAAMTDTKIKVNNLYP-SMQGDAAIID-ILKEMGANIYWNKEEGTVEVNGgKLHGITMDAGATPDLVPTVAVLGAVAEGE 324
                                   **************987.7899*88888.**********9998888877777***************************** PP

                                   HTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEEEEETTH CS
                 EPSP_synthase 324 tviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvaegeveiddie 404
                                   tvi++++++r+ketdrl+ama eL k+G  + ee+d l+i+++e  lkga v+  +DhRi m+l+lag +++g+++id +e
  gi|91773066|ref|YP_565758.1| 325 TVITNAEHVRYKETDRLHAMAVELDKMGISTSEEKDKLTIKGGE--LKGADVHGWHDHRIVMSLTLAG-MIAGDTTIDTAE 402
                                   ***************************************99985..9*********************.88888******* PP

                                   HHHHHSSSHHHHH CS
                 EPSP_synthase 405 ctdksfpefeekL 417
                                   ++ +s+p+f++ +
  gi|91773066|ref|YP_565758.1| 403 AIFISYPNFFDSM 415
                                   **********976 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   6.9e-05      0.61      16      48 ..      43      75 ..      31     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.9e-05
                    Cadherin_5 16 gseDtaltitaaqLLanasDvdgdtLsvsslta 48
                                  +s Dt+ ti+a ++L  + + dgd+L +s+++ 
  gi|91773066|ref|YP_565758.1| 43 ISADTQSTIKACEMLGAYIEKDGDKLLISGVDG 75
                                  688**************************9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2812.66
//
Query:       gi|91773067|ref|YP_565759.1|  [L=217]
Description: thymidylate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-21   74.2   0.1      1e-20   74.0   0.1    1.1  1  Thymidylat_synt  Thymidylate synthase
  ------ inclusion threshold ------
      0.025   14.7   0.0        0.7   10.1   0.0    2.3  2  T3SchapCesA      Type III secretion system filament chaperone
      0.086   12.5   0.1       0.13   11.9   0.1    1.2  1  MIX              Mitochondrial membrane-anchored proteins


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 !   74.0   0.1   1.7e-24     1e-20      80     223 ..      66     213 ..      15     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.7e-24
                                   TH.....HHHHHT..........TB-SSSHHHHHHHBTSTTTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGG.SSS- CS
               Thymidylat_synt  80 Wd.....ewadee..........gdlgpvYGkqwrkfkaeegkkidqlakvidqlkenpdsRriivsawnpaeldk.maLp 144
                                   W+     e    +          +d +  YG+ +r++      k+dq+++vi++l +n + Rr     w p+  d+ +   
  gi|91773067|ref|YP_565759.1|  66 WNherleE----YakqlitgenaQDFEYTYGQRLRNWD----GKVDQIEYVIEKLTNNKTTRRATAVTWVPTI-DTkVDEV 137
                                   44222221....1333455555589************7....79**************************875.444999* PP

                                   -SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHHHHHH CS
               Thymidylat_synt 145 pChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqvkeql 223
                                   pC+++  f+++d++   ++l+   RS D++ + p N+   + L++ +a  +gl pg+++ +   aHiY+   +++++ +
  gi|91773067|ref|YP_565759.1| 138 PCMIIDDFKIRDDT---VHLTTLFRSHDFAGAYPANLYGLSKLLEYVADKVGLAPGTITTMSVSAHIYDHDWDKIEKII 213
                                   **********7664...9*******************************************************999876 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00012       0.7      61      91 ..      88     118 ..      45     122 .. 0.85
   2 ?    2.4   0.0      0.03   1.8e+02      68      84 ..     199     215 ..     190     217 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                   T3SchapCesA  61 gytygeerklydsalskieklietlkparsk 91 
                                    ytyg+  + +d  + +ie +ie l+  ++ 
  gi|91773067|ref|YP_565759.1|  88 EYTYGQRLRNWDGKVDQIEYVIEKLTNNKTT 118
                                   5**********************99877665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.03
                   T3SchapCesA  68 rklydsalskiekliet 84 
                                    ++yd    kiek+i+ 
  gi|91773067|ref|YP_565759.1| 199 AHIYDHDWDKIEKIIKG 215
                                   679***********986 PP

>> MIX  Mitochondrial membrane-anchored proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.2e-05      0.13      52     138 ..      64     149 ..      46     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                           MIX  52 lallweqtkhyypadwlvpleltqvlkytsgaylqnyvadpdqlrkevllqllnvkygrvkdpng..grvnrdveeiisma 130
                                    a  w+  +    a  l+  e +q + yt g+ l+n+    dq+   v+ +l n k  r          ++  v+e+ +m 
  gi|91773067|ref|YP_565759.1|  64 SA--WNHERLEEYAKQLITGENAQDFEYTYGQRLRNWDGKVDQIE-YVIEKLTNNKTTRRATAVTwvPTIDTKVDEVPCMI 141
                                   44..4444444457899**************************96.6899999***99977655422689*********** PP

                           MIX 131 vddleamd 138
                                   +dd++  d
  gi|91773067|ref|YP_565759.1| 142 IDDFKIRD 149
                                   ***98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1719.34
//
Query:       gi|91773068|ref|YP_565760.1|  [L=124]
Description: hypothetical protein Mbur_1080 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 802.96
//
Query:       gi|91773069|ref|YP_565761.1|  [L=148]
Description: hypothetical protein Mbur_1081 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   72.5   0.0    6.2e-20   72.0   0.0    1.2  1  DUF488    Protein of unknown function, DUF488


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   3.5e-24   6.2e-20       2     122 .]      17     127 ..      16     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 3.5e-24
                        DUF488   2 lervydllkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdprweefferYaaeles 82 
                                   le ++d+ ++ ++ +l+D+R++P S +++f+ke+l++ l++++i Y +++ lg+ r+ +        + + f++Y+  l +
  gi|91773069|ref|YP_565761.1|  17 LEYLIDMVQSFNISYLMDIRSYPHSVREDFNKENLERMLPKNNIVYSHCPGLGGLRDGSYMDYT---KTDEFSKYYSLLVD 94 
                                   788999***************************************************9987773...34677778888887 PP

                        DUF488  83 keaakealeelkelakkgvaLlcaekdperchrvvlaeyl 122
                                   k        ++++ a +g++L+caek+p+ chr  l+++l
  gi|91773069|ref|YP_565761.1|  95 K-------IRFVNNAGSGIVLMCAEKNPKDCHRYHLSKVL 127
                                   4.......4677778888*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1088.80
//
Query:       gi|91773070|ref|YP_565762.1|  [L=285]
Description: HtpX-2 peptidase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  119.2   0.0    3.2e-34  118.4   0.0    1.4  1  Peptidase_M48  Peptidase family M48
    0.00028   20.2   0.0    0.00042   19.6   0.0    1.4  1  Peptidase_M56  BlaR1 peptidase M56
     0.0074   16.0   2.1     0.0074   16.0   2.1    2.1  2  Yip1           Yip1 domain
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.028   14.2   0.0    1.2  1  BSP            Peptidase of plants and bacteria
       0.04   14.2   0.3        0.2   11.9   0.1    2.1  2  DUF4157        Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.0     9e-38   3.2e-34       2     195 ..      65     285 .]      64     285 .] 0.79

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 9e-38
                                   --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsv 81 
                                   ++ ++l ++v++la +a+l  p++kvy+v+ +  NAFa+g+  ++  ++ t+g++ + l++eel++Vl+HEl+H+k+r+++
  gi|91773070|ref|YP_565762.1|  65 SESPQLYDIVRNLAMRAQL--PMPKVYIVETSMPNAFATGRDPKHaAVAATTGIM-NILTTEELEGVLAHELAHVKNRDTL 142
                                   6788999************..********************98888*********.************************* PP

                                   HHHHHHHHHHHHHHHHHHH....HT.T-SHHHHHTT--....S---HHHHHHHHHHTT.......HHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx....xx.xxxxxxxxxxxx....xxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                 Peptidase_M48  82 vslivsllasillllglal....li.sraeedaagafl....dalavliglliillfl.......alSRkrEyqADeagve 146
                                   +s++ +++a ++ +l+  +    ++ +  ++d+ g+       ala+++        l       a+SR+rE+ AD+ g++
  gi|91773070|ref|YP_565762.1| 143 ISAVAATIAGVITMLATWArwaaIFgGIGGRDDDGGGNivgfIALAIVAP-------LaatiiqfAISRSREFGADAEGAR 216
                                   **888777777777665331111220222222222211000012333333.......13445666**************** PP

                                   TTT.HHHHHHHHHHHHHHTT--S---HHHH....................HHS-SS--HHHHHHHHHH- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 147 llkrakdlvraliklakdlerqdvsaslrs....................ellstHPplleRiqalkel 195
                                   + +++ +l++al kl +++++++ ++   +                    +l+stHP ++eRi++l+e+
  gi|91773070|ref|YP_565762.1| 217 ISQKPWALASALSKLESGAQNYKPGKNDVQpsqntahmfivnplrgsslmKLFSTHPATEERIRRLDEM 285
                                   ********************97666666666677799*****************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-07   0.00042     187     220 ..     116     149 ..      45     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                 Peptidase_M56 187 flkklsdeeleyillHElaHlkrkDllvnllvav 220
                                   +++ l+ eele +l+HElaH+k++D+l+ +++a 
  gi|91773070|ref|YP_565762.1| 116 IMNILTTEELEGVLAHELAHVKNRDTLISAVAAT 149
                                   5667899*********************998875 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   2.7      0.31   1.1e+03      80     102 ..      14      36 ..       4      53 .. 0.41
   2 !   16.0   2.1   2.1e-06    0.0074      31     120 ..     112     201 ..     107     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.31
                          Yip1  80 lalllhliakllggkgsfkqtls 102
                                   l++ll ++++l gg++    +++
  gi|91773070|ref|YP_565762.1|  14 LTGLLIIVGRLIGGTTGMFIAFA 36 
                                   22222223333333333111111 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.1e-06
                          Yip1  31 lltlllgllaslnlgqtlasg..eevqgltlssllgaiiggylglllgllllalllhl.iakllggkgsfkqtlsvvgyal 108
                                   ++t ++ +l++  l+++la +  +  ++ tl+s+++a i+g++++l++++ +a+++   +++  +g g+   ++ ++++a 
  gi|91773070|ref|YP_565762.1| 112 ATTGIMNILTTEELEGVLAHElaHVKNRDTLISAVAATIAGVITMLATWARWAAIFGGiGGRDDDGGGN---IVGFIALAI 189
                                   4455555555555555555556766788999***************************7778888****...888888885 PP

                          Yip1 109 lPlilgaliail 120
                                   ++ + + +i ++
  gi|91773070|ref|YP_565762.1| 190 VAPLAATIIQFA 201
                                   555555555444 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.7e-06     0.028      59     131 ..      91     158 ..      53     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                           BSP  59 lrdidgvaytsGldddhkeIhlslsyiekasaekdakaevtgvLthelvhvyqweaegrapggliEGiAdyvR 131
                                   ++ +   a+++G d++h  +   +  ++  ++     +e++gvL hel+hv + ++   a ++ i+G+   ++
  gi|91773070|ref|YP_565762.1|  91 VETSMPNAFATGRDPKHAAVAATTGIMNILTT-----EELEGVLAHELAHVKNRDTLISAVAATIAGVITMLA 158
                                   44444568888889999999888888877654.....7*************9999966666666666654443 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.6e-05       0.2      40      74 ..     111     138 ..      95     142 .. 0.71
   2 ?   -1.1   0.0      0.64   2.3e+03      12      29 ..     206     223 ..     202     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.6e-05
                       DUF4157  40 AfTlgndivfaageyqpesaagrellaHELtHvvq 74 
                                   A T+g   ++       ++++ + +laHEL+Hv  
  gi|91773070|ref|YP_565762.1| 111 AATTGIMNIL-------TTEELEGVLAHELAHVKN 138
                                   5555544444.......56777889********76 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.64
                       DUF4157  12 rafgadlsdVrvhtgsaa 29 
                                   r fgad + +r+ + + a
  gi|91773070|ref|YP_565762.1| 206 REFGADAEGARISQKPWA 223
                                   789999999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1996.59
//
Query:       gi|91773071|ref|YP_565763.1|  [L=84]
Description: hypothetical protein Mbur_1083 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   12.8   0.5       0.11   12.4   0.5    1.2  1  DELLA     Transcriptional regulator DELLA protein N terminal
       0.11   12.2   0.1       0.15   11.8   0.1    1.2  1  FeoB_C    Ferrous iron transport protein B C terminus
       0.46   10.3   4.0        2.1    8.1   0.1    2.3  2  Fn_bind   Fibronectin binding repeat


Domain annotation for each model (and alignments):
>> DELLA  Transcriptional regulator DELLA protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   1.8e-05      0.11       1      36 [.      41      76 ..      41      84 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                         DELLA  1 DelLavlGYkvrssdladVAqkLEqLemvlgaaqed 36
                                  De+La  G  +  s++ad    LE+ e ++++ +ed
  gi|91773071|ref|YP_565763.1| 41 DEILADEGIELTDSEIADLEDDLEEFEAMISEIEED 76
                                  9****************************9777766 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 ?   11.8   0.1   2.5e-05      0.15       2      32 ..       2      30 ..       1      32 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                        FeoB_C  2 fslYllgilvallvalllkkttlkgepspfv 32
                                  +s+  lgi+v+ll++l+l+     gep+  v
  gi|91773071|ref|YP_565763.1|  2 VSIKHLGIVVILLMGLMLSG--CVGEPADTV 30
                                  667779************98..477776555 PP

>> Fn_bind  Fibronectin binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00036       2.1      11      28 ..      20      37 ..      18      44 .. 0.78
   2 ?    3.0   0.9     0.014        84      21      27 ..      72      78 ..      67      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00036
                                  XXXXXXXX--B----S-. CS
                       Fn_bind 11 pgmSGqnggttieEDTkk 28
                                  +g  G+ + t+ eEDT++
  gi|91773071|ref|YP_565763.1| 20 SGCVGEPADTVTEEDTAT 37
                                  4555777889******96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                                  B----S- CS
                       Fn_bind 21 tieEDTk 27
                                  +ieEDT 
  gi|91773071|ref|YP_565763.1| 72 EIEEDTE 78
                                  7999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 564.52
//
Query:       gi|91773072|ref|YP_565764.1|  [L=471]
Description: hypothetical protein Mbur_1084 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.001   19.2   7.4      0.001   19.2   7.4    2.7  2  LPD39       Large polyvalent protein associated domain 39
  ------ inclusion threshold ------
      0.019   15.1   2.5       0.12   12.5   0.2    3.0  2  DUF3567     Protein of unknown function (DUF3567)
       0.07   13.2  10.6      0.024   14.7   4.6    2.7  2  ApoLp-III   Apolipophorin-III precursor (apoLp-III)
        0.1   12.0   3.2       0.19   11.1   3.2    1.4  1  Bul1_C      Bul1 C terminus
        1.2    9.1   9.4        4.1    7.4   2.7    2.8  3  Laminin_II  Laminin Domain II
        1.6    9.4  11.6       0.23   12.1   3.3    2.8  2  DUF5344     Family of unknown function (DUF5344)
          2    8.8   9.3        1.8    9.0   4.0    2.8  2  Syntaxin_2  Syntaxin-like protein
        2.1    8.5   5.7       0.87    9.7   0.3    2.9  3  SAM_Exu     Exuperantia SAM-like domain
        2.9    8.4   5.8        1.4    9.4   0.4    2.8  3  NPV_P10     Nucleopolyhedrovirus P10 protein
          6    6.9  13.3       0.37   10.9   6.7    2.1  2  SYCE1       Synaptonemal complex central element protein 1
        7.2    4.4   5.7        1.9    6.4   2.4    1.5  1  Prominin    Prominin
        7.4    6.4  11.0        1.8    8.4   2.9    3.7  4  DivIC       Septum formation initiator
        8.9    7.0  11.7        2.4    8.9   3.2    3.0  2  KfrA_N      Plasmid replication region DNA-binding N-term


Domain annotation for each model (and alignments):
>> LPD39  Large polyvalent protein associated domain 39
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.0      0.32   4.5e+02     106     164 ..      63     124 ..      53     155 .. 0.64
   2 !   19.2   7.4   7.2e-07     0.001     102     174 ..     203     275 ..     116     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.32
                         LPD39 106 lkeeretlkeeperkaeyaeLrkrfe...aLpeeakalYkkvRdaYkkqaeelrealeenie 164
                                   +++++++ ++ +  ka+y+eLr +f+   aL ++++   +++ da k+    + e ++ ++e
  gi|91773072|ref|YP_565764.1|  63 EMKNNRARSKVQLSKAGYEELRGNFQnakALQAKGQLNTTEALDAAKEYLTGTIEYMVTRLE 124
                                   44555555566789999999999996222566666655555555555555555555555444 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.2e-07
                         LPD39 102 aeaelkeeretlkeeperkaeyaeLrkrfeaLpeeakalYkkvRdaYkkqaeelrealeenieraaeiaeaka 174
                                    +++l++e + l ee+e+ +e +e+  +++aL eeak+  + +R+aY++  e+  e l ++i+ + e++ + +
  gi|91773072|ref|YP_565764.1| 203 VSERLQNEINSLTEEGEDTEELQEMLDDYNALIEEAKQTHESAREAYQNGDEDAGEQLRKSISMTNEANIKLR 275
                                   56778888889999***************************************************66544433 PP

>> DUF3567  Protein of unknown function (DUF3567)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.35   4.8e+02      45      80 ..     111     145 ..      91     151 .. 0.81
   2 ?   12.5   0.2     9e-05      0.12      50      85 ..     203     238 ..     196     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.35
                       DUF3567  45 yldGslAesfrkevkalieeepseeevddfldeyaa 80 
                                   yl G++ e +  +++++ e+   +e+v++++d+y +
  gi|91773072|ref|YP_565764.1| 111 YLTGTI-EYMVTRLETIKEDGSYSEDVNATIDTYIN 145
                                   666665.44556788899999999********9965 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9e-05
                       DUF3567  50 lAesfrkevkalieeepseeevddfldeyaalaqqp 85 
                                   + e++++e+++l+ee  ++ee++++ld+y+al ++ 
  gi|91773072|ref|YP_565764.1| 203 VSERLQNEINSLTEEGEDTEELQEMLDDYNALIEEA 238
                                   6799**************************998765 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 ?   14.7   4.6   1.7e-05     0.024      21     106 ..     134     221 ..     119     252 .. 0.61
   2 ?    6.8   1.1    0.0049       6.7      29      83 ..     198     251 ..     190     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                     ApoLp-III  21 eevvetiKensenlvdqlkqv.ikslqeelkkksdeleealkevkkkieet.adklseenPevkkkaqelqekvQsgvqsl 99 
                                   e+v+ ti ++ + l  q  +v ++ ++ +l +++  + +++++++k+++++ a+k+++   +  +k +  +e +Q+ ++sl
  gi|91773072|ref|YP_565764.1| 134 EDVNATIDTYINRLEAQKDDVaAADTRKDLSETTRDIRKIWSDAQKDLNKMrAQKINSGLVNYLEKTDGVSERLQNEINSL 214
                                   444444444444444444443134566666677777777777777777776335677777777777777777777777777 PP

                     ApoLp-III 100 vkesqkl 106
                                    +e + +
  gi|91773072|ref|YP_565764.1| 215 TEEGEDT 221
                                   7666554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0049
                     ApoLp-III  29 ensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkk 83 
                                   e+++++ ++l++ i+sl+ee  ++  el+e+l++ ++ iee+ ++ ++++ + + 
  gi|91773072|ref|YP_565764.1| 198 EKTDGVSERLQNEINSLTEEGEDTE-ELQEMLDDYNALIEEAKQTHESAREAYQN 251
                                   5788999999********9976655.9************9998887776555554 PP

>> Bul1_C  Bul1 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.2   0.00014      0.19      83     191 ..     159     267 ..     143     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                        Bul1_C  83 tfkefekkikeykkkfeenkeklneLynlsreistkreLkFtdfiskqlanDveslanlkvkvtelnevfkkqvetlkdes 163
                                   t k++ ++ ++ +k  ++ ++ ln++ +++ ++   + L+ td +s++l n ++sl++  ++++el+e++      +++++
  gi|91773072|ref|YP_565764.1| 159 TRKDLSETTRDIRKIWSDAQKDLNKMRAQKINSGLVNYLEKTDGVSERLQNEINSLTEEGEDTEELQEMLDDYNALIEEAK 239
                                   668899999999***************999999999**********************************99988888888 PP

                        Bul1_C 164 esslseksnsssssklssstssasstea 191
                                   ++  s+ ++ +++++   ++ ++s + +
  gi|91773072|ref|YP_565764.1| 240 QTHESAREAYQNGDEDAGEQLRKSISMT 267
                                   7776666666665555444444443332 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.019        26      24      93 ..      71     141 ..      55     157 .. 0.70
   2 ?    1.1   0.4      0.27   3.8e+02      45      69 ..     161     182 ..     134     209 .. 0.45
   3 ?    7.4   2.7     0.003       4.1       4      60 ..     185     241 ..     182     284 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX--TTTTTGGGHHHHHHHHHH...HHHHHH CS
                    Laminin_II  24 qnlentkeklseinrsveetnekvkdankairdArrsv.kkLeklapqLldklkelkqleeassslsdnis 93 
                                    +++  k+ ++e++++ ++ +++  + +  + +A ++    L+ +++ ++ +l+++k+  + s+ + + i+
  gi|91773072|ref|YP_565764.1|  71 SKVQLSKAGYEELRGNFQNAKALQAKGQLNTTEALDAAkEYLTGTIEYMVTRLETIKEDGSYSEDVNATID 141
                                   556666777888888877766655533334444444440469****************9999888777776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.27
                                   XXXXXXXXXXXXXXXXXXXX--TTT CS
                    Laminin_II  45 ekvkdankairdArrsvkkLeklap 69 
                                   +   d+++++rd r+  ++ +k ++
  gi|91773072|ref|YP_565764.1| 161 K---DLSETTRDIRKIWSDAQKDLN 182
                                   2...222222222222222222111 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.003
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrs 60 
                                    a+++n+ +++ le++ ++s++l+n+ ++l e  ++ ee +e ++d+n  i++A++ 
  gi|91773072|ref|YP_565764.1| 185 RAQKINSGLVNYLEKTDGVSERLQNEINSLTEEGEDTEELQEMLDDYNALIEEAKQT 241
                                   567777777777777777777777777777666666666666666666666666543 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.7      0.27   3.7e+02       3      52 ..      61     112 ..      59     128 .. 0.77
   2 ?   12.1   3.3   0.00017      0.23      29      86 ..     201     258 ..     183     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.27
                       DUF5344   3 EIklnqaeVeqkLselktaaeelk..tsipetisgknsldvvekineleeel 52 
                                   E+ ++ + + +k++  k   eel+  +++++  + k++l+++e +   +e l
  gi|91773072|ref|YP_565764.1|  61 EMEMKNNRARSKVQLSKAGYEELRgnFQNAKALQAKGQLNTTEALDAAKEYL 112
                                   7777888888888888888888877799999999999999998776665544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                       DUF5344  29 ipetisgknsldvvekineleeeleellkaYktlllknvedtesaVdslkeaDealas 86 
                                          +n+++ +++  e  eel+e+l++Y +l+++  ++ esa + ++  De +++
  gi|91773072|ref|YP_565764.1| 201 DGVSERLQNEINSLTEEGEDTEELQEMLDDYNALIEEAKQTHESAREAYQNGDEDAGE 258
                                   5555566799999999999**********************************98876 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.0    0.0013       1.8      12      82 ..     137     214 ..     133     217 .. 0.76
   2 ?    3.0   1.1     0.095   1.3e+02      13      54 ..     205     250 ..     193     284 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                    Syntaxin_2  12 vstleklvkqLgtkkd...teelreklhelieeinelikktnellkklsqldnsssds...qqkl..qkekLkkdfkea 82 
                                   + t++ +++ L+ +kd     ++r+ l e++ +i+++ ++ +++l+k+ + + +s       +k+    e+L+++++++
  gi|91773072|ref|YP_565764.1| 137 NATIDTYINRLEAQKDdvaAADTRKDLSETTRDIRKIWSDAQKDLNKMRAQKINSG-LvnyLEKTdgVSERLQNEINSL 214
                                   5799***********97888888888888888888888888888888887665542.2467444445889999888876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.095
                    Syntaxin_2  13 stleklvkqLgtkk.dteelrekl...helieeinelikktnellk 54 
                                     l++ +++L   + dteel+e l   + liee++++ +   e  +
  gi|91773072|ref|YP_565764.1| 205 ERLQNEINSLTEEGeDTEELQEMLddyNALIEEAKQTHESAREAYQ 250
                                   4566666666555336777775554445566666555555544444 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         2   2.7e+03      34      50 ..     169     184 ..     155     192 .. 0.72
   2 ?    9.7   0.3   0.00063      0.87      42      73 .]     198     231 ..     194     231 .. 0.89
   3 ?   -0.7   0.2       1.1   1.5e+03      27      62 ..     237     271 ..     233     279 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2
                       SAM_Exu  34 sLkeiweekkkeGlekl 50 
                                    +++iw++ +k+ l+k+
  gi|91773072|ref|YP_565764.1| 169 DIRKIWSDAQKD-LNKM 184
                                   468899999887.5554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00063
                       SAM_Exu  42 kkkeGlekllkekitslke..edkeeLlelLdsh 73 
                                   +k++G+ + l+++i+sl+e  ed+eeL e+Ld +
  gi|91773072|ref|YP_565764.1| 198 EKTDGVSERLQNEINSLTEegEDTEELQEMLDDY 231
                                   5899*************984459*********87 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                       SAM_Exu  27 EngidyesLkeiweekkkeGlekllkekitslkeed 62 
                                   E++ + es +e++++  +++ e+l  ++i+ ++e++
  gi|91773072|ref|YP_565764.1| 237 EAKQTHESAREAYQNGDEDAGEQLR-KSISMTNEAN 271
                                   7777888999999999988866554.7777766665 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.5   3.5e+03      34      51 ..      99     112 ..      70     128 .. 0.51
   2 ?   -0.1   0.3      0.94   1.3e+03      41      56 ..     144     159 ..     133     193 .. 0.54
   3 ?    9.4   0.4     0.001       1.4      22      55 ..     206     239 ..     194     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.5
                       NPV_P10  34 lpdvtelnekLdaqsaqL 51 
                                   l++    +e Lda  + L
  gi|91773072|ref|YP_565764.1|  99 LNT----TEALDAAKEYL 112
                                   233....23344433333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.94
                       NPV_P10  41 nekLdaqsaqLaelet 56 
                                    ++L+aq + +a+ +t
  gi|91773072|ref|YP_565764.1| 144 INRLEAQKDDVAAADT 159
                                   3344444444444433 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.001
                       NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                    lq+++++++e+ +d++el+e Ld+ +a ++e +
  gi|91773072|ref|YP_565764.1| 206 RLQNEINSLTEEGEDTEELQEMLDDYNALIEEAK 239
                                   69************************99988765 PP

>> SYCE1  Synaptonemal complex central element protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.5      0.93   1.3e+03      71     101 ..      60      90 ..      40     121 .. 0.45
   2 ?   10.9   6.7   0.00027      0.37      20     132 ..     159     269 ..     136     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.93
                         SYCE1  71 qekeseaqrkqelseeckqrieeltskiqee 101
                                   qe e + +r ++  +  k   eel  + q++
  gi|91773072|ref|YP_565764.1|  60 QEMEMKNNRARSKVQLSKAGYEELRGNFQNA 90 
                                   2222222222222222222222333333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00027
                         SYCE1  20 akkksseELgeaqalkealkrElDsLnaEkvh..LeevlnkKqealriLqlhcqekeseaqrkqelseeckqrieeltski 98 
                                    +k +se  ++ ++++   +++l++++a k++  L + l+k +++ + Lq + +  ++e +     +ee ++ +  +++ i
  gi|91773072|ref|YP_565764.1| 159 TRKDLSETTRDIRKIWSDAQKDLNKMRAQKINsgLVNYLEKTDGVSERLQNEINSLTEEGED----TEELQEMLDDYNALI 235
                                   57888888888999*************99986559999999999999999999999888777....5666777778***** PP

                         SYCE1  99 qeeklkrrklrlefeeqleelmeqhkdlwefhve 132
                                   +e+k+++ + r + ++  e+  eq ++ +++ +e
  gi|91773072|ref|YP_565764.1| 236 EEAKQTHESAREAYQNGDEDAGEQLRKSISMTNE 269
                                   *************999999999998887776663 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.4    0.0014       1.9     163     274 ..     155     262 ..     152     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0014
                      Prominin 163 tNkaldegleesketvkrgledlrtflkdv.pqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaele 242
                                   +   +++ l e++  ++++  d+++ l++  +q+i++ lv+ y e  + vs+ L++  ++l ++ +dt e +  ++L++ +
  gi|91773072|ref|YP_565764.1| 155 AAADTRKDLSETTRDIRKIWSDAQKDLNKMrAQKINSGLVN-YLEKTDGVSERLQNEINSLTEEGEDTEELQ--EMLDDYN 232
                                   56678899999999999999999998888736779999998.999999999999999999999999998888..9999999 PP

                      Prominin 243 rllenlkeakeqLeqvnklekeLrksgsqLrd 274
                                   +l+e+ k+++e+ ++  ++  e    g+qLr+
  gi|91773072|ref|YP_565764.1| 233 ALIEEAKQTHESAREAYQNGDE--DAGEQLRK 262
                                   9999999999987776655543..45555555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.43   5.9e+02      53      71 ..      61      79 ..      48      80 .. 0.85
   2 ?   -2.0   0.0       2.2     3e+03      34      49 ..     138     153 ..     111     173 .. 0.58
   3 ?    8.4   2.9    0.0013       1.8      27      63 ..     205     240 ..     176     248 .. 0.84
   4 ?   -0.8   0.0      0.94   1.3e+03      28      50 ..     259     281 ..     256     285 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.43
                                  XXXXXXXXXXXXXXXXXXX CS
                         DivIC 53 dedyieerARselglvkpg 71
                                  + ++   rARs+ +l+k g
  gi|91773072|ref|YP_565764.1| 61 EMEMKNNRARSKVQLSKAG 79
                                  55788899*******9976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHHHCC CS
                         DivIC  34 aklkaeneeLeaevkd 49 
                                   a++   +++Lea+ +d
  gi|91773072|ref|YP_565764.1| 138 ATIDTYINRLEAQKDD 153
                                   4444444444444333 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXX CS
                         DivIC  27 aalqaelaklkaeneeLeaevkdLksdedyieerARs 63 
                                   ++lq+e+++l++e e+ e+  + L +d++++ e A++
  gi|91773072|ref|YP_565764.1| 205 ERLQNEINSLTEEGEDTEELQEML-DDYNALIEEAKQ 240
                                   679*********************.9*********96 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.94
                                   HHHHHHHHHHHHHHHHHHHHCC- CS
                         DivIC  28 alqaelaklkaeneeLeaevkdL 50 
                                   +l + +   ++ n +L a ++++
  gi|91773072|ref|YP_565764.1| 259 QLRKSISMTNEANIKLRALIQEM 281
                                   55555666666666666666555 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 ?    8.9   3.2    0.0018       2.4      33     111 ..     137     228 ..      87     230 .. 0.75
   2 ?    3.8   1.9     0.066        92      73     104 ..     225     256 ..     189     271 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                        KfrA_N  33 pntisrvlkeweaelaaalaaraapelPealaeallaalwqaale...............eaeeelaaaraelqaaraale 98 
                                   ++ti ++++++ea++   +aa+++++l+e   +   +++w+ a++               +  e+ +   ++lq +++ l 
  gi|91773072|ref|YP_565764.1| 137 NATIDTYINRLEAQKDDVAAADTRKDLSETTRDI--RKIWSDAQKdlnkmraqkinsglvNYLEKTDGVSERLQNEINSLT 215
                                   4799999999999999998888878888776664..7********555554444333333333366666777777777777 PP

                        KfrA_N  99 aeraeaearveel 111
                                   +e ++ e+ +e l
  gi|91773072|ref|YP_565764.1| 216 EEGEDTEELQEML 228
                                   7777777776666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.066
                        KfrA_N  73 qaaleeaeeelaaaraelqaaraaleaeraea 104
                                   q++l++ ++ +++a++ +++ar+a ++  ++a
  gi|91773072|ref|YP_565764.1| 225 QEMLDDYNALIEEAKQTHESAREAYQNGDEDA 256
                                   33334444455555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1902  (0.106085); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); 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):              13  [number of targets reported over threshold]
# CPU time: 0.92u 0.33s 00:00:01.25 Elapsed: 00:00:00.49
# Mc/sec: 2863.31
//
Query:       gi|91773073|ref|YP_565765.1|  [L=290]
Description: hypothetical protein Mbur_1085 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00017   21.1   0.2    0.00033   20.1   0.2    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0024   17.7   0.0     0.0042   16.9   0.0    1.3  1  MarR_2           MarR family
  ------ inclusion threshold ------
      0.027   15.0   0.0      0.051   14.1   0.0    1.4  1  HTH_27           Winged helix DNA-binding domain
      0.029   14.3   0.0      0.057   13.3   0.0    1.5  1  MarR             MarR family
      0.033   13.0   0.0      0.043   12.6   0.0    1.2  1  HTH_micro        HTH-like
      0.043   14.1   0.5          1    9.6   0.0    2.1  2  DUF4293          Domain of unknown function (DUF4293)
       0.06   13.3   0.0       0.11   12.5   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.075   13.1   0.0        0.2   11.7   0.0    1.7  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
       0.12   12.4   0.1       0.12   12.4   0.1    2.1  2  Ac76             Orf76 (Ac76)
        1.8    8.8   4.8          3    8.1   1.3    2.2  2  DUF2304          Uncharacterized conserved protein (DUF2304)


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 !   20.1   0.2   1.9e-07   0.00033       6      47 ..     230     272 ..     229     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                        HTH_24   6 rkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                   r++L ++ +n++ i+q++L  +l  S + v+  +  Le+ Gl+
  gi|91773073|ref|YP_565765.1| 230 REVLDIVIDNGGrITQKDLRGKLRYSEAKVSLIVSDLENRGLV 272
                                   7899999999999****************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.4e-06    0.0042      10      53 ..     232     274 ..     230     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                   vL  + +++gr +t+++l  +l++s + vs i+ +L+ +GLv +
  gi|91773073|ref|YP_565765.1| 232 VLDIVIDNGGR-ITQKDLRGKLRYSEAKVSLIVSDLENRGLVDK 274
                                   88888999997.9*****************************75 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   0.0   2.8e-05     0.051      15      54 ..     239     278 ..     230     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                        HTH_27  15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54 
                                   +++r +++dl+g+l ++ + +s +++ L+++GLv + ++ 
  gi|91773073|ref|YP_565765.1| 239 NGGRITQKDLRGKLRYSEAKVSLIVSDLENRGLVDKFKKG 278
                                   6778889***************************888765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.057      12      51 ..     237     276 ..     230     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                   HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                   +++ g +++++L  kl  s + v+ ++  Le +Gl+++ k
  gi|91773073|ref|YP_565765.1| 237 IDNGGRITQKDLRGKLRYSEAKVSLIVSDLENRGLVDKFK 276
                                   566678******************************9977 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.043      95     150 ..     231     285 ..     215     290 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                     HTH_micro  95 kivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeakiviki 150
                                   +++d+++ +  ++++++lr kl     k++ ++  L+++gl++ k k++   +i i
  gi|91773073|ref|YP_565765.1| 231 EVLDIVIDNGGRITQKDLRGKLRYSEAKVSLIVSDLENRGLVD-KFKKGRGNIIII 285
                                   79*****************************************.888887766655 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00058         1       5      33 ..       4      32 ..       2      73 .. 0.70
   2 ?    2.8   0.1     0.071   1.3e+02      84     113 ..     146     174 ..     144     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00058
                       DUF4293  5 QslyLllaailmaaflflplasivtedel 33
                                   sl+ +l++il+++++++p++ + t++  
  gi|91773073|ref|YP_565765.1|  4 RSLFWFLVCILALILFIVPVGAVGTATIH 32
                                  59******************995554433 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.071
                       DUF4293  84 lclinllllvllyvllallllvnkanaaae 113
                                   ++++ +lllv+++vl a+ ++ nk+ a++ 
  gi|91773073|ref|YP_565765.1| 146 MTYLAILLLVFVLVLSAY-VYSNKKGANED 174
                                   567788888888888888.44444444333 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   0.0   5.9e-05      0.11      21      61 ..     242     287 ..     226     290 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TEE..EEES- CS
                     HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis..r.grr..irild 61 
                                   ++tq++l   l  +   vs i s+L+++gl++  + gr+  i+i+d
  gi|91773073|ref|YP_565765.1| 242 RITQKDLRGKLRYSEAKVSLIVSDLENRGLVDkfKkGRGniIIIPD 287
                                   689999999999999*****************86335657788877 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011       0.2       1      54 [.      31      83 ..      31     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
               CarbopepD_reg_2  1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvG 54
                                  i+G +++ +t epl+ + + v++t  + +  + G ++l+ l +g+y++v++y+ 
  gi|91773073|ref|YP_565765.1| 31 IHGAIYEWDTFEPLENVLIEVNSTPPQSIVAKYGVYSLD-LVPGDYEIVATYYT 83
                                  7899**********************************7.556******99954 PP

>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7       1.4   2.4e+03      28      39 ..      10      21 ..       2      27 .. 0.59
   2 ?   12.4   0.1   6.8e-05      0.12      23      57 ..     142     177 ..     135     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                          Ac76 28 ltllllfvlFii 39
                                  l+++l ++lFi+
  gi|91773073|ref|YP_565765.1| 10 LVCILALILFIV 21
                                  334444455544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.8e-05
                          Ac76  23 lsellltllllfvlFiillnvy.yikteStpadlyt 57 
                                    s  + +l +l+++F+++l+ y y +++ + +dl  
  gi|91773073|ref|YP_565765.1| 142 ESPYMTYLAILLLVFVLVLSAYvYSNKKGANEDLLV 177
                                   477789999**********97637788888999864 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.3    0.0017         3      30      59 ..       4      33 ..       2      41 .. 0.80
   2 ?    1.7   0.1      0.17     3e+02       4      17 ..     151     164 ..     143     177 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                       DUF2304 30 ysllwlllalilivlslfpqiltvlanllG 59
                                  +sl+w+l+++++++l ++p  +   a++ G
  gi|91773073|ref|YP_565765.1|  4 RSLFWFLVCILALILFIVPVGAVGTATIHG 33
                                  69*****************77666666555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                       DUF2304   4 iiliivsvllllli 17 
                                   i+l++++++l +++
  gi|91773073|ref|YP_565765.1| 151 ILLLVFVLVLSAYV 164
                                   22222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        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: 00:00:00.45
# Mc/sec: 1928.75
//
Query:       gi|91773074|ref|YP_565766.1|  [L=168]
Description: hypothetical protein Mbur_1086 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   12.9   0.0      0.097   12.3   0.0    1.2  1  PapJ      Pilus-assembly fibrillin subunit, chaperone


Domain annotation for each model (and alignments):
>> PapJ  Pilus-assembly fibrillin subunit, chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-06     0.097      84     131 ..      60     107 ..      44     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-06
                          PapJ  84 yvLnlklsrCGdGlselpekrsvasynvvvkqslvlkegkddvlLser 131
                                    vL ++l + G G + + ekr ++++ v + +++v  + +d +   ++
  gi|91773074|ref|YP_565766.1|  60 EVLIVRLEENGIGVARVDEKRFTEHGAVLLIGHIVHTDIQDTIDTIDQ 107
                                   589*********************************999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1091.72
//
Query:       gi|91773075|ref|YP_565767.1|  [L=331]
Description: homoserine dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-57  193.6   0.3    3.8e-57  193.0   0.3    1.3  1  Homoserine_dh    Homoserine dehydrogenase
    7.5e-11   42.7   0.2      2e-10   41.3   0.2    1.8  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    0.00028   20.7   0.2    0.00056   19.7   0.2    1.6  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    0.00065   20.0   0.2     0.0017   18.6   0.2    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.047   13.6   0.1      0.093   12.6   0.1    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


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 !  193.0   0.3   1.1e-60   3.8e-57       1     173 []     153     326 ..     153     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 1.1e-60
                                   --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT CS
                 Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgle 81 
                                   Pii+ ++++l+g++i ++eGilngt+nyilt+m ee+as++++l+e qelG+ae+Dpt DveG+D+a Kl+ila+ +f+++
  gi|91773075|ref|YP_565767.1| 153 PIINLVRDTLAGNEILSVEGILNGTCNYILTRMMEEHASYDQMLAESQELGIAETDPTYDVEGIDTACKLVILANSIFDQN 233
                                   9**********************************9********************************************* PP

                                   --GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEEC...EEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEES-S CS
                 Homoserine_dh  82 veledvevegiskltaedikeakeegkvlklvasav...earVkpelvpkshplasvkgsenavlvetdrlgelviqGpga 159
                                    +++dv+v+gi+k+t e ++ a +eg+v+kl+++ v   ++rV+p+lvp+shpla v g+ n+ +v td +g+++++G+ga
  gi|91773075|ref|YP_565767.1| 234 ATYQDVDVTGITKVTLESLSLAYDEGYVIKLIGE-VkkdRLRVSPRLVPSSHPLA-VGGTLNVASVCTDLAGTITVTGRGA 312
                                   **********************************.44458***************.************************* PP

                                   SHHHHHHHHHHHHH CS
                 Homoserine_dh 160 GaepTAsavlsDll 173
                                   G+ +TAsavlsD++
  gi|91773075|ref|YP_565767.1| 313 GSIETASAVLSDIV 326
                                   ************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 !   41.3   0.2   5.6e-14     2e-10       1     117 []      10     145 ..      10     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 5.6e-14
                                   --SHHHHHHHHHHHH---S.....SEEEEEEEEESS.EEE-TT.........HHHHHT--CB---H.....HHHHHHHS-E CS
                 NAD_binding_3   1 GlGaiGsavleqlkrqqse.....ielelvavadrd.sllskd.........rkallasealtldl.....ddliahldpd 61 
                                   G+G +G++v+e l+r+  +     i+l++va+ad++  +++ +         r    ++e  t  +     +d+i+++d d
  gi|91773075|ref|YP_565767.1|  10 GFGSVGQGVAEVLLRKDGYlkslgIDLDVVAIADSKgAEVNPAgidlkatlgR----KRESGTVAIddltgEDIIKNIDHD 86 
                                   99***************99*****************7777777***8865443....333334444000125666666*** PP

                                   EEEE-S--HHHHT.....THHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                 NAD_binding_3  62 vvVEcasseavae.....lvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                   vv+E ++ +   +      +l+a + g +vvt nkg la   +y+eL+eaa+++++k+++e
  gi|91773075|ref|YP_565767.1|  87 VVIETTPTDIETGgcglvNMLAAFECGRHVVTSNKGPLA--LKYRELAEAAKEADRKLLFE 145
                                   *****999887653333246889999*************..*****************997 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 !   19.7   0.2   1.6e-07   0.00056      32     116 ..       3      96 ..       1     121 [. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-07
                                   TEEEEEE--SHHHHHHHHHHHHCT-.........EEEEEEESSEEEEETTEE-HHHHHHHHHCSSS..STTHSHHSTSTSE CS
                 ELFV_dehydrog  32 gkrvaisGsGnvgsyaallltelga.........kvvavsDssGviydpeGldieellelkeerks..vkeykkssekkae 101
                                   + r  i G+G vg+ +a+ l ++            vva+ Ds+G+ ++p G+d+++ l  k+e ++  +++++   e+ ++
  gi|91773075|ref|YP_565767.1|   3 KVRASIIGFGSVGQGVAEVLLRKDGylkslgidlDVVAIADSKGAEVNPAGIDLKATLGRKRESGTvaIDDLT--GEDIIK 81 
                                   6688999********999876643222222223379********************99999999995666666..455566 PP

                                   EESHHSHHHHSS-SE CS
                 ELFV_dehydrog 102 yieneeellelkvdi 116
                                    i+ +  + ++++di
  gi|91773075|ref|YP_565767.1|  82 NIDHDVVIETTPTDI 96 
                                   777764444445555 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 !   18.6   0.2   4.6e-07    0.0017       3     125 ..       8     138 ..       7     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.6e-07
                                   EE--SHHHHHHHHHHHCTCCT-G.......EEEEEESSHHHHHHHHCHH.........TTTCEEEEE--TTTHHHHHHHHH CS
               Sacchrp_dh_NADP   3 iiGaGsvGqavaellarhfdvda.......eitvadrskeklealaaka.........lgvrfeaialdaenyeavLaall 67 
                                   iiG+GsvGq+vae+l+r++ + +        +++ad + ++++     a         ++ +  ++a+d    e++++ + 
  gi|91773075|ref|YP_565767.1|   8 IIGFGSVGQGVAEVLLRKDGYLKslgidldVVAIADSKGAEVNP----AgidlkatlgRKRESGTVAIDDLTGEDIIKNI- 83 
                                   8*******************999888854333333333333222....23466888777777888888888888877776. PP

                                   TTSSEEEE-SSGG.....GHHHHHHHHHHHT-EEEESS-BCGCCSCHCCSHHHHHTHHHHHHC CS
               Sacchrp_dh_NADP  68 kegdlvvnlsppi.....ssldvlkaCietgvhyvdtsiskeertnyalreavlklkekakea 125
                                    ++d+v+  +p       ++l  + a+ e g h+v+            l  ++++l+e+akea
  gi|91773075|ref|YP_565767.1|  84 -DHDVVIETTPTDietggCGLVNMLAAFECGRHVVTSNK-------GPLALKYRELAEAAKEA 138
                                   .77999999886557777888888899999999998554.......33555666666666655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.6e-05     0.093       3      92 ..       7      98 ..       5     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                                  EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH....HHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SE CS
                       3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseealekalekiek....sleklvekgklkeeeveaalarisfttdleeavdadl 81
                                   +iG G +G+g+a+v+++++   + + i+ + ++ a +k ++     ++  +  g+ k+e+   a++ ++ ++ ++++ d d+
  gi|91773075|ref|YP_565767.1|  7 SIIGFGSVGQGVAEVLLRKDGYLKSLGIDLDVVAIADSKGAEvnpaGIDLKATLGR-KRESGTVAIDDLTGEDIIKNI-DHDV 87
                                  69*****************8888888888887777776666543333333333333.346666777888877777776.**** PP

                                  EEE-S-SSHHH CS
                       3HCDH_N 82 viEavvEnlel 92
                                  viE+ + ++e 
  gi|91773075|ref|YP_565767.1| 88 VIETTPTDIET 98
                                  ***99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2161.44
//
Query:       gi|91773076|ref|YP_565768.1|  [L=567]
Description: DNA ligase I, ATP-dependent (dnl1) [Methanococcoides burtonii DSM 6242]
Scores for complete 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-56  189.2   0.0    1.1e-55  188.4   0.0    1.4  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    3.6e-34  118.6   0.1    8.1e-34  117.4   0.1    1.6  1  DNA_ligase_A_N  DNA ligase N terminus
    9.1e-18   64.7   0.0      3e-17   63.0   0.0    1.9  2  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region


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 !  188.4   0.0   1.9e-59   1.1e-55       2     204 .]     239     435 ..     238     435 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 1.9e-59
                                   EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEE CS
                DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElva 82 
                                   mLA+ + sie a+k l  + + vE+K+DG+R+q+hk+gd++++fSRrl+++t ++p++v+a+k  +k+d  s+il+GE+va
  gi|91773076|ref|YP_565768.1| 239 MLAQVTPSIEAAIKDL--GMLAVEWKFDGARVQIHKKGDSINIFSRRLENVTLSLPDIVEAVKLHVKAD--SAILEGEAVA 315
                                   9**************8..5677****************************************9999987..9********* PP

                                   EETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESS CS
                DNA_ligase_A_M  83 vdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkd 163
                                   vd++ g+++ fq++ +r+++k++ve++++e++l l +FDiLyl+g+ l+d++l  Rr+ L   + e+ d +++ e+  ++d
  gi|91773076|ref|YP_565768.1| 316 VDEN-GAPRAFQDILKRFRRKYDVETMVREIPLTLNLFDILYLNGDVLMDQSLLRRREQLVACV-ENCDSIKVDEQVLTDD 394
                                   9888.***********************************************************.**************** PP

                                   HHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                DNA_ligase_A_M 164 veeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                   v+ ++++++ a++ g+EG+++Knp+++Y pgkr+knwlK K
  gi|91773076|ref|YP_565768.1| 395 VNVVNDIYAAALNGGHEGVMLKNPEASYSPGKRGKNWLKKK 435
                                   ***************************************87 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 !  117.4   0.1   1.4e-37   8.1e-34       2     172 ..       4     189 ..       3     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 1.4e-37
                                   CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HHH CS
                DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglskkk 78 
                                   F+e+a+++++ie+  ++ le++++++++++++     e+l  ++ +    ++P++   ++g+g sll+ al+e +gls k+
  gi|91773076|ref|YP_565768.1|   4 FKEFADVCKQIEH-ISSSLEMTDVVSDMLKSIS---TEELPVVTHFvmgdVFPAWSVEQLGVGTSLLYSALSESSGLSLKE 80 
                                   9************.7788***********8864...5689999999**********99*********************** PP

                                   HHHHHHHHS-HHHHHHHHHCCHHHH-----..............-BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS- CS
                DNA_ligase_A_N  79 ikdalakvgDlgevaeevlskrstlakksp..............ltieevnelLdklaaa.gkgsedekkkilkkllkras 144
                                   i+d  +++gD+ge+a ++l k+++++kk++              ++i +v+e + ++++  g gs+  k++ l+ l++++s
  gi|91773076|ref|YP_565768.1|  81 IEDLVRSTGDIGETAVAALGKKKKNKKKNQaslsffsedaasvsISIMDVFERFLDISRYsGAGSQSSKMRNLQFLFNSSS 161
                                   *******************8888884444444555555555555999**********98789******************* PP

                                   HHHHHHHHHHHCT---SS--HHHHHHHH CS
                DNA_ligase_A_N 145 peEakyliriilkdlriglsektvldal 172
                                   +eEa+yl+r+  +dlrig++e+ v+da+
  gi|91773076|ref|YP_565768.1| 162 SEEARYLARLTIEDLRIGVGEGIVRDAI 189
                                   **************************98 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 ?   -3.1   0.0       2.1   1.2e+04      25      50 ..      73      98 ..      56     117 .. 0.64
   2 !   63.0   0.0   5.1e-21     3e-17       2      99 .]     456     547 ..     455     547 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                                  -SS--HHHHHHHHHHHGGGEECTTCE CS
                DNA_ligase_A_C 25 gtGfsdaeleelrkklkelerkkppf 50
                                  ++G+s +e+e+l ++  ++ ++    
  gi|91773076|ref|YP_565768.1| 73 SSGLSLKEIEDLVRSTGDIGETAVAA 98
                                  57888888888877776444433333 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 5.1e-21
                                   GGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEECT CS
                DNA_ligase_A_C   2 gglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeitas 80 
                                   ++l+gs+ l++ d  dgk+  +gkv+tGfsd++l+el++ ++el   ++      + e      ++P++v+e++f+ei++s
  gi|91773076|ref|YP_565768.1| 456 ANLIGSYALACFDpeDGKFLPIGKVATGFSDEQLAELTEVFSELIIGESGR----EIE------LKPDVVFEIAFEEIQKS 526
                                   6789**************************************999999888....222......78*************** PP

                                   SSSTT..EECT-EEEEE-TTS CS
                DNA_ligase_A_C  81 gkyka..slRfPrfkrlReDk 99 
                                   ++y +  +lRfPr++++ReDk
  gi|91773076|ref|YP_565768.1| 527 TNYGSgyALRFPRLVNVREDK 547
                                   ********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3698.29
//
Query:       gi|91773077|ref|YP_565769.1|  [L=396]
Description: cell surface protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-66  222.3  11.3    6.9e-66  221.9  11.3    1.1  1  S-layer     S-layer protein
    0.00011   22.2   0.1    0.00011   22.2   0.1    1.8  2  S_layer_N   S-layer like family, N-terminal region
  ------ inclusion threshold ------
       0.15   12.4   0.1       0.42   10.9   0.1    1.8  1  Auxin_resp  Auxin response factor


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 !  221.9  11.3   1.1e-69   6.9e-66       7     257 ..      31     290 ..      24     291 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 1.1e-69
                       S-layer   7 seeltwtasnFsgfyydi.ddglssEsltlele.........sksdrtieegelvYsttpvekefef......eewgsYev 71 
                                    +++ w+ sn++++y+ + d g+++Esl++e+          + ++++i+++el+Y+t++++k++++      +++++Y+v
  gi|91773077|ref|YP_565769.1|  31 VSSIAWDGSNWNALYFALnDVGSNTESLCYENIdpenpaigvTPDNNIIDKKELIYRTHTYHKKYKLsaktdaNAVSTYSV 111
                                   45677*************889*********988898888776559**********************99999999999*** PP

                       S-layer  72 igflaekYfagydnsaetsddvsllsdekLskvlide..deektlksgssleLeegYeleikqiDvdgdkvwleLtkdgee 150
                                   i+++++kY+a+ +n+a           +k++ ++ ++    ektlk+g+s++L+++Y+l+++q+D d  k+++ L+kdg e
  gi|91773077|ref|YP_565769.1| 112 IPLFSKKYIAV-NNDA-----------SKMTTLIKEQggGAEKTLKEGESWDLGNDYSLKLNQLDADAGKAFVILYKDGIE 180
                                   ***********.7777...........8*********999***************************************** PP

                       S-layer 151 vdskvissska..dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqis.ddvleieegdefgkmevksvsen 228
                                   +ds+v++++++  d+ +++++dl++ dd+v++++++++ f++t++s+++++++++i+ d+v++i++gd+fg +++k+vsen
  gi|91773077|ref|YP_565769.1| 181 LDSDVLDMDGTddDRAFIVKDDLAGIDDLVYFVTYLENTFKSTSESFAILKYTWLIDkDNVITIKKGDKFGLLKCKDVSEN 261
                                   ********998999******************************************************************* PP

                       S-layer 229 eiemenddsitLsrdktieimddlkfkva 257
                                   +i+m+nd  itL++d+t++++dd++f+++
  gi|91773077|ref|YP_565769.1| 262 WINMSNDVVITLEMDNTVYFTDDWYFQTS 290
                                   ***************************97 PP

>> S_layer_N  S-layer like family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.9e-08   0.00011     180     283 ..      38     159 ..      11     160 .. 0.77
   2 ?   -1.9   0.4       0.4   2.4e+03     108     148 ..     193     242 ..     165     299 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.9e-08
                     S_layer_N 180 eddddavelvvaevvanvs..............ekkgddlkvkedelvyaslaykddkeafkdyq..dlieGveipllgke 244
                                    ++ +a  + +++v +n++               ++ d+  + ++el+y + +y+ + +  ++++  ++     ipl+ k+
  gi|91773077|ref|YP_565769.1|  38 GSNWNALYFALNDVGSNTEslcyenidpenpaiGVTPDNNIIDKKELIYRTHTYHKKYKLSAKTDanAVSTYSVIPLFSKK 118
                                   44567778888888888888888888888888788888899*************99984444443336777777******* PP

                     S_layer_N 245 ykivkidkDddiiylGkevy...egvikegetyslGdGytvk 283
                                   y  v+ d  + + +l ke +   e+++kege+ +lG+ y +k
  gi|91773077|ref|YP_565769.1| 119 YIAVNNDASK-MTTLIKEQGggaEKTLKEGESWDLGNDYSLK 159
                                   *998877777.667777765344899*************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.4
                     S_layer_N 108 tdkayllveaakd........dyta.klkdsswddglvdkavlgdadkvg 148
                                   +d+a+++++++           y + ++k  s + ++ + + l+d+d+v 
  gi|91773077|ref|YP_565769.1| 193 DDRAFIVKDDLAGiddlvyfvTYLEnTFKSTSESFAILKYTWLIDKDNVI 242
                                   44555555444333344433333221233333333444444444444443 PP

>> Auxin_resp  Auxin response factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1     7e-05      0.42      58      82 ..      20      44 ..      14      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7e-05
                    Auxin_resp 58 rfsGtivgvedldsvrWpgSkWrsL 82
                                  ++ Gti+  ++++s+ W gS+W  L
  gi|91773077|ref|YP_565769.1| 20 KVRGTILDSGNVSSIAWDGSNWNAL 44
                                  568*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2754.32
//
Query:       gi|91773078|ref|YP_565770.1|  [L=283]
Description: methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-11   43.4   0.0      1e-10   42.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    9.8e-10   38.5   0.0    1.7e-09   37.7   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    2.5e-08   34.6   0.0    5.7e-08   33.4   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    3.3e-07   29.7   0.0    4.7e-07   29.2   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    6.2e-07   30.0   0.0      2e-06   28.4   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
    1.9e-06   27.7   0.0    3.2e-06   27.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.2e-06   26.6   0.0    4.8e-06   26.0   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
    2.4e-05   23.8   0.0    3.6e-05   23.2   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    2.8e-05   24.0   0.0      4e-05   23.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      3e-05   23.5   0.0    3.9e-05   23.1   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00022   20.8   0.0    0.00039   20.0   0.0    1.4  1  MTS              Methyltransferase small domain
    0.00064   19.4   0.0    0.00096   18.8   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00076   19.3   0.0     0.0013   18.5   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
    0.00086   19.3   0.0     0.0014   18.6   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0045   16.8   0.0     0.0096   15.7   0.0    1.5  1  Met_10           Met-10+ like-protein
     0.0052   16.4   0.0     0.0087   15.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0062   15.7   0.0       0.01   14.9   0.0    1.4  1  DREV             DREV methyltransferase
     0.0065   16.2   0.0     0.0093   15.7   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
      0.009   15.4   0.0      0.016   14.6   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.018   14.4   0.0      0.031   13.7   0.0    1.3  1  TehB             Tellurite resistance protein TehB
       0.03   14.0   0.0      0.054   13.1   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.037   13.0   0.0      0.059   12.4   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.048   13.1   0.0      0.094   12.2   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
      0.073   12.2   0.0       0.12   11.4   0.0    1.3  1  Fibrillarin      Fibrillarin
      0.078   12.6   0.0       0.12   11.9   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
       0.12   12.1   0.0       0.56    9.8   0.0    2.0  2  GCD14            tRNA methyltransferase complex GCD14 subunit


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 !   42.2   0.0   1.5e-13     1e-10       1      90 [.      69     157 ..      69     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.5e-13
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTT...TEEEEEEESTGGGS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedg...sfDlvvssgalhhl 77 
                                   vLd+G G+G l++ l++++  a+vt+v++ ++m+e  +e++++ g+ n+ +v++  edl+ ed+    +D+v++s++l   
  gi|91773078|ref|YP_565770.1|  69 VLDIGSGPGSLAIPLSEKV--AHVTAVEPGKGMMELLQENISKYGInNIGCVNKRWEDLNVEDDlegPYDIVIASFSLG-- 145
                                   9*****************9..***********************99*************97554444*******97755.. PP

                                   SHHHHHHHHHHHH CS
               Methyltransf_25  78 sdedlekalkeia 90 
                                     +d+++a++++ 
  gi|91773078|ref|YP_565770.1| 146 -MPDIRNAIEKMQ 157
                                   .478999999886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.5e-12   1.7e-09       8     107 ..      53     158 ..      37     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.5e-12
               Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaep 79 
                                   ++ + l++l+  l++g+rvLdiG G G+l+  l+e++++vt+v++   + e+++         ++ + +k  +d + +++ 
  gi|91773078|ref|YP_565770.1|  53 RIEKTLKELP--LKKGSRVLDIGSGPGSLAIPLSEKVAHVTAVEPGKGMMELLQeniskyginNIGCVNKRWEDLNVEDDL 131
                                   3445555555..99********************************99999999*************************** PP

               Methyltransf_23  80 qgkfdlIvlrevlehvpdppellrqiat 107
                                   +g +d+++++++l+ +pd   ++ ++++
  gi|91773078|ref|YP_565770.1| 132 EGPYDIVIASFSLG-MPDIRNAIEKMQS 158
                                   *************8.5666666666666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   8.2e-11   5.7e-08       1      90 [.      70     157 ..      70     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 8.2e-11
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnve..lealdlldldggssfDlvvasnvlhhl 79 
                                   L+iG+G Gsl+ +l ek   +++t+v++ + ++e  +e ++k++ nn  +v+  +e+l+++d+ +g  +D+v+as+ l   
  gi|91773078|ref|YP_565770.1|  70 LDIGSGPGSLAIPLSEK--VAHVTAVEPGKGMMELLQENISKYGINNIGCVNkrWEDLNVEDDLEG-PYDIVIASFSLGM- 146
                                   8****************..**************************998777522677777666665.***********99. PP

               Methyltransf_12  80 kdirevldnir 90 
                                   +dir +++++ 
  gi|91773078|ref|YP_565770.1| 147 PDIRNAIEKMQ 157
                                   89999999876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   6.8e-10   4.7e-07      14      75 ..      49     110 ..      40     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.8e-10
                                   --HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTC CS
                        RrnaAD  14 knkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskd 75 
                                   knk  i++ l++l l++   vl+ig+G+G l  +L + + +v+++E  + +++llq+++sk+
  gi|91773078|ref|YP_565770.1|  49 KNKGRIEKTLKELPLKKGSRVLDIGSGPGSLAIPLSEKVAHVTAVEPGKGMMELLQENISKY 110
                                   688889999************************************************99844 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       9.2   6.4e+03      33      60 ..      43      66 ..      17      67 .. 0.61
   2 !   28.4   0.0   2.8e-09     2e-06       1      71 [.      70     144 ..      70     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9.2
                                  HHHHHCCHHT-EEEETTEECCCTSS-TT CS
               Methyltransf_11 33 lakekaseeglkvefvvadaeklpfedn 60
                                   +k+ ++++g +   ++ ++++lp++++
  gi|91773078|ref|YP_565770.1| 43 FWKRSQKNKG-R---IEKTLKELPLKKG 66
                                  3333333333.3...6777777887765 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.8e-09
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT...-EEEEEEES-C CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfedn...sfDlvvssevl 71 
                                   Ld+G+G G+la +l +++a+v++v++ k m++l +e++s+ g+ ++ +v  + e+l++ed+    +D+v++s++l
  gi|91773078|ref|YP_565770.1|  70 LDIGSGPGSLAIPLSEKVAHVTAVEPGKGMMELLQENISKYGInNIGCVNKRWEDLNVEDDlegPYDIVIASFSL 144
                                   8**********************************************************9655599999999876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.6e-09   3.2e-06       2     100 ..      64     159 ..      63     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.6e-09
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled...ekfDlil 79 
                                   +kg rvlD+G+G G l++ l e++   a+v+ ++  + + el +en +k g++n+      +e+l+  +ed    ++D+++
  gi|91773078|ref|YP_565770.1|  64 KKGSRVLDIGSGPGSLAIPLSEKV---AHVTAVEPGKGMMELLQENISKYGINNIGCVNKRWEDLN--VEDdleGPYDIVI 139
                                   7999*****************886...89***********************************99..888888******* PP

               Methyltransf_31  80 snevlnaladpdkileeierv 100
                                   +      ++d  +++e+++++
  gi|91773078|ref|YP_565770.1| 140 ASFS-LGMPDIRNAIEKMQSA 159
                                   9644.5999999999988875 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   6.9e-09   4.8e-06      44     121 ..      63     140 ..      36     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.9e-09
                                   CS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC....TTTTT-EEEEE CS
                          GidB  44 llkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee....kqeeekydvvt 120
                                   l k +  +v+D+GsG+G  +ipL+   +  ++t +e+ +  ++ L+e +++ +++n+  v++r e+     + e +yd+v+
  gi|91773078|ref|YP_565770.1|  63 LKKGS--RVLDIGSGPGSLAIPLS--EKVAHVTAVEPGKGMMELLQENISKYGINNIGCVNKRWEDlnveDDLEGPYDIVI 139
                                   33444..4*********9999987..6777899*********************************887677788899887 PP

                                   E CS
                          GidB 121 s 121
                                   +
  gi|91773078|ref|YP_565770.1| 140 A 140
                                   5 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.2e-08   3.6e-05      44     126 ..      45     127 ..      22     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.2e-08
                                   HHHHHHH..HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GG CS
                          CMAS  44 eeAqlaK..ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldye 122
                                   +  q++K  ++ +l+ l lk+G+++LdiG G Gsl++   e+  ++v ++   k  ++l ++++ + ++++   v+ + +e
  gi|91773078|ref|YP_565770.1|  45 KRSQKNKgrIEKTLKELPLKKGSRVLDIGSGPGSLAIPLSEK-VAHVTAVEPGKGMMELLQENISKYGINNIGCVN-KRWE 123
                                   5667776336789*************************9999.89*********************9999887776.4688 PP

                                   G--- CS
                          CMAS 123 dlde 126
                                   dl+ 
  gi|91773078|ref|YP_565770.1| 124 DLNV 127
                                   8764 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.9e-08     4e-05      67     146 ..      59     138 ..      52     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.9e-08
                                   HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEE...ES-GGGTTGGG-SEE CS
                          PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivv...vgDGrkGyeekaPYd 144
                                   + l lkkg+rvL++GsG G l+  l++ v +++   ++e  k ++e  ++n+ k +++n+  v     D +   + + PYd
  gi|91773078|ref|YP_565770.1|  59 KELPLKKGSRVLDIGSGPGSLAIPLSEKVAHVT---AVEPGKGMMELLQENISKYGINNIGCVnkrWEDLNVEDDLEGPYD 136
                                   5567***********************999888...9********************976544111445555555556666 PP

                                   EE CS
                          PCMT 145 ai 146
                                    +
  gi|91773078|ref|YP_565770.1| 137 IV 138
                                   55 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   5.7e-08   3.9e-05      38     140 ..      56     157 ..      42     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.7e-08
                                   HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-...T CS
               Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed...d 115
                                   ++ k    k+g++vlD+ +G g la+ ls++v    +v+ ++  + m++  ++ + + g  ni  ++   e+L+ ed   +
  gi|91773078|ref|YP_565770.1|  56 KTLKELPLKKGSRVLDIGSGPGSLAIPLSEKVA---HVTAVEPGKGMMELLQENISKYGINNIGCVNKRWEDLNVEDdleG 133
                                   5666667799*******************9986...58888999*******************************995555 PP

                                   -EEEEEEES-GGG-S-HHHHHHHHH CS
               Ubie_methyltran 116 sfDvvtvsfGlrnvtDklkaLkeay 140
                                    +D+v  sf l  ++D+ +a++++ 
  gi|91773078|ref|YP_565770.1| 134 PYDIVIASFSL-GMPDIRNAIEKMQ 157
                                   79*******99.5889988888775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.7e-07   0.00039      24     102 ..      58     139 ..      55     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.7e-07
                                   HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTST.TS-EE CS
                           MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleeve.ekkfd 99 
                                   l+ lp ++  +vlD+G+G G l++ l ++  +  vt+v+  +  +e+ +en+++ +++    v+ +++d+  e + e+ +d
  gi|91773078|ref|YP_565770.1|  58 LKELPLKKGSRVLDIGSGPGSLAIPLSEKVAH--VTAVEPGKGMMELLQENISKYGINnigcVNKRWEDLNVEDDlEGPYD 136
                                   56788889999*****************9988..9*******************999988787788888754443358899 PP

                                   EEE CS
                           MTS 100 liv 102
                                   +++
  gi|91773078|ref|YP_565770.1| 137 IVI 139
                                   888 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06   0.00096      41     117 ..      65     138 ..      50     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                   +g+rvLD+ +G G+l++  lS +++++++ve  k ++++l+en+++ ++++    +++++ e+l+ +   ++++div
  gi|91773078|ref|YP_565770.1|  65 KGSRVLDIGSGPGSLAI-PLSEKVAHVTAVEPGKGMMELLQENISKYGINN--IGCVNKRWEDLNVEDDLEGPYDIV 138
                                   6899*************.6*****************************998..444445555555554555666666 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-06    0.0013      16     127 ..      28     141 ..      15     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
               Methyltransf_16  16 sigrkvWdaavvlvkylekklake.......lganelsklsvlELGsGtGlvGlavaellpeakviltD.leellellkkn 88 
                                   +  +k+Wd+   +  + ++  +++       ++    ++ +vl++GsG G   + + e+   a+v+     + ++ell++n
  gi|91773078|ref|YP_565770.1|  28 GDCAKLWDSRENAERFWKRSQKNKgriektlKELPLKKGSRVLDIGSGPGSLAIPLSEK--VAHVTAVEpGKGMMELLQEN 106
                                   44468999999999988887666689988764455678899***********9999999..566655441566******** PP

               Methyltransf_16  89 ielnknalkskvkvevLdWgeeleedllekeevDlilaa 127
                                   i   +    +++      W++   ed l + ++D+++a+
  gi|91773078|ref|YP_565770.1| 107 ISKYG---INNIGCVNKRWEDLNVEDDL-EGPYDIVIAS 141
                                   **944...77888888999664334444.5689***997 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     2e-06    0.0014      12      65 ..      63     114 ..      51     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
               Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled 65 
                                   ++kgsrv+DiG+  g l+i l   +k+ +v+a++  +g +e  +eni+k+g+++
  gi|91773078|ref|YP_565770.1|  63 LKKGSRVLDIGSGPGSLAIPLS--EKVAHVTAVEPGKGMMELLQENISKYGINN 114
                                   46899****************8..6899**********************9965 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05    0.0096      93     151 ..      57     114 ..      19     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                   HHHTT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                        Met_10  93 rlakl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                   +l +l  ++g +V+d+  G G +aip++   k   v a++     +++l+eni    +++
  gi|91773078|ref|YP_565770.1|  57 TLKELpLKKGSRVLDIGSGPGSLAIPLSE--KVAHVTAVEPGKGMMELLQENISKYGINN 114
                                   233336789*******************9..999*******************9866665 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05    0.0087       3      85 ..      68     148 ..      66     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwGG 83 
                                    +lD+ sG G  +i + ++  +v a+e  +  +++ q+N   Yg++ +i +v   +++l  +  le   +d+v++S   G 
  gi|91773078|ref|YP_565770.1|  68 RVLDIGSGPGSLAIPLSEKVAHVTAVEPGKGMMELLQENISKYGIN-NIGCVNKRWEDLNVEDDLEGP-YDIVIASFSLGM 146
                                   69*****************************************995.699999999998777777776.999999998887 PP

               Methyltransf_15  84 ps 85 
                                   p+
  gi|91773078|ref|YP_565770.1| 147 PD 148
                                   76 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05      0.01      93     151 ..      64     128 ..      48     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                          DREV  93 qedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlk....kkkynvlsale..lqetdvk 151
                                   ++  ++ld+G+G G ++  +++ + +v a e  + m++ l+    k + n ++ ++  +++ +v+
  gi|91773078|ref|YP_565770.1|  64 KKGSRVLDIGSGPGSLAIPLSEKVAHVTAVEPGKGMMELLQenisKYGINNIGCVNkrWEDLNVE 128
                                   57789***************************999988776211145556666665456665555 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-05    0.0093       3      77 ..      43     115 ..      41     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                        DUF938   3 fapaaernrepilevLksylakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnl 77 
                                   f + +++n+  i + Lk+   k+++rvL+i+sG G  A+ + +++ +++  + ++ + ++e ++  +++ +++n+
  gi|91773078|ref|YP_565770.1|  43 FWKRSQKNKGRIEKTLKELPLKKGSRVLDIGSGPGSLAIPLSEKVAHVT--AVEPGKGMMELLQENISKYGINNI 115
                                   556799*************999999*************99998877654..455555566666666666666666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.3e-05     0.016     159     232 ..      63     140 ..      52     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.....eekadviva 232
                                   +k+g++vlD+G G G Lai  +    ++v+av   +  ++  +eN+++ ++++   v+   e l+     e+++d+++a
  gi|91773078|ref|YP_565770.1|  63 LKKGSRVLDIGSGPGSLAIPLSE-KVAHVTAVEPGKGMMELLQENISKYGINNIGCVNKRWEDLNveddlEGPYDIVIA 140
                                   78999**************9776.5679***********************9977787554444223456799****99 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-05     0.031      30     122 ..      65     158 ..      41     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                                   -S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTE...EEEE--GG.G----S-EEEEEEESSGG CS
                          TehB  30 kpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlkni...stalydin.eaklderydfilstvvlm 106
                                   k ++vld+g g g  ++ ls +  +vta++  +  ++ l+e ++k  ++ni   + +  d+n e +l+  yd+++++  l 
  gi|91773078|ref|YP_565770.1|  65 KGSRVLDIGSGPGSLAIPLSEKVAHVTAVEPGKGMMELLQENISKYGINNIgcvNKRWEDLNvEDDLEGPYDIVIASFSL- 144
                                   6789***************************************9988887711145566777345677788888776544. PP

                                   GS-GGGHHHHHHHHHH CS
                          TehB 107 fleaeripsiienmqe 122
                                         i + ie mq 
  gi|91773078|ref|YP_565770.1| 145 --GMPDIRNAIEKMQS 158
                                   ..44456666666665 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 ?   13.1   0.0   7.8e-05     0.054       4      66 ..      61     120 ..      58     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.8e-05
                                   H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES CS
               Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivlea 66 
                                   L ++++ ++lD+ ++PG+       l ++ ++v+Av+  k  ++ ++en+++ g++n+ +++ 
  gi|91773078|ref|YP_565770.1|  61 LPLKKGSRVLDIGSGPGSLAI---PLSEKVAHVTAVEPGKGMMELLQENISKYGINNIGCVNK 120
                                   56788999*********8655...5666799*************************9998875 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.5e-05     0.059     204     255 ..      68     119 ..      47     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.5e-05
               tRNA_U5-meth_tr 204 dllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiir 255
                                    +l++  G G ++++l++++ +v a e  k  +e  q ni +  i+n+  + 
  gi|91773078|ref|YP_565770.1|  68 RVLDIGSGPGSLAIPLSEKVAHVTAVEPGKGMMELLQENISKYGINNIGCVN 119
                                   6789999****************************************98776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014     0.094       4      57 ..      68     119 ..      65     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEE CS
                Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilr 57 
                                    vl+iG+G G++ + l++k ++++  ++E  + +++ + ++i +++++N+ +++
  gi|91773078|ref|YP_565770.1|  68 RVLDIGSGPGSLAIPLSEKVAHVT--AVEPGKGMMELLQENISKYGINNIGCVN 119
                                   689*****************9976..89**********************9987 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.12      43     101 ..      39      93 ..       9     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                   EEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEE CS
                   Fibrillarin  43 eEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyav 101
                                   +  R W+  + K  + i k lkelp+kkgs+vL +G++ G+ +  +s+ v     v av
  gi|91773078|ref|YP_565770.1|  39 NAERFWKRSQ-KNKGRIEKTLKELPLKKGSRVLDIGSGPGSLAIPLSEKVA---HVTAV 93 
                                   4458887544.66789*********************99987766665554...44444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.12      11      34 ..      63      86 ..      55     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                          MetW 11 ikpgsrvldlGcGdGellellkee 34
                                  +k+gsrvld+G+G G+l   l e+
  gi|91773078|ref|YP_565770.1| 63 LKKGSRVLDIGSGPGSLAIPLSEK 86
                                  5899*************8877653 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00082      0.56      33      99 ..      58     121 ..      45     169 .. 0.64
   2 ?   -0.5   0.0       1.2   8.1e+02      62     120 ..     209     266 ..     204     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00082
                         GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthr 99 
                                    ++L lk+Gs+v++ G G gsl+  ++  va   h+ ++e  +  +e  +e+  + +++++  v++r
  gi|91773078|ref|YP_565770.1|  58 LKELPLKKGSRVLDIGSGPGSLAIPLSEKVA---HVTAVEPGKGMMELLQENISKYGINNIGCVNKR 121
                                   56899******************99999887...677777777777777777777777665555444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                         GCD14  62 vaPtGhlftfefheq..raekareefrehelsqlvtvthrDvckeGfdeevsgkvDavfLD 120
                                   + P  h+f +ef ++   +++a++ fr++     +  +++++  + + ee  ++ D +f+D
  gi|91773078|ref|YP_565770.1| 209 IFPDMHVFPLEFTNDfgSMDEAIDYFRSRY---TIETEQQEIMLRNYLEETLEQQDGLFVD 266
                                   668889999999886335788999998764...5666777777777755555777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1855.48
//
Query:       gi|91773079|ref|YP_565771.1|  [L=254]
Description: cobyrinic acid a,c-diamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-10   39.5   0.0    7.7e-10   38.9   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.6e-07   31.0   0.0    7.8e-06   25.5   0.0    2.2  2  ParA             NUBPL iron-transfer P-loop NTPase
    1.7e-06   27.7   0.0    0.00065   19.3   0.0    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    8.9e-06   25.7   0.1    1.4e-05   25.1   0.1    1.5  1  AAA_31           AAA domain
    0.00012   21.3   0.2    0.00021   20.6   0.2    1.4  1  ArsA_ATPase      Anion-transporting ATPase
     0.0002   21.3   0.1     0.0003   20.7   0.1    1.2  1  APS_kinase       Adenylylsulphate kinase
    0.00029   20.2   0.0     0.0023   17.3   0.1    2.2  3  MipZ             ATPase MipZ
    0.00035   20.7   0.1    0.00057   20.0   0.1    1.3  1  DUF87            Helicase HerA, central domain
      0.001   18.4   0.0      0.002   17.5   0.0    1.4  1  Zeta_toxin       Zeta toxin
     0.0013   18.4   0.0      0.044   13.4   0.1    2.1  2  SRP54            SRP54-type protein, GTPase domain
     0.0017   17.9   0.1     0.0039   16.7   0.1    1.7  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
     0.0025   18.2   0.0     0.0081   16.6   0.0    1.7  2  AAA_16           AAA ATPase domain
     0.0036   16.8   0.0     0.0062   16.0   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
     0.0042   17.3   0.0          1    9.6   0.0    2.3  2  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.013   16.0   0.1      0.022   15.3   0.1    1.4  1  ABC_tran         ABC transporter
      0.024   14.2   0.0       0.05   13.2   0.0    1.5  2  AAA_25           AAA domain
      0.034   14.2   0.1        4.4    7.4   0.0    2.3  2  MMR_HSR1         50S ribosome-binding GTPase
      0.042   13.6   0.1      0.089   12.6   0.0    1.5  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.05   12.9   0.1      0.073   12.4   0.1    1.2  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
      0.051   13.5   0.0      0.096   12.6   0.0    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.062   13.0   0.0       0.14   11.8   0.0    1.5  1  Thymidylate_kin  Thymidylate kinase
      0.063   13.2   0.1       0.13   12.2   0.1    1.5  1  NTPase_1         NTPase
      0.064   13.0   1.4       0.11   12.2   1.4    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.066   13.8   0.1       0.12   12.9   0.1    1.4  1  AAA_18           AAA domain
      0.067   12.2   0.0       0.11   11.4   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.079   13.1   0.0       0.12   12.5   0.0    1.3  1  AAA_33           AAA domain
      0.089   11.7   0.0       0.34    9.8   0.0    1.9  3  AAA_10           AAA-like domain
       0.11   12.2   0.2       0.21   11.3   0.0    1.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.11   12.1   0.0       0.41   10.3   0.0    1.8  2  AAA_24           AAA domain
       0.12   12.0   0.2       0.79    9.3   0.1    2.0  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.17   11.9   0.0       0.47   10.4   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
       0.18   10.9   0.0       0.44    9.6   0.0    1.5  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase


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 !   38.9   0.0   1.4e-12   7.7e-10       6      87 ..       7     200 ..       3     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.4e-12
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................ 54 
                                   +kGG+GK+tl+a +a++l++rg +Vl++D D     l++ +gle   +                                 
  gi|91773079|ref|YP_565771.1|   7 GKGGSGKSTLTALIAKSLSERGCNVLVIDNDESNFGLHMQMGLELPDDFlnflggkknlvgkmmeafpkgeklslfdhkwe 87 
                                   8****************************99998888877777777777889999999999******************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|91773079|ref|YP_565771.1|  88 istipegyvtrkgnlsliavgkihefgegcacpmgalakqliqnielgendfvlvdteagiehfgrgveegcdvlfmvadp 168
                                   *****************************9999988777777777777777777777777777777777777777777777 PP

                                   ..CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS. CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ..dlkrllellealgkkkalllkiagvvlnrvdge 87 
                                       +rl+e +++l  +     k++ ++lnr +g 
  gi|91773079|ref|YP_565771.1| 169 syESIRLSEKISKLADN---SGKPLYYILNRAEGA 200
                                   55444555555555544...257777777777765 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 !   25.5   0.0   1.4e-08   7.8e-06       9      42 ..       5      38 ..       2      57 .. 0.87
   2 ?    3.4   0.0      0.08        45      99     121 ..     124     146 ..     117     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-08
                          ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDi 42
                                  l gKGG GKSt+++ +A +L+++g +v ++D D 
  gi|91773079|ref|YP_565771.1|  5 LCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDE 38
                                  68*****************************995 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.08
                          ParA  99 aikqllkdvewgelDyLiiDlPP 121
                                   + kql++++e ge D++++D+  
  gi|91773079|ref|YP_565771.1| 124 LAKQLIQNIELGENDFVLVDTEA 146
                                   569*****************965 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06   0.00065      10      47 ..       8      46 ..       2      57 .. 0.85
   2 !    6.4   0.0    0.0096       5.4     107     156 ..     127     176 ..      97     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                      CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdnl.Lrlh 47
                                  +GG G+++l+a +a++l e g +vlviD+  +n+ L+++
  gi|91773079|ref|YP_565771.1|  8 KGGSGKSTLTALIAKSLSERGCNVLVIDNDESNFgLHMQ 46
                                  7****************************9999645544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0096
                      CBP_BcsQ 107 aalkelk.eqyrwillDlpagasaltrellaladlvllvvepdanchvrLh 156
                                   + +++++ ++ +++l+D  ag ++  r + + +d+ ++v+ p   + +rL 
  gi|91773079|ref|YP_565771.1| 127 QLIQNIElGENDFVLVDTEAGIEHFGRGVEEGCDVLFMVADPSYES-IRLS 176
                                   34566777899*****************************998775.5555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   2.6e-08   1.4e-05      10      40 ..       8      38 ..       3     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.6e-08
                        AAA_31 10 KGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                  KGG GK+T +  +a++l+++g  vL++D D 
  gi|91773079|ref|YP_565771.1|  8 KGGSGKSTLTALIAKSLSERGCNVLVIDNDE 38
                                  *****************************96 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   3.8e-07   0.00021       5      38 ..       4      37 ..       1      40 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.8e-07
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  l+ GKGG GK+t+ a +a  lse g +vl+i  D
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLSERGCNVLVIDND 37
                                  679****************************887 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   5.3e-07    0.0003       6      53 ..       4      51 ..       1      60 [. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.3e-07
                                  EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                    APS_kinase  6 wltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53
                                  +l G  gsGKst++  ++k+L e+g +v ++d d+  +gL  ++g + 
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDESNFGLHMQMGLEL 51
                                  689*************************************99999865 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.1e-06    0.0023       9      40 ..       8      39 ..       3      48 .. 0.89
   2 ?   -0.7   0.0       1.2   6.9e+02      98     125 ..     135     162 ..     120     180 .. 0.76
   3 ?   -2.0   0.0       3.1   1.7e+03      47      83 ..     192     228 ..     189     249 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                                  STTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                          MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlr 40
                                  kGGsGkst +  +a +L+++G +v +id d  
  gi|91773079|ref|YP_565771.1|  8 KGGSGKSTLTALIAKSLSERGCNVLVIDNDES 39
                                  9***************************9965 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                   HH-SEEEEE--SS--HHHHHHHHT-SEE CS
                          MipZ  98 aeldfividtPGsdsalsrlahsladtl 125
                                    e df+++dt    ++  r + +  d l
  gi|91773079|ref|YP_565771.1| 135 GENDFVLVDTEAGIEHFGRGVEEGCDVL 162
                                   4689*****9888777777777777766 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.1
                                   HHHHHHHHHHHHT------EEE-SSS-HHHHTTS-HH CS
                          MipZ  47 ylenraataerkglsLplpealalseaeeaeveeeee 83 
                                   y+ nra+ a+r+ ls  ++e +++s++   e   ++ 
  gi|91773079|ref|YP_565771.1| 192 YILNRAEGASREILSCGISEDRVISTVPIYESIFKAG 228
                                   7888888888888888887777777665544444444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1     1e-06   0.00057      28      59 ..       5      35 ..       1      38 [. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-06
                         DUF87 28 ilgsTGsGKSntvavLleellekkgatililD 59
                                    g+ GsGKS+++a++ ++l  ++g ++l++D
  gi|91773079|ref|YP_565771.1|  5 LCGKGGSGKSTLTALIAKSLS-ERGCNVLVID 35
                                  56999****************.********** PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.5e-06     0.002      20      53 ..       4      38 ..       2      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                    Zeta_toxin 20 llgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                  ll G  G+GKs+l +l++++l  r+ nv+++d D+
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLSeRGCNVLVIDNDE 38
                                  899******************98889*******97 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   7.8e-05     0.044       4      39 ..       3      38 ..       1      49 [. 0.88
   2 ?    2.8   0.0      0.14        81      70      92 ..     123     146 ..     109     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  +ll+G  G+GK t +a +a+ l+++g +vl++  D 
  gi|91773079|ref|YP_565771.1|  3 TLLCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDE 38
                                  699****************************98886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHTTSSEEEEEE.- CS
                         SRP54  70 avakeavekakeekidvvlvDT.a 92 
                                   a+ak+ +++ +  + d+vlvDT a
  gi|91773079|ref|YP_565771.1| 123 ALAKQLIQNIELGENDFVLVDTeA 146
                                   5788999999999*********44 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   6.9e-06    0.0039       3      37 ..       3      37 ..       1      69 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.9e-06
                     Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                    + GkGG+Gkst ++ ++++l+e+g  vl++  D
  gi|91773079|ref|YP_565771.1|  3 TLLCGKGGSGKSTLTALIAKSLSERGCNVLVIDND 37
                                  5678***************************9877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.4e-05    0.0081      28      63 ..       4      39 ..       2      65 .. 0.81
   2 ?   -1.1   0.0       3.9   2.2e+03     117     145 ..     173     198 ..     123     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-05
                        AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  ll G  G+GKs+l   ++++l+++g+ +l  ++d++
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDES 39
                                  899*********************988877777777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.9
                        AAA_16 117 srllellkrllallsrderplvlvlDdlq 145
                                    rl e++++l+    + ++pl+ +l  ++
  gi|91773079|ref|YP_565771.1| 173 IRLSEKISKLA---DNSGKPLYYILNRAE 198
                                   45555555554...555668888876544 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05    0.0062       5      41 ..       4      40 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                                  EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                  +l+G   sGKst+++ +ak l+e++ +v vid++  +
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDESN 40
                                  79******************************98766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0018         1       8      34 ..      15      41 ..       4      50 .. 0.77
   2 ?    5.4   0.0     0.039        22       6      60 ..     121     179 ..     118     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                                  HHHHHHHHHHHH.TTEEEEEEESSHHHH CS
                        TrkA_N  8 rvGrslaeeLse.ggkdvvvidkdeerv 34
                                  +++  +a+ Lse g+ +v+vid+de+++
  gi|91773079|ref|YP_565771.1| 15 TLTALIAKSLSErGC-NVLVIDNDESNF 41
                                  556678999999666.5*******9875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                                   -SHHHHHHHHHHHHTTEEEEEEESSH..HHHHHHHHTT..SEEEES-TTSHHHHHHTTG CS
                        TrkA_N   6 lGrvGrslaeeLseggkdvvvidkde..erveelreeg..levvvgdatdeevLeeagi 60 
                                   +G ++++l+++++ g++d+v++d++   e++ +  eeg  + ++v+d++ e++  + +i
  gi|91773079|ref|YP_565771.1| 121 MGALAKQLIQNIELGENDFVLVDTEAgiEHFGRGVEEGcdVLFMVADPSYESIRLSEKI 179
                                   899999******997779******87555566667788444477788888877666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1     4e-05     0.022      14      39 ..       3      28 ..       1      52 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4e-05
                                  EEEEESTTSSHHHHHHHHTTSS--SE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 14 vaivGenGaGKStLlkllagllkpte 39
                                  + + G+ G+GKStL +l+a+ l+   
  gi|91773079|ref|YP_565771.1|  3 TLLCGKGGSGKSTLTALIAKSLSERG 28
                                  6799***************9987654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-05      0.05      36      87 ..       3      44 ..       1      56 [. 0.83
   2 ?   -3.0   0.0         8   4.5e+03     116     152 ..     134     170 ..     124     189 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                        AAA_25 36 allaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelr 87
                                  +ll+G +g+GK+tl+  +a +++ +G+           +Vl++++++s+ +l+
  gi|91773079|ref|YP_565771.1|  3 TLLCGKGGSGKSTLTALIAKSLSeRGC-----------NVLVIDNDESNFGLH 44
                                  79***************9999995555...........778888777776666 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8
                        AAA_25 116 LfakdrggtlltadvdaleaaieevegvrlvviDpls 152
                                   L ++d+    ++a +++  + +ee ++v + v Dp +
  gi|91773079|ref|YP_565771.1| 134 LGENDFVLVDTEAGIEHFGRGVEEGCDVLFMVADPSY 170
                                   4444444444555555555555555555555555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2      0.06        34       3      22 ..       4      23 ..       2      35 .. 0.82
   2 ?    7.4   0.0    0.0079       4.4      41     113 ..     132     195 ..     118     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.06
                                  EEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                  ++ G+  +GKStL   + ++
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKS 23
                                  688999*******9888776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0079
                                   EEETTEEEEEEEC.GGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                      MMR_HSR1  41 vklkgkeielvDt.pGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                   ++l++++++lvDt +G ie       +g+ +++   +d++++v d s e   +l e++ +l ++++kpl ++ln
  gi|91773079|ref|YP_565771.1| 132 IELGENDFVLVDTeAG-IE------HFGRGVEE--GCDVLFMVADPSYE-SIRLSEKISKLADNSGKPLYYILN 195
                                   5556788999999667.77......56776663..59********7744.345668888888889999999998 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00016     0.089       1      31 [.       7      37 ..       7      66 .. 0.84
   2 ?   -3.0   0.0       9.3   5.2e+03      86     118 ..     127     152 ..     122     156 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                  G+  sGKSTl++l++  + ++g +++++D D
  gi|91773079|ref|YP_565771.1|  7 GKGGSGKSTLTALIAKSLSERGCNVLVIDND 37
                                  6778*************************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.3
                        CLP1_P  86 elareveekleenkkakasgliIntpGwvkglg 118
                                   +l++++e         ++++++++t   ++ +g
  gi|91773079|ref|YP_565771.1| 127 QLIQNIE-------LGENDFVLVDTEAGIEHFG 152
                                   4444444.......2245677777776666665 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00013     0.073       1      54 [.       2      53 ..       2      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                     Gtr1_RagA  1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwD 54
                                  k LL+Gk+gsGK+++   i + ++ r +  l   id ++s++ ++ ++ l+l D
  gi|91773079|ref|YP_565771.1|  2 KTLLCGKGGSGKSTLTALIAKSLSERGCNVLV--IDNDESNFGLHMQMGLELPD 53
                                  679*********************99999986..55666666666666666655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017     0.096       4      42 ..       5      43 ..       3      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                          MobB  4 ivgksgsGKTtLleklipelkarglrvgtiKhahhgfdv 42
                                  ++gk gsGK tL   + + l++rg++v +i  ++ +f +
  gi|91773079|ref|YP_565771.1|  5 LCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDESNFGL 43
                                  799***************************999998865 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024      0.14       5      36 ..       9      39 ..       7      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                  TTSSHHHHHHHHHHHHHHTTE.EEEESSSTTS CS
               Thymidylate_kin  5 DGaGKttqaellkerlkeegikvvltrepggt 36
                                   G+GK+t ++l+++ l+e+g + vl   ++++
  gi|91773079|ref|YP_565771.1|  9 GGSGKSTLTALIAKSLSERGCN-VLVIDNDES 39
                                  59******************99.444444444 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   0.00023      0.13       3      30 ..       4      31 ..       2      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                                  EEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkv 30
                                  ++ G+ G+GK+Tl   +++ l+++g++v
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLSERGCNV 31
                                  689**********************998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4    0.0002      0.11      25      38 ..       3      16 ..       1      23 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                        AAA_29 25 tlltGpsGsGKSTl 38
                                  tll G+ GsGKSTl
  gi|91773079|ref|YP_565771.1|  3 TLLCGKGGSGKSTL 16
                                  9************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00021      0.12       2      24 ..       4      27 ..       4      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00021
                        AAA_18  2 lltGtpGvGKttlakeLskrl.gf 24
                                  ll+G+ G+GK+tl+  ++k+l + 
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLsER 27
                                  69************9999987333 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 ?   11.4   0.0    0.0002      0.11      34      67 ..       5      38 ..       2      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavDP 67
                                  l G  G+Gkstl+  ++ +l +rG  v v+  D 
  gi|91773079|ref|YP_565771.1|  5 LCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDE 38
                                  57999**********************9997775 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   0.00022      0.12       3      31 ..       4      37 ..       3      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                        AAA_33  3 llvGlpGsGKstlaerllkklg.....avllssd 31
                                  ll+G  GsGKstl   ++k l      + +++ d
  gi|91773079|ref|YP_565771.1|  4 LLCGKGGSGKSTLTALIAKSLSergcnVLVIDND 37
                                  79************99988887777544455555 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0006      0.34      23      59 ..       2      38 ..       1      58 [. 0.90
   2 ?   -1.8   0.0         2   1.1e+03     238     259 ..      74      95 ..      64     100 .. 0.76
   3 ?   -2.8   0.0         4   2.3e+03      37      81 ..     124     176 ..     122     188 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                        AAA_10 23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkk 59
                                  ++l+ G+ G GKS l+ l+   +s +g  +l+iD  +
  gi|91773079|ref|YP_565771.1|  2 KTLLCGKGGSGKSTLTALIAKSLSERGCNVLVIDNDE 38
                                  5799******************************765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                        AAA_10 238 kkefkvvifDEawiftssaeGk 259
                                    k +k   fD  w + +++eG 
  gi|91773079|ref|YP_565771.1|  74 PKGEKLSLFDHKWEISTIPEGY 95 
                                   66788899***********995 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4
                        AAA_10  37 lakllvlyisllggkaliiDpkkerekfketlpe.......iak.kinvvtLd 81 
                                   lak l+ +i l ++  +++D  +  e+f + + e       +a+ +++ ++L+
  gi|91773079|ref|YP_565771.1| 124 LAKQLIQNIELGENDFVLVDTEAGIEHFGRGVEEgcdvlfmVADpSYESIRLS 176
                                   57888888888888888888888888887777665444443222345555555 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       2      33 ..       6      37 ..       5      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                    ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                  +G  GsGK+t++  +++ l++rg +v v+  D
  gi|91773079|ref|YP_565771.1|  6 CGKGGSGKSTLTALIAKSLSERGCNVLVIDND 37
                                  7999**********************999755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00074      0.41       4      34 ..       2      39 ..       1      56 [. 0.90
   2 ?   -1.1   0.0       2.3   1.3e+03      23      36 ..     136     149 ..     124     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00074
                        AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekG 34
                                  k l+ G+ g+GK+tl + +       g ++l+id +++
  gi|91773079|ref|YP_565771.1|  2 KTLLCGKGGSGKSTLTALIakslserGCNVLVIDNDES 39
                                  789************99998999999999999999985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                        AAA_24  23 gpkplfidtekGlk 36 
                                   +++++++dte+G  
  gi|91773079|ref|YP_565771.1| 136 ENDFVLVDTEAGIE 149
                                   68999******986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0014      0.79       3      39 ..       3      41 ..       1      49 [. 0.80
   2 ?    0.6   0.0      0.64   3.6e+02      52      73 ..     109     132 ..      58     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                                  EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSC CS
                          cobW  3 tvltGflGsGKTtLlnhll..enraglklavivNefgev 39
                                  t+l+G  GsGK+tL   +     ++g ++ vi N+ +++
  gi|91773079|ref|YP_565771.1|  3 TLLCGKGGSGKSTLTALIAksLSERGCNVLVIDNDESNF 41
                                  7899********998777766667888999999997765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.64
                                   .EEEETTTTECCH..CTT-HHHHH CS
                          cobW  52 eivelenGciCct..lredllkel 73 
                                   +i e+ +Gc C    l+++l++++
  gi|91773079|ref|YP_565771.1| 109 KIHEFGEGCACPMgaLAKQLIQNI 132
                                   3899999**998733333333333 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 ?   10.4   0.0   0.00084      0.47       2      30 ..       3      34 ..       2      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00084
                                  EEEE--SSSSHHHHHHHGGGGB...S--EEEE CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyv 30
                                   lL G+ G+gKs+l+  +a+ l   +++v+++
  gi|91773079|ref|YP_565771.1|  3 TLLCGKGGSGKSTLTALIAKSLserGCNVLVI 34
                                  59*******************98766666665 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00078      0.44      46      71 ..       9      34 ..       6      35 .. 0.96
   2 ?   -2.2   0.0       3.1   1.7e+03     149     174 ..     104     129 ..      99     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00078
                                  S-HSHHHHHHHHHHHTTTS..-EEEE CS
                          LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                  GG+GK  l++ ++k l++rg++v v+
  gi|91773079|ref|YP_565771.1|  9 GGSGKSTLTALIAKSLSERGCNVLVI 34
                                  9**********************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.1
                                   EEEE..EHHHHC--BTTTSSBSS-GG CS
                          LpxK 149 ivvvdaergfgngrllPaGpLREpls 174
                                   ++ v + ++fg+g+  P G L  +l 
  gi|91773079|ref|YP_565771.1| 104 LIAVGKIHEFGEGCACPMGALAKQLI 129
                                   55555556677777777777755543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1898.26
//
Query:       gi|91773080|ref|YP_565772.1|  [L=204]
Description: hypothetical protein Mbur_1092 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1464.30
//
Query:       gi|91773081|ref|YP_565773.1|  [L=426]
Description: Fe3+-hydroxamate binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-52  176.3   0.1    1.1e-51  175.8   0.1    1.1  1  Peripla_BP_2  Periplasmic binding protein
    0.00017   21.5   0.0    0.00031   20.6   0.0    1.4  1  Acid_PPase    Acid Phosphatase


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 !  175.8   0.1   1.2e-55   1.1e-51       1     234 [.      98     360 ..      98     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 1.2e-55
                                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..............TS.........-BSBESSSB-HHHHHHH-- CS
                  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee............ai.........vevgadgeidvEklaalkP 60 
                                   i++++p++ ++ +alG++dk+v++d++t+     +++e+            +i         +e+++++eid+E++a lkP
  gi|91773081|ref|YP_565773.1|  98 IITTNPDNSRMIIALGDLDKIVATDECTRSGCILPRDENdekiaenawealQIydggqlddfPETNTRKEIDYETMAILKP 178
                                   89***************************988888888887666666665511666666666******************* PP

                                   SEEEE-GGG...GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEE CS
                  Peripla_BP_2  61 Dlvilskglgltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvl 141
                                   D++++ + +  ++ d  ++k+g+p+v+   ++t+ + +e i+  g +l+++++a++l + + sk+++++s ++++++++ +
  gi|91773081|ref|YP_565773.1| 179 DVIFDATWY--NRGDLIEEKVGCPCVVAGAGFTFTESYEHIQLMGNVLDEQKRADELENYVRSKVDMIESVTSQIDDSEKP 257
                                   *********..********************************************************************** PP

                                   EEEETTE..EEEE-TTSTTTHHHHT.S--EES.TTT--.......STT-EEE-HHHHHHH--SEEEEEEH..HHHT-S--H CS
                  Peripla_BP_2 142 vfggadeggyvvagsnsyigdllda.lgieni.aaesk.......kseyeeisaEqilasdpdvifvsgr..aeadnktgl 211
                                   ++++a++g+++ +++  +++d++++ + +e++ +a  +       ++e+++++aEqi+a++p++ifv+++   +     g+
  gi|91773081|ref|YP_565773.1| 258 IVYFAPRGAKKGFYDAVEGRDFTRTeAVYEPLdIAG-GinvakdcTGENINVPAEQIVAWEPEYIFVAWSstSSLGEPNGV 337
                                   ********************************5555.559******************************99999999*** PP

                                   HHHT-SHHHHTSHHHHTT-EEEE CS
                  Peripla_BP_2 212 eflkenpllaelpAvkngrVyal 234
                                   +f++e+ +l+e+pAv+n++Vya+
  gi|91773081|ref|YP_565773.1| 338 DFVMETAELSEIPAVRNNDVYAC 360
                                   *********************97 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.4e-08   0.00031      32     158 ..      78     212 ..      64     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.4e-08
                                   TS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G...........GGESEEEESSS-HHH CS
                    Acid_PPase  32 kksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLklleindakekekkll.dvfddveiykgsktk 111
                                    k +v+D+ + +++ly+  e+i+ +  +++  +++    d+    +e+ +   i  ++e+++k++ ++ + ++iy+g +  
  gi|91773081|ref|YP_565773.1|  78 AK-TVTDAHERKVTLYRPIERIITTNPDNSRMIIALGDLDKIVATDECTRSGCILPRDENDEKIAeNAWEALQIYDGGQLD 157
                                   33.8**********************99999999999************9998886666655555055666********** PP

                                   HHHHHHHHH---GGGE......EEEES-HHHHHH..HHTTT-EEEE-SSS--HHH CS
                    Acid_PPase 112 hfeklkkktgieyedm......lfFDdesrniev..esrlgvtfvlvpdGltree 158
                                    f + + +++i+ye m      + FD  + n+ +  e+++g+ +v+   G t +e
  gi|91773081|ref|YP_565773.1| 158 DFPETNTRKEIDYETMailkpdVIFDATWYNRGDliEEKVGCPCVVAGAGFTFTE 212
                                   ****************65555557*******98732455******9999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2711.60
//
Query:       gi|91773082|ref|YP_565774.1|  [L=373]
Description: ABC Fe3+-siderophore transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-92  309.9  33.9    1.8e-92  309.7  33.9    1.0  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
       0.17   11.4   0.0       0.37   10.3   0.0    1.5  1  DUF334    Domain of unknown function (DUF334)


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 !  309.7  33.9     2e-96   1.8e-92       1     312 []      48     366 ..      45     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 309.7 bits;  conditional E-value: 2e-96
                         FecCD   1 llllllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadP 74 
                                   l+++l ++ +++g+ +is++ev+++ll++        + l ++iv+++rlpr++a++++G++L+v+G+++Q+v++NpLa+P
  gi|91773082|ref|YP_565774.1|  48 LVIFLSAFIVTIGPLEISVAEVYKILLSSLfpgyftnEGLTSQIVWNIRLPRIIAGIMAGFGLGVCGCVMQAVLKNPLASP 128
                                   45666677789****************9999*9**99999999************************************** PP

                         FecCD  75 silGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltslllll 154
                                    +lGissga +g+++a++++     + + l+  afl+++l +l++++la + kga++++liLaGia+++l+s+l+ l+ ++
  gi|91773082|ref|YP_565774.1| 129 FTLGISSGANFGVAVAAVMGvGVIGGPYLLVGNAFLFSMLCALFIIALA-NFKGATSETLILAGIAINYLFSSLSDLFRYF 208
                                   *******************987788999999******************.******************************* PP

                         FecCD 155 lneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltava 235
                                   +++e+l+ ++ w +G+ls  sws++ +ll +++++++ll+l a++l+++a+gde+AkslG++++rvr++++ll++ll+a++
  gi|91773082|ref|YP_565774.1| 209 ATDEQLRIMVSWGMGDLSAFSWSNFSILLGVFVFCTPLLYLKANDLNIMAIGDENAKSLGIDTNRVRMFTMLLASLLIATV 289
                                   ********************************************************************************* PP

                         FecCD 236 valvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                   v+++G+i+F+GL++Ph+ar++vg+dh++l p+s++lGal+l+ ad  + ++l+pt +p+gi+t+l+G+pff+yl+l+
  gi|91773082|ref|YP_565774.1| 290 VCFTGTIAFIGLVAPHMARMVVGSDHKYLFPASGILGALILISADATGLNILRPTMIPTGIMTSLLGVPFFMYLILK 366
                                   **************************************************************************986 PP

>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.1e-05      0.37     139     204 ..      27      95 ..       7     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.1e-05
                        DUF334 139 shehyqkr.qkqlftgigamllvfmlfalimtigrdfmsflhv.dvlqnaiasklkasegfis.vlwyi 204
                                   + e yq+   k+lf  i  ++lv++l a+i+tig   +s   v  +l  ++     + eg+ s ++w i
  gi|91773082|ref|YP_565774.1|  27 AREGYQRYvGKKLFFLISMLVLVIFLSAFIVTIGPLEISVAEVyKILLSSLFPGYFTNEGLTSqIVWNI 95 
                                   568888752699**********************98888777633555666666666666665355655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2299.34
//
Query:       gi|91773083|ref|YP_565775.1|  [L=262]
Description: ABC cobalamin/Fe3+-siderophores transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  109.2   0.0    3.4e-31  108.6   0.0    1.3  1  ABC_tran      ABC transporter
    2.3e-07   30.9   0.2     0.0061   16.4   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.5e-05   24.7   0.0    2.9e-05   23.7   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    2.2e-05   25.0   0.0    2.7e-05   24.8   0.0    1.3  1  AAA_23        AAA domain
    4.6e-05   23.0   2.4     0.0015   18.0   2.4    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00073   19.4   0.5     0.0024   17.6   0.1    1.7  2  AAA_15        AAA ATPase domain
     0.0023   17.9   0.0      0.013   15.4   0.0    2.0  2  Rad17         Rad17 P-loop domain
     0.0032   17.1   0.0      0.006   16.2   0.0    1.4  1  AAA_27        AAA domain
     0.0034   16.3   1.6        1.4    7.6   1.1    2.9  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0039   17.5   0.3      0.061   13.6   0.3    2.1  1  AAA_22        AAA domain
     0.0054   16.2   0.1       0.01   15.3   0.1    1.4  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
     0.0096   16.3   0.0      0.022   15.1   0.0    1.8  1  AAA_16        AAA ATPase domain
     0.0099   15.1   1.4      0.031   13.5   1.4    1.7  1  NB-ARC        NB-ARC domain
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.055   12.8   0.0    1.7  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.03   14.0   0.0      0.073   12.8   0.0    1.6  1  AAA_30        AAA domain
      0.034   14.0   0.0      0.062   13.1   0.0    1.4  1  MukB          MukB N-terminal
      0.035   14.4   0.0      0.076   13.3   0.0    1.5  1  B5            tRNA synthetase B5 domain
      0.054   13.5   0.0       0.11   12.4   0.0    1.5  1  RRF           Ribosome recycling factor
       0.12   12.2   0.1        1.7    8.5   0.0    2.2  2  NTPase_1      NTPase
       0.14   12.3   0.0        1.2    9.3   0.0    2.1  2  AAA_33        AAA domain
       0.14   11.8   0.0       0.21   11.3   0.0    1.3  1  AAA_24        AAA domain
       0.15   12.8   0.1        1.8    9.3   0.0    2.2  2  Phage_ABA_S   Phage ABA sandwich 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 !  108.6   0.0   4.2e-34   3.4e-31       1     137 []      19     166 ..      19     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 4.2e-34
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren. 79 
                                   l+nvs++++ ++ v ivG+nGaGKSt+lk++ + l p++G+i++dg +lk+ ++ ++ k+i+++pq  +++fp++ v e+ 
  gi|91773083|ref|YP_565775.1|  19 LENVSVDIYGSSFVSIVGPNGAGKSTMLKCINKILVPDSGDIHIDGYNLKNMKRIEVAKNIAYVPQSsNRVFPTT-VFETv 98 
                                   78*****************************************************************88889988.99999 PP

                                   ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                 ++ e++ ++l+++g+++l+         +LSgGq+q++ +aral+++   +llDEpt+
  gi|91773083|ref|YP_565775.1|  99 lmgrrphigwfsneKDIEKVWQVLEEMGIEDLALCSF----DELSGGQQQKILIARALAQDTGAILLDEPTS 166
                                   *********9966555555888888888887666666....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   7.5e-06    0.0061       3      41 ..      33      58 ..      31     125 .. 0.71
   2 !   12.8   0.0   9.3e-05     0.076     232     272 ..     133     170 ..     110     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.5e-06
                        AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                   ++GpNg+GKS+ L+++             + +l + +g
  gi|91773083|ref|YP_565775.1| 33 SIVGPNGAGKSTMLKCI-------------NKILVPDSG 58
                                  69***************.............344444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.3e-05
                        AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHP 272
                                    +++elS G+++   l++  l+++   + +l+DEp ++L+ 
  gi|91773083|ref|YP_565775.1| 133 CSFDELSGGQQQK-ILIARALAQDT--GAILLDEPTSNLDI 170
                                   568899*******.88888888887..99**********97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.5e-08   2.9e-05      18      50 ..      25      57 ..      18      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.5e-08
                        AAA_29 18 eidlkg..atlltGpsGsGKSTllDAiqalLvpak 50
                                  +i   g  ++ ++Gp+G+GKST+l  i+ +Lvp++
  gi|91773083|ref|YP_565775.1| 25 DIY--GssFVSIVGPNGAGKSTMLKCINKILVPDS 57
                                  444..434889**********************87 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   3.3e-08   2.7e-05      11      48 ..      20      58 ..      10     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.3e-08
                        AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAiklaLygetp 48
                                  +++++d  ++ ++ I+GpNGaGK+T l +i  +L  +++
  gi|91773083|ref|YP_565775.1| 20 ENVSVDIyGSSFVSIVGPNGAGKSTMLKCINKILVPDSG 58
                                  56667777788999****************988876554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.4   1.9e-06    0.0015      23     189 ..      28     186 ..      19     217 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                    +sf +ivGpNG+GKs +l  i  +L  +s   +  + ++      k+ ++++ a+   ++ +++++  +  + v  ++ +
  gi|91773083|ref|YP_565775.1|  28 GSSFVSIVGPNGAGKSTMLKCINKILVPDSG-DIHIDGYN-----LKNMKRIEVAKNIAYVPQSSNR--VFPTTVFETVLM 100
                                   46899*****************888876555.44333332.....1222333333222222222222..222233333333 PP

                                   ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 104 krkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                    r  +  ++ n+k+++  +v ++le++gi+        +LSgG+++ +    l+A   ++ +   llDe  ++LD  +   
  gi|91773083|ref|YP_565775.1| 101 GRRPHIGWFSNEKDIE--KVWQVLEEMGIEDLalcsfdELSGGQQQKI----LIARALAQDTGAILLDEPTSNLDIWHQLD 175
                                   4444444555666554..455666666665433333448888887644....33444456777788888888888887777 PP

                                   HHHHHHHHCTT CS
                                   xxxxxxxxxxx RF
                         SMC_N 179 vaellkekskn 189
                                   v e +++  k+
  gi|91773083|ref|YP_565775.1| 176 VMENVQRLVKE 186
                                   77666655444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1     3e-06    0.0024      16      73 ..      21      75 ..      18      85 .. 0.69
   2 ?   -0.7   0.0       1.1   8.9e+02     321     356 ..     153     188 ..     110     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                        AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenise 73
                                  +v++d+  + +  ++G+N++GKS+ l+ ++++l  +    +  i i+  +l++++ i+ 
  gi|91773083|ref|YP_565775.1| 21 NVSVDIYGSsFVSIVGPNGAGKSTMLKCINKILVPD----SGDIHIDGYNLKNMKRIEV 75
                                  5555654444999****************9998866....3334455555555544444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                        AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                    +++  +l++EP  +L + +q  ++++ ++l++++k
  gi|91773083|ref|YP_565775.1| 153 AQDTGAILLDEPTSNLDIWHQLDVMENVQRLVKEKK 188
                                   345677999999999999999999999999999887 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   0.0   1.6e-05     0.013      47      84 ..      31      69 ..       3     103 .. 0.80
   2 ?    0.2   0.0      0.76   6.2e+02      23      75 ..     184     236 ..     165     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                         Rad17 47 iLLisGPsGCgkstvvkvLskelgiklre.wlnpvslke 84
                                   + i GP G gkst++k + k+l+++  + ++++ +lk+
  gi|91773083|ref|YP_565775.1| 31 FVSIVGPNGAGKSTMLKCINKILVPDSGDiHIDGYNLKN 69
                                  56799*******************986552566666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.76
                         Rad17  23 vhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75 
                                   v  kk+ ++    + +   +   +iL++      +  t  +vL+ e   k+ e
  gi|91773083|ref|YP_565775.1| 184 VKEKKVAAIMAVHDLNLASRYSDQILMMKDGKVVSAGTPAQVLTTENIAKVYE 236
                                   67788888888888888888888999999999999999999999988888776 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.4e-06     0.006      25      50 ..      28      53 ..      19      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.4e-06
                        AAA_27 25 eadlhliyGpNEAGKstalrAisdll 50
                                   +++  i+GpN AGKst+l+ i+++l
  gi|91773083|ref|YP_565775.1| 28 GSSFVSIVGPNGAGKSTMLKCINKIL 53
                                  577889***************99876 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.011       9.1     248     266 ..      33      51 ..      28      57 .. 0.90
   2 !    7.6   1.1    0.0018       1.4     320     429 ..     135     229 ..     126     244 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                   EEEE-TTSSHHHHHHHHHH CS
                    ABC_ATPase 248 lIvGggfhGKsTLLeAlek 266
                                    IvG++  GKsT+L+ ++k
  gi|91773083|ref|YP_565775.1|  33 SIVGPNGAGKSTMLKCINK 51 
                                   79*************9975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                                   ESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                    ABC_ATPase 320 tedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                    ++ SG   q   i++al  ++ ++L+DE ts   + ++ +                ++ v++l+k+  v  i+ v  ++ 
  gi|91773083|ref|YP_565775.1| 135 FDELSGGQQQKILIARALAQDTGAILLDEPTSNLDIWHQLDV---------------MENVQRLVKEKKVAAIMAVHDLNL 200
                                   567799999999999999999999999999997666663322...............456666777777777777777777 PP

                                   CTTT-SEEEEEETTEEEE-HHHHHHHHHC CS
                    ABC_ATPase 401 yldvAdtvilmeeykpkdvtekakeiaee 429
                                     + +d++++m++ k+  + + a+ + +e
  gi|91773083|ref|YP_565775.1| 201 ASRYSDQILMMKDGKVVSAGTPAQVLTTE 229
                                   77777777777776666666666655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.3   7.5e-05     0.061       5      43 ..      29      76 ..      25     203 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.5e-05
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee.........erpevv 43
                                   +++ ++G+ G+GK+t l+ + + l+ ++   +         +r ev+
  gi|91773083|ref|YP_565775.1| 29 SSFVSIVGPNGAGKSTMLKCINKILVPDSGDIHidgynlknmKRIEVA 76
                                  57899**************99998864433333666666666444444 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.3e-05      0.01      28     126 ..     133     232 ..     119     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                        HSM3_N  28 csln.lstvaklkedakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidslvvaa 107
                                   cs++ ls  ++ k  + r la+    ++ ++++++ld    l++++++ ++++ + v ++ +v+dl  a + + + l++  
  gi|91773083|ref|YP_565775.1| 133 CSFDeLSGGQQQKILIARALAQDTGAILLDEPTSNLDIWHQLDVMENVQRLVKEKKVAAIMAVHDLNLASRYSDQILMMKD 213
                                   55542444444444666777766655666778999********************************************** PP

                        HSM3_N 108 ckvieksyPkglfatseii 126
                                    kv++   P  +++t +i 
  gi|91773083|ref|YP_565775.1| 214 GKVVSAGTPAQVLTTENIA 232
                                   ***********99999886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.7e-05     0.022      24      52 ..      29      57 ..      18     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                        AAA_16 24 pelvllsGesGvGKsslvrellralekdg 52
                                  ++ v ++G+ G GKs++++++ + l  d 
  gi|91773083|ref|YP_565775.1| 29 SSFVSIVGPNGAGKSTMLKCINKILVPDS 57
                                  47899*****************9999883 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.4   3.8e-05     0.031      19     144 ..      28     201 ..      18     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                                   CSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE.......................................... CS
                        NB-ARC  19 qslvvalvGmgGvGKttlakqilnksdevegrFdsvawv.......................................... 57 
                                   +s +v++vG  G GK+t++k i++    v    d+++                                            
  gi|91773083|ref|YP_565775.1|  28 GSSFVSIVGPNGAGKSTMLKCINKI--LVPDSGDIHIDGynlknmkrievakniayvpqssnrvfpttvfetvlmgrrphi 106
                                   6779****************99986..444444444444445577788889999999999999999999999999999988 PP

                                   .EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE......EE-SHHH.H.....HHHH CS
                        NB-ARC  58 .vvsktdkseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlD......DVweeed.wdkigvvlpa 127
                                      s++ ++e++++ +l+e++ ++  l +++e       k  + r+L +    ++lD      D+w++ d +++++  ++ 
  gi|91773083|ref|YP_565775.1| 107 gWFSNEKDIEKVWQ-VLEEMGIEDLALCSFDELSGgqqQKILIARALAQDTGAILLDeptsnlDIWHQLDvMENVQRLVK- 185
                                   88899999999998.88888888777777777666644555677888888888888877777778877766666666655. PP

                                   CHTTSEEEEEESBCCCC CS
                        NB-ARC 128 renrlrvllTTRdeeva 144
                                    e+++  ++   d ++a
  gi|91773083|ref|YP_565775.1| 186 -EKKVAAIMAVHDLNLA 201
                                   .5555555555555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.8e-05     0.055      17      55 ..      24      62 ..      18      93 .. 0.79
   2 ?   -2.7   0.0       3.8   3.1e+03      48      82 ..     219     253 ..     210     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                  Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                  + + G+  + +vGp G+GK+ + k+++++l p s +  +
  gi|91773083|ref|YP_565775.1| 24 VDIYGSSFVSIVGPNGAGKSTMLKCINKILVPDSGDIHI 62
                                  56678888899*******************987765555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                  Mg_chelatase  48 plseeealevakiasvagkkeeekllkrrpfraph 82 
                                   + + +++l +++ia v + +++ +++ + p++ p 
  gi|91773083|ref|YP_565775.1| 219 AGTPAQVLTTENIAKVYEVEAHVHNYGETPYVMPL 253
                                   55677888888888888888888888888888875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     9e-05     0.073      20      42 ..      31      53 ..      22      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                        AAA_30 20 vavltGpAGtGKttalkalreaw 42
                                  ++ ++Gp G+GK+t+lk +++++
  gi|91773083|ref|YP_565775.1| 31 FVSIVGPNGAGKSTMLKCINKIL 53
                                  7889*************998876 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.6e-05     0.062      30      58 ..      33      61 ..      25      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-05
                                  HHHS--SHHHHHHHHHHHHHHS--TTT-- CS
                          MukB 30 tlsGgnGaGksttmaafvtaliPdlsllh 58
                                  ++ G nGaGkst++ ++  +l+Pd   +h
  gi|91773083|ref|YP_565775.1| 33 SIVGPNGAGKSTMLKCINKILVPDSGDIH 61
                                  5779********************98777 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.3e-05     0.076      18      64 ..     115     183 ..     105     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-05
                                   HHHHHHHHHHTT-E.......................EESSTTCEEEE--TT-TT--SHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5  18 eeeiikiLkrlgce......................riekdkdlllVtvPswRsDlereeDliEEvaRl 64 
                                    e++ ++L+++g+e                      +  +d+  +l   P+   D+ ++ D++E v Rl
  gi|91773083|ref|YP_565775.1| 115 IEKVWQVLEEMGIEdlalcsfdelsggqqqkiliarALAQDTGAILLDEPTSNLDIWHQLDVMENVQRL 183
                                   5778899****************************966899999**********************998 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.11       3      62 ..       4      76 ..       2      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                  HHHHHSS-SSSSCGGGTTSEEEETTE.............EEEGGGTEEEEESSTTEEEEEESSCCHHHHHHHH CS
                           RRF  3 kelsklrtgranpslldnikVeyygk.............ktpLnqlAqvsvkeartllitpfdkslvkaieka 62
                                   +++ +  g a++ +l+n++V+ yg+             +t L+ + ++ v+++  + i  ++ +++k ie a
  gi|91773083|ref|YP_565775.1|  4 IKIKDMCFGYASTPILENVSVDIYGSsfvsivgpngagkSTMLKCINKILVPDSGDIHIDGYNLKNMKRIEVA 76
                                  56777778999***************9*********997799**************************99965 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0021       1.7       2      37 ..      32      69 ..      31      87 .. 0.78
   2 ?    1.6   0.0      0.29   2.3e+02     114     154 ..     176     218 ..     148     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                                  EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfytee 37
                                  v i Gp G GK+T++k + + l  +  +++++G   ++
  gi|91773083|ref|YP_565775.1| 32 VSIVGPNGAGKSTMLKCINKILVPDsgDIHIDGYNLKN 69
                                  5689************9999885432266777766555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.29
                                   HHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE CS
                      NTPase_1 114 fkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfe 154
                                   + e v++++k +++  ++ +h  +  ++  ++i   kd+kv++
  gi|91773083|ref|YP_565775.1| 176 VMENVQRLVKeKKVAAIMAVHDLNlASRYSDQILMMKDGKVVS 218
                                   5678999999788889999999888999999999999999987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0014       1.2       3      19 ..      33      49 ..      31     132 .. 0.79
   2 ?    0.9   0.0      0.58   4.8e+02      16      33 ..     149     171 ..     143     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                        AAA_33  3 llvGlpGsGKstlaerl 19
                                   +vG++G+GKst ++ +
  gi|91773083|ref|YP_565775.1| 33 SIVGPNGAGKSTMLKCI 49
                                  589*********98865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.58
                        AAA_33  16 aerllkklgavllssdt.....l 33 
                                   a+ l++ +ga+ll+++t     +
  gi|91773083|ref|YP_565775.1| 149 ARALAQDTGAILLDEPTsnldiW 171
                                   67777777788888887444441 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.21       6      47 ..      33      71 ..      30     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                        AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie 47
                                   i+Gp+g+GK+t++k + +k+l+ d   G  ++d+ ++++++
  gi|91773083|ref|YP_565775.1| 33 SIVGPNGAGKSTMLKCI-NKILVPD--SGDIHIDGYNLKNMK 71
                                  599**************.9999865..344556665555555 PP

>> Phage_ABA_S  Phage ABA sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0022       1.8      26      69 ..     102     146 ..      69     159 .. 0.72
   2 ?    1.1   0.0      0.79   6.4e+02      19      53 ..     206     245 ..     183     255 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0022
                   Phage_ABA_S  26 geflvevfeysedisaAweVveklknegiei.kvkslekkyqvlv 69 
                                    +  +  f+  +di++ w+V+e++  e++++ ++++l+++ q ++
  gi|91773083|ref|YP_565775.1| 102 RRPHIGWFSNEKDIEKVWQVLEEMGIEDLALcSFDELSGGQQQKI 146
                                   444455555599************977776667777777766555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.79
                   Phage_ABA_S  19 ntevldegeflvevfey.....sedisaAweVveklkneg 53 
                                   ++  ++++++ v    +     +e+i++  eV  +++n+g
  gi|91773083|ref|YP_565775.1| 206 DQILMMKDGKVVSAGTPaqvltTENIAKVYEVEAHVHNYG 245
                                   4444444444444445555667899999999999999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 1753.60
//
Query:       gi|91773084|ref|YP_565776.1|  [L=414]
Description: 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-134  448.1   9.1   2.6e-134  447.9   9.1    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 !  447.9   9.1  1.4e-138  2.6e-134       2     367 .]      38     414 .]      37     414 .] 0.99

  Alignments for each domain:
  == domain 1  score: 447.9 bits;  conditional E-value: 1.4e-138
                                   HHHHHHHHHHS-HHHHHHHTT----.HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHHHHHH CS
                   HMG-CoA_red   2 veeRrklleelteeeleelkeesld.eevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsasrga 77 
                                   v+ R  ++e++++ ++e+++++++d e++++++iEn+iG++q+PlGvag + +ng+    e+++P+At+Eg+lvAs++rg+
  gi|91773084|ref|YP_565776.1|  38 VRVRKCAIEKMNGVKFEHIQNYTIDaEAATKRNIENMIGTIQIPLGVAGAIMVNGEyasgEFMLPLATTEGALVASVNRGC 118
                                   788999*******************99999*************************************************** PP

                                   HHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSEEEEEEEEE- CS
                   HMG-CoA_red  78 kainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdievvlagrlvvlrlkvdt 158
                                   ++i++sgG ++++++d mtra+v+ le+v++++e+ +w++++e +++++++a +t+r+g+l +++++++g++v+lr+ +dt
  gi|91773084|ref|YP_565776.1| 119 TVITASGGSNVRIFQDLMTRAPVFKLENVNKVKEFVDWVKREETFTNMKEKAGETTRFGELLSVDPFITGNTVFLRFAYDT 199
                                   ********************************************************************************* PP

                                   TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHHHH-HH CS
                   HMG-CoA_red 159 gDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaealvdln 239
                                   +DAmG+Nmv++at+a++++i+e fg    +s+++N+ctdkk++ain i grgk+v+a++ti++e+vek lk++++ + ++n
  gi|91773084|ref|YP_565776.1| 200 KDAMGMNMVTIATDAVLNFISEDFG-VYPISLSGNMCTDKKPAAINNILGRGKTVAADVTIPKEIVEKKLKTTPKMMEEVN 279
                                   *************************.899**************************************************** PP

                                   HH....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE.----SBSHHHHH-HHHH CS
                   HMG-CoA_red 240 ra.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPsleVGtvGGgtklppqae 318
                                    + n +g+a++G++gfnahaaN+iaA++lA+GqD+a+v+e+s ai+++e  e+gdly+svtlPs++VGtvGGgt++ +q+ 
  gi|91773084|ref|YP_565776.1| 280 YRkNlLGSARAGALGFNAHAANIIAALYLACGQDAAHVVEGSSAITTMEVNENGDLYCSVTLPSIQVGTVGGGTGIATQRD 360
                                   ********************************************************************************* PP

                                   HHHHTT---HH........HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                   HMG-CoA_red 319 llkllgvkgak.....nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                   +l+llgv+ga+     n+k+Laeiiaa++LA+e+s++ A aa++l+k+H +l+r
  gi|91773084|ref|YP_565776.1| 361 CLNLLGVAGAGevpghNSKKLAEIIAAAVLAGEISLIGAQAAGHLAKAHAELGR 414
                                   ***************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2918.53
//
Query:       gi|91773085|ref|YP_565777.1|  [L=189]
Description: hypothetical protein Mbur_1099 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1340.73
//
Query:       gi|91773086|ref|YP_565778.1|  [L=434]
Description: tryptophan synthase subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-40  137.0   0.0    9.6e-40  136.8   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.8   0.0   5.4e-44   9.6e-40       5     294 .]      77     414 ..      73     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 5.4e-44
                                   SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEE CS
                          PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallGlkvt 82 
                                    +p Pl r++rl+k l +p  +++K+E+  p gS+K ++a+   ++  keg   +  +e+++G++g al++ ++ + +++ 
  gi|91773086|ref|YP_565778.1|  77 WRPAPLFRAHRLEKMLDTPakIYYKYEGVSPAGSHKPNTAVAQAYYnMKEG-TERITTETGAGQWGSALSLSCNYFDIECK 156
                                   689**************************************9888878888.8888899999******************* PP

                                   EEEETTS-...HHHHHHHHHTT-EEEEE............CCHHHHHHHH.HH..HHHHH...STTCEE--TTTSHHHHHH CS
                          PALP  83 ivvpadas...pekvallrllGaevvev............ggdydeavaa.aa..elaae...gegaylvsqfdnptvieg 142
                                   +++ +++    p+++ l+ l+Ga+vv +            ++ +d+a ++ +a  e+ ++    ++  ++  +   +v++ 
  gi|91773086|ref|YP_565778.1| 157 VYMVRSSFeqkPYRKSLINLWGATVVPSpspdtefgrhilEKYPDTAGSLgIAigEAVEDavkHDNTKYALGSVLNHVMLH 237
                                   ****99997778****************98877777777655577777774112333333455455555555556799999 PP

                                   HHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT-EEEEEEECTTCGGTTCC...S..S.SS..B. CS
                          PALP 143 ygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke....rrpdvrvigvepegsdalarsl...ragrrvtvpvs 213
                                   ++ ig E  +ql+   + pd v+ ++GgG+++aGi+ ++++    +  d+r+i+vep+ +++l ++    + g+  ++++ 
  gi|91773086|ref|YP_565778.1| 238 QTVIGIEAQKQLDkveEYPDIVIGCCGGGSNLAGISLPYMKdkieGTHDPRIIAVEPSACPTLCDGKfqyDYGDMAKLTPL 318
                                   ********98888888*************************77654445*****************977777777777777 PP

                                   .............SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH..HHHHH CS
                          PALP 214 .............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal..klrea 279
                                                   a gl+ +  s+   +l ++++ e+ +  + e++ea + +ar egi + p s +a+  +  +++++
  gi|91773086|ref|YP_565778.1| 319 lkmyslgydfmppAIHAGGLRYHGCSPIISQLTADKLMEATSYHQIEVFEAGVMFARSEGIPPAPESNHAIKCAidEALKC 399
                                   ********999988888999999************************************************9999****** PP

                                   HCCTTCEEEEEEE-B CS
                          PALP 280 gelkegdrvvviltg 294
                                   ++ +e++++++ l+g
  gi|91773086|ref|YP_565778.1| 400 KQTGEEKTILFCLSG 414
                                   ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 00:00:00.39
# Mc/sec: 3298.56
//
Query:       gi|91773087|ref|YP_565779.1|  [L=204]
Description: endonuclease III / DNA-(apurinic or apyrimidinic site) lyase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-24   84.3   0.0      1e-23   83.8   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    7.3e-11   41.4   0.0    3.2e-10   39.3   0.0    2.1  2  HHH            Helix-hairpin-helix motif
     0.0001   22.5   4.6    0.00016   21.9   4.6    1.3  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
    0.00024   21.7   0.0      0.044   14.4   0.0    2.5  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.035   14.1   0.0       0.29   11.1   0.0    2.0  2  DUF2400        Protein of unknown function (DUF2400)
      0.077   13.1   0.0       0.89    9.7   0.0    2.2  2  HHH_2          Helix-hairpin-helix 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 !   83.8   0.0   3.4e-27     1e-23       1     107 [.      31     165 ..      31     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 3.4e-27
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   +s++lsq+t+de++ + +++lf+ f   tp ++a+ad ++++elir +Gfyr K  +++e++r+l+               
  gi|91773087|ref|YP_565779.1|  31 ISTVLSQRTRDEVTIPTTQKLFSVFD--TPPKMANADADEIQELIRNVGFYRVKSHRLIEISRMLLdeydgivpddinelv 109
                                   79**********************65..***************************************************** PP

                                   ................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                   ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                   ++ + +i+vD+hv+ri +r++++k++ t++++e +l +++e
  gi|91773087|ref|YP_565779.1| 110 klpgvgrktancvltyAFDKDAIAVDTHVHRISNRMGLVKTT-TPEETEIELGKVVE 165
                                   ****************555679*******************6.******99988776 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.94   2.8e+03      23      26 ..      61      64 ..      59      72 .. 0.53
   2 !   39.3   0.0   1.1e-13   3.2e-10       1      30 []      96     125 ..      96     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.94
                                  HHHH CS
                           HHH 23 tAea 26
                                  +A+a
  gi|91773087|ref|YP_565779.1| 61 MANA 64
                                  5554 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 1.1e-13
                                   SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                           HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                   +++g++p+++ eL++lPGVG+ktA+++l y
  gi|91773087|ref|YP_565779.1|  96 EYDGIVPDDINELVKLPGVGRKTANCVLTY 125
                                   59*************************987 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 !   21.9   4.6   5.4e-08   0.00016       1      17 []     184     200 ..     184     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.4e-08
                 EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                   C + +PkC++C ++D+C
  gi|91773087|ref|YP_565779.1| 184 CRPVSPKCDECIMNDIC 200
                                   99*************** PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.013        40      15      40 ..      48      72 ..      43      91 .. 0.86
   2 !   14.4   0.0   1.5e-05     0.044      26      48 ..      97     119 ..      83     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                                  HHHHHTTT--SHHHHHHS-HHHHHTS CS
                         HHH_5 15 AlallsaGiesvedlaaadveeLaki 40
                                    +l s  ++++ + a+ad++e++++
  gi|91773087|ref|YP_565779.1| 48 TQKLFSV-FDTPPKMANADADEIQEL 72
                                  6799999.**************9985 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.5e-05
                                   HHHHHHS-HHHHHTSTTS-HHHH CS
                         HHH_5  26 vedlaaadveeLakipGiGkktA 48 
                                   ++ ++  d++eL k+pG+G ktA
  gi|91773087|ref|YP_565779.1|  97 YDGIVPDDINELVKLPGVGRKTA 119
                                   55666679**************9 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.14   4.1e+02      32      75 ..      43      85 ..      18     100 .. 0.66
   2 ?   11.1   0.0   9.6e-05      0.29     173     194 ..     132     153 ..     127     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                       DUF2400 32 qiikkleellelmdkspydfvleeeeekdlkelekfkyRffnse 75
                                  + i + ++l++++d+ p+    +++e ++l +  +f yR+ +++
  gi|91773087|ref|YP_565779.1| 43 VTIPTTQKLFSVFDTPPKMANADADEIQELIRNVGF-YRVKSHR 85
                                  457889999999999888776666544444443445.8876654 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.6e-05
                       DUF2400 173 iPlDvHvarvarklgllkrkqa 194
                                   i +D+Hv+r+++++gl+k+++ 
  gi|91773087|ref|YP_565779.1| 132 IAVDTHVHRISNRMGLVKTTTP 153
                                   789*************987665 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.18   5.3e+02      16      41 ..      48      74 ..      45      78 .. 0.76
   2 ?    9.7   0.0    0.0003      0.89      33      58 ..     104     129 ..      93     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                         HHH_2 16 AklLakrFksldaLkkasleeLle.vd 41
                                   ++L + F++  ++++a+++e++e ++
  gi|91773087|ref|YP_565779.1| 48 TQKLFSVFDTPPKMANADADEIQElIR 74
                                  577888888888999999999987345 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0003
                         HHH_2  33 sleeLlevddiGeeiAqsivefFene 58 
                                   +++eL++++++G ++A+ + ++  ++
  gi|91773087|ref|YP_565779.1| 104 DINELVKLPGVGRKTANCVLTYAFDK 129
                                   789****************9995444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1436.65
//
Query:       gi|91773088|ref|YP_565780.1|  [L=760]
Description: ski2-like helicase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   91.2   0.1      4e-25   88.6   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
    7.2e-10   39.1   0.0      1e-08   35.4   0.0    2.4  3  ResIII           Type III restriction enzyme, res subunit
    1.2e-09   38.5   0.0    8.3e-08   32.6   0.1    3.0  2  Helicase_C       Helicase conserved C-terminal domain
    2.6e-08   34.3   0.1    9.3e-08   32.6   0.1    2.0  1  HHH_5            Helix-hairpin-helix domain
    0.00016   21.5   0.0    0.00043   20.1   0.0    1.7  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0007   19.6   0.3     0.0031   17.6   0.1    2.3  2  HHH_2            Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.06   13.2   0.0         11    6.1   0.0    3.0  2  HHH              Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   1.6e-28     4e-25       2     170 ..      26     182 ..      25     187 .. 0.87
   2 ?   -1.0   0.0      0.51   1.3e+03      97     130 ..     538     574 ..     514     607 .. 0.51

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.6e-28
                                   HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   + Qaeai+  l +++++l+a++T+sGKTl + +++++++     ++g kal+++P+r+La + ++++k++  + +++v   
  gi|91773088|ref|YP_565780.1|  26 PPQAEAIEMGLlEKKNLLAAIPTASGKTLLAELAMIKAI-----REGGKALYIVPLRALASEKFERFKELAPF-GIKVGIS 100
                                   67******9987999*********************999.....6788**********************995.7777644 PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                   +g+   ++  + l    di+v+t ++ d+ll++g+  +++++++V+DE++ l +++++++++  +++l + + d     qv
  gi|91773088|ref|YP_565780.1| 101 TGD--LDSRADWL-GVNDIIVATSEKTDSLLRNGTSWMDEITTVVVDEIHLLDSKNRGPTLEVTITKLMRLNPD----VQV 174
                                   454..44444455.338**************999988*******************************655555....56* PP

                                   EEEESSBS CS
                                   xxxxxxxx RF
                          DEAD 163 ivlSATlp 170
                                   ++lSAT+ 
  gi|91773088|ref|YP_565780.1| 175 VALSATVG 182
                                   ******86 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                                   TCSEEEEEHHHHHHHH...HCTSSHCTTEEEEEEETH CS
                                   xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                          DEAD  97 gvdivvgtpgrlddll...stgklnlsqvrflVlDEa 130
                                   g di+v+    l+ ++   + ++l l++  + ++ E 
  gi|91773088|ref|YP_565780.1| 538 GDDITVTDMTLLHLVCstpDMRQLYLRNTDYTIVNEY 574
                                   3444444443333333333233334555555555443 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   3.9e-12     1e-08       2     169 ..      22     181 ..      21     183 .. 0.88
   2 ?    0.6   0.0      0.19   4.9e+02      66      96 ..     392     423 ..     389     464 .. 0.78
   3 ?   -3.6   0.0       3.8   9.6e+03     131     147 ..     572     588 ..     539     607 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.9e-12
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                   +el++ Q+eaie  l      ++k++l +++T +GKTl+a +++i+++++ g+  k+l +vp ++l +   e+fk++++  
  gi|91773088|ref|YP_565780.1|  22 KELYPPQAEAIEMGL-----LEKKNLLAAIPTASGKTLLAeLAMIKAIRE-GG--KALYIVPLRALASEKFERFKELAPFG 94 
                                   578999999999988.....45899***************7777777776.56..8***********************99 PP

                                   ...GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHH CS
                        ResIII  82 ykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreile 155
                                      + ++ +gd +++ +     ++i+v+t ++ d+ +      + +   d++  +++DE H l +k+       +++++++
  gi|91773088|ref|YP_565780.1|  95 I--KVGISTGDLDSR-ADWLGVNDIIVATSEKTDSLL-----RNGTSWMDEITTVVVDEIHLLDSKNrgptlevTITKLMR 167
                                   7..688888888888.888899***************.....77888899999************7467777789999999 PP

                                   T---SEEEEEESS- CS
                        ResIII 156 kfkeavllglTATp 169
                                    +++  +++l+AT 
  gi|91773088|ref|YP_565780.1| 168 LNPDVQVVALSATV 181
                                   9999*********6 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                                   HHHHHHHHGGGGTGG.....GEEEESSS-B-- CS
                        ResIII  66 lleqtleefkkflseayke.igkkvsgdkkka 96 
                                   ll +t++ef++++++++++ ++ ++s+ + ++
  gi|91773088|ref|YP_565780.1| 392 LLAKTYDEFAQLMENYVEAdAEDIWSKLGTEN 423
                                   7899************9887666676665555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.8
                                   TT-SEEEEETGGGTTS. CS
                        ResIII 131 drfdviiiDEaHrlgak 147
                                   +++ v   DE H + +k
  gi|91773088|ref|YP_565780.1| 572 NEYIVAHSDEFHEIPDK 588
                                   44456667999988875 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     0.097   2.5e+02      10      52 ..      58     106 ..      52     121 .. 0.76
   2 !   32.6   0.1   3.2e-11   8.3e-08      40     109 ..     303     381 ..     228     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.097
                                   H...HHTTTTSEEEEEESSHH.HHHHHHHHHHHT..TSTEEEESTTSTH CS
                    Helicase_C  10 l...kleeeggkilifvntid.rlekvklllekk..gikvavlhgelpq 52 
                                   l   k  +eggk+l +v+ +    ek++ ++e    gikv + +g+l +
  gi|91773088|ref|YP_565780.1|  58 LamiKAIREGGKALYIVPLRAlASEKFERFKELApfGIKVGISTGDLDS 106
                                   23448889*************5444466664444669999999998865 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 3.2e-11
                                   TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE........ESSSSSS.HHHHHHHHTTSSS CS
                    Helicase_C  40 gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi........nfdlprn.vtsyiqriGRtgR 109
                                      va +h+ l++n+r+ + + f+++ ++v+ +t  ++ G+++p  +++i        nf+++   v +y+q++GR+gR
  gi|91773088|ref|YP_565780.1| 303 RKGVAFHHAGLNSNHRKLVENGFRQNLIKVISSTPTLAAGLNLPARRVIIrsyrrfdsNFGMQPIpVLEYKQMAGRAGR 381
                                   5568899*************************************99999976664444344432246************ PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   3.6e-11   9.3e-08       3      53 ..     676     724 ..     674     727 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.6e-11
                                   HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                         HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                   eL ++ G+G+++A++l++aG+ sv++l+ ad+  L+k+  +G+k A +i+ 
  gi|91773088|ref|YP_565780.1| 676 ELVGIRGVGRVRARKLYNAGFVSVAKLKGADISVLSKL--VGPKVAYNILS 724
                                   6889**********************************..******99985 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 !   20.1   0.0   1.7e-07   0.00043       3      30 ..     677     704 ..     675     713 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.7e-07
               DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra 30 
                                   + ++ GVG+++A+k+y++G+ ++  l+ 
  gi|91773088|ref|YP_565780.1| 677 LVGIRGVGRVRARKLYNAGFVSVAKLKG 704
                                   789*********************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 ?   -3.3   0.0       3.9   9.9e+03      18      35 ..     392     409 ..     390     410 .. 0.81
   2 !   17.6   0.1   1.2e-06    0.0031       6      52 ..     678     723 ..     673     726 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.9
                         HHH_2  18 lLakrFksldaLkkasle 35 
                                   lLak ++++ +L++  +e
  gi|91773088|ref|YP_565780.1| 392 LLAKTYDEFAQLMENYVE 409
                                   799999999999987665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.2e-06
                         HHH_2   6 LGIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52 
                                    GIr VG   A++L ++ F s+ +Lk a++  L+++  +G+++A +i 
  gi|91773088|ref|YP_565780.1| 678 VGIRGVGRVRARKLYNAgFVSVAKLKGADISVLSKL--VGPKVAYNIL 723
                                   6*************9866****************98..9*****9996 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0042        11      12      28 ..     676     692 ..     674     694 .. 0.90
   2 ?    3.7   0.0     0.024        62      19      29 ..     714     724 ..     712     725 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0042
                                   HHHTSTT-SHHHHHHHH CS
                           HHH  12 eLlalPGVGpktAeaIl 28 
                                   eL+ + GVG+ +A++ +
  gi|91773088|ref|YP_565780.1| 676 ELVGIRGVGRVRARKLY 692
                                   8999*********9876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.024
                                   -SHHHHHHHHH CS
                           HHH  19 VGpktAeaIls 29 
                                   VGpk+A  Ils
  gi|91773088|ref|YP_565780.1| 714 VGPKVAYNILS 724
                                   9********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 5356.83
//
Query:       gi|91773089|ref|YP_565781.1|  [L=426]
Description: histidinol dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-169  563.5   6.8   3.2e-169  563.3   6.8    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 !  563.3   6.8  1.8e-173  3.2e-169       7     409 .]      23     424 ..      19     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 563.3 bits;  conditional E-value: 1.8e-173
                                   --HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC----E CS
                 Histidinol_dh   7 dseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqkesee 87 
                                   d+ +v+ tv++il+dv+e+Gde l+eyt kFDk++  ++++vs+eeie+a++++d+el + l+ aaenir+fh+aq+++++
  gi|91773089|ref|YP_565781.1|  23 DMMDVAGTVSSILKDVQEKGDEGLREYTLKFDKAD-IHTIEVSSEEIEQAMKEVDAELLRHLKIAAENIRNFHTAQLPQKT 102
                                   5668999*************************774.689****************************************** PP

                                   EEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHCT-SEEEE CS
                 Histidinol_dh  88 evketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaaklagvdeiyk 167
                                   ++ e +pg++lgq+++p+ +vG YvPgG+a+ypSt+lm+++pAkvAgvk++v++tPp  dgkvnp +l+a k+ag+d+iyk
  gi|91773089|ref|YP_565781.1| 103 WYIEPSPGIKLGQMATPLASVGAYVPGGRASYPSTALMTIIPAKVAGVKNVVMCTPPGsDGKVNPLTLVAGKVAGADHIYK 183
                                   ********************************************************************************* PP

                                   --HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHHHHHTT-TT-E CS
                 Histidinol_dh 168 vGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLlsqaEHdedaq 248
                                   vGG+qAiaa+AyGtes+  vdkivGPGn++V+ AK++v+++ +iD++aGPsEvl+iaD++ad++++A+D+l+qaEHd+++ 
  gi|91773089|ref|YP_565781.1| 184 VGGVQAIAAMAYGTESVLSVDKIVGPGNVFVTVAKMMVRDKAEIDFPAGPSEVLIIADDSADAAMIASDILAQAEHDPKSV 264
                                   ********************************************************************************* PP

                                   EEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEESTTHHHHGGG--S-SE CS
                 Histidinol_dh 249 avlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlelqvedpeellekiknaGa 329
                                   +vlvtts+elae++++ev+kq++ + r+ei+e+sle+ +ai+++++++e+i+++n++ApEHle++ved +++l+ i+naG+
  gi|91773089|ref|YP_565781.1| 265 SVLVTTSSELAEQTNNEVKKQAAIAVRREIIEQSLEN-AAILVTDSMDECIRISNDFAPEHLEIMVEDDDAVLDMIENAGS 344
                                   *************************************.99***************************************** PP

                                   EEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                 Histidinol_dh 330 iflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavetlAeaEgLeaHaeavkvRl 409
                                   if+G+y+p+++gDYa+GtnhvLPT+g+ +++sgl++++Flk +++q+++ke+l+++++++++lAe EgL+aHa++vk Rl
  gi|91773089|ref|YP_565781.1| 345 IFVGNYAPVAAGDYASGTNHVLPTAGYPKIYSGLNIHHFLKYSTIQKITKEGLSSIGDTIIALAEKEGLQAHADSVKSRL 424
                                   *****************************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3125.47
//
Query:       gi|91773090|ref|YP_565782.1|  [L=132]
Description: hypothetical protein Mbur_1104 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-59  199.6   2.0    1.3e-59  199.5   2.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
      0.016   15.2   0.3      0.019   15.0   0.3    1.1  1  Rad33     Rad33


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 !  199.5   2.0   1.5e-63   1.3e-59       1     129 [.       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 1.5e-63
                       DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvwghrk 81 
                                   mkir+vs++eei++l+ neki+Hlafrpsn+d+++lvkkc+++++iq+p+Sy++t+sks++mfl++q+i+l+egdvwghrk
  gi|91773090|ref|YP_565782.1|   1 MKIRIVSKREEIDKLDANEKIIHLAFRPSNEDVFNLVKKCKDVEVIQIPTSYRRTVSKSIEMFLDMQNIKLIEGDVWGHRK 81 
                                   9******************************************************************************** PP

                       DUF1699  82 dineyyevseevierikelkseglseeeiaeklsketklspdlikfll 129
                                   dineyy++s+++  ri++l+seg+s++ ia+kls+e kl+++++ ++l
  gi|91773090|ref|YP_565782.1|  82 DINEYYTISTAIAGRITDLRSEGISDDVIADKLSREGKLNKEMLFYIL 129
                                   **********************************************98 PP

>> Rad33  Rad33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   2.1e-06     0.019      27     109 ..      32     116 ..       6     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-06
                         Rad33  27 qDlaLkqlpqlleeLkiPkcftkdieecidyyYelikskdvkidelnkkqeitlelieaytitssvkeeed..iiDivDid 105
                                   + + L +  + +e ++iP+ + + ++++i+ + ++ + k ++ d  +++++i      + +i+ ++++ ++  i+D v  d
  gi|91773090|ref|YP_565782.1|  32 DVFNLVKKCKDVEVIQIPTSYRRTVSKSIEMFLDMQNIKLIEGDVWGHRKDINEYYTISTAIAGRITDLRSegISDDVIAD 112
                                   445676777778999************************999*******99999988888999999887666799999899 PP

                         Rad33 106 kLik 109
                                   kL +
  gi|91773090|ref|YP_565782.1| 113 KLSR 116
                                   9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 914.64
//
Query:       gi|91773091|ref|YP_565783.1|  [L=250]
Description: uroporphyrinogen-III C-methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for 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-55  185.9   0.6      1e-54  185.7   0.6    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.041   14.3   0.3       0.22   11.9   0.3    2.1  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   0.6   1.2e-58     1e-54       1     212 [.       7     219 ..       7     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 1.2e-58
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                   k+ylVG GpGdpel+T++A+r+l tadv++ d+ +  e +l+ ++e      + gk + +++ ++ ei++a++e++++gk 
  gi|91773091|ref|YP_565783.1|   7 KVYLVGSGPGDPELMTLKARRLLDTADVIIFDQ-LPGEKILASMPEA-AEKIDAGKHAGDHTLTQSEINDAIVEKAKEGKI 85 
                                   79***************************9999.5444444444443.3445555566788889***************** PP

                  TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeeereleal 157
                                   Vv+l++GDP+ +g+g+e++e+l +  agie+e++PG++s+ aa a++gip+t+++ +++v+     ++++++e++ +++ l
  gi|91773091|ref|YP_565783.1|  86 VVRLKGGDPYMFGRGGEEAEELVK--AGIEFEIVPGITSALAATAYAGIPVTHRDHASMVTfitghEDPTKEETALDWKTL 164
                                   ************************..****************************************888899********* PP

                  TP_methylase 158 langdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                   +a g+t+v++++++ l++ + +L+++ +++ tpva+ver++++d+rv+ gt+e++
  gi|91773091|ref|YP_565783.1| 165 AAFGGTIVIFMGVKMLERNMGELMRYGKNPKTPVAMVERGTRPDQRVTIGTVETI 219
                                   **************************777788********************987 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   0.3   2.5e-05      0.22      27     136 ..      65     203 ..      48     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..........................CCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxx RF
                   Radical_SAM  27 rslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..........................vpgirit 81 
                                   ++l++ ei + + e  a+ g+ +v l gg+p +  +  e++e+l+k                            +    +t
  gi|91773091|ref|YP_565783.1|  65 HTLTQSEINDAIVEK-AKEGKIVVRLKGGDPYMFGRGGEEAEELVKAGiefeivpgitsalaatayagipvthrDHASMVT 144
                                   556666777666666.566799************************98999998888888888888888888876677777 PP

                                   EEECSSCHG....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHH CS
                                   xxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpd....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealek 136
                                   ++t +  p+       +++l+  g + ++ +g++ +      +lm+ g++++  ++ +e+
  gi|91773091|ref|YP_565783.1| 145 FITGHEDPTkeetALDWKTLAAFGgTIVIFMGVKMLERN-MGELMRYGKNPKTPVAMVER 203
                                   777777777755544445555555777888888888887.77777777777666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1848.76
//
Query:       gi|91773092|ref|YP_565784.1|  [L=266]
Description: uroporphyrinogen-III synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-40  136.6   0.0    9.9e-40  136.3   0.0    1.0  1  HEM4      Uroporphyrinogen-III synthase HemD
  ------ inclusion threshold ------
       0.04   13.8   0.0        0.2   11.5   0.0    1.9  2  DUF3916   Protein of unknown function (DUF3916)


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.0   1.1e-43   9.9e-40       5     230 ..      24     256 ..      21     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 1.1e-43
                                   HHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHH..HTT---HHHHHCSEEESSHHH CS
                          HEM4   5 ealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealk..reeedvkalaslkvaavGpaT 83 
                                   e+ e+ G+e++++P+ieie   +++  +a+ +++ +g  d++iftSan++++ + +    r++  ++al+++ v+a+Gp+T
  gi|91773092|ref|YP_565784.1|  24 ELAESFGFEVVAIPMIEIEG-MKDEYFDAFAENIFSGISDYVIFTSANGIDHTLSKITpdRHSKFIDALNNTNVVAIGPTT 103
                                   67899***************.555666666677777888*************99988899********************* PP

                                   HHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEE.EE-HHHHHHHHH CS
                          HEM4  84 araLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYet.vpaeeepeelke 163
                                   ++ Le +g+ v  +p   +++egL+e+l ++++gk++   r+  ++  l +gL+  ga+v e +vY+   p  ++++el +
  gi|91773092|ref|YP_565784.1| 104 RKQLEGIGIGVMGMPG-VYSSEGLVEYLCPDVKGKQIDTARSAYGSSLLISGLRDCGANVLETKVYTLtLPKGPLQDELIT 183
                                   ************9**9.**************************************************9788888******* PP

                                   HHHTT--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHH CS
                          HEM4 164 alkagevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvaeeptaegl 230
                                   +  +ge+d+ +ftS+ +vr+++ +++         + l++  vaaiG  Ta++lk++g++v v+++e+t + +
  gi|91773092|ref|YP_565784.1| 184 KSVNGEIDVFAFTSSMMVRSFFDRAEALCegksirEVLENSLVAAIGIPTANTLKEYGVEVNVTPDEYTFKEI 256
                                   **************************877999*************************************8875 PP

>> DUF3916  Protein of unknown function (DUF3916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.1   9.4e+02     108     139 ..      19      52 ..      15      57 .. 0.73
   2 ?   11.5   0.0   2.3e-05       0.2      83     147 ..     192     257 ..     186     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.1
                       DUF3916 108 lskerslaeewgleipr..nlkelgfeeeiyded 139
                                   + k+r+lae +g e+ +   ++ +g + e++d++
  gi|91773092|ref|YP_565784.1|  19 VVKSRELAESFGFEVVAipMIEIEGMKDEYFDAF 52 
                                   6788999999999887522567788888888765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.3e-05
                       DUF3916  83 iiiFkseeyfqsFferks..seqkwillskerslaeewgleiprnlkelgfeeeiydedeieekeiw 147
                                   +  F s    +sFf+r +   e k+i+   e+sl    g+   ++lke+g+e+++  +de++ kei+
  gi|91773092|ref|YP_565784.1| 192 VFAFTSSMMVRSFFDRAEalCEGKSIREVLENSLVAAIGIPTANTLKEYGVEVNVT-PDEYTFKEIL 257
                                   6678999999******9977799*******************************65.6677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        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: 1774.95
//
Query:       gi|91773093|ref|YP_565785.1|  [L=177]
Description: hypothetical protein Mbur_1108 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0024   18.1   2.0     0.0024   18.1   2.0    1.9  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
  ------ inclusion threshold ------
        0.2   11.6   0.1        0.2   11.6   0.1    3.1  3  ODV-E18   Occlusion-derived virus envelope protein ODV-E18
       0.21   12.0   2.7        1.7    9.0   0.4    2.3  2  DUF4281   Domain of unknown function (DUF4281)
          9    6.2   7.0         22    4.9   0.9    2.4  2  Tmemb_9   TMEM9


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 ?   -0.7   0.2      0.34   1.5e+03      75      87 ..      13      25 ..       4      52 .. 0.61
   2 !   18.1   2.0   5.5e-07    0.0024      14      84 ..      55     123 ..      47     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.34
                         PMT_2 75 daplvllwalaly 87
                                   ++l+ll++++ +
  gi|91773093|ref|YP_565785.1| 13 TVVLLLLYMALHL 25
                                  3333333333333 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.5e-07
                         PMT_2  14 tklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwal 84 
                                    ++ g+   +i+ +s+++++l  + l +l++++f+k++ l  all+a+++  ++ ++l++++++l l++ l
  gi|91773093|ref|YP_565785.1|  55 IDINGQESGSIISPSIVMTILLFFNLIFLVKNRFDKHIVLNIALLIATLL--IYHLFLNNINSTLELATKL 123
                                   578899999*******************************9999999966..4555556777777666555 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.4e-05       0.2      27      68 ..      11      52 ..       5      60 .. 0.80
   2 ?   -1.3   5.9      0.47   2.1e+03      22      40 ..      66      84 ..      55     118 .. 0.89
   3 ?   -2.2   0.3      0.89     4e+03      35      49 ..     154     168 ..     151     175 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.4e-05
                       ODV-E18 27 lltilvvlviiillvllvqssstGsdssssnannartGfvnP 68
                                  l+t++ +l+ ++l +++v+   + ++ss+ + + a++Gf+ P
  gi|91773093|ref|YP_565785.1| 11 LITVVLLLLYMALHLFIVDFEISNAQSSGGGLSYAKIGFFGP 52
                                  5666666777777777777666679***************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.47
                       ODV-E18 22 lePsllltilvvlviiill 40
                                  + Ps+++til    +i l+
  gi|91773093|ref|YP_565785.1| 66 ISPSIVMTILLFFNLIFLV 84
                                  689*******999888876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.89
                       ODV-E18  35 viiillvllvqssst 49 
                                   vi i++ +++++s  
  gi|91773093|ref|YP_565785.1| 154 VIPIIISIVYNASKL 168
                                   455556666666654 PP

>> DUF4281  Domain of unknown function (DUF4281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.028   1.2e+02      27      53 ..       4      32 ..       2      50 .. 0.67
   2 ?    9.0   0.4   0.00038       1.7       8      47 ..      71     112 ..      65     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.028
                       DUF4281 27 rrvmesllpflvlallYlvl..lvaakls 53
                                  r+++   l+++vl llY++l  ++++++ 
  gi|91773093|ref|YP_565785.1|  4 RKIIYFNLITVVLLLLYMALhlFIVDFEI 32
                                  56666678899999999998764333333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00038
                       DUF4281   8 llvlpfwllmilaPrakvtrrvmesllpflvlallYlvl..l 47 
                                   ++++++++ +i++ ++++ ++++ ++++++++ l+Y ++   
  gi|91773093|ref|YP_565785.1|  71 VMTILLFFNLIFLVKNRFDKHIVLNIALLIATLLIYHLFlnN 112
                                   678889999***************************988331 PP

>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2    0.0052        23      52      78 ..       5      32 ..       1      43 [. 0.74
   2 ?    4.9   0.9     0.005        22      51      78 ..      90     117 ..      84     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0052
                       Tmemb_9 52 vvviivivvislLviYm.lflllldpll 78
                                   ++++ ++ + lL++Ym l l ++d  +
  gi|91773093|ref|YP_565785.1|  5 KIIYFNLITVVLLLLYMaLHLFIVDFEI 32
                                  5788888888899999944688887655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.005
                       Tmemb_9  51 kvvviivivvislLviYmlflllldpll 78 
                                   k +v+ +  +i++L+iY lfl  +++ l
  gi|91773093|ref|YP_565785.1|  90 KHIVLNIALLIATLLIYHLFLNNINSTL 117
                                   678999999************8777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1318.72
//
Query:       gi|91773094|ref|YP_565786.1|  [L=237]
Description: hypothetical protein Mbur_1109 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1621.98
//
Query:       gi|91773095|ref|YP_565787.1|  [L=91]
Description: hypothetical protein Mbur_1110 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 719.35
//
Query:       gi|91773096|ref|YP_565788.1|  [L=415]
Description: YVTN beta-propeller repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-14   51.9   7.0    0.00017   21.0   0.2    3.6  3  Lactonase     Lactonase, 7-bladed beta-propeller
    2.7e-09   36.0   9.1    2.6e-05   23.0   0.8    3.5  4  Cytochrom_D1  Cytochrome D1 heme domain
      5e-07   29.5  13.6      0.014   15.0   1.5    3.3  3  SGL           SMP-30/Gluconolactonase/LRE-like region
    3.1e-06   26.9  12.9       0.36   10.9   0.3    6.1  7  NHL           NHL repeat
    2.3e-05   24.2   0.0          2    8.4   0.0    4.6  5  PD40          WD40-like Beta Propeller Repeat
  ------ inclusion threshold ------
      0.017   14.2   1.8          9    5.3   0.1    3.6  4  DUF1513       Protein of unknown function (DUF1513)
      0.022   14.8   0.1        1.9    8.6   0.0    4.0  6  P_proprotein  Proprotein convertase P-domain
       0.18   11.8   5.8        3.1    7.8   0.2    2.7  2  DUF4245       Protein of unknown function (DUF4245)


Domain annotation for each model (and alignments):
>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3     1e-05     0.023     235     320 ..      57     139 ..      36     151 .. 0.79
   2 !   21.0   0.2   7.4e-08   0.00017     248     318 ..     156     221 ..     139     229 .. 0.87
   3 !   18.9   0.2   3.2e-07   0.00072      32     123 ..     231     315 ..     225     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                                   SS-TSS-S---EEEEEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEE CS
                     Lactonase 235 tlpegftgknsaaeIrlspdgkflyvSnRgadsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnv 315
                                   ++  +++ ++ ++e++++pdg+ +yv +   d  +v  +d    t t + +v+++g      a++p+g+ ++v+ ++s n+
  gi|91773096|ref|YP_565788.1|  57 SIVTTMKIEAYSGEVAVTPDGRRIYVTDSAIDRTTVPIIDTV--TNTVHSTVNVGGS-SWGAAINPAGTRVYVSIRDSTNI 134
                                   333456667899***************************666..5666777888776.6788******************9 PP

                                   EEEEE CS
                     Lactonase 316 tvfer 320
                                    v++ 
  gi|91773096|ref|YP_565788.1| 135 LVINT 139
                                   99754 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 7.4e-08
                                   EEEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEE CS
                     Lactonase 248 eIrlspdgkflyvSnRgadsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnvtvf 318
                                    I+++pdg  lyv +  +d i+v +      t + + +v++ g+ P d a++p+g+ ++v n + +nv+v+
  gi|91773096|ref|YP_565788.1| 156 RIAITPDGTKLYVTSHKNDIISVIDT----VTNSVISTVNV-GEIPWDVAVTPDGTKVYVTNSRGNNVSVI 221
                                   699********************987....24467888888.888***********************997 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 3.2e-07
                                   EEEESS---SEEE-TTSSEEEEEET.STTTEEEEEEEETTTTEEEEEEEEE.SSS-EEEEEE-TTSSEEEEEETTTTEEEE CS
                     Lactonase  32 lvaelenPsyLalspdgktlYavnetgeeggvsafaidkdsgeltllnkvssegaspchlsvdedgkllavAnYsggsvsv 112
                                   +v  +e P  + ++pdg+ +Y+ n +  + +vs  +  ++    +++++ +  g +p  +s  +dg  ++vAnY g+svsv
  gi|91773096|ref|YP_565788.1| 231 TVNVGEYPWGVIVNPDGTKVYVTNWK--DDSVSVIDTFTN----NVIATIP-VGMHPSGVSATPDGTKVYVANYDGNSVSV 304
                                   46667777778889999999998774..666666555544....4677777.89999999999999999999999999999 PP

                                   EEB.TTSEBES CS
                     Lactonase 113 fpldadgslke 123
                                   ++ + d+ + +
  gi|91773096|ref|YP_565788.1| 305 IDTATDNVIAT 315
                                   99988877665 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.3   8.8e-06      0.02      49     217 ..      38     198 ..      28     202 .. 0.80
   2 !   10.1   0.3   9.5e-05      0.21       9     113 ..     126     230 ..     117     238 .. 0.75
   3 !   17.9   0.6     4e-07   0.00089       9     116 ..     168     275 ..     162     277 .. 0.91
   4 !   23.0   0.8   1.1e-08   2.6e-05       9     116 ..     210     317 ..     208     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-06
                                   EEEEEETTSEEEEEESSSSSEEEEEE-SSEEEEEEE--TTS..EEEEEEEETTEEEEEETTT--EEEEEE--EE-SSSS-- CS
                  Cytochrom_D1  49 yvyvigRDgkvtliDLwakeivaevkiGlnarsvavSqddr..yvivgnYlPgqlvildaetLelvkvisargltvderes 127
                                   ++yv++  g+v++iD  +  iv ++ki   + +vav  d+r  yv  ++    ++ i+d+ t     v s++++ +    s
  gi|91773096|ref|YP_565788.1|  38 FAYVMSSGGNVSVIDTATDSIVTTMKIEAYSGEVAVTPDGRriYVTDSAIDRTTVPIIDTVTNT---VHSTVNVGG---SS 112
                                   89************************99999999999999944555566667777777766643...334444444...66 PP

                                   -EEEEEE-SSSSEEEEEETTTTEEEEEE-SSSSSEEEEEEE--SSEEEEEE-TTSSEEEEEEGGGTEEEEEETTTTEEEEE CS
                  Cytochrom_D1 128 RVaaivasperpefvvnlkdtgeillvdysdlknlktrtieaakflhDggldpdkRYflaaanaedkvavvdtkegklvil 208
                                     aai  + +r    v+++d+ +il+++    +n  t +++++  ++  +++pd+  + ++   +d ++v+dt ++     
  gi|91773096|ref|YP_565788.1| 113 WGAAINPAGTRV--YVSIRDSTNILVINT--ATNSITSKVDVGWGPDRIAITPDGTKLYVTSHKNDIISVIDTVTNSVIST 189
                                   778888887777..6799******99984..578999999****9********9988888899999999999999998888 PP

                                   EE-SSSBEE CS
                  Cytochrom_D1 209 ldvgktphk 217
                                   ++vg++p +
  gi|91773096|ref|YP_565788.1| 190 VNVGEIPWD 198
                                   888887765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.5e-05
                                   EEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEET.TSEEEEEESSSSSEEEEEE-SSEEEEEEE--TT CS
                  Cytochrom_D1   9 vverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigR.DgkvtliDLwakeivaevkiGlnarsvavSqdd 88 
                                   v  rd  ++ +++  +++i+++++ g+        ++dg  +yv +     +++iD  ++ ++ +v++G     vav  d+
  gi|91773096|ref|YP_565788.1| 126 VSIRDSTNILVINTATNSITSKVDVGWGPDR-IAITPDGTKLYVTSHkNDIISVIDTVTNSVISTVNVGEIPWDVAVTPDG 205
                                   5567888888888888888888888877632.3456788888888751556788899888899999999888889988888 PP

                                   SEEEEEEEETTEEEEEETTT--EEE CS
                  Cytochrom_D1  89 ryvivgnYlPgqlvildaetLelvk 113
                                     v v n    +++++d+ t +  +
  gi|91773096|ref|YP_565788.1| 206 TKVYVTNSRGNNVSVIDTFTNNVTA 230
                                   8888888888888888877655544 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 4e-07
                                   EEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEE.ETTSEEEEEESSSSSEEEEEE-SSEEEEEEE--TT CS
                  Cytochrom_D1   9 vverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvi.gRDgkvtliDLwakeivaevkiGlnarsvavSqdd 88 
                                   v+   +  + ++d  +++ +++++  +++   +  ++dg  vyv  +R  +v++iD +++++ a+v++G    +v v  d+
  gi|91773096|ref|YP_565788.1| 168 VTSHKNDIISVIDTVTNSVISTVNV-GEIPWDVAVTPDGTKVYVTnSRGNNVSVIDTFTNNVTATVNVGEYPWGVIVNPDG 247
                                   6777888899999999999999985.5788889999*******9758999******************************* PP

                                   SEEEEEEEETTEEEEEETTT--EEEEEE CS
                  Cytochrom_D1  89 ryvivgnYlPgqlvildaetLelvkvis 116
                                     v v n+    ++++d+ t + +++i+
  gi|91773096|ref|YP_565788.1| 248 TKVYVTNWKDDSVSVIDTFTNNVIATIP 275
                                   ******************9999999987 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 1.1e-08
                                   EEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEE.TTSEEEEEESSSSSEEEEEE-SSEEEEEEE--TT CS
                  Cytochrom_D1   9 vverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvig.RDgkvtliDLwakeivaevkiGlnarsvavSqdd 88 
                                   v+ +   +v ++d  +++ +a+++ g +   +++  +dg  vyv   +D  v++iD ++++++a++ +G+   +v    d+
  gi|91773096|ref|YP_565788.1| 210 VTNSRGNNVSVIDTFTNNVTATVNVG-EYPWGVIVNPDGTKVYVTNwKDDSVSVIDTFTNNVIATIPVGMHPSGVSATPDG 289
                                   66677778999999999999998754.566789999********9768********************************* PP

                                   SEEEEEEEETTEEEEEETTT--EEEEEE CS
                  Cytochrom_D1  89 ryvivgnYlPgqlvildaetLelvkvis 116
                                     v v+nY    ++++d+ t + ++++ 
  gi|91773096|ref|YP_565788.1| 290 TKVYVANYDGNSVSVIDTATDNVIATVD 317
                                   ******************9998888775 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.5   6.4e-06     0.014     115     245 ..      46     171 ..      31     172 .. 0.79
   2 !   14.9   1.7   6.4e-06     0.014     137     223 ..     197     277 ..     175     284 .. 0.79
   3 !   12.5   0.8   3.7e-05     0.082     138     234 ..     240     329 ..     236     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-06
                           SGL 115 galyrldpd.gklervlddltipNGlawspdgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDa. 193
                                   g++ ++d+   +++ +++  + +  +a++pdg+ +Y++Ds+ ++ ++  +d+ ++++++    +++        G+a+   
  gi|91773096|ref|YP_565788.1|  46 GNVSVIDTAtDSIVTTMKIEAYSGEVAVTPDGRRIYVTDSAIDRTTVPIIDTVTNTVHS---TVNVGGS---SWGAAINPa 120
                                   6777777775566666666666666899**********************999884443...3333444...569****95 PP

                           SGL 194 eGnvwvAvwgggkvvrfdpd.GklieeiklpakrvtscaFgGpdlrtLyitsa 245
                                     +v+v + ++  + +++++  +++ ++++    +  +a   pd ++Ly+ts+
  gi|91773096|ref|YP_565788.1| 121 GTRVYVSIRDSTNILVINTAtNSITSKVDVG-WGPDRIAI-TPDGTKLYVTSH 171
                                   668*****************99999999999.78888887.6999******97 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.4e-06
                           SGL 137 NGlawspdgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeG.nvwvAvwgggkvvrfdpd.Gk 215
                                     +a++pdg+++Y+++s+ + ++++d  +  +   n +  a+++ ge +p G++v  +G +v+v+ w+++ v+++d+   +
  gi|91773096|ref|YP_565788.1| 197 WDVAVTPDGTKVYVTNSRGNNVSVIDTFT--N---NVT--ATVNVGE-YPWGVIVNPDGtKVYVTNWKDDSVSVIDTFtNN 269
                                   55789********************9953..3...334..4444454.589******7757***************99899 PP

                           SGL 216 lieeiklp 223
                                   +i++i + 
  gi|91773096|ref|YP_565788.1| 270 VIATIPVG 277
                                   99988765 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 3.7e-05
                           SGL 138 GlawspdgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeG.nvwvAvwgggkvvrfdpd.Gkl 216
                                   G+ ++pdg+++Y+++   ++++++d  +++  +    v ++       p G+  + +G +v+vA ++g+ v+++d++  ++
  gi|91773096|ref|YP_565788.1| 240 GVIVNPDGTKVYVTNWKDDSVSVIDTFTNNV-IATIPVGMH-------PSGVSATPDGtKVYVANYDGNSVSVIDTAtDNV 312
                                   8889********************9964444.444444444.......5555555544279****************9*** PP

                           SGL 217 ieeiklpakrvtscaFgG 234
                                   i+++++  +++  +a+g+
  gi|91773096|ref|YP_565788.1| 313 IATVDVG-DHPVEIALGH 329
                                   ******9.9999999985 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.5   7.9e+03       9      20 ..      42      53 ..      40      55 .. 0.75
   2 !    6.8   0.0    0.0033       7.5       7      20 ..      71      85 ..      70      86 .. 0.93
   3 ?   -2.4   0.0       2.7   6.1e+03       5      17 ..     113     126 ..     113     127 .. 0.62
   4 ?   -2.0   0.0       2.1   4.7e+03       3      13 ..     153     163 ..     152     169 .. 0.68
   5 !   10.9   0.3   0.00016      0.36       4      26 ..     196     219 ..     195     221 .. 0.83
   6 !    5.7   0.1    0.0076        17       3      20 ..     237     255 ..     236     263 .. 0.82
   7 !    7.7   0.1    0.0017       3.7       3      27 ..     279     304 ..     278     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                                  EETTTEEEEEEC CS
                           NHL  9 vdsnGdiyVaDs 20
                                  ++s+G++ V D+
  gi|91773096|ref|YP_565788.1| 42 MSSGGNVSVIDT 53
                                  349999988886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0033
                                  EEEE.TTTEEEEEEC CS
                           NHL  7 vavd.snGdiyVaDs 20
                                  vav+ ++ +iyV+Ds
  gi|91773096|ref|YP_565788.1| 71 VAVTpDGRRIYVTDS 85
                                  89**9*********7 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.7
                                   EEEEEE.TTTEEEE CS
                           NHL   5 hGvavd.snGdiyV 17 
                                   +G a++  + ++yV
  gi|91773096|ref|YP_565788.1| 113 WGAAINpAGTRVYV 126
                                   78899944445555 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.1
                                   SEEEEEEETTT CS
                           NHL   3 yPhGvavdsnG 13 
                                    P  +a++++G
  gi|91773096|ref|YP_565788.1| 153 GPDRIAITPDG 163
                                   68889999665 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00016
                                   EEEEEEE.TTTEEEEEECCCTEEE CS
                           NHL   4 PhGvavd.snGdiyVaDsenhrvq 26 
                                   P++vav+ ++  +yV++s+ + v 
  gi|91773096|ref|YP_565788.1| 196 PWDVAVTpDGTKVYVTNSRGNNVS 219
                                   9******88889*****7666665 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.0076
                                   SEEEEEEE.TTTEEEEEEC CS
                           NHL   3 yPhGvavd.snGdiyVaDs 20 
                                   yP+Gv v+ ++  +yV++ 
  gi|91773096|ref|YP_565788.1| 237 YPWGVIVNpDGTKVYVTNW 255
                                   8*******77778999875 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0017
                                   SEEEEEEE.TTTEEEEEECCCTEEEE CS
                           NHL   3 yPhGvavd.snGdiyVaDsenhrvqv 27 
                                   +P+Gv+++ ++  +yVa++  ++v v
  gi|91773096|ref|YP_565788.1| 279 HPSGVSATpDGTKVYVANYDGNSVSV 304
                                   7*******88889******9999987 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00091         2       9      25 ..      66      82 ..      62      85 .. 0.85
   2 !    6.8   0.0     0.003       6.8      14      27 ..     157     170 ..     155     174 .. 0.88
   3 ?    2.2   0.0     0.085   1.9e+02      15      30 ..     200     215 ..     198     219 .. 0.81
   4 ?   -2.5   0.0       2.4   5.4e+03      18      24 ..     245     251 ..     245     253 .. 0.85
   5 ?   -0.6   0.0       0.6   1.3e+03      16      24 ..     285     293 ..     282     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00091
                                  S.EEEEEE-TTSSEEEE CS
                          PD40  9 gnegaPsfSPDGkrlaF 25
                                  ++ g+ +++PDG+r++ 
  gi|91773096|ref|YP_565788.1| 66 AYSGEVAVTPDGRRIYV 82
                                  6788999********95 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.003
                                   EEE-TTSSEEEEEE CS
                          PD40  14 PsfSPDGkrlaFsS 27 
                                   ++++PDG++l+ +S
  gi|91773096|ref|YP_565788.1| 157 IAITPDGTKLYVTS 170
                                   6899*******998 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.085
                                   EE-TTSSEEEEEEECT CS
                          PD40  15 sfSPDGkrlaFsSdRg 30 
                                   +++PDG++ + + +Rg
  gi|91773096|ref|YP_565788.1| 200 AVTPDGTKVYVTNSRG 215
                                   689*****99876665 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.4
                                   TTSSEEE CS
                          PD40  18 PDGkrla 24 
                                   PDG++ +
  gi|91773096|ref|YP_565788.1| 245 PDGTKVY 251
                                   9**9988 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.6
                                   E-TTSSEEE CS
                          PD40  16 fSPDGkrla 24 
                                    +PDG++ +
  gi|91773096|ref|YP_565788.1| 285 ATPDGTKVY 293
                                   58***9987 PP

>> DUF1513  Protein of unknown function (DUF1513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.013        30      39      73 ..      57      88 ..      41     103 .. 0.70
   2 ?    1.3   0.0     0.067   1.5e+02     222     260 ..     157     195 ..     152     218 .. 0.68
   3 ?    5.3   0.1     0.004         9     221     268 ..     198     246 ..     196     273 .. 0.82
   4 ?    0.3   0.0      0.13   2.9e+02     222     259 ..     283     320 ..     276     360 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.013
                       DUF1513 39 eelqtlaaeedrhFyGHgvfsadGrlLyttEndle 73
                                  + ++t++    + + G +++++dGr +y+t++ ++
  gi|91773096|ref|YP_565788.1| 57 SIVTTMK---IEAYSGEVAVTPDGRRIYVTDSAID 88
                                  4444333...3468888888999999998887664 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.067
                       DUF1513 222 vavdsegrlvavtsPrgnlvavwdlasgelleeaalada 260
                                   +a++ +g+ + vts + +++ v+d+ ++++++++++ ++
  gi|91773096|ref|YP_565788.1| 157 IAITPDGTKLYVTSHKNDIISVIDTVTNSVISTVNVGEI 195
                                   788888888888999999999988888888888887765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.004
                       DUF1513 221 svavdsegrlvavtsPrgnlvavwdlasgelleeaalada.agvaaaks 268
                                   +vav+ +g+ v vt  rgn v v+d+ ++++++++++ +   gv + ++
  gi|91773096|ref|YP_565788.1| 198 DVAVTPDGTKVYVTNSRGNNVSVIDTFTNNVTATVNVGEYpWGVIVNPD 246
                                   69*****************************999988765245555555 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.13
                       DUF1513 222 vavdsegrlvavtsPrgnlvavwdlasgelleeaalad 259
                                   v ++ +g+ v v+   gn v v+d+a++++++++ + d
  gi|91773096|ref|YP_565788.1| 283 VSATPDGTKVYVANYDGNSVSVIDTATDNVIATVDVGD 320
                                   66778888888999999999999999999998887766 PP

>> P_proprotein  Proprotein convertase P-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.9   4.2e+03      23      38 ..      73      88 ..      70     115 .. 0.62
   2 ?   -2.8   0.0       2.9   6.6e+03      23      33 ..     117     127 ..      95     133 .. 0.68
   3 ?   -0.7   0.0      0.67   1.5e+03      23      53 ..     159     189 ..     158     197 .. 0.70
   4 ?    8.6   0.0   0.00085       1.9      23      63 ..     201     241 ..     198     256 .. 0.90
   5 ?   -0.6   0.0      0.59   1.3e+03      22      38 ..     242     258 ..     241     277 .. 0.75
   6 ?   -1.5   0.0       1.2   2.6e+03      24      38 ..     286     300 ..     285     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                                  E-TTS-EEEEE---TT CS
                  P_proprotein 23 vsPsGtrsvLlnrrgk 38
                                  v+P+G r+++ ++  +
  gi|91773096|ref|YP_565788.1| 73 VTPDGRRIYVTDSAID 88
                                  5789999888887666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.9
                                   E-TTS-EEEEE CS
                  P_proprotein  23 vsPsGtrsvLl 33 
                                   + P+Gtr+++ 
  gi|91773096|ref|YP_565788.1| 117 INPAGTRVYVS 127
                                   56888888765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.67
                                   E-TTS-EEEEE---TT---SS-EEEEEEEES CS
                  P_proprotein  23 vsPsGtrsvLlnrrgkdksrsgfldwtfmst 53 
                                   ++P+Gt++++ +++++  s  + ++    st
  gi|91773096|ref|YP_565788.1| 159 ITPDGTKLYVTSHKNDIISVIDTVTNSVIST 189
                                   57*******9999988666555555555555 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00085
                                   E-TTS-EEEEE---TT---SS-EEEEEEEESTTTTS---EE CS
                  P_proprotein  23 vsPsGtrsvLlnrrgkdksrsgfldwtfmsthlwgeraeGe 63 
                                   v+P+Gt++++ n+rg++ s  + ++ + + t  +ge ++G 
  gi|91773096|ref|YP_565788.1| 201 VTPDGTKVYVTNSRGNNVSVIDTFTNNVTATVNVGEYPWGV 241
                                   68**************9999999999999999999999985 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.59
                                   EE-TTS-EEEEE---TT CS
                  P_proprotein  22 LvsPsGtrsvLlnrrgk 38 
                                   +v P+Gt++++ n + +
  gi|91773096|ref|YP_565788.1| 242 IVNPDGTKVYVTNWKDD 258
                                   688******99986655 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 1.2
                                   -TTS-EEEEE---TT CS
                  P_proprotein  24 sPsGtrsvLlnrrgk 38 
                                   +P+Gt++++ n  g+
  gi|91773096|ref|YP_565788.1| 286 TPDGTKVYVANYDGN 300
                                   699***999998776 PP

>> DUF4245  Protein of unknown function (DUF4245)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0014       3.1      87     157 ..      73     143 ..      53     148 .. 0.82
   2 ?    6.2   0.5    0.0042       9.5      87     150 ..     201     262 ..     182     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                       DUF4245  87 vtpegqyisltqs..dadeddlvasvlggaeetgtvevgGrtWqvyaedkwetalvreegdvtvvvtGtasee 157
                                   vtp+g+ i +t s  d ++ ++++ v++  +   tv+vgG++W    ++++++  v+  + + ++v  ta+  
  gi|91773096|ref|YP_565788.1|  73 VTPDGRRIYVTDSaiDRTTVPIIDTVTN--TVHSTVNVGGSSWGAAINPAGTRVYVSIRDSTNILVINTATNS 143
                                   8999999999999444444455555555..78889***********9*******************9999865 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0042
                       DUF4245  87 vtpegqyisltqsdadeddlvasvlggaeetgtvevgGrtWqvyaedkwetalvreegdvtvvv 150
                                   vtp+g+ + +t s+ ++  +++  +++   t tv+vg   W v +++++++  v + +d +v v
  gi|91773096|ref|YP_565788.1| 201 VTPDGTKVYVTNSRGNNVSVIDTFTNN--VTATVNVGEYPWGVIVNPDGTKVYVTNWKDDSVSV 262
                                   8***********************995..67788**********88888888887655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 2912.69
//
Query:       gi|91773097|ref|YP_565789.1|  [L=401]
Description: hypothetical protein Mbur_1112 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   37.3   3.1      1e-08   35.8   1.0    2.7  2  Peptidase_C39_2  Peptidase_C39 like family
    0.00094   19.2   0.0     0.0021   18.1   0.0    1.6  1  Peptidase_C70    Papain-like cysteine protease AvrRpt2
  ------ inclusion threshold ------
       0.16   10.5   0.1       0.23   10.0   0.1    1.1  1  MutL             MutL protein


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.31   1.9e+03      63      99 ..     199     233 ..     172     260 .. 0.58
   2 !   35.8   1.0   1.7e-12     1e-08       1     143 [.     264     379 ..     264     380 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.31
               Peptidase_C39_2  63 lgvynepivklaekyglkvsdtrgssieevkkeidag 99 
                                   +++y +++++ +e+ ++  +++++  +++ ++ei  +
  gi|91773097|ref|YP_565789.1| 199 WSLYETMLENDMEENLA--AWQKSDEFTKSIEEIITN 233
                                   45556666666666665..333344444444444443 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 1.7e-12
               Peptidase_C39_2   1 ldvplynQldelpngCeptslamvlsyl...gkkvtqnelakelktnssgdpntgfvgnitdksglgvynepivklaekyg 78 
                                   l+vp y Q  e+ ++C pts++m+ +y+    +++tq+++ + l+  +                 +g++ + i++++e++ 
  gi|91773097|ref|YP_565789.1| 264 LSVPAYTQ--ETDYYCVPTSIQMLCEYFndpSTTPTQTYIFNYLGGLE----------------DFGLSYSDIEEWVEDVW 326
                                   68******..******************64334788888888888886................35677777777777776 PP

               Peptidase_C39_2  79 lkvsdtrgssi..eevkkeidagkPvvvsvttfkplndgeikftssgHlvvitGYdekg.krvyvnDP 143
                                    k   +r+s +   +v++eid+++P+  ++               sgH+ v++GY ++g  + y+nDP
  gi|91773097|ref|YP_565789.1| 327 DKTPTVRTSGLynIDVVTEIDNNRPFFSMI---------------SGHCRVCRGYLNSGyFYEYINDP 379
                                   65555555554446899*************...............7***********87466689999 PP

>> Peptidase_C70  Papain-like cysteine protease AvrRpt2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.5e-07    0.0021       2     131 ..     261     383 ..     260     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.5e-07
                 Peptidase_C70   2 sealdvpyllqldqaatgCwaaslsmiasyleqksidpselaal..vdkwslmdeglngeekialae.klGlveevpeppq 79 
                                   s++l vp   q  ++   C ++s+ m+  y++ +s +p +   +  +++  l d gl+  +  + +e ++     +p    
  gi|91773097|ref|YP_565789.1| 261 SKTLSVPAYTQ--ETDYYCVPTSIQMLCEYFNDPSTTPTQTYIFnyLGG--LEDFGLSYSDIEEWVEdVWDK---TPTVRT 334
                                   56789999999..*******************99988888777755666..9999*9977776665515666...666655 PP

                 Peptidase_C70  80 s..yeieklvklLraggPlivaiaspgdvvgHviVltGidedga..vivhDPesga 131
                                   s  y+i ++v+ +++++P    i      +gH++V  G  + g    +++DP  g+
  gi|91773097|ref|YP_565789.1| 335 SglYNI-DVVTEIDNNRPFFSMI------SGHCRVCRGYLNSGYfyEYINDPLTGS 383
                                   575766.68899******99888......59************977789***8875 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   3.8e-05      0.23     254     332 ..     156     236 ..     117     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.8e-05
                          MutL 254 vGGaTTdvhsvaegspek..ekvllk.lpeprakrtVegdLGmrvsaknvleeageeelareliseeelrerlenlmerpk 331
                                   vG++TT    ++ ++ ++  +  +l+ ++++ +++t  gdLG+    +++le+  ee+la++ ++++e+++++e++  +  
  gi|91773097|ref|YP_565789.1| 156 VGAMTTVKDKATGEEYRIfvDAYSLEeVQDNPINKTRFGDLGVWSLYETMLENDMEENLAAW-QKSDEFTKSIEEIITNEG 235
                                   78888877766444444322667788899999******************************.699*******99988766 PP

                          MutL 332 t 332
                                   +
  gi|91773097|ref|YP_565789.1| 236 I 236
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); 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):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2392.14
//
Query:       gi|91773098|ref|YP_565790.1|  [L=270]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-21   76.8   0.3    5.4e-21   74.5   0.0    2.3  3  DUF1724   Domain of unknown function (DUF1724)
  ------ inclusion threshold ------
      0.059   13.4   0.0       0.25   11.4   0.0    2.1  2  HemN_C    HemN C-terminal domain
       0.11   12.4   0.1       0.27   11.1   0.1    1.6  1  HxlR      HxlR-like helix-turn-helix


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 ?   -1.3   0.0      0.42   2.5e+03      13      31 ..      80      98 ..      77     106 .. 0.69
   2 ?   -2.9   0.0       1.3   7.7e+03      51      58 ..     132     139 ..     132     140 .. 0.84
   3 !   74.5   0.0     9e-25   5.4e-21       1      61 [.     205     266 ..     205     267 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.42
                       DUF1724 13 lsltvtDkflslslfdkdg 31
                                  ++  ++D+f  ++  +k +
  gi|91773098|ref|YP_565790.1| 80 VASRIADSFSTIGTINKHK 98
                                  5566778888888877764 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                       DUF1724  51 eLFeyYlk 58 
                                   eLF+ Y+ 
  gi|91773098|ref|YP_565790.1| 132 ELFNVYRT 139
                                   89**9985 PP

  == domain 3  score: 74.5 bits;  conditional E-value: 9e-25
                       DUF1724   1 tklyvydeeikplsltvtDkflslslfdkdg.kydhk.dlisfdesAlkWGeeLFeyYlkrSe 61 
                                   +kl+v+d++i  ++l+vtDk+lsl+l++kdg +yd    ++sfd+ A+ WGe+LFeyY+++S+
  gi|91773098|ref|YP_565790.1| 205 FKLMVMDGNI-RVGLIVTDKCLSLGLYKKDGvTYDIAsGIFSFDPMAVVWGERLFEYYKEQSK 266
                                   699*******.**************************99**********************97 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   4.2e-05      0.25      30      64 ..      44      77 ..      35      78 .. 0.83
   2 ?   -3.0   0.0       1.3     8e+03      28      54 ..     186     211 ..     179     216 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.2e-05
                        HemN_C 30 fgldleellaaaleklqeqGLLeldggrlrltprG 64
                                  +g + +++ ++++++l+   L+e  +++++lt+ G
  gi|91773098|ref|YP_565790.1| 44 SGSS-SQSIIPNIRRLESGQLVEAKEDGYCLTRLG 77
                                  4555.78889**********************988 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                        HemN_C  28 qrfgldleellaaaleklqeqGLLeld 54 
                                   q+ ++++ e  ++al+++++  L ++d
  gi|91773098|ref|YP_565790.1| 186 QLKQEPYVEK-INALKDYENFKLMVMD 211
                                   4444445555.5557777766665555 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.5e-05      0.27       9      53 ..      25      68 ..      22      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.5e-05
                                  HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE CS
                          HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierev 53
                                   il +l +g+k+ s+l+++ ++ sq++ + ++r+Le+ +l+e+++
  gi|91773098|ref|YP_565790.1| 25 EILLSLNEGSKKLSQLREISGSSSQSI-IPNIRRLESGQLVEAKE 68
                                  699*************99987777776.5789*********9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1745.73
//
Query:       gi|91773099|ref|YP_565791.1|  [L=143]
Description: hypothetical protein Mbur_1114 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1013.44
//
Query:       gi|91773100|ref|YP_565792.1|  [L=205]
Description: hypothetical protein Mbur_1115 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.4   0.6       0.25   11.6   0.6    1.4  1  XhlA      Haemolysin XhlA


Domain annotation for each model (and alignments):
>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   1.4e-05      0.25      15      51 ..      91     127 ..      87     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                          XhlA  15 nleervdkleekaaeaeekiknleedlkklesnqkWl 51 
                                   +l+e +++  + ++ ++  +++++e++k+les + W+
  gi|91773100|ref|YP_565792.1|  91 ELNEYLSEHGKVSTVQLDISEEINEEIKRLESKNVWQ 127
                                   55666667788999**********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1347.09
//
Query:       gi|91773101|ref|YP_565793.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.7   0.4    6.3e-67  226.0   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
      9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.2e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00011   22.5   0.3       0.17   12.1   0.2    2.8  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.067   13.8   1.4        0.3   11.7   1.4    2.2  1  BST2             Bone marrow stromal antigen 2
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.7   2.6       0.55   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.36   11.2   6.9       0.52   10.7   4.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
          1   10.1   8.9        7.1    7.4   1.5    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.1    9.0   6.0       0.65   10.7   1.1    2.7  2  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.44   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  226.0   0.0   3.5e-70   6.3e-67       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91773101|ref|YP_565793.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 226.0 bits;  conditional E-value: 3.5e-70
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91773101|ref|YP_565793.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91773101|ref|YP_565793.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierear..ea..eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++r  +   ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91773101|ref|YP_565793.1| 329 SENDN--QLWSKAMNIlLIDVKKSVDQIRgmSGcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **976..*********************964338888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91773101|ref|YP_565793.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.5e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91773101|ref|YP_565793.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7     8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91773101|ref|YP_565793.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.6     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.5   0.0    0.0025       4.5       5      45 ..     249     287 ..     245     290 .. 0.84
   3 !   12.1   0.2   9.3e-05      0.17      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91773101|ref|YP_565793.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91773101|ref|YP_565793.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91773101|ref|YP_565793.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91773101|ref|YP_565793.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00046      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91773101|ref|YP_565793.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91773101|ref|YP_565793.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00031      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    0.9   0.1      0.34   6.2e+02      11      58 ..     392     446 ..     383     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91773101|ref|YP_565793.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91773101|ref|YP_565793.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999888854444440......55555555555555555553 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?   10.7   4.5   0.00029      0.52       2      36 ..     156     213 ..     155     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91773101|ref|YP_565793.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91773101|ref|YP_565793.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCellADvCGC 213
                                   79***************99987555588888888888888887775555444446666 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 ?    3.3   0.1     0.074   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.4   1.5     0.004       7.1       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.0   0.1      0.19   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91773101|ref|YP_565793.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91773101|ref|YP_565793.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91773101|ref|YP_565793.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00036      0.65      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.6   0.3        10   1.8e+04      55      66 ..     154     165 ..     144     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91773101|ref|YP_565793.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                         PLATZ  55 kssseaCetCar 66 
                                   +++ ++C +C++
  gi|91773101|ref|YP_565793.1| 154 RAEIKSCPHCGC 165
                                   334478999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2904.52
//
Query:       gi|91773102|ref|YP_565794.1|  [L=381]
Description: hypothetical protein Mbur_1118 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-13   49.8   0.1    1.2e-12   48.6   0.1    1.7  1  Peptidase_C39_2  Peptidase_C39 like family
    2.3e-05   24.4   0.0      5e-05   23.3   0.0    1.5  1  Peptidase_C70    Papain-like cysteine protease AvrRpt2


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   1.3e-16   1.2e-12       1     144 []     212     339 ..     212     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.3e-16
               Peptidase_C39_2   1 ldvplynQlde.........lpngCeptslamvlsyl.gkkvtqnelakelktnssgdpntgfvgnitdksglgvynepiv 71 
                                   +dvp  +Q++          + + C+ t +am+ +y+ g++++ ++++  +++++             ++ +++++ ++i+
  gi|91773102|ref|YP_565794.1| 212 IDVPHRSQWELfwdlhgyaaASTACGDTVAAMLEEYYtGTSPDIWDIYLIYGSMGA------------SEAEDYLQDQSIN 280
                                   69******9767777888889999*****************************982............56778999***** PP

               Peptidase_C39_2  72 klaekyglkvsdtrgssieevkkeidagkPvvvsvttfkplndgeikftssgHlvvitGYdekgkrvyvnDPa 144
                                   +  ++ ++    + +  i+ ++ +id g+P++++ +          + + + H+vv++GY++ ++++++nDP+
  gi|91773102|ref|YP_565794.1| 281 ADKRSHTG----SLSYVIDCAQYYIDTGRPFYLIEE----------SNSGELHAVVLRGYSDAYDYFVLNDPN 339
                                   *9999888....8899*******************7..........456788********************7 PP

>> Peptidase_C70  Papain-like cysteine protease AvrRpt2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.6e-09     5e-05       3     136 ..     210     346 ..     208     353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.6e-09
                 Peptidase_C70   3 ealdvpyllqld.........qaatgCwaaslsmiasyleqksidpselaalvdkwslmdeglngeekialaeklGlveev 74 
                                   +  dvp   q++          a+t+C++++++m+  y++ +s d  ++    ++      g++  e++   ++++  +  
  gi|91773102|ref|YP_565794.1| 210 AYIDVPHRSQWElfwdlhgyaAASTACGDTVAAMLEEYYTGTSPDIWDIYLIYGS-----MGASEAEDYLQDQSINADKRS 285
                                   5679*******9********99******************999999999877776.....565656666666666663333 PP

                 Peptidase_C70  75 peppqsyeieklvklLraggPlivaiaspgdvvgHviVltGidedga.vivhDPesgakrkks 136
                                        sy i+    +++ g+P +   +s  +   H+ Vl G     + ++++DP+  + ++ +
  gi|91773102|ref|YP_565794.1| 286 HTGSLSYVIDCAQYYIDTGRPFYLIEESNSG-ELHAVVLRGYSDAYDyFVLNDPNTLSGTE-Q 346
                                   334446*****************99877776.89*******9877779*******987666.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2389.21
//
Query:       gi|91773103|ref|YP_565795.1|  [L=119]
Description: carboxymuconolactone decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   34.4   0.0    2.2e-08   34.1   0.0    1.1  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.021   14.9   0.0    1.3  1  DUF1137   Protein of unknown function (DUF1137)


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 !   34.1   0.0   2.4e-12   2.2e-08       2      76 ..      28     103 ..      27     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.4e-12
                                   HHHHHHHHHHHHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHH CS
                           CMD   2 ellraltalrealla.reggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaa 76 
                                   ++ + ++ +++a+++ re+gL+ k ++L+ +av+++++  + ++  + ++++ G+t+ e+ +++++aa+++g  ++
  gi|91773103|ref|YP_565795.1|  28 DFGQGVASFYKAIWKdREDGLSMKNKHLMVFAVACSRNNTNSAKKILVKLKNHGATRTEVLDAMMMAAWTGGIQNF 103
                                   67788999*********************************99****************************98765 PP

>> DUF1137  Protein of unknown function (DUF1137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.3e-06     0.021      43      84 ..      67     110 ..      49     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-06
                       DUF1137  43 slackellskls..ghlqtedleklmtfrgtggllnykdyslsv 84 
                                   + + k++l kl   g  +te l+ +m+   tgg+ n+ d+s ++
  gi|91773103|ref|YP_565795.1|  67 TNSAKKILVKLKnhGATRTEVLDAMMMAAWTGGIQNFTDISSDI 110
                                   345688898886337789999*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 813.15
//
Query:       gi|91773104|ref|YP_565796.1|  [L=176]
Description: Ferritin and Dps [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-41  141.2   4.4    2.3e-41  141.0   4.4    1.0  1  Ferritin  Ferritin-like domain
  ------ inclusion threshold ------
      0.038   14.1   0.1      0.065   13.3   0.1    1.4  1  ANAPC5    Anaphase-promoting complex subunit 5


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 !  141.0   4.4   2.6e-45   2.3e-41       2     141 ..       8     143 ..       7     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 2.6e-45
                                   HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.CSSH CS
                      Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke.fgsv 81 
                                   kaLn q+++e+++a++y+am++y +++gl g+a++f+ q++ee+ ha+k++++i + G+     ++el++ie+p + fg++
  gi|91773104|ref|YP_565796.1|   8 KALNGQINKEMYSAHLYMAMSAYSSNIGLSGFANWFMVQYQEEMLHAMKFYNYIVDQGA-----KVELQAIEKPAQeFGTT 83 
                                   89*********************************************************.....************9**** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  82 eevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekler 141
                                   +e+l a l hek +t+s+++l++la ee+D+at+ fl+++++eq e+e + +a+++kl++
  gi|91773104|ref|YP_565796.1|  84 LEMLNATLGHEKFITRSINDLVDLAIEEKDHATNIFLQWYITEQIEEEGNDNAIIDKLKL 143
                                   *********************************************************986 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.2e-06     0.065       6      87 ..      39     123 ..      35     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-06
                        ANAPC5   6 lnalrakdYqqaldsLhryFDyvlsqnessq....kksyqyalLnlaslhadfghneeAvkaleeairlArenkDkscLal 82 
                                   ++++   +Yq+ + + ++ + y++ q ++ +    +k  q +   l +l a++gh++  ++++++ + lA e+kD+++ ++
  gi|91773104|ref|YP_565796.1|  39 FANWFMVQYQEEMLHAMKFYNYIVDQGAKVElqaiEKPAQEFGTTLEMLNATLGHEKFITRSINDLVDLAIEEKDHAT-NI 118
                                   56777778888888888888888888888877777666666778899*****************************97.55 PP

                        ANAPC5  83 alawl 87 
                                    l+w+
  gi|91773104|ref|YP_565796.1| 119 FLQWY 123
                                   56665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1342.16
//
Query:       gi|91773105|ref|YP_565797.1|  [L=241]
Description: CRISPR-associated Cas6 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-37  129.6   0.5    4.1e-37  128.0   0.6    1.7  2  Cas_Cas6  CRISPR associated protein Cas6


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.14   2.5e+03      19      47 ..      35      62 ..      17      90 .. 0.60
   2 !  128.0   0.6   2.3e-41   4.1e-37       1     146 []      91     239 ..      91     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.14
                                  EEEE----S--TCEE.EEESS-BBEEEEE CS
                      Cas_Cas6 19 evellkepeitssevvfktlSPivvrstk 47
                                  +++l +e    ++  +f t+S +++++ +
  gi|91773105|ref|YP_565797.1| 35 NITLANEIHSHQG-FKFYTFSNLIIEDWI 62
                                  4444444444334.558899999988442 PP

  == domain 2  score: 128.0 bits;  conditional E-value: 2.3e-41
                                   HHHCS-EEEET...TEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHHHHHHHHH CS
                      Cas_Cas6   1 gllknkeirlg...nnefkveevellkepeitssevvfktlSPivvrstkkengkkktyylspddeeFsellkenlkkkyk 78 
                                   gll ++e+ lg   +++f +e++e++++ ei++s+  f tlSPi+v++ +k+n+k   ++l p+d++F+e+++ nl+ +y+
  gi|91773105|ref|YP_565797.1|  91 GLLLEPEFFLGrdkKANFIIERIEIMPNLEISESCK-FTTLSPIYVKTMRKKNDKLVEIDLYPKDSKFYENIHTNLTARYE 170
                                   689999******99*****************99966.**********99******************************** PP

                                   HHHSS..SS---EEEEEEEEE.........TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-EEE CS
                      Cas_Cas6  79 alygeekeeklsikpdkkvkkivvkkk...etyirGylgrfelegdpellklaydaGlGeknsqGFGmvev 146
                                   ++yg++ e++  +++ + vk+++ k+    + + r++l+++ele++pel+k+aydaGlGekn++GFG++e+
  gi|91773105|ref|YP_565797.1| 171 EYYGHKVEHDY-FDVLE-VKDFKPKRVsigNSFRRCSLMKLELEASPELIKFAYDAGLGEKNAMGFGCLEL 239
                                   *****944444.44444.444444444555***************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1758.58
//
Query:       gi|91773106|ref|YP_565798.1|  [L=625]
Description: hypothetical protein Mbur_1122 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   16.8   0.2      0.011   15.5   0.2    1.7  1  DUF592    Protein of unknown function (DUF592)


Domain annotation for each model (and alignments):
>> DUF592  Protein of unknown function (DUF592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2     6e-07     0.011       9      84 ..      31     108 ..      23     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6e-07
                        DUF592   9 kpiilgkdsksgkyvlpeitkedslnarlfLKkyglkkFldkY..LPeelnslyiyelIklLGFelkdkellnaiskv 84 
                                   k++++  d +++ +v+++ + +d  +++ +LK+ g+k F+ +Y  LP++ +s +i +   lL ++++  ++++a  + 
  gi|91773106|ref|YP_565798.1|  31 KTLLVPLDGSEESFVINNSNLDDEFDSKPWLKRLGKKYFMHDYfiLPTHKSSNNIGSTSALLSHSPTHYKITTAFFSK 108
                                   5666677888999*****************************9777*********99999999888888887764443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4231.62
//
Query:       gi|91773107|ref|YP_565799.1|  [L=286]
Description: hypothetical protein Mbur_1123 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  119.4   2.2    2.1e-34  119.2   2.2    1.0  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 !  119.2   2.2   1.2e-38   2.1e-34       2     235 ..       2     247 ..       1     274 [. 0.81

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 1.2e-38
                      Cas_Cas7   2 ryefvllfdvkngNpNGDpdagnkPRidpetgeglvsDvclKrkiRnyvekakeekeiyvkekkv..............ln 68 
                                   +y++++++++kn+  N+ +d    PR    +g+++ +D++lK+ iR+y++k++   +++v++ k+              l 
  gi|91773107|ref|YP_565799.1|   2 NYNGIVVVNAKNASFNAGFD--GLPRR-LPNGKIFATDKALKYCIRDYLSKNE---TVFVQRTKKedtikgaivqrhltL- 75 
                                   68999*************65..59999.79*******************9987...8****9999555555544433331. PP

                      Cas_Cas7  69 ekkeeay.........k..deekke.lreamcenffDvRtFGavmstgvngqvr.GpVqltfarslepv.lpeeqsitrma 135
                                         +         k   ++  e +    ++ f+DvR+FG v++ + n++++ Gp q++++++  +   + + +i+++ 
  gi|91773107|ref|YP_565799.1|  76 ------DenylekcnkKsiPKD--EmAVIEDLKSFIDVRLFGVVFAVKGNNISMtGPCQINYGVNRFKNsSIFSSEILSPY 148
                                   ......0333332221122111..11334446778***********877788888***********9999*********** PP

                      Cas_Cas7 136 ateekkekekkqrtmgrkhivpyglYrahgfinanlaek..tgfseeDlellkeallnmfehdrsaargemevrkllvfeh 214
                                   +++++k+k+ +q+t+g++++ +   Y++++ +n n a+k   ++s+eD+++lk+al   + + +s++  ++e+  +l+fe 
  gi|91773107|ref|YP_565799.1| 149 RNSNEKSKDVQQTTIGEESRADDVYYVYDICLNMNSAKKqeIEISDEDITKLKNALKYSVGEVNSTTMFGCETVSMLWFEN 229
                                   *999776666***************************7645889************************************9 PP

                      Cas_Cas7 215 esklgnapaaklfdlvkvekk 235
                                       ++   ++l +lv+v ++
  gi|91773107|ref|YP_565799.1| 230 ---SDDRIFNNLNSLVDVYEE 247
                                   ...566667777777887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1943.99
//
Query:       gi|91773108|ref|YP_565800.1|  [L=264]
Description: hypothetical protein Mbur_1124 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   31.8   0.0    1.5e-07   31.5   0.0    1.1  1  Cas_Cas5d       CRISPR-associated protein (Cas_Cas5)
  ------ inclusion threshold ------
       0.03   14.0   0.0       0.13   12.0   0.0    2.1  2  TPK_B1_binding  Thiamin pyrophosphokinase, vitamin B1 binding


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 !   31.5   0.0   1.7e-11   1.5e-07       2     149 ..      33     181 ..      32     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.7e-11
                                   EEEEEECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHHT--TTS-..........-CCCCTTEEEEEEEEEEEEEEETE CS
                     Cas_Cas5d   2 LllrlegplasfgrpsrkveretydvPtkSavlGllaaalGirrddd..........leelkpalrwgvrvdrrgellrgd 72 
                                   L +rl+g +a f +p     r ty +++k  +lGl++++ G++ ++           l++lk  ++ +    +++++   +
  gi|91773108|ref|YP_565800.1|  33 LTFRLYGSFAHFNQPISNRFRNTYSIIPKPQLLGLIGSIVGLSGYKNaavspefyskLSDLKVFIKCNS--LSEKKFTL-S 110
                                   89*****************************************99999*****9666666664444444..55555555.9 PP

                                   EEEECT-GGGS--BSSS----CCEEEEEEEEEEEECEEEEEECCSCCH.HHHHHHHHH.HHHTTSSSSESSSTTSEEEE CS
                     Cas_Cas5d  73 yhtvagrtlperrkektadrkkraatvlseraYladahfevalegeee.gklleelar.alrkpvwplyLGrkecivpv 149
                                   y+ ++    +++r ++       +  v+ + + l d  +ev + + e+   +le++ + ++  +v+p+y+G  e+ + v
  gi|91773108|ref|YP_565800.1| 111 YNSLN--SFLNNRIDS------GSPNVIIKEQVLLDPDYEVGIVVNENnPLHLEIIDKiRMNCGVFPIYFGKNEFFANV 181
                                   99999..666666666......344555556678899999999999998899999987468899***********7665 PP

>> TPK_B1_binding  Thiamin pyrophosphokinase, vitamin B1 binding domain
   #    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      14      21 ..     163     170 ..     156     171 .. 0.78
   2 ?   12.0   0.0   1.4e-05      0.13      10      37 ..     195     220 ..     187     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.6
                                   -EEEEEES CS
                TPK_B1_binding  14 kyvgliPl 21 
                                    ++g++P+
  gi|91773108|ref|YP_565800.1| 163 MNCGVFPI 170
                                   479*9997 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.4e-05
                                   TTB.-EEEEEESSSSEEEEEEESBSS-E CS
                TPK_B1_binding  10 eqegkyvgliPlggevtglttkGlkwnl 37 
                                   e  +k ++++P+ +ev+ ++t+ +k +l
  gi|91773108|ref|YP_565800.1| 195 E-SNKCCSIFPF-EEVESVNTRNMKLEL 220
                                   4.679*******.8********999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2017.19
//
Query:       gi|91773109|ref|YP_565801.1|  [L=880]
Description: CRISPR-associated helicase Cas3 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-09   37.7   0.0    1.5e-08   34.6   0.0    2.5  2  DEAD        DEAD/DEAH box helicase
    2.5e-09   37.4   3.8    9.2e-09   35.5   0.1    3.0  2  ResIII      Type III restriction enzyme, res subunit
    2.7e-06   27.7   0.8    2.7e-06   27.7   0.8    3.2  2  Helicase_C  Helicase conserved C-terminal domain
    0.00015   22.0   0.0    0.00023   21.3   0.0    1.2  1  HD_6        HD domain
    0.00035   20.8   0.1     0.0013   18.9   0.0    2.0  2  HD          HD domain
      0.009   15.5   0.0       0.65    9.4   0.0    2.3  2  PhoH        PhoH-like protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0     5e-12   1.5e-08      15     172 ..     293     474 ..     281     476 .. 0.63
   2 ?   -2.9   0.0       1.7   4.9e+03      82     112 ..     705     735 ..     689     758 .. 0.60

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5e-12
                                   CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT......TST.............S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxx.............x RF
                          DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk......yid.............l 76 
                                   + ++++ +TG GKT + +  vl+i+   ++++ +++++v P   ++eq ++ + + +       + +              
  gi|91773109|ref|YP_565801.1| 293 KIFMLSVPTGGGKTNISMKLVLNILE--HDNSLKRIFYVFPFINIIEQNYKSIDNTLFndsyfpN-KlglisdiysrayvN 370
                                   4456899***************9994..5788889******************887774554430.122333332222211 PP

                                   EEEEEETTSSHHHHHHHH.....................HTTCSEEEEEHHHHHHHH.....HCTSSHCTTE..EEEEEET CS
                                   xxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxx.....xxxxxxxxxx..xxxxxxx RF
                          DEAD  77 rvlliiggvaardqlskl.....................dngvdivvgtpgrlddll.....stgklnlsqv..rflVlDE 129
                                                +++++                      n++  v+++   + +++     ++   ++ ++  +++V+DE
  gi|91773109|ref|YP_565801.1| 371 -------------KYENMsdtddsdfkleqmlliqndnfLNNCVNVISNVNFFNSFIknggnNR--YKIANMcnSVVVIDE 436
                                   .............222221112222222333455443222556666666667777666664322..3355545689***** PP

                                   HHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                          DEAD 130 adrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.kd 172
                                   +++l+d++ + f+n i ++     ++  l+   i++SATlp ++
  gi|91773109|ref|YP_565801.1| 437 IQTLSDKNIRTFYNFIKETS----ES--LNIYYIIMSATLPdFN 474
                                   *******8888887755555....33..45669*******9665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddll 112
                                   i+g+ a+ q++ ++n++d++ +  g++d ++
  gi|91773109|ref|YP_565801.1| 705 IQGKIANLQYQSINNELDVIDTKVGKVDIFI 735
                                   4556666666777666777666666666644 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   3.1e-12   9.2e-09      21     170 ..     279     471 ..     252     472 .. 0.62
   2 ?    1.3   0.6       0.1     3e+02      83     140 ..     682     738 ..     651     758 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.1e-12
                                   ............TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG......... CS
                        ResIII  21 s..........krdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflseayke..... 84 
                                   +          +++k +++  +TG GKT +++kl+ ++l++ + +  +++ + p ++++eq ++ + ++l ++  +     
  gi|91773109|ref|YP_565801.1| 279 EcndnmkrlvkDGNKIFMLSVPTGGGKTNISMKLVLNILEHDN-SlkRIFYVFPFINIIEQNYKSIDNTLFNDSYFpnklg 358
                                   04444444555999999********************998644.2359999************999666666666655656 PP

                                   .GEEEESSS-B--............................-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGG CS
                        ResIII  85 .igkkvsgdkkka.....................kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHr 143
                                    i+ ++s    ++                     + ++ +n+  ++++++ +++ ++++ +++ +  +  + v++iDE   
  gi|91773109|ref|YP_565801.1| 359 lISDIYSRAYVNKyenmsdtddsdfkleqmlliqNDNFLNNCVNVISNVNFFNSFIKNGGNNRYKIANMCNSVVVIDEIQT 439
                                   533332222222222111222222334444444344444555555555555555554445555555555556********* PP

                                   TTS.T...TTHHHHHT---...SEEEEEESS-S CS
                        ResIII 144 lgakk...swreilekfke...avllglTATpe 170
                                   l++k+   +++ i+e   e    + + ++AT++
  gi|91773109|ref|YP_565801.1| 440 LSDKNirtFYNFIKETS-EslnIYYIIMSATLP 471
                                   ***52443444443333.246688888999975 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                   ...........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEET CS
                        ResIII  83 ke.........igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDE 140
                                   ++         + kk+  d+ k+      + ki   ++qs+++++     +  + + ++ d++i+DE
  gi|91773109|ref|YP_565801.1| 682 HFdtyygklseEVKKIARDNFKP-----IQGKIANLQYQSINNEL-----DVIDTKVGKVDIFICDE 738
                                   22333222322233333333333.....47788888899999999.....77888889999999999 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 ?   -1.2   0.2      0.84   2.5e+03      15      73 ..      75     140 ..      61     180 .. 0.60
   2 !   27.7   0.8     9e-10   2.7e-06      11     109 ..     526     628 ..     500     630 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.84
                                   TTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHH...........HHHHHHHTTSSS.EEEES CS
                    Helicase_C  15 eggkilifvntidrlekvklllekkgikvavlhgelpqnere...........eileqfnkgesd.vLiat 73 
                                   + ++il+f+ +  ++     +  +++++ ++++++ ++++ +             l++f +++s  +Li t
  gi|91773109|ref|YP_565801.1|  75 SIKQILLFAVYYHDI---GKI--NSNFQKVKVNSKKSSSNSNhsifsekvltsFLLNEFPNQKSIiYLIGT 140
                                   556777777777777...444..222233333333333332212233322222344444444444366666 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 9e-10
                                   HHTTTTSEEEEEESSHHHHHHHHHHHHHT......TSTEEEESTTSTHHHHHHHHHHHH...TTSSSEEEESGGGTSSSTS CS
                    Helicase_C  11 kleeeggkilifvntidrlekvklllekk......gikvavlhgelpqnereeileqfn...kgesdvLiatdvaerGidi 82 
                                   +    g k+li +n +d+    +++ e +      g+++  l++++++  r++i+e+ +   +ge+ ++++t+ +e G+di
  gi|91773109|ref|YP_565801.1| 526 NYATGGVKVLITLNVVDTSR--RVFDELRidddfnGFSFYLLNSTTSTLRRKKIIENIKkcpNGERIIIVSTQSIEAGVDI 604
                                   445667899********886..5553333445668***********************98888****************** PP

                                   TTESEEE.ESSSSSSHHHHHHHHTTSSS CS
                    Helicase_C  83 pkvnlVi.nfdlprnvtsyiqriGRtgR 109
                                   ++ ++ i ++++    +s+ q +GR+ R
  gi|91773109|ref|YP_565801.1| 605 DC-DFGIrDYSIL---DSIEQISGRINR 628
                                   64.4433145444...556666666655 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   7.8e-08   0.00023      49     155 ..      75     181 ..      34     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.8e-08
                                   HHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH...........HHHHHHHHHHHT CS
                          HD_6  49 alrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle...........evarslaaavgg 118
                                   +++++l+f +  HD+GK++++Fq+ + +  +           ++++ +H+  +  +l+           + +  + ++v  
  gi|91773109|ref|YP_565801.1|  75 SIKQILLFAVYYHDIGKINSNFQKVKVNSKK-----------SSSNSNHSIFSEKVLTsfllnefpnqkSIIYLIGTVVSL 144
                                   57899******************98833222...........226677888877776666666787776777778888999 PP

                                   TTS---HHHHHTSS-HHHHTTHHHHHHHHHHHHHHHH CS
                          HD_6 119 HHGkppkeeeekaekkssaaedweeaqkelleaaaef 155
                                   HH k  + + ++ ++++++ + ++++ +++  +++e+
  gi|91773109|ref|YP_565801.1| 145 HHTKLRDFSIKDYDESQDEIKIIQQIIQDTGLEIKEI 181
                                   9998777777666555555444444444444444444 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.4e-07    0.0013      25      93 ..      77     150 ..      63     197 .. 0.77
   2 ?   -2.1   0.0       1.4   4.3e+03      77      95 ..     686     708 ..     655     739 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.4e-07
                                   HHHHHHHHHHTTTTHHHHTS..HHH..HHHCTCCHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHTTCCHHH CS
                            HD  25 rellllaaLlHDiGkgpfgdafekk..eeefekflaHekvgaeilrevekrlgld....ledvaklirehheswe 93 
                                   +++ll+a ++HDiGk+ ++ ++  k  +++  +  +H+++++++l  +++ ++ +    + ++  +++ hh + +
  gi|91773109|ref|YP_565801.1|  77 KQILLFAVYYHDIGKINSN-FQKVKvnSKKSSSNSNHSIFSEKVLTSFLLNEFPNqksiIYLIGTVVSLHHTKLR 150
                                   57899************66.5655577444555568999999999999999988899998888888888887764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                   H....HHHHHHHHHTTCCHHHHH CS
                            HD  77 d....ledvaklirehheswegk 95 
                                   +     e+v k++r +++++ gk
  gi|91773109|ref|YP_565801.1| 686 YygklSEEVKKIARDNFKPIQGK 708
                                   13344567778888777777654 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00022      0.65      17      61 ..     289     335 ..     279     370 .. 0.87
   2 ?    3.4   0.1     0.015        45     119     144 ..     428     453 ..     425     459 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00022
                                   H.H-SEEEEE--TTSSTTHHHHHHHHHHHHT.TS-SEEEEEE-S--T CS
                          PhoH  17 k.kndivfaiGpaGtGKtylavalavealkk.kkvkriiltrpavea 61 
                                   k  n+i +   p+G GKt +++ l +++l++ +++kri ++ p +++
  gi|91773109|ref|YP_565801.1| 289 KdGNKIFMLSVPTGGGKTNISMKLVLNILEHdNSLKRIFYVFPFINI 335
                                   3568899999*******************986889999999888765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.015
                                   -SEEEEE-SGGG--HHHHHHHHTTB- CS
                          PhoH 119 ndafvilDEAQnttkeqmkmfltRlG 144
                                    +++v++DE Q ++ +++++f   + 
  gi|91773109|ref|YP_565801.1| 428 CNSVVVIDEIQTLSDKNIRTFYNFIK 453
                                   589***************99976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (880 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); 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:                         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 0.25s 00:00:00.89 Elapsed: 00:00:00.39
# Mc/sec: 6731.05
//
Query:       gi|91773110|ref|YP_565802.1|  [L=199]
Description: CRISPR-associated Cas4 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-54  184.5   3.9    1.7e-54  184.3   3.9    1.0  1  Cas_Cas4  Domain of unknown function DUF83
  ------ inclusion threshold ------
      0.043   13.7   0.1       0.05   13.5   0.1    1.2  1  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 !  184.3   3.9   1.9e-58   1.7e-54       1     162 []      34     193 ..      34     193 .. 0.99

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 1.9e-58
                      Cas_Cas4   1 tgtkiqyyliCkrklwlisheitleensetvelGkllheesyerekkevelsesikiDvvekekeklvvvEvKkskkkeea 81 
                                   tg+ki+yy+iC++klwl+sh+i le+++e+v++Gk++he+sy+++kke++++++i+iD+v+k+++ l+++E+Kk k++e+a
  gi|91773110|ref|YP_565802.1|  34 TGVKINYYHICHTKLWLFSHNIALEHENENVNIGKQIHEDSYSKNKKEITIDNTISIDFVKKRDDILELHEIKKTKSMEDA 114
                                   699****************************************************************************** PP

                      Cas_Cas4  82 aklQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCayaelCli 162
                                   +  Q+lyY+++L+k+g++   Gv++yp  ++++ev lt +++ ++e+ i +ie+ii+  ++p++k+ +iC kCay+e+C++
  gi|91773110|ref|YP_565802.1| 115 HLQQMLYYIYYLKKRGIDSY-GVMNYPLLNQTREVVLTSDDEMKIEDDIINIEKIITG-RMPHPKRIRICPKCAYFEFCFC 193
                                   ********************.************************************9.9*******************96 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.6e-06      0.05     134     254 ..      90     191 ..      44     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-06
                      PDDEXK_1 134 iDrvddkegelriiDyKtgsappkskelaelkegl.QlllYllalaegeelkeegepagalylrleepkvkdeevvkkmal 213
                                   iD v ++++ l++ + K ++     ++      +l Q+l Y ++l++    +  +   g+  + l        +++++++l
  gi|91773110|ref|YP_565802.1|  90 IDFVKKRDDILELHEIKKTK---SMED-----AHLqQMLYYIYYLKKR---G-ID-SYGVMNYPL-------LNQTREVVL 150
                                   78888778878888888555...4444.....6784666666666666...2.22.444444444.......368888889 PP

                      PDDEXK_1 214 teeeleallqeleelaeeilagefparpskk.CeyCpyksvC 254
                                   t+++  ++++++ ++ e+i  g++p     + C  C+y + C
  gi|91773110|ref|YP_565802.1| 151 TSDDEMKIEDDIINI-EKIITGRMPHPKRIRiCPKCAYFEFC 191
                                   999999*******96.9999999888888778*******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1059  (0.0590663); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1689.59
//
Query:       gi|91773111|ref|YP_565803.1|  [L=333]
Description: CRISPR-associated Cas1 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-85  286.7   0.1    1.9e-85  286.5   0.1    1.0  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 !  286.5   0.1     1e-89   1.9e-85       1     282 [.       5     287 ..       5     288 .. 0.99

  Alignments for each domain:
  == domain 1  score: 286.5 bits;  conditional E-value: 1e-89
                                   EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.SSSST CS
                      Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.eesgn 80 
                                   +y+ ++g  l++k++++++ +++e k+ +p+++i si+ +g++s+s+ ++++l+++gip++f++++g y g+++p e+  +
  gi|91773111|ref|YP_565803.1|   5 YYILQDGI-LKRKENTVYFVNKDE-KRVLPINKIYSIYAYGKLSFSSGVVSYLSKNGIPIHFFNYYGFYEGSMYPrETLIS 83 
                                   69999999.*************99.9******************************************************* PP

                                   HHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTT..HHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHH CS
                      Cas_Cas1  81 velrraQyraaddeekrlelakkivagklenqrkvlrrlkrdree..eeleeaieeleelleklekaesleeLrgiEGeaa 159
                                   ++l ++Q+ ++ d+ekr+ la k+++g+  n+ k+l++++r +e+  +++++ ++++e+ l++l++a+s+ +++++EG+++
  gi|91773111|ref|YP_565803.1|  84 GDLVIHQASHYLDSEKRMLLAGKFIEGACGNILKNLKYYSRTKEDcqDAMNSYVSSIESELSRLPNADSIPKMMNVEGRMR 164
                                   *******************************************88999********************************* PP

                                   HHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHH CS
                      Cas_Cas1 160 kaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpl 240
                                    +Y++a+d++++e++++ +R+rrpp +++N+l+sfg++l+y++vls+i++++L+P+i++LHe+ ++r+sLalD+ E+f+p+
  gi|91773111|ref|YP_565803.1| 165 YIYYNALDEIFPEDYRIVTRTRRPPGNKMNTLISFGNSLMYTTVLSEIYNTQLNPTISYLHEPFERRFSLALDVSEIFKPI 245
                                   ********************************************************************************* PP

                                   HCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHH CS
                      Cas_Cas1 241 lvDrlvlslinkrqlkekdFekeengvlLteegrkkfleafe 282
                                   ++Dr++l+l+nk++l+++ F  e + +lL+e+g+k+fl++++
  gi|91773111|ref|YP_565803.1| 246 IIDRIILKLVNKNMLDDNCFMGEIGDMLLSEKGKKIFLQEYN 287
                                   ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2536.89
//
Query:       gi|91773112|ref|YP_565804.1|  [L=87]
Description: hypothetical protein Mbur_1128 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.8e-21   73.9   3.0    1.1e-20   73.6   3.0    1.0  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
       0.14   12.7   0.1       0.17   12.4   0.1    1.1  1  IZUMO        Izumo sperm-egg fusion, Ig domain-associated


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 !   73.6   3.0   1.2e-24   1.1e-20       1      73 [.       1      70 [.       1      72 [. 0.98

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1.2e-24
                                  EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHH CS
                   CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqf 73
                                  m+v++vYD+  + +r++kv+ +lk+y +++vQ+SV egel++a++ k+++ lk++i+++edsi iy++++ ++
  gi|91773112|ref|YP_565804.1|  1 MYVIIVYDV--GVERLNKVRIFLKQY-LNWVQNSVLEGELTKAEYFKIQSHLKQLINKDEDSIFIYRVKDYKY 70
                                  9********..***************.******************************************9887 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.9e-05      0.17      55     102 ..       8      55 ..       4      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                   EEEHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHHHHHHHHH CS
                         IZUMO  55 vvdeetlekvasslkkelkrltdsdlkgelllkeLlwllqkqkkklke 102
                                    v +e+l+kv+ +lk+ l+ +++s l+gel   e +++ +++k+ +++
  gi|91773112|ref|YP_565804.1|   8 DVGVERLNKVRIFLKQYLNWVQNSVLEGELTKAEYFKIQSHLKQLINK 55 
                                   58899************************9999***999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 585.66
//
Query:       gi|91773113|ref|YP_565805.1|  [L=446]
Description: tRNA CCA-pyrophosphorylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-45  153.4   0.0    4.9e-45  152.4   0.0    1.6  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    6.1e-13   48.9   0.0    1.6e-12   47.6   0.0    1.8  1  NTP_transf_2     Nucleotidyltransferase domain
    7.3e-05   23.0   0.0    0.00016   21.9   0.0    1.5  1  SMODS            Second Messenger Oligonucleotide or Dinucleo


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.0   8.2e-49   4.9e-45       1     113 []     154     264 ..     154     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 8.2e-49
                                   HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETTEEE CS
               tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPvDpk 81 
                                   dev llK+f++g+gvYGselk++GfsGYl+Ellv++ygsfe+vleaa++w+p++ +d+ e+ +   kf++plvviDP+Dpk
  gi|91773113|ref|YP_565805.1| 154 DEVLLLKQFMRGTGVYGSELKTEGFSGYLTELLVINYGSFEKVLEAASNWRPGLLLDILEHGK--LKFEDPLVVIDPTDPK 232
                                   89***********************************************************99..99************** PP

                                   EETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
               tRNA_NucTransf2  82 RNvaaalsleklaefilaareflkkpseefff 113
                                   RNvaaalsl+k+++f+ +ar+fl +p+e++ff
  gi|91773113|ref|YP_565805.1| 233 RNVAAALSLDKFCTFVDMARSFLCNPDESMFF 264
                                   *****************************996 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   2.6e-16   1.6e-12      12      94 ..      40     140 ..      29     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.6e-16
                                   TT..TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH...............HHHEHHHHHHHHCCCEEECTTEEEEEE CS
                  NTP_transf_2  12 ep..vakvvlfGSyarGtalkg.SDiDllvvlpeevsre...............kkeegleklaeiikfleellglevdlv 74 
                                    +  ++k  l+GS+arGt+ +g +D+D+++++p+++sre               + e   e +ae++++  + +g  vdlv
  gi|91773113|ref|YP_565805.1|  40 VGlvGVKTQLVGSAARGTWISGtHDLDIFITFPDDTSREdlesyglsvgrqvakEAEHWDEHYAEHPYVKMRYKGFDVDLV 120
                                   555678999*******************************************997778889******************** PP

                                   CEEECCCCTEEEEEECEEEH CS
                  NTP_transf_2  75 trekledpllvksileerpl 94 
                                   +++++ + + ++s+++++p+
  gi|91773113|ref|YP_565805.1| 121 PCYSVSSASSIISAVDRTPF 140
                                   ***************99987 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.6e-08   0.00016       9     135 ..       7     127 ..       2     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.6e-08
                         SMODS   9 eflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegdep 89 
                                   + l++i++ +++++++++  +++  +++    +++   +++ lvGS ar+T i ++ d+d+   ++ d      ++++d  
  gi|91773113|ref|YP_565805.1|   7 SILEKIKPTEKEREHLTKVADELMYKIDCLTFKVGLVGVKTQLVGSAARGTWISGTHDLDIFITFPDD------TSREDLE 81 
                                   567889999999999999999999999988878888889999*****************999999998......4444444 PP

                         SMODS  90 sdlleklkkalkktyksseirqdrqvvvvelneikidvvPavenkd 135
                                   s  l   ++++k+     e+  +++ v ++++++++d+vP+ + ++
  gi|91773113|ref|YP_565805.1|  82 SYGLSVGRQVAKEAEHWDEHYAEHPYVKMRYKGFDVDLVPCYSVSS 127
                                   55555555555777777788999******************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 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:                        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 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3229.69
//
Query:       gi|91773114|ref|YP_565806.1|  [L=279]
Description: 8-oxoguanine DNA glycosylase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-21   76.4   0.1    3.3e-20   72.4   0.2    2.4  2  OGG_N     8-oxoguanine DNA glycosylase, N-terminal domain
    2.3e-07   31.2   0.0    3.4e-07   30.7   0.0    1.2  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    1.7e-05   24.5   0.0    4.5e-05   23.1   0.0    1.7  1  HHH       Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.045   14.4   0.2       0.17   12.5   0.1    2.0  2  HHH_5     Helix-hairpin-helix domain
      0.053   13.6   0.0          1    9.5   0.0    2.3  2  HHH_2     Helix-hairpin-helix motif
      0.062   13.5   0.0       0.12   12.6   0.0    1.6  1  DUF3669   Zinc finger protein


Domain annotation for each model (and alignments):
>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.2   1.1e-23   3.3e-20       4     121 .]       4     105 ..       1     105 [. 0.90
   2 ?   -3.3   0.0         3     9e+03      82     106 ..     223     247 ..     221     251 .. 0.72

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.1e-23
                                   ES-SS--HHHHHCSSS-SSEEE-TTS-EEEEETTEEEEEEEETTEEEEET--.............HHHHHHTHHHHTTTTS CS
                         OGG_N   4 vskeeldlkktLkcGQsFrWkktekteyvgvlgdrvveLkqeeddllyrtlesesstkasseeakeeeteeilrdYfnLdv 84 
                                   +++e+l+l+ tL cGQ FrW ++ +  ++gv+++ v  ++q +++    +              +++ +e+++++Yf+Ld 
  gi|91773114|ref|YP_565806.1|   4 IKTEDLNLEYTLDCGQVFRWDRDGDW-WTGVINGVVARISQSPETGDLLV--------------DSSLDEDFFHRYFRLDD 69 
                                   67889*********************.*************8765544333..............347799*********** PP

                                   -HHHHHHHHTT.SHHHHHHHCCTTT-------HHHHH CS
                         OGG_N  85 dleelykewskkdplfkksadkftGiRllrqdpwEcL 121
                                   dl  ++k+ +k d+++  +++k++G+Rl+rqdpwEcL
  gi|91773114|ref|YP_565806.1|  70 DLPAIFKQINK-DEHMDVAISKYRGLRLIRQDPWECL 105
                                   ******99988.************************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3
                                   TTS-HHHHHHHHTT.SHHHHHHHCC CS
                         OGG_N  82 Ldvdleelykewskkdplfkksadk 106
                                    d+ +e+++k    +dp f+  a+k
  gi|91773114|ref|YP_565806.1| 223 VDTHVEKIVKAYYGNDPYFEGNATK 247
                                   6777888888888888888876655 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.1e-10   3.4e-07      20      91 ..     125     239 ..     106     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.1e-10
                                   HHHHHHS.........HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH......................... CS
                                   xxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                       HhH-GPD  20 rlferfg.........fptpedladadeekLrelirelGfyrrKakyikelArilv......................... 66 
                                    l ++fg         fp++e+la+ ++++L e+    +++  +  +i+++A +++                         
  gi|91773114|ref|YP_565806.1| 125 MLSALFGeelekghysFPKVEALAASSCDDLCEC----KMG-FRTARIIKAANAVIngdivldelfsldygeaknelmkle 200
                                   3444444777888888******************....666.6699*********************************** PP

                                   ...............S-SSS--TTSHHHHHHHHHHTTSSS CS
                                   ...............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ...............gkpdvlivvDvhvrrilkrlrsike 91 
                                                  +k++ +++vD+hv +i+k +++ ++
  gi|91773114|ref|YP_565806.1| 201 gigekvadcillfafAKME-GFPVDTHVEKIVKAYYGNDP 239
                                   *************998887.***************99887 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.5e-08   4.5e-05      12      30 .]     195     213 ..     193     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                                   HHHTSTT-SHHHHHHHHHH CS
                           HHH  12 eLlalPGVGpktAeaIlsy 30 
                                   eL++l+G+G+k+A++Il +
  gi|91773114|ref|YP_565806.1| 195 ELMKLEGIGEKVADCILLF 213
                                   9***************986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1     3e+03      25      40 ..     143     158 ..     135     172 .. 0.69
   2 ?   12.5   0.1   5.7e-05      0.17      26      53 ..     181     212 ..     159     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                                   SHHHHHHS-HHHHHTS CS
                         HHH_5  25 svedlaaadveeLaki 40 
                                    ve+laa + ++L++ 
  gi|91773114|ref|YP_565806.1| 143 KVEALAASSCDDLCEC 158
                                   6888888888888775 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.7e-05
                                   HHHHHHS-....HHHHHTSTTS-HHHHHHHHH CS
                         HHH_5  26 vedlaaad....veeLakipGiGkktAeriil 53 
                                   +++l ++d    ++eL k+ GiG+k A+ i+l
  gi|91773114|ref|YP_565806.1| 181 LDELFSLDygeaKNELMKLEGIGEKVADCILL 212
                                   678877644433789************98887 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.11   3.2e+02      22      40 ..     140     158 ..     138     170 .. 0.86
   2 ?    9.5   0.0   0.00034         1      35      54 ..     194     213 ..     189     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                         HHH_2  22 rFksldaLkkasleeLlev 40 
                                   +F +++aL++ s ++L e 
  gi|91773114|ref|YP_565806.1| 140 SFPKVEALAASSCDDLCEC 158
                                   699************9875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00034
                         HHH_2  35 eeLlevddiGeeiAqsivef 54 
                                   +eL ++++iGe++A+ i  f
  gi|91773114|ref|YP_565806.1| 194 NELMKLEGIGEKVADCILLF 213
                                   79**************9876 PP

>> DUF3669  Zinc finger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-05      0.12       8      34 ..     217     242 ..     191     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                       DUF3669   8 acrkmtleetgiaeavkafwdndpYyP 34 
                                   +++ +  + t ++++vka++ ndpY+ 
  gi|91773114|ref|YP_565806.1| 217 KMEGFPVD-THVEKIVKAYYGNDPYFE 242
                                   44445555.889*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1905.45
//
Query:       gi|91773115|ref|YP_565807.1|  [L=196]
Description: indolepyruvate oxidoreductase subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-36  126.4   0.5    1.4e-36  126.2   0.5    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 !  126.2   0.5   7.9e-41   1.4e-36       1     176 [.      16     192 ..      16     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 7.9e-41
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                   GGqG+++a+ i++k+a+ + y v a++++g+++rGg+++ h+ri+ +   ++i+  +ad l+al++ ++ +++d l ++g+
  gi|91773115|ref|YP_565807.1|  16 GGQGAILASDIIGKSAVLENYGVRAAETHGMAQRGGSVVNHIRIGCD-LGSMIPLKGADCLLALEPVEALRYIDSLADDGV 95 
                                   9**********************************************.89****************9999*********** PP

                                   EEEECTCGTT-CCHHHCTS-HHHHHHH.....T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHHCC CS
                           POR  82 iiynseelkpdelkkakeeerelkerl.....gvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeaikkr 157
                                   +i+n+e + p +++  k e++++++         rv++++at+ a e+g  + a+N+v++Ga++  l ++ e+l+  +k++
  gi|91773115|ref|YP_565807.1|  96 VIMNTEAVYPVTVNTGKAEYPDVESIVaelkkTHRVIAFNATEKAAEAGS-RQAMNVVLVGAVSNFLPIKTETLLNRVKEM 175
                                   *********************999988****99**************888.****************************** PP

                                   S-CH.HHHHHHHHHHHHHH CS
                           POR 158 fpkkkeviekNlkafragy 176
                                   +p k   i+ N+kaf+ g+
  gi|91773115|ref|YP_565807.1| 176 VPPK--TIDTNVKAFEMGR 192
                                   **95..9*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1356.31
//
Query:       gi|91773116|ref|YP_565808.1|  [L=601]
Description: thiamine pyrophosphate enzyme-like TPP-binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-27   96.0   0.3    4.2e-27   94.8   0.3    1.6  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    3.5e-13   49.8   0.0    5.9e-13   49.1   0.0    1.3  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    2.2e-09   36.7  12.5    1.5e-05   24.6   3.3    3.4  3  Fer4          4Fe-4S binding domain
    5.7e-07   29.6  11.3    5.7e-07   29.6  11.3    2.5  2  Fer4_21       4Fe-4S dicluster domain
      1e-05   25.6  12.6    1.4e-05   25.1  11.4    1.9  2  Fer4_9        4Fe-4S dicluster domain
    1.8e-05   24.5  16.5     0.0034   17.4   2.7    3.9  3  Fer4_2        4Fe-4S binding domain
    2.5e-05   24.3  11.0    6.8e-05   22.9  11.0    1.8  1  Fer4_10       4Fe-4S dicluster domain
    0.00024   21.0  18.9      0.014   15.4   3.2    3.2  2  Fer4_6        4Fe-4S binding domain
     0.0014   19.2  12.7     0.0014   19.2  12.7    2.4  2  Fer4_7        4Fe-4S dicluster domain
     0.0042   16.7   0.1      0.072   12.7   0.0    2.6  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
  ------ inclusion threshold ------
      0.042   14.6   1.4      0.042   14.6   1.4    4.0  3  Fer4_15       4Fe-4S single cluster domain
        0.1   12.9   0.1       0.26   11.6   0.1    1.7  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 
       0.11   13.1  10.9         77    3.9  11.0    2.7  1  Fer4_17       4Fe-4S dicluster domain
       0.14   11.7   0.0       0.62    9.7   0.0    2.1  2  WHIM1         WSTF, HB1, Itc1p, MBD9 motif 1
       0.16   13.0  12.0       0.23   12.4   2.4    2.6  3  Fer4_16       4Fe-4S double cluster binding domain
       0.21   12.1  14.2       0.56   10.8   2.1    3.5  3  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
        2.3    9.3  15.2       0.13   13.2   4.0    3.2  2  Fer4_3        4Fe-4S binding domain
        5.9    7.4  14.7    1.7e+03   -0.4  14.7    2.6  1  Fer4_8        4Fe-4S dicluster domain
        6.1    7.6  20.7          2    9.2   3.5    2.9  2  Fer4_4        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.3   4.4e-30   4.2e-27       1     152 [.     386     526 ..     386     527 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 4.4e-30
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                   diGc+tl      ++  ++ +++  ++ +mG ++ +A+G+    +++++ + +GD++f+++ ++ l +av+++++itv +l
  gi|91773116|ref|YP_565808.1| 386 DIGCYTL------GI--QNGTVD--TTLCMGGSITVASGIYHSGEKQPICCSIGDSTFFHTgMNGLLNAVYNKANITVAIL 456
                                   8999999......33..667788..99***************76788********************************** PP

                                   E-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                   +N++++mtg+q++p  g +++g++   +k++d+++l+++lGa+ + +v++ dv+ + ea+k+a + +g+++i 
  gi|91773116|ref|YP_565808.1| 457 DNRITAMTGHQPNPGMGLTSTGET---TKEIDLEQLCRGLGAEfVEVVDSFDVNATVEAFKRAKDYEGTSVII 526
                                   *****************9999988...9***************888************************995 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   6.3e-16   5.9e-13       4     196 ..      18     201 ..      15     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 6.3e-16
                                   HHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHHHH CS
                         POR_N   4 iaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlglaag 84 
                                   +++g +vi++YP TPssei+++l+++ +  +    +v    +E  a+++++GA ++G+r++++    Gl  + + l+  + 
  gi|91773116|ref|YP_565808.1|  18 VEGGGRVISGYPGTPSSEIVDTLSKMKE-RD---FYVEWSVNEKVAMEVAAGAGMTGVRSVVTMKHVGLNVAADPLMTLSY 94 
                                   667779******************9983.33...47888899*****************************9998877655 PP

                                   TT-..-EEEEEEEEE-STTBEEEEE--TTCHHHHS---E.EEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HEE CS
                         POR_N  85 eel..PvvivvvaRalpstglsirtdqsDlmaardtgli.vlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshev 162
                                   + +   +v++v+    +++g    +  +D     ++ l+  l +++ qea d++  Af l+ek+++Pvi +   +++sh  
  gi|91773116|ref|YP_565808.1|  95 MGVkgGMVVIVA----DDPGCHSSQNEQDSRIYSEFSLMpCLDPSTPQEAKDMIPYAFELSEKFELPVI-FRPTTRISHGK 170
                                   544115566555....566666677888888888887663899************************98.56788999*** PP

                                   EEEEC-SGG..GS-----SBXXXXXXXXSXXXBXX CS
                         POR_N 163 ekvelpdee.delklikekleeyerkeyaldpekp 196
                                    ++el +   + ++++ ek    ++ +  + p + 
  gi|91773116|ref|YP_565808.1| 171 ADIELGEITdHRVEAKFEK----DPSRWVMVPSNA 201
                                   ****998772233333333....333333444443 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.4   5.1e+03       3      10 ..     399     406 ..     398     406 .. 0.85
   2 !   16.3   1.0   6.7e-06    0.0063       2      16 ..     546     560 ..     545     561 .. 0.91
   3 !   24.6   3.3   1.6e-08   1.5e-05       7      24 .]     580     597 ..     576     597 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.4
                                   EETTTSSS CS
                          Fer4   3 ideekCig 10 
                                   +d+ +C+g
  gi|91773116|ref|YP_565808.1| 399 VDTTLCMG 406
                                   899***97 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6.7e-06
                                   EEETTTSSS-THHHH CS
                          Fer4   2 videekCigCGaCve 16 
                                   ++d +kC+gC  Cv+
  gi|91773116|ref|YP_565808.1| 546 KVDHDKCVGCRMCVN 560
                                   79***********96 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 1.6e-08
                                   TSSS-THHHHHSTTTEEE CS
                          Fer4   7 kCigCGaCvevCPvgAIt 24 
                                    C+gCG+C+evC ++AI+
  gi|91773116|ref|YP_565808.1| 580 TCTGCGLCAEVCKFDAIK 597
                                   6****************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 !   13.6   2.8   5.8e-05     0.055      33      53 ..     544     565 ..     528     567 .. 0.76
   2 !   29.6  11.3     6e-10   5.7e-07       3      57 ..     547     596 ..     545     598 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-05
                       Fer4_21  33 vlkvvedeCvGCnlCssv.CPv 53 
                                    +kv +d+CvGC +C++  CP 
  gi|91773116|ref|YP_565808.1| 544 PFKVDHDKCVGCRMCVNLgCPA 565
                                   45899**********9865985 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 6e-10
                       Fer4_21   3 idedkCigCgkCli.aCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   +d+dkC+gC  C+   C+     aie+d++++  +++ +C+GC lC++vC   d+i
  gi|91773116|ref|YP_565808.1| 547 VDHDKCVGCRMCVNlGCP-----AIEFDKENKKSTINATCTGCGLCAEVCKF-DAI 596
                                   89**********952688.....9**************************86.776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.8   6.4e+03      35      39 ..     360     364 ..     337     366 .. 0.68
   2 !   25.1  11.4   1.5e-08   1.4e-05       1      51 []     551     596 ..     551     596 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.8
                        Fer4_9  35 aCigC 39 
                                    C gC
  gi|91773116|ref|YP_565808.1| 360 MCAGC 364
                                   46666 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.5e-08
                        Fer4_9   1 kCtgCgaCvea.CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kC+gC+ Cv+  Cpa  + +++++ +++        C+gCg C+e+C+ +ai
  gi|91773116|ref|YP_565808.1| 551 KCVGCRMCVNLgCPAIEFDKENKKSTINA------TCTGCGLCAEVCKFDAI 596
                                   7*******9988**************997......6***********99887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.82   7.7e+02       6      14 ..     357     365 ..     352     367 .. 0.80
   2 !   17.4   2.7   3.6e-06    0.0034       2      22 .]     544     565 ..     543     565 .. 0.92
   3 !   13.7   1.4   5.3e-05      0.05       9      20 ..     580     591 ..     568     593 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.82
                        Fer4_2   6 dtdrCigCg 14 
                                    +++C gC+
  gi|91773116|ref|YP_565808.1| 357 PPAMCAGCS 365
                                   6899****6 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.6e-06
                        Fer4_2   2 pvvvdtdrCigCgaCvsa.CPa 22 
                                   p++vd d+C+gC+ Cv+  CPa
  gi|91773116|ref|YP_565808.1| 544 PFKVDHDKCVGCRMCVNLgCPA 565
                                   6899************999**8 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 5.3e-05
                        Fer4_2   9 rCigCgaCvsaC 20 
                                   +C+gCg C  +C
  gi|91773116|ref|YP_565808.1| 580 TCTGCGLCAEVC 591
                                   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 !   22.9  11.0   7.2e-08   6.8e-05       4      55 ..     547     591 ..     545     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.2e-08
                       Fer4_10   4 idddtCirCgkCvka.CPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   +d d+C++C+ Cv+  CPa       +++++e+++ ++    Ctgcg C+e+C
  gi|91773116|ref|YP_565808.1| 547 VDHDKCVGCRMCVNLgCPA-------IEFDKENKK-STINATCTGCGLCAEVC 591
                                   689***********88***.......666555555.555789*********** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.6   1.8e-05     0.017       3      21 ..     546     565 ..     544     568 .. 0.89
   2 !   15.4   3.2   1.5e-05     0.014       8      24 .]     580     596 ..     577     596 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                        Fer4_6   3 eidpdkCigCgdCvrv.CPe 21 
                                    +d dkC+gC+ Cv+  CP+
  gi|91773116|ref|YP_565808.1| 546 KVDHDKCVGCRMCVNLgCPA 565
                                   699**********9988886 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.5e-05
                        Fer4_6   8 kCigCgdCvrvCPegai 24 
                                    C+gCg C+ vC ++ai
  gi|91773116|ref|YP_565808.1| 580 TCTGCGLCAEVCKFDAI 596
                                   7*************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 ?   -2.4   0.1       8.4   7.9e+03      37      42 ..     360     365 ..     350     405 .. 0.76
   2 !   19.2  12.7   1.5e-06    0.0014       1      52 []     551     595 ..     551     595 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.4
                        Fer4_7  37 kClgCg 42 
                                   +C gC 
  gi|91773116|ref|YP_565808.1| 360 MCAGCS 365
                                   566663 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.5e-06
                        Fer4_7   1 rCigCgaCvaa.CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C+gC+ Cv+  Cp  aie+d+e+++++         +C+gCg C++vC ++a
  gi|91773116|ref|YP_565808.1| 551 KCVGCRMCVNLgCP--AIEFDKENKKST------INATCTGCGLCAEVCKFDA 595
                                   7********977**..9***99854433......5689***********9987 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   7.6e-05     0.072       6     106 ..      12     114 ..       7     161 .. 0.65
   2 ?   -1.1   0.0       1.3   1.3e+03      51      95 ..     239     284 ..     237     289 .. 0.82
   3 ?    0.1   0.0      0.56   5.3e+02      79     147 ..     437     516 ..     406     527 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                                   HHHHHHHHCT--EEEE---CCCHHHHCCHHCT...TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH.HHCHHHH CS
                  TPP_enzyme_N   6 alvraLkalgvehvfgvpGsrilplldalseeq..girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa.tnaltal 83 
                                   a++r + + g +++ g+pG+ + +++d ls+ +  ++ v  +++E +a+  A g  +   + +v + ++g ++ +  l+ l
  gi|91773116|ref|YP_565808.1|  12 AIARGIVEGGGRVISGYPGTPSSEIVDTLSKMKerDFYVEWSVNEKVAMEVAAGAGMTGVRSVVTMKHVGLNVaADPLMTL 92 
                                   788888899999*******************99777777779************977766666666666764403344444 PP

                                   HHHHHHT--EEEEEEE--CCCHH CS
                  TPP_enzyme_N  84 aeAkvdriPllvlsgdrptslrg 106
                                       v +  ++v+++d p  + +
  gi|91773116|ref|YP_565808.1|  93 SYMGVKG-GMVVIVADDPGCHSS 114
                                   3333333.355555555544444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHH.TS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEE CS
                  TPP_enzyme_N  51 aafaAdgyarat.gkpgvvlvtsgpGatnaltalaeAkvdriPllv 95 
                                   aa++A+ ya+    ++gv +    +Ga  +  +l+  +++++  ++
  gi|91773116|ref|YP_565808.1| 239 AAGIASVYAKEAiDNLGVSASYLKIGAYPVPEGLIKRMYEQVDTVL 284
                                   8999*****9555999999999999999888888888888887665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.56
                                   CHHHHHHHHHHT--EEEEEEE--CCCHH............S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                  TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrg............qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirta 147
                                   ++++l +A +++  + v   d+  +               +g + +e+d ++l+r +  ++++v ++ ++  ++ +A++ a
  gi|91773116|ref|YP_565808.1| 437 GMNGLLNAVYNKANITVAILDNRITAMTghqpnpgmgltsTGETTKEIDLEQLCRGLGAEFVEVVDSFDVNATV-EAFKRA 516
                                   44444444444444433222222222222444444448887777779999999999998888888877765555.455555 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 ?   -0.3   0.0       1.9   1.8e+03      13      33 ..     328     347 ..     326     356 .. 0.81
   2 ?   14.6   1.4   4.4e-05     0.042       2      33 ..     546     577 ..     545     580 .. 0.86
   3 ?    5.5   3.9      0.03        28       7      19 ..     580     592 ..     578     598 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.9
                       Fer4_15  13 lCvaeapevfeldedglasvl 33 
                                    Cv++  +vf+++  gl++++
  gi|91773116|ref|YP_565808.1| 328 HCVKAIADVFKIE-SGLPVIK 347
                                   6**********99.8888655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.4e-05
                       Fer4_15   2 vvDrdaCigcglCvaeapevfeldedglasvl 33 
                                   +vD+d+C gc +Cv +    +e+d++ ++s++
  gi|91773116|ref|YP_565808.1| 546 KVDHDKCVGCRMCVNLGCPAIEFDKENKKSTI 577
                                   79*************977799**998887654 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.03
                       Fer4_15   7 aCigcglCvaeap 19 
                                   +C+gcglC+++++
  gi|91773116|ref|YP_565808.1| 580 TCTGCGLCAEVCK 592
                                   8*********995 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 ?   11.6   0.1   0.00027      0.26       4      99 ..     236     321 ..     233     324 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                                   EEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGGTSE CS
                       PFOR_II   4 vivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkkskvk 84 
                                    ++a G+++  ak+a+d+l   g+++ +l++ + +P Pe  +k++ ++v+ v+v++         ++ve+  + + k   +
  gi|91773116|ref|YP_565808.1| 236 GVIAAGIASVYAKEAIDNL---GVSASYLKIGA-YPVPEGLIKRMYEQVDTVLVIEELE------PIVEDRCKIIAKDMES 306
                                   6899*************87...8899****987.6********************9876......5666665555555566 PP

                                   EEEEE--GGG----H CS
                       PFOR_II  85 vvnfvaglgGrditv 99 
                                    ++++++  G +++v
  gi|91773116|ref|YP_565808.1| 307 SIKIIGKTDGTVPRV 321
                                   677777777776665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  11.0     0.081        77       2      57 ..     552     592 ..     551     596 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.081
                       Fer4_17   2 CiqCgyClp.eCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                   C +C++C++  Cp  e  ++++k++++a                +C++Cg+C+++C 
  gi|91773116|ref|YP_565808.1| 552 CVGCRMCVNlGCPAIEFDKENKKSTINA----------------TCTGCGLCAEVCK 592
                                   8888888876688888777777777776................6999999999995 PP

>> WHIM1  WSTF, HB1, Itc1p, MBD9 motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00065      0.62       9      30 ..      38      63 ..      31      63 .. 0.73
   2 ?   -2.7   0.0         5   4.7e+03      16      27 ..     321     332 ..     317     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00065
                                  CCCCC.ST...CCCS-HHHHHHHHHH CS
                         WHIM1  9 deLak.gg...YyeLspeeklkiLki 30
                                  d+L+k ++   Y+e+s++ek++++++
  gi|91773116|ref|YP_565808.1| 38 DTLSKmKErdfYVEWSVNEKVAMEVA 63
                                  55555344559************975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5
                                   CCCS-HHHHHHH CS
                         WHIM1  16 YyeLspeeklki 27 
                                   ++eL++++++k+
  gi|91773116|ref|YP_565808.1| 321 VGELNVDHCVKA 332
                                   689******986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.2     0.084        79      43      65 ..     542     564 ..     520     566 .. 0.69
   2 ?   12.4   2.4   0.00024      0.23      42      66 ..     569     593 ..     565     594 .. 0.81
   3 ?   11.8   2.5   0.00037      0.35       1      19 [.     580     598 ..     578     600 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.084
                       Fer4_16  43 edeekckkqeaitgCdiCqdv.CP 65 
                                    + +k + + ++ gC++C++  CP
  gi|91773116|ref|YP_565808.1| 542 LTPFKVD-HDKCVGCRMCVNLgCP 564
                                   5555555.78899*****985476 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00024
                       Fer4_16  42 aedeekckkqeaitgCdiCqdvCPa 66 
                                    ++++k +++  +tgC+ C++vC +
  gi|91773116|ref|YP_565808.1| 569 DKENKKSTINATCTGCGLCAEVCKF 593
                                   5667777788999**********76 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00037
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C++Cg CaevC  +aike
  gi|91773116|ref|YP_565808.1| 580 TCTGCGLCAEVCKFDAIKE 598
                                   5999999999999999986 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 ?   -0.3   0.0       1.7   1.6e+03      10      23 ..     327     340 ..     325     346 .. 0.87
   2 ?   10.8   2.1   0.00059      0.56       1      31 [.     547     577 ..     547     579 .. 0.77
   3 ?    5.2   4.1     0.033        31       2      16 ..     578     591 ..     577     593 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                       Fer4_13  10 gaCvelaPdvFeed 23 
                                   + Cv++  dvF+++
  gi|91773116|ref|YP_565808.1| 327 DHCVKAIADVFKIE 340
                                   68*********987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00059
                       Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvv 31 
                                   VD d+C++c  Cv+l     e d+e ++s +
  gi|91773116|ref|YP_565808.1| 547 VDHDKCVGCRMCVNLGCPAIEFDKENKKSTI 577
                                   9*************95555566666666655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.033
                       Fer4_13   2 DrdtCiacgaCvela 16 
                                   +  tC++cg+C+e++
  gi|91773116|ref|YP_565808.1| 578 N-ATCTGCGLCAEVC 591
                                   5.89*********99 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   3.5       1.9   1.8e+03       1       9 [.     552     560 ..     552     561 .. 0.90
   2 ?   13.2   4.0   0.00014      0.13       1      15 []     581     595 ..     581     595 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.9
                        Fer4_3   1 CtgCgaCve 9  
                                   C+gC+ Cv+
  gi|91773116|ref|YP_565808.1| 552 CVGCRMCVN 560
                                   ****99*95 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00014
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   CtgCg+C evC  +A
  gi|91773116|ref|YP_565808.1| 581 CTGCGLCAEVCKFDA 595
                                   ***********8877 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4  14.7       1.8   1.7e+03       4      62 ..     551     592 ..     548     595 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                        Fer4_8   4 kCieCgaCqsa.CpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                   kC++C +C +  Cp+++  k+    ++                ++  +Ct+cg C+evC+
  gi|91773116|ref|YP_565808.1| 551 KCVGCRMCVNLgCPAIEFDKEN---KK---------------STINATCTGCGLCAEVCK 592
                                   6666666664336644332111...11...............123468**********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 ?    9.2   3.5    0.0021         2       2      15 ..     550     564 ..     549     569 .. 0.90
   2 ?    8.9   3.5    0.0025       2.4       3      16 ..     580     593 ..     570     594 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                        Fer4_4   2 erCigCgsCvaa.CP 15 
                                   ++C+gC+ Cv+  CP
  gi|91773116|ref|YP_565808.1| 550 DKCVGCRMCVNLgCP 564
                                   89********98887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +C+gCg C  +C++
  gi|91773116|ref|YP_565808.1| 580 TCTGCGLCAEVCKF 593
                                   6***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 3374.50
//
Query:       gi|91773117|ref|YP_565809.1|  [L=645]
Description: hydantoinase/oxoprolinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  117.2   7.3    1.2e-33  116.6   2.5    2.9  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    3.4e-30  105.0   4.1    2.8e-27   95.6   0.2    3.2  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
      7e-09   34.8   1.3    0.00046   18.9   0.3    2.3  2  MutL            MutL protein
    0.00021   20.9   1.4       0.13   11.7   0.0    3.5  4  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.013   14.7   0.1      0.033   13.4   0.1    1.6  1  StbA            StbA protein
      0.018   14.5   0.3      0.036   13.5   0.0    1.7  2  ROK             ROK family
       0.53   10.3   2.1        1.2    9.2   0.3    2.2  2  LisH            LisH


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 ?    0.2   0.2      0.15   3.7e+02      82      99 ..       5      22 ..       2      37 .. 0.80
   2 !  116.6   2.5   4.7e-37   1.2e-33       1     289 [.     185     552 ..     185     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.15
                Hydantoinase_A 82 ItfDmGGTstDvslikdg 99
                                  +++D GGT tD+  +++ 
  gi|91773117|ref|YP_565809.1|  5 LGIDAGGTYTDAVIVRED 22
                                  689*********999854 PP

  == domain 2  score: 116.6 bits;  conditional E-value: 4.7e-37
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   r++ta+++A l pi  ++++ v +++e rg+ a++m++++dG++v + ea k+p+e +  GPaa++vga++   l + k++
  gi|91773117|ref|YP_565809.1| 185 RGVTAYIDAQLVPISTKFMNAVVSEIERRGIDAKIMMLKCDGSVVGIVEALKHPIESVFTGPAASLVGASY---LSKMKDC 262
                                   89*********************************************************************...888999* PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpesa.....gadpgpacy 156
                                   I++D+GGTstDv+ + dg +e++ e  + +g k++++a++++t ++gG+s ++  ++g+++vgp+ +      a   pa +
  gi|91773117|ref|YP_565809.1| 263 IVIDVGGTSTDVAKVTDGIPEITDEGAVvGGWKTKVKAIRMETSAMGGDSHIW-IKNGRISVGPRRVipicmAATKWPAIK 342
                                   *************************98879**********************5.566999999985422221566666555 PP

                Hydantoinase_A 157 rkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarraf.eelakelnlk........................... 209
                                   +k   +  +     +++ +qp +f     g+  ++ +++++++ + +++e                               
  gi|91773117|ref|YP_565809.1| 343 EKLK-RTSIPSKIQLCENIQPTKFY-VRAGHKTDRMSKTEKKLfDRIGDEPTSIneiftdglpssvfldllikkkivhaig 421
                                   5555.44444444557788888777.3444444444444444447777765444677777777777777777777777777 PP

                Hydantoinase_A 210 ...............................................veevAegilsvavenman.avrklsvergldpke 242
                                                                                   e++A+ ++s +  ++   +++k+++++   +++
  gi|91773117|ref|YP_565809.1| 422 ftptdalhvlgdytewdceasriaagilskmthsdhttfceeiknvfGENMAAYVMSYLLREIDHvHIKKIIENKDQYITK 502
                                   777777777777777777777777777777777775555555555557777777777777777542677778888777777 PP

                Hydantoinase_A 243 lt....lvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvre 289
                                   +     +v  GG+ +  +  + ++++  ++i p+ya+v +a+G+ + +v++
  gi|91773117|ref|YP_565809.1| 503 FKvgvpVVLLGGPVQAYVDNIRDAIDA-EIILPEYAEVGNAVGAIVGKVTK 552
                                   762333578999999999999999997.57888888999999999988876 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 !   95.6   0.2   1.1e-30   2.8e-27       2     177 ..       5     165 ..       4     166 .. 0.93
   2 !    8.6   0.6   0.00055       1.4       2      18 ..     263     279 ..     262     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 1.1e-30
                    Hydant_A_N   2 igIDvGGTfTDavaldeke.eevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg..... 76 
                                   +gID+GGT+TDav+++e++ +++ ++K ++t  ++  gi +al+++  +     ++++ + ++TT+atNa+le++      
  gi|91773117|ref|YP_565809.1|   5 LGIDAGGTYTDAVIVREDDgKVIDSTKSPTTYPDPLPGIQNALDSLNPSY---LNNVSKISVSTTLATNAVLENTVserss 82 
                                   69**************99988999*********************96553...67*******************9999999 PP

                    Hydant_A_N  77 .ervaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavv 156
                                      vaLi++    d+++  +++ p+                + v+++++ +g ++ +ld +++r  + + k++ v ++av+
  gi|91773117|ref|YP_565809.1|  83 gHDVALIMIG---DVIKPTDSKIPYT---------------INVQGGHSSNGMEIHSLDTKNIRDFILETKDK-VAAFAVS 144
                                   99*****975...7888888877777...............89****************************99.******* PP

                    Hydant_A_N 157 llhSylnpehElrvaeiarei 177
                                   + +S +np+hEl+ +ei++e+
  gi|91773117|ref|YP_565809.1| 145 SHFSIRNPDHELKTKEIIEEM 165
                                   ******************997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00055
                    Hydant_A_N   2 igIDvGGTfTDavalde 18 
                                   i IDvGGT TD+  +++
  gi|91773117|ref|YP_565809.1| 263 IVIDVGGTSTDVAKVTD 279
                                   79*********998874 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.9e-06      0.01       3      56 ..       6      55 ..       5      92 .. 0.85
   2 !   18.9   0.3   1.8e-07   0.00046     224     272 ..     242     285 ..     228     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
                          MutL  3 viDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklg 56
                                   iD G t+T +++v++++  ++++ ++++pTt    d l G+++al++l+ +  
  gi|91773117|ref|YP_565809.1|  6 GIDAGGTYTDAVIVREDD--GKVIDSTKSPTTYP--DPLPGIQNALDSLNPSYL 55
                                  58**************88..*************5..99*********9987754 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.8e-07
                          MutL 224 impTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspeke 272
                                   + + PaA l +++ l++     + d++v+DvGG++Tdv  v++g pe++
  gi|91773117|ref|YP_565809.1| 242 VFTGPAASLVGASYLSK-----MKDCIVIDVGGTSTDVAKVTDGIPEIT 285
                                   567899*********99.....459******************999876 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 !   11.7   0.0   5.2e-05      0.13       1      29 [.       5      34 ..       5     149 .. 0.82
   2 !    5.9   0.0    0.0031         8       3      67 ..     265     398 ..     263     457 .. 0.77
   3 ?   -0.8   0.0      0.33   8.5e+02     202     264 ..     492     546 ..     470     548 .. 0.67
   4 ?   -2.4   0.0         1   2.6e+03      57      91 ..     587     622 ..     583     637 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                                  EEEEE-SSEEEEEEEE.TTTEEEEEEEE-- CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmd.ekgevlgrgitns 29
                                  +GiD G+T t av+++ ++g+v+  +++ +
  gi|91773117|ref|YP_565809.1|  5 LGIDAGGTYTDAVIVReDDGKVIDSTKSPT 34
                                  8************99835667988777655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0031
                                   EEE-SSEEEEEEEE.......TTTEEEEEEEE--............................................... CS
                   BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitns............................................... 29 
                                   iD+G+T+t ++ ++       ++g v+g ++t+                                                
  gi|91773117|ref|YP_565809.1| 265 IDVGGTSTDVAKVTdgipeitDEGAVVGGWKTKVkairmetsamggdshiwikngrisvgprrvipicmaatkwpaikekl 345
                                   9*******9887777999999999999999999988888888888888888888888888888888888888888888888 PP

                                   .................TTS-HHH.........HHHHHHHHHHT--GGGECEE.. CS
                   BcrAD_BadFG  30 .................anlesvrfeaaekvleealtealerageeeadieetyl 67 
                                                    +++  vr   + + +++  +++++r g e+++i+e+ +
  gi|91773117|ref|YP_565809.1| 346 krtsipskiqlceniqpTKFY-VRAGHKTDRMSKTEKKLFDRIGDEPTSINEI-F 398
                                   888888888888666654444.5566777778888888888888888888877.3 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.33
                                   HHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHH CS
                   BcrAD_BadFG 202 ialrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAa 264
                                   i+++  ++i +++   + v+l GG  ++  +v ++r+ ++ ++       + ++++  a+GA+
  gi|91773117|ref|YP_565809.1| 492 IIENKDQYITKFKVGVP-VVLLGGPVQA--YVDNIRDAIDAEII-----LPEYAEVGNAVGAI 546
                                   44444444555444433.9999999888..88888777766654.....46677777777775 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1
                                   --GGGECEE..EEESTTCCCTCTTBSEEE-.....HHH CS
                   BcrAD_BadFG  57 eeeadieetylvgtgyGratlpekfekeiirs...eil 91 
                                   +eeadie   lv+++++ ++l+  +e++ i+    +i 
  gi|91773117|ref|YP_565809.1| 587 LEEADIEGNRLVMEYLNNSGLQ--IEDHKIEVikqDIK 622
                                   5789999999999999999999..77666654433554 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.3e-05     0.033     150     188 ..     246     285 ..     209     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                          StbA 150 Pagfealke.ldeleslLiiDlGGttLDvakvrgklegis 188
                                   Pa+  + ++ l+++   ++iD+GGt  Dvakv+  + +i+
  gi|91773117|ref|YP_565809.1| 246 PAASLVGASyLSKMKDCIVIDVGGTSTDVAKVTDGIPEIT 285
                                   666666666699********************99888877 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.4e-05     0.036       2      56 ..       5      60 ..       4      83 .. 0.82
   2 ?   -3.9   0.3         3   7.6e+03       2      16 ..     263     277 ..     262     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                                  EEEEE-SSEEEE.EEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTE CS
                           ROK  2 igidiGgtkial.alvdeegeilarekvetptetteetlvdaiaelvdeaerkade 56
                                  +gid+Ggt++ + ++++++g++ ++ k +t+ +++ +++++a+++l  ++ +++ +
  gi|91773117|ref|YP_565809.1|  5 LGIDAGGTYTDAvIVREDDGKVIDSTKSPTTYPDPLPGIQNALDSLNPSYLNNVSK 60
                                  69*******9761566779*************************999888776653 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                                   EEEEE-SSEEEEEEE CS
                           ROK   2 igidiGgtkialalv 16 
                                   i id+Ggt + +a v
  gi|91773117|ref|YP_565809.1| 263 IVIDVGGTSTDVAKV 277
                                   779*****9998865 PP

>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.35     9e+02       5      13 ..     474     482 ..     470     483 .. 0.83
   2 ?    9.2   0.3   0.00048       1.2       4      17 ..     595     608 ..     595     608 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.35
                                   HHHHHHHHH CS
                          LisH   5 rLIydYLvk 13 
                                   ++++ YL+ 
  gi|91773117|ref|YP_565809.1| 474 AYVMSYLLR 482
                                   79*****86 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00048
                                   HHHHHHHHHHCT-H CS
                          LisH   4 NrLIydYLvkeGye 17 
                                   NrL+++YL ++G++
  gi|91773117|ref|YP_565809.1| 595 NRLVMEYLNNSGLQ 608
                                   9***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 3533.42
//
Query:       gi|91773118|ref|YP_565810.1|  [L=152]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-24   85.2   0.0    4.3e-24   85.1   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    7.2e-05   22.9   0.0     0.0001   22.4   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
       0.11   12.1   0.1       0.45   10.1   0.1    1.8  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
       0.17   11.6   0.0       0.55    9.9   0.0    1.8  1  FMN_bind_2      Putative FMN-binding domain


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 !   85.1   0.0   9.7e-28   4.3e-24       2     140 ..       8     145 ..       7     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 9.7e-28
                                   HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SE.GG.EEEE CS
                  Pyridox_ox_2   2 reeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlars.fn.slny 79 
                                   +++++++L +++++rl++  +++p+i+P+++++ ++++y+h+++++ +++++++++ vc++v    +  ++ +  +  ++y
  gi|91773118|ref|YP_565810.1|   8 NKALEDILLDAQYLRLGLCSNEKPYIVPISFGYKDNTIYLHSSRKGTKINLIKQNKnVCFEVDTFYETLPSDEpCSyYMKY 88 
                                   6778999**********************************************6666****************9999999* PP

                                   EEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEEEE CS
                  Pyridox_ox_2  80 rSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieevsgr 140
                                   +SVv +G+a+ ++de+e +e l+ +++++ ++++      ++ ++k  +v+r++i+++ gr
  gi|91773118|ref|YP_565810.1|  89 QSVVGYGTATILEDEKEIKEGLKIIIDRYHNKEYS----IDDLDVKGVAVIRIDIDDLHGR 145
                                   *****************************887755....356789999**********999 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.3e-08    0.0001       4      87 ..      10     103 ..       7     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.3e-08
                                   HHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.............G CS
                Putative_PNPOx   4 elreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.............l 71 
                                   +l+++l ++++ +l+ ++ +  P+++p+++ + d +  i+++++++  k   +++n +v++ ++ +              +
  gi|91773118|ref|YP_565810.1|  10 ALEDILLDAQYLRLGLCSNEK-PYIVPISFGYKDNT--IYLHSSRKGTKINLIKQNKNVCFEVDTFYetlpsdepcsyymK 87 
                                   67888999999******5555.*************9..***************************999999999****999 PP

                                   SEEEEEEEEEEEESCH CS
                Putative_PNPOx  72 grgvrieGtaelvsdg 87 
                                   +++v  +Gta++++d+
  gi|91773118|ref|YP_565810.1|  88 YQSVVGYGTATILEDE 103
                                   999999*****99997 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 ?   10.1   0.1    0.0001      0.45      39     105 ..      41     120 ..       9     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                 Pyrid_ox_like  39 edgdlwfltkkdsdkvkeirkdsqvnlaf........sdeskkkyv...sv..sGtaevvedrakieelWspvvkawfpe 105
                                   +d++++  ++++  k++ i+++++v++ +        sde  ++y+   sv  +Gta++ ed++ i+e  + +++ + ++
  gi|91773118|ref|YP_565810.1|  41 KDNTIYLHSSRKGTKINLIKQNKNVCFEVdtfyetlpSDEPCSYYMkyqSVvgYGTATILEDEKEIKEGLKIIIDRYHNK 120
                                   6899******************9998754222222223444455541114434689999999999999888888877765 PP

>> FMN_bind_2  Putative FMN-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00012      0.55     103     142 ..      86     122 ..       4     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                                   EEEEEEEEEEEEEE---HHHHHHHHHHHHHHHS---...- CS
                    FMN_bind_2 103 WnYaaVhvyGkakviedeeelrkqledltdqaEaerkkpw 142
                                    +Y++V  yG+a+++ede+e+++ l+ ++d++ +   k++
  gi|91773118|ref|YP_565810.1|  86 MKYQSVVGYGTATILEDEKEIKEGLKIIIDRYHN---KEY 122
                                   5799**********************99999987...233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1077.78
//
Query:       gi|91773119|ref|YP_565811.1|  [L=70]
Description: hypothetical protein Mbur_1136 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 489.44
//
Query:       gi|91773120|ref|YP_565812.1|  [L=629]
Description: acetyl-coenzyme A synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-95  318.1   0.1    8.5e-95  317.8   0.1    1.1  1  AMP-binding    AMP-binding enzyme
    7.1e-26   91.0   0.1    1.8e-25   89.7   0.0    1.7  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.7e-19   68.4   7.1    8.7e-19   67.2   7.1    1.7  1  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 !  317.8   0.1   1.4e-98   8.5e-95       6     422 ..      89     519 ..      83     520 .. 0.86

  Alignments for each domain:
  == domain 1  score: 317.8 bits;  conditional E-value: 1.4e-98
                                   HHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                   AMP-binding   6 aktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                   + +++kva+++   +ge q +TYr+l++ v r+++gL+slGv+kgd+V i++p+ pe +va+la++++Ga+++++  +++a
  gi|91773120|ref|YP_565812.1|  89 NGRRNKVAMIWvgdNGEEQVITYRQLYRDVMRFSNGLKSLGVGKGDTVCIYMPQVPEQIVAMLACARIGAIHSVVFGGFGA 169
                                   66789*********999**************************************************************** PP

                                   HHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS......-T CS
                   AMP-binding  84 eelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae......kp 150
                                   ++l+  ++d++akv+i       +  ++++  + ++ea  +   v++++vl +  ++ e  +++e + +   e      k+
  gi|91773120|ref|YP_565812.1| 170 KALHSRIKDAQAKVVItadasirR-GKRIDlKSLVDEAVVNASCVEKIVVLRRMTPQIELFSEIEVDFY---EimedveKE 246
                                   ****************87765531.23344333444444444555555555555544444444444433...134467789 PP

                                   SCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                   AMP-binding 151 eeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGat 230
                                   +e+e  +++d+++i+YTSGTTG  KG++++  +++v ++++   ++  +lk++dv++++++  +i+g+++ ++++l+ Gat
  gi|91773120|ref|YP_565812.1| 247 CEPEIMDSEDPLFILYTSGTTGPAKGIVHTCgGYMVGTYYTT--KNVLDLKDNDVLWCTADPGWITGHSYIVYGPLSMGAT 325
                                   9999***************************88888888885..45577889***************************** PP

                                   EEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC. CS
                   AMP-binding 231 vvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge. 309
                                   + +++++++ +dp++++ +ie++ v+v++++P++++++++ g++     +++lsslr++ ++gepl+pe+ ++++++ g+ 
  gi|91773120|ref|YP_565812.1| 326 ILISETTPDyPDPGVWWSMIEEFDVSVFYTAPTAVRMFMRMGEEW--PGKYNLSSLRILGSVGEPLNPEAFKWYYRVIGKe 404
                                   *********888****************************76554..34558**************************99* PP

                                   ..EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-HHHHH CS
                   AMP-binding 310 ..evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkpeata 386
                                     +vl+++++TEt++++ + +  ++  k+g +G+p+pgv v +vDe+ g pvp g+ G l++++p  ++m+  ++++e+ +
  gi|91773120|ref|YP_565812.1| 405 kcPVLDTWWQTETGMHMLT-TAVGEPMKPGFTGRPVPGVVVDVVDEN-GDPVPAGTGGFLVIKQPwpSMMRTVYGNDERYR 483
                                   *****************73.445555689*****************9.****************9778************9 PP

                                   HHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 387 eafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                   + ++   ++++  GDl++ dedGy+ i gR++d++++
  gi|91773120|ref|YP_565812.1| 484 QYWT-TiKNYYSAGDLAVKDEDGYIMIQGRADDVLIV 519
                                   9998.4456*************************987 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 ?   -3.5   0.1         3   1.8e+04      45      66 ..     198     219 ..     182     223 .. 0.65
   2 !   89.7   0.0   2.9e-29   1.8e-25       1      76 []     528     606 ..     528     606 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                                   HHHHHHHHHT-TTTS-SEEEE- CS
                 AMP-binding_C  45 eLkahvrkelgpyavpkkvvfv 66 
                                   +Lk+ v +++    + +k+v++
  gi|91773120|ref|YP_565812.1| 198 DLKSLVDEAVVNASCVEKIVVL 219
                                   6666666666666666666655 PP

  == domain 2  score: 89.7 bits;  conditional E-value: 2.9e-29
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea.leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evEsalvsh+aVaeaaV+G+pd++kG  ++afV+l+ g  s++ l+ +L  hvr +lgp+a p++++fvd+lpktrsGK
  gi|91773120|ref|YP_565812.1| 528 EVESALVSHEAVAEAAVIGKPDPLKGDSIKAFVILRMGfnSSDkLKLDLLYHVRMNLGPIAMPSEIEFVDSLPKTRSGK 606
                                   8**********************************888743335**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   7.1   1.5e-22   8.7e-19       1      55 []      29      82 ..      29      82 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.5e-22
                                  HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                        ACAS_N  1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                  y+++y eS++dpe+ W+++a+el+W++++dkv+++ ++p++kWF+++k+Ni++Nc
  gi|91773120|ref|YP_565812.1| 29 YEKVYSESLKDPEKHWENVAEELEWFEKWDKVMEW-DHPYAKWFTNAKMNITHNC 82
                                  99*********************************.******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 4435.24
//
Query:       gi|91773121|ref|YP_565813.1|  [L=49]
Description: hypothetical protein Mbur_1138 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 337.45
//
Query:       gi|91773122|ref|YP_565814.1|  [L=219]
Description: hypothetical protein Mbur_1139 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.081   12.5   1.2       0.25   10.9   1.2    1.9  1  ArsR          ArsR transcriptional regulator
       0.15   11.9   0.1       0.34   10.8   0.0    1.6  2  Rho_RNA_bind  Rho termination factor, RNA-binding domain


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.2   2.8e-05      0.25      68      96 ..     102     130 ..      44     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.8e-05
                          ArsR  68 ekpekeYhtsYskvqanfqcsledlsdii 96 
                                   +k + +Y ++Y+k++++fq+ l+ l+di+
  gi|91773122|ref|YP_565814.1| 102 KKKNSNYISYYTKFKISFQIFLSYLADIL 130
                                   567789*********************98 PP

>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.3   1.2e+04      33      41 ..      11      19 ..       8      23 .. 0.74
   2 ?   10.8   0.0   3.8e-05      0.34      12      42 ..      68      98 ..      62     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.3
                                  CCCCTT--T CS
                  Rho_RNA_bind 33 qirkfgLrt 41
                                  +irk +L+ 
  gi|91773122|ref|YP_565814.1| 11 TIRKENLKD 19
                                  688888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.8e-05
                                  -EEEE-GTT---TT-EEE-CCCCCCTT--TT CS
                  Rho_RNA_bind 12 ygFlRtsnylpgpedvYVsasqirkfgLrtG 42
                                   gF  t++y++ ++ +YV+a+ i + +L++ 
  gi|91773122|ref|YP_565814.1| 68 SGFWLTKGYMQDSNWAYVQAKRIERERLKNE 98
                                  589999**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1615.23
//
Query:       gi|91773123|ref|YP_565815.1|  [L=115]
Description: hypothetical protein Mbur_1140 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.1   0.0    0.00027   20.7   0.0    1.1  1  MarR_2          MarR family
     0.0008   19.3   0.0     0.0015   18.5   0.0    1.6  1  HTH_36          Helix-turn-helix domain
     0.0013   18.6   0.1     0.0021   17.9   0.1    1.4  1  MarR            MarR family
     0.0022   17.9   0.0     0.0031   17.4   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0052   16.9   0.0     0.0087   16.2   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.019   14.7   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
      0.016   15.4   0.0      0.027   14.7   0.0    1.4  1  Rio2_N          Rio2, N-terminal
      0.034   13.6   0.7       0.41   10.1   0.7    2.1  1  SieB            Super-infection exclusion protein B
      0.051   13.1   0.0       0.13   11.9   0.0    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding


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 !   20.7   0.0   1.4e-07   0.00027       2      59 ..      20      77 ..      19      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.4e-07
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                   lt+a+  vL +   +p++      +a ++ l+ s+v+r +k+L ++  ++r+ +  D
  gi|91773123|ref|YP_565815.1| 20 NLTRADMKVLEYFFEEPDNWSKTERIATHMELDLSTVQRSVKKLHEKKILTRSQNNLD 77
                                  689999999999999999988999****************************988666 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.5e-07    0.0015      27      54 ..      41      68 ..      19      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.5e-07
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                    e++a++++l+ +Tv+r +k+L ++ +
  gi|91773123|ref|YP_565815.1| 41 KTERIATHMELDLSTVQRSVKKLHEKKI 68
                                  689*********************9976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.1e-06    0.0021      21      55 ..      43      77 ..      21      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTS CS
                          MarR 21 seLakklgvskstvtrvldrLekkGlieRskspeD 55
                                    +a +++++ stv r +++L +k  ++Rs++  D
  gi|91773123|ref|YP_565815.1| 43 ERIATHMELDLSTVQRSVKKLHEKKILTRSQNNLD 77
                                  479****************************9766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-06    0.0031       3      62 ..      18      85 ..      15      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                  HCHHHHHCCCHCHHHHHHCC..CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEE CS
                          TrmB  3 klGLseyEakvYlaLlklgp..atadeiaeelgvprskvYevLrsLedkGlVerekgr......pklY 62
                                  +l+L+  ++kv  +  ++    ++++ ia + +++ s+v++++++L +k + +r++ +        +Y
  gi|91773123|ref|YP_565815.1| 18 ALNLTRADMKVLEYFFEEPDnwSKTERIATHMELDLSTVQRSVKKLHEKKILTRSQNNldgggySFIY 85
                                  6899999999999999655423899************************9999999886666643355 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 !   16.2   0.0   4.4e-06    0.0087      18      49 ..      35      66 ..      27      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
                                  HHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHT CS
                Fe_dep_repress 18 eekkvvktkdlaerLnvspssVsemlkkLekd 49
                                  e  +  kt ++a  ++   s+V+ ++kkL+++
  gi|91773123|ref|YP_565815.1| 35 EPDNWSKTERIATHMELDLSTVQRSVKKLHEK 66
                                  55667799*********************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   9.7e-06     0.019       6      50 ..      26      71 ..      21      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.7e-06
                                  HHHHCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  6 laiLdalaeapqel.tlselArrtglpkStvhRlLqtLvelGyveq 50
                                  + +L+++ e+p  + +   +A +  l  Stv R ++ L+e +++++
  gi|91773123|ref|YP_565815.1| 26 MKVLEYFFEEPDNWsKTERIATHMELDLSTVQRSVKKLHEKKILTR 71
                                  579**********988899***********************9987 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-05     0.027      23      68 ..      38      85 ..      19      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                        Rio2_N 23 evVptelieeisrlkeeevkkrlsrllkaklisrktakydG..YkLty 68
                                  ++  te+i++  +l+ + v++++++l+++k++ r++ + dG  Y  +y
  gi|91773123|ref|YP_565815.1| 38 NWSKTERIATHMELDLSTVQRSVKKLHEKKILTRSQNNLDGggYSFIY 85
                                  5677899***************************88888752266665 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7   0.00021      0.41      67     136 ..      10      88 ..       1     113 [. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                          SieB  67 eqkkvekklknLteeekavLreflnqgksv...........ltlplndpavkeLlekgiltkasn.........vsniaik 127
                                   ++k v+k   nLt++  +vL  f++++ +            l l+  +  vk+L ek+ilt+++n         +      
  gi|91773123|ref|YP_565815.1|  10 KIKDVIKCALNLTRADMKVLEYFFEEPDNWskteriathmeLDLSTVQRSVKKLHEKKILTRSQNnldgggysfI------ 84 
                                   577888888899999999999999988654111111111112233445578999999999999995444444332...... PP

                          SieB 128 ettakykiq 136
                                        yki+
  gi|91773123|ref|YP_565815.1|  85 -----YKIN 88 
                                   .....3333 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.4e-05      0.13       5      47 ..      25      69 ..      21      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                        HTH_24  5 drkILelLqknpr..isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  d k+Le+  ++p+       +A +  l +stv r +k+L e+ ++
  gi|91773123|ref|YP_565815.1| 25 DMKVLEYFFEEPDnwSKTERIATHMELDLSTVQRSVKKLHEKKIL 69
                                  6666666666555555666799*****************999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 861.52
//
Query:       gi|91773124|ref|YP_565816.1|  [L=205]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-14   53.8  12.9    9.1e-12   44.7   1.5    3.1  3  Fer4_5           4Fe-4S binding domain
    1.9e-09   37.5  13.1    1.1e-06   28.7   2.7    2.7  3  Fer4_21          4Fe-4S dicluster domain
    5.1e-09   35.6  23.4    3.6e-06   26.6   3.2    3.7  4  Fer4             4Fe-4S binding domain
    9.6e-09   35.3  17.9    2.1e-05   24.6   4.7    2.8  3  Fer4_9           4Fe-4S dicluster domain
    4.3e-08   33.3  11.0    4.3e-08   33.3  11.0    1.5  1  Fer4_18          4Fe-4S dicluster domain
    5.3e-08   33.3  16.2     0.0013   19.2   1.4    3.2  3  Fer4_7           4Fe-4S dicluster domain
    1.8e-07   30.9  19.2    0.00033   20.6   2.3    3.1  3  Fer4_6           4Fe-4S binding domain
      7e-06   26.5  13.9    0.00064   20.2   3.1    2.8  3  Fer4_17          4Fe-4S dicluster domain
    0.00015   21.8  21.4    0.00051   20.1  16.0    3.3  3  Fer4_10          4Fe-4S dicluster domain
    0.00026   20.9  11.5      0.004   17.2   1.1    3.4  3  Fer4_2           4Fe-4S binding domain
    0.00078   20.3  20.1    0.00083   20.2   1.9    3.0  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0023   18.3  25.9      0.011   16.2   3.4    3.5  3  Fer4_4           4Fe-4S binding domain
     0.0032   18.3   3.0     0.0032   18.3   3.0    4.0  4  Fer4_3           4Fe-4S binding domain
     0.0073   17.1  11.0       0.14   13.0   1.3    2.5  2  Fer4_22          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.027   14.9  18.6        0.2   12.1   2.1    2.8  3  Fer4_8           4Fe-4S dicluster domain
        3.9    7.0   6.2       0.35   10.5   1.3    1.7  2  Saf_2TM          SAVED-fused 2TM effector domain
        5.2    7.7  21.8       0.51   10.9   2.8    3.1  4  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       9.3   9.8e+03       9      18 ..      11      20 ..       7      21 .. 0.56
   2 !   44.7   1.5   8.6e-15   9.1e-12       2      48 .]      26      72 ..      25      72 .. 0.90
   3 !   16.7   0.4     5e-06    0.0052      10      39 ..     123     151 ..     108     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.3
                        Fer4_5  9 flaivlvtll 18
                                  +++iv +++l
  gi|91773124|ref|YP_565816.1| 11 LVVIVSIAGL 20
                                  4456666555 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 8.6e-15
                        Fer4_5  2 allllilflaivlvtllfGRafCgWiCPfGalqellakllrrklgkp 48
                                  ++++li ++++++++++ GR+fCg++CP+G+++++    +++k+++p
  gi|91773124|ref|YP_565816.1| 26 GYFMLIVMGTLFVTSIFRGRWFCGNLCPRGSYFDYGIIKISKKRKIP 72
                                  789*******************************8776788888776 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 5e-06
                        Fer4_5  10 laivlvtllfGRafCgWiCPfGalqellak 39 
                                   ++ +l + +  R +C  +CP G++q +++ 
  gi|91773124|ref|YP_565816.1| 123 IGTLLGSYFNTRSWCN-ACPMGTMQRIIGG 151
                                   355556666889****.*********9985 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.6   4.9e+03      47      52 ..      48      53 ..      46      72 .. 0.71
   2 !   28.7   2.7     1e-09   1.1e-06      16      54 ..     138     176 ..     134     180 .. 0.92
   3 !   14.5   1.7   2.7e-05     0.029       7      21 ..     187     201 ..     181     205 .] 0.65

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.6
                       Fer4_21 47 CssvCP 52
                                  C + CP
  gi|91773124|ref|YP_565816.1| 48 CGNLCP 53
                                  666666 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1e-09
                       Fer4_21  16 iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPve 54 
                                    aC+ +++q i + +k +lk+ ++ Cv C+lC +vCP+e
  gi|91773124|ref|YP_565816.1| 138 NACPMGTMQRIIGGKKYQLKMDHEACVDCKLCEKVCPME 176
                                   58***********************************84 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.7e-05
                       Fer4_21   7 kCigCgkCliaCedt 21 
                                   +Ci+Cg+C+ +C++ 
  gi|91773124|ref|YP_565816.1| 187 DCIKCGRCIDVCPKD 201
                                   577777777777654 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.2   1.3e+03      14      21 ..      48      55 ..      47      57 .. 0.80
   2 ?   -0.7   0.4       1.4   1.5e+03      16      21 ..     138     143 ..     137     145 .. 0.71
   3 !   20.4   3.1   3.1e-07   0.00032       4      20 ..     159     175 ..     156     176 .. 0.90
   4 !   26.6   3.2   3.4e-09   3.6e-06       7      23 ..     187     203 ..     184     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
                                  HHHHSTTT CS
                          Fer4 14 CvevCPvg 21
                                  C + CP g
  gi|91773124|ref|YP_565816.1| 48 CGNLCPRG 55
                                  88889987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                   HHSTTT CS
                          Fer4  16 evCPvg 21 
                                   ++CP g
  gi|91773124|ref|YP_565816.1| 138 NACPMG 143
                                   478876 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 3.1e-07
                                   ETTTSSS-THHHHHSTT CS
                          Fer4   4 deekCigCGaCvevCPv 20 
                                   d e C+ C++C++vCP 
  gi|91773124|ref|YP_565816.1| 159 DHEACVDCKLCEKVCPM 175
                                   89**************6 PP

  == domain 4  score: 26.6 bits;  conditional E-value: 3.4e-09
                                   TSSS-THHHHHSTTTEE CS
                          Fer4   7 kCigCGaCvevCPvgAI 23 
                                   +Ci+CG+C++vCP +A+
  gi|91773124|ref|YP_565816.1| 187 DCIKCGRCIDVCPKDAL 203
                                   5***************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.7     4e+03      42      49 ..      48      55 ..      46      57 .. 0.63
   2 !   24.6   4.7   1.9e-08   2.1e-05      10      49 ..     138     176 ..     134     178 .. 0.92
   3 !   18.3   2.6   1.8e-06    0.0019      34      50 ..     186     202 ..     175     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                        Fer4_9 42 CveaCpkg 49
                                  C + Cp+g
  gi|91773124|ref|YP_565816.1| 48 CGNLCPRG 55
                                  55566664 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.9e-08
                        Fer4_9  10 eaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   +aCp+g++++  +++k +l+++ e aC++C+ C+++Cp +
  gi|91773124|ref|YP_565816.1| 138 NACPMGTMQRIIGGKKYQLKMDHE-ACVDCKLCEKVCPME 176
                                   46*****************99988.9************86 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.8e-06
                        Fer4_9  34 eaCigCgaCveaCpkga 50 
                                    +Ci+Cg+C+++Cpk+a
  gi|91773124|ref|YP_565816.1| 186 PDCIKCGRCIDVCPKDA 202
                                   47************987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3  11.0   4.1e-11   4.3e-08      51      96 ..     153     199 ..     142     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.1e-11
                       Fer4_18  51 eerkekgagdcidcescvkvcPtgidirk.Glqleciscllcidacd 96 
                                   + + + ++  c+dc+ c kvcP+++++r+ G   +ci+c++cid c 
  gi|91773124|ref|YP_565816.1| 153 KYQLKMDHEACVDCKLCEKVCPMELEVRDiGNNPDCIKCGRCIDVCP 199
                                   4555677889******************9899**************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.6   6.3e+02       7      15 ..      47      55 ..      44     121 .. 0.80
   2 !   18.8   5.1   1.7e-06    0.0018      10      50 ..     138     175 ..     132     177 .. 0.77
   3 !   19.2   1.4   1.3e-06    0.0013       2      18 ..     188     204 ..     186     205 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.6
                        Fer4_7  7 aCvaaCpvk 15
                                  +C + Cp +
  gi|91773124|ref|YP_565816.1| 47 FCGNLCPRG 55
                                  678888743 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.7e-06
                        Fer4_7  10 aaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                   +aCp+++++     +   + ++++d+e C++C+ C++vCP 
  gi|91773124|ref|YP_565816.1| 138 NACPMGTMQRIIGGK---KYQLKMDHEACVDCKLCEKVCPM 175
                                   577777777654422...24589999**************6 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.3e-06
                        Fer4_7   2 CigCgaCvaaCpvkaie 18 
                                   Ci+Cg+C ++Cp +a++
  gi|91773124|ref|YP_565816.1| 188 CIKCGRCIDVCPKDALS 204
                                   99999999999998886 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.6   1.6e+03      18      22 ..     139     143 ..     137     148 .. 0.72
   2 !   20.6   2.3   3.1e-07   0.00033       4      21 ..     158     175 ..     156     177 .. 0.90
   3 !   18.7   4.6   1.3e-06    0.0014       9      24 .]     188     203 ..     184     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                        Fer4_6  18 vCPeg 22 
                                   +CP+g
  gi|91773124|ref|YP_565816.1| 139 ACPMG 143
                                   78865 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.1e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPe 21 
                                    d ++C++C  C++vCP+
  gi|91773124|ref|YP_565816.1| 158 MDHEACVDCKLCEKVCPM 175
                                   5889*************7 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.3e-06
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   Ci Cg+C++vCP +a+
  gi|91773124|ref|YP_565816.1| 188 CIKCGRCIDVCPKDAL 203
                                   ************9986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         4   4.3e+03       8      15 ..      48      55 ..      46      74 .. 0.71
   2 !   20.2   3.1     6e-07   0.00064      21      60 ..     140     177 ..     114     178 .. 0.61
   3 !   12.0   1.9   0.00022      0.23      45      58 ..     187     200 ..     182     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4
                       Fer4_17  8 ClpeCpsy 15
                                  C + Cp++
  gi|91773124|ref|YP_565816.1| 48 CGNLCPRG 55
                                  66666653 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 6e-07
                       Fer4_17  21 epkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                   +p+ +++++  g++   + ++  + C+ C++Ce++CP++l
  gi|91773124|ref|YP_565816.1| 140 CPMGTMQRIIGGKK--YQLKMDHEACVDCKLCEKVCPMEL 177
                                   33344444322322..23357889**************98 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00022
                       Fer4_17  45 lCieCgeCerkCPq 58 
                                   +Ci+Cg+C  +CP+
  gi|91773124|ref|YP_565816.1| 187 DCIKCGRCIDVCPK 200
                                   57777777777776 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.7   2.8e+03      15      36 ..      48      63 ..      47      73 .. 0.60
   2 !   10.6   7.7   0.00044      0.46      17      56 .]     138     174 ..     135     174 .. 0.67
   3 !   20.1  16.0   4.8e-07   0.00051       4      56 .]     158     199 ..     155     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                       Fer4_10 15 CvkaCPadltsvgakgeaseee 36
                                  C + CP       +++++ ++ 
  gi|91773124|ref|YP_565816.1| 48 CGNLCPR------GSYFDYGII 63
                                  7788998......444444444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00044
                       Fer4_10  17 kaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                   +aCP+       + ++ +++ + k + e+C +c  C ++CP
  gi|91773124|ref|YP_565816.1| 138 NACPM----GTMQRIIGGKKYQLKmDHEACVDCKLCEKVCP 174
                                   57999....44444444444444448899999999999998 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 4.8e-07
                       Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    d + C+ C+ C k+CP+        + +    ++ ++  +C++cg C+++CP
  gi|91773124|ref|YP_565816.1| 158 MDHEACVDCKLCEKVCPM--------ELEV---RDIGNNPDCIKCGRCIDVCP 199
                                   6899**************........3333...33335568***********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 ?    0.4   0.1      0.82   8.6e+02      16      21 ..     137     141 ..     130     142 .. 0.67
   2 !   17.2   1.1   3.8e-06     0.004       5      21 ..     158     174 ..     154     175 .. 0.89
   3 !   15.5   3.5   1.3e-05     0.014       6      21 ..     185     199 ..     180     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.82
                        Fer4_2  16 CvsaCP 21 
                                   C +aCP
  gi|91773124|ref|YP_565816.1| 137 C-NACP 141
                                   4.4555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.8e-06
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                    d ++C+ C+ C ++CP
  gi|91773124|ref|YP_565816.1| 158 MDHEACVDCKLCEKVCP 174
                                   6789************* PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.3e-05
                        Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                   ++d Ci Cg C+++CP
  gi|91773124|ref|YP_565816.1| 185 NPD-CIKCGRCIDVCP 199
                                   778.***********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 ?   -2.0   0.1       6.9   7.2e+03      10      16 ..     138     144 ..     136     154 .. 0.71
   2 !   11.2   3.3   0.00051      0.54      50      66 ..     159     175 ..     149     176 .. 0.68
   3 !   20.2   1.9   7.9e-07   0.00083       2      18 ..     188     204 ..     187     205 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.9
                       Fer4_16  10 evCPtna 16 
                                   ++CP + 
  gi|91773124|ref|YP_565816.1| 138 NACPMGT 144
                                   4666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00051
                       Fer4_16  50 kqeaitgCdiCqdvCPa 66 
                                    +ea+  C+ C++vCP+
  gi|91773124|ref|YP_565816.1| 159 DHEACVDCKLCEKVCPM 175
                                   46777777777777776 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 7.9e-07
                       Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                   C++Cg+C++vCP +a++
  gi|91773124|ref|YP_565816.1| 188 CIKCGRCIDVCPKDALS 204
                                   **************986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.34   3.6e+02       3       8 ..     136     141 ..     134     143 .. 0.79
   2 !   16.2   3.4     1e-05     0.011       2      16 ..     161     175 ..     160     176 .. 0.92
   3 !   14.1   3.6   4.7e-05      0.05       4      16 ..     188     200 ..     184     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.34
                        Fer4_4   3 rCigCg 8  
                                   +C+ C+
  gi|91773124|ref|YP_565816.1| 136 WCNACP 141
                                   899997 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1e-05
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   e C++C+ C+ +CP+
  gi|91773124|ref|YP_565816.1| 161 EACVDCKLCEKVCPM 175
                                   78************7 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4.7e-05
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   Ci Cg+C+++CP 
  gi|91773124|ref|YP_565816.1| 188 CIKCGRCIDVCPK 200
                                   ************5 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.98     1e+03       7      14 ..      48      55 ..      46      56 .. 0.80
   2 ?   -0.8   0.6       3.8     4e+03      10      12 ..     139     141 ..     137     143 .. 0.56
   3 !    8.1   5.1    0.0056       5.9       1      12 [.     163     174 ..     163     176 .. 0.94
   4 !   18.3   3.0     3e-06    0.0032       1      15 []     188     202 ..     188     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.98
                        Fer4_3  7 CvevCPvg 14
                                  C + CP g
  gi|91773124|ref|YP_565816.1| 48 CGNLCPRG 55
                                  77889987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.8
                        Fer4_3  10 vCP 12 
                                   +CP
  gi|91773124|ref|YP_565816.1| 139 ACP 141
                                   566 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0056
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+ C +C++vCP
  gi|91773124|ref|YP_565816.1| 163 CVDCKLCEKVCP 174
                                   999********* PP

  == domain 4  score: 18.3 bits;  conditional E-value: 3e-06
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ Cg+C +vCP++A
  gi|91773124|ref|YP_565816.1| 188 CIKCGRCIDVCPKDA 202
                                   *************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   2.6     0.003       3.2      72      95 ..     153     176 ..     132     177 .. 0.85
   2 !   13.0   1.3   0.00014      0.14      78      94 ..     184     200 ..     178     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                       Fer4_22  72 efkekfgesgCvGCgRCieacpvk 95 
                                   +++ k+++++Cv C  C+++cp++
  gi|91773124|ref|YP_565816.1| 153 KYQLKMDHEACVDCKLCEKVCPME 176
                                   5677889999***********976 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00014
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                   ++  C+ CgRCi++cp+
  gi|91773124|ref|YP_565816.1| 184 NNPDCIKCGRCIDVCPK 200
                                   5678***********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 ?   -2.5   0.0       7.1   7.5e+03      11      18 ..      48      55 ..      47      77 .. 0.63
   2 ?    8.2   7.8    0.0032       3.4      46      64 ..     158     176 ..     115     177 .. 0.75
   3 ?   12.1   2.1   0.00019       0.2       5      16 ..     188     199 ..     184     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.1
                        Fer4_8 11 CqsaCpvl 18
                                  C + Cp  
  gi|91773124|ref|YP_565816.1| 48 CGNLCPRG 55
                                  55556533 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0032
                        Fer4_8  46 ealwsCttcgaCtevCpvg 64 
                                      ++C+ c+ C++vCp++
  gi|91773124|ref|YP_565816.1| 158 MDHEACVDCKLCEKVCPME 176
                                   4567888888888888875 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00019
                        Fer4_8   5 CieCgaCqsaCp 16 
                                   Ci+Cg+C + Cp
  gi|91773124|ref|YP_565816.1| 188 CIKCGRCIDVCP 199
                                   777777777776 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       1.9     2e+03      69      82 ..      27      40 ..      11      57 .. 0.65
   2 ?   10.5   1.3   0.00033      0.35      33      85 ..      75     127 ..      62     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                       Saf_2TM 69 aiilvigvllivvG 82
                                  +++l++  +l+v++
  gi|91773124|ref|YP_565816.1| 27 YFMLIVMGTLFVTS 40
                                  44444444444443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00033
                       Saf_2TM  33 llailgtdwalkialklaggslevsfssseipeivlaiilvigvllivvGavl 85 
                                   l ++ +   a++++++l  ++++v f  ++++e++ +i++  + +++++G +l
  gi|91773124|ref|YP_565816.1|  75 LSSMWVRIPAFTLMMTLMIYRISVTFAAQNTFELIGVILVSMCLTTTIIGTLL 127
                                   555556677999999***********************************776 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.5   4.7e+03      12      18 ..      48      54 ..      47      60 .. 0.84
   2 ?   -2.8   0.1       9.5     1e+04      48      53 ..     137     142 ..     134     144 .. 0.71
   3 ?   10.9   2.8   0.00048      0.51       2      22 ..     159     179 ..     158     185 .. 0.83
   4 ?    8.3   3.9    0.0033       3.5       4      18 ..     186     200 ..     184     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.5
                       Fer4_13 12 CvelaPd 18
                                  C++l+P 
  gi|91773124|ref|YP_565816.1| 48 CGNLCPR 54
                                  9999995 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.5
                       Fer4_13  48 adaCPv 53 
                                   ++aCP+
  gi|91773124|ref|YP_565816.1| 137 CNACPM 142
                                   567775 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00048
                       Fer4_13   2 DrdtCiacgaCvelaPdvFee 22 
                                   D + C++c++C +++P   e 
  gi|91773124|ref|YP_565816.1| 159 DHEACVDCKLCEKVCPMELEV 179
                                   889*************86665 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0033
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                     Ci cg C +++P+
  gi|91773124|ref|YP_565816.1| 186 PDCIKCGRCIDVCPK 200
                                   57************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1471.72
//
Query:       gi|91773125|ref|YP_565817.1|  [L=1015]
Description: FAD linked oxidase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-36  125.1   0.0    3.7e-36  123.9   0.0    1.7  1  FAD_binding_4   FAD binding domain
    4.3e-34  116.6   3.6    2.9e-16   59.4   0.7    2.8  2  CCG             Cysteine-rich domain
    4.5e-09   36.7   6.1    4.5e-09   36.7   6.1    2.4  4  Fer4_17         4Fe-4S dicluster domain
    7.5e-05   22.8   4.3    8.8e-05   22.6   2.2    2.3  2  Fer4_9          4Fe-4S dicluster domain
    9.9e-05   22.7   6.7    9.9e-05   22.7   6.7    2.0  2  Fer4_8          4Fe-4S dicluster domain
     0.0023   18.5   6.5     0.0074   16.9   6.5    1.9  1  Fer4_7          4Fe-4S dicluster domain
     0.0031   17.2   0.0     0.0072   16.0   0.0    1.7  1  FAD-oxidase_C   FAD linked oxidases, C-terminal domain
  ------ inclusion threshold ------
        0.2   10.8   0.0       0.38    9.9   0.0    1.3  1  NTP_transf_7    Nucleotidyltransferase
       0.59   10.1   4.3        6.1    6.8   0.8    3.9  4  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   0.0   1.9e-39   3.7e-36       1     138 [.      54     192 ..      54     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 1.9e-39
                                   EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                 FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                   paa+v+ ++e+++++++++a+++++p+++r+g ss  g+++ ++gg+v d+  ln+i++id e++t+tv+aG+++++l++ 
  gi|91773125|ref|YP_565817.1|  54 PAAIVKLRTEDDIVKLMEFARKYSIPIVPRAGASSGYGGVIpTKGGIVADVNLLNDIVSIDTENMTVTVGAGIIWERLERK 134
                                   899**************************************99********66**************************** PP

                                   HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                 FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                   l++++l +   p+s   +tvGG++a+n++Gygs  yG ++d+  ++++vl++Ge++++
  gi|91773125|ref|YP_565817.1| 135 LNKENLSVCSMPSSAPAATVGGWLAQNGIGYGSYEYGWSQDTMISARAVLPNGEIRDF 192
                                   *******************************************************986 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.1   7.3e-19   1.4e-15       1      82 [.     635     716 ..     635     719 .. 0.97
   2 !   59.4   0.7   1.5e-19   2.9e-16       1      85 []     763     850 ..     763     850 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 7.3e-19
                           CCG   1 vayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgC 80 
                                   +ayf gC  +    ++  +a  +ll+ +g+e+ +l ++esCCG +   +gk +++e+++++n+e+++++g++ ++t cp C
  gi|91773125|ref|YP_565817.1| 635 YAYFAGC-TASFVEKDIAEASVRLLTDAGLEITYLgKEESCCGIPMLAAGKWDVFEKIMRMNIENMKKKGVKTVITSCPAC 714
                                   79*****.89999******************************************************************** PP

                           CCG  81 ll 82 
                                    l
  gi|91773125|ref|YP_565817.1| 715 WL 716
                                   65 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 1.5e-19
                           CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                   v+++d Ch++ra   y+ +r+++k+++++++ e+e++ e+  CCG+  +   + e+a  ++++++++ae+ ga+++v+acp
  gi|91773125|ref|YP_565817.1| 763 VTIHDACHMGRAGgiYEPPRNLIKAVPGVDFREMEHNrENGHCCGSVLTLVANPEVASVVGNMRLKEAEDIGAEIMVAACP 843
                                   79******************************************************************************* PP

                           CCG  79 gCllqlk 85 
                                    C++ql+
  gi|91773125|ref|YP_565817.1| 844 CCQVQLR 850
                                   *****96 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   6.1   2.3e-12   4.5e-09       2      60 ..     506     571 ..     505     572 .. 0.83
   2 ?   -4.0   0.1         9   1.8e+04      38      49 ..     700     714 ..     689     715 .. 0.54
   3 ?   -3.0   0.0       5.6   1.1e+04      12      48 ..     769     807 ..     767     808 .. 0.70
   4 ?   -4.4   0.2         9   1.8e+04      34      49 ..     830     845 ..     817     846 .. 0.57

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.3e-12
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl......glleeaeke..ekaslCieCgeCerkCPqgl 60 
                                   C+qCgyC++eC +y+ +++e ++++ ++ +      g  +++ +e  +++  C++C++C+++C  +l
  gi|91773125|ref|YP_565817.1| 506 CAQCGYCVEECDQYYGRGWESQSPRGKWFFikeylaG-RDKMTQEqvDTFLACTTCELCDHRCQLDL 571
                                   ***************************9777777752.44443433479**************8877 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9
                       Fer4_17  38 eke...ekaslCieC 49 
                                   +k+   +++ +C  C
  gi|91773125|ref|YP_565817.1| 700 KKKgvkTVITSCPAC 714
                                   333333677777776 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.6
                       Fer4_17  12 Cpsyea..ydnepkkllraaklglleeaekeekaslCie 48 
                                   C +++a  + + p++l++a+   +++e+e +++ + C++
  gi|91773125|ref|YP_565817.1| 769 CHMGRAggIYEPPRNLIKAVPGVDFREMEHNRENGHCCG 807
                                   666666444456778888877778889988888888875 PP

  == domain 4  score: -4.4 bits;  conditional E-value: 9
                       Fer4_17  34 leeaekeekaslCieC 49 
                                    e++ +e ++  C +C
  gi|91773125|ref|YP_565817.1| 830 AEDIGAEIMVAACPCC 845
                                   4444444566667766 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.2   4.4e-08   8.8e-05       2      48 ..     506     569 ..     505     571 .. 0.74
   2 ?   -3.4   0.0       5.8   1.2e+04      34      39 ..     709     714 ..     685     721 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.4e-08
                        Fer4_9   2 CtgCgaCveaC..............pagvvvedaaerkarlraase...eaCigCgaCveaCpk 48 
                                   C++Cg+Cve C               ++ ++++  ++ +++++++     aC++C+ C ++C+ 
  gi|91773125|ref|YP_565817.1| 506 CAQCGYCVEECdqyygrgwesqsprGKWFFIKEYLAGRDKMTQEQVdtfLACTTCELCDHRCQL 569
                                   ***********9999999988887644455555555555544433377889***********86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.8
                        Fer4_9  34 eaCigC 39 
                                   ++C  C
  gi|91773125|ref|YP_565817.1| 709 TSCPAC 714
                                   333333 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   6.7     5e-08   9.9e-05       3      62 ..     504     568 ..     502     571 .. 0.80
   2 ?   -4.4   0.5         9   1.8e+04      54      59 ..     842     847 ..     839     855 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5e-08
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.........dvqeeqvleeeealwsCttcgaCtevCp 62 
                                   + C +Cg+C ++C  +  ++ +++++rg+            ++ +eq     +++ +Cttc+ C+ +C 
  gi|91773125|ref|YP_565817.1| 504 YTCAQCGYCVEECDQYYGRGWESQSPRGKWFFikeylagrdKMTQEQ----VDTFLACTTCELCDHRCQ 568
                                   68************999999999999999887777765443333333....589**************7 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 9
                        Fer4_8  54 cgaCte 59 
                                   c +C++
  gi|91773125|ref|YP_565817.1| 842 CPCCQV 847
                                   555554 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   6.5   3.7e-06    0.0074       1      48 [.     505     567 ..     505     570 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt...........ekv...eid.pekClgCgaCvavC 48 
                                   +C +Cg+Cv+ C ++  + +e+++++g+           +k+   ++d    C++C+ C  +C
  gi|91773125|ref|YP_565817.1| 505 TCAQCGYCVEECDQYYGRGWESQSPRGKwffikeylagrDKMtqeQVDtFLACTTCELCDHRC 567
                                   5***********9999999999888854444433333333333224442446********999 PP

>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.6e-06    0.0072     123     248 ..     333     453 ..     219     455 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.6e-06
                                   HHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEEEEEEEETTEEEEEEEEEEE..--T.T--THHHHHH..HHHHH CS
                 FAD-oxidase_C 123 llkagvavlseDtsvPvsrladlvrdikalldkyglevvlfgHagdgnlhlyilfdladeaee.eraeklvdev..vdlav 200
                                   +++ g+  +  ++ vP++++ ++v++ik+ +d   l   ++  a dgn++l++ ++ + +  + + a +l   +  v++a 
  gi|91773125|ref|YP_565817.1| 333 VKRLGPSFIPAEIIVPLDKVGKVVSEIKQKIDLPVLMEGMV--AKDGNVILLCFIPHSERSFKfNLAFTLG--IsiVKIAE 409
                                   467778888899*******************9888666666..57********998875543313333444..355***** PP

                                   HTT-----------------------THHHHHHHHHHHH-TT--BSTT CS
                 FAD-oxidase_C 201 elgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPkgiLNPg 248
                                   ++gG i++    Gl  +++ e+ +g   l+ m  +K+  DP++i+NP 
  gi|91773125|ref|YP_565817.1| 410 DNGGRIYAS---GLYFAKEAEKVYGN-RLKKMLDLKQQVDPADIMNPE 453
                                   *******97...44444445666666.789999**************6 PP

>> NTP_transf_7  Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00019      0.38     142     242 ..     373     474 ..     351     481 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                  NTP_transf_7 142 snekgrnvelkfvdslrRqfefsvDsfqivldsllefyevssealsesfyptvvaesvygdfeealehLekkl..iatrkP 220
                                     + g  + l f+ + +R f+f + +f + +  +   ++   +   +  y    ae vyg+  + +  L++++   +  +P
  gi|91773125|ref|YP_565817.1| 373 VAKDGNVILLCFIPHSERSFKFNL-AFTLGISIVKIAEDNGGRIYASGLYFAKEAEKVYGNRLKKMLDLKQQVdpADIMNP 452
                                   56778999999***********98.6888886665555555555888899999*****************998445779** PP

                  NTP_transf_7 221 eeiRGGGLlkYcnLlvrgykpa 242
                                   e i G G+lk    l + ++p 
  gi|91773125|ref|YP_565817.1| 453 ETITGKGILKTGITLSKAFEPM 474
                                   ***********99999999885 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      0.98     2e+03      56      67 ..     296     307 ..     280     309 .. 0.78
   2 ?    6.8   0.8    0.0031       6.1       9      47 ..     487     524 ..     485     533 .. 0.80
   3 ?    0.5   0.0      0.29   5.8e+02      10      39 ..     539     568 ..     536     579 .. 0.80
   4 ?   -1.2   0.0      0.99     2e+03      47      57 ..     709     719 ..     697     720 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.98
                OrfB_Zn_ribbon  56 adrDvnAaiNil 67 
                                     rDv A  Ni+
  gi|91773125|ref|YP_565817.1| 296 ESRDVSALENII 307
                                   67*********8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0031
                OrfB_Zn_ribbon   9 eykakeyGikveevnpayTSktCseCgsknkealsgrtf 47 
                                   e   k++ i+   v+ ayT  +C  C ++ ++   gr +
  gi|91773125|ref|YP_565817.1| 487 EKFTKQKDIEADIVSHAYTCAQCGYCVEECDQ-YYGRGW 524
                                   66788999***********9999999988877.555554 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.29
                OrfB_Zn_ribbon  10 ykakeyGikveevnpayTSktCseCgsknk 39 
                                   y a +  ++ e+v+ +   +tC  C ++ +
  gi|91773125|ref|YP_565817.1| 539 YLAGRDKMTQEQVDTFLACTTCELCDHRCQ 568
                                   666677778888999999999999999875 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.99
                OrfB_Zn_ribbon  47 fkCpnCgfead 57 
                                     Cp+C++++d
  gi|91773125|ref|YP_565817.1| 709 TSCPACWLVWD 719
                                   57999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1015 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.83u 0.27s 00:00:01.10 Elapsed: 00:00:00.46
# Mc/sec: 6567.48
//
Query:       gi|91773126|ref|YP_565818.1|  [L=128]
Description: hypothetical protein Mbur_1143 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-13   50.3   0.0    2.7e-13   49.9   0.0    1.1  1  TfoX_N    TfoX N-terminal domain
    0.00019   21.9   0.0    0.00026   21.5   0.0    1.3  1  YjbR      YjbR


Domain annotation for each model (and alignments):
>> TfoX_N  TfoX N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0     3e-17   2.7e-13      10      91 ..      25     105 ..      18     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3e-17
                                   EEEEETTEEEEEETTEEEEEEETTEEEEE--HHHHHHHHHTT--..--EEEETTEEEE-SEEE--HHHHC-HHHHHHHHHH CS
                        TfoX_N  10 tsrrmFGgyglfvdglmfalvsdgelylradeetreefeaagle..pftyakkgtpktlsYyrvpeelledpeqlarwvrl 88 
                                   ++r+mFG    fv+g+mf+ v+++ ++lr +ee+++++ a+  e  pft++ +   +  +Y  +p+++++d+ +l++w++ 
  gi|91773126|ref|YP_565818.1|  25 EFRKMFGSPVHFVKGNMFVGVHGDGIMLRLKEEDQQKLYAEHDEatPFTPNGR---RMREYAILPPSVYDDEMELRKWLDI 102
                                   79*****************************9999988777665357888744...2349*******************99 PP

                                   HHH CS
                        TfoX_N  89 ale 91 
                                   ++ 
  gi|91773126|ref|YP_565818.1| 103 SYT 105
                                   985 PP

>> YjbR  YjbR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.9e-08   0.00026      11      84 ..      29     104 ..      18     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.9e-08
                                   CTT.S-EEEECCCEEEEEEECCCCGEEEES-HHHHHHHHHSSTTEEE-T....S.TTTEEEE...ETTSS-HHHHHHHHHH CS
                          YjbR  11 pfg.pelvfkvggKmFallgleeeslnlkcdpeeaeaLreqypaiapgy....h.kkhWitv...lldgvpddeleelide 82 
                                    fg p  v  v+g mF+ ++ ++  ++l++++e+++ L +++++ +p+     + +++ i     + d  ++ el++++d 
  gi|91773126|ref|YP_565818.1|  29 MFGsP--VHFVKGNMFVGVHGDG--IMLRLKEEDQQKLYAEHDEATPFTpngrRmREYAILPpsvY-D--DEMELRKWLDI 102
                                   34444..489********98755..*****************999****87652555565546635.5..599******** PP

                                   HH CS
                          YjbR  83 SY 84 
                                   SY
  gi|91773126|ref|YP_565818.1| 103 SY 104
                                   *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 869.00
//
Query:       gi|91773127|ref|YP_565819.1|  [L=209]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-24   86.9   0.0    2.2e-24   86.5   0.0    1.1  1  ABC_tran     ABC transporter
    1.6e-07   31.4   2.4    6.8e-05   22.8   0.2    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    9.3e-07   28.5   1.4    1.3e-05   24.7   1.4    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00025   20.3   0.4       0.48    9.6   0.3    2.1  2  NB-ARC       NB-ARC domain
    0.00027   20.6   0.2    0.00053   19.7   0.2    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0034   16.6   0.0     0.0043   16.3   0.0    1.2  1  DAP3         Mitochondrial ribosomal death-associated protein
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.013   14.7   0.0    1.2  1  G-alpha      G-protein alpha subunit
      0.018   14.9   0.1      0.036   14.0   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
      0.063   12.3   0.0      0.088   11.8   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
      0.066   13.6   0.1      0.078   13.4   0.1    1.4  1  AAA_16       AAA ATPase domain
      0.067   13.2   0.0        1.4    8.9   0.0    2.3  2  AAA_5        AAA domain (dynein-related subfamily)
      0.067   13.5   0.0       0.13   12.6   0.0    1.5  2  AAA_22       AAA domain
      0.085   12.9   0.7        5.2    7.1   0.1    2.3  2  AAA_14       AAA domain
       0.11   12.4   0.1       0.19   11.6   0.1    1.4  1  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   1.7e-27   2.2e-24       2     137 .]      22     166 ..      21     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.7e-27
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   ++ +l++k+g ++ + G++G+GKStLlk+ +g  ++t+G++ +++k l++++   +rk+i++++q+  + +++ v e    
  gi|91773127|ref|YP_565819.1|  22 SHFNLDIKKGDRILLKGRSGSGKSTLLKMAIGFAHQTSGSLYYNNKLLDSNTVWDARKRIAYVSQDLDIYEGS-VNEFiee 101
                                   6789**************************************************************8888888.8888888 PP

                                   ...HHHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ...xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...esdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                      +s++e    + k+++ l   +++++v++ + + LSgG+kqr+ + +++l  ++++llDE t+
  gi|91773127|ref|YP_565819.1| 102 vfsYSSNEgkldLIKLRRLLVYLGFEKDVLDMDFEDLSGGEKQRIGIIMSVLIGKDIYLLDEITS 166
                                   9994444455668888888888889*************************************985 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.3   0.00081         1       3      24 ..      35      57 ..      34      85 .. 0.70
   2 !   22.8   0.2   5.3e-08   6.8e-05     182     299 ..      88     195 ..      57     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00081
                        AAA_21  3 vliGpNgsGKSnLLd.aldllar 24
                                  +l G+ gsGKS+LL+ a+ ++++
  gi|91773127|ref|YP_565819.1| 35 LLKGRSGSGKSTLLKmAIGFAHQ 57
                                  688***********944544444 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 5.3e-08
                        AAA_21 182 krllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgslll 262
                                   +++ ++ v+++ +  + +s ++ + +li+++ +      v++  ++d  + ++ +lS G k+ ++++ ++l      +++l
  gi|91773127|ref|YP_565819.1|  88 LDIYEGSVNEFIEEVFSYSSNEGKLDLIKLRRL-----LVYLGFEKDVLDMDFEDLSGGEKQRIGIIMSVLIGK---DIYL 160
                                   444445555555555555555544444444444.....799******************************966...**** PP

                        AAA_21 263 iDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                   +DE+ ++L+ +l ++++  +  l+r++  +++ +H+ 
  gi|91773127|ref|YP_565819.1| 161 LDEITSSLDSALKEKVANYF--LERKDWTLVIISHDD 195
                                   *****************888..444468899999986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.4   1.1e-08   1.3e-05      31     199 ..      38     195 ..      18     207 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                   ESTTSSHHHHHH.HHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEE CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  31 GpNGSGKsnlld.AilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrrvkrkges 109
                                   G+ GSGKs ll  Ai    G++++++      ++l+ + +   a+   a+v+  +d  + +           ++ + ++  
  gi|91773127|ref|YP_565819.1|  38 GRSGSGKSTLLKmAI----GFAHQTSGSLYYNNKLLDSnTVWDARKRIAYVSQDLDIYEGS-----------VNEFIEEVF 103
                                   666666666654233....433333333333344444422222333333333322222222...........333334444 PP

                                   EEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 110 eykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                   +y  n+ +    ++++ll   g++k+        LSgGek+ +   +++++     + +yllDei + LD +  +kva+++
  gi|91773127|ref|YP_565819.1| 104 SYSSNEGKLDLIKLRRLLVYLGFEKDvldmdfeDLSGGEKQRI--GIIMSVLI--GKDIYLLDEITSSLDSALKEKVANYF 180
                                   5555555666666666666666655566666669******965..55666654..4569********************** PP

                                   HHHCTTSEEEEE-SSH CS
                                   xxxxxxxxxxxxxxxx RF
                         SMC_N 184 keksknaQfivislre 199
                                    e++ +  +++is+++
  gi|91773127|ref|YP_565819.1| 181 LERK-DWTLVIISHDD 195
                                   9988.77788888876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00046      0.58      23      42 ..      34      53 ..      19     121 .. 0.83
   2 !    9.6   0.3   0.00038      0.48      84     119 ..     165     203 ..     142     209 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00046
                                  EEEEESTTSSHHHHHHHHCC CS
                        NB-ARC 23 valvGmgGvGKttlakqiln 42
                                  + l G+ G+GK+tl+k ++ 
  gi|91773127|ref|YP_565819.1| 34 ILLKGRSGSGKSTLLKMAIG 53
                                  7799**********998765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00038
                                   SSS-STTSHHHHHHHHCCCT..TEEEEE..EEE-SHHHH. CS
                        NB-ARC  84 eekeeveslkrklvrlLltk..rfllvl..DDVweeedwd 119
                                    +  ++  lk+k+ ++ l++   +l+++  DDVw++e+ +
  gi|91773127|ref|YP_565819.1| 165 TSSLDSA-LKEKVANYFLERkdWTLVIIshDDVWDKENVR 203
                                   3333333.8999999876664667777788******9874 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   4.1e-07   0.00053      17      39 ..      26      48 ..      19      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.1e-07
                        AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                  ++i+  + +ll G+sGsGKSTll
  gi|91773127|ref|YP_565819.1| 26 LDIKKGDRILLKGRSGSGKSTLL 48
                                  67775559**************8 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 !   16.3   0.0   3.4e-06    0.0043      21      50 ..      29      58 ..      19     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-06
                                  S---EEEEE-SSSSSTTTTHHHHHHHGGGS CS
                          DAP3 21 kkvkrlvltGekgsGKSvlLlqalayAlek 50
                                  kk  r++l+G+ gsGKS+lL  a+ +A++ 
  gi|91773127|ref|YP_565819.1| 29 KKGDRILLKGRSGSGKSTLLKMAIGFAHQT 58
                                  7899*******************9999875 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     1e-05     0.013      23      80 ..      31      86 ..      13     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                                  EEEEEEEESTTSSHHHHHHHHH.HHCS----HHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                       G-alpha 23 evkllllGqseSGKsTilkqlk.llykkgfseeelatwraviqlnivrsiktileales 80
                                    ++ll G s+SGKsT+lk    + ++ + s     + ++++ +n+v ++++ ++ +++
  gi|91773127|ref|YP_565819.1| 31 GDRILLKGRSGSGKSTLLKMAIgFAHQTSGSLY---YNNKLLDSNTVWDARKRIAYVSQ 86
                                  459***************987623333332211...23345555555555555554444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.8e-05     0.036      77     125 ..       8      57 ..       2      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                                   SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                   RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                   y+ + ++  +ke l++ +  +k+ + ++l G SG GKStL+++ ++ +++
  gi|91773127|ref|YP_565819.1|   8 YKDISLRYGEKEVLSHFNLDIKKgDRILLKGRSGSGKSTLLKMAIGFAHQ 57 
                                   55566666777888888888887789999************987775555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.9e-05     0.088     117     156 ..      19      58 ..       2      64 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                         T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                   ++ +  +  +++   il+ G  gsGK+tll +++ + +++
  gi|91773127|ref|YP_565819.1|  19 EVLSHFNLDIKKGDRILLKGRSGSGKSTLLKMAIGFAHQT 58 
                                   455555677788899****************999987765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.1e-05     0.078      22      46 ..      31      53 ..      15     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                        AAA_16 22 grpelvllsGesGvGKsslvrellr 46
                                  g    +ll G sG+GKs+l++++  
  gi|91773127|ref|YP_565819.1| 31 G--DRILLKGRSGSGKSTLLKMAIG 53
                                  4..3589*************87764 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 ?    8.9   0.0    0.0011       1.4       2      18 ..      34      50 ..      33     108 .. 0.86
   2 ?    2.4   0.0      0.11   1.5e+02      52      83 ..     142     173 ..     126     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                  EEEE--SSSSHHHHHHH CS
                         AAA_5  2 vlLvGppGtgKselaer 18
                                  +lL+G +G+gKs+l + 
  gi|91773127|ref|YP_565819.1| 34 ILLKGRSGSGKSTLLKM 50
                                  79***********9875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                                   .....--------G-SEEEEESGGG--HHHHH CS
                         AAA_5  52 tslvdsplvraaregeilvlDEveraesevln 83 
                                   ++ + ++++     ++i++lDE++   +++l+
  gi|91773127|ref|YP_565819.1| 142 EKQRIGIIMSVLIGKDIYLLDEITSSLDSALK 173
                                   5555566676677899*******987766554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001      0.13       8      31 ..      34      57 ..      28     111 .. 0.82
   2 ?   -3.0   0.0       6.1   7.9e+03      96     107 ..     160     175 ..     151     196 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                        AAA_22  8 lvvtGesGtGKTtllrrlleqlde 31
                                  +++ G sG+GK+tll++    +++
  gi|91773127|ref|YP_565819.1| 34 ILLKGRSGSGKSTLLKMAIGFAHQ 57
                                  7899************99888765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.1
                        AAA_22  96 iiDEaqh.lr...see 107
                                   ++DE+   l+   +e+
  gi|91773127|ref|YP_565819.1| 160 LLDEITSsLDsalKEK 175
                                   4444444443222233 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.004       5.2       5      43 ..      34      71 ..      30     115 .. 0.67
   2 ?    4.5   0.1     0.027        34      31      77 ..     128     171 ..     113     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.004
                        AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                  ++++G   +GK+tllk  i     + +  ly+n +  + 
  gi|91773127|ref|YP_565819.1| 34 ILLKGRSGSGKSTLLKMAIGFAH-QTSGSLYYNNKLLDS 71
                                  6899999********99985555.666667766554444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                        AAA_14  31 esilyinldderdkkladpekllelileklkeekktylflDEiqev...p 77 
                                   +++l ++++d +  +++     + +i++ l   +k + +lDEi  +    
  gi|91773127|ref|YP_565819.1| 128 KDVLDMDFEDLSGGEKQR----IGIIMSVL-I-GKDIYLLDEITSSldsA 171
                                   566677777766654443....47888863.3.68999*****9763331 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.19       2      18 ..      33      49 ..      32      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                  CEEEEC-TTTCHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlq 18
                                   ++l+G++GsGK+tLl+
  gi|91773127|ref|YP_565819.1| 33 RILLKGRSGSGKSTLLK 49
                                  689************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 1603.39
//
Query:       gi|91773128|ref|YP_565820.1|  [L=265]
Description: ABC transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-74  248.6  18.3    6.1e-74  248.4  18.3    1.0  1  UPF0014   Uncharacterised protein family (UPF0014)


Domain annotation for each model (and alignments):
>> UPF0014  Uncharacterised protein family (UPF0014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.4  18.3   3.4e-78   6.1e-74       2     242 .]       9     249 ..       8     249 .. 0.99

  Alignments for each domain:
  == domain 1  score: 248.4 bits;  conditional E-value: 3.4e-78
                       UPF0014   2 lqlalalllvlialllslvlklglekelliaavrmvvQLllvGyvLklifalnslllvllillvmllvAaieaakrvkkkl 82 
                                   l+l++++ll++i+ll+s++lklg+ +e++++a rm++QL++vG++L+++f+ln+ +++ll+l+vm+l+A++++ + ++ ++
  gi|91773128|ref|YP_565820.1|   9 LALVACFLLLAIPLLVSHYLKLGIIRETVVSASRMILQLIFVGFFLTVLFDLNNSIVNLLWLFVMILMATYATINDIGLDI 89 
                                   67999**************************************************************************** PP

                       UPF0014  83 kklllivllsllvstlltlllllllviqpepwyepqylIPlaGmilGnamnaialalerllselksereeiealLalGatp 163
                                   kklll++++s++v+ +l+ll+++++v++ e+ ++++ylIP++Gm lGn++ ++ +++++++++++++++++ + L+lGa++
  gi|91773128|ref|YP_565820.1|  90 KKLLLPTIFSFIVGNFLILLYFNTFVVNLENLFDARYLIPIFGMFLGNSLRGNLVSISNFYDTIRRNENRYLYSLSLGAKK 170
                                   ********************************************************************************* PP

                       UPF0014 164 keAvkeivreairaaliPtinsmatvGlVsLPGmmtGqiLaGaspleAvkyqilimfmilastalstvlvvlllyrrlf 242
                                   +eA+ +++r++i+ al P+i sm+tvG+VsLPGmmtGqi+aG+sp+ A+kyq++im++i +st++++++ ++++ r+ f
  gi|91773128|ref|YP_565820.1| 171 SEAILPYARKSIKLALKPSIASMSTVGIVSLPGMMTGQIIAGSSPILAIKYQMAIMVGIYVSTVMTVTIGIFMTTRSSF 249
                                   **********************************************************************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1793.11
//
Query:       gi|91773129|ref|YP_565821.1|  [L=160]
Description: hypothetical protein Mbur_1146 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-05   23.8   0.0    0.00011   22.5   0.0    1.6  1  YscW      Type III secretion system lipoprotein chaperone (Ys


Domain annotation for each model (and alignments):
>> YscW  Type III secretion system lipoprotein chaperone (YscW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     6e-09   0.00011       6      92 ..      49     137 ..      45     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6e-09
                                   EEEEEE...SS--TT-EEEEEEEEEE..ETTEEEEEEEE...EEEESS..SSEEEEEEEEHHHHTT--EE.EEEEEEETT- CS
                          YscW   6 vsGtVtyrerialppdavltVeLsdvSladapakvlaeq...eirtegkqvPlsFsLsydparikpraryavsArievdgk 83 
                                   v+G++ + e ++   +a++ ++++dvSl+d+ + +++e+   ++ ++++ +     L y p ++++r++y++s  + v+g 
  gi|91773129|ref|YP_565821.1|  49 VQGNIIFDEPVESFSNATIYLKVEDVSLQDVSSVTISENfisSVSMDADDIQTVPYLIYHP-ELDERMTYSLSVHVDVNGD 128
                                   99**********************************9972224456665555555689999.9***************998 PP

                                   -S--EEEEE CS
                          YscW  84 llfitdtvy 92 
                                     + + + y
  gi|91773129|ref|YP_565821.1| 129 GSLSNGDYY 137
                                   887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1176.62
//
Query:       gi|91773130|ref|YP_565822.1|  [L=109]
Description: hypothetical protein Mbur_1147 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.018   15.2   0.0    1.4  1  DprA_WH   DprA winged helix domain
      0.016   15.1   0.2      0.035   14.0   0.1    1.6  2  TrmB      Sugar-specific transcriptional regulator TrmB
      0.016   15.0   0.0      0.038   13.8   0.0    1.7  2  HTH_IclR  IclR helix-turn-helix domain
       0.02   14.8   0.1      0.077   12.9   0.1    2.0  2  HTH_5     Bacterial regulatory protein, arsR family
      0.039   14.1   0.0      0.093   12.8   0.0    1.6  2  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
      0.039   14.0   0.0      0.053   13.6   0.0    1.2  1  HTH_20    Helix-turn-helix domain
        0.1   12.2   0.0       0.26   10.9   0.0    1.7  1  HTH_24    Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   6.9e-06     0.018      16      41 ..      36      61 ..      20      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.9e-06
                       DprA_WH 16 rvLaaLgpePvhvDqLvrrtglpaae 41
                                  ++L+ L+ +P+++ q++r+tglp+  
  gi|91773130|ref|YP_565822.1| 36 KILEVLSEDPLSLRQISRKTGLPFVD 61
                                  69********************9855 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.3   3.4e+03      19      30 ..      19      30 ..      10      33 .. 0.72
   2 ?   14.0   0.1   1.4e-05     0.035      17      64 ..      40      93 ..      36      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                                  HHCCCHHCHHCC CS
                          TrmB 19 klgpatadeiae 30
                                  ++g+ t++e+ +
  gi|91773130|ref|YP_565822.1| 19 AEGSRTVTEVLS 30
                                  678888888865 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.4e-05
                                  HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE CS
                          TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYra 64
                                  +l+++p++ ++i++++g+p   v + +  L++ +lVer+  +      +++Y +
  gi|91773130|ref|YP_565822.1| 40 VLSEDPLSLRQISRKTGLPFVDVENKIMALVESDLVERKSISsgleeeKYIYGP 93
                                  7899**********************************9977788877777765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.038       6      32 ..      35      59 ..      34      79 .. 0.73
   2 ?   -3.2   0.0       2.9   7.5e+03      41      48 ..      83      90 ..      82      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-H CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpk 32
                                  + iL+ l+e p   +l++++r+tglp 
  gi|91773130|ref|YP_565822.1| 35 FKILEVLSEDPL--SLRQISRKTGLPF 59
                                  789999998876..7**********95 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.9
                                  HHHHTTSE CS
                      HTH_IclR 41 tLvelGyv 48
                                   L+e++y+
  gi|91773130|ref|YP_565822.1| 83 GLEEEKYI 90
                                  59999997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.83   2.1e+03      12      20 ..      19      27 ..      15      30 .. 0.85
   2 ?   12.9   0.1     3e-05     0.077       6      28 ..      36      58 ..      32      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.83
                                  TTSSEEHHH CS
                         HTH_5 12 aegelcvce 20
                                  aeg+++v+e
  gi|91773130|ref|YP_565822.1| 19 AEGSRTVTE 27
                                  7999**998 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3e-05
                                  HHHHHHTTSSEEHHHHHHHHTS- CS
                         HTH_5  6 kILklLaegelcvcelaeelgls 28
                                  kIL  L+e +l+  ++++++gl+
  gi|91773130|ref|YP_565822.1| 36 KILEVLSEDPLSLRQISRKTGLP 58
                                  8********************97 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.8   4.7e+03      25      34 ..      20      29 ..      18      34 .. 0.57
   2 ?   12.8   0.0   3.6e-05     0.093      23      57 ..      41      75 ..      35      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.8
                                  HSSBEHHHHH CS
                         HTH_9 25 kgrltlrelv 34
                                  +g +t++e +
  gi|91773130|ref|YP_565822.1| 20 EGSRTVTEVL 29
                                  5666666544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.6e-05
                                  HHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9 23 lrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                  l++  l+lr++++kt+L+   V +  ++L+   lV
  gi|91773130|ref|YP_565822.1| 41 LSEDPLSLRQISRKTGLPFVDVENKIMALVESDLV 75
                                  567789***********************987777 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.1e-05     0.053       3      56 ..      25      77 ..      23      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                  HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  ++e+L+ +   +il  L ++++l++ ++ +  +l+   + + + +L+e +Lve+
  gi|91773130|ref|YP_565822.1| 25 VTEVLSKEGSFKILEVL-SEDPLSLRQISRKTGLPFVDVENKIMALVESDLVER 77
                                  667788888899*****.**********************************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 ?   10.9   0.0    0.0001      0.26       6      29 ..      35      57 ..      34      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                        HTH_24  6 rkILelLqknprisqreLAerlgl 29
                                  +kILe+L ++p +s r++++++gl
  gi|91773130|ref|YP_565822.1| 35 FKILEVLSEDP-LSLRQISRKTGL 57
                                  89*******55.***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 802.53
//
Query:       gi|91773131|ref|YP_565823.1|  [L=503]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for 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-20   72.0   1.1    5.8e-10   39.5   0.1    2.3  2  Inhibitor_I42  Chagasin family peptidase inhibitor I42
    2.8e-10   40.1   0.0      5e-10   39.3   0.0    1.4  1  HTH_20         Helix-turn-helix domain
    8.2e-07   28.5   0.6    1.4e-06   27.7   0.6    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
    9.5e-07   28.6   0.3    1.8e-06   27.7   0.3    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
    3.5e-05   23.6   0.0    8.4e-05   22.4   0.0    1.6  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0011   18.8   2.0     0.0013   18.6   0.6    1.9  2  HTH_11         HTH domain
     0.0043   16.9   0.3     0.0094   15.8   0.3    1.5  1  TFIIE_alpha    TFIIE alpha subunit
     0.0044   16.9   0.2     0.0099   15.8   0.2    1.5  1  MarR           MarR family
     0.0062   16.3   0.0      0.012   15.4   0.0    1.5  1  DUF742         Protein of unknown function (DUF742)
     0.0083   16.1   0.0      0.017   15.1   0.0    1.4  1  Dimerisation2  Dimerisation domain
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.031   14.2   0.0    1.4  1  MarR_2         MarR family
      0.033   14.2   0.2      0.086   12.8   0.2    1.7  1  HTH_45         Winged helix-turn-helix
      0.034   14.6   0.1      0.074   13.6   0.1    1.5  1  HTH_27         Winged helix DNA-binding domain
      0.037   13.8   0.1      0.069   12.9   0.1    1.4  1  HTH_38         Helix-turn-helix domain
      0.045   13.6   0.0      0.086   12.7   0.0    1.5  1  HTH_IclR       IclR helix-turn-helix domain
      0.091   12.6   0.0       0.18   11.6   0.0    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
        0.1   12.7   0.3        0.2   11.7   0.3    1.4  1  Cullin_Nedd8   Cullin protein neddylation domain


Domain annotation for each model (and alignments):
>> Inhibitor_I42  Chagasin family peptidase inhibitor I42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1     2e-10   2.1e-07       1      90 [.     308     391 ..     308     392 .. 0.85
   2 !   39.5   0.1   5.5e-13   5.8e-10       2      91 .]     417     500 ..     416     500 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2e-10
                                   EEETT-EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSSEEEEEEEEEE-TTSTSS- CS
                 Inhibitor_I42   1 tvkvgetieieLpenpttGYsWtvdasdseglkllseeyipdesdelvGaggthvwtfkalkpGettiefkyarpwekate 81 
                                   +v++g++++i L + p++GY W ++  d+ +l+  + +y++++s   v  + ++ wtf+  + Ge +i+++y ++++++ +
  gi|91773131|ref|YP_565823.1| 308 SVNAGSIVRIDL-DAPSEGY-WYLSGRDDLFLNEKGYGYSSSYS--PVDDDSVYGWTFETPSIGEKSIMLEYNSWNDQT-S 383
                                   589*********.8999***.******88888888888888888..6*************************5555555.5 PP

                                   -SC.EEEEE CS
                 Inhibitor_I42  82 aeertftlt 90 
                                    ++ +f++t
  gi|91773131|ref|YP_565823.1| 384 VPS-DFEMT 391
                                   455.88776 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 5.5e-13
                                   EETT-EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSSEEEEEEEEEE-TTSTSS-- CS
                 Inhibitor_I42   2 vkvgetieieLpenpttGYsWtvdasdseglkllseeyipdesdelvGaggthvwtfkalkpGettiefkyarpwekatea 82 
                                   +++ge + i+L e     Y W+++ +  +gl+l ++++ip+++       g+h+w+++a ++Ge++i++  +++  + t  
  gi|91773131|ref|YP_565823.1| 417 LEQGEWMLIRLFESTADTYAWNMTLT--DGLQLKRDQFIPQSKG---SLYGKHEWKIEAIAAGEQNISAINMKQKVDITG- 491
                                   689***********************..9*************97...44569********************99999977. PP

                                   SC.EEEEEE CS
                 Inhibitor_I42  83 eertftltv 91 
                                    e+ f+ltv
  gi|91773131|ref|YP_565823.1| 492 YEQIFDLTV 500
                                   555999998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   4.7e-13     5e-10       3      60 ..      37      93 ..      35      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.7e-13
                                  HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                  i+  L+++  ++il++L ++e+++a+++ + l+ls +t+ y+++ L ea+L++v r +
  gi|91773131|ref|YP_565823.1| 37 ITQTLSNEKSLKILDLL-SEEPMSATDISKKLGLSITTIKYNIDSLLEADLIKVHRIK 93
                                  6678999**********.************************************9976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.6   1.4e-09   1.4e-06       2      48 .]      43      88 ..      42      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.4e-09
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +e+ +kIL lL +   +s ++++++lglS++t+++ ++ L e+ lIk
  gi|91773131|ref|YP_565823.1| 43 NEKSLKILDLLSE-EPMSATDISKKLGLSITTIKYNIDSLLEADLIK 88
                                  7899*********.77*****************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.3   1.7e-09   1.8e-06       3      46 ..      45      88 ..      43      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.7e-09
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  + lkIL lL+e+++++++++++lgls  t+ +    L ea+L++
  gi|91773131|ref|YP_565823.1| 45 KSLKILDLLSEEPMSATDISKKLGLSITTIKYNIDSLLEADLIK 88
                                  569***************************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     8e-08   8.4e-05      16      66 ..      51     108 ..      49     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE-- CS
                          TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYravd 66 
                                    Ll+++p++a++i+++lg++ +++   + sL++++l+++ + +        klY++v+
  gi|91773131|ref|YP_565823.1|  51 DLLSEEPMSATDISKKLGLSITTIKYNIDSLLEADLIKVHRIKwsakgreVKLYEPVQ 108
                                   79*************************************9999999999999999985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   1.2e-06    0.0013       3      46 ..      47      89 ..      45      93 .. 0.86
   2 ?   -3.2   0.0         8   8.5e+03      26      33 ..     119     126 ..     118     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL.eelgvpI 46
                                  l+il lL  +++p+s+ +++++L++S +t+   I++L e+ ++++
  gi|91773131|ref|YP_565823.1| 47 LKILDLL--SEEPMSATDISKKLGLSITTIKYNIDSLlEADLIKV 89
                                  7899999..6667**********************9977777665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8
                        HTH_11  26 nvSrrtvr 33 
                                   nvSr+ + 
  gi|91773131|ref|YP_565823.1| 119 NVSRASII 126
                                   99999985 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   8.9e-06    0.0094       7      67 ..      38      97 ..      34     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.9e-06
                                  HHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTT CS
                   TFIIE_alpha  7 vrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeek 67
                                   +   +e+  ++ld L  +  ++  d++k+l++ ++ ++  +  L ea l+k++r +   k
  gi|91773131|ref|YP_565823.1| 38 TQTLSNEKSLKILDLLS-EEPMSATDISKKLGLSITTIKYNIDSLLEADLIKVHRIKWSAK 97
                                  555667899999*9888.7788999******************************886555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   9.4e-06    0.0099       6      49 ..      47      89 ..      43      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.4e-06
                                  HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  ++iL +l+ ++p+s +++ kklg+s++t+   +d L +++li+ 
  gi|91773131|ref|YP_565823.1| 47 LKILDLLS-EEPMSATDISKKLGLSITTIKYNIDSLLEADLIKV 89
                                  56666665.579*****************************975 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.012      39     102 ..      39     102 ..      18     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                        DUF742  39 arlq.pehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrapvtdraaeqpdre 102
                                   ++l+ ++  +il+L +e p+s  +++ +l l +++++  + +Ll+a+l++v++      a+  + +
  gi|91773131|ref|YP_565823.1|  39 QTLSnEKSLKILDLLSEePMSATDISKKLGLSITTIKYNIDSLLEADLIKVHRIKWS--AKGREVK 102
                                   4444045679****9999*********************************998776..5555555 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.017      11      65 ..      37      90 ..      33     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                 Dimerisation2 11 aSkaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLere 65
                                  ++++L    +L++ dlL e ep+sa +++++lg+s+  ++  +d +   +L +++
  gi|91773131|ref|YP_565823.1| 37 ITQTLSNEKSLKILDLLSE-EPMSATDISKKLGLSITTIKYNIDSLLEADLIKVH 90
                                  6788888999*********.*****************999988888877777765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-05     0.031      10      52 ..      49      88 ..      46      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  +L  L  +p   ++++++ ++lgls  ++ + ++ L +a L+ 
  gi|91773131|ref|YP_565823.1| 49 ILDLLSEEP---MSATDISKKLGLSITTIKYNIDSLLEADLIK 88
                                  567777777...9****************************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 ?   12.8   0.2   8.2e-05     0.086      10      57 ..      48      95 ..      44     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-05
                        HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYv 57
                                   IL+ +se+  + T i +k  Ls  +++  +d L+e +lik +  k++
  gi|91773131|ref|YP_565823.1| 48 KILDLLSEEPMSATDISKKLGLSITTIKYNIDSLLEADLIKVHRIKWS 95
                                  79**************************************98777765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     7e-05     0.074      16      48 ..      55      87 ..      47     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                        HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                  +++++++d++++l ++ ++i y+++ L e++L+
  gi|91773131|ref|YP_565823.1| 55 EEPMSATDISKKLGLSITTIKYNIDSLLEADLI 87
                                  78999**************************** PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.5e-05     0.069       4      38 ..      40      75 ..      38      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                        HTH_38  4 hLsleeReeIerllaeG.lslreIArrLgrspsTIs 38
                                   Ls e   +I +ll+e  +s  +I ++Lg s +TI 
  gi|91773131|ref|YP_565823.1| 40 TLSNEKSLKILDLLSEEpMSATDISKKLGLSITTIK 75
                                  6999**********8888*****************6 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.1e-05     0.086       3      42 ..      44      81 ..      42      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-05
                                  HHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHH CS
                      HTH_IclR  3 dRalaiLdalaeapqeltlselArrtglpkStvhRlLqtL 42
                                  ++ l iLd+l+e+p  ++ +++++++gl+ +t    + +L
  gi|91773131|ref|YP_565823.1| 44 EKSLKILDLLSEEP--MSATDISKKLGLSITTIKYNIDSL 81
                                  689*******9976..67***********99976555555 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.18       6      35 ..      47      75 ..      43      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                 HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvl 35
                                  +kIL++L e + +s +++++++GlS +t+ 
  gi|91773131|ref|YP_565823.1| 47 LKILDLLSEEP-MSATDISKKLGLSITTIK 75
                                  79999999875.9*************9986 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00019       0.2      10      58 ..      37      88 ..      34      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                  Cullin_Nedd8 10 IVRiMKsrktlshneLvsev...ieqlskrftpsiadikkrIesLiekeYle 58
                                  I +++ ++k+l++ +L+se      ++sk+  +si+ ik +I+sL+e + ++
  gi|91773131|ref|YP_565823.1| 37 ITQTLSNEKSLKILDLLSEEpmsATDISKKLGLSITTIKYNIDSLLEADLIK 88
                                  77888899********999754466779*******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); 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: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3500.47
//
Query:       gi|91773132|ref|YP_565824.1|  [L=326]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.6e-15   55.7   0.4    8.6e-14   52.2   0.0    2.1  2  Radical_SAM  Radical SAM superfamily
     0.0039   17.3   0.7     0.0095   16.1   0.2    1.8  2  Fer4_14      4Fe-4S single cluster domain
     0.0097   15.7   0.5      0.024   14.4   0.1    1.8  2  LPD13        Large polyvalent protein-associated domain 13
     0.0098   15.1   0.1      0.022   13.9   0.1    1.5  1  DUF561       Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.013   15.7   0.1      0.025   14.9   0.1    1.5  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   2.4e-17   8.6e-14       6     153 ..      32     184 ..      29     189 .. 0.92
   2 ?    1.5   0.1     0.096   3.5e+02      80     115 ..     251     298 ..     187     308 .. 0.55

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.4e-17
                                   EESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESS.TGGGSTTHHHHHHHHHHTCCCTEEE CS
                                   xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpet....vrregrgrslsveeileevkelkaekg.vkevilggg.epllypdfvellerlaklavpgiri 80 
                                    Cn++C++C+ ++     + + +    +++ee+++ +  ++++ +  ++++++g  ep+l+ ++   +e+++ +  +++ i
  gi|91773132|ref|YP_565824.1|  32 NCNFDCVYCQLGHVdwkiSTPSEATDLVTTEEVIDSLANYHKKVDdLDYITFSGTcEPTLNLELGNMIEQIRNI--SNVPI 110
                                   7****************************************77778*****99755******************..9**** PP

                                   EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdrivglp 153
                                   +v+tn  l+++e ++  l    d v  +l ++++++++ +++   g ++++++++l+ l +  +++v + i++l 
  gi|91773132|ref|YP_565824.1| 111 CVITNSSLVNREDVRNNLS-KADLVVATLVSGNEDTFQAINRpaEGIELQDIIKGLKQLQKMKGPKVAIEIMLLD 184
                                   **********999999999.55*************88888876688889****************9999999986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.096
                                   EEEEECSSCHG..........HHHHHHHHHTT..-SEEEEEEBSSSHH CS
                                   xxxxxxxxxxx..........xxxxxxxxxxx..xxxxxxxxxxxxxx RF
                   Radical_SAM  80 itvetngtlpd..........eeklerllelg..vdrvslgleaadde 115
                                   ++++  g++            +e+ +++l+++  +d+v  +l++ ++e
  gi|91773132|ref|YP_565824.1| 251 VRLVLKGLKRKrsniehenltDEVYDLILRRPctFDQVVQSLDIDNEE 298
                                   333333333223333333333666666666666666666666666655 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 !   16.1   0.2   2.6e-06    0.0095       7     109 ..      32     129 ..      29     142 .. 0.63
   2 ?   -1.7   0.0      0.87   3.1e+03      68     110 ..     162     207 ..     154     215 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.6e-06
                       Fer4_14   7 gCnlsCkgCd.nketwks....elgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeypek 81 
                                    Cn+ C+ C   + +wk     e++   t e++ + l++ +k+  + + ++++G  eP +     el ++++++++   ++
  gi|91773132|ref|YP_565824.1|  32 NCNFDCVYCQlGHVDWKIstpsEATDLVTTEEVIDSLANYHKKVDDLDYITFSGtCEPTLN---LELGNMIEQIRNIS-NV 108
                                   7********9855556653333444444444444555444444445689*****99**955...46667777776655.78 PP

                       Fer4_14  82 kiwletngtleielektpdlkekleals 109
                                   +i + tn +l           ++++ ls
  gi|91773132|ref|YP_565824.1| 109 PICVITNSSLVNRE-------DVRNNLS 129
                                   89999999988332.......3333333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.87
                       Fer4_14  68 lklvkrlkeey.pe..kkiwl...etngtleielektpdlkeklealsk 110
                                   +k +k+l++ + p+  ++i l   + +++ + +    p+ ++++e+l+ 
  gi|91773132|ref|YP_565824.1| 162 IKGLKQLQKMKgPKvaIEIMLldsNNGYLTN-SS--DPEIDKQIEVLKF 207
                                   4555555554445522333322112333333.33..4777777777774 PP

>> LPD13  Large polyvalent protein-associated domain 13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.98   3.5e+03      24      39 ..      89     104 ..      62     127 .. 0.58
   2 !   14.4   0.1   6.7e-06     0.024       9      75 ..     214     280 ..     208     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.98
                         LPD13  24 psrdvlLptlpenven 39 
                                   p+ + +L ++ e++ n
  gi|91773132|ref|YP_565824.1|  89 PTLNLELGNMIEQIRN 104
                                   4444444444444443 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.7e-06
                         LPD13   9 eletvseipdelFtnpsrdvlLptlpenvenligaegkkvllkkniveknkrdHkeltledsrkiLn 75 
                                   e+ t+s  p e+F  p  + +L+++ ++  + +g e  +++lk    ++ +++H++lt e    iL+
  gi|91773132|ref|YP_565824.1| 214 EILTISRPPAEDFIIPVTETRLKEIAQKFDEELGRERVRLVLKGLKRKRSNIEHENLTDEVYDLILR 280
                                   67899999***********************************99999************9999997 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   6.1e-06     0.022      51     116 ..      97     169 ..      94     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-06
                        DUF561  51 klvkkvksvsniPiCv...saveakllleavkaGadlvei....GnfdslYeqgrklsseeilalvkevrkLl 116
                                   +++++++++sn+PiCv   s++  ++ ++  ++ adlv      Gn d++ + +r  +  e+  ++k +++L 
  gi|91773132|ref|YP_565824.1|  97 NMIEQIRNISNVPICVitnSSLVNREDVRNNLSKADLVVAtlvsGNEDTFQAINRPAEGIELQDIIKGLKQLQ 169
                                   689************988877777777777788888875333349*****99999999999999999888885 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 ?   14.9   0.1   6.9e-06     0.025      11     118 ..      29     142 ..      22     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.9e-06
                       Fer4_12  11 fvsgCnlsCkgCfnket.wsfksgkef.tkelleeiiedlkkesi.....egltllG.GEPllpenaeallelvkevkeek 83 
                                   f + Cn+ C +C    + w+ ++  e  +  + ee+i++l+++++     + +t++G  EP l   + +l ++++++++  
  gi|91773132|ref|YP_565824.1|  29 FRKNCNFDCVYCQLGHVdWKISTPSEAtDLVTTEEVIDSLANYHKkvddlDYITFSGtCEPTL---NLELGNMIEQIRNIS 106
                                   6689********7544325555444431467777777777775555666799*****55****...667888888888877 PP

                       Fer4_12  84 pekdiwlytgytleelskkekeellkeid....vlvdGk 118
                                     + +++++ +  +  +   +++ l++ d     lv+G+
  gi|91773132|ref|YP_565824.1| 107 NVPICVITNSSLVNRED---VRNNLSKADlvvaTLVSGN 142
                                   76677777776655443...4455555552222455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2354.75
//
Query:       gi|91773133|ref|YP_565825.1|  [L=201]
Description: hypothetical protein Mbur_1150 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-21   77.3   0.0    1.4e-21   76.8   0.0    1.2  1  DUF134          Protein of unknown function  DUF134
  ------ inclusion threshold ------
      0.022   14.2   7.1        0.6    9.6   0.1    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.024   14.3   0.1      0.036   13.8   0.1    1.2  1  Sigma70_r4_2    Sigma-70, region 4
      0.047   13.7   0.1       0.16   12.0   0.0    1.9  2  HTH_29          Winged helix-turn helix
      0.086   12.5   3.5        6.6    6.5   0.1    2.6  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.088   12.8   0.0       0.11   12.6   0.0    1.1  1  DUF45           Protein of unknown function DUF45
       0.19   11.6   0.0       0.36   10.7   0.0    1.4  1  HTH_23          Homeodomain-like domain
       0.22   11.3   8.7        1.8    8.4   1.4    2.4  2  zinc_ribbon_2   zinc-ribbon domain
       0.35   10.9   6.4        1.1    9.3   3.8    2.1  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.44   10.4   8.2       0.27   11.1   0.7    2.3  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.66   10.1   4.0        1.6    8.8   4.0    1.6  1  Zn_Tnp_IS91     Transposase zinc-binding domain
          1    9.5   7.9        2.6    8.2   7.9    1.7  1  Zn-ribbon_8     Zinc ribbon domain
        1.8    8.6   4.8        3.9    7.5   4.8    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0     1e-24   1.4e-21       1      96 [.       6     103 ..       6     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 1e-24
                        DUF134   1 msrkgrprklrdileePkvrifkPea..veetgkvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkia 79 
                                   m   grprk + +  + + r fkP +   ++ + v+i++dele++rl   e++kqe+aa+ m i ++t+ r+l+ + +kia
  gi|91773133|ref|YP_565825.1|   6 MHNMGRPRKRKMVNFDYNTRHFKPSGtcLKDMEEVNITIDELETLRLSTLEKMKQENAAQTMQIHQSTFQRTLQRTLQKIA 86 
                                   66789********************944455568*********************************************** PP

                        DUF134  80 kalveGraiilkGGeyk 96 
                                   +alv+G+ i ++GG+y+
  gi|91773133|ref|YP_565825.1|  87 DALVNGKSIRVEGGDYT 103
                                   ****************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 ?    6.6   2.6    0.0037       5.1      18      25 ..     170     177 ..     165     178 .. 0.77
   2 ?    9.6   0.1   0.00043       0.6       3      11 ..     189     197 ..     187     201 .] 0.61

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0037
                   zf-ribbon_3  18 vCpyCGtk 25 
                                   +Cp+CG++
  gi|91773133|ref|YP_565825.1| 170 KCPNCGYE 177
                                   69999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00043
                   zf-ribbon_3   3 vrCPnCGap 11 
                                   v CP+CG+p
  gi|91773133|ref|YP_565825.1| 189 VICPECGKP 197
                                   456666654 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.6e-05     0.036      19      54 .]      50      85 ..      45      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                  HHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                  Sigma70_r4_2 19 fllryleglsykEIAellgisegtVksrlsRArkkL 54
                                  + l+ le ++++ +A+ + i+ +t ++ l+R ++k+
  gi|91773133|ref|YP_565825.1| 50 LRLSTLEKMKQENAAQTMQIHQSTFQRTLQRTLQKI 85
                                  67999****************************996 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         4   5.5e+03       4      54 ..       3      13 ..       1      18 [. 0.54
   2 ?   12.0   0.0   0.00012      0.16      10      48 ..      56      93 ..      52      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                        HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrpr 54
                                  ++++++ G +                                        r
  gi|91773133|ref|YP_565825.1|  3 CIIMHNMGRP----------------------------------------R 13
                                  5555555554........................................3 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00012
                        HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrr 48
                                  e ++   ++A+ ++++ +t++r+l r  ++ ++al +++
  gi|91773133|ref|YP_565825.1| 56 EKMK-QENAAQTMQIHQSTFQRTLQRTLQKIADALVNGK 93
                                  5676.889******************9999999999866 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9    0.0076        11      23      31 ..     170     178 ..     165     178 .. 0.84
   2 ?    6.5   0.1    0.0048       6.6       6      15 ..     191     200 ..     188     201 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0076
                 zf-NADH-PPase  23 vCpaCgleh 31 
                                    Cp+Cg+e+
  gi|91773133|ref|YP_565825.1| 170 KCPNCGYEQ 178
                                   69****996 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0048
                 zf-NADH-PPase   6 CgrCGaptep 15 
                                   C+ CG p+++
  gi|91773133|ref|YP_565825.1| 191 CPECGKPMIR 200
                                   *******987 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.8e-05      0.11       3      76 ..      40     110 ..      38     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                         DUF45   3 lrlrvepdgsvevsaPkgvseeeiedfvkkkakwiekklakleerakeaekelesgesfpllGkkyrlkvekgk 76 
                                   +++++++ +++++s+ +++++e++ +  + +++  +++l++  +   +  + l++g+s+++ G +y +  ++g+
  gi|91773133|ref|YP_565825.1|  40 VNITIDELETLRLSTLEKMKQENAAQTMQIHQSTFQRTLQRTLQ---KIADALVNGKSIRVEGGDYTMPGKDGT 110
                                   7899***9999*******************************99...99*****************98887777 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.36      16      40 ..      56      80 ..      47      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                        HTH_23 16 eGlsvreIAreLgvsrrTvyrwlkr 40
                                  e++ ++ +A+ + ++++T +r l+r
  gi|91773133|ref|YP_565825.1| 56 EKMKQENAAQTMQIHQSTFQRTLQR 80
                                  5889999****************99 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4    0.0013       1.8       1       8 [.     170     177 ..     170     178 .. 0.77
   2 ?    6.8   1.0    0.0042       5.8      16      22 ..     191     197 ..     186     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                 zinc_ribbon_2   1 fCpnCGae 8  
                                   +CpnCG+e
  gi|91773133|ref|YP_565825.1| 170 KCPNCGYE 177
                                   68888876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0042
                 zinc_ribbon_2  16 CpyCGtp 22 
                                   Cp+CG p
  gi|91773133|ref|YP_565825.1| 191 CPECGKP 197
                                   5555554 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.15   2.1e+02      24      61 ..      35      73 ..      21      98 .. 0.77
   2 ?    9.3   3.8   0.00081       1.1      69      96 ..     167     198 ..     160     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
                                  .EEEEEEEEEETTCT--HHHHHHHHHHHHCC.T.TTT-E CS
                          HypA 24 rkvtkvkvevGelsgvepeaLefafellaegtv.legae 61
                                  +  ++v++++ el+++  ++Le + +  a++t+ +++++
  gi|91773133|ref|YP_565825.1| 35 KDMEEVNITIDELETLRLSTLEKMKQENAAQTMqIHQST 73
                                  567889999999999999999888777776666555555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00081
                                   -EEEETTTS-EEECHH..H..HHS-TTTSSS- CS
                          HypA  69 vkvrCreCgkefelee..k..alrCpkCgsad 96 
                                    +++C +Cg+e +++      ++ Cp+Cg+  
  gi|91773133|ref|YP_565825.1| 167 GVCKCPNCGYEQTHQPgtPcaQVICPECGKPM 198
                                   5799*****999977664256779*****975 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.5     0.061        84       3       9 ..     170     177 ..     168     181 .. 0.79
   2 ?   11.1   0.7    0.0002      0.27       2      14 ..     189     201 .]     188     201 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.061
                                   E-SSS-.- CS
                zf-C4_Topoisom   3 kCPkCg.g 9  
                                   kCP Cg +
  gi|91773133|ref|YP_565825.1| 170 KCPNCGyE 177
                                   9****944 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                                   EE-SSS--EEEEE CS
                zf-C4_Topoisom   2 ekCPkCggdLvlk 14 
                                   + CP+Cg+++++k
  gi|91773133|ref|YP_565825.1| 189 VICPECGKPMIRK 201
                                   78********987 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 ?    8.8   4.0    0.0011       1.6      39      65 ..     168     196 ..     160     201 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                   Zn_Tnp_IS91  39 ryeCeeCghe..kivyfsCksrhCpsCqk 65 
                                   + +C++Cg e  +     C +  Cp+C+k
  gi|91773133|ref|YP_565825.1| 168 VCKCPNCGYEqtHQPGTPCAQVICPECGK 196
                                   568****95521555689*********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 ?    8.2   7.9    0.0019       2.6       7      37 ..     170     199 ..     169     201 .] 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                   Zn-ribbon_8   7 rCeeCghefevlqsis.dapltaCPeCgsevr 37 
                                   +C +Cg  +e+ ++     +++ CPeCg+++ 
  gi|91773133|ref|YP_565825.1| 170 KCPNCG--YEQTHQPGtPCAQVICPECGKPMI 199
                                   7*****..554444452555666*****9654 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.8    0.0028       3.9      30      54 ..     170     196 ..     168     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0028
                OrfB_Zn_ribbon  30 tCseCgsknke..alsgrtfkCpnCgf 54 
                                   +C++Cg+++++       ++ Cp+Cg 
  gi|91773133|ref|YP_565825.1| 170 KCPNCGYEQTHqpGTPCAQVICPECGK 196
                                   7**********9888999*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1646  (0.0918066); expected 358.6 (0.02)
Passed bias filter:                     1098  (0.0612416); expected 358.6 (0.02)
Passed Vit filter:                       154  (0.00858944); 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):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1361.05
//
Query:       gi|91773134|ref|YP_565826.1|  [L=282]
Description: TatD-related deoxyribonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-22   77.7   0.0    1.3e-21   77.2   0.0    1.2  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.056   12.8   0.0      0.073   12.4   0.0    1.2  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   1.4e-25   1.3e-21       2     254 ..      11     276 ..      10     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 1.4e-25
                                   EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG.................GGHHHHHHHHTT.TTTEEEEE---GGG CS
                    TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtss.................kdskavlelakkypnkvyavlGiHPne 65 
                                   D H+H+d     ++  ++++++++ag+++++ v+  +                  +++++ + +++     ++vlG+HP+e
  gi|91773134|ref|YP_565826.1|  11 DEHMHIDP---RAKGLKAVKEFQNAGGTHIILVTKPTwtigvevtrpedykivfDETVDLANQINETGVTAFPVLGVHPAE 88 
                                   9*******...5689****************7777667777888888887665545555666666689999********** PP

                                   GGCC.CCHH.........HHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES.-H CS
                    TatD_DNase  66 vdeasedll.........eelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrk.ae 135
                                   +++ +e+++           l+ + ++v++  +v++ + G+++y+++e+ ++a ++++e+ + lAk  ++++++H+++  e
  gi|91773134|ref|YP_565826.1|  89 INKLNERMElekavelmkGGLEIAsEYVEEGLAVGL-KSGRPHYPVSEEIWDASNTIMEHGFTLAKGAGCAIQLHTESvGE 168
                                   ***777777778877777778888889*********.*****************************************899 PP

                                   HHHHHHHHHCGGCCS...EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHH..HHS-GGGEEE---TTSSEE CS
                    TatD_DNase 136 edlleilkeaaeaka...kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelv..kavpldrlLiETDaPyltp 211
                                    +l++i+++a+ +++   +vv H        +++ l  g++ ++ +          + ++  +  + +r+++ETD  y+++
  gi|91773134|ref|YP_565826.1| 169 PELIDITERAKRTGIqlnRVVKHY-APPLVNVCERL--GIFPGVLA---------GKGAIeeALEQGTRFMMETD--YIDD 235
                                   9**********99999*8888886.77777777776..9****998.........344444466789********..9999 PP

                                   CCCTT.SE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    TatD_DNase 212 kpyrg.krnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                    p r+ ++  p+++++   kl e  +  +e + +i++eN+++++
  gi|91773134|ref|YP_565826.1| 236 -PERPgAVLGPKTIPRRTLKLVEEYG--EELFWKIHKENVEEVY 276
                                   .99999***********999999766..8899999999999987 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-06     0.073      94     248 ..      53     232 ..       7     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-06
                                   HHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEET CS
                  Amidohydro_1  94 skasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgt 174
                                   +++ ++ + ++      + a+++ +++++  +  ++ ++e+ ++  e ++  + v    ++++ + e++e++ + + ++ +
  gi|91773134|ref|YP_565826.1|  53 RPEDYKIVFDET----VDLANQINETGVTAFPVLGVHPAEINKLN-ERMELEKAVELMKGGLEIASEYVEEGLAVGLKS-G 127
                                   555555554443....44555666688888889999999996665.455555555555588899999999999988888.6 PP

                                   TTTSTCCHHTTTHCCEEEHCTCEEE......HH.........HHHHHHHHHHHHCEEHHHHHHHH................ CS
                  Amidohydro_1 175 hlevaeslglldeiklilahgvhlt......pt.........eaellkerlkeagvahcpfsnsi................ 224
                                     +++ s  + d  ++i++hg +l                  e++ + er+k++g+ + +   ++                
  gi|91773134|ref|YP_565826.1| 128 RPHYPVSEEIWDASNTIMEHGFTLAkgagcaIQlhtesvgepELIDITERAKRTGIQLNRVVKHYapplvnvcerlgifpg 208
                                   67777778999999***********87666511666789999***************666666667777778888888999 PP

                                   SEHHHHHHHHHHHHTSCEEEEEEC CS
                  Amidohydro_1 225 lrsgrealrkaldeGvkvglgtDg 248
                                   +  g  a+++al++G+++++ tD 
  gi|91773134|ref|YP_565826.1| 209 VLAGKGAIEEALEQGTRFMMETDY 232
                                   5555567****************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 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:                         2  (0.000111551); expected 0.2 (1e-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: 2147.62
//
Query:       gi|91773135|ref|YP_565827.1|  [L=416]
Description: WD40-like beta propeller protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-26   91.1  20.5    2.9e-06   27.0   0.2    7.4  7  PD40             WD40-like Beta Propeller Repeat
      2e-09   36.7  10.7      0.056   12.2   0.4    7.1  9  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    3.1e-08   33.2   4.9     0.0011   18.2   0.4    4.0  4  DUF5050          Domain of unknown function (DUF5050)
    5.5e-08   31.9   3.4    2.8e-06   26.3   3.0    3.9  1  Pectate_lyase22  Oligogalacturonate lyase
    0.00045   20.2   0.6     0.0014   18.5   0.2    2.1  2  eIF2A            Eukaryotic translation initiation factor eIF
     0.0012   18.7   0.0      0.067   12.9   0.0    2.9  3  Gmad1            Lipoprotein LpqB beta-propeller domain
  ------ inclusion threshold ------
      0.013   15.6   0.0         17    5.6   0.0    3.7  4  BiPBP_C          Penicillin-Binding Protein C-terminus Family
      0.027   14.7   0.5        3.5    7.9   0.2    3.1  3  NusG_II          NusG domain II
      0.029   14.0   0.3        2.6    7.7   0.0    3.3  3  ChitinaseA_N     Chitinase A, N-terminal domain


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.3   8.6e-05      0.17       3      28 ..      26      51 ..      26      61 .. 0.89
   2 !   19.8   0.0   2.8e-07   0.00055      16      38 .]      93     114 ..      93     114 .. 0.96
   3 ?    1.6   0.2      0.14   2.8e+02      13      27 ..     143     157 ..     143     166 .. 0.83
   4 !   27.0   0.2   1.5e-09   2.9e-06       3      38 .]     202     236 ..     202     236 .. 0.96
   5 !   13.7   0.2   2.3e-05     0.046       9      27 ..     250     268 ..     249     280 .. 0.77
   6 !   24.5   0.7     9e-09   1.8e-05       2      38 .]     289     327 ..     288     327 .. 0.94
   7 ?    0.4   0.0      0.33   6.5e+02      14      24 ..     344     354 ..     342     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.6e-05
                                  E--SSSS.EEEEEE-TTSSEEEEEEE CS
                          PD40  3 rltntpgnegaPsfSPDGkrlaFsSd 28
                                  +lt  ++ +g P +S DG +++++S+
  gi|91773135|ref|YP_565827.1| 26 QLTDETESIGYPQWSTDGDKIIYTSS 51
                                  578889999***************96 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.8e-07
                                   E-TTSSEEEEEEECT.TCEEEEE CS
                          PD40  16 fSPDGkrlaFsSdRgsGkpdIyv 38 
                                   +SPDG++l F+S+ + G++++++
  gi|91773135|ref|YP_565827.1|  93 LSPDGTKLLFVSNAT-GNHELWI 114
                                   5**************.******7 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.14
                                   EEEE-TTSSEEEEEE CS
                          PD40  13 aPsfSPDGkrlaFsS 27 
                                   ++s+SP  + ++++S
  gi|91773135|ref|YP_565827.1| 143 GISWSPGSSQIVYVS 157
                                   589***99****999 PP

  == domain 4  score: 27.0 bits;  conditional E-value: 1.5e-09
                                   E--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                          PD40   3 rltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                   +lt++ +++++ ++  DG ++aF+S+ + G+  I++
  gi|91773135|ref|YP_565827.1| 202 KLTTSRKDNIGATWRSDGEKIAFVSNES-GNGGIWI 236
                                   68999**********************9.*****97 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 2.3e-05
                                   S.EEEEEE-TTSSEEEEEE CS
                          PD40   9 gnegaPsfSPDGkrlaFsS 27 
                                   g  +++ +SPDG++++++ 
  gi|91773135|ref|YP_565827.1| 250 GSAYNIDWSPDGTKIVYVK 268
                                   5667888**********85 PP

  == domain 6  score: 24.5 bits;  conditional E-value: 9e-09
                                   EE--SSSS....EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                          PD40   2 krltntpg...negaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                   k+ltn+++       P +SPDG++++F S    G ++I++
  gi|91773135|ref|YP_565827.1| 289 KPLTNNSKyfvSQSYPDWSPDGSKIVFNSGNI-GEYEIWI 327
                                   799999999999******************88.******7 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.33
                                   EEE-TTSSEEE CS
                          PD40  14 PsfSPDGkrla 24 
                                   P +SP G +++
  gi|91773135|ref|YP_565827.1| 344 PQWSPKGDKIV 354
                                   66******996 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 !    4.2   0.0    0.0073        15      31      61 ..      20      50 ..      13      56 .. 0.85
   2 ?   -0.1   0.0      0.16   3.1e+02     268     290 ..      52      69 ..      40      86 .. 0.67
   3 !    8.5   0.0   0.00037      0.74     244     285 ..      94     134 ..      86     143 .. 0.80
   4 ?    1.9   0.3     0.037        74     225     271 ..     158     210 ..     150     222 .. 0.74
   5 !    4.3   0.1    0.0068        14     227     266 ..     209     249 ..     181     255 .. 0.54
   6 !   12.2   0.4   2.8e-05     0.056      39      93 ..     248     306 ..     228     306 .. 0.74
   7 !   10.8   0.2   7.3e-05      0.15      20      77 ..     273     337 ..     271     342 .. 0.77
   8 ?    0.2   0.0      0.13   2.6e+02      46      58 ..     342     354 ..     320     359 .. 0.69
   9 ?    0.3   0.0      0.12   2.4e+02      49     121 ..     345     359 ..     337     386 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0073
                                  TTEECEEEETTTT.BSEEEEESSTTEEEEEE CS
                       DPPIV_N 31 etneveelspgeeklqlakwSPagdklafvr 61
                                  ++ e+ +l++++e + +++wS +gdk++++ 
  gi|91773135|ref|YP_565827.1| 20 NASEILQLTDETESIGYPQWSTDGDKIIYTS 50
                                  56778888889999**************975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                                   SS-C.EEESS-SSS-EEEEEEEE CS
                       DPPIV_N 268 dgkseikqlTsGeweVtsilavd 290
                                   d       +TsG+w V ++  +d
  gi|91773135|ref|YP_565827.1|  52 DL----ENITSGDWVV-DFWMMD 69 
                                   33....369*****99.444444 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00037
                                   TTTSSEEEEEEETTSSEEEEEEESSS-C.EEESS-SSS-EEE CS
                       DPPIV_N 244 krdesgflwisekdGfkHLylfdldgkseikqlTsGeweVts 285
                                   ++d++++l++s+ +G + L+++d dg+  ++qlT G+    +
  gi|91773135|ref|YP_565827.1|  94 SPDGTKLLFVSNATGNHELWIMDIDGSD-KRQLTYGAHLENN 134
                                   4688899999999999999999999999.9999998865555 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.037
                                   EEEEESSS-S......SS-S-EEE-TTTSSEEEEEEETTSSEEEEEEESSS-C CS
                       DPPIV_N 225 kleetsdgWv......elhdevhflkrdesgflwisekdGfkHLylfdldgks 271
                                   +++e++++W       ++++ ++++k ++++ +wi+++dG + L l ++++ +
  gi|91773135|ref|YP_565827.1| 158 ASSENRNVWEtveingKKEQMFNISKVSKDYDIWIVDHDGSNNLKLTTSRKDN 210
                                   44677777766666545666666668899999999999999999999888766 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.0068
                                   EEESSS-SSS-S-EEE-.TTTSSEEEEEEETTSSEEEEEEE CS
                       DPPIV_N 227 eetsdgWvelhdevhfl.krdesgflwisekdGfkHLylfd 266
                                   ++   +W +  ++++f+ +++++g +wi++kdG +++ l+d
  gi|91773135|ref|YP_565827.1| 209 DNIGATWRSDGEKIAFVsNESGNGGIWIMNKDGSDKIQLVD 249
                                   33444555555555555555666666666666666666555 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 2.8e-05
                                   ETTTT.BSEEEEESSTTEEEEE......ETTEEEEESTTTSEEEECES-STTTEEESB--H CS
                       DPPIV_N  39 spgeeklqlakwSPagdklafv......rnnnLyvrelatgkeiqlTsdgsagifnGvadW 93 
                                    +g   +  ++wSP+g+k+++v      + + ++v ++  ++++ lT++ +  ++   +dW
  gi|91773135|ref|YP_565827.1| 248 VDG--SAYNIDWSPDGTKIVYVkgdhenYTSSIWVMDTDGSNKKPLTNNSKYFVSQSYPDW 306
                                   444..67789999999999999444333356799999999999999999999999999999 PP

  == domain 7  score: 10.8 bits;  conditional E-value: 7.3e-05
                                   EETTEEEEEETTTEECEEEETT...TT.BSEEEEESSTTEEEEEETT....EEEEESTTTSEEEE CS
                       DPPIV_N  20 sytaeyyiydletneveelspg...eeklqlakwSPagdklafvrnn....nLyvrelatgkeiq 77 
                                   +yt + ++ d+   + ++l+++      +++++wSP+g k++f   n    ++++ ++    +i+
  gi|91773135|ref|YP_565827.1| 273 NYTSSIWVMDTDGSNKKPLTNNskyFVSQSYPDWSPDGSKIVFNSGNigeyEIWIMNSDGTDQIR 337
                                   688899999999999999999976666789*************7654333388888776666655 PP

  == domain 8  score: 0.2 bits;  conditional E-value: 0.13
                                   SEEEEESSTTEEE CS
                       DPPIV_N  46 qlakwSPagdkla 58 
                                    +++wSP+gdk++
  gi|91773135|ref|YP_565827.1| 342 LMPQWSPKGDKIV 354
                                   5788888888876 PP

  == domain 9  score: 0.3 bits;  conditional E-value: 0.12
                                   EEESSTTEEEEEETTEEEEESTTTSEEEECES-STTTEEESB--HHHHHHTSSSSBEEEE-TTSSEEEEEEEE CS
                       DPPIV_N  49 kwSPagdklafvrnnnLyvrelatgkeiqlTsdgsagifnGvadWvyeEEvlgsnsavwWspdgsrlaylrfd 121
                                   +                                                          Wsp+g++++ + ++
  gi|91773135|ref|YP_565827.1| 345 Q----------------------------------------------------------WSPKGDKIVTMAIN 359
                                   4..........................................................55555555555554 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.08   1.6e+02     224     257 ..      44      83 ..      38      91 .. 0.75
   2 !    4.7   0.0    0.0079        16     224     255 ..      98     128 ..      64     137 .. 0.59
   3 !   18.2   0.4   5.6e-07    0.0011     191     261 ..     182     256 ..     150     260 .. 0.75
   4 !    8.3   0.1    0.0006       1.2     107     193 ..     263     358 ..     259     381 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.08
                                   TTEEEEEE-SSS-E.......EEEEETTS---EEEEES-E CS
                       DUF5050 224 gnwiYyqkesdeeka......lyrikldGsekeklaegnv 257
                                   +++iY + + ++         + +++ dGs+k  la+g++
  gi|91773135|ref|YP_565827.1|  44 DKIIYTSSDLENITSgdwvvdFWMMDADGSNKIQLASGDS 83 
                                   4556666665555446777779999999999999999875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0079
                                   TTEEEEEE-SSS-E.EEEEETTS---EEEEES CS
                       DUF5050 224 gnwiYyqkesdeekalyrikldGsekeklaeg 255
                                    + +++++++++++ l  ++ dGs+k+ l+ g
  gi|91773135|ref|YP_565827.1|  98 TKLLFVSNATGNHE-LWIMDIDGSDKRQLTYG 128
                                   35566666666666.88888888888877655 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 5.6e-07
                                   EEGGGTT-EEEE-SSS---EE-S-S-EEEEEEE....TTEE.EEEE-SSS-E.EEEEETTS---EEEEES-EEEEE CS
                       DUF5050 191 idlsknyaLyrvklsgsekevltedkvdnyNvt....gnwi.YyqkesdeekalyrikldGsekeklaegnvsnin 261
                                    ++sk+y ++ v+++gs++ +lt+ + dn+  t    g++i ++++es+++  +  +++dGs+k  l +g+  ni 
  gi|91773135|ref|YP_565827.1| 182 SKVSKDYDIWIVDHDGSNNLKLTTSRKDNIGATwrsdGEKIaFVSNESGNGG-IWIMNKDGSDKIQLVDGSAYNID 256
                                   3569******************999988766533333766626666666655.*****************988885 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0006
                                   EEEEEEESSSS-EE.EEEEETTS---EEE.......ESS----SEEETTEEEEE-T.TT-.-EEEEETTTTEEEEEE-S-E CS
                       DUF5050 107 wiYYqhydekdglk.lykikidgkektkl.......sdeaieplsvkdgwiYytgesedh.slykldtdgksiskvseenl 178
                                   +i Y++ d++++++ +  +++dg++k+ l        ++++ + s ++ +i +++ + ++ +++ ++ dg+++ ++ e+ +
  gi|91773135|ref|YP_565827.1| 263 KIVYVKGDHENYTSsIWVMDTDGSNKKPLtnnskyfVSQSYPDWSPDGSKIVFNSGNIGEyEIWIMNSDGTDQIRIDEGLM 343
                                   566777666665543777888888888884332222223344445556666666555554478888888888888877777 PP

                                   EEEEEEETTEEEEEG CS
                       DUF5050 179 yllvvegdyiYyidl 193
                                      + +gd+i  + +
  gi|91773135|ref|YP_565827.1| 344 PQWSPKGDKIVTMAI 358
                                   777777777766555 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   3.0   1.4e-09   2.8e-06      39     271 ..      89     332 ..      62     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.4e-09
               Pectate_lyase22  39 yqkcftrdgskllfggafdgprnyylldlntqqavqltegkg.dntfggf.......lssdddalfyvk...nernlm.rv 107
                                   y+  ++ dg+kllf  +  g+++ +++d++     qlt g   +n + g+        s+    + yv    ++rn+   v
  gi|91773135|ref|YP_565827.1|  89 YNSPLSPDGTKLLFVSNATGNHELWIMDIDGSDKRQLTYGAHlENNLLGLagrwgisWSPGSSQIVYVSassENRNVWeTV 169
                                   6777899*******************************99743444333212222226899999***97222456765246 PP

               Pectate_lyase22 108 dletleetviyqvdeewvgygtwvansdctklvgieikkedwkpltdwkkfaefyft..npccrlirvdlktgeaevilke 186
                                   +++  +e  ++++++  + y  w+ + d ++ + +   ++d    t     +++ f   +     i +  k g  ++ l +
  gi|91773135|ref|YP_565827.1| 170 EINGKKE-QMFNISKVSKDYDIWIVDHDGSNNLKLTTSRKDNIGATWRSDGEKIAFVsnESGNGGIWIMNKDGSDKIQLVD 249
                                   7776655.689999999**********************998776644444444444004445567777777777665555 PP

               Pectate_lyase22 187 nqwlghpiyrpfddstvafchegphdlvdarmwlinedgsnlrkvkehaeg.escthevwvpdgsalayvsylkgstervi 266
                                    +   + i    d + + +  +g h+   + +w+++ dgsn + + + ++   s ++  w pdgs +++ s   g+ e  i
  gi|91773135|ref|YP_565827.1| 250 GS--AYNIDWSPDGTKIVY-VKGDHENYTSSIWVMDTDGSNKKPLTNNSKYfVSQSYPDWSPDGSKIVFNSGNIGEYEIWI 327
                                   44..566766656655555.579********************9998877526889999************9999999999 PP

               Pectate_lyase22 267 ysadp 271
                                   +++d 
  gi|91773135|ref|YP_565827.1| 328 MNSDG 332
                                   88775 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.9   7.8e+03      62      74 ..      34      46 ..      13      53 .. 0.57
   2 !   18.5   0.2   7.1e-07    0.0014      42     162 ..     235     357 ..     204     363 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.9
                                  EEEEEE-TTSS-E CS
                         eIF2A 62 ihdvaWspkskef 74
                                  i   +Ws++++++
  gi|91773135|ref|YP_565827.1| 34 IGYPQWSTDGDKI 46
                                  5555566655554 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 7.1e-07
                                   EESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEESSSSC...EEEEEECSCEEEEEEEEES--EEE.....E-TTSSE CS
                         eIF2A  42 yliklkkkksevvelkkegpihdvaWspkskefaviyGkmpa...kvslfdlkvkviskleeqkrNtif.....fspkgkl 114
                                   +++  +k  s+ ++l  +g ++ + Wsp++++++ ++G+ ++   ++ + d++++ ++ l ++++  +      +sp g  
  gi|91773135|ref|YP_565827.1| 235 WIM--NKDGSDKIQL-VDGSAYNIDWSPDGTKIVYVKGDHENytsSIWVMDTDGSNKKPLTNNSKYFVSqsypdWSPDGSK 312
                                   555..3444556677.46789*****************887752244455667999999999998888545555******9 PP

                                   EEEE-TTSSS-EEEEEETTTTEEEEEEE-TT--EEEE-TTSSEEEEEE CS
                         eIF2A 115 vllaGfgnlaGeleiwdvkkkkkiakaeaanatlvewspdgryvlTat 162
                                   +++ + gn+ Ge eiw ++  +   +++  +  + +wsp+g+ ++T+ 
  gi|91773135|ref|YP_565827.1| 313 IVF-NSGNI-GEYEIWIMN-SDGTDQIRIDEGLMPQWSPKGDKIVTMA 357
                                   998.569*9.******775.556688888889999**********975 PP

>> Gmad1  Lipoprotein LpqB beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   3.4e-05     0.067     119     203 ..      93     179 ..      92     216 .. 0.82
   2 ?    0.3   0.0      0.25   4.9e+02      32      67 ..     217     252 ..     213     272 .. 0.69
   3 ?    1.5   0.0       0.1   2.1e+02      30      64 ..     257     293 ..     246     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                         Gmad1 119 vSrDGtRaAvivekdgggkvyvavVvrdadGqksltapvalatglleeav..svsWrsedt..LvVlrsseggpvqalVsl 195
                                   +S+DGt ++++++ +g+ ++ +  +  d++++++lt++  l  +ll  a    +sW+ +++  + V +sse+ +v++ V++
  gi|91773135|ref|YP_565827.1|  93 LSPDGTKLLFVSNATGNHELWIMDI--DGSDKRQLTYGAHLENNLLGLAGrwGISWSPGSSqiVYVSASSENRNVWETVEI 171
                                   79**********9999999998888..556677777777777777766642279**976542267899999999**9**** PP

                         Gmad1 196 dgseseal 203
                                   +g +++ +
  gi|91773135|ref|YP_565827.1| 172 NGKKEQMF 179
                                   **888765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                         Gmad1  32 rdgqqvaavtapdggrtLvvgsyggeasevleggsl 67 
                                    dg+++a+v++++g+  +++++++g  +  l +gs 
  gi|91773135|ref|YP_565827.1| 217 SDGEKIAFVSNESGNGGIWIMNKDGSDKIQLVDGSA 252
                                   589999999999999999998777765544444444 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.1
                         Gmad1  30 vSrdgqqvaavt..apdggrtLvvgsyggeasevleg 64 
                                    S+dg++++ v+  +++ +++++v++++g  ++ l+ 
  gi|91773135|ref|YP_565827.1| 257 WSPDGTKIVYVKgdHENYTSSIWVMDTDGSNKKPLTN 293
                                   4888888888887777777888888888777766644 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 ?    5.6   0.0    0.0083        17      63      83 ..     100     120 ..      90     125 .. 0.76
   2 ?    4.7   0.0     0.015        30      31      79 ..     197     249 ..     172     251 .. 0.72
   3 ?   -2.3   0.0       2.3   4.6e+03      74      85 ..     277     288 ..     269     292 .. 0.83
   4 ?   -0.6   0.0      0.71   1.4e+03      61      82 ..     310     332 ..     296     338 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0083
                       BiPBP_C  63 elawqpepGrhrLtvvDaaGr 83 
                                    l+++   G+h+L+++D +G 
  gi|91773135|ref|YP_565827.1| 100 LLFVSNATGNHELWIMDIDGS 120
                                   45666699*********9996 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                       BiPBP_C  31 krqrlqlkargg.eaplrWlldgepl...aetkrgrelawqpepGrhrLtvvD 79 
                                     ++l+l+ + + +   +W+ dge +    + + +  ++++ + G  ++++vD
  gi|91773135|ref|YP_565827.1| 197 GSNNLKLTTSRKdNIGATWRSDGEKIafvSNESGNGGIWIMNKDGSDKIQLVD 249
                                   57788888888845599******987332344555667777799999999999 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                       BiPBP_C  74 rLtvvDaaGrvd 85 
                                   +++v+D +G  +
  gi|91773135|ref|YP_565827.1| 277 SIWVMDTDGSNK 288
                                   689999999765 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.71
                       BiPBP_C  61 grelawqp.epGrhrLtvvDaaG 82 
                                   g+++ + + + G++++++++ +G
  gi|91773135|ref|YP_565827.1| 310 GSKIVFNSgNIGEYEIWIMNSDG 332
                                   555666666889*******9999 PP

>> NusG_II  NusG domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0018       3.5      15      63 ..     156     204 ..     143     211 .. 0.82
   2 ?   -1.8   0.0       1.8   3.5e+03      64      80 ..     231     247 ..     217     257 .. 0.74
   3 ?    2.7   0.0     0.071   1.4e+02      56      84 ..     310     342 ..     262     356 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                                   ..........EEEEEETTEEEEEEEE-TT--EEEEEEE-TTSEEEEEEE CS
                       NusG_II  15 laakkkkeaktavitvdgkvvktisLskedeektieiegeegtnvieik 63 
                                   + a++++++    ++++gk  + +++sk++++++i i +++g n ++ +
  gi|91773135|ref|YP_565827.1| 156 VSASSENRNVWETVEINGKKEQMFNISKVSKDYDIWIVDHDGSNNLKLT 204
                                   4555666666678*****************************9988764 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                                   TTEEEEEEE-SSS-HHH CS
                       NusG_II  64 dgkvrvkeadCpdkiCv 80 
                                   +g +++  +d  dki  
  gi|91773135|ref|YP_565827.1| 231 NGGIWIMNKDGSDKIQL 247
                                   67788888888888754 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.071
                                   S....EEEEEEETTEEEEEEE-SSS-HHHHH-- CS
                       NusG_II  56 g....tnvieikdgkvrvkeadCpdkiCvktgw 84 
                                   g     n   i + ++++  +d  d+i +++g 
  gi|91773135|ref|YP_565827.1| 310 GskivFNSGNIGEYEIWIMNSDGTDQIRIDEGL 342
                                   244557777888999************999885 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.48   9.6e+02     103     125 ..     110     132 ..     104     136 .. 0.76
   2 ?    1.9   0.0      0.08   1.6e+02      99     125 ..     184     210 ..     149     217 .. 0.85
   3 ?    7.7   0.0    0.0013       2.6     100     122 ..     273     295 ..     240     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.48
                  ChitinaseA_N 103 keivvaDtDGshLkpLemnvden 125
                                   +e+ + D DGs  ++L++  + +
  gi|91773135|ref|YP_565827.1| 110 HELWIMDIDGSDKRQLTYGAHLE 132
                                   578899*****999999865433 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.08
                  ChitinaseA_N  99 ksapkeivvaDtDGshLkpLemnvden 125
                                    s+   i + D DGs   +L+++ ++n
  gi|91773135|ref|YP_565827.1| 184 VSKDYDIWIVDHDGSNNLKLTTSRKDN 210
                                   57778999*******999999887776 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0013
                  ChitinaseA_N 100 sapkeivvaDtDGshLkpLemnv 122
                                     +++i v DtDGs  kpL+ n 
  gi|91773135|ref|YP_565827.1| 273 NYTSSIWVMDTDGSNKKPLTNNS 295
                                   56789**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 2888.76
//
Query:       gi|91773136|ref|YP_565828.1|  [L=407]
Description: periplasmic component of the Tol biopolymer transport system-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-19   67.5   8.9    2.7e-05   24.0   0.1    6.6  6  PD40      WD40-like Beta Propeller Repeat
    1.3e-08   34.5   0.1    4.7e-05   22.8   0.0    3.2  3  DUF5050   Domain of unknown function (DUF5050)
    5.9e-07   28.6   1.0       0.92    8.2   0.0    5.3  6  DPPIV_N   Dipeptidyl peptidase IV (DPP IV) N-terminal region
  ------ inclusion threshold ------
      0.071   13.2   0.6         31    4.7   0.0    4.3  5  Inh       Protease inhibitor Inh


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.7e-06     0.025       4      25 ..      28      49 ..      26      49 .. 0.93
   2 !    5.8   0.2    0.0031        14      16      25 ..      98     107 ..      98     109 .. 0.93
   3 !   24.0   0.1   6.1e-09   2.7e-05       4      38 .]     180     213 ..     178     213 .. 0.94
   4 !   10.6   0.0   9.5e-05      0.43       3      27 ..     223     247 ..     223     247 .. 0.92
   5 !    9.0   0.1   0.00031       1.4       9      25 ..     285     301 ..     281     301 .. 0.82
   6 ?    2.8   0.0     0.026   1.1e+02      14      26 ..     332     344 ..     331     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-06
                                  --SSSS.EEEEEE-TTSSEEEE CS
                          PD40  4 ltntpgnegaPsfSPDGkrlaF 25
                                  lt +++ +g P +SPDG ++++
  gi|91773136|ref|YP_565828.1| 28 LTDGTESNGFPQWSPDGEMIVY 49
                                  789999**************98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0031
                                   E-TTSSEEEE CS
                          PD40  16 fSPDGkrlaF 25 
                                   +SPDG +l +
  gi|91773136|ref|YP_565828.1|  98 WSPDGDKLLY 107
                                   *******987 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 6.1e-09
                                   --SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                          PD40   4 ltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                   +t +++n+  + + P G++++F SdRg G+pdI+v
  gi|91773136|ref|YP_565828.1| 180 ITQGDENDSQFLWQPHGNKIVFRSDRG-GYPDIWV 213
                                   788999999******************.******8 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 9.5e-05
                                   E--SSSS.EEEEEE-TTSSEEEEEE CS
                          PD40   3 rltntpgnegaPsfSPDGkrlaFsS 27 
                                   +l n+++ e ++ +S DG+++a++S
  gi|91773136|ref|YP_565828.1| 223 QLSNSEEKELDIKWSMDGTKIAYVS 247
                                   5789999999*************98 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.00031
                                   S.EEEEEE-TTSSEEEE CS
                          PD40   9 gnegaPsfSPDGkrlaF 25 
                                    ++  P fSPDG ++aF
  gi|91773136|ref|YP_565828.1| 285 RWDARPEFSPDGEKIAF 301
                                   5666777*********9 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.026
                                   EEE-TTSSEEEEE CS
                          PD40  14 PsfSPDGkrlaFs 26 
                                   P +SP G+++aF+
  gi|91773136|ref|YP_565828.1| 332 PQWSPMGNKIAFT 344
                                   559*********9 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.026   1.2e+02     119     136 ..      61      78 ..      43      86 .. 0.63
   2 !   13.0   0.1   9.7e-06     0.043     159     260 ..     126     232 ..     122     236 .. 0.75
   3 !   22.8   0.0     1e-08   4.7e-05      27     163 ..     208     355 ..     195     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.026
                                   EEEEEEETTS---EEEES CS
                       DUF5050 119 lklykikidgkektklsd 136
                                   +k   ++idg++kt+l++
  gi|91773136|ref|YP_565828.1|  61 TKTWMMDIDGSNKTQLTS 78 
                                   445556666666666643 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.7e-06
                                   -EEEEETTTTEEEEEE...-S-EEEEEEEETTEEEEEGGGTT-EEEE-SSS---EE-....S-S-EEEEEEETTEEEEEE- CS
                       DUF5050 159 slykldtdgksiskvs...eenlyllvvegdyiYyidlsknyaLyrvklsgsekevl....tedkvdnyNvtgnwiYyqke 232
                                    +  ++ dg+s++kv+   + ++y    +  +i+ +  +k ++L+ ++ +g+ek ++    ++d+ ++   +gn+i +  +
  gi|91773136|ref|YP_565828.1| 126 DIQIMNADGTSKNKVKgssNAEYYGWAQNTTKIFMV--DKSKKLWLLNPDGTEKVLItqgdENDSQFLWQPHGNKIVFRSD 204
                                   566688888887777521144555566677788885..59999*************9555333445667789999999999 PP

                                   SSS-E.EEEEETTS---EEEEES-EEEE CS
                       DUF5050 233 sdeekalyrikldGsekeklaegnvsni 260
                                    +  +++  ++ dG++k  l++ + +++
  gi|91773136|ref|YP_565828.1| 205 RGGYPDIWVMNYDGTGKLQLSNSEEKEL 232
                                   999999***********99998876655 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 1e-08
                                   TTEEEEEETTS-S-EEEEEEEEEEEEE....-SSEEEEEEE----------SS-.SEEEEEEETTS---EEEE-.....S- CS
                       DUF5050  27 enkLYkmnsdgsnlkklsddsvsyinv....agnyiYYvrnndkkstsksllsl.ltglyriktdGtertklsd.....dk 97 
                                      +++mn+dg+ + +ls+++ + + +    +g  i Yv+ +  ++++ s + + ++++  ++ dG++++kl+      d 
  gi|91773136|ref|YP_565828.1| 208 YPDIWVMNYDGTGKLQLSNSEEKELDIkwsmDGTKIAYVSPSVLNTSNLSTFFNsSHSIWVMNSDGSDKKKLTGrhdrwDA 288
                                   3359****************999997533338*********99999666666666****************9852222234 PP

                                   EEEEEEETTEEEEEE.ESSSS-EEEEEEETTS---EEEESS----SEEETTEEEEE-T.TT--EEEE CS
                       DUF5050  98 slevslvgnwiYYqh.ydekdglklykikidgkektklsdeaieplsvkdgwiYytgesedhslykl 163
                                     e s  g++i + + y+++ + k+  +++dg+++t l++  + + s  +++i +tg+s ++s++++
  gi|91773136|ref|YP_565828.1| 289 RPEFSPDGEKIAFDTtYKNESDPKIIVMDVDGTNETVLAKGWMPQWSPMGNKIAFTGKSGNNSVVSV 355
                                   5568899****997548999**************************************999987765 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0002      0.92      27      60 ..      17      50 ..      14      83 .. 0.86
   2 ?   -1.0   0.0      0.13   5.7e+02     108     117 ..      98     107 ..      93     110 .. 0.79
   3 ?    2.1   0.1     0.015        65     225     271 ..     143     187 ..     124     203 .. 0.53
   4 !    6.0   0.1   0.00093       4.2       6      83 ..     148     229 ..     143     247 .. 0.56
   5 !    4.6   0.0    0.0026        12      38      62 ..     224     248 ..     219     301 .. 0.73
   6 !    5.1   0.0    0.0018       8.3       1      60 [.     293     344 ..     293     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0002
                                  EEETTTEECEEEETTTT.BSEEEEESSTTEEEEE CS
                       DPPIV_N 27 iydletneveelspgeeklqlakwSPagdklafv 60
                                  i  +++ne+ el++g+e   +++wSP+g+++++ 
  gi|91773136|ref|YP_565828.1| 17 ITHVSANETIELTDGTESNGFPQWSPDGEMIVYH 50
                                  677899999***********************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.13
                                   E-TTSSEEEE CS
                       DPPIV_N 108 Wspdgsrlay 117
                                   Wspdg++l+y
  gi|91773136|ref|YP_565828.1|  98 WSPDGDKLLY 107
                                   8888888887 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.015
                                   EEEEESSS-SSS-S-EEE-TTTSSEEEEEEETTSSEEEEEEESSS-C CS
                       DPPIV_N 225 kleetsdgWvelhdevhflkrdesgflwisekdGfkHLylfdldgks 271
                                    ++ +  gW + ++++ ++  d+s+ lw+++ dG +++ + + d++ 
  gi|91773136|ref|YP_565828.1| 143 SSNAEYYGWAQNTTKIFMV--DKSKKLWLLNPDGTEKVLITQGDEND 187
                                   3344555555555555544..56666666666666666655555544 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.00093
                                   EEEEEECEEEESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEETT....EEEEESTTTSEEEECES-S CS
                       DPPIV_N   6 flllatnaeknwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafvrnn....nLyvrelatgkeiqlTsdg 82 
                                   +  +a+n++k++  + ++++++ +    e + +++g+e  + + w P g+k++f  ++    +++v +     ++ql++ +
  gi|91773136|ref|YP_565828.1| 148 YYGWAQNTTKIFMVDKSKKLWLLNPDGTEKVLITQGDENDSQFLWQPHGNKIVFRSDRggypDIWVMNYDGTGKLQLSNSE 228
                                   555566666666666666666666555555556666666666666666666666666444446666666555666665554 PP

                                   T CS
                       DPPIV_N  83 s 83 
                                   +
  gi|91773136|ref|YP_565828.1| 229 E 229
                                   3 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.0026
                                   EETTTT.BSEEEEESSTTEEEEEET CS
                       DPPIV_N  38 lspgeeklqlakwSPagdklafvrn 62 
                                   ls++eek  ++kwS +g+k+a+v  
  gi|91773136|ref|YP_565828.1| 224 LSNSEEKELDIKWSMDGTKIAYVSP 248
                                   4555788889999999999999865 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.0018
                                   TTTSSEEEEEECEEEESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEE CS
                       DPPIV_N   1 spdgkflllatnaeknwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafv 60 
                                   spdg+++ +    +  +++++  + ++ d+   + + l++g     +++wSP g+k+af+
  gi|91773136|ref|YP_565828.1| 293 SPDGEKIAF----DTTYKNESDPKIIVMDVDGTNETVLAKG----WMPQWSPMGNKIAFT 344
                                   567777777....5667777888888888887776777776....89***********97 PP

>> Inh  Protease inhibitor Inh
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.6   7.1e+03      61      91 ..     126     155 ..     124     161 .. 0.70
   2 ?    1.0   0.0       0.1   4.5e+02      54      69 ..     191     206 ..     185     231 .. 0.82
   3 ?    0.6   0.0      0.14   6.1e+02      61      94 ..     210     243 ..     207     246 .. 0.87
   4 ?    0.0   0.0       0.2   9.1e+02      58      94 ..     262     299 ..     248     302 .. 0.72
   5 ?    4.7   0.0    0.0069        31      52      72 ..     331     351 ..     314     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                                   EEEEE-TTS-EEEEEEEEETTEEEEEE.CCC CS
                           Inh  61 eivLtdadGsslarlarqedgrfegvltedg 91 
                                   +i +++adG+s  +++ +++ ++ g  +++ 
  gi|91773136|ref|YP_565828.1| 126 DIQIMNADGTSKNKVKGSSNAEYYGW-AQNT 155
                                   67888888888888888888777776.3444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.1
                                   EEEEETTEEEEE-TTS CS
                           Inh  54 aWdvtgkeivLtdadG 69 
                                    W+++g++iv+ ++ G
  gi|91773136|ref|YP_565828.1| 191 LWQPHGNKIVFRSDRG 206
                                   59********998887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.14
                                   EEEEE-TTS-EEEEEEEEETTEEEEEE.CCCEEE CS
                           Inh  61 eivLtdadGsslarlarqedgrfegvltedgepl 94 
                                   +i++++ dG+  ++l+++e+++++ + + dg+++
  gi|91773136|ref|YP_565828.1| 210 DIWVMNYDGTGKLQLSNSEEKELDIKWSMDGTKI 243
                                   68899999999999*9999999999988888877 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.2
                                   ETTEEEEE-TTS-EEEEEEEEETTEEEEE..E.CCCEEE CS
                           Inh  58 tgkeivLtdadGsslarlarqedgrfegv..ltedgepl 94 
                                   + + i++++ dGs   +l+ ++d  ++++   ++dge++
  gi|91773136|ref|YP_565828.1| 262 SSHSIWVMNSDGSDKKKLTGRHDR-WDARpeFSPDGEKI 299
                                   678999999999999999877776.99872234666666 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.0069
                                   -SEEEEETTEEEEE-TTS-EE CS
                           Inh  52 iaaWdvtgkeivLtdadGssl 72 
                                   + +W+++g++i++t+++G++ 
  gi|91773136|ref|YP_565828.1| 331 MPQWSPMGNKIAFTGKSGNNS 351
                                   678**************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2543.51
//
Query:       gi|91773137|ref|YP_565829.1|  [L=241]
Description: hypothetical protein Mbur_1156 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1768.50
//
Query:       gi|91773138|ref|YP_565830.1|  [L=349]
Description: hypothetical protein Mbur_1157 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0021   17.3   0.0     0.0087   15.4   0.0    1.8  2  DUF1611       Domain of unknown function (DUF1611_C) P-loop d
  ------ inclusion threshold ------
       0.06   13.6   0.0       0.12   12.7   0.0    1.5  1  PG_binding_4  Putative peptidoglycan binding domain


Domain annotation for each model (and alignments):
>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.7e-07    0.0087      13      49 ..       6      42 ..       2      52 .. 0.88
   2 ?   -1.2   0.0      0.11     1e+03     167     191 ..     135     159 ..     133     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.7e-07
                       DUF1611 13 krvlvvGTdcavGKrttaleleealeerGlkaafvaT 49
                                  + + v+   c+ GK ttal le++++ +Glk+a + T
  gi|91773138|ref|YP_565830.1|  6 NQIYVLASPCEQGKTTTALLLEKEFKSKGLKVACLQT 42
                                  567777788************************9988 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.11
                       DUF1611 167 nlseeeakealeeleeelglpvvdp 191
                                   +++e+++++++ ++ ++++ p+vd 
  gi|91773138|ref|YP_565830.1| 135 QINEKNVQNIITKVPSKIDFPCVDT 159
                                   56788999**************995 PP

>> PG_binding_4  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.3e-05      0.12       6      78 ..      93     165 ..      88     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                  PG_binding_4   6 eelglay.dieeyvaealtygrkgnelerlsetiaawkevdlrvsldeeklkeyldeiakeidtepkdasfkl.k 78 
                                     +g++y d+   ++e ++y  k+n+ +++  ++ +    ++  +++e+ +++++ ++ ++id + +d sf+l +
  gi|91773138|ref|YP_565830.1|  93 GPIGATYiDLFHNINEVVSYEVKDNWKKFVLGISPT--FSEFWDQINEKNVQNIITKVPSKIDFPCVDTSFNLhH 165
                                   56899999******************8888777777..7779999**************************9944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2889.83
//
Query:       gi|91773139|ref|YP_565831.1|  [L=941]
Description: excinuclease ABC subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-37  126.6   0.7    9.2e-37  125.5   0.7    1.7  1  UvrA_inter       UvrA interaction domain
    7.4e-31  106.8   0.0      5e-29  100.9   0.0    2.9  2  UvrA_DNA-bind    UvrA DNA-binding domain
    7.5e-21   75.1   0.1    9.7e-09   35.9   0.1    4.3  3  ABC_tran         ABC transporter
    6.3e-13   48.7   0.5      0.058   12.8   0.1    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    5.4e-08   32.5   0.6     0.0047   16.6   0.1    2.7  2  AAA_29           P-loop containing region of AAA domain
    7.6e-08   32.9   0.5       0.05   14.0   0.0    3.8  4  AAA_16           AAA ATPase domain
    4.8e-06   26.9   0.4      0.092   13.0   0.0    3.6  4  AAA_22           AAA domain
    8.4e-06   25.8   0.3      0.044   13.7   0.1    2.5  2  RsgA_GTPase      RsgA GTPase
      1e-05   25.3   0.9     0.0035   17.2   0.2    2.5  2  BCA_ABC_TP_C     Branched-chain amino acid ATP-binding casset
    1.3e-05   25.8   0.7       0.11   13.0   0.1    2.6  2  AAA_23           AAA domain
    0.00026   20.9  13.0     0.0043   16.9   0.0    4.9  5  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00027   20.8   0.0     0.0084   15.9   0.1    2.5  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00028   21.5   0.2        1.2    9.7   0.0    2.8  2  AAA_18           AAA domain
    0.00031   21.1   8.3      0.049   14.0   0.3    3.9  3  DnaJ_CXXCXGXG    DnaJ central domain
    0.00041   20.3   0.1        1.2    9.0   0.0    2.6  2  APS_kinase       Adenylylsulphate kinase
    0.00046   20.0   2.1       0.53   10.0   0.0    3.8  3  AAA_24           AAA domain
    0.00055   20.0   0.1        4.1    7.4   0.0    3.4  3  AAA_14           AAA domain
    0.00075   19.1   1.0      0.075   12.6   0.2    2.7  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0008   19.6   0.1        2.3    8.4   0.0    3.1  3  AAA_33           AAA domain
    0.00084   19.1   3.9        2.3    7.8   0.0    4.8  5  AAA_15           AAA ATPase domain
     0.0021   17.7   0.5       0.97    9.0   0.0    3.3  3  AAA_25           AAA domain
     0.0029   17.7   0.9       0.25   11.5   0.1    3.1  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0031   16.8   0.0        1.7    7.8   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.004   17.1   0.2        2.5    8.0   0.0    2.9  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0081   15.2   0.8        1.3    8.0   0.2    2.6  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   14.9   0.1        3.7    6.6   0.0    3.2  3  NB-ARC           NB-ARC domain
      0.012   14.9   0.2        4.2    6.6   0.0    2.6  2  ATPase           KaiC
      0.015   15.2   0.0          3    7.7   0.0    2.5  2  NACHT            NACHT domain
      0.021   15.3   1.6         13    6.3   0.0    3.2  3  Cytochrom_c3_2   Cytochrome c3
       0.03   14.1   0.1        3.6    7.3   0.0    2.9  3  AAA_30           AAA domain
      0.037   13.3   0.0        6.7    5.9   0.0    2.5  2  Zeta_toxin       Zeta toxin
      0.064   13.0   0.1        7.8    6.2   0.0    2.6  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.068   13.6   0.1        4.6    7.7   0.1    2.5  2  RNA_helicase     RNA helicase
      0.068   12.7   0.3        3.2    7.2   0.1    2.5  2  AAA_7            P-loop containing dynein motor region
       0.19   11.6   3.7       0.93    9.4   0.2    3.1  3  NTPase_1         NTPase
        2.8    8.0   5.0        1.6    8.7   0.0    3.2  3  YhfH             YhfH-like protein
        2.9    8.1  12.8        5.5    7.2   1.6    4.0  4  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.7   1.9e-39   9.2e-37       1     107 [.     132     240 ..     132     242 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 1.9e-39
                    UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydlde..dieldknkkhsievvvDrlv 79 
                                   Qsv+qIvd+ilk++eg+k+ ilaP+vrerkge+kkll +l+ +Gf r r+Dgei+ l++   i l +++kh+ie vvDr+v
  gi|91773139|ref|YP_565831.1| 132 QSVDQIVDSILKIKEGSKIHILAPLVRERKGEYKKLLAELRTEGFARARVDGEIIALEDaeTIGLGRYNKHNIEAVVDRIV 212
                                   9*********************************************************988999***************** PP

                    UvrA_inter  80 vkkeersrlaesvetAlklgeglvivse 107
                                   +k++ r+r++++vetAl+ + g+++v+ 
  gi|91773139|ref|YP_565831.1| 213 IKDDIRERVTDAVETALEKSGGTLVVHV 240
                                   ************************9986 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.38   1.9e+02      76     107 ..      35      66 ..       2      68 .. 0.73
   2 !  100.9   0.0     1e-31     5e-29       1     110 []     291     399 ..     291     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.38
                                   .........---HHHHHHHHHH-------HHH CS
                 UvrA_DNA-bind  76 grkrsyektfeGvipnlerryreteSeavree 107
                                   +++ + +  f+ +  + +rry e+ S ++r+ 
  gi|91773139|ref|YP_565831.1|  35 SGSGKSSLAFDTIYAEGQRRYVESLSAYARQF 66 
                                   566777889999*****************985 PP

  == domain 2  score: 100.9 bits;  conditional E-value: 1e-31
                                   -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----................ CS
                 UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyksggrkrsy 81 
                                   Dp+l+vpd +lsl egAi+ w  kk+ yy+q l ++a++yg+++d+pf++L +e+kdi+++G+++ +  v+  ++g+ +++
  gi|91773139|ref|YP_565831.1| 291 DPELIVPDTTLSLHEGAIEHW-GKKDGYYMQSLGSIAQRYGFSMDVPFEDLAPEHKDIIFNGASGLIDYVHIGKNGGMWKH 370
                                   9********************.999****************************************99999*********** PP

                                   ...---HHHHHHHHHH-------HHHHHH CS
                 UvrA_DNA-bind  82 ektfeGvipnlerryreteSeavreelek 110
                                   +++f+Gvi n+ + y++teSe+ ++ l+k
  gi|91773139|ref|YP_565831.1| 371 KGKFNGVIANISKIYNSTESENRKDTLKK 399
                                   **********************9998875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.8e-06    0.0033       1      28 [.      16      43 ..      16     181 .. 0.94
   2 !   14.3   0.0   9.1e-05     0.044      42     136 ..     421     518 ..     409     519 .. 0.68
   3 !   35.9   0.1     2e-11   9.7e-09       1     136 [.     623     859 ..     623     860 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.8e-06
                                  EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                  lknv++++ ++++++i+G +G+GKS+L+
  gi|91773139|ref|YP_565831.1| 16 LKNVDVTFPRDKLIVITGLSGSGKSSLA 43
                                  79************************95 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.1e-05
                                   EEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  42 illdgkdlkeqeleslrkeigvlpqepqlfpeltvren....esdeeiekalsklglkelkdtvvksspssLSgGqkqrva 118
                                   ++++++++ +   ++++ ei+ l+ e +l  +lt re        +ei++ l  l +++l+  ++++s+++LSgG+ qr+ 
  gi|91773139|ref|YP_565831.1| 421 VTINEQNILK--VTRMSVEIALLFFE-ELETKLTPREYsiarLILKEIKARLGFLMDVGLDYLTLSRSAATLSGGEAQRIR 498
                                   5666666666..66666666666666.666666666665555333445555555556667777888889************ PP

                                   HHHHHHHT..SSEEEEESTT CS
                                   xxxxxxxx..xxxxxxxxxx RF
                      ABC_tran 119 larallkk..pkllllDEpt 136
                                   la  + +     l++lDEp+
  gi|91773139|ref|YP_565831.1| 499 LATQIGSSlmGVLYILDEPS 518
                                   **9987652257999***95 PP

  == domain 3  score: 35.9 bits;  conditional E-value: 2e-11
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.....................EETTCEGGGB-HHHCCHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGei.....................lldgkdlkeqeleslrke 60 
                                   lk +++++  g ++ ++G +G+GKStL++  ++++  ++ +                      ++d+ ++ +++++     
  gi|91773139|ref|YP_565831.1| 623 LKGIDVDFPLGVMTCVTGVSGSGKSTLINETLNKVLSQKLNRsrerpgkykdikglelvdkviTIDQSPIGRTPRSNPATY 703
                                   78999**********************975554444322222344456667777777777777777777777666666666 PP

                                   EEEE-SS--S-TTSBHHHH.............................................................. CS
                                   xxxxxxxxxxxxxxxxxxx.............................................................. RF
                      ABC_tran  61 igvlpqepqlfpeltvren.............................................................. 79 
                                      ++   +lf++++++++                                                              
  gi|91773139|ref|YP_565831.1| 704 TNLFTPIRELFSQTKMAKTrgykpgrfsfnvrggrcetcsgdgtitiemhflpdvyvpcevchgkrynhetlevnykdkni 784
                                   66666667777777766668**************************************************99999777777 PP

                                   ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS...SEEEEESTT CS
                                   ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                      ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp...kllllDEpt 136
                                                  e   +i + l++l +++l   ++++s ++LSgG+ qrv+la  l +++   ++++lDEpt
  gi|91773139|ref|YP_565831.1| 785 advldmtveealgffENVPKIRNKLQTLFDVGLGYIKLGQSSTTLSGGEAQRVKLATELSRRStgkTVFILDEPT 859
                                   666655555555444444446666777777779999999999*****************98752227*******9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00012     0.058       2      46 ..       3      48 ..       2      61 .. 0.82
   2 !   12.3   0.0   0.00017     0.085     135     211 ..     384     562 ..     133     567 .. 0.70
   3 ?    6.2   0.2     0.013       6.1      26      51 ..     635     661 ..     621     675 .. 0.75
   4 !   12.2   0.0   0.00019      0.09     135     210 ..     820     902 ..     707     909 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                  EEEEEEESETTEECEEEEEETT.SSEEEEEESTTSSHHHH.HHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxx RF
                         SMC_N  2 lkrleienFksyagktvilpfs.ksftaivGpNGSGKsnl.ldAilF 46
                                  lk++++++ k  + k+v++ f  +++ +i+G  GSGKs+l +d i +
  gi|91773139|ref|YP_565831.1|  3 LKNIIVKGAKEHNLKNVDVTFPrDKLIVITGLSGSGKSSLaFDTI-Y 48
                                  899*******999999999986257999***********834655.5 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                                   T................................................................................ CS
                                   x................................................................................ RF
                         SMC_N 135 e................................................................................ 135
                                                                                                                    
  gi|91773139|ref|YP_565831.1| 384 Iynstesenrkdtlkkyittkpctscngdrlkpaslavtineqnilkvtrmsveiallffeeletkltpreysiarlilke 464
                                   044444444444444444444444444444444444444444444444666666777777777777777777777777777 PP

                                   .......................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEE CS
                                   .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                         SMC_N 136 .......................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQf 192
                                                          +LSgGe + + la    i +     ly+lDe    L ++   ++ + lk+ ++    +
  gi|91773139|ref|YP_565831.1| 465 ikarlgflmdvgldyltlsrsaaTLSGGEAQRIRLATQ--IGSSLMGVLYILDEPSIGLHQRDNLRLINTLKHLRDIgNTV 543
                                   77777777778888888888888999999887766665..66777789************************99987689* PP

                                   EEE-SSHHHCCC-SCEEEE CS
                                   xxxxxxxxxxxxxxxxxxx RF
                         SMC_N 193 ivislreemlekadklvgv 211
                                   iv+ ++ee++ ++d++v +
  gi|91773139|ref|YP_565831.1| 544 IVVEHDEETIMNCDHVVDM 562
                                   *************999865 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.013
                                   EEEEEESTTSSHHHHH.HHHHHHCTT. CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                         SMC_N  26 ftaivGpNGSGKsnll.dAilFvLGer 51 
                                   +t+++G  GSGKs l+ + +  vL+++
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLInETLNKVLSQK 661
                                   79***********98725666677755 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00019
                                   T.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SC CS
                                   x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadk 207
                                           +LSgGe + v la  ++ ++   + +++lDe    L +  v+k+ ++l++  ++   +ivi ++ ++++ ad 
  gi|91773139|ref|YP_565831.1| 820 IklgqsstTLSGGEAQRVKLATELSRRST-GKTVFILDEPTTGLHFDDVNKLLDVLQRLVETgNTVIVIEHNLDVIKTADW 899
                                   045555559**************986655.567889*********************998876899**********99997 PP

                                   EEE CS
                                   xxx RF
                         SMC_N 208 lvg 210
                                   ++ 
  gi|91773139|ref|YP_565831.1| 900 VID 902
                                   765 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 !   13.2   0.0   0.00012     0.057      11      38 ..      15      42 ..       9      49 .. 0.81
   2 !   16.6   0.1   9.7e-06    0.0047      17      39 ..     628     650 ..     621     661 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                        AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTl 38
                                   +++ ++++ ++  +++tG sGsGKS+l
  gi|91773139|ref|YP_565831.1| 15 NLKNVDVTFPRDKLIVITGLSGSGKSSL 42
                                  566677888877799***********98 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.7e-06
                        AAA_29  17 ieidlkg.atlltGpsGsGKSTll 39 
                                   +++ l g +t +tG sGsGKSTl+
  gi|91773139|ref|YP_565831.1| 628 VDFPL-GvMTCVTGVSGSGKSTLI 650
                                   55553.459**************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00019     0.093      25      63 ..      27      66 ..      14     141 .. 0.79
   2 ?   -1.4   0.0       5.4   2.6e+03       3      30 ..     212     239 ..     210     240 .. 0.85
   3 !   14.0   0.0    0.0001      0.05      26      51 ..     635     660 ..     624     689 .. 0.85
   4 ?    0.4   0.0       1.5   7.3e+02     106     141 ..     844     887 ..     784     899 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                        AAA_16 25 elvllsGesGvGKsslv.rellralekdggif..lrgkcdql 63
                                   l++++G sG+GKssl+ ++++   e+++ ++  l++ ++q+
  gi|91773139|ref|YP_565831.1| 27 KLIVITGLSGSGKSSLAfDTIYA--EGQRRYVesLSAYARQF 66
                                  789**************666664..44445666688888887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.4
                        AAA_16   3 vGReeeleqLlsalervrsgrpelvlls 30 
                                   v +++ +e++++a+e++ + +++ ++++
  gi|91773139|ref|YP_565831.1| 212 VIKDDIRERVTDAVETALEKSGGTLVVH 239
                                   668899999******9999999888887 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 0.0001
                        AAA_16  26 lvllsGesGvGKsslvrellralekd 51 
                                   ++ ++G sG+GKs+l++e l+ +  +
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLINETLNKVLSQ 660
                                   6789************9999866554 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.5
                        AAA_16 106 a.............avpelagaeasrllellkrllallsrderplvlvl 141
                                   +             ++  l+ ++ + ll++l+rl+   ++ +  +v+v+
  gi|91773139|ref|YP_565831.1| 844 SrrstgktvfildePTTGLHFDDVNKLLDVLQRLV---ET-GN-TVIVI 887
                                   23333333333333333333344455555555555...22.22.34444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0029       1.4       5      28 ..      26      49 ..      24     101 .. 0.76
   2 ?   -1.8   0.0       7.2   3.5e+03      78     117 ..     496     538 ..     448     546 .. 0.65
   3 !   13.0   0.0   0.00019     0.092       7      35 ..     635     663 ..     633     721 .. 0.82
   4 ?   -1.0   0.0       3.9   1.9e+03      82     114 ..     839     872 ..     777     889 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0029
                        AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                  ++++v+tG sG+GK+ l+    + 
  gi|91773139|ref|YP_565831.1| 26 DKLIVITGLSGSGKSSLAFDTIYA 49
                                  579************998655555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.2
                        AAA_22  78 llealeqalraravielliiDEaqh.lr.s..eealeeLrslln 117
                                    +++ +q  ++ +  +l i+DE    l  +   +++++L++l +
  gi|91773139|ref|YP_565831.1| 496 RIRLATQIGSSLMG-VLYILDEPSIgLHqRdnLRLINTLKHLRD 538
                                   44566666666677.78888887666643144677777777766 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00019
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeaka 35 
                                   +++vtG sG+GK+tl+++ l++   ++  
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLINETLNKVLSQKLN 663
                                   689***************99998665544 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.9
                        AAA_22  82 leqalrarav.ielliiDEaqh.lrseealeeLrs 114
                                   l+  l++r++ + ++i+DE    l + + +++L +
  gi|91773139|ref|YP_565831.1| 839 LATELSRRSTgKTVFILDEPTTgL-HFDDVNKLLD 872
                                   334444444456999999977777.6444444433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0018      0.85      84     116 ..      10      43 ..       2      61 .. 0.77
   2 !   13.7   0.1     9e-05     0.044     100     130 ..     634     665 ..     604     674 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                                   TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                   RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                     ++++l+++   +   k++v+ G SG GKS+L 
  gi|91773139|ref|YP_565831.1|  10 GAKEHNLKNVDVTFPRdKLIVITGLSGSGKSSLA 43 
                                   55567777777666555***************95 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9e-05
                                   SEEEEECSTTSSHHHHHHHHCTT.-----S-- CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe.lelktgev 130
                                    ++++ G SG GKStLin+ l++ l++k +  
  gi|91773139|ref|YP_565831.1| 634 VMTCVTGVSGSGKSTLINETLNKvLSQKLNRS 665
                                   57899*************87664145555554 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 !   17.2   0.2   7.3e-06    0.0035       1      16 [.     572     587 ..     572     587 .. 0.91
   2 ?    6.3   0.0     0.019       9.1       1      12 [.     913     924 ..     913     925 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.3e-06
                  BCA_ABC_TP_C   1 rvIAeGtPaEvrndPr 16 
                                   ++ AeGtP+E++++P+
  gi|91773139|ref|YP_565831.1| 572 EIVAEGTPEEIMAHPD 587
                                   579***********96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                  BCA_ABC_TP_C   1 rvIAeGtPaEvr 12 
                                   +vIA GtP+ v 
  gi|91773139|ref|YP_565831.1| 913 KVIAKGTPEKVS 924
                                   79*******985 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   0.00023      0.11       4      35 ..       8      42 ..       5      45 .. 0.83
   2 !   10.6   0.1    0.0012       0.6      15      45 ..     628     660 ..     621     737 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00023
                        AAA_23  4 ienfrsf..rdqeidF.skgltlItGpNGaGKTTi 35
                                  +++ + +  +++++ F  ++l +ItG  G+GK+++
  gi|91773139|ref|YP_565831.1|  8 VKGAKEHnlKNVDVTFpRDKLIVITGLSGSGKSSL 42
                                  5666666668999999999**************98 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0012
                        AAA_23  15 idF.skgltlItGpNGaGKTTil.dAiklaLyg 45 
                                   +dF    +t++tG  G+GK+T++ + +  +L  
  gi|91773139|ref|YP_565831.1| 628 VDFpLGVMTCVTGVSGSGKSTLInETLNKVLSQ 660
                                   55533348**************95555555555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.35   1.7e+02       1      15 [.      28      42 ..      28      47 .. 0.92
   2 ?    0.8   0.1      0.71   3.4e+02     259     282 ..     439     465 ..     429     473 .. 0.80
   3 ?    2.4   0.1      0.23   1.1e+02     234     272 ..     486     523 ..     461     546 .. 0.82
   4 ?    3.3   0.5      0.12        59       1      16 [.     635     650 ..     635     651 .. 0.92
   5 !   16.9   0.0   8.9e-06    0.0043     238     298 ..     830     890 ..     822     895 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.35
                        AAA_21  1 lnvliGpNgsGKSnL 15
                                  l v++G  gsGKS+L
  gi|91773139|ref|YP_565831.1| 28 LIVITGLSGSGKSSL 42
                                  579**********98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.71
                        AAA_21 259 sllliDEpEngLHP...kllrrllell 282
                                   +ll+++E+E+ L P   ++ r +l+ +
  gi|91773139|ref|YP_565831.1| 439 ALLFFEELETKLTPreySIARLILKEI 465
                                   79************7766666666666 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.23
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP 272
                                   a+ lS G  + ++l+t + + l    l+++DEp  gLH 
  gi|91773139|ref|YP_565831.1| 486 AATLSGGEAQRIRLATQIGSSLMG-VLYILDEPSIGLHQ 523
                                   555688887777999999999999.8************7 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.12
                        AAA_21   1 lnvliGpNgsGKSnLL 16 
                                   +++++G  gsGKS+L+
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLI 650
                                   5899***********8 PP

  == domain 5  score: 16.9 bits;  conditional E-value: 8.9e-06
                        AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   S G  +  +l+t l r+    +++++DEp +gLH   + +ll++l +l ++g  vi+  H+
  gi|91773139|ref|YP_565831.1| 830 SGGEAQRVKLATELSRRSTGKTVFILDEPTTGLHFDDVNKLLDVLQRLVETGNTVIVIEHN 890
                                   566555559***********9************************8888889999987666 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.28   1.4e+02       1      15 [.      29      43 ..      29      84 .. 0.82
   2 !   15.9   0.1   1.7e-05    0.0084       2      23 ..     637     660 ..     636     689 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.28
               Viral_helicase1  1 ivvhGvpGcGKStli 15
                                  iv+ G  G+GKS+l 
  gi|91773139|ref|YP_565831.1| 29 IVITGLSGSGKSSLA 43
                                  79**********975 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.7e-05
               Viral_helicase1   2 vvhGvpGcGKStlirkllrts..l 23 
                                    v Gv G+GKStli + l++    
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLINETLNKVlsQ 660
                                   699****************94322 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0054       2.6       1      15 [.      29      43 ..      29      56 .. 0.95
   2 !    9.7   0.0    0.0024       1.2       2      17 ..     637     652 ..     637     685 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0054
                        AAA_18  1 IlltGtpGvGKttla 15
                                  I++tG +G+GK++la
  gi|91773139|ref|YP_565831.1| 29 IVITGLSGSGKSSLA 43
                                  99***********98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0024
                        AAA_18   2 lltGtpGvGKttlake 17 
                                   ++tG++G+GK+tl +e
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLINE 652
                                   79**********9876 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.025        12      36      54 ..     270     288 ..     242     294 .. 0.60
   2 ?    3.3   0.0      0.22     1e+02      57      65 ..     403     411 ..     384     423 .. 0.66
   3 !   14.0   0.3    0.0001     0.049      16      51 ..     738     769 ..     723     775 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.025
                 DnaJ_CXXCXGXG  36 fvqqsqstCpeCeGtGkvi 54 
                                    +++ q  C+eC+G G+ +
  gi|91773139|ref|YP_565831.1| 270 SFNSPQGACEECHGLGTSM 288
                                   3344566788888887765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.22
                 DnaJ_CXXCXGXG  57 kdkCkkCkG 65 
                                   +++C++C+G
  gi|91773139|ref|YP_565831.1| 403 TKPCTSCNG 411
                                   234555544 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 0.0001
                 DnaJ_CXXCXGXG  16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtG 51 
                                   +C+tC+G G+++ e++    f   +  +C+ C+G+ 
  gi|91773139|ref|YP_565831.1| 738 RCETCSGDGTITIEMH----FLPDVYVPCEVCHGKR 769
                                   6********7655553....44466789*****986 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0024       1.2       4      20 ..      28      44 ..      25      58 .. 0.85
   2 !    8.6   0.1    0.0034       1.6       3      29 ..     634     661 ..     632     668 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                                  EEEEESSTTSSHHHHHH CS
                    APS_kinase  4 vvwltGlsgsGKstian 20
                                   + +tGlsgsGKs++a+
  gi|91773139|ref|YP_565831.1| 28 LIVITGLSGSGKSSLAF 44
                                  689************97 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0034
                                   EEEEEESSTTSSHHHHHHH.HHHHHHHT CS
                    APS_kinase   3 vvvwltGlsgsGKstiana.lekkLvek 29 
                                   v+  +tG+sgsGKst+ n+ l+k L +k
  gi|91773139|ref|YP_565831.1| 634 VMTCVTGVSGSGKSTLINEtLNKVLSQK 661
                                   56679**********8765155555443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.081        39       5      20 ..      29      44 ..      25      53 .. 0.87
   2 ?    3.2   0.0      0.13        63     110     133 ..     525     551 ..     517     559 .. 0.74
   3 !   10.0   0.0    0.0011      0.53       3      28 ..     634     659 ..     632     707 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.081
                        AAA_24  5 iliyGpsgiGKTtlak 20
                                  i+i+G sg+GK++la 
  gi|91773139|ref|YP_565831.1| 29 IVITGLSGSGKSSLAF 44
                                  89***********996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                        AAA_24 110 efrrllkklqelrk...nvifiahekt 133
                                   +  rl+++l++lr+   +vi++ h ++
  gi|91773139|ref|YP_565831.1| 525 DNLRLINTLKHLRDignTVIVVEHDEE 551
                                   556888888888888868888877665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0011
                        AAA_24   3 lkiliyGpsgiGKTtlakelgpkplf 28 
                                   ++ +++G sg+GK+tl++e  +k+l 
  gi|91773139|ref|YP_565831.1| 634 VMTCVTGVSGSGKSTLINETLNKVLS 659
                                   6789**************99777775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0085       4.1       2      27 ..      26      51 ..      25      81 .. 0.84
   2 !    7.2   0.1    0.0098       4.7       5      27 ..     636     658 ..     633     687 .. 0.82
   3 ?    0.6   0.0       1.1   5.4e+02      55      92 ..     842     882 ..     816     893 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0085
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikell 27
                                  +k++vitG+  +GK+ l+++ i+ + 
  gi|91773139|ref|YP_565831.1| 26 DKLIVITGLSGSGKSSLAFDTIYAEG 51
                                  5899****************998766 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0098
                        AAA_14   5 lvitGaRrvGKTtllkqlikell 27 
                                    ++tG+  +GK+tl+++ +++ l
  gi|91773139|ref|YP_565831.1| 636 TCVTGVSGSGKSTLINETLNKVL 658
                                   689**************999888 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                        AAA_14  55 lileklkeekktylflDEiqev......pewekalkslvdegkn 92 
                                   ++ ++ +  +kt+++lDE          +++ ++l++lv++g n
  gi|91773139|ref|YP_565831.1| 842 ELSRR-S-TGKTVFILDEPTTGlhfddvNKLLDVLQRLVETG-N 882
                                   33333.3.4899999999765444444477777777777777.4 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 ?    4.2   0.0      0.06        29       3      22 ..      29      48 ..      27      56 .. 0.78
   2 !   12.6   0.2   0.00015     0.075       2      24 ..     635     657 ..     634     664 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.06
                                  EEEEESTTCCHHHHHHHHHC CS
                          cobW  3 tvltGflGsGKTtLlnhlle 22
                                  +v+tG  GsGK++L   ++ 
  gi|91773139|ref|YP_565831.1| 29 IVITGLSGSGKSSLAFDTIY 48
                                  89***********9877774 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00015
                                   EEEEEESTTCCHHHHHHHHHCT- CS
                          cobW   2 vtvltGflGsGKTtLlnhllenr 24 
                                   +t +tG  GsGK+tL+n++l++ 
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLINETLNKV 657
                                   689****************9765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0095       4.6       1      17 [.      28      44 ..      28     103 .. 0.83
   2 ?   -1.8   0.0       6.5   3.2e+03      71     111 ..     510     553 ..     493     555 .. 0.67
   3 !    8.4   0.0    0.0047       2.3       3      21 ..     637     655 ..     635     672 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0095
                        AAA_33  1 lvllvGlpGsGKstlae 17
                                  l+++ Gl+GsGKs la 
  gi|91773139|ref|YP_565831.1| 28 LIVITGLSGSGKSSLAF 44
                                  78999********9985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.5
                        AAA_33  71 rnvildatnlsrrera..rflklarrl.gvpvrivvvetdeetl 111
                                     +ild + +  ++r+  r+++ +++l +   +++vve deet+
  gi|91773139|ref|YP_565831.1| 510 VLYILDEPSIGLHQRDnlRLINTLKHLrDIGNTVIVVEHDEETI 553
                                   55788888888888852244454543313446899999999987 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0047
                        AAA_33   3 llvGlpGsGKstlaerllk 21 
                                    + G++GsGKstl+ + l+
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLINETLN 655
                                   578**********988765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3       0.5   2.4e+02       1      39 [.       1      42 [.       1      44 [. 0.77
   2 ?   -0.3   0.0       1.4   6.7e+02     317     337 ..     427     451 ..     371     463 .. 0.81
   3 ?    2.4   0.0      0.22   1.1e+02     325     362 ..     510     546 ..     489     553 .. 0.83
   4 ?    3.5   0.0     0.097        47      18      63 ..     629     690 ..     621     706 .. 0.73
   5 !    7.8   0.0    0.0048       2.3     313     365 ..     845     890 ..     773     894 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.5
                        AAA_15  1 MkIkkikikNFRs..lkdveidlsee.ltvliGkNnsGKSsi 39
                                  M +k+i++k  +   lk+v++ +  + l v+ G  +sGKSs+
  gi|91773139|ref|YP_565831.1|  1 MSLKNIIVKGAKEhnLKNVDVTFPRDkLIVITGLSGSGKSSL 42
                                  777777777777522677888887667**************8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                        AAA_15 317 k....dekeeknvilliEEPEahLH 337
                                   +    ++ + ++++l++EE E+ L 
  gi|91773139|ref|YP_565831.1| 427 NilkvTRMSVEIALLFFEELETKLT 451
                                   4444556677899999999999885 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.22
                        AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviit 362
                                   v+++++EP + LH      li++lk l + ++  vi+ 
  gi|91773139|ref|YP_565831.1| 510 VLYILDEPSIGLHQRDNLRLINTLKHLRDIGN-TVIVV 546
                                   79***********************9988887.56665 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.097
                        AAA_15  18 eidlseeltvliGkNnsGKSsil.ealdlFlnnkekkn................kkvikieke 63 
                                   + +l   +t++ G  +sGKS+++ e l++ l++k + +                +kvi+i+++
  gi|91773139|ref|YP_565831.1| 629 DFPLGV-MTCVTGVSGSGKSTLInETLNKVLSQKLNRSrerpgkykdikglelvDKVITIDQS 690
                                   344444.99************885799999999965557777777777777776666666665 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0048
                        AAA_15 313 eaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   +       ++   +++++EP + LH +  + l + l++l+++++  vi+  H+
  gi|91773139|ref|YP_565831.1| 845 RR------STGKTVFILDEPTTGLHFDDVNKLLDVLQRLVETGN-TVIVIEHN 890
                                   33......333678889**************************9.67766666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0     0.002      0.97      27      53 ..      20      46 ..       9      52 .. 0.85
   2 ?    5.0   0.0     0.033        16      30      57 ..     630     657 ..     617     672 .. 0.80
   3 ?   -2.7   0.0       7.7   3.7e+03     164     188 ..     866     889 ..     865     890 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                        AAA_25 27 kgllpagelallaGapgtGKttlaldl 53
                                  +   p+++l++++G +g+GK+ la d 
  gi|91773139|ref|YP_565831.1| 20 DVTFPRDKLIVITGLSGSGKSSLAFDT 46
                                  55679*******************986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.033
                        AAA_25  30 lpagelallaGapgtGKttlaldlalav 57 
                                    p+g  + ++G +g+GK+tl  +   +v
  gi|91773139|ref|YP_565831.1| 630 FPLGVMTCVTGVSGSGKSTLINETLNKV 657
                                   4999***************986665555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.7
                        AAA_25 164 dvgalvealeriarrtgaavllvhH 188
                                   dv++l++ l+r+  +tg +v+++ H
  gi|91773139|ref|YP_565831.1| 866 DVNKLLDVLQRL-VETGNTVIVIEH 889
                                   788899999999.799*****9999 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.19        93       2      15 ..      29      42 ..      28      56 .. 0.91
   2 !   11.5   0.1   0.00051      0.25       3      37 ..     637     676 ..     635     692 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                                  EEEEESTTSSHHHH CS
                      MMR_HSR1  2 vaivGrpNvGKStL 15
                                  ++i G + +GKS+L
  gi|91773139|ref|YP_565831.1| 29 IVITGLSGSGKSSL 42
                                  79***********9 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00051
                                   EEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSEE CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltge.....kaivsdkpgtTrdin 37 
                                   ++ G + +GKStLin  +++       +  ++pg+ +di+
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLINETLNKvlsqkLNRSRERPGKYKDIK 676
                                   789**************99643222345566666655555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.007       3.4       2      25 ..      27      50 ..      26      75 .. 0.82
   2 !    7.8   0.0    0.0036       1.7       3      32 ..     635     664 ..     633     674 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.007
                       DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                  +++++tG +G+GK+ +++  +++ 
  gi|91773139|ref|YP_565831.1| 27 KLIVITGLSGSGKSSLAFDTIYAE 50
                                  689**************9998875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0036
                       DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeer 32 
                                   +  VtGv+G+GK+ + ++ l+++ +++++r
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLINETLNKVLSQKLNR 664
                                   568*****************9994444444 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     0.026        12      20      44 ..      26      50 ..      13     118 .. 0.72
   2 !    8.0   0.0    0.0051       2.5      24      48 ..     637     661 ..     632     702 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                      ATPase_2 20 neiyfiYGpegsGKtaLlkeiienl 44
                                  ++ ++i+G  gsGK++L    i   
  gi|91773139|ref|YP_565831.1| 26 DKLIVITGLSGSGKSSLAFDTIYAE 50
                                  7889*************87777665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0051
                      ATPase_2  24 fiYGpegsGKtaLlkeiienledkd 48 
                                    ++G  gsGK++L++e +++ ++++
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLINETLNKVLSQK 661
                                   699***************9987654 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 ?    4.9   0.0     0.024        12     104     146 ..       2      43 ..       1      54 [. 0.73
   2 !    8.0   0.2    0.0026       1.3     132     156 ..     636     660 ..     630     665 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
                         T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttll 146
                                   +l+++++++a ++++++v  +   + +li+++G  gsGK+ l+
  gi|91773139|ref|YP_565831.1|   2 SLKNIIVKGAKEHNLKNVDVT-FPRDKLIVITGLSGSGKSSLA 43 
                                   566666777766666665333.35889************9886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0026
                         T2SSE 132 ilvsGgTgsGKttllyallkeinks 156
                                     v+G  gsGK+tl++  l+++ ++
  gi|91773139|ref|YP_565831.1| 636 TCVTGVSGSGKSTLINETLNKVLSQ 660
                                   579***************9998665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.29   1.4e+02      22      38 ..      28      44 ..      17      55 .. 0.83
   2 ?    6.6   0.0    0.0077       3.7      23      43 ..     636     656 ..     621     664 .. 0.84
   3 ?    2.3   0.0      0.16        79      84     137 ..     862     917 ..     851     938 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.29
                                  EEEEEESTTSSHHHHHH CS
                        NB-ARC 22 vvalvGmgGvGKttlak 38
                                  ++ + G  G+GK+ la 
  gi|91773139|ref|YP_565831.1| 28 LIVITGLSGSGKSSLAF 44
                                  6899**********984 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0077
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                     + G  G+GK+tl+++ lnk
  gi|91773139|ref|YP_565831.1| 636 TCVTGVSGSGKSTLINETLNK 656
                                   4589*************9998 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.16
                                   SSS-STTSHHHHHHHHCCCTTEEEEEE...EE-SHHHH.....HHHHCHTTSEEEEE CS
                        NB-ARC  84 eekeeveslkrklvrlLltkrfllvlD...DVweeedwdkigvvlparenrlrvllT 137
                                    ++++v++l + l+rl +t ++++v+    DV ++ dw  i +     e++ +v+  
  gi|91773139|ref|YP_565831.1| 862 LHFDDVNKLLDVLQRLVETGNTVIVIEhnlDVIKTADW-VIDLGPEGGERGGKVIAK 917
                                   57888888999***************88889*******.888777778888888765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0087       4.2      16      40 ..      23      47 ..      16      56 .. 0.86
   2 ?    5.4   0.1     0.021        10      16      36 ..     630     650 ..     623     660 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0087
                        ATPase 16 ipegrvvlitGepGtGKtifalqFl 40
                                  +p+++ + itG +G+GK+ +a   +
  gi|91773139|ref|YP_565831.1| 23 FPRDKLIVITGLSGSGKSSLAFDTI 47
                                  8*****************9987655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                        ATPase  16 ipegrvvlitGepGtGKtifa 36 
                                   +p g ++ +tG++G+GK+++ 
  gi|91773139|ref|YP_565831.1| 630 FPLGVMTCVTGVSGSGKSTLI 650
                                   788999************985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.05        24       2      17 ..      28      43 ..      27      66 .. 0.85
   2 ?    7.7   0.0    0.0062         3       3      30 ..     636     663 ..     634     668 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.05
                                  CEEEEC-TTTCHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLl 17
                                  l++++G +GsGK+ L+
  gi|91773139|ref|YP_565831.1| 28 LIVITGLSGSGKSSLA 43
                                  799***********98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0062
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegklp 30 
                                    +++G +GsGK+tL+ +   +  ++kl+
  gi|91773139|ref|YP_565831.1| 636 TCVTGVSGSGKSTLINETLNKVLSQKLN 663
                                   689***********98877766666655 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.027        13       5      35 ..     250     284 ..     241     304 .. 0.69
   2 ?    0.1   0.0       2.3   1.1e+03      20      35 ..     397     412 ..     381     430 .. 0.64
   3 ?    5.4   0.1     0.053        25       6      49 ..     736     782 ..     732     793 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.027
                                   CT.TGGGTSS...SST-SSTT.HHHHHHHHHHH-- CS
                Cytochrom_c3_2   5 egvkCadCHt...kekpkkdk.aveeekClsCHgk 35 
                                   e+++C+dC     + +p++ + +  + +C++CHg 
  gi|91773139|ref|YP_565831.1| 250 ENLACTDCEIgfeDMEPSAFSfNSPQGACEECHGL 284
                                   56778888764323334444445566678888875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.3
                                   STTHHHHHHHHHHH-- CS
                Cytochrom_c3_2  20 kdkaveeekClsCHgk 35 
                                    +k ++++ C+sC g+
  gi|91773139|ref|YP_565831.1| 397 LKKYITTKPCTSCNGD 412
                                   2345566666666655 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.053
                                   T.TGGGTSSSST-SSTTHHHHHH...HHHHH--HHHCHTTSST.TSS CS
                Cytochrom_c3_2   6 gvkCadCHtkekpkkdkaveeek...ClsCHgkleelakktkeakea 49 
                                   g +C++C ++ + + + +   +    C+ CHgk  ++++ + + k++
  gi|91773139|ref|YP_565831.1| 736 GGRCETCSGDGTITIEMHFLPDVyvpCEVCHGKRYNHETLEVNYKDK 782
                                   55899999988875544333322455*****9998887766554444 PP

>> AAA_30  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        71      17      34 ..      25      42 ..      19      66 .. 0.85
   2 ?    7.3   0.0    0.0075       3.6      20      41 ..     635     657 ..     632     667 .. 0.80
   3 ?   -1.7   0.0       4.2     2e+03      85     120 ..     846     885 ..     821     887 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                        AAA_30 17 gdrvavltGpAGtGKtta 34
                                  +d++ v+tG  G+GK+ +
  gi|91773139|ref|YP_565831.1| 25 RDKLIVITGLSGSGKSSL 42
                                  56799**********986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0075
                        AAA_30  20 vavltGpAGtGKttalkal.rea 41 
                                   ++++tG+ G+GK+t++++  +++
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLINETlNKV 657
                                   789*************9874444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.2
                        AAA_30  85 rlepgtllivDEagmv....dtkqlaallkaaekagakvi 120
                                   r + +t++i DE        d ++l ++l+++ ++g +vi
  gi|91773139|ref|YP_565831.1| 846 RSTGKTVFILDEPTTGlhfdDVNKLLDVLQRLVETGNTVI 885
                                   3455699999996654434445555555555555566655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.014       6.7      12      39 ..      22      49 ..      12      87 .. 0.78
   2 ?    4.5   0.0     0.038        18      18      40 ..     635     657 ..     631     663 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                    Zeta_toxin 12 sqerPklillgGqpGAGKselaellkde 39
                                  +  r kli++ G +G+GKs+la ++  +
  gi|91773139|ref|YP_565831.1| 22 TFPRDKLIVITGLSGSGKSSLAFDTIYA 49
                                  457889**************99665544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.038
                    Zeta_toxin  18 lillgGqpGAGKselaellkdel 40 
                                   +  + G +G+GKs+l++++ +++
  gi|91773139|ref|YP_565831.1| 635 MTCVTGVSGSGKSTLINETLNKV 657
                                   5678999**********998876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.074        36       1      16 [.      28      43 ..      28      66 .. 0.86
   2 ?    6.2   0.0     0.016       7.8       3      26 ..     637     661 ..     635     689 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.074
                           PRK  1 vIgvagsSGaGkttva 16
                                  +I ++g SG+Gk+++a
  gi|91773139|ref|YP_565831.1| 28 LIVITGLSGSGKSSLA 43
                                  589**********986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.016
                           PRK   3 gvagsSGaGkttv.arklekifgre 26 
                                    v+g SG+Gk+t+  ++l+k++ ++
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLiNETLNKVLSQK 661
                                   59**********6257888888755 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.23   1.1e+02       1      17 [.      29      45 ..      29      65 .. 0.85
   2 ?    7.7   0.1    0.0095       4.6       2      26 ..     637     661 ..     636     678 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.23
                  RNA_helicase  1 iwlyGpsgeGKStlake 17
                                  i+++G sg GKS+la +
  gi|91773139|ref|YP_565831.1| 29 IVITGLSGSGKSSLAFD 45
                                  789**********9976 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0095
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl 26 
                                   +++G sg GKStl++e  +++l++ 
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLINETLNKVLSQK 661
                                   789************9666665433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.15        74      27      55 ..      20      48 ..       1      63 [. 0.74
   2 ?    7.2   0.1    0.0065       3.2      36      61 ..     636     661 ..     631     666 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                         AAA_7 27 elllknkkpvllvGptGtGKtviikdllk 55
                                  +  + ++k ++++G +G+GK++++ d++ 
  gi|91773139|ref|YP_565831.1| 20 DVTFPRDKLIVITGLSGSGKSSLAFDTIY 48
                                  56667788999***********9988544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0065
                         AAA_7  36 vllvGptGtGKtviikdllkkldkek 61 
                                   ++++G +G+GK+++i+++l+k+ ++k
  gi|91773139|ref|YP_565831.1| 636 TCVTGVSGSGKSTLINETLNKVLSQK 661
                                   5789*************999887666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.48   2.3e+02       2      16 ..      29      43 ..      28      52 .. 0.87
   2 ?   -2.2   0.1       6.7   3.3e+03      48      98 ..     184     238 ..     169     246 .. 0.65
   3 ?    9.4   0.2    0.0019      0.93       3      26 ..     637     660 ..     635     664 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.48
                                  EEEE--TTSSHHHHH CS
                      NTPase_1  2 vfiTGppGvGKtTlv 16
                                  ++iTG +G+GK+ l 
  gi|91773139|ref|YP_565831.1| 29 IVITGLSGSGKSSLA 43
                                  79**********986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                                   EEEET.T--EEEEEETT.---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-....E CS
                      NTPase_1  48 kivdlasgeegiLarve.akreprvgkyvvdvesfeelalealrkalsead....v 98 
                                   +i++l++ e+  L r + ++ e+ v+++v++ +++ e + +a+++al++++    v
  gi|91773139|ref|YP_565831.1| 184 EIIALEDAETIGLGRYNkHNIEAVVDRIVIK-DDIRERVTDAVETALEKSGgtlvV 238
                                   5777777777777777723334456666666.777777788888888776655433 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0019
                                   EEE--TTSSHHHHHHHHHHHH... CS
                      NTPase_1   3 fiTGppGvGKtTlvkkvlellkss 26 
                                   ++TG +G+GK+Tl++  l+++ s+
  gi|91773139|ref|YP_565831.1| 637 CVTGVSGSGKSTLINETLNKVLSQ 660
                                   69**************99988665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0034       1.6       9      26 ..     115     132 ..     112     134 .. 0.81
   2 ?   -1.6   0.0       5.8   2.8e+03       6      19 ..     268     281 ..     264     288 .. 0.78
   3 ?   -2.3   0.3       9.4   4.5e+03      13      19 ..     403     409 ..     399     412 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0034
                          YhfH   9 rnLPkKkCteCGkeieEq 26 
                                    +++   C++CGk ie q
  gi|91773139|ref|YP_565831.1| 115 ARIGIRHCPKCGKAIEPQ 132
                                   5667789********987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.8
                          YhfH   6 eFfrnLPkKkCteC 19 
                                    F+ n P+  C eC
  gi|91773139|ref|YP_565831.1| 268 AFSFNSPQGACEEC 281
                                   57777788889998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.4
                          YhfH  13 kKkCteC 19 
                                   +K Ct+C
  gi|91773139|ref|YP_565831.1| 403 TKPCTSC 409
                                   7999999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.14        66      28      35 ..     121     128 ..     106     135 .. 0.69
   2 ?    7.2   1.6     0.011       5.5       7      34 ..     253     283 ..     251     287 .. 0.76
   3 ?   -0.9   0.1       3.8   1.8e+03      27      35 ..     403     413 ..     389     415 .. 0.71
   4 ?    1.9   0.4      0.52   2.5e+02       7      34 ..     738     767 ..     738     771 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                   Zn-ribbon_8  28 aCPeCgse 35 
                                   +CP+Cg++
  gi|91773139|ref|YP_565831.1| 121 HCPKCGKA 128
                                   37777764 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                   Zn-ribbon_8   7 rCeeCghefevlqsis...dapltaCPeCgs 34 
                                    C++C   fe + +++    +p+ aC eC++
  gi|91773139|ref|YP_565831.1| 253 ACTDCEIGFEDMEPSAfsfNSPQGACEECHG 283
                                   6*********555544335777888****97 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.8
                   Zn-ribbon_8  27 ta.CPeCgs.e 35 
                                   t+ C +C++ +
  gi|91773139|ref|YP_565831.1| 403 TKpCTSCNGdR 413
                                   44599998855 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.52
                   Zn-ribbon_8   7 rCeeCghefevlqsis.daplta.CPeCgs 34 
                                   rCe C  + ++  +++  ++  + C  C++
  gi|91773139|ref|YP_565831.1| 738 RCETCSGDGTITIEMHfLPDVYVpCEVCHG 767
                                   799999999999999977777778****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.83u 0.29s 00:00:01.11 Elapsed: 00:00:00.44
# Mc/sec: 6437.63
//
Query:       gi|91773140|ref|YP_565832.1|  [L=194]
Description: formylmethanofuran dehydrogenase, subunit E [Methanococcoides burtonii DSM 6242]
Scores for complete 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  144.3   0.0    2.9e-42  143.8   0.0    1.2  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
    1.1e-11   44.5   2.8    1.9e-11   43.7   2.8    1.3  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
      0.029   14.6   0.4      0.059   13.6   0.4    1.4  1  LIM           LIM domain
      0.088   11.7   0.1       0.13   11.1   0.1    1.2  1  ISN1          IMP-specific 5'-nucleotidase
       0.15   11.9   0.0       0.21   11.5   0.0    1.2  1  DUF1706       Protein of unknown function (DUF1706)
       0.18   11.8   0.1       0.54   10.3   0.0    1.8  2  Sdh5          Flavinator of succinate dehydrogenase


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 !  143.8   0.0   9.7e-46   2.9e-42       1     132 []       9     144 ..       9     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 9.7e-46
                                   HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEETTT-EE CS
                          FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkrktgka 81 
                                   fHGHlCpglv+Gyr++ +a ++++  ++++deelv++ve++sC +DAiqv+ gct+Gkgnl+++d+gk+++tf kr++ +a
  gi|91773140|ref|YP_565832.1|   9 FHGHLCPGLVIGYRIGTYAAEQFK--DRSEDEELVVVVENKSCSVDAIQVINGCTFGKGNLVFKDLGKHVYTFFKRGDRNA 87 
                                   9**********************8..34448************************************************** PP

                                   EEEEE-.......CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHEE CS
                          FmdE  82 vrlklk.......eelpelreklakgkakeekeeeeleeeleeaikkilnapeeelfe 132
                                   +r++++       e+++el+ k+ +g+a+ e e ee++++++e + +il+ p+e+lf+
  gi|91773140|ref|YP_565832.1|  88 LRISVNprkrsndEKYNELFPKVRNGTATAE-ELEEFRKRHAENAYAILDIPDEDLFT 144
                                   ****************************988.8899********************96 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 !   43.7   2.8   6.2e-15   1.9e-11       3      35 ..     159     193 ..     158     194 .] 0.94

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 6.2e-15
                  zf-dskA_traR   3 ygs..CeeCGEpIpeaRlralPgarlCveCqekae 35 
                                   y+s  C+eCGE+ +e Rlr+ +g+++C++C+e+++
  gi|91773140|ref|YP_565832.1| 159 YRSiaCAECGEEAMETRLRVKEGKIVCLSCFEGHD 193
                                   78889***************************996 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4     2e-05     0.059      28      55 ..     163     190 ..     159     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                   B-TTT-SB-CTT.CEEETTEEEEHHHHH CS
                           LIM  28 tCsdCqkeLkegsfyekdgklyCkkdyl 55 
                                    C++C++e  e+++ +k+gk++C +++ 
  gi|91773140|ref|YP_565832.1| 163 ACAECGEEAMETRLRVKEGKIVCLSCFE 190
                                   7*******99999*************95 PP

>> ISN1  IMP-specific 5'-nucleotidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.4e-05      0.13     309     351 ..      33      75 ..      20      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                          ISN1 309 areqLeevvlvvqkklelseaareikfcafnGGsDvfvDiGdk 351
                                    r + ee+v+vv++k  + +a + i+ c+f  G+ vf D+G  
  gi|91773140|ref|YP_565832.1|  33 DRSEDEELVVVVENKSCSVDAIQVINGCTFGKGNLVFKDLGKH 75 
                                   58888***********************************976 PP

>> DUF1706  Protein of unknown function (DUF1706)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.9e-05      0.21      87     134 ..     101     148 ..      76     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-05
                                   HHHHHHHHHHCTTS-HHHHHHHHHHHHHHHHHHHHHS-HHHHHSTTS- CS
                       DUF1706  87 gelnqkfyekyqdlsleelleelkesheellalieslsdeeLfekkgr 134
                                   +++n+ f +  + ++ +e lee++++h+e   +i  ++de+Lf+ + +
  gi|91773140|ref|YP_565832.1| 101 EKYNELFPKVRNGTATAEELEEFRKRHAENAYAILDIPDEDLFTVTNV 148
                                   5788999999999******************************87765 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   3.3e+03      20      35 ..      23      38 ..      21      40 .. 0.82
   2 ?   10.3   0.0   0.00018      0.54      26      64 ..     118     156 ..     114     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                  TTTHHHHHTTT--HHH CS
                          Sdh5 20 LgrFaekhlatlseee 35
                                  +g++a++++++ se+e
  gi|91773140|ref|YP_565832.1| 23 IGTYAAEQFKDRSEDE 38
                                  7899999999888776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00018
                                   HHTTT--HHHHHHHHHHHTS--HHHHHHHHT-.---S-H CS
                          Sdh5  26 khlatlseeeldaferLLdleDpdLldwltgrkeepeda 64 
                                   ++l+++ ++ ++   ++Ld++D dL+ +   ++e+pe+a
  gi|91773140|ref|YP_565832.1| 118 EELEEFRKRHAENAYAILDIPDEDLFTVTNVETEPPEKA 156
                                   688999999999999*************99997777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 1026.26
//
Query:       gi|91773141|ref|YP_565833.1|  [L=446]
Description: adenylosuccinate lyase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-56  192.0   3.8    2.5e-56  191.4   3.8    1.1  1  Lyase_1      Lyase
    1.4e-20   73.6   0.1    7.1e-20   71.3   0.0    2.2  2  ADSL_C       Adenylosuccinate lyase C-terminus
  ------ inclusion threshold ------
      0.011   16.1   0.2      0.068   13.6   0.0    2.5  2  FumaraseC_C  Fumarase C C-terminus
      0.016   15.9   0.2      0.086   13.6   0.0    2.3  2  ASL_C2       Argininosuccinate lyase C-terminal
       0.18   12.1   0.8        2.4    8.5   0.1    2.7  2  DUF1844      Domain of unknown function (DUF1844)


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 !  191.4   3.8     7e-60   2.5e-56       6     309 ..      11     293 ..       7     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 7e-60
                                   ETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHH CS
                       Lyase_1   6 kadklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmn 86 
                                    +d++  +++e +r+++ l+      +aal+ a ak ++ ++e+aa+i+k    ++  +k++   +++ i+ ++++++ + 
  gi|91773141|ref|YP_565833.1|  11 GTDEMKYVWSEANRLEKLLK-----TEAALSNAEAKIGMVPAEAAAEIEKS---IAH-VKIE---RVAEIEDEIHHDMMA- 78 
                                   58999999999999999999.....899*************8888888765...444.6777...889999999999877. PP

                                   HHHHHHHHTT.HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEE CS
                       Lyase_1  87 lnevigellg.ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPv 166
                                      vi+ +++  + +++++vh+g++snD+ +Ta +l++ +a+ + L+++ ++L d+l  ka+e+k++v +GrTh+q  +P+
  gi|91773141|ref|YP_565833.1|  79 --IVIA-ISEqCTDDAAKWVHFGATSNDILDTATALQMMDAV-AILEEKTRTLLDVLLTKAEEHKNTVCAGRTHGQIGVPT 155
                                   ..5666.33334469***************************.77************************************ PP

                                   EHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHH CS
                       Lyase_1 167 tlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavve 247
                                   t g  ++ +a ++ r++erl +l++rllv+++ g++++ ++++ d    e  a+ ++ + +    + +  +++ +rD+++e
  gi|91773141|ref|YP_565833.1| 156 TYGLRFAIWASEVARHLERLAQLTPRLLVGQMTGAVGTQAAFGKDGI--EIQAHAMEYLGL---GSVDVSNQIIQRDRHAE 231
                                   **********************************8888888888874..566666664444...667888899******** PP

                                   HHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHH CS
                       Lyase_1 248 llgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagr 309
                                   ++ +++++ t L k+a ++r l+ +e+ +ve+s+++++ GSS+MP+K+NP+++E + g a+ 
  gi|91773141|ref|YP_565833.1| 232 FVMWMANTVTTLDKIAVEIRTLQRSEIAEVEESFRKNQVGSSTMPHKRNPIKSEQISGLARI 293
                                   ********************************************************998875 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   5.2e+03      49      68 ..      21      40 ..      13      45 .. 0.67
   2 !   71.3   0.0     2e-23   7.1e-20       1      73 []     360     438 ..     360     438 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                                  HHCHHHHHT-GGGCCTTHHH CS
                        ADSL_C 49 seeeldalfdpayylgsade 68
                                  ++++l++l++ ++ l +a++
  gi|91773141|ref|YP_565833.1| 21 EANRLEKLLKTEAALSNAEA 40
                                  44577888888777777765 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 2e-23
                                   TGGGHHHHHHHHHH.TH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHHHH CS
                        ADSL_C   1 GlifservllaLvk.glgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivdrv 73 
                                   Gl + e++++ L+k g+gR+eA+e+V+  am+a e+   l+++L++ p+v+ + +e+e+++l+dp+ y+g a ++v+ v
  gi|91773141|ref|YP_565833.1| 360 GLNMGEAIMIDLAKrGVGRQEAHEIVRSSAMEAHESgkhLKDVLLSRPDVTkYlNESEINDLLDPDMYIGTAVAQVENV 438
                                   899**********66*******************99***************55*999*******************986 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1         2   7.2e+03      24      45 ..     239     260 ..     236     261 .. 0.79
   2 ?   13.6   0.0   1.9e-05     0.068      18      50 ..     389     425 ..     379     427 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                                   HT--HHHHHHHTT-.-HHHHHH CS
                   FumaraseC_C  24 egktlreavlelgllteeelde 45 
                                   + +tl  +++e   l + e+ e
  gi|91773141|ref|YP_565833.1| 239 TVTTLDKIAVEIRTLQRSEIAE 260
                                   5678999999998888888876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHT--HHHHHHH....TT-.-HHHHHHHT-HH CS
                   FumaraseC_C  18 AkeAlkegktlreavle....lgllteeeldelldpe 50 
                                   A eA+++gk l+++ l      ++l e e+++lldp 
  gi|91773141|ref|YP_565833.1| 389 AMEAHESGKHLKDVLLSrpdvTKYLNESEINDLLDPD 425
                                   789*************98888899***********95 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.4   8.8e+03      34      55 ..      52      73 ..      37      94 .. 0.65
   2 ?   13.6   0.0   2.4e-05     0.086      11      65 ..     371     425 ..     370     428 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                                  HTT--GGG--HHHHHHH-TT-- CS
                        ASL_C2 34 ekgkeleeltleelkeisplle 55
                                  e +k+++++++e ++ei++ + 
  gi|91773141|ref|YP_565833.1| 52 EIEKSIAHVKIERVAEIEDEIH 73
                                  3345566666666666655444 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.4e-05
                                   HHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHH CS
                        ASL_C2  11 LvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpe 65 
                                   L+++G+   eAHeiv + + +a e+gk+l+++ l+  + + + l+ +++++ Ldp 
  gi|91773141|ref|YP_565833.1| 371 LAKRGVGRQEAHEIVRSSAMEAHESGKHLKDVLLSRPD-VTKYLNeSEINDLLDPD 425
                                   788999999*************************9999.66677779999999996 PP

>> DUF1844  Domain of unknown function (DUF1844)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.19   6.7e+02      12      40 ..      36      62 ..      32      76 .. 0.74
   2 ?    8.5   0.1   0.00068       2.4      32      55 ..     106     129 ..      92     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.19
                       DUF1844 12 ssAlvaLGelpdpetgkkekdlelAkqsI 40
                                  s+A+++ G +p++ + + ek    A+ +I
  gi|91773141|ref|YP_565833.1| 36 SNAEAKIGMVPAEAAAEIEK--SIAHVKI 62
                                  789********998866665..4455555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00068
                       DUF1844  32 dlelAkqsIdlLamLkeKtkgnLd 55 
                                   d  +A q +d +a+L+eKt+  Ld
  gi|91773141|ref|YP_565833.1| 106 DTATALQMMDAVAILEEKTRTLLD 129
                                   6679****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2602.02
//
Query:       gi|91773142|ref|YP_565834.1|  [L=175]
Description: hypothetical protein Mbur_1161 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00011   22.0   0.0    0.00034   20.4   0.0    1.8  2  TrmB         Sugar-specific transcriptional regulator TrmB
    0.00025   21.3   0.0    0.00066   20.0   0.0    1.6  2  Rrf2         Transcriptional regulator
     0.0003   20.3   0.0    0.00058   19.4   0.0    1.5  1  HTH_24       Winged helix-turn-helix DNA-binding
    0.00054   19.8   0.0     0.0014   18.4   0.0    1.7  1  HTH_5        Bacterial regulatory protein, arsR family
    0.00056   19.7   0.0    0.00093   19.0   0.0    1.3  1  HTH_IclR     IclR helix-turn-helix domain
     0.0024   17.7   0.0     0.0049   16.7   0.0    1.6  1  TFIIE_alpha  TFIIE alpha subunit
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.02   14.8   0.1    1.5  1  HTH_11       HTH domain
      0.018   14.9   0.0      0.039   13.8   0.0    1.5  1  MarR_2       MarR family
      0.064   13.2   0.0       0.64   10.0   0.0    2.2  2  MarR         MarR family
       0.09   12.6   0.0       0.31   10.9   0.0    1.9  1  HTH_23       Homeodomain-like domain
       0.12   12.6   0.0       0.25   11.6   0.0    1.5  1  HTH_34       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 !   20.4   0.0   2.1e-07   0.00034      11      57 ..      18      64 ..      12      73 .. 0.90
   2 ?   -2.1   0.0       2.2   3.6e+03      48      66 ..     105     123 ..     103     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                                  CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                  + +Y+ L ++g+a+ ++i  +l++ +s+  ++++sL + Gl++++++
  gi|91773142|ref|YP_565834.1| 18 VLAYIGLQSEGSADFQDILDNLDIQKSTLWRYISSLREQGLIDISRS 64
                                  679***************************************99876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                   HCTSEEEESSTTTEEEE-- CS
                          TrmB  48 dkGlVerekgrpklYravd 66 
                                   d G+++r + r+k  ++++
  gi|91773142|ref|YP_565834.1| 105 DSGMIRRYRDRTKNLKPIK 123
                                   6799999999988877775 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.1e-07   0.00066      10      58 ..      15      62 ..      10      64 .. 0.94
   2 ?   -2.8   0.0         5   8.2e+03      25      35 ..     134     144 ..     111     150 .. 0.51

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.1e-07
                                  HHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 10 alhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  al++l+y+ +++e++ +  ++i ++ +i++s l + ++ Lr++gl+   
  gi|91773142|ref|YP_565834.1| 15 ALKVLAYIGLQSEGS-ADFQDILDNLDIQKSTLWRYISSLREQGLIDIS 62
                                  99***********98.******************************865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                                   -B-HHHHHHHH CS
                          Rrf2  25 pvsseeiaerq 35 
                                   ++ +e+i e  
  gi|91773142|ref|YP_565834.1| 134 KIVVETIREAE 144
                                   23334444444 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 !   19.4   0.0   3.5e-07   0.00058      12      47 ..      24      59 ..      14      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                        HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  Lq +++   +++ + l++ +st++r++  L e+GlI
  gi|91773142|ref|YP_565834.1| 24 LQSEGSADFQDILDNLDIQKSTLWRYISSLREQGLI 59
                                  78899999***************************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 !   18.4   0.0   8.8e-07    0.0014      12      45 ..      26      59 ..      24      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.8e-07
                                  TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5 12 aegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  +eg++ + ++ + l++ +st+ ++ + Lre+GL+
  gi|91773142|ref|YP_565834.1| 26 SEGSADFQDILDNLDIQKSTLWRYISSLREQGLI 59
                                  57999****************************9 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.7e-07   0.00093       4      48 ..      14      59 ..      13      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.7e-07
                                  HHHHHHCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR  4 RalaiLdalaeapqel.tlselArrtglpkStvhRlLqtLvelGyv 48
                                  Ral +L +++ + ++   ++++ +++++ kSt  R++++L e+G++
  gi|91773142|ref|YP_565834.1| 14 RALKVLAYIGLQSEGSaDFQDILDNLDIQKSTLWRYISSLREQGLI 59
                                  9**************77***************************97 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0049       6      62 ..       3      64 ..       1      88 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                                  HHHHCS-HHHHHHHHHHHCTTSEBH.....HHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                   TFIIE_alpha  6 vvrkfygeeavlvldvLlekgevte.....edlakelkidlnelrklLnrLyearlvkykrr 62
                                  v +++ +++++ +l+vL+  g  +e      d+  +l i++  l + +  L+e++l+++ r+
  gi|91773142|ref|YP_565834.1|  3 VKFEAQEDNHFRALKVLAYIGLQSEgsadfQDILDNLDIQKSTLWRYISSLREQGLIDISRS 64
                                  6678889999988888875444443222237****************************997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.2e-05      0.02      16      46 ..      30      61 ..      14      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                        HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelg.vpI 46
                                     +++ + L++ ++t +r+I +L+e+g ++I
  gi|91773142|ref|YP_565834.1| 30 ADFQDILDNLDIQKSTLWRYISSLREQGlIDI 61
                                  566889999*******************5554 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.039       9      55 ..      17      63 ..      13      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                  HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   vLa++g   ++    +++ + l++ ks++ r +  L ++GL+  ++
  gi|91773142|ref|YP_565834.1| 17 KVLAYIGLQSEGSADFQDILDNLDIQKSTLWRYISSLREQGLIDISR 63
                                  599999999999999****************************8876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00039      0.64      13      51 ..      25      63 ..      10      65 .. 0.82
   2 ?    0.4   0.0      0.38   6.2e+02      43      52 ..     105     114 ..     103     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                                  HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                   ++g++  +++ + l ++kst+ r +  L ++Gli+ s+
  gi|91773142|ref|YP_565834.1| 25 QSEGSADFQDILDNLDIQKSTLWRYISSLREQGLIDISR 63
                                  456677777**************************8665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.38
                                   HTTSEEEEEE CS
                          MarR  43 kkGlieRsks 52 
                                   + G+i+R+++
  gi|91773142|ref|YP_565834.1| 105 DSGMIRRYRD 114
                                   78******98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.31      21      47 ..      33      59 ..      32      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                        HTH_23 21 reIAreLgvsrrTvyrwlkryreeGle 47
                                  ++I + L++ ++T++r+++  re Gl 
  gi|91773142|ref|YP_565834.1| 33 QDILDNLDIQKSTLWRYISSLREQGLI 59
                                  58999******************9986 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   0.00015      0.25       3      50 ..      16      65 ..      15      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                        HTH_34  3 lavlsy..LasvdeadfvelkealeatdgnLsvhlkkLekagYievdkef 50
                                  l+vl+y  L s+ +adf+++ + l + ++ L   ++ L ++g i ++ ++
  gi|91773142|ref|YP_565834.1| 16 LKVLAYigLQSEGSADFQDILDNLDIQKSTLWRYISSLREQGLIDISRSY 65
                                  566766447789********************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1213.69
//
Query:       gi|91773143|ref|YP_565835.1|  [L=284]
Description: hypothetical protein Mbur_1162 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-28   97.6   0.0    1.6e-27   96.6   0.0    1.6  1  DUF488    Protein of unknown function, DUF488
    0.00032   20.7   0.0    0.00078   19.5   0.0    1.6  1  HemN_C    HemN C-terminal domain
  ------ inclusion threshold ------
      0.034   14.9   0.4       0.75   10.6   0.4    2.3  1  DUF4326   Domain of unknown function (DUF4326)
      0.036   12.9   0.9      0.052   12.4   0.0    1.7  2  YqfD      Putative stage IV sporulation protein YqfD
        0.5   10.4   0.1        0.5   10.4   0.1    3.0  4  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   4.3e-31   1.6e-27       2     120 ..     154     271 ..     153     273 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 4.3e-31
                        DUF488   2 lervydllkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdprweefferYaaeles 82 
                                   ++++++ll ++++++l+DVR++P S++  f+k++l+  l++ gi+Y+++++lg +++ rk+ ++ +++++ f++Ya+ +++
  gi|91773143|ref|YP_565835.1| 154 IDQFLNLLIQNNINILADVRKNPFSMKFSFTKKKLSTYLEKIGIQYIHIPDLGIESDDRKELNSMTDYQNLFKEYADSTLK 234
                                   89*************************************************************9999*************8 PP

                        DUF488  83 keaakealeelkelakkg.vaLlcaekdperchrvvlae 120
                                     ++ke+l+ + el++++ va++c+e+d   chr v+a+
  gi|91773143|ref|YP_565835.1| 235 --RNKEHLDYIYELSQSNrVAMMCFEADIDMCHRGVIAK 271
                                   ..4679******************************997 PP

>> HemN_C  HemN C-terminal 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   0.00078      34      64 ..      57      87 ..      42      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.2e-07
                        HemN_C 34 leellaaaleklqeqGLLeldggrlrltprG 64
                                  +++++ a + klq +GL+  ++++l lt++G
  gi|91773143|ref|YP_565835.1| 57 FSNAYYADITKLQSDGLIIENDHHLELTEKG 87
                                  88999888**********************9 PP

>> DUF4326  Domain of unknown function (DUF4326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00021      0.75      23      82 ..     175     270 ..      85     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                       DUF4326  23 NpFvvgqe................................lgereevvekyreyleeraekdeelkaaleeLr.gkeLaCw 70 
                                   NpF ++ +                                l++  +  + ++ey+ ++ ++++e+++ + eL   +++a +
  gi|91773143|ref|YP_565835.1| 175 NPFSMKFSftkkklstylekigiqyihipdlgiesddrkeLNSMTDYQNLFKEYADSTLKRNKEHLDYIYELSqSNRVAMM 255
                                   66666666666677777777777777777777777777776677777888999999999999**********978889966 PP

                       DUF4326  71 Ck..pk.pCHadvll 82 
                                   C   +   CH  v++
  gi|91773143|ref|YP_565835.1| 256 CFeaDIdMCHRGVIA 270
                                   65335457**99987 PP

>> YqfD  Putative stage IV sporulation protein YqfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       0.4   1.4e+03      35      66 ..      85     115 ..      77     123 .. 0.74
   2 ?   12.4   0.0   1.4e-05     0.052       5      49 ..     143     187 ..     139     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.4
                          YqfD  35 rkkdgeleakislkdfkklrkiarktgcrvki 66 
                                   +k+++ ++ k++ k+++++r++a k   + +i
  gi|91773143|ref|YP_565835.1|  85 EKGKD-VSTKTERKAIFRIRRVANKFSSDKQI 115
                                   55555.88888888888888888887766555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.4e-05
                          YqfD   5 GyvtikveGknperflnllarrgIelwdikrkkdgeleakislkd 49 
                                   G   i  eG+++ +flnll++++I++    rk+  ++++  + k+
  gi|91773143|ref|YP_565835.1| 143 GLFSIGYEGRDIDQFLNLLIQNNINILADVRKNPFSMKFSFTKKK 187
                                   6678889*******************9988888888888877765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.67   2.4e+03      13      26 ..      11      26 ..       1      37 [. 0.52
   2 ?   10.4   0.1   0.00014       0.5      40      70 ..      65      95 ..      60     101 .. 0.89
   3 ?   -1.7   0.1      0.83     3e+03      36      55 ..     120     139 ..     114     141 .. 0.82
   4 ?   -0.9   0.1      0.47   1.7e+03      36      60 ..     154     185 ..     149     195 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.67
                        HTH_45 13 eais..egeakkTkim 26
                                  ++i+  +++ + Tk m
  gi|91773143|ref|YP_565835.1| 11 SVIDrlNERGNATKFM 26
                                  3332224444555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                        HTH_45 40 LdmLvekglikkskekYvlTekGlelleklk 70
                                  + +L++ gli ++++  +lTekG+++  k +
  gi|91773143|ref|YP_565835.1| 65 ITKLQSDGLIIENDHHLELTEKGKDVSTKTE 95
                                  67899*******************9887766 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.83
                        HTH_45  36 lnkYLdmLvekglikkskek 55 
                                    +kY ++ v+ +l+++++++
  gi|91773143|ref|YP_565835.1| 120 YEKYPEFTVKSKLVDNKEKQ 139
                                   57899999999999998875 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.47
                        HTH_45  36 lnkYLdmLvekgl.i.....kk.skekYvlTe 60 
                                   ++++L+ L+++++ i     k+  + k++ T+
  gi|91773143|ref|YP_565835.1| 154 IDQFLNLLIQNNInIladvrKNpFSMKFSFTK 185
                                   56889999988875344444222345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2120.26
//
Query:       gi|91773144|ref|YP_565836.1|  [L=253]
Description: hypothetical protein Mbur_1163 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1558.22
//
Query:       gi|91773145|ref|YP_565837.1|  [L=72]
Description: hypothetical protein Mbur_1164 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00012   21.9   0.0    0.00013   21.8   0.0    1.0  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.5e-09   0.00013     101     139 ..      22      64 ..       9      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.5e-09
                                   T....TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHH CS
               Phage_integrase 101 k....rgkplsrqtvrkafkraveeagiekpltpHtlRhsfat 139
                                   k    +g++++      +++r+++  gi+k+++pH +Rhs a+
  gi|91773145|ref|YP_565837.1|  22 KgnikKGQHMQYMGCLMILRRLAKSPGINKRIHPHLFRHSRAS 64 
                                   2555599*********************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 482.84
//
Query:       gi|91773146|ref|YP_565838.1|  [L=135]
Description: hypothetical protein Mbur_1165 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.024   14.5   0.4      0.067   13.1   0.4    1.7  1  LPD15           Large polyvalent-protein-associated domain 15
      0.079   13.6   0.1        0.1   13.2   0.1    1.2  1  Cytochrom_B562  Cytochrome b562


Domain annotation for each model (and alignments):
>> LPD15  Large polyvalent-protein-associated domain 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   7.5e-06     0.067       6      92 ..      24     106 ..      19     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-06
                         LPD15   6 lakelqeelrdgiawviiykegrsW.kaeaiwldeddtleeedlkrlr...eikkaDdkAvvvnGkysgnlgedmtleela 82 
                                   l+k++ +++++gi  +++ ke+r+W ++ a+ l++ ++l ++d +++r   +++++Dd        +   + +dm+ ++l+
  gi|91773146|ref|YP_565838.1|  24 LVKQMTDDAKQGI--IALTKEDRQWfETYAFGLQQFEVLCSKDSSKMRagdWRQAVDDF------SKVRFFVDDMEEKKLV 96 
                                   79999*******9..5788******4455666999999999998888722244555553......4557889999999999 PP

                         LPD15  83 aairyhyeni 92 
                                   + + +++e i
  gi|91773146|ref|YP_565838.1|  97 KNVFWNVEGI 106
                                   9999998865 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.2e-05       0.1      33      89 ..      26      82 ..       1      86 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                Cytochrom_B562 33 raaaedakeatpsklekdseeqkdYqeGldklidqldkaealakagkleeakaalke 89
                                  +++ +dak++ ++  ++d++ +++Y  Gl+++ +   k ++++ ag+  +a    ++
  gi|91773146|ref|YP_565838.1| 26 KQMTDDAKQGIIALTKEDRQWFETYAFGLQQFEVLCSKDSSKMRAGDWRQAVDDFSK 82
                                  45678999999988888******************************9999766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 999.52
//
Query:       gi|91773147|ref|YP_565839.1|  [L=507]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-24   85.1   0.1    7.3e-13   48.5   0.0    2.9  3  PAS          PAS fold
    1.4e-21   76.5   0.0    1.3e-14   54.2   0.0    2.6  2  PAS_3        PAS fold
    3.4e-21   75.8   0.3    8.2e-21   74.6   0.3    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.7e-20   72.7   0.0      4e-11   43.1   0.0    2.4  2  PAS_4        PAS fold
    5.2e-20   71.6   0.9    1.1e-09   38.4   0.1    2.8  2  PAS_9        PAS domain
    5.7e-19   67.9   0.1    2.5e-18   65.9   0.0    2.2  2  HisKA        His Kinase A (phospho-acceptor) domain
    5.9e-08   32.5   0.1    0.00064   19.7   0.0    2.7  2  PAS_8        PAS domain
    6.6e-06   26.0   0.0    1.6e-05   24.7   0.0    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.3e-05   23.3   0.0     0.0089   16.1   0.0    2.5  2  PAS_11       PAS domain
     0.0099   16.0   0.0       0.17   12.1   0.0    2.7  1  PAS_7        PAS fold
  ------ inclusion threshold ------
      0.021   14.8   0.1       0.13   12.3   0.0    2.2  2  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   4.5e-16   7.3e-13       7     106 ..      38     134 ..      32     141 .. 0.86
   2 !   33.5   0.0     2e-11   3.2e-08       7     112 ..     162     268 ..     156     269 .. 0.74
   3 ?   -1.8   0.0       1.9   3.1e+03      51      87 ..     375     416 ..     370     435 .. 0.63

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.5e-16
                                   HHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEE CS
                           PAS   7 leslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpi 87 
                                   +e+l d if ++e+g+++y+++a+e+++G+++eev+g s++ +ih++d   l + +   le  +++ ++++  k+  g ++
  gi|91773147|ref|YP_565839.1|  38 IENLNDVIFSINEQGNFTYISPAIEDFTGYRAEEVMGTSFMQYIHPDDLPGLLQDIDLTLEGEHKPYMFRVVSKT--GNIT 116
                                   8********************************************998779999999999999999999997777..9999 PP

                                   EEEEEEEEEEETTEEEEEE CS
                           PAS  88 hlevraspvrdaggeilgf 106
                                   ++++  + ++  g+ + g+
  gi|91773147|ref|YP_565839.1| 117 YVHTSSRGILKNGKVV-GI 134
                                   9998888888775533.65 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2e-11
                                   HHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSE CS
                           PAS   7 leslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrp 86 
                                   l+ + ++i+v+D d+ri++vN++a+ llG+++ e+l+++ ++ +++e+ +  +a+ ++  ++++  s+ +e  ++++ +  
  gi|91773147|ref|YP_565839.1| 162 LDVAGVAIIVIDNDHRISLVNKKACGLLGYKEHELLNRNWFEMVVPEEIRdSVAQTFTFSCSENALSTPFECAINTKEKQN 242
                                   666899*********************************999887776554777777766666666666666666666666 PP

                                   EEEEEEEEEEEETTEEEEEEEEEEEE CS
                           PAS  87 ihlevraspvrdaggeilgflgvlrd 112
                                   + +   ++ + d+ g+  g+++ + d
  gi|91773147|ref|YP_565839.1| 243 KLCSWKCTQLKDENGNTNGYILAGED 268
                                   66666666666666666666666666 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.9
                                   STTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.........TTSSEE CS
                           PAS  51 heeddaelaelleqlleqgeesrageisfkl.........rdgrpi 87 
                                   +e+    l+e +++ l ++ e  ++ei  +          + +++ 
  gi|91773147|ref|YP_565839.1| 375 IED----LKEDIKEKLPDQAEMVSFEILTNIeniivdinkVEKSVL 416
                                   445....788888888888888888877666555555555555555 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   7.9e-18   1.3e-14       2      89 .]      55     138 ..      54     138 .. 0.95
   2 !   19.7   0.0   4.6e-07   0.00075       4      82 ..     181     259 ..     178     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 7.9e-18
                         PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengk 81 
                                   +y+s+++e+ +Gy++ee++g+  s+++++hp+D++ + ++++  l++ + py  ++R++ k G +++v+++ r i  +ngk
  gi|91773147|ref|YP_565839.1|  55 TYISPAIEDFTGYRAEEVMGT--SFMQYIHPDDLPGLLQDIDLTLEGEHkPY--MFRVVSKTGNITYVHTSSRGI-LKNGK 130
                                   79*******************..*******************9997777666..9********************.***** PP

                         PAS_3  82 pvrvigva 89 
                                   +v + g++
  gi|91773147|ref|YP_565839.1| 131 VVGINGIM 138
                                   ****9985 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.6e-07
                         PAS_3   4 vserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   v+++ + +lGy ++ell++  +w ++v pe+ r+ v +++  + ++++ +  +e  i +k  +    +++++ ++deng+ 
  gi|91773147|ref|YP_565839.1| 181 VNKKACGLLGYKEHELLNR--NWFEMVVPEEiRDSVAQTFTFSCSENAlSTPFECAINTKEKQNKLCSWKCTQLKDENGNT 259
                                   7888999************..********************8888888788889999999999999999999999999985 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   0.3     5e-24   8.2e-21       5     101 ..     410     507 .]     406     507 .] 0.92

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 5e-24
                                   HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHHHHH CS
                     HATPase_c   5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsivkkl 84 
                                   ++++ + +l++Na+kf+ k++++ev++++ ++ + ++v+D GiGi++ed+k+lf++f q d+s++r +gg G+Gl+i kk+
  gi|91773147|ref|YP_565839.1| 410 KVEKSVLHLIENAIKFSDKTQHVEVSLESVDEMIAFKVTDRGIGITEEDIKRLFKPFNQlDASSTRVYGGLGIGLYIIKKI 490
                                   56677999********88**********8557************************************************* PP

                                   HHHTTTEEEEEEETTTE CS
                     HATPase_c  85 velmgGeiwvesepgrG 101
                                   +el+gG + ++se ++G
  gi|91773147|ref|YP_565839.1| 491 AELHGGGLAIKSELEKG 507
                                   *******9999988776 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.9e-09   3.2e-06       2     108 ..      39     144 ..      38     146 .. 0.91
   2 !   43.1   0.0   2.4e-14     4e-11       1     110 []     162     274 ..     162     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-09
                         PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhye 82 
                                   ++l+d+++ ++++g+++y+++a+++  g+++ee++G ++ ++  ++d ++l ++++  lege+  ++  ++   g   ++ 
  gi|91773147|ref|YP_565839.1|  39 ENLNDVIFSINEQGNFTYISPAIEDFTGYRAEEVMGTSFMQYIHPDDLPGLLQDIDLTLEGEHKPYMFRVVSKTGNITYVH 119
                                   899*************************************98888899999999999999999988888888889999999 PP

                         PAS_4  83 lrllPlrdesGevigvlvisrDiTer 108
                                   ++ + ++  +G+v+g+ +i++ i ++
  gi|91773147|ref|YP_565839.1| 120 TSSRGIL-KNGKVVGINGIMVNIAQL 144
                                   9999997.59*****99999998876 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 2.4e-14
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll..pgee 78 
                                   ld   +a++v+d d r+  +N+ a+ l+g+  +ell++ ++e ++pee ++ +++  +   ++++  +  e+     +++ 
  gi|91773147|ref|YP_565839.1| 162 LDVAGVAIIVIDNDHRISLVNKKACGLLGYKEHELLNRNWFEmVVPEEIRDSVAQTFTFSCSENALSTPFECAINtkEKQN 242
                                   5677899**********************************946666699999999998888888888888777789**** PP

                         PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerrr 110
                                   + +++ ++ l+de+G + g+++ + DiTer++
  gi|91773147|ref|YP_565839.1| 243 KLCSWKCTQLKDENGNTNGYILAGEDITERKQ 274
                                   ******************************85 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   1.5e-10   2.4e-07       2     102 ..      43     141 ..      42     143 .. 0.85
   2 !   38.4   0.1     7e-13   1.1e-09       3     104 .]     168     271 ..     166     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.5e-10
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                   d i+ +n++g+ +y+++a ++++Gy +eev+g+s+ + + ++++    l+++  +++ + + +    + k+g+  +v+ + 
  gi|91773147|ref|YP_565839.1|  43 DVIFSINEQGNFTYISPAIEDFTGYRAEEVMGTSFMQYI-HPDDLPGLLQDIDLTLEGEHKPYMFRVVSKTGNITYVHTSS 122
                                   5566678********************************.6666666666666666657899999**************** PP

                         PAS_9  83 spvkdddgelvgiivilrDi 102
                                   + +   +g++vgi +i+++i
  gi|91773147|ref|YP_565839.1| 123 RGILK-NGKVVGINGIMVNI 141
                                   ***65.68999999999998 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 7e-13
                         PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvll 80 
                                   +i+++++d+ri  +N++a+ llGy++ e+l++++++++  ++e ++ +++ +    +       +e  + +k+ +  ++  
  gi|91773147|ref|YP_565839.1| 168 AIIVIDNDHRISLVNKKACGLLGYKEHELLNRNWFEMV-VPEEIRDSVAQTFTFSCSenaLSTPFECAINTKEKQNKLCSW 247
                                   677778********************************.5666666665555555556887888888888999999999** PP

                         PAS_9  81 taspvkdddgelvgiivilrDite 104
                                   +++ +kd++g+  g+i+  +Dite
  gi|91773147|ref|YP_565839.1| 248 KCTQLKDENGNTNGYILAGEDITE 271
                                   ***********************8 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 !   65.9   0.0   1.5e-21   2.5e-18       2      67 .]     293     360 ..     292     360 .. 0.95
   2 ?   -2.2   0.0       2.6   4.3e+03      45      59 ..     405     423 ..     371     429 .. 0.56

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.5e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   +++f+a+++HELrtPL+ai+g++e+L ++  g+l++++ +yl+ i  +++ l+++++ +L++s+ie+g
  gi|91773147|ref|YP_565839.1| 293 KSEFIANMSHELRTPLNAIIGFSEILIEKkfGDLNDKQDKYLNNIFISGKKLLEIINSILEISKIESG 360
                                   89************************66669***********************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                   HHHHH....HHHHHHHHHH CS
                         HisKA  45 esear....rldhlvedlL 59 
                                   +  ++     ++hl+e+  
  gi|91773147|ref|YP_565839.1| 405 IVDINkvekSVLHLIENAI 423
                                   3333333336667776655 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00041      0.68       7      56 ..      38      90 ..      31     101 .. 0.74
   2 !   19.7   0.0   3.9e-07   0.00064       4      55 ..     159     208 ..     156     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                         PAS_8  7 fesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg..qllpvlrpll 56
                                  +e+++d i+ ++  g +++++ +a ++++Gy+ +++ g  +   + +++l++ll
  gi|91773147|ref|YP_565839.1| 38 IENLNDVIFSINeQG-NFTYISPAIEDFTGYRaEEVMGTSFMqyIHPDDLPGLL 90
                                  689999999999455.5***************8888877774344444444444 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 3.9e-07
                         PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrpl 55 
                                   +  ++ + ++i+v+d++ ri  vN++a+ llGy+    + l +++++ + p+
  gi|91773147|ref|YP_565839.1| 159 QHYLDVAGVAIIVIDNDHRISLVNKKACGLLGYK--EHELLNRNWFEMVVPE 208
                                   555777889******999**************88..4444444666665555 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 !   24.7   0.0   9.8e-09   1.6e-05       3      77 ..     411     484 ..     408     494 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 9.8e-09
                   HATPase_c_3   3 lekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGl 77 
                                   +ek+++ l++N++    + ++v+++++  + +   ++++D G G++ee++k+ +++ ++     ++ +++G  GiGl
  gi|91773147|ref|YP_565839.1| 411 VEKSVLHLIENAIKfsDKTQHVEVSLESVD-EMIAFKVTDRGIGITEEDIKRLFKPFNQLDA--SSTRVYGGLGIGL 484
                                   4899*********96334445888887765.6899********************9888888..48999******96 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.5e-06    0.0089       9      88 ..      49     123 ..      42     137 .. 0.87
   2 ?    4.6   0.0     0.021        34       8      51 ..     172     212 ..     167     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.5e-06
                        PAS_11   9 didgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksk 88 
                                     +g+++ + +    ++  +g+  ee++g+s+ + +hp+dl  l +    ++  +ge++  ++R  ++++++ +v+t s+
  gi|91773147|ref|YP_565839.1|  49 NEQGNFTYISP---AIEDFTGYRAEEVMGTSFMQYIHPDDLPGLLQDIDLTL--EGEHKPYMFRVVSKTGNITYVHTSSR 123
                                   55677777777...66777899****************************99..99999******************997 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                        PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlst 51 
                                   +d d +I  v++   +a   lg++++el++r +++++ p++ ++
  gi|91773147|ref|YP_565839.1| 172 IDNDHRISLVNK---KACGLLGYKEHELLNRNWFEMVVPEEIRD 212
                                   566667777777...778889******************99554 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0    0.0001      0.17       7     114 ..     168     276 ..     162     277 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                         PAS_7   7 GisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg...agdveaeverrlaaaragkphsfererpd 84 
                                   +i+v+D+d+r+ ++N++ + ll++ e+ +     +e ++    +    +    + +e+++ + ++ a + k    + +  +
  gi|91773147|ref|YP_565839.1| 168 AIIVIDNDHRISLVNKKACGLLGYKEHELLNRNWFEMVVPEEIRDSVAQtftFSCSENALSTPFECAINTK--EKQNKLCS 246
                                   799*********************99988655556655544433322221111223333333333222222..22333344 PP

                         PAS_7  85 grvievrgnplpdgGfVttytDiTerrrae 114
                                    +  +++ +     G++   +DiTer++ e
  gi|91773147|ref|YP_565839.1| 247 WKCTQLKDENGNTNGYILAGEDITERKQVE 276
                                   455555555557778888888888888776 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       0.9   1.5e+03      36      52 ..     275     291 ..     272     305 .. 0.80
   2 ?   12.3   0.0   7.7e-05      0.13      42     109 ..     421     491 ..     407     494 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.9
                   HATPase_c_2  36 veEactNavehayleap 52 
                                   veEa+ Na + a + ++
  gi|91773147|ref|YP_565839.1| 275 VEEALLNAKHMAEDANR 291
                                   89******999988776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.7e-05
                   HATPase_c_2  42 NavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikglv 109
                                   Na++   +   +++vev+les +e + ++v+D+G g + e++++  ++ +      +      G+Gl++ik+++
  gi|91773147|ref|YP_565839.1| 421 NAIKFSDK---TQHVEVSLESVDEMIAFKVTDRGIGITEEDIKRLFKPFNqldassTRVYGGLGIGLYIIKKIA 491
                                   55555554...699*********************977766655444333456644444445567778888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.23s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3643.34
//
Query:       gi|91773148|ref|YP_565840.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.7   0.4    6.3e-67  226.0   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
      9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.2e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00011   22.5   0.3       0.17   12.1   0.2    2.8  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.067   13.8   1.4        0.3   11.7   1.4    2.2  1  BST2             Bone marrow stromal antigen 2
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.7   2.6       0.55   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.36   11.2   6.9       0.52   10.7   4.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
          1   10.1   8.9        7.1    7.4   1.5    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.1    9.0   6.0       0.65   10.7   1.1    2.7  2  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.44   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  226.0   0.0   3.5e-70   6.3e-67       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91773148|ref|YP_565840.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 226.0 bits;  conditional E-value: 3.5e-70
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91773148|ref|YP_565840.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91773148|ref|YP_565840.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierear..ea..eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++r  +   ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91773148|ref|YP_565840.1| 329 SENDN--QLWSKAMNIlLIDVKKSVDQIRgmSGcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **976..*********************964338888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91773148|ref|YP_565840.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.5e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91773148|ref|YP_565840.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7     8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91773148|ref|YP_565840.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.6     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.5   0.0    0.0025       4.5       5      45 ..     249     287 ..     245     290 .. 0.84
   3 !   12.1   0.2   9.3e-05      0.17      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91773148|ref|YP_565840.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91773148|ref|YP_565840.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91773148|ref|YP_565840.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91773148|ref|YP_565840.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00046      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91773148|ref|YP_565840.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91773148|ref|YP_565840.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00031      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    0.9   0.1      0.34   6.2e+02      11      58 ..     392     446 ..     383     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91773148|ref|YP_565840.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91773148|ref|YP_565840.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999888854444440......55555555555555555553 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?   10.7   4.5   0.00029      0.52       2      36 ..     156     213 ..     155     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91773148|ref|YP_565840.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91773148|ref|YP_565840.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCellADvCGC 213
                                   79***************99987555588888888888888887775555444446666 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 ?    3.3   0.1     0.074   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.4   1.5     0.004       7.1       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.0   0.1      0.19   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91773148|ref|YP_565840.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91773148|ref|YP_565840.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91773148|ref|YP_565840.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00036      0.65      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.6   0.3        10   1.8e+04      55      66 ..     154     165 ..     144     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91773148|ref|YP_565840.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                         PLATZ  55 kssseaCetCar 66 
                                   +++ ++C +C++
  gi|91773148|ref|YP_565840.1| 154 RAEIKSCPHCGC 165
                                   334478999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 3201.84
//
Query:       gi|91773149|ref|YP_565841.1|  [L=64]
Description: hypothetical protein Mbur_1168 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-06   25.8   0.0    7.7e-06   25.7   0.0    1.1  1  MarR_2          MarR family
    7.3e-06   25.8   0.1    1.1e-05   25.2   0.1    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
    2.8e-05   23.9   0.0    3.2e-05   23.7   0.0    1.1  1  TrmB            Sugar-specific transcriptional regulator TrmB
    4.2e-05   23.0   0.0    5.2e-05   22.7   0.0    1.1  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00065   20.0   0.0    0.00079   19.7   0.0    1.2  1  Rrf2            Transcriptional regulator
     0.0022   18.2   0.0     0.0027   17.9   0.0    1.1  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0032   17.9   0.0     0.0034   17.8   0.0    1.1  1  HTH_27          Winged helix DNA-binding domain
      0.008   16.0   0.0      0.012   15.5   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.033   14.2   0.0      0.041   13.9   0.0    1.1  1  z-alpha         Adenosine deaminase z-alpha domain
      0.061   13.3   0.0      0.062   13.3   0.0    1.1  1  HTH_11          HTH domain
      0.069   13.1   0.0      0.078   12.9   0.0    1.2  1  MarR            MarR family
       0.12   12.4   0.0       0.12   12.4   0.0    1.1  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.18   12.0   0.0       0.37   11.0   0.0    1.7  1  Mrr_N           Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   5.6e-09   7.7e-06       5      51 ..       7      52 ..       3      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.6e-09
                                  HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                        MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                    + ++L +L +++++ l++g++a+++g++   vs+ l+ L ++GLv
  gi|91773149|ref|YP_565841.1|  7 TNEEMILKVLEDSEEP-LRPGDVAEATGIDNKLVSKSLASLKKKGLV 52
                                  56778999******98.*****************************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 !   25.2   0.1   7.9e-09   1.1e-05       7      45 ..      12      52 ..      11      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 7.9e-09
                                  HHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  7 ILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  ILk L++  ++l  ++ ae++g+    vS  L+ L++ GLV
  gi|91773149|ref|YP_565841.1| 12 ILKVLEDseEPLRPGDVAEATGIDNKLVSKSLASLKKKGLV 52
                                  99999998788*****************************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 !   23.7   0.0   2.3e-08   3.2e-05      14      53 ..      13      53 ..       5      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.3e-08
                                  CHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB 14 YlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                   ++L  +++p++  ++ae++g++   v ++L sL++kGlV 
  gi|91773149|ref|YP_565841.1| 13 LKVLEdSEEPLRPGDVAEATGIDNKLVSKSLASLKKKGLVC 53
                                  444447899******************************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 !   22.7   0.0   3.8e-08   5.2e-05       1      47 [.       5      52 ..       5      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
                        HTH_24  1 ldetdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  ld ++  IL++L++ +  +   ++Ae++g+    v++ l  L+++Gl+
  gi|91773149|ref|YP_565841.1|  5 LDTNEEMILKVLEDsEEPLRPGDVAEATGIDNKLVSKSLASLKKKGLV 52
                                  79999*********7777****************************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.7e-07   0.00079      19      57 ..      16      54 ..       3      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.7e-07
                                  HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  +e++eep++  ++ae ++i  + ++k la L+k+glv s
  gi|91773149|ref|YP_565841.1| 16 LEDSEEPLRPGDVAEATGIDNKLVSKSLASLKKKGLVCS 54
                                  4566678999***************************77 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.9e-06    0.0027      11      53 ..      10      53 ..       5      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                                  HHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 11 etIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                  e I+++ e ++++ ++ d+ae+ ++    Vs++l  L+k+G+v 
  gi|91773149|ref|YP_565841.1| 10 EMILKVLEdSEEPLRPGDVAEATGIDNKLVSKSLASLKKKGLVC 53
                                  5677777779********************************95 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0034       3      48 ..       7      52 ..       5      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                        HTH_27  3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                  +++ ++L +++  +++ +  d+++++ ++   +s+sl  L +kGLv
  gi|91773149|ref|YP_565841.1|  7 TNEEMILKVLEDSEEPLRPGDVAEATGIDNKLVSKSLASLKKKGLV 52
                                  677899999*999999999*************************** PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.4e-06     0.012       7      48 ..      11      52 ..      11      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.4e-06
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                  +iL+ l+   ++l+  ++A++tg+    v+  L++L + G+v
  gi|91773149|ref|YP_565841.1| 11 MILKVLEDSEEPLRPGDVAEATGIDNKLVSKSLASLKKKGLV 52
                                  69**********************998888888888888887 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 ?   13.9   0.0     3e-05     0.041       5      53 ..       8      54 ..       5      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                                  HHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEE CS
                       z-alpha  5 qaekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyr 53
                                   +e il++Le+++e      +a + g+    + + + L +l++kg v++
  gi|91773149|ref|YP_565841.1|  8 NEEMILKVLEDSEEPLRPGDVAEATGID--NKLVSKSLASLKKKGLVCS 54
                                  689*************************..79***************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.062       4      43 ..      11      50 ..       8      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   il+ L ++++p+   + Ae +++  + v + +++L+++g
  gi|91773149|ref|YP_565841.1| 11 MILKVLEDSEEPLRPGDVAEATGIDNKLVSKSLASLKKKG 50
                                  59*************************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.6e-05     0.078       8      47 ..      12      52 ..       5      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                                  HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGli 47
                                  iL  l+++++ l+  + a++ g+++  v++ l  L kkGl+
  gi|91773149|ref|YP_565841.1| 12 ILKVLEDSEEpLRPGDVAEATGIDNKLVSKSLASLKKKGLV 52
                                  66677666555*****************************9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.5e-05      0.12      21      53 ..      22      55 ..       5      64 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.5e-05
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.r 53
                                  pl   + A+  G+    vs+ l+ Lk++gl+   
  gi|91773149|ref|YP_565841.1| 22 PLRPGDVAEATGIDNKLVSKSLASLKKKGLVCsP 55
                                  7777899***********************9752 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.37      58      79 ..      43      64 .]       9      64 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                         Mrr_N 58 rtyLkkagllespkrgvwkiTe 79
                                  +  Lkk gl+ spkr ++ iT+
  gi|91773149|ref|YP_565841.1| 43 LASLKKKGLVCSPKRCYYDITN 64
                                  568*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.29s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 452.43
//
Query:       gi|91773150|ref|YP_565842.1|  [L=103]
Description: 30S ribosomal protein S10P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   93.6   0.0    7.6e-27   93.4   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e


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 !   93.4   0.0   4.2e-31   7.6e-27       1      97 [.       6      99 ..       6     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 4.2e-31
                                  EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHHHS CS
                 Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidtll 82
                                  rirl+++++ +L+ ++++++ +a+++g+ ++gpvplPtk++ v+v+ksp++d + +++++e+r+hkRlidi  a+++ +++l+
  gi|91773150|ref|YP_565842.1|  6 RIRLSGTSPVNLDGVCDQVKAIANRTGVSISGPVPLPTKKLVVPVRKSPSGDgTATWDHWEMRVHKRLIDI-AADERALRQLM 87
                                  8**********************************************************************.5********** PP

                                  -...S---SS-EEEE CS
                 Ribosomal_S10 83 kllqlnlpegVsvev 97
                                  +   +++p+ +s+e+
  gi|91773150|ref|YP_565842.1| 88 R---IQVPKDISIEI 99
                                  *...*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 811.93
//
Query:       gi|91773151|ref|YP_565843.1|  [L=422]
Description: elongation factor 1-alpha [Methanococcoides burtonii DSM 6242]
Scores for 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  191.6   0.0    1.3e-56  191.2   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.9e-36  123.8   0.1    1.3e-35  122.0   0.0    2.0  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    4.6e-17   62.2   0.9    1.7e-16   60.4   0.6    2.2  2  GTP_EFTU_D2  Elongation factor Tu domain 2
      1e-06   28.8   0.0    1.2e-05   25.4   0.0    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0017   17.9   0.2      0.026   14.0   0.1    2.5  2  FeoB_N       Ferrous iron transport protein B
     0.0034   16.8   0.0       0.07   12.5   0.0    2.1  2  Gtr1_RagA    Gtr1/RagA G protein conserved region
     0.0042   17.2   0.0        2.6    8.1   0.0    2.3  2  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.026   14.4   0.3    1.6  1  GTP_EFTU_D4  Elongation factor Tu domain 4
      0.013   14.8   0.0      0.028   13.7   0.0    1.5  1  Septin       Septin
      0.022   14.3   0.7      0.068   12.8   0.1    2.0  2  Ras          Ras family
      0.045   14.0   0.1        2.7    8.2   0.1    2.5  2  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.11   12.7   0.1       0.48   10.6   0.1    2.0  1  DUF5511      Family of unknown function (DUF5511)
       0.17   11.6   0.3        1.1    9.0   0.3    2.0  1  ATP_bind_1   Conserved hypothetical ATP binding protein


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 !  191.2   0.0   9.7e-60   1.3e-56       1     186 [.       4     208 ..       4     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 9.7e-60
                                   TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST.............HCHSHHHHHHTSCSSCEEEEEETTCS CS
                      GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv.............lDtlkeErergiTiksaaisleketk 68 
                                   k+++n+++ighvDhGK+T+++rL+++tga+  +  ++ ++++             +DtlkeErerg+Ti++++  ++  t+
  gi|91773151|ref|YP_565843.1|   4 KPHMNLAVIGHVDHGKSTFVGRLMFETGAVPAHLIEKYKAEAkekgkesfafawvMDTLKEERERGVTIDISHKRFD--TD 82 
                                   579**************************999888884332336788999***************************..** PP

                                   SEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...HHHHHHHHHH CS
                      GTP_EFTU  69 kylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...kaelkeivee 145
                                   ky ++++D+PGH+dF+k++i+g++++D avlvv+a +Gv++qt+e++ l +++g++ +iv+iNKmD +   +++++e+++e
  gi|91773151|ref|YP_565843.1|  83 KYYFTVVDCPGHRDFVKNMITGASQADAAVLVVAAPDGVMAQTKEHVFLSRTLGINqLIVAINKMDAAkysEDRYNEVKKE 163
                                   *********************************************************************9999******** PP

                                   HHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHH CS
                      GTP_EFTU 146 vkqklsrkeeklekygekgekevpvvfgSalkgegvk............tlle 186
                                   v+q l         +g+k++ +vp++++Sa++g++++            +lle
  gi|91773151|ref|YP_565843.1| 164 VSQLL-------GMVGFKAD-DVPFIPTSAFEGDNITkssantpwytgpALLE 208
                                   **777.......67899985.9*************996666666666664444 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 ?   -2.3   0.0       3.9   5.3e+03       8      51 ..     108     149 ..     102     164 .. 0.61
   2 !  122.0   0.0   9.7e-39   1.3e-35       4     111 ..     313     418 ..     310     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.9
                                   EEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSS CS
                   GTP_EFTU_D3   8 feAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldk 51 
                                    +A v+++     + + +  + v+  rt  ++  +v++ +k+d 
  gi|91773151|ref|YP_565843.1| 108 ADAAVLVVAA-PDGVMAQTKEHVFLSRTLGINQLIVAI-NKMDA 149
                                   5566666666.445555556678888888888877777.55553 PP

  == domain 2  score: 122.0 bits;  conditional E-value: 9.7e-39
                                   EECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE-- CS
                   GTP_EFTU_D3   4 phtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpialek 84 
                                    +++f+ q+++l++  +++it gY+pv++++ta+ +++ +++++kld+k+++v+e++p ++k Gd++iv++++++p+++e 
  gi|91773151|ref|YP_565843.1| 313 VADEFTGQIVVLQH--PSAITVGYTPVFHCHTAQTACTLMAINKKLDPKSGQVKEENPTYIKAGDAAIVTIKPTRPMCIEP 391
                                   6789**********..***************************************************************** PP

                                   TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                   GTP_EFTU_D3  85 gseypqlGrFaiReggrTvaaGvvtei 111
                                   +se+pqlGrFaiR++g T+aaG+ +++
  gi|91773151|ref|YP_565843.1| 392 VSEIPQLGRFAIRDMGMTIAAGMCMSV 418
                                   **********************98877 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 ?   -2.4   0.0       4.8   6.7e+03      14      41 ..       4      29 ..       4      33 .. 0.78
   2 !   60.4   0.6   1.2e-19   1.7e-16       1      73 [.     238     304 ..     238     305 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.8
                                  ETTEEEEEEC.TCTTSEEEEEEEEEEEEE CS
                   GTP_EFTU_D2 14 kkGdevrilg.ndtskkeivtrissletf 41
                                  k+ +++ ++g +d +k+   t +++l  +
  gi|91773151|ref|YP_565843.1|  4 KPHMNLAVIGhVDHGKS---TFVGRLMFE 29
                                  56788889999999999...888888765 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 1.2e-19
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   Gtv  grv++G++kkG++v +++  ++ +   ++++s+e++he+ d+av+g+n+G +v+++g +d +++Gd+ 
  gi|91773151|ref|YP_565843.1| 238 GTVPVGRVETGIMKKGQKVTFMP--SGAT---GEVKSIEMHHEEWDQAVPGDNIGWNVRGIGKND-VRRGDVC 304
                                   99*******************55..5556...*********************************.*****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 !   25.4   0.0   8.5e-09   1.2e-05       2      97 ..       9     128 ..       8     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.5e-09
                                   EEEEESTTSSHHHHHHHHH....................T...........STEEESSSTTSSSSEEEEEEEETTEEEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinalt....................g...........ekaivsdkpgtTrdinegrvklkgkeielv 51 
                                    a++G+   GKSt++ +l+                    +           ++ + +++ g+T+di ++r+++++  +++v
  gi|91773151|ref|YP_565843.1|   9 LAVIGHVDHGKSTFVGRLMfetgavpahliekykaeakeKgkesfafawvmDTLKEERERGVTIDISHKRFDTDKYYFTVV 89 
                                   699***************977777777777766666555056666665554578999999************999****** PP

                                   ECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH CS
                      MMR_HSR1  52 DtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeel 97 
                                   D+pG  +    +  +++ +    +ad+++lvv a  +++ ++ +e 
  gi|91773151|ref|YP_565843.1|  90 DCPG--H----RDFVKNMITGASQADAAVLVVAAP-DGVMAQTKEH 128
                                   ****..3....224556666667789999999766.3343333332 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.3   4.2e+02       2      22 ..       8      28 ..       7      54 .. 0.74
   2 !   14.0   0.1   1.9e-05     0.026      32     136 ..      69     170 ..      67     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.3
                                  EEEEEESTTSSHHHHHHHHHT CS
                        FeoB_N  2 tvalvGnpnvGkttlfnaltg 22
                                  ++a++G  + Gk+t++ +l  
  gi|91773151|ref|YP_565843.1|  8 NLAVIGHVDHGKSTFVGRLMF 28
                                  6799**********9988864 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.9e-05
                                   TSSSEEEEEEEEETTEEEEEEE----SSS..SSSSHHHHHHHHHHHCTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEE CS
                        FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYsl..sayseeekvardflleeepdvvvnvvdatnlernLyLtlqllelgvpvvl 110
                                   Gvt++ ++ +++++++ +++vD PG  ++  + ++   +    +l+   pd v+      + + +++L  + l +  ++++
  gi|91773151|ref|YP_565843.1|  69 GVTIDISHKRFDTDKYYFTVVDCPGHRDFvkNMITGASQADAAVLVVAAPDGVMA-----QTKEHVFLS-RTLGI-NQLIV 142
                                   9************************987744556777777777777788887653.....333344443.33333.46899 PP

                                   EEETHHHHHHTTEEE-H..HHHHHHHTS CS
                        FeoB_N 111 alnmideaekkgieidl..kkLsekLgv 136
                                   a+n++d+a+ ++ + ++  k++s+ Lg+
  gi|91773151|ref|YP_565843.1| 143 AINKMDAAKYSEDRYNEvkKEVSQLLGM 170
                                   *******998887776422567777763 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   5.1e-05      0.07      29      67 ..      66     103 ..      50     117 .. 0.84
   2 ?    2.1   0.0     0.077   1.1e+02     114     161 ..     140     187 ..     122     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                     Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeyls 67 
                                   ++ g+tid++++++  +++ ++ ++Dc+G ++fv+++++
  gi|91773151|ref|YP_565843.1|  66 RERGVTIDISHKRF-DTDKYYFTVVDCPGHRDFVKNMIT 103
                                   56689********9.58999***************9765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.077
                     Gtr1_RagA 114 vfvlihKmDliqedereeifeerkeeireeiekleke..eiqffaTSiwd 161
                                   + v i+KmD    +  e+ ++e k+e+++ +  ++++  ++ f  TS ++
  gi|91773151|ref|YP_565843.1| 140 LIVAINKMDAA--KYSEDRYNEVKKEVSQLLGMVGFKadDVPFIPTSAFE 187
                                   568899***98..6777888888888888887665555589999999875 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0019       2.6       1      19 [.       9      27 ..       9      34 .. 0.89
   2 !    6.8   0.0    0.0046       6.3      52     151 ..      42     132 ..      34     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                                  EEEEEBTTTTHHHHHHHHH CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                  +av+G++ +GKS+++  L+
  gi|91773151|ref|YP_565843.1|  9 LAVIGHVDHGKSTFVGRLM 27
                                  69************98876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0046
                                   .SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEE CS
                     Dynamin_N  52 keelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadii 132
                                   k+e kek k+   f  v +++++e+e+         ++ i++k ++ ++   t+vD PG  +  k   ++++ + +  +++
  gi|91773151|ref|YP_565843.1|  42 KAEAKEKGKESFAFAWVMDTLKEERERGV-------TIDISHKRFDTDKYYFTVVDCPGHRDFVK---NMITGASQADAAV 112
                                   56667777777777888888877777776.......458999*****************988433...4677776666666 PP

                                   EEEEETTS-CCC-.CHHHHH CS
                     Dynamin_N 133 lavtsanhdlsns.ealfla 151
                                   l+v + +  ++++ e  fl+
  gi|91773151|ref|YP_565843.1| 113 LVVAAPDGVMAQTkEHVFLS 132
                                   66665555665553555555 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 ?   14.4   0.3   1.9e-05     0.026      20      76 ..     241     294 ..     223     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                   EEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TT CS
                   GTP_EFTU_D4  20 ivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivG 76 
                                    vG +v +G++k g k+        Ge+++i+ ++++ ++a  G++++  ++g  +G
  gi|91773151|ref|YP_565843.1| 241 PVG-RVETGIMKKGQKVTFMPSGATGEVKSIEMHHEEWDQAVPGDNIGWNVRG--IG 294
                                   588.9***********986655599**********************999988..34 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.1e-05     0.028       5      78 ..       7     100 ..       4     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                   EEEEEEEBTTSSCCCCCCTT.SSSS----.....................--------------S-EEEEEEEEETTCEEE CS
                        Septin   5 ftlmvvGesglGkttlintl.fetdliee.....................ekleeasekkkktveikkkkvvieedgvkln 63 
                                   ++l v+G+   Gk+t++  l fet  +++                       +++ +e+ ++ v+i+ +++  + d  k  
  gi|91773151|ref|YP_565843.1|   7 MNLAVIGHVDHGKSTFVGRLmFETGAVPAhliekykaeakekgkesfafaWVMDTLKEERERGVTIDISHKRFDTD--KYY 85 
                                   899**************87537888888889999*******99999999856677788899999999999999988..889 PP

                                   EEEEE---BSSSSSH CS
                        Septin  64 ltviDtpgfGdavdn 78 
                                   +tv+D pg+ d+v n
  gi|91773151|ref|YP_565843.1|  86 FTVVDCPGHRDFVKN 100
                                   9***********998 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.1   1.5e+03       2      19 ..       9      26 ..       8      32 .. 0.85
   2 ?   12.8   0.1   4.9e-05     0.068      11     151 ..      49     193 ..      45     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                                  EEEEESTTSSHHHHHHHH CS
                           Ras  2 lvlvGdsavGKtslllrf 19
                                  l ++G    GK++++ r 
  gi|91773151|ref|YP_565843.1|  9 LAVIGHVDHGKSTFVGRL 26
                                  679**********99876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.9e-05
                                   SHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHH CS
                           Ras  11 GKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvk 91 
                                   GK s+ + +v d+ kee e  + +d   k++  d  ++ +++ D  G  +f +   +  ++a++++lv +    +     +
  gi|91773151|ref|YP_565843.1|  49 GKESFAFAWVMDTLKEERERGVTIDISHKRF--DTDKYYFTVVDCPGHRDFVKNMITGASQADAAVLVVA--APDGVMAQT 125
                                   9*******************99888877766..5667899***********9999999999999999955..555554444 PP

                                   HHHHHHHHHSTTTSEEEEEEETTTGGG.........G-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHH CS
                           Ras  92 kwveeikrvaeenvpivLvGnKvDlee.........kravsteegeelakelglkfletSAktnenvee 151
                                   k +  ++r+     ++++  nK+D ++         k++vs+  g    k  +++f+ tSA +  n+++
  gi|91773151|ref|YP_565843.1| 126 KEHVFLSRTLGI-NQLIVAINKMDAAKysedrynevKKEVSQLLGMVGFKADDVPFIPTSAFEGDNITK 193
                                   444556666662.3566667******999999888888888888887779999**********999976 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 ?    3.2   0.0     0.073     1e+02       2      22 ..       9      29 ..       8      37 .. 0.88
   2 ?    8.2   0.1    0.0019       2.7       9     119 ..      47     148 ..      45     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.073
                                  EEEESSTTSSHHHHHHCHCT- CS
                           Roc  2 vvlvGdsgvGKtsllkrfved 22
                                  + ++G    GK++++ r++ +
  gi|91773151|ref|YP_565843.1|  9 LAVIGHVDHGKSTFVGRLMFE 29
                                  5789*************9965 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                                   TSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEEG CS
                           Roc   9 gvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalailvyds 89 
                                   + GK s++  +v d+ +e+++  + +d+++k++           ++k+ + + D  G+ +f + +    ++a++a+lv+ +
  gi|91773151|ref|YP_565843.1|  47 EKGKESFAFAWVMDTLKEERERGVTIDISHKRFD----------TDKYYFTVVDCPGHRDFVKNMITGASQADAAVLVVAA 117
                                   67**************************999872..........23578************99888888888888888774 PP

                                   HH.HHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                           Roc  90 rs.senlkeWlkelkkvagkspvilvgnkiD 119
                                    +      +    l++  g +++i+ +nk+D
  gi|91773151|ref|YP_565843.1| 118 PDgVMAQTKEHVFLSRTLGINQLIVAINKMD 148
                                   4313333344445666777778888888888 PP

>> DUF5511  Family of unknown function (DUF5511)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00035      0.48      13      44 ..     123     154 ..     120     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                       DUF5511  13 dqvknevhlskylfnkqvivkvsekeaaayae 44 
                                    q k+ v ls+ l   q+iv + + +aa y+e
  gi|91773151|ref|YP_565843.1| 123 AQTKEHVFLSRTLGINQLIVAINKMDAAKYSE 154
                                   699***************************98 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3   0.00078       1.1       1     181 [.      11     158 ..      11     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00078
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaav..direlitledvmedlglgpngalvvaleflresl 79 
                                   v+G++  GK+tfvg+l+  + +           PA  + +Y+a+     +e +  + vm+ l+ +  ++++  +++  +++
  gi|91773151|ref|YP_565843.1|  11 VIGHVDHGKSTFVGRLMFETGAV----------PAHLIEKYKAEAkeKGKESFAFAWVMDTLKEERERGVT--IDISHKRF 79 
                                   78888888888888888888877..........88777777766511457888888888886666666655..56667776 PP

                    ATP_bind_1  80 dwldeelekeeddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqrltd.ptkfisgllsalsamlrlelP 158
                                   d   ++       + ++D+PG   +++ +  +a      ++ + a+ vv   D  ++++    f+s+         +l++ 
  gi|91773151|ref|YP_565843.1|  80 D--TDKY-----YFTVVDCPGHRDFVKNMITGA------SQaDAAVLVVAAPDGVMAQTkEHVFLSR---------TLGIN 138
                                   3..2333.....6899*****999999888888......6668899999999988888756678888.........55554 PP

                    ATP_bind_1 159 .hvvvlnkfDllkeklekeleffe 181
                                     +v++nk+D +k ++    ++++
  gi|91773151|ref|YP_565843.1| 139 qLIVAINKMDAAKYSE----DRYN 158
                                   1588999999977333....3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.26s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2789.97
//
Query:       gi|91773152|ref|YP_565844.1|  [L=730]
Description: elongation factor EF-2 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  217.0   0.1    2.8e-64  216.2   0.1    1.4  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    8.8e-31  106.2   0.2    3.3e-30  104.3   0.1    2.1  2  EFG_IV       Elongation factor G, domain IV
    7.1e-26   90.1   1.3    5.6e-24   84.0   0.9    2.8  3  EFG_II       Elongation Factor G, domain II
    1.2e-23   82.9   0.1    3.1e-23   81.6   0.1    1.8  1  EFG_C        Elongation factor G C-terminus
    9.4e-15   54.8   0.2      3e-14   53.1   0.2    2.0  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    5.8e-05   23.1   0.1    0.00018   21.6   0.1    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0032   17.3   0.1      0.014   15.2   0.0    2.0  2  RF3_C        Class II release factor RF3, C-terminal domain
  ------ inclusion threshold ------
      0.053   13.1   0.0       0.11   12.1   0.0    1.4  1  Ras          Ras family
       0.17   11.8   0.5       0.63    9.9   0.3    2.0  2  RsgA_GTPase  RsgA GTPase


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 !  216.2   0.1   1.4e-67   2.8e-64       3     193 ..      21     257 ..      19     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 216.2 bits;  conditional E-value: 1.4e-67
                                   EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEEEESSSG CS
                      GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinliDtPGHv 81 
                                   irnigi++h+DhGKtTL+d+Ll+ +g+isk  e a+ + ++D+ +eE+ergiTi+s+++s+  + e+k+ylinliDtPGHv
  gi|91773152|ref|YP_565844.1|  21 IRNIGIVAHIDHGKTTLSDNLLAGAGMISK--ELAGRQLFMDSDAEEQERGITIDSSNVSMVhEyEGKEYLINLIDTPGHV 99 
                                   8*****************************..889999************************626**************** PP

                                   GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekyge 162
                                   dF  +v+r++r++Dgav+v+daveG +pqte+vlr+alke+v++++fiNK+Drl++el+   +e++ +l +  ++++k   
  gi|91773152|ref|YP_565844.1| 100 DFGGDVTRAMRAVDGAVVVIDAVEGTMPQTETVLRQALKEHVKPVLFINKVDRLINELQVDDQEMQIRLGKLIDHVNKLIK 180
                                   *********************************************************************888555554433 PP

                                   TTT............TTEEEEEEBTTTTBTHH..................................HHHHHHHHHSH CS
                      GTP_EFTU 163 kge............kevpvvfgSalkgegvk..................................tllealvellp 193
                                     +             e +v+fgSal +++++                                  ++ ++++++lp
  gi|91773152|ref|YP_565844.1| 181 GMNeerynagwrvdaAEGTVAFGSALYNWAISvpmmkktgvsfsevfnycreedmkslaekcplheAVNDMVIRFLP 257
                                   3334456666777778999**********998777777777777777777777777777777666666666666665 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 ?   -3.3   0.0       3.6   7.2e+03       2      13 ..     463     474 ..     462     480 .. 0.77
   2 !  104.3   0.1   1.7e-33   3.3e-30       3     120 ..     508     617 ..     506     618 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.6
                                   CCESCEE.SS-C CS
                        EFG_IV   2 qVayrEtirkpv 13 
                                    V yrEti+  +
  gi|91773152|ref|YP_565844.1| 463 LVVYRETITGTA 474
                                   589****99765 PP

  == domain 2  score: 104.3 bits;  conditional E-value: 1.7e-33
                                   CESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--E CS
                        EFG_IV   3 VayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepv 83 
                                   +++r    +p+ er+ekl+  +g ++++ak+i++i +     +n + d+tkg+q+++e++e++ +Gf+e++k Gpl +ep+
  gi|91773152|ref|YP_565844.1| 508 ISMR----MPEVERREKLMA-AGLNKDEAKKIVNIFE-----SNAYFDMTKGIQYLNETMELIIEGFTEVMKAGPLSKEPC 578
                                   5566....888889999999.9***************.....89************************************* PP

                                   ESEEEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                        EFG_IV  84 tdvkvtLldgslhe..vdsseaafkpaarralkeallkA 120
                                   ++vkv+L+d++lhe  v++++a+++pa+r+a+++a+l+A
  gi|91773152|ref|YP_565844.1| 579 MGVKVKLMDAKLHEdaVHRGPAQVIPASRQAIQAAMLMA 617
                                   ************************************998 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 ?   -3.9   0.0       7.6   1.5e+04      13      32 ..     215     234 ..     207     235 .. 0.77
   2 !   84.0   0.9   2.8e-27   5.6e-24       2      74 ..     388     460 ..     387     461 .. 0.97
   3 ?    3.2   0.0     0.046        92      14      53 ..     527     566 ..     521     568 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.6
                        EFG_II  13 kskadedklskaLarlleED 32 
                                     k++   +s++++ + eED
  gi|91773152|ref|YP_565844.1| 215 MMKKTGVSFSEVFNYCREED 234
                                   55677778999999999999 PP

  == domain 2  score: 84.0 bits;  conditional E-value: 2.8e-27
                        EFG_II   2 PePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                   +ePv+++a+e+k  +d  kl ++L+++++EDptl+++ deeT+e +++GmGelHle+++ r++r+ +ve++++
  gi|91773152|ref|YP_565844.1| 388 SEPVVTVAVEAKHMKDLPKLVEVLRQVAKEDPTLKITLDEETGEHLMAGMGELHLEVIAHRIERDKGVEITTT 460
                                   69*******************************************************************9986 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.046
                        EFG_II  14 skadedklskaLarlleEDptlrverdeeTketilsGmGe 53 
                                   +k++++k+ + ++  +  D t  +++ +eT e+i++G  e
  gi|91773152|ref|YP_565844.1| 527 NKDEAKKIVNIFESNAYFDMTKGIQYLNETMELIIEGFTE 566
                                   688999999999999999*******************887 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 !   81.6   0.1   1.6e-26   3.1e-23       2      87 ..     621     705 ..     620     707 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.6e-26
                                   EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE-- CS
                         EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeevp 82 
                                   l EP++kv i+vp+e +g ++++++ rrG i+dm+++ +++++ie ++P++el+gfa ++rs+T+G++++s+ef+g+e++p
  gi|91773152|ref|YP_565844.1| 621 LFEPYQKVFIQVPQEQMGGATKEIQGRRGVIIDMTSE-GDTTVIESKAPVSELFGFAGDIRSATEGRAMWSTEFAGFEPLP 700
                                   78***********************************.******************************************9 PP

                                   HHHHH CS
                         EFG_C  83 gdkld 87 
                                    ++++
  gi|91773152|ref|YP_565844.1| 701 MSLMT 705
                                   87765 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 !   53.1   0.2   1.5e-17     3e-14       1      74 []     306     373 ..     306     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.5e-17
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                   G+v++gr++sG l +G+ev++  ++ sk+    ri+++ +f+++e+ +v+  +aG+i+a+ gl da  vG+t+t
  gi|91773152|ref|YP_565844.1| 306 GEVSTGRLFSGSLSRGMEVYV--SGASKT---NRIQQVGVFMGPERLEVDAIPAGNIAAVTGLRDA-FVGATVT 373
                                   89*******************..777788...*********************************8.*****86 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   8.9e-08   0.00018       2     113 ..      24     148 ..      23     149 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.9e-08
                                   EEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSSHHHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGliegase 62 
                                   ++iv +   GK+tL   l+                 +    +++ g T+d     +      k+  i+l+DtpG ++    
  gi|91773152|ref|YP_565844.1|  24 IGIVAHIDHGKTTLSDNLLAgagmiskelagrqlfmDSDAEEQERGITIDSSNVSMVheyeGKEYLINLIDTPGHVD---F 101
                                   7888888999****99998545555555555444322334466678888885555443532223559*******665...2 PP

                                   HHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                      MMR_HSR1  63 ekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                   + ++++a++    +d +++v+da e+++ + +  l + l+e+ kp +l +n
  gi|91773152|ref|YP_565844.1| 102 GGDVTRAMR---AVDGAVVVIDAVEGTMPQTETVLRQALKEHVKP-VLFIN 148
                                   223444444...58********99665555555556666655566.44445 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.1e-06     0.014      16      80 ..     397     461 ..     386     487 .. 0.82
   2 ?   -2.6   0.0       2.3   4.6e+03      16      54 ..     542     580 ..     530     581 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.1e-06
                                   EESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE CS
                         RF3_C  16 rlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrles 80 
                                   ++k      +l + l+q+a+E  +  ++ +e++ e +++ +G+L +eV+++R+++  gve+++++
  gi|91773152|ref|YP_565844.1| 397 EAKHMKDLPKLVEVLRQVAKEDPTLKITLDEETGEHLMAGMGELHLEVIAHRIERDKGVEITTTP 461
                                   55555555678888999999999888888888999************************998876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                                   EESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEE CS
                         RF3_C  16 rlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilg 54 
                                      d +k  q+ +   +L  EG ++v+k    ++e+ +g
  gi|91773152|ref|YP_565844.1| 542 AYFDMTKGIQYLNETMELIIEGFTEVMKAGPLSKEPCMG 580
                                   555666667777777788889999999887777777776 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.3e-05      0.11      27     123 ..      67     160 ..      52     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                                   SCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHH.HHHHHHHHHSTTTSE CS
                           Ras  27 eyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvk.kwveeikrvaeenvp 106
                                   e   Ti   + +   e++gke+ +++ DT G  +f    +  +r ++g+++v d  + +   + +  + + +k+++    +
  gi|91773152|ref|YP_565844.1|  67 ERGITIDSSNVSMVHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAVVVIDAVEGT-MPQTEtVLRQALKEHV----K 142
                                   445688777888888999**********************************9987654.4444414444444444....4 PP

                                   EEEEEETTT.GGGG-SS- CS
                           Ras 107 ivLvGnKvD.leekravs 123
                                    vL  nKvD l ++ +v+
  gi|91773152|ref|YP_565844.1| 143 PVLFINKVDrLINELQVD 160
                                   678888888444445555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         3     6e+03     155     161 ..      92      98 ..      76     103 .. 0.79
   2 ?    9.9   0.3   0.00031      0.63      15      71 ..     111     165 ..     104     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3
                                   EESS-SS CS
                   RsgA_GTPase 155 liDtPGf 161
                                   liDtPG 
  gi|91773152|ref|YP_565844.1|  92 LIDTPGH 98 
                                   8999996 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00031
                                   S--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHH CS
                   RsgA_GTPase  15 NvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkee 71 
                                    vd +++v+ ++  e ++ + + +L +a +++++pv+ +nK+D l +e ++++++ +
  gi|91773152|ref|YP_565844.1| 111 AVDGAVVVIDAV--EGTMPQTETVLRQALKEHVKPVLFINKVDRLINELQVDDQEMQ 165
                                   588888888887..5566678999*******************87777656665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 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:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5010.56
//
Query:       gi|91773153|ref|YP_565845.1|  [L=186]
Description: 30S ribosomal protein S7P [Methanococcoides burtonii DSM 6242]
Scores for 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  129.1   4.2    1.2e-37  128.8   4.2    1.0  1  Ribosomal_S7  Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
      0.071   12.3   0.1       0.15   11.2   0.1    1.5  2  G-7-MTase     mRNA (guanine-7-)methyltransferase (G-7-MTase)


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 !  128.8   4.2   1.4e-41   1.2e-37      16     149 .]      44     186 .]      33     186 .] 0.94

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 1.4e-41
                                   SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE- CS
                  Ribosomal_S7  16 pkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevr 92 
                                   +k + ++ve+l+n++m+    +Gkk++A +iv +a+di+++ktkk+p++vl+eA++n+ Pr+ev ++++GG++++ +v+ +
  gi|91773153|ref|YP_565845.1|  44 NKSDITIVERLVNNVMRnaqnTGKKQIALRIVDEAFDIVNSKTKKNPVQVLVEAVSNAGPREEVVRLKYGGISVPKAVDTA 124
                                   567889***********99999*********************************************************** PP

                                   HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                  Ribosomal_S7  93 pkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                   p+Rr++ Alr+i  ++   ++++++s+ae+La+Eli+A++++  + ++++++  +r+A+a+r
  gi|91773153|ref|YP_565845.1| 125 PQRRVDHALRNISIGSnqtAFKSKRSAAECLASELIAASNRDakCFSINRKDGKERVAKAAR 186
                                   ************99998889999******************98899**************97 PP

>> G-7-MTase  mRNA (guanine-7-)methyltransferase (G-7-MTase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   1.7e-05      0.15      47     110 ..      21      87 ..      20      98 .. 0.85
   2 ?   -2.3   0.0      0.21   1.9e+03     259     274 ..     125     140 ..     112     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.7e-05
                     G-7-MTase  47 krfvnlg.vvepirgpnLaaqdfkklsldlvitsvkrflekleeg..ekleillcesdedvvderel 110
                                   kr+vnl+ v+ p  + + a q f+k  + +v   v++++++ ++   +++ + + ++  d+v+ +++
  gi|91773153|ref|YP_565845.1|  21 KRYVNLDpVIVPHTSGKHARQQFNKSDITIVERLVNNVMRNAQNTgkKQIALRIVDEAFDIVNSKTK 87 
                                   89999988999******************************96651155666778888889988765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.21
                     G-7-MTase 259 edsllshalRriGvnS 274
                                   +++ + halR i + S
  gi|91773153|ref|YP_565845.1| 125 PQRRVDHALRNISIGS 140
                                   4788999999875555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 1057.75
//
Query:       gi|91773154|ref|YP_565846.1|  [L=142]
Description: 30S ribosomal protein S12P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  157.6   0.2    1.4e-46  156.8   0.2    1.4  2  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 ?   -2.1   0.0      0.16   2.9e+03      91     108 ..       5      22 ..       1      24 [. 0.78
   2 !  156.8   0.2   7.8e-51   1.4e-46       1     114 []      27     141 ..      27     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.16
                                   EEEBETS---TSSSTTTT CS
               Ribosom_S12_S23  91 rykvvkvagvslkalsky 108
                                   +y   ++++v++ a++k 
  gi|91773154|ref|YP_565846.1|   5 KYAAHRLQQVRKDARWKD 22 
                                   788888999999999885 PP

  == domain 2  score: 156.8 bits;  conditional E-value: 7.8e-51
                                   --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--... CS
               Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk. 80 
                                   r++l++  ksd+l+gapq rG+vlekv+veak+PnsA+Rk+vr++Likng++ taf+pg+ga+nf+dEhdev+v+ i+++ 
  gi|91773154|ref|YP_565846.1|  27 RRTLGLDIKSDPLSGAPQGRGIVLEKVGVEAKQPNSAIRKCVRIQLIKNGRQATAFCPGDGAINFIDEHDEVTVERIGGRm 107
                                   67889999*******************************************************************999888 PP

                                   ...BTTSTTEEEEBETS---TSSSTTTTT----T CS
               Ribosom_S12_S23  81 gkavkDlpGvrykvvkvagvslkalskykkekpk 114
                                   g a++D+pGvr+kv+ v++vsl++++ ++kekp+
  gi|91773154|ref|YP_565846.1| 108 GGAMGDIPGVRFKVIAVNNVSLREMVIGRKEKPR 141
                                   ********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 826.62
//
Query:       gi|91773155|ref|YP_565847.1|  [L=141]
Description: transcription elongation factor NusA-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   71.2   1.5    2.7e-13   49.5   0.0    2.1  2  KH_2      KH domain
    7.1e-11   42.0   2.6    1.4e-08   34.7   0.2    2.2  2  KH_5      NusA-like KH domain
    7.9e-06   25.7   0.2      0.008   16.0   0.1    2.3  2  KH_4      KH domain
    0.00039   20.2   1.6       0.21   11.4   0.2    2.5  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 !   49.5   0.0   6.1e-17   2.7e-13       2      66 ..      12      86 ..      11      98 .. 0.86
   2 !   21.8   0.8   2.8e-08   0.00013       6      55 ..      79     130 ..      74     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.1e-17
                                  HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC............E CS
                          KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk............V 66
                                  ++++l+++++ a +++++I++  +rvi+v+ ++ +g +IGk G n+++++  + k ie +e++             V
  gi|91773155|ref|YP_565847.1| 12 RYIALFESVTHASIKDCIIDD--DRVIYVVNTGDMGAAIGKCGDNLNRVKLSVDKHIELIEYSAepvtfiknafgtV 86
                                  5789***************99..*************************************99866665555555554 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.8e-08
                                   HHHHTECETEEEEEEECCS..CEEEEEEEESCHHHHHTGGGHHHHHHHHHHH CS
                          KH_2   6 laveikkagvskveIerta..nrviiviresqpgivIGkgGsnikkigkelr 55 
                                   +++ +    v++v+I  +   n + + + ++++g++IG++Gsni+ki+  ++
  gi|91773155|ref|YP_565847.1|  79 IKNAFGTVSVRSVRISSKGdkNIAYVDVAANEKGLAIGRNGSNIDKIKRVVG 130
                                   55555566688899988443144445578899***************97665 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2   3.2e-12   1.4e-08       2      69 .]      32      93 ..      31      93 .. 0.96
   2 !    7.7   0.2   0.00082       3.7      17      35 ..     109     127 ..      99     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.2e-12
                          KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                  ++r++ +V  ++     +Ga++gk G++ + v+    ++ i+++e+s  +++fi+na+  + v+sV i
  gi|91773155|ref|YP_565847.1| 32 DDRVIYVVNTGD-----MGAAIGKCGDNLNRVKLSV-DKHIELIEYSAEPVTFIKNAFGTVSVRSVRI 93
                                  7899999*****.....*******************.****************************975 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00082
                          KH_5  17 dpvGaivgkkGsrikavss 35 
                                   ++ G ++g++Gs+i ++++
  gi|91773155|ref|YP_565847.1| 109 NEKGLAIGRNGSNIDKIKR 127
                                   358999*********9986 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00064       2.9      25      52 ..      31      56 ..      13      60 .. 0.71
   2 !   16.0   0.1   1.8e-06     0.008      19      58 ..      90     129 ..      68     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00064
                          KH_4 25 eeeeveielnvegedlGrvIGkrGrtld 52
                                  ++++v +   v++ d+G  IGk G +l+
  gi|91773155|ref|YP_565847.1| 31 DDDRVIYV--VNTGDMGAAIGKCGDNLN 56
                                  34333333..5799**********9986 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-06
                          KH_4  19 evteeeeeeeveielnvegedlGrvIGkrGrtldAlqylv 58 
                                   +v+++ + +++   ++v+ +++G+ IG++G ++d ++ +v
  gi|91773155|ref|YP_565847.1|  90 SVRISSKGDKNIAYVDVAANEKGLAIGRNGSNIDKIKRVV 129
                                   5667777889999********************9888776 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0006       2.7       5      36 ..      38      69 ..      33     103 .. 0.73
   2 !   11.4   0.2   4.7e-05      0.21       5      27 ..     105     127 ..     101     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0006
                                  EEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEE CS
                          KH_1  5 lvPsslvgriIGkgGsnIkeIreet.gakIkvp 36
                                   v++  +g+ IGk G n+++ +  +   +I ++
  gi|91773155|ref|YP_565847.1| 38 VVNTGDMGAAIGKCGDNLNRVKL-SvDKHIELI 69
                                  6778889************9876.545556655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.7e-05
                                   EEGGGHHHHHHTGGGHHHHHHHH CS
                          KH_1   5 lvPsslvgriIGkgGsnIkeIre 27 
                                    v ++  g+ IG++GsnI +I++
  gi|91773155|ref|YP_565847.1| 105 DVAANEKGLAIGRNGSNIDKIKR 127
                                   6777788999***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 966.82
//
Query:       gi|91773156|ref|YP_565848.1|  [L=95]
Description: 50S ribosomal protein L30e [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-12   47.6   0.2    1.3e-12   47.3   0.2    1.2  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 !   47.3   0.2   7.2e-17   1.3e-12       3      94 ..       5      92 ..       3      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 7.2e-17
                                  HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEEE CS
                Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsalai 85
                                  i ++l k+ ++g++++G+++++ a  ++eak+v+lA++++ +   + +ea     ++  + +++  +LG ++gk ++ +++ai
  gi|91773156|ref|YP_565848.1|  5 IDKALIKVIRTGTVIMGANRTIEAAVKNEAKMVVLASNCPANIRDQ-IEA--TSVPILNYAGTG-VDLGPVCGKAFTIATMAI 83
                                  677888999******************************9999988.654..455666678888.****************** PP

                                  EESTTTHHH CS
                Ribosomal_L7Ae 86 kdegdskdl 94
                                   d+g+s++l
  gi|91773156|ref|YP_565848.1| 84 MDAGESDIL 92
                                  ******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 712.22
//
Query:       gi|91773157|ref|YP_565849.1|  [L=386]
Description: DNA-directed RNA polymerase subunit A'' [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-54  184.1   0.9    4.5e-54  183.7   0.9    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
       0.15   12.3   0.3       0.28   11.3   0.3    1.4  1  ABC1            ABC1 family


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 !  183.7   0.9     5e-58   4.5e-54      67     265 ..      54     329 ..      21     331 .. 0.93

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 5e-58
                                   B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5  67 lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkka 147
                                    vep eavG+++aQSiGePgTQ+t++TFH+aGva+ nvtlG+prl ei+++ k+ +++++tv l +e+a++++ a+kv+ +
  gi|91773157|ref|YP_565849.1|  54 CVEPCEAVGVVSAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKTPSTPMMTVALAKEHAADRDFARKVAWE 134
                                   79**************************************************************************99999 PP

                                   HSE.............................................................................. CS
                                   xxx.............................................................................. RF
                RNA_pol_Rpb1_5 148 iek.............................................................................. 150
                                   ie                                                                               
  gi|91773157|ref|YP_565849.1| 135 IEAthiehladvttdlanmnlildlnekmllqrdidvdaiaeklaeglkvnvkipsevanqiivipkeplyrdllqlakni 215
                                   99899999************************************************************************* PP

                                   ......CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHH CS
                                   ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 151 ......gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiqev 225
                                         gi++ikr++++++  g    +e++l teg  l+e+l+ve+ +d +++ +n+i ei+e++gieaar a++ke +++
  gi|91773157|ref|YP_565849.1| 216 hgitlkGIEGIKRVVIRKD--G----DEYTLYTEGSMLKEILEVEG-IDLSRTSTNNIGEIYEVFGIEAARFAIIKEASDT 289
                                   **************99933..3....345789**************.********************************** PP

                                   HHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 226 ykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                   +++qg++v+ rHl+l+ d+mt+ ge+++++r+Gi  ++ s
  gi|91773157|ref|YP_565849.1| 290 LREQGLTVDIRHLMLVSDIMTCDGEVKQIGRHGISGEKAS 329
                                   **********************************987765 PP

>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   3.2e-05      0.28      17      99 ..     110     194 ..     105     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.2e-05
                          ABC1  17 ePiAaASiaqVhrAklksgeeVavKvqrpgvkk..riksDlellkllakllkkflkelrldleelvdefskslleEldfer 95 
                                   +P+ +  +a+ h A     ++Va  +   ++++   +++Dl++++l+++l +k+l + + d++++++++++ l+ ++    
  gi|91773157|ref|YP_565849.1| 110 TPMMTVALAKEHAADRDFARKVAWEIEATHIEHlaDVTTDLANMNLILDLNEKMLLQRDIDVDAIAEKLAEGLKVNVKIPS 190
                                   68888889999********************98225789*********************************999988777 PP

                          ABC1  96 EAkn 99 
                                   E +n
  gi|91773157|ref|YP_565849.1| 191 EVAN 194
                                   7666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2398.10
//
Query:       gi|91773158|ref|YP_565850.1|  [L=883]
Description: DNA-directed RNA polymerase subunit A' [Methanococcoides burtonii DSM 6242]
Scores for complete 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-105  350.9   0.0     1e-104  350.2   0.0    1.3  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    5.1e-69  231.7   0.2    9.2e-69  230.9   0.2    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    3.5e-32  111.5   0.0    6.3e-32  110.7   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    3.7e-32  110.5   0.0    8.4e-32  109.3   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    4.1e-28   98.6   0.1    7.5e-28   97.7   0.1    1.4  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
       0.12   11.4   0.9       0.27   10.2   0.2    1.7  2  UPF0564         Uncharacterised protein family UPF0564


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 !  350.2   0.0  3.5e-108    1e-104       2     312 .]      12     316 ..      11     316 .. 0.93

  Alignments for each domain:
  == domain 1  score: 350.2 bits;  conditional E-value: 3.5e-108
                                   E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfh 82 
                                   k+i +i+fg++sp+e+rk+Sv+ + +a+t++++   P ++Gl+D rlg+id  l+C+ Cg    eC+ghfGhieL +Pv+h
  gi|91773158|ref|YP_565850.1|  12 KRIGAIKFGLISPREVRKMSVTSIITADTYDDDG-YPIDMGLMDLRLGVIDPGLKCKSCGSRAGECPGHFGHIELVAPVIH 91 
                                   8999****************************95.9********************************************* PP

                                   HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHH.HHHCSSSCC.CCHHHHHHHHCCS-BE-SSSSB-EEEEEETTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1  83 igffklilkilecvckecskllldeekkkllsklk.krekleelk.krlkaieelckkinlcekCgavqpkleeegeklka 161
                                   +gf+k+ +kil++vc +cs+lll+e+kk+ + ++  k++ + +l  + ++++ +  +k+++c  C+  + +l+ ++ek  +
  gi|91773158|ref|YP_565850.1|  92 VGFNKILRKILRSVCCKCSSLLLEESKKRDFLEQLaKQKDMGHLPdDVINNVFKEARKSKTCPYCN--EEQLDIKFEKPSE 170
                                   *************************98876666552555555554488999999999999999999..4456667777777 PP

                                   EESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 162 alkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdii 242
                                    +++ ++     l+++++++ +++i+d+d++v+g++++ +rPew+iltvlPVpP+++RPs++l++g+rsedDlt+kl+dii
  gi|91773158|ref|YP_565850.1| 171 YIENGHK-----LTPTEIRDRFENISDDDIRVMGMNPDTARPEWMILTVLPVPPVTVRPSITLESGQRSEDDLTHKLVDII 246
                                   7777776.....********************************************************************* PP

                                   HHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 243 krNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                   ++N+r+++++++gap+liie+ +elLQ+h +t+fdne+sg++pa+++s+rplk+l+qrLkGKeGrfRg+L
  gi|91773158|ref|YP_565850.1| 247 RINQRFQENRDAGAPQLIIEDLWELLQYHLTTYFDNEVSGVPPARHRSGRPLKTLTQRLKGKEGRFRGSL 316
                                   ********************************************************************98 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.9   0.2   3.1e-72   9.2e-69       1     166 []     318     484 ..     318     484 .. 0.98

  Alignments for each domain:
  == domain 1  score: 230.9 bits;  conditional E-value: 3.1e-72
                                   SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-S.C CS
                RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkr.k 80 
                                   Gkrv++saR+v+spdpnl+++evgvP s+a+ +t+p +v + ni+ +r++v++g+ev+Pga+yv+r+d+++ k+++ ++ +
  gi|91773158|ref|YP_565850.1| 318 GKRVNFSARTVVSPDPNLSINEVGVPLSIAQHMTIPVRVISKNIDLMREYVRRGREVHPGANYVIRDDERRIKVTELNKeE 398
                                   9*************************************************************************9998878 PP

                                   HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHHH CS
                RNA_pol_Rpb1_2  81 lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEae 161
                                   l ++le g+ +er+++dgd+vl+NRqPsLhk+simahrvkvl++kt++ln +v+ +yNaDFDGDemn+h+ q+ee+raEa+
  gi|91773158|ref|YP_565850.1| 399 LLEKLEPGWSIERQMQDGDIVLFNRQPSLHKMSIMAHRVKVLPNKTFKLNPAVCPPYNADFDGDEMNMHVLQTEESRAEAS 479
                                   9******************************************************************************** PP

                                   HCSBT CS
                RNA_pol_Rpb1_2 162 elllv 166
                                    l++v
  gi|91773158|ref|YP_565850.1| 480 ILMQV 484
                                   *9976 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   2.1e-35   6.3e-32       1     156 [.     487     652 ..     487     653 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 2.1e-35
                                   CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSB.ESS.SEBEEHHHHHHCCCHCCC CS
                RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpai.lkp.kelwtgkqtfsrilpnei 79 
                                   nilsp+ g P+ig ++D+++G++llT+++ fi++++a++ll+k        v+++pa  l   ++ w gkq+fs ilp+  
  gi|91773158|ref|YP_565850.1| 487 NILSPRFGGPIIGGIHDHISGLFLLTRNEKFISKNDALELLRKSEL----RVLPEPAGhLEDgEPYWNGKQIFSQILPK-G 562
                                   9*******************************************33....467777751555777*************6.4 PP

                                   CEEEE......SSSS........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
                RNA_pol_Rpb1_3  80 nyerk......neek........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyll 146
                                   +y ++      ++++        d +v+i++gelikG+id++++g + +g +++ ++ke+g+++ ++f+d+++rl+++ ++
  gi|91773158|ref|YP_565850.1| 563 LYVEFpaqvcfKCDTckkgdceyDAYVVIEDGELIKGTIDEQAIG-AFKGRVLDKVVKEFGTTAGAKFVDDFTRLAIRGVM 642
                                   44444354444333366688999**********************.999******************************** PP

                                   HHCEB-TGGG CS
                RNA_pol_Rpb1_3 147 qsgftigigD 156
                                   + g+++gi+D
  gi|91773158|ref|YP_565850.1| 643 HTGLSFGISD 652
                                   ********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 !  109.3   0.0   2.8e-35   8.4e-32       3     108 .]     680     784 ..     678     784 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 2.8e-35
                                   HHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS CS
                RNA_pol_Rpb1_4   3 eaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkri 83 
                                   ++e+ ++le lpg++l+e+ e++i++ l kard++g +a ksl  +Ns +iM++sGa+Gsi+n++q+a+c+Gqq+v+g+ri
  gi|91773158|ref|YP_565850.1| 680 AYEN-KELEALPGRTLDETIEMRIMQTLGKARDDTGGMADKSLGLENSAVIMARSGARGSILNLTQMAACVGQQAVRGERI 759
                                   5677.99*************************************77*********************************** PP

                                   --SSTSCSSTTSSSSESSTTTSSEE CS
                RNA_pol_Rpb1_4  84 pkgfsgrtlphfkkidespesrGFv 108
                                    +g+ grtlphf k d ++ ++GFv
  gi|91773158|ref|YP_565850.1| 760 RRGYAGRTLPHFDKGDLGADAHGFV 784
                                   ************************8 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.1   2.5e-31   7.5e-28       1      66 [.     791     856 ..     791     875 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 2.5e-31
                                   B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                   GL+++e+ffh+ ggReGL+DtAv+T++sGYlqRrlv+al+d+ v+yd++vr++ g ivqf+ygedg
  gi|91773158|ref|YP_565850.1| 791 GLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDGSVRETRGVIVQFKYGEDG 856
                                   9****************************************************************8 PP

>> UPF0564  Uncharacterised protein family UPF0564
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   9.2e-05      0.27     206     258 ..     117     170 ..     115     208 .. 0.84
   2 ?   -1.4   0.0      0.31   9.1e+02      66      97 ..     383     414 ..     380     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.2e-05
                       UPF0564 206 klhetFqkelakkkk.kiepteqkpfnfqeskksasreyldsenesikeekekp 258
                                   +++++F ++lak+k+  + p  +    f+e++ks ++ y+++e  +ik ek+ +
  gi|91773158|ref|YP_565850.1| 117 SKKRDFLEQLAKQKDmGHLPDDVINNVFKEARKSKTCPYCNEEQLDIKFEKPSE 170
                                   78899*********84589****************************9555444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.31
                       UPF0564  66 eneeRReevreeskailletekPFsFyerdkq 97 
                                   + +eRR +v e  k++lle+ +P    er++q
  gi|91773158|ref|YP_565850.1| 383 RDDERRIKVTELNKEELLEKLEPGWSIERQMQ 414
                                   5689*****************99777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (883 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 5559.92
//
Query:       gi|91773159|ref|YP_565851.1|  [L=604]
Description: DNA-directed RNA polymerase subunit B' [Methanococcoides burtonii DSM 6242]
Scores for complete 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  405.5   0.0   2.8e-121  405.3   0.0    1.1  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    3.6e-30  104.2   0.1    7.8e-30  103.1   0.1    1.6  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    2.2e-17   63.1   0.1    4.6e-17   62.1   0.1    1.6  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    1.8e-09   38.0   3.2    5.6e-09   36.4   3.2    1.9  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
    0.00084   19.4   0.4     0.0015   18.6   0.4    1.3  1  DUF1451         Zinc-ribbon containing domain
  ------ inclusion threshold ------
      0.012   15.3   0.5       0.14   11.9   0.0    2.5  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.018   14.9   0.3        4.4    7.3   0.1    2.8  2  Nudix_N_2       Nudix N-terminal
        1.1    8.8   2.9          8    6.1   2.8    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.3   0.0  1.3e-124  2.8e-121       3     390 .]     137     507 ..     135     507 .. 0.96

  Alignments for each domain:
  == domain 1  score: 405.3 bits;  conditional E-value: 1.3e-124
                                   HT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEEEEEB CS
                RNA_pol_Rpb2_6   3 klapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGqnavV 83 
                                     +p++eh+ spr+++ aam kq +g+ s n   r +++ ++l+++qk++ +t+ +++a++        ++e ++Gqn+vV
  gi|91773159|ref|YP_565851.1| 137 GMVPYPEHNASPRNTMGAAMIKQCIGVSSSNLKLRPDTRAHVLHYPQKAMTRTQ-TCDAIH--------FDERPAGQNFVV 208
                                   678***************************************************.888888........************ PP

                                   BBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTSB--SS-EEE CS
                RNA_pol_Rpb2_6  84 AvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedGivrvgaevk 159
                                   AvmsyeG+niEDa+++n+ +++r++ +s++++++e e r++++g+e+ ++ ++++     s +a+++Ld dG+v++++ v 
  gi|91773159|ref|YP_565851.1| 209 AVMSYEGHNIEDALVFNKGSIQRGLGRSHFLRTFEGEERRYPGGQEDKFEIPDSEfrgarSADAYANLDIDGLVNPETVVG 289
                                   *********************************************99888888889***99******************** PP

                                   TT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEEEEEEEE-- CS
                RNA_pol_Rpb2_6 160 egdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkvyvaqkRkl 240
                                   ++d+l+gk+  ++ ++ +e+    + fg + ++ +++ ++++s+e+g+Vd+v++       +++ ++++l+kv+++++R +
  gi|91773159|ref|YP_565851.1| 290 PNDVLIGKT--SPPRFLEEQ----SDFGITIEQRRESAITMRSNEKGIVDTVIL-------TESINGTRLAKVKIRDERIP 357
                                   ********8..888888544....4455555556899*****************.......8999**************** PP

                                   -TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B--TT-...-HHH CS
                RNA_pol_Rpb2_6 241 qvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaalegkkvdatvFdgakeeei 321
                                   ++GDKfasrhGqKGv++li+p +DmPf+e G+v+D+v+NP+++PSRmt++++lE++ gk ++leg++  +t+F+g  e+ i
  gi|91773159|ref|YP_565851.1| 358 EIGDKFASRHGQKGVIGLIVPYHDMPFTELGMVPDLVINPHAIPSRMTVAHVLEMIGGKLGSLEGQRKWGTAFSGDMEDGI 438
                                   ********************************************************************************* PP

                                   HHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                RNA_pol_Rpb2_6 322 kelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390
                                   ++ L+++g++++Gkev+ dG+tG+k++a++fvGvi y+kL+h+v+ KihaRs+Gp+++lt+QP++G+a+
  gi|91773159|ref|YP_565851.1| 439 RDGLKNRGFSHTGKEVFCDGVTGKKIQADVFVGVILYQKLHHMVASKIHARSRGPVQVLTRQPTEGRAR 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 !  103.1   0.1   3.5e-33   7.8e-30       1      85 [.     509     599 ..     509     601 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 3.5e-33
                                   BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHHHHHH CS
                RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklLlqeL 75 
                                   GGlrfGEMErd+li++Gaa++Lkerl+++SD+v   vc +c+++a+ +      +C+++  e++i++ve+++afklLl+e+
  gi|91773159|ref|YP_565851.1| 509 GGLRFGEMERDVLIGHGAAMTLKERLLDESDKVVELVCAQCGMVATFDrtrnirYCSNCGAETDIHPVEMSYAFKLLLDEI 589
                                   9*********************************************99********************************* PP

                                   HHTTBEEEEE CS
                RNA_pol_Rpb2_7  76 qslgialkll 85 
                                   +slg+a++l 
  gi|91773159|ref|YP_565851.1| 590 KSLGVAPRLR 599
                                   ******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 !   62.1   0.1   2.1e-20   4.6e-17       1      62 []       6      67 ..       6      67 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.1e-20
                                  EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                  Vf++G+l+G+++dp +lve++R  RR+g ++++ +++l+e+ +ev +++D GR++RP i+Ve
  gi|91773159|ref|YP_565851.1|  6 VFLDGELIGTHNDPVELVESIRGQRRSGMLPHQLNVTLYEDIHEVILSSDIGRARRPAIVVE 67
                                  9************************************************************7 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 !   36.4   3.2   2.5e-12   5.6e-09       1      58 []      88     128 ..      88     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.5e-12
                                   HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                   + dLl+ g vEylDaeEEe+a+I +++edl+                  ++TH+EI+P
  gi|91773159|ref|YP_565851.1|  88 FRDLLDMGYVEYLDAEEEENAFIGLYEEDLTP-----------------NHTHLEIDP 128
                                   89****************************66.................589999999 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   6.6e-07    0.0015     112     141 ..     541     570 ..     535     571 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.6e-07
                       DUF1451 112 lGtlvCekCgkelalkkteeippCpkCgat 141
                                     +lvC++Cg   ++++t++i  C++Cga+
  gi|91773159|ref|YP_565851.1| 541 VVELVCAQCGMVATFDRTRNIRYCSNCGAE 570
                                   568************************986 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   0.2      0.18   4.1e+02      23      28 ..     545     550 ..     543     551 .. 0.72
   2 ?   11.9   0.0   6.2e-05      0.14       1      16 [.     559     574 ..     559     579 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                 zf-NADH-PPase  23 vCpaCg 28 
                                   vC++Cg
  gi|91773159|ref|YP_565851.1| 545 VCAQCG 550
                                   777776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.2e-05
                 zf-NADH-PPase   1 rthrFCgrCGaptepa 16 
                                   r+ r+C+ CGa+t   
  gi|91773159|ref|YP_565851.1| 559 RNIRYCSNCGAETDIH 574
                                   567*********9765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.014        32      23      31 ..     544     552 ..     529     553 .. 0.77
   2 ?    7.3   0.1     0.002       4.4       1      10 [.     562     571 ..     562     576 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.014
                                   EEETTTTEE CS
                     Nudix_N_2  23 lvCpaCgti 31 
                                   lvC++Cg++
  gi|91773159|ref|YP_565851.1| 544 LVCAQCGMV 552
                                   8******98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                                   -B-TTT--B- CS
                     Nudix_N_2   1 kFCsqCGtpv 10 
                                   ++Cs+CG+++
  gi|91773159|ref|YP_565851.1| 562 RYCSNCGAET 571
                                   8******986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.019        42      19      28 ..     543     552 ..     539     558 .. 0.88
   2 ?    6.1   2.8    0.0036         8       2      32 ..     545     574 ..     544     579 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.019
                                   CEEESSSSBE CS
                  TF_Zn_Ribbon  19 elvCtdCGlV 28 
                                   elvC  CG V
  gi|91773159|ref|YP_565851.1| 543 ELVCAQCGMV 552
                                   89******88 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
                                   EETTTTCEECHEETSTTCEEESSSSBEEEEC CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVledn 32 
                                   +C  Cg    ++D  r+  +C++CG+  + +
  gi|91773159|ref|YP_565851.1| 545 VCAQCGMVA-TFDRTRNIRYCSNCGAETDIH 574
                                   799999875.99*9***********977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4228.71
//
Query:       gi|91773160|ref|YP_565852.1|  [L=542]
Description: DNA-directed RNA polymerase subunit beta'' [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-55  187.5   0.1    2.7e-55  187.1   0.1    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    1.4e-26   92.4   0.0    2.4e-26   91.7   0.0    1.4  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    1.2e-23   83.8   0.0    1.8e-23   83.2   0.0    1.3  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2


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 !  187.1   0.1   4.4e-59   2.7e-55       4     202 ..       2     367 ..       1     368 [. 0.99

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 4.4e-59
                                   HHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1   4 sqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYsaplyvk 84 
                                   + ++dS+nkfv++ l+kii+e+  ie++ e       +++k+++ir+++Pvv+e+d++ +++yP+earlrnl+Ysapl+++
  gi|91773160|ref|YP_565852.1|   2 QHHIDSYNKFVKHGLQKIINEQGIIETDLED------IYVKLGKIRVEHPVVKEADGAIEKLYPNEARLRNLSYSAPLFLE 76 
                                   78*************************9995......9******************************************* PP

                                   EEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE.......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                RNA_pol_Rpb2_1  85 lklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek.......... 155
                                   +  v     n+ee +++e ++G+lP+M++s  c+l ++s+ e+v+++E+pld+GGyFi+nGte+v++ +e+          
  gi|91773160|ref|YP_565852.1|  77 MSVVQ----NGEEGEPKEAKVGQLPVMIKSDICNLVGISDAEMVQHGEDPLDPGGYFIVNGTERVVMTLEDlapnkiltel 153
                                   ***99....8*********************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|91773160|ref|YP_565852.1| 154 gerygdsievskvfsqrrgyralvvvergrkslleisfpsisgrinfitlmralgvetdedvakivstdpeimkfmfenle 234
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|91773160|ref|YP_565852.1| 235 eaevftiedaiekiggrvasgqareyqmkranyvidryllphlgndpadripkahflgrmaescfelalkrrsdddkdhys 315
                                   ********************************************************************************* PP

                                   .....XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1 156 .....laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                        l G+L+++lfrv++++l+rdvk +l++   ++++l+++ lv+a+ +t
  gi|91773160|ref|YP_565852.1| 316 nkrlkLTGDLMEDLFRVAFNRLARDVKYQLERANMRNRELNVATLVRADVLT 367
                                   ************************************************9876 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0     4e-30   2.4e-26       1      67 [.     388     451 ..     388     452 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 4e-30
                RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallar 67 
                                   q+ldr+ ++s+lshlrrv s+   ls+ + ++e+Rdlhp++wGr+Cp+eTPEG+ncGlvk++a++++
  gi|91773160|ref|YP_565852.1| 388 QLLDRTDYISTLSHLRRVISP---LSRAQPHFEARDLHPTQWGRLCPSETPEGPNCGLVKNFAQMVE 451
                                   89*******************...***************************************9975 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 !   83.2   0.0     3e-27   1.8e-23       6     190 .]     139     320 ..     135     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 3e-27
                                   EEEE-SSSSSE.............SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHH CS
                RNA_pol_Rpb2_2   6 yvekekdknki.............satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIleri 73 
                                   ++  + ++nki             +++v s +  +r++v++++  ++ l ++ +s+  +i+++ +++Alg+ +d+++ + +
  gi|91773160|ref|YP_565852.1| 139 MTLEDLAPNKIltelgerygdsieVSKVFSQRRGYRALVVVERGRKSLLEISFPSISGRINFITLMRALGVETDEDVAKIV 219
                                   56666777777777777777777778888888889999988888999999****************************977 PP

                                   TSSSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH CS
                RNA_pol_Rpb2_2  74 cydsedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenk 154
                                   +   +d+++++ ++e+lee+e + t e+a+++ig +va ++ +e ++++a  ++         +r+ l+ hlg +     +
  gi|91773160|ref|YP_565852.1| 220 S---TDPEIMKFMFENLEEAE-VFTIEDAIEKIGGRVASGQAREYQMKRANYVI---------DRYLLP-HLGNDPA---D 283
                                   7...79999999998888765.679**************************995.........8*****.*******...4 PP

                                   ...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                RNA_pol_Rpb2_2 155 r.lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                   r  ka++++ m++  ++l+l+rr+ DD+Dh+ nkR++
  gi|91773160|ref|YP_565852.1| 284 RiPKAHFLGRMAESCFELALKRRSDDDKDHYSNKRLK 320
                                   558********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3595.94
//
Query:       gi|91773161|ref|YP_565853.1|  [L=78]
Description: DNA-directed RNA polymerase subunit H [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-28   98.6   0.2    1.5e-28   98.5   0.2    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.2   8.2e-33   1.5e-28       2      73 .]       5      76 ..       4      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 8.2e-33
                                  .-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                RNA_pol_Rpb5_C  2 nitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                  ++++Hel+P+he+++e++ k++l+++++++eqLPk++ +Dp+a ++g+++Gdvvk++rks+tagea +YR+V
  gi|91773161|ref|YP_565853.1|  5 SLLDHELIPHHEIMDEDDLKTVLTHYNVEREQLPKLKVTDPIALEIGAEPGDVVKVIRKSQTAGEALYYRYV 76
                                  6799******************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 504.82
//
Query:       gi|91773162|ref|YP_565854.1|  [L=411]
Description: S-adenosyl-L-homocysteine hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-52  178.4   0.0    4.5e-26   91.7   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    2.6e-50  170.7   1.2    2.6e-50  170.7   1.2    1.9  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    4.1e-09   36.0   0.1    8.1e-09   35.1   0.1    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    2.8e-06   27.0   0.3    5.9e-06   25.9   0.1    1.6  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.017   15.3   0.2        1.6    9.1   0.2    2.6  2  TSCPD          TSCPD 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 !   85.1   0.1   1.3e-27   4.5e-24       8     138 ..       5     131 ..       1     135 [. 0.94
   2 !   91.7   0.0   1.3e-29   4.5e-26     174     286 ..     134     405 ..     130     409 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.3e-27
                                   GGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase   8 slaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaaaaia 88 
                                    l e G  +i    + mp l  +re++++e+plkg +ia +lh+ ++ta L+e+L   Gaev+ + Cn  stqd+++aa+ 
  gi|91773162|ref|YP_565854.1|   5 DLIESGDMKIGWVRSHMPVLSIIRENFEREQPLKGHKIAMALHVEAKTAALVEALAIGGAEVTITGCNPLSTQDDVSAALN 85 
                                   6678899999999*******************************************************************9 PP

                                   CT.TEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                   xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase  89 ea.gvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                   ++ +++ +a      +ey + i+++l++     +p++ +DdG Dl   +h+
  gi|91773162|ref|YP_565854.1|  86 TRdNINCYAKYDCCSDEYYEAIDKVLDM-----KPDITIDDGADLIFKLHT 131
                                   877***********************66.....7***********988886 PP

  == domain 2  score: 91.7 bits;  conditional E-value: 1.3e-29
                                   CCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                     AdoHcyase 174 tellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD.................................. 220
                                   t+ll++i G  eetttG+hrL+ ++k+g L++p + vnd++tk  fD                                  
  gi|91773162|ref|YP_565854.1| 134 TDLLSDIFGGCEETTTGIHRLKAMEKDGALKMPVVAVNDAMTKFLFDnrygtgqsswdgimrttnllvagktvviggygwc 214
                                   56788999************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                     AdoHcyase 221 ................................................................................. 220
                                                                                                                    
  gi|91773162|ref|YP_565854.1| 215 gkgvslrasglgadvivteidpiralearmdghrvmsmaeaakygdifvtttgnvdilskkhfevmkdgailansghfnve 295
                                   ********************************************************************************* PP

                                   ..............................................S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE-- CS
                                   ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 221 ..............................................hpsfvmsasftnqvlaqielfkkekkyekkvyvlp 255
                                                                                 hp+ vm++sf+nq+l    + +  +k e++v+ +p
  gi|91773162|ref|YP_565854.1| 296 inleeltamassvrtvrknikeynvagkrinvladgrlvnlaagdgHPAEVMDMSFANQALCVKYIAE--TKLENGVHPVP 374
                                   *************************************************************9777666..568******** PP

                                   CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 256 kklDekvarlhleklgaklteltkeqaeyig 286
                                   + lD +va+l+l+++g+++++l+ +q+ey++
  gi|91773162|ref|YP_565854.1| 375 HDLDMYVAELKLKSMGIEIDKLEPHQTEYME 405
                                   *****************************95 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 ?   -1.0   0.0      0.46   1.6e+03      40      59 ..      57      76 ..      48      88 .. 0.72
   2 !  170.7   1.2   7.2e-54   2.6e-50       1     160 [.     181     339 ..     181     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.46
                                  HHHHHCT-EEEEE-S-HHHH CS
                 AdoHcyase_NAD 40 aslkglGarvivtevdPica 59
                                  ++l   Ga v++t  +P+++
  gi|91773162|ref|YP_565854.1| 57 EALAIGGAEVTITGCNPLST 76
                                  56666778888887777654 PP

  == domain 2  score: 170.7 bits;  conditional E-value: 7.2e-54
                                   HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SE CS
                 AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadi 81 
                                   n yg+ +s  dgi+r+t++l+aGk++v+ GyG  GkG +    glGa vivte+dPi al a m+G++v+ + e++k +di
  gi|91773162|ref|YP_565854.1| 181 NRYGTGQSSWDGIMRTTNLLVAGKTVVIGGYGWCGKGVSLRASGLGADVIVTEIDPIRALEARMDGHRVMSMAEAAKYGDI 261
                                   78******************************************************************************* PP

                                   EEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS CS
                 AdoHcyase_NAD  82 vvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgca 160
                                   +vtttGn di++++h++ mkd ai++n Ghf+ ei++++l+a+a ++ +v+ ++++++++ gk+i +la+Grl+nl++ 
  gi|91773162|ref|YP_565854.1| 262 FVTTTGNVDILSKKHFEVMKDGAILANSGHFNVEINLEELTAMASSVRTVRKNIKEYNVA-GKRINVLADGRLVNLAAG 339
                                   *********************************************************985.999************976 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 !   35.1   0.1   2.3e-12   8.1e-09      22     127 ..     189     290 ..     173     308 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.3e-12
                                   CCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                  2-Hacid_dh_C  22 ewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlplt 102
                                    w+   +++   ++gktv i G+G  G+ v  r++++g++vi+++  + +  e++  g +++s+ e+ +  Di + +    
  gi|91773162|ref|YP_565854.1| 189 SWDGIMRTTNLLVAGKTVVIGGYGWCGKGVSLRASGLGADVIVTEIDPIRALEARMDGHRVMSMAEAAKYGDIFVTT---- 265
                                   55555566666899*********************************998889999999**************9975.... PP

                                   TTTTTSBSHHHHHCSTTTEEEEESS CS
                  2-Hacid_dh_C 103 petrhlinaeelakmkkgailiNta 127
                                     + +++++++++ mk+gail N +
  gi|91773162|ref|YP_565854.1| 266 TGNVDILSKKHFEVMKDGAILANSG 290
                                   56999*****************987 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 ?   -3.4   0.0       1.7   6.2e+03     138     160 ..      44      62 ..      26      65 .. 0.52
   2 !   25.9   0.1   1.6e-09   5.9e-06       2     103 ..     201     298 ..     200     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                                   EEEEE-SSS-HHHHHHHHHHHTT CS
                          IlvN 138 iaveqdasgkakelalayakgiG 160
                                   +a++ +    ak  al  a +iG
  gi|91773162|ref|YP_565854.1|  44 MALHVE----AKTAALVEALAIG 62 
                                   344444....4444444444555 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.6e-09
                                   HHTS-EEEES-SHHHHHHHHHHHHTT-..-EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHH CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgl..dvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeee 80 
                                   + gk++++ GyG  G+  +  lr sgl  dv+v+  +    + +A+ +g++v+++aea+k  d+ ++ +    + ++++++
  gi|91773162|ref|YP_565854.1| 201 VAGKTVVIGGYGWCGKGVS--LRASGLgaDVIVTEIDPI-RALEARMDGHRVMSMAEAAKYGDIFVTTT---GNVDILSKK 275
                                   579************8665..666655338888776666.7789*******************987765...567899999 PP

                                   TGGG--TT-EEEESSSHHHHTTS CS
                          IlvN  81 iepnlkegkalafahGfnihfgl 103
                                     + +k+g++la +  fn+  +l
  gi|91773162|ref|YP_565854.1| 276 HFEVMKDGAILANSGHFNVEINL 298
                                   99****************98765 PP

>> TSCPD  TSCPD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00043       1.6       9      73 ..      44     108 ..      39     109 .. 0.86
   2 ?    3.5   0.0     0.024        85      25      39 ..     140     154 ..     126     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                         TSCPD   9 reieievddkliknvkfvgGCngnlkgiskLvegmkveevikklkGikCgnkeTSCpDqlakAlk 73 
                                   + +++e +   + +   +gG +  ++g   L +  +v+ + ++ + i+C +k   C+D   +A++
  gi|91773162|ref|YP_565854.1|  44 MALHVEAKTAALVEALAIGGAEVTITGCNPLSTQDDVSAALNTRDNINCYAKYDCCSDEYYEAID 108
                                   455666665566677789****************************************9999986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.024
                         TSCPD  25 fvgGCngnlkgiskL 39 
                                   + gGC+  ++gi +L
  gi|91773162|ref|YP_565854.1| 140 IFGGCEETTTGIHRL 154
                                   68***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2327.28
//
Query:       gi|91773163|ref|YP_565855.1|  [L=434]
Description: N-ethylammeline chlorohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-69  234.4   1.0    2.6e-69  234.2   1.0    1.1  1  Amidohydro_1  Amidohydrolase family
    3.5e-22   79.5   4.3    9.3e-14   51.7   0.2    3.3  3  Amidohydro_3  Amidohydrolase family
     0.0063   15.9   0.1      0.011   15.1   0.1    1.4  1  A_deaminase   Adenosine/AMP deaminase
  ------ inclusion threshold ------
      0.023   14.8   0.0      0.078   13.1   0.0    1.9  1  VirK          VirK protein
       0.12   11.8   0.1        3.4    7.1   0.0    2.1  2  DUF3700       Aluminium induced protein
       0.16   12.0   0.2        3.1    7.9   0.0    3.0  4  RL10P_insert  Insertion domain in 60S ribosomal protein L10P


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 !  234.2   1.0   8.7e-73   2.6e-69       1     343 [.      54     400 ..      54     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.2 bits;  conditional E-value: 8.7e-73
                                   EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHH CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgieall 67 
                                   +v+PG++++H+H+ ++l+rg     +l +wl          ++ +++ ++++ ++ +++ksGt  +adm++     +e + 
  gi|91773163|ref|YP_565855.1|  54 VVMPGFVNTHTHAGMTLFRGYaddlPLAQWLqehiwpaeaeLTASDVLAGTRLACLEMIKSGTIAFADMYF----FMEEVG 130
                                   69*********************************************************************....****** PP

                                   HHHHTSSSEEEEEEESSEGGS...GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHT CS
                  Amidohydro_1  68 eaaeelplglrilggkvsldr...gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrd 145
                                   +a+ee+  glr+ +++++++    +++ +++++ +++++++     gka+g+++v  +ph++ ++s+e l+++ + a + +
  gi|91773163|ref|YP_565855.1| 131 KAVEEC--GLRAALSYGMIELwddEKGTNELKKGREFVKEW----NGKAEGRISVMYGPHAPNTCSKEFLSKVKEQAIADN 205
                                   *****6..*************99988888899999999998....************************************ PP

                                   TEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSE CS
                  Amidohydro_1 146 lpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilr 226
                                   ++++iH+let++e  ++++++g   ++   +  ++ ++++++  +++ah+++l++ ++ +l+ +  ++++ah p sn++l+
  gi|91773163|ref|YP_565855.1| 206 VKIHIHVLETEAELNQMKEQYG---MC--SVNMLDTIDFFGP-GVLAAHCIWLSDGDMDILADN--NVNIAHNPVSNMKLA 278
                                   **********************...88..99999********.***********99********..*************** PP

                                   HHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS- CS
                  Amidohydro_1 227 sgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsie 307
                                   sg++++ k+ld+G++v lgtDg+as+n+l++++e++ a++lq++  + d+++ l++k++l+maT ngAkal +  + G + 
  gi|91773163|ref|YP_565855.1| 279 SGVAPVMKLLDKGANVCLGTDGCASNNNLDMFDEMKTAALLQKVDTM-DPTA-LPAKQVLEMATVNGAKALDI--NSGVLR 355
                                   ***************************************99994444.8888.********************..****** PP

                                   TTSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEE CS
                  Amidohydro_1 308 vGkdADlvvvdl...di......laafvglkkdgnvkkvivkGkl 343
                                   + + AD +++d    ++       +++v+++  + v+++iv+G +
  gi|91773163|ref|YP_565855.1| 356 KDYNADVIIIDMnkaHLsplfdvPSQLVYSATGNDVRTTIVNGVV 400
                                   ************76622677888********************65 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.3   1.3e-09   3.9e-06       2      31 ..      47      74 ..      46      88 .. 0.83
   2 ?    1.3   0.0     0.062   1.9e+02     102     139 ..     140     177 ..     133     255 .. 0.76
   3 !   51.7   0.2   3.1e-17   9.3e-14     312     472 ..     247     401 ..     185     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.3e-09
                  Amidohydro_3  2 viDakGrlvlPGFvDsHtHlagggvnl.rll 31
                                  viDa+G++v+PGFv  HtH   +g+ l r++
  gi|91773163|ref|YP_565855.1| 47 VIDAQGGVVMPGFVNTHTH---AGMTLfRGY 74
                                  9******************...666665655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.062
                  Amidohydro_3 102 avrnsaaldlagiteatpdp.aggeilrdangegatgll 139
                                   a++++ +++l+++++ t +  +g+e +++ ng+ a+g +
  gi|91773163|ref|YP_565855.1| 140 AALSYGMIELWDDEKGTNELkKGREFVKEWNGK-AEGRI 177
                                   667788888888888888887888888888887.77755 PP

  == domain 3  score: 51.7 bits;  conditional E-value: 3.1e-17
                  Amidohydro_3 312 ehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpwprigaa 390
                                   +h+ ++++ +++ +a+ +v ++  pv+n            + a+g++pv+ ll++g +v+lg+D  a  + +d + ++ +a
  gi|91773163|ref|YP_565855.1| 247 AHCIWLSDGDMDILADNNVNIAHNPVSNM-----------KLASGVAPVMKLLDKGANVCLGTDgcASNNNLDMFDEMKTA 316
                                   56666666666666666666666666666...........779999********************9************** PP

                  Amidohydro_3 391 vmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld......adpldvdppelaear...v 462
                                     +++      + +   l+  ++l + T ++Akal      G L++ + AD++++d        ++dv+ + +++a+   v
  gi|91773163|ref|YP_565855.1| 317 ALLQK----VDTMDPTALPAKQVLEMATVNGAKALDINS--GVLRKDYNADVIIIDmnkahlSPLFDVPSQLVYSATgndV 391
                                   *****....5677999***********************..***************999999999999999999998**** PP

                  Amidohydro_3 463 rltvvdGrvv 472
                                   r t+v+G+v+
  gi|91773163|ref|YP_565855.1| 392 RTTIVNGVVL 401
                                   *******986 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.7e-06     0.011     232     304 ..     258     327 ..     188     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
                                   HHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT.-SHHHHHHHHHHHHT--HHHH CS
                   A_deaminase 232 yllalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfg.ttLieeYaiaaqvfklseedl 304
                                   + la++++ ++  P+SN++l    +    P+ ++l++g nv l+tD  +  + +++ +e++ aa   k ++ d 
  gi|91773163|ref|YP_565855.1| 258 DILADNNVNIAHNPVSNMKL----ASGVAPVMKLLDKGANVCLGTDGCASNNnLDMFDEMKTAALLQKVDTMDP 327
                                   678999**************....77889*****************9887651569****99998888888775 PP

>> VirK  VirK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.078      29      74 ..      90     135 ..      85     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                   ...ESS---SEEEEE--SEEEEETTTEEEEEEEEEES--TTS-EEE CS
                          VirK  29 paeegapasktrggvrinayrvtsdgtlafsdahftvdsdgkpile 74 
                                   pae++ +as + +g+r     +++ gt+af+d  f +++ gk++ e
  gi|91773163|ref|YP_565855.1|  90 PAEAELTASDVLAGTRLACLEMIKSGTIAFADMYFFMEEVGKAVEE 135
                                   6788999************************************987 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.033     1e+02      26      98 ..     157     229 ..     147     235 .. 0.86
   2 ?    7.1   0.0    0.0011       3.4     117     179 ..     355     419 ..     353     425 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.033
                       DUF3700  26 kkkklaeellekflslkpeavsvnlgdsallayssekespllprlfavlddifClfqGslenlasLkkqyGLs 98 
                                   ++ k+  e +++++ ++++ +sv +g +a  ++s+e  s+++++ +a   +i+     +   l ++k+qyG+ 
  gi|91773163|ref|YP_565855.1| 157 NELKKGREFVKEWNGKAEGRISVMYGPHAPNTCSKEFLSKVKEQAIADNVKIHIHVLETEAELNQMKEQYGMC 229
                                   44455668999999999******************************999999999999999*********84 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                       DUF3700 117 rgPypadqvvkdleGkfafvlydskaktvfvaldadgsvplyWGia..adgsvvisddlelvkks 179
                                   r  y ad ++ d++  +   l+d  ++ v+ a+++d +  +  G+    + +v++ +++++++++
  gi|91773163|ref|YP_565855.1| 355 RKDYNADVIIIDMNKAHLSPLFDVPSQLVYSATGNDVRTTIVNGVVlmDERKVLCMNEQQVINDA 419
                                   6679****************************************853257788888999999875 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.1   1.2e+04      10      22 ..       3      16 ..       2      18 .. 0.64
   2 ?   -0.3   0.1      0.37   1.1e+03      38      60 ..      28      50 ..      20      55 .. 0.77
   3 ?   -2.8   0.0       2.3   6.8e+03      27      45 ..     131     149 ..     113     158 .. 0.62
   4 ?    7.9   0.0     0.001       3.1      33      58 ..     390     415 ..     360     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.1
                  RL10P_insert 10 dviipag.plelaP 22
                                  d+ii+ g  l++ P
  gi|91773163|ref|YP_565855.1|  3 DIIIKNGyVLTMDP 16
                                  78888884455445 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                  RL10P_insert 38 lkkGkivleedylvckkGetlts 60
                                  ++ Gkiv  ++++ +++++++++
  gi|91773163|ref|YP_565855.1| 28 IEGGKIVEVAETTSATANTVIDA 50
                                  77788888888888888888776 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                  RL10P_insert  27 peLrklglptklkkGkivl 45 
                                   +   + gl + l  G i+l
  gi|91773163|ref|YP_565855.1| 131 KAVEECGLRAALSYGMIEL 149
                                   4445667777777777766 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.001
                  RL10P_insert  33 glptklkkGkivleedylvckkGetl 58 
                                    + t +++G++ ++e++++c + +++
  gi|91773163|ref|YP_565855.1| 390 DVRTTIVNGVVLMDERKVLCMNEQQV 415
                                   5789****************888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2778.42
//
Query:       gi|91773164|ref|YP_565856.1|  [L=212]
Description: metal-dependent phosphohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-12   45.8   2.0      9e-12   45.3   2.0    1.2  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   2.0     5e-16     9e-12       3     121 ..      25     125 ..      24     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH...HHH CS
                            HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld...led 80 
                                    H+ +V   +  ++ ++g   d ++++laaLlHD+G +++++          +  +H++++aei+++++  +gld   ++ 
  gi|91773164|ref|YP_565856.1|  25 SHIERVESTCMLIQAEEG--GDLQVIRLAALLHDVGVVKEHR----------EGGDHAVHSAEIAHDLLMKEGLDpsvVDH 93 
                                   6999**************..*******************887..........5669************************* PP

                                   HHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                            HD  81 vaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                   v+  i  h++s            ++ sle +i+++aDr++a
  gi|91773164|ref|YP_565856.1|  94 VVSCICTHRFSRG---------NMAGSLEGQILQDADRIDA 125
                                   **********996.........57***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1470.26
//
Query:       gi|91773165|ref|YP_565857.1|  [L=258]
Description: hypothetical protein Mbur_1184 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-75  251.3   0.4    4.8e-75  251.0   0.4    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase


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 !  251.0   0.4   2.7e-79   4.8e-75       1     176 []      66     240 ..      66     240 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.0 bits;  conditional E-value: 2.7e-79
                        PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseRakvs 81 
                                   llla+ p++svNGN+aaLv+e++veL+e++ga+levNlf+r++eRv++i ++lk++ga+evlg + dar+ +l++ Ra+v+
  gi|91773165|ref|YP_565857.1|  66 LLLAEYPILSVNGNAAALVPESLVELSEMVGAPLEVNLFHRSDERVARIISHLKQKGASEVLGGKGDARL-SLDHGRAIVD 145
                                   799*****************************************************************99.9********* PP

                        PPS_PS  82 keGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkskeeleeivke 162
                                   ++Giy+aDvvlvplEDGDR+++Lv+mgK+viaiDLNP+sRt+rta++tivdnvvRal n++  ++elk+ +  e+++i+ke
  gi|91773165|ref|YP_565857.1| 146 SDGIYKADVVLVPLEDGDRCQKLVDMGKTVIAIDLNPMSRTSRTASVTIVDNVVRALGNMVGLATELKELTPFEIKNIIKE 226
                                   ********************************************************************************* PP

                        PPS_PS 163 fdnkkvlkealkei 176
                                   +dn+++l+ea++ei
  gi|91773165|ref|YP_565857.1| 227 YDNERTLSEAVREI 240
                                   **********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1744.55
//
Query:       gi|91773166|ref|YP_565858.1|  [L=316]
Description: membrane protease [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  101.4   1.0    8.5e-29  100.8   1.0    1.2  1  Band_7    SPFH domain / Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   1.0   4.7e-33   8.5e-29       2     176 ..      56     247 ..      55     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 4.7e-33
                        Band_7   2 iieegevgvvvr..fGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsv...........sltvptkDglpvtidvtviy 69 
                                   ++++g+vgv +    G +++ l+ Glh++ P++ svt++svr   +++s            +++++t++gl +++d++v+y
  gi|91773166|ref|YP_565858.1|  56 SVGAGQVGVKFSqfGGVMDDELGEGLHIVPPWI-SVTKYSVRSEMYTMSGraaegevvgddQINALTNEGLTLGLDISVRY 135
                                   6899******9995666677*******977755.5666******************************************* PP

                        Band_7  70 rv.pddapklvaaveresanldnlirrvlesalrevisemtleellsn.reelaeelknelneqlrkyGvevldvritdid 148
                                   r+ +dda+++++++  +  + +++ir++++s++rev+s  t+  ++++ r+ +a e++ e+ ++l + G+ v++v +++++
  gi|91773166|ref|YP_565858.1| 136 RLvADDASVVHSKL--GTSYAQKIIRPTIKSVIREVVSGQTAMAIYGEqRDLVATEMQLEMEKALVGDGIIVEEVLLRNVQ 214
                                   **************..******************************9977******************************* PP

                        Band_7 149 pppevaqalaakqaaeaea.......qaeiaraea 176
                                   +p ++a+a+++k +a+++a       q  +++ ea
  gi|91773166|ref|YP_565858.1| 215 LPTKIADAIESKLQADQDAqrmifvkQ--KEQLEA 247
                                   *******************88877443..333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1956.50
//
Query:       gi|91773167|ref|YP_565859.1|  [L=293]
Description: pantothenate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   40.6   2.3    5.2e-10   39.4   2.3    1.7  1  GHMP_kinases_N  GHMP kinases N terminal domain
    0.00018   21.8   0.4     0.0007   19.9   0.1    2.0  2  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 !   39.4   2.3   5.8e-14   5.2e-10       1      59 [.      82     140 ..      82     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 5.8e-14
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHH.HHSHHH CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggn.gsggDv 59 
                                   +++++s iP+g+G+G SAA a+++++Al+++++l+l  ++l  +a+ + + +n +++gDv
  gi|91773167|ref|YP_565859.1|  82 RVSCTSSIPIGCGFGASAAGALSVAYALNEAFSLDLTSNQLLETAHIAEV-TNgSGMGDV 140
                                   5899****************************999966788777775555.551555555 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.23     2e+03      30      83 ..      63     113 ..      51     115 .. 0.73
   2 !   19.9   0.1   7.8e-08    0.0007      14      66 ..     213     260 ..     200     277 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.23
                GHMP_kinases_C  30 gilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83 
                                   ++l +  ++++++l +     +++s +++ p  ++++ + ++a  va al+e+f
  gi|91773167|ref|YP_565859.1|  63 PVLAETTRAVVDKLVDFP---VRVSCTSSIPIGCGFGASAAGALSVAYALNEAF 113
                                   555566666777776655...788888877888888888888888888888877 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 7.8e-08
                GHMP_kinases_C  14 gellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalf 66 
                                   ++ + ls +   + ++g  +++l +++e+  + G   +  s+a++G+t+fa+ 
  gi|91773167|ref|YP_565859.1| 213 ENFMQLSKQ--FTLRCGLASEHLLDAIESVNAIG---GMSSQAMLGDTIFAIS 260
                                   333333333..23377777777777777776666...***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2013.08
//
Query:       gi|91773168|ref|YP_565860.1|  [L=414]
Description: bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  161.1   1.1    2.5e-46  157.8   0.2    2.1  2  DFP           DNA / pantothenate metabolism flavoprotein
    2.9e-34  118.1   1.0    5.7e-34  117.1   1.0    1.5  1  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
        2.7    8.3   5.3         21    5.5   0.0    4.0  5  YqaH          Uncharacterized YqaH-like


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 ?    1.9   0.0     0.029   1.8e+02      33      55 ..      38      60 ..      29     104 .. 0.77
   2 !  157.8   0.2   4.3e-50   2.5e-46       3     186 .]     198     377 ..     196     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.029
                                  HHHHHHHHHTT-EEEEEE-S-SS CS
                           DFP 33 yalAeaaaarGaeVtlvsgpvsl 55
                                  ++lA+++++ Ga+V  v ++ + 
  gi|91773168|ref|YP_565860.1| 38 IELARELIRNGADVYGVMSEAAQ 60
                                  579************99998543 PP

  == domain 2  score: 157.8 bits;  conditional E-value: 4.3e-50
                                   T-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT- CS
                           DFP   3 gkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkea 83 
                                   gkkvl+t+G+T E+iDp+R+i+NrSSG++G ++A ++++rGa+Vt+v+   +l+   g++ + vesa +m +a+ ++l++ 
  gi|91773168|ref|YP_565860.1| 198 GKKVLITSGATAESIDPIRIITNRSSGTTGREIALEFYRRGADVTVVHKG-KLDLD-GIREILVESAGQMVDATLKELEHD 276
                                   89*********************************************976.45544.9*****************999766 PP

                                   .SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HHHHHHHHHHHT CS
                           DFP  84 .divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....ellenareklerk 159
                                    d++i+aAA++Dy+++   ++Kik    + +++l++++++++++e+ +++ +   l+GF+ae      el+++a++ +++ 
  gi|91773168|ref|YP_565860.1| 277 yDMLISAAAISDYTIDA-MDDKIKS---GGDISLKFRSTRKLIREV-RDAYPYISLIGFKAEAYisedELIARAKDSMKDA 352
                                   6**************85.788**96...4469**************.56667767*******522456************* PP

                                   T-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                           DFP 160 gldlivaNdvskeeagfgsdenevtll 186
                                   +ld++vaN+v+++  g+g+ +n+v+++
  gi|91773168|ref|YP_565860.1| 353 DLDMVVANEVGTS--GMGTIDNDVYII 377
                                   ***********87..********9986 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   1.0   9.6e-38   5.7e-34       1     155 [.      22     188 ..      22     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 9.6e-38
                                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESEEEEE CS
                  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadllvia 71 
                                   k i+l++TGs++a+ ++el ++L+++g++v  v+++aA+++i+k+ l+ a+         ++++h+++   +  adll+ia
  gi|91773168|ref|YP_565860.1|  22 KTIVLAVTGSIGAVRVIELARELIRNGADVYGVMSEAAQHIIHKDALHYATghevitdLAGEVEHVKFcgaEGCADLLLIA 102
                                   679****************************************9966666688899998899999999886779******* PP

                                   EEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHHH.T................GHHHHH CS
                  Flavoprotein  72 PasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekle.egvtvikPsegdigkgkmaeiee 149
                                   Pa+ant++k+a G+ d+++t+++    ++  p++i+Pam+ +mye+p++++n++kl+   + +++P    +g++k+a+ e+
  gi|91773168|ref|YP_565860.1| 103 PATANTIGKMAVGVDDTPVTTFATTaiGSGIPVIIVPAMHNSMYEHPAVMENIDKLKgWDISFVGPH-LSEGIAKIASNEQ 182
                                   *******************999944479****************************76889*****9.8889999999999 PP

                                   HHHHHC CS
                  Flavoprotein 150 ivgkil 155
                                   iv  + 
  gi|91773168|ref|YP_565860.1| 183 IVLAVE 188
                                   987665 PP

>> YqaH  Uncharacterized YqaH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.92   5.5e+03      65      84 ..      35      54 ..      32      58 .. 0.72
   2 ?    5.5   0.0    0.0034        21      68      86 ..     228     246 ..     203     248 .. 0.85
   3 ?    2.0   0.2     0.043   2.6e+02      18      54 ..     259     292 ..     251     310 .. 0.71
   4 ?   -1.0   0.1      0.38   2.3e+03      17      42 ..     334     358 ..     331     364 .. 0.84
   5 ?   -3.3   0.0       1.9   1.2e+04      22      35 ..     391     404 ..     387     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.92
                          YqaH 65 vrLyeiaskfakrGlnvsvv 84
                                  vr+ e+a ++ ++G +v  v
  gi|91773168|ref|YP_565860.1| 35 VRVIELARELIRNGADVYGV 54
                                  77778888888888777655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0034
                          YqaH  68 yeiaskfakrGlnvsvvkr 86 
                                    eia++f +rG +v+vv++
  gi|91773168|ref|YP_565860.1| 228 REIALEFYRRGADVTVVHK 246
                                   69**************986 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.043
                          YqaH  18 iksaeeLvselLaealkegDfegaielagsivvlskD 54 
                                   ++sa ++v   L e   e+D++  i+ a +i + + D
  gi|91773168|ref|YP_565860.1| 259 VESAGQMVDATLKE--LEHDYDMLISAA-AISDYTID 292
                                   55666665555555..389***999955.56666654 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.38
                          YqaH  17 liksaeeLvselLaealkegDfegai 42 
                                    ++s +eL++    +++k+ D + ++
  gi|91773168|ref|YP_565860.1| 334 AYISEDELIAR-AKDSMKDADLDMVV 358
                                   58899999999.89999*99998766 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 1.9
                          YqaH  22 eeLvselLaealke 35 
                                   + L++e La+ +++
  gi|91773168|ref|YP_565860.1| 391 KRLIAEALADNIED 404
                                   67899999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3270.60
//
Query:       gi|91773169|ref|YP_565861.1|  [L=339]
Description: hypothetical protein Mbur_1188 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-14   54.5   0.0    2.7e-14   53.6   0.0    1.4  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    2.4e-07   31.1   0.2    1.2e-06   28.8   0.0    2.2  2  eRF1_2          eRF1 domain 2
    8.6e-06   26.1   0.0    2.4e-05   24.6   0.0    1.7  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.024   14.7   0.0    1.6  1  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
      0.048   13.3   5.4        0.1   12.3   5.4    1.6  1  LUC7            LUC7 N_terminus
      0.049   13.8   9.5       0.32   11.1   9.5    2.5  1  HR1             Hr1 repeat
      0.057   13.7   1.2       0.15   12.4   1.2    1.7  1  ATP-synt_DE     ATP synthase, Delta/Epsilon chain, long alpha
      0.071   13.6   0.1       0.25   11.9   0.1    1.9  1  Csd3_N          Csd3 N-terminal
       0.09   10.5   2.8       0.11   10.2   2.8    1.0  1  CobN-Mg_chel    CobN/Magnesium Chelatase
       0.18   11.5   2.5       0.22   11.2   0.8    2.1  2  DAGK_cat        Diacylglycerol kinase catalytic domain
        1.1    9.0   9.7        2.5    7.9   9.7    1.6  1  DUF724          Protein of unknown function (DUF724)
        3.7    6.8  10.2       0.33   10.2   5.0    1.8  2  HemX            HemX, putative uroporphyrinogen-III C-methylt


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 !   53.6   0.0   1.8e-17   2.7e-14       3      96 ..     210     307 ..     208     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.8e-17
                       acVLRF1   3 lgvllvrrggfavgvveggelv.askvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...vvl 79 
                                   + vl  ++g   +g+ +++++  +  v ++ v+ ++ +GG+Sq+Rf+R r++ + +++++v+ a+++ll +  ae   ++l
  gi|91773169|ref|YP_565861.1| 210 VCVLATHAGESLIGISSDKNIFdEDMVIRSSVKAKHTKGGFSQRRFERLRDEDISHHADKVRSALKDLLSNSIAEidmMFL 290
                                   6788888888889999966555266799*****************************************988888999*** PP

                       acVLRF1  80 gGdrslvaevledarla 96 
                                    Gd  l++ + ++ +l+
  gi|91773169|ref|YP_565861.1| 291 CGDIVLAEHIVDEMNLE 307
                                   ****9999999997765 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.7e+03      45     110 ..      82     147 ..      55     164 .. 0.68
   2 !   28.8   0.0   8.3e-10   1.2e-06      28      98 ..     237     306 ..     212     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                                   CHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEE CS
                        eRF1_2  45 rfeRlreekleeflkkvaeaankafllvdkdklkgiilagpgfvkeefldkdlldaelkkkviklv 110
                                   ++e l+++ ++e    ++e+++ +  +  ++ l+ i  +  +f+   + +k+++ +e ++k +  +
  gi|91773169|ref|YP_565861.1|  82 QLEELKNKGTNENSFTLIEEISPTIFEPYIERLASINSGNDSFITAYITHKQMQTNEIQTKLANHL 147
                                   556666666666666666666666556666677777777777777777777777777777665544 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 8.3e-10
                                   EE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEEEESSTHHHHHHHHHHH CS
                        eRF1_2  28 ievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiilagpgfvkeefldkdll 98 
                                   i +sv  Kh +Gg s+rrfeRlr+e + +  +kv +a+++  l++ + +++ ++l+g    +e+++d++ l
  gi|91773169|ref|YP_565861.1| 237 IRSSVKAKHTKGGFSQRRFERLRDEDISHHADKVRSALKDL-LSNSIAEIDMMFLCGDIVLAEHIVDEMNL 306
                                   6788889***************************9888776.889************99999988887765 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 ?   -2.5   0.0       3.8   5.7e+03       1      32 [.     109     140 ..     109     158 .. 0.63
   2 !   24.6   0.0   1.6e-08   2.4e-05       3     107 ..     197     303 ..     196     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.8
                baeRF_family10   1 PylapLlealdeyerygvvlvdreraRlfevy 32 
                                   Py++ L+ +   ++ +  +++ ++++   e++
  gi|91773169|ref|YP_565861.1| 109 PYIERLASINSGNDSFITAYITHKQMQTNEIQ 140
                                   77777777777777777777766665554444 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.6e-08
                baeRF_family10   3 lapLlealdeyerygvvlvdreraRlfevylgelee.veevegevpgrtktggwksqdrfqrreeeqaerhlkevAellak 82 
                                   ++pL+++l +   ++v+ +++++  +   +   +    +++++ v+ ++ +gg  sq+rf+r ++e + +h+++v  +l++
  gi|91773169|ref|YP_565861.1| 197 VEPLTKLLAREMTVCVLATHAGESLIGISSDKNIFDeDMVIRSSVKAKHTKGGF-SQRRFERLRDEDISHHADKVRSALKD 276
                                   789********************9999888888766266677777767778888.************************** PP

                baeRF_family10  83 lleerg..verlvlgGdeeetaalldr 107
                                   ll+++   +++ +l+Gd   +++++d 
  gi|91773169|ref|YP_565861.1| 277 LLSNSIaeIDMMFLCGDIVLAEHIVDE 303
                                   ***987669999999998877777765 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 ?   14.7   0.0   1.6e-05     0.024       3     107 ..     210     316 ..     208     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                 baeRF_family2   3 lvvevDrtGadltlvdaggeeeeetveGghdpvhkvraggwshrryqrraeeswerNaeavAeevdrlvres..gaelVvl 81 
                                   ++v++ ++G  l   +++++  +e++  ++    k  +gg s+rr++r  +e + + a++v  ++++l   s  + ++ +l
  gi|91773169|ref|YP_565861.1| 210 VCVLATHAGESLIGISSDKNIFDEDMVIRSSVKAKHTKGGFSQRRFERLRDEDISHHADKVRSALKDLLSNSiaEIDMMFL 290
                                   6777778888888888777777888888888778888999*****************************997225579*** PP

                 baeRF_family2  82 aGDvrarsllrdeLpervrelvveve 107
                                   +GD+   + ++de+  ++  +v  ++
  gi|91773169|ref|YP_565861.1| 291 CGDIVLAEHIVDEMNLEIPLMVRNID 316
                                   ***98888888887777666665555 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.4   6.8e-05       0.1     100     163 ..      41     104 ..       5     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                                   XXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          LUC7 100 iqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelgeeGkVdeaqklmkevee 163
                                    +  k rle+++++++++ +ak++ +++l+e + ++e+l  + eel ++G  +++ +l++e+  
  gi|91773169|ref|YP_565861.1|  41 MEIDKTRLEKNENNTKKAIAAKQEAEQKLNEATVRVETLSYQLEELKNKGTNENSFTLIEEISP 104
                                   45568999999999999999999***********************************999864 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.5   0.00021      0.32      32      64 ..      53      89 ..       2      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                           HR1 32 qnkk....vrqeaeselsesnskielLreqLeelqas 64
                                  +n k    ++qeae++l+e+  ++e L  qLeel+++
  gi|91773169|ref|YP_565861.1| 53 NNTKkaiaAKQEAEQKLNEATVRVETLSYQLEELKNK 89
                                  333336789*************************985 PP

>> ATP-synt_DE  ATP synthase, Delta/Epsilon chain, long alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.2   9.8e-05      0.15       6      24 ..      56      74 ..      54      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.8e-05
                                  HHHHHHHHHHHHHHHHHHH CS
                   ATP-synt_DE  6 erAeeAkerAeerLeeasd 24
                                  ++A +Ak++Ae++L+ea+ 
  gi|91773169|ref|YP_565861.1| 56 KKAIAAKQEAEQKLNEATV 74
                                  6899************965 PP

>> Csd3_N  Csd3 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.25      14      60 ..     134     180 ..     127     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                        Csd3_N  14 leknnipeklyynldeedkellseiragvkyyelrddkgellqalip 60 
                                   +++n+i++kl   ld++  +ll+ i++++ y   +d+   + ++++p
  gi|91773169|ref|YP_565861.1| 134 MQTNEIQTKLANHLDQDTLQLLKKINTNTGYVLFYDNMKLVCEVIVP 180
                                   89*********************************988877787775 PP

>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.8   7.2e-05      0.11     500     649 ..      11     156 ..       4     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.2e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel 500 laeLeelideYeeaesldperlkalreqilelveelnldkdlg.......leeakeeeeeefeellekldgyleelkeaqi 573
                                   +++L++  ++Y   e+l++e  k +++ +   + +++l+k+ +       +++++e++ +e +  +e l+ +leelk++  
  gi|91773169|ref|YP_565861.1|  11 VENLNSIFNRYSGKEKLENEIEKLQSHLLEMEIDKTRLEKNENntkkaiaAKQEAEQKLNEATVRVETLSYQLEELKNKGT 91 
                                   6789999999**9999966544544556667899999988777788887633334444455555599************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel 574 rdglhilGeapegeqlvdlvvailrleneegesltealaealgldldeleeksekelrtagdalealeeeaeelve 649
                                   ++  ++l e  + +  + ++  ++++++++++ +t+ + ++ +++++e+++k  ++          l++ + +l++
  gi|91773169|ref|YP_565861.1|  92 NENSFTLIEEISPTIFEPYIERLASINSGNDSFITAYITHK-QMQTNEIQTKLANH----------LDQDTLQLLK 156
                                   ************************88766665555555555.45554433333333..........3333333333 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   0.00015      0.22       5      52 ..      17      64 ..      13      89 .. 0.79
   2 ?   -1.8   0.0       1.5   2.2e+03      26      52 ..     129     159 ..     121     167 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                  EE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHH CS
                      DAGK_cat  5 ivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeak 52
                                  i+N+ sGk+k e++++k++++l e +++ +  e +e++  k++a++ +
  gi|91773169|ref|YP_565861.1| 17 IFNRYSGKEKLENEIEKLQSHLLEMEIDKTRLEKNENNTKKAIAAKQE 64
                                  89********************99999666555555666666654433 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                   HHHCTCEEEEEE--STTH....HHHHHHHHH CS
                      DAGK_cat  26 leeagvelelieteepgd....akelakeak 52 
                                   +++++++++ i+t+ +++      +l+k+++
  gi|91773169|ref|YP_565861.1| 129 ITHKQMQTNEIQTKLANHldqdTLQLLKKIN 159
                                   5566666777777766663333455555555 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   9.7    0.0017       2.5     116     178 ..      15      77 ..       1      88 [. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                        DUF724 116 kkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledve 178
                                   ++i +  s k+kle+ei++l++  le+e  +++l +++++ +k ia+ +  ++kl+e++ +ve
  gi|91773169|ref|YP_565861.1|  15 NSIFNRYSGKEKLENEIEKLQSHLLEMEIDKTRLEKNENNTKKAIAAKQEAEQKLNEATVRVE 77 
                                   4677888999999***************99999999999999999999999999999888776 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.0   0.00022      0.33      37     103 ..      24      90 ..       9     100 .. 0.72
   2 ?   -2.0   0.2       1.1   1.7e+03      25      44 ..     131     151 ..     121     163 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                          HemX  37 vaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgae 103
                                   +++l++++++l++ l ++e +k++ ++ e++ +++  + +++e++l++ + ++e+l+ ql++++++ 
  gi|91773169|ref|YP_565861.1|  24 KEKLENEIEKLQSHLLEMEIDKTRLEKNENNTKKAIAAKQEAEQKLNEATVRVETLSYQLEELKNKG 90 
                                   4677788888888888877777777777777777777777777777777777777777777777763 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                          HemX  25 lgqqqvqeltaev.aelqqql 44 
                                   ++q q +e +++  ++l+q++
  gi|91773169|ref|YP_565861.1| 131 HKQMQTNEIQTKLaNHLDQDT 151
                                   333333222222233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2665  (0.148642); expected 358.6 (0.02)
Passed bias filter:                     1001  (0.0558313); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 2474.70
//
Query:       gi|91773170|ref|YP_565862.1|  [L=196]
Description: hypothetical protein Mbur_1189 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.25   12.0   0.0    1.6  2  DUF3502   Domain of unknown function (DUF3502)
       0.74   10.0   5.5       0.44   10.8   0.8    2.3  2  DUF2508   Protein of unknown function (DUF2508)


Domain annotation for each model (and alignments):
>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.61   5.5e+03      51      84 ..      48      80 ..      28      85 .. 0.49
   2 ?   12.0   0.0   2.8e-05      0.25      58     113 ..     136     191 ..      97     196 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
                       DUF3502 51 vkefneeakaspalgFtfDsspvkteiaalsnvv 84
                                  ++++ e+a+ s  l  t+ s++++ e + +++ +
  gi|91773170|ref|YP_565862.1| 48 IEKMCEKAV-SENLLETISSEELSVECETCEECM 80
                                  222222222.333333455555555666665555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.8e-05
                       DUF3502  58 akaspalgFtfDsspvkteiaalsnvveeykkaletGlvDpeetlpkfneklkaaG 113
                                    k+s+ +   +D   ++ ++++l nv+  y + le G++D+e+ +  + +++++ G
  gi|91773170|ref|YP_565862.1| 136 DKYSKNVEGILDIPTLERQYSELLNVYYDYDSWLEGGIADMENDILALSKQIDSLG 191
                                   4557777778899999*******************************999999888 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3     0.046   4.1e+02      11      33 ..      37      59 ..      31      81 .. 0.68
   2 ?   10.8   0.8   4.9e-05      0.44       8      44 ..     114     151 ..     106     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.046
                       DUF2508 11 kkeedeeLleeIektkeelesak 33
                                  ++ ede L eeIek+ e+  s++
  gi|91773170|ref|YP_565862.1| 37 ERDEDEPLNEEIEKMCEKAVSEN 59
                                  45589999999998766555544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.9e-05
                       DUF2508   8 gklkkeedeeLleeIektkeelesakslfensvD.lsd 44 
                                    klk+ + e+L + + +++ ++++  +++e ++D +  
  gi|91773170|ref|YP_565862.1| 114 EKLKQIYSERLKTRLTELRYNIDKYSKNVEGILDiPTL 151
                                   39********************************6333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1532.14
//
Query:       gi|91773171|ref|YP_565863.1|  [L=267]
Description: ribosomal RNA methyltransferase RrmJ/FtsJ [Methanococcoides burtonii DSM 6242]
Scores for 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-56  188.7   0.0    2.4e-55  187.4   0.0    1.6  2  FtsJ             FtsJ-like methyltransferase
    6.4e-06   26.1   1.5    1.1e-05   25.3   1.5    1.4  1  TRAM             TRAM domain
    6.3e-05   22.9   0.0    0.00023   21.0   0.0    1.9  1  Methyltransf_23  Methyltransferase domain
    9.3e-05   22.3   0.1      0.002   17.9   0.0    2.4  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.022   15.5   0.2        3.7    8.3   0.1    2.8  2  Methyltransf_25  Methyltransferase domain
      0.043   13.7   0.1      0.081   12.8   0.1    1.5  1  NAD_binding_10   NAD(P)H-binding


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 !  187.4   0.0     8e-59   2.4e-55       1     176 [.      18     191 ..      18     192 .. 0.98
   2 ?   -1.7   0.0      0.89   2.6e+03     118     140 ..     224     247 ..     202     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 8e-59
                                   CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCH CS
                          FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekike 81 
                                   yrsR+ayKL +i+ek++++k+++t+vDlgaaPGgw +v+ +    +gk+v+vDl+ ++ ++gv+ti+gdit+ eti+ki e
  gi|91773171|ref|YP_565863.1|  18 YRSRAAYKLFQINEKHEVIKEDDTIVDLGAAPGGWLEVAKKIS--GGKIVGVDLRRIKEIEGVETIKGDITSDETIKKIIE 96 
                                   9**************************************8885..49********************************** PP

                                   CHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEEEEEEE-SS CS
                          FtsJ  82 alserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFekvsvvkPks 162
                                   +++e ++d+v++D ap+ sg+++ld++++++L  +ale+a k+lkp+g+f++k+f+g+ +++++ ++++ F + + + Pk+
  gi|91773171|ref|YP_565863.1|  97 LVGEGGADVVICDAAPNLSGNWSLDHARSIDLTTSALECAKKILKPKGHFIVKVFQGDMFKEYMDKVRESFTYTRAFSPKA 177
                                   ********************************************************************************* PP

                                   --CCG-EEEEEEEE CS
                          FtsJ 163 srsesseeflvcrg 176
                                   sr+es+e++++ ++
  gi|91773171|ref|YP_565863.1| 178 SRPESAEIYVIGKK 191
                                   **********9875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.89
                                   HCCHCCCCECCCEEEECCCH.CCC CS
                          FtsJ 118 lelalkllkpggtfvlkifr.gee 140
                                   + ++ + +k+g ++ +ki++ ++e
  gi|91773171|ref|YP_565863.1| 224 VVFMQDEVKKGENVRIKIVDvKPE 247
                                   556667889999999999885555 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.5   3.8e-09   1.1e-05       8      61 ..     203     253 ..     198     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.8e-09
                                   EEEEEEEE-.TTSEEEEEET.TEEEEETT-.-T..TEEEEEEEEEE-SSEEEEEE CS
                          TRAM   8 qeVlveglsksegegiGrtdngkvvfvpgd.lpgIGdfVeVkItkvkrqyLrGel 61 
                                    +V++++ +  +g+gi+ ++ ++vvf ++  ++  G+ V +kI +vk+ ++++ +
  gi|91773171|ref|YP_565863.1| 203 FDVTIKKIG-AKGNGIAFVE-DFVVFMQDEvKK--GENVRIKIVDVKPEFAFAIV 253
                                   68*******.**********.********9999..*****************987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   7.8e-08   0.00023      21     124 ..      37     155 ..      10     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.8e-08
               Methyltransf_23  21 raggrvLdiGcGtGillevlren.gfsvtgvDlspeaveiae......kakkaqkdqfdeqeaae.....pqgkfdlIvlr 89 
                                   +++  ++d+G++ G +lev+++  g +++gvDl+++  +++e      +    + + +    +++      +g  d++++ 
  gi|91773171|ref|YP_565863.1|  37 KEDDTIVDLGAAPGGWLEVAKKIsGGKIVGVDLRRI--KEIEgvetikG---DITSDE---TIKKiielvGEGGADVVICD 109
                                   556699**************776377*******976..44443344431...222222...22223334488899999998 PP

               Methyltransf_23  90 evlehvpdpp...........ellrqiatllkpgGylllseplasl 124
                                      +   ++            ++l +++++lkp G++++ ++  + 
  gi|91773171|ref|YP_565863.1| 110 AAPNLSGNWSldharsidlttSALECAKKILKPKGHFIVKVFQGDM 155
                                   887777777777888888888******************9986554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.6e-07     0.002       2     130 ..      37     171 ..      36     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.6e-07
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled.......ekf 75 
                                   +++ +++DlG++ G  + ++    ++++++vG+D       +       ++++ ve  +gdi++ e+ +++          
  gi|91773171|ref|YP_565863.1|  37 KEDDTIVDLGAAPGGWLEVAK--KISGGKIVGVDLR-----RI------KEIEGVETIKGDITSDET-IKKiielvgeGGA 103
                                   567788899999987765554..5788899999953.....23......346778888888888443.55566778889** PP

               Methyltransf_31  76 Dlilsnevl...........naladpdkileeiervlkpggilliedpr..llaelpakveeeskaye 130
                                   D+++++++              +    ++le +++ lkp+g++++  ++  + +e+ +kv+e+ ++ +
  gi|91773171|ref|YP_565863.1| 104 DVVICDAAPnlsgnwsldhaRSIDLTTSALECAKKILKPKGHFIVKVFQgdMFKEYMDKVRESFTYTR 171
                                   ******888888888888878899999*******************9998888999999999999763 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0012       3.7       1      31 [.      42      71 ..      42     144 .. 0.62
   2 ?    5.5   0.0    0.0095        28      24      66 ..     123     168 ..      97     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                  EEEET-TTSHHHHHHHCTSTSSEEEEEESSH CS
               Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDise 31
                                  ++dlG+ +G +++ + k  g +k++gvD+  
  gi|91773171|ref|YP_565863.1| 42 IVDLGAAPGGWLEVAKKISG-GKIVGVDLRR 71
                                  79*******99877776656.*******854 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0095
                                   EEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC..CGBSSSTTTEE CS
               Methyltransf_25  24 vtgvDiseemleaareraeeegl.nvefvqgda..edlpfedgsfD 66 
                                      +D++ ++le a++ ++ +g   v++ qgd+  e ++   +sf 
  gi|91773171|ref|YP_565863.1| 123 ARSIDLTTSALECAKKILKPKGHfIVKVFQGDMfkEYMDKVRESFT 168
                                   456999**********999988889999999995444666666665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.7e-05     0.081      32      73 ..      72     115 ..      65     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                   CHHHHCTTTCEEEE--TT-CCHHHHHHT.....T-SEEEES---TCC CS
                NAD_binding_10  32 laeleaeeglevvegdvtdvedlaealk.....gadaVvsalggggk 73 
                                   +   ++ eg+e+++gd+t+ e++++ ++     gad+V++ ++++ +
  gi|91773171|ref|YP_565863.1|  72 I---KEIEGVETIKGDITSDETIKKIIElvgegGADVVICDAAPNLS 115
                                   3...44579******************999999*******9955433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); 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:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2018.63
//
Query:       gi|91773172|ref|YP_565864.1|  [L=96]
Description: hypothetical protein Mbur_1191 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-38  128.8   1.7    6.9e-38  128.7   1.7    1.0  1  DUF211    Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
       0.13   11.8   0.2       0.15   11.6   0.2    1.1  1  MCR_beta  Methyl-coenzyme M reductase beta subunit, C-termina


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 !  128.7   1.7   7.7e-42   6.9e-38       2      88 ..       4      90 ..       3      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 7.7e-42
                                  EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEESS- CS
                        DUF211  2 irrlvLDvlkphepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaGkki 84
                                  irrlvLDvlkph+ps++ela kl+ ++gv gvni ++evD+ ten+kitieG+ni+y+ +++++e+lg+vihSiDev+aG+ +
  gi|91773172|ref|YP_565864.1|  4 IRRLVLDVLKPHHPSTIELAGKLSGVDGVMGVNIGLYEVDQRTENIKITIEGDNIEYDVVKQELEKLGAVIHSIDEVAAGSLL 86
                                  9********************************************************************************** PP

                                  ---- CS
                        DUF211 85 veev 88
                                  veev
  gi|91773172|ref|YP_565864.1| 87 VEEV 90
                                  **97 PP

>> 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 ?   11.6   0.2   1.7e-05      0.15      38      99 ..      33      92 ..      17      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                      MCR_beta 38 mGdavGaferahllglayqGlnannlvydlvkengkegtvGtvveslveraiedkvikvekk 99
                                  mG  +G +e  +        ++ +n+ yd+vk++ +   +G+v++s+ e a    ++++ ++
  gi|91773172|ref|YP_565864.1| 33 MGVNIGLYEVDQRTENIKITIEGDNIEYDVVKQELE--KLGAVIHSIDEVAAGSLLVEEVET 92
                                  8999*****99999999999************9988..89******9998877766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 780.55
//
Query:       gi|91773173|ref|YP_565865.1|  [L=212]
Description: hypothetical protein Mbur_1192 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   35.2   0.0    1.6e-08   35.0   0.0    1.3  1  PHP          PHP domain
    1.5e-05   24.6   0.0      6e-05   22.6   0.0    1.9  1  RNase_P_p30  RNase P subunit p30
  ------ inclusion threshold ------
      0.079   12.8   0.0       0.17   11.7   0.0    1.5  1  TetR_C_1     Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   2.7e-12   1.6e-08       1      74 [.       3      98 ..       3     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.7e-12
                                  EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT...HHHHHHHHHHH.HTTTTSEEEEEEE.............. CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx...... RF
                           PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf...gyvefykaakk.kykagikpiiGleayvaddse...... 73
                                  dlH+Ht +s   + + ++elv++a  +g+  i+iTDh+++     ++  +k+ak  ++  +i++i G+e++ +  ++      
  gi|91773173|ref|YP_565865.1|  3 DLHTHTIFSDG-ELI-PSELVRRAVTFGYRGIGITDHADFTnveHILPCIKKAKYmEEVMDIRIIPGVEITHVHPEKiasfak 83
                                  79******955.234.6***********************955533333344433334489********87777666566666 PP

                                  ............... CS
                                  ..............x RF
                           PHP 74 ..............k 74
                                                +
  gi|91773173|ref|YP_565865.1| 84 marelgaeiivvhgE 98
                                  655555555555550 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 !   22.6   0.0     1e-08     6e-05      11     145 ..      13     145 ..       2     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1e-08
                                   .......HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.HHHHHHHHH-- CS
                   RNase_P_p30  11 dskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpsklqrlskvrqkfd 91 
                                   ++  +s++++++ ++gy+g+ i+ + +  +++   +    ++++ + ++e+ ++++  +v+++   p+k+ + +k++++  
  gi|91773173|ref|YP_565865.1|  13 GELIPSELVRRAVTFGYRGIGITDHADFTNVEHILP----CIKKAKYMEEVMDIRIIPGVEITHVHPEKIASFAKMARELG 89 
                                   4555678999*****************665555544....5588899999999***************9988888887654 PP

                                   ..EEEEE......--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                   RNase_P_p30  92 ..llavr......PttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                     +++v+      P+    + aa+   dvDi+ ++       +++ +++++A+++g+ +Ei+
  gi|91773173|ref|YP_565865.1|  90 aeIIVVHgespvePVAPGTNAAAIACEDVDILAHPG------FITEEEAQMAADNGTCLEIT 145
                                   44998872222225566789999999********99......79****************97 PP

>> TetR_C_1  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.8e-05      0.17      29      74 ..     165     210 ..     157     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                                   HHHHHHT-SS--HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHH CS
                      TetR_C_1  29 larlfagtprlspnelrgmErlLrllrdaGlsdedavyalslisnF 74 
                                   +a++++ t+  sp+ l + E+ L++   aGl+d++a ++l    +F
  gi|91773173|ref|YP_565865.1| 165 GATMVVNTDTHSPENLITKETALKIAMGAGLTDSQAKKVLENSVRF 210
                                   899*********************************9998766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1368.71
//
Query:       gi|91773174|ref|YP_565866.1|  [L=197]
Description: hypothetical protein Mbur_1193 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1220.33
//
Query:       gi|91773175|ref|YP_565867.1|  [L=181]
Description: deoxyribonucleotide triphosphate pyrophosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-53  181.6   0.0    1.5e-53  181.5   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.0   8.6e-58   1.5e-53       2     187 .]       5     179 ..       4     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 8.6e-58
                                   EEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTBGGG CS
                    Ham1p_like   2 vfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLnglPGvy 80 
                                   vf+TgNkgK+ e+keila +++e+ +     ++ ++E q +++e +a+  a++ ae  + pv++dDsgL+++aLng+PG+y
  gi|91773175|ref|YP_565867.1|   5 VFVTGNKGKFGEAKEILAAKDIELIQN----KDGYPELQeDELEPIAAYGAKYCAEkLKHPVMVDDSGLFINALNGFPGPY 81 
                                   8****************8766666533....33445888799999**********846888******************** PP

                                   TTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT-SS CS
                    Ham1p_like  81 sarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpeegek 161
                                   sa ++     +  +++k+l+ +  +e+dr A f++v+++++p++e+ ++f+G+veGei++e+rg+ggfGyDpiF++ + ++
  gi|91773175|ref|YP_565867.1|  82 SAFVE-----EYLGNQKVLKLMG-DESDRAAVFKSVIGYCEPGGEP-VTFTGTVEGEIAHEERGSGGFGYDPIFEY-N-GN 153
                                   **994.....345789******8.5569**************6666.99***************************.4.68 PP

                                   BTTTS.CHHHHHHSHHHHHHHHHHHH CS
                    Ham1p_like 162 tfaelskeeknaiShRgkAlekllef 187
                                   tf+el +eekn++ShR++Al+k+ ++
  gi|91773175|ref|YP_565867.1| 154 TFGELGAEEKNKMSHRKRALDKFFDW 179
                                   ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 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:                        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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1136.14
//
Query:       gi|91773176|ref|YP_565868.1|  [L=190]
Description: O-sialoglycoprotein endopeptidase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-08   33.2   0.0    0.00049   20.1   0.0    2.2  2  APH             Phosphotransferase enzyme family
    7.5e-08   32.2   0.0    1.1e-07   31.7   0.0    1.4  1  RIO1            RIO1 family
    4.6e-05   22.9   0.0    0.00057   19.3   0.0    2.1  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    8.4e-05   22.1   0.0    9.9e-05   21.8   0.0    1.3  1  Pkinase         Protein kinase domain
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.015   14.6   0.0    1.3  1  EcKinase        Ecdysteroid kinase
      0.027   13.8   0.0      0.028   13.7   0.0    1.3  1  Pkinase_Tyr     Protein tyrosine kinase
      0.041   13.5   0.0      0.082   12.5   0.0    1.5  2  Choline_kinase  Choline/ethanolamine kinase


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 !   11.7   0.0   6.9e-05      0.18      33     107 ..      37     100 ..      10     102 .. 0.86
   2 !   20.1   0.0   1.9e-07   0.00049     167     196 ..     102     128 ..     100     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                                   -HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHC CS
                           APH  33 aaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhq 107
                                    +e++r+e++l+   ++ gvp+P +++       i+     +ey++g+++       +++ ++  +g ++++lh+
  gi|91773176|ref|YP_565868.1|  37 RKERTRAEARLMSDARRCGVPTPIIHD-------IYDFTIEMEYIDGKPVKY----VIDETICKLMGKLIGRLHS 100
                                   4678899999********999988888.......8999999*********99....7999**************7 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.9e-07
                                   EEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                           APH 167 vllHgDlhpgNllvdpddgrvtGviDfeda 196
                                   +++HgDl + N+l    ++r+ ++iDf+++
  gi|91773176|ref|YP_565868.1| 102 GIIHGDLTTSNMLYS--GDRI-YLIDFGLS 128
                                   69*************..9**9.*****986 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   4.2e-11   1.1e-07      49     150 ..      35     126 ..      15     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.2e-11
                                   HHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEE CS
                          RIO1  49 klvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvH 129
                                   ++ k  ++ E r ++ +++ gvp P   ++ +  + me+i+  g +++ + d +    +     +++ +++  ++  g++H
  gi|91773176|ref|YP_565868.1|  35 RIRKERTRAEARLMSDARRCGVPTPIIHDIYDFTIEMEYID--GKPVKYVIDET----IC----KLMGKLIGRLHSGGIIH 105
                                   566778999********************************..99888777666....44....455555557889***** PP

                                   SS-STTSEEEETTEEEE--GT CS
                          RIO1 130 aDLSeyNvlvdedkvviIDvs 150
                                   +DL   N+l++ d++++ID++
  gi|91773176|ref|YP_565868.1| 106 GDLTTSNMLYSGDRIYLIDFG 126
                                   *******************97 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.059   1.5e+02      54      76 ..      37      59 ..      30      74 .. 0.85
   2 !   19.3   0.0   2.2e-07   0.00057     120     170 ..      84     129 ..      68     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.059
                           Kdo 54 grtravrEfrllkrLeeagvavp 76
                                   + r ++E rl+   ++ gv++p
  gi|91773176|ref|YP_565868.1| 37 RKERTRAEARLMSDARRCGVPTP 59
                                  5678999*************998 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.2e-07
                           Kdo 120 krallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkar 170
                                    +++ k  g+li +lh+ g+ H+dl   n+l   +     +i+liD+  ++
  gi|91773176|ref|YP_565868.1|  84 DETICKLMGKLIGRLHSGGIIHGDLTTSNMLYSGD-----RIYLIDFGLSY 129
                                   56788899***********************9988.....5******7665 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   3.9e-08   9.9e-05     107     146 ..      91     129 ..      29     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.9e-08
                                   HHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSE CS
                       Pkinase 107 ilegleylHskgiiHrDlKpeNiLidekgelKitDFGlak 146
                                   + + +  lHs giiH Dl ++N+L++  + + ++DFGl+ 
  gi|91773176|ref|YP_565868.1|  91 MGKLIGRLHSGGIIHGDLTTSNMLYS-GDRIYLIDFGLSY 129
                                   44455679******************.778********85 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     6e-06     0.015     217     264 ..     103     148 ..      83     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                      EcKinase 217 lnHGDlwvnNimfkydeegepedvilvDFQlsry....gSpalDLlyflyts 264
                                   + HGDl ++N++++ d      +++l+DF ls++     S  +D+++++ t 
  gi|91773176|ref|YP_565868.1| 103 IIHGDLTTSNMLYSGD------RIYLIDFGLSYVdgsvESRGVDIHVLFQTL 148
                                   78***********887......79*******986222268889999988775 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.028     119     151 ..      98     129 ..      31     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                   HHHTTEEEST-SGGGEEEEETTEEEE-STTTHE CS
                   Pkinase_Tyr 119 LeskklvHrdlaarNvLlsenkvvkisDfGLar 151
                                   L+s  ++H dl++ N+L s ++ + + DfGL+ 
  gi|91773176|ref|YP_565868.1|  98 LHSGGIIHGDLTTSNMLYS-GDRIYLIDFGLSY 129
                                   89999***********999.7788899****86 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.92   2.4e+03      50      81 ..      72     101 ..      66     104 .. 0.76
   2 ?   12.5   0.0   3.2e-05     0.082     149     187 ..     105     145 ..      81     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.92
                                   E--TCEE--TTGGGCHHHHHHHHHHHHHHTTC CS
                Choline_kinase  50 efiesrtlstedlrepeiskkiAkklaelHsl 81 
                                   e+i++++++   + +++i k  +k +++lHs 
  gi|91773176|ref|YP_565868.1|  72 EYIDGKPVK--YVIDETICKLMGKLIGRLHSG 101
                                   677777654..467788999999999999985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.2e-05
                                   -S--SGGGEEE.-CTTEEEE--GTT-....EEEEHHHHHHHHH CS
                Choline_kinase 149 HnDlqegNillnkeekklvlIDFEYa....gynyrgfDlanhf 187
                                   H Dl  +N+l+  + ++++lIDF  +    ++  rg D+   f
  gi|91773176|ref|YP_565868.1| 105 HGDLTTSNMLY--SGDRIYLIDFGLSyvdgSVESRGVDIHVLF 145
                                   9**********..**********76522334556666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1089.55
//
Query:       gi|91773177|ref|YP_565869.1|  [L=335]
Description: DNA-binding/iron metalloprotein/AP endonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete 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-90  301.5   0.0    7.8e-90  301.2   0.0    1.0  1  Peptidase_M22   Glycoprotease family
     0.0076   16.0   0.0       0.04   13.6   0.0    1.9  2  Carbam_trans_N  Carbamoyltransferase N-terminus


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 !  301.2   0.0   8.7e-94   7.8e-90       2     271 .]      24     295 ..      23     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 301.2 bits;  conditional E-value: 8.7e-94
                                   CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHH...TSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHH CS
                 Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaea...glsledldaIavtkgPGlftgLrvGvsfAkglala 79 
                                   v+a+v+++++   +k+GG++P++a+++H+ +   +ie++l+e    g s+e++daIa+++gPGl+ +Lr +++ A++lal+
  gi|91773177|ref|YP_565869.1|  24 VIAEVTETYR---PKTGGIHPREAAQHHALHASDVIERLLKEYrdkGHSPENIDAIAFSQGPGLGACLRTVATSARALALS 101
                                   6778888887...99**************************998889********************************** PP

                                   CT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHH CS
                 Peptidase_M22  80 lnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkiek 160
                                   l++PlvgVnh+++h++ +r +++  +Pvvl+vsGg++qv++ ++g+y+i+getld+ +g+aldk+ar  gl +pggpk+e+
  gi|91773177|ref|YP_565869.1| 102 LDIPLVGVNHCIGHVEIGRWKTPAVDPVVLYVSGGNSQVLAHRAGKYRIFGETLDIGIGNALDKFARGAGLTHPGGPKVEE 182
                                   *******************9987789****************99************************************* PP

                                   HHCTC.S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHH CS
                 Peptidase_M22 161 lakeg.kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakelvilGGvaankrL 239
                                   +a+++ +++++p+++kg+dfsfsGl ta++ +l++ + ed+++sfqe+++++lve+teral++++++e++++GGv+an rL
  gi|91773177|ref|YP_565869.1| 183 YARKAtNYVKMPYVVKGMDFSFSGLSTAATDALKDnSLEDVCYSFQENAFAMLVEVTERALAHTGKSEVLLAGGVGANMRL 263
                                   *****899*************************7756******************************************** PP

                                   HHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                 Peptidase_M22 240 realeeeaeelglkliiPplkyctdnaamiaw 271
                                   re+l  ++e++g+++++P+ +++ dn+amia+
  gi|91773177|ref|YP_565869.1| 264 REMLDLMCEDRGASFYVPERRFMGDNGAMIAY 295
                                   ******************************97 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0     0.062   5.6e+02       2      69 ..       4      80 ..       3      85 .. 0.60
   2 !   13.6   0.0   4.4e-06      0.04     266     323 ..     218     280 ..     185     294 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.062
                Carbam_trans_N  2 ilGikltlflHDgavalvddgklvaaveeErltr..ikrdqk......lpklkaidyaleea...gvelsdiDqivfde 69
                                  +lGi +t      ++a+vd+ +++a v e  + +    + ++      l   + i+  l+e+   g ++++iD i+f +
  gi|91773177|ref|YP_565869.1|  4 VLGIEGT--AWNLSAAIVDEDDVIAEVTETYRPKtgGIHPREaaqhhaLHASDVIERLLKEYrdkGHSPENIDAIAFSQ 80
                                  6788877..5566777888888888876654332112233334455555555666666665333388888888888865 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.4e-06
                Carbam_trans_N 266 e...dlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNs..allesglFedvwv 323
                                   +   d+  s+q+    ++vev++ + ++++     laGGv++N+ l     l+ +    + +v
  gi|91773177|ref|YP_565869.1| 218 NsleDVCYSFQENAFAMLVEVTERALAHTGKSEVLLAGGVGANMRLREmlDLMCEDRGASFYV 280
                                   23449**************************************98864113455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2005.76
//
Query:       gi|91773178|ref|YP_565870.1|  [L=87]
Description: hypothetical protein Mbur_1197 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 558.70
//
Query:       gi|91773179|ref|YP_565871.1|  [L=358]
Description: hypothetical protein Mbur_1198 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   14.2   0.1       0.15   12.9   0.1    1.6  1  Big_9     Bacterial Ig domain
       0.11   12.5   0.0       0.27   11.3   0.0    1.7  1  Wzt_C     Wzt C-terminal 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 ?   12.9   0.1   1.6e-05      0.15      19      68 ..     285     343 ..     274     345 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                         Big_9  19 ddsvtvt.edsv...........landtdpdgdaltvtsltvtlvtapanGtvtinadgtlt 68 
                                   dd vt++ ed++           l+ndt  d  +l  +++   +vt++++G++t+++dg+++
  gi|91773179|ref|YP_565871.1| 285 DDYVTIDvEDESsfslgervflyLNNDTWTDTKDLGPEHF---VVTGASQGKFTLTDDGRVS 343
                                   4556665444445666666789999***********9998...5789************875 PP

>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     3e-05      0.27      62     114 ..     105     158 ..      57     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
                         Wzt_C  62 evfgtntelekksfeleelkagervevefefkl.pLapGeYlltvaledrdgee 114
                                   +++g n++   +++ l el++g+++ ++f+ k+ +L +GeY l++  + + ge+
  gi|91773179|ref|YP_565871.1| 105 YICGVNSRVRLNNDVLVELHPGQSLNATFNSKCwNLDNGEYILSAVYHTSRGES 158
                                   567777744433355999*************544**********9886666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2329.43
//
Query:       gi|91773180|ref|YP_565872.1|  [L=181]
Description: hypothetical protein Mbur_1199 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00049   19.9   0.0    0.00074   19.4   0.0    1.2  1  MarR_2          MarR family
     0.0016   18.0   0.4     0.0035   16.9   0.3    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0021   18.0   0.1     0.0031   17.4   0.1    1.3  1  MarR            MarR family
     0.0042   16.9   0.1     0.0087   15.9   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.014   15.2   0.0       0.02   14.7   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
       0.04   13.8   0.2       0.16   11.9   0.0    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
      0.067   13.2   0.0       0.11   12.5   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.078   12.7   0.1        0.1   12.3   0.1    1.1  1  UNC-93          Ion channel regulatory protein UNC-93
       0.12   12.2   0.2       0.12   12.2   0.2    1.6  2  TFIIE_alpha     TFIIE alpha subunit
       0.13   12.5   0.0        0.2   11.9   0.0    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.1e-07   0.00074       5      54 ..     114     162 ..     110     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.1e-07
                                   HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2   5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                   + ++     + + +gr + ++el+  l+ sk+ vsril  L+++G v ++
  gi|91773180|ref|YP_565872.1| 114 GDERKTVEIILNKGGR-ILQNELVNSLDFSKAKVSRILINLEKRGIVKKS 162
                                   5555555566666665.9*****************************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3     2e-06    0.0035      11      48 .]     123     160 ..     116     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                        HTH_24  11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   +L k +ri q+eL   l+ S++ v+r l +Le+ G++k
  gi|91773180|ref|YP_565872.1| 123 ILNKGGRILQNELVNSLDFSKAKVSRILINLEKRGIVK 160
                                   4566778*****************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.7e-06    0.0031      10      51 ..     121     163 ..     112     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.7e-06
                                   HHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  10 rilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                   +i+ ++g+ + + eL + l  sk+ v+r+l  Lek+G +++sk
  gi|91773180|ref|YP_565872.1| 121 EIILNKGGrILQNELVNSLDFSKAKVSRILINLEKRGIVKKSK 163
                                   5666666647777**************************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 !   15.9   0.1   4.9e-06    0.0087      25      56 ..     132     163 ..     112     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                                   HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB  25 adeiaeelgvprskvYevLrsLedkGlVerek 56 
                                    +e+ + l+ +++kv ++L +Le++G+V+++k
  gi|91773180|ref|YP_565872.1| 132 QNELVNSLDFSKAKVSRILINLEKRGIVKKSK 163
                                   5789999**********************987 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 ?   14.7   0.0   1.1e-05      0.02      22      50 ..     133     161 ..     108     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  22 selArrtglpkStvhRlLqtLvelGyveq 50 
                                    el + ++ +k++v+R+L  L+++G+v++
  gi|91773180|ref|YP_565872.1| 133 NELVNSLDFSKAKVSRILINLEKRGIVKK 161
                                   6999***********************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.87   1.6e+03       7      21 ..     108     122 ..     107     124 .. 0.82
   2 ?   11.9   0.0   8.7e-05      0.16      20      47 .]     134     161 ..     132     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.87
                                   HHHHHTTSSEEHHHH CS
                         HTH_5   7 ILklLaegelcvcel 21 
                                   ILk+L   e++  e+
  gi|91773180|ref|YP_565872.1| 108 ILKALTGDERKTVEI 122
                                   99***9999877666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.7e-05
                                   HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  20 elaeelglsqstvShHLkkLreaGLVek 47 
                                   el++ l+ s+++vS+ L  L++ G+V+k
  gi|91773180|ref|YP_565872.1| 134 ELVNSLDFSKAKVSRILINLEKRGIVKK 161
                                   99************************87 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   0.0   6.1e-05      0.11      22      55 ..     130     163 ..     107     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.1e-05
                                   HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglisrgr 55 
                                   + q el + l  +   vsril  L+++g++++++
  gi|91773180|ref|YP_565872.1| 130 ILQNELVNSLDFSKAKVSRILINLEKRGIVKKSK 163
                                   56888889999999****************9653 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 ?   12.3   0.1   5.8e-05       0.1      45     115 ..       9      80 ..       5      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-05
                        UNC-93  45 iiyavftvanlvapsvvdlltakwalvigallyaifqlgF.lllnkyylyissa.llGvgaallwtgqGsyLs 115
                                   ++  +f ++++v+ +v+ + t+ + ++ g ++  i+ + +   +n++yl++ssa l G+  al+   +G + +
  gi|91773180|ref|YP_565872.1|   9 VTIGIFIISSIVVINVLLVNTPVVIQIEGDAF-KIVDIPYkYTINEAYLLLSSAfLCGFCLALILLDNGIFQT 80 
                                   6678999******9999999999888888765.555555525679999999999356*******999997765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.9   6.9e+03       9      26 ..      12      29 ..       8      33 .. 0.72
   2 ?   12.2   0.2   6.7e-05      0.12       6      59 ..     108     161 ..     104     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                                  HCS-HHHHHHHHHHHCTT CS
                   TFIIE_alpha  9 kfygeeavlvldvLlekg 26
                                  +++ ++ + v++vLl + 
  gi|91773180|ref|YP_565872.1| 12 GIFIISSIVVINVLLVNT 29
                                  566677888999998775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.7e-05
                                   HHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                   TFIIE_alpha   6 vvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvky 59 
                                   +++   g+e + v  +L + g +  ++l + l + + ++ ++L +L + ++vk 
  gi|91773180|ref|YP_565872.1| 108 ILKALTGDERKTVEIILNKGGRILQNELVNSLDFSKAKVSRILINLEKRGIVKK 161
                                   456677888888888888899****************************99985 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 ?   11.9   0.0   0.00011       0.2      22      58 ..     129     165 ..     119     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                Fe_dep_repress  22 vvktkdlaerLnvspssVsemlkkLekdGyveyekyk 58 
                                    + + +l   L+ s++ Vs  l  Lek G v+ +ky+
  gi|91773180|ref|YP_565872.1| 129 RILQNELVNSLDFSKAKVSRILINLEKRGIVKKSKYG 165
                                   5677889999***********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1194.80
//
Query:       gi|91773181|ref|YP_565873.1|  [L=288]
Description: hypothetical protein Mbur_1200 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.5   0.8       0.05   13.1   0.2    2.0  2  TcfC      E-set like domain


Domain annotation for each model (and alignments):
>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.8e-06      0.05      43      64 ..     124     145 ..     122     148 .. 0.88
   2 ?   -2.3   0.0      0.18   3.3e+03      46      58 ..     258     270 ..     257     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-06
                          TcfC  43 sGiYeveirvyengqvvrteqq 64 
                                   +G+Y+ve+++y+n+qv+ ++ +
  gi|91773181|ref|YP_565873.1| 124 TGTYDVEVKLYQNEQVIDEKVT 145
                                   7***************998866 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.18
                          TcfC  46 Yeveirvyengqv 58 
                                   Y v+++v  n+q 
  gi|91773181|ref|YP_565873.1| 258 YLVTVEVNWNEQD 270
                                   99***99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1923.72
//
Query:       gi|91773182|ref|YP_565874.1|  [L=644]
Description: HEAT repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-104  341.2  21.5      7e-19   68.0   0.4    8.8  9  HEAT_2          HEAT repeats
    7.1e-62  199.8  29.1    3.7e-06   27.1   0.0   14.7 15  HEAT_PBS        PBS lyase HEAT-like repeat
    1.9e-46  152.1   1.6    0.00011   22.1   0.0   14.7 15  HEAT            HEAT repeat
    6.4e-26   90.4  17.2      0.019   15.5   0.0   14.0 15  HEAT_EZ         HEAT-like repeat
      3e-22   77.9   3.8     0.0012   18.9   0.0   11.9 14  Arm             Armadillo/beta-catenin-like repeat
      8e-16   58.5   2.7      0.049   13.7   0.0    7.0  5  Cnd1            non-SMC mitotic condensation complex subunit 
    2.7e-11   42.6   0.2     0.0024   16.3   0.0    4.6  4  Vitellogenin_N  Lipoprotein amino terminal region
      2e-09   36.6   0.2    8.7e-05   21.3   0.0    3.7  2  Adaptin_N       Adaptin N terminal region
    3.9e-08   33.5   6.2        2.6    8.1   0.0    7.4  8  Aconitase_B_N   Aconitate B N-terminal domain
    0.00039   20.1   3.6       0.19   11.2   0.2    3.8  4  ERAP1_C         ERAP1-like C-terminal domain
      0.007   16.8   0.5        9.3    6.7   0.0    5.3  6  RasGEF_N_2      Rapamycin-insensitive companion of mTOR RasGE
  ------ inclusion threshold ------
      0.013   15.4   0.6        8.2    6.4   0.0    4.7  4  IBN_N           Importin-beta N-terminal domain
      0.015   15.3  10.7         11    6.2   0.1    7.0  7  UPF0147         Uncharacterised protein family (UPF0147)
      0.069   13.0   1.5         30    4.5   0.0    4.5  5  YmgB            Biofilm development protein YmgB/AriR
      0.069   11.9   2.8        8.2    5.1   0.0    3.2  3  API5            Apoptosis inhibitory protein 5 (API5)
       0.12   13.1   0.0         11    6.7   0.0    3.6  3  DUF2877         Protein of unknown function (DUF2877)
       0.13   12.9   2.2         89    3.8   0.0    5.7  8  Vac14_Fab1_bd   Vacuolar 14 Fab1-binding region
        0.2   11.7   2.3         19    5.4   0.1    3.3  3  TraW_N          Sex factor F TraW protein N terminal


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 !   33.6   0.0   3.7e-11   3.7e-08       6      79 ..      49     123 ..      45     128 .. 0.89
   2 ?    6.6   0.0      0.01        10       2      59 ..     109     165 ..     108     168 .. 0.85
   3 !   57.1   0.0   1.7e-18   1.7e-15       2      76 ..     170     243 ..     169     245 .. 0.95
   4 !   68.0   0.4     7e-22     7e-19      10      84 ..     241     315 ..     235     318 .. 0.92
   5 !   45.1   0.3   9.8e-15   9.8e-12       1      76 [.     325     401 ..     325     403 .. 0.95
   6 !   60.4   0.8   1.6e-19   1.6e-16       3      76 ..     391     465 ..     389     466 .. 0.92
   7 !   52.3   0.0   5.5e-17   5.5e-14       1      87 [.     453     538 ..     453     539 .. 0.96
   8 !   38.7   0.1   9.8e-13   9.7e-10       1      76 [.     515     592 ..     515     595 .. 0.92
   9 !   20.6   0.1   4.5e-07   0.00045      14      56 ..     594     638 ..     590     642 .. 0.58

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.7e-11
                        HEAT_2   6 qalendpdpevrraairaLgrignpealpaLvell..ededpavRraaaeaLgaigdpealpaLkellddddddvv 79 
                                   + + + +++ +r++ai +L +ig++++ ++L+ +l  ++e+  +R  aa+aL++ig   +++ L   l++ ++++v
  gi|91773182|ref|YP_565874.1|  49 EDI-KNENESIRQEAIGNLTKIGDEDSTDILTGILmdKNESNSIRISAADALAEIGKGGSISPLISVLQENNSALV 123
                                   556.78999************************8856668889**************************9999887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                        HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaig 59 
                                   ++L+++l +  + ++ +++ ++L ++g+p +  ++  +l++ +p+ R++    L  i+
  gi|91773182|ref|YP_565874.1| 109 SPLISVL-QENNSALVIEVSENLVQFGDPATEMLIYTFLDNGKPEFRANLMYVLCMIA 165
                                   6899999.78888999999999*******99999999999999999999877776555 PP

  == domain 3  score: 57.1 bits;  conditional E-value: 1.7e-18
                        HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddd 76 
                                   +++++ l n++d  +r++ +  L++++++++++aL+ +lede+++vRr+aa+ Lg ig++ a+p+L + + ++++
  gi|91773182|ref|YP_565874.1| 170 EYFIEKL-NSEDATTRINMAFILAEMADERTVDALIVALEDENRYVRRHAARGLGNIGNKNAIPSLIQVMSNTSE 243
                                   789999*.9************************************************************998876 PP

  == domain 4  score: 68.0 bits;  conditional E-value: 7e-22
                        HEAT_2  10 ndpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaAa 84 
                                   +++  evr +a++aLg+ig+++a++ L+++l+ded+ v   aa aLg++g++ea+paL+++l++d++ vv+e+A+
  gi|91773182|ref|YP_565874.1| 241 TSEPREVRSNAAIALGQIGDDDAVEPLIQMLKDEDWSVPSSAAIALGELGNSEAIPALTAALRRDEEFVVKESAI 315
                                   478889*****************************************************************9875 PP

  == domain 5  score: 45.1 bits;  conditional E-value: 9.8e-15
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvelled..edpavRraaaeaLgaigdpealpaLkellddddd 76 
                                   +d+L+ +l +d d+ v+++a+ aL  ig ++a+  L++lled  e+++ R+aaa +Lg ig+++a+  L ++l d+++
  gi|91773182|ref|YP_565874.1| 325 IDKLIDLL-DDNDKSVQKNAAYALRGIGGEKAIVPLIDLLEDsyEHEDARAAAASSLGTIGNKDAVLPLIQILEDKNE 401
                                   689*****.*******************************887899***************************99876 PP

  == domain 6  score: 60.4 bits;  conditional E-value: 1.6e-19
                        HEAT_2   3 aLlqalendpdpe.vrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddd 76 
                                   +L+q+le+  +pe +r+++ raL rig+++a + L+e l+de+p++R+aaa+aLg++gd++al+aL  +l d+++
  gi|91773182|ref|YP_565874.1| 391 PLIQILEDKNEPEtLRIRTTRALRRIGDERATKPLIESLKDENPDIREAAANALGEMGDESALDALILSLEDENW 465
                                   79****88666663799**************************************************99999887 PP

  == domain 7  score: 52.3 bits;  conditional E-value: 5.5e-17
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81 
                                   ldaL+  l +d+++ vr+ +++aL +++n++++  + ++l+de + vR++aa++Lg ig+++a+p L e+   +++ +v++
  gi|91773182|ref|YP_565874.1| 453 LDALILSL-EDENWRVRYSVVDALQKYDNKTVVLPISNMLDDEYWSVRKTAAQSLGTIGNQQAIPPLVEAISVEKEKDVKT 532
                                   58899999.9**********************************************************************9 PP

                        HEAT_2  82 aAaeaL 87 
                                     +++L
  gi|91773182|ref|YP_565874.1| 533 TMVRSL 538
                                   999887 PP

  == domain 8  score: 38.7 bits;  conditional E-value: 9.8e-13
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvelled..edpavRraaaeaLgaigdpealpaLkellddddd 76 
                                   +++L++a++  ++++v+ + +r+L +i+n ++ +++++ll+d  e   vR+aaa +L++ g+++a++ L + ++d++ 
  gi|91773182|ref|YP_565874.1| 515 IPPLVEAISVEKEKDVKTTMVRSLEDIDNGSSTDLFIRLLQDktEFLSVREAAAISLAKPGNEQAVDPLIQVMLDETQ 592
                                   689*****99******************************88324468*************************99876 PP

  == domain 9  score: 20.6 bits;  conditional E-value: 4.5e-07
                        HEAT_2  14 pevrraairaLgrignpealpaLvelleded..pavRraaaeaLg 56 
                                   +++r++a++aLgrig+ +a++aL ++ +d++   a R aa ea++
  gi|91773182|ref|YP_565874.1| 594 YNLRIEAAIALGRIGDYDAFDALSRISKDPNehFALRTAAEEAIA 638
                                   456666666666666666666666666665421345555555555 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.1   4.1e+03       2      21 ..      59      78 ..      58      80 .. 0.83
   2 !   10.2   0.0    0.0011       1.1       1      26 [.      91     116 ..      91     117 .. 0.94
   3 !   11.3   0.0   0.00046      0.46       2      27 .]     184     209 ..     183     209 .. 0.92
   4 !   21.2   0.0   2.9e-07   0.00029       1      25 [.     214     238 ..     214     240 .. 0.94
   5 !   27.1   0.0   3.7e-09   3.7e-06       1      27 []     247     273 ..     247     273 .. 0.98
   6 !   20.1   0.3   6.6e-07   0.00066       3      26 ..     280     303 ..     278     304 .. 0.92
   7 ?    0.5   0.0       1.4   1.4e+03       6      27 .]     314     334 ..     310     334 .. 0.85
   8 !   13.9   0.1   6.6e-05     0.065       1      27 []     339     365 ..     339     365 .. 0.95
   9 !   20.5   0.2   5.1e-07   0.00051       1      27 []     372     398 ..     372     398 .. 0.96
  10 !   12.9   0.0   0.00014      0.14       2      27 .]     406     431 ..     405     431 .. 0.92
  11 !   23.3   0.4     6e-08     6e-05       1      27 []     436     462 ..     436     462 .. 0.95
  12 ?   -0.5   0.0       2.9   2.9e+03       1      26 [.     467     492 ..     467     493 .. 0.72
  13 !   19.7   0.0   9.1e-07   0.00091       1      25 [.     498     522 ..     498     523 .. 0.95
  14 !   13.6   0.0   8.7e-05     0.087       1      27 []     563     589 ..     563     589 .. 0.94
  15 !   11.2   0.2   0.00051      0.51       1      25 [.     596     620 ..     596     640 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.1
                                  HHHHHHHHHHCTSGGGHHHH CS
                      HEAT_PBS  2 RraAakaLgqlgdeeaipaL 21
                                  R +A+  L ++gde++ ++L
  gi|91773182|ref|YP_565874.1| 59 RQEAIGNLTKIGDEDSTDIL 78
                                  77888889999999999888 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                   +R +Aa aL+++g   +i +L+ +Lq
  gi|91773182|ref|YP_565874.1|  91 IRISAADALAEIGKGGSISPLISVLQ 116
                                   599*********************98 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00046
                                   HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                   R + a+ L+++ de+ ++aL+ aL+d
  gi|91773182|ref|YP_565874.1| 184 RINMAFILAEMADERTVDALIVALED 209
                                   677799******************98 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHHHHHCTSGGGHHHHHHHC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                   vRr Aa++Lg++g + aip L+++ 
  gi|91773182|ref|YP_565874.1| 214 VRRHAARGLGNIGNKNAIPSLIQVM 238
                                   9*********************986 PP

  == domain 5  score: 27.1 bits;  conditional E-value: 3.7e-09
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   vR +Aa aLgq+gd++a+++L++ L+d
  gi|91773182|ref|YP_565874.1| 247 VRSNAAIALGQIGDDDAVEPLIQMLKD 273
                                   8************************98 PP

  == domain 6  score: 20.1 bits;  conditional E-value: 6.6e-07
                                   HHHHHHHHHCTSGGGHHHHHHHCT CS
                      HEAT_PBS   3 raAakaLgqlgdeeaipaLleaLq 26 
                                    +Aa aLg+lg  eaipaL +aL 
  gi|91773182|ref|YP_565874.1| 280 SSAAIALGELGNSEAIPALTAALR 303
                                   68********************95 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 1.4
                                   HHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   6 akaLgqlgdeeaipaLleaLqd 27 
                                   a aL +l     i+ L+ +L+d
  gi|91773182|ref|YP_565874.1| 314 AIALEKLDG-SGIDKLIDLLDD 334
                                   778888888.99********98 PP

  == domain 8  score: 13.9 bits;  conditional E-value: 6.6e-05
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   v+ +Aa+aL  +g e ai +L+ +L+d
  gi|91773182|ref|YP_565874.1| 339 VQKNAAYALRGIGGEKAIVPLIDLLED 365
                                   7889*********************98 PP

  == domain 9  score: 20.5 bits;  conditional E-value: 5.1e-07
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   +R+aAa +Lg++g ++a+ +L++ L+d
  gi|91773182|ref|YP_565874.1| 372 ARAAAASSLGTIGNKDAVLPLIQILED 398
                                   59***********************98 PP

  == domain 10  score: 12.9 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                   R + ++aL ++gde+a  +L+e L+d
  gi|91773182|ref|YP_565874.1| 406 RIRTTRALRRIGDERATKPLIESLKD 431
                                   77789*******************98 PP

  == domain 11  score: 23.3 bits;  conditional E-value: 6e-08
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   +R aAa aLg++gde a++aL+  L+d
  gi|91773182|ref|YP_565874.1| 436 IREAAANALGEMGDESALDALILSLED 462
                                   59********************99987 PP

  == domain 12  score: -0.5 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                   vR++ + aL +   + ++ ++ + L+
  gi|91773182|ref|YP_565874.1| 467 VRYSVVDALQKYDNKTVVLPISNMLD 492
                                   89****99987766666666666555 PP

  == domain 13  score: 19.7 bits;  conditional E-value: 9.1e-07
                                   HHHHHHHHHHHCTSGGGHHHHHHHC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                   vR  Aa +Lg++g ++aip+L+ea 
  gi|91773182|ref|YP_565874.1| 498 VRKTAAQSLGTIGNQQAIPPLVEAI 522
                                   8999******************996 PP

  == domain 14  score: 13.6 bits;  conditional E-value: 8.7e-05
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   vR aAa +L++ g e+a+++L+++  d
  gi|91773182|ref|YP_565874.1| 563 VREAAAISLAKPGNEQAVDPLIQVMLD 589
                                   9**********************9765 PP

  == domain 15  score: 11.2 bits;  conditional E-value: 0.00051
                                   HHHHHHHHHHHCTSGGGHHHHHHHC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                   +R +Aa aLg++gd +a +aL +  
  gi|91773182|ref|YP_565874.1| 596 LRIEAAIALGRIGDYDAFDALSRIS 620
                                   599***********88888886655 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.8   7.9e+02      10      27 ..      52      69 ..      46      71 .. 0.80
   2 !    7.5   0.0    0.0057       5.7       9      30 ..      82     105 ..      76     106 .. 0.81
   3 ?    1.8   0.0      0.37   3.7e+02       4      28 ..     171     195 ..     169     197 .. 0.87
   4 !   10.7   0.0   0.00052      0.52       4      28 ..     202     226 ..     200     228 .. 0.90
   5 !   10.5   0.0   0.00063      0.62       3      28 ..     232     259 ..     230     261 .. 0.77
   6 !   13.9   0.0     5e-05      0.05       3      28 ..     265     290 ..     263     292 .. 0.91
   7 ?    0.2   0.0       1.2   1.2e+03       2      21 ..     295     315 ..     294     317 .. 0.90
   8 !    9.0   0.0    0.0019       1.9       4      27 ..     327     350 ..     325     351 .. 0.89
   9 !    7.7   0.0    0.0048       4.7       5      28 ..     359     384 ..     356     386 .. 0.84
  10 ?   -1.4   0.0         4     4e+03       2      26 ..     390     415 ..     389     418 .. 0.60
  11 !   22.1   0.0   1.1e-07   0.00011       5      27 ..     425     447 ..     423     450 .. 0.89
  12 !   14.5   0.0   3.1e-05     0.031       3      25 ..     454     476 ..     452     478 .. 0.85
  13 !   21.3   0.0   2.1e-07   0.00021       5      28 ..     487     510 ..     484     513 .. 0.89
  14 !    7.2   0.0    0.0069       6.9       4      25 ..     549     572 ..     548     573 .. 0.89
  15 ?    2.8   0.0      0.18   1.8e+02       3      28 ..     582     608 ..     582     610 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.8
                                  T-SSHHHHHHHHHHHHHH CS
                          HEAT 10 sDpspeVReaAakaLgal 27
                                  + ++ ++R+ A+ +L+++
  gi|91773182|ref|YP_565874.1| 52 KNENESIRQEAIGNLTKI 69
                                  44999*********9988 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0057
                                   HT-..SSHHHHHHHHHHHHHHHHC CS
                          HEAT   9 lsD..pspeVReaAakaLgalaev 30 
                                   l+D  +s ++R +Aa aL+++ ++
  gi|91773182|ref|YP_565874.1|  82 LMDknESNSIRISAADALAEIGKG 105
                                   55655999************9875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.37
                                   HHHHHHT-SSHHHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                    +++ l+++++  R + a  L+++a
  gi|91773182|ref|YP_565874.1| 171 YFIEKLNSEDATTRINMAFILAEMA 195
                                   677889************9999998 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00052
                                   HHHHHHT-SSHHHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                   +l+ +l+D++  VR+ Aa+ Lg++ 
  gi|91773182|ref|YP_565874.1| 202 ALIVALEDENRYVRRHAARGLGNIG 226
                                   68889*****************995 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00063
                                   HHHHHHH.T-SSHH.HHHHHHHHHHHHH CS
                          HEAT   3 Plllkll.sDpspe.VReaAakaLgala 28 
                                   P l++ + + ++p+ VR++Aa aLg++ 
  gi|91773182|ref|YP_565874.1| 232 PSLIQVMsNTSEPReVRSNAAIALGQIG 259
                                   665555426688888***********96 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 5e-05
                                   HHHHHHHT-SSHHHHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAakaLgala 28 
                                    +l+++l+D++++V ++Aa aLg+l 
  gi|91773182|ref|YP_565874.1| 265 EPLIQMLKDEDWSVPSSAAIALGELG 290
                                   6799*******************995 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 1.2
                                   HHHHHHHH.T-SSHHHHHHHH CS
                          HEAT   2 lPlllkll.sDpspeVReaAa 21 
                                   +P+l  +l +D++  V e+A+
  gi|91773182|ref|YP_565874.1| 295 IPALTAALrRDEEFVVKESAI 315
                                   799999999********9997 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.0019
                                   HHHHHHT-SSHHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                    l+ ll D++ +V ++Aa+aL  +
  gi|91773182|ref|YP_565874.1| 327 KLIDLLDDNDKSVQKNAAYALRGI 350
                                   6899*****************866 PP

  == domain 9  score: 7.7 bits;  conditional E-value: 0.0048
                                   HHHHHT-..SSHHHHHHHHHHHHHHH CS
                          HEAT   5 llkllsD..pspeVReaAakaLgala 28 
                                   l+ ll+D  ++ + R+aAa +Lg++ 
  gi|91773182|ref|YP_565874.1| 359 LIDLLEDsyEHEDARAAAASSLGTIG 384
                                   4777888899*************995 PP

  == domain 10  score: -1.4 bits;  conditional E-value: 4
                                   HHHHHHHHT-.SSHHH.HHHHHHHHHH CS
                          HEAT   2 lPlllkllsD.pspeV.ReaAakaLga 26 
                                   lPl++  l+D ++pe  R  + +aL +
  gi|91773182|ref|YP_565874.1| 390 LPLIQI-LEDkNEPETlRIRTTRALRR 415
                                   788777.68855555336666666655 PP

  == domain 11  score: 22.1 bits;  conditional E-value: 1.1e-07
                                   HHHHHT-SSHHHHHHHHHHHHHH CS
                          HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                   l++ l+D++p++ReaAa+aLg++
  gi|91773182|ref|YP_565874.1| 425 LIESLKDENPDIREAAANALGEM 447
                                   77889****************98 PP

  == domain 12  score: 14.5 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHT-SSHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAakaLg 25 
                                   ++l+  l+D++++VR++++ aL 
  gi|91773182|ref|YP_565874.1| 454 DALILSLEDENWRVRYSVVDALQ 476
                                   5666679**************96 PP

  == domain 13  score: 21.3 bits;  conditional E-value: 2.1e-07
                                   HHHHHT-SSHHHHHHHHHHHHHHH CS
                          HEAT   5 llkllsDpspeVReaAakaLgala 28 
                                   + ++l D+ ++VR++Aa++Lg++ 
  gi|91773182|ref|YP_565874.1| 487 ISNMLDDEYWSVRKTAAQSLGTIG 510
                                   4789*****************996 PP

  == domain 14  score: 7.2 bits;  conditional E-value: 0.0069
                                   HHHHHHT-..SSHHHHHHHHHHHH CS
                          HEAT   4 lllkllsD..pspeVReaAakaLg 25 
                                   l+++ll+D  +  +VReaAa +L+
  gi|91773182|ref|YP_565874.1| 549 LFIRLLQDktEFLSVREAAAISLA 572
                                   78999***999999******9996 PP

  == domain 15  score: 2.8 bits;  conditional E-value: 0.18
                                   HHHHHHH.T-SSHHHHHHHHHHHHHHH CS
                          HEAT   3 Plllkll.sDpspeVReaAakaLgala 28 
                                   Pl++ +l + ++ + R  Aa aLg++ 
  gi|91773182|ref|YP_565874.1| 582 PLIQVMLdETQAYNLRIEAAIALGRIG 608
                                   788888844478889**********96 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.44   4.4e+02      34      55 .]      79     102 ..      76     102 .. 0.79
   2 ?   -0.1   0.0       1.4   1.4e+03      28      52 ..     167     191 ..     161     194 .. 0.80
   3 !   10.1   0.0   0.00094      0.94      30      55 .]     200     225 ..     196     225 .. 0.94
   4 !   14.3   0.0   4.3e-05     0.043      29      55 .]     230     258 ..     228     258 .. 0.85
   5 ?    3.9   0.0     0.081        81      28      55 .]     262     289 ..     261     289 .. 0.88
   6 ?    3.0   0.0      0.16   1.5e+02      28      55 .]     293     320 ..     292     320 .. 0.88
   7 !   10.5   0.0    0.0007       0.7      30      53 ..     325     348 ..     323     348 .. 0.87
   8 ?    2.3   0.0      0.26   2.6e+02      30      55 .]     356     383 ..     353     383 .. 0.77
   9 ?    6.1   0.0     0.017        17      28      55 .]     387     416 ..     386     416 .. 0.89
  10 !   15.5   0.0   1.9e-05     0.019      30      55 .]     422     447 ..     419     447 .. 0.91
  11 ?    3.6   0.0     0.099        99      29      54 ..     452     477 ..     449     478 .. 0.71
  12 ?    2.9   0.0      0.17   1.7e+02      35      55 .]     489     509 ..     483     509 .. 0.74
  13 ?    3.3   0.0      0.12   1.2e+02       1      27 [.     496     520 ..     496     539 .. 0.80
  14 ?    6.8   0.0      0.01        10      32      53 ..     549     572 ..     547     573 .. 0.91
  15 ?    3.3   0.0      0.12   1.2e+02      28      55 .]     578     607 ..     577     607 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.44
                       HEAT_EZ  34 lalLnddsd..eVRaaAagaLgnl 55 
                                      L+d++   ++R  Aa aL+ +
  gi|91773182|ref|YP_565874.1|  79 TGILMDKNEsnSIRISAADALAEI 102
                                   5678897777799*****999875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                       HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaL 52 
                                   e + +++  Ln++++++R + a  L
  gi|91773182|ref|YP_565874.1| 167 EDIEYFIEKLNSEDATTRINMAFIL 191
                                   66899**********9998766655 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00094
                       HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                                   ++aL+ +L+d++  VR  Aa+ Lgn+
  gi|91773182|ref|YP_565874.1| 200 VDALIVALEDENRYVRRHAARGLGNI 225
                                   789*********************98 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 4.3e-05
                       HEAT_EZ  29 ilpaLlalL.nddsd.eVRaaAagaLgnl 55 
                                   ++p L++ + n++++ eVR +Aa+aLg++
  gi|91773182|ref|YP_565874.1| 230 AIPSLIQVMsNTSEPrEVRSNAAIALGQI 258
                                   7899996664889999***********98 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.081
                       HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                   +++ +L+++L+d++ +V   Aa+aLg l
  gi|91773182|ref|YP_565874.1| 262 DAVEPLIQMLKDEDWSVPSSAAIALGEL 289
                                   68999******8777**********986 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.16
                       HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                   e++paL a+L+ d+  V + +a+aL++l
  gi|91773182|ref|YP_565874.1| 293 EAIPALTAALRRDEEFVVKESAIALEKL 320
                                   89************99988888888876 PP

  == domain 7  score: 10.5 bits;  conditional E-value: 0.0007
                       HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLg 53 
                                   ++ L+ lL d +++V+++Aa+aL+
  gi|91773182|ref|YP_565874.1| 325 IDKLIDLLDDNDKSVQKNAAYALR 348
                                   5678899999999*********95 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.26
                       HEAT_EZ  30 lpaLlalLnd..dsdeVRaaAagaLgnl 55 
                                   + +L+ lL+d  ++ + RaaAa  Lg +
  gi|91773182|ref|YP_565874.1| 356 IVPLIDLLEDsyEHEDARAAAASSLGTI 383
                                   5567889988777779999999999975 PP

  == domain 9  score: 6.1 bits;  conditional E-value: 0.017
                       HEAT_EZ  28 eilpaLlalLnddsd.eV.RaaAagaLgnl 55 
                                   +++ +L++ L+d++  e+ R  + +aL+++
  gi|91773182|ref|YP_565874.1| 387 DAVLPLIQILEDKNEpETlRIRTTRALRRI 416
                                   68999*******9998778********997 PP

  == domain 10  score: 15.5 bits;  conditional E-value: 1.9e-05
                       HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                                    ++L+  L+d+++++R+aAa aLg +
  gi|91773182|ref|YP_565874.1| 422 TKPLIESLKDENPDIREAAANALGEM 447
                                   5789********************86 PP

  == domain 11  score: 3.6 bits;  conditional E-value: 0.099
                       HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgn 54 
                                   +l+aL+  L+d++ +VR+ ++ aL +
  gi|91773182|ref|YP_565874.1| 452 ALDALILSLEDENWRVRYSVVDALQK 477
                                   45556666665555*********976 PP

  == domain 12  score: 2.9 bits;  conditional E-value: 0.17
                       HEAT_EZ  35 alLnddsd..eVRaaAagaLgnl 55 
                                   ++L  d+   +VR++Aa  Lg +
  gi|91773182|ref|YP_565874.1| 489 NML--DDEywSVRKTAAQSLGTI 509
                                   555..666678999999999865 PP

  == domain 13  score: 3.3 bits;  conditional E-value: 0.12
                       HEAT_EZ   1 wrvRraAawaLGrlaggepellqplvp 27 
                                   w vR  Aa  LG++   + ++++plv+
  gi|91773182|ref|YP_565874.1| 496 WSVRKTAAQSLGTIG--NQQAIPPLVE 520
                                   889999999999876..5566666655 PP

  == domain 14  score: 6.8 bits;  conditional E-value: 0.01
                       HEAT_EZ  32 aLlalLnddsd..eVRaaAagaLg 53 
                                   ++++lL+d+    +VR+aAa+ L+
  gi|91773182|ref|YP_565874.1| 549 LFIRLLQDKTEflSVREAAAISLA 572
                                   699*********9********997 PP

  == domain 15  score: 3.3 bits;  conditional E-value: 0.12
                       HEAT_EZ  28 eilpaLlalLnddsd..eVRaaAagaLgnl 55 
                                   +++++L++ + d+ +  + R  Aa+aLg++
  gi|91773182|ref|YP_565874.1| 578 QAVDPLIQVMLDETQayNLRIEAAIALGRI 607
                                   7888999888888886777*********97 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.1   6.1e+03      22      33 ..      52      63 ..      51      67 .. 0.73
   2 ?   -2.3   0.0       5.2   5.2e+03      21      39 ..      83     102 ..      82     104 .. 0.81
   3 ?   -1.1   0.0       2.3   2.3e+03      12      28 ..     106     123 ..     106     127 .. 0.71
   4 !    9.5   0.0    0.0011       1.1      10      39 ..     196     225 ..     192     226 .. 0.90
   5 !    7.0   0.0    0.0063       6.2      10      39 ..     227     258 ..     225     260 .. 0.89
   6 ?    4.9   0.0     0.028        28       8      25 ..     258     275 ..     256     278 .. 0.86
   7 ?   -1.5   0.0         3     3e+03       9      30 ..     290     312 ..     288     315 .. 0.73
   8 !   18.9   0.0   1.2e-06    0.0012      13      37 ..     324     348 ..     323     352 .. 0.93
   9 ?    2.3   0.0      0.19   1.9e+02      13      37 ..     355     381 ..     350     383 .. 0.83
  10 ?    1.6   0.0      0.31   3.1e+02      12      39 ..     387     416 ..     382     418 .. 0.82
  11 !   11.7   0.0   0.00021      0.21      10      38 ..     418     446 ..     415     449 .. 0.88
  12 ?    5.1   0.0     0.026        26       8      30 ..     509     532 ..     507     539 .. 0.77
  13 ?    1.4   0.0      0.38   3.8e+02      16      33 ..     549     568 ..     547     568 .. 0.90
  14 ?    1.3   0.0      0.38   3.8e+02      11      37 ..     577     605 ..     575     608 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.1
                                  TTSSHHHHHHHH CS
                           Arm 22 ssedeevqeeAa 33
                                  ++e+e++++eA 
  gi|91773182|ref|YP_565874.1| 52 KNENESIRQEAI 63
                                  578888888885 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.2
                                   TT.TSSHHHHHHHHHHHHHH CS
                           Arm  21 Ls.sedeevqeeAawALsNL 39 
                                   ++ +e+ +++  Aa AL+ +
  gi|91773182|ref|YP_565874.1|  83 MDkNESNSIRISAADALAEI 102
                                   556889999999****9876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.3
                                   THHHHHHHHTT.TSSHHH CS
                           Arm  12 GavppLvrLLs.sedeev 28 
                                   G + pL++ L+ + +  v
  gi|91773182|ref|YP_565874.1| 106 GSISPLISVLQeNNSALV 123
                                   5689*******6655555 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0011
                                   HTTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                           Arm  10 eaGavppLvrLLssedeevqeeAawALsNL 39 
                                   +   v++L+  L++e+  v++ Aa+ L+N+
  gi|91773182|ref|YP_565874.1| 196 DERTVDALIVALEDENRYVRRHAARGLGNI 225
                                   66679************************8 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0063
                                   HTTHHHHHHHHTT..TSSHHHHHHHHHHHHHH CS
                           Arm  10 eaGavppLvrLLs..sedeevqeeAawALsNL 39 
                                   + +a+p L++ +s  se  ev+ +Aa AL+ +
  gi|91773182|ref|YP_565874.1| 227 NKNAIPSLIQVMSntSEPREVRSNAAIALGQI 258
                                   569***********************888865 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.028
                                   HHHTTHHHHHHHHTTTSS CS
                           Arm   8 vieaGavppLvrLLssed 25 
                                   + +  av+pL+++L++ed
  gi|91773182|ref|YP_565874.1| 258 IGDDDAVEPLIQMLKDED 275
                                   667889*********876 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 3
                                   HHTTHHHHHHHHTT.TSSHHHHH CS
                           Arm   9 ieaGavppLvrLLs.sedeevqe 30 
                                    ++ a+p+L + L+ +e   v+e
  gi|91773182|ref|YP_565874.1| 290 GNSEAIPALTAALRrDEEFVVKE 312
                                   57889****99998766666655 PP

  == domain 8  score: 18.9 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHHTTTSSHHHHHHHHHHHH CS
                           Arm  13 avppLvrLLssedeevqeeAawALs 37 
                                   +++ L++LL++ d +vq++Aa AL+
  gi|91773182|ref|YP_565874.1| 324 GIDKLIDLLDDNDKSVQKNAAYALR 348
                                   899*********************8 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.19
                                   HHHHHHHHTT..TSSHHHHHHHHHHHH CS
                           Arm  13 avppLvrLLs..sedeevqeeAawALs 37 
                                   a+ pL++LL+   e+e+ + +Aa+ L+
  gi|91773182|ref|YP_565874.1| 355 AIVPLIDLLEdsYEHEDARAAAASSLG 381
                                   788*******99999998888888776 PP

  == domain 10  score: 1.6 bits;  conditional E-value: 0.31
                                   THHHHHHHHTT..TSSHHHHHHHHHHHHHH CS
                           Arm  12 GavppLvrLLs..sedeevqeeAawALsNL 39 
                                    av pL++ L+  +e e+++   ++AL+ +
  gi|91773182|ref|YP_565874.1| 387 DAVLPLIQILEdkNEPETLRIRTTRALRRI 416
                                   5788*******9999999998999888865 PP

  == domain 11  score: 11.7 bits;  conditional E-value: 0.00021
                                   HTTHHHHHHHHTTTSSHHHHHHHHHHHHH CS
                           Arm  10 eaGavppLvrLLssedeevqeeAawALsN 38 
                                   +  a +pL++ L++e+++++e+Aa AL+ 
  gi|91773182|ref|YP_565874.1| 418 DERATKPLIESLKDENPDIREAAANALGE 446
                                   556789*********************96 PP

  == domain 12  score: 5.1 bits;  conditional E-value: 0.026
                                   HHHTTHHHHHHHHTT.TSSHHHHH CS
                           Arm   8 vieaGavppLvrLLs.sedeevqe 30 
                                   + ++ a+ppLv+ +s  +  +v++
  gi|91773182|ref|YP_565874.1| 509 IGNQQAIPPLVEAISvEKEKDVKT 532
                                   67899*********9766666665 PP

  == domain 13  score: 1.4 bits;  conditional E-value: 0.38
                                   HHHHHTT..TSSHHHHHHHH CS
                           Arm  16 pLvrLLs..sedeevqeeAa 33 
                                    ++rLL+  +e  +v+e+Aa
  gi|91773182|ref|YP_565874.1| 549 LFIRLLQdkTEFLSVREAAA 568
                                   689*****999999999997 PP

  == domain 14  score: 1.3 bits;  conditional E-value: 0.38
                                   TTHHHHHHHHTT..TSSHHHHHHHHHHHH CS
                           Arm  11 aGavppLvrLLs..sedeevqeeAawALs 37 
                                     av+pL++ +   ++  +++ eAa AL+
  gi|91773182|ref|YP_565874.1| 577 EQAVDPLIQVMLdeTQAYNLRIEAAIALG 605
                                   569*******9988888888888887776 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 ?    0.4   0.2      0.61     6e+02      70      95 ..      54      79 ..      45     177 .. 0.61
   2 !   12.7   0.0   9.6e-05     0.096      10      54 ..     187     231 ..     181     261 .. 0.72
   3 !   12.4   0.0   0.00012      0.12       2      85 ..     247     350 ..     246     371 .. 0.67
   4 !   13.7   0.0   4.9e-05     0.049      21      88 ..     420     481 ..     419     485 .. 0.86
   5 !    7.4   0.0    0.0042       4.2      23     103 ..     484     560 ..     480     596 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.61
                          Cnd1 70 enprVvanalaalteiseksenaiyn 95
                                  en+++++ a+  lt+i +++++ i++
  gi|91773182|ref|YP_565874.1| 54 ENESIRQEAIGNLTKIGDEDSTDILT 79
                                  45555555555555554444333332 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.6e-05
                          Cnd1  10 lgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmv 54 
                                   ++ i  +   e +v+ L  +L+De+ yVR++aa ++ ++ +++ +
  gi|91773182|ref|YP_565874.1| 187 MAFILAEMADERTVDALIVALEDENRYVRRHAARGLGNIGNKNAI 231
                                   66666666678999*******************999887555544 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00012
                          Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakL............ilnd...mvk........ekg. 58 
                                   +R++a ++lg i  ++ ve+l+    + LkDed  V   aai++ +L            +++d   +vk          g 
  gi|91773182|ref|YP_565874.1| 247 VRSNAAIALGQIGDDDAVEPLI----QMLKDEDWSVPSSAAIALGELgnseaipaltaaLRRDeefVVKesaialekLDGs 323
                                   7888888888888777766555....5788999999999999999997777777666652222232222222222212234 PP

                          Cnd1  59 flselaklleDenprVvanalaaltei 85 
                                    +++l +ll+D++++V++na +al  i
  gi|91773182|ref|YP_565874.1| 324 GIDKLIDLLDDNDKSVQKNAAYALRGI 350
                                   577888888888888888888888766 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 4.9e-05
                          Cnd1  21 ylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                     ++pL ++LkDe+p +R+ aa ++ ++       ++  l+ l   leDen rV+ +++ al+++ +k
  gi|91773182|ref|YP_565874.1| 420 RATKPLIESLKDENPDIREAAANALGEMG------DESALDALILSLEDENWRVRYSVVDALQKYDNK 481
                                   6789*******************998754......455699999***********9999999988776 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0042
                          Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselakll.eDenprVvanalaalteisek.senaiynllpdii 101
                                   v p+ + L De   VRktaa  +  + +++       +  l +++  ++++ V +  + +l++i +  s++++++ll+d  
  gi|91773182|ref|YP_565874.1| 484 VLPISNMLDDEYWSVRKTAAQSLGTIGNQQA------IPPLVEAIsVEKEKDVKTTMVRSLEDIDNGsSTDLFIRLLQDKT 558
                                   669999**************99876644443......44444555456666666666666666666644455556665555 PP

                          Cnd1 102 sk 103
                                     
  gi|91773182|ref|YP_565874.1| 559 EF 560
                                   55 PP

>> Vitellogenin_N  Lipoprotein amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0012       1.2     539     591 ..      53     102 ..      44     123 .. 0.83
   2 !    6.0   0.0    0.0033       3.3     515     588 ..     219     255 ..     164     275 .. 0.67
   3 !    7.2   0.0    0.0014       1.4     489     588 ..     353     444 ..     335     476 .. 0.79
   4 !   16.3   0.0   2.4e-06    0.0024     443     591 ..     476     607 ..     470     629 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                                   -S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHT CS
                Vitellogenin_N 539 evstfvRlaavlaLrnlakkaprkvrsvllriyentaekpevRvaAvlalmet 591
                                   + ++ +R +a+ +L ++ + +     ++l  i+++++e + +R+ A+ al e 
  gi|91773182|ref|YP_565874.1|  53 NENESIRQEAIGNLTKIGDEDST---DILTGILMDKNESNSIRISAADALAEI 102
                                   55678899999988877777666...9*******************9888775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0033
                                   HHHHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HHHHHHHHHHH CS
                Vitellogenin_N 515 lkaLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllriyentaekpevRvaAvlal 588
                                    + LgN+G+++ + +l                                      +++ nt e+ evR  A++al
  gi|91773182|ref|YP_565874.1| 219 ARGLGNIGNKNAIPSLI-------------------------------------QVMSNTSEPREVRSNAAIAL 255
                                   45555555555555555.....................................55555555555555555554 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0014
                                   .GGTHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHH CS
                Vitellogenin_N 489 eeyipylaqklkeavekgdsekiqvylkaLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllr 569
                                   e++i +l++ l+++   ++++ +  +  +Lg +G++  +  l ++l ++++ ++++R+    aLr++ +     + + l++
  gi|91773182|ref|YP_565874.1| 353 EKAIVPLIDLLEDS--YEHEDARAAAASSLGTIGNKDAVLPLIQIL-EDKNEPETLRIRTTRALRRIGDE---RATKPLIE 427
                                   788999*******8..666777888999******************.88888899999999****66554...35566666 PP

                                   HHH-TTS-HHHHHHHHHHH CS
                Vitellogenin_N 570 iyentaekpevRvaAvlal 588
                                    +++  e+p++R aA+ al
  gi|91773182|ref|YP_565874.1| 428 SLKD--ENPDIREAAANAL 444
                                   6655..5666777776666 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 2.4e-06
                                   -HHHHHHHHHHHHHHHHHHHTT-SS..............--G.....GGTHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT- CS
                Vitellogenin_N 443 qpylntsalLafgslvrkycvnndsahnrypvhlfgratchrefvieeyipylaqklkeavekgdsekiqvylkaLgNlGh 523
                                   q+y n++++L +++++ +   + ++          + a+   ++  +++ip+l++ ++     ++++ +  ++++L  + +
  gi|91773182|ref|YP_565874.1| 476 QKYDNKTVVLPISNMLDDEYWSVRK----------TAAQSLGTIGNQQAIPPLVEAISVE---KEKDVKTTMVRSLEDIDN 543
                                   6677788888888887776666665..........2233333344458999999998886...7777888999******** PP

                                   GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHT CS
                Vitellogenin_N 524 peilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllriyentaekpevRvaAvlalmet 591
                                    ++ + + ++l ++++    vR aa  +L    k  ++++ + l++++ ++++++ +R+ A++al + 
  gi|91773182|ref|YP_565874.1| 544 GSSTDLFIRLL-QDKTEFLSVREAAAISLA---KPGNEQAVDPLIQVMLDETQAYNLRIEAAIALGRI 607
                                   ***********.777777778888877776...999999***********************999665 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0023       2.2     305     367 ..      44     102 ..      32     127 .. 0.85
   2 !   21.3   0.0   8.7e-08   8.7e-05      81     366 ..     200     540 ..     188     549 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
                                   TTCCCCSXXTTSXHHHHHHHHHHHCCCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHHHHHHHH CS
                     Adaptin_N 305 ldlkifllktdddvsirlkaldlllklvdesNvkeivkeLkkyvkevadedfksklvkaIgrl 367
                                   ++l ++ +k ++++sir++a+  l+k++de++ +++   L+    e+  +++++ +++a++++
  gi|91773182|ref|YP_565874.1|  44 KELALEDIK-NENESIRQEAIGNLTKIGDEDSTDILTGILMDKN-ES--NSIRISAADALAEI 102
                                   677788888.9999****************99999999888876.55..67888888888776 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 8.7e-08
                                   CHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSH.HHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHC CS
                     Adaptin_N  81 tnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrsp.yvrkkAalailklykkdpdllrkqlveeikel 160
                                   +++l  +l+d n ++r  A r+L++i+ ++  ++l + + +    ++p  vr++Aa+a+ ++   d d+     ve +++ 
  gi|91773182|ref|YP_565874.1| 200 VDALIVALEDENRYVRRHAARGLGNIGNKNAIPSLIQVMSN---TSEPrEVRSNAAIALGQIG--DDDA-----VEPLIQM 270
                                   56777899********************9988887665554...344468******9988774..3344.....6779*** PP

                                   TT-SSHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCHHHHH.......................................H CS
                     Adaptin_N 161 lsdkdpgvvlaAvalleeikkndrlllkllpklvrrLcnll.......................................t 202
                                   l+d+d +v ++A  +l e+  n ++ + +l    rr ++++                                       +
  gi|91773182|ref|YP_565874.1| 271 LKDEDWSVPSSAAIALGEL-GNSEA-IPALTAALRRDEEFVvkesaialekldgsgidklidllddndksvqknaayalrG 349
                                   *******************.33333.4444444455466779999999988899999999999999999999999999999 PP

                                   CS-HHHHHHHHHHHCC---SSHHHH.............................................HHHHHHHCGGC CS
                     Adaptin_N 203 eldpwlqvkiiklltrlarqepeer...........................................skkellesllnll 240
                                   +  + ++v +i+ll +  ++e++++                                           + ++  + l + l
  gi|91773182|ref|YP_565874.1| 350 IGGEKAIVPLIDLLEDSYEHEDARAaaasslgtignkdavlpliqiledknepetlrirttralrrigD-ERATKPLIESL 429
                                   999999999999997666655555579********************9999999999988887766653.57888888888 PP

                                   GCSSCHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCCCSXXTTSXHHHH CS
                     Adaptin_N 241 qssnnaVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlkifllktdddvsir 321
                                   +  n+ +  +++n++ e+ ++++l      aL+  l++++  +ry ++++l+k   k    v     ++++l+ d+  s+r
  gi|91773182|ref|YP_565874.1| 430 KDENPDIREAAANALGEMGDESAL-----DALILSLEDENWRVRYSVVDALQKYDNKT---VV--LPISNMLD-DEYWSVR 499
                                   9****************9999985.....9*******99999**********988887...33..35888888.9999*** PP

                                   HHHHHHHCCCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHHHHHHH CS
                     Adaptin_N 322 lkaldlllklvdesNvkeivkeLkkyvkevadedfksklvkaIgr 366
                                   ++a + l ++++++ +  +v+ +  +   + ++d+k  +v+++ +
  gi|91773182|ref|YP_565874.1| 500 KTAAQSLGTIGNQQAIPPLVEAISVE---K-EKDVKTTMVRSLED 540
                                   *****************999998744...4.66788888887765 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0026       2.6      64     118 ..      77     130 ..      71     135 .. 0.80
   2 ?    2.2   0.0      0.17   1.7e+02      81     119 ..     185     223 ..     169     225 .. 0.82
   3 ?    3.9   0.0      0.05        50      67     118 ..     236     286 ..     231     289 .. 0.79
   4 !    7.9   0.0    0.0031         3      92     119 ..     321     348 ..     300     350 .. 0.82
   5 ?   -0.3   0.0         1     1e+03      92     115 ..     352     375 ..     349     383 .. 0.61
   6 ?    4.3   0.0      0.04        40      94     119 ..     420     445 ..     372     448 .. 0.81
   7 ?   -0.3   0.0         1     1e+03      80     118 ..     499     538 ..     494     542 .. 0.76
   8 ?   -0.7   0.0       1.4   1.3e+03      93     140 ..     577     626 ..     548     629 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                 Aconitase_B_N  64 fLaaiakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                    L+ i+ ++ es+ i   +A + L+++  G ++++Li++l+e++++l  e+ e L
  gi|91773182|ref|YP_565874.1|  77 ILTGILMDKNESNSIR-ISAADALAEIGKGGSISPLISVLQENNSALVIEVSENL 130
                                   5778888888888775.456677788877889***********999998888877 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.17
                 Aconitase_B_N  81 eeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                    +   +L++M     v++Li +l+++++ ++++aa+ L 
  gi|91773182|ref|YP_565874.1| 185 INMAFILAEMADERTVDALIVALEDENRYVRRHAARGLG 223
                                   45556899****************9********999886 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.05
                 Aconitase_B_N  67 aiakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                   ++++++ e +++ ++ A+  Lg++    +v++Li++lk++d ++ ++aa aL
  gi|91773182|ref|YP_565874.1| 236 QVMSNTSEPREVRSNAAI-ALGQIGDDDAVEPLIQMLKDEDWSVPSSAAIAL 286
                                   566666666677666666.589999999**********99999999999887 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0031
                 Aconitase_B_N  92 GGynvksLidllkekdeelaeeaaeaLk 119
                                    G  +++Lidll+++d++++++aa aL+
  gi|91773182|ref|YP_565874.1| 321 DGSGIDKLIDLLDDNDKSVQKNAAYALR 348
                                   5789********************9996 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1
                 Aconitase_B_N  92 GGynvksLidllkekdeelaeeaa 115
                                   G  ++ +Lidll+++ e+  + aa
  gi|91773182|ref|YP_565874.1| 352 GEKAIVPLIDLLEDSYEHEDARAA 375
                                   346899******965444333333 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.04
                 Aconitase_B_N  94 ynvksLidllkekdeelaeeaaeaLk 119
                                    + k+Li+ lk+++ +++e+aa+aL 
  gi|91773182|ref|YP_565874.1| 420 RATKPLIESLKDENPDIREAAANALG 445
                                   57899******************996 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 1
                 Aconitase_B_N  80 peeAvelLgtMlGGynvksLidllkekd.eelaeeaaeaL 118
                                   +++A + Lgt+    ++ +L+++++ ++ ++++++ ++ L
  gi|91773182|ref|YP_565874.1| 499 RKTAAQSLGTIGNQQAIPPLVEAISVEKeKDVKTTMVRSL 538
                                   56899999*999999*******999554045666666555 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 1.4
                 Aconitase_B_N  93 GynvksLidllkekdee..laeeaaeaLkktllvydafedveelake.naa 140
                                     +v++Li+++ +++++  l+ eaa aL + +  ydaf+ ++  +k+ n++
  gi|91773182|ref|YP_565874.1| 577 EQAVDPLIQVMLDETQAynLRIEAAIALGR-IGDYDAFDALSRISKDpNEH 626
                                   467889999877555541145556666654.56788888888888876665 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 ?   -3.9   0.0       7.5   7.5e+03     165     206 ..      58     100 ..      51     104 .. 0.55
   2 ?    5.4   0.0     0.011        11     134     226 ..     221     275 ..     147     311 .. 0.60
   3 !   11.2   0.2   0.00019      0.19     111     217 ..     360     456 ..     323     475 .. 0.84
   4 ?    1.4   0.0      0.19   1.9e+02     165     218 ..     563     616 ..     488     633 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.5
                                   HHHHHHHHHHHHS-HHHHHHHHHHHHC-S.SHHHHHHHHHHHC CS
                       ERAP1_C 165 lrwavycalaanggeaewdallerykdts.apsekeaalrala 206
                                   +r+ ++ +l + g+e+  d l  +  d + ++s +  a+ ala
  gi|91773182|ref|YP_565874.1|  58 IRQEAIGNLTKIGDEDSTDILTGILMDKNeSNSIRISAADALA 100
                                   5556666666666666555555554222212355666666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                                   HHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHH.HHHHHHHHCC-S-HHH CS
                       ERAP1_C 134 aacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallerykdtsapse.keaalralaatpdpel 213
                                    +++                                       g+++ + +l++  ++ts p e +  a+ al+ + d ++
  gi|91773182|ref|YP_565874.1| 221 GLGNI--------------------------------------GNKNAIPSLIQVMSNTSEPREvRSNAAIALGQIGDDDA 263
                                   33333......................................34455555555554444433335555555555555555 PP

                                   HHHHHHHCTTT.. CS
                       ERAP1_C 214 lerllnfvlesde 226
                                   +e l++++  +++
  gi|91773182|ref|YP_565874.1| 264 VEPLIQMLK-DED 275
                                   555555553.222 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00019
                                   HHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC CS
                       ERAP1_C 111 aeklgwepgeshldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallerykd 191
                                   ++ l    ++s+   + r+++ s +++ g++++v  + +++++  +     p  lr +  +al + g+e   + l+e  kd
  gi|91773182|ref|YP_565874.1| 360 IDLL----EDSYEHEDARAAAASSLGTIGNKDAVLPLIQILEDK-N----EPETLRIRTTRALRRIGDERATKPLIESLKD 431
                                   5544....268899999**************9999999999999.4....4999*********777************988 PP

                                   -SSHHHHHHHHHHHCC-S-HHHHHHH CS
                       ERAP1_C 192 tsapsekeaalralaatpdpellerl 217
                                   ++  + +eaa++al+   d+ +l +l
  gi|91773182|ref|YP_565874.1| 432 ENP-DIREAAANALGEMGDESALDAL 456
                                   775.****************999984 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHHS-HHHHHHHHHHHHC-SS.HHHHHHHHHHHCC-S-HHHHHHHH CS
                       ERAP1_C 165 lrwavycalaanggeaewdallerykdtsa.psekeaalralaatpdpellerll 218
                                   +r a+  +la+ g+e+ +d l++   d+++  + +  a+ al+ + d ++  + l
  gi|91773182|ref|YP_565874.1| 563 VREAAAISLAKPGNEQAVDPLIQVMLDETQaYNLRIEAAIALGRIGDYDAFDA-L 616
                                   67777778888899999999999997777437889999999999999888776.4 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.1   5.1e+03      45      45 ..     115     115 ..      74     147 .. 0.53
   2 ?   -0.7   0.0       1.9   1.9e+03       7      32 ..     200     225 ..     169     255 .. 0.74
   3 ?   -1.7   0.0       3.7   3.7e+03       7      34 ..     264     291 ..     261     308 .. 0.81
   4 ?   -1.6   0.0       3.5   3.5e+03       6      30 ..     324     348 ..     323     362 .. 0.86
   5 !    6.7   0.0    0.0094       9.3       8      38 ..     423     453 ..     421     506 .. 0.86
   6 ?    2.1   0.0      0.25   2.5e+02      26      77 ..     515     567 ..     488     603 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.1
                    RasGEF_N_2  45 l 45 
                                   l
  gi|91773182|ref|YP_565874.1| 115 L 115
                                   1 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                    RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeea 32 
                                   ++ l+  L+d++r v+++a++ L ++
  gi|91773182|ref|YP_565874.1| 200 VDALIVALEDENRYVRRHAARGLGNI 225
                                   45667778888888888888777666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.7
                    RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacd 34 
                                   +e l++ L+d++ +v + a+ +L e  +
  gi|91773182|ref|YP_565874.1| 264 VEPLIQMLKDEDWSVPSSAAIALGELGN 291
                                   78999*******9999999998888754 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.5
                    RasGEF_N_2   6 giellvnqLydqsrevvaaaleiLe 30 
                                   gi+ l++ L d +++v++ a+ +L 
  gi|91773182|ref|YP_565874.1| 324 GIDKLIDLLDDNDKSVQKNAAYALR 348
                                   57889999*********99998875 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0094
                    RasGEF_N_2   8 ellvnqLydqsrevvaaaleiLeeacddkes 38 
                                   + l+++L+d+++++++aa+++L e+ d+ + 
  gi|91773182|ref|YP_565874.1| 423 KPLIESLKDENPDIREAAANALGEMGDESAL 453
                                   57999*****************999776544 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.25
                    RasGEF_N_2  26 leiLeeacddkeslevlvelkpslqhlge.igslLllkllstssGfkylqeln 77 
                                   +  L ea++ ++   v + +  sl+++++     L+++ll+ +++f  ++e  
  gi|91773182|ref|YP_565874.1| 515 IPPLVEAISVEKEKDVKTTMVRSLEDIDNgSSTDLFIRLLQDKTEFLSVREAA 567
                                   5556777777777788888888999997779999*******999998887764 PP

>> IBN_N  Importin-beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.3   2.9e+02      13      36 ..      73      96 ..      60     100 .. 0.80
   2 ?    6.4   0.0    0.0082       8.2      14      39 ..     230     255 ..     227     257 .. 0.90
   3 ?    0.2   0.0      0.71   7.1e+02      13      32 ..     387     406 ..     385     410 .. 0.85
   4 ?   -0.8   0.0       1.5   1.5e+03      20      39 ..     552     571 ..     547     573 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.3
                                  CHHHHHHHHHHCTTSHHHHHHHHH CS
                         IBN_N 13 gflsallqilanseselevRqlAa 36
                                  ++   l  il++++ ++++R +Aa
  gi|91773182|ref|YP_565874.1| 73 DSTDILTGILMDKNESNSIRISAA 96
                                  66677899********9***9997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0082
                                   HHHHHHHHHHCTTSHHHHHHHHHHHH CS
                         IBN_N  14 flsallqilanseselevRqlAalyL 39 
                                   + ++l+q+++n++ + evR  Aa+ L
  gi|91773182|ref|YP_565874.1| 230 AIPSLIQVMSNTSEPREVRSNAAIAL 255
                                   6789*******************987 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.71
                                   CHHHHHHHHHHCTTSHHHHH CS
                         IBN_N  13 gflsallqilanseselevR 32 
                                   ++++ l+qil++++ ++ +R
  gi|91773182|ref|YP_565874.1| 387 DAVLPLIQILEDKNEPETLR 406
                                   567779**********8888 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.5
                                   HHHHCTTSHHHHHHHHHHHH CS
                         IBN_N  20 qilanseselevRqlAalyL 39 
                                   ++l++++  l+vR +Aa+ L
  gi|91773182|ref|YP_565874.1| 552 RLLQDKTEFLSVREAAAISL 571
                                   6788888889*******998 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   1.1e+03      11      34 ..      77     100 ..      71     107 .. 0.59
   2 ?    6.2   0.1     0.011        11       6      38 ..     228     260 ..     225     299 .. 0.88
   3 ?   -3.2   0.0       9.4   9.3e+03      17      24 ..     335     342 ..     325     351 .. 0.54
   4 ?   -2.7   0.0       6.5   6.4e+03      32      51 ..     359     378 ..     353     393 .. 0.73
   5 ?    0.6   0.2       0.6     6e+02      12      40 ..     392     420 ..     384     452 .. 0.64
   6 ?    2.9   0.0      0.11   1.1e+02      33      53 ..     551     571 ..     545     587 .. 0.87
   7 ?    4.9   0.1     0.027        27      50      81 .]     612     643 ..     575     643 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                                   HHHHHHT-TTS-HHHHHHHHHHHH CS
                       UPF0147  11 lLeeiiedtsvPrniRraakeake 34 
                                   +L+ i+ d++   +iR +a +a++
  gi|91773182|ref|YP_565874.1|  77 ILTGILMDKNESNSIRISAADALA 100
                                   555555555555555555555554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT- CS
                       UPF0147   6 kevielLeeiiedtsvPrniRraakeakekLkd 38 
                                   k++i  L +++++ts Pr +R +a  a+ ++ d
  gi|91773182|ref|YP_565874.1| 228 KNAIPSLIQVMSNTSEPREVRSNAAIALGQIGD 260
                                   678889999************999888777665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9.4
                                   T-TTS-HH CS
                       UPF0147  17 edtsvPrn 24 
                                   +d+sv++n
  gi|91773182|ref|YP_565874.1| 335 NDKSVQKN 342
                                   45555555 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6.5
                                   HHHHHT-TTS-HHHHHHHHH CS
                       UPF0147  32 akekLkdekeslavraatai 51 
                                    ++ L+d  e+ + raa a 
  gi|91773182|ref|YP_565874.1| 359 LIDLLEDSYEHEDARAAAAS 378
                                   56778888888899988774 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.6
                                   HHHHHT-TTS-HHHHHHHHHHHHHHT-TT CS
                       UPF0147  12 LeeiiedtsvPrniRraakeakekLkdek 40 
                                   L +i+ed++ P + R  ++ a++++ de+
  gi|91773182|ref|YP_565874.1| 392 LIQILEDKNEPETLRIRTTRALRRIGDER 420
                                   55566666666666666666555555554 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.11
                                   HHHHT-TTS-HHHHHHHHHHH CS
                       UPF0147  33 kekLkdekeslavraataisi 53 
                                   ++ L+d++e l+vr a ais+
  gi|91773182|ref|YP_565874.1| 551 IRLLQDKTEFLSVREAAAISL 571
                                   678999*************96 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.027
                                   HHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                       UPF0147  50 aisiLdeisnDpnmPlhaRtliwevvskLEti 81 
                                   a  +L  is+Dpn  +  Rt+  e ++++E+i
  gi|91773182|ref|YP_565874.1| 612 AFDALSRISKDPNEHFALRTAAEEAIANIENI 643
                                   45678999******999999999999999986 PP

>> YmgB  Biofilm development protein YmgB/AriR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.6   2.6e+03      26      43 ..     169     186 ..     169     202 .. 0.78
   2 ?   -2.3   0.0         4     4e+03      28      46 ..     202     220 ..     194     225 .. 0.83
   3 ?    2.9   0.0     0.095        95      18      37 ..     223     242 ..     212     246 .. 0.89
   4 ?    4.5   0.0      0.03        30      16      37 ..     379     400 ..     373     408 .. 0.86
   5 ?   -0.4   0.0       1.1     1e+03      15      39 ..     504     530 ..     497     545 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.6
                                   HHHHHHHHHT---HHHHH CS
                          YmgB  26 IlkLiekLEsesdvvqld 43 
                                   I + iekL se+ +++ +
  gi|91773182|ref|YP_565874.1| 169 IEYFIEKLNSEDATTRIN 186
                                   7789******99887765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4
                                   HHHHHHHT---HHHHHHHH CS
                          YmgB  28 kLiekLEsesdvvqldvyR 46 
                                   +Li  LE e+  v+    R
  gi|91773182|ref|YP_565874.1| 202 ALIVALEDENRYVRRHAAR 220
                                   79999**999888877666 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.095
                                   ---SHHHHHHHHHHHHHT-- CS
                          YmgB  18 gkvtnKaIIlkLiekLEses 37 
                                   g++ nK+ I +Li+ ++++s
  gi|91773182|ref|YP_565874.1| 223 GNIGNKNAIPSLIQVMSNTS 242
                                   5799**********999886 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.03
                                   TT---SHHHHHHHHHHHHHT-- CS
                          YmgB  16 sggkvtnKaIIlkLiekLEses 37 
                                   s g++ nK+ +l Li+ LE  +
  gi|91773182|ref|YP_565874.1| 379 SLGTIGNKDAVLPLIQILEDKN 400
                                   66899**************876 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.1
                                   HTT---SHHHHHHHHHHHH..HT---H CS
                          YmgB  15 asggkvtnKaIIlkLiekL..Esesdv 39 
                                   +s g++ n + I  L+e +  E+e+dv
  gi|91773182|ref|YP_565874.1| 504 QSLGTIGNQQAIPPLVEAIsvEKEKDV 530
                                   666788888889999987633666666 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       0.4     4e+02      68     108 ..      51      85 ..      40     120 .. 0.69
   2 ?    5.1   0.0    0.0082       8.2      58     100 ..     197     237 ..     192     274 .. 0.85
   3 ?    5.0   0.1     0.009         9      56     109 ..     320     371 ..     317     415 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.4
                          API5  68 iedddlgirkqAikdLpslckdtkeyvskiadiLaQlLite 108
                                   i +++ +ir+ Ai +L ++  +        +diL+ +L+  
  gi|91773182|ref|YP_565874.1|  51 IKNENESIRQEAIGNLTKIGDEDS------TDILTGILMDK 85 
                                   6678889***********998766......56776666544 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0082
                          API5  58 ekaidaqlDLiedddlgirkqAikdLpslckdtkeyvskiadi 100
                                   e+++da++  +ed++  +r+ A ++L ++ + +  +++ ++++
  gi|91773182|ref|YP_565874.1| 197 ERTVDALIVALEDENRYVRRHAARGLGNIGNKN--AIPSLIQV 237
                                   6899*************************8654..46665555 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.009
                          API5  56 laekaidaqlDLiedddlgirkqAikdLpslckdtkeyvskiadiLaQlLited 109
                                   l  + id+++DL++d+d +++k A  +L  +  ++   +  ++d L      ed
  gi|91773182|ref|YP_565874.1| 320 LDGSGIDKLIDLLDDNDKSVQKNAAYALRGIGGEKA--IVPLIDLLEDSYEHED 371
                                   566789******************998888876544..5555566655555554 PP

>> DUF2877  Protein of unknown function (DUF2877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.011        11      73     107 ..      49      83 ..      40      84 .. 0.85
   2 ?   -1.4   0.0       3.9   3.9e+03      43      95 ..     177     227 ..     157     257 .. 0.64
   3 ?    1.2   0.0      0.61     6e+02      70     102 ..     424     456 ..     400     457 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                       DUF2877  73 kalsseeeeelekalekllaiGhtSGadlllGlll 107
                                   +++++e+e+  ++a+ +l++iG+   +d+l+G+l+
  gi|91773182|ref|YP_565874.1|  49 EDIKNENESIRQEAIGNLTKIGDEDSTDILTGILM 83 
                                   56677777666*********************985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                       DUF2877  43 kakkrttdvSaalLkaalegefseellallkalsseeeeelekalekllaiGh 95 
                                   ++++ tt +  a++ a ++ e  + + al+ al+ e++    +a + l +iG+
  gi|91773182|ref|YP_565874.1| 177 NSEDATTRINMAFILAEMADE--RTVDALIVALEDENRYVRRHAARGLGNIGN 227
                                   556666666666655444433..233445555555555544566666666654 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.61
                       DUF2877  70 allkalsseeeeelekalekllaiGhtSGadll 102
                                    l+++l+ e+++  e+a ++l ++G+ S  d+l
  gi|91773182|ref|YP_565874.1| 424 PLIESLKDENPDIREAAANALGEMGDESALDAL 456
                                   489999999999889*************99987 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.48   4.8e+02      26      55 ..     197     226 ..     181     241 .. 0.76
   2 ?   -2.3   0.0       7.1     7e+03      27      42 ..     262     277 ..     252     284 .. 0.74
   3 ?   -0.3   0.0       1.7   1.7e+03      71      89 ..     326     344 ..     308     349 .. 0.80
   4 ?   -1.7   0.0       4.5   4.5e+03      30      51 ..     423     444 ..     418     449 .. 0.73
   5 ?    3.8   0.0     0.089        89      29      51 ..     453     475 ..     446     502 .. 0.84
   6 ?   -1.4   0.0       3.8   3.8e+03      26      52 ..     481     507 ..     476     515 .. 0.83
   7 ?   -2.3   0.0       6.9   6.8e+03      12      37 ..     566     592 ..     561     599 .. 0.68
   8 ?   -2.5   0.0       8.4   8.3e+03      68      83 ..     611     626 ..     610     634 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.48
                 Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyacEslynia 55 
                                   e+ v+ ++ +++D+++ vR +a+  l ni 
  gi|91773182|ref|YP_565874.1| 197 ERTVDALIVALEDENRYVRRHAARGLGNIG 226
                                   567899999*************99999985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.1
                 Vac14_Fab1_bd  27 eivkpvlkcfsDkdsr 42 
                                   + v+p++++++D+d  
  gi|91773182|ref|YP_565874.1| 262 DAVEPLIQMLKDEDWS 277
                                   5677888888887755 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.7
                 Vac14_Fab1_bd  71 dalvklvaDsdesvksgae 89 
                                   d l+ l+ D+d+sv++ a+
  gi|91773182|ref|YP_565874.1| 326 DKLIDLLDDNDKSVQKNAA 344
                                   6788888899999987665 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.5
                 Vac14_Fab1_bd  30 kpvlkcfsDkdsrvRyyacEsl 51 
                                   kp++++++D++  +R  a+ +l
  gi|91773182|ref|YP_565874.1| 423 KPLIESLKDENPDIREAAANAL 444
                                   6777888888888877666655 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.089
                 Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEsl 51 
                                   ++ ++ +++D++ rvRy ++++l
  gi|91773182|ref|YP_565874.1| 453 LDALILSLEDENWRVRYSVVDAL 475
                                   66778899**********99998 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 3.8
                 Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyacEsly 52 
                                   +++v p+ ++++D+   vR +a+ sl 
  gi|91773182|ref|YP_565874.1| 481 KTVVLPISNMLDDEYWSVRKTAAQSLG 507
                                   578889999999999999999999885 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 6.9
                 Vac14_Fab1_bd  12 avaialekk.ikeyleeivkpvlkcfs 37 
                                   a+ai+l+k   ++ ++ +++++l+  +
  gi|91773182|ref|YP_565874.1| 566 AAAISLAKPgNEQAVDPLIQVMLDETQ 592
                                   567777776666777777777776554 PP

  == domain 8  score: -2.5 bits;  conditional E-value: 8.4
                 Vac14_Fab1_bd  68 eifdalvklvaDsdes 83 
                                   + fdal++++ D +e+
  gi|91773182|ref|YP_565874.1| 611 DAFDALSRISKDPNEH 626
                                   579*******998875 PP

>> TraW_N  Sex factor F TraW protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1         5     5e+03      17      25 ..     252     260 ..     251     260 .. 0.77
   2 ?    5.4   0.1     0.019        19      14      25 ..     374     385 ..     372     385 .. 0.89
   3 ?    4.4   0.0     0.037        37      15      25 ..     501     511 ..     500     511 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5
                        TraW_N  17 AkdLGviGp 25 
                                   A  LG+iG+
  gi|91773182|ref|YP_565874.1| 252 AIALGQIGD 260
                                   6669***96 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                        TraW_N  14 aAyAkdLGviGp 25 
                                   aA+A +LG+iG+
  gi|91773182|ref|YP_565874.1| 374 AAAASSLGTIGN 385
                                   8**********6 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.037
                        TraW_N  15 AyAkdLGviGp 25 
                                   ++A++LG+iG+
  gi|91773182|ref|YP_565874.1| 501 TAAQSLGTIGN 511
                                   68********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 3669.19
//
Query:       gi|91773183|ref|YP_565875.1|  [L=373]
Description: DNA topoisomerase VI subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-13   49.9   0.3    4.6e-13   48.9   0.3    1.5  1  TP6A_N    Type IIB DNA topoisomerase


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.3   2.6e-17   4.6e-13      12      61 ..      92     145 ..      81     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.6e-17
                                   HHHHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGT CS
                        TP6A_N  12 lihelleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLn 61 
                                   l++++l +++ +T+R++YY     d ++F++Qaes+rli+d+e +++++Re ++
  gi|91773183|ref|YP_565875.1|  92 LVKNHLAQDRGSTLRELYYIsenwDIAKFREQAESNRLIEDLEIITSLQREYFH 145
                                   56999***************99999**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.24s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2266.59
//
Query:       gi|91773184|ref|YP_565876.1|  [L=622]
Description: DNA topoisomerase VI subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  224.7   0.0    8.3e-67  224.0   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    3.5e-44  149.6   0.0    7.9e-44  148.5   0.0    1.6  1  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
    1.8e-10   41.3   0.0    3.7e-10   40.3   0.0    1.6  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    6.9e-07   29.2   0.0    1.4e-06   28.2   0.0    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    0.00091   18.1   0.0     0.0019   17.0   0.0    1.5  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp
  ------ inclusion threshold ------
      0.052   13.3   0.2        0.2   11.4   0.2    2.0  1  RPAP1_N         RPAP1-like, N-terminal
      0.089   13.2   0.1        1.1    9.7   0.0    2.5  3  Ribosomal_S13   Ribosomal protein S13/S18


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 !  224.0   0.0   3.2e-70   8.3e-67       1     159 []     312     475 ..     312     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 224.0 bits;  conditional E-value: 3.2e-70
                Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydegadvit 81 
                                   P+tdclspigeeli kgl+ke++++f+a++tr+p+v++g+pf+vEvgiayGG l+k+++++i+RfaNrvPLly++g++++t
  gi|91773184|ref|YP_565876.1| 312 PPTDCLSPIGEELIYKGLEKEFNVDFIATTTRSPSVFSGNPFVVEVGIAYGGVLQKDDRIDIMRFANRVPLLYQQGGCATT 392
                                   99******************************************************************************* PP

                Topo-VIb_trans  82 kavksinwkrYkleq.....pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkekekeek 157
                                   +av+ i+wk+Y+l+q     p++pvv+lvhvast+vPf+se+K+aiad++ei++e++la++ev rkL++yl+++ + k+++
  gi|91773184|ref|YP_565876.1| 393 HAVEGIKWKQYGLNQpgggmPTGPVVLLVHVASTNVPFTSESKDAIADIPEIRDEVELAIKEVSRKLNRYLNRQVSLKKRR 473
                                   **************************************************************************9999988 PP

                Topo-VIb_trans 158 ek 159
                                   ek
  gi|91773184|ref|YP_565876.1| 474 EK 475
                                   76 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 !  148.5   0.0   3.1e-47   7.9e-44       1     114 []     495     613 ..     495     613 .. 0.99

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 3.1e-47
                                   SSS---SHHHHHHHTT-EEEEEEE--SSS-.EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE- CS
                       Top6b_C   1 dreepdidpvvArimgnvlvereveengdg.vevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWels 80 
                                   +r+ pdi+pvvA++mgn+lv r+ve++++g ++v++kvkNf++k +ef+lh++lp+ei+++spe+kv++m++++d++W+++
  gi|91773184|ref|YP_565876.1| 495 ERDLPDINPVVAKVMGNLLVMRHVEHGANGdAAVTIKVKNFGSKLTEFKLHDMLPYEISDVSPEPKVISMGSDFDYVWTMK 575
                                   79******************************************************************************* PP

                                   --TT-EEEE----SS-GGGS--....B----------- CS
                       Top6b_C  81 vsageskvleYsvdseaeeels....liveGveeekvT 114
                                   vs++ sk+++Ys++s++e+e++    liveG++ee+vT
  gi|91773184|ref|YP_565876.1| 576 VSPEGSKAVTYSLSSMSEDEIKrlpqLIVEGLDEELVT 613
                                   *************************************9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   1.4e-13   3.7e-10       4      86 ..      36     128 ..      33     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.4e-13
                                   HHHHHHHHHHHHHHHHHHSTTT....EEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCS.TTCH.....HCSTCHTSTS CS
                     HATPase_c   4 krLrqiisnlvdNavkfatkag....eieveika.seddlvisveDnGiGipkedlkklfe.kfsq.....ddstkrgggg 73 
                                   + L   ++++vdN++++  ++     +i ++i++  +d++++ veDnG+Gi ke+++k+f+          + +++rg++g
  gi|91773184|ref|YP_565876.1|  36 RSLITTVKEAVDNSLDA-CEEAeilpDILLHIERvGKDNVSVIVEDNGPGIVKEQIPKVFAkL-LYgsrfhALKQSRGQQG 114
                                   678899**********8.33331222556666654348*******************999953.33368877788888899 PP

                                   SSHHHHHHHH.HHH CS
                     HATPase_c  74 tGlGlsivkk.lve 86 
                                    G+++s+  + l+ 
  gi|91773184|ref|YP_565876.1| 115 IGISASVLYAqLTA 128
                                   99998888775554 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 !   28.2   0.0   5.4e-10   1.4e-06       6      85 ..      41     124 ..      37     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 5.4e-10
                   HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklA 80 
                                    + e vdNsldA  e      + +++++  +++ ++ +eD+G G+ +e++ +++ +l   s+  +  ++s+G+ GiG+ +A
  gi|91773184|ref|YP_565876.1|  41 TVKEAVDNSLDACEEAeilpdILLHIERVGKDNVSVIVEDNGPGIVKEQIPKVFaKLLYGSRF-HALKQSRGQQGIGI-SA 119
                                   689*********9998999885555555546679******************77589999988.57899********4.44 PP

                   HATPase_c_3  81 slslg 85 
                                   s+  +
  gi|91773184|ref|YP_565876.1| 120 SVLYA 124
                                   43322 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 !   17.0   0.0   7.6e-07    0.0019     179     238 ..     250     307 ..     227     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.6e-07
                                   HHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHH CS
                          FbpA 179 kellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqel 238
                                     +  +  ++l+ +L  +f+ ++ l+aee+++ agld+e   ++l+ ++ ++l +a++++
  gi|91773184|ref|YP_565876.1| 250 LRY--TDRQKLAPFLRYSFSKIGLLTAEEICKAAGLDTEMLPSKLTRDQTKKLLDAFKKV 307
                                   333..256899**********************************************986 PP

>> RPAP1_N  RPAP1-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   7.9e-05       0.2      11      35 ..     588     612 ..     587     614 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                       RPAP1_N  11 LasMspeEIeeereeLlesLdPkll 35 
                                   L+sMs++EI++  + + e Ld  l+
  gi|91773184|ref|YP_565876.1| 588 LSSMSEDEIKRLPQLIVEGLDEELV 612
                                   99*******************9998 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00043       1.1      22      64 ..     268     310 ..     254     317 .. 0.87
   2 ?   -0.4   0.1      0.54   1.4e+03      54      88 ..     444     481 ..     432     499 .. 0.54
   3 ?   -2.7   0.0       2.9   7.5e+03      43      58 ..     588     603 ..     581     610 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00043
                 Ribosomal_S13  22 GiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqy 64 
                                    iG  +a++i+k+a++d+++  ++lt ++ +k+ +  ++ + +
  gi|91773184|ref|YP_565876.1| 268 KIGLLTAEEICKAAGLDTEMLPSKLTRDQTKKLLDAFKKVKIM 310
                                   58999*****************************999986554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.54
                 Ribosomal_S13  54 ieeive...nkaqykipnwinrqkdikdGkdshvvend 88 
                                   i+++ve   ++++ k + ++nrq  +k+ +++  + ++
  gi|91773184|ref|YP_565876.1| 444 IRDEVElaiKEVSRKLNRYLNRQVSLKKRREKEIIITK 481
                                   44444411122344566667887777766655544333 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.9
                 Ribosomal_S13  43 igelteeeiekieeiv 58 
                                   ++ ++e+ei+++ +++
  gi|91773184|ref|YP_565876.1| 588 LSSMSEDEIKRLPQLI 603
                                   5567788888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4090.48
//
Query:       gi|91773185|ref|YP_565877.1|  [L=143]
Description: CMP/dCMP deaminase, zinc-binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-20   71.7   0.0    4.5e-20   71.4   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.2e-18   67.2   0.0    1.5e-18   66.9   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.036   14.2   0.0    1.6  2  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
      0.026   14.6   0.0      0.038   14.1   0.0    1.3  1  Bd3614-deam      Bd3614-like deaminase
       0.15   12.1   0.0       0.53   10.4   0.0    1.7  2  NAD1             Novel AID APOBEC clade 1


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.3e-23   4.5e-20       6     100 ..       3      95 ..       1      96 [. 0.95

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.3e-23
                                   HHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEEEE--BHHHH CS
               dCMP_cyt_deam_1   6 kllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyvtlePCsmCa 86 
                                   +++++a+++a+   +   +++G+v+v+++ ii++g+n + ++ ++++HAE+++++ a++  g + ++ +ly tl PC  Ca
  gi|91773185|ref|YP_565877.1|   3 EFMQVAIDEARSGLNSGGIPIGSVLVRDDLIIGKGHNLRVQQDDPMAHAEISCLRDAGRV-G-SYRDSILYSTLMPCYLCA 81 
                                   79*********999********************************************99.4.5679************** PP

                                   HHHHHHT-SEEEEE CS
               dCMP_cyt_deam_1  87 kaiiqsgikkvvvg 100
                                    a++q+gikkv+vg
  gi|91773185|ref|YP_565877.1|  82 GAVVQFGIKKVIVG 95 
                                   ************97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   4.2e-22   1.5e-18       4     135 ..       2     131 ..       1     133 [. 0.88

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 4.2e-22
                   MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlepCdm 84 
                                   +++++ a+ e++ +++ ++ +ig v v d+ +i++g+n + ++ ++ aHaEi  l+ A   ++     d +ly tl pC  
  gi|91773185|ref|YP_565877.1|   2 DEFMQVAIDEARSGLNSGGIPIGSVLVRDDLIIGKGHNLRVQQDDPMAHAEISCLRDAGRVGSY---RDSILYSTLMPCYL 79 
                                   5789999***************************************************444444...6************* PP

                   MafB19-deam  85 CagaivqaglkklvygagnpkslnkLkvkekngrvelv...eddckeilkgffk 135
                                   Caga+vq g+kk++ g +   + +      +++ ve+v    d+c +++ +f+ 
  gi|91773185|ref|YP_565877.1|  80 CAGAVVQFGIKKVIVGES--RTFSGAREFMESHGVEVVdldLDECVAMMDDFIS 131
                                   ****************99..5555555556778888887878999999999986 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     1e-05     0.036      18      64 ..      44      88 ..      31      94 .. 0.74
   2 ?   -2.2   0.0       1.2   4.4e+03      55      69 ..     121     135 ..     120     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                         SNAD4 18 knkke.haEllflekikseldpsqeyrvtwylswsPCaeCaekiaefl 64
                                  +++   haE+  l++   ++      + ++y +  PC+ Ca ++++f 
  gi|91773185|ref|YP_565877.1| 44 QDDPMaHAEISCLRDA-GRV--GSYRDSILYSTLMPCYLCAGAVVQFG 88
                                  333337********99.333..34445579***************995 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                         SNAD4  55 eCaekiaeflaehpn 69 
                                   eC++ + +f++++p+
  gi|91773185|ref|YP_565877.1| 121 ECVAMMDDFISKEPE 135
                                   699999999999886 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    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      76      99 ..      66      89 ..      36     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                   Bd3614-deam 76 egarllvtlqcCkmCAalvvaaad 99
                                   ++ l++tl +C +CA+ vv+++ 
  gi|91773185|ref|YP_565877.1| 66 RDSILYSTLMPCYLCAGAVVQFGI 89
                                  5889***************99875 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.53      46      92 ..      46      87 ..      29      94 .. 0.77
   2 ?   -0.7   0.0      0.37   1.3e+03     127     149 ..     111     133 ..      96     139 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                          NAD1 46 eskcHaEllflnkikslklldpsqkykvtwylswSPCseCasklaef 92
                                  +  +HaE+  l+    ++       ++ ++y++  PC  Ca  +++f
  gi|91773185|ref|YP_565877.1| 46 DPMAHAEISCLRDAGRVGS-----YRDSILYSTLMPCYLCAGAVVQF 87
                                  3345999999888866666.....46668****************99 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.37
                          NAD1 127 gvklsimkyeefeycwetfVene 149
                                   gv++  ++++e+  + + f+++e
  gi|91773185|ref|YP_565877.1| 111 GVEVVDLDLDECVAMMDDFISKE 133
                                   55555566666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1008.48
//
Query:       gi|91773186|ref|YP_565878.1|  [L=406]
Description: peptidase U32 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-81  271.7   0.0    5.2e-81  271.2   0.0    1.2  1  Peptidase_U32  Peptidase family U32


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 !  271.2   0.0   2.9e-85   5.2e-81       2     231 ..      82     304 ..      81     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 271.2 bits;  conditional E-value: 2.9e-85
                 Peptidase_U32   2 eklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikekv 82 
                                   ++l   ++++a+ +vdavi +Dp+v++ a +    l++h+Stqan++n+++v+f+ +lGasrvvlaREls+e+ik+i+ ++
  gi|91773186|ref|YP_565878.1|  82 DDLDVVIDSVASSDVDAVIAWDPAVITKAVDA--GLRVHISTQANVSNWQTVEFYGSLGASRVVLARELSMENIKEIRWNT 160
                                   566778999*******************9999..*********************************************** PP

                 Peptidase_U32  83 pdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkdlclieelp 163
                                    dvelEvf+hGa+c a+sGrc+ls+y+ g+s+n+gec+qpcr+ ++l+ e+ ++         +g+ylls++dlc+ie++p
  gi|91773186|ref|YP_565878.1| 161 -DVELEVFIHGAMCQAISGRCYLSAYILGKSGNCGECSQPCRWGWKLVGEDGSEVD------LEGKYLLSARDLCMIEHIP 234
                                   .*********************************************9888754333......3477*************** PP

                 Peptidase_U32 164 elleaGvdslKIeGRmkspeyvatvvrvYreaidallagr..eevkeelkeeleklanrgltsgfllgrk 231
                                   el++ Gv+++K+eGR+k+++y++ v r+Yrea++++++g    e++ ++k+el++++nrg+++gf++g +
  gi|91773186|ref|YP_565878.1| 235 ELIDTGVNAFKVEGRLKDARYTSIVSRCYREALNSYCDGSytLEKARSWKDELASVFNRGFSTGFYFGVP 304
                                   ****************************************8888889*******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2577.45
//
Query:       gi|91773187|ref|YP_565879.1|  [L=132]
Description: transcription activator, effector binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-18   66.9   0.1    2.7e-18   66.7   0.1    1.1  1  GyrI-like  GyrI-like small molecule binding domain
    1.2e-07   32.0   0.1    1.4e-07   31.8   0.1    1.1  1  Cass2      Integron-associated effector binding protein


Domain annotation for each model (and alignments):
>> GyrI-like  GyrI-like small molecule binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.1     3e-22   2.7e-18      60     155 .]      34     132 .]       2     132 .] 0.84

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 3e-22
                                   -....STTCCCEEEEEEEECCCCCCGBTTSEEEEE-SEEEEEEEEECEGGGHHHHHHHHHHTHHHHTT-EEEESEEEEEEE CS
                     GyrI-like  60 e....etedeelkydigvtveirvegpeglefleipageyAvfrhkGpyddlqatyaklygewlpesgyerrdgpsiEiYl 136
                                   e    +  ++  + ++++ v+++ eg ++++ +e+p+g+++++ h+Gpy+d  +ty++l++ w++ +g+  + g  +E Yl
  gi|91773187|ref|YP_565879.1|  34 EdimrANSEGNADLEAVIPVSEKIEGVGDVKCYELPGGNMVKVVHNGPYEDTGPTYQELFA-WIDVNGL-KITGLKREAYL 112
                                   444456667778889999999999*************************************.*******.*********** PP

                                   CCCTS.SCGCEEEEEEEEEC CS
                     GyrI-like 137 sdpre.reeelkteiyipvk 155
                                   +dp++ ++e+  teiy+p+k
  gi|91773187|ref|YP_565879.1| 113 NDPHDvPPEDILTEIYVPIK 132
                                   ******************97 PP

>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   1.5e-11   1.4e-07      59     149 .]      34     131 ..       3     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.5e-11
                                   T......-CCGEEEEEEEEE-TTSSS-TT-EEEEE--EEEEEEEEESSSTT-HHHHHHHHHHCHCCHCTEEE-SSEEEEEE CS
                         Cass2  59 s......eenkfsyyagvevpsdsevpeglvkkeiPggkYavftiegdfeedlaeaweaiygellpnsnyerrggpdfEvy 133
                                   +       e++ + +a+++v+++ e   ++   e+Pgg+++++ ++g+ e+    ++++++ ++   ++++   g + E y
  gi|91773187|ref|YP_565879.1|  34 EdimranSEGNADLEAVIPVSEKIEGVGDVKCYELPGGNMVKVVHNGPYED-TGPTYQELFAWID-VNGLKI-TGLKREAY 111
                                   356666689999**************************************8.***********96.588888.66****** PP

                                   STTHHH....TEEEEEEEEE CS
                         Cass2 134 keepae....kseielyIPv 149
                                    ++p +    +   e+y+P+
  gi|91773187|ref|YP_565879.1| 112 LNDPHDvppeDILTEIYVPI 131
                                   7777667777*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1014.02
//
Query:       gi|91773188|ref|YP_565880.1|  [L=112]
Description: hypothetical protein Mbur_1207 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.8   7.6      0.029   14.6   7.6    1.0  1  DUF2878   Protein of unknown function (DUF2878)


Domain annotation for each model (and alignments):
>> DUF2878  Protein of unknown function (DUF2878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   7.6   1.6e-06     0.029       5      96 ..      13     101 ..       9     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-06
                       DUF2878   5 allfqlgWlaavlgaarglllllllllllllllhlalspsrkaelklllavlllGlllDslllalgvlsfaalsasllPlW 85 
                                   +l+f l+ ++avl+ +++ll l++l+l ++ +    ++ s+k +  + +  +++G+  + + ++lgv ++aa+    +PlW
  gi|91773188|ref|YP_565880.1|  13 LLIFALALIVAVLFWENNLL-LTFLILSIYGI--REYFWSEKGDNIVFVSGVIIGCSAEFIGTYLGVWTYAAPFFFNIPLW 90 
                                   688999999****9998644.44444555555..245677777777777***********************778889*** PP

                       DUF2878  86 lllLWllfalt 96 
                                   l   W l+ + 
  gi|91773188|ref|YP_565880.1|  91 LPFAWGLVSVI 101
                                   *9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 813.76
//
Query:       gi|91773189|ref|YP_565881.1|  [L=80]
Description: hypothetical protein Mbur_1209 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.038   14.0   0.0      0.043   13.8   0.0    1.1  1  Thioredoxin  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 ?   13.8   0.0   2.4e-06     0.043      19      60 ..      22      63 ..      10      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-06
                                  SEEEEE.EE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTT CS
                   Thioredoxin 19 klvlve.FyApwCghCkalaPeleklaeelkdkvklakvdvde 60
                                  ++vlve Fy + C +C++ +P+++++   +   +  ++ ++ +
  gi|91773189|ref|YP_565881.1| 22 DEVLVEyFYEDGCLKCQQTSPVIDSVIGSYD-SINYINHNIAT 63
                                  5677764899*****************9999.66666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 590.27
//
Query:       gi|91773190|ref|YP_565882.1|  [L=146]
Description: hypothetical protein Mbur_1210 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   33.9   7.2    3.9e-08   33.4   7.2    1.3  1  DUF2178   Predicted membrane protein (DUF2178)
  ------ inclusion threshold ------
       0.16   11.3   5.9       0.97    8.7   1.2    2.0  2  DUF4191   Domain of unknown function (DUF4191)
        1.3    9.4  12.6        1.8    8.9   7.2    2.2  2  DUF1430   Protein of unknown function (DUF1430)
        3.5    7.0   7.6       0.93    8.9   2.9    1.9  2  DUF2417   Region of unknown function (DUF2417)


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   7.2   8.7e-12   3.9e-08       9     100 ..      34     128 ..      24     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 8.7e-12
                       DUF2178   9 alvglgiwa...aignvllaviavaaGvllaillkkkve..evveDERlariaekAsrktlqillfliallgvvlivlksd 84 
                                    + ++++++   +ig  + ++++v++G  ++++++k +   ev +DE ++ri+  +s +tl i +++i+ll vvl  + + 
  gi|91773190|ref|YP_565882.1|  34 GIAAIALYSygdIIG--GNMMASVVIGLSISYIIRKAMLkdEVKKDEMVKRISGMSSDITLYISIISIGLLTVVLHFFPTL 112
                                   333444444544433..45778999**********998778************************************8888 PP

                       DUF2178  85 fpeytrvgfllafsal 100
                                   f  +  +++lla+ +l
  gi|91773190|ref|YP_565882.1| 113 FDVFEILAILLAVMLL 128
                                   8888888888887755 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0023        10      23      83 ..      23      85 ..      12      89 .. 0.68
   2 ?    8.7   1.2   0.00022      0.97      34      86 ..      97     145 ..      86     146 .] 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0023
                       DUF4191 23 kkllwlllaaflvvvvvfvvlglllg.slilllilgillgllvalivltrraeka.ayaqieg 83
                                  +++  +l ++f ++++++  +g ++g +++  +++g+ ++ ++   +l+  ++k  + ++i g
  gi|91773190|ref|YP_565882.1| 23 NRIYLILNMIFGIAAIALYSYGDIIGgNMMASVVIGLSISYIIRKAMLKDEVKKDeMVKRISG 85
                                  4444444444544555555666666527999*****************999987514566666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00022
                       DUF4191  34 lvvvvvfvvlglllgslilllilgillgllvalivltrraekaayaqiegqpG 86 
                                   + + +++vvl ++   + l+ ++ i l++l+a+++l++ a +  y++++++ G
  gi|91773190|ref|YP_565882.1|  97 ISIGLLTVVLHFF---PTLFDVFEI-LAILLAVMLLSKIALQMYYTKMKDEIG 145
                                   2222222222222...344444443.78999999***************9987 PP

>> DUF1430  Protein of unknown function (DUF1430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.3     0.022        99      22      62 ..      23      66 ..      18      74 .. 0.52
   2 ?    8.9   7.2    0.0004       1.8      21      89 ..      73     141 ..      56     146 .] 0.61

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.022
                       DUF1430 22 fkkkilikkihGyslfk..rhkeyliiqli.vllillvlifilt 62
                                  ++ ++++  i+G+ +++  ++   +  +++ +++i+l +++i++
  gi|91773190|ref|YP_565882.1| 23 NRIYLILNMIFGIAAIAlySYGDIIGGNMMaSVVIGLSISYIIR 66
                                  66666666777766544114455555444303334444444444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0004
                       DUF1430  21 qfkkkilikkihGysl.fkrhkeyliiqlivllillvlifiltk.ekiillvvlvlllielllillvqeki 89 
                                   + kk+ ++k+i+G+s  ++ + + + i l+++++ +  +  l +  +i+++++ v+ll ++ l++++ + +
  gi|91773190|ref|YP_565882.1|  73 EVKKDEMVKRISGMSSdITLYISIISIGLLTVVLHFFPT--LFDvFEILAILLAVMLLSKIALQMYYTKMK 141
                                   679999********9634555554444444444444333..333366666666666667777766665443 PP

>> DUF2417  Region of unknown function (DUF2417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2     0.067     3e+02      91     116 ..      26      55 ..      23      73 .. 0.71
   2 ?    8.9   2.9   0.00021      0.93      82     136 ..      92     146 .]      77     146 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.067
                       DUF2417  91 anllnllf....fglpSkldrvlnivlavL 116
                                   +++ln++f    ++l+S+ d + + ++a +
  gi|91773190|ref|YP_565882.1|  26 YLILNMIFgiaaIALYSYGDIIGGNMMASV 55 
                                   567777777777999999999887776654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00021
                       DUF2417  82 lalillslianllnllffglpSkldrvlnivlavLllvnllllllvkytReregf 136
                                   l + ++s++ + + l ff +   +  +l i lav+ll  ++l +  +++++++gf
  gi|91773190|ref|YP_565882.1|  92 LYISIISIGLLTVVLHFFPTLFDVFEILAILLAVMLLSKIALQMYYTKMKDEIGF 146
                                   66789************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1074.39
//
Query:       gi|91773191|ref|YP_565883.1|  [L=67]
Description: XRE family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-15   56.5   0.3    2.5e-15   56.3   0.3    1.1  1  HTH_3           Helix-turn-helix
    4.1e-10   39.5   0.2    4.4e-10   39.4   0.2    1.0  1  HTH_19          Helix-turn-helix domain
    2.4e-05   24.7   0.0    2.8e-05   24.5   0.0    1.1  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00013   22.2   0.0    0.00015   22.0   0.0    1.1  1  HTH_31          Helix-turn-helix domain
     0.0028   17.5   0.2     0.0042   17.0   0.2    1.3  1  HTH_11          HTH domain
     0.0059   16.5   0.1     0.0099   15.8   0.0    1.3  2  HTH_37          Helix-turn-helix domain
     0.0074   16.2   0.0      0.011   15.7   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.017   15.0   0.0    1.2  1  HTH_25          Helix-turn-helix domain
      0.015   15.1   0.0      0.018   14.9   0.0    1.2  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.028   14.0   0.0      0.038   13.5   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.048   13.2   0.0      0.072   12.6   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4
      0.067   13.3   0.0      0.073   13.2   0.0    1.1  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
        0.1   12.4   0.1       0.18   11.6   0.1    1.4  1  HTH_38          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.3   1.8e-18   2.5e-15       1      55 []       8      62 ..       8      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.8e-18
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                  +kelR + +l+q++LAek+Gv r ti  +E+G+ nPsl+ ++ +a+++  +++e+
  gi|91773191|ref|YP_565883.1|  8 IKELRAKYDLTQKDLAEKIGVRRETIVFLEKGKYNPSLKLAYDIAQVFESKIEEI 62
                                  8***********************************************9998885 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.2   3.2e-13   4.4e-10       3      62 ..       7      65 ..       6      67 .] 0.94

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.2e-13
                        HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqg 62
                                  ++ke+R ++ ltq++lae++g++r  i  +E+gk+ +ps +l ++ia+ ++  +e+++ +
  gi|91773191|ref|YP_565883.1|  7 KIKELRAKYDLTQKDLAEKIGVRRETIVFLEKGKY-NPSLKLAYDIAQVFESKIEEIFLF 65
                                  69********************************9.***************999999865 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 !   24.5   0.0     2e-08   2.8e-05       1      60 [.       7      65 ..       7      67 .] 0.95

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2e-08
                        HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLley 60
                                  k++el a+ ++t+++La+++g+ + t+  l kgk  ++sl+    i+++++ ++++++ +
  gi|91773191|ref|YP_565883.1|  7 KIKELRAKYDLTQKDLAEKIGVRRETIVFLEKGK-YNPSLKLAYDIAQVFESKIEEIFLF 65
                                  799******************************9.6********************9976 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.1e-07   0.00015       7      53 ..       9      54 ..       4      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                        HTH_31  7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealara 53
                                  ++lR++  L+q+++Ae +gv + t+  lE G+  +ps+     +a++
  gi|91773191|ref|YP_565883.1|  9 KELRAKYDLTQKDLAEKIGVRRETIVFLEKGKY-NPSLKLAYDIAQV 54
                                  789******************************.6*99876666665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   3.1e-06    0.0042       2      32 ..       4      33 ..       3      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                        HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtv 32
                                  l++ ++ L +a+ +++ ++LAe+++v r t+
  gi|91773191|ref|YP_565883.1|  4 LRTKIKEL-RAKYDLTQKDLAEKIGVRRETI 33
                                  6889999*.99999****************9 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.2e-06    0.0099      17      56 ..       2      41 ..       1      43 [. 0.90
   2 ?   -3.0   0.0       5.2   7.1e+03      19      28 ..      47      56 ..      45      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                                  HHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                        HTH_37 17 aqlalaiaeliekrelsqseaaqllgiaqPkvsrllrgkl 56
                                  ++l  +i+el++k +l+q+++a++ g+ +  ++ l++gk 
  gi|91773191|ref|YP_565883.1|  2 SKLRTKIKELRAKYDLTQKDLAEKIGVRRETIVFLEKGKY 41
                                  567778***********************99999999986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.2
                                  HHHHHHHHHH CS
                        HTH_37 19 lalaiaelie 28
                                  la+ ia++ e
  gi|91773191|ref|YP_565883.1| 47 LAYDIAQVFE 56
                                  7778888766 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 !   15.7   0.0     8e-06     0.011      19      38 ..      14      33 ..       2      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8e-06
                                  EEEHHHHHHHHHTTSSHHHH CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretv 38
                                  + +ltq++lA+ +G++ret+
  gi|91773191|ref|YP_565883.1| 14 KYDLTQKDLAEKIGVRRETI 33
                                  5689***************7 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.2e-05     0.017       3      36 ..       9      42 ..       7      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                  HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                        HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                  ++ R +  l+ +++a+++ +r +++  lE+++++
  gi|91773191|ref|YP_565883.1|  9 KELRAKYDLTQKDLAEKIGVRRETIVFLEKGKYN 42
                                  789****************************997 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.3e-05     0.018      10      51 ..      18      59 ..       8      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpaervpeIekatnGeV 51
                                  +qk LAe++gv ++++ ++ kgk + + +   +I ++ + ++
  gi|91773191|ref|YP_565883.1| 18 TQKDLAEKIGVRRETIVFLEKGKYNPSLKLAYDIAQVFESKI 59
                                  69*****************99999988888888888766555 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 ?   13.5   0.0   2.8e-05     0.038      10      29 ..       9      28 ..       8      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                        HTH_24 10 elLqknprisqreLAerlgl 29
                                  ++L+++ +++q++LAe++g+
  gi|91773191|ref|YP_565883.1|  9 KELRAKYDLTQKDLAEKIGV 28
                                  799999************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.2e-05     0.072      14      37 ..      10      33 ..       3      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                                  HHHHTTT--HHHHHHHHTS-HHHH CS
                    Sigma70_r4 14 elrfgeglTleEIgerlgiSrerV 37
                                  elr   +lT+++++e+ g+ re++
  gi|91773191|ref|YP_565883.1| 10 ELRAKYDLTQKDLAEKIGVRRETI 33
                                  5777889****************8 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 ?   13.2   0.0   5.3e-05     0.073      72     113 ..       6      47 ..       2      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                MqsA_antitoxin  72 afiarvrkkleldqreaaeifGgGvnafsryekGkvrpplal 113
                                   ++i+++r k +l+q+++ae  G+  ++    ekGk +p+l l
  gi|91773191|ref|YP_565883.1|   6 TKIKELRAKYDLTQKDLAEKIGVRRETIVFLEKGKYNPSLKL 47 
                                   67999********************************99876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.18      10      37 ..       5      33 ..       3      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                        HTH_38 10 ReeIerllaeG.lslreIArrLgrspsTI 37
                                  R +I  l+a+  l++++ A ++g+ + TI
  gi|91773191|ref|YP_565883.1|  5 RTKIKELRAKYdLTQKDLAEKIGVRRETI 33
                                  899****97666****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 422.51
//
Query:       gi|91773192|ref|YP_565884.1|  [L=177]
Description: heat shock protein DnaJ-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   34.7   2.0    2.3e-08   34.1   1.2    1.7  2  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.29   5.1e+03      32      44 ..     116     128 ..     113     132 .. 0.67
   2 !   34.1   1.2   1.3e-12   2.3e-08      12      55 ..     134     174 ..     125     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.29
                                   TSCCHHHHHHHHH CS
                          DnaJ  32 knpkdpeaeekFk 44 
                                    ++k +ea+e F 
  gi|91773192|ref|YP_565884.1| 116 IHDKRKEAREFFD 128
                                   4556668888876 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 1.3e-12
                                   G-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTS CS
                          DnaJ  12 asedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsd 55 
                                    + + I k+Y+++a+++HPDk    +  +ekFk++n A+++L+ 
  gi|91773192|ref|YP_565884.1| 134 NDFEAINKKYKEMAKELHPDKP---TGDTEKFKQLNVAHKILKR 174
                                   46678*****************...6677*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1276.34
//
Query:       gi|91773193|ref|YP_565885.1|  [L=1074]
Description: HsdR family type I site-specific deoxyribonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete 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-132  440.6  16.8   4.1e-132  440.6  16.8    1.6  2  DUF3387         Domain of unknown function (DUF3387)
      1e-80  270.6   0.1      1e-80  270.6   0.1    2.0  2  SWI2_SNF2       SWI2/SNF2 ATPase
    9.7e-49  166.0   7.9    4.1e-48  163.9   0.1    3.6  4  HSDR_N          Type I restriction enzyme R protein N terminu
    2.9e-15   56.7   0.0    2.9e-15   56.7   0.0    2.9  2  ResIII          Type III restriction enzyme, res subunit
    0.00063   20.1   0.2      0.041   14.2   0.0    3.4  3  Helicase_C      Helicase conserved C-terminal domain
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.43   10.5   0.0    1.9  2  Glyco_hydro_44  Glycoside hydrolase family 44


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 ?   -3.7   0.2         2   6.1e+03     153     175 ..     547     569 ..     534     572 .. 0.82
   2 !  440.6  16.8  1.4e-135  4.1e-132       1     330 [.     741    1068 ..     741    1069 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2
                       DUF3387 153 iLseefleevkkmkeknlavelL 175
                                    L++e l+e +k k k +++e+L
  gi|91773193|ref|YP_565885.1| 547 ELEKENLAETQKAKAKWTQLEAL 569
                                   47788899999999999999988 PP

  == domain 2  score: 440.6 bits;  conditional E-value: 1.4e-135
                       DUF3387    1 sggkgkptedieeavavlkeklevvrellhgfdyskfftadpkeklellleaaehilsleegkkrFlklvkaLkkayal 79  
                                    sggkg+p+  +e av++++ekle+v++++hgf+y+++f ad+++kl+++l+a+ehil le+gkkr++++v+aL++a+++
  gi|91773193|ref|YP_565885.1|  741 SGGKGDPAVLQESAVQLMLEKLEIVSQMFHGFSYEHYFAADTSTKLSIILAAEEHILGLENGKKRYIDEVTALSRAFSI 819 
                                    689**************************************************************************** PP

                       DUF3387   80 capseeaeelrdevaffqavrailvKltaaeegkspdteeleaavrqlidkaiaseevvdifaaaglekpdisiLseef 158 
                                    ++p+eea++++de++f+qa++a+lvK++++ +gk+   ee+e+a+rq+id+a+++e+v+d+f+aag++kpdisiLse+f
  gi|91773193|ref|YP_565885.1|  820 AIPHEEAMDVKDEISFYQAIKARLVKFDSTGTGKTD--EEIETAIRQVIDQALVTEQVIDVFDAAGIKKPDISILSEDF 896 
                                    ****************************98777766..5**************************************** PP

                       DUF3387  159 leevkkmkeknlavelLkklLadeikarsrkNlvkskkFserLeelikkYnnraltsaevieeLielakeikeekkrge 237 
                                    l ev++m++kn+a+e+LkklL+deikar +kNlv+sk+++e+Le++ikkY+n+ +t+aevieeLiel+keik  +k+  
  gi|91773193|ref|YP_565885.1|  897 LLEVQNMEHKNIALEVLKKLLNDEIKARVKKNLVQSKSLMEMLEDSIKKYHNKVITAAEVIEELIELSKEIKRMDKEPL 975 
                                    ******************************************************************************* PP

                       DUF3387  238 elgLseeElAFYdaLaenesavevmgddkLkelAkelvetvrknatiDWtkresvrAklrvavkrlLrkygYPpdkqee 316 
                                    e+gLse E+AFY+a+a+n+sa+e+m+++kL+elA  l +++++na+iDWt++esvrAkl+v vkr+Lr+ygYPpd q+ 
  gi|91773193|ref|YP_565885.1|  976 EMGLSEFEYAFYTAIADNDSARELMQKEKLRELAVVLFDKIKQNASIDWTIKESVRAKLKVIVKRTLRQYGYPPDLQAL 1054
                                    ******************************************************************************* PP

                       DUF3387  317 aveeVleQaellak 330 
                                    a+e+Vl+Qael+++
  gi|91773193|ref|YP_565885.1| 1055 ATETVLKQAELITD 1068
                                    ***********986 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.6   0.1   3.4e-84     1e-80       1     214 [.     276     551 ..     276     561 .. 0.93
   2 ?   -2.2   1.2      0.88   2.6e+03      55     110 ..     865     923 ..     852     968 .. 0.63

  Alignments for each domain:
  == domain 1  score: 270.6 bits;  conditional E-value: 3.4e-84
                     SWI2_SNF2   1 qQyravekavervke.................................gdrkgGviWHtqGSGKsltmvflakklleeelk 48 
                                   +Qy+av++ave++ +                                 gdrkgGv+WHtqGSGKsl+mvf++ k++  +++
  gi|91773193|ref|YP_565885.1| 276 HQYYAVNRAVESTLRasgyaaakdwqifglhhespesyglpgvteqpiGDRKGGVVWHTQGSGKSLSMVFYTGKIVL-AMD 355
                                   8************999********************************99***************************.*** PP

                     SWI2_SNF2  49 npkvvvvtDRkdLdkQlsktfaka...geekpkqaesrkeLkellekesekiifttiqKfeeeekeklevlsereniivlv 126
                                   np+vvv+tDR+dLd+Ql++tfa++    +++p+qae+r +Lkell+ +s++++fttiqKf++ee + +++ls+r+niiv++
  gi|91773193|ref|YP_565885.1| 356 NPTVVVITDRNDLDDQLFDTFAASkqlLRQEPVQAENRGHLKELLNVASGGVVFTTIQKFQPEEGNVYPKLSDRRNIIVIA 436
                                   **********************975556999******************************999999************** PP

                     SWI2_SNF2 127 DEaHRsqyg......................elakklrkalpnaafigFTGTPilkkdkktkevFgeyidkYtikeaveDg 185
                                   DEaHR+qyg                      ++ak+ r+alpna+++gFTGTPi+k+d +t +vFg+y+d Y+i++aveDg
  gi|91773193|ref|YP_565885.1| 437 DEAHRTQYGfkaktidikdeqgnvigqkivyGFAKYTRDALPNATYLGFTGTPIEKTDVNTPAVFGNYVDIYDISQAVEDG 517
                                   ********************************************************************************* PP

                     SWI2_SNF2 186 avvpilYesrlaklelkeeek.....ldeefeei 214
                                   a+v+i+Yesrlak+ l++e k     ldee+e+ 
  gi|91773193|ref|YP_565885.1| 518 ATVKIYYESRLAKIILSKEGKklvseLDEELEKE 551
                                   **************99998755333333333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.88
                     SWI2_SNF2  55 vtDRkdLdkQlsktfakageekpk.qaesrkeLkellekesekiifttiqKfeee..ek 110
                                   v+D     +Q+ + f++ag +kp+ ++ s++ L e  + e+++i + +++K+ ++  ++
  gi|91773193|ref|YP_565885.1| 865 VIDQALVTEQVIDVFDAAGIKKPDiSILSEDFLLEVQNMEHKNIALEVLKKLLNDeiKA 923
                                   67777778888888888876666524555555555556668888888888886331222 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.9   0.1   1.4e-51   4.1e-48       3     191 ..       2     205 ..       1     208 [. 0.95
   2 ?   -1.6   0.1      0.73   2.2e+03      38      83 ..     540     582 ..     524     624 .. 0.55
   3 ?   -0.5   0.0      0.35     1e+03      59     131 ..     801     894 ..     763     929 .. 0.69
   4 ?    4.2   0.2     0.012        37      38     106 ..     943    1019 ..     925    1028 .. 0.79

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 1.4e-51
                                   SHHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH...........-HHHHHHHH..TT CS
                        HSDR_N   3 sEaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgaln...........ikkltkrla..ls 70 
                                   +E+++e+ +++ell+++Gyq+    d+++++++pe r++ ++v l ++lr+++g++n           i++++++ +  l 
  gi|91773193|ref|YP_565885.1|   2 TESAIEE-FAIELLEHQGYQYIYAPDITPDSDTPE-RERFEDVLLSERLRKSIGRINptipadaredaIRQIQRLNSpeLI 80 
                                   8998888.***************************.99*****************************9999999999**** PP

                                   --HHHHHHHHHTS.-EEEE...TS-EEEEESS-SSSGGGS-EEEEE----S.SSS---EEEEEEETTEEEEEEEE--T... CS
                        HSDR_N  71 dgnkefyellkeg.kvkfk...egrkknikLiDkknlenNrfqvvnQvtvt.gnqkrrpDivlfvnglplvviElKrp... 143
                                   ++n++f+++l+eg kv ++    +r + ++L+D++++enN+f v+nQ+tv  +n ++rpDi+lfvnglplvviElK+p   
  gi|91773193|ref|YP_565885.1|  81 ANNEAFHRMLTEGiKVSYQkdgADRGDLVWLVDFNDPENNEFLVTNQFTVIeNNVNKRPDIILFVNGLPLVVIELKNPade 161
                                   *****************87799899999**********************98999***********************886 PP

                                   T.-HHHHHHHHTSS---.---SSSGGGGG--EEEEE-SS-EEEEE--SS CS
                        HSDR_N 144 g.tieeAinQikryrkeksdvsipqlfrYlqfgvisngketrfyaktkr 191
                                   + t++ A++Q+++y+++     i +lf+Y+ f+vis+g e++ ++ +++
  gi|91773193|ref|YP_565885.1| 162 NaTVRSAFRQLQTYKQA-----ISSLFAYNGFMVISDGLEAKSGSLSAG 205
                                   26*************88.....9******************99887765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.73
                                   .----SHHHHHHHHHHHHHHHH..............-HHHHHHHHTT--HHHHHHHHHTS CS
                        HSDR_N  38 vrkskaevaleknlreqlgaln..............ikkltkrlalsdgnkefyellkeg 83 
                                   ++++++e+  ++nl e+++a+               i                 + ++++
  gi|91773193|ref|YP_565885.1| 540 LVSELDEELEKENLAETQKAKAkwtqlealigsegrI-----------------RQIAQD 582
                                   4455555555555555555433333333333333332.................333333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.35
                                   H.....-HHHHHHHH............TT--HHHHHHHHHTS-EEEE.TS-EEEEESS-SSSGGGS-EEEEE----S.... CS
                        HSDR_N  59 n.....ikkltkrla............lsdgnkefyellkegkvkfk.egrkknikLiDkknlenNrfqvvnQvtvt.... 117
                                   n     i+++t++ +              + + +fy+ +k   vkf+  g+ k+      +++e  + qv+ Q+ vt    
  gi|91773193|ref|YP_565885.1| 801 NgkkryIDEVTALSRafsiaipheeamDVKDEISFYQAIKARLVKFDsTGTGKT-----DEEIETAIRQVIDQALVTeqvi 876
                                   455555344433333333555555555556667788888888888887444444.....6688888888888888888888 PP

                                   ....SSS---EEEEEEET CS
                        HSDR_N 118 ....gnqkrrpDivlfvn 131
                                         + ++pDi+++  
  gi|91773193|ref|YP_565885.1| 877 dvfdAAGIKKPDISILSE 894
                                   888888888888888765 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.012
                                    .----SHHHHHHHHHHHHHHHH..-HHHHHHHH...TT--HHHHHHHHHTS.-EE.EE.TS-EEEEESS-SSSGGGS CS
                        HSDR_N   38 vrkskaevaleknlreqlgaln..ikkltkrla...lsdgnkefyellkeg.kvk.fk.egrkknikLiDkknlenN 106 
                                     +k +++v++ +++ e l +l   ik + k++    ls+ +++fy+ ++++ +   ++ +++ ++  ++ ++++++N
  gi|91773193|ref|YP_565885.1|  943 IKKYHNKVITAAEVIEELIELSkeIKRMDKEPLemgLSEFEYAFYTAIADNdSAReLMqKEKLRELAVVLFDKIKQN 1019
                                    5788889999999999999999999999999999*****************88776668666666665655555555 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 !   56.7   0.0   9.7e-19   2.9e-15      21     170 ..     290     490 ..     252     491 .. 0.75
   2 ?   -3.4   3.1       2.9   8.7e+03      99      99 ..     901     901 ..     840    1015 .. 0.59

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 9.7e-19
                                   ...................................TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHH CS
                        ResIII  21 s.................................krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslle 68 
                                                                      ++k g+++++ G+GK+l ++  + ++  + ++  ++++ +r++l +
  gi|91773193|ref|YP_565885.1| 290 RasgyaaakdwqifglhhespesyglpgvteqpiGDRKGGVVWHTQGSGKSLSMVFYTGKIVLAMDNPTVVVITDRNDLDD 370
                                   2345555555566666666666666666666666688999***************************************** PP

                                   HHHHHGGGGTGG.........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGT CS
                        ResIII  69 qtleefkkflseayke.....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrl 144
                                   q+ ++f+  ++  ++e     + + +++        +  +  +++ttiq+++ ++    +   +l++ r+ ++i DEaHr+
  gi|91773193|ref|YP_565885.1| 371 QLFDTFAASKQLLRQEpvqaeNRGHLKEL------LNVASGGVVFTTIQKFQPEE---GNVYPKLSDRRNIIVIADEAHRT 442
                                   ******77777666555322233333333......35569***************...7777788888888********** PP

                                   TS.........T................TTHHHHHT---SEEEEEESS-S CS
                        ResIII 145 gak........k................swreilekfkeavllglTATpe 170
                                   ++         k                ++++  +++++a+ lg+T+Tp 
  gi|91773193|ref|YP_565885.1| 443 QYGfkaktidiKdeqgnvigqkivygfaKYTR--DALPNATYLGFTGTPI 490
                                   **988766665155566665566665445555..99999*********96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.9
                                   . CS
                        ResIII  99 k 99 
                                   +
  gi|91773193|ref|YP_565885.1| 901 Q 901
                                   2 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 ?    1.7   0.0      0.11   3.3e+02      28      75 ..      38      84 ..       5     100 .. 0.71
   2 ?   -3.6   0.0       4.7   1.4e+04      12      30 ..     255     273 ..     243     287 .. 0.61
   3 !   14.2   0.0   1.4e-05     0.041      45     110 ..     648     712 ..     584     713 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                  HHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG CS
                    Helicase_C 28 rlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdv 75
                                  r+e   ll e+   ++ +++ ++p++ re++++q ++ +s  Lia + 
  gi|91773193|ref|YP_565885.1| 38 RFE-DVLLSERLRKSIGRINPTIPADAREDAIRQIQRLNSPELIANNE 84
                                  443.2334455589999*****************98777778887665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.7
                                   HTTTTSEEEEEESSHHHHH CS
                    Helicase_C  12 leeeggkilifvntidrle 30 
                                   ++e++ + +i ++t+++l 
  gi|91773193|ref|YP_565885.1| 255 KKEDRTTGIITIQTVKKLA 273
                                   3444555588888888774 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.4e-05
                                   EESTTSTHHHHHHHHHHHH..TTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  45 vlhgelpqnereeileqfn..kgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   ++h  +++++r++  e+++  ++e +++i  d+  +G d+p+++++ + d p + ++++q+i R+ R+
  gi|91773193|ref|YP_565885.1| 648 KHH--TTKEQRRALAERMKdpEDELKLVIVRDMWLTGFDVPCLHTMYI-DKPMKGHTLMQAIARVNRV 712
                                   333..69***********98789999***************9999875.7777779999*****9997 PP

>> Glyco_hydro_44  Glycoside hydrolase family 44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   4.8e+03     161     180 ..     468     487 ..     463     527 .. 0.86
   2 ?   10.5   0.0   0.00014      0.43     146     194 ..     947     994 ..     940    1021 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                                   HHHHHHHHH-TT-EEEEEEE CS
                Glyco_hydro_44 161 dlAkavkaadpdaevlGpas 180
                                    +Ak  ++a p+a+ lG+  
  gi|91773193|ref|YP_565885.1| 468 GFAKYTRDALPNATYLGFTG 487
                                   58999999*****9999875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                                   --S---HHHHHHHHHHHHHHHHHH-TT-EEEEEEE-SHHHHTTT-..TT CS
                Glyco_hydro_44 146 hpekvtydellertidlAkavkaadpdaevlGpaswgwtayfqsaaepd 194
                                   h + +t++e++e  i+l+k +k++d +   +G +++ +++y   a ++d
  gi|91773193|ref|YP_565885.1| 947 HNKVITAAEVIEELIELSKEIKRMDKEPLEMGLSEFEYAFYTAIA-DND 994
                                   78889***********************************96665.344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1074 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1359  (0.075799); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); 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):               6  [number of targets reported over threshold]
# CPU time: 0.84u 0.28s 00:00:01.12 Elapsed: 00:00:00.44
# Mc/sec: 7336.97
//
Query:       gi|91773194|ref|YP_565886.1|  [L=342]
Description: hypothetical protein Mbur_1214 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-108  360.5   5.0     5e-108  360.1   5.0    1.1  1  Virulence_RhuM  Virulence protein RhuM family
  ------ inclusion threshold ------
      0.084   12.4   0.0       0.26   10.9   0.0    1.8  1  GerE            Bacterial regulatory proteins, luxR family


Domain annotation for each model (and alignments):
>> Virulence_RhuM  Virulence protein RhuM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.1   5.0  5.6e-112    5e-108       2     251 ..      69     322 ..      68     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 360.1 bits;  conditional E-value: 5.6e-112
                Virulence_RhuM   2 vvkkfrtvakegkreverevklynLdaiiavGyrvkskratqFRkWatkvlkeylikGfvldderlkngkklgkdyfdell 82 
                                   + +++++v+ eg+rev+r+vk+y+L+aiiavGyrv+s+r++qFR+Wa ++l++y+ kGf++d++r+k g++++++yfd+ll
  gi|91773194|ref|YP_565886.1|  69 TAEDLSVVQIEGDREVTRTVKCYSLEAIIAVGYRVNSERGIQFRQWAISILQQYIHKGFAIDSDRFKYGSRFSTRYFDDLL 149
                                   788999*************************************************************************** PP

                Virulence_RhuM  83 erirdiRasErrfyqkvtdiyatsiDYdkkseatkeFfatvqnklhyavtgktaaeliveradaekenmgLttwkga...k 160
                                   e+irdiR+sEr++yqk+tdiyatsiDY++k++ t++Ffa vqnklh+a+tg+taae+i +ra ++k+nmgLt+w++    k
  gi|91773194|ref|YP_565886.1| 150 EEIRDIRSSERMLYQKITDIYATSIDYSPKAQDTQKFFAVVQNKLHFAITGQTAAEIINTRARSDKQNMGLTSWRKGpdgK 230
                                   ***************************************************************************98899* PP

                Virulence_RhuM 161 vlksdvtiakNYLseeelkeLnrivsayldlaelqakrrkeltmedwaekldeflelndkevLkdaGkisaeqakekaeke 241
                                   ++  dv+iakNYL+++el++Lnriv++yld aelqa r+k+++m+dw+ kl++fl+++++e+L++aG+is+e a + ++ke
  gi|91773194|ref|YP_565886.1| 231 IMPGDVAIAKNYLDKTELDHLNRIVTMYLDHAELQAIRNKPMYMKDWIGKLNAFLKFSEYEILTNAGQISHEVALALVSKE 311
                                   ********************************************************************************* PP

                Virulence_RhuM 242 yekfk.kqrkk 251
                                   ye fk  q+k+
  gi|91773194|ref|YP_565886.1| 312 YEVFKkIQDKN 322
                                   *****667665 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.9e-05      0.26      20      43 ..      37      60 ..      35      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.9e-05
                                  HHHHHHHHTS-HHHHHHHHHHHHH CS
                          GerE 20 nkeIAeelniSekTVkvhksnimk 43
                                   k IAe  ++S+ +++ h++ni+k
  gi|91773194|ref|YP_565886.1| 37 QKRIAELFGCSADNISLHLKNIYK 60
                                  689*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2305.98
//
Query:       gi|91773195|ref|YP_565887.1|  [L=344]
Description: hypothetical protein Mbur_1215 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-115  385.2   9.1   1.5e-115  384.8   9.1    1.1  1  Virulence_RhuM  Virulence protein RhuM family
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.091   12.5   0.0    1.6  1  HTH_38          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Virulence_RhuM  Virulence protein RhuM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.8   9.1  1.6e-119  1.5e-115       1     251 [.      69     324 ..      69     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 384.8 bits;  conditional E-value: 1.6e-119
                Virulence_RhuM   1 avvkkfrtvakegkreverevklynLdaiiavGyrvkskratqFRkWatkvlkeylikGfvldderlkn.gkklgkdyfde 80 
                                   ++v++frtv++eg+r+ver++++ynLda+i+vGyrv+s +atqFR+Watk+lkey+ikGfvldderlk+ ++ +gkdyf+e
  gi|91773195|ref|YP_565887.1|  69 STVRNFRTVQAEGSRQVERDLEYYNLDAVISVGYRVNSYQATQFRIWATKILKEYIIKGFVLDDERLKQgNQVFGKDYFEE 149
                                   699******************************************************************88899******* PP

                Virulence_RhuM  81 llerirdiRasErrfyqkvtdiyatsiDYdkkseatkeFfatvqnklhyavtgktaaeliveradaekenmgLttwkga.. 159
                                   llerir+iRasErrfyqk+tdiya+s+DYdk++ +tkeFfa+vqnklh+a+tgktaae+i++ ada+k +mgLt+wk+a  
  gi|91773195|ref|YP_565887.1| 150 LLERIREIRASERRFYQKITDIYALSADYDKNAPVTKEFFASVQNKLHWAITGKTAAEIIYDSADATKIHMGLTNWKQApd 230
                                   *****************************************************************************9999 PP

                Virulence_RhuM 160 .kvlksdvtiakNYLseeelkeLnrivsayldlaelqakrrkeltmedwaekldeflelndkevLkdaGkisaeqakekae 239
                                    k++ksdv+iakNYL e +++eLn+i+sayldlae++a+r++ ++m+dw++ l++flel+++ +L+d+Gk+s  +ak kae
  gi|91773195|ref|YP_565887.1| 231 gKIMKSDVSIAKNYLGEAHIRELNQIISAYLDLAENRAQRHILMKMQDWSKFLHSFLELSSYPILNDKGKVSGLEAKLKAE 311
                                   9******************************************************************************** PP

                Virulence_RhuM 240 keyekfk.kqrkk 251
                                   +eye+++ +q+k+
  gi|91773195|ref|YP_565887.1| 312 QEYEEYRvTQDKN 324
                                   *******777665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05     0.091      21      42 ..      36      57 ..      29      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                        HTH_38 21 lslreIArrLgrspsTIsRElk 42
                                  l++++I+++ g+s+ TIs ++k
  gi|91773195|ref|YP_565887.1| 36 LTQKAIGKLFGKSKATISEHIK 57
                                  689***************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2011.54
//
Query:       gi|91773196|ref|YP_565888.1|  [L=274]
Description: hypothetical protein Mbur_1216 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1882.29
//
Query:       gi|91773197|ref|YP_565889.1|  [L=183]
Description: hypothetical protein Mbur_1217 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.5    7.1  28.3         13    5.6  28.3    1.7  1  DUF4271   Domain of unknown function (DUF4271)


Domain annotation for each model (and alignments):
>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  28.3   0.00075        13      53     188 ..       8     140 ..       2     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00075
                       DUF4271  53 flllltclllglllylllsefgslfgsylassllllliiflilllylllKlllykllgwlFfdkkkirqwifsylsylsll 133
                                   f l l++lll+l+++l+ +e  +++   + s+l ++++++l +l++l++ +l ++l+++l  d ++i++   s++   + +
  gi|91773197|ref|YP_565889.1|   8 FVLTLNSLLLSLMVFLVKEEIVINSLHPYISNLPNIITYILYFLVILIFTWLSMQLTNTL--DTDEIDEGSISVIEPANDA 86 
                                   4556778999*********97766665555999999*******************99987..8888999999999999999 PP

                       DUF4271 134 glllfplvlllvyfplssqillililiillliklllllyksirifkrkkfsllYl 188
                                   +l  ++  ++++++ +++++++++++ii+++i++ + + ++  if+   f+++Y+
  gi|91773197|ref|YP_565889.1|  87 FLPSYLGYFFVALSVPNIEVFFYVFTIICVFIFYSR-ISYFNPIFFLFGFNFYYI 140
                                   9999999*****************************.999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1410.10
//
Query:       gi|91773198|ref|YP_565890.1|  [L=351]
Description: restriction modification system DNA specificity subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-39  134.4   0.8    2.3e-21   76.8   0.0    2.1  2  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   1.3e-25   2.3e-21       3     167 ..       4     157 ..       2     158 .. 0.94
   2 !   56.6   0.1   1.9e-19   3.5e-15       2     139 ..     174     299 ..     173     328 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 1.3e-25
                                   T-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HHHCCTEE-HHHHCCTT---B-TT-EEEE-SSSTT-EEEESS-BEE- CS
                   Methylase_S   3 dwevvkLgdvfeikkgktpkkkelkengkypyiragilnnkvvkdglgykkkyilpkgdilissratiGkvayrdkkyyln 83 
                                   +w++ kLgdv  ++ gk+++   ++ +gk+p++++         + +gy ++ +++++ ++i+ ++t+Gk+ y++ ++++ 
  gi|91773198|ref|YP_565890.1|   4 KWKKCKLGDVLVLNYGKSLPE-RKRVEGKIPVYSSA--------GLTGYHNETLVNSEGLIIGRKGTVGKIYYSKTPFFCI 75 
                                   7*******************7.**************........9999********************************* PP

                                   TTEEEEEEST.TT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Methylase_S  84 qsvivlipkn.kkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldntielekkik 163
                                   + ++++ p + k  + +f+y++l+++   l+ l+  s+ p+l+  +  ++ I lPpl+eQ  Ia+ Ls+ld++i+l ++++
  gi|91773198|ref|YP_565890.1|  76 DTAYYILPEEtKYYL-NFIYYLLKTI--GLEELNEDSAVPRLNRNTAYSQDILLPPLPEQRAIASVLSSLDDKIDLLHRQN 153
                                   ********8755555.9999999988..88888889********************************************9 PP

                                   HHHH CS
                   Methylase_S 164 neie 167
                                   +++e
  gi|91773198|ref|YP_565890.1| 154 KTLE 157
                                   9998 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 1.9e-19
                                   TT-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HHHCCTEE-HHHHCCTT---B-TT-EEEE-S.SSTT-EEEESS-BE CS
                   Methylase_S   2 edwevvkLgdvfeikkgktpkkkelkengkypyiragilnnkvvkdglgykkkyilpkgdilissr.atiGkvayrdkkyy 81 
                                   e+we+ +Lgdv+ +++gk+ +  ++  +g++p+++ +        ++lgy++k ++++ +++i+   a++G+  +  ++++
  gi|91773198|ref|YP_565890.1| 174 EGWEEGTLGDVASFHNGKKRP--DDIIEGNIPIYGGN--------GILGYSDKSNNEGVTVIIGRVgAYCGSLYIERNPVW 244
                                   79************9999888..57889*********........9*****************9668************** PP

                                   E-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--H CS
                   Methylase_S  82 lnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpl 139
                                    ++++ v +p+ +k++++fl+++l+ +  +l+ +  gs +p lt+  lk+i+I lPp 
  gi|91773198|ref|YP_565890.1| 245 ISDNALVAKPI-NKEHSSFLFFLLKSL--QLNEIAEGSSHPLLTQNLLKSIQIILPPE 299
                                   **********9.566667777777655..8999999********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2363.07
//
Query:       gi|91773199|ref|YP_565891.1|  [L=381]
Description: hypothetical protein Mbur_1219 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-66  223.4   3.3    1.3e-66  223.2   1.7    1.8  2  YhcG_C        YhcG PDDEXK nuclease domain
    1.2e-43  148.5   6.5      2e-43  147.8   6.5    1.3  1  DUF1016_N     DUF1016 N-terminal domain
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.21   11.7   0.0    1.3  1  Alpha-L-AF_C  Alpha-L-arabinofuranosidase C-terminal domain


Domain annotation for each model (and alignments):
>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.3   1.8e+03       8      43 ..      25      62 ..      18      80 .. 0.67
   2 !  223.2   1.7   2.2e-70   1.3e-66       2     155 .]     213     366 ..     212     366 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.3
                        YhcG_C  8 yvldflelkeeykErelekal..ieklkkfllelGkgF 43
                                  y + + elk++++  +++ a+   ++l +f  elG++ 
  gi|91773199|ref|YP_565891.1| 25 YSVWLNELKNKVRLVQIKAAVkvNSELLQFYWELGQDI 62
                                  55556666666666666655411567889999999874 PP

  == domain 2  score: 223.2 bits;  conditional E-value: 2.2e-70
                        YhcG_C   2 eilkdpyvldflelkeeykErelekalieklkkfllelGkgFafvgrqyrleveekefyidLlfYhlklkcyvvieLKvge 82 
                                   e+lkdpy++dfl+l+e+++E+ele+ali+++++fllelG+gF+++g+qy+lev+++ef+idLlfYh+kl+cyvv+eLK+ +
  gi|91773199|ref|YP_565891.1| 213 ETLKDPYNFDFLTLTEKHNEKELEDALINHVTHFLLELGAGFSYLGKQYKLEVSGDEFFIDLLFYHVKLHCYVVVELKAVK 293
                                   689****************************************************************************** PP

                        YhcG_C  83 fkpedagklnlYlsaldeelkkeednptiGiilckekdktvveyalkeinkpigvseYelpkelpeelkeklp 155
                                   fkpe+agkln+Y+sa+de lk+e+d++tiGi++ck+k++tvvey+lk+++kpigvseY ++k+lp+e+k++lp
  gi|91773199|ref|YP_565891.1| 294 FKPEFAGKLNFYISAVDEILKSEQDDTTIGILICKSKNDTVVEYSLKDVHKPIGVSEYIITKNLPDEFKSSLP 366
                                   *********************************************************************9996 PP

>> DUF1016_N  DUF1016 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   6.5   3.3e-47     2e-43       2     137 .]      32     191 ..      31     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 3.3e-47
                     DUF1016_N   2 ikelieqarqkaakavnselvelyweiGkrivekqeraeyGkkvikkLsedLkkefpevkGFsernlknmrqfyeayk.ee 81 
                                   +k++++  ++kaa++vnsel+++ywe+G++iv+kq+++++G++++k+Ls dL++efp++kGFs +nlk+++q+y +y+ e 
  gi|91773199|ref|YP_565891.1|  32 LKNKVRLVQIKAAVKVNSELLQFYWELGQDIVNKQKNTKWGAGFLKQLSIDLSSEFPDTKGFSLSNLKYIKQWYLFYSrEF 112
                                   7899999**********************************************************************9788 PP

                     DUF1016_N  82 eilqqlvaq.......................lsWshnllllekvkdeeerefYleeaieegWsrreLerqiksklyer 137
                                   e+ qq+v q                       ++W+hn+++++k+k+ +e+ fY++++i+++Wsr++L+++i+s+l++r
  gi|91773199|ref|YP_565891.1| 113 EKSQQAVGQnssksllqseksfeqqavaqltqVPWGHNIVIISKCKNLNEALFYIQKTIQNNWSRSVLTHHIESNLFKR 191
                                   99999998556666666666666666666777*********************************************98 PP

>> Alpha-L-AF_C  Alpha-L-arabinofuranosidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.5e-05      0.21      46     105 ..     137     288 ..     136     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                                   -SBSTT-......SEEEETTE.EEE-HHHHHHHHHHHS--SEEEEEEEE--EEEEEEEET..................... CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                  Alpha-L-AF_C  46 plvnviaatqWs.pdliwdngkvvgtpsYyvqklfsknaggtvlpvelespkyeikgege..................... 104
                                   + v+ ++++ W  +++i  + k ++ + +y+qk +++n   +vl  ++es+ ++ +g+                       
  gi|91773199|ref|YP_565891.1| 137 QAVAQLTQVPWGhNIVIISKCKNLNEALFYIQKTIQNNWSRSVLTHHIESNLFKREGKAItnfkatlpepqsdlaietlkd 217
                                   6788899999*96666669999***************************99885555443567777777777777777777 PP

                                   ......................................................................S CS
                                   ......................................................................x RF
                  Alpha-L-AF_C 105 ......................................................................a 105
                                                                                                         +
  gi|91773199|ref|YP_565891.1| 218 pynfdfltltekhnekeledalinhvthfllelgagfsylgkqyklevsgdeffidllfyhvklhcyvvvE 288
                                   77777777666666666666666666666666666666666555555555555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2793.61
//
Query:       gi|91773200|ref|YP_565892.1|  [L=132]
Description: hypothetical protein Mbur_1220 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00014   22.3   0.2    0.00035   21.1   0.0    1.7  2  Phage_pRha  Phage regulatory protein Rha (Phage_pRha)
     0.0013   18.9   0.4     0.0039   17.4   0.0    1.9  2  ORF6N       ORF6N domain
  ------ inclusion threshold ------
      0.036   14.9   0.1       0.04   14.7   0.1    1.1  1  DKNYY       DKNYY family


Domain annotation for each model (and alignments):
>> Phage_pRha  Phage regulatory protein Rha (Phage_pRha)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.8e-08   0.00035      47      87 ..       3      43 ..       1      44 [. 0.92
   2 ?   -1.6   0.0      0.68   4.1e+03      17      21 ..      73      77 ..      50     102 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.8e-08
                    Phage_pRha 47 gretkvylltrdgftllvmgftgkkavefkaayidrFnele 87
                                  gr+tk   +t++g+ +l +gf ++ av++ +++i++F +++
  gi|91773200|ref|YP_565892.1|  3 GRRTKPCVFTEQGVAMLSAGFRNETAVKMSIQIINAFVAMR 43
                                  677788889******************************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.68
                    Phage_pRha 17 VlrdI 21
                                  +l++I
  gi|91773200|ref|YP_565892.1| 73 ILNAI 77
                                  33322 PP

>> ORF6N  ORF6N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.6e-07    0.0039      64      82 ..       2      20 ..       1      21 [. 0.90
   2 ?   -1.6   0.1      0.54   3.3e+03      30      40 ..      80      90 ..      66      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.6e-07
                         ORF6N 64 skskylpylfTEqGvlmla 82
                                  s+++++p +fTEqGv+ml+
  gi|91773200|ref|YP_565892.1|  2 SGRRTKPCVFTEQGVAMLS 20
                                  57899*************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.54
                         ORF6N 30 qavkrnkeRFp 40
                                  +++++  +RF+
  gi|91773200|ref|YP_565892.1| 80 KQFRNSHDRFI 90
                                  46777777775 PP

>> DKNYY  DKNYY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   6.7e-06      0.04      56     125 ..      36     114 ..      11     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.7e-06
                         DKNYY  56 lesfelik.kikdknnvY.......vkdekkekekkkkikkadsktFeildsgya.kDknnvYykgkkiegadaksFkv 125
                                   ++ f  +   i  + +v+        ++ +++++ +k ++ +++k+F+  +++++  D++ vY +g  +++  +k F  
  gi|91773200|ref|YP_565892.1|  36 INAFVAMRrFIASNAQVFqrlealeIEQLETDTKMDKILNAIEIKQFRNSHDRFIiIDNTTVYHFGASLKDLGKKWFAF 114
                                   34443333337788888899888888888999999999************666554*************9998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 1048.53
//
Query:       gi|91773201|ref|YP_565893.1|  [L=358]
Description: filamentation induced by cAMP protein Fic [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-23   82.6   0.0    2.7e-23   81.8   0.0    1.4  1  Fic_N           Fic/DOC family N-terminal
      4e-15   56.5   0.0    8.2e-15   55.5   0.0    1.6  1  Fic             Fic/DOC family
  ------ inclusion threshold ------
      0.033   14.8   0.1       0.11   13.2   0.0    1.9  2  Ribosomal_S20p  Ribosomal protein S20


Domain annotation for each model (and alignments):
>> Fic_N  Fic/DOC family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   4.5e-27   2.7e-23       2      81 ..      29     107 ..      28     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 4.5e-27
                         Fic_N   2 kllseAnralgeLdgllrllpnpelLirplvrkEAvlSSeIEgtqttlddlleaeadeeeekskdvkEVlnYvkAleyGl 81 
                                   ++ ++Anra++eL+g l+++pnp+++i++l+++EA++SS+IE++ tt d+l++a + ++++++  +kEVl+Y kAl +G+
  gi|91773201|ref|YP_565893.1|  29 EQANKANRAMAELKGRLSAIPNPDIFINTLSLQEAKDSSSIENVFTTNDKLFKAFTLDSTADP-HTKEVLRYGKALVDGF 107
                                   7889*********************************************************99.************9997 PP

>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   1.4e-18   8.2e-15      13      97 .]     123     212 ..     115     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.4e-18
                                   HS-S------TS--SS-S....T..EEEE---SCCCHHHHHHHHHHHHC.HHT-S-HHHHHHHHHHHHHHH--SSS-HHHH CS
                           Fic  13 lllqdigeeagefrdeev....segklesalappeevpaeleelleyln.elekeeplekaaalhyefekiHPFaDGNgRt 88 
                                   l++++i ee+  +rd +v    + +++++ ++  + +  +l+++++  n ++++++pl+k+a+lhy+fe iHPF DGNgR 
  gi|91773201|ref|YP_565893.1| 123 LIYRNIKEENDGIRDFPVyignDYRRIYTPPCCRDVILDKLNNWISVANsKSDEIDPLIKMAILHYQFEVIHPFKDGNGRA 203
                                   5566666666777776667776556777777777788889999999999******************************** PP

                                   HHHHHHHHH CS
                           Fic  89 arlllnllL 97 
                                   +r++  llL
  gi|91773201|ref|YP_565893.1| 204 GRVINVLLL 212
                                   ***988876 PP

>> Ribosomal_S20p  Ribosomal protein S20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.4   8.5e+03      67      78 ..      31      42 ..      28      45 .. 0.71
   2 ?   13.2   0.0   1.8e-05      0.11      28      78 ..     265     331 ..     255     333 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                                  CCHHHHHHHHHH CS
                Ribosomal_S20p 67 kNtAaRkkSrla 78
                                   N+A+R  + l 
  gi|91773201|ref|YP_565893.1| 31 ANKANRAMAELK 42
                                  588888777765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHHC...-HHH.............HHHHHHHHHHHHHHHHCTTSSTCCHHHHHHHHHH CS
                Ribosomal_S20p  28 rtaiKkvraaiea...dkek.............aqealkkaiskidkaakkgvihkNtAaRkkSrla 78 
                                   ++++ kv++ ie    +kek             +++++ +++ k   +++kg+  +NtA+++ +rl 
  gi|91773201|ref|YP_565893.1| 265 KYTLDKVLTIIELfndTKEKmqgevpdiysfelLETLFTQVYCKYAFLVEKGIASRNTASKYLNRLV 331
                                   5555566666655654444466777777777779*****************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2778.99
//
Query:       gi|91773202|ref|YP_565894.1|  [L=519]
Description: N-6 DNA methylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-115  383.3   0.0   1.1e-114  383.0   0.0    1.1  1  N6_Mtase       N-6 DNA Methylase
    1.5e-27   96.8   0.0    4.2e-27   95.4   0.0    1.8  1  HsdM_N         HsdM N-terminal domain
    6.9e-06   25.7   0.0    1.8e-05   24.4   0.0    1.7  1  MTS            Methyltransferase small domain
     0.0083   15.8   0.0      0.029   14.0   0.0    1.9  1  Cons_hypoth95  Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.012   15.3   0.8       0.06   13.0   0.8    2.0  1  UPF0020        Putative RNA methylase family UPF0020
      0.022   14.2   0.0      0.039   13.4   0.0    1.3  1  AviRa          RRNA methyltransferase AviRa


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 !  383.0   0.0  3.6e-118  1.1e-114       2     311 ..     156     475 ..     155     476 .. 0.98

  Alignments for each domain:
  == domain 1  score: 383.0 bits;  conditional E-value: 3.6e-118
                      N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyG 82 
                                   s d+lG+v+Ey+l++fa +egk+gG+f+TPr+v++l+ve+lep++g+ v+Dp+cGsgg++vq+ek++ ++ gk +++siyG
  gi|91773202|ref|YP_565894.1| 156 SADILGHVFEYFLGEFALAEGKRGGQFYTPRSVVELLVEMLEPYNGR-VFDPCCGSGGMFVQSEKFVADHRGKVNDISIYG 235
                                   68********************************************8.********************************* PP

                      N6_Mtase  83 qeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekderfreavapksnadl 163
                                   qe+n+tt+rLakmNl+++gi+ ++vk +++ ++ ++ ++ d k+d+v+aNppfn+++w+ + l kd r++++v+p++na++
  gi|91773202|ref|YP_565894.1| 236 QESNQTTWRLAKMNLAIRGIDSSQVKWNNEGSFLNDSHK-DLKADYVIANPPFNDSDWSGDLLRKDGRWKYGVPPAGNANY 315
                                   ***************************************.***************************************** PP

                      N6_Mtase 164 afllhiieslkpkGraavvlangvLfr.ggkegkIrkalvekdlveavialpeklFyntsiptcilvlkkekae.....rk 238
                                   a+++h++++l+p+G+a++vla+g+L + ++ eg+Irk+lve  +v+++++lp+klF nt+ip+++++l+++ka+     r+
  gi|91773202|ref|YP_565894.1| 316 AWIQHFLYHLSPNGQAGFVLAKGSLTSkSSGEGDIRKELVESRMVDCIVNLPPKLFLNTQIPASLWFLSRNKANgkyrnRT 396
                                   *************************987999*****************************************99******* PP

                      N6_Mtase 239 gkvlfidaseefkkkdrkknklteediekildtykek......skevdkfskvveleeiaendynlnvgryveteeeee 311
                                   +++lfida++  +  +r+++++++edi+k++dty+++      +++v++f+++ ++e ++e dy+ ++gryv+   ee+
  gi|91773202|ref|YP_565894.1| 397 DEILFIDARNMGHLINRRTREFSPEDIQKVADTYHNWrnpdgnYEDVKGFCNSTSIERVHELDYVVTPGRYVGLPVEED 475
                                   ************************************************************************9876665 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   1.4e-30   4.2e-27       1     136 [.      13     143 ..      13     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.4e-30
                                   HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC...........--..--------....S-CCCSHHH CS
                        HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereeklleeyken....aleeleeklkskeafyipeelrWke 77 
                                   +e++lwkaad+LR+++da+eyk  +lgL+FlK+++d +ee  +kl +         a+ e ++++k+++ f++p+ +rW++
  gi|91773202|ref|YP_565894.1|  13 IEKQLWKAADKLRKNIDAAEYKHIVLGLIFLKYISDSFEELYQKLQKGD--GdytgADPEDRDEYKAENVFFVPAIARWSY 91 
                                   689**********99******************************4443..2346655678899***************** PP

                                   HHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS......S-----SSHHHHHHHHHH CS
                        HsdM_N  78 lakkkdddelgenlnkafpaleelnkslkgvfmkddfnafalgeitkkspalLskviek 136
                                   l  k+++ e+g+++++a++a+e++n+ lkgv+ k     fa+g+    +p  L  +i+ 
  gi|91773202|ref|YP_565894.1|  92 LQSKAKQPEIGKDVDRAMDAIERENPLLKGVLPKV----FARGN---LDPTSLGGLIDL 143
                                   ***97777************************755....66655...699999999886 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     6e-09   1.8e-05      21     109 ..     190     289 ..     187     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6e-09
                                   HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC........EEEEE-S....T CS
                           MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle........vevvasd....v 89 
                                   +lL+e l+   +g+v D +cG G + ++  k+  +++ ++ d++ +  es +++++  k++         +v +++    +
  gi|91773202|ref|YP_565894.1| 190 ELLVEMLEP-YNGRVFDPCCGSGGMFVQSEKFVADHRGKVNDISIYGQESNQTTWRLAKMNlairgidsSQVKWNNegsfL 269
                                   689999999.9999*************999998888888888777777777776666666555555558888888844433 PP

                                   TTTSTTS-EEEEEE---STT CS
                           MTS  90 leeveekkfdlivsNPPfha 109
                                    +  ++ k d+++ NPPf +
  gi|91773202|ref|YP_565894.1| 270 NDSHKDLKADYVIANPPFND 289
                                   455668899*********87 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   9.7e-06     0.029      34     128 ..     194     292 ..     184     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.7e-06
                                   HHHCCCHCC-EEEETT-TTSHHHHH.....HHHTT-SEEEEE...ES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCT CS
                 Cons_hypoth95  34 nilaaeiegarvLDlfaGsGalglE.....AlSRgakkavlv...ekdkeavkilkenleelkleeetaelkedaleallk 106
                                   ++l+++  + rv D ++GsG++ +      A  Rg  + + +   e+++++ ++ k nl+  ++++  +++k +++ ++l+
  gi|91773202|ref|YP_565894.1| 194 EMLEPY--NGRVFDPCCGSGGMFVQsekfvADHRGKVNDISIygqESNQTTWRLAKMNLAIRGIDS--SQVKWNNEGSFLN 270
                                   555554..5667999999999986522433667886655544344888888889999999999886..9999999999*9* PP

                                   S--SS-EEEEEEE--SSSTTCH CS
                 Cons_hypoth95 107 lakkkeefdivflDPPyakell 128
                                    ++k+ + d+v  +PP++++++
  gi|91773202|ref|YP_565894.1| 271 DSHKDLKADYVIANPPFNDSDW 292
                                   *9****************9987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.8     2e-05      0.06      31     133 ..     202     289 ..     192     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                   -EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGG.EEEEE- CS
                       UPF0020  31 pllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdl.iefsqa 110
                                   + +DP CGsG++ +     +a+                    + +++++yg ++++   + a+ N+   g++ + +++++ 
  gi|91773202|ref|YP_565894.1| 202 RVFDPCCGSGGMFVQSEKFVADHR-----------------GKVNDISIYGQESNQTTWRLAKMNLAIRGIDSSqVKWNN- 264
                                   678*********998777766666.................3448999*******************9999864155655. PP

                                   -GGG--..STTS---EEEE------ CS
                       UPF0020 111 daakLr..lkegevdvivtnpPYGe 133
                                   +   L+  +k+ + d +++npP+ +
  gi|91773202|ref|YP_565894.1| 265 EGSFLNdsHKDLKADYVIANPPFND 289
                                   4445666556679*********965 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.039      56     101 ..     202     252 ..     187     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                         AviRa  56 tlyDpCCGgayLltv.lgll..hgkkik..kvlasDvdeevlelakkNLsL 101
                                   +++DpCCG++ +      ++  h+ k++  ++++ + ++++ +lak NL++
  gi|91773202|ref|YP_565894.1| 202 RVFDPCCGSGGMFVQsEKFVadHRGKVNdiSIYGQESNQTTWRLAKMNLAI 252
                                   79******9987654144554478888733579***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 3504.06
//
Query:       gi|91773203|ref|YP_565895.1|  [L=127]
Description: hypothetical protein Mbur_1223 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 897.30
//
Query:       gi|91773204|ref|YP_565896.1|  [L=259]
Description: dihydroorotate dehydrogenase electron transfer subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-11   42.4   9.5      1e-09   38.0   4.2    2.4  2  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    0.00099   19.4   0.0      0.038   14.4   0.0    2.4  1  FAD_binding_6    Oxidoreductase FAD-binding domain
     0.0043   17.7   0.2      0.017   15.7   0.2    2.0  1  NAD_binding_1    Oxidoreductase NAD-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 !    7.3   0.2   0.00069       4.1      22      40 ..     169     187 ..     154     189 .. 0.67
   2 !   38.0   4.2   1.7e-13     1e-09       2      40 ..     207     239 ..     206     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00069
                                   TT.CEEETTTT-CEEECCC CS
               DHODB_Fe-S_bind  22 dggeykrvCkdGPvFdade 40 
                                   d   y r+C+ GP++ +  
  gi|91773204|ref|YP_565896.1| 169 DVSVYDRICVCGPEIMMAN 187
                                   333899*******997765 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 1.7e-13
                                   ---SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCC CS
               DHODB_Fe-S_bind   2 erMaCGvGaClgCvvktkggdggeykrvCkdGPvFdade 40 
                                   ++ +C++G+C++C+++ +g       rvCkdGPv++++ 
  gi|91773204|ref|YP_565896.1| 207 RYFKCAIGVCGACCMDPDG------LRVCKDGPVLNGSL 239
                                   799**************65......9*********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 !   14.4   0.0   6.3e-06     0.038       3      96 ..       7      85 ..       5      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.3e-06
                                  EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEEC.ETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-T CS
                 FAD_binding_6  3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlk.ikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelki 84
                                  k++e  e s+ +r+frf+++ +++    ++Gq+v++ ++ +++        p+ s+  +G       v + G  ++ L  +k+
  gi|91773204|ref|YP_565896.1|  7 KIVEIVEESPTIRTFRFDISFDDA----LPGQFVMVWVRgVDE-------VPMGSSYLNGIT-----VQNVGDATSKLFDMKV 73
                                  678888899999999999998777....569999999994444.......466677777755.....6677************ PP

                                  T-EEEEEEEE-S CS
                 FAD_binding_6 85 gdtleikGPlGk 96
                                  gd++ ++GP+Gk
  gi|91773204|ref|YP_565896.1| 74 GDSVGLRGPFGK 85
                                  **********97 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 !   15.7   0.2   2.9e-06     0.017       2     107 ..      99     188 ..      98     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-06
                                   EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHHH CS
                 NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdall 82 
                                   iagG+G aP+  + + ++e      kv+ + G r+  +l++++++ ++     g+l+++ +    ++g++g  g+v++ l+
  gi|91773204|ref|YP_565896.1|  99 IAGGVGAAPLGPLADYAAE---CGAKVTTILGSRECYELVFEDRFSSA-----GELHIT-T----DDGSAGTCGFVTTVLA 166
                                   9*********999999998...589********************999.....444333.3....4555566899988885 PP

                                   HHHHHHSSTTEEEEEECSHHHHHHH CS
                 NAD_binding_1  83 eellslkkeethvyvCGppgMikav 107
                                   ++ +s     + ++vCGp+ M++ v
  gi|91773204|ref|YP_565896.1| 167 DMDVS---VYDRICVCGPEIMMANV 188
                                   55555...7899**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2030.30
//
Query:       gi|91773205|ref|YP_565897.1|  [L=300]
Description: dihydroorotate dehydrogenase 1B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-68  229.8   0.9    4.4e-68  229.7   0.9    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
      6e-11   42.0   1.2      2e-05   23.9   0.1    2.2  2  Dus           Dihydrouridine synthase (Dus)
    3.6e-06   26.6   0.9    5.4e-05   22.8   0.1    2.8  3  His_biosynth  Histidine biosynthesis protein
    1.5e-05   24.5   7.4    0.00013   21.5   7.4    2.5  1  NMO           Nitronate monooxygenase
     0.0023   17.2   0.7     0.0051   16.0   0.1    1.8  2  DUF561        Protein of unknown function (DUF561)
     0.0033   16.5   2.0     0.0064   15.5   1.9    1.6  1  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0048   16.1   0.6      0.021   14.0   0.3    2.1  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0051   16.2   0.2     0.0051   16.2   0.2    2.4  3  ThiG          Thiazole biosynthesis protein ThiG
     0.0071   15.8   0.7       0.48    9.8   0.1    2.8  4  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
  ------ inclusion threshold ------
       0.14   11.3   0.0       0.21   10.7   0.0    1.3  1  IGPS          Indole-3-glycerol phosphate synthase


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 !  229.7   0.9   2.4e-71   4.4e-68       4     293 ..       2     279 ..       1     281 [. 0.94

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 2.4e-71
                                   EEETTEEESSSEEE-TTSSTTS.SSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHHH CS
                        DHO_dh   4 tkvlglkfknpiglAaGfdkeg.eeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavlek 83 
                                   ++++g++fknp +lA+G+++ +  ++l++ + g+g + ++s++p+p+ G+p+P +++l+ +  +lN++Gl+n+   +  ++
  gi|91773205|ref|YP_565897.1|   2 VTITGIDFKNPTMLASGIMGTTgASLLRIAECGAGGVVTKSIGPEPKAGHPNPSMIKLECG--FLNAMGLPNPSYTEFDNE 80 
                                   789****************97615678889999****************************..***************999 PP

                                   HHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHG.GGESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHHHHS CS
                        DHO_dh  84 llkrrkeqeekkelginlskakktenavddyvevvrkig.pfadilelNvSsPntp.glrdlqekeelkaillkvvkevsk 162
                                   ++ +r+     +++++++s+ + +   ++d+v+v++ ++     ++elNvS+P++  +++++++++ + + ++++v ++ +
  gi|91773205|ref|YP_565897.1|  81 IKTVRSG----TDVPVIASIFGGN---AEDFVKVAEGLAdSEPAAFELNVSCPHAEgYGATIGTDTCMVESITAAVCDAVD 154
                                   9999966....479*********9...***********9777889***********889********************** PP

                                   SEEEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHHTT CS
                        DHO_dh 163 vpvlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirelykrlk 242
                                   vpv+vKl+P++td++ + +a++   ++ + +i+    t++++aid++s  ++  n++GGlsG+a+k++a+k +++ly+ l+
  gi|91773205|ref|YP_565897.1| 155 VPVWVKLTPNVTDIKAIGKAAQNGgADAVVAIN----TLRGMAIDINSGYPILGNRFGGLSGPAVKPVAIKCVYDLYEALD 231
                                   **************9999988887777777777....89****************************************** PP

                                   T.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHH CS
                        DHO_dh 243 keipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkelee 293
                                     ip+IgvGG+++ eDa+e+++aGAs+vq+++a+  e + i+++i  ++e 
  gi|91773205|ref|YP_565897.1| 232 --IPVIGVGGVSTWEDAVEMMMAGASAVQIGSAV-HESVDIFSDIASGIEL 279
                                   ..*******************************9.9*********999975 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   1.1e-08     2e-05      53     156 ..      89     184 ..      73     187 .. 0.89
   2 !   16.8   0.1   1.6e-06    0.0028     170     216 ..     218     263 ..     212     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.1e-08
                                   TSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESES CS
                           Dus  53 etplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigi 133
                                   + p++  ++g +++  ++ A+  ad++  + +lNv CP      +g+Ga+   +  +v++i +av +av++Pv vk    +
  gi|91773205|ref|YP_565897.1|  89 DVPVIASIFGGNAEDFVKVAEGLADSEPAAFELNVSCPHA----EGYGATIGTDTCMVESITAAVCDAVDVPVWVKLTPNV 165
                                   4589999*******************************75....799*****************************99988 PP

                                   STTTC.HHHHHHHHHHCT-SEEE CS
                           Dus 134 ddeeenalelakiveaaGaqalt 156
                                    d +     ++k++++ Ga+a++
  gi|91773205|ref|YP_565897.1| 166 TDIKA----IGKAAQNGGADAVV 184
                                   87766....99999999999885 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.6e-06
                                   --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHH CS
                           Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrga 216
                                   + ++ ++++ +a+ ipvi+ G++ ++eda +++   Ga +v ig + 
  gi|91773205|ref|YP_565897.1| 218 VAIKCVYDLYEALDIPVIGVGGVSTWEDAVEMMMA-GASAVQIGSAV 263
                                   567889***************************99.*******9876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.22     4e+02     183     210 ..      81     108 ..      75     116 .. 0.80
   2 ?   -0.8   0.1      0.49   8.8e+02     103     132 ..     162     190 ..     136     199 .. 0.59
   3 !   22.8   0.1     3e-08   5.4e-05      60     116 ..     218     274 ..     209     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.22
                                   HHHHHHHHSSEEEEESS--SHHHHHHHH CS
                  His_biosynth 183 tkelaeavkipviasGGvgsledlkelk 210
                                   +k++++ +++pvias   g+ ed+ +++
  gi|91773205|ref|YP_565897.1|  81 IKTVRSGTDVPVIASIFGGNAEDFVKVA 108
                                   47899999*******8888899988876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                                   HHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
                  His_biosynth 103 taavknpelikelaekfgsqkivvaiDarr 132
                                   t  v++ + i ++a++ g+   vvai + r
  gi|91773205|ref|YP_565897.1| 162 TPNVTDIKAIGKAAQNGGA-DAVVAINTLR 190
                                   4445555666666665444.5666666555 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 3e-08
                                   HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                  His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                   + +++v  + e+++ipv   GG+++ ed+ e++ aga+ v ig+a+ ++ ++++++a
  gi|91773205|ref|YP_565897.1| 218 VAIKCVYDLYEALDIPVIGVGGVSTWEDAVEMMMAGASAVQIGSAVHESVDIFSDIA 274
                                   566677777777777777777777777777777777777777777777777777766 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   7.4   7.2e-08   0.00013     132     224 ..     175     262 ..      62     266 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.2e-08
                           NMO 132 lkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaL 212
                                    +++g+ +++ i +   + + +++G     + G   GG  G p+v+    ++ v    +a+diPvi  GG+ + ++   ++
  gi|91773205|ref|YP_565897.1| 175 AQNGGADAVVAINTLRGMAIDINSGYP---ILGNRFGGLSG-PAVK-PVAIKCVYDLYEALDIPVIGVGGVSTWEDAVEMM 250
                                   223333333333333333333333333...33778888888.5553.56788999999*********************** PP

                           NMO 213 alGAsgvqigtr 224
                                    +GAs+vqig++
  gi|91773205|ref|YP_565897.1| 251 MAGASAVQIGSA 262
                                   **********98 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   0.0       2.5   4.6e+03      25      41 ..     164     180 ..     161     186 .. 0.81
   2 !   16.0   0.1   2.8e-06    0.0051     174     223 ..     219     269 ..     213     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.5
                        DUF561  25 nveqvlkiaraaekaka 41 
                                   nv+++++i +aa+++ a
  gi|91773205|ref|YP_565897.1| 164 NVTDIKAIGKAAQNGGA 180
                                   78899999999998876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.8e-06
                        DUF561 174 tlastyeiskkvslPvicasGlsdvtvplal.slgasGiGigsavsklnde 223
                                   ++ ++y + +++++Pvi   G+s+    + +  +gas + igsav++  d+
  gi|91773205|ref|YP_565897.1| 219 AIKCVYDLYEALDIPVIGVGGVSTWEDAVEMmMAGASAVQIGSAVHESVDI 269
                                   678********************99877765168***********987766 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.9   3.6e-06    0.0064     194     239 ..     218     263 ..     136     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 194 tAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                    A+  v++  +  ++pvi  GG+++ +d v  + aGa+av +Gs +
  gi|91773205|ref|YP_565897.1| 218 VAIKCVYDLYEALDIPVIGVGGVSTWEDAVEMMMAGASAVQIGSAV 263
                                   58888999999********************************975 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.42   7.5e+02      22      38 ..      79      95 ..      76     113 .. 0.86
   2 !   14.0   0.3   1.2e-05     0.021      81     184 ..     168     271 ..     137     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.42
                                  HHHHHHHTT--S-EEEE CS
                          NanE 22 edikaikavvdlPiiGi 38
                                  ++ik +++ +d+P+i  
  gi|91773205|ref|YP_565897.1| 79 NEIKTVRSGTDVPVIAS 95
                                  6899*********9975 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHT.T--EEEES---SHHHHH CS
                          NanE  81 ieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalsea.glkviaeGrintPekak 160
                                   i+++ k+ ++ +  ++  i tl    +  + G  i+G  + G  + + k    ++ v +l ea ++ vi  G + t e a 
  gi|91773205|ref|YP_565897.1| 168 IKAIGKAAQNGGADAVVAINTLRGMAIDINSGYPILGNRFGGLSGPAVKPV-AIKCVYDLYEAlDIPVIGVGGVSTWEDAV 247
                                   555555555555666666777776666678888889988888888877644.467777777764899************** PP

                                   HHHTT--SEEEE-HHHH-HHHHHH CS
                          NanE 161 kaieiGvdavvvGsaitrleeiak 184
                                   +++  G+ av +Gsa+    +i +
  gi|91773205|ref|YP_565897.1| 248 EMMMAGASAVQIGSAVHESVDIFS 271
                                   ***************988777765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   2.4e+03     166     193 ..      80     107 ..      76     115 .. 0.72
   2 ?    0.3   0.6      0.19   3.5e+02     150     181 ..     130     160 ..     113     197 .. 0.67
   3 !   16.2   0.2   2.8e-06    0.0051     168     214 ..     224     270 ..     203     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                                   HHHHHHHH-SS-BEEES---SHHHHHHH CS
                          ThiG 166 alkiiieeakvPvivDAGigspsdaaqa 193
                                    +k++++ ++vPvi     g+++d +++
  gi|91773205|ref|YP_565897.1|  80 EIKTVRSGTDVPVIASIFGGNAEDFVKV 107
                                   6788889999999976666666666555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                                   EBSSSTTS----S-HHHHHHHHHH-SS-BEEE CS
                          ThiG 150 PlaapiGsglGllnkealkiiieeakvPvivD 181
                                    ++a iG+   +++      +++ ++vPv v 
  gi|91773205|ref|YP_565897.1| 130 GYGATIGTDTCMVES-ITAAVCDAVDVPVWVK 160
                                   578999998887765.4567889999999885 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 2.8e-06
                                   HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHH CS
                          ThiG 168 kiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpv 214
                                     + e +++Pvi   G+ + +da++ m  Ga+av + +av e+ d+ 
  gi|91773205|ref|YP_565897.1| 224 YDLYEALDIPVIGVGGVSTWEDAVEMMMAGASAVQIGSAVHESVDIF 270
                                   4467889**********************************999875 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 ?   -3.3   0.0       2.9   5.2e+03      62      87 ..       6      31 ..       5      38 .. 0.67
   2 ?   -2.9   0.0       2.1   3.8e+03     131     148 ..      81      98 ..      77     109 .. 0.74
   3 ?    3.2   0.0     0.028        50      18      59 ..     154     195 ..     142     200 .. 0.85
   4 !    9.8   0.1   0.00027      0.48     128     167 ..     220     259 ..     213     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.9
                                  HHHHHHH.TT-SEEEES-HHHHHHHH CS
                  G3P_antiterm 62 aveflkkeikvdGiistksslikkak 87
                                  +++f + ++ ++Gi+ t  + + +  
  gi|91773205|ref|YP_565897.1|  6 GIDFKNPTMLASGIMGTTGASLLRIA 31
                                  56777777888899887766555444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                   HCTSTTS...EEEEESS- CS
                  G3P_antiterm 131 ikeikkelkipiiaGGLi 148
                                   ik +++ +++p+ia+ + 
  gi|91773205|ref|YP_565897.1|  81 IKTVRSGTDVPVIASIFG 98 
                                   778889999999998555 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.028
                                   -SSEEEE--EETTTHHHHHHHHHHTT-EEEEEGGGEET--SS CS
                  G3P_antiterm  18 evevvfllegdilnlkeiveklkkagkkvfvhiDlieGlskd 59 
                                   +v v + l+ +++++k i + +++ g  ++v i+ ++G++ d
  gi|91773205|ref|YP_565897.1| 154 DVPVWVKLTPNVTDIKAIGKAAQNGGADAVVAINTLRGMAID 195
                                   56677778999***************************9866 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00027
                                   HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                    k++ ++ ++l+ip+i  G ++t ed  e++ aGa+av  
  gi|91773205|ref|YP_565897.1| 220 IKCVYDLYEALDIPVIGVGGVSTWEDAVEMMMAGASAVQI 259
                                   56777888999**************************976 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012      0.21     146     246 ..     167     268 ..     141     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-.TTSEEEEESSS-SHHHHH CS
                          IGPS 146 eleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvp.kdvllvaeSGiktredve 225
                                    ++++ +aa++ g +++v +++   +++ +++g +i+G     L    v+    + + +l++  d+ ++   G++t ed+ 
  gi|91773205|ref|YP_565897.1| 167 DIKAIGKAAQNGGADAVVAINTLRGMAIDINSGYPILGNRFGGLSGPAVKPVAIKCVYDLYEaLDIPVIGVGGVSTWEDAV 247
                                   4678889999999999999999999999999999999988889999888877777777777734699************** PP

                                   HHCCTT-SEEEESHHHHC-TT CS
                          IGPS 226 klkeegvnafLvGeslmrqed 246
                                   ++  +g++a+ +G+++ ++ d
  gi|91773205|ref|YP_565897.1| 248 EMMMAGASAVQIGSAVHESVD 268
                                   ***************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1890.09
//
Query:       gi|91773206|ref|YP_565898.1|  [L=309]
Description: porphobilinogen deaminase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-72  241.0   0.1    1.1e-71  240.6   0.1    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    1.6e-09   38.0   0.1    3.8e-09   36.8   0.1    1.6  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 !  240.6   0.1   1.2e-75   1.1e-71       2     201 ..       2     203 ..       1     206 [. 0.96

  Alignments for each domain:
  == domain 1  score: 240.6 bits;  conditional E-value: 1.2e-75
                Porphobil_deam   2 rigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlptel 81 
                                    +gtR+S+LA+aqa+lv ++L+e  +e++   ikt+GD  +d+pL+++ g g+F++el+++++ege+d+aVhS+KDlpt  
  gi|91773206|ref|YP_565898.1|   2 ILGTRGSALAIAQADLVTKMLEEkGHELTRNVIKTSGDVFTDRPLHEVAGVGVFVRELDDRMIEGEVDIAVHSMKDLPTVR 82 
                                   58*******************6634558999************************************************** PP

                Porphobil_deam  82 peglelaavlkredprDvlvvks..sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLA 160
                                   p++l +aavlkr++p Dvl++ +  +l+elp+ga++gT+S+RR+aql ++rpdl+v+dlRGn++tR++kl++g+yd+i+LA
  gi|91773206|ref|YP_565898.1|  83 PPELAIAAVLKRDSPYDVLLTADgsTLDELPDGAIIGTTSMRRRAQLLRYRPDLNVEDLRGNINTRIQKLKAGQYDGILLA 163
                                   ********************844669******************************************************* PP

                Porphobil_deam 161 aAGLkRlgleerisevlspeellpavgQGalavevrkedee 201
                                   +AGL+R+g++ ++++ l+ e ++p++ QG++ v +r++de+
  gi|91773206|ref|YP_565898.1| 164 EAGLQRMGWDMDVQR-LPAEAFCPSANQGTIVVVTRADDEA 203
                                   *************99.**********************985 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 !   36.8   0.1   4.2e-13   3.8e-09       4      73 ..     219     287 ..     217     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 4.2e-13
                                   HHHHHHHHHHTT--TTSSEEEEEEEE.TTE.EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHHHHHH CS
               Porphobil_deamC   4 vlaERallkeLeGGCsvPiGvyaeve.aneelkLkglvlsldglksaveeaeakgeleeaeelGkklaeel 73 
                                     +ER l+++ eGGC vPiG++a+++ +++e+     vl+ dg++  ++++e  +++++ +e  ++++ +l
  gi|91773206|ref|YP_565898.1| 219 TEVERLLITDVEGGCIVPIGSFAQMNeDGDEIHVLVEVLAVDGTR--EIRIEDDIPVKNYREHALSIGRML 287
                                   579**********************997778************99..888888887777777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2139.77
//
Query:       gi|91773207|ref|YP_565899.1|  [L=422]
Description: glutamate-1-semialdehyde aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  221.7   0.0    1.6e-65  221.4   0.0    1.1  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.063   12.4   0.0      0.084   12.0   0.0    1.2  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 !  221.4   0.0   1.7e-69   1.6e-65      10     335 ..      33     342 ..      25     391 .. 0.91

  Alignments for each domain:
  == domain 1  score: 221.4 bits;  conditional E-value: 1.7e-69
                                   CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEE CS
                   Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkv 90 
                                   ++  + a+G++++dvdg++y+D   ++ +++lGha+P + +a+ +q++k ++     + +   + l ek+++l p  +d++
  gi|91773207|ref|YP_565899.1|  33 PFYTESANGCRIKDVDGNEYIDYCLAYGPNILGHANPVIKQAIIDQLDKGWLYG---TPTGLEVTLGEKIASLYPS-IDML 109
                                   46677899******************************************9887...66777789**********9.**** PP

                                   EEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-H CS
                   Aminotran_3  91 flansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlken 171
                                    ++ +G+eA+++Al++ar        t k+k+++++g+fHG   + l  +gs  +  t  +p + +++    + + ++ +n
  gi|91773207|ref|YP_565899.1| 110 RFVSTGTEATMSALRAARG------FTCKNKFVKIEGGFHGAHDAVLVKAGS--GATTHGKPDSLGIPEDFTKNTLQVAYN 182
                                   *******************......9*************************9..666666666666666666666777888 PP

                                   HHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..TTTSSSSGGGGC CS
                   Aminotran_3 172 eeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf..GrTGklfAleha 250
                                   +      +e+++++++  +d+ aAvi+Ep+ g+ G + ++ ++l+++r++++++dv+li+DEv tGf  +  G   A e++
  gi|91773207|ref|YP_565899.1| 183 D------IEAMTEVIESNQDDMAAVIMEPVLGNIGPILPEGDYLKEVRKVTEENDVVLIFDEVITGFrlAMGG---AQEYF 254
                                   8......7888899999**************************************************888888...***** PP

                                   TS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                   Aminotran_3 251 gvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekllenaqelgaalkegL 328
                                   gv+pD++tl+K ++gGlp+ ++ +++e+ ++++p++   +++Tf+G p   a+ +a+++++e+ek+ e+ +++g++l++gL
  gi|91773207|ref|YP_565899.1| 255 GVTPDMTTLGKIVGGGLPIGVFGGKREILEMISPSGsvyQAGTFSGSPASVAAGIAAVDVLEKEKVHEKLEATGNMLRAGL 335
                                   *********************************9999******************************************** PP

                                   HHHCTT- CS
                   Aminotran_3 329 eelqkky 335
                                   +++ +++
  gi|91773207|ref|YP_565899.1| 336 NDIIADK 342
                                   **98776 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.4e-06     0.084     130     300 ..     182     349 ..     172     416 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.4e-06
                                   E-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTT CS
                 Aminotran_1_2 130 ldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatranvee 209
                                   +d+ea+ e +++++ + +    ++ e +  + G ++++ + l+++ ++++++ ++l++De+  gf +   +a++ +++v +
  gi|91773207|ref|YP_565899.1| 182 NDIEAMTEVIESNQDDMA---AVIMEPVLGNIGPILPEGDyLKEVRKVTEENDVVLIFDEVITGFRLAMGGAQE-YFGVTP 258
                                   89*********9887777...************999986538999999***************99998446666.888888 PP

                                   STTEEEEEESSSTTSSGGG-EEEEEEEH...HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 210 epnllivgslsKafGlaGeRvGyilgna...avvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrke 287
                                   +      ++l+K  G  G+ +G + g+    +++s   ++ +++++s   +a vaa + +++    e e+  ++l++    
  gi|91773207|ref|YP_565899.1| 259 DM-----TTLGKIVG-GGLPIGVFGGKReilEMISPSGSVYQAGTFSG-SPASVAAGIAAVDVL--EKEKVHEKLEATGNM 330
                                   65.....59999887.47777888887734444444444444445433.333333333333322..555555666666666 PP

                                   HHHHHHHS......TEEEE CS
                 Aminotran_1_2 288 lrdeLael......glkvl 300
                                   lr++L+++      ++ v 
  gi|91773207|ref|YP_565899.1| 331 LRAGLNDIiadkrlDFHVG 349
                                   6666665555556555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2522.15
//
Query:       gi|91773208|ref|YP_565900.1|  [L=318]
Description: delta-aminolevulinic acid dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   1.3e-144  481.2   0.2    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.17   11.7   0.0    1.2  1  Mob_Pre   Plasmid recombination enzyme


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  1.5e-148  1.3e-144       5     316 ..       2     315 ..       1     316 [. 0.97

  Alignments for each domain:
  == domain 1  score: 481.2 bits;  conditional E-value: 1.5e-148
                                   GGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS-BSS- CS
                          ALAD   5 rrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeekdeeg 85 
                                   rrlr+ + +r+lvret+l ++dli+p+fv+e+++++ +i+smpg++rl++d++v+ ++e+++lgi+a++lFg+p++kd+ g
  gi|91773208|ref|YP_565900.1|   2 RRLRSGK-IRDLVRETSLGVDDLIYPMFVDETTDSSVDISSMPGIQRLPLDKVVDDAKEAADLGIPALVLFGIPKHKDAVG 81 
                                   7777655.9************************************************************************ PP

                                   GGGGSTTSHHHHHHHHHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS...EEHHHHHHHHHHHHHHHHHCT-SEEEE-S- CS
                          ALAD  86 sealnedglvqrairaikeev.pelvvitDvclceytshGhcgileeke..vdndetlellakvavsqaeaGadivapSdm 163
                                   + +  ed +vq+a+r ike++ +++vvitDvc+ceyt+hGhcgi++ ++  v+nd tl++l k+a s++eaGadivapS+m
  gi|91773208|ref|YP_565900.1|  82 TCSHGEDDIVQQAVRSIKEDLgKDMVVITDVCMCEYTDHGHCGIVDMDTedVLNDPTLDILGKIATSHVEAGADIVAPSGM 162
                                   ********************9899*********************643345****************************** PP

                                   -TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-SBEEEE CS
                          ALAD 164 mDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldleeGADivmvK 244
                                   mDg+++air++Lde++fe+++i+sY+aKy+SafYgPFr+aa+s  +fgdr+tYqmdpans+ea+re+eld+ eGADi+mvK
  gi|91773208|ref|YP_565900.1| 163 MDGMIGAIRNSLDENHFENTPIMSYAAKYTSAFYGPFREAADSGFQFGDRSTYQMDPANSNEAIREAELDILEGADIIMVK 243
                                   ********************************************************************************* PP

                                   S-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHHHHH CS
                          ALAD 245 PalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfakevak 316
                                   Pal+ylDii ++k+ef++p+aay+vSGEY+m+kaaae+gwldek v++EsllsikRAGad+iltYfak++a+
  gi|91773208|ref|YP_565900.1| 244 PALPYLDIIYRIKNEFKMPTAAYNVSGEYSMLKAAAEKGWLDEKLVMYESLLSIKRAGADMILTYFAKDLAR 315
                                   *********************************************************************997 PP

>> Mob_Pre  Plasmid recombination enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.9e-05      0.17     102     150 ..      89     137 ..      85     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHHHHH-GGGEEEEEEETSSSS-EEEEEE--EETT.EE-HH CS
                       Mob_Pre 102 effeealkffeeryGkenvlsAvvHlDEatpHmHlgvvpvtekerlsak 150
                                   ++ ++a+  ++e  Gk+ v+   v + E t H H+g+v ++ + +l++ 
  gi|91773208|ref|YP_565900.1|  89 DIVQQAVRSIKEDLGKDMVVITDVCMCEYTDHGHCGIVDMDTEDVLNDP 137
                                   57899************************************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1961.90
//
Query:       gi|91773209|ref|YP_565901.1|  [L=422]
Description: glutamyl-tRNA reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  134.2   1.8    2.5e-38  131.2   0.2    2.5  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.3e-36  125.5   0.2    2.6e-36  124.6   0.2    1.5  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    5.4e-21   74.9   1.2      1e-20   73.9   1.2    1.5  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    5.8e-09   36.4   1.3    3.5e-08   33.9   0.0    2.8  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.1e-06   27.4   0.0    7.2e-06   26.3   0.0    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    4.9e-06   26.0   0.1    9.4e-06   25.1   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00014   21.4   0.3    0.00031   20.3   0.3    1.5  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    0.00028   21.3   0.0    0.00089   19.7   0.0    1.8  1  NAD_binding_7    Putative NAD(P)-binding
    0.00029   21.0   0.3    0.00084   19.5   0.0    2.0  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0004   20.3   0.5     0.0022   17.9   0.5    2.0  1  DFP              DNA / pantothenate metabolism flavoprotein
    0.00041   19.4   0.0     0.0008   18.4   0.0    1.4  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    0.00075   19.4   0.5     0.0039   17.1   0.1    2.2  2  NAD_binding_10   NAD(P)H-binding
     0.0018   19.1   0.2     0.0058   17.5   0.0    2.0  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0024   17.2   0.2        1.3    8.3   0.0    3.2  3  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0069   15.2   0.1      0.017   13.8   0.1    1.6  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
       0.01   16.1   0.0       0.01   16.1   0.0    2.9  4  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.025   14.1   0.0        0.1   12.2   0.0    2.0  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.039   14.5   0.2      0.082   13.5   0.2    1.5  1  PRESAN           Plasmodium RESA N-terminal
      0.048   13.9   1.4       0.55   10.5   0.1    3.1  3  TrkA_N           TrkA-N domain
      0.057   13.8   0.4        4.3    7.8   0.0    2.7  2  Rimk_N           RimK PreATP-grasp domain


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 !  131.2   0.2   2.8e-41   2.5e-38       1     137 [.     162     295 ..     162     296 .. 0.98
   2 ?    1.6   0.1       0.3   2.7e+02      73     101 ..     328     356 ..     302     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 2.8e-41
                                   HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
                  Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81 
                                   +la+++l+ l++k++l+iG+Gem++lv+++L+++ ++ +  aNRt+e+a++laeel+ge   a+ +++l++++++advvis
  gi|91773209|ref|YP_565901.1| 162 DLAEDILDGLNDKHILVIGTGEMGTLVTRALSHRDMHVIYLANRTYEKARDLAEELGGE---AVMFDQLEKYVRAADVVIS 239
                                   59******************************************************999...******************* PP

                                   -SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHH CS
                  Shikimate_DH  82 ataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLke 137
                                   at++++++l+ + v ++++ r+++lll+Dia PRd++p+v+e+ +v l ++D L+ 
  gi|91773209|ref|YP_565901.1| 240 ATSAPHYVLKGDLVAKVMEGRENELLLIDIASPRDIDPAVEEIPHVILRNIDGLRV 295
                                   ****************************************************9986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.3
                                   HHT-SEEEE-SSSSS-SB-HHHHHCCHHH CS
                  Shikimate_DH  73 laeadvvisataseepilekeeveealkk 101
                                    ++ad +is   s+++ l+++e+e+a +k
  gi|91773209|ref|YP_565901.1| 328 RQKADAIISNLYSQSHGLRHNEMEHAINK 356
                                   4789*****************99999865 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 !  124.6   0.2   2.9e-39   2.6e-36       3     146 .]       9     147 ..       7     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.9e-39
                       GlutR_N   3 inhktapvelreklafseeelkellkel.ee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkeklyvl 81 
                                   i+h +a+ve +e  +    +++ +l++l ++  v e+++L+TCNR+Eiy++++   + s+ l+++ +e+     ++ ++++
  gi|91773209|ref|YP_565901.1|   9 ITHAKATVEEMEDSWHG--DIDLVLSQLySNeLVYECAVLKTCNRVEIYVVSS---KGSSVLFHYAKEMG--VSAKIVEFY 82 
                                   7999******9999886..5666777775442566**************6543...45666666665553..2347899** PP

                       GlutR_N  82 egeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                   +++e++rHl+r+a+GL+S+++GEdqIlgQ+k+ + +ak agt+gkvL++ f+kai+v+krvrtet
  gi|91773209|ref|YP_565901.1|  83 DHDESLRHLLRLACGLESMIIGEDQILGQIKDFFLMAKGAGTVGKVLSTAFSKAIQVGKRVRTET 147
                                   ****************************************************************8 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   1.2   1.2e-23     1e-20       1      96 [.     310     410 ..     310     411 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.2e-23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHHHHHH CS
                   GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllheptarL 77 
                                   kAe iI++e++  +a++k+++++ +I++l+++ + +r +e+e a++kl+    + + +r++le+lt++++nk+l ept++L
  gi|91773209|ref|YP_565901.1| 310 KAEIIIDDELDMVKAQYKRQKADAIISNLYSQSHGLRHNEMEHAINKLSayhtIGEIERKVLEDLTHAITNKILAEPTKKL 390
                                   79**************************************************999999999******************** PP

                                   HSS.-TTTTHHHHHHHHH.. CS
                   GlutR_dimer  78 kea.edeeeellealrrlFn 96 
                                   ++a e +++++l+ ++rlF+
  gi|91773209|ref|YP_565901.1| 391 RNAaEYDDDKFLDSVSRLFD 410
                                   ***766666**********8 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 ?   -0.7   0.0       2.4   2.2e+03      26      53 ..      52      79 ..      40      84 .. 0.82
   2 ?   -2.3   0.0       7.9   7.1e+03       6      21 ..     121     136 ..     121     165 .. 0.73
   3 !   33.9   0.0     4e-11   3.5e-08       2      96 ..     176     271 ..     175     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.4
                                  GCEEEEEESSCCCHHHHHHHHC-EEECE CS
                 F420_oxidored 26 heivvansrnpekaeelaeelgvkvtav 53
                                   ei+v++s+  + + + a+e+gv+++ v
  gi|91773209|ref|YP_565901.1| 52 VEIYVVSSKGSSVLFHYAKEMGVSAKIV 79
                                  5899999999999999999999988765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.9
                                   TTSHHHHHHHHHHHHT CS
                 F420_oxidored   6 GaGnmgealasgllaa 21 
                                   GaG +g+ l   +++a
  gi|91773209|ref|YP_565901.1| 121 GAGTVGKVLSTAFSKA 136
                                   7888888888777766 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 4e-11
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE.CHHHHHHH-SEEEE-S-HHHHH...HHH CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtav.dneeaaeeadvvvlavkpedve...evl 78 
                                   i +iG+G+mg  +++ l++++   h i++a +r+ eka+ laeelg ++    + e+ ++ advv+ a    ++    +++
  gi|91773209|ref|YP_565901.1| 176 ILVIGTGEMGTLVTRALSHRD--MHVIYLA-NRTYEKARDLAEELGGEAVMFdQLEKYVRAADVVISATSAPHYVlkgDLV 253
                                   679******************..6777766.***************65555405688999******999887774334788 PP

                                   HHCGHHHHTTSEEEEESS CS
                 F420_oxidored  79 selakdalkgklvisvla 96 
                                   +++++   ++ l+i+++ 
  gi|91773209|ref|YP_565901.1| 254 AKVMEGRENELLLIDIAS 271
                                   888999999999999986 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     8e-09   7.2e-06       2      90 ..     176     270 ..     175     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8e-09
                                   EEEE--SHHHHHHHHHHHHTT-EE.EEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHHHH..HHHHSH CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykv.avynrtkekveelvaeg...akaaesieelvasldvvitmvkagkavd..eviegl 76 
                                   i +iG+G+MG+   + l +++++v ++ nrt ek+++l++e    a++++++e+ v+++dvvi   +a + v   +++ ++
  gi|91773209|ref|YP_565901.1| 176 ILVIGTGEMGTLVTRALSHRDMHViYLANRTYEKARDLAEELggeAVMFDQLEKYVRAADVVISATSAPHYVLkgDLVAKV 256
                                   669**************877766527889***********95567******************998888877522466667 PP

                                   CCC--TT-EEEE-S CS
                 NAD_binding_2  77 lealkkgdilidgs 90 
                                   +e  +++ +lid +
  gi|91773209|ref|YP_565901.1| 257 MEGRENELLLIDIA 270
                                   77777777777765 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   0.1   1.1e-08   9.4e-06      32      99 ..     169     241 ..     137     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                                   S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTC...EECSHHHHHHH-SEEEE-S CS
                  2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgv...elvsleellaesDivslhl 99 
                                     l++k + +iG+G++G+ v + l+  +m+vi+   +  +++   +eelg     +++le+ ++ +D+v+ ++
  gi|91773209|ref|YP_565901.1| 169 DGLNDKHILVIGTGEMGTLVTRALSHRDMHVIYLANRTYEKArdLAEELGGeavMFDQLEKYVRAADVVISAT 241
                                   56899***************************98766554444544444431116679999999999998765 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   3.5e-07   0.00031      10     116 ..     154     249 ..     152     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-07
                   Glu_dehyd_C  10 isiveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretp 90 
                                   +si+  a++lae + +    + +  lv+G+G +G L + +l++  r+++ +y  + r + +++ dl eelG+  v      
  gi|91773209|ref|YP_565901.1| 154 VSIASAAVDLAEDILDG--LNDKHILVIGTGEMGTLVTRALSH--RDMHVIYLAN-RTY-EKARDLAEELGGEAVM----- 223
                                   57777777777776554..467899************9***86..7787565555.444.67889******99885..... PP

                   Glu_dehyd_C  91 vdeipeaseemdlvvEaTGsakhafe 116
                                    d++ +  +  d+v+ aT +++ +++
  gi|91773209|ref|YP_565901.1| 224 FDQLEKYVRAADVVISATSAPHYVLK 249
                                   6888888999********99988875 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 !   19.7   0.0   9.9e-07   0.00089       5      72 ..     171     244 ..     168     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.9e-07
                 NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk......laeeelekdlegadlviaatddr 72 
                                   l++k++lv+G Ge+++   r l   + +v+ +a+++ e++ +l +      +  ++lek +  ad+vi at+ +
  gi|91773209|ref|YP_565901.1| 171 LNDKHILVIGTGEMGTLVTRALSHRDMHVIYLANRTYEKARDLAEelggeaVMFDQLEKYVRAADVVISATSAP 244
                                   689********************************5444444444322222223557999***********876 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.4e-07   0.00084       2      77 ..     175     243 ..     174     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.4e-07
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-H CS
                        DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtp 77 
                                   +++v+G  G mG+ v++a+++ +d+++    +r+    +++d+ e lg    +  ++d+le+ +++adv+i  T+ 
  gi|91773209|ref|YP_565901.1| 175 HILVIGT-GEMGTLVTRALSH-RDMHVIYLANRTY--EKARDLAEELGG---EAVMFDQLEKYVRAADVVISATSA 243
                                   699***8.***********99.7777777777776..356677776665...77889**************99953 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   2.5e-06    0.0022      28     180 ..     181     349 ..     175     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                                   --HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S--EEES---------- CS
                           DFP  28 SGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkeadivimaAAvaDyrpkeaaeeKikke 108
                                   +G+mG  + +a+ +r ++V + +  +  ++       +    + m +++e+ +++ad+vi+a     y  k     K+   
  gi|91773209|ref|YP_565901.1| 181 TGEMGTLVTRALSHRDMHVIYLANRTYEKAR--DLAEELGGEAVMFDQLEKYVRAADVVISATSAPHYVLKGDLVAKVMEG 259
                                   8**********************99643333..3356899999***********************************999 PP

                                   ---..----EEE---HHHHHHHC-S..................S-EEEEEEE-S..S-HHHHHHHHHHHTT-SEEEEEEGG CS
                           DFP 109 eeeeeltleleknpdilaelaekkk.................kkqllvGFaaet..eellenareklerkgldlivaNdvs 170
                                   +e+e l +++ + +di   ++e  +                 + +++ + +ae   ++ l+  +++ +r+++d+i+ N  s
  gi|91773209|ref|YP_565901.1| 260 RENELLLIDIASPRDIDPAVEEIPHvilrnidglrvineknlQMRMVEAKKAEIiiDDELDMVKAQYKRQKADAIISNLYS 340
                                   9999999*********99887666577888888888876433223455677775446999999999999999999999999 PP

                                   GTTGGG-SS- CS
                           DFP 171 keeagfgsde 180
                                   ++ +g+ ++e
  gi|91773209|ref|YP_565901.1| 341 QS-HGLRHNE 349
                                   87.6655554 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 !   18.4   0.0     9e-07    0.0008     130     214 ..     174     254 ..     157     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9e-07
                                   -EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-G CS
               OCD_Mu_crystall 130 svlaiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilka 210
                                   + + +iG G +  + ++al+  +d++ + + +r+ e+a  +ae+l +   e +  ++ e+ v  ad+v+ +T a + +lk 
  gi|91773209|ref|YP_565901.1| 174 KHILVIGTGEMGTLVTRALS-HRDMHVIYLANRTYEKARDLAEELGG---EAVMFDQLEKYVRAADVVISATSAPHYVLKG 250
                                   56779*************97.58999999999999999999999987...99999*************************9 PP

                                   GGS- CS
               OCD_Mu_crystall 211 ewvk 214
                                   ++v 
  gi|91773209|ref|YP_565901.1| 251 DLVA 254
                                   9985 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 !   17.1   0.1   4.4e-06    0.0039       2      73 ..     180     246 ..     180     265 .. 0.76
   2 ?   -0.7   0.0       1.3   1.2e+03      35      79 ..     306     351 ..     293     370 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-06
                                   TTSHHHHHHHHHHHHC-T-EEEEEE.TTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                NAD_binding_10   2 AtGkvGrllvkellargghevtalv.RnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                   +tG  G l+++ l +r +++v  l+ R+ ek+ +l++e     + g++   ++l++ ++ ad+V+sa+++ + 
  gi|91773209|ref|YP_565901.1| 180 GTGEMGTLVTRALSHR-DMHVIYLAnRTYEKARDLAEE-----LGGEAVMFDQLEKYVRAADVVISATSAPHY 246
                                   79*************9.577777653778999999754.....56666667899**************88765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                   HHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HHHHHH CS
                NAD_binding_10  35 leaeeglevvegdvtdvedlaealkgadaVvsalggggk..deegak 79 
                                   +e ++++e++  d +d  + +   + ada++s+l +++   +++ ++
  gi|91773209|ref|YP_565901.1| 306 VE-AKKAEIIIDDELDMVKAQYKRQKADAIISNLYSQSHglRHNEME 351
                                   43.57778888888888888888889999999994433333333333 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 !   17.5   0.0   6.4e-06    0.0058       2      72 ..     175     243 ..     174     260 .. 0.83
   2 ?   -2.5   0.0       9.9   8.8e+03      25      79 ..     328     351 ..     297     368 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.4e-06
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE-S-G CS
                  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpeidavivatpn 72 
                                   ++++iG+G +g+   r+l ++  + +v+ l ++  e+a+++ae++g e   +++le+ ++  ++d+vi at +
  gi|91773209|ref|YP_565901.1| 175 HILVIGTGEMGTLVTRALSHR--DMHVIYLANRTYEKARDLAEELGGEavMFDQLEKYVR--AADVVISATSA 243
                                   89*************999888..99***********************888888998888..77777766654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.9
                                   TEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHH CS
                  GFO_IDH_MocA  25 leevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheela 79 
                                   +++  a++++  ++++ ++                               h+e++
  gi|91773209|ref|YP_565901.1| 328 RQKADAIISNLYSQSHGLR-------------------------------HNEME 351
                                   3333344443333333333...............................33333 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 ?    0.3   0.0      0.43   3.8e+02      36      62 ..      97     123 ..      88     146 .. 0.81
   2 ?    4.2   0.0     0.026        24      19      72 ..     156     208 ..     135     217 .. 0.82
   3 !    8.3   0.0    0.0014       1.3      71      95 ..     225     249 ..     220     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.43
                                   T-EEEEE---TTTHHHHHHHHHCTT-E CS
                 THF_DHG_CYH_C  36 gkkvvvvGrsnivgkplallLleknat 62 
                                   g + +++G+ +i+g+   ++L++k+a 
  gi|91773209|ref|YP_565901.1|  97 GLESMIIGEDQILGQIKDFFLMAKGAG 123
                                   77889**********999999998663 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.026
                                   HHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCC CS
                 THF_DHG_CYH_C  19 tpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkd 72 
                                    + + v+l ++    l++k+++v+G ++ +g  ++  L+++++ V ++ ++t +
  gi|91773209|ref|YP_565901.1| 156 IASAAVDLAEDILDGLNDKHILVIGTGE-MGTLVTRALSHRDMHVIYLANRTYE 208
                                   5677888999999999*********997.6999999999999999999999854 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0014
                                   CCHHHHHCCSSEEEE-SS-TT-B-G CS
                 THF_DHG_CYH_C  71 kdlaeitreadivvvavGkpelika 95 
                                   ++l++++r ad+v++a+  p+ + +
  gi|91773209|ref|YP_565901.1| 225 DQLEKYVRAADVVISATSAPHYVLK 249
                                   5899****************98844 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 !   13.8   0.1   1.9e-05     0.017     259     352 ..     160     340 ..     140     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHH.H.......................... CS
                Oxidored_nitro 259 lldaladyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrdde.e.......................... 312
                                   ++d  +d+ + l+ k ++++g +++   ++r+l    m+v++++ +t +++ + +                          
  gi|91773209|ref|YP_565901.1| 160 AVDLAEDILDGLNDKHILVIGTGEMGTLVTRALSHRDMHVIYLANRTYEKARDlAeelggeavmfdqlekyvraadvvisa 240
                                   5677778888999******************************98887776664258************************ PP

                                   ...............................................................HHHHHS.TT.SEEEES.C CS
                Oxidored_nitro 313 ...............................................................rlkaeleegepeviddad 330
                                                                                                  r+    e+++ e+i+d +
  gi|91773209|ref|YP_565901.1| 241 tsaphyvlkgdlvakvmegrenelllidiasprdidpaveeiphvilrnidglrvineknlqmRMV---EAKKAEIIIDDE 318
                                   *********************************************************998744333...233457888889 PP

                                   HHHHHHHHHHHT-SEEEE-CCH CS
                Oxidored_nitro 331 leeleelikelkpdlllggske 352
                                   l+ +++  k+ k+d ++++ + 
  gi|91773209|ref|YP_565901.1| 319 LDMVKAQYKRQKADAIISNLYS 340
                                   9999**************9875 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 ?   -2.3   0.0       5.7   5.1e+03      71      97 ..      28      57 ..       6      86 .. 0.68
   2 ?   -2.4   0.1         6   5.3e+03       5      23 ..     121     139 ..     121     147 .. 0.78
   3 ?   16.1   0.0   1.1e-05      0.01       1      76 [.     176     240 ..     176     260 .. 0.80
   4 ?   -2.0   0.0       4.4   3.9e+03      30      42 ..     324     336 ..     284     394 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.7
                                  SEEEE-SSGG...GHHHHHHHHHHHT-EEE CS
               Sacchrp_dh_NADP 71 dlvvnlsppi...ssldvlkaCietgvhyv 97
                                  dlv++ + +    +  +vlk+C +  + +v
  gi|91773209|ref|YP_565901.1| 28 DLVLSQLYSNelvYECAVLKTCNRVEIYVV 57
                                  666666666556677777788777665554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                                   --SHHHHHHHHHHHCTCCT CS
               Sacchrp_dh_NADP   5 GaGsvGqavaellarhfdv 23 
                                   GaG vG+++    ++  +v
  gi|91773209|ref|YP_565901.1| 121 GAGTVGKVLSTAFSKAIQV 139
                                   99****9988777777666 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.1e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE- CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnl 76 
                                   +l+iG G +G  v++ l+ ++ +   i +a r+ ek++ la+++ g+ + +         + L+++++ +d+v+++
  gi|91773209|ref|YP_565901.1| 176 ILVIGTGEMGTLVTRALSHRDMH--VIYLANRTYEKARDLAEELGGEAVMFD--------Q-LEKYVRAADVVISA 240
                                   89****************99887..9*************9988766654443........3.55555555666655 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.4
                                   EESSHHHHHHHHC CS
               Sacchrp_dh_NADP  30 adrskeklealaa 42 
                                   a  +++k++a+++
  gi|91773209|ref|YP_565901.1| 324 AQYKRQKADAIIS 336
                                   2333333333333 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       2.3   2.1e+03     104     136 ..      46      76 ..      33      97 .. 0.73
   2 ?   12.2   0.0   0.00011       0.1       2      66 ..     171     239 ..     170     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                                   S---TTSEEEEEEESS-SHHHHHHHHTT----E CS
                          IlvN 104 ikppkdvdvvlvAPkgpGhlvreeyeegkGvpa 136
                                   +k+ ++v++++v  k  G+ v  +y++  Gv a
  gi|91773209|ref|YP_565901.1|  46 LKTCNRVEIYVVSSK--GSSVLFHYAKEMGVSA 76 
                                   556667777777766..5677778888888865 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00011
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEE.EE-TT-HHHHHHHHTT-EEE...EHHHHHHT-SEEEE CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvv.glregsksvkkAkeegfevl...tvaeavkkadvvmi 66 
                                   l++k+i viG G  G   ++ l    ++v++ ++r+ +k  + A+e g e +   ++++ v++advv+ 
  gi|91773209|ref|YP_565901.1| 171 LNDKHILVIGTGEMGTLVTRALSHRDMHVIYlANRTYEKARDLAEELGGEAVmfdQLEKYVRAADVVIS 239
                                   789**************99999999999885377888889999**988776612245667899999985 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   9.2e-05     0.082      22      93 ..     334     405 ..     312     416 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        PRESAN  22 dmyiiwnyvmknekkkyknmikkLsnyleelakkynipeeykkklwkeckneitkelkklekeynknfynll 93 
                                    + +++++ +++  +++++ i+kLs y +    ++++ e+    + +++  e tk+l++  +++ ++f + +
  gi|91773209|ref|YP_565901.1| 334 IISNLYSQSHGLRHNEMEHAINKLSAYHTIGEIERKVLEDLTHAITNKILAEPTKKLRNAAEYDDDKFLDSV 405
                                   5789***************************************************************98766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.84   7.5e+02      26     107 ..       8      93 ..       3     102 .. 0.70
   2 ?   10.5   0.1   0.00062      0.55       1      44 [.     176     221 ..     176     248 .. 0.70
   3 ?   -1.5   0.0       3.3   2.9e+03      34      34 ..     303     303 ..     246     343 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.84
                                   EEESSHHHHHHHHHTT...SE.EEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEEESSGGGH CS
                        TrkA_N  26 vidkdeerveelreeg...le.vvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpkkkiiaraqdpeha 102
                                   vi + +++vee+++     ++ v+   +++e v e a +++++ v + + + + + ++ ++ake+   +ki+   +++e  
  gi|91773209|ref|YP_565901.1|   8 VITHAKATVEEMEDSWhgdIDlVLSQLYSNELVYECAVLKTCNRVEIYVVSSKGSSVLFHYAKEMGVSAKIVEFYDHDESL 88 
                                   666666666666655443433456666677777777777888777777777777778889999999999999888888776 PP

                                   HHHHH CS
                        TrkA_N 103 ellkk 107
                                   + l +
  gi|91773209|ref|YP_565901.1|  89 RHLLR 93 
                                   66655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00062
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSH.HHHHHHHHTT.SEE CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkde.erveelreeg.lev 44 
                                   i++iG G++G+ +++ Ls++ ++v+   ++  e+++ l+ee   e+
  gi|91773209|ref|YP_565901.1| 176 ILVIGTGEMGTLVTRALSHRDMHVIYLANRTyEKARDLAEELgGEA 221
                                   79*****************663455444433377777766653444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.3
                                   H CS
                        TrkA_N  34 v 34 
                                   +
  gi|91773209|ref|YP_565901.1| 303 M 303
                                   1 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0048       4.3      39      90 ..       7      59 ..       2      62 .. 0.81
   2 ?    3.2   0.2      0.13   1.1e+02      22      66 ..     296     339 ..     293     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
                        Rimk_N 39 lkieaekpevyykg.ekleefdavipRigasitfygtavlrqFemmgvfvlne 90
                                  + i+++k +v   + +   ++d v+ ++ +++  y +avl+  ++ +++v+ +
  gi|91773209|ref|YP_565901.1|  7 MVITHAKATVEEMEdSWHGDIDLVLSQLYSNELVYECAVLKTCNRVEIYVVSS 59
                                  66777777775444266679*****************************9875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                        Rimk_N  22 aekrghevevldplrcylkieaekpevyykgekleefdavipRig 66 
                                   +++++ ++++++ ++ ++ i++ + +++  + k ++ da+i  + 
  gi|91773209|ref|YP_565901.1| 296 INEKNLQMRMVEAKKAEIIIDD-ELDMVKAQYKRQKADAIISNLY 339
                                   5678889999999999999988.6666666678889999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 2763.46
//
Query:       gi|91773210|ref|YP_565902.1|  [L=226]
Description: siroheme synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-19   68.4   0.0    9.7e-19   67.7   0.0    1.3  1  NAD_binding_7   Putative NAD(P)-binding
    5.7e-05   22.5   0.1    9.9e-05   21.7   0.1    1.4  1  Sirohm_synth_M  Sirohaem biosynthesis protein central
     0.0027   17.0   0.0     0.0045   16.3   0.0    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.032   13.8   0.0      0.047   13.3   0.0    1.2  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
        0.1   12.9   0.0       0.15   12.3   0.0    1.3  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   2.7e-22   9.7e-19       1      95 [.      13     119 ..      13     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 2.7e-22
                 NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.....elvklaeeelekd............legadl 64 
                                   lf+d++g+kv+v+GgG+v+ rk++ ++e+ a+ +v++ ++++ele     ++v+l+++    d            +e+a+l
  gi|91773210|ref|YP_565902.1|  13 LFIDMEGRKVVVFGGGSVGFRKASLFAEY-AETVVISIDLSPELEelassSKVELIKS----DlssvsdesildlMEDAFL 88 
                                   79***************************.9999999999888884444433333343....2333344566666999*** PP

                 NAD_binding_7  65 viaatddrelneriaeaakarrilvnvadkp 95 
                                   vi at+ ++ln+ri e+a+  +ilvn+ d +
  gi|91773210|ref|YP_565902.1|  89 VIPATNVPSLNDRIRELAQGCGILVNRIDMA 119
                                   *****************************65 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 !   21.7   0.1   2.8e-08   9.9e-05       1      27 [.     130     156 ..     130     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.8e-08
                Sirohm_synth_M   1 rGpLQIaiSTnGksPrLAaliRreier 27 
                                   r +L+I iST G+sP+ ++  Rr++e+
  gi|91773210|ref|YP_565902.1| 130 RNGLSIGISTFGSSPAVSKYTRRKLEA 156
                                   678***********************7 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 !   16.3   0.0   1.2e-06    0.0045      29     103 ..      20      97 ..      12     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                                   -EEEEESTSHHHHHHHH.HHHHTT-EEEEEESSHHHHHHHHHTTTCECEE..HCHHHHHHHHHHHH-SEEEE---BTT CS
                   AlaDh_PNT_C  29 akvlviGgGvaGlqAia.takglgakVtvlDvrparleqleslgakfvev..lksqeellaeavkeadvvigtvlipG 103
                                    kv+v+GgG +G   ++  a   + +V  +D++p+  e  +s + + ++    + + e++ + +++a +vi +  +p 
  gi|91773210|ref|YP_565902.1|  20 RKVVVFGGGSVGFRKASlFAEYAETVVISIDLSPELEELASSSKVELIKSdlSSVSDESILDLMEDAFLVIPATNVPS 97 
                                   59**********97555168888999999******999999988887776557889999************9999985 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05     0.047       2      57 ..      21      77 ..      20      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                  EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHH CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiyepgLeelvkk 57
                                  k++v+G G vG   a ++ae     vi +D + e  +   s+k++++  +L+++  +
  gi|91773210|ref|YP_565902.1| 21 KVVVFGGGSVGFRKASLFAEYAeTVVISIDLSPELEELASSSKVELIKSDLSSVSDE 77
                                  899*****************99567789**999877777778888888888877655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05      0.15       1      52 [.      22      74 ..      22     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                                  EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSH CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatde 52
                                  +++ G G vG + a  + e ++  v+ id ++e  e ++  ++e ++ d ++ 
  gi|91773210|ref|YP_565902.1| 22 VVVFGGGSVGFRKASLFAEyAETVVISIDLSPELEELASSSKVELIKSDLSSV 74
                                  79*****************66666777999999888889999*9999886643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1421.37
//
Query:       gi|91773211|ref|YP_565903.1|  [L=159]
Description: AsnC family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-31  108.9   0.0    1.5e-31  108.4   0.0    1.3  1  AsnC_trans_reg2  AsnC-like ligand binding domain
    2.7e-07   30.3   0.0    5.9e-07   29.2   0.0    1.6  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.023   14.3   0.0        3.2    7.4   0.0    2.5  2  HTH_24           Winged helix-turn-helix DNA-binding
       0.05   13.2   0.0      0.082   12.5   0.0    1.2  1  DDRGK            DDRGK domain
      0.092   12.9   0.0       0.28   11.3   0.0    1.7  2  HEPN             HEPN domain
       0.16   11.9   0.0        0.8    9.6   0.0    1.9  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 !  108.4   0.0   5.1e-35   1.5e-31       2      82 .]      69     153 ..      68     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 5.1e-35
               AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyevLpst 78 
                                   +G++ana++ w+vp+e veev++v+a ++evtHcYeR    +wpynl++mvh  ++e++e v++ei+ atg++dy++L+s+
  gi|91773211|ref|YP_565903.1|  69 IGITANAMCTWNVPDELVEEVGAVMAGFSEVTHCYERprypDWPYNLFTMVHSYTREDCEHVAKEISIATGISDYNLLYSV 149
                                   8************************************88888*************************************** PP

               AsnC_trans_reg2  79 refK 82 
                                   refK
  gi|91773211|ref|YP_565903.1| 150 REFK 153
                                   ***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 !   29.2   0.0     2e-10   5.9e-07       1      42 []       8      52 ..       8      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2e-10
                 HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                  +De+D ++L++ q        ++a++A+++G++e+ v  R++ L+
  gi|91773211|ref|YP_565903.1|  8 MDELDTRLLKLTQDGipfTHSPFADVAKELGMTEEDVVDRIKHLQ 52
                                  9*****************************************996 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 ?    7.4   0.0    0.0011       3.2       1      48 []       8      58 ..       8      58 .. 0.88
   2 ?    4.3   0.0    0.0096        29      16      46 ..     127     157 ..     120     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                        HTH_24  1 ldetdrkILelLqk...nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +de+d ++L+l q+     + + +++A++lg++   v  r+k L+ +G+I+
  gi|91773211|ref|YP_565903.1|  8 MDELDTRLLKLTQDgipFTHSPFADVAKELGMTEEDVVDRIKHLQVNGFIR 58
                                  68888888888888888888999***********99999999999999996 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0096
                        HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeGl 46 
                                        +e++ ++g+S  ++++ ++++++ G+
  gi|91773211|ref|YP_565903.1| 127 CEHVAKEISIATGISDYNLLYSVREFKKTGV 157
                                   555569********************99996 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05     0.082     117     143 ..      31      57 ..      27      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                   HHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                         DDRGK 117 eelavkfklktqevierikeLeeqgsl 143
                                    ++a +++++ ++v++rik+L+ +g +
  gi|91773211|ref|YP_565903.1|  31 ADVAKELGMTEEDVVDRIKHLQVNGFI 57 
                                   699*******************99977 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.62   1.9e+03      77     101 ..      15      44 ..       3      54 .. 0.49
   2 ?   11.3   0.0   9.3e-05      0.28      70     106 ..      89     132 ..      56     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.62
                                   HHHHHCCCHHCCCTSS--S.....--HHHH CS
                          HEPN  77 leeLekayiesrYpdakee.....yteeda 101
                                   l +L++  i+    +++       +teed+
  gi|91773211|ref|YP_565903.1|  15 LLKLTQDGIPFTHSPFADVakelgMTEEDV 44 
                                   444444444444444444334444444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.3e-05
                                   -HHHHHHHHHHHCCCHHCCCTSS--S.......--HHHHHHHHH CS
                          HEPN  70 seelreeleeLekayiesrYpdakee.......yteedaeealk 106
                                      +   ++e+++ y   rYpd  ++       yt+ed+e++ k
  gi|91773211|ref|YP_565903.1|  89 VGAVMAGFSEVTHCYERPRYPDWPYNlftmvhsYTREDCEHVAK 132
                                   3344445599************9999**************9866 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00027       0.8      24      53 ..      30      59 ..      13      68 .. 0.90
   2 ?   -0.1   0.0       0.3   9.1e+02      24      49 ..     131     156 ..     116     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                                  HHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2 24 vgelarrlglsksavsrilkrLvaaGLver 53
                                   +++a++lg++   v  ++k L+  G+++r
  gi|91773211|ref|YP_565903.1| 30 FADVAKELGMTEEDVVDRIKHLQVNGFIRR 59
                                  689*************************98 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.3
                                   HHHHHHHHTSSHHHHHHHHHHHHHTT CS
                        MarR_2  24 vgelarrlglsksavsrilkrLvaaG 49 
                                   ++e+  ++g+s  ++ + ++++ + G
  gi|91773211|ref|YP_565903.1| 131 AKEISIATGISDYNLLYSVREFKKTG 156
                                   67888899999999999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1102.47
//
Query:       gi|91773212|ref|YP_565904.1|  [L=151]
Description: AsnC family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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   86.0   0.0    2.6e-24   85.2   0.0    1.4  1  AsnC_trans_reg2  AsnC-like ligand binding domain
    1.7e-07   31.0   0.0    3.1e-07   30.1   0.0    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0057   16.2   2.1      0.077   12.6   2.1    2.2  1  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.011   15.8   0.0       0.02   15.0   0.0    1.5  1  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
      0.024   14.6   0.1      0.048   13.6   0.1    1.5  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
       0.11   12.4   0.1        0.3   11.0   0.0    1.7  2  RuvB_C           RuvB C-terminal winged helix 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 !   85.2   0.0   8.8e-28   2.6e-24       2      82 .]      65     143 ..      64     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 8.8e-28
               AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLpstrefK 82 
                                   +G   ++lva++vpe+r++evae +++++ev+H+Y+R+ +yn++f+v+a+++e++e+++ +++++tg+  +  Lp++r fK
  gi|91773212|ref|YP_565904.1|  65 VGGI-STLVAMEVPESRIDEVAELINSHQEVSHNYLRQADYNIWFTVSAANRERLEQIIYDLKDETGCP-LIDLPTKRLFK 143
                                   7888.9***************************************************************.99******999 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 !   30.1   0.0     1e-10   3.1e-07       1      41 [.       4      47 ..       4      48 .. 0.98

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1e-10
                 HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrL 41
                                  LDe+D+ IL+++q d      ++++L++++G+Se+  l R++rL
  gi|91773212|ref|YP_565904.1|  4 LDEVDKSILNLIQLDfplDPHPFEKLSQQLGISEEDLLVRMERL 47
                                  8******************************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.1   2.6e-05     0.077       1      48 []       4      54 ..       4      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                        HTH_24  1 ldetdrkILelLqk...nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  lde d+ IL+l+q        +   L+++lg+S   ++ r++rL ++G I+
  gi|91773212|ref|YP_565904.1|  4 LDEVDKSILNLIQLdfpLDPHPFEKLSQQLGISEEDLLVRMERLSRKGAIR 54
                                  79999*********76646679**************************886 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   6.5e-06      0.02      21      57 ..      26      62 ..       7      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.5e-06
                Sulfolobus_pRN 21 leeleektGiekeellvyltrlykrGlisrkWrkiaG 57
                                  +e+l ++ Gi  e+llv + rl ++G i r    i  
  gi|91773212|ref|YP_565904.1| 26 FEKLSQQLGISEEDLLVRMERLSRKGAIRRIGPVINT 62
                                  79**************************996555555 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.6e-05     0.048       7      56 ..      78     124 ..      68     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                   GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHH CS
                AsnC_trans_reg   7 pghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflre 56 
                                    +    ++e++e +  + eV + y    dy++ + v +++ e le+++ +
  gi|91773212|ref|YP_565904.1|  78 ES---RIDEVAELINSHQEVSHNYLRQADYNIWFTVSAANRERLEQIIYD 124
                                   34...49***************************************9755 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 ?   11.0   0.0    0.0001       0.3       4      46 ..       4      46 ..       3      56 .. 0.92
   2 ?   -2.1   0.0       1.3   3.7e+03      26      45 ..      68      86 ..      62      93 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                  --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHH CS
                        RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedviEP 46
                                  Lde d+++L+l++  f   p   + l++ lg+++e +   +E 
  gi|91773212|ref|YP_565904.1|  4 LDEVDKSILNLIQLDFPLDPHPFEKLSQQLGISEEDLLVRMER 46
                                  89**********************************9999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                  HHHHHHHTT--HHHHHHTTH CS
                        RuvB_C 26 lktlaailgeeketiedviE 45
                                  ++tl+a ++++++ i +v E
  gi|91773212|ref|YP_565904.1| 68 ISTLVA-MEVPESRIDEVAE 86
                                  455443.4555566655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 00:00:00.41
# Mc/sec: 1098.86
//
Query:       gi|91773213|ref|YP_565905.1|  [L=346]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-22   80.9   0.3    6.1e-22   78.8   0.0    2.1  3  Radical_SAM  Radical SAM superfamily
    4.9e-10   39.8   0.0    9.6e-10   38.9   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    1.4e-08   35.1   2.3    2.8e-08   34.2   2.3    1.5  1  SPASM        Iron-sulfur cluster-binding domain
    4.5e-07   30.0   0.0      1e-06   28.9   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
        0.1   12.1   0.1       0.16   11.4   0.1    1.2  1  DUF5046      Domain of unknown function (DUF5046)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   1.7e-25   6.1e-22       4     150 ..      13     152 ..      10     168 .. 0.89
   2 ?   -0.3   0.0      0.35   1.3e+03      31      86 ..     158     247 ..     148     251 .. 0.47
   3 ?   -2.1   0.1       1.2   4.3e+03       4      19 ..     252     267 ..     250     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.7e-25
                                   ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvet 84 
                                   t gCnl+C++C  ++t  +e ++ +ls+ e ++ v+e+ +e+g   +il+ggepl+++d +e+++ +  +   g+r+++ t
  gi|91773213|ref|YP_565905.1|  13 TWGCNLACVHCRGSST--SEIPEGELSTSEAKHFVDEI-VEMGDPILILTGGEPLVRKDVYEIARYATDK---GLRVALAT 87 
                                   559************8..********************.9********************9999999998...******** PP

                                   CSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  85 ngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdriv 150
                                   ngtl+++ ++++l+++gv rvs++++  +   +++ ++  ++ fe  ++++e+l++ g+    ++++
  gi|91773213|ref|YP_565905.1|  88 NGTLLNDGVVKKLKDAGVQRVSISIDGSTAQ-THDDFRgVPGAFESSMRGIEYLKAGGLG-FQINTT 152
                                   *******************************.777777799**************99987.444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....................................TTHHHHHHHHHHTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxxx RF
                   Radical_SAM  31 veeileevkelkaekgvkevilgggeplly.....................................pdfvellerlakla 74 
                                   ++ei ++++++  + g++  +++   p+ +                                     p++ ++++++ak+ 
  gi|91773213|ref|YP_565905.1| 158 IDEIPAILEIA-TNIGAEAHHIFLLVPTGRgkeleneeippaeyervlnwfydqqkhvkiqlkatcaPHYFRIMRQRAKR- 236
                                   55666666666.45553333333333333333333333333333333333333333333333333335555555555555. PP

                                   CCTEEEEEEECS CS
                                   xxxxxxxxxxxx RF
                   Radical_SAM  75 vpgiritvetng 86 
                                    +g ++tv t g
  gi|91773213|ref|YP_565905.1| 237 -EGTEVTVKTHG 247
                                   .57777776665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
                                   ESEESS--TTTSCCTT CS
                                   xxxxxxxxxxxxxxxx RF
                   Radical_SAM   4 trgCnlrCsfCarpet 19 
                                   trgC ++ sfC +++t
  gi|91773213|ref|YP_565905.1| 252 TRGCLGGISFCFVSST 267
                                   8999999999999976 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.7e-13   9.6e-10      12     123 ..      13     120 ..       5     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.7e-13
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                   + gCnl+C  C   +t +  +g+  t+e++ + ++++ +  ++ l+l+GGEPl+   +++++e++++   +++  + ++++
  gi|91773213|ref|YP_565905.1|  13 TWGCNLACVHCRGSSTSEIPEGELSTSEAK-HFVDEIVEMGDPILILTGGEPLV---RKDVYEIARYATDKGL-RVALATN 88 
                                   67************************9885.778999999**************...****************.69***** PP

                       Fer4_12  93 gytleelskk.ekeellkeidvlvdGkfeesl 123
                                   g+ l++   k  k+  ++ + + +dG  ++  
  gi|91773213|ref|YP_565905.1|  89 GTLLNDGVVKkLKDAGVQRVSISIDGSTAQTH 120
                                   ****9977664677789999999999887765 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   2.3   7.7e-12   2.8e-08       1      67 [.     255     314 ..     255     324 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 7.7e-12
                         SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefrkskkfplielCrnC 67 
                                   C  + + +f++s GdV pC     +   +++ Gni+e+s++eIw+++  ++++r+   ++l   C +C
  gi|91773213|ref|YP_565905.1| 255 CLGGISFCFVSSTGDVQPC----GYL--PVIAGNIKEKSFKEIWEDSvLFNDLRD--YDKLGGKCGRC 314
                                   66667788***********....233..7***************99989*****4..44444557777 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.8e-10     1e-06       7     101 ..      15     101 ..      12     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.8e-10
                       Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwlet 87 
                                   gCnl+C+ C  ++t +   g+ +t+e   + +  ++  e+    l ltGGePL     k+++++ ++  +++  +++ l t
  gi|91773213|ref|YP_565905.1|  15 GCNLACVHCRGSSTSEIPEGELSTSEAK-HFV--DEIVEMGDPILILTGGEPLV---RKDVYEIARYATDKG--LRVALAT 87 
                                   9*********999999888888887765.555..33334444559********5...599************..******* PP

                       Fer4_14  88 ngtleielektpdl 101
                                   ngtl  +  + +  
  gi|91773213|ref|YP_565905.1|  88 NGTLLNDGVVKKLK 101
                                   ***98776643333 PP

>> DUF5046  Domain of unknown function (DUF5046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.4e-05      0.16      93     135 ..      71     113 ..      59     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                       DUF5046  93 tvavyatdgilrvydkttGalltdvevepveeqqsvrvsavge 135
                                   ++a yatd  lrv   t+G ll d  v+ + ++   rvs   +
  gi|91773213|ref|YP_565905.1|  71 EIARYATDKGLRVALATNGTLLNDGVVKKLKDAGVQRVSISID 113
                                   6999************************999987777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2530.09
//
Query:       gi|91773214|ref|YP_565906.1|  [L=126]
Description: hypothetical protein Mbur_1234 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   57.3   0.0    1.7e-15   57.1   0.0    1.0  1  CcmE      CcmE
  ------ inclusion threshold ------
       0.56   10.1   2.6         10    6.0   0.0    2.2  2  DUF4307   Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> CcmE  CcmE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.9e-19   1.7e-15       5     126 ..       5     125 ..       1     126 [] 0.81

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.9e-19
                                   XXXXXXXXXXXXXXXXXXXXXXXXXSSSXXBXTTTTTS--S-.TTSEEEEEEEE-TTT-EE-TTSSEEEEEEE-...T.-E CS
                          CcmE   5 rlklivllllvlaavvvlvlsalqenlvyfltpsevlekkae.egrrlrvgGlVkegsvkrdpesleveFvvtd...leke 81 
                                   r +++ +l+  ++av+v+ l ++  + + +l +s++++++++ +g+++   GlVk+g+++ +pe   v+F+++d   +e+e
  gi|91773214|ref|YP_565906.1|   5 RKAILTILA--IVAVMVIGLWGVDVE-QGYLMVSDITTSPQDhVGQKVSTMGLVKNGTLSISPE--MVSFTLVDaedKEHE 80 
                                   444443333..444444444444444.56999******97777****************99765..58******877689* PP

                                   EEEEEES---TT--TTSEEEEEEEE-TTSEEEECCEEESS-XXXX CS
                          CcmE  82 lkVeYegilPdlFregqgvvveGrleedgvfeAeevlaKhdekYm 126
                                   + +eY+  lP +  eg+++  +G++ +++ +eAe++++ +++kY 
  gi|91773214|ref|YP_565906.1|  81 IDIEYTADLPANIVEGNSISLTGTMISESKIEAEQIVIGCPSKYS 125
                                   ********************************************5 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.8    0.0093        83       6      27 ..       6      27 ..       2      50 .. 0.60
   2 ?    6.0   0.0    0.0011        10      24      58 ..      54      88 ..      45      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0093
                       DUF4307  6 villvvlvvvalalvawigysq 27
                                  +++l++l++va+++++  g++ 
  gi|91773214|ref|YP_565906.1|  6 KAILTILAIVAVMVIGLWGVDV 27
                                  4455555555555555555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0011
                       DUF4307 24 gysqgsadvsaevvgfevvddstvevtfeVtrddg 58
                                  ++++g+ ++s e+v+f+ vd++  e +++++  ++
  gi|91773214|ref|YP_565906.1| 54 LVKNGTLSISPEMVSFTLVDAEDKEHEIDIEYTAD 88
                                  45668999***********9888877777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 963.62
//
Query:       gi|91773215|ref|YP_565907.1|  [L=300]
Description: polyprenyl synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-51  173.9   0.1    3.8e-51  173.6   0.1    1.2  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.064   12.3   0.0          7    5.6   0.0    2.1  2  Biopterin_H      Biopterin-dependent aromatic amino acid hydr
        0.1   12.2   0.0        0.2   11.2   0.0    1.5  1  Peptidase_C47    Staphopain peptidase C47


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 !  173.6   0.1   6.3e-55   3.8e-51       3     205 ..      28     218 ..      26     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 6.3e-55
                                   HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHH CS
               polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklA 83 
                                   ++++++ +++ +gGK++Rp+++lla++++++ +   e+  ++a ++el+h+asL+hDDi D+  +RRG ++ah+++G ++A
  gi|91773215|ref|YP_565907.1|  28 QMKKVVGHICRSGGKKVRPIILLLASRICGKGS---ENCTNAALAIELIHSASLIHDDILDEGVMRRGVESAHKKFGPAAA 105
                                   6889999***********************444...7899***************************************** PP

                                   HHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHH CS
               polyprenyl_synt  84 indgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaal 164
                                   +++gd++ +++ el++ +   s+ +++ f ++ + ++eG+ +d++++ ++d++   + +y + + +KTa+lfa+++ ++a+
  gi|91773215|ref|YP_565907.1| 106 MLAGDYMISKSIELISIY---STPVVQEFGRAGMAMAEGETIDIKST-SEDFA---EMNYFDCIDKKTASLFAASAVMGAY 179
                                   *****************9...569********************555.57777...************************* PP

                                   HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS CS
               polyprenyl_synt 165 lagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgK 205
                                   +aga+++++++lk++g++lG a+Qi+DD+l ++++ ++  K
  gi|91773215|ref|YP_565907.1| 180 IAGADEKTASKLKNYGRKLGRAYQIVDDLLEYTQNIDN--K 218
                                   ****99***************************66332..2 PP

>> Biopterin_H  Biopterin-dependent aromatic amino acid hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0012         7      88     134 ..       9      54 ..       4      59 .. 0.81
   2 ?    4.7   0.1    0.0023        14     268     316 ..     178     228 ..     129     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0012
                   Biopterin_H  88 yleafkllekecgysedniPqledvskfLkektGfklRPvaGllsaR 134
                                   y+++ + +++ ++   d+ Pq+++v  ++ ++ G k+RP+  ll++R
  gi|91773215|ref|YP_565907.1|   9 YRQITDAMNE-MISDMDDSPQMKKVVGHICRSGGKKVRPIILLLASR 54 
                                   5555555544.45567888*************************999 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0023
                   Biopterin_H 268 Yfvaesfedakeklrkfaktlkrpfsvryd..pytqsvevldskekikkll 316
                                    ++a + e++ +kl+++ ++l r +++  d   ytq+++  +s +k  ++l
  gi|91773215|ref|YP_565907.1| 178 AYIAGADEKTASKLKNYGRKLGRAYQIVDDllEYTQNIDNKKSDNKSISIL 228
                                   56777789999****************987557999998877777665555 PP

>> Peptidase_C47  Staphopain peptidase C47
   #    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      66     107 ..     187     229 ..     177     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                 Peptidase_C47  66 tpnemiefGksqGrdiqylervtsyee.vdqltknnkGiavlg 107
                                   t+ ++ ++G+  Gr  q+ + +  y + +d+   +nk i +l 
  gi|91773215|ref|YP_565907.1| 187 TASKLKNYGRKLGRAYQIVDDLLEYTQnIDNKKSDNKSISILQ 229
                                   5677889***************9996449************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2534.43
//
Query:       gi|91773216|ref|YP_565908.1|  [L=397]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-15   55.6   0.0    1.3e-14   55.0   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
      8e-09   35.9   0.0    2.1e-08   34.6   0.0    1.8  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.065   13.2   0.4       0.18   11.7   0.0    1.9  2  Imm51        Immunity protein 51
       0.13   12.5   0.0       0.25   11.6   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 !   55.0   0.0   2.8e-18   1.3e-14       3     165 ..      94     246 ..      92     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.8e-18
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                   +t  C+++C++C         +   +l++ee+ + v e+  + g+  + + gge +l++d+++ ++   k    +   t+ 
  gi|91773216|ref|YP_565908.1|  94 ITDRCPYNCIHCGAA----GIVADPELTLEEVNRVVNEA-IDLGAYLISFDGGETMLRSDIADMVASVDKT---KAIATCF 166
                                   6899***********....69******************.8**99999999*******************8...9999999 PP

                                   ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                   t+g+++++e ++ l+ +g+   +++++++d++++ +  +r + f+  + ++++  +agi    d+ v++   n ++lee++
  gi|91773216|ref|YP_565908.1| 167 TSGFKLTPERAQDLKTAGLYSAHISVDSPDEKEHDRVRGREGAFQNSMTGIRNTLNAGIM--ADMFVVVSPDNIDDLEEFY 245
                                   ********************************7777777******************999..788888888*******998 PP

                                   H CS
                                   x RF
                   Radical_SAM 165 e 165
                                    
  gi|91773216|ref|YP_565908.1| 246 T 246
                                   6 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   4.6e-12   2.1e-08       1      47 [.     313     353 ..     313     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.6e-12
                         SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse 47 
                                   Cfa++r + +++ GdV+pC +      ++l++Gn+re+ leeIw+  
  gi|91773216|ref|YP_565908.1| 313 CFAGRRWVHVAAGGDVMPCAY------TPLSFGNVRENGLEEIWKRM 353
                                   9******************33......37***************654 PP

>> Imm51  Immunity protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.18      51     101 ..     212     263 ..     207     265 .. 0.88
   2 ?   -2.3   0.1      0.92   4.1e+03      17      41 ..     341     365 ..     340     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                         Imm51  51 ekapelleklefDpEagmFvay.sedkealkelaellkelledeeklrelie 101
                                   +++  + ++l+    a+mFv+  ++++++l+e+ +l  +l   e  ++e+i 
  gi|91773216|ref|YP_565908.1| 212 NSMTGIRNTLNAGIMADMFVVVsPDNIDDLEEFYTLADNLSMQEMSIYEIIA 263
                                   566677888888999*****9978899**********************995 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.92
                         Imm51  17 leddkveeveerfeeegaegnGydW 41 
                                   + ++  ee+ +r+ ++ a+  + d+
  gi|91773216|ref|YP_565908.1| 341 VRENGLEEIWKRMGKHAAYKGSADY 365
                                   5678889999999999999888776 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.6e-05      0.25      14     132 ..      97     207 ..      90     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                       Fer4_12  14 gCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgy 94 
                                   +C+ +C  C    +    +  e t e  +++++++ +     +++ GGE +l   +++++++v +v ++k       ++g+
  gi|91773216|ref|YP_565908.1|  97 RCPYNCIHCG---AAGIVADPELTLEEVNRVVNEAIDLGAYLISFDGGETML---RSDIADMVASVDKTKA-IATCFTSGF 170
                                   6777777777...45555677899999999999*99****************...999********99999.556667788 PP

                       Fer4_12  95 tleelskk.ekeellkeidvlvdGkfeesledeslrfrg 132
                                   +l   +++  k   l   ++ vd +   ++e+++ r r 
  gi|91773216|ref|YP_565908.1| 171 KLTPERAQdLKTAGLYSAHISVDSPD--EKEHDRVRGRE 207
                                   88777766433333445556665554..44444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2649.70
//
Query:       gi|91773217|ref|YP_565909.1|  [L=108]
Description: H(+)-transporting ATP synthase, subunit H [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-07   29.9  18.1      7e-07   29.6  18.1    1.0  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
    1.4e-06   28.4  24.6    1.6e-05   25.0  17.9    2.0  2  ATP-synt_B      ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
      0.042   14.4  17.2       0.06   13.9  17.2    1.3  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
       0.14   12.8  13.0       0.85   10.3  13.0    2.2  1  Ribosomal_S20p  Ribosomal protein S20
       0.16   12.0  10.5       0.58   10.2   0.6    2.1  2  HOIP-UBA        HOIP UBA domain pair
       0.41   10.5  10.4       0.47   10.3  10.4    1.0  1  PIN_8           PIN like domain
        0.8   10.5   6.6        9.8    7.0   0.2    2.4  2  dsrm            Double-stranded RNA binding motif
       0.91   10.2   9.3        2.6    8.7   9.3    1.8  1  DUF883          Bacterial protein of unknown function (DUF883
        1.5    7.6   8.3        1.6    7.6   8.3    1.0  1  LMBR1           LMBR1-like membrane protein
          3    8.6   9.6       0.46   11.3   1.9    2.4  2  DUF2462         Protein of unknown function (DUF2462)
        3.3    8.0   7.2        1.2    9.4   3.0    1.8  2  Pro_CA          Carbonic anhydrase
        3.9    8.1  12.3       0.27   11.8   5.0    2.2  2  YtxH            YtxH-like protein
        7.4    6.3   9.3        2.6    7.8   3.2    2.0  2  PRKCSH-like     Glucosidase II beta subunit-like


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 !   29.6  18.1     5e-10     7e-07       1     101 [.       1     101 [.       1     102 [. 0.96

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5e-10
                                   XXXXHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  V-ATPase_G_2   1 dessrllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaq 81 
                                   +++ ++l+e++e E+  ++ +E+  k+ +++  aA+ eA+ i+++Ae++a + +++  +  +e ++++ e++ + + +ea+
  gi|91773217|ref|YP_565909.1|   1 MAKDKILSEIKEAEQSAAKMVEEGLKNKNERNLAARNEAREIIKQAENDAAKSAQNALKSAEETIKQESEDIISNGVNEAK 81 
                                   67889***********************99999*****************9999999999********************* PP

                                   HHHHHHHCSHHHHHHHHHHH CS
                  V-ATPase_G_2  82 avrkraearlqqAvelilka 101
                                   +++ +aea +++Ave+ + +
  gi|91773217|ref|YP_565909.1|  82 RISVKAEANVDKAVENLITE 101
                                   ***************98765 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 !   25.0  17.9   1.2e-08   1.6e-05      33      96 ..       4      68 ..       3      71 .. 0.91
   2 !    9.1   1.8   0.00098       1.4      64     100 ..      66     102 ..      63     108 .] 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.2e-08
                    ATP-synt_B 33 ekIadeiaeAeerrkea.aallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerl 96
                                  +kI +ei+eAe++++++ ++ l+++ ++   Ar eA+eiik+A+++a+k+++++ ++ae+ +++ 
  gi|91773217|ref|YP_565909.1|  4 DKILSEIKEAEQSAAKMvEEGLKNKNERNLAARNEAREIIKQAENDAAKSAQNALKSAEETIKQE 68
                                  79**********9988648899**************************************99875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00098
                    ATP-synt_B  64 raeAaeiiknAkkeaeklkeeieaeaeaeaerlkesA 100
                                   ++e+++ii n+ +ea+++  ++ea++ +++e l+ + 
  gi|91773217|ref|YP_565909.1|  66 KQESEDIISNGVNEAKRISVKAEANVDKAVENLITEF 102
                                   7899999999999999999999999999999988765 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 ?   13.9  17.2   4.3e-05      0.06      11      99 ..      12     100 ..       3     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHHHHHH CS
                    V-ATPase_G  11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelkesvkknke 91 
                                   +AE++Aa++v+e  k+k++r   A++eA++ i++  +   k  ++  +++  + ++ +++i ++  ++ k+++ ++++n +
  gi|91773217|ref|YP_565909.1|  12 EAEQSAAKMVEEGLKNKNERNLAARNEAREIIKQAENDAAKSAQNALKSAEETIKQESEDIISNGVNEAKRISVKAEANVD 92 
                                   8*********************************99999999999999999999999999999999999************ PP

                                   HHHHHHHH CS
                    V-ATPase_G  92 avvkellk 99 
                                   + v++l++
  gi|91773217|ref|YP_565909.1|  93 KAVENLIT 100
                                   ****9996 PP

>> Ribosomal_S20p  Ribosomal protein S20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  13.0   0.00062      0.85       4      60 ..      15      69 ..       8     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                                  CCCHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHHHHHHHHH CS
                Ribosomal_S20p  4 kSakKrirqn.ekrrlrNrsyksavrtaiKkvraaieadkekaqealkkaiskidkaa 60
                                  +Sa K ++   +++++rN + ++++r +iK++++ +   +++aq+alk+a  +i +  
  gi|91773217|ref|YP_565909.1| 15 QSAAKMVEEGlKNKNERNLAARNEAREIIKQAENDA---AKSAQNALKSAEETIKQES 69
                                  6888888876256799********************...6788888888888776644 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.3    0.0097        13      58     103 ..      17      64 ..       3      67 .. 0.67
   2 ?   10.2   0.6   0.00042      0.58      62      99 ..      64     101 ..      59     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0097
                      HOIP-UBA  58 aaseqkekke.....nevgklsraEakealleagGdvekAvkqclreRrkK 103
                                   aa+  +   e     ne     r+Ea+e  ++a+ d+ k+++++l+  ++ 
  gi|91773217|ref|YP_565909.1|  17 AAKMVE---EglknkNERNLAARNEAREIIKQAENDAAKSAQNALKSAEET 64 
                                   222222...1233337777889**********************9976665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00042
                      HOIP-UBA  62 qkekkenevgklsraEakealleagGdvekAvkqclre 99 
                                     +++ +++ +   +Eak+  ++a+ +v+kAv+++++e
  gi|91773217|ref|YP_565909.1|  64 TIKQESEDIISNGVNEAKRISVKAEANVDKAVENLITE 101
                                   44556688888999********************9986 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  10.4   0.00034      0.47      59     159 ..       3     103 ..       1     107 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                         PIN_8  59 yedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeelkaeleelkksskadkeedpilkkleelle 139
                                   ++++ +e+++++++a+k +ee lk++++++  +++e+r+ +k++ +++ ++ ++ l+++++++k++ +ed i++ ++e  +
  gi|91773217|ref|YP_565909.1|   3 KDKILSEIKEAEQSAAKMVEEGLKNKNERNLAARNEAREIIKQAENDAAKSAQNALKSAEETIKQE-SEDIISNGVNEAKR 82 
                                   678889999999999999999******9999999***************99988888888888877.68**********99 PP

                         PIN_8 140 gkigealskeel.eelvkege 159
                                     + ++ + ++  e+l+ e e
  gi|91773217|ref|YP_565909.1|  83 ISVKAEANVDKAvENLITEFE 103
                                   999888888887677777655 PP

>> dsrm  Double-stranded RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0071       9.8      52      62 ..      10      20 ..       7      23 .. 0.88
   2 ?    5.9   1.6     0.016        22      52      64 ..      43      55 ..      31      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0071
                                  HHHHHHHHHHH CS
                          dsrm 52 KKeAeqsAAed 62
                                   KeAeqsAA+ 
  gi|91773217|ref|YP_565909.1| 10 IKEAEQSAAKM 20
                                  6********96 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                                  HHHHHHHHHHHHH CS
                          dsrm 52 KKeAeqsAAedal 64
                                   K+Ae++AA+ a 
  gi|91773217|ref|YP_565909.1| 43 IKQAENDAAKSAQ 55
                                  59********995 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   9.3    0.0019       2.6       3      71 ..       6      67 ..       3     108 .] 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                        DUF883  3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVre 71
                                  + +e++++ ++++++++e  ++ +e   ++R++++e +++a + +++ ++++ ++a+e        +++
  gi|91773217|ref|YP_565909.1|  6 ILSEIKEAEQSAAKMVEEGLKNKNERNLAARNEAREIIKQAENDAAKSAQNALKSAEE-------TIKQ 67
                                  4455555555555555555555555555555555555555555555555555555555.......4444 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.3    0.0012       1.6     211     308 ..       5      99 ..       1     107 [. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                         LMBR1 211 klntekeeaereledllkevkklrksisesdp.lrkyleeilkkvPeeiaeklksnenkteeslaklekqlika.lqkrer 289
                                   k+ +e +eae+   ++++e  k   +++e +   r+   ei+k+  +++a+ +++  +++ee+++++ +++i++ +++ +r
  gi|91773217|ref|YP_565909.1|   5 KILSEIKEAEQSAAKMVEEGLK---NKNERNLaARNEAREIIKQAENDAAKSAQNALKSAEETIKQESEDIISNgVNEAKR 82 
                                   4555666666666633333333...333333336888999***************9999*****999988887669***** PP

                         LMBR1 290 tekqwkrllekaleledii 308
                                   ++ + + +++ka  +e++i
  gi|91773217|ref|YP_565909.1|  83 ISVKAEANVDKA--VENLI 99 
                                   ************..55554 PP

>> DUF2462  Protein of unknown function (DUF2462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.9   0.00033      0.46      41      75 ..      14      46 ..       7      48 .. 0.86
   2 ?    1.3   2.2      0.44     6e+02      20      60 ..      54      99 ..      43     106 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                       DUF2462 41 qqklkkklsaglnkktEkelasrAgsskLellkgg 75
                                  +q+  k+++ gl++k+E++la+r +    e++k+ 
  gi|91773217|ref|YP_565909.1| 14 EQSAAKMVEEGLKNKNERNLAARNE--AREIIKQA 46
                                  58999******************99..88888875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.44
                       DUF2462 20 kaknpkkgarviaPKkaklvkq.....qklkkklsaglnkktEkel 60
                                  +++  k ++ +i+  ++ ++ +     + +  k +a++ k +E+++
  gi|91773217|ref|YP_565909.1| 54 AQNALKSAEETIKQESEDIISNgvneaKRISVKAEANVDKAVENLI 99
                                  3333455555555555544433333336666666666666666665 PP

>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5      0.17   2.4e+02      86     125 ..       5      47 ..       2      48 .. 0.44
   2 ?    9.4   3.0   0.00086       1.2      74     130 ..      45     101 ..      35     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHH....CHHHHHTTSSHHHHHHHHHHHHHHHHHH CS
                        Pro_CA  86 kwlekirealek....veeelesekekearerlleeenVaeqle 125
                                   k+l++i+ea ++    vee   ++k++ +++++ e +++ +q e
  gi|91773217|ref|YP_565909.1|   5 KILSEIKEAEQSaakmVEEG-LKNKNERNLAARNEAREIIKQAE 47 
                                   45555555555522123322.22234444444446666666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00086
                                   HHCCSTTSSHHHHHHHHHHHHHHHCHHHHHTTS.SHHHHHHHHHHHHHHHHHHHHHCS CS
                        Pro_CA  74 aekseeeagaidkwlekirealekveeelesek.ekearerlleeenVaeqlenLlek 130
                                   +  ++++a+  ++ l++++e++++ +e++ s+  ++++r  + +e+nV++ +enL+++
  gi|91773217|ref|YP_565909.1|  45 Q-AENDAAKSAQNALKSAEETIKQESEDIISNGvNEAKRISVKAEANVDKAVENLITE 101
                                   3.446668888999999999888866554444357788888889***********985 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.7      0.56   7.7e+02      49      70 ..       3      24 ..       1      31 [. 0.55
   2 ?   11.8   5.0    0.0002      0.27      24      73 ..      37      86 ..      34      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.56
                          YtxH 49 kekakekaedlkekvkekadel 70
                                  k+k  ++++++ +++++ ++e 
  gi|91773217|ref|YP_565909.1|  3 KDKILSEIKEAEQSAAKMVEEG 24
                                  4555555555555555555554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                          YtxH 24 ketRkdlkekaddlkekakelleeakekakekaedlkekvkekadelkek 73
                                  +e R+ +k++ +d++++a+++l++a+e+ k+++ed+ ++  ++a++++ k
  gi|91773217|ref|YP_565909.1| 37 NEAREIIKQAENDAAKSAQNALKSAEETIKQESEDIISNGVNEAKRISVK 86
                                  799**************************999999988888777777655 PP

>> PRKCSH-like  Glucosidase II beta subunit-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.2    0.0019       2.6     123     165 ..       7      49 ..       2      60 .. 0.83
   2 ?    2.7   0.8     0.072        99     125     160 ..      61      96 ..      50     108 .] 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0019
                   PRKCSH-like 123 arkfeelleeankkvkkglkikeelllaakkkldelkkklkel 165
                                     +++e ++ a k v++glk k+e  laa++  +e++k+ ++ 
  gi|91773217|ref|YP_565909.1|   7 LSEIKEAEQSAAKMVEEGLKNKNERNLAARNEAREIIKQAEND 49 
                                   5677888899999***********************9997654 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.072
                   PRKCSH-like 125 kfeelleeankkvkkglkikeelllaakkkldelkk 160
                                     e++++e ++ +++g++  + + ++a+  +d+  +
  gi|91773217|ref|YP_565909.1|  61 AEETIKQESEDIISNGVNEAKRISVKAEANVDKAVE 96 
                                   345667888999999999999999999888776433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2696  (0.150371); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 726.22
//
Query:       gi|91773218|ref|YP_565910.1|  [L=646]
Description: V-type ATP synthase subunit I [Methanococcoides burtonii DSM 6242]
Scores for complete 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-28   96.9   5.6    1.7e-16   59.4   0.1    3.0  3  V_ATPase_I   V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
       0.16   12.4   0.6       0.32   11.4   0.6    1.4  1  V-SNARE      Vesicle transport v-SNARE protein N-terminus
        2.7    8.4  10.1        1.6    9.1   3.0    3.5  3  DUF2929      Protein of unknown function (DUF2929)
        5.4    7.0   7.7         11    6.0   1.3    2.4  2  Prefoldin_2  Prefoldin subunit


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.1   3.9e-20   1.7e-16     301     413 ..     264     375 ..     150     413 .. 0.85
   2 ?   -1.5   0.1       0.1   4.5e+02     518     543 ..     464     489 ..     458     499 .. 0.80
   3 !   38.7   0.0   6.8e-14   3.1e-10     717     812 ..     548     638 ..     545     639 .. 0.72

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 3.9e-20
                    V_ATPase_I 301 nldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNp 381
                                   ++ ++++++i +gW+p ++   ++k++++at+ +   +++ +++ +t +  P      k+ + fQei+d Y+ ++Y+E+ p
  gi|91773218|ref|YP_565910.1| 264 KIATSEHTFIIDGWIPDDQFPILEKTIESATSGRAFVSKQEIENADT-DIIPIKYDNPKVSQPFQEIMDLYARPKYKEIDP 343
                                   5677899***********************97776555666666565.6789***************************** PP

                    V_ATPase_I 382 alftiitFPFlFavMFGDiGHGlllllfalll 413
                                   + +  i+FP  +++  GDiG +++ll++a+ +
  gi|91773218|ref|YP_565910.1| 344 TSLIFISFPLFYGMILGDIGYAAILLALAFGI 375
                                   *************************9998754 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.1
                    V_ATPase_I 518 ilGviqMlfgvllslvNalyfkkkld 543
                                   ++G+++  fg++l ++N   ++   +
  gi|91773218|ref|YP_565910.1| 464 LIGLLHINFGYVLGFINENRKHGFAT 489
                                   79999999999999999877665555 PP

  == domain 3  score: 38.7 bits;  conditional E-value: 6.8e-14
                    V_ATPase_I 717 iSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhWVEfq 797
                                   +Sn  SY RL A+ L+   +++ +    +++         g il vi+ ++ +++  a   ++  +   LHaLRL+ VEf 
  gi|91773218|ref|YP_565910.1| 548 LSNALSYTRLIAVGLSSIYIASTVNLIAFDM-----ILPQGGILAVIGAIIVFIFGHALNTVLSIIAPGLHALRLQYVEFF 623
                                   79999******99876665555444444444.....334444555555555555555666666778899************ PP

                    V_ATPase_I 798 sKFykgdGykFepfs 812
                                    KFy+g G k++pf 
  gi|91773218|ref|YP_565910.1| 624 GKFYEGGGRKYNPFG 638
                                   **************6 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 ?   11.4   0.6   7.1e-05      0.32      35      66 ..      87     117 ..      85     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-05
                       V-SNARE  35 deaeelldqMelEvrnlpsserasykaklrey 66 
                                   +e++++ldq+++Ev  + +  r+++ ++l+e 
  gi|91773218|ref|YP_565910.1|  87 NELDSMLDQLDIEVT-VKTEKRSELDSRLKEL 117
                                   69************9.8889********9975 PP

>> DUF2929  Protein of unknown function (DUF2929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.097   4.4e+02       4      24 ..     396     416 ..     394     420 .. 0.87
   2 ?   -1.7   0.2      0.83   3.7e+03      31      51 ..     455     475 ..     450     477 .. 0.74
   3 ?    9.1   3.0   0.00036       1.6      19      52 ..     566     601 ..     564     603 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.097
                       DUF2929   4 ivtifWsfiLgevvgYIgsaL 24 
                                   i t++ ++++ge +g+ +++L
  gi|91773218|ref|YP_565910.1| 396 ISTLIFGVLYGEFLGFSLASL 416
                                   789999*********988887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.83
                       DUF2929  31 fttalilavvfgvlviliial 51 
                                   ++t++  ++++g+l i+++++
  gi|91773218|ref|YP_565910.1| 455 VMTMIAATALIGLLHINFGYV 475
                                   577777888888888888766 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00036
                       DUF2929  19 YIgsaLtgvtydft..talilavvfgvlviliiali 52 
                                   YI+s+++   +d+   + +ilav+ +++v+++++++
  gi|91773218|ref|YP_565910.1| 566 YIASTVNLIAFDMIlpQGGILAVIGAIIVFIFGHAL 601
                                   9***********653389*************99875 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.3    0.0025        11       8      48 ..      87     127 ..      79     130 .. 0.77
   2 ?    4.1   0.6    0.0094        42      10      44 ..     223     257 ..     215     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EE CS
                   Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvleelelldedtkvy 48 
                                   ++l + l+ql+ +++ + ++ +el++ l+ele l++d + +
  gi|91773218|ref|YP_565910.1|  87 NELDSMLDQLDIEVTVKTEKRSELDSRLKELEALKKDLTPF 127
                                   67777888888899999999999999999999998886655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0094
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT CS
                   Prefoldin_2  10 lqqqlqqlaqqikqletqlkelelvleelellded 44 
                                   ++qq+  l+++i +++++  e  l++eel +++ +
  gi|91773218|ref|YP_565910.1| 223 IKQQMVLLETDIISIKEKYFEFILASEELLTIEAE 257
                                   79***************************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 4319.91
//
Query:       gi|91773219|ref|YP_565911.1|  [L=79]
Description: H+-transporting two-sector ATPase, C subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-17   64.2  11.0      1e-17   64.2  11.0    1.3  2  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.86   1.5e+04      26      29 ..       6       9 ..       3      13 .. 0.46
   2 !   64.2  11.0   5.6e-22     1e-17       1      60 []      19      78 ..      19      78 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.86
                                  HHHH CS
                    ATP-synt_C 26 irav 29
                                  + a+
  gi|91773219|ref|YP_565911.1|  6 AAAT 9 
                                  2333 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 5.6e-22
                                  HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                  +gaglavGl++l+sGi+   +g+a+i+a+a+n +lf+k li+ +++e+i ++gL+val++
  gi|91773219|ref|YP_565911.1| 19 IGAGLAVGLTGLASGIAEKDIGAAAIGAMAENESLFGKGLILTVIPETIVIFGLVVALLI 78
                                  7*********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 557.62
//
Query:       gi|91773220|ref|YP_565912.1|  [L=183]
Description: V-type ATP synthase subunit E [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-21   76.0  12.9      1e-19   70.7  12.9    2.0  1  vATP-synt_E  ATP synthase (E/31 kDa) subunit
     0.0068   16.5   6.9      0.012   15.6   6.9    1.5  1  ATP-synt_B   ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
      0.012   15.7   4.4      0.012   15.7   4.4    1.8  2  DivIVA       DivIVA protein
      0.039   12.9   0.3      0.055   12.4   0.3    1.2  1  UPF0261      Uncharacterised protein family (UPF0261)
        0.1   12.0   7.8       0.17   11.3   7.8    1.4  1  DUF3552      Domain of unknown function (DUF3552)
       0.11   12.6   0.1          1    9.5   0.0    2.2  2  DUF2856      Protein of unknown function (DUF2856)
       0.32   10.8   8.1       0.63    9.8   8.1    1.6  1  Phage_GP20   Phage minor structural protein GP20


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 !   70.7  12.9     4e-23     1e-19       1     199 []       9     182 ..       9     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 4e-23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   vATP-synt_E   1 fIrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeea 81 
                                   +I++ A+ +++ I+a+a++e+ ++++ + +++++ +  +++k+e  +++ ++++iS+a ++ ++++L+ar+evl++v ++a
  gi|91773220|ref|YP_565912.1|   9 DIMSAAQTEVNVINADADAEVSQILDDARQTAKKIMGDRLAKAEDDIKRLRQQEISSANLEVKRAMLNARKEVLDKVYNNA 89 
                                   5999***************************************************************************** PP

                                   HHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTTSSS CS
                   vATP-synt_E  82 ekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedfledvlG 162
                                      +  ++  k       ++L+++ + ++ ++   ++++k+ ++lv+++    +            ++++ +    +d++G
  gi|91773220|ref|YP_565912.1|  90 IDSIVSLPGSK--Q----EELLKAIIDENDSNGSNIYSNKDSEKLVRKL---SS------------LEYAGN----IDCIG 145
                                   *********99..4....5555555557899*****************5...22............233445....7**** PP

                                   EEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                   vATP-synt_E 163 GvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                   G  +e++dg ++++ T + +L+ v eq l++ +  LF
  gi|91773220|ref|YP_565912.1| 146 GLTIENSDGTVRLDYTYDMILKNVNEQSLKQTSDILF 182
                                   *******************************999998 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 !   15.6   6.9   4.9e-06     0.012      51     122 ..      13      84 ..       5      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                    ATP-synt_B  51 allaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvval 122
                                   a++ e     ++A ae ++i ++A++ a+k+  ++ a+ae +++rl+++     + e +ra+ + r++v + 
  gi|91773220|ref|YP_565912.1|  13 AAQTEVNVINADADAEVSQILDDARQTAKKIMGDRLAKAEDDIKRLRQQEISSANLEVKRAMLNARKEVLDK 84 
                                   55555566668999999********************************99999999999999999999775 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   4.4   4.7e-06     0.012      62     123 ..       4      62 ..       2      68 .. 0.89
   2 ?   -3.0   0.0       2.8   7.2e+03      90     102 ..     108     120 ..      99     135 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.7e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  62 eetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrqa 123
                                   e+ +k+ + +aq   + + a a +e ++i+++A+++a+ki+    ++++k++++i++l++q+
  gi|91773220|ref|YP_565912.1|   4 ETVIKDIMSAAQTEVNVINADADAEVSQILDDARQTAKKIM---GDRLAKAEDDIKRLRQQE 62 
                                   7788999999999***************************8...779999999999999986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                                   XXXXXXXXXXXXX CS
                        DivIVA  90 iikeAekkaekiv 102
                                   ii+e + + ++i 
  gi|91773220|ref|YP_565912.1| 108 IIDENDSNGSNIY 120
                                   4444444444443 PP

>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.1e-05     0.055      25     110 ..      13     108 ..       5     113 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                       UPF0261  25 eegvevlliDvgtree........ekeaidisreevleaagkeae..eelesldrgeaieamseaaaklvkelyeekidgv 95 
                                   ++++ev +i++    e        +++a +i  +++++a+ + ++  ++  s+   e+ +am +a ++++ ++y+++id++
  gi|91773220|ref|YP_565912.1|  13 AAQTEVNVINADADAEvsqilddaRQTAKKIMGDRLAKAEDDIKRlrQQEISSANLEVKRAMLNARKEVLDKVYNNAIDSI 93 
                                   5555555555444333333333323334445566666655553334333445667789999******************** PP

                       UPF0261  96 islGGsggtslataa 110
                                   +sl Gs+  +l+ a+
  gi|91773220|ref|YP_565912.1|  94 VSLPGSKQEELLKAI 108
                                   ******999888776 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.8   6.5e-05      0.17      24      97 ..      15      85 ..       3     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.5e-05
                       DUF3552 24 iaekkiaeAeeeA..kkiieeAkkeAeakkkealleakeeihklreelekelkerrnelqrlekRllqkeetLdrk 97
                                  ++e ++ +A ++A  ++i+++A+++A+++    l +a ++i++lr++   e+ + + e++r    l+ ++e Ld+ 
  gi|91773220|ref|YP_565912.1| 15 QTEVNVINADADAevSQILDDARQTAKKIMGDRLAKAEDDIKRLRQQ---EISSANLEVKRA--MLNARKEVLDKV 85
                                  55555656555552279****************************85...888877777774..688888888875 PP

>> DUF2856  Protein of unknown function (DUF2856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.22   5.5e+02      18      36 ..      28      46 ..      21      74 .. 0.72
   2 ?    9.5   0.0   0.00041         1      12      43 ..      71     103 ..      61     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                       DUF2856 18 svsevldkfrknydlimsl 36
                                   vs++ld  r+    im  
  gi|91773220|ref|YP_565912.1| 28 EVSQILDDARQTAKKIMGD 46
                                  6899999999999998863 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00041
                       DUF2856  12 rrcsgnsvsevldkfrkn.ydlimslpqetkee 43 
                                   +r+  n+  evldk+ +n  d i+slp   +ee
  gi|91773220|ref|YP_565912.1|  71 KRAMLNARKEVLDKVYNNaIDSIVSLPGSKQEE 103
                                   78888999******877637*******987776 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.1   0.00025      0.63       3     107 ..       7     112 ..       5     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                    Phage_GP20   3 ikkvm..kaengkditkakldeveeerdtlkeqlkdrdkqL..edLkkkakdneeL.qkqieelqaknkkakaeyeakiad 78 
                                   ik++m  ++ + ++i+ +    +++e+ ++ ++  +  k++  + L k+  d + L q++i + + ++k+a  ++ +++ d
  gi|91773220|ref|YP_565912.1|   7 IKDIMsaAQTEVNVINAD----ADAEVSQILDDARQTAKKImgDRLAKAEDDIKRLrQQEISSANLEVKRAMLNARKEVLD 83 
                                   777883333333444433....33444444444444444443356888888888884567********************* PP

                    Phage_GP20  79 lkldnaielaLkeakaknekavkalldkd 107
                                      +nai++  +  + k+e+++ka++d +
  gi|91773220|ref|YP_565912.1|  84 KVYNNAIDSIVSLPGSKQEELLKAIIDEN 112
                                   ***************************54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1113.05
//
Query:       gi|91773221|ref|YP_565913.1|  [L=357]
Description: V-type ATP synthase subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete 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   5.8    2.4e-75  254.2   5.8    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
      0.071   12.8   0.0       0.15   11.7   0.0    1.5  1  OxoGdeHyase_C   2-oxoglutarate dehydrogenase C-terminal
       0.12   12.3   0.3       0.42   10.6   0.3    1.9  1  LisH            LisH


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 !  254.2   5.8     4e-79   2.4e-75       2     335 ..      26     353 ..      25     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 254.2 bits;  conditional E-value: 4e-79
                                   HHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.HHHH CS
                vATP-synt_AC39   2 eArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgpsref 82 
                                   +Arvram+s+lL++e y +L  ++ ++++ r+++e+ Y++++ + + ++ +++ +e+al+++la +f kl ++++g+++ +
  gi|91773221|ref|YP_565913.1|  26 TARVRAMKSNLLPREVYPRL-MNMGIDEITRFIEESQYKQDVDELARTYDGVDLFEHALNRNLAVTFTKLINISEGELNYL 105
                                   7*******************.556*****************6666699*****************************88** PP

                                   HHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHHHCC...-- CS
                vATP-synt_AC39  83 ldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakyleealdeleetg 163
                                   ++ +l++ydi+ +k++lrgk+  +++ ee+ + ++ +g+ls   l  l+e++s+e++++al+gt y++ l+e    ++   
  gi|91773221|ref|YP_565913.1| 106 ISEYLRKYDIWSIKTILRGKYC-GASVEEINDSIVSAGQLSYPFLLSLSEKESYESIIDALSGTDYYPTLKE----YDG-T 180
                                   **********************.5777******************************************998....555.5 PP

                                   SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-.S--HHHHHHH CS
                vATP-synt_AC39 164 dleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkllipgg.slypegleal 243
                                   +l++ien+Ldk+y++ l   +++ ++++++++++++++eiD++n+++++r+k++g   k+++++l+++gg +l+ +++e+l
  gi|91773221|ref|YP_565913.1| 181 NLSDIENKLDKMYYTGLSTTVNNPKSNDSKLFSKFIRTEIDIKNLSTLFRLKNAG-VEKDEIADLILEGGlHLSIKEIEKL 260
                                   67******************999999999************************77.67888******************** PP

                                   HTT-G.....GG.GGSSTSSTTGGGTT-.-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHHHHHHHHHHHHHHHHHHH CS
                vATP-synt_AC39 244 aeaedveellaalkyteygelleealee.agslksledaldealvkllkk.afrqqfsvgvfyaYlklkeqEirnlrwIae 322
                                   +    ++e+++ l++++y+e ++ ++++  +sl +le++l +  +k +++ ++ +++s+ +++ Y++ k +E+ nlr+I++
  gi|91773221|ref|YP_565913.1| 261 LPL-PFSEFVQSLEKYPYWEDISGIVKTeMDSLIELETQLTRSNIKSASSfSHVYPLSIVPIMDYILNKTNEVHNLRIILR 340
                                   ***.8********9999999999888887777************************************************* PP

                                   HHHHT--SHHHHG CS
                vATP-synt_AC39 323 giaqglpkekIre 335
                                   g+a++l++e Ir+
  gi|91773221|ref|YP_565913.1| 341 GKAANLDEEIIRN 353
                                   ***********98 PP

>> OxoGdeHyase_C  2-oxoglutarate dehydrogenase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.5e-05      0.15      58      86 ..     252     280 ..     246     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.5e-05
                 OxoGdeHyase_C  58 vaivriEqlyPfpfeelkeelekYpnake 86 
                                   + i  iE+l P+pf+e+ ++lekYp  ++
  gi|91773221|ref|YP_565913.1| 252 LSIKEIEKLLPLPFSEFVQSLEKYPYWED 280
                                   56889*******************98766 PP

>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   7.1e-05      0.42       2      13 ..     101     112 ..     101     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.1e-05
                                   HHHHHHHHHHHH CS
                          LisH   2 eLNrLIydYLvk 13 
                                   eLN+LI++YL+k
  gi|91773221|ref|YP_565913.1| 101 ELNYLISEYLRK 112
                                   8*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2636.05
//
Query:       gi|91773222|ref|YP_565914.1|  [L=99]
Description: V-type ATP synthase subunit F [Methanococcoides burtonii DSM 6242]
Scores for complete 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   63.4   0.1      2e-17   63.2   0.1    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
    0.00072   19.9   0.0      0.033   14.5   0.0    2.1  2  YcgL        YcgL domain


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 !   63.2   0.1   2.3e-21     2e-17       2      87 ..       4      89 ..       3      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.3e-21
                                  EEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEESCSCCGGSHH CS
                    ATP-synt_F  2 avIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIPskegpydee 83
                                  av+G++++vtgfrlaG++++++++ +e+e++++++l+++d+gi +i+e+ +++++e ++++ +e + P+++++ + +++ +  
  gi|91773222|ref|YP_565914.1|  4 AVVGSSEFVTGFRLAGIKKIYEAKSDELESVVTKVLKDSDVGIFVIHEDDFNKLPEILRDTLSEsVDPTVVTLGGTGESSNL- 85
                                  9******************************************************9999988888*******9666554322. PP

                                  CHHH CS
                    ATP-synt_F 84 kdsv 87
                                  ++++
  gi|91773222|ref|YP_565914.1| 86 REKI 89
                                  4455 PP

>> YcgL  YcgL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0066        59      31      60 ..       4      33 ..       3      38 .. 0.85
   2 !   14.5   0.0   3.6e-06     0.033       5      37 ..      37      69 ..      33      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0066
                          YcgL 31 esfGkpefvmeleLskerkLaradaekVla 60
                                  +  G+ efv  + L+  +k+ +a+ +++ +
  gi|91773222|ref|YP_565914.1|  4 AVVGSSEFVTGFRLAGIKKIYEAKSDELES 33
                                  56899***************9999888765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.6e-06
                          YcgL  5 ksskkeetYLYvekkddfsevPeeLlesfGkpe 37
                                  k  k +++ ++v ++ddf+++Pe L++++ +  
  gi|91773222|ref|YP_565914.1| 37 KVLKDSDVGIFVIHEDDFNKLPEILRDTLSESV 69
                                  788999999******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 666.86
//
Query:       gi|91773223|ref|YP_565915.1|  [L=578]
Description: V-type ATP synthase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-95  318.2   0.0    3.5e-95  317.7   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    2.6e-45  153.2   0.1    4.7e-45  152.4   0.1    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.9e-14   53.9   2.1    1.9e-14   53.9   2.1    2.0  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
     0.0031   17.5   1.0      0.029   14.3   0.1    2.3  2  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.026   14.0   0.1      0.049   13.1   0.1    1.3  1  NQRA             Na(+)-translocating NADH-quinone reductase s
      0.026   14.8   0.0      0.056   13.7   0.0    1.5  1  AAA_22           AAA domain
       0.15   12.3   0.2         12    6.2   0.0    2.6  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 !  317.7   0.0   1.4e-98   3.5e-95       1     213 []     208     429 ..     208     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 317.7 bits;  conditional E-value: 1.4e-98
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH....SS...GGGGEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx...xxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe....gt...imkrtvl 74 
                                   G+r+lD +fpi++G++ +ipg fg Gktv +q+l+k+s++d +++y+g+Gergne+a+vl+efpe    +t   +m+rtvl
  gi|91773223|ref|YP_565915.1| 208 GQRILDGMFPIAKGGTAAIPGPFGSGKTVTQQQLAKWSDTD-IVVYIGCGERGNEMADVLNEFPEledpKTgrpLMERTVL 287
                                   9************************************9888.***********************988822468******* PP

                                   EEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  75 vantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagka 155
                                   +antsn+pvaareas+ytgit+AEy+rd+g++v+l+ads+srwaeA+reis rl+emp+++gypayl a+l+++yERag +
  gi|91773223|ref|YP_565915.1| 288 IANTSNMPVAAREASVYTGITIAEYYRDMGYDVSLMADSSSRWAEAMREISSRLEEMPGEEGYPAYLSARLSEFYERAGAV 368
                                   ********************************************************************************* PP

                                   ...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 156 ...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                          Gs+t++ avsp+ggDfs+pvt++tl+i+++f+ Ld kl qr+hfP+in+l+S+S
  gi|91773223|ref|YP_565915.1| 369 nslAGLDGSITVIGAVSPPGGDFSEPVTQNTLRIVKVFWALDAKLSQRRHFPSINWLTSYS 429
                                   6555559*****************************************************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 !  152.4   0.1   1.8e-48   4.7e-45       1     121 []      84     199 ..      84     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.8e-48
                                   EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE--E CS
               ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiaee 81 
                                   yDGiqrpL  ++ek+g+fi+rGv+++ ldre+ wefkp+v++gd+v+gg+ilG vqet+ iehkimvpp+++g++kei+ +
  gi|91773223|ref|YP_565915.1|  84 YDGIQRPLPVLQEKMGNFIQRGVTANGLDRERVWEFKPTVSKGDEVKGGNILGLVQETKNIEHKIMVPPSISGTIKEIK-A 163
                                   9*****************************************************************************9.* PP

                                   EEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
               ATP-synt_ab_Xtn  82 geytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                   g+++v++ti+++++++    e++++qkwPvr prpv++kl
  gi|91773223|ref|YP_565915.1| 164 GSFKVDETICVLTDGT----EISMMQKWPVRGPRPVAKKL 199
                                   *************766....8*****************97 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   2.1   7.6e-18   1.9e-14       1      69 []       7      68 ..       7      68 .. 0.98
   2 ?   -3.9   0.1         7   1.8e+04      31      46 ..     459     474 ..     455     475 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 7.6e-18
                                  EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                 ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                  i++v Gpvv v  gi   p +y++++v+  +  ++l+g+++++ ++++ v+v+++t+Gl++G++V +TG
  gi|91773223|ref|YP_565915.1|  7 IYRVAGPVVTV-IGIK--PRMYDVVKVG--H--EGLMGEVIRIKGEQATVQVYEDTSGLKPGEPVMNTG 68
                                  789********.9999..**********..9..9**********************************8 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7
                                   TCSTEEEEEEEEEETT CS
                 ATP-synt_ab_N  31 efgtlllgvalnlged 46 
                                   ++++ l++ ++ +g d
  gi|91773223|ref|YP_565915.1| 459 QQESELQEIVQLVGSD 474
                                   4578899999988876 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 ?    1.1   0.1      0.15   3.9e+02      45      75 ..      27      57 ..       9      58 .. 0.84
   2 !   14.3   0.1   1.1e-05     0.029      42      84 ..     119     165 ..     114     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.15
                        RnfC_N 45 lvkvgdkVlkGqkiaeaegfvsapvhasvsG 75
                                  +vkvg + l+G++i  +++  +++v+  +sG
  gi|91773223|ref|YP_565915.1| 27 VVKVGHEGLMGEVIRIKGEQATVQVYEDTSG 57
                                  8*************99999889999999999 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.1e-05
                        RnfC_N  42 akplvkvgdkVlkGqkiaeaeg..fv..sapvhasvsGtVkaiekrl 84 
                                    kp v++gd+V+ G++++  ++   +  +  v  s+sGt+k+i+   
  gi|91773223|ref|YP_565915.1| 119 FKPTVSKGDEVKGGNILGLVQEtkNIehKIMVPPSISGTIKEIKAGS 165
                                   589*************9976542244114556679********9755 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.9e-05     0.049      42     103 ..     120     185 ..     106     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                          NQRA  42 klkvkegdkVkkGqvl...fedKknpgvlftsp.asGevveinrGekRvlqsvvievdgdeeeefe 103
                                   k +v++gd+Vk G++l    e K+ +  +++ p +sG+++ei+ G+ +v +++ + +dg+e   ++
  gi|91773223|ref|YP_565915.1| 120 KPTVSKGDEVKGGNILglvQETKNIEHKIMVPPsISGTIKEIKAGSFKVDETICVLTDGTEISMMQ 185
                                   55799********9863325778877767776647************9999999999977665555 PP

>> AAA_22  AAA 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     0.056       6      59 ..     222     268 ..     219     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllre 59 
                                   g  ++ G+ G+GKT++ ++l+++ d         + vv++ + + + + +d+l+e
  gi|91773223|ref|YP_565915.1| 222 GTAAIPGPFGSGKTVTQQQLAKWSD--------TDIVVYIGCGERGnEMADVLNE 268
                                   66799******************97........8888899998888555555555 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.044   1.1e+02      24      61 ..      27      62 ..      24      67 .. 0.83
   2 ?    6.2   0.0    0.0046        12      56      77 ..     122     143 ..     113     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.044
                                  EEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTE CS
                 Peptidase_M23 24 VvfagkkegyGnvviidhgdgystlyahlskisvkegq 61
                                  Vv++g ++ +G+v++i+ ++ ++++y   s   +k+g+
  gi|91773223|ref|YP_565915.1| 27 VVKVGHEGLMGEVIRIKGEQATVQVYEDTSG--LKPGE 62
                                  8999998677****************98877..56665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0046
                                   SS-TTEEE-TTCEEEEEBSTSS CS
                 Peptidase_M23  56 svkegqkVkaGqvIGtvgstgr 77 
                                   +v++g++Vk G+++G v +t++
  gi|91773223|ref|YP_565915.1| 122 TVSKGDEVKGGNILGLVQETKN 143
                                   59***************99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3914.50
//
Query:       gi|91773224|ref|YP_565916.1|  [L=460]
Description: V-type ATP synthase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-64  216.3   0.0    5.2e-64  215.8   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      4e-10   40.1   2.2      4e-10   40.1   2.2    1.8  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    5.1e-05   23.3   0.8    0.00019   21.5   0.5    2.2  3  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.8   0.0   8.7e-68   5.2e-64       1     213 []     130     348 ..     130     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.8 bits;  conditional E-value: 8.7e-68
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlva 76 
                                   Gi+++D   ++v+Gq++ i++++g+++++i+ ++++q++        a++++++G  ++e++ ++++f+++++++r v+++
  gi|91773224|ref|YP_565916.1| 130 GISTIDGTNTLVRGQKLPIFSGSGLPHNEIALQIARQAKVPgsdePfAVVFAAMGITNEEAQYFMDDFEKTGALERAVVFL 210
                                   899**********************************8755777537********************************** PP

                                   EETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  77 ntsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkap 156
                                   n +++p+++r+ ++++++t+AEy+++ ++++vl+i++++++++eAlr+++++ +e+p+++gyp+y++++laslyERag ++
  gi|91773224|ref|YP_565916.1| 211 NLADDPAVERIVTPRMALTAAEYLAYeHDMHVLVILTDITNYCEALRQMGAAREEVPGRRGYPGYMYTDLASLYERAGVIK 291
                                   *************************9899**************************************************** PP

                                   SSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 157 drtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                     +Gsvt++ +++++g+D+++p+++   +it+g+iv++++l++++++P+invl S+S
  gi|91773224|ref|YP_565916.1| 292 GIKGSVTQFSILTMPGDDITHPIPDLSGYITEGQIVVSRELHRKGIYPPINVLPSLS 348
                                   9******************************************************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 !   40.1   2.2   6.7e-14     4e-10       1      69 []       8      73 ..       8      73 .. 0.89
   2 ?   -3.7   0.0         3   1.8e+04      53      64 ..     134     145 ..     130     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 6.7e-14
                                  EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                 ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                  iv+v+Gp++  e+ +    g+ ++++++l++ gt  +g++l  + d+V+v+v+++t Gl + + V++ G
  gi|91773224|ref|YP_565916.1|  8 IVEVSGPLIFLEKTEP--VGYGELVQINLPD-GTTKRGQVLDTSADMVVVQVFEGTVGLNEESGVVFSG 73
                                  89**************..5555556666559.********************************99987 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|91773224|ref|YP_565916.1| 134 IDGTNTLVRGQK 145
                                   688999999985 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.5   3.2e-08   0.00019       3      83 ..       3      68 ..       1      89 [. 0.81
   2 ?   -3.8   0.0       2.4   1.5e+04       5      21 ..     129     145 ..     129     149 .. 0.81
   3 ?   -3.1   0.0       1.5   9.1e+03      27      55 ..     232     258 ..     222     264 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.2e-08
                    HAS-barrel  3 evigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt.. 82
                                  +++ +    s++++++e +++v++Ge+V+i+lpdg+   G+v+d ++                       d +v++++e+t  
  gi|91773224|ref|YP_565916.1|  3 KEYKTIVEvSGPLIFLEKTEPVGYGELVQINLPDGTTKRGQVLDTSA-----------------------DMVVVQVFEGTvg 62
                                  5666666669************************************9.......................8888888887765 PP

                    HAS-barrel 83 .....g 83
                                       g
  gi|91773224|ref|YP_565916.1| 63 lneesG 68
                                  555553 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.4
                    HAS-barrel   5 igestssslifrvegsk 21 
                                   +g st++++ + v+g+k
  gi|91773224|ref|YP_565916.1| 129 TGISTIDGTNTLVRGQK 145
                                   68899999999999987 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                    HAS-barrel  27 eyVeielpdgeivlGmvtdirrgnselsn 55 
                                   ey+ +e++   +vl + tdi ++++ l++
  gi|91773224|ref|YP_565916.1| 232 EYLAYEHD--MHVLVILTDITNYCEALRQ 258
                                   67777766..6777788999997755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2940.90
//
Query:       gi|91773225|ref|YP_565917.1|  [L=206]
Description: V-type ATP synthase subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-54  183.1   8.5    5.8e-54  182.9   8.5    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.016   15.9   0.2        1.8    9.2   0.0    2.2  2  Ead_Ea22    Ead/Ea22-like protein


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 !  182.9   8.5   6.4e-58   5.8e-54       1     196 []      12     205 ..      12     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 6.4e-58
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS CS
                    ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvv 81 
                                   eLi+lkk++kl + gh+lLk+Krd Lilef++il ++k+ r el+ ++++a+ ++  a +++g+ +i+s++ + ++     
  gi|91773225|ref|YP_565917.1|  12 ELIELKKKIKLSEGGHKLLKMKRDGLILEFFDILSKAKDVRSELDAAYEKANVKIGIAESVEGRITIKSTAFAMKD---AP 89 
                                   79********************************************************99999*********7777...47 PP

                                   -SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D  82 kvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNaL 161
                                   ++ l+++n++GV vp++e ++  k  +++ ygll+t++++deav++++el+e+++ +a++et++++L + i+kt+rRvNaL
  gi|91773225|ref|YP_565917.1|  90 QIVLESHNIMGVVVPKIESSSVrKPINKRGYGLLGTSSYIDEAVDSYEELVEKIILAAEIETTMKKLLDDIEKTKRRVNAL 170
                                   8****************8876675555677*************************************************** PP

                                   HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D 162 ekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                   e +vIP+l e++ +I+ +L+E+ere++frlk++kk
  gi|91773225|ref|YP_565917.1| 171 EFKVIPELTEAMVFIRLRLEEMERENTFRLKRIKK 205
                                   *********************************97 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0041        37      89     132 ..      33      80 ..      11      87 .. 0.75
   2 ?    9.2   0.0    0.0002       1.8      56      87 ..     132     171 ..      96     202 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0041
                      Ead_Ea22  89 e.....aenedialtvgklrveleaaekrlekenveqadaaeveitalr 132
                                         +e++di +++ + r+el+aa + +   ++  a++ e+ it  +
  gi|91773225|ref|YP_565917.1|  33 KrdgliLEFFDILSKAKDVRSELDAAYEKA-NVKIGIAESVEGRITIKS 80 
                                   1555568899999***********998877.677888888888888766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                      Ead_Ea22  56 h........daefiaaanpatvlaLLDelekkqqrikele 87 
                                   +         +  +aa+   t+  LLD++ek ++r+ +le
  gi|91773225|ref|YP_565917.1| 132 AvdsyeelvEKIILAAEIETTMKKLLDDIEKTKRRVNALE 171
                                   2223356656666666667777788888888777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1319.63
//
Query:       gi|91773226|ref|YP_565918.1|  [L=706]
Description: flagella protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-27   95.7   0.2    2.9e-27   94.3   0.2    1.8  1  Arch_fla_DE      Archaeal flagella protein
    9.7e-06   25.7  17.9    0.00019   21.4   6.9    2.8  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    1.8e-05   24.2   2.6    1.8e-05   24.2   2.6    2.6  2  GAS              Growth-arrest specific micro-tubule binding
    0.00012   21.5  14.4    0.00027   20.4   7.6    2.4  2  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
    0.00027   18.9  12.3     0.0004   18.4  12.3    1.2  1  Myosin_tail_1    Myosin tail
    0.00036   20.6  11.4      0.006   16.6   2.3    3.1  3  DUF1664          Protein of unknown function (DUF1664)
    0.00039   20.6   8.8    0.00039   20.6   8.8    2.6  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0021   17.9  13.1       0.02   14.7   2.2    2.7  2  DUF724           Protein of unknown function (DUF724)
      0.005   17.1   8.2      0.005   17.1   8.2    2.5  2  ATG16            Autophagy protein 16 (ATG16)
     0.0067   16.7  14.9        0.3   11.4   3.4    4.2  5  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0077   16.0   1.2     0.0077   16.0   1.2    3.4  3  Nsp1_C           Nsp1-like C-terminal region
  ------ inclusion threshold ------
      0.011   16.1   1.2      0.011   16.1   1.2    4.6  3  FlaC_arch        Flagella accessory protein C (FlaC)
      0.015   14.4  10.8      0.031   13.4  10.8    1.5  1  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.018   14.3   9.8      0.021   14.1   1.8    2.8  2  DUF3450          Protein of unknown function (DUF3450)
      0.022   14.9   2.5      0.022   14.9   2.5    2.4  2  Uds1             Up-regulated During Septation
      0.027   14.3  11.5      0.025   14.4   9.0    2.2  2  TACC_C           Transforming acidic coiled-coil-containing p
       0.03   14.2   3.0       0.13   12.2   0.3    2.3  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
      0.045   14.0   8.0       0.13   12.6   2.0    2.9  2  DUF4164          Domain of unknown function (DUF4164)
      0.055   13.1   8.1       0.17   11.4   8.1    1.9  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
      0.059   13.4  14.6       0.32   11.1   0.7    3.5  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.079   13.5  15.0       0.82   10.3   2.4    3.8  3  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.093   13.1   4.9        2.1    8.8   0.1    3.4  3  CLZ              C-terminal leucine zipper domain of cyclic n
       0.15   12.0  14.4       0.31   11.0   0.5    4.2  3  Prefoldin        Prefoldin subunit
       0.27   11.2  16.0       0.72    9.9   4.9    3.5  3  Laminin_II       Laminin Domain II
        0.3   11.5  13.4       0.04   14.3   2.1    3.8  2  Snapin_Pallidin  Snapin/Pallidin
       0.35   10.9   1.3          3    7.9   0.1    2.6  2  DUF1515          Protein of unknown function (DUF1515)
       0.37   10.0  11.3        1.1    8.4   2.3    2.5  2  TMPIT            TMPIT-like protein
       0.43   10.2   2.7       0.89    9.2   2.7    1.5  1  DUF484           Protein of unknown function, DUF484
       0.52   10.5   6.0        1.1    9.5   6.0    1.5  1  Cornifin         Cornifin (SPRR) family
       0.59   10.2   3.3        1.2    9.3   2.4    2.0  1  Nup54            Nucleoporin complex subunit 54
       0.63   10.2   7.6        1.6    8.9   0.3    3.3  3  TolA_bind_tri    TolA binding protein trimerisation
       0.73   10.3   6.2        0.6   10.6   0.3    3.3  3  DUF4208          Domain of unknown function (DUF4208)
       0.82    9.5  11.1       0.12   12.1   1.0    3.7  4  DivIC            Septum formation initiator
       0.85    9.3   9.8       0.91    9.2   1.4    2.8  3  DUF745           Protein of unknown function (DUF745)
       0.94    9.2   9.3        4.5    7.0   0.9    2.6  2  Lectin_N         Hepatic lectin, N-terminal domain
        1.2    9.1  16.4       0.56   10.2   9.7    2.8  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        1.3    9.7   8.9        5.4    7.8   1.2    3.5  3  Occludin_ELL     Occludin homology domain
        1.5    7.7  22.4      0.014   14.3   8.8    2.7  2  Spc7             Spc7 kinetochore protein
        1.8    9.5  13.0       0.56   11.1   2.2    3.5  3  PRKG1_interact   cGMP-dependent protein kinase interacting do
        2.8    8.4  12.5       0.33   11.4   3.7    3.1  3  CENP-H           Centromere protein H (CENP-H)
        3.1    6.8  19.5       0.31   10.1   5.3    3.4  3  APG17            Autophagy protein Apg17
        3.1    6.6  14.5        4.1    6.2  13.3    1.7  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC
        3.2    8.3  19.2        0.9   10.1   5.8    2.9  3  APG6_N           Apg6 coiled-coil region
        3.4    5.5  13.0       0.64    7.9   8.2    1.5  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        3.9    7.9  17.6       0.38   11.1   2.4    3.4  3  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        4.1    7.8  14.1        4.7    7.6   3.8    2.4  2  Fez1             Fez1
        4.1    7.5   6.9        1.2    9.3   1.2    2.7  2  CHDCT2           CHDCT2 (NUC038) domain
        4.4    7.3  16.0       0.14   12.1   2.7    4.1  4  Prefoldin_2      Prefoldin subunit
        4.6    7.5  16.7        5.5    7.3   2.5    3.9  3  Cortex-I_coil    Cortexillin I, coiled coil
          5    7.3  20.0       0.55   10.4   7.9    3.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
          6    6.7   8.1       0.71    9.7   1.0    2.9  3  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
          6    7.0  11.3        1.3    9.2   1.6    3.2  3  CREPT            Cell-cycle alteration and expression-elevate
        8.9    6.4   9.2         53    3.9   3.8    4.1  3  DASH_Dad4        DASH complex subunit Dad4
        9.3    6.5  15.9       0.92    9.7   4.6    2.5  3  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        9.5    6.2  12.5        4.8    7.2   7.7    2.2  2  Rootletin        Ciliary rootlet component, centrosome cohesi
        9.9    6.3  12.0    1.1e+02    3.0  12.0    2.5  1  RasGAP_C         RasGAP C-terminus


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.2   9.2e-30   2.9e-27       2      95 .]     590     679 ..     589     679 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 9.2e-30
                   Arch_fla_DE   2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelkkseltved 82 
                                   e+++L+++ ++++++ +++eWlefL+e vg+++++++l++Yee+gWi+e+vr eL++y++gi++ + ek+++k   l ++d
  gi|91773226|ref|YP_565918.1| 590 ENVHLNNIIKNSTNMKLCMEWLEFLMELVGCNHLSDILSFYEELGWINEDVRVELIRYAEGIDY-YIEKSDWK---LPPDD 666
                                   6899***********************************************************9.999999*8...***** PP

                   Arch_fla_DE  83 HvkSllyieklag 95 
                                   HvkS+++ie+lag
  gi|91773226|ref|YP_565918.1| 667 HVKSIWFIEQLAG 679
                                   ***********96 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 !   21.4   6.9   6.1e-07   0.00019       7     111 ..     378     486 ..     374     505 .. 0.88
   2 !    9.0   3.3    0.0041       1.3      84     140 .]     515     571 ..     499     571 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.1e-07
                CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelemseenqekvileaEtsk....aevetlkeeieelaeelreleldLvalrseke 83 
                                   +++++L  s+r+++sL   +  L  ++ ++e++++ ++ + E+      a +e+  ++i +++++ +ele  L+++ s++ 
  gi|91773226|ref|YP_565918.1| 378 EIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNssinARIEESTNHIAKIEKRISELEDTLENIHSDNS 458
                                   67899*************************************9872222556779999*********************** PP

                CENP-F_leu_zip  84 eLekelqkkqervseLeslnsslenlle 111
                                   eL+  l    e + eL s+n  + + ++
  gi|91773226|ref|YP_565918.1| 459 ELQTGLASIEENIAELTSSNAMIFSHIQ 486
                                   *******************988777666 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0041
                CENP-F_leu_zip  84 eLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtqlkelne 140
                                    L++   ++q+ ++eL s+ s++ + le++ + +++ k e++++ e+++++l  l+e
  gi|91773226|ref|YP_565918.1| 515 LLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELFKNELISLTE 571
                                   577778899*****************************************9988876 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 !   24.2   2.6   5.7e-08   1.8e-05      26     144 ..     374     493 ..     371     502 .. 0.94
   2 ?    1.7   2.2      0.45   1.4e+02      28      80 ..     506     558 ..     498     568 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.7e-08
                           GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlk.nyekdkqslknlkarlkelekelkdlk 105
                                   e  ++ K+e+++ k+ +e+   ++  ++ +  +l++ L+  +++ e+ +  ++ + e+  + ++++++r++ele+ l++++
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINaRIEESTNHIAKIEKRISELEDTLENIH 454
                                   667899********************************************8862568889999****************** PP

                           GAS 106 wehevleqrfekvekerdelykkfeaaiqevqqktglkn 144
                                    ++  l+  ++++e+ + el+++  + + ++q+ t++ n
  gi|91773226|ref|YP_565918.1| 455 SDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGN 493
                                   ********************************9999876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.45
                           GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlkny 80 
                                   I++  e ++ l + +++ +k+++e+ +  +++   L+ka + ++e +++  + 
  gi|91773226|ref|YP_565918.1| 506 IDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDER 558
                                   66667778888899999999999999999999999999999999999887765 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.8      0.05        16     165     235 ..     336     411 ..     332     430 .. 0.66
   2 !   20.4   7.6   8.3e-07   0.00027      68     203 ..     430     572 ..     420     579 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.05
                ALIX_LYPXL_bnd 165 ekaendDitpkl......ltekkrdiaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksd 235
                                   e++  dDi++++      + ek++ i  + +++ +   +e  d+++++l++s+++qe+l  +i ++  ++ +  +s 
  gi|91773226|ref|YP_565918.1| 336 ENVNLDDIRTVVpienaiIIEKEE-IIEKVESSPLTLSIEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSL 411
                                   556666665544322221555555.554555777777888999*******************987766665555544 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 8.3e-07
                ALIX_LYPXL_bnd  68 qpSseltaelraelqkyreileeAsesDkivrqklqenkedlelLsgpeeeleaalp......ssssaaasesveeqirkl 142
                                   ++S  + a++ +++++++ +le+  + ++ ++  l++++e++++L+++++ + + +       +s+sa++  ++ + i k+
  gi|91773226|ref|YP_565918.1| 430 EESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMIFSHIQkitefgNSRSAEI-FETNDRIDKI 509
                                   57888999*************************************9999999999887778877676666.89999***** PP

                ALIX_LYPXL_bnd 143 rsllekldelkaereqllkdlkekaendDitpklltekkr....diaanefealfeeelekydpl 203
                                    + l  l ++++e ++ +++l+ ++++d i   l ++       + +++e  +lf++el  + ++
  gi|91773226|ref|YP_565918.1| 510 DESLTLLTQIQDESQKNIHELR-SVASD-IIRSLEKAHNTnkefKAETDERGELFKNELISLTEF 572
                                   *********************9.35555.544443222224556667777788888888755554 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  12.3   1.3e-06    0.0004     356     528 ..     374     543 ..     367     582 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                 Myosin_tail_1 356 qaleelseqleqakrskaslekakqaLesenkelqaelkslqqakqdseqkrkkleaqlqelqvklseserqreelaekvs 436
                                   +a++e++++l ++krs+ sl  +  +L  +  el++    l+  k+dse+    ++a+++e   ++++ e++ +el++ ++
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQS---LTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLE 451
                                   689*******************************975...566699*********************************** PP

                 Myosin_tail_1 437 klqaelesvsslleeaegksiklskdvsslesqlqDtqellqeetrqkLalssrlrqleeeknalkeqleeeeeakknvek 517
                                   ++ ++  ++++ l + e++   l+   + + s++q + e  +    +  +   r+ +++e  + l+  ++e +++ +++  
  gi|91773226|ref|YP_565918.1| 452 NIHSDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQKNIHELRS 532
                                   **********************************************************99999888888877666555544 PP

                 Myosin_tail_1 518 qlstlqaqlsd 528
                                     s +   l+ 
  gi|91773226|ref|YP_565918.1| 533 VASDIIRSLEK 543
                                   44333333333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.26        83      78     120 ..     372     414 ..     352     426 .. 0.58
   2 !   16.6   2.3   1.9e-05     0.006      38     121 ..     392     475 ..     386     478 .. 0.92
   3 !    8.4   1.0    0.0068       2.2      65     110 ..     503     548 ..     483     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.26
                       DUF1664  78 qkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                   ++e+  eik+e+++ ++  +++ +++ ++   + +le++l+ i
  gi|91773226|ref|YP_565918.1| 372 SIEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVI 414
                                   4455555555555555555555555555555555555555544 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.9e-05
                       DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                   sl   + +++ ++ ++ +sl+  k++ ++   +++++++e+++ +++i++ ++e+++ l++i++d +++++   ++e++++
  gi|91773226|ref|YP_565918.1| 392 SLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIA 472
                                   66667778899999999***************************************************************9 PP

                       DUF1664 119 rie 121
                                   ++ 
  gi|91773226|ref|YP_565918.1| 473 ELT 475
                                   986 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0068
                       DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                   ++rid++d++l   ++i+ e +++++e+r+  s+i + +e+ +++ 
  gi|91773226|ref|YP_565918.1| 503 NDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTN 548
                                   68*********************************99999988765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   6.5      0.29        94      67     161 ..     351     446 ..     275     447 .. 0.76
   2 !   20.6   8.8   1.2e-06   0.00039      38     164 ..     397     533 ..     395     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.29
                       UPF0242  67 kskleekeaklteld.eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLae 146
                                   +  + eke+ + + +  +l+   ea+ e ++e  + k+ +++  +++  l+ +  +L++ l  i++d e+    ++++++e
  gi|91773226|ref|YP_565918.1| 351 NAIIIEKEEIIEKVEsSPLTLSIEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEE 431
                                   444555555555444434555566666666666666777777777777777777777777777777777777777777777 PP

                       UPF0242 147 kqellqeyqetieeq 161
                                    ++ + + ++ i+e+
  gi|91773226|ref|YP_565918.1| 432 STNHIAKIEKRISEL 446
                                   777777777777664 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.2e-06
                       UPF0242  38 iGlllaaaGsLlllllllkwekalkeklekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkee 118
                                   iG l   +G+L   l ++k +++ ++   +  +ee  + + + ++ +++ e++le+  +++ eL+  l++ ee++++l+  
  gi|91773226|ref|YP_565918.1| 397 IGTLTGNIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSS 477
                                   677777788886655555555555555567789999999999999************************************ PP

                       UPF0242 119 nqqLqekleaiae..........dfeelkleleeqLaekqellqeyqetieeqrsv 164
                                   n+ + +  ++i e          + ++   +++e L   ++  +e+q++i+e+rsv
  gi|91773226|ref|YP_565918.1| 478 NAMIFSHIQKITEfgnsrsaeifETNDRIDKIDESLTLLTQIQDESQKNIHELRSV 533
                                   ********************99999999999***********************97 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.2   6.3e-05      0.02     109     186 ..     374     455 ..     367     457 .. 0.85
   2 !   10.2   8.9    0.0016       0.5      62     180 ..     428     547 ..     426     555 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-05
                        DUF724 109 eerkklekkieeeesekrkleeeidelekkilelerqlallk....ekkeaadkeiarlkseaekleeeledveqeFeava 185
                                   e++ +++k++++ + ++++l ++i  l  +i ele+ l+++k    + +++ +++i ++  + +k+e+++++ e+  e++ 
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKndseNTNSSINARIEESTNHIAKIEKRISELEDTLENIH 454
                                   67788999**********************************877655666677788888888999999999999888887 PP

                        DUF724 186 s 186
                                   s
  gi|91773226|ref|YP_565918.1| 455 S 455
                                   6 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0016
                        DUF724  62 siddsrseleslkeslaeLekhGFdVkalqsrl.nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkile 141
                                   +i++s++ + ++ + ++eLe    ++++  s l + L s+ ++ ++l +    + ++i++ ++  ++ ++ei e++ +i +
  gi|91773226|ref|YP_565918.1| 428 RIEESTNHIAKIEKRISELEDTLENIHSDNSELqTGLASIEENIAELTSSNAMIFSHIQKITEFGNSRSAEIFETNDRIDK 508
                                   78999****************************445899*******************99999999999************ PP

                        DUF724 142 lerqlallkekkeaadkeiarlkseaekleeeledveqe 180
                                   + + l+ll + +++++k+i +l+s a+++ ++le++++ 
  gi|91773226|ref|YP_565918.1| 509 IDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNT 547
                                   *****************************9999987654 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   8.2   1.6e-05     0.005      67     182 ..     328     479 ..     273     484 .. 0.72
   2 ?    0.9   2.2       1.5   4.7e+02      68     135 ..     501     569 ..     483     583 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-05
                         ATG16  67 q................................snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkle 115
                                   +                                 ++++s+ ++ + +++ ++++ela++ +s++ l + + +l+  + +le
  gi|91773226|ref|YP_565918.1| 328 AippidisenvnlddirtvvpienaiiiekeeiIEKVESSPLTLSIEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELE 408
                                   2445666666666666666666666666666655556666666666778899************************99999 PP

                         ATG16 116 eklk...ed.eerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENk 182
                                   ++l+   +d e++  +++a++++ +  +++ e+++ e+e ++++++ + s Lq  l ++Ee+  +l+  N+
  gi|91773226|ref|YP_565918.1| 409 QSLTvikNDsENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNA 479
                                   9764222441455667899**********************************************999886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.5
                         ATG16  68 snskqsakiqsleqklaqlreela.elyksrgelaqrllelneelqkleeklkedeerlaeleaeraal 135
                                   +++++ +ki ++ ++l+q+++e + + +  r+  ++ +++l++++ + +e   e +er +  ++e  +l
  gi|91773226|ref|YP_565918.1| 501 ETNDRIDKIDESLTLLTQIQDESQkNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELFKNELISL 569
                                   344444555555555555555533133333444444444444444444444444444444445555444 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.36   1.2e+02      36      75 ..     373     412 ..     365     419 .. 0.70
   2 !   11.4   3.4   0.00093       0.3      33      91 ..     401     460 ..     379     465 .. 0.84
   3 ?    1.3   0.1       1.3   4.2e+02      38      72 ..     459     493 ..     450     509 .. 0.80
   4 ?    4.5   0.2      0.13        42      43      80 ..     482     519 ..     465     522 .. 0.72
   5 !    8.6   1.2    0.0068       2.2      19      65 ..     510     556 ..     503     575 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.36
                       BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                   +++++++ ++l+++    +++y ++  +  +i ++e+++t
  gi|91773226|ref|YP_565918.1| 373 IEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLT 412
                                   4566666677777777777777777777777777777766 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00093
                       BLOC1_2  33 sekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                   + ++ +l++++  +++++e++n+  +  +++  ++i +iek+++eLe++ + + +  +eL
  gi|91773226|ref|YP_565918.1| 401 TGNIGELEQSLTVIKNDSENTNSSINaRIEESTNHIAKIEKRISELEDTLENIHSDNSEL 460
                                   56788999*************9987769********************998876655555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.3
                       BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiek 72 
                                   +l++ +as+e+++ +l + ++ + +++q+i ++ +
  gi|91773226|ref|YP_565918.1| 459 ELQTGLASIEENIAELTSSNAMIFSHIQKITEFGN 493
                                   67788899999999999999999999999988755 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.13
                       BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                    ++++k  e  n++++e+ +  ++id+i++++t L+++
  gi|91773226|ref|YP_565918.1| 482 FSHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQI 519
                                   45556666666788888999999999999999988775 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0068
                       BLOC1_2  19 vedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylq 65 
                                    e + lL+++  ++++++++l++va+++ ++lek  ++++e++   +
  gi|91773226|ref|YP_565918.1| 510 DESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETD 556
                                   57899************************************998765 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 ?    2.0   0.4      0.52   1.7e+02      59     109 ..     376     426 ..     368     434 .. 0.78
   2 !   16.0   1.2   2.4e-05    0.0077      58     108 ..     428     478 ..     424     485 .. 0.89
   3 ?    2.3   0.7      0.43   1.4e+02      65     112 ..     498     545 ..     483     550 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.52
                        Nsp1_C  59 IskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskle 109
                                   + ++++e+ + +++q+ +  ++  ++ +  eLe+ L+ + ++ e+ +s+++
  gi|91773226|ref|YP_565918.1| 376 MDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSIN 426
                                   567788888888899999999999999999999999988888888777665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.4e-05
                        Nsp1_C  58 kIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskl 108
                                   +I++  +++ ++e+  ++++++Le i+s+ +eL++ L+++E+++ el s+ 
  gi|91773226|ref|YP_565918.1| 428 RIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSN 478
                                   567777889999**********************************99765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.43
                        Nsp1_C  65 evleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesqk 112
                                   e++e++    kid++L+++++ qde ++ ++++ + ++++  +le+++
  gi|91773226|ref|YP_565918.1| 498 EIFETNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAH 545
                                   56777788899**************99999998888777776666555 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 ?    1.5   0.5       1.3   4.1e+02      10      37 ..     377     404 ..     361     434 .. 0.64
   2 ?   16.1   1.2   3.4e-05     0.011       2      40 ..     436     474 ..     435     476 .. 0.94
   3 ?   -0.3   0.7       4.6   1.5e+03       8      33 ..     505     530 ..     493     576 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.3
                     FlaC_arch  10 sklsteletvkkeneelsksveelkenV 37 
                                   ++++ el+  k+++e+l +++ +l  n+
  gi|91773226|ref|YP_565918.1| 377 DEIKKELADSKRSQESLYTNIGTLTGNI 404
                                   4444445555555555554444444444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.4e-05
                     FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                   i ++E+++s+l+ +le++ ++n+el++ +  ++en+ +l
  gi|91773226|ref|YP_565918.1| 436 IAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAEL 474
                                   678*********************************987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 4.6
                     FlaC_arch   8 klsklsteletvkkeneelsksveel 33 
                                   +++k++ +l+ + + ++e +k+++el
  gi|91773226|ref|YP_565918.1| 505 RIDKIDESLTLLTQIQDESQKNIHEL 530
                                   44455555555555555555555554 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 ?   13.4  10.8   9.7e-05     0.031      28     183 ..     380     563 ..     370     597 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.7e-05
                         Atg14  28 rerlaklksekeslkkkiekalegke........eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                   +++la+ k  +esl++ i  +  +           ++++e+   + +a++ee  ++ia++++r++el+d+l++  + + e 
  gi|91773226|ref|YP_565918.1| 380 KKELADSKRSQESLYTNIGTLTGNIGeleqsltvIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSEL 460
                                   6666677777777776666555444455556667777888888888999******************************** PP

                         Atg14 101 kkklaklsdklk.....................kRrsdleslqneleerrkk..qiaklqdaikrieqklsslssktlesr 158
                                   +  la+  ++++                      R +++  +++++ +  ++  +++++qd+ ++  + l s+ s+++  +
  gi|91773226|ref|YP_565918.1| 461 QTGLASIEENIAeltssnamifshiqkitefgnSRSAEIFETNDRIDKIDESltLLTQIQDESQKNIHELRSVASDIIR-S 540
                                   **********************************************998776226899999999999999999999999.9 PP

                         Atg14 159 sslcselaklyglrrtsyergkwvf 183
                                   +++++  +k +++     erg+ ++
  gi|91773226|ref|YP_565918.1| 541 LEKAHNTNKEFKAET--DERGELFK 563
                                   999999999999988..66664443 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.8   6.5e-05     0.021      25      91 ..     415     481 ..     393     491 .. 0.86
   2 ?    4.4   0.7     0.062        20      15      73 ..     503     561 ..     494     575 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-05
                       DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                   ++ + ++ ++++++i+++++  +++++++ +l++ le++   n++l+  +as e++ia+l+ + + i
  gi|91773226|ref|YP_565918.1| 415 KNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMI 481
                                   45667788999*************************************************9987655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.062
                       DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerl 73 
                                   ++ +d++++  +  ++++ +sqk+i +l   ++++ + ++++++ +++ +++ ++  +l
  gi|91773226|ref|YP_565918.1| 503 NDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGEL 561
                                   5778899999999999**************************99999999988876665 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.5   6.8e-05     0.022      17     119 ..     370     464 ..     369     466 .. 0.87
   2 ?    1.1   0.8       1.3   4.1e+02      33      89 ..     502     550 ..     493     579 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.8e-05
                          Uds1  17 iLsleeVeelkkelkaLeerlealrkkL.aletklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeser 96 
                                   +Ls+e ++e+kkel+  ++  e+l +++ +l   + +  +sL   + +++++        +++s+++  +++++++a+ e+
  gi|91773226|ref|YP_565918.1| 370 TLSIEAMDEIKKELADSKRSQESLYTNIgTLTGNIGELEQSLTVIK-NDSEN--------TNSSINARIEESTNHIAKIEK 441
                                   69*************************95688899*******9999.44444........345566799************ PP

                          Uds1  97 kvdelaselekleeraaevrrrL 119
                                   ++ el+++le++++   e+++ L
  gi|91773226|ref|YP_565918.1| 442 RISELEDTLENIHSDNSELQTGL 464
                                   ***************99999765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.3
                          Uds1  33 LeerlealrkkLaletklrda.arsLsrlyssskksak....ssaarsnskssreslakaee 89 
                                    ++r++++ + L+l t+++d   +++++l  s +++      +    +       ++++++e
  gi|91773226|ref|YP_565918.1| 502 TNDRIDKIDESLTLLTQIQDEsQKNIHELR-SVASD-IirslE----K-------AHNTNKE 550
                                   578899999999999999985145788887.44333.111111....1.......2222222 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.7   8.8e+02      96     143 ..     374     421 ..     351     434 .. 0.56
   2 ?   14.4   9.0   7.7e-05     0.025       6     171 ..     425     586 ..     419     603 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.7
                        TACC_C  96 kryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeek 143
                                   + ++  k+ l + k+ +esl + +  +  ++ + eq    +k+  e+ 
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENT 421
                                   344555555666666666666666666666666666666666555544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.7e-05
                        TACC_C   6 ldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlns 86 
                                   ++a +e+ ++ + + e++i+el+++ e+ + +n e++  +a+ e+ ia+l++++     +   +iqk++e  +  +a++ +
  gi|91773226|ref|YP_565918.1| 425 INARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSN----AMIFSHIQKITEFGNSRSAEIFE 501
                                   567889999999*************************************99988....56668899999999999999999 PP

                        TACC_C  87 veksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeekLekAneeiaqvrskakaetaalqa 167
                                   ++  ++++ + +  + +  ++ +kn   l+++a++++  ++k+ +  +++ka ++e+ e   +e+    +  ++e +a+ a
  gi|91773226|ref|YP_565918.1| 502 TNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELFKNELISLTEFVEKEFKAIGA 582
                                   99999999999999999999*************************************999999999999999999998887 PP

                        TACC_C 168 sLrk 171
                                      k
  gi|91773226|ref|YP_565918.1| 583 RSYK 586
                                   6555 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3    0.0004      0.13      89     183 ..     375     476 ..     371     482 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0004
                                   CHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..---...--SSSHHHHHHHTS-T. CS
                Apolipoprotein  89 daeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeve...erlssrveelreklee. 165
                                   +++e+++ la  ++  +e+l +++++l  +++++ ++l   ++   e+ ++s++++ ee+    +++++r++el+++le  
  gi|91773226|ref|YP_565918.1| 375 AMDEIKKELAD-SKRSQESLYTNIGTLTGNIGELEQSLTV-IKNDSENTNSSINARIEESTnhiAKIEKRISELEDTLENi 453
                                   6899****998.9999****************99999997.*******************9999***************97 PP

                                   .....TSHHHHHS--XXXXXXXX CS
                Apolipoprotein 166 .....qaeelrerleanleelka 183
                                        +++   +++e+n++el++
  gi|91773226|ref|YP_565918.1| 454 hsdnsELQTGLASIEENIAELTS 476
                                   77555455445555555556655 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0    0.0004      0.13      10      87 ..     397     475 ..     388     477 .. 0.90
   2 ?    3.8   0.4      0.23        72      36      82 ..     501     547 ..     489     551 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0004
                       DUF4164  10 ltrLeaaldsLEkavdr.rleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietiravL 87 
                                      L++ + +LE++++  + ++e+++++++a+ie+ ++  +++++++ + e+ ++++ + n+E++  L +  e+i +++
  gi|91773226|ref|YP_565918.1| 397 IGTLTGNIGELEQSLTViKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELT 475
                                   567899999****9985488999999*************************************************9876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.23
                       DUF4164  36 eleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaiet 82 
                                   e + +i +++e  + L +  d+++    +l +v++++ r L+ a +t
  gi|91773226|ref|YP_565918.1| 501 ETNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNT 547
                                   6678999999999****************************999776 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 ?   11.4   8.1   0.00053      0.17      48     166 ..     406     525 ..     398     617 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00053
                  HAUS-augmin3  48 aLeeaLktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeek...ea 125
                                   +Le+ L  i+ +d++ ++++++++ +ee ++ + + e+ ++eL+ + + + +  ++Lq   as++++  +l++++    + 
  gi|91773226|ref|YP_565918.1| 406 ELEQSLTVIK-NDSE-NTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAmifSH 484
                                   7999999999.3333.478899999************************************************99922234 PP

                  HAUS-augmin3 126 kkklkeaqeelraenaetnavLqqlteeakqlaeyfeeaek 166
                                    +k++e  ++ +ae++etn   +++ e+ + l++  +e++k
  gi|91773226|ref|YP_565918.1| 485 IQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQK 525
                                   566667777999*************9988777777777766 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5     0.014       4.6      56     116 ..     373     433 ..     370     436 .. 0.95
   2 ?   11.1   0.7     0.001      0.32      79     128 ..     438     487 ..     432     488 .. 0.91
   3 ?    3.0   1.4      0.31     1e+02      63     106 ..     524     567 ..     497     575 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                    TPR_MLP1_2  56 vkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedln 116
                                   ++++ ++++el++ k   ++l ++  +++ ++ e e+s++  k+  e+  s++++rie+ +
  gi|91773226|ref|YP_565918.1| 373 IEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEEST 433
                                   78999*****************************************************965 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.001
                    TPR_MLP1_2  79 eaesakaeleeseesweeqkeelekelselekriedlneqNklLhdQlEs 128
                                   + e+  +ele   e++++  +el++ l+++e+ i +l++ N++  +++++
  gi|91773226|ref|YP_565918.1| 438 KIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMIFSHIQK 487
                                   667778899999999*********************************97 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.31
                    TPR_MLP1_2  63 reelnelkaeiaelkaeaesakaeleeseesweeqkeelekels 106
                                    + ++el++ ++++  ++e+a+++++e +++ +e+ e +++el 
  gi|91773226|ref|YP_565918.1| 524 QKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELFKNELI 567
                                   22234455555555555555555555555555555555555554 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.4    0.0026      0.82      34      98 ..     381     446 ..     356     447 .. 0.81
   2 ?   10.0   2.5     0.003      0.97       8      70 ..     427     484 ..     424     512 .. 0.71
   3 ?    2.4   1.2      0.72   2.3e+02      25      61 ..     517     552 ..     496     581 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0026
                  Syntaxin-6_N  34 stseeldetrteLrkalrsiewdledLeetvriveknpsk.fkidekelsrrrafveevreevkem 98 
                                   ++  ++++ ++ L ++++++  ++ +Le++  +++++ ++  +  ++ +++  + +++++++++e+
  gi|91773226|ref|YP_565918.1| 381 KELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENtNSSINARIEESTNHIAKIEKRISEL 446
                                   356778889999**********************999999677778999************99986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.003
                  Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivekn 70 
                                   + +++s n ++++ +r ++l ++      e++++ ++eL++ l sie+++ +L  + +++ ++
  gi|91773226|ref|YP_565918.1| 427 ARIEESTNHIAKIEKRISELEDT-----LENIHSDNSELQTGLASIEENIAELTSSNAMIFSH 484
                                   56777777777777777775544.....78888999999999999999999998887666443 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.72
                  Syntaxin-6_N  25 erlledtssstseeldetrteLrkalrsiewdledLe 61 
                                   ++++++++++  +el++  +++ ++l+++ ++ ++++
  gi|91773226|ref|YP_565918.1| 517 TQIQDESQKN-IHELRSVASDIIRSLEKAHNTNKEFK 552
                                   4444443332.44444444444444444444433333 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0066       2.1      16      67 ..     380     431 ..     374     435 .. 0.90
   2 ?    5.0   0.3       0.1        32      27      60 ..     437     470 ..     430     488 .. 0.76
   3 ?   -1.0   0.1       7.2   2.3e+03      28      44 ..     501     517 ..     489     544 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0066
                           CLZ  16 DeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitk 67 
                                    +e a+++  q++l +++  L +++  L++ l  + ++ e++++ +++Ri++
  gi|91773226|ref|YP_565918.1| 380 KKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEE 431
                                   4557788899****************************************85 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.1
                           CLZ  27 keleekverLessLeaLqtrlarLlaeyessqrk 60 
                                    ++e+++++Le +Le+++     L + + s ++ 
  gi|91773226|ref|YP_565918.1| 437 AKIEKRISELEDTLENIHSDNSELQTGLASIEEN 470
                                   5788888888888888888777777777766654 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 7.2
                           CLZ  28 eleekverLessLeaLq 44 
                                   e++++++++++sL  L+
  gi|91773226|ref|YP_565918.1| 501 ETNDRIDKIDESLTLLT 517
                                   67788888888887764 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.093        30      77     116 ..     374     413 ..     372     417 .. 0.85
   2 ?   11.0   0.5   0.00097      0.31      80     118 ..     437     475 ..     430     477 .. 0.92
   3 ?    3.8   0.8      0.16        50      84     115 ..     504     535 ..     500     558 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.093
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  77 eAiellkkkleelekqlekleeeleklkdqittleanlaq 116
                                   eA++ +kk+l++ ++++e+l  ++  l+ +i +le+ l  
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTV 413
                                   7899999999999999999999999999999999987765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00097
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                   + ++k+++ele++le++  +  +l++ + ++e+n+a+l+
  gi|91773226|ref|YP_565918.1| 437 AKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELT 475
                                   5589*******************************9975 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  84 kkleelekqlekleeeleklkdqittleanla 115
                                   +++++++++l+ l++  ++ +++i++l+  ++
  gi|91773226|ref|YP_565918.1| 504 DRIDKIDESLTLLTQIQDESQKNIHELRSVAS 535
                                   77888888888888888888888888776654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.3     0.059        19      40      94 ..     376     431 ..     357     438 .. 0.86
   2 ?    9.9   4.9    0.0022      0.72      10      88 ..     420     499 ..     412     509 .. 0.85
   3 ?    4.4   1.6      0.11        35      33      81 ..     499     547 ..     492     575 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.059
                                   XXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....HHHHHHH CS
                    Laminin_II  40 veetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.lsdnise 94 
                                   ++e+++++ d+++  ++  +++ +L+ ++ +L++ l  +k+ +e+ +s + + i+e
  gi|91773226|ref|YP_565918.1| 376 MDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSsINARIEE 431
                                   589999999999999999999999****************9999998889999987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0022
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....H CS
                    Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.l 88 
                                   +t +++ + +++  + + ++++ +se+++++e+++ + +++++++++ ++++ +L+     +++ ++++ +  + +s+ +
  gi|91773226|ref|YP_565918.1| 420 NTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGNSRSAeI 499
                                   56677788888999999***************************************************999887776652 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.11
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                    Laminin_II  33 lseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                   + e n+ +++++e +  ++++ ++ ++++ +L  +a +++  l++  + 
  gi|91773226|ref|YP_565918.1| 499 IFETNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNT 547
                                   5556666666666677777777777777777777777777666654443 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.1   0.00013      0.04      13      89 ..     374     453 ..     368     461 .. 0.62
   2 ?    3.0   0.3      0.43   1.4e+02      14      41 ..     505     532 ..     498     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00013
               Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeya.kKLvnikkrmsslnerlqklkkRaekL 89 
                                    ++de++++l++ ++sQe L  ++ +l+ ++ ele+     ++  +++++ + +++ +  +++ ++++r+++l++ +e++
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTviKNDSENTNSSInARIEESTNHIAKIEKRISELEDTLENI 453
                                   6789999***********99999999988888777654422111222222222455555555555555555555555544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.43
               Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlne 41 
                                    +d++de+l  l+q Q+e ++++++l++
  gi|91773226|ref|YP_565918.1| 505 RIDKIDESLTLLTQIQDESQKNIHELRS 532
                                   6899999999999999999999999876 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0094         3       4      74 ..     405     475 ..     389     488 .. 0.68
   2 ?    0.9   0.1       1.4   4.4e+02       9      47 ..     519     560 ..     512     575 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0094
                       DUF1515   4 agvlqqlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtalegsvvklkaditsvkevtedvk 74 
                                   + + q+l  ++++ ++    ++   + s    ak+ +++ el + ++ + +  ++l++ ++s+ e  ++++
  gi|91773226|ref|YP_565918.1| 405 GELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELT 475
                                   44555555555566666666655556666677788888888888888888888888888888777666665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.4
                       DUF1515   9 qlgtllaevkelr...edlkrsedrsdasrakmyrkmdelve 47 
                                     ++ +++++elr    d+ rs +++  +  + +  +de  e
  gi|91773226|ref|YP_565918.1| 519 IQDESQKNIHELRsvaSDIIRSLEKAHNTNKEFKAETDERGE 560
                                   33344566666662226899******9999999999998655 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.3    0.0034       1.1      16      90 ..     374     451 ..     358     458 .. 0.72
   2 ?    5.8   1.9     0.021       6.8       5      83 ..     465     542 ..     456     564 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0034
                         TMPIT  16 etakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvlkevesllp 90 
                                   e+ +e+k++l++ +++q+++ ++i + + ++ el++sl+ +k++++   ++ + ++ee ++++++++k ++e+e++l 
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSEntnSSINARIEESTNHIAKIEKRISELEDTLE 451
                                   455789999999999999999999999999999999999999986633333334455555566666666666666654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                         TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                   +++e+++ el +++  + +++++++++ ++ s ei + + r+ ++++sl+ l++  ++e++++++el++  +++ ++l+
  gi|91773226|ref|YP_565918.1| 465 ASIEENIAELTSSNAMIFSHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQI-QDESQKNIHELRSVASDIIRSLE 542
                                   5778888888888888889999999999999999999999999999998888766.45666666666655544444443 PP

>> DUF484  Protein of unknown function, DUF484
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.7    0.0028      0.89      34     134 ..     414     519 ..     406     549 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0028
                        DUF484  34 lphqaantvsLvevqlararerireleeelaalmel....AraNerlfarllalqldlldarsledvlrrleasarelfla 110
                                   ++ + +nt s  + +++   ++i ++e+++++l++       +N++l+ +l  + +++ + +s ++++    +++ e+++ 
  gi|91773226|ref|YP_565918.1| 414 IKNDSENTNSSINARIEESTNHIAKIEKRISELEDTleniHSDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGNS 494
                                   5667778888888888888888888888888876641111568************************************** PP

                        DUF484 111 aavrlllfhdskvk.gesatdevil 134
                                     +++   +d+  k  es+t+   +
  gi|91773226|ref|YP_565918.1| 495 RSAEIFETNDRIDKiDESLTLLTQI 519
                                   ***********99977775443322 PP

>> Cornifin  Cornifin (SPRR) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.0    0.0034       1.1      35     119 ..     156     240 ..     131     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0034
                      Cornifin  35 tkvpepcqtkvpepcqtkvpepcqtkvpepcqtkvpepcytkvpepcsikvpepcfikapepcaikvpeqcltkapepcqt 115
                                   + + e   t + ep  + + e   t   ep  + + e  +t   ep  + + e  f  + ep  + + e  +t + +p ++
  gi|91773226|ref|YP_565918.1| 156 PSINEDEFTVAEEPVFPSINEDEFTATEEPVFPSINEFEFTATEEPVFPSINEDEFTATEEPVFPSINETEFTATEKPVFP 236
                                   445556666677777777777777777777777777777777777777777777777777777777777777777777776 PP

                      Cornifin 116 vvpe 119
                                    + e
  gi|91773226|ref|YP_565918.1| 237 PINE 240
                                   6655 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.4    0.0036       1.2      34     129 ..     425     519 ..     420     534 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHH CS
                         Nup54  34 LakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelra 114
                                   ++ R +   +++a+ ++r++e++d le+++ + + e+++ l+ +  + +el++    ++++++ +  +g + +ae  e   
  gi|91773226|ref|YP_565918.1| 425 INARIEESTNHIAKIEKRISELEDTLENIH-SDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGNSRSAEIFETND 504
                                   67899999**********************.********************************887888887778888888 PP

                                   HHHHHHHHHS-HHH. CS
                         Nup54 115 rletleaqlndpaql 129
                                   r+++++++l+  +q+
  gi|91773226|ref|YP_565918.1| 505 RIDKIDESLTLLTQI 519
                                   888888888743333 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.6   8.5e+02      41      68 ..     376     403 ..     374     433 .. 0.79
   2 ?    8.9   0.3    0.0049       1.6       2      38 ..     439     475 ..     438     490 .. 0.90
   3 ?    3.1   0.7      0.31     1e+02      18      65 ..     511     558 ..     501     565 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.6
                 TolA_bind_tri  41 iEelqyqleqleerQrdlYldlDerlrk 68 
                                   ++e + +l + ++ Q  lY+++ ++ + 
  gi|91773226|ref|YP_565918.1| 376 MDEIKKELADSKRSQESLYTNIGTLTGN 403
                                   5677788888888888888887766554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0049
                 TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLR 38 
                                   +e+r+++LE  le+  + + elq+ l + ++ ++eL 
  gi|91773226|ref|YP_565918.1| 439 IEKRISELEDTLENIHSDNSELQTGLASIEENIAELT 475
                                   79********************************996 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.31
                 TolA_bind_tri  18 qlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDer 65 
                                   ++l+ l q  ++ q+ + eLR    +    le++ +  +++  + Der
  gi|91773226|ref|YP_565918.1| 511 ESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDER 558
                                   344445555577899999999999999999999999999999999998 PP

>> DUF4208  Domain of unknown function (DUF4208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       5.1   1.6e+03       5      38 ..     264     295 ..     260     302 .. 0.72
   2 ?   -0.1   0.3         4   1.3e+03      34      65 ..     423     456 ..     404     490 .. 0.58
   3 ?   10.6   0.3    0.0019       0.6       7      61 ..     526     580 ..     520     593 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 5.1
                       DUF4208   5 smdeeeckellrpvkksLkrLkkltkekllskke 38 
                                   s+ +++ k +l  + ++Lkr+ + +k  l ++ e
  gi|91773226|ref|YP_565918.1| 264 SIPNKKGKGFLASITDALKRIAQKKK--LIDRME 295
                                   55566678899999*******97744..455555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 4
                       DUF4208  34 lskkerakilkkeLlkiGdfIdellkekke..ek 65 
                                    s + r+++  + + ki ++I+el ++ ++  ++
  gi|91773226|ref|YP_565918.1| 423 SSINARIEESTNHIAKIEKRISELEDTLENihSD 456
                                   5555555555555555555555555554443222 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0019
                       DUF4208   7 deeeckellrpvkksLkrLkkltkekl.lskkerakilkkeLlkiGdfIdellkek 61 
                                   +  e++++ +++ +sL++ ++++ke +  +++er + +k+eL+++ +f++++ k  
  gi|91773226|ref|YP_565918.1| 526 NIHELRSVASDIIRSLEKAHNTNKE-FkAETDERGELFKNELISLTEFVEKEFKAI 580
                                   333599999***********99988.669********************9998875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       3.4   1.1e+03      16      51 ..     373     408 ..     370     416 .. 0.75
   2 ?   12.1   1.0   0.00038      0.12      15      55 ..     418     458 ..     407     462 .. 0.86
   3 ?    1.6   0.4      0.74   2.4e+02      11      52 ..     491     532 ..     481     544 .. 0.85
   4 ?   -0.9   0.3       4.4   1.4e+03      16      47 ..     524     555 ..     512     557 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.4
                                   XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                         DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                   + a+ ++k+e+a+ ++  ++l   +  L+ ++ +L+
  gi|91773226|ref|YP_565918.1| 373 IEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELE 408
                                   667788888888888888888887777777776665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00038
                                   XXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                         DivIC  15 gllaykqlkqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                   + ++ +++++ i++ ++++ak+ +++ eLe+ +++ +sd +
  gi|91773226|ref|YP_565918.1| 418 SENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNS 458
                                   5678899*****************************88866 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.74
                                   XXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                         DivIC  11 fgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                   fg++    +++++  i+++ + l  l++ ++e ++++ +L+s
  gi|91773226|ref|YP_565918.1| 491 FGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQKNIHELRS 532
                                   7788888999999************************99975 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 4.4
                                   XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaev 47 
                                   + ++++l++   ++ + l+k +++n+e +ae 
  gi|91773226|ref|YP_565918.1| 524 QKNIHELRSVASDIIRSLEKAHNTNKEFKAET 555
                                   56677777777788888999999999999885 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         8   2.5e+03      30      38 ..     257     265 ..     246     325 .. 0.58
   2 ?    9.2   1.4    0.0028      0.91      55     164 ..     352     459 ..     350     466 .. 0.85
   3 ?    4.9   0.2      0.06        19      80     141 ..     501     562 ..     484     571 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8
                        DUF745  30 AaeaAakqv 38 
                                   Aa++A+k +
  gi|91773226|ref|YP_565918.1| 257 AAQEASKSI 265
                                   333333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0028
                        DUF745  55 AaLaGKqqlveqleqe.lreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqel 134
                                   A++  K+ ++e++e++ l+   ++++e+kk+l+ s+++ ++  +   + + ++  l++ l  +k+  en+   +++ ++ +
  gi|91773226|ref|YP_565918.1| 352 AIIIEKEEIIEKVESSpLTLSIEAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENT---NSSINARI 429
                                   6667789999999987345566899****************99999999999999999999998876665...56778899 PP

                        DUF745 135 aektqlleaAkkRveeLkkqlkearkdlek 164
                                   +e t+ +++ +kR+ eL+  l++ ++d  +
  gi|91773226|ref|YP_565918.1| 430 EESTNHIAKIEKRISELEDTLENIHSDNSE 459
                                   999*******************99999766 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.06
                        DUF745  80 eekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqll 141
                                   e ++ + +  +++++ ++++++ q++++ l+++   +  +le+a++++++ ++e +e+ +l 
  gi|91773226|ref|YP_565918.1| 501 ETNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELF 562
                                   55566666677778888888888888888888888888888888888888888888887776 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.9     0.014       4.5      52      98 ..     406     452 ..     396     456 .. 0.92
   2 ?    6.4   2.3     0.021       6.8      46     104 ..     453     514 ..     452     582 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                      Lectin_N  52 qLqreLetLketfsnfssstlaeiqalssqggslsekvtsleaklek 98 
                                   +L + L+ +k++ +n+ ss++a i++ + +  +++++++ le +le+
  gi|91773226|ref|YP_565918.1| 406 ELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLEN 452
                                   688999***************************************97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.021
                      Lectin_N  46 igsqnsqLqreLetLketfsnfssstla...eiqalssqggslsekvtsleaklekkqqdlk 104
                                   i s ns+Lq  L +++e++ +++ss  +   +iq+++  g+s s ++   + +++k +++l+
  gi|91773226|ref|YP_565918.1| 453 IHSDNSELQTGLASIEENIAELTSSNAMifsHIQKITEFGNSRSAEIFETNDRIDKIDESLT 514
                                   6799*******************998872225666777788888888888888877777664 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   9.7    0.0017      0.56      25     104 ..     397     481 ..     382     490 .. 0.59
   2 ?    1.9   0.7      0.65   2.1e+02       5      63 ..     486     546 ..     482     582 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0017
                  Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq...dtlrneLtnlnsiltnLls 99 
                                   i +++ +i ++l++ l+ i++  ++ ++++++ ++e ++   ++++ +++L+d+l ++     +l++ L +++ ++++L+s
  gi|91773226|ref|YP_565918.1| 397 IGTLTGNI-GELEQSLTVIKNDSENTNSSINARIEESTNhiaKIEKRISELEDTLENIHsdnSELQTGLASIEENIAELTS 476
                                   33444455.666666666666666666666666665555444445555555555555556556666666666666666666 PP

                  Baculo_PEP_C 100 svtNi 104
                                   s + i
  gi|91773226|ref|YP_565918.1| 477 SNAMI 481
                                   65554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.65
                  Baculo_PEP_C   5 qqL...nggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt 63 
                                   q++   + + + + ++ ++ ++ i   + ++l+q++   ++   +L ++++d+ ++l++ ++
  gi|91773226|ref|YP_565918.1| 486 QKItefGNSRSAEIFETNDRIDKI-DESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHN 546
                                   555432445566677777778888.5555666888877777777788888877776665544 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.77   2.5e+02      26      79 ..     392     447 ..     372     459 .. 0.59
   2 ?    4.8   0.1      0.14        46      28      71 ..     433     476 ..     424     491 .. 0.81
   3 ?    7.8   1.2     0.017       5.4      26      92 ..     501     569 ..     489     578 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.77
                  Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklkk.dpeyqekk 79 
                                   +l++++ +++ ++ eLe+ l   k++s+ + ++i+++i ++ +++ k +++  e +
  gi|91773226|ref|YP_565918.1| 392 SLYTNIGTLTGNIGELEQSLTVIKNDSEnTNSSINARIEESTNHIAKiEKRISELE 447
                                   56666666777777777777777776664444555555544444444333333333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.14
                  Occludin_ELL  28 haeleevskkfseLerelkelkegskeykkieeeilqeykklkk 71 
                                    +++++++k++seLe+ l++ + +++e ++  ++i ++ ++l++
  gi|91773226|ref|YP_565918.1| 433 TNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTS 476
                                   67889999999999999999999999999988888888777765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.017
                  Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekk.krceyLkekLshi 92 
                                   e +++++++ + ++ L +  +e++++ +e ++++++i+++++k ++ ++e++++  +r e  k++L  +
  gi|91773226|ref|YP_565918.1| 501 ETNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNtNKEFKAETdERGELFKNELISL 569
                                   677899999999999999999***********************9989999876525667777777665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   8.8   4.4e-05     0.014     151     280 ..     376     511 ..     357     515 .. 0.59
   2 ?    1.7   4.1       0.3        96     145     221 ..     503     579 ..     497     616 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                          Spc7 151 leedkelLekqe...eeldellpeleeekaeleeeleklqeaaeeles.......idkeeLeelreelaelkaeieekkke 221
                                   ++e k++L++++   e l +    l+ +  ele+ l+ +++ +e+ +s          + ++++ ++++el+ ++e+   +
  gi|91773226|ref|YP_565918.1| 376 MDEIKKELADSKrsqESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSsinarieESTNHIAKIEKRISELEDTLENIHSD 456
                                   334344443333000333333344555556677777777776666666222222144556666666666666666666666 PP

                          Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkalee 280
                                    +elq+ l+++ee+i+el+++ + + + i+     + e  ++++ e+ + +++ ++++e
  gi|91773226|ref|YP_565918.1| 457 NSELQTGLASIEENIAELTSSNAMIFSHIQ----KITEFGNSRSAEIFETNDRIDKIDE 511
                                   666666666666666666666666666666....4555677888888888888888876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.3
                          Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                   ++++++++e  +lL++ ++e ++  +el++  +++ + lek  + ++e+++ + e+ e +++el +l + +e+  k 
  gi|91773226|ref|YP_565918.1| 503 NDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELFKNELISLTEFVEKEFKA 579
                                   56677777888888888888888888888888888888888888888888888777777888887777777655554 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.2    0.0018      0.56       4      77 ..     381     454 ..     378     461 .. 0.85
   2 ?    6.1   0.7     0.064        20       7      80 ..     451     531 ..     450     539 .. 0.57
   3 ?   -0.2   1.9       5.7   1.8e+03      22      56 ..     522     555 ..     501     605 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0018
                PRKG1_interact   4 kLYeeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkele 77 
                                   k   ++k+ +e L +++ +l+ ++ el+++l+ +k+ +++ +s+ ++ +e + ++  ++e++isele+ l++++
  gi|91773226|ref|YP_565918.1| 381 KELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIH 454
                                   5567889999***********************998877778888889999999999**********9988775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.064
                PRKG1_interact   7 eeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkisel...........eeelkel 76 
                                   e+ +++n++L++ L ++e++++el+s+ + + ++    ++k ++  + ++ e  +++ +i ++           +e++k++
  gi|91773226|ref|YP_565918.1| 451 ENIHSDNSELQTGLASIEENIAELTSSNAMIFSH----IQKITEFGNSRSAEIFETNDRIDKIdesltlltqiqDESQKNI 527
                                   567889999**99999999999999977776633....3333333333333334444444444000222233445555666 PP

                PRKG1_interact  77 eeLr 80 
                                   +eLr
  gi|91773226|ref|YP_565918.1| 528 HELR 531
                                   6665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 5.7
                PRKG1_interact  22 elekelselkseleklkqqrqesvskrssllelek 56 
                                   e++k+++el+s  + + ++  e+ +++++  ++e 
  gi|91773226|ref|YP_565918.1| 522 ESQKNIHELRSVASDIIRS-LEKAHNTNKEFKAET 555
                                   2333344444433333322.222222222222222 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 ?    1.3   0.3       1.4   4.5e+02      46      86 ..     375     415 ..     356     438 .. 0.54
   2 ?   11.4   3.7     0.001      0.33       6      93 ..     441     538 ..     436     540 .. 0.89
   3 ?    3.0   1.6      0.42   1.3e+02       5      76 ..     506     578 ..     502     584 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.4
                        CENP-H  46 laael.lelakekesekeklkeelekleaelkksrqrwrvvk 86 
                                    + e+  ela  k+s++  l   + +l  ++ + +q  +v+k
  gi|91773226|ref|YP_565918.1| 375 AMDEIkKELADSKRSQE-SLYTNIGTLTGNIGELEQSLTVIK 415
                                   34444334444444444.122223333333333333333333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.001
                        CENP-H   6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek..........eklkeelekleaelk 76 
                                   +++ el  +l++++++ +elq  l+++e+++ +l+  n+ +++++++ ++  +s++          +k +e+l  l +  +
  gi|91773226|ref|YP_565918.1| 441 KRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGNSRSaeifetndriDKIDESLTLLTQIQD 521
                                   5688999**************************************988888888888999999888888899999999999 PP

                        CENP-H  77 ksrqrwrvvknvasaii 93 
                                   +s++++  ++ vas ii
  gi|91773226|ref|YP_565918.1| 522 ESQKNIHELRSVASDII 538
                                   99999999999999998 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.42
                        CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.lelakekesek...eklkeelekleaelk 76 
                                   i+++de  + l +++ e+++   el +v  +++r  +k ++  +e  +e+ +     +   ++l +  e +e+e+k
  gi|91773226|ref|YP_565918.1| 506 IDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFkAETDERG---ElfkNELISLTEFVEKEFK 578
                                   677888888888999999999999999999999998888888888822333222...2333555555555555555 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.5   4.8e+02     240     304 ..     251     313 ..     248     329 .. 0.69
   2 ?    4.3   2.8     0.057        18     126     186 ..     377     445 ..     370     453 .. 0.54
   3 ?   10.1   5.3   0.00096      0.31     224     317 ..     444     537 ..     436     554 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHH CS
                         APG17 240 ledVvkelqerleem.ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeefle 304
                                   l+ + k  qe  +++ +k+ k + +  +++ k +++ kk+++++ee++   pey     + +e  +
  gi|91773226|ref|YP_565918.1| 251 LPPIAKAAQEASKSIpNKKGKGFLASITDALKRIAQKKKLIDRMEEFQPIAPEYTD---QDKESPA 313
                                   66677777777777786666666777777778888999999999999999999999...3333333 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.057
                                   HHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH........-------..STCCHHHHHHHHHHHHHHH CS
                         APG17 126 ealkesidelqaaqkkldssllefdtdlrelkkel........sksksks..essslipellkelesleee 186
                                   +++k++ ++ ++ q++l++++ ++  ++ el+++l        ++++  s  +  +  ++++++ e++ +e
  gi|91773226|ref|YP_565918.1| 377 DEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLtvikndseNTNS--SinARIEESTNHIAKIEKRISE 445
                                   45666677777788888888888888888888888765543221111..1123333333344444444444 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00096
                                   CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHH CS
                         APG17 224 eereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeefle 304
                                   +e e+ le ++ D++el+  +++++e+++e++++++ + ++ ++i+++ ++ ++ + e ++  +k++e l++++++++  +
  gi|91773226|ref|YP_565918.1| 444 SELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQ 524
                                   4667889999**************************************9999888888888889***************99 PP

                                   H...HHHHHHHHH CS
                         APG17 305 rweeekekieekl 317
                                   +  +e  ++++++
  gi|91773226|ref|YP_565918.1| 525 KNIHELRSVASDI 537
                                   9866666655543 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   6.7     0.042        14     133     282 ..     321     472 ..     271     476 .. 0.71
   2 ?    6.2  13.3     0.013       4.1      81     260 ..     375     551 ..     356     563 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.042
                      CALCOCO1 133 ELEeDiktltqralekEteLeRlkerak..kalaqrkeeeaerkqlqakleqseeelrslskelqelrnslaerdtqvlqL 211
                                    +  + k++    +  +++L+ ++  +    a+   kee  e+ ++   l  s e + ++ kel + + s++   t++ +L
  gi|91773226|ref|YP_565918.1| 321 GISSENKAIPPIDISENVNLDDIRTVVPieNAIIIEKEEIIEKVESS-PLTLSIEAMDEIKKELADSKRSQESLYTNIGTL 400
                                   44445666666677778888888877644488888999999998887.899999999999999999999999999999999 PP

                      CALCOCO1 212 qdtittltqkLttAqr.keaenEallkelrslqerlaaSerkvegLkeeLssvaaqrdrtqaeLHqaRleaA 282
                                     +i +l+q Lt  +   e  n ++ + +  + + +a  e++   L++ L+++ +  ++ q+ L     + A
  gi|91773226|ref|YP_565918.1| 401 TGNIGELEQSLTVIKNdSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIA 472
                                   999999999999876514566677788899999999999999999999999999988888887765555555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                      CALCOCO1  81 rveelkeelkesrekveeleekqkelerlseelaeeksalleakeesearirELEeDiktltqralekEteLeRlkerakk 161
                                    ++e+k+el+ s+  +e+l ++   l+   +el +  +++ + +e+ ++    ++  i+  t++  + E ++  l ++ + 
  gi|91773226|ref|YP_565918.1| 375 AMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNS---SINARIEESTNHIAKIEKRISELEDTLEN 452
                                   5778888888888877777665555555444454444444444444444...44456777788888888888889999999 PP

                      CALCOCO1 162 alaqrkeeeaerkqlqakleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttAqrkeaenEallkelrsl 242
                                   ++    e ++   +++ ++ +  + +  + + +q++ +  + r++++ + +d i ++ + Lt   + + e+ +  +elrs+
  gi|91773226|ref|YP_565918.1| 453 IHSDNSELQTGLASIEENIAELTSSNAMIFSHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQKNIHELRSV 533
                                   9999999999999999999999999999999*************************************************9 PP

                      CALCOCO1 243 qerlaaSerkvegLkeeL 260
                                      +  S  k+   ++e 
  gi|91773226|ref|YP_565918.1| 534 ASDIIRSLEKAHNTNKEF 551
                                   988888877776666655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2       2.1   6.7e+02      47      92 ..     374     419 ..     356     426 .. 0.67
   2 ?   10.1   5.8    0.0028       0.9      13      98 ..     378     478 ..     372     488 .. 0.73
   3 ?    3.0   5.3      0.43   1.4e+02      45     118 ..     502     575 ..     483     584 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.1
                        APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                   e ++e+++el++ ++ +e+l +++  l  +  ele+ l  +++ +e
  gi|91773226|ref|YP_565918.1| 374 EAMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSE 419
                                   5666777777777777777777777777777777776666665555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0028
                        APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeek...............qdeeleeleeeleklekeeeelleeLkelekere 78 
                                   e++k+l+++++  +++ +   +l+ +  e e+                +  +ee+ + ++k+ek  +el+  L+++ + ++
  gi|91773226|ref|YP_565918.1| 378 EIKKELADSKRSQESLYTNIGTLTGNIGELEQsltvikndsentnssINARIEESTNHIAKIEKRISELEDTLENIHSDNS 458
                                   5555555555555555555555555555544466666666666555667777888888*********************** PP

                        APG6_N  79 eleaelaaleeelealeeee 98 
                                   el+  la++ee  ++l   +
  gi|91773226|ref|YP_565918.1| 459 ELQTGLASIEENIAELTSSN 478
                                   *************9998765 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.43
                        APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleee 118
                                   +++ +++++e+l  l + ++e ++++ el +  +++ + l++++++ ++ ++e ++  + +++  + l+e+ e+
  gi|91773226|ref|YP_565918.1| 502 TNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELFKNELISLTEFVEK 575
                                   5678999999*******************************************999999999988888888765 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.2     0.002      0.64      32     154 ..     404     526 ..     376     544 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                    V_ATPase_I  32 cdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavl.ek 111
                                   + e+e++l+++++  e++++ +  + e+++++ a+ ek+++ele++le+++++ +el++ l +++++  el+  +a++ ++
  gi|91773226|ref|YP_565918.1| 404 IGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMIfSH 484
                                   678999999999999998888888888788888888899999999999999999999999999999999999887766244 PP

                    V_ATPase_I 112 akefleeeeeeeeeeeseeeeeekeeeeeeeseeeeeeellee 154
                                   ++++ e  +++++e  +++++ +k  +e+ +  ++ ++e++++
  gi|91773226|ref|YP_565918.1| 485 IQKITEFGNSRSAEIFETNDRIDK-IDESLTLLTQIQDESQKN 526
                                   555544335544444433333322.222222222223333333 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.4    0.0012      0.38       3      73 ..     376     448 ..     374     452 .. 0.94
   2 ?    9.2   1.5    0.0048       1.5       4      85 ..     444     530 ..     441     543 .. 0.90
   3 ?    1.1   1.7       1.5   4.8e+02      10      66 ..     516     571 ..     507     588 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0012
                   Uso1_p115_C   3 aseleseaaslkdeneklkaelqslskalesleqk..eakkaaesqakeleaenkklekeleklraelkeeke 73 
                                     e+++e a+ k+ +e+l ++++ l+ ++ +leq+    k+++e+ +++++a+++++++ + k++++++e + 
  gi|91773226|ref|YP_565918.1| 376 MDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSltVIKNDSENTNSSINARIEESTNHIAKIEKRISELED 448
                                   57999*******************************99*****************************999775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0048
                   Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqk.....eakkaaesqakeleaenkklekeleklraelkeekekekekq 79 
                                   sele + +++ + n++l++ l s ++++ +l ++     +  +++++  ++ +ae+ +++++++k+++ l    + ++e+q
  gi|91773226|ref|YP_565918.1| 444 SELEDTLENIHSDNSELQTGLASIEENIAELTSSnamifSHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQ 524
                                   899*******************************999988888889999999999999999*********99999999999 PP

                   Uso1_p115_C  80 kEldDL 85 
                                   k + +L
  gi|91773226|ref|YP_565918.1| 525 KNIHEL 530
                                   988776 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.5
                   Uso1_p115_C  10 aaslkdeneklkaelqslsk.alesleqkeakkaaesqakeleaenkklekeleklra 66 
                                    ++++de++k   el+s ++  ++sle++  ++ +++ + e++++ +  ++el  l +
  gi|91773226|ref|YP_565918.1| 516 LTQIQDESQKNIHELRSVASdIIRSLEKA--HNTNKEFKAETDERGELFKNELISLTE 571
                                   45667777777777776544044455555..444444333433333333444444443 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.8     0.015       4.7      49     152 ..     356     458 ..     343     468 .. 0.72
   2 ?    3.9   5.1      0.21        66      34     128 ..     465     559 ..     443     590 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                          Fez1  49 ekeeeikeleesleektle.levcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeae 128
                                   ekee i+++e+s  + + e ++++++el+ +k ++e l  ++++l  ++ el ++l+  ++++e+++ +s +a+ +++ ++
  gi|91773226|ref|YP_565918.1| 356 EKEEIIEKVESSPLTLSIEaMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTN-SSINARIEES-TN 434
                                   5666666666665554443378999999999999999999999999999999999999876666554.4444444443.46 PP

                          Fez1 129 eleelkreverlraeLkeerqkke 152
                                   ++++ ++++ +l+  L++ +  + 
  gi|91773226|ref|YP_565918.1| 435 HIAKIEKRISELEDTLENIHSDNS 458
                                   778888888888888877665544 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.21
                          Fez1  34 valkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa 114
                                    ++  ++ el+++     ++i+++ e  +++++e+ + ++++++  ++ +ll + +++ +++++elr+ +s+  ++ e+a+
  gi|91773226|ref|YP_565918.1| 465 ASIEENIAELTSSNAMIFSHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAH 545
                                   3333344444444444445788888999999***********************99************9999888888877 PP

                          Fez1 115 lesdeakaqrqeae 128
                                   ++ +e ka+ +e+ 
  gi|91773226|ref|YP_565918.1| 546 NTNKEFKAETDERG 559
                                   77777777766632 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.5   7.9e+02      70     120 ..     276     327 ..     273     346 .. 0.81
   2 ?    9.3   1.2    0.0036       1.2      82     169 ..     396     483 ..     373     485 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.5
                        CHDCT2  70 vieeqlrraallnl.qeekekvgslaqrfaelellaeshqkllkesaagnkn 120
                                   +i + l+r a+ ++  ++ e+ +++a ++++ +  +++ +++++++ +++++
  gi|91773226|ref|YP_565918.1| 276 SITDALKRIAQKKKlIDRMEEFQPIAPEYTDQDKESPAVSEQNHKGISSENK 327
                                   588899999988877999999********99999999888888777665444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0036
                        CHDCT2  82 nlqeekekvgslaqrfaelellaeshqkllkesaagnknanavlekvLnqleelLsdmkadvsrlpatlsrlrpvaeRLqm 162
                                   n+ + + ++g+l+q+++ +++ +e  ++ ++   +++ n  a +ek +++le+ L+++++d s l + l+ ++   + L  
  gi|91773226|ref|YP_565918.1| 396 NIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTS 476
                                   556667889999999999999999999999999999999999999*************************99988778888 PP

                        CHDCT2 163 sersiLs 169
                                   s+  i s
  gi|91773226|ref|YP_565918.1| 477 SNAMIFS 483
                                   8777766 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.7   0.00044      0.14      56     101 ..     407     452 ..     365     465 .. 0.62
   2 ?   -0.9   0.0       4.9   1.6e+03      65      86 ..     458     479 ..     454     490 .. 0.72
   3 ?    1.3   1.2      0.99   3.2e+02      12      44 ..     504     536 ..     496     578 .. 0.69
   4 ?   -1.6   0.1       8.2   2.6e+03       7      26 ..     680     699 ..     674     704 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00044
                                   EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Prefoldin_2  56 vkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                   ++q+++ +k++ e++  +++++i++ ++ + k+ek+++el+++l +
  gi|91773226|ref|YP_565918.1| 407 LEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLEN 452
                                   5666666777777777777777777777777777777777666654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.9
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  65 eeLeerketlekeiktlekqle 86 
                                   +eL++ ++++e++i++l+++  
  gi|91773226|ref|YP_565918.1| 458 SELQTGLASIEENIAELTSSNA 479
                                   5788888888888888887655 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.99
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT CS
                   Prefoldin_2  12 qqlqqlaqqikqletqlkelelvleelellded 44 
                                   ++++++++ ++ l +  +e+++ + el ++++d
  gi|91773226|ref|YP_565918.1| 504 DRIDKIDESLTLLTQIQDESQKNIHELRSVASD 536
                                   445555555555555555555555555554444 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 8.2
                                   HHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   7 fqqlqqqlqqlaqqikqlet 26 
                                   ++  +++l+ ++++ik++++
  gi|91773226|ref|YP_565918.1| 680 LKVDKNRLSIIEKDIKKVKM 699
                                   44445666666666666665 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   4.9      0.19        61      12     103 ..     377     465 ..     362     469 .. 0.77
   2 ?    7.3   2.5     0.017       5.5      38      78 ..     505     545 ..     468     558 .. 0.77
   3 ?   -1.4   0.0       8.4   2.7e+03      76      94 ..     674     693 ..     658     699 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.19
                                   XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil  12 nelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealknleleklarlelesrlskte 92 
                                   +e+ + la  ++s es  +    l  +  ele++l+++++++++ +     ++a+++e  + + +      ele  l  + 
  gi|91773226|ref|YP_565918.1| 377 DEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNS---SINARIEESTNHIAKIEKRISELEDTLENIH 454
                                   56777888888899999999999999999999999999999888876...5678888888887665555567888888877 PP

                                   HHCHHHHHHHH CS
                 Cortex-I_coil  93 kdkailelkla 103
                                    d++ l+  la
  gi|91773226|ref|YP_565918.1| 455 SDNSELQTGLA 465
                                   77776666555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil  38 qkdelesllasleseaaerekrlreleakldealknlelek 78 
                                   + d+++++l++l + ++e +k ++el++   +++++le+ +
  gi|91773226|ref|YP_565918.1| 505 RIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAH 545
                                   4478999******************************9865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 8.4
                                   HHHHHHHHHH.HHHHHHHHH CS
                 Cortex-I_coil  76 leklarlele.srlsktekd 94 
                                    e+la l+++  rls +ekd
  gi|91773226|ref|YP_565918.1| 674 IEQLAGLKVDkNRLSIIEKD 693
                                   58899998863699999999 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.5    0.0095         3      36     122 ..     375     461 ..     370     465 .. 0.89
   2 ?   10.4   7.9    0.0017      0.55      32     125 ..     438     534 ..     433     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0095
                                   HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHH CS
                     Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneq 116
                                    ++++++el++ ++s+++ ++ + +++  + e ++s +  +n  ++ +++++ +i++  + i + e++i +L ++le+ ++
  gi|91773226|ref|YP_565918.1| 375 AMDEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHS 455
                                   5789999**********9999999999999999999998899999999999999********9999*******99999998 PP

                                   HHHHHH CS
                     Fib_alpha 117 kiqkLe 122
                                   + ++L+
  gi|91773226|ref|YP_565918.1| 456 DNSELQ 461
                                   877776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0017
                                   CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                     Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqesnirvLqn 109
                                   +++k++++le++le+i++ ++e ++   +i++ ++e  +s++      + i+++ ++   ei + +++id+  +++  L++
  gi|91773226|ref|YP_565918.1| 438 KIEKRISELEDTLENIHSDNSELQTGLASIEENIAELTSSNAMIfshIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQ 518
                                   68999*************************9999999988887533344555555566678899999999999******** PP

                                   HHHHHHHHHHHHHHHH CS
                     Fib_alpha 110 vlesneqkiqkLeqdi 125
                                   + ++ +++i++L++  
  gi|91773226|ref|YP_565918.1| 519 IQDESQKNIHELRSVA 534
                                   **********998755 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.1      0.12        38       7      49 ..     403     445 ..     354     453 .. 0.90
   2 ?    9.7   1.0    0.0022      0.71       6      78 ..     434     512 ..     429     518 .. 0.73
   3 ?    0.5   0.2       1.5   4.8e+02       4      44 ..     502     542 ..     499     580 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                          ACCA   7 piaeleekieelkklaeesevdlseeieklekkleklkkeiyk 49 
                                   +i ele+ ++ +k+ +e+++ +++++ie+  ++++k++k+i +
  gi|91773226|ref|YP_565918.1| 403 NIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISE 445
                                   7889999999999999999999999999999999999988754 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                          ACCA   6 kpiaeleekieelkklaee...sevdlseeieklekkleklkk...eiyknltpwqkvqlaRhpeRpktldyiealfed 78 
                                   ++ia++e++i+el+++ e+   ++ +l++ ++++e+++++l++    i+++++++ +   +R++e  +t d i+++ e 
  gi|91773226|ref|YP_565918.1| 434 NHIAKIEKRISELEDTLENihsDNSELQTGLASIEENIAELTSsnaMIFSHIQKITEFGNSRSAEIFETNDRIDKIDES 512
                                   667777777777777755533355567788888888888777633378899999999999*****99999999998665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.5
                          ACCA   4 fekpiaeleekieelkklaeesevdlseeieklekkleklk 44 
                                   ++++i++++e ++ l+++++es+ +++e  +  ++ +++l+
  gi|91773226|ref|YP_565918.1| 502 TNDRIDKIDESLTLLTQIQDESQKNIHELRSVASDIIRSLE 542
                                   56667777777777777766666553322222222222222 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 ?   -0.5   0.1       4.1   1.3e+03      25      73 ..     249     296 ..     241     325 .. 0.73
   2 ?    9.2   1.6    0.0039       1.3      39     122 ..     382     466 ..     343     481 .. 0.84
   3 ?    2.6   0.5      0.44   1.4e+02      35      87 ..     514     572 ..     483     606 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 4.1
                         CREPT  25 aklPpevsdvsllekikdkeeaekllkqveealellaeYnkrLeaelee 73 
                                   + lPp  + ++ ++k   +++++ +l ++ +al+ +a+  k+L + +ee
  gi|91773226|ref|YP_565918.1| 249 STLPPIAKAAQEASKSIPNKKGKGFLASITDALKRIAQ-KKKLIDRMEE 296
                                   67888888888888877788888888888888888877.4455555554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0039
                         CREPT  39 kik.dkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelks 118
                                   ++  +k ++e+l +++ +    + e  ++L+   ++ ++ ++ +++ +e   +++ak e++++el++ le+++s ++el++
  gi|91773226|ref|YP_565918.1| 382 ELAdSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQT 462
                                   454367889999999999999999********99*********************************************99 PP

                         CREPT 119 hiqs 122
                                    + s
  gi|91773226|ref|YP_565918.1| 463 GLAS 466
                                   8877 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.44
                         CREPT  35 sllekikdkeeae..kl...lkqveealellaeYnkrLeaeleeRkklak.mledflea 87 
                                    ll++i+d+++++  +l   ++ +  +le  ++ nk  +ae++eR +l k  l +++e 
  gi|91773226|ref|YP_565918.1| 514 TLLTQIQDESQKNihELrsvASDIIRSLEKAHNTNKEFKAETDERGELFKnELISLTEF 572
                                   45666665544321133000344445555566778888888888888754134455544 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.38   1.2e+02      18      45 ..     395     422 ..     391     432 .. 0.85
   2 ?    3.9   3.8      0.17        53       6      45 ..     419     461 ..     415     473 .. 0.81
   3 ?   -0.3   0.1       3.2     1e+03      18      44 ..     525     551 ..     505     557 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.38
                     DASH_Dad4  18 knvekLnesvvelnkeleeinkkNknve 45 
                                   +n+  L+ ++ el+++l  i+++ +n++
  gi|91773226|ref|YP_565918.1| 395 TNIGTLTGNIGELEQSLTVIKNDSENTN 422
                                   6899999999********9999887764 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.17
                     DASH_Dad4   6 eeqqsalLsRI...iknvekLnesvvelnkeleeinkkNknve 45 
                                   e++ s + +RI    + + k+ + + el+ +le+i ++N++++
  gi|91773226|ref|YP_565918.1| 419 ENTNSSINARIeesTNHIAKIEKRISELEDTLENIHSDNSELQ 461
                                   5556666677744456799********************9987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.2
                     DASH_Dad4  18 knvekLnesvvelnkeleeinkkNknv 44 
                                   kn++ L +   ++ ++le++ + Nk+ 
  gi|91773226|ref|YP_565918.1| 525 KNIHELRSVASDIIRSLEKAHNTNKEF 551
                                   577777777777788888888877765 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.6    0.0029      0.92      46     146 ..     377     477 ..     362     490 .. 0.85
   2 ?    2.5   7.1      0.48   1.5e+02      38     146 ..     450     564 ..     449     578 .. 0.61
   3 ?    1.5   3.2      0.96   3.1e+02      36     102 ..     511     577 ..     506     606 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0029
                 Jnk-SapK_ap_N  46 eeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleeke 126
                                   +e + el + ++  e+L+t+    +    + e+ l  i +  e+ ++ +++++e+ ++++ ++e+++++++d l+++ + +
  gi|91773226|ref|YP_565918.1| 377 DEIKKELADSKRSQESLYTNIGTLTGNIGELEQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDN 457
                                   566778888888888888888888888888899999********************************************* PP

                 Jnk-SapK_ap_N 127 aelkkeysklheretellkk 146
                                   +el++  ++ +e+  el  +
  gi|91773226|ref|YP_565918.1| 458 SELQTGLASIEENIAELTSS 477
                                   ****9999999977777655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.48
                 Jnk-SapK_ap_N  38 LeslasrneeeeaeleelreeleqLet.......eyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelk 111
                                   Le+++s+n e ++ l   +e++ +L++       + ++ +e+ +    e+ e+ d +++  + l    +  +e +++++  
  gi|91773226|ref|YP_565918.1| 450 LENIHSDNSELQTGLASIEENIAELTSsnamifsHIQKITEFGNSRSAEIFETNDRIDKIDESLTLLTQIQDESQKNIH-E 529
                                   7777777777777766666666666651000000555555555555599999999999877766655555555555666.5 PP

                 Jnk-SapK_ap_N 112 aknaadqlsrleekeaelkkeysklheretellkk 146
                                   ++++a  + r  ek ++ +ke ++ +++  el+k+
  gi|91773226|ref|YP_565918.1| 530 LRSVASDIIRSLEKAHNTNKEFKAETDERGELFKN 564
                                   55666555555556666667888877877777664 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.96
                 Jnk-SapK_ap_N  36 ElLeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqle 102
                                   E+L  l++ ++e + ++ elr   +++   +e+ ++ +k+++ e  e  + +++e   l e ve+  
  gi|91773226|ref|YP_565918.1| 511 ESLTLLTQIQDESQKNIHELRSVASDIIRSLEKAHNTNKEFKAETDERGELFKNELISLTEFVEKEF 577
                                   6666667777777777888888888888777777777777776666666666666666666665544 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.9     0.074        24      55     122 ..     399     475 ..     359     480 .. 0.69
   2 ?    7.2   7.7     0.015       4.8      23     112 ..     434     556 ..     423     579 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.074
                     Rootletin  55 l.........ssareleeeesadleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlr 122
                                   +         +s   +++++++   ++ a+ ee  +  +k+++  s L + le+ ++ n +L++ l  +++++ +l+
  gi|91773226|ref|YP_565918.1| 399 TltgnigeleQSLTVIKNDSENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELT 475
                                   24455555544445555555555568999999999999999999999999999999999999999999888877765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.015
                     Rootletin  23 aKvlqYkkrcseleqrlle...ktselektkltlll...................................ssareleeee 65 
                                   + + +  kr+sele+ l++   ++sel++      l                                    +++ + ++ 
  gi|91773226|ref|YP_565918.1| 434 NHIAKIEKRISELEDTLENihsDNSELQTG-----LasieeniaeltssnamifshiqkitefgnsrsaeiFETNDRIDKI 509
                                   334455556666665555544422222222.....1334456666665555566555444444443333222224444444 PP

                     Rootletin  66 sadleealakLeeErqrs.eklaqvnslLreqleearqaneaLtedlq 112
                                    ++l ++l++ ++E q++ ++l +v s     le+a+++n++++ + +
  gi|91773226|ref|YP_565918.1| 510 DESL-TLLTQIQDESQKNiHELRSVASDIIRSLEKAHNTNKEFKAETD 556
                                   4444.88999999988764899****99999**********9999876 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  12.0      0.33   1.1e+02      11      84 ..     403     475 ..     398     602 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.33
                      RasGAP_C  11 nlkeLeelgvisrennyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvl 84 
                                   n+ eLe++  + ++++ ++  ++I++ i +  +++ k+++ ++ le+tl+++++ n+ l++ l+s ++ i +  
  gi|91773226|ref|YP_565918.1| 403 NIGELEQSLTVIKNDS-ENTNSSINARIEESTNHIAKIEKRISELEDTLENIHSDNSELQTGLASIEENIAELT 475
                                   6778888777776666.556899*******************************************99997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1329  (0.0741257); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        77  (0.00429472); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              56  [number of targets reported over threshold]
# CPU time: 1.22u 0.33s 00:00:01.55 Elapsed: 00:00:00.54
# Mc/sec: 3899.72
//
Query:       gi|91773227|ref|YP_565919.1|  [L=607]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-25   87.7   0.1    1.9e-24   86.3   0.1    1.8  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.6e-13   49.8   0.1      5e-13   48.9   0.1    1.5  1  HisKA        His Kinase A (phospho-acceptor) domain
      6e-10   39.3   1.1    9.3e-09   35.5   0.1    2.9  3  PAS_9        PAS domain
    7.6e-10   39.5   0.0    1.3e-09   38.7   0.0    1.4  1  GAF          GAF domain
    6.8e-09   35.7   0.0      2e-08   34.2   0.0    1.8  2  PAS          PAS fold
    4.6e-06   27.0   0.0    8.3e-06   26.1   0.0    1.4  1  GAF_2        GAF domain
    1.3e-05   25.0   0.0    3.2e-05   23.9   0.0    1.6  1  PAS_8        PAS domain
    2.7e-05   24.4   0.0    5.9e-05   23.3   0.0    1.6  1  PAS_3        PAS fold
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.037   14.3   0.0    1.6  1  PAS_4        PAS fold
      0.022   14.7   0.0      0.056   13.4   0.0    1.7  1  HATPase_c_5  GHKL domain
      0.031   14.4   0.0      0.076   13.1   0.0    1.6  1  PAS_11       PAS domain
      0.041   14.2   0.0       0.14   12.5   0.0    1.9  2  GAF_3        GAF domain
      0.063   13.2   0.0       0.14   12.1   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
      0.071   12.8   0.4       0.16   11.6   0.0    1.7  2  PAS_12       UPF0242 C-terminal PAS-like domain


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 !   86.3   0.1   1.5e-27   1.9e-24       1     109 [.     497     606 ..     497     607 .] 0.96

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 1.5e-27
                                   EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHH CS
                     HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsi 80 
                                   gd+  L++++ +l++Na+kf++ +g+++v ++++ d l+i ++D+G G+  ++++ +f kf q d+s +r++gg+G+Gl+i
  gi|91773227|ref|YP_565919.1| 497 GDKVYLEKVFVHLLGNAIKFTPASGTVSVFMDRTRDSLHIAIKDTGVGVASDQIPYMFHKFRQlDGSLTRKYGGVGIGLYI 577
                                   688899**************88**********8779********************************************* PP

                                   HHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlp 109
                                   +k +v+ ++G+iw+ese+g Gt++++ lp
  gi|91773227|ref|YP_565919.1| 578 CKHIVDAHKGKIWMESEEGTGTDIHIILP 606
                                   *************************9887 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 !   48.9   0.1   3.9e-16     5e-13       1      65 [.     383     449 ..     383     451 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 3.9e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65 
                                   ++ +fla+++HELrtPL++i+g+  ++++e  gkl+e+++++ + + +++  l +lve lL +++ +
  gi|91773227|ref|YP_565919.1| 383 MKDEFLANLSHELRTPLNVIKGFGGLMSEErfGKLDERQRKAMDAVMRNTTILIELVESLLYITSVQ 449
                                   689************************88889*****************************998765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.44   5.6e+02      64     103 ..      12      51 ..       5      52 .. 0.76
   2 !   35.5   0.1   7.2e-12   9.3e-09       2     104 .]      79     180 ..      78     180 .. 0.88
   3 ?   -1.9   0.0         3   3.9e+03       4      23 ..     204     222 ..     201     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.44
                         PAS_9  64 vevvlirkngetfwvlltaspvkdddgelvgiivilrDit 103
                                   ++++l+  ng+t++++++  +   +++ ++++ + + D++
  gi|91773227|ref|YP_565919.1|  12 FDLELVQVNGNTIPIHMNTKAASIGGRSYQLVNFMFSDVS 51 
                                   778889999*****99988777666666666667777777 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 7.2e-12
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirkngetfwv 78 
                                   dg++++  d ++ ++N ++l+++Gy+++ev+g +++ l+  +p ++++l ++++ +         ++++ li k g+ ++v
  gi|91773227|ref|YP_565919.1|  79 DGVVLI-YDLKVKFVNSKVLNITGYDRDEVMGSDFFKLI--SPGDRSTLMKLYQKILHkdknVRDRYDTFLISKYGKNIPV 156
                                   677776.466577**************************..99999999999999999999888899999*********** PP

                         PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                   ++t+s +  +    v+  +i+rDi++
  gi|91773227|ref|YP_565919.1| 157 EITVSFIEFNMVPAVM--IIFRDISD 180
                                   *******877655555..******96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3
                         PAS_9   4 ilidnpdgril.yaNeaalrl 23 
                                    +i  pdg i   +N+a++++
  gi|91773227|ref|YP_565919.1| 204 LFI-APDG-IDvAINKALEKI 222
                                   455.49**.999*****9987 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.1e-12   1.3e-09       3     133 .]     212     354 ..     210     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.1e-12
                                   HHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC..........EEEETTSHHHH...HHHHHSSSEEESTGGTS CS
                           GAF   3 eelldtvveelrellgadrvalylpdydGlhydipqasrw..........lfmkngrgicg...qvlatgqplvipdstpd 70 
                                   + + ++++e+++ l+++drv  ++  +dG  +  ++  +w            +k + +i+    + l++gq++ ++d+ + 
  gi|91773227|ref|YP_565919.1| 212 DVAINKALEKIGLLCECDRVGMFMLCQDG-FV-ADNTNEWcgkgvlchkeELQKIPVSIIPwimEQLSKGQVVFVTDVGKL 290
                                   66788999***********9998857777.55.777777788888877765566677777788899999*******86644 PP

                                   TTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHHH CS
                           GAF  71 prfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvaval 133
                                   p  a  +++dl+   girs+++ P+  d +  G ++l+n s+  +++++el  +q++   +++a+
  gi|91773227|ref|YP_565919.1| 291 PSQAS-KEKDLFMKKGIRSFISFPIYIDSKFAGFICLYNVSDceEWDENELTTMQMIMGIIGMAI 354
                                   44333.679******************************666778*************9999997 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.1   6.6e+03      82      94 ..      19      31 ..       6      39 .. 0.69
   2 !   34.2   0.0   1.6e-11     2e-08       2     112 ..      69     177 ..      68     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.1
                                  TTSSEEEEEEEEE CS
                           PAS 82 rdgrpihlevras 94
                                  ++g +i+++++++
  gi|91773227|ref|YP_565919.1| 19 VNGNTIPIHMNTK 31
                                  6888888888765 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 1.6e-11
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC. CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl. 81 
                                   ++++i+e + d+++++  d ++ +vN++   ++G++r+ev+g+ ++ li++ d+++l +l+++ l+  ++ r+   +f   
  gi|91773227|ref|YP_565919.1|  69 QYSTIVEKSNDGVVLI-YDLKVKFVNSKVLNITGYDRDEVMGSDFFKLISPGDRSTLMKLYQKILHKDKNVRDRYDTFLIs 148
                                   799*************.*************************************************************99* PP

                                   TTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                           PAS  82 rdgrpihlevraspvrdaggeilgflgvlrd 112
                                   + g+ i++e+++s + +       ++ ++rd
  gi|91773227|ref|YP_565919.1| 149 KYGKNIPVEITVSFIEFNMVP--AVMIIFRD 177
                                   **********99876666443..55555555 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   6.5e-09   8.3e-06      63     138 .]     276     355 ..     257     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.5e-09
                                   HHHTS-EEES-GGG-S-HHHHH...HHHHTT--EEEEEE-TTS---EEEEES.......--HHHHHHHHHHHHHHHHHHH CS
                         GAF_2  63 lrtgrpvilndleedpdkkglp...aghaglrsflavPlisegrvvGvlnlyankppa.fdeedlelLeelaeqiaiaie 138
                                   l +g+ v+++d+   p++ + +     + g+rsf+++P++ + +  G+++ly   + + +de +l+ ++++++ i+ aie
  gi|91773227|ref|YP_565919.1| 276 LSKGQVVFVTDVGKLPSQASKEkdlFMKKGIRSFISFPIYIDSKFAGFICLYNVSDCEeWDENELTTMQMIMGIIGMAIE 355
                                   456999*****99988888888888**************9999********86665556*******************98 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.5e-08   3.2e-05       2      46 ..      69     113 ..      68     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.5e-08
                         PAS_8   2 rlralfesspdgiavvdlgd.rivdvNqaalellGys.adlkgellg 46 
                                   ++ +++e s+dg+++++  d ++ +vN + l ++Gy+ +++ g+++ 
  gi|91773227|ref|YP_565919.1|  69 QYSTIVEKSNDGVVLIY--DlKVKFVNSKVLNITGYDrDEVMGSDFF 113
                                   699************98..557***************7777776663 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.6e-08   5.9e-05       3      69 ..      91     157 ..      89     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.6e-08
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyR..irrkdGeyrwve 69 
                                   +v+ +v +i+Gy+++e++g+  ++ +l+ p Dr+ +++ +q++l k++ +   y   ++ k G+ + ve
  gi|91773227|ref|YP_565919.1|  91 FVNSKVLNITGYDRDEVMGS--DFFKLISPGDRSTLMKLYQKILHKDKNVRDRYDtfLISKYGKNIPVE 157
                                   89******************..**********************9999775554311555566555555 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.9e-05     0.037      13     106 ..      85     179 ..      74     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                         PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...pgeerhyelrllPlrd 90 
                                    d++v ++N     + g++++e++G+ ++ l +++d+  l+  +++ l  ++ +++   + l    g+  ++e++++ +  
  gi|91773227|ref|YP_565919.1|  85 YDLKVKFVNSKVLNITGYDRDEVMGSDFFKLISPGDRSTLMKLYQKILHKDKNVRDRYDTFLiskYGKNIPVEITVSFI-- 163
                                   4899**********************************************99998877666677778888888888776.. PP

                         PAS_4  91 esGevigvlvisrDiT 106
                                   e   v +v++i+rDi+
  gi|91773227|ref|YP_565919.1| 164 EFNMVPAVMIIFRDIS 179
                                   5567888888888886 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.3e-05     0.056       8      93 ..     504     597 ..     498     605 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                   HATPase_c_5   8 vilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...........ekkkle.sskskkeehGiGlksire 76 
                                    ++  lL NAi    +       +++ + ++ +sl i i+ +  g           + ++l  s ++k +  GiGl   ++
  gi|91773227|ref|YP_565919.1| 504 KVFVHLLGNAIKFTPAS----GTVSVFMDRTRDSLHIAIKDTGVGvasdqipymfhKFRQLDgSLTRKYGGVGIGLYICKH 580
                                   57888888888766554....4788999999999999999996665555454444333555556688999*********** PP

                   HATPase_c_5  77 ivkkykgnlsieaedgl 93 
                                   iv+ +kg++++e e+g+
  gi|91773227|ref|YP_565919.1| 581 IVDAHKGKIWMESEEGT 597
                                   ************99985 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     6e-05     0.076      27      69 ..      99     140 ..      82     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-05
                        PAS_11  27 slglekeelvgrsiydLchpqdlstlkshlrevissngeatss 69 
                                    +g+ ++e++g  +++L++p d+stl++ +++++ +++++  +
  gi|91773227|ref|YP_565919.1|  99 ITGYDRDEVMGSDFFKLISPGDRSTLMKLYQKIL-HKDKNVRD 140
                                   5799******************************.76665544 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.14      80     129 .]     306     356 ..     270     356 .. 0.82
   2 ?   -2.3   0.0         4   5.2e+03     104     127 ..     413     436 ..     400     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                         GAF_3  80 draalavPLvagrqviGvlal.astkprafdaedlelleslArqiataier 129
                                    r+ +  P+++ ++  G+++l + ++++++d+ +l  ++ +++ i++aier
  gi|91773227|ref|YP_565919.1| 306 IRSFISFPIYIDSKFAGFICLyNVSDCEEWDENELTTMQMIMGIIGMAIER 356
                                   4888999****99********55779************************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4
                         GAF_3 104 kprafdaedlelleslArqiatai 127
                                   + +++d++++  +++++r + + i
  gi|91773227|ref|YP_565919.1| 413 RFGKLDERQRKAMDAVMRNTTILI 436
                                   345799**********99887766 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.14      53     115 ..     520     593 ..     510     604 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                   HATPase_c_2  53 egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikglvDev..ey...d 115
                                   +g+v+v ++++ ++l++ ++D G g    ++p    +        + +    G+Gl++ k++vD    ++   +
  gi|91773227|ref|YP_565919.1| 520 SGTVSVFMDRTRDSLHIAIKDTGVGVASDQIPYMFHKFRqldgslTRKYGGVGIGLYICKHIVDAHkgKIwmeS 593
                                   689**********************88888887766555788867777777889999*******9844335653 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 ?   11.6   0.0   0.00012      0.16      54     139 ..      77     164 ..      67     175 .. 0.73
   2 ?   -3.8   0.1       6.9   8.8e+03     108     132 ..     461     485 ..     450     489 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                        PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkfl.qdfseivqegleeWkralaklsskteskir....lvlKtKagqev 129
                                    n g++l+y     k+ f+N+++ +++G+  d+++ +df++++++g  +   +l +   ++++++r      l +K g+++
  gi|91773227|ref|YP_565919.1|  77 SNDGVVLIYD---LKVKFVNSKVLNITGYDRDEVMgSDFFKLISPGDRSTLMKLYQKILHKDKNVRdrydTFLISKYGKNI 154
                                   5778888885...5799**************9977489******9976655555554444444443111145567889999 PP

                        PAS_12 130 llncllgiip 139
                                   ++++++  i+
  gi|91773227|ref|YP_565919.1| 155 PVEITVSFIE 164
                                   8888888776 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.9
                        PAS_12 108 klsskteskirlvlKtKagqevlln 132
                                   +++s+ e+ i+lv+ + + + ++l+
  gi|91773227|ref|YP_565919.1| 461 NVESSLERAISLVASNIEKKRLMLK 485
                                   4556666777777666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3820.63
//
Query:       gi|91773228|ref|YP_565920.1|  [L=79]
Description: hypothetical protein Mbur_1248 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.5   0.2    7.1e-05   22.7   0.2    1.8  1  PAS_8     PAS domain
    9.2e-05   22.7   0.0    0.00019   21.6   0.0    1.5  2  PAS_9     PAS domain
     0.0019   18.2   0.0     0.0021   18.0   0.0    1.1  1  PAS       PAS fold


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 !   22.7   0.2   1.2e-08   7.1e-05       7      49 ..      33      77 ..       8      79 .] 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.2e-08
                         PAS_8  7 fesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqll 49
                                  +  +p g+++vd    ++vd+N+  +e+ G+s +d++g+++++++
  gi|91773228|ref|YP_565920.1| 33 LSLLPGGLVLVDvQTSQVVDMNPEGIEMIGLSkDDVLGKDCHTFF 77
                                  55678899999964448***********************98766 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.56   3.4e+03      76      92 ..      14      30 ..       5      36 .. 0.68
   2 !   21.6   0.0   3.2e-08   0.00019       5      40 ..      41      77 ..      37      79 .] 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.56
                         PAS_9 76 fwvlltaspvkdddgel 92
                                  +++ +  +p+ d+++ +
  gi|91773228|ref|YP_565920.1| 14 IPIGIASTPFDDAERSV 30
                                  66667778886666554 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 3.2e-08
                         PAS_9  5 li.dnpdgrilyaNeaalrllGyspeevlgksitdlf 40
                                  ++ d     ++++N+  ++++G s+++vlgk+++++f
  gi|91773228|ref|YP_565920.1| 41 VLvDVQTSQVVDMNPEGIEMIGLSKDDVLGKDCHTFF 77
                                  44244555799*************************9 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.6e-07    0.0021       5      46 ..      31      73 ..      27      79 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-07
                                  HHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCTTSBG CS
                           PAS  5 aileslpdpifvvD.edgrilyvNaaaeellGlsreevlgksl 46
                                  ++l+ lp + ++vD     ++ +N++  e+ Gls ++vlgk  
  gi|91773228|ref|YP_565920.1| 31 SFLSLLPGGLVLVDvQTSQVVDMNPEGIEMIGLSKDDVLGKDC 73
                                  678889********9999**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 552.83
//
Query:       gi|91773229|ref|YP_565921.1|  [L=195]
Description: hypothetical protein Mbur_1249 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-08   34.2  14.9      1e-07   31.1   7.7    2.1  2  GPDPase_memb   Membrane domain of glycerophosphoryl diester p
    0.00024   21.0  15.8    0.00024   21.0  15.8    2.4  2  UPF0259        Uncharacterised protein family (UPF0259)
     0.0012   18.7  18.4     0.0042   16.9  18.5    1.8  1  DUF975         Protein of unknown function (DUF975)
  ------ inclusion threshold ------
      0.029   13.6  13.2      0.043   13.0  13.2    1.2  1  CitMHS         Citrate transporter
      0.087   12.9  10.4       0.95    9.6   2.7    3.4  3  DUF624         Protein of unknown function, DUF624


Domain annotation for each model (and alignments):
>> GPDPase_memb  Membrane domain of glycerophosphoryl diester phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   2.6   0.00075       2.7     201     242 ..       8      51 ..       3      84 .. 0.59
   2 !   31.1   7.7   2.9e-11     1e-07     162     242 ..      82     163 ..      74     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00075
                  GPDPase_memb 201 keSwqltkknflrlllklllliliivivltvi..lsllllllql 242
                                   ++Sw+  k n+ ++++  +++++  ++++t++  +++l+++++ 
  gi|91773229|ref|YP_565921.1|   8 SRSWNAFKDNVAAFIVATIIVVFGSIFIVTIAplFYGLTYMAVK 51 
                                   68999999999988888888777777777765114555555544 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.9e-11
                  GPDPase_memb 162 ilivllylifylivfylaiRliftLPliilekkslkeAlkeSwqltkknflrlllkll.lliliivivltvilsllllllq 241
                                   ili ++y++++l  ++l+i li++ Pl++++++ + +A+keS  + k nf+  l+  + + i++++  +t+i+sl+++ ++
  gi|91773229|ref|YP_565921.1|  82 ILIGIGYMLLVLPGLILSILLIYSFPLLVIKDYGAMDAIKESIDISKPNFVDSLVLFIiVAIISAIGGITYIVSLVTIPII 162
                                   77899**********************************************984433303344445567788888877766 PP

                  GPDPase_memb 242 l 242
                                   +
  gi|91773229|ref|YP_565921.1| 163 T 163
                                   5 PP

>> UPF0259  Uncharacterised protein family (UPF0259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.7      0.17   5.9e+02     215     241 ..      11      37 ..       5      48 .. 0.64
   2 !   21.0  15.8   6.7e-08   0.00024     131     198 ..      71     136 ..      54     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.17
                       UPF0259 215 fsllskkiaflllnllsnlisailiiY 241
                                    +++++++a++++ +++ +  +i+i+ 
  gi|91773229|ref|YP_565921.1|  11 WNAFKDNVAAFIVATIIVVFGSIFIVT 37 
                                   455666666666666666666666654 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 6.7e-08
                       UPF0259 131 PklliLiflttlliqlGllllliPGiivaillslsPiillkekksildsikasvnitfknikliaPav 198
                                    k  +L+ ++ +li +G +ll++PG+i++ill +s  +l++++ + +d+ik s+ i+  n+  +   v
  gi|91773229|ref|YP_565921.1|  71 VKSWVLLLVSVILIGIGYMLLVLPGLILSILLIYSFPLLVIKDYGAMDAIKESIDISKPNF--VDSLV 136
                                   56678999***************************9999999**************98886..22222 PP

>> DUF975  Protein of unknown function (DUF975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  18.5   1.2e-06    0.0042      44     161 ..      19     150 ..       6     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                        DUF975  44 etilvssllellivlllgtl..ltlsavfvviklvkrkekvelkeslasfke..knfiklLvllllkelflllwsliallg 120
                                     ++v +++ +  +++++t+  l  ++ ++ +k  +  ekve+++ + +f++  k  + lLv  +l+++  +l++l+ l+ 
  gi|91773229|ref|YP_565921.1|  19 AAFIVATIIVVFGSIFIVTIapLFYGLTYMAVKGLRG-EKVEINDVFEGFNRfvKSWVLLLVSVILIGIGYMLLVLPGLIL 98 
                                   4555556666666677777655778999999999999.************4433444445566677777778888888888 PP

                        DUF975 121 lliiiislsla...........llsseieenlvvvllvlliilllivlilai 161
                                   ++++i+s+ l+             s  i++++ v+ lvl+ii+ +i +i +i
  gi|91773229|ref|YP_565921.1|  99 SILLIYSFPLLvikdygamdaiKESIDISKPNFVDSLVLFIIVAIISAIGGI 150
                                   8888888888899***999887667778888888888877776666555443 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  13.2   1.2e-05     0.043     116     281 ..      24     165 ..      12     181 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 116 lliplalaaniggaltpiGtpttraa.....arpglslpnllllalllvgllplvllfmfgvalalpvnapkvkkqkaiie 191
                                   ++i++++++    ++ p +  +t +a                                             ++ + ++++e
  gi|91773229|ref|YP_565921.1|  24 ATIIVVFGSIFIVTIAPLFYGLTYMAvkglrG---------------------------------------EKVEINDVFE 65 
                                   34444444444444444444444444444440.......................................5555555555 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxx.x.xxxxxxxxx RF
                        CitMHS 192 aiarsllpvatilllaykkveWsvlllfaGvfll................vgaleqtGilealadllga.g.gplvalalv 254
                                     +r++++++++l+++        +l+ +G +ll                  ++++ G ++a+ +++ + + +++v  +++
  gi|91773229|ref|YP_565921.1|  66 GFNRFVKSWVLLLVSV--------ILIGIGYMLLvlpglilsilliysfpLLVIKDYGAMDAIKESI-DiSkPNFVDSLVL 137
                                   5555555555555222........2222222222444444444444444445999999999999999.4433555554444 PP

                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                        CitMHS 255 lgliallsafisnvava.almapialgm 281
                                   ++++a++sa+ + + ++ ++++pi+  +
  gi|91773229|ref|YP_565921.1| 138 FIIVAIISAIGGITYIVsLVTIPIITLA 165
                                   4444444444444444423333333222 PP

>> DUF624  Protein of unknown function, DUF624
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.6     0.008        29      43      73 ..       5      34 ..       2      36 .. 0.67
   2 ?    9.6   2.7   0.00026      0.95       4      74 ..      24      91 ..      19      93 .. 0.69
   3 ?    5.8   0.1    0.0041        15      41      72 ..     116     147 ..      89     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.008
                        DUF624 43 sifktFweaYKknfkksnllglillliglil 73
                                   if++ w+a+K+n      +  i++++g i+
  gi|91773229|ref|YP_565921.1|  5 DIFSRSWNAFKDNVAAFI-VATIIVVFGSIF 34
                                  589999*******65555.555555555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00026
                        DUF624  4 lNllwllftllglvvfglfPAtaAlfavvrkwirkee.dssifktFweaYKknfkksnllglillliglill 74
                                   +++ +   + ++++++++P +  l+++  k +r+e+ +++ + + ++ + k ++   l+ +il+ ig++ll
  gi|91773229|ref|YP_565921.1| 24 ATIIVV---FGSIFIVTIAPLFYGLTYMAVKGLRGEKvEINDVFEGFNRFVKSWVLL-LVSVILIGIGYMLL 91
                                  444444...8899***********************555554445566777777654.44455555555554 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0041
                        DUF624  41 dssifktFweaYKknfkksnllglillligli 72 
                                       +k+ ++  K nf++s +l++i+++i +i
  gi|91773229|ref|YP_565921.1| 116 AMDAIKESIDISKPNFVDSLVLFIIVAIISAI 147
                                   55566777777799*************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 1375.80
//
Query:       gi|91773230|ref|YP_565922.1|  [L=361]
Description: MscS mechanosensitive ion channel [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  161.8   2.2    1.6e-47  161.8   2.2    2.2  3  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.017   15.4   1.7      0.017   15.4   1.7    2.4  3  EbsA        EbsA-like 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 ?   -3.2   0.4      0.55     5e+03      29      45 ..      34      50 ..      22      56 .. 0.56
   2 ?   -2.7   2.1      0.38   3.4e+03       4      24 ..      74      94 ..      72     118 .. 0.77
   3 !  161.8   2.2   1.8e-51   1.6e-47       4     206 .]     151     350 ..     148     350 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.55
                                  HHHHHHHHHHHHHHCHH CS
                    MS_channel 29 avlGalglalglalkdl 45
                                   +  +l++++ l++k++
  gi|91773230|ref|YP_565922.1| 34 ISSIILAFGVDLVFKKV 50
                                  22234555566666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.38
                                  HHHHHHHHHHHHHHHTTT--S CS
                    MS_channel  4 lkiliivvgilivlsllgvnv 24
                                  +++++i++gi ++ls++g+  
  gi|91773230|ref|YP_565922.1| 74 IYYTLIFFGIFLALSVVGIGE 94
                                  679999999999999999865 PP

  == domain 3  score: 161.8 bits;  conditional E-value: 1.8e-51
                                   HHHHHHHHHHHHHH.HTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS.SEEEEEEEE-SS CS
                    MS_channel   4 lkiliivvgilivl.sllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig.dieGtVediglr 82 
                                     i+i++vg+ +++  ++g+nv+ l+a++G++g+a+++a+kd is++++G+ ++++kpfk GD++eig + +G V+++g+r
  gi|91773230|ref|YP_565922.1| 151 SDIIIVLVGLGMIIeGVWGINVGPLFASAGIVGIAIAFAAKDAISQFFGGLSIYYDKPFKNGDRIEIGdGQIGLVQEVGIR 231
                                   5678888887666626899*************************************************999********** PP

                                   EEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE CS
                    MS_channel  83 ttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldef 163
                                   +t+i +f +++++iPns +++++i+N++  ++++ +k++igv+y+sd   ++kv e+l+++ +    vl+d+ + v++d+ 
  gi|91773230|ref|YP_565922.1| 232 STRILDFYNNMIIIPNSIIANNKIINYTSPQPQMMVKITIGVEYGSD---VSKVKEVLLKIGNDIDLVLDDPSPSVRFDNH 309
                                   ***********************************************...******************************* PP

                                   -SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                    MS_channel 164 gdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                   gd sl+f +  +vk   p+e++sv +e+n  i  +++++gi i
  gi|91773230|ref|YP_565922.1| 310 GDFSLDFALILWVKY--PSEKFSVINEVNTMIDIEFKKAGIGI 350
                                   ***************..***********************976 PP

>> EbsA  EbsA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.74   6.7e+03      43      56 ..      28      41 ..      18      57 .. 0.53
   2 ?   15.4   1.7   1.9e-06     0.017      33      87 ..      66     122 ..      64     127 .. 0.77
   3 ?   -1.7   0.1      0.38   3.4e+03      55      85 ..     229     259 ..     224     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.74
                          EbsA 43 snlvlllflvlvil 56
                                  ++ ++++  ++++ 
  gi|91773230|ref|YP_565922.1| 28 VAALIIISSIILAF 41
                                  33333333333333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.9e-06
                          EbsA  33 llEnt.riylksnlvlllflvlvilgfkryliieedkliiks.lrffkkkkielseI 87 
                                   +lE   r+   +++++++fl+l ++g+  y+ i  ++l+++  ++++  + +++++I
  gi|91773230|ref|YP_565922.1|  66 VLEAVkRPIYYTLIFFGIFLALSVVGIGEYFFIATNNLLLTLlALVWLFALVNINKI 122
                                   56654145667899***********************88876356666666666655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.38
                          EbsA  55 ilgfkryliieedkliikslrffkkkkiels 85 
                                   ++   r l + ++ +ii +  + ++k i++ 
  gi|91773230|ref|YP_565922.1| 229 GIRSTRILDFYNNMIIIPNSIIANNKIINYT 259
                                   5666788888888888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2366.61
//
Query:       gi|91773231|ref|YP_565923.1|  [L=107]
Description: hypothetical protein Mbur_1251 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.029   14.3   0.2       0.18   11.7   0.1    1.9  2  DUF1899         Domain of unknown function (DUF1899)
       0.08   12.6   0.0       0.12   12.0   0.0    1.2  1  DNA_pol3_theta  DNA polymerase III, theta subunit


Domain annotation for each model (and alignments):
>> DUF1899  Domain of unknown function (DUF1899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     2e-05      0.18      11      55 ..       4      46 ..       3      52 .. 0.90
   2 ?    0.6   0.0      0.06   5.4e+02      12      26 ..      52      66 ..      50      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                       DUF1899 11 vfgkpakkeecydnirvsknawdsnlikaNpkflAvnwessGGGa 55
                                  v+ k+ak e+ ++ ++v+  a +  ++  N+ flA+n e  G  +
  gi|91773231|ref|YP_565923.1|  4 VYIKAAKDENIFTPCNVNVDAIKYIHCIENKVFLALNPEDVG--S 46
                                  899**********************************99885..3 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.06
                       DUF1899 12 fgkpakkeecydnir 26
                                   g+p + ee++dni 
  gi|91773231|ref|YP_565923.1| 52 AGEPINGEEQIDNIV 66
                                  5899999******84 PP

>> DNA_pol3_theta  DNA polymerase III, theta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.4e-05      0.12      12      45 ..      62      95 ..      56      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                DNA_pol3_theta 12 mdkinvdlaasgvafkERynmPVvaeqver.eqPe 45
                                   d i v l+as+ a  E y+mP++ +  e+ +qP+
  gi|91773231|ref|YP_565923.1| 62 IDNI-VSLIASAKAESETYDMPIILDFSEQiDQPK 95
                                  4444.99*****************99887646776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 743.50
//
Query:       gi|91773232|ref|YP_565924.1|  [L=189]
Description: hypothetical protein Mbur_1252 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.7   0.1       0.67   10.4   0.0    1.9  2  COX7a     Cytochrome c oxidase subunit VII


Domain annotation for each model (and alignments):
>> COX7a  Cytochrome c oxidase subunit VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.09   1.6e+03      21      35 ..      62      76 ..      55      79 .. 0.86
   2 ?   10.4   0.0   3.7e-05      0.67      13      37 ..      89     113 ..      86     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.09
                         COX7a 21 rgprsklylypyyal 35
                                   g r+ l +  yyal
  gi|91773232|ref|YP_565924.1| 62 DGNRDELCILGYYAL 76
                                  5889999999***98 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.7e-05
                         COX7a  13 sdkkplwlrgprsklylypyyalfa 37 
                                   ++ k l+l++p +k++ + y+al+a
  gi|91773232|ref|YP_565924.1|  89 KQAKKLHLKNPEDKYLPTYYIALLA 113
                                   55679**********9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 1380.63
//
Query:       gi|91773233|ref|YP_565925.1|  [L=63]
Description: excinuclease ABC (subunit A) [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00014   22.4   0.1    0.00015   22.3   0.1    1.1  1  ABC_tran     ABC transporter
     0.0069   16.1   0.1     0.0079   15.9   0.1    1.2  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.038   14.5   0.1      0.045   14.2   0.1    1.1  1  AAA_23       AAA domain
      0.066   13.1   0.0      0.066   13.1   0.0    1.1  1  RsgA_GTPase  RsgA GTPase
       0.07   13.0   0.0       0.11   12.4   0.0    1.4  2  APS_kinase   Adenylylsulphate kinase
      0.098   13.0   0.0       0.11   12.9   0.0    1.1  1  AAA_16       AAA ATPase domain
       0.16   12.2   0.0       0.19   12.0   0.0    1.2  1  AAA_22       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   5.8e-08   0.00015       2      36 ..      17      52 ..      16      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.8e-08
                                  EEEEEEEETTSEEEEEESTTSSHHHH.HHHHTTSS- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      ABC_tran  2 knvslklkegekvaivGenGaGKStL.lkllagllk 36
                                  kn+ lk++ +++++i+G +G+GKS+L + +++ +++
  gi|91773233|ref|YP_565925.1| 17 KNIGLKFSCDKLIVITGLSGSGKSSLpFDMIYAEVQ 52
                                  89***********************96778877765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.1e-06    0.0079      18      38 ..      22      42 ..      15      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.1e-06
                        AAA_29 18 eidlkgatlltGpsGsGKSTl 38
                                  +++ +  +++tG sGsGKS+l
  gi|91773233|ref|YP_565925.1| 22 KFSCDKLIVITGLSGSGKSSL 42
                                  566566899**********98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.8e-05     0.045      16      35 ..      22      42 ..      12      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                        AAA_23 16 dF.skgltlItGpNGaGKTTi 35
                                   F  ++l +ItG  G+GK+++
  gi|91773233|ref|YP_565925.1| 22 KFsCDKLIVITGLSGSGKSSL 42
                                  564569*************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.066      99     115 ..      26      42 ..       6      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                   TSEEEEECSTTSSHHHH CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStL 115
                                   dk++v+ G SG GKS+L
  gi|91773233|ref|YP_565925.1|  26 DKLIVITGLSGSGKSSL 42 
                                   599*************9 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         3   7.7e+03     126     133 ..      11      18 ..       6      20 .. 0.51
   2 ?   12.4   0.0   4.2e-05      0.11       4      22 ..      28      46 ..      25      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3
                                   HHTTSSSS CS
                    APS_kinase 126 areGeike 133
                                   are +ik+
  gi|91773233|ref|YP_565925.1|  11 ARECNIKN 18 
                                   45555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                                  EEEEESSTTSSHHHHHHHH CS
                    APS_kinase  4 vvwltGlsgsGKstianal 22
                                   + +tGlsgsGKs++ + +
  gi|91773233|ref|YP_565925.1| 28 LIVITGLSGSGKSSLPFDM 46
                                  689***********98765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.1e-05      0.11      25      40 ..      27      42 ..      20      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                        AAA_16 25 elvllsGesGvGKssl 40
                                   l++++G sG+GKssl
  gi|91773233|ref|YP_565925.1| 27 KLIVITGLSGSGKSSL 42
                                  6899***********9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.4e-05      0.19       6      21 ..      27      42 ..      24      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                        AAA_22  6 gilvvtGesGtGKTtl 21
                                  +++v+tG sG+GK+ l
  gi|91773233|ref|YP_565925.1| 27 KLIVITGLSGSGKSSL 42
                                  789***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 382.56
//
Query:       gi|91773234|ref|YP_565926.1|  [L=294]
Description: heat shock protein HtpX [Methanococcoides burtonii DSM 6242]
Scores for complete 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  135.2   0.2      4e-39  134.4   0.0    1.5  2  Peptidase_M48  Peptidase family M48
    4.8e-07   29.3   0.2    1.5e-05   24.4   0.0    2.2  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.029   14.8   3.4      0.029   14.8   3.4    2.0  2  PhoR           Phosphate regulon sensor protein PhoR
       0.16   11.9   0.6       0.57   10.2   0.0    2.2  2  Sugarporin_N   Maltoporin periplasmic N-terminal extension
       0.17   12.1   0.1       0.32   11.2   0.1    1.4  1  DUF4157        Domain of unknown function (DUF4157)
        0.9    9.0   7.9        2.1    7.8   0.5    3.0  3  DUF1129        Protein of unknown function (DUF1129)


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 ?   -3.0   0.3       1.8   5.3e+03      99     125 ..      18      44 ..      12      58 .. 0.50
   2 !  134.4   0.0   1.4e-42     4e-39       2     195 ..      72     288 ..      71     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                                   HHHTT-SHHHHHTT--S---HHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48  99 allisraeedaagafldalavliglli 125
                                   +ll ++  ++ a+ f++ +++++++l 
  gi|91773234|ref|YP_565926.1|  18 FLLAAVYLAFLAFLFYAGAPQMFMVLF 44 
                                   344444445555555555555444443 PP

  == domain 2  score: 134.4 bits;  conditional E-value: 1.4e-42
                                   --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsv 81 
                                   +++++l++++ +l + a+l  p+++v+vvn +  NAFa+g+g ++  +++t+gL+ + l++ el+aVl+HEl+H+k+r+++
  gi|91773234|ref|YP_565926.1|  72 QEAPDLHQTITRLCAIADL--PMPRVAVVNTSIPNAFATGRGPKNaVVAVTTGLM-DQLNQGELEAVLAHELSHVKNRDMA 149
                                   7899***************..********************98888*********.************************* PP

                                   HHHHHHHHHHHHHHHHHHH.....HTT-SHHHHHTT--S---HHHHHHHHHHTT...HHHHHHHHHHHHHHHHTTT.HHHH CS
                                   xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48  82 vslivsllasillllglal.....lisraeedaagafldalavliglliillfl...alSRkrEyqADeagvellkrakdl 154
                                   + +i s ++++++++++       +++  ++++ ++ + a+ ++ +l+ i++fl   alSR+rE+ AD+ ++ ++ ++ +l
  gi|91773234|ref|YP_565926.1| 150 ILTIASFISTMAFYIVRYSfyfggMGGMGGRRKESGGIVAIWIVSLLVWIISFLlirALSRYREFAADKGSAVITGQPSNL 230
                                   *********999998865411111333334444444444444444444444444889************************ PP

                                   HHHHHHHHHHTT--S---HHHH.................HHS-SS--HHHHHHHHHH- CS
                                   xxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 155 vraliklakdlerqdvsaslrs.................ellstHPplleRiqalkel 195
                                   ++al k++  + r ++++  +                   llstHP +++Ri+al+++
  gi|91773234|ref|YP_565926.1| 231 ASALTKISGIMPRIPKDDLREVegmnaffifpavsgsfmSLLSTHPTIEKRIAALEKI 288
                                   *************999999887999******************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     5e-09   1.5e-05     178     227 ..     114     163 ..      59     164 .. 0.90
   2 ?    3.0   0.1     0.016        49     106     128 ..     188     206 ..     181     239 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5e-09
                 Peptidase_M56 178 kprIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclfwf 227
                                     ++ + + ++ +l++ ele +l+HEl+H+k++D+ +  ++ +++ + ++
  gi|91773234|ref|YP_565926.1| 114 NAVVAVTTGLMDQLNQGELEAVLAHELSHVKNRDMAILTIASFISTMAFY 163
                                   556677788899*****************************999988776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.016
                 Peptidase_M56 106 lliWivgalilllyliaallvlk 128
                                   ++iWiv  l+     i ++l+++
  gi|91773234|ref|YP_565926.1| 188 VAIWIVSLLVW----IISFLLIR 206
                                   44455444442....22222221 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.4   9.6e-06     0.029       6      51 ..      17      62 ..      14      82 .. 0.90
   2 ?   -1.8   0.6       1.5   4.5e+03      31      39 ..     192     200 ..     184     211 .. 0.44

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.6e-06
                          PhoR  6 llrlallllaallvgllvgalaallllalllllawhlyqllrLsrW 51
                                  +++la+++la+l++ +++ga++++++l++ ++++ ++y+  rL  W
  gi|91773234|ref|YP_565926.1| 17 MFLLAAVYLAFLAFLFYAGAPQMFMVLFIGAFMGLQYYYSDRLVLW 62
                                  6789***************************************888 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                          PhoR  31 llallllla 39 
                                   +++ll++++
  gi|91773234|ref|YP_565926.1| 192 IVSLLVWII 200
                                   222222222 PP

>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       2.9   8.6e+03       5      14 ..     152     161 ..     148     165 .. 0.47
   2 ?   10.2   0.0   0.00019      0.57      22      37 ..     272     287 ..     259     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.9
                  Sugarporin_N   5 tlalaialll 14 
                                   t+a+ i+ ++
  gi|91773234|ref|YP_565926.1| 152 TIASFISTMA 161
                                   3444444444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                  Sugarporin_N  22 aaasltiEaRLaaLEk 37 
                                    ++  tiE R+aaLEk
  gi|91773234|ref|YP_565926.1| 272 LSTHPTIEKRIAALEK 287
                                   44556**********8 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.32      57      75 ..     128     146 ..     112     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                       DUF4157  57 esaagrellaHELtHvvqq 75 
                                   ++ + +++laHEL+Hv  +
  gi|91773234|ref|YP_565926.1| 128 NQGELEAVLAHELSHVKNR 146
                                   5556689*********765 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.3     0.033        99      86     135 ..      15      61 ..       9     108 .. 0.72
   2 ?    7.8   0.5   0.00071       2.1     113     170 ..     148     208 ..     115     218 .. 0.79
   3 ?    1.4   0.0     0.063   1.9e+02      90     132 ..     232     274 ..     229     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.033
                       DUF1129  86 LlllalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrllt 135
                                   L+++ l a+  ++la++  + + ++     +l++++ +Gl +++  rl+ 
  gi|91773234|ref|YP_565926.1|  15 LTMFLLAAVYLAFLAFLFYAGAPQM---FMVLFIGAFMGLQYYYSDRLVL 61 
                                   4455555555566666666556665...7778888899999999888765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00071
                       DUF1129 113 litlllvalvgGlamvlvyrlltre...kkkkkrpplwkrllilllllvvwlvlftlvall 170
                                   +  l++ ++++ +a+++v + ++         +r++   +++i +++l+vw++ f+l+  l
  gi|91773234|ref|YP_565926.1| 148 MAILTIASFISTMAFYIVRYSFYFGgmgGMGGRRKESGGIVAIWIVSLLVWIISFLLIRAL 208
                                   3445667888888999988888876777777888888888999999999999999887665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.063
                       DUF1129  90 alfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyr 132
                                   + ++ ++gi+  + k+   +  G+ + +++ +v+G +m l+ +
  gi|91773234|ref|YP_565926.1| 232 SALTKISGIMPRIPKDDLREVEGMNAFFIFPAVSGSFMSLLST 274
                                   5678899999999999988889****************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1858.74
//
Query:       gi|91773235|ref|YP_565927.1|  [L=190]
Description: hypothetical protein Mbur_1256 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.021   14.6   0.0    1.2  1  HeLo      Prion-inhibition and propagation


Domain annotation for each model (and alignments):
>> HeLo  Prion-inhibition and propagation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-06     0.021     108     173 ..      49     114 ..      15     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-06
                                   ....G-B--GGGS-HHHHHHH.HHHHHHHHHS----S-----EEE-SHHHHHHHHHHHHHHHHHHH CS
                          HeLo 108 sslalssereksfraefellkrlmrkaakkrqkrtslpkrlrWaivdkkkfeelvkdlkelvdsLe 173
                                   + +++s  + ++ r+e+e+l   ++k + ++ ++ + +  + W+i d k fe+lv++++ +  +L+
  gi|91773235|ref|YP_565927.1|  49 CFKSMSLSQYENTRKEIEGLLSYSTKETGTKYHIEKDKYNFLWVILDDKDFEDLVTNIHMISQTLI 114
                                   5556666777888899999988889999999999999*********************98777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1151.18
//
Query:       gi|91773236|ref|YP_565928.1|  [L=92]
Description: hypothetical protein Mbur_1257 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       354  (0.0197445); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 590.79
//
Query:       gi|91773237|ref|YP_565929.1|  [L=232]
Description: Phage shock protein A PspA/IM30 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-24   84.5  22.9    8.8e-24   84.3  22.9    1.0  1  PspA_IM30     PspA/IM30 family
    5.5e-05   23.4   8.5      0.039   14.3   0.6    3.4  3  Flagellin_C   Bacterial flagellin C-terminal helical region
     0.0093   16.0  11.4       0.12   12.4   3.3    3.0  3  DUF1664       Protein of unknown function (DUF1664)
  ------ inclusion threshold ------
      0.032   14.5  10.5       0.71   10.2   3.3    2.9  2  DUF5082       Domain of unknown function (DUF5082)
      0.046   13.5   0.0       0.24   11.2   0.0    2.2  2  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
       0.13   12.9   8.4        3.3    8.4   0.5    3.1  3  YabA          Initiation control protein YabA
       0.14   12.2   6.0         13    5.9   3.4    3.0  3  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
       0.76    8.6  17.4       0.27   10.0   7.1    2.3  2  Spc7          Spc7 kinetochore protein
        1.7    8.5  15.4       0.66    9.8   2.1    3.7  4  DivIC         Septum formation initiator
        1.7    8.3  11.2        2.1    8.0   6.9    2.8  2  SHE3          SWI5-dependent HO expression protein 3
        2.6    8.2   6.7        1.9    8.7   0.1    3.1  3  MbeD_MobD     MbeD/MobD like
        2.6    5.9   8.6          3    5.6   0.5    2.0  2  V_ATPase_I    V-type ATPase 116kDa subunit family
        3.2    7.8  14.1       0.77    9.8   9.1    2.5  3  FlxA          FlxA-like protein
        4.4    7.1  12.7        8.2    6.2   0.6    2.9  2  DUF724        Protein of unknown function (DUF724)
        4.7    7.6   9.7        3.5    8.0   0.4    3.2  2  CCDC-167      Coiled-coil domain-containing protein 167
        6.2    7.3  14.7       0.19   12.1   1.5    4.1  3  CLZ           C-terminal leucine zipper domain of cyclic nucl
        8.1    7.0  21.0       0.44   11.1   9.5    3.2  2  APG6_N        Apg6 coiled-coil region
        8.2    6.8  10.1         16    5.8   0.4    4.6  4  Osmo_CC       Osmosensory transporter coiled coil


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 !   84.3  22.9   8.9e-27   8.8e-24       1     220 [.       2     231 ..       2     232 .] 0.94

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 8.9e-27
                     PspA_IM30   1 gifkrllrllraniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkg 81 
                                   ++f+r+ ++l+a++++ +  +eDP   l+   +   + l+ +++ +a+v +++k+l+ +  +  + + kl  +A+ A +  
  gi|91773237|ref|YP_565929.1|   2 SLFNRMETVLKAKMNKIVNRMEDPRETLDYSYEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSIDKLAGQARDAIKSD 82 
                                   58*******************************999********************************************* PP

                     PspA_IM30  82 eeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqkslgkls..t 160
                                   +e+LAr al+++  l  q+++l++q a++ +  ++l ++ ++l tk+e +++kke++ka+  aa aq ++++s+ ++s   
  gi|91773237|ref|YP_565929.1|  83 REDLARLALERKGALDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTAAEAQVNISESVSGISeeM 163
                                   ******************************************************************************555 PP

                     PspA_IM30 161 esatdslerieeKieerearadaaaelae.........saqd..ldakleaagiqkevseqvlarlkaeqg 220
                                   ++   + er e+K e+++ara+a  el +         s  +   d +l+   ++ +v e +la+l++e+g
  gi|91773237|ref|YP_565929.1| 164 ADVGLAVERAENKTEDMKARASALDELIDagtlddftsS--GddIDRELAKISAESNV-ETELAKLRQEEG 231
                                   5556678********************977788776533..15699999999999999.********9886 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 ?    2.7   0.4      0.17   1.7e+02       8      45 ..      40      77 ..      34      86 .. 0.82
   2 !   14.3   0.6     4e-05     0.039       4      52 ..      97     145 ..      95     153 .. 0.85
   3 !   10.2   0.1   0.00073      0.73       4      41 ..     152     189 ..     149     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCH CS
                   Flagellin_C  8 itdldkvrselGavqnRlesaitnlkaqsenlkaaesr 45
                                  +++++   +++ ++++Rl+ + ++l++ ++ l+ + ++
  gi|91773237|ref|YP_565929.1| 40 LQGVKRGVADVATSKKRLQLQRSKLMQSIDKLAGQARD 77
                                  67788888999999999999999999999999888776 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHHHH CS
                   Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrledvDpa 52 
                                   +d ++++ld++ +elG  q +l  a ++l++ +e + ++++ ++   +a
  gi|91773237|ref|YP_565929.1|  97 LDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTA 145
                                   5667899*********************************999865444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00073
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHH CS
                   Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaqsenlka 41 
                                   ++e +++++++ +++G++ +R e+ ++ +ka  + l++
  gi|91773237|ref|YP_565929.1| 152 ISESVSGISEEMADVGLAVERAENKTEDMKARASALDE 189
                                   8999**************************99888765 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   0.7    0.0059       5.9      55     116 ..      13      74 ..       2      81 .. 0.80
   2 ?    5.6   0.6     0.015        15      56     124 .]      49     115 ..      40     115 .. 0.73
   3 !   12.4   3.3   0.00012      0.12      49     121 ..     110     181 ..     101     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0059
                       DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                   +++++  +++++  +++d + ++q e+ + +k+ v++v    ++++ + +++ + + +l+++
  gi|91773237|ref|YP_565929.1|  13 AKMNKIVNRMEDPRETLDYSYEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSIDKLAGQ 74 
                                   455566666666668899999**********************9999999999999999876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                       DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve.svkeaveglesklerieekQ 124
                                   ++a+ k++L+ +  ++ +++d   +++ + ++ +++ redl+++  + + +++  v+gl+++++++ ++Q
  gi|91773237|ref|YP_565929.1|  49 DVATSKKRLQLQRSKLMQSID---KLAGQARDAIKSDREDLARLALERKgALDIQVQGLDQQIAELGKEQ 115
                                   566667777666666555555...4677888999999999999987654278889999999999998887 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00012
                       DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                   +l + +++l a+ ++Ls +++   +k +  k+  ++ +++v+ ++e +s i+e++  v  ave  e+k e+++
  gi|91773237|ref|YP_565929.1| 110 ELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTAAEAQVN-ISESVSGISEEMADVGLAVERAENKTEDMK 181
                                   455667899999999*****9999999999999999999885.8999****************9999999886 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.7    0.0038       3.8       2      75 ..      12      86 ..      11      92 .. 0.85
   2 ?   10.2   3.3   0.00071      0.71      13      58 ..      95     140 ..      90     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                       DUF5082  2 ktkisklqaqiaelrseia.aleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnl 75
                                  k+k +k  +++++ r++++ ++e+++e L+ +k+ + d+  s k  + + +k   s + + G++++  +++r++l
  gi|91773237|ref|YP_565929.1| 12 KAKMNKIVNRMEDPRETLDySYEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSIDKLAGQARDAIKSDREDL 86
                                  5666777777888887776479*****************9999999999999999999*****999999999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00071
                       DUF5082  13 aelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse 58 
                                   + l  ++++l+++I++L +  +kl++++++l++k +  +++  + +
  gi|91773237|ref|YP_565929.1|  95 GALDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIK 140
                                   567789************9999999999999998877777766553 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 ?   11.2   0.0   0.00024      0.24      15      47 ..      17      49 ..       8      54 .. 0.84
   2 ?   -1.2   0.0       1.8   1.8e+03      28      43 ..     143     158 ..     139     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                          NOG1 15 davlFllDpseecgysleeQlsLleeikelfan 47
                                  ++v  + Dp e+  ys e+Ql++l+ +k  +a+
  gi|91773237|ref|YP_565929.1| 17 KIVNRMEDPRETLDYSYEKQLEMLQGVKRGVAD 49
                                  5556677********************998875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                          NOG1  28 gysleeQlsLleeike 43 
                                   ++  e Q+++ e++  
  gi|91773237|ref|YP_565929.1| 143 YTAAEAQVNISESVSG 158
                                   567899**99999865 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0033       3.3      11      76 ..      27      89 ..      14      93 .. 0.77
   2 ?    7.8   0.8    0.0049       4.9      13      61 ..      97     145 ..      88     162 .. 0.59
   3 ?    0.4   0.1      0.99   9.9e+02      16      52 ..     155     191 ..     148     230 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0033
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA 11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76
                                  e+l+ + e+ le l+ +k+ +a++    ++L+l+ +kl + ++   k + + + ++++ +e Larl
  gi|91773237|ref|YP_565929.1| 27 ETLDYSYEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSID---KLAGQARDAIKSDREDLARL 89
                                  4577778889999***************************994...44444555566666666665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0049
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXX CS
                          YabA  13 leeqleelleeleelkeelaelleenaeLeleneklrerleeeekkeke 61 
                                   l+ q++ l ++++el +e  +l+  +++L++  e +r++ e+ +++ ++
  gi|91773237|ref|YP_565929.1|  97 LDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTA 145
                                   5566666777777777777777777777777766666665332222222 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.99
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA  16 qleelleeleelkeelaelleenaeLeleneklrerl 52 
                                   +++ ++ee++++  ++++  ++ +++++  + l e++
  gi|91773237|ref|YP_565929.1| 155 SVSGISEEMADVGLAVERAENKTEDMKARASALDELI 191
                                   4555555555555555555555555555555555554 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 ?    5.5   0.2     0.017        17      44      97 ..      34      89 ..       3      92 .. 0.76
   2 ?    5.9   3.4     0.013        13      41     113 ..      95     168 ..      57     193 .. 0.76
   3 ?    4.9   0.3     0.024        24      24     106 ..     138     221 ..     137     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                  Baculo_PEP_C 44 etqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltnL 97
                                  e+qL+ l+  +k+ +a+++t   rl+ + ++L +++ +l+ + r ++++   +l+ L
  gi|91773237|ref|YP_565929.1| 34 EKQLEMLQG-VKRGVADVATskkRLQLQRSKLMQSIDKLAGQARDAIKSDREDLARL 89
                                  556666554.77777887777779999999999999999999998888877777776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                  Baculo_PEP_C  41 daietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllq 113
                                    a++ q++ l++++ +l +e +++l ++ ++L++++  +    +t++ + t+ ++++ n+  sv +i + ++ +  
  gi|91773237|ref|YP_565929.1|  95 GALDIQVQGLDQQIAELGKE-QDKLVAAEKRLSTKVEVFRtkkETIKAQYTAAEAQV-NISESVSGISEEMADVGL 168
                                   46777888888888885554.557888999999999988888899999999999998.578888888877766555 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.024
                  Baculo_PEP_C  24 airlqnvqilaq..latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq.dtlrneLtnlnsiltnLlssv 101
                                   +i++q +   aq  +++ +  i +++ ++  ++++  ++ ++++++ +++L++ + a + d++++  + ++ +l+ + ++ 
  gi|91773237|ref|YP_565929.1| 138 TIKAQYTAAEAQvnISESVSGISEEMADVGLAVER-AENKTEDMKARASALDELIDAGTlDDFTSSGDDIDRELAKISAE- 216
                                   56777666666522578888899999999999988.55566688888889988888777766776666666666666543. PP

                  Baculo_PEP_C 102 tNins 106
                                    N+++
  gi|91773237|ref|YP_565929.1| 217 SNVET 221
                                   45544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.4     0.016        16     140     216 ..      11      87 ..       5      95 .. 0.52
   2 ?   10.0   7.1   0.00028      0.27     144     239 ..      97     194 ..      93     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.016
                          Spc7 140 LkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeie 216
                                   Lk +++++++ +e+ +e+L+ + e+  e+l+ +++  a++    ++lq ++ +l ++  +   ++r+++++  ++++
  gi|91773237|ref|YP_565929.1|  11 LKAKMNKIVNRMEDPRETLDYSYEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSIDKLAGQARDAIKSDREDLA 87 
                                   66777777777777777776555555555555555555555555555443333333332333444444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00028
                          Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.id.keeLeelreelaelkaeieekkkel 222
                                   l+ +++gl+++ ++L k++++l ++ ++l+++ +  + + e+++++++  e+ ++ +e++  + ee+a++   +e+ ++++
  gi|91773237|ref|YP_565929.1|  97 LDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTAAEAqVNiSESVSGISEEMADVGLAVERAENKT 177
                                   555666666666666666666666666666666666666666666444443335558899999999999999999999999 PP

                          Spc7 223 aelqeqleeleekieel 239
                                   ++++++  +l+e i++ 
  gi|91773237|ref|YP_565929.1| 178 EDMKARASALDELIDAG 194
                                   99999999998877765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.015        15      12      54 ..      33      74 ..      31      90 .. 0.85
   2 ?    9.8   2.1   0.00066      0.66      18      60 ..     100     142 ..      98     143 .. 0.91
   3 ?   -0.1   0.0      0.81   8.1e+02      26      50 ..     163     187 ..     155     195 .. 0.62
   4 ?   -1.2   0.1       1.8   1.8e+03      29      39 ..     219     229 ..     204     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                                  XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                         DivIC 12 gkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54
                                  ++k+l  ++ +k+ +a+     ++l+ ++ +L + +++L  ++
  gi|91773237|ref|YP_565929.1| 33 YEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSIDKL-AGQ 74
                                  678999999999999999999999999999999999999.444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00066
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                         DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                   +++ l+q+ia+l +e +kl a +++L  +v+  +  ++ i+++
  gi|91773237|ref|YP_565929.1| 100 QVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQ 142
                                   57889**************************999999999865 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.81
                                   HHHHHHHHHHHHHHHHHHHHHHCC- CS
                         DivIC  26 iaalqaelaklkaeneeLeaevkdL 50 
                                   +a+    +++  ++ e+++a+ + L
  gi|91773237|ref|YP_565929.1| 163 MADVGLAVERAENKTEDMKARASAL 187
                                   5555555666666666666666665 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHH CS
                         DivIC  29 lqaelaklkae 39 
                                    + elakl++e
  gi|91773237|ref|YP_565929.1| 219 VETELAKLRQE 229
                                   34555555555 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.1       0.6   5.9e+02     180     205 ..       6      33 ..       2      71 .. 0.54
   2 ?    8.0   6.9    0.0021       2.1      49     117 ..      78     150 ..      48     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.6
                                   XXXXXXXXXXXXXXXXXXXXXXXXX..X CS
                          SHE3 180 nlesieeeknkkllkkleslaseld..l 205
                                   ++e + + k++k+ + +e  ++ ld   
  gi|91773237|ref|YP_565929.1|   6 RMETVLKAKMNKIVNRMEDPRETLDysY 33 
                                   5555555555555555555555555331 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                                   HHHHHHHHHHHH.HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH CS
                          SHE3  49 slkhENdnLssl.LkRK...errlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqY 117
                                    +k + + L  l L+RK   + +++ l+++++el ++ ++l + +k l++++e    ++++ ++++   ++q 
  gi|91773237|ref|YP_565929.1|  78 AIKSDREDLARLaLERKgalDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTAAEAQV 150
                                   4677777777655899944446899*****************************9999999999998887775 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.1      0.33   3.2e+02      45      65 ..      48      75 ..      15      80 .. 0.60
   2 ?    8.7   0.1    0.0019       1.9      42      68 ..      92     118 ..      76     120 .. 0.81
   3 ?   -1.5   0.0       2.8   2.8e+03      46      55 ..     151     160 ..     123     173 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
                     MbeD_MobD 45 a.......aLseqvtgLsqQVesLseqv 65
                                  a        L+ q  +L q +++L++q 
  gi|91773237|ref|YP_565929.1| 48 AdvatskkRLQLQRSKLMQSIDKLAGQA 75
                                  2222222257777777888888877775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                     MbeD_MobD  42 renaaLseqvtgLsqQVesLseqvrRl 68 
                                     ++aL  qv+gL qQ+ +L ++ ++l
  gi|91773237|ref|YP_565929.1|  92 ERKGALDIQVQGLDQQIAELGKEQDKL 118
                                   45679**************98876665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.8
                     MbeD_MobD  46 aLseqvtgLs 55 
                                    +se v g+s
  gi|91773237|ref|YP_565929.1| 151 NISESVSGIS 160
                                   3444444444 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 ?    5.6   0.5    0.0031         3     217     287 ..       9      79 ..       3      93 .. 0.86
   2 ?    3.9   2.8      0.01        10      74     138 ..      97     163 ..      79     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0031
                    V_ATPase_I 217 eqlkekikkicesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewklkv 287
                                   + lk+k++ki++ ++    +l+ s e++ e+l++v++ ++d+ +  ++ + ++++++++i k   + +  +
  gi|91773237|ref|YP_565929.1|   9 TVLKAKMNKIVNRMEDPRETLDYSYEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSIDKLAGQARDAI 79 
                                   56899**************************************9999999999999999877665555554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.01
                    V_ATPase_I  74 leeelekleeelkelnenleklkkelnelvelkavlekakefleee.eeeeeeeeseeeeee..keee 138
                                   l+ +++ l++++ el ++++kl +  ++l  + +v+++ ke ++++ ++ e++  + +e+ +  +ee 
  gi|91773237|ref|YP_565929.1|  97 LDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQyTAAEAQ-VNISESVSgiSEEM 163
                                   55677888889999999999999999999999999998888888774333333.33333222232222 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   9.1   0.00077      0.77      17      96 ..      52     140 ..      44     145 .. 0.75
   2 ?    8.6   3.5    0.0018       1.8      22      65 ..      97     150 ..      90     188 .. 0.71
   3 ?   -2.4   0.0       4.7   4.6e+03      60      67 ..     218     225 ..     201     231 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00077
                          FlxA  17 sqiasLqkQiknlqkqLkelses...deltkeekk.......kqqqliqaQIqqlqaQIaqlqqqqae.kaqekqqsekee 86 
                                   +  ++Lq Q ++l +++++l+ +     +++   +       +++  +  Q+q l +QIa l ++q++  a+ek+ s+k e
  gi|91773237|ref|YP_565929.1|  52 TSKKRLQLQRSKLMQSIDKLAGQardAIKSDR--EdlarlalERKGALDIQVQGLDQQIAELGKEQDKlVAAEKRLSTKVE 130
                                   55678999999999999999888763223333..234678899*******************8777652688888888888 PP

                          FlxA  87 kskskqegvn 96 
                                     ++k+e+++
  gi|91773237|ref|YP_565929.1| 131 VFRTKKETIK 140
                                   8888877765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0018
                          FlxA  22 LqkQiknlqkqLkelses.deltkeekk.........kqqqliqaQIqqlqaQI 65 
                                   L  Q++ l +q+ el+++ d+l + ek+         +++++i+aQ ++ +aQ+
  gi|91773237|ref|YP_565929.1|  97 LDIQVQGLDQQIAELGKEqDKLVAAEKRlstkvevfrTKKETIKAQYTAAEAQV 150
                                   444555555555555555455555555555555556677777777777777776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.7
                          FlxA  60 qlqaQIaq 67 
                                   +++ ++a+
  gi|91773237|ref|YP_565929.1| 218 NVETELAK 225
                                   22222222 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.6    0.0082       8.2     102     149 ..      31      78 ..      14      99 .. 0.82
   2 ?    4.2   5.8     0.035        34     131     181 ..     100     150 ..      92     230 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0082
                        DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlall 149
                                    +++k le+++++++ +++ +++k++l+ + ++l + i +l  q+  +
  gi|91773237|ref|YP_565929.1|  31 YSYEKQLEMLQGVKRGVADVATSKKRLQLQRSKLMQSIDKLAGQARDA 78 
                                   578999**********************************99887432 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.035
                        DUF724 131 eidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181
                                   +++ l+++i+el ++++ l + +++ + ++   ++++e+++ ++ ++e ++
  gi|91773237|ref|YP_565929.1| 100 QVQGLDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTAAEAQV 150
                                   455555556665555555554444444444444444444444444444433 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   3.0      0.27   2.7e+02      36      70 ..      75     120 ..      19     132 .. 0.69
   2 ?    8.0   0.4    0.0036       3.5       5      67 ..     155     232 .]     151     232 .] 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                      CCDC-167  36 e.......Resle....eEeaslkeqleenekeLksLrkeNrksml 70 
                                   +       Re+l     e +++l  q++  +++ ++L ke  k ++
  gi|91773237|ref|YP_565929.1|  75 ArdaiksdREDLArlalERKGALDIQVQGLDQQIAELGKEQDKLVA 120
                                   1222222244444555558999999999999999999999988766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0036
                      CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseee................ResleeEeaslkeqleenekeLksLrkeNrk 67 
                                    ++++ e++a++   +e+ e++ ++ +    +                 +++ +E+a+++ + ++ e eL++Lr+e +k
  gi|91773237|ref|YP_565929.1| 155 SVSGISEEMADVGLAVERAENKTEDMKARASAldelidagtlddftssGDDIDRELAKISAE-SNVETELAKLRQEEGK 232
                                   56667777777777777777777777766666666667677666667788888999999987.789**********987 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7      0.54   5.4e+02      37      44 ..      34      41 ..       4      74 .. 0.57
   2 ?   12.1   1.5   0.00019      0.19      15      60 ..     104     149 ..      91     152 .. 0.91
   3 ?    0.9   0.5       0.6   5.9e+02      43      43 ..     187     187 ..     154     229 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.54
                           CLZ 37 essLeaLq 44
                                  e++Le+Lq
  gi|91773237|ref|YP_565929.1| 34 EKQLEMLQ 41
                                  33333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
                           CLZ  15 LDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrk 60 
                                   LD++ a+ g+eq++l    +rL +++e++ t+ + + a+y++++++
  gi|91773237|ref|YP_565929.1| 104 LDQQIAELGKEQDKLVAAEKRLSTKVEVFRTKKETIKAQYTAAEAQ 149
                                   9999*************************************99886 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.6
                           CLZ  43 L 43 
                                   L
  gi|91773237|ref|YP_565929.1| 187 L 187
                                   2 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.5   0.00044      0.44      44     132 ..      49     149 ..       9     150 .. 0.74
   2 ?   -0.7   4.1         2     2e+03      50      75 ..     204     228 ..     149     232 .] 0.50

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                        APG6_N  44 k..........qdee.leeleeeleklekeeeelleeLkelekere.eleaelaaleeelealeeeeerfwreynelqlel 112
                                   +          q+++ ++++++   + +++ ++  e L++l  er+ +l+ +++ l ++ ++l +e+++ +   + l++++
  gi|91773237|ref|YP_565929.1|  49 DvatskkrlqlQRSKlMQSIDKLAGQARDAIKSDREDLARLALERKgALDIQVQGLDQQIAELGKEQDKLVAAEKRLSTKV 129
                                   144444444443333034444445678888888899999999988758********************************* PP

                        APG6_N 113 leleeeldsleaqyehaqnq 132
                                   + +  +++ ++aqy+ a++q
  gi|91773237|ref|YP_565929.1| 130 EVFRTKKETIKAQYTAAEAQ 149
                                   ***************99887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                        APG6_N  50 eeleeeleklekeeeelleeLkelek 75 
                                   +++++el+k+++e ++ ++eL++l +
  gi|91773237|ref|YP_565929.1| 204 DDIDRELAKISAE-SNVETELAKLRQ 228
                                   3333333333322.223333333333 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.77   7.7e+02      21      40 ..      47      66 ..      37      67 .. 0.82
   2 ?    5.8   0.4     0.016        16      20      39 ..     100     119 ..      84     122 .. 0.91
   3 ?    0.7   0.0      0.63   6.2e+02      16      30 ..     151     165 ..     141     175 .. 0.87
   4 ?    1.8   0.3      0.28   2.8e+02      22      32 ..     204     214 ..     197     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.77
                                  HHHHHHHHHHHHHHHHHHHH CS
                       Osmo_CC 21 vedideeIaaLeekRqrLvd 40
                                  v d+ +  ++L+ +R +L++
  gi|91773237|ref|YP_565929.1| 47 VADVATSKKRLQLQRSKLMQ 66
                                  7888888899*****99976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHHHHH CS
                       Osmo_CC  20 kvedideeIaaLeekRqrLv 39 
                                   +v+ +d++Ia+L + +++Lv
  gi|91773237|ref|YP_565929.1| 100 QVQGLDQQIAELGKEQDKLV 119
                                   68889*********999998 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.63
                                   HHHHHHHHHHHHHHH CS
                       Osmo_CC  16 nIEqkvedideeIaa 30 
                                   nI ++v  i ee+a+
  gi|91773237|ref|YP_565929.1| 151 NISESVSGISEEMAD 165
                                   8999********997 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHH CS
                       Osmo_CC  22 edideeIaaLe 32 
                                   +did e+a++ 
  gi|91773237|ref|YP_565929.1| 204 DDIDRELAKIS 214
                                   89999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1423  (0.0793686); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 1395.91
//
Query:       gi|91773238|ref|YP_565930.1|  [L=1280]
Description: hypothetical protein Mbur_1259 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-21   75.0   0.2    4.3e-20   72.2   0.0    2.6  2  AAA_27          AAA domain
    4.7e-15   56.6   4.8    4.7e-15   56.6   4.8    6.7  3  AAA_23          AAA domain
     0.0094   16.1   0.0      0.028   14.5   0.0    1.8  1  EELM2           Extended EGL-27 and MTA1 homology domain
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.051   13.3   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
       0.16   12.3   0.2       0.33   11.3   0.2    1.4  1  DUF3040         Protein of unknown function (DUF3040)
       0.28   10.6  18.3        1.3    8.4   0.1    2.5  2  SMC_N           RecF/RecN/SMC N terminal domain
       0.96   10.0   0.0       0.96   10.0   0.0    4.0  3  ABC_tran        ABC transporter
        2.6    8.3  17.0          2    8.7   0.3    4.3  4  BORCS7          BLOC-1-related complex sub-unit 7
        4.7    7.1  26.5        0.8    9.6   0.1    5.8  6  STAT_alpha      STAT protein, all-alpha domain
        5.3    7.3   5.6        4.1    7.7   0.1    3.7  4  Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_


Domain annotation for each model (and alignments):
>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   2.4e-23   4.3e-20       1     199 [.       1     198 [.       1     204 [. 0.86
   2 ?   -2.4   0.3       1.6   2.9e+03     164     207 .]     709     752 ..     705     752 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.4e-23
                        AAA_27   1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGiper.tkdnflhdakkLrigavle..ead 78 
                                   Mr++ L+++ +Gkf+d s++     ++l++++G NEAGKst+l+ i++++fG+p + ++ n   + k    g++l+   ++
  gi|91773238|ref|YP_565930.1|   1 MRITDLNIDGFGKFNDFSIND--LGEGLTVLHGENEAGKSTLLSFIRRMFFGFPDKrSNINHYPPFKGGLHGGRLSiqVDA 79 
                                   ****************99864..479***************************9751555665566655556665422677 PP

                        AAA_27  79 geelefaRrkgrkktlldaddqalpeevlaallggldretFealFgLdherLreGGealleaegelgqlLfeasaGl..as 157
                                   g   +++R  ++  ++  +d+   +e+ + ++lg++d++ Fe++++   ++L++  +  l + + +   L++a++G+  as
  gi|91773238|ref|YP_565930.1|  80 GIGYTIERYAQNGLNIYLPDGIIKDENEIGKILGNADKDVFENVYAFGLDELQDFNK--L-NGDSINGKLYSAGTGIgaAS 157
                                   8889************************************************98655..3.566788889***99873357 PP

                        AAA_27 158 lrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                   +  +++ +e+++ ++fkp+++k+ +in+  +el++ ++e+++
  gi|91773238|ref|YP_565930.1| 158 IPYIQNLFEKKKGAIFKPTGKKP-QINTLFTELNKIEQEIND 198
                                   77889999999************.**************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                        AAA_27 164 aLeaeadelfkprkskkrainealeeleeakkelreaqvraeew 207
                                    L+ e+d+l k++k+++ +++  +++l++++ ++++ q++ +ew
  gi|91773238|ref|YP_565930.1| 709 YLNLERDKLEKDKKASSDQYAFLEAKLDDMRYSYQNIQIEWNEW 752
                                   57788899999999999999999999999999999999998888 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   4.8   2.6e-18   4.7e-15       2     199 ..       6     234 ..       5     238 .. 0.63
   2 ?  -11.6  21.8        10   1.8e+04     131     198 ..     318     412 ..     265     573 .. 0.49
   3 ?  -30.5  41.0        10   1.8e+04      87     157 ..    1047    1119 ..     638    1155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 2.6e-18
                        AAA_23   2 Lkienfrsfrdqei.dFskgltlItGpNGaGKTTildAiklaLygetprlsrks.....grgfeksdveiesegkvkay.v 75 
                                   L i +f++f+d++i d++ glt+++G+N+aGK+T+l +i+ +++g++ + s+ +     ++g+  +  +i+ +  + +y +
  gi|91773238|ref|YP_565930.1|   6 LNIDGFGKFNDFSInDLGEGLTVLHGENEAGKSTLLSFIRRMFFGFPDKRSNINhyppfKGGLHGGRLSIQVD-AGIGYtI 85 
                                   789**********99******************************9988888887777755666566556555.3444557 PP

                        AAA_23  76 eltfenkdgry..trsiererelsk..kkgkttkkaklelleideleqfisellgskki..............ilnlilfl 138
                                   e+  +n  ++y  + +i++e e  k  +++++  +++   ++ del++f +   + + i              ++++i+ l
  gi|91773238|ref|YP_565930.1|  86 ERYAQNGLNIYlpDGIIKDENEIGKilGNADKDVFENVYAFGLDELQDFNKL--NGDSIngklysagtgigaaSIPYIQNL 164
                                   7777666666687666666555444114555556666666666888777664..444443345556666666644555544 PP

                        AAA_23 139 gqer....feefel.kdkkerleelekeleeledekkllekl........eqekekekeleeleeeleeilkel 199
                                    +++    f    +   kk +++ l +el+++e+e++ +e+         +++  keke+++l+++   +l++ 
  gi|91773238|ref|YP_565930.1| 165 FEKKkgaiF----KpTGKKPQINTLFTELNKIEQEINDIEDGqyaydqlhNDIRYKEKEISDLKNKKSALLEKQ 234
                                   444422222....2222333555555555555555555555545554446455556668888888877777765 PP

  == domain 2  score: -11.6 bits;  conditional E-value: 10
                        AAA_23 131 ilnlilflgqerfeefel.......kdkke.......................................rleelekeleel 165
                                   i++l   + + r+e++el       +                                           +l+++ +e++  
  gi|91773238|ref|YP_565930.1| 318 IFELGKGIEKYRAEKEELpkvkvslQ---TekkrfdsllqelgpdwdegklngfdrsipaidtvrkrhsELQAIDDEIKNT 395
                                   22222222222222222222211110...0122222333333333444433333333333333333333222222222222 PP

                        AAA_23 166 edekkllekleqekekekeleeleeeleeilke 198
                                    +  k +e+l                +  i+k+
  gi|91773238|ref|YP_565930.1| 396 RQNLKRIEDL----------------ISRINKK 412
                                   2222222222................2222221 PP

  == domain 3  score: -30.5 bits;  conditional E-value: 10
                        AAA_23   87 trsiererelskkkgkttkka..klelleideleqfisellgskkiilnlilflgqerfeefelkdkkerlee 157 
                                    + +i +e ++sk +  +++++  ++++ eid+  + +s++ gs k++++++  + ++++ ++el   ke+l+e
  gi|91773238|ref|YP_565930.1| 1047 HLIIMDELKNSKHDLLKVQESeiAENINEIDDELESLSNEKGSIKNQITQLEGYNEGSTLRLELGMLKEELNE 1119
                                    1222222222222222222221122222223333333333333333444444444444444444444444444 PP

>> EELM2  Extended EGL-27 and MTA1 homology 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       8      76 ..     464     532 ..     458     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                         EELM2   8 nvgenfqvpkvpkffldrssrsfkevtkaeaknedetskaltarLvYspsalervkekilkegakdkvi 76 
                                   ++g+n++ +++ +f+l++s ++++++++++ kn + + ++l+a+L ++  +++r++++ilk  +k ++i
  gi|91773238|ref|YP_565930.1| 464 DIGSNWDESSLGDFHLSSSAKEYSNAMASNFKNAELNIHDLEAKLEWAMLEINRINNNILKIDSKINAI 532
                                   69*******************************9999***********************955554444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.8e-05     0.051      11      39 ..      13      41 ..       3      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                        AAA_29 11 tfdghtieidlkg..atlltGpsGsGKSTll 39
                                   f++  ++i+  g   t+l G++++GKSTll
  gi|91773238|ref|YP_565930.1| 13 KFND--FSINDLGegLTVLHGENEAGKSTLL 41
                                  4444..3443333349**************9 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00018      0.33      21      79 ..     570     629 ..     561     634 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                       DUF3040  21 eDPklaaalrggaararrrslrrlavlavllfvaGllllvlG.vaaaa...vvlgvvGfvvml 79 
                                    D ++a+ + g+ + + +++++   + a + +v+G+++l +G v  +    +++ +v f+v++
  gi|91773238|ref|YP_565930.1| 570 RDDNFASIM-GKVPVTVSQHMPM--WPAGAFVVLGFAVLAAGfVYENLhggIIVCIVLFIVAI 629
                                   566899999.6666677776644..777778888********665555888666666666655 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 ?    8.4   0.1   0.00073       1.3       2      45 ..       3      45 ..       2      56 .. 0.88
   2 ?    4.0  14.0     0.016        30      41     211 ..     977    1271 ..     438    1277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00073
                                  EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAil 45
                                  ++ l i++F  ++ +  i ++ +++t++ G+N +GKs ll  i+
  gi|91773238|ref|YP_565930.1|  3 ITDLNIDGFGKFN-DFSINDLGEGLTVLHGENEAGKSTLLSFIR 45
                                  78899*******5.99999*******************997765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.016
                                    HHHHHHHCTT.TTTTTTC.HCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETT CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   41 ldAilFvLGersakklrs.eklsdlihk...skekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseyking 115 
                                    +d ++F L e+++k+l + +++s l+++    +e ++v++a++   +++  +    +  e+ +++   +++e  + +++
  gi|91773238|ref|YP_565930.1|  977 MDKLSFSLKEAENKHLDHlNDMSTLLKEgvaDSEDDFVSNAKIWDDLSQARNG--YNIAELHLRKLSGNDDEHLIIMDE 1053
                                    45556666666666664324566666655444444455555554433333222..344444444444444444444455 PP

                                    EEE-HHHHHHHHHCTT-STT........................................................... CS
                                    xxxxxxxxxxxxxxxxxxxx........................................................... RF
                         SMC_N  116 kevtkkevsellesagiske........................................................... 135 
                                     + +k+++ ++ ++++i ++                                                           
  gi|91773238|ref|YP_565930.1| 1054 LKNSKHDLLKV-QESEIAENineiddeleslsnekgsiknqitqlegynegstlrlelgmlkeelneksrewatysiaq 1131
                                    55555555443.3334444477788888888888889999999999999999999999999999999999999999999 PP

                                    ...........................................................CS-HHHHHHHHHHHHHH... CS
                                    ...........................................................xxxxxxxxxxxxxxxxx... RF
                         SMC_N  136 ...........................................................lLSgGektLvalaLlfA... 152 
                                                                                               +LS+G    + laL+f    
  gi|91773238|ref|YP_565930.1| 1132 hilskameryekerqpaviteaqsffinitggkyeriyspldssdifvedksgthknivELSRGTAEQLYLALRFGfik 1210
                                    9999999999999999999999999999999999999999999999999***************************966 PP

                                    .HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-.SCEEEE CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                         SMC_N  153 .iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka.dklvgv 211 
                                     + k + +   ++D+i  + D  + ++  + + e s++ Q++  + + +++e   d + gv
  gi|91773238|ref|YP_565930.1| 1211 eLGKHSESLPIVFDDILVNFDPVRSRNAISSISELSSSNQVLYFTCHPRTVEMFrDVVHGV 1271
                                    655555555679*********************************9999999874455555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00054      0.96      13      33 ..      26      46 ..      17      49 .. 0.88
   2 ?   -4.5   4.9        10   1.8e+04      41      41 ..     377     377 ..     174     503 .. 0.64
   3 ?   -0.7   0.2       1.1   1.9e+03      37      80 ..    1085    1152 ..    1061    1205 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                                  EEEEEESTTSSHHHHHHHHTT CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllag 33
                                  ++++ Gen aGKStLl+ + +
  gi|91773238|ref|YP_565930.1| 26 LTVLHGENEAGKSTLLSFIRR 46
                                  5789*************9977 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 10
                                   E CS
                                   x RF
                      ABC_tran  41 e 41 
                                   +
  gi|91773238|ref|YP_565930.1| 377 T 377
                                   0 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                                    -SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH.......................H CS
                                    xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................x RF
                      ABC_tran   37 pteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren.......................e 80  
                                    +++G+i+ + ++l+  +e + lr e+g+l++e + +++  +  +                       e
  gi|91773238|ref|YP_565930.1| 1085 NEKGSIKNQITQLEGyNEGSTLRLELGMLKEELNEKSREWATYSiaqhilskameryekerqpavitE 1152
                                    46666644444443356666777777777777444444322222334455555544432333333220 PP

>> BORCS7  BLOC-1-related complex sub-unit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0011         2      55      90 ..     385     420 ..     374     433 .. 0.83
   2 ?    8.5   1.5    0.0013       2.3      11      93 ..     449     532 ..     443     554 .. 0.88
   3 ?   -3.2   0.1       5.8     1e+04      69      94 ..     974     999 ..     965    1018 .. 0.57
   4 ?   -0.8   0.3      0.99   1.8e+03      66      95 ..    1070    1099 ..    1052    1103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                        BORCS7  55 faqqedaienteesLkkmsllttelnyqveaisksi 90 
                                   + + +d i+nt ++Lk+++ l+ ++n+++e +s ++
  gi|91773238|ref|YP_565930.1| 385 LQAIDDEIKNTRQNLKRIEDLISRINKKHEVVSGKL 420
                                   66789*************************998665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                        BORCS7  11 alfqeSKkeLtervevivndis.svakqvvkgSksseilmkaaksfaqqedaienteesLkkmsllttelnyqveaisksi 90 
                                   + ++  KkeLt+  ++i +++  s++   + +S  +e  +++a +f   e +i+  e+ L+   l ++++n++  +i ++i
  gi|91773238|ref|YP_565930.1| 449 TKLDSKKKELTDILQDIGSNWDeSSLGDFHLSSSAKEYSNAMASNFKNAELNIHDLEAKLEWAMLEINRINNNILKIDSKI 529
                                   446666***************62567889999999*************************999999999999999999988 PP

                        BORCS7  91 kql 93 
                                   + +
  gi|91773238|ref|YP_565930.1| 530 NAI 532
                                   776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.8
                        BORCS7  69 Lkkmsllttelnyqveaisksikqle 94 
                                   + +m +l+ +l++ +++  ++++ ++
  gi|91773238|ref|YP_565930.1| 974 ISEMDKLSFSLKEAENKHLDHLNDMS 999
                                   55555555555544444444443333 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.99
                        BORCS7   66 eesLkkmsllttelnyqveaisksikqlee 95  
                                     e+++++   +++l++++ +i+++i qle 
  gi|91773238|ref|YP_565930.1| 1070 AENINEIDDELESLSNEKGSIKNQITQLEG 1099
                                    467777777788888899999998888886 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.026        47       8      62 ..     182     238 ..     179     254 .. 0.69
   2 ?    0.1   1.2      0.35   6.3e+02      42     149 ..     388     409 ..     280     450 .. 0.65
   3 ?    0.7   1.0      0.25   4.4e+02       9      40 ..     386     417 ..     379     498 .. 0.54
   4 ?    9.6   0.1   0.00045       0.8       3      93 ..     786     891 ..     784     898 .. 0.88
   5 ?    2.1   0.2     0.091   1.6e+02      17      88 ..     907    1000 ..     892    1009 .. 0.49
   6 ?    5.9   1.2    0.0061        11       3      82 ..    1018    1097 ..    1016    1119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.026
                    STAT_alpha   8 leelrskvqeteqdirkLedeqeeFdfqyqelqkl..eqeraesekkelkkqkellq 62 
                                   +++l  + +++eq+i+++ed q  +d  ++ ++ +  e +  +++k+ l +++e+++
  gi|91773238|ref|YP_565930.1| 182 INTLFTELNKIEQEINDIEDGQYAYDQLHNDIRYKekEISDLKNKKSALLEKQEHVR 238
                                   66777788999***********99998888887772222233444444445555444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.35
                    STAT_alpha  42 leqeraesekkelkkqkellqqmlnaLdqkRkelvdklkellnlleslqeklldeeLieWKrrQqlagiGapfnesLDqlq 122
                                   +     + e k+ +++ + +++++++                                                       
  gi|91773238|ref|YP_565930.1| 388 I-----DDEIKNTRQNLKRIEDLISR------------------------------------------------------- 408
                                   2.....22222222222222222222....................................................... PP

                    STAT_alpha 123 kwfealaeliwqlrqqlkkleelrqkl 149
                                                             +
  gi|91773238|ref|YP_565930.1| 409 --------------------------I 409
                                   ..........................2 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.25
                    STAT_alpha   9 eelrskvqeteqdirkLedeqeeFdfqyqelq 40 
                                   + + +++++t q+++++ed+  + + +++ ++
  gi|91773238|ref|YP_565930.1| 386 QAIDDEIKNTRQNLKRIEDLISRINKKHEVVS 417
                                   44444444444444444444433332222222 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00045
                    STAT_alpha   3 eieqrleelrskvqeteqdirkLedeq.................eeFdfqyqelqkleqeraesekkelkkqkellqqmln 66 
                                   +++++l   +++v++ e+d +kL d+                  ++ + +y +  k   e+ +++++el +q e+l+  l+
  gi|91773238|ref|YP_565930.1| 786 DLHSQLLMCEKSVEDFEEDAKKLLDLCkcditgrpidldiiklhDDVNAEYANTGKV--EQLQQDHEELVEQSEMLNVALK 864
                                   677888888999999999999999999999999999999999999999999999999..899999999************* PP

                    STAT_alpha  67 aLdqkRkelvdklkellnlleslqekl 93 
                                   +   +R  +++k ke l +++   ++ 
  gi|91773238|ref|YP_565930.1| 865 EKEAERSVVLNKWKEWLAKYDLSSNMT 891
                                   ****************99998666655 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.091
                    STAT_alpha   17 eteqdirkLedeqeeFdfqyqelqkl.....................eqeraesekkelkkqkellqqmlna...Ldqk 71  
                                    e++ +i++L ++ e++   +  ++ +                     e  + + + ++   +k++l++++++   L+ +
  gi|91773238|ref|YP_565930.1|  907 EIQDNIKNLAENIESYTSSIDVYEDKirgtldvcgrkgsgfgfdtelE--TLRDDVEKAVSEKNQLDSLISEmdkLSFS 983 
                                    455666666666666666666655555666666666666666665431..22222222334444444444443333333 PP

                    STAT_alpha   72 Rkelvdklkellnlles 88  
                                     ke  +k+ + ln +++
  gi|91773238|ref|YP_565930.1|  984 LKEAENKHLDHLNDMST 1000
                                    33333333333333333 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.0061
                    STAT_alpha    3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlnaLdqkRkelvdklke 81  
                                    +i + l++ r+  +  e ++rkL  + +e+ + + el++ +++  + +++e++++ +++++ l++L++++ ++ +++ +
  gi|91773238|ref|YP_565930.1| 1018 KIWDDLSQARNGYNIAELHLRKLSGNDDEHLIIMDELKNSKHDLLKVQESEIAENINEIDDELESLSNEKGSIKNQITQ 1096
                                    566788899999999999**********************99****************************999888877 PP

                    STAT_alpha   82 l 82  
                                    l
  gi|91773238|ref|YP_565930.1| 1097 L 1097
                                    6 PP

>> Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_RAQPRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.4   2.6e+03      39      50 ..     203     214 ..     180     222 .. 0.68
   2 ?   -3.7   0.1       8.3   1.5e+04      24      52 ..     393     402 ..     382     411 .. 0.46
   3 ?   -1.5   0.0       1.7     3e+03       9      50 ..     784     833 ..     779     834 .. 0.70
   4 ?    7.7   0.1    0.0023       4.1       3      30 ..     963     991 ..     961     999 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                Plasmid_RAQPRD  39 hfdYdrlrrDle 50 
                                   +  Yd+l++D++
  gi|91773238|ref|YP_565930.1| 203 QYAYDQLHNDIR 214
                                   557899999986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.3
                Plasmid_RAQPRD  24 eraeaqakqeekaRvhfdYdrlrrDleri 52 
                                   ++++                   + l+ri
  gi|91773238|ref|YP_565930.1| 393 KNTR-------------------QNLKRI 402
                                   3333...................233333 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.7
                Plasmid_RAQPRD   9 LakllkqLdqlqalveraeaqakqe........ekaRvhfdYdrlrrDle 50 
                                   +  l++qL   +++ve+ e+ ak+         +   + +d+ +l++D++
  gi|91773238|ref|YP_565930.1| 784 INDLHSQLLMCEKSVEDFEEDAKKLldlckcdiTGRPIDLDIIKLHDDVN 833
                                   66788899999999999998888765555555433357788888888876 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0023
                Plasmid_RAQPRD   3 a.aEreeLakllkqLdqlqalveraeaqa 30 
                                   a +E+++L +l++++d+l+ ++++ae++ 
  gi|91773238|ref|YP_565930.1| 963 AvSEKNQLDSLISEMDKLSFSLKEAENKH 991
                                   669**********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1810  (0.100954); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); 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):              10  [number of targets reported over threshold]
# CPU time: 1.46u 0.36s 00:00:01.81 Elapsed: 00:00:00.57
# Mc/sec: 6737.15
//
Query:       gi|91773239|ref|YP_565931.1|  [L=436]
Description: metallophosphoesterase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-14   54.6   0.3    3.2e-14   53.9   0.3    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    7.4e-06   26.3   0.0    1.1e-05   25.7   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.3   3.5e-18   3.2e-14       3     203 ..      17     214 ..      15     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.5e-18
                                   EEEEESBTB................TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH... CS
                   Metallophos   3 ilvigDlHl................algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky... 63 
                                   +++ +DlHl                  + + +d++++++d ++++ ++d++l+ GD++d  d + + +   l+ l ++   
  gi|91773239|ref|YP_565931.1|  17 FVHAADLHLdspflglseintklsqVMAKATFDAYNNIIDLCIEK-NADFLLISGDIYDSADKSLYAQLKfLEGLKRLssa 96 
                                   79***********************9999**********888777.**************966664444423333333666 PP

                                   TSEEEEEC-TTSCHHHHHHHHHHHHHHH..HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCH CS
                   Metallophos  64 pipvylllGNHegfeeellnkygylgif..sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnlele 142
                                   +i  y+++GNH+      ln       +  s  w  +++ f++  +         ++  +G+       + +++++++++ 
  gi|91773239|ref|YP_565931.1|  97 GIAAYITHGNHD-----PLNG------WsaSLEWPANVKIFSGDDVET------VFVEKDGN------VIASINGISYRTK 154
                                   ************.....2222......222555666666665555555......55555555......8899999999999 PP

                                   HHHCCHHHHHH.HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                   Metallophos 143 apepgdewlkd.lekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                    +++  ++ k+ ++k +  +++i + H  + +g+g++   ++    lk+ + d++  GH+H 
  gi|91773239|ref|YP_565931.1| 155 HIQE--NLAKRfQKKDALSPFTIGMLHCTVDSGGGHYPYAPCSIQDLKETNYDYWALGHIHY 214
                                   8885..44444555899999999999*****888888888888877899999*********6 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.2e-09   1.1e-05       3     158 ..      17     244 ..      15     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.2e-09
                 Metallophos_2   3 laiiSDlH.....................snldaleavlealkevgvdaiihaGDl.eeeep.......evleellela.. 52 
                                   +++ +DlH                     + +da +++++   e ++d ++ +GD+   ++        ++le l++l   
  gi|91773239|ref|YP_565931.1|  17 FVHAADLHldspflglseintklsqvmakATFDAYNNIIDLCIEKNADFLLISGDIyD-SADkslyaqlKFLEGLKRLSsa 96 
                                   57788888888888888888888888888888999999999999999********842.3332344444566666666699 PP

                 Metallophos_2  53 ..pvlaVrGNnD....................................eev.veedvlreaaelgtdlpeeaelelagekv 94 
                                       ++ +GN+D                                    ++  +  +  + ++ l++++++++ l+   +++
  gi|91773239|ref|YP_565931.1|  97 giAAYITHGNHDplngwsaslewpanvkifsgddvetvfvekdgnviaSINgISYRTKHIQENLAKRFQKKDALS--PFTI 175
                                   9*******************************9999999988877765444677788888888888887777777..788* PP

                 Metallophos_2  95 lliHgdpl....gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..tya 158
                                   +++H + +    ++++a  +  + +e + d+ ++GH+H p+v ++ + ++v+ G ++++  g+ +  ++ 
  gi|91773239|ref|YP_565931.1| 176 GMLHCTVDsgggHYPYAPCSIQDLKETNYDYWALGHIHYPQVLET-DPYIVYSGNPQGRNPGELGerGCT 244
                                   *****9779976555555555555566777**********99988.566666666665544443333555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 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:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2569.47
//
Query:       gi|91773240|ref|YP_565932.1|  [L=118]
Description: hypothetical protein Mbur_1261 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-06   28.1   0.2    1.8e-06   27.6   0.2    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.046   13.7   1.2      0.068   13.2   1.2    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
      0.085   12.7   0.1      0.085   12.7   0.1    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   3.1e-10   1.8e-06      27      71 ..       6      46 ..       2      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.1e-10
                                  -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCC CS
                 Lactamase_B_2 27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavle 71
                                  e + +daVl++h H DH + +  lr+    ++p+y++kg+  +l+
  gi|91773240|ref|YP_565932.1|  6 EYRVVDAVLISHTHGDHAQYIHILRT----DIPIYCTKGTKTILQ 46
                                  66789*************88888888....59********99886 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   1.1e-05     0.068      41      58 ..       6      23 ..       1      33 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                                  GGGGEEEEE-SBSSHHHH CS
                   Lactamase_B 41 kpkdvdavilTHlHlDHi 58
                                  + + vdav+++H H DH+
  gi|91773240|ref|YP_565932.1|  6 EYRVVDAVLISHTHGDHA 23
                                  55679************8 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.4e-05     0.085      35      57 ..       8      30 ..       1     107 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                 Lactamase_B_3 35 eeaDlvlisqaledHahletlkq 57
                                  + +D+vlis+ + dHa+   + +
  gi|91773240|ref|YP_565932.1|  8 RVVDAVLISHTHGDHAQYIHILR 30
                                  679************98766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 825.23
//
Query:       gi|91773241|ref|YP_565933.1|  [L=173]
Description: hypothetical protein Mbur_1262 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-16   60.4   0.0    2.7e-16   59.9   0.0    1.1  1  DUF98       p-hydroxybenzoic acid synthase
     0.0073   16.0   0.0     0.0093   15.6   0.0    1.1  1  Chor_lyase  Chorismate lyase
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.028   14.3   0.0    1.5  1  UTRA        UTRA domain


Domain annotation for each model (and alignments):
>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   4.5e-20   2.7e-16       3     143 ..      27     167 ..      26     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 4.5e-20
                                   --S-HHHHHHHHHSS-EEEEEEEEEEEE--HHHHHHHTS-TT-EEEEEEEEEEETTEEEEEEEEEEEGGGS-HHHHH.... CS
                         DUF98   3 gDGsvTrhlelltqekveveliemeaeeseeeeapkeveelkkpllrRqVwlrangqklayAeSwwneeelekylke.... 79 
                                   +DGsvT  le++t+++v+v + +++++++++e         ++ +++R V l a++ +++ A S  ++e++  ++++    
  gi|91773241|ref|YP_565933.1|  27 TDGSVTFLLEIMTRKDVSVVTEAQHIVKADTEMSSLLKVPEGSDVNYRLVTLFAGDIPFVRALSLSPIERMPGNIRQdmmr 107
                                   8********************99999999999999999999****************************998888777777 PP

                                   SSS-HHHHHHHTT--BEEEEEEEEEEE--HHHHHHTSS-EEEEEEEEEEETTEEEEEEEEEEEG CS
                         DUF98  80 kdqpiwksLtkerlelfReirglalgeadeLeeafgekgpfwsRhYrlfhkgkpltvirEvFsp 143
                                   +d+pi+k+L+++ +e++R+ + +++ + d + +     ++++sR Y ++h+++ ++ i E F++
  gi|91773241|ref|YP_565933.1| 108 ADIPIGKILRNSGIETRRDFDNINITDDDPIFD----ISRVLSRSYHIVHDNNTMMWINERFPV 167
                                   9***************************98744....479**********************97 PP

>> Chor_lyase  Chorismate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.5e-06    0.0093      28     152 ..      29     159 ..      20     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                    Chor_lyase  28 gsLtrrlkalae.elrvelLaeswitlrddeeqllaseealsgwvRevilkgddrPlvfartliprssletqgfdlaqlGk 107
                                   gs+t  l+ ++  ++ v   a+ ++    +   ll+++e++    R v l + d+P+v a +l p   + ++  +  +  +
  gi|91773241|ref|YP_565933.1|  29 GSVTFLLEIMTRkDVSVVTEAQHIVKADTEMSSLLKVPEGSDVNYRLVTLFAGDIPFVRALSLSPIERMPGNIRQDMMRAD 109
                                   6666666665554677777777777788888899*******************************9999988887788899 PP

                    Chor_lyase 108 raLGellfsds.dvkR..dklevtrveae..leaLyaRRsrlsigaknvl 152
                                   +++G++l     + +R  d++++t ++    + ++++R   +  +++ ++
  gi|91773241|ref|YP_565933.1| 110 IPIGKILRNSGiETRRdfDNINITDDDPIfdISRVLSRSYHIVHDNNTMM 159
                                   9***9997654133332256777777655567888888888887777776 PP

>> UTRA  UTRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.7e-06     0.028      14      87 ..      51     125 ..      40     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-06
                                   EEEE--HHHHHHHTS-TTSEEEEEEEEEEETTEEEEEEEEEEEGGGTTTCHHHHHH..CS-HHHHHHHHHTTSEEE CS
                          UTRA  14 eevpasaeiaeaLglpagepvlrieRlrladgepvaleesylpaslvpdlleedle..egslyayleerlgvpitr 87 
                                     v+a+ e++ +L++p+g++v +     +a++ p++ + s  p ++ p+   +d+   + ++ ++l++  g++ +r
  gi|91773241|ref|YP_565933.1|  51 HIVKADTEMSSLLKVPEGSDVNYRLVTLFAGDIPFVRALSLSPIERMPGNIRQDMMraDIPIGKILRN-SGIETRR 125
                                   5689*********************************************9999986568888888888.7776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1333.41
//
Query:       gi|91773242|ref|YP_565934.1|  [L=103]
Description: hypothetical protein Mbur_1263 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-33  114.6   0.1    3.7e-33  114.5   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 !  114.5   0.1   2.1e-37   3.7e-33       1     103 []       1      99 [.       1      99 [. 0.99

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 2.1e-37
                                   -EEE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHHHHHH CS
                       DUF5611   1 mreYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaaldtvkk 81 
                                   m+eYk+KrGf++++ er++e++ ++f+++++++gd+l +s+g+ik+l+v++  ++k+lvvdt+  d +++dd+ +ldt+k+
  gi|91773242|ref|YP_565934.1|   1 MQEYKLKRGFSPDI-ERIYEEVGKCFPVDIDRDGDKLSISYGVIKELSVSM--NGKMLVVDTVM-DVSSDDDDLILDTNKR 77 
                                   9*************.************************************..***********.999************* PP

                                   HHHHHHHHH---GGGHHHHH-- CS
                       DUF5611  82 fndFLeeaTGydaKeRkkkakk 103
                                   f+dFL  aTGy+aKeR+++akk
  gi|91773242|ref|YP_565934.1|  78 FRDFLLLATGYTAKERRNQAKK 99 
                                   ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 611.72
//
Query:       gi|91773243|ref|YP_565935.1|  [L=561]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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    3.9e-18   66.0   0.0    1.6  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.1e-12   48.1   0.1      1e-08   35.4   0.0    3.0  3  PAS_9         PAS domain
    7.4e-11   41.8   0.1    1.1e-07   31.7   0.0    2.7  2  PAS_8         PAS domain
      1e-08   35.4   0.0     0.0011   19.2   0.0    3.1  2  PAS_4         PAS fold
    1.7e-06   28.0   0.0    6.7e-05   22.9   0.0    3.0  2  PAS           PAS fold
    0.00013   22.0   0.1     0.0015   18.5   0.0    2.3  2  HisKA         His Kinase A (phospho-acceptor) domain
    0.00017   21.7   0.0      0.026   14.7   0.0    3.2  2  PAS_7         PAS fold
    0.00096   18.9   0.0     0.0015   18.3   0.0    1.2  1  DDE_Tnp_ISL3  Transposase


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 !   66.0   0.0   1.8e-21   3.9e-18       8     110 ..     458     559 ..     453     561 .] 0.92

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.8e-21
                                   HHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHH CS
                     HATPase_c   8 qiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklve 86 
                                    ++ n ++Na+k++++++++e  ++  +  d  ++ v+DnGiG+  ed + +fe+f++   +++  +g GlGl+ivk+++e
  gi|91773243|ref|YP_565935.1| 458 TVFANYLSNAIKYSPEGSKVEFDVD--DlgDMCKVLVKDNGIGVLDEDKPFVFERFTR--LNSVHIKGAGLGLAIVKRIAE 534
                                   6899*********999999999999..44599**************************..7788899************** PP

                                   HTTTEEEEEEET.TTEEEEEEEEES CS
                     HATPase_c  87 lmgGeiwvesep.grGttftftlpl 110
                                   l++G++ v+++p g+G+ f++ l++
  gi|91773243|ref|YP_565935.1| 535 LHNGQVGVDDNPdGKGCAFWVILKK 559
                                   ********99999********9986 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00047       1.1       2     104 .]      26     129 ..      25     129 .. 0.76
   2 ?   -3.1   0.0       4.2   9.5e+03      34      57 ..     168     191 ..     161     207 .. 0.70
   3 !   35.4   0.0   4.5e-12     1e-08       2     104 .]     224     323 ..     223     323 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00047
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkng.etfwvll 80 
                                   +g+++ ++d ++ +aN  ++  l  + + v+g  i++++++ +++ e +r++  + +  + ++v ++   kng +  w + 
  gi|91773243|ref|YP_565935.1|  26 VGVAVLDSDLKVKWANHFLMHELCGQINHVVGVEISQILSSISNSSECFRHFDVTDQLcNGERVVLHTPLKNGvGHRWLEH 106
                                   57888889998889999999998889*************44444444444444444435467777777777889******* PP

                         PAS_9  81 taspvkdd.dgelvgiivilrDite 104
                                   ++sp+ +d    + g+i+ + Dit+
  gi|91773243|ref|YP_565935.1| 107 RLSPISSDiY--NEGWIGYFYDITD 129
                                   *****66544..55577******96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.2
                         PAS_9  34 ksitdlfvtdpeanerlraaleqg 57 
                                   k++tdl+ + + ++er++a+ e  
  gi|91773243|ref|YP_565935.1| 168 KKYTDLLLDGEVNEERIHAIEEIQ 191
                                   456777767777777777766655 PP

  == domain 3  score: 35.4 bits;  conditional E-value: 4.5e-12
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvllt 81 
                                   d+++i + dg+i  +N+ a+++lGys  e+lg + ++++  d  +  +  ++l++ +k +    e  + +++g  ++v+l+
  gi|91773243|ref|YP_565935.1| 224 DPMVIFDLDGKIWEINQVACDVLGYSYFELLGMDHSMIY--DGGSLTETINILKDSEKkPSILLESFCNTRDGVCIPVELN 302
                                   7899977********************************..8888888888888888889********************* PP

                         PAS_9  82 aspvkdddgelvgiivilrDite 104
                                   ++ +  +++ +v+  +++rD++e
  gi|91773243|ref|YP_565935.1| 303 CRLIDYEEKPVVL--ITSRDMSE 323
                                   *************..******97 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0022       4.8       5      27 ..      19      41 ..      16      59 .. 0.91
   2 !   31.7   0.0   4.9e-11   1.1e-07       2      45 ..     214     258 ..     214     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0022
                         PAS_8  5 alfesspdgiavvdlgdrivdvN 27
                                   +++++ +g+av+d + ++ ++N
  gi|91773243|ref|YP_565935.1| 19 DILDHLKVGVAVLDSDLKVKWAN 41
                                  589***********8889***99 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 4.9e-11
                         PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgell 45 
                                   ++++lfe+ +d+++++dl+++i ++Nq a++ lGys  +l+g++ 
  gi|91773243|ref|YP_565935.1| 214 KFKTLFENTSDPMVIFDLDGKIWEINQVACDVLGYSyFELLGMDH 258
                                   699**************7778***************999999876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.8e-07    0.0011       1     108 [.      21     130 ..      21     132 .. 0.81
   2 !   12.7   0.0     5e-05      0.11       1      41 [.     219     259 ..     219     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.8e-07
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.....pg 76 
                                   ld+l +++avld+d++v +aN   ++ +  +  +++G    ++l+     + ++  r+   +++ +  + ++l+     + 
  gi|91773243|ref|YP_565935.1|  21 LDHLKVGVAVLDSDLKVKWANHFLMHELCGQINHVVGVEISQILSS--ISNSSECFRHFDVTDQLCNGERVVLHtplknGV 99 
                                   79********************988778889999*********996..555555566666666666666666666666599 PP

                         PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTer 108
                                   ++r++e rl+P+  ++    g++++++DiT++
  gi|91773243|ref|YP_565935.1| 100 GHRWLEHRLSPIS-SDIYNEGWIGYFYDITDQ 130
                                   ************5.455579**********86 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5e-05
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla 41 
                                   +++++d+ +++d dg++  +N+ a++++g++ +ellG+   
  gi|91773243|ref|YP_565935.1| 219 FENTSDPMVIFDLDGKIWEINQVACDVLGYSYFELLGMDHS 259
                                   799**********************************8665 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.12   2.6e+02       6      28 ..      20      42 ..      17      94 .. 0.85
   2 !   22.9   0.0     3e-08   6.7e-05       3      94 ..     215     304 ..     214     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                                  HHHHSSSEEEEEETTSBEEEECH CS
                           PAS  6 ileslpdpifvvDedgrilyvNa 28
                                  il++l +++ v+D d ++ ++N+
  gi|91773243|ref|YP_565935.1| 20 ILDHLKVGVAVLDSDLKVKWANH 42
                                  78899999999999998888885 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3e-08
                                   HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.T CS
                           PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl.r 82 
                                   +++++e++ dp+++ D dg+i ++N+ a++ lG+s  e+lg   ++ +   +   l e +  l  + +++++   sf+  r
  gi|91773243|ref|YP_565935.1| 215 FKTLFENTSDPMVIFDLDGKIWEINQVACDVLGYSYFELLGMDHSMIYDGGS---LTETINILKDSEKKPSILLESFCNtR 292
                                   68899***********************************988776666664...66666666666666666666666666 PP

                                   TSSEEEEEEEEE CS
                           PAS  83 dgrpihlevras 94 
                                   dg  i++e++++
  gi|91773243|ref|YP_565935.1| 293 DGVCIPVELNCR 304
                                   666666666655 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 ?    0.7   0.1      0.24   5.4e+02      20      56 ..     167     202 ..     160     207 .. 0.79
   2 !   18.5   0.0   6.9e-07    0.0015       4      66 ..     346     407 ..     343     408 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.24
                                   HHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHH CS
                         HisKA  20 ilgnaeaLkregklteelkeyletiesearrldhlve 56 
                                   i+ ++++L + g+ +ee   ++e i+ +a+ l+ lv 
  gi|91773243|ref|YP_565935.1| 167 IKKYTDLLLD-GEVNEERIHAIEEIQANAEKLNGLVR 202
                                   5557777777.466788888999*****999999986 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 6.9e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                         HisKA   4 rflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                    f+  + H+L +P  +++g++e+L+++     + ++y++ i+++ + + +l+e    ++++e+
  gi|91773243|ref|YP_565935.1| 346 VFVDILRHDLMNPAGVVKGYSELLSKQ-VEGSMMEKYVRMIRKNNNKIIDLIESASKYAKLES 407
                                   589999******************886.44588888*****************9999998886 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.026       1     113 [.      21     133 ..      21     135 .. 0.73
   2 ?    3.4   0.0     0.038        85       2      49 ..     220     275 ..     219     293 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                         PAS_7   1 lenmsqGisvfDadlrLvawNrryl.elldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfer 80 
                                   l++++ G++v+D+dl++   N+  + el +  +++  vgv+++++l  +++  e+    ++  v+  l + ++   h+  +
  gi|91773243|ref|YP_565935.1|  21 LDHLKVGVAVLDSDLKVKWANHFLMhELCGQINHV--VGVEISQILSSISNSSECF---RHFDVTDQLCNGERVVLHTPLK 96 
                                   7999*****************97651455555555..5************999999...2233333333444455555555 PP

                         PAS_7  81 erpdgrvievrgnpl....pdgGfVttytDiTerrra 113
                                   +   +r++e r +p+     + G++  + DiT++ ++
  gi|91773243|ref|YP_565935.1|  97 NGVGHRWLEHRLSPIssdiYNEGWIGYFYDITDQMKS 133
                                   5666678888877774444789***********9886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.038
                         PAS_7   2 enmsqGisvfDadlrLvawNr........rylelldlpeelvqvgvpleellryna 49 
                                   en s+ +++fD d+++  +N+         y ell++  ++++ g +l+e +++++
  gi|91773243|ref|YP_565935.1| 220 ENTSDPMVIFDLDGKIWEINQvacdvlgySYFELLGMDHSMIYDGGSLTETINILK 275
                                   67777788888888888888822222222455666666666666666666666655 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.7e-07    0.0015     127     216 ..     321     408 ..     308     412 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.7e-07
                  DDE_Tnp_ISL3 127 lteeqkqrldelleaspelekaYelkeelrevfrkk..dkeearkalkewiekaersglkefkklaktlknhreeIlnyfd 205
                                   +  ++++ +++l ++++el++ + +k  +++++r++  +++ + k ++e+++k  + +   ++k +++++++ ++I+  ++
  gi|91773243|ref|YP_565935.1| 321 M--SERKHIEHLSRTNKELKCLHDTKDVFVDILRHDlmNPAGVVKGYSELLSK--QVEGSMMEKYVRMIRKNNNKIIDLIE 397
                                   3..45556669**********************96666566666666665555..444557******************** PP

                  DDE_Tnp_ISL3 206 srlsngpvEgi 216
                                   s    + +E+i
  gi|91773243|ref|YP_565935.1| 398 SASKYAKLESI 408
                                   99999*99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3486.09
//
Query:       gi|91773244|ref|YP_565936.1|  [L=231]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-10   39.5   0.0    9.8e-10   39.1   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    2.4e-05   24.6   0.0    3.8e-05   24.0   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    0.00039   20.5   0.7     0.0007   19.7   0.6    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.6e-13   9.8e-10       6     121 ..      19     118 ..      17     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.6e-13
                                   EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                   gCn++C++C   +      + +++svee+++++k        k v+lgg ep+l+++++ l+++l +    g ++ + +ng
  gi|91773244|ref|YP_565936.1|  19 GCNMKCPYCVHIH-----QPFKEVSVEEVVDLAKNSL----SKAVHLGGAEPTLQKELIPLIKALNEV---GKEVLLKSNG 87 
                                   9********9997.....8**************9998....9*************************7...********** PP

                                   SCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  87 tlpdeeklerllelgvdrvslgleaaddekvlklm 121
                                   ++  + +le  l++    + l l+a+ d   + +m
  gi|91773244|ref|YP_565936.1|  88 MK--PGVLEDALPYV-HGFVLELKAPLDN-LKAIM 118
                                   **..58888888888.9999999998887.55555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.4e-09   3.8e-05      13      95 ..      18      89 ..      10     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.4e-09
                       Fer4_12 13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgyt 95
                                   gCn++C++C+       + +++f++   ee+++ +k++  + + l G EP l   +++l++l+k + e + e + ++++g +
  gi|91773244|ref|YP_565936.1| 18 FGCNMKCPYCV-------HIHQPFKEVSVEEVVDLAKNSLSKAVHLGGAEPTL---QKELIPLIKALNEVGKE-VLLKSNGMK 89
                                  59*******99.......8999*************999999************...99*********999985.899999976 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 !   19.7   0.6   1.2e-07    0.0007       5      90 ..      17      88 ..      13     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-07
                       Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwlet 87
                                  + gCn++C+ C +        ++p++e  +e++++ +k+s +  + + l G eP     +kel++l+k l e +  k++ l++
  gi|91773244|ref|YP_565936.1| 17 FFGCNMKCPYCVH-------IHQPFKEVSVEEVVDLAKNSLS--KAVHLGGAEPT---LQKELIPLIKALNEVG--KEVLLKS 85
                                  569********75.......5688988888888855555555..55999999**8...469***********99..99*9999 PP

                       Fer4_14 88 ngt 90
                                  ng+
  gi|91773244|ref|YP_565936.1| 86 NGM 88
                                  996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1577.13
//
Query:       gi|91773245|ref|YP_565937.1|  [L=98]
Description: hypothetical protein Mbur_1266 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 634.84
//
Query:       gi|91773246|ref|YP_565938.1|  [L=331]
Description: AIR synthase related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-17   63.4   1.4      5e-17   62.3   1.4    1.6  1  AIRS      AIR synthase related protein, N-terminal domain
    7.4e-15   55.4   0.0    1.3e-14   54.7   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   1.4   5.6e-21     5e-17       1      93 [.      45     150 ..      45     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 5.6e-21
                                   SSSEE.........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHHHHT CS
                          AIRS   1 dDaav.........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaaeel 69 
                                   dDaav         ++++d    ++++e     G+++v vn++D+ amG+rP+a++++++      ++e++rg++++++++
  gi|91773246|ref|YP_565938.1|  45 DDAAVldtggdeviLFAADAIWGKIAMESQWWTGYTSVVVNVNDISAMGGRPVAMVNVMSSCdtdACKEMMRGIKDGVKKF 125
                                   8999555555555599***9999****999999*********************666666659****************** PP

                                   T-EEEEEEEEEESS.EEEEEEEEEE CS
                          AIRS  70 gvplvgGdtsfsne.ptisvtavGl 93 
                                   gvp+vgG+++ ++   ++ v+++G+
  gi|91773246|ref|YP_565938.1| 126 GVPMVGGHIHPDTPyNSLGVAIIGV 150
                                   **********996557899999997 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 !   54.7   0.0   1.4e-18   1.3e-14      38     149 ..     191     299 ..     163     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.4e-18
                                   HHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEE CS
                        AIRS_C  38 lgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllva 118
                                     d++ ++ +  v++ +a++ +l+ a +D+++ G +g+l ++++ s+vga +d+dk+pi + l  +le +l  +   ++v+
  gi|91773246|ref|YP_565938.1| 191 FKDAQTVRDRFLVMQTIAEK-KLAIAGKDISNPGTIGTLGMLCETSKVGASVDVDKIPIPEYL--ELEQWLKIYPATGYVI 268
                                   56888889999999999997.99999***********************************98..6777777777777777 PP

                                   EEHGGH.HHHHHHHHHTTCCCEEEEEEEEESS CS
                        AIRS_C 119 vppeea.davlaileeeglpeaavIGevtake 149
                                     ++e+ d++++i+e+ g+ +aav+G + +++
  gi|91773246|ref|YP_565938.1| 269 TTKPENcDECIRIFEDVGI-TAAVVGNINDSG 299
                                   7777777************.7******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2341.15
//
Query:       gi|91773247|ref|YP_565939.1|  [L=312]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for 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   91.0   0.1    1.7e-25   90.3   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    2.1e-06   27.9   0.0    6.6e-06   26.3   0.0    1.8  1  Fer4_14      4Fe-4S single cluster domain
     0.0015   18.8   0.0     0.0032   17.7   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.034   14.2   0.0      0.068   13.2   0.0    1.5  1  TFIIB        Transcription factor TFIIB repeat


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.1   3.8e-29   1.7e-25       3     166 ..      46     226 ..      44     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.8e-29
                                   EESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                   xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekg..vkevilgggepllypdfvellerlaklavpg 77 
                                   v + Cn +C++C+r+++    +r+++++++l+++e le+ +++ +++   + + + g g+pl++++  e le ++ +  p+
  gi|91773247|ref|YP_565939.1|  46 VAPKCNIQCNYCDRKFDcvneSRPGVTSEILTPQEALEKTRQVLKDHPfiKVVAVAGPGDPLANDETFETLELIKNE-FPD 125
                                   6789***************************************955555566677789*****99887776666666.6** PP

                                   EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH...............HHHHHHHHHHHHTTSE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxx RF
                   Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf...............eevlealeklreagik 143
                                   ++++++tng+ + ++k+++ll+ gv +++++l+a+d++ ++  + +  ++                 +le+++k+ eag+ 
  gi|91773247|ref|YP_565939.1| 126 VTLCLSTNGLAL-PDKMDELLRVGVSTLTVTLNAIDPK-IQAQIVDHISYkgksytgveaaeiliANQLEGIKKAVEAGMV 204
                                   ************.*************************.55555333333666669999999999**************** PP

                                   TEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 144 rvvdrivglpGendeeleellel 166
                                    +++++v++p  n+++++e+++ 
  gi|91773247|ref|YP_565939.1| 205 -IKVNTVLIPEINKDHIVEVAKK 226
                                   .******************9986 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 !   26.3   0.0   1.5e-09   6.6e-06       7      92 ..      49     137 ..      45     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.5e-09
                       Fer4_14   7 gCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeype 80 
                                   +Cn++C  Cd      n++    +++    +e le+  + lk++ + i+ + + G G+PL  +n+++ ++ ++ +k+e+p+
  gi|91773247|ref|YP_565939.1|  49 KCNIQCNYCDrkfdcvNESRPGVTSEILTPQEALEKTRQVLKDHPF-IKVVAVAGpGDPL--ANDET-FETLELIKNEFPD 125
                                   8*********554444444444455555556666555556777777.8889*********..55555.5677999****** PP

                       Fer4_14  81 kkiwletngtle 92 
                                   +   l tng++ 
  gi|91773247|ref|YP_565939.1| 126 VTLCLSTNGLAL 137
                                   ********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 !   17.7   0.0   7.1e-07    0.0032      12     100 ..      47     141 ..      35     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.1e-07
                       Fer4_12  12 vsgCnlsCkgCfnketwsfk.......sgkeftkelleeiiedlkk.esiegltllG.GEPllpenaeallelvkevkeek 83 
                                   +  Cn++C++C  ++  +++       s+  +++e+le+  + lk+ + i+ + + G G+Pl+  n+e++ e ++ +k+e+
  gi|91773247|ref|YP_565939.1|  47 APKCNIQCNYCD-RKFDCVNesrpgvtSEILTPQEALEKTRQVLKDhPFIKVVAVAGpGDPLA--NDETF-ETLELIKNEF 123
                                   458******985.4444444333444266666799999999999976899*************..66555.5568899999 PP

                       Fer4_12  84 p.ekdiwlytgytleels 100
                                   p    +++++g  l + +
  gi|91773247|ref|YP_565939.1| 124 PdVTLCLSTNGLALPDKM 141
                                   965678888888776655 PP

>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-05     0.068      23      56 ..     165     198 ..     153     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                   HHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS-- CS
                         TFIIB  23 klaleekvlkGrspagiaAAclyiAcrkeevkrt 56 
                                    + ++   +kG+s +g+ AA ++iA ++e+ k+ 
  gi|91773247|ref|YP_565939.1| 165 AQIVDHISYKGKSYTGVEAAEILIANQLEGIKKA 198
                                   567788889********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2273.13
//
Query:       gi|91773248|ref|YP_565940.1|  [L=116]
Description: 6-pyruvoyl tetrahydropterin synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  100.2   0.1      9e-29   99.9   0.1    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.1     5e-33     9e-29       7     121 ..      11     113 ..       6     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 5e-33
                                   EEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.--HHHHH CS
                          PTPS   7 eFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkflnaddpeleellspTaEnla 87 
                                    +d+aH+l++he  c+ +HGH+yk+ev +ege ++e+gmv+df  +k+++keil+++Dhk+ln d+  +     p+aEn++
  gi|91773248|ref|YP_565940.1|  11 YIDSAHYLPEHE-TCGIVHGHTYKIEVVLEGE-KQENGMVMDFYIIKKIVKEILKTYDHKLLN-DVLPF-----PSAENIC 83 
                                   689******998.*******************.******************************.99999.....9****** PP

                                   HHHHHHHHHHHGCCCGCEEEEEEEEETTEEEEEE CS
                          PTPS  88 klifeelkerlqekevklskvrvwEtpnswaeyr 121
                                   ++++ +l e+l   ++   +v+vwE +++w+e +
  gi|91773248|ref|YP_565940.1|  84 EHMHGQLFEQL---GLP-VSVKVWEGHGKWCELN 113
                                   ***********...555.56***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 838.57
//
Query:       gi|91773249|ref|YP_565941.1|  [L=238]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-10   41.5   0.3    3.2e-10   40.7   0.3    1.5  1  Radical_SAM  Radical SAM superfamily
    1.6e-07   31.5   0.0    3.3e-07   30.5   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
    1.8e-06   28.2   0.1    6.9e-06   26.4   0.0    1.9  2  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.3   5.3e-14   3.2e-10       3     145 ..      27     166 ..      25     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 5.3e-14
                                   EESEESS--TTTSCCTT.............HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet.............vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfveller 69 
                                    + gCnl+Cs+C++                 + e  +  l + ++ e++  +    g ++ v l+ggepll++df+ +++ 
  gi|91773249|ref|YP_565941.1|  27 RFIGCNLNCSYCDTEPAdpsvcmfertpgsNSFENIPNPLVTSQVSELLGNY----GnIHSVSLTGGEPLLHADFISKMDI 103
                                   567**********************976666666666666666666666555....44*********************** PP

                                   HHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                   Radical_SAM  70 laklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.v 145
                                    + l        +e+n tl  + ++e++++  v +vs +++ +d+++  +l+     +e+++e++++lr+   +r +
  gi|91773249|ref|YP_565941.1| 104 PHLL-------YLESNMTL--PHMAEKIKD-KVSYVSGDIKLIDEFEGEDLV---THLEQTIECFRTLRQT-KDReC 166
                                   ***8.......89999999..6999*****.88*************666666...7899999*99999998.44444 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 !   30.5   0.0   5.5e-11   3.3e-07       2      62 ..      25      95 ..      24     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.5e-11
                       Fer4_14  2 fvrlsgCnlsCkgCd..........nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhye 62
                                  fvr+ gCnl+C  Cd           + t  s++ +   + l+ +++++l  ++ +i+ ++ltGGePL+++
  gi|91773249|ref|YP_565941.1| 25 FVRFIGCNLNCSYCDtepadpsvcmFERTPGSNSFENIPNPLVTSQVSELLGNYGNIHSVSLTGGEPLLHA 95
                                  9***********999666655444444444456666666777788888999999999***********994 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 !   26.4   0.0   1.1e-09   6.9e-06       2      69 ..      13      95 ..      12     103 .. 0.64
   2 ?   -1.8   0.0      0.58   3.5e+03      74     106 ..     134     165 ..     118     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-09
                       Fer4_12  2 nGeG....vr.lslfvsgCnlsCkgCfnketwsfk........sgkef...t.kelleeiiedlkkesi.egltllGGEPllp 66
                                  +GeG    vr +++++ gCnl+C++C  + +  ++        +++ f   +   +  ++ e l ++ +   ++l+GGEPll 
  gi|91773249|ref|YP_565941.1| 13 QGEGphvgVRqAFVRFIGCNLNCSYCDTEPAD-PSvcmfertpGSNSFeniPnPLVTSQVSELLGNYGNiHSVSLTGGEPLL- 93
                                  677755556656999**********9855555.33455555553333322241445556666666644349**********9. PP

                       Fer4_12 67 ena 69
                                   +a
  gi|91773249|ref|YP_565941.1| 94 -HA 95
                                  .33 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.58
                       Fer4_12  74 elvkevkeekpekdiwlytgytleelskkekee 106
                                   +l++e++ e +  ++++ t   + +l++++ +e
  gi|91773249|ref|YP_565941.1| 134 KLIDEFEGEDL-VTHLEQTIECFRTLRQTKDRE 165
                                   56666666666.466666666666666654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1745.03
//
Query:       gi|91773250|ref|YP_565942.1|  [L=185]
Description: hypothetical protein Mbur_1271 [Methanococcoides burtonii DSM 6242]
Scores for 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-71  238.3   3.1    4.5e-71  238.1   3.1    1.0  1  DUF366    Domain of unknown function (DUF366)


Domain annotation for each model (and alignments):
>> DUF366  Domain of unknown function (DUF366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.1   3.1   2.5e-75   4.5e-71       1     183 []       1     180 [.       1     180 [. 0.99

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 2.5e-75
                        DUF366   1 mkvlvleekikYdGsqlsslwaykefgiqgdsivafrGecevkleelvDleDvkeeeeIksedmlhfivehFdstdlklav 81 
                                   m+++vl+ek++YdGsq+sslway+  g+q dsivafrG c+vk+e+++DleD++ +++I+s+dmlhf++ehFdstdlkl++
  gi|91773250|ref|YP_565942.1|   1 MECIVLDEKVHYDGSQISSLWAYNLKGVQYDSIVAFRGGCDVKIEHMIDLEDKRMGDSIYSTDMLHFLIEHFDSTDLKLVY 81 
                                   89******************************************************************************* PP

                        DUF366  82 lrQrllvaivkevleekgvklkreGdDlyvndkKLsvsiataslvsvkiHlglNvesegtpvetigLkdlgi.eedieela 161
                                   +rQrl+++iv+e l+++g+ ++r+GdDl+vn+kKL++sia++s vs+kiH+g+Nv ++     + +L+d+gi e++  +l 
  gi|91773250|ref|YP_565942.1|  82 ARQRLFTSIVAESLSDTGIVTTRQGDDLFVNGKKLTISIASTSSVSQKIHFGINVYHD----FYGNLNDIGIdENKAVSLL 158
                                   **********************************************************....9*********888999*** PP

                        DUF366 162 eevakkyaeeiediekdirKvr 183
                                   +++ k+y++ei+diekd+rK+r
  gi|91773250|ref|YP_565942.1| 159 ADIGKRYVAEIHDIEKDLRKSR 180
                                   ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1266.06
//
Query:       gi|91773251|ref|YP_565943.1|  [L=233]
Description: ATPase ExsB [Methanococcoides burtonii DSM 6242]
Scores for complete 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-62  210.0   0.0    3.2e-62  209.8   0.0    1.0  1  QueC             Queuosine biosynthesis protein QueC
    6.8e-05   22.5   0.1     0.0091   15.6   0.0    2.6  2  ThiI             Thiamine biosynthesis protein (ThiI)
    0.00062   19.5   0.0     0.0011   18.7   0.0    1.3  1  Asn_synthase     Asparagine synthase
  ------ inclusion threshold ------
        0.1   12.1   0.5        3.3    7.1   0.0    2.8  4  Diphthami_syn_2  Diphthamide synthase
       0.12   11.2   0.0       0.17   10.7   0.0    1.2  1  tRNA_Me_trans    tRNA methyl transferase


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.8   0.0   8.8e-66   3.2e-62       2     208 ..       3     217 ..       2     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 8.8e-66
                                   EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG--------- CS
                          QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeeievpk 81 
                                   +++llS GlDS ++la+a+++ +  +altfdYgqr  kke+e+ + +++++g+ eh+i++l++l+++++++L++++ +vp+
  gi|91773251|ref|YP_565943.1|   3 SILLLSSGLDSVAALAIALDNSDVFMALTFDYGQRsVKKEIEYSRMVCEHYGI-EHRIITLSWLSSITNTSLVNKDLDVPE 82 
                                   799********************************99****************.*************************** PP

                                   --.............--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS-- CS
                          QueC  82 eelee..........eelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkki 152
                                    ++++          +++++++Vp+RN +f+ +aas+ae+ g+e +i G+n e+++++PD+++efv+a+++  ++++++ +
  gi|91773251|ref|YP_565943.1|  83 LSINDlidgpdniteDSAKSVWVPNRNGVFINIAASFAESHGCEYVIAGFNGEEAKTFPDNSKEFVNAVDECFSYSTANGV 163
                                   5555555566666669***************************************************************** PP

                                   EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHH CS
                          QueC 153 eieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfee 208
                                   ++ aPlid++K  iv+ ++elg+ple+++sCY+g ee  +Cg C++C++Rk++f +
  gi|91773251|ref|YP_565943.1| 164 KVLAPLIDMDKVSIVRKAMELGAPLEYSWSCYHGAEE--PCGVCESCMRRKRAFLA 217
                                   **********************************555..**************975 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0069        25       6      69 ..       3      61 ..       1      80 [. 0.71
   2 !   15.6   0.0   2.5e-06    0.0091     135     161 ..     160     186 ..      82     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0069
                          ThiI  6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvv 69
                                   ++LlS G+DS  a  ++l       +++++   + +  +++ +e    +  +y+   e ++++
  gi|91773251|ref|YP_565943.1|  3 SILLLSSGLDSVAALAIALDNSDVFMALTFD---YGQRSVKKEIEYSRMVCEHYGI--EHRIIT 61
                                  689********88888888877777778886...5666666666666666666663..555555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.5e-06
                          ThiI 135 vvnllilrPLigldKeeiiklAkeigt 161
                                   +  + +l PLi +dK  i++ A e+g 
  gi|91773251|ref|YP_565943.1| 160 ANGVKVLAPLIDMDKVSIVRKAMELGA 186
                                   33468*******************996 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     3e-07    0.0011      22      79 ..       5      62 ..       3      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3e-07
                  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfee.kgsdeakyakevaehlgtehtelvl 79
                                  +lLS GlDS +  a+a   s+  + + + ++ +    +e++y + v+eh+g+eh+ + l
  gi|91773251|ref|YP_565943.1|  5 LLLSSGLDSVAALAIALDNSD-VFMALTFDYGQrSVKKEIEYSRMVCEHYGIEHRIITL 62
                                  58*******999999999998.999999999555999*****************98766 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00093       3.3       1      27 [.       1      27 [.       1      34 [. 0.92
   2 ?    1.8   0.0      0.04   1.4e+02     153     175 ..      35      57 ..      28      86 .. 0.86
   3 ?   -2.7   0.0      0.92   3.3e+03      47      76 ..     113     142 ..     108     160 .. 0.73
   4 ?   -1.5   0.0      0.42   1.5e+03     110     131 ..     161     182 ..     155     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00093
               Diphthami_syn_2  1 mkvavlysGGkDsilaLykalkeseve 27
                                  m+++ l s G Ds+ aL  al++s+v 
  gi|91773251|ref|YP_565943.1|  1 MRSILLLSSGLDSVAALAIALDNSDVF 27
                                  89*********************9995 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.04
               Diphthami_syn_2 153 Grridkklidelkklsekygidk 175
                                   G+r  kk i+  + ++e+ygi++
  gi|91773251|ref|YP_565943.1|  35 GQRSVKKEIEYSRMVCEHYGIEH 57 
                                   88889999*************86 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.92
               Diphthami_syn_2  47 vhlvellaesvGiplikletaGeeekeved 76 
                                   +++ +  aes G + +    +Gee k   d
  gi|91773251|ref|YP_565943.1| 113 INIAASFAESHGCEYVIAGFNGEEAKTFPD 142
                                   677778888888888888888877766544 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.42
               Diphthami_syn_2 110 lGlksvaPLWkkdpeelleeiv 131
                                    G+k +aPL + d   ++ + +
  gi|91773251|ref|YP_565943.1| 161 NGVKVLAPLIDMDKVSIVRKAM 182
                                   699******9999877776665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.7e-05      0.17       4      69 ..       4      61 ..       1      68 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.7e-05
                 tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvd 69
                                  + +lS+G DS  a+a+ +    +   vf++l+ + ++ +     ++++++ ++v+e+ gi+++++ 
  gi|91773251|ref|YP_565943.1|  4 ILLLSSGLDSVAALAI-A---LDNSDVFMALTFDYGQRS----VKKEIEYSRMVCEHYGIEHRIIT 61
                                  6789*****8655554.3...456789****99966555....899***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 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:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1582.82
//
Query:       gi|91773252|ref|YP_565944.1|  [L=275]
Description: PKD repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for 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   60.5   8.2    3.4e-10   39.6   0.3    2.3  2  PKD         PKD domain
    7.5e-06   25.6   0.3      0.032   14.0   0.0    2.5  2  PKD_3       PKD-like domain
  ------ inclusion threshold ------
      0.061   13.5   1.1        0.9    9.8   0.1    2.6  2  Dockerin_1  Dockerin type I domain
      0.085   12.4   0.2        1.4    8.4   0.1    2.0  2  FmrO        Ribosomal RNA methyltransferase (FmrO)
       0.62   10.3   0.1       0.62   10.3   0.1    4.2  3  He_PIG      Putative Ig domain


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.3   9.6e-14   3.4e-10      25      70 ..     105     149 ..      90     150 .. 0.90
   2 !   24.2   2.3   6.2e-09   2.2e-05      10      67 ..     181     235 ..     169     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 9.6e-14
                                   -SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD  25 nvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                    +++ Wdf+  +   +++   + h+Y++pG+Y+V++ta+n+ gs t
  gi|91773252|ref|YP_565944.1| 105 ATSWAWDFDG-DSLIDSTDAMFVHIYTTPGTYNVSLTATNPNGSDT 149
                                   589*****99.********************************976 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 6.2e-09
                                   SSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
                           PKD  10 pgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                                   +  +v ft  +   + ++ sWd++  +   ++  +++ ++Y  pG+Y+V++ a+n+ g
  gi|91773252|ref|YP_565944.1| 181 TPLSVKFTDLS--LDAANVSWDVNE-DGIEDSNASEFVYVYGVPGTYNVSLAATNSNG 235
                                   45678888888..8888889*****.*****************************987 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     9e-06     0.032      32      68 .]     104     143 ..      98     143 .. 0.86
   2 !    9.3   0.0   0.00027      0.95      30      68 .]     192     232 ..     182     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9e-06
                         PKD_3  32 naa.faWtieGk..ivsteptytfteeelgsyevtleven 68 
                                   +a+ +aW  +G   i st++ ++   ++ g+y+v l+++n
  gi|91773252|ref|YP_565944.1| 104 GATsWAWDFDGDslIDSTDAMFVHIYTTPGTYNVSLTATN 143
                                   4556******996446**********************98 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00027
                         PKD_3  30 aenaafaWtie..Gkivsteptytfteeelgsyevtleven 68 
                                   ++ a+ +W ++  G + s+  +++++  + g+y+v l ++n
  gi|91773252|ref|YP_565944.1| 192 LDAANVSWDVNedGIEDSNASEFVYVYGVPGTYNVSLAATN 232
                                   688999**9997677899********************998 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00025       0.9      31      54 ..     104     127 ..      85     150 .. 0.77
   2 ?    1.8   0.2      0.08   2.9e+02      37      43 ..     199     205 ..     186     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                                   CCCHGGGSTT-SSCESHHHHHHHH CS
                    Dockerin_1  31 ssngkaaDvNgDGrvnalDallvi 54 
                                        a D +gD  ++++Da+ v+
  gi|91773252|ref|YP_565944.1| 104 GATSWAWDFDGDSLIDSTDAMFVH 127
                                   555567788888888888888875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.08
                                   GSTT-SS CS
                    Dockerin_1  37 aDvNgDG 43 
                                    DvN+DG
  gi|91773252|ref|YP_565944.1| 199 WDVNEDG 205
                                   6777777 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.028        99     100     150 ..      74     125 ..      69     164 .. 0.77
   2 ?    8.4   0.1   0.00038       1.4     103     161 ..     166     226 ..     147     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.028
                          FmrO 100 vyaalPapasvlDvaCgLnpLavpwlllaadatylasDidsd.lvefldrfl 150
                                   v ++ P  +   +++ g  pL+v ++ +++ at  a D d d l++  d+++
  gi|91773252|ref|YP_565944.1|  74 VISMEPVSDFTSNITSGDVPLSVKFIDMSSGATSWAWDFDGDsLIDSTDAMF 125
                                   6677788888899999999*********************873566666543 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00038
                          FmrO 103 alPapasvlDvaCgLnpLavpwlllaadatylasDidsdlvefldr..flalvevegrvev 161
                                   ++P  +   +v+ gL pL+v +  l+ da  ++ D++ d +e  ++  f+ + +v+g  +v
  gi|91773252|ref|YP_565944.1| 166 VMPVANFTSNVTVGLTPLSVKFTDLSLDAANVSWDVNEDGIEDSNAseFVYVYGVPGTYNV 226
                                   6788888999*******************************97765336666666665555 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2       0.2   7.1e+02      27      40 ..      57      70 ..      55      72 .. 0.87
   2 ?   10.3   0.1   0.00017      0.62      34      49 .]     131     146 ..      98     146 .. 0.85
   3 ?    2.2   3.6     0.057   2.1e+02      35      49 .]     221     235 ..     147     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.2
                        He_PIG 27 GtpdqtvapGsytf 40
                                  G+p   v+ Gsyt 
  gi|91773252|ref|YP_565944.1| 57 GSPQLRVTSGSYTP 70
                                  789999999***95 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                        He_PIG  34 apGsytftVtatdgsg 49 
                                   +pG+y++ +tat+ +g
  gi|91773252|ref|YP_565944.1| 131 TPGTYNVSLTATNPNG 146
                                   58**********9775 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.057
                        He_PIG  35 pGsytftVtatdgsg 49 
                                   pG+y++ + at+++g
  gi|91773252|ref|YP_565944.1| 221 PGTYNVSLAATNSNG 235
                                   6**********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1521.39
//
Query:       gi|91773253|ref|YP_565945.1|  [L=326]
Description: alanine dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.3e-114  380.7   0.8   5.2e-114  380.5   0.8    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    0.00027   21.0   0.0    0.00055   20.0   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.055   14.1   0.0       0.13   12.9   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.5   0.8  8.7e-118  5.2e-114       7     317 ..       7     317 ..       2     318 .. 0.97

  Alignments for each domain:
  == domain 1  score: 380.5 bits;  conditional E-value: 8.7e-118
                                   -HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSEEE CS
               OCD_Mu_crystall   7 taveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglptvta 87 
                                    +++v++++ l+ +++ave+af++  + kv++pp+ +l + +++g+l+ mpayl++++  gvK+vn+hp+n ++glp+v+a
  gi|91773253|ref|YP_565945.1|   7 DQNDVRSLIGLSSAMEAVEKAFEQHGNKKVQMPPKSYLYFDKHNGDLRTMPAYLEEQDISGVKIVNVHPDNRDKGLPSVMA 87 
                                   6789********************9999***************************************************** PP

                                   EEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHH CS
               OCD_Mu_crystall  88 lvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevriydrdeeaae 168
                                   lv+Ln++etG pla+md+t+lt+lRT+A+++vaakyLarkd++ ++iiGaG qa+tql+al+ ++d+++v +yd+++   +
  gi|91773253|ref|YP_565945.1|  88 LVILNSTETGQPLAVMDGTYLTDLRTGAAGGVAAKYLARKDSHIVGIIGAGNQAKTQLLALSLIFDLHRVNVYDVSKDRCD 168
                                   ********************************************************************************* PP

                                   HHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHCCEEEESHHH CS
               OCD_Mu_crystall 169 kfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddilkradifvdsea 248
                                    f e++ + ++  + + + +++a  ++di+vtvT+ ++p++kaew+k+G+hina+gada gk+eLd+ ++  a++fvd+  
  gi|91773253|ref|YP_565945.1| 169 DFREEMMQkMDATIIVTSTVKDAC-DCDILVTVTPVREPLVKAEWIKQGTHINAIGADAVGKEELDPTLITSAKVFVDDIV 248
                                   ***998886899999888888875.8******************************************************* PP

                                   HHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHHHHCCC CS
               OCD_Mu_crystall 249 qareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvyeraeek 317
                                   qa ++Ge++v++++g++ +d++ ae+geviaG k GR++++eit+fds+Gla++D+aaa+lvy+ a++k
  gi|91773253|ref|YP_565945.1| 249 QASHSGEVNVPLSNGIITVDDIWAEIGEVIAGIKIGRENESEITVFDSTGLAIQDIAAATLVYDAAKSK 317
                                   ******************************************************************987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.3e-08   0.00055       4     100 ..     121     218 ..     118     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.3e-08
                                   HHHHS..TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                  Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83 
                                    k l + +++ v +iGaG+ a+  + +L+    +++v v   + +r ++++ee+ ++   ++ +++  +   ++d++++ t
  gi|91773253|ref|YP_565945.1| 121 AKYLARKDSHIVGIIGAGNQAKTQLLALSLIfDLHRVNVYDVSKDRCDDFREEMMQKMDATIIVTSTVKDACDCDILVTVT 201
                                   5556666777899******99877777765448999******************7776677777888888999******** PP

                                   SSSS-SB-HHHHHCCHH CS
                  Shikimate_DH  84 aseepilekeeveealk 100
                                     +ep++++e++++  +
  gi|91773253|ref|YP_565945.1| 202 PVREPLVKAEWIKQGTH 218
                                   ************99765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05      0.13       2      69 ..     132     201 ..     131     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlav 69 
                                   +giiGaGn++++ ++ l+   ++ h + v  + ++++ + ++ee+       + v +++ ++a++ +d++v   
  gi|91773253|ref|YP_565945.1| 132 VGIIGAGNQAKTQLLALSLI-FDLHRVNVY-DVSKDRCDDFREEMMqkmdatIIV-TSTVKDACD-CDILVTVT 201
                                   8*********8755544433.345777744.777777777777777777774444.448899997.99887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2089.27
//
Query:       gi|91773254|ref|YP_565946.1|  [L=130]
Description: hypothetical protein Mbur_1275 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       546  (0.0304535); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 880.17
//
Query:       gi|91773255|ref|YP_565947.1|  [L=310]
Description: SSU ribosomal protein S6P modification protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-26   92.4   0.1    4.7e-26   91.6   0.1    1.4  1  RimK            RimK-like ATP-grasp domain
    1.7e-15   56.9   0.1    4.2e-15   55.6   0.1    1.5  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    1.5e-08   34.2   0.0    5.8e-08   32.3   0.0    1.8  2  ATPgrasp_YheCD  YheC/D like ATP-grasp
    6.4e-08   32.9   0.0    1.1e-07   32.1   0.0    1.4  1  Rimk_N          RimK PreATP-grasp domain
    2.6e-05   23.6   0.1    0.00015   21.1   0.1    2.2  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
      0.003   17.6   0.0      0.013   15.5   0.0    2.0  1  ATP-grasp_3     ATP-grasp 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 !   91.6   0.1   1.6e-29   4.7e-26       1     188 []     101     306 ..     101     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 1.6e-29
                                   HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-S...........HHHHHHHHH CS
                          RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakk...........eqklkqvle 70 
                                   a +K+ +  l+aka++++p+t +++d  +a +++++++     v+K ++g  G  +v  k+             +l+ +++
  gi|91773255|ref|YP_565947.1| 101 AANKYYASSLMAKAGLPIPKTMVVQDTGNALNILDRME---DAVIKPIFGYKGKDIVRIKDgtiinndgttnDSELEGTID 178
                                   67999********************************6...89**********9887665411111111111345555555 PP

                                   HGGG--.......EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT- CS
                          RimK  71 alkeai.......lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamel 144
                                   a    i        +qeyi++  ++diR +vv+++v+aa+ r++ eG +  nl +Gg  ++ +ls  + el ika++ ++ 
  gi|91773255|ref|YP_565947.1| 179 A----IleqrgmlYIQEYIAN-PGRDIRAFVVNGKVIAAIYRTAPEGAWINNLSQGGNESRCELSSYQIELCIKASRSVGT 254
                                   5....333334447999*986.579******************************************************** PP

                                   SEEEEEEEEE........TTEEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                          RimK 145 vvaGvDllra........krgllvlEvnsspglekiektlgidiakklieai 188
                                    +aGvDl+++         +  l+lE+n+ p + +i k  gi++ak +i+ i
  gi|91773255|ref|YP_565947.1| 255 YFAGVDLIEElngsnngnGDKSLILEINATPSVAGIYKAWGINAAKYIIKNI 306
                                   ******99852222221124579*************************9876 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 !   55.6   0.1   1.4e-18   4.2e-15      12     154 ..     118     264 ..     110     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.4e-18
                                   S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-T..........T-TTHHHHHHHHTTTTTS-EEEEE--GGGG CS
                     GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkk..........sdpnlksilellteegkepviaqrylpeik 82 
                                   ipkt+v +d+ +  ++l++++d+++KP+ g+ G+ ++r+k+          +d++l+  ++++ e+   ++ +q+y+ +  
  gi|91773255|ref|YP_565947.1| 118 IPKTMVVQDTGNALNILDRMEDAVIKPIFGYKGKDIVRIKDgtiinndgttNDSELEGTIDAILEQRG-MLYIQEYIANPG 197
                                   79************************************975333332222256778888888877655.7889****9987 PP

                                   G-EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT CS
                     GSH-S_ATP  83 eGDkRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd 154
                                   + D R ++v+G+ i  a+ R + eg   +nl+ gg+++  el++ + e++ + +   ++ G +f+G+D+i++
  gi|91773255|ref|YP_565947.1| 198 R-DIRAFVVNGKVIA-AIYRTAPEGAWINNLSQGGNESRCELSSYQIELCIKAS---RSVGTYFAGVDLIEE 264
                                   7.*************.**********************************8876...678**********86 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 !   32.3   0.0   1.9e-11   5.8e-08      29     165 ..     118     234 ..     110     243 .. 0.88
   2 ?   -2.2   0.0      0.68     2e+03     220     238 ..     277     295 ..     273     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.9e-11
                ATPgrasp_YheCD  29 LPetellesledleemlekyksvylKpanGskGkgilriekeekellllsrekkkkkkkrlaslselesllkkllkkkr.y 108
                                   +P+t  ++++ +  ++l++ ++ ++Kp+ G kGk+i+ri+            ++  ++  +++ sele  ++  l+++   
  gi|91773255|ref|YP_565947.1| 118 IPKTMVVQDTGNALNILDRMEDAVIKPIFGYKGKDIVRIKD-----------GTIINNDGTTNDSELEGTIDAILEQRGmL 187
                                   8****************************************...........4445566777899**********999955 PP

                ATPgrasp_YheCD 109 lvQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalp 165
                                    +Q++i          D+R++v        +v++++ R+a++g+ + nls+GG+  +
  gi|91773255|ref|YP_565947.1| 188 YIQEYIANPG-----RDIRAFVVN-----GKVIAAIYRTAPEGAWINNLSQGGNESR 234
                                   69**997665.....7******93.....3599********************9765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.68
                ATPgrasp_YheCD 220 WllEvNskpgrsifkeagd 238
                                    +lE+N+ p+ +   +a  
  gi|91773255|ref|YP_565947.1| 277 LILEINATPSVAGIYKAWG 295
                                   699******9887776655 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   3.8e-11   1.1e-07       3      94 .]       4      98 ..       1      98 [. 0.91

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.8e-11
                        Rimk_N  3 iaiLsrnpelystrrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipR.igasi...tfygtavlrqFe 81
                                  i+i+ ++++  + + +++a+ + +++ +++d ++ ++ i + + ++ + +++l+++d++i+R +ga     + ++ +vlrq+e
  gi|91773255|ref|YP_565947.1|  4 IGIIITDRNDPTAQAFQNACVSNNIKPHMIDLREKKVIIGE-SLSLQIADRDLQQLDVIIVRdVGAGGfdgVSFRFDVLRQLE 85
                                  78888889999999***********************9998.99******************99775434599********** PP

                        Rimk_N 82 mmgvfvlneseAi 94
                                  + gv+++n++ +i
  gi|91773255|ref|YP_565947.1| 86 QEGVPIINSPVSI 98
                                  *********9987 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1     5e-08   0.00015      10      91 ..      92     165 ..      84     230 .. 0.78
   2 ?   -0.5   0.0      0.19   5.7e+02     257     270 ..     276     289 ..     268     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5e-08
                   ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylks 90 
                                   +N+   +++ ++K   ++l+ +agl++pk+++v +++    ++ +++ ++ e+ viKp+ g  Gk+i+ i++     ++++
  gi|91773255|ref|YP_565947.1|  92 INSPVSIQNAANKYYASSLMAKAGLPIPKTMVVQDTG----NALNILDRM-EDAVIKPIFGYKGKDIVRIKD---GTIINN 164
                                   78888999999******************88775555....555677788.6699************99955...333333 PP

                   ATPgrasp_ST  91 s 91 
                                    
  gi|91773255|ref|YP_565947.1| 165 D 165
                                   3 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                   ATPgrasp_ST 257 plllElNarpglai 270
                                    l+lE+Na+p++a 
  gi|91773255|ref|YP_565947.1| 276 SLILEINATPSVAG 289
                                   689*******9975 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.5e-06     0.013       1     156 [.     101     283 ..     101     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
                                   HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS--TTE.................. CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........... 64 
                                   a++K+     + +ag+++P      ++ +a ++    +  v+Kp+ G  g+ ++ ++++   ++   ++            
  gi|91773255|ref|YP_565947.1| 101 AANKYYASSLMAKAGLPIPktmvvqDTGNALNILDRMEDAVIKPIFGYKGKDIVRIKDGTIINNDGTTNDselegtidail 181
                                   689***9999*********87777655566667777999*****************9997777666655577889777776 PP

                                   ......EEEE--..-SEEEEEEEEE.SSSEEEEEEEEEEEET.....TEEEEEEES----HHHHHHHHHHHHHTTSTT--E CS
                   ATP-grasp_3  65 ......lvqefi..eGkplSvsllsdgekvlvlavnrqliekaeke.fvyaGnvtpietelkeevvelaeevvekleglaG 136
                                          +qe+i  +G+++ + ++  +   ++ a+ r   e a+ + ++  Gn  +++ el++  +el+ ++ +++ g+  
  gi|91773255|ref|YP_565947.1| 182 eqrgmlYIQEYIanPGRDIRAFVVNGK---VIAAIYRTAPEGAWINnLSQGGN--ESRCELSSYQIELCIKASRSV-GTY- 255
                                   666666666666222444444333322...33333333333333332444444..455568888899999999999.554. PP

                                   EEEEEEE........ESS.SEEEEEEES CS
                   ATP-grasp_3 137 yvGvDlv........lkdeepyviEvNP 156
                                   ++GvDl+         + ++  ++E+N+
  gi|91773255|ref|YP_565947.1| 256 FAGVDLIeelngsnnGNGDKSLILEINA 283
                                   89****9998887654447999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2213.54
//
Query:       gi|91773256|ref|YP_565948.1|  [L=115]
Description: peptidyl-tRNA hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  134.0   0.1    3.1e-39  133.9   0.1    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.1   1.7e-43   3.1e-39       1     116 [.       4     114 ..       4     115 .] 0.97

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.7e-43
                                   EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEE CS
                          PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaali 81 
                                   +k+++++r DLk+skGk+a+q+ahAav++++ ++++  +   l++W+e gqkk+vl+ve+ ++L el++ka+++gl++ali
  gi|91773256|ref|YP_565948.1|   4 YKQCIIIRDDLKLSKGKLAVQVAHAAVSAAEWASRS--D---LENWKEGGQKKVVLRVEKLQDLFELKEKARREGLSTALI 79 
                                   79*****************************98886..4...899*999******************************** PP

                                   EETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB CS
                          PTH2  82 rDagrtqiepgtkTvlaigPapksivdkvtgkLkl 116
                                   +Dag t+i+pgt+Tvl+igPa ++ +dkvtg+Lkl
  gi|91773256|ref|YP_565948.1|  80 TDAGLTEIAPGTVTVLGIGPARADYIDKVTGNLKL 114
                                   **********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 792.80
//
Query:       gi|91773257|ref|YP_565949.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91773257|ref|YP_565949.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91773257|ref|YP_565949.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91773257|ref|YP_565949.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91773257|ref|YP_565949.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91773257|ref|YP_565949.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91773257|ref|YP_565949.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91773257|ref|YP_565949.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91773257|ref|YP_565949.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2025.61
//
Query:       gi|91773258|ref|YP_565950.1|  [L=439]
Description: tRNA pseudouridine synthase D [Methanococcoides burtonii DSM 6242]
Scores for complete 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-165  551.0   0.1   1.8e-165  550.8   0.1    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 !  550.8   0.1    1e-169  1.8e-165       2     416 .]      11     430 ..      10     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 550.8 bits;  conditional E-value: 1e-169
                          TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDk 82 
                                   +gi+ly+t+t+gigG+lr++ eDF V Ei   +++ee +eg+yl+l+++krnw+t++l+r+l+r l+is+krvgfaGtKDk
  gi|91773258|ref|YP_565950.1|  11 IGIDLYTTKTPGIGGKLRQQTEDFGVIEI---TNREEGTEGKYLILELTKRNWETHHLIRDLTRILRISQKRVGFAGTKDK 88 
                                   89***************************...6667899****************************************** PP

                          TruD  83 rAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileeleekggvPN 162
                                   rAvTtQ isi+++e+e+l+++++kd+el+ +gr++++l+lGdL+GN+F i+vrd+  +e+e+++r+++++++++e+ggvPN
  gi|91773258|ref|YP_565950.1|  89 RAVTTQKISIYDMEEEALQNVHLKDTELKILGRSNKSLELGDLTGNEFIITVRDIdLDEKELESRLSQTTASIKEQGGVPN 169
                                   ********************************************************************************* PP

                          TruD 163 yfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslryErallkrLae 243
                                   +fG+QRFG+ rp+th+vG+ iv++d+e+A+++y++ ++++e+edt+e+r+ v et+d+ e+l+ +p +lryEra++++L++
  gi|91773258|ref|YP_565950.1| 170 FFGIQRFGALRPITHVVGESIVRNDIEKAAMAYIAASYPDEPEDTQEVRNRVFETKDYIEGLKGYPLQLRYERAMMHHLVS 250
                                   ********************************************************************************* PP

                          TruD 244 kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer.lpdtdrlqlvteknveevkrli 323
                                   kp+dy++++e+lp n++++FvhAyqSy++N+++++R+++glpl+++v GD+v+f++++ lpd++r ++vte+n++ +++l+
  gi|91773258|ref|YP_565950.1| 251 KPEDYAGSFETLPANIRKMFVHAYQSYIYNTIICSRIKKGLPLNRAVVGDIVCFKNKAgLPDKSRNERVTEDNIDGMNNLV 331
                                   *******************************************************9999********************** PP

                          TruD 324 ergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrve......dlelsaeedelt 398
                                   +r+rafvtaplvG+++ela+g +geierev+ee ++  e Fk+p++ elsskG rR+ill+++      ++el++ + ++t
  gi|91773258|ref|YP_565950.1| 332 KRNRAFVTAPLVGYSSELASGVPGEIEREVIEELNVPIEGFKVPSMEELSSKGLRREILLSTDpkyfieEDELNEGKYRVT 412
                                   ********************************************************************98899999999** PP

                          TruD 399 leFsLpkGsYATvvlrEi 416
                                   l+FsLpkGsYAT++lrE+
  gi|91773258|ref|YP_565950.1| 413 LDFSLPKGSYATTILREY 430
                                   *****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3054.53
//
Query:       gi|91773259|ref|YP_565951.1|  [L=534]
Description: CTP synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-124  414.7   0.9   1.9e-124  414.3   0.9    1.2  1  CTP_synth_N    CTP synthase N-terminus
      8e-56  188.8   0.0    1.5e-55  187.9   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    8.5e-05   22.6   0.0    0.00036   20.6   0.0    2.1  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00049   19.9   0.0     0.0033   17.2   0.0    2.2  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.085   11.8   0.2        0.2   10.6   0.2    1.6  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
       0.12   12.3   0.1       0.33   10.8   0.1    1.8  1  AAA_31         AAA domain


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.3   0.9  6.2e-128  1.9e-124       1     264 [.       2     264 ..       2     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 414.3 bits;  conditional E-value: 6.2e-128
                                   EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT--- CS
                   CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikl 81 
                                   kyi+vtGGv+SglGkGi++as+g+ lk++g+kvt+ikiDPY+n+dagt+sp++hGEv+vl+dG+e+DlDlGnYeRfld++l
  gi|91773259|ref|YP_565951.1|   2 KYIIVTGGVMSGLGKGITTASVGRNLKNKGYKVTAIKIDPYINIDAGTMSPYQHGEVYVLKDGGEVDLDLGNYERFLDTEL 82 
                                   8******************************************************************************** PP

                                   -GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHH CS
                   CTP_synth_N  82 tkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlkle 162
                                   t+++n+ttGkiy++vi+ker+G+ylGktvq+iph+t+eik+ri+++a k+ adv+++e+gGtvgdies+pflea+rq+  e
  gi|91773259|ref|YP_565951.1|  83 TRDHNLTTGKIYQTVIDKERKGEYLGKTVQIIPHITNEIKDRIRRIAAKSGADVCLIEVGGTVGDIESMPFLEAVRQMYRE 163
                                   ***********************************************9999****************************** PP

                                   H-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-G CS
                   CTP_synth_N 163 lgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesi 243
                                    + en++l+hvtlvp+ +++g++ktkptqhsvkelr+lG++p++iv r++k+l e++++kialfc+v+ eavis++d  +i
  gi|91773259|ref|YP_565951.1| 164 ESPENIALLHVTLVPI-DSQGDQKTKPTQHSVKELRELGLTPHVIVSRCKKALMESTRSKIALFCDVPVEAVISAHDSADI 243
                                   ***************6.57************************************************************** PP

                                   GGHHHHHHHCTHHHHHHHHTT CS
                   CTP_synth_N 244 yevpllleeqglaelileklk 264
                                   yevpl le++gl++++l+kl 
  gi|91773259|ref|YP_565951.1| 244 YEVPLQLENEGLSNYLLKKLI 264
                                   *****************9985 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9   0.0     5e-59   1.5e-55       2     188 ..     299     521 ..     298     523 .. 0.93

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 5e-59
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH....THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile....llknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                   l D+y s++e+l+h ++e+g+k e+ ++da+    +     +l+++dgilv+gG+g++g+egk+ aik+aren+iP+LG C
  gi|91773259|ref|YP_565951.1| 299 LEDSYISIVESLKHGAIEIGCKFEITWFDAESFDDDPseveKLNGFDGILVPGGFGERGTEGKMLAIKYARENNIPYLGLC 379
                                   78***************************97766633445469************************************** PP

                                   HHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEE CS
                        GATase  79 LGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknevierhrH 128
                                   LGmQl++ief+r+vv                       ++++  ++g+tmrlgd+e+        + +yg  + ++erhrH
  gi|91773259|ref|YP_565951.1| 380 LGMQLAVIEFARNVVgldganssefdentpypvidllpEQEDVVDMGATMRLGDYEAtlkagslaESIYGA-SLITERHRH 459
                                   ************999999999999999999********9999**********************9999999.********* PP

                                   EEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHH CS
                        GATase 129 ryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnfli 188
                                   ryevnp+   ++e++g+++++k+++   +mei e ++   +++ QFHPE++s+p++p+++f+ ++
  gi|91773259|ref|YP_565951.1| 460 RYEVNPNyvdRIEEHGMIFSGKNKN---RMEIAEVPSkDfYFASQFHPEFKSRPGRPSPPFKAFM 521
                                   ***********************55...6888888885579********************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 !   20.6   0.0   1.2e-07   0.00036       5      55 ..       9     123 ..       4     431 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                                   ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                          CbiA   5 stkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                   +  +G GK  ++a+ +r l+++g++V +++ Dp  n +a   g+    +                                
  gi|91773259|ref|YP_565951.1|   9 GVMSGLGKGITTASVGRNLKNKGYKVTAIKIDPYINIDA---GTMSPYQHgevyvlkdggevdldlgnyerfldteltrdh 86 
                                   4579*****************************999887...333333323555555566666655666666666666666 PP

                                   ....................................C CS
                                   ....................................x RF
                          CbiA  55 ....................................d 55 
                                                                       d
  gi|91773259|ref|YP_565951.1|  87 nlttgkiyqtvidkerkgeylgktvqiiphitneikD 123
                                   6655555555555555555555555555555555550 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06    0.0033      96     216 .]     363     505 ..     355     505 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                 Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..................q..saashavkvekg 156
                                     i+ a e+++P lg C+G+ql  + +  +++    +  + +++ e++                  +       + +++ g
  gi|91773259|ref|YP_565951.1| 363 LAIKYARENNIPYLGLCLGMQLAVIEFARNVVGLDGA--NSSEFDENTpypvidllpeqedvvdmgAtmRLGDYEATLKAG 441
                                   55788999**************988877666543222..23333333344677777766555544414456677788889* PP

                 Peptidase_C26 157 sllaellgseeievnslHhqaike.....laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   sl ++++g++ i     H+  ++      ++e+  + +  + + +E  e+++++ f+++ Q+HPE
  gi|91773259|ref|YP_565951.1| 442 SLAESIYGASLITERHRHRYEVNPnyvdrIEEHGMIFSGKNKNRMEIAEVPSKD-FYFASQFHPE 505
                                   *******9888888888887765444444999********************66.*********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 ?   10.6   0.2   6.8e-05       0.2      35      74 ..       7      48 ..       2      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.8e-05
                                  EE..-TTSSHHHHHHHHHHHHHCTT--EEEEEE--------- CS
                          MeaB 35 tG..vPGaGkstlvealglelrrrGkrvavlavDPsspftGG 74
                                  tG  + G Gk  ++  +g +l+++G++v+ + +DP  ++  G
  gi|91773259|ref|YP_565951.1|  7 TGgvMSGLGKGITTASVGRNLKNKGYKVTAIKIDPYINIDAG 48
                                  5433579****************************8777666 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00011      0.33      10      48 ..      11      49 ..       2     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                        AAA_31 10 KGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattgl 48
                                    G GK  t+  ++  l ++g+kv  + +Dp  n   g+
  gi|91773259|ref|YP_565951.1| 11 MSGLGKGITTASVGRNLKNKGYKVTAIKIDPYINIDAGT 49
                                  5699***************************99987643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3445.45
//
Query:       gi|91773260|ref|YP_565952.1|  [L=224]
Description: hypothetical protein Mbur_1283 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.015   14.5   5.7       0.02   14.1   5.7    1.1  1  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
       0.14   11.6   0.0       0.21   11.0   0.0    1.2  1  DUF4349        Domain of unknown function (DUF4349)
       0.14   12.2   1.0       0.22   11.6   1.0    1.3  1  Vma12          Endoplasmic reticulum-based factor for assembl


Domain annotation for each model (and alignments):
>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   5.7   3.3e-06      0.02     190     255 ..     153     218 ..     135     224 .] 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-06
                 MIG-14_Wnt-bd 190 wssal....ilkilaiilavlyflyLlylifrsfseirskrvkegdiRfkf.lilltllvlavlvifiilg 255
                                    ss      ++k l+i+l ++ ++ L+y+++rs+s+++ +    ++i++ f +++++++++++lv++++  
  gi|91773260|ref|YP_565952.1| 153 YSS-IgqtiGTKHLIILLSFVAIVALIYMVIRSLSSVDMN----YSINLSFyTAIVISILFTSLVAYMFTK 218
                                   222.023349999*******************99999993....467666603444444444444444443 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.5e-05      0.21     150     210 ..     117     180 ..     110     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.5e-05
                       DUF4349 150 tvtvtlrepeaeteaeeee..gegflealsggwnalveflagllv..vlgallPwllvlalvlal 210
                                    v +++ e+ +++++ ++   ++gf++++s+g++a+++++ + +    l++ll +++++a ++++
  gi|91773260|ref|YP_565952.1| 117 PVAIDIDESLSSPSPVNPMqnINGFGRQFSDGLSAMYSSIGQTIGtkHLIILLSFVAIVA-LIYM 180
                                   57788888888888777778899**************99998854114555666666666.4444 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   3.7e-05      0.22      83     122 ..     167     206 ..     128     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                         Vma12  83 iliSvvavffavwialrsartpslpvrvllslvvallVgv 122
                                   il+S va ++ +++++rs+ + ++ + + ls+  a+++ +
  gi|91773260|ref|YP_565952.1| 167 ILLSFVAIVALIYMVIRSLSSVDMNYSINLSFYTAIVISI 206
                                   89**********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1646.45
//
Query:       gi|91773261|ref|YP_565953.1|  [L=60]
Description: hypothetical protein Mbur_1284 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   45.0   0.9    2.3e-11   44.1   0.9    1.5  1  Trm112p          Trm112p-like protein
     0.0022   18.3   0.1     0.0025   18.2   0.1    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0022   18.0   0.0     0.0023   17.9   0.0    1.1  1  Elf1             Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
      0.016   15.3   0.8      0.031   14.4   0.8    1.6  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
       0.03   13.9   0.7       0.15   11.7   0.0    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.032   14.0   1.6      0.072   12.9   1.6    1.6  1  Cys_rich_KTR     Cysteine-rich KTR
      0.054   12.9   1.8        2.4    7.7   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.087   13.1   0.9       0.22   11.8   0.9    1.6  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
      0.094   12.5   2.2        1.7    8.5   2.2    2.1  1  A2L_zn_ribbon    A2L zinc ribbon domain
       0.11   12.3   0.2       0.11   12.3   0.2    1.0  1  CK_II_beta       Casein kinase II regulatory subunit
       0.13   11.8   2.8        0.4   10.2   2.8    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.9   1.4e-14   2.3e-11       1      68 []       2      49 ..       2      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.4e-14
                                  BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                       Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                  k++l++iLaCp+ckg L   +l  +++              +   e +i++g+L+C++c+  +pI dG
  gi|91773261|ref|YP_565953.1|  2 KKDLMDILACPICKGDL---VLNITKE--------------D---EKEIISGTLYCSKCNEYFPITDG 49
                                  789**************...3333332..............1...349*******************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 !   18.2   0.1   1.5e-06    0.0025       2      36 ..       7      42 ..       6      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
               Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigq.cvyCadCga 36
                                  +++ CP C+g+ vl  ++   +ei   + yC +C+ 
  gi|91773261|ref|YP_565953.1|  7 DILACPICKGDLVLNITKEDEKEIISgTLYCSKCNE 42
                                  6889**********9998888887778*******96 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0023      18      56 ..       5      45 ..       1      54 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                          Elf1 18 lptkFdCpfCnheksvevkldkkek..iaevsCkvCgesfe 56
                                  l     Cp C+ + +++++ + +++   +++ C++C+e+f 
  gi|91773261|ref|YP_565953.1|  5 LMDILACPICKGDLVLNITKEDEKEiiSGTLYCSKCNEYFP 45
                                  677889*******888887777777888*********9986 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 ?   14.4   0.8   1.9e-05     0.031      12      33 ..      28      49 ..       8      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                    zf-RRPl_C4 12 lknlnetvyCeaCeiyfkvkne 33
                                   + ++ t+yC++C+ yf ++++
  gi|91773261|ref|YP_565953.1| 28 KEIISGTLYCSKCNEYFPITDG 49
                                  4567789**********98875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.31   5.1e+02       4       9 ..      10      15 ..       7      17 .. 0.85
   2 ?   11.7   0.0   9.3e-05      0.15       2      16 ..      34      48 ..      33      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.31
                        zf_UBZ  4 lCerCg 9 
                                   C+ C+
  gi|91773261|ref|YP_565953.1| 10 ACPICK 15
                                  6****7 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.3e-05
                        zf_UBZ  2 tylCerCgkeipese 16
                                  t  C++C++++p+++
  gi|91773261|ref|YP_565953.1| 34 TLYCSKCNEYFPITD 48
                                  678*********985 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.6   4.4e-05     0.072       4      35 ..       9      42 ..       6      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
                  Cys_rich_KTR  4 vlcPvCgnkTRlkired..TvLknfpLfCPKCkq 35
                                  + cP+C++   l i ++   ++    L+C KC +
  gi|91773261|ref|YP_565953.1|  9 LACPICKGDLVLNITKEdeKEIISGTLYCSKCNE 42
                                  68********9999875125677889******75 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.011        18      18      26 .]      10      18 ..       9      18 .. 0.68
   2 ?    7.7   0.1    0.0015       2.4       2      14 ..      34      48 ..      33      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                   zf-ribbon_3 18 vCpyCGtkl 26
                                  +Cp C ++l
  gi|91773261|ref|YP_565953.1| 10 ACPICKGDL 18
                                  578887765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                   zf-ribbon_3  2 tvrCPnCGa.p.lss 14
                                  t +C++C++   +++
  gi|91773261|ref|YP_565953.1| 34 TLYCSKCNEyFpITD 48
                                  679*****9864655 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.9   0.00014      0.22       5      32 ..      10      41 ..       9      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                  --TTTT-TTTEEETT........S-EEETTTT CS
                Prim_Zn_Ribbon  5 pCPvCGGrDrFrfddkdgr....GtwfCrqCg 32
                                  +CP+C+G     ++++d +    Gt  C++C+
  gi|91773261|ref|YP_565953.1| 10 ACPICKGDLVLNITKEDEKeiisGTLYCSKCN 41
                                  7******9999999999989***********4 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 ?    8.5   2.2     0.001       1.7       2      32 ..       7      45 ..       6      46 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                 A2L_zn_ribbon  2 nlkvCsvCggngiln..seq......gylvCieCgasfp 32
                                  ++  C  C+g+ +ln  +e+      g l+C +C+  fp
  gi|91773261|ref|YP_565953.1|  7 DILACPICKGDLVLNitKEDekeiisGTLYCSKCNEYFP 45
                                  5566889********875542233335677888876665 PP

>> CK_II_beta  Casein kinase II regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2     7e-05      0.11     104     135 ..      13      44 ..       2      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                    CK_II_beta 104 lCekqkvLPvGlsdkpgektvklyCpkCedvY 135
                                   +C++  vL +   d+ +  +  lyC kC++ +
  gi|91773261|ref|YP_565953.1|  13 ICKGDLVLNITKEDEKEIISGTLYCSKCNEYF 44 
                                   7****************************987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.8   0.00024       0.4       2      25 ..      10      40 ..       9      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                                  EETTTTCEE.C......HEETSTTCEEESSS CS
                  TF_Zn_Ribbon  2 kCPnCgstn.l......veDpergelvCtdC 25
                                   CP+C+++  l      + +  +g+l+C++C
  gi|91773261|ref|YP_565953.1| 10 ACPICKGDLvLnitkedEKEIISGTLYCSKC 40
                                  5******9844999777777889******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 453.81
//
Query:       gi|91773262|ref|YP_565954.1|  [L=314]
Description: nucleoside recognition [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   30.5  12.6     0.0001   22.5   3.3    3.1  2  Gate      Nucleoside recognition


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   3.3   5.8e-09    0.0001       4      90 ..      15     182 ..      12     202 .. 0.65
   2 !    8.7   6.2   0.00011         2       3     111 ..     181     282 ..     179     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.8e-09
                          Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtly................ 68 
                                   ++ +i+++++  ++l + +++++++++ ep+f+     l+  ++ +++++++  +v++ ++ +                  
  gi|91773262|ref|YP_565954.1|  15 VIITIFIGLFGTGILIEMGIMQKLSRFTEPIFKHTH--LPQSCASAFMVSLG-STVAANSMVVKVkdegfiddremmlcai 92 
                                   7789******************************88..99999999999988.4555555544434555566666666666 PP

                          Gate  69 ....................................................................tsalgellqgfdt 81 
                                                                                                       + +l+e+++++++
  gi|91773262|ref|YP_565954.1|  93 lnstpayireiltyqipivlpalgpivggfyvmvfiisalvkvsvviilsriwfkehngalpepekieRPKLREAIRKAFN 173
                                   666666666666666666666666666666666666666666666666666666666666666666665555555555555 PP

                          Gate  82 pksalafll 90 
                                   ++++l + +
  gi|91773262|ref|YP_565954.1| 174 RQKRLFTKI 182
                                   555555444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00011
                          Gate   3 kagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpk 83 
                                   k+  i + +++l+  l++ ++++ +  l  p+   +g   + +++++l+t +a+  +++++lg l        + g  t  
  gi|91773262|ref|YP_565954.1| 181 KIAIIYITMTTLVFALRERGAFETFNVL--PLADIFG--IPAESIIPLTTYVASPIIGISLLGPLI-------SDGGITYL 250
                                   5666778888888888888888888877..99999**..**************************6.......89999999 PP

                          Gate  84 sal.afllfvllytpcvat...lavivrelgs 111
                                   +a+ +++l ++++ p +++   l+ +v+++g 
  gi|91773262|ref|YP_565954.1| 251 QAMiVLMLGSMFMLPILSIrsiLPRYVSIFGP 282
                                   97725555566666777665557778777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2134.02
//
Query:       gi|91773263|ref|YP_565955.1|  [L=116]
Description: F420H2 dehydrogenase subunit O [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-53  180.1   3.5    1.4e-53  179.9   3.5    1.0  1  FpoO      F420H2 dehydrogenase subunit FpoO
  ------ inclusion threshold ------
        0.6   10.2   6.7        4.4    7.4   2.6    2.9  2  DZR       Double zinc ribbon
        1.3    9.0  11.1       0.28   11.1   2.0    3.3  3  DUF4428   Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.9   3.5   2.3e-57   1.4e-53       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 2.3e-57
                          FpoO   1 madcdlcgvsiPtviPvrvfkPrlelsyPeGvwkGlcekclkaakktydelskeeasgtaGkcdlcgkktrlydvevqvPs 81 
                                   madcdlcgvsiPtv+Pvrvf+Pr+elsyPeGvwkGlc  cl+aakk+yde+s+++a+gt+Gkcdlcg+kt+l+dv v+vPs
  gi|91773263|ref|YP_565955.1|   1 MADCDLCGVSIPTVCPVRVFSPRFELSYPEGVWKGLCGGCLAAAKKAYDESSEKVAAGTFGKCDLCGTKTQLQDVGVNVPS 81 
                                   9******************************************************************************** PP

                          FpoO  82 fskgsekktaklckrcleaveeayekkke 110
                                   fsk+s  kt+k+c +cle+++e++ekk+e
  gi|91773263|ref|YP_565955.1|  82 FSKRSIVKTRKICLKCLEETSESFEKKDE 110
                                   **************************986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.1     0.018   1.1e+02      15      32 ..       4      16 ..       2      48 .. 0.66
   2 ?    7.4   2.6   0.00074       4.4      15      40 ..      63     103 ..      33     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.018
                           DZR 15 CseCgtklkavaaedrCp 32
                                  C+ Cg +++     ++Cp
  gi|91773263|ref|YP_565955.1|  4 CDLCGVSIP-----TVCP 16
                                  999999996.....4444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00074
                           DZR  15 CseCgtklkavaa................edrCpsCgekvdp 40 
                                   C+ Cgtk + + +                 + C +C e++++
  gi|91773263|ref|YP_565955.1|  63 CDLCGTKTQLQ-DvgvnvpsfskrsivktRKICLKCLEETSE 103
                                   99999996522.246688888999999999999999877665 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.4     0.035   2.1e+02       1       9 [.       3      11 ..       3      19 .. 0.83
   2 ?   -1.4   0.0      0.39   2.3e+03      22      29 ..      36      43 ..      25      55 .. 0.76
   3 ?   11.1   2.0   4.7e-05      0.28       1      35 [.      62     106 ..      62     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.035
                       DUF4428  1 iCaiCgkKi 9 
                                  +C++Cg  i
  gi|91773263|ref|YP_565955.1|  3 DCDLCGVSI 11
                                  6****9655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.39
                       DUF4428 22 vCkdClkK 29
                                  +C  Cl  
  gi|91773263|ref|YP_565955.1| 36 LCGGCLAA 43
                                  78888764 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.7e-05
                       DUF4428   1 iCaiCgkKigll..........krlkleDgyvCkdClkKlsefls 35 
                                   +C++Cg+K+ l           kr  ++  ++C +Cl++ se+++
  gi|91773263|ref|YP_565955.1|  62 KCDLCGTKTQLQdvgvnvpsfsKRSIVKTRKICLKCLEETSESFE 106
                                   7********9944455555554446666669*******9888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 846.63
//
Query:       gi|91773264|ref|YP_565956.1|  [L=480]
Description: F420H2 dehydrogenase subunit N [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-74  251.1  30.1    1.2e-74  251.1  30.1    2.1  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0076   16.3   1.8      0.088   12.9   1.8    3.0  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
       0.16   11.5   0.0       0.26   10.8   0.0    1.2  1  DUF4739          Domain of unknown function (DUF4739)
        6.3    7.0   8.4       0.56   10.3   1.0    3.3  2  DUF962           Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   3.7      0.41   1.8e+03     119     150 ..      44      74 ..       4     115 .. 0.57
   2 !  251.1  30.1   2.7e-78   1.2e-74       1     292 [.     119     419 ..     119     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.41
               Proton_antipo_M 119 llAatlvkagvlllirlllllavssneisqll 150
                                   l+ a+l++++ ++ +++++  + s  ++sq++
  gi|91773264|ref|YP_565956.1|  44 LV-AMLLTISSFGTTAVMFSNSLSIDALSQFF 74 
                                   33.22334444443333333333333333333 PP

  == domain 2  score: 251.1 bits;  conditional E-value: 2.7e-78
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslel 81 
                                   andL+ l++++El +l++y L+g+ kk+p s+eAs+k+f++++l+  +LLlgi ++y++tgt+++e ++++++l lns++ 
  gi|91773264|ref|YP_565956.1| 119 ANDLMVLFVAFELASLATYALAGFEKKNPASIEASMKYFIIGSLSAALLLLGIGYVYGATGTTNIEGIAQNIDLLLNSPMG 199
                                   89******************************************************************************* PP

               Proton_antipo_M  82 llllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiismllg 161
                                    l l+ll++g+ +K+a+vp+h+W pd y++aP  vsallAa   k+g+++ ++++       + ++++ ++ila+++m +g
  gi|91773264|ref|YP_565956.1| 200 ILSLVLLIAGFGFKIALVPFHMWAPDTYQGAPSLVSALLAAGSKKMGIIAAFKVFIGALiALQADWQIAFAILAVLTMTYG 280
                                   ***************************************999*******9998776555589******************* PP

               Proton_antipo_M 162 slvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyere.......ktrdiray 235
                                   ++val+qt++Kr+lAySs+++ Gy+++a++v+t +++++ i++ l+h+++ka+ F++  +v+y  +       +++ +++ 
  gi|91773264|ref|YP_565956.1| 281 NIVALSQTSVKRMLAYSSLAQAGYITMAFVVMTPMALTGGILYALSHGFMKAGAFIATAAVVYMVTsenkdilNADHLDNF 361
                                   *********************************************************9999998555789999999***** PP

               Proton_antipo_M 236 ggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvl 292
                                   +gL  +mPi+al ++v++++l+G+Pptag++skf ++++ ++ +l++l+++ ++ s+l
  gi|91773264|ref|YP_565956.1| 362 KGLGRRMPITALSMTVFVFALSGIPPTAGYMSKFILFSSTIQSGLVWLAVIaILNSAL 419
                                   *************************************************997777766 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 !   12.9   1.8     2e-05     0.088      10      55 ..      59     104 ..      47     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
               Proton_antipo_N  10 lsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                   + ++ ++ +D ls  + +v  +v++lv++ S++Y ++ ++   +++
  gi|91773264|ref|YP_565956.1|  59 VMFSNSLSIDALSQFFKIVFLTVTTLVCIASVKYTDGNDHADEYYV 104
                                   5678899***************************987667666665 PP

>> DUF4739  Domain of unknown function (DUF4739)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.7e-05      0.26     195     217 ..     176     198 ..     166     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.7e-05
                       DUF4739 195 tspgpanisqieqnidlivkspl 217
                                   +++g++ni  i qnidl++ sp+
  gi|91773264|ref|YP_565956.1| 176 GATGTTNIEGIAQNIDLLLNSPM 198
                                   568*******************8 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   0.00013      0.56      28      91 ..     106     168 ..      12     171 .. 0.75
   2 ?   -1.2   1.3       0.5   2.2e+03      44      44 ..     371     371 ..     246     434 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                        DUF962  28 vplilltvlllllraklklllalfvvgyifafvGHfvfEkrkPAlfknplqsllidplmvllel 91 
                                   v ++ + +++++ + +l +l+++f ++  + ++  + fEk++PA+++  +++++i+ l ++l l
  gi|91773264|ref|YP_565956.1| 106 VLFATIGMMMVASANDLMVLFVAFELASLATYALAG-FEKKNPASIEASMKYFIIGSLSAALLL 168
                                   222223333333333355666666666555555555.******************988776665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.5
                        DUF962  44 l 44 
                                    
  gi|91773264|ref|YP_565956.1| 371 T 371
                                   0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); 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:                         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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3236.73
//
Query:       gi|91773265|ref|YP_565957.1|  [L=495]
Description: F420H2 dehydrogenase subunit M [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-69  234.5  33.7    1.5e-69  234.5  33.7    1.8  3  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
       0.15   11.5   0.1        0.3   10.6   0.1    1.4  1  DUF3343          Protein of unknown function (DUF3343)


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.7      0.27   2.4e+03      64      64 ..      58      58 ..       8     100 .. 0.61
   2 ?   -3.6   0.0      0.55   4.9e+03       8      23 ..      74      89 ..      69     120 .. 0.76
   3 !  234.5  33.7   1.6e-73   1.5e-69       1     293 []     127     424 ..     127     424 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.27
               Proton_antipo_M 64 e 64
                                  +
  gi|91773265|ref|YP_565957.1| 58 Q 58
                                  1 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.55
               Proton_antipo_M  8 ylglElvllplylLig 23
                                   lg ++v++pl+lL +
  gi|91773265|ref|YP_565957.1| 74 HLGVDGVSMPLILLNA 89
                                  5777777777777754 PP

  == domain 3  score: 234.5 bits;  conditional E-value: 1.6e-73
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg......tlefeelskalelg 75 
                                   + d +l+y+++El+l+pl++++++w+   ++ +A++k+f++t ++sl++Llgi+ ly ++       ++++++l++++++ 
  gi|91773265|ref|YP_565957.1| 127 SLDFFLFYVFWELTLVPLFFMVNIWGGA-NKKHAAIKFFIYTHVASLVMLLGIFGLYFNAWslsgvpNMDMTYLISQFQFL 206
                                   56899********************988.999**********************998554323347777788888888*** PP

               Proton_antipo_M  76 lnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssneisq.lllil 153
                                    +++++ l++l+ll+g++vK+++vp+h Wlpday eaPt++s+l+  +l+k+g+++l+r++l++   ++++ +++ ++ +l
  gi|91773265|ref|YP_565957.1| 207 ESEIARDLIFLALLFGFIVKTPVVPFHSWLPDAYSEAPTAGSVLF--ILLKIGGYGLFRVMLPMLpfTATPSLMItIMGAL 285
                                   *********************************************..*****************97656666555155589 PP

               Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdira 234
                                   ++is+++g+++alaq d+Kr++AySsish+Gy+++++a   + ++++a+++ ++h+l+ + +F+   +vi+ ++ t  i++
  gi|91773265|ref|YP_565957.1| 286 GAISIIYGAFLALAQKDLKRMIAYSSISHMGYVTLGCAGLVSLSISGAMFQQFSHGLIMSIMFMSC-GVIQTKTGTSIINN 365
                                   9************************************999999*********************99.7779999******* PP

               Proton_antipo_M 235 yggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvlt 293
                                   +ggLa++mP l +++++++++  GlP+++gF+++fl+L+ ++   +i +++a++a+v+t
  gi|91773265|ref|YP_565957.1| 366 LGGLAQRMPKLTVIMVLGFMASLGLPGLTGFIAEFLVLTFSFINVPIYVIIALLAIVIT 424
                                   ******************************************99999999999999997 PP

>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   3.3e-05       0.3       1      20 [.      45      64 ..      45      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.3e-05
                       DUF3343  1 yyvitFssthhAiaaekalk 20
                                  y +++F+st+ A+++e+a++
  gi|91773265|ref|YP_565957.1| 45 YMYFSFDSTSAAMQFEEAAN 64
                                  689**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3168.80
//
Query:       gi|91773266|ref|YP_565958.1|  [L=665]
Description: F420H2 dehydrogenase subunit L [Methanococcoides burtonii DSM 6242]
Scores for complete 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-72  244.3  23.6    1.5e-72  244.3  23.6    2.0  2  Proton_antipo_M  Proton-conducting membrane transporter
    3.9e-18   65.3   0.5    3.9e-18   65.3   0.5    4.0  5  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
      0.054   13.1   5.8       0.45   10.1   4.2    2.9  2  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2      0.83   4.9e+03     199     214 ..      82      97 ..      67     119 .. 0.55
   2 !  244.3  23.6   2.5e-76   1.5e-72       1     277 [.     130     434 ..     130     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.83
               Proton_antipo_M 199 eaaiihllthalfkal 214
                                   +a++++++t++ + + 
  gi|91773266|ref|YP_565958.1|  82 AAVMLLMVTFVSLLIH 97 
                                   2333333333333333 PP

  == domain 2  score: 244.3 bits;  conditional E-value: 2.5e-76
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllyn.....ltg.......tlefeels 69 
                                   ++++l+l++ +Elv+l++ylLig+w++kp +++A+ k+fl+t++g++++L gi+ll++     l+g        l+fee++
  gi|91773266|ref|YP_565958.1| 130 SDNILQLFVCWELVGLSSYLLIGFWFHKPGAASAAKKAFLTTRIGDVMFLAGIVLLFAdifaiLEGklpegvyLLQFEEIF 210
                                   789***************************************************999733333445888889999****** PP

               Proton_antipo_M  70 kal.........elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla 140
                                   k++          lg++ + l++++ll++ g++ Ks+q+plh+Wlpda +e+Pt vsal+ Aat+v+agv+l++r+++++ 
  gi|91773266|ref|YP_565958.1| 211 KFIpdlvainstVLGMEVSHLTIVTLLFFGGAVGKSGQFPLHVWLPDA-MEGPTTVSALIhAATMVTAGVYLVARTFPMFL 290
                                   *********998888999999***************************.*******************************9 PP

               Proton_antipo_M 141 vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygvea...aiihllthalfkallFll 218
                                    +++   ++++il++ ++l++++++++ +d+Kr+lAyS+is+lGym+++l+++ ++g ea   +++hl+ ha+fkallFl+
  gi|91773266|ref|YP_565958.1| 291 -AAPSTLIVVAILGAFTALFAATMGIVMNDLKRVLAYSTISQLGYMVLGLGLGAVIGAEAvgvSMFHLINHAFFKALLFLC 370
                                   .*************************************************996666555522279**************** PP

               Proton_antipo_M 219 agsviyerektrdirayggLakkmPilalvllvlllsla..GlPpt....agFlskfliLeaava 277
                                   agsvi++   t+d+r++gg +k+mPi++++++ ++l+la  G+P+t    +gFlsk+ i+e a+ 
  gi|91773266|ref|YP_565958.1| 371 AGSVIHAV-GTHDMRQLGGVRKVMPITFATMTAAALALAgfGIPGTsigfSGFLSKDPIIEYAYV 434
                                   ****9987.9****************************9889****99999*********98764 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 !   65.3   0.5   6.5e-22   3.9e-18      12      55 ..      72     115 ..      65     117 .. 0.94
   2 ?   -3.7   0.1       2.2   1.3e+04      14      28 ..     224     238 ..     221     240 .. 0.77
   3 ?   -3.0   0.1       1.4   8.3e+03      30      37 ..     263     270 ..     263     271 .. 0.91
   4 ?   -2.1   0.4      0.73   4.3e+03      22      39 ..     539     556 ..     536     559 .. 0.70
   5 ?   -0.4   0.2      0.21   1.3e+03      26      38 ..     645     657 ..     643     657 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 6.5e-22
               Proton_antipo_N  12 ieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                   +++g+l+D+l a+mll+vtfvsll+h+Y++gYM++d+ ++R+fa
  gi|91773266|ref|YP_565958.1|  72 LNLGILIDPLAAVMLLMVTFVSLLIHIYAVGYMSHDPAKPRYFA 115
                                   589****************************************8 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
               Proton_antipo_N  14 igfllDklsalmllv 28 
                                   +g+ ++ l+++ ll+
  gi|91773266|ref|YP_565958.1| 224 LGMEVSHLTIVTLLF 238
                                   577888899888875 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.4
               Proton_antipo_N  30 tfvsllvh 37 
                                   t+vs+l+h
  gi|91773266|ref|YP_565958.1| 263 TTVSALIH 270
                                   89*****9 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.73
               Proton_antipo_N  22 salmllvvtfvsllvhlY 39 
                                    +l + ++  v+ lv+ Y
  gi|91773266|ref|YP_565958.1| 539 LILWMPLIVAVAGLVIAY 556
                                   567777777788787777 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.21
               Proton_antipo_N  26 llvvtfvsllvhl 38 
                                   ++vv +v+llv+l
  gi|91773266|ref|YP_565958.1| 645 AAVVAGVGLLVIL 657
                                   689*******975 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 ?   10.1   4.2   7.5e-05      0.45      92     181 ..     476     563 ..     455     598 .. 0.62
   2 ?    1.5   2.4     0.032   1.9e+02     163     203 ..     545     586 ..     537     620 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.5e-05
               Proton_antipo_C  92 yPhEsdntmlfpllvLvlftlfvGliGip.fnqegidldilskwLtpsinllhknsnesvdwyefltnaifSvsialfGif 171
                                     hEs+++m++pl++L++f ++ G++    f    i+++  +  ++   +l   +        e l    + + +a+ G++
  gi|91773266|ref|YP_565958.1| 476 GGHESPSSMTIPLAILAVFAVIFGALSRGkFM-TFIESNFEHLDMNALAQLGGYHLGA--HGHEPLLILWMPLIVAVAGLV 553
                                   359*********************99753243.3333333333333333333333322..456667777788899999999 PP

               Proton_antipo_C 172 iAsllYkpvy 181
                                   iA+l+Y++  
  gi|91773266|ref|YP_565958.1| 554 IAYLIYNKRV 563
                                   9999997643 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.032
               Proton_antipo_C 163 vsialfGifiAsllYkpvyssl.qnldlinsfvkkgpkrill 203
                                   + +a+ G++iA+l+Y++    + + +   n + k  ++r   
  gi|91773266|ref|YP_565958.1| 545 LIVAVAGLVIAYLIYNKRVIDMsRIVSSENPVYKLLYNRYYQ 586
                                   578999999999999874333303334444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 4799.63
//
Query:       gi|91773267|ref|YP_565959.1|  [L=100]
Description: F420H2 dehydrogenase subunit K [Methanococcoides burtonii DSM 6242]
Scores for complete 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-26   91.2   4.8      3e-26   91.1   4.8    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.086   12.8   0.0       0.11   12.4   0.0    1.2  1  BMC          BMC domain


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 !   91.1   4.8   3.3e-30     3e-26       2     103 ..       7      95 ..       6     100 .] 0.97

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 3.3e-30
                                   HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHH CS
                   Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaeta 82 
                                   +l+l+a++f iGlyg+++++n +++l+++el++n++n++lv+++++              +d+ +q+++L+ i+++aae+a
  gi|91773267|ref|YP_565959.1|   7 YLALSAIVFSIGLYGLMTHKNGIRMLMCVELMLNSANINLVAFSSYN-------------NDMTGQVFALFSIALAAAEAA 74 
                                   899*******************************************9.............********************* PP

                                   HHHHHHHHHHHHSSS-BCCG- CS
                   Oxidored_q2  83 vgLallvrlyreygtddvqel 103
                                   +g a+l+++yr ++ +dv++l
  gi|91773267|ref|YP_565959.1|  75 IGFAILMSIYRMRDMIDVDKL 95 
                                   *******************98 PP

>> BMC  BMC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.11       3      56 ..      21      77 ..      20      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                  EEEEEESHHHHHHHHHHHHHHSSEEEEEEEECTTT...CEEEEEEESHHHHHHHHHH CS
                           BMC  3 GlietrglaaaieaaDaalKaAnVelvgvekvggg...kvtviitGdvaaVkaAvea 56
                                  Gl++ +++  +++++  +l +An++lv +++ ++    +v+++++  +aa +aA+  
  gi|91773267|ref|YP_565959.1| 21 GLMTHKNGIRMLMCVELMLNSANINLVAFSSYNNDmtgQVFALFSIALAAAEAAIGF 77
                                  8999999999*******************9999944778999999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 694.44
//
Query:       gi|91773268|ref|YP_565960.1|  [L=135]
Description: F420H2 dehydrogenase subunit I [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   56.6  11.2    2.3e-08   33.5   2.9    2.3  2  Fer4      4Fe-4S binding domain
    5.6e-12   46.1   8.0    7.9e-12   45.6   8.0    1.2  1  Fer4_7    4Fe-4S dicluster domain
    2.1e-11   43.8  17.6    7.7e-09   35.6   8.3    1.6  2  Fer4_9    4Fe-4S dicluster domain
      2e-09   38.3   5.0     0.0004   21.3   1.2    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    3.7e-09   36.6   7.5    5.6e-09   36.0   7.5    1.3  1  Fer4_21   4Fe-4S dicluster domain
    1.2e-08   34.9  10.1    2.9e-08   33.7  10.4    1.5  1  Fer4_10   4Fe-4S dicluster domain
    2.2e-07   30.5   9.0    6.2e-05   22.9   1.6    2.3  2  Fer4_2    4Fe-4S binding domain
    2.7e-07   30.9   7.7    3.6e-05   24.1  10.9    2.0  2  Fer4_8    4Fe-4S dicluster domain
    1.1e-05   25.2  13.7    0.00011   22.1   4.3    2.3  2  Fer4_6    4Fe-4S binding domain
    3.6e-05   23.9   9.6     0.0026   18.1   1.2    2.3  2  Fer4_4    4Fe-4S binding domain
      4e-05   24.1  10.0     0.0025   18.3  10.9    2.2  2  Fer4_17   4Fe-4S dicluster domain
    4.1e-05   24.2   6.1     0.0086   16.8   0.4    2.5  2  Fer4_15   4Fe-4S single cluster domain
    5.3e-05   24.0   7.6      0.014   16.2   1.5    2.1  2  Fer4_22   4Fe-4S dicluster domain
      0.001   19.6  12.1     0.0019   18.7   2.4    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.002   18.9  15.8       0.05   14.6   3.3    2.2  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.12   12.6   9.5         11    6.2   9.5    2.1  1  Fer4_18   4Fe-4S dicluster domain
       0.14   12.1   0.0        0.2   11.5   0.0    1.2  1  TRSP      TRSP domain C terminus to PRTase_2


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 !   33.5   2.9   2.2e-11   2.3e-08       3      24 .]      39      60 ..      38      60 .. 0.94
   2 !   28.1   1.2   1.1e-09   1.1e-06       2      23 ..      78      99 ..      77     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.2e-11
                                  EETTTSSS-THHHHHSTTTEEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                   d++kCigCG+C++ CP+ AI+
  gi|91773268|ref|YP_565960.1| 39 LDKSKCIGCGICANTCPNSAIK 60
                                  699*****************96 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.1e-09
                                  EEETTTSSS-THHHHHSTTTEE CS
                          Fer4  2 videekCigCGaCvevCPvgAI 23
                                   id + C++CG+C++ CP +A+
  gi|91773268|ref|YP_565960.1| 78 AIDISHCMFCGLCIDQCPQDAL 99
                                  68999****************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 !   45.6   8.0   7.5e-15   7.9e-12       1      52 []      43      98 ..      43      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 7.5e-15
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekv....eidpekClgCgaCvavCPtga 52
                                  +CigCg C+++Cp++ai++  + ++k  +k+    +id + C++Cg C++ CP +a
  gi|91773268|ref|YP_565960.1| 43 KCIGCGICANTCPNSAIKIVRARVNKDSDKTrwfpAIDISHCMFCGLCIDQCPQDA 98
                                  7******************998888866555557799****************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 !   19.9   1.8   5.7e-07    0.0006      33      51 .]      36      59 ..      18      59 .. 0.72
   2 !   35.6   8.3   7.3e-12   7.7e-09       1      50 [.      43      98 ..      43      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.7e-07
                        Fer4_9 33 e.....eaCigCgaCveaCpkgai 51
                                        ++CigCg C++ Cp+ ai
  gi|91773268|ref|YP_565960.1| 36 LqkldkSKCIGCGICANTCPNSAI 59
                                  13334489************9987 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 7.3e-12
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase......eaCigCgaCveaCpkga 50
                                  kC+gCg C + Cp+ +++  +a+     +++++      + C++Cg C++ Cp++a
  gi|91773268|ref|YP_565960.1| 43 KCIGCGICANTCPNSAIKIVRARVNKDSDKTRWfpaidiSHCMFCGLCIDQCPQDA 98
                                  7****************99999999999999999*****99*************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.2   3.8e-07    0.0004       1      24 [.      43      65 ..      43      77 .. 0.79
   2 !   18.7   0.1   2.4e-06    0.0025       1      21 [.      83     103 ..      83     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.8e-07
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkeke 24
                                  +C++Cg Ca++CP +aik  + ++
  gi|91773268|ref|YP_565960.1| 43 KCIGCGICANTCPNSAIKIVR-AR 65
                                  5****************9773.33 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.4e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                   +C  Cg C++ CP++a++++k
  gi|91773268|ref|YP_565960.1|  83 HCMFCGLCIDQCPQDALSSTK 103
                                   79***************9983 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   7.5   5.3e-12   5.6e-09       3      57 ..      39      99 ..      37     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.3e-12
                       Fer4_21  3 idedkCigCgkCliaCedtshqai......eidaktvlkvv.edeCvGCnlCssvCPvedci 57
                                  +d++kCigCg C+ +C++++++ +      + d+ + ++ +  ++C+ C lC++ CP +d++
  gi|91773268|ref|YP_565960.1| 39 LDKSKCIGCGICANTCPNSAIKIVrarvnkDSDKTRWFPAIdISHCMFCGLCIDQCP-QDAL 99
                                  799***************99999977664334444556666269*************.5765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7  10.4   2.8e-11   2.9e-08       4      56 .]      39      95 ..      36      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.8e-11
                       Fer4_10  4 idddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +d+++Ci+Cg C + CP ++    ++ ++k+ ++      +++++C++cg C+++CP
  gi|91773268|ref|YP_565960.1| 39 LDKSKCIGCGICANTCPNSAikivRARVNKDSDKTRWFPAIDISHCMFCGLCIDQCP 95
                                  799***************99988888888888888888999***************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 !   22.9   1.6   5.9e-08   6.2e-05       5      22 .]      39      56 ..      36      56 .. 0.90
   2 !   12.0   1.0   0.00017      0.18       3      22 .]      77      96 ..      75      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.9e-08
                        Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                   d  +CigCg+C + CP+
  gi|91773268|ref|YP_565960.1| 39 LDKSKCIGCGICANTCPN 56
                                  6899*************5 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00017
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +++d  +C+ Cg C++ CP+
  gi|91773268|ref|YP_565960.1| 77 PAIDISHCMFCGLCIDQCPQ 96
                                  789999*************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 !   24.1  10.9   3.4e-08   3.6e-05       3      64 ..      42      97 ..      40      98 .. 0.70
   2 !   15.8   0.5   1.4e-05     0.014       2      17 ..      81     109 ..      80     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.4e-08
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  +kCi+Cg C ++Cp    +  +   +++  +   +       +  + +C+ cg C ++Cp++
  gi|91773268|ref|YP_565960.1| 42 SKCIGCGICANTCPNSAIKIVRARVNKDSDKT-RWFP-----AIDISHCMFCGLCIDQCPQD 97
                                  79************555554333333333333.2222.....4579**************85 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.4e-05
                        Fer4_8   2 lekCieCgaCqsaCp.............v 17 
                                   +++C+ Cg+C ++Cp             v
  gi|91773268|ref|YP_565960.1|  81 ISHCMFCGLCIDQCPqdalsstkvyttgV 109
                                   68999999999999977555555444444 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   4.3   1.1e-07   0.00011       5      24 .]      40      59 ..      40      59 .. 0.94
   2 !    8.4   1.9    0.0022       2.4       2      24 .]      77      99 ..      76      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                        Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                  d++kCigCg C++ CP  ai
  gi|91773268|ref|YP_565960.1| 40 DKSKCIGCGICANTCPNSAI 59
                                  89**************9887 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  ++id + C  Cg C++ CP +a+
  gi|91773268|ref|YP_565960.1| 77 PAIDISHCMFCGLCIDQCPQDAL 99
                                  6777777888*********8875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.2   2.5e-06    0.0026       2      15 ..      42      55 ..      41      72 .. 0.89
   2 !   10.2   1.7   0.00083      0.88       4      16 ..      84      96 ..      81     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  ++CigCg C ++CP
  gi|91773268|ref|YP_565960.1| 42 SKCIGCGICANTCP 55
                                  79************ PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00083
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C  Cg C++ CPq
  gi|91773268|ref|YP_565960.1| 84 CMFCGLCIDQCPQ 96
                                  66699*******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 !   14.1   2.5   4.9e-05     0.051      43      58 ..      41      56 ..      12      59 .. 0.78
   2 !   18.3  10.9   2.4e-06    0.0025       1      59 [.      43      97 ..      43      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-05
                       Fer4_17 43 aslCieCgeCerkCPq 58
                                   s+Ci+Cg C+  CP+
  gi|91773268|ref|YP_565960.1| 41 KSKCIGCGICANTCPN 56
                                  5789999999999987 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.4e-06
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaeke..ekaslCieCgeCerkCPqg 59
                                  +Ci+Cg C++ Cp  ++      k++ra  +++ +++       +s C+ Cg+C  +CPq+
  gi|91773268|ref|YP_565960.1| 43 KCIGCGICANTCPNSAI------KIVRARVNKDSDKTRWFpaIDISHCMFCGLCIDQCPQD 97
                                  6************8776......4555555555666555433599**************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 !   16.8   0.4   8.1e-06    0.0086       3      20 ..      39      56 ..      38      69 .. 0.92
   2 !    9.9   0.8    0.0011       1.2       3      19 ..      79      95 ..      78     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.1e-06
                       Fer4_15  3 vDrdaCigcglCvaeape 20
                                  +D+++Cigcg C+  +p+
  gi|91773268|ref|YP_565960.1| 39 LDKSKCIGCGICANTCPN 56
                                  8***************96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                       Fer4_15  3 vDrdaCigcglCvaeap 19
                                  +D + C+ cglC++ +p
  gi|91773268|ref|YP_565960.1| 79 IDISHCMFCGLCIDQCP 95
                                  8999***********98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.5   1.3e-05     0.014      75      94 ..      37      56 ..      11      59 .. 0.85
   2 !   12.0   0.5   0.00028       0.3      71      95 ..      73      97 ..      56      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                       Fer4_22 75 ekfgesgCvGCgRCieacpv 94
                                  +k ++s+C+GCg C ++cp+
  gi|91773268|ref|YP_565960.1| 37 QKLDKSKCIGCGICANTCPN 56
                                  57799*************97 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00028
                       Fer4_22 71 sefkekfgesgCvGCgRCieacpvk 95
                                  + +   ++ s+C+ Cg Ci++cp++
  gi|91773268|ref|YP_565960.1| 73 TRWFPAIDISHCMFCGLCIDQCPQD 97
                                  467778899*************985 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.4   1.8e-06    0.0019       2      18 ..      40      56 ..      39      57 .. 0.94
   2 ?    6.2   2.4     0.014        15       1      18 [.      79      96 ..      79      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.8e-06
                       Fer4_13  2 DrdtCiacgaCvelaPd 18
                                  D+++Ci+cg+C++++P+
  gi|91773268|ref|YP_565960.1| 40 DKSKCIGCGICANTCPN 56
                                  99**************7 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  +D + C+ cg+C + +P+
  gi|91773268|ref|YP_565960.1| 79 IDISHCMFCGLCIDQCPQ 96
                                  68899************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   4.8    0.0012       1.3       1      15 []      44      58 ..      44      58 .. 0.93
   2 !   14.6   3.3   4.7e-05      0.05       1      15 []      84      98 ..      84      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg C + CP+ A
  gi|91773268|ref|YP_565960.1| 44 CIGCGICANTCPNSA 58
                                  ************876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.7e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg+C + CP +A
  gi|91773268|ref|YP_565960.1| 84 CMFCGLCIDQCPQDA 98
                                  99**********998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   9.5     0.011        11      54      97 ..      37      96 ..      19     115 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                       Fer4_18 54 kekgagdcidcescvkvcPtg.idi...r...kGlq.........l.eciscllcidacdk 97
                                  ++ ++++ci c+ c + cP   i i   r   +            + +c+ c+lcid c +
  gi|91773268|ref|YP_565960.1| 37 QKLDKSKCIGCGICANTCPNSaIKIvraRvnkDS-DktrwfpaidIsHCMFCGLCIDQCPQ 96
                                  4567889************643665322121111.11112222222369999999999954 PP

>> TRSP  TRSP domain C terminus to PRTase_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019       0.2      28      55 ..     101     128 ..      91     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                          TRSP  28 aalekaervlvLGteElmylPlrlAaal 55 
                                   +++  ++ v+ L +eEl+y+P +lA+++
  gi|91773268|ref|YP_565960.1| 101 STKVYTTGVIRLTHEELLYTPDMLAREI 128
                                   4444678899***************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1002.31
//
Query:       gi|91773269|ref|YP_565961.1|  [L=344]
Description: F420H2 dehydrogenase subunit H [Methanococcoides burtonii DSM 6242]
Scores for complete 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-106  353.8  22.4   8.9e-106  353.5  22.4    1.0  1  NADHdh      NADH dehydrogenase
  ------ inclusion threshold ------
        1.8    6.4   3.2        2.6    5.8   3.2    1.1  1  V_ATPase_I  V-type ATPase 116kDa subunit family


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 !  353.5  22.4  9.9e-110  8.9e-106       5     297 ..      21     334 ..      17     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 353.5 bits;  conditional E-value: 9.9e-110
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTT CS
                        NADHdh   5 lllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafav 85 
                                   +l+ v++  +++++++eRk+++ iq RlGP++vGp+Gl+q++aDa+Kl++Ked+ip+kad+llf+ ap++++ +++l++++
  gi|91773269|ref|YP_565961.1|  21 CLIGVVFGGAMIVVWFERKLSGDIQFRLGPKYVGPFGLFQLVADAIKLMTKEDLIPSKADRLLFVSAPIVLMGSVFLMLVA 101
                                   56667778888********************************************************************** PP

                                   S-SSS..........SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S CS
                        NADHdh  86 iPfge..........vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllags 156
                                   iPfg+          v +++++++l+i a+ss++++g ++ +++sn+kY+llGa+R+ a mi yEv+lg+++++v++++gs
  gi|91773269|ref|YP_565961.1| 102 IPFGAvfvngveypiVGTEMDISILYIEAVSSISIIGAFMYAYSSNNKYSLLGAFRNFARMIGYEVPLGITIVSVAVMVGS 182
                                   ****5556678889999999************************************************************* PP

                                   S-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHH CS
                        NADHdh 157 lslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsalavl 237
                                   l++ ei +aq+ iwfi+lq+l+fi+f+ial+a ++r PFD  e+e+ELvaG+ tEY+gm+f+l f+aey++++l s+l+vl
  gi|91773269|ref|YP_565961.1| 183 LNIVEIAQAQSPIWFIFLQPLGFIVFFIALMADMGRLPFDQNESEEELVAGWITEYTGMRFGLGFFAEYIHLILGSMLVVL 263
                                   ********************************************************************************* PP

                                   HCT.SS-HCCS...........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                        NADHdh 238 lFlgGwllpfs...........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                   lFlgGw+lp             ++l++llKv+l+++++i++r+++pR+R+dq+++l+wk llpl+l+nl +
  gi|91773269|ref|YP_565961.1| 264 LFLGGWNLPSFltnvtilgvflPTLFYLLKVALVILTIIMLRWAVPRFRIDQVVDLSWKRLLPLSLLNLGW 334
                                   ********98899*******9999********************************************976 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 ?    5.8   3.2   0.00029       2.6     525     573 ..     261     309 ..     252     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00029
                    V_ATPase_I 525 lfgvllslvNalyfkkkldiilefiPqllfllsifgYlvlliiyKWlvd 573
                                   ++ ++l ++N   f  +++i+  f+P l++ll +   +  +i+++W+v 
  gi|91773269|ref|YP_565961.1| 261 VVLLFLGGWNLPSFLTNVTILGVFLPTLFYLLKVALVILTIIMLRWAVP 309
                                   34578999**************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2254.25
//
Query:       gi|91773270|ref|YP_565962.1|  [L=374]
Description: F420H2 dehydrogenase subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete 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-85  284.5   0.1    4.3e-83  278.5   0.1    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.9e-07   30.4   0.0    2.4e-07   30.1   0.0    1.3  1  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.5   0.1   4.8e-87   4.3e-83       2     271 .]     124     374 .]     124     374 .] 0.97

  Alignments for each domain:
  == domain 1  score: 278.5 bits;  conditional E-value: 4.8e-87
                                   TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSS CS
                Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkg 82 
                                   +G +++f+y+++eRe il+l+++vtGaR+t++++r+GGv+ Dlpeg+ ek  +++ +l++++++++kl+++++i+k R+ g
  gi|91773270|ref|YP_565962.1| 124 IGFVSMFMYTIKEREDILSLMDMVTGARITHTFLRFGGVRDDLPEGFKEKSVAVFASLREQIADYDKLFNHDEIYKLRCFG 204
                                   799****************************************************************************** PP

                                   SS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S- CS
                Complex1_49kDa  83 vgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpegp 163
                                   vgvl++++a +lg++Gp lRa+Gv++D+Rk+epY +Y++ldf+v+++++gD+ +R+ vr+eEm +++ Iieq+l+++p+gp
  gi|91773270|ref|YP_565962.1| 205 VGVLDSKTARDLGVSGPALRATGVPFDIRKDEPYLVYKDLDFKVCTATDGDIAARINVRLEEMLEAMYIIEQCLDQMPSGP 285
                                   ********************************************************************************* PP

                                   SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHH CS
                Complex1_49kDa 164 vlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqale 244
                                   +  ed+ + +                    t  ++vp+g+++++vE p+Ge+g+y+vsdgs+kp+r+kir p + ++qal+
  gi|91773270|ref|YP_565962.1| 286 IFFEDSLYGVR-------------------TPVMRVPEGDIFHRVEDPRGEMGFYVVSDGSDKPHRVKIRGPVYPTMQALP 347
                                   99988666433...................23468********************************************** PP

                                   HHTTTS-SGGGTHHHHTT---HHHHH- CS
                Complex1_49kDa 245 ellkgellaDvvailgsldivlgevDR 271
                                    l+kg+++aDv ai gs+d +++e+DR
  gi|91773270|ref|YP_565962.1| 348 PLIKGTTIADVAAIAGSMDGCTSEADR 374
                                   **************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.7e-11   2.4e-07       1      68 [.      48     115 ..      48     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.7e-11
                                   --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                  NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                   +G+E+il++++  +   +v+RiC   +++   a v ave+  +i++p+++++ir +++    l++h++
  gi|91773270|ref|YP_565962.1|  48 KGIEKILENKTYLQGIPIVDRICYLTAMTNEEAYVGAVEKLADIEVPEKSQYIRVIVEELSRLQSHLL 115
                                   59****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 00:00:00.39
# Mc/sec: 2892.99
//
Query:       gi|91773271|ref|YP_565963.1|  [L=158]
Description: NADH dehydrogenase subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete 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  126.1   0.1    1.5e-36  125.7   0.1    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.032   14.2   0.0       0.04   13.9   0.0    1.1  1  RNase_H_2       RNase_H superfamily


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   0.1   1.7e-40   1.5e-36       2     117 ..      32     147 ..      31     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 1.7e-40
                                   E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHHHHH CS
                Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgadwyE 81 
                                   ++epe+++ev++++kd  el fd+ls+ tavD++ ++++ vvyh+ s+++ + +++k+++++++pe++S+++++ +a+wyE
  gi|91773271|ref|YP_565963.1|  32 YLEPEKIVEVCQYMKD--ELLFDHLSSETAVDYPkRNEIVVVYHIGSYDHSVLMTIKIKLPRDAPEIESIVPVYWNANWYE 110
                                   689*************..599***********99999******************************************** PP

                                   HHHHHHSHHBCTTSSTSS-SSSSTT.SSS-TTSTTS- CS
                Complex1_30kDa  82 REayDmfGivfeghpdlrrillped.feghPLRkdfp 117
                                   RE+y++fG++f++hp+l+ ++lp++ +  +PLRkd++
  gi|91773271|ref|YP_565963.1| 111 RETYELFGVKFNNHPNLKPLVLPDElMGDWPLRKDYE 147
                                   *************************56777*****96 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.5e-06      0.04      22      89 ..      31      97 ..      19     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-06
                     RNase_H_2 22 vldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlfkkykldeeefr 89
                                  ++  + ++i++++q++++e    +  +e++++  ++++ +v+++  s+D ++l +   k + d +e++
  gi|91773271|ref|YP_565963.1| 31 AY-LEPEKIVEVCQYMKDELLFDHLSSETAVDYPKRNEIVVVYHIGSYDHSVLMTIKIKLPRDAPEIE 97
                                  44.46688899*****************99*********************99887755555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 865.87
//
Query:       gi|91773272|ref|YP_565964.1|  [L=184]
Description: F420H2 dehydrogenase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-21   75.2   0.1    5.8e-21   74.7   0.1    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.1   3.2e-25   5.8e-21      32     130 ..      85     169 ..      60     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 3.2e-25
                                   S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.E CS
                   Oxidored_q6  32 adskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevvpvdi 112
                                   ++++          adv++++G vt+k  +al++l+e+++ +k+vi++G+C+++GG +  ++++s+   v+++++  p+d+
  gi|91773272|ref|YP_565964.1|  85 NSPR---------AADVMIISGYVTKKYLPALNTLWEQMAAPKWVICMGDCSISGGPF--YESYST---VQNIDKMFPIDV 151
                                   3344.........89*******************************************..664444...579********* PP

                                   EE-SSS--HHHHHHHHHH CS
                   Oxidored_q6 113 nipGCPphpeailetlla 130
                                   +ipGCPp+pea+l+++ +
  gi|91773272|ref|YP_565964.1| 152 FIPGCPPRPEALLQGFIE 169
                                   *************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.44
# Mc/sec: 1266.38
//
Query:       gi|91773273|ref|YP_565965.1|  [L=131]
Description: F420H2 dehydrogenase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  122.4   1.8    6.8e-36  122.4   1.8    1.5  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
       0.18   11.1   0.1        0.2   11.0   0.1    1.1  1  Foamy_BEL    Foamy virus BEL 1/2 protein


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 ?   -2.3   0.1      0.56     5e+03      73      83 ..      13      23 ..       3      27 .. 0.59
   2 !  122.4   1.8   7.6e-40   6.8e-36       4      99 .]      31     129 ..      28     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.56
                                  HHHHHHHHHHH CS
                   Oxidored_q4 73 gliemllFlli 83
                                  ++i +++Fl++
  gi|91773273|ref|YP_565965.1| 13 SYIPVAVFLVV 23
                                  45666666655 PP

  == domain 2  score: 122.4 bits;  conditional E-value: 7.6e-40
                                   HHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST.....HHHHHHHHHHHH CS
                   Oxidored_q4   4 llllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkel...glfgliemllFl 81 
                                   ++++ +l++p++++++k ++YEcG +p+g+ar++f+v++yl+a+ F++FD+ev+fl+pwa+ ++ +    +++++eml+F+
  gi|91773273|ref|YP_565965.1|  31 TMAMVKLVSPRSKSPNKYTTYECGSDPLGDARIQFNVEYYLYAIAFVLFDIEVLFLYPWAMIYQGTsvdMVTAIVEMLIFI 111
                                   577889999****************************************************999776666888******** PP

                                   HHHHHHHHHHHHH-S-XX CS
                   Oxidored_q4  82 lillvglvYewkkgaLeW 99 
                                   ++ll+g++Y wkkgaL+W
  gi|91773273|ref|YP_565965.1| 112 FVLLFGYAYLWKKGALKW 129
                                   ****************** PP

>> Foamy_BEL  Foamy virus BEL 1/2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   2.2e-05       0.2     131     205 ..      25     107 ..       9     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.2e-05
                     Foamy_BEL 131 ylenpatfivwkftcqedpsgkrylgtqfwvpplgqvniqfyknyqivifcdal........dplavvfhgteeelydids 203
                                    l  pat+ + k       s ++y   +    plg+  iqf  +y +  +   l         p a +++gt  ++     
  gi|91773273|ref|YP_565965.1|  25 LLMPPATMAMVKLVSPRSKSPNKYTTYECGSDPLGDARIQFNVEYYLYAIAFVLfdievlflYPWAMIYQGTSVDMVTAIV 105
                                   5678999999999999999**********************8887654443332222234668999999999999976655 PP

                     Foamy_BEL 204 ev 205
                                   e+
  gi|91773273|ref|YP_565965.1| 106 EM 107
                                   55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 919.37
//
Query:       gi|91773274|ref|YP_565966.1|  [L=168]
Description: hypothetical protein Mbur_1298 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   4.2       0.11   12.6   0.2    2.7  3  DZR              Double zinc ribbon
      0.015   14.8  13.2       0.35   10.4   2.3    3.0  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.017   14.5  10.1       0.66    9.5   0.2    3.9  4  zf-ribbon_3      zinc-ribbon domain
      0.039   13.7   0.6         11    5.8   0.0    3.0  3  zinc_ribbon_5    zinc-ribbon domain
      0.098   13.1   0.9      0.098   13.1   0.9    2.4  2  Lar_restr_allev  Restriction alleviation protein Lar
        0.1   13.0   1.1        2.1    8.8   0.2    2.7  2  zf-IS66          zinc-finger binding domain of transposase IS
       0.11   12.3   2.0       0.18   11.7   0.3    2.2  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.21   12.1   8.8       0.39   11.2   1.4    2.6  2  zf-CHY           CHY zinc finger
       0.22   11.6  12.0        1.3    9.2   0.2    3.6  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.29   11.1   2.4        9.7    6.2   0.0    2.9  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
        0.5   11.2   6.6        1.6    9.6   0.8    2.7  2  zinc_ribbon_15   zinc-ribbon family
        1.7    8.4   3.2        7.9    6.3   0.1    2.7  3  RecO_C           Recombination protein O C terminal
        2.7    8.1   7.9        7.4    6.7   0.0    3.5  3  zf-C2HC5         Putative zinc finger motif, C2HC5-type
        3.4    7.9  12.3       0.54   10.5   0.7    3.3  4  Prok-RING_2      Prokaryotic RING finger family 2
        5.1    7.1   8.4        0.8    9.6   0.9    2.6  3  C1_1             Phorbol esters/diacylglycerol binding domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6     0.055        65      15      35 ..       4      26 ..       1      33 [. 0.65
   2 ?    4.2   0.1     0.038        45      28      37 ..     125     134 ..     111     142 .. 0.76
   3 ?   12.6   0.2     9e-05      0.11      13      40 ..     126     161 ..     119     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.055
                           DZR 15 CseCgtk..lkavaaedrCpsCg 35
                                  C  Cg +   k++++ + C sC 
  gi|91773274|ref|YP_565966.1|  4 CVICGDDqdFKQYESYNICTSCA 26
                                  66677664455566677777776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.038
                           DZR  28 edrCpsCgek 37 
                                    ++CpsC+++
  gi|91773274|ref|YP_565966.1| 125 YYKCPSCDTS 134
                                   5789999877 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 9e-05
                           DZR  13 rfCseCgtklkavaa........edrCpsCgekvdp 40 
                                     C+ C t++    +         + C++Cg++v++
  gi|91773274|ref|YP_565966.1| 126 YKCPSCDTSIFDKYEseevgewlVISCSNCGAMVKK 161
                                   56*******765555699999***********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 ?   10.4   2.3   0.00029      0.35       2      31 ..       3      31 ..       2      35 .. 0.79
   2 ?    8.0   3.4    0.0017         2       1      30 [.     126     160 ..     126     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                                  EETTTTCEECHEETSTTCE..EESSSSBEEEE CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergel..vCtdCGlVled 31
                                  kC +Cg +++   +e      +Ct+C  ++ed
  gi|91773274|ref|YP_565966.1|  3 KCVICGDDQDFKQYE---SynICTSCADIMED 31
                                  8*****997555555...335*****999998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0017
                                   EEETTTTCEECHEE....TSTTC...EEESSSSBEEE CS
                  TF_Zn_Ribbon   1 ykCPnCgstnlveD....perge...lvCtdCGlVle 30 
                                   ykCP C ++  ++D    +e ge   + C++CG+++ 
  gi|91773274|ref|YP_565966.1| 126 YKCPSCDTS--IFDkyesEEVGEwlvISCSNCGAMVK 160
                                   89*****87..55552236666666568*****9985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.099   1.2e+02       2       9 ..       1       8 [.       1      15 [. 0.80
   2 ?   -0.2   0.4      0.62   7.4e+02      17      22 ..      20      25 ..      17      25 .. 0.86
   3 ?    6.7   0.1    0.0041       4.9       2      10 ..     125     133 ..     124     138 .. 0.79
   4 ?    9.5   0.2   0.00055      0.66       3      13 ..     150     160 ..     149     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.099
                   zf-ribbon_3 2 tvrCPnCG 9
                                 + +C  CG
  gi|91773274|ref|YP_565966.1| 1 MEKCVICG 8
                                 67899999 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.62
                   zf-ribbon_3 17 nvCpyC 22
                                  n+C++C
  gi|91773274|ref|YP_565966.1| 20 NICTSC 25
                                  89*999 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0041
                   zf-ribbon_3   2 tvrCPnCGa 10 
                                   +++CP+C++
  gi|91773274|ref|YP_565966.1| 125 YYKCPSCDT 133
                                   689****97 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00055
                   zf-ribbon_3   3 vrCPnCGa.pls 13 
                                   ++C+nCGa + +
  gi|91773274|ref|YP_565966.1| 150 ISCSNCGAmV-K 160
                                   79*****944.5 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.8   2.1e+03      28      34 ..      22      28 ..       9      29 .. 0.75
   2 ?    4.6   0.1     0.022        27       4      11 ..     127     134 ..     126     147 .. 0.81
   3 ?    5.8   0.0    0.0096        11       1      13 [.     148     160 ..     148     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.8
                 zinc_ribbon_5 28 CakCaev 34
                                  C  Ca++
  gi|91773274|ref|YP_565966.1| 22 CTSCADI 28
                                  8888876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.022
                 zinc_ribbon_5   4 rCpdCdtk 11 
                                   +Cp Cdt 
  gi|91773274|ref|YP_565966.1| 127 KCPSCDTS 134
                                   7*****95 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0096
                 zinc_ribbon_5   1 LiirCpdCdtkFk 13 
                                   L+i+C +C+ + k
  gi|91773274|ref|YP_565966.1| 148 LVISCSNCGAMVK 160
                                   78*******9966 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 ?    0.3   0.4      0.77   9.2e+02       8      32 ..       6      26 ..       1      51 [. 0.60
   2 ?   13.1   0.9   8.2e-05     0.098       3      37 ..     125     158 ..     123     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.77
               Lar_restr_allev  8 fCggravlersqrvvaeigqcvyCa 32
                                   Cg ++  ++ ++       c +Ca
  gi|91773274|ref|YP_565966.1|  6 ICGDDQDFKQYESYNI----CTSCA 26
                                  4444444443333332....44443 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.2e-05
               Lar_restr_allev   3 LkpCPfCggravlersqrvvaeigq..cvyCadCgas 37 
                                    + CP C   ++ +++++ ++e+g+  +++C +Cga+
  gi|91773274|ref|YP_565966.1| 125 YYKCPSC---DTSIFDKYESEEVGEwlVISCSNCGAM 158
                                   5677777...56777777777777777*********3 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 ?    8.8   0.2    0.0018       2.1      17      46 .]     102     132 ..      97     132 .. 0.89
   2 ?    1.9   0.1      0.24   2.9e+02       3      10 ..     151     158 ..     150     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                       zf-IS66  17 drvreeldipPakfrViehirp.kyaCpcCe 46 
                                   +r  e+ld+ + ++   +++    y+Cp+C+
  gi|91773274|ref|YP_565966.1| 102 ERMHEVLDWLEGTPQFYHYYFKeYYKCPSCD 132
                                   44789***************9989******6 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.24
                       zf-IS66   3 tCpcCGgl 10 
                                   +C++CG+ 
  gi|91773274|ref|YP_565966.1| 151 SCSNCGAM 158
                                   69999974 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         1   1.2e+03      85      95 ..      17      27 ..      11      47 .. 0.74
   2 ?   11.7   0.3   0.00015      0.18      82     116 ..     120     157 ..      90     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                                  HHHTSTSSSTS CS
                  eIF-5_eIF-2B 85 eeyVlCkeCks 95
                                  e+y +C++C  
  gi|91773274|ref|YP_565966.1| 17 ESYNICTSCAD 27
                                  56778888875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                                   HHHHHHTSTSSSTSTCEEECC...SSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  82 kyieeyVlCkeCkspetelek...eerllvlkCkaCga 116
                                    y +ey  C++C+    +       ++ lv++C++Cga
  gi|91773274|ref|YP_565966.1| 120 YYFKEYYKCPSCDTSIFDKYEseeVGEWLVISCSNCGA 157
                                   699*********875443333333488999*******7 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.0     0.039        47      57      73 ..       4      26 ..       1      42 [. 0.50
   2 ?   11.2   1.4   0.00033      0.39      17      70 ..     123     165 ..     114     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                        zf-CHY 57 CkkCkk..efaey....fCpiCk 73
                                  C  C+   +f++y     C+ C 
  gi|91773274|ref|YP_565966.1|  4 CVICGDdqDFKQYesynICTSCA 26
                                  44444333333333323344443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00033
                        zf-CHY  17 kklyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCp 70 
                                   k++y+C +C +      ++++e +ev        +  ++ C++C+  +++yf p
  gi|91773274|ref|YP_565966.1| 123 KEYYKCPSCDT----SIFDKYESEEV-------GEWLVISCSNCGAMVKKYFSP 165
                                   789******98....67888888876.......3457999******99999876 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       6.1   7.3e+03       3       8 ..       3       8 ..       3       9 .. 0.80
   2 ?    2.6   0.1      0.13   1.5e+02      19      26 .]      18      25 ..      16      28 .. 0.84
   3 ?    9.2   0.2    0.0011       1.3       3      13 ..     127     137 ..     126     138 .. 0.88
   4 ?    6.5   0.5    0.0073       8.7       2      13 ..     150     161 ..     150     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.1
                        zf-ACC 3 KCpsCg 8
                                 KC  Cg
  gi|91773274|ref|YP_565966.1| 3 KCVICG 8
                                 898898 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                        zf-ACC 19 nlyVCPkC 26
                                  ++++C++C
  gi|91773274|ref|YP_565966.1| 18 SYNICTSC 25
                                  78899999 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0011
                        zf-ACC   3 KCpsCgemlyk 13 
                                   KCpsC ++++ 
  gi|91773274|ref|YP_565966.1| 127 KCPSCDTSIFD 137
                                   9******9985 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0073
                        zf-ACC   2 tKCpsCgemlyk 13 
                                   + C  Cg+m+ k
  gi|91773274|ref|YP_565966.1| 150 ISCSNCGAMVKK 161
                                   67*******976 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       3.6   4.4e+03      28      31 ..      22      25 ..      20      27 .. 0.61
   2 ?    6.2   0.0    0.0081       9.7      12      22 ..     126     136 ..     124     138 .. 0.86
   3 ?    3.8   0.0     0.045        54       7      19 ..     145     157 ..     142     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
                       DUF35_N 28 CphC 31
                                  C+ C
  gi|91773274|ref|YP_565966.1| 22 CTSC 25
                                  6666 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0081
                       DUF35_N  12 qrCpdCGtvqf 22 
                                    +Cp+C+t +f
  gi|91773274|ref|YP_565966.1| 126 YKCPSCDTSIF 136
                                   59******988 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.045
                       DUF35_N   7 grLvgqrCpdCGt 19 
                                   g+ ++  C++CG+
  gi|91773274|ref|YP_565966.1| 145 GEWLVISCSNCGA 157
                                   7778888999996 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.067        80       3      24 ..       4      25 ..       2      49 .. 0.69
   2 ?    9.6   0.8    0.0013       1.6      35      79 ..     123     163 ..     114     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.067
                zinc_ribbon_15  3 CpkCgklskaelvkkkkvlklf 24
                                  C  Cg+ ++ + ++++++++ +
  gi|91773274|ref|YP_565966.1|  4 CVICGDDQDFKQYESYNICTSC 25
                                  6666666666666666666655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                zinc_ribbon_15  35 kpylacskCkslleaskelgkeiekkessekkeCknCgkeveeef 79 
                                   k y++c +C + + ++     e e+  +  + +C+nCg+ v++ f
  gi|91773274|ref|YP_565966.1| 123 KEYYKCPSCDTSIFDKY----ESEEVGEWLVISCSNCGAMVKKYF 163
                                   6799******9998887....33444445599******9998765 PP

>> RecO_C  Recombination protein O C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0066       7.9      69     100 ..       2      30 ..       1      34 [. 0.85
   2 ?    1.6   0.0      0.18   2.2e+02      17      45 ..      85     115 ..      81     123 .. 0.66
   3 ?   -0.9   0.2         1   1.2e+03      69      97 ..     126     157 ..     121     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0066
                                   SB-TTT--BS--EE-TTT.....SSEE-TTT- CS
                        RecO_C  69 dsCaacgekialaafspswggllcsecaakap 100
                                   ++C+ cg +++   + ++   ++c++ca+  +
  gi|91773274|ref|YP_565966.1|   2 EKCVICGDDQDFKQYESY---NICTSCADIME 30 
                                   68*******999999998...68999998765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.18
                                   HHHHS-SSS.--.HHHHHHHHHHHHHHHHSS CS
                        RecO_C  17 ldrllpeee.pn.peLFdlllatLdaLdeas 45 
                                   +d++l+e   p+ ++ F+   ++Ld+L++++
  gi|91773274|ref|YP_565966.1|  85 ADNALHESKiPSkQRYFERMHEVLDWLEGTP 115
                                   566664433144257999*********9876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1
                                   SB-TTT--BS--EE-TTT........SSEE-T CS
                        RecO_C  69 dsCaacgekialaafspswgg...llcsecaa 97 
                                   ++C  c ++i + + s+  g+   + cs+c+a
  gi|91773274|ref|YP_565966.1| 126 YKCPSCDTSIFDKYESEEVGEwlvISCSNCGA 157
                                   67889999999999998888886655555554 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 ?    1.0   2.0      0.35   4.2e+02      18      26 ..      20      28 ..       1      34 [. 0.59
   2 ?    6.7   0.0    0.0062       7.4      35      52 ..     126     143 ..     121     145 .. 0.82
   3 ?    1.6   0.1      0.24   2.9e+02      19      26 ..     151     158 ..     146     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.35
                      zf-C2HC5 18 pnClnCGki 26
                                   +C++C  i
  gi|91773274|ref|YP_565966.1| 20 NICTSCADI 28
                                  345555544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0062
                      zf-C2HC5  35 kpCsfCgspllsseerqe 52 
                                    +C++C+++++ + e +e
  gi|91773274|ref|YP_565966.1| 126 YKCPSCDTSIFDKYESEE 143
                                   69********99888766 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.24
                      zf-C2HC5  19 nClnCGki 26 
                                    C nCG  
  gi|91773274|ref|YP_565966.1| 151 SCSNCGAM 158
                                   68888865 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 ?   10.5   0.7   0.00045      0.54      24      52 ..       3      30 ..       1      33 [. 0.79
   2 ?   -3.0   0.0       7.1   8.4e+03      12      21 ..      57      66 ..      47      70 .. 0.55
   3 ?    4.0   1.0     0.049        58      39      48 ..     123     132 ..     119     136 .. 0.84
   4 ?   -2.1   0.2       3.8   4.6e+03      44      52 ..     152     160 ..     147     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                   Prok-RING_2 24 qcvlcGrWacdacWkdeyytckscaGlik 52
                                  +cv+cG    d    + y +c sca +++
  gi|91773274|ref|YP_565966.1|  3 KCVICGDDQ-DFKQYESYNICTSCADIME 30
                                  7*****854.555557899*******995 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.1
                   Prok-RING_2 12 lcatahplag 21
                                  l +t+  +++
  gi|91773274|ref|YP_565966.1| 57 LDNTSRYVSD 66
                                  5555555544 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.049
                   Prok-RING_2  39 deyytcksca 48 
                                    eyy c sc 
  gi|91773274|ref|YP_565966.1| 123 KEYYKCPSCD 132
                                   59*******6 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.8
                   Prok-RING_2  44 ckscaGlik 52 
                                   c  c+ ++k
  gi|91773274|ref|YP_565966.1| 152 CSNCGAMVK 160
                                   777777665 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 ?   -0.6   1.6         1   1.2e+03       7      18 ..      15      26 ..       1      29 [. 0.51
   2 ?    1.5   0.1      0.23   2.8e+02       7      21 ..      15      29 ..      11      42 .. 0.76
   3 ?    9.6   0.9   0.00067       0.8       2      38 ..     116     159 ..     116     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1
                                  --SS--B-TTT- CS
                          C1_1  7 nfkqptfCkhCg 18
                                  ++++ + C+ C+
  gi|91773274|ref|YP_565966.1| 15 QYESYNICTSCA 26
                                  334444555555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.23
                                  --SS--B-TTT-SB- CS
                          C1_1  7 nfkqptfCkhCgefl 21
                                  ++++ + C+ C++++
  gi|91773274|ref|YP_565966.1| 15 QYESYNICTSCADIM 29
                                  6678889****9988 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00067
                                   -EEEE--SS--B-TTT-SB-......-S.SSS-EEEETTT--EE CS
                          C1_1   2 hwvhrnfkqptfCkhCgefl......wg.kekqglkCswCkllv 38 
                                   ++ h  fk+  +C  C+ ++      ++ +e   ++Cs+C+  v
  gi|91773274|ref|YP_565966.1| 116 QFYHYYFKEYYKCPSCDTSIfdkyesEEvGEWLVISCSNCGAMV 159
                                   58899999***************998667888999*****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1334  (0.0744046); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1202.18
//
Query:       gi|91773275|ref|YP_565967.1|  [L=139]
Description: hypothetical protein Mbur_1299 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-37  127.1   0.3      3e-37  126.6   0.3    1.3  1  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.3   1.6e-41     3e-37       2     106 .]       6     110 ..       5     110 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 1.6e-41
                         DUF22   2 vkivyrkdgeivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvldvve 82 
                                   +++v rk+ge+v++kv+++p+++t++t+akwe++i++ed+e+++Ge+kki ike++l+++t+++p++++ ha+++vl+v +
  gi|91773275|ref|YP_565967.1|   6 IQVVARKEGEMVSKKVKAAPYEFTIATRAKWEMVISNEDLELRAGEYKKIAIKEVTLDADTLAIPCAFTYHAVASVLKVSS 86 
                                   79******************************************************************************* PP

                         DUF22  83 kgkpkkveeereiteavflpvedG 106
                                   k++++ ve+ r+i++a+++++e+G
  gi|91773275|ref|YP_565967.1|  87 KEGNCLVESPRTISHAYVFGQETG 110
                                   **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 950.74
//
Query:       gi|91773276|ref|YP_565968.1|  [L=53]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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-12   44.4  16.4    1.1e-06   28.2   4.5    2.1  2  Fer4       4Fe-4S binding domain
    1.3e-08   34.7  12.7    2.1e-05   24.6   2.0    2.1  2  Fer4_4     4Fe-4S binding domain
    2.2e-08   34.1  14.5    2.8e-08   33.8  14.5    1.1  1  Fer4_21    4Fe-4S dicluster domain
      4e-08   32.9  13.7    4.4e-05   23.3   2.9    2.2  2  Fer4_2     4Fe-4S binding domain
    9.1e-08   32.6  13.7    0.00037   21.0   3.9    2.0  2  Fer4_7     4Fe-4S dicluster domain
    1.1e-07   31.6  16.1    0.00014   21.8   4.5    2.1  2  Fer4_6     4Fe-4S binding domain
      6e-07   29.5  14.1    1.6e-06   28.2  14.1    1.6  1  Fer4_9     4Fe-4S dicluster domain
    2.2e-06   28.5  13.2     0.0017   19.2   3.7    2.0  2  Fer4_16    4Fe-4S double cluster binding domain
    4.9e-05   23.4  15.7     0.0062   16.6   3.7    2.0  2  Fer4_10    4Fe-4S dicluster domain
    0.00024   21.6  13.9     0.0033   17.9   2.2    2.1  2  Fer4_17    4Fe-4S dicluster domain
    0.00049   20.5  14.4      0.011   16.2   2.6    2.0  2  Fer4_8     4Fe-4S dicluster domain
     0.0069   17.2  14.9       0.26   12.1   4.5    2.1  2  Fer4_22    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.027   15.4  17.9       0.38   11.8   4.4    2.2  2  Fer4_3     4Fe-4S binding domain
      0.068   13.7  14.6        1.1    9.9   3.6    2.2  2  Fer4_13    4Fe-4S single cluster domain of Ferredoxin I
       0.21   12.3  14.0       0.61   10.9   3.1    2.3  2  Fer4_15    4Fe-4S single cluster domain
        0.6   10.1   8.2        2.6    8.1   1.1    2.2  2  ADD_DNMT3  Cysteine rich ADD domain in DNMT3
          1    9.6  13.2        4.1    7.6  13.2    1.8  1  Fer4_18    4Fe-4S dicluster domain
        2.8    8.1   9.9          5    7.2   9.9    1.5  1  Elf1       Transcription elongation factor Elf1 like


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   4.0   6.9e-08   6.9e-05       4      23 ..       3      22 ..       1      23 [. 0.92
   2 !   28.2   4.5   1.1e-09   1.1e-06       4      24 .]      30      50 ..      28      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.9e-08
                                  ETTTSSS-THHHHHSTTTEE CS
                          Fer4  4 deekCigCGaCvevCPvgAI 23
                                  + + C+gCG+C   C  +AI
  gi|91773276|ref|YP_565968.1|  3 INDNCVGCGQCTAFCKIDAI 22
                                  5799***************9 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.1e-09
                                  ETTTSSS-THHHHHSTTTEEE CS
                          Fer4  4 deekCigCGaCvevCPvgAIt 24
                                  +++ C++CG+C+  CP  AI+
  gi|91773276|ref|YP_565968.1| 30 ITDACVNCGICATYCPMKAIE 50
                                  689****************96 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.0   2.2e-08   2.1e-05       2      15 ..       5      18 ..       4      26 .. 0.93
   2 !   15.9   3.3   1.4e-05     0.014       2      16 ..      32      46 ..      31      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  ++C+gCg+C+a+C+
  gi|91773276|ref|YP_565968.1|  5 DNCVGCGQCTAFCK 18
                                  89***********6 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.4e-05
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  + C++Cg C  +CP+
  gi|91773276|ref|YP_565968.1| 32 DACVNCGICATYCPM 46
                                  89************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8  14.5   2.8e-11   2.8e-08       5      58 ..       4      50 ..       2      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.8e-11
                       Fer4_21  5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  +d+C+gCg+C+  C+   ++ai +++k++   ++d Cv C +C++ CP+ ++ie
  gi|91773276|ref|YP_565968.1|  4 NDNCVGCGQCTAFCK---IDAIIVKSKAH---ITDACVNCGICATYCPM-KAIE 50
                                  489************...9****998888...89**************7.7775 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   3.1   1.3e-05     0.013       8      20 ..       5      17 ..       1      18 [. 0.87
   2 !   23.3   2.9   4.4e-08   4.4e-05       6      21 ..      30      45 ..      26      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                        Fer4_2  8 drCigCgaCvsaC 20
                                  d+C+gCg C+  C
  gi|91773276|ref|YP_565968.1|  5 DNCVGCGQCTAFC 17
                                  78*******9999 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.4e-08
                        Fer4_2  6 dtdrCigCgaCvsaCP 21
                                   td+C++Cg+C + CP
  gi|91773276|ref|YP_565968.1| 30 ITDACVNCGICATYCP 45
                                  589************* PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.3   4.4e-06    0.0043       2      20 ..       7      25 ..       6      31 .. 0.84
   2 !   21.0   3.9   3.7e-07   0.00037       1      20 [.      33      52 ..      33      53 .] 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                        Fer4_7  2 CigCgaCvaaCpvkaield 20
                                  C+gCg+C+a C+ +ai ++
  gi|91773276|ref|YP_565968.1|  7 CVGCGQCTAFCKIDAIIVK 25
                                  ************9998665 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 3.7e-07
                        Fer4_7  1 rCigCgaCvaaCpvkaield 20
                                  +C++Cg C+ +Cp+kaie d
  gi|91773276|ref|YP_565968.1| 33 ACVNCGICATYCPMKAIEAD 52
                                  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 !   15.8   3.7   1.1e-05     0.011       6      24 .]       4      22 ..       3      22 .. 0.89
   2 !   21.8   4.5   1.4e-07   0.00014       5      24 .]      30      49 ..      28      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                        Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                   d+C+gCg C++ C  +ai
  gi|91773276|ref|YP_565968.1|  4 NDNCVGCGQCTAFCKIDAI 22
                                  59************98776 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.4e-07
                        Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                    d+C+ Cg C++ CP++ai
  gi|91773276|ref|YP_565968.1| 30 ITDACVNCGICATYCPMKAI 49
                                  579**************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 !   28.2  14.1   1.6e-09   1.6e-06       1      51 []       6      49 ..       6      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.6e-09
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  +C+gCg+C++ C+ ++++ ++++ +          C+ Cg C+  Cp +ai
  gi|91773276|ref|YP_565968.1|  6 NCVGCGQCTAFCKIDAIIVKSKAHITDA-------CVNCGICATYCPMKAI 49
                                  6*****************9999999885.......*************987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.1   3.1e-05     0.031       1      23 [.       6      28 ..       6      32 .. 0.85
   2 !   19.2   3.7   1.7e-06    0.0017       2      20 ..      34      52 ..      33      53 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkek 23
                                  +C++Cg+C+  C  +ai  k+++
  gi|91773276|ref|YP_565968.1|  6 NCVGCGQCTAFCKIDAIIVKSKA 28
                                  6***************9988655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++Cg Ca  CP +ai+++
  gi|91773276|ref|YP_565968.1| 34 CVNCGICATYCPMKAIEAD 52
                                  ****************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 !   13.8   4.0   4.6e-05     0.046       6      19 ..       4      17 ..       1      31 [. 0.72
   2 !   16.6   3.7   6.3e-06    0.0062       6      22 ..      31      47 ..      26      53 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                       Fer4_10  6 ddtCirCgkCvkaC 19
                                   d C++Cg+C+++C
  gi|91773276|ref|YP_565968.1|  4 NDNCVGCGQCTAFC 17
                                  48899999999999 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.3e-06
                       Fer4_10  6 ddtCirCgkCvkaCPad 22
                                  +d C++Cg C + CP++
  gi|91773276|ref|YP_565968.1| 31 TDACVNCGICATYCPMK 47
                                  699*************3 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   3.7    0.0007       0.7      44      57 ..       5      18 ..       1      22 [. 0.80
   2 !   17.9   2.2   3.3e-06    0.0033      40      59 ..      28      47 ..      18      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0007
                       Fer4_17 44 slCieCgeCerkCP 57
                                  ++C++Cg+C++ C 
  gi|91773276|ref|YP_565968.1|  5 DNCVGCGQCTAFCK 18
                                  68999999999985 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.3e-06
                       Fer4_17 40 eekaslCieCgeCerkCPqg 59
                                   +  + C++Cg C+++CP++
  gi|91773276|ref|YP_565968.1| 28 AHITDACVNCGICATYCPMK 47
                                  366799************96 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.8   0.00057      0.57      49      63 ..       5      19 ..       2      21 .. 0.66
   2 !   16.2   2.6   1.1e-05     0.011      45      64 ..      28      47 ..      20      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00057
                        Fer4_8 49 wsCttcgaCtevCpv 63
                                  ++C++cg+Ct  C++
  gi|91773276|ref|YP_565968.1|  5 DNCVGCGQCTAFCKI 19
                                  567777777777764 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-05
                        Fer4_8 45 eealwsCttcgaCtevCpvg 64
                                  +++ ++C++cg C++ Cp++
  gi|91773276|ref|YP_565968.1| 28 AHITDACVNCGICATYCPMK 47
                                  57788899999999999976 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   4.5   0.00026      0.26      80      94 ..       5      19 ..       2      23 .. 0.86
   2 !   11.4   2.7   0.00043      0.43      79      94 ..      31      46 ..      21      48 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                       Fer4_22 80 sgCvGCgRCieacpv 94
                                    CvGCg C++ c+ 
  gi|91773276|ref|YP_565968.1|  5 DNCVGCGQCTAFCKI 19
                                  57**********975 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00043
                       Fer4_22 79 esgCvGCgRCieacpv 94
                                  + +Cv Cg C + cp+
  gi|91773276|ref|YP_565968.1| 31 TDACVNCGICATYCPM 46
                                  5678888888888876 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.4   0.00038      0.38       1      15 []       7      21 ..       7      21 .. 0.92
   2 ?    9.7   5.7    0.0018       1.8       1      15 []      34      48 ..      34      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg+C   C  +A
  gi|91773276|ref|YP_565968.1|  7 CVGCGQCTAFCKIDA 21
                                  ***********8776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0018
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C++Cg C   CP +A
  gi|91773276|ref|YP_565968.1| 34 CVNCGICATYCPMKA 48
                                  ************987 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.3    0.0012       1.2       1      16 [.       3      17 ..       3      18 .. 0.90
   2 ?    9.9   3.6    0.0011       1.1       4      17 ..      32      45 ..      30      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                       Fer4_13  1 VDrdtCiacgaCvela 16
                                  ++ d+C++cg+C +++
  gi|91773276|ref|YP_565968.1|  3 IN-DNCVGCGQCTAFC 17
                                  56.9**********99 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                       Fer4_13  4 dtCiacgaCvelaP 17
                                  d C++cg+C+  +P
  gi|91773276|ref|YP_565968.1| 32 DACVNCGICATYCP 45
                                  79************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.1   0.00061      0.61       6      28 ..       5      29 ..       4      32 .. 0.79
   2 ?    7.5   3.4    0.0067       6.7       6      19 ..      32      45 ..      31      53 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                       Fer4_15  6 daCigcglCvaea..pevfeldedg 28
                                  d+C gcg+C a +  + ++++ +++
  gi|91773276|ref|YP_565968.1|  5 DNCVGCGQCTAFCkiDAIIVKSKAH 29
                                  89*********99766777777666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0067
                       Fer4_15  6 daCigcglCvaeap 19
                                  daC  cg C++ +p
  gi|91773276|ref|YP_565968.1| 32 DACVNCGICATYCP 45
                                  89***********7 PP

>> ADD_DNMT3  Cysteine rich ADD domain in DNMT3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.6     0.012        12      15      26 ..       2      13 ..       1      18 [. 0.85
   2 ?    8.1   1.1    0.0026       2.6       9      25 ..      23      39 ..      17      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                     ADD_DNMT3 15 niEdiClsCGsl 26
                                  +i d C+ CG+ 
  gi|91773276|ref|YP_565968.1|  2 KINDNCVGCGQC 13
                                  799*******86 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0026
                     ADD_DNMT3  9 vkenkrniEdiClsCGs 25
                                  + + k +i d C+ CG 
  gi|91773276|ref|YP_565968.1| 23 IVKSKAHITDACVNCGI 39
                                  678899**********6 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  13.2    0.0041       4.1      58      96 ..       4      45 ..       1      52 [. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0041
                       Fer4_18 58 agdcidcescvkvcPtgidirkG...lqleciscllcidacd 96
                                  + +c+ c++c + c ++  i k    +   c++c+ c   c 
  gi|91773276|ref|YP_565968.1|  4 NDNCVGCGQCTAFCKIDAIIVKSkahITDACVNCGICATYCP 45
                                  679***********9876554431115568*******99995 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   9.9     0.005         5      24      61 ..      13      50 ..       5      53 .] 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.005
                          Elf1 24 CpfCnheksvevkldkkekiaevsCkvCgesfetkvna 61
                                  C   ++ +++ vk +     a v+C++C +++ +k+ +
  gi|91773276|ref|YP_565968.1| 13 CTAFCKIDAIIVKSKAHITDACVNCGICATYCPMKAIE 50
                                  66555556**********************99998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 395.37
//
Query:       gi|91773277|ref|YP_565969.1|  [L=425]
Description: amine oxidase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-17   61.7   0.0    1.1e-16   61.2   0.0    1.2  1  Amino_oxidase  Flavin containing amine oxidoreductase
    3.8e-11   43.1   0.0      1e-10   41.6   0.1    1.7  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.5e-08   34.7   1.3      5e-06   26.3   0.0    2.1  2  DAO            FAD dependent oxidoreductase
      1e-06   28.2   0.7     0.0093   15.2   0.0    3.2  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.2e-06   26.1   2.0       0.01   15.0   0.7    3.0  3  FAD_binding_2  FAD binding domain
    0.00013   20.8   1.8      0.013   14.2   0.7    2.2  2  HI0933_like    HI0933-like protein
      0.001   19.6   3.9      0.022   15.3   0.2    2.6  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.012   15.0   0.6      0.022   14.2   0.1    1.5  2  GMC_oxred_N    GMC oxidoreductase
       0.16   11.2   1.0       0.37   10.0   0.9    1.7  2  FAD_binding_3  FAD binding domain
       0.16   11.0   1.6       0.28   10.2   0.2    1.9  2  GIDA           Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   6.3e-20   1.1e-16       2     430 ..      11     399 ..      10     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 6.3e-20
                                   HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET..TTHHHHHHHHHTTCCCCEEEESCCGCEEEEE CS
                 Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg..agnpllellkelgledslslpdpgapkrvls 80 
                                    GL  A +L+ +G++V v+E    +GGR   +  +Gy + +Ga  + +     pl +l++e+g +   +  d++a+ r+++
  gi|91773277|ref|YP_565969.1|  11 GGLLSAAKLSGKGYEVEVFERLAMIGGRFTNFDIKGYQLTTGALHMLPhgPTGPLAQLIREVGADVTIERQDDTAFMRIHE 91 
                                   7***********************************************77778*************999999998888888 PP

                                   TTEECCTTEECHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHH CS
                 Amino_oxidase  81 kggrefpgdlspv.paewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgdvevwdrl 160
                                        ++g++++v  +e+ +  +          +  +++l+l ++     ++ ++++ s+ e++ ++ + +  +  + d +
  gi|91773277|ref|YP_565969.1|  92 ---DLENGIYKDVsFGEFGSTFS----------VWNRIKLALLLIS---TRKWPPKNCSFGEWITKNLNMPIAH-QMADSF 155
                                   ...4559******7777888777..........7789999999999...9999*********************.555555 PP

                                   HHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETT CS
                 Amino_oxidase 161 iepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealae..elrgldirlntrVkeikregd 239
                                             +a+ l a+d + ++a   +  l++  g g    +p gG +++ +ala+  ++ g++i + t+V+ei  e++
  gi|91773277|ref|YP_565969.1| 156 CG--------WALSLKAADTPVEEAFEIFENLYRHGGPG----VPIGGCKAVTDALADvvRKNGGSIETKTEVTEILVENG 224
                                   55........77777777776666665555555544444....4589*******************************999 PP

                                   CEEEEETTSTEEEESEEEE-S-HHHHHSSEEES.CC.SH..HHHHHHHHSEEEEEEEEEEEESSGGSGCSTSECE.CECCC CS
                 Amino_oxidase 240 gvtvtledgevveaDaVvvTvplgvlkailfsP.pl.pd..ekaeairnlgfgsvnkvilefdrkfwednalgqg.vlvse 315
                                   +    l dg++   D V++ +  +  +  l++  p  p+  +  + ir ++    +k+ l+  ++   +     g    ++
  gi|91773277|ref|YP_565969.1| 225 KAVGVLIDGQKHMSDIVISNIGHPFTS-DLYKDaPTtPQykQYIDKIRTIKPSAGVKICLAANEPLIGHG----GvLFTPS 300
                                   9555589*****************999.666666776776688899999999**************5442....3456666 PP

                                   EEETTTEEEEECCECCCSTTTEEEEEEEEEC.HHHHHHHTTS-HHHHHHHHHHHHHHHHTGTSSTCSEEEEEECCTETTTS CS
                 Amino_oxidase 316 ltttlgeafissdfpsrappgkglvllvyvg.gdaaneleslsdeelvqavlrdLrklfgeevpepkatlvtrWhtdplar 395
                                     ++ g + + +  p  ap gk+lv+ + ++  d +++l     ee ++  + dL+++f+ + ++++  ++++++   ++ 
  gi|91773277|ref|YP_565969.1| 301 AKRVNGINEVTNIDPKLAPRGKHLVMAHQTVqWDKIPYL-----EEEIDMGIADLKQIFP-NKDYEIILTQSYYG--GWP- 372
                                   6666677777766***********999999977888877.....99999***********.99999998888875..666. PP

                                   SSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGC CS
                 Amino_oxidase 396 gsysyvsvgpghedydplakpegdprlffAGehts 430
                                          v+ ++   d  + + ++++l++ G+   
  gi|91773277|ref|YP_565969.1| 373 -------VNRSSSGTDIGNTT-PIKGLYVVGDGAK 399
                                   .......77777777778888.8999999998855 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1   5.8e-14     1e-10       1      67 [.       5      71 ..       5      72 .. 0.94
   2 ?   -3.3   0.0       6.4   1.1e+04      27      46 ..     151     170 ..     150     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 5.8e-14
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                  ++GaGl+Gl+ A+ L+ +g++v+++e+   +GGr + ++++g+ + +ga  + + g+   + +l+re
  gi|91773277|ref|YP_565969.1|  5 VIGAGLGGLLSAAKLSGKGYEVEVFERLAMIGGRFTNFDIKGYQLTTGALHMLPHGPTGPLAQLIRE 71
                                  8***********************************************9999888888888888876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.4
                                   SSSSSSGGG-EECETTCEEC CS
                 NAD_binding_8  27 krdrlGGraasyevpgvrvd 46 
                                   ++d+++G+a s +  + +v+
  gi|91773277|ref|YP_565969.1| 151 MADSFCGWALSLKAADTPVE 170
                                   56778888888776555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.4    0.0019       3.4       2      29 ..       3      32 ..       2      41 .. 0.89
   2 !   26.3   0.0   2.8e-09     5e-06     146     332 ..     193     395 ..     166     403 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0019
                                  EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekg 29
                                   ++iG+G  Gl  A  L+ +g  V ++e+ 
  gi|91773277|ref|YP_565969.1|  3 AIVIGAGLGGLLSAAKLSGKGyeVEVFERL 32
                                  58****************999******995 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.8e-09
                                   HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--.GGGHHHHHTTCTT..TSEEEEEEE CS
                           DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaa.Gawsdllgllkel..dlpispvrg 222
                                    ++t ala+ ++++G+ i ++tevt++  e+gk++gv  +   g+++    +V+++ G+   ++    +l  d p++p   
  gi|91773277|ref|YP_565969.1| 193 KAVTDALADVVRKNGGSIETKTEVTEILVENGKAVGVLiD---GQKH-MSDIVISNiGHP--FT---SDLykDAPTTPQYK 264
                                   689***********************98889999999554...6654.345666651533..44...33333448888777 PP

                                   EE...EEE.EECCTHSTGSGCSEEEEEEEETTTTEEEEEE..................TTSEEEEEESSEEETTCSSTSCS CS
                           DAO 223 qv...lvl.kplseklvspaailpvpetdddgrgvyvtpr..................kdgrvlvGgtadeesgdddpevd 281
                                   q+   +++ kp     v  +  l+  e+  +++gv +tp+                  + g++lv ++   + ++d  +  
  gi|91773277|ref|YP_565969.1| 265 QYidkIRTiKPSAG--V--KICLAANEPLIGHGGVLFTPSakrvnginevtnidpklaPRGKHLVMAHQ--TVQWDKIPYL 339
                                   77333233244333..2..3445555588999*******988888888888888888855777776665..899******* PP

                                   HHHHHHHHHHHHHHSGGG.CG..EEEEEEEEEE.E.TTSSEEEEEEETEEEEEEEE CS
                           DAO 282 eedidellealrklfPql.gd..vlrkwaGlrp.l.pdglpligetpgvkglylat 332
                                   ee+id  +  l+++fP++  +  ++++++G  p +  + +  ig+t+  kgly++ 
  gi|91773277|ref|YP_565969.1| 340 EEEIDMGIADLKQIFPNKdYEiiLTQSYYGGWPvNrSSSGTDIGNTTPIKGLYVVG 395
                                   *****************534443447999888854357799999976688999984 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.2e-06    0.0093       2      52 ..       2      56 ..       1      96 [. 0.84
   2 !    6.2   0.0    0.0029       5.2     183     244 ..     193     254 ..     183     267 .. 0.89
   3 ?    3.6   0.0     0.018        32     264     285 ..     384     405 ..     367     412 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.2e-06
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaed 52
                                  + +viG+G +Gl  a +l+ +g++v ++e     +g + n+++  ++  +g+ + 
  gi|91773277|ref|YP_565969.1|  2 KAIVIGAGLGGLLSAAKLSGKGYEVEVFErlamIGGRFTNFDIKGYQLTTGALHM 56
                                  679*************************999999999999988888877777665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0029
                                   HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstell 244
                                   k++++al+++++k+G  + ++t+v+ei  ++ k+  vl dg++   d v+  +G    ++l+
  gi|91773277|ref|YP_565969.1| 193 KAVTDALADVVRKNGGSIETKTEVTEILVENGKAVGVLIDGQKHMSDIVISNIGHPFTSDLY 254
                                   578999*********************999996779999999999*****999987777766 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.018
                                   SBESSTTEEE-GGGCTECCSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 264 lrtnvpgiyaiGDvaggkggpe 285
                                     t ++g+y++GD a+gkgg+e
  gi|91773277|ref|YP_565969.1| 384 NTTPIKGLYVVGDGAKGKGGIE 405
                                   4566***********9988887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.7   5.7e-06      0.01       2      35 ..       3      36 ..       2      41 .. 0.88
   2 !    7.5   0.0     0.001       1.9     136     186 ..     188     238 ..     159     306 .. 0.89
   3 ?    1.1   0.0     0.089   1.6e+02     373     405 ..     368     400 ..     338     408 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.7e-06
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                  +iViG+Gl+GL +A++++ +G +v v e     g
  gi|91773277|ref|YP_565969.1|  3 AIVIGAGLGGLLSAAKLSGKGYEVEVFERLAMIG 36
                                  69**********************9999876655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.001
                                   ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTC CS
                 FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgr 186
                                   +++  +a+  +l++ +rk+g  + ++te++e++ve+g+++G+ +  ++ ++
  gi|91773277|ref|YP_565969.1| 188 PIGGCKAVTDALADVVRKNGGSIETKTEVTEILVENGKAVGVLIDGQKHMS 238
                                   5677899999*******************************9988665444 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.089
                                   S-EEEBETTSBE.STTEEESSBTEEE-STCEESS CS
                 FAD_binding_2 373 mgGvetdengrv.ldadgqpipGLYAaGevaagg 405
                                    gG +++ ++   +  + +pi+GLY +G  a  g
  gi|91773277|ref|YP_565969.1| 368 YGGWPVNRSSSGtDIGNTTPIKGLYVVGDGA-KG 400
                                   5677777666542567789*********988.44 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.7   7.4e-06     0.013       2      37 ..       2      37 ..       1      41 [. 0.91
   2 !    5.4   0.0    0.0034       6.2     109     158 ..     193     241 ..     189     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                  + iviG+G  Gl+ A++++ +g +V ++e+   +g 
  gi|91773277|ref|YP_565969.1|  2 KAIVIGAGLGGLLSAAKLSGKGYEVEVFERLAMIGG 37
                                  689**************************9988876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEE CS
                   HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadkl 158
                                   + + dal   ++++g +++++tev+++  e+++++ v + ++++  +d +
  gi|91773277|ref|YP_565969.1| 193 KAVTDALADVVRKNGGSIETKTEVTEILVENGKAVGVLI-DGQKHMSDIV 241
                                   67899****************************999999.5555444444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.2e-05     0.022       1      37 [.       2      39 ..       2      48 .. 0.88
   2 ?   -3.5   0.0       9.1   1.6e+04      15      27 ..      66      78 ..      65      85 .. 0.77
   3 ?    4.7   0.2     0.025        44      42      77 ..     195     230 ..     193     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TT CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rl 37
                                  k++v+G+G+ gl  A+ l+  g +V v+er  ++  r 
  gi|91773277|ref|YP_565969.1|  2 KAIVIGAGLGGLLSAAKLSGKGYEVEVFERLAMIGgRF 39
                                  579****************************9998554 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.1
                                  HHHHHHTTSEEEE CS
                     Pyr_redox 15 AgalaelgkkVtv 27
                                  A+ ++e g++Vt+
  gi|91773277|ref|YP_565969.1| 66 AQLIREVGADVTI 78
                                  7788999999996 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.025
                                   HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                     Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesvk 77 
                                   + ++l++ ++kng  + ++t+v+ei  ++ +  +v 
  gi|91773277|ref|YP_565969.1| 195 VTDALADVVRKNGGSIETKTEVTEILVENGKAVGVL 230
                                   567899999****************98888755665 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   2.7e+03       1      22 [.       1      22 [.       1      42 [. 0.86
   2 ?   14.2   0.1   1.2e-05     0.022     197     239 ..     197     237 ..     193     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                   GMC_oxred_N  1 vdelveggGsagsvvAaRLsed 22
                                  ++++v+g+G+ g   Aa+Ls +
  gi|91773277|ref|YP_565969.1|  1 MKAIVIGAGLGGLLSAAKLSGK 22
                                  6789999999999999999965 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.2e-05
                   GMC_oxred_N 197 awLrpalerpnleiltgakaekiilegrkkravGVeasdkkgt 239
                                     L + +++++  i t+++++ i++e  +++avGV +  +k  
  gi|91773277|ref|YP_565969.1| 197 DALADVVRKNGGSIETKTEVTEILVE--NGKAVGVLIDGQKHM 237
                                   67999*********************..*******99887765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   0.00021      0.37       3      34 ..       2      33 ..       1      36 [. 0.92
   2 ?   -3.5   0.0       2.5   4.6e+03     107     132 ..     195     220 ..     191     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  + +++GaG+ Gl++a  Ls +G +v + e+ +
  gi|91773277|ref|YP_565969.1|  2 KAIVIGAGLGGLLSAAKLSGKGYEVEVFERLA 33
                                  578**********************9999975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.5
                                   HHHHHHHHHHHHTEEETCSEEEECCE CS
                 FAD_binding_3 107 leriLvehaeerglqvrfktevesle 132
                                   ++ +L++  ++ g +++ ktev+ ++
  gi|91773277|ref|YP_565969.1| 195 VTDALADVVRKNGGSIETKTEVTEIL 220
                                   56678888888888899999887655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00016      0.28       2      35 ..       3      35 ..       2      57 .. 0.83
   2 ?   -0.7   0.1      0.33     6e+02     115     140 ..     213     238 ..     205     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                                  EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                          GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldti 35
                                   iViG+G+ G+  A++++ +G++v  + ++l +i
  gi|91773277|ref|YP_565969.1|  3 AIVIGAGLGGLLSAAKLSGKGYEVEVF-ERLAMI 35
                                  69**********************998.555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.33
                                   ES-EEEEEECTTEEEEEEETTS-EEE CS
                          GIDA 115 eeeveeliveekkvkgvvtedgetik 140
                                   + ev+e++ve++k  gv+ + +++++
  gi|91773277|ref|YP_565969.1| 213 KTEVTEILVENGKAVGVLIDGQKHMS 238
                                   5799************9998777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.36
# Mc/sec: 3544.27
//
Query:       gi|91773278|ref|YP_565970.1|  [L=330]
Description: FO synthase subunit 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   55.9   0.1    1.7e-14   54.5   0.1    1.7  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1   9.8e-19   1.7e-14       1     165 [.      13     184 ..      13     186 .. 0.86
   2 ?   -3.4   0.0      0.61   1.1e+04     125     143 ..     218     235 ..     206     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 9.8e-19
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE............SSTGGGSTTHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx............xxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilg............ggepllypdfvelle 68 
                                   ++vt+ C++ C +C+++++ + ++ ++ +s+ ei  +++++ ++ g ++ ++++              e l y+  ve+++
  gi|91773278|ref|YP_565970.1|  13 IPVTNICRNLCGYCTFRRD-AGHPEAHLMSMSEIRPILERG-EKAGcTEALFVFgeyaeevpeyllELEKLGYSTTVEYVA 91 
                                   689***************8.*********************.9***77777777566555555555555555566666666 PP

                                   HHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  69 rlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdri 149
                                    l+kla  +i +   tn++ ++++ le l++l+   + l le++ + k +    +g+ ++ ++e ++++ ++ i+  +++i
  gi|91773278|ref|YP_565970.1|  92 DLCKLA-IEIGLLPHTNAGILNRKELEILKPLN-ISMGLMLETTAELKAHSES-PGKKPSTRIEMIRTAGKLKIP-FTTGI 168
                                   666665.888888888888888***********.************9999999.*********************.***** PP

                                   EEBTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                   Radical_SAM 150 vglpGendeeleelle 165
                                   +++ Ge++++++  l+
  gi|91773278|ref|YP_565970.1| 169 LVGIGETKDDRKRSLN 184
                                   **********988775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.61
                                   SHHHHHHHHHHHHHHTTSE CS
                                   xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 125 htfeevlealeklreagik 143
                                   ++ ee ++++ ++re  ++
  gi|91773278|ref|YP_565970.1| 218 PSKEEMIDTVAIAREI-LP 235
                                   5667778888888776.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2415.14
//
Query:       gi|91773279|ref|YP_565971.1|  [L=356]
Description: FO synthase subunit 2 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-18   67.6   0.2    2.4e-18   67.1   0.2    1.3  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.2   1.3e-22   2.4e-18       1     164 [.      55     222 ..      55     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.3e-22
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiri 80 
                                   +++t  C + C fCa++      ++g+ ls+++i++++ke++   g ++++i+gg  p++  d++ ++++++k + p i++
  gi|91773279|ref|YP_565971.1|  55 INFTDICIGTCGFCAFKD-----KKGYLLSIDQIKDKIKEAH-VSGaTEVCIQGGLLPNVKIDLYIDILKAVKSDYPHIHT 129
                                   689**************5.....9*****************6.5566***************************9888888 PP

                                   EEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                   xxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdriv 150
                                   ++ ++  +           ee l++l+  g  +     +e++ d+ v+++++ ++ t++e+++++ +++++gi  ++ +++
  gi|91773279|ref|YP_565971.1| 130 HCFSPMEVNHaakasglsvEETLKTLKANGlNTMPGTAAEILVDK-VRNIICpDKLTRQEWIDTVTLAHKLGIQ-TTATMM 208
                                   8888877766888888888***********777777778888887.****************************.9***** PP

                                   EBTTTSHHHHHHHH CS
                                   xxxxxxxxxxxxxx RF
                   Radical_SAM 151 glpGendeeleell 164
                                    ++  ++e++ e++
  gi|91773279|ref|YP_565971.1| 209 YGHVDTWEDRIEHI 222
                                   *********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2774.63
//
Query:       gi|91773280|ref|YP_565972.1|  [L=356]
Description: FO synthase subunit 2 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   66.6   0.2    5.2e-18   66.0   0.2    1.3  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.2   2.9e-22   5.2e-18       2     160 ..      57     219 ..      56     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2.9e-22
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgirit 81 
                                    +t+ C ++C fC ++e     ++g++l++eeile+v ++ ++ g v+ +i+gg  p l+ +f+ ++ + ++ + p+++i+
  gi|91773280|ref|YP_565972.1|  57 YITNMCKGNCGFCGFRE-----EKGYILTIEEILEQVGQA-EKAGaVEICIQGGYLPQLDLEFYNDIVKSIHTKYPNMTIH 131
                                   6899************5.....9*****************.9***9******************99999999885666666 PP

                                   EEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                   xxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivg 151
                                     ++    +         e+   +l++ g  +    ++e++ d+ v+k+++ ++ t ++++e++++ +++g++ +  +i+ 
  gi|91773280|ref|YP_565972.1| 132 GFSPMEIYYasslsktpiEDAFSELKKSGlGTLTGTSAEILVDR-VRKIICeDKITTDQWIETIKASHRVGLR-TNATIMY 210
                                   666666655777777779***********9999999*******9.****************************.999**** PP

                                   BTTTSHHHH CS
                                   xxxxxxxxx RF
                   Radical_SAM 152 lpGendeel 160
                                   ++ e++ee+
  gi|91773280|ref|YP_565972.1| 211 GHVETWEER 219
                                   ******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2454.54
//
Query:       gi|91773281|ref|YP_565973.1|  [L=220]
Description: hypothetical protein Mbur_1305 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-51  172.8   0.5    6.6e-51  172.6   0.5    1.0  1  CofC          Guanylyl transferase CofC like
     0.0021   18.5   0.0     0.0026   18.1   0.0    1.2  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.6   0.5   7.4e-55   6.6e-51       1     197 [.       6     197 ..       6     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 172.6 bits;  conditional E-value: 7.4e-55
                          CofC   1 mkviiPvsainsaktrlseilseeerkellkamlldvidalkrldvl...vvsedeevleyaldelgvevvkekekdlnta 78 
                                   m+++iP+++ n ak+rls+ils+++r+e++ +ml+dvi+al+  +v+   +++   e ++ +    g  ++ e   +ln++
  gi|91773281|ref|YP_565973.1|   6 MRAVIPYKNEN-AKSRLSPILSKKDREEFVELMLKDVIKALDDAEVVnidILTTSAEGIPNDF--NGNVTITEP--GLNDS 81 
                                   899*****999.*****************************9966661114444444444444..555566666..***** PP

                          CofC  79 vekafeeieekeviiipsdiPlikkedvkdllelekradvviaPargGGtnllllr.ksalevkyedfsflkhleearkrg 158
                                   +++ + +  +++++ii++d+Pl++ +++++++  ++  dvvi P++gGGtn+l++r ++ + vky+d+sf+ h e + + +
  gi|91773281|ref|YP_565973.1|  82 INEYL-QNANEPILIIMADLPLVTGDHIRKIISFSE--DVVIVPGKGGGTNILFIRhPNEFTVKYHDCSFISHCEITDELD 159
                                   ***95.578899***********************9..******************99*********************** PP

                          CofC 159 lkvkiydsfylsvdinteedlgeillhGegtkakeylrk 197
                                    +++i+dsf+ s di++++d+ e++lhG+g+ akey  k
  gi|91773281|ref|YP_565973.1| 160 KSMHIFDSFLASTDIDEPHDIVELMLHGKGQ-AKEYAEK 197
                                   *****************************96.7888654 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 !   18.1   0.0   2.9e-07    0.0026      26     127 ..      37     128 ..      26     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHHHCTT.-CEEEEECSH.CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHH CS
                  NTP_transf_3  26 llervldalraagvdevvvvggd.eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelve 105
                                   +l+ v++al +a+v ++ + + + e +    ++++  v+  e    g   s+   l++a  ++++l++++D+Pl+t ++++
  gi|91773281|ref|YP_565973.1|  37 MLKDVIKALDDAEVVNIDILTTSaEGIP---NDFNGNVTITE---PGLNDSINEYLQNA--NEPILIIMADLPLVTGDHIR 109
                                   7777778888887777766665524444...34555555554...59999******987..7******************* PP

                                   HHHHCHHHHTSSEEEEESSSEE CS
                  NTP_transf_3 106 rllaaaaasgadvvvptyeger 127
                                   +++      ++ v+vp   g+ 
  gi|91773281|ref|YP_565973.1| 110 KIISFS---EDVVIVPGKGGGT 128
                                   ***974...4556666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1725.55
//
Query:       gi|91773282|ref|YP_565974.1|  [L=103]
Description: CutA1 divalent ion tolerance protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  103.1   0.3    6.4e-30  102.9   0.3    1.0  1  CutA1        CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
      0.066   13.2   0.7       0.13   12.3   0.3    1.7  2  SCAPER_N     S phase cyclin A-associated protein in the endop
      0.096   13.1   0.0       0.14   12.6   0.0    1.3  1  Caskin-tail  C-terminal region of Caskin


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 !  102.9   0.3   1.1e-33   6.4e-30       1      98 [.       4      98 ..       4      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 1.1e-33
                                  EEEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEEEE CS
                         CutA1  1 vlvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeiial 83
                                  ++v++t+++++ea+ l ++lv+++laAC+ni+  i+SvYrW  ki edkEv+l++kt +e ++el+++v++lh+y++p+i+ +
  gi|91773282|ref|YP_565974.1|  4 IMVYITVENMDEAQMLGKELVSSNLAACANIHR-IDSVYRWGCKIVEDKEVVLILKTISEMFDELKETVRSLHSYDLPCIC-W 84
                                  68****************************999.*********************************************97.7 PP

                                  EESEEEHHHHHHHHH CS
                         CutA1 84 pieagseaYlkWiee 98
                                  +i+ g+e+Yl+W+++
  gi|91773282|ref|YP_565974.1| 85 NIS-GDEDYLQWVSD 98
                                  988.*********97 PP

>> SCAPER_N  S phase cyclin A-associated protein in the endoplasmic reticulum
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.29   1.7e+03      29      46 ..       6      24 ..       5      43 .. 0.69
   2 ?   12.3   0.3   2.1e-05      0.13      37      70 ..      45      78 ..      24      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                      SCAPER_N 29 iYqtces.desvveCkevi 46
                                  +Y t+e+ de+++  ke +
  gi|91773282|ref|YP_565974.1|  6 VYITVENmDEAQMLGKELV 24
                                  6777774266666666655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.1e-05
                      SCAPER_N 37 esvveCkevilvLdnylrdfeaLierlrlkkdye 70
                                    +ve kev+l+L+++ + f++L e +r  ++y+
  gi|91773282|ref|YP_565974.1| 45 CKIVEDKEVVLILKTISEMFDELKETVRSLHSYD 78
                                  468999*******************999887775 PP

>> Caskin-tail  C-terminal region of Caskin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-05      0.14      31      54 ..      45      68 ..      23      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                   Caskin-tail 31 ssaaevksaknILdDIgnMFDdLA 54
                                  +++ e+k  + IL  I+ MFD+L 
  gi|91773282|ref|YP_565974.1| 45 CKIVEDKEVVLILKTISEMFDELK 68
                                  6678899999************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 692.10
//
Query:       gi|91773283|ref|YP_565975.1|  [L=57]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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   51.4  16.6    6.4e-07   28.9   4.1    2.1  2  Fer4      4Fe-4S binding domain
    3.3e-12   46.8  34.0      4e-07   30.5  12.6    2.0  3  Fer4_7    4Fe-4S dicluster domain
    6.4e-10   39.8  22.3    3.9e-05   24.5   0.8    2.1  3  Fer4_16   4Fe-4S double cluster binding domain
      4e-09   36.0  11.5    3.2e-05   23.7   1.6    2.2  2  Fer4_2    4Fe-4S binding domain
      9e-09   35.3  24.5    1.9e-05   24.7  13.8    2.0  2  Fer4_10   4Fe-4S dicluster domain
    1.9e-08   34.1  13.0     0.0002   21.3   3.5    2.2  2  Fer4_6    4Fe-4S binding domain
      2e-07   31.1  21.9    5.8e-06   26.4  12.2    1.9  2  Fer4_9    4Fe-4S dicluster domain
    6.6e-07   29.4  12.1    2.6e-06   27.5  12.1    1.8  1  Fer4_21   4Fe-4S dicluster domain
    2.8e-05   24.3  12.4     0.0037   17.7   3.1    2.3  2  Fer4_4    4Fe-4S binding domain
    0.00017   22.0  12.8       0.02   15.3   3.2    2.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00019   22.2  20.1       0.03   15.3   4.4    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0014   19.1  11.7       0.12   12.9   3.1    2.1  2  Fer4_17   4Fe-4S dicluster domain
     0.0018   18.8  10.4      0.016   15.7   2.4    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.016   15.4  11.1       0.38   11.0   1.8    2.0  2  Fer4_18   4Fe-4S dicluster domain
      0.074   13.8  11.6       0.98   10.2   0.5    2.7  2  Fer4_15   4Fe-4S single cluster domain
       0.18   12.7  14.8       0.31   11.9   3.6    2.1  2  Fer4_22   4Fe-4S dicluster domain
        4.6    7.4  10.8        1.1    9.3   0.5    3.3  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 !   28.9   4.1     6e-10   6.4e-07       2      24 .]       4      26 ..       3      26 .. 0.90
   2 !   28.8   4.6   6.8e-10   7.2e-07       6      24 .]      36      54 ..      32      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6e-10
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                   +++  C +CGaCv vCP+gA++
  gi|91773283|ref|YP_565975.1|  4 SVNKYICGYCGACVGVCPTGALE 26
                                  578889***************86 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 6.8e-10
                                  TTSSS-THHHHHSTTTEEE CS
                          Fer4  6 ekCigCGaCvevCPvgAIt 24
                                  +kC+gCG+C ++CP gAI+
  gi|91773283|ref|YP_565975.1| 36 NKCTGCGICQKICPLGAIE 54
                                  79****************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.2   4.9e-06    0.0051      36      52 .]       8      24 ..       2      24 .. 0.82
   2 !   30.5  12.6   3.8e-10     4e-07       2      52 .]      10      52 ..       9      52 .. 0.94
   3 !   20.6   2.6   4.6e-07   0.00049       1      20 [.      37      56 ..      37      57 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.9e-06
                        Fer4_7 36 ekClgCgaCvavCPtga 52
                                    C +CgaCv vCPtga
  gi|91773283|ref|YP_565975.1|  8 YICGYCGACVGVCPTGA 24
                                  56999*********997 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 3.8e-10
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  C  CgaCv +Cp++a+el e         +  + +kC+gCg C++ CP ga
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTGALELVET--------WIEVDNKCTGCGICQKICPLGA 52
                                  999***************875........88899**************987 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 4.6e-07
                        Fer4_7  1 rCigCgaCvaaCpvkaield 20
                                  +C+gCg C++ Cp +aie++
  gi|91773283|ref|YP_565975.1| 37 KCTGCGICQKICPLGAIEVN 56
                                  7************9999875 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 !   24.5   0.8   3.7e-08   3.9e-05       2      20 ..      10      28 ..       9      37 .. 0.85
   2 !   18.1   3.5   3.8e-06     0.004      51      66 ..      35      50 ..      29      51 .. 0.85
   3 !   17.8   3.6   4.4e-06    0.0047       1      19 [.      37      55 ..      37      57 .] 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.7e-08
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  Cg Cg+C+ vCPt+a++  
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTGALELV 28
                                  ****************987 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.8e-06
                       Fer4_16 51 qeaitgCdiCqdvCPa 66
                                   +++tgC+iCq++CP 
  gi|91773283|ref|YP_565975.1| 35 DNKCTGCGICQKICPL 50
                                  5799***********6 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 4.4e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                  +C++Cg C ++CP +ai+ 
  gi|91773283|ref|YP_565975.1| 37 KCTGCGICQKICPLGAIEV 55
                                  5888888888888888875 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   2.7   2.5e-06    0.0027       5      22 .]       5      22 ..       2      22 .. 0.88
   2 !   23.7   1.6   3.1e-08   3.2e-05       5      21 ..      32      49 ..      29      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.5e-06
                        Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                  v+  +C  CgaCv +CP+
  gi|91773283|ref|YP_565975.1|  5 VNKYICGYCGACVGVCPT 22
                                  78889************7 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.1e-08
                        Fer4_2  5 vdtd.rCigCgaCvsaCP 21
                                  ++ d +C+gCg+C++ CP
  gi|91773283|ref|YP_565975.1| 32 IEVDnKCTGCGICQKICP 49
                                  554449***********9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7  13.8   1.8e-08   1.9e-05       3      56 .]       4      49 ..       2      49 .. 0.82
   2 !   21.5   2.9   1.8e-07   0.00018       2      22 ..      31      51 ..      30      57 .] 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.8e-08
                       Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +++  C  Cg+Cv +CP+        g+ +  e+  ++  kCtgcg C+++CP
  gi|91773283|ref|YP_565975.1|  4 SVNKYICGYCGACVGVCPT--------GALELVETWIEVDNKCTGCGICQKICP 49
                                  567789*************........555555555566678***********9 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.8e-07
                       Fer4_10  2 vvidddtCirCgkCvkaCPad 22
                                  ++  d++C++Cg C+k CP  
  gi|91773283|ref|YP_565975.1| 31 WIEVDNKCTGCGICQKICPLG 51
                                  566789*************94 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.0   1.5e-06    0.0016       4      24 .]       5      25 ..       2      25 .. 0.83
   2 !   21.3   3.5   1.9e-07    0.0002       6      24 .]      35      53 ..      34      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +++  C  Cg+Cv vCP+ga+
  gi|91773283|ref|YP_565975.1|  5 VNKYICGYCGACVGVCPTGAL 25
                                  66667777***********97 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.9e-07
                        Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                  ++kC+gCg C ++CP gai
  gi|91773283|ref|YP_565975.1| 35 DNKCTGCGICQKICPLGAI 53
                                  59*************7665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.1   1.5e-05     0.015      36      50 ..      10      24 ..       2      25 .. 0.83
   2 !   26.4  12.2   5.5e-09   5.8e-06       2      51 .]      10      53 ..       9      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                        Fer4_9 36 CigCgaCveaCpkga 50
                                  C  CgaCv +Cp+ga
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTGA 24
                                  989*********997 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 5.5e-09
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  C  CgaCv +Cp+g+ +  +   ++ +      +C+gCg C ++Cp gai
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTGALELVETWIEVDN------KCTGCGICQKICPLGAI 53
                                  889************998877777776......6************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 !   27.5  12.1   2.5e-09   2.6e-06       3      58 ..       5      54 ..       3      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.5e-09
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  +++  C  Cg C+ +C++++ + +e+     +  v+++C+GC +C ++CP+ ++ie
  gi|91773283|ref|YP_565975.1|  5 VNKYICGYCGACVGVCPTGALELVET-----WIEVDNKCTGCGICQKICPL-GAIE 54
                                  67778999*********877777764.....456799*************8.9997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   2.0   0.00027      0.28       7      17 .]      13      23 ..      10      23 .. 0.93
   2 !   17.7   3.1   3.5e-06    0.0037       2      16 ..      36      50 ..      35      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                        Fer4_4  7 CgsCvaaCPqg 17
                                  Cg+Cv +CP+g
  gi|91773283|ref|YP_565975.1| 13 CGACVGVCPTG 23
                                  *********86 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.5e-06
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  ++C+gCg C  +CP 
  gi|91773283|ref|YP_565975.1| 36 NKCTGCGICQKICPL 50
                                  79************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 !   11.5   2.7   0.00029      0.31      51      64 ..      10      23 ..       5      24 .. 0.69
   2 !   15.3   3.2   1.9e-05      0.02       3      17 ..      36      50 ..      34      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                        Fer4_8 51 CttcgaCtevCpvg 64
                                  C  cgaC+ vCp+g
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTG 23
                                  77777777777765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.9e-05
                        Fer4_8  3 ekCieCgaCqsaCpv 17
                                  +kC++Cg Cq+ Cp+
  gi|91773283|ref|YP_565975.1| 36 NKCTGCGICQKICPL 50
                                  579999999999986 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   7.8   0.00015      0.16       3      15 .]      12      24 ..      10      24 .. 0.87
   2 !   15.3   4.4   2.8e-05      0.03       1      15 []      38      52 ..      38      52 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                        Fer4_3  3 gCgaCvevCPvgA 15
                                   CgaCv vCP+gA
  gi|91773283|ref|YP_565975.1| 12 YCGACVGVCPTGA 24
                                  4***********9 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.8e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  CtgCg C + CP gA
  gi|91773283|ref|YP_565975.1| 38 CTGCGICQKICPLGA 52
                                  ************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 !   11.1   1.4   0.00041      0.44       2      16 ..      10      24 ..       9      36 .. 0.80
   2 !   12.9   3.1   0.00011      0.12       1      15 [.      37      51 ..      37      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                       Fer4_17  2 CiqCgyClpeCpsye 16
                                  C  Cg+C+ +Cp+++
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTGA 24
                                  888888888888765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                       Fer4_17  1 rCiqCgyClpeCpsy 15
                                  +C++Cg C + Cp +
  gi|91773283|ref|YP_565975.1| 37 KCTGCGICQKICPLG 51
                                  588888888888876 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 !    8.1   1.1    0.0037       3.9       1      17 [.       5      21 ..       5      23 .. 0.87
   2 !   15.7   2.4   1.5e-05     0.016       1      17 [.      34      49 ..      34      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  V++  C  cgaCv ++P
  gi|91773283|ref|YP_565975.1|  5 VNKYICGYCGACVGVCP 21
                                  67778999********* PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.5e-05
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  VD ++C++cg+C +++P
  gi|91773283|ref|YP_565975.1| 34 VD-NKCTGCGICQKICP 49
                                  89.*************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 ?   10.8   1.7    0.0004      0.43      61      74 ..      10      23 ..       3      31 .. 0.88
   2 ?   11.0   1.8   0.00036      0.38      57      74 ..      34      51 ..      24      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                       Fer4_18 61 cidcescvkvcPtg 74
                                  c  c++cv vcPtg
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTG 23
                                  889**********8 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00036
                       Fer4_18 57 gagdcidcescvkvcPtg 74
                                   +++c+ c+ c k+cP g
  gi|91773283|ref|YP_565975.1| 34 VDNKCTGCGICQKICPLG 51
                                  5789************87 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00093      0.98       1      20 [.       3      22 ..       3      27 .. 0.89
   2 ?    7.1   4.8    0.0087       9.2       6      19 ..      36      49 ..      31      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00093
                       Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                  + v++  C  cg+Cv ++p+
  gi|91773283|ref|YP_565975.1|  3 ISVNKYICGYCGACVGVCPT 22
                                  6789999***********96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0087
                       Fer4_15  6 daCigcglCvaeap 19
                                  ++C+gcg C + +p
  gi|91773283|ref|YP_565975.1| 36 NKCTGCGICQKICP 49
                                  68*********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 ?    8.1   2.6    0.0046       4.8       2      15 ..      10      23 ..       9      37 .. 0.82
   2 ?   11.9   3.6   0.00029      0.31      80      94 ..      36      50 ..      25      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0046
                       Fer4_22  2 ClsCgaCtlvCptC 15
                                  C  CgaC  vCpt 
  gi|91773283|ref|YP_565975.1| 10 CGYCGACVGVCPTG 23
                                  889*********96 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00029
                       Fer4_22 80 sgCvGCgRCieacpv 94
                                  ++C+GCg C++ cp 
  gi|91773283|ref|YP_565975.1| 36 NKCTGCGICQKICPL 50
                                  68***********95 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 ?    9.3   0.5    0.0011       1.1      50      63 ..      16      29 ..      13      30 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                       Fer4_19 50 vverCPSGALsyve 63
                                   v  CP GAL++ve
  gi|91773283|ref|YP_565975.1| 16 CVGVCPTGALELVE 29
                                  6889*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 429.76
//
Query:       gi|91773284|ref|YP_565976.1|  [L=406]
Description: geranylgeranyl reductase [Methanococcoides burtonii DSM 6242]
Scores for 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-17   63.5   2.1    6.5e-09   35.5   0.3    3.0  2  FAD_binding_3   FAD binding domain
    2.7e-10   39.9   1.7    3.8e-07   29.5   0.2    2.3  2  FAD_binding_2   FAD binding domain
    2.8e-10   40.1   2.6    1.3e-09   37.9   2.6    1.9  1  FAD_oxidored    FAD dependent oxidoreductase
    8.3e-08   31.3   0.1    2.8e-07   29.6   0.0    1.8  2  HI0933_like     HI0933-like protein
    1.1e-06   28.8   0.0    2.7e-06   27.5   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.6e-06   26.9   2.5    8.5e-06   25.2   0.4    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.7e-06   26.3   1.0    6.8e-06   25.4   1.0    1.4  1  GIDA            Glucose inhibited division protein A
    9.2e-06   24.9   0.4      0.019   14.1   0.9    2.5  2  Lycopene_cycl   Lycopene cyclase protein
    7.8e-05   22.0   0.3    0.00027   20.3   0.1    1.9  2  Thi4            Thi4 family
     0.0005   19.8   0.5      0.044   13.4   0.2    2.2  2  DAO             FAD dependent oxidoreductase
    0.00087   18.3   0.1       0.32    9.8   0.1    2.2  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.011   15.0   0.5      0.018   14.3   0.5    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.082   12.2   0.4       0.17   11.1   0.1    1.8  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.15   11.9   0.5       0.32   10.9   0.1    1.7  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.89   10.2   3.0       0.82   10.3   0.1    2.3  2  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 !   23.7   0.1   2.2e-08   2.6e-05       2      35 ..       5      38 ..       4      46 .. 0.94
   2 !   35.5   0.3   5.4e-12   6.5e-09      94     336 ..      89     325 ..      67     337 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-08
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                  +dV++VGaGp G ++a+  ++ G +v+++ekr++
  gi|91773284|ref|YP_565976.1|  5 YDVIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQE 38
                                  69*****************************986 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 5.4e-12
                                   HCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTG CS
                 FAD_binding_3  94 sspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgi 174
                                   s++e  +v+  + ++r+L+++ + +g++vr kt+ + l  ++++v    + +  g+e++vr+k ++GaDG+ S+v + +gi
  gi|91773284|ref|YP_565976.1|  89 SGGEVGYVLERKIFDRALANESALAGAEVRVKTRATDLIIENDTVCGIKLMH-LGKEYEVRSKIVIGADGVESKVGRWAGI 168
                                   455555677777889******************************9998888.5*************************** PP

                                   GEEEEEEEEEEEEEEEEEEC-SCCCTTC..CEEEEEC..CTTEEEEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHH CS
                 FAD_binding_3 175 efegeetvyeagvldvlfdadlsdivep..lvlilsa..esrgvmviPlentlerfyvqvearaekeersekfteeevkar 251
                                   e + + +++e     ++ +a+++   ++   ++++++  + + v + P     ++ + +  ++        +  +++ ++ 
  gi|91773284|ref|YP_565976.1| 169 ETSVKPSDIETCAQYLVSNANID---QEfcYFYLGNEiaPAGYVWMFPKGG-NKANVGIGILGS-------RAGKDKPIEL 238
                                   *9888888555444445455887...3323333433311223335555555.333333344433.......3444445566 PP

                                   HHHHHTTSSCEEEEEEEEEEEEEEE.EESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHH..HHTTSS-GG CS
                 FAD_binding_3 252 lreivgektldveieevsawtvaqr.vaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaa..vlkGeAkee 329
                                   l+  ++++  d++i e+ + +v    + e+   + ++l+GDAa    P +G G+  a +Da ++a  +aa    kG+ + +
  gi|91773284|ref|YP_565976.1| 239 LNDFIEKNMPDAKIIEMVIGGVPVCgTIERTIANGLMLVGDAARQSDPITGGGIINA-MDAGKIAGEIAAkaIRKGDCSID 318
                                   66666666666677777776665542567777889****************999555.58888877777521346777888 PP

                                   GGHHHHH CS
                 FAD_binding_3 330 lLdtYee 336
                                    L+ Ye+
  gi|91773284|ref|YP_565976.1| 319 TLQEYED 325
                                   8888875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   3.2e-10   3.8e-07       1      47 [.       6      52 ..       6      68 .. 0.90
   2 !    9.3   0.1   0.00045      0.53     147     200 ..     106     157 ..      89     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.2e-10
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE- CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgida 47
                                  DviV+G+G +G  AA +aa++Gl+v+++ek qe g  + +++G   +
  gi|91773284|ref|YP_565976.1|  6 DVIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQEIGDPIRCAEGVGKF 52
                                  9********************************99999999997655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00045
                                   HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                 FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                   l+++   ag +++ +t+a++Li+e++ v G+ ++  + g+e ++r+k v+ a g
  gi|91773284|ref|YP_565976.1| 106 LANESALAGAEVRVKTRATDLIIENDTVCGIKLM--HLGKEYEVRSKIVIGADG 157
                                   5555656679************************..999999999998887766 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   2.6   1.1e-12   1.3e-09       1     164 [.       6     178 ..       6     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.1e-12
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll..tsglvatdignkaee......qvvtgiareflerlrqrgga 73 
                                   Dv+VvG+gp+G +AA +Aa++G  vl++e+r+ +G     + g++   +++++e       +    + + ++   +     
  gi|91773284|ref|YP_565976.1|   6 DVIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQEIGDPIrcAEGVGKFHLKQHIEPdprwicA---DVKGSYIISPDG---T 80 
                                   9**********************************865213444444444444445653332...222222222211...1 PP

                  FAD_oxidored  74 ..rlkkrskwn......tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg.d 145
                                     ++++++  +      + e +++ ++l +  a ag +v  +tr+++ + e++++ ++++ +  +++++r+k++i A g +
  gi|91773284|ref|YP_565976.1|  81 riEMAEEM--SggevgyVLERKIFDRALANESALAGAEVRVKTRATDLIIENDTVCGIKLMHLGKEYEVRSKIVIGADGvE 159
                                   11111222..0222355899999999999999999****************999******77667************8768 PP

                  FAD_oxidored 146 GdlaalaGvpyrvGresre 164
                                    +++ +aG+++ v   + e
  gi|91773284|ref|YP_565976.1| 160 SKVGRWAGIETSVKPSDIE 178
                                   9999999999988655555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   2.3e-10   2.8e-07       1      49 [.       5      54 ..       5      70 .. 0.87
   2 ?   -1.6   0.0      0.67     8e+02     114     158 ..     105     150 ..     101     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.3e-10
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC.GGGT-EE CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis.GgGrcNv 49
                                  +dviv+G+G+ G  aA +aak+g +Vl++ek +++g  i+ + G G+  +
  gi|91773284|ref|YP_565976.1|  5 YDVIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQEIGDPIRCAeGVGKFHL 54
                                  59***********************************9998757787655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.67
                                   HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEE CS
                   HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvkt.kseeeleadkl 158
                                   al +e   ag ++r++t+ +++  e+d +  +k+ + ++e+e ++ 
  gi|91773284|ref|YP_565976.1| 105 ALANESALAGAEVRVKTRATDLIIENDTVCGIKLmHLGKEYEVRSK 150
                                   7888899999999999999999999999999998655555544332 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 !   27.5   0.0   2.3e-09   2.7e-06       1      32 [.       9      40 ..       9      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.3e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  +vGaG +G+ aA ++ak+g+dvl +ekr+ +G
  gi|91773284|ref|YP_565976.1|  9 VVGAGPGGSIAAKTAAKEGLDVLMIEKRQEIG 40
                                  8******************************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 !   25.2   0.4   7.1e-09   8.5e-06       1      33 [.       5      37 ..       5      49 .. 0.90
   2 ?    0.8   0.1       0.2   2.4e+02     191     240 ..     108     161 ..      94     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 7.1e-09
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                  +dv+v+G+Gp+G  aa+t+a+ g++v+++e+++
  gi|91773284|ref|YP_565976.1|  5 YDVIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQ 37
                                  69***************************7544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                                   HHHHHTTEEEEESCEEEEEEETTE...EEE.EEETTSCEEEESEEEE-S-EEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx...xxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 191 ealekeGvevklgtsvkeidgnge...kle.vvledgeeidadlvvvavGvrps 240
                                   ++    G ev+++t++++++ +++    ++ ++l+++ e+  + v+ a Gv+ +
  gi|91773284|ref|YP_565976.1| 108 NESALAGAEVRVKTRATDLIIENDtvcGIKlMHLGKEYEVRSKIVIGADGVESK 161
                                   444445666666677776555555569888999999999999999999998865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.0   5.7e-09   6.8e-06       1     150 [.       6     158 ..       6     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.7e-09
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHH........HHT-SHHHHHHHHEEE CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEid........alggliikaadkagiq 73 
                                   dviV+G+G  G+ AA +aa+ G++vl+i +k ++i+         g++k +l++ i+         ++g  i   d ++i 
  gi|91773284|ref|YP_565976.1|   6 DVIVVGAGPGGSIAAKTAAKEGLDVLMI-EKRQEIGDP--IRCAEGVGKFHLKQHIEpdprwicaDVKGSYIISPDGTRI- 82 
                                   8***************************.777888875..4445677777777777533333322466777777888888. PP

                                   EEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHT.STTEEEEES-EEEEEECTTEEEEEEET.TS-EE..EECEEEE--TT CS
                          GIDA  74 frilNrskGpavralraqvdrelyskevteklen.epnleiieeeveeliveekkvkgvvte.dgeti..kakavviatGt 150
                                    ++  +  G  v++     +r+ + +++ ++      ++ + ++ +++li+e+++v+g+++   g+++  ++k+v+ a G 
  gi|91773284|ref|YP_565976.1|  83 -EMAEEMSGGEVGYV---LERKIFDRALANESALaGAEVRVKTR-ATDLIIENDTVCGIKLMhLGKEYevRSKIVIGADGV 158
                                   .77767777777766...89999999987764431467777655.566668899999987541455540055577767776 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.9   1.6e-05     0.019       1      36 [.       6      39 ..       6     174 .. 0.60
   2 !    7.8   0.0    0.0012       1.5     231     310 ..     248     329 ..     238     357 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                  Dv+v+GaGp g s+Aa+  +ak gl v++ie  +++
  gi|91773284|ref|YP_565976.1|  6 DVIVVGAGPGG-SIAAKT-AAKEGLDVLMIEKRQEI 39
                                  9********88.566665.6**********987765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0012
                 Lycopene_cycl 231 kvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres........slsar 302
                                     ++++e   g +Pv   g ++r+ ++  + +G aa    P TG  + +++ + + +a  iaa + ++        +    
  gi|91773284|ref|YP_565976.1| 248 PDAKIIEMVIGGVPV--CGTIERTIANgLMLVGDAARQSDPITGGGIINAMDAGK-IAGEIAAKAIRKgdcsidtlQE--- 322
                                   5578888888999**..99999988887999********************8777.7777777766665775444433... PP

                 Lycopene_cycl 303 awatlwpr 310
                                     ++lw++
  gi|91773284|ref|YP_565976.1| 323 -YEDLWRA 329
                                   .3444443 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.2e-07   0.00027      18      54 ..       5      40 ..       3      58 .. 0.92
   2 ?   -1.6   0.0       1.1   1.3e+03     114     135 ..     116     136 ..      85     169 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.2e-07
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                   Dv++vGaG+ G  aa++ ak+ +l v+++e++  +G
  gi|91773284|ref|YP_565976.1|  5 YDVIVVGAGPGGSIAAKTAAKE-GLDVLMIEKRQEIG 40
                                  59********************.*********98887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                   EEEESEEEEEEEEETBTEEEEE CS
                          Thi4 114 kllnavaveDlivregegvaGv 135
                                    +   + + Dli+ + ++v G+
  gi|91773284|ref|YP_565976.1| 116 EVRVKTRATDLIIEN-DTVCGI 136
                                   444444444555544.444444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   3.7e-05     0.044       1      33 [.       6      40 ..       6      43 .. 0.96
   2 ?    4.6   0.0     0.017        20     148     227 ..     102     186 ..      63     264 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  dv+++G+G  G+ +A  +a++g  V+ +ek+ ++g
  gi|91773284|ref|YP_565976.1|  6 DVIVVGAGPGGSIAAKTAAKEGldVLMIEKRQEIG 40
                                  9******************************8887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHTT-EEEESECEEEEEEEE.....TCEEEEEEECTEEEEEEEE..EEE--GGGHH..HHHTTCTTTSEEEE CS
                           DAO 148 ltaalaraaealGveilegtevtgleeed.....gkvwgverttpgendaada..vVnaaGawsd..llgllkeldlpisp 219
                                   + +ala++ + +G+e++ +t++t+l  e+     +k++++     g + +++   v+ a G+ s+   +     ++  ++p
  gi|91773284|ref|YP_565976.1| 102 FDRALANESALAGAEVRVKTRATDLIIENdtvcgIKLMHL-----GKEYEVRSkiVIGADGVESKvgRW---AGIETSVKP 174
                                   568999999999************7454423544444554.....444223334488888888875444...222222233 PP

                                   ....EEEEEEEE CS
                           DAO 220 ....vrgqvlvl 227
                                       + +q+lv 
  gi|91773284|ref|YP_565976.1| 175 sdieTCAQYLVS 186
                                   222255555555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00026      0.32       1      35 [.       6      37 ..       6      48 .. 0.89
   2 !    6.3   0.0     0.003       3.6     142     341 ..      88     297 ..      73     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00026
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                  ++++vG+G+ G++aA + ak +   l+v+++e+ +
  gi|91773284|ref|YP_565976.1|  6 DVIVVGAGPGGSIAAKTAAKEG---LDVLMIEKRQ 37
                                  699*************999999...9******864 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.003
                                   -B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-IIIIIIT- CS
                Trp_halogenase 142 lsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgllieqaLk 219
                                   +s+ + +y l+++ +++ L + +  +G +++  + ++  + e++ v +++l     + ev   ++i + G ++++   a  
  gi|91773284|ref|YP_565976.1|  88 MSGGEVGYVLERKIFDRALANESALAGAEVRVKTRATDLIIENDTVCGIKLMHlgkEYEVRSKIVIGADGVESKVGRWAGI 168
                                   566678999*******************98877777777777777777776656447778889**********99888766 PP

                                   --EEE-TTT----EEEEEEEE--H.---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--TTT CS
                Trp_halogenase 220 tgfedwsdvLltdrAlavqvesee.lvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgklea 298
                                   ++  + sd+  + + l+ + + ++     y +     aG +W  P  ++  n G+    ++a +d+ ++ l   ++++   
  gi|91773284|ref|YP_565976.1| 169 ETSVKPSDIETCAQYLVSNANIDQeFCYFYLGNEIAPAGYVWMFPKGGNKANvGIGILGSRAGKDKPIELLNDFIEKN-MP 248
                                   666677777777777777776666466677778888899999999888888888888888888888887666666644.44 PP

                                   S-EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH CS
                Trp_halogenase 299 eprkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa 341
                                   +++ i++  G        +++  ++++++G+a+   +P+ + +i  ++ 
  gi|91773284|ref|YP_565976.1| 249 DAKIIEMVIGGvpvcgtIERTIANGLMLVGDAARQSDPITGGGIINAMD 297
                                   5577788777767777788889999999999999999998888876655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   1.5e-05     0.018       1      36 [.       8      43 ..       8      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nignsi 36
                                  i++GaGP G  aa ++ k gl d+l +Ek  +ig+ i
  gi|91773284|ref|YP_565976.1|  8 IVVGAGPGGSIAAKTAAKEGL-DVLMIEKRqEIGDPI 43
                                  89*******************.8*****987787765 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   0.1   0.00015      0.17      30      62 ..       6      38 ..       2     133 .. 0.93
   2 ?   -2.1   0.1       1.6   1.9e+03      33      71 ..     287     327 ..     273     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                   v+v+G+G  G  A++ta++ g +V ++++r++
  gi|91773284|ref|YP_565976.1|  6 DVIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQE 38
                                  69***************************9987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                                   EESTSHH.HHHHHHHHHHTT-E.EEEEESSHHHHHHHHHTT CS
                   AlaDh_PNT_C  33 viGgGva.GlqAiatakglgak.VtvlDvrparleqleslg 71 
                                   + GgG+   + A ++a ++ ak ++  D ++++l++ e+l 
  gi|91773284|ref|YP_565976.1| 287 ITGGGIInAMDAGKIAGEIAAKaIRKGDCSIDTLQEYEDLW 327
                                   67888753677888888888763677888888888888844 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00027      0.32       2      34 ..       7      39 ..       6      57 .. 0.92
   2 ?   -3.7   0.0       7.9   9.4e+03      14      33 ..     106     125 ..     104     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                  v v+GaG  G+  a+ +a++gl+V +++ ++e+
  gi|91773284|ref|YP_565976.1|  7 VIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQEI 39
                                  78**************************99875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.9
                                   HHHHHHHTT-EEEEE-S-HH CS
                       3HCDH_N  14 iaavfasagleVvlvdisee 33 
                                   +a+  a ag eV++  ++++
  gi|91773284|ref|YP_565976.1| 106 LANESALAGAEVRVKTRATD 125
                                   56777888888888776655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00069      0.82       2      35 ..       7      40 ..       6      58 .. 0.93
   2 ?   -1.1   0.4       2.5     3e+03       4      19 ..     287     302 ..     287     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00069
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  v+vvG+G  g  +A+++a+ g +V ++e + ++ 
  gi|91773284|ref|YP_565976.1|  7 VIVVGAGPGGSIAAKTAAKEGLDVLMIEKRQEIG 40
                                  89****************************9997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                                   EECSSHHHHHHHHHHH CS
                     Pyr_redox   4 vvGgGyiglElAgala 19 
                                   + GgG i+ + Ag +a
  gi|91773284|ref|YP_565976.1| 287 ITGGGIINAMDAGKIA 302
                                   5699999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2647.63
//
Query:       gi|91773285|ref|YP_565977.1|  [L=479]
Description: K+ transporter Trk [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-69  235.0  22.9    4.1e-68  230.1  22.9    2.0  1  TrkH          Cation transport protein
  ------ inclusion threshold ------
        2.9    7.0  11.9       0.06   12.5   1.2    2.5  2  Bac_export_2  FlhB HrpN YscU SpaS Family


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 !  230.1  22.9   4.5e-72   4.1e-68       7     489 ..      41     471 ..      37     478 .. 0.94

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 4.5e-72
                          TrkH   7 kggiitialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivvees 87 
                                     +++t ++g++l f++  s+ + + +++f iv   + a    g+++ +++   ++ l+alfe++sg+tttg++ +v+ es
  gi|91773285|ref|YP_565977.1|  41 VSFAVTTVIGSLLSFKFISSEDEWEKREGFAIVAFGWFAAALFGSIPYMFD--GVTPLNALFESMSGFTTTGATIFVDIES 119
                                   5789999****************************************9965..5778************************ PP

                          TrkH  88 lprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvvl 168
                                    +rs l++r+++q+iGg+g++ l  ++lp lg  + ++ ++ea+++  ++   ++++e++kil+ +yv++ +l ++ll   
  gi|91773285|ref|YP_565977.1| 120 HSRSLLFWRSMTQWIGGMGIIMLFIAILPKLGVAGRQMFRAEAPGPQEDQL-KPRIRETAKILWAVYVSISVLELILL--- 196
                                   ********************************************9987665.599***********************... PP

                          TrkH 169 iytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrviiaikkkil 249
                                           +++      + ++a  h+++++  +Gfs++++S a fn+ ++i+ ++++f+++ + +F ++++++   kk+  
  gi|91773285|ref|YP_565977.1| 197 ------LAAGM------SFYDASTHTFTTMACGGFSTYADSVAAFNS-PLIEGIITLFMFIAGANFALHYKTLYSDKKSL- 263
                                   ......88999......9*****************************.************************99877766. PP

                          TrkH 250 rdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfilldegslvvksipkgsrvlkalFqsvstrta. 329
                                               l+d ++++ + ++a++++ l+ + l                   + + ip  ++++ a+Fq+ s +t+ 
  gi|91773285|ref|YP_565977.1| 264 ------------LKDNEFKFYFAIVAISTILLTGILLR-----------------DSYDTIP--TAFRYAVFQVLSILTTt 313
                                   ............679*****977777777666665544.................6778999..88899************ PP

                          TrkH 330 GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksidgkhlerqllvdlwsl 410
                                   G++++d+  ++++ kv+l+ +m+igg++gStaggI+ ++v+++ +  ++e+ +  +pka++++++ gk +  ++++++ s+
  gi|91773285|ref|YP_565977.1| 314 GYATADFNLWSDSGKVILLAIMFIGGCAGSTAGGIKVVRVLILLKYARRELFKAIHPKAIRPVKFNGKSVPGDVMHAIISF 394
                                   ********************************************************************************* PP

                          TrkH 411 flvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGa.knaslsaqlttisklvlialmirGrlrglpvlld 489
                                   ++++++i+++++  l   +   +++  ++ ++++++g++G+++     ++ + +++ ++kl+lia+m++Grl++++v++ 
  gi|91773285|ref|YP_565977.1| 395 VVIYFLIFLFSSSILAILG---MDLTSSITASIATLGNIGPGFNVvGPMANFSTVPVLGKLILIANMWIGRLEVFTVIVM 471
                                   ***********99998888...9*******************9844899*****************************97 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 ?   12.5   1.2   6.7e-06      0.06      34     200 ..      76     257 ..      65     270 .. 0.75
   2 ?   -1.2   3.6       0.1   9.4e+02     121     163 ..     378     417 ..     270     473 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX.................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X CS
                  Bac_export_2  34 laglllllllgpslveelaellrevlsa.................lelllelllallllllplllvlllaallanllqv.g 96 
                                     ++++l+  +p++++ ++  l++++++                 ++  l +  ++++ +  + +++l++a+l +l    +
  gi|91773285|ref|YP_565977.1|  76 GWFAAALFGSIPYMFDGVTP-LNALFESmsgftttgatifvdiesHSRSLLFWRSMTQWIGGMGIIMLFIAILPKLGVAgR 155
                                   44455566666777766665.333344445567677666655543222233333444556677888888888888876658 PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Bac_export_2  97 flfstkalkpklsklnplkglkrifslrslvellksllkvvlvgavaylvlkseleellalaeldleaalelllslllkll 177
                                    +f ++a  p+ ++l+p   ++   ++  +v +  s+l+++l++a+++ +++++ ++++++a   +++ ++ ++ +   l+
  gi|91773285|ref|YP_565977.1| 156 QMFRAEAPGPQEDQLKP--RIRETAKILWAVYVSISVLELILLLAAGMSFYDASTHTFTTMACGGFSTYADSVAAFNSPLI 234
                                   9****************..566666666789999*********************************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXX CS
                  Bac_export_2 178 llvllallviallDlllqrwefe 200
                                     ++ ++++ia + ++l +    
  gi|91773285|ref|YP_565977.1| 235 EGIITLFMFIAGANFALHYKTLY 257
                                   *************9999876655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.1
                                   XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Bac_export_2 121 fslrslv.ellksllkvvlvgavaylvlkseleellalaeldle 163
                                   f+ +s+  +++ +++ +v++ ++++l+ +s + ++l    +dl+
  gi|91773285|ref|YP_565977.1| 378 FNGKSVPgDVMHAIISFVVIYFLIFLFSSS-ILAIL---GMDLT 417
                                   333333212333333332222222222222.11111...12222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3198.13
//
Query:       gi|91773286|ref|YP_565978.1|  [L=444]
Description: potassium transporter peripheral membrane component [Methanococcoides burtonii DSM 6242]
Scores for complete 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-51  171.9   4.8    1.2e-26   93.3   0.1    2.3  2  TrkA_N           TrkA-N domain
    8.9e-31  105.5   1.2    1.9e-14   53.2   0.1    3.0  3  TrkA_C           TrkA-C domain
    1.8e-11   44.2   3.4    9.7e-05   22.4   0.1    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    6.5e-11   42.6   1.5      5e-05   23.7   0.1    2.7  2  NAD_binding_7    Putative NAD(P)-binding
    4.7e-10   39.1   2.1     0.0005   19.4   0.0    2.3  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    3.4e-09   37.0   3.7     0.0015   18.8   0.1    2.7  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    8.7e-07   29.5   0.7     0.0038   17.8   0.1    2.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.2e-05   24.5   0.2       0.13   12.2   0.0    2.4  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0001   22.2   0.8       0.28   11.1   0.1    3.1  4  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00011   22.4   0.1      0.032   14.4   0.0    2.7  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    0.00015   22.4   0.1       0.04   14.6   0.0    2.9  3  Methyltransf_25  Methyltransferase domain
    0.00022   21.1   0.2       0.63   10.0   0.1    2.6  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
    0.00031   20.1   0.8       0.03   13.5   0.1    2.2  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00034   20.0   0.0      0.054   12.7   0.0    2.3  2  FAD_binding_3    FAD binding domain
    0.00055   20.5   1.9       0.11   13.1   0.0    3.6  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00094   18.9   0.2        1.1    8.9   0.0    2.4  2  ApbA             Ketopantoate reductase PanE/ApbA
     0.0012   18.4   1.0      0.074   12.6   0.4    3.0  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0016   18.1   0.3        1.9    8.0   0.2    2.4  2  DAO              FAD dependent oxidoreductase
     0.0029   16.4   0.1       0.16   10.6   0.0    2.2  2  HI0933_like      HI0933-like protein
     0.0029   17.2   4.9       0.54    9.8   0.3    2.3  2  DUF1188          Protein of unknown function (DUF1188)
      0.006   16.5   2.4        1.5    8.7   0.2    2.6  2  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.025   13.4   0.2       0.33    9.8   0.0    2.2  2  Trp_halogenase   Tryptophan halogenase
      0.026   13.9   0.6        9.9    5.4   0.1    3.2  3  ThiF             ThiF family
      0.036   13.6   1.7          1    8.8   0.3    2.3  2  NmrA             NmrA-like family
      0.043   13.1   2.6        1.5    8.0   0.0    3.0  3  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      0.044   14.4   4.3        1.9    9.2   1.2    2.6  2  PglD_N           PglD N-terminal domain
      0.044   14.3   0.1         11    6.6   0.0    2.5  2  XdhC_C           XdhC Rossmann domain
      0.066   13.3   0.4      0.066   13.3   0.4    2.8  3  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
      0.087   12.6   0.2       0.49   10.2   0.1    2.2  2  Methyltransf_31  Methyltransferase domain
       0.51    9.7   4.3       0.94    8.8   0.4    2.6  2  Spermine_synth   Spermine/spermidine synthase 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 !   79.7   1.5   3.3e-25     2e-22       1     116 []       3     123 ..       3     123 .. 0.91
   2 !   93.3   0.1   1.9e-29   1.2e-26       1     116 []     230     346 ..     230     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3.3e-25
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavl 81 
                                   iii+G+G+vG ++a  L  ++ dvvvid de++++++ e  ++v++g++++ ++Le++ i++ad+++a+tg+de ni+++ 
  gi|91773286|ref|YP_565978.1|   3 IIIVGAGEVGFHIASSLYLNN-DVVVIDIDEDACARADELDVQVIQGNGANVSILERL-INDADLLVAVTGSDELNIVTCT 81 
                                   8******************99.7*********************************98.9********************* PP

                                   HHHHHTSS...SEEEEEESSGGG....HHHHHHHTTSEEEEH CS
                        TrkA_N  82 lakelnpk...kkiiaraqdpeh....aellkklgadvvisp 116
                                   +ak + p    +k++ar+ +p++    +    ++g+dv+i p
  gi|91773286|ref|YP_565978.1|  82 TAKLISPLhkqLKTMARVTNPDYidrpVATRTQVGIDVMICP 123
                                   ***9999987889**********7643333344888988876 PP

  == domain 2  score: 93.3 bits;  conditional E-value: 1.9e-29
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgddeanila 79 
                                   ++iiG G+vG  la+ L++++ ++ +i+k+ +r+e++++    + v++g++td ++L+e g++++d+vi +t++de+n+l+
  gi|91773286|ref|YP_565978.1| 230 VLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLDRCESIADLLpkVLVLKGNGTDIHLLKEEGVQNMDVVISVTDSDEKNLLC 310
                                   68*****************6667*****************96666999********************************* PP

                                   HHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                        TrkA_N  80 vllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                   +ll k+l   kk+i+ra++ +++ l++ +g+d+++sp
  gi|91773286|ref|YP_565978.1| 311 ALLSKQLGA-KKVIVRADHLDYVPLFELVGVDRAVSP 346
                                   *****9777.79***********************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       8.3     5e+03      50      65 ..      23      38 ..      22      41 .. 0.79
   2 !   53.2   0.1   3.2e-17   1.9e-14       1      69 [.     153     220 ..     153     221 .. 0.96
   3 !   50.3   0.0   2.7e-16   1.6e-13       2      69 ..     377     443 ..     376     444 .] 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.3
                                  T-EEEEEEEHHHHHHH CS
                        TrkA_C 50 GDvllvvgspsdlael 65
                                  +Dv+++  + ++ a++
  gi|91773286|ref|YP_565978.1| 23 NDVVVIDIDEDACARA 38
                                  7999999999987776 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 3.2e-17
                                   CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                   ++e++v+ +s lv+k++k+l++ +  ++v a+ R+  +iip gd+v+++GD+++v+g+++++ ++ +l+
  gi|91773286|ref|YP_565978.1| 153 MMEFVVSDESDLVDKKMKDLDISE-CCIVSALYRDSNIIIPHGDDVIHKGDHVVVIGKSDAMMDIGNLF 220
                                   69**********************.**********9**************************9998887 PP

  == domain 3  score: 50.3 bits;  conditional E-value: 2.7e-16
                                   EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                   +e+  ++ s++ Gk+lk +++++ g+lv  ++++g+ ++p+g+++++eGD++lv+  ps+ +++++l+
  gi|91773286|ref|YP_565978.1| 377 IEYNASSTSKVTGKPLKNVRFPE-GALVCMVVHKGDTFVPRGNYIIKEGDRVLVFLLPSAHQKVERLF 443
                                   6888999****************.***************************************99998 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.6     2e-07   0.00012      14     126 ..       2     114 ..       1     120 [. 0.80
   2 !   22.4   0.1   1.6e-07   9.7e-05      12      90 ..     227     308 ..     219     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-07
                                   EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-.SB- CS
                  Shikimate_DH  14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisataseep.ile 91 
                                   k++++GaGe++  +a+ L+ +  v  + +     +ra+el  ++ +g   +  +++ l++l+++ad++++ t+s e  i++
  gi|91773286|ref|YP_565978.1|   2 KIIIVGAGEVGFHIASSLYLNnDVVVIDIDEDACARADELDVQViQG---NGANVSILERLINDADLLVAVTGSDELnIVT 79 
                                   89****************85426777778889999*****9888344...599999*****************98862666 PP

                                   HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTT CS
                  Shikimate_DH  92 keeveealkkrkkplllvDiavPRdvepevaeled 126
                                       + ++  +k+ + +  +++P  ++  va+ ++
  gi|91773286|ref|YP_565978.1|  80 CTTAKLISPLHKQLKTMARVTNPDYIDRPVATRTQ 114
                                   66666555555466699999999989888877655 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.6e-07
                                   T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHH....HHHHT-SEEEE-SSSSS- CS
                  Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelk....ellaeadvvisataseep 88 
                                    k+vl+iG G ++  +ak L +++ +++ ++  +l+r +++a+ l ++ +   + ++++    e ++++dvvis t s e 
  gi|91773286|ref|YP_565978.1| 227 VKRVLIIGGGTVGFYLAKLLEKSN-TSIKIIEKNLDRCESIADLLPKVLVLKGNGTDIHllkeEGVQNMDVVISVTDSDEK 306
                                   689***********9999777555.55****************998887766666665322226799*********99886 PP

                                   SB CS
                  Shikimate_DH  89 il 90 
                                    l
  gi|91773286|ref|YP_565978.1| 307 NL 308
                                   55 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 !   17.3   0.2   8.1e-06    0.0049       9      83 ..       2      84 ..       1     103 [. 0.73
   2 !   23.7   0.1   8.4e-08     5e-05       8      84 ..     228     316 ..     223     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.1e-06
                 NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvklaeee......lekdlegadlviaatddrelneri 78
                                  k+++vG+Gev+ + +++l  +  +v+v++ +  +++        + ++    +      le+ +++adl++a+t  +eln   
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYLN-NDVVVIDIDE-DACAradeldvQVIQ---GNganvsiLERLINDADLLVAVTGSDELNIVT 79
                                  689**********99999998.8899987773.233333233232222...222222224888****************9877 PP

                 NAD_binding_7 79 aeaak 83
                                  + +ak
  gi|91773286|ref|YP_565978.1| 80 CTTAK 84
                                  77665 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 8.4e-08
                 NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvklaeee..l....ekdlegadlviaatddreln 75 
                                   k+vl++GgG+v+   ++ l +++  ++++ +++ + +e       + + l+ +   +    e+ ++++d+vi +td +e n
  gi|91773286|ref|YP_565978.1| 228 KRVLIIGGGTVGFYLAKLLEKSNTSIKIIEKNL-DRCEsiadllpKVLVLKGNGtdIhllkEEGVQNMDVVISVTDSDEKN 307
                                   89******************************6.445522233332222333332224455667***********999998 PP

                 NAD_binding_7  76 eriaeaaka 84 
                                      a + k+
  gi|91773286|ref|YP_565978.1| 308 LLCALLSKQ 316
                                   776666665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   1.1e-06   0.00067      30      97 ..       2      68 ..       1      96 [. 0.90
   2 !   19.4   0.0   8.4e-07    0.0005      28      97 ..     227     299 ..     211     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvig 97
                                  k++++G+G +G + ia +  l+ +V+v+D+++++  + ++l  ++++   ++ + l++ +++ad+++ 
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFH-IASSLYLNNDVVVIDIDEDACARADELDVQVIQGNGANVSILERLINDADLLVA 68
                                  899********98.88899**********************************************985 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 8.4e-07
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHH....HHHHHH-SEEEE CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeell....aeavkeadvvig 97 
                                     +vl+iGgG++G   ++   + + ++++++++ +r e + +l  k v vlk +   +    +e v+++dvvi+
  gi|91773286|ref|YP_565978.1| 227 VKRVLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLDRCESIADLLPK-VLVLKGNGTDIhllkEEGVQNMDVVIS 299
                                   458***************************************9999.666555544432222567999***997 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 !   18.0   0.9   4.3e-06    0.0026       1      78 [.       3      71 ..       3      83 .. 0.93
   2 !   18.8   0.1   2.4e-06    0.0015       1      76 [.     230     300 ..     230     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                                  ++i+GaG vG  +a  l  ++dv    +v+d +++ ++++     + +++ i+ + +n++  L++l++++dl+v +++
  gi|91773286|ref|YP_565978.1|  3 IIIVGAGEVGFHIASSLYLNNDV----VVIDIDEDACARA----DELDVQVIQGNGANVSI-LERLINDADLLVAVTG 71
                                  89******************986....*********9999....689*************8.***********97765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.4e-06
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE- CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnl 76 
                                   vliiG+G vG  +a+ll++++     i +++++++++e +a+  l +++   + +  ++   L++  ++  d+v+++
  gi|91773286|ref|YP_565978.1| 230 VLIIGGGTVGFYLAKLLEKSNT---SIKIIEKNLDRCESIAD--LLPKVLVLKGNGTDIHL-LKEEgVQNMDVVISV 300
                                   89*****************987...5**************98..66777777777777776.444436666777776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0027       1.6       1      52 [.       2      47 ..       2      67 .. 0.79
   2 !   17.8   0.1   6.3e-06    0.0038       2      91 ..     230     323 ..     229     326 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0027
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvta 52
                                  ki i+GaG++g+ +as l  ++    ++vv+ + +++ a + a+el v+v++
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYLNN----DVVVI-DIDED-ACARADELDVQVIQ 47
                                  67899***********999996....88878.55544.55666777777776 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.3e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S-HHH CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlavkped 73 
                                   + iiG+G +g+ la+ l +++   ++i ++ ++n ++ e++a+ l           ++ +  +ee +++ dvv+ +v  +d
  gi|91773286|ref|YP_565978.1| 230 VLIIGGGTVGFYLAKLLEKSN---TSIKII-EKNLDRCESIADLLPkvlvlkgngTDI-HLLKEEGVQNMDVVI-SVTDSD 304
                                   679*****************9...****88.************999999999885444.447789999999876.444444 PP

                                   HHHHHHHC.GHHHHTTSEE CS
                 F420_oxidored  74 veevlsel.akdalkgklv 91 
                                    +++l +l  k++ ++k++
  gi|91773286|ref|YP_565978.1| 305 EKNLLCALlSKQLGAKKVI 323
                                   4444444414444444444 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 !    9.9   0.1    0.0011      0.68       1      91 [.       2      95 ..       2     104 .. 0.66
   2 !   12.2   0.0   0.00022      0.13       2     100 ..     230     324 ..     229     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                                  -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H...HHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EE..EE--- CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvree...elieeineehenvkyLpgiklpenlvattdlaealkgadii..vlvvP 78
                                  ki ++GaG  G  +A +l  n+ +v+++  +e   + ++e++ +    +   ++++ e l   +dl  a++g+d +  v   +
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYLNN-DVVVIDIDEdacARADELDVQVIQGN-GANVSILERLINDADLLVAVTGSDELniVTCTT 82
                                  799*****************99.77777888845533344444333333.234666678889999999999998651144444 PP

                                  HHHHHHHHHHHCC CS
                NAD_Gly3P_dh_N 79 sqalrevlkklkg 91
                                   + +    k+lk+
  gi|91773286|ref|YP_565978.1| 83 AKLISPLHKQLKT 95
                                  5555555555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHH CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqal 82 
                                   + ++G+G  G  lAk+l++ + +++++ ++ + +e+i +    v  L+g   + +l      +e +++ d+++ v  s   
  gi|91773286|ref|YP_565978.1| 230 VLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLDRCESIADLLPKVLVLKGNGTDIHLLK----EEGVQNMDVVISVTDSDEK 306
                                   779**********************************999999999998666555554....4677777888888877777 PP

                                   HHHHHHHCCC--TT-EEE CS
                NAD_Gly3P_dh_N  83 revlkklkgllkkkailv 100
                                   +  ++ l++ l +k+++v
  gi|91773286|ref|YP_565978.1| 307 NLLCALLSKQLGAKKVIV 324
                                   777777777776666666 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 !   11.1   0.1   0.00046      0.28       1      40 [.       2      40 ..       2      64 .. 0.88
   2 !    7.8   0.0    0.0047       2.8       2      43 ..     230     271 ..     229     313 .. 0.83
   3 ?   -1.6   0.0       3.5   2.1e+03     131     171 ..     322     362 ..     286     370 .. 0.72
   4 ?   -0.6   0.0       1.8   1.1e+03       9      38 ..     358     387 ..     356     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                  k+ ++GaG +G  ia+ +   + +Vv++di+e+a ++a e
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYL-NNDVVVIDIDEDACARADE 40
                                  5789***********98876.569**********999865 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0047
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekie 43 
                                   v +iG Gt+G  +a+++ +++ ++++++ + ++ e+ ++ + 
  gi|91773286|ref|YP_565978.1| 230 VLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLDRCESIADLLP 271
                                   789*************************99999888776665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.5
                                   GEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHHHHHHTT CS
                       3HCDH_N 131 rviglHFfnPpplmkLvEvvrgekTseetvatvvelakkig 171
                                    ++ +  +  +pl++Lv v r+ + +e+t+++v +l+  +g
  gi|91773286|ref|YP_565978.1| 322 VIVRADHLDYVPLFELVGVDRAVSPREATINEVLKLTMGTG 362
                                   55555555567788888888888888888888888776655 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.8
                                   CCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                       3HCDH_N   9 tmGagiaavfasagleVvlvdiseealeka 38 
                                   tmG+gi a+++ +g +  +++ ++++  k+
  gi|91773286|ref|YP_565978.1| 358 TMGTGIEALTMIEGEKAEIIEYNASSTSKV 387
                                   8************99999999988877766 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 ?    5.2   0.1     0.042        25       1      38 [.       5      41 ..       5      58 .. 0.85
   2 !   14.4   0.0   5.4e-05     0.032       1      28 [.     232     259 ..     232     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.042
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  IvGaG  G  +A+ L   + dv++++  ++ + ra   
  gi|91773286|ref|YP_565978.1|  5 IVGAGEVGFHIASSLYL-NNDVVVIDIDEDACARADEL 41
                                  9************9987.48*********999998765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.4e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekr 28 
                                   I+G+G  G ++A lL k + ++ ++ek+
  gi|91773286|ref|YP_565978.1| 232 IIGGGTVGFYLAKLLEKSNTSIKIIEKN 259
                                   9*************************96 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.6e-05      0.04       6      95 ..       6     102 ..       4     103 .. 0.76
   2 ?    4.3   0.0      0.11        65       7      71 ..     234     300 ..     230     313 .. 0.78
   3 ?   -1.9   0.0       9.7   5.8e+03       1      24 [.     354     376 ..     354     388 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-05
                                   -TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHH....TTTTEEEEESBCCGBS.....SSTTTEEEEEEESTGGG CS
               Methyltransf_25   6 cGtGrltlalakrlg.kakvtgvDiseemleaareraee....eglnvefvqgdaedlp.....fedgsfDlvvssgalhh 76 
                                    G G++ +++a  l  + +v+ +Di+e+++++a e   +    +g+nv++++  ++d +       +++ ++v+++    +
  gi|91773286|ref|YP_565978.1|   6 VGAGEVGFHIASSLYlNNDVVVIDIDEDACARADELDVQviqgNGANVSILERLINDADllvavTGSDELNIVTCTT-AKL 85 
                                   59999999999998447*****************7665555458889999887776654323334777999999964.566 PP

                                   SSHHHHHHHHHHHHHHEEE CS
               Methyltransf_25  77 lsdedlekalkeiarvLkp 95 
                                   +s   l+k lk +arv++p
  gi|91773286|ref|YP_565978.1|  86 IS--PLHKQLKTMARVTNP 102
                                   76..467889999999998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                                   TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS....SSTTTEEEEEEE CS
               Methyltransf_25   7 GtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp....fedgsfDlvvss 71 
                                   G G++ ++lak l +++ t + i e+ l+++++ a+   ++v +++g+ +d++    +  + +D+v+s+
  gi|91773286|ref|YP_565978.1| 234 GGGTVGFYLAKLL-EKSNTSIKIIEKNLDRCESIAD-LLPKVLVLKGNGTDIHllkeEGVQNMDVVISV 300
                                   7888999999998.6999999999999999999884.4469********99873222234489999986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 9.7
                                   EEEET-TTSHHHHHHHCTSTSSEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakv 24 
                                   vL l  GtG  +l + +  +ka++
  gi|91773286|ref|YP_565978.1| 354 VLKLTMGTGIEALTMIEG-EKAEI 376
                                   899999***999888765.34554 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0011      0.63      31      92 ..     155     212 ..     150     220 .. 0.77
   2 !    8.4   0.0    0.0034       2.1      31      87 ..     378     430 ..     368     441 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
               Castor_Poll_mid  31 efylkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegdkllviaeddd 92 
                                   ef + +++ l +kk +d+ ++ +  +v  +  +++++i++ P+ d v+++gd+++vi++ d 
  gi|91773286|ref|YP_565978.1| 155 EFVVSDESDLVDKKMKDLDIS-ECCIVSAL--YRDSNIII-PHGDDVIHKGDHVVVIGKSDA 212
                                   777888888888888887654.33455555..88888866.99**************99876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0034
               Castor_Poll_mid  31 efylkelpelegkkyedvllafqe.avviGikvassgkiylnPeddevlqegdkllvi 87 
                                   e++  + ++++gk  ++v+  f+e a v+ +  +++g  ++ P+ +++++egd++lv 
  gi|91773286|ref|YP_565978.1| 378 EYNASSTSKVTGKPLKNVR--FPEgALVCMV--VHKGD-TFVPRGNYIIKEGDRVLVF 430
                                   5567778888888888876..5551556655..56676.689*************985 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.017        10       2      58 ..       2      84 ..       1     134 [. 0.71
   2 !   13.5   0.1   5.1e-05      0.03     139     231 ..     222     313 ..     184     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH.......................... CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.legtclnggcllskallgvaedaeias.......................... 57
                                  +++++G+G  G++ a  l   + +v++++ +e++c   + l  +++ g +++ +i++                          
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYL-NNDVVVIDiDEDACARADELDVQVIQGNGANVSILErlindadllvavtgsdelnivtctta 83
                                  78999999999999988877.67888888788888888777777777777777777766666666666666655555555555 PP

                                  H CS
                                  x RF
                   Pyr_redox_2 58 e 58
                                  +
  gi|91773286|ref|YP_565978.1| 84 K 84
                                  4 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.1e-05
                                   SS-T..SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHH..HHTTEEEEESCEEEEEEETTEE CS
                                   xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 139 kllp..krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleeal..ekeGvevklgtsvkeidgngek 215
                                     ++  kr++++GgG +G  lA  l k +  + ++e +   +    +++++ l ++l  + +G +++l ++   +++ +  
  gi|91773286|ref|YP_565978.1| 222 GHTDnvKRVLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLDRC----ESIADLLPKVLvlKGNGTDIHLLKEE-GVQNMDVV 297
                                   444466889999999999999999999988888888765555....67777777754115668888876665.77766666 PP

                                   EEEEETTSCEEEESEE CS
                                   xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 216 levvledgeeidadlv 231
                                   ++v+++d++ + + l+
  gi|91773286|ref|YP_565978.1| 298 ISVTDSDEKNLLCALL 313
                                   6688888887777665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.022        13       3      34 ..       2      32 ..       1      47 [. 0.86
   2 !   12.7   0.0     9e-05     0.054       3      33 ..     229     259 ..     228     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.022
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  +++IVGaG +G+  a+ L     +vv+++  +
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYLN-NDVVVIDIDE 32
                                  689***************999.8999998655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9e-05
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                    VlI+G+G +G+ la+lL +   +  ++ek 
  gi|91773286|ref|YP_565978.1| 229 RVLIIGGGTVGFYLAKLLEKSNTSIKIIEKN 259
                                   59******************99999999986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.081        49       1      29 [.       2      29 ..       2      46 .. 0.80
   2 ?   -1.3   0.0       5.4   3.2e+03       1      21 [.     203     223 ..     200     228 .. 0.64
   3 !   13.1   0.0   0.00018      0.11       1      31 [.     229     259 ..     229     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.081
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvve 29
                                  k+++vG+G +g   A+ l  l+++V v++
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLY-LNNDVVVID 29
                                  799************9983.555666665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.4
                                   EEEEECSSHHHHHHHHHHHHT CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalael 21 
                                   +vvv+G ++  ++ ++ +a +
  gi|91773286|ref|YP_565978.1| 203 HVVVIGKSDAMMDIGNLFAGH 223
                                   677777777666666666555 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00018
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvvers 31 
                                   +v+++GgG++g  lA+ l + + +++++e +
  gi|91773286|ref|YP_565978.1| 229 RVLIIGGGTVGFYLAKLLEKSNTSIKIIEKN 259
                                   79**************************975 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0018       1.1       1      41 [.       3      43 ..       3      94 .. 0.78
   2 !    7.9   0.0    0.0038       2.3       1      38 [.     230     268 ..     230     319 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCE CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGl 41
                                  i i+GaG +G  +a +L+  ++dv++i+ ++  +++  + ++
  gi|91773286|ref|YP_565978.1|  3 IIIVGAGEVGFHIASSLYL-NNDVVVIDIDEdACARADELDV 43
                                  89***************66.8899999988866665554444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0038
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38 
                                   ++i+G G +G +la  L k +  + +i ++  r+e++ +
  gi|91773286|ref|YP_565978.1| 230 VLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLdRCESIAD 268
                                   68****************999999999999888888754 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.4   0.00012     0.074       1      43 [.       1      42 [.       1      59 [. 0.85
   2 ?   -0.4   0.0       1.2   7.5e+02     142     161 ..     112     131 ..      91     141 .. 0.71
   3 ?    2.3   0.0      0.18   1.1e+02       2      39 ..     229     266 ..     228     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                  SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS CS
                UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgk 43
                                  mki ++G+G vG   a  l  + ++v+++Dide + +   + +
  gi|91773286|ref|YP_565978.1|  1 MKIIIVGAGEVGFHIASSL-YLNNDVVVIDIDEDACARADELD 42
                                  89***********999998.5679*********9887666555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                   S-TTCEEEEE------TTSH CS
                UDPG_MGDP_dh_N 142 kkgvdfdvvsnPEflregsa 161
                                   +++v +dv+ +PE  + +++
  gi|91773286|ref|YP_565978.1| 112 RTQVGIDVMICPELALASEV 131
                                   347899*******8876654 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.18
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdkl 39 
                                   ++ +iG G vG   a +l +    + ++ ++  + +++
  gi|91773286|ref|YP_565978.1| 229 RVLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLDRCESI 266
                                   899***************99999999998887776665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0032       1.9       1      33 [.       2      35 ..       2      54 .. 0.89
   2 !    7.8   0.0    0.0035       2.1       1      29 [.     229     259 ..     229     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0032
                                  EEEEECTSHHHHHHHHHHHHTT.EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekgdiag 33
                                  +++i+G+G +G  +A  L   + V++++ +++a+
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYLNNdVVVIDIDEDAC 35
                                  59****************98878****9886665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0035
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                   +v+iiGGG +G   A  L + +  + ++ek+
  gi|91773286|ref|YP_565978.1| 229 RVLIIGGGTVGFYLAKLLEKSNtsIKIIEKN 259
                                   59****************776689*****98 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.034        20       2      31 ..       2      30 ..       1      37 [. 0.84
   2 !   10.6   0.0   0.00027      0.16       2      32 ..     229     259 ..     228     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.034
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                  ++i++G+G  G+  A s+   +++V++++ 
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSL-YLNNDVVVIDI 30
                                  79*************999.67778888885 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00027
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVllleka 32 
                                   +v++iGgG  G++ A  ++k + ++ ++ek+
  gi|91773286|ref|YP_565978.1| 229 RVLIIGGGTVGFYLAKLLEKSNTSIKIIEKN 259
                                   699**************************98 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.5    0.0013       0.8      45      77 ..       2      34 ..       1      79 [. 0.67
   2 !    9.8   0.3    0.0009      0.54      40     105 ..     224     301 ..     203     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                  EEEEES-CCCHHHHHHHHCCCEEEEEEESSGGG CS
                       DUF1188 45 nvlviGaYltGaaiakkLskkeevtlvDiephl 77
                                  +++++Ga  +G  ia++L  +++v+++Di++  
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYLNNDVVVIDIDEDA 34
                                  79***************************8753 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0009
                                   -E..EEEEEES-CCCHHHHHHHHCCC.EEEEEE....ESSGGGGGGSSST.......HHHHHHHHTTS---SEEEE-- CS
                       DUF1188  40 eleeknvlviGaYltGaaiakkLskk.eevtlv....Diephlkellekd.......vefklsleevernadlviDlt 105
                                   + + k+vl+iG   +G ++ak L+k+ + + ++    D  + +++ll+k         +++l  ee  +n+d+vi +t
  gi|91773286|ref|YP_565978.1| 224 TDNVKRVLIIGGGTVGFYLAKLLEKSnTSIKIIeknlDRCESIADLLPKVlvlkgngTDIHLLKEEGVQNMDVVISVT 301
                                   446799*******************99999997333356678888888877777766666666667788999999877 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 !    8.7   0.2    0.0025       1.5       3      73 ..       8      75 ..       7     100 .. 0.76
   2 !    7.2   0.0    0.0069       4.1       4      82 ..     236     323 ..     234     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                                  TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73
                                   G vG ++++ l  ++  +v+++  +++  a+ ++e  ++v++g+  +v+ l++ +++ad  v+ +g+++ 
  gi|91773286|ref|YP_565978.1|  8 AGEVGFHIASSLYLNN--DVVVIDIDEDACAR-ADELDVQVIQGNGANVSILERLINDADLLVAVTGSDEL 75
                                  6899999999998885..45555445555554.46799**********************99988887654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0069
                                   SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT.TTCEEEE--TT-CCHHHH.HHTT-SEEEES---TCC........H CS
                NAD_binding_10   4 GkvGrllvkellargghevtalvRnpeklaeleae.eglevvegdvtdvedlae.alkgadaVvsalggggk........d 74 
                                   G vG +l+k ll++++++++++  n ++ +++++  +++ v++g+ td   l+e  +++ d+V+s + +++k        +
  gi|91773286|ref|YP_565978.1| 236 GTVGFYLAK-LLEKSNTSIKIIEKNLDRCESIADLlPKVLVLKGNGTDIHLLKEeGVQNMDVVISVTDSDEKnllcallsK 315
                                   888888887.555558************999987679***********999865169**********87776455555432 PP

                                   HHHHHHHH CS
                NAD_binding_10  75 eegakniv 82 
                                   + gak+++
  gi|91773286|ref|YP_565978.1| 316 QLGAKKVI 323
                                   22355554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.21   1.2e+02       1      20 [.       2      21 ..       2      36 .. 0.80
   2 ?    9.8   0.0   0.00055      0.33       1      33 [.     229     258 ..     229     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                                  EEEEE--SHHHHHHHHHHHH CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalak 20
                                  ki+ivG+G  G+  A+ l  
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYL 21
                                  79**********99998854 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00055
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                   +++i+GGGt G+  A +l+k     ++++++e+
  gi|91773286|ref|YP_565978.1| 229 RVLIIGGGTVGFYLAKLLEKSN---TSIKIIEK 258
                                   699****************998...78998887 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.028        17      20      39 ..       2      21 ..       1      39 [. 0.85
   2 ?    5.4   0.1     0.017       9.9      19      38 ..     228     247 ..     202     256 .. 0.79
   3 ?   -0.8   0.0       1.3   7.9e+02      32      55 ..     353     376 ..     352     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.028
                                  EEEEE--SHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                          ThiF 20 kvllvGaGglGsellknLal 39
                                  k+ +vGaG +G  ++  L l
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYL 21
                                  89*************99977 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                                   SEEEEE--SHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          ThiF  19 skvllvGaGglGsellknLa 38 
                                   ++vl++G G++G +l+k+L 
  gi|91773286|ref|YP_565978.1| 228 KRVLIIGGGTVGFYLAKLLE 247
                                   89***************995 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.3
                                   HHHHHHHHHTTTEEEEEESSB--G CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  32 ellknLalsGvgkltlvDnDkiel 55 
                                   e+lk+ +++G++ lt++  +k e+
  gi|91773286|ref|YP_565978.1| 353 EVLKLTMGTGIEALTMIEGEKAEI 376
                                   899999***********9999887 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3    0.0017         1       4      80 ..       5      76 ..       3      83 .. 0.77
   2 ?    3.8   0.1     0.058        35       2      77 ..     231     306 ..     230     327 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                                  SSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GGS-HHH CS
                          NmrA  4 iGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfyskeie 80
                                  i ++G+ G ++++ l   +++  ++v d ++++ +   e  v++++g+  + ++l+++++++d+  +vtg  s+e++
  gi|91773286|ref|YP_565978.1|  5 IVGAGEVGFHIASSLYL-NND--VVVIDIDEDACARADELDVQVIQGNGANVSILERLINDADLLVAVTG--SDELN 76
                                  44557777777665443.333..345688888999999999*****************************..66654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.058
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S.-SHHHHHHHHSTTEEE.ES-TT-HHHHH.HHHTT-SEEEE---GGS- CS
                          NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdt.kselakslkeaGvelv.kgdlddkeslv.ealkgvdvvfsvtgfysk 77 
                                   l+iG+ G  G ++++ l k++ +++++ +++ + e ++ l   + +lv kg+  d  +l+ e +++ dvv+svt + +k
  gi|91773286|ref|YP_565978.1| 231 LIIGG-GTVGFYLAKLLEKSNTSIKIIEKNLdRCESIADL--LPKVLVlKGNGTDIHLLKeEGVQNMDVVISVTDSDEK 306
                                   66765.9999999999999999999999998433444444..466777799988888776268999*******996633 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.059        35     166     193 ..       2      29 ..       1      84 [. 0.74
   2 ?   -0.7   0.0       1.1   6.6e+02     163     180 ..     200     217 ..     192     229 .. 0.80
   3 ?    8.0   0.0    0.0025       1.5       1      31 [.     231     261 ..     231     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.059
                   Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvv 193
                                   k++++G+++ ++ +A  l+ ++  V + 
  gi|91773286|ref|YP_565978.1|   2 KIIIVGAGEVGFHIASSLYLNNDVVVID 29 
                                   5778888888888888887664444333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                   Pyr_redox_3 163 agqkvvViGgknSavDaA 180
                                   +g++vvViG+++  +D+ 
  gi|91773286|ref|YP_565978.1| 200 KGDHVVVIGKSDAMMDIG 217
                                   6889*******9999975 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0025
                   Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.n 31 
                                   +IiG+G  G   a  l+k++  ++ i+Ek+  
  gi|91773286|ref|YP_565978.1| 231 LIIGGGTVGFYLAKLLEKSNT-SIKIIEKNlD 261
                                   6*******************9.79*****855 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.2    0.0031       1.9       1      64 [.       2      68 ..       2      72 .. 0.67
   2 ?    5.6   0.1     0.041        25       1      67 [.     229     302 ..     229     310 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0031
                        PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk.tevegypvlgk...aiellkslseeeyevviA 64
                                  ki+I+GaG  g  +a  +  n++  +i +  d+ +   + +++v+++    +++l++l  ++ ++ +A
  gi|91773286|ref|YP_565978.1|  2 KIIIVGAGEVGFHIASSLYLNNDVVVIDIDEDACArADELDVQVIQGngaNVSILERLI-NDADLLVA 68
                                  8*********************8777777777655233445566554111455566664.34456666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.041
                        PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk..teveg.......ypvlgkaiellkslseeeyevviAIGn 67 
                                   +++IiG G  g   a+++e+++    i ++ +n +  +++ +       +++ g++i+llk+   ++++vvi++ +
  gi|91773286|ref|YP_565978.1| 229 RVLIIGGGTVGFYLAKLLEKSNT--SIKIIEKNLDrcESIADllpkvlvLKGNGTDIHLLKEEGVQNMDVVISVTD 302
                                   589****************9993..444444443211122222333333555555666666655568889998876 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.04        24       2      53 ..       4      72 ..       3     119 .. 0.66
   2 ?    6.6   0.0     0.018        11       1      45 [.     230     295 ..     230     325 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.04
                                  EEE--STTHHHHHHHHHHHTEEEEEEES-G.GGG-GGG-TT-SE....................-EEEE--S- CS
                        XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpre.efatkerfpeade....................tavvvlthd 53
                                  +i+Gag+v+ ++a+ +  l+ +v+v+d +e + a+++++                         + +v++t +
  gi|91773286|ref|YP_565978.1|  4 IIVGAGEVGFHIASSL-YLNNDVVVIDIDEdACARADELD---VqviqgnganvsilerlindaDLLVAVTGS 72
                                  89***********988.57889999999994555444444...123455643334444444444333333333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG......-GGG-TT-SE.......................- CS
                        XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa......tkerfpeade.......................t 45 
                                   ++i+G+g v+  la+l+++ + ++ +++++ +                                         +
  gi|91773286|ref|YP_565978.1| 230 VLIIGGGTVGFYLAKLLEKSNTSIKIIEKNLDRCesiadlL--------PkvlvlkgngtdihllkeegvqnmD 295
                                   68*************************99874222322330........1233344444444444445555334 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   0.00011     0.066      26      91 ..       3      75 ..       1     106 [. 0.76
   2 ?   -1.3   0.0       3.3     2e+03      18      33 ..     196     211 ..     185     232 .. 0.60
   3 ?   -0.3   0.1       1.7     1e+03      24      53 ..     228     257 ..     215     331 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                  EEEE--SHHHHHHHHHHHHCT-EEEEE-S-H.HHH......HHHHC.TT-EE--HHHCTTT-SEEEE-SSSSSS CS
                 AdoHcyase_NAD 26 avvaGyGdvGkGcaaslkglGarvivtevdP.ica......lqaam.eGfevvtleevvkkadivvtttGnkdi 91
                                  ++++G G+vG   a+sl      v+v ++d   ca      +q +  +G +v  le ++++ad++v++tG++++
  gi|91773286|ref|YP_565978.1|  3 IIIVGAGEVGFHIASSLYLN-NDVVVIDIDEdACAradeldVQVIQgNGANVSILERLINDADLLVAVTGSDEL 75
                                  6899************9866.56677778752566333322333223799********************9753 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                                   -S--TTSEEEEE--SH CS
                 AdoHcyase_NAD  18 dvllaGkvavvaGyGd 33 
                                   dv+  G  +vv+G  d
  gi|91773286|ref|YP_565978.1| 196 DVIHKGDHVVVIGKSD 211
                                   5555555555555433 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.7
                                   SEEEEE--SHHHHHHHHHHHHCT-EEEEE- CS
                 AdoHcyase_NAD  24 kvavvaGyGdvGkGcaaslkglGarvivte 53 
                                   k ++++G G vG   a+ l++  + + + e
  gi|91773286|ref|YP_565978.1| 228 KRVLIIGGGTVGFYLAKLLEKSNTSIKIIE 257
                                   567777777777777777766666665554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00082      0.49      13     103 ..       7     102 ..       4     105 .. 0.75
   2 ?   -1.1   0.0       2.4   1.5e+03      15      80 ..     236     299 ..     229     345 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00082
               Methyltransf_31  13 GtGeltfelaeelgpkaevvGiDiseeaielAre....naqklgldnveFeqgdieeleklled...ekfDlilsnevlna 86 
                                   G+Ge +f +a+ l+ + +vv iDi+e+a  +A e      q +g  nv+  +  i++++ l++    +  +++++  +  +
  gi|91773286|ref|YP_565978.1|   7 GAGEVGFHIASSLYLNNDVVVIDIDEDACARADEldvqVIQGNGA-NVSILERLINDADLLVAVtgsDELNIVTCT-TAKL 85 
                                   7899*******9999*****************9966644444444.788888777776644332456777777774.5567 PP

               Methyltransf_31  87 ladpdkileeiervlkp 103
                                   ++ + k l+ + rv +p
  gi|91773286|ref|YP_565978.1|  86 ISPLHKQLKTMARVTNP 102
                                   77777778888887776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
               Methyltransf_31  15 GeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeq...gdieelekl.ledekfDlils 80 
                                   G+ +f la +l +k++ ++i i e+ + +++++a+ l  + v + +    di+ l++  +  ++ D+++s
  gi|91773286|ref|YP_565978.1| 236 GTVGFYLA-KLLEKSN-TSIKIIEKNLDRCESIADLL-PK-VLVLKgngTDIHLLKEEgV--QNMDVVIS 299
                                   55566666.4444444.56666666666666654422.22.2222212244444444333..35666665 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.27   1.6e+02      30      56 ..      12      36 ..       1      41 [. 0.68
   2 ?    8.8   0.4    0.0016      0.94       8      65 ..     216     273 ..     210     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.27
                                  SHHHHHHTTSTT-SEEEEEES-HHHHH CS
                Spermine_synth 30 GgvlrevvkhntvekitlvdiDqkvid 56
                                  G  +   + +n  ++++++diD++++ 
  gi|91773286|ref|YP_565978.1| 12 GFHIASSLYLN--NDVVVIDIDEDACA 36
                                  44445555556..899********995 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
                                   HHHHHHCCSSST-EEEEESSTT.SHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHH CS
                Spermine_synth   8 iahvplmlhknpkevLiiGGgD.GgvlrevvkhntvekitlvdiDqkvidfskkflpsl 65 
                                   i+++ +    n k+vLiiGGg  G  l +++  +  ++i +++   + +++    lp++
  gi|91773286|ref|YP_565978.1| 216 IGNLFAGHTDNVKRVLIIGGGTvGFYLAKLLEKS-NTSIKIIEKNLDRCESIADLLPKV 273
                                   555555556689********97677888887655.677877776666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2940.94
//
Query:       gi|91773287|ref|YP_565979.1|  [L=396]
Description: chaperone protein DnaJ [Methanococcoides burtonii DSM 6242]
Scores for complete 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-40  137.8   0.1      4e-40  137.3   0.1    1.2  1  DnaJ_C          DnaJ C terminal domain
    1.6e-27   95.4   5.0    2.6e-27   94.7   5.0    1.4  1  DnaJ            DnaJ domain
    1.1e-14   54.5  17.0    2.4e-14   53.4  17.0    1.6  1  DnaJ_CXXCXGXG   DnaJ central domain
  ------ inclusion threshold ------
      0.028   14.4  19.2        0.5   10.4   0.3    3.3  4  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
       0.17   12.6   0.2       0.27   11.9   0.2    1.3  1  LprI            Lysozyme inhibitor LprI
       0.23   11.9   5.1       0.58   10.7   5.1    1.7  1  Cytochrom_c3_2  Cytochrome c3
        1.5    8.7   7.4        3.7    7.5   1.6    2.5  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
          2    8.4   7.4        1.7    8.5   1.0    2.2  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
        2.3    8.3  12.2         91    3.2  12.2    2.2  1  DZR             Double zinc ribbon
        8.8    6.4  10.0         42    4.3  10.0    2.1  1  Cytochrome_C7   Cytochrome c7 and related cytochrome c


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 !  137.3   0.1   2.2e-43     4e-40       2     148 .]     129     345 ..     128     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 2.2e-43
                                   EEEEEE-HHHHHH-.EEE.EEEE.......................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                        DnaJ_C   2 eveleisleelykGktkkikikrnvi....................................................... 27 
                                   +++l ++le++++G +  i++ r ++                                                       
  gi|91773287|ref|YP_565979.1| 129 RYDLGVTLEQAAFGEKVHINVPRAENcetcggtgakegtspktcatcrgsgqvtharrtplgnfmttttcdachgkgqvie 209
                                   799********************999******************************************************* PP

                                   ..............T.EEEEEE-TT--TT-EEEETT-SS.SS...S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHH CS
                                   ..........xxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaJ_C  28 ..........kkekk.tlevkipaGikdgqkirlegeGd.eeg.gepGDlivtikvkphpvFkrkgndlyveveislaeal 95 
                                             k++k  ++ v+ip+G ++g +++++geG+  ++ +++GDl+++i+vk+h+ F+r g+d+++ ++is+++a+
  gi|91773287|ref|YP_565979.1| 210 spcpvcrgsgKQKKVrKMGVSIPKGADTGLRLKMSGEGEaGSPgAPSGDLYIVIHVKQHDEFERIGDDIVYGIPISFSQAA 290
                                   *********84444469**********************74447************************************* PP

                                   HTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                   xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaJ_C  96 lGgklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                   lG++++vptl+gkvk+ki   tq+ ++lr+kgkGmp+l+ ++++Gd++v+v ve+P
  gi|91773287|ref|YP_565979.1| 291 LGAEIKVPTLHGKVKMKIkpgTQTHSILRLKGKGMPRLH-GHGQGDQLVKVIVETP 345
                                   **************************************8.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   5.0   1.5e-30   2.6e-27       1      63 []       6      67 ..       6      67 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 1.5e-30
                                  HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                          DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                  dyYeiLgvskdas+ e+kkaYrkla+k+HPDkn k+ +aeekFkei+eAy vLsd+ek++qYD
  gi|91773287|ref|YP_565979.1|  6 DYYEILGVSKDASDTELKKAYRKLAMKFHPDKN-KEADAEEKFKEISEAYAVLSDAEKKAQYD 67
                                  8********************************.9999************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4  17.0   1.3e-17   2.4e-14       1      67 []     155     219 ..     155     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.3e-17
                 DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                   C++C G+gak+g+ +ktC tC+GsG+v++ ++t lg+f+  +++tC++C+G+G+vi  +++C+ C+G+g
  gi|91773287|ref|YP_565979.1| 155 CETCGGTGAKEGTsPKTCATCRGSGQVTHARRTpLGNFM--TTTTCDACHGKGQVI--ESPCPVCRGSG 219
                                   **********9777***********88777777799977..579************..789******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 ?    8.1   6.3    0.0014       2.6      11      45 ..     153     184 ..     145     195 .. 0.80
   2 ?    7.4   4.3    0.0024       4.3      12      41 ..     171     206 ..     168     208 .. 0.86
   3 ?    9.4   4.9   0.00056         1      11      40 ..     196     219 ..     193     221 .. 0.92
   4 ?   10.4   0.3   0.00028       0.5       9      40 ..     208     238 ..     206     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                                   EE-TTTTTTSEETTE......E-TTTTTSSEEE-H CS
                     Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkglipTa 45 
                                   ++C++C g+G  e++ p     C  C G g +  a
  gi|91773287|ref|YP_565979.1| 153 ENCETCGGTGAKEGTSP---KTCATCRGSGQVTHA 184
                                   58*************55...58******9987655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0024
                                   E-TTTTTTSEETTE............E-TTTTTSSE CS
                     Anti-TRAP  12 kCdaCngsGkiepe......eprasleCPkCsGkgl 41 
                                   +C +C gsG++  +      +  ++  C +C Gkg 
  gi|91773287|ref|YP_565979.1| 171 TCATCRGSGQVTHArrtplgNFMTTTTCDACHGKGQ 206
                                   8**********9998877777778889*******96 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00056
                                   EE-TTTTTTSEETTE......E-TTTTTSS CS
                     Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkg 40 
                                   t+CdaC+g G++         +CP C G g
  gi|91773287|ref|YP_565979.1| 196 TTCDACHGKGQVIES------PCPVCRGSG 219
                                   79*********9999......9*****987 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00028
                                   CEEE-TTTTTTSEETTE......E-TTTTTSS CS
                     Anti-TRAP   9 LEtkCdaCngsGkiepeeprasleCPkCsGkg 40 
                                   +E +C+ C gsGk +    + ++  Pk    g
  gi|91773287|ref|YP_565979.1| 208 IESPCPVCRGSGKQKKV-RKMGVSIPKGADTG 238
                                   699**********9988.66777777765555 PP

>> LprI  Lysozyme inhibitor LprI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00015      0.27      15      75 ..      10      71 ..       1      87 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                  HHHHHHHHHHHHHHHHHHHHH....HHHHHTT....HHHHHHHHHHHHHHHHHHHHHHHTTTS-T CS
                          LprI 15 CasaalkaadaeLnkaykalk....eekekkavssearkaLkdaqraWikyRdaeCalakspake 75
                                   +    +a+d+eL+kay++l+     +   k+++++a++++k+   a+    dae ++++  ++ 
  gi|91773287|ref|YP_565979.1| 10 ILGVSKDASDTELKKAYRKLAmkfhPD---KNKEADAEEKFKEISEAYAVLSDAEKKAQYDRFGH 71
                                  55666789*********9999755422...44577888888888888887777777776666665 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.1   0.00032      0.58       8      78 ..     154     215 ..     146     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                   TGGGTSSSST-SSTTHHHHHHHHHHH--HHHCHTTSST.TSSBTTSSCTSSS-GGGTS-TTTSBT-GGGGT CS
                Cytochrom_c3_2   8 kCadCHtkekpkkdkaveeekClsCHgkleelakktkeakeanphkshekeleCteCHkeHkksekvCaeC 78 
                                   +C++C ++  +   + ++ ++C +C g+ + +++++      +p  +++++++C++CH + +  e+ C  C
  gi|91773287|ref|YP_565979.1| 154 NCETCGGTGAK---EGTSPKTCATCRGSGQVTHARR------TPLGNFMTTTTCDACHGKGQVIESPCPVC 215
                                   79999888886...5667899*****9999876664......5889999*********9999888888877 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.6    0.0021       3.7       4      27 ..     155     175 ..     153     176 .. 0.95
   2 ?    4.1   0.4     0.025        44       2       9 ..     210     217 ..     209     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                                   -TTT--BBEEEECTTEEEEE-TTT CS
                  zf-FPG_IleRS   4 CpRCwryiervgqagrstyfCprC 27 
                                   C++C+++ +++g    s+  C +C
  gi|91773287|ref|YP_565979.1| 155 CETCGGTGAKEGT---SPKTCATC 175
                                   *************...*******9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.025
                                   SB-TTT-- CS
                  zf-FPG_IleRS   2 epCpRCwr 9  
                                   +pCp+C++
  gi|91773287|ref|YP_565979.1| 210 SPCPVCRG 217
                                   59****96 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 ?    3.1   0.7     0.047        84      26      45 ..     155     177 ..     153     180 .. 0.88
   2 ?    8.5   1.0   0.00096       1.7      24      46 ..     196     218 ..     193     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.047
                                   -HHHHHHHHH...TT-B-TTT-- CS
                    zf-C3HC4_3  26 CeeCaekllk...rkkkCpiCrr 45 
                                   Ce+C  +  k   + k+C  Cr 
  gi|91773287|ref|YP_565979.1| 155 CETCGGTGAKegtSPKTCATCRG 177
                                   999999998889999******96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00096
                                   EE-HHHHHHHHHTT-B-TTT--B CS
                    zf-C3HC4_3  24 vlCeeCaekllkrkkkCpiCrrp 46 
                                    +C +C  k +  +  Cp+Cr +
  gi|91773287|ref|YP_565979.1| 196 TTCDACHGKGQVIESPCPVCRGS 218
                                   58********88*********75 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  12.2     0.051        91      10      48 ..     150     215 ..     145     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.051
                           DZR  10 pdarfCseCgtklkavaa...........................edrCpsCgekvdpearfCpeC 48 
                                   p+a+ C++Cg +  ++ +                            ++C++C+ k +  ++ Cp C
  gi|91773287|ref|YP_565979.1| 150 PRAENCETCGGTGAKEGTspktcatcrgsgqvtharrtplgnfmtTTTCDACHGKGQVIESPCPVC 215
                                   555666666555443333444444444444444468888888888888888888888888888888 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  10.0     0.023        42       3      60 ..     141     208 ..     135     224 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.023
                 Cytochrome_C7   3 fshkshlka.tgykCtdCHsklfeskak.......kk.maemekgkskkaeves.ltCgaCHdgknaf 60 
                                   f +k h+++ ++ +C++C ++ ++++++       ++  + +++++    ++ + +tC+aCH + ++ 
  gi|91773287|ref|YP_565979.1| 141 FGEKVHINVpRAENCETCGGTGAKEGTSpktcatcRGsGQVTHARRTPLGNFMTtTTCDACHGKGQVI 208
                                   66778888887889999988885333322345444222222222333333444445599999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2643.58
//
Query:       gi|91773288|ref|YP_565980.1|  [L=620]
Description: molecular chaperone DnaK [Methanococcoides burtonii DSM 6242]
Scores for complete 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-245  814.2  15.4   8.4e-218  724.4   9.1    2.0  2  HSP70            Hsp70 protein
    6.4e-17   61.4   1.4    6.4e-17   61.4   1.4    2.2  2  MreB_Mbl         MreB/Mbl protein
    0.00013   22.3   5.0      0.068   13.6   0.1    3.9  3  FtsA             Cell division protein FtsA
     0.0013   18.5   0.0      0.003   17.3   0.0    1.6  1  FGGY_C           FGGY family of carbohydrate kinases, C-termi
  ------ inclusion threshold ------
       0.19   11.9  12.7       0.33   11.1   8.8    2.2  2  DUF3347          Protein of unknown function (DUF3347)
        2.7    8.6   8.7        7.8    7.1   0.7    3.2  3  Phage_connect_1  Phage gp6-like head-tail connector protein
        9.5    6.5   8.4         17    5.7   8.4    1.4  1  Vfa1             AAA-ATPase Vps4-associated protein 1


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 !   94.3   0.4     2e-30   5.2e-27       1      71 [.       4      75 ..       4      79 .. 0.98
   2 !  724.4   9.1  3.3e-221  8.4e-218     100     599 .]      79     578 ..      75     578 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2e-30
                                  EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTX CS
                         HSP70  1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGr 71
                                  ++GiDLGttns++av+eggk++vi n+eg rttPsvv+F+kk ++lvG++Akrq++ np n v s+Kr+iG+
  gi|91773288|ref|YP_565980.1|  4 ILGIDLGTTNSCMAVIEGGKPTVIPNAEGGRTTPSVVGFSKKgDKLVGQVAKRQMIANPGNSVSSIKRHIGE 75
                                  68*********************************************************************7 PP

  == domain 2  score: 724.4 bits;  conditional E-value: 3.3e-221
                                   EEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTC CS
                         HSP70 100 eveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGld 180
                                   +v+  g+++tp+++sam+L+klk++aeaylg+++t+ vitvPaYfnd+qRqatkdAg+iAGL+vlRi+NepTAa+laYGld
  gi|91773288|ref|YP_565980.1|  79 KVNLSGKDYTPQEVSAMILRKLKDDAEAYLGETITQTVITVPAYFNDSQRQATKDAGQIAGLEVLRIINEPTAASLAYGLD 159
                                   56777**************************************************************************** PP

                                   CSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHH CS
                         HSP70 181 kkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaae 261
                                   k++ ++++lvyDlGggtfdvSilel++Gvfev++T+g+thlGG+dfD++++e+lveefkk egidls+dk alqrl++aae
  gi|91773288|ref|YP_565980.1| 160 KEEGDHKILVYDLGGGTFDVSILELGDGVFEVLSTSGNTHLGGDDFDQRITEFLVEEFKKAEGIDLSNDKAALQRLNDAAE 240
                                   ********************************************************************************* PP

                                   HHHHHTTTSSCSEEEEEEEEEETTT..EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSH CS
                         HSP70 262 kaKkeLSsskqteinleietvdedg..kdlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlvGGstRiP 340
                                   kaK+eLS +++t++nl+++t+d++g  k+++++++Ra+fe+++edl+++tle+++ al+dakl++++id v+l+GGstR P
  gi|91773288|ref|YP_565980.1| 241 KAKIELSGVASTNVNLPFITADSNGqpKHIDIDITRAQFEKMTEDLVAKTLESMKMALSDAKLTTKDIDRVLLIGGSTRTP 321
                                   ************************999****************************************************** PP

                                   HHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEE CS
                         HSP70 341 kvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkliernttiptkksqvf 421
                                   +v +lvk+++gk+p k++npDeava+GAA+qagvlsg  ev+d+lllDvtpL++gietlggv+t liernttip kksq+f
  gi|91773288|ref|YP_565980.1| 322 AVYNLVKNFIGKDPYKNINPDEAVAVGAAIQAGVLSG--EVHDVLLLDVTPLTMGIETLGGVATPLIERNTTIPVKKSQIF 400
                                   *************************************..****************************************** PP

                                   EESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSS CS
                         HSP70 422 staadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeitieasegl 502
                                   staad+q++vei++lqger +++ nk+lg+f ldgippaprG pqieVtfdid nGil+v+akd +tgke++i+i++  gl
  gi|91773288|ref|YP_565980.1| 401 STAADSQPSVEIHILQGERGIASANKTLGRFVLDGIPPAPRGLPQIEVTFDIDSNGILHVNAKDLGTGKEQSISIQKPGGL 481
                                   ********************************************************************************* PP

                                   BHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHH CS
                         HSP70 503 seeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakt 583
                                   s+eeie+mvkdae +aeedk++ke++e++n+a++lv+ +e++l+e+++ +++++ke++e+ai++Lk++le+e+ e+i++kt
  gi|91773288|ref|YP_565980.1| 482 SDEEIERMVKDAELHAEEDKARKEEVETRNNADSLVNAAENTLKEAGDVATNEQKEQIEAAIADLKTALEGEDLEAIKSKT 562
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHH CS
                         HSP70 584 eelkkvvekiaeklye 599
                                   e+l+++v+k+ +++ye
  gi|91773288|ref|YP_565980.1| 563 EALQESVYKVSAAMYE 578
                                   ***********99985 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   1.4   2.5e-20   6.4e-17       3     317 ..       4     351 ..       2     357 .. 0.73
   2 ?   -1.9   0.6      0.45   1.2e+03     200     257 ..     519     576 ..     516     585 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2.5e-20
                                   EEEEEE-SSEEEE..EETTTEEEE.......EEES-EEEETTT--EEEESHHHH.TTTTS-GTTEEEE.-SEETT....EE CS
                      MreB_Mbl   3 dlgiDLGtantlv..yvkgkgivl.......nepsvvAikkktkkvlavGeeAk.kmlgktpgnikav.rPlkdG....vi 68 
                                    lgiDLGt+n  +     gk  v+       + psvv ++kk  k+  vG+ Ak +m+    ++++ + r + +G     +
  gi|91773288|ref|YP_565980.1|   4 ILGIDLGTTNSCMavIEGGKPTVIpnaeggrTTPSVVGFSKKGDKL--VGQVAKrQMIANPGNSVSSIkRHIGEGdykvNL 82 
                                   589*******876114456667763333333469******998887..799997468887777776552778888433212 PP

                                   S..SH...HHHHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSS CS
                      MreB_Mbl  69 a..dl...evaeellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveep 144
                                   +  d+   ev + +l+++ ++++     + ++ vi+vP   ++ +r+A k+a + aG +   +i+ep aA +  gl+ ee 
  gi|91773288|ref|YP_565980.1|  83 SgkDYtpqEVSAMILRKLKDDAEAYLGETITQTVITVPAYFNDSQRQATKDAGQIAGLEVLRIINEPTAASLAYGLDKEEG 163
                                   311331112333444444444444445578899*********************************************998 PP

                                   S-E.EEEEE-SS-EEEEEEETTEEE.....EEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHHE CS
                      MreB_Mbl 145 sgn.mvvdiGggttevavislggiv.....tsksvrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeeek 219
                                     + +v d+Gggt +v+++ lg+ v     ts   +++Gd++d+ i++++ ++++ + G   +++ k ++  +   +e+ k
  gi|91773288|ref|YP_565980.1| 164 DHKiLVYDLGGGTFDVSILELGDGVfevlsTSGNTHLGGDDFDQRITEFLVEEFKKAEGIDLSND-KAALQRLNDAAEKAK 243
                                   7762678***************966333224667899******************9988876554.667777777777777 PP

                                   EEEEEEET...........TTTCEEEEEE..EHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSB CS
                      MreB_Mbl 220 meikGrdl...........vtglpkevev..sseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallk 287
                                   +e++G               +g pk++ +  + ++ +++ ++ v++ +e++k +L ++   L++  +dr ++l GG++   
  gi|91773288|ref|YP_565980.1| 244 IELSGVAStnvnlpfitadSNGQPKHIDIdiTRAQFEKMTEDLVAKTLESMKMALSDA--KLTTKDIDR-VLLIGGSTRTP 321
                                   7777754311111221112468888776511567788888888999999999988764..577776777.5667****999 PP

                                   THHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
                      MreB_Mbl 288 gldkllseetglpvkvaedpltcvakGtgk 317
                                    + +l+++ +g   +   +p ++va G+++
  gi|91773288|ref|YP_565980.1| 322 AVYNLVKNFIGKDPYKNINPDEAVAVGAAI 351
                                   999999999999999999999999999875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.45
                                   HHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                      MreB_Mbl 200 taekikieigsavkeeeeekmeikGrdlvtglpkevevsseevrealkepvsaiveav 257
                                    ae+  +e g ++++e++e++e    dl t l  e     ++ +eal+e+v ++  a+
  gi|91773288|ref|YP_565980.1| 519 AAENTLKEAGDVATNEQKEQIEAAIADLKTALEGEDLEAIKSKTEALQESVYKVSAAM 576
                                   5788888899999999999999999999999987766666666788888888877665 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0017       4.3       2      22 ..       6      26 ..       5     141 .. 0.84
   2 !   13.6   0.1   2.6e-05     0.068       4      86 ..     171     246 ..     168     350 .. 0.68
   3 ?    0.4   0.5      0.33   8.5e+02      37      88 ..     486     526 ..     451     598 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                                  EEEE-SSSEEEEEEETTEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                          FtsA  2 lvDiGagktdvavaedgalvh 22
                                  ++D+G++ +++av+e+g+++ 
  gi|91773288|ref|YP_565980.1|  6 GIDLGTTNSCMAVIEGGKPTV 26
                                  79***************8765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.6e-05
                                   EE-SSSEEEEEEETTEEEEEEEES-......-HHHHHHHHHHHHT--HHHHHHHHHHH--S--EEEEEHHHHHGGGGSTTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA   4 DiGagktdvavaedgalvhlrvigv......ggngitkdiakalrtaveeAerikikyGsalaekeigrkelsggsalpnl 78 
                                   D+G+g+ dv+++e g  v ++v+ +      gg+ +++ i + l + +++Ae i  +                +++al+ l
  gi|91773288|ref|YP_565980.1| 171 DLGGGTFDVSILELGDGV-FEVLSTsgnthlGGDDFDQRITEFLVEEFKKAEGIDLSN---------------DKAALQRL 235
                                   9*************9644.555555555666***********************9332...............44444444 PP

                                   HHHHHHH...H CS
                                   xxxxxxx...x RF
                          FtsA  79 eelaera...l 86 
                                   +++ae+a   l
  gi|91773288|ref|YP_565980.1| 236 NDAAEKAkieL 246
                                   44444443221 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.33
                                   HHHHHT--HHHHHHHHHHH--S--EEEEEHHHHHGGGGSTTHHHHHHHHHT- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA  37 iakalrtaveeAerikikyGsalaekeigrkelsggsalpnleelaeralsp 88 
                                   i+++++ a   Ae+ k             ++e++  ++   l+++ae+ l+ 
  gi|91773288|ref|YP_565980.1| 486 IERMVKDAELHAEEDK-----------ARKEEVETRNNADSLVNAAENTLKE 526
                                   5666666666666666...........3334455444444444444444422 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 !   17.3   0.0   1.2e-06     0.003     141     196 ..     281     355 ..     273     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                        FGGY_C 141 alekd..................sgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                                   ++++d                  + k++dr+++ GG ++ +++  l  + +g  p +   ++ea+a+GaAi A+v
  gi|91773288|ref|YP_565980.1| 281 KMTEDlvaktlesmkmalsdaklTTKDIDRVLLIGGSTRTPAVYNLVKNFIGkDPYKNINPDEAVAVGAAIQAGV 355
                                   554445555555555556666668999*************************888888888************97 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.079     2e+02     105     135 ..     258     288 ..     220     299 .. 0.68
   2 ?   11.1   8.8   0.00013      0.33      24      99 ..     499     585 ..     480     603 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.079
                       DUF3347 105 elkekaekiaeskdieeqReaFkklsedlik 135
                                    ++++ +   ++ di+  R++F+k++edl++
  gi|91773288|ref|YP_565980.1| 258 FITADSNGQPKHIDIDITRAQFEKMTEDLVA 288
                                   45555555556669*************9875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                       DUF3347  24 eeeeeeeeekekkkekse........eeee.........kdeklkevlesYlklkdALvaddakeakkaakkleeklkavd 87 
                                   e+++++ee ++++    +        e  +         ++e+ +++ ++  +lk+AL  +d +++k+++++l+e++ +v+
  gi|91773288|ref|YP_565980.1| 499 EDKARKEEVETRN----NadslvnaaE--NtlkeagdvaTNEQKEQIEAAIADLKTALEGEDLEAIKSKTEALQESVYKVS 573
                                   1111111111111....0112222221..1334455666888889999999*****************************8 PP

                       DUF3347  88 tsklkekekkel 99 
                                   ++ +++ +k++ 
  gi|91773288|ref|YP_565980.1| 574 AAMYEKAQKEAS 585
                                   877766665443 PP

>> Phage_connect_1  Phage gp6-like head-tail connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   4.2e+03      26      56 ..      97     129 ..      94     134 .. 0.52
   2 ?    5.2   0.2     0.011        29       4      33 ..     214     243 ..     212     309 .. 0.69
   3 ?    7.1   0.7    0.0031       7.8      24      84 ..     537     592 ..     523     600 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
               Phage_connect_1  26 iqaAeeyikdylgrkl..eadedgielpedlkt 56 
                                   +++ ++ ++ ylg +   ++++ + ++ ++ ++
  gi|91773288|ref|YP_565980.1|  97 LRKLKDDAEAYLGETItqTVITVPAYFNDSQRQ 129
                                   555666777777766643333344444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
               Phage_connect_1   4 LeeiKlhLrIdddddDalLesliqaAeeyi 33 
                                   +ee+K+  +Id ++d+a L++l +aAe++ 
  gi|91773288|ref|YP_565980.1| 214 VEEFKKAEGIDLSNDKAALQRLNDAAEKAK 243
                                   6999*********************99764 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0031
               Phage_connect_1  24 sliqaAeeyikdylgrkl.eadedgielpedlktavlelaahryenr..egtssdssegkslse 84 
                                   + i+aA + +k++l+ +  e     ++ +e l ++v+ + a++ye+   e++      g+  se
  gi|91773288|ref|YP_565980.1| 537 EQIEAAIADLKTALEGEDlE---AIKSKTEALQESVYKVSAAMYEKAqkEASA-----GAEASE 592
                                   56899999999999988743...44455788***************9544443.....555555 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 ?    5.7   8.4    0.0068        17      68     159 ..     482     586 ..     462     600 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0068
                          Vfa1  68 leeeiekvkkeyeekqkkkkekekkk...kekd....kkdkdkkkekekdkkkekekeeekkkelkkaeeelee....... 134
                                   ++eeie++ k+ e + +++k ++++    +++d    + +++ k+  +  ++++ke+ e+++++lk+a e ++        
  gi|91773288|ref|YP_565980.1| 482 SDEEIERMVKDAELHAEEDKARKEEVetrNNADslvnAAENTLKEAGDVATNEQKEQIEAAIADLKTALEGEDLeaikskt 562
                                   667777777766666555554444442222222555322222222223333333333222333333222222222222232 PP

                          Vfa1 135 .keeprvkkykLhkefyqsRlerkrq 159
                                    + +++v  yk +  +y++ +++  +
  gi|91773288|ref|YP_565980.1| 563 eALQESV--YKVSAAMYEKAQKEASA 586
                                   1344444..77777777766655533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1448  (0.080763); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.48
# Mc/sec: 3903.09
//
Query:       gi|91773289|ref|YP_565981.1|  [L=191]
Description: heat shock protein GrpE [Methanococcoides burtonii DSM 6242]
Scores for complete 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  180.0   5.1    3.3e-53  179.8   5.1    1.0  1  GrpE            GrpE
  ------ inclusion threshold ------
      0.015   15.1   0.5      0.083   12.7   0.2    2.3  2  Heme_oxygenase  Heme oxygenase
      0.031   14.1   2.9      0.055   13.3   2.8    1.5  1  Mer2            Mer2
       0.98    9.9   3.5        3.2    8.2   1.2    2.2  2  Goodbye         fungal STAND N-terminal Goodbye domain


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 !  179.8   5.1   7.3e-57   3.3e-53       5     166 .]      25     186 ..      12     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 7.3e-57
                                   ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HH CS
                          GrpE   5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksaken 85 
                                   + e+ +e++ ++ e   ++ +++++el+e+++r++aefen+r+r  +ekee +kfa+e+++ +LL+v+Dn++ral+sak++
  gi|91773289|ref|YP_565981.1|  25 NAEALKENASDSTEDLHTSCDSQIAELNEQIMRQRAEFENFRNRSLREKEEFRKFALEEIMVELLEVRDNFDRALESAKKA 105
                                   3444455555555555667888*********************************************************** PP

                                   H-HHHHHHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEEE CS
                          GrpE  86 eeekslleGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVsk 166
                                   ++++s++eGvem+ kq+ +iLek+g++ i+++g++FDp++hea+++v+++e++++++v+v++ GY l+++v+R+AmV+V++
  gi|91773289|ref|YP_565981.1| 106 DDVNSIIEGVEMVFKQFTSILEKEGLKMIDCEGKEFDPHFHEAMMHVQTTEHADQHIVDVCKAGYELNSKVIRHAMVTVAQ 186
                                   *******************************************************************************86 PP

>> Heme_oxygenase  Heme oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.65   2.9e+03       9      21 ..      35      47 ..      27      67 .. 0.65
   2 ?   12.7   0.2   1.9e-05     0.083     148     204 ..     127     178 ..      54     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.65
                                  HHTHHHHHHHHTS CS
                Heme_oxygenase  9 eaTkdvHneaenl 21
                                  ++T+d+H++ ++ 
  gi|91773289|ref|YP_565981.1| 35 DSTEDLHTSCDSQ 47
                                  5788888888764 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.9e-05
                                   SSSSSGGGGH-TTSSSHHHHHHHHHHHHHCS---HHHHHHHHHHHHHHHHHHHHHHH CS
                Heme_oxygenase 148 eeceatafyefesisdrkvfkqeYreaLdslelddearaavveeAreaFrlnievvr 204
                                   e+ e++++ + e+    k+f  ++ ea+ +++ +++a +++v+ +++ ++ln +v+r
  gi|91773289|ref|YP_565981.1| 127 EK-EGLKMIDCEG----KEFDPHFHEAMMHVQTTEHADQHIVDVCKAGYELNSKVIR 178
                                   33.4555555555....99***********************************987 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.8   1.2e-05     0.055      10     105 ..      37     133 ..      30     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                          Mer2  10 ssgslnsgakklsEaDKqILeWAgKLE.LEsvdLrEksskLinvlkenskeLlkvisklnellidlkeeesdnskekeikd 89 
                                   +++++ s ++++ E   qI++  +  E      LrEk +     l+e   eLl+v +++   l + k+ +  ns ++++  
  gi|91773289|ref|YP_565981.1|  37 TEDLHTSCDSQIAELNEQIMRQRAEFEnFRNRSLREKEEFRKFALEEIMVELLEVRDNFDRALESAKKADDVNSIIEGVEM 117
                                   457889999***********9777666456779******9999*************************9999********* PP

                          Mer2  90 likdLsvkienqlskv 105
                                   + k+ ++ +e++  k+
  gi|91773289|ref|YP_565981.1| 118 VFKQFTSILEKEGLKM 133
                                   *****99999854444 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2   0.00072       3.2       3      57 ..      27      78 ..      25      89 .. 0.77
   2 ?    0.7   0.0      0.16   7.1e+02      93     116 ..     104     127 ..     100     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00072
                       Goodbye  3 eAlkeyekeTgkdlkdealkelssvedllkqieaekdkfeefrekkeklkealkk 57
                                  eAlke ++ + +dl   +++  s++ +l +qi +++++fe+fr+++ + ke + k
  gi|91773289|ref|YP_565981.1| 27 EALKENASDSTEDL---HTSCDSQIAELNEQIMRQRAEFENFRNRSLREKEEFRK 78
                                  66777777777777...7778899*******************776665555544 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                       Goodbye  93 aakkvseiydaieeLfeelsdfle 116
                                    a++v++i + +e +f++   +le
  gi|91773289|ref|YP_565981.1| 104 KADDVNSIIEGVEMVFKQFTSILE 127
                                   577888888888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1515  (0.0845); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1325.09
//
Query:       gi|91773290|ref|YP_565982.1|  [L=137]
Description: hypothetical protein Mbur_1314 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        4.3    6.8  14.5        6.7    6.2  14.5    1.3  1  ABC2_membrane_5  ABC-2 family transporter protein
        7.2    6.7   7.5        4.1    7.4   0.0    2.7  3  FixQ             Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  14.5   0.00075       6.7      89     200 ..      14     132 ..       9     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00075
               ABC2_membrane_5  89 liliailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgri.......vliiiifgiifllv 162
                                   l ++++l ++++++  ++++   t ++ + s++i l++a++f++ +  +  +   + g +       ++ +i+++ +f++v
  gi|91773290|ref|YP_565982.1|  14 LAVSGTLSLFMIGMALGVMHIFETGKSPMPSSMILLIFAVLFIVGSVFFEMRGADQVGALiggcvvsFAATISIFSFFGGV 94 
                                   566777888888888889999999999999999999999999999999999999999987788887766777777889999 PP

               ABC2_membrane_5 163 aifslsklelslidlsnyilliillviillliivSyfi 200
                                   +++ + +l +   d    +l+++ ++ +ll+ ++Sy+ 
  gi|91773290|ref|YP_565982.1|  95 EFVRTGGLGVLGWDKIVSALALCMIASMLLVKLLSYKM 132
                                   99999999887777778888999999999999999986 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00046       4.1       6      34 ..      11      39 ..       9      42 .. 0.92
   2 ?    3.3   0.5    0.0094        84      13      27 ..      47      61 ..      43      65 .. 0.56
   3 ?   -2.9   0.4       0.8   7.2e+03       8      19 ..      80      91 ..      78      94 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00046
                          FixQ  6 lrgfadswgllflvllfygvviyafrpgn 34
                                  ++++a s  l ++++ ++  v ++f  g+
  gi|91773290|ref|YP_565982.1| 11 VQALAVSGTLSLFMIGMALGVMHIFETGK 39
                                  7999*********************9887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0094
                          FixQ 13 wgllflvllfygvvi 27
                                  ++l+f vl+ +g v+
  gi|91773290|ref|YP_565982.1| 47 ILLIFAVLFIVGSVF 61
                                  445555555555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.8
                          FixQ  8 gfadswgllflv 19
                                   fa ++ ++ ++
  gi|91773290|ref|YP_565982.1| 80 SFAATISIFSFF 91
                                  455555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 881.93
//
Query:       gi|91773291|ref|YP_565983.1|  [L=307]
Description: hypothetical protein Mbur_1315 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-40  136.6   0.0    1.1e-39  136.0   0.0    1.2  1  ATP-grasp_3      ATP-grasp domain
    8.5e-08   32.4   0.0    1.9e-07   31.3   0.0    1.6  1  preATP-grasp_3   pre ATP-grasp 3 domain
     0.0001   22.0   0.0     0.0002   21.1   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    0.00084   18.7   0.0       0.26   10.5   0.0    2.5  3  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.023   14.2   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
       0.11   12.1   0.0       0.39   10.3   0.0    1.9  2  RimK             RimK-like ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0   0.0   3.8e-43   1.1e-39       1     161 []     109     265 ..     109     265 .. 0.95

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 3.8e-43
                                   HTSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEEEEE CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvslls 81 
                                   +sdKl++++ L++ag+ vP ++   e  + +  +v Kpr+G+++e ++v +        i  ++++ e+ieG++lSvsl++
  gi|91773291|ref|YP_565983.1| 109 CSDKLECTRILENAGLAVPRTYAFGESMPFKGCWVTKPRYGCASEDTFVCHRP-----DIRRDHIATEYIEGEHLSVSLIC 184
                                   8*******************************************999998877.....466678***************** PP

                                   .SSSEEEEEEEEEEEET........TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS- CS
                   ATP-grasp_3  82 dgekvlvlavnrqliekaeke....fvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRl 158
                                    g++ l+l+vn q++e    +    + y+G++tp++t++++e++++a++++++l g++Gy GvD++l d  py+++vNPR+
  gi|91773291|ref|YP_565983.1| 185 -GKEQLPLTVNAQRMEIDPAKdaskIDYCGCTTPYRTDREQELYDVAKKATRAL-GCNGYIGVDIILGD-RPYIVDVNPRP 262
                                   .8899*********99876667888*****************************.**************.*********** PP

                                   -GG CS
                   ATP-grasp_3 159 tts 161
                                   tts
  gi|91773291|ref|YP_565983.1| 263 TTS 265
                                   *97 PP

>> preATP-grasp_3  pre ATP-grasp 3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   6.2e-11   1.9e-07      23      75 ..      55     104 ..      28     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.2e-11
                preATP-grasp_3  23 vvdseedvdetfrrlaaeaDaVlvIAPEtdgiLarltrlveaagkrlLGsssk 75 
                                   v++seed  +t r++a+e+Da lvIAPE  +iL  lt+++e++  ++LG+s++
  gi|91773291|ref|YP_565983.1|  55 VRSSEEDIEATIRKCAKECDAGLVIAPE--DILPGLTAIIEEN-TLNLGCSPD 104
                                   567899999******************9..8***********9.9******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 !   21.1   0.0   6.5e-08    0.0002       4     110 ..     166     287 ..     164     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.5e-08
                  ATPgrasp_Ter   4 allvmeyLegpEySvDvlaek.......gevlaavpRrKekgglq........elekdeelielaerlaeefgldglvnvQ 69 
                                   + + +ey+eg+  Sv  +++k       +   + +  +K+++++         ++++++el ++a++ ++++g++g+++v 
  gi|91773291|ref|YP_565983.1| 166 DHIATEYIEGEHLSVSLICGKeqlpltvNAQRMEIDPAKDASKIDycgcttpyRTDREQELYDVAKKATRALGCNGYIGVD 246
                                   567899*************9834444444444555556667777788999999999************************* PP

                  ATPgrasp_Ter  70 vrededgpkLLEiNpRasGGl.gysalaGvnlpylalklllg 110
                                   +   +d+p++ ++NpR+   l g++     ++++l lk  +g
  gi|91773291|ref|YP_565983.1| 247 IIL-GDRPYIVDVNPRPTTSLvGITKIMDKEIAELLLKNGMG 287
                                   965.688**********9876135555556666665555555 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      0.87   2.6e+03      47      72 ..      61      86 ..      42      98 .. 0.72
   2 !    5.2   0.0    0.0035        10      16      42 ..     106     132 ..     100     137 .. 0.88
   3 !   10.5   0.0   8.6e-05      0.26     226     271 ..     224     267 ..     216     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.87
                   ATPgrasp_ST 47 aeiseleafvkeleegvviKpakgsg 72
                                  +  ++++++ ke++ g+vi p +   
  gi|91773291|ref|YP_565983.1| 61 DIEATIRKCAKECDAGLVIAPEDILP 86
                                  44567899999999999998877555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0035
                   ATPgrasp_ST  16 fplvddKlkfkelalraglkvpkllgv 42 
                                   + +  dKl +++++++agl vp++++ 
  gi|91773291|ref|YP_565983.1| 106 ASICSDKLECTRILENAGLAVPRTYAF 132
                                   56789******************9975 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 8.6e-05
                   ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgplllElNarpglaiv 271
                                   +e+ ++a+ka   l + gy+G+Di l + + p+++ +N rp  ++v
  gi|91773291|ref|YP_565983.1| 224 QELYDVAKKATRALGCNGYIGVDIILGD-R-PYIVDVNPRPTTSLV 267
                                   578899******************8865.6.8********988775 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 ?   14.2   0.0   7.7e-06     0.023     126     176 ..     214     262 ..     170     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                                   SS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS- CS
               Dala_Dala_lig_C 126 vpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlP 176
                                   +++   +++e+++ ++a+ka +al+++G   vD++l   +++++ +vN+ P
  gi|91773291|ref|YP_565983.1| 214 CTTPYRTDREQELYDVAKKATRALGCNGYIGVDIILG--DRPYIVDVNPRP 262
                                   56677889999*************************8..89*******999 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.52   1.6e+03       2      21 ..     110     129 ..     109     134 .. 0.89
   2 ?   10.3   0.0   0.00013      0.39     128     181 ..     223     278 ..     203     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.52
                                   H-HHHHHHHHHHTT-----E CS
                          RimK   2 rdKlkslklLakakikvpnt 21 
                                   +dKl + ++L  a++ vp+t
  gi|91773291|ref|YP_565983.1| 110 SDKLECTRILENAGLAVPRT 129
                                   79************999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                                   -HHHHHHHHHHHHHCT-S.EEEEEEEEETTEEEEEEEESS--SH..HHHHHHT--HH CS
                          RimK 128 seeekelAikaakamelv.vaGvDllrakrgllvlEvnsspgle..kiektlgidia 181
                                   ++e+ ++A ka++a++   ++GvD++  +r + +++vn  p +   +i k +  +ia
  gi|91773291|ref|YP_565983.1| 223 EQELYDVAKKATRALGCNgYIGVDIILGDRPY-IVDVNPRPTTSlvGITKIMDKEIA 278
                                   5778899*******998559******998865.679**9997651144444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2063.49
//
Query:       gi|91773292|ref|YP_565984.1|  [L=325]
Description: hydantoinase/oxoprolinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-30  105.3   0.9    2.3e-29  102.6   0.1    1.9  2  Hydantoinase_A   Hydantoinase/oxoprolinase
    4.2e-05   22.3   0.3      0.012   14.2   0.0    2.5  3  MutL             MutL protein
  ------ inclusion threshold ------
      0.062   14.0   0.0        0.7   10.6   0.0    2.4  2  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.025   1.5e+02      80     100 ..       2      21 ..       1      27 [. 0.85
   2 !  102.6   0.1   3.9e-33   2.3e-29       4     271 ..      53     299 ..      50     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.025
                Hydantoinase_A  80 kvItfDmGGTstDvslikdge 100
                                   ++I++D+GG  t+v+  + ge
  gi|91773292|ref|YP_565984.1|   2 RYIGVDIGGANTKVASSD-GE 21 
                                   58************9876.66 PP

  == domain 2  score: 102.6 bits;  conditional E-value: 3.9e-33
                Hydantoinase_A   4 tavvnAylspilreylesvekslekrgak..arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkvI 82 
                                   ++v++++l++++ ++ e+++ +++ ++ +  +++ +++  G++ +  + ++   e++++++aa++  + +   + g+  +I
  gi|91773292|ref|YP_565984.1|  53 AVVMTGELADCFVDKEEGINFIMDAVNNAfdCEVRYVNNTGNFQKSTQNNR---ELAAANWAASARLIGE---EVGD--CI 125
                                   78*********************998877779***********99997777...6***************...6666..** PP

                Hydantoinase_A  83 tfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsil.vvdeggklrvgpesagadpgpacyrkGgte 162
                                   ++D+G+T+ Dv++ik+g++         +  +++ +l  +++ ++G++++ +    ++++++   ++++++         +
  gi|91773292|ref|YP_565984.1| 126 FVDVGSTTSDVIPIKNGKH--------VAGHTDFSRLLRDELFYAGTLRTnLAALLETVNLDAGTCRVSSEL--------F 190
                                   *******************........57789****************************************........9 PP

                Hydantoinase_A 163 ltvTDanlvLGrlqpedfls.gpdgdqkldvelarraf.eelakelnlk...veevAegilsvavenmanavrklsvergl 238
                                   + ++Da+++LG +++e +++ + dg++k++ +++rr +   +a+  + +   +  +A+++ + + e ++n v  +     +
  gi|91773292|ref|YP_565984.1| 191 ANTADAYMMLGDIDKELYTCeTSDGAGKDRIDCMRRLArVVCADLTEISeedIYRLAKNVKERQIELLCNSVSAV-----A 266
                                   99************************************999999998887779999*******************.....9 PP

                Hydantoinase_A 239 dpkeltlvvfGGaGaqhaaalaeelgvkkvivp 271
                                   + +el ++v +G G+++++ +a++lg  ++ + 
  gi|91773292|ref|YP_565984.1| 267 EANELDMIVSAGLGEFMIEKAAKRLGYDCFSTA 299
                                   **************************9998753 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0   0.00077       4.6     250     266 ..       4      19 ..       2      34 .. 0.83
   2 !   14.2   0.0   2.1e-06     0.012     199     271 ..      78     146 ..      67     182 .. 0.76
   3 ?   -2.8   0.0       0.3   1.8e+03      47      91 ..     242     290 ..     230     293 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00077
                          MutL 250 lvvDvGGaTTdvhsvae 266
                                   ++vD+GGa T v s  +
  gi|91773292|ref|YP_565984.1|   4 IGVDIGGANTKVASS-D 19 
                                   79***********98.3 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.1e-06
                          MutL 199 IrevFlehivkakglskleelvsaeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspek 271
                                   ++++F  ++  + +  + ++ +++++   +a     ++l+ e    ++gd++ vDvG++T+dv+ + +g++  
  gi|91773292|ref|YP_565984.1|  78 VNNAFDCEVRYVNNTGNFQKSTQNNRELAAANWAASARLIGE----EVGDCIFVDVGSTTSDVIPIKNGKHVA 146
                                   555665555666666677777777777777777788888888....89****************997766554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.3
                          MutL  47 aleeleeklgktevdevlatSSA...aGgLkmvv.iGlvedltaeaarr 91 
                                    + +l+++ ++ +++ ++ + SA   a  L m+v +Gl e +  +aa+r
  gi|91773292|ref|YP_565984.1| 242 DIYRLAKNVKERQIELLCNSVSAvaeANELDMIVsAGLGEFMIEKAAKR 290
                                   4555566655556666666666633345688877357777788888887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.22   1.3e+03      78      97 .]      32      51 ..       4      51 .. 0.83
   2 ?   10.6   0.0   0.00012       0.7       7      74 ..     215     280 ..     211     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                                  SHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25 78 sdedlekalkeiarvLkpgG 97
                                  +d  l+ alke+a+ L+p+G
  gi|91773292|ref|YP_565984.1| 32 KDTILPSALKELADRLQPDG 51
                                  45567899**********99 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                                   TTSHHHHHHHCTSTSSEEEEEES...SHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTG CS
               Methyltransf_25   7 GtGrltlalakrlgkakvtgvDi...seemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgal 74 
                                   G G++ +++ +rl  a+v++ D+   see + + +++++e+  ++e+++ +++++ + +++ D++vs+g  
  gi|91773292|ref|YP_565984.1| 215 GAGKDRIDCMRRL--ARVVCADLteiSEEDIYRLAKNVKER--QIELLCNSVSAVAE-ANELDMIVSAGLG 280
                                   7888889999998..89999887333666677777777544..8**********985.56*******7553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2495.88
//
Query:       gi|91773293|ref|YP_565985.1|  [L=210]
Description: aspartate/glutamate/uridylate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-20   72.8   0.6    4.6e-09   36.2   0.1    2.1  2  AA_kinase  Amino acid kinase family
     0.0082   16.5   0.2      0.015   15.6   0.2    1.4  1  DUF4258    Domain of unknown function (DUF4258)


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 !   35.0   0.1   1.2e-12   1.1e-08       1      87 [.       1      78 [.       1      83 [. 0.76
   2 !   36.2   0.1   5.1e-13   4.6e-09     150     211 ..     109     171 ..      85     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.2e-12
                                  TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHHH CS
                     AA_kinase  1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevatrd 80
                                  ++vV+KlGGs+++ + e   ++++ +  aa  e ++++++V Ggg f+d + ++  ++ l+++ ++          + +a ++
  gi|91773293|ref|YP_565985.1|  1 MKVVLKLGGSLIDrSSEL--IKAISDHFAAT-EGNMQVIIVPGGGIFADTIRRIskEYSLTEKAAH---------WMAIAAME 71
                                  789**********77777..***********.*******************999554444444444.........34444444 PP

                                  HHHHHHH CS
                     AA_kinase 81 alaslge 87
                                  + a l e
  gi|91773293|ref|YP_565985.1| 72 QYAHLLE 78
                                  4444444 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 5.1e-13
                                   ETTTE..EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.........CS CS
                     AA_kinase 150 deege..lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.........sa 211
                                   de     ++ ++sDtiaa++A+ ++A +l+ +tdVdG++++        ++++ei+ +e+e           +
  gi|91773293|ref|YP_565985.1| 109 DE--LphSWDVTSDTIAAWVAQRMSA-RLVKATDVDGIFNNG-------KMIEEITLKELEVmgetcadrmLS 171
                                   33..255999****************.************764.......9***********933333333222 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.7e-06     0.015       6      62 ..     127     196 ..     126     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                       DUF4258   6 rermaeRgIseedieevlenGeiieeys....lvlgktsegrpl.........hvvvapdedpvvviTvy 62 
                                    +rm++R ++ +d+  + +nG+ iee      +v+g t  +r l         ++v+++ ++p +vi ++
  gi|91773293|ref|YP_565985.1| 127 AQRMSARLVKATDVDGIFNNGKMIEEITlkelEVMGETCADRMLstmlikhgmECVIVNGDHPERVIAAI 196
                                   59************************99****9********************99999999999888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1580.75
//
Query:       gi|91773294|ref|YP_565986.1|  [L=54]
Description: hypothetical protein Mbur_1318 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00087   19.2   3.3    0.00087   19.2   3.3    2.4  2  DUF1610         Domain of unknown function (DUF1610)
      0.006   16.9   3.7      0.006   16.9   3.7    1.7  2  DUF2039         Uncharacterized conserved protein (DUF2039)
     0.0088   16.4   0.5     0.0088   16.4   0.5    2.0  2  zf-UBP          Zn-finger in ubiquitin-hydrolases and other p
  ------ inclusion threshold ------
       0.01   16.3  10.0      0.032   14.7  10.0    1.7  1  zf-CHY          CHY zinc finger
      0.018   14.8   4.0      0.018   14.8   4.0    1.9  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.043   13.9  15.2        1.1    9.4  15.2    2.2  1  DZR             Double zinc ribbon
       0.08   12.7  12.3          3    7.7   9.7    2.2  2  zf-HYPF         HypF finger
       0.17   11.9  11.1        0.6   10.1  11.1    1.8  1  zinc-ribbons_6  zinc-ribbons
       0.18   12.1  10.0       0.58   10.5   6.3    2.2  2  C1_2            C1 domain
       0.23   11.9   8.9       0.26   11.7   8.9    1.1  1  Rhodanese_C     Rhodanase C-terminal
       0.49   10.5  10.5        0.9    9.7   7.2    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
        0.5   10.4  10.0       0.88    9.6  10.0    1.4  1  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.53   10.1  12.3        3.2    7.6   0.1    3.7  4  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
        0.6   10.2  12.5       0.86    9.6   0.8    2.0  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.85    9.1  12.6        1.5    8.3   0.6    3.7  4  zf-ribbon_3     zinc-ribbon domain
        1.6    8.7  14.1        4.2    7.4   0.1    3.8  3  Nudix_N_2       Nudix N-terminal
        1.8    6.3   7.1        1.8    6.3   7.1    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
        2.5    8.3   8.8        2.2    8.4   4.3    2.1  2  Spt4            Spt4/RpoE2 zinc finger
        2.5    8.1  18.4       0.57   10.1   7.0    3.1  2  zf-HIT          HIT zinc finger
        2.5    7.9  18.4         13    5.6   0.1    3.9  3  zinc_ribbon_2   zinc-ribbon domain
        2.5    7.7  11.4       0.58    9.7   1.3    3.3  3  zf_C2H2_10      C2H2 type zinc-finger
        3.9    6.9   8.6        4.2    6.8   8.6    1.0  1  NMD3            NMD3 family
        4.2    7.4  12.1         32    4.5  12.1    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        4.7    6.9  17.2        3.2    7.4   0.1    3.2  3  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
        6.7    6.8   9.6        3.1    7.9   0.3    2.9  3  DUF2752         Protein of unknown function (DUF2752)
        7.1    6.6  17.2        8.6    6.4   0.1    4.0  4  zinc_ribbon_4   zinc-ribbon domain
        7.2    6.0  17.8         27    4.2   0.0    3.9  2  zf-TFIIB        Transcription factor zinc-finger
        7.4    6.8  18.0        1.9    8.6   2.8    3.2  3  Zn-ribbon_8     Zinc ribbon 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 !   19.2   3.3   1.4e-06   0.00087       1      22 [.       7      27 ..       7      27 .. 0.99
   2 ?    6.2   2.2     0.015       9.9      18      23 ..      45      50 ..      42      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                       DUF1610  1 CtSCGaelaprEravvFpCPNC 22
                                  CtSCG+ l++ +  +  pCP C
  gi|91773294|ref|YP_565986.1|  7 CTSCGIHLVEKG-FTRLPCPTC 27
                                  ************.*******99 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                       DUF1610 18 pCPNCG 23
                                   CP+CG
  gi|91773294|ref|YP_565986.1| 45 TCPKCG 50
                                  6****9 PP

>> DUF2039  Uncharacterized conserved protein (DUF2039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.7   9.3e-06     0.006      53      88 ..       3      39 ..       1      40 [. 0.91
   2 ?   -0.2   0.3       2.1   1.3e+03      82      86 ..      45      49 ..      39      51 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.3e-06
                       DUF2039 53 kkkkCvkCeektvkkaYhki.CkkCakekkvCakCsk 88
                                  k ++C++C  + v+k + ++ C +C +e+  C+kC +
  gi|91773294|ref|YP_565986.1|  3 KVEQCTSCGIHLVEKGFTRLpCPTCETELGRCTKCRQ 39
                                  6689*************8877**************87 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.1
                       DUF2039 82 vCakC 86
                                  +C+kC
  gi|91773294|ref|YP_565986.1| 45 TCPKC 49
                                  56666 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.8       2.5   1.6e+03      14      19 ..       7      12 ..       5      31 .. 0.60
   2 !   16.4   0.5   1.4e-05    0.0088       1      21 [.      34      53 ..      34      54 .] 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.5
                                  ETTT-- CS
                        zf-UBP 14 CLkCgh 19
                                  C +Cg 
  gi|91773294|ref|YP_565986.1|  7 CTSCGI 12
                                  444443 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.4e-05
                                  -TTTH--.SSEEEETTT--EE CS
                        zf-UBP  1 CseCnsenknlWlCLkCghvg 21
                                  C++C+++ +n++ C kCg+vg
  gi|91773294|ref|YP_565986.1| 34 CTKCRQQ-SNPYTCPKCGFVG 53
                                  *****88.***********97 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7  10.0     5e-05     0.032      21      74 ..       6      51 ..       1      52 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5e-05
                        zf-CHY 21 aCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCkl 74
                                  +C +C      h + ++  +++ c +Cete      C+kC+++ + y+Cp+C +
  gi|91773294|ref|YP_565986.1|  6 QCTSCGI----HLV-EKGFTRLPCPTCETE---LGRCTKCRQQSNPYTCPKCGF 51
                                  5777766....644.445556789999996...999****************75 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2         1   6.7e+02      47      52 ..       7      12 ..       6      14 .. 0.69
   2 ?   14.8   4.0   2.8e-05     0.018      22      52 ..      21      51 ..      15      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1
                zinc_ribbon_10 47 CpkCga 52
                                  C +Cg 
  gi|91773294|ref|YP_565986.1|  7 CTSCGI 12
                                  888874 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.8e-05
                zinc_ribbon_10 22 alICskChshnGlapkeeleevkyrCpkCga 52
                                   l C++C +  G  +k + +   y CpkCg+
  gi|91773294|ref|YP_565986.1| 21 RLPCPTCETELGRCTKCRQQSNPYTCPKCGF 51
                                  677***********999999*********97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  15.2    0.0016       1.1       1      49 []       7      50 ..       2      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                           DZR  1 CpqCgeelppdar...fCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                  C +Cg  l ++      C++C t+l       rC +C ++ +p   +Cp+CG
  gi|91773294|ref|YP_565986.1|  7 CTSCGIHLVEKGFtrlPCPTCETEL------GRCTKCRQQSNPY--TCPKCG 50
                                  7777755444333245699999999......79*****999888..899998 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.018        12      24      31 ..       7      14 ..       2      15 .. 0.87
   2 ?    7.7   9.7    0.0047         3       2      28 ..      24      50 ..      24      51 .. 0.99

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.018
                                  -TTTS--E CS
                       zf-HYPF 24 CtnCGPrl 31
                                  Ct+CG +l
  gi|91773294|ref|YP_565986.1|  7 CTSCGIHL 14
                                  *****886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                                  -HHHHHHHC-TTSTTTT-TT---TTTS CS
                       zf-HYPF  2 CedClrEykdpldRRfhaqfisCtnCG 28
                                  C+ C+ E+   +  R +  + +C++CG
  gi|91773294|ref|YP_565986.1| 24 CPTCETELGRCTKCRQQSNPYTCPKCG 50
                                  **************************9 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  11.1   0.00093       0.6      18      55 ..       6      49 ..       2      52 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00093
                                  E-TTT--EEEEEEE....-SSS-S---EEEETTEEE..E--TTT CS
                zinc-ribbons_6 18 hCeaCqedlkkeal....CpeCeqelevlkaCgavd..yfCnkc 55
                                  +C +C  +l ++ +    Cp+Ce el ++ +C   +  y C kc
  gi|91773294|ref|YP_565986.1|  6 QCTSCGIHLVEKGFtrlpCPTCETELGRCTKCRQQSnpYTCPKC 49
                                  67777776665544444488888888888888654434777777 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   5.0      0.54   3.5e+02      20      42 ..       6      31 ..       2      38 .. 0.59
   2 ?   10.5   6.3    0.0009      0.58      16      41 ..      29      52 ..      16      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.54
                          C1_2 20 nCsaCgrk..idgff.YsCseCdfsl 42
                                  +C  Cg     +gf    C++C+  l
  gi|91773294|ref|YP_565986.1|  6 QCTSCGIHlvEKGFTrLPCPTCETEL 31
                                  57777777654555567777776444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0009
                          C1_2 16 sesfnCsaCgrkidgffYsCseCdfs 41
                                   e ++C  C+++++   Y+C++C f+
  gi|91773294|ref|YP_565986.1| 29 TELGRCTKCRQQSN--PYTCPKCGFV 52
                                  56689999999974..4******995 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   8.9    0.0004      0.26      18      63 ..       4      49 ..       1      50 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0004
                   Rhodanese_C 18 vgkCieCgkpvdelrkrnCanedCnelvlvCeeCaeklkgvcseeC 63
                                  v +C  Cg +  e  +++  +++C++ +  C++C+++ + + + +C
  gi|91773294|ref|YP_565986.1|  4 VEQCTSCGIHLVEKGFTRLPCPTCETELGRCTKCRQQSNPYTCPKC 49
                                  789*******998889998899*****************9966689 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 ?    2.3   0.1      0.29   1.9e+02      18      24 ..       6      12 ..       2      17 .. 0.86
   2 ?    9.7   7.2    0.0014       0.9       2      24 ..      24      51 ..      23      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.29
                      zf-Mss51 18 eCpdCGi 24
                                  +C  CGi
  gi|91773294|ref|YP_565986.1|  6 QCTSCGI 12
                                  7*****8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                      zf-Mss51  2 CPvpkhkqt.....apkhvdfeCpdCGi 24
                                  CP+++++ +      +++  ++Cp+CG+
  gi|91773294|ref|YP_565986.1| 24 CPTCETELGrctkcRQQSNPYTCPKCGF 51
                                  ****9988899988888999*******8 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  10.0    0.0014      0.88      23      64 ..       3      50 ..       1      52 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                   Zn_Tnp_IS91 23 avekilrCrta..alGfaryeCeeCghekivyfsCksrh....CpsCq 64
                                  +ve+ ++C+ +  + Gf+r+ C++C+ e   + +C++++    Cp+C+
  gi|91773294|ref|YP_565986.1|  3 KVEQCTSCGIHlvEKGFTRLPCPTCETELGRCTKCRQQSnpytCPKCG 50
                                  678889999852268********************98755556****7 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 ?    7.6   0.1     0.005       3.2       1      14 [.       4      17 ..       4      19 .. 0.91
   2 ?    2.1   1.2      0.26   1.6e+02       4      11 ..      24      31 ..      22      36 .. 0.86
   3 ?   -0.3   0.3       1.4   9.3e+02       3       9 ..      33      39 ..      32      41 .. 0.74
   4 ?    6.4   0.2     0.012       7.8       3       8 ..      45      50 ..      44      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.005
                                  -EE-SSS--EEEEE CS
                zf-C4_Topoisom  1 vekCPkCggdLvlk 14
                                  ve+C +Cg +Lv+k
  gi|91773294|ref|YP_565986.1|  4 VEQCTSCGIHLVEK 17
                                  589*********98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                                  -SSS--EE CS
                zf-C4_Topoisom  4 CPkCggdL 11
                                  CP C  +L
  gi|91773294|ref|YP_565986.1| 24 CPTCETEL 31
                                  ****9876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                                  E-SSS-- CS
                zf-C4_Topoisom  3 kCPkCgg 9 
                                   C kC++
  gi|91773294|ref|YP_565986.1| 33 RCTKCRQ 39
                                  6999975 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.012
                                  E-SSS- CS
                zf-C4_Topoisom  3 kCPkCg 8 
                                  +CPkCg
  gi|91773294|ref|YP_565986.1| 45 TCPKCG 50
                                  7****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 ?    9.6   0.8    0.0013      0.86      72      94 ..       6      29 ..       2      32 .. 0.81
   2 ?    5.9   5.2     0.019        12      71      93 ..      32      50 ..      28      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                                  EETTTS-EEECHHH.HHS-TTTSS CS
                          HypA 72 rCreCgkefeleek.alrCpkCgs 94
                                  +C++Cg +  ++   +l Cp+C++
  gi|91773294|ref|YP_565986.1|  6 QCTSCGIHLVEKGFtRLPCPTCET 29
                                  7*****88887764589*****87 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                                  EEETTTS-EEECHHHHHS-TTTS CS
                          HypA 71 vrCreCgkefeleekalrCpkCg 93
                                   rC++C+++ +     ++CpkCg
  gi|91773294|ref|YP_565986.1| 32 GRCTKCRQQSNP----YTCPKCG 50
                                  58*****88874....48****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 ?    4.4   0.1      0.04        26      19      24 ..       7      12 ..       4      17 .. 0.82
   2 ?    3.3   0.2     0.091        58      19      24 ..      24      29 ..      22      31 .. 0.57
   3 ?   -0.6   0.2       1.6     1e+03      19      22 ..      34      37 ..      33      40 .. 0.75
   4 ?    8.3   0.6    0.0024       1.5       4      23 ..      45      50 ..      44      52 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.04
                   zf-ribbon_3 19 CpyCGt 24
                                  C++CG 
  gi|91773294|ref|YP_565986.1|  7 CTSCGI 12
                                  999996 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.091
                   zf-ribbon_3 19 CpyCGt 24
                                  Cp C t
  gi|91773294|ref|YP_565986.1| 24 CPTCET 29
                                  555554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                   zf-ribbon_3 19 CpyC 22
                                  C++C
  gi|91773294|ref|YP_565986.1| 34 CTKC 37
                                  7777 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0024
                   zf-ribbon_3  4 rCPnCGaplssddnvCpyCG 23
                                  +              Cp+CG
  gi|91773294|ref|YP_565986.1| 45 T--------------CPKCG 50
                                  3..............56665 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   3.3     0.057        37       3      30 ..       7      29 ..       6      29 .. 0.67
   2 ?    0.6   0.4      0.88   5.7e+02      25      28 ..      34      37 ..      32      39 .. 0.74
   3 ?    7.4   0.1    0.0066       4.2      23      31 ..      44      52 ..      43      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.057
                                  -TTT--B-EEE--TT-SS-EEEETTTTE CS
                     Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgt 30
                                  C++CG  +  +       +Rl Cp C+t
  gi|91773294|ref|YP_565986.1|  7 CTSCGIHLVEKG-----FTRLPCPTCET 29
                                  677776644443.....47999999975 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.88
                                  ETTT CS
                     Nudix_N_2 25 CpaC 28
                                  C++C
  gi|91773294|ref|YP_565986.1| 34 CTKC 37
                                  8888 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0066
                                  EEETTTTEE CS
                     Nudix_N_2 23 lvCpaCgti 31
                                  ++Cp+Cg++
  gi|91773294|ref|YP_565986.1| 44 YTCPKCGFV 52
                                  58****998 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 ?    6.3   7.1    0.0029       1.8     619     662 ..       5      50 ..       1      53 [. 0.57

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0029
                      PolC_DP2 619 rkCkkCgketle.....arCeeCgekteeklvCkkceeeveeekcekce 662
                                   ++C++Cg + +e       C++C+++      C+kc+++++  +c+kc+
  gi|91773294|ref|YP_565986.1|   5 EQCTSCGIHLVEkgftrLPCPTCETELGR---CTKCRQQSNPYTCPKCG 50 
                                   56777775544311111346666655554...77777777777777775 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.3    0.0035       2.2       4      25 ..       7      29 ..       4      42 .. 0.83
   2 ?    1.0   2.5      0.73   4.7e+02       4      25 ..      34      50 ..      32      53 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
                          Spt4  4 CllCklvktedqFeeegCpnC.e 25
                                  C++C++   e+ F++  Cp C +
  gi|91773294|ref|YP_565986.1|  7 CTSCGIHLVEKGFTRLPCPTCeT 29
                                  *********************33 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.73
                          Spt4  4 CllCklvktedqFeeegCpnCe 25
                                  C++C+   +       +Cp C 
  gi|91773294|ref|YP_565986.1| 34 CTKCRQQSN-----PYTCPKCG 50
                                  555553333.....46699994 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   3.1      0.25   1.6e+02      14      21 ..      22      29 ..       5      31 .. 0.57
   2 ?   10.1   7.0   0.00088      0.57       4      20 ..      33      50 ..      30      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.25
                                  EE-TTT-- CS
                        zf-HIT 14 YkCpkCnt 21
                                    Cp+C+t
  gi|91773294|ref|YP_565986.1| 22 LPCPTCET 29
                                  44888876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00088
                                  B-TTT-S.B-SEE-TTT- CS
                        zf-HIT  4 lCgvCgf.pakYkCpkCn 20
                                   C  C +    Y+CpkC+
  gi|91773294|ref|YP_565986.1| 33 RCTKCRQqSNPYTCPKCG 50
                                  7999***9999******8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.021        13       2       7 ..       7      12 ..       3      19 .. 0.73
   2 ?    2.4   0.3      0.21   1.3e+02       2       9 ..      24      31 ..      22      32 .. 0.80
   3 ?    2.9   8.7      0.15        94       2      21 ..      34      51 ..      33      53 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.021
                 zinc_ribbon_2  2 CpnCGa 7 
                                  C++CG 
  gi|91773294|ref|YP_565986.1|  7 CTSCGI 12
                                  777774 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.21
                 zinc_ribbon_2  2 CpnCGael 9 
                                  Cp C +el
  gi|91773294|ref|YP_565986.1| 24 CPTCETEL 31
                                  88888776 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
                 zinc_ribbon_2  2 CpnCGaelqdnakF.CpyCGt 21
                                  C++C  +    +++ Cp+CG+
  gi|91773294|ref|YP_565986.1| 34 CTKCRQQ---SNPYtCPKCGF 51
                                  6666665...66667999996 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.18   1.2e+02       5      10 ..      24      29 ..      21      31 .. 0.80
   2 ?    1.0   0.3      0.47     3e+02       5      11 ..      34      40 ..      33      41 .. 0.82
   3 ?    9.7   1.3    0.0009      0.58       3      13 ..      44      54 .]      43      54 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.18
                    zf_C2H2_10  5 CPKCqe 10
                                  CP C+ 
  gi|91773294|ref|YP_565986.1| 24 CPTCET 29
                                  ****86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                    zf_C2H2_10  5 CPKCqek 11
                                  C KC  +
  gi|91773294|ref|YP_565986.1| 34 CTKCRQQ 40
                                  99**875 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0009
                    zf_C2H2_10  3 fsCPKCqeklP 13
                                  + CPKC+ + P
  gi|91773294|ref|YP_565986.1| 44 YTCPKCGFVGP 54
                                  78****98866 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.6    0.0066       4.2       1      43 [.       7      51 ..       7      54 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0066
                          NMD3  1 CcrCGkeieeling....lCedCllkevditegiekievevCkeCgr 43
                                  C  CG+   e  +g     C+ C ++  + t++ ++ +   C++Cg 
  gi|91773294|ref|YP_565986.1|  7 CTSCGIHLVE--KGftrlPCPTCETELGRCTKCRQQSNPYTCPKCGF 51
                                  99****9942..3345579**************************96 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  12.1      0.05        32      21      55 ..      14      52 ..       4      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.05
                OrfB_Zn_ribbon 21 evnpayTSktCseCgsknke....alsgrtfkCpnCgfe 55
                                  +v++ +T   C+ C  ++ +    +++++ ++Cp+Cgf+
  gi|91773294|ref|YP_565986.1| 14 LVEKGFTRLPCPTCETELGRctkcRQQSNPYTCPKCGFV 52
                                  5666677778*******99999999************96 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.005       3.2      10      18 ..       4      12 ..       2      19 .. 0.87
   2 ?    2.2   4.7      0.22   1.4e+02      13      29 ..      24      39 ..      22      45 .. 0.83
   3 ?    5.2   1.6     0.025        16      13      18 ..      46      51 ..      44      54 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.005
                       zf-tcix 10 vrkCpkCGt 18
                                  v +C++CG+
  gi|91773294|ref|YP_565986.1|  4 VEQCTSCGI 12
                                  679*****8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                       zf-tcix 13 CpkCGtyNGtRglsCkN 29
                                  Cp+C t+ G R+  C+ 
  gi|91773294|ref|YP_565986.1| 24 CPTCETELG-RCTKCRQ 39
                                  ******999.8999985 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.025
                       zf-tcix 13 CpkCGt 18
                                  CpkCG 
  gi|91773294|ref|YP_565986.1| 46 CPKCGF 51
                                  *****5 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.77   4.9e+02      10      16 ..       6      12 ..       5      13 .. 0.87
   2 ?    7.9   0.3    0.0048       3.1       5      14 ..      18      27 ..      16      29 .. 0.87
   3 ?    2.7   0.8       0.2   1.3e+02      10      16 ..      45      51 ..      43      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.77
                       DUF2752 10 pCPGCGl 16
                                  +C  CG+
  gi|91773294|ref|YP_565986.1|  6 QCTSCGI 12
                                  6*****6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0048
                       DUF2752  5 altGipCPGC 14
                                   +t +pCP+C
  gi|91773294|ref|YP_565986.1| 18 GFTRLPCPTC 27
                                  589******* PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.2
                       DUF2752 10 pCPGCGl 16
                                   CP CG 
  gi|91773294|ref|YP_565986.1| 45 TCPKCGF 51
                                  7*****6 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.21   1.4e+02      27      32 ..       6      11 ..       2      12 .. 0.79
   2 ?    3.5   0.1       0.1        67       5      10 ..      24      29 ..      15      30 .. 0.73
   3 ?    2.7   3.4      0.18   1.2e+02      27      33 ..      33      39 ..      33      40 .. 0.86
   4 ?    6.4   0.1     0.013       8.6       4      10 ..      45      51 ..      44      53 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                 zinc_ribbon_4 27 rCskCg 32
                                  +C+ Cg
  gi|91773294|ref|YP_565986.1|  6 QCTSCG 11
                                  688886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                 zinc_ribbon_4  5 CpsCka 10
                                  Cp C++
  gi|91773294|ref|YP_565986.1| 24 CPTCET 29
                                  777776 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.18
                 zinc_ribbon_4 27 rCskCgh 33
                                  rC+kC++
  gi|91773294|ref|YP_565986.1| 33 RCTKCRQ 39
                                  8****97 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.013
                 zinc_ribbon_4  4 tCpsCka 10
                                  tCp+C++
  gi|91773294|ref|YP_565986.1| 45 TCPKCGF 51
                                  5777765 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.041        27      19      26 ..       4      11 ..       2      19 .. 0.76
   2 ?   -1.0  14.9       1.7   1.1e+03       2      26 ..      24      50 ..      23      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.041
                      zf-TFIIB 19 idyCpqCr 26
                                  +++C++C+
  gi|91773294|ref|YP_565986.1|  4 VEQCTSCG 11
                                  67777775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                      zf-TFIIB  2 CPkCqdeleeser..ggveidyCpqCr 26
                                  CP+C +el    +  +    ++Cp+C+
  gi|91773294|ref|YP_565986.1| 24 CPTCETELGRCTKcrQQSNPYTCPKCG 50
                                  *********5555559999*******7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.07        45      28      34 ..       6      12 ..       2      19 .. 0.62
   2 ?    8.6   2.8     0.003       1.9       7      36 ..       6      31 ..       6      33 .. 0.71
   3 ?    2.4   7.1      0.28   1.8e+02       8      33 ..      34      50 ..      30      52 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.07
                   Zn-ribbon_8 28 aCPeCgs 34
                                  +C +Cg 
  gi|91773294|ref|YP_565986.1|  6 QCTSCGI 12
                                  4777765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.003
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgsev 36
                                  +C++Cg  + v   +++    +CP+C  e+
  gi|91773294|ref|YP_565986.1|  6 QCTSCG-IHLVEKGFTRL---PCPTCETEL 31
                                  6*****.66666656644...4****8876 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.28
                   Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                                  C++C ++ +         + +CP+Cg
  gi|91773294|ref|YP_565986.1| 34 CTKCRQQSN---------PYTCPKCG 50
                                  666653333.........34599998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 359.59
//
Query:       gi|91773295|ref|YP_565987.1|  [L=89]
Description: elongation factor 1-beta [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-18   67.3   0.0    1.2e-18   67.1   0.0    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   6.6e-23   1.2e-18       2      88 ..       6      86 ..       5      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 6.6e-23
                                  EEEEEEESSS---HHHHHHHHHH.HS-TSEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SEEEEE CS
                       EF1_GNE  2 vvlevkPeddetdleelekkvksikleglvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVqsvei 84
                                  ++++++Pe ++tdl++l+ +++++  eg+ +   s++ep+afGlk+L++ + + d +++t+ +ee+++++ g     V+sv++
  gi|91773295|ref|YP_565987.1|  6 ATMKIMPEGVDTDLDDLKIRLEAVLPEGASIFG-SEIEPVAFGLKALKLVVLVGDLEGGTEPVEEAFAAVPG-----VESVQV 82
                                  689********************9999999995.**************************************.....****** PP

                                  EEEE CS
                       EF1_GNE 85 vsfn 88
                                  +++ 
  gi|91773295|ref|YP_565987.1| 83 TELG 86
                                  9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); 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 0.35s 00:00:00.81 Elapsed: 00:00:00.53
# Mc/sec: 507.43
//
Query:       gi|91773296|ref|YP_565988.1|  [L=309]
Description: thiamine biosynthesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-33  114.7   0.0    5.7e-33  114.2   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
    8.2e-19   68.1   0.0    1.1e-16   61.2   0.0    2.1  2  THUMP          THUMP domain
      3e-05   23.0   0.1    7.1e-05   21.8   0.0    1.6  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.026   14.0   0.0    1.3  1  QueC           Queuosine biosynthesis protein QueC
      0.055   13.6   0.1        0.1   12.8   0.1    1.3  1  Mtf2_C         Polycomb-like MTF2 factor 2
       0.12   11.5   0.0       0.33   10.0   0.0    1.7  2  NAD_synthase   NAD synthase


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.0   1.9e-36   5.7e-33       1     130 [.     177     306 ..     177     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 1.9e-36
                          ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeile 81 
                                   g+qg  ++L+SgGiDSpVaa+l++kRG++v  v+ +n p+  ++a e+  k++e l +++ +  +k++ v++ + l+e ++
  gi|91773296|ref|YP_565988.1| 177 GSQGIMIVLMSGGIDSPVAAWLMMKRGVKVIPVYANNIPFSDDRALERAIKAVERLQKWSPADPMKMYEVPHGKNLDEFMK 257
                                   7899***************************************************************************** PP

                          ThiI  82 kvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlr 130
                                   k   k t++l+kr+m+r+A ++ ++e+a+ ++tG+s+gqVaSqt  N++
  gi|91773296|ref|YP_565988.1| 258 KCIVKNTCLLCKRTMYRMAYEIMKKENADGIITGSSIGQVASQTAANMH 306
                                   **********************************************986 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   3.8e-20   1.1e-16       1     143 [.      29     166 ..      29     167 .. 0.93
   2 !    5.0   0.0    0.0083        25      23      68 ..     205     256 ..     199     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 3.8e-20
                                   HHHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                         THUMP   1 geieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfee 81 
                                   +++e++l  ++v  +rv +++gri++ +  +     e++   a   ++g+++ + +   + ad+++  ++   i  + + e
  gi|91773296|ref|YP_565988.1|  29 RNLEAMLRQKNVSFSRVHREWGRIFITSDDP-----EAA--IAAADVFGVVSTSAA-KMIDADVDEAAKLCADIGVDIINE 101
                                   699************************9733.....333..3566889********.*******************99988 PP

                                   CT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT.....-EE-SSS-SEEEEEEEETTEEEEEEE CS
                         THUMP  82 eketFaVrvkrrgkhfeftsreinrevGkaivektg.....lkVdlenPdivvrveiikdkayisid 143
                                   ++ +F +r++r+gk+   +s +i r  G+a++ +++     +kVdl+nPd  + ve +++kay+++d
  gi|91773296|ref|YP_565988.1| 102 GE-SFGIRARRVGKE-GPSSTDIGRLCGDAVWTRLEsigrtPKVDLSNPDREISVEMRQNKAYVFTD 166
                                   75.************.************************************************987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0083
                                   EEEEECTEEEEEETHHHHHHHHHTSTTECEEEEE......EEEEESSHHHHH CS
                         THUMP  23 rivvelkgekpeedeellkealekargiqrvipv......cevceadledil 68 
                                   +++ ++ +  p+ d+++l++a++ ++ +q+++p+      +   +++l+++ 
  gi|91773296|ref|YP_565988.1| 205 KVIPVYANNIPFSDDRALERAIKAVERLQKWSPAdpmkmyEVPHGKNLDEFM 256
                                   46667778899***********************988877767777777765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1      0.93   2.8e+03      45      65 ..      78      98 ..      72     100 .. 0.81
   2 !   21.8   0.0   2.4e-08   7.1e-05       4      41 ..     183     220 ..     181     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.93
                 tRNA_Me_trans 45 ccaeedlkdaervaeklgipl 65
                                  +  ++d+ +a + +  +g+ +
  gi|91773296|ref|YP_565988.1| 78 KMIDADVDEAAKLCADIGVDI 98
                                  56789999*******999975 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.4e-08
                 tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqgyevigvflklweeedee 41 
                                   +v++SgG+DS vaa l+ ++g +vi v+ +++  +d+ 
  gi|91773296|ref|YP_565988.1| 183 IVLMSGGIDSPVAAWLMMKRGVKVIPVYANNIPFSDDR 220
                                   89**************************9998776655 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.8e-06     0.026       2      30 ..     182     210 ..     181     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-06
                                   EEEE--SSHHHHHHHHHHHHH-SEEEEEE CS
                          QueC   2 avvllSGGlDSttvlalakkegkevealt 30 
                                    +vl+SGG+DS ++++l++k+g +v+ + 
  gi|91773296|ref|YP_565988.1| 182 MIVLMSGGIDSPVAAWLMMKRGVKVIPVY 210
                                   59********************9998764 PP

>> Mtf2_C  Polycomb-like MTF2 factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.4e-05       0.1      19      36 ..      99     116 ..      96     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                        Mtf2_C  19 iasGEkfavlAkRvtpnG 36 
                                   i+ GE+f ++A+Rv+ +G
  gi|91773296|ref|YP_565988.1|  99 INEGESFGIRARRVGKEG 116
                                   788************999 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00011      0.33      22      94 ..     183     254 ..     176     294 .. 0.66
   2 ?   -2.0   0.0      0.51   1.5e+03      11      35 ..     278     303 ..     267     307 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                                   EEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHHH CS
                  NAD_synthase  22 vlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpivrafeqelke 94 
                                   ++ +SGG+DS ++a l  k     +v+ ++     +s+++ +e a++ +e+l+  +   ++k +     ++l+e
  gi|91773296|ref|YP_565988.1| 183 IVLMSGGIDSPVAAWLMMKRG--VKVIPVYANnIPFSDDRALERAIKAVERLQKWSPADPMKMYEVPHGKNLDE 254
                                   5668**********9987754..577777777567889999999999999988666555555444444444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.51
                                   HHHHHCTTSEEEEEE-SSH.HHHHHH CS
                  NAD_synthase  11 eyvkkagakgvvlGlSGGv.DSslva 35 
                                   e +kk++a+g++ G S G+  S ++a
  gi|91773296|ref|YP_565988.1| 278 EIMKKENADGIITGSSIGQvASQTAA 303
                                   45678888888888886651444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1904.66
//
Query:       gi|91773297|ref|YP_565989.1|  [L=74]
Description: hypothetical protein Mbur_1321 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   23.4   4.1    5.9e-05   22.9   4.1    1.2  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0006   19.6   3.0    0.00097   19.0   3.0    1.3  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0012   18.5   1.8      0.002   17.8   1.8    1.4  1  A2L_zn_ribbon    A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.023   14.6   0.8      0.031   14.2   0.8    1.3  1  Prok-RING_1      Prokaryotic RING finger family 1
      0.072   12.9   0.0      0.078   12.8   0.0    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase
       0.12   11.7   2.2       0.22   10.9   2.2    1.5  1  zf-TFIIB         Transcription factor zinc-finger
       0.73   10.0  10.6          2    8.7   6.8    2.4  2  zf-Dof           Dof domain, zinc finger
       0.94    9.1   5.1        1.2    8.7   0.9    2.8  2  zf_C2H2_10       C2H2 type zinc-finger
        1.3    8.6   5.4        3.9    7.1   5.4    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   4.1     3e-08   5.9e-05       4      27 ..      35      58 ..      32      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3e-08
                PhnA_Zn_Ribbon  4 kCplCaSeytYedgallvCpeCah 27
                                  kCp+C+Se ++e+++l vC  C++
  gi|91773297|ref|YP_565989.1| 35 KCPKCNSELELENDSLQVCKVCKY 58
                                  9*********************86 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 !   19.0   3.0   4.9e-07   0.00097       4      29 ..      36      58 ..      35      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.9e-07
                                  ESTTTSBEEEEECSCCCEEEESSSS- CS
                RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgY 29
                                  CpkC++ L+  +d + +   C  C+Y
  gi|91773297|ref|YP_565989.1| 36 CPKCNSELELENDSLQV---CKVCKY 58
                                  ****************8...****** PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.8   9.9e-07     0.002       4      29 ..      34      58 ..      31      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.9e-07
                 A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCga 29
                                   +C +C+++ +l  +++  vC+ C +
  gi|91773297|ref|YP_565989.1| 34 DKCPKCNSELEL-ENDSLQVCKVCKY 58
                                  59**********.*********9965 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 ?   14.2   0.8   1.6e-05     0.031       4      27 ..      33      57 ..      30      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                   Prok-RING_1  4 gkkCpvCgkelkeedD.iVvCpeCg 27
                                   +kCp C+ el+ e+D + vC +C+
  gi|91773297|ref|YP_565989.1| 33 LDKCPKCNSELELENDsLQVCKVCK 57
                                  589*********99773679****7 PP

>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.9e-05     0.078      27      71 ..      15      64 ..       7      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
                                  E-SSSB-BSSEEEEETT--BT.....CCBEETSSSEEEEEESSS---TTE CS
               Pyrophosphatase 27 vlftskgypanYGfipqTled.....telkGDgDPlDvlvlgeeplspge 71
                                  ++  + +++  +G+i +Tl++     +el+ ++D l v+++++  ++ g+
  gi|91773297|ref|YP_565989.1| 15 IIRYYLHIMDRWGYIMKTLDKcpkcnSELELENDSLQVCKVCKYWTKAGT 64
                                  6677899999***************999**************98877764 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.2   0.00011      0.22       1      14 [.      35      48 ..      35      58 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                      zf-TFIIB  1 kCPkCqdeleeser 14
                                  kCPkC++ele  + 
  gi|91773297|ref|YP_565989.1| 35 KCPKCNSELELEND 48
                                  8********95444 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       5.1     1e+04      13      17 ..       9      13 ..       8      19 .. 0.67
   2 ?    8.7   6.8   0.00098         2       4      45 ..      34      66 ..      31      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.1
                        zf-Dof 13 ntkFc 17
                                  nt Fc
  gi|91773297|ref|YP_565989.1|  9 NTLFC 13
                                  67777 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00098
                        zf-Dof  4 lkCprCestntkFcYyNNyslsqPRyfCkaCrryWtkgGklR 45
                                   kCp+C+s+        N+sl+    +Ck C+ yWtk+G+ R
  gi|91773297|ref|YP_565989.1| 34 DKCPKCNSELE----LENDSLQ----VCKVCK-YWTKAGTAR 66
                                  57888888643....4677775....8****6.9*****988 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.15   2.9e+02      20      24 ..      20      24 ..      19      25 .. 0.88
   2 ?    8.7   0.9   0.00061       1.2       5      19 ..      36      51 ..      35      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.15
                    zf_C2H2_10 20 IHvMd 24
                                   H+Md
  gi|91773297|ref|YP_565989.1| 20 LHIMD 24
                                  5***9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00061
                    zf_C2H2_10  5 CPKCqeklP.DiDtLQ 19
                                  CPKC+  l    D+LQ
  gi|91773297|ref|YP_565989.1| 36 CPKCNSELElENDSLQ 51
                                  ****987732556666 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.4     0.002       3.9       2      25 ..      35      56 ..      35      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.002
                                  EETTTTCEE.CHEETSTTCE.EESSS CS
                  TF_Zn_Ribbon  2 kCPnCgstn.lveDpergel.vCtdC 25
                                  kCP+C+s+  l++D     l vC+ C
  gi|91773297|ref|YP_565989.1| 35 KCPKCNSELeLEND----SLqVCKVC 56
                                  8******8544444....56688888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 501.46
//
Query:       gi|91773298|ref|YP_565990.1|  [L=158]
Description: hypothetical protein Mbur_1322 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-05   25.8   0.0      2e-05   24.9   0.0    1.4  1  Toprim_4  Toprim domain
      0.001   19.5   0.0     0.0014   19.0   0.0    1.3  1  Toprim_2  Toprim-like
      0.002   18.3   0.2      0.032   14.4   0.2    2.3  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.4e-09     2e-05       2      78 ..      46     111 ..      45     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.4e-09
                      Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaell 78 
                                   +ii+ Eg  D ++l k gi++ +  +  +  pl +i+ e+  +e         ++vi+++d D +G+  a +l+e+l
  gi|91773298|ref|YP_565990.1|  46 AIILAEGKRDIISLKKLGINGPIELVTQS--PLTEIS-ERVASE--------KRRVIILTDWDRRGNILAAKLSEDL 111
                                   79**********************77644..588888.555553........4********************9965 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.4e-07    0.0014       1      73 [.      48     116 ..      48     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.4e-07
                      Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagv 73 
                                   +++Eg  D +Sl++lgi+     + + +  lte   ++ +++  ++v++ +D D+ G+  a++l+e l + g+
  gi|91773298|ref|YP_565990.1|  48 ILAEGKRDIISLKKLGIN-GPIELVTQSP-LTEISERVASEK--RRVIILTDWDRRGNILAAKLSEDLVYLGA 116
                                   689**************7.3444445555.899999998888..99*******************99987773 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   5.4e-06     0.032      56      85 ..      80     109 ..      46     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
                                   HHHHHHHHSEEEEECSSSHHHHHHHHHHHH CS
                        Toprim  56 lkelakradeiilatDpDreGeaiawelle 85 
                                    ++ a++  ++i++tD Dr G  +a +l e
  gi|91773298|ref|YP_565990.1|  80 SERVASEKRRVIILTDWDRRGNILAAKLSE 109
                                   335568889*************99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1125.34
//
Query:       gi|91773299|ref|YP_565991.1|  [L=96]
Description: acylphosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   91.4   0.0    3.9e-26   91.3   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 !   91.3   0.0   2.2e-30   3.9e-26       2      85 .]      11      94 ..      10      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2.2e-30
               Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdFe 84
                                  +++v+GrVQgv+FR f+++ A++lgl Gy++Nl+dg+V++va+g+++ ++++l++l+ gp+ ++v+ +ev ++   ++f+dF 
  gi|91773299|ref|YP_565991.1| 11 EIYVSGRVQGVYFRGFTQKTATSLGLMGYAQNLPDGRVKVVAQGKRSCISELLDHLHIGPELSNVECIEVGWMGLSDTFTDFF 93
                                  799*******************************************************************************8 PP

               Acylphosphatase 85 i 85
                                  i
  gi|91773299|ref|YP_565991.1| 94 I 94
                                  7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 691.19
//
Query:       gi|91773300|ref|YP_565992.1|  [L=635]
Description: threonyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-52  177.4   0.1    2.6e-52  176.5   0.1    1.5  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    2.7e-19   69.1   0.3    5.9e-19   68.0   0.3    1.6  1  HGTP_anticodon  Anticodon binding domain
      1e-15   58.2   0.3    1.9e-15   57.3   0.3    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.5   0.1   4.4e-56   2.6e-52       1     137 []       1     137 [.       1     137 [. 0.98

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 4.4e-56
                                   -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE- CS
                   tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlypy 79 
                                   m+lLlih+d++eye+kk++ ++ae  ee+ k+grle+al++F+avE+ De+++++++++av+ei++va +vka++++lypy
  gi|91773300|ref|YP_565992.1|   1 MQLLLIHSDYIEYEVKKST-PVAEeiEESFKQGRLEDALTAFMAVESFDEANPQEIIDRAVSEIENVAGQVKAENIMLYPY 80 
                                   9******************.7777699999*************************************************** PP

                                   STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                   tRNA-Thr_ED  80 aHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                   aHLss+l+sp+va+++lk +e++l+ k ++v+raPFGwyk+f+isckGhpL+elsr+i
  gi|91773300|ref|YP_565992.1|  81 AHLSSDLSSPKVAVSVLKGIENALEGK-YNVMRAPFGWYKAFRISCKGHPLSELSRTI 137
                                   **************************8.****************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.3   9.9e-23   5.9e-19       1      90 [.     521     609 ..     521     613 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 9.9e-23
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET.....TT CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr.....dt 76 
                                   qv vip++e   +++++a+++a+ L+   +r+++dd++e++gkkir+a + +ip++ v+G+ e+e+g+vtv  r     ++
  gi|91773300|ref|YP_565992.1| 521 QVRVIPIAE---RHMDFAQEVADSLL---CRADIDDREETVGKKIRDAGREWIPYVAVIGDSEVESGKVTVTIRaesepKK 595
                                   89*******...**************...88*******************************************6444444 PP

                                   CEEEEEETTHHHHH CS
                HGTP_anticodon  77 reqervsldelvek 90 
                                    ++++++ +el e 
  gi|91773300|ref|YP_565992.1| 596 PMKVEMTAEELSER 609
                                   44466666666655 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 !   57.3   0.3   3.1e-19   1.9e-15       1     178 [.     291     500 ..     291     501 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3.1e-19
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easldd 78 
                                   Y +e++ +r + L+  ++ +   +  d ++  k+LPlk++++++  +R+E++ ++ GL R+r F++ d +  +   + + +
  gi|91773300|ref|YP_565992.1| 291 YSIESD-KRHMFLRFAACFGQFLMNHDMTISYKNLPLKMIEMTRYsFRKEQRgELVGLRRLRAFTMPDMHTLCPdMEAAIS 370
                                   556666.5899999999999999999998888*********99854******8999******************8677888 PP

                                   HHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETT.............................TSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxx RF
                  tRNA-synt_2b  79 slrdlikaisriferlglefraiielmsaksadykdkkefeavses.............................ltkgie 130
                                   ++ +      +i++++g+ +   +   +++  +y+d  ef     +                             + k+  
  gi|91773300|ref|YP_565992.1| 371 QFGEQYSMCIDILRKIGIDVSDFEVAIRFTREFYDDNREFITELAKkvdkpvlvemwdtrffyfvlkfefnfvdaIAKASA 451
                                   88888888889*******995554444444455666666655444455666666666666666666666666666888888 PP

                                   EEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                  tRNA-synt_2b 131 igtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                   ++t+q +  + +er +++++d n++ +++ +++ +  g +eR + a+le+
  gi|91773300|ref|YP_565992.1| 452 LSTVQID-VENAERYDINYVDANGKINRPTILHCSpSGaIERCIYALLEK 500
                                   *******.999************************9999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4259.49
//
Query:       gi|91773301|ref|YP_565993.1|  [L=106]
Description: hypothetical protein Mbur_1325 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 801.73
//
Query:       gi|91773302|ref|YP_565994.1|  [L=354]
Description: hypothetical protein Mbur_1326 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  133.9  46.2    8.6e-39  133.6  46.2    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6  46.2   4.8e-43   8.6e-39       4     326 ..      23     339 ..      18     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 4.8e-43
               AI-2E_transport   4 ilvllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltqlvk 84 
                                   + + ll++l ++ ++ ++   +++++v+ay+  p+++f+   ++kr l +l+ ++++++ +v+++++ + ++++ql  + +
  gi|91773302|ref|YP_565994.1|  23 VALVLLFSLFIIILL-PIADGIMLGIVFAYIGRPIYNFI---KMKRHLGALVATMFIVIPIVMILGMGIIEIANQLMWIAE 99 
                                   333444444444444.5889*******************...8889999999999999988888888888999******** PP

               AI-2E_transport  85 slpayidslqnilnelpslleele.nliqalkqslskilsnilssilnsllsllasllglilslvlvllllffllldgekl 164
                                   +  a+i+sl++++ +l    +  + ++i++  ++ s ++  +l+++   ++s+++ +++++++l++ +l+++fll+dg+ l
  gi|91773302|ref|YP_565994.1| 100 NQGAVIESLLDFIRNLN--IPDAYyENIRQTIWNSSISILPLLGNL--VFVSYARGIAMFMINLLVAVLVCYFLLADGDGL 176
                                   **************997..444442334444444444444444444..4899999************************** PP

               AI-2E_transport 165 rqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliPyiGavivlip 245
                                   ++ +l+++p+++++ vk+++ +++ +lsg+++g++  al ++ l+ i+++++g+ + l la l+++a++iP++ +++vl++
  gi|91773302|ref|YP_565994.1| 177 YRSVLRIIPKGNQHLVKRYVHHMDIILSGVFIGNAYAALSVSTLSVIVFYAFGLSHVLALATLIFVASVIPMFAGYMVLVV 257
                                   ********************************************************************************* PP

               AI-2E_transport 246 iaiialltggikevlivliv.vllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlilavpltavikailea 325
                                   + i+ ++  g++ +li+++v  +++ +  + +l+P+l + + ++hp++i+l++l+g+ ++G+ G++ a++l++++  ++++
  gi|91773302|ref|YP_565994.1| 258 LTIVRYFSLGFESALIFFVVsSIIIYAPPEFFLRPYLASIKSHIHPFLIMLAFLGGAFVGGIAGFFAAPILLGTLVSAYRV 338
                                   999999888877777766651566777889**********************************************99998 PP

               AI-2E_transport 326 y 326
                                   y
  gi|91773302|ref|YP_565994.1| 339 Y 339
                                   7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2243.87
//
Query:       gi|91773303|ref|YP_565995.1|  [L=667]
Description: hypothetical protein Mbur_1327 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-39  136.0   0.0    1.8e-39  135.5   0.0    1.2  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
    1.2e-06   28.6   9.6    1.2e-06   28.6   9.6    3.2  3  Fer4_9       4Fe-4S dicluster domain
    1.2e-06   28.0   3.0    1.2e-06   28.0   3.0    3.9  4  Fer4         4Fe-4S binding domain
    3.3e-06   27.3   3.1    9.5e-06   25.8   3.1    1.7  1  Fer4_18      4Fe-4S dicluster domain
    4.5e-06   26.7   9.1    4.5e-06   26.7   9.1    2.6  2  Fer4_10      4Fe-4S dicluster domain
    7.1e-06   26.5  10.3    7.1e-06   26.5  10.3    2.5  2  Fer4_7       4Fe-4S dicluster domain
    0.00018   22.3   1.5    0.00018   22.3   1.5    3.9  3  Fer4_16      4Fe-4S double cluster binding domain
     0.0003   20.8   3.3     0.0003   20.8   3.3    4.2  5  Fer4_21      4Fe-4S dicluster domain
    0.00086   19.3   3.6    0.00086   19.3   3.6    3.7  3  Fer4_6       4Fe-4S binding domain
      0.002   18.5  16.9       0.04   14.4   1.2    4.1  3  Fer4_8       4Fe-4S dicluster domain
     0.0022   18.0   2.1     0.0022   18.0   2.1    4.0  2  Fer4_2       4Fe-4S binding domain
      0.003   17.5   0.1     0.0076   16.2   0.1    1.6  1  PUA          PUA domain
  ------ inclusion threshold ------
      0.027   15.0  14.3       0.17   12.5   1.9    3.2  4  Fer4_17      4Fe-4S dicluster domain
      0.034   13.9   0.0       0.06   13.1   0.0    1.4  1  ATP_bind_3   PP-loop family
      0.053   13.8   0.1       0.15   12.3   0.1    1.7  1  UPF0113      UPF0113 PUA domain
       0.99   10.3   8.8          4    8.4   0.7    2.7  2  Fer4_22      4Fe-4S dicluster domain
        2.5    8.7  11.4         11    6.7   1.5    2.8  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.0   1.7e-42   1.8e-39       3     173 ..     269     444 ..     267     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 1.7e-42
                                   EEE--SSCTCHHHHHHHHHHCTTH..EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHCH CS
                   PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv..pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyeea 81 
                                    vs+sgGkdslV+l+L+l+a+k +  + +f++tg efpet+efv    e+ g++l+  + e+ ++e+++ ++ + +++++ 
  gi|91773303|ref|YP_565995.1| 269 HVSFSGGKDSLVVLDLTLSALKGRdvRAFFLNTGIEFPETVEFVHSHCENRGIELIESKAENAFWENLESFGPPAKDFRW- 348
                                   69*******************995449*****************************************************. PP

                                   HHHHHTHHHHHHHHHCT....TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CC CS
                   PAPS_reduct  82 aeriaKveplkkaLekl....dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpL 158
                                   +++++K+ p+   +++     +  +++ G R+ es+sr++++  e++   +++l++fP+ +W   +vw yi+ ++++ynpL
  gi|91773303|ref|YP_565995.1| 349 CCKVCKLGPAGAIIDQCsengGVCLTIDGKRKFESFSRSNISASEKNPFVPNQLNIFPIRDWRAIEVWLYIYWRKLDYNPL 429
                                   *********999999884444556899****************************************************** PP

                                   CCTT-SS--BCTTB- CS
                   PAPS_reduct 159 ydqgfrsiGcvpctg 173
                                   yd gf+++Gc+ c++
  gi|91773303|ref|YP_565995.1| 430 YDVGFERVGCYLCPA 444
                                   ************985 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   0.2       1.9     2e+03       2      13 ..      40      56 ..      19      71 .. 0.65
   2 ?   -1.7   1.1       3.3   3.4e+03       8      24 ..     349     368 ..     345     375 .. 0.74
   3 !   28.6   9.6   1.1e-09   1.2e-06       1      46 [.     608     649 ..     608     652 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                        Fer4_9  2 CtgC......gaCveaCp 13
                                  C +C      ++C   C+
  gi|91773303|ref|YP_565995.1| 40 CKNCnvplldKNCGV-CE 56
                                  444433333333443.44 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                        Fer4_9   8 CveaC...pagvvvedaaer 24 
                                   C ++C   pag+++++++e+
  gi|91773303|ref|YP_565995.1| 349 CCKVCklgPAGAIIDQCSEN 368
                                   77777777888888777665 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 1.1e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaC 46 
                                   kCt+Cg C ++Cp ++++  + ++ + ++     +Ci+Cg+C++ C
  gi|91773303|ref|YP_565995.1| 608 KCTECGICLKVCPVNAIELGSEKGRVYIND----SCISCGKCTDGC 649
                                   7************************99976....6*********** PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.9       1.5   1.6e+03      10      15 ..      51      56 ..      50      58 .. 0.85
   2 ?   -3.1   0.8       7.8   8.3e+03       9      14 ..     437     442 ..     437     442 .. 0.90
   3 !   28.0   3.0   1.2e-09   1.2e-06       6      24 .]     607     625 ..     604     625 .. 0.93
   4 !    8.8   4.7    0.0014       1.4       2      18 ..     633     649 ..     632     649 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                                  S-THHH CS
                          Fer4 10 gCGaCv 15
                                  +CG C+
  gi|91773303|ref|YP_565995.1| 51 NCGVCE 56
                                  6****7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.8
                                   SS-THH CS
                          Fer4   9 igCGaC 14 
                                   +gC +C
  gi|91773303|ref|YP_565995.1| 437 VGCYLC 442
                                   79***9 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 1.2e-09
                                   TTSSS-THHHHHSTTTEEE CS
                          Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                   +kC+ CG+C +vCPv+AI+
  gi|91773303|ref|YP_565995.1| 607 SKCTECGICLKVCPVNAIE 625
                                   8*****************6 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0014
                                   EEETTTSSS-THHHHHS CS
                          Fer4   2 videekCigCGaCvevC 18 
                                   v++ + Ci CG+C + C
  gi|91773303|ref|YP_565995.1| 633 VYINDSCISCGKCTDGC 649
                                   56789********9988 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   3.1     9e-09   9.5e-06      40      96 ..     588     650 ..     561     661 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9e-09
                       Fer4_18  40 rkkekkalkekeerkekgagdcidcescvkvcPtg.idi..rkG...lqleciscllcidacd 96 
                                   +k+ +++  e   ++   a++c++c+ c+kvcP++ i++   kG   +  +cisc++c d c 
  gi|91773303|ref|YP_565995.1| 588 SKEYAHSCLEATAKQLLRASKCTECGICLKVCPVNaIELgsEKGrvyINDSCISCGKCTDGCV 650
                                   33444444555566777899*************853555334563225568***********6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.5       7.7   8.1e+03      45      48 ..      40      43 ..      23      56 .. 0.57
   2 !   26.7   9.1   4.3e-09   4.5e-06       6      55 ..     606     649 ..     601     651 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.7
                       Fer4_10 45 Ctgc 48
                                  C +c
  gi|91773303|ref|YP_565995.1| 40 CKNC 43
                                  4443 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 4.3e-09
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaC 55 
                                   +++C++Cg C k+CP+       ++++ ++e+ r+   ++C+ cg+C++ C
  gi|91773303|ref|YP_565995.1| 606 ASKCTECGICLKVCPV-------NAIELGSEKGRVyINDSCISCGKCTDGC 649
                                   789*************.......6666666666666799**********99 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.4       7.1   7.5e+03      40      44 ..      51      55 ..      22      57 .. 0.65
   2 !   26.5  10.3   6.7e-09   7.1e-06       1      48 [.     608     649 ..     608     651 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.1
                        Fer4_7 40 gCgaC 44
                                  +Cg+C
  gi|91773303|ref|YP_565995.1| 51 NCGVC 55
                                  34444 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 6.7e-09
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                   +C++Cg C ++Cpv+aiel  e   kg  +v+   ++C++Cg+C + C
  gi|91773303|ref|YP_565995.1| 608 KCTECGICLKVCPVNAIELGSE---KG--RVY-INDSCISCGKCTDGC 649
                                   7******************886...44..455.569**********99 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.64   6.7e+02      36      61 ..      19      44 ..       3      45 .. 0.61
   2 !   22.3   1.5   1.7e-07   0.00018       1      22 [.     608     629 ..     608     638 .. 0.85
   3 ?    2.8   4.7      0.23   2.4e+02       2      12 ..     639     649 ..     638     651 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.64
                       Fer4_16 36 aekkdlaedeekckkqeaitgCdiCq 61
                                    +k+ + ++   ++q  i+ C++C+
  gi|91773303|ref|YP_565995.1| 19 VVDKKKHSRNPVSNEQSTIYWCKNCN 44
                                  44455555555556678888898885 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.7e-07
                       Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                   +C++Cg C++vCP+nai+  +e
  gi|91773303|ref|YP_565995.1| 608 KCTECGICLKVCPVNAIELGSE 629
                                   5****************98743 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.23
                       Fer4_16   2 CgtCgkCaevC 12 
                                   C++CgkC++ C
  gi|91773303|ref|YP_565995.1| 639 CISCGKCTDGC 649
                                   999****9999 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       2.8     3e+03      17      34 ..     315     332 ..     311     361 .. 0.59
   2 ?   -2.1   0.9       4.3   4.6e+03      16      33 ..     363     380 ..     345     387 .. 0.66
   3 ?   -2.5   0.1       5.5   5.8e+03      42      47 ..     437     442 ..     435     444 .. 0.82
   4 !   20.8   3.3   2.9e-07    0.0003      20      58 ..     590     625 ..     583     626 .. 0.85
   5 ?    6.1   4.2     0.012        12       5      18 ..     636     649 ..     632     655 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                       Fer4_21  17 aCedtshqaieidaktvl 34 
                                    Ce+ +++ ie +a++ +
  gi|91773303|ref|YP_565995.1| 315 HCENRGIELIESKAENAF 332
                                   688888888876655543 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                       Fer4_21  16 iaCedtshqaieidaktv 33 
                                     C++++  +++id+k++
  gi|91773303|ref|YP_565995.1| 363 DQCSENGGVCLTIDGKRK 380
                                   356677777777776665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.5
                       Fer4_21  42 vGCnlC 47 
                                   vGC lC
  gi|91773303|ref|YP_565995.1| 437 VGCYLC 442
                                   899999 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 2.9e-07
                       Fer4_21  20 dtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   + +h ++e +ak+   +++++C+ C +C++vCPv ++ie
  gi|91773303|ref|YP_565995.1| 590 EYAHSCLEATAKQL--LRASKCTECGICLKVCPV-NAIE 625
                                   67899999888887..6789*************9.9987 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.012
                       Fer4_21   5 edkCigCgkCliaC 18 
                                   +d+Ci+CgkC+  C
  gi|91773303|ref|YP_565995.1| 636 NDSCISCGKCTDGC 649
                                   47899999998888 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.9       6.6     7e+03       9      16 ..      43      56 ..      41      56 .. 0.64
   2 !   19.3   3.6   8.2e-07   0.00086       7      24 .]     607     624 ..     605     624 .. 0.94
   3 !    9.6   4.5    0.0009      0.95       4      19 ..     634     649 ..     633     651 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.6
                        Fer4_6  9 Ci......gCgdCv 16
                                  C+       Cg C+
  gi|91773303|ref|YP_565995.1| 43 CNvplldkNCGVCE 56
                                  55555544799996 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8.2e-07
                        Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                   +kC+ Cg C +vCP +ai
  gi|91773303|ref|YP_565995.1| 607 SKCTECGICLKVCPVNAI 624
                                   89**************98 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0009
                        Fer4_6   4 idpdkCigCgdCvrvC 19 
                                   +  d+Ci+Cg+C++ C
  gi|91773303|ref|YP_565995.1| 634 YINDSCISCGKCTDGC 649
                                   5689********9988 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2       1.2   1.3e+03      36      55 ..      25      44 ..       3      58 .. 0.63
   2 !   14.4   1.2   3.8e-05      0.04       2      17 ..     606     621 ..     583     632 .. 0.84
   3 !   13.1   0.7   9.3e-05     0.098       3      25 ..     637     659 ..     636     667 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                        Fer4_8 36 vqeeqvleeeealwsCttcg 55
                                    ++ v +e+ +++ C +c+
  gi|91773303|ref|YP_565995.1| 25 HSRNPVSNEQSTIYWCKNCN 44
                                  33344444477888888885 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.8e-05
                        Fer4_8   2 lekCieCgaCqsaCpv 17 
                                   ++kC+eCg C + Cpv
  gi|91773303|ref|YP_565995.1| 606 ASKCTECGICLKVCPV 621
                                   5678888888888876 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 9.3e-05
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhl 25 
                                   ++Ci Cg C++ C vl+ ++k l
  gi|91773303|ref|YP_565995.1| 637 DSCISCGKCTDGCVVLKYSDKIL 659
                                   58***********9999887754 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.1   2.1e-06    0.0022       8      21 ..     607     620 ..     602     621 .. 0.91
   2 !   11.8   3.6    0.0002      0.21       4      20 ..     634     649 ..     631     650 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                    +C++Cg+C+++CP
  gi|91773303|ref|YP_565995.1| 607 SKCTECGICLKVCP 620
                                   59************ PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                        Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                   ++  d+Ci+Cg+C++ C
  gi|91773303|ref|YP_565995.1| 634 YI-NDSCISCGKCTDGC 649
                                   44.488*********99 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.2e-06    0.0076      14      63 ..     162     209 ..     158     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-06
                                   HTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHC CS
                           PUA  14 lsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakik 63 
                                   l+g+++    + +   d++ gd V +v++  +lv+vG+++++s+ +a+++
  gi|91773303|ref|YP_565995.1| 162 LNGKKVSSELIESSTNDIKTGDPVIVVSG--NLVGVGISLVDSDNMATAD 209
                                   5677888888888899********99998..***************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 ?   12.4   3.4   0.00017      0.18      41      58 ..     604     621 ..     580     624 .. 0.71
   2 ?   12.5   1.9   0.00016      0.17       1      19 [.     608     626 ..     608     637 .. 0.77
   3 ?    5.8   3.3     0.019        20      44      56 ..     637     649 ..     622     651 .. 0.77
   4 ?    4.4   3.9     0.051        54       2      14 ..     639     651 ..     638     658 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                       Fer4_17  41 ekaslCieCgeCerkCPq 58 
                                    +as+C+eCg C ++CP 
  gi|91773303|ref|YP_565995.1| 604 LRASKCTECGICLKVCPV 621
                                   478999999999999995 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                       Fer4_17   1 rCiqCgyClpeCpsyeayd 19 
                                   +C++Cg Cl++Cp +++  
  gi|91773303|ref|YP_565995.1| 608 KCTECGICLKVCPVNAIEL 626
                                   6999999999999987754 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.019
                       Fer4_17  44 slCieCgeCerkC 56 
                                   ++Ci+Cg+C+  C
  gi|91773303|ref|YP_565995.1| 637 DSCISCGKCTDGC 649
                                   6888888888888 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.051
                       Fer4_17   2 CiqCgyClpeCps 14 
                                   Ci+Cg C++ C  
  gi|91773303|ref|YP_565995.1| 639 CISCGKCTDGCVV 651
                                   7777777777765 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.7e-05      0.06       3      68 ..     269     330 ..     267     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                   EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H CS
                    ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv 68 
                                    v +SgG DS++ l l+ +  k  g +++a+ ++ g+     e  e+v++ c++ +i+l+ +k++ 
  gi|91773303|ref|YP_565995.1| 269 HVSFSGGKDSLVVLDLTLSALK--GRDVRAFFLNTGIE--FPETVEFVHSHCENRGIELIESKAEN 330
                                   699*************999965..7899*****99996..556789***********999888775 PP

>> UPF0113  UPF0113 PUA 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      63 ..     156     212 ..     152     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                       UPF0113   7 kaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt.k.aspgkiv 63 
                                   k+ k  L G++v  e i++ t ++k+++ v+V++ n  ++G+G++  d+ + a ++++v
  gi|91773303|ref|YP_565995.1| 156 KKTKMHLNGKKVSSELIESSTNDIKTGDPVIVVSGN--LVGVGISLVDSdNmATADCPV 212
                                   55666688************************8877..899999988886556666655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.7    0.0038         4      76      95 ..     603     622 ..     575     623 .. 0.70
   2 ?    5.1   1.9     0.038        40      80      93 ..     637     650 ..     629     653 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0038
                       Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                      +s+C+ Cg C ++cpv+
  gi|91773303|ref|YP_565995.1| 603 LLRASKCTECGICLKVCPVN 622
                                   34778888888888888875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.038
                       Fer4_22  80 sgCvGCgRCieacp 93 
                                    +C+ Cg+C++ c 
  gi|91773303|ref|YP_565995.1| 637 DSCISCGKCTDGCV 650
                                   56888888887775 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 ?    5.9   2.8     0.017        18       4      17 ..     607     620 ..     606     622 .. 0.92
   2 ?    6.7   1.5      0.01        11       1      16 [.     635     649 ..     635     661 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                       Fer4_13   4 dtCiacgaCvelaP 17 
                                   ++C++cg+C +++P
  gi|91773303|ref|YP_565995.1| 607 SKCTECGICLKVCP 620
                                   68***********9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                       Fer4_13   1 VDrdtCiacgaCvela 16 
                                   ++ d+Ci+cg+C + +
  gi|91773303|ref|YP_565995.1| 635 IN-DSCISCGKCTDGC 649
                                   56.9********8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4516.06
//
Query:       gi|91773304|ref|YP_565996.1|  [L=455]
Description: oxidoreductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-44  149.5   5.6    4.1e-44  148.9   5.6    1.3  1  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
    1.6e-35  122.7   2.2    2.5e-35  122.1   2.2    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.1e-12   46.2   3.6    2.7e-06   27.8   0.3    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.9e-11   43.8   1.5    7.5e-06   25.4   0.0    3.5  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-08   35.2   0.5     0.0021   18.4   0.0    2.6  2  NAD_binding_7   Putative NAD(P)-binding
    6.4e-08   32.7   0.6    6.4e-08   32.7   0.6    1.9  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.8e-07   30.1   1.8    0.00063   19.1   0.0    2.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    9.1e-07   28.6   3.6    0.00013   21.4   0.1    2.4  2  FAD_oxidored    FAD dependent oxidoreductase
    1.8e-06   27.4   0.8    4.8e-05   22.7   0.2    2.5  2  Thi4            Thi4 family
    9.6e-06   25.1   0.4    7.3e-05   22.2   0.1    2.0  2  FAD_binding_3   FAD binding domain
    2.1e-05   23.8   2.5    2.1e-05   23.8   2.5    2.5  3  FAD_binding_2   FAD binding domain
    3.8e-05   23.0   2.5     0.0018   17.5   0.2    2.9  3  GIDA            Glucose inhibited division protein A
    5.4e-05   22.1   0.4    5.4e-05   22.1   0.4    2.0  2  HI0933_like     HI0933-like protein
    0.00013   21.4   0.3    0.00013   21.4   0.3    1.9  2  Amino_oxidase   Flavin containing amine oxidoreductase
    0.00031   20.8   0.1        5.6    7.0   0.0    4.5  4  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    0.00063   19.8   1.0       0.07   13.1   0.3    3.1  3  NAD_binding_9   FAD-NAD(P)-binding
    0.00088   19.0   0.8    0.00088   19.0   0.8    2.7  3  DAO             FAD dependent oxidoreductase
     0.0012   19.4   1.6        1.1    9.9   0.1    3.0  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0025   17.3   0.2        2.1    7.7   0.0    2.9  3  PALP            Pyridoxal-phosphate dependent enzyme
     0.0046   16.3   0.1          1    8.7   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0048   16.7   0.2        1.3    8.7   0.0    2.3  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
  ------ inclusion threshold ------
      0.024   14.5   0.4        1.5    8.6   0.2    2.4  2  Rossmann-like   Rossmann-like domain
      0.027   15.1   0.6      0.027   15.1   0.6    2.4  2  Fer4_7          4Fe-4S dicluster domain
      0.027   14.3   0.3        0.3   11.0   0.1    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.038   13.6   0.2        1.6    8.3   0.0    3.1  3  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.04   14.2   0.6         10    6.4   0.0    2.9  2  TrkA_N          TrkA-N domain
      0.045   12.9   0.1        4.3    6.4   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.065   12.1   1.0       0.12   11.2   0.2    1.7  2  Trp_halogenase  Tryptophan halogenase
        0.3   10.1   3.0       0.14   11.2   0.3    1.8  2  Lycopene_cycl   Lycopene cyclase protein
          4    7.7   8.4       0.18   11.9   2.0    2.1  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 !  148.9   5.6   6.9e-47   4.1e-44       1     111 [.      15     124 ..      15     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 6.9e-47
                                   HTTS-S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-GGGTG CS
                       Fer4_20   1 raknfkevalglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpqeelC 81 
                                   r++nf+evalg+tee+a+ eA+RCl+Ck+++cv+gCPv+idip+fi+ki+eg+++ea++iik+tn+lpavcgrvCpqee+C
  gi|91773304|ref|YP_565996.1|  15 RITNFDEVALGYTEEQAILEAERCLECKNPKCVEGCPVNIDIPGFISKIKEGDFQEAINIIKATNILPAVCGRVCPQEEQC 95 
                                   6789***************************************************************************** PP

                                   CCS-GGGTTB.----HHHHHHHHHHHHHHT CS
                       Fer4_20  82 egaCvlekkgkepvaigklerfvadaaree 111
                                   e+ C+l+kk+ ep+aig+ler +ad +r+ 
  gi|91773304|ref|YP_565996.1|  96 EKLCILGKKS-EPIAIGRLERICADIERKV 124
                                   ******9777.**************99875 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 !  122.1   2.2   4.2e-38   2.5e-35       2     294 .]     138     442 ..     137     442 .. 0.83

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 4.2e-38
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgk 82 
                                    v+++G+GpAGl+aa +la+ag+ vt++   ++++  g +l + + +++ ++ i++e+v+    +i++l +  ++++  g+
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKAGHSVTIF---EALHEAGGVLVYGIPEFRLPKAIVKEEVD----HIRKLGADIKMDYVIGR 211
                                   69**************************...88999999999**********99996544....68888884455565666 PP

                                   EEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC..TTBEECCSECHHHHHHCCSS-T........SEEEEES-SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx RF
                   Pyr_redox_2  83 kkvklekkkegdeekiaydklvlAtGs.sprdlgipGv.aenvgklvrtldsaealklkllp........krivvvGgGyi 153
                                     ++l       + +  +d+++l tG+  p+ +gi+G+  ++v+   + l+ ++ +k  +++         +++vvGgG++
  gi|91773304|ref|YP_565996.1| 212 -ILTLD------QLTDRFDAVFLGTGAgLPKFMGIEGEnLNGVYSANEFLTRVNLMKAYNNDfdtpikrgSNVIVVGGGNV 285
                                   .77774......34679*********8467777*****4344444556677777777777779999999************ PP

                                   HHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.........EEEEEETTSC CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx RF
                   Pyr_redox_2 154 GvElAaalaklgke.vtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.........klevvledge 224
                                   +++ A  + +lg++ v +v++r+         ++++  e+ ++eG+ ++l t++++i++ ++         k  ++l++ +
  gi|91773304|ref|YP_565996.1| 286 AMDAARSALRLGADeVSIVYRRSDEE----LPARREEIEHAKEEGIVFRLLTNPVRIIEGENmsvngveciK--MELGEPD 360
                                   ***********8866******99986....45777777999999**************99989999666441..5555555 PP

                                   E...............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHH CS
                                   x...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 225 e...............idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaA 290
                                                   +dad v++a+G +p++ +++ + gle++++g ivvde++ ++++g+ a GD +   +g +++  A
  gi|91773304|ref|YP_565996.1| 361 DsgrrrpevvegsehiVDADIVIMAIGTSPNPIIFDGSKGLEVTPWGTIVVDESGMSSIEGVCAGGDAV---TGAATVISA 438
                                   5666677777777777****************99889******************************99...888888888 PP

                                   HHHH CS
                                   xxxx RF
                   Pyr_redox_2 291 vqqG 294
                                   + +G
  gi|91773304|ref|YP_565996.1| 439 MGAG 442
                                   7765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2     4e-06    0.0024       2      33 ..     139     170 ..     138     217 .. 0.90
   2 !   27.8   0.3   4.5e-09   2.7e-06       1      77 [.     276     350 ..     276     353 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdk 33 
                                   v++vG+G  gl +A+ la+ g++Vt++e+  +
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDLAKAGHSVTIFEALHE 170
                                   89*************************98766 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 4.5e-09
                                   EEEEECSSHHHHHHHHHHHHTT.SEEEEEESS.SSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelg.kkVtvvers.dkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvk 77 
                                   +v+vvGgG++++++A  + +lg ++V++v r+ d+ l      a+++  e+ +++gi ++l t++++i + e+  v++v+
  gi|91773304|ref|YP_565996.1| 276 NVIVVGGGNVAMDAARSALRLGaDEVSIVYRRsDEEL-----PARREEIEHAKEEGIVFRLLTNPVRIIEGENMsVNGVE 350
                                   599*******************67**99988714455.....7999999******************9977776688886 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 !   13.9   0.3     4e-05     0.024       2      29 ..     141     167 ..     140     177 .. 0.90
   2 !   25.4   0.0   1.3e-08   7.5e-06     151     296 ..     261     418 ..     214     422 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                   Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEk 29 
                                   I+G GPaGl+aa  l kag  +++i E 
  gi|91773304|ref|YP_565996.1| 141 IVGSGPAGLTAASDLAKAGH-SVTIFEA 167
                                   9******************9.7999985 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.3e-08
                   Pyr_redox_3 151 khyskvkefhkyagqkvvViGgknSavDaAlelvrkga.eVtvvtrgseiekeesdpsyslkpdienrl.eelvke..... 224
                                   k y ++ +    +g +v+V+Gg+n a+DaA    r ga eV++v+r+s  e        +++   e+ +  +l+++     
  gi|91773304|ref|YP_565996.1| 261 KAYNNDFDTPIKRGSNVIVVGGGNVAMDAARSALRLGAdEVSIVYRRSDEEL--PARREEIEHAKEEGIvFRLLTNpvrii 339
                                   233333333334589*********************9846******974332..222233333333222022222233344 PP

                   Pyr_redox_3 225 ..ekikvlfnaevk.eikekeeey..kvktedgkkvev.kddvvlatGykpdlsflkk.slfeldedgrpvlteeteet 296
                                     e++ v   +++k e+ e++ +   + +  +g+++ v  d v++a+G +p+  +++  +++e + +g++v++e+ +++
  gi|91773304|ref|YP_565996.1| 340 egENMSVNGVECIKmELGEPDDSGrrRPEVVEGSEHIVdADIVIMAIGTSPNPIIFDGsKGLEVTPWGTIVVDESGMSS 418
                                   4455666655555433444444331133455555555524555566999999888887788999999999999999887 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 !   14.4   0.1   6.5e-05     0.039       3      36 ..     132     165 ..     130     214 .. 0.89
   2 !   18.4   0.0   3.6e-06    0.0021       7      70 ..     274     387 ..     272     393 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.5e-05
                 NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvv 36 
                                    + +gk+v +vG G+ +++ ++ l++ag  vt+ 
  gi|91773304|ref|YP_565996.1| 132 AQSTGKTVAIVGSGPAGLTAASDLAKAGHSVTIF 165
                                   6889****************************96 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.6e-06
                 NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagak.vtvvapevkeele...elvklaeee............................. 54 
                                   g +v+vvGgG+vA+  +r+ l+ ga+ v +v  ++ eel+   e +++a+ee                             
  gi|91773304|ref|YP_565996.1| 274 GSNVIVVGGGNVAMDAARSALRLGADeVSIVYRRSDEELParrEEIEHAKEEgivfrlltnpvriiegenmsvngvecikm 354
                                   789*********************854999988865555555544555555567777777777776666777666666666 PP

                 NAD_binding_7  55 ...............l..ekdlegadlviaatd 70 
                                                  +  ++++ +ad+vi+a+ 
  gi|91773304|ref|YP_565996.1| 355 elgepddsgrrrpevVegSEHIVDADIVIMAIG 387
                                   666666666665554223455888999998875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.6   1.1e-10   6.4e-08       1      33 [.     141     173 ..     141     180 .. 0.97
   2 ?   -1.2   0.1       4.2   2.5e+03       1      20 [.     279     298 ..     279     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.1e-10
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33 
                                   IvG+G +Gl+aA+ Lakag++v+++e+ +  GG
  gi|91773304|ref|YP_565996.1| 141 IVGSGPAGLTAASDLAKAGHSVTIFEALHEAGG 173
                                   9*******************************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.2
                                   EE--SHHHHHHHHHHHCCTE CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagf 20 
                                   +vG+G  ++ aA+ + + g+
  gi|91773304|ref|YP_565996.1| 279 VVGGGNVAMDAARSALRLGA 298
                                   8****999999987777666 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 !    9.4   0.7     0.001       0.6      30      59 ..     138     167 ..     125     182 .. 0.89
   2 !   19.1   0.0   1.1e-06   0.00063      28      99 ..     274     386 ..     250     414 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDv 59 
                                   +v ++G G aGl A++  ++ g +Vt+++ 
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKAGHSVTIFEA 167
                                   699************************986 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.1e-06
                                   --EEEEESTSHHHHHHHHHHHHTT-E.EEEEESS.....HHHHHHHHHTTTCECEE......................... CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgak.VtvlDvr.....parleqleslgakfvev......................... 77 
                                    ++v+v+GgG + + A++ a +lga+ V ++  r     par+e++e+ +++ +                           
  gi|91773304|ref|YP_565996.1| 274 GSNVIVVGGGNVAMDAARSALRLGADeVSIVYRRsdeelPARREEIEHAKEEGIVFrlltnpvriiegenmsvngvecikm 354
                                   578**********************63666654422222466777777666655558899999999999999999999999 PP

                                   ..........HCHHHHHHHHHHHH-SEEEE-- CS
                   AlaDh_PNT_C  78 ..........lksqeellaeavkeadvvigtv 99 
                                             ++ +  + +e++ +ad+vi ++
  gi|91773304|ref|YP_565996.1| 355 elgepddsgrRRPEVVEGSEHIVDADIVIMAI 386
                                   99999998766666667788999999999885 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   2.2e-07   0.00013       2      42 ..     139     179 ..     138     198 .. 0.93
   2 !    7.6   0.6    0.0035       2.1       2      28 ..     277     304 ..     276     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.2e-07
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42 
                                   v +vG+gpaG++AA   a+aG +v + e     GG l  g+
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDLAKAGHSVTIFEALHEAGGVLVYGI 179
                                   89*********************************998775 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0035
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGa.kvlLv 28 
                                   v+VvGGg   + AA +A r Ga +v +v
  gi|91773304|ref|YP_565996.1| 277 VIVVGGGNVAMDAARSALRLGAdEVSIV 304
                                   9********************9445555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2     8e-08   4.8e-05      19      76 ..     138     196 ..     130     207 .. 0.82
   2 ?    2.4   0.0      0.13        80       5      35 ..     260     292 ..     257     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8e-08
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB..SEEEEETTTHHH CS
                          Thi4  19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf..saivvrkpakel 76 
                                    v+ivG+G++GLtaa  lak+ +  v+i+e+    GG    G   f   + +v+++ +++
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKA-GHSVTIFEALHEAGGVLVYGIPEFrlPKAIVKEEVDHI 196
                                   699******************.*********99999988888766622477777777665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHTE..EEEEEE--SHHHHHHHHH CS
                          Thi4   5 veryfedllkyae..sDvvivGaGssGLtaayy 35 
                                   +++y +d+++ ++  s+v++vG+G   + aa+ 
  gi|91773304|ref|YP_565996.1| 260 MKAYNNDFDTPIKrgSNVIVVGGGNVAMDAARS 292
                                   56666666665543389***********99986 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   0.1   1.2e-07   7.3e-05       3      34 ..     138     169 ..     137     172 .. 0.92
   2 ?    0.5   0.0      0.46   2.8e+02       3      35 ..     276     309 ..     275     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                   +V+IVG+GpaGl++a+ L++aG +v++ e   
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKAGHSVTIFEALH 169
                                   699************************99765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.46
                                   EEEEE--SHHHHHHHHHHHHTTHH.EEEEESSSS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvr.vvlvekrst 35 
                                   +V++VG+G + + +a+   + G + v +v +rs+
  gi|91773304|ref|YP_565996.1| 276 NVIVVGGGNVAMDAARSALRLGADeVSIVYRRSD 309
                                   69**************999999985666666665 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   2.5   3.5e-08   2.1e-05       2      38 ..     139     175 ..     138     179 .. 0.92
   2 ?    1.4   0.1      0.22   1.3e+02       2      28 ..     277     304 ..     276     310 .. 0.87
   3 ?   -2.1   0.0       2.5   1.5e+03     173     240 ..     345     444 ..     319     452 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.5e-08
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38 
                                   v ++GsG AGL+AA  +a+aG++v++ e  +e gg +
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDLAKAGHSVTIFEALHEAGGVL 175
                                   89****************************9999865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                                   EEEE--SHHHHHHHHHHHHTTT.-EEEE CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavv 28 
                                   viV+G+G   + AA +a + G+ +v +v
  gi|91773304|ref|YP_565996.1| 277 VIVVGGGNVAMDAARSALRLGAdEVSIV 304
                                   9*************99999998777666 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
                                   EEEEEEEEET...............TTTCEEEEEESEEEE-----GG...........................GSSSBSS CS
                 FAD_binding_2 173 rvtGavvenp...............esgrevrirakavvlatgGfgr.................allkellgaaaeaettn 221
                                    v+G+++ ++                +g+e+ + a+ v++a g  ++                   ++e   +  e  + +
  gi|91773304|ref|YP_565996.1| 345 SVNGVECIKMelgepddsgrrrpevVEGSEHIVDADIVIMAIGTSPNpiifdgskglevtpwgtIVVDESGMSSIEGVCAG 425
                                   666666665566666655555555555555555666666666666666666666555555555555555556667777777 PP

                                   GTT-S-HHHHHHHCTTSSE CS
                 FAD_binding_2 222 apavtGdglalalragaal 240
                                     avtG ++ + ++ +++l
  gi|91773304|ref|YP_565996.1| 426 GDAVTGAATVISAMGAGKL 444
                                   7777777776666666555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2     3e-06    0.0018       2      58 ..     139     195 ..     138     205 .. 0.73
   2 ?    3.7   0.0     0.045        27       1      24 [.     276     299 ..     276     313 .. 0.88
   3 ?    0.0   0.0      0.59   3.5e+02     130     156 ..     368     394 ..     333     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3e-06
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SS.SSEEE-TTHHHHHHHHHH CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsC.npsiggiakgllvrEida 58 
                                   v ++G G AG+ AA  +a++G++v+++    +  + l++  p ++ + k+++++E+d+
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDLAKAGHSVTIFEALHEAGGVLVYgIPEFRLP-KAIVKEEVDH 195
                                   89*************************55444444444425666654.6666666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.045
                                   CEEEE-SSHHHHHHHHHHHHTT-- CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGak 24 
                                   +viV+GgG   + AA  a rlGa+
  gi|91773304|ref|YP_565996.1| 276 NVIVVGGGNVAMDAARSALRLGAD 299
                                   59*******************985 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.59
                                   EEEETTS-EEEECEEEE--TT-BT-EE CS
                          GIDA 130 gvvtedgetikakavviatGtflkgki 156
                                    vv  +++++ a++v++a Gt  +  i
  gi|91773304|ref|YP_565996.1| 368 EVVEGSEHIVDADIVIMAIGTSPNPII 394
                                   57888899999*********9444444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.4   9.1e-08   5.4e-05       2      36 ..     138     172 ..     137     177 .. 0.92
   2 ?    0.1   0.1      0.42   2.5e+02       2      24 ..     276     298 ..     275     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.1e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                   +v+++G G+AGl aA  +ak+g++V+++e+ +++g
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKAGHSVTIFEALHEAG 172
                                   69***************************988776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.42
                                   SEEEE--SHHHHHHHHHHHHTT- CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgk 24 
                                   +viv+GgG   + aA sa + g+
  gi|91773304|ref|YP_565996.1| 276 NVIVVGGGNVAMDAARSALRLGA 298
                                   79**********99999976654 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.3   2.2e-07   0.00013       2      28 ..     147     173 ..     146     176 .. 0.97
   2 ?   -0.7   0.5       1.1   6.7e+02     418     451 ..     418     449 ..     410     450 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                 Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                   aGL+aA+ L+ aG++Vt++Ea   +GG
  gi|91773304|ref|YP_565996.1| 147 AGLTAASDLAKAGHSVTIFEALHEAGG 173
                                   9*************************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                   CSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                 Amino_oxidase 418 gdprlffAGehtsreypgtvegAilSGlraAari 451
                                    + +++  G++++    +tv  A+ +G+ aA+ i
  gi|91773304|ref|YP_565996.1| 418 SIEGVCAGGDAVT--GAATVISAMGAGKLAADTI 449
                                   47899999***99..9999************987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.052        31       9      42 ..     133     165 ..     127     172 .. 0.87
   2 ?   -0.9   0.0       2.7   1.6e+03      46      86 ..     193     232 ..     187     240 .. 0.76
   3 !    7.0   0.0    0.0094       5.6      12      46 ..     274     308 ..     267     335 .. 0.87
   4 ?    2.4   0.0      0.24   1.5e+02      70      90 ..     373     394 ..     366     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.052
                                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                   + ++k+v ++G G  +  +a+ L+++g   v+++
  gi|91773304|ref|YP_565996.1| 133 QSTGKTVAIVGSGPAGLTAASDLAKAGHS-VTIF 165
                                   56789*******************99887.7775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                  Shikimate_DH  46 lerakelaeelkgeeiealkleelkellaeadvvisatase 86 
                                   +++ ++l  ++k + + + ++  l++l +++d v+  t++ 
  gi|91773304|ref|YP_565996.1| 193 VDHIRKLGADIKMD-YVIGRILTLDQLTDRFDAVFLGTGAG 232
                                   56667777777444.777788889999999*****999985 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0094
                                   T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                  Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46 
                                   +++v+++G G++a  +a+  l+ g+++v ++ R  
  gi|91773304|ref|YP_565996.1| 274 GSNVIVVGGGNVAMDAARSALRLGADEVSIVYRRS 308
                                   679*************************9998865 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.24
                                   HHHHHT-SEEEE-SS.SSS-SB CS
                  Shikimate_DH  70 kellaeadvvisata.seepil 90 
                                   +e++ +ad+vi+a++ s++pi+
  gi|91773304|ref|YP_565996.1| 373 SEHIVDADIVIMAIGtSPNPII 394
                                   68999********973678877 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 !   13.1   0.3   0.00012      0.07       1      39 [.     140     174 ..     140     180 .. 0.87
   2 ?   -0.6   0.0       1.9   1.2e+03     130     155 ..     206     231 ..     186     232 .. 0.69
   3 ?    3.2   0.0      0.13        80     131     155 ..     363     388 ..     344     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                 NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgag 39 
                                   aivG Gp+Gl+++  L++       +++t+f+  +e+g  
  gi|91773304|ref|YP_565996.1| 140 AIVGSGPAGLTAASDLAKA-----GHSVTIFEAlHEAGGV 174
                                   8****************99.....599******9998834 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                 NAD_binding_9 130 radgqavlladgaslaadaVvLAlGh 155
                                   +    ++l+ d+ + ++daV+L +G 
  gi|91773304|ref|YP_565996.1| 206 DYVIGRILTLDQLTDRFDAVFLGTGA 231
                                   44445677888889999999999995 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
                 NAD_binding_9 131 adgq.avlladgaslaadaVvLAlGh 155
                                   ++++ +v++ +++ ++ad V++A+G 
  gi|91773304|ref|YP_565996.1| 363 GRRRpEVVEGSEHIVDADIVIMAIGT 388
                                   44445899999999**********96 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.8   1.5e-06   0.00088       2      33 ..     139     172 ..     138     217 .. 0.93
   2 ?    0.1   0.5      0.77   4.6e+02       2      29 ..     277     307 ..     276     314 .. 0.85
   3 ?   -2.5   0.0       4.9   2.9e+03     241     269 ..     389     428 ..     369     438 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                   v+i+G+G +Gl++A +La++g  Vt++e+ ++ag
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDLAKAGhsVTIFEALHEAG 172
                                   99******************99******987777 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.77
                                   EEEECTSHHHHHHHHHHHHTT...EEEEESS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg...Vtllekg 29 
                                   v+++GGG + + +A+ + r g   V ++ ++
  gi|91773304|ref|YP_565996.1| 277 VIVVGGGNVAMDAARSALRLGadeVSIVYRR 307
                                   9********9999999988888898888776 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.9
                                   EEEEEEEETTTTEEEEEE............TTSEEEEEESS CS
                           DAO 241 lpvpetdddgrgvyvtpr............kdgrvlvGgta 269
                                    p+p++ d+++g++vtp+             +g v++Gg+a
  gi|91773304|ref|YP_565996.1| 389 SPNPIIFDGSKGLEVTPWgtivvdesgmssIEG-VCAGGDA 428
                                   566678888999999998666666666665445.6666655 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 ?    7.5   0.1      0.01       6.1       1      31 [.     138     165 ..     138     172 .. 0.90
   2 !    9.9   0.1    0.0018       1.1       3      47 ..     278     320 ..     276     392 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                 F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivva 31 
                                   +++i+G+G  g + as l++ag   h++++ 
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKAG---HSVTIF 165
                                   58********************...999975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0018
                                   EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                 F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47 
                                    ++G+Gn++   a+ +l+ g  + e+ ++ +r+ e++ + +ee++
  gi|91773304|ref|YP_565996.1| 278 IVVGGGNVAMDAARSALRLG--ADEVSIVYRRSDEELPARREEIE 320
                                   467*****************..9999999******9999888887 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0035       2.1      52     104 ..     134     203 ..     113     206 .. 0.90
   2 ?   -0.6   0.0       1.2   7.2e+02     151     168 ..     215     232 ..     208     239 .. 0.85
   3 ?    5.9   0.0     0.012       7.2      53      95 ..     272     317 ..     242     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0035
                                   TTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE..................EETTS-HHHHHHHHHTT-EE CS
                          PALP  52 gtgaktvveassGNhgralAaaaallGlkvtiv..................vpadaspekvallrllGaev 104
                                      +ktv+  +sG +g+ +A   a++G  vti+                  +p+   +e v+ +r lGa++
  gi|91773304|ref|YP_565996.1| 134 S-TGKTVAIVGSGPAGLTAASDLAKAGHSVTIFealheaggvlvygipefrLPKAIVKEEVDHIRKLGADI 203
                                   3.689*******************************9999999999999999999999***********98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                                   HHHTTTTEEEEEEE-SSS CS
                          PALP 151 leqlggkpdavvvpvGgG 168
                                   l+ql +++dav++++G G
  gi|91773304|ref|YP_565996.1| 215 LDQLTDRFDAVFLGTGAG 232
                                   38999***********98 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.012
                                   TTTSEEEEEBSSHHHHHHHHHHHHHT-.EEEEEEETTS-..HHHHH CS
                          PALP  53 tgaktvveassGNhgralAaaaallGl.kvtivvpadas..pekva 95 
                                   +++ +v++ ++GN ++ +A  a +lG  +v iv  +++   p++++
  gi|91773304|ref|YP_565996.1| 272 KRGSNVIVVGGGNVAMDAARSALRLGAdEVSIVYRRSDEelPARRE 317
                                   68899*********************99999998888774545554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0017         1      31      67 ..     131     167 ..     113     184 .. 0.87
   2 ?    5.3   0.0     0.019        12      35      75 ..     273     314 ..     248     328 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                                   BS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                  2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                     + +gktv+i+G G  G ++a  l++ g  v++++ 
  gi|91773304|ref|YP_565996.1| 131 VAQSTGKTVAIVGSGPAGLTAASDLAKAGHSVTIFEA 167
                                   56779************************99998765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                   TTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCH CS
                  2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeee 75 
                                   +g+ v ++G G+++  +a+ +  +g+ +v ++ r+ ++e  +
  gi|91773304|ref|YP_565996.1| 273 RGSNVIVVGGGNVAMDAARSALRLGAdEVSIVYRRSDEELPA 314
                                   7999**********************7665555554433333 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 ?    5.6   0.1     0.018        11      29      59 ..     133     163 ..     122     196 .. 0.87
   2 !    8.7   0.0    0.0021       1.3      29      62 ..     271     304 ..     250     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
                                   -STTEEEEEE--SHHHHHHHHHHHHCT-EEE CS
                 ELFV_dehydrog  29 slegkrvaisGsGnvgsyaallltelgakvv 59 
                                   + +gk+vai GsG  g  aa  l+++g++v+
  gi|91773304|ref|YP_565996.1| 133 QSTGKTVAIVGSGPAGLTAASDLAKAGHSVT 163
                                   4789*******************99998875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                                   -STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEE CS
                 ELFV_dehydrog  29 slegkrvaisGsGnvgsyaallltelgakvvavs 62 
                                     +g++v++ G Gnv+  aa+ + +lga  v+++
  gi|91773304|ref|YP_565996.1| 271 IKRGSNVIVVGGGNVAMDAARSALRLGADEVSIV 304
                                   457899***********************99986 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0026       1.5       8      45 ..     134     171 ..     126     198 .. 0.84
   2 ?    3.6   0.0     0.097        58      59     110 ..     369     420 ..     356     428 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0026
                 Rossmann-like   8 sarlsvGiisaGrvGtalgaaleraghvvvgisaisaa 45 
                                   s+  +v i+++G  G + +  l++agh v+   a+ +a
  gi|91773304|ref|YP_565996.1| 134 STGKTVAIVGSGPAGLTAASDLAKAGHSVTIFEALHEA 171
                                   555689************************99998877 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.097
                 Rossmann-like  59 vlevedvaaraellllavPdaelpglvkglaatgavraGtivahtsganGve 110
                                   v+e  + +  a+++++a+  +  p + +g    +++  Gtiv+  sg   +e
  gi|91773304|ref|YP_565996.1| 369 VVEGSEHIVDADIVIMAIGTSPNPIIFDGSKGLEVTPWGTIVVDESGMSSIE 420
                                   5677788999***********************************9987765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.6   4.4e-05     0.027      29      52 .]      29      54 ..       6      54 .. 0.77
   2 ?    0.0   0.5       2.2   1.3e+03      44      50 ..      85      91 ..      71     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-05
                        Fer4_7 29 ekveidpekClgCga..CvavCPtga 52
                                  e++ +++e+Cl C++  Cv+ CP+++
  gi|91773304|ref|YP_565996.1| 29 EQAILEAERCLECKNpkCVEGCPVNI 54
                                  5556789*******999******986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.2
                        Fer4_7 44 CvavCPt 50
                                  C +vCP 
  gi|91773304|ref|YP_565996.1| 85 CGRVCPQ 91
                                  4445543 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   0.1    0.0005       0.3       1      32 [.     138     169 ..     138     219 .. 0.90
   2 ?    0.7   0.0      0.69   4.1e+02       1      44 [.     276     321 ..     276     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdise 32 
                                   +va++G+G  G   a+ +a+ag++V++++  +
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKAGHSVTIFEALH 169
                                   69*************************98755 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.69
                                   EEEEE--SCCHHHHHHHHHHTT-.EEEEE-S.-HHHHHHHHHHHHH CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagl.eVvlvdi.seealekalekiek 44 
                                   +v v+G G +    a  +++ g  eV +v + s+e l + +e+ie+
  gi|91773304|ref|YP_565996.1| 276 NVIVVGGGNVAMDAARSALRLGAdEVSIVYRrSDEELPARREEIEH 321
                                   588***************9999834776655367777777777776 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 ?    8.3   0.0    0.0027       1.6       2      28 ..     138     164 ..     137     170 .. 0.93
   2 ?    0.1   0.0      0.83     5e+02     137     162 ..     320     344 ..     300     349 .. 0.71
   3 ?    0.1   0.0      0.89   5.3e+02      70      87 ..     372     389 ..     361     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                                   EEEEE--STTHHHHHHHHHHCTSEEEE CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevig 28 
                                   +++++G+G  Gl+ a  la++gh v++
  gi|91773304|ref|YP_565996.1| 138 TVAIVGSGPAGLTAASDLAKAGHSVTI 164
                                   79***********************96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.83
                                   HHHCSS-TTCEEEEE------TTSHH CS
                UDPG_MGDP_dh_N 137 eeaskkkgvdfdvvsnPEflregsav 162
                                   e+a+ ++g+ f++++nP ++ eg+ +
  gi|91773304|ref|YP_565996.1| 320 EHAK-EEGIVFRLLTNPVRIIEGENM 344
                                   3233.348999999999999999865 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.89
                                   HHHHHHC-SEEEE----- CS
                UDPG_MGDP_dh_N  70 vekaveeadvifiaVgTP 87 
                                    ++++ +ad++++a+gT 
  gi|91773304|ref|YP_565996.1| 372 GSEHIVDADIVIMAIGTS 389
                                   578999**********95 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.017        10       1      29 [.     139     167 ..     139     172 .. 0.86
   2 ?    4.9   0.1     0.049        29       1      41 [.     277     318 ..     277     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                   ++i+G G  G + a  L + g+ +v++ + 
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDLAKaGH-SVTIFEA 167
                                   68*****************666.6**9986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.049
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg 41 
                                   +i++G G+v++  a+   + g ++v+++ ++ +    +r+e+
  gi|91773304|ref|YP_565996.1| 277 VIVVGGGNVAMDAARSALRlGADEVSIVYRRSDEELPARREE 318
                                   79*************999988888999988877655555555 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.054        32     188     218 ..     133     163 ..     112     170 .. 0.84
   2 ?    6.4   0.0    0.0072       4.3     187     226 ..     259     308 ..     213     316 .. 0.73
   3 ?   -2.2   0.0         3   1.8e+03     141     161 ..     371     391 ..     363     453 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.054
                   K_oxygenase 188 llakkriaVvGsGqSaaeifedllrrqkkve 218
                                   + ++k++a+vGsG  +   + dl++  ++v+
  gi|91773304|ref|YP_565996.1| 133 QSTGKTVAIVGSGPAGLTAASDLAKAGHSVT 163
                                   678899*******999999999999877655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0072
                   K_oxygenase 187 e...........llakkriaVvGsGqSaaeifedllrrqkkvelklvtrse 226
                                                +++ +++VvG+G  a + ++ +lr  +  e+++v r++
  gi|91773304|ref|YP_565996.1| 259 LmkaynndfdtpIKRGSNVIVVGGGNVAMDAARSALRLGA-DEVSIVYRRS 308
                                   34444455555678899*****************998865.6888888876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3
                   K_oxygenase 141 egeeeelearnlvlgvGtepk 161
                                   eg+e+ + a  +++++Gt+p+
  gi|91773304|ref|YP_565996.1| 371 EGSEHIVDADIVIMAIGTSPN 391
                                   566677777777777777664 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2    0.0002      0.12       2      32 ..     139     166 ..     138     185 .. 0.89
   2 ?   -1.2   0.0       1.2   7.1e+02       1      27 [.     276     302 ..     276     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlve 32 
                                   + ivG G+aG +aA+ laka+   ++vt+ e
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDLAKAG---HSVTIFE 166
                                   89******************9...7787766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                   EEEEE--SHHHHHHHHHHHHHTTTSSE CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgkle 27 
                                   ++++vGGG  +  aA    + + ++++
  gi|91773304|ref|YP_565996.1| 276 NVIVVGGGNVAMDAARSALRLGADEVS 302
                                   599******999999776666655454 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00023      0.14       2      32 ..     139     167 ..     138     172 .. 0.92
   2 ?   -4.0   0.2       9.2   5.5e+03     121     143 ..     420     443 ..     410     447 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvliea 32 
                                   v+++G+GpAgl  A  l  ak+g +v++ ea
  gi|91773304|ref|YP_565996.1| 139 VAIVGSGPAGLTAASDL--AKAGHSVTIFEA 167
                                   89***************..999999999987 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.2
                 Lycopene_cycl 121 lvvleggrkir.arlvvdarglas 143
                                     v++gg  +  a +v+ a g+++
  gi|91773304|ref|YP_565996.1| 420 EGVCAGGDAVTgAATVISAMGAGK 443
                                   457888886542778999999776 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0   0.00031      0.18       5      21 ..      33      51 ..      29      52 .. 0.89
   2 ?   -1.9   0.5       7.7   4.6e+03      16      22 .]      85      91 ..      84      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                        Fer4_2  5 vdtdrCigCg..aCvsaCP 21
                                   +++rC++C+  +Cv  CP
  gi|91773304|ref|YP_565996.1| 33 LEAERCLECKnpKCVEGCP 51
                                  5789*****999******* PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.7
                        Fer4_2 16 CvsaCPa 22
                                  C  +CP+
  gi|91773304|ref|YP_565996.1| 85 CGRVCPQ 91
                                  7789995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2704.08
//
Query:       gi|91773305|ref|YP_565997.1|  [L=283]
Description: ferredoxin-NADP(+) reductase subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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-12   46.0   4.6    5.4e-12   45.3   4.6    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    1.9e-06   28.5   0.0    4.2e-06   27.4   0.0    1.6  1  NAD_binding_1    Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
      0.088   12.9   0.1       0.15   12.2   0.1    1.3  1  NAD_binding_6    Ferric reductase NAD binding domain
       0.16   12.0   0.3       0.31   11.1   0.3    1.4  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   4.6   1.2e-15   5.4e-12       2      42 .]     214     250 ..     213     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.2e-15
                                   ---SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB. CS
               DHODB_Fe-S_bind   2 erMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadevd 42 
                                    +M++G+G+C+gC+v + g    e k++C+dGP+F+a++vd
  gi|91773305|ref|YP_565997.1| 214 PIMVDGTGMCGGCRVNVGG----EVKFACVDGPEFNAKDVD 250
                                   68***************66....59*************995 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 !   27.4   0.0   9.4e-10   4.2e-06       1     108 [.     104     198 ..     104     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.4e-10
                                   EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHH CS
                 NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdal 81 
                                   +++gG+GiaP++   ++  ++    +kv+ + G+r+++ l++++e+ ++    +++  +va+    ++g++g  g+v+d +
  gi|91773305|ref|YP_565997.1| 104 LVGGGVGIAPIYPQAKEYRAA---GNKVISIIGARNKDMLILEDEMIAA----SDE-VLVAT----DDGSKGHHGFVTDLV 172
                                   79***********99999987...689******************9988....443.45666....6666678******99 PP

                                   HHHHHHHSSTTEEEEEECSHHHHHHHH CS
                 NAD_binding_1  82 leellslkkeethvyvCGppgMikavr 108
                                    + l++ ++  + ++  Gpp M++av+
  gi|91773305|ref|YP_565997.1| 173 KQLLDG-DEHIDRIVAIGPPIMMRAVA 198
                                   555555.7788889999*******985 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.2e-05      0.15       3      24 ..     101     122 ..      99     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_6   3 nvllvagGiGitpfisilkdll 24 
                                   +v+lv+gG+Gi+p+++ +k++ 
  gi|91773305|ref|YP_565997.1| 101 TVVLVGGGVGIAPIYPQAKEYR 122
                                   69**************999875 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 ?   11.1   0.3   6.9e-05      0.31      54      73 ..     220     239 ..     212     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.9e-05
                        Fer2_3  54 egiCGscavainGkptlaCt 73 
                                    g+CG c v++ G+++ aC 
  gi|91773305|ref|YP_565997.1| 220 TGMCGGCRVNVGGEVKFACV 239
                                   79*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1999.85
//
Query:       gi|91773306|ref|YP_565998.1|  [L=401]
Description: S-adenosylmethionine synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-176  585.3   1.7   5.6e-176  585.2   1.7    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.2   1.7  3.1e-180  5.6e-176       1     396 []       3     397 ..       3     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 585.2 bits;  conditional E-value: 3.1e-180
                                   --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE CS
               AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGevie 81 
                                   rni+ve+l+++p+e+qe+E+vErKG+GHPDsi+Dg+aeavsral+key++k+gailhhn+D++++vaG+s+p+fgGGev++
  gi|91773306|ref|YP_565998.1|   3 RNIKVEHLHETPIEKQETELVERKGVGHPDSISDGLAEAVSRALCKEYIDKCGAILHHNTDETQIVAGRSRPEFGGGEVLK 83 
                                   79******************************************************************************* PP

                                   -EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEE CS
               AdoMet_Synthase  82 pieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfgvg 162
                                   pi+ ll+grat+e++g +ip+e++al+aa+ey++++++a+dle+d+i+d+klg+gs+dL+dvf+r  ++vp+aNDtSfgvg
  gi|91773306|ref|YP_565998.1|  84 PIYTLLVGRATMEFDGMEIPAETVALQAAREYVRNTIPAMDLERDMIIDCKLGTGSSDLRDVFTR--DHVPMANDTSFGVG 162
                                   *****************************************************************..468*********** PP

                                   EES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHHHHHH CS
               AdoMet_Synthase 163 yaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeeveelakk 243
                                   +ap+sele++v++ter+l ++  kkk+p +GeDiKvmglRe+++i+lT+++ +v r+++d+++Y+++kee++e+v +la+k
  gi|91773306|ref|YP_565998.1| 163 HAPFSELEQVVYNTERQLLTDLKKKKIPGIGEDIKVMGLRENNDISLTICCGMVGRHIDDMDHYINAKEEMTEYVLDLATK 243
                                   ********************************************************************************* PP

                                   HSTTSEEEEEE-TT-BGG..GTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHHHH CS
               AdoMet_Synthase 244 ltkerevevevNtaDkke..eesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvlane 322
                                   +t+ r+v+ ++N+aDk++   ++v+ltvtGtsaE+gDdGsvGRGNR+nGlitp+rpms+EA++GKNP++H+GKiYn+l+++
  gi|91773306|ref|YP_565998.1| 244 YTD-RTVSARINAADKVDggCDCVFLTVTGTSAEMGDDGSVGRGNRSNGLITPSRPMSMEATSGKNPINHIGKIYNLLSTQ 323
                                   ***.************9988899********************************************************** PP

                                   HHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHTTT- CS
               AdoMet_Synthase 323 iakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteeliegk 396
                                   +a+++v+ v++v++v+++llsqiG pid+Plvas+qvi+e+g++++++++e+  +id++le+i++it+++++g+
  gi|91773306|ref|YP_565998.1| 324 MARDVVSAVDEVSDVHIKLLSQIGMPIDQPLVASAQVIPEDGANFAHIQSEAVVVIDDWLENITKITDMVVKGE 397
                                   ***********************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2797.99
//
Query:       gi|91773307|ref|YP_565999.1|  [L=284]
Description: ATP phosphoribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-51  172.3   0.6      1e-50  171.9   0.6    1.2  1  HisG          ATP phosphoribosyltransferase
    1.7e-23   82.5   0.5    4.5e-23   81.2   0.5    1.8  1  HisG_C        HisG, C-terminal domain
     0.0054   16.7   0.1        5.1    7.0   0.0    3.0  2  NMT1          NMT1/THI5 like
  ------ inclusion threshold ------
      0.019   15.1   0.2      0.029   14.5   0.2    1.3  1  P_gingi_FimA  Major fimbrial subunit protein (FimA)


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 !  171.9   0.6   2.2e-54     1e-50       1     159 [.      50     203 ..      50     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 2.2e-54
                                   -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHHHHHH CS
                          HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnlakky 81 
                                   raadip+yV++ga+d+GitG D++ E+  e++ve+lldL++g ++lv+avpees+++s++dl    g+r+aT++p ++++y
  gi|91773307|ref|YP_565999.1|  50 RAADIPEYVQDGAADVGITGLDLISET--ESDVEMLLDLKYGGADLVLAVPEESDISSANDL---DGMRVATEFPGITARY 125
                                   89************************7..468*************************99998...567************* PP

                                   HHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHSHHHHHHHHHHHH CS
                          HisG  82 feekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkkkekieellerlr 159
                                   f+++g+k++++k+sG++E++p++g+aDaIvD+ ++G+TL  n+Lk+ie++++ss  Lian++  k++ekie++ + l+
  gi|91773307|ref|YP_565999.1| 126 FKDLGIKIDVVKVSGACEMTPHVGIADAIVDISSSGTTLVMNHLKVIEKVFSSSIYLIANHETAKTEEKIEHIKTALE 203
                                   **************************************************************999889*****99886 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.5     1e-26   4.5e-23       1      73 []     208     281 ..     208     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1e-26
                                   TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-..SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                        HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspla.degwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                   A+ +++lm+n+p + +++++++lPGl +PT+++++ +e+ vaV+avv+ + ++ +i +LkaaGA dIlv+pie+
  gi|91773307|ref|YP_565999.1| 208 AKAKRYLMMNAPITVVDDLKEVLPGLAGPTIMKVEsKEDIVAVHAVVDADIIFATITKLKAAGAFDILVMPIER 281
                                   899*******************************9899**********************************96 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0011       5.1      32      98 ..      52     116 ..      43     123 .. 0.73
   2 !    6.3   0.0    0.0018       8.2      15      54 ..     125     164 ..     118     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                                   THHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--.EEEEEECCC--SSGGGGTTSEEEE CS
                          NMT1  32 sdatelvasgkadfgvsyqesllaarakglpvvsvaallqepl.sglivlkdsgikspkDLkGkrigy 98 
                                   +d +e+v  g+ad+g++  + +    +   +v ++  l        l+v ++s+i+s +DL+G r+++
  gi|91773307|ref|YP_565999.1|  52 ADIPEYVQDGAADVGITGLDLIS---ETESDVEMLLDLKYGGAdLVLAVPEESDISSANDLDGMRVAT 116
                                   78899999999999999887666...4555666666665544404566677777**********9986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0018
                                   HHHHTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHH CS
                          NMT1  15 YFkeeGldVeivepadpsdatelvasgkadfgvsyqesll 54 
                                   YFk+ G+++++v+ ++ ++ t++v+  +a + +s++ ++l
  gi|91773307|ref|YP_565999.1| 125 YFKDLGIKIDVVKVSGACEMTPHVGIADAIVDISSSGTTL 164
                                   ************************9998888888877776 PP

>> P_gingi_FimA  Major fimbrial subunit protein (FimA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   6.5e-06     0.029      76     146 ..     178     242 ..     155     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.5e-06
                                   EEEEEEESCTTTCCTTSCHHHHHT-EEEGGGCCTT.BTTB--EEEEEEEEEE-SCEEEEESSCTCCEEEEC CS
                  P_gingi_FimA  76 kkvvviANatgldaigktlgdvkalleelssdgknvtknnlpMtsklvtvtllagktnyygykgttesken 146
                                   + +++iAN ++  ++ ++++ +k++le+++ +     k +l+M+ +++ v  l++   ++g +g+t +k++
  gi|91773307|ref|YP_565999.1| 178 SSIYLIAN-HETAKTEEKIEHIKTALESVMHAKA---KRYLMMNAPITVVDDLKEV--LPGLAGPTIMKVE 242
                                   679*****.6677777888888888888888844...6**********99766666..4777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1886.28
//
Query:       gi|91773308|ref|YP_566000.1|  [L=246]
Description: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-78  263.5   0.9    1.6e-78  263.3   0.9    1.0  1  His_biosynth     Histidine biosynthesis protein
    7.1e-10   38.5   0.1    0.00021   20.5   0.1    2.4  2  Dus              Dihydrouridine synthase (Dus)
    4.9e-07   29.5   0.2    2.9e-06   26.9   0.1    1.9  2  NMO              Nitronate monooxygenase
      1e-06   28.2   0.6    0.00023   20.5   0.1    2.1  2  DHO_dh           Dihydroorotate dehydrogenase
    2.2e-05   23.9   1.1    0.00021   20.7   0.1    2.2  2  TMP-TENI         Thiamine monophosphate synthase
    2.9e-05   23.4   0.3      0.066   12.4   0.1    2.2  2  NanE             Putative N-acetylmannosamine-6-phosphate epi
    3.5e-05   23.2   0.3       0.14   11.5   0.1    2.1  2  ThiG             Thiazole biosynthesis protein ThiG
    4.1e-05   23.1   0.6     0.0041   16.6   0.1    2.2  2  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
    9.8e-05   21.9   0.4     0.0088   15.5   0.0    2.2  2  PcrB             PcrB family
    0.00022   20.4   0.3       0.02   13.9   0.0    2.1  2  IMPDH            IMP dehydrogenase / GMP reductase domain
    0.00024   20.2   0.3        0.1   11.6   0.0    2.2  2  FMN_dh           FMN-dependent dehydrogenase
     0.0012   18.1   0.0      0.005   16.0   0.0    1.9  2  IGPS             Indole-3-glycerol phosphate synthase
     0.0018   17.5   0.1     0.0033   16.6   0.1    1.4  1  DUF561           Protein of unknown function (DUF561)
     0.0067   15.3   0.4       0.03   13.2   0.1    1.9  2  Trp_syntA        Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.013   15.3   0.1        5.6    6.9   0.0    3.2  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.058   13.0   0.0       0.25   10.9   0.0    1.9  2  DeoC             DeoC/LacD family aldolase
       0.16   12.4   0.0       0.29   11.5   0.0    1.4  1  DinI             DinI-like family


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 !  263.3   0.9   1.6e-81   1.6e-78       1     229 []       4     234 ..       4     234 .. 0.99

  Alignments for each domain:
  == domain 1  score: 263.3 bits;  conditional E-value: 1.6e-81
                                   EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S...SEEEE CS
                  His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevf...ipvqv 78 
                                   ++ipa+D+k Gk+V+lv+G+  +e    +dpve+a ++ ++ga+ lh++Dld+a eg+++n  ++++i+e+++   i +qv
  gi|91773308|ref|YP_566000.1|   4 EVIPAVDMKGGKCVQLVQGVPGSEMISLDDPVEVALDWVSQGARTLHLIDLDGAIEGNRTNAPIIKKIVEKCKpqgIYIQV 84 
                                   59**********************************************************************9999***** PP

                                   ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHT CS
                  His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleel 159
                                   GGGIrs+ed+++ll++g+dkvi++taa+k+pelik+l+++fgs++i va+D+++g k+ i+gw++e++ +ave+ +++ee+
  gi|91773308|ref|YP_566000.1|  85 GGGIRSFEDAATLLDIGIDKVILSTAALKDPELIKKLSDEFGSEHINVALDSKNG-KISIEGWTKESEHTAVEMGSQFEEK 164
                                   *******************************************************.************************* PP

                                   T-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS- CS
                  His_biosynth 160 gageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegelt 229
                                   gag+il+t+id++G l+G++ + t+el +av+ipviasGGv++led+ +lk++g+++v+vgsaly++++t
  gi|91773308|ref|YP_566000.1| 165 GAGSILFTNIDSEGLLNGVNPKPTEELVNAVTIPVIASGGVTTLEDIVTLKNTGAAGVVVGSALYKKRFT 234
                                   ******************************************************************9886 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.9e-06    0.0062     169     226 ..      62     122 ..      56     135 .. 0.86
   2 !   20.5   0.1     2e-07   0.00021     173     219 ..     186     231 ..     134     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.9e-06
                                   G--CHHHHHHHHH-S...S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.H CS
                           Dus 169 tadweaIkevkqavs...ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.s 226
                                   + +   Ik++ ++ +   i + + G+I+++eda   l+  G+d v+ + +al++P l+++ s
  gi|91773308|ref|YP_566000.1|  62 RTNAPIIKKIVEKCKpqgIYIQVGGGIRSFEDAATLLDI-GIDKVILSTAALKDPELIKKlS 122
                                   566677999999998899*****************9999.*****************98644 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2e-07
                                   HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCS CS
                           Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgn 219
                                   +  +e+ +av+ipvia G+++++ed+   l++tGa gv++g + +++
  gi|91773308|ref|YP_566000.1| 186 KPTEELVNAVTIPVIASGGVTTLEDIV-TLKNTGAAGVVVGSALYKK 231
                                   55678999*****************97.58889********999876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.31   3.3e+02     194     226 ..      80     112 ..      55     125 .. 0.69
   2 !   26.9   0.1   2.8e-09   2.9e-06     187     225 ..     190     228 ..     153     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.31
                           NMO 194 iPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                   i +   GGi   ++ a+ L +G   v + t+ L
  gi|91773308|ref|YP_566000.1|  80 IYIQVGGGIRSFEDAATLLDIGIDKVILSTAAL 112
                                   555566888888888888888888888877755 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 2.8e-09
                           NMO 187 qvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                   + ++av iPviA GG+ + +++ +    GA+gv +g+++
  gi|91773308|ref|YP_566000.1| 190 ELVNAVTIPVIASGGVTTLEDIVTLKNTGAAGVVVGSAL 228
                                   5689*********************************97 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0054       5.7     234     291 ..      68     125 ..      55     128 .. 0.81
   2 !   20.5   0.1   2.1e-07   0.00023     238     285 ..     192     237 ..     183     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0054
                                   HHHHHHHTTT..S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHH CS
                        DHO_dh 234 irelykrlkke.ipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkel 291
                                   i ++ ++ k++ i i   GGi s eDa   +  G   v + ta   ++p ++kk+ +e 
  gi|91773308|ref|YP_566000.1|  68 IKKIVEKCKPQgIYIQVGGGIRSFEDAATLLDIGIDKVILSTAA-LKDPELIKKLSDEF 125
                                   55555555554366777799*********************999.89999999999886 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.1e-07
                                   HHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHH CS
                        DHO_dh 238 ykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiak 285
                                    + +   ip+I++GG+++ eD +   + GA+ v v++al+++  ++ +
  gi|91773308|ref|YP_566000.1| 192 VNAVT--IPVIASGGVTTLEDIVTLKNTGAAGVVVGSALYKKRFTLTE 237
                                   55555..********************************776655555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.12   1.3e+02     141     179 ..      67     109 ..      59     111 .. 0.83
   2 !   20.7   0.1     2e-07   0.00021     121     181 .]     165     228 ..     142     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.12
                      TMP-TENI 141 glkelaeale...iPvvaiGGitl.envaevleagadgvavvs 179
                                    +k+++e+++   i + + GGi+  e++a++l+ g+d v + +
  gi|91773308|ref|YP_566000.1|  67 IIKKIVEKCKpqgIYIQVGGGIRSfEDAATLLDIGIDKVILST 109
                                   6889999999888999999***85499*********9998765 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2e-07
                      TMP-TENI 121 gvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGit.lenvaevleagadgvavvsai 181
                                   g+G+i  T+  ++   + ++ +  +el++a++iPv+a GG+t le++ ++ ++ga+gv v sa+
  gi|91773308|ref|YP_566000.1| 165 GAGSILFTNIDSEGllNGVNPKPTEELVNAVTIPVIASGGVTtLEDIVTLKNTGAAGVVVGSAL 228
                                   678888888887776677788889****************96379***************9985 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 !    9.1   0.0   0.00065      0.68     135     186 ..      70     121 ..      52     127 .. 0.80
   2 !   12.4   0.1   6.2e-05     0.066     140     179 ..     191     231 ..     182     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00065
                                   HHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHH CS
                          NanE 135 alvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkf 186
                                   ++v++ + +g+ + + G i + e a++ ++iG+d v++ +a  +  e++kk 
  gi|91773308|ref|YP_566000.1|  70 KIVEKCKPQGIYIQVGGGIRSFEDAATLLDIGIDKVILSTAALKDPELIKKL 121
                                   578899999****************************998877766666665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.2e-05
                                   HHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
                          NanE 140 lsea.glkviaeGrintPekakkaieiGvdavvvGsaitrl 179
                                   l++a  + via G + t e   +  ++G++ vvvGsa+ + 
  gi|91773308|ref|YP_566000.1| 191 LVNAvTIPVIASGGVTTLEDIVTLKNTGAAGVVVGSALYKK 231
                                   44442688*****************************9765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00035      0.36     164     208 ..      65     112 ..      50     123 .. 0.80
   2 !   11.5   0.1   0.00013      0.14     163     208 ..     184     229 ..     155     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
                                   HHHHHHHHHH-...SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
                          ThiG 164 kealkiiieea...kvPvivDAGigspsdaaqamelGadavllntava 208
                                   +  +k i+e++    + + v  Gi+s +daa+ +++G+d v+l ta  
  gi|91773308|ref|YP_566000.1|  65 APIIKKIVEKCkpqGIYIQVGGGIRSFEDAATLLDIGIDKVILSTAAL 112
                                   4567777777633347788999***********************964 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                                   -HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
                          ThiG 163 nkealkiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                                   n++  + +++ +++Pvi   G+ + +d+++  + Ga +v++ +a+ 
  gi|91773308|ref|YP_566000.1| 184 NPKPTEELVNAVTIPVIASGGVTTLEDIVTLKNTGAAGVVVGSALY 229
                                   566778899*********************************9985 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 ?    4.8   0.1     0.016        17     127     171 ..      68     111 ..      64     112 .. 0.84
   2 !   16.6   0.1   3.9e-06    0.0041     122     168 ..     179     225 ..     157     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                                   GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--HH CS
                  G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnke 171
                                   ++k+++++k +  i i  GG i++ ed  ++l+ G++ v  s+ +
  gi|91773308|ref|YP_566000.1|  68 IKKIVEKCKPQ-GIYIQVGGGIRSFEDAATLLDIGIDKVILSTAA 111
                                   46677777766.899999*********************999876 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.9e-06
                                   EESGGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                  G3P_antiterm 122 vlPglvpkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                   +l g+ pk ++e+ ++++ip+ia+G ++t ed+ ++ + Ga +v ++
  gi|91773308|ref|YP_566000.1| 179 LLNGVNPKPTEELVNAVTIPVIASGGVTTLEDIVTLKNTGAAGVVVG 225
                                   677889999*********************************99865 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.3e-06    0.0088     154     215 ..      49     115 ..      19     125 .. 0.72
   2 ?    4.7   0.1     0.017        18     180     215 ..     196     232 ..     174     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.3e-06
                                   -SEEEEE-..TTSSS-HHHHHHHHHHHSSS..EEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                          PcrB 154 lrliYlEa..sGaledveevialkkkleka..rlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                   l li l+    G   +   +++++ k++ +   + vGGGirs E+A+  +    D ++  ++  +++
  gi|91773308|ref|YP_566000.1|  49 LHLIDLDGaiEGNRTNAPIIKKIVEKCKPQgiYIQVGGGIRSFEDAATLLDIgIDKVILSTAALKDP 115
                                   555555543467777777889999999765116679***************9999999988777666 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                                   SSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                          PcrB 180 karlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                   ++ +i  GG+   E+     +  A  +vvG ++++k 
  gi|91773308|ref|YP_566000.1| 196 TIPVIASGGVTTLEDIVTLKNTgAAGVVVGSALYKKR 232
                                   4668999********999999999**********997 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.01        11     196     235 ..      68     107 ..      55     133 .. 0.86
   2 !   13.9   0.0   1.9e-05      0.02     200     240 ..     189     229 ..     144     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.01
                                   HHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaaGadavml 235
                                   + +++e +k +g+ +   GGi++ +d +  l +G d v+l
  gi|91773308|ref|YP_566000.1|  68 IKKIVEKCKPQGIYIQVGGGIRSFEDAATLLDIGIDKVIL 107
                                   6778888999999999999999999999999999888887 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.9e-05
                                   HHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 200 aeaakkagvpviaDGGikysgdivkAlaaGadavmlGslla 240
                                    e ++   +pvia GG+++ +div     Ga  v++Gs l 
  gi|91773308|ref|YP_566000.1| 189 EELVNAVTIPVIASGGVTTLEDIVTLKNTGAAGVVVGSALY 229
                                   56678889******************************985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0031       3.3     260     300 ..      67     108 ..      54     113 .. 0.69
   2 !   11.6   0.0   9.5e-05       0.1     263     302 ..     190     227 ..     185     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                                   CHHHHHHHH..S.S-EEEESS--SHHHHHHHHHTT-SEEEES CS
                        FMN_dh 260 vLpeiveavggr.ievlvDgGirrGsDvlkAlalGAdavllG 300
                                   ++ +ive+++ + i + v gGir+ +D++  l +G d v+l 
  gi|91773308|ref|YP_566000.1|  67 IIKKIVEKCKPQgIYIQVGGGIRSFEDAATLLDIGIDKVILS 108
                                   556777777765577777777777777777777777776654 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.5e-05
                                   HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                        FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                   e+v+av   i+v+++gG+++ +D++     GA +v++G +
  gi|91773308|ref|YP_566000.1| 190 ELVNAVT--IPVIASGGVTTLEDIVTLKNTGAAGVVVGSA 227
                                   5666775..*****************************76 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.67     7e+02      59      97 ..      24      61 ..      20     122 .. 0.64
   2 !   16.0   0.0   4.8e-06     0.005     198     244 ..     187     231 ..     182     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.67
                                  TTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC--- CS
                          IGPS 59 PskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGs 97
                                  P  ++i  d dp+e+A ++ + gA ++  +      +G+
  gi|91773308|ref|YP_566000.1| 24 PGSEMISLD-DPVEVALDWVSQGARTLHLIDLDGAIEGN 61
                                  556667766.77777777777777666544333334444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.8e-06
                                   HHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC- CS
                          IGPS 198 tteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrq 244
                                    teeL++ v   + ++a  G++t ed+ +lk++g+ ++ vG++l ++
  gi|91773308|ref|YP_566000.1| 187 PTEELVNAVT--IPVIASGGVTTLEDIVTLKNTGAAGVVVGSALYKK 231
                                   5777888777..899*****************************886 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.1e-06    0.0033     179     220 ..     189     231 ..     184     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.1e-06
                        DUF561 179 yeiskkvslPvicasGlsdvtvplals.lgasGiGigsavskl 220
                                    e++++v++Pvi++ G++++   ++l+  ga+G+ +gsa+ k 
  gi|91773308|ref|YP_566000.1| 189 EELVNAVTIPVIASGGVTTLEDIVTLKnTGAAGVVVGSALYKK 231
                                   6799*****************999997479********98654 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   3.7e+02     186     230 ..      68     112 ..      50     132 .. 0.73
   2 !   13.2   0.1   2.8e-05      0.03     192     231 ..     190     230 ..     181     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHH CS
                     Trp_syntA 186 vdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalv 230
                                   ++++ve+ k      + vG Gi++ e+++++   + d vi   a +
  gi|91773308|ref|YP_566000.1|  68 IKKIVEKCKPQG-IYIQVGGGIRSFEDAATLLdIGIDKVILSTAAL 112
                                   455555555443.668899999999999998866677777766655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.8e-05
                                   HHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHH CS
                     Trp_syntA 192 rlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvk 231
                                   +l ++ + Pv    G+ t e++ ++  ++a+Gv+vGSal k
  gi|91773308|ref|YP_566000.1| 190 ELVNAVTIPVIASGGVTTLEDIVTLKnTGAAGVVVGSALYK 230
                                   45555679999999********99998***********976 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 ?    6.9   0.0    0.0053       5.6      14      26 ..      38      50 ..      35      56 .. 0.88
   2 ?    1.0   0.0      0.35   3.7e+02      21      30 ..      87      96 ..      84     109 .. 0.83
   3 ?    3.1   0.0     0.078        83      21      31 ..     204     215 ..     200     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0053
               DNA_pol_lambd_f 14 AkkwyakGirtle 26
                                  A +w+++G rtl 
  gi|91773308|ref|YP_566000.1| 38 ALDWVSQGARTLH 50
                                  99*********96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.35
               DNA_pol_lambd_f 21 Girtledlra 30
                                  Gir++ed+ +
  gi|91773308|ref|YP_566000.1| 87 GIRSFEDAAT 96
                                  9******876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.078
               DNA_pol_lambd_f  21 Girtledlra.k 31 
                                   G++tled+++ k
  gi|91773308|ref|YP_566000.1| 204 GVTTLEDIVTlK 215
                                   9*******9942 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.72   7.6e+02     110     130 ..      59      80 ..      33     124 .. 0.78
   2 ?   10.9   0.0   0.00024      0.25     188     235 .]     189     231 ..     184     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.72
                                   H.HHHHHHHHHHHHHHHHHHTE CS
                          DeoC 110 e.eqqklaeikrvkeacheegl 130
                                   e ++++   ik++ e+c+  g+
  gi|91773308|ref|YP_566000.1|  59 EgNRTNAPIIKKIVEKCKPQGI 80 
                                   3377777778888888876665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00024
                                   HHHHHCHSSTEEEEETTSSHHHHHHHHHHHHH..HHTHCEEEESHHHHTT CS
                          DeoC 188 kdvikaapvpgvvlsGGvseedfletvedAvk..eagasGvlsGRaifqk 235
                                   +++++a+ +p v+ sGGv       t+ed v   + ga+Gv++G a ++k
  gi|91773308|ref|YP_566000.1| 189 EELVNAVTIP-VIASGGV------TTLEDIVTlkNTGAAGVVVGSALYKK 231
                                   57889999**.*******......66666666668*********999986 PP

>> DinI  DinI-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.29      11      48 ..     116     155 ..     110     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                   HHHHHHHHH-SS-EEEEEEESS.-EEEEES.--HHHHHHH CS
                          DinI  11 ELskRiqevfPdaevrvrkasa.nglsveG.askedkeri 48 
                                   EL k+++  f + +++v+ +s+  ++s+eG  +++++ ++
  gi|91773308|ref|YP_566000.1| 116 ELIKKLSDEFGSEHINVALDSKnGKISIEGwTKESEHTAV 155
                                   9*********************457*****7777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1620.11
//
Query:       gi|91773309|ref|YP_566001.1|  [L=191]
Description: imidazoleglycerol-phosphate dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  213.9   1.6    1.4e-63  213.5   1.6    1.1  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 !  213.5   1.6   7.6e-68   1.4e-63       1     144 []      31     173 ..      31     173 .. 1.00

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 7.6e-68
                                   ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE--S CS
                          IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevaldlsg 81 
                                   Tgigf+dhmL+++akhg++dl ++++gdl vd+Hh++ed++i+lGqal+ealgdk gi+Rfg+a +pmDeala v+ldl g
  gi|91773309|ref|YP_566001.1|  31 TGIGFFDHMLTSFAKHGNLDLIIEATGDLIVDEHHLIEDTAIVLGQALSEALGDKDGIARFGDARIPMDEALADVVLDLGG 111
                                   9******************************************************************************** PP

                                   S-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                          IGPD  82 rpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                   r ylv++ae++ +++ge++t+lv++ffesl+++++++lh+ v+ g n+hh++ealfKafa aL
  gi|91773309|ref|YP_566001.1| 112 RTYLVMKAEFEAPRVGEMNTQLVRHFFESLTDNSKMNLHIAVT-GYNDHHKIEALFKAFAYAL 173
                                   ******************************************9.*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 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:                        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 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1342.09
//
Query:       gi|91773310|ref|YP_566002.1|  [L=700]
Description: DNA mismatch repair protein MutS-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.5   0.0    3.1e-07   30.6   0.0    1.4  1  MutS_V    MutS domain V
      2e-07   31.5   0.1     0.0015   19.1   0.0    3.0  2  HHH_5     Helix-hairpin-helix domain
    0.00039   20.5   0.1     0.0011   19.0   0.1    1.7  1  HHH_2     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   5.1e-11   3.1e-07       2     135 ..     515     643 ..     514     669 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5.1e-11
                                   EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSEEE CS
                        MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatekslvi 82 
                                   l+ G n +Gk ++l  va +v+la++G   pa ++ei+++++ +    ++ +l     +F + +++ + + +++    lv+
  gi|91773310|ref|YP_566002.1| 515 LLSGVNSGGKTSLLELVAQCVILAHMGFPTPAVNMEIGLAEEFYHFGKSKGTLDA--GAFETTLVDFSVVANDS--PKLVL 591
                                   799***************************************8876555555554..57999999988876654..56*** PP

                                   EESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEE CS
                        MutS_V  83 lDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevkn 135
                                    DEl   t       i   ++e l+e+ + +++f  H  el   +++  +v+ 
  gi|91773310|ref|YP_566002.1| 592 ADELESITEPGASAKIISGILEVLSENDNGMSIFVSHLSELILENTE-CNVRV 643
                                   *****9999999999*************************9865544.34444 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.5e-07    0.0015       4      54 ..       4      57 ..       2      60 .. 0.86
   2 !    9.2   0.0    0.0003       1.8      21      39 ..     261     280 ..     254     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.5e-07
                                  HHTSTT--HHHHHHHHTT.T--S..HHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
                         HHH_5  4 LlsvsGiGpktAlallsa.Gies..vedlaaadveeLakipGiGkktAeriile 54
                                  L++++ iG+k+A++  ++ G e    +++++ d++ ++++ G+G++ A +++ e
  gi|91773310|ref|YP_566002.1|  4 LQDIPRIGEKMAKRFQEHfGGEDraMDAILSGDIASISEVEGVGQRYAISLVHE 57
                                  899***************887762257*****************9988777655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0003
                                   T.T--SHHHHHHS-HHHHHT CS
                         HHH_5  21 a.GiesvedlaaadveeLak 39 
                                     Gi+s+ed+a+ d+e+L +
  gi|91773310|ref|YP_566002.1| 261 CsGICSLEDIADDDIERLKQ 280
                                   438**************975 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.9e-07    0.0011       8      52 ..       7      55 ..       5      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-07
                         HHH_2  8 IrhVGektAklLakrFk....sldaLkkasleeLlevddiGeeiAqsiv 52
                                  I+ +Gek+Ak   ++F+     +da+ + ++  ++ev+++G++ A s v
  gi|91773310|ref|YP_566002.1|  7 IPRIGEKMAKRFQEHFGgedrAMDAILSGDIASISEVEGVGQRYAISLV 55
                                  99**************877668**********************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4557.00
//
Query:       gi|91773311|ref|YP_566003.1|  [L=277]
Description: hypothetical protein Mbur_1335 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   30.0   0.0    6.3e-07   29.5   0.0    1.2  1  DUF4130   Domain of unknown function (DUF4130


Domain annotation for each model (and alignments):
>> DUF4130  Domain of unknown function (DUF4130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   3.5e-11   6.3e-07      17     138 ..     109     248 ..      98     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.5e-11
                       DUF4130  17 agkkvledladpdvlrleelarkvsreahrmkgfvRFreledgiyvakiePkhnvlellaehFadRfadekwlIldekrkl 97 
                                    ++++l + +d    r  ++ r+v++  +r+  f R  el++gi+   i   h++ ++ +++  ++ +d   ++++   + 
  gi|91773311|ref|YP_566003.1| 109 GDSDILYSGNDMIAKRYYNYMREVGKAYERLCMFARP-ELKGGILSVVIDTPHDIADMFCRWLVRKNPDVPVAVIK--NDS 186
                                   556777788888999999******************5.6778*********************************7..444 PP

                       DUF4130  98 alvyd.....................lseeedefeelWktyfksiaikeRknpklqrqemPk 138
                                   a v +                      ++++d++++lW  y++s  i +R+np l +++ Pk
  gi|91773311|ref|YP_566003.1| 187 AWVGNgdligldrfakitasfveslrSTSRSDDVDKLWDLYYNSQMIDSRRNPGLAKKMQPK 248
                                   4555455888888888888888899888999***************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1976.56
//
Query:       gi|91773312|ref|YP_566004.1|  [L=379]
Description: hypothetical protein Mbur_1336 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-08   34.3   0.0    4.9e-08   33.1   0.0    1.6  1  HHH_3           Helix-hairpin-helix motif
    1.2e-05   25.7   0.5    0.00011   22.6   0.4    2.6  1  Radical_SAM     Radical SAM superfamily
     0.0054   16.5   0.0      0.013   15.4   0.0    1.6  1  HHH             Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.073   13.0   0.7       0.23   11.4   0.0    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.11   12.6   0.0       0.23   11.6   0.0    1.4  1  HHH_2           Helix-hairpin-helix motif
       0.14   12.7   0.0       0.33   11.6   0.0    1.6  1  HHH_5           Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.6e-11   4.9e-08       5      49 ..     310     350 ..     307     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.6e-11
                         HHH_3   5 gvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlkv 49 
                                   +vdiN+A  +eL ++pG+gp  A++Iv++R    p+ s +eL +v
  gi|91773312|ref|YP_566004.1| 310 PVDINSAEMSELLMVPGIGPISANRIVRAR----PIVSEQELCRV 350
                                   69****************************....99999999877 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.4   3.7e-08   0.00011       4     140 ..      53     188 ..      50     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.7e-08
                                   ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE...SSTGGGSTTHHHHHHHHHHTC..CCTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx...xxxxxxxxxxxxxxxxxxxxx..xxxx RF
                   Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilg...ggepllypdfvellerlakla..vpgi 78 
                                   ++ C++ C +C+++   +re + ++l + ei+++  ++ ++++ +++++l+   +g+  + + ++ ++ +l + +  +  i
  gi|91773312|ref|YP_566004.1|  53 SNSCAGECAYCPNRC--ERETKRAFLEPVEIAKITWSF-YRRNaIDGLFLSsgiMGDAEYTSQKQLEVVELLRGQgfKGYI 130
                                   678***********9..5********************.67777*******555555555555555555555555764555 PP

                                   EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH.HHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf.eevlealeklrea 140
                                   +i+v    ++     le +++   d + +++e++++  + +++ ++ ++  +vl+ l+  r++
  gi|91773312|ref|YP_566004.1| 131 NIRVMPGTPKY---LLEQIADHA-DKFGVNAETTNSVNYSEIC-PNFDYkNDVLQRLKWTRDL 188
                                   55554444444...789999966.***********99777777.4333335666666666655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.3e-06     0.013       8      28 ..     316     336 ..     311     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.3e-06
                                   SSHHHHHTSTT-SHHHHHHHH CS
                           HHH   8 asreeLlalPGVGpktAeaIl 28 
                                   a + eLl +PG+Gp  A++I 
  gi|91773312|ref|YP_566004.1| 316 AEMSELLMVPGIGPISANRIV 336
                                   55789**************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   1.2       2.3   6.9e+03      30      45 ..      59      73 ..      53      76 .. 0.65
   2 ?   11.4   0.0   7.8e-05      0.23       3      44 ..     141     181 ..     140     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                OrfB_Zn_ribbon 30 tCseCgsknkealsgr 45
                                  +C+ C  + ++  ++r
  gi|91773312|ref|YP_566004.1| 59 ECAYCPNRCER-ETKR 73
                                  57777776666.4444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.8e-05
                OrfB_Zn_ribbon   3 klkeqleykakeyGikveevnpayTSktCseCgsknkealsg 44 
                                    l eq+++ a ++G++ e+ n  + S  C++  +kn+  l++
  gi|91773312|ref|YP_566004.1| 141 YLLEQIADHADKFGVNAETTNSVNYSEICPNFDYKNDV-LQR 181
                                   5889***************************9999987.444 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.6e-05      0.23      29      53 ..     313     337 ..     311     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.6e-05
                         HHH_2  29 LkkasleeLlevddiGeeiAqsive 53 
                                   + +a++ eLl v++iG++ A+ iv+
  gi|91773312|ref|YP_566004.1| 313 INSAEMSELLMVPGIGPISANRIVR 337
                                   6789******************985 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.33      28      53 ..     312     337 ..     295     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                   HHHHS-HHHHHTSTTS-HHHHHHHHH CS
                         HHH_5  28 dlaaadveeLakipGiGkktAeriil 53 
                                   d+ +a+  eL  +pGiG+  A ri+ 
  gi|91773312|ref|YP_566004.1| 312 DINSAEMSELLMVPGIGPISANRIVR 337
                                   677788889999*********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2885.60
//
Query:       gi|91773313|ref|YP_566005.1|  [L=65]
Description: hypothetical protein Mbur_1337 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.5e-09   34.5   0.1    8.5e-09   34.5   0.1    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   4.7e-13   8.5e-09     391     423 ..      25      57 ..       5      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.7e-13
                                   ETTEEEEEEE-B--SS-S--TTHHHHHHHHHHH CS
                    ADP_PFK_GK 391 leevevclaPvlvckkpkkTvGlGDtISaaglv 423
                                   +  ++vc+ P+l+c++p +TvGlGDt+ +a+++
  gi|91773313|ref|YP_566005.1|  25 YGCLNVCILPTLLCDDPISTVGLGDTVMSAAFL 57 
                                   45689**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); 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: 0.32u 0.18s 00:00:00.50 Elapsed: 00:00:00.33
# Mc/sec: 587.97
//
Query:       gi|91773314|ref|YP_566006.1|  [L=384]
Description: ADP-dependent glucokinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-70  237.3   0.0    2.7e-70  237.1   0.0    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.1   0.0   1.5e-74   2.7e-70       3     357 ..       3     372 ..       1     382 [. 0.87

  Alignments for each domain:
  == domain 1  score: 237.1 bits;  conditional E-value: 1.5e-74
                                   EEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHHH.... CS
                    ADP_PFK_GK   3 vavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeelvkaak 78 
                                    ++Gyn n+Da+     +d+ elle ++ + + ++ +  +  i+s +dl+++++ ++++G +aE+f+++  +f+ l++  +
  gi|91773314|ref|YP_566006.1|   3 FLCGYNMNLDAVysitgEDIAELLELVDGDVLFDSFQRSSGAITSISDLIAGLVGCMQDGTGAEWFIQEVSVFRFLMD--H 81 
                                   68****************************9899999*****************************************..9 PP

                                   CC--SEEEEESHHHHHHHHHCCTT-.EEEEE----H..HHHTTS-SSEE........EEEEGGG-S-.---EEEEEEE-TT CS
                    ADP_PFK_GK  79 klkkaelrmGGnagimanrlakega.kvllgaklsk..klkellsekiv........vlgkpseaskekdeiHlIlEykkg 148
                                   ++++a +r+GGn++iman+++++ga +v+++ ++++    + l+s k v         l+++ +  k ++ +H+++++k+g
  gi|91773314|ref|YP_566006.1|  82 FYDRAVIRVGGNMAIMANVMSEMGAeEVVVN-PVGDvgSIRPLISGKNVifpeerdnNLKSSLKGAK-EKIVHFVFDFKEG 160
                                   *************************777765.44443479999999944344443334444444444.4689********* PP

                                   -EE...TE.EE-SS-EEEEEE--STCGGTS--HHHCTTHHH.HH.-SEEEE--GGG--TB-TTSTCHHHHHHHHHHHHHHH CS
                    ADP_PFK_GK 149 ekw...ge.ieapraNRfIissdpenlrlsileefkealke.fk.pdllvlsGlqmleeqykegkereerlekvkeqlksl 223
                                    ++   g+ i++pr+NRfI+++d+ n++l i+  f+++  e +k  +++++sG++ l+++y +++   e++ek+  ++k++
  gi|91773314|ref|YP_566006.1| 161 LSFelfGKnITVPRENRFIATYDNVNTELYISPAFEDYSLEyVKvANGAIVSGFNQLRSSYPDSSGPVEKFEKALFLIKEW 241
                                   ******777***************************998662669************************************ PP

                                   C..C.T-EEEEE----S-HHHHHHHHHHCGGG-SEEEE-HHHHHHHHHHTT-HHHCCSS...CC--HHHHHHHHHHHHH.. CS
                    ADP_PFK_GK 224 k..n.kikiHlElAsfqdeellkeilekilpyvdslGlnEqElanllsvlggeekeltevsdkepriakvlealrkllkll 301
                                   k  n ++ +H El++f+  e++  i++++   vds+G+nE+E+a+l ++ g ++++++e      +   ++ea++k+++  
  gi|91773314|ref|YP_566006.1| 242 KelNsDLLVHAELGHFSTYEMAVFIFTELSGIVDSIGMNEDEIAMLFEIHGIPKERFQE-----INSIVIVEACVKCIH-- 315
                                   ***77***********************************************9999955.....5668899********.. PP

                                   ...HHTT-SEEEEEETTEEEEEEETT.SSS-HHHHHHHHHHHHHHHHHHHHH.-.....SHHH CS
                    ADP_PFK_GK 302 kkskkrkltrihvHtlayqiiltkke.sewkneaakkalakaallAarkacn.s.....dlek 357
                                       + +l+++ vHt++++i++ +++ s+ ++e++  +l++++++Aa  a++ +     d+e+
  gi|91773314|ref|YP_566006.1| 316 ---AT-GLKKMVVHTRDFIISVFRDTvSSCNHEMQ--SLEFGIMCAAFFAATgKlpyrpDIES 372
                                   ...78.*****************774145555555..*************9952453344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2544.18
//
Query:       gi|91773315|ref|YP_566007.1|  [L=485]
Description: ADP-specific phosphofructokinase [Methanococcoides burtonii DSM 6242]
Scores for 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-115  383.6   0.0     1e-114  383.4   0.0    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.4   0.0  5.8e-119    1e-114       2     423 ..      26     478 ..      25     479 .. 0.92

  Alignments for each domain:
  == domain 1  score: 383.4 bits;  conditional E-value: 5.8e-119
                                   EEEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHHH... CS
                    ADP_PFK_GK   2 kvavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeelvkaa 77 
                                    ++v+yn+n+Dai     +d++ ll++++++ev++k  e++++i+s++dl++++++++++G+aaE+++++++++e+l++  
  gi|91773315|ref|YP_566007.1|  26 GMFVAYNSNIDAIkhvseEDISMLLAQVDQNEVQDKLFEYPRQIDSPSDLMARLIIAMRDGKAAEVPTNTTDIHEWLTD-- 104
                                   589***************************************************************************9.. PP

                                   .CC--SEEEEESHHHHHHHHHCCTT-EEEEE-.---HHHHTTS-SS.......EE....EEEEGGG-S-...---EEEEEE CS
                    ADP_PFK_GK  78 kklkkaelrmGGnagimanrlakegakvllga.klskklkellsek.......iv....vlgkpseaske..kdeiHlIlE 144
                                    +l ++++rmGG+agi++n+la+ g +v++++ +ls +++e++ ++       ++    +l +p++a++   k+++++IlE
  gi|91773315|ref|YP_566007.1| 105 -HLGFDNARMGGQAGIISNLLASIGQNVITYVpWLSAEQAEYFVDSdnllfpvVEgdqlRLVRPRDAYDPqnKSKVNWILE 184
                                   .*********************************************8888775116667666777777666678******* PP

                                   E-TT-EE...TE.EE-SS-EEEEEE--STCGGTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTSTCHHHHHHHHHHH CS
                    ADP_PFK_GK 145 ykkgekw...ge.ieapraNRfIissdpenlrlsileefkealkefk..pdllvlsGlqmleeqykegkereerlekvkeq 219
                                   ++kg  +   ge + +pr+NR+Iiss+p+++r+++  e++e +++++  +d+++l+G+qm++e+y++g++++++++k++++
  gi|91773315|ref|YP_566007.1| 185 FSKGMGVnfkGEhFIVPRDNRLIISSRPKWIRIEMVPELYERIPSLQanIDGALLAGYQMIKEKYEDGSTYMDYIDKAVNV 265
                                   *****9999*778********************************9999******************************** PP

                                   HHHHC..C.T-EEEEE----S-HHHHHHHHHHCGGG.-SEEEE-HHHHHHHHHHTT-HHHCCSS...CC--HHHHHHHHHH CS
                    ADP_PFK_GK 220 lkslk..n.kikiHlElAsfqdeellkeilekilpy.vdslGlnEqElanllsvlggeekeltevsdkepriakvlealrk 296
                                   +++lk  n +i+iH+E++s+q++ ++++il++i+++ v+slGl++ E+an l+vlg+ee   + + ++e+ i +++e+++k
  gi|91773315|ref|YP_566007.1| 266 IERLKegNpNIRIHVEFTSIQNKLIRQSILKYIVKKhVHSLGLDTVEVANALNVLGYEELAYSVINKGENAIVSLFEGAVK 346
                                   *******88***********************99887********************9999999999************** PP

                                   HHH.....HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH-...SHHHHHHHH..........HS CS
                    ADP_PFK_GK 297 llkllkkskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacns...dleklelklddsfsvskskki 374
                                   llk     +  +l+r+hvH+l+++i+++ k+ +++  +++kal +a+++Aa++a      +le+  ++l          ++
  gi|91773315|ref|YP_566007.1| 347 LLK-----EL-ELERVHVHSLGFYICVVAKDCPVSVLDHRKALLFASTTAASQALLGeivSLESTVAGL----------DV 411
                                   ***.....99.*********************************************5356888888888..........55 PP

                                   -B-TT..HHHHHHHHCC................EETTEEEEEEE-B--SS-S--TTHHHHHHHHHHH CS
                    ADP_PFK_GK 375 plnek..epvscweeei................eleevevclaPvlvckkpkkTvGlGDtISaaglv 423
                                   p+++k   ++ ++e++                 ++ +++ +++P++v+ +p++TvG+GD ISaa+++
  gi|91773315|ref|YP_566007.1| 412 PVSDKghGDLGRLEDHLvnsgmccmedfengciRTPQYDAIVIPTKVVSEPVATVGIGDVISAAAFA 478
                                   5555555555555555555555555555799**99******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3499.09
//
Query:       gi|91773316|ref|YP_566008.1|  [L=394]
Description: bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-138  459.5   3.5   7.9e-138  459.3   3.5    1.0  1  ArgJ      ArgJ family
     0.0088   16.1   0.8        2.8    7.9   0.1    2.5  2  HAP       Hydrophobic abundant protein (HAP)


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 !  459.3   3.5  8.8e-142  7.9e-138       6     376 .]      16     394 .]      11     394 .] 0.94

  Alignments for each domain:
  == domain 1  score: 459.3 bits;  conditional E-value: 8.8e-142
                                   XXSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHSEEEEEEEEEEXXXSXHHHHHHHHHHHHHHHHHH CS
                          ArgJ   6 aagikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkgaravvvnsgnANavtgeqGledaeemaeavaea 86 
                                   a gik  k+ la+iv+  + +aa+vfT+nkv Aap+ v+re+l k+ ++ av++nsgnANa+tgeqGl+da+em++ ++e 
  gi|91773316|ref|YP_566008.1|  16 AFGIKPGKMGLAIIVA--EGNAAGVFTRNKVIAAPLIVTREALGKNGRLAAVIANSGNANAFTGEQGLADAREMVSILSER 94 
                                   679**99********9..5789*********************88878********************************* PP

                                   HTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEETEEEEEEEEEEXSSS CS
                          ArgJ  87 lgikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevelgkevtiagiaKGaGm 161
                                   lg++++ v+vasTGviG++l+++ i+++++++++ l       ++aa+AimTTDt+pK++a+e++    v i+giaKG+Gm
  gi|91773316|ref|YP_566008.1|  95 LGVDSDLVAVASTGVIGRKLDIDWIRDNVDEVMSGLVaspqgnSHAARAIMTTDTFPKMTAIELD--CGVCIGGIAKGSGM 173
                                   *********************************98845666779******************996..69************ PP

                                   XXXXEE--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT.STTHHHHHHHHHHHHHHHHH CS
                          ArgJ 162 ihPnmaTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeeeeedleefeealtevlqeLak 242
                                   i+Pnm+TmL+f++tDaa+s+++l+ +l+eavd+sFn++ vDgdtSTnD+vll A+ga+   ++d++ef+e l++vl +Lak
  gi|91773316|ref|YP_566008.1| 174 IEPNMGTMLGFVYTDAALSSDVLDGCLREAVDRSFNMVVVDGDTSTNDMVLLTATGAT-GISPDINEFKEGLEHVLVDLAK 253
                                   *********************************************************8.4499****************** PP

                                   HHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS---TTS-EE......TTEE CS
                          ArgJ 243 qivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagaeldpekvsv....llgevk 319
                                   qi++DGEGat+l+e +V+ga see+A+ vak++++s+LvK+A+fG+D+nwGR++aa+Gy+gael+++++s+     +++v 
  gi|91773316|ref|YP_566008.1| 254 QIAKDGEGATRLIEAQVTGAISEEDARLVAKAIVRSPLVKSAIFGKDPNWGRVVAAAGYSGAELEQDRLSLafsnGVDTVY 334
                                   ***********************************************************************6665555699 PP

                                   EEETTE...E----HHHHHHHHH-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                          ArgJ 320 vlekge...peevdeerakeilkeeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                   +++ g+   +++ + ++ ++i+ + ev i v l  g+++a++w+cDL+y+Yv+iN++Y+t
  gi|91773316|ref|YP_566008.1| 335 LVDGGKilsEDKEHLQKLEAIMGSLEVIIMVGLALGSANAKAWGCDLTYDYVRINSEYTT 394
                                   999999653344456778899*************************************98 PP

>> HAP  Hydrophobic abundant protein (HAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0011       9.7      87     120 ..      99     132 ..      86     145 .. 0.86
   2 !    7.9   0.1   0.00031       2.8      56      97 ..     162     203 ..     157     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0011
                           HAP  87 ldlvkssvtgilsdlldldavlelveevlrvlla 120
                                    dlv  + tg++   ld+d + + v+ev+  l+a
  gi|91773316|ref|YP_566008.1|  99 SDLVAVASTGVIGRKLDIDWIRDNVDEVMSGLVA 132
                                   699*************************987765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00031
                           HAP  56 viiglvvtlsgvleivvgvvlllvdvlaalaldlvkssvtgi 97 
                                   v ig +   sg++e  +g++l++v + aal+ d++++++   
  gi|91773316|ref|YP_566008.1| 162 VCIGGIAKGSGMIEPNMGTMLGFVYTDAALSSDVLDGCLREA 203
                                   789999999*************************99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2491.92
//
Query:       gi|91773317|ref|YP_566009.1|  [L=154]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   3.4    3.1e-16   59.5   0.2    2.2  2  CBS            CBS domain
  ------ inclusion threshold ------
        0.1   12.5   0.4       0.98    9.3   0.0    2.1  2  Peptidase_S55  SpoIVB peptidase S55
       0.62   10.0   3.9         13    5.8   0.3    2.2  2  DUF3659        Protein of unknown function (DUF3659)


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 !   59.5   0.2   5.3e-20   3.1e-16       1      55 [.       3      56 ..       3      57 .. 0.96
   2 !   56.5   0.3   4.7e-19   2.8e-15       1      56 [.      98     152 ..      98     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 5.3e-20
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                  V+dim+++v++++p++t++  ++l+++k++s++PVV ++gk+vGiv++ Dll++l
  gi|91773317|ref|YP_566009.1|  3 VKDIMSSNVIVCSPQDTISSTAQLLKKKNISGVPVV-DEGKVVGIVSEVDLLKLL 56
                                  89***********************9999*******.6**************987 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 4.7e-19
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V+dim +dv+t+  ++++e+a + m +++++rlPVV ++g++vG++t+ D++r l+
  gi|91773317|ref|YP_566009.1|  98 VSDIMEKDVFTIGLESSVEDASRSMSRHKINRLPVV-DNGEIVGLITRGDIIRGLA 152
                                   89***********************9999*******.6**************9876 PP

>> Peptidase_S55  SpoIVB peptidase S55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00016      0.98     175     193 ..      32      50 ..      12      60 .. 0.91
   2 ?    1.2   0.0      0.05     3e+02     179     192 ..     131     144 ..     128     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                 Peptidase_S55 175 mSGsPiiqngklvGavthv 193
                                   +SG P++ +gk+vG v+ v
  gi|91773317|ref|YP_566009.1|  32 ISGVPVVDEGKVVGIVSEV 50 
                                   7***************988 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.05
                 Peptidase_S55 179 PiiqngklvGavth 192
                                   P++ ng++vG +t 
  gi|91773317|ref|YP_566009.1| 131 PVVDNGEIVGLITR 144
                                   9**********995 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3    0.0022        13      14      42 ..      37      62 ..      28      65 .. 0.73
   2 ?    5.4   0.3     0.003        18      14      30 ..     132     147 ..     131     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0022
                       DUF3659 14 vvdeeGnvvGrvveGdlkkLaGkkvdedG 42
                                  vv +eG+vvG v e dl kL    + e G
  gi|91773317|ref|YP_566009.1| 37 VV-DEGKVVGIVSEVDLLKLL--NIPEHG 62
                                  44.599999999999988887..555555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.003
                       DUF3659  14 vvdeeGnvvGrvveGdl 30 
                                   vvd +G++vG ++ Gd+
  gi|91773317|ref|YP_566009.1| 132 VVD-NGEIVGLITRGDI 147
                                   565.***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 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:                        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 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1029.57
//
Query:       gi|91773318|ref|YP_566010.1|  [L=340]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-33  115.9   0.0    2.4e-33  115.2   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    4.5e-21   75.8   0.0    6.5e-21   75.2   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
  ------ inclusion threshold ------
        0.1   13.4   0.0       0.22   12.3   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.13   12.9   0.0       0.25   11.9   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


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 !  115.2   0.0   5.3e-37   2.4e-33       1     117 [.       6     137 ..       6     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 5.3e-37
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHH CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagvsk 80 
                                   +++ivGa+Gy+G el+rlL +hp+v++ +++s++   G+++++ +k+l++  d+++ed ++e++  ++d+vf a+p+g+++
  gi|91773318|ref|YP_566010.1|   6 NAGIVGASGYTGGELMRLLLNHPYVNIETATSRRL-SGEAVSDTHKHLRGLVDIEFEDLSPEDIrGRCDVVFVAVPHGTAM 85 
                                   579*****************************999.**********************99999989*************** PP

                                   HHHHHHHHTTSEEEESSSTTTTST...............TSEBE-HHHHGGG CS
                Semialdhyde_dh  81 elapklaeagvkviDlssdfRlkd...............davyvlpevnrea 117
                                   +++p+l++ ++kviDls+d+Rlk+               dav++l e+++e 
  gi|91773318|ref|YP_566010.1|  86 NIVPELIDDNTKVIDLSADYRLKTsvfeqvynmehvdprDAVFGLVELHPEV 137
                                   *************************************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   1.5e-24   6.5e-21       2     184 .]     158     311 ..     157     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.5e-24
                                   HHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHH CS
               Semialdhyde_dhC   2 kPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkava 82 
                                   +PL +a   l+  i+++++++ GaG +                 +++  ++ + a N+ +y+ + ++++  e+ +el+ ++
  gi|91773318|ref|YP_566010.1| 158 APLTAA-KLLKMAIFDSKSGITGAGIN-----------------PTMVSHYPNMAENVQAYKLT-THRHREEILQELNRLD 219
                                   589998.668999*************6.................99999999************.**************** PP

                                   HHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHTTCSSSEEEE CS
               Semialdhyde_dhC  83 etkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaapevkvvvneeedrPtpaavaggtnsvsVG 161
                                   +  + ++ft+      + VP +rG+++++++ +k   + ++v+  + ++++  +++v+v +  d+P + av g +n++++G
  gi|91773318|ref|YP_566010.1| 220 NAFTDVNFTP------HVVPSIRGILTTAHLFTKekMSLEDVRGLYHEFYKN-KPFVRVVD--DIPSLSAVKG-SNFCDIG 290
                                   *********9......78***************9666667777777788888.*******8..*********9.9****** PP

                                   EEEEETTCTTEEEEEEEEETTTT CS
               Semialdhyde_dhC 162 RirkdemgdeglklvvvgDNllk 184
                                    +++d  + + +++v+++DNl+k
  gi|91773318|ref|YP_566010.1| 291 -FEVDANTGR-VVVVSAIDNLVK 311
                                   .********8.**********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 ?   12.3   0.0     5e-05      0.22       1      90 [.       5      99 ..       5      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                                  EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..HHHHHTCT...TESEEEE-S-GGGHHH CS
                  GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..leelladp...eidavivatpngthee 77
                                  ++ +i+Ga G+ g + +r l ++ +  ++  + +++ +       + ++    d  +e+l+ ++   ++d+v+va+p gt ++
  gi|91773318|ref|YP_566010.1|  5 INAGIVGAsGYTGGELMRLLLNH-PYVNIETATSRRLSGEAVSDTHKHLRGLVDieFEDLSPEDirgRCDVVFVAVPHGTAMN 86
                                  58899**9777788888666666.88899999999886666555555555444434667777667779*************** PP

                                  HHHHHHHTT-EEE CS
                  GFO_IDH_MocA 78 lakaaleagkhvl 90
                                  ++ +++  + +v+
  gi|91773318|ref|YP_566010.1| 87 IVPELIDDNTKVI 99
                                  **99999888776 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 ?   11.9   0.0   5.6e-05      0.25       8      95 ..      14     102 ..       6     104 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.6e-05
                                   SHHHHHHHHHHHHTTS-GGCEEEEEESSC..CCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCG CS
                 F420_oxidored   8 Gnmgealasgllaagaqpheivvansrnp..ekaeelaeelg....vkvtavdneeaaeeadvvvlavkpedveevlsela 82 
                                   G  g  l++ ll++     +i  a+sr    e +  ++++l     ++ +  + e+   ++dvv++av+   + +++ el 
  gi|91773318|ref|YP_566010.1|  14 GYTGGELMRLLLNHP--YVNIETATSRRLsgEAVSDTHKHLRglvdIEFEDLSPEDIRGRCDVVFVAVPHGTAMNIVPEL- 91 
                                   566666666666664..333333434432113334444444456557888888999999*********************. PP

                                   HHHHTTSEEEEES CS
                 F420_oxidored  83 kdalkgklvisvl 95 
                                      + ++ vi+ +
  gi|91773318|ref|YP_566010.1|  92 --IDDNTKVIDLS 102
                                   ..66677777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2650.51
//
Query:       gi|91773319|ref|YP_566011.1|  [L=142]
Description: nucleoside 2-deoxyribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  101.1   0.0    5.2e-29  100.9   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
    8.3e-22   77.5   0.0      1e-21   77.3   0.0    1.1  1  Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
    6.7e-05   23.5   0.0    0.00016   22.2   0.0    1.6  1  TIR_2            TIR domain
     0.0011   18.5   0.0     0.0014   18.3   0.0    1.2  1  LDcluster4       SLOG cluster4 family
  ------ inclusion threshold ------
      0.039   14.3   0.0      0.063   13.6   0.0    1.3  1  DUF4062          Domain of unknown function (DUF4062)
      0.062   13.8   0.0      0.074   13.6   0.0    1.1  1  Reprolysin_3     Metallo-peptidase family M12B Reprolysin-lik


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   1.7e-32   5.2e-29       1     106 [.       7     110 ..       7     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.7e-32
                                   EEEESGGGCSCCCHHHHHHHHHHHHTTTTEEE-CCTT-TT.....--SSHHHHHHHHHHHHHC-SEEEEE--SSSSSS--H CS
               Nuc_deoxyrib_tr   1 iYLAgplvFrpdakalaarlkallaengldglaPldneaelel.paeetaraiyeadialirqaDavianldpfrgpeaDs 80 
                                   iYLA+pl F++++++++++l  +l++ g+d+++P+++ ++ e+ ++e ++++i++ +++ ++++D+v+a+ld+  g ++Ds
  gi|91773319|ref|YP_566011.1|   7 IYLAAPL-FSEAEQDYNRKLETALKDLGFDVFVPQEDSNDTEAaREEMDSNKIFQLNLEAVDNCDIVVAVLDG--GSDIDS 84 
                                   9******.***************************8888888889999*************************..88**** PP

                                   HHHHHHHHHHHCT-EEEEE-S-GCGH CS
               Nuc_deoxyrib_tr  81 GtafEvGyavalgkpvlayttdarel 106
                                   Gta+E+Gya++ +k ++++ td+r+l
  gi|91773319|ref|YP_566011.1|  85 GTAWEIGYAYSKKKTIIGLKTDFRTL 110
                                   ************************84 PP

>> Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   3.4e-25     1e-21       2     108 .]       5     107 ..       4     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 3.4e-25
                                   EEEEEEE---SSSST-HHHHHHHHHHTSSS-EEEEE----SS-----HHHHH.....HHHHHHHHHHHH-SEEEEEE-TT- CS
               Nuc_deoxyri_tr2   2 ksvFLaGsteseaetdWredlteaLsaipklgvtvfnPqredwdseleedrskkrfreqvewelealekAdvvvfvfdged 82 
                                   k+++La++++seae+d++++l +aL++   lg++vf+Pq++  d+e  + r++ +++++++++lea +++d+vv+v+dg +
  gi|91773319|ref|YP_566011.1|   5 KNIYLAAPLFSEAEQDYNRKLETALKD---LGFDVFVPQEDSNDTE--AAREEMDSNKIFQLNLEAVDNCDIVVAVLDGGS 80 
                                   79***********************88...9***********9985..599****************************77 PP

                                   -.-HHHHHHHHHHTTSS-EEEEE-TT- CS
               Nuc_deoxyri_tr2  83 s.atrslvElglaaakgkkvvlvpkgf 108
                                   + +  + +E+g+a++k+k++++++++f
  gi|91773319|ref|YP_566011.1|  81 DiDSGTAWEIGYAYSKKKTIIGLKTDF 107
                                   7688899*****************997 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.5e-08   0.00016       5      92 ..      14     106 ..      13     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.5e-08
                         TIR_2   5 yssedkewaeklaeaLeaagirvwldrwdl..........kpgedweeeieeaiessdvvlvvlspaylesewcreeleaa 75 
                                   +s++++++ +kl +aL++ g++v++ ++d            + + ++ ++ ea++++d+v++vl   +  +  +  e+ +a
  gi|91773319|ref|YP_566011.1|  14 FSEAEQDYNRKLETALKDLGFDVFVPQEDSndteaareemDSNKIFQLNL-EAVDNCDIVVAVLDGGSDIDSGTAWEIGYA 93 
                                   678899999****************7776522222222103333444444.68****************999999****** PP

                         TIR_2  76 leaaeegkkrlipvlle 92 
                                   ++    +kk++i +  +
  gi|91773319|ref|YP_566011.1|  94 YS----KKKTIIGLKTD 106
                                   *6....45558887777 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.6e-07    0.0014      90     129 ..      62     106 ..      40     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.6e-07
                    LDcluster4  90 nlilvlssdvviai.....ggrsGTlsEialaleegkpvivlkgt 129
                                   nl  v  +d+v+a+     ++ sGT+ Ei +a++++k++i lk++
  gi|91773319|ref|YP_566011.1|  62 NLEAVDNCDIVVAVldggsDIDSGTAWEIGYAYSKKKTIIGLKTD 106
                                   5667889*****98554334679*******************954 PP

>> DUF4062  Domain of unknown function (DUF4062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.1e-05     0.063      18      61 ..      25      77 ..      14      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                       DUF4062 18 lieallelglepvgmee.........faardqsqlelcleevdecdifililg 61
                                  l +al+ lg++ +  +e         +++++++ ++l le vd+cdi++++l 
  gi|91773319|ref|YP_566011.1| 25 LETALKDLGFDVFVPQEdsndteaarEEMDSNKIFQLNLEAVDNCDIVVAVLD 77
                                  55555555666533333566666677899999******************985 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.5e-05     0.074       8      94 ..      14      99 ..      10     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                  Reprolysin_3  8 vnranqiyerdlgirlqlvaiiitdkasdpytkkdatealdelaevtaeaergqagyDlvhlftardesgvgGlAyvgsvcns 90
                                  +++a q y+r+l++ l+  +   + +++d++ ++ a+e +d+++ ++ +     ++ D+v+++ +  +++  G A+  +  +s
  gi|91773319|ref|YP_566011.1| 14 FSEAEQDYNRKLETALKDLGFDVFVPQEDSNDTEAAREEMDSNKIFQLNL-EAVDNCDIVVAVLDGGSDIDSGTAWEIGYAYS 95
                                  677889999888888777799999999999999999*****998777664.479***********999********9888777 PP

                  Reprolysin_3 91 skka 94
                                  +kk+
  gi|91773319|ref|YP_566011.1| 96 KKKT 99
                                  7773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1202.91
//
Query:       gi|91773320|ref|YP_566012.1|  [L=200]
Description: hypothetical protein Mbur_1344 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-45  154.2   0.0    2.7e-45  154.0   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 !  154.0   0.0   1.5e-49   2.7e-45       1     166 []      11     181 ..      11     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 1.5e-49
                                   HHHHHHHHHHHTTSS-S-H.H---HHHHSEEEEEEEEEEE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS----HH CS
                       AMMECR1   1 lklareaieealkeekkle.eeakeelkekaglFVtlkekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFspvtae 80 
                                   ++lar++ie++lk++++ +  + +e + e +g+FVtl+ k+g+LRGCiG+  ++  L++++++ A++aA++DpRF+ v  +
  gi|91773320|ref|YP_566012.1|  11 VRLARNTIESFLKDGEQSDsIDLPEVFGELRGVFVTLT-KNGNLRGCIGHPYADSVLESAIVDSAISAATRDPRFPMVDIS 90 
                                   689*************99978888899999********.77**************************************** PP

                                   HHTTEEEEEEEE---EE--......GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TTCCCSTT CS
                       AMMECR1  81 ElpeleveVsvLtepepiv......ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpdewkdse 155
                                   E++++ veV+vLt+pe ++      +e +e+g+hGli + g ++++lLPqva+e++ d  + l++++ Kagl++d+w  + 
  gi|91773320|ref|YP_566012.1|  91 EMSDIIVEVTVLTQPELVDvlpdklPEVIEIGRHGLIAKMGMYQGLLLPQVAPENDFDAIDLLNHTCLKAGLPQDAW-LTG 170
                                   ******************4455566888**********************************************99*.67* PP

                                   SEEEEE-EEEE CS
                       AMMECR1 156 ikltryevekf 166
                                    +++ +e+++f
  gi|91773320|ref|YP_566012.1| 171 AQMYWFEGQIF 181
                                   *******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1326.15
//
Query:       gi|91773321|ref|YP_566013.1|  [L=413]
Description: phosphoglycerate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-104  348.6   0.0   4.3e-104  348.5   0.0    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 !  348.5   0.0  2.4e-108  4.3e-104       1     377 [.      12     393 ..      12     394 .. 0.93

  Alignments for each domain:
  == domain 1  score: 348.5 bits;  conditional E-value: 2.4e-108
                                   GGGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHTT CS
                           PGK   1 vkdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellgk 81 
                                   ++d+d+ ++++lvRvD+N+p++  g i dd ri++++pT+  l  ++akvvll+H++rp g+++ ++++ +a+ +s+ lg+
  gi|91773321|ref|YP_566013.1|  12 IDDFDIGDRTILVRVDLNSPMSPGGGILDDMRIKSHIPTLMDL--EDAKVVLLAHQSRP-GKNDFTTMQLHADVMSSSLGR 89 
                                   689****************************************..899***********.89******************* PP

                                   -EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS--TTTTHHH CS
                           PGK  82 eVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahrahaStvgia 155
                                   +V++++d++g+++++ ia++++g+v+lLeNvrfy+eE+ +++       ++++kla l+d++ nDAF+++hr+h S++g++
  gi|91773321|ref|YP_566013.1|  90 KVTYIDDIFGTHARDSIASMEKGDVILLENVRFYSEESLRRPvdehqgtHMVRKLAPLFDIFLNDAFAVSHRSHLSITGFS 170
                                   *************************************8654444455557******************************* PP

                                   HCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT-B-TTSS-. CS
                           PGK 156 kvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlkaqgleigkslv. 233
                                    vl++ aG+lme+E++ l+  l+  e p++++lGGakv+d +kv e++l++   d+++++G++an+ l+a+g++ig   + 
  gi|91773321|ref|YP_566013.1| 171 GVLPSGAGRLMEREITSLDVSLKGSESPCIFVLGGAKVDDSLKVAEHVLSSGgaDRVLVTGVVANVVLAASGVDIGGPNMk 251
                                   ***88********************************************99778**********************66553 PP

                                   ..-G....GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-.EEEEE-HHHHHHHHHHHCC-SEE CS
                           PGK 234 ..ee....dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipede.malDigpktielfaeaikeaktv 307
                                     e+    d+++ ak++le+++    k+ +p Dv+++++    e+  ++++++ +++  + Dig +ti +++++i++aktv
  gi|91773321|ref|YP_566013.1| 252 fiESqgylDQIDKAKNILERFD---GKLGFPRDVALNDNG---ERIEANIDDVASSNlPINDIGLETIVAYSSEIENAKTV 326
                                   3355667678***********8...89**********932...2233467777655559********************** PP

                                   EEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
                           PGK 308 vwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsLelLeg 377
                                   v+nGp+Gv eie f+ GT +i+ka+++a    +si+GGg+  a v+++g+++ +sh+StGGgA++++L g
  gi|91773321|ref|YP_566013.1| 327 VLNGPAGVSEIEGFEIGTSEIIKAATNA---GYSIAGGGHITAEVRNMGYEKMFSHISTGGGACIDYLAG 393
                                   *************************996...49***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3189.99
//
Query:       gi|91773322|ref|YP_566014.1|  [L=355]
Description: cobyrinic acid ac-diamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-33  113.5   0.3    7.1e-33  112.5   0.3    1.5  1  DRTGG         DRTGG domain
    2.6e-32  112.3   0.0    5.1e-32  111.3   0.0    1.5  2  AAA_26        AAA domain
    0.00014   21.9   0.0    0.00056   20.0   0.0    2.1  2  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0049   16.9   0.0      0.019   15.0   0.0    1.9  2  Hpr_kinase_N  HPr Serine kinase N terminus


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 !  112.5   0.3   1.6e-36   7.1e-33       1     104 [.     215     320 ..     215     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 1.6e-36
                                   HHHHHTT-EEEE--..SS--E-EEEE-SS-HHHHHHHHHT..SEEEEEETT-HHHHHHHTT-TEEEEEEETT----HHHHH CS
                         DRTGG   1 eiaealgaevlnggeeelrrvekvvvgamsvenmlerlke..gdlvivpGDRediqlaaleagiaalilTgglepseevlk 79 
                                   ei+e+l+aevl+g+e+    v++++vgam+v+++++++++  +++vi++GDR+diq+aa+ea++++l+lTg+l+ps++vl 
  gi|91773322|ref|YP_566014.1| 215 EIVEDLHAEVLAGSENLDVLVDHYLVGAMEVNSAIKYFRRtpNSVVITGGDRSDIQMAAIEARVKCLVLTGNLQPSAAVLG 295
                                   79************877777*******************999*************************************** PP

                                   HHHHHT--EEE-SS-HHHHHHHHHT CS
                         DRTGG  80 laeeaglpvlsveldtfttakrinq 104
                                    a+ea++pv+ v+ dt++t++r+++
  gi|91773322|ref|YP_566014.1| 296 SADEAQIPVILVRGDTMSTIERMER 320
                                   **********************997 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   1.1e-35   5.1e-32       2     196 ..       3     210 ..       2     212 .. 0.91
   2 ?   -3.5   0.0       1.7   7.6e+03     127     145 ..     300     318 ..     297     336 .. 0.69

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.1e-35
                        AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie......ededselikellgldqtyelpeplalsaplspe 76 
                                   +i++++ ++++GK++++ g+  +lk+kg+++gy+KP+++ ++      +ded+e ++++++l+++++ ++p++l++ l   
  gi|91773322|ref|YP_566014.1|   3 SILISSSEKYSGKSSLCIGIGTILKDKGYSIGYMKPVGNMLVdvngvlSDEDAEQARKVFDLKDDIKNITPILLTDNL--- 80 
                                   69***************************************9888887888***********************9875... PP

                        AAA_26  77 laarqegedidlekiv....kelekdadivvVEGagglgvpiteellnadiaknlgapvilVarggl.gtinqllltieal 152
                                   + +++ g++ +l+k +     e++ d+d+v+ EG+gg+g + +++l++ ++a   g +++lVar+++ ++++++l  ie+ 
  gi|91773322|ref|YP_566014.1|  81 VEDALAGVEKHLDKTIldayGEISRDKDVVLLEGTGGIGGGAIYGLSDPQVASIVGTKILLVARYESiHAVDRILSDIELI 161
                                   556666777788888888889**********************************************89************ PP

                        AAA_26 153 rqknvrvlGvilNkvrnp......envetlekksgipvlGvvPylpdlea 196
                                   ++     +GvilN+v +       e +  + +++g++vlGv+P +++l++
  gi|91773322|ref|YP_566014.1| 162 HD-PDMFAGVILNEVDEGqleyvcELLVPFLENKGVKVLGVLPKDTTLRS 210
                                   99.5789*******755567666668999999999************987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                        AAA_26 127 lgapvilVargglgtinql 145
                                    ++pvilV   + +ti+++
  gi|91773322|ref|YP_566014.1| 300 AQIPVILVRGDTMSTIERM 318
                                   6789999876666777665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.2e-07   0.00056      10     121 ..      13     211 ..       4     216 .. 0.84
   2 ?   -2.4   0.0         1   4.6e+03      54      63 ..     301     322 ..     255     348 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-07
                                   SSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx................................... RF
                          CbiA  10 vGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep................................... 54 
                                   +GK++l+++++++l+++g+ +   + ++++      + g+  d++                                    
  gi|91773322|ref|YP_566014.1|  13 SGKSSLCIGIGTILKDKGYSIGYMKpVGNMLVD---VNGVLSDEDAeqarkvfdlkddiknitpilltdnlvedalagvek 90 
                                   7************************77777444...457776666678999999999************************ PP

                                   ...........................................................CCHCCCHHHHHHCHCHHHH..E CS
                                   ...........................................................xxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...........................................................dlkrllellealgkkkalllki 76 
                                                                                               ++r+l  +e +  +     ++
  gi|91773322|ref|YP_566014.1|  91 hldktildaygeisrdkdvvllegtggigggaiyglsdpqvasivgtkillvaryesihAVDRILSDIELIHDP----DMF 167
                                   ****************************************************9999555555555555555555....99* PP

                                   EEEEEEEESS...-...TTCHHHHHHHHHHCTS-EEEEEE--CCHCCC CS
                                   xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  77 agvvlnrvdgenee...tllkealeelkqrygvpvlgviprdeavaea 121
                                   agv+ln vd+ + e   +ll  +le+     gv+vlgv+p+d+ +   
  gi|91773322|ref|YP_566014.1| 168 AGVILNEVDEGQLEyvcELLVPFLENK----GVKVLGVLPKDTTLRSV 211
                                   *********985432224444555443....***********998655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                   H............CCHCCCHHH CS
                                   x............xxxxxxxxx RF
                          CbiA  54 p............dlkrllell 63 
                                   +            +++r+++l+
  gi|91773322|ref|YP_566014.1| 301 QipvilvrgdtmsTIERMERLI 322
                                   1444445554444555555555 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.36   1.6e+03       1      22 [.     211     232 ..     211     265 .. 0.75
   2 !   15.0   0.0   4.2e-06     0.019      77     123 ..     274     320 ..     260     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.36
                                   EEHHHHHHHTTEEEEEGGTT-E CS
                  Hpr_kinase_N   1 vtvkelieklklelllgeegld 22 
                                   v ++e++e+l+ e+l g+e+ld
  gi|91773322|ref|YP_566014.1| 211 VPISEIVEDLHAEVLAGSENLD 232
                                   5689999999999999998886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.2e-06
                                   HTT--S-EEEETTT---HHHHHHHHHH---EEEESS-HHHHHTTHHH CS
                  Hpr_kinase_N  77 fskkipciiltrgleppeellelaeeygvpllrtklstsefiaelir 123
                                   ++ ++ c++lt +l+p   +l  a+e+++p++  +  t ++i+++ r
  gi|91773322|ref|YP_566014.1| 274 IEARVKCLVLTGNLQPSAAVLGSADEAQIPVILVRGDTMSTIERMER 320
                                   678899*********************************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.25s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2284.63
//
Query:       gi|91773323|ref|YP_566015.1|  [L=696]
Description: Acyl-CoA synthetase [Methanococcoides burtonii DSM 6242]
Scores for 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-74  248.8   0.0    6.3e-74  248.2   0.0    1.3  1  ATP-grasp_5    ATP-grasp domain
    1.6e-55  186.7   4.5    4.3e-55  185.3   0.3    3.0  3  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    2.2e-25   89.4   0.5    8.9e-25   87.4   0.1    2.3  2  CoA_binding_2  CoA binding domain
      3e-13   50.3   0.4    1.1e-12   48.5   0.1    2.2  2  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.28   10.6   0.0    1.5  1  F_bP_aldolase  Fructose-bisphosphate aldolase class-II


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 !  248.2   0.0   1.7e-77   6.3e-74       2     222 .]     473     693 ..     472     693 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.2 bits;  conditional E-value: 1.7e-77
                   ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaae 82 
                                   a+++gr++L   e+ ++l+aygipvvet  +++ +  ++a+e++gypvv+K+ s+di+hKtdvgGvr++l++a++v++a+ 
  gi|91773323|ref|YP_566015.1| 473 AISNGRRTL-GLESFDILRAYGIPVVETLNVKTLQGTLDACENMGYPVVMKVLSADISHKTDVGGVRIGLENADDVERAYL 552
                                   678888888.79********************************************************************* PP

                   ATP-grasp_5  83 eilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertka 163
                                   +++++v+++ p+a ++gv+Vq+m + gg E+i+g+++D +FGp+++fGlGGt+vevlkdv++ ++p+     +++++++++
  gi|91773323|ref|YP_566015.1| 553 TMMSDVRRYMPHAVVSGVQVQKMIT-GGKEVIIGMNRDVQFGPLLMFGLGGTYVEVLKDVSFSVAPVGVDVLKKMVSSIRT 632
                                   *************************.******************************************************* PP

                   ATP-grasp_5 164 skllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeeg..vvalDarirl 222
                                   +++l+g+rge+++d+a+++++l+r+sqLv+d+peI e +inPl+v +eg  +va+D+r++l
  gi|91773323|ref|YP_566015.1| 633 YPILTGIRGESPSDIASIVDTLCRVSQLVSDFPEILEFEINPLMVLPEGqgCVAMDIRLTL 693
                                   *********************************************884445*******986 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2   7.1e+03      81      95 ..      89     103 ..      86     107 .. 0.78
   2 !  185.3   0.3   1.2e-58   4.3e-55       1     138 []     150     287 ..     150     287 .. 0.99
   3 ?    1.7   0.1     0.058   2.1e+02       3      31 ..     297     325 ..     295     327 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                  Succ_CoA_lig  81 kkpvvvlksGrseag 95 
                                    k vvv+ +G +eag
  gi|91773323|ref|YP_566015.1|  89 VKNVVVISAGFKEAG 103
                                   488999999988877 PP

  == domain 2  score: 185.3 bits;  conditional E-value: 1.2e-58
                  Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark 81 
                                   +G+i+++sqSGa++++ ldwa +rg+gfsk++slGn+ad++++d+l  +++d++t vi++ylE+++dg kf+++ar+++rk
  gi|91773323|ref|YP_566015.1| 150 KGNISMMSQSGAICTSTLDWADARGVGFSKFISLGNKADLSENDFLLEMEDDENTAVIAAYLEGVKDGPKFMEIARKVSRK 230
                                   69******************************************************************************* PP

                  Succ_CoA_lig  82 kpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                   kp++v+ksGr++ g+ra++shtg lagsd++++aaf q+ v+r+ds+e+l+d+++++
  gi|91773323|ref|YP_566015.1| 231 KPIIVIKSGRTAVGSRAVSSHTGTLAGSDEAYNAAFSQSNVIRADSVEQLMDLMRAF 287
                                   *****************************************************9986 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.058
                  Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfskv 31 
                                   +ia+i+  G+l++  +d+++  gl +s++
  gi|91773323|ref|YP_566015.1| 297 NIAIITNAGGLGILAADACQFAGLSLSSF 325
                                   8*********************9999987 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.1   2.5e-28   8.9e-25       2     114 ..      10     133 ..       9     135 .. 0.97
   2 ?   -2.3   0.0       1.7   5.9e+03      50      71 ..     366     386 ..     356     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 2.5e-28
                                   -EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH-- CS
                 CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalga 80 
                                   ++aV+Gas ++gk g+ vl++lle  +g +++p+npk++eilg ++y+++ ++p+  +l++v++p+  +p+ +++++ +g+
  gi|91773323|ref|YP_566015.1|  10 SVAVIGASRTEGKVGRAVLDNLLEsySG-RIIPINPKADEILGLPCYPTILDAPGGAELAVVVVPAVLVPDALEKCGLAGV 89 
                                   79**********************9888.**********************878*************************** PP

                                   SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                 CoA_binding_2  81 kavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                   k v++ ++            ++ +ae+++e+g+r+vg++C++++
  gi|91773323|ref|YP_566015.1|  90 KNVVVISAgfkeagiegsKLERRCAEIVKEHGMRMVGPNCLGII 133
                                   *****9999********************************996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                   T....T--EEEE-S-HHHHGGG CS
                 CoA_binding_2  50 aedpepvdlvdvftppeatpei 71 
                                    + + +vd v ++t p+a+ ei
  gi|91773323|ref|YP_566015.1| 366 LD-DPNVDGVILLTSPQAMTEI 386
                                   43.3689999999999999887 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1     3e-16   1.1e-12       4      96 .]       9      98 ..       6      98 .. 0.97
   2 ?   -2.3   0.0         2   7.3e+03      73      93 ..     387     407 ..     362     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3e-16
                                  EEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHT CS
                   CoA_binding  4 tkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelvea 85
                                   +v+viGa++++++++  + ++ l+     ++++np+  ++e+lglp+y+++ +++    ++ av++vPa  + +a +++  a
  gi|91773323|ref|YP_566015.1|  9 ASVAVIGASRTEGKVGrAVLDNLLESYSGRIIPINPK--ADEILGLPCYPTILDAPGG--AELAVVVVPAVLVPDALEKCGLA 87
                                  68***********************9999********..*******************..*********************** PP

                                  T-SEEEEESST CS
                   CoA_binding 86 gikgiviiteg 96
                                  g+k +v+i++g
  gi|91773323|ref|YP_566015.1| 88 GVKNVVVISAG 98
                                  ********976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHTT-SEEEEE CS
                   CoA_binding  73 esaqeavdelveagikgivii 93 
                                   ++++e+v e  ++  k+i++ 
  gi|91773323|ref|YP_566015.1| 387 KNIAEVVAEKCAHTKKPILCS 407
                                   567788888888888888886 PP

>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.7e-05      0.28      14      53 ..     491     530 ..     489     567 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.7e-05
                                   T--EEEEE--SHHHHHHHHHHHHHHTS-EEEEE-HHHHHH CS
                 F_bP_aldolase  14 gyavgafnvtnletvkavleaaeeaksPvIlqlsegaaak 53 
                                    y+++ + + n++t++++l+a+e++  Pv++++    +++
  gi|91773323|ref|YP_566015.1| 491 AYGIPVVETLNVKTLQGTLDACENMGYPVVMKVLSADISH 530
                                   69*****************************998877743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 4144.73
//
Query:       gi|91773324|ref|YP_566016.1|  [L=174]
Description: bifunctional deaminase-reductase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-22   80.5   0.0    1.5e-21   77.1   0.0    1.9  1  RibD_C    RibD C-terminal domain
    6.5e-06   25.9   0.0      9e-06   25.5   0.0    1.1  1  DHFR_1    Dihydrofolate reductase


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 !   77.1   0.0   1.7e-25   1.5e-21       4     199 ..       6     166 ..       4     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.7e-25
                                   EEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEH...HHHHHHT--SS--SSCHSCHHHTT.GSS-EEEE CS
                        RibD_C   4 ilklavSlDGklaaaggeskwitgeearadvhelraeadailvGr...gtvladnpsltvrwvkkreaeadaearqpvrvV 81 
                                   il +a+SlDG++a+++g+ +w+ +   + + ++  ++ +++++Gr   +++l ++     +w+ k            + +V
  gi|91773324|ref|YP_566016.1|   6 ILYIAMSLDGYIATKSGSVDWLIDIPGYDFYDRFIENIGVVVMGRksyEMILSFDV----EWPYKF----------ARSYV 72 
                                   6779*****************************************99989888888....666665..........779** PP

                                   EETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCCESE-HHHHHHHHHHTT--EEEEEETHHHHHHHHHTTT-SEEEEE CS
                        RibD_C  82 vdstlrvpldakvltddaptlvatteeadkekveklkvrvdlkelleeLkergirsllveGGatLagsllraglvDelrly 162
                                   +++ ++ +++  v  +                      ++  k l+eeL+ +  ++++v+GG+ +++++l+++l+De+++ 
  gi|91773324|ref|YP_566016.1|  73 LTHGNKFEDTDLVKFT----------------------NISVKGLVEELSSETEKDIWVLGGGEVVREFLDSKLIDEIIIG 131
                                   *****95444444444......................488**************************************** PP

                                   EESCE--TTSBCSSSSST-SSEEEEEEEEEEETTEEE CS
                        RibD_C 163 iaPkllGgagktlfdgegfkalklklvksealgegvv 199
                                   ++P+llG+ g +lf ++  + ++lkl  ++++ +g+v
  gi|91773324|ref|YP_566016.1| 132 VMPILLGE-GIPLFREYAHQ-TELKLLDVKQYEKGMV 166
                                   ********.**********9.7**********99986 PP

>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     1e-09     9e-06      39     108 ..      45     121 ..      35     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1e-09
                                   EEEEEHHHHHCC-.....S--TTCEEEEE-S-TT---TTEE..EESSHHHHCC.CCTTS.SEEEEEE-HHHHHHCGG CS
                        DHFR_1  39 pvimGrkTfeslg....krpLpnrkniVltrnedlkvegve..vvssleeala.lakeekeevfviGGaeiYkqalp 108
                                    v+mGrk +e +     + p +  +++Vlt+ ++++  + +  +  s++ +++ l +e++++++v+GG+e+ +++l+
  gi|91773324|ref|YP_566016.1|  45 VVVMGRKSYEMILsfdvEWPYKFARSYVLTHGNKFEDTDLVkfTNISVKGLVEeLSSETEKDIWVLGGGEVVREFLD 121
                                   69********77544466699999**********988655523444666677635555589*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1011.18
//
Query:       gi|91773325|ref|YP_566017.1|  [L=368]
Description: hypothetical protein Mbur_1349 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 2413.16
//
Query:       gi|91773326|ref|YP_566018.1|  [L=351]
Description: hypothetical protein Mbur_1350 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2075.58
//
Query:       gi|91773327|ref|YP_566019.1|  [L=187]
Description: NADPH-dependent FMN reductase [Methanococcoides burtonii DSM 6242]
Scores for 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-38  129.4   0.0    1.2e-37  129.1   0.0    1.1  1  FMN_red         NADPH-dependent FMN reductase
    1.5e-13   50.9   0.0    1.9e-13   50.6   0.0    1.2  1  Flavodoxin_2    Flavodoxin-like fold
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.036   14.3   0.0    1.4  1  Flavodoxin_5    Flavodoxin domain
      0.029   14.9   0.7      0.056   14.0   0.5    1.6  2  Fer4_17         4Fe-4S dicluster domain
        0.1   12.2   1.7       0.27   10.8   1.7    1.7  1  RecR            RecR protein
       0.11   12.7   0.0       0.19   11.9   0.0    1.5  1  T2SS_PulS_OutS  Type II secretion system pilotin lipoprotein 
       0.34   11.0   1.5       0.59   10.3   1.5    1.4  1  zf_CCCH_4       Zinc finger domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.0   4.6e-41   1.2e-37       1     146 [.       1     150 [.       1     157 [. 0.94

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 4.6e-41
                                   -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--...---HCHGHTCGGSHHHHHHHHHHHH-SCEEEE CS
                       FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc.alcdkdlesegqtsddvaellekiaaadaliiv 79 
                                   mkil+isGS+++++n++++++ ++e +k +g+e++ i ++++ i+pc a  ++   ++++ +dd++e++ k+ +ada++++
  gi|91773327|ref|YP_566019.1|   1 MKILGISGSPKQEGNNETIIKNVLEVAKSKGFETDSIMISQKkIAPCiACGTCARGEKCPINDDMQEVYGKLVEADAIVFS 81 
                                   9*********************************************9844444444469********************** PP

                                   EEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECS CS
                       FMN_red  80 tPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpra 146
                                   tP+Y+g+++++lK+++Dr +  +r++ +lrgK +a++avgg+r+gg++ + q  + ++ ++g+i+v+++
  gi|91773327|ref|YP_566019.1|  82 TPVYFGGMTAQLKALFDRSVLlRRQGFQLRGKFGAVMAVGGSRNGGQEKTIQNVHDCMmVHGMIPVGDG 150
                                   *******************99*************************************77*****9986 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   7.5e-17   1.9e-13       1     137 [.       1     123 [.       1     167 [. 0.74

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 7.5e-17
                                   -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTT.CHHHHHHH.HHHHHCS CS
                  Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeek.padveseq.iekllaa 78 
                                   mkiL i ++p++e  ++  + + ++e ++++g  e + + + +    p +         a  ek p++ ++++   kl +a
  gi|91773327|ref|YP_566019.1|   1 MKILGISGSPKQE-GNNETIIKNVLEVAKSKG-FETDSIMISQKkIAPCIACGTC----ARGEKcPINDDMQEvYGKLVEA 75 
                                   9***********5.999***************.9*********755554443333....3344446777777779****** PP

                                   SEEEEEEE-BTTB--HHHHHHHHHHS-TTT.SCEETTCSSCCCCTTT.TSEEEEEEEESS- CS
                  Flavodoxin_2  79 daivlqfPlwwfgvPailKgwiDrvltagf.afyteeggegrgggLk.gkkalvivttGgp 137
                                   daiv+++P+++ g+ a+lK+ +Dr +   +  f             +   k   ++++Gg+
  gi|91773327|ref|YP_566019.1|  76 DAIVFSTPVYFGGMTAQLKALFDRSVLLRRqGF-------------QlRGKFGAVMAVGGS 123
                                   ***********************9654444133.............222235555555555 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.4e-05     0.036      12      69 ..      42     100 ..      39     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                  Flavodoxin_5  12 kkiaeriaeelreegelvdved.vekesedlesydavvigasvyygkllpelakFvekh 69 
                                   kkia  ia  + ++ge + ++d +++   +l ++da+v+ ++vy g++  +l+++ ++ 
  gi|91773327|ref|YP_566019.1|  42 KKIAPCIACGTCARGEKCPINDdMQEVYGKLVEADAIVFSTPVYFGGMTAQLKALFDRS 100
                                   78999999999999999999995544555*********************999887754 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   2.2e-05     0.056      37      57 ..      38      60 ..      11      64 .. 0.69
   2 ?   -3.2   0.0       5.2   1.3e+04      39      47 ..     130     139 ..     109     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                       Fer4_17 37 aekeekaslCieCgeCe..rkCP 57
                                  ++ ++k+  Ci Cg C+  +kCP
  gi|91773327|ref|YP_566019.1| 38 MISQKKIAPCIACGTCArgEKCP 60
                                  34458***********98899*9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                       Fer4_17  39 ke.ekaslCi 47 
                                   k  +++++C+
  gi|91773327|ref|YP_566019.1| 130 KTiQNVHDCM 139
                                   2235666665 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.7   0.00011      0.27      12      33 ..      40      61 ..      34      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                  HHHH-EE-TTT--EESSSS-CC CS
                          RecR 12 akekvrhCsrCgnlteedlCaI 33
                                    +k+ +C  Cg+ +  + C+I
  gi|91773327|ref|YP_566019.1| 40 SQKKIAPCIACGTCARGEKCPI 61
                                  5789*****************9 PP

>> T2SS_PulS_OutS  Type II secretion system pilotin lipoprotein (PulS_OutS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.4e-05      0.19      46      68 ..      14      36 ..       7      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-05
                                  --HHHHHHHHHHHHHHTT--GGG CS
                T2SS_PulS_OutS 46 pddatilkvalkvakqrgWdtde 68
                                  ++++ti+k +l+vak++g++td 
  gi|91773327|ref|YP_566019.1| 14 GNNETIIKNVLEVAKSKGFETDS 36
                                  7899****************975 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.5   0.00023      0.59       7      16 ..      51      60 ..      48      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                     zf_CCCH_4  7 GtCkkGdkCr 16
                                  GtC +G+kC+
  gi|91773327|ref|YP_566019.1| 51 GTCARGEKCP 60
                                  9********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1049.64
//
Query:       gi|91773328|ref|YP_566020.1|  [L=577]
Description: Cl- channel, voltage gated [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-90  303.1  41.8    7.1e-88  295.2  33.4    2.0  2  Voltage_CLC  Voltage gated chloride channel
    6.7e-26   90.5   1.6    2.6e-12   47.0   0.3    2.7  2  CBS          CBS domain


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.9   3.5e-06     0.031     167     220 ..      26      81 ..      22      88 .. 0.88
   2 !  295.2  33.4   7.9e-92   7.1e-88      22     353 ..      89     410 ..      83     411 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCHH.CHHHHHHH.HHHHHHHHHHHHCCCS CS
                   Voltage_CLC 167 fvllGilgGllgalfvrlllkverlfrkle.klkikkrl.epalvgllvgllglll 220
                                   ++l+Gi+ Gl  ++++ +l  +e +f ++   ++ + ++  pa++gllvg+++++ 
  gi|91773328|ref|YP_566020.1|  26 AILIGIFTGLTIVAYNICLKYAEDIFWSNSdITSSYIVIlIPAIGGLLVGIIVFFS 81 
                                   79**********************9999887777775556**************97 PP

  == domain 2  score: 295.2 bits;  conditional E-value: 7.9e-92
                                   HHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHHTT.--SHHHHHHHHHHHHHHHHHH CS
                   Voltage_CLC  22 ipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrllklsrndrdrrlvaaGaAAGiAAa 102
                                   +pev++  + + g++s+r ++  +++s++++++G+s+G+e+p + +G+ +gs++++ lk+ +++r r+l+ +GaA+GiAAa
  gi|91773328|ref|YP_566020.1|  89 VPEVIEGTALHGGRISVRGAFREVVLSIISIATGGSVGKEAPGILAGSGIGSIFAKALKA-PDHRYRTLIGCGAAGGIAAA 168
                                   79*********************************************************5.5554777************* PP

                                   HT-HHHHHHHHCTTTSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S....-.T---...--GGGHHHHHHHHHHHHHHHH CS
                   Voltage_CLC 103 FnaPlgGvlfalEevsrefslrallpvfvasvvaalvlrlllgeepa....fgeveslfalsllelilfvllGilgGllga 179
                                   FnaPl+Gv+f++E++++e+++r+++p+++++v+a+lv++l++  +p+    +g ++     ++ e il+++lG l+G+ ++
  gi|91773328|ref|YP_566020.1| 169 FNAPLAGVVFVVEVILGELETRTFIPIVISAVFATLVANLIFEVKPIqisyYG-LVD----PIGESILYLILGTLCGITSV 244
                                   *********************************************99877666.664....8******************* PP

                                   HHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCCHHHHHCTT-S-HHHHHH...HHHHHHHHHH CS
                   Voltage_CLC 180 lfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlgggyeliasllegstlllsllllllllllkllata 260
                                   l +r+l +v+  f kl   +i+  ++pa++gllvgl+g+++p+ + g gy+ ia++l++s   +++ lll+l++lk+la +
  gi|91773328|ref|YP_566020.1| 245 LLIRTLFTVHDGFSKL---PIHSAFKPAIGGLLVGLMGYFYPQ-IRGIGYDVIADVLTNS---FTIQLLLVLFVLKILAFS 318
                                   **************99...999999******************.***************9...****************** PP

                                   HHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHHHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHH CS
                   Voltage_CLC 261 ltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgafalvGmaaflagvtrapltaiviviEltgdlelllpl 341
                                   +t+gsg +gG ++Ps++ GA+lG ++g+++++++p +++   ga+alvGm+a+lag++raplta++i++Elt++++++lpl
  gi|91773328|ref|YP_566020.1| 319 FTIGSGGAGGSIVPSMFAGAMLGGAYGTLVHSIFPTSTA-AAGAYALVGMGATLAGTARAPLTAVLILFELTQNYNIILPL 398
                                   ***********************************6555.57*************************************** PP

                                   HHHHHHHHHHHC CS
                   Voltage_CLC 342 mlavliAkavad 353
                                   m+a+++++ +++
  gi|91773328|ref|YP_566020.1| 399 MFACVVSNSISN 410
                                   *******99875 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   1.3e-14   1.1e-10       5      55 ..     447     497 ..     439     499 .. 0.92
   2 !   47.0   0.3   2.9e-16   2.6e-12       2      53 ..     507     560 ..     506     563 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.3e-14
                                   SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   m+++v+t++ d+t +++l+lm ++++ ++PV+d+++kl+Givtl+D  +++
  gi|91773328|ref|YP_566020.1| 447 MRTNVHTISDDDTAKDLLDLMQSSRHAGFPVLDGNKKLCGIVTLEDMREKV 497
                                   9********************988899*******************98875 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 2.9e-16
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53 
                                   ++i t++v++++pd+tl  +l++++ ++v+rlPVV  d+d+ l+Gi+t++D+++
  gi|91773328|ref|YP_566020.1| 507 SQIATHNVISAYPDETLDVVLKRFAMRDVGRLPVVsrDDDKSLLGIITRSDIVK 560
                                   7999********************6556********998999**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3844.42
//
Query:       gi|91773329|ref|YP_566021.1|  [L=430]
Description: MiaB-like tRNA modifying enzyme [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-23   81.4   0.3      8e-23   80.3   0.3    1.6  1  UPF0004        Uncharacterized protein family UPF0004
    1.2e-18   68.1   0.1    1.4e-17   64.6   0.0    2.2  2  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
       0.13   12.4   0.1       0.24   11.6   0.1    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd


Domain annotation for each model (and alignments):
>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.3   1.3e-26     8e-23       1      94 [.       2      91 ..       2      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.3e-26
                                  XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-H CS
                       UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrek 83
                                  kv+i+t+GC+ N++ se++++++++ gyelv++  +A+vv++nTC+v+ ++e+k+++++++l a+      vvv+GCm+q + 
  gi|91773329|ref|YP_566021.1|  2 KVHITTYGCSANQASSEIMIASVRDLGYELVDE-MDAEVVVINTCTVKYTTEQKILHKIEDLGAKG---IDVVVTGCMPQVQL 80
                                  79*****************************98.59**************************9977...89************ PP

                                  HHHHHH-TTS- CS
                       UPF0004 84 eellkeepevd 94
                                  e++l+++p ++
  gi|91773329|ref|YP_566021.1| 81 ETILERNPDAH 91
                                  ******99744 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.071   4.2e+02      73     115 ..      62     101 ..      26     124 .. 0.60
   2 !   64.6   0.0   2.3e-21   1.4e-17       3     167 .]     147     317 ..     145     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.071
                                   TCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  73 lavpgiritvetngtlpdeeklerllelgvdrvslgleaadde 115
                                   l      i v++ g +p   +le++le+++d   lg++++ + 
  gi|91773329|ref|YP_566021.1|  62 L--GAKGIDVVVTGCMP-QVQLETILERNPDAHILGVNSIAKI 101
                                   2..33334444444444.4466666666666666666666555 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 2.3e-21
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.TTHHHHHHHHHHTC........ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx........ RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.pdfvellerlakla........ 74 
                                   +++gC + C +C+++     +g+ rs + ++i+e ++ + ++ g++e++l++++   y  d  +ll +l ++         
  gi|91773329|ref|YP_566021.1| 147 ISQGCDYSCAYCIVTI---ARGKLRSFDADSIVEDIRMA-VDEGCREIWLTSQDNGQYgTDRDVLLPELLRRIvaipgdfk 223
                                   789************8...8*******************.9**********776555555555555555555556657666 PP

                                   .CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEE CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                   Radical_SAM  75 .vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdriv 150
                                      g+ + +++ ++l  ++ +e ++       v+l++++a+d  vlk+mnr h++ee    + +lrea +++    +d+iv
  gi|91773329|ref|YP_566021.1| 224 iRVGMMNPFSVTPIL--DDLIEVFRSDKiYKIVHLPIQSASDN-VLKKMNRYHSIEEANGIVFRLREA-FPDltlFTDIIV 300
                                   666666666666666..899999999889**************.******99****************.************ PP

                                   EBTTTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                   Radical_SAM 151 glpGendeeleellell 167
                                   g+  e+d +++ +le++
  gi|91773329|ref|YP_566021.1| 301 GFSSESDNDFNMTLEWV 317
                                   **************996 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 ?   11.6   0.1     4e-05      0.24      68     120 ..      23      75 ..      18      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                                   HHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHH CS
                 NAD_binding_2  68 avdeviegllealkkgdilidgstsspedtrelakelkekglkfldaPVSGGe 120
                                    v+++  +l+++++++ ++i++ t+++++ +++ +++++ g+k +d+ V+G  
  gi|91773329|ref|YP_566021.1|  23 SVRDLGYELVDEMDAEVVVINTCTVKYTTEQKILHKIEDLGAKGIDVVVTGCM 75 
                                   577777789****************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2583.26
//
Query:       gi|91773330|ref|YP_566022.1|  [L=362]
Description: fructose 1,6-bisphosphatase II [Methanococcoides burtonii DSM 6242]
Scores for complete 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-114  382.2   5.9   1.6e-114  382.0   5.9    1.0  1  FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-enco


Domain annotation for each model (and alignments):
>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.0   5.9  8.8e-119  1.6e-114       4     307 ..      22     350 ..      19     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 382.0 bits;  conditional E-value: 8.8e-119
                   FBPase_glpX   4 alelvrvteaAAlaaarlvGrgdkeaadqaAveamrkalneleikgevviGegekdeapmLyiGekvGsgeg.pevdiavd 83 
                                      l++vteaAA+aa+ ++G+g+k+ adq++veamr+++n+l++kg++ iGege+deapmL+iGe+vG+g+g   vdiavd
  gi|91773330|ref|YP_566022.1|  22 LPSLIHVTEAAAIAASYQMGKGNKNYADQVSVEAMRRMMNTLDFKGVIKIGEGERDEAPMLFIGEEVGTGKGdIVVDIAVD 102
                                   56799*******************************************************************99******* PP

                   FBPase_glpX  84 pleGttlvAkglpnaisviAvaekgsllkapdvYmeKlvvgpeak........gvidldapveenlkavakalgkevedlt 156
                                   pleGt+l+A+g p++isv+A+ae g l++ pdvYm+K+vvgp++         ++idldap+ +nl++vakal++++ +++
  gi|91773330|ref|YP_566022.1| 103 PLEGTNLTADGIPGSISVMAMAEPGGLFHGPDVYMDKIVVGPDVVryekehpdEKIDLDAPIIKNLEIVAKALERDIGEIV 183
                                   ******************************************99559999999**************************** PP

                   FBPase_glpX 157 vvvLdrpRheelieeireagarvklisdGDvaaaiaaaleesgvdvllGiGgapEGvlaAaalkclgGemqarlvpr.... 233
                                   vv+L+r+Rh+++ieeir++garv+l+sdGD+++ +++a+++sg++v++G+Gg+ E+vl+Aaa+k+lgG++ arlv+     
  gi|91773330|ref|YP_566022.1| 184 VVILERDRHKNMIEEIRATGARVNLVSDGDLMPGVSTAIRGSGIHVVMGSGGSGEAVLTAAAIKILGGKVLARLVLPtvan 264
                                   **************************************************************************97779** PP

                   FBPase_glpX 234 ..........keeereraekmgi..edldkvltledLvkgddvifaatgvTdgelLkgvrfkggg.arteslvmrsksgtv 301
                                             k+e++ r+++mgi  ++++++l++++Lv g d ifaa+gvT+g++L+ v+++ggg ar++s++m s sg+v
  gi|91773330|ref|YP_566022.1| 265 ggseeeiaeeKAEKMPRLATMGIteDNINDILDTDKLVPGTDFIFAASGVTSGQFLNQVNLFGGGnARVHSICMGS-SGVV 344
                                   ********9999999********77789********************************999888********99.5999 PP

                   FBPase_glpX 302 rfiesi 307
                                   +  +si
  gi|91773330|ref|YP_566022.1| 345 KLTDSI 350
                                   988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2702.24
//
Query:       gi|91773331|ref|YP_566023.1|  [L=184]
Description: hypothetical protein Mbur_1355 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   37.9   0.1    3.1e-09   37.1   0.1    1.3  1  CGI-121   Kinase binding protein CGI-121


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 !   37.1   0.1   1.7e-13   3.1e-09      25     161 ..      50     179 ..      28     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.7e-13
                                   EE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS--HHHHHH CS
                       CGI-121  25 fldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvssseadeeevlk 105
                                     da +i  k h+ +A+ +a+ a ++g+   k l  E++ + s++++Igea+   g+s+   +++ + ++++  +  e  k
  gi|91773331|ref|YP_566023.1|  50 GMDAGKIAGKAHIDHAISKAMKAMENGTNIAKDLGVEMMRYASGKKQIGEAFS-IGLSEGRLDVVFIIIGAP-VNVGEAAK 128
                                   579*************************************************9.*****************9.78888899 PP

                                   HHHHHS-SEEE.--SHHHHHH--HHHHHHHTT--..TT---SSHHH.HHHHHHHHHHT CS
                       CGI-121 106 slkevvegelv.pleeeleeltdwkkikkiYklneleeekeeevke.ledlvvsaval 161
                                   +++++ve + v + +      +  +++   + ++  ++e e+  ++ + +lv+++val
  gi|91773331|ref|YP_566023.1| 129 KISSLVELSDVlKYSV-----SKNEQLISQFSIT--DAELEAVGEDrIPELVLERVAL 179
                                   9999999555524443.....6788999999999..3344444445599999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1327.72
//
Query:       gi|91773332|ref|YP_566024.1|  [L=962]
Description: leucyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-62  209.9   1.6    5.2e-44  150.5   0.4    2.7  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    3.9e-26   91.7   0.5    6.6e-11   41.6   0.0    3.3  3  tRNA-synt_1g   tRNA synthetases class I (M)
    6.6e-20   71.6   0.2    1.4e-19   70.6   0.2    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    6.8e-10   38.8   0.1    4.4e-07   29.5   0.0    2.4  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    2.5e-06   27.1   0.0    6.3e-06   25.8   0.0    1.6  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.022   14.9   0.1         14    5.9   0.0    3.9  4  DUF1858        Domain of unknown function (DUF1858)
      0.026   13.5   0.0      0.045   12.7   0.0    1.3  1  tRNA-synt_1d   tRNA synthetases class I (R)
      0.039   12.9   0.0      0.091   11.7   0.0    1.5  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 !  150.5   0.4   2.3e-47   5.2e-44       1     304 [.      13     326 ..      13     332 .. 0.86
   2 !   57.3   0.0   3.9e-19   8.8e-16     321     601 ..     396     670 ..     374     671 .. 0.84

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 2.3e-47
                   tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                   k+++kW+e++vf++e    ++++++ ++++ Py +G+lH Gh  + t+ d+v rykrm G++vly +G+   G +i    e
  gi|91773332|ref|YP_566024.1|  13 KWQQKWNESKVFEAE---ADDRDKYFITIPYPYLNGNLHAGHTRTFTIGDVVARYKRMMGNNVLYPMGFHVTGTPIVGLAE 90 
                                   589***********9...788999***************************************************976544 PP

                   tRNA-synt_1  82 kklgakekkerkklg......re..efrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                     + +++ ++ k ++      +e  + ++   +++++++ e +++++ +G s+D+ r+  T d+++++ +++ f  l++k+
  gi|91773332|ref|YP_566024.1|  91 -LIQNRDPETMKVYTefhgipVEtlKGMDTPEKIVDYFSVEAERSMRSIGYSIDWRRKFTTTDPNYKKFIEWQFNLLYEKD 170
                                   .3445555454444411111133114457778999********************************************** PP

                   tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpl...adkeevklviaTTtPeTllgdtavavnpeldyv..... 227
                                   li +g+++v+w+++   ++ + ++ + ++      + + l   + +  + +  aT +PeT++g t + +np+l++v     
  gi|91773332|ref|YP_566024.1| 171 LIVKGSHPVKWCPNDDNPVEDHDILHGEEATI---IDYTLvkfKYDG-MIIPCATLRPETVFGVTNLWINPDLEHVkikvt 247
                                   ************************87776543...344431102222.36778***********************99999 PP

                   tRNA-synt_1 228 ..itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDye 304
                                      ++e +++ +   ++l+  + e +  ed+ +++L+g +v++pl++ ++  +   +v+ e+G+G+V   P h + Dy 
  gi|91773332|ref|YP_566024.1| 248 feGREEVWVVSKEAYRKLIFTDREVEFIEDVDASSLIGIKVTNPLNDAQVITLPASFVKGENGSGIVMSVPSHAPYDYL 326
                                   8778888999999999999999999****************************************************96 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 3.9e-19
                   tRNA-synt_1 321 gtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkp.iiyrateqWfvrvke..ladaalkavekv 398
                                   g+l+e++++++g+ v + ++ ++++l e g        e s p+  r ++p ++ +++ qWf + ++   +d++ + +e++
  gi|91773332|ref|YP_566024.1| 396 GVLKENTGKYSGMAVSKIKDVLTRDLIEMGIGE--VFYEFSEPVVCRCGTPcVVNMVKGQWFLNYSNpeWKDKVYRCIENM 474
                                   899**************************9755..566778899889888835667778*****998789*********** PP

                   tRNA-synt_1 399 qfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkalekeakdklkke 476
                                    ++p+  + ++++ +   +d +  R++  G+ +p+   +  ++ ++ ++     ++ a+  +   e+++l  e  d++  +
  gi|91773332|ref|YP_566024.1| 475 DIIPEDLRVEFNNKVDWLKDKACARKKGLGTLLPFdnqWLIESLGDSTIYM-SYYIIAKFIAMGIETEQLVPELFDHVLLK 554
                                   **********************************86668888888777733.34455556666666677777888888555 PP

                   tRNA-synt_1 477 kgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglv 556
                                   k +le   +       Sg     +++   + +++++  +p d+ ++G D i   +   ++  +a++++  + + + ++g+v
  gi|91773332|ref|YP_566024.1| 555 KCSLETAAE------RSGI-DANIIE---QISSDFEYWYPVDLRSSGKDLIPNHLLFFLFHHVAIFDEDKWpRAIAINGFV 625
                                   555555554......3554.555555...45789*******************************9998663788999*99 PP

                   tRNA-synt_1 557 rdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                      eG+KmSKs+g  +  +d i++ygad+ R++++ ++++++d ++
  gi|91773332|ref|YP_566024.1| 626 S-LEGKKMSKSKGPLLTLNDAITNYGADISRMYILsSAEQMQDADW 670
                                   6.68******************************988889999877 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 !   38.4   0.1   2.7e-13   6.1e-10       1      58 [.      34      91 ..      34     107 .. 0.89
   2 !    8.3   0.0   0.00037      0.83      48     133 ..     107     192 ..     100     198 .. 0.83
   3 !   41.6   0.0   2.9e-14   6.6e-11     288     369 ..     590     673 ..     569     685 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.7e-13
                                  EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH CS
                  tRNA-synt_1g  1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek 58
                                  +++t + pY ng+lH Gh ++  ++D++aRykr+ g++vl+  g    Gtpi   Ae 
  gi|91773332|ref|YP_566024.1| 34 YFITIPYPYLNGNLHAGHTRTFTIGDVVARYKRMMGNNVLYPMGFHVTGTPIVGLAEL 91
                                  58**************************************************988774 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00037
                                   -SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTT CS
                  tRNA-synt_1g  48 hGtpielkAekegvtpeelvekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkd 126
                                   hG+p+e+   k   tpe++v+ ++ e ++ +++++ s d     +tt+ + k++ +  f+ l+ek+li +++  + +cp+d
  gi|91773332|ref|YP_566024.1| 107 HGIPVET--LKGMDTPEKIVDYFSVEAERSMRSIGYSIDwrRKFTTTDPNYKKFIEWQFNLLYEKDLIVKGSHPVKWCPND 185
                                   7777654..566679******************98888733334588899999***************************9 PP

                                   TEEE-GG CS
                  tRNA-synt_1g 127 erflpdr 133
                                   ++   d 
  gi|91773332|ref|YP_566024.1| 186 DNPVEDH 192
                                   9877776 PP

  == domain 3  score: 41.6 bits;  conditional E-value: 2.9e-14
                                   EEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE CS
                  tRNA-synt_1g 288 igkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldf 366
                                    gkd i+ H +f+     +   e k p++++ ++++ +egkK+SkS+g + + ++a++++ ad+ R y++++a++++D+d+
  gi|91773332|ref|YP_566024.1| 590 SGKDLIPNHLLFFLFHHVAifDEDKWPRAIAINGFVSLEGKKMSKSKGPLLTLNDAITNYGADISRMYILSSAEQMQDADW 670
                                   49***********999999988999******************************************************99 PP

                                   -HH CS
                  tRNA-synt_1g 367 swe 369
                                   + +
  gi|91773332|ref|YP_566024.1| 671 KNS 673
                                   876 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 !   70.6   0.2   6.1e-23   1.4e-19       1     119 [.     709     814 ..     709     851 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 6.1e-23
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   d+w+ls+l++ + e++ea++  r ++a++++y ++ nd+ +wy +   +              ++l evl+ ++rl+aPf+
  gi|91773332|ref|YP_566024.1| 709 DKWMLSRLQQRILETNEALDTIRTRNALQNAYFLLFNDI-RWYQKRGGN--------------ALLCEVLDVWIRLMAPFT 774
                                   9**************************************.9**777555..............569*************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkk..esimlaewpe.kaeelekel...e 119
                                   P+i+Ee+w    e +g+   + i+la++p+ +++  ++++   e
  gi|91773332|ref|YP_566024.1| 775 PHICEEIW----EAIGHTdnDLISLADYPQyDESLVDTQAeftE 814
                                   ********....66654444999******755544444331221 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 !    6.7   0.0    0.0018       4.1      21      50 ..      45      74 ..      36      83 .. 0.91
   2 !   29.5   0.0     2e-10   4.4e-07     207     299 ..     584     678 ..     574     680 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0018
                                  S--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                  tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqf 50
                                   + h Gh+R++ + D+++r+ +++g +v +
  gi|91773332|ref|YP_566024.1| 45 GNLHAGHTRTFTIGDVVARYKRMMGNNVLY 74
                                  578**********************99987 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 2e-10
                                   SEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS.S-T CS
                  tRNA-synt_1e 207 eidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls.ahy 285
                                    +d+ s G+DL+  h    l  + a fd  ++ +    ng++++eg+kmsks + ++t++d+++++ + + R+++ls a+ 
  gi|91773332|ref|YP_566024.1| 584 PVDLRSSGKDLIPNHLLFFLFHHVAIFDeDKWPRAIAINGFVSLEGKKMSKSKGPLLTLNDAITNYGADISRMYILSsAEQ 664
                                   58999******999999999********999*****************************************887751566 PP

                                   TS-EEE-HHHHHHH CS
                  tRNA-synt_1e 286 rsqldfkeelleea 299
                                    +  d+k++ +e+a
  gi|91773332|ref|YP_566024.1| 665 MQDADWKNSGIETA 678
                                   77789999988877 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 !   25.8   0.0   2.8e-09   6.3e-06      23     126 ..     217     325 ..     205     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.8e-09
                 tRNA-synt_1_2  23 levfttrpdtlfGvtfvalapehplvekl..aekkkelaafieevkkk.sesereletke..keGvftglkaihPitgeki 98 
                                   +   t rp+t+fGvt + + p+ + v+     e ++e+    +e+ +k   ++re+e  e        g+k+++P+++ ++
  gi|91773332|ref|YP_566024.1| 217 IPCATLRPETVFGVTNLWINPDLEHVKIKvtFEGREEVWVVSKEAYRKlIFTDREVEFIEdvDASSLIGIKVTNPLNDAQV 297
                                   666799**************976555433347778888777666555413444555555522556689************* PP

                 tRNA-synt_1_2  99 piwvanyvlmeygtgavmavPahdqrDf 126
                                       a +v  e g+g vm+vP+h   D+
  gi|91773332|ref|YP_566024.1| 298 ITLPASFVKGENGSGIVMSVPSHAPYDY 325
                                   ***********************98887 PP

>> DUF1858  Domain of unknown function (DUF1858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0063        14       6      33 ..      56      85 ..      52     114 .. 0.90
   2 ?    3.9   0.0     0.027        60      37      56 ..     551     570 ..     549     572 .. 0.87
   3 ?   -1.8   0.0       1.6   3.5e+03      25      52 ..     623     650 ..     619     655 .. 0.80
   4 ?   -3.0   0.0       3.9   8.8e+03      40      51 ..     847     858 ..     843     859 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0063
                                  BHHHHHHH-GGGH..HHHHHTTGGGGGSCC CS
                       DUF1858  6 tIgelleeyPela..evLvelGfhclgcps 33
                                  tIg+++ +y  ++  +vL  +Gfh  g p+
  gi|91773332|ref|YP_566024.1| 56 TIGDVVARYKRMMgnNVLYPMGFHVTGTPI 85
                                  9*************************9999 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.027
                                   THHHHSBHHHHHHHHT--HH CS
                       DUF1858  37 tvakvetleqaakvhgidld 56 
                                   ++ k+ +le+aa+  gid +
  gi|91773332|ref|YP_566024.1| 551 VLLKKCSLETAAERSGIDAN 570
                                   578899************87 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.6
                                   TGGGGGSCCHHTTHHHHSBHHHHHHHHT CS
                       DUF1858  25 Gfhclgcpsllktvakvetleqaakvhg 52 
                                   Gf  l+ +++ k+ ++ +tl +a    g
  gi|91773332|ref|YP_566024.1| 623 GFVSLEGKKMSKSKGPLLTLNDAITNYG 650
                                   88889999999999******99976665 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3.9
                                   HHSBHHHHHHHH CS
                       DUF1858  40 kvetleqaakvh 51 
                                   k+et ++a+ + 
  gi|91773332|ref|YP_566024.1| 847 KMETFKKALSMQ 858
                                   89******9986 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     2e-05     0.045      14      61 ..      26      73 ..      15     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                  ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEE CS
                  tRNA-synt_1d 14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvi 61
                                   ++ ++ k  +    P +  ++h+Gh r+  iGd+v+r   ++G +v+
  gi|91773332|ref|YP_566024.1| 26 AEADDRDKYFITIPYPYLNGNLHAGHTRTFTIGDVVARYKRMMGNNVL 73
                                  55666777777777899999*************************997 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 ?   -3.7   0.0       1.9   4.3e+03      34      60 ..      44      70 ..      20      72 .. 0.81
   2 ?   11.7   0.0   4.1e-05     0.091     265     312 ..     615     661 ..     582     691 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.9
                  tRNA-synt_1f 34 SGliHiGnlrevltadlvaralrkrge 60
                                   G +H G  r    +d+var  r +g+
  gi|91773332|ref|YP_566024.1| 44 NGNLHAGHTRTFTIGDVVARYKRMMGN 70
                                  5999***********999998877776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.1e-05
                  tRNA-synt_1f 265 aPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrk 312
                                    P  +  + +   +g+kms+SkG  ltl+d+++ +  ++ r +il+  
  gi|91773332|ref|YP_566024.1| 615 WPRAIAINGFVSLEGKKMSKSKGPLLTLNDAITNYGADISRMYILS-S 661
                                   4665555544444555*****************9999999998887.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (962 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 5814.00
//
Query:       gi|91773333|ref|YP_566025.1|  [L=202]
Description: hypothetical protein Mbur_1357 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1494.54
//
Query:       gi|91773334|ref|YP_566026.1|  [L=168]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  225.4   0.5    2.9e-67  225.2   0.5    1.0  1  ArsR      ArsR transcriptional regulator
  ------ inclusion threshold ------
      0.057   13.3   0.2          2    8.3   0.0    2.2  2  Clathrin  Region in Clathrin and VPS


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 !  225.2   0.5   3.3e-71   2.9e-67       1     158 [.       8     165 ..       8     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.2 bits;  conditional E-value: 3.3e-71
                          ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgeeveealklLkkikliEsqWrmpepgekpekeYhtsYskv 81 
                                   indp+eLvpllq+f+s+++k+v++ l++eWlt+ ++e+k+g +++e++++Lkk++l+EsqW+mp+pg++pekeYh+sYskv
  gi|91773334|ref|YP_566026.1|   8 INDPSELVPLLQTFQSKEHKQVFNLLLEEWLTKGDIEDKMGFDATESISILKKCGLLESQWHMPKPGKMPEKEYHSSYSKV 88 
                                   8******************************************************************************** PP

                          ArsR  82 qanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkGqrlelv 158
                                   q nfqcs+edlsdii ++f ++ee+++l++++e+ ve+gn+s+s+l+r+++++pl+ir+la+rs+kl+v+Gqrl+++
  gi|91773334|ref|YP_566026.1|  89 QSNFQCSFEDLSDIIILTFNKYEEISDLITELEELVEKGNHSMSSLTRAMNKNPLYIRSLARRSSKLSVMGQRLKMN 165
                                   **************************************************************************986 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00022         2      23      58 ..      11      43 ..       8      64 .. 0.85
   2 ?    3.2   0.1    0.0085        76      13      48 ..     103     138 ..      94     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00022
                                  HHHHCHHHCCHHHCHTS--HHHHHHHHHHHHHTT-H CS
                      Clathrin 23 leelleyLekvlkedskenpalqtallelyakyddp 58
                                  + el ++L+  +   ske+++++++lle  ++ +d+
  gi|91773334|ref|YP_566026.1| 11 PSELVPLLQTFQ---SKEHKQVFNLLLEEWLTKGDI 43
                                  679*********...99**********976666665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0085
                                   CHHHHHCTT-HHHHCHHHCCHHHCHTS--HHHHHHH CS
                      Clathrin  13 vvklfeeaglleelleyLekvlkedskenpalqtal 48 
                                   ++  f +++ +  l+  Le++++++++  ++l  a+
  gi|91773334|ref|YP_566026.1| 103 IILTFNKYEEISDLITELEELVEKGNHSMSSLTRAM 138
                                   677899999999999999999987777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1360.06
//
Query:       gi|91773335|ref|YP_566027.1|  [L=262]
Description: Crp/FNR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-10   40.2   0.2    5.3e-10   38.7   0.0    2.0  1  HTH_24          Winged helix-turn-helix DNA-binding
      1e-07   31.7   0.0    2.4e-07   30.5   0.0    1.6  1  MarR_2          MarR family
    1.2e-07   31.6   0.0    2.6e-07   30.5   0.0    1.6  1  HTH_11          HTH domain
    4.5e-07   29.7   0.1    1.5e-06   28.0   0.0    1.9  1  MarR            MarR family
    4.6e-06   26.6   0.3     0.0016   18.4   0.0    3.0  3  HTH_3           Helix-turn-helix
    9.7e-06   25.5   0.1    0.00011   22.1   0.0    2.6  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      2e-05   25.0   0.0    4.5e-05   23.9   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
    0.00022   21.1   0.0    0.00062   19.7   0.0    1.9  1  HTH_45          Winged helix-turn-helix
    0.00055   19.7   0.0     0.0012   18.5   0.0    1.6  1  HTH_23          Homeodomain-like domain
    0.00076   19.6   0.0     0.0035   17.5   0.0    2.0  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0011   19.3   0.0     0.0036   17.6   0.0    1.9  1  Rrf2            Transcriptional regulator
     0.0028   17.4   0.0     0.0076   16.0   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain
     0.0038   17.3   0.0     0.0087   16.2   0.0    1.6  1  HTH_28          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.025   14.2   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
      0.023   15.3   0.0      0.057   14.0   0.0    1.7  1  Phage_rep_O     Bacteriophage replication protein O
      0.027   14.3   0.0       0.06   13.2   0.0    1.5  1  HTH_10          HTH DNA binding domain
       0.03   14.0   0.0      0.097   12.4   0.0    1.8  2  DUF4423         Domain of unknown function (DUF4423)
      0.032   14.5   0.0       0.16   12.3   0.0    2.1  2  Mnd1            Mnd1 HTH domain
      0.033   14.1   0.0      0.084   12.7   0.0    1.7  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.038   13.9   0.0       0.17   11.8   0.0    2.0  2  HTH_36          Helix-turn-helix domain
      0.049   13.8   0.1       0.32   11.1   0.1    2.2  1  Mrr_N           Mrr N-terminal domain
      0.056   13.8   0.2       0.16   12.4   0.0    1.9  1  FaeA            FaeA-like protein
      0.089   12.8   0.1       0.23   11.5   0.1    1.7  1  HU-DNA_bdg      DNA-binding domain
        0.1   12.5   0.0       0.24   11.2   0.0    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.12   12.5   0.0       0.28   11.3   0.0    1.6  1  HTH_13          HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   7.5e-13   5.3e-10       4      47 ..      12      56 ..       4      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 7.5e-13
                        HTH_24  4 tdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  t+++IL ++ + +p+  q+e+Ae++g++p++v++++k+L+ eG+I
  gi|91773335|ref|YP_566027.1| 12 TKFQILTEVAAhQPNVRQKEIAEKIGVTPQAVSEYIKELTAEGFI 56
                                  89****999998999****************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.3e-10   2.4e-07       6      51 ..      12      56 ..      10      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.3e-10
                                  HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                  + +++L +++++ ++ ++++e+a++ g++++avs  +k+L a G++
  gi|91773335|ref|YP_566027.1| 12 TKFQILTEVAAHQPN-VRQKEIAEKIGVTPQAVSEYIKELTAEGFI 56
                                  789**********97.9***************************99 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.6e-10   2.6e-07       2      46 ..      13      56 ..      12      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.6e-10
                        HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                  ++qil+ + ++++++  +e+Ae+++v+ ++v  +Ik+L++ g+ I
  gi|91773335|ref|YP_566027.1| 13 KFQILTEVAAHQPNVRQKEIAEKIGVTPQAVSEYIKELTAEGF-I 56
                                  579*****888888****************************3.3 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.1e-09   1.5e-06       4      47 ..      12      56 ..      11      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.1e-09
                                  HHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  4 tqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGli 47
                                  t f iL+ ++ ++p  +++e+a+k+gv++ +v++ +++L  +G+i
  gi|91773335|ref|YP_566027.1| 12 TKFQILTEVAAHQPnVRQKEIAEKIGVTPQAVSEYIKELTAEGFI 56
                                  789999999877766*****************************9 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.3e-06    0.0016      10      31 ..      27      48 ..      24      52 .. 0.88
   2 ?   -1.3   0.0       3.3   2.4e+03      25      37 ..     136     147 ..     134     156 .. 0.74
   3 ?    4.6   0.0     0.047        34      30      46 ..     171     188 ..     170     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                                  HHHHHHHHHHTSSHHHHHHHHT CS
                         HTH_3 10 lsqeeLAeklGvsrstisriEn 31
                                    q+e+Aek+Gv+++++s +++
  gi|91773335|ref|YP_566027.1| 27 VRQKEIAEKIGVTPQAVSEYIK 48
                                  579*****************87 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                                   HHHHHHTTSSCSB CS
                         HTH_3  25 tisriEnGernPs 37 
                                   tis  E+G+    
  gi|91773335|ref|YP_566027.1| 136 TISSVEKGDD-VG 147
                                   8999**9943.55 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.047
                                   HTT.SSCSBHHHHHHHHH CS
                         HTH_3  30 EnG.ernPsletlkklak 46 
                                   E+G  rn +le+l+kla 
  gi|91773335|ref|YP_566027.1| 171 ERGgSRNVDLERLEKLAS 188
                                   7888************95 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.6e-07   0.00011      21      57 ..      26      62 ..      11      69 .. 0.83
   2 ?   -0.5   0.0       1.8   1.3e+03      20      38 ..     122     140 ..     106     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.6e-07
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrri 57
                                  ++ q+e+A+ +G+t++ vs  ++eL  eg i   gr +
  gi|91773335|ref|YP_566027.1| 26 NVRQKEIAEKIGVTPQAVSEYIKELTAEGFIFsDGR-V 62
                                  789***************************986454.2 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                                   EEHHHHHHHHHTTSSHHHH CS
                     HTH_Crp_2  20 lpltqeelAsmlGltretv 38 
                                   l ++++ + s  G+t ++v
  gi|91773335|ref|YP_566027.1| 122 LYVSKTNITSATGITISSV 140
                                   7899999999999999998 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 !   23.9   0.0   6.3e-08   4.5e-05       7      68 .]      15      70 ..      13      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.3e-08
                        HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  ++L  ++  +  +++++++++  v+ +++s+ +k+Lt+ G++       +++++r+r+T kG
  gi|91773335|ref|YP_566027.1| 15 QILTEVAAHQPNVRQKEIAEKIGVTPQAVSEYIKELTAEGFI------FSDGRVRYRITKKG 70
                                  788888888899999***************************......88899********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 !   19.7   0.0   8.7e-07   0.00062      21      65 ..      28      73 ..       3      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.7e-07
                        HTH_45 21 kkTkimykanLsykllnkYLdmLvekgli.kkskekYvlTekGlel 65
                                  ++ +i  k   + + +++Y++ L+ +g+i ++    Y++T+kG e 
  gi|91773335|ref|YP_566027.1| 28 RQKEIAEKIGVTPQAVSEYIKELTAEGFIfSDGRVRYRITKKGVEW 73
                                  45567777777888999************88999*********985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-06    0.0012       5      46 ..      11      55 ..       7      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                        HTH_23  5 reRlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  + +++il  +a      +++eIA++ gv+++ v+ ++k   +eG+
  gi|91773335|ref|YP_566027.1| 11 ITKFQILTEVAAhqpNVRQKEIAEKIGVTPQAVSEYIKELTAEGF 55
                                  67999******888************************9988986 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 !   17.5   0.0   4.9e-06    0.0035      22      52 ..      26      56 ..      15      61 .. 0.89
   2 ?   -0.9   0.0       2.8     2e+03      19      41 ..     120     142 ..     113     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.9e-06
                                  SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyv 52
                                   v++k++ae ++v p  Vse +k+L  +G++
  gi|91773335|ref|YP_566027.1| 26 NVRQKEIAEKIGVTPQAVSEYIKELTAEGFI 56
                                  6899************************985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                                   HHSSB-HHHHHHHHTS-HHHHHH CS
                Fe_dep_repress  19 ekkvvktkdlaerLnvspssVse 41 
                                   +  +v+++++ ++ ++  ssV +
  gi|91773335|ref|YP_566027.1| 120 GLLYVSKTNITSATGITISSVEK 142
                                   56689999999999999999976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     5e-06    0.0036      11      57 ..      14      58 ..       6      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5e-06
                                  HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  +++l++ a+++ +  v+ +eiae+ ++ p+ ++  +++L+ +g++ s
  gi|91773335|ref|YP_566027.1| 14 FQILTEVAAHQPN--VRQKEIAEKIGVTPQAVSEYIKELTAEGFIFS 58
                                  6899999999995..8****************************966 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05    0.0076       6      48 ..      14      56 ..      14      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                  ++iL  +a++++ ++ +e+A+++g+++ +v+ +++ L+ +G++
  gi|91773335|ref|YP_566027.1| 14 FQILTEVAAHQPNVRQKEIAEKIGVTPQAVSEYIKELTAEGFI 56
                                  7999999**********************************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05    0.0087       2      40 ..      13      54 ..      12      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                        HTH_28  2 RleiikllaaGh...svreaArelgisrrtvyrWikryeegG 40
                                  +++i+ ++aa+    +++e+A++ g++++ v+  ik + ++G
  gi|91773335|ref|YP_566027.1| 13 KFQILTEVAAHQpnvRQKEIAEKIGVTPQAVSEYIKELTAEG 54
                                  899******9755459999************99999877777 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.5e-05     0.025      24      61 ..      27      63 ..      13      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                                  ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                          GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrqgrG 61
                                    +++e+a+++gV+ + v e +++L+aeg + +  ++ 
  gi|91773335|ref|YP_566027.1| 27 V-RQKEIAEKIGVTPQAVSEYIKELTAEGFIFSDGRVR 63
                                  5.789*************************99888765 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     8e-05     0.057      49      86 ..      26      63 ..      21      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                   Phage_rep_O 49 wisnsqlveltgisrtkvskalkeLirekviikegrkv 86
                                   +++++++e +g+++++vs+ +keL++e+ i+ +gr +
  gi|91773335|ref|YP_566027.1| 26 NVRQKEIAEKIGVTPQAVSEYIKELTAEGFIFSDGRVR 63
                                  67899******************************533 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.4e-05      0.06      24      46 ..      27      49 ..      25      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.4e-05
                        HTH_10 24 vtlkeLAkelGIskstlsehLrk 46
                                  v+ ke+A+++G++++++se++++
  gi|91773335|ref|YP_566027.1| 27 VRQKEIAEKIGVTPQAVSEYIKE 49
                                  6679****************986 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.097      24      84 ..      15      72 ..      12      86 .. 0.87
   2 ?   -2.7   0.0       5.7   4.1e+03     118     129 ..     228     239 ..     199     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                       DUF4423 24 pvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt 84
                                   ++ e+++ +++    +e+a++++  ++ + v++ ++ L+  g++  d+  +yr t+k ++
  gi|91773335|ref|YP_566027.1| 15 QILTEVAAHQPN-VRQKEIAEKIG--VTPQAVSEYIKELTAEGFIFSDGRVRYRITKKGVE 72
                                  567787777777.999********..*******************************9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                       DUF4423 118 dissltlaiske 129
                                    +ssl+lai++e
  gi|91773335|ref|YP_566027.1| 228 GLSSLVLAIDEE 239
                                   456777777654 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00022      0.16      20      48 ..      31      59 ..      28      60 .. 0.85
   2 ?   -2.1   0.1       6.7   4.8e+03      17      32 ..     183     198 ..     180     209 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                          Mnd1 20 lapkekgivsqsVkdvlqsLvdDglveve 48
                                  +++ + g+++q V +++++L+++g + ++
  gi|91773335|ref|YP_566027.1| 31 EIAEKIGVTPQAVSEYIKELTAEGFIFSD 59
                                  555559*******************9876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.7
                          Mnd1  17 leklapkekgivsqsV 32 
                                   lekla+++  i    V
  gi|91773335|ref|YP_566027.1| 183 LEKLASSKSFIAVIGV 198
                                   7788877555555444 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.084      11      30 ..      29      48 ..      26      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlk 30
                                  qk+ Ae++gv++qaVs  +k
  gi|91773335|ref|YP_566027.1| 29 QKEIAEKIGVTPQAVSEYIK 48
                                  899*************9874 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024      0.17      25      55 .]      26      56 ..      14      56 .. 0.87
   2 ?   -1.1   0.0       2.6   1.9e+03      24      43 ..     122     141 ..     116     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                        HTH_36 25 fpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  +  q+ +a++ g+  + vs +ikeL   G+i
  gi|91773335|ref|YP_566027.1| 26 NVRQKEIAEKIGVTPQAVSEYIKELTAEGFI 56
                                  5579*********************988876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                        HTH_36  24 cfpsqetlakrlglsknTvs 43 
                                    + s+  + +++g+  ++v 
  gi|91773335|ref|YP_566027.1| 122 LYVSKTNITSATGITISSVE 141
                                   68899999999999988876 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00045      0.32      55      85 ..      44      74 ..       3      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
                         Mrr_N 55 gWartyLkkagllespkrgvwkiTekGrevl 85
                                  + ++++L+ +g++ s+ r  ++iT+kG e++
  gi|91773335|ref|YP_566027.1| 44 SEYIKELTAEGFIFSDGRVRYRITKKGVEWV 74
                                  556899*********************9985 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00022      0.16       5      45 ..      16      56 ..      12      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
                                  HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                          FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegki 45
                                  Il+ +   +  ++ +eiA+ +g++   +  Y++ L +eg i
  gi|91773335|ref|YP_566027.1| 16 ILTEVAAHQPNVRQKEIAEKIGVTPQAVSEYIKELTAEGFI 56
                                  666666656679**************************977 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00032      0.23      26      85 ..       8      71 ..       3      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                                  --EE-HHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHH....TTT-EEE-SSEEEEEEEES- CS
                    HU-DNA_bdg 26 sgsltledIidemvkegtevrketienilnlykrevseai....leGysVntglgrasltikGv 85
                                  ++ +t  +I+ e+++ + +vr+  i++ + +  + vse+i    +eG+  ++g +r+ +t kGv
  gi|91773335|ref|YP_566027.1|  8 KSGITKFQILTEVAAHQPNVRQKEIAEKIGVTPQAVSEYIkeltAEGFIFSDGRVRYRITKKGV 71
                                  56688889******************************99333347**************9998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00034      0.24      18      41 ..      27      50 ..      14      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                 HTH_AsnC-type 18 isyaeLAervGlSestvlrRvrrL 41
                                     +e+Ae++G+++++v + ++ L
  gi|91773335|ref|YP_566027.1| 27 VRQKEIAEKIGVTPQAVSEYIKEL 50
                                  5679*************9866655 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00039      0.28       7      49 ..      20      65 ..      16      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                        HTH_13  7 lvlsrPlVsagmvakeLkvtpraalklvkelglREl...TGRgrfr 49
                                      +P V  + +a+++ vtp+a+ + +kel         GR r+r
  gi|91773335|ref|YP_566027.1| 20 VAAHQPNVRQKEIAEKIGVTPQAVSEYIKELTAEGFifsDGRVRYR 65
                                  556689999999*******************764331125777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1914.89
//
Query:       gi|91773336|ref|YP_566028.1|  [L=176]
Description: hypothetical protein Mbur_1360 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-29  102.9   0.0    2.3e-29  102.7   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
      2e-05   25.2   0.5      0.034   14.6   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 !  102.7   0.0   2.6e-33   2.3e-29       1     164 [.       1     148 [.       1     149 [. 0.93

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 2.6e-33
                 Metallophos_2   1 MklaiiSDlH.snldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaaelgtd 80 
                                   M++++iSD+H + +d+++++   ++++  d+i haGD+  ++ e+ +++ +  +++aV+GN D           + el++ 
  gi|91773336|ref|YP_566028.1|   1 MRILAISDTHlKGGDIPPTFRGLVDDC--DMIAHAGDF--TSNECYNAFAATGKLKAVHGNSD-----------NSELKQL 66 
                                   9*********88889999999999999..********9..9999*******99**********...........99***** PP

                 Metallophos_2  81 lpeeaelelagekvlliHgdpl..gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpetyai 159
                                   lpe+ ++e +g k++++H+  l   ++ al++l+ e  +g+dv+++GH+H+p +ek  +v+++ PGs++epr++dp ++++
  gi|91773336|ref|YP_566028.1|  67 LPERLVFETEGIKIGIVHEGSLsiMDTTALRYLALE--MGVDVLIFGHIHRPLIEKS-DVILICPGSPTEPRQSDP-SVVL 143
                                   *******************98877777777777777..*******************.8****************9.**** PP

                 Metallophos_2 160 ldtde 164
                                   +d+++
  gi|91773336|ref|YP_566028.1| 144 IDIKD 148
                                   ***97 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.8e-06     0.034       1      75 [.       1      59 [.       1      81 [. 0.65
   2 !    9.0   0.1   0.00021       1.9     182     204 .]      94     116 ..      71     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-06
                                  EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS CS
                   Metallophos  1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe 75
                                  +ril i+D+H  l gg+++ + + l       ++d++ +aGD++        + + +aa +k    + +++GN +
  gi|91773336|ref|YP_566028.1|  1 MRILAISDTH--LKGGDIPPTFRGL---V--DDCDMIAHAGDFTSNE-----CYNAFAATGK----LKAVHGNSD 59
                                  89********..5555555444444...2..358********88776.....4444455555....356677777 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00021
                                   HHHHHHHHHTTESEEEEESSSSE CS
                   Metallophos 182 ealedllkkygvdlvisGHtHvy 204
                                    al+ l  + gvd+ i+GH+H++
  gi|91773336|ref|YP_566028.1|  94 TALRYLALEMGVDVLIFGHIHRP 116
                                   5566779999***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1120.94
//
Query:       gi|91773337|ref|YP_566029.1|  [L=188]
Description: hypothetical protein Mbur_1361 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1229.97
//
Query:       gi|91773338|ref|YP_566030.1|  [L=426]
Description: replication factor A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00055   19.7   3.2       0.37   10.6   0.1    3.3  4  NTR       UNC-6/NTR/C345C module


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 !    8.0   0.1   0.00013       2.4      13      96 ..      77     167 ..      75     173 .. 0.78
   2 !   10.6   0.1     2e-05      0.37      12      97 ..     187     279 ..     185     287 .. 0.73
   3 ?   -3.3   0.0      0.43   7.7e+03      23      38 ..     324     339 ..     319     349 .. 0.72
   4 ?   -3.0   0.1      0.36   6.5e+03      61      81 ..     381     397 ..     378     403 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00013
                                   EEEEEEEEETTEEEEEEEEEEEEEES...STTTSTTTSEEEEEEETT...SSSS-C-TTSEEEEEEEEE.EETSSEEEEES CS
                           NTR  13 vkVlsveeegsfdkytvkvkevlKeg...stdkvrkgkerlfvkrkd...CrcpkLklgkeYLimGkss.keegrgryvlg 86 
                                   vk+++++e+g+++++ +kv++   ++    ++    g+e+  +k  +      p++++gk+Y     +s +++gr++++l+
  gi|91773338|ref|YP_566030.1|  77 VKLNEIDEGGKWVNIRAKVLQLWDSShesVSQVGIIGDETATIKFIKwsrDIIPDVEEGKSYYFKNIVSnEWNGRFEVTLN 157
                                   7899999999**********99999933333334457888888887773334477888*****99888888999999**** PP

                                   TTCEEEEE-C CS
                           NTR  87 kkslveewpd 96 
                                   k+++vee  +
  gi|91773338|ref|YP_566030.1| 158 KNTVVEELDE 167
                                   ******9866 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 2e-05
                                   EEEEEEEEEETTEEEEEEEEEEEEEES......STTTSTTTSEEEEEEETTSSSS-C-TTSEEEEEEEEE.EETSSEEEEE CS
                           NTR  12 kvkVlsveeegsfdkytvkvkevlKeg......stdkvrkgkerlfvkrkdCrcpkLklgkeYLimGkss.keegrgryvl 85 
                                   +v+V++++e+g+++ +++kv +   ++           +++ +  f+k ++ +  +L +g++YL    ++ +++++++++l
  gi|91773338|ref|YP_566030.1| 187 MVNVVDITEDGKWVSIKAKVAQLWDNShesisqVGLVGDSTGTIKFIKWTSADLLDLTEGNSYLFNNVVAqEWNDKFEITL 267
                                   689999***************99999844432222233333444444444455555666******9777788999999*** PP

                                   STTCEEEEE-CC CS
                           NTR  86 gkkslveewpdk 97 
                                   +k+s +ee  ++
  gi|91773338|ref|YP_566030.1| 268 NKNSSIEELDED 279
                                   *******98665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.43
                                   TEEEEEEEEEEEEEES CS
                           NTR  23 sfdkytvkvkevlKeg 38 
                                      +y++++k+vl  g
  gi|91773338|ref|YP_566030.1| 324 VDGTYDLRIKAVLDDG 339
                                   5668999999999887 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 0.36
                                   -C-T.TSEEEEEEEEEEETSSE CS
                           NTR  61 kLkl.gkeYLimGksskeegrg 81 
                                   kLkl gk +++ G++      +
  gi|91773338|ref|YP_566030.1| 381 KLKLlGKYFMVTGSKV-----D 397
                                   5778899999999988.....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2564.63
//
Query:       gi|91773339|ref|YP_566031.1|  [L=610]
Description: sodium/hydrogen exchanger [Methanococcoides burtonii DSM 6242]
Scores for complete 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-40  136.7  53.9    1.2e-39  136.2  53.9    1.1  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
    1.6e-28   99.3   0.6      3e-28   98.4   0.6    1.4  1  TrkA_N           TrkA-N domain
    9.1e-13   47.8   0.3    2.3e-12   46.5   0.3    1.8  1  TrkA_C           TrkA-C domain
    8.3e-07   29.4   1.8    8.5e-07   29.4   0.4    1.7  1  NAD_binding_7    Putative NAD(P)-binding
    1.2e-05   24.9   0.4    2.8e-05   23.8   0.2    1.7  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00043   20.5   0.1     0.0009   19.4   0.1    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00047   20.4   0.2    0.00096   19.4   0.2    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00061   20.3   0.6     0.0021   18.6   0.1    2.2  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00072   19.2   0.5    0.00072   19.2   0.5    1.9  2  NmrA             NmrA-like family
     0.0011   18.3   0.0     0.0015   17.8   0.0    1.2  1  FAD_binding_3    FAD binding domain
     0.0011   18.5   0.3     0.0027   17.3   0.3    1.6  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0014   18.6   0.2     0.0023   17.9   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
     0.0027   17.8   0.8      0.013   15.6   0.2    2.2  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0062   15.8   0.3      0.011   15.0   0.3    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
       0.01   16.4   0.6      0.028   15.0   0.6    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.031   14.8   0.0       0.07   13.6   0.0    1.6  1  XdhC_C           XdhC Rossmann domain
      0.032   14.1   0.1       0.06   13.2   0.1    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.044   13.2   0.2       0.07   12.6   0.2    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.049   12.3   0.1      0.069   11.8   0.1    1.3  1  HI0933_like      HI0933-like protein
      0.097   12.6   0.2       0.27   11.2   0.0    1.9  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.14   11.2   0.0       0.22   10.5   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


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 !  136.2  53.9   1.4e-42   1.2e-39       3     374 ..      12     382 ..       9     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 1.4e-42
                                   HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHH CS
                Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknlksill 81 
                                   ++++ +l++  l+r +k+p++++l++ G++ Gp +lgl++ps   e l  +  l + +++F+ Gl++dl+++r+    +l 
  gi|91773339|ref|YP_566031.1|  12 AVLVMSLVAQSLSRLFKMPVLIFLLAEGIIAGPEVLGLLDPSllGEGLAAIVSLCVAVIVFDGGLHIDLKSIRSIQQGVLS 92 
                                   455557777779*****************************9999999999999*************************** PP

                                   HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHH CS
                Na_H_Exchanger  82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavl 162
                                   l ++gv+it+++ +l++++  i+g++l  + +fga+++at p v+++++ ++ rv+ r+  +l+ e+vlnDav+v+l a++
  gi|91773339|ref|YP_566031.1|  93 LITVGVIITFIFATLFTHY--IVGLSLEISAVFGALVTATGPTVITPVV-RQVRVNHRVSKTLELEGVLNDAVCVILAALV 170
                                   ******************8..89**************************.******************************* PP

                                   HHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTS.XXXHHHHHH CS
                Na_H_Exchanger 163 lalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaell.gvsgilgaf 242
                                    +++      + s + ++ ++++   +gl++g++ g+ll +++ ++  ++++  ++++  +++++ +ae+l   sgil++ 
  gi|91773339|ref|YP_566031.1| 171 FEVI----ISQLSGFEAVSFIVYRTMIGLTMGIASGLLLTRFLSSSVLSEQVVRFVTFTSVIATFVIAESLgAESGILAVA 247
                                   ***8....77889999****************************98677777777777778888*******44589***** PP

                                   HHHHHHHHHHHHTTHHHHHHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSS CS
                Na_H_Exchanger 243 laGlvlseyefsnklseklesfre...glfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllgl 320
                                   l G++++ ++++ k  + l+ f +     ++ l+F+l+ + l ++ ++   +  i+v+l+lv++  +r+l+vf+ + ++++
  gi|91773339|ref|YP_566031.1| 248 LFGIIVGSSNVRYK--AALKEFKSdlvLMMLSLIFILLAAMLKFEDIFRIGFAGIIVVLLLVFF--VRPLSVFVSTARTNF 324
                                   *******8888886..4455566555599**************999964555555555555555..8************** PP

                                   XHHHHHHCCCCSS.BHHHHHHHHHHHHHH....XHHHHTT.SSTTTCSTSXHHHHHHHH CS
                Na_H_Exchanger 321 slrealiigfgglqrgavalalaalgpal....gllarel.yallivvvlftvlvqGls 374
                                    ++e+l+i+f g  rg v + +a  +  +    ++   +  + l++++v++tvl  G+ 
  gi|91773339|ref|YP_566031.1| 325 RTKEKLFISFVGP-RGVVPASIATYFAIKmnslNIEGGQElVGLVFLTVIITVLMTGSL 382
                                   *************.***988887766666445566666777*************87765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.6   3.5e-31     3e-28       1     108 [.     397     506 ..     397     512 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 3.5e-31
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavl 81 
                                   i+++G G+vGr lae+++++g++vvv++++ee++++l + g++vv+gda d +vL++agie+a++v+a t++d +n+l+++
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRGENVVVVESSEEHCQRLMKSGIRVVHGDAEDVNVLKKAGIENAKYVVASTNQDNTNLLVCQ 477
                                   79*****************7778********************************************************** PP

                                   HHHHHTSS..SEEEEEESSGGGHHHHHHH CS
                        TrkA_N  82 lakelnpk..kkiiaraqdpehaellkkl 108
                                   +ak+ ++    +i+ar+++ e+ +++ +l
  gi|91773339|ref|YP_566031.1| 478 IAKTKFGFkeDQIVARVNNMENLHAFWDL 506
                                   **9998876688**********9987655 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.3   2.7e-15   2.3e-12       3      67 ..     544     606 ..     542     609 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.7e-15
                                   EEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                        TrkA_C   3 evtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                   ev+v+ + +++Gk++kel l++ + l++ +rRg++ +i++g++vLe +Dv++v+g+ ++ + +++
  gi|91773339|ref|YP_566031.1| 544 EVKVT-NPKVAGKSIKELSLPE-DSLLLMVRRGDQSFIANGNLVLEFDDVVTVIGEGDAAKIVAD 606
                                   78887.999*************.********************************9998765555 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 !   29.4   0.4   9.9e-10   8.5e-07       9      84 ..     396     481 ..     389     502 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.9e-10
                 NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekd...........legadlviaatddrelneri 78 
                                   ++lvvGgGev+   ++++ + g +v+vv    +e +++l+k   + +++d           +e+a+ v+a t++++ n  +
  gi|91773339|ref|YP_566031.1| 396 EILVVGGGEVGRILAERFEKRGENVVVVESS-EEHCQRLMKSGIRVVHGDaedvnvlkkagIENAKYVVASTNQDNTNLLV 475
                                   79**************************888.67888888866666655545556666677999***************** PP

                 NAD_binding_7  79 aeaaka 84 
                                   ++ ak+
  gi|91773339|ref|YP_566031.1| 476 CQIAKT 481
                                   **9986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.9     5e+03      11      46 ..     121     157 ..     119     165 .. 0.70
   2 !   23.8   0.2   3.2e-08   2.8e-05       1      72 [.     397     473 ..     397     479 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.9
                                   HHHHHHHHHHTHC.EEEE-SCHHHHHHHHHCEEEEET CS
                          ApbA  11 sllaakLakagad.vtlilrsrrlealkknGlrltse 46 
                                    +++a  +++g + +t ++r+ r+++ +++ l+l+++
  gi|91773339|ref|YP_566031.1| 121 AVFGALVTATGPTvITPVVRQVRVNHRVSKTLELEGV 157
                                   5666777776655467788877999988888888765 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.2e-08
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCH...SCCCCS-ESEE CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsae...ekselepidlv 72 
                                   i+++G G +G++la +  k g++v+++  s+ ++++l k G+r+   + +++++++++ ++++     s +++  ++
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRGENVVVVESSEeHCQRLMKSGIRVVHGDaEDVNVLKKAGIENAkyvVASTNQDNTNL 473
                                   89*********************************************999999988888888777733344444444 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 !   19.4   0.1   1.1e-06    0.0009       2      56 ..     397     451 ..     396     497 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasl 56 
                                   i ++G G+ G+ +a++++k+g +v+v++ ++e++++l+++g+++++  +e v+ l
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRGENVVVVESSEEHCQRLMKSGIRVVHGDAEDVNVL 451
                                   6699*************************************99988777666554 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 !   19.4   0.2   1.1e-06   0.00096       1      70 [.     397     459 ..     397     487 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTS CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkeg 70 
                                   +l++G+G vG+ +ae  +++++   +++v++ s+e++++l +    + +  +  dae++   L+++ ++ +
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRGE---NVVVVESSEEHCQRLMK----SGIRVVHGDAEDVNV-LKKAgIENA 459
                                   89******************98...5**************85....345555556666655.444435555 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 !   18.6   0.1   2.4e-06    0.0021       2      58 ..     397     448 ..     396     466 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHH CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneea 58 
                                   i ++G+G++g+ la+++ ++g   +++vv+ ++++e  + l ++ g++v ++d+e++
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRG---ENVVVV-ESSEEHCQRLMKS-GIRVVHGDAEDV 448
                                   6689*****************...****88.9999999999877.688888888775 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.7   1.4e+03     132     151 ..      96     115 ..      82     123 .. 0.79
   2 !   19.2   0.5   8.5e-07   0.00072       1      75 [.     397     469 ..     397     480 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                                   CTS-EEEEEE-EEGGG-BSS CS
                          NmrA 132 lgipytfvyagffmenflsl 151
                                    g++ tf+ a++f++++ +l
  gi|91773339|ref|YP_566031.1|  96 VGVIITFIFATLFTHYIVGL 115
                                   38999*********998765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 8.5e-07
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---GG CS
                          NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgfy 75 
                                   Ilv+G+ G+ G+ +++ + k+g +v   v ++++e  + l ++G  +v+gd++d ++l++a +++++ v ++t+  
  gi|91773339|ref|YP_566031.1| 397 ILVVGG-GEVGRILAERFEKRGENVV--VVESSEEHCQRLMKSGIRVVHGDAEDVNVLKKAgIENAKYVVASTNQD 469
                                   788886.9**************9985..5699***************************9989********99944 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-06    0.0015       3      84 ..     396     488 ..     394     525 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.....S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.....radglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                   ++l+VG+G +G +la    ++G +vv+ve  ++  +       r    + + +++l+++G+e+  +  +++n+ ++ +l +
  gi|91773339|ref|YP_566031.1| 396 EILVVGGGEVGRILAERFEKRGENVVVVESSEEHCQRLmksgiRVVHGDAEDVNVLKKAGIENAKYVVASTNQDNTNLLVC 476
                                   79****************************9999887664455556668999************99999999999999999 PP

                                   ECCCC......C CS
                 FAD_binding_3  79 elsdt......p 84 
                                   ++ +t       
  gi|91773339|ref|YP_566031.1| 477 QIAKTkfgfkeD 488
                                   966665544442 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 !   17.3   0.3   3.2e-06    0.0027       1      54 [.     395     448 ..     395     476 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHH CS
                UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeel 54 
                                   m+i v+G G vG + a  + ++g +v++v  +ee+ + l ++ i +++ + e++
  gi|91773339|ref|YP_566031.1| 395 MEILVVGGGEVGRILAERFEKRGENVVVVESSEEHCQRLMKSGIRVVHGDAEDV 448
                                   789*******************************************99887765 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 !   17.9   0.2   2.7e-06    0.0023       3      73 ..     402     471 ..     401     500 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                                   TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCC CS
                NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggk 73 
                                    G vGr l+++  +rg  +v+++  ++e+ ++l  ++g++vv+gd++dv+ l++a +++a  Vv++++++++
  gi|91773339|ref|YP_566031.1| 402 GGEVGRILAERFEKRG-ENVVVVESSEEHCQRLM-KSGIRVVHGDAEDVNVLKKAgIENAKYVVASTNQDNT 471
                                   599************6.899999999******97.7****************99978999999999987665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.5e-05     0.013      14      88 ..     396     471 ..     386     490 .. 0.84
   2 ?   -0.8   0.0       1.7   1.4e+03      14      31 ..     591     608 ..     586     609 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                                   EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHH.HHT-SEEEE-SSSSS- CS
                  Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkel.laeadvvisataseep 88 
                                   ++l++G Ge+++ +a+ + ++g + vvv+  + e+ ++l ++  + ++  a +++ lk++ +++a  v+++t+  + 
  gi|91773339|ref|YP_566031.1| 396 EILVVGGGEVGRILAERFEKRGEN-VVVVESSEEHCQRLMKSGiRVVHGDAEDVNVLKKAgIENAKYVVASTNQDNT 471
                                   79***************9866655.**************99864777788999999987559999999999988765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                   EEEEES-SHHHHHHHHHH CS
                  Shikimate_DH  14 kvlliGaGemaelvakhL 31 
                                    v++iG G  a+ va  L
  gi|91773339|ref|YP_566031.1| 591 VVTVIGEGDAAKIVADLL 608
                                   589********9999765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   1.3e-05     0.011     142     188 ..     394     441 ..     379     491 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                   TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                   Pyr_redox_2 142 pkrivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaa 188
                                   p  i+vvGgG +G  lA  + k g++v++ve  ++ + r +++ ++  
  gi|91773339|ref|YP_566031.1| 394 PMEILVVGGGEVGRILAERFEKRGENVVVVESSEEHCqRLMKSGIRVV 441
                                   5679**************************999998867777666544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   3.3e-05     0.028       2      37 ..     397     433 ..     396     467 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TT CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rl 37 
                                   ++vvGgG +g  lA+ + + g +V vve s++ + rl
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRGENVVVVESSEEHCqRL 433
                                   89****************************9988444 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.2e-05      0.07       2      97 ..     398     489 ..     397     514 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                                   EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHSSS--SEEEESS-HHHHH CS
                        XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeadetavvvlthdhklDaealeaalrkkaayigllGSrkkaa 82 
                                   +++G+g+v++ la+  ++ g +v+vv++ ee+   +r+     +  + + h+ + D ++l++a  ++a+y+ +   + +++
  gi|91773339|ref|YP_566031.1| 398 LVVGGGEVGRILAERFEKRGENVVVVESSEEH--CQRLM----KSGIRVVHGDAEDVNVLKKAGIENAKYVVASTNQDNTN 472
                                   79****************************84..45666....56788889999999999999988899998888888777 PP

                                   HHCTTS.--........ CS
                        XdhC_C  83 rrlerlraa..glseee 97 
                                    ++ ++++   g++e++
  gi|91773339|ref|YP_566031.1| 473 LLVCQIAKTkfGFKEDQ 489
                                   77776665535556655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     7e-05      0.06       2      42 ..     397     437 ..     396     474 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42 
                                   + v+G G +G+ +a+ f ++g +Vv+v+ see  ++ +++ 
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRGENVVVVESSEEHCQRLMKSG 437
                                   679*****************************999988765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   8.2e-05      0.07       1      68 [.     397     462 ..     397     471 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.2e-05
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEE CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdav 68 
                                   ilV+G+ G +G+ l+++++++g +v+++ + ++  ++  +  +++v++d  d + l+++  e ++ +v
  gi|91773339|ref|YP_566031.1| 397 ILVVGG-GEVGRILAERFEKRGENVVVVESSEEHCQRLMKSGIRVVHGDAEDVNVLKKAGIE-NAKYV 462
                                   899**9.************************888888888888*******999988887664.56665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   8.1e-05     0.069       2      43 ..     396     437 ..     395     480 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43 
                                   +++v+GgG  G   A++ +krg++V+++e+ ++  ++++ sG
  gi|91773339|ref|YP_566031.1| 396 EILVVGGGEVGRILAERFEKRGENVVVVESSEEHCQRLMKSG 437
                                   689********************************9999998 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.1   4.4e+03      50      91 ..     141     180 ..     138     219 .. 0.65
   2 ?   11.2   0.0   0.00032      0.27       2      40 ..     397     435 ..     396     469 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.1
                                   T----TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCC CS
                NAD_Gly3P_dh_N  50 giklpenlvattdlaealkgadiivlvvPsqalrevlkklkg 91 
                                   ++++++ +  t +l+ +l++a +++l+    +++ ++ +l+g
  gi|91773339|ref|YP_566031.1| 141 QVRVNHRVSKTLELEGVLNDAVCVILA--ALVFEVIISQLSG 180
                                   566777888888888888877666654..4445555555554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00032
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHH CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeine 40 
                                   i v+G+G  G  lA  ++++g++v++   +ee+++++ +
  gi|91773339|ref|YP_566031.1| 397 ILVVGGGEVGRILAERFEKRGENVVVVESSEEHCQRLMK 435
                                   88*****************************99998765 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00026      0.22      43     130 ..     408     485 ..     394     501 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                   CCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHH CS
                        RrnaAD  43 ilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqll 123
                                   il e++ kr ++vvv+E+ e+ +++l k     + + vvh D+ + ++ +    k+ i++   vva++    +  lv q+ 
  gi|91773339|ref|YP_566031.1| 408 ILAERFEKRGENVVVVESSEEHCQRLMK-----SGIRVVHGDAEDVNVLK----KAGIENAKYVVASTNQDNTNLLVCQIA 479
                                   5667777777****************99.....69***************....77899999999*999999****99998 PP

                                   HGGGGCE CS
                        RrnaAD 124 eesrfgl 130
                                   +  +fg+
  gi|91773339|ref|YP_566031.1| 480 K-TKFGF 485
                                   6.44544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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):              21  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.52
# Mc/sec: 3545.73
//
Query:       gi|91773340|ref|YP_566032.1|  [L=251]
Description: dimethylamine corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-27   95.6   0.4    4.2e-27   94.6   0.4    1.5  1  B12-binding    B12 binding domain
    4.9e-19   68.5   0.7    4.9e-19   68.5   0.7    1.9  3  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.4   4.7e-31   4.2e-27       2     120 ..     131     243 ..     130     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 4.7e-31
                   B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrirp 80 
                                    ++ +tv+gd+h++G+a++  +l++agfeV+++g +v++++++++i+++++d+vglSal+t++l++ ke++el  + + r+
  gi|91773340|ref|YP_566032.1| 131 VIVNGTVEGDVHDIGKAIVSTMLQAAGFEVHDIGRDVPVQNFIDKIKETNADMVGLSALMTTTLQGQKEVIELlkENGLRD 211
                                   57899********************************************************************8888999* PP

                   B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   +vkv+vGGa+++ +++    +  g+d+    ++e+a ea+
  gi|91773340|ref|YP_566032.1| 212 KVKVMVGGAPATDAWAK---K-CGADC----YAENASEAV 243
                                   *********98888888...6.99777....999998887 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.7   5.4e-23   4.9e-19       3      74 ..      45     115 ..      43     116 .. 0.96
   2 ?   -2.6   0.0       0.9   8.1e+03      21      62 ..     144     154 ..     132     166 .. 0.59
   3 ?   -2.9   0.0       1.1     1e+04      37      49 ..     191     203 ..     169     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 5.4e-23
                 B12-binding_2   3 erlhwaivhgdkegieelidealaqgsa.avdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74 
                                   + l +a+v  +k+++ +++++a   g+a av++++++l+++m+eVG lf++g+lflp+v+++a++m ++v++L
  gi|91773340|ref|YP_566032.1|  45 KTLSDAVVSCKKDEVIAAVEKAK--GKApAVELIDNGLAAGMNEVGVLFERGKLFLPHVMMAADAMSAGVEML 115
                                   6799*******************..8889*****************************************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.9
                 B12-binding_2  21 idealaqgsaavdvlndvllpamkeVGdlfgagelflpqvll 62 
                                   i                               g+ ++  +l+
  gi|91773340|ref|YP_566032.1| 144 I-------------------------------GKAIVSTMLQ 154
                                   3...............................4444444444 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                 B12-binding_2  37 dvllpamkeVGdl 49 
                                   +  l + keV +l
  gi|91773340|ref|YP_566032.1| 191 TTTLQGQKEVIEL 203
                                   4445556666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1859.83
//
Query:       gi|91773341|ref|YP_566033.1|  [L=98]
Description: hypothetical protein Mbur_1366 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 736.78
//
Query:       gi|91773342|ref|YP_566034.1|  [L=348]
Description: transmembrane protein MttP [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-14   51.9  46.1    2.1e-06   27.9  14.3    3.1  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4  23.8   3.4e-10   6.2e-06       2     135 ..      17     176 ..      16     178 .. 0.74
   2 !   27.9  14.3   1.2e-10   2.1e-06       2     136 ..     193     335 ..     192     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.4e-10
                          EamA   2 lgillallaalfwaiyfvlskillrkv...............spltltfvrfliagillliiallkegkl.......akls 60 
                                   +g+++al  a++w+i++v   i+ +                 s  t+++  +++a+ +l +i +l  ++         k +
  gi|91773342|ref|YP_566034.1|  17 KGYMWALFCAILWGIWYVPGTIIWAVPpfdamwvdidathggSMATIVVALLIAAFNALTVIVALLIWNAylgkfgeMKRT 97 
                                   799****************99984444445557777777665333333333333333333332222222223444464445 PP

                          EamA  61 lkd....wllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                   lk+     ++++l +++g+ +a l  f+a+  ++a++a+++ ++ Pv+  +l+  ++ge+++++ ++gi++i++G l i
  gi|91773342|ref|YP_566034.1|  98 LKEfhpcSKWFFLASIFGGPIAILGSFIAIGFIGAGFAAVAALMYPVIGSVLARQWYGEQISKRAWMGILVIIVGGLTI 176
                                   55567888999***************************************************************97766 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.2e-10
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfl....iagillliiallkegkl.....aklslkdwllllllgll 73 
                                   lg+l  l aal w+i + ++ ++l   +p    ++rfl    +  ++l++ia++ + ++     + +++ ++l l + g +
  gi|91773342|ref|YP_566034.1| 193 LGYLGGLMAALGWGIEGAIAGKGLDIAEPDVGITIRFLgeslLYWVILIPIAAIAGYPIleyalQAFNPLSILVLGFAG-I 272
                                   59999**********************9998888888866668888889999999999977655555555555544444.5 PP

                          EamA  74 gtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    +  +++ +++++  +++++   i +l  ++++i+ +l+  + + ++ l+g +l++lG ++++
  gi|91773342|ref|YP_566034.1| 273 TFGYCYVSWYKSFPLIGVGRGQGIGNLYGLCAVIFMYLFMAQVPAWTVLVGGALCVLGSFVMI 335
                                   777777*****************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); 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:                        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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 2521.36
//
Query:       gi|91773343|ref|YP_566035.1|  [L=216]
Description: trimethylamine corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-20   73.9   1.4    2.1e-20   72.9   1.1    1.7  2  B12-binding_2  B12 binding domain
    5.7e-20   71.6   1.2    5.7e-20   71.6   1.2    2.1  3  B12-binding    B12 binding domain
  ------ inclusion threshold ------
        2.4    8.1   8.7        1.5    8.8   1.7    2.6  3  EspB           Enterobacterial EspB protein


Domain annotation for each model (and alignments):
>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   1.1   3.5e-24   2.1e-20       5      74 ..      11      80 ..       7      81 .. 0.96
   2 ?   -2.9   0.0       1.7     1e+04      12      30 ..     169     185 ..     167     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 3.5e-24
                 B12-binding_2  5 lhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                   + a++++d+e +ee+++eal+++ + v +++d+l ++m+eVGd f++g+lflp+v+ ++e+m ++va+L
  gi|91773343|ref|YP_566035.1| 11 AKAAVMEFDDELVEEICEEALEAKVDIVSLIQDGLTAGMNEVGDQFEQGTLFLPHVIAASEAMSAGVAIL 80
                                  5789******************99********************************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                 B12-binding_2  12 gdkegieelidealaqgsa 30 
                                   ++++gi++ + +++  g a
  gi|91773343|ref|YP_566035.1| 169 LKEAGIRDSVMTMV--GGA 185
                                   68888888888877..555 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.13   7.8e+02      41      57 ..      24      40 ..       6      59 .. 0.72
   2 ?   -3.8   0.0       2.1   1.3e+04      11      28 ..      71      88 ..      65      91 .. 0.68
   3 !   71.6   1.2   9.6e-24   5.7e-20       2     120 ..      96     208 ..      95     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                   B12-binding 41 edivaairaekpdvvgl 57
                                  e+i +++ + k+d+v l
  gi|91773343|ref|YP_566035.1| 24 EEICEEALEAKVDIVSL 40
                                  88888888888888876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.1
                   B12-binding 11 dlhplGlavlaaalrdag 28
                                  ++ + G+a+l  al+++g
  gi|91773343|ref|YP_566035.1| 71 EAMSAGVAILTPALEAQG 88
                                  455667888888888776 PP

  == domain 3  score: 71.6 bits;  conditional E-value: 9.6e-24
                   B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrirp 80 
                                   +++++t++gd+h++G++++a +l+ agf++++lg +v   + v+a++++kp +vg Sal+t+++    ++ e+  +++ir+
  gi|91773343|ref|YP_566035.1|  96 TIVIGTIEGDIHSIGKDIVATMLKIAGFKIVDLGRDVAIGAYVDAVKEHKPMIVGSSALMTTTMILQMNIEEQlkEAGIRD 176
                                   6899*********************************************************************9999**** PP

                   B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                    v ++vGGa+++ d+++   + +g  d    ++e+a +a+
  gi|91773343|ref|YP_566035.1| 177 SVMTMVGGAPVTQDWAD---K-IG-SD---IYAENATDAV 208
                                   ****************9...7.99.66...5888887765 PP

>> EspB  Enterobacterial EspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.011        68     147     182 ..       8      43 ..       2      61 .. 0.84
   2 ?    8.8   1.7   0.00025       1.5      48     119 ..      71     142 ..      55     146 .. 0.86
   3 ?   -1.7   0.0      0.39   2.4e+03     107     116 ..     201     210 ..     163     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.011
                          EspB 147 neqrakavedlqesnleeykktvresqDkiasvlqd 182
                                   n++++ av ++  + +ee  +++ e++ +i+s +qd
  gi|91773343|ref|YP_566035.1|   8 NAKAKAAVMEFDDELVEEICEEALEAKVDIVSLIQD 43 
                                   889999**************************9998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00025
                          EspB  48 ekkAgAtaallegvlsivlGilgsaaaiasgaie.elatkGasvvvdkatsasaksVntasEvsvkAlvkasE 119
                                   e+   A  a+l  +l+  +G ++s ++i  g ie  +   G+ +v+ +   a +k V    +v++ A v+a+ 
  gi|91773343|ref|YP_566035.1|  71 EAM-SAGVAILTPALEAQGGSVKSKGTIVIGTIEgDIHSIGKDIVATMLKIAGFKIVDLGRDVAIGAYVDAVK 142
                                   334.567788888***************999986268899******************************996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.39
                          EspB 107 sEvsvkAlvk 116
                                   +E +++A+vk
  gi|91773343|ref|YP_566035.1| 201 AENATDAVVK 210
                                   5677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1518.51
//
Query:       gi|91773344|ref|YP_566036.1|  [L=540]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-68  228.9   9.1    2.4e-67  226.8   9.1    1.9  1  RACo_C_ter   C-terminal domain of RACo the ASKHA domain
    6.4e-12   45.5   0.0    2.3e-11   43.7   0.0    2.0  2  Raco_middle  RACo middle region
    2.1e-10   40.6   9.7    3.9e-10   39.7   9.0    1.8  1  Fer4_21      4Fe-4S dicluster domain
    6.6e-09   36.2  10.1    1.4e-08   35.2  10.1    1.6  1  Fer4_7       4Fe-4S dicluster domain
    7.9e-09   35.0  14.9    0.00014   21.6   5.1    2.9  2  Fer4         4Fe-4S binding domain
    1.4e-07   31.2  15.7    0.00012   22.0   2.6    2.5  2  Fer4_6       4Fe-4S binding domain
    2.6e-07   30.7   9.7    5.5e-07   29.7   9.7    1.6  1  Fer4_9       4Fe-4S dicluster domain
    1.7e-05   25.3   3.5     0.0029   18.1   0.2    2.6  2  Fer4_17      4Fe-4S dicluster domain
    3.5e-05   23.8  12.0    0.00049   20.2  12.9    2.3  2  Fer4_10      4Fe-4S dicluster domain
      4e-05   24.5  11.7      0.035   15.0   1.7    2.6  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00011   22.4  13.4      0.073   13.6   2.4    2.6  2  Fer4_4       4Fe-4S binding domain
     0.0014   18.6  15.0      0.032   14.3   3.8    2.6  2  Fer4_2       4Fe-4S binding domain
     0.0053   17.6  16.4       0.36   11.9   4.7    2.7  2  Fer4_3       4Fe-4S binding domain
     0.0075   16.7  11.4       0.16   12.4   2.4    2.6  2  Fer4_8       4Fe-4S dicluster domain
  ------ inclusion threshold ------
         10    6.8  11.1         34    5.1  11.1    1.9  1  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
         10    7.1  11.1         17    6.4   1.1    2.5  2  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.8   9.1   2.1e-70   2.4e-67       3     259 ..     171     427 ..     169     428 .. 0.95

  Alignments for each domain:
  == domain 1  score: 226.8 bits;  conditional E-value: 2.1e-70
                                   EEEEEESSSEEEEEE-SS-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGGSSEEEEECTSS-............. CS
                    RACo_C_ter   3 slliDiGTNaEivlgnkdellaasaaaGPAlEGaeikcGmrAapgAIedveidpetlevelkvigdek............. 70 
                                   s+++D+GTNaE++++++d++++asaaaGPA+EG++ikcGm+A+pgAI+dv++++    +++++++++              
  gi|91773344|ref|YP_566036.1| 171 SMVTDYGTNAEMAIKVGDKIITASAAAGPAIEGQGIKCGMLASPGAISDVTVEDGL--WRVTILDESMteckghlidpvtg 249
                                   89************************************************999998..99999987666788999999999 PP

                                   .........-SEEEHHHHHHHHHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSSS-EEEEHHHHHHHHHH CS
                    RACo_C_ter  71 .........akGicGsGiidliaelleagiidkkgklnkelkserireeeetleyvlakaeetetkdivitekDieelika 142
                                            akG++G+G+i+++a +le gi++k + l              + ++ l   e     +i i ekDiee++ka
  gi|91773344|ref|YP_566036.1| 250 eikessdvvAKGVTGTGVISALALALECGIMKKIPVL-------------PNGKLFLD--E-----GIEIFEKDIEEAGKA 310
                                   999****************************999999.............44555563..3.....8************** PP

                                   HHHHHHHHHHHHHHTT--GGG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHHHHHCBHHHHHHHHHH CS
                    RACo_C_ter 143 kaAiyagiktLleevglevediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAreallseealeeleei 223
                                   ++Ai+a+  tL+ e g +++d++++y+AGa+G+y+da+kA+++G +P+  ++++vq+GNts+a+Ar+++l+e++l+e+ e+
  gi|91773344|ref|YP_566036.1| 311 IGAIRAAQLTLMIESGTAYSDLDNMYMAGATGAYVDANKARKLGSCPN-FAHNIVQFGNTSVALARDLVLDESKLDEVIEM 390
                                   ************************************************.999***************************** PP

                                   HHHE..EE--TTSSSHHHHHHHHHSSSS-SSGGG-ST- CS
                    RACo_C_ter 224 arki..tyielateeeFqeeyvaalflphtdlelfpsv 259
                                   a+ki  +++++at++ F++ y+++l+++++++ +++++
  gi|91773344|ref|YP_566036.1| 391 AHKItaDHLMMATSTVFSNIYMCELSYWTQGM-PIEMY 427
                                   ****999*************************.88887 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0     2e-14   2.3e-11       1     160 [.       2     164 ..       2     167 .. 0.83
   2 ?   -3.4   0.0       6.1   6.8e+03      12      48 ..     239     274 ..     232     287 .. 0.61

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2e-14
                   Raco_middle   1 yGlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleeagiek 81 
                                   yG+a+D+Gt+   a+L+dle++k+l++a ++ +    G +v+  + +a +   g +  ++ +     + ++++ +e g+++
  gi|91773344|ref|YP_566036.1|   2 YGIALDLGTSGFRAQLIDLESKKVLKTAITMKHPLP-GGNVMDHLDFAIQ--IGEDVANEIM----LDTVKRIFDEFGVDP 75 
                                   9***************************99987765.789*********9..3333333444....45677778888**** PP

                   Raco_middle  82 eeiyevvvagNttMlhlllgldpkslakap........yvpvvseavelkakel..glkinpeakvyvlpnvssyvGgDiv 152
                                   + i++++v+gN + l l+ +++ + la a            vv+ + +++a+el  g+   p+++v+v p++ + +G+D++
  gi|91773344|ref|YP_566036.1|  76 SLIKRLAVCGNPIQLSLFQNMEIRDLAYAGenkqkklgVENVVRGSRVFPANELfeGIMDLPNCTVIVPPAIKHEIGADAL 156
                                   **************************876422222222567899999******944566689******************* PP

                   Raco_middle 153 agilasgl 160
                                   a ++ +++
  gi|91773344|ref|YP_566036.1| 157 AMMIKTDF 164
                                   ****9986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.1
                   Raco_middle  12 vvaaLvdletgkelaeasalNpQikyGeDvlsRiaya 48 
                                     ++L+d  tg+ ++e+s++ ++   G+ v+s +a a
  gi|91773344|ref|YP_566036.1| 239 CKGHLIDPVTGE-IKESSDVVAKGVTGTGVISALALA 274
                                   555666666664.455555666666666666655554 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   9.0   3.5e-13   3.9e-10       6      58 ..     479     532 ..     474     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3.5e-13
                       Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvG..CnlCssvCPvedcie 58 
                                    +Ci Cg+C + C++ +++ ie d++ ++++ +++C G  C  C++vCPv d+i+
  gi|91773344|ref|YP_566036.1| 479 PECIRCGQCEVECPEDAIKIIERDGELYANYNSERCLGtsCRRCVAVCPV-DAIH 532
                                   58**********************************8777*********9.8885 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2  10.1   1.2e-11   1.4e-08       2      52 .]     481     530 ..     480     530 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.2e-11
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClg..CgaCvavCPtga 52 
                                   Ci Cg+C++ Cp +ai++ e+   +g  ++++++e+Clg  C++CvavCP++a
  gi|91773344|ref|YP_566036.1| 481 CIRCGQCEVECPEDAIKIIER---DGELYANYNSERCLGtsCRRCVAVCPVDA 530
                                   ******************998...688899*******7444**********97 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   5.1   1.2e-07   0.00014       7      24 .]     480     497 ..     478     497 .. 0.95
   2 !   18.8   1.2   9.1e-07     0.001      10      23 ..     518     531 ..     517     532 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                                   TSSS-THHHHHSTTTEEE CS
                          Fer4   7 kCigCGaCvevCPvgAIt 24 
                                    Ci+CG+C+  CP +AI+
  gi|91773344|ref|YP_566036.1| 480 ECIRCGQCEVECPEDAIK 497
                                   5****************6 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 9.1e-07
                                   S-THHHHHSTTTEE CS
                          Fer4  10 gCGaCvevCPvgAI 23 
                                    C +Cv vCPv+AI
  gi|91773344|ref|YP_566036.1| 518 SCRRCVAVCPVDAI 531
                                   7************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   5.4   2.9e-05     0.032       9      24 .]     481     496 ..     478     496 .. 0.97
   2 !   22.0   2.6   1.1e-07   0.00012       4      24 .]     509     531 ..     507     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   Ci Cg C++ CPe+ai
  gi|91773344|ref|YP_566036.1| 481 CIRCGQCEVECPEDAI 496
                                   **************98 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-07
                        Fer4_6   4 idpdkCig..CgdCvrvCPegai 24 
                                   ++ ++C+g  C++Cv+vCP +ai
  gi|91773344|ref|YP_566036.1| 509 YNSERCLGtsCRRCVAVCPVDAI 531
                                   789****666**********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 !   29.7   9.7   4.9e-10   5.5e-07       1      51 []     480     531 ..     480     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.9e-10
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaC..igCgaCveaCpkgai 51 
                                   +C++Cg+C+  Cp ++++  +  ++   +  se +C  ++C++Cv++Cp +ai
  gi|91773344|ref|YP_566036.1| 480 ECIRCGQCEVECPEDAIKIIERDGELYANYNSE-RClgTSCRRCVAVCPVDAI 531
                                   5****************9998888888766665.9*7778**********987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   2.6e-06    0.0029      39      59 ..     474     494 ..     446     496 .. 0.86
   2 !    7.3   0.4    0.0061       6.9      41      58 ..     509     528 ..     497     531 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-06
                       Fer4_17  39 keekaslCieCgeCerkCPqg 59 
                                    ee a +Ci Cg+Ce +CP++
  gi|91773344|ref|YP_566036.1| 474 IEEHAPECIRCGQCEVECPED 494
                                   4578899************97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0061
                       Fer4_17  41 ekaslC..ieCgeCerkCPq 58 
                                    + ++C  ++C++C+++CP 
  gi|91773344|ref|YP_566036.1| 509 YNSERClgTSCRRCVAVCPV 528
                                   56677744579999999996 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2  12.9   4.4e-07   0.00049       7      56 .]     479     527 ..     473     527 .. 0.86
   2 !   14.6   2.1   2.4e-05     0.027       3      26 ..     508     533 ..     506     538 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.4e-07
                       Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                     CirCg+C   CP       ++ e+++e   + ++e+C g  c  Cv++CP
  gi|91773344|ref|YP_566036.1| 479 PECIRCGQCEVECPE---DAIKIIERDGELYANYNSERCLGtsCRRCVAVCP 527
                                   57*************...7777777888888899*****9988********9 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.4e-05
                       Fer4_10   3 vidddtC..irCgkCvkaCPadltsv 26 
                                    +++++C  + C++Cv++CP+d+ ++
  gi|91773344|ref|YP_566036.1| 508 NYNSERClgTSCRRCVAVCPVDAIHY 533
                                   578999*7779**********76554 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 !   13.1   3.8   0.00013      0.14       2      19 ..     481     498 ..     480     516 .. 0.81
   2 !   15.0   1.7   3.1e-05     0.035       3      20 ..     517     534 ..     513     539 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                       Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                   C++Cg+C   CP++aik 
  gi|91773344|ref|YP_566036.1| 481 CIRCGQCEVECPEDAIKI 498
                                   ***************984 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.1e-05
                       Fer4_16   3 gtCgkCaevCPtnaikek 20 
                                   ++C++C+ vCP++ai+ k
  gi|91773344|ref|YP_566036.1| 517 TSCRRCVAVCPVDAIHYK 534
                                   68*************977 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   2.4   6.5e-05     0.073       4      16 ..     481     493 ..     478     501 .. 0.93
   2 !   13.5   3.4   6.9e-05     0.077       1      16 [.     511     528 ..     511     529 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   Ci+Cg+C+  CP 
  gi|91773344|ref|YP_566036.1| 481 CIRCGQCEVECPE 493
                                   ************5 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.9e-05
                        Fer4_4   1 qerC..igCgsCvaaCPq 16 
                                   +erC  + C++Cva+CP+
  gi|91773344|ref|YP_566036.1| 511 SERClgTSCRRCVAVCPV 528
                                   599*666**********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 !    9.3   3.4    0.0011       1.2      10      22 .]     481     493 ..     475     493 .. 0.87
   2 !   14.3   3.8   2.8e-05     0.032       5      21 ..     509     527 ..     507     528 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                        Fer4_2  10 CigCgaCvsaCPa 22 
                                   Ci+Cg C   CP+
  gi|91773344|ref|YP_566036.1| 481 CIRCGQCEVECPE 493
                                   *******888**5 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.8e-05
                        Fer4_2   5 vdtdrCig..CgaCvsaCP 21 
                                   ++++rC+g  C+ Cv +CP
  gi|91773344|ref|YP_566036.1| 509 YNSERCLGtsCRRCVAVCP 527
                                   799***9999********* PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   3.8   0.00066      0.73       1      15 []     481     495 ..     481     495 .. 0.97
   2 !   11.9   4.7   0.00032      0.36       1      15 []     514     530 ..     514     530 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00066
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ Cg+C++ CP++A
  gi|91773344|ref|YP_566036.1| 481 CIRCGQCEVECPEDA 495
                                   ************998 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00032
                        Fer4_3   1 Ctg..CgaCvevCPvgA 15 
                                   C+g  C++Cv vCPv+A
  gi|91773344|ref|YP_566036.1| 514 CLGtsCRRCVAVCPVDA 530
                                   6655599********98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.4   0.00014      0.16      45      63 ..     475     493 ..     445     498 .. 0.70
   2 !    9.6  13.0    0.0011       1.2       4      64 ..     480     529 ..     477     530 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                        Fer4_8  45 eealwsCttcgaCtevCpv 63 
                                   ee + +C  cg+C+++Cp+
  gi|91773344|ref|YP_566036.1| 475 EEHAPECIRCGQCEVECPE 493
                                   5556677777777777776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                        Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsC..ttcgaCtevCpvg 64 
                                   +Ci+Cg C+ +Cp   + +  + +  ge  + + ++++         C  t+c++C+ vCpv+
  gi|91773344|ref|YP_566036.1| 480 ECIRCGQCEVECP---EDAIKIIERDGELYA-NYNSER---------ClgTSCRRCVAVCPVD 529
                                   7***********9...222334444555555.555545.........6559**********96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  11.1      0.03        34       5      57 ..     480     532 ..     478     533 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                       Fer4_13   5 tCiacgaCvelaP.dvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57 
                                   +Ci cg+C   +P d  ++ + +g  + a+ ++   +   +++ ++ CPv++I+
  gi|91773344|ref|YP_566036.1| 480 ECIRCGQCEVECPeDAIKIIERDGELY-ANYNSERCLGTSCRRCVAVCPVDAIH 532
                                   8************54788888888766.5889999999***************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.0     0.038        43       2      13 ..     481     492 ..     472     496 .. 0.66
   2 ?    6.4   1.1     0.015        17      72      95 ..     504     529 ..     495     530 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                       Fer4_22   2 ClsCgaCtlvCp 13 
                                   C++Cg+C + Cp
  gi|91773344|ref|YP_566036.1| 481 CIRCGQCEVECP 492
                                   555555555555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                       Fer4_22  72 efkekfgesgCvG..CgRCieacpvk 95 
                                   e+ ++++++ C G  C RC+++cpv+
  gi|91773344|ref|YP_566036.1| 504 ELYANYNSERCLGtsCRRCVAVCPVD 529
                                   5667889999988889*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3767.39
//
Query:       gi|91773345|ref|YP_566037.1|  [L=196]
Description: hypothetical protein Mbur_1371 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1285.05
//
Query:       gi|91773346|ref|YP_566038.1|  [L=104]
Description: hypothetical protein Mbur_1372 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 743.75
//
Query:       gi|91773347|ref|YP_566039.1|  [L=287]
Description: hypothetical protein Mbur_1373 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.04   13.9   0.0    1.6  1  S19       Chorion protein S19 C-terminal
       0.03   15.0   0.0       0.11   13.2   0.0    1.8  2  RPA_C     Replication protein A C terminal
      0.054   13.3   0.0       0.08   12.8   0.0    1.3  1  RMI2      RecQ-mediated genome instability protein 2


Domain annotation for each model (and alignments):
>> S19  Chorion protein S19 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.7e-06      0.04      20      54 ..      74     113 ..      65     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-06
                           S19  20 tvqPaGatllyPGqnnyray.....vsPpeyskvilPvra 54 
                                    v P+Ga  ly Gq +  a+     v Ppey  v+  vr+
  gi|91773347|ref|YP_566039.1|  74 VVDPSGAFTLYAGQYQSDAIaflssVVPPEYVSVVGKVRS 113
                                   599***********8766652232267********99997 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.62   3.7e+03      74      93 ..      12      31 ..       6      34 .. 0.61
   2 ?   13.2   0.0   1.8e-05      0.11      47      98 ..     223     276 ..     195     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.62
                                  HHHSTSXHHHHHHHHHHHHH CS
                         RPA_C 74 aqklrlsvndvkqavdeLsn 93
                                  a++l+ s +++ ++vde ++
  gi|91773347|ref|YP_566039.1| 12 AKELNDSSSTIHSTVDEAID 31
                                  56666666666666666555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.8e-05
                                   SXHHHHHHHHHHHH.SXSTTTEEHHHHH.HHS..TSXHHHHHHHHHHHHHTTSEE CS
                         RPA_C  47 ltalaqqvlnlikqspeseeGvhvdeia.qkl..rlsvndvkqavdeLsneGiiY 98 
                                    ++l++ vlnl+ +   + +Gv   e+   ++  ++++++v ++v++L+++G+ Y
  gi|91773347|ref|YP_566039.1| 223 EKDLDTLVLNLMSE-LGGGKGVDYAELMsVAVsrQINEKTVDSVVRSLLTKGLCY 276
                                   5788999*****99.********999874333569*****************999 PP

>> RMI2  RecQ-mediated genome instability protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05      0.08      31     106 ..      40     123 ..       7     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                          RMI2  31 avgreglevsrvWlQGtvvevdaske.....sllldDgtgvfvveglnelpktk...kclkeGkYVmVvGvvqssspepvl 103
                                     +  g+ v+rv + G++ ev++ ++     + ++ D +g f+  + +  +      +++ + +YV+VvG v+s ++e+ l
  gi|91773347|ref|YP_566039.1|  40 LLTPGGVMVNRVFVTGVLTEVENIDSdgdtwRARVVDPSGAFTLYAGQYQSDAIaflSSVVPPEYVSVVGKVRSYKSEDGL 120
                                   44468999**********99988666677999*********99876555444446779999************99999666 PP

                          RMI2 104 kav 106
                                    ++
  gi|91773347|ref|YP_566039.1| 121 VVI 123
                                   555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2131.09
//
Query:       gi|91773348|ref|YP_566040.1|  [L=450]
Description: replication factor A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-09   36.2   2.6        0.1   12.6   0.0    3.6  4  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0     9e-06      0.16       2      71 ..      87     158 ..      86     163 .. 0.83
   2 !    9.8   0.0   4.3e-05      0.77      18      72 ..     216     265 ..     197     271 .. 0.89
   3 ?   -3.2   0.1      0.48   8.6e+03       1      18 [.     306     321 ..     306     323 .. 0.76
   4 !   12.6   0.0   5.8e-06       0.1      19      68 ..     351     423 ..     327     431 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9e-06
                                   EEEEEEEEEE......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTS.SEEEEEE CS
               tRNA_anti-codon   2 tvaGrvtsis......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpgg.elelkve 71 
                                   +++ r+ +is      +++   +++ +l D++g    + ++      +  l +Gd vr++   v+ ++++ e+++++ 
  gi|91773348|ref|YP_566040.1|  87 SLEVRILKISektvdlKGERTIIFSGILADRSGLCPFTSWK------QLALNVGDAVRISnASVRNWYNRtEVSISAY 158
                                   5677888888888887677777888889*************......999*******************956666554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 4.3e-05
                                   EEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEE CS
               tRNA_anti-codon  18 vifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkvee 72 
                                   +i  +l D+tgr+  v ++      ++ +++G+++r +   v+ ++g  ++++ ++
  gi|91773348|ref|YP_566040.1| 216 IIEGVLADETGRLPFVSWS-----PLDGVDIGSIIRFKdASVRVYRGV-PSIHLDS 265
                                   66778**************.....**********************99.9999876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.48
                                   EEEEEEEEEEEEEEETTE CS
               tRNA_anti-codon   1 VtvaGrvtsisdrsggkv 18 
                                   V+++G ++s+  r g+++
  gi|91773348|ref|YP_566040.1| 306 VVLVGNIVSV--RPGSGL 321
                                   7789999999..777665 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 5.8e-06
                                   EEEEEEETTEEEEEEEET........................HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEE CS
               tRNA_anti-codon  19 ifidlrDgtgriqvvlfr........................eeatklaenlkeGdvvrvtGrvkrrpggelel 68 
                                   i ++l+Dgtg++ v+l+r                        ++ ++ ++++  G +++v+G  +r++ g ++ 
  gi|91773348|ref|YP_566040.1| 351 IKLVLDDGTGSVLVMLNRelseivygktlhesfsllgktmsmNAIFEDMKRVLTGRYIGVRGNTSRSEFG-VTF 423
                                   6789***********************************99999999999999**********9999888.655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3259.19
//
Query:       gi|91773349|ref|YP_566041.1|  [L=73]
Description: histone [Methanococcoides burtonii DSM 6242]
Scores for complete 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-16   58.0   0.2    9.5e-16   57.8   0.2    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    2.2e-09   37.8   0.1    2.4e-09   37.7   0.1    1.0  1  Histone        Core histone H2A/H2B/H3/H4
    3.8e-08   33.4   0.0    4.2e-08   33.3   0.0    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
      1e-07   32.1   0.0    1.2e-07   31.9   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    5.8e-07   29.8   0.0    6.8e-07   29.6   0.0    1.1  1  CENP-S         CENP-S protein
    1.4e-05   25.0   0.0    1.8e-05   24.7   0.0    1.0  1  Bromo_TP       Bromodomain associated
  ------ inclusion threshold ------
      0.035   13.9   0.0       0.28   11.0   0.0    2.0  2  AAA_lid_2      AAA lid domain
      0.073   13.6   0.0      0.089   13.3   0.0    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 


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 !   57.8   0.2   4.2e-19   9.5e-16       3      64 ..       4      64 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 4.2e-19
                                  XXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                 CBFD_NFYB_HMF  3 LPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                  LP+a v+++++s+ da+++++ A   + e++e + +++++eA  ++++++rKt+k+e+iklA
  gi|91773349|ref|YP_566041.1|  4 LPLASVERLIRSA-DAERVSEPAASALLEIIEAYGTKISKEAIIYANHAGRKTVKEEDIKLA 64
                                  9************.**********************************************98 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 !   37.7   0.1   1.1e-12   2.4e-09      70     128 ..       9      65 ..       2      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.1e-12
                                   HHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHH CS
                       Histone  70 vvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlAr 128
                                   v r i++   +  r+s  a  al e++Ea+ + + +eA ++a+ha R+T+  +Di+lA+
  gi|91773349|ref|YP_566041.1|   9 VERLIRS--ADAERVSEPAASALLEIIEAYGTKISKEAIIYANHAGRKTVKEEDIKLAY 65 
                                   4455555..7789********************************************97 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 !   33.3   0.0   1.9e-11   4.2e-08       8      72 ..       4      63 ..       1      70 [. 0.89

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.9e-11
                      CENP-T_C  8 lPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvil 72
                                  lP a+v +l +++       +++++ a +al ++ + +  +++++   ya+HagRKt++e+D+ l
  gi|91773349|ref|YP_566041.1|  4 LPLASVERLIRSA-----DAERVSEPAASALLEIIEAYGTKISKEAIIYANHAGRKTVKEEDIKL 63
                                  7888888887666.....5679****************************************965 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 !   31.9   0.0   5.2e-11   1.2e-07      10      69 ..       8      67 ..       5      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.2e-11
                   TFIID-31kDa 10 lihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqs 69
                                   ++ +++s   + ++e   + Ll+++  y +++ ++A ++a+ha++k+v+ +d++lA ++
  gi|91773349|ref|YP_566041.1|  8 SVERLIRSADAERVSEPAASALLEIIEAYGTKISKEAIIYANHAGRKTVKEEDIKLAYEM 67
                                  57889999999**********************************************776 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0     3e-10   6.8e-07      22      69 ..      17      64 ..       6      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3e-10
                        CENP-S 22 keveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLl 69
                                     ++++ + +al e++ +   +++k   ++a+HA+R+t++ +D++L 
  gi|91773349|ref|YP_566041.1| 17 DAERVSEPAASALLEIIEAYGTKISKEAIIYANHAGRKTVKEEDIKLA 64
                                  4456999999************************************96 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   7.8e-09   1.8e-05      13      67 ..      10      64 ..       4      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.8e-09
                                  HHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHH CS
                      Bromo_TP 13 sqileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvlt 67
                                    + ++a+ +++ e+a  +L ei++ Y ++++++a  +a+hagR +++ +D+ l+
  gi|91773349|ref|YP_566041.1| 10 ERLIRSADAERVSEPAASALLEIIEAYGTKISKEAIIYANHAGRKTVKEEDIKLA 64
                                  5677899999999**************************************9887 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.18     4e+02      46      67 ..       3      24 ..       2      31 .. 0.73
   2 ?   11.0   0.0   0.00013      0.28      28      54 ..      46      72 ..      40      73 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.18
                     AAA_lid_2 46 aaplVLaHRlrrepeaegette 67
                                  + pl+   Rl+r++ ae++++ 
  gi|91773349|ref|YP_566041.1|  3 ILPLASVERLIRSADAERVSEP 24
                                  5677777899988888876554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                     AAA_lid_2 28 AlAalegrdyVtpeDvkeaaplVLaHR 54
                                   +A  +gr++V +eD+k a ++   +R
  gi|91773349|ref|YP_566041.1| 46 IYANHAGRKTVKEEDIKLAYEMLTKPR 72
                                  578889*************99988777 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     4e-05     0.089       6      63 ..      10      66 ..       7      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                                  HHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH CS
                   TFIID_20kDa  6 qdLvqqvdsetkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhle 63
                                  + L++  d+e + ++     Llei++++ + ++k a   a h   +++   Di+l  e
  gi|91773349|ref|YP_566041.1| 10 ERLIRSADAERVSEPA-ASALLEIIEAYGTKISKEAIIYANHAGRKTVKEEDIKLAYE 66
                                  5688888887766665.55688********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 569.66
//
Query:       gi|91773350|ref|YP_566042.1|  [L=168]
Description: small multi-drug exporter [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-39  135.2   5.5    2.3e-39  134.8   5.5    1.2  1  Sm_multidrug_ex  Putative small multi-drug export protein
     0.0055   17.2   7.8      0.011   16.2   2.7    2.2  2  SNARE_assoc      SNARE associated Golgi 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 !  134.8   5.5   2.6e-43   2.3e-39       1     121 []      30     152 ..      30     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 2.6e-43
               Sm_multidrug_ex   1 Elrgaiplgi.llgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaek.ksekiekygflGLll 79 
                                   Elrgaip++i ++++ p++a+l++vlgnllpv+ +llfl++++ +l+++k+ + +f++l +++++ +se++ekyg+l+L+l
  gi|91773350|ref|YP_566042.1|  30 ELRGAIPIAIgVYEIGPVEAYLLAVLGNLLPVIPLLLFLEPVSAFLRRFKIGDMFFTWLFTRTRQkHSESMEKYGTLALTL 110
                                   9*********777**************************************************995666778********* PP

               Sm_multidrug_ex  80 FvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                   FvaiPLp+TGawtG+++a+++g+k+++al+ai++Gvliag++
  gi|91773350|ref|YP_566042.1| 111 FVAIPLPVTGAWTGCAAAFVFGIKFRHALIAIVAGVLIAGIV 152
                                   ****************************************86 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.2    0.0086        77      68     116 ..      17      66 ..       4      70 .. 0.78
   2 !   16.2   2.7   1.2e-06     0.011      44     117 ..      81     156 ..      71     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0086
                   SNARE_assoc  68 flallllrllpi..vPrdlvnyvaGltrvsfkrFflatfiGsipwalvyay 116
                                   +l +++l  lpi  + r +++++ G+ ++ + +  l +++G +++++ +++
  gi|91773350|ref|YP_566042.1|  17 WLSTIILSALPIseL-RGAIPIAIGVYEIGPVEAYLLAVLGNLLPVIPLLL 66 
                                   666777777777334.89999999999999999999999999988877665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.2e-06
                   SNARE_assoc  44 kalrrkllsekrvkalerlverygflallllrllpivPrdlvn..yvaGltrvsfkrFflatfiGsipwalvyayl 117
                                    ++ + +l  ++ ++ ++++e+yg+lal l+  +p   + + +  ++a +++++f++ ++a ++G +++ +v+++l
  gi|91773350|ref|YP_566042.1|  81 GDMFFTWLFTRTRQKHSESMEKYGTLALTLFVAIPLPVTGAWTgcAAAFVFGIKFRHALIAIVAGVLIAGIVVTLL 156
                                   567777888889999999*******9988777777544444433366667*****************998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 1313.28
//
Query:       gi|91773351|ref|YP_566043.1|  [L=110]
Description: hypothetical protein Mbur_1378 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 764.80
//
Query:       gi|91773352|ref|YP_566044.1|  [L=265]
Description: ferredoxin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-19   66.9  51.4    2.2e-07   30.4   8.2    6.0  6  Fer4      4Fe-4S binding domain
    4.6e-14   51.8   5.5    4.6e-14   51.8   5.5    4.4  6  FeS       Putative Fe-S cluster
    1.9e-13   49.9  47.7    2.8e-05   24.0   0.7    5.8  5  Fer4_6    4Fe-4S binding domain
    2.7e-13   50.3  40.0    7.5e-07   29.6  14.8    4.8  4  Fer4_7    4Fe-4S dicluster domain
    8.8e-12   45.0  43.8    4.6e-07   29.9  17.3    4.3  4  Fer4_21   4Fe-4S dicluster domain
    8.8e-12   45.0  31.9    7.2e-07   29.3  16.7    3.7  3  Fer4_9    4Fe-4S dicluster domain
    2.6e-08   33.5  53.0    7.5e-05   22.6   2.7    6.1  6  Fer4_2    4Fe-4S binding domain
    7.7e-07   30.0  42.7     0.0098   16.8   1.4    5.3  6  Fer4_16   4Fe-4S double cluster binding domain
    2.2e-06   27.7  59.5     0.0006   19.9  16.4    5.1  3  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.3  49.2      0.016   15.7  16.3    5.0  5  Fer4_17   4Fe-4S dicluster domain
      0.016   15.8  45.2       0.17   12.4   7.3    5.7  5  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.018   15.5   0.7      0.018   15.5   0.7    6.4  7  Fer4_4    4Fe-4S binding domain
      0.033   13.4   0.0        0.1   11.8   0.0    1.7  2  NanE      Putative N-acetylmannosamine-6-phosphate epimerase
      0.056   14.4   3.4      0.056   14.4   3.4    6.7  7  Fer4_3    4Fe-4S binding domain
       0.07   13.6  46.2      0.051   14.0  15.0    4.5  3  Fer4_8    4Fe-4S dicluster domain
       0.78   10.6  39.6       0.21   12.5   1.9    5.3  6  Fer4_22   4Fe-4S dicluster domain
        3.4    8.5  44.8       0.22   12.3   4.5    6.3  7  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.4      0.92   9.7e+02      11      14 ..      52      55 ..      51      58 .. 0.77
   2 ?   -2.7   0.1         6   6.3e+03      18      21 ..      77      80 ..      76      81 .. 0.89
   3 !   16.3   1.2   6.1e-06    0.0064      12      24 .]     147     159 ..     143     159 .. 0.92
   4 !   26.2   0.9   4.5e-09   4.7e-06       2      23 ..     167     188 ..     166     189 .. 0.91
   5 !   20.2   5.6   3.4e-07   0.00036       8      24 .]     218     234 ..     217     234 .. 0.97
   6 !   30.4   8.2   2.1e-10   2.2e-07       2      24 .]     241     263 ..     240     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.92
                                  -THH CS
                          Fer4 11 CGaC 14
                                  CGaC
  gi|91773352|ref|YP_566044.1| 52 CGAC 55
                                  9999 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6
                                  STTT CS
                          Fer4 18 CPvg 21
                                  CPvg
  gi|91773352|ref|YP_566044.1| 77 CPVG 80
                                  **97 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 6.1e-06
                                   THHHHHSTTTEEE CS
                          Fer4  12 GaCvevCPvgAIt 24 
                                   G+Cv +CP+gAI+
  gi|91773352|ref|YP_566044.1| 147 GTCVRACPFGAIS 159
                                   99*********96 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 4.5e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    +++++C+ CG+C  +CP++ +
  gi|91773352|ref|YP_566044.1| 167 SVNKNLCTSCGLCLAACPNDIL 188
                                   699****************976 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 3.4e-07
                                   SSS-THHHHHSTTTEEE CS
                          Fer4   8 CigCGaCvevCPvgAIt 24 
                                   CigC++C++ CP +AI+
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPEDAIK 234
                                   ****************6 PP

  == domain 6  score: 30.4 bits;  conditional E-value: 2.1e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   ++d++kC++CG+Cve CP ++I+
  gi|91773352|ref|YP_566044.1| 241 EVDQDKCTACGICVEKCPQNCIE 263
                                   79*******************96 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   5.5   4.4e-17   4.6e-14       1      33 []      47      79 ..      47      79 .. 0.98
   2 ?   -3.4   0.0       7.6   8.1e+03      28      32 ..     123     127 ..     122     128 .. 0.77
   3 ?   -2.9   1.5       5.5   5.8e+03       8      15 ..     138     144 ..     133     145 .. 0.71
   4 ?   -2.0   1.0       2.7   2.9e+03       6      11 ..     173     178 ..     170     182 .. 0.68
   5 ?   -2.1   0.7         3   3.2e+03       6      23 ..     221     237 ..     219     249 .. 0.54
   6 ?   -3.1   3.0       6.4   6.7e+03       6      10 ..     247     251 ..     243     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.4e-17
                           FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                  LPg+NCgaCGy+gC +fAe++v+ +a+l+ Cp+
  gi|91773352|ref|YP_566044.1| 47 LPGANCGACGYAGCADFAEKVVAEDAPLDGCPV 79
                                  9******************************96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.6
                           FeS  28 ledCp 32 
                                   +edC+
  gi|91773352|ref|YP_566044.1| 123 IEDCT 127
                                   78997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.5
                           FeS   8 aCGypgCm 15 
                                   +C y gCm
  gi|91773352|ref|YP_566044.1| 138 GCNY-GCM 144
                                   5777.777 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.7
                           FeS   6 CgaCGy 11 
                                   C  CG 
  gi|91773352|ref|YP_566044.1| 173 CTSCGL 178
                                   666663 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 3
                           FeS   6 CgaCGypgCmafAealve 23 
                                   C+ C  ++C + A ++ +
  gi|91773352|ref|YP_566044.1| 221 CKICE-KNCPEDAIKVTN 237
                                   66663.366666666555 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 6.4
                           FeS   6 CgaCG 10 
                                   C aCG
  gi|91773352|ref|YP_566044.1| 247 CTACG 251
                                   88887 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.3       1.1   1.2e+03      11      19 ..      51      60 ..      49      65 .. 0.77
   2 !   12.5   3.5   0.00011      0.12       9      24 .]     139     158 ..     138     158 .. 0.83
   3 !   24.0   0.7   2.7e-08   2.8e-05       2      22 ..     166     186 ..     165     189 .. 0.89
   4 !   16.7   5.7   5.4e-06    0.0057       9      24 .]     218     233 ..     218     233 .. 0.98
   5 !   18.5   6.8   1.4e-06    0.0015       2      22 ..     240     260 ..     239     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                        Fer4_6 11 gCgdC.vrvC 19
                                   Cg+C ++ C
  gi|91773352|ref|YP_566044.1| 51 NCGACgYAGC 60
                                  5999977777 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                        Fer4_6   9 Ci.gC.gd..CvrvCPegai 24 
                                   C+ gC g+  Cvr+CP+gai
  gi|91773352|ref|YP_566044.1| 139 CNyGCmGRgtCVRACPFGAI 158
                                   6668855588*********8 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 2.7e-08
                        Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                   + +++++C++Cg C ++CP +
  gi|91773352|ref|YP_566044.1| 166 PSVNKNLCTSCGLCLAACPND 186
                                   679****************65 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 5.4e-06
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   CigC  C+++CPe+ai
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPEDAI 233
                                   **************98 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 1.4e-06
                        Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                   +e+d+dkC+ Cg Cv  CP +
  gi|91773352|ref|YP_566044.1| 240 AEVDQDKCTACGICVEKCPQN 260
                                   79*****************76 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  12.7      0.34   3.6e+02       5      52 .]      52     157 ..      50     157 .. 0.40
   2 !   27.6   7.5   3.1e-09   3.3e-06       2      51 ..     143     186 ..     139     187 .. 0.89
   3 !   19.0   2.1   1.5e-06    0.0016       2      26 ..     173     197 ..     172     215 .. 0.79
   4 !   29.6  14.8   7.1e-10   7.5e-07       2      51 ..     218     260 ..     217     261 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.34
                        Fer4_7   5 CgaCvaa.C.................pvkaielde.........e.enekgtekv.............eidpekCl..... 39 
                                   CgaC  a C                 pv+ +++ +         + e+ek+ ++v             ++  e+C+     
  gi|91773352|ref|YP_566044.1|  52 CGACGYAgCadfaekvvaedapldgcPVGGFDTAKeigaiigqeVsESEKEYPYVrcgggircvdrfdYVGIEDCTaviml 132
                                   555553324444455555555555554444433321222222112122222222244444444554443334444422222 PP

                        Fer4_7  40 .....gC.......gaCvavCPtga 52 
                                        gC       g Cv++CP+ga
  gi|91773352|ref|YP_566044.1| 133 sdgekGCnygcmgrGTCVRACPFGA 157
                                   2222212333333389*******97 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3.1e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   C+g g Cv+aCp +ai+++e       + + ++ + C++Cg C a+CP +
  gi|91773352|ref|YP_566044.1| 143 CMGRGTCVRACPFGAISINEN------RLPSVNKNLCTSCGLCLAACPND 186
                                   88889*************986......45788999*************87 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.5e-06
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek 26 
                                   C+ Cg C aaCp++ +++ +++++ 
  gi|91773352|ref|YP_566044.1| 173 CTSCGLCLAACPNDILMFAKDSEQV 197
                                   ******************9875543 PP

  == domain 4  score: 29.6 bits;  conditional E-value: 7.1e-10
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   CigC+ C+++Cp +ai+++++        +e+d++kC+ Cg Cv+ CP +
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPEDAIKVTNF-------LAEVDQDKCTACGICVEKCPQN 260
                                   ******************987.......4789****************87 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4      0.73   7.7e+02      10      27 ..      51      69 ..      49      80 .. 0.75
   2 !   25.6   6.8   9.6e-09     1e-05       8      53 ..     143     185 ..     136     189 .. 0.92
   3 !   14.2   8.1   3.3e-05     0.035      23      58 ..     199     234 ..     192     235 .. 0.75
   4 !   29.9  17.3   4.4e-10   4.6e-07       8      59 .]     218     264 ..     217     264 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.73
                       Fer4_21 10 gCgkC.liaCedtshqaie 27
                                  +Cg C +  C d + + + 
  gi|91773352|ref|YP_566044.1| 51 NCGACgYAGCADFAEKVVA 69
                                  7999945569988777664 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 9.6e-09
                       Fer4_21   8 CigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                   C+g g C+ aC+     ai+i++++   v ++ C+ C lC++ CP 
  gi|91773352|ref|YP_566044.1| 143 CMGRGTCVRACP---FGAISINENRLPSVNKNLCTSCGLCLAACPN 185
                                   9999********...89****************************3 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.3e-05
                       Fer4_21  23 hqaieid.aktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   +q+ + d +k+v +v e  C+GC++C + CP ed+i+
  gi|91773352|ref|YP_566044.1| 199 VQCNSHDkGKAVKAVCEVGCIGCKICEKNCP-EDAIK 234
                                   566665514455567799*************.89997 PP

  == domain 4  score: 29.9 bits;  conditional E-value: 4.4e-10
                       Fer4_21   8 CigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                   CigC+ C + C++   +ai+++ +  ++v +d+C++C +C++ CP ++ciem
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPE---DAIKVT-NFLAEVDQDKCTACGICVEKCP-QNCIEM 264
                                   ************7...99*986.7788******************.7****9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   4.6       7.7   8.1e+03       4      12 ..      51      60 ..      48     129 .. 0.74
   2 !   28.9   7.3     9e-10   9.4e-07       2      50 ..     143     187 ..     137     188 .. 0.84
   3 !   29.3  16.7   6.8e-10   7.2e-07       2      51 .]     218     262 ..     217     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.7
                        Fer4_9  4 gCgaCvea.C 12
                                  +CgaC +a C
  gi|91773352|ref|YP_566044.1| 51 NCGACGYAgC 60
                                  5777744335 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 9e-10
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   C+g g+Cv+aCp+g+++  +++    +++     C++Cg C++aCp+++
  gi|91773352|ref|YP_566044.1| 143 CMGRGTCVRACPFGAISINENRLPSVNKN----LCTSCGLCLAACPNDI 187
                                   444489**********9999888888765....6************994 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 6.8e-10
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C+gC+ C++ Cp ++++  ++  ++ ++     +C+ Cg Cve+Cp+++i
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPEDAIKVTNFLAEVDQD-----KCTACGICVEKCPQNCI 262
                                   *********************9999974.....6*************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.9       1.5   1.5e+03      12      19 ..      51      58 ..      50      61 .. 0.68
   2 ?   -2.1   0.5       5.2   5.5e+03      12      17 ..     107     115 ..     106     116 .. 0.71
   3 !    9.3   2.4    0.0012       1.3      10      21 ..     139     154 ..     134     155 .. 0.84
   4 !   19.7   2.2   5.8e-07   0.00061       3      22 .]     166     185 ..     164     185 .. 0.90
   5 !   11.3   5.4   0.00028       0.3      10      22 .]     218     230 ..     208     230 .. 0.86
   6 !   22.6   2.7   7.1e-08   7.5e-05       4      22 .]     241     259 ..     239     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                        Fer4_2 12 gCgaCvsa 19
                                  +CgaC  a
  gi|91773352|ref|YP_566044.1| 51 NCGACGYA 58
                                  79999555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.2
                        Fer4_2  12 gCg...aCv 17 
                                   +Cg    Cv
  gi|91773352|ref|YP_566044.1| 107 RCGggiRCV 115
                                   787778887 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0012
                        Fer4_2  10 Ci.gC...gaCvsaCP 21 
                                   C+ gC   g+Cv aCP
  gi|91773352|ref|YP_566044.1| 139 CNyGCmgrGTCVRACP 154
                                   888998767******* PP

  == domain 4  score: 19.7 bits;  conditional E-value: 5.8e-07
                        Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                   + v+ + C++Cg C+ aCP+
  gi|91773352|ref|YP_566044.1| 166 PSVNKNLCTSCGLCLAACPN 185
                                   67999**************5 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00028
                        Fer4_2  10 CigCgaCvsaCPa 22 
                                   CigC++C ++CP+
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPE 230
                                   ************5 PP

  == domain 6  score: 22.6 bits;  conditional E-value: 7.1e-08
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   +vd d+C++Cg+Cv  CP+
  gi|91773352|ref|YP_566044.1| 241 EVDQDKCTACGICVEKCPQ 259
                                   79****************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 ?   -2.2   0.9         8   8.4e+03       2       7 ..      52      57 ..      49      63 .. 0.60
   2 ?   -2.0   0.0       6.7     7e+03      12      22 ..      77      87 ..      74     117 .. 0.51
   3 !   10.5   0.1   0.00085       0.9       2      20 ..     143     161 ..     142     171 .. 0.81
   4 !   13.9   3.7   7.4e-05     0.078       2      30 ..     173     201 ..     172     215 .. 0.73
   5 !   16.8   1.4   9.3e-06    0.0098       2      20 ..     218     236 ..     217     245 .. 0.88
   6 !   11.0   8.0   0.00061      0.65       1      19 [.     246     264 ..     246     265 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8
                       Fer4_16  2 CgtCgk 7 
                                  Cg Cg 
  gi|91773352|ref|YP_566044.1| 52 CGACGY 57
                                  666665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.7
                       Fer4_16 12 CPtnaikekke 22
                                  CP++ +++ ke
  gi|91773352|ref|YP_566044.1| 77 CPVGGFDTAKE 87
                                  55555544433 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00085
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C + g C+ +CP +ai+ +
  gi|91773352|ref|YP_566044.1| 143 CMGRGTCVRACPFGAISIN 161
                                   788899*********9976 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 7.4e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearec 30 
                                   C++Cg C+ +CP + +   k+ e    +c
  gi|91773352|ref|YP_566044.1| 173 CTSCGLCLAACPNDILMFAKDSEQVHVQC 201
                                   **************998775555444444 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 9.3e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C++C+ C + CP++aik +
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPEDAIKVT 236
                                   ****************976 PP

  == domain 6  score: 11.0 bits;  conditional E-value: 0.00061
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C+ Cg C+e CP+n+i++
  gi|91773352|ref|YP_566044.1| 246 KCTACGICVEKCPQNCIEM 264
                                   5****************86 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  11.0   4.7e-06     0.005       9      56 .]     143     184 ..     136     184 .. 0.81
   2 !   17.2  16.0   3.8e-06     0.004       4      56 .]     168     229 ..     165     229 .. 0.78
   3 !   19.9  16.4   5.7e-07    0.0006       8      56 .]     217     258 ..     211     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.7e-06
                       Fer4_10   9 CirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   C++ g+Cv+aCP+      +   ++e+   +++   Ct cg C +aCP
  gi|91773352|ref|YP_566044.1| 143 CMGRGTCVRACPF------GAISINENRLPSVNKNLCTSCGLCLAACP 184
                                   99999********......44455555555667788***********9 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.8e-06
                       Fer4_10   4 idddtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++++ C+ Cg C +aCP d+          +v+ +  +++++++ +    C+gc  C + CP
  gi|91773352|ref|YP_566044.1| 168 VNKNLCTSCGLCLAACPNDIlmfakdseqVHVQCNSHDKGKAVKAVCEVGCIGCKICEKNCP 229
                                   68999*********************985444444444444444444458***********9 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 5.7e-07
                       Fer4_10   8 tCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    Ci+C+ C k CP         +++  +   +++ +kCt+cg Cve+CP
  gi|91773352|ref|YP_566044.1| 217 GCIGCKICEKNCPE-------DAIKVTNFLAEVDQDKCTACGICVEKCP 258
                                   5*************.......666666666666888************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 ?   -0.9   1.3       2.4   2.6e+03       2      10 ..      52      62 ..      50     105 .. 0.75
   2 ?    6.0   1.1     0.016        17      45      58 ..     142     155 ..     127     158 .. 0.83
   3 ?   11.7   8.2   0.00028      0.29      35      60 ..     162     187 ..     142     188 .. 0.68
   4 ?   15.7  16.3   1.5e-05     0.016       2      59 ..     173     231 ..     172     233 .. 0.82
   5 ?   10.6   6.5    0.0006      0.63      44      59 ..     245     260 ..     234     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.4
                       Fer4_17  2 CiqCgy..Clp 10
                                  C  Cgy  C++
  gi|91773352|ref|YP_566044.1| 52 CGACGYagCAD 62
                                  66666655555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                       Fer4_17  45 lCieCgeCerkCPq 58 
                                    C++ g C+r+CP 
  gi|91773352|ref|YP_566044.1| 142 GCMGRGTCVRACPF 155
                                   69999999999996 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00028
                       Fer4_17  35 eeaekeekaslCieCgeCerkCPqgl 60 
                                   e+   + + +lC++Cg+C ++CP+++
  gi|91773352|ref|YP_566044.1| 162 ENRLPSVNKNLCTSCGLCLAACPNDI 187
                                   33333346799************997 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 1.5e-05
                       Fer4_17   2 CiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   C++Cg Cl++Cp  +    ++ +++  + +++++++a k      Ci+C+ Ce+ CP++
  gi|91773352|ref|YP_566044.1| 173 CTSCGLCLAACPNDILmFAKDSEQVHVQCNSHDKGKAVKAVCEVGCIGCKICEKNCPED 231
                                   ************977745566778999999988888766545568************97 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0006
                       Fer4_17  44 slCieCgeCerkCPqg 59 
                                   ++C+ Cg C++kCPq+
  gi|91773352|ref|YP_566044.1| 245 DKCTACGICVEKCPQN 260
                                   78************97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.1       4.9   5.2e+03       8      17 ..      51      60 ..      50      73 .. 0.58
   2 ?   -1.2   0.1       2.9   3.1e+03      47      53 ..      72      79 ..      63      80 .. 0.74
   3 ?    4.6   0.3     0.045        48       5      17 ..     142     154 ..     140     155 .. 0.92
   4 ?    7.4  13.2    0.0063       6.6       1      51 [.     168     221 ..     168     234 .. 0.75
   5 ?   12.4   7.3   0.00016      0.17       1      18 [.     242     259 ..     242     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.9
                       Fer4_13  8 acgaCvelaP 17
                                  +cgaC+ +  
  gi|91773352|ref|YP_566044.1| 51 NCGACGYAGC 60
                                  4666655433 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                       Fer4_13 47 A.adaCPv 53
                                  A +d+CPv
  gi|91773352|ref|YP_566044.1| 72 ApLDGCPV 79
                                  44899**8 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.045
                       Fer4_13   5 tCiacgaCvelaP 17 
                                    C++ g+Cv ++P
  gi|91773352|ref|YP_566044.1| 142 GCMGRGTCVRACP 154
                                   6***********9 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0063
                       Fer4_13   1 VDrdtCiacgaCvelaPd...vFeeddeggasvvaeqptseeekadaeeAadaC 51 
                                   V+++ C++cg+C +++P+   +F+ d e+ +++   ++++++ ka +e  + +C
  gi|91773352|ref|YP_566044.1| 168 VNKNLCTSCGLCLAACPNdilMFAKDSEQVHVQCNSHDKGKAVKAVCEVGCIGC 221
                                   899**************8777899999999888888888876666666555444 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00016
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   VD+d+C+acg+Cve +P+
  gi|91773352|ref|YP_566044.1| 242 VDQDKCTACGICVEKCPQ 259
                                   9****************7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.3       3.3   3.5e+03       6      10 ..      51      55 ..      50      62 .. 0.79
   2 ?   -2.3   0.0       8.7   9.2e+03      13      16 ..      76      79 ..      75      80 .. 0.65
   3 ?   -1.8   0.3       6.1   6.4e+03       6      12 ..     107     116 ..     106     116 .. 0.59
   4 ?    9.3   2.9    0.0016       1.7       6      17 .]     142     156 ..     136     156 .. 0.70
   5 ?   15.5   0.7   1.7e-05     0.018       2      15 ..     171     184 ..     170     195 .. 0.89
   6 ?    8.2   5.8    0.0037       3.9       4      16 ..     218     230 ..     211     236 .. 0.93
   7 ?   11.9   5.2   0.00025      0.26       1      17 []     244     260 ..     244     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.3
                        Fer4_4  6 gCgsC 10
                                  +Cg+C
  gi|91773352|ref|YP_566044.1| 51 NCGAC 55
                                  69999 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.7
                        Fer4_4 13 aCPq 16
                                   CP+
  gi|91773352|ref|YP_566044.1| 76 GCPV 79
                                  6886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 6.1
                        Fer4_4   6 gCg...sCva 12 
                                   +Cg   +Cv+
  gi|91773352|ref|YP_566044.1| 107 RCGggiRCVD 116
                                   6775555775 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0016
                        Fer4_4   6 gCg...sCvaaCPqg 17 
                                   gC+    Cv+aCP+g
  gi|91773352|ref|YP_566044.1| 142 GCMgrgTCVRACPFG 156
                                   5664448******86 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 1.7e-05
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   + C+ Cg C aaCP
  gi|91773352|ref|YP_566044.1| 171 NLCTSCGLCLAACP 184
                                   78************ PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0037
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   CigC+ C+  CP 
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPE 230
                                   ************5 PP

  == domain 7  score: 11.9 bits;  conditional E-value: 0.00025
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   q++C+ Cg Cv  CPq+
  gi|91773352|ref|YP_566044.1| 244 QDKCTACGICVEKCPQN 260
                                   79*************86 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   1.2e+03      58     111 ..      12      72 ..       3      82 .. 0.60
   2 ?   11.8   0.0   9.7e-05       0.1      11      64 ..     194     249 ..     187     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                   HHHHTTT-SE.EEEE--SS--T--HHHHHHHHHHH-......-EEEEE-SSHHHHHHHHHT CS
                          NanE  58 deLaaagadi.ialDatdrerpvtieelikkikeky......qllmaDistleeglvakkl 111
                                     L   g  i i l a++r  +v+ + l++++ e         +  a ++ + e +va+++
  gi|91773352|ref|YP_566044.1|  12 ATLGGLGLVIgIMLIAASRMFKVETNPLVEEVVEILpgancgACGYAGCADFAEKVVAEDA 72 
                                   5555555444455556666666666666666655433333336777888888888887766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.7e-05
                                   HT-SEEEEESHHHHHHHHTT--S-EEE..E-B---TTS---BS-SHHHHHHHHTTT CS
                          NanE  11 aGavgiriegvedikaikavvdlPiiG..ivkrdlpdsevritatlkdideLaaag 64 
                                   +  v ++ ++ +  ka+kav ++  iG  i  ++ p+  +++t +l ++d+   ++
  gi|91773352|ref|YP_566044.1| 194 SEQVHVQCNSHDKGKAVKAVCEVGCIGckICEKNCPEDAIKVTNFLAEVDQDKCTA 249
                                   55677888999999*************8899*******************865555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.7       1.7   1.8e+03       3       7 ..      51      55 ..      51      58 .. 0.78
   2 ?   -0.5   0.1         3   3.2e+03      11      14 ..      77      80 ..      74      81 .. 0.79
   3 ?   -1.5   0.1       6.2   6.5e+03       4       9 ..     108     116 ..     106     117 .. 0.76
   4 ?   12.2   4.4   0.00026      0.27       1      15 []     139     157 ..     138     157 .. 0.81
   5 ?   14.4   3.4   5.4e-05     0.056       1      14 [.     173     186 ..     173     187 .. 0.93
   6 ?   10.4   2.9     0.001       1.1       1      15 []     218     232 ..     218     232 .. 0.96
   7 ?    3.8   9.6      0.13   1.3e+02       1      14 [.     247     260 ..     247     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.7
                        Fer4_3  3 gCgaC 7 
                                  +CgaC
  gi|91773352|ref|YP_566044.1| 51 NCGAC 55
                                  6**** PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3
                        Fer4_3 11 CPvg 14
                                  CPvg
  gi|91773352|ref|YP_566044.1| 77 CPVG 80
                                  **98 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 6.2
                        Fer4_3   4 Cg...aCve 9  
                                   Cg   +Cv+
  gi|91773352|ref|YP_566044.1| 108 CGggiRCVD 116
                                   877788985 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00026
                        Fer4_3   1 Ct.gCg...aCvevCPvgA 15 
                                   C+ gC+   +Cv++CP gA
  gi|91773352|ref|YP_566044.1| 139 CNyGCMgrgTCVRACPFGA 157
                                   6558955669*******98 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 5.4e-05
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   Ct Cg+C+ +CP++
  gi|91773352|ref|YP_566044.1| 173 CTSCGLCLAACPND 186
                                   ************87 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.001
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gC  C++ CP++A
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPEDA 232
                                   ****99******998 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.13
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   Ct Cg Cve CP +
  gi|91773352|ref|YP_566044.1| 247 CTACGICVEKCPQN 260
                                   9***********87 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   8.6      0.66     7e+02      44      64 ..     122     156 ..      50     157 .. 0.50
   2 ?   14.0  15.0   4.8e-05     0.051       5      64 ..     173     231 ..     169     235 .. 0.67
   3 ?    4.1  17.5     0.061        64       5      64 ..     218     260 ..     216     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.66
                        Fer4_8  44 e..............eealwsCttcgaCtevCpvg 64 
                                   +              +   + C++ g C+++Cp g
  gi|91773352|ref|YP_566044.1| 122 GiedctavimlsdgeKGCNYGCMGRGTCVRACPFG 156
                                   144555556666665677899***********975 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.8e-05
                        Fer4_8   5 CieCgaCqsaCp.....vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   C+ Cg+C +aCp     +++++ + + + +   ++++++      +     C +c+ C+++Cp++
  gi|91773352|ref|YP_566044.1| 173 CTSCGLCLAACPndilmFAKDSEQVHVQCNSHDKGKAVK------AVCEVGCIGCKICEKNCPED 231
                                   ***********9777655555553333333333331222......223579************85 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.061
                        Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   Ci+C  C+++Cp      ++  +  +  ae    +q        ++Ct+cg C+e+Cp++
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCP------EDAIKVTNFLAE---VDQ--------DKCTACGICVEKCPQN 260
                                   ***********9......332333333233...222........58************87 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       7.8   8.2e+03       4      11 ..      51      58 ..      49      72 .. 0.63
   2 ?   -0.3   0.0         2   2.1e+03      68      90 ..      94     116 ..      82     120 .. 0.79
   3 ?    3.4   2.3      0.13   1.4e+02      79      94 ..     140     155 ..     129     157 .. 0.85
   4 ?    9.8   0.3    0.0014       1.4      76      96 .]     167     187 ..     160     187 .. 0.85
   5 ?    6.6   5.7     0.014        14      67      94 ..     203     230 ..     189     233 .. 0.74
   6 ?   12.5   1.9    0.0002      0.21      69      95 ..     234     260 ..     231     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.8
                       Fer4_22  4 sCgaCtlv 11
                                  +CgaC ++
  gi|91773352|ref|YP_566044.1| 51 NCGACGYA 58
                                  46666543 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2
                       Fer4_22  68 hklsefkekfgesgCvGCgRCie 90 
                                   + +se ++++    C G  RC++
  gi|91773352|ref|YP_566044.1|  94 QEVSESEKEYPYVRCGGGIRCVD 116
                                   5667778888999999999*986 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.13
                       Fer4_22  79 esgCvGCgRCieacpv 94 
                                   ++gC+G g C++acp 
  gi|91773352|ref|YP_566044.1| 140 NYGCMGRGTCVRACPF 155
                                   579***********95 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0014
                       Fer4_22  76 kfgesgCvGCgRCieacpvki 96 
                                   +++++ C+ Cg C +acp++i
  gi|91773352|ref|YP_566044.1| 167 SVNKNLCTSCGLCLAACPNDI 187
                                   568899***********9876 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.014
                       Fer4_22  67 lhklsefkekfgesgCvGCgRCieacpv 94 
                                    h   + ++ + e gC+GC  C+++cp+
  gi|91773352|ref|YP_566044.1| 203 SHDKGKAVKAVCEVGCIGCKICEKNCPE 230
                                   45555667778899************97 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.0002
                       Fer4_22  69 klsefkekfgesgCvGCgRCieacpvk 95 
                                   k+++f +++++ +C+ Cg C+e+cp++
  gi|91773352|ref|YP_566044.1| 234 KVTNFLAEVDQDKCTACGICVEKCPQN 260
                                   8889999*****************986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       4.6   4.9e+03      13      26 ..      59      72 ..      51      90 .. 0.69
   2 ?    0.7   0.9      0.86   9.1e+02       7      38 ..     107     136 ..     105     139 .. 0.81
   3 ?    5.0   0.3      0.04        42      56      66 .]     150     160 ..     141     160 .. 0.71
   4 ?   12.1   3.4   0.00024      0.25       3      33 ..     168     198 ..     167     219 .. 0.70
   5 ?    1.0   3.2      0.69   7.3e+02       8      20 ..     218     230 ..     215     230 .. 0.91
   6 ?    3.1   0.1      0.15   1.6e+02      57      66 .]     226     235 ..     225     235 .. 0.88
   7 ?   12.3   4.5   0.00021      0.22       2      20 ..     241     259 ..     241     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.6
                       Fer4_15 13 lCvaeapevfelde 26
                                   C++ a++v+ +d 
  gi|91773352|ref|YP_566044.1| 59 GCADFAEKVVAEDA 72
                                  47777777776664 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.86
                       Fer4_15   7 aCigcglCvaeapevfeldedglasvllddge 38 
                                   +C g  +Cv++  +++ ++ d  a++ l+dge
  gi|91773352|ref|YP_566044.1| 107 RCGGGIRCVDRF-DYVGIE-DCTAVIMLSDGE 136
                                   799999****95.699888.888888887776 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.04
                       Fer4_15  56 araCPvdAIrv 66 
                                   +raCP +AI++
  gi|91773352|ref|YP_566044.1| 150 VRACPFGAISI 160
                                   57777777765 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00024
                       Fer4_15   3 vDrdaCigcglCvaeapevfeldedglasvl 33 
                                   v++++C++cglC+a++p+ + +  ++  +v+
  gi|91773352|ref|YP_566044.1| 168 VNKNLCTSCGLCLAACPNDILMFAKDSEQVH 198
                                   7899************875444444444444 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.69
                       Fer4_15   8 CigcglCvaeape 20 
                                   Cigc  C +++pe
  gi|91773352|ref|YP_566044.1| 218 CIGCKICEKNCPE 230
                                   ********99996 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.15
                       Fer4_15  57 raCPvdAIrv 66 
                                   ++CP+dAI v
  gi|91773352|ref|YP_566044.1| 226 KNCPEDAIKV 235
                                   58******87 PP

  == domain 7  score: 12.3 bits;  conditional E-value: 0.00021
                       Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                   +vD+d+C+ cg Cv+ +p+
  gi|91773352|ref|YP_566044.1| 241 EVDQDKCTACGICVEKCPQ 259
                                   59***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1432.72
//
Query:       gi|91773353|ref|YP_566045.1|  [L=196]
Description: electron transport complex, RnfABCDGE type, A subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-54  184.2  22.4    2.3e-54  184.0  22.4    1.0  1  Rnf-Nqr          Rnf-Nqr subunit, membrane protein


Domain annotation for each model (and alignments):
>> Rnf-Nqr  Rnf-Nqr subunit, membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.0  22.4   1.3e-58   2.3e-54       2     171 ..       8     191 ..       7     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.0 bits;  conditional E-value: 1.3e-58
                                   -HHHHHHHHHTS-TTTTT--HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHH------.....---HHHHHHHHHHHH CS
                       Rnf-Nqr   2 lkillsgilkeNpvlvqflGiCpflavskklknalgmglavtfvlvlsnlvisllrklipk.....klriivfilviAalv 77 
                                   ++i+++g++++N++++qflG+C+f++v+k++k+a gm+ av+fv++l+++v++l++++++      +l +i+fi+viAalv
  gi|91773353|ref|YP_566045.1|   8 FQIFMDGVFIKNFLIIQFLGLCSFVGVTKDTKSAAGMSGAVIFVMTLAATVSFLIYNFVLVplkleFLDLISFIVVIAALV 88 
                                   89********************************************************99999****************** PP

                                   HHHHHHT------THHHHHHHHHHHHS-HHHHHHHHT-----.---THHHHHHHHHHHHHHHHHHHHHHHHHHT....... CS
                       Rnf-Nqr  78 tlvelvlkaflpslykaLgiflpLivvNCiilgraeafaskn.svleslldglgsglGftlalvllaairellg....... 150
                                   +lve+v+++ +psly++Lgi+lpLi++NC++lg++++++ ++ s+++s+++g+ +g+G++l+++++++ire+         
  gi|91773353|ref|YP_566045.1|  89 QLVEFVVRKNVPSLYRSLGIYLPLITTNCAVLGVVLLNVLNEySFIQSVVFGVSAGIGYALVMLMMSGIRERTTlvnvpss 169
                                   ***************************************9889************************************** PP

                                   .S-SSS.-----SHHHHHHHHH CS
                       Rnf-Nqr 151 .kGtliglilagllagaFlglg 171
                                    +G++ ++++a++l++aF+   
  gi|91773353|ref|YP_566045.1| 170 mRGLPHAFLIATMLSMAFVNYF 191
                                   ******************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1315.01
//
Query:       gi|91773354|ref|YP_566046.1|  [L=203]
Description: electron transport complex RsxE subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  207.6  17.4    1.6e-61  207.3  17.4    1.0  1  Rnf-Nqr   Rnf-Nqr subunit, membrane protein


Domain annotation for each model (and alignments):
>> Rnf-Nqr  Rnf-Nqr subunit, membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3  17.4   8.9e-66   1.6e-61       3     174 .]       5     188 ..       4     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 8.9e-66
                                   HHHHHHHHHTS-TTTTT--HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHH CS
                       Rnf-Nqr   3 killsgilkeNpvlvqflGiCpflavskklknalgmglavtfvlvlsnlvisllrklipkklriivfilviAalvtlvelv 83 
                                   + +++gi k+Np++  +lG+Cp+lav+++++na+gm++ + fvl++snl++s lrk ip+++r+++fil+iA++v +v++v
  gi|91773354|ref|YP_566046.1|   5 SEFIRGITKDNPIFGLVLGLCPTLAVTTSIDNAIGMSAGTAFVLICSNLMVSGLRKQIPASVRLPIFILIIATFVSIVKMV 85 
                                   679****************************************************************************** PP

                                   T------THHHHHHHHHHHHS-HHHHHHHHT--------THHHHHHHHHHHHHHHHHHHHHHHHHHTS-SSS......... CS
                       Rnf-Nqr  84 lkaflpslykaLgiflpLivvNCiilgraeafasknsvleslldglgsglGftlalvllaairellgkGtlig........ 156
                                   ++a++p +y+aLg+f+pLivvNCii+graea+a+kn+++ sl+d+lgs++Gf+l+lvl+++irellg+G +          
  gi|91773354|ref|YP_566046.1|  86 MEAYFPPMYAALGVFIPLIVVNCIIIGRAEAYANKNNMFYSLIDALGSSAGFLLVLVLIGGIRELLGTGGIAIfgtqlvsi 166
                                   *******************************************************************8877555689999* PP

                                   ....-----SHHHHHHHHHHHH CS
                       Rnf-Nqr 157 ....lilagllagaFlglggli 174
                                       +++++l +gaFl++g+l+
  gi|91773354|ref|YP_566046.1| 167 pinpITFMILSPGAFLTIGILM 188
                                   ******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1408.90
//
Query:       gi|91773355|ref|YP_566047.1|  [L=190]
Description: electron transport complex, RnfABCDGE type, G subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-15   55.1   1.3    1.5e-14   54.3   1.3    1.4  1  FMN_bind  FMN-binding domain


Domain annotation for each model (and alignments):
>> FMN_bind  FMN-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   1.3   8.5e-19   1.5e-14       1      66 [.      99     180 ..      99     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 8.5e-19
                                   SSSSEEEEEEEEETTTSBEEEEEEEESSS-TTTGGG..................CTTHHHHSSEEETCTTBHHHHHHHHHH CS
                      FMN_bind   1 GyggtikvlvtvkdgdgtItgievlehsETpglgsk..................avkkdggdqevDaiSGATissravkda 63 
                                   G +g i+v+ +v+++ + Itgi ++ h ETpglgsk                  + +k+gg   +D i+GATiss+av+da
  gi|91773355|ref|YP_566047.1|  99 GAQGLIEVAGGVDSSFNAITGIGIMAHTETPGLGSKiaddpfksqftnvkvadlSLSKSGG--AIDSITGATISSQAVIDA 177
                                   6688999*****554559*****************88999988777655443332344455..8***************** PP

                                   HHH CS
                      FMN_bind  64 vna 66 
                                   +n+
  gi|91773355|ref|YP_566047.1| 178 LNE 180
                                   996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1303.27
//
Query:       gi|91773356|ref|YP_566048.1|  [L=309]
Description: NADH--ubiquinone oxidoreductase subunit RnfD [Methanococcoides burtonii DSM 6242]
Scores for complete 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-71  241.7  25.7    1.3e-71  241.4  25.7    1.1  1  NQR2_RnfD_RnfE  NQR2, RnfD, RnfE family


Domain annotation for each model (and alignments):
>> NQR2_RnfD_RnfE  NQR2, RnfD, RnfE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4  25.7   7.3e-76   1.3e-71       2     292 .]       5     281 ..       4     281 .. 0.96

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 7.3e-76
                NQR2_RnfD_RnfE   2 vsssphvrdkestkrimldvliallpallfgvynfglqalllilvavvvavlaEvlfaklrkkevkvtdlsavvtglLlal 82 
                                   +s+ ph +++++ k+im+  ++al+p++l++vy+fgl a+ l++ ++++a+++E+ ++k  +++++++d++av+ gl++a+
  gi|91773356|ref|YP_566048.1|   5 ISAPPHKKENITFKKIMWAKVLALMPVVLLSVYLFGLPAIGLVAASIFAAIATEATIQKAFGQKITIADGHAVLIGLMVAM 85 
                                   6789***************************************************************************** PP

                NQR2_RnfD_RnfE  83 ilPptlplwvvvigsvfaivvvKelfGGlGqNifNPAlvgrafllisfpaqmtwvaDavsgatpLaalksaslldlflgni 163
                                   i+Pp++plw+++ig+vfa+ ++K++fGG+G+ +fNP l++++fl +++ + m        +  p +    + l++l+l+n 
  gi|91773356|ref|YP_566048.1|  86 IIPPEVPLWIPMIGTVFAVGIGKHAFGGIGSYVFNPVLAAWLFLSLAWGSIMA------PASYPQT----SALFELVLENG 156
                                   ****************************************************4......2222333....35889*****9 PP

                NQR2_RnfD_RnfE 164 agsigetsalalllgglyLlvrkiiswripvsvlatvavlsllfnllaapplfhllsGglllgafFmatdpvtspitkkGk 244
                                   ag +  +s + +ll+g++L++r++i+wripv++++t+++l++l+++     l  +++G +++g++F+atd +tsp+tk+G+
  gi|91773356|ref|YP_566048.1| 157 AGVMAGVSPFFILLAGAVLIFRRYIEWRIPVTFFVTTVLLAFLLGD----SLSYVVLGVVVFGVLFIATDTSTSPTTKNGR 233
                                   *********************************************6....899**************************** PP

                NQR2_RnfD_RnfE 245 lifglliGlltvliRvfgaypeGvafaiLlmNllvplidkltrprnfg 292
                                   +i+g+++G+l+v+   f +y +G+++   l+N+++ lid+ t p+ +g
  gi|91773356|ref|YP_566048.1| 234 VIYGIVCGVLVVVYGHFANYVDGTFYGLFLANCVASLIDNNTLPASYG 281
                                   ****************************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2090.55
//
Query:       gi|91773357|ref|YP_566049.1|  [L=453]
Description: electron transport complex, RnfABCDGE type, C subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   93.9   0.0    1.3e-26   93.3   0.0    1.3  1  Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subu
    4.5e-22   77.9   1.4    1.5e-21   76.2   0.3    2.2  2  RnfC_N        RnfC Barrel sandwich hybrid domain
      2e-11   43.6   0.8    5.3e-11   42.2   0.8    1.8  1  SLBB          SLBB domain
    3.5e-08   33.4  10.9    1.5e-06   28.2  12.8    2.4  2  Fer4_10       4Fe-4S dicluster domain
    6.3e-08   33.1  12.2    2.1e-07   31.4  12.2    2.0  1  Fer4_7        4Fe-4S dicluster domain
    1.2e-06   28.1  14.8     0.0017   18.1   3.7    2.7  2  Fer4          4Fe-4S binding domain
    1.5e-06   28.2  12.8    1.8e-05   24.8  13.9    2.2  2  Fer4_9        4Fe-4S dicluster domain
    2.1e-06   27.8  10.7     0.0062   17.0   1.7    3.2  2  Fer4_4        4Fe-4S binding domain
    2.5e-06   28.3   9.4      0.011   16.7   2.0    2.6  2  Fer4_16       4Fe-4S double cluster binding domain
    4.6e-06   26.7  10.5     0.0032   17.6   2.2    2.8  2  Fer4_21       4Fe-4S dicluster domain
    1.1e-05   25.8  11.8     0.0011   19.3  13.8    2.4  3  Fer4_8        4Fe-4S dicluster domain
    1.3e-05   25.1  14.8      0.011   15.8   2.2    2.7  2  Fer4_6        4Fe-4S binding domain
    2.8e-05   24.6  12.5    0.00046   20.7  13.5    2.3  2  Fer4_17       4Fe-4S dicluster domain
    5.5e-05   23.0  14.3      0.031   14.4   3.2    3.0  2  Fer4_2        4Fe-4S binding domain
    0.00027   21.7   7.1      0.058   14.2   2.1    2.7  2  Fer4_22       4Fe-4S dicluster domain
     0.0062   16.0   0.0     0.0087   15.5   0.0    1.2  1  NQRA          Na(+)-translocating NADH-quinone reductase subu
  ------ inclusion threshold ------
      0.022   15.7   6.2      0.022   15.7   6.2    3.5  2  Fer4_3        4Fe-4S binding domain
      0.081   13.1  21.0      0.091   13.0   2.8    3.4  4  Fer4_18       4Fe-4S dicluster domain
        1.3    8.8   8.8          2    8.2   0.8    2.5  2  Fer4_20       Dihydroprymidine dehydrogenase domain II, 4Fe-4


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.0   1.4e-29   1.3e-26       1     151 [.     106     269 ..     106     270 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 1.4e-29
                  Complex1_51K   1 vkeagivGrGGagfPthvKlkakakkkkkylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvigvrdekp 81 
                                   +k+agiv+++G+  Pth+ l+++ k +++++++Na+ +E ++  ++++ ++++++++++lk++++a ga+kg +++r+++ 
  gi|91773357|ref|YP_566049.1| 106 IKDAGIVEHYGT--PTHKVLRPEGK-QIDTVLINATSSE-WIGGHYDTSAQYASQMIDALKLLMKAAGASKGAVVLRNDDL 182
                                   79**********..**********8.89***********.***************************************** PP

                  Complex1_51K  82 eaiealeka......laeakaagl...........ldievvklagkYpaGeekaLiesltgrevprgkppadvgvvvnNve 145
                                   e+i+a+++       l+ a+ +g             di vv+ ++ Y +   + L+++ltgr+v+ ++ p+dvgv++++v+
  gi|91773357|ref|YP_566049.1| 183 ESINAFDHLrvdgklLTVAPLMGKrklsyyfkdmgSDIIVVSQERIYGQKILDLLTYNLTGRRVSFCCDPTDVGVAICGVK 263
                                   ********977777766666555588999**************************************************** PP

                  Complex1_51K 146 Tlaavy 151
                                   +++a+y
  gi|91773357|ref|YP_566049.1| 264 SAKALY 269
                                   ***998 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.3   1.6e-24   1.5e-21      25      99 ..       9      83 ..       3      85 .. 0.96
   2 ?   -1.0   0.0       1.8   1.7e+03      71      88 ..     283     300 ..     270     308 .. 0.66

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.6e-24
                        RnfC_N 25 plpkelvlplsqhiGapakplvkvgdkVlkGqkiaeaegfvsapvhasvsGtVkaiekrlvahgsgveavvienD 99
                                  ++p+++++pl+qh G  ++plv++gd V +Gqki+e e + sa+vh+sv G+V++iek+++++g++v++v+i++ 
  gi|91773357|ref|YP_566049.1|  9 KIPEKIIIPLKQHDGCLCTPLVNKGDMVSMGQKIGECECYDSAAVHSSVCGEVISIEKAANPNGTKVNSVIIKPT 83
                                  689*********************************************************************975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                        RnfC_N  71 asvsGtVkaiekrlvahg 88 
                                    svsG+V + +k+lv+ g
  gi|91773357|ref|YP_566049.1| 283 VSVSGKVNSPKKILVKIG 300
                                   367777776666655554 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.8   5.7e-14   5.3e-11       1      57 [.     282     329 ..     282     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 5.7e-14
                                   EEEEESSBSS-EEEEEETT-BHHHHHHTTT-SBSS.........-EEEE-SSSSS-- CS
                          SLBB   1 vVtVtGeVkrPgnyevpigttlsdlieqaGGltddadlksvnLarlavipgGpmmgi 57 
                                   vV V+G+V+ P+ + v+igt+++d+i+++GG++ d           ++i +G+++g+
  gi|91773357|ref|YP_566049.1| 282 VVSVSGKVNSPKKILVKIGTPFKDVIDACGGYMGDTG---------KLIANGAVTGV 329
                                   79*********************************99.........7899****998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2  12.8   1.6e-09   1.5e-06       8      56 .]     360     411 ..     352     411 .. 0.77
   2 !   15.7   3.5   1.3e-05     0.012       8      24 ..     399     423 ..     392     442 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.6e-09
                       Fer4_10   8 tCirCgkCvkaCPadltsvgakgease...eeavrkkvekCtgcgaCveaCP 56 
                                    C++C++Cv++CP+dl  ++ +++a++   +e  + ++ +C +cg C ++CP
  gi|91773357|ref|YP_566049.1| 360 DCTHCARCVDVCPVDLIPSRITAFADQgrfDECRQMNILNCVECGRCSAVCP 411
                                   4***************6666666665511155666799*************9 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                       Fer4_10   8 tCirCgkCvkaCPadl........t 24 
                                    C++Cg+C ++CP+++         
  gi|91773357|ref|YP_566049.1| 399 NCVECGRCSAVCPSKIhllqliryA 423
                                   5*************77555554430 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4  12.2   2.2e-10   2.1e-07       2      51 ..     361     413 ..     360     414 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.2e-10
                        Fer4_7   2 CigCgaCvaaCpvkaield..eeenekgtekv.eidpekClgCgaCvavCPtg 51 
                                   C++C +Cv++Cpv+ i  +   ++++ +++++ +++  +C+ Cg+C avCP++
  gi|91773357|ref|YP_566049.1| 361 CTHCARCVDVCPVDLIPSRitAFADQGRFDECrQMNILNCVECGRCSAVCPSK 413
                                   ***************98553245555566666357899*************97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   3.7   1.8e-06    0.0017       7      22 ..     360     375 ..     359     376 .. 0.91
   2 !   14.8   3.4     2e-05     0.019       7      20 ..     399     412 ..     396     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                                   TSSS-THHHHHSTTTE CS
                          Fer4   7 kCigCGaCvevCPvgA 22 
                                   +C++C +Cv+vCPv+ 
  gi|91773357|ref|YP_566049.1| 360 DCTHCARCVDVCPVDL 375
                                   5*************96 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2e-05
                                   TSSS-THHHHHSTT CS
                          Fer4   7 kCigCGaCvevCPv 20 
                                    C+ CG+C  vCP 
  gi|91773357|ref|YP_566049.1| 399 NCVECGRCSAVCPS 412
                                   5************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 !   16.2   2.0   9.2e-06    0.0087      34      50 ..     359     375 ..     336     376 .. 0.72
   2 !   24.8  13.9   1.9e-08   1.8e-05       1      49 [.     360     413 ..     360     415 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.2e-06
                        Fer4_9  34 eaCigCgaCveaCpkga 50 
                                    +C++C +Cv++Cp + 
  gi|91773357|ref|YP_566049.1| 359 IDCTHCARCVDVCPVDL 375
                                   47***********9885 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.9e-08
                        Fer4_9   1 kCtgCgaCveaC.....pagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   +Ct C +Cv++C     p+ ++   +++r++++r+ +  +C++Cg+C ++Cp++
  gi|91773357|ref|YP_566049.1| 360 DCTHCARCVDVCpvdliPSRITAFADQGRFDECRQMNILNCVECGRCSAVCPSK 413
                                   5***********5555545555555666666666666699************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.7   6.6e-06    0.0062       4      16 ..     361     373 ..     356     380 .. 0.94
   2 !   14.0   2.0     6e-05     0.057       3      16 ..     399     412 ..     397     416 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-06
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C++C +Cv++CP+
  gi|91773357|ref|YP_566049.1| 361 CTHCARCVDVCPV 373
                                   ************7 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6e-05
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +C++Cg+C a+CP+
  gi|91773357|ref|YP_566049.1| 399 NCVECGRCSAVCPS 412
                                   7************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 !   16.7   2.0   1.2e-05     0.011       2      20 ..     361     379 ..     360     396 .. 0.82
   2 !   15.5   0.9   2.7e-05     0.025       1      19 [.     399     417 ..     399     448 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C+ C +C++vCP++ i ++
  gi|91773357|ref|YP_566049.1| 361 CTHCARCVDVCPVDLIPSR 379
                                   **************99877 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.7e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C++Cg+C  vCP++    
  gi|91773357|ref|YP_566049.1| 399 NCVECGRCSAVCPSKIHLL 417
                                   6************987444 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   2.2   3.4e-06    0.0032      28      56 ..     348     375 ..     339     378 .. 0.79
   2 !   12.9   1.4   9.9e-05     0.094       7      22 ..     399     414 ..     390     434 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-06
                       Fer4_21  28 idaktvlkvvedeCvGCnlCssvCPvedc 56 
                                   ++a++v++ v+ +C+ C+ C++vCPv d 
  gi|91773357|ref|YP_566049.1| 348 LSADEVIRDVSIDCTHCARCVDVCPV-DL 375
                                   456677888899*************9.65 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.9e-05
                       Fer4_21   7 kCigCgkCliaCedts 22 
                                   +C++Cg+C  +C+ + 
  gi|91773357|ref|YP_566049.1| 399 NCVECGRCSAVCPSKI 414
                                   5666666666666554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.8   7.6e-05     0.072      46      64 ..     356     374 ..     322     375 .. 0.77
   2 !   19.3  13.8   1.2e-06    0.0011       4      65 .]     360     414 ..     358     414 .. 0.87
   3 !   17.3   1.8   5.3e-06     0.005       3      33 ..     398     428 ..     396     447 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.6e-05
                        Fer4_8  46 ealwsCttcgaCtevCpvg 64 
                                   +    Ct+c +C++vCpv+
  gi|91773357|ref|YP_566049.1| 356 DVSIDCTHCARCVDVCPVD 374
                                   5566899999999999986 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-06
                        Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                   +C++C +C + Cpv     +    a +++ + + ++++      + +C++cg+C+ vCp +i
  gi|91773357|ref|YP_566049.1| 360 DCTHCARCVDVCPVDLIPSRITAFADQGRFD-ECRQMN------ILNCVECGRCSAVCPSKI 414
                                   6************999999888888888787.666666......89*************997 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 5.3e-06
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaa 33 
                                    +C+eCg+C + Cp+  +  + + +a++  +
  gi|91773357|ref|YP_566049.1| 398 LNCVECGRCSAVCPSKIHLLQLIRYAKNSIE 428
                                   5899999999999966665555555555444 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   5.0   4.6e-05     0.044       9      24 .]     361     376 ..     360     376 .. 0.91
   2 !   15.8   2.2   1.1e-05     0.011       8      21 ..     399     412 ..     395     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   C++C +Cv+vCP + i
  gi|91773357|ref|YP_566049.1| 361 CTHCARCVDVCPVDLI 376
                                   ************8765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.1e-05
                        Fer4_6   8 kCigCgdCvrvCPe 21 
                                   +C+ Cg+C +vCP 
  gi|91773357|ref|YP_566049.1| 399 NCVECGRCSAVCPS 412
                                   7************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 !   12.5   1.6   0.00018      0.17      44      60 ..     359     375 ..     337     376 .. 0.78
   2 !   20.7  13.5   4.9e-07   0.00046       2      60 ..     361     414 ..     360     415 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                       Fer4_17  44 slCieCgeCerkCPqgl 60 
                                    +C++C +C+ +CP +l
  gi|91773357|ref|YP_566049.1| 359 IDCTHCARCVDVCPVDL 375
                                   57888888888888765 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.9e-07
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                   C++C+ C+++Cp   + +    ++ + a  g+++e  +++++ +C+eCg+C+++CP+++
  gi|91773357|ref|YP_566049.1| 361 CTHCARCVDVCPVDLIPS----RITAFADQGRFDEC-RQMNILNCVECGRCSAVCPSKI 414
                                   ************987733....45555555888885.778****************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 !   13.1   3.5   8.5e-05      0.08      10      21 ..     361     372 ..     353     373 .. 0.91
   2 !   14.4   3.2   3.3e-05     0.031       8      21 ..     398     411 ..     393     412 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                        Fer4_2  10 CigCgaCvsaCP 21 
                                   C++C  Cv++CP
  gi|91773357|ref|YP_566049.1| 361 CTHCARCVDVCP 372
                                   ************ PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.3e-05
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                    +C++Cg C  +CP
  gi|91773357|ref|YP_566049.1| 398 LNCVECGRCSAVCP 411
                                   57************ PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2    0.0021         2      79      95 ..     358     374 ..     335     375 .. 0.81
   2 !   14.2   2.1   6.2e-05     0.058      75      96 .]     393     414 ..     380     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                       Fer4_22  79 esgCvGCgRCieacpvk 95 
                                   +  C+ C RC+++cpv+
  gi|91773357|ref|YP_566049.1| 358 SIDCTHCARCVDVCPVD 374
                                   5679**********986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.2e-05
                       Fer4_22  75 ekfgesgCvGCgRCieacpvki 96 
                                   ++++   Cv CgRC+++cp+ki
  gi|91773357|ref|YP_566049.1| 393 RQMNILNCVECGRCSAVCPSKI 414
                                   5778899************987 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.3e-06    0.0087      27     131 ..      12     115 ..       3     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.3e-06
                          NQRA  27 kkvallgedyvglkpklkvkegdkVkkGqvlfedKknpgvlftspasGevveinrGek...Rvlqsvvievdgdeeeefek 104
                                   +k+ +  +++ g   + +v++gd V  Gq + e    ++  + s + Gev +i++ +     +++sv+i+ +  e +e  +
  gi|91773357|ref|YP_566049.1|  12 EKIIIPLKQHDGCLCTPLVNKGDMVSMGQKIGECECYDSAAVHSSVCGEVISIEKAANpngTKVNSVIIKPT--EDVECVD 90 
                                   566677777778888889************************************9876333689******99..5555555 PP

                          NQRA 105 fskkelaslsreevkeqLlksGlwtal 131
                                   f+   ++++s++++++ + ++G+    
  gi|91773357|ref|YP_566049.1|  91 FT--PVKDVSASKLVDVIKDAGIVEHY 115
                                   55..36677888888888888876655 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   6.2   2.4e-05     0.022       1      14 [.     361     374 ..     361     374 .. 0.95
   2 ?   12.4   4.6   0.00026      0.24       1      14 [.     400     413 ..     400     414 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-05
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   Ct+C +Cv+vCPv+
  gi|91773357|ref|YP_566049.1| 361 CTHCARCVDVCPVD 374
                                   ************85 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00026
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+ Cg+C  vCP++
  gi|91773357|ref|YP_566049.1| 400 CVECGRCSAVCPSK 413
                                   ************97 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       7.9   7.4e+03      68      79 ..      55      66 ..      36      97 .. 0.58
   2 ?   -3.1   0.0       9.6     9e+03      91     104 ..     306     319 ..     304     322 .. 0.81
   3 ?   13.0   2.8   9.6e-05     0.091      49      74 ..     349     374 ..     329     380 .. 0.80
   4 ?   12.1   2.0   0.00018      0.17      51      77 ..     390     416 ..     378     424 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.9
                       Fer4_18 68 vkvcPtgidirk 79
                                   +vc   i i k
  gi|91773357|ref|YP_566049.1| 55 SSVCGEVISIEK 66
                                  345555555544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.6
                       Fer4_18  91 cidacdkvmeklgk 104
                                    idac   m+  gk
  gi|91773357|ref|YP_566049.1| 306 VIDACGGYMGDTGK 319
                                   69***999988765 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 9.6e-05
                       Fer4_18  49 ekeerkekgagdcidcescvkvcPtg 74 
                                   + +e  ++ + dc++c  cv+vcP++
  gi|91773357|ref|YP_566049.1| 349 SADEVIRDVSIDCTHCARCVDVCPVD 374
                                   55666778889*************86 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00018
                       Fer4_18  51 eerkekgagdcidcescvkvcPtgidi 77 
                                   +e ++ +  +c++c+ c +vcP +i +
  gi|91773357|ref|YP_566049.1| 390 DECRQMNILNCVECGRCSAVCPSKIHL 416
                                   6677888899*************9976 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 ?    4.1   1.8      0.04        38      23      48 ..     360     382 ..     339     399 .. 0.70
   2 ?    8.2   0.8    0.0021         2      24      65 ..     400     438 ..     394     449 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.04
                                   T----TT-HHHHCSTT---HHHHHHH CS
                       Fer4_20  23 RClqCkkapcvkgCPveidipefikk 48 
                                    C +C  a cv+ CPv++ ip+ i++
  gi|91773357|ref|YP_566049.1| 360 DCTHC--ARCVDVCPVDL-IPSRITA 382
                                   58999..89*******97.4444443 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0021
                                   ----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH- CS
                       Fer4_20  24 ClqCkkapcvkgCPveidipefikkiaegnleeaakiiketn 65 
                                   C++C    c++ CP +i+  + i+   ++ +e+a++ +++++
  gi|91773357|ref|YP_566049.1| 400 CVEC--GRCSAVCPSKIHLLQLIRYA-KNSIENAYEDLSSKE 438
                                   9999..78***************975.567899988776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3260.77
//
Query:       gi|91773358|ref|YP_566050.1|  [L=490]
Description: hypothetical protein Mbur_1385 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0013   18.7  26.0       0.18   11.8  11.4    4.7  5  Cytochrome_C7    Cytochrome c7 and related cytochrome c
  ------ inclusion threshold ------
      0.018   14.8   8.3      0.018   14.8   8.3    4.9  5  Cytochrom_NNT    NapC/NirT cytochrome c family, N-terminal re
      0.023   15.4  10.7         17    6.0   0.0    5.7  5  CCP_MauG         Di-haem cytochrome c peroxidase
      0.086   13.8  23.7       0.24   12.3   4.6    5.1  5  Cytochrome_C554  Cytochrome c554 and c-prime
       0.13   11.8   0.1       0.29   10.7   0.1    1.6  1  EF-hand_5        EF hand
       0.21   12.0  27.0         22    5.6  17.3    4.5  3  Cytochrom_c3_2   Cytochrome c3
       0.53   11.5   5.8         77    4.5   0.4    4.7  5  Cytochrom_C      Cytochrome c
        2.3    8.8   6.3        1.3    9.6   2.1    2.5  2  Flocculin_t3     Flocculin type 3 repeat
        4.5    7.7  20.6         17    5.8   0.0    5.8  6  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III


Domain annotation for each model (and alignments):
>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.9    0.0047       9.4      33      72 ..      31     115 ..      18     121 .. 0.66
   2 ?    3.0   0.1      0.05     1e+02      14      23 ..     109     118 ..     100     158 .. 0.64
   3 !    5.8   5.4    0.0068        13      13      59 ..     184     228 ..     172     235 .. 0.63
   4 !   11.8  11.4   8.9e-05      0.18       6      72 ..     210     276 ..     204     277 .. 0.69
   5 !    6.3   0.0    0.0049       9.7      13      24 ..     433     444 ..     417     461 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0047
                 Cytochrome_C7  33 aemekgkskkaevesltCgaCHdgknaf.............................................svakkaeC 68 
                                   ++++++ +++ e+++ +Cg CH                                                   ++    +C
  gi|91773358|ref|YP_566050.1|  31 EAIATHYMTEGEWSDASCGGCHFTAPDHvatnthiqrdigewdpltnfdievegedewvknfgayhpgggeleAYGVDVDC 111
                                   555666677777888889999966655444455555556666666666666666666666677777777777655667777 PP

                 Cytochrome_C7  69 akCH 72 
                                   + CH
  gi|91773358|ref|YP_566050.1| 112 MICH 115
                                   7777 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.05
                 Cytochrome_C7  14 ykCtdCHskl 23 
                                    +C  CH++ 
  gi|91773358|ref|YP_566050.1| 109 VDCMICHEQY 118
                                   4566666655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0068
                 Cytochrome_C7  13 gykCt.dCHsklfeskakkkmaemekgkskkaeves.ltCgaCHdgkna 59 
                                   + +C+ +CH + +e++a       +++ ++k + ++ ++C +CH+ ++ 
  gi|91773358|ref|YP_566050.1| 184 KESCSdNCHVTNVETTA----VTWASEDYHKFDAHAdVNCVECHEISQS 228
                                   55775259998843333....223344555556666788*****87665 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 8.9e-05
                 Cytochrome_C7   6 kshlkatgykCtdCHsklfeska.kkkmaemekgkskkaevesltCga..CHdgknaf...svakkaeCakCH 72 
                                   k  ++ +  +C +CH+   +s++ +k+    + ++++++e e+++C++  CH+g  +    + +++ +C++CH
  gi|91773358|ref|YP_566050.1| 210 KFDAH-ADVNCVECHEIS-QSSMfVKQ----DLENIHEVEAETKSCDDpgCHKGISHGpivDAHETVACESCH 276
                                   44444.4789*****988.33332333....23345555556677*9999****999777767899******* PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.0049
                 Cytochrome_C7  13 gykCtdCHsklf 24 
                                     +C+dCH++++
  gi|91773358|ref|YP_566050.1| 433 PLACADCHGSTA 444
                                   456777777763 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.5      0.56   1.1e+03      65      76 ..      45      56 ..      25     121 .. 0.53
   2 ?   -0.4   0.2      0.42   8.3e+02      61      76 ..     180     196 ..     174     202 .. 0.69
   3 ?   14.8   8.3   8.9e-06     0.018     106     170 ..     197     261 ..     191     266 .. 0.78
   4 ?    1.4   0.7      0.11   2.3e+02      66      75 ..     270     279 ..     265     285 .. 0.84
   5 ?   -0.1   0.1      0.33   6.6e+02     159     166 ..     435     442 ..     420     449 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.56
                 Cytochrom_NNT 65 raeCsdCHvPke 76
                                   a+C  CH    
  gi|91773358|ref|YP_566050.1| 45 DASCGGCHFTAP 56
                                  455555554432 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.42
                 Cytochrom_NNT  61 rsgvraeCsd.CHvPke 76 
                                      v+ +Csd CHv + 
  gi|91773358|ref|YP_566050.1| 180 GAPVKESCSDnCHVTNV 196
                                   44589999877999874 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 8.9e-06
                 Cytochrom_NNT 106 eakrlelaerewarmkandsreCrnCHseeamdlekqkkkaakahkkaaeeektCid..CHkgiaHk 170
                                   e    ++a++ ++++ a+ + +C +CH+ ++ ++   k++  ++ +++++e+k+C d  CHkgi H 
  gi|91773358|ref|YP_566050.1| 197 ETTAVTWASEDYHKFDAHADVNCVECHEISQSSM-FVKQDL-ENIHEVEAETKSCDDpgCHKGISHG 261
                                   56667899********************995544.333333.45556667889**9888*******5 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.11
                 Cytochrom_NNT  66 aeCsdCHvPk 75 
                                   + C++CH+P 
  gi|91773358|ref|YP_566050.1| 270 VACESCHIPA 279
                                   68******96 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.33
                 Cytochrom_NNT 159 tCidCHkg 166
                                   +C dCH  
  gi|91773358|ref|YP_566050.1| 435 ACADCHGS 442
                                   46666654 PP

>> CCP_MauG  Di-haem cytochrome c peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.34   6.7e+02      21      35 ..      45      61 ..      38      87 .. 0.71
   2 ?    2.3   0.0      0.12   2.4e+02      21      61 ..     108     150 ..     105     166 .. 0.66
   3 ?   -1.1   4.7       1.3   2.6e+03      19      29 ..     214     224 ..     171     252 .. 0.63
   4 ?    6.0   0.0    0.0084        17      19      36 ..     267     284 ..     256     331 .. 0.82
   5 ?    3.3   0.0     0.061   1.2e+02      18      33 ..     430     445 ..     420     475 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.34
                                  S--HHHHS..GCCCTTS CS
                      CCP_MauG 21 kisCasCH..dpaagft 35
                                  + sC  CH   p++  t
  gi|91773358|ref|YP_566050.1| 45 DASCGGCHftAPDHVAT 61
                                  789*****664444333 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                                   S--HHHHSGC..CCTTS-SSS.SBBEGGGEBSSS----STTGGG CS
                      CCP_MauG  21 kisCasCHdp..aagftdglk.vslgvegrlgarnaptllnaaf 61 
                                   ++ C  CH++  + gf+   + ++ g + +  +  a+ ++n+++
  gi|91773358|ref|YP_566050.1| 108 DVDCMICHEQygEYGFDARAElFAAG-DFENANAAAMEAANIKV 150
                                   578*****763345555555555555.34556666666666665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                                   TSS--HHHHSG CS
                      CCP_MauG  19 ngkisCasCHd 29 
                                     +++C  CH+
  gi|91773358|ref|YP_566050.1| 214 HADVNCVECHE 224
                                   34556666664 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0084
                                   TSS--HHHHSGCCCTTS- CS
                      CCP_MauG  19 ngkisCasCHdpaagftd 36 
                                    ++++C sCH pa  + d
  gi|91773358|ref|YP_566050.1| 267 HETVACESCHIPALPGGD 284
                                   6899******99876655 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.061
                                   TTSS--HHHHSGCCCT CS
                      CCP_MauG  18 gngkisCasCHdpaag 33 
                                     g  +Ca CH  +a 
  gi|91773358|ref|YP_566050.1| 430 LAGPLACADCHGSTAN 445
                                   566789*****64433 PP

>> Cytochrome_C554  Cytochrome c554 and c-prime
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.12   2.4e+02      45      60 ..      42      57 ..      27      69 .. 0.70
   2 ?    1.7   0.0      0.25     5e+02      77      83 ..     109     115 ..      95     157 .. 0.68
   3 ?   12.3   4.6   0.00012      0.24      50      83 ..     186     223 ..     175     224 .. 0.76
   4 ?    4.1   2.5     0.046        92      50      83 ..     245     276 ..     226     277 .. 0.60
   5 ?    1.8   0.1      0.24   4.7e+02       1      11 [.     435     445 ..     435     454 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                                  -TT-TTTGGGSBSTTT CS
               Cytochrome_C554 45 aeeapeClkCHatgag 60
                                  + +++ C +CH t+ +
  gi|91773358|ref|YP_566050.1| 42 EWSDASCGGCHFTAPD 57
                                  4567899999999765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.25
                                   S-HHHHH CS
               Cytochrome_C554  77 VqCesCH 83 
                                   V C  CH
  gi|91773358|ref|YP_566050.1| 109 VDCMICH 115
                                   5555555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00012
                                   TTG.GGSBSTTTSTT--...-SSS--GGGBSS-HHHHH CS
               Cytochrome_C554  50 eCl.kCHatgagkdkgf...vlkektkllagVqCesCH 83 
                                    C  +CH+t+++   ++   +  +k+++ a+V+C +CH
  gi|91773358|ref|YP_566050.1| 186 SCSdNCHVTNVETTAVTwasEDYHKFDAHADVNCVECH 223
                                   55427******9888773334456788899******** PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.046
                                   TTGGGSBSTTTSTT---SSS--GGGBSS-HHHHH CS
               Cytochrome_C554  50 eClkCHatgagkdkgfvlkektkllagVqCesCH 83 
                                   e  +C  +g +k  g++     ++ + V CesCH
  gi|91773358|ref|YP_566050.1| 245 ETKSCDDPGCHK--GISHGPIVDAHETVACESCH 276
                                   444455554443..3445555556689******* PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.24
                                   HHHHHTHHHHH CS
               Cytochrome_C554   1 aCaeCHeeqye 11 
                                   aCa+CH + ++
  gi|91773358|ref|YP_566050.1| 435 ACADCHGSTAN 445
                                   69999987654 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00014      0.29       6      24 ..     377     395 ..     377     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                   HHH-SS-SSCE-HHHHHHH CS
                     EF-hand_5   6 qaiDlNgDGkIskeELktl 24 
                                   +a+D N DG ++++E + +
  gi|91773358|ref|YP_566050.1| 377 KAADSNDDGVVTADEMRSF 395
                                   589************9976 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.6     0.023        45      28      38 ..      68     120 ..      31     147 .. 0.55
   2 ?    5.6  17.3     0.011        22      10      79 ..     189     276 ..     181     277 .. 0.74
   3 ?    3.9   0.0     0.038        75       8      15 ..     435     442 ..     418     451 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.023
                                   H..........................................HHHHH--HHH CS
                Cytochrom_c3_2  28 k..........................................ClsCHgklee 38 
                                   +                                          C+ CH+++ e
  gi|91773358|ref|YP_566050.1|  68 DigewdpltnfdievegedewvknfgayhpgggeleaygvdvdCMICHEQYGE 120
                                   23444444444444444444444444444444444444444446666666655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                                   GGTSSSST-SSTTHHHHHH...........HHHHH--HHHCHTTSST.TSSBTTSSCTSSS-GGG..TS-TTT.......S CS
                Cytochrom_c3_2  10 adCHtkekpkkdkaveeek...........ClsCHgkleelakktkeakeanphkshekeleCte..CHkeHk.......k 70 
                                   ++CH ++  +++ +  +e+           C++CH+  ++    +++   +n h+  +++ +C++  CHk+ +       +
  gi|91773358|ref|YP_566050.1| 189 DNCHVTNVETTAVTWASEDyhkfdahadvnCVECHEISQSSMFVKQD--LENIHEVEAETKSCDDpgCHKGIShgpivdaH 267
                                   469998876665555555567788888888******88877776664..688888888888998777**986544777655 PP

                                   BT-GGGGT- CS
                Cytochrom_c3_2  71 sekvCaeCH 79 
                                   ++  C++CH
  gi|91773358|ref|YP_566050.1| 268 ETVACESCH 276
                                   5699***** PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.038
                                   TGGGTSSS CS
                Cytochrom_c3_2   8 kCadCHtk 15 
                                   +CadCH++
  gi|91773358|ref|YP_566050.1| 435 ACADCHGS 442
                                   45555543 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.4   2.7e+03       9      20 ..      45      56 ..      41      79 .. 0.76
   2 ?    0.8   0.0      0.56   1.1e+03      11      20 ..     110     120 ..     103     161 .. 0.70
   3 ?    4.5   0.4     0.039        77      10      38 ..     217     243 ..     209     249 .. 0.79
   4 ?   -0.4   0.0       1.3   2.6e+03      11      38 ..     271     298 ..     265     334 .. 0.65
   5 ?    3.2   0.0     0.098   1.9e+02      11      22 ..     435     446 ..     429     466 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                                  HTTGGGTB-SSS CS
                   Cytochrom_C  9 tanCaaCHgveg 20
                                  +a C +CH  + 
  gi|91773358|ref|YP_566050.1| 45 DASCGGCHFTAP 56
                                  689*****6554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.56
                                   TGGGTB.-SSS CS
                   Cytochrom_C  11 nCaaCH.gveg 20 
                                   +C+ CH + ++
  gi|91773358|ref|YP_566050.1| 110 DCMICHeQYGE 120
                                   7*****44444 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.039
                                   TTGGGTB-SSSBSSS....--HHHHHHHT CS
                   Cytochrom_C  10 anCaaCHgvegggakqgggptlsgaaera 38 
                                    nC+ CH +          ++l +++e +
  gi|91773358|ref|YP_566050.1| 217 VNCVECHEISQSSMFVK--QDLENIHEVE 243
                                   49******999988877..8888888765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.3
                                   TGGGTB-SSSBSSS....--HHHHHHHT CS
                   Cytochrom_C  11 nCaaCHgvegggakqgggptlsgaaera 38 
                                    C +CH ++  g   gg+ +l+   + +
  gi|91773358|ref|YP_566050.1| 271 ACESCHIPALPGGDLGGVIPLASFDWSN 298
                                   699***7766665555555555544444 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.098
                                   TGGGTB-SSSBS CS
                   Cytochrom_C  11 nCaaCHgveggg 22 
                                    Ca CHg ++++
  gi|91773358|ref|YP_566050.1| 435 ACADCHGSTANA 446
                                   6*****998776 PP

>> Flocculin_t3  Flocculin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.1   0.00067       1.3       8      28 ..     186     206 ..     185     210 .. 0.87
   2 ?   -0.2   0.1      0.75   1.5e+03       8      17 ..     248     257 ..     246     271 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00067
                  Flocculin_t3   8 sCsdnkCset.tvttgvstvTt 28 
                                   sCsdn C+ t + tt v+ + +
  gi|91773358|ref|YP_566050.1| 186 SCSDN-CHVTnVETTAVTWASE 206
                                   9****.****999999998776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.75
                  Flocculin_t3   8 sCsdnkCset 17 
                                   sC+d +C++ 
  gi|91773358|ref|YP_566050.1| 248 SCDDPGCHKG 257
                                   9**666*984 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.6     0.084   1.7e+02      12      39 ..      46      79 ..      40     108 .. 0.68
   2 ?    2.5   0.1     0.093   1.9e+02      13      28 ..     110     130 ..     100     165 .. 0.63
   3 ?   -3.9   0.1         9   1.8e+04      11      19 ..     184     193 ..     183     200 .. 0.71
   4 ?    0.3   2.7      0.44   8.7e+02      12      20 ..     217     226 ..     206     269 .. 0.79
   5 ?    5.8   0.0    0.0086        17      13      39 ..     271     303 ..     265     327 .. 0.72
   6 ?    5.5   0.0     0.011        21      13      25 ..     435     447 ..     431     482 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.084
               Cytochrome_CBB3 12 knCasCH.g.kggagpsla..gr..dwepdalvd 39
                                  ++C +CH + ++ ++ + +  ++  +w+p + +d
  gi|91773358|ref|YP_566050.1| 46 ASCGGCHfTaPDHVATNTHiqRDigEWDPLTNFD 79
                                  69*****536666664444434468888844444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.093
               Cytochrome_CBB3  13 nCasCHg.kggag....psla 28 
                                   +C  CH   g  g    ++l+
  gi|91773358|ref|YP_566050.1| 110 DCMICHEqYGEYGfdarAELF 130
                                   8*****965555555665555 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 9
               Cytochrome_CBB3  11 kknCa.sCHg 19 
                                   k++C+  CH 
  gi|91773358|ref|YP_566050.1| 184 KESCSdNCHV 193
                                   5678856995 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.44
               Cytochrome_CBB3  12 knCasCHg.k 20 
                                    nC+ CH  +
  gi|91773358|ref|YP_566050.1| 217 VNCVECHEiS 226
                                   59*****843 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.0086
               Cytochrome_CBB3  13 nCasCHg....kggag..pslagrdwepdalvd 39 
                                   +C sCH      g +g   +la  dw++ + vd
  gi|91773358|ref|YP_566050.1| 271 ACESCHIpalpGGDLGgvIPLASFDWSNGERVD 303
                                   7*****866744444578889999999744444 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.011
               Cytochrome_CBB3  13 nCasCHgkggagp 25 
                                   +Ca CHg+ +++ 
  gi|91773358|ref|YP_566050.1| 435 ACADCHGSTANAI 447
                                   6******766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3578.47
//
Query:       gi|91773359|ref|YP_566051.1|  [L=134]
Description: hypothetical protein Mbur_1386 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1019.83
//
Query:       gi|91773360|ref|YP_566052.1|  [L=350]
Description: ApbE-like lipoprotein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-75  253.3   0.1      3e-75  253.1   0.1    1.0  1  ApbE      ApbE family


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 !  253.1   0.1   1.7e-79     3e-75       1     257 [.      53     328 ..      53     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 253.1 bits;  conditional E-value: 1.7e-79
                                   TTEEEEEEEE.......HH..HHHHHHHHHHHHHC-SS-TTSHHHHHHCTSS-EEE-HHHHHHHHHHHHHHHHTTTSS-TT CS
                          ApbE   1 mgttvsitly..g....le..aaieaelerlekllsryrpdSelsrlNrakkevkvspelaellkaaleiseltdgafdpt 73 
                                   m+ttv+ ++y  +    ++   +++ +++++++l+s+y++dS+l+ lN++++  ++s+el+ ++ +++++s+ ++gafd+t
  gi|91773360|ref|YP_566052.1|  53 MDTTVTAAIYdsDtdhaVQtvGKAFGRVAQTDELMSSYKNDSQLNMLNENNRLENASEELLFVIGRSIYYSNISNGAFDIT 133
                                   99*******965155663345444599*********************88666899************************* PP

                                   THHHHHHHC..TTSG.G.----HHHHHHHHTT.-GGGEEE...EESTT..-----TTTHHHHHHHHHHHHHHH.TT-EEEE CS
                          ApbE  74 vgplvklwg..fgee.karvpsaeeidaalalvgykkiel...lakkgpgmkLDlggiaKGyavdrvaellka.giksalv 147
                                   ++p+++lw   f+++ ++r ps+eeid+ l+lv++kki +     +++pgmk+ lggiaKGyavd+++e l + gi+s++v
  gi|91773360|ref|YP_566052.1| 134 IKPILDLWSakFSPGgTYRPPSQEEIDTTLELVDCKKIVIegnTISTEPGMKVVLGGIAKGYAVDQAIESLIDnGIESCFV 214
                                   ********744666645588******************9999*6666789******************************* PP

                                   EETTEEEEEC..-ECT-EEEEEE-TTS..SEEEEEEESSSEEEEEETTSSEEE.TEEEES-B-TTTSSB---SECEEEEEE CS
                          ApbE 148 nlGGdiralG..pdgkpwrvgiedPra..ellavlslsddavaTSGdyeryfe.gkryhHiidprtgyPaesglasvtVia 223
                                   ++GGd r +G  pdg +w+vg+++P++  e+++v++l++ avaTSG+yeryf    +++Hi dprtgy   ++l+s+tVia
  gi|91773360|ref|YP_566052.1| 215 DAGGDGRYIGtkPDGIKWTVGLQNPDKqgEIITVMRLENMAVATSGNYERYFSdAAKVSHISDPRTGYLS-RELISATVIA 294
                                   **********999999*********94589********88************5588************99.8********9 PP

                                   SC.HHHHHHHHHHHHHHHHHHHHHHCCGGGTCTEE CS
                          ApbE 224 ds.alADalaTalfvlgeekalellekkeegveal 257
                                   ++ ++ADalaT++fvlge+++ el+e+  eg+e+l
  gi|91773360|ref|YP_566052.1| 295 ETtMDADALATTVFVLGEKEGTELIESL-EGIECL 328
                                   766***********************75.579886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2533.04
//
Query:       gi|91773361|ref|YP_566053.1|  [L=183]
Description: 2',5' RNA ligase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-27   95.2   0.0    4.8e-16   58.7   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
      1e-10   41.7   0.0    1.2e-10   41.5   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    5.8e-08   32.9   0.0    8.8e-08   32.3   0.0    1.3  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.025   14.2   0.0    1.2  1  MIF4G            MIF4G domain


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 !   58.7   0.0   1.1e-19   4.8e-16       1      87 []       8      88 ..       8      88 .. 0.95
   2 !   34.8   0.0     3e-12   1.4e-08      10      87 .]      94     172 ..      89     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.1e-19
                                  EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSC CS
                    LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrp 83
                                  +++p++i++el  + + +e    +++lk v p+  HiTL+flgev++++vp++ ++l++i  + +pf+ +++gvg+f++ ++p
  gi|91773361|ref|YP_566053.1|  8 VDLPSSIRRELIDVLSLFE----GFKLKIVSPELIHITLKFLGEVSDDMVPDIASSLDGI--ECMPFNANIKGVGVFSNLRSP 84
                                  6789999999999999999....9999999******************************..999************9999** PP

                                  CEEE CS
                    LigT_PEase 84 rviy 87
                                  rv++
  gi|91773361|ref|YP_566053.1| 85 RVVW 88
                                  ***9 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3e-12
                                   HHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEESHHHHH...HHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCE CS
                    LigT_PEase  10 elarlaaeleralaklglkpv.rpfnpHiTLaflgevdeekvp...ellealaeiasgaepfelkvdgvglfpsrl.rprv 85 
                                   +  +l++e+e  l+kl +  + r+f  H TLa+++  ++e+ +    +l++l++++ g    e++vd+v l +s+l + ++
  gi|91773361|ref|YP_566053.1|  94 NFKKLHEEVETSLSKLRFDKDkREFAAHATLARIKFMPKEQMKgllYVLDKLKDVDLG----EIRVDKVLLKKSTLtPDGP 170
                                   67899*********************************99999444566666666444....5****************** PP

                                   EE CS
                    LigT_PEase  86 iy 87 
                                   +y
  gi|91773361|ref|YP_566053.1| 171 VY 172
                                   99 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 !   41.5   0.0   2.6e-14   1.2e-10      25     121 ..      37     132 ..      10     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.6e-14
               2_5_RNA_ligase2  25 ppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsvsdsealqalraallealpeagdke 102
                                     HitL+++++ ++d  +d+a+ l  +  e+ pf++ ++g+gvF+  ++  vv+l +  +  +++l++++++ l + + ++
  gi|91773361|ref|YP_566053.1|  37 LIHITLKFLGEVSDDMvPDIASSLDGI--ECMPFNANIKGVGVFSNlRSPrVVWLGA--EGNFKKLHEEVETSLSKLRFDK 113
                                   48***********99889999999887..899***************7777******..9********************* PP

               2_5_RNA_ligase2 103 dsgeftPHlTiaqsadsts 121
                                   d++ef  H+T+a+ + +  
  gi|91773361|ref|YP_566053.1| 114 DKREFAAHATLARIKFMPK 132
                                   ************8765544 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0     2e-11   8.8e-08      25     206 ..      21     179 ..       5     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2e-11
                                   HHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE.....TTTEEEEEE CS
                     AKAP7_NLS  25 vlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpakarVlYakv 105
                                   vls ++g + ++ ++pe +H+Tl  l   +++++ + ++ L  ++      +   p++ ++kG+++f  +  + rV++++ 
  gi|91773361|ref|YP_566053.1|  21 VLSLFEGFKLKI-VSPELIHITLKFLGEVSDDMVPDIASSLDGIE------C--MPFNANIKGVGVF-SNLRSPRVVWLGA 91 
                                   677788888889.99999999999999999999999999998884......4..79***********.57777******** PP

                                   --SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEEEEE--EEEE CS
                     AKAP7_NLS 106 eeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefgeekineihL 186
                                   e     +++++l++ + + +++  l  +kdk+++  HaTl+ +++  k+q+k         +l++ kd ++ge+++ ++ L
  gi|91773361|ref|YP_566053.1|  92 E-----GNFKKLHEEVETSLSK--LRFDKDKREFAAHATLARIKFMPKEQMKGL-----LYVLDKLKDVDLGEIRVDKVLL 160
                                   8.....7899999999999955..5666777779*****************988.....78******************** PP

                                   EESSS---TTS--EEEEEEE CS
                     AKAP7_NLS 187 sqlesddesdgyYkviasvk 206
                                    + + + +    Y++i +v 
  gi|91773361|ref|YP_566053.1| 161 KKSTLTPD-GPVYETIHEVL 179
                                   99999988.88999988875 PP

>> MIF4G  MIF4G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.7e-06     0.025     101     203 ..      14     132 ..       9     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-06
                                   HHHHHHHHHHHHHHHHTTSSEHHHHHHHHHHHHHGGCCCCSCCHSCHHHHHHHHHHHHHHHHHHHC............... CS
                         MIF4G 101 rrrrlglvrflgelfklkmltskilldclkellssltketaddppqdleeieilltllttigktle............... 166
                                    rr l  v+ l+e+fklk+++   l+++  ++l ++ ++  +d   +l+ ie++    +  g   +               
  gi|91773361|ref|YP_566053.1|  14 IRRELIDVLSLFEGFKLKIVSP-ELIHITLKFLGEVSDDMVPDIASSLDGIECMPFNANIKGVGVFsnlrsprvvwlgaeg 93 
                                   5677777889***********9.9999999********8888***********999999999999999************* PP

                                   CCHHHHHHHHHHHHHHHHHHHCCH..CSSSSHHHHHHHH CS
                         MIF4G 167 nnekakkeldqffkriqkiledat..rqelssrirfmlk 203
                                   n++k+++e+++ ++++++ + ++    + + +ri+fm k
  gi|91773361|ref|YP_566053.1|  94 NFKKLHEEVETSLSKLRFDKDKREfaAHATLARIKFMPK 132
                                   **********************9999999999****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1337.43
//
Query:       gi|91773362|ref|YP_566054.1|  [L=293]
Description: hypothetical protein Mbur_1389 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   73.8   2.3    1.8e-20   72.7   0.2    2.5  3  DisA_N    DisA bacterial checkpoint controller nucleotide-bin


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0     0.055   9.9e+02      90     105 ..      14      29 ..       4      33 .. 0.85
   2 ?   -1.4   0.0     0.094   1.7e+03      15      37 ..     104     120 ..      65     144 .. 0.57
   3 !   72.7   0.2     1e-24   1.8e-20       3     118 ..     153     278 ..     151     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.055
                                   HHHHHHHSSSEEEEE- CS
                        DisA_N  90 AlgiseetdalvivVS 105
                                   A++i+ee  +++i+VS
  gi|91773362|ref|YP_566054.1|  14 AIKIAEELCSTAIIVS 29 
                                   8999999999999999 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.094
                                   EEEEESSSCCCTTCCTSEEEEEE CS
                        DisA_N  15 liviereeelkeiietgvkldae 37 
                                   ++ i +++      e+g  ++ e
  gi|91773362|ref|YP_566054.1| 104 IVGIIQTR------ESGAIVTHE 120
                                   33222222......233333333 PP

  == domain 3  score: 72.7 bits;  conditional E-value: 1e-24
                                   HHHHHHHHT--EEEEEESSSC............CCTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.ETTEEEEEEE CS
                        DisA_N   3 aveelskkkiGaliviereee............lkeiietgvkldaevskellkeifekksplhDGAvii.rdgrivaagv 70 
                                   a ++++++kiG+ +++++ ee                 ++  +l ++ ++e +ke+     +l+DG ++i ++g + aag+
  gi|91773362|ref|YP_566054.1| 153 ASSGREGHKIGTAFILGDIEEvlqrshqmilnpYAGHKDEHRNLLNKKNWESVKEF-----ALLDGVFVIsKEGIVQAAGR 228
                                   678899*************9988887777644323455778889999999999999.....*********88********* PP

                                   EE--.TT-TTS.ST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTE CS
                        DisA_N  71 iLpl.senkel.kelGtRHraAlgiseetdalvivVSeetgkislakdgk 118
                                   +L++ +++ ++ ++lG RH +A++i+++t a+++++Se+ g++++++dgk
  gi|91773362|ref|YP_566054.1| 229 YLDVdAKEIDIeQGLGGRHVSAAAITRDTFAIAVTISESGGTVRIYMDGK 278
                                   ****877889977***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1772.75
//
Query:       gi|91773363|ref|YP_566055.1|  [L=347]
Description: cell division protein pelota [Methanococcoides burtonii DSM 6242]
Scores for complete 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   98.2   0.6    5.6e-28   97.5   0.6    1.4  1  eRF1_1    eRF1 domain 1
    2.7e-24   85.8   0.2    6.9e-24   84.5   0.2    1.7  1  eRF1_3    eRF1 domain 3
    1.7e-08   34.9   0.0    3.6e-07   30.6   0.0    2.4  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 !   97.5   0.6   9.3e-32   5.6e-28       1     128 [.       1     125 [.       1     126 [. 0.94

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 9.3e-32
                                   HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECTTSSE CS
                        eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdkdagv 80 
                                   m+++krdl+++ +g ++L pe+ +dlwhl  +i++gd v + t+rk  +   +    + e+++++L ++ve+v+f+k +++
  gi|91773363|ref|YP_566055.1|   1 MRVTKRDLKHNREGEISLTPETLDDLWHLKYIIEKGDLVFSLTKRKADNaADKLRPEKAEKKTVRLGVRVEDVEFHKFSNR 81 
                                   9*********************************************9883344455559********************** PP

                                   EEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                        eRF1_1  81 lrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                   lr++G + ++ +    g +htl++e + +++i+k  w++ +ler++ea
  gi|91773363|ref|YP_566055.1|  82 LRVHGLIEHGMD---AGFYHTLNIEDGTNLSITK-YWKKDQLERVNEA 125
                                   ***********9...9******************.5**********98 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.2   1.2e-27   6.9e-24       1     113 []     251     347 .]     251     347 .] 0.95

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 1.2e-27
                                   HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHT CS
                        eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenvees 81 
                                   +++e++l++ +l+e+a d gk++YG++ev++a+ +gAvetLLv +e+ r +   +e+    g        i+ l++nve s
  gi|91773363|ref|YP_566055.1| 251 IARESSLMDSLLKEIALD-GKVAYGMDEVKQAIDFGAVETLLVADEMLRLE---RES----G-------NIDGLIQNVERS 316
                                   689***************.******************************97...444....4.......499********* PP

                                   T-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                        eRF1_3  82 gakveiisseseeGeqlvkafgGiaaiLRykv 113
                                   ++k++++s+e+e G++l +++gGiaaiLR+kv
  gi|91773363|ref|YP_566055.1| 317 QGKMVVFSTEFEPGQRL-HSLGGIAAILRFKV 347
                                   *****************.************97 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     6e-11   3.6e-07       2     128 ..     134     242 ..     133     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 6e-11
                                   EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEE CS
                        eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiil 82 
                                   v+l+ ++eg A ig+++++ +e+ ++i++s  k +  G              +e f+  + +++++a      +  + +++
  gi|91773363|ref|YP_566055.1| 134 VILVAIEEGDADIGFVRHYGIEIYSHITQSSGKGE--GT------------LREVFFSTILDQLTHA-----MSGTESVVV 195
                                   67899999999999999999999999998843322..22............2467999999999888.....46789**** PP

                                   EESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC.CH CS
                        eRF1_2  83 agpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek.aa 128
                                    gpgf+k++f+++   ++    + i + d+s+ g sg++evl+  a 
  gi|91773363|ref|YP_566055.1| 196 SGPGFTKDDFMKYASSKNSDLVAGILVEDTSSIGMSGFQEVLRRgAV 242
                                   ********************99********************98643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2348.92
//
Query:       gi|91773364|ref|YP_566056.1|  [L=663]
Description: hypothetical protein Mbur_1391 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-99  332.8   0.9    3.9e-99  332.5   0.9    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
    4.7e-28   98.0   0.0    1.6e-27   96.3   0.0    1.9  1  NFACT-R_1      NFACT protein RNA binding domain
    1.8e-05   24.9   0.1    6.9e-05   23.0   0.0    2.0  2  NFACT-R_2      NFACT protein RNA binding domain
      0.008   16.0   0.9      0.014   15.2   0.8    1.4  1  HGD-D          2-hydroxyglutaryl-CoA dehydratase, D-component
  ------ inclusion threshold ------
       0.13   12.7   3.1       0.13   12.7   0.0    2.5  3  Ribosomal_S13  Ribosomal protein S13/S18
       0.13   12.2   0.0       0.43   10.6   0.0    1.8  1  H2TH           Formamidopyrimidine-DNA glycosylase H2TH domai
       0.23   11.7   1.5       0.46   10.7   0.1    2.0  2  Hydin_ADK      Hydin Adenylate kinase-like domain
       0.78    9.5   2.9       0.33   10.7   0.2    1.7  2  HDV_ag         Hepatitis delta virus delta antigen


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 !  332.5   0.9  1.8e-102   3.9e-99       2     416 ..       7     445 ..       6     453 .. 0.93

  Alignments for each domain:
  == domain 1  score: 332.5 bits;  conditional E-value: 1.8e-102
                                   HHHHHHHHHHHHHH...HTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHH CS
                          FbpA   2 glvlaavvaELqke...llggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRk 78 
                                   ++++aa+v+EL +    l++++i kiyqp +de++++l  +++gr++L+++a   ++r h++++ +e+pk+p++F+mlLRk
  gi|91773364|ref|YP_566056.1|   7 SADVAALVSELGDGegsLIDSKIGKIYQPAPDEIRINLFiFGKGRYNLVIEA---GKRAHMSNYVRESPKTPQAFPMLLRK 84 
                                   6799*******998888**********************9************...************************** PP

                                   HHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXX CS
                          FbpA  79 yLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYe 159
                                   ++ g+ri+si+q +fdRi+e+++ +        e  L++E++ r +Ni+L+++++kIi ++k v++k    R++ +ge+Ye
  gi|91773364|ref|YP_566056.1|  85 HILGGRITSIKQYDFDRIIEMGVIRG-----GIETILVCELFSR-GNIVLLNSDRKIILPMKPVTFK---GRRVRSGEIYE 156
                                   **************************.....9999*********.**********************...9********** PP

                                   XSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHT CS
                          FbpA 160 lPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelle 240
                                   +P++  +l+Pl++++ + ++e++  ++ ++v+++++++ +l+++laee++ rag+dk+tsak++s+e++ +l +a++++++
  gi|91773364|ref|YP_566056.1| 157 YPEA--QLSPLDVDA-NIMSERFLSSDSNVVRTIATSY-NLGGVLAEEVCLRAGVDKNTSAKDASSEEVAALSKAVTDVFA 233
                                   ****..******999.88899977799***********.****************************************** PP

                                   XXX....XXEE.......XSSSEESSX..XTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHH...HHHHHHHHHHHHHHH CS
                          FbpA 241 eleeekfepqlvlkee..kpeefsvvp..lkslselekesfdslsealdeyYakkaerdrveq...krsdlekrvenelek 314
                                   ++ +++++p++++k+   + ++++v+p  l+++s++eke ++s+++alde+++kka ++++eq   k+++ e ++e++l+k
  gi|91773364|ref|YP_566056.1| 234 PIVNHELNPCIIKKTVkdELQAVDVLPleLTQYSDAEKEFYPSFNKALDEFFGKKASEEVIEQvvaKKKEKEDVFERRLRK 314
                                   **********987766556777888888899999****************************965556666666******* PP

                                   HHHHHHHHHHHHHCCGGH.....HHHHCCHH-----------------------..--....................... CS
                          FbpA 315 lekklkklekelekaeka.....enyrligelltaylyaikkgmsevelenyyde.ge....................... 366
                                   +++ + k+e++  +          ny+ ++e+l+++  a+ kg+s+ ++ +++++ +                        
  gi|91773364|ref|YP_566056.1| 315 QQEAILKFETDSTRYTLIaesiyGNYQTVEEVLSVLEAARDKGYSWKDIWDTLKKaKDtlpaakaivsidpaegsvvvdld 395
                                   ********987555444444555*******************************85449*********************9 PP

                                   ---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          FbpA 367 evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesv 416
                                    v+ +++ rk++++nAq y++k+kK+ ++++++  +ie tk+ +++ e++
  gi|91773364|ref|YP_566056.1| 396 VVNANINVRKTIPQNAQMYYNKAKKISKKRDGALIAIEDTKRAMQKREQK 445
                                   9999*****************************************99986 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 !   96.3   0.0   7.1e-31   1.6e-27       2     109 .]     462     571 ..     461     571 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 7.1e-31
                     NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnkl 81 
                                   ++wF ssdg+lvi+G+D+ +nee++kky+e++d++fh  + +++ ++++ +eg+  +ipe++leeaa +++++S+  ++ +
  gi|91773364|ref|YP_566056.1| 462 FRWFFSSDGFLVIGGRDSDTNEEIVKKYMEKRDIVFHTQVPGAPITVIK-TEGK--DIPETTLEEAARFVVSYSSVwKSGQ 539
                                   99***********************************************.7777..9************************ PP

                     NFACT-R_1  82 ssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                    s d+++++++++skt++    l++Gs++++g
  gi|91773364|ref|YP_566056.1| 540 FSGDCYWIKPEQVSKTPEsgeyLKKGSFIIRG 571
                                   *****************************986 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       4.9   1.1e+04      67     104 .]     422     459 ..     418     459 .. 0.70
   2 !   23.0   0.0   3.1e-08   6.9e-05       2      69 ..     463     534 ..     463     543 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.9
                     NFACT-R_2  67 skgkeeeevevkvkkkegeeekeievkplseeei.ekwr 104
                                   sk ++ + ++++ +k+  ++ +e +v++ ++    ++w+
  gi|91773364|ref|YP_566056.1| 422 SKKRDGALIAIEDTKRAMQK-REQKVSKRRKAVFkKHWY 459
                                   67777778888877777777.677888777777767775 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3.1e-08
                     NFACT-R_2   2 RhfrlsekaklIvgReeeEnkfl.kgll.kkdfvslrakshkGplvlid..g.elseedlelaarivarYskg 69 
                                   R f  s+++ +I gR+++ n+++ k+++ k+d+v ++++   +p+++i+  g ++ e++le aar+v+ Ys+ 
  gi|91773364|ref|YP_566056.1| 463 RWFFSSDGFLVIGGRDSDTNEEIvKKYMeKRDIV-FHTQVPGAPITVIKteGkDIPETTLEEAARFVVSYSSV 534
                                   77889999*********99998736677666666.99999999*****54565777***************85 PP

>> HGD-D  2-hydroxyglutaryl-CoA dehydratase, D-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.8   6.1e-06     0.014      94     242 ..     270     415 ..     246     453 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.1e-06
                                   HHHHH.HHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHTTSSS-SS-H.HHHH.HHHHHTT.S-HHHHHHHHHH CS
                         HGD-D  94 edele.nliaaleeitgkrideesleaaikeanetrellkelytllpqspapihg.fdll.llakvvf.lgkeeatealee 170
                                   e+e+   + +al e++gk+ +ee +e+++++++e+++ +++  +l++q++a + + +d   +++ +   +g  + +e +  
  gi|91773364|ref|YP_566056.1| 270 EKEFYpSFNKALDEFFGKKASEEVIEQVVAKKKEKEDVFER--RLRKQQEAILKFeTDSTrYTLIAESiYGNYQTVEEVLS 348
                                   5667668999*****************************99..9**88889999988888888888887788888888888 PP

                                   HHHHHHHHT.STS-EEEEEES---TT--HHHHHHHHT.T-EEEEEESTTTHHHHS-.....SSHHH.HHHHHHHHHT CS
                         HGD-D 171 lleeleerskseriRllltGipvellaaklmkaleaglgavvvnndacypsrlvry.....vgdvgqplealasgyy 242
                                   +le++++ ++       +++  ++  ++k +++l a +   +v+ d   +s  v+      + +v + + + a+ yy
  gi|91773364|ref|YP_566056.1| 349 VLEAARD-KG-------YSWKDIWDTLKKAKDTLPAAKA--IVSIDPAEGSVVVDLdvvnaNINVRKTIPQNAQMYY 415
                                   9988888.33.......6677777777777666666655..666666666666622334443344444555554455 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05      0.13       9      62 ..     179     232 ..     172     258 .. 0.85
   2 ?   -2.2   0.1       2.2   4.9e+03      24      58 ..     286     319 ..     282     334 .. 0.58
   3 ?   -1.6   0.1       1.5   3.4e+03      36      59 ..     431     454 ..     396     488 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                 Ribosomal_S13   9 gkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenka 62 
                                   ++ +v+ ++++ + +G   a++++ +a+vd+++ +++ + ee+  + + v    
  gi|91773364|ref|YP_566056.1| 179 SDSNVVRTIATSYNLGGVLAEEVCLRAGVDKNTSAKDASSEEVAALSKAVTDVF 232
                                   677888899999999*******************************99998754 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                 Ribosomal_S13  24 Grrkakiilkkadvdedkrigelteeeiekieeiv 58 
                                   G+++++++++++ v ++k  +++ e  + k +e +
  gi|91773364|ref|YP_566056.1| 286 GKKASEEVIEQV-VAKKKEKEDVFERRLRKQQEAI 319
                                   555555555554.4444555555555555555544 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.5
                 Ribosomal_S13  36 dvdedkrigelteeeiekieeive 59 
                                    ++ +kr+ +  e++++k ++ v 
  gi|91773364|ref|YP_566056.1| 431 AIEDTKRAMQKREQKVSKRRKAVF 454
                                   244444444444444444444444 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.43      39      79 ..     193     233 ..     185     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                   --HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHH CS
                          H2TH  39 lGNiyadEvLfrakihPerlakslskeelellhqeikevlk 79 
                                   lG + a+Ev  ra+++ +++ak  s ee+++l +++++v+ 
  gi|91773364|ref|YP_566056.1| 193 LGGVLAEEVCLRAGVDKNTSAKDASSEEVAALSKAVTDVFA 233
                                   7999*********************************9986 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00021      0.46      27      79 ..     176     240 ..     169     344 .. 0.66
   2 ?   -0.8   0.1      0.71   1.6e+03      99     132 ..     416     449 ..     382     460 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                     Hydin_ADK  27 lltiDsvvleAisdgnssaGlrArelCaeaaieqaekekeeaaeeaekkegq............l 79 
                                   +l+ Ds v+  i+ + +  G+ A e+C++a +++++  k+ ++ee+++ + +            l
  gi|91773364|ref|YP_566056.1| 176 FLSSDSNVVRTIATSYNLGGVLAEEVCLRAGVDKNTSAKDASSEEVAALSKAvtdvfapivnheL 240
                                   6889*****************************99999999988887654444555555433330 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.71
                     Hydin_ADK  99 aasskiskkkktsvvsgkkkaesegaksqkqkek 132
                                   ++++kiskk+ + ++  ++++ + ++ +qk +++
  gi|91773364|ref|YP_566056.1| 416 NKAKKISKKRDGALIAIEDTKRAMQKREQKVSKR 449
                                   2237788888888887777776666666665443 PP

>> HDV_ag  Hepatitis delta virus delta antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00015      0.33      12      49 ..     289     327 ..     284     354 .. 0.82
   2 ?   -3.1   0.3       2.5   5.5e+03      29     107 ..     441     452 ..     416     483 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                        HDV_ag  12 greevleqwvsgrkklee.lerdlrkvkkkikkledehp 49 
                                     eev+eq v+ +k+ e+ +er lrk ++ i k+e +  
  gi|91773364|ref|YP_566056.1| 289 ASEEVIEQVVAKKKEKEDvFERRLRKQQEAILKFETDST 327
                                   579********999887736*************997765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                        HDV_ag  29 elerdlrkvkkkikkledehpwlgnikgilgkkdkdgegappakrartdqmevdsgprkrpsrggftdkerqdhrrrka 107
                                   + e+ +                                                                    +rrka
  gi|91773364|ref|YP_566056.1| 441 KREQKV-------------------------------------------------------------------SKRRKA 452
                                   222222...................................................................222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1279  (0.0713369); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4311.54
//
Query:       gi|91773365|ref|YP_566057.1|  [L=390]
Description: DNA primase small subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-22   78.1   0.0    1.4e-21   77.4   0.0    1.4  1  DNA_primase_S  DNA primase small subunit
    0.00052   20.6   0.2     0.0066   17.0   0.1    2.3  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.016   15.6   0.1      0.031   14.7   0.1    1.4  1  DUF3140        Protein of unknown function (DUF3140)


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 !   77.4   0.0   2.3e-25   1.4e-21       1     176 [.      97     325 ..      97     326 .. 0.71

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2.3e-25
                                   EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH.. CS
                 DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaivnyln 79 
                                   FD+D+d+ ++   +++  ++ ++ +++ k+ d ll++dfgfk  di  vfsg+rG+H ++sd ++ +l ++er++iv+y++
  gi|91773365|ref|YP_566057.1|  97 FDLDADHIPG-APNSYSDMLDHVKKETLKLYD-LLTDDFGFKeeDIGAVFSGGRGYHFHISDPRVLSLESAERREIVDYIS 175
                                   9********9.777788888888888888886.999******************************************655 PP

                                   .....................................................................HCHHHHCT---- CS
                 DNA_primase_S  80 ly.....................................rplhpflsrsmlkivkpvveeiileeqdpfeikkllrllpdk 123
                                                                          r  h+ ++++                          r l  k
  gi|91773365|ref|YP_566057.1| 176 GRglnldkifvkkgvsgdagsekatmnvfpseddggwggRINHHMIAYL--------------------------RELAAK 230
                                   4466666666655555555555555555555555555443344444444..........................333333 PP

                                   ----..............................................................--------------- CS
                 DNA_primase_S 124 slrekkkw............................................eakedivlvllyprldeqvtkgikhllka 160
                                   +++e k +                                              + +  ++ l  + de+vt +ik+l+++
  gi|91773365|ref|YP_566057.1| 231 EDAE-K-LftgfdrigkktakriveilrdetqvdllkkgnmealsrvnkdiiQTLAERSVTELSASVDEPVTGDIKRLIRL 309
                                   3333.1.123333333333444444444444445555556677788888889778888899999***************** PP

                                   --....---------. CS
                 DNA_primase_S 161 pfcihgktgnvcvpld 176
                                   p+++hgk+g +++ l+
  gi|91773365|ref|YP_566057.1| 310 PGSLHGKSGMCVTSLS 325
                                   *********9999875 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.1e-06    0.0066      27      57 .]     225     257 ..     216     257 .. 0.79
   2 ?    0.9   0.0      0.12   7.3e+02      25      42 ..     294     311 ..     268     316 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                                   HHHHHS.-HHHHHT.STTS-HHHHHHHHHHHHH CS
                         HHH_5  27 edlaaa.dveeLak.ipGiGkktAeriilelkd 57 
                                    +laa+ d+e+L +    iGkktA+ri++ l+d
  gi|91773365|ref|YP_566057.1| 225 RELAAKeDAEKLFTgFDRIGKKTAKRIVEILRD 257
                                   5776653777766669***************98 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                   SHHHHHHS-HHHHHTSTT CS
                         HHH_5  25 svedlaaadveeLakipG 42 
                                   sv++ +  d+++L ++pG
  gi|91773365|ref|YP_566057.1| 294 SVDEPVTGDIKRLIRLPG 311
                                   344445579999999998 PP

>> DUF3140  Protein of unknown function (DUF3140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   5.2e-06     0.031      15      76 ..     222     286 ..     217     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.2e-06
                       DUF3140  15 eWLkteeSkevgekkdg.gesvghesGrkiveilr..kkkadltdddlehmrkVvgyvkrhlaqe 76 
                                    +L++ ++ke++ek  +  +++g+++ ++iveilr  ++ + l++ ++e++ +V + + + la++
  gi|91773365|ref|YP_566057.1| 222 AYLRELAAKEDAEKLFTgFDRIGKKTAKRIVEILRdeTQVDLLKKGNMEALSRVNKDIIQTLAER 286
                                   6888889999998854468****************87777788999********99999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2996.05
//
Query:       gi|91773366|ref|YP_566058.1|  [L=235]
Description: hypothetical protein Mbur_1393 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.7   0.2       0.07   13.6   0.2    1.6  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.9e-06      0.07      27     108 ..       3     101 ..       1     102 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-06
                                   HHHHHHCCCHHTTSSSSTTTTTTHHHHH.HHHHHHHT................HCHHHHH...HHHHHHHHHHHHHHTHCH CS
                          Sld5  27 pesleailedetkssdlpslpphflela.vkllelard...............ldelkrl...lrdllevRlakirkfaen 88 
                                    ++l++il +e++s  l+ lp  f+ l  +++ el+ +                del++    ++ ++  R++ki++ a +
  gi|91773366|ref|YP_566058.1|   3 RNELKSILREENSS-ALRGLPHGFYGLVdKYIHELEGEirqisnqrspeskilEDELQSAindVETIFIRRIRKITSRATS 82 
                                   5789**********.*************54488888765555555656677776777766333666777788888888877 PP

                                   HHHHHHTS-TCCHCCS-HHH CS
                          Sld5  89 ledaagggggellsglseeE 108
                                   ++ ++ +++ ++l++l + E
  gi|91773366|ref|YP_566058.1|  83 NAFSS-SSPKQDLDKLLPAE 101
                                   77777.88888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 00:00:00.43
# Mc/sec: 1641.69
//
Query:       gi|91773367|ref|YP_566059.1|  [L=92]
Description: 50S ribosomal protein L44e [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   87.0   9.0    1.3e-24   86.4   9.0    1.3  1  Ribosomal_L44   Ribosomal protein L44
  ------ inclusion threshold ------
      0.058   13.1   0.5        1.7    8.4   0.0    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.067   13.0   2.1        6.4    6.6   0.3    2.3  2  zinc_ribbon_5   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   9.0   2.2e-28   1.3e-24       1      75 [.      16      90 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 2.2e-28
                                  EEEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EE CS
                 Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfel 75
                                  +Hteh  e++kkgk+s +++++R+++r q g+g  G++++v+++ +K+tK+++l+++C +C+k+++++++Rakkfe+
  gi|91773367|ref|YP_566059.1| 16 THTEHIAERVKKGKASAMTHIARQKKR-QTGIGnsGKFSKVPGG-DKPTKRVQLKYRCATCNKSHQRPCFRAKKFEF 90
                                  6**************************.****************.*******************************8 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.012        71      46      52 ..      10      16 ..       2      27 .. 0.68
   2 ?    8.4   0.0   0.00029       1.7      40      52 ..      64      76 ..      55      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.012
                zinc_ribbon_10 46 rCpkCga 52
                                  +Cp+C++
  gi|91773367|ref|YP_566059.1| 10 YCPSCKT 16
                                  5666653 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00029
                zinc_ribbon_10 40 leevkyrCpkCga 52
                                    ++kyrC+ C+ 
  gi|91773367|ref|YP_566059.1| 64 RVQLKYRCATCNK 76
                                  56789******96 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0018        11       2      11 ..       8      17 ..       7      29 .. 0.83
   2 ?    6.6   0.3    0.0011       6.4      20      32 ..      63      75 ..      59      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0018
                 zinc_ribbon_5  2 iirCpdCdtk 11
                                  ++ Cp C+t 
  gi|91773367|ref|YP_566059.1|  8 RTYCPSCKTH 17
                                  899*****96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0011
                 zinc_ribbon_5 20 KksgkkVrCakCa 32
                                  K  + k rCa C 
  gi|91773367|ref|YP_566059.1| 63 KRVQLKYRCATCN 75
                                  78899*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 644.26
//
Query:       gi|91773368|ref|YP_566060.1|  [L=58]
Description: 30S ribosomal protein S27e [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-23   81.4   0.8      3e-23   81.3   0.8    1.0  1  Ribosomal_S27e  Ribosomal protein S27
     0.0033   17.0   0.1     0.0054   16.3   0.0    1.4  1  zf-C2H2_12      Zinc-finger C2H2-type
     0.0058   16.7   0.5     0.0074   16.4   0.5    1.2  1  FYVE            FYVE zinc finger
     0.0072   16.3   0.2     0.0072   16.3   0.2    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
  ------ inclusion threshold ------
      0.019   15.0   0.4      0.021   14.9   0.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.11   12.0   0.1       0.11   12.0   0.1    2.2  2  Sgf11           Sgf11 (transcriptional regulation protein)
       0.13   12.3   4.7        1.7    8.7   4.7    2.0  1  zf-BED          BED zinc finger
       0.15   12.1   2.6       0.27   11.3   2.3    1.7  2  zinc_ribbon_6   Zinc-ribbon


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.8   1.3e-26     3e-23       1      54 [.       4      57 ..       4      58 .] 0.98

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.3e-26
                                  -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                  p+s+Fl+vkC dC ne+v+F++a++ v+C+ Cg++L+e tGGk+ ++ +ile+l
  gi|91773368|ref|YP_566060.1|  4 PKSRFLRVKCNDCSNEQVIFGSASRKVNCLVCGRTLAESTGGKSTITTHILEVL 57
                                  89*************************************************997 PP

>> zf-C2H2_12  Zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.4e-06    0.0054      17      46 ..      24      55 ..      20      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                    zf-C2H2_12 17 dpqrrglvCmvCgeslaslk..lstikrHIrq 46
                                  +++ r++ C+vCg++la+     sti  HI++
  gi|91773368|ref|YP_566060.1| 24 GSASRKVNCLVCGRTLAESTggKSTITTHILE 55
                                  6778999*********987533699*****98 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   3.3e-06    0.0074      11      38 ..      12      42 ..       6      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-06
                                  B-TTT--B...--SSS--EE-TTT--EE-ST CS
                          FYVE 11 kCeiCakk...FsllrrrhhCrlCGkvvCek 38
                                  kC+ C+++   F   +r+  C +CG+ + e+
  gi|91773368|ref|YP_566060.1| 12 KCNDCSNEqviFGSASRKVNCLVCGRTLAES 42
                                  688887762225556***********98765 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 !   16.3   0.2   3.2e-06    0.0072      36      70 ..       7      42 ..       2      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.2e-06
                   Zn_Tnp_IS91 36 GfaryeCeeCghekivyfsCksrh.CpsCqkkatee 70
                                   f r++C++C++e++++ s  ++  C  C++  +e 
  gi|91773368|ref|YP_566060.1|  7 RFLRVKCNDCSNEQVIFGSASRKVnCLVCGRTLAES 42
                                  57899*******9999999988888*****987665 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 ?   14.9   0.4   9.3e-06     0.021      69     106 ..       9      49 ..       3      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.3e-06
                                   -EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEESSSEE CS
                          HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadveivsGeell 106
                                   ++v+C++C++e  +    + +++C  Cg++  e ++G+   
  gi|91773368|ref|YP_566060.1|   9 LRVKCNDCSNEQVIFGsaSrKVNCLVCGRTLAESTGGKSTI 49 
                                   689******9987444333588********99999998765 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.9       0.2   4.4e+02       5      11 ..      11      17 ..      10      19 .. 0.85
   2 ?   12.0   0.1   5.1e-05      0.11       2      17 ..      27      42 ..      26      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                                  EE-TTTS CS
                         Sgf11  5 vtCpnCg 11
                                  v+C+ C+
  gi|91773368|ref|YP_566060.1| 11 VKCNDCS 17
                                  78**997 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.1e-05
                                  C-EEE-TTTSSEEEGG CS
                         Sgf11  2 seyvtCpnCgRqiaas 17
                                  s+ v+C+ CgR+ a s
  gi|91773368|ref|YP_566060.1| 27 SRKVNCLVCGRTLAES 42
                                  7889********9976 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.7   0.00075       1.7      14      39 ..      27      53 ..       3      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00075
                                  SS--EETTTTEE----.SSTHHHHHHH CS
                        zf-BED 14 eqkavCryCgkilsrg.ggttnLkrHL 39
                                  + k+ C  Cg++l+ + gg +   +H+
  gi|91773368|ref|YP_566060.1| 27 SRKVNCLVCGRTLAEStGGKSTITTHI 53
                                  5799************99999999997 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   0.00012      0.27      24      40 ..       5      21 ..       1      37 [. 0.71
   2 ?   -3.3   0.0       4.3   9.6e+03      38      46 ..      46      54 ..      44      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                 zinc_ribbon_6 24 knkkvkilCnDCekkse 40
                                  k++  ++ CnDC++++ 
  gi|91773368|ref|YP_566060.1|  5 KSRFLRVKCNDCSNEQV 21
                                  678899******98764 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.3
                 zinc_ribbon_6 38 ksevkfhvl 46
                                  ks++  h+l
  gi|91773368|ref|YP_566060.1| 46 KSTITTHIL 54
                                  677777876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 438.72
//
Query:       gi|91773369|ref|YP_566061.1|  [L=265]
Description: translation initiation factor IF-2 subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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-24   84.0   0.1    1.4e-23   83.2   0.1    1.4  1  EIF_2_alpha     Eukaryotic translation initiation factor 2 al
    6.1e-11   42.5   0.2    6.1e-11   42.5   0.2    1.7  2  S1              S1 RNA binding domain
  ------ inclusion threshold ------
      0.036   14.4   0.0      0.075   13.3   0.0    1.5  1  TFIIE_beta      TFIIE beta subunit core domain
      0.045   14.2   0.0       0.12   12.8   0.0    1.7  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
       0.83   10.3   4.5        0.8   10.4   2.5    2.0  2  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


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 !   83.2   0.1   3.8e-27   1.4e-23       5     116 .]     122     229 ..     119     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 3.8e-27
                                   THHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHHST CS
                   EIF_2_alpha   5 vgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkagee 84 
                                   v   l +++g++y aF ++ai++e++++++ i++e++e++ +i+++++k + v i ++++lt+  +dG+e Ik+aLka+++
  gi|91773369|ref|YP_566061.1| 122 VTATLSNEFGSCYIAFeEAAINGEDAFEDIVISKELAEKIASIAQENIKLPFVDIAGYVDLTSNLPDGIELIKKALKAAAK 202
                                   5678999**********************************************************************8888 PP

                                   .S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                   EIF_2_alpha  85 asneeeveeeeevkikliapPeYvltvetldk 116
                                   ++ ++     +++++++ ++P+Y+++v ++++
  gi|91773369|ref|YP_566061.1| 203 VKIDD-----VRIDVTYTGAPRYRIKVIAPEY 229
                                   76666.....*****************99886 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.2   1.7e-14   6.1e-11       2      75 .]       7      81 ..       7      81 .. 0.96
   2 ?   -3.7   0.2       4.6   1.7e+04      57      64 ..     202     209 ..     201     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.7e-14
                                  STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                            S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                  pe g+ v  +V++v+++Ga+  l+  +g egf+++se+++   v+   + +++G+++  kvl+vd +rr i+ls+k
  gi|91773369|ref|YP_566061.1|  7 PESGDFVVCTVKNVVDFGAYTTLEeyGGKEGFIHISEVKAG-WVKYVRDYVREGQKIVCKVLNVDPNRRHIDLSLK 81
                                  688999999****************99*************9.9999****************************86 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.6
                                   EEEEEEEE CS
                            S1  57 kvkvlkvd 64 
                                   kvk+++v+
  gi|91773369|ref|YP_566061.1| 202 KVKIDDVR 209
                                   68888876 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.075      18      66 ..     170     220 ..     159     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                    TFIIE_beta  18 plsleeIlsylslqldlsdknwllleaLknnpkieyDpk..kgkfsfkPly 66 
                                    l++ +I+ y++l  +l+d  +l+ +aLk   k+++D++  + ++   P y
  gi|91773369|ref|YP_566061.1| 170 KLPFVDIAGYVDLTSNLPDGIELIKKALKAAAKVKIDDVriDVTYTGAPRY 220
                                   799**********8888899****************986555566555555 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.4e-05      0.12      16      75 ..      63     123 ..      60     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                PrlF_antitoxin  16 vRkaLklkkgrdkiaytilddgkv.visraeeeaeDpvleqFLeFlakdllknperlrpve 75 
                                   v k+L+++++r +i   ++d ++    ++ ++ ++++   ++L+F+a+d+ + pe++ +v+
  gi|91773369|ref|YP_566061.1|  63 VCKVLNVDPNRRHIDLSLKDVNEHqKRAKIQDWKNEQKATKWLQFVAEDMGTSPEEMGAVT 123
                                   779999999999999999886554145666888999999*****************99886 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 ?   -0.9   0.0       0.7   2.5e+03      46      59 ..      72      85 ..      15     107 .. 0.53
   2 ?   10.4   2.5   0.00022       0.8      88     125 ..     216     253 ..     159     256 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.7
                                  .---EEEEHHHHHH CS
                Ribosomal_L27A 46 kkeykvvnlkdLde 59
                                  ++++  ++lkd++e
  gi|91773369|ref|YP_566061.1| 72 NRRHIDLSLKDVNE 85
                                  22234444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00022
                                   .....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-E CS
                Ribosomal_L27A  88 k..kdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGk 125
                                   +  +  +Kv++ +   k  +   +k+S+kA+e Ie+ GGk
  gi|91773369|ref|YP_566061.1| 216 GapRYRIKVIAPEY--KTAEAALKKASEKAIETIEKKGGK 253
                                   34555667776553..345566789**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1725.54
//
Query:       gi|91773370|ref|YP_566062.1|  [L=56]
Description: nucleolar RNA-binding protein Nop10p [Methanococcoides burtonii DSM 6242]
Scores for complete 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   82.6   1.0    1.5e-23   82.5   1.0    1.0  1  Nop10p    Nucleolar RNA-binding protein, Nop10p family
     0.0078   15.8   1.8     0.0096   15.5   1.8    1.2  1  RecR      RecR protein
       0.01   13.8   0.3       0.01   13.8   0.3    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
       0.13   11.9   5.1        3.4    7.4   0.4    2.2  2  zf-tcix   Putative treble-clef, zinc-finger, Zn-binding


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 !   82.5   1.0   3.4e-27   1.5e-23       1      51 [.       1      51 [.       1      52 [. 0.97

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 3.4e-27
                                  .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHHH CS
                        Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRralKkr 51
                                  m  +lrkc++c++YTLk+ cpecg+   ++ PaRFSP D+y+kyRr  Kkr
  gi|91773370|ref|YP_566062.1|  1 MGNKLRKCTQCNIYTLKDNCPECGESSGNPLPARFSPLDTYGKYRRISKKR 51
                                  6779**********************************************8 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.8   2.1e-06    0.0096      14      35 ..       3      24 ..       1      27 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-06
                                  HH-EE-TTT--EESSSS-CCCC CS
                          RecR 14 ekvrhCsrCgnlteedlCaICs 35
                                  +k+r C +C+ +t +d C+ C 
  gi|91773370|ref|YP_566062.1|  3 NKLRKCTQCNIYTLKDNCPECG 24
                                  689****************995 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.3   2.2e-06      0.01     618     640 ..       5      27 ..       2      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-06
                      PolC_DP2 618 rrkCkkCgketlearCeeCgekt 640
                                    rkC++C+  tl+ +C+eCge+ 
  gi|91773370|ref|YP_566062.1|   5 LRKCTQCNIYTLKDNCPECGESS 27 
                                   69******************975 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4   0.00075       3.4      10      19 ..       5      14 ..       3      15 .. 0.87
   2 ?    6.9   0.5    0.0011       4.8      12      21 ..      19      28 ..      16      30 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00075
                       zf-tcix 10 vrkCpkCGty 19
                                  +rkC++C +y
  gi|91773370|ref|YP_566062.1|  5 LRKCTQCNIY 14
                                  8******877 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0011
                       zf-tcix 12 kCpkCGtyNG 21
                                   Cp+CG   G
  gi|91773370|ref|YP_566062.1| 19 NCPECGESSG 28
                                  5*****8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 379.66
//
Query:       gi|91773371|ref|YP_566063.1|  [L=261]
Description: hypothetical protein Mbur_1398 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-52  178.4   0.1    2.2e-52  178.1   0.1    1.1  1  PAC2             PAC2 family
  ------ inclusion threshold ------
      0.053   13.5   0.2       0.81    9.7   0.0    2.2  2  Cyclophil_like2  Cyclophilin-like family
      0.057   13.7   0.7       0.12   12.6   0.7    1.5  1  BLOC1_2          Biogenesis of lysosome-related organelles co
        0.1   12.5   0.0       0.56   10.1   0.0    2.2  2  NAD_binding_10   NAD(P)H-binding


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 !  178.1   0.1     5e-56   2.2e-52       1     211 [.      20     232 ..      20     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 5e-56
                                   EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT.SEEEEEEE....E CS
                          PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsgsrdllvlqg....r 75 
                                   L++G+pg+G+Vg+l+vd+Lie+l+aekv ei+s++ +p     p+v+v+e+  ++l ++++y+ +++++d+++l g     
  gi|91773371|ref|YP_566063.1|  20 LLVGLPGVGHVGKLVVDHLIEKLDAEKVFEIYSPH-FP-----PQVMVNEEstVKLVNNEIYICKANGNDIVLLAGdhqsT 94 
                                   799********************************.**.....*******************99989*********87777 PP

                                   -HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT........-CEEEEHHHH CS
                          PAC2  76 epilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees........eyggivgitg 148
                                   + +++ye +    +d+aeelgvk++++Lgg+++g+++   ht++  ++gaa+d e+++el+e         ++ggivg++g
  gi|91773371|ref|YP_566063.1|  95 STEGHYE-LGAIYIDIAEELGVKRIFTLGGFPTGQLT---HTDE--IMGAANDLEMVTELKEYevtfkpnePGGGIVGASG 169
                                   7777777.9999*********************9995...6666..9*************64444566677********** PP

                                   HHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHH CS
                          PAC2 149 lLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqlee 211
                                   lLl+++k ++i a++l++ +++yl+dPk+a+all  lsk+l +evd+++Lee+a+ +e+ ++ 
  gi|91773371|ref|YP_566063.1| 170 LLLGLSKFKNIRAACLMGLTSGYLVDPKSAQALLALLSKILSIEVDVSELEERAKDMEKIVAN 232
                                   **********************************************************99876 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00018      0.81      43     102 ..      55     111 ..      38     120 .. 0.73
   2 ?    1.3   0.1      0.07   3.2e+02      12      52 ..     193     238 ..     190     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00018
               Cyclophil_like2  43 lpeklptddapegssikaGdla.yyapwgnlvlfykdfeesysygltrlGrieedaeelae 102
                                   +p ++  +++ ++ +  + +++ + a+++++vl+ +d+++  ++g+++lG i     ++ae
  gi|91773371|ref|YP_566063.1|  55 FPPQVMVNEE-STVKLVNNEIYiCKANGNDIVLLAGDHQSTSTEGHYELGAI---YIDIAE 111
                                   7777777777.6666666777625678899********99889********9...233333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.07
               Cyclophil_like2  12 Lednaaarallekl....PltltmedyngnEkiay.lpeklptdda 52 
                                   L d ++a+all++l     +++++++++++ k ++ +  +l  +++
  gi|91773371|ref|YP_566063.1| 193 LVDPKSAQALLALLskilSIEVDVSELEERAKDMEkIVANLMEAKQ 238
                                   6678899999999988889999999999866655434444444444 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   2.8e-05      0.12      58      91 ..     200     233 ..     194     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                       BLOC1_2  58 eelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                   ++l  +l++i  ie +v+eLee ++ +++++ +L
  gi|91773371|ref|YP_566063.1| 200 QALLALLSKILSIEVDVSELEERAKDMEKIVANL 233
                                   678899************************9988 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 ?   10.1   0.0   0.00013      0.56      52     103 ..      73     128 ..      26     152 .. 0.64
   2 ?   -1.8   0.0      0.53   2.4e+03      51      73 ..     216     238 ..     193     252 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                                   CHHHHHHTT-SEEEES---TCCHHHH....HHHHHHHHHHCT--EEEEEEETTTTS CS
                NAD_binding_10  52 edlaealkgadaVvsalggggkdeeg....aknivdaakeagvkRfvlvsaigvgd 103
                                   e      +g d+V+ a+ ++++ +eg     +  +d a+e gvkR+ +++++ +g+
  gi|91773371|ref|YP_566063.1|  73 EIYICKANGNDIVLLAGDHQSTSTEGhyelGAIYIDIAEELGVKRIFTLGGFPTGQ 128
                                   444555689********88888777755556777***************9999885 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.53
                                   CCHHHHHHTT-SEEEES---TCC CS
                NAD_binding_10  51 vedlaealkgadaVvsalggggk 73 
                                   v++l+e  k+ + +v++l   ++
  gi|91773371|ref|YP_566063.1| 216 VSELEERAKDMEKIVANLMEAKQ 238
                                   44555555555555555543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1356  (0.0756317); expected 358.6 (0.02)
Passed bias filter:                     1039  (0.0579508); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1615.14
//
Query:       gi|91773372|ref|YP_566064.1|  [L=409]
Description: PHP-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   18.2   0.0     0.0065   16.2   0.0    2.0  2  PHP_C     PHP-associated
  ------ inclusion threshold ------
      0.019   15.2   0.2       0.03   14.6   0.2    1.4  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.57   5.1e+03      42      51 ..      91     100 ..      83     102 .. 0.63
   2 !   16.2   0.0   7.2e-07    0.0065       7      53 ..     176     224 ..     172     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.57
                         PHP_C  42 atpdelleai 51 
                                    +++el ea+
  gi|91773372|ref|YP_566064.1|  91 SKAEELAEAM 100
                                   4456666665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.2e-07
                         PHP_C   7 ArrfAeklglpgtgGSDAHrle..eVGrayTefeepiatpdelleaire 53 
                                   A+r+ e + l ++ +SDAH+++  ++ r +T fe p+ +++ l +ai +
  gi|91773372|ref|YP_566064.1| 176 ADRISELHRLTFLTNSDAHSPWsnKLAREFTRFEVPSIDFEGLEKAILR 224
                                   9999****************98556*************99999999976 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   3.3e-06      0.03       1      83 [.       6      87 ..       6     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                                  EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE................. CS
                                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                           PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse...kerpsh 79
                                  dlH+H++ys + + +++++ +  +ak++g++ +a  D  +  + +e++k+a +++    + i+  e  +++ +e   k+r +h
  gi|91773372|ref|YP_566064.1|  6 DLHLHSKYSmACSKNMELSTISIEAKKKGIDLVATGDCIH-PKWLEEIKQAATNN----ETIFINETHFIPTTEiedKNRVHH 83
                                  89********8889*******************9888775.66777777774444....333333433333333333445555 PP

                                  .... CS
                                  xxxx RF
                           PHP 80 ltll 83
                                  l++l
  gi|91773372|ref|YP_566064.1| 84 LLIL 87
                                  5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2732.62
//
Query:       gi|91773373|ref|YP_566065.1|  [L=315]
Description: hypothetical protein Mbur_1401 [Methanococcoides burtonii DSM 6242]
Scores for 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-08   32.4   0.0    1.4e-07   31.9   0.0    1.3  1  Reprolysin_5     Metallo-peptidase family M12
      1e-05   26.1   0.0    2.1e-05   25.0   0.0    1.6  1  Reprolysin_3     Metallo-peptidase family M12B Reprolysin-lik
     0.0006   20.1   0.0    0.00098   19.4   0.0    1.3  1  Pep_M12B_propep  Reprolysin family propeptide
  ------ inclusion threshold ------
      0.025   14.2   0.1       0.05   13.2   0.1    1.4  1  Peptidase_M57    Dual-action HEIGH metallo-peptidase
      0.035   13.7   0.0       0.11   12.1   0.0    1.8  2  Reprolysin_4     Metallo-peptidase family M12B Reprolysin-lik


Domain annotation for each model (and alignments):
>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   3.8e-11   1.4e-07       5     161 ..     108     254 ..     106     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.8e-11
                  Reprolysin_5   5 vallvaaDcsfvaafgg.daaaqanivnlvnrasnvyeresnislglanvtildeedpstaseasstgdaselLnefqsas 84 
                                   +++l+ +D  + + +g+ +  ++  i +++n+a n   ++++  l++  ++ + + d+         g+++e+++ f+++ 
  gi|91773373|ref|YP_566065.1| 108 FNILLCYDSAYKDVYGSyT-LVEMEISDMINTA-NLGLDDHDAMLTFDYYKRYGSLDN---------GTSQEIIDFFKDDI 177
                                   6789999999999997755.9************.***********************9.........77999999999999 PP

                  Reprolysin_5  85 salrgqqnddlailflmtnfsgg.vGlAwlgqlcnsgsagsvstrveksnsvvvstatevqvvaHElGHnfGavHDcd 161
                                      r+  + dl  lf  ++f+ + +G+++ ++  ++ + + +++ +++  ++++  ++  +v++HE+GHn+ a+ D  
  gi|91773373|ref|YP_566065.1| 178 PPYRDITDSDLTTLFYGQDFDDNtLGRGSTYNGSSDRAYSVLQMVPSTGSYGAS-YSERCIVLTHEIGHNLDARYDEH 254
                                   9999999999************98999998777666655555555555566666.8999**************98865 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 !   25.0   0.0   5.9e-09   2.1e-05      41     122 ..     164     250 ..     123     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5.9e-09
                  Reprolysin_3  41 kdatealdelaevtaeaergqagyDlvhlftarde.sgvgGlAyv..gsvcnsskkagvnsgssvlgkvga...dtvaHEi 115
                                     ++e++d +++++  + r+  + Dl +lf ++d+ + ++G      gs  + ++  +++ +++ +g++     ++++HEi
  gi|91773373|ref|YP_566065.1| 164 GTSQEIIDFFKDDIPPY-RDITDSDLTTLFYGQDFdDNTLGRGSTynGSSDRAYSVLQMVPSTGSYGASYSercIVLTHEI 243
                                   23478999999999988.9****************977777766632444444444677777777777555789******* PP

                  Reprolysin_3 116 GHnfgan 122
                                   GHn++a+
  gi|91773373|ref|YP_566065.1| 244 GHNLDAR 250
                                   ****997 PP

>> Pep_M12B_propep  Reprolysin family propeptide
   #    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      87     140 .]      11      62 ..       5      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.7e-07
               Pep_M12B_propep  87 yYqGevrgeegssvalstCsGl.rGvirteneeYfIePleeeeeeeeekkpHvvY 140
                                    Y+G+v g+e+s+va++  + l  G+i ++++ Y+I   +   +e  +k+ H +Y
  gi|91773373|ref|YP_566065.1|  11 TYHGKVVGDEDSKVAMTISNNLlIGMIDVDENAYYIDFTK---NEIGGKNIHNIY 62 
                                   6******************99559************9884...335567788887 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 ?   13.2   0.1   1.4e-05      0.05     111     154 ..     211     256 ..     190     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                 Peptidase_M57 111 sgGlPykviqigtglesysvdvneh..vithelGhtvGlRhsDyyn 154
                                   s  + y v+q+  ++ sy+    e   v+the+Gh +  R+ ++y+
  gi|91773373|ref|YP_566065.1| 211 SSDRAYSVLQMVPSTGSYGASYSERciVLTHEIGHNLDARYDEHYE 256
                                   56678999999889999999999974478**************997 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 ?   -1.6   0.0       0.5   1.8e+03       7      37 ..     110     140 ..     107     142 .. 0.89
   2 ?   12.1   0.0   3.2e-05      0.11      87     156 ..     181     256 ..     163     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.5
                  Reprolysin_4   7 vavavdpeyvaelgsvdevraainalvtvln 37 
                                   +++ +d  y    gs   v  +i  +++++n
  gi|91773373|ref|YP_566065.1| 110 ILLCYDSAYKDVYGSYTLVEMEISDMINTAN 140
                                   7889999999999999999999999999998 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.2e-05
                  Reprolysin_4  87 rdskdyDlaallrdtrasqqnvgvawvgalcls.arq..nk..kasgvaasrdeydi.fAHEiGHtfGaaHdlsde 156
                                   rd  d Dl  l+  +  + +  g +  + + ++ a+   ++    + + as +e  i + HEiGH++ a  d  +e
  gi|91773373|ref|YP_566065.1| 181 RDITDSDLTTLFYGQDFDDNTLGRGSTYNGSSDrAYSvlQMvpSTGSYGASYSERCIvLTHEIGHNLDARYDEHYE 256
                                   7778888888887776677778888888777666665333333446666665555555**********99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2322.33
//
Query:       gi|91773374|ref|YP_566066.1|  [L=77]
Description: hypothetical protein Mbur_1402 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 565.43
//
Query:       gi|91773375|ref|YP_566067.1|  [L=170]
Description: hypothetical protein Mbur_1403 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.5   0.0       0.12   13.1   0.0    1.2  1  fn3_5     Fn3-like domain


Domain annotation for each model (and alignments):
>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.7e-06      0.12       2      97 ..      52     148 ..      51     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-06
                         fn3_5   2 aLkeigdkfsftltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldl 82 
                                   ++kei++  + +ltlkN +n ++  ++ ++   T      +g+ i+ ++ p+     l  ++s v +++n+s  ++v+   
  gi|91773375|ref|YP_566067.1|  52 SIKEINELSTLQLTLKNEGNYTVNVAILEE-FSTYNIIYSNGSDIEYEHMPAL---DLMGDESLVELKPNESLSINVNPIG 128
                                   79****************************.9999988899999999999987...899******************9766 PP

                         fn3_5  83 psdakk.....kngyfveGf 97 
                                    + ++k     + +yfv G 
  gi|91773375|ref|YP_566067.1| 129 WNPFSKgnhslSAKYFVRGL 148
                                   66666666666566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1151.66
//
Query:       gi|91773376|ref|YP_566068.1|  [L=104]
Description: hypothetical protein Mbur_1404 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 779.90
//
Query:       gi|91773377|ref|YP_566069.1|  [L=74]
Description: hypothetical protein Mbur_1405 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 562.15
//
Query:       gi|91773378|ref|YP_566070.1|  [L=320]
Description: ribonuclease BN [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-47  162.7  28.5    1.6e-47  162.3  28.5    1.1  1  Virul_fac_BrkB  Virulence factor BrkB


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.3  28.5   8.7e-52   1.6e-47       3     255 ..      62     316 ..      60     318 .. 0.90

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 8.7e-52
                Virul_fac_BrkB   3 ddlsllAaalayytllSlfPlllvllavlgllglddelqeqlldllaevlpegaaevvedilqrllnqa...slgllglav 80 
                                   dd++ ++aal++y++lSl  lll++ ++ g++++ + lq++++d+++ ++ e++++ ++ ++++l +++    + ++++++
  gi|91773378|ref|YP_566070.1|  62 DDGTSFSAALSFYLILSLPSLLLFSSSLGGMFLKVELLQATIIDYISPFADEEIINSFNLLFHQLPETSsltFGLIISFLL 142
                                   8999**************************966699***************9999****9999999999673444455555 PP

                Virul_fac_BrkB  81 llwsasggvsalrralnkiygv....eesrs....flrkrllsllllllllvllllslvlsvflqslllasapllglglel 153
                                   +lwsa +++ ++++++++++gv    +   +    +++kr+ s+++++++ +ll++s+++ +fl +++++++ + +l+le 
  gi|91773378|ref|YP_566070.1| 143 FLWSAGNIFLQFQKTIDHMWGVldskK---GwsqrLFKKRISSFVAVFIFSLLLIISILAEIFLVVISNMLTIIHPLPLE- 219
                                   55********************85432...34555*******************************99877644444433. PP

                Virul_fac_BrkB 154 sellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgaliill 234
                                       l+q+++ +v++++l+++f++lY+ lp++kv+++++ +G++l++++++l+k+lfsly+s+ ++++++Y  +ga+++++
  gi|91773378|ref|YP_566070.1| 220 ----LMQYISSIVTFFVLIFFFIYLYMALPDKKVKIKYIGIGSFLTVFFITLGKHLFSLYISY-SNFTTVYTKIGAFLAIF 295
                                   ....799****9**************************************************9.89*************** PP

                Virul_fac_BrkB 235 lWlylsalilLlGaelnaelq 255
                                   lW+y+s++i+ l ae+++ ++
  gi|91773378|ref|YP_566070.1| 296 LWMYYSSIIVTLMAEFIKIYS 316
                                   ****************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1227  (0.0684366); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2057.24
//
Query:       gi|91773379|ref|YP_566071.1|  [L=64]
Description: hypothetical protein Mbur_1407 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-24   85.7   0.2    1.7e-24   85.4   0.2    1.1  1  DUF1508          Domain of unknown function (DUF1508)
     0.0021   18.3   0.0     0.0022   18.2   0.0    1.2  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0068   16.4   0.0     0.0071   16.3   0.0    1.2  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
  ------ inclusion threshold ------
      0.084   13.1   0.0       0.12   12.6   0.0    1.3  1  ACI44            Metallo-carboxypeptidase inhibitor


Domain annotation for each model (and alignments):
>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.2   3.8e-28   1.7e-24       1      48 []       9      56 ..       9      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 3.8e-28
                                  ETTTEEEEEEE-TTS-EEEEEEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                       DUF1508  1 DknGefrFrLkaaNgevIatsegYsskaaaenGIesVkknapdaeveD 48
                                  Dk+G++rFrLka+Nge++at++gY++ka+++nGI sVk+na dae+++
  gi|91773379|ref|YP_566071.1|  9 DKSGKYRFRLKAKNGEIVATGQGYATKAGCMNGIKSVKNNAMDAEIVE 56
                                  89********************************************97 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.9e-07    0.0022      30      63 ..       4      36 ..       2      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.9e-07
               CarboxypepD_reg 30 astttdadGafrlrglppgtysvtvsapGyatat 63
                                   +  td++G++r+r l++ + +++++ +Gyat +
  gi|91773379|ref|YP_566071.1|  4 FEIYTDKSGKYRFR-LKAKNGEIVATGQGYATKA 36
                                  5689*********9.****************986 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-06    0.0071      25      59 ..       3      36 ..       1      60 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
               CarbopepD_reg_2 25 kkgtvTdenGnFelknlpagkytLvvsyvGyktqe 59
                                  k+  +Td++G+++++ l+a++ ++v++  Gy t+ 
  gi|91773379|ref|YP_566071.1|  3 KFEIYTDKSGKYRFR-LKAKNGEIVATGQGYATKA 36
                                  67789*********7.999999**********964 PP

>> ACI44  Metallo-carboxypeptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.6e-05      0.12      10      33 ..      36      59 ..      32      64 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                                  GG--TT-EEETTTTEEE-HHHHHH CS
                         ACI44 10 tdctnGekcvqknkicstiveiqr 33
                                  + c nG k v+ n + + ivei+ 
  gi|91773379|ref|YP_566071.1| 36 AGCMNGIKSVKNNAMDAEIVEIET 59
                                  57********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 438.29
//
Query:       gi|91773380|ref|YP_566072.1|  [L=269]
Description: secreted protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-24   85.2   0.1    8.9e-24   83.7   0.1    1.8  2  Inhibitor_I42  Chagasin family peptidase inhibitor I42


Domain annotation for each model (and alignments):
>> Inhibitor_I42  Chagasin family peptidase inhibitor I42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.1   4.9e-28   8.9e-24       2      91 .]      60     145 ..      59     145 .. 0.96
   2 ?   -2.3   0.0      0.36   6.4e+03       1      72 [.     205     218 ..     194     227 .. 0.67

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 4.9e-28
                                   EETT-EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSSEEEEEEEEEE-TTSTSS-- CS
                 Inhibitor_I42   2 vkvgetieieLpenpttGYsWtvdasdseglkllseeyipdesdelvGaggthvwtfkalkpGettiefkyarpwekatea 82 
                                   +k g++i+++L+enp+tGYsW+++    eg+ l+++e++ ++++ ++Gagg+h+wt+ka ++G+++i++ y+ +we++t +
  gi|91773380|ref|YP_566072.1|  60 LKMGDSIVLKLNENPSTGYSWDLSLP--EGIVLVKDEFVGPDEP-MPGAGGVHEWTLKASSEGNYQINAIYKMSWENVTGN 137
                                   899*******************9999..***************9.*********************************986 PP

                                   SC.EEEEEE CS
                 Inhibitor_I42  83 eertftltv 91 
                                   e+ tft++v
  gi|91773380|ref|YP_566072.1| 138 ED-TFTMNV 145
                                   66.***997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.36
                                   EEETT-EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSSEEEEEEEEE CS
                 Inhibitor_I42   1 tvkvgetieieLpenpttGYsWtvdasdseglkllseeyipdesdelvGaggthvwtfkalkpGettiefky 72 
                                   tv++g+ + i L+                                                           
  gi|91773380|ref|YP_566072.1| 205 TVNTGNGFDIALK----------------------------------------------------------T 218
                                   3555555555555..........................................................3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2143.06
//
Query:       gi|91773381|ref|YP_566073.1|  [L=306]
Description: LPPG:FO 2-phospho-L-lactate transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  160.5   0.1    6.2e-47  160.2   0.1    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 !  160.2   0.1   3.5e-51   6.2e-47       2     263 ..       2     272 ..       1     293 [. 0.85

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 3.5e-51
                                   EEEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C..........HHH CS
                       UPF0052   2 vvlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlval...idder..........lle 67 
                                   ++++GGtG++kll+gl+++   +elt+vv++a+d++ sG        l+ +Di+++l+ l   id+++          +++
  gi|91773381|ref|YP_566073.1|   2 IIFSGGTGTPKLLDGLRHIVpeDELTVVVNTAEDVWVSG-------NLITPDIDTILYLLsgrIDRDKwwgvkddtfqTHR 75 
                                   68******************999****************.......99************999888889996555555444 PP

                                   HHCH-B-SS...........SSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-E CS
                       UPF0052  68 eLfqyRfkg...........dgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledGee 136
                                   e+      +           d d  +h+++  lL++     g sl+e+i++l ++ +++++vlP++dd+v++ +e+  G+ 
  gi|91773381|ref|YP_566073.1|  76 EM------KelghdesmmigDLDRVTHIMRSDLLRQ-----GlSLSESIHELLSVYGIGVNVLPMSDDSVRTIVETPSGH- 144
                                   44......34445557777777888***********.....99*************************************. PP

                                   EE.STTTGGGG-S...-EEE.EEEESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE-- CS
                       UPF0052 137 it.geskisearklkapikr.vflepegaeaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskakkvlvsn 215
                                   ++ ++ +++++    +++ +  + + e+a++ + vlea+++ d +++gp++++tSi+Pi+ +pg+++ l  +k+k+v+vs+
  gi|91773381|ref|YP_566073.1| 145 VHfQDFWVKQH--GVPEVLSvEQEGIEEASICSLVLEALESDDEVLIGPSNPITSIGPIISLPGMSRIL--RKKKVVAVSP 221
                                   666*****333..35778887888999999***************************************..669******* PP

                                   SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S...-SEEEEE-S.---HHHH CS
                       UPF0052 216 imtqkGetdgfsvsdhvkaieravg.....kgvakay...vdavlvnts.evpeell 263
                                   i++      + +vs+++ + ++a g     +g+a+ y   +d+++++++ ++++e +
  gi|91773381|ref|YP_566073.1| 222 IIG------NEAVSGPAGKFMTARGfdvssRGIADCYrefLDVLVLDDRdTTSPEQF 272
                                   **9......****************988874444444666*****988823333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 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:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2122.47
//
Query:       gi|91773382|ref|YP_566074.1|  [L=400]
Description: metal-dependent phosphohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   2.9    1.1e-13   51.4   2.9    2.6  2  HD             HD domain
    0.00074   19.1   0.0     0.0018   17.8   0.0    1.7  1  HDOD           HDOD domain
  ------ inclusion threshold ------
      0.084   12.5   0.0       0.25   11.0   0.0    1.7  1  Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
       0.15   12.6   0.9       0.35   11.4   0.1    2.1  2  DUF2482        Hypothetical protein of unknown function (DUF2


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 !   51.4   2.9   2.5e-17   1.1e-13       1     121 [.      50     163 ..      50     164 .. 0.76
   2 ?    0.3   0.1      0.17   7.7e+02      56      77 ..     283     304 ..     265     382 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.5e-17
                                   HHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHTTTTHHHHTS..HHH......HHHCTCCHHHHHHHHHHHHHHHHH CS
                            HD   1 rleHsleVaklarrlaedlge..eedrellllaaLlHDiGkgpfgdafekk......eeefekflaHekvgaeilrevekr 73 
                                   r+eHsl+V++la +l  +++   +e++e l++aaLlHDiG+gp ++a e+       e         +++  +ilr+ e++
  gi|91773382|ref|YP_566074.1|  50 RFEHSLGVMHLATMLTSQIDSieNEEKEELRAAALLHDIGHGPLSHATENLirhytrE--------RHEDVKSILRKGEIS 122
                                   79********************************************999995543321........334444444444444 PP

                                   HHHH.....HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                            HD  74 lgld.....ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                   + l       +++a+ i+  ++               + +++++v+++D+l +
  gi|91773382|ref|YP_566074.1| 123 EILEdngldPMTIAAHIKGETDLGK------------IVNSEIDVDRMDYLVR 163
                                   4333333335778888888888885............899*********9966 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                                   CHHHHHHHHHHHHHHHHHHHHH CS
                            HD  56 flaHekvgaeilrevekrlgld 77 
                                   +++He+vg+ + r ++k++++ 
  gi|91773382|ref|YP_566074.1| 283 HVGHEVVGEGVMRYRGKVERVE 304
                                   4567777777777777777553 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     4e-07    0.0018      96     152 ..      51     110 ..      40     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-07
                                   HHHHHHHHHHHHHHHHHT...T-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHH CS
                          HDOD  96 wehslavAlvarelaeel...gledpeeaflaGLLhdiGklvllsllpeeleellekvae 152
                                    ehsl v  +a++l +++   + e++ee+  a+LLhdiG   l ++ ++ +   +++ +e
  gi|91773382|ref|YP_566074.1|  51 FEHSLGVMHLATMLTSQIdsiENEEKEELRAAALLHDIGHGPLSHATENLIRHYTRERHE 110
                                   58**************9954444555*****************99999988887775554 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 ?   11.0   0.0   5.5e-05      0.25      40      56 ..     339     355 ..     337     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.5e-05
                 Prot_ATP_OB_N  40 GqeVlLnEalvvVealg 56 
                                   G  V+L+Ea+++V++l+
  gi|91773382|ref|YP_566074.1| 339 GKMVRLDEASNIVATLE 355
                                   99************986 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 ?   -2.6   0.1       1.8     8e+03       5      24 ..      62      81 ..      58      85 .. 0.74
   2 ?   11.4   0.1   7.9e-05      0.35       8      67 ..     118     176 ..     110     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                       DUF2482  5 dmtqeeikdllaeKskeLye 24
                                   m  ++i  + +e ++eL++
  gi|91773382|ref|YP_566074.1| 62 TMLTSQIDSIENEEKEELRA 81
                                  57778888888888888876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.9e-05
                       DUF2482   8 qeeikdllaeKskeLyelieeikeetdFdillfsaigvsdgdaqvsssslvvGkivglan 67 
                                   + ei ++l++   +   ++ +ik+etd   +++s i v+  d ++      +G ++gl++
  gi|91773382|ref|YP_566074.1| 118 KGEISEILEDNGLDPMTIAAHIKGETDLGKIVNSEIDVDRMD-YLVRDAHYTGVAFGLVD 176
                                   569999999999999***************************.77777777899998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2704.74
//
Query:       gi|91773383|ref|YP_566075.1|  [L=120]
Description: hypothetical protein Mbur_1413 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   0.3       0.16   11.6   0.3    1.4  1  DAGK_cat  Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3     9e-06      0.16      46     110 ..      14      79 ..       5      90 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9e-06
                                   HHHHHHHHCC-SEEEE.EESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HHHHHCT--SSHHHHH CS
                      DAGK_cat  46 elakeakeegvdlivv.aGGDGtvsevlnglleelatkpplgiiPlGtgNdlaralgigkdieeal 110
                                   el+ e+++ g d+iv   GGDG v++v+ g  ++++ +   ++i l +  d a al   ++i++a+
  gi|91773383|ref|YP_566075.1|  14 ELVLEHRNIGDDIIVTlTGGDGHVGAVAVGHYDNTGGHASSSVITLPSHRDDAIALDAARKITSAT 79 
                                   667777777777777526**********99998777777777777766666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 727.53
//
Query:       gi|91773384|ref|YP_566076.1|  [L=183]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-27   96.1   0.1    1.9e-27   95.9   0.1    1.0  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 !   95.9   0.1   1.1e-31   1.9e-27       1     125 [.       1     163 [.       1     181 [. 0.85

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.1e-31
                                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.GS....TCSSHHHHHHCT...............TE CS
                  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.klklaaredpilhielrr...............wa 65 
                                   ++i++gi+G+++a ++++lle L + +i++++vlt+aAkk+++ e +++ ++    i+++  +                ++
  gi|91773384|ref|YP_566076.1|   1 MEIVIGISGASGAQYGIRLLEVLSEMDIDTHLVLTEAAKKILKVEtDYTTED----IEDMATAVydekdftapiasgshPF 77 
                                   68*****************************************885444433....33333333444577777777777** PP

                                   SEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTEEEEE.--HHCCTCS CS
                  Flavoprotein  66 dllviaPasantlakianGiadnll..............................tlilratakkpiliaPamnpamyenp 116
                                   ++++iaP+s++tla +anG +dnl+                              +  lra ++++++++P + p +y++p
  gi|91773384|ref|YP_566076.1|  78 EGMIIAPCSMKTLASVANGTSDNLIaraadvclkerrklilmtretplsgihienM--LRA-HNAGAILLP-ACPGFYNRP 154
                                   ***************************************************99555..544.669******.********* PP

                                   TCHHHHHHH CS
                  Flavoprotein 117 qtlknlekl 125
                                   + +++l ++
  gi|91773384|ref|YP_566076.1| 155 NAMEELIDF 163
                                   *******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1474.87
//
Query:       gi|91773385|ref|YP_566077.1|  [L=112]
Description: molybdopterin converting factor small subunit MoaD [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   74.5   0.2      1e-20   74.1   0.2    1.1  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.022   15.1   0.2      0.026   14.9   0.2    1.2  1  Urm1      Urm1 (Ubiquitin related modifier)
      0.047   13.9   0.1      0.065   13.4   0.1    1.3  1  DUF4279   Domain of unknown function (DUF4279)


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 !   74.1   0.2   1.8e-24     1e-20       1      77 []      24     112 .]      24     112 .] 0.97

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1.8e-24
                                   EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG............TTTTEEEEETTEEEGC.CTTTSB--TTCEE CS
                          ThiS   1 vllfaelrelageeelelaegstvaelleaLgerypela............lerrvavavNgeivpr.lwldtelkdgDev 68 
                                   ++lfa+lre+ag   +++ eg++++e+l+ L+ ++p+++             ++ +++++Ng+++++ ++ dt+l++gDe+
  gi|91773385|ref|YP_566077.1|  24 IKLFANLREIAG-VSELELEGENIQEILDILQNDHPQIQeliydddrgkkeIRAYINILINGNNIQHlEGSDTVLNEGDEI 103
                                   79**********.8888999*******************************99**************99************ PP

                                   EEEESTTC- CS
                          ThiS  69 ailppVaGG 77 
                                   ai+ppV+GG
  gi|91773385|ref|YP_566077.1| 104 AIFPPVSGG 112
                                   ********9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   4.3e-06     0.026      27      96 .]      40     112 .]      14     112 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-06
                                   SSSS-BHHHHHHHHCCCC-SSGHHHCBS...TTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                          Urm1  27 eseevnleeliayikknlikerkevFle...kdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96 
                                   e e  n++e+++ +++++ + ++ ++ +   k+++r  i +Lin  +++ l+  d++l+++D+i     + GG
  gi|91773385|ref|YP_566077.1|  40 ELEGENIQEILDILQNDHPQIQELIYDDdrgKKEIRAYINILINGNNIQHLEGSDTVLNEGDEIAIFPPVSGG 112
                                   4556788888888888887777777743234899******************************987777766 PP

>> DUF4279  Domain of unknown function (DUF4279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.065      54      93 ..      44      88 ..      33     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                       DUF4279 54 eqldklldrlepkaekikelak.....kygleiylqvviyiedge 93
                                  e ++++ld l+++  +i+el       k ++++y+ + i+ ++ +
  gi|91773385|ref|YP_566077.1| 44 ENIQEILDILQNDHPQIQELIYdddrgKKEIRAYINILINGNNIQ 88
                                  789*******************998888899*****999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 814.58
//
Query:       gi|91773386|ref|YP_566078.1|  [L=125]
Description: camphor resistance protein CrcB [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.3  10.3    2.3e-21   75.9  10.3    1.1  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)
  ------ inclusion threshold ------
      0.024   15.0   6.1      0.028   14.7   6.1    1.1  1  DUF3021   Protein of unknown function (DUF3021)


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9  10.3   2.6e-25   2.3e-21       3      94 ..      13     113 ..      12     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.6e-25
                                   HHHHHHHHHHHHHHH.HHHHBEBHHHHHHHHHHHHHHHHHHH..............HHTTTHHHHHS-SHHHHHHHHHHHH CS
                          CRCB   3 valggalGallRyllssllnkrplgtlavNvlGsfllgllla..............llttGflGglTTfStfvlelvslle 69 
                                   +a+gg+lGa+ Ryl++s++++ p+gtl+vNvlGs+l+g+l++              +++tGflG++TTfStfv++++sl  
  gi|91773386|ref|YP_566078.1|  13 IAAGGFLGAISRYLITSTIVS-PTGTLIVNVLGSLLIGMLMYdneyigyvdqrtrlIIGTGFLGSFTTFSTFVVQTYSLGG 92 
                                   689************888777.55***************999999999888888877*********************965 PP

                                   HT-HHHHHHHHHHHHHHHHHHHHHH CS
                          CRCB  70 egellaallyvllsvvlgllavvlg 94 
                                   +     a++++l+++++++lav++g
  gi|91773386|ref|YP_566078.1|  93 T----PAIVNILANILMTILAVFAG 113
                                   4....57788888888888888776 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.1   3.1e-06     0.028      10     111 ..      11     114 ..       7     125 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                       DUF3021  10 iGiligliislvislfsgettllestavlkqvllsaliGvlfalasli.feserlsllkqtlihflvv.lllvlllalllg 88 
                                    Gi+ g +++ +  +++++t++  +  ++ +vl+s+liG+l+    +i + ++r  l + t +   ++ + ++++ ++ lg
  gi|91773386|ref|YP_566078.1|  11 SGIAAGGFLGAISRYLITSTIVSPTGTLIVNVLGSLLIGMLMYDNEYIgYVDQRTRLIIGTGFLGSFTtFSTFVVQTYSLG 91 
                                   5888888888899999999988899999********************99999********96555550555555559999 PP

                       DUF3021  89 Wfplsvigiliv.ilifiiiylii 111
                                    +p  +++il+  +++ +++++  
  gi|91773386|ref|YP_566078.1|  92 GTPA-IVNILANiLMTILAVFAGR 114
                                   7776.5555555244445555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 912.57
//
Query:       gi|91773387|ref|YP_566079.1|  [L=102]
Description: hypothetical protein Mbur_1418 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-35  119.8   0.4    5.3e-35  119.6   0.4    1.0  1  DUF190    Uncharacterized ACR, COG1993


Domain annotation for each model (and alignments):
>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   0.4   2.9e-39   5.3e-35       1      97 []       4     100 ..       4     100 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2.9e-39
                                   EEEEEEEETT-EETTEEHHHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHHHHH CS
                        DUF190   1 klLrIyigesdrlegkplyeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieaflpel 81 
                                   k+LrI+++e+  ++gk ++eai+el++e+ ++gatvl+GieG+g +++ihta++l+l ++lP+++e++d+eeki+++lp++
  gi|91773387|ref|YP_566079.1|   4 KILRIFLNENCIFDGKVAHEAILELLKEARVSGATVLHGIEGYGVHNKIHTASILRLGTQLPIIVEAIDSEEKIREILPNI 84 
                                   68******************************************************************************* PP

                                   HT----SEEEEEEEE- CS
                        DUF190  82 kelvkeglvtlekvev 97 
                                   +++v egl+tl++ve+
  gi|91773387|ref|YP_566079.1|  85 RKMVPEGLITLQEVEI 100
                                   **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 716.17
//
Query:       gi|91773388|ref|YP_566080.1|  [L=86]
Description: hypothetical protein Mbur_1419 [Methanococcoides burtonii DSM 6242]
Scores for 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-20   70.5   0.8    1.1e-19   70.4   0.8    1.0  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.8   5.9e-24   1.1e-19       2      84 .]       2      86 .]       1      86 [] 0.93

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 5.9e-24
                     CRS1_YhbY  2 tekelrrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkc..egppalnmkrmaeiLeektgglviqrsgtsivL 82
                                   ++ l +Lr+ a ++kp++++Gk G+t++++ e+++++k++ lvkvk+      ++ ++ +ae L+e+t+ +vi+++g+s+vL
  gi|91773388|ref|YP_566080.1|  2 DKERLYKLRSEATNIKPIINVGKGGITDQLIMELKKHIKERHLVKVKVlkSASYEDGIDAIAENLAEATRTTVIDVRGSSVVL 84
                                  578899******************************************984445666************************** PP

                     CRS1_YhbY 83 YR 84
                                  YR
  gi|91773388|ref|YP_566080.1| 85 YR 86
                                  *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 672.00
//
Query:       gi|91773389|ref|YP_566081.1|  [L=233]
Description: hypothetical protein Mbur_1420 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-09   36.5   0.1    4.1e-09   36.1   0.1    1.1  1  ATPase       KaiC
    0.00041   20.1   0.0      0.001   18.8   0.0    1.6  2  DUF835       Protein of unknown function (DUF835)
     0.0005   19.3   0.7    0.00069   18.9   0.0    1.6  2  PAXNEB       PAXNEB protein
     0.0026   16.7   0.0     0.0045   15.9   0.0    1.3  1  AAA_35       AAA-like domain
  ------ inclusion threshold ------
      0.033   13.5   0.0      0.044   13.1   0.0    1.2  1  DnaB_C       DnaB-like helicase C terminal domain
      0.051   13.2   0.0      0.074   12.7   0.0    1.4  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi


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 !   36.1   0.1   1.4e-12   4.1e-09       4     221 ..       7     224 ..       5     233 .] 0.80

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.4e-12
                        ATPase   4 gIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegkla 84 
                                   gI++lD+++ gG+ eg+   + G p +GK  +  + + +g+++  e  ++v++ e+ e + e ++  + d+e  +    l 
  gi|91773389|ref|YP_566081.1|   7 GIKELDDLI-GGVREGTNLMLIGPPMCGKDELINKIVHTGLKN-MESSIIVSTRETGERILEWFSLNDFDVETAN----LG 81 
                                   9*******9.******************************999.9*****************9998888876543....55 PP

                        ATPase  85 iidasesaeesaee........kdkedleelieelaeaikeika......krvviDsitgl.ayeekeavaReilrqlvrv 150
                                   i+d ++++ +++++         +  dl  +  ++ ++++e+ +       r+ i s++++ +y++ + v+R  l+  + +
  gi|91773389|ref|YP_566081.1|  82 IVDCVTKTLGISTQdtaqikraASPVDLTGIGVRMGQYLEEFLVqkespgLRLCINSLSTIlMYSNLQTVFR-FLHVYTGR 161
                                   7777776666655566667557777788888888999888887754455679*********77777777776.79999*** PP

                        ATPase 151 lkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte 221
                                   +k  +   i+v e +++++  +   +++ + dg+i ++ ++ +++  R l i     t+  +k + feI+ 
  gi|91773389|ref|YP_566081.1| 162 VKAAKAFGIFVVE-DETHDPQTVATLKQ-LFDGMIEIK-ETDSGHALRLLGI-----TPKPTKWYDFEING 224
                                   *************.66678888889999.*******99.5555677777776.....45555666666655 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.73   2.2e+03      14      35 ..      45      66 ..      34      76 .. 0.64
   2 !   18.8   0.0   3.5e-07     0.001      65     136 .]     117     190 ..      85     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.73
                        DUF835 14 dlvkegvkvlaitRenpkkire 35
                                   l++ ++++++ tRe+ + i e
  gi|91773389|ref|YP_566081.1| 45 GLKNMESSIIVSTRETGERILE 66
                                  4555556777778887776655 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 3.5e-07
                        DUF835  65 tetivkflkeaekg..vvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136
                                    + +++fl ++e+      i +l  ++++++ ++v++fl+    +v + +++ i+v++ e+ +++ +a Lk+ f
  gi|91773389|ref|YP_566081.1| 117 GQYLEEFLVQKESPglRLCINSLSTILMYSNLQTVFRFLHVYTGRVKAAKAFGIFVVEDETHDPQTVATLKQLF 190
                                   4556666666666677889***************************************************9877 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3      0.48   1.4e+03      22      36 ..       7      20 ..       6      27 .. 0.72
   2 !   18.9   0.0   2.3e-07   0.00069     185     282 ..     110     197 ..      37     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.48
                        PAXNEB 22 GtpsLDklLgGGLpl 36
                                  G+++LD+l+gG +  
  gi|91773389|ref|YP_566081.1|  7 GIKELDDLIGG-VRE 20
                                  999******66.443 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.3e-07
                        PAXNEB 185 ssllnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarss 265
                                   + +  ++ q l++   +++++   lR++i+sL   l+       s+ +++++FLh   + ++  ++  +  +  + +  ++
  gi|91773389|ref|YP_566081.1| 110 TGIGVRMGQYLEEFLVQKESP--GLRLCINSLSTILM------YSNLQTVFRFLHVYTGRVKAAKAFGIFVVEDETH--DP 180
                                   555556666666655555555..79************......369*****************************99..** PP

                        PAXNEB 266 slvrkieqlvDtvieLe 282
                                   + v  ++ql+D++ie++
  gi|91773389|ref|YP_566081.1| 181 QTVATLKQLFDGMIEIK 197
                                   **************986 PP

>> AAA_35  AAA-like 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    0.0045      29     164 ..      19     166 ..      17     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-06
                        AAA_35  29 kpGalirikapkkmGKtSLlarilakakqqgyktvsldlqladkeils..dldkf...lrw..fcanvsrqLklen....k 98 
                                   ++G+ + + +p   GK  L+++i+++  ++  +++ ++ +++ ++il+  +l+ f        +   v++ L++++    +
  gi|91773389|ref|YP_566081.1|  19 REGTNLMLIGPPMCGKDELINKIVHTGLKNMESSIIVSTRETGERILEwfSLNDFdveTANlgIVDCVTKTLGISTqdtaQ 99 
                                   5688888899999*****************************999976444555421133311445689999998533345 PP

                        AAA_35  99 ldeyWd..eelgskvsctayleeylLkeidkplvLaldevdrlfeypeiakdflslLRswheeaknke 164
                                   ++      +  g  v+  +ylee+l ++ +  l L+++ +++++ y+++ + +++ L+++  + k  +
  gi|91773389|ref|YP_566081.1| 100 IKRAASpvDLTGIGVRMGQYLEEFLVQKESPGLRLCINSLSTILMYSNL-QTVFRFLHVYTGRVKAAK 166
                                   66555555788999**********************************9.688999999888777655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.044       5      79 ..       7      80 ..       5     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                  STHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  5 gfkdLDkltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskkl 79
                                  g k+LD+l++G+++g+ +++ + p +Gk  l  +i+++  ++ +   +++s   + e++++ +  ++ ++++ +l
  gi|91773389|ref|YP_566081.1|  7 GIKELDDLIGGVREGTNLMLIGPPMCGKDELINKIVHTGLKNMES-SIIVSTRETGERILEWFSLNDFDVETANL 80
                                  789*************99******************998875554.55556655666666655555555555555 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.5e-05     0.074       1      49 [.       7     112 ..       7     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                                   SSHHHHHHS-EB.TT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEE............................... CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx............................... RF
                   ATP-synt_ab   1 GirvlDalfpiv.qGqrtlipgafgvGktvisqslskqsnsdd.aiiyvg............................... 48 
                                   Gi+ lD l+  v +G +++++g   +Gk ++++++++   ++   +i+v                                
  gi|91773389|ref|YP_566081.1|   7 GIKELDDLIGGVrEGTNLMLIGPPMCGKDELINKIVHTGLKNMeSSIIVStretgerilewfslndfdvetanlgivdcvt 87 
                                   78889988876515888999*************999986555347788873444444444444444444444444444444 PP

                                   ........................E CS
                                   ........................x RF
                   ATP-synt_ab  49 ........................i 49 
                                                           i
  gi|91773389|ref|YP_566081.1|  88 ktlgistqdtaqikraaspvdltgI 112
                                   4444444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.44
# Mc/sec: 1589.77
//
Query:       gi|91773390|ref|YP_566082.1|  [L=177]
Description: molybdopterin binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  117.4   0.2    4.4e-34  117.2   0.2    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 !  117.2   0.2   2.4e-38   4.4e-34       1     143 [.      19     170 ..      19     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 2.4e-38
                                   EEEEE-HHHH........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH.HHHHHTSSEEEEESS-SSSTT- CS
                 MoCF_biosynth   1 avitvGdell........sgkieDtngpllaellkelgvevskytvvpDdeeeikeal.laaleeadviittGGtGptpdD 72 
                                   a+i+++++++        +  ++D +g+++++l++e g+++ +y +v D+ ++ikea+ +a l++ad++ittGGtG+tp D
  gi|91773390|ref|YP_566082.1|  19 AIISISTSRYekygsgtsPVGADDISGKIMMDLVEENGHNLVDYCLVSDEMSAIKEAVtEAILKGADIVITTGGTGLTPSD 99 
                                   79********777755553335************************************64445666*************** PP

                                   -HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                 MoCF_biosynth  73 vtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpale 143
                                   vt e + ++fek+++gf+e+fr  s ++     ++p+++l ra      g+ +++LPGsp+av+ al +i+lp++ 
  gi|91773390|ref|YP_566082.1| 100 VTIESIVPMFEKQMPGFGELFRYKSTEQ-----IGPAVMLTRADagimgGSAVFCLPGSPGAVELALSKIILPEVG 170
                                   ***************************8.....*********99****6556*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1189.05
//
Query:       gi|91773391|ref|YP_566083.1|  [L=172]
Description: 50S ribosomal protein L10e [Methanococcoides burtonii DSM 6242]
Scores for 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  112.9   0.7    1.2e-32  112.6   0.7    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 !  112.6   0.7   6.9e-37   1.2e-32       2     132 .]      13     163 ..      12     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 6.9e-37
                                   XSSXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXX CS
                 Ribosomal_L16   2 krkkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfph 70 
                                   k + +++++  y+ gv+ ++  ++++g+        + L a e++q++++aleaari++nr +++  g+   ++++rv+ph
  gi|91773391|ref|YP_566083.1|  13 KSRSFTRRK--YMGGVPgSQVIHFDMGNktadfpvkITLLADERCQIRHTALEAARITANRAMTTAAGRsgfHMKLRVYPH 91 
                                   567788888..***********************9999**************************88777889********* PP

                                   EEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                 Ribosomal_L16  71 hpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpiktkiv 132
                                    +++++     ag+dR+++G+    Gk   ++arv++ q if+i  ++ +  iak+alrra +Klp+++ iv
  gi|91773391|ref|YP_566083.1|  92 EVLRENkqatgAGADRVSSGMraayGKNVSTAARVSARQKIFTIsVNKEHFIIAKDALRRAGQKLPTPVTIV 163
                                   ********************************************42223566****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1274.99
//
Query:       gi|91773392|ref|YP_566084.1|  [L=202]
Description: translation initiation factor IF-2 subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  132.5   0.0    8.6e-39  132.0   0.0    1.2  1  eIF-5_eIF-2B    Domain found in IF2B/IF5
    6.4e-11   42.1   0.4    1.3e-10   41.1   0.4    1.6  1  TRAM            TRAM domain
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.023   14.3   0.0    1.3  1  YscJ_FliF       Secretory protein of YscJ/FliF family
       0.09   12.7   0.0       0.47   10.4   0.0    2.0  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
       0.21   12.0   1.2       0.48   10.8   1.4    1.6  1  ZF-HD_dimer     ZF-HD protein dimerisation region


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 !  132.0   0.0   2.4e-42   8.6e-39       5     117 .]      19     129 ..      16     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 2.4e-42
                                   CSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHH CS
                  eIF-5_eIF-2B   5 edkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyie 85 
                                   e+++ r+ +p++++ +egk +tv++Nf++ia+ Lnrdp+h++kyl++e+gt++++ e++r+i++gkf ++++++ +d+y+e
  gi|91773392|ref|YP_566084.1|  19 ETTDVRFVIPEPRIFIEGK-TTVLENFANIADVLNRDPDHLMKYLTREMGTAAKL-EGSRAIFQGKFPKENIKSNIDAYVE 97 
                                   56778**************.***********************************.999********************** PP

                                   HHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                  eIF-5_eIF-2B  86 eyVlCkeCkspetelekeerllvlkCkaCgak 117
                                   eyV+C+eC++p+t+l+k++r+++lkC+aCga+
  gi|91773392|ref|YP_566084.1|  98 EYVICSECNRPDTQLVKSDRVIILKCSACGAH 129
                                   ******************************85 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.4   3.6e-14   1.3e-10       3      60 ..     147     200 ..     145     202 .] 0.96

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.6e-14
                                   XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEE CS
                          TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGe 60 
                                   ++G+++eV +  ++ s+g+gi+++  ++++fvpg+ +  Gd++++kI++   + +++e
  gi|91773392|ref|YP_566084.1| 147 EEGEEYEVRIDAVG-SKGDGIAKLA-KFTIFVPGATK--GDVLKIKIKRISGNLAFAE 200
                                   79************.**********.***********..****************998 PP

>> YscJ_FliF  Secretory protein of YscJ/FliF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.5e-06     0.023     109     141 ..       5      37 ..       2      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-06
                     YscJ_FliF 109 egeLartiesldgVesArVhlalPeksvfvreq 141
                                   e+ L r ie+l +Ve  +V  ++Pe ++f++ +
  gi|91773392|ref|YP_566084.1|   5 ETMLNRAIENLPDVETTDVRFVIPEPRIFIEGK 37 
                                   889**************************9865 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 ?   10.4   0.0   0.00013      0.47      47      73 ..       1      27 [.       1      29 [. 0.95
   2 ?   -0.4   0.0      0.33   1.2e+03      40      63 ..      48      71 ..      44      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                  HHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                AsnC_trans_reg 47 lealerflreklaslpgvartetsivl 73
                                  ++++e+ l++ + +lp+v+ t+  +v+
  gi|91773392|ref|YP_566084.1|  1 MDDYETMLNRAIENLPDVETTDVRFVI 27
                                  89*********************9996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                                  EEEEESSHHHHHHHHHHTTTTSTT CS
                AsnC_trans_reg 40 lkvvvrdlealerflreklaslpg 63
                                  + v  rd ++l + l +++++   
  gi|91773392|ref|YP_566084.1| 48 ADVLNRDPDHLMKYLTREMGTAAK 71
                                  567889999999999888776655 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 ?   10.8   1.4   0.00013      0.48      37      53 ..     120     136 ..     102     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                   ZF-HD_dimer  37 aLkCaaCgChrnFHrre 53 
                                    LkC aCg hr   +r+
  gi|91773392|ref|YP_566084.1| 120 ILKCSACGAHRPVKKRR 136
                                   69*********877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1427.71
//
Query:       gi|91773393|ref|YP_566085.1|  [L=81]
Description: hypothetical protein Mbur_1424 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-05   24.8   0.0    1.3e-05   24.7   0.0    1.0  1  ATPase    KaiC


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 !   24.7   0.0   7.3e-10   1.3e-05       3      73 ..       6      77 ..       5      81 .] 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.3e-10
                        ATPase  3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa.edlrenakslGwd 73
                                  t I+++ e++ +   ++ ++l+tG+  +G  +f  qFl++g+   ge   + t+e ++ + ++ + ++lG d
  gi|91773393|ref|YP_566085.1|  6 TSIPEFHELIGNEALDNDAILLTGGLESGIATFKVQFLYEGVIGNGELKAYRTIENKEaHRIQPDEQTLGED 77
                                  99********99999****************************99**********98845566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 593.15
//
Query:       gi|91773394|ref|YP_566086.1|  [L=403]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-14   54.0   0.1    3.8e-14   53.4   0.1    1.3  1  Radical_SAM      Radical SAM superfamily
    3.9e-07   30.5   0.2    9.7e-07   29.2   0.2    1.7  1  SPASM            Iron-sulfur cluster-binding domain
    0.00098   19.4   0.0     0.0021   18.3   0.0    1.5  1  Fer4_12          4Fe-4S single cluster domain
     0.0015   18.7   0.1     0.0042   17.2   0.1    1.7  1  Fer4_14          4Fe-4S single cluster domain
  ------ inclusion threshold ------
        0.1   12.1   0.1        1.6    8.2   0.1    2.0  1  Peripla_BP_4     Periplasmic binding protein domain
        0.1   12.6   0.0       0.32   11.1   0.0    1.7  2  QCR10            Ubiquinol-cytochrome-c reductase complex sub
       0.11   12.7   0.0       0.21   11.8   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.12   12.2   0.0       0.21   11.4   0.0    1.4  1  POT1             Telomeric single stranded DNA binding POT1/C
       0.12   11.7   0.0       0.36   10.1   0.0    1.7  2  Methyltrans_RNA  RNA methyltransferase
       0.18   11.6   0.1       0.45   10.3   0.1    1.7  1  IDEAL            IDEAL 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 !   53.4   0.1   2.1e-17   3.8e-14       2     166 ..     109     261 ..     108     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.1e-17
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                   ++tr Cn +C +C+ +      g + +l++  i++ ++e+  ++g+ +++++ g+pll+ d+ el+e   k    +  + +
  gi|91773394|ref|YP_566086.1| 109 EITRNCNCNCEHCIMS------GGEGDLDTATIKKAIDEA-LDMGAVVITFTEGDPLLREDIFELIEYVDKD---KAIVNI 179
                                   79**************......688888999999999999.7999*************99997777777776...****** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleel 163
                                    t+gt  ++e++++l++ g+  + +++ ++ +e++    + ++ fe+   a+++  +ag+   v++++     n+++le +
  gi|91773394|ref|YP_566086.1| 180 YTPGTEMTPEVAQKLKDTGLHNLLVSIYSTVPEEHDSVRKLKGAFEKATGAIKYGLDAGLL--VTMCTHASPKNMKKLESM 258
                                   *********************************666666699****************999..455554444677777776 PP

                                   HHH CS
                                   xxx RF
                   Radical_SAM 164 lel 166
                                   +++
  gi|91773394|ref|YP_566086.1| 259 YQF 261
                                   665 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.2   5.4e-10   9.7e-07       1      53 [.     322     369 ..     322     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.4e-10
                         SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefr 53 
                                   C+a++r l + ++G V pC  +  ++  ++++Gni+++sl++Iw++  +  +f+
  gi|91773394|ref|YP_566086.1| 322 CMAGQRWLHVCVEGSVKPC--P--YI--PFSFGNIQTDSLRSIWSKIrKVSDFK 369
                                   999****************..2..34..6***************6544444455 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 !   18.3   0.0   1.2e-06    0.0021      12      93 ..     111     183 ..     103     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                   +  Cn +C+ C+        ++ + ++++++++i+++ +     +t++ G+Pll   +e++ el+++v + k   + + + 
  gi|91773394|ref|YP_566086.1| 111 TRNCNCNCEHCI-----MSGGEGDLDTATIKKAIDEALDMGAVVITFTEGDPLL---REDIFELIEYVDKDKA-IVNIYTP 182
                                   568*******99.....455666788899999999999****************...9999999999999887.4445444 PP

                       Fer4_12  93 g 93 
                                   g
  gi|91773394|ref|YP_566086.1| 183 G 183
                                   5 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.4e-06    0.0042       5      92 ..     111     186 ..     108     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwl 85 
                                   +  Cn++C  C  +       +   +  ++++ +  +++ ++ +  +++t G+PL+    +++++l++++ + +    + +
  gi|91773394|ref|YP_566086.1| 111 TRNCNCNCEHCIMSG-----GEGDLDTATIKKAI--DEALDMGAVVITFTEGDPLLR---EDIFELIEYVDKDK--AIVNI 179
                                   568********9777.....44444555666777..55666777889********55...99**********99..99999 PP

                       Fer4_14  86 etngtle 92 
                                   +t gt +
  gi|91773394|ref|YP_566086.1| 180 YTPGTEM 186
                                   9999877 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 ?    8.2   0.1    0.0009       1.6     178     210 ..     166     202 ..     120     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0009
                                   HHH...TTT.ECEEEESSCCHHHCHHHHHHHTTTTST CS
                  Peripla_BP_4 178 llt...anp.ldgilaandgmaegalealeaaglagk 210
                                   l+    +++ ++ i++++++m++ ++++l+++gl + 
  gi|91773394|ref|YP_566086.1| 166 LIEyvdKDKaIVNIYTPGTEMTPEVAQKLKDTGLHNL 202
                                   3334545545999******************999776 PP

>> QCR10  Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.32      23      49 ..     145     171 ..     142     173 .. 0.89
   2 ?   -3.2   0.0         5     9e+03      10      35 ..     224     249 ..     220     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                         QCR10  23 agvavlfftsgvPrvqkdiLqkiPvig 49 
                                    g+ v++ft+g P+ ++di++ i +++
  gi|91773394|ref|YP_566086.1| 145 MGAVVITFTEGDPLLREDIFELIEYVD 171
                                   5899****************9998776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5
                         QCR10  10 trygptlalfGgaagvavlfftsgvP 35 
                                   ++ ++ ++ +G  ag  v + t   P
  gi|91773394|ref|YP_566086.1| 224 FEKATGAIKYGLDAGLLVTMCTHASP 249
                                   55666677788888887777776666 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 ?   11.8   0.0   0.00011      0.21      43     112 ..     133     202 ..     111     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEE CS
                 NAD_binding_2  43 akaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspedtrelakelkekglkfl 112
                                   a++ + i e+++   vvit+ + ++  +e i++l+e+++k++ +++  t   e t e+a++lk++gl+ l
  gi|91773394|ref|YP_566086.1| 133 ATIKKAIDEALDMGAVVITFTEGDPLLREDIFELIEYVDKDKAIVNIYTPGTEMTPEVAQKLKDTGLHNL 202
                                   444444555555559999999999999***************************************9865 PP

>> POT1  Telomeric single stranded DNA binding POT1/CDC13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.21       7      86 ..     135     207 ..     129     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                   HT.CTTEEEEEEEEEEEEEECCCSCCEEEEECCCCCTTTSCCHCTTTEEEEEEEECCCCCCCCGGCCCCEEECCCCEEEES CS
                          POT1   7 ae.aekkvvnviGvVidasfpkktggsdyvctfkivDpsknkgdendglrvvlFsknfedLpivkkvgdiirlhraklqsy 86 
                                   ++ a     ++ +vVi+++ + ++  +d +++++ vD++        ++ v+++ +  e  p+v++  ++  lh++ ++ y
  gi|91773394|ref|YP_566086.1| 135 IKkAIDEALDMGAVVITFTEGDPLLREDIFELIEYVDKD--------KAIVNIYTPGTEMTPEVAQKLKDTGLHNLLVSIY 207
                                   445667777889***************************........********************99999999988876 PP

>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.6   2.9e+03     177     197 ..     119     139 ..      93     152 .. 0.69
   2 ?   10.1   0.0    0.0002      0.36      68      95 ..     247     275 ..     240     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                   EEEEEE--TT---HHHHHHHH CS
               Methyltrans_RNA 177 kvlliiGPEGGfsekEiellk 197
                                   + +++ G EG + ++ i+++ 
  gi|91773394|ref|YP_566086.1| 119 EHCIMSGGEGDLDTATIKKAI 139
                                   566777777777766665554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                                   E--SS.HHHHHHHHHHHHTT-SEEEEEE- CS
               Methyltrans_RNA  68 alpkg.dklelilqkatElGvseivplis 95 
                                   a pk+ +kle + q atElGv+e+ ++ s
  gi|91773394|ref|YP_566086.1| 247 ASPKNmKKLESMYQFATELGVHEFSLWES 275
                                   6677779******************9986 PP

>> IDEAL  IDEAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00025      0.45      13      25 ..     134     146 ..     131     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                         IDEAL  13 kLlreIDeALdnr 25 
                                   ++++ IDeALd++
  gi|91773394|ref|YP_566086.1| 134 TIKKAIDEALDMG 146
                                   799********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3297.75
//
Query:       gi|91773395|ref|YP_566087.1|  [L=432]
Description: tryptophanyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-36  126.5   0.0    1.2e-20   74.0   0.0    2.0  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   6.7e-25   1.2e-20       2     177 ..      62     231 ..      60     251 .. 0.89
   2 !   50.7   0.0   8.7e-18   1.6e-13     145     292 ..     267     413 ..     265     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 6.7e-25
                                   HHS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHH.HHHHHHHHHHHHHTCH CS
                  tRNA-synt_1b   2 kerplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkre.evlenaikaqlakgld 81 
                                   +++p++v+sG++PTg  HlG+ ++++ +++ qk+g ++f+ iaD +A+ ++    ++ k r+   e++  +   ++a g++
  gi|91773395|ref|YP_566087.1|  62 NKEPFSVMSGFMPTGGGHLGHKMVMEEIIWHQKMGADAFVGIADREAYSVRGI--SWDKCRQIGiEDYIVS---LIALGFE 137
                                   589************************************************99..7888887651555555...9****** PP

                                   TTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.S.C--BHHHHHHHHHHHHHHHHTCHSEEEEEGGG CS
                  tRNA-synt_1b  82 pekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.g.egislgeftYplLqaaDilllkadlvpgGsDQ 160
                                   p + ++++qse  + ++la  l+  +++ +l+ ++ f   ++++++      + ++++ p+L ++     k+++ p+G DQ
  gi|91773395|ref|YP_566087.1| 138 P-DGHIYFQSESENVKDLAFELSAKANFSELSAIYGFSG-ETNVAHmVsAITQSADILQPQLSEYGGP--KPTVIPVGADQ 214
                                   *.789**********************************.888888644677899***********99..9********** PP

                                   HHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 161 kqnielgrdlarrfnkk 177
                                   + +++l+r la ++n  
  gi|91773395|ref|YP_566087.1| 215 DPHMRLTRGLAHKMNMF 231
                                   ************99865 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 8.7e-18
                                   HHHHTCHSEEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHC CS
                  tRNA-synt_1b 145 DilllkadlvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqka 225
                                   D  l++ ++ + G D +  +  ++  ++  n   +f +p+++++++++gl+G+ KmS+S ++s I L ++++ + kk+++a
  gi|91773395|ref|YP_566087.1| 267 DTKLFEGHIDIYGADDYNKLLETVREVEIENGGYAFVPPSSTYHRFMSGLQGG-KMSSSVPESLISLKEDPKLAAKKVKRA 346
                                   66666667778888888877777777777777789******************.*************************** PP

                                   HCSTTC..SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 226 vtdsde..evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                   +t  +   e +k l +    +  ++e l+ ++ +++ +e+ e++ e+v ++ ++g++k  ++e ++e+l
  gi|91773395|ref|YP_566087.1| 347 KTGGRVslEEQKKLGGEADKCS-VYELLMFHLVEND-NELAEIYDECVCGKRMCGTCKALASELMEEFL 413
                                   ******6666677777777777.9*******99999.9****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3427.99
//
Query:       gi|91773396|ref|YP_566088.1|  [L=493]
Description: phenylalanyl-tRNA synthetase subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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-93  311.0   0.0    7.3e-93  310.6   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    1.6e-09   37.5   0.0    2.5e-06   27.1   0.0    2.5  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00078   18.6   0.4      0.031   13.4   0.1    2.9  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0055   16.5   0.1       0.81    9.6   0.0    3.0  3  DUF1495          Winged helix DNA-binding domain (DUF1495)
  ------ inclusion threshold ------
      0.079   13.1   0.3        7.1    6.8   0.1    2.8  2  Mrr_N            Mrr N-terminal domain
       0.14   12.2   1.5          1    9.4   0.3    2.5  2  HTH_45           Winged helix-turn-helix
       0.19   11.7   0.2       0.56   10.1   0.1    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm


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 !  310.6   0.0   2.8e-96   7.3e-93       2     244 ..     218     485 ..     217     486 .. 0.98

  Alignments for each domain:
  == domain 1  score: 310.6 bits;  conditional E-value: 2.8e-96
                                   .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-...... CS
                  tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka...... 76 
                                   ++++ p k+++ +k+hp++++++++++ifle+gf+e++g+ v+s+f+nfdaL++pqdhpaR+mqdtF l+++++       
  gi|91773396|ref|YP_566088.1| 218 YNIQTPPKPVYGAKIHPYQRLIDQMRQIFLEMGFTEIKGDVVQSSFWNFDALFQPQDHPAREMQDTFHLDTKSELpekyke 298
                                   89*******************************************************************6666669***** PP

                                   ........................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEE CS
                  tRNA-synt_2d  77 ........................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqveglvv 132
                                                           ++++ +LRthttav+i++l ++++pp+k ++i+r++Rr+++D th++eF q+eg+++
  gi|91773396|ref|YP_566088.1| 299 girdmhehggdlqstgwggkwsedIAKRDVLRTHTTAVTIKYLtDNPNPPVKAFCIDRAYRRETIDPTHTPEFEQLEGVIM 379
                                   ************************999****************9999********************************** PP

                                   ETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEE CS
                  tRNA-synt_2d 133 denvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfa 213
                                   den+s+a+l+g+lee+++++ g+e +vrfrp yfp+tePs+e +vy+  ++ +w+El+gaG++r+ev+e++gi  +++++a
  gi|91773396|ref|YP_566088.1| 380 DENMSFANLLGCLEEFYHRM-GFE-DVRFRPGYFPYTEPSVEPEVYI--EGLGWVELGGAGVFRKEVTEPLGI--KQPVLA 454
                                   ********************.***.**********************..************************..****** PP

                                   EEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                  tRNA-synt_2d 214 fGlGveRlamlkygieDiRelvendlrflrq 244
                                   +GlGv R+amlk+g++D+Rel++ d+++lr+
  gi|91773396|ref|YP_566088.1| 455 WGLGVSRVAMLKLGLKDLRELYQADIDWLRK 485
                                   ****************************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 !    7.7   0.0   0.00082       2.1       5      38 ..     223     255 ..     220     283 .. 0.75
   2 !   27.1   0.0   9.7e-10   2.5e-06      76     209 ..     331     454 ..     324     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00082
               tRNA_synthFbeta   5 lPkapttegelnkeqklrrklrdllagaGlnEvi 38 
                                    Pk + + ++ ++ q+l +++r++  ++G++E+ 
  gi|91773396|ref|YP_566088.1| 223 PPKPVYG-AKIHPYQRLIDQMRQIFLEMGFTEIK 255
                                   4454445.5599********************84 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 9.7e-10
               tRNA_synthFbeta  76 tsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealle 155
                                   t  ++  ++   +  ++ n+ v++F i + ++ +  + +   e ++l +v++ ++           ++f++l g +e++  
  gi|91773396|ref|YP_566088.1| 331 THTTAVTIK---YLTDNPNPPVKAFCIDRAYRREtIDPTHTPEFEQLEGVIMDEN-----------MSFANLLGCLEEFYH 397
                                   555554444...44556788899***********87778899*************...........*************** PP

               tRNA_synthFbeta 156 slgiekvefepaehpalhpgrsAeikvdgk...evGvlGelhpevleafdlkqrvyv 209
                                   ++g+e+v+f+p   p+ +p    e++++g    e+G +G + +ev e +++kq+v +
  gi|91773396|ref|YP_566088.1| 398 RMGFEDVRFRPGYFPYTEPSVEPEVYIEGLgwvELGGAGVFRKEVTEPLGIKQPVLA 454
                                   ***************************885555*********************986 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 ?    1.2   0.0      0.06   1.5e+02      25      49 ..     235     259 ..     217     272 .. 0.81
   2 !   13.4   0.1   1.2e-05     0.031      93     120 ..     350     376 ..     349     399 .. 0.80
   3 ?   -1.0   0.0      0.29   7.4e+02     287     307 ..     455     475 ..     451     477 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.06
                                   HHHHHHHHHHHHHHTT-EE----SE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  25 rstvtkavrkyleengfieietPiL 49 
                                    +++++++r+++ e gf+ei+  ++
  gi|91773396|ref|YP_566088.1| 235 YQRLIDQMRQIFLEMGFTEIKGDVV 259
                                   578899**************86555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.2e-05
                                   EEEEEEEEE--S--BTTB-S-CEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqiea 120
                                   + f+i ra+R E ++ ++ + EF q+e 
  gi|91773396|ref|YP_566088.1| 350 KAFCIDRAYRRETIDPTHTP-EFEQLEG 376
                                   68******************.****984 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.29
                                   EEEEHHHHHHHHCT-SSGGGC CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                   +glG++R+ ml lg+++ r++
  gi|91773396|ref|YP_566088.1| 455 WGLGVSRVAMLKLGLKDLREL 475
                                   79**************99986 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00032      0.81      50      88 ..      37      73 ..      24      74 .. 0.90
   2 ?    2.8   0.0     0.041   1.1e+02      54      88 ..     156     188 ..     142     189 .. 0.78
   3 ?   -0.8   0.0      0.55   1.4e+03      32      54 ..     378     400 ..     366     411 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                       DUF1495 50 gkrynsessLielGLveeeeeseglklYklteeGieive 88
                                  ++ ++s+ sL e GL e    +  +++Y+lt eG++++e
  gi|91773396|ref|YP_566088.1| 37 ETAMQSAFSLSENGLTE--VTDVVTEIYSLTSEGRTYAE 73
                                  5678999********96..6899999**********998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.041
                       DUF1495  54 nsessLielGLveeeeeseglklYklteeGieive 88 
                                   n+ + Li++ L +  + ++ +++ ++t+eG+++v+
  gi|91773396|ref|YP_566088.1| 156 NTINDLIKRKLLS--KTEDKYRTVSITDEGRQLVK 188
                                   5566788888885..578889999********997 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.55
                       DUF1495  32 srrvrskpsnvkGaleGmgkryn 54 
                                   + + +++  n+ G+le + +r+ 
  gi|91773396|ref|YP_566088.1| 378 IMDENMSFANLLGCLEEFYHRMG 400
                                   555677889******98888876 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.032        81      57      85 ..      42      72 ..       8      74 .. 0.71
   2 ?    6.8   0.1    0.0028       7.1      59      86 ..     159     188 ..     157     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.032
                         Mrr_N 57 artyLkkagllespk..rgvwkiTekGrevl 85
                                      L++ gl e ++    ++++T +Gr++ 
  gi|91773396|ref|YP_566088.1| 42 SAFSLSENGLTEVTDvvTEIYSLTSEGRTYA 72
                                  4456888899888888899999999999875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0028
                         Mrr_N  59 tyLkkagllespk..rgvwkiTekGrevlk 86 
                                   ++L k +ll++++    +++iT++Gr+++k
  gi|91773396|ref|YP_566088.1| 159 NDLIKRKLLSKTEdkYRTVSITDEGRQLVK 188
                                   678999999998866888*********986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.18   4.7e+02      43      67 ..      46      73 ..      13      76 .. 0.75
   2 ?    9.4   0.3   0.00039         1      38      69 ..     156     190 ..     152     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.18
                        HTH_45 43 Lvekgl..ikk.skekYvlTekGlelle 67
                                  L e+gl  +++  +e Y+lT +G+ + e
  gi|91773396|ref|YP_566088.1| 46 LSENGLteVTDvVTEIYSLTSEGRTYAE 73
                                  67777744333367889****9998765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00039
                        HTH_45  38 kYLdmLvekglikkskekYv...lTekGlellekl 69 
                                   + ++ L++++l++k+++kY+   +T++G++l+++ 
  gi|91773396|ref|YP_566088.1| 156 NTINDLIKRKLLSKTEDKYRtvsITDEGRQLVKTG 190
                                   56999*******999999964448*******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 ?   10.1   0.1   0.00022      0.56       3      63 ..       3      63 ..       1      66 [. 0.92
   2 ?   -3.4   0.0       3.6   9.2e+03      30      45 ..     149     164 ..     147     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                  HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                          TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                  +++L+ ++  v +a+ +l + t +e+ae++     ++ ++  sL++ Gl e+ +  + +Y+
  gi|91773396|ref|YP_566088.1|  3 DYNLTNNDKNVLIAMDELSSTTPEELAEKTSMKVETAMQSAFSLSENGLTEVTDVVTEIYS 63
                                  799**********************************************999988777776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
                                   CCTTSSCHCHHHHHHH CS
                          TrmB  30 eelgvprskvYevLrs 45 
                                   ee+g +++++++ +++
  gi|91773396|ref|YP_566088.1| 149 EEIGTDQNTINDLIKR 164
                                   6677777888777653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3792.07
//
Query:       gi|91773397|ref|YP_566089.1|  [L=379]
Description: hypothetical protein Mbur_1428 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-48  163.8   0.3    7.3e-48  163.5   0.3    1.1  1  DUF362    Domain of unknown function (DUF362)
    1.5e-08   34.1  11.9    0.00024   20.8   4.4    2.4  2  Fer4      4Fe-4S binding domain
      8e-06   26.4  11.6    1.6e-05   25.4  11.6    1.6  1  Fer4_7    4Fe-4S dicluster domain
      1e-05   25.3  13.1     0.0055   16.7   2.2    2.6  2  Fer4_2    4Fe-4S binding domain
    3.8e-05   23.7  11.5    6.5e-05   23.0  11.5    1.4  1  Fer4_21   4Fe-4S dicluster domain
    0.00023   21.1  11.6     0.0016   18.4   0.9    2.4  2  Fer4_6    4Fe-4S binding domain
    0.00034   20.7  13.0    0.00058   20.0  13.0    1.4  1  Fer4_9    4Fe-4S dicluster domain
      0.001   19.1  14.4     0.0035   17.4  14.8    1.7  2  Fer4_10   4Fe-4S dicluster domain
      0.009   16.5   8.0        0.6   10.7   2.3    2.3  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.037   15.0  12.0        1.2   10.1   3.0    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
       0.08   13.7   8.4       0.19   12.5   0.5    2.6  2  Fer4_15   4Fe-4S single cluster domain
       0.15   11.2   0.1       0.21   10.7   0.1    1.2  1  Lar_N     Lactate racemase N-terminal domain
       0.26   12.3  19.1        1.9    9.6   6.8    2.5  2  Fer4_3    4Fe-4S binding domain
       0.37   11.0   6.3        1.4    9.1   6.2    1.9  2  Fer4_18   4Fe-4S dicluster domain
       0.77    9.9   4.6        1.1    9.4   3.6    1.8  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
        1.3    9.7  16.3        1.3    9.7   2.1    2.4  2  Fer4_4    4Fe-4S binding domain
        3.9    8.1  11.2        6.4    7.4   4.0    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        6.2    7.3  17.6         12    6.5   5.7    2.3  3  Fer4_8    4Fe-4S dicluster domain


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 !  163.5   0.3   7.3e-51   7.3e-48       1     202 [.      42     243 ..      42     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 163.5 bits;  conditional E-value: 7.3e-51
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                        DUF362   1 VaiKpNlgeagnpe.gatthpevvravvellkeagagkiivgdspglyvsrgkahrevaeeagydelae..gadiadgleg 78 
                                   V++KpN++ a +pe ++tthp++v+a++el+ eag g +i+gd+ g++    + ++e+++ +g++e+a+  ga++ + +++
  gi|91773397|ref|YP_566089.1|  42 VLLKPNVLAAVPPEkAVTTHPSIVEAMCELVIEAG-GVPIIGDGAGITH--PGVTDEALDISGIREAAQraGAEVLNFETS 119
                                   99******9999999******************99.99********732..24489**********999777788888888 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF362  79 edevvvpvkgkhlkkelkiakavleaDviInlpklKgHalagvtgalKnlfGcisgsgkaeiHskrdsekfaekiadlaka 159
                                    ++ v+ v+  +l++ ++ ak+vleaDv+I+lpklK+H+l+++tga+Kn+fG ++ + +++ H   + + fa++++d++++
  gi|91773397|ref|YP_566089.1| 120 GYISVDVVNSVQLSH-IYYAKPVLEADVVISLPKLKTHELTKYTGAVKNMFGGLPLKFRKQAHVLGKIDLFADALVDVYSV 199
                                   878777776657777.***********************************************433599************ PP

                                   .xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                        DUF362 160 .lkpdlnvvdgikamegegpsggs.kelglvlaStDpvalDaaaa 202
                                    + p+l+v+dg+ +meg+gp+ g  ++++lv+aS+Dpv lD +a 
  gi|91773397|ref|YP_566089.1| 200 kV-PHLAVMDGVVGMEGNGPALGHpVNSHLVMASFDPVSLDIVAS 243
                                   44.9*************************************9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.8   2.1e-06    0.0021       2      23 ..     311     332 ..     310     333 .. 0.87
   2 !   20.8   4.4   2.4e-07   0.00024       2      23 ..     340     361 ..     339     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    i+++ C+ CG Cv  C   AI
  gi|91773397|ref|YP_566089.1| 311 FINTSSCTLCGSCVLNCSPKAI 332
                                   69***************77777 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.4e-07
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   +i+ ekCi C  C e CP gA 
  gi|91773397|ref|YP_566089.1| 340 QINDEKCILCYCCRELCPSGAV 361
                                   79******************97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4  11.6   1.6e-08   1.6e-05       1      52 []     316     360 ..     316     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.6e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C+ Cg Cv +C+ kaie ++        k++i+ ekC+ C+ C + CP+ga
  gi|91773397|ref|YP_566089.1| 316 SCTLCGSCVLNCSPKAIEQED-------GKLQINDEKCILCYCCRELCPSGA 360
                                   5*****************966.......489*******************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.2   5.5e-06    0.0055       2      20 ..     309     327 ..     309     329 .. 0.92
   2 !   13.4   3.4   6.4e-05     0.064       3      21 ..     339     357 ..     337     358 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.5e-06
                        Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                   +++++t +C+ Cg+Cv +C
  gi|91773397|ref|YP_566089.1| 309 RPFINTSSCTLCGSCVLNC 327
                                   589**************** PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.4e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    +++ ++Ci C  C+  CP
  gi|91773397|ref|YP_566089.1| 339 LQINDEKCILCYCCRELCP 357
                                   6899*************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0  11.5   6.5e-08   6.5e-05       2      59 .]     311     363 ..     310     363 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.5e-08
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                   +i+ ++C  Cg+C++ C+    +aie + + +l++ +++C+ C  C + CP ++++em
  gi|91773397|ref|YP_566089.1| 311 FINTSSCTLCGSCVLNCS---PKAIEQE-DGKLQINDEKCILCYCCRELCP-SGAVEM 363
                                   6999*************9...6999975.66679*****************.699998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   1.6e-06    0.0016       2      24 .]     310     332 ..     309     332 .. 0.90
   2 !    7.2   4.0    0.0059       5.8       3      23 ..     340     360 ..     338     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   + i+ ++C+ Cg Cv +C  +ai
  gi|91773397|ref|YP_566089.1| 310 PFINTSSCTLCGSCVLNCSPKAI 332
                                   789***************97776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0059
                        Fer4_6   3 eidpdkCigCgdCvrvCPega 23 
                                   +i+++kCi C+ C   CP ga
  gi|91773397|ref|YP_566089.1| 340 QINDEKCILCYCCRELCPSGA 360
                                   79*********9999999987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0  13.0   5.9e-07   0.00058       2      50 ..     317     360 ..     316     361 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.9e-07
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   Ct Cg+Cv  C  +++++++++  ++ +     +Ci C  C e Cp+ga
  gi|91773397|ref|YP_566089.1| 317 CTLCGSCVLNCSPKAIEQEDGKLQINDE-----KCILCYCCRELCPSGA 360
                                   ****************999999999974.....6************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  14.8   3.5e-06    0.0035       3      56 .]     311     357 ..     309     357 .. 0.91
   2 !   13.0   4.9   8.4e-05     0.084       2      22 ..     339     359 ..     338     371 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    i++++C+ Cg Cv  C       + k+++ e+++ +++ ekC+ c  C e CP
  gi|91773397|ref|YP_566089.1| 311 FINTSSCTLCGSCVLNC-------SPKAIEQEDGKLQINDEKCILCYCCRELCP 357
                                   6899*************.......4788888889999999*************9 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.4e-05
                       Fer4_10   2 vvidddtCirCgkCvkaCPad 22 
                                   ++i+d++Ci C  C++ CP+ 
  gi|91773397|ref|YP_566089.1| 339 LQINDEKCILCYCCRELCPSG 359
                                   679****************94 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.3    0.0023       2.3      42      57 ..     313     328 ..     300     332 .. 0.85
   2 !   10.7   2.3    0.0006       0.6       1      17 [.     345     361 ..     344     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                       Fer4_17  42 kaslCieCgeCerkCP 57 
                                   + s+C+ Cg C+  C 
  gi|91773397|ref|YP_566089.1| 313 NTSSCTLCGSCVLNCS 328
                                   5789*******99995 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0006
                       Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                   +Ci C +C++ Cps++ 
  gi|91773397|ref|YP_566089.1| 345 KCILCYCCRELCPSGAV 361
                                   69999999999999765 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 ?   10.1   3.0    0.0012       1.2       2      28 ..     317     342 ..     316     346 .. 0.83
   2 ?    8.0   4.0    0.0057       5.6       1      20 [.     345     364 ..     345     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                   C+ Cg C+  C  +ai+++ + +++++
  gi|91773397|ref|YP_566089.1| 317 CTLCGSCVLNCSPKAIEQE-DGKLQIN 342
                                   *****************99.6666655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0057
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C+ C  C e CP++a+++k
  gi|91773397|ref|YP_566089.1| 345 KCILCYCCRELCPSGAVEMK 364
                                   5***************9988 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   0.00019      0.19       3      30 ..     312     339 ..     311     344 .. 0.83
   2 ?    5.0   2.2     0.042        42       3      28 ..     341     367 ..     339     378 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                       Fer4_15   3 vDrdaCigcglCvaea.pevfeldedgla 30 
                                   ++ + C+ cg Cv ++ p+ +e++ dg+ 
  gi|91773397|ref|YP_566089.1| 312 INTSSCTLCGSCVLNCsPKAIEQE-DGKL 339
                                   67889***********99999998.7775 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.042
                       Fer4_15   3 vDrdaCigcglCvaeape.vfeldedg 28 
                                   ++ ++Ci c  C +++p   +e+++  
  gi|91773397|ref|YP_566089.1| 341 INDEKCILCYCCRELCPSgAVEMKSSL 367
                                   7789************75144444455 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00021      0.21     143     182 ..     133     172 ..      50     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                         Lar_N 143 tpveinklvaeadlviltGfiepHyfaGfsGGrKsilpGv 182
                                     ++  k v+ead vi + + + H +  ++G  K ++ G+
  gi|91773397|ref|YP_566089.1| 133 SHIYYAKPVLEADVVISLPKLKTHELTKYTGAVKNMFGGL 172
                                   56888999**************************999875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.4     0.005         5       1      15 []     317     331 ..     317     331 .. 0.94
   2 ?    9.6   6.8    0.0019       1.9       1      15 []     346     360 ..     346     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.005
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   Ct Cg Cv  C ++A
  gi|91773397|ref|YP_566089.1| 317 CTLCGSCVLNCSPKA 331
                                   ***********9887 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C+ C e CP+gA
  gi|91773397|ref|YP_566089.1| 346 CILCYCCRELCPSGA 360
                                   **************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 ?   -3.0   0.0       8.2   8.2e+03      82     103 ..       6      27 ..       3      32 .. 0.74
   2 ?    9.1   6.2    0.0014       1.4      58      96 ..     314     357 ..     308     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.2
                       Fer4_18  82 qleciscllcidacdkvmeklg 103
                                   +++ + c+   da d v e+++
  gi|91773397|ref|YP_566089.1|   6 RVSIVRCTDYSDAKDAVREAIS 27 
                                   5667889999999998888776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                       Fer4_18  58 agdcidcescvkvc.PtgidirkG.lql...eciscllcidacd 96 
                                   ++ c+ c+scv  c P  i+  +G lq+   +ci c  c + c 
  gi|91773397|ref|YP_566089.1| 314 TSSCTLCGSCVLNCsPKAIEQEDGkLQIndeKCILCYCCRELCP 357
                                   678********8887999*****977884445999999988885 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.5   7.4e+03       2      19 ..     121     138 ..     120     163 .. 0.77
   2 ?    9.4   3.6    0.0011       1.1      48      89 ..     318     360 ..     307     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.5
                                   SSS--HHHHHHTTT-B-- CS
                        ETF_QO   2 kltfdklssvflsgtnhe 19 
                                    ++ d ++sv ls+++++
  gi|91773397|ref|YP_566089.1| 121 YISVDVVNSVQLSHIYYA 138
                                   578899999998887654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                                   HH-TTS-EEEEETT.TTSSEEEEE-CCC--S--HHHHH-TT-- CS
                        ETF_QO  48 ryCPagvyeivede.eakekklqinaqnCvhCktCdikdpsqn 89 
                                     C + v ++  ++ e+++ klqin + C+ C  C    ps  
  gi|91773397|ref|YP_566089.1| 318 TLCGSCVLNCSPKAiEQEDGKLQINDEKCILCYCCRELCPSGA 360
                                   5788899999888878999****************86666655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.1    0.0013       1.3       2      15 ..     315     328 ..     314     335 .. 0.89
   2 ?    5.0   6.6     0.041        41       2      17 .]     344     359 ..     343     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   ++C+ CgsCv  C+
  gi|91773397|ref|YP_566089.1| 315 SSCTLCGSCVLNCS 328
                                   58********9996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.041
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   e+Ci C +C+  CP+g
  gi|91773397|ref|YP_566089.1| 344 EKCILCYCCRELCPSG 359
                                   79************85 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 ?    4.6   0.7     0.048        48       1      16 [.     312     327 ..     312     340 .. 0.85
   2 ?    7.4   4.0    0.0064       6.4       1      18 [.     341     358 ..     341     359 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.048
                       Fer4_13   1 VDrdtCiacgaCvela 16 
                                   ++ ++C+ cg+Cv  +
  gi|91773397|ref|YP_566089.1| 312 INTSSCTLCGSCVLNC 327
                                   68899*******9877 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0064
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   ++ ++Ci c  C+el+P 
  gi|91773397|ref|YP_566089.1| 341 INDEKCILCYCCRELCPS 358
                                   677**************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 ?    5.6   4.3     0.021        21      49      61 ..     315     327 ..     312     332 .. 0.74
   2 ?    6.3   5.5     0.013        13      49      63 ..     344     358 ..     328     360 .. 0.71
   3 ?    6.5   5.7     0.012        12       4      18 ..     345     359 ..     342     372 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.021
                        Fer4_8  49 wsCttcgaCtevC 61 
                                    sCt cg+C+ +C
  gi|91773397|ref|YP_566089.1| 315 SSCTLCGSCVLNC 327
                                   5788888888777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                        Fer4_8  49 wsCttcgaCtevCpv 63 
                                   ++C  c +C+e Cp 
  gi|91773397|ref|YP_566089.1| 344 EKCILCYCCRELCPS 358
                                   467777777777775 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.012
                        Fer4_8   4 kCieCgaCqsaCpvl 18 
                                   kCi C +C++ Cp+ 
  gi|91773397|ref|YP_566089.1| 345 KCILCYCCRELCPSG 359
                                   677777777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2788.91
//
Query:       gi|91773398|ref|YP_566090.1|  [L=185]
Description: hypothetical protein Mbur_1429 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-80  269.2   0.0    1.8e-80  269.0   0.0    1.0  1  DUF531         Protein of unknown function (DUF531)
     0.0094   15.3   0.0      0.012   15.0   0.0    1.1  1  SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP


Domain annotation for each model (and alignments):
>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.0   0.0     2e-84   1.8e-80       1     169 [.       1     169 [.       1     170 [. 0.99

  Alignments for each domain:
  == domain 1  score: 269.0 bits;  conditional E-value: 2e-84
                        DUF531   1 mltlglvntYDkkklheaHkRaiARaapicyafdfnLalldFplkkeekelvdvvaekttiGesGkylkelaeknrllvld 81 
                                   mltlgl+ntYDk+k+++aH+RaiARaapicya++++L+l+dFp+k++++elv+++++kttiG sGkylk+l+e+nrl+++d
  gi|91773398|ref|YP_566090.1|   1 MLTLGLINTYDKIKVLDAHYRAIARAAPICYAYGLTLCLFDFPFKMTPEELVEYIMDKTTIGGSGKYLKALHENNRLFIFD 81 
                                   89******************************************************************************* PP

                        DUF531  82 lpkkgfpaqfGevvattskpdekkaitpeevaeeilrkksvllliGlGrkGlPkellklakyhlditekgvslEtctAiga 162
                                   lpkkgf++qfG++v+tts p++k ++tpe++a  ++r++s+llliGlGrkGlPk+l++l+++hldit +g+slEtctA+g+
  gi|91773398|ref|YP_566090.1|  82 LPKKGFQSQFGTAVVTTSMPEDKFTVTPEDIAGGMMRNRSYLLLIGLGRKGLPKKLYSLTDHHLDITCDGISLETCTAMGI 162
                                   ********************************************************************************* PP

                        DUF531 163 iaaviat 169
                                   i+a+i+ 
  gi|91773398|ref|YP_566090.1| 163 IPAYIMG 169
                                   ****986 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-06     0.012      97     160 ..      95     160 ..      69     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-06
                 SPOUT_MTase_2  97 livtdPeGeeisevkeelaealrkakevvvlvG.sReGiPkGlfrfadfvvDlaP.gvtlateyai 160
                                   ++ t    ++++   e++a  + +++   +l+G  R+G+Pk l+ ++d+ +D++  g+ l t +a+
  gi|91773398|ref|YP_566090.1|  95 VVTTSMPEDKFTVTPEDIAGGMMRNRSYLLLIGlGRKGLPKKLYSLTDHHLDITCdGISLETCTAM 160
                                   44455445677777888888888888888999967*****************97527888777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1314.65
//
Query:       gi|91773399|ref|YP_566091.1|  [L=144]
Description: GCN5-related N-acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-14   51.8   0.0    1.3e-13   51.2   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.9e-11   44.2   0.0    2.4e-11   43.9   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      2e-10   40.7   0.0    3.1e-10   40.1   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.2e-05   23.1   0.2    0.00039   20.5   0.2    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00062   19.8   0.0    0.00098   19.2   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.062   13.3   0.0    1.7  1  FR47             FR47-like protein
      0.071   12.5   0.0        0.1   12.0   0.0    1.2  1  GNAT_acetyltr_2  GNAT acetyltransferase 2
      0.075   12.5   0.0       0.11   12.0   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   5.8e-17   1.3e-13       3      76 .]      37     110 ..      35     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 5.8e-17
                                   EEEEEEEETTEEEEEEEEEEES.TCTEEEEE-GGGTTSSHHHHHHH.HTTSEEEEE.EEEETHHHHHHHHHHTTEEE CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslld.aeitrlaVdpeyrgkGiGraLle.aaekgiile.qlelnaekaikfYeklGFee 76 
                                   + ++Vae +gkivG +a+s+ + +e + +aV+p yrg GiG++++  + ++ +  + +l++++ ++  f++k+GF+e
  gi|91773399|ref|YP_566091.1|  37 EDFIVAEVEGKIVGVAAVSVKEcCEVHSIAVHPTYRGLGIGSKMISrL-IEDVS-HeRLYVRT-TSPLFFRKMGFVE 110
                                   6799***********9999998666666*****************844.22222.22344433.3455*******96 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.1e-14   2.4e-11      32     117 .]      36     108 ..      10     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.1e-14
                                   TCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHH CS
                Acetyltransf_1  32 aegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlY 112
                                    e ++vae +g+++G + ++ +       ++++s+aV+p+yrg G+Gs+++  l+e + +e   ++++ ++++      ++
  gi|91773399|ref|YP_566091.1|  36 IEDFIVAEVEGKIVGVAAVSVKEC-----CEVHSIAVHPTYRGLGIGSKMISRLIEDVSHE---RLYVRTTSPL-----FF 103
                                   346888***********9999999.....***************************99999...5577776776.....77 PP

                                   HHTTE CS
                Acetyltransf_1 113 eklGF 117
                                   +k+GF
  gi|91773399|ref|YP_566091.1| 104 RKMGF 108
                                   67887 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.4e-13   3.1e-10      33     109 ..      39     111 ..      33     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.4e-13
               Acetyltransf_10  33 llvaeeggkivGvielrdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkav 109
                                   ++vae++gkivGv++++ ++  +++ ++V+p yrg Gig++++ +++e ++++    +l v+ ++    f++k+GF+++
  gi|91773399|ref|YP_566091.1|  39 FIVAEVEGKIVGVAAVSVKEccEVHSIAVHPTYRGLGIGSKMISRLIEDVSHE----RLYVRTTSP--LFFRKMGFVEL 111
                                   89************88555545***************************9766....888887766..59******987 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   1.7e-07   0.00039      73     125 ..      59     108 ..      32     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                                   EEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT- CS
                Acetyltransf_9  73 aagvtgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGy 125
                                   +  v ++av+p++rg g+ sk++ r++e++  e+  + +  P    ++r++G+
  gi|91773399|ref|YP_566091.1|  59 CCEVHSIAVHPTYRGLGIGSKMISRLIEDVSHERLYVRTTSP---LFFRKMGF 108
                                   556889*************************85555555555...48999998 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.4e-07   0.00098       9      65 ..      46     100 ..      39     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.4e-07
               Acetyltransf_CG   9 geevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvptCs 65 
                                   g+ v+++  +  ke   +++ + V++ +rG Gi++k++ + ++d+ +e+l v+ t +
  gi|91773399|ref|YP_566091.1|  46 GKIVGVAAVS-VKE-CCEVHSIAVHPTYRGLGIGSKMISRLIEDVSHERLYVRTTSP 100
                                   5556666655.333.7889999****************************9998765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.8e-05     0.062      20      53 ..      58      91 ..      45     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                                  TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS CS
                          FR47 20 dggelgalqvlpehrrrGlgsrlvkalakeiaer 53
                                  +  e+ ++ v+p+ r+ G gs++++ l+++++++
  gi|91773399|ref|YP_566091.1| 58 ECCEVHSIAVHPTYRGLGIGSKMISRLIEDVSHE 91
                                  5678899*********************999864 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.5e-05       0.1     100     127 ..      64      91 ..      58     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
               GNAT_acetyltr_2 100 RiAvhpelqkmGYGsralellekyyegk 127
                                    iAvhp ++++G Gs+++++l++ ++ +
  gi|91773399|ref|YP_566091.1|  64 SIAVHPTYRGLGIGSKMISRLIEDVSHE 91 
                                   59*******************9987665 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.7e-05      0.11      69     102 ..      56      89 ..      39     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
               Acetyltransf_15  69 eknvleiYtlyvsekyrgkGlakklLeeslkelk 102
                                    k+  e+ ++ v++ yrg G+  k++ + ++ + 
  gi|91773399|ref|YP_566091.1|  56 VKECCEVHSIAVHPTYRGLGIGSKMISRLIEDVS 89 
                                   577889********************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1095.12
//
Query:       gi|91773400|ref|YP_566092.1|  [L=267]
Description: hypothetical protein Mbur_1431 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-08   32.0   0.0    3.7e-07   29.5   0.0    2.1  3  NAD_synthase   NAD synthase
    4.2e-07   30.0   0.0    6.2e-07   29.4   0.0    1.2  1  Asn_synthase   Asparagine synthase
    1.2e-06   28.1   0.0    1.8e-05   24.4   0.0    2.3  2  QueC           Queuosine biosynthesis protein QueC
    9.1e-06   24.7   0.0     0.0014   17.5   0.0    2.3  2  tRNA_Me_trans  tRNA methyl transferase
    0.00014   21.5   0.0    0.00022   20.9   0.0    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.039   13.7   0.0    1.8  2  ATP_bind_3     PP-loop family


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 !   29.5   0.0   1.2e-10   3.7e-07      17      80 ..      16      78 ..       8      90 .. 0.90
   2 ?   -1.9   0.0      0.48   1.4e+03     153     167 ..     152     166 ..     151     177 .. 0.85
   3 ?   -2.3   0.0      0.65   1.9e+03      62      85 ..     196     219 ..     181     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.2e-10
                                  TTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                  NAD_synthase 17 gakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktid 80
                                  + ++v++  SGGvDSs+ aala  al  +n+la+ l s + +++++e a+  ae +gi+  ++d
  gi|91773400|ref|YP_566092.1| 16 KKEKVLVAFSGGVDSSTLAALAFAAL-GDNALAVTLYSPMIPQSELEYAKRTAEVIGIKHIVLD 78
                                  4589**********************.6899**************************9987665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.48
                                   TS-HHHHHHHHHHTT CS
                  NAD_synthase 153 ellKtevkeLakeln 167
                                   ++ K+ev+++a +l+
  gi|91773400|ref|YP_566092.1| 152 DVSKREVRQMASYLG 166
                                   689*********998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.65
                                   HHHHHHHHHHHTSEEEE---HHHH CS
                  NAD_synthase  62 vedalalaenlgievktidikpiv 85 
                                   +e a  l+++lgi +  + +++ +
  gi|91773400|ref|YP_566092.1| 196 IETAEDLIHSLGISSVRVRVHDDI 219
                                   678999999999999988887655 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.1e-10   6.2e-07      17      77 ..      17      77 ..      10      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.1e-10
                  Asn_synthase 17 dvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtel 77
                                    +v + +SGG+DSS++aala + +  ++ ++++       +e++yak++ae +g++h+ l
  gi|91773400|ref|YP_566092.1| 17 KEKVLVAFSGGVDSSTLAALAFAALGDNALAVTLYSPMIPQSELEYAKRTAEVIGIKHIVL 77
                                  6678999*****************9989999999996699*****************9654 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     6e-09   1.8e-05       1      65 [.      19      83 ..      19      88 .. 0.85
   2 ?    1.3   0.0      0.07   2.1e+02     153     183 ..     143     177 ..      97     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6e-09
                                  EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGG CS
                          QueC  1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqr.hkkeleaakkiakelgveehkildldllk 65
                                  k++v +SGG+DS+t++ala ++  ++  a+t+ Y     ++ele+ak+ a+ +g+ +h +ld d+l+
  gi|91773400|ref|YP_566092.1| 19 KVLVAFSGGVDSSTLAALAFAALgDNALAVTL-YSPMiPQSELEYAKRTAEVIGI-KHIVLDHDILS 83
                                  6799**************98775267777776.66665*****************.******99886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.07
                                   EEE-TTTT..--HHHHHHHHHHTT..HHHHH-B-S CS
                          QueC 153 eieaPlid..lsKaeivklgkelg..vpleetlsC 183
                                   +i +P +d  +sK+e+ +++  lg  v  + + sC
  gi|91773400|ref|YP_566092.1| 143 SIFTPYVDfdVSKREVRQMASYLGldVANRPSNSC 177
                                   67778765226799999999999955555667888 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.8e-07    0.0014       2      69 ..      19      78 ..      18      85 .. 0.77
   2 !    4.9   0.0    0.0033       9.8     170     192 ..     152     174 ..     142     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-07
                 tRNA_Me_trans  2 kvvvalSgGVDSsv.aaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvd 69
                                  kv+va+SgGVDSs  aa+ ++  g +  +v+l               +++l++a+r ae++gi++ v+d
  gi|91773400|ref|YP_566092.1| 19 KVLVAFSGGVDSSTlAALAFAALGDNALAVTLYSPMI---------PQSELEYAKRTAEVIGIKHIVLD 78
                                  8**********99626667888899999998865443.........34667888888888888888776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0033
                 tRNA_Me_trans 170 eltKeevrkiAkeaglavaekkd 192
                                   ++ K+evr++A+  gl+va+++ 
  gi|91773400|ref|YP_566092.1| 152 DVSKREVRQMASYLGLDVANRPS 174
                                   578****************9984 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   7.5e-08   0.00022       3     172 ..      17     177 ..      15     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.5e-08
                          ThiI   3 qgkvlaLlSgGiDSp.VaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilek 82 
                                   ++kvl+  SgG+DS   aa      G ++ +v+l  +p+ ++ + e  ++ ae++        +k +v+d+ ++l++ + +
  gi|91773400|ref|YP_566092.1|  17 KEKVLVAFSGGVDSStLAALAFAALGDNALAVTLY-SPMIPQSELEYAKRTAEVIG-------IKHIVLDH-DILSDERIR 88 
                                   689**********862677777889*********6.99999999999999998874.......66788886.567777889 PP

                          ThiI  83 vkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigld..KeeiiklAkeigt 161
                                   +++++++  +k+++++  + va eeg + +++G + + ++    + l++++++    i+ P + +d  K e+ ++A  +g 
  gi|91773400|ref|YP_566092.1|  89 INDPQRCYYCKKQFVKKLKGVASEEGLNVIMEGTNASEITGRR-PGLEALREAG-SSIFTPYVDFDvsKREVRQMASYLG- 166
                                   99*********************************99998764.5566666553.4678888765444888888888887. PP

                          ThiI 162 yeisiekedkC 172
                                    +++ ++++ C
  gi|91773400|ref|YP_566092.1| 167 LDVANRPSNSC 177
                                   57777777777 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.039       1      25 [.      19      43 ..      19      94 .. 0.76
   2 ?   -1.6   0.0      0.66     2e+03     137     169 ..     141     175 ..      98     178 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                  EEEEE--SCHHHHHHHHHHHHHCTT CS
                    ATP_bind_3  1 kvlvAvSgGlDSmaLllllaklkkk 25
                                  kvlvA+SgG+DS +L  l+     +
  gi|91773400|ref|YP_566092.1| 19 KVLVAFSGGVDSSTLAALAFAALGD 43
                                  689************9988766544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                                   TCCEE-CCC..T--HHHHHHHHHHTT---B--CGG CS
                    ATP_bind_3 137 sirlvRPlL..kvskeeleeylkekkikwveDesN 169
                                   +  +  P++  +vsk e++++++  +++ ++ +sN
  gi|91773400|ref|YP_566092.1| 141 GSSIFTPYVdfDVSKREVRQMASYLGLDVANRPSN 175
                                   34444555422456666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1843.02
//
Query:       gi|91773401|ref|YP_566093.1|  [L=134]
Description: hypothetical protein Mbur_1432 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   9.3      0.017   15.1   9.3    1.1  1  Claudin_3        Tight junction protein, Claudin-like
      0.021   14.7   0.2      0.036   14.0   0.2    1.3  1  Propeptide_C1    Peptidase family C1 propeptide
      0.027   13.7  11.1      0.035   13.3  11.1    1.2  1  MIG-14_Wnt-bd    Wnt-binding factor required for Wnt secretio
       0.84    9.7  12.4       0.11   12.6   7.1    2.0  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        1.3    7.7   8.1        1.5    7.5   8.1    1.1  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   9.3   4.6e-06     0.017       8     114 ..      20     131 ..       9     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.6e-06
                     Claudin_3   8 lgvlvvisfilnivgl.ftpaWiteest..kkeksiGivPfss..teagwleaasimmyislalflvviliyivivrkvkk 83 
                                   l+++ + s+i+ ++ + +t  Wit+  +  +k+++i ++  +    +a ++ +a+ +m++s ++fl++++  +v  + v+ 
  gi|91773401|ref|YP_566093.1|  20 LMATAICSAIMGAAEIaYTMLWITSAYErhGKNFFIDLINAKAltWTAEFVIVAGSLMLLSSMMFLITMFYSLVELNAVRD 100
                                   44444444444444433799999999888867777776666665556679999**************************98 PP

                     Claudin_3  84 ngysksvrklffliallslliviltviavil 114
                                        ++  +f l+ l+++l +i ++ a+il
  gi|91773401|ref|YP_566093.1| 101 PSKKIRMNIIFLLFILAMILLIIALISALIL 131
                                   8777777777777666666666666666665 PP

>> Propeptide_C1  Peptidase family C1 propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2     1e-05     0.036       5      19 ..      54      68 ..      52      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                                  HHHHHHHCT-SEEE- CS
                 Propeptide_C1  5 fIdyiNsknttWkAg 19
                                  fId iN k+ tW+A 
  gi|91773401|ref|YP_566093.1| 54 FIDLINAKALTWTAE 68
                                  9************95 PP

>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  11.1   9.8e-06     0.035     167     256 ..      37     129 ..      14     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.8e-06
                 MIG-14_Wnt-bd 167 wlvllvlalyerleqlkdpfysiwss.al....ilkilaiilavlyflyLlylifrsfseirskrvkegdiRfkflilltl 242
                                   + +l ++  yer  + k+ f++  ++ al     + i+a+ l++l  ++ l+ +f s+ e++++r ++ +iR+ +++ll++
  gi|91773401|ref|YP_566093.1|  37 YTMLWITSAYER--HGKNFFIDLINAkALtwtaEFVIVAGSLMLLSSMMFLITMFYSLVELNAVRDPSKKIRMNIIFLLFI 115
                                   334444445555..6678888777666224445677777777777777778888889************************ PP

                 MIG-14_Wnt-bd 243 lvlavlvifiilgl 256
                                   l +++l+i++i+ l
  gi|91773401|ref|YP_566093.1| 116 LAMILLIIALISAL 129
                                   **********9987 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 ?   -0.3   0.2       0.3   1.1e+03      79      87 ..      23      31 ..      14      50 .. 0.42
   2 ?   12.6   7.1     3e-05      0.11      30      88 ..      60     132 ..      58     134 .] 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.3
               Phage_holin_3_6 79 lagvlalvg 87
                                   a+  a++g
  gi|91773401|ref|YP_566093.1| 23 TAICSAIMG 31
                                  111111111 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3e-05
               Phage_holin_3_6  30 akragsgagllgaagvlallalllllvalalal..........aa....lwlaalivaavllvlagvlalvgl 88 
                                   ak +   a ++++ag l+ll+ +++l+++++ l          +       +  +i+a +ll++a++ al+ +
  gi|91773401|ref|YP_566093.1|  60 AKALTWTAEFVIVAGSLMLLSSMMFLITMFYSLvelnavrdpsKKirmnIIFLLFILAMILLIIALISALILR 132
                                   7888889999*******************85554444444333103444445557799*********999876 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.1   0.00041       1.5     356     430 ..      38     131 ..      24     134 .] 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00041
                       DUF2207 356 alkkwksavkkkergyfdkkgkkklkklsalglgliilglili.llallllvll....................lvfllil 415
                                   ++  ++sa++++ +++f +  ++k+ ++ a  ++++  +++l+ +++l+++  +                    +++l+il
  gi|91773401|ref|YP_566093.1|  38 TMLWITSAYERHGKNFFIDLINAKALTWTAEFVIVAGSLMLLSsMMFLITM--FyslvelnavrdpskkirmniIFLLFIL 116
                                   667788888889999999998888877777655555444444303333333..3569999**********88854444444 PP

                       DUF2207 416 llillliaiivlllf 430
                                   ++ill+ia+i +l++
  gi|91773401|ref|YP_566093.1| 117 AMILLIIALISALIL 131
                                   444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1223  (0.0682135); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 935.05
//
Query:       gi|91773402|ref|YP_566094.1|  [L=337]
Description: protoporphyrin IX magnesium-chelatase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-23   81.0   0.7    7.7e-23   80.1   0.7    1.5  1  AAA_lid_2        AAA lid domain
    2.5e-09   36.8   1.7    7.2e-06   25.5   0.0    3.1  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.7e-09   35.7   0.1      2e-05   24.6   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
    8.6e-05   21.7   0.1     0.0005   19.2   0.0    2.1  2  MCM              MCM P-loop domain
    0.00053   19.8   0.0      0.069   13.0   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
     0.0054   16.5   0.0       0.12   12.0   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
      0.008   16.6   0.0      0.021   15.2   0.0    1.7  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.085   12.6   0.2        8.1    6.1   0.0    2.3  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.7   3.4e-26   7.7e-23       2      71 ..     261     330 ..     260     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 3.4e-26
                     AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeive 71 
                                   +t+a+++++++v+g+Rad+++ r+Ar++Aa+egr+++t eD+ eaa++VL+HR+r++p++e+e + e+++
  gi|91773402|ref|YP_566094.1| 261 RTIAKICVAFNVDGHRADIMIERTARTNAAYEGRERITNEDIIEAAEMVLPHRMRKKPFEEEEFSAEQLR 330
                                   79************************************************************99988877 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1   0.00086       1.9       4      50 ..       6      54 ..       4      61 .. 0.85
   2 !   25.5   0.0   3.2e-09   7.2e-06      93     158 ..     118     183 ..     111     190 .. 0.93
   3 ?    0.9   0.0      0.11   2.5e+02     187     202 ..     190     205 ..     185     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00086
                  Mg_chelatase  4 dvkGqeeakraleiaaaG..gHnlllvGppGsGKtmlakrlpsllppls 50
                                   ++Gqe   ral + a+      +l+ G  G+ K+   + l+++lp+++
  gi|91773402|ref|YP_566094.1|  6 GIVGQEMMLRALILNAINpsIGGVLVRGQKGTAKSTAVRGLAEILPDIE 54
                                  689999999999998875114579**********************986 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 3.2e-09
                  Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                   g +  +pG ++ a++ +L++DE+  ++  v+++L +    +  t++r   +v++pa+f +v +mNp
  gi|91773402|ref|YP_566094.1| 118 GTQAFEPGILANANRNILYVDEINLLDDFVVDALLDAAAMNVNTVEREGISVSHPANFIIVGSMNP 183
                                   677899***********************************************************9 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.11
                  Mg_chelatase 187 gplldRidlqvevkkl 202
                                     lldRi lqvev+ +
  gi|91773402|ref|YP_566094.1| 190 PQLLDRIALQVEVEGI 205
                                   579*********9866 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00097       2.2       2      23 ..      29      50 ..      28      61 .. 0.89
   2 !   24.6   0.0   8.9e-09     2e-05      29     137 ..      93     195 ..      86     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00097
                                  EEEE--SSSSHHHHHHHGGGGB CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                  vl+ G++Gt+Ks+ ++ la+ l
  gi|91773402|ref|YP_566094.1| 29 VLVRGQKGTAKSTAVRGLAEIL 50
                                  8999***************998 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 8.9e-09
                                   EEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE- CS
                         AAA_5  29 yvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggelvka 105
                                   +v l+ + te+ ++g+++i+    +gt+++++++l +a r   il++DE++ +++ v+++Ll     +   +e  g  v++
  gi|91773402|ref|YP_566094.1|  93 VVDLPVGATEDRVVGSLDIEkavkEGTQAFEPGILANANR--NILYVDEINLLDDFVVDALLDAAAMNVNTVEREGISVSH 171
                                   66777789****************************7755..7******************99999999999999999999 PP

                                   --......-EEEEEESS--.-TT-TTHHHHTT CS
                         AAA_5 106 knddllerfrviatanpldrslnelspalrsR 137
                                   +++     f +++++np +    el p+l++R
  gi|91773402|ref|YP_566094.1| 172 PAN-----FIIVGSMNPEE---GELRPQLLDR 195
                                   988.....*********99...5666777777 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.22   4.9e+02      60      83 ..      29      52 ..      10      60 .. 0.81
   2 !   19.2   0.0   2.2e-07    0.0005     103     180 ..     113     190 ..      88     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.22
                                  EEEEESSTSTHHHHHHHHHHHSSS CS
                           MCM 60 vllvgdpgtaKsqlLkyveklapr 83
                                  vl+ g  gtaKs+ ++ +++++p 
  gi|91773402|ref|YP_566094.1| 29 VLVRGQKGTAKSTAVRGLAEILPD 52
                                  788899999999988888887775 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.2e-07
                                   EESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCT CS
                           MCM 103 rdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydk 180
                                   +  ++g  ++e G l  a++ ++++De++  ++   +al++a   +  ++ + Gi ++ +a   ++ ++np++g+  +
  gi|91773402|ref|YP_566094.1| 113 KAVKEGTQAFEPGILANANRNILYVDEINLLDDFVVDALLDAAAMNVNTVEREGISVSHPANFIIVGSMNPEEGELRP 190
                                   5556777899*********************************99*99************************998665 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 ?    4.6   0.0     0.012        27       2      46 ..      29      75 ..      28      95 .. 0.67
   2 !   13.0   0.0   3.1e-05     0.069      63     115 ..     132     186 ..     103     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                         AAA_3  2 vllegvPGlaktllvkalakal.dle.fkriqftpdllPsdilGtev 46
                                  vl++g  G+ak ++v+ la++l d+e ++  q+  d l  +    e 
  gi|91773402|ref|YP_566094.1| 29 VLVRGQKGTAKSTAVRGLAEILpDIEvIDGCQYNCDPLDPNTFCWEC 75
                                  799*****************983333145567776655544444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.1e-05
                         AAA_3  63 anllladeinrappktqsallea..meerqvtvegethklpepflvlatqnPieq 115
                                    n+l +dein     +  all+a  m+ ++v  eg + + p +f+++   nP e 
  gi|91773402|ref|YP_566094.1| 132 RNILYVDEINLLDDFVVDALLDAaaMNVNTVEREGISVSHPANFIIVGSMNPEEG 186
                                   589******************9633788888888888899999*********875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.077   1.7e+02      21      41 ..      25      45 ..       7      64 .. 0.78
   2 !   12.0   0.0   5.4e-05      0.12      79     144 ..     117     184 ..      91     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.077
                                  SSS-EEEECSTTSSHHHHHHH CS
               Sigma54_activat 21 tdlsvlitGesGtGKellara 41
                                  +   vl++G++Gt K++  r 
  gi|91773402|ref|YP_566094.1| 25 SIGGVLVRGQKGTAKSTAVRG 45
                                  44579**********987765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.4e-05
                                   TTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHH..HHHHSEEESBTSSSEEE--EEEEEEESS- CS
               Sigma54_activat  79 tGAekekkGlfekadgGtlfLDeigelplelQekLlr..vlqegevervGsskeikvdvriiaatned 144
                                    G+++ + G + +a+  +l++Dei+ l+  +   Ll   +++ ++ver G s ++++++ i+ + n +
  gi|91773402|ref|YP_566094.1| 117 EGTQAFEPGILANANRNILYVDEINLLDDFVVDALLDaaAMNVNTVEREGISVSHPANFIIVGSMNPE 184
                                   57788889***************************963368999**************9999988754 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.3e-06     0.021      12      88 ..      14      87 ..       8     169 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.3e-06
                        AAA_16 12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy..sa.laqalareellrqllde 88
                                  L++++ ++  ++ + vl++G++G+ Ks+ vr l++ +  d + ++ g    +    p+   +  +++ ++ +   q++ e
  gi|91773402|ref|YP_566094.1| 14 LRALILNAINPSIGGVLVRGQKGTAKSTAVRGLAE-ILPD-IEVIDGCQYNC---DPLdpNTfCWECVDK-QRKGQIKVE 87
                                  556666666777799*******************5.5555.33433333333...222112235555544.555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0036       8.1      21      42 ..      29      50 ..      14      56 .. 0.86
   2 ?    4.0   0.0     0.016        35      86     114 ..     129     157 ..      97     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0036
                        AAA_30 21 avltGpAGtGKttalkalreaw 42
                                  +++ G  Gt K+ta+++l+e++
  gi|91773402|ref|YP_566094.1| 29 VLVRGQKGTAKSTAVRGLAEIL 50
                                  6799**************9986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.016
                        AAA_30  86 lepgtllivDEagmvdtkqlaallkaaek 114
                                    +++++l vDE+ ++d   ++all+aa+ 
  gi|91773402|ref|YP_566094.1| 129 NANRNILYVDEINLLDDFVVDALLDAAAM 157
                                   445699*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2147.47
//
Query:       gi|91773403|ref|YP_566095.1|  [L=190]
Description: adenine phosphoribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-17   63.8   0.2    1.7e-17   63.4   0.2    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00089   18.8   0.1     0.0012   18.3   0.1    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.024   14.6   0.0       0.16   11.9   0.0    2.1  2  SAM_LFY       Floricaula / Leafy protein SAM domain
      0.031   13.8   0.1       0.04   13.4   0.1    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 !   63.4   0.2   3.8e-21   1.7e-17      23     146 ..      50     174 ..      34     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3.8e-21
                                   EEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE............EE----TTSEEEEE-SEESS CS
                  Pribosyltran  23 leeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes....rlledpagkkVliVDDildt 99 
                                       +   d +v i+  G+p+a+ l+ + + p+ +vrk+ y  +g    +++    s       ++ +g++Vl+VDD+++t
  gi|91773403|ref|YP_566095.1|  50 A---GKDYDRIVSIEAMGIPLATVLSMKTGKPMSIVRKRQYGLEGEVILSQST-GYSkgelYINGISKGETVLVVDDVIST 126
                                   3...336788*******************************999876665443.3445878999***************** PP

                                   SHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......E CS
                  Pribosyltran 100 GgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pd 146
                                   GgTl+a l +L++ g+ +  ++v++ +++++ + +   ++v +l  +d
  gi|91773403|ref|YP_566095.1| 127 GGTLKALLPALENMGANICNVIVVISRGDGAAKMSDMGYNVNTLVkID 174
                                   *************************99999888776666666666555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.7e-07    0.0012     120     178 ..     113     169 ..      92     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-07
                       UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkv 178
                                   + +tvl++D vi+TGg++ a +  L + g++     v+ v++   g++++++   +v+ 
  gi|91773403|ref|YP_566095.1| 113 KGETVLVVDDVISTGGTLKALLPALENMGAN--ICNVIVVISRGDGAAKMSDMGYNVNT 169
                                   5679***********************7765..45556677777788877776666664 PP

>> SAM_LFY  Floricaula / Leafy protein SAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.22     1e+03      17      38 ..      54      75 ..      40      82 .. 0.80
   2 ?   11.9   0.0   3.7e-05      0.16      20      36 ..     157     173 ..     152     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.22
                       SAM_LFY 17 yltvakiaelGftvstlvnmke 38
                                  y  +  i  +G    t++ mk 
  gi|91773403|ref|YP_566095.1| 54 YDRIVSIEAMGIPLATVLSMKT 75
                                  5566778899999999999985 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.7e-05
                       SAM_LFY  20 vakiaelGftvstlvnm 36 
                                   +ak++++G+ v+tlv++
  gi|91773403|ref|YP_566095.1| 157 AAKMSDMGYNVNTLVKI 173
                                   89*************86 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     9e-06      0.04     119     157 ..     112     152 ..     105     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-06
                      PRTase_2 119 aaakelvLvDDEistGktalnliralqeklpr..kryvvvs 157
                                   ++ +++++vDD istG t+ +l+ al++   +  + +vv+s
  gi|91773403|ref|YP_566095.1| 112 SKGETVLVVDDVISTGGTLKALLPALENMGANicNVIVVIS 152
                                   56789999******************998777434444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1422.82
//
Query:       gi|91773404|ref|YP_566096.1|  [L=331]
Description: diphthamide biosynthesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-83  279.2   0.0    5.2e-83  279.0   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.0   0.0   2.9e-87   5.2e-83       1     300 [.      30     322 ..      30     325 .. 0.95

  Alignments for each domain:
  == domain 1  score: 279.0 bits;  conditional E-value: 2.9e-87
               Diphthamide_syn   1 fPegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd.rlpvlYvfveieldvehl 79 
                                   fPeg+++ s++ia+++ e++g+e++i+++++YGaC++d   +e+  +dll H+Gh+ l   + + +v+++ ++++ dv+ +
  gi|91773404|ref|YP_566096.1|  30 FPEGFKRRSPAIASEIsEATGVEIIISANPCYGACDLDIPILEN--VDLLFHFGHAQLDDNRySDKVIFIETRSDADVKGV 108
                                   9***************9999*******************99999..9************8666****************** PP

               Diphthamide_syn  80 vetlkknfkekkkivlvstiqyahaleevkeeleeegyevv..kvpqsekplspgevlgctspklkeeeeevdailyigdg 158
                                   v ++ +++ ++kk++l++t+q++h+l+ev+e+le++g +vv    ++s k+ ++g+vlgc+++ +++   +++++lyig+g
  gi|91773404|ref|YP_566096.1| 109 VVKALEEL-QGKKVGLLTTVQHVHKLPEVREILENNG-KVVaiGRGDS-KIAYAGQVLGCNFSVADDL--DCEEFLYIGSG 184
                                   ********.7999*********************885.5554466677.99**************955..9********** PP

               Diphthamide_syn 159 rfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagk 239
                                    fh+l++ l++ k +v+ +dp+sk+++  + d + ++r+R aai+k+ da+++Giiv+++ +q+r+el+++lk l++e+gk
  gi|91773404|ref|YP_566096.1| 185 GFHPLGVSLATGK-RVLIADPFSKDVR--EVDPSLIMRQRSAAIAKSLDAESFGIIVSSKPGQYRMELARELKGLAEEKGK 262
                                   ***********77.9*********887..55699*********************************************** PP

               Diphthamide_syn 240 ksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalgerewte 300
                                   ++y+++++ ++p+++ +f ++dafV +aCprl++d+  +F+ P+ltp+E+e++lg+rew++
  gi|91773404|ref|YP_566096.1| 263 TAYILILDLITPDQMLQF-KVDAFVSTACPRLAVDEVGRFSAPMLTPQEFEIVLGKREWED 322
                                   ******************.9***************************************74 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2479.32
//
Query:       gi|91773405|ref|YP_566097.1|  [L=203]
Description: methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   55.4   0.0    6.4e-15   55.1   0.0    1.1  1  MTS              Methyltransferase small domain
    7.2e-15   55.1   0.1    9.7e-15   54.7   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.6e-11   44.7   0.1    3.7e-11   43.6   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
    1.8e-09   37.6   1.3    2.3e-08   34.0   1.3    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    3.1e-09   36.8   0.2    5.8e-09   35.9   0.1    1.5  2  Methyltransf_31  Methyltransferase domain
    1.1e-05   26.0   0.1    2.9e-05   24.6   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
    1.7e-05   24.5   0.0    2.6e-05   23.9   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00081   19.3   0.0     0.0012   18.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0028   17.0   0.0     0.0058   15.9   0.0    1.4  1  N6_Mtase         N-6 DNA Methylase
      0.005   16.3   0.0      0.012   15.1   0.0    1.6  2  AviRa            RRNA methyltransferase AviRa
     0.0053   16.3   0.1      0.011   15.3   0.1    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0059   17.3   0.0      0.011   16.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.036   13.8   0.0    1.2  1  Met_10           Met-10+ like-protein
      0.029   14.4   0.0      0.037   14.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.044   13.7   0.0       0.07   13.1   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
        0.2   11.1   0.0       0.48    9.9   0.0    1.5  2  FmrO             Ribosomal RNA methyltransferase (FmrO)


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   5.7e-18   6.4e-15      27     139 ..      42     154 ..      32     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 5.7e-18
                                   CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                           MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                   ++ +l+g+v DlGcG+G+l++ +a    e +v+ +d d  Al++a+en+e  +++ve+  +d+ + v  ++ d++v+NPPf
  gi|91773405|ref|YP_566097.1|  42 MKGDLEGTVYDLGCGTGMLAIGAAMLGAE-KVVGFDSDSGALDIARENAEIFGVDVEFECKDIRQ-VR-GHADTVVMNPPF 119
                                   5566999***************9998887.8*******************************876.55.6*********** PP

                                   TTTCHCHHHH..HHHH.HHHHHHHEEEEEEEEEEE CS
                           MTS 108 hagkatelav..aeel.iaeAkeaLkegGeLliVa 139
                                    a+ + +++    +++ +a+     +++G+L +V 
  gi|91773405|ref|YP_566097.1| 120 GAQVKGSDRPflKTAMrVADVTYSIHNSGSLAFVK 154
                                   99987554430022222344445567777777765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   8.6e-18   9.7e-15     163     233 ..      48     116 ..      30     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 8.6e-18
                          PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.eekadvivaN 233
                                    +v D+G+G+G+Lai+aa+Lga+kvv+ D D+ A+++a+eNae+ +v+ ++e    +++ + +++ad +v N
  gi|91773405|ref|YP_566097.1|  48 GTVYDLGCGTGMLAIGAAMLGAEKVVGFDSDSGALDIARENAEIFGVDVEFEC---KDIRQvRGHADTVVMN 116
                                   499************************************************86...444433589****998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.1   3.3e-14   3.7e-11       1      92 [.      50     137 ..      50     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.3e-14
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG.SSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh.lsd 79 
                                   v dlGcGtG l++ +a   g++kv+g+D ++++l++are+ae  g++vef+++d++++    g+ D vv++   +   ++ 
  gi|91773405|ref|YP_566097.1|  50 VYDLGCGTGMLAIGAAML-GAEKVVGFDSDSGALDIARENAEIFGVDVEFECKDIRQVR---GHADTVVMN-PpFGAqVKG 125
                                   78**************88.79********************999*************97...778999995.447764554 PP

                                   HHHHHHHHHHHHH CS
               Methyltransf_25  80 edlekalkeiarv 92 
                                   +d + +lk + rv
  gi|91773405|ref|YP_566097.1| 126 SD-RPFLKTAMRV 137
                                   44.5577777776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   1.3     2e-11   2.3e-08      16     136 ..      32     124 ..      23     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2e-11
                                   HHHHHHHHTT--TT..S-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHH CS
                       UPF0020  16 LAaalvrlagwkpg..epllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgare 94 
                                   LAa ++  a +k +   + +D  CG+G ++I aa+lga+ +                         +g+D+d+ +++ are
  gi|91773405|ref|YP_566097.1|  32 LAAEMLHFAFMKGDleGTVYDLGCGTGMLAIGAAMLGAEKV-------------------------VGFDSDSGALDIARE 87 
                                   78888888877765226899999***************999.........................8************** PP

                                   HHHHTT-GGGEEEEE--GGG--STTS---EEEE--------- CS
                       UPF0020  95 NaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlg 136
                                   Nae  gv+  +ef+++d++++r   g  d++v npP+G  ++
  gi|91773405|ref|YP_566097.1|  88 NAEIFGVD--VEFECKDIRQVR---GHADTVVMNPPFGAQVK 124
                                   ***99886..7899999**999...678**********9875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   5.2e-12   5.8e-09       6      81 ..      49     116 ..      45     146 .. 0.85
   2 ?   -2.7   0.0       3.9   4.4e+03      56      70 ..     176     188 ..     173     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.2e-12
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                   +v+DlGCGtG l++ +a  +    +vvG+D +  a+  Arena+  g+d veFe  di +          D ++ n
  gi|91773405|ref|YP_566097.1|  49 TVYDLGCGTGMLAIGAA--MLGAEKVVGFDSDSGALDIARENAEIFGVD-VEFECKDIRQVR-----GHADTVVMN 116
                                   79***************..445678***********************8.********9876.....446666666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.9
               Methyltransf_31  56 veFeqgdieelekll 70 
                                   ++F++ d+e +e  +
  gi|91773405|ref|YP_566097.1| 176 FKFHKKDVERIE--I 188
                                   689999999988..3 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.5e-08   2.9e-05       2      66 ..      52     114 ..      51     140 .. 0.87
   2 ?   -2.1   0.0       5.7   6.3e+03      73      88 ..     179     194 ..     172     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-08
                                   EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEE CS
               Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvv 66 
                                   d+GcGtG la   a  g ++vvg+D +  +l++a+e+a+  g+ vef + d++++    +  D vv
  gi|91773405|ref|YP_566097.1|  52 DLGCGTGMLAIGAAMLGaEKVVGFDSDSGALDIARENAEIFGVDVEFECKDIRQVR---GHADTVV 114
                                   9*************9999**********************99999*******9963...4555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.7
                                   C-CCHHHHHHHHHHHE CS
               Methyltransf_11  73 hvedpekalkeiaRvL 88 
                                   h +d+e++  ei+R+ 
  gi|91773405|ref|YP_566097.1| 179 HKKDVERIEIEIYRII 194
                                   4478888888999886 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.3e-08   2.6e-05      33     126 ..      39     122 ..      29     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.3e-08
                                   HHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-E CS
                 Cons_hypoth95  33 FnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkee 113
                                   F  ++ ++eg  v Dl +G+G l++ A+  ga+k+v +++d+ a+ i +en e ++++    e+  ++ ++++      ++
  gi|91773405|ref|YP_566097.1|  39 FAFMKGDLEGT-VYDLGCGTGMLAIGAAMLGAEKVVGFDSDSGALDIARENAEIFGVD---VEFECKDIRQVR------GH 109
                                   55566667666.99******************************************77...466666666664......45 PP

                                   EEEEEE--SSSTT CS
                 Cons_hypoth95 114 fdivflDPPyake 126
                                    d v ++PP+ ++
  gi|91773405|ref|YP_566097.1| 110 ADTVVMNPPFGAQ 122
                                   799*******887 PP

>> Methyltransf_23  Methyltransferase domain
   #    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      12      89 ..      36     116 ..      25     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
               Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                    l++++ k +  g v d+GcGtG l+  ++  g+ +v+g+D ++ a +ia+    ++ +++ f   ++++  g+ d++v++
  gi|91773405|ref|YP_566097.1|  36 MLHFAFMKGDLEGTVYDLGCGTGMLAIGAAMLGAeKVVGFDSDSGALDIARenAEIFGVDVEFECKDIRQVRGHADTVVMN 116
                                   56677777888999***********99999999999*************99876666677777777888999999999986 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.1e-06    0.0058      28     170 ..      26     157 ..      22     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                      N6_Mtase  28 ffTPrevsklivell..epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykk 106
                                   + TP  +   + + +  +   + +vyD  cG+g l + a+  l        + ++ G ++++ +  +a+ N  + g++++ 
  gi|91773405|ref|YP_566097.1|  26 YPTPALLAAEMLHFAfmKGDLEGTVYDLGCGTGMLAIGAAM-L-------GAEKVVGFDSDSGALDIARENAEIFGVDVE- 97 
                                   667777776666666655555567********877777665.4.......467899**********************99. PP

                      N6_Mtase 107 vkirlgdtlekpkfekdkkfdvvvaNppfnqkew..kektlekderfrea.vapksnadlafllhii 170
                                      + +d       +   ++d+vv Nppf+++    +   l+   r ++     +++  laf+  +i
  gi|91773405|ref|YP_566097.1|  98 --FECKD-----IRQVRGHADTVVMNPPFGAQVKgsDRPFLKTAMRVADVtYSIHNSGSLAFVKKFI 157
                                   ..34444.....44456678**********9833434445566667766655556667777777766 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05     0.012      34     101 ..      32      91 ..      24      96 .. 0.77
   2 ?   -1.9   0.0       1.6   1.8e+03     162     181 ..     105     124 ..      89     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                         AviRa  34 lasEilqralellekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLsL 101
                                   la E+l+ a+        +   t+yD  CG++ L+   ++l ++   kv++ D d+ +l++a++N ++
  gi|91773405|ref|YP_566097.1|  32 LAAEMLHFAFMKG-----DLEGTVYDLGCGTGMLAIGAAMLGAE---KVVGFDSDSGALDIARENAEI 91 
                                   5555555444333.....23458***********9999999875...79****************876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                         AviRa 162 eaekevdivitDlPYGelvs 181
                                   ++  ++d v++  P+G +v+
  gi|91773405|ref|YP_566097.1| 105 QVRGHADTVVMNPPFGAQVK 124
                                   33334899999999999876 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   9.7e-06     0.011       3      82 ..      49     120 ..      47     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.7e-06
               Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwG 82 
                                   ++ Dl +G+G  +i  a+   ekv++ +++   l +a +Nae++gv+ +    + d+ ++       + + d v++ pP G
  gi|91773405|ref|YP_566097.1|  49 TVYDLGCGTGMLAIGAAMLgAEKVVGFDSDSGALDIARENAEIFGVDVEF--ECKDIRQV-------RGHADTVVMNPPFG 120
                                   57799************996789*********************997543..33333322.......22345667777766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.8e-06     0.011       2      73 ..      52     116 ..      51     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.8e-06
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                   ++GcGtG l+   +      +++g D ++ a++ a+e     +      ve+e +d+ +  g  + D+vv++
  gi|91773405|ref|YP_566097.1|  52 DLGCGTGMLAIGAAML-GAEKVVGFDSDSGALDIARENAEIFG----VDVEFECKDIRQVRG--HADTVVMN 116
                                   89********999999.777788*********55555444444....579999999876665..99999996 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.2e-05     0.036     102     179 ..      48     120 ..      31     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                                   -EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TTT CS
                        Met_10 102 evVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpks 179
                                    +V d+  G G +ai +a ++ +k v++ d +  +    +en +   v+   +  ++D r+v  +  ad vvmn p  
  gi|91773405|ref|YP_566097.1|  48 GTVYDLGCGTGMLAIGAAMLGAEK-VVGFDSDSGALDIARENAEIFGVDV--EFECKDIRQV--RGHADTVVMNPPFG 120
                                   4799**************977665.********************99985..5589******..599*******8854 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.037      26      88 ..      47     106 ..      32     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
               Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88 
                                   + tv D+G+G g L+   a        kvvg+d+ +   + a++ ae +g +++ +++ + + 
  gi|91773405|ref|YP_566097.1|  47 EGTVYDLGCGTGMLAIGAAM---LGAEKVVGFDSDSGALDIARENAEIFGVDVEFECKDIRQV 106
                                   5689***************9...77889******************99995554444444443 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.2e-05      0.07      17      73 ..      49     102 ..      39     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-05
               Methyltransf_18  17 rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73 
                                   +v D G+  g+l+i ++  g a+kv+  D  +g+l+ a+en+e  g++  +e+ + d
  gi|91773405|ref|YP_566097.1|  49 TVYDLGCGTGMLAIGAAMLG-AEKVVGFDSDSGALDIARENAEIFGVD--VEFECKD 102
                                   799************99766.789********************9996..5555554 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00042      0.48     109     164 ..      49     103 ..      45     115 .. 0.87
   2 ?   -2.2   0.0       2.1   2.4e+03      61      96 ..     120     156 ..     110     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00042
                          FmrO 109 svlDvaCgLnpLavpwlllaadatylasDidsdlvefldrflalvevegrvevrDl 164
                                   +v D++Cg   La++   l a+ + +++D ds  +++     ++ +v+ + e +D+
  gi|91773405|ref|YP_566097.1|  49 TVYDLGCGTGMLAIGAAMLGAEKV-VGFDSDSGALDIARENAEIFGVDVEFECKDI 103
                                   89*************999999987.799*********9999999999999988886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                          FmrO  61 qaavttgDpdalkaavar...vlarhastrerLpfLref 96 
                                   +a+v ++D   lk a++        h s    L+f+++f
  gi|91773405|ref|YP_566097.1| 120 GAQVKGSDRPFLKTAMRVadvTYSIHNS--GSLAFVKKF 156
                                   5788899999999888742223333333..346666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        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: 00:00:00.46
# Mc/sec: 1339.22
//
Query:       gi|91773406|ref|YP_566098.1|  [L=237]
Description: RNA binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-09   36.2   0.1    7.2e-09   35.3   0.1    1.5  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
    0.00021   21.2   0.7    0.00041   20.2   0.7    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
     0.0011   19.0   1.6     0.0015   18.5   0.2    1.9  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0012   18.8   1.7     0.0029   17.5   1.7    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0016   19.0   1.6     0.0016   19.0   1.6    2.7  3  EXOSC1          Exosome component EXOSC1/CSL4
     0.0023   18.1   3.0     0.0096   16.1   0.2    2.3  2  zf-RING_7       C4-type zinc ribbon domain
     0.0032   17.5   0.6     0.0055   16.7   0.6    1.3  1  DZR             Double zinc ribbon
     0.0045   16.6   2.4     0.0085   15.8   2.4    1.5  1  zinc_ribbon_2   zinc-ribbon domain
     0.0097   16.2  10.9      0.021   15.2   4.8    2.9  2  S1              S1 RNA binding domain
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.018   14.7   0.1    1.3  1  TackOD1         Thaumarchaeal output domain 1
      0.016   15.3   0.2      0.016   15.3   0.2    1.8  2  DUF1451         Zinc-ribbon containing domain
      0.017   14.6   1.1        1.4    8.5   0.1    2.8  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.024   14.7   6.4      0.024   14.7   6.4    1.8  2  YscO-like       YscO-like protein
      0.051   13.7   0.2        0.4   10.9   0.3    2.2  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.085   13.0   2.0        6.8    6.9   0.2    3.3  3  HupF_HypC       HupF/HypC family
       0.11   11.9   4.7       0.43   10.0   4.7    1.9  1  zf-ribbon_3     zinc-ribbon domain
       0.12   12.5   4.1       0.58   10.3   4.3    2.0  2  Zn-ribbon_8     Zinc ribbon domain
       0.17   11.8   0.8       0.29   11.1   0.8    1.3  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.19   11.4   2.9       0.48   10.1   2.9    1.6  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.23   11.4   1.5        3.1    7.8   0.2    2.2  2  HalOD2          Halobacterial output domain 2
       0.36   10.8   2.2        0.8    9.7   2.2    1.6  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.62   10.2   3.5         19    5.5   0.2    2.5  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        1.1   10.0   3.9         19    6.0   0.5    2.5  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        8.6    6.6   9.0       0.92    9.7   0.3    2.7  2  DUF678          Protein of unknown function (DUF678)


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   9.7e-12   7.2e-09       1      37 [.      56      92 ..      56      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 9.7e-12
                                  EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                        ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                  +V+PG++++t+eef +G++TY  +g i++  +G+v v
  gi|91773406|ref|YP_566098.1| 56 LVMPGDIIGTTEEFEAGANTYNVRGDIHSLATGFVMV 92
                                  69*********************************86 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 !   20.2   0.7   5.5e-07   0.00041       6      29 ..     200     223 ..     197     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.5e-07
                   Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtp 29 
                                    C  Cg +lk++d +  CpeCg  
  gi|91773406|ref|YP_566098.1| 200 TCANCGSTLKKDDQVLKCPECGRT 223
                                   7*********************65 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   0.1       3.1   2.3e+03      39      58 ..      10      30 ..       3      42 .. 0.46
   2 !   18.5   0.2     2e-06    0.0015      26      97 ..     149     225 ..     130     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.1
                                  --HHHHHHHHHHHHCC.T.TT CS
                          HypA 39 vepeaLefafellaegtv.le 58
                                  ve+e+L++a e ++  +  +e
  gi|91773406|ref|YP_566098.1| 10 VEEEVLSTASEKVNVAEKkVE 30
                                  555555555444432222233 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2e-06
                                   EEEEEEEEETTCT--HHHHHHHHHHHHCC.T..TTT-EEEEEEE-...-EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                          HypA  26 vtkvkvevGelsgvepeaLefafellaegtv..legaeLeieevp...vkvrCreCgkefeleekalrCpkCgsadv 97 
                                   + +++v+  + s v++ + efa   + + +v  le+ +++ +  +   ++ +C +Cg++ +++++ l+Cp+Cg+++ 
  gi|91773406|ref|YP_566098.1| 149 IAAIHVSNVKESYVKEMSKEFAVADVVKAKVinLENMRMTTSGNElgvMVSTCANCGSTLKKDDQVLKCPECGRTES 225
                                   5666666666666666666666655555555355666666544431115668********9887789******9865 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 !   17.5   1.7   3.9e-06    0.0029      30      58 ..     200     226 ..     198     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.9e-06
                OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                   tC++Cgs++k+  +++++kCp+Cg +  r
  gi|91773406|ref|YP_566098.1| 200 TCANCGSTLKK--DDQVLKCPECGRTESR 226
                                   9**********..***********98776 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.3       1.7   1.3e+03      79     101 ..      33      62 ..       9      85 .. 0.55
   2 !   19.0   1.6   2.2e-06    0.0016       3      50 ..     112     165 ..     108     182 .. 0.89
   3 ?    0.1   0.1       1.7   1.2e+03       5      19 ..     172     186 ..     167     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.7
                                   CCCTECCSSSTT-.......GGCTEECTTE CS
                        EXOSC1  79 sqdvRatekdrvk.......viemfrpGDI 101
                                   + +v  t+k+           +  + pGDI
  gi|91773406|ref|YP_566098.1|  33 KTEVTKTDKEDDHveeeqhgDKVLVMPGDI 62 
                                   444444555444412222211123445555 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.2e-06
                                   -TT-EEEEEEEEEESSEEEEEEEEECTB......SBCCCEEECCCTTSS--STS CS
                        EXOSC1   3 kegdvVLarvtrlrkkqalveilsvege......nnvlsdsgvgangegavkei 50 
                                   k+gd+ ++ v+++r + alv+i  ++g       +++++  +v++++e++vke+
  gi|91773406|ref|YP_566098.1| 112 KKGDILIGTVVNVRDSMALVQIEGIKGVvdrqfiKPGIAAIHVSNVKESYVKEM 165
                                   45***********************9999999********************97 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.7
                                   T-EEEEEEEEEESSE CS
                        EXOSC1   5 gdvVLarvtrlrkkq 19 
                                    dvV a+v++l++ +
  gi|91773406|ref|YP_566098.1| 172 ADVVKAKVINLENMR 186
                                   688888888888766 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 ?    2.1   0.2      0.31   2.3e+02      23      30 ..     198     205 ..     189     206 .. 0.80
   2 !   16.1   0.2   1.3e-05    0.0096      16      31 ..     207     222 ..     206     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.31
                                   -EE-TTT- CS
                     zf-RING_7  23 vvtCpeCG 30 
                                   v tC +CG
  gi|91773406|ref|YP_566098.1| 198 VSTCANCG 205
                                   79*****9 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.3e-05
                                   HHCCSTB-EE-TTT-- CS
                     zf-RING_7  16 elragdevvtCpeCGR 31 
                                    l++ d+v +CpeCGR
  gi|91773406|ref|YP_566098.1| 207 TLKKDDQVLKCPECGR 222
                                   57899**********9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6   7.4e-06    0.0055      14      37 ..     200     223 ..     191     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.4e-06
                           DZR  14 fCseCgtklkavaaedrCpsCgek 37 
                                   +C +Cg++lk+  +  +Cp+Cg+ 
  gi|91773406|ref|YP_566098.1| 200 TCANCGSTLKKDDQVLKCPECGRT 223
                                   799999999999999999999976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.4   1.1e-05    0.0085       2      20 ..     201     221 ..     200     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                 zinc_ribbon_2   2 CpnCGaelq.dnakF.CpyCG 20 
                                   C nCG +l+ d+++  Cp+CG
  gi|91773406|ref|YP_566098.1| 201 CANCGSTLKkDDQVLkCPECG 221
                                   ********7355555*****9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.4       5.6   4.2e+03      58      64 ..      34      40 ..      15      49 .. 0.58
   2 !   15.2   4.8   2.8e-05     0.021       3      65 ..     112     184 ..     110     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.6
                                  EEEEEEE CS
                            S1 58 vkvlkvd 64
                                   +v+k+d
  gi|91773406|ref|YP_566098.1| 34 TEVTKTD 40
                                  2333333 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.8e-05
                                   TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS...........CEESCHHHCEETTEEEEEEEEEEET CS
                            S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrd...........arvedpdevlkvGdevkvkvlkvdk 65 
                                   +kg+++ G+V++v +  a V+++ g++g v +  ++               v++ ++++ v d vk+kv+++++
  gi|91773406|ref|YP_566098.1| 112 KKGDILIGTVVNVRDSMALVQIE-GIKGVVDRQFIKPGiaaihvsnvkeSYVKEMSKEFAVADVVKAKVINLEN 184
                                   89*********************.******99999988999999999887889999999999999999999876 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.4e-05     0.018      55     114 ..     165     225 ..     135     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                       TackOD1  55 lleelvkrglleeelvdrirlCpsCksghln.vrevCpkCkSidieeqelihhftCgnvgp 114
                                   + +e++  +++++++++   +  + ++++l  +  +C +C+S+  + ++++++ +Cg++++
  gi|91773406|ref|YP_566098.1| 165 MSKEFAVADVVKAKVINLENMRMTTSGNELGvMVSTCANCGSTLKKDDQVLKCPECGRTES 225
                                   445555556666666655555555566666514689*********************9875 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.5       5.6   4.2e+03      23      23 ..      31      31 ..       7      58 .. 0.51
   2 ?   15.3   0.2   2.1e-05     0.016      98     142 ..     182     224 ..     154     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.6
                       DUF1451 23 e 23
                                  +
  gi|91773406|ref|YP_566098.1| 31 K 31
                                  1 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.1e-05
                       DUF1451  98 lehagvyqsGevvglGtlvCekCgkelalkkteeippCpkCgate 142
                                   le++   +sG+  g  + +C++Cg +  lkk +++ +Cp+Cg te
  gi|91773406|ref|YP_566098.1| 182 LENMRMTTSGNELGVMVSTCANCGST--LKKDDQVLKCPECGRTE 224
                                   566777889999999999******86..7899**********997 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.054        41      21      29 ..     200     208 ..     199     213 .. 0.65
   2 ?    8.5   0.1    0.0019       1.4       2      10 ..     216     224 ..     215     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.054
                                   EESSSSBEE CS
                  TF_Zn_Ribbon  21 vCtdCGlVl 29 
                                   +C +CG+ l
  gi|91773406|ref|YP_566098.1| 200 TCANCGSTL 208
                                   577777655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                                   EETTTTCEE CS
                  TF_Zn_Ribbon   2 kCPnCgstn 10 
                                   kCP+Cg t+
  gi|91773406|ref|YP_566098.1| 216 KCPECGRTE 224
                                   9*****986 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.4   3.2e-05     0.024      84     127 ..       6      49 ..       1      55 [. 0.86
   2 ?   -1.1   0.0       2.2   1.7e+03     125     140 ..     155     170 ..     151     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     YscO-like  84 eelkqeekkvekQkekVkvAerkvEqareelakkrkeveklekh 127
                                   e+ ++ee+ +    ekV+vAe+kvE++++e++k  ke + +e++
  gi|91773406|ref|YP_566098.1|   6 EKPEVEEEVLSTASEKVNVAEKKVEKRKTEVTKTDKEDDHVEEE 49 
                                   5566788888999*************************999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHHHHH CS
                     YscO-like 125 ekhkeewlkevkkeee 140
                                   ++ ke ++ke+ ke +
  gi|91773406|ref|YP_566098.1| 155 SNVKESYVKEMSKEFA 170
                                   5668889999888854 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.1   1.6e+03      54      67 ..      73      86 ..      56      88 .. 0.79
   2 ?   10.9   0.3   0.00053       0.4       8      38 ..     198     229 ..     192     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                  NOB1_Zn_bind 54 nfqlnlrGtkyslp 67
                                   + +n rG+++sl+
  gi|91773406|ref|YP_566098.1| 73 ANTYNVRGDIHSLA 86
                                  45699******996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00053
                  NOB1_Zn_bind   8 vlrChaCfkvtkd.mtkkFCpkCGnktLkrva 38 
                                   v  C  C ++ k+  +   Cp+CG    ++++
  gi|91773406|ref|YP_566098.1| 198 VSTCANCGSTLKKdDQVLKCPECGRTESRKIS 229
                                   789******9977366667*****99888876 PP

>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.093        69      33      58 ..      46      71 ..      13      76 .. 0.83
   2 ?   -1.0   0.0       2.7     2e+03      16      42 ..      87     117 ..      80     120 .. 0.75
   3 ?    6.9   0.2    0.0091       6.8       7      33 ..     119     145 ..     117     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.093
                                  CTTB-TT-EEEEETTEEEEEE-HHHH CS
                     HupF_HypC 33 veevkvGdyVLvhvGfAiekideeea 58
                                  vee + Gd VLv  G  i   +e ea
  gi|91773406|ref|YP_566098.1| 46 VEEEQHGDKVLVMPGDIIGTTEEFEA 71
                                  68999********9999988888777 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                                   EEEEECTTEEEEEEGTTC....TTB-TT-EE CS
                     HupF_HypC  16 lAlvdvgGvrrevslalv....eevkvGdyV 42 
                                   ++ v v+  rr +s++ +    + +k Gd +
  gi|91773406|ref|YP_566098.1|  87 TGFVMVNNKRRMISVKPTtsmpPTIKKGDIL 117
                                   5678888999999988777776778888876 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0091
                                   EEEEEEETTEEEEECTTEEEEEEGTTC CS
                     HupF_HypC   7 gkvveiedelAlvdvgGvrrevslalv 33 
                                   g vv++ d++Alv+++G++  v+ +++
  gi|91773406|ref|YP_566098.1| 119 GTVVNVRDSMALVQIEGIKGVVDRQFI 145
                                   679***************999887766 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.7   0.00058      0.43       4      23 ..     200     221 ..     197     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00058
                   zf-ribbon_3   4 rCPnCGa.plssddn..vCpyCG 23 
                                   +C nCG+ + ++dd+  +Cp CG
  gi|91773406|ref|YP_566098.1| 200 TCANCGStL-KKDDQvlKCPECG 221
                                   699****77.65555227****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.081        61      28      38 ..     200     210 ..     195     211 .. 0.80
   2 ?   10.3   4.3   0.00078      0.58       8      38 ..     201     227 ..     200     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.081
                   Zn-ribbon_8  28 aCPeCgsevrr 38 
                                   +C +Cgs++++
  gi|91773406|ref|YP_566098.1| 200 TCANCGSTLKK 210
                                   59999999887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00078
                   Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evrr 38 
                                   C +Cg++     +  d+   +CPeCg  e r+
  gi|91773406|ref|YP_566098.1| 201 CANCGSTLK---K--DDQVLKCPECGRtESRK 227
                                   999995555...3..444556******88777 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 ?   11.1   0.8   0.00039      0.29      12      36 ..     199     222 ..     196     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                                   -B-TTT-SB--SSSS-EEEETTT-- CS
                          C1_1  12 tfCkhCgeflwgkekqglkCswCkl 36 
                                   ++C+ Cg+ l +k  q lkC +C++
  gi|91773406|ref|YP_566098.1| 199 STCANCGSTL-KKDDQVLKCPECGR 222
                                   68********.************97 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.9   0.00065      0.48       2      24 ..     200     221 ..     200     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00065
                                   B-SSS--B----SSS----SSS- CS
                DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCG 24 
                                   +C++Cg+  + +   +++C eCG
  gi|91773406|ref|YP_566098.1| 200 TCANCGSTLKKD-DQVLKCPECG 221
                                   5*****987643.3478*****9 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0042       3.1      26      42 ..     193     209 ..     189     213 .. 0.87
   2 ?    2.6   0.1      0.17   1.3e+02      31      42 ..     214     225 ..     212     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0042
                        HalOD2  26 qLGayvWkCtrCGevqa 42 
                                   +LG  v  C++CG +++
  gi|91773406|ref|YP_566098.1| 193 ELGVMVSTCANCGSTLK 209
                                   79***********9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                        HalOD2  31 vWkCtrCGevqa 42 
                                   v kC +CG +  
  gi|91773406|ref|YP_566098.1| 214 VLKCPECGRTES 225
                                   678999998865 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.2    0.0011       0.8       3      26 ..     199     221 ..     193     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                PhnA_Zn_Ribbon   3 pkCplCaSeytY.edgallvCpeCa 26 
                                   + C +C+S  t+  d+++l CpeC+
  gi|91773406|ref|YP_566098.1| 199 STCANCGS--TLkKDDQVLKCPECG 221
                                   78999998..8889**********7 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.025        19       3      15 ..     200     212 ..     199     212 .. 0.87
   2 ?    5.0   0.4     0.034        26       3       8 ..     216     221 ..     215     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                        zf-ACC   3 KCpsCgemlykke 15 
                                    C  Cg++l k +
  gi|91773406|ref|YP_566098.1| 200 TCANCGSTLKKDD 212
                                   6********9976 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                        zf-ACC   3 KCpsCg 8  
                                   KCp+Cg
  gi|91773406|ref|YP_566098.1| 216 KCPECG 221
                                   9****9 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.053        40       3      16 ..     199     212 ..     198     216 .. 0.79
   2 ?    6.0   0.5     0.026        19       4      14 ..     216     226 ..     213     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.053
                       zf-ISL3   3 hrCPnCgsktvvkh 16 
                                    +C nCgs+ +++ 
  gi|91773406|ref|YP_566098.1| 199 STCANCGSTLKKDD 212
                                   59*******76665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.026
                       zf-ISL3   4 rCPnCgsktvv 14 
                                   +CP+Cg++  +
  gi|91773406|ref|YP_566098.1| 216 KCPECGRTESR 226
                                   7******9433 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.1      0.45   3.4e+02       6      24 ..      25      44 ..      20      54 .. 0.73
   2 ?    9.7   0.3    0.0012      0.92      33      70 ..     166     210 ..     163     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.45
                        DUF678  6 gkkkrrkrkpkttvede.dd 24
                                  ++kk  krk+++t  d+ dd
  gi|91773406|ref|YP_566098.1| 25 AEKKVEKRKTEVTKTDKeDD 44
                                  78999999999884443244 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                        DUF678  33 SkLvkvsdvskvslsklkva..vgkgntl.....rCaACgSsLtl 70 
                                   Sk   v dv k ++ +l+++  ++ gn l     +Ca CgS+L++
  gi|91773406|ref|YP_566098.1| 166 SKEFAVADVVKAKVINLENMrmTTSGNELgvmvsTCANCGSTLKK 210
                                   67778999999999999988877888877556667*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1643  (0.0916392); expected 358.6 (0.02)
Passed bias filter:                      864  (0.0481901); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1522.50
//
Query:       gi|91773407|ref|YP_566099.1|  [L=91]
Description: DNA-directed RNA polymerase, subunit L [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-18   66.3   0.6      2e-18   65.9   0.6    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    0.00016   21.0   0.2    0.00029   20.2   0.2    1.4  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.6   2.2e-22     2e-18       2      72 ..      13      82 ..      12      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.2e-22
                                  EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHH CS
                   RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdel 72
                                  +++ei+gE hTL+n+L+ +ll++++V+ a+Y+++H  +++  l i+t+ + +p++++k a+ +l+ +c+e+
  gi|91773407|ref|YP_566099.1| 13 MKMEIAGESHTLLNMLKIILLEDERVHTASYDMKHVTISEPVLFIKTE-NADPIDVVKAAVAKLITECEEF 82
                                  789*********************************999999999996.79******************98 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 !   20.2   0.2   3.3e-08   0.00029       2      69 .]      15      79 ..      14      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-08
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_L  2 fllrgvdhtlgNaLRrillsevpgvaiea..........pvvkvntdkdklilevetdgslkPeealkeAlkiLkekl 69
                                   ++ g++htl N+L+ ill e + v  ++          pv         l+++ e     +P +++k A+ +L+  +
  gi|91773407|ref|YP_566099.1| 15 MEIAGESHTLLNMLKIILL-EDERVHTASydmkhvtisePV---------LFIKTE---NADPIDVVKAAVAKLITEC 79
                                  5789***************.998888888877777666688.........999999...89*************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 631.37
//
Query:       gi|91773408|ref|YP_566100.1|  [L=387]
Description: Sep-tRNA:Cys-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-45  154.9   0.0    8.7e-45  153.1   0.0    1.8  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    8.7e-17   61.1   0.0    1.3e-16   60.5   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    2.3e-12   46.8   0.0    3.2e-12   46.3   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
      9e-05   21.9   0.0    0.00014   21.3   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00034   19.5   0.0    0.00067   18.5   0.0    1.4  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
     0.0063   15.3   0.0     0.0091   14.8   0.0    1.2  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.0   2.9e-48   8.7e-45      19     388 ..      57     383 ..      45     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 2.9e-48
                                   -S-HHHHHCCCCHHCTBSBTTBTTS-CCCCCCCCCHCCCCCHHHHHHHHHTTHCCHHEECCCSS-HHHHHHHHHHHHHHHC CS
                       SepSecS  19 vlselkeesvfdfiHgvGrsGnlvdvqPKalGasvlakltNklvkdilkllGlrevknafvvPlatGlslaLClsalrkrs 99 
                                   vl+ +k+++v +fiH            P +lG +   ++t           G+re k  f+v           + a+   +
  gi|91773408|ref|YP_566100.1|  57 VLDLIKKPPVQKFIHE---------ALPEFLGVDE-VRITH----------GARESK--FAV-----------MHAIA--Q 102
                                   5555555555555555.........3455555555.45555..........555444..555...........55555..7 PP

                                   C--CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHH...HHHHHHHHCCTCCCEEEEEECSSTTTTB----HHHH CS
                       SepSecS 100 kakkviwvridekSslkavelaGleialvekvlegDelitdv...edveeiiekkreevilavlstlsffaprspDdvkei 177
                                   ++++vi   +++ Ss++a+++a lei+ v++ +++D+ i ++    ++ee i + ++   la+l+++++++++++D  k+i
  gi|91773408|ref|YP_566100.1| 103 EGDTVILDGLAHYSSVVAAQRARLEIRKVPHSEKPDYHIDPEaygTAIEETISETGKAPALALLTYPDGNYGNLAD-AKKI 182
                                   8999*********************************9988733347999999999999*****************.9*** PP

                                   HHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCCCCCHC...CCHCHCTS CS
                       SepSecS 178 akiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfikeisk...eypgrasa 255
                                   a +C+eydvP+l+N AY++               GR++v  k+l+ +++ ++G++++a+ +++++ ++++    y++++ +
  gi|91773408|ref|YP_566100.1| 183 ASVCHEYDVPLLLNCAYSV---------------GRMPVDAKELGVDFIAGSGHKSMASCGPIGVLGVNNdngDYSDIIFR 248
                                   *******************...............*********************************9873336******* PP

                                   CHCCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC..............EEESSSTT-SSEEEEE-CCCHCC CS
                       SepSecS 256 apskdvlisllllGskaykkllkeqkesfkllreklkklaeeve..............ekllevpeNpissaltletldei 322
                                   ++ ++++++++llG++a+ ++l +  +sf+ + ++ +++ +ev                +++++p+N++++++ +  l+ei
  gi|91773408|ref|YP_566100.1| 249 KSPTNKNKEIELLGCTARSATLMTMIASFPEVVKRTRNWGNEVAdarwfsekletmglIQMGQKPHNHDLMFFEAPNLYEI 329
                                   *****************************************9999***********9999********************* PP

                                   CC...THHHHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE-TT--HHHHHHHHHHHHHHH CS
                       SepSecS 323 kk...karldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkiasaiGlkdedvdkvlerldeil 388
                                   +    k+r +l++eL+sr+++G++       +lT        +++k+ s++ +  e++ ++++ +dei+
  gi|91773408|ref|YP_566100.1| 330 STrvkKGRYFLYKELKSRNIHGIK------AGLT--------KFFKL-STFEVGRENLSYIVDSFDEII 383
                                   988889******************......7788........88888.888888888888888888887 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   4.4e-20   1.3e-16      52     215 ..      74     237 ..      68     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 4.4e-20
                                   HHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE..TTSCBEGG CS
                   Aminotran_5  52 vaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipld..eegeldld 130
                                   + e+++++   e+  t+G+ e+  +v++++    ++gd++++  + h + +v++q+++    ++++++p    ++ ++d++
  gi|91773408|ref|YP_566100.1|  74 LPEFLGVD---EVRITHGARESKFAVMHAI---AQEGDTVILDGLAHYSSVVAAQRAR----LEIRKVPHSekPDYHIDPE 144
                                   55666666...5888***************...89****************9999998....6677776551156788888 PP

                                   GHHHH-.......-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTS CS
                   Aminotran_5 131 elekll.......nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllg 204
                                   ++ +++        + ++l  +t      G++ + ++i+++++++++ +l+  a +vg +p+d k+lgvDf+a sghK ++
  gi|91773408|ref|YP_566100.1| 145 AYGTAIeetisetGKAPALALLTYPDGNYGNLADAKKIASVCHEYDVPLLLNCAYSVGRMPVDAKELGVDFIAGSGHKSMA 225
                                   776666555566446678889999999***************************************************777 PP

                                   STT.-EEEEEEH CS
                   Aminotran_5 205 PtG.iGvlyvrk 215
                                     G iGvl v +
  gi|91773408|ref|YP_566100.1| 226 SCGpIGVLGVNN 237
                                   777799998766 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   1.1e-15   3.2e-12      45     235 ..      66     235 ..      49     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.1e-15
                                   HHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET CS
                 Aminotran_1_2  45 glpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyse 125
                                   +++   eal +flg         + +v  + Ga +   a++ ++ ++ gd ++++ + + s   +++ +++e++++p +++
  gi|91773408|ref|YP_566100.1|  66 VQKFIHEALPEFLG--------VD-EVRITHGARESKFAVMHAI-AQEGDTVILDGLAHYSSVVAAQRARLEIRKVPHSEK 136
                                   55667788889999........66.9******************.9*******************************9999 PP

                                   TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGG CS
                 Aminotran_1_2 126 edfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatran 206
                                   +d+h+d ea+ +a++e  ++    k  +++    P+G   +l++ +k+++++++y + l++  aY+++ +         ++
  gi|91773408|ref|YP_566100.1| 137 PDYHIDPEAYGTAIEETISETG--KAPALALLTYPDGNYGNLADAKKIASVCHEYDVPLLLNCAYSVGRMP--------VD 207
                                   ***************9877776..777777788888888888888888888*****************997........33 PP

                                   STTSTTEEEEEESSSTTSSGGG-EEEEEE CS
                 Aminotran_1_2 207 veeepnllivgslsKafGlaGeRvGyilg 235
                                   ++e   ++i+gs  K++++ G  +G + +
  gi|91773408|ref|YP_566100.1| 208 AKELGVDFIAGSGHKSMASCG-PIGVLGV 235
                                   444334599999999999998.7777766 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 !   21.3   0.0   4.6e-08   0.00014      23     150 ..      64     202 ..      55     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.6e-08
                                   HHHHHH.HHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE.-B-TTTSSB-G CS
               DegT_DnrJ_EryC1  23 peveeF.EkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfv.Dvdpdtynidp 101
                                   p v++F  +a+ ++lgv+ +  +  + ++   +++a+  + gd+VI   l   +++ a++++ ++   v   ++ +y idp
  gi|91773408|ref|YP_566100.1|  64 PPVQKFiHEALPEFLGVDEVRITHGARESKFAVMHAIAQE-GDTVILDGLAHYSSVVAAQRARLEIRKVpHSEKPDYHIDP 143
                                   5566664578999999999888888888888888888765.**********************999988346788****** PP

                                   GGCGGG--TTE........EE..EEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
               DegT_DnrJ_EryC1 102 aaieaaitert........ka..IlpVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                   +a   ai+e           a    p   yG+ ad +++  ++++++++++  +A ++G
  gi|91773408|ref|YP_566100.1| 144 EAYGTAIEETIsetgkapaLAllTYPDGNYGNLADAKKIASVCHEYDVPLLLNCAYSVG 202
                                   987766666545556554322112344569*************************9999 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 !   18.5   0.0   2.2e-07   0.00067      87     256 ..      85     238 ..      77     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-07
                                   ESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E..B-TTS-BE---GGGGSHHHHHHHHHHSTT CS
                      OKR_DC_1  87 vvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe..rnalgiiggidlkefeeetlkekikevpd 165
                                   +++G   s  +v++a++++gd+v++d  +H S   a   +  + +   p+  +  ++i  + +        ++e i+e+ +
  gi|91773408|ref|YP_566100.1|  85 ITHGARESKFAVMHAIAQEGDTVILDGLAHYSSVVAAQRARLE-IRKVPHseKPDYHIDPEAYG-----TAIEETISETGK 159
                                   5788999999*********************998877666554.33333312666666555555.....899999999987 PP

                                   TGSESEEEEESS.-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEEEEEHCCCCS-- CS
                      OKR_DC_1 166 akaprlavitns.TYdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilvtqSvHKllaal 245
                                   a a  la++t +   +G l++ak+i    +++++++l+  A+        +++da +l+ +       + + S HK  a+ 
  gi|91773408|ref|YP_566100.1| 160 APA--LALLTYPdGNYGNLADAKKIASVCHEYDVPLLLNCAYS----VGRMPVDAKELGVD-------FIAGSGHKSMASC 227
                                   766..88888773468************************996....47899999999999.......9999999998887 PP

                                   TT-EEEEEES- CS
                      OKR_DC_1 246 sqaSlihvkee 256
                                       ++ v+++
  gi|91773408|ref|YP_566100.1| 228 GPIGVLGVNND 238
                                   66666666555 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 !   14.8   0.0     3e-06    0.0091     154     238 ..     113     200 ..      88     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-06
                                   S-HHHHHHHHHHT-EEEEE--BTT..TBB-HHHHHHHHHHHH.CTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EE CS
                 Pyridoxal_deC 154 ahssvekaalvlgvklrviplden..gklrgaalekaieedk.ekGlipffvvatlGttvlgaFddlkelgdicekydlwl 231
                                   ah+s   aa+ + +++r +p  e+  +++ ++a   aiee + e G  p  +  t    ++g+  d k+++ +c++yd++l
  gi|91773408|ref|YP_566100.1| 113 AHYSSVVAAQRARLEIRKVPHSEKpdYHIDPEAYGTAIEETIsETGKAPALALLTYPDGNYGNLADAKKIASVCHEYDVPL 193
                                   899999**************98762255667788899*9986378************************************ PP

                                   EEE-TTG CS
                 Pyridoxal_deC 232 HvDAAya 238
                                       Ay 
  gi|91773408|ref|YP_566100.1| 194 LLNCAYS 200
                                   9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2806.87
//
Query:       gi|91773409|ref|YP_566101.1|  [L=259]
Description: 3-methyladenine DNA glycosylase-like protein [Methanococcoides burtonii DSM 6242]
Scores for 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   56.4   1.5    9.3e-14   51.6   1.5    2.1  1  Adenine_glyco  Methyladenine glycosylase
  ------ inclusion threshold ------
      0.042   14.2   2.0      0.077   13.4   2.0    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
      0.084   13.3   0.0       0.15   12.5   0.0    1.4  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p


Domain annotation for each model (and alignments):
>> Adenine_glyco  Methyladenine glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   1.5   1.6e-17   9.3e-14      22     123 ..      42     141 ..      26     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.6e-17
                 Adenine_glyco  22 ddkklFelLvLegfqaglswetilkkreafreafdgFdlekvakydeekveelladegiirnrlKieavisnAravlalqe 102
                                    d++ F++L+   f +g+  et+ kk +  + +f +F  e++++yde +++e+++de++i+n++Ki a+++n+ ++  + e
  gi|91773409|ref|YP_566101.1|  42 SDDEYFDKLTKVVFYSGFKAETVTKKLDIIKYHFPDF--ETISNYDEGRINEIFNDESMIKNKKKILACVNNSIVFKGIVE 120
                                   68899*****************************988..58**************************************** PP

                 Adenine_glyco 103 efgsfseylwsfvdgkpivee 123
                                   ++gsf +y+ sf  +++ ++ 
  gi|91773409|ref|YP_566101.1| 121 KYGSFRSYVDSFEIDNSFENL 141
                                   ************965444443 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 ?   13.4   2.0   1.3e-05     0.077       5      17 .]     242     254 ..     242     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                 EndIII_4Fe-2S   5 kPkCeaCPLaDlC 17 
                                   +PkC +C + ++C
  gi|91773409|ref|YP_566101.1| 242 NPKCHICGIKEYC 254
                                   9************ PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.15      24      92 ..      72     191 ..      51     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                   HHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH...................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                       HhH-GPD  24 rfgfptpedladadeekLrelirelGfyrrKakyikelArilv...................................... 66 
                                   ++ fp++e++ ++de  ++e+     + ++K k +  +   +v                                      
  gi|91773409|ref|YP_566101.1|  72 KYHFPDFETISNYDEGRINEIFNDESMIKNKKKILACVNNSIVfkgivekygsfrsyvdsfeidnsfenlmlfkeeiqyrf 152
                                   2339************************9**999999999999************************************** PP

                                   ...............S-SSS--TTSHHHHHHHHHHTTSSSS CS
                                   ...............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ...............gkpdvlivvDvhvrrilkrlrsikek 92 
                                                  g   ++   D +++ri+krl++i++ 
  gi|91773409|ref|YP_566101.1| 153 aflgeitsyhfmtdiGL--PVLKPDRVIARIFKRLNLIEDE 191
                                   *********98765542..33337*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1483.85
//
Query:       gi|91773410|ref|YP_566102.1|  [L=68]
Description: hypothetical protein Mbur_1442 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   30.5   0.1    3.2e-07   30.5   0.1    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.1   1.8e-11   3.2e-07       1      61 [.       3      63 ..       3      68 .] 0.91

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.8e-11
               HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssi 61
                                  y ia+e  e+  ++    +lp ++s gdt eea++n+keaiel le + e+ + + e+ ++
  gi|91773410|ref|YP_566102.1|  3 YTIALEAAEEGGFTARCLELPAAISEGDTREEALENIKEAIELVLEVTQEQARILGEVAKV 63
                                  89*********************************************99988777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 435.70
//
Query:       gi|91773411|ref|YP_566103.1|  [L=270]
Description: molybdenum ABC transporter, periplasmic molybdate-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-44  151.8   0.0    2.7e-44  151.6   0.0    1.0  1  SBP_bac_11       Bacterial extracellular solute-binding prote
    8.4e-10   39.1   0.2      9e-05   22.6   0.0    2.1  2  SBP_bac_1        Bacterial extracellular solute-binding prote
    2.1e-08   34.1   0.1    2.9e-08   33.6   0.1    1.3  1  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
    0.00054   19.5   0.0    0.00079   18.9   0.0    1.3  1  SBP_bac_6        Bacterial extracellular solute-binding prote
  ------ inclusion threshold ------
      0.058   12.8   0.1       0.11   11.9   0.1    1.4  1  SBP_bac_3        Bacterial extracellular solute-binding prote
      0.064   11.8   0.4        0.1   11.1   0.4    1.2  1  DUF5357          Family of unknown function (DUF5357)
      0.097   12.3   0.1       0.16   11.7   0.1    1.5  1  PBP_like_2       PBP superfamily domain
       0.11   11.6   4.8       0.21   10.6   4.9    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.22   12.5   3.2        1.8    9.5   3.2    2.4  1  Pilin_N          Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.0   1.4e-47   2.7e-44       4     229 ..      40     260 ..      37     261 .. 0.95

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 1.4e-47
                                   EE-SSTHHHHHHHHHHHHH.HH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEE CS
                    SBP_bac_11   4 aaagslaaalrelaaaFea.htgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplvi 83 
                                    a++ l+++++++ ++Fea +++++v + ++++g l+ qi++g + Dv++pa+  +++ l +ag+v ++s++++a+s lvi
  gi|91773411|ref|YP_566103.1|  40 SASAVLTEVFTDMEEEFEAeNPDIDVIMNFANAGSLRMQIEGGGPIDVYAPADRVQMDILTSAGFVYNDSRKDFAGSYLVI 120
                                   5788899**********6637************************************************************ PP

                                   EESTT-TT---SHHHHHHSS-.-EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEE CS
                    SBP_bac_11  84 avpkgnpkkikgwadLlkpgl.klavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltaveageadagi 163
                                   +vpkgn  +i++++dL kp++ ++a++d ++s++G++a++ l   g   l++++++k+   g+++ +++  ve+ge+dag+
  gi|91773411|ref|YP_566103.1| 121 IVPKGNVLNITTMEDLSKPEVkRIAFTDTEASTVGKYAKQSLIEKG---LWNSVQNKMI-IGDTVKNAMVHVERGEVDAGF 197
                                   *********************88****************999999*...*********9.9******************** PP

                                   EEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                    SBP_bac_11 164 vyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrkyGf 229
                                   v  +++k+ +++d +e+++  ++    ++ yp+av+++++++++ ++F++f++++++  il++yGf
  gi|91773411|ref|YP_566103.1| 198 VFMTDVKT-AKPDTIELITSVPMSE--TINYPIAVVTSTQHQKESQRFVDFVTGEKGSSILEQYGF 260
                                   *******5.4688899998777777..499************************************ 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 !   14.8   0.0     1e-05     0.021      16      71 ..      54     105 ..      40     133 .. 0.78
   2 !   22.6   0.0   4.5e-08     9e-05     211     313 ..     169     251 ..     134     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                                   HHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSB CS
                     SBP_bac_1  16 kafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakagll 71 
                                   ++fe+e+p+i+V  ++   gsl+     +i++G  p+Dv a  d  +++ l +ag++
  gi|91773411|ref|YP_566103.1|  54 EEFEAENPDIDVIMNFANAGSLRM----QIEGGG-PIDVYAPaDRVQMDILTSAGFV 105
                                   56***************8888888....******.*******888888888888543 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 4.5e-08
                                   HHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEE CS
                     SBP_bac_1 211 kelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglai 291
                                       +k   + ++ +a   +e+Ge+++++v+ +++++a+   ++  + +++++                     ++y++a+
  gi|91773411|ref|YP_566103.1| 169 NSVQNKMIIGDTVKNAMVHVERGEVDAGFVFMTDVKTAKPDTIELITSVPMSET--------------------INYPIAV 229
                                   455666677777777777788*************88888888888888888888....................******* PP

                                   BTTCSTHHHHHHHHHHHTSHHH CS
                     SBP_bac_1 292 pkgsknpeaAkkFldfllspea 313
                                   +++++++++ + F+df++++++
  gi|91773411|ref|YP_566103.1| 230 VTSTQHQKESQRFVDFVTGEKG 251
                                   ******************9986 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 !   33.6   0.1   1.4e-11   2.9e-08      83     232 ..     114     260 ..      41     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.4e-11
                                   SEEEEEEEEETTS..S--SHHHH...GG-EEEE--TT.-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTS CS
                Phosphonate-bd  83 asyrsviivrads..diqsledL...kgktiafvsps.StsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgd 157
                                   a+ + viiv++++  +i+++edL   + k+iaf++++ St G ++ + l+  e+gl  + + +   +++  +a++ v +g+
  gi|91773411|ref|YP_566103.1| 114 AGSYLVIIVPKGNvlNITTMEDLskpEVKRIAFTDTEaSTVGKYAKQSLI--EKGLWNSVQNKMIIGDTVKNAMVHVERGE 192
                                   567899******966699*****************853788888888866..89**999999999**************** PP

                                   SSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHH---SHHHHHHHHHTTE CS
                Phosphonate-bd 158 adaaavsadaledlvaegpedkdelrviassppipndpvvvrkelseelkekiqdallslaeteegkkllealgi 232
                                   +da++v+ + ++  +   p+  + ++ +  s+ i+ ++ vv+++  +++ ++  d+ ++ +    g+ +le++g+
  gi|91773411|ref|YP_566103.1| 193 VDAGFVFMTDVKTAK---PDTIELITSVPMSETINYPIAVVTSTQHQKESQRFVDFVTGEK----GSSILEQYGF 260
                                   ******999887764...5678888999999999888888888888877777666665554....6777777665 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 !   18.9   0.0     4e-07   0.00079     129     217 ..     180     263 ..     116     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4e-07
                     SBP_bac_6 129 paqmvkaagslesgepavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkgkkkelakafidfllspevqail 209
                                    +   +a+ ++e ge  v+ ++ f++d+  +k +   l   +P + ++ +pi+++  ++ ++++ ++f+df +++++ +il
  gi|91773411|ref|YP_566103.1| 180 TV--KNAMVHVERGE--VDAGFVFMTDVKTAKPDTIELITSVPMSETINYPIAVVTSTQ-HQKESQRFVDFVTGEKGSSIL 255
                                   33..47778899999..***************98888888899999*************.********************* PP

                     SBP_bac_6 210 akaggvfP 217
                                   +  g+++P
  gi|91773411|ref|YP_566103.1| 256 EQYGFTIP 263
                                   ****9988 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.4e-05      0.11      85     158 ..     116     198 ..     101     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                                   EEEEEEEEETTSHGTCCHSSCGCG...TTSEEEEETT..SHHHHHHHHHHHC.......TSEEEEESSHHHHHHHHHTTSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx..xxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3  85 agqvllvrkkdaskissiksladL...kgkkvgvqag..staeellkeelkk.......gaeivefdtleealqaLkngrv 153
                                   + +v++v+k++   + +i++++dL   + k+++ +    st  +++k++l +       + +++  dt  +a+  ++ g+v
  gi|91773411|ref|YP_566103.1| 116 SYLVIIVPKGN---VLNITTMEDLskpEVKRIAFTDTeaSTVGKYAKQSLIEkglwnsvQNKMIIGDTVKNAMVHVERGEV 193
                                   56799***864...4566666677543558999654435888889999776689998887777889*************** PP

                                   SEEEE CS
                                   xxxxx RF
                     SBP_bac_3 154 davva 158
                                   da ++
  gi|91773411|ref|YP_566103.1| 194 DAGFV 198
                                   **775 PP

>> DUF5357  Family of unknown function (DUF5357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   5.1e-05       0.1      76     134 ..       6      59 ..       2      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                       DUF5357  76 gtflpvgalitgflvsvfafgeeedeitprtivlwptisavitaipeflegtdtdlkak 134
                                    t + v+a+i  +++s+f + ++++e tp++i++ +  sav+t + + +e++   ++a+
  gi|91773411|ref|YP_566103.1|   6 QTLMVVTAIIILIVISAFSINSNDEEQTPTSIIISA--SAVLTEVFTDMEEE---FEAE 59 
                                   689*****************************9976..66766655555444...4443 PP

>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.8e-05      0.16       3     114 ..      30     138 ..      27     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
                    PBP_like_2   3 aaeatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngd.......vdfagsdrplteseiaag 76 
                                   +++++++  i +++s  + ++++++ + fe ++p+++v       g+ + ++ +g        +d + +d  lt++ +  +
  gi|91773411|ref|YP_566103.1|  30 EEQTPTS--IIISASAVLTEVFTDMEEEFEAENPDIDVIMNFANAGSLRMQIEGGGpidvyapADRVQMD-ILTSAGF--V 105
                                   5667777..****************999***************************9*8888887777777.7777778..7 PP

                    PBP_like_2  77 waangaggliqvpvaigaialvvnkdnpln.lsreaLak 114
                                   ++  +       ++a + ++++v+k n ln  ++e+L+k
  gi|91773411|ref|YP_566103.1| 106 YNDSR------KDFAGSYLVIIVPKGNVLNiTTMEDLSK 138
                                   88888......*******************955555543 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 ?   10.6   4.9   0.00011      0.21       8      76 ..       9      81 ..       6     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
               ABC2_membrane_3  8 lllPiilvlllglifsnsveddentpiavvdedn...sslsqqlvealea.spsvelvyevdseeeakkalkn 76
                                   +++ i++l+++++fs++++d e+tp+ ++ +     ++ +  + e++ea +p+++++ ++++  +++ +++ 
  gi|91773411|ref|YP_566103.1|  9 MVVTAIIILIVISAFSINSNDEEQTPTSIIISASavlTEVFTDMEEEFEAeNPDIDVIMNFANAGSLRMQIEG 81
                                  4577788888899999999999999996655555466667888889999989999988888888777766664 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.2   0.00091       1.8      11      42 ..       8      39 ..       6      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00091
                       Pilin_N 11 LmvaitvIlaAviaafvlglasneekapq.asi 42
                                  Lmv+  +I++ vi+af ++  ++ee++p  + i
  gi|91773411|ref|YP_566103.1|  8 LMVVTAIIILIVISAFSINS-NDEEQTPTsIII 39
                                  9***************9998.555555541444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1811.40
//
Query:       gi|91773412|ref|YP_566104.1|  [L=63]
Description: RNA-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-17   63.7   1.4    1.3e-17   63.6   1.4    1.0  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 !   63.6   1.4     7e-22   1.3e-17       3      62 .]       8      63 .]       6      63 .] 0.96

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 7e-22
                                  XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                          TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62
                                  + G+ ++V++e+ + +eg+gi+r+  g+v+fvp+++   Gd+V++k+tkv r++++Ge++
  gi|91773412|ref|YP_566104.1|  8 EAGESYDVTIEDTA-REGDGIARVS-GFVIFVPNTSV--GDEVTIKVTKVARKFAFGEVV 63
                                  679**********9.**********.********999..*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 416.36
//
Query:       gi|91773413|ref|YP_566105.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91773413|ref|YP_566105.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91773413|ref|YP_566105.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91773413|ref|YP_566105.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91773413|ref|YP_566105.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91773413|ref|YP_566105.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91773413|ref|YP_566105.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91773413|ref|YP_566105.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91773413|ref|YP_566105.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1832.34
//
Query:       gi|91773414|ref|YP_566106.1|  [L=226]
Description: hypothetical protein Mbur_1449 [Methanococcoides burtonii DSM 6242]
Scores for 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-14   52.0   0.0    1.5e-13   51.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.3e-13   51.5   0.0    2.5e-13   50.5   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    2.2e-12   47.5   0.0    3.7e-12   46.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.7e-09   37.6   0.0    2.2e-09   37.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.1e-05   22.5   0.0    8.6e-05   22.0   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00031   20.6   0.0    0.00035   20.4   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00072   18.9   0.0    0.00099   18.5   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.015   14.6   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.092   12.2   0.0       0.42   10.0   0.0    2.0  2  Pet127           Mitochondrial protein Pet127


Domain annotation for each model (and alignments):
>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   7.3e-17   1.5e-13       1      99 []      45     144 ..      45     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 7.3e-17
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl.. 79 
                                   L+ GcGtGsl++   e + +++++  D+s++++  ak++l k+e++++++ ++++ dl  + g    D+v+a++  h+l  
  gi|91773414|ref|YP_566106.1|  45 LDTGCGTGSLIELANETFDECNFYLNDPSEEMLSYAKTRLEKYEAERFKFTNYTTADLPLS-GVPECDVVTAIQSHHYLnr 124
                                   899***************************************************9998754.446***************9 PP

               Methyltransf_12  80 kdirevldnirklLkpgGrl 99 
                                   ++++++ ++++  Lk++G++
  gi|91773414|ref|YP_566106.1| 125 EERASITAKCYGILKKEGIF 144
                                   9999*************975 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   1.3e-16   2.5e-13       2      97 .]      45     142 ..      45     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.3e-16
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTT.TEEEEEEESTGGGSSHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedg.sfDlvvssgalhhlsde 80 
                                   Ld GcGtG l++ + + + +++++  D+seeml +a++r+e+ ++ +++f +    dlp+    ++D+v+++++ h+l++e
  gi|91773414|ref|YP_566106.1|  45 LDTGCGTGSLIELANETFDECNFYLNDPSEEMLSYAKTRLEKYEAeRFKFTNYTTADLPLSGVpECDVVTAIQSHHYLNRE 125
                                   8*******999999999989********************998889*************855449******988999**** PP

                                   HHHHHHHHHHHHEEEEE CS
               Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                   +++ + ++++ +Lk++G
  gi|91773414|ref|YP_566106.1| 126 ERASITAKCYGILKKEG 142
                                   **************998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.9e-15   3.7e-12       1      95 [.      45     145 ..      45     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.9e-15
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEEES-CCC-..C CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvssevlhhv..e 75 
                                   Ld GcGtG+l e   +++  ++ +  D+s+eml +ak++ ++ +  +++f   +  +lp+     +D+v++ ++ h++  e
  gi|91773414|ref|YP_566106.1|  45 LDTGCGTGSLIELANETFdeCNFYLNDPSEEMLSYAKTRLEKYEAeRFKFTNYTTADLPLSGvPECDVVTAIQSHHYLnrE 125
                                   89*************9999*********************9999999999999999***998669*************999 PP

                                   CHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                   +++++ ++++ +Lk++G++v
  gi|91773414|ref|YP_566106.1| 126 ERASITAKCYGILKKEGIFV 145
                                   ******************98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.1e-12   2.2e-09       8     111 ..      45     148 ..      42     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.1e-12
               Methyltransf_31   8 lDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsnevlnal 87 
                                   lD GCGtG l+  ++ e ++++++++ D see++++A+++++k + ++++F      +l+ + + +   D++++ +  ++l
  gi|91773414|ref|YP_566106.1|  45 LDTGCGTGSLIELAN-ETFDECNFYLNDPSEEMLSYAKTRLEKYEAERFKFTNYTTADLPLSgVPE--CDVVTAIQSHHYL 122
                                   9*******9987777.99******************************************988885..9999998887555 PP

               Methyltransf_31  88 a..dpdkileeiervlkpggillied 111
                                   +  + ++i  +    lk++gi+++ +
  gi|91773414|ref|YP_566106.1| 123 NreERASITAKCYGILKKEGIFVTFE 148
                                   41145667777888888888888655 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.3e-08   8.6e-05      49     159 ..      42     154 ..      19     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.3e-08
                                   TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-.T-EEEEEE..ES-G CS
               Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed.dsfDvvtv..sfGl 126
                                   +  lD  +Gtg l ++l+++  ++ +  + D +e+mL+ ++ +l++    + +f +  + +Lp +     Dvvt   s+  
  gi|91773414|ref|YP_566106.1|  42 ELWLDTGCGTGSL-IELANETFDECNFYLNDPSEEMLSYAKTRLEKYEAERFKFTNYTTADLPLSGvPECDVVTAiqSHHY 121
                                   3679*******97.8999999999****************************************998899**996458889 PP

                                   GG-S-HHHHHHHHHHHEEEEEEEEEEEE----S CS
               Ubie_methyltran 127 rnvtDklkaLkeayrvlkpGGrlvvlefskvel 159
                                    n  ++     + y +lk  G++v +e + +e+
  gi|91773414|ref|YP_566106.1| 122 LNREERASITAKCYGILKKEGIFVTFENTAPET 154
                                   9999***********************988876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.8e-07   0.00035      25      95 ..      43     122 ..       7     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
               Methyltransf_23  25 rvLdiGcGtGillevlreng..fsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqg............k 82 
                                    +Ld GcGtG+l e++ e +  +++++ D+s+e+ + a+                 +f         +             
  gi|91773414|ref|YP_566106.1|  43 LWLDTGCGTGSLIELANETFdeCNFYLNDPSEEMLSYAKtrlekyeaeR------FKF--------TNyttadlplsgvpE 109
                                   69************997774337***********999987664433321......222........112222344444556 PP

               Methyltransf_23  83 fdlIvlrevlehv 95 
                                   +d+++++++ + +
  gi|91773414|ref|YP_566106.1| 110 CDVVTAIQSHHYL 122
                                   6666666655544 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     5e-07   0.00099      66     173 ..      44     155 ..      23     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5e-07
                                   EEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS-----TTEEEEE...S-TTTS-----SEEEEESSGGGS-H CS
                Methyltransf_2  66 lvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsageeervefvg...GdffkdslPeaDaillkrvlhDwsd 142
                                    +D G GtG l++ + +++ +++  + D + e  + Ak++l+  e+er++f++    d+  + +Pe D++   +  h  + 
  gi|91773414|ref|YP_566106.1|  44 WLDTGCGTGSLIELANETFDECNFYLNDPSeEMLSYAKTRLEKYEAERFKFTNyttADLPLSGVPECDVVTAIQSHHYLNR 124
                                   579*************************7636899*************998642228999999****************** PP

                                   HHHHHHHHHHHHH--TT-EEEEEE----TTS CS
                Methyltransf_2 143 ekcvklLkrvkkalpagGkvivveavlgadp 173
                                   e+ + + ++++  l+++G  +  e   ++  
  gi|91773414|ref|YP_566106.1| 125 EERASITAKCYGILKKEGIFVTFENTAPETE 155
                                   ******************9998888776655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   7.6e-06     0.015      66     173 ..      44     155 ..      29     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.6e-06
                                   EEEES-TTSHHHHHHHHHH--EEEEE.ES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---....--SEEEEES-GGGTS CS
                          CMAS  66 lLdiGcGWGslvrraverydvkvvgl.TlSkeqaklakkrvdeldlerkvevklldyedlde....kvdrvvsvgafehvg 141
                                    Ld GcG Gsl+  a e +d   + l   S+e   +ak r+++ + er +  +     dl+     + d v +++    + 
  gi|91773414|ref|YP_566106.1|  44 WLDTGCGTGSLIELANETFDECNFYLnDPSEEMLSYAKTRLEKYEAERFK-FTNYTTADLPLsgvpECDVVTAIQSHHYLN 123
                                   59*****************96555551689999**********9955443.33333355554668899999999999999* PP

                                   GGGHHHHHHHHHHHS-TT-EEEEEEEEE--HH CS
                          CMAS 142 kenydtffkklkkllkedGllllhtitslhkk 173
                                    e+ +   +k++ +lk++G+++    t+++++
  gi|91773414|ref|YP_566106.1| 124 REERASITAKCYGILKKEGIFVTFENTAPETE 155
                                   ********************998777766655 PP

>> Pet127  Mitochondrial protein Pet127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00021      0.42     180     206 ..      11      37 ..       2      40 .. 0.83
   2 ?   -1.5   0.0      0.69   1.4e+03     220     230 ..     141     151 ..     136     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                        Pet127 180 etgyeikklkgefeSferEyydlirsa 206
                                   + + +i+++  +++Sf+rE+ dlir++
  gi|91773414|ref|YP_566106.1|  11 HYEKNIHRTIPHYSSFQREIIDLIRTT 37 
                                   45667999999**************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.69
                        Pet127 220 dGifvaYHnik 230
                                   +Gifv++ n++
  gi|91773414|ref|YP_566106.1| 141 EGIFVTFENTA 151
                                   8*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1382.37
//
Query:       gi|91773415|ref|YP_566107.1|  [L=198]
Description: hypothetical protein Mbur_1450 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-30  104.0   0.0    6.7e-30  103.5   0.0    1.2  1  UPF0029   Uncharacterized protein family UPF0029
    8.5e-12   44.8   0.0    1.5e-11   43.9   0.0    1.5  1  DUF1949   Domain of unknown function (DUF1949)


Domain annotation for each model (and alignments):
>> UPF0029  Uncharacterized protein family UPF0029
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.5   0.0   7.5e-34   6.7e-30       1     105 []      16     122 ..      16     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 7.5e-34
                                   TTEEEEEEEEE-SSHHHHHHHHHHH--..TTSSEEEEEE....EE....TTEE-TTSST..SHHHHHHHHHHTTB-SEEEE CS
                       UPF0029   1 kkSrFiavlaaveseeevkaileelkkenkkathniyAyrlrqkvekvnedsdddgEpa..AGkkllelLekeklenvlvv 79 
                                   ++S+F++++ +++se+e++a++++lk ++++a+hn++Ay +++ + ++ +++dddgEpa  +Gk++ ++Le ++l+n++vv
  gi|91773415|ref|YP_566107.1|  16 RNSTFVGHVRSIDSEAEARAFIDHLKGQYSDANHNVSAYLIKNDN-ALVAKYDDDGEPAgsSGKPVFKVLELKGLSNTVVV 95 
                                   78*************************************555555.69999****************************** PP

                                   EEEE--SS--HHHHH.HHHHHHHHHHH CS
                       UPF0029  80 vtRwfGGikLGpgrl.raiseaareaL 105
                                   vtR+fGGikLG g+l ra++e+a  a+
  gi|91773415|ref|YP_566107.1|  96 VTRYFGGIKLGFGGLsRAYRETAVAAI 122
                                   *********************998775 PP

>> DUF1949  Domain of unknown function (DUF1949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.7e-15   1.5e-11       1      56 []     138     192 ..     138     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.7e-15
                       DUF1949   1 ltvdYadlgkverlLeqfgativdteYtddVtltlavpeeeveafkaaLtdltsGr 56 
                                   +++dY+d+  ++rl e++ ++++ + Y d V+l++ v+++e++ f ++Lt+lt +r
  gi|91773415|ref|YP_566107.1| 138 VRFDYSDMHSIKRLAEEY-GQVTGESYCDVVELSVKVRKGEEDGFADKLTNLTKDR 192
                                   689***************.**********************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1261.14
//
Query:       gi|91773416|ref|YP_566108.1|  [L=384]
Description: aldo/keto reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-37  128.9   0.1      1e-35  123.4   0.1    2.1  1  Aldo_ket_red  Aldo/keto reductase family
    1.5e-10   41.5   7.7    3.2e-10   40.4   7.7    1.6  1  Fer4_17       4Fe-4S dicluster domain
    3.5e-10   39.9   6.8    6.7e-10   39.0   6.8    1.4  1  Fer4_9        4Fe-4S dicluster domain
    4.6e-07   30.0   5.9     0.0011   19.1   0.3    2.4  2  Fer4_18       4Fe-4S dicluster domain
    1.5e-06   28.5   6.3    3.5e-06   27.4   6.3    1.6  1  Fer4_8        4Fe-4S dicluster domain
    0.00026   20.7   2.0    0.00026   20.7   2.0    2.8  2  Fer4          4Fe-4S binding domain
     0.0003   20.8  11.5      0.003   17.6  12.2    2.1  2  Fer4_10       4Fe-4S dicluster domain
     0.0012   18.9   5.0       0.14   12.3   0.3    2.4  2  Fer4_21       4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   15.9  12.4      0.076   13.1   2.6    2.5  2  Fer4_2        4Fe-4S binding domain
      0.011   15.5   9.8      0.075   12.8   2.2    2.3  2  Fer4_20       Dihydroprymidine dehydrogenase domain II, 4Fe-4
      0.014   16.2   2.7        1.2   10.0   0.1    2.7  2  Fer4_22       4Fe-4S dicluster domain
      0.017   15.2   2.1      0.017   15.2   2.1    2.6  2  Fer4_6        4Fe-4S binding domain
       0.03   14.9  14.5       0.48   11.0  14.6    2.3  2  Fer4_7        4Fe-4S dicluster domain
       0.21   12.2   0.3       0.21   12.2   0.3    2.4  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
        2.5    9.1  14.8        1.5    9.9   3.5    2.5  3  Fer4_16       4Fe-4S double cluster binding domain
        3.8    8.3  17.9       0.15   12.6   2.7    2.8  3  Fer4_4        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.1   8.9e-39     1e-35       2     278 ..      16     267 ..      15     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 8.9e-39
                                   EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                  Aldo_ket_red   2 lglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                   lg+G ++l       ++i++eea ++++ a+e G+n+fDtA  Y+ g se ++G++l+k  + r++v++atK+     +  
  gi|91773416|ref|YP_566108.1|  16 LGFGCMRLPVIdgkeDQIDEEEATRMIEFAIEKGVNYFDTAYPYHAGMSEPFVGKVLAK--GYRDKVLLATKL-----PLW 89 
                                   7899998875567789*******************************************..************.....666 PP

                                   SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-....HHHHHHHHHHHHHTTSEEEEEEES--.HHHHHHHHHTTT- CS
                  Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslp...sieevldaleelvkeGkiraiGvSnfs.veqlekakkkkkv 155
                                      ++e++++ l+++l+rL+td++D +l+H  ++ +    + +  ++++e  +++Gki++iG+S ++ +   +++    ++
  gi|91773416|ref|YP_566108.1|  90 LVQTREDMDRFLDDQLERLQTDHIDFYLMHGFTRGYWnkmRELGMFEFIENAISSGKIKYIGFSFHDdITVFKEI--IDGY 168
                                   667899************************9987544444444579*****************************..9999 PP

                                   -EEEEE-B-BTT..-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHH CS
                  Aldo_ket_red 156 kivavqveynll..releeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelse 234
                                   ++ + +++yn++  + ++ ++ l+++k+kg+++  ++pl gG l                             +  e++++
  gi|91773416|ref|YP_566108.1| 169 DWDFCMIQYNFMdeDYQAGKQGLQYAKQKGIDVAIMEPLRGGNLV----------------------------QVPETVQR 221
                                   ************766677777899*********************............................55556666 PP

                                   HHHHTT-..-HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG CS
                  Aldo_ket_red 235 lakehgv..slaqlalryalsqpavgivipgasnieqlednldale 278
                                   +  + ++  ++a ++ +y+  qp  +iv+ g+s+ eq+e+n+++ e
  gi|91773416|ref|YP_566108.1| 222 IWDSAKIkrTPANWCFQYLWDQPEISIVLSGMSTFEQVEQNIAYAE 267
                                   6655444449********************************9874 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   7.7   2.9e-13   3.2e-10       1      60 [.     296     362 ..     296     363 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.9e-13
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraakl.glleeaeke........ekaslCieCgeCerkCPqgl 60 
                                   +C++C+yC+p Cp++ +++    ++l+ a++   +e+a+ +        e+as+C+eCg+Ce+ CPq++
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCMP-CPTGVNIPAAF-TYLNSASMyDNVEKASFQyglfvppeEAASKCTECGLCEEHCPQHI 362
                                   6*********.******88743.344444442444444333566677768*****************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   6.8     6e-13   6.7e-10       1      49 [.     296     361 ..     296     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6e-13
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..................eaCigCgaCveaCpkg 49 
                                   +Ct+C++C++ Cp+gv+++ a+++ ++  ++++                  ++C++Cg C+e+Cp++
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCMP-CPTGVNIPAAFTYLNSASMYDNvekasfqyglfvppeeaaSKCTECGLCEEHCPQH 361
                                   6*********.*******************999********************************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 !   19.1   0.3     1e-06    0.0011      27      80 ..     263     315 ..     249     331 .. 0.76
   2 !   13.1   0.9   7.2e-05     0.081      55      81 ..     342     368 ..     320     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                       Fer4_18  27 vvydakrGekia.grkkekkalkekeerkekgagdcidcescvkvcPtgidirkG 80 
                                   ++y a+rGe  +  ++ +++ +k ++  +ek + +c++c++c+  cPtg++i   
  gi|91773416|ref|YP_566108.1| 263 IAY-AERGEANSlTSNDKEVLQKVRKFYNEKMEVNCTNCKYCMP-CPTGVNIPAA 315
                                   444.57999877245555566677778899999*********85.*****99665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.2e-05
                       Fer4_18  55 ekgagdcidcescvkvcPtgidirkGl 81 
                                   e++a++c++c+ c + cP +i i++ l
  gi|91773416|ref|YP_566108.1| 342 EEAASKCTECGLCEEHCPQHIRIQEML 368
                                   577899****************99866 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   6.3   3.1e-09   3.5e-06       4      65 .]     296     362 ..     293     362 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.1e-09
                        Fer4_8   4 kCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvlee.....eealwsCttcgaCtevCpvgi 65 
                                   +C++C +C+  Cp+  +    + + +     + v++   +++     eea+ +Ct+cg C+e Cp++i
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCMP-CPTGVNIPaAFTYLNSASMYDNVEKASFQYGlfvppEEAASKCTECGLCEEHCPQHI 362
                                   7*********.**6666543333333333333233333433377788*******************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   4.0      0.17   1.9e+02       7      16 ..     296     305 ..     292     310 .. 0.85
   2 !   20.7   2.0   2.3e-07   0.00026       6      20 ..     346     360 ..     344     363 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                                   TSSS-THHHH CS
                          Fer4   7 kCigCGaCve 16 
                                    C++C++C+ 
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCMP 305
                                   6*******85 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.3e-07
                                   TTSSS-THHHHHSTT CS
                          Fer4   6 ekCigCGaCvevCPv 20 
                                   +kC+ CG+C+e CP 
  gi|91773416|ref|YP_566108.1| 346 SKCTECGLCEEHCPQ 360
                                   7*************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  12.2   2.7e-06     0.003       8      56 .]     296     359 ..     290     359 .. 0.91
   2 !   16.3   2.6   6.8e-06    0.0076       6      26 ..     345     365 ..     340     380 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                       Fer4_10   8 tCirCgkCvkaCPadl...............tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                    C++C+ C+  CP+ +               ++v++  ++ +  +  + + +kCt+cg C e+CP
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCMP-CPTGVnipaaftylnsasmyDNVEKASFQYGLFVPPEeAASKCTECGLCEEHCP 359
                                   6********9.***99*************998899999999998887779**************9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6.8e-06
                       Fer4_10   6 ddtCirCgkCvkaCPadltsv 26 
                                   +++C++Cg C + CP++++ +
  gi|91773416|ref|YP_566108.1| 345 ASKCTECGLCEEHCPQHIRIQ 365
                                   578999999999999977333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.7    0.0025       2.8      27      53 ..     283     308 ..     273     312 .. 0.76
   2 !   12.3   0.3   0.00013      0.14      38      53 ..     345     360 ..     328     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0025
                       Fer4_21  27 eidaktvlkvvedeCvGCnlCssvCPv 53 
                                   ++  k + + +e +C+ C+ C+ +CP+
  gi|91773416|ref|YP_566108.1| 283 QKVRKFYNEKMEVNCTNCKYCM-PCPT 308
                                   5555666778899********7.7996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                       Fer4_21  38 edeCvGCnlCssvCPv 53 
                                   +++C+ C lC + CP 
  gi|91773416|ref|YP_566108.1| 345 ASKCTECGLCEEHCPQ 360
                                   5799999999999994 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.3    0.0041       4.6       9      22 .]     296     308 ..     287     308 .. 0.83
   2 ?   13.1   2.6   6.8e-05     0.076       8      22 .]     346     360 ..     338     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                        Fer4_2   9 rCigCgaCvsaCPa 22 
                                   +C++C+ C   CP+
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYC-MPCPT 308
                                   6*******.99997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.8e-05
                        Fer4_2   8 drCigCgaCvsaCPa 22 
                                    +C++Cg C   CP+
  gi|91773416|ref|YP_566108.1| 346 SKCTECGLCEEHCPQ 360
                                   59************6 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.0    0.0042       4.7      22      58 ..     295     328 ..     275     338 .. 0.72
   2 ?   12.8   2.2   6.7e-05     0.075      19      48 ..     343     370 ..     338     378 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0042
                                   TT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHH CS
                       Fer4_20  22 sRClqCkkapcvkgCPveidipefikkiaegnleeaa 58 
                                     C +C  ++c+  CP+ ++ip   + +++  +++ +
  gi|91773416|ref|YP_566108.1| 295 VNCTNC--KYCM-PCPTGVNIPAAFTYLNSASMYDNV 328
                                   358888..6788.9********988777777666555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.7e-05
                                   HHHTT----TT-HHHHCSTT---HHHHHHH CS
                       Fer4_20  19 eeAsRClqCkkapcvkgCPveidipefikk 48 
                                   e As+C +C    c+++CP +i+i+e++k+
  gi|91773416|ref|YP_566108.1| 343 EAASKCTEC--GLCEEHCPQHIRIQEMLKR 370
                                   5699*****..89*************9986 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   0.4     0.028        31      60      93 ..     275     307 ..     252     310 .. 0.73
   2 ?   10.0   0.1    0.0011       1.2      76      96 .]     342     362 ..     320     362 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.028
                       Fer4_22  60 erlrqrllhklsefkekfgesgCvGCgRCieacp 93 
                                   +   + +l+k+++f ++  e  C+ C  C+  cp
  gi|91773416|ref|YP_566108.1| 275 TSNDKEVLQKVRKFYNEKMEVNCTNCKYCMP-CP 307
                                   4456788999999999999999999999963.55 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                       Fer4_22  76 kfgesgCvGCgRCieacpvki 96 
                                   +  +s+C+ Cg C+e+cp++i
  gi|91773416|ref|YP_566108.1| 342 EEAASKCTECGLCEEHCPQHI 362
                                   557789***********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 ?    0.3   3.3      0.75   8.5e+02       8      16 ..     296     304 ..     293     311 .. 0.75
   2 ?   15.2   2.1   1.5e-05     0.017       7      20 ..     346     359 ..     344     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.75
                        Fer4_6   8 kCigCgdCv 16 
                                   +C+ C  C+
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCM 304
                                   688888886 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                        Fer4_6   7 dkCigCgdCvrvCP 20 
                                   +kC+ Cg C+ +CP
  gi|91773416|ref|YP_566108.1| 346 SKCTECGLCEEHCP 359
                                   89************ PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.4     0.027        31      33      52 .]     292     310 ..     260     310 .. 0.65
   2 ?   11.0  14.6   0.00043      0.48       2      50 ..     297     360 ..     296     362 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                        Fer4_7  33 idpekClgCgaCvavCPtga 52 
                                     + +C++C+ C+  CPtg+
  gi|91773416|ref|YP_566108.1| 292 KMEVNCTNCKYCMP-CPTGV 310
                                   23448999999986.88875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00043
                        Fer4_7   2 CigCgaCvaaCpvkaield..........eeenekgtekv..........eidpekClgCgaCvavCPt 50 
                                   C++C++C++ Cp+++              ++++ek    +          e  ++kC+ Cg C++ CP 
  gi|91773416|ref|YP_566108.1| 297 CTNCKYCMP-CPTGVNIPAaftylnsasmYDNVEK----AsfqyglfvppEEAASKCTECGLCEEHCPQ 360
                                   *******98.9855433221121222222122222....2334455555588899*************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 ?   -1.7   2.9       3.9   4.3e+03       5      13 ..     296     304 ..     294     308 .. 0.80
   2 ?   12.2   0.3   0.00019      0.21       4      25 ..     346     367 ..     345     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                       Fer4_13   5 tCiacgaCv 13 
                                   +C++c+ C 
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCM 304
                                   699999995 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                       Fer4_13   4 dtCiacgaCvelaPdvFeedde 25 
                                   ++C++cg+C e +P++ ++++ 
  gi|91773416|ref|YP_566108.1| 346 SKCTECGLCEEHCPQHIRIQEM 367
                                   68************99777765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   4.9      0.35   3.9e+02       1       9 [.     296     304 ..     255     311 .. 0.48
   2 ?    6.1  14.1      0.02        22       1      65 [.     296     359 ..     296     361 .. 0.61
   3 ?    9.9   3.5    0.0013       1.5       1      16 [.     347     362 ..     347     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.35
                       Fer4_16   1 rCgtCgkCa 9  
                                   +C++C+ C+
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCM 304
                                   233333333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy....ntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                   +C++C+ C+  CPt++    + +++ + +++      +  +   + + ee+   + ++t C+ C++ CP
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCMP-CPTGVNIPAA-FTYLNSASMYDnvekASFQYGLFVPPEEA---ASKCTECGLCEEHCP 359
                                   6*******86.***9955553.44444444333122233333333344433...358************ PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0013
                       Fer4_16   1 rCgtCgkCaevCPtna 16 
                                   +C++Cg C e CP++ 
  gi|91773416|ref|YP_566108.1| 347 KCTECGLCEEHCPQHI 362
                                   5************865 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       9.2     1e+04       2       6 ..     234     238 ..     233     238 .. 0.80
   2 ?    3.4   4.0      0.12   1.3e+02       3      17 .]     296     309 ..     292     309 .. 0.89
   3 ?   12.6   2.7   0.00013      0.15       2      16 ..     346     360 ..     345     365 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.2
                        Fer4_4   2 erCig 6  
                                   ++C++
  gi|91773416|ref|YP_566108.1| 234 NWCFQ 238
                                   89*96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                        Fer4_4   3 rCigCgsCvaaCPqg 17 
                                   +C++C+ C+  CP+g
  gi|91773416|ref|YP_566108.1| 296 NCTNCKYCMP-CPTG 309
                                   6*******99.8875 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00013
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++C++Cg C+  CPq
  gi|91773416|ref|YP_566108.1| 346 SKCTECGLCEEHCPQ 360
                                   68************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2215.34
//
Query:       gi|91773417|ref|YP_566109.1|  [L=55]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for 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   40.6   0.1    3.1e-10   40.5   0.1    1.0  1  HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like A


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 !   40.5   0.1   1.7e-14   3.1e-10      57     110 ..       2      54 ..       1      55 [] 0.91

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.7e-14
                                   TCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEET.TTEEEEEEEEES CS
                     HATPase_c  57 lfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesep.grGttftftlpl 110
                                   +fe+f +    +++ +g+GlGl+ivk++v+l++G++ ve++p g+G+ f++tl++
  gi|91773417|ref|YP_566109.1|   2 VFERFKR--VGNSSIKGSGLGLAIVKRIVDLHKGKVGVEDNPeGQGSVFWVTLKK 54 
                                   8999999..6677889**********************99999*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       146  (0.00814323); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); 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 0.27s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 366.47
//
Query:       gi|91773418|ref|YP_566110.1|  [L=77]
Description: cytochrome b5 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-11   43.4   0.5    3.5e-11   43.1   0.5    1.2  1  Cyt-b5    Cytochrome b5-like Heme/Steroid binding domain


Domain annotation for each model (and alignments):
>> Cyt-b5  Cytochrome b5-like Heme/Steroid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.5   1.9e-15   3.5e-11       1      73 [.       5      75 ..       5      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.9e-15
                                  EHHHHTTTECTT..EEEEEETTEEEECTTTC....CCSTTCSHHHHTTTTSBBHHHHHHTTGGCHHHHHHHHGGEEEEE CS
                        Cyt-b5  1 tleelskhngkn..dlwvairgkVYDvskfl....skhpGgesailkyaGkDateafksvvhsekdaekllkkylvGkl 73
                                  t eel+k+ngk+  ++++a++gkVYDv++ +    ++h+G ++      G D+t++ ++  h+++++e++   ++vG+l
  gi|91773418|ref|YP_566110.1|  5 TTEELAKYNGKDgeKCYFAYKGKVYDVTESMlwedGDHQGMHE-----GGIDLTADHEDAPHDDDVLEDF---PVVGTL 75
                                  679******99889***************99766666666555.....999**************99999...999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 481.76
//
Query:       gi|91773419|ref|YP_566111.1|  [L=417]
Description: L-threonine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  124.3   0.0    7.8e-36  124.0   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.17   11.5   0.0       0.31   10.6   0.0    1.4  1  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   0.0   8.7e-40   7.8e-36      24     294 .]      90     372 ..      71     372 .. 0.91

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 8.7e-40
                                   EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EE CS
                          PALP  24 lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGaev 104
                                    +  +E++  t+SfKd+     ++rl e+++++++v+as+GN++ra A++a+  G+++ + vp++++  ++  +++    v
  gi|91773419|ref|YP_566111.1|  90 YWPENEGFIRTCSFKDLESFPTMQRLLENNERRVLVVASAGNTARAFAHVASITGYPLLLIVPKNST-HRLWTTEEDTSSV 169
                                   78899********************88888************************************9.999***9999999 PP

                                   EEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSS.HHHHHHHHHHHH.. CS
                          PALP 105 vev..ggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgG.gliaGiaaglke.. 180
                                     v  +gdy +a a+a+++aa+ +g++      n+++ +g+gt++l  +  ++  p + + +vG+G g i+++ a+++   
  gi|91773419|ref|YP_566111.1| 170 CTVtvDGDYYQAIAMAEKIAAR-DGFVSEGGARNVARRDGMGTVMLDAVLTTKSLPQHYFQAVGSGtGGISAWEAAMRLie 249
                                   99999*****************.9988888888*********************************9************99 PP

                                   ..HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.....CGTTCCHHHHSEEEEEEEEEEHHHHHHHH CS
                          PALP 181 ..rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavg.....spselafelldrlvdeivtvsdeealeam 252
                                     r+++  +r+  +++  +++l++++ +g++++   ++ + d +  +      ++  + ++ld++++ i++++++ea ea 
  gi|91773419|ref|YP_566111.1| 250 dgRFGNnmPRLHLAQNLPCAPLYSTW-TGEQTNGNCPEEMYDDVLFNrkppyLATGGVKDALDDTNGIIYGITNKEADEAR 329
                                   88666688******************.8888888877666666666665444444466678899999************** PP

                                   HHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                          PALP 253 rllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                   + + ++egi + p+ a+a aa+ k++e+ge+k+++++v+ +tg
  gi|91773419|ref|YP_566111.1| 330 KIFEENEGIDILPAPAIACAAImKALEKGEIKADENIVLNITG 372
                                   ****************************************998 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.5e-05      0.31      47     129 ..     116     191 ..     101     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.5e-05
                                   HHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHH CS
                          AIRC  47 aeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqil 127
                                   +e+ e+r    ++a AG+ a     vas+t +P + + +k+    +++ l+ + +  s v  +tv+ g+ ++A  +A +i 
  gi|91773419|ref|YP_566111.1| 116 LENNERR--VLVVASAGNTARAFAHVASITGYPLLLIVPKN----STHRLWTTEEDTSSVCTVTVD-GDYYQAIAMAEKIA 189
                                   3433333..457899******************98776666....478999999999999999998.78888888888887 PP

                                   TT CS
                          AIRC 128 al 129
                                   a+
  gi|91773419|ref|YP_566111.1| 190 AR 191
                                   75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); 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: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2674.75
//
Query:       gi|91773420|ref|YP_566112.1|  [L=254]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-14   54.6   0.0    2.4e-14   54.0   0.0    1.2  1  ABC_tran     ABC transporter
    2.5e-09   37.4   0.8    0.00042   20.2   0.0    2.9  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.6e-06   25.6   0.0    1.8e-05   24.4   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00012   22.7   0.0    0.00016   22.2   0.0    1.3  1  AAA_23       AAA domain
    0.00013   22.0   0.1    0.00069   19.6   0.0    1.9  1  ATPase_2     ATPase domain predominantly from Archaea
    0.00023   21.4   0.1     0.0013   19.0   0.1    1.9  1  AAA_22       AAA domain
     0.0003   21.2   0.0    0.00049   20.5   0.0    1.3  1  AAA_16       AAA ATPase domain
    0.00061   19.3   0.4      0.085   12.3   0.4    2.4  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0025   17.6   0.0     0.0072   16.1   0.0    1.7  1  AAA_30       AAA domain
     0.0048   16.1   0.0     0.0099   15.1   0.0    1.4  1  NB-ARC       NB-ARC domain
     0.0049   16.0   0.0      0.008   15.3   0.0    1.3  1  T2SSE        Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.053   13.1   0.0    1.9  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.023   15.3   0.0      0.067   13.7   0.0    2.0  1  AAA_18       AAA domain
      0.024   14.6   0.1        1.2    9.1   0.0    2.5  2  AAA_5        AAA domain (dynein-related subfamily)
       0.03   14.2   0.0      0.064   13.2   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.032   14.0   0.0      0.067   12.9   0.0    1.6  2  DEAD         DEAD/DEAH box helicase
      0.055   13.5   0.0        1.1    9.2   0.0    2.3  2  AAA_14       AAA domain
      0.067   13.1   0.8        2.2    8.1   0.1    2.2  2  NTPase_1     NTPase
      0.068   13.1   0.0      0.096   12.6   0.0    1.6  1  NACHT        NACHT domain
       0.13   12.4   0.0       0.51   10.4   0.0    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
       0.14   12.3   0.1       0.32   11.1   0.1    2.0  1  AAA_33       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 !   54.0   0.0   2.8e-17   2.4e-14       7     135 ..      26     168 ..      23     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.8e-17
                                   EEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren.... 79 
                                   ++++g +++ivG++G+GKStL+  + +l +    t+ +il+++++ ++  +    rk i+ l+q+ ++  ++tv e     
  gi|91773420|ref|YP_566112.1|  26 EMNPGDILGIVGPTGSGKSTLIDDIEQLAQGdtpTQRRILINDTEPEMgLRVDPRRKLIAQLSQNMHFLADMTVSEFlqmh 106
                                   789******************9887777654444********9999997888889999********************998 PP

                                   ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHH.HHHHTSSEEEEEST CS
                                   ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                      ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalar.allkkpkllllDEp 135
                                           e   ++ +++++l  + ++++ +    + LSgGq + ++ a  a++++++++l+DE 
  gi|91773420|ref|YP_566112.1| 107 arsrgkdpELMHRVIELANRLTGEPIHEDEQ---LTVLSGGQSRSLMTADiAVISDSPIVLIDEI 168
                                   7766544433333444444444444333332...49*********9999637899********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 !   20.2   0.0   4.9e-07   0.00042       2      40 ..      33      65 ..      32      88 .. 0.78
   2 !   13.8   0.4   4.4e-05     0.038     187     269 ..     115     171 ..      86     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.9e-07
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40
                                   +++Gp gsGKS+L+d ++ la+      g+t++++++ 
  gi|91773420|ref|YP_566112.1| 33 LGIVGPTGSGKSTLIDDIEQLAQ------GDTPTQRRIL 65
                                  579***************99975......6666665554 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.4e-05
                        AAA_21 187 rlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpE 267
                                   +l++++ +  ++l+ + + e++                        +++ lS G+ r   + + ++   ++ +++liDE+E
  gi|91773420|ref|YP_566112.1| 115 ELMHRVIELANRLTGEPIHEDE------------------------QLTVLSGGQSRS-LMTADIAVISDS-PIVLIDEIE 169
                                   5566666666666666555544........................45677*******.***********9.********* PP

                        AAA_21 268 ng 269
                                   n 
  gi|91773420|ref|YP_566112.1| 170 NA 171
                                   96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.1e-08   1.8e-05      17      49 ..      25      57 ..      19      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.1e-08
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  +e+++ ++  ++Gp+GsGKSTl+D i  l  ++
  gi|91773420|ref|YP_566112.1| 25 VEMNPGDILGIVGPTGSGKSTLIDDIEQLAQGD 57
                                  6788888889**************999887665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.9e-07   0.00016      21      61 ..      32      69 ..      21     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.9e-07
                        AAA_23 21 ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeks 61
                                  +  I+Gp+G+GK+T++d i     g+tp+ +r     +++ 
  gi|91773420|ref|YP_566112.1| 32 ILGIVGPTGSGKSTLIDDIEQLAQGDTPTQRR---ILINDT 69
                                  567*******************9999886655...344444 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 !   19.6   0.0   8.1e-07   0.00069       8     141 ..      18     181 ..      15     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.1e-07
                      ATPase_2   8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienl..edkdkyviyyialreesiskldefie....eeeekkklekal 82 
                                   ++e  +++e++p +i+ i Gp gsGK++L+  i +    +   +++i +++ + e   ++d   +     +++       +
  gi|91773420|ref|YP_566112.1|  18 IEEPVKLVEMNPGDILGIVGPTGSGKSTLIDDIEQLAqgDTPTQRRILINDTEPEMGLRVDPRRKliaqLSQN-------M 91 
                                   56667899**********************9987766323334499999999999888888773344442222.......2 PP

                      ATPase_2  83 .....................................giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiD 125
                                                                        g+++ ++e  ++l+        ++ +l+ ++i      +i++iD
  gi|91773420|ref|YP_566112.1|  92 hfladmtvseflqmharsrgkdpelmhrvielanrltGEPIHEDEQLTVLSgG------QSRSLMTADIAVISDSPIVLID 166
                                   33344447777777789999999999998777666666666666665554431......3444556666666667999999 PP

                      ATPase_2 126 elqklidlglngaell 141
                                   e+ +++ ++ ++a +l
  gi|91773420|ref|YP_566112.1| 167 EIENAG-IKKQEALSL 181
                                   999999.655555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.5e-06    0.0013       7     112 ..      32     182 ..      27     199 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee....................................erpevvfvtlpsst 51 
                                   il ++G++G+GK+tl+  + + ++ +  +++                                      +e++ + + s +
  gi|91773420|ref|YP_566112.1|  32 ILGIVGPTGSGKSTLIDDIEQLAQGD-TPTQrrilindtepemglrvdprrkliaqlsqnmhfladmTVSEFLQMHARSRG 111
                                   7779***************9998533.333356777777777777776544444444444444433333333344444444 PP

                        AAA_22  52 sskdllrellralglelka.........................erlsseellealeqalrarav........ielliiDE 99 
                                   +  +                                        ++++s+ l+           +         ++++iDE
  gi|91773420|ref|YP_566112.1| 112 KDPE--------------LmhrvielanrltgepihedeqltvlSGGQSRSLM-----------TadiavisdSPIVLIDE 167
                                   3333..............15555555544444555445544444333333333...........23344455457789999 PP

                        AAA_22 100 aqhlr..seealeeL 112
                                   +++    ++eal+ L
  gi|91773420|ref|YP_566112.1| 168 IENAGikKQEALSLL 182
                                   999844346666666 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   5.8e-07   0.00049      26     162 ..      32     186 ..      22     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.8e-07
                        AAA_16  26 lvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                   ++ ++G+ G+GKs+l++ + + +++d    + i+++ +  +          +++  r++l++ql ++    +    +e+l+
  gi|91773420|ref|YP_566112.1|  32 ILGIVGPTGSGKSTLIDDIEQLAQGDtptqRRILINDTEPEM--------GLRVDPRRKLIAQLSQNMHFLADMTVSEFLQ 104
                                   6779****************9998886665455555555555........6777778899999999955544455555555 PP

                        AAA_16 103 eala............................avpelagaea.....srllellkrllallsrderplvlvlDdlqwadea 150
                                     ++                            +               + + l+++ +a +s      ++++D+++ a   
  gi|91773420|ref|YP_566112.1| 105 MHARsrgkdpelmhrvielanrltgepihedeQ--------LtvlsgGQSRSLMTADIAVISD---SPIVLIDEIENAGIK 174
                                   544422333334444444555554443332222........0333334444444444444443...368889999999999 PP

                        AAA_16 151 slqllaaLlrll 162
                                    +++l++L  ++
  gi|91773420|ref|YP_566112.1| 175 KQEALSLLSGEG 186
                                   999999988765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.4    0.0001     0.085      28      45 ..      34      51 ..      24     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                  EEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxx RF
                         SMC_N 28 aivGpNGSGKsnlldAil 45
                                   ivGp GSGKs l+d i 
  gi|91773420|ref|YP_566112.1| 34 GIVGPTGSGKSTLIDDIE 51
                                  69*************984 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.4e-06    0.0072      18     114 ..      30     185 ..      20     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.4e-06
                        AAA_30  18 drvavltGpAGtGKttalkalreaweaag.............grviglAptgkaAkvLaeelgi.eastiakllkrlk... 81 
                                     +  ++Gp G+GK+t++  ++++++ +              +  + + p  k  ++L++++ + + +t+ ++l+ ++   
  gi|91773420|ref|YP_566112.1|  30 GDILGIVGPTGSGKSTLIDDIEQLAQGDTptqrrilindtepEMGLRVDPRRKLIAQLSQNMHFlADMTVSEFLQMHArsr 110
                                   457789******************998856898888888876444556788888888888888746789999999999999 PP

                        AAA_30  82 ..........................................grarlepgtllivDEagmvdtkqlaallkaaek 114
                                                                             + a ++++ ++++DE+  +++k+ +al     +
  gi|91773420|ref|YP_566112.1| 111 gkdpelmhrvielanrltgepihedeqltvlsggqsrslmtaDIAVISDSPIVLIDEIENAGIKKQEALSLLSGE 185
                                   999999999999999999999999999999999999999998767788889999999999999998887655544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05    0.0099      11      41 ..      23      51 ..      19      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                  HHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                        NB-ARC 11 kLlekdelqslvvalvGmgGvGKttlakqil 41
                                  kL+e++  +  ++++vG  G+GK+tl+ +i 
  gi|91773420|ref|YP_566112.1| 23 KLVEMNPGD--ILGIVGPTGSGKSTLIDDIE 51
                                  788665555..***************99885 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.4e-06     0.008     134     198 ..      35     109 ..       7     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.4e-06
                         T2SSE 134 vsGgTgsGKttllyallkeinks..derivtvEDp.vEiqleganqvqlnak.......kakvtfadllraaLRl 198
                                   + G+TgsGK+tl+  + +  + +  ++r +++ D+  E+ l+ + + +l a+        a++t+++ l+   R 
  gi|91773420|ref|YP_566112.1|  35 IVGPTGSGKSTLIDDIEQLAQGDtpTQRRILINDTePEMGLRVDPRRKLIAQlsqnmhfLADMTVSEFLQMHARS 109
                                   78***********77766555444488888899984588888887777777776667777788888877776665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.3e-05     0.053       3      36 ..      33      69 ..      31      90 .. 0.79
   2 ?   -1.4   0.1       1.8   1.5e+03      54      62 ..     206     214 ..     150     234 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.3e-05
                                  EEEEESTTCCHHHHHHHHH...CT--SS-EEEEESS- CS
                          cobW  3 tvltGflGsGKTtLlnhll...enraglklavivNef 36
                                  ++++G+ GsGK+tL+  +    +     +  +++N+ 
  gi|91773420|ref|YP_566112.1| 33 LGIVGPTGSGKSTLIDDIEqlaQGDTPTQRRILINDT 69
                                  789***********99887444666667777888876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                                   EEETTTTEC CS
                          cobW  54 velenGciC 62 
                                   + + nG++C
  gi|91773420|ref|YP_566112.1| 206 IVIRNGGMC 214
                                   334444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.9e-05     0.067       2      49 ..      34      74 ..      33     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.9e-05
                        AAA_18  2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdes 49
                                  ++ G+ G+GK+tl + ++++       +d+ +++++l+ ++++  +  
  gi|91773420|ref|YP_566112.1| 34 GIVGPTGSGKSTLIDDIEQLA-----QGDTPTQRRILINDTEP--EMG 74
                                  589**************7774.....55555555555555555..222 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 ?    9.1   0.0    0.0014       1.2       4      24 ..      35      57 ..      32      73 .. 0.78
   2 ?    3.3   0.0     0.086        74      64      87 ..     154     180 ..      81     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                                  EE--SSSSHHHHHHHGGGGB..S CS
                         AAA_5  4 LvGppGtgKselaerlaaal..n 24
                                  +vGp+G+gKs+l++ + ++    
  gi|91773420|ref|YP_566112.1| 35 IVGPTGSGKSTLIDDIEQLAqgD 57
                                  79************999987543 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.086
                                   -....G-SEEEEESGGG--HHHHHHHHH CS
                         AAA_5  64 r....egeilvlDEveraesevlnsLls 87 
                                         + i+++DE+e+a  + +++L s
  gi|91773420|ref|YP_566112.1| 154 IavisDSPIVLIDEIENAGIKKQEAL-S 180
                                   3555678899******9998777777.3 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.5e-05     0.064      93     122 ..      24      53 ..       7      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-05
                                   HHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  93 lkellkdktsvlvGqSGvGKStLinallpe 122
                                   l e+  +++  +vG++G GKStLi+ + + 
  gi|91773420|ref|YP_566112.1|  24 LVEMNPGDILGIVGPTGSGKSTLIDDIEQL 53 
                                   566666788899************998764 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-05     0.067      15      94 ..      30     121 ..      19     178 .. 0.69
   2 ?   -2.5   0.0       4.3   3.6e+03      85     112 ..     173     201 ..     156     210 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                                   CEEE.EEESTTSSHHHHHHHHHHHHHHHS..........TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST...SEEEEE CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                          DEAD  15 gdvl.vaaeTGsGKTlaflipvlqivyet..........kgktgpkalivePtreLaeqtlnnlkkfkkyid...lrvlli 81 
                                   gd+l + ++TGsGK++   i  ++++++           ++++  + l v P r+L+ q  +n+  + + +    l++++ 
  gi|91773420|ref|YP_566112.1|  30 GDILgIVGPTGSGKSTL--IDDIEQLAQGdtptqrriliNDTEPEMGLRVDPRRKLIAQLSQNMHFLADMTVsefLQMHAR 108
                                   45554789******987..8888888776788888888777777899*****************88877522345555555 PP

                                   ETTSSHHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskl 94 
                                     g++ +  ++++
  gi|91773420|ref|YP_566112.1| 109 SRGKDPELMHRVI 121
                                   5555555555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                                   SSHHHHHHHHH.TTCSEEEEEHHHHHHHH CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          DEAD  85 vaardqlskld.ngvdivvgtpgrlddll 112
                                    ++++ ls l+ +g  +vv t++ ++ l+
  gi|91773420|ref|YP_566112.1| 173 IKKQEALSLLSgEGKIVVVVTHDPVLALM 201
                                   44555566664233555666666666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0013       1.1       3      36 ..      31      66 ..      29      99 .. 0.71
   2 ?    2.1   0.0      0.21   1.8e+02      63      77 ..     158     172 ..     133     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                        AAA_14  3 kilvitGaRrvGKTtllkqlikell..vkkesilyi 36
                                   il i+G+  +GK+tl+ ++ +     ++ ++ + i
  gi|91773420|ref|YP_566112.1| 31 DILGIVGPTGSGKSTLIDDIEQLAQgdTPTQRRILI 66
                                  5899************98774333354444444444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.21
                        AAA_14  63 ekktylflDEiqevp 77 
                                   ++  ++++DEi ++ 
  gi|91773420|ref|YP_566112.1| 158 SDSPIVLIDEIENAG 172
                                   4567899***99983 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0026       2.2       3      23 ..      34      54 ..      32      61 .. 0.84
   2 ?    3.5   0.1     0.071        61      93     137 ..     157     199 ..     133     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                                  EEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlell 23
                                   i Gp G+GK+Tl++ + +l 
  gi|91773420|ref|YP_566112.1| 34 GIVGPTGSGKSTLIDDIEQLA 54
                                  588***********9997765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.071
                                   HHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.- CS
                      NTPase_1  93 lseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrk.d 137
                                   +s++ +++iDEi   E    k +ea+  +  ++k+v++v h +   
  gi|91773420|ref|YP_566112.1| 157 ISDSPIVLIDEI---ENAGIKKQEALSLLSGEGKIVVVVTHDPVlA 199
                                   366779999998...7777777777765555999999999988433 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   0.00011     0.096       4      32 ..      34      62 ..      31     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                  EEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                         NACHT  4 ilqGeaGsGKTtLlqklalawaegklpqg 32
                                   + G+ GsGK+tL+  + ++++ +++ q 
  gi|91773420|ref|YP_566112.1| 34 GIVGPTGSGKSTLIDDIEQLAQGDTPTQR 62
                                  589*************9888777776664 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0006      0.51       3      19 ..      34      50 ..      32      71 .. 0.88
   2 ?   -0.8   0.0       1.8   1.5e+03      80      84 ..     162     166 ..     123     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0006
                                  EEEESTTSSHHHHHHHH CS
                      MMR_HSR1  3 aivGrpNvGKStLinal 19
                                  +ivG + +GKStLi  +
  gi|91773420|ref|YP_566112.1| 34 GIVGPTGSGKSTLIDDI 50
                                  8************9765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                                   EEEEE CS
                      MMR_HSR1  80 llvvd 84 
                                   ++++d
  gi|91773420|ref|YP_566112.1| 162 IVLID 166
                                   23333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00038      0.32       4      20 ..      35      51 ..      32     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                        AAA_33  4 lvGlpGsGKstlaerll 20
                                  +vG+ GsGKstl++ + 
  gi|91773420|ref|YP_566112.1| 35 IVGPTGSGKSTLIDDIE 51
                                  69**********98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1917.47
//
Query:       gi|91773421|ref|YP_566113.1|  [L=232]
Description: cobalamin synthesis protein, P47K [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-12   46.0   0.0    1.1e-11   44.7   0.0    1.7  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    7.7e-05   21.8   0.2      0.027   13.5   0.1    2.2  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00011   22.5   0.1    0.00047   20.5   0.1    1.8  2  AAA_19           AAA domain
     0.0021   18.1   0.1     0.0031   17.6   0.1    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0024   17.2   0.0     0.0085   15.4   0.0    1.8  2  Zeta_toxin       Zeta toxin
      0.006   15.9   0.1     0.0081   15.4   0.1    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0064   16.3   0.0     0.0094   15.7   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.028   14.8   0.0    1.6  1  AAA_16           AAA ATPase domain
      0.018   14.9   0.0       0.03   14.2   0.0    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.037   14.6   0.1      0.073   13.6   0.1    1.7  1  AAA_18           AAA domain
      0.037   13.3   0.0       0.06   12.7   0.0    1.3  1  DnaB_C           DnaB-like helicase C terminal domain
      0.046   13.2   0.0      0.073   12.5   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
       0.05   13.1   0.2      0.077   12.5   0.2    1.3  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
      0.056   13.6   0.1        0.1   12.8   0.1    1.4  1  ALS_ss_C         Small subunit of acetolactate synthase
      0.069   13.1   0.1       0.22   11.4   0.0    1.8  2  NACHT            NACHT domain
      0.093   12.5   0.0       0.15   11.8   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
       0.12   12.1   0.0       0.15   11.8   0.0    1.2  1  AAA_11           AAA domain
       0.12   12.2   0.0       0.18   11.6   0.0    1.3  1  TK               Thymidine kinase
       0.15   11.8   0.1       0.27   10.9   0.1    1.4  1  AAA_30           AAA domain
       0.16   11.7   0.1        1.3    8.8   0.0    2.0  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.16   10.8   0.0       0.24   10.3   0.0    1.1  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.17   12.2   0.0       0.31   11.3   0.0    1.4  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   1.3e-14   1.1e-11       3     176 ..       4     164 ..       2     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.3e-14
                                   EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT..EEEETTTTECCHCTT-HHHHHHHHHHHH CS
                          cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve.ivelenGciCctlredllkelealeere 80 
                                   +v++G +GsGKT++l h++    r+++k av+  +   +  D ++  + gv+  v l++  ++       ++ + + +ere
  gi|91773421|ref|YP_566113.1|   4 VVVAGTPGSGKTSVLLHTIkaLIRRENKPAVVKVDCLWT-DDDKRFGRLGVPiRVGLAKDMCPDHFTIYNTEPMIEWAERE 83 
                                   799****************887899************55.55555566667747999999999887766677777777777 PP

                                   TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HH CS
                          cobW  81 erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeealle 160
                                      +v+l Et G  +  ap                 v+v+D+    + + +++ k++  l++ad++v++K D +++++  e
  gi|91773421|ref|YP_566113.1|  84 -GANVLLNETAGlCLRCAPY----------PDSCLAVCVIDV----TTGPNTPLKVGPLLTTADVVVMTKGDIVSQAER-E 148
                                   .69*********87888888..........4456789*****....99*****************************88.* PP

                                   HHHHHHHHHHTTS-EE CS
                          cobW 161 kleerlrqlnpeakvl 176
                                   +++er+ ++np+  v+
  gi|91773421|ref|YP_566113.1| 149 VFRERVLEVNPDSMVI 164
                                   **********988776 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   3.3e-05     0.027      32      66 ..       4      38 ..       1      42 [. 0.93
   2 !    6.4   0.0    0.0047       3.8     154     234 ..     116     190 ..      70     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                  EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                  v + G+PG+Gk  ++ + +  l+rr ++ av+ vD
  gi|91773421|ref|YP_566113.1|  4 VVVAGTPGSGKTSVLLHTIKALIRRENKPAVVKVD 38
                                  6799******************************9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0047
                                   TTTTTTT--CC.CHHH-SEEEEE---.HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHH CS
                          MeaB 154 aGDelqgikkG.ileiaDiivvnkaD.kkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehrevl 232
                                   +G +   +k G +l  aD++v+ k D  ++ae+     + +le+      +  + v+++ +++g+G  el++ ie+  e++
  gi|91773421|ref|YP_566113.1| 116 TGPNT-PLKVGpLLTTADVVVMTKGDiVSQAERE-VFRERVLEV------NPDSMVIEANGLTGKGAIELAELIENSVETV 188
                                   44443.4555548899**********54445443.233333433......3356899999999999999999999988887 PP

                                   HH CS
                          MeaB 233 kk 234
                                   ++
  gi|91773421|ref|YP_566113.1| 189 ED 190
                                   65 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   5.8e-07   0.00047      11      41 ..       2      32 ..       1      42 [. 0.86
   2 ?   -0.7   0.0       1.9   1.6e+03      39      71 ..     156     187 ..     145     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.8e-07
                        AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvk 41
                                  k+++v + pG+GKT vl h ++ l+++++ +
  gi|91773421|ref|YP_566113.1|  2 KLVVVAGTPGSGKTSVLLHTIKALIRRENKP 32
                                  67899********************998664 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                        AAA_19  39 gvkpeeillva..ftgrAakelrerlaalgaeatT 71 
                                   +v+p+++++ a  +tg+ a el+e +   + + +T
  gi|91773421|ref|YP_566113.1| 156 EVNPDSMVIEAngLTGKGAIELAELI---ENSVET 187
                                   45555554443227999999999877...444444 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 !   17.6   0.1   3.8e-06    0.0031       1      37 [.       3      39 ..       3     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.8e-06
                                  EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDp 37
                                  +++++++ G+GKT+++++ ++al rr+++ ++v++D 
  gi|91773421|ref|YP_566113.1|  3 LVVVAGTPGSGKTSVLLHTIKALIRRENKPAVVKVDC 39
                                  579999****************************996 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05    0.0085      17      45 ..       2      30 ..       2      41 .. 0.78
   2 ?   -1.5   0.0       1.6   1.3e+03      29      54 ..     138     162 ..     138     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                    Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgn 45
                                  kl++++G pG+GK++++  + ++l r++n
  gi|91773421|ref|YP_566113.1|  2 KLVVVAGTPGSGKTSVLLHTIKALIRREN 30
                                  689*************9999999884443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                    Zeta_toxin  29 KselaellkdelerqgnvvrldpDdl 54 
                                   K+ + + +++e+  +++v++++pD++
  gi|91773421|ref|YP_566113.1| 138 KGDIVSQAEREVF-RERVLEVNPDSM 162
                                   6777888888885.889999999976 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     1e-05    0.0081       2      29 ..       2      29 ..       1      39 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                       DUF2075  2 avvlVtGvaGtGKtvvllnllaeledde 29
                                  ++v+V G +G+GKt vll+ + +l + e
  gi|91773421|ref|YP_566113.1|  2 KLVVVAGTPGSGKTSVLLHTIKALIRRE 29
                                  689*****************99993333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05    0.0094       2      33 ..       5      35 ..       4      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
               Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptae 33
                                  vv+G pG+GK++++ + ++  li ++n+p+++
  gi|91773421|ref|YP_566113.1|  5 VVAGTPGSGKTSVLLHTIKA-LIRRENKPAVV 35
                                  9*****************99.88889998654 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   3.5e-05     0.028      26      55 ..       3      34 ..       1      93 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-05
                        AAA_16 26 lvllsGesGvGKsslvrellralekd..ggif 55
                                  lv++ G +G+GK+s++ +  +al ++  +  +
  gi|91773421|ref|YP_566113.1|  3 LVVVAGTPGSGKTSVLLHTIKALIRRenKPAV 34
                                  799*************6666666665442333 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.7e-05      0.03       2      36 ..       4      38 ..       3      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKha 36
                                  + ++g+ gsGKT+ l + i++l +r+ + +++K +
  gi|91773421|ref|YP_566113.1|  4 VVVAGTPGSGKTSVLLHTIKALIRRENKPAVVKVD 38
                                  6789****************************976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.9e-05     0.073       1      17 [.       4      20 ..       4     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-05
                        AAA_18  1 IlltGtpGvGKttlake 17
                                  ++++GtpG+GKt++  +
  gi|91773421|ref|YP_566113.1|  4 VVVAGTPGSGKTSVLLH 20
                                  78**********99644 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.4e-05      0.06      20      52 ..       2      34 ..       1      43 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                                  XEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 20 dliiiAarpsmGktalalniaenaavkeklpva 52
                                  +l+++A+ p+ Gkt++ l+ +++   +e++p +
  gi|91773421|ref|YP_566113.1|  2 KLVVVAGTPGSGKTSVLLHTIKALIRRENKPAV 34
                                  69******************9998877776633 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     9e-05     0.073       1      36 [.       1      36 [.       1      49 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                                  E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                         KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvvid 36
                                  M Lvv+ G P sGK+++  +  kal  ++ +  v++
  gi|91773421|ref|YP_566113.1|  1 MKLVVVAGTPGSGKTSVLLHTIKALIRRENKPAVVK 36
                                  99************9987665555555444444444 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   9.4e-05     0.077      16      41 ..       4      29 ..       1      37 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-05
                                  EEEEE-TTSSHHHHHHHHHHHHHHTS CS
                 UvrD-helicase 16 ilveAsAGsGKTfvlaerilrlikee 41
                                  ++v+  +GsGKT vl + i  li+ e
  gi|91773421|ref|YP_566113.1|  4 VVVAGTPGSGKTSVLLHTIKALIRRE 29
                                  4566679***************9987 PP

>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00012       0.1      23      47 ..     148     172 ..     133     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                   HHTT-EEEEEETTEEEEEEEE-HHH CS
                      ALS_ss_C  23 eifrakivdvspdsliieltgteek 47 
                                   e+fr ++++v+pds++ie+ g ++k
  gi|91773421|ref|YP_566113.1| 148 EVFRERVLEVNPDSMVIEANGLTGK 172
                                   79*****************998876 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   0.00027      0.22       2      30 ..       3      32 ..       2      41 .. 0.77
   2 ?   -1.8   0.0       3.2   2.6e+03     117     149 ..     127     159 ..     124     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                  CEEEEC-TTTCHHH.HHHHHHHHHCTS-SC CS
                         NACHT  2 lvilqGeaGsGKTt.Llqklalawaegklp 30
                                  lv++ G +GsGKT  Ll+ +  ++++++ p
  gi|91773421|ref|YP_566113.1|  3 LVVVAGTPGSGKTSvLLHTIKALIRRENKP 32
                                  799*********962677777777766655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
                                   TTT--EEEEEEECCCHHHHCTTSSCE..EEEE- CS
                         NACHT 117 llpeasllltvrpralrdleeqleeaivleveg 149
                                   ll++a +++ ++ + ++++e+ + +++vlev++
  gi|91773421|ref|YP_566113.1| 127 LLTTADVVVMTKGDIVSQAEREVFRERVLEVNP 159
                                   788999999999999999999999999999986 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.15       2      34 ..       4      36 ..       3      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                           PRK  2 IgvagsSGaGkttva.rklekifgrekvkaaeie 34
                                  + vag  G+Gkt+v  ++++ +++re+++a+ ++
  gi|91773421|ref|YP_566113.1|  4 VVVAGTPGSGKTSVLlHTIKALIRRENKPAV-VK 36
                                  569**********963788888898888854.43 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.15      20      44 ..       4      28 ..       1      89 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                        AAA_11 20 tliqGPPGtgKTktivellsqllsr 44
                                  +++ G PG+gKT+++++ +++l+ r
  gi|91773421|ref|YP_566113.1|  4 VVVAGTPGSGKTSVLLHTIKALIRR 28
                                  6899************999999744 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.18       2      48 ..       2      53 ..       1      90 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                            TK  2 sielilgpmfaGKsteLlrrvkryqlaekkvvvika.....akdnRysegkv 48
                                  ++ ++ g+  +GK++ Ll+++k + ++e k  v+k        d+R++   v
  gi|91773421|ref|YP_566113.1|  2 KLVVVAGTPGSGKTSVLLHTIKALIRRENKPAVVKVdclwtDDDKRFGRLGV 53
                                  678999999********************99999962222145677776555 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   0.00033      0.27      20      46 ..       3      30 ..       1      38 [. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                        AAA_30 20 vavltGpAGtGKttalkal.reaweaag 46
                                  ++v+ G +G+GKt +l +  ++++++++
  gi|91773421|ref|YP_566113.1|  3 LVVVAGTPGSGKTSVLLHTiKALIRREN 30
                                  789**********998766366666664 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0016       1.3       1      33 [.       6      38 ..       6      40 .. 0.88
   2 ?    0.6   0.0      0.48   3.9e+02     159     206 ..     132     183 ..     123     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                  v+G++GsGKt+     ++ l  r+ ++avv  D
  gi|91773421|ref|YP_566113.1|  6 VAGTPGSGKTSVLLHTIKALIRRENKPAVVKVD 38
                                  89*********9988888888888999999877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                    ATP_bind_1 159 hvvvlnkfDllkek.lekeleffedvealslllekee...ekykklaeaiae 206
                                    vvv++k D++++  +e   e++ +v+  s ++e +    +   +lae i +
  gi|91773421|ref|YP_566113.1| 132 DVVVMTKGDIVSQAeREVFRERVLEVNPDSMVIEANGltgKGAIELAELIEN 183
                                   6899999999997666666666777666555555443444333334444433 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 ?   10.3   0.0   0.00029      0.24      19      49 ..       5      35 ..       2      46 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                 TrwB_AAD_bind 19 livGttGsGKtqalekllrairargdraivl 49
                                  +++Gt GsGKt +l + ++a+ +r+++  v+
  gi|91773421|ref|YP_566113.1|  5 VVAGTPGSGKTSVLLHTIKALIRRENKPAVV 35
                                  789*************999977776655444 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   0.00038      0.31       7      47 ..       3      39 ..       1      60 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47
                                  ++vv G +G+GKT +l    + l ++    e++p vv+v++
  gi|91773421|ref|YP_566113.1|  3 LVVVAGTPGSGKTSVLLHTIKALIRR----ENKPAVVKVDC 39
                                  689***********999999888333....35888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1430.06
//
Query:       gi|91773422|ref|YP_566114.1|  [L=208]
Description: Fe-S cluster protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   37.3   3.8      2e-09   36.9   0.9    2.4  2  FeS        Putative Fe-S cluster
  ------ inclusion threshold ------
       0.17   11.7   2.4       0.16   11.8   0.8    1.8  2  zf-RING_4  RING/Ubox like zinc-binding domain


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 !   36.9   0.9   2.2e-13     2e-09       1      33 []       8      39 ..       8      39 .. 0.95
   2 ?    0.3   0.1     0.062   5.6e+02      10      15 ..      83      88 ..      83      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.2e-13
                           FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                  LPg+NCg+CGy+ C+++Ae +   + ++++Cp+
  gi|91773422|ref|YP_566114.1|  8 LPGYNCGKCGYQQCRDLAENIRTAD-DISRCPF 39
                                  9********************9998.8999996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.062
                           FeS 10 GypgCm 15
                                  G+p+C+
  gi|91773422|ref|YP_566114.1| 83 GEPTCR 88
                                  9****8 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   1.8e-05      0.16      18      41 ..      13      38 ..      10      42 .. 0.88
   2 ?   -3.1   0.0      0.78     7e+03      41      46 ..      85      90 ..      85      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                     zf-RING_4 18 C.eCgyqiClfCyhrile.eeegrCP 41
                                  C +Cgyq C++  ++i++ +   rCP
  gi|91773422|ref|YP_566114.1| 13 CgKCGYQQCRDLAENIRTaDDISRCP 38
                                  779**************955689999 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.78
                     zf-RING_4 41 PaCree 46
                                  P Cre+
  gi|91773422|ref|YP_566114.1| 85 PTCRED 90
                                  889975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1332.37
//
Query:       gi|91773423|ref|YP_566115.1|  [L=168]
Description: sulfopyruvate decarboxylase subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-13   50.7   0.0    1.7e-13   50.6   0.0    1.0  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 !   50.6   0.0   9.4e-18   1.7e-13       3     162 ..       6     163 ..       4     168 .] 0.83

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 9.4e-18
                                   HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHH CS
                  TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalta 82 
                                   +++a+++ Lk  gv+ v+ vp+ +++++l ++++ +  +++ ++r E+g+++ A +y  + g++ v l+++  G+ n ++a
  gi|91773423|ref|YP_566115.1|   6 ASTAVFDSLKLTGVDLVVSVPCINLKDVLTMIDNDPtMLHIPVTREEEGVGICAGAY--MGGRIPVMLMQN-SGLGNSINA 83 
                                   789*********************************777778889999999999999..999999999988.599999999 PP

                                   HHHHH.HHT--EEEEEEE--CCCHH......S..TC--T.-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EE CS
                  TPP_enzyme_N  83 laeAk.vdriPllvlsgdrptslrg......qgvlqqel.dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPv 155
                                   la+ + + +iPll++  +r+ + +        g + + l d l++  p++     v + ++++ a++ A+r+a  ++++Pv
  gi|91773423|ref|YP_566115.1|  84 LASLNnLFHIPLLLIMSHRGCEGETicaqypMGQMTPSLlDTLGI--PYV-----VPTIDTVEDAIHYAWRIA-IEKKRPV 156
                                   99876156*****************99865533333333577777..777.....******************.8888888 PP

                                   EEEEEHH CS
                  TPP_enzyme_N 156 ylelpkd 162
                                   ++ l   
  gi|91773423|ref|YP_566115.1| 157 AVLLEIG 163
                                   8877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 980.14
//
Query:       gi|91773424|ref|YP_566116.1|  [L=189]
Description: sulfopyruvate decarboxylase subunit beta [Methanococcoides burtonii DSM 6242]
Scores for complete 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-20   71.3   0.5    1.4e-19   70.3   0.5    1.5  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 !   70.3   0.5   8.1e-24   1.4e-19      20     153 .]      38     157 ..      24     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 8.1e-24
                                   EEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHHHHTCCT CS
                  TPP_enzyme_C  20 syltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnl.pitvvvlnNegygmtggqqepfggkr 99 
                                   +  + ++lg+mG + ++++G++l  pdr+v+ai GDG+ lm++  lat++ ++  + ++vv++N++yg tg+q + +    
  gi|91773424|ref|YP_566116.1|  38 RSANFYMLGSMGLSSSIGLGVALSVPDRHVIAIDGDGSVLMNMGSLATIAHQHPeNYLLVVIDNGAYGSTGNQLTATAL-- 116
                                   3445678****************99***********************9988888******************877653.. PP

                                   TTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C 100 ksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                              +d+a +a+++G++ +    + + ee++e+lk     +g+ +++v
  gi|91773424|ref|YP_566116.1| 117 ----------GTDLAIVAKGAGIDeVHN--TFSEEEFREKLKNV--DRGVIVVHV 157
                                   ..........469***********7766..55559******998..356777765 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:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1333.10
//
Query:       gi|91773425|ref|YP_566117.1|  [L=427]
Description: hypothetical protein Mbur_1460 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-106  356.5   0.0   1.4e-106  356.3   0.0    1.0  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    0.00013   22.5   8.2    0.00022   21.8   7.0    2.1  2  Fer4_7    4Fe-4S dicluster domain
     0.0014   19.1   3.5        2.7    8.5   0.0    2.5  2  Fer4_8    4Fe-4S dicluster domain
     0.0058   16.8   7.2      0.013   15.6   7.2    1.6  1  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.016   15.3  12.4       0.24   11.6   3.0    2.7  3  Fer4_21   4Fe-4S dicluster domain
      0.025   14.4  11.6       0.63    9.9   3.6    3.1  2  Fer4      4Fe-4S binding domain
      0.027   14.6  10.4       0.24   11.6  11.0    2.2  2  Fer4_10   4Fe-4S dicluster domain
       0.15   12.2  13.1       0.78   10.0   1.8    2.9  3  Fer4_2    4Fe-4S binding domain
       0.46   11.3   7.5        0.5   11.1   0.1    3.0  2  Fer4_15   4Fe-4S single cluster domain
        3.2    8.4  12.9         14    6.3   3.7    2.5  2  Fer4_17   4Fe-4S dicluster domain
          4    8.1  13.0        2.8    8.6   0.5    3.2  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        4.4    8.1  11.2        3.4    8.4   1.7    2.7  2  Fer4_4    4Fe-4S binding domain
        4.8    8.2   8.6         29    5.7   0.7    2.5  4  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 !  356.3   0.0    1e-109  1.4e-106       1     347 []      17     418 ..      17     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: 356.3 bits;  conditional E-value: 1e-109
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx......xxxxxx RF
                        HcyBio   1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkiki..ekvwLngvpayag......laavdl 73 
                                   avVlta+++++lv++ ge+ +ae+vDVVt++T+++ms+++a+l+++v++++++   ++v++ngvpa++g      l+++dl
  gi|91773425|ref|YP_566117.1|  17 AVVLTAQQVCDLVDS-GEDIRAEDVDVVTAATRAIMSGTYAILSFPVKSSHSFLraKEVYMNGVPAHVGpcpnerLGILDL 96 
                                   8**************.***********************************999889************************ PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio  74 ylgataeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNsse 154
                                   +l++t++s d   +++yG+gh+++dL ++ +ve+++ ++++     ++++t++tld +++a+l+++R+a++nY+a+vN+s+
  gi|91773425|ref|YP_566117.1|  97 MLFGTDHSVD---DSRYGAGHLFRDLAERMTVEVKVITDNG-----ESFKTQVTLDGMPYAMLYGTRHAFKNYSAFVNTSD 169
                                   *********4...459*************************.....*********************************** PP

                                   x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 155 e...tiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLa 232
                                   e   +i++ ++e+ p+l++at+sg+G+++P++nDp l+ igiGtr+l++G+eG+++g+GT+ss+ek+           +L+
  gi|91773425|ref|YP_566117.1| 170 EpaaSIFH-AMEFGPRLTEATISGCGQINPVKNDPLLESIGIGTRMLMNGSEGFIMGSGTRSSAEKP-----------NLT 238
                                   ********.**********************************************************...........*** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                        HcyBio 233 vigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael..... 308
                                   +++d++eM+pey+ g+f ts+Gpe+iv++++p+Pv++++vle+++ +d+++++pv+ v++r      +g+ +Y+++     
  gi|91773425|ref|YP_566117.1| 239 AFADMHEMKPEYM-GGFSTSAGPECIVSWAVPVPVTSDSVLESIKERDRQLKMPVMAVDNR----ACVGYSDYGDVwegtd 314
                                   *************.*********************************************99....89************** PP

                                   ............................................................xxxxxxxx....xx.xxxxxx RF
                        HcyBio 309 ............................................................Gkieiegk....ev.ktarls 324
                                                                                               G+i++e      +v +++r+s
  gi|91773425|ref|YP_566117.1| 315 laidfspdecigctlcepaemcpmasisfgdgevkldrytcfncglcstlcvtdvftanlGSINFELGgestNVpIVLRQS 395
                                   ***************************************************************9986666779999***** PP

                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 325 slkrareiaeeLkewiekgeflL 347
                                   + kra e++e+Lke+i++g+f++
  gi|91773425|ref|YP_566117.1| 396 DKKRALELSEKLKEQILDGSFRM 418
                                   *********************86 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.5   7.6e+03      20      40 ..     282     302 ..     275     304 .. 0.74
   2 !   21.8   7.0   1.6e-07   0.00022       2      51 ..     324     368 ..     317     369 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.5
                        Fer4_7  20 deeenekgtekveidpekClg 40 
                                   +e++++ +++ +++d + C+g
  gi|91773425|ref|YP_566117.1| 282 KERDRQLKMPVMAVDNRACVG 302
                                   455555577889999999986 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.6e-07
                        Fer4_7   2 CigCgaCvaa..CpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   CigC  C++a  Cp+  i++ +        +v++d  +C +Cg C + C t+
  gi|91773425|ref|YP_566117.1| 324 CIGCTLCEPAemCPMASISFGD-------GEVKLDRYTCFNCGLCSTLCVTD 368
                                   *******96555********77.......4799****************887 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  11.7      0.13   1.8e+02       4      63 ..     323     367 ..     321     369 .. 0.73
   2 !    8.5   0.0    0.0019       2.7       4      16 ..     354     366 ..     351     417 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                        Fer4_8   4 kCieCgaCq..saCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                   +Ci+C +C+  ++Cp+++ +        ge+     + ++       ++C +cg C++ C +
  gi|91773425|ref|YP_566117.1| 323 ECIGCTLCEpaEMCPMASISF-----GDGEV-----KLDR-------YTCFNCGLCSTLCVT 367
                                   7********9899**888762.....22333.....3456.......788888888888865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                        Fer4_8   4 kCieCgaCqsaCp 16 
                                    C +Cg+C + C 
  gi|91773425|ref|YP_566117.1| 354 TCFNCGLCSTLCV 366
                                   6888888888883 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   7.2   9.6e-06     0.013       1      49 [.     323     368 ..     323     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.6e-06
                        Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   +C+gC+ C++a  Cp+  ++  ++e k          C+ Cg C   C ++
  gi|91773425|ref|YP_566117.1| 323 ECIGCTLCEPAemCPMASISFGDGEVKLDRY-----TCFNCGLCSTLCVTD 368
                                   5*******76555*****9999888887764.....5***********887 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.9   6.7e+03      33      43 ..     292     302 ..     274     304 .. 0.61
   2 ?   11.6   3.0   0.00017      0.24      37      53 ..     320     338 ..     311     343 .. 0.76
   3 ?    8.2   1.5    0.0019       2.7       3      19 ..     350     366 ..     346     374 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.9
                       Fer4_21  33 vlkvvedeCvG 43 
                                   v++v +  CvG
  gi|91773425|ref|YP_566117.1| 292 VMAVDNRACVG 302
                                   34566778887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                       Fer4_21  37 vedeCvGCnlC..ssvCPv 53 
                                     deC+GC+lC  +++CP+
  gi|91773425|ref|YP_566117.1| 320 SPDECIGCTLCepAEMCPM 338
                                   579********55579*97 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0019
                       Fer4_21   3 idedkCigCgkCliaCe 19 
                                   +d+ +C +Cg+C + C 
  gi|91773425|ref|YP_566117.1| 350 LDRYTCFNCGLCSTLCV 366
                                   56677888888888885 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.6   0.00046      0.63       3      17 ..     319     333 ..     317     342 .. 0.87
   2 ?    7.9   1.1     0.002       2.8       3      18 ..     350     365 ..     348     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00046
                                   EETTTSSS-THHHHH CS
                          Fer4   3 ideekCigCGaCvev 17 
                                   + ++ CigC +C+ +
  gi|91773425|ref|YP_566117.1| 319 FSPDECIGCTLCEPA 333
                                   789*********975 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.002
                                   EETTTSSS-THHHHHS CS
                          Fer4   3 ideekCigCGaCvevC 18 
                                    d   C +CG+C   C
  gi|91773425|ref|YP_566117.1| 350 LDRYTCFNCGLCSTLC 365
                                   67788*******9999 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  11.0   0.00017      0.24       4      55 ..     319     365 ..     316     366 .. 0.84
   2 ?    8.7   1.2    0.0013       1.8       2      19 ..     348     365 ..     347     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                       Fer4_10   4 idddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   + +d Ci+C+ C  a  CP+         +  ++++v+ + + C +cg C   C
  gi|91773425|ref|YP_566117.1| 319 FSPDECIGCTLCEPAemCPM-------ASISFGDGEVKLDRYTCFNCGLCSTLC 365
                                   5689********97555***.......777788888888999******999888 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                       Fer4_10   2 vvidddtCirCgkCvkaC 19 
                                   v++d+ tC +Cg C + C
  gi|91773425|ref|YP_566117.1| 348 VKLDRYTCFNCGLCSTLC 365
                                   678999************ PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.5   4.8e+03       2      12 ..     292     302 ..     291     302 .. 0.77
   2 ?    8.6   1.7    0.0015       2.1       5      21 ..     319     337 ..     315     338 .. 0.84
   3 ?   10.0   1.8   0.00056      0.78       3      20 ..     348     365 ..     346     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                        Fer4_2   2 pvvvdtdrCig 12 
                                   +++vd ++C+g
  gi|91773425|ref|YP_566117.1| 292 VMAVDNRACVG 302
                                   57889999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                        Fer4_2   5 vdtdrCigCgaCvsa..CP 21 
                                   + +d CigC  C  a  CP
  gi|91773425|ref|YP_566117.1| 319 FSPDECIGCTLCEPAemCP 337
                                   66899*******9887899 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00056
                        Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                   v+ d+ +C +Cg C + C
  gi|91773425|ref|YP_566117.1| 348 VKLDRYTCFNCGLCSTLC 365
                                   678999********9999 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   3.5      0.73     1e+03       5      14 ..     321     330 ..     317     337 .. 0.83
   2 ?   11.1   0.1   0.00036       0.5       1      24 [.     348     372 ..     348     405 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.73
                       Fer4_15   5 rdaCigcglC 14 
                                    d+Cigc lC
  gi|91773425|ref|YP_566117.1| 321 PDECIGCTLC 330
                                   599******* PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
                       Fer4_15   1 VvvDrdaCigcglCvaea.pevfel 24 
                                   V++Dr +C  cglC +++ ++vf+ 
  gi|91773425|ref|YP_566117.1| 348 VKLDRYTCFNCGLCSTLCvTDVFTA 372
                                   89***************98888875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.7    0.0099        14      44      58 ..     322     338 ..     289     341 .. 0.77
   2 ?   -1.7  12.8       3.1   4.3e+03       2      57 ..     324     366 ..     323     370 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0099
                       Fer4_17  44 slCieCgeCe..rkCPq 58 
                                   ++Ci+C +Ce  + CP+
  gi|91773425|ref|YP_566117.1| 322 DECIGCTLCEpaEMCPM 338
                                   56666666665555665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                       Fer4_17   2 CiqCgyClp..eCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                   Ci+C  C+p  +Cp+            + +++g+ e    +    +C +Cg+C++ C 
  gi|91773425|ref|YP_566117.1| 324 CIGCTLCEPaeMCPM------------ASISFGDGEV---KLDRYTCFNCGLCSTLCV 366
                                   777777777444444............3333332222...223345666666666665 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   5.4      0.16   2.2e+02       4      17 ..     322     337 ..     317     339 .. 0.80
   2 ?    1.3   0.1      0.38   5.3e+02      48      57 ..     333     342 ..     331     343 .. 0.87
   3 ?    8.6   0.5     0.002       2.8       2      21 ..     351     371 ..     350     380 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                       Fer4_13   4 dtCiacgaC..velaP 17 
                                   d+Ci+c++C  +e++P
  gi|91773425|ref|YP_566117.1| 322 DECIGCTLCepAEMCP 337
                                   89*******5557777 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.38
                       Fer4_13  48 adaCPvesIg 57 
                                   a++CP++sI 
  gi|91773425|ref|YP_566117.1| 333 AEMCPMASIS 342
                                   789*****96 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.002
                       Fer4_13   2 DrdtCiacgaCvela.PdvFe 21 
                                   Dr tC +cg+C  l+  dvF 
  gi|91773425|ref|YP_566117.1| 351 DRYTCFNCGLCSTLCvTDVFT 371
                                   899**********99446775 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.7    0.0024       3.4       1      16 [.     321     338 ..     321     343 .. 0.91
   2 ?    3.9   2.4     0.068        94       3      10 ..     354     361 ..     350     366 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                        Fer4_4   1 qerCigCgsCvaa..CPq 16 
                                   ++ CigC  C+ a  CP+
  gi|91773425|ref|YP_566117.1| 321 PDECIGCTLCEPAemCPM 338
                                   689*********999996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.068
                        Fer4_4   3 rCigCgsC 10 
                                   +C++Cg C
  gi|91773425|ref|YP_566117.1| 354 TCFNCGLC 361
                                   5******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 ?    2.0   3.4       0.3   4.1e+02      50      66 ..     320     338 ..     290     339 .. 0.58
   2 ?    5.4   1.6     0.025        35       2      20 ..     324     344 ..     323     353 .. 0.78
   3 ?    4.1   1.3     0.065        89      52      65 ..     353     366 ..     346     368 .. 0.73
   4 ?    5.7   0.7     0.021        29       2      20 ..     355     373 ..     354     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.3
                       Fer4_16  50 kqeaitgCdiCq..dvCPa 66 
                                   +  +++gC  C+  ++CP+
  gi|91773425|ref|YP_566117.1| 320 SPDECIGCTLCEpaEMCPM 338
                                   4567788888853367775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                       Fer4_16   2 CgtCgkC..aevCPtnaikek 20 
                                   C++C+ C  ae+CP + i+  
  gi|91773425|ref|YP_566117.1| 324 CIGCTLCepAEMCPMASISFG 344
                                   9******66678**9999865 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.065
                       Fer4_16  52 eaitgCdiCqdvCP 65 
                                   + ++ C+ C + C+
  gi|91773425|ref|YP_566117.1| 353 YTCFNCGLCSTLCV 366
                                   56888888888886 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.021
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C +Cg C   C t++++++
  gi|91773425|ref|YP_566117.1| 355 CFNCGLCSTLCVTDVFTAN 373
                                   9999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2739.82
//
Query:       gi|91773426|ref|YP_566118.1|  [L=636]
Description: sodium/hydrogen exchanger [Methanococcoides burtonii DSM 6242]
Scores for 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  47.9    2.8e-59  200.8  47.9    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    2.3e-21   76.2   0.0    4.3e-21   75.3   0.0    1.5  1  TrkA_N          TrkA-N domain
    8.9e-13   47.9   0.1    2.1e-12   46.7   0.1    1.7  1  TrkA_C          TrkA-C domain


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.8  47.9   4.7e-63   2.8e-59      22     374 ..       1     344 [.       1     348 [. 0.96

  Alignments for each domain:
  == domain 1  score: 200.8 bits;  conditional E-value: 4.7e-63
                                   HHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHHHHHHHHHHHHH.HH CS
                Na_H_Exchanger  22 eivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksilllallgvlitvvliGlllylll 102
                                   +ivg++++G+l+Gp+g g+i+   e +evl+e+g++lllF +G+el++++l+k++++++ ++ ++v++t++++  ++++  
  gi|91773426|ref|YP_566118.1|   1 MIVGFLFTGMLVGPHGYGFIDAV-EEVEVLAEIGIVLLLFTIGVELSIKDLWKMKRAVVFGGSIQVFLTTIAVFSIANY-- 78 
                                   58*********************.************************************************5555664.. PP

                                   TXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTX.XXXXTSSSTSXHHHH CS
                Na_H_Exchanger 103 ilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalak.eeaggetslllllli 182
                                    lg+ + e++++g+++s++++++vl++l+++g+++   g+  l++++ +D+++v+++ + + la+ +++++++ +  l++ 
  gi|91773426|ref|YP_566118.1|  79 -LGYGIGESIFIGFLFSLSSTAIVLKLLQNRGELQAPHGRFSLAVLLYQDVIVVPMILITPFLAGaGSMSDAAFIPILAKG 158
                                   .789************************************************************888888888888999** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                Na_H_Exchanger 183 flvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklsekles 263
                                   + +v++++  ++++++ +l+ it++  +d+el++l +++++l++a+l+++lg+s +lgaflaGl++se+e+s+++  ++ +
  gi|91773426|ref|YP_566118.1| 159 IGLVILVFASAKWIVPQVLFQITKT--RDSELFFLSIIVICLSVAWLTSSLGLSLALGAFLAGLIISESEYSHQALSNMIP 237
                                   *************************..9**********************************************9999*** PP

                                   HHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHH CS
                Na_H_Exchanger 264 freglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaa 344
                                   fr ++f  +fF+++G+ ldl  +   ++ ++l ++i + +ll + + + l ++llg++l++a+i+g+g++q+g+++++l  
  gi|91773426|ref|YP_566118.1| 238 FR-DIFMSFFFISIGMLLDLDYF---FNDPFLFIIIAACVLLLKSVIAGLSSYLLGFPLHTAVIAGLGLAQVGEFSFVLST 314
                                   **.9***************9999...8888888888888889*************************************** PP

                                   HHHHHXHHHHTTSSTTTCSTSXHHHHHHHH CS
                Na_H_Exchanger 345 lgpalgllarelyallivvvlftvlvqGls 374
                                   +g   gll+ e+y l++vv ++t+ v  ++
  gi|91773426|ref|YP_566118.1| 315 FGVEYGLLTDEVYQLFLVVSILTMAVTSSV 344
                                   ************************987765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   7.2e-25   4.3e-21       2     114 ..     388     500 ..     387     502 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 7.2e-25
                                   EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHH CS
                        TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavll 82 
                                   ii+G+G  Gr++a+  + +g++++v d+++e+v++ + +g  +++gd +++ vLe+a+i++a++++++++d + +  a+ l
  gi|91773426|ref|YP_566118.1| 388 IIAGFGFNGRTVAKAATIAGIPYLVLDTNPETVRKEQLKGELIYYGDSSQRGVLEHADIKDARVMVVCISDPAGTRRAISL 468
                                   9*****************8888******************99*************************************** PP

                                   HHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                        TrkA_N  83 akelnpkkkiiaraqdpehaellkklgadvvi 114
                                   a+++np+++iiar+q+ ++ e l++lga++vi
  gi|91773426|ref|YP_566118.1| 469 ARKMNPNIHIIARTQYLQEMEPLYELGANEVI 500
                                   *******************************9 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.1   3.5e-16   2.1e-12       4      69 ..     564     631 ..     561     632 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 3.5e-16
                                   EEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C   4 vtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                   ++v+a+s  vGk l +l+lr++ +v+++airR+ +++ +p+ d vL +GDvl+++gsp+ +++++ l+
  gi|91773426|ref|YP_566118.1| 564 LRVRASSFAVGKNLLQLDLRKKySVTLLAIRRNsEVIANPDADAVLISGDVLVLMGSPEMISKVTPLF 631
                                   78999***********************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 3710.45
//
Query:       gi|91773427|ref|YP_566119.1|  [L=378]
Description: hypothetical protein Mbur_1462 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2486.31
//
Query:       gi|91773428|ref|YP_566120.1|  [L=317]
Description: tyrosyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-56  191.8   0.0    1.9e-56  191.5   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.011   14.7   0.0       0.34    9.8   0.0    2.1  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5   0.0   2.2e-60   1.9e-56       3     293 .]      27     310 ..      25     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 2.2e-60
                                   HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTT CS
                  tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpe 83 
                                   +++ ++y+G +P+gk+H G+++ ++kl++lqkag e+++l+aD+hA+++++   ++ ++rk +++ ++     la gldpe
  gi|91773428|ref|YP_566120.1|  27 KKHPSAYTGYEPSGKIHMGHVLTVNKLLDLQKAGFEITVLLADVHAYLNQKG--TMDEVRKTADYNKKC---FLALGLDPE 102
                                   57899********************************************999..9**************...********* PP

                                   TEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH.CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHH CS
                  tRNA-synt_1b  84 kaevvlqsewlehlelaellrdlgklgslnrmlqfks.vkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqn 163
                                    +++v++s+ + + e++  + +l++ +slnr  +  + v +++e  +  +++++ Yp++qa Di+ll +d+ +gG DQ+++
  gi|91773428|ref|YP_566120.1| 103 MTNFVYGSDFQLSPEYMLNVLKLTQATSLNRAKRSMDeVGRKMED-P--KVSQMVYPIMQAVDIALLGVDVAVGGIDQRKI 180
                                   ********************************8755538888888.4..7******************************* PP

                                   HHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHT CS
                  tRNA-synt_1b 164 ielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklkte 242
                                     l+r+ ++ ++ k     p ++ +p+l gldG+ KmS+S +n +I  dd+++  kkk++ka++  ++  ++  l+  k+ 
  gi|91773428|ref|YP_566120.1| 181 HMLAREGLPGLGFK----APLCIHTPILLGLDGT-KMSSSNEN-YISVDDDEAALKKKFKKAFCPAEDieNNPVLELFKYH 255
                                   ***********766....****************.********.********************99999788888888999 PP

                                   HHH....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 243 lsn....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                   +++     ++er e+++g    +++ el++ ++++ +h++dlk+++a+ lne+le
  gi|91773428|ref|YP_566120.1| 256 ITPrydeMVFERPEKFGGDLVCKSYAELEKVFADGSLHPMDLKNGAAKYLNEILE 310
                                   999999899*********99999*****************************985 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   3.8e-05      0.34      17      45 ..      21      50 ..       6      90 .. 0.70
   2 ?    3.0   0.0    0.0045        40     261     294 ..     191     224 ..     157     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.8e-05
                  tRNA-synt_1f 17 kkka.ekdevvvesGispSGliHiGnlrev 45
                                   k   +k++    +G+ pSG+iH+G +  v
  gi|91773428|ref|YP_566120.1| 21 TKLLeTKKHPSAYTGYEPSGKIHMGHVLTV 50
                                  2222355667788************87554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0045
                  tRNA-synt_1f 261 lggeaPekvvYelillkggekmssSkGnvltled 294
                                   lg++aP  +   ++l   g kmssS+ n+++++d
  gi|91773428|ref|YP_566120.1| 191 LGFKAPLCIHTPILLGLDGTKMSSSNENYISVDD 224
                                   67888887777766666677***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2165.52
//
Query:       gi|91773429|ref|YP_566121.1|  [L=243]
Description: hypothetical protein Mbur_1464 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   79.3   0.0    3.1e-22   78.9   0.0    1.2  1  Thg1      tRNAHis guanylyltransferase
    4.9e-09   36.4   0.2      1e-08   35.4   0.1    1.6  2  Thg1C     Thg1 C terminal domain


Domain annotation for each model (and alignments):
>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   3.5e-26   3.1e-22       4     124 ..       1     118 [.       1     119 [. 0.94

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 3.5e-26
                          Thg1   4 vkefeqddkllpntlivvRiDGrgFhkfskkhkfekPnDeralklmneaakelvkefe.divlaYgqSDEislvlsketkl 83 
                                   +k+ e  ++l    +++vR+DGr+F++  ++++ ekP+De+++++m ++ + ++k+   ++ laY++SDE s+++ +    
  gi|91773429|ref|YP_566121.1|   1 MKKREVYSDLRCIPPVIVRLDGRTFKHTLSRLGCEKPYDEKFASAMADSLELFFKKSGiNAALAYTFSDEASILFFDLP-- 79 
                                   678888888888899**********999999*************************9669****************999.. PP

                          Thg1  84 ynrraqklvslvaslftaafvkllskafeelpsFDarvvly 124
                                   +++r++kl s+++s++++af+ ++        sFD+r+v++
  gi|91773429|ref|YP_566121.1|  80 FDGRVEKLDSVISSYLSSAFTIKMGLDEP--VSFDSRIVPV 118
                                   **********************9998877..9******975 PP

>> Thg1C  Thg1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.58   5.2e+03      49      62 ..      48      61 ..      42      77 .. 0.72
   2 !   35.4   0.1   1.1e-12     1e-08       2      84 ..     122     202 ..     121     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.58
                         Thg1C 49 dkneiLfsefginY 62
                                  d  e++f++ gin 
  gi|91773429|ref|YP_566121.1| 48 DSLELFFKKSGINA 61
                                  55688888888885 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 1.1e-12
                         Thg1C   2 nlrDYlsWRqvDchinnlYNttFWalvqkgglteqeaeeeLkgtlskdkneiLfsefginYnnepeifrkGsvlvrekeke 82 
                                   n+ +Yl WRq ++  n +    +++l+  +g+++++a +++kg  ++  +e+Lf++ gin ++ p   r+G  ++++  k 
  gi|91773429|ref|YP_566121.1| 122 NVAEYLIWRQSEAWRNCVSSYGYYTLL-SEGMSKKDAASAIKGKKAQGIHELLFQR-GINLDKVPMWQRRGILVYKDDYKV 200
                                   899***********************9.89************************76.**************9999976555 PP

                         Thg1C  83 ek 84 
                                   + 
  gi|91773429|ref|YP_566121.1| 201 AG 202
                                   43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1437.85
//
Query:       gi|91773430|ref|YP_566122.1|  [L=90]
Description: PRC-barrel protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-14   53.1   2.0    3.1e-14   52.8   2.0    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 !   52.8   2.0   1.7e-18   3.1e-14       6      74 ..       5      74 ..       2      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.7e-18
                                  S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.......-EEEEEGG.CEECCCTEEEETT CS
                           PRC  6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..gekevliPfdlavkigkdriivda 74
                                  +++l G+ Vyt++G+++GkV+D+v+d +e  v +l +s+ +++ +  + + v++P++ +v + +d++i++ 
  gi|91773430|ref|YP_566122.1|  5 ITSLFGLNVYTNQGTYVGKVNDLVFDVDERLVSGLALSDINRDIFdvQTRGVILPYR-WVVTTGDIVIIRD 74
                                  689***************************************666************.8888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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 0.27s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 569.00
//
Query:       gi|91773431|ref|YP_566123.1|  [L=253]
Description: hypothetical protein Mbur_1466 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-37  127.6   0.7    8.3e-37  126.7   0.2    1.7  2  RNase_H_2       RNase_H superfamily
  ------ inclusion threshold ------
      0.013   15.2   0.0       0.26   11.0   0.0    2.3  2  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.28   2.5e+03     130     141 ..      26      37 ..      22      69 .. 0.83
   2 !  126.7   0.2   9.3e-41   8.3e-37       2     165 ..      89     238 ..      88     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.28
                     RNase_H_2 130 klyqeylrtgde 141
                                   +++++yl+ +de
  gi|91773431|ref|YP_566123.1|  26 CTWDKYLEHQDE 37 
                                   689999988886 PP

  == domain 2  score: 126.7 bits;  conditional E-value: 9.3e-41
                     RNase_H_2   2 ffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlfkkyk 82 
                                   ++DiEttGlsp++++i++iG++d ++   ++++    ++ + e+ ++e     l+k++ lv+fng++FD+pf+++ + +++
  gi|91773431|ref|YP_566123.1|  89 YVDIETTGLSPSSSYITVIGIYDGED--AKTYV----KGIDLEDVVEE-----LQKYELLVSFNGARFDLPFIQKEYPQIE 158
                                   99********************7555..45455....58999999999.....9***********************9977 PP

                     RNase_H_2  83 ldeeefrhiDLlkelrkkklesysLksvekelgierreed..lsGsqavklyqeylrtgdeellekilaYNedDvralatl 161
                                   +++    hiDL+++lr+ +l++ +Lk++ek+l+i+r++e   + G +av+l++ey ++g+e++le +l+YN++D+++l+t+
  gi|91773431|ref|YP_566123.1| 159 FNQ---LHIDLMYPLRRIGLSG-GLKAIEKKLEINRTDETvgITGFDAVRLWHEY-ERGNEASLELLLEYNREDIVNLKTI 234
                                   775...****************.*************6554349************.69*********************** PP

                     RNase_H_2 162 yekl 165
                                   +ek 
  gi|91773431|ref|YP_566123.1| 235 IEKT 238
                                   9975 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 ?   11.0   0.0   2.9e-05      0.26      45      69 ..     128     151 ..      92     157 .. 0.83
   2 ?    1.9   0.0     0.017   1.5e+02     101     165 ..     159     230 ..     152     234 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.9e-05
                DNA_pol_B_exo2  45 fegvekkkpqlVsfngrgfDlpvle 69 
                                    e ++k++  lVsfng  fDlp ++
  gi|91773431|ref|YP_566123.1| 128 VEELQKYE-LLVSFNGARFDLPFIQ 151
                                   55556666.79***********875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.017
                DNA_pol_B_exo2 101 ystrhlDLmdllseyg....aranakLdelakllglPGKlgvdGskVaelyqegklkeir...eYcetDvln 165
                                   +++ h+DLm  l + g     +a +k  e+ ++    G +g d+ + ++ y++g+ ++++   eY++ D++n
  gi|91773431|ref|YP_566123.1| 159 FNQLHIDLMYPLRRIGlsggLKAIEKKLEINRTDETVGITGFDAVRLWHEYERGNEASLElllEYNREDIVN 230
                                   566677777766665521112233333345555666677889999999999988765543333999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1576.55
//
Query:       gi|91773432|ref|YP_566124.1|  [L=604]
Description: excinuclease ABC subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete 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-56  188.2   0.3    4.6e-55  185.8   0.0    2.3  2  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    8.1e-12   45.6   0.0    2.3e-11   44.1   0.0    1.8  1  HHH_5       Helix-hairpin-helix domain
    1.8e-11   44.1   0.2    2.3e-10   40.6   0.1    2.7  2  GIY-YIG     GIY-YIG catalytic domain
      3e-11   43.2   0.8    8.5e-11   41.8   0.2    2.1  2  HHH_2       Helix-hairpin-helix motif
    4.4e-08   32.6   0.4    1.1e-07   31.3   0.4    1.7  1  UVR         UvrB/uvrC motif
    5.6e-08   32.3   0.0    0.00027   20.6   0.1    3.1  2  HHH         Helix-hairpin-helix motif
    5.5e-05   23.3   0.1     0.0021   18.2   0.0    2.7  2  HHH_3       Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.28   11.8   2.8       0.75   10.4   0.0    3.1  3  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
       0.42   10.6   2.5          6    6.9   0.0    3.0  2  DUF2335     Predicted membrane protein (DUF2335)


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.24   4.8e+02      97     147 ..     329     380 ..     325     382 .. 0.70
   2 !  185.8   0.0   2.3e-58   4.6e-55       2     154 .]     380     530 ..     379     530 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.24
                                   HHHHTT----EEEEES............SSSEE.EE--TT-HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                    UvrC_HhH_N  97 vleelglkipvvglaKdkkrktrakaeereeev.lelkkssealkllqrird 147
                                   + +++++++p  g +K  ++  +++a+ + e+  l+ + +++al+ l ++rd
  gi|91773432|ref|YP_566124.1| 329 AARSVQIQVPQRGNKKRLMEMAEQNAQMTLEQShLKQSDKEQALQALLQLRD 380
                                   566777788888878866665555554444443588999999*****99999 PP

  == domain 2  score: 185.8 bits;  conditional E-value: 2.3e-58
                                   HHTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS.....---SEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    UvrC_HhH_N   2 ellglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllkefsklPdLi 82 
                                   ++l l++ p +ie++DiS+i+gt++vgsmvvfe+g p++s+yR+f+ik+vk+ dD+a+m+ev++Rr+++ ++e++klPdLi
  gi|91773432|ref|YP_566124.1| 380 DALALSTLPAHIEGFDISNISGTDAVGSMVVFENGLPANSKYRHFNIKTVKGIDDFAMMAEVVKRRYTHQKAEKDKLPDLI 460
                                   6899***************************************************************************** PP

                                   EESSSHHHHHHHHHHHHHTT----EEEEES..............SSSEEEE--TT-HHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    UvrC_HhH_N  83 liDGGkgqlnaakevleelglkipvvglaKdkkrktraka..eereeevlelkkssealkllqrirdeaHrfAI 154
                                   liDGG gq++aa+  l+el+l+ip+vglaK  ++     +  ++ ++ev++l+++sealk+l+r+rde+HrfA+
  gi|91773432|ref|YP_566124.1| 461 LIDGGPGQVSAAMGSLKELQLDIPLVGLAKRFEHI----IvpKDGTDEVVILPHTSEALKVLMRVRDESHRFAV 530
                                   ******************************55554....3454666789************************7 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.1e-14   2.3e-11       3      53 ..     545     594 ..     544     598 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.1e-14
                                   HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                         HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                   eL +++GiG+++ +all++ ++s+e++ +a+veeL+++ Gi+k +Aeri+ 
  gi|91773432|ref|YP_566124.1| 545 ELDTIPGIGASRKKALLNH-FSSIEQIRHASVEELTAVEGISKGLAERIVA 594
                                   799****************.*****************************85 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   1.2e-13   2.3e-10       3      78 .]      13      88 ..      11      88 .. 0.88
   2 ?   -0.1   0.0      0.56   1.1e+03      18      35 ..     583     600 ..     582     604 .] 0.88

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.2e-13
                                  EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-H.S.STEEEEEEEE----HHHHHHHHHHHHHHTTSSSS CS
                       GIY-YIG  3 gvYiirskenkliYvGstknlekRlkqHnagkkakytrkk.gkkpfeliileifptksealelEkklikkyksnkyn 78
                                  gvY+++++ +++iY+G++k+l+kR +q+++++k++  +++ ++++ + + + + +++  al lE+ l kk+++ +yn
  gi|91773432|ref|YP_566124.1| 13 GVYLMKDISDNIIYIGKAKSLKKRVSQYFQSSKNHSSKTRaMVRKIADVDYIVTESEVAALILEANLVKKNRP-HYN 88
                                  9***************************99998888877667777777777777777777*************.998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.56
                                   EEESSHHHHHHHHHHHHH CS
                       GIY-YIG  18 GstknlekRlkqHnagkk 35 
                                   G++k l +R+  H+++++
  gi|91773432|ref|YP_566124.1| 583 GISKGLAERIVAHFNKER 600
                                   8999*********99986 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.9   9.8e+03      50      61 ..      36      47 ..      33      48 .. 0.84
   2 !   41.8   0.2   4.3e-14   8.5e-11       8      61 ..     549     602 ..     548     604 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.9
                         HHH_2 50 sivefFeneknr 61
                                   + ++F+++kn+
  gi|91773432|ref|YP_566124.1| 36 RVSQYFQSSKNH 47
                                  6899***99986 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 4.3e-14
                         HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFeneknr 61 
                                   I+ +G++  k+L ++F s++++++as+eeL++v++i +  A+ iv  F++e+++
  gi|91773432|ref|YP_566124.1| 549 IPGIGASRKKALLNHFSSIEQIRHASVEELTAVEGISKGLAERIVAHFNKERVE 602
                                   99************************************************9876 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.4   5.6e-11   1.1e-07       4      35 ..     202     233 ..     200     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.6e-11
                           UVR   4 ikeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                   ikeL+e+m+  a ++++E AA +RDqi alk 
  gi|91773432|ref|YP_566124.1| 202 IKELQEKMNIHAIAQEYESAAVIRDQIDALKS 233
                                   9*****************************96 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0012       2.3       9      29 ..     542     562 ..     540     563 .. 0.86
   2 !   20.6   0.1   1.4e-07   0.00027       1      29 [.     566     594 ..     566     595 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                                   SHHHHHTSTT-SHHHHHHHHH CS
                           HHH   9 sreeLlalPGVGpktAeaIls 29 
                                   s  eL ++PG+G ++  a l+
  gi|91773432|ref|YP_566124.1| 542 SHSELDTIPGIGASRKKALLN 562
                                   678*********999888775 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.4e-07
                                   SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                           HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                   s+e ++ as+eeL+a++G+ +  Ae+I +
  gi|91773432|ref|YP_566124.1| 566 SIEQIRHASVEELTAVEGISKGLAERIVA 594
                                   5788899********************86 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.14   2.7e+02      12      26 ..     542     556 ..     540     564 .. 0.78
   2 !   18.2   0.0   1.1e-06    0.0021       8      33 ..     570     595 ..     565     600 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.14
                         HHH_3  12 saeeLqklpGlgpkl 26 
                                   s +eL+++pG+g++ 
  gi|91773432|ref|YP_566124.1| 542 SHSELDTIPGIGASR 556
                                   6799*******9875 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.1e-06
                         HHH_3   8 iNtAsaeeLqklpGlgpklAknIvay 33 
                                   i  As+eeL+ ++G+++ lA++Iva+
  gi|91773432|ref|YP_566124.1| 570 IRHASVEELTAVEGISKGLAERIVAH 595
                                   668*********************98 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 ?   -1.6   0.1       2.1   4.2e+03      35      63 ..     215     243 ..     190     253 .. 0.65
   2 ?   -1.4   0.1       1.8   3.7e+03      44      82 ..     346     384 ..     328     399 .. 0.64
   3 ?   10.4   0.0   0.00038      0.75      20      52 ..     546     579 ..     542     603 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                    5_3_exonuc  35 lkeygsleeilenldelkekklkekLeen 63 
                                    +ey+s + i +++d lk+ +++++ +++
  gi|91773432|ref|YP_566124.1| 215 AQEYESAAVIRDQIDALKSLSRQQTATAG 243
                                   36777777777777777765555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                    5_3_exonuc  44 ilenldelkekklkekLeenkeearlskkLatiktdvpl 82 
                                   ++e +++ ++ +l+++  ++ ++ +  + L ++++ + l
  gi|91773432|ref|YP_566124.1| 346 LMEMAEQNAQMTLEQSHLKQSDKEQALQALLQLRDALAL 384
                                   444444434445555555666666667777777766554 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00038
                    5_3_exonuc  20 ipGvpgiGektAakLlkeygsleeilenld.elk 52 
                                   +  +pgiG+   ++Ll+++ s+e+i ++   el+
  gi|91773432|ref|YP_566124.1| 546 LDTIPGIGASRKKALLNHFSSIEQIRHASVeELT 579
                                   56799********************985422333 PP

>> DUF2335  Predicted membrane protein (DUF2335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.3      0.17   3.4e+02      19      46 ..     345     370 ..     341     374 .. 0.70
   2 ?    6.9   0.0     0.003         6       5      27 ..     577     599 ..     574     601 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                       DUF2335  19 RIiamaekEqehRheleeklldaqires 46 
                                   R ++ma  Eq+ ++ le+  l+ +++e+
  gi|91773432|ref|YP_566124.1| 345 RLMEMA--EQNAQMTLEQSHLKQSDKEQ 370
                                   666666..57778888888887777765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.003
                       DUF2335   5 vLeqYesilPGaAeRIiamaekE 27 
                                   +L + e i  G+AeRI+a + kE
  gi|91773432|ref|YP_566124.1| 577 ELTAVEGISKGLAERIVAHFNKE 599
                                   5666688999**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1152  (0.0642534); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3649.71
//
Query:       gi|91773433|ref|YP_566125.1|  [L=229]
Description: hypothetical protein Mbur_1468 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   45.0   2.7    1.4e-11   45.0   2.7    2.0  2  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.058   11.8   2.6        1.6    7.0   0.1    2.1  2  TATR      Trans-activating transcriptional regulator


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 !   45.0   2.7   1.5e-15   1.4e-11       1      73 [.      34     127 ..      34     139 .. 0.83
   2 ?   -1.1   0.0      0.36   3.2e+03      13      28 ..     148     163 ..     143     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.5e-15
                      CxxCxxCC   1 eCkeCgaCCk...elkvklteedlerlkaaevaeeeeeskkiak..................adgrCvfldeetklCkiYe 60 
                                   eC+ Cg+CC+   + +v l e+d+e +k+ +   +  +   +++                  +dg Cv+l+++  +C+iY 
  gi|91773433|ref|YP_566125.1|  34 ECDLCGMCCTrqfNDHVFLLEKDVEAMKQIDA--SLITPAPYYEfcdqkgnfyvsgyslrtkEDGSCVLLENN--RCTIYD 110
                                   6*********9998999999999999998887..44444444445678999999*******************..9***** PP

                      CxxCxxCC  61 eRpkicrlfpas....e 73 
                                   +Rp+ic l+p +    +
  gi|91773433|ref|YP_566125.1| 111 KRPTICSLYPYMlhreT 127
                                   **********9955431 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.36
                      CxxCxxCC  13 kvklteedlerlkaae 28 
                                   ++++t+ed++ ++   
  gi|91773433|ref|YP_566125.1| 148 HNEITDEDTKVIASDI 163
                                   5566666666554322 PP

>> TATR  Trans-activating transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00018       1.6      24      54 ..      72     102 ..      60     111 .. 0.86
   2 ?    4.9   0.4   0.00078         7     452     489 ..     178     218 ..     156     229 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00018
                          TATR  24 sysefcdkqsndylsyynhptpdngadtvis 54 
                                    y efcd++ n y+s y   t ++g+  ++ 
  gi|91773433|ref|YP_566125.1|  72 PYYEFCDQKGNFYVSGYSLRTKEDGSCVLLE 102
                                   599*******************999876655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.00078
                          TATR 452 lkkvk...kedgsmhiveqyltqnvdnvkghnfivlsfkne 489
                                   +kkvk   ke+gs h+   y  q     kg++++v  f+n+
  gi|91773433|ref|YP_566125.1| 178 FKKVKehfKENGSRHVKSVYDRQIRAFEKGKEIVVYVFHNN 218
                                   566665559*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1350.26
//
Query:       gi|91773434|ref|YP_566126.1|  [L=368]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-19   70.2   0.0    4.2e-19   69.5   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    1.5e-05   25.0   0.0      3e-05   24.1   0.0    1.5  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   4.6e-23   4.2e-19       1     166 [.     144     313 ..     144     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 4.6e-23
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlakla.vpgi 78 
                                   ++++rgC+ +C++C++p+    +   r++s+++i+  +k++   +    + +  gg      p+f +  + l+kl    g 
  gi|91773434|ref|YP_566126.1| 144 IEISRGCPWNCKYCQTPRI--FGHEMRHRSIDSIVSFAKYYNdLRFTsSNAFAYGGNGIQ--PRFDKVEALLSKLSsIVGK 220
                                   6899**************7..9*******************7555554444444444444..5454444444444456999 PP

                                   EEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                   xxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglp 153
                                   +i++ t +  ++      e l++++++    ++slg+++++d  +lk m rght e+v  a+e++ e+ i +vvd+i+g+p
  gi|91773434|ref|YP_566126.1| 221 NIFFGTFPSEIRpefvtHEGLDLIDKYCsNRTISLGAQSGSDI-ILKEMLRGHTSEDVNIAVERCFEHEIIPVVDFIFGFP 300
                                   99999999999999*****************************.888888******************************* PP

                                   TTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                   Radical_SAM 154 Gendeeleellel 166
                                   +e +e+ + +le 
  gi|91773434|ref|YP_566126.1| 301 NEAEEDQQRTLEQ 313
                                   ******9998875 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.3e-09     3e-05      77     120 ..      54      94 ..      36      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.3e-09
                   B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   ++ ++++ ++GG+hps   e+tl +   + +vv+gege++l++l
  gi|91773434|ref|YP_566126.1|  54 SRPSGTICIAGGPHPSGSVEDTLDH---FNFVVIGEGEETLPHL 94 
                                   55568899*************9975...789**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2234.79
//
Query:       gi|91773435|ref|YP_566127.1|  [L=369]
Description: peptidase M50 [Methanococcoides burtonii DSM 6242]
Scores for 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-15   54.5  13.5    1.1e-08   34.6   0.5    2.5  2  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   7.7   2.2e-09     4e-05       2     108 ..     130     208 ..     129     231 .. 0.89
   2 !   34.6   0.5   6.3e-13   1.1e-08     176     233 ..     237     291 ..     210     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.2e-09
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp....LGGyVkmageepeeelseeeaka 78 
                                   f l++++++  HE+GH++vAk++g++                  +++Y+i++      +G+++k +g  p+++        
  gi|91773435|ref|YP_566127.1| 130 FTLAIMFVLGSHEMGHYIVAKMHGMRT-----------------SLPYFIPFPTiigtMGAVIKHRGVIPDRK-------- 185
                                   8999**********************9.................67888888777888***********9999........ PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  79 flkkspwqrllivlAGplanfilailvfvv 108
                                          + + +++AGpl++++ +++v ++
  gi|91773435|ref|YP_566127.1| 186 -------ALFDVAVAGPLVGLVASVIVTFI 208
                                   .......99*****************9987 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 6.3e-13
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 176 iaqlaseaaeaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkplse 233
                                   i  ++++++e+   ++++++ ++++ +++lNLlP  +LDGgh+++a+l + + k +s+
  gi|91773435|ref|YP_566127.1| 237 INTISGNTVETM--HPVAFAGWVGMLVTVLNLLPSGQLDGGHIVRAMLGERA-KHVSM 291
                                   334445555444..9*********************************9988.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2278.85
//
Query:       gi|91773436|ref|YP_566128.1|  [L=137]
Description: hypothetical protein Mbur_1471 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  119.8   0.3    4.3e-35  119.4   0.3    1.2  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.3   2.4e-39   4.3e-35       1      80 []      27     106 ..      27     106 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 2.4e-39
                                   --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--EE CS
                        DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPlv 80 
                                   lSflg+vdp+tG+v+d+gh+++g++i +kiLv+p+gkGStvgsyv+++l+kn+++PaA+i+ + +pi+a+Gai++diPlv
  gi|91773436|ref|YP_566128.1|  27 LSFLGNVDPKTGVVVDPGHAIYGECIRDKILVFPHGKGSTVGSYVIYQLKKNNVSPAAMINIDSEPIVAVGAIISDIPLV 106
                                   8*****************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 884.87
//
Query:       gi|91773437|ref|YP_566129.1|  [L=395]
Description: aconitase subunit 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-161  535.9   0.2   5.8e-161  535.7   0.2    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 !  535.7   0.2  3.2e-165  5.8e-161       1     401 []       1     389 [.       1     389 [. 0.98

  Alignments for each domain:
  == domain 1  score: 535.7 bits;  conditional E-value: 3.2e-165
                        DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvpttlnpi 81 
                                   m+Lt+eee++l+Ge+Ge+l+kameilvalG+i+gA++L+pv+sa+++gvsyktigdagle++++l+   ++v+vp++lnp+
  gi|91773437|ref|YP_566129.1|   1 MYLTSEEENILDGEQGETLRKAMEILVALGDIYGADSLIPVKSAQIAGVSYKTIGDAGLEWISDLE---GTVKVPSILNPA 78 
                                   9*****************************************************************...************ PP

                        DUF521  82 gvdlerweelgvdeefaekqeriieayeklGveltftCtpyll.gnapkkGehlawsESsavvyaNSvlGarTnreggpsa 161
                                   g+d+ rw+e+g+++efaekq +ii+ayeklG+++++tCtpy+l g   + G+hlawsESsav+yaNSv+GarTnreggpsa
  gi|91773437|ref|YP_566129.1|  79 GMDMVRWKEMGIEPEFAEKQLEIIAAYEKLGISSKCTCTPYYLeGFSATCGDHLAWSESSAVSYANSVIGARTNREGGPSA 159
                                   ******************************************87999********************************** PP

                        DUF521 162 laaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKalgAalaasgava 242
                                   l aA++G+t +yG+hldenR+ptv v v++e  + +dygalGy++Gk++g+r+P+++  ++p++delK lgAa+aasgava
  gi|91773437|ref|YP_566129.1| 160 LSAALVGKTGNYGYHLDENRVPTVSVVVDHE-LSGSDYGALGYIAGKEIGNRVPMFHLASTPTSDELKGLGAAMAASGAVA 239
                                   ****************************999.9************************************************ PP

                        DUF521 243 lfhiegvTPeaetleealgekekaekititkedleevleel.skakeekvdlvalGcPhlsleElrelaellkgkkkkvkv 322
                                   l+h+egvTPea    ++++  +++e+iti++++l+ev+e++  ++++ ++d+va+GcPh+s eEl+++a+ll  ++k+ ++
  gi|91773437|ref|YP_566129.1| 240 LYHVEGVTPEA----KQVHFDKPDETITIQRSQLDEVYETIiGNEDDLECDIVAVGCPHCSPEELNRIADLL--EGKRIEK 314
                                   **********4....444446789*****************9999999************************..99999** PP

                        DUF521 323 elwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpgltgvkvalgsleecve 401
                                   elwv+tsrev++++ ++  v+++e++G kvl+dtCmvvsp+++    +++++nSgKa+ Y+pg+++v +++gsle+c++
  gi|91773437|ref|YP_566129.1| 315 ELWVCTSREVAQRYPDV--VKRIEESGSKVLCDTCMVVSPATEG--HNCMMVNSGKALAYVPGMCKVPAKIGSLETCIK 389
                                   ***************99..***********************94..8******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2509.49
//
Query:       gi|91773438|ref|YP_566130.1|  [L=425]
Description: carboxylyase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-114  381.3   3.2   5.6e-114  381.2   3.2    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.2   3.2  3.1e-118  5.6e-114       1     406 []       7     383 ..       7     383 .. 0.95

  Alignments for each domain:
  == domain 1  score: 381.2 bits;  conditional E-value: 3.1e-118
                                   HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHH CS
                          UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklae 81 
                                   +++l++ g lv+++e+v+  +E++ +a++ +      +lF++++g     ++++nl+g+r+ +a ++g+   + i+++l++
  gi|91773438|ref|YP_566130.1|   7 IDHLRTSGRLVEVTEPVSKVFEAPRLAKKSN----APILFHDIDG----QKAIMNLLGSRDELADMFGVP-KDGIIQRLSD 78 
                                   689**************************97....689*****43....589****************85.5********* PP

                                   HHHS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEE CS
                          UbiD  82 llepkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklg 162
                                   ++      + k v+  + p++ ev+  ++dvdLskLP++t++++DgGpyit+g+v+++   +g  n++i+R++v++k+kl+
  gi|91773438|ref|YP_566130.1|  79 IRPD---GEVKIVD--TSPTM-EVI--ENDVDLSKLPLMTHFEKDGGPYITAGVVVSEY--GGMMNASIHRLMVVGKDKLA 149
                                   9876...7899995..58999.564..69****************************95..99****************** PP

                                   E--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEE CS
                          UbiD 163 lhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEiv 243
                                    ++++ +++   ++ka++++ eplpva+++G+dP++t+a+++++P   +E+e+a+alrg+pvel++ce+ +++vp +AEi+
  gi|91773438|ref|YP_566130.1| 150 ARLVPPRHSYVLHKKAAENN-EPLPVAIVLGADPVITFASTTRVP-AGKEFEYAAALRGAPVELFECEN-GVKVP-HAEII 226
                                   ********************.9***********************.669******************65.9****.***** PP

                                   EEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEE CS
                          UbiD 244 leGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalealflpllkkqvpevk 324
                                   leG++dp+e+++EGPf+d+tG+y+ vr+e pv+++t+i+hRkdpiy+ +++    e+ +++g+++e+ +++++ + v +vk
  gi|91773438|ref|YP_566130.1| 227 LEGYVDPTERVDEGPFVDITGTYDLVRKE-PVITITKIMHRKDPIYHGILPAGA-EHLLMMGVPYEPKIYNAVAE-VTTVK 304
                                   **************************996.*****************9978877.******************55.778** PP

                                   EEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCC CS
                          UbiD 325 dvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdrDlviiegt 405
                                   +v l+e g+++l+avv+i+k+++g+ak++++a++a+++  sl K+v++vDed+d++++ +v+ aiatrv++d D++ii+++
  gi|91773438|ref|YP_566130.1| 305 NVVLTEGGCCYLHAVVQIEKQTEGDAKNAIMAAFAAHT--SL-KHVVIVDEDIDIFNIMDVEFAIATRVKADLDVMIIPNV 382
                                   ************************************99..99.************************************98 PP

                                   E CS
                          UbiD 406 r 406
                                   r
  gi|91773438|ref|YP_566130.1| 383 R 383
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2493.96
//
Query:       gi|91773439|ref|YP_566131.1|  [L=153]
Description: hypothetical protein Mbur_1474 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.044   13.1   0.1      0.058   12.7   0.1    1.1  1  Glyco_hydro_64  Beta-1,3-glucanase
        0.1   12.7   0.5        2.4    8.3   0.0    2.7  3  RPN5_C          26S proteasome regulatory subunit RPN5 C-term


Domain annotation for each model (and alignments):
>> Glyco_hydro_64  Beta-1,3-glucanase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.4e-06     0.058     286     346 ..      30      96 ..      11      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-06
                                   .HHHHHHHHHHHH....HTT-TT-.....GGGTT.GGGTT.S..SS-HHHHHHHHTBGGG----STT CS
                Glyco_hydro_64 286 aekavqarLaAAf....nRstllltadaqpskee.astyY.kkeptNhYarlvHensvdgkgYaFaY 346
                                   a++ v+arL+A f    nRs ++  +++ p+    +++ Y ++e+ N  a++ H+ +  g ++ +aY
  gi|91773439|ref|YP_566131.1|  30 AREWVIARLCADFknlsNRSEMTWIGENLPELVPfVDEPYtRQEVSNAHAAFKHKIERSGTTFFYAY 96 
                                   4889********988888*****988999*99999*****55558***********99999988887 PP

>> RPN5_C  26S proteasome regulatory subunit RPN5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00027       2.4      18      33 .]      22      37 ..      20      37 .. 0.90
   2 ?    1.6   0.1     0.034     3e+02      24      31 ..     100     107 ..      99     109 .. 0.90
   3 ?   -3.2   0.0       1.1     1e+04      17      26 ..     139     148 ..     138     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                        RPN5_C 18 vekttHLInKEeMvhk 33
                                  ++kttHL ++E+++++
  gi|91773439|ref|YP_566131.1| 22 LKKTTHLTAREWVIAR 37
                                  68***********985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.034
                        RPN5_C  24 LInKEeMv 31 
                                   LI  EeM+
  gi|91773439|ref|YP_566131.1| 100 LIGQEEMI 107
                                   89*****9 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.1
                        RPN5_C  17 lvekttHLIn 26 
                                   lv  t H In
  gi|91773439|ref|YP_566131.1| 139 LVADTLHRIN 148
                                   6888889887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 830.49
//
Query:       gi|91773440|ref|YP_566132.1|  [L=386]
Description: cytidyltransferase-related [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-10   41.2   0.0    3.4e-10   40.3   0.0    1.5  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
        0.1   12.2   0.2       0.27   10.8   0.2    1.7  1  CinA             Competence-damaged protein


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 !   40.3   0.0   3.8e-14   3.4e-10       1     142 [.     221     382 ..     221     383 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.8e-14
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
               CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                   ++ G+FDp H+ H++++eqa+++l++++   +   +++k    +l+s++eRl+ l+++ ++  ++     ++ + +++k +
  gi|91773440|ref|YP_566132.1| 221 IFSGSFDPCHKNHIQMAEQAFNKLGKKVHFEISLTNVDKPS-IDLISLQERLDSLRKY-KDYVFFGGVLLTVAPLFIQKVN 299
                                   689***********************777777777777766.9***************.5555677777788889999999 PP

                                   TT.EEEEEEEHHHHHHHHCHH......HHHHHHHHHHHEEEEEE.....................HTTCEEEEEEECCTTT CS
               CTP_transf_like  82 pd.klylvigadvledfsewk......eleeilgnvklvvvsrp.....................ekqanvllkaekrtng 134
                                      k  +++gad++  + +++      ++++        ++ r+                        ++v+ ++++  ng
  gi|91773440|ref|YP_566132.1| 300 LFeKATFIVGADTVNRLFKTRyyrnveDMRDM------LQYFRNrnthflvfqrkgvdlelepdiLDLCEVVPLDDYLDNG 374
                                   97799***********8666656644433333......3332223344555555588888888875556666777788888 PP

                                   CSHHHHHH CS
               CTP_transf_like 135 iSstkire 142
                                    Sst ir+
  gi|91773440|ref|YP_566132.1| 375 TSSTSIRN 382
                                   89988886 PP

>> CinA  Competence-damaged protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2     3e-05      0.27      25      89 ..      14      75 ..       8      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3e-05
                          CinA 25 cTGGllaa..altsvpGaSavfeggvvtYsneaKeelLgvseetleehgavSeevaeemaegarerl 89
                                  +TGG  +a  +l++  G Sa + +++v Ys++a  el+g ++e     + vS  ++++ma  a +r+
  gi|91773440|ref|YP_566132.1| 14 ATGGGAGAidQLLRYGGGSATVLEALVPYSSKALDELIGKKPE-----KYVSPVTVRAMAMAAYRRA 75
                                  456555432278999999***********************99.....5899999999998876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2566.91
//
Query:       gi|91773441|ref|YP_566133.1|  [L=117]
Description: cupin family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-10   38.1   0.2    1.4e-09   37.6   0.2    1.3  1  Cupin_2       Cupin domain
    4.9e-06   26.1   0.0    7.4e-06   25.6   0.0    1.2  1  Cupin_3       Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.035   14.0   0.1      0.047   13.6   0.1    1.2  1  AraC_binding  AraC-like ligand binding domain
      0.079   12.2   0.0      0.089   12.1   0.0    1.2  1  GPI           Glucose-6-phosphate isomerase (GPI)
        0.1   12.5   0.0       0.13   12.1   0.0    1.1  1  DUF577        Family of unknown function (DUF577)


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 !   37.6   0.2   3.8e-13   1.4e-09      17      70 ..      61     115 ..      48     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.8e-13
                                   SSEEEEEEEEESEEEEE.ECTEEEEEETTEEEEE-TT-EEEEEE-SSS.-EEEEEE CS
                       Cupin_2  17 pgedeffyVleGegelt.vdgeeveleaGdsvyfpagtpHrfrNtgde.parllvv 70 
                                   +++ e+++Vl+Ge++l   d e+v+l +Gd + +pa+  Hr++ t+d+ +  +l v
  gi|91773441|ref|YP_566133.1|  61 DRS-EWVMVLQGEAKLVfEDLEVVHLAPGDHINIPAHCKHRVIWTSDTtETLWLAV 115
                                   445.*************999***************************999999987 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.1e-09   7.4e-06      13      66 ..      50     105 ..      45     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.1e-09
                                   EEECEEEEECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE..EECCCE CS
                       Cupin_3  13 ectpGkfrltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgl..sgtwdv 66 
                                   ++tpG++  + +++E + +l+Ge k++ e+ e v+l +GD + +p+    ++ w+ 
  gi|91773441|ref|YP_566133.1|  50 HVTPGGQWYDQDRSEWVMVLQGEAKLVFEDLEVVHLAPGDHINIPAHCkhRVIWTS 105
                                   79****9999999********************************98866666665 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.3e-05     0.047      22      74 ..      61     113 ..      46     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                   -SEEEEEEEEE-EEE.EETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEE CS
                  AraC_binding  22 deyvihyvteGtgrl.rlngrtydlgpGdlfLlppgepHdyesdsedgweyrwl 74 
                                   d  +++ v++G+++l + + + ++l pGd + +p ++ H+    s+   e+ wl
  gi|91773441|ref|YP_566133.1|  61 DRSEWVMVLQGEAKLvFEDLEVVHLAPGDHINIPAHCKHRVIWTSD-TTETLWL 113
                                   5678999********5555566******************987775.6666666 PP

>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.5e-05     0.089      87     134 ..      58     105 ..      31     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                           GPI  87 YevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinig 134
                                   Y+  + e +m+L+    l+ +d+ vv    ++ + +P +  H+ i  +
  gi|91773441|ref|YP_566133.1|  58 YDQDRSEWVMVLQGEAKLVFEDLEVVHLAPGDHINIPAHCKHRVIWTS 105
                                   677778889*****999*************************998655 PP

>> DUF577  Family of unknown function (DUF577)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.6e-05      0.13      63     117 ..      16      78 ..       2      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                        DUF577  63 vyvFidLpmpldeefikkvlenlleeiekvLlppeel........dneeWvLAlegavklaiq 117
                                    ++F ++p+ l +e  ++++++    ie+++ +++ +        d +eWv+ l+g  kl+ +
  gi|91773441|ref|YP_566133.1|  16 HNIFNQIPVDLTHEVFEPLVDQHGVSIERIISKKHVTpggqwydqDRSEWVMVLQGEAKLVFE 78 
                                   589*******************99999988888776677778888999********9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 766.66
//
Query:       gi|91773442|ref|YP_566134.1|  [L=143]
Description: iron dependent repressor [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-18   66.7   0.0    3.3e-18   65.6   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    2.4e-06   27.4   0.0    4.5e-06   26.5   0.0    1.4  1  MarR             MarR family
    3.7e-05   23.5   0.0    5.6e-05   23.0   0.0    1.3  1  MarR_2           MarR family
    5.3e-05   22.7   0.0     0.0001   21.8   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00077   19.4   0.0     0.0013   18.6   0.0    1.3  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0019   18.5   0.0     0.0035   17.6   0.0    1.5  1  Rrf2             Transcriptional regulator
     0.0034   17.1   0.0     0.0058   16.4   0.0    1.4  1  LexA_DNA_bind    LexA DNA binding domain
     0.0056   16.7   0.1       0.01   15.9   0.1    1.5  1  FeoC             FeoC like transcriptional regulator
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.028   14.1   0.0    1.4  1  Crp              Bacterial regulatory proteins, crp family
      0.021   13.7   0.0      0.024   13.5   0.0    1.1  1  HTH_micro        HTH-like
      0.043   14.1   0.0      0.068   13.4   0.0    1.3  1  FeoA             FeoA domain
      0.064   13.1   0.0       0.11   12.5   0.0    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.067   12.6   0.0       0.13   11.7   0.0    1.5  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.089   12.6   0.0       0.15   11.9   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
      0.091   12.5   0.0       0.18   11.6   0.0    1.5  1  HTH_38           Helix-turn-helix domain
      0.095   12.5   0.0       0.17   11.7   0.0    1.4  1  HTH_23           Homeodomain-like domain
      0.099   12.7   0.0       0.17   11.9   0.0    1.4  1  Phage_terminase  Phage terminase small subunit
       0.12   12.3   0.0       0.23   11.4   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
       0.13   12.4   0.0       0.21   11.8   0.0    1.4  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
       0.16   12.0   0.0       0.42   10.6   0.0    1.7  2  HTH_6            Helix-turn-helix domain, rpiR family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   3.7e-21   3.3e-18       2      60 .]       4      62 ..       3      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 3.7e-21
                                  --HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                Fe_dep_repress  2 LvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                  ++e+tEdYL++I t+ e+k++  +kd+a++L+vspssV+ m kkL k+G+++ eky+g+
  gi|91773442|ref|YP_566134.1|  4 TTERTEDYLKAIDTIIEKKGYSLVKDIARFLDVSPSSVTGMFKKLTKEGFINCEKYGGV 62
                                  589******************************************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0     5e-09   4.5e-06      20      48 ..      27      55 ..      14      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5e-09
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 20 vseLakklgvskstvtrvldrLekkGlie 48
                                  v+++a++l vs+s+vt + ++L k+G+i+
  gi|91773442|ref|YP_566134.1| 27 VKDIARFLDVSPSSVTGMFKKLTKEGFIN 55
                                  78**************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   6.2e-08   5.6e-05      23      51 ..      26      54 ..      12      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.2e-08
                                  EHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                        MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLv 51
                                   v+++ar l++s+s+v+ + k+L + G++
  gi|91773442|ref|YP_566134.1| 26 LVKDIARFLDVSPSSVTGMFKKLTKEGFI 54
                                  699*************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.1e-07    0.0001      11      47 ..      18      54 ..      12      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
                        HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +++k++    +++A+ l++Sps v+   k+L++eG+I
  gi|91773442|ref|YP_566134.1| 18 IIEKKGYSLVKDIARFLDVSPSSVTGMFKKLTKEGFI 54
                                  6888999999**************************9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0013      25      58 ..      28      63 ..      27      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EE CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.ir 58
                                  +++A++l +++++v+ ++++L +eg i   +++ ++
  gi|91773442|ref|YP_566134.1| 28 KDIARFLDVSPSSVTGMFKKLTKEGFINcEKYGgVT 63
                                  69*************************974432254 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.9e-06    0.0035      26      70 ..      25      67 ..       1      72 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.9e-06
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSH CS
                          Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakp 70
                                    +++ia+  ++sps +  +++kL+k+g+++ ++   GG++La +
  gi|91773442|ref|YP_566134.1| 25 SLVKDIARFLDVSPSSVTGMFKKLTKEGFINCEK--YGGVTLAPD 67
                                  4689***************************995..899999876 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.4e-06    0.0058       5      58 ..       5      56 ..       1      59 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
                                  -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                 LexA_DNA_bind  5 TerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                                  Ter ++ l+ i   ie++gy   +++iar l ++ ps+v    k+L + G+i+ 
  gi|91773442|ref|YP_566134.1|  5 TERTEDYLKAIDTIIEKKGYS-LVKDIARFLDVS-PSSVTGMFKKLTKEGFINC 56
                                  89999***************8.79********96.*****************86 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.1e-05      0.01       2      50 ..      12      60 ..      11      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                          FeoC  2 LtelkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                  L+ +   +e++g   +k+++r +++sp+ + +m   +++ G +++++ +
  gi|91773442|ref|YP_566134.1| 12 LKAIDTIIEKKGYSLVKDIARFLDVSPSSVTGMFKKLTKEGFINCEKYG 60
                                  78888999*********************************99988765 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.1e-05     0.028       7      32 .]      29      54 ..      28      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                                  HHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           Crp  7 dIAdylGlTrETVSRlLtrLrekGLI 32
                                  dIA++l  ++ +V+ ++++L ++G I
  gi|91773442|ref|YP_566134.1| 29 DIARFLDVSPSSVTGMFKKLTKEGFI 54
                                  9***********************88 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-05     0.024      88     140 ..       7      58 ..       2      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                     HTH_micro  88 ftskeyykivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqkt 140
                                    t++ y k +d ++++k y  ++++   l++ p  +  + kkL k+g+i+ ++
  gi|91773442|ref|YP_566134.1|   7 RTED-YLKAIDTIIEKKGYSLVKDIARFLDVSPSSVTGMFKKLTKEGFINCEK 58 
                                   4444.899*****************************************9665 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.6e-05     0.068      30      73 ..     101     141 ..      96     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                                   HHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                          FeoA  30 emGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73 
                                   +mG+ p   +  v+ +     +v  ++ tr a++re+A++I+V+
  gi|91773442|ref|YP_566134.1| 101 AMGVLPVIPVNFVQ-SY--PSYVFDLNHTRYAVDREIAESIFVR 141
                                   67777766777773.32..3689999*****************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.11      19      56 ..      21      58 ..      14      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  k+g + +++ia+ l+v+ s+v  + ++L + G+++ ek
  gi|91773442|ref|YP_566134.1| 21 KKGYSLVKDIARFLDVSPSSVTGMFKKLTKEGFINCEK 58
                                  56777899**************************9776 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 ?   11.7   0.0   0.00014      0.13      30      50 ..      27      47 ..      27      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                  HTH_Tnp_ISL3 30 vkavArqlgvSwtTVwrildr 50
                                  vk++Ar l+vS+++V  +++ 
  gi|91773442|ref|YP_566134.1| 27 VKDIARFLDVSPSSVTGMFKK 47
                                  89**************99986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.15      21      48 ..      27      54 ..      12      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR 21 lselArrtglpkStvhRlLqtLvelGyv 48
                                  ++++Ar +++++S+v ++ + L+++G++
  gi|91773442|ref|YP_566134.1| 27 VKDIARFLDVSPSSVTGMFKKLTKEGFI 54
                                  789***********************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.18      18      37 ..      21      41 ..      13      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                        HTH_38 18 aeGlslr.eIArrLgrspsTI 37
                                  ++G+sl  +IAr L++sps++
  gi|91773442|ref|YP_566134.1| 21 KKGYSLVkDIARFLDVSPSSV 41
                                  58999988***********97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.17      20      46 ..      27      53 ..      24      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                        HTH_23 20 vreIAreLgvsrrTvyrwlkryreeGl 46
                                  v++IAr L+vs++ v    k+  +eG+
  gi|91773442|ref|YP_566134.1| 27 VKDIARFLDVSPSSVTGMFKKLTKEGF 53
                                  79*************999999888886 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.17      11      41 ..      13      43 ..       4      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
               Phage_terminase 11 kAyelykEsggtlklkdIAkvLdvsestvrk 41
                                  kA     E+ g  ++kdIA  Ldvs s v +
  gi|91773442|ref|YP_566134.1| 13 KAIDTIIEKKGYSLVKDIARFLDVSPSSVTG 43
                                  6777778999999*************99975 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 ?   11.4   0.0   0.00025      0.23      18      46 ..      27      55 ..      20      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 18 vcelaeelglsqstvShHLkkLreaGLVe 46
                                  v ++a+ l++s+s v   +kkL ++G+++
  gi|91773442|ref|YP_566134.1| 27 VKDIARFLDVSPSSVTGMFKKLTKEGFIN 55
                                  89************************996 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.21      21      53 ..      27      59 ..      21      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                B-block_TFIIIC 21 qsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                   +d+a+ ++ +p+s+++  k+L+k g+I   ++
  gi|91773442|ref|YP_566134.1| 27 VKDIARFLDVSPSSVTGMFKKLTKEGFINCEKY 59
                                  57899999*******************987666 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047      0.42      35      64 ..      25      54 ..       7      57 .. 0.84
   2 ?   -2.4   0.0       5.6     5e+03      19      34 ..      69      84 ..      63      90 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                                  --HHHHHHHTT--HHHHHHHH---S-SSHH CS
                         HTH_6 35 lsikalAkaaavSeativrfakkLGfkGFs 64
                                  + +k++A  + vS ++++ + kkL  +GF 
  gi|91773442|ref|YP_566134.1| 25 SLVKDIARFLDVSPSSVTGMFKKLTKEGFI 54
                                  4589************************96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                                  HHHHHHHHH-S---TT CS
                         HTH_6 19 kkiaeyilaspdkaie 34
                                  +k+a+  ++s   +++
  gi|91773442|ref|YP_566134.1| 69 RKLAKSTRKSSVCCMS 84
                                  4555544444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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):              20  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 974.30
//
Query:       gi|91773443|ref|YP_566135.1|  [L=323]
Description: hypothetical protein Mbur_1478 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-10   41.1  14.0    1.8e-08   34.2   4.4    2.6  3  GXGXG        GXGXG motif
  ------ inclusion threshold ------
       0.13   12.4   0.5       0.45   10.7   0.2    2.1  2  HCV_NS5a_1a  Hepatitis C virus non-structural 5a zinc finger 
       0.78    8.3  12.4       0.86    8.1   5.6    2.3  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 !   12.5   1.1   1.4e-05     0.081     103     170 ..      54     118 ..      48     128 .. 0.83
   2 !   34.2   4.4   2.9e-12   1.8e-08      88     163 ..     181     259 ..     151     271 .. 0.81
   3 ?   -3.5   0.0       1.1   6.6e+03      57      76 ..     301     320 ..     297     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                                   EEEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE.-SSSTHH CS
                         GXGXG 103 klfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvl.dedekfe 170
                                    ++i+g++g+Rfa    +  a  +g  +      + G + v g++g + + Gms G+ y+  d ++ f 
  gi|91773443|ref|YP_566135.1|  54 DVHIKGSIGSRFAYSLGVDLAHFGGSAKTE----AAGNIFVEGNVGPEAGMGMSAGSLYITgDIEQPFG 118
                                   578999999999998888888777775554....78************************988887765 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.9e-12
                                   SB-S-SS...TTTT--SEEEEESSB--SSTTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE CS
                         GXGXG  88 niivGnv...vlygatgGklfirgkageRfavrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvl 163
                                    i+ G+v   +   +  G++ ++g+ag  ++ + +g  +vvegv g++ + Ym  G+++  +    +++aGm gG++y  
  gi|91773443|ref|YP_566135.1| 181 VIVKGDVyngTGLLMERGNVNVQGNAGLNTGAHLNGGSVVVEGVvGEFSGAYMKAGTLIF-NYAKGYVGAGMLGGTIYSK 259
                                   34446551113455899***************************************9975.666679***********65 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.1
                                   EEEE-STTTTT-ESSEEEEE CS
                         GXGXG  57 eGdandyvGkglsgGkivik 76 
                                     + ++yv   + +G iv++
  gi|91773443|ref|YP_566135.1| 301 GEEKEQYVKVKMRDGSIVMR 320
                                   55677888889999999875 PP

>> HCV_NS5a_1a  Hepatitis C virus non-structural 5a zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.2   1.3e+04      42      57 ..      94     109 ..      93     113 .. 0.66
   2 ?   10.7   0.2   7.6e-05      0.45      18      38 ..     169     191 ..     164     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.2
                   HCV_NS5a_1a  42 vgprtckdmvsstffi 57 
                                   vgp +   m  +  +i
  gi|91773443|ref|YP_566135.1|  94 VGPEAGMGMSAGSLYI 109
                                   6777777777776666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.6e-05
                   HCV_NS5a_1a  18 GivearCtCGaei..tGevkdGe 38 
                                   G + +rC+C ae+   G+v++G+
  gi|91773443|ref|YP_566135.1| 169 GTLASRCNCDAEVivKGDVYNGT 191
                                   78899*****985337******8 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7    0.0024        14     201     244 ..      52      94 ..      46     146 .. 0.71
   2 ?    8.1   5.6   0.00014      0.86     178     258 ..     175     262 ..     136     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0024
                          FapA 201 G.sViikGnVeegmkVkasgditikGvvesatieAggnItikgGi 244
                                   G +V+ikG++  g +  +s  +    +  sa+ eA gnI ++g++
  gi|91773443|ref|YP_566135.1|  52 GnDVHIKGSI--GSRFAYSLGVDLAHFGGSAKTEAAGNIFVEGNV 94 
                                   5578888888..444445555778888888888888888888776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00014
                          FapA 178 isVdpvleikgdVdlstGnIkfkGsViikGnV..eegmkVkasgditikGvv...esatieAggnI.tikgGiigkgk..s 250
                                    + d ++ +kgdV   tG +   G+V+++Gn    +g + + +g++ ++Gvv   ++a  +Ag  I +  +G +g+g   +
  gi|91773443|ref|YP_566135.1| 175 CNCDAEVIVKGDVYNGTGLLMERGNVNVQGNAglNTGAHLN-GGSVVVEGVVgefSGAYMKAGTLIfNYAKGYVGAGMlgG 254
                                   66788999**********************97224555555.469****99964457888887777334566666665667 PP

                          FapA 251 kikAggni 258
                                   +i++++++
  gi|91773443|ref|YP_566135.1| 255 TIYSKKKV 262
                                   77777766 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:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2338.56
//
Query:       gi|91773444|ref|YP_566136.1|  [L=122]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-09   36.8   8.6    3.1e-09   36.8   8.6    2.1  3  Fer4_21   4Fe-4S dicluster domain
    1.5e-08   34.3  16.1    4.9e-06   26.4   3.5    3.1  3  Fer4_6    4Fe-4S binding domain
    1.6e-08   34.0  12.0    1.7e-06   27.6   4.0    3.4  4  Fer4      4Fe-4S binding domain
    5.4e-08   33.3   9.7    0.00071   20.1   1.0    2.7  2  Fer4_7    4Fe-4S dicluster domain
    1.4e-07   31.5  17.7    9.5e-06   25.7   6.6    2.9  3  Fer4_9    4Fe-4S dicluster domain
      2e-05   25.5  12.2      0.021   15.7   3.1    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
    4.2e-05   23.6   8.4    4.2e-05   23.6   8.4    2.9  2  Fer4_10   4Fe-4S dicluster domain
    9.2e-05   23.1  15.5      0.002   18.8   9.6    2.7  1  Fer4_15   4Fe-4S single cluster domain
    0.00011   22.1   2.3    0.00011   22.1   2.3    3.9  4  Fer4_2    4Fe-4S binding domain
     0.0052   17.3  10.2      0.099   13.2   0.8    2.7  3  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.046   14.2   4.3      0.046   14.2   4.3    3.9  4  Fer4_4    4Fe-4S binding domain
      0.083   13.7   1.9      0.083   13.7   1.9    3.1  4  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   8.6   2.1e-12   3.1e-09       2      58 ..       8      60 ..       7      61 .. 0.89
   2 ?   -1.0   0.0       1.3     2e+03       9      14 ..      85      90 ..      65      93 .. 0.62
   3 ?   -2.6   0.1       4.2   6.2e+03      11      14 ..     112     115 ..     109     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.1e-12
                       Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  +idedkC gCg+C+  C ++++q i+++a     v ed C G   C+ +CP e++i+
  gi|91773444|ref|YP_566136.1|  8 KIDEDKCTGCGQCVSPCAEGAIQIIDGKA---KVVSEDLCDGMGFCIGICP-EGAIT 60
                                  69*****************9999998754...35689**************.89998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                       Fer4_21  9 igCgkC 14
                                  i+C +C
  gi|91773444|ref|YP_566136.1| 85 ISCFSC 90
                                  233333 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.2
                       Fer4_21  11 CgkC 14 
                                   C++C
  gi|91773444|ref|YP_566136.1| 112 CTRC 115
                                   6666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   3.5   3.3e-09   4.9e-06       1      24 []       6      29 ..       6      29 .. 0.96
   2 !   16.4   0.4   4.7e-06     0.007       3      24 .]      38      59 ..      37      59 .. 0.94
   3 ?   -1.9   0.4       2.8   4.1e+03      12      15 ..     112     115 ..     111     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.3e-09
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  +v id+dkC+gCg Cv+ C egai
  gi|91773444|ref|YP_566136.1|  6 IVKIDEDKCTGCGQCVSPCAEGAI 29
                                  699*******************98 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.7e-06
                        Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                  ++ +d+C+g g C+ +CPegai
  gi|91773444|ref|YP_566136.1| 38 VVSEDLCDGMGFCIGICPEGAI 59
                                  6889*****************8 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.8
                        Fer4_6  12 CgdC 15 
                                   C +C
  gi|91773444|ref|YP_566136.1| 112 CTRC 115
                                   7777 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   4.0   1.2e-09   1.7e-06       1      23 [.       7      29 ..       7      30 .. 0.91
   2 !   17.5   1.1   1.7e-06    0.0025       2      24 .]      38      60 ..      37      60 .. 0.94
   3 ?   -1.0   0.3       1.2   1.8e+03       8      13 ..      87      92 ..      86      92 .. 0.84
   4 ?   -1.7   0.4         2     3e+03       8      11 ..     112     115 ..     111     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  v+ide+kC+gCG+Cv+ C  gAI
  gi|91773444|ref|YP_566136.1|  7 VKIDEDKCTGCGQCVSPCAEGAI 29
                                  68****************88888 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.7e-06
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  v+ e++C g G C+ +CP gAIt
  gi|91773444|ref|YP_566136.1| 38 VVSEDLCDGMGFCIGICPEGAIT 60
                                  789*******************7 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.2
                                  SSS-TH CS
                          Fer4  8 CigCGa 13
                                  C  CGa
  gi|91773444|ref|YP_566136.1| 87 CFSCGA 92
                                  999*97 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2
                                   SSS- CS
                          Fer4   8 CigC 11 
                                   C++C
  gi|91773444|ref|YP_566136.1| 112 CTRC 115
                                   8988 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.0   4.7e-07   0.00071      30      52 .]       6      28 ..       2      33 .. 0.82
   2 !   17.1   2.1   4.3e-06    0.0064       2      43 ..      44      92 ..      43     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.7e-07
                        Fer4_7 30 kveidpekClgCgaCvavCPtga 52
                                   v+id++kC+gCg+Cv+ C  ga
  gi|91773444|ref|YP_566136.1|  6 IVKIDEDKCTGCGQCVSPCAEGA 28
                                  57889999999999999997775 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.3e-06
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenek.......gtekveidpekClgCga 43
                                  C g g+C   Cp +ai+++e++  +        ++k +  + +C +Cga
  gi|91773444|ref|YP_566136.1| 44 CDGMGFCIGICPEGAITIEERQTVEfnlekaeAQPKSTDISISCFSCGA 92
                                  9999**************9986555444322222333333456999986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.2   1.9e-06    0.0029      29      51 .]       8      29 ..       3      29 .. 0.77
   2 !   25.7   6.6   6.4e-09   9.5e-06       1      51 []      13      59 ..      13      59 .. 0.94
   3 !    6.8   5.7     0.005       7.5       2      41 ..      44      92 ..      43     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                        Fer4_9 29 raaseeaCigCgaCveaCpkgai 51
                                  ++++ ++C+gCg+Cv  C +gai
  gi|91773444|ref|YP_566136.1|  8 KIDE-DKCTGCGQCVSPCAEGAI 29
                                  3333.59************9987 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 6.4e-09
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kCtgCg+Cv+ C  g+++  +++ k+  +      C g g C+ +Cp+gai
  gi|91773444|ref|YP_566136.1| 13 KCTGCGQCVSPCAEGAIQIIDGKAKVVSED----LCDGMGFCIGICPEGAI 59
                                  7************************99876....6*************997 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.005
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.........eaCigCga 41
                                  C g g C+  Cp g+++ ++ ++   + ++ e          +C++Cga
  gi|91773444|ref|YP_566136.1| 44 CDGMGFCIGICPEGAITIEERQTVEFNLEKAEaqpkstdisISCFSCGA 92
                                  555566*********9766655554443333359*******88999986 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 !   14.5   1.8   3.4e-05     0.051       1      18 [.      13      30 ..      13      42 .. 0.84
   2 !   15.7   3.1   1.4e-05     0.021       2      49 ..      44      91 ..      43     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                  +C++Cg+C++ C ++ai+
  gi|91773444|ref|YP_566136.1| 13 KCTGCGQCVSPCAEGAIQ 30
                                  6***************97 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-05
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekck 49
                                  C + g C+ +CP++ai+ ++++++e + ++++++++  d++++ ++c 
  gi|91773444|ref|YP_566136.1| 44 CDGMGFCIGICPEGAITIEERQTVEFNLEKAEAQPKSTDISISCFSCG 91
                                  888889*************9*****99999998888888887777765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   8.4   2.8e-08   4.2e-05       2      56 .]       7      55 ..       6      55 .. 0.81
   2 !    6.5   5.4    0.0061       9.2       3      50 ..      38      92 ..      36     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.8e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  v+id+d+C++Cg+Cv+ C a     ga+++++++++v    + C+g g C+ +CP
  gi|91773444|ref|YP_566136.1|  7 VKIDEDKCTGCGQCVSPC-A----EGAIQIIDGKAKVVS-EDLCDGMGFCIGICP 55
                                  78****************.5....566666666555554.567***********9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0061
                       Fer4_10  3 vidddtCirCgkCvkaCPadl......tsvgakgeaseeeavrk.kvekCtgcga 50
                                  v+ +d C + g C   CP  +      ++v+ + e+ e +++++  + +C  cga
  gi|91773444|ref|YP_566136.1| 38 VVSEDLCDGMGFCIGICPEGAitieerQTVEFNLEKAEAQPKSTdISISCFSCGA 92
                                  567899*************889999885555555555555555534455555554 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   9.6   1.3e-06     0.002       1      34 [.       7      44 ..       7      83 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                       Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvl....l 34
                                  V++D+d+C+gcg+Cv  + e   +  dg+a+v+     
  gi|91773444|ref|YP_566136.1|  7 VKIDEDKCTGCGQCVSPCAEGAIQIIDGKAKVVsedlC 44
                                  89****************77666667****99833330 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   2.3   7.5e-08   0.00011       3      20 ..       7      24 ..       5      26 .. 0.91
   2 ?    5.3   0.1     0.016        24       5      21 ..      39      55 ..      35      56 .. 0.80
   3 ?   -0.4   0.2       1.1   1.6e+03       9      14 ..      86      91 ..      82      92 .. 0.77
   4 ?    1.6   0.1      0.24   3.6e+02       9      14 ..     111     116 ..     103     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.5e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                  v++d+d+C+gCg Cvs C
  gi|91773444|ref|YP_566136.1|  7 VKIDEDKCTGCGQCVSPC 24
                                  789************999 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                        Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                  v +d C g g C+  CP
  gi|91773444|ref|YP_566136.1| 39 VSEDLCDGMGFCIGICP 55
                                  66889999899999999 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.1
                        Fer4_2  9 rCigCg 14
                                  +C +Cg
  gi|91773444|ref|YP_566136.1| 86 SCFSCG 91
                                  488888 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.24
                        Fer4_2   9 rCigCg 14 
                                    C++C 
  gi|91773444|ref|YP_566136.1| 111 VCTRCL 116
                                   699995 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.8   6.6e-05     0.099      44      58 ..      12      26 ..       2      33 .. 0.81
   2 !   10.4   0.3   0.00049      0.73       2      50 ..      44      91 ..      43      96 .. 0.74
   3 ?   -2.5   0.1       5.2   7.8e+03       2       5 ..     112     115 ..     110     117 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  ++C++Cg+C++ C +
  gi|91773444|ref|YP_566136.1| 12 DKCTGCGQCVSPCAE 26
                                  679999999988876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00049
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaeke.ekaslCieCg 50
                                  C + g+C+  Cp ++++ +e++++  +  l++ e++ k+ +   +C +Cg
  gi|91773444|ref|YP_566136.1| 44 CDGMGFCIGICPEGAITIEERQTVEFN--LEKAEAQPKStDISISCFSCG 91
                                  9999************99999876554..555555545523556888887 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.2
                       Fer4_17   2 CiqC 5  
                                   C++C
  gi|91773444|ref|YP_566136.1| 112 CTRC 115
                                   3333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.3   3.1e-05     0.046       2      14 ..      12      24 ..      11      27 .. 0.89
   2 ?    5.0   0.1     0.028        42       4      16 ..      44      56 ..      41      67 .. 0.80
   3 ?    2.6   0.1      0.17   2.5e+02       3       9 ..      86      92 ..      80      92 .. 0.90
   4 ?   -0.3   0.2       1.4   2.1e+03       4       7 ..     112     115 ..     106     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                        Fer4_4  2 erCigCgsCvaaC 14
                                  ++C+gCg+Cv+ C
  gi|91773444|ref|YP_566136.1| 12 DKCTGCGQCVSPC 24
                                  89********966 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.028
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C g g C+ +CP 
  gi|91773444|ref|YP_566136.1| 44 CDGMGFCIGICPE 56
                                  444468******5 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.17
                        Fer4_4  3 rCigCgs 9 
                                  +C+ Cg+
  gi|91773444|ref|YP_566136.1| 86 SCFSCGA 92
                                  6****95 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.4
                        Fer4_4   4 CigC 7  
                                   C++C
  gi|91773444|ref|YP_566136.1| 112 CTRC 115
                                   8888 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.9   5.6e-05     0.083      72      94 ..       4      26 ..       1      28 [. 0.84
   2 ?    4.6   0.2      0.04        59      76      94 ..      38      56 ..      29      58 .. 0.83
   3 ?   -0.1   0.0       1.2   1.7e+03      80      86 ..      85      91 ..      60      97 .. 0.57
   4 ?   -2.7   0.0       7.5   1.1e+04      85      88 ..     112     115 ..     102     118 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                       Fer4_22 72 efkekfgesgCvGCgRCieacpv 94
                                   +  k++e +C+GCg C++ c +
  gi|91773444|ref|YP_566136.1|  4 RMIVKIDEDKCTGCGQCVSPCAE 26
                                  56678899*************86 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.04
                       Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                   ++e  C G g Ci  cp+
  gi|91773444|ref|YP_566136.1| 38 VVSEDLCDGMGFCIGICPE 56
                                  457889***********97 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.2
                       Fer4_22 80 sgCvGCg 86
                                   +C  Cg
  gi|91773444|ref|YP_566136.1| 85 ISCFSCG 91
                                  4566665 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 7.5
                       Fer4_22  85 CgRC 88 
                                   C RC
  gi|91773444|ref|YP_566136.1| 112 CTRC 115
                                   5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 883.19
//
Query:       gi|91773445|ref|YP_566137.1|  [L=67]
Description: hypothetical protein Mbur_1480 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-20   73.2   0.4    1.8e-20   73.1   0.4    1.0  1  CGGC      CGGC domain


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.4     1e-24   1.8e-20      39     106 .]       1      66 [.       1      66 [. 0.95

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1e-24
                          CGGC  39 lvgfvtCggCpgkkvveklkelkkegvdvihlssCiktkkakkeCpeieeikeaieeklgievvegth 106
                                   +++f+tCggC+g++v + +++lkk+++dvihlssC+   k+++eCp+i++ik++i+++ gie+vegth
  gi|91773445|ref|YP_566137.1|   1 MIAFFTCGGCSGRRVFRLVRSLKKHDIDVIHLSSCM-IMKNYPECPHIDSIKKTITDA-GIEIVEGTH 66 
                                   689********************************8.33689***************9.********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 509.63
//
Query:       gi|91773446|ref|YP_566138.1|  [L=250]
Description: hypothetical protein Mbur_1481 [Methanococcoides burtonii DSM 6242]
Scores for 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-81  270.5   0.0    1.1e-80  270.3   0.0    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.3   0.0   6.1e-85   1.1e-80       2     219 ..       5     246 ..       4     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 270.3 bits;  conditional E-value: 6.1e-85
                        DUF166   2 vltsgeyGervvenilnepdfersl.................ivavvevpeeldefiedpeelLpe.lkeaDiviaytlhp 64 
                                   ++++ge+G++v++ni n+++f++s+                 iv+++e+p++l+efi+dp +++p+ + e+D++ia++lhp
  gi|91773446|ref|YP_566138.1|   5 FYYNGEFGKKVIGNIVNSSTFCTSCgdlcdhcrelkishadsIVDLYEFPDDLPEFIDDPFDHIPKnVGECDLLIAMDLHP 85 
                                   79******************************************************************************* PP

                        DUF166  65 Dlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCsleeegkpkideFlee.fGkPelevev 141
                                   D+  +l+e+a+++k+ka+i p+e pk   agl +++k kle++gi++++pkpfCsl+++gk+ ideF+++ fG+P l++e+
  gi|91773446|ref|YP_566138.1|  86 DIFSVLPEIAANAKAKAVIAPVEVPKlapAGLVQQVKGKLESAGIDCEFPKPFCSLTKTGKALIDEFVDMgFGRPLLRIEI 166
                                   ********************************************************************************* PP

                        DUF166 142 kdgki..kkVeVlrsapCGstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                   ++++   ++V+Vlr+apCGstwyvakkl+++++e+++e+ + ah++YpC+Asm++d++lk+t+lh+Agyi++ +ve+A +
  gi|91773446|ref|YP_566138.1| 167 DSDRRifSHVQVLRDAPCGSTWYVAKKLRWTDIEDYKEIVSGAHHAYPCTASMDKDTQLKDTILHEAGYIIRGSVEEASG 246
                                   *999889**********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1789.75
//
Query:       gi|91773447|ref|YP_566139.1|  [L=219]
Description: nitrite and sulphite reductase, 4Fe-4S subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  106.0   0.0    1.9e-30  105.4   0.0    1.3  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.1e-14   54.0   0.0    2.1e-14   53.1   0.0    1.5  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.45   10.6   0.0    1.8  2  DUF2059       Uncharacterized protein conserved in bacteria (


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 !  105.4   0.0   3.3e-34   1.9e-30       4     152 ..      86     218 ..      83     219 .] 0.97

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 3.3e-34
                                   SCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR   4 nlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeigfnil 84 
                                   ++r+v++cpg+++c+    D+  l  +++    ++y+ ++lP KfKi vsgc n c++  ++D+g++g+ k     gf+++
  gi|91773447|ref|YP_566139.1|  86 CVRSVKICPGTTFCKRGQQDSVGLGIKLD----EKYHGMELPSKFKIGVSGCMNSCAENAIKDVGIMGTPK-----GFTVM 157
                                   89***************************....**************************************.....***** PP

                                   E--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  85 vGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                   vGG++g +++ + t+a    ++e+evl++v++i+ +y+     +  kk+R+++++e++G++ F+++v+
  gi|91773447|ref|YP_566139.1| 158 VGGSAGLKPRLADTIA--EELDEDEVLSLVDTIISFYK-----SHAKKQRIGKVIEEIGLDAFKKEVG 218
                                   ****************..5788889*************.....99999*****************995 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 !   53.1   0.0   3.5e-18   2.1e-14       2      66 ..      12      75 ..      11      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3.5e-18
                  NIR_SIR_ferr  2 kqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66
                                   q+d++++ ++  ++ +G+ t+++lr++ad++ekyg   i++T+ Q l + g++e+dl++ +++L
  gi|91773447|ref|YP_566139.1| 12 VQRDKETF-AIAPHITGGIATPDLLRKIADVSEKYGAAAIKVTSAQRLAIVGLKEDDLDNAWDDL 75
                                  699*9999.*****************************************************998 PP

>> DUF2059  Uncharacterized protein conserved in bacteria (DUF2059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.5     3e+03      39      57 ..      31      49 ..      30      51 .. 0.82
   2 ?   10.6   0.0   7.5e-05      0.45       3      29 ..     164     194 ..     163     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.5
                                  HHHHHHHHHHHHHHHHCTT CS
                       DUF2059 39 epaataesmqaaqeaaqel 57
                                  +p + ++ +++ +++++++
  gi|91773447|ref|YP_566139.1| 31 TPDLLRKIADVSEKYGAAA 49
                                  7899999999999999876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.5e-05
                                   HHHHHHHHHHHHS-HHH....HHHHHHHHHS CS
                       DUF2059   3 mkdllaaiyaktfteae....lkailaFYkS 29 
                                   +k++la+  a++++e+e    ++ i+ FYkS
  gi|91773447|ref|YP_566139.1| 164 LKPRLADTIAEELDEDEvlslVDTIISFYKS 194
                                   6899*************9999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1318.94
//
Query:       gi|91773448|ref|YP_566140.1|  [L=118]
Description: HxlR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for 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-24   83.0   0.2    1.2e-23   82.8   0.2    1.0  1  HxlR          HxlR-like helix-turn-helix
    0.00023   21.4   0.0    0.00028   21.1   0.0    1.1  1  DUF2513       Hypothetical protein (DUF2513)
    0.00026   20.5   0.0    0.00051   19.6   0.0    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.003   17.4   0.1     0.0042   17.0   0.1    1.3  1  MarR          MarR family
     0.0052   16.8   0.0     0.0074   16.3   0.0    1.2  1  HTH_20        Helix-turn-helix domain
     0.0065   16.3   0.0      0.009   15.9   0.0    1.3  1  MarR_2        MarR family
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.018   15.2   0.1    1.2  1  HTH_34        Winged helix DNA-binding domain
      0.014   15.4   0.0      0.024   14.6   0.0    1.4  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.039   13.9   0.0       0.06   13.3   0.0    1.4  1  PadR          Transcriptional regulator PadR-like family
      0.065   13.3   0.0      0.071   13.2   0.0    1.2  1  Replic_Relax  Replication-relaxation
       0.13   11.9   0.0       0.16   11.7   0.0    1.1  1  DUF4423       Domain of unknown function (DUF4423)


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.2   7.1e-27   1.2e-23       1      87 [.      12     102 ..      12     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 7.1e-27
                                   HHHSTTHHHHHHHHTTS...-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES.SSS-EEEEEE-TCGGGGHHHHH CS
                          HxlR   1 liggkWkllilvellkg...kkRfselkralpkisqkmLaqrLreLeqdglierevyp.evPpkveYsltekGrslepvlq 77 
                                   +ig++W++ il el kg   +kRf+elk+++ +i+ k+L++rL+eLe+dgli+r+  + + P    Ysl+e G + ++++q
  gi|91773448|ref|YP_566140.1|  12 IIGKRWTMCILLELYKGnnsEKRFNELKKKVAGITPKTLSTRLKELEADGLIKRTLDEaTYPMVYTYSLSESGAEFMEIIQ 92 
                                   79*************9733359********************************987615688889*************** PP

                                   HHHHHHHHHH CS
                          HxlR  78 elkkwgeeyl 87 
                                    +kkwg e+ 
  gi|91773448|ref|YP_566140.1|  93 SIKKWGLEWK 102
                                   ******9996 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.7e-07   0.00028      10      91 ..      21      97 ..      16     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                       DUF2513 10 iLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiRddtvW 91
                                  iLl+l + +++e+ ++  +   ++++g + ++++  lk l+ +gLi+ + ++a+    ++  ++L+ +G +F++ i++ + W
  gi|91773448|ref|YP_566140.1| 21 ILLELYKGNNSEKRFNELK---KKVAGITPKTLSTRLKELEADGLIKRTLDEATYP--MVYTYSLSESGAEFMEIIQSIKKW 97
                                  6777777777777766644...49************************99999887..9999*****************999 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 !   19.6   0.0   3.1e-07   0.00051      28      48 .]      44      64 ..      41      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.1e-07
                        HTH_24 28 glSpstvnrrlkrLeeeGlIk 48
                                  g++p t+++rlk+Le +GlIk
  gi|91773448|ref|YP_566140.1| 44 GITPKTLSTRLKELEADGLIK 64
                                  9*******************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.6e-06    0.0042      25      50 ..      41      66 ..      21      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-06
                                  HHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR 25 kklgvskstvtrvldrLekkGlieRs 50
                                  k  g+++ t+++ l++Le +Gli+R+
  gi|91773448|ref|YP_566140.1| 41 KVAGITPKTLSTRLKELEADGLIKRT 66
                                  4469*********************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 !   16.3   0.0   4.5e-06    0.0074      28      57 ..      36      66 ..      29      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.5e-06
                                  HHHHHHH.TS-HHHHHHHHHHHHHCTTEEEE CS
                        HTH_20 28 selaerl.dlskntlsyHLrvLeeagLvevv 57
                                  +el++ + +++++tls +L++Le  gL++++
  gi|91773448|ref|YP_566140.1| 36 NELKKKVaGITPKTLSTRLKELEADGLIKRT 66
                                  577777779*******************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.5e-06     0.009      30      55 ..      42      67 ..      19      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                                  HHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 30 rlglsksavsrilkrLvaaGLverrp 55
                                    g+++ ++s +lk+L+a GL+ r+ 
  gi|91773448|ref|YP_566140.1| 42 VAGITPKTLSTRLKELEADGLIKRTL 67
                                  569*******************9984 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.1e-05     0.018       8      69 ..      24      87 ..      19      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                        HTH_34  8 yLas..vdeadfvelkeal.eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreaf 69
                                   L++  ++e  f+elk+++ ++t   Ls+ lk Le+ g i+++++        ++++ + G e f
  gi|91773448|ref|YP_566140.1| 24 ELYKgnNSEKRFNELKKKVaGITPKTLSTRLKELEADGLIKRTLDEATYPMVYTYSLSESGAE-F 87
                                  56666688999****9987479*********************99988877778888888854.4 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 ?   14.6   0.0   1.5e-05     0.024      31      53 ..      43      65 ..      41      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                  TTSSHHHHHHHHHHHHHTTSEEE CS
                     HTH_Crp_2 31 lGltretvsrilseLkreglisr 53
                                   G+t+ t+s  l+eL+ +gli+r
  gi|91773448|ref|YP_566140.1| 43 AGITPKTLSTRLKELEADGLIKR 65
                                  79*******************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 ?   13.3   0.0   3.7e-05      0.06      30      73 ..      46      88 ..      30      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                                  THHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR 30 seGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                   + +l + Lk+Le++gl++++ +e ++ p   +Y l + G + +
  gi|91773448|ref|YP_566140.1| 46 TPKTLSTRLKELEADGLIKRTLDE-ATYPMVYTYSLSESGAEFM 88
                                  55577789*************998.599************9876 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.4e-05     0.071      26      69 ..      49      88 ..      25     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                  Replic_Relax 26 tarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarll 69
                                  t+++rL++L++ gl++r l++  + +      y Y L + Ga+++
  gi|91773448|ref|YP_566140.1| 49 TLSTRLKELEADGLIKRtLDEATYPMV-----YTYSLSESGAEFM 88
                                  6999*************8888844444.....5999******998 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-05      0.16      19      73 ..      15      68 ..       9      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                       DUF4423 19 ssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                  ++W + +++el + ++ ++  +el+k++   i+ +  ++ l+ L+  gl+k++ d
  gi|91773448|ref|YP_566140.1| 15 KRWTMCILLELYKGNNSEKRFNELKKKVA-GITPKTLSTRLKELEADGLIKRTLD 68
                                  57**************************9.9********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 740.44
//
Query:       gi|91773449|ref|YP_566141.1|  [L=241]
Description: hypothetical protein Mbur_1484 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1511.58
//
Query:       gi|91773450|ref|YP_566142.1|  [L=141]
Description: peptidylprolyl isomerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  165.1   0.5    1.7e-48  164.9   0.5    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 !  164.9   0.5   9.2e-53   1.7e-48       3     142 ..       5     132 ..       3     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 164.9 bits;  conditional E-value: 9.2e-53
                 Pro_isomerase   3 dietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipdEitsk 83 
                                    iet+ kG+iv+eLf+++aPktv+nF kl+k+gfY+g+tFhRvi +fm+q+G p+g+++       gg   + i+ Ei+  
  gi|91773450|ref|YP_566142.1|   5 IIETN-KGTIVLELFEKDAPKTVANFEKLIKQGFYNGLTFHRVISNFMIQAGCPKGNGT-------GG-PGYSIKCEIN-P 75 
                                   589*7.***********************************************999866.......33.23589****6.4 PP

                 Pro_isomerase  84 lkhkrGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvet 142
                                    kh++Gal+ma++g  +n++gsqFfIt +++phldg +tvFGkV+eGmdvv++i++ ++
  gi|91773450|ref|YP_566142.1|  76 KKHTKGALSMAHAG--KNTGGSQFFITHSPQPHLDGVHTVFGKVIEGMDVVNAIKQSDV 132
                                   48***********8..6**************************************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 884.93
//
Query:       gi|91773451|ref|YP_566143.1|  [L=315]
Description: hypothetical protein Mbur_1486 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2072.61
//
Query:       gi|91773452|ref|YP_566144.1|  [L=171]
Description: hypothetical protein Mbur_1487 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.8   1.9       0.31   11.3   0.2    2.2  2  DUF4361   Domain of unknown function (DUF4361)


Domain annotation for each model (and alignments):
>> DUF4361  Domain of unknown function (DUF4361)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   1.7e-05      0.31      40      86 ..      20      65 ..       2     108 .. 0.85
   2 ?    2.0   0.1     0.013   2.3e+02      45      90 ..     116     169 ..     110     171 .] 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                                  EEEEEEEETTEEEEESTT--TT-TTGGGGEEE.....EEEES..EEE CS
                       DUF4361 40 tktlypvdentvrfyagnedeedtkrakykinknsiiltvnedntvt 86
                                  t t+ +v + +v ++ ++e++ + +  k+kin+  +il v++d+t++
  gi|91773452|ref|YP_566144.1| 20 TLTVLAVAQSSVVIIPQTENFLEVQ-MKQKINDALVILDVTPDTTIE 65
                                  568899***************8888.99**************99764 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.013
                                   EEETTEEEEESTT--TT-TTG....GGGEEE.....EEEES......EEEEE-T CS
                       DUF4361  45 pvdentvrfyagnedeedtkr....akykinknsiiltvnedn....tvtlkpy 90 
                                   +v +ntv+  a +e++ + +r    +++++n+++ +  v +d+    +v l+++
  gi|91773452|ref|YP_566144.1| 116 VVVKNTVFNGAPTENSITANRlvalSNSTVNSYGGTWVVADDElkviEVRLTAW 169
                                   556666666666666654443222245566666666666666665555666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1106.65
//
Query:       gi|91773453|ref|YP_566145.1|  [L=152]
Description: hypothetical protein Mbur_1488 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.7   0.6      0.039   13.9   0.1    1.8  2  DUF5453   Family of unknown function (DUF5453)
      0.094   12.7   0.7      0.094   12.7   0.7    1.9  2  PilX_N    PilX N-terminal
       0.23   11.7   3.1        0.6   10.4   3.1    1.7  1  DUF948    Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> DUF5453  Family of unknown function (DUF5453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.11   6.7e+02      87     112 ..      17      34 ..       9      57 .. 0.53
   2 ?   13.9   0.1   6.6e-06     0.039     100     156 ..      68     127 ..      63     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                       DUF5453  87 Gvivfllnillgvlllvllvnfltnq 112
                                   G++v ++        lv+lv  ++n+
  gi|91773453|ref|YP_566145.1|  17 GLVVAIA--------LVFLVTLMNNA 34 
                                   3333333........33333333333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.6e-06
                       DUF5453 100 lllvllvnfltnqileekysll...ltnalpllyssvGvsivlslisiglsklarlfidl 156
                                   + ++  +n+  nq + e  + +   ++   +lly+s G ++v+s+ +i++   a  f d+
  gi|91773453|ref|YP_566145.1|  68 VHIAHQINQSSNQTIPEITTSIiddFNRQTSLLYASHGQTVVISVSNITINESASSFGDM 127
                                   567778999999999998888878899999*********************999988774 PP

>> PilX_N  PilX N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   1.6e-05     0.094       4      29 ..      17      42 ..      16      44 .. 0.92
   2 ?   -3.0   0.2       1.2   7.3e+03      14      26 ..     109     121 ..     107     123 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                        PilX_N  4 aLvvtllllavltllgvatiqgslle 29
                                   Lvv++ l++++tl ++a+++g++++
  gi|91773453|ref|YP_566145.1| 17 GLVVAIALVFLVTLMNNAAVTGYHSS 42
                                  599*******************9987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                        PilX_N  14 vltllgvatiqgs 26 
                                   v+++ ++++ +++
  gi|91773453|ref|YP_566145.1| 109 VISVSNITINESA 121
                                   4777777766665 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 ?   10.4   3.1    0.0001       0.6       1      69 [.      15      80 ..      15     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                        DUF948  1 IAglIaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69
                                  ++gl++AiA+v+Lv ++  + +       + ++++e  +++++ ++ +++d+++++  ++ ++n+ +++
  gi|91773453|ref|YP_566145.1| 15 LSGLVVAIALVFLVTLMNNAAVTG---YHSSNNALEFPKDDIRDLVSQSRDATSQAVHIAHQINQSSNQ 80
                                  589*********998876665554...666677777777777777777777777777777777775543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1191  (0.0664287); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1006.21
//
Query:       gi|91773454|ref|YP_566146.1|  [L=148]
Description: hypothetical protein Mbur_1489 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 975.35
//
Query:       gi|91773455|ref|YP_566147.1|  [L=246]
Description: hypothetical protein Mbur_1490 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.31   12.0   6.1        1.6    9.7   6.0    2.5  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   6.0     9e-05       1.6       1      25 [.      11      35 ..      11     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9e-05
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaa 25
                                  +AVS+ +G iL+  ++vI +++i +
  gi|91773455|ref|YP_566147.1| 11 KAVSETVGFILLFGVVVIGMSFIYV 35
                                  69******************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1697.04
//
Query:       gi|91773456|ref|YP_566148.1|  [L=1258]
Description: hypothetical protein Mbur_1491 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   35.2   1.1      1e-07   32.4   0.1    2.3  2  VWA           von Willebrand factor type A domain
    6.5e-05   22.9   0.0    0.00013   21.9   0.0    1.5  1  VWA_3         von Willebrand factor type A domain
     0.0095   15.3   0.2      0.017   14.5   0.2    1.3  1  VWA_CoxE      VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.025   14.6   0.0        5.1    7.2   0.0    3.1  2  P_proprotein  Proprotein convertase P-domain
      0.029   15.0   0.2        1.8    9.3   0.0    2.6  2  VWA_2         von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.14   5.1e+02      23      52 ..     352     380 ..     326     400 .. 0.63
   2 !   32.4   0.1   2.8e-11     1e-07      54     173 ..     898    1011 ..     879    1012 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                                   HHHHHHHHHTBTTTTEEEEEEEESSS.EEEE CS
                           VWA  23 fikklveklevgpegtrvglvqfsse.vkte 52 
                                   + k ++++++  ++g+  glv +s++ v + 
  gi|91773456|ref|YP_566148.1| 352 ASKAFISSFD-ESRGDLSGLVLYSDNhV-VT 380
                                   3456777777.89999999999999953.33 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 2.8e-11
                                    ETTSHCHHHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS..HTHHHHHHHHGC CS
                           VWA   54 slndysskeellsalnnlkysgggttntgkalkyaleklfkssagaRenakkviilltdGksndg..dpkeaaneakeq 130 
                                    sl++ +s  +l ++++++ +++g t+ ++++l +a ++l   +       ++ ++l++dG +n g  ++ e+a +ake 
  gi|91773456|ref|YP_566148.1|  898 SLSN-NSLVHLSNSIDTI-TADGLTA-IDEGLYEANNELSAITG------NSTVVLMSDGLDNAGhhSLIEEALRAKEH 967 
                                    3333.3456777888885.5555555.99999888775554444......69************88************* PP

                                    TEEEEEEEESSSHHHHH..HHHHSSSSCHHCEEEESSHHHHHHHH CS
                           VWA  131 gikvfavGvgnadekel..Lnkiasepgeghvftvtdfeeleelf 173 
                                    +  +++vG gn+ ++ +  L +ia+ +g g+++++++++ le++f
  gi|91773456|ref|YP_566148.1|  968 NTVIYTVGLGNNEDEVDpiLCEIANITG-GKYYFAPNSTVLEDIF 1011
                                    *********55554432229999*****.**********999986 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 !   21.9   0.0   3.7e-08   0.00013      56     155 .]     899    1000 ..     887    1000 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.7e-08
                         VWA_3   56 vsaaelqealqkikelelslgasnlegaLkealrqpakpgevrsvilltDgssaqgeervsdlisrarek.irfhalgl 133 
                                    +s  +l  +  +i+++++ +g +     L ea    +  +  ++v+l++Dg + +g ++++++  ra+e+   + ++gl
  gi|91773456|ref|YP_566148.1|  899 LSNNSLVHLSNSIDTITA-DGLTAIDEGLYEANNELSAITGNSTVVLMSDGLDNAGHHSLIEEALRAKEHnTVIYTVGL 976 
                                    567788888999999999.99999999999999998888999**********988999999999998866388899*** PP

                         VWA_3  134 gsslsa..amlqaLAeasgGtyef 155 
                                    g+  ++  ++l ++A ++gG y+f
  gi|91773456|ref|YP_566148.1|  977 GNNEDEvdPILCEIANITGGKYYF 1000
                                    **777555**************87 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 !   14.5   0.2   4.7e-06     0.017     103     172 ..     895     960 ..     891     972 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.7e-06
                      VWA_CoxE 103 lTralrerDpaeaLarvsaavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellae 172
                                   +T+ l++++++ + +++       +G T i ++l e+++  +  a+   ++vvl+sDgl+   +  l +e
  gi|91773456|ref|YP_566148.1| 895 VTSSLSNNSLVHLSNSID--TITADGLTAIDEGLYEANNELS--AITGNSTVVLMSDGLDNAGHHSLIEE 960
                                   677777555555444444..33389*************9999..7779************9888777654 PP

>> P_proprotein  Proprotein convertase P-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0014       5.1      16      30 ..      58      72 ..      50     138 .. 0.85
   2 ?    3.7   0.0     0.017        62      61      81 ..     321     341 ..     307     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                                  GGEEEEEE-TTS-EE CS
                  P_proprotein 16 gdlritLvsPsGtrs 30
                                   dl ++L+sPsGt++
  gi|91773456|ref|YP_566148.1| 58 NDLDVRLTSPSGTSY 72
                                  79***********87 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.017
                                   -EEEEEEEEESSTT--EEEEE CS
                  P_proprotein  61 eGeWkLevkdseeedtgtlks 81 
                                   +G+W+L+v+ s++++  tl++
  gi|91773456|ref|YP_566148.1| 321 AGNWTLQVSSSSSDEPFTLTT 341
                                   8*********99888877765 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.048   1.7e+02      17      55 ..     345     383 ..     326     399 .. 0.65
   2 ?    9.3   0.0   0.00049       1.8      50     106 ..     894     948 ..     886     949 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.048
                         VWA_2  17 gptrleaakdaveallkslpgdrvglvtfsdgpevlipl 55 
                                   +++  ++a +a ++ +++ +gd  glv +sd+  v ++ 
  gi|91773456|ref|YP_566148.1| 345 KKSATQIASKAFISSFDESRGDLSGLVLYSDNHVVTSDN 383
                                   34445555555555555559***********99888765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00049
                         VWA_2  50 evliplt.kdkakilnalrnleakgggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                   +v ++l+  +  ++ n ++ ++a+ g t ++++L  a+++l++ +   ++++vl++Dg
  gi|91773456|ref|YP_566148.1| 894 TVTSSLSnNSLVHLSNSIDTITAD-GLTAIDEGLYEANNELSAIT--GNSTVVLMSDG 948
                                   555666535678999*******96.*****************997..99********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.84u 0.27s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 7802.07
//
Query:       gi|91773457|ref|YP_566149.1|  [L=892]
Description: von Willebrand factor, type A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-27   95.5   0.7    1.4e-26   93.9   0.2    2.1  2  VWA         von Willebrand factor type A domain
    3.1e-16   59.9   1.0    2.8e-14   53.7   0.2    2.6  2  VWA_2       von Willebrand factor type A domain
    2.9e-12   46.8   0.0    4.4e-12   46.2   0.0    1.3  1  VWA_3       von Willebrand factor type A domain
    2.7e-11   43.6  19.0     0.0012   19.1   0.2    5.8  5  Invasin_D3  Invasin, domain 3
    4.5e-09   36.2  31.8    1.5e-05   24.9   4.4    6.8  7  Big_1       Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.048   13.1   8.9       0.17   11.2   4.4    3.4  2  VWA_CoxE    VWA domain containing CoxE-like protein
      0.059   13.0   0.5        0.3   10.7   0.1    2.2  3  CobT_C      Cobalamin biosynthesis protein CobT VWA domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.88   2.2e+03       3      15 ..     598     610 ..     598     612 .. 0.85
   2 !   93.9   0.2   5.3e-30   1.4e-26       1     174 [.     618     795 ..     618     796 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.88
                                   EEEEE-STTSCHH CS
                           VWA   3 vfvlDgSgsmgee 15 
                                   +++lD Sgsm+++
  gi|91773457|ref|YP_566149.1| 598 MLILDRSGSMDPD 610
                                   589*******875 PP

  == domain 2  score: 93.9 bits;  conditional E-value: 5.3e-30
                                   EEEEEEE-STTS......CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS..EEEE.EETTSHCHHHHHHHHHHTGS CS
                           VWA   1 DivfvlDgSgsm......geenfekvkefikklveklevgpegtrvglvqfsse..vkte.fslndysskeellsalnnlk 72 
                                   Div+vlD Sgsm       e+ ++ +k+++k ++e+l     +t vg+v+fss+  v  + +sln   +k+ l++a+++ +
  gi|91773457|ref|YP_566149.1| 618 DIVLVLDRSGSMkflgnaPEQPLTDAKSAAKIFMENLL---SNTEVGVVSFSSTstVDRQpVSLNISGNKDLLHNAIDS-M 694
                                   9****************999******************...***********9977555569999999***********.7 PP

                                   GGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS...HTHHHHHHHHGCTEEEEEEEE..SSSHHHHHH CS
                           VWA  73 ysgggttntgkalkyaleklfkssagaRenakkviilltdGksndg...dpkeaaneakeqgikvfavGv..gnadekelL 148
                                   +++ggt+ +g+a++ a + l++++      akk++i+ltdG  + g   d ++a+ +a  ++i+++++G   ++  ++ +L
  gi|91773457|ref|YP_566149.1| 695 VADGGTA-IGDAMADANNLLINGRPD----AKKIMIVLTDGVATAGsdrDGSDAISTANLNNIRIYSIGLgsSEYIDEPML 770
                                   *******.********9999888777....9************99779**********************8877778888* PP

                                   HHHSSSSCHHCEEEESSHHHHHHHHH CS
                           VWA 149 nkiasepgeghvftvtdfeeleelfe 174
                                   ++iase+g g ++++++ +el+++++
  gi|91773457|ref|YP_566149.1| 771 KRIASETG-GSYYNAPSGSELQTVYN 795
                                   ********.*************9987 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 ?    4.6   0.0     0.019        49       2      21 ..     598     617 ..     597     619 .. 0.80
   2 !   53.7   0.2   1.1e-17   2.8e-14       1     106 [.     619     730 ..     619     731 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.019
                         VWA_2   2 vfvlDtSgSmrngdygptrl 21 
                                   +++lD SgSm ++ y  t l
  gi|91773457|ref|YP_566149.1| 598 MLILDRSGSMDPDYYAGTAL 617
                                   89*********986666655 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 1.1e-17
                         VWA_2   1 lvfvlDtSgSmrng.dygptrleaakdaveallksl.pgdrvglvtfsdgpevlipl.....tkdkakilnalrnleakgg 74 
                                   +v+vlD SgSm    +  ++ l  ak+a++ ++++l  ++ vg+v+fs++++v  ++     + +k+ + na++++ a+ g
  gi|91773457|ref|YP_566149.1| 619 IVLVLDRSGSMKFLgNAPEQPLTDAKSAAKIFMENLlSNTEVGVVSFSSTSTVDRQPvslniSGNKDLLHNAIDSMVAD-G 698
                                   79*********665233689**************885799*********8866655533333599999*********96.* PP

                         VWA_2  75 gtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                   gt +++a+  a+++l ++r  +k++++++tDg
  gi|91773457|ref|YP_566149.1| 699 GTAIGDAMADANNLLINGRPDAKKIMIVLTDG 730
                                   *************9977778***********9 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 !   46.2   0.0   1.7e-15   4.4e-12       2     154 ..     618     782 ..     617     783 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.7e-15
                         VWA_3   2 evvivvDvsssmsaen.......klvkdaLsvalrqLptndkiavllfgt.kprplfpgsravsaaelqealqkikelels 74 
                                   ++v+v+D s sm+  +       + +k+a + +++ L +n+++ v++f + +++  +p s ++s   ++ +  +i+ + + 
  gi|91773457|ref|YP_566149.1| 618 DIVLVLDRSGSMKFLGnapeqplTDAKSAAKIFMENLLSNTEVGVVSFSStSTVDRQPVSLNIS-GNKDLLHNAIDSMVA- 696
                                   89**********9765567778999***********************9956666777777887.9***********999. PP

                         VWA_3  75 lgasnlegaLkealrqp..akpgevrsvilltDgss.aqgeervsdlisrar.ekirfhalglgs..slsaamlqaLAeas 149
                                   +g++    a+++a       +p   +  i+ltDg + a ++ + sd+is a   +ir+ ++glgs   ++++ml+++A ++
  gi|91773457|ref|YP_566149.1| 697 DGGTAIGDAMADANNLLinGRPDAKKIMIVLTDGVAtAGSDRDGSDAISTANlNNIRIYSIGLGSseYIDEPMLKRIASET 777
                                   *************997777889999999********6667799******988799**********76689*********** PP

                         VWA_3 150 gGtye 154
                                   gG+y+
  gi|91773457|ref|YP_566149.1| 778 GGSYY 782
                                   ***96 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   2.0   0.00033      0.85      32      80 ..      49      99 ..      25     112 .. 0.78
   2 ?    2.4   0.1     0.077     2e+02      23      54 ..     134     165 ..     120     170 .. 0.74
   3 !    6.9   0.0    0.0031       7.9      20      68 ..     249     299 ..     242     323 .. 0.68
   4 !   13.6   0.3   2.5e-05     0.064       6      94 ..     347     444 ..     343     446 .. 0.74
   5 !   19.1   0.2   4.6e-07    0.0012       7      79 ..     453     541 ..     449     555 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
                    Invasin_D3 32 ngnp.vsgltvtfsttsag..tlsavtdngdGtytatLtattagtatitptv 80
                                  ng   + + +v+fst+  g  + s+ t+n++G  t+ + +t +g++ ++++ 
  gi|91773457|ref|YP_566149.1| 49 NGTLpLNNTSVNFSTN-FGmlSSSSSTTNDSGFATVFINSTISGNLVVNASS 99
                                  5555599999****99.8867667899*******************999876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.077
                    Invasin_D3  23 tltvtlkDangnpvsgltvtfsttsag.tlsav 54 
                                    + vtl+D+ gn     t+++  t  + +ls++
  gi|91773457|ref|YP_566149.1| 134 DVNVTLRDQYGNINNTPTINLYLT-MVdVLSEL 165
                                   589*********988888888777.33355555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0031
                    Invasin_D3  20 ststltvtlkDangnpvsgltvtfstt..sag.tlsavtdngdGtytatLta 68 
                                   +ts + v l D  +np+ g+t  f++t   ++   s vt  ++   ++ L +
  gi|91773457|ref|YP_566149.1| 249 TTSEIVVSLHDRYDNPIEGATLIFNATypIDTiYNSPVT-YNSSWLSSSLES 299
                                   79999****************999988542232333333.333444555555 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 2.5e-05
                    Invasin_D3   6 tftaspasivAdGkststltvtlkDangnp.vsgltvtfstt.....sag.tlsavtdngdGtytatLtatt.agtatitp 78 
                                   t++ +p+s  A+++++  l++++ D++ np + g + +++ +     s g tl  +  n++G+ t+++  t  +++++it+
  gi|91773457|ref|YP_566149.1| 347 TLSSTPSSCYANNEDAYRLSAQIIDQFLNPlLPG-SFQIKDQvlfesSLGsTLIPL--NDYGVATTVVGPTPyVENISITA 424
                                   78899*************************7554.444443333333477566655..999****99977656******** PP

                    Invasin_D3  79 tvnG....vaiaatatvtlt 94 
                                   t+++    + i++++++++t
  gi|91773457|ref|YP_566149.1| 425 TYKNetgtTNINTSKELSFT 444
                                   **885555555666666666 PP

  == domain 5  score: 19.1 bits;  conditional E-value: 4.6e-07
                    Invasin_D3   7 ftaspasivAd...GkststltvtlkDangnpvsgltvtfstt..sagtls..........avtdngdGtytatLta.tta 71 
                                   f a+p+ ++A+   G+  st+t+ + Da g  +++ +vt++ t  s gtls          + t++++G  ++++t+ + +
  gi|91773457|ref|YP_566149.1| 453 FYANPNVVLANnlsGNHDSTVTLIALDAWGHSLQNINVTLNNTapSLGTLSldgsnesnliNFTTDQYGRVITEFTSsNFV 533
                                   668888888885557899***********************88886776666666666666899*************566* PP

                    Invasin_D3  72 gtatitpt 79 
                                   g+ ti   
  gi|91773457|ref|YP_566149.1| 534 GNCTIIGL 541
                                   **999765 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 !   24.9   4.4   5.9e-09   1.5e-05      19      64 .]      52      97 ..      35      97 .. 0.86
   2 ?    3.5   0.2     0.027        70       6      21 ..     132     147 ..     130     164 .. 0.79
   3 !   11.1   0.1   0.00012       0.3       5      38 ..     249     284 ..     248     291 .. 0.79
   4 ?    1.3   0.0      0.14   3.6e+02       1      21 [.     357     377 ..     357     380 .. 0.96
   5 ?   -3.4   0.3       4.1   1.1e+04       7      19 ..     420     432 ..     417     437 .. 0.60
   6 !   11.0   1.4   0.00013      0.32       4      55 ..     468     530 ..     466     532 .. 0.85
   7 ?   -3.5   0.1       4.2   1.1e+04      46      56 ..     661     671 ..     657     674 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.9e-09
                         Big_1 19 npvagatVtfsvsggalsassgtTdanGkatvtltstkagtvtvtA 64
                                   p+++++V+fs++ g ls+ss+tT+++G atv + st +g   v+A
  gi|91773457|ref|YP_566149.1| 52 LPLNNTSVNFSTNFGMLSSSSSTTNDSGFATVFINSTISGNLVVNA 97
                                  69**************************************988876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.027
                         Big_1   6 tntltatvkDangnpv 21 
                                   ++ +++t++D++gn  
  gi|91773457|ref|YP_566149.1| 132 AVDVNVTLRDQYGNIN 147
                                   6789**********65 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00012
                         Big_1   5 dtntltatvkDangnpvagatVtfsvsg..galsas 38 
                                   +t+++ + + D++ np++gat  f+++   +++ +s
  gi|91773457|ref|YP_566149.1| 249 TTSEIVVSLHDRYDNPIEGATLIFNATYpiDTIYNS 284
                                   78999********************99874444444 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.14
                         Big_1   1 AdGvdtntltatvkDangnpv 21 
                                   A++ d+ +l+a + D++ np+
  gi|91773457|ref|YP_566149.1| 357 ANNEDAYRLSAQIIDQFLNPL 377
                                   9******************97 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 4.1
                         Big_1   7 ntltatvkDangn 19 
                                   + +tat k++ g+
  gi|91773457|ref|YP_566149.1| 420 ISITATYKNETGT 432
                                   5566666666554 PP

  == domain 6  score: 11.0 bits;  conditional E-value: 0.00013
                         Big_1   4 vdtntltatvkDangnpvagatVtfsvsg...gals........assgtTdanGkatvtltst 55 
                                   +  +t+t ++ Da g+ +++++Vt++ ++   g+ls          + tTd+ G++ +++ts+
  gi|91773457|ref|YP_566149.1| 468 NHDSTVTLIALDAWGHSLQNINVTLNNTApslGTLSldgsnesnLINFTTDQYGRVITEFTSS 530
                                   5568*********************888877888889997765555669*********99997 PP

  == domain 7  score: -3.5 bits;  conditional E-value: 4.2
                         Big_1  46 Gkatvtltstk 56 
                                   G+++++ tst+
  gi|91773457|ref|YP_566149.1| 661 GVVSFSSTSTV 671
                                   77788888876 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 ?   -0.3   0.1      0.23   5.9e+02      93     116 ..      14      37 ..       7      61 .. 0.87
   2 ?   11.2   4.4   6.6e-05      0.17      59     165 ..     618     735 ..     577     747 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.23
                      VWA_CoxE  93 vfaFdtrlvdlTralrerDpaeaL 116
                                   +f+F t ++ +T +++++D    +
  gi|91773457|ref|YP_566149.1|  14 LFLFTTPVMAVTLEFSASDTSAQV 37 
                                   79**************99987765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.6e-05
                      VWA_CoxE  59 elvllvDvSgSmaaysaiflallhAllqqlp..........rtevfaFd.trlvd.lTralrerDpaeaLarvsaavedlg 127
                                   ++vl++D SgSm+   +   + l  +   ++          ++ v+ F+ t++vd     l+ +  +++L+++       +
  gi|91773457|ref|YP_566149.1| 618 DIVLVLDRSGSMKFLGNAPEQPLTDAKSAAKifmenllsntEVGVVSFSsTSTVDrQPVSLNISGNKDLLHNAI-DSMVAD 697
                                   79999999999997655433222211111111112334444888999963555541556789999999**9996.345589 PP

                      VWA_CoxE 128 GgTrigaalaeflelvtrpaLsrravvvlvsDglergd 165
                                   GgT ig+a+a++++l        + ++++++Dg  +  
  gi|91773457|ref|YP_566149.1| 698 GGTAIGDAMADANNLLINGRPDAKKIMIVLTDGVATAG 735
                                   ************9987654446899*******876654 PP

>> CobT_C  Cobalamin biosynthesis protein CobT VWA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.58   1.5e+03      15      25 ..     619     629 ..     592     633 .. 0.58
   2 ?   -1.1   0.0      0.46   1.2e+03      16      26 ..     620     630 ..     611     674 .. 0.69
   3 ?   10.7   0.1   0.00012       0.3     119     148 ..     703     733 ..     688     746 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.58
                        CobT_C  15 vtllldlsGsm 25 
                                   + l+ld sGsm
  gi|91773457|ref|YP_566149.1| 619 IVLVLDRSGSM 629
                                   23455555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.46
                        CobT_C  16 tllldlsGsmr 26 
                                    l+ld sGsm+
  gi|91773457|ref|YP_566149.1| 620 VLVLDRSGSMK 630
                                   589*******7 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00012
                        CobT_C 119 Gealdqlaklll.GrmedkkillvisdGaPv 148
                                   G+a++ +++ll+ Gr++ kki++v++dG   
  gi|91773457|ref|YP_566149.1| 703 GDAMADANNLLInGRPDAKKIMIVLTDGVAT 733
                                   7888888876644***************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (892 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         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: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 5221.23
//
Query:       gi|91773458|ref|YP_566150.1|  [L=121]
Description: hypothetical protein Mbur_1493 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.0   0.1      0.022   13.8   0.1    1.1  1  Tox-ODYAM1  Toxin in Odyssella and Amoebophilus


Domain annotation for each model (and alignments):
>> Tox-ODYAM1  Toxin in Odyssella and Amoebophilus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.2e-06     0.022     325     380 ..      28      84 ..      16      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-06
                    Tox-ODYAM1 325 lakvaitqmidyalklw.ernatqtinainlllkgtqhkpswlkeitqavslekedG 380
                                   + k+ +t+mi+ +l++     ++q+++   +ll ++     w+++it+ +++e++d 
  gi|91773458|ref|YP_566150.1|  28 VVKMGVTKMINSILEMIkTVPEGQELSGYIYLLDSASSSIIWYDNITDCSQVEEDDI 84 
                                   67999***********7477899******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 757.38
//
Query:       gi|91773459|ref|YP_566151.1|  [L=427]
Description: thiamine biosynthesis protein ThiC [Methanococcoides burtonii DSM 6242]
Scores for complete 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-166  552.6   2.4   5.8e-166  552.4   2.4    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 !  552.4   2.4  3.2e-170  5.8e-166       3     417 ..       4     420 ..       2     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 552.4 bits;  conditional E-value: 3.2e-170
                  ThiC_Rad_SAM   3 leaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEveKlkv 83 
                                   +e+a++g+ite+m+ va+ e++epef+++++a+Grivip+   ++ k ++iG+gl+tkvna+iG+s+d+ d ++Ev+K+k+
  gi|91773459|ref|YP_566151.1|   4 VEDAKAGKITEAMKVVANVEGLEPEFIMRGIAAGRIVIPTSPYRDVKLCGIGEGLTTKVNASIGASSDIIDEDMEVAKAKA 84 
                                   789****************************************************************************** PP

                  ThiC_Rad_SAM  84 alkagadtvmdLstggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvdfltiHagv 161
                                   a++agadt+m+L tggd+  ir+k++++ +++vg+vp+Yqa+     +++++ ++te++l ++ e+qa+ G +f++iH+g+
  gi|91773459|ref|YP_566151.1|  85 AEAAGADTLMELGTGGDFLGIRKKVCDAISLSVGSVPLYQAFIGaakRDGSIIHMTEDDLWNATEQQAKLGTNFMAIHTGI 165
                                   *****************************************976666999******************************* PP

                  ThiC_Rad_SAM 162 tlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlaeliv 242
                                   ++ +l++lk+++R+ gi+SrgG+++++wml+nekenply+efd+l+eilke++v+lS g+g+R+G+i+Datd+aq++eli+
  gi|91773459|ref|YP_566151.1| 166 NNIVLDRLKAHGRYGGICSRGGAFMTTWMLHNEKENPLYAEFDYLCEILKEHEVVLSTGNGMRAGAIHDATDRAQVQELII 246
                                   ********************************************************************************* PP

                  ThiC_Rad_SAM 243 lgelvkrarea.gvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGadllCy 322
                                   ++e +++a+++ + qv+veGPGHvplde+e+nvkl+k+++ ++Pfy+lGplvtDi+pg Dhi++aiGaa++a++G+d+lCy
  gi|91773459|ref|YP_566151.1| 247 NSECAQKAHDKyNLQVIVEGPGHVPLDEVEMNVKLMKSMSGHKPFYMLGPLVTDISPGRDHIVTAIGAATSASHGCDFLCY 327
                                   ********97549******************************************************************** PP

                  ThiC_Rad_SAM 323 vtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelaldpekareireeklpeeeea 403
                                   vtpaEHl+lP+ edv eGv ++kiaah++d++k   ++r++d a+ +aR++ldw+k+f+laldpe ar+ir+e+++++e+a
  gi|91773459|ref|YP_566151.1| 328 VTPAEHLALPNIEDVIEGVQTSKIAAHVGDMVKL--GKRDQDLAMGRARRDLDWKKMFSLALDPELARKIRTERSSADEDA 406
                                   *********************************8..7889***************************************** PP

                  ThiC_Rad_SAM 404 CsmCgekCavkive 417
                                   C+mCg++Cavkiv+
  gi|91773459|ref|YP_566151.1| 407 CTMCGDFCAVKIVN 420
                                   ***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2702.63
//
Query:       gi|91773460|ref|YP_566152.1|  [L=308]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-16   59.4   0.0    5.2e-16   58.9   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      3e-05   24.0   0.0    4.5e-05   23.5   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0012   19.3   0.0     0.0023   18.4   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.015   14.0   0.0      0.022   13.4   0.0    1.1  1  Tweety           Tweety
      0.099   13.2   0.1       0.23   12.0   0.1    1.6  1  YflT             Heat induced stress protein YflT
       0.12   11.9   0.1       0.25   11.0   0.1    1.6  1  DAGK_cat         Diacylglycerol kinase catalytic 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 !   58.9   0.0   1.8e-19   5.2e-16       1     132 [.      13     135 ..      13     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.8e-19
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES.-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDg.StDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                   ++ ipt Nee t+ ++++  ++      fe i+v Dg S+D+t++++ee      + +vi +e + Gk+ a+ ++++    
  gi|91773460|ref|YP_566152.1|  13 CILIPTLNEEVTIVQLIKDFRSE----GFENILVIDGhSSDNTRKLAEEN-----GAKVIVQEGK-GKGQAVQEAFQLIED 83 
                                   699*******************9....888888888857***********.....9*******55.*************** PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                    yi+ +D D ++   ++  +++++ ++ a   lg+r+++f    + + n+  
  gi|91773460|ref|YP_566152.1|  84 PYIVMIDGDGTYLASDVHAVLQPILDGHAEHTLGNRMANFEAGAFTKLNLAG 135
                                   *****************************************99999998863 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 !   23.5   0.0   1.5e-08   4.5e-05       3      98 ..      11      93 ..       9     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.5e-08
               Glyco_tranf_2_3  3 dlavlVptfneedvlgevlesllaqeyprvevvvvvde.sdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealr 84
                                  d+ +l+pt+nee +++ ++ ++ +     +e ++v d+ s++ t++ aee      + + +v+v++     +gk +a++ea++
  gi|91773460|ref|YP_566152.1| 11 DVCILIPTLNEEVTIVQLIKDFRS---EGFENILVIDGhSSDNTRKLAEE------N-GAKVIVQEG----KGKGQAVQEAFQ 79
                                  6899*******9999999999988...45666666655499999999988......4.678987755....69********** PP

               Glyco_tranf_2_3 85 avksdlvllvDdDt 98
                                   +++ +++++D+D 
  gi|91773460|ref|YP_566152.1| 80 LIEDPYIVMIDGDG 93
                                  ************94 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.5e-07    0.0023       2      49 ..      20      68 ..      19     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.5e-07
               Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkel.pevkllhvd 49
                                  ne+ ++ + ++  ++ gf++ilv+d +s+D+tr++ +e+ ++v + + +
  gi|91773460|ref|YP_566152.1| 20 NEEVTIVQLIKDFRSEGFENILVIDGHSSDNTRKLAEENgAKVIVQEGK 68
                                  889999999999999********************99973445554443 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.4e-06     0.022      72     126 ..     244     298 ..     237     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-06
                        Tweety  72 vccaaigvGfYGNsetndGvlqltyslrkanhtlagikklvseteesleekleee 126
                                   ++ ++i+vG+Y  +e  +Gv+++ +++  a  +l+gi+  +  + ++l  +l++e
  gi|91773460|ref|YP_566152.1| 244 LTLSGIAVGLYVVNEWMNGVTRIPMTILTALLILTGIQMFIFGMLSDLIVSLHRE 298
                                   6779***********************************9999999888777665 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.6e-05      0.23       5      68 ..      20      82 ..      16      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                          YflT  5 eneeellsaieelkaeGyneddiyvvakdkdrlerlaentdaetettseeglwdsiknlfrskg 68
                                  + e + ++ i+++++eG+++  +++  +  d++++lae+ +a+++  + +g ++++ ++f+  +
  gi|91773460|ref|YP_566152.1| 20 NEEVTIVQLIKDFRSEGFEN-ILVIDGHSSDNTRKLAEENGAKVIVQEGKGKGQAVQEAFQLIE 82
                                  677888999*********64.46666899*****************999**9999999998655 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.2e-05      0.25      21      68 ..      50      95 ..       8     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.2e-05
                                  HCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHH CS
                      DAGK_cat 21 kvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtv 68
                                  + r+l ee+g ++ ++e +++g+a + a ++ e+    iv++ GDGt 
  gi|91773460|ref|YP_566152.1| 50 NTRKLAEENGAKVIVQEGKGKGQAVQEAFQLIED--PYIVMIDGDGTY 95
                                  67889999999*************9999999998..9**********4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1960.19
//
Query:       gi|91773461|ref|YP_566153.1|  [L=206]
Description: transcription factor [Methanococcoides burtonii DSM 6242]
Scores for complete 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-56  186.8   0.9    4.7e-27   93.8   0.0    3.0  3  TBP       Transcription factor TFIID (or TATA-binding protein
    2.4e-07   30.8   0.0      0.013   15.6   0.0    2.4  2  DUF3378   Domain of unknown function (DUF3378)
    0.00093   18.8   0.0        1.1    9.0   0.0    2.5  2  NdhS      NAD(P)H dehydrogenase subunit S


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 !    3.8   0.0    0.0092        55       2      13 ..       6      17 ..       5      22 .. 0.86
   2 !   86.8   0.2   1.2e-28   7.2e-25       2      83 ..      29     108 ..      28     110 .. 0.95
   3 !   93.8   0.0   7.8e-31   4.7e-27       2      83 ..     120     201 ..     119     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0092
                                  EEEEEEEEEEE- CS
                           TBP  2 fkiqNvvasanl 13
                                  +ki+Nvvas++l
  gi|91773461|ref|YP_566153.1|  6 IKIENVVASTEL 17
                                  89*******988 PP

  == domain 2  score: 86.8 bits;  conditional E-value: 1.2e-28
                                   EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHH CS
                           TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapil 82 
                                   +ki+Nvvas++l  e+dL k++ +   ++aeY++++fpglvyr+ +pk+++l+F+sGkvv+tGak++ +++ ++ ++a++l
  gi|91773461|ref|YP_566153.1|  29 IKIENVVASTKLAEEFDLIKIEAEF--EGAEYNKQKFPGLVYRVTDPKAAFLVFTSGKVVCTGAKNVADVHIVIGNMAKKL 107
                                   89*******************8665..***************************************************998 PP

                                   H CS
                           TBP  83 k 83 
                                   +
  gi|91773461|ref|YP_566153.1| 108 N 108
                                   6 PP

  == domain 3  score: 93.8 bits;  conditional E-value: 7.8e-31
                                   EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHH CS
                           TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapil 82 
                                   +++qN+vasa+l+ +l+L+++a  +  +n+eYepe+fpglvyr+ +pkv++liFssGk+v+tG ks+ ++++ ++ + + l
  gi|91773461|ref|YP_566153.1| 120 ITVQNIVASADLHATLNLNAIAIGLGLENIEYEPEQFPGLVYRIADPKVVVLIFSSGKLVVTGGKSPAHCDQGVEVVRQQL 200
                                   89********************99779*********************************************999888777 PP

                                   H CS
                           TBP  83 k 83 
                                    
  gi|91773461|ref|YP_566153.1| 201 D 201
                                   5 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.6e-05     0.093      22      55 ..      58      91 ..      40      98 .. 0.82
   2 !   15.6   0.0   2.2e-06     0.013      24      55 ..     153     184 ..     148     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                       DUF3378 22 lrskkppyavfaakkndttItaYtSgKVlFQGkn 55
                                   +++k p+ v++  ++++   ++tSgKV+  G++
  gi|91773461|ref|YP_566153.1| 58 YNKQKFPGLVYRVTDPKAAFLVFTSGKVVCTGAK 91
                                  456679***********************98876 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.2e-06
                       DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGkn 55 
                                    ++ p+ v+++ ++++++ ++ SgK+++ G +
  gi|91773461|ref|YP_566153.1| 153 PEQFPGLVYRIADPKVVVLIFSSGKLVVTGGK 184
                                   5789***********************99976 PP

>> NdhS  NAD(P)H dehydrogenase subunit S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00018       1.1      18      34 ..      62      78 ..      53      84 .. 0.86
   2 !    7.3   0.0    0.0006       3.6      18      34 ..     155     171 ..     147     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                          NdhS 18 gfeGlvQrvsdgkaaVl 34
                                  +f Glv rv+d kaa l
  gi|91773461|ref|YP_566153.1| 62 KFPGLVYRVTDPKAAFL 78
                                  799************76 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0006
                          NdhS  18 gfeGlvQrvsdgkaaVl 34 
                                   +f Glv r++d k+ Vl
  gi|91773461|ref|YP_566153.1| 155 QFPGLVYRIADPKVVVL 171
                                   799***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1356.14
//
Query:       gi|91773462|ref|YP_566154.1|  [L=367]
Description: condensin subunit ScpB [Methanococcoides burtonii DSM 6242]
Scores for complete 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  130.9   0.1    1.3e-37  128.9   0.0    2.0  3  SMC_ScpB        Segregation and condensation complex subunit 
      0.001   19.1   0.0     0.0029   17.7   0.0    1.8  1  HTH_20          Helix-turn-helix domain
     0.0096   15.8   0.1       0.25   11.3   0.0    2.7  3  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.057   13.6   0.0         18    5.6   0.0    2.5  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.55   10.6   2.7        1.8    8.9   0.2    2.8  3  YozD            YozD-like protein


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 !  128.9   0.0   3.5e-41   1.3e-37       2     153 ..       6     149 ..       5     153 .. 0.98
   2 ?   -2.7   0.0       1.1   3.9e+03      49      68 ..     211     230 ..     210     245 .. 0.72
   3 ?   -2.1   0.0      0.73   2.6e+03      21      44 ..     259     281 ..     238     289 .. 0.63

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 3.5e-41
                      SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkktrLs 82 
                                   iiEA+Lf+age ++ ++Lak+++ s ++v  ++ +L+eey+++++g+e++ ++g+y +++kp++ +v++ ++++    +L+
  gi|91773462|ref|YP_566154.1|   6 IIEAVLFAAGEAVDTQTLAKLINKSAKNVTPVIRSLMEEYSTRESGMEIIDLGGRYVMQVKPKYTDVISPIAPK----ELK 82 
                                   8*********************999*************************************************....*** PP

                      SMC_ScpB  83 qaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglks 153
                                      l+tL+++ay+qpv ++e+ ++RG ++++++r+L +rg+ie +     +gr+ l++tT  F +yfgl+ 
  gi|91773462|ref|YP_566154.1|  83 APILRTLSMVAYHQPVVQSELVDMRGNSVYDHIRELKDRGFIEAVP----HGRTKLLQTTPLFADYFGLDR 149
                                   **********************************************....9******************86 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                      SMC_ScpB  49 elvevaggyrlvtkpelaev 68 
                                   el e+a+ y+lv+++ + e 
  gi|91773462|ref|YP_566154.1| 211 ELDELADVYKLVISKGYVEK 230
                                   57788888888877766443 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.73
                      SMC_ScpB  21 kilels.keeveealeeLkeeyeee 44 
                                   ++++ +  +e  e++ e++e+y   
  gi|91773462|ref|YP_566154.1| 259 NVADPErVKESIELITEMRERY--V 281
                                   4443334556666777777777..3 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     8e-07    0.0029      32      61 .]     102     131 ..      84     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8e-07
                                   HHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                        HTH_20  32 erldlskntlsyHLrvLeeagLvevvregr 61 
                                   e++d++ n++++H+r+L + g++e v +gr
  gi|91773462|ref|YP_566154.1| 102 ELVDMRGNSVYDHIRELKDRGFIEAVPHGR 131
                                   45699*********************9997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.12   4.1e+02      22      48 ..      17      43 ..       7      47 .. 0.84
   2 !   11.3   0.0   6.8e-05      0.25      31      60 ..     103     133 ..     101     140 .. 0.77
   3 ?   -2.9   0.0       1.8   6.6e+03      47      55 ..     223     231 ..     217     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                                  CCHHCHHCCCTTSSCHCHHHHHHHHHH CS
                          TrmB 22 patadeiaeelgvprskvYevLrsLed 48
                                    +++++a+ ++ +  +v  v+rsL++
  gi|91773462|ref|YP_566154.1| 17 AVDTQTLAKLINKSAKNVTPVIRSLME 43
                                  567889999999999999999999986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.8e-05
                                   CTTSSCHCHHHHHHHHHHCTSEEEES.STTT CS
                          TrmB  31 elgvprskvYevLrsLedkGlVerek.grpk 60 
                                    ++   ++vY+ +r+L+d+G++e ++ gr+k
  gi|91773462|ref|YP_566154.1| 103 LVDMRGNSVYDHIRELKDRGFIEAVPhGRTK 133
                                   56667789***************99844444 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.8
                                   HHCTSEEEE CS
                          TrmB  47 edkGlVere 55 
                                   ++kG+Ve++
  gi|91773462|ref|YP_566154.1| 223 ISKGYVEKV 231
                                   578999986 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 ?    5.6   0.0    0.0049        18      21      44 ..      20      43 ..      17      56 .. 0.91
   2 ?    5.3   0.0    0.0061        22      27      53 ..     103     129 ..      98     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0049
                B-block_TFIIIC 21 qsdLakeskqdprslfyrlksLek 44
                                  ++ Lak++++++++++ +++sL++
  gi|91773462|ref|YP_566154.1| 20 TQTLAKLINKSAKNVTPVIRSLME 43
                                  6789******************87 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0061
                B-block_TFIIIC  27 eskqdprslfyrlksLekkgLIvkqsi 53 
                                   ++++ ++s++ +++ L++ g+I+ +++
  gi|91773462|ref|YP_566154.1| 103 LVDMRGNSVYDHIRELKDRGFIEAVPH 129
                                   5678899***************99988 PP

>> YozD  YozD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.6   9.3e+03      19      27 ..     116     124 ..     115     126 .. 0.83
   2 ?    8.9   0.2    0.0005       1.8      26      47 ..     205     225 ..     202     234 .. 0.77
   3 ?    1.1   0.1      0.14     5e+02      21      52 ..     222     258 ..     219     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.6
                          YozD  19 kELvkRGyv 27 
                                   +EL  RG++
  gi|91773462|ref|YP_566154.1| 116 RELKDRGFI 124
                                   68999**98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0005
                          YozD  26 yvPaeeEleelADitFdYllek 47 
                                   y P+e+El+elAD+ +  ++ k
  gi|91773462|ref|YP_566154.1| 205 YDPTEDELDELADV-YKLVISK 225
                                   88***********7.5555655 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                          YozD  21 LvkRGyvPa.....eeEleelADitFdYllekciidE 52 
                                   ++ +Gyv +     + E+ e+   tFd ll+   + E
  gi|91773462|ref|YP_566154.1| 222 VISKGYVEKvinnyDGEIIEVRSTTFDDLLDAIKLLE 258
                                   566677654232226799999999***9998765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2276.96
//
Query:       gi|91773463|ref|YP_566155.1|  [L=285]
Description: condensin subunit ScpA [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-20   72.0   3.3    2.1e-18   67.1   3.3    2.2  1  SMC_ScpA  Segregation and condensation protein ScpA


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   3.3   1.2e-22   2.1e-18       1     238 [.      68     273 ..      68     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.2e-22
                                   HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeeleleelrdkLiar 81 
                                   L+ ++ ++++d+++++vtd+flayi+ l + ++l +s+  l+ as l+++K+  L + e+ve+  d +l+++e+       
  gi|91773463|ref|YP_566155.1|  68 LAKNGDINPWDIDIVEVTDKFLAYIEDL-KIMDLRISGRTLLYASILLRMKSTGLAQ-EEVEL--DDDLLDDEMDF----- 139
                                   567899**********************.************************9976.45555..56655666543..... PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...HHHH CS
                      SMC_ScpA  82 LleYrkykeeaklfkeleaerlksfskarsdleefikeveevavkieksvfklieafnkllkrakivalaekqiseleisi 162
                                         y+ e     +l + r +   + +++l+e+i e+++ + k+e         +  +++r   v+ + ++   l i++
  gi|91773463|ref|YP_566155.1| 140 ------YDIEEYPVPKLPIRRTAT--R-PVTLQELITELKKAE-KVETR------RKDRRIRRRLEVFDRVTTDDVLGIAH 204
                                   ......455555566777666666..5.5**********9854.78877......678899999889999988899***** PP

                                   HHHHHHHH...............HHHTS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEESSTTS-EEE CS
                      SMC_ScpA 163 eeqleellaqleqflqarlkevLldlrswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQeeflddLqv 238
                                   ee     +      l ++l+e++   r  v +s+L+      ++ e   +++ lL L ++++v l+Qee +++L+v
  gi|91773463|ref|YP_566155.1| 205 EEDIRGRVD----TLYTSLEELF-RTRDEVMFSDLVDW--SGSRSERLMTYISLLFLASEKKVLLAQEELFGELFV 273
                                   ***999885....7889998544.44799********9..9999999***************************98 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:                      422  (0.0235373); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1960.63
//
Query:       gi|91773464|ref|YP_566156.1|  [L=1174]
Description: condensin subunit Smc [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  232.8  14.3    8.1e-69  231.4  14.3    1.9  1  SMC_N          RecF/RecN/SMC N terminal domain
    1.5e-34  118.8   0.2    1.3e-33  115.8   0.0    2.7  3  SMC_hinge      SMC proteins Flexible Hinge Domain
      1e-13   52.2  20.2      1e-13   52.2  20.2    5.9  4  AAA_23         AAA domain
      3e-08   33.8  30.7      3e-08   33.8  30.7    4.3  3  AAA_15         AAA ATPase domain
    3.8e-08   33.5   0.3     0.0001   22.2   0.1    4.2  5  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    2.9e-07   30.1   0.0    6.4e-07   29.0   0.0    1.6  1  AAA_29         P-loop containing region of AAA domain
  ------ inclusion threshold ------
        0.6    8.2  83.6       0.26    9.4   4.9    5.4  5  EzrA           Septation ring formation regulator, EzrA
        1.6    9.3 108.4       0.75   10.3   1.4    8.5  7  APG6_N         Apg6 coiled-coil region


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 !  231.4  14.3   3.6e-72   8.1e-69       1     219 [.       2    1166 ..       2    1167 .. 1.00

  Alignments for each domain:
  == domain 1  score: 231.4 bits;  conditional E-value: 3.6e-72
                                    EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaev 79  
                                    ++k++e  nFks+ gk+v++pf + ft i GpNGSGKsn++d ilFvLG +++++lr+ekl+dli++ ++ ++ ++a+v
  gi|91773464|ref|YP_566156.1|    2 YIKEIEFINFKSF-GKKVKIPFFDDFTTISGPNGSGKSNIIDGILFVLGLSNSRTLRAEKLTDLIYNGDKAKRPDFAQV 79  
                                    79***********.5**************************************************************** PP

                                    EEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STT.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                         SMC_N   80 eitfdnedkklkiekeevsisrrvkrkge...seykingkevtkkevsellesagiske.................... 135 
                                    +i fdn+d++++++++ev isr++ ++++   s +++ngk v+ +e+++ l++a++++e                    
  gi|91773464|ref|YP_566156.1|   80 TIKFDNTDREMPVDADEVIISRKIRETDNgyySYFYFNGKAVSLTELHNYLSKARVTPEgynvvmqgdvtriitmtpne 158 
                                    ************************9988878889999****************************************** PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  159 rrkiideiagvaefdnkrdralneleivrerveradilieevekqleklklerdqavkyqalkqekmkfegfvllsklk 237 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  238 dakvelenvdkdisfkkevqeklqlsieerkeklagiekelteltseiqrmgedeqiqvkrdieeikgevsrcvnsiel 316 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  317 adneiedidsrrkkafldiegtknkindvnsklseeslrkdsilseiserktermilqsrisdvdekfaqtrdellvfk 395 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  396 seletvkndkselmrqedrlldslrrksaevrdieneitdakgksessdsdtksaqydieklteqinahtrdlddlesn 474 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  475 cfqiksvvtdldvtlrkhqqdyallearvraaedtsnyskavdmiiaekkhhglpgiygtiaelgsvdqkyanalsvaa 553 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  554 ggrmqavvvetdedasraihflkqqrggratflplnkmesrrpykdlsdrkgvvgyaidlidfeykfeaafwyvfrdtl 632 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  633 ivdtlenarrligglrmvtlegevieksgamtggsmgrnsglsfaaaekdklfkiaeqltefesrrntaikkldavegh 711 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  712 iadinreihefekeiskkemifeeiggraerltqlieaknneleqiegeraklreemeqvasrkvdvegrskeleaeia 790 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  791 vldeklsdsevpelnkqadrideelrrldgrirdieadinalnldheyaskkieddrqlikemeekksthrvrvaefkt 869 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  870 kiaeleltledkqkreeelteelrdmqqkralkqteynlaekdfasvrsklddadkammvleatrnalvdqtkdlkeel 948 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|91773464|ref|YP_566156.1|  949 vrrgieevedvpnyetvstriasiekamerlepvnmraideydevdgrvvdlktrrailfnereqiltridqyetlkkd 1027
                                    ******************************************************************************* PP

                                    .......................................................CS-HHHHHHHHHHHHHHHHCCS-- CS
                                    .......................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  136 .......................................................lLSgGektLvalaLlfAiqkvkpa 159 
                                                                                           ++SgGek+L+ala++fAiq+++pa
  gi|91773464|ref|YP_566156.1| 1028 afmetfhginepfkeifhelsdgsgelvlddndepfnggltlraqpkektlqrleAMSGGEKSLTALAFVFAIQQYRPA 1106
                                    ******************************************************************************* PP

                                    SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  160 plyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkvengvs 219 
                                    p+y +Deid+ LD +n  +va+++k+++ +aQfiv+slr+ m+e a++++gv ++en+++
  gi|91773464|ref|YP_566156.1| 1107 PFYAFDEIDMFLDGANADRVAQRVKKAKGKAQFIVVSLRKPMIEAAERTIGVAMQENNIT 1166
                                    ******************************************************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 !  115.8   0.0   5.7e-37   1.3e-33       2     116 ..     529     643 ..     528     644 .. 0.96
   2 ?   -3.6   0.0         6   1.3e+04      69      92 ..     712     752 ..     681     756 .. 0.55
   3 ?   -1.6   0.0       1.4   3.2e+03      40      68 ..    1122    1148 ..    1119    1161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 5.7e-37
                     SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgavp 82 
                                   +g++G++a+l +vd++y  A+++a+g+r+qa+vve++e+a ++i flk++++gratflpl++++++++ ++  d++  +++
  gi|91773464|ref|YP_566156.1| 529 PGIYGTIAELGSVDQKYANALSVAAGGRMQAVVVETDEDASRAIHFLKQQRGGRATFLPLNKMESRRPYKDLSDRKGVVGY 609
                                   79************************************************************999988888888777**** PP

                     SMC_hinge  83 lidlvevddelrkalryllgdtlvvdsldeAeel 116
                                   +idl++++ ++++a+ y+++dtl+vd+l++A++l
  gi|91773464|ref|YP_566156.1| 610 AIDLIDFEYKFEAAFWYVFRDTLIVDTLENARRL 643
                                   ********************************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6
                     SMC_hinge  69 kadgandkns.................gavplidlvevdde 92 
                                    ad ++++++                 +a++l++l+e +++
  gi|91773464|ref|YP_566156.1| 712 IADINREIHEfekeiskkemifeeiggRAERLTQLIEAKNN 752
                                   44444443334444455555667777788888888888776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                     SMC_hinge   40 takkiieflkkknagratflpldrikqkn 68  
                                     a +  + +kk+ +g+a+f++ + +++++
  gi|91773464|ref|YP_566156.1| 1122 NADRVAQRVKKA-KGKAQFIVVS-LRKPM 1148
                                    677778888999.9******995.45444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2  20.2   4.6e-17     1e-13       2     200 .]       6     286 ..       5     286 .. 0.63
   2 ?   -7.2  24.4         8   1.8e+04      75     193 ..     296     462 ..     286     469 .. 0.35
   3 ?   -6.3  16.4         8   1.8e+04     108     180 ..     720     796 ..     658     830 .. 0.39
   4 ?   -8.3  23.2         8   1.8e+04      56     192 ..     813     969 ..     799    1027 .. 0.62

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.6e-17
                        AAA_23   2 Lkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfen 81 
                                   ++  nf+sf ++++i F + +t I+GpNG+GK+ i+d i ++L+   +r+ r ++    ++ +  ++++k + ++++t++ 
  gi|91773464|ref|YP_566156.1|   6 IEFINFKSFgKKVKIPFFDDFTTISGPNGSGKSNIIDGILFVLGLSNSRTLRAEK---LTDLIYNGDKAKRPDFAQVTIKF 83 
                                   7889*****77788******************************99988888764...56666666667777775555555 PP

                        AAA_23  82 kdgry............................................................trsiererelskkkgk 102
                                   +++++                                                            tr+i+ + ++++k  +
  gi|91773464|ref|YP_566156.1|  84 DNTDRempvdadeviisrkiretdngyysyfyfngkavsltelhnylskarvtpegynvvmqgdvTRIITMTPNERRKIID 164
                                   444444577776666666666666666888888888888888888888888888888777777773333333333333333 PP

                        AAA_23 103 tt.........kkaklellei.deleqfisellgskkiilnlilflgqer...feefelkdkke................. 153
                                   ++         ++ +l++lei +e+ ++ + l++  +++l+ + +  ++    +   +lk   +                 
  gi|91773464|ref|YP_566156.1| 165 EIagvaefdnkRDRALNELEIvRERVERADILIEEVEKQLEKLKLERDQAvkyQ---ALK---Qekmkfegfvllsklkda 239
                                   332222221112222222222344444444455555555555554444443332...221...022233366666644455 PP

                        AAA_23 154 ..rleelekeleeledekkllekleqekekekeleeleeeleeilkele 200
                                     +le++ k++  +++++++l+    ++e++++l  +e+el+e+++e++
  gi|91773464|ref|YP_566156.1| 240 kvELENVDKDISFKKEVQEKLQL--SIEERKEKLAGIEKELTELTSEIQ 286
                                   56888888888888887777774..557889999999999999999986 PP

  == domain 2  score: -7.2 bits;  conditional E-value: 8
                        AAA_23  75 veltfenkdgry..........trsiererelskkkgkttkkaklellei.....deleqfisellgskkiilnlilflgq 140
                                   v++++e ++g+           + +ie+         ++++k+++  +e      ++ + ++se+  +k++il+ i+  + 
  gi|91773464|ref|YP_566156.1| 296 VKRDIEEIKGEVsrcvnsielaDNEIED--------IDSRRKKAFLDIEGtknkiNDVNSKLSEESLRKDSILSEISERKT 368
                                   5555555555543332221111111111........111122211111111222244445555555555555555555555 PP

                        AAA_23 141 er.............feefelkdkkerleelekeleeledekkllekl................................. 175
                                   er             f     +++ ++l  ++ ele+ +++k++l ++                                 
  gi|91773464|ref|YP_566156.1| 369 ERmilqsrisdvdekF-----AQTRDELLVFKSELETVKNDKSELMRQedrlldslrrksaevrdieneitdakgksessd 444
                                   5544433333332110.....222333333333333333333333333233322212112111111111222233333333 PP

                        AAA_23 176 eqekekekeleeleeele 193
                                    + k+ +  +e+l e+++
  gi|91773464|ref|YP_566156.1| 445 SDTKSAQYDIEKLTEQIN 462
                                   444555556666666666 PP

  == domain 3  score: -6.3 bits;  conditional E-value: 8
                        AAA_23 108 klelleideleqfisellgskkiilnlilflgqer..feefelkdkkerleelekeleeledekkllekl...eqeke 180
                                    +++ ei++ +++i e++g + ++l++++  +  +  + e e+++  e++e++   + + e + k+le++   ++ek 
  gi|91773464|ref|YP_566156.1| 720 HEFEKEISK-KEMIFEEIGGRAERLTQLIEAKNNEleQIEGERAKLREEMEQVASRKVDVEGRSKELEAEiavLDEKL 796
                                   111111122.22222233333333322222222221111111122333333333333333333333333344433333 PP

  == domain 4  score: -8.3 bits;  conditional E-value: 8
                        AAA_23  56 rgfeksdveiesegkvkayveltfenkdgrytrsiererelskkkgkttkka....klelleideleqfisellgskkiil 132
                                   + + + d +i + + + + + l+ e+ ++    +ie++r+l+k+++++++      ++++++i+ele +++++ +++++  
  gi|91773464|ref|YP_566156.1| 813 EELRRLDGRIRDIEADINALNLDHEYASK----KIEDDRQLIKEMEEKKSTHrvrvAEFKTKIAELELTLEDKQKREEELT 889
                                   45555555666666666667777777777....599999999988888876666666777777777777777666666655 PP

                        AAA_23 133 nlilflgqer........feefelkdkke........rleelekeleeledekkllekl.eqekekek...........el 185
                                   + +  ++q+r         +        e        +l+++ k++  le++++ l ++ +++ke+             ++
  gi|91773464|ref|YP_566156.1| 890 EELRDMQQKRalkqteynLA--------EkdfasvrsKLDDADKAMMVLEATRNALVDQtKDLKEELVrrgieevedvpNY 962
                                   55666666663333223322........12223444466666666666666666555553222222223333333333444 PP

                        AAA_23 186 eeleeel 192
                                   e++  ++
  gi|91773464|ref|YP_566156.1| 963 ETVSTRI 969
                                   4444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8  30.7   1.3e-11     3e-08       1     261 [.       1     389 [.       1     517 [. 0.69
   2 ?   -4.0  10.0         4   9.1e+03     138     280 ..     712     842 ..     667     846 .. 0.46
   3 ?   -1.5  14.5      0.69   1.6e+03     108     262 ..     811     959 ..     775    1116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.3e-11
                        AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn......................kkvi 58 
                                   M+Ik+i+  NF+s+ + v+i++ +++t++ G+N+sGKS+i++ + + l  + +                        +   
  gi|91773464|ref|YP_566156.1|   1 MYIKEIEFINFKSFGKkVKIPFFDDFTTISGPNGSGKSNIIDGILFVLGLSNSRTlraekltdliyngdkakrpdfaQ--- 78 
                                   **************888***************************9999988333355544444444444333333331... PP

                        AAA_15  59 kiekedleifeniseskdikIdvef........................................................ 83 
                                                       ++++f                                                        
  gi|91773464|ref|YP_566156.1|  79 --------------------VTIKFdntdrempvdadeviisrkiretdngyysyfyfngkavsltelhnylskarvtpeg 139
                                   ....................4444444556666666666677777777799999999999999999999999999999999 PP

                        AAA_15  84 .................................aek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkkne 130
                                                                    ++k + a + e +  +++ + ad+l+++ e++l k++ ++++++k + 
  gi|91773464|ref|YP_566156.1| 140 ynvvmqgdvtriitmtpnerrkiideiagvaefDNKrDRALN-ELEIVRERVERADILIEEVEKQLEKLKLERDQAVKYQA 219
                                   999999999999999999999999999998865222322222.23333455566788999999999999999999999999 PP

                        AAA_15 131 lsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee........................... 184
                                   l++ek + e      +l++ k e ++  +++++++ke ++kl   +ee ++k +                           
  gi|91773464|ref|YP_566156.1| 220 LKQEKMKFEGFVLLSKLKDAKVELEN-VDKDISFKKEVQEKLQLSIEERKEKLAgiekelteltseiqrmgedeqiqvkrd 299
                                   99999888888888777777666665.555666888888888887777777666666777766665555555555665665 PP

                        AAA_15 185 .........elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl....eeelteklkeiqeklkei 252
                                            +  n+++ a  +++ i ++R+    d e +++ ++ + +k++ee+l++      + e + +   +q+ +++ 
  gi|91773464|ref|YP_566156.1| 300 ieeikgevsRCVNSIELADNEIEDIDSRRKKAFLDIEGTKNKINDVNSKLSEESLRKDSilseISERKTERMILQSRISDV 380
                                   555555555444444444444444444444444444444444444444444444444444444333333333333333333 PP

                        AAA_15 253 dkklaeelk 261
                                   d+k+a+   
  gi|91773464|ref|YP_566156.1| 381 DEKFAQTRD 389
                                   333333333 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4
                        AAA_15 138 vekkkskkelpkekeeklekekeelkid..kedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkss 216
                                   + ++  ++e+ ++++e ++ke    +i    e l+ li+  ++ l+  +   +   +++++     a R+v+ e   k+ +
  gi|91773464|ref|YP_566156.1| 712 IADI--NREIHEFEKEISKKEMIFEEIGgrAERLTQLIEAKNNELE--Q--IEGERAKLREEMEQVASRKVDVEGRSKELE 786
                                   2222..2333333333333333333333225555555552222221..1..223333333333444444444444444444 PP

                        AAA_15 217 llgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkik.kfnykgkk 280
                                   + +++++++l+++       el++++++i+e+l+ +d+ +     ++++ +i+ ++ + +y +kk
  gi|91773464|ref|YP_566156.1| 787 AEIAVLDEKLSDS----EVPELNKQADRIDEELRRLDGRI-----RDIEADINALNlDHEYASKK 842
                                   4444444444442....35677888888888888888888.....66666666666666666655 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.69
                        AAA_15 108 lkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee.... 184
                                   ++++ ++l+ +i+d + ++++ +l+                          +e  +++ ed + lik++ee+++ +     
  gi|91773464|ref|YP_566156.1| 811 IDEELRRLDGRIRDIEADINALNLD--------------------------HEYASKKIEDDRQLIKEMEEKKSTHRvrva 865
                                   3334444555555555555544444..........................444444444444555555555544444111 PP

                        AAA_15 185 ..............elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklke 251
                                                  +++  +++ ++l+  + kR  ++++++  ++ + ++ +k+ +        ++  + l+ + ++l +
  gi|91773464|ref|YP_566156.1| 866 efktkiaeleltleDKQKREEELTEELRDMQQKRALKQTEYNLAEKDFASVRSKLDD-------ADKAMMVLEATRNALVD 939
                                   111111111111111112223455555556666666666666666666665555544.......68999999999999999 PP

                        AAA_15 252 idkklaeelk.........k 262
                                   + k+l+eel           
  gi|91773464|ref|YP_566156.1| 940 QTKDLKEELVrrgieevedV 959
                                   99999998874444333330 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   4.6e-08    0.0001       1      26 [.      26      61 ..      26     129 .. 0.69
   2 ?   -1.7   0.4      0.88     2e+03     107     199 ..     171     274 ..     140     336 .. 0.65
   3 ?   -1.6   0.7      0.84   1.9e+03     133     191 ..     321     379 ..     294     452 .. 0.57
   4 ?   -3.1   0.4       2.4   5.4e+03     102     149 ..     823     870 ..     779     926 .. 0.54
   5 !   18.8   0.0   5.1e-07    0.0011     165     296 ..    1044    1143 ..     971    1143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.6e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..........d 26
                                  ++ + GpNgsGKSn++d + ++ +l          +
  gi|91773464|ref|YP_566156.1| 26 FTTISGPNGSGKSNIIDGILFVLGLsnsrtlraekL 61
                                  68899*****************88655443333331 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.88
                        AAA_21 107 eedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke...........rigllnifadyf 176
                                   e+d++ ++a ++ ++v+++++++ +++e+ ++q +k+ ++ +    + +l ++++  e           +  l n  +d  
  gi|91773464|ref|YP_566156.1| 171 EFDNKRDRALNELEIVRERVERADILIEEVEKQLEKLKLERDQAVKYQALKQEKMKFEgfvllsklkdaKVELENVDKDIS 251
                                   556666666666666666666666666666666665555444444444444444444444444444444555555555555 PP

                        AAA_21 177 gfakekrllqrlvrslklveiel 199
                                   +++++++ lq  + ++k+  + +
  gi|91773464|ref|YP_566156.1| 252 FKKEVQEKLQLSIEERKEKLAGI 274
                                   55555555555555555555444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.84
                        AAA_21 133 sepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrs 191
                                   +e++d  ++ka++di  +++++++ + +l +e  +  +i  +    + e+ +lq +++ 
  gi|91773464|ref|YP_566156.1| 321 IEDIDSRRKKAFLDIEGTKNKINDVNSKLSEESLRKDSILSEISERKTERMILQSRISD 379
                                   44444444444444444444444444444444333333333333333333333333333 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.4
                        AAA_21 102 krsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltdits 149
                                   ++++ ++++ n +++++ + + + ++  ++ +e  + ++++++ + t+
  gi|91773464|ref|YP_566156.1| 823 RDIEADINALNLDHEYASKKIEDDRQLIKEMEEKKSTHRVRVAEFKTK 870
                                   444444444444444444444444444444444444444444444444 PP

  == domain 5  score: 18.8 bits;  conditional E-value: 5.1e-07
                        AAA_21  165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkr 243 
                                     + l + +++++  ++  ++ ++l+ + ++ e  l+ l+                                 +S G k+
  gi|91773464|ref|YP_566156.1| 1044 FHELSDGSGELVLDDNDEPFNGGLTLRAQPKEKTLQRLE--------------------------------AMSGGEKS 1090
                                    666667777777777777777777777777777777775................................56****** PP

                        AAA_21  244 l.l.alltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                    l + a++ a+ + ++  +++++DE++ +L+ +   r+++ +k+++  +aQ+i+++
  gi|91773464|ref|YP_566156.1| 1091 LtAlAFVFAIQQYRPA-PFYAFDEIDMFLDGANADRVAQRVKKAKG-KAQFIVVS 1143
                                    *743666666666666.************************99988.9****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 !   29.0   0.0   2.9e-10   6.4e-07       2      46 ..       4      48 ..       3      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.9e-10
                        AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                  k+++ +N  +f +  +i++  +++t ++Gp+GsGKS ++D i ++L
  gi|91773464|ref|YP_566156.1|  4 KEIEFINFKSFGKkVKIPFF-DDFTTISGPNGSGKSNIIDGILFVL 48
                                  6899*********8889997.569*******************998 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6  22.1     0.027        60     304     463 ..     186     352 ..     182     365 .. 0.82
   2 ?    2.2  13.6     0.018        41     374     489 ..     377     490 ..     336     503 .. 0.78
   3 ?    7.6   6.1   0.00041      0.92     341     417 ..     700     777 ..     698     789 .. 0.91
   4 ?    9.4   4.9   0.00012      0.26      76     154 ..     781     859 ..     776     861 .. 0.92
   5 ?    4.6  12.5    0.0033       7.4      89     208 ..     857     981 ..     853     994 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.027
                                   HTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTH.HHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHH CS
                          EzrA 304 veknlkelkeklehlekqnkelkeeldrlkqsYeLseeelekl.relekelkelekdyeeleekleekkvaYSelqeelee 383
                                   v +++++    +e++ekq+++lk e d+  +   L++e+++     l ++lk+ + ++e+++++++ kk +  +lq  +ee
  gi|91773464|ref|YP_566156.1| 186 VRERVERADILIEEVEKQLEKLKLERDQAVKYQALKQEKMKFEgFVLLSKLKDAKVELENVDKDISFKKEVQEKLQLSIEE 266
                                   67888888999****************9998888877777643146789******************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHSSS.....-SS-S-TTTHHHHSTTTSTTTHHHHH CS
                          EzrA 384 leekleeieekqeeileslkslrkdEk.rAreqldeikkelkeikrkiek.....snLPgiPesyleelkeasdeieelak 458
                                    +ekl+ ie+++ e+  +++ + +dE+ + ++ ++eik e++ + ++ie      + + +  ++ + +++ ++++i++++ 
  gi|91773464|ref|YP_566156.1| 267 RKEKLAGIEKELTELTSEIQRMGEDEQiQVKRDIEEIKGEVSRCVNSIELadneiEDIDSRRKKAFLDIEGTKNKINDVNS 347
                                   **************************8689************999998741111134555555666666666777777777 PP

                                   HHT-T CS
                          EzrA 459 eLekk 463
                                   +L+++
  gi|91773464|ref|YP_566156.1| 348 KLSEE 352
                                   77666 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.018
                                   -STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS-S-TTTHHHHSTTTSTTTH CS
                          EzrA 374 YSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLPgiPesyleelkeasdeie 454
                                    S++ e++ ++ ++l  +++++e+++++ ++l ++E r  ++l + + e+++i+++i + +  g +es  ++ k a+  ie
  gi|91773464|ref|YP_566156.1| 377 ISDVDEKFAQTRDELLVFKSELETVKNDKSELMRQEDRLLDSLRRKSAEVRDIENEITDAK--GKSESSDSDTKSAQYDIE 455
                                   4667778888888888888888999999999999999999999999999999999999998..999999999999999999 PP

                                   HHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHHH CS
                          EzrA 455 elakeLekkpinikevnkrldeardlveklyektn 489
                                   +l ++++    +++++++ + +++++v  l+ +  
  gi|91773464|ref|YP_566156.1| 456 KLTEQINAHTRDLDDLESNCFQIKSVVTDLDVTLR 490
                                   99999999999999999999999999998877655 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00041
                                   TTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHH CS
                          EzrA 341 eeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkd.EkrAreqld 417
                                   + ++kl+ +e ++ +++++++e e+++++k++ + e+  + e+l++ +e+ ++++e+i+ + ++lr++ E+ A +++d
  gi|91773464|ref|YP_566156.1| 700 TAIKKLDAVEGHIADINREIHEFEKEISKKEMIFEEIGGRAERLTQLIEAKNNELEQIEGERAKLREEmEQVASRKVD 777
                                   56899999*********************************************************9874777777765 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00012
                                   HTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--T CS
                          EzrA  76 klpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkklla 154
                                   + +e+e ++  ++e l+  ++ +++k+ + ++eel +++ +i++i ++++ l   +e  +++ie+ ++  +e+++k  +
  gi|91773464|ref|YP_566156.1| 781 RSKELEAEIAVLDEKLSDSEVPELNKQADRIDEELRRLDGRIRDIEADINALNLDHEYASKKIEDDRQLIKEMEEKKST 859
                                   568999*************************************************************999999887665 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.0033
                                   --S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTH...HHHHHHHH CS
                          EzrA  89 elldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfs...ygealeel 166
                                   +++++ ++ + k+k+aele +l++ +++ +++ eel++++++   +++e++ +++++ ++r kl +  ++   ++ + ++l
  gi|91773464|ref|YP_566156.1| 857 KSTHRVRVAEFKTKIAELELTLEDKQKREEELTEELRDMQQKRALKQTEYNLAEKDFASVRSKLDDADKAmmvLEATRNAL 937
                                   56789999********************************************************98887622256788899 PP

                                   HHHHHHH------..----------HHHHHHHHHHHHHHHHHHH CS
                          EzrA 167 ekqleniekefse..feeltengdyveakeilkkleeeidelee 208
                                    +q +++++e+    +ee+ +  +y++++  + ++e+ +++le 
  gi|91773464|ref|YP_566156.1| 938 VDQTKDLKEELVRrgIEEVEDVPNYETVSTRIASIEKAMERLEP 981
                                   999999999986544899999999**999999999999999985 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.9      0.01        23      51     116 ..     161     228 ..     123     229 .. 0.77
   2 ?    4.0  21.6     0.031        69       7     102 ..     193     296 ..     190     323 .. 0.76
   3 ?   -0.1  12.8      0.57   1.3e+03      47     126 ..     354     433 ..     295     437 .. 0.59
   4 ?    9.6   9.4   0.00056       1.3      18     127 ..     398     504 ..     395     509 .. 0.56
   5 ?   10.3   1.4   0.00033      0.75      46      95 ..     681     730 ..     653     736 .. 0.89
   6 ?    7.3   8.5    0.0028       6.4      49      97 ..     747     795 ..     734     798 .. 0.89
   7 ?    3.9  14.3     0.033        75      12     122 ..     872     979 ..     871     988 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.01
                        APG6_N  51 eleee...leklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellele 116
                                   ++ +e   +++ +++++++l+eL+ + +  e+ +  +++ e++le+l+ e ++ + +y++l+ e++++e
  gi|91773464|ref|YP_566156.1| 161 KIIDEiagVAEFDNKRDRALNELEIVRERVERADILIEEVEKQLEKLKLERDQAV-KYQALKQEKMKFE 228
                                   444443337788899999999999999999999999*********9999988877.5777777777765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.031
                        APG6_N   7 tdlLleeldkqleqaekerdaYeeflkklkkekkeeek.........qdeeleeleeeleklekeeeelleeLkelekere 78 
                                   +d+L+ee++kqle+++ erd+  ++ + lk+ek + e           + ele+ +++++  ++ +e+l+  ++e +++ +
  gi|91773464|ref|YP_566156.1| 193 ADILIEEVEKQLEKLKLERDQAVKYQA-LKQEKMKFEGfvllsklkdAKVELENVDKDISFKKEVQEKLQLSIEERKEKLA 272
                                   79***********************87.77776666569*88888886667777777777777777777777777777777 PP

                        APG6_N  79 eleaelaaleeelealeeeeerfw 102
                                    +e+el +l++e +++ e+e+  +
  gi|91773464|ref|YP_566156.1| 273 GIEKELTELTSEIQRMGEDEQIQV 296
                                   777777777777777777766544 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.57
                        APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqy 126
                                      +++  e+++ + e+  l++ + +++++ ++ ++el   ++ele +++++ + +r+   l   l ++  e + +e+++
  gi|91773464|ref|YP_566156.1| 354 LRKDSILSEISERKTERMILQSRISDVDEKFAQTRDELLVFKSELETVKNDKSELMRQEDRLLDSLRRKSAEVRDIENEI 433
                                   22234455566666666666666666666666666666666666666666666666666666666666666666666665 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00056
                        APG6_N  18 leqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                                   le++++++ ++++ +++l ++ + ++    e++++e+e+ + + + e+  +  k ++   e+l ++++a ++ l++le + 
  gi|91773464|ref|YP_566156.1| 398 LETVKNDKSELMRQEDRLLDSLRRKS---AEVRDIENEITDAKGKSESSDSDTKSAQYDIEKLTEQINAHTRDLDDLESNC 475
                                   55555555555555555555544433...4666666666666666666666666666666666666666666666666666 PP

                        APG6_N  99 erfwreynelqlelleleeeldsleaqye 127
                                    +  +   +l+++l +++++ + lea+++
  gi|91773464|ref|YP_566156.1| 476 FQIKSVVTDLDVTLRKHQQDYALLEARVR 504
                                   66666666666666666666666666655 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00033
                        APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                   +++l ++ e+l + e+ +++++++L+++e + +++++e+++ e+e +++e
  gi|91773464|ref|YP_566156.1| 681 KDKLFKIAEQLTEFESRRNTAIKKLDAVEGHIADINREIHEFEKEISKKE 730
                                   5677789999***********************************99876 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0028
                        APG6_N  49 leeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                   +e+ ++ele++e e+++l ee++++ + + ++e   ++le+e + l+e+
  gi|91773464|ref|YP_566156.1| 747 IEAKNNELEQIEGERAKLREEMEQVASRKVDVEGRSKELEAEIAVLDEK 795
                                   6788999************************************999986 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.033
                        APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                    el+  le+ +k  ++++e l+ +++++  +   ++e + +e++++ ++++ +++ + +  le++r +l ++ ++l+eel 
  gi|91773464|ref|YP_566156.1| 872 AELELTLEDKQKREEELTEELRDMQQKRALK---QTEYNLAEKDFASVRSKLDDADKAMMVLEATRNALVDQTKDLKEELV 949
                                   5778889999999999999999999886664...58999999*************************************** PP

                        APG6_N  93 aleeeeerfwreynelqlelleleeeldsl 122
                                   ++  ee + +  y   ++  ++ e+ ++ l
  gi|91773464|ref|YP_566156.1| 950 RRGIEEVEDVPNYETVSTRIASIEKAMERL 979
                                   **9999999999999988888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2151  (0.119973); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        87  (0.00485247); 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: 2.56u 0.43s 00:00:02.99 Elapsed: 00:00:00.73
# Mc/sec: 4876.82
//
Query:       gi|91773465|ref|YP_566157.1|  [L=258]
Description: hypothetical protein Mbur_1500 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.3   1.9       0.13   12.4   1.9    1.4  1  COG2      COG (conserved oligomeric Golgi) complex component,
       0.13   12.1   1.9       0.26   11.1   1.9    1.5  1  SKA2      Spindle and kinetochore-associated protein 2


Domain annotation for each model (and alignments):
>> 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 ?   12.4   1.9   1.4e-05      0.13      30      93 ..      19      82 ..       6      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                          COG2 30 slrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvrekls 93
                                  +   ++e +++ l++++++  ++d+++ +++ ++L  ++++++e++s+++ +++++ + +++l 
  gi|91773465|ref|YP_566157.1| 19 EKEGEMEVMSTTLRDSIMRELRNDLKNDLDINNRLNKIEQDVKELSSNISGMMDELLDQKSQLR 82
                                  5567899999************************************************999986 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 ?   11.1   1.9   2.9e-05      0.26       4      69 ..      10      79 ..       9      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.9e-05
                          SKA2  4 vdklealFqkaesdLdyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqc....eellaekk 69
                                  ++ le  + + e ++++ +  L + ++++++++ +N + + +rl+k+ +++++L++++    +ell +k 
  gi|91773465|ref|YP_566157.1| 10 IERLERKLFEKEGEMEVMSTTLRDSIMRELRNDLKNDLDINNRLNKIEQDVKELSSNIsgmmDELLDQKS 79
                                  577888777889999*************************************998875111145555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1496.12
//
Query:       gi|91773466|ref|YP_566158.1|  [L=888]
Description: SMC-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-22   78.6   7.4    8.5e-22   78.6   7.4    4.7  2  AAA_23          AAA domain
    1.6e-21   76.8   0.0      3e-21   75.9   0.0    1.5  1  SMC_N           RecF/RecN/SMC N terminal domain
    4.6e-10   39.7   9.7    4.6e-10   39.7   9.7    3.3  1  AAA_15          AAA ATPase domain
    2.4e-08   34.2   7.3    0.00016   21.6   0.0    3.8  3  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    2.4e-05   24.0   0.0    6.6e-05   22.6   0.0    1.7  2  AAA_29          P-loop containing region of AAA domain
    0.00017   21.7   0.0      0.048   13.9   0.0    2.6  2  SbcCD_C         Putative exonuclease SbcCD, C subunit
     0.0031   17.1   0.0      0.011   15.3   0.0    1.9  1  AAA_27          AAA domain
      0.007   16.8   0.0      0.024   15.0   0.0    2.0  1  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
       0.05   13.4   2.0        0.5   10.1   0.0    3.4  3  MukB            MukB N-terminal
      0.055   13.3   1.1        8.5    6.1   0.0    3.3  2  USP8_interact   USP8 interacting
       0.87    9.5   8.2        1.3    8.9   1.8    4.7  3  Rad50_zn_hook   Rad50 zinc hook motif
        2.3    8.2   5.5        4.4    7.3   1.7    3.7  2  Pox_A_type_inc  Viral A-type inclusion protein repeat
        7.7    6.0  14.4       0.45   10.0   0.1    4.2  4  Fzo_mitofusin   fzo-like conserved region
        8.5    6.2  37.2       0.65    9.8   9.2    4.7  5  DUF724          Protein of unknown function (DUF724)


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   7.4   6.6e-25   8.5e-22       1     193 [.       5     273 ..       5     293 .. 0.74
   2 ?   -0.2   9.6      0.96   1.2e+03     111     196 ..     351     452 ..     311     458 .. 0.65

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 6.6e-25
                        AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfen 81 
                                   ++++en+rs+ d +i F++g+t+++G NG+GK+++l+A+  +L+g      r  +++f+ sd+    +g +ka++ ++fen
  gi|91773466|ref|YP_566158.1|   5 RVRVENIRSYIDLDISFDDGVTVVSGVNGSGKSSLLEACFTGLFGS-----RALSKDFVISDIIR--KGATKASIVVDFEN 78 
                                   689******************************************4.....4445689****984..56999********* PP

                        AAA_23  82 kdgrytrsiererelskkkgkttkkaklellei.......deleqfisellgskkiilnlilflgqerfeefelkdkke.. 153
                                   +++  ++sie+  ++   +gk  ++   +++++       +++ + ++ ll+ +++  ++++++ q++ + + ++++k+  
  gi|91773466|ref|YP_566158.1|  79 QGN--YYSIEQGYKVDARSGKASNNRSVFKVNDevmvdqaNQTYEAVKALLKMDEEAYTNCVYIRQGEIDVLINAKTKDrq 157
                                   **9..58999988888888888887777777776677677777888888*******************8788887777788 PP

                        AAA_23 154 ................................................................................. 153
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 158 rmidgllqigkleeyrerassarvgvgrhqreadsrlkdniadievledskpyqllnglrtevtgiekaildlgskkerak 238
                                   888999999999999999999999999988888887777888888888888888777777755533333333333333222 PP

                        AAA_23 154 ...rleelekeleeledekkllekl............eqekekekeleeleeele 193
                                      +                                 eq+k+   e+++ + ++ 
  gi|91773466|ref|YP_566158.1| 239 eliE--------------------SigdrigkyseilEQKKKADSEIKDFKTNIS 273
                                   2220....................1344454444444444444444444444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.96
                        AAA_23 111 lleideleqfisellgskkiilnlilflgqerfeefel...kdkke..............rleelekeleeledekkllek 174
                                   +    +l++++++++gs  i+++ ++f + + ++++e+                       +e+  +++++++ + ++ ++
  gi|91773466|ref|YP_566158.1| 351 NNFLLNLNKQLNNSVGSIRIRNEKVVFAKNDLKKYLEDveqI---GsfiqnkygdakelgFVEDKLDQIDDISGFVNEKQT 428
                                   333367889999999999999999999999998887775550...344444555555333666666666666665555555 PP

                        AAA_23 175 l..eqekekekeleeleeeleeil 196
                                   +   +eke  ++  ele+++++ +
  gi|91773466|ref|YP_566158.1| 429 KlhGKEKEISATVVELEKKIQKSK 452
                                   543377788888888888888754 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 !   75.9   0.0   2.4e-24     3e-21       2     213 ..       3     876 ..       2     882 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.4e-24
                                   EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTT.TCHCCCCCC--BTTCSSTTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakkl.rseklsdlihkskekasvkkaevei 81 
                                   lkr+++en +sy     ++ f++++t++ G NGSGKs+ll+A  F+ G   +++l +   +sd+i k      ++ka++ +
  gi|91773466|ref|YP_566158.1|   3 LKRVRVENIRSYI--DLDISFDDGVTVVSGVNGSGKSSLLEAC-FT-GLFGSRALsKDFVISDIIRK-----GATKASIVV 74 
                                   89**********5..9**************************9.64.43345445134456777776.....8999***** PP

                                   EEEETTEESSSSSS.CEEEEEEEETTSEEEEEETTEEE......-HHHHHHHHHCTT-STT.................... CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxx.................... RF
                         SMC_N  82 tfdnedkklkieke.evsisrrvkrkgeseykingkev......tkkevsellesagiske.................... 135
                                    f+n+++  +ie+  +v  +  + ++++s +k+n++ +      t++ v+ ll++     +                    
  gi|91773466|ref|YP_566158.1|  75 DFENQGNYYSIEQGyKVDARSGKASNNRSVFKVNDEVMvdqanqTYEAVKALLKM-----Deeaytncvyirqgeidvlin 150
                                   ******9966655415666666667777777776665411000044555555544.....3446668************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 151 aktkdrqrmidgllqigkleeyrerassarvgvgrhqreadsrlkdniadievledskpyqllnglrtevtgiekaildlg 231
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 232 skkerakeliesigdrigkyseileqkkkadseikdfktniskehaniessrdqvnsgnndilalhssnvslfgvvevadg 312
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 313 sdiegcvtdlekqevsardgfsgvvkkrelalnneaaqnnfllnlnkqlnnsvgsirirnekvvfakndlkkyledveqig 393
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 394 sfiqnkygdakelgfvedkldqiddisgfvnekqtklhgkekeisatvvelekkiqkskdllskglcptcgqdlqgskvce 474
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 475 enagdedrktelineleliradqdkikvkvelirnvrdiikaiaeaekllllkkneitsiekgieehlssikeendkvidi 555
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 556 ekqideckrsigelksgmeslkseetaaqefhgkllhklevarqirsnilkarniqnninrlqdgvknglekielfesqin 636
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 637 erkqrilkldealggvdlkelqadmsqyerayngivsemgmrdmrkgelhkeigriegniqrlnelkikqkmlvnkkdfla 717
                                   ********************************************************************************* PP

                                   .....................................................................CS-HHHHHHHHH CS
                                   .....................................................................xxxxxxxxxxxx RF
                         SMC_N 136 .....................................................................lLSgGektLval 147
                                                                                                        lLSgGe+++  l
  gi|91773466|ref|YP_566158.1| 718 avygdaeeletmylrlrvelraknidaldrllneifsfmytnnayshisldpeynltiyekdgtplepkLLSGGERAIFNL 798
                                   ********************************************************************************* PP

                                   HHHHH..........HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                   xxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 148 aLlfA..........iqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvtk 213
                                    L+ A                 p  ++De    LD  +v+++ +l++  +     Q++++s++e ++  ad+++ v k
  gi|91773466|ref|YP_566158.1| 799 VLRCAiyrllahapgSTGSAELPPLIFDEPTVFLDRGHVHQLIKLIDMMRGIgvGQILIVSHDESLIDSADHVFVVEK 876
                                   *****88877777776666778889*********************977654449****************9998876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   9.7   3.6e-13   4.6e-10       1     273 [.       1     453 [.       1     459 [. 0.70

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3.6e-13
                        AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsileal.d.lFlnnkekkn......................... 54 
                                   Mk+k+++++N Rs+ d +i++++ +tv+ G N+sGKSs+lea    lF ++  +k+                         
  gi|91773466|ref|YP_566158.1|   1 MKLKRVRVENIRSYIDLDISFDDGVTVVSGVNGSGKSSLLEACfTgLFGSRALSKDfvisdiirkgatkasivvdfenqgn 81 
                                   *****************************************9613133333333336777776666666666666666666 PP

                        AAA_15  55 ............................kkvikiekedleifeniseskdikIdvef........................ 83 
                                                               +                                                    
  gi|91773466|ref|YP_566158.1|  82 yysieqgykvdarsgkasnnrsvfkvndE---------------------------Vmvdqanqtyeavkallkmdeeayt 135
                                   66666666666666666665554444440...........................0444444444444444444446666 PP

                        AAA_15  84 ................................................................................. 83 
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 136 ncvyirqgeidvlinaktkdrqrmidgllqigkleeyrerassarvgvgrhqreadsrlkdniadievledskpyqllngl 216
                                   666666666666667777*************************************************************** PP

                        AAA_15  84 ...............aek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelp 148
                                                    k e ake +++  ++  k++++l +kk+   ++ ikd+k++++k+  + e+  ++ +  ++++ 
  gi|91773466|ref|YP_566158.1| 217 rtevtgiekaildlgS-KkERAKELIESIGDRIGKYSEILEQKKKA--DSEIKDFKTNISKEHANIESSRDQVNSGNNDIL 294
                                   ******9999999854.35999***************966666655..778888888888888888777777777777777 PP

                        AAA_15 149 kekeeklekekeelkidkedlkklikkleeslkkee.........................elknvlksaiiklllisakR 204
                                    + +++  +       d +d++    +le++  +                            l++ l+++   +++ ++k 
  gi|91773466|ref|YP_566158.1| 295 ALHSSNVSLFGVVEVADGSDIEGCVTDLEKQEVSARdgfsgvvkkrelalnneaaqnnfllNLNKQLNNSVGSIRIRNEKV 375
                                   665555544444444457777777777777766666777777788878888888888888855555555555555555555 PP

                        AAA_15 205 nvsdedsekkss...llgklkekileealqekl...eeelteklkeiqeklkeidkklaeelk......kilkkkidkikk 273
                                    + ++d +k  +    +g+ +++++ +a+        e++ +++++i   ++e++ kl  ++k       +l+kki+k+k+
  gi|91773466|ref|YP_566158.1| 376 VFAKNDLKKYLEdveQIGSFIQNKYGDAK---ElgfVEDKLDQIDDISGFVNEKQTKLHGKEKeisatvVELEKKIQKSKD 453
                                   55554444444400044445555555544...2355666777777777777777777777777666777667777777665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   5.8e-05     0.074       1      19 [.      25      43 ..      25      93 .. 0.76
   2 ?    1.2   0.9       0.2   2.6e+02     158     220 ..     208     284 ..     186     410 .. 0.73
   3 !   21.6   0.0   1.3e-07   0.00016     155     303 .]     601     866 ..     573     866 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                        AAA_21  1 lnvliGpNgsGKSnLLdal 19
                                  ++v+ G NgsGKS+LL+a 
  gi|91773466|ref|YP_566158.1| 25 VTVVSGVNGSGKSSLLEAC 43
                                  69999************95 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                        AAA_21 158 ldglrke..rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer............g 220
                                   +  ++++  r  +  i ++ +   ++k+++++l+ s+ ++  ++s ++e++++ +s++ + + +            +
  gi|91773466|ref|YP_566158.1| 208 KPYQLLNglRTEVTGIEKAILDLGSKKERAKELIESIGDRIGKYSEILEQKKKADSEIKDFKTNiskehaniessrD 284
                                   33333334578888888888888888888888888888888888888888888888888877765555555554440 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.3e-07
                        AAA_21 155 lllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer................ 219
                                   +++  + r+ + + +++++   ++ ++++l++  ++++k++ ++l+  + g++l ++ ++ ++++                
  gi|91773466|ref|YP_566158.1| 601 RSNILKARNIQNNINRLQDGVKNGLEKIELFESQINERKQRILKLDEALGGVDLKELQADMSQYErayngivsemgmrdmr 681
                                   444444444444444444444444444444444444444444444444444444444444444447777777777777777 PP

                        AAA_21 220 ................................................................................. 219
                                                                                                                    
  gi|91773466|ref|YP_566158.1| 682 kgelhkeigriegniqrlnelkikqkmlvnkkdflaavygdaeeletmylrlrvelraknidaldrllneifsfmytnnay 762
                                   777777777777777777777777777777777777777777777777777777777777777777777778888888888 PP

                        AAA_21 220 ........gvvflengdgqelparelSdGtkrllalltallralkkg...........sllliDEpEngLHPkllrrllel 281
                                           +  +  ++dg +l +  lS G + ++ l++ ++  +  +           + l++DEp  +L+   ++ l++l
  gi|91773466|ref|YP_566158.1| 763 shisldpeYNLTIYEKDGTPLEPKLLSGGERAIFNLVLRCAIYRLLAhapgstgsaelPPLIFDEPTVFLDRGHVHQLIKL 843
                                   888888878899999***********************999999999999******************************* PP

                        AAA_21 282 lkelsr.ngaQviltTHSpllld 303
                                   ++  +  + +Q+++++H+ +l+d
  gi|91773466|ref|YP_566158.1| 844 IDMMRGiGVGQILIVSHDESLID 866
                                   *99999999**********9997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.2e-08   6.6e-05       1      49 [.       3      50 ..       3      55 .. 0.89
   2 ?   -3.4   0.0       6.7   8.6e+03      37      58 ..     863     884 ..     863     886 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.2e-08
                        AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  Lkr+++ N  ++ + +i++d +g+t+++G +GsGKS+ll A  + L ++
  gi|91773466|ref|YP_566158.1|  3 LKRVRVENIRSYIDLDISFD-DGVTVVSGVNGSGKSSLLEACFTGLFGS 50
                                  789999999999999999*9.789*****************98877776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.7
                        AAA_29  37 TllDAiqalLvpakkvrfNkaa 58 
                                   +l+D+   ++v +k+   N+++
  gi|91773466|ref|YP_566158.1| 863 SLIDSADHVFVVEKDPITNSSS 884
                                   599**999*9999988888887 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 ?    5.1   0.0     0.021        27      60      83 ..     636     659 ..     628     666 .. 0.78
   2 !   13.9   0.0   3.7e-05     0.048      33      89 ..     788     845 ..     771     846 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                       SbcCD_C  60 repalrlvfLDEAFsklDeesiat 83 
                                   +e++ r++ LDEA +++D + +++
  gi|91773466|ref|YP_566158.1| 636 NERKQRILKLDEALGGVDLKELQA 659
                                   57889*************887765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.7e-05
                       SbcCD_C  33 lSGGekqflaylalaaalaalyssaeg..repalrlvfLDEAFsklDeesiatllelle 89 
                                   lSGGe+  ++ l+l  a+  l+ +a+g   +  l ++++DE    lD   +++l++l++
  gi|91773466|ref|YP_566158.1| 788 LSGGER-AIFNLVLRCAIYRLLAHAPGstGSAELPPLIFDEPTVFLDRGHVHQLIKLID 845
                                   8*****.******************965566779*******************999975 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.6e-06     0.011       1      58 [.       1      55 [.       1      61 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.6e-06
                        AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertk 58
                                  M+l+r ++e   ++ d  ++f+   ++++++ G N +GKs++l+A    lfG  + +k
  gi|91773466|ref|YP_566158.1|  1 MKLKRVRVENIRSYIDLDISFD---DGVTVVSGVNGSGKSSLLEACFTGLFGSRALSK 55
                                  8888888888888889899997...89************************9776554 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   1.9e-05     0.024      12      78 ..      11      69 ..       4     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                        AAA_16 12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalar 78
                                  ++s+++   s + +++++sG  G+GKssl++++++ l ++   +l+ +++ +      +++ + +++
  gi|91773466|ref|YP_566158.1| 11 IRSYIDLDISFDDGVTVVSGVNGSGKSSLLEACFTGLFGS--RALSKDFVIS------DIIRKGATK 69
                                  56666644555558999*****************977665..3455555544......345555555 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00039       0.5      23      56 ..      20      53 ..       2     119 .. 0.84
   2 ?   -1.0   0.1      0.97   1.2e+03     121     158 ..     226     263 ..     183     279 .. 0.72
   3 ?    0.1   0.1      0.46   5.9e+02     123     182 ..     619     677 ..     543     698 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00039
                                  -HHHHHHHHHS--SHHHHHHHHHHHHHHS--TTT CS
                          MukB 23 dldelvttlsGgnGaGksttmaafvtaliPdlsl 56
                                   +d+ vt +sG nG+Gks  + a +t l    +l
  gi|91773466|ref|YP_566158.1| 20 SFDDGVTVVSGVNGSGKSSLLEACFTGLFGSRAL 53
                                  67999******************99999876555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.97
                                   EEES--TT--HHHHHEE--SSS--EE--HHHHHHHHHT CS
                          MukB 121 alqgleedvkltdvlleklddkkarvrelnelkeklee 158
                                   a+ +l ++++  + l+e+++d+ ++  e+ e k+k+++
  gi|91773466|ref|YP_566158.1| 226 AILDLGSKKERAKELIESIGDRIGKYSEILEQKKKADS 263
                                   46666666777777777788877777777777776665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.46
                                   ES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT-EEEE-S-HHHHHHHHHHTTS CS
                          MukB 123 qgleedvkltdvlleklddkkarvrelnelkekleelegvrlkkfnsvtdyhallfdlGv 182
                                    g+++ ++ ++++ ++++++k+r+++l e    ++  ++++    +  + y  ++ ++G+
  gi|91773466|ref|YP_566158.1| 619 DGVKNGLEKIELFESQINERKQRILKLDEALGGVDL-KELQADMSQYERAYNGIVSEMGM 677
                                   467888889999999999999999999997766653.34444433344556677777776 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0067       8.5       7      75 ..     259     327 ..     253     335 .. 0.88
   2 ?    3.8   0.4     0.035        45       9      63 ..     541     596 ..     533     619 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0067
                 USP8_interact   7 qkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrstnpvlraladqlerdevlrWveslklarv 75 
                                   +k  ++i+++k+++++++ ++++ +++++  ++ i al s+n +l  + +  + ++++  v+ l++ +v
  gi|91773466|ref|YP_566158.1| 259 KKADSEIKDFKTNISKEHANIESSRDQVNSGNNDILALHSSNVSLFGVVEVADGSDIEGCVTDLEKQEV 327
                                   566789****************************************99999999999988888887766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.035
                 USP8_interact   9 qqqkiaelkkevaeqkqqlseqkrelellkeyiralrstnpvlraladql.erdev 63 
                                     ++i+e +++v + ++q+ e kr +  lk+ + +l+s +++ ++ + +l ++ ev
  gi|91773466|ref|YP_566158.1| 541 HLSSIKEENDKVIDIEKQIDECKRSIGELKSGMESLKSEETAAQEFHGKLlHKLEV 596
                                   55556666666666666666666666666666666666655555554444333444 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 ?    8.9   1.8     0.001       1.3       2      33 ..     438     471 ..     437     492 .. 0.86
   2 ?   -3.0   0.0       5.3   6.8e+03       2      17 ..     556     571 ..     555     572 .. 0.80
   3 ?   -1.1   0.1       1.3   1.7e+03       2      18 ..     632     648 ..     631     649 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                                   HHHHHHHHHHHHHHTT..-SEE-TTT--EE-HHH CS
                 Rad50_zn_hook   2 hqeteelnkkieelke..akgcCPlCgReldeeh 33 
                                   +++ +el+kki + k+  +kg CP Cg++l   +
  gi|91773466|ref|YP_566158.1| 438 SATVVELEKKIQKSKDllSKGLCPTCGQDLQGSK 471
                                   68999********99855677********98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.3
                                   HHHHHHHHHHHHHHTT CS
                 Rad50_zn_hook   2 hqeteelnkkieelke 17 
                                   +++++e ++ i elk+
  gi|91773466|ref|YP_566158.1| 556 EKQIDECKRSIGELKS 571
                                   7788999999999886 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHHHTT- CS
                 Rad50_zn_hook   2 hqeteelnkkieelkea 18 
                                   +++++e +++i++l ea
  gi|91773466|ref|YP_566158.1| 632 ESQINERKQRILKLDEA 648
                                   6889999****999885 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.4   1.8e+03       4      14 ..     192     202 ..     192     202 .. 0.93
   2 ?    7.3   1.7    0.0034       4.4       3      22 ..     545     564 ..     543     565 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                Pox_A_type_inc   4 srlRsRIsDLE 14 
                                   srl++ I D+E
  gi|91773466|ref|YP_566158.1| 192 SRLKDNIADIE 202
                                   79*******98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0034
                Pox_A_type_inc   3 msrlRsRIsDLErqLseCrr 22 
                                   + ++ +++ D+E+q +eC+r
  gi|91773466|ref|YP_566158.1| 545 IKEENDKVIDIEKQIDECKR 564
                                   667889*************9 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.4   3.1e+03      98      98 ..     253     253 ..     213     298 .. 0.56
   2 ?    3.0   0.1     0.051        65     106     144 ..     419     457 ..     407     460 .. 0.85
   3 ?   -0.8   1.9      0.77   9.8e+02     115     144 ..     560     589 ..     519     651 .. 0.63
   4 ?   10.0   0.1   0.00035      0.45     111     150 ..     679     718 ..     655     731 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                 Fzo_mitofusin  98 e 98 
                                   e
  gi|91773466|ref|YP_566158.1| 253 E 253
                                   1 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.051
                 Fzo_mitofusin 106 lcqqvdetekeleeeikelekeiekleevqkkakllrnk 144
                                   ++  v+e +++l+ + ke+++++ +le+ ++k+k l  k
  gi|91773466|ref|YP_566158.1| 419 ISGFVNEKQTKLHGKEKEISATVVELEKKIQKSKDLLSK 457
                                   5566999999******************99999998766 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.77
                 Fzo_mitofusin 115 keleeeikelekeiekleevqkkakllrnk 144
                                   +e +++i el++ +e+l++ ++ a+ ++ k
  gi|91773466|ref|YP_566158.1| 560 DECKRSIGELKSGMESLKSEETAAQEFHGK 589
                                   244444444444444444444444444433 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00035
                 Fzo_mitofusin 111 detekeleeeikelekeiekleevqkkakllrnkaslles 150
                                   d+ + el++ei ++e +i++l+e++ k k+l nk  +l++
  gi|91773466|ref|YP_566158.1| 679 DMRKGELHKEIGRIEGNIQRLNELKIKQKMLVNKKDFLAA 718
                                   567889****************************999986 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.4     0.001       1.3     129     182 ..     217     287 ..     187     292 .. 0.77
   2 ?   -1.0   2.3         1   1.3e+03     101     142 ..     410     451 ..     358     487 .. 0.55
   3 ?    9.8   9.2   0.00051      0.65      83     162 ..     509     589 ..     482     606 .. 0.81
   4 ?    3.7   2.4     0.037        47      95     176 ..     612     698 ..     598     708 .. 0.72
   5 ?    1.6   0.2      0.17   2.2e+02      98     150 ..     655     707 ..     652     729 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                        DUF724 129 eeeidelekkilelerqlallk.................ekkeaadkeiarlkseaekleeeledveqeFe 182
                                    +e+  +ek+il+l  +++++k                 e+k++ad+ei++ k++ +k + ++e+ +++++
  gi|91773466|ref|YP_566158.1| 217 RTEVTGIEKAILDLGSKKERAKeliesigdrigkyseilEQKKKADSEIKDFKTNISKEHANIESSRDQVN 287
                                   4555566666666666666666666666666666666668999*************999999999998876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                        DUF724 101 kdeqtklleerkklekkieeeesekrkleeeidelekkilel 142
                                    d+ +++ + +  +++k ++ + +++++++ + elekki++ 
  gi|91773466|ref|YP_566158.1| 410 EDKLDQIDDISGFVNEKQTKLHGKEKEISATVVELEKKIQKS 451
                                   333333333333333333333333444444444444444443 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00051
                        DUF724  83 hGFdVkalqsrlnkLlslk.deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiar 162
                                   +  d+    +  +kLl lk +e t++++ +++  ++i+ee+++   +e++ide ++ i el+   ++lk+++ aa++   +
  gi|91773466|ref|YP_566158.1| 509 NVRDIIKAIAEAEKLLLLKkNEITSIEKGIEEHLSSIKEENDKVIDIEKQIDECKRSIGELKSGMESLKSEETAAQEFHGK 589
                                   4455555556668999886257899********************************************888777765544 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.037
                        DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeeid.....elekkilelerqlallkekkeaadkeiarlkseaekl 170
                                   n++  l+d  ++ le+++ +e++i e +++  kl+e +      el+  +++ er    + +++   d +  +l++e  ++
  gi|91773466|ref|YP_566158.1| 612 NNINRLQDGVKNGLEKIELFESQINERKQRILKLDEALGgvdlkELQADMSQYERAYNGIVSEMGMRDMRKGELHKEIGRI 692
                                   555567888888889999999999999999999998877555556666677777776666677777777777777777777 PP

                        DUF724 171 eeeled 176
                                   e ++++
  gi|91773466|ref|YP_566158.1| 693 EGNIQR 698
                                   776665 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.17
                        DUF724  98 lslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk 150
                                    +l+ + ++++++ +++ +++   +++k +l++ei  +e +i++l++ +   k
  gi|91773466|ref|YP_566158.1| 655 KELQADMSQYERAYNGIVSEMGMRDMRKGELHKEIGRIEGNIQRLNELKIKQK 707
                                   56788888999999999999999999*****************8887664333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1435  (0.0800379); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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):              14  [number of targets reported over threshold]
# CPU time: 1.26u 0.35s 00:00:01.61 Elapsed: 00:00:00.57
# Mc/sec: 4717.67
//
Query:       gi|91773467|ref|YP_566159.1|  [L=485]
Description: metallophosphoesterase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   49.4   0.6    7.6e-13   49.4   0.6    1.7  2  Metallophos     Calcineurin-like phosphoesterase
    5.8e-10   39.6   0.7    1.6e-09   38.2   0.3    1.9  2  Metallophos_2   Calcineurin-like phosphoesterase superfamily 
  ------ inclusion threshold ------
       0.12   12.7   0.3        2.5    8.4   0.0    2.9  3  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
       0.23   11.4   1.3         16    5.5   0.5    2.3  2  HEPN_AbiA_CTD   HEPN like, Abia C-terminal domain


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.6   1.7e-16   7.6e-13       1     123 [.       5     120 ..       5     189 .. 0.73
   2 ?   -2.5   0.0       1.4   6.2e+03     129     156 ..     426     463 ..     395     475 .. 0.58

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.7e-16
                                   EEEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHH...TSEEE CS
                   Metallophos   1 lrilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrg..dlekellellaalvky...pipvy 68 
                                   +ril++gD+H+         ++   +d++  ++dd+++  k+d+v++aGDl+d     le  +l+ ++ l+k+   +ip+ 
  gi|91773467|ref|YP_566159.1|   5 IRILHTGDTHIgyrqyhseVRRQDFIDAFSSVIDDAIDM-KVDVVVHAGDLFDSRnpTLED-ILDTIKVLLKLkqqKIPFL 83 
                                   59*************887777777777777888888777.**************9885555.6666666666666799*** PP

                                   EEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                   Metallophos  69 lllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                    + GNHe                s+++ +  + f+ + +as  ++  k +l++G 
  gi|91773467|ref|YP_566159.1|  84 SIVGNHE----------------SKQHTQWLDLFESMDIASRLGT--KPFLIDGV 120
                                   *******................3333333777888888887777..44444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHSCHHHHCC...........HHHHHHHHH CS
                   Metallophos 129 vsldklgslnleleapepg...........dewlkdlek 156
                                   +++++++  n+++ +++++           de+l+d  +
  gi|91773467|ref|YP_566159.1| 426 EQVSEVKDSNMITASTTERvsndetskesdDEILQD-TE 463
                                   445555555555555555555555555566888888.22 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 !   38.2   0.3   3.5e-13   1.6e-09       2     164 ..       6     226 ..       5     227 .. 0.75
   2 ?   -2.7   0.0       1.3     6e+03      57      84 ..     276     306 ..     272     338 .. 0.56

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.5e-13
                 Metallophos_2   2 klaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep.........evleellela....pvl 55 
                                   ++++  D+H             + +da   v++++ + +vd ++haGDl   ++p         +vl +l   +    p+l
  gi|91773467|ref|YP_566159.1|   6 RILHTGDTHigyrqyhsevrrqDFIDAFSSVIDDAIDMKVDVVVHAGDLfDSRNPtledildtiKVLLKL---KqqkiPFL 83 
                                   789999****999999999988889999999*****************9988888665555333344444...3666**** PP

                 Metallophos_2  56 aVrGNnD..............................eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl.... 102
                                    + GN++                               ++ ++ v r++ +l ++  +    +++++++l++H+       
  gi|91773467|ref|YP_566159.1|  84 SIVGNHEskqhtqwldlfesmdiasrlgtkpflidgvAIYGIDNVPRSKIPLYDYS-DFTAENCGKWNLLVMHQLMApfpf 163
                                   *******8888888888877777777777777665432225666666666665554.44444579*********9669995 PP

                 Metallophos_2 103 ...gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..tyaildtde 164
                                        +d +++l ++       +++G  H++e++k g+++  + Gs ++ + ++    ty i+++++
  gi|91773467|ref|YP_566159.1| 164 gewDCEDVISSLPFD----LHAILLGDYHKHEKTKVGSTWATYCGSTERNSASESDprTYNIITIND 226
                                   555555555555555....4499*************************9955544444**9999987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                 Metallophos_2  57 VrGNnD...eevveedvlreaaelgtdlpee 84 
                                   + GN D   ++ ++e +l++++ l t++ + 
  gi|91773467|ref|YP_566159.1| 276 ISGNSDvsiSYNEIEGLLAKQEALVTRIRDM 306
                                   7788886542224455555555555544333 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 ?    0.7   0.0      0.15   6.7e+02      23      52 ..      23      52 ..      18      55 .. 0.87
   2 ?   -2.4   0.0       1.4   6.2e+03      28      44 ..      78      93 ..      63      95 .. 0.70
   3 ?    8.4   0.0   0.00056       2.5       8      38 ..     290     320 ..     279     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                                  HHCCTTSS-TT-EEEE-TTT--EEEE-SSE CS
                RNA_pol_Rpb2_4 23 elRRkgkiseevsivlnekqkevkiatDgG 52
                                  e+RR+  i+ + s++ +  + +v +   +G
  gi|91773467|ref|YP_566159.1| 23 EVRRQDFIDAFSSVIDDAIDMKVDVVVHAG 52
                                  68************9999999998887777 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                  TSS-TT-EEEE-TTT-- CS
                RNA_pol_Rpb2_4 28 gkiseevsivlnekqke 44
                                  +ki ++ siv n++ k+
  gi|91773467|ref|YP_566159.1| 78 QKI-PFLSIVGNHESKQ 93
                                  333.7999999998775 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00056
                                   EEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE CS
                RNA_pol_Rpb2_4   8 lGvtrdpkklvetlRelRRkgkiseevsivl 38 
                                    G+  +++ lv+++R++R ++ +se++ + +
  gi|91773467|ref|YP_566159.1| 290 EGLLAKQEALVTRIRDMRHSEGVSEDMDVEV 320
                                   5888999*************99996655433 PP

>> HEPN_AbiA_CTD  HEPN like, Abia C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0082        37      77     128 ..      30      80 ..      12      82 .. 0.73
   2 ?    5.5   0.5    0.0035        16      81     117 ..     422     458 ..     410     464 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0082
                 HEPN_AbiA_CTD  77 iddseeiiekahklrnanPlshssselldkentskelkesikelsklideyi 128
                                   id  +++i++a +++  + + h+   + +++ t +++ ++ik l kl +++i
  gi|91773467|ref|YP_566159.1|  30 IDAFSSVIDDAIDMKV-DVVVHAGDLFDSRNPTLEDILDTIKVLLKLKQQKI 80 
                                   3444889999999975.56788865444556689**********99988876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0035
                 HEPN_AbiA_CTD  81 eeiiekahklrnanPlshssselldkentskelkesi 117
                                   ++i e+  +++++n ++ s++e +++++tske  + i
  gi|91773467|ref|YP_566159.1| 422 DNISEQVSEVKDSNMITASTTERVSNDETSKESDDEI 458
                                   78999**************************976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2890.20
//
Query:       gi|91773468|ref|YP_566160.1|  [L=243]
Description: glucose-6-phosphate isomerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-42  143.8   0.3    4.5e-42  143.4   0.3    1.1  1  GPI       Glucose-6-phosphate isomerase (GPI)
    6.6e-05   22.6   0.3    0.00038   20.1   0.3    2.2  2  Cupin_2   Cupin domain
  ------ inclusion threshold ------
      0.058   13.0   0.0      0.094   12.3   0.0    1.3  1  Cupin_1   Cupin


Domain annotation for each model (and alignments):
>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.3   7.4e-46   4.5e-42       4     176 ..      19     189 ..      16     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 7.4e-46
                           GPI   4 ardlaavladeealkaltetldddvaYevsdslktaeegerlaadqliydvtvilPgkiGeEriktrGHyHkevd.rrstr 83 
                                     d++ v+ d e ++      d + +Y++++   ++e+  +++++ l+yd+tvi+P   G E ikt GHyH++v  +   +
  gi|91773468|ref|YP_566160.1|  19 LHDMKEVVYDHEWFRS---VDDMELYYMFRHLSLSEEDLKIINKSHLRYDITVIPPAMFGSEFIKTAGHYHPNVPgQEISY 96 
                                   6788999999977777...67889*************************************************988999** PP

                           GPI  84 PEvYevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdagqdYdviakarGmaay 164
                                   PEvY+vl+Gea ++L+k  g  v d +v++ k++++ ++PP ygHv++n ++e L man+v+ d+++ Y ++  ++G a+y
  gi|91773468|ref|YP_566160.1|  97 PEVYQVLEGEATYILQKHVGDDVVDTVVIKAKKGDIALIPPDYGHVTVNASDEILKMANWVCCDFSSSYAPFRDMEGGAYY 177
                                   *****************9998999999****************************************************** PP

                           GPI 165 iieegevlrkrk 176
                                   + e g ++ +r 
  gi|91773468|ref|YP_566160.1| 178 LLESGFMKNHRY 189
                                   **8877666554 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.3   6.4e-08   0.00038      21      67 ..      98     153 ..      82     158 .. 0.83
   2 ?   -1.5   0.0      0.36   2.2e+03      41      59 ..     171     191 ..     169     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.4e-08
                                   EEEEEEESEEEEEECTE.........EEEEETTEEEEE-TT-EEEEEE-SSS-EEE CS
                       Cupin_2  21 effyVleGegeltvdge.........eveleaGdsvyfpagtpHrfrNtgdeparl 67 
                                   e++ VleGe+++++  +         +++ ++Gd++++p+   H  +N++de +++
  gi|91773468|ref|YP_566160.1|  98 EVYQVLEGEATYILQKHvgddvvdtvVIKAKKGDIALIPPDYGHVTVNASDEILKM 153
                                   7788999999999774444456776799************************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.36
                                   EETTEEEEE-TT..-EEEEEE CS
                       Cupin_2  41 leaGdsvyfpag..tpHrfrN 59 
                                   +e G +++ ++g    Hr++N
  gi|91773468|ref|YP_566160.1| 171 MEGGAYYLLESGfmKNHRYEN 191
                                   677888888888889999998 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05     0.094      52     105 ..      94     149 ..      84     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                                   SSS-EEEEEEESEEEEEEEETTSS.EEEEEE...EETTEEEEE-TT-EEEEEEESSS CS
                       Cupin_1  52 pnateiayvlqGegrvgfvvpgngnrdfhkk...lreGdvfvvPaglvhfqynsgde 105
                                    +++e+  vl+Ge++  ++  + g  + + +    ++Gd+  +P+ + h+++n  de
  gi|91773468|ref|YP_566160.1|  94 ISYPEVYQVLEGEAT-YILQKHVGDDVVDTVvikAKKGDIALIPPDYGHVTVNASDE 149
                                   46789999*******.888888888888888988*******************9754 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:                        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 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1629.13
//
Query:       gi|91773469|ref|YP_566161.1|  [L=252]
Description: hypothetical protein Mbur_1504 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-95  317.1   1.2    6.6e-95  316.9   1.2    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 !  316.9   1.2   3.7e-99   6.6e-95       1     238 []       8     247 ..       8     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 316.9 bits;  conditional E-value: 3.7e-99
                                   ---HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE..........EEEE CS
                        NRD1_2   1 vgfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek..elevpegkvgia 79 
                                   v+f++s+ie+l+y++tfdp +++G+ ivN sl++++dle +le+ + vi+sglsvs+ +ki+++ge+  +l++ +g vgia
  gi|91773469|ref|YP_566161.1|   8 VQFTSSRIEDLMYRTTFDPVNMTGELIVNQSLVKEKDLEAVLEVYNLVIRSGLSVSPFLKIIKSGETigDLKIAQGDVGIA 88 
                                   79******************************************************************************* PP

                                   EE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEEEEET CS
                        NRD1_2  80 tvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlReipv 160
                                   tvCSitidgvLlk G++++p++GG+++i++++pvrFt++++Y +t+idPlev++s+++Tsv+++++tg+gkilAnlRe p 
  gi|91773469|ref|YP_566161.1|  89 TVCSITIDGVLLKGGVMINPRFGGVVQIKNGQPVRFTDVVTYASTTIDPLEVLMSQDITSVTKMLRTGSGKILANLREAPL 169
                                   ********************************************************************************* PP

                                   TTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEGGGSEE CS
                        NRD1_2 161 sarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidiselkk 238
                                   +ar+++++il++l +ag+sg++e+gepn++vl+vpve++++g+vv+gG+np+a++ke+g++++++a+s li i ++k+
  gi|91773469|ref|YP_566161.1| 170 VARDDIDHILSDLMEAGLSGIMEVGEPNTRVLDVPVERDHLGVVVIGGTNPMAMAKEQGFEISTSAMSALIGIDSMKH 247
                                   ****************************************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1819.88
//
Query:       gi|91773470|ref|YP_566162.1|  [L=461]
Description: phosphoesterase, RecJ-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   58.2   2.0    1.3e-15   58.0   0.7    1.8  2  DHHA1     DHHA1 domain
     0.0072   16.6   0.2      0.014   15.6   0.2    1.5  1  DHH       DHH family
  ------ inclusion threshold ------
       0.15   11.7   0.1        3.4    7.3   0.0    2.2  2  DUF1847   Protein of unknown function (DUF1847)
       0.25    9.6   0.0        1.4    7.1   0.0    1.9  2  CDC45     CDC45-like protein


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.4   1.1e+04      39      64 ..      22      47 ..       5      66 .. 0.56
   2 !   58.0   0.7     3e-19   1.3e-15      51     138 .]     363     455 ..     320     455 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                                  TCEEEEEECHCCHHH.HHHHHHHHHHH CS
                         DHHA1 39 gvkvlvaevgeewda.galgiaadklk 64
                                  +v+v+v+    ++d  +  gi++  l 
  gi|91773470|ref|YP_566162.1| 22 QVSVYVVSH-IDADGlTSAGIICKALE 47
                                  566666666.66666444455554444 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 3e-19
                                   HHHHHHHHHHHHHHTHG..BT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEH CS
                         DHHA1  51 wdagalgiaadklkskl..kk.pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipa 124
                                   +  +++gi+a++  s +   + p+i+f+ +++g  vkvsar ++d    g++++e+++  aa++ g GGGHd AaGa+ip+
  gi|91773470|ref|YP_566162.1| 363 ILETIVGIIAGMSTSVIgnRNlPIIAFADAKDG--VKVSARGTQDlirrGLNLSEAMSMTAAEFDGAGGGHDIAAGATIPE 441
                                   334466666666666555556699999999987..********************************************** PP

                                   CHHHHHHHHHHHHH CS
                         DHHA1 125 ekleealealeeai 138
                                   +  ee++ +l+++i
  gi|91773470|ref|YP_566162.1| 442 SAKEEFIMKLDAVI 455
                                   *******9999876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   3.1e-06     0.014       2      94 ..      25     146 ..      22     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-06
                                   EEEE-ECSSSHHHHHHHHHHHH.................................CECS--TCGGCGCCHHCCCSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH   2 ilivghknpDtDsigSaialan.................................llvDhneksqavegeakeeaedviii 49 
                                   +++  + + D+D+++Sa  + +                                 +  D ++   +    +++++ + +i 
  gi|91773470|ref|YP_566162.1|  25 VYV--VSHIDADGLTSAGIICKaleregiehsihfvkqldeveiesianlnpelvIFTDLGSGMIDS---LNSHGINAVIA 100
                                   455..999********665555467777777776666666666666666666555566666555444...67********* PP

                                   E-S---S..S---SS--E.EEE-SSS-HHHHHHHHHHHTT----HHHH CS
                                   xxxxxxx..xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  50 DHHrlge..efetlapil.flnepvgstaeivaelleekkeeiskeia 94 
                                   DHH++    +++ + +++ f  ++  s++++ + l+++ +++  k++a
  gi|91773470|ref|YP_566162.1| 101 DHHQPRGelDYHLNPHLYgFNGSYELSGSGMTYILANALGDN--KDLA 146
                                   ****98877333333333144445557777777776663333..4445 PP

>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.032   1.4e+02      73     113 ..      27      67 ..      13      74 .. 0.72
   2 ?    7.3   0.0   0.00076       3.4      44      77 ..     295     328 ..     267     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.032
                       DUF1847  73 lakileakgfevvsviCkvgsvdkeelgieeeekvkkkkke 113
                                   +++ ++a g++ +++iCk+ + +  e +i+  +++++ + e
  gi|91773470|ref|YP_566162.1|  27 VVSHIDADGLTSAGIICKALEREGIEHSIHFVKQLDEVEIE 67 
                                   56778999**********99887776666666665555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00076
                       DUF1847  44 eeiiefakrmgykkiGiafCvglleeakalakil 77 
                                   + +++ + r g   iG+a+C+g + ea + ak l
  gi|91773470|ref|YP_566162.1| 295 STLLNATARYGHADIGLAVCMGDRGEAYESAKKL 328
                                   55667778999***************98776544 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00031       1.4       1      64 [.      25      84 ..      25     110 .. 0.73
   2 ?   -0.0   0.0     0.045     2e+02     225     256 ..     123     153 ..     115     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00031
                         CDC45  1 VlilvaldvDalCAariLtsLLkkdliphkivPVsGyedlekaleelveegeelrsvvllnlGa 64
                                  V +++  d+D l +a i+ + L+++ i+h+i+ V+  +++e           + + v++  lG+
  gi|91773470|ref|YP_566162.1| 25 VYVVSHIDADGLTSAGIICKALEREGIEHSIHFVKQLDEVEIESIANL----NPELVIFTDLGS 84
                                  678888****************************98888864433333....336777777774 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.045
                         CDC45 225 sygesvsslmYsLaselgredndlLWlAIvGl 256
                                   sy  s s + Y La++lg  ++dl  lAIvG+
  gi|91773470|ref|YP_566162.1| 123 SYELSGSGMTYILANALGD-NKDLADLAIVGA 153
                                   6777999**********95.7899999***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3033.82
//
Query:       gi|91773471|ref|YP_566163.1|  [L=166]
Description: hypothetical protein Mbur_1506 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.2   0.0       0.03   14.3   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 ?   14.3   0.0   1.7e-06      0.03      32      82 ..      39     104 ..       3     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-06
                                   SEE..EEETTEEEEEEEEEESSS....EEEE.........EHHHHHHHHHHHHHHTCEEEEEEEET CS
                           Hjc  32 Dvi..AirgdvvlviEvKsskke....riyl.........kkeqvekllefarkaggelllavklq 82 
                                   Dv+   ++ d +l iE+Ks + e     +y           ++q++++ +f r++g   +lav l+
  gi|91773471|ref|YP_566163.1|  39 DVLvdSLNPDYYLGIECKSISVEkganALYFtqhftvdkkGAHQIDRISDFLRRSGRTGYLAVELR 104
                                   55433578999*******9664424446777******99889********************9873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1150.67
//
Query:       gi|91773472|ref|YP_566164.1|  [L=89]
Description: hypothetical protein Mbur_1507 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.6   1.7      0.047   12.5   1.7    1.1  1  CreD      Inner membrane protein CreD
      0.058   12.8   1.2      0.064   12.6   1.2    1.0  1  TssN      Type VI secretion system, TssN


Domain annotation for each model (and alignments):
>> CreD  Inner membrane protein CreD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.7   5.2e-06     0.047     351     402 ..       9      60 ..       4      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-06
                          CreD 351 elAYliaalavvllislYlssvlkskkrgllfaallallYgllyvlLqledy 402
                                    ++Y+ ++  v+l+  +Y    +++k++ +l+a++ ++++++l +++++ d+
  gi|91773472|ref|YP_566164.1|   9 GFSYIPSSTGVTLMYQAYNVGTMNKKTMEILLAIGSVVVFVVLLIMVHATDM 60 
                                   468*******************************************999886 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.2   7.2e-06     0.064      77     138 ..      19      80 ..       8      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-06
                          TssN  77 lylllkkffkelkekkilfeilltlivillglvlfvlvfnllselq.ygvwaatsllvfiipl 138
                                   ++l+++ ++    +kk ++eill++ ++++ +vl ++v     e q yg++ a +l+v ++ l
  gi|91773472|ref|YP_566164.1|  19 VTLMYQAYNVGTMNKK-TMEILLAIGSVVVFVVLLIMVHATDMEPQgYGFLGALALFVLTVSL 80 
                                   5678899999999999.999999999999999999999888777777***8888888877755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 586.82
//
Query:       gi|91773473|ref|YP_566165.1|  [L=131]
Description: hypothetical protein Mbur_1508 [Methanococcoides burtonii DSM 6242]
Scores for 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-64  215.1   1.6    2.3e-64  214.9   1.6    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.9   1.6   1.3e-68   2.3e-64       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 214.9 bits;  conditional E-value: 1.3e-68
                       DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvwghrk 81 
                                   mkirvvsskeei+tl+ene+ivHlafrpsntdi+slv kcp++ka+++p+Sykkt+sksakm+le+qgi+llegdvwghrk
  gi|91773473|ref|YP_566165.1|   1 MKIRVVSSKEEIKTLSENEEIVHLAFRPSNTDIFSLVVKCPSVKALHIPSSYKKTISKSAKMYLEMQGINLLEGDVWGHRK 81 
                                   9******************************************************************************** PP

                       DUF1699  82 dineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                   diney+evs+ v++rike++++g+seeei ek+ +et+lspd+i+fl+k
  gi|91773473|ref|YP_566165.1|  82 DINEYSEVSQGVYDRIKEYRDSGISEEEINEKMVRETRLSPDFIEFLMK 130
                                   ***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 00:00:00.43
# Mc/sec: 909.96
//
Query:       gi|91773474|ref|YP_566166.1|  [L=218]
Description: hypothetical protein Mbur_1509 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  119.7   0.0    1.3e-34  119.4   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.5e-15   57.3   0.0    2.1e-15   56.8   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0036   17.3   0.3       0.06   13.3   0.1    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.0   2.2e-38   1.3e-34       1     163 []      10     188 ..      10     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 2.2e-38
                 Lactamase_B_3   1 eltwlghnsflletagarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql..................aenvk 63 
                                   +++wlgh+ f ++++ ++i++DP++   +   p++eaD++l+++++ dH++++ ++++                   +  +
  gi|91773474|ref|YP_566166.1|  10 SIEWLGHAGFIFRGQKKVIYIDPYQ-IPDEISPEDEADIILLTHEHFDHCNPDSIRKIrgsmtttlipenmslqfkGDARR 89 
                                   599*********************9.56677788************************98777777766666666544444 PP

                 Lactamase_B_3  64 vlee...geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggplt 141
                                   ++e+   +++l+++g++i+ v++++ +++ ++rge++g+++e +g++iyh G+ +     +e +e+ ++Dv l+P+   +t
  gi|91773474|ref|YP_566166.1|  90 IIEGdklKGDLAIKGVNIEVVPSYNLNKPNHPRGEGVGYIVELEGIKIYHAGDSDL---IPEMAEI-HADVALLPISADFT 166
                                   4544666688*********************************************9...8999999.************** PP

                 Lactamase_B_3 142 lgqeealelakrLkpklvlPmh 163
                                   ++ eea++++  + pk+ +Pmh
  gi|91773474|ref|YP_566166.1| 167 MSEEEAADATVSIGPKIAIPMH 188
                                   *********************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 !   56.8   0.0   3.5e-19   2.1e-15      21     201 .]      36     189 ..      15     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 3.5e-19
                                   --S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECS CS
                 Lactamase_B_2  21 Pve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgd 100
                                   P e   ++  + d +llth+H+DH+ + +++r++r+         ++   + +n++  +++ + +  ++  ++++ ++++ 
  gi|91773474|ref|YP_566166.1|  36 PDEiSPED--EADIILLTHEHFDHC-NPDSIRKIRG--------SMTTTLIPENMSLQFKGDA-RRIIEGDKLKGDLAIK- 103
                                   44544555..89*************.79*****877........5788888888888888888.4444555588899998. PP

                                   TTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---S CS
                 Lactamase_B_2 101 ggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltp 181
                                    g++i+++p     ++  +  +g+ +G+++e +g ++y++gD+  ipe++  +++ ad++ll+i           +++++ 
  gi|91773474|ref|YP_566166.1| 104 -GVNIEVVPSYNLNKP--NHPRGEGVGYIVELEGIKIYHAGDSDLIPEMA--EIH-ADVALLPIS---------ADFTMSE 169
                                   .788999999988888..78889************************884..466.9******99.........6799*** PP

                                   TSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 182 eeaveaaadlgakrlvliHi 201
                                   eea++a   +g+k+++++H+
  gi|91773474|ref|YP_566166.1| 170 EEAADATVSIGPKIAIPMHY 189
                                   *******************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1     1e-05      0.06      42      58 ..      42      58 ..      20      59 .. 0.86
   2 ?    2.5   0.0     0.022   1.3e+02     128     163 ..     120     186 ..      80     218 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                  GGGEEEEE-SBSSHHHH CS
                   Lactamase_B 42 pkdvdavilTHlHlDHi 58
                                   ++ d ++lTH H+DH+
  gi|91773474|ref|YP_566166.1| 42 EDEADIILLTHEHFDHC 58
                                  566799**********7 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.022
                                   TTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC................................ CS
                   Lactamase_B 128 gpghghghgvveygggkvlftGDallagetgridl...............................t 163
                                   +p   +++++ve++g k+  +GD  l++e ++i+                                +
  gi|91773474|ref|YP_566166.1| 120 HPRGEGVGYIVELEGIKIYHAGDSDLIPEMAEIHAdvallpisadftmseeeaadatvsigpkiaiP 186
                                   5666678889999999999999999999999999866555555555555555555555555555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1523.44
//
Query:       gi|91773475|ref|YP_566167.1|  [L=108]
Description: RNAse P, Rpr2/Rpp21 subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   55.4   0.1    9.2e-15   54.7   0.1    1.4  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
       0.12   12.1   0.4        4.8    7.0   0.1    2.2  2  Ribosomal_S27e  Ribosomal protein S27


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 !   54.7   0.1     1e-18   9.2e-15       1      90 []      21      97 ..      21      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1e-18
                                  HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EE CS
                          Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlv 83
                                  r++ L+++a+  + +++p  s ++++ +r++ +k+++r p  +kr++C+ C+s+l+pg++++vr++   +           ++
  gi|91773475|ref|YP_566167.1| 21 RIERLFKLAAE-EYSSNPGRSDRYVHLARRIGMKYRIRFPSPLKRKMCRGCSSYLVPGSSSRVRLHG--R----------YMT 90
                                  78999999998.999**************************************************53..2..........266 PP

                                  EEETTTT CS
                          Rpr2 84 vtClaCg 90
                                  +tCl+Cg
  gi|91773475|ref|YP_566167.1| 91 ITCLKCG 97
                                  ******7 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0057        52      20      37 ..      58      75 ..      52      86 .. 0.78
   2 ?    7.0   0.1   0.00053       4.8       2      16 ..      85      99 ..      84     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0057
                                  ESS-SS-EEESSSTCEEE CS
                Ribosomal_S27e 20 FshaatvvkCisCgkvLv 37
                                  F ++ +  +C  C++ Lv
  gi|91773475|ref|YP_566167.1| 58 FPSPLKRKMCRGCSSYLV 75
                                  667777779*****9998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00053
                                  S--EEEEE-TTTS-E CS
                Ribosomal_S27e  2 rskFldvkCpdCene 16
                                  +++++ + C +C++e
  gi|91773475|ref|YP_566167.1| 85 HGRYMTITCLKCGRE 99
                                  677888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 727.39
//
Query:       gi|91773476|ref|YP_566168.1|  [L=80]
Description: hypothetical protein Mbur_1511 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.6    7.9   3.4        2.5    8.0   1.6    1.8  2  B12D      NADH-ubiquinone reductase complex 1 MLRQ subunit


Domain annotation for each model (and alignments):
>> B12D  NADH-ubiquinone reductase complex 1 MLRQ subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0     0.071   1.3e+03      13      31 ..      29      47 ..      26      52 .. 0.67
   2 ?    8.0   1.6   0.00014       2.5       8      27 ..      55      74 ..      53      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.071
                          B12D 13 gagvggavfylvRllltnP 31
                                  g  +g +  +++R  + + 
  gi|91773476|ref|YP_566168.1| 29 GCSGGTCGAFGIRAGSEKN 47
                                  5566778888888766555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00014
                          B12D  8 LfvfigagvggavfylvRll 27
                                  +f+++g+g+   vf++v+ll
  gi|91773476|ref|YP_566168.1| 55 IFAIMGIGMLVGVFFIVKLL 74
                                  79***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 535.11
//
Query:       gi|91773477|ref|YP_566169.1|  [L=79]
Description: hypothetical protein Mbur_1512 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   21.6   0.1    0.00017   21.5   0.1    1.2  1  HTH_45    Winged helix-turn-helix
     0.0077   16.1   0.1      0.011   15.6   0.1    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.029   14.3   0.0    1.2  1  AvrM_N    Flax-rust effector AvrM N-terminal domain
      0.062   13.2   0.2        0.1   12.6   0.2    1.4  1  TBPIP     TBPIP/Hop2 winged helix domain
      0.078   13.5   0.0      0.098   13.2   0.0    1.3  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   4.9e-08   0.00017      21      69 ..      28      76 ..      14      79 .] 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.9e-08
                        HTH_45 21 kkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlellekl 69
                                  +  +i ++  +    ++k L+ L ek+li ++++ Y+lTe G  + +++
  gi|91773477|ref|YP_566169.1| 28 EGVRIAKNMHIAKISADKILEELAEKDLIVEENGFYKLTELGTTVERSV 76
                                  55678888888888999*************************9877666 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     3e-06     0.011      15      59 ..      18      63 ..      11      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-06
                                  HHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                          TrmB 15 laLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                  l Ll ++g+++   ia++  + + ++ ++L++L +k+l+  e g +
  gi|91773477|ref|YP_566169.1| 18 LSLLgSRGQLEGVRIAKNMHIAKISADKILEELAEKDLIVEENGFY 63
                                  678889*********************************9987755 PP

>> AvrM_N  Flax-rust effector AvrM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.1e-06     0.029      20      54 ..      34      69 ..      26      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
                        AvrM_N 20 kpaevekLspdeliRYvaerdtnvekma.rkLykaa 54
                                  k  +++k+s d+++  +ae+d +ve +   kL +++
  gi|91773477|ref|YP_566169.1| 34 KNMHIAKISADKILEELAEKDLIVEENGfYKLTELG 69
                                  889*********************998524666666 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.8e-05       0.1      28      50 ..      35      58 ..      26      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                         TBPIP 28 k.klgKtavqkaLdeLvdegkiie 50
                                  + ++ K ++ k+L+eL+++++i+e
  gi|91773477|ref|YP_566169.1| 35 NmHIAKISADKILEELAEKDLIVE 58
                                  446999****************87 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.7e-05     0.098      15      68 .]      23      69 ..       8      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                        HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   r++ +  ++++ + + ++++ ++l++L ek+L++++         +++lT+ G
  gi|91773477|ref|YP_566169.1| 23 SRGQLEGVRIAKNMHIAKISADKILEELAEKDLIVEE--N-----GFYKLTELG 69
                                  55555556899999999*****************443..3.....788888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 564.91
//
Query:       gi|91773478|ref|YP_566170.1|  [L=459]
Description: KaiC [Methanococcoides burtonii DSM 6242]
Scores for complete 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-71  238.5   0.5    6.1e-43  146.8   0.1    2.9  2  ATPase           KaiC
    2.6e-12   46.7   0.0    2.4e-06   27.1   0.0    2.3  2  DnaB_C           DnaB-like helicase C terminal domain
    3.6e-09   36.5   0.0    0.00038   20.1   0.1    3.1  2  AAA_25           AAA domain
      9e-07   29.4   0.0     0.0018   18.7   0.0    2.3  2  AAA_16           AAA ATPase domain
    2.8e-06   27.2   0.0      0.016   15.0   0.0    2.5  2  AAA_24           AAA domain
    8.1e-06   24.7   0.9       0.03   12.9   0.0    3.2  4  GvpD             GvpD gas vesicle protein
    1.4e-05   25.1   0.0      0.018   15.0   0.0    2.7  2  NACHT            NACHT domain
    1.4e-05   24.9   0.2     0.0089   15.8   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    6.8e-05   23.2   0.0      0.043   14.1   0.0    2.4  2  AAA_22           AAA domain
     0.0001   21.7   0.0       0.34   10.1   0.0    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00025   20.9   0.0     0.0015   18.4   0.0    2.2  2  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
    0.00029   20.4   0.6      0.055   13.0   0.1    2.4  2  AAA_7            P-loop containing dynein motor region
    0.00029   20.2   0.0      0.045   13.0   0.0    2.6  2  Rad51            Rad51
     0.0003   20.5   0.1       0.17   11.5   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
    0.00048   19.4   0.7       0.77    8.9   0.1    3.0  3  TIP49            TIP49 P-loop domain
    0.00052   20.5   0.0       0.13   12.7   0.0    2.4  2  AAA              ATPase family associated with various cellul
    0.00057   20.2   0.0       0.13   12.6   0.0    2.3  2  AAA_19           AAA domain
    0.00062   18.9   0.1       0.05   12.7   0.1    2.3  2  T2SSE            Type II/IV secretion system protein
     0.0007   19.6   0.0      0.006   16.6   0.0    2.4  2  AAA_14           AAA domain
     0.0007   19.6   0.4     0.0018   18.4   0.4    2.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00077   18.8   0.6       0.44    9.8   0.1    2.4  2  Zeta_toxin       Zeta toxin
     0.0011   17.9   0.0     0.0041   16.1   0.0    1.8  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0011   18.7   0.0        1.6    8.5   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
     0.0016   18.1   0.0     0.0057   16.3   0.0    1.9  2  SRP54            SRP54-type protein, GTPase domain
     0.0017   18.3   0.3       0.44   10.4   0.2    3.3  3  NTPase_1         NTPase
     0.0024   18.4   0.0      0.058   14.0   0.0    2.6  2  AAA_18           AAA domain
     0.0025   17.5   0.0        1.1    8.9   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0035   17.9   0.2          2    9.0   0.0    2.7  2  ABC_tran         ABC transporter
     0.0036   17.3   0.0       0.22   11.5   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
     0.0043   17.0   0.0      0.014   15.4   0.0    1.8  2  AAA_31           AAA domain
     0.0062   16.3   0.1       0.19   11.4   0.0    2.2  2  AAA_30           AAA domain
     0.0081   15.4   0.1      0.072   12.3   0.0    2.3  2  ArsA_ATPase      Anion-transporting ATPase
     0.0089   15.7   0.0      0.091   12.4   0.0    2.1  2  Zot              Zonular occludens toxin (Zot)
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.021   14.8   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
      0.012   14.8   0.1       0.71    8.9   0.0    2.6  3  PAXNEB           PAXNEB protein
      0.013   15.8   0.0        3.1    8.2   0.0    2.4  2  RNA_helicase     RNA helicase
      0.014   15.6   0.1        6.1    7.0   0.0    2.5  2  AAA_33           AAA domain
      0.015   14.7   1.1        1.3    8.4   0.2    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.019   14.2   0.2       0.09   12.0   0.0    2.0  2  NB-ARC           NB-ARC domain
      0.023   14.7   0.2        9.5    6.2   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.026   14.5   0.3       0.49   10.4   0.1    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
       0.03   13.5   0.1       0.44    9.7   0.1    2.2  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.03   13.1   0.0      0.056   12.3   0.0    1.3  1  AAA_35           AAA-like domain
      0.042   13.3   0.5        0.2   11.1   0.0    2.0  2  RecA             recA bacterial DNA recombination protein
      0.045   14.0   0.0        3.4    7.9   0.0    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.046   13.5   1.4       0.18   11.6   0.2    2.1  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.059   12.8   0.3        1.7    8.0   0.1    2.2  2  PhoH             PhoH-like protein
      0.064   12.4   1.2       0.83    8.7   0.1    2.3  2  PIF1             PIF1-like helicase
       0.11   12.0   0.0       0.21   11.0   0.0    1.5  1  KdpD             Osmosensitive K+ channel His kinase sensor d
       0.17   11.8   1.5       0.73    9.7   0.1    2.6  2  RsgA_GTPase      RsgA GTPase
       0.18   11.5   0.0        1.4    8.6   0.0    2.1  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.21   11.0   1.0         15    4.9   0.2    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.58    9.9   3.3        9.4    6.1   0.2    2.6  2  AAA_29           P-loop containing region of 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 !   87.7   0.1   2.2e-27   7.3e-25       2     229 ..       8     224 ..       7     226 .. 0.85
   2 !  146.8   0.1   1.8e-45   6.1e-43       1     226 [.     238     453 ..     238     456 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 2.2e-27
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegk 82 
                                   +  IeglDeil gG+ + +++l++G++G GKt++alq l + a++ ge+++++ +    +   e        +ekl++   
  gi|91773478|ref|YP_566170.1|   8 PCCIEGLDEIL-GGFKSPSTILVAGTAGVGKTTMALQMLSNAAKS-GEKVLYIPLTTVTS---E-------RFEKLQAVFP 76 
                                   567*******9.******************************999.*******9865443...3.......3566667777 PP

                        ATPase  83 laiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvse 163
                                   +++ ++s++  ++  +  ++d+ + + e+ ++i + +  r+viD+it++     e++ R+ + +l ++lk+ +   +l+ e
  gi|91773478|ref|YP_566170.1|  77 FIFENISTHPLNR--QAAEKDPLSTLIEMGNVITSENPDRIVIDPITPIGFGFVEQERRRFFYTLDSMLKESNALVMLTGE 155
                                   8888888888664..4578889999999*********************66667777899999999999************ PP

                        ATPase 164 kssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhsk......kehpfeIteegikvlee 229
                                       ee++ g  v++ + dg+i L ++   +++   l+++km g++ +k      +e+ ++++++g +++++
  gi|91773478|ref|YP_566170.1| 156 L--LEEQIHGSVVSH-LTDGIIYLSKENSGYHTAHKLRVLKMLGSNLQKsgmstsREYSYDVSSDGFVIYPR 224
                                   5..778*********.**************************998876422222267778888888777775 PP

  == domain 2  score: 146.8 bits;  conditional E-value: 1.8e-45
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   +++g+e +D +l+gG+  g+++l++GepG+GKtif+  F+++g+++ ge+gv+v+  e++e+++++a+++ w+++++ ++g
  gi|91773478|ref|YP_566170.1| 238 IRSGVENFDLMLYGGMIAGNSMLVAGEPGAGKTIFSWSFIMEGLSN-GENGVIVSYGERPEQIIREAAKFNWNMQQYVDSG 317
                                   579****************************************999.********************************** PP

                        ATPase  82 klaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgvTailv 161
                                   +l +i+   +++          + e + +l+  ++e++++r+v+D + +l  +  ++ ++R +l  l++ lk +gv ++++
  gi|91773478|ref|YP_566170.1| 318 QLQFIHSNPEEI---------HPAEHAIKLKGLVEELGITRIVVDGLVNLeITFPDNIKLRGYLLSLINYLKSMGVSSVFT 389
                                   *****9988865.........58889999*********************667777778********************** PP

                        ATPase 162 sekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikv 226
                                   +e + + +++  ++ + fi+d v+ L++ + ++e++R+l+++k  g++h   + ++ I++ gik 
  gi|91773478|ref|YP_566170.1| 390 TELDPQTGSIMSNE-ASFIMDSVVTLEQILCSNEVKRYLRVLKSKGSRHGLIMREYVISDTGIKL 453
                                   **999988888887.567*********************************************96 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 !   27.1   0.0   7.2e-09   2.4e-06       5      62 ..      10      66 ..       7     138 .. 0.79
   2 !   17.4   0.0   6.3e-06    0.0021       2      85 ..     238     320 ..     237     386 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.2e-09
                                  STHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  5 gfkdLDkltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeq 62
                                    + LD++++G+++   i++A+ +++Gkt++al++ +naa++   +v+++ l   +++
  gi|91773478|ref|YP_566170.1| 10 CIEGLDEILGGFKSPSTILVAGTAGVGKTTMALQMLSNAAKS-GEKVLYIPLTTVTSE 66
                                  5678**********************************9974.557777766555554 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 6.3e-06
                                   BXSSTHHHH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHH CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C   2 lstgfkdLD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrt 81 
                                   +++g +++D  l +G+  g+ +++A+ p+ Gkt +  +++ +   + +++v+ +s     eq+++     + ++ ++ + +
  gi|91773478|ref|YP_566170.1| 238 IRSGVENFDlMLYGGMIAGNSMLVAGEPGAGKTIFSWSFIMEGLSNGENGVI-VSYGERPEQIIREAAKFNWNM-QQYVDS 316
                                   678999999445689************************9998876666665.566666667766555544443.444555 PP

                                   TTSX CS
                                   xxxx RF
                        DnaB_C  82 gklk 85 
                                   g+l+
  gi|91773478|ref|YP_566170.1| 317 GQLQ 320
                                   5554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.1e-06   0.00038      18     184 ..      10     151 ..       2     155 .. 0.56
   2 !   11.6   0.0   0.00043      0.15      25     108 ..     249     324 ..     246     358 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-06
                        AAA_25  18 pppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsed....elrrRlrav 93 
                                    ++ ++ +++g+    +++l+aG  g+GKtt+al++    a +G+           kVly+ +    +     l+  +  +
  gi|91773478|ref|YP_566170.1|  10 CIEGLDEILGGF-KSPSTILVAGTAGVGKTTMALQMLSNAAkSGE-----------KVLYIPLTTVTSerfeKLQAVFPFI 78 
                                   566677777888.67899***********************8888...........4555554333320000222222222 PP

                        AAA_25  94 gealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealer 174
                                   +e++   ++ ++     +       +  +++l  + + ++ ++i++ e+++ +viDp++ +  g  +   + ++++  l++
  gi|91773478|ref|YP_566170.1|  79 FENI---STHPLNR---Q-------AAEKDPL--STLIEMGNVITS-ENPDRIVIDPITPIGFGFVE--QERRRFFYTLDS 141
                                   2332...2222221...1.......1112222..222355677777.77777777777776666333..234555555555 PP

                        AAA_25 175 iarrtgaavl 184
                                   + ++ +a v+
  gi|91773478|ref|YP_566170.1| 142 MLKESNALVM 151
                                   5555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00043
                        AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelr..rRlravgealrddar 102
                                   l++g++ ag   l+aG pg+GKt +  +   + +  G+            V++  +E +e+ +r   ++ + ++++ d ++
  gi|91773478|ref|YP_566170.1| 249 LYGGMI-AGNSMLVAGEPGAGKTIFSWSFIMEGLsNGE----------NGVIVSYGERPEQIIReaAKFNWNMQQYVDSGQ 318
                                   567776.8*****************9888777773333..........256666677777766633566667777777777 PP

                        AAA_25 103 llvldl 108
                                   l++++ 
  gi|91773478|ref|YP_566170.1| 319 LQFIHS 324
                                   777764 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   5.4e-06    0.0018      23      88 ..      23      94 ..      11     153 .. 0.65
   2 !    8.7   0.0    0.0062       2.1      24      44 ..     256     276 ..     248     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.4e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekd........ggiflrgkcdqlesaipysalaqalareellrqllde 88
                                  +p+ +l+ G +GvGK++++ + l  + k+           ++++++++l++  p+  + + ++++ l rq +++
  gi|91773478|ref|YP_566170.1| 23 SPSTILVAGTAGVGKTTMALQMLSNAAKSgekvlyipLTTVTSERFEKLQAVFPF--IFENISTHPLNRQAAEK 94
                                  5689***************998888888866444332122355555555555555..55555555555555544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0062
                        AAA_16  24 pelvllsGesGvGKsslvrel 44 
                                   ++++l+ Ge+G GK+   +++
  gi|91773478|ref|YP_566170.1| 256 GNSMLVAGEPGAGKTIFSWSF 276
                                   389************876655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.7e-05     0.016       4      31 ..      26      60 ..      23     134 .. 0.72
   2 !   10.0   0.0    0.0015      0.52       3      22 ..     257     276 ..     255     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.7e-05
                        AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidt 31
                                   il+ G +g+GKTt+a+++       g+k+l+i +
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMlsnaaksGEKVLYIPL 60
                                  699****************9999999999999943 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0015
                        AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                   +++l+ G++g+GKT + +++
  gi|91773478|ref|YP_566170.1| 257 NSMLVAGEPGAGKTIFSWSF 276
                                   789**************999 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0025      0.86      11      44 ..      25      59 ..      21      78 .. 0.80
   2 ?   -2.7   0.0         5   1.7e+03     154     194 ..     158     197 ..     140     202 .. 0.72
   3 !   12.9   0.0     9e-05      0.03       9      31 ..     255     277 ..     250     306 .. 0.80
   4 ?   -1.0   0.0       1.5   5.2e+02     161     197 ..     403     438 ..     375     452 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0025
                          GvpD 11 ktllikGaPGtGktlftlrgldvlrr.esdvlyvs 44
                                   t+l+ G  G Gkt+++l+ l    +  ++vly+ 
  gi|91773478|ref|YP_566170.1| 25 STILVAGTAGVGKTTMALQMLSNAAKsGEKVLYIP 59
                                  699******************8766515689**95 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5
                          GvpD 154 letaansrleyivdGvvtlnvkeddrgrlrrdlrleklrGv 194
                                    e  + s + ++ dG++ l  ke+    +  +lr+ k+ G 
  gi|91773478|ref|YP_566170.1| 158 EEQIHGSVVSHLTDGIIYLS-KENSGYHTAHKLRVLKMLGS 197
                                   45556677889999999997.55657789999999999885 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 9e-05
                          GvpD   9 aGktllikGaPGtGktlftlrgl 31 
                                   aG+++l+ G+PG+Gkt+f   ++
  gi|91773478|ref|YP_566170.1| 255 AGNSMLVAGEPGAGKTIFSWSFI 277
                                   79****************98875 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.5
                          GvpD 161 rleyivdGvvtl.nvkeddrgrlrrdlrleklrGvrig 197
                                   +  +i+d vvtl ++       ++r lr+ k +G r g
  gi|91773478|ref|YP_566170.1| 403 EASFIMDSVVTLeQILCS--NEVKRYLRVLKSKGSRHG 438
                                   456999******866544..467888888888777655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.2e-05     0.018       2      59 ..      26      79 ..      25     120 .. 0.74
   2 ?    7.5   0.1     0.011       3.6       3      23 ..     259     279 ..     257     393 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.2e-05
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHC CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllf 59
                                  ++++ G aG+GKTt++ ++ + +a++  +     l + l+  + +r ++   +  ++f
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAKSGEKV----LYIPLTTVTSERFEKLQAVFPFIF 79
                                  899***********9999999999888332....344444444444444455555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.011
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   +++ Ge+G GKT++  +++++
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFSWSFIME 279
                                   789**********98777765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-05    0.0089      49      86 ..      26      63 ..      21      74 .. 0.88
   2 ?    6.6   0.0     0.018         6      48      76 ..     257     285 ..     249     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                     IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrvedL 86
                                   i++ G +GvGK+ +a  +  +a+++g +vl++ ++ +
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTV 63
                                  7899****************************977655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                     IstB_IS21  48 enivllGpsGvGKshlaialgveavragl 76 
                                   +++++ G +G+GK+ ++ ++ +e+  +g 
  gi|91773478|ref|YP_566170.1| 257 NSMLVAGEPGAGKTIFSWSFIMEGLSNGE 285
                                   578999*************9999887664 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   0.00013     0.043       6      70 ..      25      88 ..      21     154 .. 0.70
   2 ?    6.7   0.0     0.024       8.1       6      20 ..     257     271 ..     254     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00013
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsst..sskdllrellralglelka 70
                                  + ++v G +G+GKTt + ++l+++ +       + +v+   + t++s+   +++ ++  +++++     +
  gi|91773478|ref|YP_566170.1| 25 STILVAGTAGVGKTTMALQMLSNAAKS------GEKVLyipLTTVTSERfeKLQAVFPFIFENISTHPLN 88
                                  6799*************9999998432......5555512533333333557777777777777655555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.024
                        AAA_22   6 gilvvtGesGtGKTt 20 
                                   ++++v Ge+G+GKT 
  gi|91773478|ref|YP_566170.1| 257 NSMLVAGEPGAGKTI 271
                                   6799**********7 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0015      0.51       3      30 ..      26      51 ..      24      73 .. 0.81
   2 !   10.1   0.0     0.001      0.34       4      52 ..     259     305 ..     257     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                       DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddee 30
                                   +lV G aG GKt ++l++l ++ +  +
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAK--S 51
                                  699*****************99833..3 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.001
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlreala 52 
                                   +lV G++G+GKt+   +++ e    +++++ v++s  ++  +++rea +
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFSWSFIMEG--LSNGENGVIVSYGERPEQIIREAAK 305
                                   69***************99998..7888888888888888888888765 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 ?   -1.2   0.0       4.8   1.6e+03      16      37 ..      40      61 ..      38      75 .. 0.74
   2 !   18.4   0.0   4.5e-06    0.0015      19      69 ..     275     325 ..     272     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.8
                          MEDS 16 alvpfikaglargekvlyvasa 37
                                  ++++ ++++ ++gekvly+  +
  gi|91773478|ref|YP_566170.1| 40 MALQMLSNAAKSGEKVLYIPLT 61
                                  67788999999*******9764 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.5e-06
                          MEDS  19 pfikaglargekvlyvasastldelrealrkagldvdaalesgqleildae 69 
                                   +fi +gl++ge  ++v   ++ +++ ++ +k + + +++++sgql++++++
  gi|91773478|ref|YP_566170.1| 275 SFIMEGLSNGENGVIVSYGERPEQIIREAAKFNWNMQQYVDSGQLQFIHSN 325
                                   8**********99999999***************************99965 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 !   13.0   0.1   0.00016     0.055      34      74 ..      25      65 ..      20      75 .. 0.87
   2 ?    5.2   0.0     0.039        13      32      58 ..     255     282 ..     244     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                         AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqts 74
                                    +l+ G++G+GKt+++ ++l++  k+  ++l i ++  ts
  gi|91773478|ref|YP_566170.1| 25 STILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTS 65
                                  6799*******************999999999999988876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.039
                         AAA_7  32 nkkpvllvGptGtGKtviikd.llkkld 58 
                                   +++++l+ G+ G GKt+   + +++ l+
  gi|91773478|ref|YP_566170.1| 255 AGNSMLVAGEPGAGKTIFSWSfIMEGLS 282
                                   57899***********998887777766 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.051        17      19      58 ..       7      45 ..       1     122 [. 0.70
   2 !   13.0   0.0   0.00013     0.045      14      59 ..     230     278 ..     217     358 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.051
                                  E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHH CS
                         Rad51 19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlc 58
                                  l    + lDe+L GG+++ s   + G  + Gkt ++ ++ 
  gi|91773478|ref|YP_566170.1|  7 LPCCIEGLDEIL-GGFKSPSTILVAGTAGVGKTTMALQML 45
                                  555667799998.89******************9887653 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00013
                                   HSS-E...E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHH CS
                         Rad51  14 sellq...lttGskklDelLgGGietgsiteifGefrsGktqlchtlcv 59 
                                    ++++   +  G +++D +L GG+ +g+   + Ge ++Gkt ++ ++ +
  gi|91773478|ref|YP_566170.1| 230 LDIISetkIRSGVENFDLMLYGGMIAGNSMLVAGEPGAGKTIFSWSFIM 278
                                   5555444499*******************************99988643 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00051      0.17      20      57 ..      22      59 ..       9      71 .. 0.81
   2 ?    6.5   0.0     0.018         6      24      66 ..     258     300 ..     239     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00051
                                  TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
               Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavn 57
                                  k+++++l+ G  G+GK+++a ++ ++  ++ ++++ + 
  gi|91773478|ref|YP_566170.1| 22 KSPSTILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIP 59
                                  7889******************9998888887776665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                                   -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCH CS
               Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaaipeell 66 
                                   s+l+ Ge G+GK++++ +   +   + ++ v v  ++ pe+++
  gi|91773478|ref|YP_566170.1| 258 SMLVAGEPGAGKTIFSWSFIMEGLSNGENGVIVSYGERPEQII 300
                                   78*************9888887777777778888888888876 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.015       5.2      52      74 ..      26      48 ..      19      82 .. 0.72
   2 ?    0.7   0.0      0.69   2.3e+02     185     211 ..     198     224 ..     185     236 .. 0.85
   3 !    8.9   0.1    0.0023      0.77      31      66 ..     237     272 ..     226     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                                  XXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 52 avLlaGpsgtGktalaiaiskel 74
                                  ++L+aG +g Gkt +a+ +  + 
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNA 48
                                  79**************9874333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.69
                                   -EEE-SSS-SS------S--------S CS
                         TIP49 185 kvkklGrsearakefDiekdefvelPk 211
                                   +++k G s++r+ ++D+++d fv  P+
  gi|91773478|ref|YP_566170.1| 198 NLQKSGMSTSREYSYDVSSDGFVIYPR 224
                                   68999*****************99885 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0023
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  31 kareaagvivelikekklaGravLlaGpsgtGktal 66 
                                   k r  +  +  ++  + +aG ++L+aG++g+Gkt  
  gi|91773478|ref|YP_566170.1| 237 KIRSGVENFDLMLYGGMIAGNSMLVAGEPGAGKTIF 272
                                   55555555666778899****************976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00038      0.13       1      46 [.      27      75 ..      27     103 .. 0.77
   2 ?    5.4   0.0     0.067        23       1      14 [.     259     272 ..     259     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00038
                                  EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSSSTTHHHHHH CS
                           AAA  1 vllyGppGtGKTllakavakel...gvefleisgsellskyvgesekki 46
                                  +l+ G+ G+GKT++a ++ +++   g ++l i +++++s+ +++ ++ +
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSNAaksGEKVLYIPLTTVTSERFEKLQAVF 75
                                  699************9999886444688999999888855444444444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.067
                                   EEEESSTTSSHHHH CS
                           AAA   1 vllyGppGtGKTll 14 
                                   +l+ G pG GKT++
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIF 272
                                   799*********86 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00039      0.13      11      71 ..      25      84 ..      17     199 .. 0.81
   2 ?    5.6   0.0     0.055        19      10      33 ..     256     279 ..     252     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00039
                        AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatT 71
                                  +++lv + +G GKT++  ++++ + + g+ k+  i l ++t+   ++l+     + ++++T
  gi|91773478|ref|YP_566170.1| 25 STILVAGTAGVGKTTMALQMLSNAAKSGE-KVLYIPLTTVTSERFEKLQAVFPFIFENIST 84
                                  67899999********9999999999984.5678888888888777777766666666655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.055
                        AAA_19  10 ekvllvtaGpGtGKTrvlkhival 33 
                                    + +lv + pG GKT      + +
  gi|91773478|ref|YP_566170.1| 256 GNSMLVAGEPGAGKTIFSWSFIME 279
                                   57799**********865555554 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 !   12.7   0.1   0.00015      0.05     127     162 ..      22      57 ..       2      61 .. 0.83
   2 ?    4.0   0.0     0.063        21     121     150 ..     248     277 ..     189     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                         T2SSE 127 rerglilvsGgTgsGKttllyallkeinksderivt 162
                                   ++  +ilv+G+ g GKtt++  +l+  +ks e+++ 
  gi|91773478|ref|YP_566170.1|  22 KSPSTILVAGTAGVGKTTMALQMLSNAAKSGEKVLY 57 
                                   55689***************9999999999888775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.063
                         T2SSE 121 vlrkavrerglilvsGgTgsGKttllyall 150
                                   +l   + +  ++lv+G  g GKt++  + +
  gi|91773478|ref|YP_566170.1| 248 MLYGGMIAGNSMLVAGEPGAGKTIFSWSFI 277
                                   555566667899************986655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-05     0.006       4      62 ..      26      84 ..      23     176 .. 0.73
   2 ?   -0.4   0.0       3.2   1.1e+03       6      47 ..     260     301 ..     256     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-05
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke 62
                                   +++ G   vGKTt++ q++++   + e++lyi l + + +++++ + +  +i+e++++
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTSERFEKLQAVFPFIFENIST 84
                                  57899***************9999999*********99998887777677777766443 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.2
                        AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47 
                                   ++ G   +GKT +   +i e l + e+ + ++  + +++ ++
  gi|91773478|ref|YP_566170.1| 260 LVAGEPGAGKTIFSWSFIMEGLSNGENGVIVSYGERPEQIIR 301
                                   67777789*****99999999866666666666555554444 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4   5.2e-06    0.0018       3      33 ..      28      58 ..      26     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.2e-06
                                  EEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  3 iastkGGvGKTtlaanLaralarrglrVllv 33
                                  +++++ GvGKTt+a+ ++   a+ g +Vl +
  gi|91773478|ref|YP_566170.1| 28 LVAGTAGVGKTTMALQMLSNAAKSGEKVLYI 58
                                  678999**********************977 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0013      0.44      14      45 ..      22      54 ..      15      63 .. 0.76
   2 ?    6.8   0.0     0.011       3.6      19      33 ..     259     273 ..     256     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                    Zeta_toxin 14 erPklillgGqpGAGKselaellkdele.rqgn 45
                                  ++P  il++G  G GK+++a  +  + + ++++
  gi|91773478|ref|YP_566170.1| 22 KSPSTILVAGTAGVGKTTMALQMLSNAAkSGEK 54
                                  78****************987665554424444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                    Zeta_toxin  19 illgGqpGAGKsela 33 
                                   +l++G pGAGK+  +
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFS 273
                                   79*********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 !   16.1   0.0   1.2e-05    0.0041      17      60 ..      26      69 ..      22      86 .. 0.88
   2 ?   -1.8   0.0       3.3   1.1e+03      18      43 ..     259     284 ..     256     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                 TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivlDltGafvsrfy 60
                                   il++Gt+G GKt+++ ++l ++ + g++++ + lt    +rf 
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTSERFE 69
                                  5899************************9998877777777775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.3
                 TrwB_AAD_bind  18 ilivGttGsGKtqalekllrairarg 43 
                                   +l++G  G+GKt    +++ +  + g
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFSWSFIMEGLSNG 284
                                   7899********87766654444444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0046       1.6      15      94 ..      25     100 ..      11     123 .. 0.67
   2 !    7.9   0.0    0.0071       2.4      12      52 ..     254     288 ..     243     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0046
                                   CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEEEEETTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                          DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid..lrvlliiggvaardqlsk 93 
                                     +lva+  G GKT+++l  + ++      k+g k+l++ P++  + + +++l+ ++ +i   ++++ +  + a++d ls+
  gi|91773478|ref|YP_566170.1|  25 STILVAGTAGVGKTTMALQMLSNA-----AKSGEKVLYI-PLTTVTSERFEKLQAVFPFIFenISTHPLNRQAAEKDPLST 99 
                                   6799***********976666544.....4788888886.88888888888888888764323444444445555666666 PP

                                   H CS
                                   x RF
                          DEAD  94 l 94 
                                   l
  gi|91773478|ref|YP_566170.1| 100 L 100
                                   5 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0071
                                   HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkali 52 
                                   + g+++lva+e G+GKT   +  +++ +++  g++g    +
  gi|91773478|ref|YP_566170.1| 254 IAGNSMLVAGEPGAGKTIFSWSFIMEGLSN--GENG----V 288
                                   36899************9998888888865..5544....3 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.7e-05    0.0057       2      90 ..      25     118 ..      24     121 .. 0.80
   2 ?   -2.2   0.0         8   2.7e+03       3      15 ..     258     270 ..     257     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-05
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHH....HHTTE.EEEESSTTSCHHHHHHHHHH CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktla....eklgv.pvikkkeeadpaavakeave 77 
                                   + il++G+ G+GKTt + ++     k+g+kvl + + t     +e L+++     e++   p+ ++  e+dp +++ e  +
  gi|91773478|ref|YP_566170.1|  25 STILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTSERFEKLQAVFpfifENISThPLNRQAAEKDPLSTLIEMGN 105
                                   789*******************************99999999999999765111133332033347777899999999888 PP

                                   HHHHTTSSEEEEE CS
                         SRP54  78 kakeekidvvlvD 90 
                                      +e+ d +++D
  gi|91773478|ref|YP_566170.1| 106 VITSENPDRIVID 118
                                   8888888888888 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8
                                   EEEEEESTTSSHH CS
                         SRP54   3 villvGlqGaGKT 15 
                                    +l++G  GaGKT
  gi|91773478|ref|YP_566170.1| 258 SMLVAGEPGAGKT 270
                                   57899*******9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2    0.0013      0.44       2      30 ..      27      55 ..      26      67 .. 0.89
   2 ?    1.4   0.0      0.79   2.7e+02      94     131 ..     110     152 ..      83     185 .. 0.78
   3 ?    2.4   0.0      0.39   1.3e+02       2      17 ..     259     274 ..     258     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                                  EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                  +++ G  GvGKtT+  ++l++ ++sg kv
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSNAAKSGEKV 55
                                  899**************999999988776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.79
                                   HHH-EEEE---.....STTGGG-HHHHHHHHHHHTTTSEEEEE CS
                      NTPase_1  94 seadviviDEi.....GkmElkskkfkeaveevLksekpvlav 131
                                   +++d iviD i     G  E + ++f  +++ +Lk+++ +++ 
  gi|91773478|ref|YP_566170.1| 110 ENPDRIVIDPItpigfGFVEQERRRFFYTLDSMLKESNALVML 152
                                   7889999998866666889****************65555543 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.39
                                   EEEE--TTSSHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvk 17 
                                   +++ G+pG GKt +  
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFSW 274
                                   6799********8754 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   0.00017     0.058       1      17 [.      27      43 ..      27     125 .. 0.80
   2 ?    1.8   0.0      0.97   3.3e+02       2      13 ..     260     271 ..     259     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00017
                        AAA_18  1 IlltGtpGvGKttlake 17
                                  Il++Gt+GvGKtt+a  
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQ 43
                                  99***********9855 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.97
                        AAA_18   2 lltGtpGvGKtt 13 
                                   l++G pG+GKt 
  gi|91773478|ref|YP_566170.1| 260 LVAGEPGAGKTI 271
                                   699*******96 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 !    8.9   0.0    0.0031       1.1      15      47 ..      25      58 ..      13      91 .. 0.82
   2 ?    6.1   0.0     0.022       7.5      11      58 ..     253     301 ..     241     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0031
                                  -EEEEEESTTSSHHHHH.HHHHHHSSTSSEEEEE CS
                                  xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 15 qrtlipgafgvGktvis.qslskqsnsddaiiyv 47
                                   ++l+ g +gvGkt+++ q+ls+ ++s + + y+
  gi|91773478|ref|YP_566170.1| 25 STILVAGTAGVGKTTMAlQMLSNAAKSGEKVLYI 58
                                  58899***********999999999887766665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                                   EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEEESEEHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  11 ivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvgiGergnevae 58 
                                   ++ G+ +l+ g+ g Gkt  s s + +  s+    ++v  Ger +++ +
  gi|91773478|ref|YP_566170.1| 253 MIAGNSMLVAGEPGAGKTIFSWSFIMEGLSNGeNGVIVSYGERPEQIIR 301
                                   6789***************995544444444339999******887655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0058         2       7      67 ..      20      81 ..      14     202 .. 0.77
   2 ?    6.3   0.0      0.04        13      10      63 ..     255     308 ..     250     361 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0058
                                  EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqe 67
                                   +k  +++ + G  G GK+t++  ++ +  +  +++l+   + +++++ e+l++ + +++++
  gi|91773478|ref|YP_566170.1| 20 GFKSPSTILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIpLTTVTSERFEKLQAVFPFIFEN 81
                                  6777789999***********88888888777777766546666667777777777777777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.04
                                   TTSEEEEEESTTSSHHHHHH..HHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEE CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  10 egekvaivGenGaGKStLlk..llagllkpteGeilldgkdlkeqeleslrkeigv 63 
                                   +g+ + + Ge GaGK+ +    ++ gl++ ++G i   g+  +++ +e   +++ +
  gi|91773478|ref|YP_566170.1| 255 AGNSMLVAGEPGAGKTIFSWsfIMEGLSNGENGVIVSYGERPEQIIREA--AKFNW 308
                                   67888999*******9875422677888889999966677766633333..33333 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 !   11.5   0.0   0.00065      0.22      22      60 ..      22      58 ..       4     114 .. 0.77
   2 ?    3.5   0.0      0.19        63      27      53 ..     259     285 ..     239     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00065
                                  .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                        ResIII 22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                  k    +l++ + G+GKT +a+++  + +k+g+  k+l +
  gi|91773478|ref|YP_566170.1| 22 KSPSTILVAGTAGVGKTTMALQMLSNAAKSGE--KVLYI 58
                                  467789999********************977..77654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                                   EEEEESTTSTHHHHHHHHHHHH-S... CS
                        ResIII  27 glikmaTGtGKTlvaaklierllkkgk 53 
                                   +l++ + G+GKT+ + ++i + l++g+
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFSWSFIMEGLSNGE 285
                                   5778889********888777666544 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     4e-05     0.014      12      38 ..      34      60 ..      27     103 .. 0.92
   2 ?   -2.2   0.0       9.9   3.3e+03      33      50 ..     387     404 ..     373     449 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4e-05
                        AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDl 38
                                  GvGKTT ++++ +  ak+g+kvL + l
  gi|91773478|ref|YP_566170.1| 34 GVGKTTMALQMLSNAAKSGEKVLYIPL 60
                                  9**********************9965 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.9
                        AAA_31  33 vLlvDlDpQanattglgi 50 
                                   v   +lDpQ+ + ++ + 
  gi|91773478|ref|YP_566170.1| 387 VFTTELDPQTGSIMSNEA 404
                                   667788888877665543 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00055      0.19      20      63 ..      26      69 ..      21     118 .. 0.82
   2 ?    2.5   0.0      0.31   1.1e+02      21      33 ..     259     271 ..     253     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00055
                        AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa 63
                                  + ++ G AG GKtt+  ++   ++++g++v+ +  t   +++ +
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTSERFE 69
                                  56899*********988888888889999998888877777655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.31
                        AAA_30  21 avltGpAGtGKtt 33 
                                   +++ G +G+GKt 
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTI 271
                                   7899*******96 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00021     0.072       3      35 ..      26      58 ..      25     112 .. 0.90
   2 ?    0.2   0.1      0.98   3.3e+02       4      35 ..     259     290 ..     257     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvlli 35
                                   ilv+G  GVGKtt++  +  + +++g+kvl i
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAKSGEKVLYI 58
                                  599***************************987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.98
                                   EEEEESTTSSHHHHHHHHHHH.HHHTTS-EEEE CS
                   ArsA_ATPase   4 ilvgGKGGVGKttvsaatavk.lsekgkkvlli 35 
                                   +lv+G  G GKt  s ++ ++ ls+ ++ v ++
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFSWSFIMEgLSNGENGV-IV 290
                                   6899*************9998566555444.44 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00027     0.091       2      70 ..      26      93 ..      25     110 .. 0.73
   2 ?    0.8   0.0      0.98   3.3e+02       4      20 ..     260     276 ..     258     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                           Zot  2 islvtGapGsgKtsgavkkdllpalke.gRkiitnidGlrlerieqvlgekvstarlirid.npegaetlk 70
                                  + lv G  G gKt  a+++ l +a k+ +++++  +   + er+e+ l+ +++     +i+ +p+ ++  +
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQM-LSNAAKSgEKVLYIPLTTVTSERFEK-LQAVFP-FIFENIStHPLNRQAAE 93
                                  7799***************.77777762566777999999888888.677776.23445555776666555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.98
                           Zot   4 lvtGapGsgKtsgavkk 20 
                                   lv G+pG+gKt  + ++
  gi|91773478|ref|YP_566170.1| 260 LVAGEPGAGKTIFSWSF 276
                                   789********987666 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 ?   14.8   0.0   6.1e-05     0.021      20      68 ..      24      71 ..      11     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.1e-05
                      ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                   + +++ G  g+GKt++  ++++n  ++++ ++ yi+l ++ ++++++ 
  gi|91773478|ref|YP_566170.1| 24 PSTILVAGTAGVGKTTMALQMLSNAAKSGE-KVLYIPLTTVTSERFEKL 71
                                  5668899******************88886.555679999888888776 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.16        54     236     282 ..     134     177 ..     117     223 .. 0.70
   2 ?    8.9   0.0    0.0021      0.71      19      84 ..     238     302 ..     233     328 .. 0.88
   3 ?   -1.6   0.0       3.5   1.2e+03     208     283 ..     347     416 ..     308     440 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                        PAXNEB 236 kFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieLe 282
                                   +F+++L ++l++sn+ ++ t   +l+ +++ + + + +l D++i L+
  gi|91773478|ref|YP_566170.1| 134 RFFYTLDSMLKESNALVMLT--GELL-EEQIHGSVVSHLTDGIIYLS 177
                                   7999*******999988877..6788.78888889999999999986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                        PAXNEB  19 tStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlre 84 
                                   + +G++++D +L GG+  G+++l+  +     +++    F+ eG+ ++ + +++s+ + pe+++re
  gi|91773478|ref|YP_566170.1| 238 IRSGVENFDLMLYGGMIAGNSMLVAGE-PGAGKTIFSWSFIMEGLSNGENGVIVSYGERPEQIIRE 302
                                   569*********************955.44557888899*****************9****99987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.5
                        PAXNEB 208 vlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieLes 283
                                   + Riv+  L++  ++  p++ +    ll+++  L+++     +  + t  l+     s + ++   ++D+v++Le 
  gi|91773478|ref|YP_566170.1| 347 ITRIVVDGLVNLEITF-PDNIKLRGYLLSLINYLKSMG----VSSVFTTELDPQ-TGSIMSNEASFIMDSVVTLEQ 416
                                   7788888888888844.444444445555555555443....333333222222.334444555556666666665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0093       3.1       1      26 [.      27      52 ..      27     108 .. 0.78
   2 ?    5.3   0.0     0.074        25       2      23 ..     260     281 ..     259     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0093
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                  i++ G +g+GK+t+a ++ ++ +k+ 
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSNAAKSG 52
                                  6789***********99888777554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.074
                  RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                                   ++ G++g GK+ ++ +++ + l
  gi|91773478|ref|YP_566170.1| 260 LVAGEPGAGKTIFSWSFIMEGL 281
                                   689***********99887655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.018       6.1       2      22 ..      27      47 ..      27     105 .. 0.87
   2 ?    6.1   0.0     0.035        12       3      19 ..     260     276 ..     259     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.018
                        AAA_33  2 vllvGlpGsGKstlaerllkk 22
                                  +l+ G +G+GK+t a ++l +
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSN 47
                                  6789***********999865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.035
                        AAA_33   3 llvGlpGsGKstlaerl 19 
                                   l+ G pG+GK+ ++++ 
  gi|91773478|ref|YP_566170.1| 260 LVAGEPGAGKTIFSWSF 276
                                   6789**********985 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0037       1.3      37      64 ..      22      49 ..       9      55 .. 0.87
   2 ?    4.8   0.0     0.046        15      40      61 ..     257     278 ..     234     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0037
                                  GS-.SEEEE--TTSSHHHHHHHHHHHHH CS
                  FtsK_SpoIIIE 37 kmashllvaGatgsGKStalntLilSla 64
                                  k++s +lvaG+ g GK+t+   ++ ++a
  gi|91773478|ref|YP_566170.1| 22 KSPSTILVAGTAGVGKTTMALQMLSNAA 49
                                  56788*************9999998887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.046
                                   .SEEEE--TTSSHHHHHHHHHH CS
                  FtsK_SpoIIIE  40 shllvaGatgsGKStalntLil 61 
                                   + +lvaG +g GK+ +  ++i+
  gi|91773478|ref|YP_566170.1| 257 NSMLVAGEPGAGKTIFSWSFIM 278
                                   569***********99888776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00027      0.09      22      49 ..      26      53 ..      11     106 .. 0.66
   2 ?   -0.8   0.1       2.1     7e+02      23      36 ..     259     272 ..     252     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                                  EEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                        NB-ARC 22 vvalvGmgGvGKttlakqilnksdeveg 49
                                   + + G +GvGKtt+a q+l++ ++  +
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTMALQMLSNAAKSGE 53
                                  67899**************999554443 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                                   EEEEESTTSSHHHH CS
                        NB-ARC  23 valvGmgGvGKttl 36 
                                   + + G +G GKt+ 
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIF 272
                                   7899********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 ?    6.2   0.0     0.028       9.5      19      42 ..      24      47 ..       5      59 .. 0.79
   2 ?    5.8   0.0     0.039        13      19      40 ..     256     277 ..     234     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.028
                                  TEEEEEEESTTSSHHHHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrglaka 42
                                   ++il  G  G+GKTt++ +++++
  gi|91773478|ref|YP_566170.1| 24 PSTILVAGTAGVGKTTMALQMLSN 47
                                  456999***********9887765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.039
                                   TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrgla 40 
                                   g+ +l  G+ GaGKT ++ +++
  gi|91773478|ref|YP_566170.1| 256 GNSMLVAGEPGAGKTIFSWSFI 277
                                   5668999**********87665 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 ?   10.4   0.1    0.0014      0.49       2      38 ..      27      66 ..      26      69 .. 0.88
   2 ?    1.3   0.0      0.96   3.2e+02       2      15 ..     259     272 ..     258     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                                  EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--H CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtte 38
                                  +l+ G  G+gK+++a ++++     + +v+y+ lt  t+e
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSNAaksGEKVLYIPLTTVTSE 66
                                  6788***********9998777799*********998877 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.96
                                   EEEE--SSSSHHHH CS
                         AAA_5   2 vlLvGppGtgKsel 15 
                                   +l+ G+pG gK+ +
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIF 272
                                   6889*******965 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 ?    9.7   0.1    0.0013      0.44      26      58 ..      27      59 ..      10      65 .. 0.88
   2 ?    1.3   0.0      0.47   1.6e+02      24      51 ..     257     286 ..     254     316 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                                  EEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES CS
                          DAP3 26 lvltGekgsGKSvlLlqalayAlekgwvvlhvp 58
                                  +++ G  g+GK+++ lq+l  A+++g  vl +p
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIP 59
                                  6789*********************99999998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.47
                                   -EEEEE-SSSSSTTTTHHHHHHHGGGS..- CS
                          DAP3  24 krlvltGekgsGKSvlLlqalayAlek..g 51 
                                   + +++ Ge+g GK++     +  +l++  +
  gi|91773478|ref|YP_566170.1| 257 NSMLVAGEPGAGKTIFSWSFIMEGLSNgeN 286
                                   67899*********9877777777776553 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016     0.056      32      90 ..      25      83 ..      20      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                        AAA_35 32 alirikapkkmGKtSLlarilakakqqgyktvsldlqladkeilsdldkflrwfcanvs 90
                                  ++i + +   +GKt +  ++l++a+++g k++++ l ++ +e +++l+ ++  +  n+s
  gi|91773478|ref|YP_566170.1| 25 STILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTSERFEKLQAVFPFIFENIS 83
                                  5788889999*************************************998887777776 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00058       0.2      40      87 ..      13      58 ..       2      70 .. 0.84
   2 ?   -0.5   0.1         2   6.6e+02      34      82 ..     238     285 ..     226     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                                  HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE CS
                          RecA 40 aldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafi 87
                                  +ld  lG  G+     i + G+   Gktt+al+++++a k+g  + +i
  gi|91773478|ref|YP_566170.1| 13 GLDEILG--GFKSPSTILVAGTAGVGKTTMALQMLSNAAKSGEKVLYI 58
                                  5666665..999999999************************999887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                                   E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT- CS
                          RecA  34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkgg 82 
                                   i sG   +d+ l  GG+  G  + + G   +Gkt ++ + i e   +g 
  gi|91773478|ref|YP_566170.1| 238 IRSGVENFDLMLY-GGMIAGNSMLVAGEPGAGKTIFSWSFIMEGLSNGE 285
                                   6678888888775.99*******************99999988766655 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 ?    7.9   0.0      0.01       3.4       2      28 ..      27      53 ..      26      73 .. 0.82
   2 ?    3.7   0.0       0.2        69       3      28 ..     260     285 ..     258     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
                                  EEEESSTTSSHHHHHHCHCT-CCC-EE CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkfseke 28
                                  +++ G +gvGKt+++ +++++  ++ e
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSNAAKSGE 53
                                  7889*************9999887655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.2
                                   EEESSTTSSHHHHHHCHCT-CCC-EE CS
                           Roc   3 vlvGdsgvGKtsllkrfvedkfseke 28 
                                   ++ G+ g+GKt +  +f+ +  s+ e
  gi|91773478|ref|YP_566170.1| 260 LVAGEPGAGKTIFSWSFIMEGLSNGE 285
                                   678***********999988776655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00053      0.18       1      32 [.      29      60 ..      29      66 .. 0.89
   2 ?    0.5   0.1       1.2   4.2e+02       1      13 [.     261     273 ..     261     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00053
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNL 32
                                  v+G+aG+GKtt+  ++ + + ++g +v ++ L
  gi|91773478|ref|YP_566170.1| 29 VAGTAGVGKTTMALQMLSNAAKSGEKVLYIPL 60
                                  89*************99999999999988755 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                    ATP_bind_1   1 vvGpaGsGKttfv 13 
                                   v+G +G+GKt f 
  gi|91773478|ref|YP_566170.1| 261 VAGEPGAGKTIFS 273
                                   89********885 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0051       1.7      20      47 ..      25      52 ..      15      72 .. 0.80
   2 ?    2.4   0.0      0.27        90      22      49 ..     259     286 ..     248     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0051
                                  SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                          PhoH 20 divfaiGpaGtGKtylavalavealkkk 47
                                  + + ++G aG GKt +a+++  +a k++
  gi|91773478|ref|YP_566170.1| 25 STILVAGTAGVGKTTMALQMLSNAAKSG 52
                                  567889************9987777664 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                                   EEEE--TTSSTTHHHHHHHHHHHHTTS- CS
                          PhoH  22 vfaiGpaGtGKtylavalavealkkkkv 49 
                                   + ++G+ G+GKt ++ +  +e l++++ 
  gi|91773478|ref|YP_566170.1| 259 MLVAGEPGAGKTIFSWSFIMEGLSNGEN 286
                                   5678*********999888887777665 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0025      0.83      20      64 ..      22      66 ..      14      74 .. 0.87
   2 ?    1.8   0.1      0.31   1.1e+02      22      54 ..     256     289 ..     252     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                                  HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHH CS
                          PIF1 20 ekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAal 64
                                  +++ ++ v G +G gKt +  ++l+   ++g++vl +  + v + 
  gi|91773478|ref|YP_566170.1| 22 KSPSTILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTSE 66
                                  67899**************999999999999****9988888775 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                                   TS-EEEEESTTSSCHHH.HHHHHHHCHCTCCCEE CS
                          PIF1  22 gklfFvtGsgGtgKtfl.wkallkklrsegkivl 54 
                                   g+++ v G  G+gKt++ w  +++ l + ++ v+
  gi|91773478|ref|YP_566170.1| 256 GNSMLVAGEPGAGKTIFsWSFIMEGLSNGENGVI 289
                                   88999**********6549999988887776665 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 ?   11.0   0.0   0.00062      0.21       6      89 ..      26     118 ..      22     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00062
                          KdpD   6 kiflGaapGvGktyamLeeaqelkeegvdvviglvethgrketealleglevi.......prkevey.kgkeleeldldai 78 
                                   +i +  ++GvGkt   L+   +++++g +v+   + t + ++ e+l + ++ i       p ++ +  k+   + +++ ++
  gi|91773478|ref|YP_566170.1|  26 TILVAGTAGVGKTTMALQMLSNAAKSGEKVLYIPLTTVTSERFEKLQAVFPFIfenisthPLNRQAAeKDPLSTLIEMGNV 106
                                   5788889************99999***999988888777777777765555553333333443333303333333455555 PP

                          KdpD  79 la.rkpevvlvD 89 
                                   ++ ++p+ +++D
  gi|91773478|ref|YP_566170.1| 107 ITsENPDRIVID 118
                                   432556666666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0021      0.73      89     124 ..      13      49 ..       8      57 .. 0.78
   2 ?   -1.3   0.1       5.3   1.8e+03      97     113 ..     254     270 ..     251     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0021
                                   THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                   gl+e+   +k+ +t++++G  GvGK+t+  ++l+++ 
  gi|91773478|ref|YP_566170.1|  13 GLDEILGGFKSpSTILVAGTAGVGKTTMALQMLSNAA 49 
                                   56666666777689999***********988887754 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.3
                                   CTTSEEEEECSTTSSHH CS
                   RsgA_GTPase  97 lkdktsvlvGqSGvGKS 113
                                   ++++ ++++G+ G+GK+
  gi|91773478|ref|YP_566170.1| 254 IAGNSMLVAGEPGAGKT 270
                                   67788999********7 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0041       1.4       1      22 [.      27      48 ..      27      92 .. 0.72
   2 ?    0.2   0.0       1.5   5.1e+02       2      12 ..     260     270 ..     259     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0041
               Viral_helicase1  1 ivvhGvpGcGKStlirkllrts 22
                                  i+v+G +G GK+t+  + l++ 
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQMLSNA 48
                                  68************99999884 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
               Viral_helicase1   2 vvhGvpGcGKS 12 
                                   +v+G pG+GK+
  gi|91773478|ref|YP_566170.1| 260 LVAGEPGAGKT 270
                                   799*******9 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.065        22      25      43 ..      27      45 ..      23      74 .. 0.84
   2 ?    4.9   0.2     0.045        15      22      39 ..     256     273 ..     249     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.065
                  Mg_chelatase 25 lllvGppGsGKtmlakrlp 43
                                  +l++G++G GKt +a ++ 
  gi|91773478|ref|YP_566170.1| 27 ILVAGTAGVGKTTMALQML 45
                                  899**********997765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.045
                  Mg_chelatase  22 gHnlllvGppGsGKtmla 39 
                                   g ++l++G pG+GKt+  
  gi|91773478|ref|YP_566170.1| 256 GNSMLVAGEPGAGKTIFS 273
                                   45899**********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 ?    6.1   0.2     0.028       9.4      24      38 ..      26      40 ..      20      50 .. 0.83
   2 ?    3.7   0.3      0.16        53      23      36 ..     256     270 ..     251     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.028
                        AAA_29 24 atlltGpsGsGKSTl 38
                                  ++l++G+ G+GK+T+
  gi|91773478|ref|YP_566170.1| 26 TILVAGTAGVGKTTM 40
                                  589***********8 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.16
                        AAA_29  23 g.atlltGpsGsGKS 36 
                                   g ++l++G+ G+GK+
  gi|91773478|ref|YP_566170.1| 256 GnSMLVAGEPGAGKT 270
                                   5579**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              53  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 3021.22
//
Query:       gi|91773479|ref|YP_566171.1|  [L=89]
Description: exodeoxyribonuclease VII small subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   62.3   3.9    5.2e-17   61.6   3.9    1.3  1  Exonuc_VII_S  Exonuclease VII small subunit
  ------ inclusion threshold ------
      0.078   13.1   0.2       0.14   12.3   0.2    1.4  1  COMM_domain   COMM domain
       0.16   12.3   1.0        0.2   12.0   1.0    1.2  1  KxDL          Uncharacterized conserved protein


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 !   61.6   3.9   8.7e-21   5.2e-17       1      52 []      20      71 ..      20      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 8.7e-21
                  Exonuc_VII_S  1 FEealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkvek 52
                                  FE++l eLe +v++LE+g+l+L+es++ +e+G+kL+  C++++++ e+kve+
  gi|91773479|ref|YP_566171.1| 20 FEASLGELEHLVDQLEKGQLTLDESIETFEKGMKLALLCNQMIEDSEKKVEV 71
                                  9*************************************************85 PP

>> COMM_domain  COMM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.3e-05      0.14      33      63 ..       8      37 ..       5      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                   COMM_domain 33 klqngsgnsenvtlelskeqLqeLlneLeei 63
                                  k+++g  ++e  t+e s  +L++L+++Le+ 
  gi|91773479|ref|YP_566171.1|  8 KVEKGAAEKE-QTFEASLGELEHLVDQLEKG 37
                                  5677777555.9*****************85 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0   3.3e-05       0.2      30      77 ..      28      75 ..       3      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                          KxDL 30 reLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkak 77
                                  + L ++ ++ q  l +  + f++g+kl+   ++ +e + kk++ l +k
  gi|91773479|ref|YP_566171.1| 28 EHLVDQLEKGQLTLDESIETFEKGMKLALLCNQMIEDSEKKVEVLMEK 75
                                  4555566677789******************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 648.26
//
Query:       gi|91773480|ref|YP_566172.1|  [L=407]
Description: exodeoxyribonuclease VII large subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-83  280.1   0.0    4.2e-77  259.7   0.1    2.1  2  Exonuc_VII_L     Exonuclease VII, large subunit
      2e-30  104.9   0.6      4e-30  103.9   0.6    1.6  1  tRNA_anti_2      OB-fold nucleic acid binding domain
      7e-08   32.4   0.1    1.6e-07   31.2   0.1    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0023   17.7   0.1     0.0051   16.6   0.1    1.5  1  RMI2             RecQ-mediated genome instability protein 2
  ------ inclusion threshold ------
      0.076   13.3   0.0       0.15   12.3   0.0    1.5  1  RecJ_OB          RecJ OB domain
       0.44   10.7   5.1       0.59   10.3   0.8    2.4  2  Myc-LZ           Myc leucine zipper 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 !  259.7   0.1   1.4e-80   4.2e-77       1     215 [.     122     336 ..     122     340 .. 0.95
   2 !   19.6   0.0   1.8e-07   0.00055     249     303 ..     335     390 ..     329     391 .. 0.90

  Alignments for each domain:
  == domain 1  score: 259.7 bits;  conditional E-value: 1.4e-80
                  Exonuc_VII_L   1 lfdeerkkplpklpkrigvvtsptgaairDilrtlkrrgplveillfpalvQGeeaaaeiikalekanalkeaDvliiaRG 81 
                                   lf++ +k p+p +p rigvvtsptgaai+Dil++++rr+p v+ill p+ vQGe++a++i++ +e +n+++ +Dv+i++RG
  gi|91773480|ref|YP_566172.1| 122 LFSDVHKIPIPGYPLRIGVVTSPTGAAIHDILNVIRRRYP-VNILLSPTIVQGERSAESIVRSIELLNQTD-VDVIIVGRG 200
                                   79999***********************************.***********************9999665.5******** PP

                  Exonuc_VII_L  82 GGSleDLwaFndeelaraiaaskiPvisavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeqleelerrlekaikr 162
                                   GGSleDLw+Fn+e +arai++sk P++savGHEtD+tiaDf Ad+rapTP+aaAelvvpd++e++++l++l++rle+++++
  gi|91773480|ref|YP_566172.1| 201 GGSLEDLWSFNEEVVARAIFNSKKPIVSAVGHETDFTIADFTADMRAPTPSAAAELVVPDQKEVKRHLATLSSRLENEVEH 281
                                   ********************************************************************************* PP

                  Exonuc_VII_L 163 lleekkqrleklasrl..kspeellerkrqrldeleerleralkkqlkkkrerle 215
                                    +++ k rle+++++l  ++  ++l +++q ldel+ +l++++ k++  k+ +l+
  gi|91773480|ref|YP_566172.1| 282 VISQGKGRLEQIRKKLepQHIMDMLLQDSQYLDELTMKLTSSMGKTIVDKTFELK 336
                                   ****************6557788999****************9999877776665 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.8e-07
                  Exonuc_VII_L 249 leeleeklealsplkvLkrGyaivrk.edgkvvtsakdlkkgdeleirladgevka 303
                                   l+  ++kl+a+spl+++ rGy+i  +  ++  ++s+++l  +d+l++ ++dg +++
  gi|91773480|ref|YP_566172.1| 335 LKFHSSKLNAVSPLNTILRGYSIAIDpVNDLSISSVTELGDNDQLDVIVNDGIFEC 390
                                   666789********************999**********************97765 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 !  103.9   0.6   1.3e-33     4e-30       1      95 []       4      99 ..       4      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1.3e-33
                   tRNA_anti_2  1 lsVseltraikell..eaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvY 81
                                  ++V+el++ ik++l  +++l +++wv+Geisnl++++sgh+Yft kD k++is+v f+s +++l+f+le+ mkVlv g+++vY
  gi|91773480|ref|YP_566172.1|  4 YTVTELNNLIKNTLtnNPKL-NQIWVQGEISNLTKHSSGHYYFTVKDGKSQISCVSFKSVNRNLRFELESSMKVLVFGSVDVY 85
                                  79************877888.66**********8788********************************************** PP

                   tRNA_anti_2 82 eprGsyqlivedie 95
                                    rG+yql+v+di+
  gi|91773480|ref|YP_566172.1| 86 VVRGQYQLYVQDIR 99
                                  ***********995 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 !   31.2   0.1   5.2e-11   1.6e-07       2      74 ..      27      99 ..      26     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.2e-11
                                  EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC..TTSSEEEEEEEEE CS
               tRNA_anti-codon  2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr..pggelelkveeie 74
                                  +v+G++++   ++++++ +++++Dg  +i +v f++  ++l  +l+  + v v+G v  +  +g+ ++l+v++i+
  gi|91773480|ref|YP_566172.1| 27 WVQGEISNLT-KHSSGHYYFTVKDGKSQISCVSFKSVNRNLRFELESSMKVLVFGSVDVYvvRGQ-YQLYVQDIR 99
                                  89*******6.**************************************************8887.*******97 PP

>> RMI2  RecQ-mediated genome instability protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.7e-06    0.0051      34      94 ..      18      82 ..       5      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                          RMI2 34 reglevsrvWlQGtvvevdaske...sllldDgtgvfvveglnelpktk.kclkeGkYVmVvGvv 94
                                  +++ +++++W+QG + +++++++    ++++Dg   ++  + +++ ++   +l++ + V+V G+v
  gi|91773480|ref|YP_566172.1| 18 TNNPKLNQIWVQGEISNLTKHSSghyYFTVKDGKSQISCVSFKSVNRNLrFELESSMKVLVFGSV 82
                                  577899*********999988878899******************99875799**********98 PP

>> RecJ_OB  RecJ OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.15      46     108 .]      36      97 ..      17      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                       RecJ_OB  46 vgkeknhlklkledesgksleaiaFnlaekleelekgdkvdiaytleinefngretlqlrikd 108
                                    ++ + h  ++++d++  +++++ F+  ++  ++e ++ +++++  +++ +  r ++ql ++d
  gi|91773480|ref|YP_566172.1|  36 TKHSSGHYYFTVKDGK-SQISCVSFKSVNRNLRFELESSMKVLVFGSVDVYVVRGQYQLYVQD 97 
                                   455678********98.****************999999999999999999999999999987 PP

>> Myc-LZ  Myc leucine zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8    0.0002      0.59      15      26 ..     108     119 ..     105     119 .. 0.86
   2 ?    1.6   0.2       0.1     3e+02      21      28 ..     287     294 ..     284     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                        Myc-LZ  15 krrEqLKhkLeQ 26 
                                   k  EqLK+kLeQ
  gi|91773480|ref|YP_566172.1| 108 KAYEQLKNKLEQ 119
                                   667********9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                        Myc-LZ  21 KhkLeQLr 28 
                                   K +LeQ+r
  gi|91773480|ref|YP_566172.1| 287 KGRLEQIR 294
                                   89****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2781.01
//
Query:       gi|91773481|ref|YP_566173.1|  [L=164]
Description: CoB--CoM heterodisulfide reductase subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete 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   47.8   7.9    2.3e-12   47.2   7.9    1.3  1  Fer4_8    4Fe-4S dicluster domain
    4.6e-10   39.5   7.1    7.2e-10   38.8   7.1    1.3  1  Fer4_10   4Fe-4S dicluster domain
    9.3e-10   38.9   7.8    1.4e-09   38.3   7.8    1.3  1  Fer4_17   4Fe-4S dicluster domain
    2.8e-08   33.8   8.0    5.9e-08   32.7   8.0    1.5  1  Fer4_9    4Fe-4S dicluster domain
    5.7e-07   30.0  11.6    3.8e-06   27.4  12.3    1.9  2  Fer4_7    4Fe-4S dicluster domain
    0.00011   22.2   5.8    0.00021   21.4   5.8    1.4  1  Fer4_21   4Fe-4S dicluster domain
    0.00077   19.2  13.8      0.019   14.8   3.0    2.4  2  Fer4      4Fe-4S binding domain
     0.0015   18.5  13.5     0.0073   16.3   3.0    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0035   17.7   3.0     0.0035   17.7   3.0    2.4  2  Fer4_4    4Fe-4S binding domain
     0.0042   17.3   7.9       0.01   16.0   0.6    2.2  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.065   13.2   0.3      0.065   13.2   0.3    2.3  2  SCIFF     Six-cysteine peptide SCIFF
      0.067   14.2  18.7       0.24   12.4   3.3    2.3  2  Fer4_3    4Fe-4S binding domain
      0.079   13.9  14.4        2.6    9.0  14.5    2.3  1  Fer4_16   4Fe-4S double cluster binding domain
       0.21   12.4   3.5        1.3    9.9   0.1    2.3  2  Fer4_15   4Fe-4S single cluster domain
       0.29   10.9   6.0       0.68    9.7   0.9    2.2  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
        3.3    8.0  12.8        1.4    9.1   2.4    2.3  2  Fer4_6    4Fe-4S binding domain
        4.9    7.8   9.6        7.8    7.1   1.1    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
          6    7.8  13.4         11    7.0   4.3    2.2  2  Fer4_22   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 !   47.2   7.9   2.3e-15   2.3e-12       2      65 .]      20      79 ..      19      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2.3e-15
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                  + kC++Cg C+ +Cp+ r+t  + ++  r+ +++ +         e+lw+Cttc +C+e+Cp gi
  gi|91773481|ref|YP_566173.1| 20 ILKCMHCGVCTGSCPSGRHTSlNVRNLLRKARKG-ESVLSD----ETLWTCTTCYNCQERCPRGI 79
                                  579******************9999999999888.333333....57***************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   7.1   7.3e-13   7.2e-10       7      56 .]      21      76 ..      15      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.3e-13
                       Fer4_10  7 dtCirCgkCvkaCPadl.....tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                   +C++Cg C+ +CP+        ++  ++++++e++ ++  ++ Ct+c +C+e CP
  gi|91773481|ref|YP_566173.1| 21 LKCMHCGVCTGSCPSGRhtslnVRNLLRKARKGESVLSDeTLWTCTTCYNCQERCP 76
                                  58*************889**99999999********9999***************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 !   38.3   7.8   1.4e-12   1.4e-09       1      61 []      22      80 ..      22      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.4e-12
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61
                                  +C++Cg C+ +Cps++ ++ + ++llr+a+    e +  +e+  +C++C +C+++CP g+d
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSGRHTSLNVRNLLRKARK--GESVLSDETLWTCTTCYNCQERCPRGID 80
                                  6***************************655..5888999******************997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   8.0     6e-11   5.9e-08       1      49 [.      22      78 ..      22      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6e-11
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkg 49
                                  kC+ Cg C+ +Cp+g ++  ++++  r  +++e        + C++C  C e+Cp+g
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSGRHTSLNVRNLLRKARKGEsvlsdetlWTCTTCYNCQERCPRG 78
                                  7************************99998888**********************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 !   14.8   3.0   3.2e-05     0.031      33      51 ..      18      36 ..      10      37 .. 0.82
   2 !   27.4  12.3   3.9e-09   3.8e-06       1      52 []      22      79 ..      22      79 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                        Fer4_7 33 idpekClgCgaCvavCPtg 51
                                   d  kC++Cg+C   CP+g
  gi|91773481|ref|YP_566173.1| 18 TDILKCMHCGVCTGSCPSG 36
                                  6778999999999999987 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 3.9e-09
                        Fer4_7  1 rCigCgaCvaaCpvkaie...ldeeenekgt.ekv..eidpekClgCgaCvavCPtga 52
                                  +C++Cg C+  Cp++  +   +++  +++++ e+v  +   ++C++C++C+++CP g+
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSGRHTslnVRNLLRKARKgESVlsDETLWTCTTCYNCQERCPRGI 79
                                  7************777662223333344443133322334568************986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   5.8   2.1e-07   0.00021       7      52 ..      22      76 ..      18      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.1e-07
                       Fer4_21  7 kCigCgkCliaCedtshqai......eidaktvlkvved....eCvGCnlCssvCP 52
                                  kC++Cg C+ +C+ + h+ +      + +a++   v++d    +C+ C  C + CP
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSGRHTSLnvrnllR-KARKGESVLSDetlwTCTTCYNCQERCP 76
                                  8*******************5444321.1223335554423447************ PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.0   1.9e-05     0.019       7      21 ..      22      36 ..      18      36 .. 0.90
   2 !    9.8   3.2   0.00069      0.69       8      21 ..      65      78 ..      64      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                  TSSS-THHHHHSTTT CS
                          Fer4  7 kCigCGaCvevCPvg 21
                                  kC++CG C   CP g
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSG 36
                                  9************76 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00069
                                  SSS-THHHHHSTTT CS
                          Fer4  8 CigCGaCvevCPvg 21
                                  C+ C +C e CP g
  gi|91773481|ref|YP_566173.1| 65 CTTCYNCQERCPRG 78
                                  ************87 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.0   7.3e-06    0.0073       8      21 ..      21      34 ..      16      35 .. 0.88
   2 !    7.5   2.9    0.0047       4.6       9      21 ..      64      76 ..      58      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.3e-06
                        Fer4_2  8 drCigCgaCvsaCP 21
                                   +C++Cg C+ +CP
  gi|91773481|ref|YP_566173.1| 21 LKCMHCGVCTGSCP 34
                                  59************ PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0047
                        Fer4_2  9 rCigCgaCvsaCP 21
                                  +C+ C  C+  CP
  gi|91773481|ref|YP_566173.1| 64 TCTTCYNCQERCP 76
                                  7*********9*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 !   17.7   3.0   3.6e-06    0.0035       3      17 .]      22      36 ..      20      37 .. 0.93
   2 ?    3.8   1.8       0.1     1e+02       3      16 ..      64      77 ..      60      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                        Fer4_4  3 rCigCgsCvaaCPqg 17
                                  +C +Cg+C+ +CP+g
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSG 36
                                  7************85 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.1
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                  +C+ C  C   CP 
  gi|91773481|ref|YP_566173.1| 64 TCTTCYNCQERCPR 77
                                  49999999988995 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.1     0.017        17      58      74 ..      20      36 ..       5      47 .. 0.76
   2 !   16.0   0.6     1e-05      0.01      47      86 ..      51      91 ..      37     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                       Fer4_18 58 agdcidcescvkvcPtg 74
                                    +c++c++c   cP g
  gi|91773481|ref|YP_566173.1| 20 ILKCMHCGVCTGSCPSG 36
                                  45788888888888865 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1e-05
                       Fer4_18 47 lkekeerkekgagdcidcescvkvcPtgidirkGl.qleci 86
                                   k +   ++++   c++c  c + cP gidi + +  +  i
  gi|91773481|ref|YP_566173.1| 51 RKGESVLSDETLWTCTTCYNCQERCPRGIDIVDAIfEIRAI 91
                                  45555556677789*****************9874255555 PP

>> SCIFF  Six-cysteine peptide SCIFF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   6.5e-05     0.065      15      39 ..      21      45 ..      13      48 .. 0.87
   2 ?    0.9   1.7      0.46   4.5e+02      17      27 ..      65      75 ..      55      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                         SCIFF 15 lkkggCgeCqtSCqSACKTSctVgN 39
                                  lk   Cg C  SC S   TS  V N
  gi|91773481|ref|YP_566173.1| 21 LKCMHCGVCTGSCPSGRHTSLNVRN 45
                                  67789****************9988 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.46
                         SCIFF 17 kggCgeCqtSC 27
                                   + C +Cq  C
  gi|91773481|ref|YP_566173.1| 65 CTTCYNCQERC 75
                                  46799999988 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   7.5    0.0091         9       1      14 [.      23      36 ..      23      36 .. 0.97
   2 ?   12.4   3.3   0.00024      0.24       1      14 [.      65      78 ..      65      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0091
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C++Cg C  +CP+g
  gi|91773481|ref|YP_566173.1| 23 CMHCGVCTGSCPSG 36
                                  ************97 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00024
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  Ct C+ C e CP g
  gi|91773481|ref|YP_566173.1| 65 CTTCYNCQERCPRG 78
                                  ************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 ?    9.0  14.5    0.0026       2.6       1      65 [.      22      76 ..      22      78 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                  +C  Cg C+ +CP++  ++      + r+   ++ +++  l+    ++   + +t C +Cq+ CP
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSGRHTSL-----NVRNLLRKARKGESVLS---DET--LWTCTTCYNCQERCP 76
                                  5*************976666.....33333333223333332...223..488************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.8      0.16   1.6e+02       7      19 ..      22      34 ..      18      43 .. 0.88
   2 ?    9.9   0.1    0.0013       1.3       6      24 ..      63      81 ..      59     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.16
                       Fer4_15  7 aCigcglCvaeap 19
                                  +C+ cg+C   +p
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCP 34
                                  7*******99998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                       Fer4_15  6 daCigcglCvaeapevfel 24
                                  ++C+ c +C +++p+ + +
  gi|91773481|ref|YP_566173.1| 63 WTCTTCYNCQERCPRGIDI 81
                                  68***********987765 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 ?    4.0   0.3     0.041        41      23      43 ..      22      40 ..      11      64 .. 0.65
   2 ?    9.7   0.9   0.00068      0.68      24      56 ..      65      95 ..      60     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.041
                                  T----TT-HHHHCSTT---HH CS
                       Fer4_20 23 RClqCkkapcvkgCPveidip 43
                                  +C++C    c+ +CP   +  
  gi|91773481|ref|YP_566173.1| 22 KCMHC--GVCTGSCPSGRHTS 40
                                  68888..67888888654333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00068
                                  ----TT-HHHHCSTT---HHHHHHHHHTT-HHH CS
                       Fer4_20 24 ClqCkkapcvkgCPveidipefikkiaegnlee 56
                                  C +C   +c++ CP  idi + i +i++  ++e
  gi|91773481|ref|YP_566173.1| 65 CTTC--YNCQERCPRGIDIVDAIFEIRAIAVHE 95
                                  8888..67************9999998766665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.4    0.0014       1.4       8      22 ..      22      36 ..      19      38 .. 0.90
   2 ?    4.2   3.0     0.052        52       9      22 ..      65      78 ..      64      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                        Fer4_6  8 kCigCgdCvrvCPeg 22
                                  kC +Cg C+  CP g
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSG 36
                                  8************87 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.052
                        Fer4_6  9 CigCgdCvrvCPeg 22
                                  C+ C++C   CP g
  gi|91773481|ref|YP_566173.1| 65 CTTCYNCQERCPRG 78
                                  99*******9*965 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.9     0.035        35       5      17 ..      22      34 ..      19      36 .. 0.90
   2 ?    7.1   1.1    0.0079       7.8       5      18 ..      64      77 ..      62      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.035
                       Fer4_13  5 tCiacgaCvelaP 17
                                  +C+ cg+C   +P
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCP 34
                                  7*********999 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0079
                       Fer4_13  5 tCiacgaCvelaPd 18
                                  tC+ c +C e +P 
  gi|91773481|ref|YP_566173.1| 64 TCTTCYNCQERCPR 77
                                  8************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 ?    7.0   4.3     0.011        11       1      16 [.      22      37 ..      22      56 .. 0.78
   2 ?    6.9   1.5     0.011        11      67      96 .]      50      79 ..      37      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                       Fer4_22  1 rClsCgaCtlvCptCs 16
                                  +C++Cg Ct  Cp+  
  gi|91773481|ref|YP_566173.1| 22 KCMHCGVCTGSCPSGR 37
                                  7************865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                       Fer4_22 67 lhklsefkekfgesgCvGCgRCieacpvki 96
                                   +k +++ +     +C+ C  C+e+cp +i
  gi|91773481|ref|YP_566173.1| 50 ARKGESVLSDETLWTCTTCYNCQERCPRGI 79
                                  456666666777789999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1158.19
//
Query:       gi|91773482|ref|YP_566174.1|  [L=306]
Description: CoB--CoM heterodisulfide reductase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-35  119.4   1.1    6.5e-19   67.9   0.2    2.3  2  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.2e-17   2.2e-13       3      84 ..      16      96 ..      14      97 .. 0.94
   2 !   67.9   0.2   3.6e-23   6.5e-19       1      85 []     158     250 ..     158     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.2e-17
                           CCG  3 yfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelae.alakrnvetaeetgadaivtacpgCllql 84
                                  +f gC ++ ++yp  +k++k  le+l ++ ++le++sCC+a+g+ ++++++++ al  rn++  e++g d i+t+c+gC+++l
  gi|91773482|ref|YP_566174.1| 16 LFLGC-VIPNRYPGIEKSTKLCLEKLDIDCVDLEGASCCPAPGILRSFDKTTWlALSSRNISLTEDLGRD-ILTICNGCYGSL 96
                                  699**.********************************************5555*************988.*********987 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 3.6e-23
                           CCG   1 vayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                   va+++gChll+++      + e +  + +l+ea+g+  +++ +k +CCGaggg+++    +a+al++++++++e +++d+i
  gi|91773482|ref|YP_566174.1| 158 VAVHYGCHLLKPSkgrvgmSVERPSFFDELVEATGAVSVDYpDKMECCGAGGGVRSALSdEALALTEHKLSMIEAAEVDCI 238
                                   89***********99999999999***********9999999***********9999666********************* PP

                           CCG  74 vtacpgCllqlk 85 
                                   v+acp+C++ql+
  gi|91773482|ref|YP_566174.1| 239 VNACPFCHMQLD 250
                                   **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2183.68
//
Query:       gi|91773483|ref|YP_566175.1|  [L=318]
Description: methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-134  446.9   1.7   3.2e-134  446.7   1.7    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 !  446.7   1.7  1.8e-138  3.2e-134       1     298 [.       6     307 ..       6     308 .. 0.97

  Alignments for each domain:
  == domain 1  score: 446.7 bits;  conditional E-value: 1.8e-138
                          MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGeteeaivk 81 
                                   k+q+v+e++Gvk+GGqpG+yPt+l+g++fy +hkiv+de++G+fdkeaa++l++++ e++d+tGnP ++q+vGet +ai k
  gi|91773483|ref|YP_566175.1|   6 KKQEVFEVGGVKFGGQPGQYPTILIGSMFYNRHKIVTDEDEGVFDKEAADNLWNHMLEMTDVTGNPCVNQIVGETTQAIKK 86 
                                   79******************************************************************************* PP

                          MtrH  82 yidfvadvtd.aPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmdptvegkl 161
                                   yid+++  +d +P+lids+++ev++aaa+y+te+G+adr+iynsin si+d+eiea+ +sd++a+ivlafn++dptv+gkl
  gi|91773483|ref|YP_566175.1|  87 YIDWFVAEDDkTPFLIDSSAGEVRAAAAEYVTEIGVADRAIYNSINGSIHDHEIEAIRKSDINASIVLAFNATDPTVKGKL 167
                                   ***98777777********************************************************************** PP

                          MtrH 162 kileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdwlrefkk...ke 239
                                   ++le+g+ +++ g+l++a+++Gi+kpl+dva+tplg+gaga+++a++avk+++GlPvG+g+hn++saWdw++++kk   ++
  gi|91773483|ref|YP_566175.1| 168 EVLETGGPGQTMGMLDIAKDCGITKPLVDVAATPLGAGAGASMRAVIAVKGHFGLPVGGGYHNLASAWDWMKDYKKgfaTK 248
                                   **************************************************************************9944345 PP

                          MtrH 240 kekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgvel 298
                                   +e++a y+++d+g+nlv ++lgs+f l+GPien+ +v+Pa amvdi+++e+akelg+e+
  gi|91773483|ref|YP_566175.1| 249 EERKAVYMPTDIGTNLVPQTLGSNFQLFGPIENTDTVYPATAMVDIILAETAKELGLEI 307
                                   556666***************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2045.72
//
Query:       gi|91773484|ref|YP_566176.1|  [L=75]
Description: tetrahydromethanopterin S-methyltransferase subunit G [Methanococcoides burtonii DSM 6242]
Scores for complete 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-32  111.0   0.4      2e-32  110.8   0.4    1.0  1  MtrG      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.4   1.1e-36     2e-32       1      64 []       7      70 ..       7      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.1e-36
                          MtrG  1 kiPsvvvdpddfnevkkrLdeieekvefvnsEiaqriGkkvGRdiGilYGlviGliillvyill 64
                                  ++Psvv+dp dfnev ++L+ i+ek+efvnsEiaqriGkk+GRdiGi+YG+v+G++i+l+yi+l
  gi|91773484|ref|YP_566176.1|  7 TTPSVVTDPVDFNEVLEKLNLIDEKIEFVNSEIAQRIGKKLGRDIGIMYGAVAGILIFLIYISL 70
                                  58***********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 516.50
//
Query:       gi|91773485|ref|YP_566177.1|  [L=79]
Description: tetrahydromethanopterin S-methyltransferase subunit F [Methanococcoides burtonii DSM 6242]
Scores for complete 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  102.9   1.6    5.2e-30  102.6   1.6    1.1  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu
  ------ inclusion threshold ------
       0.48   10.5   5.2        1.2    9.3   5.2    1.8  1  YqzM      YqzM-like 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 !  102.6   1.6   5.8e-34   5.2e-30       1      62 []      10      72 ..      10      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 5.8e-34
                          MtrF  1 gvptvnkpnmkaiksvvedirYraqLiaReqkLdSGvsatgivGfaiGfvlAllLvv.lPvll 62
                                  gvp+v++p+m+ai++vv+ irYraqLiaR+qkLdSGv+at+ +Gf++Gf +A+l+v+ lP+++
  gi|91773485|ref|YP_566177.1| 10 GVPMVINPQMGAIENVVDRIRYRAQLIARNQKLDSGVNATAATGFIVGFGFAVLMVLiLPLII 72
                                  8********************************************************9**986 PP

>> YqzM  YqzM-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.2   0.00013       1.2      17      34 ..      50      67 ..      36      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00013
                          YqzM 17 SgvGFvvsFgFFavlFiI 34
                                  ++ GF+v+FgF +++ +I
  gi|91773485|ref|YP_566177.1| 50 AATGFIVGFGFAVLMVLI 67
                                  678********8888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 586.28
//
Query:       gi|91773486|ref|YP_566178.1|  [L=241]
Description: tetrahydromethanopterin S-methyltransferase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-84  281.6   4.2    2.6e-84  281.1   4.2    1.1  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.049   13.0   0.7       0.14   11.6   0.1    2.2  2  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu
      0.094   12.5   0.0        1.3    8.8   0.0    2.6  2  GP57      Phage Tail fiber assembly helper gene product 57


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 !  281.1   4.2   4.3e-88   2.6e-84       1     171 [.       4     173 ..       4     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 281.1 bits;  conditional E-value: 4.3e-88
                                   -----TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE---TT CS
                          MtrA   1 kkepaegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGaevkG 81 
                                   k+epa +WP++kG+y+vGd++++vav+t+gsh+ + ++leaGaai+Gp+ktenlG+ekvva++i npnirf+i+tG+evkG
  gi|91773486|ref|YP_566178.1|   4 KREPAVDWPTLKGEYDVGDVKNCVAVITCGSHIPSGPQLEAGAAITGPCKTENLGLEKVVAQIIGNPNIRFVIITGSEVKG 84 
                                   89******************************************************************************* PP

                                   T-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHHHHHHHT-----SS---- CS
                          MtrA  82 hitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqvelvdlidtedvgaikakikelvakdpgafeeeplv 162
                                   hitG+a+ ++h+nGv ++++ivga+GaiP++enlt++aver+q+qve++++i+ted+g+i+akike+vakdpga++ +p+v
  gi|91773486|ref|YP_566178.1|  85 HITGEAFIMVHKNGV-SDNRIVGATGAIPYVENLTDAAVERLQQQVEMINMIGTEDMGQIVAKIKECVAKDPGALDVDPMV 164
                                   ***************.9**************************************************************** PP

                                   ---XXXXXX CS
                          MtrA 163 ievkeeeee 171
                                   +ev e+++e
  gi|91773486|ref|YP_566178.1| 165 VEVGEAGGE 173
                                   ****99876 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.78   4.6e+03      36      45 ..      98     107 ..      96     109 .. 0.85
   2 ?   11.6   0.1   2.3e-05      0.14      31      57 ..     209     235 ..     183     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.78
                          MtrF  36 GvsatgivGf 45 
                                   Gvs+ +ivG 
  gi|91773486|ref|YP_566178.1|  98 GVSDNRIVGA 107
                                   99999*9996 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.3e-05
                          MtrF  31 qkLdSGvsatgivGfaiGfvlAllLvv 57 
                                   +k  +Gv a ++ G++iG+ ++l L++
  gi|91773486|ref|YP_566178.1| 209 NKYHAGVHAGKVEGIMIGLAITLSLLG 235
                                   7999****************9999887 PP

>> GP57  Phage Tail fiber assembly helper gene product 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.14   8.1e+02      47      64 ..     103     120 ..      98     128 .. 0.82
   2 ?    8.8   0.0   0.00021       1.3      10      25 ..     184     199 ..     177     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                          GP57  47 ravGitGdtikveeivea 64 
                                   r vG tG    ve++ +a
  gi|91773486|ref|YP_566178.1| 103 RIVGATGAIPYVENLTDA 120
                                   899****99999999876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00021
                          GP57  10 lsaeivtlksrildtq 25 
                                   ++aei t++srild  
  gi|91773486|ref|YP_566178.1| 184 MAAEIATIRSRILDID 199
                                   78************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1755.16
//
Query:       gi|91773487|ref|YP_566179.1|  [L=107]
Description: tetrahydromethanopterin S-methyltransferase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  133.0   0.1    4.2e-39  132.8   0.1    1.0  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 !  132.8   0.1   2.4e-43   4.2e-39       1      94 []       3      96 ..       3      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 2.4e-43
                          MtrB  1 lvkvlpelnlvldpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlfyGfi 83
                                  +v+v+pe++lvldp t+v+a++red++++s+dp++e++++L+kiaddlvnsL+p+++ll+++pgRe+t + aG++ n+fyG+i
  gi|91773487|ref|YP_566179.1|  3 MVHVAPEAHLVLDPLTSVLAAEREDIICYSMDPIMEQVNELDKIADDLVNSLSPDMKLLNAFPGREETALKAGFYGNTFYGVI 85
                                  8********************************************************************************** PP

                          MtrB 84 vglviaallal 94
                                  vglv+++++al
  gi|91773487|ref|YP_566179.1| 86 VGLVFSGMIAL 96
                                  *******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 747.92
//
Query:       gi|91773488|ref|YP_566180.1|  [L=269]
Description: tetrahydromethanopterin S-methyltransferase subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete 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-112  375.0  32.4   1.8e-112  374.8  32.4    1.0  1  MtrC      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
        3.6    7.9   5.2        1.6    9.0   0.3    2.9  2  DUF1294   Protein of unknown function (DUF1294)


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 !  374.8  32.4    2e-116  1.8e-112       1     268 []       1     266 [.       1     266 [. 0.99

  Alignments for each domain:
  == domain 1  score: 374.8 bits;  conditional E-value: 2e-116
                          MtrC   1 msaggggkeaeeaipekkllalgivggligiylasvl...epalgsllaalgaicaivwGadavrrvasYglGTGVPSigm 78 
                                   msagg+g+ea+  ip+++l+alg +ggl g y++++l   +p  +++l+algaicaivwG++avrrvasYglGTGVPSigm
  gi|91773488|ref|YP_566180.1|   1 MSAGGAGGEATGGIPQNQLIALGSLGGLAGAYAGHFLsitSP-AFAFLGALGAICAIVWGSAAVRRVASYGLGTGVPSIGM 80 
                                   9************************************99555.5************************************* PP

                          MtrC  79 lalgmGivaalaglavgsalkllagpiialvvaliiglvvgvlakkvikmkipileksttelaaagalsiiglsvaiagsf 159
                                   +algmG+va+++glavg+    +agpi+a+++a+iiglv+gvla+kv++m+ipi+e+s+te+a+ag+l+iiglsva++g+f
  gi|91773488|ref|YP_566180.1|  81 MALGMGVVASMFGLAVGG----IAGPIVAFITASIIGLVIGVLANKVLGMGIPIMEQSMTEIAGAGTLTIIGLSVAMTGTF 157
                                   ******************....9********************************************************** PP

                          MtrC 160 eikailskviatGliallfilaglailhPfNaclGPdEkqdRTLklalekgalaliivgivsletesaaalvviivgliiW 240
                                   +++a+l++v+atG+ia++fi++g+ailhPfNa+lGPdEkqdRTL++alekga+a++++giv++ +++a+a+ +i++g++iW
  gi|91773488|ref|YP_566180.1| 158 MFDAVLETVVATGYIAVIFIAGGMAILHPFNANLGPDEKQDRTLMTALEKGAIAMVVAGIVATVVDGASAVPSIMIGVFIW 238
                                   ********************************************************************************* PP

                          MtrC 241 lisfkkfvklvkrdaakvkgtgllPkee 268
                                   +i+f+k+vklv+rda+kv gtgllP+ee
  gi|91773488|ref|YP_566180.1| 239 YIAFTKYVKLVNRDAYKVLGTGLLPTEE 266
                                   *************************987 PP

>> DUF1294  Protein of unknown function (DUF1294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3   0.00018       1.6      22      44 ..      14      36 ..       9      38 .. 0.91
   2 ?   -1.5   0.7      0.35   3.1e+03      33      43 ..      46      56 ..      43      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                       DUF1294 22 ipEktLlllallgGslGallgmr 44
                                  ip + L++l  lgG +Ga++g  
  gi|91773488|ref|YP_566180.1| 14 IPQNQLIALGSLGGLAGAYAGHF 36
                                  899*****************975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.35
                       DUF1294 33 lgGslGallgm 43
                                  + G+lGa+++ 
  gi|91773488|ref|YP_566180.1| 46 FLGALGAICAI 56
                                  45999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1795.99
//
Query:       gi|91773489|ref|YP_566181.1|  [L=239]
Description: tetrahydromethanopterin S-methyltransferase subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete 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-102  342.3  26.3   1.4e-102  342.1  26.3    1.0  1  MtrD      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.1  26.3  7.6e-107  1.4e-102       2     218 .]      12     225 ..      11     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 342.1 bits;  conditional E-value: 7.6e-107
                          MtrD   2 illliliviggvligvgvhfvPvGGapaamaqatGvgtGtaqlaaGagltGlltaaalaektdslllillsGavgamlmla 82 
                                   il+++++++gg+li+++vhfvPvGGapaamaqatG+gtGt+qlaaGagltGl+ta+a+++++dslll+++sG+vgam+m+a
  gi|91773489|ref|YP_566181.1|  12 ILYIAMVTLGGMLISWSVHFVPVGGAPAAMAQATGIGTGTVQLAAGAGLTGLVTAGAVMAVSDSLLLVVASGGVGAMIMIA 92 
                                   899****************************************************************************** PP

                          MtrD  83 itmlvgnliyvygvGvvaasakvekdpitgdkqekyvsqGteGhgiPtvsfvsGviGgllgGiGGalvyyallellkaalk 163
                                   +tm+vg+++yvygvGv++asakv++dpit+d+q+ yvsqGteGhg+Ptvs+vsGviGg+lgGiGG+ +y+al+++   +++
  gi|91773489|ref|YP_566181.1|  93 VTMIVGTWVYVYGVGVPPASAKVDYDPITKDRQDIYVSQGTEGHGLPTVSYVSGVIGGALGGIGGSAIYFALMST---STT 170
                                   ************************************************************************954...568 PP

                          MtrD 164 laaaaavalaailavglflvnavlasynigGtieGfhdpkfkrlpkavvaslvas 218
                                   l++++ vala+i+avg+f+vnav++synigGtieGfhdpkfk++pkav+as+va+
  gi|91773489|ref|YP_566181.1| 171 LIQSDLVALASIFAVGIFFVNAVIPSYNIGGTIEGFHDPKFKKWPKAVLASFVAT 225
                                   89999************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1714.09
//
Query:       gi|91773490|ref|YP_566182.1|  [L=301]
Description: tetrahydromethanopterin S-methyltransferase subunit E [Methanococcoides burtonii DSM 6242]
Scores for complete 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-140  466.1  12.9   3.8e-140  465.9  12.9    1.0  1  MtrE         Tetrahydromethanopterin S-methyltransferase, sub
  ------ inclusion threshold ------
        0.8   10.2  13.7       0.18   12.3   8.0    2.3  2  SNARE_assoc  SNARE associated Golgi 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 !  465.9  12.9  4.2e-144  3.8e-140       1     271 []       7     279 ..       7     279 .. 0.99

  Alignments for each domain:
  == domain 1  score: 465.9 bits;  conditional E-value: 4.2e-144
                          MtrE   1 lGvlalmgalatiagaaedlesdvgsqsnpnsqvqLapqmgylhrifnkaisGePvaygllaavagavalvllsalklnvv 81 
                                   +Gvlalmga+atiag++edlesdvgsqsnpnsqvqLapqm+y+hri+nkaisGeP++++l++a++g+va+vl+ + +l+v+
  gi|91773490|ref|YP_566182.1|   7 MGVLALMGAAATIAGTTEDLESDVGSQSNPNSQVQLAPQMMYPHRIYNKAISGEPPSNALICAIGGTVASVLM-TANLSVI 86 
                                   8************************************************************************.78***** PP

                          MtrE  82 laivlgalvaalvhgvyavtaylGriasqakfkqpvyldvlkshlgaivahafiavfaivvlsylmtlvlkhpfplpllal 162
                                   +ai++galva+ vhg+y++tay+Gr+asq++f+qp+yld+l+sh+++++++afi++f+i+v+sy+m++vl+hpfpl+lla+
  gi|91773490|ref|YP_566182.1|  87 FAIAIGALVASAVHGTYCITAYMGRTASQKRFRQPIYLDILRSHTPVMMGYAFITTFCILVVSYIMVAVLAHPFPLTLLAF 167
                                   ********************************************************************************* PP

                          MtrE 163 iwGitvGaiGsstGdvhyGaereyqkkefGaGvpvaasGdivrkaeaGlrnsidnalfcakfggpltGlafglivflelWr 243
                                   iwGitvGaiGsstGdvhyGaere+q++efG+G+++a+sG+ivrkae+Glrn+idn++fcakfggp+tGlafg++vfl+ W+
  gi|91773490|ref|YP_566182.1| 168 IWGITVGAIGSSTGDVHYGAEREFQNVEFGSGLNAANSGNIVRKAESGLRNGIDNSWFCAKFGGPVTGLAFGMTVFLSGWV 248
                                   ********************************************************************************* PP

                          MtrE 244 tivfekv...tagwlavivgliivllliiln 271
                                   t vf+++   t+gwl+v +g+i+vlllii+n
  gi|91773490|ref|YP_566182.1| 249 TAVFNPAislTMGWLSVAAGVILVLLLIIWN 279
                                   *****998889******************98 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   8.0     2e-05      0.18       5     118 ..      65     186 ..      61     188 .. 0.72
   2 ?    0.8   0.3     0.073   6.6e+02      71      92 ..     242     263 ..     208     290 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                   SNARE_assoc   5 vll.vaaGvlfglll.....gtlvtslgallGasl..ayllgrylgrkalrrkllsekrvkalerlverygflallllrll 77 
                                   +l+ +++G ++++l+     ++++ ++gal+++ +  +y + +y+gr a +++++++ +++ l ++      +a ++   +
  gi|91773490|ref|YP_566182.1|  65 ALIcAIGGTVASVLMtanlsVIFAIAIGALVASAVhgTYCITAYMGRTASQKRFRQPIYLDILRSHTPVMMGYAFITTFCI 145
                                   55534555555444455566999999999999998456***********************96666644444444444444 PP

                   SNARE_assoc  78 pivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylG 118
                                    +v + +v+++a  +++ +  F+++  +G+i  ++ ++  G
  gi|91773490|ref|YP_566182.1| 146 LVVSYIMVAVLAHPFPLTLLAFIWGITVGAIGSSTGDVHYG 186
                                   55555555566667****************98888777665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.073
                   SNARE_assoc  71 llllrllpivPrdlvnyvaGlt 92 
                                   ++l+ ++  v+++++++++G +
  gi|91773490|ref|YP_566182.1| 242 VFLSGWVTAVFNPAISLTMGWL 263
                                   2333333333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2287.10
//
Query:       gi|91773491|ref|YP_566183.1|  [L=128]
Description: hypothetical protein Mbur_1526 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-46  156.4   0.0    3.1e-46  156.2   0.0    1.0  1  DUF5402   Family of unknown function (DUF5402)


Domain annotation for each model (and alignments):
>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.2   0.0   1.7e-50   3.1e-46       1     119 []       3     124 ..       3     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 1.7e-50
                       DUF5402   1 lkdkllkdreklekklqnllgkevfvsevdifalrcGcvGilievrGlevddveifkekileklkelakdleikadvvyar 81 
                                   +++ +lk r+ le+kl++llg +vf++e+difal+cGc+G++i++rGl++dd+eif+e+i +++ e   +lei++ ++++r
  gi|91773491|ref|YP_566183.1|   3 MTQDMLKARGALENKLRELLGIPVFLIEMDIFALPCGCSGVTINTRGLQLDDLEIFEEHIIKYFTETVISLEIDPAFLFVR 83 
                                   7899***************************************************************************** PP

                       DUF5402  82 vvPGtaevidlavrklcnrcrkef...sgkkPrPdllvlkf 119
                                   ++PGtae++++++r lcn c+++f   sg++PrPd+++lkf
  gi|91773491|ref|YP_566183.1|  84 LIPGTAEIASVNARMLCNNCYMDFsrgSGRQPRPDIYILKF 124
                                   ************************9999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 899.14
//
Query:       gi|91773492|ref|YP_566184.1|  [L=347]
Description: peptidase U32 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-11   41.2   0.0    1.2e-09   37.7   0.0    2.0  2  Peptidase_U32   Peptidase family U32
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.24   10.6   0.0    1.4  1  Glyco_hydro_97  Glycoside hydrolase 97


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 !   37.7   0.0   1.3e-13   1.2e-09       3      91 ..      89     177 ..      87     201 .. 0.91
   2 ?    1.2   0.0     0.018   1.6e+02     170     193 ..     245     268 ..     232     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.3e-13
                 Peptidase_U32   3 klrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaREl..sleeikaikek 81 
                                   ++  y++kl+++g+d + v+Dp+ +e++ ++  ++ + +S+   + ++++++f+++lGa+ +v+   +  ++++++ai+++
  gi|91773492|ref|YP_566184.1|  89 TIDWYFDKLNNIGIDSITVADPFFVEMLAKD-YDMDVVVSVLSFVDSPQKAEFYEQLGATTIVIDPVVnrQFDKLEAIRDA 168
                                   567799**********************999.8********************************9998899********9 PP

                 Peptidase_U32  82 vpdvelEvfv 91 
                                   v +++l  +v
  gi|91773492|ref|YP_566184.1| 169 V-SCDLKLLV 177
                                   9.77776666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.018
                 Peptidase_U32 170 vdslKIeGRmkspeyvatvvrvYr 193
                                    d++KI GR++  + v   v++Y 
  gi|91773492|ref|YP_566184.1| 245 TDTFKIGGRTQFVNWVLDAVDAYA 268
                                   589*********999999999995 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.7e-05      0.24      85     132 ..      57     107 ..      41     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.7e-05
                Glyco_hydro_97  85 lvaYakekgvgvelwlhsetsgnvan...lekqldkafklyeklGvkgvKv 132
                                    ++Ya++kgv++e++l+s+++g ++      + +d  f++++++G++++ v
  gi|91773492|ref|YP_566184.1|  57 QTEYAHDKGVKMEIILNSSCMGGQQLtpeGYRTIDWYFDKLNNIGIDSITV 107
                                   479****************97766544457778999**********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2593.30
//
Query:       gi|91773493|ref|YP_566185.1|  [L=269]
Description: xylose isomerase-like TIM barrel [Methanococcoides burtonii DSM 6242]
Scores for complete 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   93.5   0.1    1.4e-26   93.2   0.1    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
    0.00014   21.2   0.1    0.00019   20.8   0.1    1.1  1  UvdE          UV-endonuclease UvdE
     0.0024   17.5   0.3     0.0056   16.3   0.0    1.7  2  HMGL-like     HMGL-like


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 !   93.2   0.1   2.4e-30   1.4e-26       9     210 .]      19     231 ..      12     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 2.4e-30
                                   -SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC......HTTCS..HHHHHHHHHHHHHHH CS
                  AP_endonuc_2   9 fdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypded......erear..reesvdalkraiela 79 
                                   +++vEl+++ l  +  +  ++ +l+++   l   +l  +++  +  +                +  +  +++ ++++iela
  gi|91773493|ref|YP_566185.1|  19 VRSVELYMPKLGVYEGNclQKNRLEQILDELSTCDLDTSMHAHYFADVPTY-PkglvvdT---AsmEPIHFKLMEECIELA 95 
                                   577777777777776667777777777777777777733333333332222.13554330...2444558999******** PP

                                   HHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC...HHHHHHHHHHTTTTEE CS
                  AP_endonuc_2  80 aaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd...eelarlldavdspnvg 157
                                    +L ++ +v+hpG    + +++++  + r+  +l++la++a +++v+l+lE+   ++  +++   eel++++++vds n+g
  gi|91773493|ref|YP_566185.1|  96 GKLETKAVVIHPG----RVGDDRQRSLGRMTTNLKRLAAFASENNVMLGLENKEATDPGNLCceaEELLKVVNEVDSSNLG 172
                                   *************....99*************************************988888******************* PP

                                   EEEEHHHHHHH....TTTHHHHHHHHHGGEEEEEE.EESS..TTTTSSTTEESTTSSSS CS
                  AP_endonuc_2 158 vclDtgHllia....eedvddalraladrikhvHikDakg..dlgagrdrhvpigeGei 210
                                   v++D+gH+++     +e +++++r++ + + hvH++D++g  + +  +d+h+ +g+G+i
  gi|91773493|ref|YP_566185.1| 173 VTFDIGHANLTcggdHEKLNEFIRTVSEQVIHVHLHDNYGtwTSNYDGDEHMAPGTGTI 231
                                   ****************************************9999999**********97 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   3.1e-08   0.00019      88     230 ..      41     199 ..      29     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-08
                          UvdE  88 eleevGelakelglRltfHPeqftll.nSdrkevtesairdlayHdklld.alklaeqq.davliiHvGGkfgdkeaaler 165
                                   +le++   +++ +l +++H   f  + + ++  v++ a  +   H kl++  ++la +   + ++iH G   +d++ +l r
  gi|91773493|ref|YP_566185.1|  41 RLEQILDELSTCDLDTSMHAHYFADVpTYPKGLVVDTASME-PIHFKLMEeCIELAGKLeTKAVVIHPGRVGDDRQRSLGR 120
                                   56666666777888899999999877356777777776443.57999997269***9998899******99999******* PP

                          UvdE 166 fkenikrlpd...svkerlvLENDdks......ytvadlLpvcee...lniPlVlDyHHhnvld.lreesldeslp.lv 230
                                   ++ n+krl+    +   +l LEN + +         ++lL+v +e    n+ + +D+ H n +   ++e+l+e  + + 
  gi|91773493|ref|YP_566185.1| 121 MTTNLKRLAAfasENNVMLGLENKEATdpgnlcCEAEELLKVVNEvdsSNLGVTFDIGHANLTCgGDHEKLNEFIRtVS 199
                                   *******975221566799****98864433335689****987722257999******99876577778877776344 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.32   1.9e+03     179     199 ..      40      61 ..      35      62 .. 0.76
   2 !   16.3   0.0   9.3e-07    0.0056     110     224 ..     112     235 ..      86     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.32
                                   HHHHHHHHHS-..GGGEEEEEB CS
                     HMGL-like 179 elisalkervk.dkvilsvHcH 199
                                   ++++++ ++++   +++s+H+H
  gi|91773493|ref|YP_566185.1|  40 NRLEQILDELStCDLDTSMHAH 61 
                                   56777777777667899****9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.3e-07
                                   STHHHHHHHHHHHHHHHHHTT-E..TTT-BTTTBS--HHHHHHHHHHHHHH..T-SEEEEEETTS-....--HHHHHHHHH CS
                     HMGL-like 110 kdreevakkaeeavkaarslgkd..velsledasrtdleflaevveaaeea..GatriniaDtvGv....ltPneaaelis 182
                                    dr+ ++ +++  +k+   ++ +  v l+le   +td+ +l+  +e++ ++   +++ n+  t  +    lt    +e ++
  gi|91773493|ref|YP_566185.1| 112 DDRQRSLGRMTTNLKRLAAFASEnnVMLGLENKEATDPGNLCCEAEELLKVvnEVDSSNLGVTFDIghanLTCGGDHEKLN 192
                                   577777778888888777777777899************999888888888777888888888776222234556799*** PP

                                   HHHHHS-.GGGEEEEEB-TTS-HHHHHH..HHHHTT--EEEEBT CS
                     HMGL-like 183 alkervkdkvilsvHcHndlGlAvantl..aAveaGadrvdgtv 224
                                   ++ + v+ +  ++vH H+++G+ + n    + +  G   +d +v
  gi|91773493|ref|YP_566185.1| 193 EFIRTVS-EQVIHVHLHDNYGTWTSNYDgdEHMAPGTGTIDYSV 235
                                   *******.999**********99998642244555666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1900.75
//
Query:       gi|91773494|ref|YP_566186.1|  [L=136]
Description: hypothetical protein Mbur_1529 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-24   85.5   0.5    5.9e-24   85.2   0.5    1.1  1  Usp             Universal stress protein family
      0.001   19.1   0.1     0.0011   18.9   0.1    1.1  1  ADH_zinc_N      Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.025   14.8   0.1       0.25   11.6   0.0    2.0  2  PTS-HPr         PTS HPr component phosphorylation site
      0.062   13.4   0.2      0.088   12.9   0.2    1.2  1  CheD            CheD chemotactic sensory transduction
       0.17   11.9   0.0       0.21   11.6   0.0    1.1  1  DNA_photolyase  DNA photolyase


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 !   85.2   0.5   1.6e-27   5.9e-24       4     141 .]       2     131 ..       1     131 [. 0.93

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 1.6e-27
                                   EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEE CS
                           Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvev 84 
                                   +Il+++Dgs +s++A+  A + a ++++e+i++hv++++  g   + +  ae      +e+ l++         ++ +   
  gi|91773494|ref|YP_566186.1|   2 KILLPTDGSGYSENAAMVAGQIASKHDSEVIIVHVVEDKGLGRKTWRENGAEHVINSVREELLKR-------GCKEQNIIS 75 
                                   9**************************************99999999888888888888887764.......457888888 PP

                                   EEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  85 vveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                   ++++g++ae+i+++a+++++d iV+G+rg++g+++ ++GSv+ +vl+ +p+ VlvV+
  gi|91773494|ref|YP_566186.1|  76 ETVGGHAAEMIVKTAKKHNVDRIVIGTRGHTGIKQ-IMGSVTLKVLQLSPILVLVVP 131
                                   899*******************************9.99******************7 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   3.1e-07    0.0011       5      96 ..      19     109 ..      17     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.1e-07
                                   HHHHHHHHTT-EEEEEESSHHHH...HHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEE CS
                    ADH_zinc_N   5 aavqlAkalGaeviavdsseekl...elakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpg 82 
                                    a q+A     evi v + e+k    +  +++Ga++vin+    + e++ +    +  +++ e+vG g++ e+ +k +k++
  gi|91773494|ref|YP_566186.1|  19 VAGQIASKHDSEVIIVHVVEDKGlgrKTWRENGAEHVINS----VREELLKRG-CKEQNIISETVG-GHAAEMIVKTAKKH 93 
                                   68899999999999999999986666**************....666666666.56999*******.*******9999987 PP

                                   .EEEEECSC.TSSEEE CS
                    ADH_zinc_N  83 .GrlvvvGg.gkgeee 96 
                                        v+G+ g+ + +
  gi|91773494|ref|YP_566186.1|  94 nVDRIVIGTrGHTGIK 109
                                   5445555555555555 PP

>> PTS-HPr  PTS HPr component phosphorylation site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.13   4.5e+02      17      36 ..      16      35 ..       8      46 .. 0.74
   2 ?   11.6   0.0   7.1e-05      0.25      14      64 ..      81     129 ..      69     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                                  HHHHHHHHHTTSSSEEEEEE CS
                       PTS-HPr 17 pAamlvqaasefksevtlek 36
                                  +A +  q+as+ +sev + +
  gi|91773494|ref|YP_566186.1| 16 AAMVAGQIASKHDSEVIIVH 35
                                  45555689999999999877 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.1e-05
                                   SHHHHHHHHHHHTTSS.SEEEEEE....EETTSHHHHHHCTCSTT-EEEEEE CS
                       PTS-HPr  14 haRpAamlvqaasefk.sevtlekkdkpvnaksilglmsLgvkkGeevtvsa 64 
                                   h  +A m+v++a++ +  ++ +  +      k+i+g ++L+v + + + v +
  gi|91773494|ref|YP_566186.1|  81 H--AAEMIVKTAKKHNvDRIVIGTR-GHTGIKQIMGSVTLKVLQLSPILVLV 129
                                   4..59**********9899999985.778999***99999998877776665 PP

>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.4e-05     0.088      20      83 ..      52     119 ..      44     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHHHHHHHTTT--GGG-EEEEEE-..---S.......---SS-HHHHHHHHHHHHHHHTT--E CS
                          CheD  20 adtaielLinellklgakkerleaklaGG..Aqmfafes..sksdvlniGerNveavkelLkeegipi 83 
                                   a++ i+ + +ellk+g+k++++  + +GG  A+m+  ++  ++ d + iG+r    +k+++ +  +++
  gi|91773494|ref|YP_566186.1|  52 AEHVINSVREELLKRGCKEQNIISETVGGhaAEMIVKTAkkHNVDRIVIGTRGHTGIKQIMGSVTLKV 119
                                   5677888999******************9878888665544445566699999999998887777766 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.8e-05      0.21      13      95 ..      14     101 ..      12     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                                   T-HHHH...HHHCTTSEEEEEEEE-HH..HHTCGS-CHHHHHHHHHHHHH..HHHHHHHTT--EEEEESSHHHHHHHHHHH CS
                DNA_photolyase  13 DNpALa...aAaasgepvipvfvldpe..kahklrvgaarvdfllesLad..LdeeLrelgirLvvrrgdpadvlpelake 86 
                                    N+A+     A +++++vi v v++++  +++++    + ++ ++ s+++  L++ ++e++i    + g +a+ +++ ak+
  gi|91773494|ref|YP_566186.1|  14 ENAAMVagqIASKHDSEVIIVHVVEDKglGRKTW--RENGAEHVINSVREelLKRGCKEQNIISETVGGHAAEMIVKTAKK 92 
                                   57777733345888999*********98766666..88888899999987679999*****999999999*********** PP

                                   CTECEEEEE CS
                DNA_photolyase  87 lgasavvan 95 
                                   ++++++v+ 
  gi|91773494|ref|YP_566186.1|  93 HNVDRIVIG 101
                                   *****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 943.96
//
Query:       gi|91773495|ref|YP_566187.1|  [L=185]
Description: hypothetical protein Mbur_1530 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.8   0.3      0.017   14.8   0.3    1.5  2  Wzy_C      O-Antigen ligase
        0.1   12.5   0.0       0.25   11.2   0.1    1.7  2  zf-C2H2_9  C2H2 type zinc-finger (1 copy)


Domain annotation for each model (and alignments):
>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   1.8e-06     0.017      19      70 ..      18      75 ..      13     132 .. 0.85
   2 ?   -2.9   0.0      0.51   4.5e+03      41      51 ..     148     159 ..     140     179 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-06
                         Wzy_C 19 iigllvalivlliifykrri......pfllllgilvgvilliilfvlstnletlknit 70
                                  +i+++++l ++ ++  ++ +        ++++++ ++v+l+++ +++ ++++++k  +
  gi|91773495|ref|YP_566187.1| 18 VISVPIGLSIYSWLKTREWLlyiekiELKYWIVLCLLVLLWYTAIIIKSRYYKIKMAN 75
                                  667777777777777666668888889***************************9864 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.51
                         Wzy_C  41 llllg.ilvgvi 51 
                                   ++++g +lv+++
  gi|91773495|ref|YP_566187.1| 148 RGIVGhVLVVAL 159
                                   444443333333 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 ?   -2.5   0.0      0.53   4.7e+03       8      19 ..      84      95 ..      78     100 .. 0.74
   2 ?   11.2   0.1   2.8e-05      0.25       3      46 ..     132     178 ..     130     185 .] 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.53
                                  --B-SSHHHHHH CS
                     zf-C2H2_9  8 evkfnswkdlse 19
                                  +  +n+wk++++
  gi|91773495|ref|YP_566187.1| 84 RFPINGWKNIAK 95
                                  556889999986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.8e-05
                                   B-TTT--B-S....SHHHHHHHHHHHTSSS--HHHHHHHHHT-SS--- CS
                     zf-C2H2_9   3 lCPvCevkfn....swkdlseHilsaasksdaeHvmWLNRniskkrls 46 
                                   +CP Cev+++     w+ +  H+l  a +   + v  L Rn+ k  l+
  gi|91773495|ref|YP_566187.1| 132 RCPKCEVELEenknLWRGIVGHVLVVALRKIIKIVGTLKRNVLK-NLQ 178
                                   7********8777679999****999999888888888888854.455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1172.23
//
Query:       gi|91773496|ref|YP_566188.1|  [L=136]
Description: histidine triad (HIT) protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-25   89.3   0.0    2.5e-25   89.1   0.0    1.1  1  HIT       HIT domain
    1.7e-14   54.2   0.0    2.1e-14   54.0   0.0    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
     0.0042   16.9   0.1     0.0069   16.3   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 !   89.1   0.0   4.2e-29   2.5e-25       2      96 ..      11     105 ..      10     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 4.2e-29
                                   GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT CS
                           HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahag 82 
                                   ++ips+++yed++++afldi+p ++gh+ v+pkkh++ ++d++ e+ + l+++vk++   l++ ++++g +v  nn a+ag
  gi|91773496|ref|YP_566188.1|  11 GKIPSHKIYEDEETYAFLDINPCSRGHTVVVPKKHYDSFTDMPTEDAGSLFATVKMLTGMLEDAMSADGSNVGLNNKAAAG 91 
                                   679****************************************************************************** PP

                                   -SSSS-EEEEEEC- CS
                           HIT  83 qsvahlHiHviprr 96 
                                   q v+h+H+H+ipr 
  gi|91773496|ref|YP_566188.1|  92 QLVPHVHVHIIPRM 105
                                   ************96 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 !   54.0   0.0   3.5e-18   2.1e-14       2     101 ..       3     103 ..       2     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.5e-18
                                   -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EEEE CS
                        DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vdaee 81 
                                   ++f++++kgk+p+  +yede++ ++ Di+p ++ h +v+pk++ +s +d+ +e+   l + ++ +  ++e+ +++ +    
  gi|91773496|ref|YP_566188.1|   3 CLFCNIIKGKIPSHKIYEDEETYAFLDINPCSRGHTVVVPKKHYDSFTDMPTEDAGSLFATVKMLTGMLEDAMSAdGSNVG 83 
                                   99*********************************************************************9977666777 PP

                                   E--SCCCT--S-S--EEEEE CS
                        DcpS_C  82 lrvgvhyqPsvyhlHlHvis 101
                                   l+    + + v h+H+H+i 
  gi|91773496|ref|YP_566188.1|  84 LNNKAAAGQLVPHVHVHIIP 103
                                   888888899*********97 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-06    0.0069      13     108 ..       2     103 ..       1     110 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                                   H-S--.--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHH...HHHTT--E CS
                      CwfJ_C_1  13 sClfC.lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalvkm...ykkqdkda 89 
                                   +ClfC + + k ++h i    +++Y+ l  +p s gH +++p +H  + + ++ e   ++ +  k l+ m     + d   
  gi|91773496|ref|YP_566188.1|   2 DCLFCnIIKGKIPSHKIYE-DEETYAFLDINPCSRGHTVVVPKKHYDSFTDMPTEDAGSLFATVKMLTGMledAMSADGSN 81 
                                   5788855667777887754.789*************************************999999999954334556667 PP

                                   EEEEE-...SSS-----EEEEE CS
                      CwfJ_C_1  90 vvfEis...sersvHlaiqvip 108
                                   v + ++    +  +H+++++ip
  gi|91773496|ref|YP_566188.1|  82 VGLNNKaaaGQLVPHVHVHIIP 103
                                   7777766666778999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 904.20
//
Query:       gi|91773497|ref|YP_566189.1|  [L=438]
Description: filamentation induced by cAMP protein Fic [Methanococcoides burtonii DSM 6242]
Scores for complete 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   72.3   0.0    1.5e-19   70.7   0.0    1.9  1  Fic            Fic/DOC family
    9.4e-06   25.3   0.0    2.7e-05   23.8   0.0    1.8  1  HTH_DeoR       DeoR-like helix-turn-helix domain
     0.0014   18.9   0.0     0.0036   17.6   0.0    1.7  1  DUF4172        Domain of unknown function (DUF4172)
     0.0016   18.5   0.9     0.0062   16.6   0.3    2.2  2  Fic_N          Fic/DOC family N-terminal
  ------ inclusion threshold ------
      0.025   14.4   0.5        0.3   11.0   0.2    2.9  4  Dioxygenase_N  Catechol dioxygenase N terminus
      0.026   14.6   1.0      0.083   12.9   0.3    2.3  2  DUF2089        Protein of unknown function (DUF2089)
      0.049   14.1   2.7        4.8    7.7   0.1    3.4  3  PhoU           PhoU domain
       0.14   12.0   0.1       0.26   11.2   0.1    1.4  1  VbhA           Antitoxin VbhA


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   6.7e-23   1.5e-19       2      96 ..     179     283 ..     178     284 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 6.7e-23
                                   -SHHHHHHHHCHS-S----...--TS--SS-S.....T..EEEE---SCCCHHHHHHHHHHHHC..HHT-S-HHHHHHHHH CS
                           Fic   2 ltledllelhrlllqdige...eagefrdeev.....segklesalappeevpaeleelleyln..elekeeplekaaalh 72 
                                   +t+e lle+++++++++++   ++g frd+++     + g++ +++++ eev++ ++el+++ n  ++  ++p++k  +lh
  gi|91773497|ref|YP_566189.1| 179 MTPELLLEIQKRMTEGTFDdpeDEGVFRDNDEirvfdNDGEVLHTPPKKEEVSELVSELCNFANndDQFFIHPIIKGIFLH 259
                                   6899***************98877*****888*****99*************************77777788********* PP

                                   HHHHHH--SSS-HHHHHHHHHHHH CS
                           Fic  73 yefekiHPFaDGNgRtarlllnll 96 
                                   y +++iHPF+DGNgRt+r l+ ++
  gi|91773497|ref|YP_566189.1| 260 YLLNYIHPFNDGNGRTGRSLFYWY 283
                                   ********************9997 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 !   23.8   0.0   1.2e-08   2.7e-05      12      50 ..     388     426 ..     375     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                      HTH_DeoR  12 qgklsveelvellgvSeaTiRRDLneLeeqglltRthGG 50 
                                   + ++ v+e+++  gvS aT+R DL +Lee g l++   G
  gi|91773497|ref|YP_566189.1| 388 HKTMAVKEVMNTQGVSYATARSDLFYLEEIGHLKKQKSG 426
                                   899*****************************9997766 PP

>> DUF4172  Domain of unknown function (DUF4172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.6e-06    0.0036      19      66 ..      90     137 ..      80     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                       DUF4172  19 aellaevrr.kqGrllGklealgfelreealletlteevvksseIEGek 66 
                                   +e+l ++ + ++G+l   ++a+ +++re+ +l++l+ee+++ss+IEG +
  gi|91773497|ref|YP_566189.1|  90 QEKLYTLDKgAAGTLASVIDAI-SDNREKYILNSLMEEAIASSQIEGAT 137
                                   5555555551456677777666.899*********************86 PP

>> Fic_N  Fic/DOC family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   2.8e-06    0.0062      12      81 ..     102     172 ..      98     173 .. 0.69
   2 ?   -1.1   0.0      0.89     2e+03      47      72 ..     374     398 ..     370     405 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.8e-06
                         Fic_N  12 geLdgllrllp.npelLirplvrkEAvlSSeIEgtqttlddlleaeadeeee.kskdvkEVlnYvkAleyGl 81 
                                   g L++++ ++  n e  i   +++EA +SS+IEg+  + + + ++  +++++ ++kd + ++n  + ++y l
  gi|91773497|ref|YP_566189.1| 102 GTLASVIDAISdNREKYILNSLMEEAIASSQIEGATPS-RRVAKEMLRKSKKpENKDERMIINNYNTMKYVL 172
                                   667777777764666677777899**********8655.444444444444424468899999999998865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.89
                         Fic_N  47 ttlddlleaeadeeeekskdvkEVln 72 
                                   t ++++l+   + ++++  +vkEV+n
  gi|91773497|ref|YP_566189.1| 374 TRQREILRQFIKYPHKTM-AVKEVMN 398
                                   678889999999999987.9****98 PP

>> Dioxygenase_N  Catechol dioxygenase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.4   9.9e+03       1      13 [.     113     125 ..     113     128 .. 0.82
   2 ?   -2.9   0.0       2.9   6.5e+03       8      20 ..     230     242 ..     227     244 .. 0.81
   3 ?   11.0   0.2   0.00013       0.3       8      41 ..     338     371 ..     334     382 .. 0.84
   4 ?    0.4   0.0      0.27   6.1e+02       2      45 ..     374     423 ..     373     433 .. 0.50

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
                                   -HHHHHHHHHHHH CS
                 Dioxygenase_N   1 dpRlkeiverlvr 13 
                                   d+R k+i+++l++
  gi|91773497|ref|YP_566189.1| 113 DNREKYILNSLME 125
                                   6799999999987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHHH CS
                 Dioxygenase_N   8 verlvrhlhdfir 20 
                                   v++lv++l++f++
  gi|91773497|ref|YP_566189.1| 230 VSELVSELCNFAN 242
                                   7899999999986 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
                 Dioxygenase_N   8 verlvrhlhdfirevdlteeEwwaavdfLtrvGq 41 
                                   ++++++ lh++ + ++++++E  +a++++++  +
  gi|91773497|ref|YP_566189.1| 338 LTAIIESLHEILKYLEIKQQEQYQALKYMNESDE 371
                                   6899**************************9776 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.27
                                   HHHHHHHHHHHHHHHHHH..HHT....T--HHHHHHHHHHHHHHHH.... CS
                 Dioxygenase_N   2 pRlkeiverlvrhlhdfi..rev....dlteeEwwaavdfLtrvGqisdd 45 
                                    R +ei++++++  h+++  +ev     ++++  +  + +L ++G+  ++
  gi|91773497|ref|YP_566189.1| 374 TRQREILRQFIKYPHKTMavKEVmntqGVSYATARSDLFYLEEIGHLKKQ 423
                                   67777777777777765411222111123333334444566666665555 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3   7.3e+03      89     105 ..     113     129 ..      85     132 .. 0.65
   2 ?   12.9   0.3   3.7e-05     0.083      28      71 ..     366     412 ..     337     429 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                       DUF2089  89 eeerkeileklekgeis 105
                                   ++++k il++l +  i 
  gi|91773497|ref|YP_566189.1| 113 DNREKYILNSLMEEAIA 129
                                   56778888888887775 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.7e-05
                       DUF2089  28 lsefarLskeqlefvelfikarGn...lkevekelgisYpTvrnrld 71 
                                   ++e ++L++ q e ++ fik   +   +kev ++ g+sY T+r+ l 
  gi|91773497|ref|YP_566189.1| 366 MNESDELNTRQREILRQFIKYPHKtmaVKEVMNTQGVSYATARSDLF 412
                                   677789*************9754322289999999********9885 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.32   7.3e+02      17      49 ..       8      40 ..       5      55 .. 0.85
   2 ?    7.7   0.1    0.0021       4.8      10      75 ..      84     146 ..      81     155 .. 0.70
   3 ?    3.4   0.2     0.047   1.1e+02       8      52 ..     341     387 ..     338     418 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.32
                                  HHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU 17 ealeekdtelarevierddeidrlekeiersll 49
                                  ++l+++d   a + i + d i+   + ++r+l 
  gi|91773497|ref|YP_566189.1|  8 SSLSTEDGTEAMKYIHDQDVINFVSEYNRRYLH 40
                                  6899*****************998888887765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                                   HHHHHHHHHHHCT-HHHHHHHH.HHHHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHHHHHHHHHH CS
                          PhoU  10 emlddalealeekdtelarevi.erddeidrlekeierslleal.akrqplaedlrellsllriardl 75 
                                   +mld+  e l++ d+ +a  +    d   d+ ek i +sl+e++ a +     +++ ++ ++r+a+++
  gi|91773497|ref|YP_566189.1|  84 TMLDEFQEKLYTLDKGAAGTLAsVIDAISDNREKYILNSLMEEAiASS-----QIEGATPSRRVAKEM 146
                                   7999999*******9888777413477777777777777777774433.....344456666777665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.047
                                   HHHHHHHHHHHHHCT-HHHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   8 veemlddalealeekdtelarev..ierddeidrlekeierslleal 52 
                                   + e l++ l+ le k  e  +++  +++ de++  ++ei r+ ++  
  gi|91773497|ref|YP_566189.1| 341 IIESLHEILKYLEIKQQEQYQALkyMNESDELNTRQREILRQFIKYP 387
                                   56889999999988876665544116778888888888888865544 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012      0.26       6      22 ..     125     141 ..     123     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                          VbhA   6 rqAlAsnelEGlepsae 22 
                                   ++A+As+++EG +ps++
  gi|91773497|ref|YP_566189.1| 125 EEAIASSQIEGATPSRR 141
                                   79*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2989.55
//
Query:       gi|91773498|ref|YP_566190.1|  [L=150]
Description: T/G mismatch-specific endonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-18   66.7   0.0    2.2e-18   65.9   0.0    1.3  1  Vsr        DNA mismatch endonuclease Vsr
  ------ inclusion threshold ------
      0.064   13.4   0.7       0.12   12.5   0.7    1.5  1  MTES_1575  REase_MTES_1575


Domain annotation for each model (and alignments):
>> Vsr  DNA mismatch endonuclease Vsr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   2.4e-22   2.2e-18      10      69 ..      21      81 ..      15      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.4e-22
                                  HHHHHTXXSSSXHHHHHHHHHHHHTT-.-EEES-TTSTT--SEEEGGGTEEEEEE-TTTTT CS
                           Vsr 10 skvmakikskdtkpElrlaklltglGl.ryRkndkslaGkPDvvlkkykvvvFvhGcFWHg 69
                                  s vm+++  kdtkpEl+l+k+l   G+  yR++ k+++G+PD+  ++ k+++Fv+Gc+WH 
  gi|91773498|ref|YP_566190.1| 21 SRVMSANVGKDTKPELLLRKALRYIGIpGYRLHWKKVPGRPDITYPGGKIAIFVNGCYWHR 81
                                  88************************956*******************************6 PP

>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   1.4e-05      0.12      52      93 ..     102     143 ..      93     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                     MTES_1575  52 keardrdierqevLerlGWkilRiwssdwyrnpeeeleklve 93 
                                   k++++rd e  + L++ GWki+  w+ + +r+  e+ e++++
  gi|91773498|ref|YP_566190.1| 102 KRNKERDDENIRLLKAEGWKIIVLWECEIKRDVMECAERVRN 143
                                   67889999999**********************999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1029.20
//
Query:       gi|91773499|ref|YP_566191.1|  [L=224]
Description: hypothetical protein Mbur_1535 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-07   29.3   0.0    1.2e-06   28.2   0.0    1.6  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 !   28.2   0.0   6.6e-11   1.2e-06       1      37 []      59      95 ..      59      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 6.6e-11
                       DUF1232  1 aklliagalaYlisPiDlIPDfiPvlGflDDlavltl 37
                                  +k+l+ +al Yl++  D+I D     G+lDDl+++++
  gi|91773499|ref|YP_566191.1| 59 TKMLVNAALSYLVLEEDIITDKRSKDGYLDDLYICAY 95
                                  699*******************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1663.46
//
Query:       gi|91773500|ref|YP_566192.1|  [L=246]
Description: hypothetical protein Mbur_1536 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-07   28.5   0.3    9.3e-07   28.5   0.3    1.9  2  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 !   28.5   0.3   5.2e-11   9.3e-07       1      36 [.      51      86 ..      51      87 .. 0.93
   2 ?   -3.4   0.1      0.51   9.1e+03      19      26 ..     110     117 ..     108     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.2e-11
                       DUF1232  1 aklliagalaYlisPiDlIPDfiPvlGflDDlavlt 36
                                  ak  i +++ Y+  P D IPD  ++ GflDD++v++
  gi|91773500|ref|YP_566192.1| 51 AKFKINSCFSYFAIPDDYIPDDEGPEGFLDDFFVCV 86
                                  5788999***************************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.51
                       DUF1232  19 IPDfiPvl 26 
                                   I ++iP++
  gi|91773500|ref|YP_566192.1| 110 IMELIPFV 117
                                   67788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1778.53
//
Query:       gi|91773501|ref|YP_566193.1|  [L=732]
Description: type III restriction enzyme, res subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-23   83.2   0.4    1.7e-22   79.8   0.0    2.7  2  Helicase_C     Helicase conserved C-terminal domain
    2.1e-23   83.2   0.0    7.1e-23   81.5   0.0    2.0  1  ResIII         Type III restriction enzyme, res subunit
    2.1e-13   50.4   0.0    6.7e-13   48.8   0.0    1.9  2  DEAD           DEAD/DEAH box helicase
      2e-08   34.2   0.6    7.5e-08   32.3   0.2    2.1  2  PLDc_2         PLD-like domain
    7.8e-07   28.1   0.0    1.6e-06   27.1   0.0    1.4  1  SNF2_N         SNF2 family N-terminal domain
    8.3e-07   28.5   0.3    1.6e-06   27.5   0.3    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.3e-05   25.0   0.0      3e-05   23.8   0.0    1.6  1  SWI2_SNF2      SWI2/SNF2 ATPase
  ------ inclusion threshold ------
      0.082   13.2   0.5        0.7   10.2   0.0    2.5  2  AAA_22         AAA domain
       0.13   12.0   0.0       0.31   10.7   0.0    1.7  1  AAA_30         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 ?   -0.1   0.1      0.57   1.1e+03      32      68 ..     400     435 ..     365     443 .. 0.60
   2 !   79.8   0.0   8.6e-26   1.7e-22       1     110 [.     549     659 ..     549     660 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.57
                                   HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS CS
                    Helicase_C  32 vklllekkgikvavlhgelpqnereeileqfnkgesd 68 
                                    +ll+e+  + +  +h  + ++e+++il+qf + +++
  gi|91773501|ref|YP_566193.1| 400 GNLLRENMYLIIDEVHE-IGSSENRKILSQFTDIKYR 435
                                   34444444555555665.9999999******876666 PP

  == domain 2  score: 79.8 bits;  conditional E-value: 8.6e-26
                                   HHHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                    Helicase_C   1 dkleallell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                   dk++ l+e+l +++ + +k+l+++n +d++++v  + e++g+k+ +++g+l+ +++e+++++f++g+ ++L+a + + +Gi
  gi|91773501|ref|YP_566193.1| 549 DKFRVLKEILvEESDSLNKCLVYCNDKDHMNEVAEMIEREGFKCRKFYGDLNPKNKEHVFDSFKNGDLQFLVAIKCLDQGI 629
                                   6889999998899999************998855555999***************************************** PP

                                   TSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   dip +n  i++   rn+++yiqr+GR+ R 
  gi|91773501|ref|YP_566193.1| 630 DIPVCNSAIILTSSRNPREYIQRRGRILRL 659
                                   ***************************995 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 !   81.5   0.0   3.6e-26   7.1e-23       2     171 .]     278     444 ..     277     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 3.6e-26
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   ++lr+yQeeai++++     +++ rg+++maTGtGKT++a+++i++l  k k    l+ vp+++l +q+ ee k+++ +  
  gi|91773501|ref|YP_566193.1| 278 KSLRNYQEEAIQAWV-----DNEYRGILEMATGTGKTFTALNAIKQLDLKSK--LLLIGVPQRELANQWTEECKSVFGDVP 351
                                   789***********9.....8999*************************955..67777******************9998 PP

                                   .........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT CS
                        ResIII  83 ke.......igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilek 156
                                   ++       +g k++ +++++++k+++   i+++   ++  ++      +  +l  ++ ++iiDE+H +g+ ++ r+il +
  gi|91773501|ref|YP_566193.1| 352 NRmilcysnTGWKMNIEREIRQSKREKALCIIIVVFGTMRGNE---FVSKIGNLLRENMYLIIDEVHEIGS-SENRKILSQ 428
                                   8888776544444444444445555555556666666666555...6788999999999************.999***999 PP

                                   ---.SEEEEEESS-S- CS
                        ResIII 157 fke.avllglTATper 171
                                   f + +++lgl+ATper
  gi|91773501|ref|YP_566193.1| 429 FTDiKYRLGLSATPER 444
                                   97769*********86 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   3.4e-16   6.7e-13       2     171 ..     282     444 ..     281     448 .. 0.73
   2 ?   -2.4   0.1       1.8   3.6e+03      82     134 ..     515     566 ..     493     589 .. 0.48

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.4e-16
                                   HHHHHHHHHHHTTC.EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplilggg.dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   ++Q+eai++ ++++   +++++TG+GKT  + + +++++    + + +  li +P reLa+q  +++k+++  +  r+ l+
  gi|91773501|ref|YP_566193.1| 282 NYQEEAIQAWVDNEyRGILEMATGTGKTFTA-LNAIKQL----DLKSKLLLIGVPQRELANQWTEECKSVFGDVPNRMILC 357
                                   58*********776699************96.5666677....466669999********************877777777 PP

                                   ET....TSSHHHHHHHHHTT....CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                   xx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 ig....gvaardqlskldng....vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                   ++    + + ++++++ +++    + ivv  + r  +++s+    l++  +l++DE++++ +++ ++ +++ ++ +     
  gi|91773501|ref|YP_566193.1| 358 YSntgwKMNIEREIRQSKREkalcIIIVVFGTMRGNEFVSKIGNLLRENMYLIIDEVHEIGSSENRKILSQ-FTDI----- 432
                                   76444533334444444322346666666666688888865554599999************955555555.5555..... PP

                                   TSTTTSEEEEEESSBSH CS
                                   xxxxxxxxxxxxxxxxx RF
                          DEAD 155 dgklqrqvivlSATlpk 171
                                     k     + lSAT+++
  gi|91773501|ref|YP_566193.1| 433 --K---YRLGLSATPER 444
                                   ..2...37999999875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                   ETTSSHHHHHHHHHTT..CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHH CS
                                   xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldng..vdivvgtpgrlddllstgklnlsqvrflVlDEadrll 134
                                   i+ +  + ++++++ng  ++i++     +++ ++  k  ++ ++ + + E d l 
  gi|91773501|ref|YP_566193.1| 515 IKTNGGHIDIQNIENGtyLQILLNQRADIIKECK-DK--FRVLKEILVEESDSLN 566
                                   3333333444455544344444444444444332.23..5555555556665555 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.2   3.7e-11   7.5e-08       4     133 .]      31     208 ..      28     208 .. 0.82
   2 ?   -1.5   0.0         1   2.1e+03      35      73 ..     529     593 ..     524     608 .. 0.59

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.7e-11
                        PLDc_2   4 liksAkksidiatyyfvsdrei...ldallkaakrgvkvrilldskkd.............................daga 52 
                                   ++++++++ +ia ++   + +i   ++ + +  ++g k  ++++s+ +                             ++++
  gi|91773501|ref|YP_566193.1|  31 ALSRSRYYYRIAGFFS--STAIaaaARGISAFVENGEKMYLIIGSQLSqedvdaintgtkkidatlyekwdvckedfENNV 109
                                   6888889999998855..7777443444566899***********999*************************99875555 PP

                        PLDc_2  53 vdeaslkelkellleagvevrvfe...tll........gslHaKlylid....gktvivGSsNltkrgldlnlElnvvied 118
                                   v ++++  l+ l+++ ++e+++     + +        + +H+K+++++    +++ i GS N t ++++ n+E+  v  +
  gi|91773501|ref|YP_566193.1| 110 V-KKRFELLAWLIANDKLEIKIGVnkdK-NgnylssedSLFHEKVLIFEdydgNRIQIDGSINETGKAWRENRESFCVHRS 188
                                   4.588999999**********9764331.1344556779*********65888889999*********************9 PP

                        PLDc_2 119 k.....elakeleeeFerlw 133
                                   +     e+++   + F+++w
  gi|91773501|ref|YP_566193.1| 189 WekghkEFINSAMDDFNKIW 208
                                   98888777777777788877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                        PLDc_2  35 rgvkvrilldskkd..........................dagavdeaslkelkellleagvevr 73 
                                   +g  ++ill++++d                            +++d+++ +e +e++ ++g + r
  gi|91773501|ref|YP_566193.1| 529 NGTYLQILLNQRADiikeckdkfrvlkeilveesdslnkcLVYCNDKDHMNEVAEMIEREGFKCR 593
                                   56667777777554555555555555555555555555554455555555566666666666555 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 !   27.1   0.0   7.9e-10   1.6e-06      57     215 ..     297     442 ..     281     449 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.9e-10
                                   -EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH-TT...S-EEE--SSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                        SNF2_N  57 GGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierhvss...salrvlvyggqk 133
                                    GiL   +G GKT ++l  i+++      ++         +  Li vP+ +l++qW++e ++   +     + ++  +g  
  gi|91773501|ref|YP_566193.1| 297 RGILEMATGTGKTFTALNAIKQLDL----KS---------KLLLIGVPQrELANQWTEECKSVFGDvpnRMILCYSNTGW- 363
                                   58999999*************4333....22.........348999***************9865410044434444443. PP

                                   H-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH.---S-EEEE-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                        SNF2_N 134 kmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavsk.LstsnrwiltG 213
                                   km+ +++  + k  ++  ++i+ + +++  +e++ k+  l +    ++++DE h +++s+++  +++s+  + ++r+ l++
  gi|91773501|ref|YP_566193.1| 364 KMNIEREIRQSKREKALCIIIVVFGTMR-GNEFVSKIGNLLRE-NMYLIIDEVHEIGSSENR--KILSQfTDIKYRLGLSA 440
                                   4666666677777788888999999999.66688888888765.56999*********9554..3444423699******* PP

                                   -- CS
                                   xx RF
                        SNF2_N 214 TP 215
                                   TP
  gi|91773501|ref|YP_566193.1| 441 TP 442
                                   *9 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 !   27.5   0.3   8.2e-10   1.6e-06      27     155 ..     532     663 ..     526     674 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 8.2e-10
                 ERCC3_RAD25_C  27 ylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkp.....yiyGetseaerlkilqkfk 102
                                   yl+   ++++ ++    +kfr+++ ++       +k +v++++   ++e+a++++++       yG+ + +++ +++++fk
  gi|91773501|ref|YP_566193.1| 532 YLQILLNQRADIIKECKDKFRVLKEILVEESDSLNKCLVYCNDKDHMNEVAEMIEREgfkcrKFYGDLNPKNKEHVFDSFK 612
                                   888888888888888999***99988888888999****************99877522222589***************9 PP

                 ERCC3_RAD25_C 103 knpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkks 155
                                   + + ++ ++  k  D+ iD+P  n  i + s     r   qr GriLr  k++
  gi|91773501|ref|YP_566193.1| 613 NGD-LQFLVAIKCLDQGIDIPVCNSAIILTSSRNP-REYIQRRGRILRLHKNK 663
                                   885.6677777999**********99988776655.6789********87764 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.5e-08     3e-05      15     205 ..     289     498 ..     274     518 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.5e-08
                     SWI2_SNF2  15 e...gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageekp.......kqaesrke 85 
                                   +   +++  G++   +G GK++t + + k+l     k++ +++ +  ++L +Q +++ +++  + p       +++  + +
  gi|91773501|ref|YP_566193.1| 289 QawvDNEYRGILEMATGTGKTFTALNAIKQLDL---KSKLLLIGVPQRELANQWTEECKSVFGDVPnrmilcySNTGWKMN 366
                                   13444578899999**********999999887...667777778999************954444112222235555668 PP

                     SWI2_SNF2  86 Lkelleke.sekiifttiqKfeeeekekl....evlsereniivlvDEaHRsqygelakklrkalpnaafigFTGTPilkk 161
                                   ++++++++ +ek ++ +i  f + + +++         ren+++++DE H   ++e +k l ++     ++g+  TP  + 
  gi|91773501|ref|YP_566193.1| 367 IEREIRQSkREKALCIIIVVFGTMRGNEFvskiGN-LLRENMYLIIDEVHEIGSSENRKILSQFTDIKYRLGLSATPERAW 446
                                   89999544388899999999985544333221133.34788************************************9984 PP

                     SWI2_SNF2 162 d....kktkevFg.eyidkYtikeave..Dgavvp.ilYesrlaklelkeee 205
                                   d       +e Fg e i  +++++a++  Dg      +Y+ +l++ +l+ +e
  gi|91773501|ref|YP_566193.1| 447 DeegnSAIQEYFGkEPIFVWDMEKAIRppDGYEPClCQYKYHLHDCSLTGDE 498
                                   4223244688998567999999999973344332235566666666666555 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   0.00035       0.7      14     114 ..     304     428 ..     295     444 .. 0.77
   2 ?   -0.5   0.1      0.68   1.4e+03      63     115 ..     512     584 ..     491     593 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00035
                        AAA_22  14 sGtGKTtllrrlleqldeeakaee.............erpevvfvtlpsst....sskdllrellralglelka....... 70 
                                   +GtGKT+++ +  +qld  +k                e+ + vf ++p+ +    s +    ++ r++ +++ +       
  gi|91773501|ref|YP_566193.1| 304 TGTGKTFTALNAIKQLDLKSKLLLigvpqrelanqwtEECKSVFGDVPNRMilcySNTGWKMNIEREIRQSKREkalciii 384
                                   8***************98766666999999999999977777777777777776666666677777777766668889999 PP

                        AAA_22  71 ...erlsseellealeqalraravielliiDEaqhlrseealeeLrs 114
                                       + +  e+++++ + lr+ +    liiDE++ + s e+ + L++
  gi|91773501|ref|YP_566193.1| 385 vvfGTMRGNEFVSKIGNLLRENMY---LIIDEVHEIGSSENRKILSQ 428
                                   999999999999999999999988...********963333333333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                        AAA_22  63 alglelka.........erlsseellealeqalrarav....ielliiDEaqhlr......s.eealeeLrsl 115
                                   ++  ++++         ++  ++ ll++ ++ ++++++     + ++++E + l+      + +++++e+ ++
  gi|91773501|ref|YP_566193.1| 512 QIAIKTNGghidiqnieNGTYLQILLNQRADIIKECKDkfrvLKEILVEESDSLNkclvycNdKDHMNEVAEM 584
                                   4444444455556666544555666677777777777777677779999999997555444157777776555 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   0.00016      0.31       2     114 ..     280     431 ..     279     439 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                        AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKt.talkalreaweaaggrviglAptgkaAkvLaeelg.i............ 68 
                                   l++ Q++a++a + ++    +l+ + GtGKt tal+a++++  +++  +ig+ p+ + A++ +ee+  +            
  gi|91773501|ref|YP_566193.1| 280 LRNYQEEAIQAWVDNEY-RGILEMATGTGKTfTALNAIKQLDLKSKLLLIGV-PQRELANQWTEECKsVfgdvpnrmilcy 358
                                   6788*****99999996.899**********557899999998888766666.7777777777655532222222222222 PP

                        AAA_30  69 ....eastiakllkrlk........................grarlepgtllivDEagmvdtkqlaallkaaek 114
                                         ++i++ +++ k                        g + l+++  li+DE+  +++++ +++l++ ++
  gi|91773501|ref|YP_566193.1| 359 sntgWKMNIEREIRQSKrekalciiivvfgtmrgnefvskiG-NLLRENMYLIIDEVHEIGSSENRKILSQFTD 431
                                   211133444444444448888888888888888888888753.4566668889999988888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 5110.44
//
Query:       gi|91773502|ref|YP_566194.1|  [L=657]
Description: DNA repair ATPase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-18   66.7  26.1    3.8e-18   66.7  26.1    4.0  2  AAA_23           AAA domain
    6.2e-05   22.5   0.0    6.2e-05   22.5   0.0    2.6  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00079   19.1   3.8    0.00079   19.1   3.8    3.1  3  AAA_27           AAA domain
     0.0061   16.3   0.0       0.01   15.5   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.2      0.012   15.4   0.2    3.7  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.078   13.2   0.2       0.42   10.8   0.2    2.3  1  zinc_ribbon_16   Zinc-ribbon like family
        0.1   12.8   0.3       0.34   11.1   0.3    1.9  1  FAA_hydrolase_N  Fumarylacetoacetase N-terminal
       0.18   11.9   0.8        1.4    9.1   0.0    2.4  2  Phage_Treg       Lactococcus bacteriophage putative transcrip
        8.4    6.0  76.6        1.5    8.4  39.4    2.5  2  AAA_15           AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7  26.1   1.9e-21   3.8e-18       1     195 [.       8     239 ..       8     271 .. 0.60
   2 ?  -25.5  50.6         9   1.8e+04      79     198 ..     270     427 ..     224     540 .. 0.60

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 1.9e-21
                        AAA_23   1 kLkienfrsf.rdqeidF....skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese...gkvka 73 
                                   ++++ nf ++ ++ ++dF    +k+++l+  pNG+GKTT++ Aik+++yge+ +  ++s  ++   d+    +    k++ 
  gi|91773502|ref|YP_566194.1|   8 RITLFNFACYyGENTLDFttktDKNIFLFNVPNGSGKTTLFHAIKWGFYGESIEYFKDS-DKISIKDFLND-RldpSKDMC 86 
                                   7999******55667***********************************985444443.34555555422.235578899 PP

                        AAA_23  74 yveltfenkdgrytrsierere..lskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer.......... 142
                                   +ve+tfe+ +++  ++++r+ +  ++k+++ + +k + ++l++de +++++++ +   +++  +++++ e+          
  gi|91773502|ref|YP_566194.1|  87 FVEITFEYGNKT--YTLKRKYQpgVKKTSELSLSKGQDDILDVDEAQEMLNHI-NP--QNFADFFMFDGEQlsrfmtaqkn 162
                                   9**********6..6777766621555555555677889*******9999985.43..45656666666663444444333 PP

                        AAA_23 143 .feefelkdkke.......................rlee.lekeleeledekkllekl........eqekekekeleelee 190
                                    +         +                       +le+ + +el +++ ++k +e++        ++++++  ++e+ +e
  gi|91773502|ref|YP_566194.1| 163 iE---------QnyrdsilqllglkqiqilkddlsKLEKrYDNELTQQKSTNKDVETKkkvinrlnKDINNEDVKIEKHNE 234
                                   30.........1444455555544433333332222222233333332222222222234444444222333334444444 PP

                        AAA_23 191 eleei 195
                                    +e+ 
  gi|91773502|ref|YP_566194.1| 235 SIEQN 239
                                   44443 PP

  == domain 2  score: -25.5 bits;  conditional E-value: 9
                        AAA_23  79 fenkdgry...............trsiererelskkkgkttkkaklelleideleqfisellg.skkiilnlilflgqer. 142
                                   ++++d+r+                ++ier+ +++ ++++++  +  ++++ ++ +  +++  + + k++++ +  +g +  
  gi|91773502|ref|YP_566194.1| 270 IRKQDKRSsdiesklsssstnffIKFIERDLKRYIDENNNKIRDLQDICGLSDMQADTQSAKEdILKKSIPKCEVCGHKLs 350
                                   222333225555555555555566666666666666666665555555555444444444333122233333333333333 PP

                        AAA_23 143 .feefelkdkkerleelekeleeledekkllekl....................eqekekekeleeleeeleeilke 198
                                     e  +lkd++er+ e  k +e++++e++ l+++                     ++ e ++++++le++ ++++ke
  gi|91773502|ref|YP_566194.1| 351 dSEISKLKDEQERISESLKLFEKNKNERDNLKDEnqqfmsslrlldgcdfglemDNLDELKNKIHNLEKAKKDLDKE 427
                                   34444445555555555555555555555555555555555555555555555533333333444444433333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.1e-08   6.2e-05       2      92 ..       6     101 ..       5     142 .. 0.75
   2 ?  -11.2  38.2         9   1.8e+04      41     196 ..     168     622 ..     164     642 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.1e-08
                                   EEEEEEESETTEECEEE...EEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH...CCCCCC--BTTCSSTTE CS
                                   xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                         SMC_N   2 lkrleienFksyagktv...ilpfsksftaivGpNGSGKsnlldAilFvLGersakklrse...klsdlihkskekasvkk 76 
                                   l r+++ nF  y g+++   +++ +k++     pNGSGK+ l+ Ai++ +  +s + ++ +   +++d ++  +  +s + 
  gi|91773502|ref|YP_566194.1|   6 LIRITLFNFACYYGENTldfTTKTDKNIFLFNVPNGSGKTTLFHAIKWGFYGESIEYFKDSdkiSIKDFLND-RLDPSKDM 85 
                                   568899999999876652224455666677778***************998888889997622257888887.999***** PP

                                   EEEEEEEEETTEESSS CS
                                   xxxxxxxxxxxxxxxx RF
                         SMC_N  77 aeveitfdnedkklki 92 
                                   + veitf+  +k+ + 
  gi|91773502|ref|YP_566194.1|  86 CFVEITFEYGNKTYTL 101
                                   *******999998322 PP

  == domain 2  score: -11.2 bits;  conditional E-value: 9
                                   HHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEEEEETTSEEEE...EET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx...xxx RF
                         SMC_N  41 ldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkk.lkiekeevsisrrvkrkgesey...kin 114
                                    d+il +LG ++  ++ +++ls+l ++   + +++++++ +ve   +  ++    i++e+v+i+++ ++ ++++    k++
  gi|91773502|ref|YP_566194.1| 168 RDSILQLLGLKQI-QILKDDLSKLEKRydnELTQQKSTNKDVETKKKVINRLnKDINNEDVKIEKHNESIEQNDNyieKLE 247
                                   5777777777666.5555666666655444223333333334333222222123577777777766554444433011456 PP

                                   TEEE-HHHHHHHHHCT.T-STT........................................................... CS
                                   xxxxxxxxxxxxxxxx.xxxxx........................................................... RF
                         SMC_N 115 gkevtkkevsellesa.giske........................................................... 135
                                   +++ +++++ +++e+  +i+k+                                                           
  gi|91773502|ref|YP_566194.1| 248 EQRTRYAKLPKVMEDLdKINKDirkqdkrssdiesklsssstnffikfierdlkryidennnkirdlqdicglsdmqadtq 328
                                   677777777777776525666699999999999999999999999999999999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773502|ref|YP_566194.1| 329 sakedilkksipkcevcghklsdseisklkdeqeriseslklfeknknerdnlkdenqqfmsslrlldgcdfglemdnlde 409
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773502|ref|YP_566194.1| 410 lknkihnlekakkdldkesqreeygdlakinreisslqiqntknedkikiakyniksskrekeditrdikrlghddtntvr 490
                                   99999999999999999999999999999999999999999999999999999999999999999999999999999**** PP

                                   ........................................................................CS-HHHHHH CS
                                   ........................................................................xxxxxxxxx RF
                         SMC_N 136 ........................................................................lLSgGektL 144
                                                                                                           + S+Gek++
  gi|91773502|ref|YP_566194.1| 491 itrnidylsklirlldealeigteskrhqilkksnelfneitnkpdeysgigfedeesyafiiktkdnspvkNPSRGEKQV 571
                                   ********************************************************************************* PP

                                   HHHHHHHHHHCCS.--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 145 valaLlfAiqkvk.paplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                   +a+++l+ ++++  ++ + l+D   a LD+ + + + + l + +   Q+i  +
  gi|91773502|ref|YP_566194.1| 572 LAMSFLLGLNQYTgRNNVILMDTPVASLDDVHSAGIGSALANLN--NQVIFLA 622
                                   ********999872678999********************9999..6776655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   3.8     4e-07   0.00079       5     206 ..       8     231 ..       4     232 .. 0.74
   2 ?   -3.4   0.1       2.9   5.8e+03     152     180 ..     250     278 ..     236     286 .. 0.56
   3 ?   -3.4   0.1         3     6e+03     155     189 ..     354     387 ..     350     392 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4e-07
                        AAA_27   5 rLdLeryGkf.tdrsldfsa.eeadlhliyGpNEAGKstalrAisdllfG.....ip...ertkdnflhd....akkLrig 71 
                                   r++L  +  +  +++ldf + +++++ l   pN +GK+t+++Ai+  ++G     ++   + + ++fl d     k++   
  gi|91773502|ref|YP_566194.1|   8 RITLFNFACYyGENTLDFTTkTDKNIFLFNVPNGSGKTTLFHAIKWGFYGesieyFKdsdKISIKDFLNDrldpSKDMCFV 88 
                                   555666654414679***9845778899999**************999995533322111334567876522225778766 PP

                        AAA_27  72 avleeadgeelefaRr......kgrkktlldaddqalpeevlaallggldretFealFgLdherLreGGealleaegelgq 146
                                    +  e  +++ +++R+      k+++ +l + +d+ l+ +  +++l++++ + F + F  d e+L +  +a  + e +   
  gi|91773502|ref|YP_566194.1|  89 EITFEYGNKTYTLKRKyqpgvkKTSELSLSKGQDDILDVDEAQEMLNHINPQNFADFFMFDGEQLSRFMTAQKNIEQNYRD 169
                                   55557777899999954444437778899999999******************************9876666666666666 PP

                        AAA_27 147 lLfe..asaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelreaqvraee 206
                                   ++++      ++ l++ l +Le++ d+  +++ks+++ + ++++ +++++k +++++v+ e+
  gi|91773502|ref|YP_566194.1| 170 SILQllGLKQIQILKDDLSKLEKRYDNELTQQKSTNKDVETKKKVINRLNKDINNEDVKIEK 231
                                   6555113345667788888999999999999999999*****************99998765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.9
                        AAA_27 152 saGlaslrevleaLeaeadelfkprkskk 180
                                   ++ +a+l +v+e+L++  +++ k+ k+++
  gi|91773502|ref|YP_566194.1| 250 RTRYAKLPKVMEDLDKINKDIRKQDKRSS 278
                                   44445555566666655555555555544 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3
                        AAA_27 155 laslrevleaLeaeadelfkprkskkrainealee 189
                                   +++l++ +e++++   +lf+++k+++ ++++++++
  gi|91773502|ref|YP_566194.1| 354 ISKLKDEQERISE-SLKLFEKNKNERDNLKDENQQ 387
                                   5666666666654.446777777777666665555 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 !   15.5   0.0   5.2e-06      0.01       3      50 ..       8      59 ..       6      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.2e-06
                        AAA_29  3 rlqlvNWgtfdg.htieidlkg...atlltGpsGsGKSTllDAiqalLvpak 50
                                  r+ l+N   + g +t+++++k    ++l+  p+GsGK+Tl+ Ai+  +++++
  gi|91773502|ref|YP_566194.1|  8 RITLFNFACYYGeNTLDFTTKTdknIFLFNVPNGSGKTTLFHAIKWGFYGES 59
                                  889999999999899999887777799999**************98888776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   6.1e-06     0.012       7      72 ..      39      99 ..      39     146 .. 0.83
   2 ?   -1.2   5.7      0.72   1.4e+03      41     147 ..     186     299 ..     170     314 .. 0.40
   3 ?   -1.3   4.7      0.74   1.5e+03      62     129 ..     367     431 ..     347     582 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.1e-06
                        AAA_21  7 pNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72
                                  pNgsGK++L+ a+++ +    ++e  +d++    +i++ ++l d+ dp+++++f  + f+  ++ y
  gi|91773502|ref|YP_566194.1| 39 PNGSGKTTLFHAIKWGFY-GESIEYFKDSD----KISIKDFLNDRLDPSKDMCFVEITFEYGNKTY 99
                                  8**************987.77777777777....88888888888888888888888666666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.72
                        AAA_21  41 girkipslldlydpeipfefeieeflsqgvryryglrlersqv.....eeklssvetllesgll...ldkrsleeedvfnp 113
                                   +++k ++++d+  + ++++  +    +++v  r + ++++++v      e++ ++++  e+ +    ++ + ++ + + + 
  gi|91773502|ref|YP_566194.1| 186 DLSKLEKRYDNELTQQKSTNKDV-ETKKKVINRLNKDINNEDVkiekhNESIEQNDNYIEKLEEqrtRYAKLPKVMEDLDK 265
                                   33333333333333333333333.334444444444444444443333333332222222222200022222222333333 PP

                        AAA_21 114 eargirggvsvfslkelsvsepndlqfgkaltdi 147
                                     ++ir++ +  s++e+ +s++++++f+k++ ++
  gi|91773502|ref|YP_566194.1| 266 INKDIRKQDKRSSDIESKLSSSSTNFFIKFIERD 299
                                   3344444444444444445555555555555444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.74
                        AAA_21  62 ieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslke 129
                                     ++++++++ r +l+ e++q+    ss++ l ++ + l  ++l+e ++++++ + ++++++ +s++e
  gi|91773502|ref|YP_566194.1| 367 SLKLFEKNKNERDNLKDENQQF---MSSLRLLDGCDFGLEMDNLDELKNKIHNLEKAKKDLDKESQRE 431
                                   4557888999999999999999...9999999999999999999999999999998888888877754 PP

>> zinc_ribbon_16  Zinc-ribbon like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00021      0.42      42      79 ..     333     370 ..     294     384 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                zinc_ribbon_16  42 prcskplpkcavcglslGtsdvtnkdskrksvvkevss 79 
                                      +k +pkc vcg  l +s++++ +++++ + + ++ 
  gi|91773502|ref|YP_566194.1| 333 DILKKSIPKCEVCGHKLSDSEISKLKDEQERISESLKL 370
                                   445789***************99866444444444444 PP

>> FAA_hydrolase_N  Fumarylacetoacetase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00017      0.34      24      88 ..     122     186 ..     120     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                   TEEEEHHHHHHTTSS-STGG...SSSGTTSSSSSHHHHHT-HHHHHHHHHHHHHHHBT..SHHHHT- CS
               FAA_hydrolase_N  24 dqvldLsalaeaglfsqleedaeekesvfsqptLnafaalgrevwravRaalqelLsa..eeelrdn 88 
                                   d +ld+++++e  ++++++ +  ++  +f+ ++L +f+  ++++ ++ R  + +lL     + l+d+
  gi|91773502|ref|YP_566194.1| 122 DDILDVDEAQE--MLNHINPQNFADFFMFDGEQLSRFMTAQKNIEQNYRDSILQLLGLkqIQILKDD 186
                                   67888888744..555443433455556799************************965432244444 PP

>> Phage_Treg  Lactococcus bacteriophage putative transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00068       1.4      15      40 ..      56      81 ..      49      83 .. 0.83
   2 ?    0.2   0.2      0.41   8.2e+02       4      32 ..     212     240 ..     209     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00068
                    Phage_Treg 15 yqesvefYkkkLsvqskdflkdsLlP 40
                                  y es+e++k+   +  kdfl+d L P
  gi|91773502|ref|YP_566194.1| 56 YGESIEYFKDSDKISIKDFLNDRLDP 81
                                  789******98666666*****9866 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
                    Phage_Treg   4 ekvvthlGevvyqesvefYkkkLsvqskd 32 
                                   +kv++ l + +  e v   k++ s++ +d
  gi|91773502|ref|YP_566194.1| 212 KKVINRLNKDINNEDVKIEKHNESIEQND 240
                                   69***************999999987655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  39.4   0.00076       1.5       4     270 ..       7     298 ..       5     317 .. 0.65
   2 ?   -3.2  37.5       2.6   5.2e+03      58     332 ..     294     595 ..     278     599 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00076
                        AAA_15   4 kkikikNFRslkd.veidlsee....ltvliGkNnsGKSsilealdl.Flnnkekknkkvikiekedleife.niseskd. 76 
                                    +i++ NF ++    ++d+  +    + ++  +N+sGK+++ +a+++ F  ++ +++k+ +ki  +d+ + + + s++++ 
  gi|91773502|ref|YP_566194.1|   7 IRITLFNFACYYGeNTLDFTTKtdknIFLFNVPNGSGKTTLFHAIKWgFYGESIEYFKDSDKISIKDFLNDRlDPSKDMCf 87 
                                   567777888877667777777777666677779************996777777777555555544433332033333331 PP

                        AAA_15  77 ikIdvef.........aek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkel 147
                                   ++I++e+         +++ + +k+ e +l    k ++d+l  ++ +++ ++i+ +++++    ++ e  s ++  +k++ 
  gi|91773502|ref|YP_566194.1|  88 VEITFEYgnktytlkrKYQpGVKKTSELSLS---KGQDDILDVDEAQEMLNHINPQNFAD-FFMFDGEQLSRFMTAQKNIE 164
                                   4677777777776655444444444333333...34556677777777777777777775.47777777777777777766 PP

                        AAA_15 148 pkekee.klekekeelkidkedlkklikkleeslkkee......elknvlksaiiklllisakRnvsdedsekkssllgkl 221
                                    +++++  + +  + ++i k+dl kl k++ + l++++      e k++  + + k   +++++  ++++s +++++++++
  gi|91773502|ref|YP_566194.1| 165 QNYRDSiLQLLGLKQIQILKDDLSKLEKRYDNELTQQKstnkdvETKKKVINRLNKDINNEDVKIEKHNESIEQNDNYIEK 245
                                   6666551566789*************************6666666666666666666666666666666666666666666 PP

                        AAA_15 222 kekileealqekleeelteklkeiqeklkeidkklaeelk.......kilkkkidk 270
                                   +e+    +++     ++ e+l++i+++++++dk  ++ ++       + ++k+i+ 
  gi|91773502|ref|YP_566194.1| 246 LEEQRTRYAK---LPKVMEDLDKINKDIRKQDKRSSDIESklsssstNFFIKFIER 298
                                   6666555443...8899999********9999998766666777766555555544 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.6
                        AAA_15  58 ikiekedleifeniseskdikIdvef......aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknels 132
                                   ++ie +  ++ ++ +++k  +++         a  + +   e++lk++  k++ +  k  +s+++k++ +++   ++ +l 
  gi|91773502|ref|YP_566194.1| 294 KFIERDLKRYIDE-NNNKIRDLQDICglsdmqA--DTQSAKEDILKKSIPKCEVCGHKLSDSEISKLKDEQERISESLKLF 371
                                   2222222222222.2222222222222333210..2222223455555555555555555555555444444444444433 PP

                        AAA_15 133 dekisvekkks.....................kkelpkekeeklekekeelkidkedlkklikkleeslkkee.....elk 187
                                    ++++  ++ +                     + +l+++k++ +++ek++ ++dke++++ + +l ++  + +       k
  gi|91773502|ref|YP_566194.1| 372 EKNKNERDNLKdenqqfmsslrlldgcdfgleMDNLDELKNKIHNLEKAKKDLDKESQREEYGDLAKINREISslqiqNTK 452
                                   333333333333333447777777777777777777777777777777777777777777777555555444444344444 PP

                        AAA_15 188 nvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl..eeelteklkeiqeklkeidkklaeelk..... 261
                                   n  k +i k+ + s+kR+ +d + + k+                  l  ++ +t  + +  + l++++  l+e l+     
  gi|91773502|ref|YP_566194.1| 453 NEDKIKIAKYNIKSSKREKEDITRDIKR------------------LghDDTNTVRITRNIDYLSKLIRLLDEALEigtes 515
                                   4444444445555555554443333322..................13322222222222222222222222222233333 PP

                        AAA_15 262 .............kilkkkidkikkfnykgkkneeieikddeelplnknGsGvqrllllillileaekkdekeeknvilli 329
                                                +++++k d+   +++  +++    ik+++++p+++ + G ++ l +++l+  ++       +n+++l+
  gi|91773502|ref|YP_566194.1| 516 krhqilkksnelfNEITNKPDEYSGIGFEDEESYAFIIKTKDNSPVKNPSRGEKQVLAMSFLLGLNQYT----GRNNVILM 592
                                   334333333322344555555555555555555555555**********************98777777....67777777 PP

                        AAA_15 330 EEP 332
                                   + P
  gi|91773502|ref|YP_566194.1| 593 DTP 595
                                   666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2867  (0.159909); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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):               9  [number of targets reported over threshold]
# CPU time: 1.04u 0.31s 00:00:01.35 Elapsed: 00:00:00.50
# Mc/sec: 3927.42
//
Query:       gi|91773503|ref|YP_566195.1|  [L=569]
Description: DNA-cytosine methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  133.4   0.5    1.2e-37  130.0   0.0    2.5  2  DNA_methylase    C-5 cytosine-specific DNA methylase
    0.00097   18.7   0.0     0.0019   17.8   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.0   1.4e-41   1.2e-37       1     335 []       5     355 ..       5     355 .. 0.78
   2 ?   -0.1   0.2     0.053   4.8e+02     200     261 ..     367     425 ..     356     493 .. 0.63

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.4e-41
                                   -EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...........-SEEEES-TTTS-....GS--.-SEEEE CS
                 DNA_methylase   1 lkfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..........kvsigDitkidkk....klpediDlLvg 67 
                                   +++ d+f+G+GG + g+++agfe+v+a +i++ a +t + n++          k + gDi ki+ +     +p d+D++vg
  gi|91773503|ref|YP_566195.1|   5 FTVADFFCGAGGSSEGFRQAGFEIVFALDIWNPARETHKLNHPncahfgldcyKDKDGDILKIETTdiddVIP-DVDVIVG 84 
                                   6899********************************************9*99999999999999996765566.7****** PP

                                   ---GGGTECTSEE--TTSGGG.HHHHHHHHHHHHH-......-SEEEEEEEGGGGGGCCS....HHHHHHHHHHHHHTEEE CS
                 DNA_methylase  68 GfPCqpfSvaGkqkgfedtrg.tLffeiiriikekk......PkvfllENVkgLlkhdkg....ktlkvilekleelGYev 137
                                   ++PC +fS +     +++t g  L+ ++ +ii  kk       k+ llENV++ +k+ ++    ++l+   e l +lG + 
  gi|91773503|ref|YP_566195.1|  85 SPPCVSFSSSNRAGKADKTHGiRLIKKYLQIISIKKhkpgsiLKYWLLENVPNTMKQLQEeytfRELELTNEILLSLGIQK 165
                                   ***********8888888888**********987776654444999*****998888777677788888888899999776 PP

                                   E............EEEEEGGGTT-SB--EEEEEEEEEGGG----------SS---GGG.....TSGGGTTS-EEBTTTB-- CS
                 DNA_methylase 138 s............ykllnasdyGvpQnReRvfivgirkdlelnvlvkvkefrfpkkkdleasktlrdlleekseldeekta 206
                                                 +++na+dyG+pQ+R+R++i  +  +       ++ ++++ + +     ++++  + +   +++ +  
  gi|91773503|ref|YP_566195.1| 166 RetdialkidisdENIYNAADYGIPQRRKRLVIGDYPRPD------PTHKDKWISLS-----EVINAFDYD---ITDPNFG 232
                                   67899999999999******************98776653......45555555554.....455555555...4555555 PP

                                   GGGSSSTT-EE--.......S---HHHTS--.B--TTS...-B----S-STT--B-TTS---EEEETTEEE--T.TTGGG- CS
                 DNA_methylase 207 lsdklvekeekikkttkaseegypkelsrnr.idkveelkglsatrrksgrgeklekelaeagklqknkerfkpviekkri 286
                                   +s ++ e   ++ +t+++  +  +   +r++  +++  + ++ +t+  s+      + +a ++++ ++++ f+  +++  +
  gi|91773503|ref|YP_566195.1| 233 FSIDTEELTDHFYDTSIHEYDWLQ-ARDRKQqARYYGRMAFPEETSVPSR------TVMAMRTTSSREAMIFEG-NNPGSY 305
                                   555555555555544443333333.2222211344444444444444444......466666666677777764.8899** PP

                                   -B-BHHHHHHHHT--TT-----SBH.HHHHHHHTS--HHHHHHHHHHHHH CS
                 DNA_methylase 287 RrLtprEaarlqGfPddfefgskks.aaykqiGnsVpvpvieaiakeikk 335
                                   R+ t rE a l++fP ++ f++k++  +yk++Gn+V +++++a a+ei k
  gi|91773503|ref|YP_566195.1| 306 RAPTIREIATLMSFPITYLFQGKSEgIKYKLVGNAVCPKLAYAFAEEILK 355
                                   **********************************************9975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.053
                                   BTTTB--GGGSSSTT-EE--.......S---HHHTS--B--TTS...-B----S-STT--B- CS
                 DNA_methylase 200 ldeektalsdklvekeekikkttkaseegypkelsrnridkveelkglsatrrksgrgekle 261
                                    +++k++l+ +l+  ++++ +++k+ + ++  e++ n   k+++ + + +++r    ++++ 
  gi|91773503|ref|YP_566195.1| 367 PNSDKNKLEFDLTGWDSRKIPQNKHEKANFT-EIVPN--MKYKNFRVELDNSRPRYTDDSIV 425
                                   6778888888888888888888888888888.77766..34444343333333333333222 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.1e-07    0.0019       4      81 ..       7      88 ..       4     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-07
               Methyltransf_15  4 ilDlfsGaGGnviqfalv.fekviaiei...nleklacaqhNaevYgvsdkitlvlgdvfellaklkleki.kvdlvflSpPw 81
                                  + D f+GaGG +  f +  fe v+a++i    +e+ ++ + N+  +g  d  + + gd++++  +   ++i  vd+++ SpP+
  gi|91773503|ref|YP_566195.1|  7 VADFFCGAGGSSEGFRQAgFEIVFALDIwnpARETHKLNHPNCAHFGL-DCYKDKDGDILKIETTDIDDVIpDVDVIVGSPPC 88
                                  67**************999********954457899999*******76.6778899***998766555555899********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3578.26
//
Query:       gi|91773504|ref|YP_566196.1|  [L=173]
Description: GCN5-related N-acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for 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-08   32.1   0.0    5.1e-07   29.7   0.0    1.9  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.5e-07   31.6   0.0      2e-07   31.2   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.2e-06   26.8   0.1      1e-05   25.9   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0065   15.5   0.1     0.0079   15.2   0.1    1.1  1  Bmp              ABC transporter substrate-binding protein Pn


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.1e-10   5.1e-07      16     111 ..      33     153 ..      19     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.1e-10
               Acetyltransf_10  16 fispealrerieegealllvaeeggkivGvielrdgs.......................hisllfVdpeyrgqGigkaLl 73 
                                   f+ ++al+++  +    ++v++ ++ +vG+ +l+++                        ++++l+Vd +y  +Gig+ Ll
  gi|91773504|ref|YP_566196.1|  33 FLIEDALDDQE-QMVSATFVCYHEDYLVGYFTLTTDTlevvavgdgdgvdefeyakypalKLARLAVDMDYACKGIGRHLL 112
                                   55667777776.6667789999999*****99966666999999999********************************** PP

               Acetyltransf_10  74 eaveeeaekdgikl...eltvnaspyavpfYeklGFkavge 111
                                    +++  a +         ltv++++  ++fY++  F  v++
  gi|91773504|ref|YP_566196.1| 113 TTAIGLALDVSKTAgcrYLTVDSKSCSIGFYKRNTFILVEK 153
                                   *****975554444688****************99988854 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   4.5e-11     2e-07      32     114 ..      46     145 ..      14     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.5e-11
                                   TCEEEEEEETTEEEEEEEEEEEET................TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.... CS
                Acetyltransf_1  32 aegllvaeedgeliGfisllkipd................ekggvayieslaVspeyrgkGlGsaLlealeeraree.... 92 
                                    + ++v+++++ l+G+ +l+ ++                  k++   + +laV+ +y  kG+G++Ll++++  a++     
  gi|91773504|ref|YP_566196.1|  46 VSATFVCYHEDYLVGYFTLTTDTLevvavgdgdgvdefeyAKYPALKLARLAVDMDYACKGIGRHLLTTAIGLALDVskta 126
                                   3367889999**************8888888888888877777778888**********************7777775443 PP

                                   TESEEEEEEETTEHHHHHHHHH CS
                Acetyltransf_1  93 gikkivlaveedndaairlYek 114
                                   g++  +l+v ++   +i++Y++
  gi|91773504|ref|YP_566196.1| 127 GCR--YLTV-DSKSCSIGFYKR 145
                                   554..5644.556788****66 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   2.3e-09     1e-05       5      74 ..      49     148 ..      46     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.3e-09
                                   EEEEEETTEEEEEEEEEEES......................TCTEEEEE-GGGTTSSHHHHHHHH.......TT..SEEE CS
                Acetyltransf_7   5 vfVaeddgkivGfialslld......................aeitrlaVdpeyrgkGiGraLlea.......ae..kgii 54 
                                   +fV+++++  vG+  l+ +                         + rlaVd +y  kGiGr Ll+        +    g++
  gi|91773504|ref|YP_566196.1|  49 TFVCYHEDYLVGYFTLTTDTlevvavgdgdgvdefeyakypaLKLARLAVDMDYACKGIGRHLLTTaiglaldVSktAGCR 129
                                   57888887777777666666777777777777776666655555556*****************95356554411557776 PP

                                   EEEEEETHH.HHHHHHHHTTE CS
                Acetyltransf_7  55 leqlelnae.kaikfYeklGF 74 
                                       +++++  +i+fY+++ F
  gi|91773504|ref|YP_566196.1| 130 YL--TVDSKsCSIGFYKRNTF 148
                                   22..3333246799***9866 PP

>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.8e-06    0.0079      61     119 ..       7      63 ..       2      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                                   -SEEEEESCCHHHHHHHHHHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHH CS
                           Bmp  61 sdlivatgfalqdalqevssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaa 119
                                   sdl+v+   +  d++   s++    +Fli Da+ ++e  +++s++F  + + +L+G+++
  gi|91773504|ref|YP_566196.1|   7 SDLLVSKLTKNDDLSAFDSENAELNGFLIEDALDDQE--QMVSATFVCYHEDYLVGYFT 63 
                                   67777777777777777777888889***********..9*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1182.74
//
Query:       gi|91773505|ref|YP_566197.1|  [L=363]
Description: small GTP-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-33  114.5   1.9    3.7e-33  113.7   1.9    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    3.5e-21   75.4   0.0    7.4e-21   74.4   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    2.2e-17   62.9   0.0    4.3e-17   61.9   0.0    1.5  1  TGS           TGS domain
    1.1e-13   51.0   0.9    3.8e-13   49.3   0.0    2.1  2  FeoB_N        Ferrous iron transport protein B
    1.4e-05   25.0   0.8      0.017   15.0   0.1    2.4  2  RsgA_GTPase   RsgA GTPase
      0.003   17.2   0.5        2.5    7.7   0.0    2.5  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.004   17.2   1.0      0.094   12.8   0.1    2.6  3  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
      0.034   13.9   0.8       0.79    9.4   0.1    2.6  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.05   14.1   0.1       0.16   12.5   0.0    1.9  2  ABC_tran      ABC transporter
      0.059   12.3   0.4       0.28   10.1   0.0    2.0  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.088   11.9   0.0       0.41    9.7   0.0    1.9  2  MCM           MCM P-loop domain
       0.14   11.3   0.0       0.31   10.2   0.0    1.7  1  NB-ARC        NB-ARC domain
       0.15   11.6   0.3          4    6.9   0.0    2.7  3  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.17   11.5   0.4         20    4.8   0.0    2.4  2  Ras           Ras family


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 !  113.7   1.9   2.9e-36   3.7e-33       1     105 [.     182     286 ..     182     287 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.9e-36
                  MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelare.p 80 
                                   +gG++i++t++l+ l+++ +k++l eykihna+vlir++++vD+lidvi+gnrvY+p+++v+NK+Dl++++ l++++   p
  gi|91773505|ref|YP_566197.1| 182 RGGVTISTTMELE-LTDDLIKAVLGEYKIHNAHVLIRDNINVDELIDVIMGNRVYVPSIIVVNKVDLANEDILNKMEYLfP 261
                                   69*********88.***************************************************************9769 PP

                  MMR_HSR1_Xtn  81 nsvviSaekelnldeLkekiweeLn 105
                                   ++++iSa++e+nl+++k+ i+++L+
  gi|91773505|ref|YP_566197.1| 262 DATFISANEEKNLEAVKDLIYDSLD 286
                                   ***********************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 !   74.4   0.0   5.8e-24   7.4e-21       2      99 ..      64     163 ..      63     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 5.8e-24
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlill 81 
                                   va+vG p vGKStL+n++tg++++v+d+ +tT+d++ g +++k+  i+++D+pGl+ ga +++g g+++ a+ + ++l+l+
  gi|91773505|ref|YP_566197.1|  64 VALVGFPSVGKSTLLNKITGANSEVGDYEFTTLDVIPGVLDYKDATIQVLDVPGLVRGAASGRGRGREVIAVVRnSNLVLF 144
                                   9*****************************************************999*************988879***** PP

                                   EEETT.TTCSHHHHHHHHH CS
                      MMR_HSR1  82 vvdas.eeklkpldeelee 99 
                                   ++d+   e++k l +el +
  gi|91773505|ref|YP_566197.1| 145 LLDVFqPEHYKVLIQELYD 163
                                   ***8864456666666655 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   3.4e-20   4.3e-17       1      59 [.     288     360 ..     288     361 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 3.4e-20
                                   EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                           TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                   irvy+ P+G + d      ++ g tv D++ ++hr++ +kf+y +V+G       qr gldh Ledgd ++++
  gi|91773505|ref|YP_566197.1| 288 IRVYLkPQGGLADmdepliVTDGVTVGDICERLHRDFRDKFRYSQVWGasakhpgQRAGLDHYLEDGDLLTLI 360
                                   89*******************************************************************9987 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 !   49.3   0.0     3e-16   3.8e-13       2      58 ..      63     119 ..      62     171 .. 0.76
   2 ?   -0.1   0.1      0.46   5.9e+02     104     121 ..     234     251 ..     192     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 3e-16
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----S CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiY 58 
                                   tvalvG p vGk+tl+n++tga+++vg +  +t +   g l++k+ +++++D+PG  
  gi|91773505|ref|YP_566197.1|  63 TVALVGFPSVGKSTLLNKITGANSEVGDYEFTTLDVIPGVLDYKDATIQVLDVPGLV 119
                                   79*****************************************************75 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.46
                                   TTSSEEEEEETHHHHHHT CS
                        FeoB_N 104 lgvpvvlalnmideaekk 121
                                   + vp ++++n++d a+++
  gi|91773505|ref|YP_566197.1| 234 VYVPSIIVVNKVDLANED 251
                                   457889999999999875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.4e-05     0.017      69     125 ..      31      86 ..      12      95 .. 0.67
   2 !    8.3   0.1    0.0016         2      47      99 ..     236     283 ..     218     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                   HHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                   RsgA_GTPase  69 keelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelel 125
                                   k++l++l  ev++  ++++ g     ++  d t++lvG   vGKStL+n++++  + 
  gi|91773505|ref|YP_566197.1|  31 KAKLARLREEVVKKASTKSGGDGYSVKKSGDATVALVGFPSVGKSTLLNKITGA-NS 86 
                                   5555555555555433333333333445566899*****************997.44 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                                   -EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                   ++ +iv+nK+Dl++e+       +++e l  + +++sa+++++le++k+l+ d
  gi|91773505|ref|YP_566197.1| 236 VPSIIVVNKVDLANEDI-----LNKMEYLFPDATFISANEEKNLEAVKDLIYD 283
                                   6789*********9988.....5555556667799999999999999988766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0     0.002       2.5       3      22 ..      64      84 ..      62      93 .. 0.83
   2 !    7.3   0.1    0.0026       3.3     129     162 ..     224     256 ..     188     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                                  EEEEESTTCCHHHHHHHHH.C CS
                          cobW  3 tvltGflGsGKTtLlnhll.e 22
                                  + l+Gf+  GK+tLln+++ +
  gi|91773505|ref|YP_566197.1| 64 VALVGFPSVGKSTLLNKITgA 84
                                  679**************9853 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                                   CCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHH CS
                          cobW 129 ekieekaedqlaaadllvlnKtDlldeeallekl 162
                                   e i   +++ + + +++v+nK+Dl++e+ l +k+
  gi|91773505|ref|YP_566197.1| 224 ELIDVIMGNRVYVPSIIVVNKVDLANEDIL-NKM 256
                                   56667788889999***********99843.555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       4.3   5.5e+03      65      80 ..       7      22 ..       4      52 .. 0.47
   2 !   12.8   0.1   7.4e-05     0.094       1      22 [.      64      85 ..      64     100 .. 0.84
   3 ?    2.4   0.0      0.11   1.5e+02      98     137 ..     105     147 ..      98     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.3
                                  CHHHHHHHHHHHHHHH CS
                     Dynamin_N 65 fsevreeieketekia 80
                                  +++v++ei+k + ++a
  gi|91773505|ref|YP_566197.1|  7 IQAVEDEIRKTSYNKA 22
                                  4444444444333332 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.4e-05
                                  EEEEEBTTTTHHHHHHHHHTS- CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                  +a+vG  S GKS++ln+++g++
  gi|91773505|ref|YP_566197.1| 64 VALVGFPSVGKSTLLNKITGAN 85
                                  799*****************98 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.11
                                   TTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEE CS
                     Dynamin_N  98 llvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavts 137
                                    ++ ++ ++D+PGl + ++      + v   +++++++l++++
  gi|91773505|ref|YP_566197.1| 105 YKDATIQVLDVPGLVRGAASGRgrgREVIAVVRNSNLVLFLLD 147
                                   56778999********988877778777777788888887765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.096   1.2e+02       2      22 ..      67      87 ..      66     115 .. 0.83
   2 ?    9.4   0.1   0.00062      0.79     150     198 ..     229     278 ..     218     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.096
                    ATP_bind_1  2 vGpaGsGKttfvgalseilel 22
                                  vG +++GK+t+ ++++   ++
  gi|91773505|ref|YP_566197.1| 67 VGFPSVGKSTLLNKITGANSE 87
                                  899*********998766555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00062
                    ATP_bind_1 150 samlrlelPhvvvlnkfDllkek.lekeleffedvealslllekeeekyk 198
                                    +  r+ +P ++v+nk+Dl++e+ l+k    f+d   +s+ +ek+ e++k
  gi|91773505|ref|YP_566197.1| 229 IMGNRVYVPSIIVVNKVDLANEDiLNKMEYLFPDATFISANEEKNLEAVK 278
                                   55567889***********9999655555557777666665554434443 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.16       5      36 ..      55      86 ..      52     109 .. 0.85
   2 ?   -2.2   0.0       4.3   5.5e+03      29      50 ..     201     223 ..     199     286 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                  EEEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  5 slklkegekvaivGenGaGKStLlkllagllk 36
                                  s+k + + +va+vG    GKStLl+ ++g  +
  gi|91773505|ref|YP_566197.1| 55 SVKKSGDATVALVGFPSVGKSTLLNKITGANS 86
                                  555666789*******************9765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                                   HHHTTSS--SEEEEEET.TCEGG CS
                                   xxxxxxxxxxxxxxxxx.xxxxx RF
                      ABC_tran  29 kllagllkpteGeilld.gkdlk 50 
                                   k+++g++k  + ++l++ + +++
  gi|91773505|ref|YP_566197.1| 201 KAVLGEYKIHNAHVLIRdNINVD 223
                                   55555555555555444232322 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00021      0.28      25      52 ..      58      84 ..      54      99 .. 0.83
   2 ?   -0.5   0.1      0.39   4.9e+02     168     183 ..     236     251 ..     215     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                                  G-S-SEEEEEEE-TTSSHHHHHHHHHHH CS
                          MeaB 25 kaGraqvvGltGvPGaGkstlvealgle 52
                                  k+G a+ v l G+P +Gkstl+++++  
  gi|91773505|ref|YP_566197.1| 58 KSGDAT-VALVGFPSVGKSTLLNKITGA 84
                                  677775.6899************99865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.39
                                   H-SEEEEE---HHHHH CS
                          MeaB 168 iaDiivvnkaDkkeae 183
                                   +  iivvnk D+++ +
  gi|91773505|ref|YP_566197.1| 236 VPSIIVVNKVDLANED 251
                                   5679*******76644 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00032      0.41      52      79 ..      56      83 ..      12      95 .. 0.80
   2 ?   -0.6   0.0      0.45   5.7e+02      59      92 ..     238     271 ..     189     287 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00032
                                  SBBCSS-EEEEEESSTSTHHHHHHHHHH CS
                           MCM 52 tklrgdinvllvgdpgtaKsqlLkyvek 79
                                  +k  gd  v lvg p+++Ks+lL++++ 
  gi|91773505|ref|YP_566197.1| 56 VKKSGDATVALVGFPSVGKSTLLNKITG 83
                                  45679******************99864 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.45
                                   EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSS CS
                           MCM  59 nvllvgdpgtaKsqlLkyveklapravytsgkgs 92 
                                    +++v  + +a   +L+++e l+p a+++s++  
  gi|91773505|ref|YP_566197.1| 238 SIIVVNKVDLANEDILNKMEYLFPDATFISANEE 271
                                   4677777788888888888888888888887765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00024      0.31      20      51 ..      61      93 ..      54     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                                  SEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CB CS
                        NB-ARC 20 slvvalvGmgGvGKttlakqilnksdeveg.rF 51
                                     valvG + vGK+tl+++i    +ev   +F
  gi|91773505|ref|YP_566197.1| 61 DATVALVGFPSVGKSTLLNKITGANSEVGDyEF 93
                                  3579*****************999777765444 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.12   1.6e+02       7      29 ..      65      87 ..      62     101 .. 0.77
   2 ?   -2.1   0.0       1.8   2.3e+03      66      79 ..     104     117 ..      91     120 .. 0.75
   3 ?    6.9   0.0    0.0031         4     121     142 ..     234     255 ..     219     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                                  EEEESTTSSHHHHHHHHHHHTTS CS
                      GTP_EFTU  7 giighvDhGKtTLtdrLlyktga 29
                                  +++g    GK+TL+ +++ ++++
  gi|91773505|ref|YP_566197.1| 65 ALVGFPSVGKSTLLNKITGANSE 87
                                  56666778********9966655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                   TCSSEEEEEEEESS CS
                      GTP_EFTU  66 etkkylinliDtPG 79 
                                   ++k+ +i+++D PG
  gi|91773505|ref|YP_566197.1| 104 DYKDATIQVLDVPG 117
                                   47889999999999 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0031
                                   TTTEEEEEEESCGSTHHHHHHH CS
                      GTP_EFTU 121 egvpiivfiNKmDrlkaelkei 142
                                   + vp i+++NK+D +++++ + 
  gi|91773505|ref|YP_566197.1| 234 VYVPSIIVVNKVDLANEDILNK 255
                                   45789*********96665444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.015        20       2      21 ..      64      83 ..      63     120 .. 0.67
   2 ?    4.6   0.1     0.017        22      79     124 ..     207     255 ..     194     283 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                                  EEEEESTTSSHHHHHHHHHH CS
                           Ras  2 lvlvGdsavGKtslllrfvk 21
                                  + lvG  +vGK++ll++ + 
  gi|91773505|ref|YP_566197.1| 64 VALVGFPSVGKSTLLNKITG 83
                                  679************99874 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                                   EETTBHHHHHTHHHHHHHHHHHST...TTSEEEEEEETTTGGGG-SS-H CS
                           Ras  79 yditsresfenvkkwveeikrvae...envpivLvGnKvDleekravst 124
                                   y i++++ + + +  v+e+ +v       vp ++v nKvDl+++  +++
  gi|91773505|ref|YP_566197.1| 207 YKIHNAHVLIRDNINVDELIDVIMgnrVYVPSIIVVNKVDLANEDILNK 255
                                   55555555544444444444444433346999**********9655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2617.31
//
Query:       gi|91773506|ref|YP_566198.1|  [L=405]
Description: molybdopterin molybdochelatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.2    3.3e-38  130.9   0.2    1.4  1  MoeA_N         MoeA N-terminal region (domain I and II)
    9.5e-26   90.2   0.0      2e-25   89.1   0.0    1.6  1  MoCF_biosynth  Probable molybdopterin binding domain
    2.8e-09   37.0   0.1    6.7e-09   35.8   0.1    1.7  1  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 !  130.9   0.2   5.5e-42   3.3e-38       2     157 .]      11     173 ..      10     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 5.5e-42
                                   -HHHHHHHHHHH-HH.-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--................. CS
                        MoeA_N   2 sveealaiilaalel.eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep.......saage 73 
                                   s+e+a+ +  + +++ ++ + +p+ +++ grvlaedvv+++dvP+fd+S  DGYAvr+e+ ++a            s+ g+
  gi|91773506|ref|YP_566198.1|  11 SIEDARTL-FKGVKVrTHIVfIPI-ERSTGRVLAEDVVSTIDVPGFDKSLRDGYAVRSEDVASAGDAPVslklvgfSPVGR 89 
                                   66777774.333433355567999.8899**********************************9665559******99999 PP

                                   .-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHH CS
                        MoeA_N  74 eperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeig 151
                                   +p+ ++ +  av+++TG+p+P+gadaVv+vEdte +    +tv v ++vk+g++   aG+di++++ ll++g  ++++e+g
  gi|91773506|ref|YP_566198.1|  90 PPQYSVGKMeAVEVATGGPIPDGADAVVMVEDTElN---GDTVLVkTSVKAGKFLILAGSDISKNTCLLSRGLTIGAREVG 167
                                   9999988888***********************653...334444589********************************* PP

                                   HHHHCT CS
                        MoeA_N 152 llasvG 157
                                   +la++G
  gi|91773506|ref|YP_566198.1| 168 VLAAIG 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 !   89.1   0.0   3.4e-29     2e-25       1     143 [.     185     321 ..     185     322 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 3.4e-29
                                   EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--H CS
                 MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvt 74 
                                   ++i++G+el+       +g ++Dtn++ l+++ ++lgv++++y++++Dd + ++  +++a+ e d+++t+G t+++pdD++
  gi|91773506|ref|YP_566198.1| 185 GIISTGNELTmpgtslqPGMVYDTNSYSLYAAATKLGVDTIAYGLIKDDQDTVSGVVKKAIGECDIVLTSGSTSAGPDDFM 265
                                   69**********************************************************9999***************** PP

                                   HHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                 MoCF_biosynth  75 pealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                   ++++++ ++       ++ ++++ kpgkpv+++++   ++    +i++LPG p ++ +++ e++lp ++
  gi|91773506|ref|YP_566198.1| 266 YDIIEEQGN-------VLAHGLNFKPGKPVILGMI---NKI---PIVALPGHPTSSLTVFYEFILPLIR 321
                                   *********.......8**************9999...543...6*******************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 !   35.8   0.1   1.1e-12   6.7e-09       2      71 ..     336     399 ..     335     400 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.1e-12
                                   EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                        MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                   a+l+ed+ s   r e+l v+l+    + v+ +t +++S+++++la A+g+i+ip+++  +++G eV v +
  gi|91773506|ref|YP_566198.1| 336 AVLGEDVISGT-RHELLAVRLE----NGVVFST-SRSSAAITTLAYADGFIEIPADVPMVKKGMEVVVSF 399
                                   88999999999.**********....5699999.********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2969.61
//
Query:       gi|91773507|ref|YP_566199.1|  [L=292]
Description: branched-chain amino acid aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-55  186.0   0.0      1e-54  185.8   0.0    1.0  1  Aminotran_4  Amino-transferase class IV


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 !  185.8   0.0   5.7e-59     1e-54       1     221 [.      32     256 ..      32     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 5.7e-59
                   Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg.aatsepsva 80 
                                   g+fE++r+yng++f ldeH++RL  sa+++ le+p+++ e+++++ e+l++nn   +++r++v+rg g+lg ++ ++p   
  gi|91773507|ref|YP_566199.1|  32 GVFEGIRAYNGRVFKLDEHVDRLYDSAKAIALEVPLTKAEMTEAILETLRKNNLTDAYIRPIVTRGIGDLGlDPRKCPIPS 112
                                   8**************************9999*****************************************999999999 PP

                   Aminotran_4  81 vyvsalppgpeseke....lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtEgstsNvfi 157
                                   +y+++ ++g+ + +     l+++t   +r  +    p++K+lnyl+n+la+ ea+++g de++++d++g+v+Egs  N+f+
  gi|91773507|ref|YP_566199.1| 113 IYIISQEWGAMYGDLyevgLKAITVGIRRNAPDALSPNIKSLNYLNNILAKIEANAKGGDEAIFLDQNGFVSEGSGDNIFV 193
                                   99999999999999999*988888887888888999********************************************* PP

                   Aminotran_4 158 vkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvr 221
                                   +k+g+++tPp  +  L+Gitr++++el++++g ev  +++ l d   ade+f+t+t+++  p++
  gi|91773507|ref|YP_566199.1| 194 IKNGKIYTPPTIN-NLKGITRATAIELLEERGYEVVVQNLGLFDMYTADEIFVTGTAAEAAPIT 256
                                   *********9988.7***********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1981.28
//
Query:       gi|91773508|ref|YP_566200.1|  [L=176]
Description: hypothetical protein Mbur_1544 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.051   13.7   0.8      0.051   13.7   0.8    2.0  2  LAB_N            Lipid A Biosynthesis N-terminal domain
       0.37    9.0  15.1       0.55    8.5  15.1    1.2  1  DUF2070          Predicted membrane protein (DUF2070)
        1.7    9.0   8.2       0.29   11.5   2.5    2.1  2  DUF3981          Domain of unknown function (DUF3981)
        2.2    7.5   6.3        7.5    5.8   0.5    2.1  2  DUF4191          Domain of unknown function (DUF4191)
        4.5    7.8  10.8       0.68   10.4   2.9    2.5  2  MerC             MerC mercury resistance protein
        4.6    6.5   9.4       0.17   11.2   1.2    2.0  2  S_4TM            SMODS-associating 4TM effector domain
        5.2    6.9   7.8          5    7.0   0.2    3.5  4  Phage_holin_2_3  Bacteriophage holin family HP1


Domain annotation for each model (and alignments):
>> LAB_N  Lipid A Biosynthesis N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8     2e-05     0.051       3      45 ..       7      49 ..       5      70 .. 0.86
   2 ?   -3.0   0.1       3.1     8e+03      43      57 ..     154     168 ..     146     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                         LAB_N  3 flgqllFtlRfvvQwiasekkkksvlpvlFWvlSllGslllli 45
                                  ++g ++F +  ++  ++s ++kks+lp++F +l  l+  l+l+
  gi|91773508|ref|YP_566200.1|  7 IIGIIFFAAISLYNLVHSIRHKKSYLPSVFGILMALATALILF 49
                                  578999************************9999888888775 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                         LAB_N  43 lliYailrkDpvlil 57 
                                   l+++ +  +++v+i+
  gi|91773508|ref|YP_566200.1| 154 LVLFLMSLREYVIIF 168
                                   455555556666665 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  15.1   0.00021      0.55      40     168 ..       4     160 ..       2     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00021
                       DUF2070  40 gillfglpalvaflltlpvlrilggr..ltykrs..lflalltelivviisllaillsallqalvllalvls......... 107
                                   +il++g+ +++a+ l++ v +i +++  l       +++al+t+li++   l++ ++++++   +lla++ s         
  gi|91773508|ref|YP_566200.1|   4 AILIIGIIFFAAISLYNLVHSIRHKKsyL--PSVfgILMALATALILFDRPLIGGFAFVII---FLLAIFSSgkifgirkr 79 
                                   68999999*******99999999999544..444458888888888888777777777544...23333333666669999 PP

                       DUF2070 108 ................lalvfalrllvlvavsdesllkavlpaliqpllailllvly.....fspesfllllllslifala 167
                                                   l  v+ + +   +a+ +   + av  +liq++l++l+lv++       p++fl l+ ++l+++l+
  gi|91773508|ref|YP_566200.1|  80 sflkamegveinskfsLRYVTNIKYWAAYALNNGPKKAAVGYSLIQTVLIALVLVIFtyvfpR-PTNFLTLVPFILVLFLM 159
                                   999999999999998888888888888888888888899999***************776532.33333333333333332 PP

                       DUF2070 168 v 168
                                   +
  gi|91773508|ref|YP_566200.1| 160 S 160
                                   2 PP

>> DUF3981  Domain of unknown function (DUF3981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.5   0.00011      0.29      30      87 ..       4      61 ..       1      79 [. 0.85
   2 ?    1.0   0.5      0.21   5.4e+02      59      77 ..     118     136 ..      66     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                       DUF3981 30 silvipvlfwigiaiyeyfwliddrvdsilthysvavailiglvlfsqdqigklegtl 87
                                  +il+i ++f+  i++y+ +  i  +   + + + + +a+   l+lf +  ig +   +
  gi|91773508|ref|YP_566200.1|  4 AILIIGIIFFAAISLYNLVHSIRHKKSYLPSVFGILMALATALILFDRPLIGGFAFVI 61
                                  79***********************99999******************9999776554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.21
                       DUF3981  59 lthysvavailiglvlfsq 77 
                                      ys+  ++li lvl+  
  gi|91773508|ref|YP_566200.1| 118 AVGYSLIQTVLIALVLVIF 136
                                   4568888888888887654 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5    0.0029       7.5      27      71 ..       6      51 ..       1      55 [. 0.68
   2 ?    4.7   0.9    0.0063        16      11      62 ..     104     154 ..      98     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0029
                       DUF4191 27 wlllaaflvvvvvfvvlglllg.slilllilgillgllvalivltr 71
                                   ++ ++f +++ +  ++  + + + +l  ++gil++l +ali++ r
  gi|91773508|ref|YP_566200.1|  6 LIIGIIFFAAISLYNLVHSIRHkKSYLPSVFGILMALATALILFDR 51
                                  34444445555555555545442699999***************98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0063
                       DUF4191  11 iaqvfkltrkedkkllwlllaaflvvvvvfvvlglllgslilllilgillgl 62 
                                    + ++ l +  +k+ + + l+  +++++v+v++++++ ++  +l l  ++ l
  gi|91773508|ref|YP_566200.1| 104 YWAAYALNNGPKKAAVGYSLIQTVLIALVLVIFTYVFPRPTNFLTLV-PFIL 154
                                   58999999999999998988888888888888888884322222221.1111 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.9   0.00027      0.68      40      82 ..       7      49 ..       2     110 .. 0.81
   2 ?    1.8   1.3      0.12   3.1e+02      43      79 ..     123     159 ..      99     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                          MerC 40 qvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalf 82
                                   + +i+++ai+l+ lv++ r+ +++++ v g+l  l+ ++ lf
  gi|91773508|ref|YP_566200.1|  7 IIGIIFFAAISLYNLVHSIRHKKSYLPSVFGILMALATALILF 49
                                  567899***********************99987776665544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                          MerC  43 lilvvaigllalvvgyrrhrktsvlvlgalGllillv 79 
                                   li  v+i+l+ ++++y   r t  l+l  + l+++l+
  gi|91773508|ref|YP_566200.1| 123 LIQTVLIALVLVIFTYVFPRPTNFLTLVPFILVLFLM 159
                                   5667888888888888766666666665555555554 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.5      0.19   4.8e+02      23      72 ..      19      68 ..       4      84 .. 0.60
   2 ?   11.2   1.2   6.5e-05      0.17      13      72 ..     102     161 ..      99     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                         S_4TM 23 Ysrakrlqalrvilsvvlaivlsvlavlvpslktylallgllwllldvlv 72
                                  Y+ +  ++  +  l  v+ i+++++++l+  ++++++ +++++++l +++
  gi|91773508|ref|YP_566200.1| 19 YNLVHSIRHKKSYLPSVFGILMALATALILFDRPLIGGFAFVIIFLLAIF 68
                                  44444444444455555666666666655555555555555555555444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.5e-05
                         S_4TM  13 lellaAqrqlYsrakrlqalrvilsvvlaivlsvlavlvpslktylallgllwllldvlv 72 
                                   ++  aA++      k   ++++i +v++a+vl++++ ++p+ +++l+l++++++l+ + +
  gi|91773508|ref|YP_566200.1| 102 IKYWAAYALNNGPKKAAVGYSLIQTVLIALVLVIFTYVFPRPTNFLTLVPFILVLFLMSL 161
                                   666666666666778899999********************9999999999998887654 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.059   1.5e+02      26      42 ..       4      20 ..       1      31 [. 0.69
   2 ?    7.0   0.2    0.0019         5      28      41 ..      34      47 ..      32      49 .. 0.91
   3 ?   -2.5   0.1       1.8   4.6e+03      19      29 ..     120     129 ..     115     139 .. 0.55
   4 ?    0.1   0.1      0.28   7.1e+02      19      30 ..     157     168 ..     148     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.059
               Phage_holin_2_3 26 WAiviGIicgvvTfliN 42
                                    ++iGIi+ ++  l N
  gi|91773508|ref|YP_566200.1|  4 AILIIGIIFFAAISLYN 20
                                  5689****976655555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0019
               Phage_holin_2_3 28 iviGIicgvvTfli 41
                                  +v+GI+++++T li
  gi|91773508|ref|YP_566200.1| 34 SVFGILMALATALI 47
                                  59*********987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.8
               Phage_holin_2_3  19 GllsLseWAiv 29 
                                   G+ sL + +++
  gi|91773508|ref|YP_566200.1| 120 GY-SLIQTVLI 129
                                   66.66665544 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.28
               Phage_holin_2_3  19 GllsLseWAivi 30 
                                    l+sL e++i++
  gi|91773508|ref|YP_566200.1| 157 FLMSLREYVIIF 168
                                   355******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1273.59
//
Query:       gi|91773509|ref|YP_566201.1|  [L=268]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-33  115.8   0.2    2.7e-33  115.4   0.2    1.1  1  ABC_tran         ABC transporter
    3.3e-11   43.6   4.2    3.9e-05   23.6   0.8    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    8.8e-08   31.8   2.9    4.5e-07   29.5   2.9    1.9  1  SMC_N            RecF/RecN/SMC N terminal domain
    3.3e-05   23.8   0.1    0.00071   19.4   0.0    2.1  2  AAA_15           AAA ATPase domain
    0.00013   21.7   0.2    0.00048   19.8   0.1    1.9  2  AAA_29           P-loop containing region of AAA domain
    0.00014   21.7   0.1    0.00035   20.3   0.1    1.6  1  AAA_30           AAA domain
    0.00018   21.9   0.0    0.00039   20.8   0.0    1.6  1  AAA_16           AAA ATPase domain
    0.00048   20.6   0.7     0.0042   17.5   0.7    2.2  1  AAA              ATPase family associated with various cellul
     0.0009   19.8   0.8     0.0012   19.4   0.8    1.4  1  AAA_23           AAA domain
     0.0026   16.6   0.0     0.0042   15.9   0.0    1.2  1  RNA12            RNA12 protein
     0.0027   16.9   0.5      0.004   16.4   0.5    1.5  1  NB-ARC           NB-ARC domain
      0.004   17.4   0.6      0.017   15.4   0.6    2.0  1  AAA_22           AAA domain
     0.0058   16.4   0.0      0.007   16.1   0.0    1.3  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.012   14.6   0.1      0.018   14.1   0.1    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.012   15.3   0.8        1.8    8.3   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.014   15.2   0.4      0.035   13.9   0.0    1.9  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.032   13.4   0.2       0.14   11.3   0.1    1.9  2  PIF1             PIF1-like helicase
      0.035   13.9   0.2      0.056   13.2   0.2    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.036   14.0   0.3      0.093   12.6   0.1    1.7  2  ATPase_2         ATPase domain predominantly from Archaea
      0.043   14.1   1.6       0.11   12.9   1.6    1.7  1  AAA_19           AAA domain
      0.048   13.8   0.2       0.96    9.6   0.0    2.7  3  Sigma54_activ_2  Sigma-54 interaction domain
       0.05   13.6   0.1       0.46   10.5   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
      0.055   13.5   0.4       0.37   10.8   0.0    2.1  2  AAA_14           AAA domain
      0.056   13.2   0.3       0.16   11.7   0.1    2.0  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.058   13.3   0.4        0.1   12.5   0.1    1.6  2  NACHT            NACHT domain
      0.063   11.9   0.9       0.47    9.0   0.1    2.0  2  AAA_13           AAA domain
      0.065   13.4   0.0        0.2   11.8   0.0    1.9  1  AAA_33           AAA domain
      0.071   12.5   0.0       0.11   11.9   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.073   13.6   0.6       0.18   12.3   0.6    1.9  1  AAA_18           AAA domain
      0.078   12.9   1.5       0.15   11.9   0.2    2.1  2  NTPase_1         NTPase
      0.079   12.5   0.0       0.12   11.9   0.0    1.2  1  AAA_27           AAA domain
       0.13   12.5   0.3       0.45   10.7   0.3    1.9  1  AAA_28           AAA domain
       0.22   11.1   1.6       0.29   10.7   0.6    1.7  2  DUF1280          Protein of unknown function (DUF1280)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.2   4.9e-36   2.7e-33       1     137 []      17     164 ..      17     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 4.9e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l++v+l  ++g+ v+i+G+nG+GK+tL+k++ +  kp++G+i++dg++l++    +  k+i++++q  +++ e tv++   
  gi|91773509|ref|YP_566201.1|  17 LNQVDLRAEKGTFVGIIGPNGSGKTTLVKTINNIIKPNSGSITIDGRSLDTMGSVEIAKNIAMVSQVISINFEFTVEDVvl 97 
                                   789*************************************************************************999** PP

                                   .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                e+ e +++a++k ++ +lkd+ v    ++LSgG+ q+v +aral+++pk+l+lDEpt+
  gi|91773509|ref|YP_566201.1|  98 mgrtpyikgaethEDMEIVQDAMKKTKILHLKDRFV----TQLSGGELQKVIIARALAQDPKILILDEPTS 164
                                   ******9998775555559*****************....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.8   7.2e-08   3.9e-05       1      79 [.      29      93 ..      29     124 .. 0.65
   2 !   21.5   0.1   3.1e-07   0.00017     235     294 ..     134     190 ..     111     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.2e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrle 79
                                  + ++iGpNgsGK++L +++  +            +++++g+i+++ ++ld+    + ++      +sq + +++++++e
  gi|91773509|ref|YP_566201.1| 29 FVGIIGPNGSGKTTLVKTINNI------------IKPNSGSITIDGRSLDTMGSVEIAKNIAM--VSQVISINFEFTVE 93
                                  678****************544............55555555555555554444444333333..55555555555555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.1e-07
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                   ++lS G ++   ++ al++++   ++l++DEp ++L+   +  +l l+ke+sr+g  vi+
  gi|91773509|ref|YP_566201.1| 134 TQLSGGELQKVIIARALAQDP---KILILDEPTSHLDITNQIDILNLVKEASRKGMLVIA 190
                                   678999999944444444444...8***************************97655555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   2.9   8.3e-10   4.5e-07      24     198 ..      27     192 ..      11     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8.3e-10
                                   SSEEEEEESTTSSHHHHHHHHHHHCTT.TTT.TTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersak.klrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                     f  i+GpNGSGK+ l+  i  ++  +s + ++  ++l+ + +    + + + a v+ +++ + +   + ++ v + r+ 
  gi|91773509|ref|YP_566201.1|  27 GTFVGIIGPNGSGKTTLVKTINNIIKPNSGSiTIDGRSLDTMGS---VEIAKNIAMVSQVISINFEF--TVEDVVLMGRTP 102
                                   35889****************99988766531344444444433...45555666676665544443..555667788888 PP

                                   ETTSE...EEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                   xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 104 krkge...seykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181
                                   + kg     +++i +  ++k++   +l+ ++   ++LSgGe + v +a  +A    +   + +lDe  ++LD +n   + +
  gi|91773509|ref|YP_566201.1| 103 YIKGAethEDMEIVQDAMKKTK---ILHLKDRFVTQLSGGELQKVIIARALA----QDPKILILDEPTSHLDITNQIDILN 176
                                   8888722233444444444444...45555555679****988666555544....5556899****************** PP

                                   HHHHHCTTSEEEEE-SS CS
                                   xxxxxxxxxxxxxxxxx RF
                         SMC_N 182 llkeksknaQfivislr 198
                                   l+ke+s +  ++vi++ 
  gi|91773509|ref|YP_566201.1| 177 LVKEASRK-GMLVIAVI 192
                                   ***99954.55565554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.3e-06   0.00071      24      84 ..      25     106 ..      14     142 .. 0.57
   2 ?    2.3   0.1       0.2   1.1e+02     322     355 ..     152     185 ..     141     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-06
                        AAA_15  24 e...ltvliGkNnsGKSsilealdlFlnnkekkn.......kkvikiekedleifenis.eskdikIdvef.......... 83 
                                   e   +  +iG+N+sGK+++++ ++ +++ +   +            +   ++ei +ni+  s+ i I++ef          
  gi|91773509|ref|YP_566201.1|  25 EkgtFVGIIGPNGSGKTTLVKTINNIIKPN---SgsitidgR--SLDTMGSVEIAKNIAmVSQVISINFEFtvedvvlmgr 100
                                   44567779***************9888877...222455331..2222233333333321455666666665555555555 PP

                        AAA_15  84 .....a 84 
                                         
  gi|91773509|ref|YP_566201.1| 101 tpyikG 106
                                   554431 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandn 355
                                   ++++il+++EP  hL + +q  + +l ke+++++
  gi|91773509|ref|YP_566201.1| 152 QDPKILILDEPTSHLDITNQIDILNLVKEASRKG 185
                                   6899**********************99999876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   8.9e-07   0.00048      20      50 ..      25      55 ..      14      60 .. 0.80
   2 ?   -1.6   0.0       4.2   2.3e+03      45      55 ..     222     233 ..     220     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.9e-07
                        AAA_29 20 dlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                  + kg ++ ++Gp+GsGK+Tl+  i+ ++ p++
  gi|91773509|ref|YP_566201.1| 25 E-KGtFVGIIGPNGSGKTTLVKTINNIIKPNS 55
                                  3.4557789***************99999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.2
                        AAA_29  45 lLvpak.kvrfN 55 
                                   +L+p++ k+++N
  gi|91773509|ref|YP_566201.1| 222 VLTPSNiKTAYN 233
                                   89****999999 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   6.5e-07   0.00035      15     122 ..      24     191 ..      11     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.5e-07
                        AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaa.g............grviglAptgkaAkvLa................... 63 
                                   +++  ++ + Gp G+GKtt++k+++++++ + g            g+v ++   + +++v++                   
  gi|91773509|ref|YP_566201.1|  24 AEKGTFVGIIGPNGSGKTTLVKTINNIIKPNsGsitidgrsldtmGSVEIAKNIAMVSQVISinfeftvedvvlmgrtpyi 104
                                   55667999*********************9967877777777776555555555555555556666666555555555555 PP

                        AAA_30  64 ......eelgi..eastiakllkrlk................grarlepgtllivDE.agmv...dtkqlaallkaaekag 116
                                         e+++i  +a+   k+l+  +                +ra  ++ ++li DE ++ +   ++ ++ +l+k+a+++g
  gi|91773509|ref|YP_566201.1| 105 kgaethEDMEIvqDAMKKTKILHLKDrfvtqlsggelqkviiARALAQDPKILILDEpTSHLditNQIDILNLVKEASRKG 185
                                   555444455545566666666666669999999****99998644555559******445554445566777777777778 PP

                        AAA_30 117 akvilv 122
                                   + vi v
  gi|91773509|ref|YP_566201.1| 186 MLVIAV 191
                                   877765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   7.3e-07   0.00039      11      63 ..      15      67 ..      12     189 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.3e-07
                        AAA_16 11 qLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                  q+l+ ++ r+ +g    v ++G+ G+GK++lv+++ + ++ + g i++ g+  + 
  gi|91773509|ref|YP_566201.1| 15 QILNQVDlRAEKG--TFVGIIGPNGSGKTTLVKTINNIIKPNsGSITIDGRSLDT 67
                                  5566666344444..7899*****************9999995477777777666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.7   7.6e-06    0.0042       3      53 ..      32      84 ..      30     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.6e-06
                                  EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfkea 53
                                  ++Gp G GKT+l+k + + ++  +  ++i+g +l  +   e +k+i+++ + +
  gi|91773509|ref|YP_566201.1| 32 IIGPNGSGKTTLVKTINNIIKpnSGSITIDGRSLDTMGSVEIAKNIAMVSQVI 84
                                  78*****************9744667999999999887777777777776654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.8   2.3e-06    0.0012      20      43 ..      28      51 ..      12     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.3e-06
                        AAA_23 20 gltlItGpNGaGKTTildAiklaL 43
                                   ++ I+GpNG+GKTT++  i  + 
  gi|91773509|ref|YP_566201.1| 28 TFVGIIGPNGSGKTTLVKTINNII 51
                                  4567************99887665 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.7e-06    0.0042      12      53 ..      22      65 ..      13      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.7e-06
                         RNA12 12 leEnvntFivvkGPrGSGkkeLv..ldrvlkdrkkvlvidCdel 53
                                  l+ +  tF+ + GP GSGk+ Lv  +++++k ++  ++id ++l
  gi|91773509|ref|YP_566201.1| 22 LRAEKGTFVGIIGPNGSGKTTLVktINNIIKPNSGSITIDGRSL 65
                                  677889****************9555677777777888887665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   7.4e-06     0.004       8      43 ..      16      50 ..      10     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.4e-06
                                  HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                  + ++ +   e +  +v++ G  G+GKttl+k i+n 
  gi|91773509|ref|YP_566201.1| 16 ILNQVDLRAEKG-TFVGIIGPNGSGKTTLVKTINNI 50
                                  555555556666.89******************985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   3.2e-05     0.017       4      53 ..      26      70 ..      23     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-05
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..ss 53
                                  + +++ ++G+ G+GKTtl++++ +  +       ++++ ++++  s+   +s
  gi|91773509|ref|YP_566201.1| 26 KGTFVGIIGPNGSGKTTLVKTINNIIK-------PNSGSITIDGRSLDtmGS 70
                                  567888***************999764.......366666666666654444 PP

>> AAA_24  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     0.007       5      40 ..      30      70 ..      26     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                        AAA_24  5 iliyGpsgiGKTtlakel....gpkplfidtek.Glkslda 40
                                  + i+Gp+g+GKTtl+k++    +p+   i +++ +l+ +  
  gi|91773509|ref|YP_566201.1| 30 VGIIGPNGSGKTTLVKTInniiKPNSGSITIDGrSLDTMGS 70
                                  679***************66666666666666633333333 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   0.1   3.3e-05     0.018      15      54 ..      13      52 ..       5      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                                  HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                          MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealglelr 54
                                  ++++l+++  +a + + vG+ G  G+Gk tlv+ +   ++
  gi|91773509|ref|YP_566201.1| 13 SRQILNQVDLRAEKGTFVGIIGPNGSGKTTLVKTINNIIK 52
                                  89******************************98876554 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 ?    8.3   0.0    0.0033       1.8      28      58 ..      22      52 ..      13      86 .. 0.83
   2 ?    5.5   0.2     0.024        13       9      98 ..     103     197 ..     100     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
                        RuvB_N 28 kreealdhvllyGpPGlGkttlakiiakelg 58
                                   r e+   v ++Gp G Gkttl k i + ++
  gi|91773509|ref|YP_566201.1| 22 LRAEKGTFVGIIGPNGSGKTTLVKTINNIIK 52
                                  67788888999************99988665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                        RuvB_N   9 yigqekvkeklkifieaakkre..ealdhvlly.GpPGlGkttlakiiakelgvkl..kitsgPvlekagdlaalltnlee 84 
                                   yi  ++ +e+++i+ +a kk +  +  d  + +     l k  +a+ +a++ ++ +  + ts   + ++ d+  l+++ ++
  gi|91773509|ref|YP_566201.1| 103 YIKGAETHEDMEIVQDAMKKTKilHLKDRFVTQlSGGELQKVIIARALAQDPKILIldEPTSHLDITNQIDILNLVKEASR 183
                                   5666677777888777766654222345444330334599999999999998887744578999999************** PP

                        RuvB_N  85 kdvlfideihrlsr 98 
                                   k +l i  ih l+ 
  gi|91773509|ref|YP_566201.1| 184 KGMLVIAVIHDLNL 197
                                   **********9985 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.5e-05     0.035       1      22 [.      32      53 ..      32      61 .. 0.87
   2 ?   -2.5   0.0       6.7   3.7e+03      25      55 ..     152     182 ..     139     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilel 22
                                  ++Gp GsGKtt+v+++++i++ 
  gi|91773509|ref|YP_566201.1| 32 IIGPNGSGKTTLVKTINNIIKP 53
                                  79***************99875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.7
                    ATP_bind_1  25 rsvavvNLDPAaeelpYeaavdirelitled 55 
                                   ++++++ LD   ++l    ++di +l+++++
  gi|91773509|ref|YP_566201.1| 152 QDPKILILDEPTSHLDITNQIDILNLVKEAS 182
                                   5566677777777888888888888888776 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00025      0.14       8      50 ..      15      55 ..      11      65 .. 0.80
   2 ?   -0.8   0.0       1.2   6.4e+02     262     288 ..     221     247 ..     185     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                  HHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTC CS
                          PIF1  8 kvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrseg 50
                                  ++++++   + +ekg ++ + G  G+gKt l k++ ++++++ 
  gi|91773509|ref|YP_566201.1| 15 QILNQV--DLRAEKGTFVGIIGPNGSGKTTLVKTINNIIKPNS 55
                                  445555..556799999999*******************9853 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                   ......EEEESSCCHHHHHHHHHHCCS CS
                          PIF1 262 eyleerailcptnedvdeiNnyvlskl 288
                                   e l+   i ++ n dv+ iNn++ + l
  gi|91773509|ref|YP_566201.1| 221 EVLTPSNIKTAYNIDVEVINNQITNSL 247
                                   555556677788999999999998876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2    0.0001     0.056       2      45 ..      30      72 ..      29      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldrae 45
                                  +g+ g+ G+Gktt+ +++++i++  +  + +i+g s+ ++ ++e
  gi|91773509|ref|YP_566201.1| 30 VGIIGPNGSGKTTLVKTINNIIK-PNSGSITIDGRSLDTMGSVE 72
                                  89********************9.66666778777766665554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017     0.093      16      42 ..      23      49 ..      15      63 .. 0.81
   2 ?   -1.5   0.0       3.5   1.9e+03      94      94 ..     158     158 ..      97     203 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                      ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiie 42
                                  + e+ +++ i Gp gsGKt+L+k i +
  gi|91773509|ref|YP_566201.1| 23 RAEKGTFVGIIGPNGSGKTTLVKTINN 49
                                  4456788999************98865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
                      ATPase_2  94 i 94 
                                   i
  gi|91773509|ref|YP_566201.1| 158 I 158
                                   2 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.6    0.0002      0.11       9     128 ..      26     181 ..      19     200 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0002
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelre.....rlaalgae................ 68 
                                   k + + ++++ G+GKT+++k+i ++++ + g        ++  gr+ + +       ++a++ +                 
  gi|91773509|ref|YP_566201.1|  26 KGTFVGIIGPNGSGKTTLVKTINNIIKPNSGS-------ITIDGRSLDTMGSveiakNIAMVSQVisinfeftvedvvlmg 99 
                                   567889***************99999888865.......444455444444311111443333335555555555555555 PP

                        AAA_19  69 .......atTiHrlal..........ldfddlltealelle.............eaeeekkl.qeeellivDE.fqdvd.e 116
                                          a+T   + +          l            l+             +    + l q+ ++li DE ++ +d  
  gi|91773509|ref|YP_566201.1| 100 rtpyikgAETHEDMEIvqdamkktkiL-----------HLKdrfvtqlsggelqKVIIARALaQDPKILILDEpTSHLDiT 169
                                   555555544444442233332222221...........1224444455555554333333330334477777755677776 PP

                        AAA_19 117 lqyrLlkallge 128
                                    q  +l+ +++ 
  gi|91773509|ref|YP_566201.1| 170 NQIDILNLVKEA 181
                                   676666666644 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 ?    9.6   0.0    0.0018      0.96       9      70 ..      15      76 ..      12      85 .. 0.82
   2 ?    0.7   0.0      0.96   5.2e+02      59      81 ..     169     195 ..     109     200 .. 0.57
   3 ?   -0.9   0.0         3   1.6e+03      48      86 ..     222     261 ..     218     268 .] 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                                  HHHHHHHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-HHHHHHHTTT CS
               Sigma54_activ_2  9 elkerLeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklpldlleqakg 70
                                  ++ ++++  a++ + v ++G++Gsgk++  +++ +   p++   +++  +  ++ ++e ak+
  gi|91773509|ref|YP_566201.1| 15 QILNQVDLRAEKGTFVGIIGPNGSGKTTLVKTINNIIKPNSGSITIDGRSLDTMGSVEIAKN 76
                                  677888888999999******************99999988877777777777777776666 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.96
                                   H-HHHHHHH....TTTSEEEEEE-TT- CS
               Sigma54_activ_2  59 klpldlleq....akggtLylkdiadl 81 
                                   +   d+l+     ++ g+L++  i+dl
  gi|91773509|ref|YP_566201.1| 169 TNQIDILNLvkeaSRKGMLVIAVIHDL 195
                                   122222222111135666666666655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3
                                   EE--SSTTHHHH-HHHHHHH.TTTSEEEEEE-TT--HHHH CS
               Sigma54_activ_2  48 wleifvverlaklpldlleq.akggtLylkdiadlskaeq 86 
                                   +l + ++++  ++  +++++ +++ + +++ ++ lsk+e 
  gi|91773509|ref|YP_566201.1| 222 VLTPSNIKTAYNIDVEVINNqITNSLYVIPRLEPLSKQEP 261
                                   5667777777777777665438999999999999999875 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   0.00084      0.46       4      24 ..      32      54 ..      30      68 .. 0.83
   2 ?    0.1   0.0       1.3   7.2e+02      46      73 ..     133     161 ..      72     176 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00084
                                  EE--SSSSHHHHHHHGGGGB..S CS
                         AAA_5  4 LvGppGtgKselaerlaaal..n 24
                                  ++Gp G+gK++l++ +   +  n
  gi|91773509|ref|YP_566201.1| 32 IIGPNGSGKTTLVKTINNIIkpN 54
                                  79*************99988543 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                                   --.........--------.G-SEEEEES CS
                         AAA_5  46 eikngttslvdsplvraar.egeilvlDE 73 
                                    ++ ++ +l++ ++ ra    ++il+lDE
  gi|91773509|ref|YP_566201.1| 133 VTQLSGGELQKVIIARALAqDPKILILDE 161
                                   33323333333333333224667777776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00068      0.37       4      34 ..      29      58 ..      26      92 .. 0.72
   2 ?    0.6   0.0      0.99   5.4e+02      51      77 ..     140     166 ..     110     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00068
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesil 34
                                   + i G+  +GKTtl+k++  + + +++  +
  gi|91773509|ref|YP_566201.1| 29 FVGIIGPNGSGKTTLVKTIN-NIIKPNSGSI 58
                                  688************98874.3333444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.99
                        AAA_14  51 kllelilek.lkeekktylflDEiqevp 77 
                                   +l ++i ++ l  ++ ++l+lDE     
  gi|91773509|ref|YP_566201.1| 140 ELQKVIIARaLA-QDPKILILDEPTSHL 166
                                   455566665333.488999999976654 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0003      0.16       6      48 ..      32      72 ..      28     105 .. 0.71
   2 ?   -2.4   0.0       6.7   3.6e+03      55      73 ..     193     211 ..     168     225 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                     PduV-EutP  6 liGkvgsGKttLtqalkgeelkYkktqaiefsdeviDtPGeyl 48
                                  +iG+ gsGKttL +++++  ++     +i +  + +Dt G   
  gi|91773509|ref|YP_566201.1| 32 IIGPNGSGKTTLVKTINN--IIKPNSGSITIDGRSLDTMGSVE 72
                                  79**************86..66667778888888888888543 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.7
                     PduV-EutP  55 salivtsaeadvialvqda 73 
                                   + l+ +++ +d i l+ d 
  gi|91773509|ref|YP_566201.1| 193 HDLNLAAYYCDKICLIRDG 211
                                   4566666667777666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00019       0.1       4      22 ..      31      49 ..      28      56 .. 0.84
   2 ?   -2.8   0.0       9.9   5.4e+03      70      88 ..     142     160 ..     124     192 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                                  EEEC-TTTCHHHHHHHHHH CS
                         NACHT  4 ilqGeaGsGKTtLlqklal 22
                                   + G++GsGKTtL++ +  
  gi|91773509|ref|YP_566201.1| 31 GIIGPNGSGKTTLVKTINN 49
                                  589************9965 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.9
                                   -CCHHHHCCSCCCEEEEEE CS
                         NACHT  70 sevwavllelperlLlilD 88 
                                   ++v++ ++  ++   lilD
  gi|91773509|ref|YP_566201.1| 142 QKVIIARALAQDPKILILD 160
                                   4455555555566666666 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00087      0.47      21      39 ..      32      50 ..      30      81 .. 0.84
   2 ?    1.5   0.0      0.17        92     526     555 ..     153     182 ..     141     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00087
                        AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                  i G NG+GKTtL + ++++
  gi|91773509|ref|YP_566201.1| 32 IIGPNGSGKTTLVKTINNI 50
                                  569***********99987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                        AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrl 555
                                     ki ++D P S LD + +  + +l+k+  
  gi|91773509|ref|YP_566201.1| 153 DPKILILDEPTSHLDITNQIDILNLVKEAS 182
                                   679***********************9875 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   0.00037       0.2       4      19 ..      32      47 ..      30     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                        AAA_33  4 lvGlpGsGKstlaerl 19
                                  ++G++GsGK+tl++ +
  gi|91773509|ref|YP_566201.1| 32 IIGPNGSGKTTLVKTI 47
                                  69**********9875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.11      27      59 ..      32      64 ..      12     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                  Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseeealevak 59
                                  ++Gp GsGKt l k +++++ p s + +++ ++
  gi|91773509|ref|YP_566201.1| 32 IIGPNGSGKTTLVKTINNIIKPNSGSITIDGRS 64
                                  79*****************99988766666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   0.00034      0.18       1      25 [.      30      83 ..      30     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00034
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf............................g 25
                                  +++ G+ G+GKttl k +++    +                            +
  gi|91773509|ref|YP_566201.1| 30 VGIIGPNGSGKTTLVKTINNIIkPNsgsitidgrsldtmgsveiakniamvsqV 83
                                  689*************99655322244455555555555554444445555554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00028      0.15       2      26 ..      30      54 ..      29      68 .. 0.82
   2 ?   -1.0   0.1       2.6   1.4e+03     114     134 ..     174     194 ..     129     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                                  EEEE--TTSSHHHHHHHHHHHH... CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                  v i Gp G+GKtTlvk + + +k +
  gi|91773509|ref|YP_566201.1| 30 VGIIGPNGSGKTTLVKTINNIIKPN 54
                                  5688**************9999754 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.6
                                   HHHHHHHHHTTTSEEEEE--S CS
                      NTPase_1 114 fkeaveevLksekpvlavihr 134
                                   + + v+e+ +++  v+avih 
  gi|91773509|ref|YP_566201.1| 174 ILNLVKEASRKGMLVIAVIHD 194
                                   445566666677777777776 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.12      17      48 ..      18      49 ..       7      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                        AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisd 48
                                  +++d++ae+  +  i+GpN +GK+t+++ i++
  gi|91773509|ref|YP_566201.1| 18 NQVDLRAEKGTFVGIIGPNGSGKTTLVKTINN 49
                                  6899***********************99976 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00083      0.45       3      21 ..      31      49 ..      29     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00083
                        AAA_28  3 vitGgestGKTtlleaLaa 21
                                   i+G+ ++GKTtl++ +++
  gi|91773509|ref|YP_566201.1| 31 GIIGPNGSGKTTLVKTINN 49
                                  59************98874 PP

>> DUF1280  Protein of unknown function (DUF1280)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00054      0.29     157     185 ..      27      55 ..      15      60 .. 0.88
   2 ?   -2.9   0.0       7.8   4.3e+03      12      40 ..     112     140 ..     106     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                       DUF1280 157 divlgigGDkGgdetKlcliieNvekPNs 185
                                      +gi G  G+++t l+  i+N+ kPNs
  gi|91773509|ref|YP_566201.1|  27 GTFVGIIGPNGSGKTTLVKTINNIIKPNS 55 
                                   5679************************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.8
                       DUF1280  12 vleaiqeivgeedvdeFlkdfvkflakse 40 
                                    +e +q+ ++++++ ++ ++fv+ l+  e
  gi|91773509|ref|YP_566201.1| 112 DMEIVQDAMKKTKILHLKDRFVTQLSGGE 140
                                   56777777888888888888887776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 1796.10
//
Query:       gi|91773510|ref|YP_566202.1|  [L=387]
Description: ABC transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-84  282.4  39.5    2.4e-78  263.3  32.6    2.7  3  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 ?   -1.1   0.9     0.042   7.5e+02     108     136 ..      11      39 ..       4      52 .. 0.62
   2 !  263.3  32.6   1.4e-82   2.4e-78       6     290 ..      55     333 ..      18     349 .. 0.95
   3 !   22.4   0.7   2.9e-09   5.2e-05     276     312 .]     343     380 ..     331     380 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.042
                         FecCD 108 flgallalllvlllarkrkgasplkliLa 136
                                   ++ al+++ll++++++   g+++++ +L+
  gi|91773510|ref|YP_566202.1|  11 LIIALAVILLIVVVSNTAIGTTNISPVLT 39 
                                   45555555555555655555555555555 PP

  == domain 2  score: 263.3 bits;  conditional E-value: 1.4e-82
                         FecCD   6 lllslllgavkispsevfeallgka..dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaa 84 
                                   +l +l+l  ++++ s +f++++ +   ++ +++i++ +rlprvl+a+lvGaaLa+aG+++Q++++NpLadP+i+G+ssgaa
  gi|91773510|ref|YP_566202.1|  55 ILWTLSLLGIPFDGSALFNSISPDRtwTDGQEMIIMGIRLPRVLLAALVGAALATAGCSMQGLLKNPLADPYIIGMSSGAA 135
                                   677778888888888888887655577788889************************************************ PP

                         FecCD  85 lgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilf 165
                                   lga+++++ll        + l++f++a +++++v+ +++ +++    +l+LaGia+s++lsalts++l++  +e+l++i++
  gi|91773510|ref|YP_566202.1| 136 LGAAIGFTLL------LPVQLISFIFATITIFVVYNISKVGGKVPVDTLLLAGIAISFFLSALTSFFLFF--SESLHQIIY 208
                                   *******996......7789************************************************99..68******* PP

                         FecCD 166 wllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvG 246
                                   w++G + +asw+kv + +++++ ++l+++ ++  l+++ lg+e+A+slGvn+e v+  +l+++al+ta+av+++G+igFvG
  gi|91773510|ref|YP_566202.1| 209 WMMGGFWNASWDKVKITMLVVFTGILFSYRHSWILNVMLLGEEQAQSLGVNIESVKKQILVISALITAAAVSVSGIIGFVG 289
                                   ********************************************************************************* PP

                         FecCD 247 LivPhiarllvgadhrkllplsallGallllladllarlllspt 290
                                   Li+Phi+r l+g+dhr llp+s+l+Ga++l+++d++ar++ s +
  gi|91773510|ref|YP_566202.1| 290 LIIPHIMRNLIGPDHRGLLPASTLMGAIFLVISDTFARTFPSMV 333
                                   ***************************************96644 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 2.9e-09
                         FecCD 276 llladllarll.lsptelpvgivtaliGapffiylllr 312
                                   +l+  +l r+  l+ ++lpvgivtal+Gapff+yll++
  gi|91773510|ref|YP_566202.1| 343 MLFQVILERVGsLQGVDLPVGIVTALFGAPFFVYLLRK 380
                                   55555555543145899*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2919.45
//
Query:       gi|91773511|ref|YP_566203.1|  [L=363]
Description: ligand binding protein [Methanococcoides burtonii DSM 6242]
Scores for 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-42  143.6   0.2    8.8e-42  143.3   0.2    1.1  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
        0.1   13.0   0.1       0.18   12.2   0.1    1.3  1  Radical_SAM   Radical SAM superfamily
       0.17   11.9   0.3       0.33   11.0   0.3    1.5  1  PGF-CTERM     PGF-CTERM motif


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 !  143.3   0.2   1.5e-45   8.8e-42       1     235 [.      51     276 ..      51     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 1.5e-45
                                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHH CS
                  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellks 81 
                                   i++l ps+tei++ +Ga dkvvg  + +++p +a+    + ++vg +++i++E++a l PDl++l++     d +++l+++
  gi|91773511|ref|YP_566203.1|  51 IVCLMPSITEIVFTVGAGDKVVGGTEDDNYPPEAE----NLTKVGRYTTINYETVAGLEPDLILLDEAN-GEDTIKRLEEL 126
                                   8*********************************9....99*************************999.89********* PP

                                   HS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTT CS
                  Peripla_BP_2  82 giptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsnsyi 160
                                   +i+t+  +++   +++ e+i  +g+++++ed+a+++v  + +++ ++ ++++ +   ++p ++++ +d+ +++ ag ++y 
  gi|91773511|ref|YP_566203.1| 127 NIQTLMINPKT-MDEIIESILLVGTITNNEDNAQEIVDGMRQTISNITDSTKGItdEERPRVLYIVWDD-PIYSAGKYTYP 205
                                   **********5.6*****************************************987777777777777.8********** PP

                                   THHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                  Peripla_BP_2 161 gdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyald 235
                                   +dl+  +g++ni+++   +++ +i+ E ++++dp++i++sg+      +++    +n++l+ + A+kn rVy ++
  gi|91773511|ref|YP_566203.1| 206 NDLITMAGGQNIIEA---NGWPTINLESVVSADPQIIICSGM-GGLSYQIANNTRNNDALQTVSAIKNDRVYSIK 276
                                   ************999...5***********************.9999999**********************986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.9e-05      0.18      50     136 ..      70     167 ..      50     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                                   EEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG..........HHHHHHHHHTT-SEEEEEEBSSSHH..... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                   Radical_SAM  50 vilgggepllypdfvellerlaklavpgiritvetngtlpd..........eeklerllelgvdrvslgleaadde..... 115
                                    ++gg e + yp+++e l +  +      +i +et ++l            e+ ++rl el++ ++ ++ ++ d+      
  gi|91773511|ref|YP_566203.1|  70 KVVGGTEDDNYPPEAENLTKVGR----YTTINYETVAGLEPdlilldeangEDTIKRLEELNIQTLMINPKTMDEIiesil 146
                                   46789999999999999999999....577777776666446888889999*************************88888 PP

                                   HHHHHHTCTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 116 kvlklmnrghtfeevlealek 136
                                    v  ++n  ++ +e++++++ 
  gi|91773511|ref|YP_566203.1| 147 LVGTITNNEDNAQEIVDGMRQ 167
                                   777788777788888877764 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   5.5e-05      0.33       1      10 [.     341     350 ..     341     351 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.5e-05
                     PGF-CTERM   1 tPGFGavlAl 10 
                                   tPGFG++lA+
  gi|91773511|ref|YP_566203.1| 341 TPGFGVLLAI 350
                                   9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2681.13
//
Query:       gi|91773512|ref|YP_566204.1|  [L=534]
Description: hypothetical protein Mbur_1548 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  11.6    2.4e-05   24.8   0.3    3.6  3  DUF4430    Domain of unknown function (DUF4430)
    6.1e-06   26.0   4.8    1.1e-05   25.3   0.1    2.3  2  PGF-CTERM  PGF-CTERM motif
     0.0019   18.4   0.2         18    5.6   0.0    3.3  3  OspE       Borrelia outer surface protein E
  ------ inclusion threshold ------
        8.5    5.8  10.3        3.4    7.1   0.2    3.0  3  Rax2       Cortical protein marker for cell polarity


Domain annotation for each model (and alignments):
>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.8   1.4e-08   6.4e-05      27      73 ..      91     140 ..      65     141 .. 0.81
   2 !   24.2   0.4   8.2e-09   3.7e-05      41      72 ..     245     276 ..     207     277 .. 0.88
   3 !   24.8   0.3   5.3e-09   2.4e-05      41      72 ..     379     413 ..     337     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.4e-08
                       DUF4430  27 yitsIngl...eqdtakksyWmyevNGepsdvGagsyklkdgdkivfryt 73 
                                    i++ ng     + t+++s W +++N++++++G g   +++gdki f+y 
  gi|91773512|ref|YP_566204.1|  91 SINALNGTnnePWGTGNSSSWYLYINDVYASRGLGGNPVSNGDKISFWYA 140
                                   466667765556677777******************************95 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 8.2e-09
                       DUF4430  41 ksyWmyevNGepsdvGagsyklkdgdkivfry 72 
                                   +++W++++NG+p+  G g   +++gdki+f+y
  gi|91773512|ref|YP_566204.1| 245 SRGWSLFINGVPAPMGLGGNSVSNGDKITFWY 276
                                   58*****************************9 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 5.3e-09
                       DUF4430  41 k...syWmyevNGepsdvGagsyklkdgdkivfry 72 
                                   +   ++W++++NG+p+  G g   +++gdki+f+y
  gi|91773512|ref|YP_566204.1| 379 GgisRGWSLFINGVPAPMGLGGNSVSNGDKITFWY 413
                                   15559*****************************9 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   1.8     0.069   3.1e+02       7      20 ..       7      20 ..       7      20 .. 0.88
   2 !   25.3   0.1   2.4e-09   1.1e-05       1      22 [.     510     532 ..     510     533 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.069
                     PGF-CTERM  7 vlAlaGLLaaalLa 20
                                  +++ ++L++a++La
  gi|91773512|ref|YP_566204.1|  7 IICMIALASAVFLA 20
                                  57889********7 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.4e-09
                     PGF-CTERM   1 tPGFGavlAlaGLLaaa.lLaRR 22 
                                   tPGF+ ++A+ GLL +a ++++R
  gi|91773512|ref|YP_566204.1| 510 TPGFEGIFAVSGLLLSAmFIMKR 532
                                   9****************666665 PP

>> OspE  Borrelia outer surface protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0     0.004        18      14      37 ..      57      80 ..      46     114 .. 0.83
   2 !    4.4   0.0    0.0097        43      13      37 ..     193     217 ..     182     249 .. 0.76
   3 !    4.4   0.0    0.0093        42      13      37 ..     330     354 ..     319     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.004
                                  TS-EEEEEEEEEEE-SSSEEEEEE CS
                          OspE 14 ssnwidlgdlvvrkeedgietgln 37
                                  + n++dlg l ++ e +gi+ ++ 
  gi|91773512|ref|YP_566204.1| 57 TYNFTDLGALMLVNESQGISYNIS 80
                                  469****************98765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0097
                                   TTS-EEEEEEEEEEE-SSSEEEEEE CS
                          OspE  13 nssnwidlgdlvvrkeedgietgln 37 
                                   +++n++dlg +  + e +gi  ++ 
  gi|91773512|ref|YP_566204.1| 193 EINNFTDLGAFMFVNESQGIGYNIS 217
                                   689****************977664 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0093
                                   TTS-EEEEEEEEEEE-SSSEEEEEE CS
                          OspE  13 nssnwidlgdlvvrkeedgietgln 37 
                                   +++n++dlg +  + e +gi+ ++ 
  gi|91773512|ref|YP_566204.1| 330 EINNFTDLGAFMFVNESQGISYNIS 354
                                   689*****************87764 PP

>> Rax2  Cortical protein marker for cell polarity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.8      0.41   1.8e+03     103     122 ..      83     102 ..      40     120 .. 0.61
   2 ?    4.5   0.2    0.0047        21     103     124 ..     220     241 ..     218     249 .. 0.89
   3 ?    7.1   0.2   0.00076       3.4     103     124 ..     357     378 ..     354     386 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.41
                          Rax2 103 nlpdfGnasaalyngtswiP 122
                                   ++++fG++s    ngt+ +P
  gi|91773512|ref|YP_566204.1|  83 YFSSFGSFSINALNGTNNEP 102
                                   34445555555555555555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0047
                          Rax2 103 nlpdfGnasaalyngtswiPYl 124
                                   ++++fG++s+  +ngt  +PY+
  gi|91773512|ref|YP_566204.1| 220 YFSSFGSFSMNAFNGTINEPYV 241
                                   6799*****************8 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00076
                          Rax2 103 nlpdfGnasaalyngtswiPYl 124
                                   ++++fG++s+  +ngts +PY+
  gi|91773512|ref|YP_566204.1| 357 YFSSFGSFSMNAFNGTSNEPYV 378
                                   6799*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3531.37
//
Query:       gi|91773513|ref|YP_566205.1|  [L=656]
Description: Pyrrolo-quinoline quinone [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-28  100.4   1.5    1.1e-11   44.7   0.0    2.5  3  PQQ_2      PQQ-like domain
    5.5e-28   96.7  18.3    3.4e-05   24.2   0.0    8.3  8  PQQ_3      PQQ-like domain
      6e-13   48.0  17.9    1.7e-08   34.0   0.1    7.7  9  PQQ        PQQ enzyme repeat
  ------ inclusion threshold ------
      0.024   14.6   1.2      0.029   14.3   0.0    1.8  2  PGF-CTERM  PGF-CTERM motif


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.5e-15   1.1e-11      55     157 ..      57     155 ..      54     166 .. 0.83
   2 !   39.2   0.0   1.3e-13   5.6e-10      32     187 ..     117     272 ..     113     283 .. 0.84
   3 !   30.8   0.1   4.8e-11   2.1e-07       6     232 ..     184     422 ..     179     424 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.5e-15
                         PQQ_2  55 tGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklv 135
                                   + +  We++l+  +  +p v ++ v+v+++d+++ a+ +++G+  W+  +++    +   ++  a++ d ++v++ +g ++
  gi|91773513|ref|YP_566205.1|  57 DNSMSWEKQLSDGIDCTPIVIDDLVYVATGDNTVFAIHKKTGEIEWESSSSG----SGFLVSNLAYGNDMIFVPTMNGYIY 133
                                   5677899999999999999999999999999999999999999999944444....4455788888899999999999999 PP

                         PQQ_2 136 aldpkdGkvlWerelaaprgts 157
                                   a+d+++G++ W++++++++ ++
  gi|91773513|ref|YP_566205.1| 134 AFDADNGNEKWNAKVSDAQLNT 155
                                   9999999999999998777555 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.3e-13
                         PQQ_2  32 avlsggtlfvatgggrlvaldaatGkvlWettl.egpvvgaplvaegrvvvva..........sdgqlialdaedGkrlWs 101
                                   a+ +++ +fv t  g ++a+da +G ++W++++ ++++ ++   +++++++ +          s g+++ +d + Gk++W+
  gi|91773513|ref|YP_566205.1| 117 AY-GNDMIFVPTMNGYIYAFDADNGNEKWNAKVsDAQLNTPVKYDNNKIFFGDcsvggasetsSAGTYYCYD-DEGKEVWN 195
                                   67.899***************************7777777779******999999999988888889999**.******** PP

                         PQQ_2 102 tqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyassgq 182
                                   + ++s   +     a  av g++++ g+ +++l+ ++  +G+ ++e   ++  g      vg i ++   +++++y+ s++
  gi|91773513|ref|YP_566205.1| 196 RTSNS--GTG-YYWAGAAVKGKYLIYGDDGSNLTSVNKNTGDTVDEIDASSVYGI----DVGNIRSSIMYDDNKIYFTSKS 269
                                   55555..333.3356667779**********************999977653433....58999999999999****9999 PP

                         PQQ_2 183 grlla 187
                                   g   +
  gi|91773513|ref|YP_566205.1| 270 G--YC 272
                                   9..44 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 4.8e-11
                         PQQ_2   6 saldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvga........plvaegr 78 
                                   +++d   G+e+W  + + + g   ++a ++g++l+ +++g +l++++++tG  + e ++++   g+           ++++
  gi|91773513|ref|YP_566205.1| 184 YCYDD-EGKEVWNRTSNSGTGYYWAGAAVKGKYLIYGDDGSNLTSVNKNTGDTVDEIDASSV-YGIdvgnirssIMYDDNK 262
                                   67885.7*******998888888899999*****************************9553.333366666669****** PP

                         PQQ_2  79 vvvvasdgqlialdaedGkrlWstqqrseepae.lrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprgts 157
                                   +++ +  g  +al  e+ + l+ t +   + a+  +s+++p++++++++vg+ s++  +l ++d   +W+ +  +a + + 
  gi|91773513|ref|YP_566205.1| 263 IYFTSKSGYCYALGFESSTGLFDTTDKH-K-ANiGISTSTPVIYKERIYVGH-SNGFSCLKASDLTSIWDFSTdGAVQSSP 340
                                   *****99988887777777788844444.3.44379999*************.999***************9977766555 PP

                         PQQ_2 158 elsrvgdisgrpvvaegtVyassgqgrllal.dlatgr..rl.wskeiss.......inglpildgdllyvvsa.gelial 226
                                   ++s+ +d     v    +    + +g++ ++ d ++++  +l ws    +         g +  +++++y++++ ++l+ l
  gi|91773513|ref|YP_566205.1| 341 AISSHDDAGNGDVYI--YFTTNTAEGKVYCIkDDGENNdpELkWSYG--NpdktaysLAG-VSISDGWVYYGTDsNYLFGL 416
                                   555444443333333..233333445589999999999884457321..12224553555.89999999999977***999 PP

                         PQQ_2 227 dratGa 232
                                     ++++
  gi|91773513|ref|YP_566205.1| 417 TNKEKT 422
                                   888776 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   7.6e-09   3.4e-05       5      40 .]      62      97 ..      61      97 .. 0.97
   2 !   21.7   0.0   4.7e-08   0.00021       1      39 [.      98     138 ..      98     139 .. 0.79
   3 !    8.6   0.0   0.00061       2.7       1      37 [.     140     187 ..     140     189 .. 0.92
   4 !   12.7   0.9     3e-05      0.13       1      40 []     190     232 ..     190     232 .. 0.87
   5 !    7.6   0.0    0.0012       5.5      12      37 ..     251     276 ..     245     279 .. 0.88
   6 ?    2.6   0.0     0.046     2e+02      14      31 ..     298     315 ..     293     322 .. 0.88
   7 !   12.1   0.1   4.9e-05      0.22       4      36 ..     327     369 ..     325     371 .. 0.83
   8 !   12.1   0.6   4.6e-05      0.21       2      33 ..     379     413 ..     379     417 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.6e-09
                         PQQ_3  5 WsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40
                                  W++ql + + ++p v ++lvyv+tgd+t++A++ +t
  gi|91773513|ref|YP_566205.1| 62 WEKQLSDGIDCTPIVIDDLVYVATGDNTVFAIHKKT 97
                                  ********************************9876 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 4.7e-08
                         PQQ_3   1 GevlWsvqlpg..pvnsspavdgglvyvgtgdGtlyAlDae 39 
                                   Ge+ W+ +  g   ++s +a++++ ++v t++G +yA+Da+
  gi|91773513|ref|YP_566205.1|  98 GEIEWESSSSGsgFLVSNLAYGNDMIFVPTMNGYIYAFDAD 138
                                   6777777554433555778*********************8 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00061
                         PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtg..........dGtlyAlD 37 
                                   G ++W+ ++ + ++n+++ +d++++++g+            Gt y++D
  gi|91773513|ref|YP_566205.1| 140 GNEKWNAKVSDaQLNTPVKYDNNKIFFGDCsvggasetssAGTYYCYD 187
                                   889******887999999***********9999999999999999999 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 3e-05
                         PQQ_3   1 GevlWsv....qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                   G+++W++    +  g++++++av g ++  g++  +l++++ +t
  gi|91773513|ref|YP_566205.1| 190 GKEVWNRtsnsG-TGYYWAGAAVKGKYLIYGDDGSNLTSVNKNT 232
                                   99*****77733.45899********************999776 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0012
                         PQQ_3  12 pvnsspavdgglvyvgtgdGtlyAlD 37 
                                    + ss  +d++++y+++  G  yAl 
  gi|91773513|ref|YP_566205.1| 251 NIRSSIMYDDNKIYFTSKSGYCYALG 276
                                   68899*******************96 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.046
                         PQQ_3  14 nsspavdgglvyvgtgdG 31 
                                   +s+p+++  ++yvg ++G
  gi|91773513|ref|YP_566205.1| 298 TSTPVIYKERIYVGHSNG 315
                                   5899***********987 PP

  == domain 7  score: 12.1 bits;  conditional E-value: 4.9e-05
                         PQQ_3   4 lWsvqlpgpvnsspavd.......gg.lvyvgtg..dGtlyAl 36 
                                   +W ++++g+v+sspa++       g+ ++y++t    G++y++
  gi|91773513|ref|YP_566205.1| 327 IWDFSTDGAVQSSPAISshddagnGDvYIYFTTNtaEGKVYCI 369
                                   8*************88777666543357999999*******97 PP

  == domain 8  score: 12.1 bits;  conditional E-value: 4.6e-05
                         PQQ_3   2 evlWsvqlpgpvnssp...avdgglvyvgtgdGtl 33 
                                   e++Ws++ p+++ +s+    +++g vy gt+ + l
  gi|91773513|ref|YP_566205.1| 379 ELKWSYGNPDKTAYSLagvSISDGWVYYGTDSNYL 413
                                   689***7777555555555***********97766 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.45     2e+03      21      37 ..      59      75 ..      56      76 .. 0.82
   2 !   14.6   0.0   5.2e-06     0.023       2      25 ..      80     103 ..      79     108 .. 0.92
   3 !   34.0   0.1   3.8e-12   1.7e-08       2      38 .]     122     158 ..     121     158 .. 0.93
   4 ?    0.2   0.1      0.19   8.7e+02      13      24 ..     184     194 ..     176     197 .. 0.82
   5 ?   -1.3   0.2      0.56   2.5e+03       5      22 ..     218     235 ..     216     236 .. 0.80
   6 ?    0.2   0.1      0.19   8.6e+02       1      15 [.     261     275 ..     261     276 .. 0.92
   7 ?    2.6   0.0     0.032   1.4e+02      23      37 ..     327     341 ..     321     342 .. 0.93
   8 ?   -1.6   0.0       0.7   3.1e+03      21      30 ..     379     388 ..     379     390 .. 0.82
   9 ?   -0.2   0.0      0.26   1.1e+03       3      15 ..     404     416 ..     404     429 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.45
                                  CEEEEEESSSCGSSESE CS
                           PQQ 21 kvlWrfktggpvlslpi 37
                                   + W++++++ ++ +pi
  gi|91773513|ref|YP_566205.1| 59 SMSWEKQLSDGIDCTPI 75
                                  566**********9998 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.2e-06
                                   EEEEEETTSEEEEEETTTCCEEEE CS
                           PQQ   2 vvylgsadGylyAlDadTGkvlWr 25 
                                    vy+++ d++++A+  +TG++ W+
  gi|91773513|ref|YP_566205.1|  80 LVYVATGDNTVFAIHKKTGEIEWE 103
                                   79*********************8 PP

  == domain 3  score: 34.0 bits;  conditional E-value: 3.8e-12
                                   EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESEE CS
                           PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlslpik 38 
                                    +++++ +Gy+yA+Dad+G+++W  k++++ l++p+k
  gi|91773513|ref|YP_566205.1| 122 MIFVPTMNGYIYAFDADNGNEKWNAKVSDAQLNTPVK 158
                                   6999**************************9999975 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.19
                                   EEEETTTCCEEE CS
                           PQQ  13 yAlDadTGkvlW 24 
                                   y +D d Gk++W
  gi|91773513|ref|YP_566205.1| 184 YCYD-DEGKEVW 194
                                   8899.99***** PP

  == domain 5  score: -1.3 bits;  conditional E-value: 0.56
                                   EEETTSEEEEEETTTCCE CS
                           PQQ   5 lgsadGylyAlDadTGkv 22 
                                   +g+++ +l  ++ +TG+ 
  gi|91773513|ref|YP_566205.1| 218 YGDDGSNLTSVNKNTGDT 235
                                   56778899999*****86 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.19
                                   TEEEEEETTSEEEEE CS
                           PQQ   1 gvvylgsadGylyAl 15 
                                   +++y +s+ Gy yAl
  gi|91773513|ref|YP_566205.1| 261 NKIYFTSKSGYCYAL 275
                                   78***********98 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.032
                                   EEEEESSSCGSSESE CS
                           PQQ  23 lWrfktggpvlslpi 37 
                                   +W f t+g+v+s+p+
  gi|91773513|ref|YP_566205.1| 327 IWDFSTDGAVQSSPA 341
                                   7************96 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 0.7
                                   CEEEEEESSS CS
                           PQQ  21 kvlWrfktgg 30 
                                   +++W++ +++
  gi|91773513|ref|YP_566205.1| 379 ELKWSYGNPD 388
                                   689***9986 PP

  == domain 9  score: -0.2 bits;  conditional E-value: 0.26
                                   EEEEETTSEEEEE CS
                           PQQ   3 vylgsadGylyAl 15 
                                   vy+g++ +yl+ l
  gi|91773513|ref|YP_566205.1| 404 VYYGTDSNYLFGL 416
                                   89********987 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.8       2.3     1e+04       1       4 [.     587     590 ..     587     590 .. 0.95
   2 ?   14.3   0.0   6.5e-06     0.029       2      23 .]     633     654 ..     633     654 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                     PGF-CTERM   1 tPGF 4  
                                   tPGF
  gi|91773513|ref|YP_566205.1| 587 TPGF 590
                                   9*** PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.5e-06
                     PGF-CTERM   2 PGFGavlAlaGLLaaalLaRRr 23 
                                   PGF+ ++ ++GLL +++ ++++
  gi|91773513|ref|YP_566205.1| 633 PGFEGIFMVIGLLLSVFCIKKK 654
                                   9******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 3652.73
//
Query:       gi|91773514|ref|YP_566206.1|  [L=809]
Description: Pyrrolo-quinoline quinone [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-69  227.4  43.0    5.7e-08   33.0   0.3   16.2 16  PQQ_3      PQQ-like domain
    2.3e-64  217.2   6.8    7.6e-17   61.7   0.1    6.6  6  PQQ_2      PQQ-like domain
    5.8e-40  133.4  40.6    0.00018   21.3   0.5   14.2 15  PQQ        PQQ enzyme repeat
  ------ inclusion threshold ------
      0.035   14.3   0.0       0.15   12.3   0.0    2.1  1  Pepsin-I3  Pepsin inhibitor-3-like repeated domain
       0.74   10.2  11.2          5    7.6   0.1    6.5  7  Kelch_6    Kelch motif
        2.1    8.4   3.6         12    6.0   3.6    2.1  1  PGF-CTERM  PGF-CTERM motif


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.2e-06    0.0067      12      38 ..      68      94 ..      54      96 .. 0.84
   2 !   27.7   0.1   8.6e-10   2.6e-06       1      39 [.      97     138 ..      97     139 .. 0.86
   3 ?    4.2   0.0     0.022        65       1      35 [.     140     181 ..     140     185 .. 0.78
   4 !   10.4   0.0   0.00025      0.76       1      40 []     186     228 ..     186     228 .. 0.91
   5 !    7.5   0.0     0.002       5.8       6      32 ..     245     271 ..     241     275 .. 0.82
   6 !   17.2   0.1   1.8e-06    0.0053      13      37 ..     298     326 ..     291     329 .. 0.86
   7 !   19.2   0.1   4.2e-07    0.0012       1      37 [.     330     372 ..     330     374 .. 0.86
   8 !   23.8   0.8   1.5e-08   4.6e-05       1      36 [.     375     413 ..     375     414 .. 0.88
   9 ?    4.8   0.0     0.014        41       4      37 ..     445     478 ..     443     481 .. 0.73
  10 ?    3.3   0.0     0.041   1.2e+02      11      29 ..     495     513 ..     491     514 .. 0.80
  11 !   16.9   0.0   2.1e-06    0.0064       9      37 ..     512     540 ..     505     543 .. 0.93
  12 !   33.0   0.3   1.9e-11   5.7e-08       1      40 []     544     589 ..     544     589 .. 0.98
  13 !   16.2   0.0   3.6e-06     0.011      14      38 ..     604     632 ..     590     634 .. 0.80
  14 !   14.0   0.3   1.8e-05     0.053       1      38 [.     635     676 ..     635     678 .. 0.90
  15 !   13.7   0.1   2.2e-05     0.065       1      29 [.     679     710 ..     679     728 .. 0.80
  16 !   17.8   0.0   1.1e-06    0.0034       1      36 [.     731     762 ..     731     766 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                         PQQ_3 12 pvnsspavdgglvyvgtgdGtlyAlDa 38
                                   +n +p+++g+lvy+ t++G++ A++ 
  gi|91773514|ref|YP_566206.1| 68 GINVPPVIAGDLVYTHTTNGSVWAFNK 94
                                  788899*******************86 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 8.6e-10
                         PQQ_3   1 GevlWsvqlpg..pvn.sspavdgglvyvgtgdGtlyAlDae 39 
                                   G ++W+ ++ g  +++ s+pa+++g+++v++  G l+A+Da 
  gi|91773514|ref|YP_566206.1|  97 GALIWRSKTSGgsALQsSTPAYGDGKLFVASNSGDLFAFDAS 138
                                   889******66576664666********************97 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.022
                         PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtg......dGtlyA 35 
                                   Ge+lWs  + +    ++ ++ + ++y+g+g          y+
  gi|91773514|ref|YP_566206.1| 140 GEELWSEHVTDsNFECPITYFDHRLYIGDGlrggidTKYYYC 181
                                   9999*9988765888999***********9876665555555 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00025
                         PQQ_3   1 GevlWsv...qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                   G++lW++   +  g ++ ++ v g+ ++ +t+ G+l +lD et
  gi|91773514|ref|YP_566206.1| 186 GQLLWKYangNSAGFLWNGASVIGDFLVYSTHEGKLLSLDKET 228
                                   99*****8775567999***********************998 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.002
                         PQQ_3   6 svqlpgpvnsspavdgglvyvgtgdGt 32 
                                   s++ pg   ss+++ +g++y++++ G 
  gi|91773514|ref|YP_566206.1| 245 SKEDPGMFRSSVTYHDGYIYTTSERGQ 271
                                   5677787789*************9886 PP

  == domain 6  score: 17.2 bits;  conditional E-value: 1.8e-06
                         PQQ_3  13 vnsspavdgglvyvgtg....dGtlyAlD 37 
                                    +s+pav +g+vyvg g     G+l++lD
  gi|91773514|ref|YP_566206.1| 298 STSTPAVHDGKVYVGQGehgyTGHLTCLD 326
                                   4699************************9 PP

  == domain 7  score: 19.2 bits;  conditional E-value: 4.2e-07
                         PQQ_3   1 GevlWsvqlpgpvnssp..avdgg..lvyvgtg..dGtlyAlD 37 
                                   G+vlWs+ +++ v+ssp  av +   ++y+++   dG+ly+l+
  gi|91773514|ref|YP_566206.1| 330 GDVLWSYFVDAGVKSSPvlAVENEitYIYFTGAesDGSLYCLE 372
                                   99***************7666665557999999********97 PP

  == domain 8  score: 23.8 bits;  conditional E-value: 1.5e-08
                         PQQ_3   1 GevlWsv.qlpg..pvnsspavdgglvyvgtgdGtlyAl 36 
                                   G++ W++ ++++  ++  ++a+++g++y+gt+ G ly++
  gi|91773514|ref|YP_566206.1| 375 GTLAWEYdPTDDvgYILQGAAISDGKIYFGTDGGYLYCI 413
                                   999****955544488899*******************7 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.014
                         PQQ_3   4 lWsv.qlpgpvn.sspavdgglvyvgtgdGtlyAlD 37 
                                   lW+  ++++ v+ ss+++++++vyv +g   +++lD
  gi|91773514|ref|YP_566206.1| 445 LWASeDIGA-VKgSSTVIANNKVYVNCG-DYVRSLD 478
                                   677734454.443999*********988.6666666 PP

  == domain 10  score: 3.3 bits;  conditional E-value: 0.041
                         PQQ_3  11 gpvnsspavdgglvyvgtg 29 
                                   ++  +spa+ +g v +g +
  gi|91773514|ref|YP_566206.1| 495 YKSIASPAYHDGNVWCGLP 513
                                   55679*********99965 PP

  == domain 11  score: 16.9 bits;  conditional E-value: 2.1e-06
                         PQQ_3   9 lpgpvnsspavdgglvyvgtgdGtlyAlD 37 
                                   lp+ vns+++v++g+++ g +dG+ y++D
  gi|91773514|ref|YP_566206.1| 512 LPDSVNSATTVADGKLFEGEWDGNYYCFD 540
                                   7999************************9 PP

  == domain 12  score: 33.0 bits;  conditional E-value: 1.9e-11
                         PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg......dGtlyAlDaet 40 
                                   Ge++W++++ g ++++pa+d+ +vy++t+       G++y++Da+t
  gi|91773514|ref|YP_566206.1| 544 GEEIWNFSTEGNAQATPAYDNERVYFTTWiygqtyGGNVYCVDANT 589
                                   9*******************************************98 PP

  == domain 13  score: 16.2 bits;  conditional E-value: 3.6e-06
                         PQQ_3  14 nsspavdgglvyvgtg....dGtlyAlDa 38 
                                    ssp+++g++vyv+t+     G +yAl+ 
  gi|91773514|ref|YP_566206.1| 604 CSSPTIYGDIVYVTTYnfygEGEIYALNK 632
                                   59*************************86 PP

  == domain 14  score: 14.0 bits;  conditional E-value: 1.8e-05
                         PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg.....dGtlyAlDa 38 
                                   G +lW+ ++++ + s+pav+ g vyv++g     d   y++Da
  gi|91773514|ref|YP_566206.1| 635 GSILWKEDIHS-TDSTPAVAYGNVYVAGGcygysDLQTYCFDA 676
                                   889*******6.6699*************99999999999997 PP

  == domain 15  score: 13.7 bits;  conditional E-value: 2.2e-05
                         PQQ_3   1 GevlWsv....qlpgpvnsspavdgglvyvgtg 29 
                                   Ge++W++    +++g + +s+a+++ +++vgt 
  gi|91773514|ref|YP_566206.1| 679 GELKWNTtpedGIGGWL-CSVAIADEKIFVGTA 710
                                   9******9766666655.**************8 PP

  == domain 16  score: 17.8 bits;  conditional E-value: 1.1e-06
                         PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                   Ge++W+ +++g   sspav++  v++ ++ G++yA+
  gi|91773514|ref|YP_566206.1| 731 GELIWNSPFGG---SSPAVADEMVFTIAD-GKVYAF 762
                                   99********7...58***********95.*****9 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   2.3e-15   6.9e-12      67     152 ..      68     150 ..      54     154 .. 0.84
   2 !   58.0   0.1   3.3e-19     1e-15       2     183 ..      86     270 ..      85     280 .. 0.79
   3 !   38.2   0.0   3.8e-13   1.1e-09      24     136 ..     296     412 ..     259     416 .. 0.76
   4 ?    1.6   0.0     0.057   1.7e+02     116     194 ..     457     483 ..     434     517 .. 0.49
   5 !   61.7   0.1   2.6e-20   7.6e-17       5     180 ..     474     661 ..     471     662 .. 0.78
   6 !   47.5   0.0   5.5e-16   1.7e-12       2     136 ..     624     761 ..     623     767 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.3e-15
                         PQQ_2  67 pvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWe 147
                                    +  +p +a++ v+ ++ +g+++a+++++G + W+ + ++++   +++s++pa+++++++v+  sg+l a+d+++G++lW+
  gi|91773514|ref|YP_566206.1|  68 GINVPPVIAGDLVYTHTTNGSVWAFNKHNGALIWRSKTSGGS---ALQSSTPAYGDGKLFVASNSGDLFAFDASSGEELWS 145
                                   444569*****************************4444434...446********************************* PP

                         PQQ_2 148 relaa 152
                                   + +++
  gi|91773514|ref|YP_566206.1| 146 EHVTD 150
                                   99854 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 3.3e-19
                         PQQ_2   2 egvvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgap.lvaegrvvv 81 
                                   +g+v a+++ +Ga++Wr++   ++   +s++  ++g+lfva+ +g l a+da++G++lW+  ++  + + p +  + r++ 
  gi|91773514|ref|YP_566206.1|  86 NGSVWAFNKHNGALIWRSKTSGGSALQSSTPAYGDGKLFVASNSGDLFAFDASSGEELWSEHVTDSNFECPiTYFDHRLYI 166
                                   799***************774444444444777******************************777666665999999999 PP

                         PQQ_2  82 va......sdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprg 155
                                    +      + + ++ +d ++G++lW  + ++  +a ++ +++++++ d +v  ++ gkl  ld ++G++ +e  l +++  
  gi|91773514|ref|YP_566206.1| 167 GDglrggiDTKYYYCYD-DTGQLLWK-YANG-NSAGFLWNGASVIG-DFLVYSTHEGKLLSLDKETGELTDEIDLgSEDI- 242
                                   99998885555888899.********.8888.78888888888888.66667777******************9955443. PP

                         PQQ_2 156 tselsrvgdisgrpvvaegtVyassgqg 183
                                   + + +  g   ++++  +g++y  s  g
  gi|91773514|ref|YP_566206.1| 243 RFSKEDPGMFRSSVTYHDGYIYTTSERG 270
                                   3333455666666666666777776666 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 3.8e-13
                         PQQ_2  24 plgggvsravlsggtlfva....tgggrlvaldaatGkvlWettlegpvvgap.lvaegrv...vvva...sdgqlialda 93 
                                   ++++ +  + +++g+++v+    +++g l++ld ++G vlW++ +++ v+++p l  e+++   ++ +   sdg+l+ l+ 
  gi|91773514|ref|YP_566206.1| 296 GFSTST--PAVHDGKVYVGqgehGYTGHLTCLDDSNGDVLWSYFVDAGVKSSPvLAVENEItyiYF-TgaeSDGSLYCLE- 372
                                   344444..788********777779***************************97888888866533.2578999******. PP

                         PQQ_2  94 edGkrlWstqqrseepaelrssaspavagdtvvvgessgklva 136
                                   edG+++W+ ++ +  ++  + +++ + +++++++g+ +g l++
  gi|91773514|ref|YP_566206.1| 373 EDGTLAWE-YDPT-DDVGYILQGAAI-SDGKIYFGTDGGYLYC 412
                                   ********.7777.677744444444.4689999998877765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.057
                         PQQ_2 116 aspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyassgqgrllal.dlatgr 194
                                   +                                                   ++v+a+++Vy+  g++  +   d+ tg+
  gi|91773514|ref|YP_566206.1| 457 S---------------------------------------------------STVIANNKVYVNCGDY--VRSlDQYTGE 483
                                   2...................................................2222233444444444..2222444433 PP

  == domain 5  score: 61.7 bits;  conditional E-value: 2.6e-20
                         PQQ_2   5 vsaldaatGaelWrvdlar....................plgggvsravlsggtlfvatgggrlvaldaatGkvlWettle 65 
                                   v+ ld+ tG+ l   + +                     p +  ++++v ++g+lf ++  g+ +++d  tG+++W+++ e
  gi|91773514|ref|YP_566206.1| 474 VRSLDQYTGEFLSNHSNGStkyksiaspayhdgnvwcglPDSVNSATTV-ADGKLFEGEWDGNYYCFDEVTGEEIWNFSTE 553
                                   6666666666666664422233444444444333333332233333466.******************************* PP

                         PQQ_2  66 gpvvgaplvaegrvvvva......sdgqlialdaedGkrlWstqqrse.epaelrssaspavagdtvvvges....sgklv 135
                                   g ++++p  +++rv++ +       +g+++ +da++G++lW  q +    +      +sp+++gd v+v +      g+++
  gi|91773514|ref|YP_566206.1| 554 GNAQATPAYDNERVYFTTwiygqtYGGNVYCVDANTGELLWD-QNEIInNCC-----SSPTIYGDIVYVTTYnfygEGEIY 628
                                   **************9999998887888***************.888853444.....59***********999999***** PP

                         PQQ_2 136 aldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyass 180
                                   al+  +G+ lW++ + ++             ++p va g+Vy+++
  gi|91773514|ref|YP_566206.1| 629 ALNKNNGSILWKEDIHSTD------------STPAVAYGNVYVAG 661
                                   *************996655............79999988999887 PP

  == domain 6  score: 47.5 bits;  conditional E-value: 5.5e-16
                         PQQ_2   2 egvvsaldaatGaelWrvdlarplgggvsravlsggtlfvat.....gggrlvaldaatGkvlWettlegpvvga...plv 74 
                                   eg+++al++++G++lW+ d++ + ++ +  av + g ++va+        + +++da tG+++W+tt+e  + g      +
  gi|91773514|ref|YP_566206.1| 624 EGEIYALNKNNGSILWKEDIH-STDSTP--AV-AYGNVYVAGgcygySDLQTYCFDAITGELKWNTTPEDGIGGWlcsVAI 700
                                   79****************993.244444..66.8899999954444466799****************55555544445** PP

                         PQQ_2  75 aegrvvvva.....sdg....qlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklva 136
                                   a+++++v +     +d+      +alda +G++ W+       p    + +spava d+ v+  ++gk++a
  gi|91773514|ref|YP_566206.1| 701 ADEKIFVGTafeteDDYtglnGTCALDAFTGELIWNS------P---FGGSSPAVA-DEMVFTIADGKVYA 761
                                   *********99997444667799*************2......2...235555555.44444444666655 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.6e-07   0.00077       2      32 ..      79     109 ..      78     114 .. 0.91
   2 !   20.6   0.0     1e-07    0.0003       1      25 [.     121     145 ..     121     149 .. 0.95
   3 !    8.8   0.3   0.00054       1.6      13      30 ..     180     196 ..     176     202 .. 0.89
   4 ?    0.4   0.0      0.25   7.3e+02      10      21 ..     219     230 ..     213     231 .. 0.88
   5 !   14.4   0.1   8.9e-06     0.027       6      37 ..     316     347 ..     307     348 .. 0.89
   6 !   10.6   0.1   0.00015      0.44       5      32 ..     360     387 ..     357     388 .. 0.86
   7 ?    3.8   0.3      0.02        59       1      14 [.     399     412 ..     399     413 .. 0.91
   8 ?   -2.7   0.0       2.4   7.2e+03      18      25 ..     440     447 ..     440     457 .. 0.84
   9 ?    2.8   0.0     0.041   1.2e+02       1      23 [.     464     485 ..     464     494 .. 0.89
  10 !   17.7   0.0   8.2e-07    0.0024       1      36 [.     525     560 ..     525     561 .. 0.92
  11 !   21.3   0.5   5.9e-08   0.00018       5      26 ..     574     596 ..     572     598 .. 0.86
  12 !   13.2   0.1   2.2e-05     0.066       9      25 ..     624     640 ..     613     649 .. 0.90
  13 !   11.7   0.1   6.4e-05      0.19      11      35 ..     670     694 ..     656     695 .. 0.88
  14 !    5.5   0.0    0.0061        18      12      24 ..     723     735 ..     718     744 .. 0.88
  15 ?   -2.7   0.1       2.3   6.9e+03       8      15 ..     755     762 ..     755     763 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.6e-07
                                   EEEEEETTSEEEEEETTTCCEEEEEESSSCG CS
                           PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpv 32 
                                    vy ++ +G ++A++  +G ++Wr kt+g  
  gi|91773514|ref|YP_566206.1|  79 LVYTHTTNGSVWAFNKHNGALIWRSKTSGGS 109
                                   79*************************9975 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1e-07
                                   TEEEEEETTSEEEEEETTTCCEEEE CS
                           PQQ   1 gvvylgsadGylyAlDadTGkvlWr 25 
                                   g+++++s+ G l+A+Da++G++lW+
  gi|91773514|ref|YP_566206.1| 121 GKLFVASNSGDLFAFDASSGEELWS 145
                                   789*********************7 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00054
                                   EEEETTTCCEEEEEESSS CS
                           PQQ  13 yAlDadTGkvlWrfktgg 30 
                                   y +D dTG++lW++ +g+
  gi|91773514|ref|YP_566206.1| 180 YCYD-DTGQLLWKYANGN 196
                                   7899.*********9986 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.25
                                   SEEEEEETTTCC CS
                           PQQ  10 GylyAlDadTGk 21 
                                   G+l+ lD +TG+
  gi|91773514|ref|YP_566206.1| 219 GKLLSLDKETGE 230
                                   89999******9 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 8.9e-06
                                   EETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                           PQQ   6 gsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                   + + G+l  lD ++G+vlW++ +++ v s+p+
  gi|91773514|ref|YP_566206.1| 316 HGYTGHLTCLDDSNGDVLWSYFVDAGVKSSPV 347
                                   5799*******999**************9997 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.00015
                                   EE.ETTSEEEEEETTTCCEEEEEESSSCG CS
                           PQQ   5 lg.sadGylyAlDadTGkvlWrfktggpv 32 
                                    g   dG ly l  ++G++ W++++ ++v
  gi|91773514|ref|YP_566206.1| 360 TGaESDGSLYCLE-EDGTLAWEYDPTDDV 387
                                   55678********.**********99876 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.02
                                   TEEEEEETTSEEEE CS
                           PQQ   1 gvvylgsadGylyA 14 
                                   g++y g+++Gyly 
  gi|91773514|ref|YP_566206.1| 399 GKIYFGTDGGYLYC 412
                                   79***********7 PP

  == domain 8  score: -2.7 bits;  conditional E-value: 2.4
                                   TTCCEEEE CS
                           PQQ  18 dTGkvlWr 25 
                                   dT+++lW 
  gi|91773514|ref|YP_566206.1| 440 DTNNMLWA 447
                                   699****7 PP

  == domain 9  score: 2.8 bits;  conditional E-value: 0.041
                                   TEEEEEETTSEEEEEETTTCCEE CS
                           PQQ   1 gvvylgsadGylyAlDadTGkvl 23 
                                   ++vy+ + d y++ lD +TG+ l
  gi|91773514|ref|YP_566206.1| 464 NKVYVNCGD-YVRSLDQYTGEFL 485
                                   789******.**********976 PP

  == domain 10  score: 17.7 bits;  conditional E-value: 8.2e-07
                                   TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                           PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                   g+++ g  dG+ y +D  TG+++W f t+g+ +++p
  gi|91773514|ref|YP_566206.1| 525 GKLFEGEWDGNYYCFDEVTGEEIWNFSTEGNAQATP 560
                                   57788899************************9998 PP

  == domain 11  score: 21.3 bits;  conditional E-value: 5.9e-08
                                   EE.ETTSEEEEEETTTCCEEEEE CS
                           PQQ   5 lg.sadGylyAlDadTGkvlWrf 26 
                                   +g +++G++y +Da+TG++lW  
  gi|91773514|ref|YP_566206.1| 574 YGqTYGGNVYCVDANTGELLWDQ 596
                                   455******************75 PP

  == domain 12  score: 13.2 bits;  conditional E-value: 2.2e-05
                                   TSEEEEEETTTCCEEEE CS
                           PQQ   9 dGylyAlDadTGkvlWr 25 
                                    G +yAl+ ++G +lW+
  gi|91773514|ref|YP_566206.1| 624 EGEIYALNKNNGSILWK 640
                                   699*************8 PP

  == domain 13  score: 11.7 bits;  conditional E-value: 6.4e-05
                                   EEEEEETTTCCEEEEEESSSCGSSE CS
                           PQQ  11 ylyAlDadTGkvlWrfktggpvlsl 35 
                                   + y +Da TG+++W + +++ + ++
  gi|91773514|ref|YP_566206.1| 670 QTYCFDAITGELKWNTTPEDGIGGW 694
                                   689***********99999988775 PP

  == domain 14  score: 5.5 bits;  conditional E-value: 0.0061
                                   EEEEETTTCCEEE CS
                           PQQ  12 lyAlDadTGkvlW 24 
                                    +AlDa TG+++W
  gi|91773514|ref|YP_566206.1| 723 TCALDAFTGELIW 735
                                   68*********** PP

  == domain 15  score: -2.7 bits;  conditional E-value: 2.3
                                   TTSEEEEE CS
                           PQQ   8 adGylyAl 15 
                                   adG++yA+
  gi|91773514|ref|YP_566206.1| 755 ADGKVYAF 762
                                   59****97 PP

>> Pepsin-I3  Pepsin inhibitor-3-like repeated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     5e-05      0.15      21      59 ..     458     497 ..     441     501 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                     Pepsin-I3  21 GCvVqdNklyvg.giylRdLtseEqsELktydaevtkYke 59 
                                     v+ +Nk+yv+ g y+R L     + L  + +++tkYk 
  gi|91773514|ref|YP_566206.1| 458 STVIANNKVYVNcGDYVRSLDQYTGEFLSNHSNGSTKYKS 497
                                   5699*******9899*******99999***********96 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.95   2.8e+03       6      17 ..     255     266 ..     252     278 .. 0.80
   2 ?   -1.6   0.0       1.3   3.8e+03       8      20 ..     303     315 ..     297     329 .. 0.77
   3 ?   -3.1   0.0       3.8   1.1e+04      13      33 ..     356     371 ..     352     384 .. 0.66
   4 ?    7.6   0.1    0.0017         5       4      23 ..     456     475 ..     454     492 .. 0.82
   5 ?    2.4   0.1     0.072   2.2e+02       6      39 ..     650     680 ..     645     689 .. 0.66
   6 ?   -1.7   0.0       1.4   4.2e+03       4      16 ..     695     707 ..     693     711 .. 0.88
   7 ?    0.1   0.0      0.38   1.1e+03       8      18 ..     753     763 ..     751     773 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.95
                       Kelch_6   6 slvsvggkiYif 17 
                                   s++ ++g+iY  
  gi|91773514|ref|YP_566206.1| 255 SVTYHDGYIYTT 266
                                   5566999***75 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                       Kelch_6   8 vsvggkiYifGGy 20 
                                   ++++gk+Y+  G 
  gi|91773514|ref|YP_566206.1| 303 AVHDGKVYVGQGE 315
                                   6799****96555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.8
                       Kelch_6  13 kiYifGGytdsspylnkvwvy 33 
                                   +iY  G  +d      +++++
  gi|91773514|ref|YP_566206.1| 356 YIYFTGAESD-----GSLYCL 371
                                   6787888777.....555555 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0017
                       Kelch_6   4 ghslvsvggkiYifGGytds 23 
                                   g s+v++++k+Y+ +G +  
  gi|91773514|ref|YP_566206.1| 456 GSSTVIANNKVYVNCGDYVR 475
                                   6899************9764 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.072
                       Kelch_6   6 slvsvggkiYifGGytdsspylnkvwvydpetks 39 
                                   ++v++g+ +Y++GG +++  +  + +++d +t+ 
  gi|91773514|ref|YP_566206.1| 650 PAVAYGN-VYVAGGCYGY--SDLQTYCFDAITGE 680
                                   5677777.9999987663..22455777777765 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 1.4
                       Kelch_6   4 ghslvsvggkiYi 16 
                                    +s++++++ki++
  gi|91773514|ref|YP_566206.1| 695 LCSVAIADEKIFV 707
                                   5899*******98 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 0.38
                       Kelch_6   8 vsvggkiYifG 18 
                                   ++++gk+Y+fG
  gi|91773514|ref|YP_566206.1| 753 TIADGKVYAFG 763
                                   5699******8 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.6     0.004        12       2      11 ..     777     786 ..     776     799 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.004
                     PGF-CTERM   2 PGFGavlAla 11 
                                   PGFG+++A++
  gi|91773514|ref|YP_566206.1| 777 PGFGSLFAIV 786
                                   *********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (809 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 5170.08
//
Query:       gi|91773515|ref|YP_566207.1|  [L=366]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  102.4   0.0    4.9e-29  101.6   0.0    1.4  1  ABC_tran     ABC transporter
    1.1e-10   41.9   0.3    3.4e-06   27.1   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      2e-08   34.3   0.0    6.4e-08   32.7   0.0    1.9  2  TOBE_2       TOBE domain
    0.00027   20.4   0.0      0.013   15.0   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0009   19.8   0.0     0.0014   19.2   0.0    1.3  1  AAA_23       AAA domain
     0.0032   17.7   0.1     0.0061   16.8   0.1    1.5  1  TOBE         TOBE domain
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.026   14.9   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.016   15.5   0.4      0.052   13.8   0.4    1.9  1  AAA_22       AAA domain
      0.055   13.2   0.0      0.097   12.4   0.0    1.3  1  AAA_30       AAA domain
      0.064   13.5   0.5       0.68   10.2   0.5    2.4  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.07   12.9   0.0       0.16   11.8   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
      0.095   13.1   0.0          1    9.8   0.0    2.5  1  AAA          ATPase family associated with various cellular a
       0.11   12.4   0.0       0.26   11.2   0.0    1.5  2  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0   3.6e-32   4.9e-29      11     136 ..      34     170 ..      25     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 3.6e-32
                                   TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHHHH........ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                      ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvren........ 79 
                                   +e+v+++G++G+GK+t l+++agl++p+ G+i ++gk   +    ++l+   ++ g+++q+  lfp++ v++n        
  gi|91773515|ref|YP_566207.1|  34 DELVVLFGRSGSGKTTTLRCIAGLETPECGNIVVNGKTYYDsesgIDLKPQYRRPGYVFQNYALFPHMDVGKNivyglkgw 114
                                   5899*******************************999999999*9*********************************** PP

                                   ...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                      +++e++ ++l+ l +++l+ +      s+LSgGqkqrvalaral+  p++lllDEp+
  gi|91773515|ref|YP_566207.1| 115 speKKKERLFEMLRLLHIEGLEGRYP----SQLSGGQKQRVALARALAPSPDILLLDEPF 170
                                   99888888999999999999888888....*****************************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 !   13.1   0.0   4.4e-05     0.061       1      22 [.      36      57 ..      36      80 .. 0.90
   2 !   27.1   0.0   2.5e-09   3.4e-06     220     300 ..     126     204 ..      74     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                        AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                  l vl G+ gsGK++ L+++ +l
  gi|91773515|ref|YP_566207.1| 36 LVVLFGRSGSGKTTTLRCIAGL 57
                                  579****************998 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 2.5e-09
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                    +++l+ ++   + +++lS G+k+  al+ al+  +   ++ll+DEp + L+  +  rl e +k  ++  g+ +++ THSp
  gi|91773515|ref|YP_566207.1| 126 MLRLLHIEGLEGRYPSQLSGGQKQRVALARALAPSP---DILLLDEPFSALDMVVRMRLRERIKVIQKeLGIPIMFITHSP 203
                                   7888999999999************89999999877...************************8888889*********** PP

                        AAA_21 300 l 300
                                   +
  gi|91773515|ref|YP_566207.1| 204 E 204
                                   6 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.1     7e+03      35      53 ..     139     157 ..     134     162 .. 0.69
   2 !   32.7   0.0   4.6e-11   6.4e-08       2      76 .]     286     365 ..     285     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.1
                        TOBE_2  35 yvvelaggqlvvvrqpnad 53 
                                   y  +l ggq+++v+ + a 
  gi|91773515|ref|YP_566207.1| 139 YPSQLSGGQKQRVALARAL 157
                                   5557888998888877664 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 4.6e-11
                        TOBE_2   2 aiRPEklrla.......aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsala..pGdtVelswdpdda 73 
                                   ++RPE+++l        +++g n ++Gt+ dv+  Gss ++ vel+g + v+   ++ +r   l+   G++V + + + d+
  gi|91773515|ref|YP_566207.1| 286 GVRPENIHLMvynedslSDEG-NVFAGTILDVTDKGSSKLMAVELDGSNVVL-FCDVPTR--LLDdvQGSRVIVKIAANDV 362
                                   79**********998655555.9************************98855.5555554..444459************* PP

                        TOBE_2  74 vvl 76 
                                   +v+
  gi|91773515|ref|YP_566207.1| 363 LVF 365
                                   998 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.04        55      19      44 ..      29      54 ..      24      56 .. 0.81
   2 !   15.0   0.0   9.1e-06     0.013     133     209 ..     139     214 ..      92     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.04
                                  EEETTSSEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 19 ilpfsksftaivGpNGSGKsnlldAi 44
                                  + ++ +++ ++ G+ GSGK+  l  i
  gi|91773515|ref|YP_566207.1| 29 SFEVGDELVVLFGRSGSGKTTTLRCI 54
                                  5667788999*********9877665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 9.1e-06
                                   STTCS-HHHHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SS.HHHCCC-SCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.xxxxxxxxxxx RF
                         SMC_N 133 skelLSgGektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkekskn..aQfivislr.eemlekadklv 209
                                   ++++LSgG+k+ vala  +A     p+p + llDe  +aLD   + ++ e++k  +k+    ++ i+++ ee ++ ad++v
  gi|91773515|ref|YP_566207.1| 139 YPSQLSGGQKQRVALARALA-----PSPdILLLDEPFSALDMVVRMRLRERIKVIQKElgIPIMFITHSpEEAFSLADRVV 214
                                   4669*********9997765.....6665899*********************8877733556666765256777777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     1e-06    0.0014      12      40 ..      27      55 ..      11      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-06
                        AAA_23 12 dqeidFskgltlItGpNGaGKTTildAik 40
                                  d++++ ++ l++++G  G+GKTT l++i 
  gi|91773515|ref|YP_566207.1| 27 DVSFEVGDELVVLFGRSGSGKTTTLRCIA 55
                                  45667799*******************97 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   4.4e-06    0.0061       4      63 ..     306     363 ..     303     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.4e-06
                          TOBE   4 rNqlpgtVvvveplgseveVrvdlggga.tLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                    N++ gt++ v+++gs+ +  v+l+g +  L + v++r  ++     G++V + i a++v 
  gi|91773515|ref|YP_566207.1| 306 GNVFAGTILDVTDKGSSKLMAVELDGSNvVLFCDVPTRLLDD---VQGSRVIVKIAANDVL 363
                                   69****************************************...99*********99986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.9e-05     0.026      25      62 ..      35      73 ..      25      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                        AAA_16 25 elvllsGesGvGKsslvrellralekd..ggiflrgkcdq 62
                                  elv+l G sG+GK++ +r+++  le+   g i+++gk+  
  gi|91773515|ref|YP_566207.1| 35 ELVVLFGRSGSGKTTTLRCIAG-LETPecGNIVVNGKTYY 73
                                  79******************94.55554656777777655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   3.8e-05     0.052       6      26 ..      35      55 ..      31     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                        AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                   ++v++G sG+GKTt+lr ++
  gi|91773515|ref|YP_566207.1| 35 ELVVLFGRSGSGKTTTLRCIA 55
                                  6789*************9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     7e-05     0.097      17      45 ..      33      61 ..      28      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7e-05
                        AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa 45
                                  gd ++vl G+ G+GKtt+l+ ++ + + +
  gi|91773515|ref|YP_566207.1| 33 GDELVVLFGRSGSGKTTTLRCIAGLETPE 61
                                  67799***************998877666 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 ?   10.2   0.5    0.0005      0.68      61      81 ..     158     178 ..     137     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                       SbcCD_C  61 epalrlvfLDEAFsklDeesi 81 
                                    p++++++LDE Fs lD   +
  gi|91773515|ref|YP_566207.1| 158 APSPDILLLDEPFSALDMVVR 178
                                   5789*************8665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.16      18      45 ..      29      57 ..      24      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                        AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqal 45
                                  ++++ +  ++l G+sGsGK+T l  i+ l
  gi|91773515|ref|YP_566207.1| 29 SFEVGDeLVVLFGRSGSGKTTTLRCIAGL 57
                                  5555566899***********88666655 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 ?    9.8   0.0   0.00074         1       1      22 [.      37      58 ..      37     192 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00074
                                  EEEESSTTSSHHHHHHHHHHHH CS
                           AAA  1 vllyGppGtGKTllakavakel 22
                                  v+l+G  G GKT++ + +a   
  gi|91773515|ref|YP_566207.1| 37 VVLFGRSGSGKTTTLRCIAGLE 58
                                  689***************9863 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.26      93     128 ..      28      63 ..      18      70 .. 0.82
   2 ?   -3.7   0.0       7.1   9.8e+03      61      85 ..     178     202 ..     171     214 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                   HHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S CS
                   RsgA_GTPase  93 lkellkdktsvlvGqSGvGKStLinallpelelktg 128
                                   ++ ++ d+++vl G SG GK+t +  +++ ++ + g
  gi|91773515|ref|YP_566207.1|  28 VSFEVGDELVVLFGRSGSGKTTTLRCIAGLETPECG 63 
                                   56677899***************9999886665555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.1
                                   HHHHHHHHHHHHHHTTSEEEE--TT CS
                   RsgA_GTPase  61 eeeeleelkeelealgyevllvsak 85 
                                   +++  e++k   ++lg++++++  +
  gi|91773515|ref|YP_566207.1| 178 RMRLRERIKVIQKELGIPIMFITHS 202
                                   5554566677777888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2357.28
//
Query:       gi|91773516|ref|YP_566208.1|  [L=222]
Description: molybdate ABC transporter inner membrane protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-21   75.8  17.5    4.1e-21   75.5  17.5    1.2  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5  17.5   2.3e-25   4.1e-21       1     181 [.      27     218 ..      13     222 .] 0.84

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.3e-25
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilg..hlilpviillllsaapyvr 69 
                                   gil+++ +a +r +++++l ++l+ ++l lP+ v + llv+++          + ++++   +++ +++i++++ ++p+++
  gi|91773516|ref|YP_566208.1|  27 GILISYALA-RRDFRGKWLADILVTLPLVLPPTVTGYLLVVLLgrngaigsflFEITGWSllFTWHAAVIAAFVVSLPLMV 106
                                   566667777.******************************999********99444444422555569************* PP

                  BPD_transp_1  70 lirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgy 148
                                    ++++a+++++++l+ aa++lG s+ +++  v+lP+a+  i++g++l+f++++g++ ++++++++ +   +t+ l+++ ++
  gi|91773516|ref|YP_566208.1| 107 KTTASAISAVDRELEYAAYTLGHSELETMLFVTLPLAKKGILAGIVLSFARAVGEFGATLMVAGNIPgkTNTMSLSIYTAF 187
                                   **************************************************************9887745555555555555 PP

                  BPD_transp_1 149 dyseisnggvlalviavlllnlvadilqrlldp 181
                                   +  +   +++ +lvi +++++lv++++++ +  
  gi|91773516|ref|YP_566208.1| 188 QSGND--ALANILVITLVVVSLVSMAMAAKFVD 218
                                   55444..48888888888888888887766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1578.85
//
Query:       gi|91773517|ref|YP_566209.1|  [L=266]
Description: molybdenum ABC transporter, periplasmic molybdate-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-47  162.8   0.0    1.2e-47  162.6   0.0    1.0  1  SBP_bac_11      Bacterial extracellular solute-binding protei
    2.4e-15   57.3   0.0    2.1e-13   50.9   0.0    2.0  1  SBP_bac_1       Bacterial extracellular solute-binding protei
    2.2e-05   24.2   0.3    2.9e-05   23.8   0.3    1.3  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0048   16.3   0.1     0.0074   15.7   0.1    1.3  1  SBP_bac_6       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.016   14.8   0.0       0.02   14.5   0.0    1.3  1  OpuAC           Substrate binding domain of ABC-type glycine 
      0.019   14.8   0.2      0.037   13.8   0.2    1.7  1  SBP_bac_8       Bacterial extracellular solute-binding protei
      0.056   14.1   0.0       0.12   13.0   0.0    1.5  1  DUF4404         Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.0   4.7e-51   1.2e-47       1     229 [.      37     260 ..      37     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 4.7e-51
                                   .EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEE CS
                    SBP_bac_11   1 ltvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassp 80 
                                   +tv aa+sl++ ++e+ ++F e h+++++++  +gsg+l+ qi++ga+ Dv+++as+++++ll +++l+ a++++++a + 
  gi|91773517|ref|YP_566209.1|  37 VTVSAAASLTESFTEIENKFeEGHPDIDIVLNLAGSGTLRMQIEAGAPIDVFASASQKHMDLLGSENLIYADTRNDFAENS 117
                                   5999****************555********************************************************** PP

                                   EEEEESTT-TT---SHHHHHHSS-.-EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHHHTTT-S CS
                    SBP_bac_11  81 lviavpkgnpkkikgwadLlkpgl.klavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltaveagead 160
                                   lv++vp+++ ++ik+++dL++ ++ k+a+ dP+ +p+G++++ +le a    l++ +++k   ++es+ q+l +ve+ge+d
  gi|91773517|ref|YP_566209.1| 118 LVMIVPEPSRNDIKSLEDLADGSItKIAIGDPEIAPVGRYTKDALETAF---LWDDVSDKLI-YAESVKQVLVYVESGEVD 194
                                   ***********************999***********************...*********9.****************** PP

                                   EEEEEHHHHH..HSTTSSEEE.E--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                    SBP_bac_11 161 agivyeseakaaengdkleav.ylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrkyGf 229
                                   ag+vy ++a+  +  dk+++v  +p ++    + yp+av++ ++k  a ++F++++ s+e+++i+ kyGf
  gi|91773517|ref|YP_566209.1| 195 AGFVYMTDAM-SSDMDKIDVVaQIPVSTS---ISYPIAVVSFSDKTIASQEFIDYVISDEGKDIFVKYGF 260
                                   *********9.356777777777777777...79************************************ 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 !   50.9   0.0   8.1e-17   2.1e-13       2     314 ..      43     252 ..      40     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 8.1e-17
                                   GSHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHT..TSBECCHHHHH CS
                     SBP_bac_1   2 gsltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlaka..glllpldpyvk 79 
                                   +slte  ++ ++  ++fe+ hp+i+++++  gsg+l+     +i+aG+ p+Dv+a+ +  +++ l ++   ++   +++++
  gi|91773517|ref|YP_566209.1|  43 ASLTE--SFTEIE-NKFEEGHPDIDIVLNLAGSGTLRM----QIEAGA-PIDVFASaSQKHMDLLGSEnlIYADTRNDFAE 115
                                   67778..888888.88**********************....******.*******9999999999998889999999999 PP

                                   HTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEE CS
                     SBP_bac_1  80 aylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggs 160
                                   + l+ +v++   ++++                                      + ++l++     ++ g  +        
  gi|91773517|ref|YP_566209.1| 116 NSLVMIVPEPSRNDIK--------------------------------------SLEDLADGSITKIAIGDPE-------- 150
                                   9998888887777655......................................6667776666666666666........ PP

                                   HHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEE CS
                     SBP_bac_1 161 asgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivg 241
                                                               ++p+g +++++l+ ++    l ++ ++k  + +++ ++l  +e+Ge+++++v+
  gi|91773517|ref|YP_566209.1| 151 ----------------------------IAPVGRYTKDALETAF----LWDDVSDKLIYAESVKQVLVYVESGEVDAGFVY 199
                                   ............................6666666666666666....4449****************************9 PP

                                   HHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                     SBP_bac_1 242 lwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                    ++               ++++ +++++v +   + +      ++y++a+++ s++  a ++F+d++ s+e++
  gi|91773517|ref|YP_566209.1| 200 MTD---------------AMSSDMDKIDVVAQIPVST-----SISYPIAVVSFSDKTIASQEFIDYVISDEGK 252
                                   877...............3333333333333222222.....39***************************97 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.3   1.1e-08   2.9e-05      84     198 ..     115     229 ..      34     264 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.1e-08
                                   EEEEEEEEETTS..S--SHHHH...GG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEE.EE--HHHHHHHHHTTSS CS
                Phosphonate-bd  84 syrsviivrads..diqsledL...kgktiafvspsStsGylvpaalLvkeagldpeddfsev.fsgshdaavlavlsgda 158
                                   + + v+iv++ s  di+sledL      +ia+++p+ +    + +  L + a l  +d  ++  ++ s  ++++ v sg++
  gi|91773517|ref|YP_566209.1| 115 ENSLVMIVPEPSrnDIKSLEDLadgSITKIAIGDPEIAPVGRYTKDAL-ETAFLW-DDVSDKLiYAESVKQVLVYVESGEV 193
                                   677899***998556*******8666689*******99999999999*.899887.45555556***************** PP

                                   SEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEE...EE--EEEE CS
                Phosphonate-bd 159 daaavsadaledlvaegpedkdelrviasspp...ipndpvvv 198
                                   da++v+ + +++       d+d++ v+a++p+   i ++p++v
  gi|91773517|ref|YP_566209.1| 194 DAGFVYMTDAMSS------DMDKIDVVAQIPVstsI-SYPIAV 229
                                   *****98866542......45566666554431104.344444 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 !   15.7   0.1   2.9e-06    0.0074     139     214 ..     188     260 ..     164     266 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-06
                     SBP_bac_6 139 lesgepavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkgkkkelakafidfllspevqailakagg 214
                                   +esge  v+ ++ +++d++ ++ +   +   +P + ++ +pi+++  ++ k    ++fid+  s+e+  i++k g+
  gi|91773517|ref|YP_566209.1| 188 VESGE--VDAGFVYMTDAMSSDMDKIDVVAQIPVSTSISYPIAVVSFSD-KTIASQEFIDYVISDEGKDIFVKYGF 260
                                   78999..9**************9666777779*****************.**********************9997 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.9e-06      0.02      85     187 ..     115     209 ..      51     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.9e-06
                                   EECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSCEEEEHH....H CS
                         OpuAC  85 gnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgldkvelvegseaamda....e 161
                                   +n   ++vp+    +++iks++DL++ +       ++  +g p  +++ + t+ +l++  l  + +v  s + ++a    +
  gi|91773517|ref|YP_566209.1| 115 ENSLVMIVPEPS--RNDIKSLEDLADGSI------TKIAIGDPEIAPVGRYTKDALETAFL--WDDV--SDKLIYAesvkQ 183
                                   444445555444..79********88888......78999999999999999988888888..7776..666666655778 PP

                                   HHHHHHTTCSSEEEEETTSTHHHHTT CS
                         OpuAC 162 lyaaykrgepvvvyawtPdwaikkyd 187
                                   +   +++ge+++++++ +d++ +++d
  gi|91773517|ref|YP_566209.1| 184 VLVYVESGEVDAGFVYMTDAMSSDMD 209
                                   88899*****************9997 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 ?   13.8   0.2   1.5e-05     0.037     159     258 ..     162     258 ..      36     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS-HHHHHH CS
                     SBP_bac_8 159 kealellkklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavpknaknedlaA 239
                                    e++ l+++ +d+  + ++  ++   + +Gev +++ +  d+ + + ++ ++ a +p ++s++    +av + +++   a+
  gi|91773517|ref|YP_566209.1| 162 LETAFLWDDVSDKLIYAESVKQVLVYVESGEVDAGFVYMTDAMSSDMDKIDVVAQIPVSTSISYP--IAVVSFSDKTI-AS 239
                                   55566788888888888888999999999999999999999999888788888889877666554..99*******99.6* PP

                                   HHHHHHHTTSHHHHHHHHH CS
                     SBP_bac_8 240 ldFlkwltspenqaalaek 258
                                   ++F+ ++ s+e+   +++ 
  gi|91773517|ref|YP_566209.1| 240 QEFIDYVISDEGKDIFVKY 258
                                   ************9998884 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.8e-05      0.12      43      72 ..      39      68 ..      30      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                       DUF4404 43 aaeeeelaerlneaverFeeeHPklagvlr 72
                                   +++++l+e  +e+ ++Fee HP+++ vl+
  gi|91773517|ref|YP_566209.1| 39 VSAAASLTESFTEIENKFEEGHPDIDIVLN 68
                                  455556********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1947.90
//
Query:       gi|91773518|ref|YP_566210.1|  [L=116]
Description: hypothetical protein Mbur_1554 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 803.13
//
Query:       gi|91773519|ref|YP_566211.1|  [L=135]
Description: phenylacetic acid degradation-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   38.3   0.1    1.7e-09   37.9   0.1    1.2  1  4HBT      Thioesterase superfamily
    0.00059   20.0   0.2     0.0008   19.5   0.2    1.2  1  DUF4442   Domain of unknown function (DUF4442)
     0.0049   16.1   0.0     0.0064   15.8   0.0    1.2  1  PS-DH     Polyketide synthase dehydratase


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   2.8e-13   1.7e-09       2      77 ..      44     115 ..      43     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.8e-13
                                   SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                          4HBT   2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                   G+v gG++++l+D a +aa +s+g    ++v+++ +i f+ + + g +l+++ar +    ++a+++v+++de+g  
  gi|91773519|ref|YP_566211.1|  44 GIVQGGAIFTLADFAFAAASNSHGT---VAVAINANISFVTSTTSG-TLYAQARENSKNPKIATYTVDITDEEGNA 115
                                   8999********************6...9*****************.*************************9975 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.3e-07    0.0008      18     122 ..      16     115 ..       6     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                                   GG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-.--S-EEEEEE CS
                       DUF4442  18 tvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlak.atgdltavae 97 
                                    + ++  e++ g+a++++     + N +g v ++Ai++la++a+     a+  ++ + +  +++++++   + g+l a+a+
  gi|91773519|ref|YP_566211.1|  16 HIDIKLLEVSEGYAKAKMDIHEHHLNGVGIVQGGAIFTLADFAFA---AASNSHGTVAVAINANISFVTStTSGTLYAQAR 93 
                                   5788999***********************************986...566678889999999****98736688999997 PP

                                   -TTS-TT--EEEEEEEEEEETTE.E CS
                       DUF4442  98 lepedvgekeelvvevevrdekgee 122
                                    ++++    +  + +v+++de+g+ 
  gi|91773519|ref|YP_566211.1|  94 ENSKN---PKIATYTVDITDEEGNA 115
                                   66543...44556677777777755 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-06    0.0064     239     289 ..      77     125 ..      46     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-06
                                   EEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEESEEEE CS
                         PS-DH 239 lrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieglrlr 289
                                   +++   +s+  ++l+++ar ++++ + +++ ++++de+G+++a ++g+  r
  gi|91773519|ref|YP_566211.1|  77 ISFV--TSTTSGTLYAQARENSKNPKIATYTVDITDEEGNAIAIFQGMAYR 125
                                   3333..467889***********************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 958.95
//
Query:       gi|91773520|ref|YP_566212.1|  [L=232]
Description: HAD family hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-29  102.4   0.0    3.7e-29  102.1   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    7.3e-14   52.6   0.2    1.7e-12   48.1   0.2    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    5.3e-05   23.2   0.0    0.00012   22.1   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
     0.0019   18.7   0.1     0.0036   17.7   0.1    1.5  1  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   8.2e-33   3.7e-29       1     178 []       5     183 ..       5     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 8.2e-33
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee...kieellrkyneekkk.ke 77 
                                   +iFD+Dg+l+d+ +++ +a+ ++++e+g+ +++  ++ ++ g ++ e++r l e++  +    +++el+++y++e  +  e
  gi|91773520|ref|YP_566212.1|   5 LIFDMDGVLVDSMPYHTEALSHVFAEMGF-SMDARHVYNMEGSKTVEIVRFLLEKDGIDLlevDVDELIHRYRDEFARiVE 84 
                                   69**************************9.9***********************988777999***************999 PP

                         HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyv 158
                                   +k +++v e L  L ++++ l++v+  +r+ v++ +++l    +Fdv++++edv + KP+p++++ a + ++l+++e+++v
  gi|91773520|ref|YP_566212.1|  85 LKAFSEVLECLPIL-KERFMLAVVSGADRNIVQDIITNLY-GGIFDVVISGEDVDNGKPAPDPFLSAADMFGLDANECLVV 163
                                   **************.789********************98.69************************************** PP

                         HAD_2 159 GDsptDieaakkagikviav 178
                                   +    ++eaa +ag+ ++av
  gi|91773520|ref|YP_566212.1| 164 ENAAMGVEAANRAGMFCLAV 183
                                   ***************99987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.2   3.7e-16   1.7e-12       2     210 .]       3     177 ..       2     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.7e-16
                                   SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltaldi 82 
                                   k+++fD+dG+L+++ p +++++  +                      a  + s +   +             +e ++ l  
  gi|91773520|ref|YP_566212.1|   3 KALIFDMDGVLVDSMPYHTEALSHV---------------------FAEMGFSMDARHVYN-----MEGSKTVEIVRFL-- 55 
                                   89********************999.....................444444555544444.....2223333344444.. PP

                                   HHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TTGGGESE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                     Hydrolase  83 ppdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lGddyfda 162
                                      l+++  ++ + + ++ ++  r++ +f+   +lk + e+ e++  Lk++   +++++g +++ ++ ++ + +G  +fd+
  gi|91773520|ref|YP_566212.1|  56 ---LEKDGIDLLEVDVDELIH--RYRDEFARIVELKAFSEVLECLPILKERFM-LAVVSGADRNIVQDIITNlYG-GIFDV 129
                                   ...555889999999999999..***************************977.*************66666599.***** PP

                                   EEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 163 viasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   vi+++++  +kp p+ ++ a++ ++ + +e+++V+  + +++a+ +Ag
  gi|91773520|ref|YP_566212.1| 130 VISGEDVDNGKPAPDPFLSAADMFGLDANECLVVENAAMGVEAANRAG 177
                                   *********************************************998 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.7e-08   0.00012       3      56 ..     139     191 ..     138     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.7e-08
                                   STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TT CS
                Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpe 56 
                                   gKP+p  + +a+  +g+d +e+l++    a  +++An+aG+ +++V t v++++
  gi|91773520|ref|YP_566212.1| 139 GKPAPDPFLSAADMFGLDANECLVVENA-AMGVEAANRAGMFCLAVPTYVSKES 191
                                   9*************************99.*****************99887764 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   7.9e-07    0.0036       2     139 ..       6     137 ..       5     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.9e-07
                           HAD   2 lfDfDgTLldgdsle......lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerf 76 
                                   +fD+Dg L+d+ +++      ++++    ++a++ + +   k+ +++   ++ l+++g++ l+       +e ++++ ++f
  gi|91773520|ref|YP_566212.1|   6 IFDMDGVLVDSMPYHtealshVFAEMGFSMDARHVYNMEGSKTVEIV---RFLLEKDGIDLLEVD----VDELIHRYRDEF 79 
                                   8**********999999666555555555555555555555566666...444433344433333....333333333333 PP

                           HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepll.aelg..adevlatelevddrlt 139
                                    + v ++ ++  ++le l    ++ + ++vvSg+ r +v+ +  +++g  +d v++ e     +++
  gi|91773520|ref|YP_566212.1|  80 ARIVELK-AF-SEVLECLPIL-KERFMLAVVSGADRNIVQDIItNLYGgiFDVVISGE-----DVD 137
                                   3222222.36.5666666633.6779*****************99*****9*999995.....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1756.17
//
Query:       gi|91773521|ref|YP_566213.1|  [L=131]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for 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-25   86.9   0.1    1.1e-24   86.7   0.1    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.1   6.2e-29   1.1e-24       1     111 [.       7     117 ..       7     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 6.2e-29
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEEEESS CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpg.mdGlellkeireedpelpviiltah 80 
                                   +l+v+D+ +v+  +++ le+ gy++  +a++g+ea+ +++   +dl+l+Di++ g mdG+e+++eir++  ++pvi+lta+
  gi|91773521|ref|YP_566213.1|   7 ILVVEDENIVALSIKNKLESLGYSVPSTASSGEEAITKADLFYPDLVLMDIMLRGdMDGIEAANEIRTKF-DIPVIFLTAY 86 
                                   8**********************7777**************************999************99.********** PP

                                   TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                   ++++++++a  a+ ++++sKpf++++L++ +
  gi|91773521|ref|YP_566213.1|  87 TDDNTLEKAKVAEPYGYISKPFKEQDLKSNI 117
                                   ***************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1063.11
//
Query:       gi|91773522|ref|YP_566214.1|  [L=142]
Description: rhodanese-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-19   68.7   0.0    7.1e-19   68.3   0.0    1.2  1  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.045   13.6   0.0    1.5  1  DUF4307    Domain of unknown function (DUF4307)


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 !   68.3   0.0     8e-23   7.1e-19       2     106 ..      46     135 ..      45     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 8e-23
                     Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaa 82 
                                   ++e+k++++kg+v llDvR++ e++ gh++gAvn+             +  +l ++l e     +k + vyc++g r+ +a
  gi|91773522|ref|YP_566214.1|  46 VHEAKDIFDKGDVFLLDVRTESEFNSGHLEGAVNI-------------EVSQLGTRLNEA--PADKVILVYCRTGVRSVRA 111
                                   6899********99*********************.............888888888888..8899***********9999 PP

                     Rhodanese  83 aallkklGyknvsvldGGfkawke 106
                                    ++l  +Gy++v++++GG++aw +
  gi|91773522|ref|YP_566214.1| 112 SKTLVNAGYTDVYNMKGGIMAWMS 135
                                   887777**999***********86 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     5e-06     0.045       7      48 ..       9      50 ..       7      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-06
                       DUF4307  7 illvvlvvvalalvawigysqgsadvsaevvgfevvddstve 48
                                   +lv+l+v+a +++++igy++ +++ ++++v++++v+ ++++
  gi|91773522|ref|YP_566214.1|  9 TMLVILLVIACIALGFIGYDKFAPNQNGTDVSYTDVSVHEAK 50
                                  5799*******************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1086.07
//
Query:       gi|91773523|ref|YP_566215.1|  [L=80]
Description: hypothetical protein Mbur_1560 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   47.6  10.4    1.9e-12   47.6  10.4    1.8  2  DUF2769   Protein of unknown function (DUF2769)


Domain annotation for each model (and alignments):
>> DUF2769  Protein of unknown function (DUF2769)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.12   2.2e+03       6      11 ..      17      22 ..      15      25 .. 0.72
   2 !   47.6  10.4   1.1e-16   1.9e-12       1      57 [.      26      75 ..      26      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.12
                       DUF2769  6 Cpsyta 11
                                  Cps+++
  gi|91773523|ref|YP_566215.1| 17 CPSFHH 22
                                  999984 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 1.1e-16
                       DUF2769  1 CiCkkCpsytaeckkkelellFCargksekcieeekgClCpeCevykeykLkeeyyC 57
                                  C+Ck+Cpsy+   ++    ++FCarg+  +   e+k+ClC+eC vyk+++++++++C
  gi|91773523|ref|YP_566215.1| 26 CNCKRCPSYP---GDG---YMFCARGND-RPLPEKKECLCRECYVYKQFGFEGDFFC 75
                                  **********...444...5********.8888888********************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 671.63
//
Query:       gi|91773524|ref|YP_566216.1|  [L=230]
Description: fibrillarin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-93  311.2   0.1    3.1e-93  311.0   0.1    1.0  1  Fibrillarin  Fibrillarin
     0.0016   18.2   0.0     0.0021   17.8   0.0    1.2  1  GCD14        tRNA methyltransferase complex GCD14 subunit


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 !  311.0   0.1   3.5e-97   3.1e-93       4     225 ..       4     226 ..       1     227 [. 0.97

  Alignments for each domain:
  == domain 1  score: 311.0 bits;  conditional E-value: 3.5e-97
                                   ECSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHH CS
                   Fibrillarin   4 heklegvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGtt 84 
                                   +e  eg+++v++ g++ latkn++pg++vYgE+l++ e+eEyR W+++rsKlaa+++k++k +pik++s+vLYlGaasGtt
  gi|91773524|ref|YP_566216.1|   4 NEISEGIFEVRKGGKKILATKNANPGSNVYGENLLEEEGEEYRAWDARRSKLAAMVIKKMK-VPIKSNSRVLYLGAASGTT 83 
                                   67899******999999*******************************************8.9****************** PP

                                   HHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHHE CS
                   Fibrillarin  85 vsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklfl 165
                                   vsHvsD++  +g+vyavefspr++reli+++++R+nivPil+DA++P+ Y+++ve+vDvif+Dvaqp+qa+i+a na  fl
  gi|91773524|ref|YP_566216.1|  84 VSHVSDMLP-NGIVYAVEFSPRTMRELIQLCDTRSNIVPILADASRPKLYAHIVEQVDVIFQDVAQPNQAQIAAVNAGQFL 163
                                   *******98.*********************************************************************** PP

                                   EEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHH...TTEEEEEEEE-TTTSTTEEEEEEEEE CS
                   Fibrillarin 166 keggyllisikarsidvtkepeevfkeeveklke...eglkvleqvklepyekdhalvvgkyk 225
                                   ke+gyll+sikarsid++++p++vfkeev+kl++   +++kv+++++l p+++dh+ +++k+k
  gi|91773524|ref|YP_566216.1| 164 KEDGYLLLSIKARSIDTVANPSKVFKEEVNKLEKdfdTQFKVIKKYDLAPFHEDHLGLIAKKK 226
                                   *********************************86668********************99875 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-07    0.0021      33     161 ..      62     190 ..      53     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-07
                         GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgk 113
                                    mk+ +k  s+v+  G+ sg+  + ++  + P G ++++ef  + +++ +   +  +  +++     D+ +  + +++ ++
  gi|91773524|ref|YP_566216.1|  62 KMKVPIKSNSRVLYLGAASGTTVSHVS-DMLPNGIVYAVEFSPRTMRELI---QLCDTRSNIVPILADASRPKLYAHIVEQ 138
                                   35667899************8777666.577**********876554444...44455566666678999888889999** PP

                         GCD14 114 vDavfLDlPaPweaiphaa...kalkkeggrlCsf.sPCieqvqrtceaLre 161
                                   vD +f D+ +P +a   a+   + lk++g  l s  +  i+ v +  ++++e
  gi|91773524|ref|YP_566216.1| 139 VDVIFQDVAQPNQAQIAAVnagQFLKEDGYLLLSIkARSIDTVANPSKVFKE 190
                                   ***********99865554011557777777666523456666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1649.08
//
Query:       gi|91773525|ref|YP_566217.1|  [L=354]
Description: rRNA biogenesis protein Nop56/Nop58 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-53  180.2   0.0    5.7e-53  179.7   0.0    1.2  1  Nop            snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
        1.8    7.9   3.4         26    4.1   0.6    2.3  2  Transcrip_reg  Transcriptional regulator


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 !  179.7   0.0   6.3e-57   5.7e-53       2     229 ..     116     325 ..     115     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 6.3e-57
                                   HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH-SSS-S-H CS
                           Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedeelakevimaakvtastsmgaelse 82 
                                   ld+id+ +n l++r+ ewY+ hFpEL     ++   a+ v+++g +r+++         ++ + + a+     smg+el +
  gi|91773525|ref|YP_566217.1| 116 LDDIDDVVNVLSERLSEWYGLHFPELGL---SSEPLARFVSEFG-SRNNV-------PAEHPMFEKATS----SMGSELPS 181
                                   79************************94...456679*******.88888.......145667777777....******** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCH CS
                           Nop  83 edlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfral 163
                                    d + ik +++++ el+++r++++  + ++m+++APN++ + G+ ++ar+is +GgL +L+++P+st+q++Ga++alf++l
  gi|91773525|ref|YP_566217.1| 182 ADEELIKGFASNACELYDSRHSIEASIVRNMEKMAPNVTLITGSLIGARFISMTGGLARLSQLPSSTVQVMGANRALFKHL 262
                                   ********************************************************************************* PP

                                   H.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                           Nop 164 k.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                   + +  +pk+G+i++++lv+++ p+++++kiaR+laaK++laaR+D +   +g+l  +++ ++ekk++
  gi|91773525|ref|YP_566217.1| 263 RgRAPSPKHGIIFNNPLVKNS-PWWQRGKIARALAAKISLAARMDVY---SGELHPEIKVDLEKKVN 325
                                   *5559**************77.***********************88...58888888888888875 PP

>> Transcrip_reg  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.6    0.0029        26     219     237 ..     108     126 ..      41     128 .. 0.83
   2 ?    4.0   0.1    0.0032        28      11      57 ..     282     331 ..     280     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0029
                                   HHHHHHHHHHTSTTEEEEE CS
                 Transcrip_reg 219 kleklidaLeeldDVqnvy 237
                                   ++ + ++aL+++dDV nv 
  gi|91773525|ref|YP_566217.1| 108 QIIQAVEALDDIDDVVNVL 126
                                   677889***********97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0032
                                   CHCCCCHHHHHHHHHHHHHHHHHT...HH-S-GGG-HHHHHHHHHHHHTT CS
                 Transcrip_reg  11 aandakkgklftklakeItvaake...eggpDpesNprLraaiekakkan 57 
                                   +  + ++gk+   la +I++aa++   +g+  pe  + L++ ++++k+an
  gi|91773525|ref|YP_566217.1| 282 NSPWWQRGKIARALAAKISLAARMdvySGELHPEIKVDLEKKVNSIKAAN 331
                                   566779*****************833334468888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2402.97
//
Query:       gi|91773526|ref|YP_566218.1|  [L=319]
Description: beta-ribofuranosylaminobenzene 5'-phosphate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-09   35.6   0.0      2e-08   34.5   0.0    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
    4.9e-07   29.9   3.8    1.1e-06   28.8   3.8    1.6  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   2.2e-12     2e-08       1      82 [.     215     295 ..     215     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.2e-12
                GHMP_kinases_C   1 llealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralr 80 
                                   +l+a+++gd+e +g ++  +q+   +k +v+  ++ +++l e++++lG +ga++s    Gp+vf+++++++ aeq++++++
  gi|91773526|ref|YP_566218.1| 215 MLPAILEGDIENFGFAVDHLQNVgFKKREVALQSRQVRDLMEFMQDLGTCGAGMSSF--GPAVFGFIDNRNMAEQIRDEVQ 293
                                   789***************88888*9999********************777777766..********************98 PP

                GHMP_kinases_C  81 ee 82 
                                    +
  gi|91773526|ref|YP_566218.1| 294 HF 295
                                   66 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 !   28.8   3.8   1.2e-10   1.1e-06       2      66 .]      75     135 ..      74     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.2e-10
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHH.HHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleae.rlaqggngsggDvaasvyGg 66 
                                   i+++ ++P + GLGS++  a++++aA+++l+gl      l+++    ++++g +sg+ va +  Gg
  gi|91773526|ref|YP_566218.1|  75 IHVEEDMPAHVGLGSGTQSALSAAAAVNELYGL-----GLTVRELaIAVGRGGTSGIGVASFESGG 135
                                   899****************************94.....343333314447788******9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2477.93
//
Query:       gi|91773527|ref|YP_566219.1|  [L=216]
Description: hypothetical protein Mbur_1564 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-12   45.6   0.0    2.1e-11   43.7   0.0    2.0  2  DUF2953   Protein of unknown function (DUF2953)
  ------ inclusion threshold ------
      0.072   14.1   0.0       0.14   13.1   0.0    1.5  1  DUF4834   Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.74   6.6e+03      17      28 ..     109     120 ..     109     123 .. 0.79
   2 !   43.7   0.0   2.4e-15   2.1e-11       1      53 []     129     175 ..     129     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.74
                       DUF2953  17 liwaikgllygl 28 
                                   +++ +kgll+ l
  gi|91773527|ref|YP_566219.1| 109 FLHLMKGLLFQL 120
                                   678999999765 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 2.4e-15
                       DUF2953   1 leiGleDaadTgilyGliwaikgllygllsnlfnikkpeievtPvFneevfeg 53 
                                   l++Gl+D+adTg+l+G+++++ +++ g++      + ++++  PvF+ee f++
  gi|91773527|ref|YP_566219.1| 129 LTYGLSDPADTGMLCGYLHTLASIVRGRA------RSFSYSLYPVFMEEAFDM 175
                                   69**************************9......889***********9986 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05      0.14       3      69 ..       3      85 ..       1     102 [. 0.42

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                       DUF4834  3 fLlfi.lifiiailviglsilsvilrtvfg.lgsrkkss..............ksaqkqfgnstnsnqqksqsrsetkeegei 69
                                  fL +i li+++++++i l+ ++v +    g  g r++ s              +s++   +n+t+s+++ ++++++tke+++ 
  gi|91773527|ref|YP_566219.1|  3 FLYVIvLIILFLLALILLAPIAVAFDVNGGlSGVRSNVSlkwmflsysfsgqpDSKEVPVTNGTTSTEEGTTKENTTKENTTK 85
                                  55566444555555555555555555553333333333333333333333323333333333333333333333333222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1681.31
//
Query:       gi|91773528|ref|YP_566220.1|  [L=130]
Description: hypothetical protein Mbur_1565 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-26   92.1   3.3    2.5e-26   91.6   3.3    1.2  1  Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)


Domain annotation for each model (and alignments):
>> Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   3.3   1.4e-30   2.5e-26       3      79 ..      30     106 ..      28     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 1.4e-30
                    Spore_YtfJ   3 tgdgtviiPvskvsfGfgaGgsefkskkekepfgggsgaGvsitPvAfLvikkgevkllpvkk.ssldklidlvpdvv 79 
                                   +gd ++i+P++kvsfGfg+Gg+e+++  ++++fggg+g+G++i+PvAfLvi++++v+l+ +   s+l kl+d+vp v 
  gi|91773528|ref|YP_566220.1|  30 AGD-KTILPITKVSFGFGSGGGEGSKGGSESGFGGGGGGGAKIEPVAFLVISDEGVRLMTLAGnSDLGKLLDAVPGVY 106
                                   567.9*******************7777*********************************99************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 921.48
//
Query:       gi|91773529|ref|YP_566221.1|  [L=726]
Description: Rad3-related DNA helicases [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-27   95.2   0.0    1.5e-26   93.6   0.0    1.9  2  Helicase_C_2  Helicase C-terminal domain
    2.4e-19   69.6   3.7    6.6e-19   68.2   3.7    1.7  1  DEAD_2        DEAD_2
    8.3e-08   32.4   4.1    0.00037   20.6   0.2    3.2  3  ResIII        Type III restriction enzyme, res subunit
    1.3e-07   31.6   0.7    0.00014   21.7   0.2    3.2  3  DEAD          DEAD/DEAH box helicase
    0.00055   19.4   0.2     0.0093   15.4   0.1    2.5  2  PhoH          PhoH-like protein
     0.0016   17.7   0.3       0.32   10.2   0.0    2.3  2  DUF2075       Uncharacterized conserved protein (DUF2075)
     0.0067   16.1   0.1      0.017   14.8   0.1    1.6  1  HBB           Helical and beta-bridge domain
  ------ inclusion threshold ------
      0.012   15.3   0.1       0.75    9.4   0.0    2.4  2  Zot           Zonular occludens toxin (Zot)
      0.074   12.8   0.3       0.26   11.0   0.1    2.0  3  AAA_30        AAA domain
      0.081   12.3   0.5       0.15   11.3   0.1    1.6  2  ATPase        KaiC
      0.098   11.5   0.0       0.17   10.7   0.0    1.4  1  AAA_34        P-loop containing NTP hydrolase pore-1
       0.39   11.1   3.2         48    4.4   1.1    3.7  3  AAA           ATPase family associated with various cellular 


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 ?   -2.7   0.0       3.9   5.8e+03      44      83 ..     127     168 ..      66     173 .. 0.50
   2 !   93.6   0.0     1e-29   1.5e-26       2     162 ..     527     685 ..     526     690 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.9
                  Helicase_C_2  44 e.....keesrekvleeykekkkkgaillavcrGklsEGidfsdd 83 
                                   e     k+++ ++  ++yk+  ++  +++  +r +ls  id  ++
  gi|91773529|ref|YP_566221.1| 127 EreiylKRQELNSARDSYKK--SHDPAFVT-LRDELSKEIDAVEE 168
                                   22333344444555555555..43333333.34555555555555 PP

  == domain 2  score: 93.6 bits;  conditional E-value: 1e-29
                  Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeyke..kkkkgaillavcrGklsEGidf 80 
                                   l+ +e  +g+v++ff+S    ++ +++++      ++++f  e   s+++v ee+ +  +++ +a+ll+ + G+lsEGid+
  gi|91773529|ref|YP_566221.1| 527 LDSIENSKGNVILFFQSAFEAKRYYSKIEPLV---NVPVFLDEVGISSQDVREEFFSigEENGKAVLLSYLWGTLSEGIDY 604
                                   66788999********************9987...6899988777799999999998655999****************** PP

                  Helicase_C_2  81 sddllraviivglPfpnpkdpeveakreyldekgkknsgkew.ylpealravnQaiGRliRhkdDygaivllDeRfakeei 160
                                   +d ++r vii+g+++p ++d   +a  + +d+ ++  +g+e+  + +++r+++Qa+GR++R+ +Dyga +llD Rf +++ 
  gi|91773529|ref|YP_566221.1| 605 RDGRGRTVIIIGVGYPALNDRM-NAVESAYDHVFGYGAGWEFaIQVPTIRKIRQAMGRVVRSPTDYGARILLDGRFLTDS- 683
                                   ******************8765.677788899999788887615779*****************************9977. PP

                  Helicase_C_2 161 re 162
                                   ++
  gi|91773529|ref|YP_566221.1| 684 KK 685
                                   44 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   3.7   4.4e-22   6.6e-19       3     176 .]      70     285 ..      68     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 4.4e-22
                                   ESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH............. CS
                        DEAD_2   3 sRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek............. 70 
                                   +  h+q+ q+++e + +++++    +vkv +++++  +C +e+  +e ++k+ n++  + ++ +   +             
  gi|91773529|ref|YP_566221.1|  70 TNVHQQMVQFINEARDIKKVQ----DVKVAVIKGKTAMCPQEADYEECSVKRENTFELMETEREI--Ylkrqelnsardsy 144
                                   5679*************7655....5**************9887777666665543322222222..22355788999*** PP

                                   ..............................TTTTTT-SCC..CCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHH CS
                        DEAD_2  71 ..............................eekCsffenl..eelkklkkllleevvdiedlvelgeklklCPYylsrell 119
                                                                 + +C+   ++  ++++k ++ l +ev + e++ +   k ++C Y l+++ l
  gi|91773529|ref|YP_566221.1| 145 kkshdpafvtlrdelskeidaveekarglrDRACNDLYEVlrSDSEKFREWLYKEVRSPEEINDHAIKDGMCGYELVKREL 225
                                   ******************************999*97777756777777********************************* PP

                                   CCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHHHHHCC-EEEECHHH CS
                        DEAD_2 120 edadiiilpYqyLldekireslk...gislknsivilDEAhNiedvceeaasveiseesl 176
                                   ++ad+ i+ Y+ +l++ i +++    + + +++ivi+DEAhN+e+ +++  s++++e+s+
  gi|91773529|ref|YP_566221.1| 226 KHADLLICNYHHVLNPDIFSTVLgwiEKEPQETIVIFDEAHNLESAARSHSSLSLTEHSI 285
                                   ********************99876656889*************************9975 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   2.4e-07   0.00037       4     140 ..      16     158 ..      13     168 .. 0.56
   2 !    8.9   0.1   0.00096       1.4      66     148 ..     181     272 ..     173     298 .. 0.62
   3 ?    2.7   0.0     0.074   1.1e+02      82     129 ..     344     391 ..     321     407 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.4e-07
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH.HHHHHHHHHGGGGTGG... CS
                        ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk.slleqtleefkkflseayk 83 
                                    ++ Q+ea++++ ++l   +++ +l++ a+GtGKTl a+  + ++ k  +  k+++++ +  + + q ++e +++++ ++ 
  gi|91773529|ref|YP_566221.1|  16 CYPNQQEAMDRIHSAL--MQQQLVLFEGACGTGKTLSALVPALHVGKMLG--KTVIIATNVhQQMVQFINEARDIKKVQDV 92 
                                   5789************..599*****************999999999877..77777754313444444444444433322 PP

                                   .GEEEESSS-B--...............-SEEEEEHHHHHHTH........HHHTTT-S..EEEEET CS
                        ResIII  84 eigkkvsgdkkka........kekdstnkkilvttiqsldadseeeeeeseellrdrfd..viiiDE 140
                                    +  +++g++ +          + +++n+  l++t+ +++ +++e +++++++++++ +  v + DE
  gi|91773529|ref|YP_566221.1|  93 -KVAVIKGKTAMCpqeadyeeCSVKRENTFELMETEREIYLKRQELNSARDSYKKSHDPafVTLRDE 158
                                   .222233333332222233332222233333333333333333222222222222222233555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00096
                                   HHHHHHHHGGGGTGG......GEEEESSS-B--..............-SEEEEEHHHHHHTH........HHHTTT-SEEE CS
                        ResIII  66 lleqtleefkkflseayke..igkkvsgdkkka.......kekdstnkkilvttiqsldadseeeeeeseellrdrfdvii 137
                                   l+e ++++ +kf +  yke    +++++   k         +++ +++++l+ +++ + ++    +      ++ ++ ++i
  gi|91773529|ref|YP_566221.1| 181 LYEVLRSDSEKFREWLYKEvrSPEEINDHAIKDgmcgyelVKRELKHADLLICNYHHVLNPDIFSTVLGWIEKEPQETIVI 261
                                   555555444444444444444445555554444666666666777888888888888888775555555555666677*** PP

                                   EETGGGTTS.T CS
                        ResIII 138 iDEaHrlgakk 148
                                   +DEaH+l +++
  gi|91773529|ref|YP_566221.1| 262 FDEAHNLESAA 272
                                   ******99862 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.074
                                   .......GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHH CS
                        ResIII  82 yke....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseell 129
                                   y++     gk++++ k ++  +++++++il+++ ++l a+++e+   +++++
  gi|91773529|ref|YP_566221.1| 344 YERndivRGKFLRQAKGDF--GEKDDIQILLSEASELGAKLDETY--RDQYK 391
                                   3223455566666666666..99******************6553..33333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2     9e-08   0.00014       2      94 ..      18     110 ..      17     135 .. 0.84
   2 ?    3.9   0.0     0.027        40     123     140 ..     258     275 ..     219     294 .. 0.79
   3 ?    2.3   0.0     0.082   1.2e+02     160     173 ..     459     473 ..     382     476 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9e-08
                                   HHHHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                   xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                   + Q+ea++ i     +++ vl +++ G+GKTl +l+p+l +v    +  g+ ++i +  ++ + q +n+++ +kk  d++v
  gi|91773529|ref|YP_566221.1|  18 PNQQEAMDRIHsalmQQQLVLFEGACGTGKTLSALVPAL-HV---GKMLGKTVIIATNVHQQMVQFINEARDIKKVQDVKV 94 
                                   6799999988877778899********************.55...35677788888899****************999999 PP

                                   EEEETTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          DEAD  79 lliiggvaardqlskl 94 
                                    +i g++a   q ++ 
  gi|91773529|ref|YP_566221.1|  95 AVIKGKTAMCPQEADY 110
                                   9888877766666555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.027
                                   EEEEEETHHHHHHTTTHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          DEAD 123 rflVlDEadrlldqgfsd 140
                                   +++++DEa++l +  +s 
  gi|91773529|ref|YP_566221.1| 258 TIVIFDEAHNLESAARSH 275
                                   689********9986654 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.082
                                   SEEEEEESSBS.HHH CS
                                   xxxxxxxxxxx.xxx RF
                          DEAD 160 rqvivlSATlp.kdv 173
                                     vi++SATl+ +++
  gi|91773529|ref|YP_566221.1| 459 FSVILMSATLHpFEM 473
                                   349********8765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.2e-06    0.0093       9      46 ..      20      61 ..      16      84 .. 0.76
   2 ?    1.1   0.0      0.16   2.3e+02     120     134 ..     257     271 ..     255     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                                  HHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                          PhoH  9 Qkeylealk....kndivfaiGpaGtGKtylavalavealkk 46
                                  Q+e+++ ++    ++++v   G  GtGKt+ a++ a+++ k 
  gi|91773529|ref|YP_566221.1| 20 QQEAMDRIHsalmQQQLVLFEGACGTGKTLSALVPALHVGKM 61
                                  55555544444449********************99987654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                                   SEEEEE-SGGG--HH CS
                          PhoH 120 dafvilDEAQnttke 134
                                   +++vi+DEA n++++
  gi|91773529|ref|YP_566221.1| 257 ETIVIFDEAHNLESA 271
                                   689********9876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0058       8.6       2      46 ..      35      78 ..      34     124 .. 0.68
   2 !   10.2   0.0   0.00022      0.32      65     109 ..     226     277 ..     176     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0058
                       DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlv 46
                                  ++vl +G+ GtGKt+ +l  +  +  + +++t+++++  h+++  
  gi|91773529|ref|YP_566221.1| 35 QLVLFEGACGTGKTLSALVPALHV-GKMLGKTVIIATNVHQQMVQ 78
                                  68999**********998877777.56666666666555555444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00022
                       DUF2075  65 eklssfinnlsef.......kkaeekkeepkedvvivDEAhrlltksdqaek 109
                                   +  + +i n+++              ++ep+e++vi+DEAh l + ++++ +
  gi|91773529|ref|YP_566221.1| 226 KHADLLICNYHHVlnpdifsTVLGWIEKEPQETIVIFDEAHNLESAARSHSS 277
                                   55555555566556555554444556789**************995544433 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.1e-05     0.017      88     177 ..     400     499 ..     377     504 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHHHHHT.S.TTTEEEEEE...STT.....EECCCCS-TCCHHHHHHHCH.CCCCCCTS-SSHHHHHHHHT. CS
                           HBB  88 rsflsrlaefllawls.sdeedYvrlvs..keeg....esLeavcldPskalrflkerl.ssllmsgtltpleeysdiiGl 160
                                   rs++  +a f+ a+++ s + +Y  +++  ++ +      +e+    P++++++l ++l s++lms tl p+e  ++ +G+
  gi|91773529|ref|YP_566221.1| 400 RSHIRYVADFMSAYIElSHNLNYYPILNvrRDMNdeiyGRVELFTCIPKNVTEPLFNSLfSVILMSATLHPFEMVKKTLGI 480
                                   799999999999999998888998886511333321223456654456*****986654399******************* PP

                                   .....EEE.S..S.GGHCC CS
                           HBB 161 e..aklkkfpspfpkEnli 177
                                      +    +   fp+E+++
  gi|91773529|ref|YP_566221.1| 481 TrdTCEMSYGTSFPEEKRL 499
                                   99888899********986 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0005      0.75       2      53 ..      36      85 ..      35     158 .. 0.68
   2 ?    3.5   0.0     0.033        49      61      97 ..     234     273 ..     213     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0005
                           Zot  2 islvtGapGsgKtsgavkkdllpalk..egRkiitnidGlrlerieqvlgekvs 53
                                  ++l++Ga G+gKt+ a+   l   ++  +  +i+tn++    +++ q ++e+  
  gi|91773529|ref|YP_566221.1| 36 LVLFEGACGTGKTLSALVPALHVGKMlgKTVIIATNVH----QQMVQFINEARD 85
                                  6899************9887776444336777889**9....444444444433 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.033
                           Zot  61 d..npegaetlkefakwatid.kgallviDEcqeifpvra 97 
                                   +  + + + + + +  w   + ++ ++++DE++++ ++ +
  gi|91773529|ref|YP_566221.1| 234 NyhHVLNPDIFSTVLGWIEKEpQETIVIFDEAHNLESAAR 273
                                   3347777777788888888666***********9866555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.26       4      55 ..      18      72 ..      15     100 .. 0.71
   2 ?   -2.8   0.0       2.9   4.3e+03      85     100 ..     252     268 ..     227     275 .. 0.73
   3 ?   -3.8   0.0       5.8   8.7e+03      93     120 ..     563     590 ..     562     591 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                        AAA_30  4 aeQaaaveallts..gdrvavltGpAGtGKttalkalreaweaa.ggrviglApt 55
                                  ++Q++a++++++   ++++++ +G+ GtGKt +  + + ++ +  g++vi+++  
  gi|91773529|ref|YP_566221.1| 18 PNQQEAMDRIHSAlmQQQLVLFEGACGTGKTLSALVPALHVGKMlGKTVIIATNV 72
                                  6789998877654226679************765444444444448888877665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.9
                        AAA_30  85 rlepg.tllivDEagmv 100
                                   + ep+ t++i DEa  +
  gi|91773529|ref|YP_566221.1| 252 EKEPQeTIVIFDEAHNL 268
                                   34556599*****9655 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.8
                        AAA_30  93 ivDEagmvdtkqlaallkaaekagakvi 120
                                     DE+g  +++  ++++++ e++g  v+
  gi|91773529|ref|YP_566221.1| 563 FLDEVGISSQDVREEFFSIGEENGKAVL 590
                                   679******9999999999998776665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.15       8     101 ..      24     117 ..      20     161 .. 0.70
   2 ?   -3.3   0.1       3.1   4.7e+03      81     120 ..     257     294 ..     248     307 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                        ATPase   8 lDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa..edlrenakslGwdlekleeegklaii 86 
                                   +D+i +  +++++ vl  G  GtGKt+ al  +++  + +  ++v+++++ ++  ++++++a     d++k+++  k+a+i
  gi|91773529|ref|YP_566221.1|  24 MDRI-HSALMQQQLVLFEGACGTGKTLSALVPALHVGK-MLGKTVIIATNVHQqmVQFINEA----RDIKKVQDV-KVAVI 97 
                                   7777.68999*******************999988744.46678888888887334555554....477777776.77777 PP

                        ATPase  87 dasesaeesaee.....kdk 101
                                      + +  ++++      ++
  gi|91773529|ref|YP_566221.1|  98 KGKTAMCPQEADyeecsVKR 117
                                   66666655554443333333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.1
                        ATPase  81 gklaiidasesaeesaeekdkedleelieelaeaikeika 120
                                   + ++i d +++ e   +++++++l+   +++++ai e++a
  gi|91773529|ref|YP_566221.1| 257 ETIVIFDEAHNLES--AARSHSSLSLTEHSIEKAITELEA 294
                                   45666666666554..345677777777788888888776 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012      0.17     161     207 ..     244     294 ..     179     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                        AAA_34 161 leqlveWlg.edfdGvivfDEchkaknlakse...ekkatktgkavlelqk 207
                                   ++ ++ W++ e  + +++fDE+h+++++a s+   + ++    ka++el+ 
  gi|91773529|ref|YP_566221.1| 244 FSTVLGWIEkEPQETIVIFDEAHNLESAARSHsslSLTEHSIEKAITELEA 294
                                   567899***77788999**********998774443444555666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.1     0.032        48       1      21 [.      37      57 ..      37     196 .. 0.83
   2 ?    4.0   0.0     0.043        64      55      76 ..     253     275 ..     227     305 .. 0.75
   3 ?   -1.0   0.0       1.4   2.2e+03      38      68 ..     529     568 ..     506     619 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.032
                                  EEEESSTTSSHHHHHHHHHHH CS
                           AAA  1 vllyGppGtGKTllakavake 21
                                  vl+ G  GtGKTl a   a +
  gi|91773529|ref|YP_566221.1| 37 VLFEGACGTGKTLSALVPALH 57
                                  7999********998765555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.043
                                   HTSTSEEEEEETGGGHHHHH.TT CS
                           AAA  55 ekakpsilfiDEidalaksr.sg 76 
                                   ++ + +i+++DE+++l ++  s+
  gi|91773529|ref|YP_566221.1| 253 KEPQETIVIFDEAHNLESAArSH 275
                                   433469**********8877422 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.4
                                   STTHHHHHHHHHHHHHHHTS.........TSEEEEEETGG CS
                           AAA  38 yvgesekkirelfkeakeka.........kpsilfiDEid 68 
                                    +++s+ ++  +f++a e +           + +f+DE+ 
  gi|91773529|ref|YP_566221.1| 529 SIENSKGNVILFFQSAFEAKryyskieplVNVPVFLDEVG 568
                                   4455555555666665555455555533222336666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 5291.12
//
Query:       gi|91773530|ref|YP_566222.1|  [L=213]
Description: hypothetical protein Mbur_1567 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-18   65.8   4.8      5e-18   65.8   2.2    2.0  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   2.2   2.8e-22     5e-18       1      80 [.       9      93 ..       9      94 .. 0.94
   2 ?    0.2   0.0     0.085   1.5e+03      33      57 ..     162     189 ..     155     196 .. 0.63

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.8e-22
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl...asneekapqasievk..idssastgknavslehkgGdsidtkdlkivlns 78
                                  +AV+pV G++L+v +tv+la+ +a++v++     s ++++p+a+iev+  +++ +s+++n vslehkgGd++d++++ ivl++
  gi|91773530|ref|YP_566222.1|  9 NAVTPVLGAVLLVLLTVVLAGAVAVIVISNgsaLSLSSSTPMAMIEVSdvVGYASSYKNNFVSLEHKGGDPLDLDSTFIVLSG 91
                                  69***************************98644899*********999999999999999********************99 PP

                       Pilin_N 79 eg 80
                                  eg
  gi|91773530|ref|YP_566222.1| 92 EG 93
                                  86 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.085
                       Pilin_N  33 neekapqasievkidssastgkna...v 57 
                                   +  ++ ++s++  +++s+++g n    v
  gi|91773530|ref|YP_566222.1| 162 TDASTVHVSVDGYSNTSNNYGFNDgetV 189
                                   4455666677666888887776655553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1510.21
//
Query:       gi|91773531|ref|YP_566223.1|  [L=58]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-18   64.8  18.7    1.5e-09   37.3   5.9    2.1  2  Fer4          4Fe-4S binding domain
    4.3e-14   52.3  24.9      2e-10   40.6  13.5    1.6  2  Fer4_10       4Fe-4S dicluster domain
      1e-12   48.0  13.7    1.1e-12   47.9  13.7    1.0  1  Fer4_21       4Fe-4S dicluster domain
    3.7e-12   45.8  20.4    3.9e-06   26.7   7.1    2.1  2  Fer4_6        4Fe-4S binding domain
      1e-11   44.8  11.0    1.3e-11   44.4  11.0    1.2  1  Fer4_9        4Fe-4S dicluster domain
    3.1e-11   43.7  11.8      8e-11   42.4  12.1    1.5  1  Fer4_7        4Fe-4S dicluster domain
    5.9e-11   41.8  16.2    1.7e-05   24.6   4.6    2.1  2  Fer4_2        4Fe-4S binding domain
      1e-10   42.4  10.2    2.8e-05   25.0   2.3    2.1  2  Fer4_16       4Fe-4S double cluster binding domain
    3.7e-10   39.5  14.2    2.6e-05   24.4   3.9    2.1  2  Fer4_4        4Fe-4S binding domain
    2.8e-06   27.7  12.8     0.0015   19.0   1.9    2.1  2  Fer4_17       4Fe-4S dicluster domain
      7e-06   26.4  13.2     0.0064   16.9   3.1    2.1  2  Fer4_8        4Fe-4S dicluster domain
    2.5e-05   24.9  16.7    0.00086   20.1   3.9    2.2  2  Fer4_3        4Fe-4S binding domain
    4.3e-05   24.3   9.6     0.0097   16.7   1.9    2.0  2  Fer4_22       4Fe-4S dicluster domain
    0.00011   22.6  22.4      0.069   13.7   5.9    3.0  3  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    0.00011   22.8  16.7    0.00044   20.9   3.1    2.9  2  Fer4_15       4Fe-4S single cluster domain
    0.00038   20.6  14.6     0.0044   17.2   3.4    2.0  1  Fer4_18       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   15.7   5.3      0.014   15.5   5.3    1.2  1  Fer4_11       4Fe-4S dicluster domain
      0.018   15.2   3.5       0.24   11.5   3.8    1.9  2  Furin-like_2  Furin-like repeat, cysteine-rich
       0.11   12.7   7.5        1.9    8.7   0.7    2.0  2  ETF_QO        Electron transfer flavoprotein-ubiquinone oxido


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   4.9   1.8e-11   1.7e-08       2      24 .]       4      26 ..       3      26 .. 0.95
   2 !   37.3   5.9   1.6e-12   1.5e-09       2      24 .]      34      56 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.8e-11
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  vi+ + C+gCG+Cv+ CP +AI+
  gi|91773531|ref|YP_566223.1|  4 VINRDECVGCGTCVDDCPSEAIS 26
                                  8********************96 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 1.6e-12
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  v++ + Ci CGaCv+ CP++AI+
  gi|91773531|ref|YP_566223.1| 34 VVNADECIDCGACVDSCPTDAIS 56
                                  89********************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6  13.5   2.2e-13     2e-10       2      56 .]       3      51 ..       2      51 .. 0.84
   2 !   22.7   3.5   8.2e-08   7.7e-05       2      22 ..      33      53 ..      32      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.2e-13
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                  +vi++d C++Cg+Cv+ CP+       +++ +++e + + + ++C++cgaCv++CP
  gi|91773531|ref|YP_566223.1|  3 AVINRDECVGCGTCVDDCPS-------EAISMDGENIAVvNADECIDCGACVDSCP 51
                                  589*****************.......55555555555559**************9 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 8.2e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPad 22
                                  +v+++d Ci Cg+Cv++CP+d
  gi|91773531|ref|YP_566223.1| 33 AVVNADECIDCGACVDSCPTD 53
                                  678999*************94 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9  13.7   1.2e-15   1.1e-12       1      59 []       3      57 ..       3      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.2e-15
                       Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                  A+i++d+C+gCg C+  C+    +ai++d+++++ v +deC+ C  C++ CP+ d+i+m
  gi|91773531|ref|YP_566223.1|  3 AVINRDECVGCGTCVDDCP---SEAISMDGENIAVVNADECIDCGACVDSCPT-DAISM 57
                                  89*****************...6*****************************6.***98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   5.4     1e-08   9.6e-06       1      24 []       2      25 ..       2      25 .. 0.95
   2 !   26.7   7.1   4.1e-09   3.9e-06       1      24 []      32      55 ..      32      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1e-08
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  v++i++d C+gCg Cv+ CP  ai
  gi|91773531|ref|YP_566223.1|  2 VAVINRDECVGCGTCVDDCPSEAI 25
                                  689*****************9998 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 4.1e-09
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  ++++++d Ci+Cg+Cv+ CP++ai
  gi|91773531|ref|YP_566223.1| 32 IAVVNADECIDCGACVDSCPTDAI 55
                                  689*******************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4  11.0   1.4e-14   1.3e-11       1      51 []       9      55 ..       7      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.4e-14
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  +C+gCg+Cv+ Cp++++++d  +  + +      +Ci+CgaCv+ Cp++ai
  gi|91773531|ref|YP_566223.1|  9 ECVGCGTCVDDCPSEAISMDGENIAVVNAD----ECIDCGACVDSCPTDAI 55
                                  5******************99999988765....5*************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 !   42.4  12.1   8.5e-14     8e-11       2      52 .]      10      54 ..       9      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 8.5e-14
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  C+gCg Cv+ Cp++ai++d e        +++++++C++CgaCv+ CPt+a
  gi|91773531|ref|YP_566223.1| 10 CVGCGTCVDDCPSEAISMDGE------NIAVVNADECIDCGACVDSCPTDA 54
                                  ******************886......568899****************97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   3.8   4.2e-08     4e-05       3      21 ..       3      21 ..       1      22 [. 0.92
   2 !   24.6   4.6   1.8e-08   1.7e-05       3      22 .]      33      52 ..      31      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.2e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  +v+++d C+gCg+Cv+ CP
  gi|91773531|ref|YP_566223.1|  3 AVINRDECVGCGTCVDDCP 21
                                  689**************** PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.8e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +vv++d Ci CgaCv++CP+
  gi|91773531|ref|YP_566223.1| 33 AVVNADECIDCGACVDSCPT 52
                                  689****************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 !   25.0   2.3     3e-08   2.8e-05       2      31 ..      10      41 ..       9      42 .. 0.86
   2 !   24.0   2.5   5.9e-08   5.6e-05       2      20 ..      40      58 .]      39      58 .] 0.93

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3e-08
                       Fer4_16  2 CgtCgkCaevCPtnaikek..kekeieareci 31
                                  C++Cg C++ CP++ai+++  + ++++a+eci
  gi|91773531|ref|YP_566223.1| 10 CVGCGTCVDDCPSEAISMDgeNIAVVNADECI 41
                                  *****************986567778888886 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 5.9e-08
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++Cg+C+++CPt+ai+++
  gi|91773531|ref|YP_566223.1| 40 CIDCGACVDSCPTDAISME 58
                                  ****************975 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.7   3.3e-07   0.00031       2      16 ..       8      22 ..       7      28 .. 0.92
   2 !   24.4   3.9   2.8e-08   2.6e-05       2      16 ..      38      52 ..      37      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.3e-07
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  + C+gCg Cv+ CP+
  gi|91773531|ref|YP_566223.1|  8 DECVGCGTCVDDCPS 22
                                  78************7 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.8e-08
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  + Ci+Cg+Cv++CP+
  gi|91773531|ref|YP_566223.1| 38 DECIDCGACVDSCPT 52
                                  89************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 !   14.9   3.3   3.2e-05      0.03      44      59 ..       8      23 ..       3      24 .. 0.82
   2 !   19.0   1.9   1.6e-06    0.0015      40      59 ..      34      53 ..      22      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
                       Fer4_17 44 slCieCgeCerkCPqg 59
                                  ++C++Cg C+ +CP++
  gi|91773531|ref|YP_566223.1|  8 DECVGCGTCVDDCPSE 23
                                  6899999999999975 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.6e-06
                       Fer4_17 40 eekaslCieCgeCerkCPqg 59
                                    +a++Ci Cg C+ +CP +
  gi|91773531|ref|YP_566223.1| 34 VVNADECIDCGACVDSCPTD 53
                                  358999***********976 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.6   1.7e-05     0.016       4      17 ..       9      22 ..       6      36 .. 0.79
   2 !   16.9   3.1   6.7e-06    0.0064       2      17 ..      37      52 ..      36      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                        Fer4_8  4 kCieCgaCqsaCpv 17
                                  +C++Cg C + Cp+
  gi|91773531|ref|YP_566223.1|  9 ECVGCGTCVDDCPS 22
                                  68888888888884 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.7e-06
                        Fer4_8  2 lekCieCgaCqsaCpv 17
                                  +++Ci CgaC ++Cp+
  gi|91773531|ref|YP_566223.1| 37 ADECIDCGACVDSCPT 52
                                  5789999999999994 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   5.0   0.00083      0.78       1      15 []      10      24 ..      10      24 .. 0.92
   2 !   20.1   3.9   9.1e-07   0.00086       1      15 []      40      54 ..      40      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00083
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg+Cv+ CP+ A
  gi|91773531|ref|YP_566223.1| 10 CVGCGTCVDDCPSEA 24
                                  ************866 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 9.1e-07
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ CgaCv++CP++A
  gi|91773531|ref|YP_566223.1| 40 CIDCGACVDSCPTDA 54
                                  9************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.9     1e-05    0.0097      77      95 ..       5      23 ..       1      24 [. 0.85
   2 !   12.7   1.1   0.00019      0.18      81      94 ..      39      52 ..      29      55 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                       Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                  +++  CvGCg C++ cp++
  gi|91773531|ref|YP_566223.1|  5 INRDECVGCGTCVDDCPSE 23
                                  67899***********975 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00019
                       Fer4_22 81 gCvGCgRCieacpv 94
                                   C+ Cg C+++cp+
  gi|91773531|ref|YP_566223.1| 39 ECIDCGACVDSCPT 52
                                  55555555555554 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   5.9   7.3e-05     0.069       1      18 [.       5      22 ..       5      34 .. 0.91
   2 !   13.7   7.9   7.4e-05     0.069       1      17 [.      35      51 ..      35      52 .. 0.94
   3 !    7.6   0.2     0.006       5.7      49      57 ..      48      56 ..      47      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  ++rd+C++cg+Cv+ +P 
  gi|91773531|ref|YP_566223.1|  5 INRDECVGCGTCVDDCPS 22
                                  89**************95 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.4e-05
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  V+ d+Ci+cgaCv+ +P
  gi|91773531|ref|YP_566223.1| 35 VNADECIDCGACVDSCP 51
                                  899*************9 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.006
                       Fer4_13 49 daCPvesIg 57
                                  d+CP+++I 
  gi|91773531|ref|YP_566223.1| 48 DSCPTDAIS 56
                                  8*******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 !   20.9   3.1   4.7e-07   0.00044       2      34 ..       4      37 ..       3      39 .. 0.88
   2 !    7.7   6.7    0.0065       6.1       2      20 ..      34      52 ..      34      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.7e-07
                       Fer4_15  2 vvDrdaCigcglCvaea.pevfeldedglasvll 34
                                  v++rd+C gcg Cv+ + +e + +d++ +a+v +
  gi|91773531|ref|YP_566223.1|  4 VINRDECVGCGTCVDDCpSEAISMDGENIAVVNA 37
                                  699**************6699*******998765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0065
                       Fer4_15  2 vvDrdaCigcglCvaeape 20
                                  vv+ d+Ci cg+Cv+ +p+
  gi|91773531|ref|YP_566223.1| 34 VVNADECIDCGACVDSCPT 52
                                  5889************985 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.4   4.7e-06    0.0044      50      74 ..      29      53 ..      22      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.7e-06
                       Fer4_18 50 keerkekgagdcidcescvkvcPtg 74
                                   e+ +  +a +cidc++cv+ cPt+
  gi|91773531|ref|YP_566223.1| 29 GENIAVVNADECIDCGACVDSCPTD 53
                                  5666778899*************96 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   5.3   1.5e-05     0.014       8      59 ..       8      55 ..       1      58 [] 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                       Fer4_11  8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykiv 59
                                  ++C  C    Cv+ +pseai  d e+ aV+  ++    ++ ++v++cP +++
  gi|91773531|ref|YP_566223.1|  8 DECVGCG--TCVDDCPSEAISMDGENIAVVNADECI--DCGACVDSCPTDAI 55
                                  5566664..7*************9887777666655..7999*****98876 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 ?   11.5   3.8   0.00026      0.24      23      65 ..       4      46 ..       1      50 [. 0.71
   2 ?    6.5   0.4    0.0095         9      26      42 ..      37      53 ..      31      58 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                  Furin-like_2 23 lleregirqiGvclascpaGyfgvrnkevnrctkckaeecesc 65
                                  +++r++    G+c+++cp+    + ++++      +  +c +c
  gi|91773531|ref|YP_566223.1|  4 VINRDECVGCGTCVDDCPSEAISMDGENIAVVNADECIDCGAC 46
                                  799*****************99998887654443333344444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0095
                  Furin-like_2 26 regirqiGvclascpaG 42
                                   ++  + G+c++scp+ 
  gi|91773531|ref|YP_566223.1| 37 ADECIDCGACVDSCPTD 53
                                  56667789999999974 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.7     0.002       1.9      69      91 ..       4      26 ..       1      32 [. 0.86
   2 ?    8.5   2.0    0.0022       2.1      65      91 ..      30      56 ..      19      58 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                                  EE-CCC--S--HHHHH-TT--EE CS
                        ETF_QO 69 qinaqnCvhCktCdikdpsqnie 91
                                  +in  +Cv C tC    ps+ i+
  gi|91773531|ref|YP_566223.1|  4 VINRDECVGCGTCVDDCPSEAIS 26
                                  79***********8888888886 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0022
                                  SEEEEE-CCC--S--HHHHH-TT--EE CS
                        ETF_QO 65 ekklqinaqnCvhCktCdikdpsqnie 91
                                  e+  ++na +C+ C +C    p++ i+
  gi|91773531|ref|YP_566223.1| 30 ENIAVVNADECIDCGACVDSCPTDAIS 56
                                  455689***********9888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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):              19  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 394.07
//
Query:       gi|91773532|ref|YP_566224.1|  [L=234]
Description: uridylate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  102.5   4.1    5.4e-29  101.5   4.1    1.5  1  AA_kinase    Amino acid kinase family
  ------ inclusion threshold ------
      0.035   14.2   0.1       0.12   12.5   0.0    2.0  2  SKI          Shikimate kinase
        1.3    8.3  10.0       0.11   11.7   1.5    2.3  2  AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-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 !  101.5   4.1   9.1e-33   5.4e-29       1     240 [.       1     201 [.       1     202 [. 0.95

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 9.1e-33
                                   TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHH CS
                     AA_kinase   1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrd 80 
                                   +++V+ +GGs+l+ + + + + ++a  +++l  +++++vvV+Ggg  ++++++ ++g+ ++e                  d
  gi|91773532|ref|YP_566224.1|   1 MLIVLSVGGSILAkNLDPKHFSAYASALKEL-ARKHQIVVVTGGGVAARNYIDVARGVGANEVVC---------------D 65 
                                   789**********77777*************.9999******************99****99994...............* PP

                                   HHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HH CS
                     AA_kinase  81 alaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssD 161
                                   ++++  +rl+a+ll a+l +   +  +++                   ++ e  l++g+++v++g i    +g+    ++D
  gi|91773532|ref|YP_566224.1|  66 FIGIDITRLNAQLLIAALGNTAHPEPPTT------------------YKEAESALASGKIVVMGGVI----PGQ----TTD 120
                                   ******************88888888777..................778999************99....888....9** PP

                                   HHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                     AA_kinase 162 tiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvIt 240
                                    +aa+lAe+l+Ad+++i+t+VdGVy++dp+++p+a++++ ++++e+    ++ e+  g+  +++p a ++++r +i+++I+
  gi|91773532|ref|YP_566224.1| 121 AVAAILAEYLNADMMVIATSVDGVYSSDPREDPNAKKFDVMTAKELVGivISTEMKAGSKSPVDPLASKIIERCNIDTIIM 201
                                   *******************************************************************************97 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12      52      76 ..      25      49 ..       4      75 .. 0.86
   2 ?   -2.3   0.0      0.69   4.1e+03      53      68 ..     124     139 ..     120     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                                  HHHHHHHCCCSSEEEEE-TTGGGSH CS
                           SKI 52 sevlkelleeeglViatGGGavlse 76
                                  + +lkel++++++V+ tGGG++ ++
  gi|91773532|ref|YP_566224.1| 25 ASALKELARKHQIVVVTGGGVAARN 49
                                  5789****************98776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.69
                                   HHHHHHCCCSSEEEEE CS
                           SKI  53 evlkelleeeglViat 68 
                                   ++l+e+l+ + +Viat
  gi|91773532|ref|YP_566224.1| 124 AILAEYLNADMMVIAT 139
                                   5678888888899988 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 ?   11.7   1.5   1.9e-05      0.11      28      58 ..      35      65 ..      11      78 .. 0.84
   2 ?    1.0   1.7     0.038   2.2e+02      27      59 ..     103     139 ..      98     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                  --EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                   AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlD 58
                                  +  v+v GgGva  + i +a+g+ga+ +v+D
  gi|91773532|ref|YP_566224.1| 35 HQIVVVTGGGVAARNYIDVARGVGANEVVCD 65
                                  456999*******************988887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.038
                                   ---EEEEESTSHHHHH....HHHHHHHTT-EEEEEES CS
                   AlaDh_PNT_C  27 epakvlviGgGvaGlq....AiatakglgakVtvlDv 59 
                                   + +k++v+Gg + G+     A+  a  l+a+ +v+ +
  gi|91773532|ref|YP_566224.1| 103 ASGKIVVMGGVIPGQTtdavAAILAEYLNADMMVIAT 139
                                   4689999999998876222245556666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1483.22
//
Query:       gi|91773533|ref|YP_566225.1|  [L=428]
Description: flagella protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29   99.5   0.1    2.1e-28   98.0   0.1    1.8  1  Arch_fla_DE      Archaeal flagella protein
    2.3e-21   75.9   4.0    2.3e-21   75.9   4.0    5.1  5  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00027   20.9  14.8      0.045   13.8   3.0    3.4  3  DUF1664          Protein of unknown function (DUF1664)
  ------ inclusion threshold ------
      0.026   15.0  18.3       0.49   10.9   3.6    3.4  4  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.31   10.9  12.5       0.93    9.4   1.6    3.1  3  Sec34            Sec34-like family
       0.35   10.7  16.1        0.8    9.5   3.2    3.0  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.48    9.8  17.4        1.1    8.6   6.2    2.3  2  GAS              Growth-arrest specific micro-tubule binding
        1.2    9.2   8.0    1.1e+02    2.9   8.0    2.6  1  Nup54            Nucleoporin complex subunit 54
        1.4    8.7  18.4        1.4    8.7   1.8    2.9  3  DUF724           Protein of unknown function (DUF724)
        1.7    8.8  20.3      0.037   14.2   2.3    2.8  2  Tropomyosin_1    Tropomyosin like
          2    8.7  14.2        2.4    8.5   0.5    4.0  4  ABC_tran_CTD     ABC transporter C-terminal domain
        2.1    8.2  18.1       0.22   11.4   3.8    2.8  3  NleF_casp_inhib  NleF caspase inhibitor
        2.3    8.6  16.2        5.4    7.4   1.9    3.5  3  BLOC1_2          Biogenesis of lysosome-related organelles co
        2.4    8.2  18.8        4.9    7.2   2.8    2.5  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        3.2    7.4  13.0       0.37   10.4   0.5    2.6  2  Lebercilin       Ciliary protein causing Leber congenital ama
        4.4    5.1  10.2        6.6    4.5  10.2    1.2  1  Prominin         Prominin
        7.7    7.0  12.2        3.4    8.1   0.3    3.5  3  Snapin_Pallidin  Snapin/Pallidin
        8.3    6.9  19.3         14    6.2   0.1    3.5  3  ZapB             Cell division protein ZapB
        9.4    4.0  17.0        1.9    6.3   9.3    2.0  2  V_ATPase_I       V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.1   2.2e-31   2.1e-28       4      94 ..     313     399 ..     310     400 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 2.2e-31
                   Arch_fla_DE   4 pyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelkkseltvedHv 84 
                                   ++Le++++++++ +v+l+W+efL+ervg++n+++aldyY +i+Wiseevr+e+++y++gi++ + ek +++   l +edH+
  gi|91773533|ref|YP_566225.1| 313 VRLESIKKNPMSVVVLLNWIEFLMERVGRNNLMDALDYYVDIEWISEEVRSEIMAYARGIDY-YVEKPTWR---LLPEDHT 389
                                   68***********************************************************9.99999997...******* PP

                   Arch_fla_DE  85 kSllyiekla 94 
                                   kSll+ie+l 
  gi|91773533|ref|YP_566225.1| 390 KSLLFIERLC 399
                                   ********96 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 !   75.9   4.0   2.4e-24   2.3e-21       1      55 []     105     159 ..     105     159 .. 0.99
   2 ?    2.1   0.3      0.27   2.6e+02       9      37 ..     172     200 ..     168     202 .. 0.79
   3 !    7.7   0.9    0.0048       4.5       6      40 ..     210     251 ..     207     254 .. 0.75
   4 ?   -0.2   2.1       1.4   1.3e+03      22      28 ..     261     267 ..     242     295 .. 0.52
   5 ?   -0.1   0.0       1.4   1.3e+03      15      33 ..     407     425 ..     402     426 .. 0.59

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.4e-24
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPFv 55 
                                   +i+ lEnklsk+++ +++v++en++++++ve+++++V +llsLYE+VsnqvNPFv
  gi|91773533|ref|YP_566225.1| 105 KIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELLSLYEIVSNQVNPFV 159
                                   89****************************************************8 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.27
                     FlaC_arch   9 lsklsteletvkkeneelsksveelkenV 37 
                                   ++k++ +++ v +    l+++v+ l+++ 
  gi|91773533|ref|YP_566225.1| 172 FDKTEKRISEVADYTMMLKNDVDALNQSM 200
                                   56788888888888889999999999876 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0048
                     FlaC_arch   6 Enklsklst.......eletvkkeneelsksveelkenVkdl 40 
                                   E k+s+++t        l t++++++ +s+  ++++ n++d+
  gi|91773533|ref|YP_566225.1| 210 EAKISNIDTkidvfadALITLQENINVISERSDQIEANINDI 251
                                   556666666444444489999999999999999999999875 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.4
                     FlaC_arch  22 eneelsk 28 
                                   ++eel+k
  gi|91773533|ref|YP_566225.1| 261 KIEELEK 267
                                   3333322 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.4
                     FlaC_arch  15 eletvkkeneelsksveel 33 
                                   +l++v +e+ +++  +eel
  gi|91773533|ref|YP_566225.1| 407 MLSMVDREMAKVKHGLEEL 425
                                   4556666666666555554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.2   0.00019      0.18      72     120 ..      96     144 ..      91     147 .. 0.92
   2 ?    1.3   0.1      0.35   3.3e+02      80     109 ..     170     199 ..     152     206 .. 0.62
   3 !   13.8   3.0   4.8e-05     0.045      65     122 ..     210     267 ..     198     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                       DUF1664  72 dkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                   dk++de+++ +k+++++++++   +s+++++ + vk++ve++++++ ++
  gi|91773533|ref|YP_566225.1|  96 DKRVDENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLEL 144
                                   6789***************************************998665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.35
                       DUF1664  80 eiskeikeevtevredlseigedvesvkea 109
                                   e   ++++ ++ev + +  +++dv+++++ 
  gi|91773533|ref|YP_566225.1| 170 ERFDKTEKRISEVADYTMMLKNDVDALNQS 199
                                   334455555666666666666666555554 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 4.8e-05
                       DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                   +++i ++d+k+d  +++   ++e+++ ++e  ++i+ +++ + ++ + + +k+e++e+
  gi|91773533|ref|YP_566225.1| 210 EAKISNIDTKIDVFADALITLQENINVISERSDQIEANINDIAQTTSVFSEKIEELEK 267
                                   579****************************************************996 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.6   0.00052      0.49      12      60 ..     105     153 ..     103     159 .. 0.92
   2 ?    7.6   0.9    0.0054       5.1      35      62 ..     211     238 ..     173     239 .. 0.66
   3 ?   10.5   3.6    0.0007      0.66      11      53 ..     211     253 ..     200     274 .. 0.72
   4 ?    3.1   0.6      0.14   1.3e+02       8      46 ..     243     279 ..     242     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                       NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                    ika+++k++ ++ ++ +vq + +dv+   ek+d+   +L +l + v+n
  gi|91773533|ref|YP_566225.1| 105 KIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELLSLYEIVSN 153
                                   69********************************999999999888875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0054
                       NPV_P10  35 pdvtelnekLdaqsaqLaeletkvenIq 62 
                                    +++++ +k+d  +++L +l+++++ I+
  gi|91773533|ref|YP_566225.1| 211 AKISNIDTKIDVFADALITLQENINVIS 238
                                   3567777888888888888888777775 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0007
                       NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLae 53 
                                   a i+++d+k+d+  +++  +qen++ ++e +++++a  + +a+
  gi|91773533|ref|YP_566225.1| 211 AKISNIDTKIDVFADALITLQENINVISERSDQIEANINDIAQ 253
                                   5799*******************99988766666654333332 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.14
                       NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLda 46 
                                   +I a+i+++ +  ++ +++++++++   d++el++kL++
  gi|91773533|ref|YP_566225.1| 243 QIEANINDIAQTTSVFSEKIEELEK--IDISELEKKLEQ 279
                                   7889999999999999999999998..789999999985 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.3    0.0022       2.1       6      66 ..     121     181 ..      96     191 .. 0.63
   2 ?    9.4   1.6   0.00098      0.93       6      84 ..     121     199 ..     116     221 .. 0.85
   3 ?    7.1   1.8     0.005       4.8       9      65 ..     210     266 ..     205     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0022
                         Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                   +s ++e +++ + ++++ +++ el + ++ vs++ + +  + ++ ++  +r++++ + i+e
  gi|91773533|ref|YP_566225.1| 121 SSVQRENQDVKTTVEKIDQSVLELLSLYEIVSNQVNPFVGDEQNSTATIERFDKTEKRISE 181
                                   4455566666666666666666666666666666666666666666666666666666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00098
                         Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLnsp 84 
                                   +s ++e +++ + ++++ +++ el + ++ vs++ + +  + ++ ++  +r++++ + i+e  +y   l++    Ln++
  gi|91773533|ref|YP_566225.1| 121 SSVQRENQDVKTTVEKIDQSVLELLSLYEIVSNQVNPFVGDEQNSTATIERFDKTEKRISEVADYTMMLKNDVDALNQS 199
                                   67789999****************************************************9988877777766666665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.005
                         Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                   e+++ ++ +++d   + L +l+e+ + +se++ +++++ +++ + ++ ++e  ee+e
  gi|91773533|ref|YP_566225.1| 210 EAKISNIDTKIDVFADALITLQENINVISERSDQIEANINDIAQTTSVFSEKIEELE 266
                                   566677777788888888888888888888888888888888887777777777665 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.0    0.0039       3.7     113     159 ..      96     142 ..      82     153 .. 0.74
   2 ?    0.8   0.2       0.4   3.7e+02     114     151 ..     163     200 ..     146     214 .. 0.75
   3 ?    9.5   3.2   0.00085       0.8     106     162 ..     210     266 ..     200     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0039
                                   HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 113 rqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasie 159
                                    +rv+e +++++  +++l++i  a+++v+ + q++++++e++ +s+ 
  gi|91773533|ref|YP_566225.1|  96 DKRVDENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVL 142
                                   56788888888888888888888888888888888888887776664 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 114 qrveegselveetgealkeiveavaevadlvqeiaaas 151
                                   q+   + e  ++t++ ++e+++ +  +++ v+ ++++ 
  gi|91773533|ref|YP_566225.1| 163 QNSTATIERFDKTEKRISEVADYTMMLKNDVDALNQSM 200
                                   44556677788888888888888888888887777664 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00085
                                   ....HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 106 vesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevn 162
                                    + +++  +++++ ++   + +e+++ i+e+ +++++ +++ia++++  s+ iee  
  gi|91773533|ref|YP_566225.1| 210 EAKISNIDTKIDVFADALITLQENINVISERSDQIEANINDIAQTTSVFSEKIEELE 266
                                   467888899999999999999*****************************9999875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.4    0.0041       3.9      23     121 ..     101     199 ..      96     227 .. 0.75
   2 ?    8.6   6.2    0.0012       1.1      30      93 ..     229     291 ..     225     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0041
                           GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                   +N ++Ik l +++ +++    + ++e +++++  +++ + + ++    e   +q++ +  d q  +++ +r  ++ek +++
  gi|91773533|ref|YP_566225.1| 101 ENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELLSLYEIVSNQVNPFVGDEQNSTATIERFDKTEKRISE 181
                                   677778888888888888888888888888888888888888888888888888888888999999999999999999988 PP

                           GAS 104 lkwehevleqrfekveke 121
                                   +     +l+  ++++ ++
  gi|91773533|ref|YP_566225.1| 182 VADYTMMLKNDVDALNQS 199
                                   888888888888888773 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                           GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaee.eveeLrkqlknyekdkqslknlkar 93 
                                   +l e+i+ + ++ ++ e ++++i+q  +  +e+++++e+ ++ eL+k+l++   +++  +++k+ 
  gi|91773533|ref|YP_566225.1| 229 TLQENINVISERSDQIEANINDIAQTTSVFSEKIEELEKiDISELEKKLEQTFLERN--QQSKKT 291
                                   688999999999999999999999999999999999876489999999988655444..333333 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   8.0      0.11   1.1e+02      43     120 ..      97     173 ..      92     297 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHH CS
                         Nup54  43 kevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletle 120
                                   k v++  +++k+++++l+++      +++ + +++k++  ++ + +l+ll+  ei++++  +   +E++  a++e  +
  gi|91773533|ref|YP_566225.1|  97 KRVDENANKIKALENKLSKID-VAISSVQRENQDVKTTVEKIDQSVLELLSLYEIVSNQVNPFVGDEQNSTATIERFD 173
                                   555555666666666666666.55556666666666666666666666666666666666655555555555444433 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.8    0.0014       1.4     115     172 ..      96     153 ..      83     168 .. 0.83
   2 ?    0.3   0.1      0.57   5.4e+02     124     151 ..     164     197 ..     152     224 .. 0.62
   3 ?    6.8   5.7    0.0056       5.3      95     162 ..     225     293 ..     213     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                        DUF724 115 ekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaeklee 172
                                   +k++ e++++ + le+++++++ +i+ ++r+++ +k+  e+ d+++ +l s  e +++
  gi|91773533|ref|YP_566225.1|  96 DKRVDENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELLSLYEIVSN 153
                                   567788888899999*********************9999999999988877766655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.57
                        DUF724 124 ekrkleeeidelekkilelerqlallk......e 151
                                   +++   e +d++ek+i+e+    ++lk      +
  gi|91773533|ref|YP_566225.1| 164 NSTATIERFDKTEKRISEVADYTMMLKndvdalN 197
                                   3444556778888888888888888874444332 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0056
                        DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeeidelek.kilelerqlallkekkeaadkeiar 162
                                   + L+ l+++ + + e++ ++e +i + ++  + ++e+i+elek  i+ele++l+++  ++++++k+  +
  gi|91773533|ref|YP_566225.1| 225 DALITLQENINVISERSDQIEANINDIAQTTSVFSEKIEELEKiDISELEKKLEQTFLERNQQSKKTNN 293
                                   57999************************************9857*******99877444444444333 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.3   3.9e-05     0.037      14      61 ..      97     144 ..      93     156 .. 0.91
   2 ?   -1.5  10.5       2.6   2.5e+03      36      99 ..     212     280 ..     161     297 .. 0.43

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                 Tropomyosin_1  14 ekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkea 61 
                                   ++++e  +k+K+le++  + +  i+s ++ nq +   vek+++++ e 
  gi|91773533|ref|YP_566225.1|  97 KRVDENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLEL 144
                                   6999**************************************999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                 Tropomyosin_1  36 eiksLtkknqqleeevekleeklkeakekaeesekkktnne.......altrkiqlLEe.eleesdkkLket 99 
                                   +i+++ +k+++  + + +l+e+++   e +++    ++n +        ++ ki+ LE  ++ e +kkL++t
  gi|91773533|ref|YP_566225.1| 212 KISNIDTKIDVFADALITLQENINVISERSDQI---EANINdiaqttsVFSEKIEELEKiDISELEKKLEQT 280
                                   333333333333333333333332222221111...111110001111222222222222222222222222 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 ?    8.5   0.5    0.0025       2.4      10      62 ..      99     149 ..      95     150 .. 0.77
   2 ?   -0.3   0.0       1.4   1.3e+03      22      46 ..     191     216 ..     168     227 .. 0.62
   3 ?    2.6   5.2      0.17   1.6e+02      12      59 ..     229     279 ..     207     284 .. 0.76
   4 ?   -0.5   0.0       1.6   1.6e+03      45      61 ..     410     426 ..     403     427 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0025
                  ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                                    +e  ++I aLE+++++++ ++++ +     + ++ + +++++   eL  lye
  gi|91773533|ref|YP_566225.1|  99 VDENANKIKALENKLSKIDVAISSVQ--RENQDVKTTVEKIDQSVLELLSLYE 149
                                   5566689****************987..6667777777777777777777776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                  ABC_tran_CTD  22 eeiaeleaeladpelysdp.eklael 46 
                                   ++  +l++ ++ p++     +k++ +
  gi|91773533|ref|YP_566225.1| 191 NDVDALNQSMEMPGISGETeAKISNI 216
                                   45556666666666553332444444 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.17
                  ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdp..eklaelsae.leeleaeLee 59 
                                   +l + I+ + e+  ++ea ++d + ++    ek+ el +  + ele++Le+
  gi|91773533|ref|YP_566225.1| 229 TLQENINVISERSDQIEANINDIAQTTSVfsEKIEELEKIdISELEKKLEQ 279
                                   6889999999999999**999998554433555555554346666666665 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.6
                  ABC_tran_CTD  45 elsaeleeleaeLeely 61 
                                    + +e++++++ Leely
  gi|91773533|ref|YP_566225.1| 410 MVDREMAKVKHGLEELY 426
                                   567899********998 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.6     0.028        26      54     148 ..     109     203 ..      82     205 .. 0.69
   2 ?   11.4   3.8   0.00023      0.22       6      63 ..     206     263 ..     204     291 .. 0.79
   3 ?   -3.3   0.0       7.9   7.5e+03      83     104 ..     341     361 ..     338     378 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.028
               NleF_casp_inhib  54 eredlYevedykleggqkveLkegitaedRdnylkdlvalyqik.navkekidnakikt.....ikdsvkkvvdeihngkv 128
                                     ++l   +d+ ++++q+ +     t+e+ d+ + +l+ ly+i+ n v+  + ++++ t     +++  k++ ++  + + 
  gi|91773533|ref|YP_566225.1| 109 LENKL-SKIDVAISSVQRENQDVKTTVEKIDQSVLELLSLYEIVsNQVNPFVGDEQNSTatierFDKTEKRISEVADYTM- 187
                                   44444.3589999999999999999***************9997356777776555443000004444444444444444. PP

               NleF_casp_inhib 129 svdaklagDlkAleknrkvP 148
                                        l +D+ Al++  ++P
  gi|91773533|ref|YP_566225.1| 188 ----MLKNDVDALNQSMEMP 203
                                   ....5999999999998888 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00023
               NleF_casp_inhib   6 teetektlkdIkdklklifereiastTaeekikElsdkltklknsvlseredlYeved 63 
                                     ete  + +I+ k+++  +  i +    + i E sd++++ +n++ ++ +   e ++
  gi|91773533|ref|YP_566225.1| 206 SGETEAKISNIDTKIDVFADALITLQENINVISERSDQIEANINDIAQTTSVFSEKIE 263
                                   679****************999999999999****************99876666533 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.9
               NleF_casp_inhib  83 Rdnylkdlvalyqiknavkeki 104
                                   R+n++  l ++  i+  ++e++
  gi|91773533|ref|YP_566225.1| 341 RNNLMDALDYYVDIE-WISEEV 361
                                   777777776666553.344444 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 ?    7.4   1.9    0.0058       5.4      31      75 ..     101     145 ..      96     153 .. 0.74
   2 ?    4.7   1.9     0.039        37      39      95 ..     189     248 ..     162     249 .. 0.55
   3 ?    5.5   3.7     0.022        21      50      92 ..     224     266 ..     208     279 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0058
                       BLOC1_2  31 aasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                   + ++k+k+l+++++++ + ++ ++++++ ++  +++idq   ++ 
  gi|91773533|ref|YP_566225.1| 101 ENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELL 145
                                   567899999999999999999999977777777777776544444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.039
                       BLOC1_2  39 lkdvaaslekklek..ln.ekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                   lk+ ++ l++++e   ++ e+++++++  ++id + + + +L+e+++++ e s ++Ea++
  gi|91773533|ref|YP_566225.1| 189 LKNDVDALNQSMEMpgISgETEAKISNIDTKIDVFADALITLQENINVISERSDQIEANI 248
                                   333333333333321111133446666667777777777788888888888888888765 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.022
                       BLOC1_2  50 leklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                   +++l  ++e+++   ++ dqie++++++ ++ s+  e + eLE
  gi|91773533|ref|YP_566225.1| 224 ADALITLQENINVISERSDQIEANINDIAQTTSVFSEKIEELE 266
                                   3333333333333333334444444444444444433333333 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.8    0.0052       4.9      56     108 ..     101     153 ..      93     166 .. 0.84
   2 ?    4.9   9.5     0.026        24       5     123 ..     165     290 ..     161     297 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0052
                CENP-F_leu_zip  56 tlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslen 108
                                   +  ++i+ l+++l+++ + ++++++e+++++  ++k  + v eL sl + ++n
  gi|91773533|ref|YP_566225.1| 101 ENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELLSLYEIVSN 153
                                   55678999999999999999999999999999999999999999877666655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.026
                CENP-F_leu_zip   5 klhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeL 85 
                                      + e++ ++e++ + + d    L+ ++  ++++ e   +  Et+ a+++++ ++i+  a  l  l+ +++ +++  +++
  gi|91773533|ref|YP_566225.1| 165 STATIERFDKTEKRISEVADYTMMLKNDVDALNQSMEMPGISGETE-AKISNIDTKIDVFADALITLQENINVISERSDQI 244
                                   5555666666666666666667777777777777777777777665.5677777777777777777777777777555554 PP

                CENP-F_leu_zip  86 e.......kelqkkqervseLeslnss.lenlleekEqekvqmkee 123
                                   e       +      e+++eLe++  s le+ le+   e+ q +++
  gi|91773533|ref|YP_566225.1| 245 EanindiaQTTSVFSEKIEELEKIDISeLEKKLEQTFLERNQQSKK 290
                                   4000000044444567788887765332555555544443333333 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00039      0.37       8      39 ..     101     132 ..      95     142 .. 0.90
   2 ?    0.3   6.4      0.51   4.8e+02      80     164 ..     210     294 ..     162     298 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                    Lebercilin   8 arllkikeLqnelaelqskleelrkEnklLkr 39 
                                   ++ +kik L+n+l++++  ++ +++En+ +k+
  gi|91773533|ref|YP_566225.1| 101 ENANKIKALENKLSKIDVAISSVQRENQDVKT 132
                                   6789************************9997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.51
                    Lebercilin  80 qekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekee.kikeLerkleleeksfrrqla 159
                                   ++k ++ + k+    ++l  l+++++  ++ s++ +    +++++  +  ++k+ee e+ +i+eLe+kle++  ++++q +
  gi|91773533|ref|YP_566225.1| 210 EAKISNIDTKIDVFADALITLQENINVISERSDQIEA-NINDIAQTTSVFSEKIEELEKiDISELEKKLEQTFLERNQQSK 289
                                   4455555555555555555555555555555433332.4455555555556666654432677777777777666666666 PP

                    Lebercilin 160 aekkk 164
                                   +++++
  gi|91773533|ref|YP_566225.1| 290 KTNNS 294
                                   66554 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  10.2     0.007       6.6     242     413 ..     100     267 ..      86     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.007
                      Prominin 242 erllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcl.dqlpnv 320
                                   ++ ++++k+ +++L++++   ++++ + ++ ++ ++++ +++ ++ls  ++ s++ +         ++  +++   +++  
  gi|91773533|ref|YP_566225.1| 100 DENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELLSLyEIVSNQVNP--------FVGDEQNStATIERF 172
                                   4556778888888888888888888888888888888888888888875555444444........444444443567788 PP

                      Prominin 321 devlealeevletnlssivkeglarlneipek..vknqtaevvpdlkkalakgreqikklakkip..realdavisdlent 397
                                   d+  +++ ev  ++++ + k++++ ln+  e+  +  +t+  ++++  +++   +++ +l+++i   +e+ d++  +++++
  gi|91773533|ref|YP_566225.1| 173 DKTEKRISEV--ADYTMMLKNDVDALNQSMEMpgISGETEAKISNIDTKIDVFADALITLQENINviSERSDQIEANINDI 251
                                   8888888888..788888888888888776654588888888888888888888888888888866667777777777777 PP

                      Prominin 398 erssktfddvvekyek 413
                                    ++++ f++++e++ek
  gi|91773533|ref|YP_566225.1| 252 AQTTSVFSEKIEELEK 267
                                   7888888888888776 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5     0.022        21      52      89 ..     100     137 ..      93     152 .. 0.84
   2 ?    8.1   0.3    0.0036       3.4      15      88 ..     172     250 ..     166     252 .. 0.77
   3 ?    1.2   0.6      0.53     5e+02      16      67 ..     242     293 ..     237     297 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.022
               Snapin_Pallidin  52 aevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                   +e  +++k   +KL++i   +ss++   q +k  +ek+
  gi|91773533|ref|YP_566225.1| 100 DENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKI 137
                                   45678999999999999999999999999998888877 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0036
               Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLk....eleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88 
                                    d+++++++e+ +    L++++d ln++++    + e +++ +++ ++++  a+ L++++ +++ ++er+ ++++ ++ 
  gi|91773533|ref|YP_566225.1| 172 FDKTEKRISEVADYTMMLKNDVDALNQSMEmpgiSGETEAKiSNIDTKIDVFADALITLQENINVISERSDQIEANIND 250
                                   58899999*******************9982222234445556666778888888999999999999999988877665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.53
               Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlne.kLkeleeaqeaevlpdlkeyakKLvn 67 
                                   d+++++++++ q+ +  +e++++l + ++ ele+  e +++ + ++  kK +n
  gi|91773533|ref|YP_566225.1| 242 DQIEANINDIAQTTSVFSEKIEELEKiDISELEKKLE-QTFLERNQQSKKTNN 293
                                   6788888888888888888888875424444444444.666666666666665 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.7     0.024        22       7      45 ..     107     145 ..      97     166 .. 0.66
   2 ?    6.2   0.1     0.015        14       3      34 ..     169     200 ..     167     240 .. 0.91
   3 ?    0.8   8.9       0.7   6.6e+02       7      58 ..     242     295 ..     210     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                          ZapB   7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenrele 45 
                                   + LE+k +k    i++ q e++++k  +e+  +   el 
  gi|91773533|ref|YP_566225.1| 107 KALENKLSKIDVAISSVQRENQDVKTTVEKIDQSVLELL 145
                                   456666666666666666666666666666666655554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                          ZapB   3 lelLeqLEskiqkaidtitlLqmeieeLkeen 34 
                                   +e +++ E++i++  d    L++ +++L +  
  gi|91773533|ref|YP_566225.1| 169 IERFDKTEKRISEVADYTMMLKNDVDALNQSM 200
                                   799*************************9976 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.7
                          ZapB   7 eqLEskiqkaidtitlLqmeieeLkeen.eelkeenrele.eeneqlkeereaw 58 
                                   +q E+ i+   +t +  +++ieeL++   +el+++ ++   e n+q k++ +++
  gi|91773533|ref|YP_566225.1| 242 DQIEANINDIAQTTSVFSEKIEELEKIDiSELEKKLEQTFlERNQQSKKTNNSQ 295
                                   788999999999999999999999886647777776665469999998877765 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 ?    2.4   1.3      0.03        28      62     104 ..      97     139 ..      81     167 .. 0.46
   2 ?    6.3   9.3     0.002       1.9      17     146 ..     164     294 ..     154     346 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.03
                    V_ATPase_I  62 sleapeekeldeleeelekleeelkelnenleklkkelnelve 104
                                   ++ ++++++++ le++l+k++  +++++++++++k++++++ +
  gi|91773533|ref|YP_566225.1|  97 KRVDENANKIKALENKLSKIDVAISSVQRENQDVKTTVEKIDQ 139
                                   3333444444444444444444444444444444433333322 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.002
                    V_ATPase_I  17 dvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea..eesleapeekeldeleeelekleeelkelnenlekl 95 
                                   + +a   +f k  +r+ e+     +l++ ++ l++ +     +  +e + ++ ++++d   + l +l+e+++ ++e ++++
  gi|91773533|ref|YP_566225.1| 164 NSTATIERFDKTEKRISEVADYTMMLKNDVDALNQSMEMPGISgeTEAKISNIDTKIDVFADALITLQENINVISERSDQI 244
                                   445555668888888888888888888888886555544433232333334445556666666666666666666666666 PP

                    V_ATPase_I  96 kkelnelvelkavlekakefleeeeeeeeeeeseeeeeekeeeeeeeseee 146
                                   +++ n++ ++++v+++  e le+ + +e e++ e++  e+ ++++++++++
  gi|91773533|ref|YP_566225.1| 245 EANINDIAQTTSVFSEKIEELEKIDISELEKKLEQTFLER-NQQSKKTNNS 294
                                   6666666666666655555554332222221111111111.1111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2120  (0.118244); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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):              19  [number of targets reported over threshold]
# CPU time: 0.98u 0.34s 00:00:01.32 Elapsed: 00:00:00.55
# Mc/sec: 2337.95
//
Query:       gi|91773534|ref|YP_566226.1|  [L=146]
Description: flagellar protein F [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.5   3.9    0.00026   21.2   3.9    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
       0.11   12.2   0.6       0.18   11.4   0.6    1.4  1  AbrB_C          AbrB C-terminal domain


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   3.9   2.9e-08   0.00026       8     132 ..      10     127 ..       2     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.9e-08
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--EEGGG-E CS
                Arch_flagellin   8 lIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspidlnktt 88 
                                    I fI  ++  +  + v+ ++ + ++++ + ++    ++++s+++i ++  d++++     + i ++ n G  +i l++++
  gi|91773534|ref|YP_566226.1|  10 SIFFITSLVLGTHSYAVMSTSNDIVTDAEDMKYNMQYQKLNSKITINSMALDDTSSI----LDINIT-NNG--NIVLASDE 83 
                                   599***********************************************9666664....******.***..9******* PP

                                   EEEEESS--EE--E..................T-EE-TT-EEEE CS
                Arch_flagellin  89 isvtddgqetlltadefgivvisdtdgsltngdevlekgekvel 132
                                   is++ dg++ ++t++  +  ++ d++  ++++d+   k+++v++
  gi|91773534|ref|YP_566226.1|  84 ISILLDGKVINYTYTPETRKWYPDETKMFSVTDDSGFKDKRVKV 127
                                   *******8888888855555555555555555555555555555 PP

>> AbrB_C  AbrB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   2.1e-05      0.18      16      32 ..      73      89 ..      63      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.1e-05
                        AbrB_C 16 anGkivLSkeGAeiLik 32
                                  +nG+ivL ++++ iL++
  gi|91773534|ref|YP_566226.1| 73 NNGNIVLASDEISILLD 89
                                  6**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 902.03
//
Query:       gi|91773535|ref|YP_566227.1|  [L=167]
Description: flagellar protein G [Methanococcoides burtonii DSM 6242]
Scores for complete 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  102.3   0.2    3.3e-29  102.2   0.2    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.036   14.2   2.9          2    8.6   0.2    2.7  2  Dexa_ind        Dexamethasone-induced
      0.079   11.7   0.3        0.1   11.3   0.3    1.1  1  HlyD_2          HlyD family secretion protein
      0.097   12.7   1.0       0.22   11.6   0.5    1.8  2  TPPK_C          Thiamine pyrophosphokinase C terminal


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.2   7.4e-33   3.3e-29       1     164 []      18     165 ..      18     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 7.4e-33
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                   +++ i ++I fI ++l A++++ v++ +++ l+++  s g+  +eq++++++i++d+  +++++t++++t+y k n+G++ 
  gi|91773535|ref|YP_566227.1|  18 AETAITHMIFFITAILLAMTVVAVMTSNVQSLTSATVSNGKVLSEQLKTDITIISDPELIPYDTTMEQYTFYAK-NTGKT- 96 
                                   6899**********************************************************************.***99. PP

                                   EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--EEE CS
                Arch_flagellin  82 idlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGastti 162
                                    +l+++ ++v++dg           +v +++ d sl ++d ++++g+++ ++v+v   +++  ++++++ + +enG s+++
  gi|91773535|ref|YP_566227.1|  97 -ELDSEYLDVLIDG----------LYVYPDELDISLFDQDVLWRPGDLLMINVTV---TEPLSDGDHRLLIAAENGRSDSM 163
                                   .999**********..........899****************************...79*******************99 PP

                                   EE CS
                Arch_flagellin 163 ef 164
                                   +f
  gi|91773535|ref|YP_566227.1| 164 DF 165
                                   87 PP

>> Dexa_ind  Dexamethasone-induced
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00044         2      59      84 ..      62      87 ..      19      91 .. 0.83
   2 ?    5.3   0.3    0.0047        21      44      75 ..     102     134 ..      98     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00044
                      Dexa_ind 59 dqalvdlgvlsdpgsvlydtdaeldv 84
                                  +q   d+ ++sdp  ++ydt  e   
  gi|91773535|ref|YP_566227.1| 62 EQLKTDITIISDPELIPYDTTMEQYT 87
                                  4666899*************988655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0047
                      Dexa_ind  44 yi.vlnvgivflpedmdqalvdlgvlsdpgsvl 75 
                                   y+ vl  g+   p+++d +l d  vl  pg  l
  gi|91773535|ref|YP_566227.1| 102 YLdVLIDGLYVYPDELDISLFDQDVLWRPGDLL 134
                                   5437778999*****************999765 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   2.2e-05       0.1      13      67 ..      19      77 ..      13      97 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.2e-05
                        HlyD_2 13 fnvlillvviiliYivvnlvisiikstieT...eivkngei.eesikkkgliirdekvi 67
                                   + +  ++++i ++++  +v+ ++ s+++     +v ng++ +e++k++ +ii d ++i
  gi|91773535|ref|YP_566227.1| 19 ETAITHMIFFITAILLAMTVVAVMTSNVQSltsATVSNGKVlSEQLKTDITIISDPELI 77
                                  44555555667777777777777777777511256888875499*********997765 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5     5e-05      0.22      14      42 ..      23      51 ..      17      59 .. 0.86
   2 ?   -1.4   0.0      0.56   2.5e+03      38      47 ..     100     109 ..      96     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                        TPPK_C 14 gallllvlAaLvAvavallvspagqsfld 42
                                   +++  + A+L+A+ v++++++ +qs++ 
  gi|91773535|ref|YP_566227.1| 23 THMIFFITAILLAMTVVAVMTSNVQSLTS 51
                                  689999****************9999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.56
                        TPPK_C  38 qsfldllidt 47 
                                   +++ld+lid 
  gi|91773535|ref|YP_566227.1| 100 SEYLDVLIDG 109
                                   689*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1097.52
//
Query:       gi|91773536|ref|YP_566228.1|  [L=231]
Description: ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   62.9   0.4    3.4e-17   62.6   0.4    1.1  1  ATPase     KaiC
    0.00043   19.7   0.0    0.00086   18.7   0.0    1.5  1  DnaB_C     DnaB-like helicase C terminal domain
     0.0021   17.7   0.0       0.46   10.0   0.0    2.2  2  AAA_25     AAA domain
     0.0041   17.6   0.1     0.0066   17.0   0.1    1.4  1  ABC_tran   ABC transporter
  ------ inclusion threshold ------
      0.013   15.3   0.4      0.057   13.1   0.1    1.9  2  IstB_IS21  IstB-like ATP binding protein
      0.015   14.8   0.2      0.054   13.0   0.0    1.8  2  RecA       recA bacterial DNA recombination protein
      0.024   14.3   0.2      0.078   12.7   0.2    1.9  1  AAA_24     AAA domain
      0.032   13.5   0.3      0.053   12.8   0.3    1.3  1  Rad51      Rad51
      0.042   13.8   0.1      0.074   13.0   0.1    1.6  1  NACHT      NACHT domain
      0.052   13.8   0.5       0.15   12.4   0.5    1.7  1  AAA_22     AAA domain
      0.061   13.8   1.1      0.091   13.2   1.0    1.5  1  AAA_23     AAA domain
       0.08   13.5   0.2       0.19   12.3   0.2    1.7  1  AAA_18     AAA domain
       0.11   12.4   3.4        1.6    8.6   0.8    2.3  2  NTPase_1   NTPase
       0.27   11.5   0.4       0.41   10.9   0.4    1.3  1  AAA_28     AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.4   2.6e-20   3.4e-17       7     211 ..      13     208 ..       9     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.6e-20
                        ATPase   7 glDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiid 87 
                                   +l + l gG+p+g+ v i G++G GK++++++ ++  +ek +  + f+++  + +  ++++ sl+  +     +g+l +i 
  gi|91773536|ref|YP_566228.1|  13 ELNDKLGGGFPKGSLVVIEGGSGGGKSTICQRITYGMIEK-DTSVTFISTQLTTKGYINQMYSLDYPIAPHLLKGRLLYIP 92 
                                   5778889****************************99999.***************************************9 PP

                        ATPase  88 asesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssse 168
                                   +    +        ++   +ie+l+ a + ++   +viD+i++l +++ + +    l  +++ l+++g + il+ e +s+ 
  gi|91773536|ref|YP_566228.1|  93 VIPLVQS------AKSRIDFIERLMGAKELFEKDVIVIDTISSLIKYSANTEKSLDLISFFKKLNGMGKVIILTIE-PSEL 166
                                   9999765......55666799***********************5555555556778899****************.4544 PP

                        ATPase 169 eaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhs 211
                                   ++         ++d  + L+ k    e++Rtl + k  g++  
  gi|91773536|ref|YP_566228.1| 167 GEDIASMFRS-SCDVYMTLKSKALGAEVKRTLVVNKFTGANGP 208
                                   4445555556.7999999******************8777655 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 !   18.7   0.0   6.7e-07   0.00086      10      82 ..      16      86 ..       9     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.7e-07
                                  HHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 10 DkltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtg 82
                                  Dkl +G+ kg l++i + ++ Gk++++  i   + + ++++v+++s   +++  ++++ s +  i  + l+ g
  gi|91773536|ref|YP_566228.1| 16 DKLGGGFPKGSLVVIEGGSGGGKSTICQRITYGMIE-KDTSVTFISTQLTTKGYINQMYSLDYPIAPHLLK-G 86
                                  78899**************************98885.6789*****************9999888777664.3 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00036      0.46      25      57 ..      17      49 ..       3      65 .. 0.79
   2 !    5.7   0.0    0.0078        10     129     164 ..     106     140 ..      82     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00036
                        AAA_25 25 lvkgllpagelallaGapgtGKttlaldlalav 57
                                   ++g  p+g+l+++ G +g GK+t++  + + +
  gi|91773536|ref|YP_566228.1| 17 KLGGGFPKGSLVVIEGGSGGGKSTICQRITYGM 49
                                  444445******************998776665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0078
                        AAA_25 129 dvdaleaaieevegvrlvviDplsralggdensnsd 164
                                   ++++l+ a +e  + +++viD++s++   + n ++ 
  gi|91773536|ref|YP_566228.1| 106 FIERLMGA-KELFEKDVIVIDTISSLIKYSANTEKS 140
                                   44444433.4445589*********99987776655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   5.2e-06    0.0066       7      51 ..      21      65 ..      16     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                                  EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                   + +g++v+i G +G GKSt+++ ++  +  +  ++++ +++l++
  gi|91773536|ref|YP_566228.1| 21 GFPKGSLVVIEGGSGGGKSTICQRITYGMIEKDTSVTFISTQLTT 65
                                  6889*******************9998888777777776666655 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   0.1   4.5e-05     0.057      49      84 ..      27      62 ..      22      68 .. 0.91
   2 ?   -0.1   0.0      0.53   6.8e+02     103     134 ..     113     144 ..      86     161 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                     IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                   +v+ G+sG GKs +   + +  +++++sv+f++++
  gi|91773536|ref|YP_566228.1| 27 LVVIEGGSGGGKSTICQRITYGMIEKDTSVTFISTQ 62
                                  58999***************************9975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.53
                     IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfevi 134
                                   +k+l + d++++D ++ l   +a++e+ +++i
  gi|91773536|ref|YP_566228.1| 113 AKELFEKDVIVIDTISSLIKYSANTEKSLDLI 144
                                   46788889999999987766666555555555 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.2e-05     0.054      41      90 ..      14      62 ..       3      81 .. 0.87
   2 ?   -0.8   0.0      0.68   8.8e+02     133     145 ..     120     132 ..      89     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                                  HHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS CS
                          RecA 41 ldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidae 90
                                  l+  lG GG+pkG ++ i G   +Gk+t++ ++   + +k+  ++fi ++
  gi|91773536|ref|YP_566228.1| 14 LNDKLG-GGFPKGSLVVIEGGSGGGKSTICQRITYGMIEKDTSVTFISTQ 62
                                  667788.************************9999999999999999765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.68
                                   SEEEEE-TTT--- CS
                          RecA 133 dlivvdsvaalvp 145
                                   d+iv+d++++l+ 
  gi|91773536|ref|YP_566228.1| 120 DVIVIDTISSLIK 132
                                   8999999988874 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   6.1e-05     0.078       5      80 ..      28     133 ..      24     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                        AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfi....dtekGlksldadkfpdie.................swedfldevv 57 
                                   ++i G sg GK+t++ ++         ++ fi     t +  ++++  ++p ++                 s +  +d+++
  gi|91773536|ref|YP_566228.1|  28 VVIEGGSGGGKSTICQRItygmiekDTSVTFIstqlTTKGYINQMYSLDYPIAPhllkgrllyipviplvqSAKSRIDFIE 108
                                   6889**************777776555555554442222334556666666555888999988888886655555555555 PP

                        AAA_24  58 el..aaeladyktlviDtideleel 80 
                                    l  a+el + +++viDti+ l ++
  gi|91773536|ref|YP_566228.1| 109 RLmgAKELFEKDVIVIDTISSLIKY 133
                                   5599999999**********99775 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   4.2e-05     0.053      24      58 ..      12      46 ..       3      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                                  HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHH CS
                         Rad51 24 kklDelLgGGietgsiteifGefrsGktqlchtlc 58
                                   +l++ LgGG++ gs+  i G ++ Gk+ +c+ ++
  gi|91773536|ref|YP_566228.1| 12 DELNDKLGGGFPKGSLVVIEGGSGGGKSTICQRIT 46
                                  578999*************************9875 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   5.8e-05     0.074       2      94 ..      27     131 ..      26     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-CCHHHHCCSCC CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvsevwavllelpe 81 
                                   lv+++G +G GK+t  q++   + e++      ++ F  ++ +++   n  +sl++ ++ +l++      +v+ ++++ + 
  gi|91773536|ref|YP_566228.1|  27 LVVIEGGSGGGKSTICQRITYGMIEKD-----TSVTFISTQLTTKGYINQmYSLDYPIAPHLLKGRLLYIPVIPLVQSAKS 102
                                   79*****************99888777.....3566666555555443334777777777776666555554444444444 PP

                                   CEE................EEEE-STT-S CS
                         NACHT  82 rlL................lilDglDelv 94 
                                   r+                 +++D +  l 
  gi|91773536|ref|YP_566228.1| 103 RIDfierlmgakelfekdvIVIDTISSLI 131
                                   44444444455555555555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   0.00011      0.15       6     131 ..      26     163 ..      23     168 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............erls 74 
                                   +++v+ G sG GK+t ++r+++   e       +++ v++  +++t+   + ++   ++    +               +s
  gi|91773536|ref|YP_566228.1|  26 SLVVIEGGSGGGKSTICQRITYGMIE-------KDTSVTFISTQLTTKGYINQMYSLDYPIAPHLlkgrllyipvipLVQS 99 
                                   678999***************99732.......444444444444444444444433333222223344555777743333 PP

                        AAA_22  75 seellealeqalrarav..ielliiDEaqhlr..s...eealeeLrsllnlsrkgvqliLvGtp 131
                                    +  ++ +e+ + a+    + +++iD +  l+  s   e+ l  ++ + +l+  g  +iL + p
  gi|91773536|ref|YP_566228.1| 100 AKSRIDFIERLMGAKELfeKDVIVIDTISSLIkySantEKSLDLISFFKKLNGMGKVIILTIEP 163
                                   3344477777777777777788888887777666333344444443332224666666666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.0   7.1e-05     0.091      20      53 ..      26      59 ..      21     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                        AAA_23 20 gltlItGpNGaGKTTildAiklaLygetprlsrk 53
                                   l++I G  G GK+Ti + i++++ ++ +     
  gi|91773536|ref|YP_566228.1| 26 SLVVIEGGSGGGKSTICQRITYGMIEKDTSVTFI 59
                                  589********************99876555544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00015      0.19       1     106 [.      28     166 ..      28     171 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                        AAA_18   1 IlltGtpGvGKttlakeL.....skrlgf........................gvnlrdvakenglllevdpealdeskrl 52 
                                   +++ G +G GK+t+++++     +                               +  +++k + l+++v p    +s + 
  gi|91773536|ref|YP_566228.1|  28 VVIEGGSGGGKSTICQRItygmiE----KdtsvtfistqlttkgyinqmysldYPIAPHLLKGRLLYIPVIPL--VQSAKS 102
                                   7899**************555542....144445565555555555555555444455555555555555555..444444 PP

                        AAA_18  53 dedkldklldaleenssaleegknlvidghlaeleseaakdikk...............vvLtaspeel 106
                                   ++d+ ++l+ a e       e +++vid + +   + a++++                 ++Lt +p+el
  gi|91773536|ref|YP_566228.1| 103 RIDFIERLMGAKELF-----EKDVIVIDTISSLIKYSANTEKSLdlisffkklngmgkvIILTIEPSEL 166
                                   444433333333333.....3478888888777777766665556666666666666666666666665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.8    0.0013       1.6       2      35 ..      28      61 ..      27      70 .. 0.84
   2 ?    4.3   0.1     0.027        34      94     147 ..     117     177 ..      97     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                                  EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                  v+i G +G GK+T++++++  + +++ +v+ + t
  gi|91773536|ref|YP_566228.1| 28 VVIEGGSGGGKSTICQRITYGMIEKDTSVTFIST 61
                                  7899**************9999899988875555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.027
                                   HHH-EEEE---STTGGG-HHHHHHHHHH.....HT.TTSEEEEE--SS-.-SHHHHHHHT- CS
                      NTPase_1  94 seadviviDEiGkmElkskkfkeaveev.....Lk.sekpvlavihrrk.dlalveeirer 147
                                    e+dviviD i ++   s++ +++++ +     L+  +k+++ +i  ++  +++   +r++
  gi|91773536|ref|YP_566228.1| 117 FEKDVIVIDTISSLIKYSANTEKSLDLIsffkkLNgMGKVIILTIEPSElGEDIASMFRSS 177
                                   689********99999998888888754333336667778888887766666666666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00032      0.41       2      20 ..      28      46 ..      27      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  +vi Gg+++GK+t++++++
  gi|91773536|ref|YP_566228.1| 28 VVIEGGSGGGKSTICQRIT 46
                                  8*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1470.24
//
Query:       gi|91773537|ref|YP_566229.1|  [L=549]
Description: type II secretion system protein E [Methanococcoides burtonii DSM 6242]
Scores for complete 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-44  150.9   0.0    4.9e-44  150.4   0.0    1.1  1  T2SSE        Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.024   14.4   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.051   13.5   0.1       0.23   11.4   0.1    1.9  2  Microtub_bd  Microtubule binding
       0.11   12.1   0.1       0.31   10.5   0.0    1.7  2  AAA_7        P-loop containing dynein motor region
       0.13   12.6   0.0       0.24   11.7   0.0    1.5  1  AAA_16       AAA ATPase 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 !  150.4   0.0   1.4e-47   4.9e-44       4     245 ..     170     415 ..     167     439 .. 0.92

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 1.4e-47
                         T2SSE   4 lleallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvl 84 
                                   ++e++++d+   dih      +++  ++ g++  ++++ ++a l + ++ +    ++ +s+ +p+ d++lp +g r++++ 
  gi|91773537|ref|YP_566229.1| 170 PIEPIIRDPYLEDIHSIGVVGIFIVHKIFGMMKTDLSFGDEAGLDQWLRSMSERIGRPVSDAKPIADGALP-DGSRINIIY 249
                                   7889999999*****999888555566666799**************************************.9****9987 PP

                         T2SSE  85 lPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtv 163
                                      v +   ++++Rk s+  +++ +l++ +al+ ++a+ +   +++ ++i +sG T sGKtt+l+a+l ++n +  +i t+
  gi|91773537|ref|YP_566229.1| 250 SLDVSKrgSSFTMRKFSEVPVSIIELIMWGALSSEMAAYMWMCLENGMSIFFSGETASGKTTMLNACLPFVNPT-AKIFTA 329
                                   5544444799****************************************************************.****** PP

                         T2SSE 164 EDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaaga 239
                                   ED++E+q+ ++   ql ++     + +v++ +ll+aaLR rP  i+vGEiR++e + + + ++TGH++ l+T Ha ++++ 
  gi|91773537|ref|YP_566229.1| 330 EDTAEVQPPHPVWQQLITRedgppESRVDTFALLKAALRSRPNYIIVGEIRGAEGAVAFQGMQTGHPV-LATFHASAVTKM 409
                                   *******************9************************************************.************ PP

                         T2SSE 240 lerLeq 245
                                   ++rL  
  gi|91773537|ref|YP_566229.1| 410 IQRLTG 415
                                   ***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 ?   14.4   0.0   6.7e-06     0.024       4      49 ..     273     323 ..     270     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.7e-06
                        AAA_29   4 lqlvNWgtfdght....ieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                   ++l+ Wg ++ +     ++  ++g +++++G++ sGK+T+l A      p+
  gi|91773537|ref|YP_566229.1| 273 IELIMWGALSSEMaaymWMCLENGmSIFFSGETASGKTTMLNACLPFVNPT 323
                                   677788877764311225555688899**************9987666655 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.49   1.8e+03      70     105 ..     230     267 ..     228     280 .. 0.68
   2 ?   11.4   0.1   6.5e-05      0.23      67      99 ..     281     312 ..     277     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.49
                                   CCHHHHHHHH.TT--EEEEE.EES.............. CS
                   Microtub_bd  70 eisqlvqsal.dgynvcifa.ygqTGsGKtyTmegeee 105
                                   + + +++ al dg+ ++i+  +     G ++Tm + +e
  gi|91773537|ref|YP_566229.1| 230 DAKPIADGALpDGSRINIIYsLDVSKRGSSFTMRKFSE 267
                                   56777888898999999985223333788999998443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.5e-05
                                   CCCCCHHHHHHHHTT--EEEEEEES........ CS
                   Microtub_bd  67 vfeeisqlvqsaldgynvcifaygqTGsGKtyT 99 
                                   + +e+++++ ++l++  ++if+ g+T sGKt  
  gi|91773537|ref|YP_566229.1| 281 LSSEMAAYMWMCLEN-GMSIFFSGETASGKTTM 312
                                   56899********54.479************44 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.6e-05      0.31      22      55 ..     285     318 ..     271     333 .. 0.86
   2 ?   -2.5   0.0      0.84     3e+03     103     112 ..     422     431 ..     403     433 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.6e-05
                         AAA_7  22 ysyllelllknkkpvllvGptGtGKtviikdllk 55 
                                   +   + ++l+n++++++ G+t +GKt++++ +l 
  gi|91773537|ref|YP_566229.1| 285 MAAYMWMCLENGMSIFFSGETASGKTTMLNACLP 318
                                   55678899********************998775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.84
                         AAA_7 103 vvFvDDlnmp 112
                                   v+F+D+ln+ 
  gi|91773537|ref|YP_566229.1| 422 VTFIDNLNVA 431
                                   78*****986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.8e-05      0.24      25      81 ..     297     350 ..     286     431 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareel 81 
                                    ++++sGe ++GK+++++++l  ++ +  if+++++ +     p  +++q+l ++e 
  gi|91773537|ref|YP_566229.1| 297 MSIFFSGETASGKTTMLNACLPFVNPTAKIFTAEDTAEV---QPPHPVWQQLITRED 350
                                   5899*****************777777555555444444...355554444434354 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 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:                        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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3475.97
//
Query:       gi|91773538|ref|YP_566230.1|  [L=551]
Description: flagellar assembly protein J [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-17   62.5   0.0    2.8e-12   46.7   0.1    3.6  5  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.1   1.5e-16   2.8e-12       2     122 ..      86     211 ..      85     217 .. 0.97
   2 ?   -5.6   3.0         1   1.8e+04     106     116 ..     227     237 ..     218     243 .. 0.61
   3 ?   -4.3   1.8      0.96   1.7e+04     100     118 ..     286     304 ..     275     309 .. 0.69
   4 !   22.0   0.0   6.7e-09   0.00012      14     120 ..     344     453 ..     330     460 .. 0.70
   5 ?   -4.5   1.4         1   1.8e+04     104     121 ..     490     507 ..     488     511 .. 0.50

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.5e-16
                                   HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-H CS
                         T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnL 77 
                                   ++++++ + a  p ++++++++++ ++g la+e ++i++ +  +  sls+a +    rtps  + ++++++ +  ++g ++
  gi|91773538|ref|YP_566230.1|  86 ITHMGVISTAETPRLDIIKIVSQNESYGFLAKESEKIYDLVTVWNmSLSDACRftskRTPSILYEDFLDRFAHGLQSGEDI 166
                                   789*****************************************99**************9888***************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                         T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillai 122
                                     +L++ +  +++e+e+ +++++  +e++ +l++ l+++li+la 
  gi|91773538|ref|YP_566230.1| 167 KSFLKAEQNVVMNEYESMYDSALYAIEVIKELFISLIMALIFLAS 211
                                   *****************************************9975 PP

  == domain 2  score: -5.6 bits;  conditional E-value: 1
                                   XXXXXXXXXXX CS
                         T2SSF 106 llllvvallvl 116
                                   l+++vv+++++
  gi|91773538|ref|YP_566230.1| 227 LMSVVVVVFIV 237
                                   44444444444 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 0.96
                                   HHHHTTXXXXXXXXXXXXX CS
                         T2SSF 100 aallepllllvvallvlli 118
                                   a +l+ +l+l++a++v++ 
  gi|91773538|ref|YP_566230.1| 286 AVILYGKLELAIAVAVVIT 304
                                   4566777777777777664 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 6.7e-09
                                   -HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHH CS
                         T2SSF  14 plveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeggnLaevLerlaeylee 90 
                                    ++eaL++l+ ++ +gpl++ ++++++rl+   +  +++     +t+s+ + ++ +++++a   gg+ + + + +a ++ +
  gi|91773538|ref|YP_566230.1| 344 LIDEALKSLQIHD-FGPLTKDVNALYKRLNTRVDKTKSWNffaaNTGSNLIQRFSAMFVEATNLGGQPEVIGDMIANNFHR 423
                                   4789*********.*****************************98887555777777777777777666666666666666 PP

                                   HHHHHHHHHHHHHTTXXXXXXXXXXXXXXX CS
                         T2SSF  91 erelrrkllaallepllllvvallvllill 120
                                     +lr+k+  +  + + +l+ +   +++ l
  gi|91773538|ref|YP_566230.1| 424 IVNLRKKRYQSASSLVGVLYGLTGGIGFTL 453
                                   666665555555555555554444444433 PP

  == domain 5  score: -4.5 bits;  conditional E-value: 1
                                   TTXXXXXXXXXXXXXXXX CS
                         T2SSF 104 epllllvvallvllilla 121
                                   e+l  ++++++v+  l++
  gi|91773538|ref|YP_566230.1| 490 EVLSAMILLIMVAHSLMS 507
                                   444555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3455.64
//
Query:       gi|91773539|ref|YP_566231.1|  [L=286]
Description: hypothetical protein Mbur_1577 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1700.14
//
Query:       gi|91773540|ref|YP_566232.1|  [L=163]
Description: 3-isopropylmalate dehydratase, small subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-18   65.9   0.0      8e-18   65.0   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 !   65.0   0.0   4.4e-22     8e-18      61     123 ..      41     102 ..      20     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 4.4e-22
                                   EHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                   Aconitase_C  61 dvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                   + +d  +  k+++ ++vv +g nfG+GSSRe+AA+al+  G+  via+ F+rIf +n+i+ gl
  gi|91773540|ref|YP_566232.1|  41 EGIDPDFSKKVHKGDVVV-GGSNFGCGSSREQAALALKYAGVSCVIAKFFGRIFFRNAINVGL 102
                                   566677777888888666.55***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1055.01
//
Query:       gi|91773541|ref|YP_566233.1|  [L=824]
Description: transmembrane oligosaccharyl transferase [Methanococcoides burtonii DSM 6242]
Scores for 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-30  103.9  33.5    3.9e-29  101.9  33.5    1.9  1  STT3      Oligosaccharyl transferase STT3 subunit
      3e-27   94.7   0.8    6.1e-27   93.7   0.8    1.6  1  AglB_L1   Archaeal glycosylation protein B long peripheral do
     0.0089   15.3   1.6     0.0089   15.3   1.6    2.5  3  7tm_7     7tm Chemosensory receptor


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 !  101.9  33.5   6.5e-33   3.9e-29      31     475 ..      48     566 ..      20     572 .. 0.73

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 6.5e-33
                                   -SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC.....HHHHHHHHCC CS
                          STT3  31 sefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld.....vsirevclwl 106
                                     +Dp+Y +R +e +++n       +++  wfd ++ yP G    + pl+ +    ++ ii+++         i  vc ++
  gi|91773541|ref|YP_566233.1|  48 GGNDPWYHLRNVESIVHN-------YPHMLWFDAYTNYPMGTGQVFAPLYDMF---LATIIWLIGFgnpsqDLIYTVCAYF 118
                                   568***************.......9***************999999999766...56666666554556556899***** PP

                                   HHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CC.CCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCS........ CS
                          STT3 107 pallgsLlaIpiyflvrelksdiaGllAAlllaiaPg.YlsrtvaGfyDtdmfeivlllfvlffflkaiktks........ 178
                                   p +l+ L++Ip+y++ + l++ +aGllAA++++++ g +lsr++ Gf+D+++ e +l+ ++ +f++ a+kt          
  gi|91773541|ref|YP_566233.1| 119 PVVLAALVVIPAYYIGKWLFDRRAGLLAAFFVSVSSGqFLSRSMIGFNDHHIAETLLSTVTAMFLIMAVKTARdhdisfeg 199
                                   ************************************************************************9******** PP

                                   ..........TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT............................ CS
                          STT3 179 ..........nkislaviaaliiflivlaWggyailiyallllfilalLiigr............................ 221
                                                +++ +a++++  + laW g   ++  ++ +++ +  i                               
  gi|91773541|ref|YP_566233.1| 200 lkngkfsslrSSLPYFILAGISLGAYTLAWKGA-LFFSLIIGVYVTVQHILDHmhgkktdymaiggmiifavalimvamtp 279
                                   *********999********************8.66666666666655544444445555555555555555555555555 PP

                                   .......S-CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHH.STTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC... CS
                          STT3 222 .......felklkiavtfsviiaflviaiivllflgfqvva.vseiigalgifgllqlvafgsvvvlvaelkfyqfis... 291
                                            lk+++a +f+  i++lv  +i ++  gf++    + +i ++  + l+  +a++s + l+  + +y +++   
  gi|91773541|ref|YP_566233.1| 280 ylggtkaLHLKALLAGLFAFPIMTLV--SIEMNRRGFNKYYyPGSLIVSFVAVVLISKIALPSAYDLIISVFSYFMRTggg 358
                                   55556667777777779999999999..99999999998777788888888888888889988888866666666666888 PP

                                   ..CHHTT.HHHHTT--..GGGHHHHHHHHHHHHCCCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCC CS
                          STT3 292 ..lfqpgilsevlgli..gevvtalavlglialwlgilyslldleyaklkikiiilvsvwlpvgllaltkglrfl.iftvP 367
                                     +   + l  ++g+    ++    a++g+++ ++  l+     e  k + +   ++ vw ++ + a+++  rf+  ++++
  gi|91773541|ref|YP_566233.1| 359 lsIAEAAPLLSRGGVFtlAPLWYNFALFGYVSFIALALF---AYEATKKNSQEKTFLIVWTVMIIWAMLQQNRFAyYYSIN 436
                                   884444444444444334666677777888887774444...44567777777888889999999**************** PP

                                   CHH..HCHHCCHHCTCHHHHHHH.........HHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHH.. CS
                          STT3 368 lgi..ifvgllleflavfvkiys.........vsqilfsgvvvillmltllpvlallaavkiskifstykdekeakikv.. 435
                                   ++i   ++g++l +la  +k             + + f  +v ++ +l l+  +  la        s+ ++  +a+     
  gi|91773541|ref|YP_566233.1| 437 AAIlsAYLGIKLLDLAGWSKLQDdvrtrkksvTTYTSFMENVKPIHILSLILIVGALA------YPSYGMAVQQAQGVSgp 511
                                   ***9999999999999999998888777776544444555555555555544443332......22222222222222211 PP

                                   ...HHHHH............HHHHCT.TTTTHHHTTHHHCHHHHHHHHHHHHHHH CS
                          STT3 436 ...aakav............aptksnglkeslewkantnrdsvvitwwdyghila 475
                                       + a                ++  +  s e+ +  ++   v++wwdygh + 
  gi|91773541|ref|YP_566233.1| 512 ngyWIDATlwlrnntpdpglDYYENYDVPVSGESYQYPEESYGVMSWWDYGHWIE 566
                                   1111222244444445666533444444455555333444455888888888765 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 !   93.7   0.8     1e-30   6.1e-27       1      92 []     733     822 ..     733     822 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1e-30
                                   -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETTEEEEE-- CS
                       AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagnvtaeveV 81 
                                   GAti+G+a+a++++t+s++++t q r+f+Y+q++   +dG+fe++vPYs++g  +getn+ v+a +pY+++++n++ +++V
  gi|91773541|ref|YP_566233.1| 733 GATIRGNAPADEKITLSTTIQTPQMRSFSYSQTM--ISDGSFEFVVPYSMTGPIEGETNFVVRAVEPYTISYENTSVQITV 811
                                   9*********************************..59******************************************* PP

                                   -HHHHHHT-EE CS
                       AglB_L1  82 pEeaVlsgetv 92 
                                   +E+aVl+g+++
  gi|91773541|ref|YP_566233.1| 812 SEKAVLEGDVI 822
                                   ********987 PP

>> 7tm_7  7tm Chemosensory receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.4      0.76   4.5e+03     145     174 ..     103     132 ..      90     146 .. 0.47
   2 !   15.3   1.6   1.5e-06    0.0089      38     156 ..     232     348 ..     223     361 .. 0.80
   3 !    3.3   1.7    0.0067        40     120     199 ..     380     459 ..     367     491 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.76
                         7tm_7 145 llsqyftlvlllllyllpylvlqlllllyf 174
                                   +  +++ l+++++ y+ + l   +++  y+
  gi|91773541|ref|YP_566233.1| 103 FGNPSQDLIYTVCAYFPVVLAALVVIPAYY 132
                                   444444444333333333333333333333 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.5e-06
                         7tm_7  38 lllvllvllvlflivlkreeyffrrsallevvynlqlvlglltvlvillsllfqrrrlarllnellkldrrlkrlgnrrnk 118
                                   +l+++l++ v+++++++ ++ + + ++++ + +++++ + l++v ++++    ++ +l  ll  l+++  + + + ++ + 
  gi|91773541|ref|YP_566233.1| 232 ALFFSLIIGVYVTVQHILDHMHGKKTDYMAIGGMIIFAVALIMVAMTPYLGGTKALHLKALLAGLFAFPIMTLVSIEMNR- 311
                                   799**************************************************************988877777777755. PP

                         7tm_7 119 rrfnrllllllvliillllvtllgylllsqyftlvlll 156
                                   r fn++++  +++++++++v +     l++ + l++ +
  gi|91773541|ref|YP_566233.1| 312 RGFNKYYYPGSLIVSFVAVVLIS-KIALPSAYDLIISV 348
                                   66666666666666666665555.44444444444444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.0067
                         7tm_7 120 rfnrllllllvliillllvtll.gylllsqyftlvlllllyllpylvlqlllllyfllllliy.ellrllnerLkqlvrel 198
                                   ++n+ l+ ++ +i+l+ l+++  +  ++++ ++l++++++ ++++l  q  + +y+ +   i   +l + +  L+ + + +
  gi|91773541|ref|YP_566233.1| 380 WYNFALFGYVSFIALA-LFAYEaTKKNSQEKTFLIVWTVMIIWAML-QQNRFAYYYSINAAILsAYLGIKLLDLAGWSKLQ 458
                                   5555555544444444.44444466667777777777777777777.8888888888888888788877777776665554 PP

                         7tm_7 199 r 199
                                   +
  gi|91773541|ref|YP_566233.1| 459 D 459
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (824 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); 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:                         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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 5999.60
//
Query:       gi|91773542|ref|YP_566234.1|  [L=634]
Description: asparagine synthase, glutamine-hydrolyzing [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-93  314.3   0.0    1.8e-93  314.0   0.0    1.1  1  Asn_synthase  Asparagine synthase
    1.7e-50  170.0   0.0      3e-50  169.2   0.0    1.4  1  GATase_7      Glutamine amidotransferase domain
      4e-45  153.3   0.0    7.1e-45  152.5   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
      5e-06   26.1   0.0    1.1e-05   25.0   0.0    1.5  1  DUF3700       Aluminium induced protein
     0.0019   17.8   0.0     0.0033   17.0   0.0    1.3  1  DUF1933       Domain of unknown function (DUF1933)
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.021   14.3   0.0    1.3  1  QueC          Queuosine biosynthesis protein QueC
       0.04   13.0   0.0      0.079   12.1   0.0    1.5  1  NAD_synthase  NAD synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.0   0.0   7.1e-97   1.8e-93       2     355 .]     235     629 ..     234     629 .. 0.89

  Alignments for each domain:
  == domain 1  score: 314.0 bits;  conditional E-value: 7.1e-97
                  Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfee.kgsdeakyakevaehlgtehtelvlte 81 
                                    r lLe++Vk+rl+++vp+G++LSGG+DS++++ l++++ ++p+ tFs+gf e  +  e++ a+e+a+ +gt+h+e+++++
  gi|91773542|ref|YP_566234.1| 235 TRLLLEESVKMRLMSEVPLGIYLSGGIDSGIVTGLMSKMVDEPIETFSVGFGErGEIGELSQAQEAADFFGTNHHEIIVDQ 315
                                   5789***********************************************6658899*********************** PP

                  Asn_synthase  82 eelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklp......... 153
                                    ++ + l+d+i+h +ep+ad+sa++++ ls++a +k+v+vvL G G+DE+fgGY   yk  l ++++ + +p         
  gi|91773542|ref|YP_566234.1| 316 GAFKQNLKDIIWHNDEPIADPSALAMFQLSKMA-SKHVTVVLNGAGGDEVFGGYI-SYKVGLANQKYHKIVPkvirqglvr 394
                                   *********************************.888*****************9.************9999999999999 PP

                  Asn_synthase 154 ....................................larslrasllarklrklaellelaeardleelaelyrlkasdsae 198
                                                                       ++++ +++ + +k++++ +  ++ +a                  +
  gi|91773542|ref|YP_566234.1| 395 pfvnaisphlsskmyvgiqsatqeveehgflftksvFSEEDKEDIYTDKIKDKIHHNTFEKA------------------T 457
                                   98887777777666666666555555555555555555555555555555555555554444..................0 PP

                  Asn_synthase 199 ................aelegedelhrelyldlktllpgdllrk.DrasmahglEaRvPflDhrlvevalrlppelklrgg 262
                                                      +++d l++++y d+k++l +++l + D+++m+ ++EaRvP +Dh++ve+a+++p elklrg 
  gi|91773542|ref|YP_566234.1| 458 tslfrgkrysgaiderSSAKNTDLLSKMMYADTKSYLVDHILLEtDKLTMSSSIEARVPIIDHKVVEFAASIPQELKLRGM 538
                                   44445555555555558899************************************************************* PP

                  Asn_synthase 263 ieKyiLRealegylPeeileRpKegfsapvgewklkgelrelaeellsdsrlakeglldreaveelleeheagkrnesrql 343
                                   +eKyiL+++ +g+lP++ ++R+K++f+ p+++w +k+el+e+ ++ l++s   ++g++++e+v++++++he+++  +++q+
  gi|91773542|ref|YP_566234.1| 539 TEKYILKKVGQGMLPPAAQNRKKRPFRIPIDTW-FKDELHEMSQQVLDESSIVEQGYFRPEVVKDIMKKHERAELLYNHQM 618
                                   *********************************.**************************************999****** PP

                  Asn_synthase 344 wslllsleawle 355
                                     ll  +e+w+e
  gi|91773542|ref|YP_566234.1| 619 YALL-VFEMWHE 629
                                   ***9.*****97 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0   1.2e-53     3e-50       1     122 [.      43     161 ..      43     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 1.2e-53
                      GATase_7   1 hrrlsiidseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewgeealerlnGmfAfa 81 
                                   hrrlsiid+e+g+QP++ +edg++ +v+nGeiyN+ +lr+eLe++ghrf+t+sDtev+++l+e+ +g++++++l+GmfAfa
  gi|91773542|ref|YP_566234.1|  43 HRRLSIIDLEGGHQPVC-NEDGTIYVVYNGEIYNFLSLRDELEKRGHRFQTSSDTEVIVHLYEE-YGKDLVHHLRGMFAFA 121
                                   99***************.79******************************************97.**************** PP

                      GATase_7  82 iwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                   +wd+++++lllaRDrlG+kPLyy++ + ++llfaSe+k++ 
  gi|91773542|ref|YP_566234.1| 122 LWDSNTRTLLLARDRLGVKPLYYTTID-NRLLFASEIKSIV 161
                                   **************************6.7*********985 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   0.0   2.8e-48   7.1e-45       1     134 []      28     156 ..      28     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 2.8e-48
                      GATase_6   1 pdasglaslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall 81 
                                   pd+sg   +++++++l+H+Rl+i++l+   g+qP+ +edg++++v+NGeiyn+ +lr+el++ +g++f++ sDtev+++l+
  gi|91773542|ref|YP_566234.1|  28 PDDSGS--FTDKGIGLGHRRLSIIDLE--GGHQPVCNEDGTIYVVYNGEIYNFLSLRDELEK-RGHRFQTSSDTEVIVHLY 103
                                   678888..9999**************7..999******************************.****************** PP

                      GATase_6  82 eelGeevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                   ee+G++++++lrGmfafa+wd+ ++tl lardrlgvkplyy++ +++l+fase
  gi|91773542|ref|YP_566234.1| 104 EEYGKDLVHHLRGMFAFALWDSNTRTLLLARDRLGVKPLYYTTIDNRLLFASE 156
                                   ****************************************************8 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.3e-09   1.1e-05      77     177 ..      65     162 ..      53     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.3e-09
                       DUF3700  77 ifClfqGslenlasLkkqy...GL.sktanevllvieayrtLrdrgPypadqvvkdleGkfafvlydskaktvfvaldadg 153
                                   i+ +++G++ n  sL+ +    G   +t+++  +++  y        y  + +v++l+G faf l+ds+++t+++a+d+ g
  gi|91773542|ref|YP_566234.1|  65 IYVVYNGEIYNFLSLRDELekrGHrFQTSSDTEVIVHLYEE------YG-KDLVHHLRGMFAFALWDSNTRTLLLARDRLG 138
                                   77788888888777764321114434556666666666653......43.5689*************************** PP

                       DUF3700 154 svplyWGiaadgsvvisdd.lelvk 177
                                     ply+ +  d +++++ + + +v+
  gi|91773542|ref|YP_566234.1| 139 VKPLYYTTI-DNRLLFASEiKSIVQ 162
                                   *****9765.555555555055555 PP

>> DUF1933  Domain of unknown function (DUF1933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.3e-06    0.0033      47     185 ..      63     206 ..      55     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                       DUF1933  47 ysayli..GslrnkrllrslltkieGrvsvlsdveilllirdklGsailslaeGdyclfiedkkG.tlelltearGlnlvy 124
                                   ++ y++  G+++n   lr+ l k   r    sd+e+++   +++G+ ++    G + + + d +  tl l  +  G  ++y
  gi|91773542|ref|YP_566234.1|  63 GTIYVVynGEIYNFLSLRDELEKRGHRFQTSSDTEVIVHLYEEYGKDLVHHLRGMFAFALWDSNTrTLLLARDRLGVKPLY 143
                                   6666654599***************************************************99972566667889****** PP

                       DUF1933 125 lvqadliwi.tdklklvskled.dkafdik..peseviktalktdnfspirnvsrlkPGtlnklr 185
                                       d++ + + ++k + +  + +ka+di   ++  + + al t++      +++l+PG +  +r
  gi|91773542|ref|YP_566234.1| 144 YTTIDNRLLfASEIKSIVQYSGyEKAVDIGtlHDYLTFRHALGTET--MFAGIKKLLPGHVMTYR 206
                                   **99998762566886666655389***964488889999999998..778999*****886665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.1e-06     0.021       5      59 ..     256     312 ..     254     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
                                   E--SSHHHHHHHHHHHHH-SE.EEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEE CS
                          QueC   5 llSGGlDSttvlalakkegke.vealtfdYgqr.hkkeleaakkiakelgveehkil 59 
                                    lSGG+DS +v+ l++k ++e +e+ ++ +g+r +  el+ a++ a+ +g ++h+i+
  gi|91773542|ref|YP_566234.1| 256 YLSGGIDSGIVTGLMSKMVDEpIETFSVGFGERgEIGELSQAQEAADFFGTNHHEII 312
                                   59***************997669**********8999*************9555543 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.1e-05     0.079       2      82 ..     232     314 ..     231     371 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHHHHHHHCTTSEEEEE..E-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                  NAD_synthase   2 ieelvdflkeyvkkagakgvvlG..lSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievkti 79 
                                   i++    l+e vk + +++v lG  lSGG+DS +v  l  k++ +e + +  +  ++  +  ++ +a++ a+ +g + ++i
  gi|91773542|ref|YP_566234.1| 232 IKKTRLLLEESVKMRLMSEVPLGiyLSGGIDSGIVTGLMSKMV-DEPIETFSVGfGERGEIGELSQAQEAADFFGTNHHEI 311
                                   6677889999*************556*********99999988.4444444444366666666777777777777776666 PP

                                   --H CS
                  NAD_synthase  80 dik 82 
                                    ++
  gi|91773542|ref|YP_566234.1| 312 IVD 314
                                   554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 3710.21
//
Query:       gi|91773543|ref|YP_566235.1|  [L=359]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-35  121.1   0.0    4.8e-35  120.6   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.5e-27   96.7   0.0    2.4e-27   96.0   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.6e-22   79.3   1.2    2.6e-22   79.3   1.2    2.0  3  Glyco_trans_4_2  Glycosyl transferase 4-like
    7.8e-20   71.6   0.5    1.3e-19   70.9   0.5    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    6.8e-13   49.4   0.0    9.4e-13   48.9   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      4e-08   33.6   0.0    8.6e-08   32.5   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.14   11.1   0.0       0.23   10.4   0.0    1.2  1  PDH              Prephenate dehydrogenase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0   1.9e-38   4.8e-35       7     171 ..     168     331 ..     163     332 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 1.9e-38
                                   HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
               Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                   ++++++++k  +ls  ++ ++ ++++l++a++l+ ++  +n++++i G g+ e +lk+la+ l++++ + f+g +++++++
  gi|91773543|ref|YP_566235.1| 168 NEKEWPHEKVQVLSNRNFYEVYNIETLLHAIPLVVEK-YENINFIIKGTGPLESSLKQLAKDLNIEKFIDFVGWIEYKEMP 247
                                   567789999***************************9.******************************************* PP

                                   HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHH CS
               Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgen 168
                                   ++l++ di+v +++s+g ++++lEAma+++++i++++gg++e ++dg +G+l++p n+e lae+i +l + +++rerlg++
  gi|91773543|ref|YP_566235.1| 248 KYLHKGDIYVSTATSDGTPVSVLEAMACKKACIVTDVGGVKEWIEDGMNGILIPPRNPEILAEKILDLARFPDERERLGNQ 328
                                   ********************************************************************************* PP

                                   HHH CS
               Glycos_transf_1 169 ark 171
                                   a+k
  gi|91773543|ref|YP_566235.1| 329 AYK 331
                                   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 !   96.0   0.0   9.4e-31   2.4e-27      10     132 ..     185     316 ..     176     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 9.4e-31
                                   --GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEEE--..- CS
               Glyco_trans_1_4  10 leenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadvfvaPs..e 81 
                                   ++ +v +++ ll+a+pl+ +k + ++++i G gp + ++l++la+  ++e+ + f+G++  ++++++l++ d++v +    
  gi|91773543|ref|YP_566235.1| 185 FY-EVYNIETLLHAIPLVVEKyEnINFIIKGTGPlE-SSLKQLAKdlNIEKFIDFVGWIeyKEMPKYLHKGDIYVSTAtsD 263
                                   53.56899***********99736**********66.599998877889888*******9889*************99878 PP

                                   --SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  82 gfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                   g+++++lEama+++++++tdvgg++e +  g ng+l+pp++pe lae+il+L 
  gi|91773543|ref|YP_566235.1| 264 GTPVSVLEAMACKKACIVTDVGGVKEWIedGMNGILIPPRNPEILAEKILDLA 316
                                   *****************************99*******************985 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   1.2     1e-25   2.6e-22       1     138 [.       2     134 ..       2     135 .. 0.90
   2 ?   -1.4   0.0      0.87   2.2e+03      26      53 ..     176     203 ..     174     232 .. 0.69
   3 ?   -3.0   0.0       2.6   6.6e+03      13      45 ..     243     275 ..     234     289 .. 0.64

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1e-25
               Glyco_trans_4_2   1 killlanlssvhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkgpleylk.a...fklkklikkikPDv 77 
                                   ki+l+a++ svht+r+a+++a++g eVh+it + +   ++   g+++h ++  +++   yl+ +   +k+++l+k++kPD+
  gi|91773543|ref|YP_566235.1|   2 KICLIADAISVHTVRWAEYFAQQGDEVHLITYESP---IQDISGVTIHAIR--SRFDSLYLAfIprhLKIYSLVKRLKPDI 77 
                                   8**********************************...77889*******9..666444444234448************* PP

               Glyco_trans_4_2  78 vhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksklkklllklalkkatkvist 138
                                   vhah +++ g+++++    +++ pvv+s+wG d+l  p  sk+  +  k +lk+a+k+++ 
  gi|91773543|ref|YP_566235.1|  78 VHAHFISKFGFHAAF----LNFRPVVMSAWGDDILIIPYWSKVLWYFTKKSLKRADKIYAV 134
                                   *********999966....69********************999999***********975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.87
               Glyco_trans_4_2  26 eVhvitpkkgakdeleaegihvhrlkvd 53 
                                   +V+v+++++ ++ + ++  +h ++l v+
  gi|91773543|ref|YP_566235.1| 176 KVQVLSNRNFYEVYNIETLLHAIPLVVE 203
                                   6999999999999999999998888544 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.6
               Glyco_trans_4_2  13 tlrlakeLakrgyeVhvitpkkgakdeleaegi 45 
                                   ++++ k+L+k ++ V+ +t+++    +lea+ +
  gi|91773543|ref|YP_566235.1| 243 YKEMPKYLHKGDIYVSTATSDGTPVSVLEAMAC 275
                                   556667777777777777776655555555444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.5   4.9e-23   1.3e-19       5     168 ..      11     162 ..      10     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 4.9e-23
                Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalg 85 
                                    +h+++ a+++a++G eV+++t +   p+++    +v +++++ +++  +l  ++ ++++  l+kr kpD+vHah+   +g
  gi|91773543|ref|YP_566235.1|  11 SVHTVRWAEYFAQQGDEVHLITYE--SPIQDI--SGVTIHAIRSRFDSLYLAFIPRHLKIYSLVKRLKPDIVHAHFISKFG 87 
                                   69********************55..445555..56888999989999999************************987776 PP

                Glyco_transf_4  86 aallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGv 166
                                   + + a +     p+V ++ g +           +s++l+++ ++ l+rad++ avS+ +a+ ++  +g+++++++Vip Gv
  gi|91773543|ref|YP_566235.1|  88 FHA-AFL--NFRPVVMSAWGDDI-----LIIPYWSKVLWYFTKKSLKRADKIYAVSDDIAQKIIFDFGISADHVEVIPFGV 160
                                   553.333..578**********5.....22234567888889999************************************ PP

                Glyco_transf_4 167 Dl 168
                                   D 
  gi|91773543|ref|YP_566235.1| 161 DS 162
                                   *6 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 !   48.9   0.0   3.7e-16   9.4e-13       3     160 .]      10     159 ..       8     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 3.7e-16
               Glyco_trans_4_4   3 igryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrll.rqrrerpdvvhahs. 81 
                                   i++++ ++a+ +a++G eV+++t + + ++      gv++h ++ +  +     la++++   +   ++r +pd+vhah  
  gi|91773543|ref|YP_566235.1|  10 ISVHTVRWAEYFAQQGDEVHLITYESPIQD----ISGVTIHAIRSRFDS---LYLAFIPRHLKIYsLVKRLKPDIVHAHFi 83 
                                   689********************9444443....69*****99988776...5677877665544455************6 PP

               Glyco_trans_4_4  82 ptaglaarlarrrrgiplvvtlhgll..lrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrvvvvpn 159
                                   ++ g+ a+++  r   p+v +++g++    ++  +++ l+  + + +l+rad + +vs+++a++++  +g+ ad+v+v+p 
  gi|91773543|ref|YP_566235.1|  84 SKFGFHAAFLNFR---PVVMSAWGDDilIIPY--WSKVLW-YFTKKSLKRADKIYAVSDDIAQKIIFdFGISADHVEVIPF 158
                                   6788866666655...*******987432234..666666.789**********************88************7 PP

               Glyco_trans_4_4 160 g 160
                                   g
  gi|91773543|ref|YP_566235.1| 159 G 159
                                   6 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 !   32.5   0.0   3.3e-11   8.6e-08       7      86 ..     261     342 ..     255     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.3e-11
               Glyco_trans_1_2   7 rsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                    s++  + ++Ea+ac    +++d  g+ e++++g  +il+   ++e laeki  l + p+er++++++a++ + ++ ++ +
  gi|91773543|ref|YP_566235.1| 261 TSDGTPVSVLEAMACKKACIVTDVGGVKEWIEDGMNGILIPprNPEILAEKILDLARFPDERERLGNQAYKVIDERGDWYR 341
                                   556666779******99888888************************************************9999988876 PP

               Glyco_trans_1_2  86 r 86 
                                    
  gi|91773543|ref|YP_566235.1| 342 I 342
                                   5 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     9e-05      0.23      60      90 ..     268     296 ..     250     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9e-05
                                   HHHHHHHHHS-TT-EEEE--S--CHHHHHHH CS
                           PDH  60 evlkelaphlkedalitDvgsvKekvvrele 90 
                                    vl+++a   k+++++tDvg+vKe + + ++
  gi|91773543|ref|YP_566235.1| 268 SVLEAMAC--KKACIVTDVGGVKEWIEDGMN 296
                                   57888887..**************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2090.62
//
Query:       gi|91773544|ref|YP_566236.1|  [L=303]
Description: NAD-dependent epimerase/dehydratase [Methanococcoides burtonii DSM 6242]
Scores for 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-48  162.7   0.0    1.3e-47  162.3   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
      2e-45  155.7   0.0    5.2e-43  147.7   0.0    2.2  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    8.5e-17   61.2   0.0    1.2e-16   60.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    8.6e-15   54.5   0.0    4.2e-13   48.9   0.0    2.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.8e-11   43.7   0.0    7.8e-10   38.4   0.0    2.6  2  NAD_binding_4    Male sterility protein
    3.8e-09   36.1   0.0    6.6e-08   32.0   0.0    2.5  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.063   13.3   0.0       0.11   12.5   0.0    1.4  1  FERM_F1          FERM F1 ubiquitin-like domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.3   0.0     5e-51   1.3e-47       1     240 [.      13     224 ..      13     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 5e-51
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   i +tG +GfiG+ l+ +l  kg +++ +++              l  +d+t+ ++++ + k+   d+ +hlA+  ++++s+
  gi|91773544|ref|YP_566236.1|  13 IAITGSRGFIGTRLTAQLRLKGLDLLEISHS-------------LDSIDITNWEQVKTIPKR---DVLVHLAGMTNIPESF 77 
                                   689****************************.............779*********999996...**************** PP

                                   HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT- CS
                     Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqygl 162
                                   ++p d++ +n+ gtln+le++r ++vkr++++s+  vYG+++ +p +e+    p+ pn+pY+ +Kl ge+l+ ay ++yg+
  gi|91773544|ref|YP_566236.1|  78 NHPRDVYTINTFGTLNMLEWCRLNDVKRFIYAST-FVYGNPQYTPVDEKH---PTLPNNPYSQSKLIGEELCNAYCRDYGI 154
                                   **********************************.9*******9999999...99************************** PP

                                   EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
                     Epimerase 163 naiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                                   ++i+lrlfn+yGp+   ++ + +ip++ir++ +gk   + l+d  ++Rdf+y++Dv++ + ++l+    g   +++ni
  gi|91773544|ref|YP_566236.1| 155 DVISLRLFNVYGPH---QKGDYLIPHIIRQLESGK---VSLKDPLPKRDFVYIDDVIDSFECALDSGLGG--CNVFNI 224
                                   **************...99***************9...77799*********************993222..347777 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 !    9.4   0.0   0.00024      0.63       2      47 ..      15      60 ..      14      63 .. 0.91
   2 !  147.7   0.0     2e-46   5.2e-43      58     331 ..      46     292 ..      39     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
                                  EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT.. CS
                 GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpk 47
                                  iTG  GfiG  l+ +L  kg +   i +  +s ++++ e++++ pk
  gi|91773544|ref|YP_566236.1| 15 ITGSRGFIGTRLTAQLRLKGLDLLEISHSLDSIDITNWEQVKTIPK 60
                                  9*************************99999999999999887665 PP

  == domain 2  score: 147.7 bits;  conditional E-value: 2e-46
                                   E--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SS CS
                 GDP_Man_Dehyd  58 kgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqe 138
                                   + D+t+ ++++ +    + d  ++LA++  +++sf++P  ++ +n  Gtl++Le +r   +   +rf+ aSt  vYG++q 
  gi|91773544|ref|YP_566236.1|  46 SIDITNWEQVKTI---PKRDVLVHLAGMTNIPESFNHPRDVYTINTFGTLNMLEWCRLNDV---KRFIYAST-FVYGNPQY 119
                                   3455555555444...455899**********************************98765...6*****99.6******* PP

                                   SSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT- CS
                 GDP_Man_Dehyd 139 vpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnlda 219
                                   +p++E++p+ P++PY+ +Kl+ + ++ +y + yg+ +++ +lfn ++p+++ ++    i++++ + + gk   + l +  +
  gi|91773544|ref|YP_566236.1| 120 TPVDEKHPTLPNNPYSQSKLIGEELCNAYCRDYGIDVISLRLFNVYGPHQKGDYL---IPHIIRQLESGK---VSLKDPLP 194
                                   **************************************************99976...666666666666...55667779 PP

                                   EEEEEEHHHHHHHHHHHHHC..SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG- CS
                 GDP_Man_Dehyd 220 kRdwghvkDyveamwlmlqq..dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyf 298
                                   kRd+ +++D+++ +  +l +  +  + ++ia+g++ svre++++ ++       +e+            ++  + ++    
  gi|91773544|ref|YP_566236.1| 195 KRDFVYIDDVIDSFECALDSglGGCNVFNIANGKSNSVREIADMLAETY----FFEK-----------GQRADIDYT-CEK 259
                                   *******************9334458899*************9865554....3431...........122334443.567 PP

                                   -SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                 GDP_Man_Dehyd 299 rpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                   r++ev  ++++++kak+ + W+pk+++++++++
  gi|91773544|ref|YP_566236.1| 260 RQSEVSDTIANIEKAKNIIKWEPKTDIKTGLAQ 292
                                   999**************************9987 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.0   4.8e-20   1.2e-16       3     157 ..      13     170 ..      11     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 4.8e-20
                                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHH CS
                 RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre..eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaea 81 
                                   i +tG++G +G+ L++ql+ +gl++l ++ +  ++d+t+ e+v+++ k    dv+v++A  t++ +  ++++  y +n  +
  gi|91773544|ref|YP_566236.1|  13 IAITGSRGFIGTRLTAQLRLKGLDLLEISHSldSIDITNWEQVKTIPKR---DVLVHLAGMTNIPESFNHPRDVYTINTFG 90 
                                   89************************99666669999999999988776...9**************************** PP

                                   HHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEE....EEE-SEESSSSS CS
                 RmlD_sub_bind  82 vealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkali....vRtswvygekgk 157
                                   + ++ e+++  +++ +i+ St +V+   + +p  e+++t P n Y ++Kl GE+  +a++ ++ i    +R   vyg ++k
  gi|91773544|ref|YP_566236.1|  91 TLNMLEWCRLNDVKrFIYAST-FVYGNPQYTPVDEKHPTLPNNPYSQSKLIGEELCNAYCRDYGIdvisLRLFNVYGPHQK 170
                                   ************964888888.9**999***************************99977765444344899999998654 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 !   48.9   0.0   1.6e-16   4.2e-13      51     228 ..      46     211 ..      14     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.6e-16
                     3Beta_HSD  51 egDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeil 130
                                     D+t+ ++++  + + dv++hla+++++     +   ++++n  GT n+le c+ ++v++++Y S+   v++n +  ++ 
  gi|91773544|ref|YP_566236.1|  46 SIDITNWEQVK-TIPKRDVLVHLAGMTNIPEsFNHPRDVYTINTFGTLNMLEWCRLNDVKRFIYASTF--VYGNPQYTPVD 123
                                   45999999986.57889************984455667****************************97..66666777776 PP

                     3Beta_HSD 131 ngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigde 209
                                        +++++l++++y++sK + E+l    N    ++   +  ++LR   +yG+ +k   l p + + + +g  ++++ d+
  gi|91773544|ref|YP_566236.1| 124 -----EKHPTLPNNPYSQSKLIGEELC---NA-YCRDY-GIDVISLRLFNVYGPHQKgdYLIPHIIRQLESG--KVSLKDP 192
                                   .....5678899*************96...44.55666.477799*********986226777787777777..8899999 PP

                     3Beta_HSD 210 evlsdrvYvgNvawahilA 228
                                     + d+vY + v +   +A
  gi|91773544|ref|YP_566236.1| 193 LPKRDFVYIDDVIDSFECA 211
                                   9999******998876666 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.038        96       1      16 [.      15      30 ..      15      36 .. 0.92
   2 !   38.4   0.0     3e-13   7.8e-10      85     213 ..      58     171 ..      33     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.038
                                  EE-TTSHHHHHHHHHH CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekL 16
                                  +TG+ GF+G++L ++L
  gi|91773544|ref|YP_566236.1| 15 ITGSRGFIGTRLTAQL 30
                                  8***********9887 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 3e-13
                                   HHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH CS
                 NAD_binding_4  85 aeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekld 162
                                   + + dv +h a+ +n+ e+ +    ++ +N+ Gt ++le+++ l+  k +++ ST +  + +++ v+e             
  gi|91773544|ref|YP_566236.1|  58 IPKRDVLVHLAGMTNIPESFNHprdVYTINTFGTLNMLEWCR-LNDVKRFIYASTFVYGNPQYTPVDE------------- 124
                                   56779***********9987653338889*************.55556*******7777777767633............. PP

                                   --EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST CS
                 NAD_binding_4 163 ederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktG 213
                                       ++ +  +n Y+qsK ++E+l++++ r  g+ v+ +R+ +++g  ++G
  gi|91773544|ref|YP_566236.1| 125 ----KHPTLPNNPYSQSKLIGEELCNAYCRDYGIDVISLRLFNVYGPHQKG 171
                                   ....45555566************************999999998865555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.15   3.7e+02       1      19 [.      13      31 ..      13      43 .. 0.84
   2 !   32.0   0.0   2.6e-11   6.6e-08      62     259 ..      48     255 ..      36     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                                  EEEETTTSHHHHHHHHHHH CS
               Polysacc_synt_2  1 vlvtGagGsiGselvrqil 19
                                  + +tG+ G iG +l+ q+ 
  gi|91773544|ref|YP_566236.1| 13 IAITGSRGFIGTRLTAQLR 31
                                  679***********99975 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 2.6e-11
                                   -TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE............GG CS
               Polysacc_synt_2  62 dvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt............DK 130
                                   d+++ e+++++ +    dv++h A + ++P   ++p ++ + N +gt n++e +  ++vk++++ St             K
  gi|91773544|ref|YP_566236.1|  48 DITNWEQVKTIPK---RDVLVHLAGMTNIPESFNHPRDVYTINTFGTLNMLEWCRLNDVKRFIYASTfvygnpqytpvdEK 125
                                   5666666666655...89************************************************966666655555323 PP

                                   .GSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG..TTS.SHHHHHHHHHTTSSEEES-TT-EEEEE-HH CS
               Polysacc_synt_2 131 .AvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgS..rGS.viplFkkqikeggpvtvTdpemtRyfmtie 207
                                       P n +  +K++ e l+ a+ +        ++  R  NV g   +G  +ip   +q+++g +v++ dp   R f+ i+
  gi|91773544|ref|YP_566236.1| 126 hPTLPNNPYSQSKLIGEELCNAYCRDY---GIDVISLRLFNVYGPhqKGDyLIPHIIRQLESG-KVSLKDPLPKRDFVYID 202
                                   145688****************99998...899**********962257449********998.8**************** PP

                                   HHHHHHHHHHHH--SS.-EEEE--.-EEEHHHHHHHH..........SSSS-E CS
               Polysacc_synt_2 208 eavqLvlqalalakgg.eifvldmGepvkivdlakalielsgleekkeediei 259
                                   + ++    al  + gg ++f    G++ +++++a  l e++ +e+ +++di+ 
  gi|91773544|ref|YP_566236.1| 203 DVIDSFECALDSGLGGcNVFNIANGKSNSVREIADMLAETYFFEKGQRADIDY 255
                                   **********99998847********************999998888777654 PP

>> FERM_F1  FERM F1 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.5e-05      0.11      18      68 ..     133     183 ..     119     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                       FERM_F1  18 syskgelvaEelcieaakkvgitpvylslFalasekekvWypPnhvfevde 68 
                                    ys+ +l+ Eelc + ++  gi  + l lF ++ +++k  y   h+++  e
  gi|91773544|ref|YP_566236.1| 133 PYSQSKLIGEELCNAYCRDYGIDVISLRLFNVYGPHQKGDYLIPHIIRQLE 183
                                   58999*****************************99998777667766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1900.53
//
Query:       gi|91773545|ref|YP_566237.1|  [L=330]
Description: NAD-dependent epimerase/dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  208.8   0.0    1.7e-61  208.4   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    8.2e-50  169.5   0.0      1e-49  169.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.8e-25   87.8   0.0    8.1e-25   87.4   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.7e-17   61.7   0.0    3.7e-16   59.1   0.0    2.2  1  NAD_binding_4    Male sterility protein
    1.3e-15   57.3   0.2      5e-15   55.4   0.2    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.9e-10   39.9   0.0    5.4e-10   39.5   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    4.3e-09   35.9   0.0    5.5e-09   35.5   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    2.9e-08   33.4   0.4    4.2e-07   29.6   0.4    2.6  1  adh_short        short chain dehydrogenase
    8.5e-05   22.2   0.2     0.0013   18.3   0.2    2.1  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.073   13.0   0.0    1.9  1  KR               KR domain
       0.07   13.4   0.1        1.1    9.5   0.0    2.2  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


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 !  208.4   0.0   1.1e-64   1.7e-61       2     332 .]      10     312 ..       9     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 208.4 bits;  conditional E-value: 1.1e-64
                                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                 GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynL 82 
                                   +TG  Gfi s+l+e L+++g +v  +v+++s  + g +e  +kd    l +++++++gD+tD   ++++ +++  d v++L
  gi|91773545|ref|YP_566237.1|  10 VTGAGGFIASHLTEELVRRGANVKAFVHYNSRNDWGLLELAEKD----LLDKVEVISGDVTDPFFVNSVTKDT--DIVFHL 84 
                                   9*******************************998888765543....4579*******************99..89**** PP

                                   -S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHH CS
                 GDP_Man_Dehyd  83 AAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwi 163
                                   AA   +++s+  Pe +++vnv Gtl++L+a+ + g+    +++++StsE YG+++ +p++E++p++ +sPY+a+K+ ad +
  gi|91773545|ref|YP_566237.1|  85 AALIGIPYSYVAPEHYVNVNVKGTLNVLQACLDNGVG---KMVHTSTSETYGTAEYTPIDEKHPLKGQSPYSASKIGADKM 162
                                   ********************************99985...9**************************************** PP

                                   HHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS--- CS
                 GDP_Man_Dehyd 164 vvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkped 244
                                   +++y+++++l++ + + fn+ +pr++++ +   i++++++++   ++ +++G l ++Rd ++vkD+v+++  +  +++   
  gi|91773545|ref|YP_566237.1| 163 AESYYRSFDLPVATIRPFNTFGPRQSARAI---IPTIISQALT--RDEIHVGSLTPVRDMTYVKDTVNGFIEVGLSER--- 235
                                   ************************977644...6666676665..46889*******************999876665... PP

                                   EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--S..S--SB--B-THHHHHHH----SS CS
                 GDP_Man_Dehyd 245 yviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrp..gevdlllgdaskakeeLgWkpkv 323
                                      ++get +v++   +++  + ++i +   g+e         ++ v  +++++rp  +ev +l+ d+skak  L+W+p++
  gi|91773545|ref|YP_566237.1| 236 ---SSGETINVGTGSGATIGVILEKILKI-LGKE---------DIPVIEEQNRVRPgkSEVMELICDNSKAKDLLNWSPEY 303
                                   ...35666666666555555554444332.2222.........233334456666644789999***************** PP

                                   -HHHHHHHH CS
                 GDP_Man_Dehyd 324 sfeelvrem 332
                                   s++++++e+
  gi|91773545|ref|YP_566237.1| 304 SLDNGLKET 312
                                   ******986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0   6.2e-53     1e-49       1     241 []       8     244 ..       8     244 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 6.2e-53
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkeeqpdavihlAa 73 
                                   ++VtGa Gfi s+l+++l ++g +v ++ +++s++ +++le +        e++ +d+td+  ++ + k  + d+v+hlAa
  gi|91773545|ref|YP_566237.1|   8 VVVTGAGGFIASHLTEELVRRGANVKAFVHYNSRNDWGLLELAekdlldkvEVISGDVTDPFFVNSVTK--DTDIVFHLAA 86 
                                   68*****************************999999998877999***********************..79******** PP

                                   ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                     Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                     g++ s   p+ +++ n++gtln+l+a+ ++gv ++++ s+se+YG  + +p +e+    plk +spY+a+K+ ++k++e
  gi|91773545|ref|YP_566237.1|  87 LIGIPYSYVAPEHYVNVNVKGTLNVLQACLDNGVGKMVHTSTSETYGTAEYTPIDEKH---PLKGQSPYSASKIGADKMAE 164
                                   ***********************************************99999******...******************** PP

                                   HHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STT CS
                     Epimerase 155 ayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkg 235
                                   +y ++++l++ ++r+fn +Gpr   ++ + +ip +i+++l++  e+ + g++t++Rd  yv+D +++++ v     +  +g
  gi|91773545|ref|YP_566237.1| 165 SYYRSFDLPVATIRPFNTFGPR---QSARAIIPTIISQALTRD-EIHV-GSLTPVRDMTYVKDTVNGFIEVGLS--ERSSG 238
                                   **********************...99**************98.6665.9*******************99888..33579 PP

                                   EEEEES CS
                     Epimerase 236 eiyniG 241
                                   e++n+G
  gi|91773545|ref|YP_566237.1| 239 ETINVG 244
                                   999998 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 !   87.4   0.0     5e-28   8.1e-25       1     220 [.       9     222 ..       9     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 5e-28
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee.lkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlaslvd 78 
                                   vvtG++GF+ ++l +eLvr++  +k    +  r++  lle ++k   +k  vi gDvtd   ++ ++++ d+v+hla+l+ 
  gi|91773545|ref|YP_566237.1|   9 VVTGAGGFIASHLTEELVRRGAnVKAFVHYNSRNDWGLLELAEKDLLDKveVISGDVTDPFFVNSVTKDTDIVFHLAALIG 89 
                                   8*******************9856666667788888888988886555556****************************99 PP

                     3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvl 158
                                   +    +  +++ +vnvkGT nvl+ac+++gv ++v+tS+ e  g   +  +i   dE+  ++ + q++y+ sK  a+k+  
  gi|91773545|ref|YP_566237.1|  90 IPYsYVAPEHYVNVNVKGTLNVLQACLDNGVGKMVHTSTSETYGT-AEYTPI---DEK--HPLKGQSPYSASKIGADKMAE 164
                                   9763778999**********************************9.344444...565..566789***********9965 PP

                     3Beta_HSD 159 kaNgrtlknggrlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYvgN 220
                                   +          +l    +Rp   +G+++  + + p++   a ++   +++g+   + d++Yv  
  gi|91773545|ref|YP_566237.1| 165 SYYR-----SFDLPVATIRPFNTFGPRQsaRAIIPTIISQALTR-DEIHVGSLTPVRDMTYVKD 222
                                   4433.....33899999*********972245666666655555.5678888888899999876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   2.3e-19   3.7e-16       1     206 [.      10     182 ..      10     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.3e-19
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHH CS
                 NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedl 81 
                                   +TGa GF++++L e+L+r+ ++vk  + v+ +s         + +   el ++ l   +++++v++GD+++p +      +
  gi|91773545|ref|YP_566237.1|  10 VTGAGGFIASHLTEELVRRGANVK--AFVHYNSR--------NDWGLLELAEKDL---LDKVEVISGDVTDPFF------V 71 
                                   7*******************9655..55555543........4455566666665...9************997......7 PP

                                   HHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H...... CS
                 NAD_binding_4  82 qelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekee 159
                                   + +++ +d+++h aA + + ++y      ++vNv+Gt +vl+ +        ++h ST+  +g+ e +             
  gi|91773545|ref|YP_566237.1|  72 NSVTKDTDIVFHLAALIGIPYSYVApehYVNVNVKGTLNVLQACLDNGVG-KMVHTSTSETYGTAEYT------------- 138
                                   999******************99654459****************87777.89*****6666666632............. PP

                                   HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EE CS
                 NAD_binding_4 160 kldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsii 206
                                        ++++  + +  Y+ sK  a+k+ +++ r+ +lpv+ +Rp + 
  gi|91773545|ref|YP_566237.1| 139 ---PIDEKHPLKGQSPYSASKIGADKMAESYYRSFDLPVATIRPFNT 182
                                   ...3455667777889***************************9665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.2   3.1e-18     5e-15       1     250 [.       8     265 ..       8     298 .. 0.65

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 3.1e-18
                                   EEEETTTSHHHHHHHHHHHHH..B-SEEEEE.ES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk..kpkkiill.erdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                   v+vtGagG i s+l+++++++  ++k  + + +r++  l e++++    l +     ++ ++ gdv+d   ++++ +  + 
  gi|91773545|ref|YP_566237.1|   8 VVVTGAGGFIASHLTEELVRRgaNVKAFVHYnSRNDWGLLELAEKD---LLD-----KVEVISGDVTDPFFVNSVTK--DT 78 
                                   79******************95444444433245566666666553...222.....334568**************..** PP

                                   SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS.....S--S....H.....HHHHHHHH CS
               Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv.....nPtn....v.....mGatKrla 145
                                   d+vfh AAl  +P     p + ++ Nv gt nv++a++++gv k+v  St          P++    +     + a+K  a
  gi|91773545|ref|YP_566237.1|  79 DIVFHLAALIGIPYSYVAPEHYVNVNVKGTLNVLQACLDNGVGKMVHTSTSETYgtaeyTPIDekhpLkgqspYSASKIGA 159
                                   **************************************************7653111112332111121111133444444 PP

                                   HHHHHHGGG--SSS--EEEEEEE-EETTGTTS...SHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHH.HHHHHHHH--S CS
               Polysacc_synt_2 146 ekllqalakeseekktkfvvvRfGNVlgSrGS...viplFkkqikeggpvtvTdpemtRyfmtieeavq.Lvlqalalakg 222
                                   +k++ ++ ++    +  ++++R  N +g r S   +ip+  +q  + +++ v   + +R +  ++++v+ ++   l++ ++
  gi|91773545|ref|YP_566237.1| 160 DKMAESYYRSF---DLPVATIRPFNTFGPRQSaraIIPTIISQALTRDEIHVGSLTPVRDMTYVKDTVNgFIEVGLSERSS 237
                                   44444433333...4666677766776654443336777777777777777777777777777777776234444466666 PP

                                   S-EEEE--.-EEEHHHHHHHH....... CS
               Polysacc_synt_2 223 geifvldmGepvkivdlakalielsgle 250
                                   ge   +  G   +i  + ++++++ g+e
  gi|91773545|ref|YP_566237.1| 238 GETINVGTGSGATIGVILEKILKILGKE 265
                                   7776677777777777777777777643 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 !   39.5   0.0   3.3e-13   5.4e-10       1     144 [.      12     180 ..      12     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3.3e-13
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH....HHHCT...TTCEEEE--TT-CCHHHHHHTT-SEEEES-...... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla....eleae...eglevvegdvtdvedlaealkgadaVvsal...... 68 
                                   GA G ++++l++el++rg  +v+a+v   ++ +    el+++   +++ev++gdvtd+  + ++ k++d+V+  +      
  gi|91773545|ref|YP_566237.1|  12 GAGGFIASHLTEELVRRG-ANVKAFVHYNSRNDwgllELAEKdllDKVEVISGDVTDPFFVNSVTKDTDIVFHLAaligip 91 
                                   9****************5.*******887777666555554434579************************9887678555 PP

                                   ...--TCC.......HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCC...HHH....HHHHHHHHHHHH CS
                NAD_binding_10  69 ...ggggk.......deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkell...kay....laakraaeellr 132
                                                  + +g+ n+++a+  +gv ++v  s+  ++  ++  ++   k+ l   ++y    + a + ae + r
  gi|91773545|ref|YP_566237.1|  92 ysyV---ApehyvnvNVKGTLNVLQACLDNGVGKMVHTSTSETYGTAEY-TPIDEKHPLkgqSPYsaskIGADKMAESYYR 168
                                   5442...033355555556*********************999964322.2222222221113331111456677777788 PP

                                   HSSSEEEEEEE- CS
                NAD_binding_10 133 asgldwTivrpg 144
                                   + +l    +rp 
  gi|91773545|ref|YP_566237.1| 169 SFDLPVATIRPF 180
                                   888888888885 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 !   35.5   0.0   3.3e-12   5.5e-09       2     136 ..       7     163 ..       6     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.3e-12
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.......................T--TTSHHHHHHHHHHH--SEEEE-- CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre.......................eldltdaeavaellkeakpdvvvnaA 59 
                                   +++vtGa+G ++s+L+++l ++g++v a+                          + d+td+  v+++ k+   d+v ++A
  gi|91773545|ref|YP_566237.1|   7 NVVVTGAGGFIASHLTEELVRRGANVKAFVHYnsrndwgllelaekdlldkveviSGDVTDPFFVNSVTKD--TDIVFHLA 85 
                                   689************************995446789*****************9999***********999..899***** PP

                                   ----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHH CS
                 RmlD_sub_bind  60 AytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqav 136
                                   A   +      +e+  +vn++++ ++ +a+   g+ +++h St   +  ++ +p  e+++ + ++ Y ++K+   ++ 
  gi|91773545|ref|YP_566237.1|  86 ALIGIPYSYVAPEHYVNVNVKGTLNVLQACLDNGVgKMVHTSTSETYGTAEYTPIDEKHPLKGQSPYSASKIGADKMA 163
                                   **********************************868**********999999999999999999*****98776655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.4   2.6e-10   4.2e-07       1     163 [.       6     166 ..       6     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.6e-10
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkld 79 
                                   k v+vtGa++ I   + +el+++Ga+v + v +++++   +++  +++  +k+ +i++Dvtd   v+ + ++        d
  gi|91773545|ref|YP_566237.1|   6 KNVVVTGAGGFIASHLTEELVRRGANVKAfVHYNSRNDWGLLELAEKDlLDKVEVISGDVTDPFFVNSVTKDT-------D 79 
                                   789************************997777766655555555555899***********99988888877.......5 PP

                                   EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHH....HH....HCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                     adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpa....ml....kqssGrIvnvsSvagkvpvagvaaYsAs 152
                                   ++ + A++        +s  + e +++vN++g++++ +a+l++    m+    ++  G+    + +  k p++g+++YsAs
  gi|91773545|ref|YP_566237.1|  80 IVFHLAALI----GIPYSYVAPEHYVNVNVKGTLNVLQACLDNgvgkMVhtstSETYGT-AEYTPIDEKHPLKGQSPYSAS 155
                                   555555552....12467778899*****************994444443332222222.3444556788999******** PP

                                   HHHHHHHHHHH CS
                     adh_short 153 Kaavagltrsl 163
                                   K + +++++s 
  gi|91773545|ref|YP_566237.1| 156 KIGADKMAESY 166
                                   *****999875 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   8.1e-07    0.0013       1      74 [.       8      87 ..       8     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.1e-07
                                  EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S......-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---G CS
                          NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt......kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgf 74
                                  ++v+Ga G +++++++ l+++g +v+a v+          ela++     ve+++gd+ d   ++++ k+ d vf   ++
  gi|91773545|ref|YP_566237.1|  8 VVVTGAGGFIASHLTEELVRRGANVKAFVHYNsrndwgLLELAEKDLLDKVEVISGDVTDPFFVNSVTKDTDIVFHLAAL 87
                                  68***************************9886766663333333333459************************87664 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.5e-05     0.073       3      76 ..       8      79 ..       7     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-05
                                  EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-..EEEE----TT-HHHHHHHHHHHH CS
                            KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga..evevvaaDvsdkdavealleeik 76
                                  +++tG+ G ++ +l++ l+++ga+  +++  +  +++d    + el++++   +vev++ Dv+d+  v+++ ++ +
  gi|91773545|ref|YP_566237.1|  8 VVVTGAGGFIASHLTEELVRRGANVKAFVHYN--SRNDW--GLLELAEKDLldKVEVISGDVTDPFFVNSVTKDTD 79
                                  58********************9877777666..33333..355666665445************99999888776 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00066       1.1       1      77 [.       8      85 ..       8      91 .. 0.91
   2 ?    1.4   0.0      0.22   3.6e+02      81     101 ..     107     128 ..     100     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00066
                                  EEEE--.SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
               Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                  v++ Ga G++++ ++e+l+r++   +  ++  +r++ +l +la+k l  ++e i+ d+ ++   + ++ k++d+v +l+
  gi|91773545|ref|YP_566237.1|  8 VVVTGAgGFIASHLTEELVRRGANVKaFVHYNSRNDWGLLELAEKDLLDKVEVISGDVTDPFF-VNSVTKDTDIVFHLA 85
                                  7999*****************98877799999**********99999999***9999999998.999999999998886 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                                   GHHHHHHHHHHHT-.EEEESS- CS
               Sacchrp_dh_NADP  81 ssldvlkaCietgv.hyvdtsi 101
                                    +l+vl+aC+++gv  +v ts 
  gi|91773545|ref|YP_566237.1| 107 GTLNVLQACLDNGVgKMVHTST 128
                                   5789*********933444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2129.04
//
Query:       gi|91773546|ref|YP_566238.1|  [L=238]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  148.3   0.0    3.4e-43  148.0   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    9.3e-10   39.1   0.0    1.1e-09   38.8   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
       0.01   15.8   0.0      0.026   14.5   0.0    1.6  1  DUF3963          Protein of unknown function (DUF3963)


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 !  148.0   0.0   5.7e-47   3.4e-43       2     243 ..       8     228 ..       7     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 5.7e-47
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   avILaGG+GtRL P t  l+k+l+p+++  +++++++ +l ++g+++ iv    + + l+e ++++gsk+gv++++++e+e
  gi|91773546|ref|YP_566238.1|   8 AVILAGGKGTRLAPYTTVLPKPLMPIGDM-PILEIVIRQLKKNGFTD-IVLAVGHLAGLIEAYFGDGSKWGVNITYSIEDE 86 
                                   8****************************.*****************.7788889************************** PP

                                   --BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEE CS
               NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfv 163
                                   + gtA+++ l+ +l    +  e++lv++gD l++ +y+++++++ e++a  + t+ ++ ++ + + Gv e d++g++++ +
  gi|91773546|ref|YP_566238.1|  87 PLGTAGPLSLIDDL----D--ENFLVMNGDLLTNVNYSDLMRFHLENDA--LSTVSVYTKDVPISLGVLELDDNGKITDYI 159
                                   *******9877654....3..469*************************..9999999999******************** PP

                                   CS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHH CS
               NTP_transferase 164 EKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleane 243
                                   EKP  +   + +s+GiYvfn+++l+ + k     k +  ++ d+++ +++  ++   ++f++  yW+D+G  +++ ++ e
  gi|91773546|ref|YP_566238.1| 160 EKPTLK---YKVSMGIYVFNRKILEHI-K-----KGEYLDFPDLIKNLISLNENVSGYMFEG--YWMDIGRYEDYSKVLE 228
                                   ***994...58****************.4.....6788999999999999999999******..9*********998766 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   1.9e-13   1.1e-09       1      66 [.       8      83 ..       8     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.9e-13
                                  EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-EEE-T CS
                  NTP_transf_3  1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrvvede 66
                                  aviLAGG+++R+       +K+l+p+g+ p+le v+++l++ g+ ++v+++g+    ++a++    + gv +++  
  gi|91773546|ref|YP_566238.1|  8 AVILAGGKGTRLAPyttvlPKPLMPIGDMPILEIVIRQLKKNGFTDIVLAVGHlaGLIEAYFgdgSKWGVNITYSI 83
                                  79**********9444689*********************************974334443321133345554443 PP

>> DUF3963  Protein of unknown function (DUF3963)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.4e-06     0.026       8      25 ..      64      81 ..      60      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-06
                       DUF3963  8 FiEkYFgDiqKWiRNitf 25
                                   iE YFgD  KW  Nit+
  gi|91773546|ref|YP_566238.1| 64 LIEAYFGDGSKWGVNITY 81
                                  7****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 1925.49
//
Query:       gi|91773547|ref|YP_566239.1|  [L=238]
Description: acylneuraminate cytidylyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-28   97.9   0.0    8.3e-28   97.8   0.0    1.1  1  CTP_transf_3     Cytidylyltransferase
      0.003   17.9   0.0     0.0036   17.7   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
      0.004   16.9   0.0     0.0054   16.5   0.0    1.2  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.055   13.0   0.0      0.079   12.5   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0   1.8e-31   8.3e-28       2     122 ..       8     144 ..       7     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1.8e-31
                                   EEEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHH... CS
                  CTP_transf_3   2 aIipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterfle... 79 
                                   aIipARsgSk++ gKn+++l+gkpli +++e+a+ks  +e+v+++TD+  i+ + k+ ga++++++ +l +d + + +   
  gi|91773547|ref|YP_566239.1|   8 AIIPARSGSKGIAGKNIRSLNGKPLICHTIEEAVKSRYLERVFISTDDPLIAKISKQCGAKIINRPAELAEDESPTINaif 88 
                                   8***********************************************************************986665111 PP

                                   .HHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTS............S CS
                  CTP_transf_3  80 .vvkaflmseneeiivnlqGdnPllqeevikkaietlkenqed............y 122
                                    ++  +++  + eii+ lq ++Pl +  +i+ka+++  + + d            y
  gi|91773547|ref|YP_566239.1|  89 hAIDTIKNAYDTEIIILLQPTSPLRNAADIDKALDMFMKTDCDsvismckvehspY 144
                                   1567888888889************************9998875555555555543 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 !   17.7   0.0   8.1e-07    0.0036      16     126 ..      22     140 ..      12     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.1e-07
                                   HHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-TTS....S-SHHHHHHHHHHHH....SSSC CS
                  NTP_transf_3  16 Kallplggkpllervldalraag.vdevvvvggdeevlaalarlgvrvvededp....gkgplaslaaalraaa...dada 88 
                                   K    l+gkpl+ ++++ + ++  +++v+++++d+ +++  ++ g+++++ + +    +  ++ ++ +a++ ++   d++ 
  gi|91773547|ref|YP_566239.1|  22 KNIRSLNGKPLICHTIEEAVKSRyLERVFISTDDPLIAKISKQCGAKIINRPAElaedESPTINAIFHAIDTIKnayDTEI 102
                                   667789*************999758**************999999999888665422123344455555544334457777 PP

                                   EEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSE CS
                  NTP_transf_3  89 vlvlacDmPlltpelverllaaaaasgadvvvptyege 126
                                   +++l    Pl +++ +++ l+ + ++++d v+   + e
  gi|91773547|ref|YP_566239.1| 103 IILLQPTSPLRNAADIDKALDMFMKTDCDSVISMCKVE 140
                                   88888888888888888888888888888777666554 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 !   16.5   0.0   1.2e-06    0.0054       3     127 ..       8     136 ..       6     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-06
                                   EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.......CCEEEEE--SS CS
                          IspD   3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.......ksiqlvaGGde 76 
                                   ++ipA  sG++  ag  K  ++l+g++l+ ht++ + +s+ ++++ +  ++   + +++++ +       ++++l +  + 
  gi|91773547|ref|YP_566239.1|   8 AIIPAR-SGSKGIAG--KNIRSLNGKPLICHTIEEAVKSRYLERVFISTDD---PLIAKISKQcgakiinRPAELAEDESP 82 
                                   566653.55555554..7789***********************9886554...555555555444788888999999999 PP

                                   HHHHHHHHHHTTSSTT..SEEEE--TT-TT--HHHHHHHHHH.HHTTCSEEEEE CS
                          IspD  77 RaesVlnglkalegea..kfVLvHDaARpllkaadiaellaa.aeqstqgaila 127
                                     ++++++++ +++    +++++     pl +aadi++ l + +++++ ++i  
  gi|91773547|ref|YP_566239.1|  83 TINAIFHAIDTIKNAYdtEIIILLQPTSPLRNAADIDKALDMfMKTDCDSVISM 136
                                   999999999999986556888888899999999999999876244556666655 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05     0.079      19     132 ..      18     131 ..      16     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                   TSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTT CS
               NTP_transferase  19 tlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelled 99 
                                    +a k +  l++++li +t++++++s++ e ++++t++  +l+++  k+     ++  + l + +  t +A+  a++ +++
  gi|91773547|ref|YP_566239.1|  18 GIAGKNIRSLNGKPLICHTIEEAVKSRYLERVFISTDD--PLIAKISKQCGAKIINRPAELAEDESPTINAIFHAIDTIKN 96 
                                   5677888999999*****************99999955..444444444443346778888888889************** PP

                                   SSE..EEEEETTEEEEST..THHHHHHHHHTHSST CS
               NTP_transferase 100 eksdelvlvLggDhlikd..ayeeavkkaiekaak 132
                                    ++ e+++ L      ++  ++ +a++ +++++ +
  gi|91773547|ref|YP_566239.1|  97 AYDTEIIILLQPTSPLRNaaDIDKALDMFMKTDCD 131
                                   **888877776655555556677777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1583.35
//
Query:       gi|91773548|ref|YP_566240.1|  [L=347]
Description: N-acetylneuraminate synthase [Methanococcoides burtonii DSM 6242]
Scores for 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-103  346.0   0.6   1.2e-103  345.7   0.6    1.1  1  NeuB      NeuB family
    1.2e-08   35.4   0.0    2.4e-08   34.5   0.0    1.5  1  SAF       SAF domain


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.7   0.6  1.4e-107  1.2e-103       1     241 []      33     273 ..      33     273 .. 0.99

  Alignments for each domain:
  == domain 1  score: 345.7 bits;  conditional E-value: 1.4e-107
                                   HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHH CS
                          NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdles 81 
                                   li++Aa++ adavKfQtf +e++vs +++kaeyqk+++e++esq+e++kklels+ +hkel++++e+k+i+flstpfd++s
  gi|91773548|ref|YP_566240.1|  33 LIDVAAKSNADAVKFQTFVTEDVVSINTPKAEYQKHTTESSESQFEMIKKLELSKTDHKELMKHAEQKNIMFLSTPFDERS 113
                                   79******************************************************************************* PP

                                   HHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS--GGG--TH CS
                          NeuB  82 vdlleslgveayKiaSgeltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPapledvnLk 162
                                   vdll +lgv+++Ki+Sge+tn+pll++i ++g p+ilStGm+tlee++eav+v+++ag+e+l+llhCts+YPa++ed+nL 
  gi|91773548|ref|YP_566240.1| 114 VDLLVELGVPLIKISSGEITNHPLLKYISRKGIPIILSTGMSTLEEVAEAVSVIKDAGCEDLTLLHCTSSYPARVEDCNLL 194
                                   ********************************************************************************* PP

                                   HHHHHHHH-TSEEEEE--SSSSHHHHHHHHHT--EEEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS--TT CS
                          NeuB 163 aietlkeafgvpvGySDHtlgiavaiaAvalGAkviEkHftldrnlegpDhkaSlepeelkelveairnvekalgegek 241
                                   ++et+++ f+v+vGySDHt+gi v++aA+a+GA+viEkHftld+nl gpDh+aSlep+el+e+v++ir veka g+++k
  gi|91773548|ref|YP_566240.1| 195 TMETMADVFDVQVGYSDHTSGICVPLAAAAMGACVIEKHFTLDKNLTGPDHMASLEPTELEEMVRGIRLVEKARGSSVK 273
                                   ***************************************************************************9875 PP

>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   2.7e-12   2.4e-08       2      62 ..     288     344 ..     287     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.7e-12
                                   EEEEESSTB-TT-BEBTTTEEEECECGGCCTSCCCGGHHHHTTEEESS-B-TT-B-BGGGE CS
                           SAF   2 nVvvAardikaGeviteddltlkrpiashkigllpiaygeviGkratrdikaGepvhahnl 62 
                                   +++vA+ +i+aG+vi ed l  krp+    +g +p++++++iGk+ +++ik++++++  ++
  gi|91773548|ref|YP_566240.1| 288 RSIVAKVNIPAGTVIAEDLLAFKRPG----VGMPPKYLDRLIGKVPISEIKKDSLINFEMF 344
                                   799**********************8....*************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2179.48
//
Query:       gi|91773549|ref|YP_566241.1|  [L=369]
Description: UDP-N-acetylglucosamine 2-epimerase [Methanococcoides burtonii DSM 6242]
Scores for 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-91  307.4   0.2    1.1e-91  307.2   0.2    1.0  1  Epimerase_2  UDP-N-acetylglucosamine 2-epimerase


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 !  307.2   0.2   6.4e-96   1.1e-91       1     347 []      23     367 ..      23     367 .. 0.93

  Alignments for each domain:
  == domain 1  score: 307.2 bits;  conditional E-value: 6.4e-96
                                   HHHTTS-..EEEEEEE-S--SGGGTHHHHH....HTT-.---SEEE---S.--HHHHHHHHHHHHHHHHHHH--SEEEEES CS
                   Epimerase_2   1 kalkaeselelqlvvtGqHldremgdtvfe....elei.ekpdydlnsds.qslakstgrvligleevleeekpDlvlvlG 75 
                                   ka++++s+l+l+l+vtG+Hl++++g+tv+e    +++i +k+ + l +ds  s+a  +g ++ gl+++l++ kpD++lvlG
  gi|91773549|ref|YP_566241.1|  23 KAIQRSSKLDLSLIVTGMHLSETFGHTVDEiekdGFSIdAKIPLGLLEDSgASMALDVGICILGLTDALKKIKPDILLVLG 103
                                   6899**********************************9999999999998****************************** PP

                                   SSHHHHHHHHHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHH CS
                   Epimerase_2  76 DtnetlagalaAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviD 156
                                   D+ e+la+++a+++++ipvaH+++G    +++ g+++E++Rh+i+kls++hf +tee++e+++++ge+e ri+vvG++++D
  gi|91773549|ref|YP_566241.1| 104 DRGEMLATTIAGIYMNIPVAHLHGG----EVS-GTVDESIRHAITKLSHIHFPATEESAERIRNLGEDEFRIYVVGAPALD 179
                                   *************************....**9.************************************************ PP

                                   HHHHHHHHHH...T-HHHHHH.--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHHHHHH CS
                   Epimerase_2 157 alllskeeieeklkaseilke.lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrlleel 236
                                   ++l +    +e++   ++  + + +k+++lv+ H++++e   +  ++i e+++a+ +    ++vv+++n+++++++++e++
  gi|91773549|ref|YP_566241.1| 180 TILSETFVPKEEM--GHFF-DiDINKPIILVVQHPVTTEV-GAVERHIRETMDAVVEL-GEQTVVIYPNADAGGRKIIETI 255
                                   **65543333333..2232.23699**************9.889*************9.44579999999*******9999 PP

                                   HH-.T..TEEEE----HHHHHHHHHC-SEEEES-H.HHHHHHHHCT--EEESSSS-S-THHHHTTSEEE.-TT-HHHHHHH CS
                   Epimerase_2 237 eel.e..nvtlieplgyldflsllknaklvltdSg.GiqeEapslgvpvvnlReeteRpegveagtnvl.vgtdkeeIvaa 312
                                   e++ +   ++++++++++d+lsl++++++++++S+ Gi+ Eaps+g+pvvn+   ++R++g+++g+n++ v++dk+eI++a
  gi|91773549|ref|YP_566241.1| 256 EQYrNyaFIKIFKNIRHVDYLSLMRTTNVMVGNSSsGII-EAPSFGLPVVNI---GTRQTGRQRGQNTIdVDYDKDEIIKA 332
                                   99954889*******************************.************...************************** PP

                                   HHHHCT-..--......--TT-SS-HHHHHHHHHH CS
                   Epimerase_2 313 leklledkkelekmanaknpYgdGkaseriveile 347
                                   ++  l dk+  +k ++  +pYg+G+a   i+eile
  gi|91773549|ref|YP_566241.1| 333 IKVGLYDKDFKRKASKCISPYGNGHAGTAIAEILE 367
                                   *****99777777778999*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2375.14
//
Query:       gi|91773550|ref|YP_566242.1|  [L=212]
Description: hexapaptide repeat-containing transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   4.3    4.8e-17   62.4   4.3    1.7  2  PglD_N      PglD N-terminal domain
      9e-17   60.1  48.7    3.1e-06   26.7   6.5    4.8  6  Hexapep     Bacterial transferase hexapeptide (six repeats)
      3e-05   23.7   7.3      3e-05   23.7   7.3    4.7  6  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.35    9.8   1.6       0.86    8.5   0.8    2.1  2  Fucokinase  L-fucokinase


Domain annotation for each model (and alignments):
>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   4.3   1.1e-20   4.8e-17       1      78 []       4      83 ..       4      83 .. 0.88
   2 ?   -2.8   0.1       2.4   1.1e+04      50      50 ..     172     172 ..     152     191 .. 0.58

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.1e-20
                        PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk...tevegypvlgkaiellkslseeeyevviAIGnnkvRkkiaekl 78
                                  k vIi a+Ghgkvv+d++++n++ ei gf+Ddn++   + v+g++++g+ +   + +  +    ++AIG+n +R ++++k+
  gi|91773550|ref|YP_566242.1|  4 KTVIIAASGHGKVVLDVLQQNENIEITGFIDDNSNlhgKRVDGIHIIGDFSMVSNII-DKIDRGIVAIGDNHIRAEFFKKM 83
                                  569******************************975556799******998877777.445558*************9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                        PglD_N  50 l 50 
                                   +
  gi|91773550|ref|YP_566242.1| 172 I 172
                                   3 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   5.8e+03      10      16 ..      50      56 ..      49      58 .. 0.47
   2 !   21.9   1.4   2.2e-08   9.9e-05      10      35 ..      94     119 ..      90     120 .. 0.94
   3 !   26.7   6.5     7e-10   3.1e-06       2      35 ..     104     137 ..     103     138 .. 0.94
   4 !   17.5   2.6   5.7e-07    0.0025       1      35 [.     121     155 ..     121     156 .. 0.93
   5 !   17.4   0.3     6e-07    0.0027       4      29 ..     142     167 ..     142     167 .. 0.96
   6 !   25.0   9.0   2.4e-09   1.1e-05       1      36 []     157     192 ..     157     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                  E-TTEEE CS
                       Hexapep 10 Igpfavi 16
                                  Ig f+++
  gi|91773550|ref|YP_566242.1| 50 IGDFSMV 56
                                  4555544 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.2e-08
                                   E-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep  10 IgpfaviggnVkIGdnvkIgagvvig 35 
                                   I+p avi+  +kIG++++++a++vi+
  gi|91773550|ref|YP_566242.1|  94 IHPDAVIARTAKIGNGTIVAANAVIN 119
                                   9************************7 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 7e-10
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   ++IG+++++ ++avi + ++IG+n++I  g+ i 
  gi|91773550|ref|YP_566242.1| 104 AKIGNGTIVAANAVINPSAEIGENCIINTGAIID 137
                                   79****************************9995 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 5.7e-07
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   s+ IG+n++I  +a+i ++  I d+v+I +g+ ++
  gi|91773550|ref|YP_566242.1| 121 SAEIGENCIINTGAIIDHDNCIADHVHISPGANLA 155
                                   689****************************9876 PP

  == domain 5  score: 17.4 bits;  conditional E-value: 6e-07
                                   EETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIg 29 
                                   I ++v+I p+a ++gnV +G++++Ig
  gi|91773550|ref|YP_566242.1| 142 IADHVHISPGANLAGNVSVGKYSHIG 167
                                   6799*********************8 PP

  == domain 6  score: 25.0 bits;  conditional E-value: 2.4e-09
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   ++ +G+ ++Ig +a i ++++IG nv++gag+v+++
  gi|91773550|ref|YP_566242.1| 157 NVSVGKYSHIGIGASIINGIIIGQNVTVGAGAVVTK 192
                                   5789******************************86 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 ?   -3.4   0.0         2   8.9e+03       5      12 ..      34      41 ..      33      42 .. 0.73
   2 ?   -1.0   0.1      0.35   1.6e+03      18      23 ..      68      73 ..      63      74 .. 0.67
   3 !    9.1   0.6   0.00024       1.1      10      33 ..      94     119 ..      92     120 .. 0.90
   4 !   12.2   7.3   2.6e-05      0.12       3      33 ..     105     137 ..     103     138 .. 0.94
   5 !   23.7   7.3   6.7e-09     3e-05       1      34 []     157     192 ..     157     192 .. 0.93
   6 ?   -1.6   0.1      0.52   2.3e+03      21      27 ..     195     201 ..     193     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                                  -TT-EE-T CS
                     Hexapep_2  5 GdnCliGa 12
                                   dn++++ 
  gi|91773550|ref|YP_566242.1| 34 DDNSNLHG 41
                                  58999885 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.35
                                  EEE-TT CS
                     Hexapep_2 18 vslGdn 23
                                  v +Gdn
  gi|91773550|ref|YP_566242.1| 68 VAIGDN 73
                                  455555 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00024
                                   E-TT-EE..SEEE-TT-EE-TT-EE- CS
                     Hexapep_2  10 iGanagi..GvslGdncvvgaGvvit 33 
                                   i+++a+i    ++G++ +v+a+ vi 
  gi|91773550|ref|YP_566242.1|  94 IHPDAVIarTAKIGNGTIVAANAVIN 119
                                   89999997779*************96 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 2.6e-05
                                   EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                     Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                   +IG+ +++ ana+i    ++G+nc++  G +i+
  gi|91773550|ref|YP_566242.1| 105 KIGNGTIVAANAVInpSAEIGENCIINTGAIID 137
                                   8**************99************9986 PP

  == domain 5  score: 23.7 bits;  conditional E-value: 6.7e-09
                                   .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                     Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                   +v++G+ + iG  a i  G+++G n++vgaG v+t+
  gi|91773550|ref|YP_566242.1| 157 NVSVGKYSHIGIGASIinGIIIGQNVTVGAGAVVTK 192
                                   699**********7755******************7 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 0.52
                                   -TT-EE- CS
                     Hexapep_2  21 Gdncvvg 27 
                                    dn+vv+
  gi|91773550|ref|YP_566242.1| 195 TDNAVVA 201
                                   69***97 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.32   1.4e+03     300     318 ..      45      64 ..       9      89 .. 0.62
   2 ?    8.5   0.8   0.00019      0.86     279     320 ..      98     141 ..      70     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.32
                    Fucokinase 300 gnvs.igsnsivsgleless 318
                                   ++++ ig  s+vs++  + +
  gi|91773550|ref|YP_566242.1|  45 DGIHiIGDFSMVSNIIDKID 64 
                                   34445777777777765554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00019
                    Fucokinase 279 Svlessvsvgegsvie.hsslkgnvsigsnsivs.glelessee 320
                                   +v++ ++++g+g+++  +  ++++ +ig+n+i+  g  ++++++
  gi|91773550|ref|YP_566242.1|  98 AVIARTAKIGNGTIVAaNAVINPSAEIGENCIINtGAIIDHDNC 141
                                   45555555665555543455555555666666531222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1330.22
//
Query:       gi|91773551|ref|YP_566243.1|  [L=370]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-130  433.6   0.0   7.6e-130  433.4   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.2e-06   28.0   0.0    1.9e-06   27.3   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
      7e-06   25.5   0.1    1.9e-05   24.1   0.1    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
    3.1e-05   22.7   0.0    4.8e-05   22.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00063   18.8   0.0     0.0012   17.8   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
     0.0089   15.7   0.0       0.02   14.5   0.0    1.5  1  ComK             ComK protein


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 !  433.4   0.0  2.5e-133  7.6e-130       2     360 ..       9     361 ..       8     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 433.4 bits;  conditional E-value: 2.5e-133
                                   HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHH CS
               DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavle 82 
                                   i+eee++ v+evl+sgwl++gp+v eFEk fa+y+g+khaia++sGt++lhl ++ l++++gdeVI+ +++F+a+ n+++ 
  gi|91773551|ref|YP_566243.1|   9 IGEEEIRLVNEVLRSGWLSMGPKVIEFEKLFAKYMGTKHAIAINSGTSGLHLCIKSLNISKGDEVITSPFSFIASSNCIMF 89 
                                   789****************************************************************************** PP

                                   TT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSS CS
               DegT_DnrJ_EryC1  83 lgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgd 163
                                    g +pvfvD+dpdt+n+d+++ie aite+tkaIlpVh++G++++mda+ +ia++h+l v+eDa++A+Ga+ykgkk+G++g+
  gi|91773551|ref|YP_566243.1|  90 EGGTPVFVDIDPDTLNLDAKQIEDAITENTKAILPVHVFGHPCEMDAIMDIAEEHDLAVVEDACEAIGAEYKGKKAGTFGN 170
                                   ********************************************************************************* PP

                                   EEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHH CS
               DegT_DnrJ_EryC1 164 aavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarR 244
                                   a+vf Fyp+K++ttGeG ++vt+d+ +a+ ++ +rn+G++  ++ ++ ++++lGynyrl+e+++A+g+ qL+r+del+ +R
  gi|91773551|ref|YP_566243.1| 171 ASVFAFYPNKQITTGEGAMIVTDDDHIAKLCKSMRNQGRS--EDAEWLNHIMLGYNYRLDEMSCALGIGQLDRIDELLGKR 249
                                   **************************************99..5677777777***************************** PP

                                   HHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCC CS
               DegT_DnrJ_EryC1 245 reiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerkeea 325
                                    ++ae y+++L++++g++++ ++++ k ++w+ y+v+v +e  ++r+e+++ l+e+ +++r+++ +p+h+qp+y+e+++++
  gi|91773551|ref|YP_566243.1| 250 SRVAEKYTKKLNGVDGIVTQYLSQDVK-MSWFVYVVQVSQE--IDRNEVMKYLREHDVSCRPYF-TPIHLQPFYKETFGYK 326
                                   ****************99888888888.9**********88..99*******************.6*************** PP

                                   CHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
               DegT_DnrJ_EryC1 326 sgdlpnaerlaervlsLplypelteedvdrVveal 360
                                   +gd+p  er++e++++Lp y +++e+++++V++ l
  gi|91773551|ref|YP_566243.1| 327 EGDFPICERVCESTIALPFYGNIDEQTIEEVCSVL 361
                                   *******************************9876 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 !   27.3   0.0   6.2e-10   1.9e-06      47     153 ..      33     123 ..      20     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.2e-10
                                   HHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTT CS
                 Aminotran_1_2  47 peleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseed 127
                                    e+e+  ak++g        ++ a+   sG++ l   ++ l  + +gde++ +  ++   +n++   gg+ v + ++ +++
  gi|91773551|ref|YP_566243.1|  33 IEFEKLFAKYMG--------TKHAIAINSGTSGLHLCIKSLN-ISKGDEVITSPFSFIASSNCIMFEGGTPVFVDID-PDT 103
                                   69**********........777****************999.********************************66.9** PP

                                   TEE-HHHHHHHHTTHHCTTETEEEEE CS
                 Aminotran_1_2 128 fhldlealeealkeapegnkktkvil 153
                                    +ld++++e+a++e       tk il
  gi|91773551|ref|YP_566243.1| 104 LNLDAKQIEDAITE------NTKAIL 123
                                   **************......455554 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   6.4e-09   1.9e-05      32     278 ..      30     268 ..      27     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.4e-09
                                   HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.TBE- CS
               Beta_elim_lyase  32 ktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.Gkmd 110
                                   ++v ++e+ +a+++g+++a+ + +Gt + ++++k l   +g+evi    + + f    +   ++g +++ ++++ +  ++d
  gi|91773551|ref|YP_566243.1|  30 PKVIEFEKLFAKYMGTKHAIAINSGTSGLHLCIKSLNiSKGDEVIT---SPFSFIASSNCIMFEGGTPVFVDIDPDtLNLD 107
                                   5677899999***********************8887699999965...5555666667777888888888877765899* PP

                                   HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSE CS
               Beta_elim_lyase 111 lekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDs 191
                                   ++++e+ai+e      ++k+i+         G + ++   +++ +ia+++++ ++ D++  + a    + + +  f  + +
  gi|91773551|ref|YP_566243.1| 108 AKQIEDAITE------NTKAILPVHV--F--GHPCEM---DAIMDIAEEHDLAVVEDACEAIGAE--YKGKKAGTFGNASV 173
                                   *********9......5666654332..2..777765...5678899***********9777665..77777889999*** PP

                                   EEEESSSTT--SS-EEEEE-HH...................HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHH CS
               Beta_elim_lyase 192 vtmslkKdllanvGgvlafrddel...............edylaerveqrkylggglrqagvlaaleagiraleeglasle 257
                                   + +   K +++  G++++++dd++                      +  + +lg + r  ++ +a   gi  l++ +++l+
  gi|91773551|ref|YP_566243.1| 174 FAFYPNKQITTGEGAMIVTDDDHIaklcksmrnqgrsedA-----EWLNHIMLGYNYRLDEMSCA--LGIGQLDRIDELLG 247
                                   **********************664444444443322111.....11123344444444444455..99999999999999 PP

                                   HHHHHHHHHHHHHHHCT--EE CS
               Beta_elim_lyase 258 rdhktaeqlaeklelvrlaip 278
                                   +  + ae+ ++kl+ v++++ 
  gi|91773551|ref|YP_566243.1| 248 KRSRVAEKYTKKLNGVDGIVT 268
                                   999999999999999988655 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.6e-08   4.8e-05      50     175 ..      28     153 ..      26     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.6e-08
                                   --HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHH...TTCEEEEESTTS CS
               Cys_Met_Meta_PP  50 gnptrsvleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkk...lgievkfvdtsd 126
                                   + p +  +e+  a+  g+++a+a++sG++ +++ i +l +++Gde+++s   +  +++ +         + i+ +  +  d
  gi|91773551|ref|YP_566243.1|  28 MGPKVIEFEKLFAKYMGTKHAIAINSGTSGLHLCIKSLnISKGDEVITSPFSFIASSNCIMFEGGTpvfVDIDPDTLNL-D 107
                                   56788899***************************9995678*******999998888765543322134455555555.8 PP

                                   HHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
               Cys_Met_Meta_PP 127 leelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                   ++++e ai+entk+++   p   + + + + +i+++a ++++ vv D++
  gi|91773551|ref|YP_566243.1| 108 AKQIEDAITENTKAIL---PVHVFGHPCEMDAIMDIAEEHDLAVVEDAC 153
                                   99************98...566666667788888888888888887765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.1e-07    0.0012      49     182 ..      36     158 ..      28     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.1e-07
                                   HHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTS.CBE CS
                   Aminotran_5  49 rekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeeg.eld 128
                                   ++ +a+ ++++     i + ++t+++ l ++sl  ++++gde++++     a  +    +  ++g + +++ +d++  +ld
  gi|91773551|ref|YP_566243.1|  36 EKLFAKYMGTKH---AIAINSGTSGLHLCIKSL--NISKGDEVITSPFSFIASSN---CI-MFEGGTPVFVDIDPDTlNLD 107
                                   566666666664...677788888*********..6***********99999883...33.3566666688888765289* PP

                                   GGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTT CS
                   Aminotran_5 129 ldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavgh 182
                                    +++e++++e+tk++   h   v G   ++++i ++a +++  v+ Da+ a+g 
  gi|91773551|ref|YP_566243.1| 108 AKQIEDAITENTKAILPVH---VFGHPCEMDAIMDIAEEHDLAVVEDACEAIGA 158
                                   **************99999...59*************************99985 PP

>> ComK  ComK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.6e-06      0.02       6      64 ..     115     169 ..     111     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.6e-06
                          ComK   6 ineeTmailpkydekkklvskvieeede.flvkqkplqiiekScryygssyegrkegtke 64 
                                   i+e+T ailp+     +++++  e ++   + +++ l ++e++c+ +g++y+g+k+gt  
  gi|91773551|ref|YP_566243.1| 115 ITENTKAILPV-----HVFGHPCEMDAImDIAEEHDLAVVEDACEAIGAEYKGKKAGTFG 169
                                   89999999999.....6677778888886788999**********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2166.32
//
Query:       gi|91773552|ref|YP_566244.1|  [L=236]
Description: methyltransferase FkbM [Methanococcoides burtonii DSM 6242]
Scores for complete 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   49.6   0.8    5.4e-12   46.1   0.8    2.2  1  Methyltransf_21  Methyltransferase FkbM domain
    2.3e-06   27.5   0.1    3.8e-06   26.8   0.1    1.3  1  Met_10           Met-10+ like-protein
    3.3e-05   23.6   0.0    5.1e-05   23.0   0.0    1.3  1  Methyltransf_22  Methyltransferase domain
    0.00052   19.2   0.0    0.00081   18.5   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.019   15.1   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
      0.028   13.5   0.0       0.06   12.4   0.0    1.5  1  DREV             DREV 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 !   46.1   0.8   1.8e-15   5.4e-12       1     163 [.      86     211 ..      86     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.8e-15
               Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksggkyfpfavgdtngf 81 
                                   d+Ganig   + +++    ++++++v+a+EP       f+k  +n  ++ ++ ++++y+ i +g       ++ +  +++ 
  gi|91773552|ref|YP_566244.1|  86 DIGANIG--GFSVRV----ANKCKHVYAVEP------LFNKQLEN--NFKLN-GITNYTIIPKGL----GSGYKDLQYENL 147
                                   9*****9..777755....567*********......88888888..68888.778888887777....555555555444 PP

               Methyltransf_21  82 stssvlggedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfkefetelfdei 162
                                                + v++v l s+ +e   ++id+lkiD+EG+E+++  ++  g++r     i +E h f+ + +++f +i
  gi|91773552|ref|YP_566244.1| 148 E------------KSVECVSLESIKKEV-GGKIDFLKIDCEGGEWSIRSSELSGVRR-----IEMELHLFNRENKNDFLKI 210
                                   4............559******998888.9*****************999*******.....899***9996666666665 PP

               Methyltransf_21 163 r 163
                                   +
  gi|91773552|ref|YP_566244.1| 211 L 211
                                   4 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.3e-09   3.8e-06      72     152 ..      48     128 ..      35     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.3e-09
                                   EEEEEETTTS---GGGHHHHHHHHTT.....--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHT CS
                        Met_10  72 crfklDvskvyfsskleaErerlakl.....veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklN 147
                                   c++k+D  + y  ++  +E  ++ +      ++++++Vvd+ A iG f++ +a   k k v+a++  P  +k l++n klN
  gi|91773552|ref|YP_566244.1|  48 CTYKIDGYRFYV-TRCMHEADTINEAynysdIKKDDIVVDIGANIGGFSVRVAN--KCKHVYAVE--PLFNKQLENNFKLN 123
                                   777777655443.3344444444332111227899******************9..999****96..************** PP

                                   T-TTC CS
                        Met_10 148 kvekv 152
                                    + ++
  gi|91773552|ref|YP_566244.1| 124 GITNY 128
                                   99886 PP

>> Methyltransf_22  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.7e-08   5.1e-05     139     231 ..     133     216 ..     109     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.7e-08
               Methyltransf_22 139 wGlassydkaytpklkskgeiltlqdtlkklghklrtidvlkidcekcewenykdwvevdirqilvevhglpskkaaplaa 219
                                    Gl+s y++   ++l+++ e ++l+ ++k++g     id lkidce  ew+     +  ++r+i +e+h    +++     
  gi|91773552|ref|YP_566244.1| 133 KGLGSGYKDLQYENLEKSVECVSLESIKKEVGG---KIDFLKIDCEGGEWSIRSSEL-SGVRRIEMELHLFNRENKN---- 205
                                   5999****99999*****9********999876...59************9877666.699********99887776.... PP

               Methyltransf_22 220 sdffdafrkasy 231
                                    df + +++a++
  gi|91773552|ref|YP_566244.1| 206 -DFLKILEDAQF 216
                                   .44444444333 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.7e-07   0.00081      13      59 ..      63     109 ..      54     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.7e-07
                                   E--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE- CS
                        RrnaAD  13 lknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlE 59 
                                   +++  +ine+ + +++++++ v++ig+  G +++++a+ +k+v ++E
  gi|91773552|ref|YP_566244.1|  63 MHEADTINEAYNYSDIKKDDIVVDIGANIGGFSVRVANKCKHVYAVE 109
                                   567789***************************************99 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   6.2e-06     0.019       1      57 [.      58     113 ..      58     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-06
                                   CCCCHHHHHHHHHHHHT-S-..TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS CS
                          FtsJ   1 yrsRsayKLleidekfklfk..pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm 57 
                                   y++R+++    i+e+++  +  +++ vvD+ga  Gg+s  +++++   ++v+av    +
  gi|91773552|ref|YP_566244.1|  58 YVTRCMHEADTINEAYNYSDikKDDIVVDIGANIGGFSVRVANKC---KHVYAVEPLFN 113
                                   7888888889999**99654449999************9999996...46999976555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05      0.06      90     124 ..      76     110 ..      63     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                          DREV  90 asdqedkklldlGaGdGeitkrvaptfeevyatel 124
                                   +  ++d  ++d+Ga  G  + rva+  ++vya e 
  gi|91773552|ref|YP_566244.1|  76 SDIKKDDIVVDIGANIGGFSVRVANKCKHVYAVEP 110
                                   333577889***********************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1412.53
//
Query:       gi|91773553|ref|YP_566245.1|  [L=344]
Description: polysaccharide biosynthesis protein CapD [Methanococcoides burtonii DSM 6242]
Scores for complete 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-112  373.8   0.4   6.5e-112  373.5   0.4    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    8.4e-28   97.4   0.0    7.3e-27   94.4   0.0    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    9.7e-24   83.8   0.1    2.4e-21   76.0   0.1    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.9e-19   69.6   0.0      5e-19   68.9   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.3e-13   49.9   0.0    5.2e-13   49.3   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    4.8e-13   48.9   0.0    1.3e-11   44.1   0.0    2.1  1  RmlD_sub_bind    RmlD substrate binding domain
    8.9e-10   38.2   0.3    1.1e-07   31.3   0.3    2.9  2  NAD_binding_4    Male sterility protein
    1.1e-08   35.0   0.0    2.1e-08   34.0   0.0    1.5  1  NmrA             NmrA-like family
      6e-08   32.4   0.1    1.2e-07   31.4   0.1    1.5  1  adh_short        short chain dehydrogenase
    2.9e-05   24.1   0.0    4.7e-05   23.4   0.0    1.4  1  KR               KR domain
    0.00074   19.6   0.7     0.0025   17.9   0.2    2.0  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0019   18.5   0.1     0.0061   16.8   0.0    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.002   18.5   0.0     0.0045   17.4   0.0    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.041   13.6   0.3       0.11   12.3   0.3    1.6  1  Polysacc_syn_2C  Polysaccharide biosynthesis protein C-termin
      0.046   13.9   0.0       0.11   12.7   0.0    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.068   13.4   0.2       0.22   11.8   0.2    2.0  1  TrkA_N           TrkA-N domain
       0.11   12.3   0.2       0.38   10.5   0.0    1.9  2  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.5   0.4  6.1e-115  6.5e-112       1     292 [.      10     292 ..      10     294 .. 0.96

  Alignments for each domain:
  == domain 1  score: 373.5 bits;  conditional E-value: 6.1e-115
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +lvtG++GsiGse+vr +l+ +pk +++l+rdE k++e+e+e+  +l  +++++     igd+rdk+rl++a+e  ++d+v
  gi|91773553|ref|YP_566245.1|  10 ILVTGGTGSIGSEIVRLVLRYNPKVVRILSRDESKQFELEQEIG-HL--DNVRFL----IGDIRDKSRLQRAFE--GIDIV 81 
                                   89****************************************83.33..346555....***************..***** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SHHHHHHHHHHHHHHHGGG--SSS--E CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnvmGatKrlaekllqalakeseekktk 162
                                   fhaAA+KhVP++e+np+ea+ktNv+gt+nvi+aa++++++kv++iStDKA++P+n+mGatK+laekl+  ++ +++ +kt 
  gi|91773553|ref|YP_566245.1|  82 FHAAAMKHVPACEYNPFEAVKTNVMGTQNVIDAALDNDIEKVIAISTDKAASPINTMGATKLLAEKLILDANFYKGPRKTV 162
                                   ********************************************************************************* PP

                                   EEEEEE-EETTGTTSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH CS
               Polysacc_synt_2 163 fvvvRfGNVlgSrGSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakal 243
                                   f++vRfGNV+gSrGSviplF kqik+ggpvtvTd+emtR++m+i++av+Lv++a+++a+ggeif+ +m + vk+ dla+ +
  gi|91773553|ref|YP_566245.1| 163 FSCVRFGNVMGSRGSVIPLFAKQIKNGGPVTVTDSEMTRFMMSIPQAVNLVFKATKIARGGEIFIFKM-PVVKLGDLAQVM 242
                                   ********************************************************************.************ PP

                                   ...........SSSS-EEE----TT--SS-EEE-GGGGGGEEE-SSEEEE CS
               Polysacc_synt_2 244 i.elsgleekkeedieikitGlRpGEklyEeLlieeesveetelekilra 292
                                   i +l+ +   k edi+i+ +G+R+GEk+yE+L++ ee+  ++++e+++++
  gi|91773553|ref|YP_566245.1| 243 IeKLAPKYGYKPEDIQITNIGIRNGEKMYEHLMNLEEALYAYKTEDMYIV 292
                                   *556666677799******************************9999876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   6.9e-30   7.3e-27       1     205 [.      10     197 ..      10     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 6.9e-30
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAavg 75 
                                   ilVtG+tG iGs +v+ +l+ + +v+ + ++ +++++++++++      ++  +d++d+s+l+r+f+  ++d+v+h+Aa +
  gi|91773553|ref|YP_566245.1|  10 ILVTGGTGSIGSEIVRLVLRYNPKVVRILSRDESKQFELEQEIghldnvRFLIGDIRDKSRLQRAFE--GIDIVFHAAAMK 88 
                                   8*********************9988888888999999999999***********************..************ PP

                                   -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHH CS
                     Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveay 156
                                   +v+a   +p + +++n++gt+n+++aa ++++++++ +s++     +a              p +  +a+Kl++ekl+ ++
  gi|91773553|ref|YP_566245.1|  89 HVPACEYNPFEAVKTNVMGTQNVIDAALDNDIEKVIAISTD-----KAA------------SPINTMGATKLLAEKLILDA 152
                                   ****************************************3.....222............3557779***********99 PP

                                   HHHHT...-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETT CS
                     Epimerase 157 aaqyg...lnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgd 205
                                   +   g   + + ++r  n++G r       +vip ++++i++g  +vt+ ++
  gi|91773553|ref|YP_566245.1| 153 NFYKGprkTVFSCVRFGNVMGSR------GSVIPLFAKQIKNGG-PVTVTDS 197
                                   8777777799************9......**************9.9999764 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.1   2.3e-24   2.4e-21       1     122 [.      11     134 ..      11     139 .. 0.88
   2 !    6.4   0.0    0.0037       3.9     145     200 ..     137     190 ..     129     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 2.3e-24
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlresp..elleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdv 79 
                                   +vtGg+G +G+++v+ ++r ++ k vr+l  +es+  el +e+ ++++  ++ gD++dk++l++a eg+d+v+h a++  v
  gi|91773553|ref|YP_566245.1|  11 LVTGGTGSIGSEIVRLVLRYNP-KVVRILSRDESKqfELEQEIGHLDNVRFLIGDIRDKSRLQRAFEGIDIVFHAAAMKHV 90 
                                   69*******************8.788887666655115566666777777******************************* PP

                     3Beta_HSD  80 ag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                      +++  e  k nv GT+nv++a++++++++++  S+ +++ p
  gi|91773553|ref|YP_566245.1|  91 PAcEYNPFEAVKTNVMGTQNVIDAALDNDIEKVIAISTDKAASP 134
                                   987999999****************************9888766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0037
                     3Beta_HSD 145 aypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklg 200
                                   +   +K laEkl+l aN    k++ + +  ++R   + G + +++  ++kq+++ g
  gi|91773553|ref|YP_566245.1| 137 TMGATKLLAEKLILDANF--YKGPRKTVFSCVRFGNVMGSRGSVIPLFAKQIKNGG 190
                                   55679************9..888888888899999999999888877777766554 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 !   68.9   0.0   4.8e-22     5e-19       1     130 [.      11     129 ..      11     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 4.8e-22
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG++G iGs +++l l+ + +v+ i  r++s +++  +++      +l +n+++  gD++D+s+l+r+++ +  d v++
  gi|91773553|ref|YP_566245.1|  11 LVTGGTGSIGSEIVRLVLRYNPKVVRILSRDESKQFELEQEIG-----HL-DNVRFLIGDIRDKSRLQRAFEGI--DIVFH 83 
                                   9*******************************99877666664.....43.69*******************98..89*** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEG CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaSts 130
                                    AA++hV+    +P + +++nv+Gt+++++a+ +  +e   +++ +St+
  gi|91773553|ref|YP_566245.1|  84 AAAMKHVPACEYNPFEAVKTNVMGTQNVIDAALDNDIE---KVIAISTD 129
                                   ********************************998776...78899998 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 !   49.3   0.0   4.9e-16   5.2e-13       1     103 [.      14     133 ..      14     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 4.9e-16
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT....TTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleae....eglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                   G+tG++G+++v+  l+ +   v++l R+++k  ele+e    ++++ + gd+ d++ l++a++g+d+V+ a++ ++     
  gi|91773553|ref|YP_566245.1|  14 GGTGSIGSEIVRLVLRYNPKVVRILSRDESKQFELEQEighlDNVRFLIGDIRDKSRLQRAFEGIDIVFHAAAMKHVpace 94 
                                   9****************98899*******9998787433225899***************************666655655 PP

                                   .....HHHH......HHHHHHHHHHCT--EEEEEEETTTTS CS
                NAD_binding_10  74 .....deeg......aknivdaakeagvkRfvlvsaigvgd 103
                                           +      ++n++daa  +++++++ +s+ ++  
  gi|91773553|ref|YP_566245.1|  95 ynpfeA--VktnvmgTQNVIDAALDNDIEKVIAISTDKAAS 133
                                   555440..1445578********************988764 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 !   44.1   0.0   1.3e-14   1.3e-11       2     155 ..       9     175 ..       8     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.3e-14
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE---- CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavaellkeakpdvvvnaAAy 61 
                                   +ilvtG++G +Gse+++++ + + +v+ + ++                       d++d+++++++++    d+v +aAA 
  gi|91773553|ref|YP_566245.1|   9 NILVTGGTGSIGSEIVRLVLRYNPKVVRILSRdeskqfeleqeighldnvrflIGDIRDKSRLQRAFEG--IDIVFHAAAM 87 
                                   69*******************99999998444599****************9999************99..789******* PP

                                   --HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH... CS
                 RmlD_sub_bind  62 tavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla... 138
                                   + v ++E ++ +a + n+ +++++ +aa   ++ ++i +StD               + sP+n+ G+tKl+ E+ +l+   
  gi|91773553|ref|YP_566245.1|  88 KHVPACEYNPFEAVKTNVMGTQNVIDAALDNDIeKVIAISTD--------------KAASPINTMGATKLLAEKLILDanf 154
                                   *****************************999846999**98..............3678999999999999999998555 PP

                                   .H-SSEEE...EEE-SEESSS CS
                 RmlD_sub_bind 139 .agkkali...vRtswvygek 155
                                    +g++ ++   vR++ v g++
  gi|91773553|ref|YP_566245.1| 155 yKGPRKTVfscVRFGNVMGSR 175
                                   534444442225666666665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.3   1.1e-10   1.1e-07       1     137 [.      12     131 ..      12     140 .. 0.79
   2 ?    3.8   0.0     0.026        27     166     208 ..     128     173 ..     122     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.1e-10
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHH CS
                 NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedl 81 
                                   +TG+TG +G+ +++  Lr +p+  + +l R +s+            ++el++++    +++++++ GD+ ++      ++l
  gi|91773553|ref|YP_566245.1|  12 VTGGTGSIGSEIVRLVLRYNPK-VVRILSRDESK------------QFELEQEIG--HLDNVRFLIGDIRDK------SRL 71 
                                   7********************7.56666676655............233333332..46899*******975......69* PP

                                   HHHHHH--EEEE--SS-S.ST.TSS..EEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..G CS
                 NAD_binding_4  82 qelaeevdviihsaAtvnfde.pyk..ellrvNveGtrevlelakklkklkvllhvST..a 137
                                   q+  e +d+++h aA  ++ + +y+  e++++Nv+Gt++v++ a        ++ +ST  a
  gi|91773553|ref|YP_566245.1|  72 QRAFEGIDIVFHAAAMKHVPAcEYNpfEAVKTNVMGTQNVIDAALDNDIE-KVIAISTdkA 131
                                   ***************99986654442269****************88777.9999**9633 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.026
                                   EEETTTCCCHHHHHHHHHHHHHHHHHHHH---...EEEEEE-EEE- CS
                 NAD_binding_4 166 raklkglpntYeqsKalaEklvrearrrsglp...vvivRpsiitg 208
                                    +k ++  nt   +K laEkl+ +a+  +g +   ++ vR ++++g
  gi|91773553|ref|YP_566245.1| 128 TDKAASPINTMGATKLLAEKLILDANFYKGPRktvFSCVRFGNVMG 173
                                   567778889999**********999855443322245567777777 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0     2e-11   2.1e-08       1      98 [.      10     124 ..      10     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2e-11
                                   EEESSTTSHHHHHHHHHHHH.HT-EEEEEES-S..-SHHHHHHHHST.TEEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                          NmrA   1 IlviGaTGrqGksvvrallk.aghkvralvRdt..kselakslkeaG.velvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                   Ilv+G+TG++G+ +vr +l+ +   vr+l Rd+  + el +++ +   v ++ gd+ dk+ l++a++g d vf + +++  
  gi|91773553|ref|YP_566245.1|  10 ILVTGGTGSIGSEIVRLVLRyNPKVVRILSRDEskQFELEQEIGHLDnVRFLIGDIRDKSRLQRAFEGIDIVFHAAAMKhv 90 
                                   9*******************444558******96644566777665416778*********************99997778 PP

                                   ...........S-HHHHHHHHHHHHHHHS-SEEE CS
                          NmrA  76 ...........skeiedgkklvdAakeaGvkhfi 98 
                                              ++++   ++++dAa    ++++i
  gi|91773553|ref|YP_566245.1|  91 paceynpfeavKTNVMGTQNVIDAALDNDIEKVI 124
                                   8888888888777777788888888887777766 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   1.1e-10   1.2e-07       1     122 [.       8     118 ..       8     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.1e-10
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                   k +lvtG+++ IG +i++ +++ + kvv  ++r e+k  e+ +e++ + +++ ++ +D++d++++++++e +       d+
  gi|91773553|ref|YP_566245.1|   8 KNILVTGGTGSIGSEIVRLVLRYNPKVVRiLSRDESKQFELEQEIGHL-DNVRFLIGDIRDKSRLQRAFEGI-------DI 80 
                                   789*************************989***************97.89*************99998866.......99 PP

                                   EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHH CS
                     adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpa 122
                                   + + A++ + +p+ e++   + + +++N++g+ +++ a+l++
  gi|91773553|ref|YP_566245.1|  81 VFHAAAM-KHVPACEYNP--F-EAVKTNVMGTQNVIDAALDN 118
                                   9999999.3444433333..4.45789999999988888876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.4e-08   4.7e-05       4     132 ..      11     124 ..       9     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.4e-08
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---E CS
                            KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikG 84 
                                   l+tGG+G++G e++r  ++   + + +lsR+++++ + +++i +l     +v+++  D+ dk+ +++++e i+        
  gi|91773553|ref|YP_566245.1|  11 LVTGGTGSIGSEIVRLVLRYNPKVVRILSRDESKQFELEQEIGHLD----NVRFLIGDIRDKSRLQRAFEGID-------I 80 
                                   9******************************554444444444443....7******************9987.......5 PP

                                   EEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEE CS
                            KR  85 vihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffv 132
                                   v+haA +     +  ++ + +e+v +  v G++n+  +  d++++ ++
  gi|91773553|ref|YP_566245.1|  81 VFHAAAMK---HVPACEYNPFEAV-KTNVMGTQNVIDAALDNDIEKVI 124
                                   77777653...3444444444433.34456666666666666655555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   2.4e-06    0.0025      10     122 ..       5     125 ..       1     138 [. 0.77
   2 ?   -1.0   0.0       1.6   1.7e+03      17      56 ..     232     274 ..     225     297 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.4e-06
                                   .TT-EEEEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET.-E.....EEEGCGHHHHHHT-SEEEE-S CS
                  Shikimate_DH  10 lkekkvlli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgee.ie.....alkleelkellaeadvvisat 83 
                                   +k+k++l+  G+G +++++++  l+ + k v ++ R+ ++  el +e+++ + ++     +++ + l+++ + +d+v+ a 
  gi|91773553|ref|YP_566245.1|   5 FKNKNILVTgGTGSIGSEIVRLVLRYNPKVVRILSRDESKQFELEQEIGHLDnVRfligdIRDKSRLQRAFEGIDIVFHAA 85 
                                   578899998458***********************************95543132111113455679999999******99 PP

                                   SSSS.-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGG CS
                  Shikimate_DH  84 asee.pilekeeveealkkrkkplllvDiavPRdvepeva 122
                                   a ++ p  e + +e+++++    + ++D a+  d+e+ +a
  gi|91773553|ref|YP_566245.1|  86 AMKHvPACEYNPFEAVKTNVMGTQNVIDAALDNDIEKVIA 125
                                   988735666666776665555888999*999999997665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                                   EES-SHHHHHHHHHHHCC...T-CEEEEEESSHHHHHHHHHHH CS
                  Shikimate_DH  17 liGaGemaelvakhLlak...gvkkvvvaNRtlerakelaeel 56 
                                   ++  G +a+ ++++L+ k   + +++ ++N  +++ +++ e+l
  gi|91773553|ref|YP_566245.1| 232 VVKLGDLAQVMIEKLAPKygyKPEDIQITNIGIRNGEKMYEHL 274
                                   6666778888888887665446678888886666666665555 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 !   16.8   0.0   5.8e-06    0.0061       1      77 [.      10      85 ..      10      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
                                  EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
               Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.lgvrfeaialdaenyeavLaallkegdlvvnls 77
                                  +l+ G+ Gs+G+ +++l++r ++    + + +r+++k  +l +++ +  ++ +   d+ +++  L+++ ++ d+v +++
  gi|91773553|ref|YP_566245.1| 10 ILVTGGtGSIGSEIVRLVLRYNPK--VVRILSRDESKQFELEQEIgHLDNVRFLIGDIRDKSR-LQRAFEGIDIVFHAA 85
                                  6888888**************998..9**********7777766699999************9.*******9*998876 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 !   17.4   0.0   4.2e-06    0.0045       2      77 ..      10      88 ..       9     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-06
                                  EEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEB..EEE..GGGGGCTT-SEEEE-SCHH CS
                Semialdhyde_dh  2 vaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlk..ved..vdeeelkevdivflalpag 77
                                  + + G+tG +G+e++rl+ + +p  ++v++ls+++s+  +l++  ++l++++ l   ++d    + +++++divf a+  +
  gi|91773553|ref|YP_566245.1| 10 ILVTGGTGSIGSEIVRLVLRyNP--KVVRILSRDESKQFELEQEIGHLDNVRFLIgdIRDksRLQRAFEGIDIVFHAAAMK 88
                                  6789**************99788..6788899999999999999997777665431133333666778*******996544 PP

>> Polysacc_syn_2C  Polysaccharide biosynthesis protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3    0.0001      0.11       7      42 ..     298     332 ..     294     334 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
               Polysacc_syn_2C   7 YdkYfseGeekiseledYnShNTerLdveeikelLl 42 
                                   Y+ Yf eG ek ++ + Y S+N++  +  eik+lL 
  gi|91773553|ref|YP_566245.1| 298 YSDYFLEGIEKAKQ-KVYSSDNVKVFTQLEIKDLLN 332
                                   99*********997.99****************996 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001      0.11       2      93 ..       9      99 ..       8     134 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                  EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTT..TTTBHHHHSSSS--S-BEB.....SSHHHHHHH-SEEEE-S-H CS
                        DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkesel..egkdagellglgklgvavt.....ddleevlekadvliDFTtp 77
                                  +++v+G +G +G+e+v++v +  + ++v  ++r+es+    ++++g+l +++   + +      ++l++++e  d++     +
  gi|91773553|ref|YP_566245.1|  9 NILVTGGTGSIGSEIVRLVLR-YNPKVVRILSRDESKQfeLEQEIGHLDNVR---FLIGdirdkSRLQRAFEGIDIV----FH 83
                                  699*****************9.777888888888743211455666555554...4443211224555555544444....44 PP

                                  HHHHHHHHHHHHTT-E CS
                        DapB_N 78 eavlenlklalekgvk 93
                                  +a+++++ ++  ++ +
  gi|91773553|ref|YP_566245.1| 84 AAAMKHVPACEYNPFE 99
                                  5555555555444333 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2    0.0002      0.22       5      58 ..      15      74 ..      10     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                  S-SHHHHHHHHHHHHTT.EEEEEEESSHHH.HHHHHHTT....SEEEES-TTSHHHHHHT CS
                        TrkA_N  5 GlGrvGrslaeeLsegg.kdvvvidkdeer.veelreeg....levvvgdatdeevLeea 58
                                  G G +G+++++ + +++ k v +  +de++ +e  +e g    +++++gd  d++ L++a
  gi|91773553|ref|YP_566245.1| 15 GTGSIGSEIVRLVLRYNpKVVRILSRDESKqFELEQEIGhldnVRFLIGDIRDKSRLQRA 74
                                  79*************773545566777766344444444656777************998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00036      0.38      53      90 ..      55      93 ..      38     105 .. 0.88
   2 ?   -2.0   0.0       2.7   2.8e+03      39      70 ..     304     335 ..     298     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
               Methyltransf_31 53 ldnveFeqgdieeleklled..ekfDlilsnevlnaladp 90
                                  ldnv+F +gdi +++  l++  e +D+++  +++ +++++
  gi|91773553|ref|YP_566245.1| 55 LDNVRFLIGDIRDKSR-LQRafEGIDIVFHAAAMKHVPAC 93
                                  89***********887.566679********999999987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
               Methyltransf_31  39 eaielArenaqklgldnve.Feqgdieelekl.l 70 
                                   e ie+A+++     +dnv+ F q +i +l ++ +
  gi|91773553|ref|YP_566245.1| 304 EGIEKAKQK--VYSSDNVKvFTQLEIKDLLNSaF 335
                                   567777774..33455776477788888555545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2251.17
//
Query:       gi|91773554|ref|YP_566246.1|  [L=392]
Description: hypothetical protein Mbur_1592 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2482.33
//
Query:       gi|91773555|ref|YP_566247.1|  [L=504]
Description: polysaccharide biosynthesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   83.9  18.7    1.1e-23   83.9  18.7    3.9  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    3.5e-17   62.6  12.4    3.5e-17   62.6  12.4    2.1  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    3.9e-17   62.5  25.2    3.9e-17   62.5  25.2    2.2  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.5e-07   31.3   8.2    1.5e-07   31.3   8.2    3.6  3  MatE             MatE
    2.3e-07   29.8  35.3    4.4e-06   25.6  35.3    2.1  1  MurJ             Lipid II flippase MurJ
  ------ inclusion threshold ------
        1.4    7.7  35.8       0.12   11.2   9.7    3.4  3  EcsB             Bacterial ABC transporter protein EcsB


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   7.2         6   1.8e+04      97     102 ..      59      64 ..      11     125 .. 0.50
   2 !   12.1   9.6   5.1e-05      0.15       2      99 ..     136     234 ..     135     291 .. 0.72
   3 ?   -3.7   0.1       3.9   1.2e+04      91     100 ..     315     324 ..     300     334 .. 0.52
   4 !   83.9  18.7   3.6e-27   1.1e-23       1     141 [.     345     481 ..     345     483 .. 0.94

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 6
               Polysacc_synt_C  97 aalvmg 102
                                    a+++g
  gi|91773555|ref|YP_566247.1|  59 GAAILG 64 
                                   111111 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.1e-05
               Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrrll 81 
                                   + +l+++++++ +  + s+ + g+g+  i l +++ g +  +il++l i   + + G a + v++ l++ ++ +++   +l
  gi|91773555|ref|YP_566247.1| 136 FIWLIIALLVSLFEGPISTGIAGTGKMGIRLTCAAMGNISRVILQVLAIyFGYEAAGLAGGAVAGILLSVIIEYRFFDLHL 216
                                   56778888888778***********************************44555688888888888888888877766554 PP

               Polysacc_synt_C  82 gikl.ellrrllkpllaal 99 
                                   +    + l++l  ++ + +
  gi|91773555|ref|YP_566247.1| 217 KRFKwHHLKSL-SVFSFWI 234
                                   43333435544.2222222 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.9
               Polysacc_synt_C  91 llkpllaalv 100
                                   l  p+l++ v
  gi|91773555|ref|YP_566247.1| 315 LAAPILIGGV 324
                                   1223333333 PP

  == domain 4  score: 83.9 bits;  conditional E-value: 3.6e-27
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrll 81 
                                   +L+il  + i+ +++ +++ +L++++++k+ +k+++ig++++++ln++lipl+gi Gaaiat++++++  +l  +al++ +
  gi|91773555|ref|YP_566247.1| 345 LLVILLAVQIVNVFQYFFTMYLNAIDHPKESFKVTFIGVAANIALNFILIPLIGISGAAIATLITMTLNGLLARRALSQFI 425
                                   5899***************************************************************************** PP

               Polysacc_synt_C  82 giklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                    i+le  ++ll ++ a++vmg++v   ++ll++l++l+  ++l  v++g+ +Y++++l+l
  gi|91773555|ref|YP_566247.1| 426 TIRLE-SQSLLNIITASVVMGLIVG-GYRLLIPLSNLW--VTLPVVVIGGGLYGVVVLKL 481
                                   ****5.89999************66.777777777655..9999999***********98 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6  12.4   1.2e-20   3.5e-17      12     291 ..      64     342 ..      58     344 .. 0.89
   2 ?   -2.8   0.7      0.96   2.9e+03     119     146 ..     453     480 ..     399     487 .. 0.71

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.2e-20
               Polysacc_synt_3  12 GvvaialvvislanlfvdmGlssaliqkedltee...dlstvftfnlvlgllialvlfllapliasfynqpelvtvlrvla 89 
                                   G + + ++ +s++++++d G++ a i++ +  ee   ++s  f++ lv+ ++i ++l++++++  ++ n   +   l ++ 
  gi|91773555|ref|YP_566247.1|  64 GAYFLFMAYTSIFSMVADGGFGAAAIKRISEGEEpdaYFSASFVLRLVFTIVIVIALLVFRDYFVDL-NTSGMFIWLIIAL 143
                                   88889999******************99865555555999*********************999885.6667777777777 PP

               Polysacc_synt_3  90 lvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwrprlkfs 170
                                   lv +++g +s+  a   +            ++++  vi+ +++ ++g+ +  L+ g ++  lls+++ + + +  ++  f+
  gi|91773555|ref|YP_566247.1| 144 LVSLFEGPISTGIAGTGKMG---IRLTCAAMGNISRVILQVLAIYFGYEAAGLAGGAVAGILLSVIIEYRFFDLHLKR-FK 220
                                   88899****99999887643...23334456778889999999999******************************97.** PP

               Polysacc_synt_3 171 lkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsviakVlfPalSrlqd..dkkk 249
                                   +++lk+l  f+ +++l+     +++++d+++iG+++++a++G+Y v  ++++ + +  t ++ + l P +S+ ++  d   
  gi|91773555|ref|YP_566247.1| 221 WHHLKSLSVFSFWIFLTAGGSLVFSQADTVMIGYFMENADVGVYRVVLQFTT-VATFTTYALRNTLWPRISHWSKsgDLGL 300
                                   ***********************************************99876.56788999**********9875338889 PP

               Polysacc_synt_3 250 lrelylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                   ++e++ ++++ + +++ Pi++g +++ + l+ +++Gs++ ++
  gi|91773555|ref|YP_566247.1| 301 VEESLSRAISYSLILAAPILIGGVMLGDKLLFLFYGSEFADS 342
                                   **************************************9876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.96
               Polysacc_synt_3 119 lvssvvgvivaivlAllglgvwALvigt 146
                                   l+  +  + v++ ++++g g++ +v+ +
  gi|91773555|ref|YP_566247.1| 453 LLIPLSNLWVTLPVVVIGGGLYGVVVLK 480
                                   4444555666777777777777766655 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5  25.2   1.3e-20   3.9e-17       5     272 ..      33     291 ..      29     293 .. 0.78
   2 ?    2.4  15.1     0.029        87      74     226 ..     306     460 ..     294     470 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.3e-20
                 Polysacc_synt   5 vivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.kelvslillnvllv 84 
                                   +++ l  q++  +++f+ + y+a ++g++  G + l +a ++++++++d G++aa++++i++ +e   + +++++l ++++
  gi|91773555|ref|YP_566247.1|  33 SLIALFWQIAFTGIGFLSTMYFAHTVGAAILGAYFLFMAYTSIFSMVADGGFGAAAIKRISEGEEPdAYFSASFVLRLVFT 113
                                   566667788888**************************************************9985556666666666666 PP

                 Polysacc_synt  85 llvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfld 165
                                   ++++++l ++ +++  +  ++   +++li+al +     +   ++    g  +m   +      ++srvil ++a++ ++ 
  gi|91773555|ref|YP_566247.1| 114 IVIVIALLVFRDYF--VDLNTSGMFIWLIIALLVS---LFEGPISTGIAGTGKMGIRLTCAAMGNISRVILQVLAIYFGY- 188
                                   66666666666666..3334444444444444444...444444444567889999999999999999999999998887. PP

                 Polysacc_synt 166 ivaavlgavlaalvggivslavlrkkf.rprfvilslklvrellsfsapltisslaillytyidsillglllgaeavGiYn 245
                                       ++g++ +a++g+++s ++ +++f    + ++  ++ + l  fs++++++  ++l++ + d++++g++ ++ +vG Y+
  gi|91773555|ref|YP_566247.1| 189 ---EAAGLAGGAVAGILLSVIIEYRFFdLHLKRFK-WHHLKSLSVFSFWIFLTAGGSLVFSQADTVMIGYFMENADVGVYR 265
                                   ...56666777777777777777777753444444.56******************************************* PP

                 Polysacc_synt 246 aayqllvaisgllapivtaalfPvfse 272
                                   ++ q++++++ + ++++  +l P++s 
  gi|91773555|ref|YP_566247.1| 266 VVLQFTTVAT-FTTYALRNTLWPRISH 291
                                   *****99987.556666669*999995 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.029
                 Polysacc_synt  74 vslillnvllvllvlvllfllllliaaflglpelavlylilalmll..llvgvasfrrglfqglermkyaavsqvveqlsr 152
                                   ++ i  +++l+  +l+  + l + +  +++++e+a  yl+l + l+  +++ ++ f+++++++    k  +  +++ + + 
  gi|91773555|ref|YP_566247.1| 306 SRAISYSLILAAPILIGGVMLGDKLLFLFYGSEFADSYLLLVILLAvqIVNVFQYFFTMYLNAIDHPKESFKVTFIGVAAN 386
                                   5555555555555555555555544446666666666666666665569******************************** PP

                 Polysacc_synt 153 vilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvils.lklvrellsfsapltisslaillyty 226
                                   ++l +i++ l++ i +a++++++ + ++g+++   l  + + r    s l  ++ ++ +++ + + +l+i+l++ 
  gi|91773555|ref|YP_566247.1| 387 IALNFILIPLIG-ISGAAIATLITMTLNGLLARRALSQFITIRLESQSlLNIITASVVMGLIVGGYRLLIPLSNL 460
                                   ************.*******************99999666777777777999******************99985 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2  17.4      0.18   5.3e+02       4     158 ..      38     179 ..      36     182 .. 0.71
   2 !   31.3   8.2   4.9e-11   1.5e-07      11     161 .]     243     392 ..     235     392 .. 0.95
   3 ?   -2.7   0.2       1.3   3.9e+03      10      10 ..     433     433 ..     399     465 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.18
                          MatE   4 lenllesllslidtllvgrl.gskalAavsialsilsllfvfl.lglstalttlvgqalGaknfkrakealrqglilllll 82 
                                   + +++++ +++++t+  ++  g+  l+a+ +++  +s++ +++  g+++a+  +++    ++   +a++++   l l++  
  gi|91773555|ref|YP_566247.1|  38 FWQIAFTGIGFLSTMYFAHTvGAAILGAYFLFMAYTSIFSMVAdGGFGAAAIKRIS----EGEEPDAYFSASFVLRLVFT- 113
                                   668999***********************************661566777776666....56655666655555555555. PP

                          MatE  83 sliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnipl 158
                                    ++i++++l+f+++++ l t         + +  +li+ +++ ++  ++s+   g+gk+ + l +++ +++ +++l
  gi|91773555|ref|YP_566247.1| 114 -IVIVIALLVFRDYFVDLNT---------SGMFIWLIIALLVSLFEGPISTGIAGTGKMGIRLTCAAMGNISRVIL 179
                                   .5555555599999999874.........44566666666666666777777777777776666666666666665 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 4.9e-11
                          MatE  11 llslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallv 90 
                                   ++s +dt+++g++    +++++ ++l+++ + ++   +l + l +++++   +++   ++e+l +++  +l+l+++i + +
  gi|91773555|ref|YP_566247.1| 243 VFSQADTVMIGYFmENADVGVYRVVLQFTTVATFTTYALRNTLWPRISHWSKSGDLGLVEESLSRAISYSLILAAPILIGG 323
                                   57889**************************************************************************** PP

                          MatE  91 llfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161
                                   +++ +++l lf  +e   + +  +l il+ +++++++q  ++ +l+++  +k ++ +++i++  ni ln++
  gi|91773555|ref|YP_566247.1| 324 VMLGDKLLFLFYGSE--FADSYLLLVILLAVQIVNVFQYFFTMYLNAIDHPKESFKVTFIGVAANIALNFI 392
                                   ***********9888..5666666777777899************************************97 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.3
                          MatE  10 s 10 
                                   s
  gi|91773555|ref|YP_566247.1| 433 S 433
                                   2 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6  35.3   1.5e-09   4.4e-06       2     434 ..      55     456 ..      54     470 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.5e-09
                          MurJ   2 aallGaglladaFnvAfklPnllrrlfaegalssaFvPvlaeakkkdeekaaefvrkvltllilvlllvtligilaaplli 82 
                                   a++ Ga+ l++ F   f+  + ++ ++a+g++ +a +   +e +++d+   a+f   vl+l+++++++++l+  ++  +++
  gi|91773555|ref|YP_566247.1|  55 AHTVGAAILGAYFL--FMAYTSIFSMVADGGFGAAAIKRISEGEEPDAYFSASF---VLRLVFTIVIVIALL--VFRDYFV 128
                                   55666666666433..44455566666666666666655555553333333333...233333333333333..6666666 PP

                          MurJ  83 rllatgfdeetlelavsllrillpylllvsls.avfgavLnarkkFfapafsPvllNvsvIltllllanklgeeailaLai 162
                                   +l ++g+             i l  +llvsl  + +++     +k ++    + + N+s ++ l +la ++g  + ++La 
  gi|91773555|ref|YP_566247.1| 129 DLNTSGM------------FIWLIIALLVSLFeGPISTGIAGTGKMGIRLTCAAMGNISRVI-LQVLAIYFG-YEAAGLAG 195
                                   6666666............2223333333333132233333445555555555666776443.333444555.44667888 PP

                          MurJ 163 GvliGgvlqllvqlpalkkaglllkprfafrdeglkkflklllptllgvsvsqlnllvdtalAsflaegsvsilayadril 243
                                   G ++G +l +++     + ++l+lk rf+++    k +    ++ +l+ + s++ ++ dt++  +++e++   ++  ++ +
  gi|91773555|ref|YP_566247.1| 196 GAVAGILLSVII---EYRFFDLHLK-RFKWHHL--KSLSVFSFWIFLTAGGSLVFSQADTVMIGYFMENADVGVYRVVLQF 270
                                   888888877654...4566777755.4777665..5555555666677777788899999999999999999988777777 PP

                          MurJ 244 qlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataev 324
                                   ++     + ++ ++l Pr+S   k++d   v++ ls ai+ +l+l+ p+ +g ++l+++++ l++  ++F +      +++
  gi|91773555|ref|YP_566247.1| 271 TTVATFTTYALRNTLWPRISHWSKSGDLGLVEESLSRAISYSLILAAPILIGGVMLGDKLLFLFY-GSEFAD------SYL 344
                                   7777777789**************************************************99999.666655......566 PP

                          MurJ 325 LaayalgLipyal.vklllrvfYAredtktPvkislislvlnillsllllpplgvvglalatslsaliglvllyvllrkrl 404
                                   L + +l++  + + +++++ ++ A    k+ +k+++i +  ni+l+++l+p +g  g a+at +  +++ +l+ + l +  
  gi|91773555|ref|YP_566247.1| 345 LLVILLAVQIVNVfQYFFTMYLNAIDHPKESFKVTFIGVAANIALNFILIPLIGISGAAIATLITMTLNGLLARRALSQFI 425
                                   66666666555441567777778*******************************************999999999999988 PP

                          MurJ 405 klteargiktflak.lvvllalaavvillls 434
                                    +  ++  ++++    vv+ +++++  ll+ 
  gi|91773555|ref|YP_566247.1| 426 TIRLESQSLLNIITaSVVMGLIVGGYRLLIP 456
                                   7666555555555522444444444444443 PP

>> EcsB  Bacterial ABC transporter protein EcsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.3      0.19   5.6e+02     168     203 ..      35      70 ..      16      80 .. 0.50
   2 ?   10.3   6.4   7.5e-05      0.22      99     217 ..     102     224 ..      99     228 .. 0.79
   3 ?   11.2   9.7   4.1e-05      0.12      95     224 ..     305     433 ..     301     469 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                          EcsB 168 irlllnalllylllalapllalllilllllvlllll 203
                                   i l +++++  + +  ++++a  + +++l +++l++
  gi|91773555|ref|YP_566247.1|  35 IALFWQIAFTGIGFLSTMYFAHTVGAAILGAYFLFM 70 
                                   334444444444444444444433333333333332 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.5e-05
                          EcsB  99 iryslllqllllllvllillPlllettglsiaelllllllllllkllnlllkweelrlqgkkkrridr....lirlllnal 175
                                   +  s++l+l+++++++++ll +      l+ ++++++l+++ll++l++  ++       +  +r++      + r++l++l
  gi|91773555|ref|YP_566247.1| 102 FSASFVLRLVFTIVIVIALLVFRDYFVDLNTSGMFIWLIIALLVSLFEGPISTGIAGTGKMGIRLTCAamgnISRVILQVL 182
                                   567999999999999999999988888888888888888888888877777777666666666666558888********* PP

                          EcsB 176 llylllalapllalllilllllvlllllkrkkkkklldWekl 217
                                   ++y+ +++a l++ ++  +ll v++ +  +  + k+++W +l
  gi|91773555|ref|YP_566247.1| 183 AIYFGYEAAGLAGGAVAGILLSVIIEYRFFDLHLKRFKWHHL 224
                                   **********99999966666666666666667788899775 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 4.1e-05
                          EcsB  95 lkksiryslllqllllllvllillPlllettglsiaelllllllllllkllnlllkweelrlqgkkkrridrlirlllnal 175
                                   l+++i ysl+l++ +l+  +++   ll+  +g+++a+  lll++ll+++++n++  +  ++l+  ++    + + ++  a+
  gi|91773555|ref|YP_566247.1| 305 LSRAISYSLILAAPILIGGVMLGDKLLFLFYGSEFADSYLLLVILLAVQIVNVFQYFFTMYLNAIDHPKESFKVTFIGVAA 385
                                   789********9999999999988888889********************************9988888888777777777 PP

                          EcsB 176 llylllalapllalllilllllvlllllkrkkkkklldWeklieeEqkr 224
                                    ++l ++l pl+++   ++++ +++++l+ +  +++l     i++E + 
  gi|91773555|ref|YP_566247.1| 386 NIALNFILIPLIGISG-AAIATLITMTLNGLLARRALSQFITIRLESQS 433
                                   7778888888888877.88888888888777777777666777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 3173.81
//
Query:       gi|91773556|ref|YP_566248.1|  [L=238]
Description: acylneuraminate cytidylyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   94.0   0.8    1.4e-26   93.8   0.8    1.0  1  CTP_transf_3  Cytidylyltransferase


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.8   7.7e-31   1.4e-26       2     213 ..      18     234 ..      17     238 .] 0.78

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 7.7e-31
                                   EEEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT.SEEEE-.-TTCSSHHHHHHHH CS
                  CTP_transf_3   2 aIipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg.asvlvt.rsslesdterflev 80 
                                   a+ p+  +S+R+p+Kn++ ++g+pl++ +l+++l+sk ++k++v TDse ikn + +    sv+v+ r+++  ++  ++++
  gi|91773556|ref|YP_566248.1|  18 ALLPMKGNSQRVPNKNMKLFAGNPLYHAILDELLESKYISKIVVNTDSETIKNDVSKNYyDSVIVInRPNELCGDFVSMNE 98 
                                   789************************************************997755444555544367777888888888 PP

                                   HHHHTTT.TTS.EEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETTSHHHHTSTTSTEEEETTTSBEEEEESSES CS
                  CTP_transf_3  81 vkaflmsenee.iivnlqGdnPllqeevikkaietlkenqedylstlvkkvgkeeevlnandlkvllddagkalyfeesvi 160
                                   + ++++++ +  + ++++++nPll+ ++i++ai ++ ++    +++l+ +++ ++++++ n  +v++  +   ++ +++++
  gi|91773556|ref|YP_566248.1|  99 LIKYDIDQVDYqYFIQTHSTNPLLKAQTIDEAIIKYIKSLA-TYDSLFSVTKLQTRLYDENGEAVNHNPD---ELIRTQDL 175
                                   888888744446*******************9999999965.7788888888888888888888888777...44444444 PP

                                   SEEHHHHHCTS...........TTTSEEEEEEEEEEHHHHHHHHHHSHHHHHSHHHHHT-TTHH CS
                  CTP_transf_3 161 pyireeplels...........rrlylshagiytfrkeqplkelvidtptseilekiekleqlr 213
                                    + +ee+++++           ++ + sh ++++  k   l+  +id p++  +e +e l+ +r
  gi|91773556|ref|YP_566248.1| 176 EPLYEENSNIYifskesfkkagNKRIGSHPQMFEVNK---LEAIDIDEPED--FELAELLYKKR 234
                                   4444444444444455554567666899999999988...89999999999..99999887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1536.67
//
Query:       gi|91773557|ref|YP_566249.1|  [L=255]
Description: 2-dehydro-3-deoxyglucarate aldolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-37  128.7   0.0      2e-37  128.5   0.0    1.0  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
       0.56    9.0   3.6       0.28   10.0   0.1    1.9  2  PK         Pyruvate kinase, barrel domain


Domain annotation for each model (and alignments):
>> 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 !  128.5   0.0   2.2e-41     2e-37       2     207 ..      14     227 ..      13     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 2.2e-41
                                   EEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGGHHH CS
                     HpcH_HpaI   2 iglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdlevld 82 
                                   ig ++   +++++e++a ag+ +++iD+E+           ++v++++ +++a      ++ VRv+++++++ik+   vld
  gi|91773557|ref|YP_566249.1|  14 IGSWITIGHPNVVEIMASAGFEWLVIDIEHTS------IDLTTVQSLISTIQA---SGIKALVRVSKNEEVIIKK---VLD 82 
                                   56799999***********************9......444666666666666...456****************...*** PP

                                   TTSSEEEESS--SHHHHHHHHHHTSHTTTS---...................HCCC-EEEEEE-SHHHHHTHHHHHTSTTE CS
                     HpcH_HpaI  83 lgaqvvlvPkvetaeealevvsalrepekgirg...................anketrllaqiEsaegvknaeeIaavegl 144
                                   +ga++++vP+++++++al++  + ++p+ g rg                    ++e++++aqiE  e+vkn+eeI++++g+
  gi|91773557|ref|YP_566249.1|  83 SGADGIVVPMIKCRADALKAIDYSKYPPVGKRGvglyraqkygtsfeeykkwVEEELVIIAQIEHIEAVKNIEEIITTDGI 163
                                   ********************************************************************************* PP

                                   EEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEE.EEEE.E-SSHHHHHHHHHTTHC CS
                     HpcH_HpaI 145 dgvflGaeDlsadlgtkrspegtevldareriltaaraagi.aaldtvasdiddaegflaegal 207
                                   dgv++G+ Dls ++g+ ++   ++v +a++ +l  ++  ++ + + ++ sd ++  + +++g +
  gi|91773557|ref|YP_566249.1| 164 DGVIIGPYDLSGSMGHPGEFYRKDVENAINDVLESCKRHNFpSGFHVIESDPHNLIQRIEQGCT 227
                                   *************************************999822344444444444444455555 PP

>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.6     0.065   5.8e+02     189     245 ..      33      90 ..      24      94 .. 0.73
   2 ?   10.0   0.1   3.2e-05      0.28     216     246 ..     137     169 ..     129     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.065
                                   T-SEEEETTE-SHHHHHHHHHHHTCCC.TTSEEEEEE-SCHHHHTHHHHHH.HSSEEEE CS
                            PK 189 gvdliaasfvrkasDvkevrevleeeg.keikiiakienqegvenldeile.asDgimv 245
                                   g + +++    ++ D+++v++++   + + ik + ++ ++e v  +  +l   +Dgi+v
  gi|91773557|ref|YP_566249.1|  33 GFEWLVIDIEHTSIDLTTVQSLISTIQaSGIKALVRVSKNEEVI-IKKVLDsGADGIVV 90 
                                   56667777778899999999998876659999999999988886.44555414677766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 3.2e-05
                                   TTSEEEEEE-SCHHHHTHHHHHHH..SSEEEEE CS
                            PK 216 keikiiakienqegvenldeilea..sDgimva 246
                                   +e+ iia+ie+ e+v+n++ei+ +   Dg+++ 
  gi|91773557|ref|YP_566249.1| 137 EELVIIAQIEHIEAVKNIEEIITTdgIDGVIIG 169
                                   56789*****************75224666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1684.62
//
Query:       gi|91773558|ref|YP_566250.1|  [L=317]
Description: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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  177.8   0.0      2e-51  173.9   0.0    2.0  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.5e-27   93.6   0.0    9.3e-27   93.3   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
      7e-05   22.9   0.1    0.00027   21.0   0.0    1.9  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
  ------ inclusion threshold ------
       0.07   13.3   0.0       0.15   12.2   0.0    1.5  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
      0.092   13.1   0.5        0.4   11.0   0.5    2.3  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
      0.096   12.9   0.0        0.4   10.9   0.0    2.1  2  TrkA_N         TrkA-N 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 ?    1.8   0.0     0.045   1.4e+02      26      56 ..      38      68 ..      21      75 .. 0.79
   2 !  173.9   0.0   6.7e-55     2e-51       2     178 .]     112     282 ..     111     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.045
                                  TCCGSBS-GTTSEEEEES-SHHHHHHHHHHH CS
                  2-Hacid_dh_C 26 ekallgkelsgktvGiiGlGrIGqavakrlk 56
                                   ++ l +++ ++ v i G+ rI ++v+k + 
  gi|91773558|ref|YP_566250.1| 38 TTRELASDIGNSDVLIAGTERITEEVIKNAP 68
                                  5566778999****************99875 PP

  == domain 2  score: 173.9 bits;  conditional E-value: 6.7e-55
                                   HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEE CS
                  2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvel 82 
                                   +++l+l+r+++++d++vr+g w   ++++g+ l+gktvGi+G+GrIG+++ ++l++f++k ++ d +++ +   + +++e+
  gi|91773558|ref|YP_566250.1| 112 GIILDLSRKISYTDRNVRKGVW---DRYMGNLLYGKTVGIFGMGRIGKSLVHLLSSFNVKFLVNDITPDFSF-GRLYNIEF 188
                                   789*******************...9*****************************************99776.777889** PP

                                   CSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTCH CS
                  2-Hacid_dh_C  83 vsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpeds 163
                                   vs +++l++sDi+s+++pl+++t+++i+ +e++km+++ailiNtaRGg+v+e +L+eaLk+  i+ga++Dvfeeep++   
  gi|91773558|ref|YP_566250.1| 189 VSKNDVLEKSDIISINIPLKKDTYDFITLNEIKKMRSNAILINTARGGIVNESDLYEALKNSMISGAGIDVFEEEPYK--G 267
                                   ******************************************************************************..6 PP

                                   HHHHSTTEEE-SS-T CS
                  2-Hacid_dh_C 164 pllelpnviltPHia 178
                                   +l+el n++lt H++
  gi|91773558|ref|YP_566250.1| 268 KLTELGNCVLTCHVG 282
                                   8************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 !   93.3   0.0   3.1e-30   9.3e-27       8     133 ..      14     313 ..       5     314 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 3.1e-30
                                   CHHHHHHHHHTTEEEEEES...CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT- CS
                                   xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh   8 reeelellkeegvevevkd...ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGi 85 
                                   ++  lellk ++++v +++   +++t el++++ + d+li  +++ +t+ev++++p+Lk+i+r+gvG D v++++++++Gi
  gi|91773558|ref|YP_566250.1|  14 SQTPLELLKSNEIDVILNSherKITTRELASDIGNSDVLIAGTER-ITEEVIKNAPNLKLISRVGVGLDGVNFELCNKYGI 93 
                                   7788899999888888888899*********************99.*********************************** PP

                                   EEEE-TTTTHHHHHHHH................................................................ CS
                                   xxxxxxxxxxxxxxxxx................................................................ RF
                    2-Hacid_dh  86 lVtnvpgystesvAElt................................................................ 102
                                   +Vt +p++ t +vAEl+                                                                
  gi|91773558|ref|YP_566250.1|  94 KVTYTPDAPTMAVAELCvgiildlsrkisytdrnvrkgvwdrymgnllygktvgifgmgrigkslvhllssfnvkflvndi 174
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                    2-Hacid_dh 103 ................................................................................. 102
                                                                                                                    
  gi|91773558|ref|YP_566250.1| 175 tpdfsfgrlyniefvskndvleksdiisiniplkkdtydfitlneikkmrsnailintarggivnesdlyealknsmisga 255
                                   ********************************************************************************* PP

                                   ...........................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                   ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 103 ...........................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                              a+T +++ ++ ++a+e++++f ++++++n+v
  gi|91773558|ref|YP_566250.1| 256 gidvfeeepykgkltelgncvltchvgASTINSRTEMETQAVEEVIRFKNERPLKNEV 313
                                   ***************************************************9999987 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.77   2.3e+03      90     117 ..      27      54 ..      22      77 .. 0.70
   2 !   21.0   0.0   9.2e-08   0.00027      17     110 ..     137     233 ..     123     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.77
                                   SSB-HHHHCCS-TTEEEEE-SSTTTTBT CS
                 AdoHcyase_NAD  90 diitlehlkkmkddaivcniGhfdseid 117
                                   d+i + h +k+  + + ++iG +d  i 
  gi|91773558|ref|YP_566250.1|  27 DVILNSHERKITTRELASDIGNSDVLIA 54 
                                   6777777777777777777777776554 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 9.2e-08
                                   H-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-....SSSSSSB- CS
                 AdoHcyase_NAD  17 tdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtt....tGnkdiit 93 
                                      ll Gk++ + G G +Gk   + l ++  + +v ++ P  ++  +    e v  ++v++k+di+         + d it
  gi|91773558|ref|YP_566250.1| 137 MGNLLYGKTVGIFGMGRIGKSLVHLLSSFNVKFLVNDITPDFSFGRLY-NIEFVSKNDVLEKSDIISINiplkKDTYDFIT 216
                                   556899**********************************99997665.5788889********986541111456799** PP

                                   HHHHCCS-TTEEEEE-S CS
                 AdoHcyase_NAD  94 lehlkkmkddaivcniG 110
                                   l+++kkm+ +ai+ n  
  gi|91773558|ref|YP_566250.1| 217 LNEIKKMRSNAILINTA 233
                                   *************9963 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.1e-05      0.15       2     109 ..     146     252 ..     145     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC-- CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealk 81 
                                   +g+ G+G +G++++  l + + k  v + t++     +      + s ++++++ d++ + ++ +k++ ++i+   +++++
  gi|91773558|ref|YP_566250.1| 146 VGIFGMGRIGKSLVHLLSSFNVKFLVNDITPDFSFGRL--YNIEFVSKNDVLEKSDIISINIPLKKDTYDFITLnEIKKMR 224
                                   89***************************987544333..2345567789******************99998778899** PP

                                   TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                 NAD_binding_2  82 kgdilidgstsspedtrelakelkekgl 109
                                   +++ili+++   + +  +l+++lk++ +
  gi|91773558|ref|YP_566250.1| 225 SNAILINTARGGIVNESDLYEALKNSMI 252
                                   ******9999988888888888887655 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   0.00014       0.4       2      21 ..     145     164 ..     144     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                   EEEEESTSHHHHHHHHHHHH CS
                       Gp_dh_N   2 kvainGfGRIGrlvlralle 21 
                                    v+i G+GRIG+ ++  l +
  gi|91773558|ref|YP_566250.1| 145 TVGIFGMGRIGKSLVHLLSS 164
                                   59**********99987763 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.91   2.7e+03       1      15 [.      51      65 ..      18      76 .. 0.75
   2 ?   10.9   0.0   0.00013       0.4       3      32 ..     148     177 ..     146     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.91
                                  EEEES-SHHHHHHHH CS
                        TrkA_N  1 iiiiGlGrvGrslae 15
                                  ++i+G  r+++++++
  gi|91773558|ref|YP_566250.1| 51 VLIAGTERITEEVIK 65
                                  456666666666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                   EES-SHHHHHHHHHHHH.TTEEEEEEESSHH CS
                        TrkA_N   3 iiGlGrvGrslaeeLse.ggkdvvvidkdee 32 
                                   i G+Gr+G+sl++ Ls+ +  +++v d  ++
  gi|91773558|ref|YP_566250.1| 148 IFGMGRIGKSLVHLLSSfNV-KFLVNDITPD 177
                                   89***************666.5888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2046.02
//
Query:       gi|91773559|ref|YP_566251.1|  [L=294]
Description: NAD-dependent epimerase/dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  141.6   0.3    1.4e-40  139.2   0.3    1.9  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-29  103.9   1.0    1.3e-27   97.1   1.0    2.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      2e-17   63.1   3.7    6.7e-16   58.1   3.7    2.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    3.1e-15   56.1   0.4    1.2e-14   54.2   0.4    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.1e-14   54.2   0.0    1.5e-13   50.5   0.0    2.0  1  RmlD_sub_bind    RmlD substrate binding domain
    1.7e-13   50.4   1.9    5.5e-05   22.5   0.0    3.2  3  NAD_binding_4    Male sterility protein
    9.6e-13   48.4   0.0    1.9e-12   47.5   0.0    1.5  1  NAD_binding_10   NAD(P)H-binding
    8.3e-09   35.3   0.1    2.5e-08   33.8   0.1    1.7  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.042   14.2   0.0    1.5  1  DUF4378          Domain of unknown function (DUF4378)
      0.089   12.2   0.2       0.17   11.3   0.2    1.5  1  adh_short        short chain dehydrogenase


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 !  139.2   0.3   8.1e-44   1.4e-40       1     237 [.       5     214 ..       5     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 8.1e-44
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   +lV G+ Gf+Gs+lv++l  k+yev++ d + s    + +++  +ve++++d+ ++++l+k  ++d+v+++A+ ++ +  +
  gi|91773559|ref|YP_566251.1|   5 VLVFGGCGFLGSYLVERLCMKKYEVTVADLNLS----KYINKDIFVECNILDKIKVAELVK--NADIVYNFAGMANLDKAV 79 
                                   79***************************8833....3333449*****************..9***************** PP

                                   HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT- CS
                     Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqygl 162
                                   edp  +ie n++g+ln+l+a+ ++gv+r++++sS   Y  +++               s Y+++Kl++ekl+e+y+a+y+l
  gi|91773559|ref|YP_566251.1|  80 EDPCGTIELNVIGNLNILDACMQSGVERFVYASS--AYSMSDK--------------GSFYGISKLTSEKLIEEYNAKYDL 144
                                   **********************************..5654444..............456********************* PP

                                   EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEE CS
                     Epimerase 163 naiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgei 237
                                   +++i+r+ ++y++r    ++++ i  l++++     +++ +gdg++ R++++++Dva++++ ++e  ++ ++ +i
  gi|91773559|ref|YP_566251.1| 145 KYTIIRYGSVYSER---ISENNYIYNLLKNAIISG-KIKHFGDGEEIREYIHASDVAQLSVEIIESNQF-ENEHI 214
                                   **************...555555555555555555.5****************************9776.34344 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 !   97.1   1.0   7.3e-31   1.3e-27       1     276 [.       6     245 ..       6     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 7.3e-31
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+ G+ Gf Gsyl+e+L+ k+yev++ + + s+ +   i    k           ++++++ D+ ++ +l++++  d vyn
  gi|91773559|ref|YP_566251.1|   6 LVFGGCGFLGSYLVERLCMKKYEVTVADLNLSK-Y---I---NK---------DIFVECNILDKIKVAELVKNA--DIVYN 68 
                                   89**********************875433332.2...2...11.........259****************99..89*** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadw 162
                                   +A++   d+ +e+P  t+e nv+G l++L+a+ + g+e   rf+ aS++                 +  s Y+++Kl+++ 
  gi|91773559|ref|YP_566251.1|  69 FAGMANLDKAVEDPCGTIELNVIGNLNILDACMQSGVE---RFVYASSAYS-------------MSDKGSFYGISKLTSEK 133
                                   ************************************97...9*****9732.............2345689********** PP

                                   HHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS-. CS
                 GDP_Man_Dehyd 163 ivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkp. 242
                                   ++++y+ +y+l  ++ ++   +s r +e+   + i + + ++     ++ ++G+++++R + h++D+++  + ++++++  
  gi|91773559|ref|YP_566251.1| 134 LIEEYNAKYDLKYTIIRYGSVYSERISEN---NYIYNLLKNAIISG-KIKHFGDGEEIREYIHASDVAQLSVEIIESNQFe 210
                                   *************************8876...55555555544433.45567***********************987642 PP

                                   --EEE-TT.-EEECHHCHHCCHHCCCHHHHHH... CS
                 GDP_Man_Dehyd 243 edyviatg.ethsvrefvelaflelgktiewegkg 276
                                   ++++i tg e ++ +e++e+ +  lg+++e e ++
  gi|91773559|ref|YP_566251.1| 211 NEHIILTGmERMKRKELFEMINDILGNKLEIELND 245
                                   34555555277888999999999999988876543 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 !   58.1   3.7   3.7e-19   6.7e-16       1     121 [.       6     118 ..       6     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 3.7e-19
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                   +v Gg+GFlG++lv++L   +   ev v+Dl+ s+ +       n + ++e+ ++dk k+ e ++++d+v   a++ ++ +
  gi|91773559|ref|YP_566251.1|   6 LVFGGCGFLGSYLVERLCMKK--YEVTVADLNLSKYI-------NKDIFVECNILDKIKVAELVKNADIVYNFAGMANLDK 77 
                                   699**************9888..6*******988777.......555589*****************************99 PP

                     3Beta_HSD  82 .kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvg 121
                                    +       + nv G  n+l+ac+++gv+++vY Ssa  + 
  gi|91773559|ref|YP_566251.1|  78 aVEDPCGTIELNVIGNLNILDACMQSGVERFVYASSAYSMS 118
                                   33333345789*************************87655 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.4   6.4e-18   1.2e-14      37     248 ..      32     236 ..       5     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 6.4e-18
                                   HHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHH CS
               Polysacc_synt_2  37 yeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaie 117
                                    +++ +   ++ +k++      v +++ dk +++++++  + d+v++ A + ++  + e p+ +i+ Nv+g  n+++a+++
  gi|91773559|ref|YP_566251.1|  32 ADLNLS---KYINKDI-----FVECNILDKIKVAELVK--NADIVYNFAGMANLDKAVEDPCGTIELNVIGNLNILDACMQ 102
                                   222222...1223334.....3458999**********..9**************************************** PP

                                   TT-SEEEEEEEGGGSS.--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGTTS....SHHHHHHHHHTTSSEE CS
               Polysacc_synt_2 118 agvkkvvliStDKAvn.PtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgSrGS....viplFkkqikeggpvt 193
                                   +gv+++v+ S+   ++   + +G++K+++ekl+ +++++    + k++++R+G V   r S    +  l k+ i +g+   
  gi|91773559|ref|YP_566251.1| 103 SGVERFVYASSAYSMSdKGSFYGISKLTSEKLIEEYNAKY---DLKYTIIRYGSVYSERISennyIYNLLKNAIISGKIKH 180
                                   *********998887615699***************9998...99**********98776644447778888888888778 PP

                                   ES-TT-EEEEE-HHHHHHHHHHHH..HH--SS-EEEE--.-EEEHHHHHHHH..... CS
               Polysacc_synt_2 194 vTdpemtRyfmtieeavqLvlqal..alakggeifvldmGepvkivdlakalielsg 248
                                     d e +R ++  ++ +qL ++ +  ++ ++ +i ++ m e +k ++l + + ++ g
  gi|91773559|ref|YP_566251.1| 181 FGDGEEIREYIHASDVAQLSVEIIesNQFENEHIILTGM-ERMKRKELFEMINDILG 236
                                   888888888888888888877665113445566777777.77777777776666666 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   8.2e-17   1.5e-13       2     199 ..       4     206 ..       3     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 8.2e-17
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSH CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...........eldltdaeavaellkeakpdvvvnaAAytavDkaEsee 71 
                                   k+lv+G+ G lGs L+++l  +++ev+  + +           e+++ d+ +vael+k+   d+v+n A   + Dka +++
  gi|91773559|ref|YP_566251.1|   4 KVLVFGGCGFLGSYLVERLCMKKYEVTVADLNlskyinkdifvECNILDKIKVAELVKN--ADIVYNFAGMANLDKAVEDP 82 
                                   79************************99998899***********************99..899***************** PP

                                   HHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SEEEEE CS
                 RmlD_sub_bind  72 eaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....kalivR 147
                                       ++n+ +  ++ +a+ + g+  +++ S+           Y+ +d+    ++YG +Kl  E+ ++++++    k++i+R
  gi|91773559|ref|YP_566251.1|  83 CGTIELNVIGNLNILDACMQSGVErFVYASSA----------YSMSDKG---SFYGISKLTSEKLIEEYNAkydlKYTIIR 150
                                   **********************9548888875..........6666664...79*************9655233379**** PP

                                   E-SEESS..SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHH CS
                 RmlD_sub_bind 148 tswvyge..kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllek 199
                                    + vy+e  +++n++ ++l+ a  + ++k + D   +++  +a d+A+  ++++e 
  gi|91773559|ref|YP_566251.1| 151 YGSVYSEriSENNYIYNLLKNAIISGKIKHFGDgeEIREYIHASDVAQLSVEIIES 206
                                   *****99889**********998888888777633466666777777777777665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00031      0.56       3      25 ..       9      31 ..       7      38 .. 0.86
   2 !   22.5   0.0   3.1e-08   5.5e-05      76     143 ..      51     120 ..      37     123 .. 0.90
   3 !   17.2   0.1   1.3e-06    0.0023     176     236 ..     124     180 ..     119     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                                  -TTSHHHHHHHHHHHHHS-.TEE CS
                 NAD_binding_4  3 GaTGFLGkvLlekLLrttpevki 25
                                  G+ GFLG++L+e+L  ++ ev++
  gi|91773559|ref|YP_566251.1|  9 GGCGFLGSYLVERLCMKKYEVTV 31
                                  99************988877655 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.1e-08
                                   --HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS- CS
                 NAD_binding_4  76 LseedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvnger 143
                                   L++ ++ el+++ d++++ a+  n+d+ +++    ++ Nv G  ++l+ + +      +++ S+ay+  ++
  gi|91773559|ref|YP_566251.1|  51 LDKIKVAELVKNADIVYNFAGMANLDKAVEDpcgTIELNVIGNLNILDACMQSGVE-RFVYASSAYSMSDK 120
                                   6677899***********************97778899*************99888.*********97765 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES CS
                 NAD_binding_4 176 YeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpe 236
                                   Y  sK  +Ekl++e++ + +l+ +i+R + +++e  +   +++  ++++l+ +i  g++++
  gi|91773559|ref|YP_566251.1| 124 YGISKLTSEKLIEEYNAKYDLKYTIIRYGSVYSERIS---ENNY-IYNLLKNAIISGKIKH 180
                                   99*****************************997655...4444.7777777777777774 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.1e-15   1.9e-12       1     182 [.       9     205 ..       9     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.1e-15
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHH.... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeeg.... 77 
                                   G+ G  G++lv++l  ++ +evt+   n +k       ++   ve +++d+ ++ae +k+ad+V+  +g  + d+ +    
  gi|91773559|ref|YP_566251.1|   9 GGCGFLGSYLVERLCMKK-YEVTVADLNLSKYI-----NKDIFVECNILDKIKVAELVKNADIVYNFAGMANLDKAVedpc 83 
                                   8899*************5.***99877777765.....234589********************99998777766667778 PP

                                   .........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-CEE-S CS
                NAD_binding_10  78 .........aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpggLtde 149
                                              ni+da+ ++gv+Rfv+ s++ +    +g+f  +      + l   +  ee+  + +l++Ti+r g    e
  gi|91773559|ref|YP_566251.1|  84 gtielnvigNLNILDACMQSGVERFVYASSAYSMS-DKGSFYGI------SKLTSEKLIEEYNAKYDLKYTIIRYGSVYSE 157
                                   888999999*********************98773.45555333......3456677777888889***********7666 PP

                                   T..--SEEEE..............ETTSS----EEEHHHHHHHHHHHCT CS
                NAD_binding_10 150 p..ttkyrvv..............ekgepfkggsisradVAdvlvavld 182
                                      +++y                  +ge++ ++ i  +dVA++ v++++
  gi|91773559|ref|YP_566251.1| 158 RisENNYIYNllknaiisgkikhfGDGEEI-REYIHASDVAQLSVEIIE 205
                                   532222221122333333222211444443.468999999999999987 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   1.4e-11   2.5e-08       1     228 [.       5     238 ..       5     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.4e-11
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG...... CS
                          NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy...... 75 
                                   +lv+G+ G +G+++v+ l  ++++v +   ++++   k +      +v+ ++ dk  ++e++k++d v+   g++      
  gi|91773559|ref|YP_566251.1|   5 VLVFGGCGFLGSYLVERLCMKKYEVTVADLNLSKYINKDI------FVECNILDKIKVAELVKNADIVYNFAGMAnldkav 79 
                                   79***********************998888877777665......7888889999*************999988999999 PP

                                   .......S-HHHHHHHHHHHHHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEE.EE-EEGGG- CS
                          NmrA  76 .......skeiedgkklvdAakeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfv.yagffmenf 148
                                          + ++    ++ dA  + Gv++f+y+s +      ++++ +++   s   ieey  +  + yt++ y  ++ e +
  gi|91773559|ref|YP_566251.1|  80 edpcgtiELNVIGNLNILDACMQSGVERFVYASSAYSM-SDKGSFYGISKLTSEKLIEEYNAKYDLKYTIIrYGSVYSERI 159
                                   999998888888899****************9988887.5568999***********************9945679***99 PP

                                   BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS- CS
                          NmrA 149 lsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigkt 228
                                   + + +  +  + a    k++  g+g+    ++ +  D+++  ++i++  +  + ++i    + +  +e+ e+++  +g +
  gi|91773559|ref|YP_566251.1| 160 SENNYIYNLLKNAIISGKIKHFGDGEEIREYI-HASDVAQLSVEIIESNQFENEHIILTGMERMKRKELFEMINDILGNK 238
                                   999999888888888889********877777.**************999889999999999999999999888777765 PP

>> DUF4378  Domain of unknown function (DUF4378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.042      49      80 ..     213     250 ..     161     285 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                       DUF4378  49 sekkrreerserklLFDlvneiLaeilalel......k 80 
                                   +   +  er++rk LF ++n iL  +l+ el      +
  gi|91773559|ref|YP_566251.1| 213 HIILTGMERMKRKELFEMINDILGNKLEIELndngyeH 250
                                   34445679*******************98886655531 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   9.4e-05      0.17       1     159 [.       3     134 ..       3     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.4e-05
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                   k vlv G+++ +G  ++++l  + ++v+v+d + +k       +++     +++++++ d+ +v +lv++a       d++
  gi|91773559|ref|YP_566251.1|   3 KKVLVFGGCGFLGSYLVERLCMKKYEVTVADLNLSKY------INK----DIFVECNILDKIKVAELVKNA-------DIV 66 
                                   689**************************99996665......554....69*****************99.......*** PP

                                   EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                     adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                   +n AG+    +  +   e+   +ie+N+ g +++  a+++        r v  sS  +   +  ++ Y+ sK   ++l
  gi|91773559|ref|YP_566251.1|  67 YNFAGM----ANLDKAVEDPCGTIELNVIGNLNILDACMQS----GVERFVYASSAYS--MSDKGSFYGISKLTSEKL 134
                                   ******....3555556667778999999999999988776....3445555555555..455556666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1854.19
//
Query:       gi|91773560|ref|YP_566252.1|  [L=223]
Description: cyclase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-15   55.3   0.0    9.7e-15   55.0   0.0    1.1  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 !   55.0   0.0   5.4e-19   9.7e-15       3     134 ..       4     155 ..       2     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 5.4e-19
                       Cyclase   3 Lshplsedtpvwp....dp.................islsehtGTHlDapgHfae..ktidel.pleelvgpavvldvsak 59 
                                   Ls+ l+edtp+++     +                 i+++ h+GTHlD p+Hf+e  +t+ +  p  ++++  +  +++  
  gi|91773560|ref|YP_566252.1|   4 LSYILEEDTPTYGniskFWiekrssikngdiannssIHTTAHVGTHLDMPYHFYEngQTVIDFdPNFWIFNYILFFEIET- 83 
                                   8999********6475522777899999***************************8755544404445666666677732. PP

                       Cyclase  60 aaaedyeiitaedleaalakqgveikpgdivlirTgwskrledkeky..rnpglseeaaewlaekg..vkavGvDtlsv 134
                                      ed  ii+ e le  ++ ++   ++ ++++++Tg+ +  ++++ky  +n g+s+e+a++l +    ++++G D +sv
  gi|91773560|ref|YP_566252.1|  84 ---EDI-IIKNEILEILEEVEN--KEKYEMLIVKTGACNI-RKEQKYweENKGFSPEIADYLKKYFpnIRIFGFDSISV 155
                                   ...455.556666666655555..469*********9866.6677777999************97777********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1571.75
//
Query:       gi|91773561|ref|YP_566253.1|  [L=211]
Description: haloacid dehalogenase-like hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-16   59.3   2.0    6.3e-16   59.0   2.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    9.5e-06   26.0   0.0    0.00011   22.6   0.0    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
     0.0018   18.1   5.9     0.0048   16.7   5.9    1.7  1  Hydrolase_3     haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.022   15.1   0.0       0.93    9.9   0.0    2.2  1  HAD             haloacid dehalogenase-like hydrolase
       0.03   14.4   0.0      0.057   13.5   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   2.0   1.7e-19   6.3e-16       1     173 [.       6     181 ..       6     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.7e-19
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee.........kieellrkynee 72 
                                   iiFD+Dg++l++  +  +af+ l+ +y ++++ ++ ++ ++       +rk+   +  ++          i e+ +ky + 
  gi|91773561|ref|YP_566253.1|   6 IIFDFDGVILNSMAIKTKAFRDLFSSY-PKNVVDDFIEYHLKNGGVSRYRKID--YFHKQllgidisekEILEYAQKYSSL 83 
                                   8***********************999.5566665555444444422222222..22222445556777888888888887 PP

                         HAD_2  73 kkkkevkpydgvkelLeeL..keagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklk 151
                                     ++ + p   ++++ + +  ++ +y++ i++  +++ +    + l+i +yF +i +s  ++ +     +i ++l+ +k k
  gi|91773561|ref|YP_566253.1|  84 TRNELTDPNYLIQDTFNFIkcNHSRYNMHIASGADEKDLIYICNGLEISKYFMTINGSPIIKSE-----IIDTILTTYKYK 159
                                   777777766666666665533799*******************************999887766.....************ PP

                         HAD_2 152 keeviyvGDsptDieaakkagi 173
                                   kee+  +GDs++D eaakk  i
  gi|91773561|ref|YP_566253.1| 160 KEETCLIGDSINDHEAAKKNSI 181
                                   ******************9766 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     3e-08   0.00011       1     207 [.       3     177 ..       3     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3e-08
                                   SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE.HHHHTHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg.ayaigkpewltal 80 
                                   ik ++fD+dG+++++    +++++ +                   +  + k++  +  +++  +  g +    k ++++++
  gi|91773561|ref|YP_566253.1|   3 IKNIIFDFDGVILNSMAIKTKAFRDL-------------------FSSYPKNVVDDFIEYHL-KN-GgVSRYRKIDYFHKQ 62 
                                   7899*********9998888899888...................66677776555544444.12.135666666666666 PP

                                   HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                     Hydrolase  81 dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyf 160
                                        lg +i++ +     +       l   ++ dp+++ +++  +++  +++ +++ +++g +++    + n l   +yf
  gi|91773561|ref|YP_566253.1|  63 ----LLGIDISEKEILEYAQK---YSSLTRNELTDPNYLIQDTFNFIKCNHSR-YNMHIASGADEKDLIYICNGLEiSKYF 135
                                   ....34444444433333333...4589999999***************8877.789*******************43333 PP

                                   SEEEEHHCES.STTT..SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHH CS
                                   xxxxxxxxxx.xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 161 daviasdiet.vakp..spegkvaaireLqgkpeevamVGDgvnDaaala 207
                                            t  + p  + e+   ++  ++ k+ee++ +GD++nD +a++
  gi|91773561|ref|YP_566253.1| 136 --------MTiNGSPiiKSEIIDTILTTYKYKKEETCLIGDSINDHEAAK 177
                                   ........333333344889999999999*******************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 !   16.7   5.9   1.3e-06    0.0048      79     217 ..      32     174 ..       2     178 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                                   B-HHHHHHHHHHHHHTT.....CEEEEEESSEEEESTT.THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEE.EES-HHH CS
                   Hydrolase_3  79 iskedvkeiikllkenn.....veillytedkvyvlnkeksekkkkeeektkkkkeeidseeeledeeiakil.ilkdkek 153
                                    +k+ v+++i++  +n+      +i  y ++++++++  +++++ ++++k+++  ++  ++ +   ++ ++++ + +++ +
  gi|91773561|ref|YP_566253.1|  32 YPKNVVDDFIEYHLKNGgvsryRKID-YFHKQLLGIDI-SEKEILEYAQKYSSLTRNELTDPNYLIQDTFNFIkCNHSRYN 110
                                   34777777777777777665532233.33555555555.444555555555444444444444444455555523444444 PP

                                   HHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHH CS
                   Hydrolase_3 154 ldelekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDie 217
                                   +  +  + +++l    +  + sk+++ i+   + K + + +++ ++++++ee+  +GD+ ND e
  gi|91773561|ref|YP_566253.1| 111 MHIASGADEKDLIYICNGLEISKYFMTINGSPIIKSEIIDTILTTYKYKKEETCLIGDSINDHE 174
                                   4444444444444445999*******************************************87 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00026      0.93       1     187 [.       6     176 ..       6     177 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                           HAD   1 alfDfDgTLldgdsle..lllrfllrrgaprl.wralreklllalfrellrldraglaellealla.glseelaaelerfv 77 
                                   ++fDfDg +l++  +   +       r+  +   + +   + +++++ ++ +++++++ +   ll+ + se+ + e ++ +
  gi|91773561|ref|YP_566253.1|   6 IIFDFDGVILNSMAIKtkA------FRDLFSSyPKNVVDDFIEYHLKNGGVSRYRKIDYFHKQLLGiDISEKEILEYAQKY 80 
                                   6889999999883333442......33333330333333366666666666666666655555444222233333333333 PP

                           HAD  78 aevirpklldp.....galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgeg 153
                                    +  r  l dp     +   ++++ +++ +   + Sg+ +  +  +++ l     ++        +++   + g+p+ +  
  gi|91773561|ref|YP_566253.1|  81 SSLTRNELTDPnyliqDTFNFIKCNHSR-YNMHIASGADEKDLIYICNGLE----ISK-------YFMT--INGSPIIK-- 145
                                   3333333333333333666666655444.4445666666666666666666....555.......4444..55555555.. PP

                           HAD 154 kvaalrewlaaegegidleevvayGDspsDlpll 187
                                     +++ +    + ++ + ee++ +GDs++D +++
  gi|91773561|ref|YP_566253.1| 146 --SEIID-TILTTYKYKKEETCLIGDSINDHEAA 176
                                   ..33333.23333444445578888888887776 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.6e-05     0.057       8      41 ..     147     179 ..     145     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHH---GGGEEEEES-TTTHHHHHHHC CS
                Hydrolase_like   8 emydfalevlgsdpeevlmiGDrlatDiagAnna 41 
                                   e++d +l  ++ ++ee+++iGD+   D ++A++ 
  gi|91773561|ref|YP_566253.1| 147 EIIDTILTTYKYKKEETCLIGDS-INDHEAAKKN 179
                                   57899999999************.*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 1450.57
//
Query:       gi|91773562|ref|YP_566254.1|  [L=323]
Description: hypothetical protein Mbur_1600 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-12   46.0   0.0    8.5e-08   32.8   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
    5.3e-11   43.1   0.0    1.3e-06   29.0   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
    1.2e-07   31.3   0.1    0.00052   19.4   0.1    2.3  2  CMAS             Mycolic acid cyclopropane synthetase
    2.1e-07   30.8   0.1    0.00043   20.1   0.1    2.3  2  Methyltransf_31  Methyltransferase domain
    5.6e-05   23.0   0.0    9.3e-05   22.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00012   22.7   0.0      0.017   15.8   0.0    2.5  2  Methyltransf_12  Methyltransferase domain
    0.00022   20.6   0.1     0.0018   17.7   0.0    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0045   16.2   0.1     0.0079   15.4   0.1    1.4  1  Glyco_transf_11  Glycosyl transferase family 11
  ------ inclusion threshold ------
      0.012   15.0   0.0       0.17   11.2   0.0    2.4  2  TehB             Tellurite resistance protein TehB
      0.048   13.5   0.0        0.1   12.5   0.0    1.6  1  Methyltransf_8   Hypothetical methyltransferase
      0.081   13.3   0.0      0.081   13.3   0.0    2.1  3  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00034      0.55       1      31 [.      60      90 ..      60     119 .. 0.85
   2 !   32.8   0.0   5.2e-11   8.5e-08      26      96 .]     155     228 ..     148     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                                  EEET-TTSHHHHHHHHTTSEEEEEES-HHHH CS
               Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskeml 31
                                  Ld G+G G  +  la+rg++v+ +D++k+ l
  gi|91773562|ref|YP_566254.1| 60 LDTGAGYGMTQFILASRGYNVISMDFTKRNL 90
                                  89**************************998 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 5.2e-11
                                   S-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  26 lskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                   +s +++++ ++k+   ++ k+ef+++++ ++p+ d+++D+ +s ++++h   ed+ + ++e+ R+Lk  G++++
  gi|91773562|ref|YP_566254.1| 155 ISSYFINYTEKKQDHTKFgKIEFIRGTFNDIPLDDGTIDALISISAFEHNiyEDMPSSVNEFNRILKDKGVMFV 228
                                   6777888887888787789******************************99*******************9875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00021      0.34       1      54 [.      59     106 ..      59     120 .. 0.79
   2 !   29.0   0.0     8e-10   1.3e-06      29      97 .]     155     224 ..     154     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESB CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgd 54 
                                   +Ld G+G G + + la r+  ++v+ +D++++ l + ++ +    +++e+++ d
  gi|91773562|ref|YP_566254.1|  59 ILDTGAGYGMTQFILASRG--YNVISMDFTKRNLPEKAKGI----FDIEIIKND 106
                                   8*****************5..********998875544444....356666655 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8e-10
                                   SSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  29 iseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                   is+ ++++++++ ++ ++ ++ef++g ++d+p++dg++D+ +s+ a++h   ed++  ++e+ r+Lk++G
  gi|91773562|ref|YP_566254.1| 155 ISSYFINYTEKKQDHTKFgKIEFIRGTFNDIPLDDGTIDALISISAFEHNIYEDMPSSVNEFNRILKDKG 224
                                   6778899999999998899************************999***7779**************998 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00027      0.45      55      95 ..      48      87 ..      43     120 .. 0.80
   2 !   19.4   0.1   3.2e-07   0.00052     126     187 ..     189     251 ..     148     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00027
                                  HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-H CS
                          CMAS 55 leklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSk 95
                                  le  ++ pG t+Ld G+G+G +    ++r + +v+++ + k
  gi|91773562|ref|YP_566254.1| 48 LESNGILPGATILDTGAGYGMTQFILASR-GYNVISMDFTK 87
                                  5666788**************99888877.77777766555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 3.2e-07
                                   -.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHH CS
                          CMAS 126 e.kvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklkfidk 187
                                   +  +d+++s+ afeh  +e  +  +++++++lk+ G++ + t  +++k++ +e  +  +f++k
  gi|91773562|ref|YP_566254.1| 189 DgTIDALISISAFEHNIYEDMPSSVNEFNRILKDKGVMFVTTSAAKNKDWYQESSKGWNFTKK 251
                                   3589***********************************************999888888877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00086       1.4       4      41 ..      56      90 ..      53     105 .. 0.84
   2 !   20.1   0.1   2.6e-07   0.00043      41     127 ..     160     244 ..     155     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00086
               Methyltransf_31  4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeai 41
                                  g ++lD G+G G   f la++     +v++ D++++ +
  gi|91773562|ref|YP_566254.1| 56 GATILDTGAGYGMTQFILASRG---YNVISMDFTKRNL 90
                                  6789***************874...4699999998765 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.6e-07
               Methyltransf_31  41 ielArenaqklgldnveFeqgdieeleklledekfDlilsnevl..naladpdkileeiervlkpggilliedprllaelp 119
                                   i++ +++ ++ ++  +eF +g +++++  l d ++D ++s +++  n   d+++  +e  r lk++g++ +++    a+++
  gi|91773562|ref|YP_566254.1| 160 INYTEKKQDHTKFGKIEFIRGTFNDIP--LDDGTIDALISISAFehNIYEDMPSSVNEFNRILKDKGVMFVTTSA--AKNK 236
                                   77788889999****************..99**************9999**********************9999..4444 PP

               Methyltransf_31 120 akveeesk 127
                                   +  +e+sk
  gi|91773562|ref|YP_566254.1| 237 DWYQESSK 244
                                   33333333 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.7e-08   9.3e-05      22     148 ..      55     259 ..      44     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.7e-08
               Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspe.aveiae........................................ 61 
                                   +g+ +Ld G+G+G +  +l+ +g++v+ +D   + + e+a+                                        
  gi|91773562|ref|YP_566254.1|  55 PGATILDTGAGYGMTQFILASRGYNVISMDFTKRnLPEKAKgifdieiikndlgsytseymeymtygkssnglintlksvp 135
                                   5789*********777777999********87550455555**************************************** PP

               Methyltransf_23  62 ...........................kakkaqkdqfdeqeaae...............pqgkfdlIvlrevlehvp..dp 98 
                                                              + kk+ +++       +               ++g++d  +++  +eh    d+
  gi|91773562|ref|YP_566254.1| 136 kallhpikiikfikkmeqkissyfinyTEKKQDHTK-------FgkiefirgtfndiplDDGTIDALISISAFEHNIyeDM 209
                                   ****99977776666666665555444333333333.......0333334445555555888**********99987679* PP

               Methyltransf_23  99 pellrqiatllkpgGylllseplaslkedrllldw..lylvpagrhisffsa 148
                                   p+ ++ ++++lk+ G++++++++a  k++ ++++   ++ +++ +++ +f+ 
  gi|91773562|ref|YP_566254.1| 210 PSSVNEFNRILKDKGVMFVTTSAA--KNKDWYQESskGWNFTKKTLSDWFNI 259
                                   *********************976..56666665431333444467777765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.044        72       1      37 [.      60      94 ..      60     107 .. 0.82
   2 !   15.8   0.0     1e-05     0.017      28      98 ..     155     225 ..     154     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.044
               Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedak 37
                                  L+ G+G G + + l+ +  + +++ +D+ ++ ++ ++
  gi|91773562|ref|YP_566254.1| 60 LDTGAGYGMTQFILASR--GYNVISMDFTKRNLPEKA 94
                                  899*****877777777..**********99995444 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1e-05
               Methyltransf_12  28 ispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl..kdirevldnirklLkpgGr 98 
                                   is+ +i+ +++k  + +  + ++++ + +d+  +dg  + D+ +++++++h   +d+ ++++++ + Lk+ G+
  gi|91773562|ref|YP_566254.1| 155 ISSYFINYTEKKQDHTKFGKIEFIRGTFNDIPLDDG--TIDALISISAFEHNiyEDMPSSVNEFNRILKDKGV 225
                                   79999*999******************999987777..************999*****************997 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.19   3.1e+02      34      85 ..      42      90 ..      23     113 .. 0.75
   2 !   17.7   0.0   1.1e-06    0.0018      79     158 ..     154     235 ..     136     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.19
                                  HHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHH CS
               Ubie_methyltran 34 lWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmL 85
                                  +W  +  + ++ ++ga++lD  +G g   f l++   + ++v+ +D+ +  L
  gi|91773562|ref|YP_566254.1| 42 IWIVKQLESNGILPGATILDTGAGYGMTQFILAS---RGYNVISMDFTKRNL 90
                                  6777777788888999999999998877777654...334566666665555 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.1e-06
                                   ES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEE.EEEES-GGG.-S-HHHHHHHHHHHEEEEEEEEEEEE--- CS
               Ubie_methyltran  79 DinenmLkvgekklkeegkinieflqanaeeLpfeddsfDv.vtvsfGlrn.vtDklkaLkeayrvlkpGGrlvvlefskv 157
                                    i++  ++ +ekk  ++ + +ief+ +  +++p +d++ D  + +s    n   D++ +++e  r+lk  G ++v   +  
  gi|91773562|ref|YP_566254.1| 154 KISSYFINYTEKKQDHTKFGKIEFIRGTFNDIPLDDGTIDAlISISAFEHNiYEDMPSSVNEFNRILKDKGVMFVTTSAAK 234
                                   57777888999999999999********************63678755555168*****************9988655544 PP

                                   - CS
               Ubie_methyltran 158 e 158
                                   +
  gi|91773562|ref|YP_566254.1| 235 N 235
                                   4 PP

>> Glyco_transf_11  Glycosyl transferase family 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   4.8e-06    0.0079      16      98 ..      82     165 ..      58     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.8e-06
               Glyco_transf_11  16 qaawalkiqklks.kkglftvnlng.rlgnqkgeyatllalak.llgrlafipasmeeiLaPfritlkvlakevklrkils 93 
                                    + ++  +++l++  kg+f++++++  lg +  ey + +   k  +g  +++    ++ L P++i + +++ e k+    +
  gi|91773562|ref|YP_566254.1|  82 SMDFT--KRNLPEkAKGIFDIEIIKnDLGSYTSEYMEYMTYGKsSNGLINTLKSVPKALLHPIKIIKFIKKMEQKISSYFI 160
                                   33333..466666589*****986527************999988999999999999*******************99999 PP

               Glyco_transf_11  94 nyhlk 98 
                                   ny  k
  gi|91773562|ref|YP_566254.1| 161 NYTEK 165
                                   98755 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.17      27      77 ..      52     103 ..      35     171 .. 0.78
   2 ?    1.2   0.0      0.13   2.1e+02       4      23 ..     284     303 ..     281     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                   CCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHH.HHHHHHHHHTT- CS
                          TehB  27 kivkpgkvldlgcgqgrnslylsllgydvtawdknensi.afleeikekenl 77 
                                    i+  + +ld g g g   + l+  gy+v ++d  +  + +  + i ++e +
  gi|91773562|ref|YP_566254.1|  52 GILPGATILDTGAGYGMTQFILASRGYNVISMDFTKRNLpEKAKGIFDIEII 103
                                   56666789*************************8776652334455555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                                   CGCCHHHHHHT-----HHHH CS
                          TehB   4 kkedyfskkynltathsevv 23 
                                   + edy+++k nlt   ++++
  gi|91773562|ref|YP_566254.1| 284 RLEDYYKDKSNLTIPNGDLK 303
                                   56999999999998877765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-05       0.1     114     158 ..     183     230 ..     174     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                                   TS-S--TT-EEEEEEES---SS-HH....HHHHHHHHHEEEEEEEEEEE CS
                Methyltransf_8 114 akvPledesvdvavfclslmgtnla....dflkeanrvlkvGGllkvae 158
                                   + +Pl+d+++d  +  +s    n++    + ++e nr+lk  G+++v+ 
  gi|91773562|ref|YP_566254.1| 183 NDIPLDDGTIDALI-SISAFEHNIYedmpSSVNEFNRILKDKGVMFVTT 230
                                   689********655.55665555541111789************99975 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-05     0.081      60      94 ..      57      91 ..      12     105 .. 0.81
   2 ?   -3.7   0.1         9   1.5e+04      15      34 ..     152     171 ..     146     173 .. 0.51
   3 ?   -2.2   0.1       3.1     5e+03      17      32 ..     247     262 ..     231     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                  AdoMet_MTase 60 tsfvdvgcgngllvyvlaaegykgygidlrkrklw 94
                                   ++ d g g g+  ++la+ gy+   +d  kr l 
  gi|91773562|ref|YP_566254.1| 57 ATILDTGAGYGMTQFILASRGYNVISMDFTKRNLP 91
                                  5789****************************875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9
                  AdoMet_MTase  15 kqkyakrlvenwvestdplk 34 
                                    qk +  +++  +++ d +k
  gi|91773562|ref|YP_566254.1| 152 EQKISSYFINYTEKKQDHTK 171
                                   45555555544444445444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.1
                  AdoMet_MTase  17 kyakrlvenwvestdp 32 
                                   +++k+ ++ w + td 
  gi|91773562|ref|YP_566254.1| 247 NFTKKTLSDWFNITDK 262
                                   5788899999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1922.67
//
Query:       gi|91773563|ref|YP_566255.1|  [L=548]
Description: hypothetical protein Mbur_1601 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 3169.56
//
Query:       gi|91773564|ref|YP_566256.1|  [L=487]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-23   81.5   0.6    2.4e-22   80.1   0.5    1.8  2  Radical_SAM  Radical SAM superfamily
    4.9e-19   68.5   0.0      1e-18   67.5   0.0    1.5  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.013   15.6   0.6       0.24   11.6   0.1    2.8  3  Fer4_14      4Fe-4S single cluster domain
       0.04   14.2   0.7       0.11   12.7   0.1    2.0  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 !   80.1   0.5   5.3e-26   2.4e-22       1     166 [.     223     388 ..     223     389 .. 0.95
   2 ?   -2.5   0.0       1.3     6e+03     110     130 ..     439     459 ..     426     465 .. 0.69

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 5.3e-26
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiri 80 
                                   ++++rgC+ +C+fC+ ++   +++++r++s+e+++ee+k++k ek  ++e+++  ++ +++p+ +e++  l+ +  +++++
  gi|91773564|ref|YP_566256.1| 223 IITSRGCPAKCTFCTAYRV--WGRKYRHRSPENVIEEMKYVK-EKYnIEELLIEDDNFTANPKRAEKICDLMIE--NKFNF 298
                                   5789**************7..********************7.5555***************************..8**** PP

                                   EEEECSSCHG....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                   xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpd....eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                      t+ +       e+ +++++++g+  +++ +e+++  +  ++++++  +e+v e + ++r+++i+  ++ i+g+pG n 
  gi|91773564|ref|YP_566256.1| 299 KWDTPNGIAAfalnEKLIRKMKNAGCYKINIAVESGNQNTLNNIIKKPLKLEKVEEIVNICRKVDIDFGIFLILGMPGDNL 379
                                   *******988*****************************999999999*******************9************* PP

                                   HHHHHHHHH CS
                                   xxxxxxxxx RF
                   Radical_SAM 158 eeleellel 166
                                   e +++ +++
  gi|91773564|ref|YP_566256.1| 380 EAMWDNYKF 388
                                   ***999887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                   BSSSHHHHHHHHTCTSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 110 eaaddekvlklmnrghtfeev 130
                                   e +++e+++klm++g+ + ++
  gi|91773564|ref|YP_566256.1| 439 EQWTPEDIQKLMKKGYIYLKF 459
                                   556777788888766665555 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   2.3e-22     1e-18      11     117 ..      26     149 ..      23     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.3e-22
                   B12-binding  11 dlhplGlavlaaalrdagfeVqllganven..................edivaairaekpdvvglSalltsqleavkelve 73 
                                   +l+p+Gl ++a ++++ g+eV+++++  e                    +i + i + +pd+v++   +++q+e+++ + +
  gi|91773564|ref|YP_566256.1|  26 PLPPIGLGYIASVIEKLGVEVKIIDCLMEGwnqreeigdgliriglseNQIRDIISDYQPDLVCVNNQFSKQYENAHLIYR 106
                                   689************************999999*********************************99************* PP

                   B12-binding  74 llkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedal 117
                                   l+k++++++++ +GG hps++p+etl+    +d+vv+gege  +
  gi|91773564|ref|YP_566256.1| 107 LVKEVDSNIITQAGGGHPSVMPKETLQD-QNLDFVVLGEGEIVV 149
                                   **************************98.666********9766 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.68   3.1e+03      61      78 ..      98     115 ..      96     139 .. 0.79
   2 ?   11.6   0.1   5.3e-05      0.24       6      49 ..     227     268 ..     223     273 .. 0.77
   3 ?    0.5   0.0      0.15   6.5e+02      14      39 ..     323     357 ..     311     393 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.68
                       Fer4_14  61 yenkkellklvkrlkeey 78 
                                   yen + +++lvk++  ++
  gi|91773564|ref|YP_566256.1|  98 YENAHLIYRLVKEVDSNI 115
                                   778888888888887765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.3e-05
                       Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiq 49 
                                    gC+ +C++C     w  ++ + + e+++ +++k +k+++  i+
  gi|91773564|ref|YP_566256.1| 227 RGCPAKCTFCTAYRVWGRKYRHRSPENVI-EEMKYVKEKYN-IE 268
                                   59*************************99.55555544443.44 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.15
                       Fer4_14  14 gCd.........nketwkselgkpqteelleqilk 39 
                                   gC+         n++t ++  +kp + e +e+i++
  gi|91773564|ref|YP_566256.1| 323 GCYkiniavesgNQNTLNNIIKKPLKLEKVEEIVN 357
                                   34433333333334444444444444444444443 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 ?   -3.7   0.0       2.9   1.3e+04      66      83 ..      98     115 ..      92     120 .. 0.77
   2 ?   12.7   0.1   2.6e-05      0.11      12      54 ..     226     268 ..     213     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.9
                       Fer4_12  66 penaeallelvkevkeek 83 
                                   +ena  +++lvkev ++ 
  gi|91773564|ref|YP_566256.1|  98 YENAHLIYRLVKEVDSNI 115
                                   568888888888887665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.6e-05
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesie 54 
                                     gC+ +C +C +  +w  k+ +  +++++ee+    +k++ie
  gi|91773564|ref|YP_566256.1| 226 SRGCPAKCTFCTAYRVWGRKYRHRSPENVIEEMKYVKEKYNIE 268
                                   57****************************9976544455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2914.21
//
Query:       gi|91773565|ref|YP_566257.1|  [L=371]
Description: NAD-dependent epimerase/dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-34  119.5   0.0    2.6e-34  119.1   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.2e-27   94.6   0.0    8.4e-27   94.2   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.9e-11   43.1   0.0    1.9e-10   40.4   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    9.1e-08   31.5   0.0    1.3e-07   31.1   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    0.00031   19.8   0.0    0.00052   19.1   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0012   18.1   0.3     0.0066   15.6   0.0    2.2  2  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.0   8.6e-38   2.6e-34       1     330 [.      16     328 ..      16     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 8.6e-38
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   ++TG +Gf Gs+l  +L   g +v+g+ ++  s      +h ++   ++l+e++   + D++    +++l++e++pd v++
  gi|91773565|ref|YP_566257.1|  16 IVTGNTGFKGSWLSIWLSLLGAKVYGLSNDIPSK----PSHFET---ASLDEHIIHNEIDIRCLYDVRELINEIEPDFVFH 89 
                                   59************************98866553....344432...23456677789*********************** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSS.B-TTS-----SHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevp.qtEttpfyPrsPYaaaKlyad 161
                                   LAAq  V+ s+++P +t+e+nv+Gt+++Lea r  +  + +  + + ++ +Y +v+ v  ++Et p+  + PY+a+K +a+
  gi|91773565|ref|YP_566257.1|  90 LAAQPIVRASYNDPVETIETNVIGTMNILEALRLSN--HPCIAIMITSDKCYDNVEWVWgYRETDPLGGEDPYSASKGAAE 168
                                   *********************************987..57888999**********66549******************** PP

                                   HHHHHHHHH......H---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHH CS
                 GDP_Man_Dehyd 162 wivvnyrea......yglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyveamwl 235
                                    i++ y ++       ++ + + +  n  +     +    r +++++     g +e++++   +a+R w+hv +  +++  
  gi|91773565|ref|YP_566257.1| 169 LIIKTYARSffdkpnSNVKIASVRAGNVIGGG---DwAKDRIVPDCIRA--WGVKEKVQIRSPNATRPWQHVLEPLSGYLY 244
                                   ********964332233444444444444444...41445566666654..556678889999***************977 PP

                                   HHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEEC.GG--SS--SB--B-THHHHH CS
                 GDP_Man_Dehyd 236 mlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdp.kyfrpgevdlllgdaskake 315
                                   + q+  +ed    +ge ++ +   + +   + + i  ++++          ++ ++++d  +  +++e++ll   ++ka +
  gi|91773565|ref|YP_566257.1| 245 LGQK-LNEDKS-LNGEPFNFGPATNQN-YTVAELI-SKMQEYW--------EDAEIQIDTgNASKQKEANLLKLCCDKALH 313
                                   5555.455555.479999998777644.4444333.3332222........2345666662455678999999******** PP

                                   HH----SS-HHHHHH CS
                 GDP_Man_Dehyd 316 eLgWkpkvsfeelvr 330
                                    LgW+++ +fe++v+
  gi|91773565|ref|YP_566257.1| 314 VLGWQATLDFEKTVK 328
                                   ***********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 !   94.2   0.0   2.8e-30   8.4e-27       1     239 [.      15     261 ..      15     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 2.8e-30
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                   ++VtG tGf Gs l   l   g +v gl+++  ++++  +           e+d++   ++++l++e +pd v+hlAa+  
  gi|91773565|ref|YP_566257.1|  15 VIVTGNTGFKGSWLSIWLSLLGAKVYGLSNDIPSKPSHFETASldehiIHNEIDIRCLYDVRELINEIEPDFVFHLAAQPI 95 
                                   68****************************9666655444444677778889***************************** PP

                                   HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSS.SBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                     Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeq.pkeettltgplkpnspYaaaKlageklvea 155
                                   v+as +dp ++ie+n++gt+n+lea+r ++     + + S+  Y +++ +    et    pl    pY+a+K a+e +++ 
  gi|91773565|ref|YP_566257.1|  96 VRASYNDPVETIETNVIGTMNILEALRLSNHPcIAIMITSDKCYDNVEWVwGYRETD---PLGGEDPYSASKGAAELIIKT 173
                                   ***************************8877768999***********952355555...********************* PP

                                   HHHHH.T.....-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                     Epimerase 156 yaaqy.g.....lnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                   ya+++ +     +++ ++r  n++G +  +   +r++p  ir    ++ +v +  + +a R++ +v +   ++l++ ++ +
  gi|91773565|ref|YP_566257.1| 174 YARSFfDkpnsnVKIASVRAGNVIGGG--DWAKDRIVPDCIRAWGVKE-KVQI-RSPNATRPWQHVLEPLSGYLYLGQKLN 250
                                   ****96589999***************..888***********99988.7777.679************999999999987 PP

                                   T-ST..TEEEE CS
                     Epimerase 231 agdk..geiyn 239
                                   ++++  ge +n
  gi|91773565|ref|YP_566257.1| 251 EDKSlnGEPFN 261
                                   75544455665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   6.4e-14   1.9e-10      50     173 ..      56     198 ..      15     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 6.4e-14
                                   TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE.EEEEEG CS
               Polysacc_synt_2  50 kklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv.vliStD 129
                                    +l+ +i+    d+r    ++++++e+++d+vfh AA   V +  + p+e+i+tNv+gt+n++ea   ++   + ++i +D
  gi|91773565|ref|YP_566257.1|  56 ASLDEHIIHNEIDIRCLYDVRELINEIEPDFVFHLAAQPIVRASYNDPVETIETNVIGTMNILEALRLSNHPCIaIMITSD 136
                                   44445555555799999999********************************************9987777664499**** PP

                                   GGSS--SH.........HH......HHHHHHHHHHHHGGG--SSS-...-EEEEEEE-EETT CS
               Polysacc_synt_2 130 KAvnPtnv.........mG......atKrlaekllqalakeseekk...tkfvvvRfGNVlg 173
                                   K  + +           +G      a+K +ae+++ ++a++  +k     k++ vR GNV+g
  gi|91773565|ref|YP_566257.1| 137 KCYDNVEWvwgyretdpLGgedpysASKGAAELIIKTYARSFFDKPnsnVKIASVRAGNVIG 198
                                   *98776532222222222233333399********9999987554455599*********98 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   4.2e-11   1.3e-07       2     139 ..      14     174 ..      13     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.2e-11
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE----- CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAyt 62 
                                   k++vtG++G  Gs L   l+  g++v++l+++                    e+d++    v+el++e++pd+v ++AA  
  gi|91773565|ref|YP_566257.1|  14 KVIVTGNTGFKGSWLSIWLSLLGAKVYGLSNDipskpshfetasldehiihnEIDIRCLYDVRELINEIEPDFVFHLAAQP 94 
                                   7899*************************8889999********************************************* PP

                                   -HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EE..EEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHHHHHHH CS
                 RmlD_sub_bind  63 avDkaEseeeaayavnaeavealAeaaaavgalL..ihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEqavlaa 139
                                    v +  +++ +  + n+ +++++ ea +  + +   i + +D  +d  +    Y+e+d+ +    Y ++K a E  ++ +
  gi|91773565|ref|YP_566257.1|  95 IVRASYNDPVETIETNVIGTMNILEALRLSNHPCiaIMITSDKCYDNVEWVWgYRETDPLGGEDPYSASKGAAELIIKTY 174
                                   ***********************99998877765116789******9987767*********************999865 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 !   19.1   0.0   1.7e-07   0.00052       1     187 [.      16     202 ..      16     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-07
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlaslvdv 79 
                                   +vtG +GF G+ l   L  l+ +    + D+  +p+  e++s  + +   e D++   +++e ++++  d v+hla+   v
  gi|91773565|ref|YP_566257.1|  16 IVTGNTGFKGSWLSIWLSLLGAKVYGLSNDIPSKPSHFETASLDEHIIHNEIDIRCLYDVRELINEIepDFVFHLAAQPIV 96 
                                   699999***9988877777776455557788888888777766666657899*************984479****988888 PP

                     3Beta_HSD  80 agklte.deimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlk 159
                                   +  +++  e  + nv GT n+lea + ++ + +  + + +  ++n   e +    E+   +   +d+y+ sK  aE +++ 
  gi|91773565|ref|YP_566257.1|  97 RASYNDpVETIETNVIGTMNILEALRLSNHPCIAIMITSDKCYDN--VEWVWGYRETD--PLGGEDPYSASKGAAELIIKT 173
                                   8755541467899************99999999999999999994..45666334443..455789999999999988888 PP

                     3Beta_HSD 160 aNgrtlkngg.rlyTcaLRpagiyGegdk 187
                                      + +  ++ ++   ++R   + G gd 
  gi|91773565|ref|YP_566257.1| 174 YARSFFDKPNsNVKIASVRAGNVIGGGDW 202
                                   77777777766777777888888887765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.77   2.3e+03       1      11 [.      17      27 ..      17      28 .. 0.84
   2 !   15.6   0.0   2.2e-06    0.0066      81     193 ..      75     177 ..      73     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.77
                                  EE-TTSHHHHH CS
                 NAD_binding_4  1 lTGaTGFLGkv 11
                                  +TG TGF G+ 
  gi|91773565|ref|YP_566257.1| 17 VTGNTGFKGSW 27
                                  7******8876 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.2e-06
                                   HHHHHHH-..-EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H... CS
                 NAD_binding_4  81 lqelaeev..dviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeege 156
                                   ++el++e+  d ++h aA+  + ++y++    +++Nv Gt ++le  +  ++    + + +  ++++ e            
  gi|91773565|ref|YP_566257.1|  75 VRELINEIepDFVFHLAAQPIVRASYNDpveTIETNVIGTMNILEALRLSNHPCIAIMITSDKCYDNVEW----------- 144
                                   566666664489*******9999999986567899**********9998777744455555666666664........... PP

                                   ...HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHH CS
                 NAD_binding_4 157 keekldederaklkglpntYeqsKalaEklvrearrr 193
                                       + +  +++  g ++ Y+ sK +aE ++++++r+
  gi|91773565|ref|YP_566257.1| 145 ----VWGYRETDPLGGEDPYSASKGAAELIIKTYARS 177
                                   ....568889999999****************99964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2213.30
//
Query:       gi|91773566|ref|YP_566258.1|  [L=145]
Description: dTDP-4-dehydrorhamnose epimerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-09   37.4   0.0    2.3e-09   37.1   0.0    1.2  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.016   14.9   0.1    1.2  1  FdtA             WxcM-like, C-terminal


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 !   37.1   0.0   2.6e-13   2.3e-09       5     152 ..       3     144 ..       1     145 [] 0.80

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.6e-13
                                   TTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEEE-BT CS
               dTDP_sugar_isom   5 egvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaVDlRk 85 
                                   egv++   k+++ e G ++++ ++e+ + +g    f ++  s+ + g ++      ++++ +  + v +Ge++ v+ D R 
  gi|91773566|ref|YP_566258.1|   3 EGVIVNPVKIITGENGNVMHALKAEDDSYHG----FGEAYFSTVNCGAIKAWK---RHHEMTLNIVVPQGEIMFVLYDDRL 76 
                                   6666666666666666666666666666555....335666666666666655...334556668899************* PP

                                   TSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEES.S---GGGEEEE-TT-TTTT--- CS
               dTDP_sugar_isom  86 gSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvt.eyyapesergirwnDpelgidw 152
                                   +S+t g++++++Ls en + l ip+ +  Gf  + ++a++l  +    ++p++   ++ + ++++ dw
  gi|91773566|ref|YP_566258.1|  77 ESNTRGQIMEIKLSTENYQRLTIPPMVWMGFKGMGKDANILINIAnIQHDPNESDHLDSHKNNINYDW 144
                                   ******************************************99944699999999*99999999999 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.8e-06     0.016      40     118 ..      42     129 ..      11     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                                   --TTTEEEEEEESS--EEEEEEES-EEEEEE-SS-E.......EEEEE-STT.EEEEE-TT-EEEEE---TT-EEEE.EES CS
                          FdtA  40 vpegeerGeHahkkleqllialsGsvevllddgkkk.......keilldsps.kglyipkmiWrelinfsedavllv.las 111
                                   v+ g+ +    h++++  +++ +G++ ++l d + +        ei l + + + l ip+m+W     + +da +l+ +a+
  gi|91773566|ref|YP_566258.1|  42 VNCGAIKAWKRHHEMTLNIVVPQGEIMFVLYDDRLEsntrgqiMEIKLSTENyQRLTIPPMVWMGFKGMGKDANILInIAN 122
                                   5555666666788888889999999998886654321111222467787655599*****************887765899 PP

                                   S---GGG CS
                          FdtA 112 esydeed 118
                                    ++d+++
  gi|91773566|ref|YP_566258.1| 123 IQHDPNE 129
                                   9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 920.78
//
Query:       gi|91773567|ref|YP_566259.1|  [L=257]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   75.7   0.0    5.5e-21   75.3   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    2.1e-07   31.4   0.0    3.2e-07   30.9   0.0    1.4  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 !   75.3   0.0   6.1e-25   5.5e-21       1     193 [.       2     203 ..       2     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 6.1e-25
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT......... CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg......... 72 
                                   k+vILaGG GtRL   t  ++k++v ++g+ +++ + ++  a  g ++  +v   ++ + ++e++ + + ++         
  gi|91773567|ref|YP_566259.1|   2 KTVILAGGLGTRLAEYTDIRPKPMVEIGGQ-PILWHIMNLYAHYGNKD-FFVALGYKGEVIKEYFLNYYSLKsdftvnlgn 80 
                                   68****************************.************99999.999999**************9999999***** PP

                                   ..........SEEEEEEESS--..BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEE CS
               NTP_transferase  73 ..........vevlialepegk..gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivp 141
                                             v+ +++l + g    t + ++  +e++ed+     ++v  gD + + ++e+++++++ +++    +  ++ 
  gi|91773567|ref|YP_566259.1|  81 gdvdclekktVDWNVTLVDTGLnsMTGGRIKRLKEYIEDDT----FMVTYGDGVSNVNIEKLIEFHKTHGK----MATVTA 153
                                   99999999998888888888873245666777777777666....8*************************....555678 PP

                                   SS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHC CS
               NTP_transferase 142 veeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevllflakd 193
                                   v+++ ++G   ++++++v++f+EKP++++   +++ G +vf++e l+++ +d
  gi|91773567|ref|YP_566259.1| 154 VHPSARFGELVISDKNEVISFKEKPQTNQ--GWINGGFFVFEPEFLDYIGSD 203
                                   99*************************88..8***************99443 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 !   30.9   0.0   3.5e-11   3.2e-07       2      53 ..       4      61 ..       3     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.5e-11
                                  EEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHH CS
                  NTP_transf_3  2 viLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd.eevla 53
                                  viLAGG ++R+ +     +K+++++gg+p+l+++++  ++ g ++ +v+ g+  ev +
  gi|91773567|ref|YP_566259.1|  4 VILAGGLGTRLAEytdirPKPMVEIGGQPILWHIMNLYAHYGNKDFFVALGYkGEVIK 61
                                  9**********9555666***********************99999999888423333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1577.61
//
Query:       gi|91773568|ref|YP_566260.1|  [L=372]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for 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-101  339.9   0.0   2.2e-101  339.8   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    5.8e-13   48.5   0.0    8.8e-13   47.9   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
      3e-08   33.2   0.0    5.1e-08   32.5   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    0.00084   18.7   0.1     0.0019   17.6   0.1    1.7  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0022   16.6   0.1     0.0039   15.8   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.034   14.3   0.0       0.08   13.1   0.0    1.6  1  DUF2684          Protein of unknown function (DUF2684)
      0.061   12.9   0.0       0.14   11.7   0.0    1.6  2  SGL              SMP-30/Gluconolactonase/LRE-like region
      0.069   11.7   0.0        0.1   11.2   0.0    1.2  1  AMP-binding      AMP-binding 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 !  339.8   0.0  9.9e-105  2.2e-101       2     360 ..      13     366 ..      12     367 .. 0.96

  Alignments for each domain:
  == domain 1  score: 339.8 bits;  conditional E-value: 9.9e-105
                                   HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHH CS
               DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavle 82 
                                   i+eee++av +vl+ + l +g+ v  FE+++a+y  ++ a+ v++GtaAlhlaL+algvgpgdeV+v slt+va+ +a++ 
  gi|91773568|ref|YP_566260.1|  13 IGEEEKKAVLDVLDRQYLGMGQDVLYFEQELATYF-AREAVCVNTGTAALHLALQALGVGPGDEVLVQSLTYVASFQAISA 92 
                                   689*******************************9.5789***************************************** PP

                                   TT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSS CS
               DegT_DnrJ_EryC1  83 lgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgd 163
                                   +ga+pv++D+dpdt++++++++++ ite t+ ++pVh+++ v  +d++ + a++ +l v+eDaA+A+G+ y++kkvG++gd
  gi|91773568|ref|YP_566260.1|  93 TGARPVPCDIDPDTITLNVDDAKKRITEHTRVVMPVHYASSVGPLDEIYEFAQDNDLRVVEDAAQAFGTYYNDKKVGSFGD 173
                                   ********************************************************************************* PP

                                   EEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCS.......S---B-B-BHHHHHHHHHHHCTH CS
               DegT_DnrJ_EryC1 164 aavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgev.......elGynyrlteiqAAiglaqLerl 237
                                   +a+fSF + Kn+t GeGGavvt+d+e+ ++++  r  G++++ ekry g+        + G  y ++++ AAig++q++++
  gi|91773568|ref|YP_566260.1| 174 IACFSFDGIKNITSGEGGAVVTDDKEVLQRVKDARLLGVEKDTEKRYSGDRswdfdvsMQGWRYHMSNVMAAIGIEQFKKF 254
                                   *********************************************************99********************** PP

                                   HHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCH CS
               DegT_DnrJ_EryC1 238 delvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvy 318
                                     + ++R+e++++y+++La+++ ++ l+ + ++   + h +++ +++    +r++l + l++ gi t +hy +p h++++y
  gi|91773568|ref|YP_566260.1| 255 PIFAEKRKELLKRYQSNLANINSIELLKQDANQ--IVPHIFVIKLKNY---DRNTLRKMLEDVGIPTGIHY-KPNHKLSYY 329
                                   **********************76444444433..799********77...9*******************.7******** PP

                                   HHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
               DegT_DnrJ_EryC1 319 aerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                   ++ +     +lp ++++a+++l+Lpl+pel+  dvd+++e l
  gi|91773568|ref|YP_566260.1| 330 DTGV-----ELPCTDTVAKEILTLPLHPELQISDVDHICEML 366
                                   9995.....58****************************987 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.9e-16   8.8e-13      62     333 ..      49     314 ..      39     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.9e-16
                                   GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTS.CBEGGGHHHH--TTEE CS
                   Aminotran_5  62 eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeeg.eldldelekllnektk 141
                                    e + +  +t a+ l++++l+  + pgde++v+++ + a +   q+++ +tga+ +   +d++  +l++d+++k ++e t+
  gi|91773568|ref|YP_566260.1|  49 REAVCVNTGTAALHLALQALG--VGPGDEVLVQSLTYVASF---QAIS-ATGARPVPCDIDPDTiTLNVDDAKKRITEHTR 123
                                   67788889999*********5..9*****************...6676.99*********98763788************* PP

                                   EEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HH..HHTESEEEEE..TTT.TTSSTT-EEEEEEHHH CS
                   Aminotran_5 142 lvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvk..klgvDflafs..ghK.llgPtGiGvlyvrkel 217
                                   +v+  h  ++ G   p++ei + a++++  v+ Daaqa+g +  d k   +g D++ fs  g K +   +G  v+   ke+
  gi|91773568|ref|YP_566260.1| 124 VVMPVHYASSVG---PLDEIYEFAQDNDLRVVEDAAQAFGTYYNDKKvgSFG-DIACFSfdGIKnITSGEGGAVVTDDKEV 200
                                   **********99...56666666699**************998874411332.5555443399*89999************ PP

                                   HHTS..SS.STTSEEEEET.TEEE.......EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH CS
                   Aminotran_5 218 lekleplllggemveevsl.eett.......faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyller 290
                                   l++++ + l g   ++ +     +       ++ + ++++    nv+++ig+++        ++   +++ kel ++ ++ 
  gi|91773568|ref|YP_566260.1| 201 LQRVKDARLLGVEKDTEKRyS--GdrswdfdVSMQGWRYH--MSNVMAAIGIEQFK------KFPIFAEKRKELLKRYQSN 271
                                   ****99999887444333212..22344555566677777..56777776665544......44577899999******** PP

                                   HCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTE CS
                   Aminotran_5 291 lkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegI 333
                                   l+++++++l+++d ++  ++i+ +++k+++ + ++++L++ gI
  gi|91773568|ref|YP_566260.1| 272 LANINSIELLKQDANQIVPHIFVIKLKNYDRNTLRKMLEDVGI 314
                                   **************************************99665 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 !   32.5   0.0   2.3e-11   5.1e-08      48     143 ..      38     122 ..      13     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.3e-11
                                   HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTT CS
                 Aminotran_1_2  48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedf 128
                                    +e++la ++         re av+v +G+ al  al +l  + pgde+lv ++ty    +++ + g+  v++ ++ +++ 
  gi|91773568|ref|YP_566260.1|  38 YFEQELATYFA--------RE-AVCVNTGTAALHLALQALG-VGPGDEVLVQSLTYVASFQAISATGARPVPCDID-PDTI 107
                                   58999******........**.*******************.9*******************************66.9*** PP

                                   EE-HHHHHHHHTTHH CS
                 Aminotran_1_2 129 hldlealeealkeap 143
                                   +l++++ ++ ++e++
  gi|91773568|ref|YP_566260.1| 108 TLNVDDAKKRITEHT 122
                                   ************954 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   8.3e-07    0.0019      29     216 ..      31     208 ..       2     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.3e-07
                                   T--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.T CS
               Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.G 107
                                   g  ++v  +e+++a +f +  a+ v +GtaA +++l++l   +g+ev+v++    +    +ai    g+++++++++ +  
  gi|91773568|ref|YP_566260.1|  31 GMGQDVLYFEQELATYF-AREAVCVNTGTAALHLALQALGvGPGDEVLVQSLT--YVASFQAI-SATGARPVPCDIDPDtI 107
                                   55667777888888888.5667789*************9989*****998665..55555555.45788899999988657 PP

                                   BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTT CS
               Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsy 188
                                   ++++++ ++ i+e+ +       +++ v        + s+  l+e++++a++++++++ D+A  +          k++ s 
  gi|91773568|ref|YP_566260.1| 108 TLNVDDAKKRITEHTR-------VVMPVHY------ASSVGPLDEIYEFAQDNDLRVVEDAAQAFGTY----YNDKKVGSF 171
                                   8888999999999555.......4444433......34788999******************988766....667888999 PP

                                   SSEEEEESS..STT--SS-EEEEE-HH.......... CS
               Beta_elim_lyase 189 vDsvtmslk..KdllanvGgvlafrddel.......e 216
                                    D+ ++s+   K+++   Gg ++++d+e         
  gi|91773568|ref|YP_566260.1| 172 GDIACFSFDgiKNITSGEGGAVVTDDKEVlqrvkdaR 208
                                   9998888644499999999999999995533333330 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-06    0.0039      66     175 ..      47     156 ..      35     212 .. 0.77
   2 ?   -3.6   0.0       1.3     3e+03     148     165 ..     351     368 ..     348     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                                   T-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHH...TTCEEEEESTTSHHHHHHHCCTTEEEEE CS
               Cys_Met_Meta_PP  66 ggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkk...lgievkfvdtsdleelekaikentklvy 142
                                    + +a++v++G+aA+++a++al +  Gde++v++  Y  +++ ++ +  +     i+ + +   ++++ +k i+e+t++v 
  gi|91773568|ref|YP_566260.1|  47 FAREAVCVNTGTAALHLALQALgVGPGDEVLVQSLTYVASFQAISATGARpvpCDIDPDTIT-LNVDDAKKRITEHTRVVM 126
                                   57899****************96788*******************99998633445555554.58999999******9995 PP

                                   EESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
               Cys_Met_Meta_PP 143 lEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                      p     +v  + +i ++a+++++ vv D++
  gi|91773568|ref|YP_566260.1| 127 ---PVHYASSVGPLDEIYEFAQDNDLRVVEDAA 156
                                   ...555555666666666666666666666655 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.3
                                   TTTT----HHHHHHHHHH CS
               Cys_Met_Meta_PP 148 npllkvvDiekiaklakk 165
                                    p l++ D+ +i+++ k+
  gi|91773568|ref|YP_566260.1| 351 HPELQISDVDHICEMLKQ 368
                                   5899*********99885 PP

>> DUF2684  Protein of unknown function (DUF2684)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.6e-05      0.08      20      59 ..     235     274 ..     228     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                       DUF2684  20 nryGwiniwtailGqffalfplffesrlillktqlvivsd 59 
                                    ry   n+  ai  + f +fp+f e r+ llk +  ++++
  gi|91773568|ref|YP_566260.1| 235 WRYHMSNVMAAIGIEQFKKFPIFAEKRKELLKRYQSNLAN 274
                                   578889**99*999******************99988865 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2   4.4e+03      90     111 ..     148     169 ..     138     207 .. 0.52
   2 ?   11.7   0.0   6.4e-05      0.14     123     174 ..     301     360 ..     282     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                           SGL  90 DgvvdpdGrlwfGtmgdeeakg 111
                                   D++v +d +  fGt  ++++ g
  gi|91773568|ref|YP_566260.1| 148 DLRVVEDAAQAFGTYYNDKKVG 169
                                   4444444444444444433322 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.4e-05
                           SGL 123 d.gklervlddltipNGlawspdgktlYl........aDsltrkiwaydvdaeggklsnrr 174
                                   d ++l+++l+d++ip G++ +p +k  Y+        +D+++++i   ++  e + +s+ +
  gi|91773568|ref|YP_566260.1| 301 DrNTLRKMLEDVGIPTGIHYKPNHKLSYYdtgvelpcTDTVAKEILTLPLHPELQ-ISDVD 360
                                   23589****************************************9998865444.66655 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.4e-05       0.1      38      80 ..      64     103 ..      54     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                                   HHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                   AMP-binding  38 gLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                   +L++lGv++gd V++    s+ +v++++ai   Ga +vp++ +
  gi|91773568|ref|YP_566260.1|  64 ALQALGVGPGDEVLVQ---SLTYVASFQAISATGARPVPCDID 103
                                   799**********995...799*****************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2270.42
//
Query:       gi|91773569|ref|YP_566261.1|  [L=280]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-27   95.4   0.2    5.5e-27   94.6   0.1    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-15   57.3   2.7    1.9e-15   57.1   2.7    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.5e-07   31.6   0.0      2e-07   31.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00057   20.3   1.4     0.0025   18.3   0.2    2.5  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.33   11.2   1.1        2.1    8.7   1.1    2.1  1  MamL-1           MamL-1 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 !   94.6   0.1   1.5e-30   5.5e-27       1     109 [.      13     117 ..      13     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.5e-30
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   s+++ ++N +k+l+e+++s+ aq +y+d+eii+ D+ StD+++ei+ ++   d ++r++  ++nv ++ a+n ++++ +g+
  gi|91773569|ref|YP_566261.1|  13 SIIMNCFNCSKYLKEAIDSVYAQ-TYEDWEIIFWDNVSTDNSAEIANSY---DNKLRYFCGNKNVPLGYARNLAIEKIQGK 89 
                                   8**********************.*************************...78*************************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TT CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdga 109
                                   yi+flD Dd + p +lek ++ +e + +
  gi|91773569|ref|YP_566261.1|  90 YIAFLDCDDMWLPTKLEKQMAIFESTSN 117
                                   ***********************99644 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 !   57.1   2.7   5.3e-19   1.9e-15      11     218 ..      21     213 ..      11     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 5.3e-19
               Glyco_tranf_2_2  11 erhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaD 91 
                                     +y++e +     +  e+ e+i+ d+ S+++   e+ +  d +l+ +  +   k   l+ arN+ ++k ++ ++ FlD D
  gi|91773569|ref|YP_566261.1|  21 CSKYLKEAIDSVYAQTYEDWEIIFWDNVSTDN-SAEIANSYDNKLRYFCGN---KNVPLGYARNLAIEKIQGKYIAFLDCD 97 
                                   4568999996666666699*************.678888888777766444...58899********************** PP

               Glyco_tranf_2_2  92 cfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdve..dltassrvledllaakstlvkffapssssili 170
                                   +++ + k+ek++ +     ++   +  +v++  ++++ + +++ +    +  a+++v e+ll  ++     f+p   +++i
  gi|91773569|ref|YP_566261.1|  98 DMWLPTKLEKQMAI-----FESTSNVKLVFSDCNIVDSQHNIINRSFavQTPARGNVFEKLLMSYN-----FIPLV-TAMI 167
                                   *************5.....55667999**************9998641145689********9554.....67765.689* PP

               Glyco_tranf_2_2 171 nrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykar 218
                                   ++  +  vG +D+ +    aE++d++lR+a +++   +  +   y+ +
  gi|91773569|ref|YP_566261.1| 168 EKDVLDDVGCFDNTY--RIAEEYDMFLRIAYKYPIDFVDEPLAEYRVH 213
                                   ***************..89***********998743233333344444 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   5.5e-11     2e-07       1     121 [.      10     122 ..       9     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.5e-11
               Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                   p+ ++++  +fn +++l e ++s+ aq+y + e+++ ++ s++  +e a      +++ ++r+    +n  + g++r  n 
  gi|91773569|ref|YP_566261.1|  10 PT-ISIIMNCFNCSKYLKEAIDSVYAQTYEDWEIIFWDNVSTDNSAEIA----NSYDN-KLRYFCGNKNV-PLGYAR--NL 81 
                                   45.999*********************************9999966655....56988.9**99998865.568888..88 PP

               Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavg 121
                                   a++ +++++++++D D+ + P+ l+++ ++f  t++v+ v 
  gi|91773569|ref|YP_566261.1|  82 AIEKIQGKYIAFLDCDDMWLPTKLEKQMAIFeSTSNVKLVF 122
                                   99*****************************9999999885 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   6.9e-07    0.0025       2      84 ..      20     100 ..      19     109 .. 0.78
   2 ?   -0.2   0.0      0.42   1.5e+03      10      10 ..     216     216 ..     171     266 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.9e-07
               Glyco_tranf_2_4   2 neadiLpeflahhlalgfd..rilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvDa 80 
                                   n+ ++L+e ++  +a  ++  +i+++dn stD++++i  ++++ kl ++ ++   ++ +  + ++l+ +  ++++++++D+
  gi|91773569|ref|YP_566261.1|  20 NCSKYLKEAIDSVYAQTYEdwEIIFWDNVSTDNSAEIANSYDN-KLRYFCGN---KNVPLGYARNLAIEKIQGKYIAFLDC 96 
                                   7888999999987777776246****************99655.44444443...3577889999999999********** PP

               Glyco_tranf_2_4  81 DEfl 84 
                                   D + 
  gi|91773569|ref|YP_566261.1|  97 DDMW 100
                                   *974 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.42
               Glyco_tranf_2_4  10 f 10 
                                    
  gi|91773569|ref|YP_566261.1| 216 N 216
                                   2 PP

>> MamL-1  MamL-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.1   0.00058       2.1      15      35 ..     208     228 ..     207     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00058
                        MamL-1  15 ElyRrhhsdCesryertqaer 35 
                                     yR h s+C+ r++ +++e 
  gi|91773569|ref|YP_566261.1| 208 AEYRVHDSNCSHRQDIGIKEE 228
                                   57*************998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1779.10
//
Query:       gi|91773570|ref|YP_566262.1|  [L=373]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   80.6   0.1    1.8e-22   80.0   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    2.2e-15   57.1   0.4      4e-15   56.3   0.4    1.6  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.3e-14   54.6   0.0    1.9e-14   54.1   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-07   31.1   0.1      2e-07   30.8   0.1    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.2e-05   24.0   0.0    8.7e-05   22.1   0.0    1.9  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.069   12.3   0.3       0.11   11.7   0.3    1.3  1  CofC             Guanylyl transferase CofC like
       0.12   12.2   0.0       0.22   11.4   0.0    1.4  1  DUF5591          Domain of unknown function (DUF5591)
       0.12   11.6   0.0       0.17   11.1   0.0    1.2  1  Peptidase_U57    YabG peptidase U57


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 !   80.0   0.1   7.9e-26   1.8e-22       1     109 [.      44     152 ..      44     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 7.9e-26
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglraatg 80 
                                   s+vip+yNee+ ++  ++ l++++p +++eiiv +DgS D+t+ei+++  k  +   +v+++++  G  +a+n+g+ +++ 
  gi|91773570|ref|YP_566262.1|  44 SIVIPAYNEEEVIEDRINNLAEIYPIDKMEIIVSNDGSVDNTEEIARSVLKkHSIEGKVLTHDRS-GVNKAINRGINETSQ 123
                                   8**************************************************99999999999966.*************** PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TT CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdga 109
                                   d++++  +D  +d+d+++ l++ l   ++
  gi|91773570|ref|YP_566262.1| 124 DLVIITGSDGLFDKDTIPNLLGVLLSSDD 152
                                   **********************9988444 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 !   56.3   0.4   1.8e-18     4e-15      10     195 ..     134     315 ..     125     358 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.8e-18
               Glyco_trans_2_3  10 vlppdclreiaaela.spevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalqevg 88 
                                   + + d +  ++  l  s+++++v+g  +++  + +++++  a+ ++  +gk++ + ++ +++  + G ++++  +a +++ 
  gi|91773570|ref|YP_566262.1| 134 LFDKDTIPNLLGVLLsSDDIGAVSGDLVPVaKGESIFSNSEAAYRS-IYGKICTWESNVHSTYCFNGPVVAFKKEASSSLN 213
                                   5555555555554442789*******99864889999999998887.79*******************************6 PP

               Glyco_trans_2_3  89 gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGcel.eklillvrllgylgsllwsalp 168
                                   + +      ++D +m+l+  +kGyr+ +vp++ ++e++p+ +   +rQ+ R a    l    + + +l+   g++ ++ +p
  gi|91773570|ref|YP_566262.1| 214 TRR-----GADDASMALSVIKKGYRCQYVPSAKFYEYVPDKFHEQRRQKIRRATRL-LeATFFNRNVLSTNCGRFRTVVFP 288
                                   555.....78*****************************************99994.222223334455666777777788 PP

               Glyco_trans_2_3 169 lhlallllfsllalalvlllllllaal 195
                                   l+l++l+l + l ++ ++l++++l+++
  gi|91773570|ref|YP_566262.1| 289 LRLMMLFLVPTLVFLSIVLWMAYLFTV 315
                                   888888888877777777777777764 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 !   54.1   0.0   8.6e-18   1.9e-14       1     226 [.      41     259 ..      41     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 8.6e-18
               Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaq.eyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                   p  +++++p++nee+v+++ +++l+ + + +  e++v  d+s + t e a+ + ++++ ++ +v++ +r   s g   a+n
  gi|91773570|ref|YP_566262.1|  41 PK-ISIVIPAYNEEEVIEDRINNLAEIyPIDKMEIIVSNDGSVDNTEEIARSVLKKHSIEG-KVLTHDR---S-GVNKAIN 115
                                   55.9*********************8735688*********************99999654.7775555...4.445889* PP

               Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralg.vl 158
                                   ++++ +++dlv++  +D + ++dt++ ll ++  ++++gav ++   +  +++ +s + a  +   + +++     +  + 
  gi|91773570|ref|YP_566262.1| 116 RGINETSQDLVIITGSDGLFDKDTIPNLLGVLlSSDDIGAVSGDLvPVAKGESIFSNSEA-AYRSIYGKICTWESNVHsTY 195
                                   ********************************8999******98868899******7777.34444446666665554389 PP

               Glyco_tranf_2_3 159 tlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnR 226
                                   ++nG  +++  e    l + ++    +dD++++l++ + g+r +yvp a  +e+ p+++ + ++q+ R
  gi|91773570|ref|YP_566262.1| 196 CFNGPVVAFKKEASSSLNTRRG----ADDASMALSVIKKGYRCQYVPSAKFYEYVPDKFHEQRRQKIR 259
                                   *****************55555....8**************************************988 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 !   30.8   0.1   8.8e-11     2e-07       1     106 [.      44     147 ..      44     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 8.8e-11
               Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska 80 
                                   s+vip +++ee   ie+r+ + a  y  +++e+iv +dgS +++ ee+   + +++ +  k   +   +  +a NrG++++
  gi|91773570|ref|YP_566262.1|  44 SIVIPAYNEEEV--IEDRINNLAEIYpIDKMEIIVSNDGSVDNT-EEIARSVLKKHSIEGKVLTHDRSGVNKAINRGINET 121
                                   79********99..************87889************5.56655555666665566655678999********** PP

               Glyco_tranf_2_2  81 esdlvlFlDaDcfissDkfekilkli 106
                                     dlv+   +D ++  D + ++l ++
  gi|91773570|ref|YP_566262.1| 122 SQDLVIITGSDGLFDKDTIPNLLGVL 147
                                   *****************998888654 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 ?   -0.6   0.0      0.37   8.2e+02      10      41 ..      51      82 ..      41     105 .. 0.78
   2 !   22.1   0.0   3.9e-08   8.7e-05      15     165 ..     110     258 ..      96     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.37
               Glyco_transf_21 10 gdpvgvnpKvnnllqaleaakydllvisDsdv 41
                                   +++ +  ++nnl+  ++  k +++v +D  v
  gi|91773570|ref|YP_566262.1| 51 NEEEVIEDRINNLAEIYPIDKMEIIVSNDGSV 82
                                  566777889*****************999665 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 3.9e-08
               Glyco_transf_21  15 vnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVts.lpvgsdakglaaaleaaflntlagvlqa 93 
                                   vn     +++++++  +dl++i  sd ++++d++ +ll+ l + +++g V++ l+ +++ +++ ++ eaa+ +++ ++ + 
  gi|91773570|ref|YP_566262.1| 110 VNKA---INRGINETSQDLVIITGSDGLFDKDTIPNLLGVLLSsDDIGAVSGdLVPVAKGESIFSNSEAAYRSIYGKICTW 187
                                   4433...5789999************************99877689******5555999*************888777666 PP

               Glyco_transf_21  94 ..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvpr..rsslrall 165
                                     ++  + + +G ++a+++ea  ++   +      A+D++++  + ++G++   +p + + + vp+   +  r+  
  gi|91773570|ref|YP_566262.1| 188 esNVHSTYCFNGPVVAFKKEASSSLNTRRG-----ADDASMALSVIKKGYRCQYVPSAKFYEYVPDkfHEQRRQKI 258
                                   669*****************9999966655.....********************999888888875544444444 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   4.8e-05      0.11      52     112 ..      85     146 ..      52     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-05
                          CofC  52 deevleya..ldelgvevvkekekdlntavekafeeieekeviiipsdiPlikkedvkdllel 112
                                    ee+  +   +++ + +v+  + +++n+a+++ + e+ ++ vii+ sd  l +k+++ +ll  
  gi|91773570|ref|YP_566262.1|  85 TEEIARSVlkKHSIEGKVLTHDRSGVNKAINRGINETSQDLVIITGSD-GLFDKDTIPNLLGV 146
                                   45555544113455668999999**********9*9999999999999.79999999999865 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.8e-05      0.22      67     150 ..      62     143 ..      61     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.8e-05
                                   GGTT----------------HHHHHHHHHHHHHHHHHHT-SE.EEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHH CS
                       DUF5591  67 eleevYPaaqYdiavtgewseeeiefvaellakylektkyek.viahleeeyreiveevaeelgleiiytvvedkptskes 146
                                   +l e+YP+ + +i v+       ++ ++e+ +++l+k++ e  v+ h  ++ ++++++  +e+++++++ + +d   +k+ 
  gi|91773570|ref|YP_566262.1|  62 NLAEIYPIDKMEIIVSN---DGSVDNTEEIARSVLKKHSIEGkVLTHDRSGVNKAINRGINETSQDLVIITGSDGLFDKDT 139
                                   6899************5...6666666777777888888865499999999999999999888888877776888888888 PP

                                   HHHH CS
                       DUF5591 147 lknL 150
                                   + nL
  gi|91773570|ref|YP_566262.1| 140 IPNL 143
                                   8877 PP

>> Peptidase_U57  YabG peptidase U57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.8e-05      0.17     119     168 ..      89     138 ..      54     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.8e-05
                 Peptidase_U57 119 clklYkklgleavgvvvkEkeqpekvkellekvkpdilvlTGHDgllkkk 168
                                   + ++ kk ++e ++ + + +   +++++ +++++ d++++TG Dgl  k+
  gi|91773570|ref|YP_566262.1|  89 ARSVLKKHSIEGKVLTHDRSGVNKAINRGINETSQDLVIITGSDGLFDKD 138
                                   556778999999999999999************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2280.14
//
Query:       gi|91773571|ref|YP_566263.1|  [L=207]
Description: acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  24.8    2.6e-07   30.1   2.1    5.3  5  Hexapep     Bacterial transferase hexapeptide (six repeats)
    5.3e-11   42.1  14.8    6.1e-05   22.7   0.3    5.3  5  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
        0.1   11.5   0.4       0.17   10.8   0.1    1.5  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 ?    3.3   0.1     0.013        76       1      17 [.       5      21 ..       5      22 .. 0.80
   2 !   12.0   0.1   2.2e-05      0.13      20      34 ..      30      44 ..      28      46 .. 0.74
   3 !   15.6   2.5   1.6e-06    0.0095       4      36 .]      56      88 ..      46      88 .. 0.82
   4 !   21.9   0.5   1.6e-08   9.9e-05       3      35 ..      85     117 ..      85     118 .. 0.94
   5 !   30.1   2.1   4.4e-11   2.6e-07       1      36 []     133     168 ..     133     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.013
                                  TEEEETTEEE-TTEEEE CS
                       Hexapep  1 stvIGsnvlIgpfavig 17
                                  +++IG+n +I   + ig
  gi|91773571|ref|YP_566263.1|  5 NAIIGKNPVIQDLVEIG 21
                                  57899999998888776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.2e-05
                                  EEE-TTEEEETTEEE CS
                       Hexapep 20 VkIGdnvkIgagvvi 34
                                  ++IGdn++I +++vi
  gi|91773571|ref|YP_566263.1| 30 TIIGDNATIRSHSVI 44
                                  578888888888887 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.6e-06
                                  EETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep  4 IGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                  +G + l++ + +ig++V IG ++++++  +ig+
  gi|91773571|ref|YP_566263.1| 56 TGHGILLRENNKIGNDVSIGTHSIVERENTIGN 88
                                  566667777999999999999999999888875 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 1.6e-08
                                   EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   +IG+nv I++++ + + V+I d+v Ig+ ++i 
  gi|91773571|ref|YP_566263.1|  85 TIGNNVRIHSNCFVPEFVIIDDDVWIGPSTTIL 117
                                   69**************************99996 PP

  == domain 5  score: 30.1 bits;  conditional E-value: 4.4e-11
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   s++I ++++Ig +++ig+ V IG+++ Ig g+v+++
  gi|91773571|ref|YP_566263.1| 133 SVHIKKGAKIGGNVTIGPRVSIGERSFIGMGSVVTK 168
                                   689*******************************86 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.046   2.8e+02       7      20 ..       5      20 ..       3      22 .. 0.60
   2 !    5.6   0.2    0.0022        13      18      32 ..      30      44 ..      29      52 .. 0.57
   3 ?    2.6   0.2     0.019   1.2e+02       2      15 ..      66      79 ..      59      81 .. 0.81
   4 !   16.7   0.1   7.7e-07    0.0046       3      28 ..      85     112 ..      83     117 .. 0.90
   5 !   22.7   0.3     1e-08   6.1e-05       2      34 .]     134     168 ..     133     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.046
                                  T-EE-TT-EE.S.EEE CS
                     Hexapep_2  7 nCliGanagi.G.vsl 20
                                  n +iG+n +i   v++
  gi|91773571|ref|YP_566263.1|  5 NAIIGKNPVIqDlVEI 20
                                  6777777666444555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0022
                                  EEE-TT-EE-TT-EE CS
                     Hexapep_2 18 vslGdncvvgaGvvi 32
                                  +++Gdn+++ + +vi
  gi|91773571|ref|YP_566263.1| 30 TIIGDNATIRSHSVI 44
                                  355666655544444 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.019
                                  EEE-TT-EE-TT-E CS
                     Hexapep_2  2 viIGdnCliGanag 15
                                   +IG+++ iG  ++
  gi|91773571|ref|YP_566263.1| 66 NKIGNDVSIGTHSI 79
                                  58999999987766 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 7.7e-07
                                   EE-TT-EE-TT-EES..EEE-TT-EE-T CS
                     Hexapep_2   3 iIGdnCliGanagiG..vslGdncvvga 28 
                                   +IG+n+ i++n+ ++  v++ d++ +g+
  gi|91773571|ref|YP_566263.1|  85 TIGNNVRIHSNCFVPefVIIDDDVWIGP 112
                                   8*************999******99986 PP

  == domain 5  score: 22.7 bits;  conditional E-value: 1e-08
                                   EEE-TT-EE-TT-EES..EEE-TT-EE-TT-EE-S CS
                     Hexapep_2   2 viIGdnCliGanagiG..vslGdncvvgaGvvita 34 
                                   v+I +   iG n +iG  vs+G+++ +g+G+v+t+
  gi|91773571|ref|YP_566263.1| 134 VHIKKGAKIGGNVTIGprVSIGERSFIGMGSVVTK 168
                                   56667777*******99*****************7 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   2.8e-05      0.17     278     318 ..      65     106 ..      15     125 .. 0.66
   2 ?   -2.6   0.0      0.33     2e+03     297     311 ..     147     161 ..     130     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                    Fucokinase 278 nSvlessvsvgegsvie.hsslkgnvsigsnsivsgleless 318
                                   n ++ ++vs+g++s++e + ++++nv+i+sn++v +  +  +
  gi|91773571|ref|YP_566263.1|  65 NNKIGNDVSIGTHSIVErENTIGNNVRIHSNCFVPEFVIIDD 106
                                   556777888888888884556668888888888877666654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.33
                    Fucokinase 297 slkgnvsigsnsivs 311
                                   +++++vsig++s++ 
  gi|91773571|ref|YP_566263.1| 147 TIGPRVSIGERSFIG 161
                                   566778888888873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1305.81
//
Query:       gi|91773572|ref|YP_566264.1|  [L=357]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-128  428.4   0.0   2.8e-128  428.2   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.9e-09   37.2   0.1      4e-09   36.1   0.1    1.7  1  Aminotran_1_2    Aminotransferase class I and II
    1.3e-08   34.5   0.0    2.1e-08   33.8   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    1.3e-08   33.8   0.0    1.5e-08   33.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    2.6e-08   33.2   0.0    4.8e-08   32.4   0.0    1.4  2  Aminotran_5      Aminotransferase class-V
    0.00027   19.8   0.0    0.00032   19.5   0.0    1.1  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
     0.0012   17.7   0.1     0.0021   16.9   0.1    1.3  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
     0.0045   16.5   0.0      0.014   14.9   0.0    1.7  2  PALP             Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.036   14.5   0.0      0.069   13.6   0.0    1.5  1  NYN              NYN domain
       0.15   12.4   0.0        1.3    9.4   0.0    2.3  2  Toxin_38         Potassium channel toxin


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 !  428.2   0.0  1.6e-131  2.8e-128       3     361 .]      11     353 ..       9     353 .. 0.96

  Alignments for each domain:
  == domain 1  score: 428.2 bits;  conditional E-value: 1.6e-131
                                   HHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHT CS
               DegT_DnrJ_EryC1   3 keeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlel 83 
                                   ++++++ave+vl+sg +++g++ + +E++fa+++++k+a++vssGt+A++l+++alg+g+gde+Ivps+tF+a+a+++  l
  gi|91773572|ref|YP_566264.1|  11 DDDIKRAVEQVLDSGRFIKGEQLRLLEQEFADFCNAKNAVGVSSGTSAILLTMMALGIGKGDEIIVPSHTFIASASPAKFL 91 
                                   678999*************************************************************************** PP

                                   T-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSE CS
               DegT_DnrJ_EryC1  84 gakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgda 164
                                   ga+pv+vD+dpdty++dp++ie+aite+tkaI++VhlyG++adm+++++ia+k+g++v+eD+++A+ a+ykgk++Galgd+
  gi|91773572|ref|YP_566264.1|  92 GATPVYVDIDPDTYTVDPNKIEEAITENTKAIIAVHLYGHPADMNSINDIASKYGIPVVEDSCQAHAAKYKGKRTGALGDI 172
                                   ********************************************************************************* PP

                                   EEEE-BTTSSS.-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHH CS
               DegT_DnrJ_EryC1 165 avfSFyptKnl.ttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarR 244
                                   avfSF+p+Kn+  +G+GG+ vtn+eelaek+ +lr hG++    ++y++++ lG n+rl+ei AAig++qL++l++++++R
  gi|91773572|ref|YP_566264.1| 173 AVFSFFPSKNMtVAGDGGIAVTNNEELAEKIAMLRDHGRN----NKYTSDL-LGLNLRLSEIPAAIGRQQLSHLSDWTDKR 248
                                   ***********778************************99....7******.***************************** PP

                                   HHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCC CS
               DegT_DnrJ_EryC1 245 reiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerkeea 325
                                   r++a++y+e+L+++ +t  + ++++++ ha+hly++++e     +rd+l++ l+++gi+t +hyp+p+hrqp  +  k   
  gi|91773572|ref|YP_566264.1| 249 RQAAARYNELLRGVVET--PFEAQWAT-HAYHLYVIQTE-----ARDDLAKYLNDNGISTGIHYPVPVHRQPCMEAGKV-- 319
                                   *************9964..44555555.9*********9.....89***************************998853.. PP

                                   CHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHHH CS
               DegT_DnrJ_EryC1 326 sgdlpnaerlaervlsLplypelteedvdrVvealr 361
                                      lp+++++++r+lsLp++p+lt+e+++ V+e+++
  gi|91773572|ref|YP_566264.1| 320 --TLPVTDKVVDRILSLPMHPQLTDEQIKFVAEKIQ 353
                                   ..49*****************************985 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   2.2e-12     4e-09      47     187 ..      34     152 ..      12     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.2e-12
                                   HHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTT CS
                 Aminotran_1_2  47 peleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseed 127
                                     le++ a+f +        ++ av v+sG++a++ + ++l  + +gdei+vp+ t+      ++  g++ v++ ++ +++
  gi|91773572|ref|YP_566264.1|  34 RLLEQEFADFCN--------AKNAVGVSSGTSAILLTMMALG-IGKGDEIIVPSHTFIASASPAKFLGATPVYVDID-PDT 104
                                   568999******........888*******************.********************************66.*** PP

                                   TEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                 Aminotran_1_2 128 fhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                   +++d +++eea++e       tk i+        G  a+ + + ++   a ky++ ++ D
  gi|91773572|ref|YP_566264.1| 105 YTVDPNKIEEAITE------NTKAIIAVHL---YGHPADMNSINDI---ASKYGIPVVED 152
                                   **************......6777775433...3555666666666...66666666666 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   1.2e-11   2.1e-08      33     252 ..      32     241 ..      17     295 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.2e-11
                                   HHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.TBE-H CS
               Beta_elim_lyase  33 tvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.Gkmdl 111
                                   + + Le+++a+ + ++ a+ v +Gt A  + +++l   +g+e+iv  p+h++   +  ++ + g++++ ++++ +  ++d+
  gi|91773572|ref|YP_566264.1|  32 QLRLLEQEFADFCNAKNAVGVSSGTSAILLTMMALGiGKGDEIIV--PSHTFIASASPAK-FLGATPVYVDIDPDtYTVDP 109
                                   56779****************************998899999997..7999887766555.55666888887776589*** PP

                                   HHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEE CS
               Beta_elim_lyase 112 ekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsv 192
                                   +k+e+ai+e      ++k+i+    + +  G +  +   + + +ia kygip++ D++  a aa   + + k+  +  D+ 
  gi|91773572|ref|YP_566264.1| 110 NKIEEAITE------NTKAIIAV--HLY--GHPADM---NSINDIASKYGIPVVEDSCQ-AHAA---KYKGKRTGALGDIA 173
                                   *********......45565432..233..666655...5667899************6.4455...56667888888888 PP

                                   EEES..SSTT--SS-.EEEEE-HH...........HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHS CS
               Beta_elim_lyase 193 tmsl..kKdllanvG.gvlafrddel.......edylaerveqrkylggglrqagvlaaleagiraleeg 252
                                   ++s+  +K++++  + g+ +++++el        d  ++   +   lg +lr ++++aa   g   l + 
  gi|91773572|ref|YP_566264.1| 174 VFSFfpSKNMTVAGDgGIAVTNNEELaekiamlRDHGRNNKYTSDLLGLNLRLSEIPAA--IGRQQLSHL 241
                                   88866699998754438888888877666666533333344445566777777777777..444444333 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 !   33.6   0.0   8.5e-12   1.5e-08      55     226 ..      34     206 ..      12     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 8.5e-12
                                   HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEE.ESTTSHHHHHH CS
               Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkk.lgievkf.vdtsdleelek 132
                                   + le++ a+  ++++a+ vssG++Ai ++++al + +Gdei+v ++ +  + +  k +    + ++++  + t d++++e+
  gi|91773572|ref|YP_566264.1|  34 RLLEQEFADFCNAKNAVGVSSGTSAILLTMMALgIGKGDEIIVPSHTFIASASPAKFLGATpVYVDIDPdTYTVDPNKIEE 114
                                   579************************9999996789***********9998876665443244444431224699***** PP

                                   HCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-..SEEEEET..TTTTTCSSS--EE CS
               Cys_Met_Meta_PP 133 aikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklga..DivvhSa..TKylgGhsdvvaG 209
                                   ai+entk++          + +D+++i ++a k g++vv D + a  +  +  + ga  Di v S   +K +   +d  +G
  gi|91773572|ref|YP_566264.1| 115 AITENTKAIIAVH---LYGHPADMNSINDIASKYGIPVVEDSCQAHAAKYKGKRTGAlgDIAVFSFfpSKNMTVAGD--GG 190
                                   *******996533...334557********************99999888888888555888888423454444444..56 PP

                                   EEEESSCHHHHHHHHHH CS
               Cys_Met_Meta_PP 210 vivvkgkeelkkelkfl 226
                                   ++v+++ eel++++++l
  gi|91773572|ref|YP_566264.1| 191 IAVTNN-EELAEKIAML 206
                                   777666.7777777766 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.7e-11   4.8e-08      48     180 ..      36     157 ..      29     197 .. 0.86
   2 ?   -4.0   0.0       2.9   5.2e+03     320     333 ..     285     298 ..     248     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.7e-11
                                   HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETT.SCB CS
                   Aminotran_5  48 arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldee.gel 127
                                    ++++a++ na++    + +s++t+ai l +++l+  + +gdei+v +    a   p++ l    ga+ +++ +d++  ++
  gi|91773572|ref|YP_566264.1|  36 LEQEFADFCNAKN---AVGVSSGTSAILLTMMALG--IGKGDEIIVPSHTFIASASPAKFL----GATPVYVDIDPDtYTV 107
                                   5789999999997...889999999*********5..9*********99988888777776....5666677777551689 PP

                                   EGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTT CS
                   Aminotran_5 128 dldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqav 180
                                   d++++e++++e+tk+++  h     G   ++++i+++a k+g+ v+ D++qa 
  gi|91773572|ref|YP_566264.1| 108 DPNKIEEAITENTKAIIAVHL---YGHPADMNSINDIASKYGIPVVEDSCQAH 157
                                   9****************9996...8**************************85 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.9
                                   SHHHHHHHHHHTTE CS
                   Aminotran_5 320 haedvatlLdeegI 333
                                     +d+a++L+++gI
  gi|91773572|ref|YP_566264.1| 285 ARDDLAKYLNDNGI 298
                                   34677888888877 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.8e-07   0.00032      74     246 ..      46     204 ..      37     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.8e-07
                                   HHEECCCSS-HHHH.HHHHHHHHHHHCC--CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTC CS
                       SepSecS  74 vknafvvPlatGls.laLClsalrkrskakkviwvridekSslkavelaGleialvekvlegDelitdvedveeiiekkre 153
                                   +kna+ v  + G s + L ++al+   k++++i +     +s   +++ G  ++ v+  +++D+  +d++++ee+i++ + 
  gi|91773572|ref|YP_566264.1|  46 AKNAVGV--SSGTSaILLTMMALG-IGKGDEIIVPSHTFIASASPAKFLGATPVYVD--IDPDTYTVDPNKIEEAITE-NT 120
                                   5555555..666653667888888.789999999988888888899999*9999998..79***************99.45 PP

                                   CCEEEEEECSSTTTTB----HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCC CS
                       SepSecS 154 evilavlstlsffaprspDdvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaii 234
                                    +i+av+      ++  +D ++ i  i ++y++P +  +    q +    k k++   G + v+     kn+ v   g+i 
  gi|91773572|ref|YP_566264.1| 121 KAIIAVHL-----YGHPAD-MNSINDIASKYGIPVVEDSC---QAHAAKYKGKRTGALGDIAVFSFFPSKNMTVAGDGGIA 192
                                   55666664.....566677.999***********876654...44555666677888899999988899999998777777 PP

                                   CESSCHCCCCCH CS
                       SepSecS 235 aasdesfikeis 246
                                    +++e+  ++i+
  gi|91773572|ref|YP_566264.1| 193 VTNNEELAEKIA 204
                                   777777666654 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   0.1   1.2e-06    0.0021      75     205 ..      40     154 ..       6     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                   HHHHCT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS-BE---GGGGSHHH CS
                      OKR_DC_1  75 aarvfgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepernalgiiggidlkefeeet 155
                                    a   +a ++  v  GTs+   +++   + +gd ++v+  +  + +    + gatPvy+  + + + +    d      + 
  gi|91773572|ref|YP_566264.1|  40 FADFCNAKNAVGVSSGTSAILLTMMALGIGKGDEIIVPSHTFIASASPAKFLGATPVYVDIDPDTYTV----DP-----NK 111
                                   4667789999999*************************999988888999**********99888864....44.....78 PP

                                   HHHHHHHSTTTGSESEEEEESS-TTSEEE-HHHHHHHHTTSESEEEEE-T CS
                      OKR_DC_1 156 lkekikevpdakaprlavitnsTYdGvlynakeivdkleklsdrilfDeA 205
                                   ++e+i+e ++a        +    +G+ +++++i d + k+++++  D+ 
  gi|91773572|ref|YP_566264.1| 112 IEEAITENTKAI-------IAVHLYGHPADMNSINDIASKYGIPVVEDSC 154
                                   899998876543.......3445579999999999999999999999985 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.6e-06     0.014      50     140 ..      37     135 ..      17     144 .. 0.82
   2 ?   -1.9   0.0      0.97   1.7e+03     177     240 ..     266     331 ..     261     335 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.6e-06
                                   HTT....TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEE...CCHHHHHHHH.HHHHH CS
                          PALP  50 keg....tgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGaevvev...ggdydeavaa.aaela 122
                                   +++    + ak+ v  ssG  ++ l ++a  +G   +i vp+++  + +   + lGa+ v v   +++y+   ++  ++++
  gi|91773572|ref|YP_566264.1|  37 EQEfadfCNAKNAVGVSSGTSAILLTMMALGIGKGDEIIVPSHTFIASASPAKFLGATPVYVdidPDTYTVDPNKiEEAIT 117
                                   33466778999***************************************************8875556666666155666 PP

                                   HHSTTCEE--TTTSHHHH CS
                          PALP 123 aegegaylvsqfdnptvi 140
                                   ++++ ++ v+ +++p+ +
  gi|91773572|ref|YP_566264.1| 118 ENTKAIIAVHLYGHPADM 135
                                   668888999999998866 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.97
                                   HHHHHSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS..CGTTCCHHHHSEEEEEE CS
                          PALP 177 glkerrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavg..spselafelldrlvdei 240
                                   ++ +++ +   +++++++e  d la++l  ++    +  +  ++  + +  +++  ++++ d+ vd+i
  gi|91773572|ref|YP_566264.1| 266 PFEAQWAThaYHLYVIQTEARDDLAKYL--NDNGISTGIHYPVPVHRQPcmEAGKVTLPVTDKVVDRI 331
                                   5566555556889999999999999999..33333333344444444445566666666666666666 PP

>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.069      17      74 ..     104     163 ..      93     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                           NYN  17 gkevdyrklleeirskge.lvraraygnwedeeqnkfqdalsstgikvkhkplkkrg...gs 74 
                                    + vd++k+ e+i+++ + ++  + yg    +++n+++d+ s++gi+v+   +++++   ++
  gi|91773572|ref|YP_566264.1| 104 TYTVDPNKIEEAITENTKaIIAVHLYGH--PADMNSINDIASKYGIPVVEDSCQAHAakyKG 163
                                   34499**********6555999******..8899*************999998877654433 PP

>> Toxin_38  Potassium channel toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.81   1.4e+03      34      45 ..      42      53 ..      36      58 .. 0.81
   2 ?    9.4   0.0    0.0007       1.3      20      39 ..     142     162 ..     133     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.81
                      Toxin_38 34 dHCaakkkeGkC 45
                                  d C+ak+++G  
  gi|91773572|ref|YP_566264.1| 42 DFCNAKNAVGVS 53
                                  78******9975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0007
                      Toxin_38  20 kseygCpviekyCedHCaa.k 39 
                                    s+yg pv+e+ C+ H a+ k
  gi|91773572|ref|YP_566264.1| 142 ASKYGIPVVEDSCQAHAAKyK 162
                                   589*************98744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2154.51
//
Query:       gi|91773573|ref|YP_566265.1|  [L=335]
Description: oxidoreductase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  107.3   0.1    2.4e-30  105.8   0.0    1.8  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0016   18.9   0.0     0.0065   17.0   0.0    1.9  2  CoA_binding_2    CoA binding domain
  ------ inclusion threshold ------
      0.066   12.8   0.3       0.54    9.8   0.1    2.4  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.086   13.4   0.0       0.72   10.5   0.0    2.5  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.15   12.1   0.0       0.47   10.5   0.0    1.9  1  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta
       0.19   10.9   0.3        6.9    5.8   0.0    2.2  2  Polysacc_deac_2  Divergent polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0   8.1e-34   2.4e-30       3     120 .]       4     123 ..       2     123 .. 0.97
   2 ?   -1.9   0.0         2   5.9e+03      83     111 ..     293     329 ..     286     334 .. 0.66

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 8.1e-34
                                   EEEETTSHHHHHHHHHHHHTTTTE..EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                  GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrle..evvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelaka 81 
                                   +a+iG+G+ g++h+r + e   +   + v ++d++++ra+++ ++f++e  +d++++l+dp+idav+++tp+ th+ lak+
  gi|91773573|ref|YP_566265.1|   4 IAVIGTGYWGKNHVRTYSELVAEGiiDHVKICDINEKRAQELGKAFNIEYLTDYKDILSDPDIDAVSIVTPSPTHFPLAKE 84 
                                   89***************99966668999***************************************************** PP

                                   HHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                  GFO_IDH_MocA  82 aleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                   ++eagk+vl+EKP++++++ea++l e+a+++g++++vg+
  gi|91773573|ref|YP_566265.1|  85 FMEAGKDVLVEKPMTMDYTEAEKLTEIAKSTGQILMVGH 123
                                   *************************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                                   HHTT-EEEE..ESSS-S......SHHHHHHHHHHHHH CS
                  GFO_IDH_MocA  83 leagkhvll..EKPlat......tveeakelvelaek 111
                                   l++++h ++  E+Pl++       v++a++++e a++
  gi|91773573|ref|YP_566265.1| 293 LKNFVHCIQtrERPLSDgfigqrAVKMAEAVLESAKT 329
                                   6777777765588888777666667777777776654 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.2e-06    0.0065       3     102 ..       4     116 ..       2     123 .. 0.79
   2 ?   -1.2   0.0      0.93   2.8e+03      20      47 ..     245     272 ..     232     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.2e-06
                                   EEEET--....S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEE.......S----T....T--EEEE-S-HHHHGGGH CS
                 CoA_binding_2   3 iaVvGas....dnpgkfgykvlryllehglpvvpVnpkeeeilgek.......vyaslaedpepvdlvdvftppeatpeiv 72 
                                   iaV+G      +    ++  v++ + +h  +++ +n k+ + lg+         y+++ + + ++d+v+++tp+ +  +++
  gi|91773573|ref|YP_566265.1|   4 IAVIGTGywgkNHVRTYSELVAEGIIDHV-KICDINEKRAQELGKAfnieyltDYKDILS-DPDIDAVSIVTPSPTHFPLA 82 
                                   67787765555667789999999999998.*********777777777766768888885.589***************** PP

                                   HHHHHH--SEEEE-TT....---HHHHHHHHHTT CS
                 CoA_binding_2  73 kealalgakavwlqpg....sedeeaaelaeeag 102
                                   ke+ ++g  +++  p     +e e++ e+a++ g
  gi|91773573|ref|YP_566265.1|  83 KEFMEAGKDVLVEKPMtmdyTEAEKLTEIAKSTG 116
                                   ******9888888887666677777777777654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.93
                                   HHHHHHHT--EEEESSS-SEETTEES-- CS
                 CoA_binding_2  20 lryllehglpvvpVnpkeeeilgekvya 47 
                                   ++yl+ ++l+++ +   e+  +g+++y 
  gi|91773573|ref|YP_566265.1| 245 IDYLKPQELHIYDIRIEETDFDGKTAYS 272
                                   6788889999999999999999988775 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 ?    9.8   0.1   0.00018      0.54       3      40 ..       4      46 ..       2      78 .. 0.85
   2 ?    0.0   0.0      0.18   5.4e+02      26      53 ..     234     262 ..     225     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                                  EEEE--STTHHHHHHHHHHCT.....SEEEEE-S-HHHHHHHC CS
                UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeig.....hevigvDideekvdkln 40
                                  i+viG+GY G  +   ++e+       +v ++Di+e++ ++l 
  gi|91773573|ref|YP_566265.1|  4 IAVIGTGYWGKNHVRTYSELVaegiiDHVKICDINEKRAQELG 46
                                  99********9998888876544466789999***99988875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.18
                                   EEEE-S.-HHHHHHHCTTS-SS--TTHHH CS
                UDPG_MGDP_dh_N  26 vigvDi.deekvdklnsgkipiyepgLee 53 
                                   +++v    ++k+d l+ ++++iy+  +ee
  gi|91773573|ref|YP_566265.1| 234 LVVVGSeKAAKIDYLKPQELHIYDIRIEE 262
                                   44444404679***********9987766 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00024      0.72       2      64 ..       4      66 ..       3      94 .. 0.79
   2 ?   -1.3   0.0       1.2   3.5e+03      14      39 ..      81     102 ..      78     121 .. 0.57
   3 ?   -1.5   0.0       1.3   3.9e+03      25      45 ..     231     251 ..     225     265 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                                  EEEETTSHHHHHHHH...HHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SE CS
                 F420_oxidored  2 igiiGaGnmgealas...gllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadv 64
                                  i++iG+G  g+  ++    l+a+g    ++  +++ n+++a+el ++++++  + d+++ +++ d+
  gi|91773573|ref|YP_566265.1|  4 IAVIGTGYWGKNHVRtysELVAEG-IIDHVK-ICDINEKRAQELGKAFNIEYLT-DYKDILSDPDI 66
                                  89*********9876222677788.677777.6799****************99.99999997765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                   HHHHHHHTTS-GGCEEEEEESSCCCH CS
                 F420_oxidored  14 lasgllaagaqpheivvansrnpeka 39 
                                   la+ +++ag   ++++v  +++    
  gi|91773573|ref|YP_566265.1|  81 LAKEFMEAG---KDVLVE-KPMTMDY 102
                                   788899999...666632.3333322 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.3
                                   GGCEEEEEESSCCCHHHHHHH CS
                 F420_oxidored  25 pheivvansrnpekaeelaee 45 
                                   ++++vv++s +  k+++l+ +
  gi|91773573|ref|YP_566265.1| 231 QRDLVVVGSEKAAKIDYLKPQ 251
                                   455666669999999999843 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.47      37      59 ..     160     182 ..     135     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                   HCSTSHHHHTCHHHHHHHHHHHT CS
                GFO_IDH_MocA_C  37 kksgGvlgdlgiHdiDllqwLfG 59 
                                   +k+ Gv++ lgiH+ D+  +L+ 
  gi|91773573|ref|YP_566265.1| 160 RKDMGVVYALGIHEVDMFCYLLD 182
                                   6789**************99985 PP

>> Polysacc_deac_2  Divergent polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.011        33      25      57 ..      69     100 ..      54     107 .. 0.84
   2 ?    5.8   0.0    0.0023       6.9     166     205 ..     106     147 ..     102     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                                   EEEETTSTTHHHHHHHHHHCT-EEEEEEEE--T CS
               Polysacc_deac_2  25 lAilPyaphskelaeaaraaghevllhlPmepk 57 
                                   ++i+  +p    la++  +ag++vl++ Pm  +
  gi|91773573|ref|YP_566265.1|  69 VSIVTPSPTHFPLAKEFMEAGKDVLVEKPMT-M 100
                                   7888888999999*****************7.3 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0023
                                   HHHHHHHHCCSEEEEEEE-SCC..HHHHHHHHHHHHHHCTEE CS
               Polysacc_deac_2 166 kklaklakkkGsaiaighprpe..tieaLkewlpeleaegie 205
                                   +kl ++ak+ G+++++gh   +   ++ Lk+ ++  e  +i+
  gi|91773573|ref|YP_566265.1| 106 EKLTEIAKSTGQILMVGHIFRHhpAVKELKNRIDIGEFGNIR 147
                                   7999**************996644677788777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2074.33
//
Query:       gi|91773574|ref|YP_566266.1|  [L=290]
Description: UDP-glucose pyrophosphorylase [Methanococcoides burtonii DSM 6242]
Scores for 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-30  106.2   0.0      3e-30  105.6   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    3.8e-09   37.1   0.0    6.1e-09   36.4   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    9.2e-06   25.6   0.0    1.8e-05   24.6   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
     0.0052   16.5   0.0     0.0093   15.7   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.022   14.7   0.1      0.037   13.9   0.1    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 !  105.6   0.0   8.4e-34     3e-30       1     241 [.       5     263 ..       5     271 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 8.4e-34
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT......... CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg......... 72 
                                   kavI a G GtR+ P t++++k ++p+ +k ++i ++++++++sgi++ii+v+ + +   +e+++ e  +++         
  gi|91773574|ref|YP_566266.1|   5 KAVIPAAGLGTRFLPATKSMPKEMLPIIDK-PVIHYVVEEAIASGIDDIIFVTGRSK-RAIEDYFDESPELQmhlkehhkd 83 
                                   799***************************.*****************888888555.56899999999988999999999 PP

                                   ............SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST..THHHHHHHHHTHSSTTSEEEEE CS
               NTP_transferase  73 ............vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikd..ayeeavkkaiekaakgtvtfgi 139
                                               v++ ++ ++e++g+ dA++ a++ +  +     ++ Lg+D++++d    +++++ +++++   t+++  
  gi|91773574|ref|YP_566266.1|  84 sllkmvedissmVDIHYIRQKEPRGLGDAIMTAKKHISGDPF---AVLLGDDIIVNDvpCTKQLIEVFQKYRC-STIAVEE 160
                                   9*************************************9996...999*********9777778888877776.6****** PP

                                   EESS-CTTSEEEEEC...TTS.BEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTT CS
               NTP_transferase 140 vpveeateyGviead...eeg.rverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleeg 215
                                   vp+e+ ++yG+i  +   ++    e+++EKP+ ++a s++ + G Yvf++e+++ + k  +    ge ++td ++ + e+ 
  gi|91773574|ref|YP_566266.1| 161 VPREKVSSYGIISGKpidDSLcILEDIIEKPSVEEApSNIGAIGRYVFTPEIFDCINK-TSTGVGGEIQLTDGIRLLNEQ- 239
                                   ************9887745557899********999899*****************65.88888999*******988666. PP

                                   EEEEEECSTTEE-EEEXSSHHHHHHH CS
               NTP_transferase 216 kvalaflfkdaeyWsDvGtldsllea 241
                                   ++ +a+ f +++   D+G+   +++a
  gi|91773574|ref|YP_566266.1| 240 QKVYAYRFAGQR--YDTGDKLGYVKA 263
                                   566678999976..899987666665 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 !   36.4   0.0   1.7e-12   6.1e-09       1     122 [.       6     159 ..       6     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.7e-12
                                   EEEEEESS-TTT....TT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHH..................... CS
                  NTP_transf_3   1 aviLAGGrSsRm....gg.dKallplggkpllervldalraagvdevvvvggd..eevla..................... 53 
                                   avi A+G ++R+    ++ +K +lp+ +kp++++v++ + a+g+d+++ v+g+  +++++                     
  gi|91773574|ref|YP_566266.1|   6 AVIPAAGLGTRFlpatKSmPKEMLPIIDKPVIHYVVEEAIASGIDDIIFVTGRskRAIEDyfdespelqmhlkehhkdsll 86 
                                   7899********7765448*******************************9995445666666666666666666666555 PP

                                   .....HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT.-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                  NTP_transf_3  54 .....alarlgvrvvededpgkgplaslaaalraaadadavlvlacD.mPlltpelverllaaaaasgadvvvpt 122
                                             +++++++++  +g + ++ +a +++ + d+++vl++D ++  +    ++l++ +++ ++++++++
  gi|91773574|ref|YP_566266.1|  87 kmvedISSMVDIHYIRQKE-PRGLGDAIMTAKKHI-SGDPFAVLLGDdIIVNDVPCTKQLIEVFQKYRCSTIAVE 159
                                   5444333344899999986.59************9.799999999985777788889999999998888877665 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     5e-09   1.8e-05      39     111 ..      82     155 ..      78     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5e-09
                                   SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS.EEEEEESSEEE-TT.HHHHHHHHHHH.TTCE CS
               Glycos_transf_2  39 tDetveileelakedprvrvirreenvGkagalnaglraatgd.yilflDaDdepdpd.wleklvealekdgadv 111
                                   +D++ +++e+++ +  ++++ir++e +G++ a++++ ++ +gd + ++l +D ++++  + ++l+e ++k + + 
  gi|91773574|ref|YP_566266.1|  82 KDSLLKMVEDIS-SMVDIHYIRQKEPRGLGDAIMTAKKHISGDpFAVLLGDDIIVNDVpCTKQLIEVFQKYRCST 155
                                   688999999997.599****************************9999****99999899999***999977654 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-06    0.0093       3      52 ..       6      57 ..       4      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                                  EEEECTTSSCT...T-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE- CS
                          IspD  3 vvipAAGsGkR...mkaglpKqflelkgqtllehtvdallaskavdkivvvvs 52
                                  +vipAAG G+R   + + +pK  l + ++++++  v+ + as+ +d i+ v  
  gi|91773574|ref|YP_566266.1|  6 AVIPAAGLGTRflpATKSMPKEMLPIIDKPVIHYVVEEAIASG-IDDIIFVTG 57
                                  89*********44447899******************999955.666665544 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     1e-05     0.037      16      51 ..      26      61 ..      24     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                                  GGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HH CS
                  CTP_transf_3 16 KnlldlggkpliayvleaalkskafekvivaTDsee 51
                                  K +l++ +kp i+yv+e+a+ s+  + ++v   s++
  gi|91773574|ref|YP_566266.1| 26 KEMLPIIDKPVIHYVVEEAIASGIDDIIFVTGRSKR 61
                                  899********************9777888765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1829.80
//
Query:       gi|91773575|ref|YP_566267.1|  [L=456]
Description: mannose-1-phosphate guanylyltransferase (GDP) [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-57  193.0   0.6      4e-57  192.3   0.6    1.3  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    5.4e-44  150.6   0.0    2.6e-43  148.4   0.0    1.9  1  NTP_transferase  Nucleotidyl transferase
    6.8e-10   38.5   0.2    1.8e-09   37.2   0.2    1.8  1  Cupin_2          Cupin domain
  ------ inclusion threshold ------
      0.056   13.4   0.3        0.1   12.5   0.3    1.4  1  AraC_binding     AraC-like ligand binding domain


Domain annotation for each model (and alignments):
>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.3   0.6     9e-61     4e-57       3     151 .]     293     441 ..     291     441 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.3 bits;  conditional E-value: 9e-61
               MannoseP_isomer   3 vedlvvvetkdavlvadkdkvqdvkkvveelkaegreeaelhrevyrPWGsyevldegeryqvkritvkPgeklslqkhhh 83 
                                   ++d+vvv+t da+lv  +++ q+vk+vv++l+ eg+e+ +lh++vyrPWG+y+ l+++er+++k+itv P++kls q hhh
  gi|91773575|ref|YP_566267.1| 293 INDMVVVDTPDALLVCPRKSSQKVKDVVNSLSVEGDERISLHQTVYRPWGTYTILESTERHKIKNITVMPQKKLSYQLHHH 373
                                   79******************************************************************************* PP

               MannoseP_isomer  84 raehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylgeddivrled 151
                                   r+ehWvvv+G+a v+++ + + l++ est+i+ g  hrl npGk+ple+ievq G+ ++eddivr++d
  gi|91773575|ref|YP_566267.1| 374 RSEHWVVVEGIACVQIEGKHFYLRQGESTFIRPGDKHRLLNPGKLPLEIIEVQLGESVDEDDIVRFDD 441
                                   ******************************************************************98 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.0   5.9e-47   2.6e-43      13     245 ..       1     259 [.       1     262 [. 0.90

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 5.9e-47
                                   GTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHH CS
               NTP_transferase  13 LwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAval 92 
                                   +wPL+r+ ++k++++lgk++l+q t+ r+++ s++ +i vv+++ ++f v  q+ke       +++++ep gk+t +A+  
  gi|91773575|ref|YP_566267.1|   1 MWPLSREYYPKQFLKLGKSSLFQDTFLRCLKlSECSDIFVVTNETQKFFVLGQIKELGYDLPVENVLIEPVGKNTLPAIFF 81 
                                   6*****************************99***********************986444578999************** PP

                                   THHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTS....BEEEEECS-SSH CS
               NTP_transferase  93 aaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeeg....rverfvEKPkea 169
                                   +   +++++ + +v ++++Dh+ + + +e++++a + a++++vtfg+vp +++t+yG+i ++++     +v +f+EKP+++
  gi|91773575|ref|YP_566267.1|  82 GMHEINERFGKSIVGIFSSDHVLDADSMETIADASNLASDYLVTFGVVPSSPHTGYGYIHPGNDIgfgnEVLEFKEKPDGE 162
                                   ***************************************9**********************5444667************ PP

                                   SHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE...................... CS
               NTP_transferase 170 kaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalaflfkdae...................... 227
                                    a+ ++++G Y++ns+++lf  + + ee ++ e+++ d++       ++ +++     +                      
  gi|91773575|ref|YP_566267.1| 163 IAKMYVKQG-YLWNSGMFLFDTDiFFEEVRKYEPSMFDAFCGDEGVIRNIVSIYS---Slpsisidygimersnkvavvkl 239
                                   ********9.************************999987543333333333333...2344778999************* PP

                                   ..-EEEXSSHHHHHHHHHHH CS
               NTP_transferase 228 ..yWsDvGtldslleanekl 245
                                     +WsD+G++d+++  ++k+
  gi|91773575|ref|YP_566267.1| 240 ehKWSDLGNFDAIYGESDKD 259
                                   *************9988876 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.2     4e-13   1.8e-09       4      70 ..     359     425 ..     356     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 4e-13
                                   EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2   4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                   ++ p+ +     H++  e  +V+eG + ++++g+ + l++G+s ++ +g  Hr+ N+g+ p++++ v
  gi|91773575|ref|YP_566267.1| 359 TVMPQKKLSYQLHHHRSEHWVVVEGIACVQIEGKHFYLRQGESTFIRPGDKHRLLNPGKLPLEIIEV 425
                                   566666666666555559*****************************************9***9876 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   2.2e-05       0.1      15      61 ..     367     412 ..     363     429 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                                   SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEE CS
                  AraC_binding  15 sfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdy 61 
                                   s++ h+h   +++ v+eG + ++++g+++ l++G+  +++pg+ H++
  gi|91773575|ref|YP_566267.1| 367 SYQLHHHRSEHWV-VVEGIACVQIEGKHFYLRQGESTFIRPGDKHRL 412
                                   6777888888875.668****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2829.98
//
Query:       gi|91773576|ref|YP_566268.1|  [L=320]
Description: hypothetical protein Mbur_1614 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-60  204.7  26.1    2.6e-60  204.5  26.1    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
      0.065   13.0   6.8       0.84    9.5   0.1    2.9  3  TMEM132D_C       Mature oligodendrocyte transmembrane protein


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 !  204.5  26.1   2.9e-64   2.6e-60       2     301 .]      18     310 ..      17     310 .. 0.99

  Alignments for each domain:
  == domain 1  score: 204.5 bits;  conditional E-value: 2.9e-64
               LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnn 82 
                                   ++++++s ++l++ll+ vd++ ++++ r+++ +++ la++++  s+l+r+lrW+ llr+l+ +is++ +  ++++++f+n+
  gi|91773576|ref|YP_566268.1|  18 IISFLVSFSILFFLLKYVDIEGVIEVSRNANIGIFCLAIIVHYASFLVRGLRWQNLLRGLNIKISIGVSSEMVFLSWFANS 98 
                                   799****************************************************************************** PP

               LPG_synthase_TM  83 vtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllavlalll 163
                                   ++P+++ G+v+r ++lk ++g + s + +++vverl+d+l l+ll+ ++ l ++   +++  ++  + +++lll+v+al l
  gi|91773576|ref|YP_566268.1|  99 IVPAKI-GDVYRSHMLKMYNGTPISVSIGTLVVERLFDILLLMLLLTITGLTVFKDKMPEE-IMQSIEIGYLLLGVIALCL 177
                                   ******.***************************************************998.******************* PP

               LPG_synthase_TM 164 llllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylllralgvdvslalllli 244
                                   ++++  r++  + + +r++ + + + ++l s     +l++p +l+ +  ++++ w +e +++ ++ r+lg+++sla+++++
  gi|91773576|ref|YP_566268.1| 178 VFFYVLRHHIGRIIPERFMIHYSNLHDGLYS-----SLSNPATLVSVAVFTIFSWTFESARFLFVTRSLGIELSLAAIIFV 253
                                   *****************************97.....699****************************************** PP

               LPG_synthase_TM 245 llaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                   +la++l++a+p++P+GlG++E++ +++l+ lGv+++ a+++all+rli+++ +l+ G
  gi|91773576|ref|YP_566268.1| 254 VLASSLLTAIPLTPAGLGAVEVSIVFILGILGVDPTVAASVALLDRLISYWSILVSG 310
                                   ****************************************************99987 PP

>> TMEM132D_C  Mature oligodendrocyte transmembrane protein, TMEM132D, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2      0.92   8.2e+03      43      54 ..      24      35 ..      19      36 .. 0.79
   2 ?    9.5   0.1   9.4e-05      0.84      32      58 ..      42      68 ..      39      96 .. 0.76
   3 ?    6.7   0.1    0.0007       6.2      26      51 ..     158     182 ..     152     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.92
                    TMEM132D_C 43 ClAilvflincv 54
                                  ++ il fl++ v
  gi|91773576|ref|YP_566268.1| 24 SFSILFFLLKYV 35
                                  688999998865 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.4e-05
                    TMEM132D_C 32 EiGmYaLlgvfClAilvflincvvyal 58
                                  E+   a +g+fClAi+v   +  v  l
  gi|91773576|ref|YP_566268.1| 42 EVSRNANIGIFCLAIIVHYASFLVRGL 68
                                  66666789*******997666665555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0007
                    TMEM132D_C  26 raltdLEiGmYaLlgvfClAilvfli 51 
                                   + + ++EiG Y Llgv  l ++ f +
  gi|91773576|ref|YP_566268.1| 158 EIMQSIEIG-YLLLGVIALCLVFFYV 182
                                   5799*****.********99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1946.52
//
Query:       gi|91773577|ref|YP_566269.1|  [L=359]
Description: dolichyl-phosphate beta-D-mannosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-36  123.8   0.4    9.2e-36  123.2   0.4    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      2e-22   79.6  15.8    3.7e-22   78.7  15.8    1.5  1  GtrA             GtrA-like protein
    3.9e-10   40.0   0.0    5.6e-10   39.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0022   17.6   1.1     0.0026   17.3   0.1    1.6  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.056   12.9   0.0       0.12   11.8   0.0    1.5  1  Glyco_transf_21  Glycosyl transferase family 21
      0.094   13.2   0.0       0.21   12.1   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.31   10.6   1.7       0.68    9.4   0.5    2.1  3  DUF166           Domain of unknown function


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 !  123.2   0.4   3.6e-39   9.2e-36       1     168 [.       4     169 ..       4     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 3.6e-39
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   s+++p++Ne ++++  ++ l +  ++ d+eiivvDD+S+D+t++++e+ ++ed rv+virr  ++G+++a+ +g+ aatg+
  gi|91773577|ref|YP_566269.1|   4 SIIVPSFNERENIPVIVDKLQNVLKDIDYEIIVVDDNSPDKTWDLVEQMSHEDSRVKVIRRIGRNGLSSAVIEGFLAATGE 84 
                                   8******************************************************************************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEE CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallr 162
                                   y+ ++DaD+++dp  l ++++++e+++ d+v+++r+   ++   ++r++   + + + +k  +  +k+++++  +++++l+
  gi|91773577|ref|YP_566269.1|  85 YLGVIDADLQHDPVLLTEMLNEIENNDLDIVIASRYTETKDVEGWSRTRL--FISDVATKLAQLVIKYKVTDPMSGYFVLK 163
                                   *************************************************9..8**************************** PP

                                   EHHHHH CS
               Glycos_transf_2 163 realee 168
                                   +++++e
  gi|91773577|ref|YP_566269.1| 164 KSVVQE 169
                                   **9976 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7  15.8   1.5e-25   3.7e-22       1     117 []     238     354 ..     238     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.5e-25
                          GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl..lkqflkFvlvsllglllnl 79 
                                   +++ivG +g+l+++ +l+l+++++g +y ++ aia++vailfn+i n++wtFkd + +++  +  +lk+ l++++g+l+n+
  gi|91773577|ref|YP_566269.1| 238 KYMIVGSFGALLHFSILTLFYKNIGYTYSISLAIAILVAILFNYIYNNIWTFKDYRLTDIslITGYLKYNLLCFVGALANY 318
                                   79*******************************************************99999******************* PP

                          GtrA  80 lilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                    ++++l++++++  ++a++vg +v++ +ny++++++++
  gi|91773577|ref|YP_566269.1| 319 SVSMYLIDHMSW--IIASMVGAFVGANWNYLTNSIYTW 354
                                   *********887..89********************98 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   2.2e-13   5.6e-10       4     127 ..       3     122 ..       2     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.2e-13
               Glyco_tranf_2_3   4 lavlVptfneed...vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                   ++++Vp+fne +   v+++ l ++l+   +++e++vv+d+s ++t + +e++   ++d rv+v+   r+ g++g s a+ e
  gi|91773577|ref|YP_566269.1|   3 FSIIVPSFNEREnipVIVDKLQNVLK--DIDYEIIVVDDNSPDKTWDLVEQM--SHEDSRVKVI---RRIGRNGLSSAVIE 76 
                                   89**********55555555555555..69********************97..99999****9...667889999***** PP

               Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll 127
                                   ++ a++++++ ++D+D   +P +l  +l+ ++  + ++v ++++++
  gi|91773577|ref|YP_566269.1|  77 GFLAATGEYLGVIDADLQHDPVLLTEMLNEIENNDLDIVIASRYTE 122
                                   *********************9999988888777777776666655 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 !   17.3   0.1     1e-06    0.0026       1     108 [.       4     109 ..       4     125 .. 0.76
   2 ?   -3.3   0.1       1.9   4.8e+03     125     170 ..     278     325 ..     230     331 .. 0.47

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-06
               Glyco_tranf_2_2   1 svviplras.eerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrGask 79 
                                   s+++p  ++ e+ + i +++ +  k  d + e+ivvdd S++k+ + v+++ +   +v  ++       +l+ a   G+  
  gi|91773577|ref|YP_566269.1|   4 SIIVPSFNErENIPVIVDKLQNVLK--DIDYEIIVVDDNSPDKTWDLVEQMSHEDSRVkVIRRI--GRNGLSSAVIEGFLA 80 
                                   5677755540555788888766655..67899*****************999999888443444..35677777889**** PP

               Glyco_tranf_2_2  80 aesdlvlFlDaDcfissDkfekilkliti 108
                                   a ++++  +DaD    +  +  +l+ i+ 
  gi|91773577|ref|YP_566269.1|  81 ATGEYLGVIDADLQHDPVLLTEMLNEIEN 109
                                   ************98888888888775554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
               Glyco_tranf_2_2 125 dlnkedsevlkdvedltassrvledllaaks..tlvkffapss.ssili 170
                                    +n   +++    ++  +++ +    l  ++   +v  +a++s s  li
  gi|91773577|ref|YP_566269.1| 278 LFNYIYNNIWTFKDYRLTDISLITGYLK-YNllCFVGALANYSvSMYLI 325
                                   3344445555555555555555544444.44112344666666555555 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.12      21      77 ..      73     130 ..      54     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
               Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaa 77 
                                   +++ ++ aa  ++l + D+d   +p  L+e+l+++e ++  +V +  ++  ++   ++
  gi|91773577|ref|YP_566269.1|  73 AVIEGFLAATGEYLGVIDADLQHDPVLLTEMLNEIENNDLDIVIASRYTETKDvEGWS 130
                                   6788899999*********************************998875444323343 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05      0.21      17      81 ..      30      92 ..      11      93 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
               Glyco_tranf_2_4 17 lgfdrilvydndstDgtrailkel..pevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                  +++ +i+v+d++s D+t+++++++  ++ ++  ++  + +     ++++ +l  +a ++++ v+DaD
  gi|91773577|ref|YP_566269.1| 30 IDY-EIIVVDDNSPDKTWDLVEQMshEDSRVKVIRR-IGRNGLSSAVIEGFL--AATGEYLGVIDAD 92
                                  333.4****************995213333444443.333445555555555..3468888888888 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5   0.00027      0.68      26      84 ..       5      62 ..       1      85 [. 0.79
   2 ?   -1.0   0.0       0.4     1e+03      64      88 ..      97     121 ..      70     156 .. 0.73
   3 ?   -1.9   0.0       0.8     2e+03     172     205 ..     136     169 ..     132     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00027
                        DUF166 26 livavvevpeeldefiedpeelLpelkeaDiviaytlhpDlllelaekakekkvkaliv 84
                                  +iv  ++  e+++  +++ +++L+   ++ i++  +  pD + +l+e++++++ ++ ++
  gi|91773577|ref|YP_566269.1|  5 IIVPSFNERENIPVIVDKLQNVLK-DIDYEIIVVDDNSPDKTWDLVEQMSHEDSRVKVI 62
                                  4566666677*************9.6799999999**************9876666555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.4
                        DUF166  64 pDlllelaekakekkvkalivpaea 88 
                                   p ll e+++++++++ +++i +  +
  gi|91773577|ref|YP_566269.1|  97 PVLLTEMLNEIENNDLDIVIASRYT 121
                                   4477788888887777777766544 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.8
                        DUF166 172 veeaeekageahqsYpClAsmerdfelketklhk 205
                                   ++++ +k ++ + +Y  +++m   f lk++ +++
  gi|91773577|ref|YP_566269.1| 136 ISDVATKLAQLVIKYKVTDPMSGYFVLKKSVVQE 169
                                   6788999999999999999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2307.25
//
Query:       gi|91773578|ref|YP_566270.1|  [L=238]
Description: hypothetical protein Mbur_1616 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   64.0   0.0    2.6e-17   63.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.4e-14   54.5   0.0    3.6e-14   53.2   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    6.8e-10   39.0   0.0    8.6e-10   38.7   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.3e-08   34.8   0.0    1.9e-08   34.2   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    6.1e-08   33.3   0.1    3.7e-07   30.8   0.0    2.1  2  Methyltransf_12  Methyltransferase domain
      1e-06   28.2   0.0    1.9e-06   27.4   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.2e-05   22.4   0.0    9.1e-05   21.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00082   19.3   0.0     0.0011   18.9   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
     0.0036   16.9   0.0     0.0075   15.9   0.0    1.5  1  MetW             Methionine biosynthesis protein MetW
     0.0055   15.3   0.0     0.0061   15.2   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
  ------ inclusion threshold ------
      0.054   14.1   0.2       0.46   11.1   0.0    2.5  2  Bin3             Bicoid-interacting protein 3 (Bin3)
        0.1   11.9   0.0        5.8    6.2   0.0    2.1  2  Methyltransf_2   O-methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   1.8e-20   2.6e-17       1      96 []      49     142 ..      49     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.8e-20
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edpek 79 
                                   L+++c +G l + +   g  v+g+D+s ++l +a +++s+ ++   ++++da +lp++++sfD+v++se+++h+  +  + 
  gi|91773578|ref|YP_566270.1|  49 LNIACSAGTLDALID--GDLVTGLDFSFKQLVYADQNNSTGNN--HYICGDACRLPLKSESFDMVIASEFIEHIdeHSISL 125
                                   678888888777777..888**************999999985..69***************************99899** PP

                                   HHHHHHHHEEEEEEEEE CS
               Methyltransf_11  80 alkeiaRvLkpgGllvi 96 
                                   +l+e++RvL+pgG l++
  gi|91773578|ref|YP_566270.1| 126 FLDEVYRVLEPGGELIL 142
                                   *************9985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   2.4e-17   3.6e-14       1      97 []      48     138 ..      48     138 .. 0.91
   2 ?   -2.7   0.0       6.6   9.9e+03      33      58 ..     170     182 ..     158     197 .. 0.52

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.4e-17
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   +L ++c  G+l + +        vtg+D+s ++l +a ++++    n ++++gda +lp++++sfD+v++s  ++h++++ 
  gi|91773578|ref|YP_566270.1|  48 ILNIACSAGTLDALIDG----DLVTGLDFSFKQLVYADQNNS--TGNNHYICGDACRLPLKSESFDMVIASEFIEHIDEHS 122
                                   89999999977666653....67******************4..3499**********************866******** PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                   +  +l+e++rvL+pgG
  gi|91773578|ref|YP_566270.1| 123 ISLFLDEVYRVLEPGG 138
                                   ***************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.6
                                   HHHHHHHHHHHTTTTEEEEESBCCGB CS
               Methyltransf_25  33 mleaareraeeeglnvefvqgdaedl 58 
                                    + + +             + ++ dl
  gi|91773578|ref|YP_566270.1| 170 HISKFN-------------KRKLYDL 182
                                   443333.............3333344 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   5.8e-13   8.6e-10      20     163 ..      42     192 ..      21     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 5.8e-13
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg.................kf 83 
                                      ++++L i+c  G+l  ++   g  vtg D s+++   a  ++++              g                 +f
  gi|91773578|ref|YP_566270.1|  42 IHNQKKILNIACSAGTLDALI--DGDLVTGLDFSFKQLVYA--DQNNST------------GnnhyicgdacrlplkseSF 106
                                   455667777777777655555..444677777777533332..111111............122333333333333334** PP

               Methyltransf_23  84 dlIvlrevlehvp..dppellrqiatllkpgGylllseplasl..kedrllldwlylvpag.rhisffsarslkelleeaG 159
                                   d ++++e++eh++  +    l+ +++ l+pgG l+l++p+ s+  + ++ ll+ +  v+ + +his f+ r l +l e++G
  gi|91773578|ref|YP_566270.1| 107 DMVIASEFIEHIDehSISLFLDEVYRVLEPGGELILTTPNYSSlwPLLETLLNKAGNVDYSdQHISKFNKRKLYDLIEKNG 187
                                   *************6457789*******************99985545566666666666657*****************99 PP

               Methyltransf_23 160 .levv 163
                                    +++v
  gi|91773578|ref|YP_566270.1| 188 kFNIV 192
                                   66666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.3e-11   1.9e-08       2     119 ..      43     158 ..      42     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.3e-11
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                   ++ +++l ++C +G+l   +         v+G+D+s + + +A +n   +   n +   gd+  l+  l+ e+fD++++ e
  gi|91773578|ref|YP_566270.1|  43 HNQKKILNIACSAGTLDALIDGD-----LVTGLDFSFKQLVYADQN---NSTGNNHYICGDACRLP--LKSESFDMVIASE 113
                                   66789999999999987776643.....39***************6...66779999*********..999********** PP

               Methyltransf_31  83 vl..naladpdkileeiervlkpggilliedpr......llaelp 119
                                   ++   +  +   +l e+ rvl+pgg+l++++p+      ll+ l+
  gi|91773578|ref|YP_566270.1| 114 FIehIDEHSISLFLDEVYRVLEPGGELILTTPNysslwpLLETLL 158
                                   **6666666778999******************554444222222 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.5e-10   3.7e-07      21      99 .]      65     140 ..      49     140 .. 0.68
   2 ?   -0.2   0.0       1.2   1.8e+03      26      50 ..     164     189 ..     153     202 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.5e-10
               Methyltransf_12  21 ieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhl..kdirevldnirklLkpgGr 98 
                                     +tg+D+s +++   + + ++ +n     +++   d+  l+ + +sfD+v+as++++h+    i  +ld+++++L pgG 
  gi|91773578|ref|YP_566270.1|  65 DLVTGLDFSFKQL-VYADQNNSTGN-----NHYICGDACRLPLKsESFDMVIASEFIEHIdeHSISLFLDEVYRVLEPGGE 139
                                   3466999999999.44444444443.....3344444443433446**************999999**************7 PP

               Methyltransf_12  99 l 99 
                                   l
  gi|91773578|ref|YP_566270.1| 140 L 140
                                   6 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
               Methyltransf_12  26 vDispsai.edakeklakrennnnnn 50 
                                   vD+s + i +  k+kl + +++n ++
  gi|91773578|ref|YP_566270.1| 164 VDYSDQHIsKFNKRKLYDLIEKNGKF 189
                                   67777777555666666666555544 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.2e-09   1.9e-06      34     150 ..      29     141 ..      18     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.2e-09
                                   HHHH.HHHHH--S.--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TT CS
               Ubie_methyltran  34 lWkk.fveklvav.krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpf 112
                                   +W++ + ++++ + ++ +k+l++a+ +g l + +     +   v++lD++ + L  + +    +++ n ++++++a +Lp 
  gi|91773578|ref|YP_566270.1|  29 KWHHlKFKRITDKiHNQKKILNIACSAGTLDALI-----DGDLVTGLDFSFKQLVYADQN---NSTGNNHYICGDACRLPL 101
                                   55553333332220334589*****999765444.....4456999********999875...4555779*********** PP

                                   S-T-EEEEEEES-GGG-S-HHHH..HHHHHHHEEEEEEEE CS
               Ubie_methyltran 113 eddsfDvvtvsfGlrnvtDklka..LkeayrvlkpGGrlv 150
                                   + +sfD+v  s  +  + +++ +  L e+yrvl pGG+l+
  gi|91773578|ref|YP_566270.1| 102 KSESFDMVIASEFIEHIDEHSISlfLDEVYRVLEPGGELI 141
                                   ***********9999998876542279**********986 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    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      30     166 ..      10     144 ..       2     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.1e-08
                                   --S----SSTT--HHHHHHH....HHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHH CS
                          CMAS  30 tYsCAyferddmtLeeAqla....KldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvd 106
                                     sC y++++ ++ +  q++    K+++i +k++  + +++L+i c  G+l   a    +  v gl +S +q  +a ++ +
  gi|91773578|ref|YP_566270.1|  10 LISCGYYDEAYKNEKGLQSKwhhlKFKRITDKIH--NQKKILNIACSAGTLD--ALID-GDLVTGLDFSFKQLVYADQN-N 84 
                                   569***9996555444444411127777777765..5579*******99874..4445.5689**********999886.6 PP

                                   TS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEE CS
                          CMAS 107 eldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGllllht 166
                                   ++++++    + +     +e +d v++ + +eh+ +++   f ++++++l+++G l+l t
  gi|91773578|ref|YP_566270.1|  85 STGNNHYICGDACRLPLKSESFDMVIASEFIEHIDEHSISLFLDEVYRVLEPGGELILTT 144
                                   67778888888898888899***********************************99876 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.3e-07    0.0011     104     188 ..      87     176 ..       6     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.3e-07
                                   SSTTEEES-TTS-S--TT-EEEEE...EES---SS-HHHHHHHHHHHEEEEEEEEEE..EEGGG-S-HHHHHHHHHCTTEE CS
                Methyltransf_8 104 vnervvacdlakvPledesvdvav...fclslmgtnladflkeanrvlkvGGllkva..evksrfesvklfaraltklGfe 179
                                    n++ +  d  ++Pl+ es d+++   f   +    +  fl e++rvl +GG l ++  + +s  +  ++++++  ++ + 
  gi|91773578|ref|YP_566270.1|  87 GNNHYICGDACRLPLKSESFDMVIaseFIEHIDEHSISLFLDEVYRVLEPGGELILTtpNYSSLWPLLETLLNKAGNVDYS 167
                                   4677888899*************9333334555677999*************88765225677777888888888888887 PP

                                   EEEEE--ST CS
                Methyltransf_8 180 vkskdlsnk 188
                                    +++   nk
  gi|91773578|ref|YP_566270.1| 168 DQHISKFNK 176
                                   777777666 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     5e-06    0.0075       4     122 ..      35     158 ..      32     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                          MetW   4 feliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlen..fedksfdyvvls 82 
                                   f+ i++ i+++ ++l++ c  G+l  l+ +       Gl+ + + ++ + +   +  +  +  d      +++sfd+v+ s
  gi|91773578|ref|YP_566270.1|  35 FKRITDKIHNQKKILNIACSAGTLDALI-DGDL--VTGLDFSFKQLVYADQNNSTGNNHYICGDACRlpLKSESFDMVIAS 112
                                   7899999****************98888.4344..46788888888877777666666655555443116799******** PP

                          MetW  83 qtlqat..rnpkevldellri...grraivsfPnfG.hWrvrlsll 122
                                     +  +  +  +  lde+ r+   g + i++ Pn+   W +  +ll
  gi|91773578|ref|YP_566270.1| 113 EFIEHIdeHSISLFLDEVYRVlepGGELILTTPNYSsLWPLLETLL 158
                                   ***998335567899*****9777789*******963577665555 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.1e-06    0.0061     173     257 ..      97     191 ..      37     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.1e-06
               Methyltransf_29 173 krlpyPsrsfdlihCsrCridwteed.gilllevdRvlRpgGyfvlsappvy..........erkeeelkeeqkeleeltk 242
                                    rlp  s+sfd++  s    + +e+  +++l ev Rvl pgG ++l++p+            + k  +   + ++++++ k
  gi|91773578|ref|YP_566270.1|  97 CRLPLKSESFDMVIASEFIEHIDEHSiSLFLDEVYRVLEPGGELILTTPNYSslwplletllN-KAGNVDYSDQHISKFNK 176
                                   59************999766666555245677**************99987788888887743.44466667778888888 PP

               Methyltransf_29 243 slCwklvakkkdvai 257
                                   +  ++l++k+++  i
  gi|91773578|ref|YP_566270.1| 177 RKLYDLIEKNGKFNI 191
                                   888888888877665 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.7   4.1e+03      61      68 ..      28      35 ..      15      56 .. 0.51
   2 ?   11.1   0.0   0.00031      0.46      20      48 ..     121     149 ..     106     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                          Bin3 61 enykelkl 68
                                  ++ ++lk+
  gi|91773578|ref|YP_566270.1| 28 SKWHHLKF 35
                                  33333322 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00031
                          Bin3  20 eglkrlfkkiyellkpgGvlilEpqewks 48 
                                   + +  +++++y++l+pgG lil   +++s
  gi|91773578|ref|YP_566270.1| 121 HSISLFLDEVYRVLEPGGELILTTPNYSS 149
                                   4578899***************8766655 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0039       5.8     128     165 ..     106     143 ..      75     149 .. 0.76
   2 ?    3.6   0.0     0.023        35     139     167 ..     165     194 ..     156     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0039
                                   -SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEE CS
                Methyltransf_2 128 aDaillkrvlhDwsdekcvklLkrvkkalpagGkvivv 165
                                    D+++ +  +   ++++++ +L++v++ l +gG++i+ 
  gi|91773578|ref|YP_566270.1| 106 FDMVIASEFIEHIDEHSISLFLDEVYRVLEPGGELILT 143
                                   467777777777777788999**************985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.023
                                   GS-HHHHHHHHHH.HHHH--TT-EEEEEE- CS
                Methyltransf_2 139 DwsdekcvklLkr.vkkalpagGkvivvea 167
                                   D+sd++++k+ kr +++ + ++Gk  +vea
  gi|91773578|ref|YP_566270.1| 165 DYSDQHISKFNKRkLYDLIEKNGKFNIVEA 194
                                   9*********98649************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1645.61
//
Query:       gi|91773579|ref|YP_566271.1|  [L=531]
Description: hypothetical protein Mbur_1617 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-25   89.4  15.3    2.8e-25   89.4  15.3    2.9  3  PMT_2        Dolichyl-phosphate-mannose-protein mannosyltrans
     0.0016   18.4   9.1     0.0016   18.4   9.1    2.2  2  DUF2723      Protein of unknown function (DUF2723)
  ------ inclusion threshold ------
      0.025   14.5   0.1       0.14   12.0   0.0    2.4  2  UPF0139      Uncharacterised protein family (UPF0139)
       0.37   11.1   0.1       0.37   11.1   0.1    4.4  5  Sigma_reg_N  Sigma factor regulator N-terminal
        0.5   10.5  11.4         10    6.4   0.0    3.7  3  Pox_A14      Poxvirus virion envelope protein A14
        5.9    7.4  16.9       0.69   10.4   4.6    3.0  3  MerC         MerC mercury resistance protein


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 !   89.4  15.3   9.4e-29   2.8e-25       2     159 .]      90     254 ..      89     254 .. 0.91
   2 ?   -1.6   3.2      0.91   2.7e+03      31     102 ..     294     324 ..     272     361 .. 0.44
   3 ?   -1.9   0.1       1.2   3.5e+03      50      64 ..     392     406 ..     386     417 .. 0.62

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 9.4e-29
                         PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllw 82 
                                   hPPl++ +l++++++  +se+a+rl+sa++g+l+i l+yl+ ++l++k++a++a++ll+v+++ +++s++++ +a+++ll+
  gi|91773579|ref|YP_566271.1|  90 HPPLYYSILHFVMMV-SQSEFALRLPSAIFGSLSIPLIYLVGKELLDKKTAIIASFLLSVSTFHINYSQEGRSYALMMLLV 169
                                   9**************.89*************************************************************** PP

                         PMT_2  83 alalylllraleknklkywllagvlfGlgflsKytaallliaallyllis.......arrilkekkpylalllalllfs.p 155
                                   +l++yl++ a  k+++ +w ++++++ + ++++++ ++++ a+ ly li+       + r + e+k+ l+++la++++s p
  gi|91773579|ref|YP_566271.1| 170 LLTIYLFINAYNKKSTLHWTITAISASVLVYTHFFGFFVIAAMGLYYLINefdikilKFRSFEESKIALIGTLAFIVMSlP 250
                                   ******************************************888666655877674444888899999888877776526 PP

                         PMT_2 156 vliw 159
                                   +++w
  gi|91773579|ref|YP_566271.1| 251 MIVW 254
                                   6666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.91
                         PMT_2  31 agvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkyw....l 102
                                    ++l i+++ + +++ f k+  ll++                                            w    l
  gi|91773579|ref|YP_566271.1| 294 YAILLIIGILFCMKD-FRKSLTLLSI--------------------------------------------WlflpL 324
                                   222222222222222.2222222222............................................112222 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                         PMT_2  50 raallaalllavvpl 64 
                                   ++a++a++ll v+ +
  gi|91773579|ref|YP_566271.1| 392 EIAVIAVILLVVCSI 406
                                   556666666666543 PP

>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   9.1   5.5e-07    0.0016      21     165 ..      92     221 ..      86     224 .. 0.86
   2 ?   -2.2   0.7       1.2   3.4e+03     141     159 ..     281     299 ..     240     320 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.5e-07
                       DUF2723  21 PlflllgrlfslladaekvalrvnllsalssaltilflfltitlllrskakkiailgaglvgalafafsdtfWfsaveaeV 101
                                   Pl+  + +++ ++    +  +++ l sa++++l+i +++l+ + ll+        + +++++++++++s+     + e+  
  gi|91773579|ref|YP_566271.1|  92 PLYYSILHFVMMVS---QSEFALRLPSAIFGSLSIPLIYLVGKELLD--------KKTAIIASFLLSVSTFHINYSQEGRS 161
                                   57777777776666...777888899********************8........4567788888888887778899**** PP

                       DUF2723 102 YalsslftalvlwlilkweeeadekrsdrwlvliayligLslgvhllnllllpaiallyyfkky 165
                                   Yal +l++ l ++l+++ ++++++      +++ a+ + + + +h++ + ++ a+ l y+++++
  gi|91773579|ref|YP_566271.1| 162 YALMMLLVLLTIYLFINAYNKKST----LHWTITAISASVLVYTHFFGFFVIAAMGLYYLINEF 221
                                   *******************99987....7788889999999999**************998865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                       DUF2723 141 Lslgvhllnllllpaiall 159
                                   Ls++     ll + ai+l+
  gi|91773579|ref|YP_566271.1| 281 LSFSSYSNLLLYIYAILLI 299
                                   3333333333333333332 PP

>> UPF0139  Uncharacterised protein family (UPF0139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8   8.4e+03      26      26 ..      35      35 ..       6      62 .. 0.46
   2 ?   12.0   0.0   4.7e-05      0.14      27      92 ..      91     158 ..      78     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                       UPF0139 26 l 26
                                  l
  gi|91773579|ref|YP_566271.1| 35 L 35
                                  2 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.7e-05
                       UPF0139  27 tpdymnllg..mifsllglmlklkwcaWvalvcslisfanskssddlkqilssfmlsvsalvmsYlqn 92 
                                   +p y+++l   m++s   + l+l  +   +l + li++      d +++i+ sf+lsvs++  +Y q+
  gi|91773579|ref|YP_566271.1|  91 PPLYYSILHfvMMVSQSEFALRLPSAIFGSLSIPLIYLVGKELLDKKTAIIASFLLSVSTFHINYSQE 158
                                   55678887611556778899*********************************************886 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.7         6   1.8e+04      18      27 ..      42      51 ..      39      64 .. 0.48
   2 ?    0.5   1.2      0.25   7.4e+02       4      32 ..     177     207 ..     174     228 .. 0.71
   3 ?   -1.3   0.3      0.91   2.7e+03      16      37 ..     234     255 ..     223     267 .. 0.67
   4 ?   -1.5   0.6       1.1   3.3e+03      16      30 ..     289     303 ..     273     312 .. 0.56
   5 ?   11.1   0.1   0.00012      0.37      15      59 ..     393     437 ..     386     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 6
                   Sigma_reg_N 18 islivlllif 27
                                  i ++++ll +
  gi|91773579|ref|YP_566271.1| 42 ILIAITLLGT 51
                                  2333333322 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                   Sigma_reg_N   4 lkkakrksilrivlislivlllifvil..vv 32 
                                   ++ + +ks+l  +++++++ +l++  +  ++
  gi|91773579|ref|YP_566271.1| 177 INAYNKKSTLHWTITAISASVLVYTHFfgFF 207
                                   6677889999999999988877765553333 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.91
                   Sigma_reg_N  16 vlislivlllifvilvvtllyl 37 
                                   + i+li +l+++v+++  + ++
  gi|91773579|ref|YP_566271.1| 234 SKIALIGTLAFIVMSLPMIVWV 255
                                   5677777777777775555444 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.1
                   Sigma_reg_N  16 vlislivlllifvil 30 
                                    l+ + ++lli+ il
  gi|91773579|ref|YP_566271.1| 289 LLLYIYAILLIIGIL 303
                                   334444444444443 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00012
                   Sigma_reg_N  15 ivlislivlllifvilvvtllylaekegnklrevlelaveitsPN 59 
                                   i++i++i+l++ ++ ++ +++y+++ ++n+ r+++  + eit+P 
  gi|91773579|ref|YP_566271.1| 393 IAVIAVILLVVCSISFIPLNNYYTSMSKNDWRSAALALEEITQPG 437
                                   667777777777777799**************************6 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.7     0.068     2e+02      17      68 ..     163     212 ..     148     239 .. 0.73
   2 ?    6.1   1.1    0.0043        13       3      38 ..     279     314 ..     277     332 .. 0.83
   3 ?    6.4   0.0    0.0033        10      35      70 ..     380     416 ..     377     433 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.068
                       Pox_A14  17 aGiiLLilacifafvdfskststtdkawralsivsFilgivillglllfsmy 68 
                                   a ++LL+l  i+ f++   ++st    w   +i + +l      g ++ ++ 
  gi|91773579|ref|YP_566271.1| 163 ALMMLLVLLTIYLFINAYNKKSTL--HWTITAISASVLVYTHFFGFFVIAAM 212
                                   4578999999*****988777744..67777777777777777777666554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0043
                       Pox_A14   3 ilellknyystvliaGiiLLilacifafvdfsksts 38 
                                   il  +++y + +l++  iLLi+ ++f   df ks +
  gi|91773579|ref|YP_566271.1| 279 ILLSFSSYSNLLLYIYAILLIIGILFCMKDFRKSLT 314
                                   5677889999999*******************9977 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0033
                       Pox_A14  35 kstst.tdkawralsivsFilgivillglllfsmygr 70 
                                   k++++  ++++r +++++ il +v  ++ +  + y+ 
  gi|91773579|ref|YP_566271.1| 380 KNKTPgNNNTLREIAVIAVILLVVCSISFIPLNNYYT 416
                                   6666667788999999999999999998887777754 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0         6   1.8e+04      67      75 ..      44      52 ..      38      67 .. 0.52
   2 ?   10.4   4.6   0.00023      0.69      39     114 ..     136     204 ..     111     218 .. 0.80
   3 ?    4.2   1.8     0.019        57      38      85 ..     286     352 ..     241     407 .. 0.71

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 6
                          MerC 67 lvlgalGll 75
                                  +++++lG +
  gi|91773579|ref|YP_566271.1| 44 IAITLLGTI 52
                                  233333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                          MerC  39 hqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetllfgslwqvltvlGaalLaiahvl 114
                                   +++++i + ++++ ++ ++y +  + + l+++++ l+i+l+   ++         + l+ ++t+++a +L+++h++
  gi|91773579|ref|YP_566271.1| 136 KKTAIIASFLLSVSTFHINYSQEGRSYALMMLLVLLTIYLFINAYN--KK-----STLHWTITAISASVLVYTHFF 204
                                   456777799999********99999999999999999999988888..34.....455888999999999999986 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.019
                          MerC  38 lhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflg...................t 85 
                                     ++ll++ +++ ++++++ ++  rk + l+  +l l ++    ++g                    
  gi|91773579|ref|YP_566271.1| 286 YSNLLLYIYAILLIIGILFCMKDFRKSLTLLSIWLFLPLVTGYFLAGsmpfqpryllfvlpaylllI 352
                                   5678999999999**********************99999877666644444444444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1265  (0.0705561); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 3056.26
//
Query:       gi|91773580|ref|YP_566272.1|  [L=131]
Description: hypothetical protein Mbur_1618 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.1   4.0       0.23   11.5   4.0    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
          2    7.7   4.9        2.8    7.2   4.9    1.2  1  DUF3810          Protein of unknown function (DUF3810)
        5.5    6.9   7.7        2.8    7.8   1.0    2.0  2  60KD_IMP         60Kd inner membrane protein


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.0   3.8e-05      0.23      35      87 ..      51     118 ..      42     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
               Phage_holin_3_6  35 sgagllgaagvlallalllllvalalal.............aa.lwlaaliva.avllvlagvlalvg 87 
                                    +a++++  gv +l+al l++v++++++             ++ +++  liv+ +++lv+  +l+++g
  gi|91773580|ref|YP_566272.1|  51 FMALVMAEFGVWTLFALKLVFVLIVYWIykgafsssekqktDLwPMMKNLIVFvGIFLVINNLLVIWG 118
                                   5677888889***************999998888877755332799*****88689999999999987 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.9   0.00047       2.8      20      77 ..      57     114 ..      48     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00047
                       DUF3810  20 fpFSvgellivllillvilylvlaiklkkrkkkkkrllkvllrvllvllvvyflftll 77 
                                     F v+ l+ + l++++i+y ++   + + +k+k+ l+ +++++++++ +++++  ll
  gi|91773580|ref|YP_566272.1|  57 AEFGVWTLFALKLVFVLIVYWIYKGAFSSSEKQKTDLWPMMKNLIVFVGIFLVINNLL 114
                                   5799999999999999999999998889999999****************99987654 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.0   0.00046       2.8     105     158 ..      28      85 ..       3      92 .. 0.59
   2 ?    3.6   0.7     0.009        54      70      94 ..      93     117 ..      87     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00046
                      60KD_IMP 105 illavttflqqklsksk..kmqkmmlyvmplm..ilffslsfpaglvlYwlvsnllsi 158
                                   +++++  f+++    +   + + +m +vm  +   ++f+l++   l++Yw+ +  +s 
  gi|91773580|ref|YP_566272.1|  28 VFYVLGDFITTAKALNYgvEANGFMALVMAEFgvWTLFALKLVFVLIVYWIYKGAFSS 85 
                                   333333444433332212222456666666541156677888899*******999985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.009
                      60KD_IMP  70 clplLiqlpifialyrvlrslasfw 94 
                                   ++p++  l++f++++ v+++l  +w
  gi|91773580|ref|YP_566272.1|  93 LWPMMKNLIVFVGIFLVINNLLVIW 117
                                   68999**************966445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:01.23
# Mc/sec: 322.01
//
Query:       gi|91773581|ref|YP_566273.1|  [L=441]
Description: peptidase M24 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-49  166.8   1.1    7.3e-49  166.3   1.1    1.3  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
      0.076   13.6   3.3       0.13   12.9   1.4    2.2  2  ATP-cone       ATP cone domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3   1.1   8.1e-53   7.3e-49       1     208 [.     205     425 ..     205     426 .. 0.91

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 8.1e-53
                                   HHHHHHHHHHHHHHHHHHHH.....HHTTC........BHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSS CS
                 Peptidase_M24   1 elirkaariasaaleavlea.....ikpgv........terelaaeieattlkrhgarglafppivasgenaavlhytpnd 68 
                                   e+i++a+ ++++a+e +++      +k+gv        t++ +   ie+t l +hg++    ++iva+g+n+a +h++  +
  gi|91773581|ref|YP_566273.1| 205 EKIKEAQFACEKAMETAIDIiaeaeVKEGVlynnevpiTSESIRTSIEHT-LLDHGCEAE--STIVACGINSANPHWEG-E 281
                                   6899***********99865111125556444444455**********88.99***9988..599************99.7 PP

                                   SB--TTEEEEEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTB.. CS
                 Peptidase_M24  69 rvlkegdlvlidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesagl.. 145
                                    ++k++++++id+ ++ +  +y +D+trTvl G+ ++e +++yeav +aqeaa++ +kpG+ +s++++a+++ +e++g+  
  gi|91773581|ref|YP_566273.1| 282 GDIKANQPIVIDIFPRNKrnRYFADMTRTVLKGEASEELKKMYEAVHAAQEAAFAILKPGILYSDVHNAVCDEFEKRGYdt 362
                                   99**************9999************************************************************* PP

                                   .....CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                 Peptidase_M24 146 .....akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                        +  f h++GHgvGl++h+  psvs    +++++eeG+v+tiEpg+y  p+ gg+ried+v++t
  gi|91773581|ref|YP_566273.1| 363 irsdsKVGFIHSTGHGVGLDIHEL-PSVS---LQEVEVEEGHVVTIEPGLY-YPEYGGIRIEDMVVIT 425
                                   ****99999*************98.**98...469****************.9999***********9 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   1.4e-05      0.13      15      70 ..     204     260 ..     197     265 .. 0.77
   2 ?   -1.2   0.0      0.34   3.1e+03      55      85 ..     318     349 ..     307     364 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH.HIIT...-BHHHHHHHHHHHHHHSS- CS
                      ATP-cone  15 vekIkraiekAcegseeeideiaeeveaevrkr.lrdg...isteeIqdlvektliehpd 70 
                                   +ekIk+a ++Ace+ +e++ +i++e   ev+++ l+++   i++e I++ +e+tl +h+ 
  gi|91773581|ref|YP_566273.1| 204 IEKIKEA-QFACEKAMETAIDIIAEA--EVKEGvLYNNevpITSESIRTSIEHTLLDHGC 260
                                   5777777.889999888877774444..6666555555588***************9985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHHH.HSS-HHHHHHHHHHHHHHH CS
                      ATP-cone  55 eeIqdlvektli.ehpdyavaaayilyrnlrk 85 
                                   ee+ ++ e + + ++  +a+++  ily++ ++
  gi|91773581|ref|YP_566273.1| 318 EELKKMYEAVHAaQEAAFAILKPGILYSDVHN 349
                                   56666666554446777777777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2628.99
//
Query:       gi|91773582|ref|YP_566274.1|  [L=297]
Description: methionine aminopeptidase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  135.6   0.1    2.1e-39  135.4   0.1    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.4   0.1   1.2e-43   2.1e-39       3     209 .]      15     289 ..      13     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 1.2e-43
                                   HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..SSSB--TTEEEEEEE CS
                 Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..ndrvlkegdlvlida 81 
                                   + +a++i s ++ +++e++k g+t  e+a+++e++t++   ++ +afp  + ++ n++++h+tp  +d+++ ++d+v++d+
  gi|91773582|ref|YP_566274.1|  15 YMQAGEILSTVRSEAKEKVKIGTTLLEVADFVEQRTIEL--GGLPAFP--CNISRNDEAAHATPliGDETVFAEDVVKLDL 91 
                                   779******************************985544..4579***..9999**********9955555566******* PP

                                   EEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS.SS CS
                 Peptidase_M24  82 gaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl.ev 161
                                   g+++dgy++D++ Tv +   t+e  +l++a ++a++aai+ +k G++++ei+a+++++++ +g+ k++ +++GHgvG+   
  gi|91773582|ref|YP_566274.1|  92 GVHIDGYIADSAITVDL---TNENSDLVKASEAALYAAIDIIKNGINTAEIGAVIEDTITGHGF-KPIANLTGHGVGQyLA 168
                                   ***************99...778889**********************************99**.************9566 PP

                                   SEEEEEESSSTT..CSSB--TTBEEEEEE......EEEEETTT...................................... CS
                 Peptidase_M24 162 hdegpsvsresn..dgrkleeGmvftiEp......giyfapge...................................... 196
                                   h + ps+++ ++  +g++++ G++f+iEp      g      +                                      
  gi|91773582|ref|YP_566274.1| 169 H-VPPSIPN-RHigQGVTIKTGDIFAIEPfatdgaG------Kvadgtlteifqvighkpirlpavrkvlkeleqyktlpf 241
                                   6.5488875.33459**************6666552......133333566666677778888888888888999999999 PP

                                   ..................................E.EEEEBEEEEEES CS
                 Peptidase_M24 197 ..................................g.gvriedtvlvte 209
                                                                     g + + e+tv+vt+
  gi|91773582|ref|YP_566274.1| 242 arrwlksdkldyslmqlekagiitsypvlkdvggGlVSQTEHTVIVTD 289
                                   9999*****************************9889*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1748.87
//
Query:       gi|91773583|ref|YP_566275.1|  [L=206]
Description: hypothetical protein Mbur_1621 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1301.07
//
Query:       gi|91773584|ref|YP_566276.1|  [L=95]
Description: hypothetical protein Mbur_1622 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-25   88.9   0.4    3.3e-25   88.2   0.4    1.4  1  DUF1805   Domain of unknown function (DUF1805)
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.043   13.8   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 !   88.2   0.4   3.7e-29   3.3e-25       1      63 []      36      94 ..      36      94 .. 0.99

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 3.7e-29
                                  E-TT--HHHHHHTT--EEE-....-S--SHHHHHHSB-SEE-HHHHHTT--TT-BHHHHGGGG CS
                       DUF1805  1 mCGaLdvealeklgdlaarvivagsGVrtledllaapvesvteaAeelGikeGmtgkeaLekl 63
                                  mCG+Ld e++ek+gd+aa+v    +GV+ +ed+l+ +v +vt +A++lG+k+Gm+g+eaLe++
  gi|91773584|ref|YP_566276.1| 36 MCGYLDTEMAEKFGDVAAKV----RGVNYFEDVLHTEVIDVTGHAKALGVKPGMKGHEALELM 94
                                  9*******************....*************************************88 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-06     0.043      31      59 ..      33      93 ..      16      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-06
                                  ..................................TEEEEE-HHHHTTT--TTSBHHHHHTT CS
                           IMS 31 k................................rgiviavsyeArayGvkrgmrikeakkl 59
                                                                   +  vi v+  A+a Gvk gm+ +ea++l
  gi|91773584|ref|YP_566276.1| 33 GfvmcgyldtemaekfgdvaakvrgvnyfedvlHTEVIDVTGHAKALGVKPGMKGHEALEL 93
                                  355666666666666677777777777778888999**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 649.75
//
Query:       gi|91773585|ref|YP_566277.1|  [L=344]
Description: RNA methylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-26   93.7   0.0    1.3e-25   90.3   0.0    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    4.4e-13   49.6   2.8    4.6e-13   49.5   1.3    1.7  2  THUMP            THUMP domain
    1.6e-07   31.3   0.0     0.0025   17.6   0.0    2.2  2  N6_N4_Mtase      DNA methylase
    3.1e-06   26.7   0.0    4.9e-06   26.0   0.0    1.3  1  N6_Mtase         N-6 DNA Methylase
    3.2e-06   27.7   0.1    1.4e-05   25.7   0.0    2.2  2  Methyltransf_11  Methyltransferase domain
    8.4e-05   23.2   0.0    0.00049   20.8   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
     0.0016   18.0   0.0       0.11   12.0   0.0    2.2  2  AviRa            RRNA methyltransferase AviRa
     0.0022   17.7   0.0     0.0032   17.1   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0082   16.0   0.0      0.015   15.1   0.0    1.4  1  N6-adenineMlase  Probable N6-adenine methyltransferase
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.98    9.0   0.0    2.1  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase


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 !   90.3   0.0   7.1e-29   1.3e-25       1     196 [.     170     338 ..     170     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 7.1e-29
                                   -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEE CS
                       UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklyg 81 
                                   +++++f++p+ L++++A+alv++a +k+g++ +DP+CG+ +il+Ea+l+ga++                           g
  gi|91773585|ref|YP_566277.1| 170 PHKKPFFYPGVLRPRVARALVNMALIKEGDVVFDPFCGTAGILVEAGLVGATVL--------------------------G 224
                                   5789**************************************************..........................* PP

                                   EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHHH-TT..- CS
                       UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkrvlrgggr 161
                                   ++   ++  ga  N+++ + ++++ +   da+k++l +++vd+++++pPYG++   +++  ++LY++   e+ rvl+    
  gi|91773585|ref|YP_566277.1| 225 LEVRYKIAVGADMNLRHFNADQTMMMG--DACKVPLVDESVDAVIADPPYGRSARIEGESlHHLYEHSFAEMFRVLKP--G 301
                                   ********************9998876..5999998888**************99776555*****************..6 PP

                                   EEEEEESSHHHHHCC---..ESEEEEEEETTEEEEEE CS
                       UPF0020 162 lvlltsenkalekaleer..alrkvkeknvklglllk 196
                                    ++++ ++ ++++++e+   +++ + +++v+ +l++k
  gi|91773585|ref|YP_566277.1| 302 KLAIIVSEIDVTELVEKVgfTIKDRFLQRVHKSLTRK 338
                                   6667777899999999988899999999999999886 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   1.3   2.6e-16   4.6e-13      14     134 ..      30     148 ..      18     156 .. 0.87
   2 ?   -1.9   0.0       1.8   3.3e+03      92     119 ..     299     330 ..     282     333 .. 0.69

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.6e-16
                                   -SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESS CS
                         THUMP  14 verveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrg 94 
                                   + + e+   ++v ++kge p+e  ++l e  ++++  + ++ v  vc++++edi+e a+  +  ++ +e++++ Vr+kr++
  gi|91773585|ref|YP_566277.1|  30 YGESEYFEHCLVADIKGE-PQEILHKLREVAKRIAMTHYILKVIDVCPTEIEDIIEVAEGCDISEHLNEGQKYVVRAKRVR 109
                                   556677777777788777.788888888999999999999999******************9999999999********** PP

                                   STSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEE CS
                         THUMP  95 khfeftsreinrevGkaivektglkVdlenPdivvrveii 134
                                   ++ ++ +++i+r vG+ai +k+    dl++Pd+ +r+ + 
  gi|91773585|ref|YP_566277.1| 110 HNTTIKCVDIERRVGGAIYRKGF-NADLKDPDVEFRAILS 148
                                   **********************9.**********998544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                   ESSSTS....SSHHHHHHHHHHHHHHCCTT-E CS
                         THUMP  92 rrgkhf....eftsreinrevGkaivektglk 119
                                   ++gk +    e++  e+  +vG  i++++  +
  gi|91773585|ref|YP_566277.1| 299 KPGKLAiivsEIDVTELVEKVGFTIKDRFLQR 330
                                   44444455667777888888888888777655 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0025     173     224 ..     178     230 ..     125     238 .. 0.82
   2 !   11.8   0.0   8.2e-05      0.15       1      55 [.     263     307 ..     263     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                   SS---HHHHHHHHHHH.S-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHH CS
                   N6_N4_Mtase 173 paqkPvallerlIkls.tkkgdivlDpFaGSGtTavaakelgrkfiGieieee 224
                                   p +     ++ l+++   k+gd+v+DpF+G+  ++v+a   g   +G e+  +
  gi|91773585|ref|YP_566277.1| 178 PGVLRPRVARALVNMAlIKEGDVVFDPFCGTAGILVEAGLVGATVLGLEVRYK 230
                                   55555667788886651566********************9999999998655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.2e-05
                                   EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEE CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifin 55 
                                   vd +++dpPY+ + +      +e+e+ ++ y    e  ++e+ rvLk+++ ++i 
  gi|91773585|ref|YP_566277.1| 263 VDAVIADPPYGRSAR------IEGESLHHLY----EHSFAEMFRVLKPGKLAIIV 307
                                   799************......8888888777....678999********999885 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.7e-09   4.9e-06      33     138 ..     184     275 ..     167     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.7e-09
                      N6_Mtase  33 evsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgd 113
                                    v + +v+++  k+g +v+Dp cG++g+lv+a  v           ++ G+e+  + +  a mNl   ++++    + +gd
  gi|91773585|ref|YP_566277.1| 184 RVARALVNMALIKEGDVVFDPFCGTAGILVEAGLV---------GATVLGLEVRYKIAVGADMNLRHFNADQT---MMMGD 252
                                   588999999999*******************9874.........57999***************877777666...99*** PP

                      N6_Mtase 114 tlekpkfekdkkfdvvvaNppfnqk 138
                                   + + p  +  +++d+v+a pp++ +
  gi|91773585|ref|YP_566277.1| 253 ACKVPLVD--ESVDAVIADPPYGRS 275
                                   ******98..9***********987 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       5.6     1e+04      72      87 ..      93     108 ..      88     120 .. 0.73
   2 !   25.7   0.0   7.7e-09   1.4e-05       5      95 ..     206     305 ..     202     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.6
                                   CC-CCHHHHHHHHHHH CS
               Methyltransf_11  72 hhvedpekalkeiaRv 87 
                                   +h+++ +k++  ++Rv
  gi|91773585|ref|YP_566277.1|  93 EHLNEGQKYVVRAKRV 108
                                   6777777777777776 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 7.7e-09
                                   -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES...........-CCC- CS
               Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse...........vlhhv 74 
                                   cGt  ++ +    ga+v+g+++  +    a ++ +  +   +++ +da k+p+ d+s+D+v++             +lhh+
  gi|91773585|ref|YP_566277.1| 206 CGTAGILVEAGLVGATVLGLEVRYKIAVGADMNLRHFNADQTMMMGDACKVPLVDESVDAVIADPpygrsariegeSLHHL 286
                                   8877777777778899*****9999997787777777665689********************9999999999999***** PP

                                   CCHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                      e+ ++e+ RvLkpg l +
  gi|91773585|ref|YP_566277.1| 287 Y--EHSFAEMFRVLKPGKLAI 305
                                   5..899**********97766 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   3.3e+03      55      55 ..     119     119 ..      86     163 .. 0.56
   2 !   20.8   0.0   2.7e-07   0.00049       1      96 [.     201     301 ..     201     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                                   C CS
               Methyltransf_25  55 a 55 
                                   +
  gi|91773585|ref|YP_566277.1| 119 I 119
                                   2 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.7e-07
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE..........E CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs..........s 71 
                                   v d  cGt  ++ ++    g a+v+g+++  +    a  ++++ +++ +++ gda ++p+ d+s+D+v++           
  gi|91773585|ref|YP_566277.1| 201 VFDPFCGTAGILVEAGLV-G-ATVLGLEVRYKIAVGADMNLRHFNADQTMMMGDACKVPLVDESVDAVIAdppygrsariE 279
                                   567789*99999998855.6.********************99999************************99999877764 PP

                                   ST.GGGSSHHHHHHHHHHHHHHEEEE CS
               Methyltransf_25  72 ga.lhhlsdedlekalkeiarvLkpg 96 
                                   g+ lhhl     e+ ++e++rvLkpg
  gi|91773585|ref|YP_566277.1| 280 GEsLHHLY----EHSFAEMFRVLKPG 301
                                   45577764....678**********8 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.017        31      53      76 ..     197     220 ..     184     244 .. 0.76
   2 !   12.0   0.0   5.9e-05      0.11     149     210 ..     246     307 ..     232     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                         AviRa  53 apltlyDpCCGgayLltvlgllhg 76 
                                   ++  ++Dp CG+a +l   gl+ +
  gi|91773585|ref|YP_566277.1| 197 EGDVVFDPFCGTAGILVEAGLVGA 220
                                   34579**********999998765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.9e-05
                         AviRa 149 ievfkaditekeeeaekevdivitDlPYGelvswqges.eepvkqlleslaavldpeesvvav 210
                                    +++  d   k + + ++vd vi+D PYG  ++ +ges ++  ++ ++++ +vl+p +  ++v
  gi|91773585|ref|YP_566277.1| 246 QTMMMGDAC-KVPLVDESVDAVIADPPYGRSARIEGESlHHLYEHSFAEMFRVLKPGKLAIIV 307
                                   456666766.55667778*******************63667788899999999876644443 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.8e-06    0.0032      41     130 ..     197     279 ..     180     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                   eg  v D f+G++++ +EA   ga  ++ +e   + +     nl++++++   +++ + ++ +++     +e++d v  DP
  gi|91773585|ref|YP_566277.1| 197 EGDVVFDPFCGTAGILVEAGLVGA-TVLGLEVRYKIAVGADMNLRHFNAD---QTMMMGDACKVPLV---DESVDAVIADP 270
                                   456689*************99995.6788899999999999*******77...45555555555544...5789******* PP

                                   SSSTTCH.H CS
                 Cons_hypoth95 122 Pyakellie 130
                                   Py +++ ie
  gi|91773585|ref|YP_566277.1| 271 PYGRSARIE 279
                                   **9997755 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.6e-06     0.015      59     148 ..     227     335 ..     211     342 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
               N6-adenineMlase  59 krFealyge.ekfvfYdlnnpeelpeel.....kgkfdviviDPPF..........lseeclkklaktaklllk..klilc 121
                                    r++  +g   + ++++  ++  + + +     ++++d +++DPP+          l +   +++a++ + l k  kl ++
  gi|91773585|ref|YP_566277.1| 227 VRYKIAVGAdMNLRHFNADQTMMMGDACkvplvDESVDAVIADPPYgrsariegesLHHLYEHSFAEMFRVL-KpgKLAII 306
                                   5554444431357899999988444333334579*************9999999988888888899999988.45854444 PP

               N6-adenineMlase 122 tgevmee.lekllgvkkt.kfepehenkl 148
                                    +e+  + l +++g+++  +f  + +++l
  gi|91773585|ref|YP_566277.1| 307 VSEIDVTeLVEKVGFTIKdRFLQRVHKSL 335
                                   44444444666676655446665555555 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 ?    0.2   0.0      0.27   4.8e+02      56      95 ..      89     137 ..      57     158 .. 0.68
   2 ?    9.0   0.0   0.00055      0.98       3      82 ..     200     273 ..     198     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.27
               Methyltransf_15  56 gdvfe..........llaklklekikvdlvflSpPwGGpsYkkqekfdlk 95 
                                   +d+ e            ++++ ++ ++ +v +   +GG  Y+k  + dlk
  gi|91773585|ref|YP_566277.1|  89 CDISEhlnegqkyvvRAKRVRHNT-TIKCVDIERRVGGAIYRKGFNADLK 137
                                   444445555555532334444444.4899999999999999998888884 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00055
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwG 82 
                                   v+ D+f+G+ G  ++  lv+ +v ++e+  +    a  N + ++     t+++gd  ++      e+  vd v++ pP G
  gi|91773585|ref|YP_566277.1| 200 VVFDPFCGTAGILVEAGLVGATVLGLEVRYKIAVGADMNLRHFN--ADQTMMMGDACKVPL--VDES--VDAVIADPPYG 273
                                   789***************************99999********5..555778899776422..2233..58888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2216.43
//
Query:       gi|91773586|ref|YP_566278.1|  [L=187]
Description: hypothetical protein Mbur_1624 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  114.2   2.9    1.9e-31  109.8   2.2    2.0  2  DUF45          Protein of unknown function DUF45
    0.00034   21.4   0.0     0.0006   20.6   0.0    1.3  1  DUF4037        Domain of unknown function (DUF4037)
     0.0011   18.8   1.3     0.0021   17.9   0.3    1.8  2  SprT-like      SprT-like family
  ------ inclusion threshold ------
      0.056   14.0   0.1       0.11   13.0   0.1    1.5  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
      0.065   13.1   0.1       0.15   11.9   0.0    1.3  1  Peptidase_M10  Matrixin
       0.23   11.1   0.0       0.37   10.4   0.0    1.3  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.015        44       7      57 ..      30      78 ..      24      86 .. 0.75
   2 !  109.8   2.2   6.2e-35   1.9e-31     110     206 ..      82     178 ..      73     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.015
                         DUF45  7 vepdgsvevsaPkgvseeeiedfvkkkakwiekklakleer.akeaekeles 57
                                   +  g++e+ +P+++  ++ e++++k++ wi ++  ++ ++ + +++kel +
  gi|91773586|ref|YP_566278.1| 30 YSC-GKLELLVPTNF--KTPEELLHKHKLWIYRRHVEYTNAiHGSSSKELLN 78
                                  555.78889999986..5678***********99999988766666666655 PP

  == domain 2  score: 109.8 bits;  conditional E-value: 6.2e-35
                         DUF45 110 keakeeleerlaklaaklgvkprsvsikdmktrWGscsskgkirlnwrLvkappevidYVvvHElaHlleknHskrFwalv 190
                                   +e++e +   +++++ +l+v p++v++++mkt+WGscssk++++ln +L+++p ++i+YVv+HE+aHl+e nHs+rFw+++
  gi|91773586|ref|YP_566278.1|  82 EELRELVMFHVKNISTELEVMPEKVTFRKMKTKWGSCSSKKRVNLNRHLMHLPDSLIEYVVFHEMAHLIELNHSPRFWNVI 162
                                   56666666679999******************************************************************* PP

                         DUF45 191 ekllPdwkeakkeLkr 206
                                   ++ + d ke+ ++L +
  gi|91773586|ref|YP_566278.1| 163 DSRYADRKEYDRQLSA 178
                                   ************9975 PP

>> DUF4037  Domain of unknown function (DUF4037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     2e-07    0.0006      25      80 ..      92     147 ..      88     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-07
                       DUF4037  25 fteireklekayPedvrlkklaarlakiaqegqynleralkrg.delaarlalaefv 80 
                                   +++i ++l + +Pe+v+ +k+++++ +++ ++ +nl+r l +  d+l  +++++e++
  gi|91773586|ref|YP_566278.1|  92 VKNISTEL-EVMPEKVTFRKMKTKWGSCSSKKRVNLNRHLMHLpDSLIEYVVFHEMA 147
                                   78899999.99***************************9886527777777777665 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.37   1.1e+03      74     104 ..      51      85 ..      48     102 .. 0.62
   2 !   17.9   0.3   7.1e-07    0.0021      25      77 ..     108     151 ..      86     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.37
                     SprT-like  74 Hlalfvisgvr....nnpHGaeFkawaakvekala 104
                                   H + + i++++    n  HG + k++ ++ ++ l+
  gi|91773586|ref|YP_566278.1|  51 HKHKLWIYRRHveytNAIHGSSSKELLNRSDEELR 85 
                                   55554444422234488899998888887776664 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 7.1e-07
                     SprT-like  25 wskrlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHlal 77 
                                   ++ +++t+ G ++ k+       ++ L+++l+   +++ ++ ++ HE++Hl+ 
  gi|91773586|ref|YP_566278.1| 108 FR-KMKTKWGSCSSKK-------RVNLNRHLMHL-PDSLIEYVVFHEMAHLIE 151
                                   44.7899*****9999.......*********99.9999999********986 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.8e-05      0.11      87     124 .]     117     155 ..     110     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                  Reprolysin_3  87 vcnsskkagvnsgssvlgk.vgadtvaHEiGHnfganHt 124
                                    c+s+k++++n+  + l + +  ++v HE+ H + +nH+
  gi|91773586|ref|YP_566278.1| 117 SCSSKKRVNLNRHLMHLPDsLIEYVVFHEMAHLIELNHS 155
                                   6999999999999988888355599*************6 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.1e-05      0.15     109     142 ..     138     171 ..     133     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHHHHHTTBESXSSTTSTTSSSCTXTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M10 109 lflVaaHEiGHalGLeHssdkdalmyplykeekk 142
                                   +++V+ HE++H++ L+Hs +   ++ + y ++k+
  gi|91773586|ref|YP_566278.1| 138 IEYVVFHEMAHLIELNHSPRFWNVIDSRYADRKE 171
                                   5789**************9988888888875554 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 ?   10.4   0.0   0.00012      0.37     117     154 ..     122     159 ..     116     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                 Peptidase_M57 117 kviqigtglesysvdvnehvithelGhtvGlRhsDyyn 154
                                   k++++   l   +  ++e+v+ he+ h + l hs  + 
  gi|91773586|ref|YP_566278.1| 122 KRVNLNRHLMHLPDSLIEYVVFHEMAHLIELNHSPRFW 159
                                   5666777777778889*****************97554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1201.87
//
Query:       gi|91773587|ref|YP_566279.1|  [L=275]
Description: tRNA pseudouridine synthase A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-29  101.0   0.0    4.6e-23   81.7   0.0    2.2  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.9e-07    0.0053       4      81 ..       8      79 ..       6      97 .. 0.72
   2 !   81.7   0.0   2.6e-27   4.6e-23       1     108 []     128     229 ..     128     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-07
               PseudoU_synth_1  4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.favgqgklspedvkel 81
                                  +++G+++ g   +q q +  tv   l   ++e+   e++  ++++ +sg++d++V+am++v+ f+    +l    ++++
  gi|91773587|ref|YP_566279.1|  8 AYIGSNFHG---SQVQLNDPTVEGELFKVLKELGIMEDPR-TANFISSGRTDSGVHAMGQVVaFDTDAPNL---AMPRV 79
                                  588888888...5666667777777777777666665554.89******************9666655443...34444 PP

  == domain 2  score: 81.7 bits;  conditional E-value: 2.6e-27
               PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvkel 81 
                                   A+k l+G+hdf++f +  + +k+tvr +++++i+     +++l++++v++++Fl+++VR +v++l+ vg g +++e++ ++
  gi|91773587|ref|YP_566279.1| 128 ASKLLLGSHDFSNF-STSRGSKKTVRIVKRIDIR----VSGNLTRIDVEANSFLWNMVRKIVAALMMVGSGVRDEEWLGHM 203
                                   7899**********.56666689***********....666799************************************* PP

               PseudoU_synth_1  82 lnakkrkkiavetapavglvlfhvrYd 108
                                   l+ ++ ++   e a   glvl++v+Y+
  gi|91773587|ref|YP_566279.1| 204 LDPESYEE-GLEPAHGYGLVLMDVNYP 229
                                   *****999.9****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1799.31
//
Query:       gi|91773588|ref|YP_566280.1|  [L=355]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  182.2   0.0    9.5e-54  181.8   0.0    1.1  1  DUF1297      Domain of unknown function (DUF1297)
    1.5e-44  150.9   0.0      3e-44  149.9   0.0    1.5  1  DUF1246      Protein of unknown function (DUF1246)
    0.00018   21.6   0.0    0.00038   20.5   0.0    1.5  1  ATP-grasp_3  ATP-grasp domain
     0.0011   18.6   0.0     0.0025   17.5   0.0    1.5  1  RimK         RimK-like ATP-grasp domain
     0.0082   15.7   0.0      0.015   14.8   0.0    1.3  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.8   0.0   2.7e-57   9.5e-54      21     187 ..     181     354 ..     171     355 .] 0.94

  Alignments for each domain:
  == domain 1  score: 181.8 bits;  conditional E-value: 2.7e-57
                                   CCEEEEE---SEEEEEEEEEETTT........TEEEEEEEEEEEEEECCCHCCS-HHHHHC.CT----EEEEEEEEEEE-G CS
                       DUF1297  21 kkasieeyvvGanfnlnyfysplk........eevellgidrRyesnldglvrlpakeqle.levepeyvvvGnipvvlRE 92 
                                   +k +++e++vG++++l++fysp++        + +e+l++drR+esn d++ rl + ++le + ++p+yvv+Gn+p+v RE
  gi|91773588|ref|YP_566280.1| 181 EKHTVQEFIVGTRYYLHFFYSPIReegyklseGILEMLSMDRRVESNADEIFRLGSPKELEdAGIHPTYVVTGNVPLVARE 261
                                   6789********************9999999889********************88776652778**************** PP

                                   GGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS---HHHHHHHH CS
                       DUF1297  93 sllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfgeplsmGrrialE 173
                                   sll+++f lgek+ve++  l+  G+iGpFcL++v+t++le+ vf++saRiv+gtn+y++gspys  + +e+ls+G+ria E
  gi|91773588|ref|YP_566280.1| 262 SLLPRIFALGEKVVEESLGLFG-GMIGPFCLETVFTDKLEIKVFEISARIVAGTNLYTSGSPYSD-MIEENLSTGKRIAQE 340
                                   ******************9997.****************************************97.5799*********** PP

                                   HHHHHHCT-GGGCE CS
                       DUF1297 174 ikeaiekdrleeiv 187
                                   ik  +++++l+ i+
  gi|91773588|ref|YP_566280.1| 341 IKLGAKTGKLDLIL 354
                                   **********9886 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.9   0.0   8.3e-48     3e-44       1     121 [.      21     141 ..      21     142 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.9 bits;  conditional E-value: 8.3e-48
                                   EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-..SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC CS
                       DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvi..devivldkfkdilkeevqeklreenailvPhgsfveYv 79 
                                   iat++SHs+lqi++gA+keg+rt+ +c  +  ++Y++f+ +  de+iv+++++di   +++e+l+++nai++PhgsfveY+
  gi|91773588|ref|YP_566280.1|  21 IATVCSHSSLQIFDGARKEGLRTIGICVGQPPRFYDAFPKAkpDEYIVVESYSDIP--KIAEELVRKNAIVIPHGSFVEYM 99 
                                   89************************************77777************9..567******************** PP

                                   -HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--B CS
                       DUF1246  80 giekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkk 121
                                   g+e++ el+vp+fGnr++l+wE++r+k+r++Le Agi++Pk+
  gi|91773588|ref|YP_566280.1| 100 GTESFAELAVPTFGNREVLEWESDRDKEREWLEGAGIHMPKI 141
                                   ****************************************97 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.1e-07   0.00038       5     158 ..     125     310 ..     122     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.........EEEE---SEEEEEEEEE.S CS
                   ATP-grasp_3   5 lktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..lvqefieGkplSvsllsdg 83 
                                    k  ++L+ ag+++P   +   +e+ e+++ vK   + gg + +++++ ee ++ i+ +e   vqefi G+ + + +  + 
  gi|91773588|ref|YP_566280.1| 125 DKEREWLEGAGIHMP---KIVDPEKIESPVMVKYHGAKGGRGFFIAKDYEEFKQYIDPNEkhTVQEFIVGTRYYLHFFYSP 202
                                   56679**********...89999999*************************99998877677***********99999888 PP

                                   SSEEEEEEEEEEEET...............................TEEEEEEES----H.HHHHHHHHHHHHTTSTT--E CS
                   ATP-grasp_3  84 ekvlvlavnrqliekaeke...........................fvyaGnvtpietel.keevvelaeevvekleglaG 136
                                    +     +++ ++e+ +++                           +v +Gnv  +  e    ++++l e+vve+  gl+G
  gi|91773588|ref|YP_566280.1| 203 IREEGYKLSEGILEMLSMDrrvesnadeifrlgspkeledagihptYVVTGNVPLVARESlLPRIFALGEKVVEESLGLFG 283
                                   888888888888877666677777888888888888888888888777788876554444477888888888775444442 PP

                                   .EEE...EEEEESS..SEEEEEEESS- CS
                   ATP-grasp_3 137 .yvG...vDlvlkd.eepyviEvNPRl 158
                                    + G    + v +d  e+ v E+ +R+
  gi|91773588|ref|YP_566280.1| 284 gMIGpfcLETVFTDkLEIKVFEISARI 310
                                   133322266667775577777777776 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.9e-07    0.0025      32      82 ..     140     189 ..     130     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.9e-07
                                   HHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEEEE- CS
                          RimK  32 kliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvqeyi 82 
                                   k+++  k+++Pv+vK   ++ G + ++ak++++ kq ++   e+  vqe+i
  gi|91773588|ref|YP_566280.1| 140 KIVDPEKIESPVMVKYHGAKGGRGFFIAKDYEEFKQYIDPN-EKHTVQEFI 189
                                   566667789****************************9985.555789999 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 !   14.8   0.0   4.1e-06     0.015      35      78 ..     145     188 ..     140     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                                   HHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                   CPSase_L_D2  35 keigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                   ++i  Pv++k   + GG+G  +a++ ee+++ +    +++   f
  gi|91773588|ref|YP_566280.1| 145 EKIESPVMVKYHGAKGGRGFFIAKDYEEFKQYIDPNEKHTVQEF 188
                                   67899**************************9998888776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2319.74
//
Query:       gi|91773589|ref|YP_566281.1|  [L=160]
Description: hypothetical protein Mbur_1627 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.026   14.3   0.8       0.79    9.5   0.0    2.4  2  DASH_Duo1  DASH complex subunit Duo1


Domain annotation for each model (and alignments):
>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   4.4e-05      0.79      16      52 ..      29      65 ..      23      87 .. 0.83
   2 ?    3.1   0.2    0.0044        78      14      41 ..     133     160 .]     129     160 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 4.4e-05
                     DASH_Duo1 16 ienviesLkkaksniervketvestntLLdkWirIls 52
                                  ++ + +s+ +a+++i+ ++ + +st  +Ld +++I  
  gi|91773589|ref|YP_566281.1| 29 VDELGDSISQARTDIQFLQWAANSTGIILDDYSNIKD 65
                                  5677899****************************76 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0044
                     DASH_Duo1  14 evienviesLkkaksniervketvestn 41 
                                   e++e++ e L+++++ +++++e  e+tn
  gi|91773589|ref|YP_566281.1| 133 EALEKSLEMLNETSELLSEISELAEQTN 160
                                   5678888888888888888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1034.18
//
Query:       gi|91773590|ref|YP_566282.1|  [L=170]
Description: hypothetical protein Mbur_1628 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.6    5.9   8.9          1    8.3   1.3    2.0  2  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.9     0.006   1.1e+02     127     172 ..      10      67 ..       6      82 .. 0.80
   2 ?    8.3   1.3   5.7e-05         1      64     107 ..     101     144 ..      73     170 .] 0.65

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.006
                          PHO4 127 llggiiaallfllvkrl............ilvkeklknalralpvlvlvtiailalsi 172
                                    lg++ + ll++lv  +            +l++e+  +++ ++p+l+l++i++l+l+ 
  gi|91773590|ref|YP_566282.1|  10 ALGMVSSLLLLFLVTEFskplltkyslfqVLWRESEFRSFALAPFLYLISILFLLLLS 67 
                                   6899999999999999977777777666666668888999999999999998887765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 5.7e-05
                          PHO4  64 lgmlaallgaavwlllatvlglPvStthslvGaliGaalaaegg 107
                                    g    l g+ + l+ a ++++P     s+vG+l+G+ l ++++
  gi|91773590|ref|YP_566282.1| 101 KGSSKTLEGTLAGLIGAIIFSYPLVGYLSIVGGLVGMYLELKSK 144
                                   56666777888999999********************9987552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1147.17
//
Query:       gi|91773591|ref|YP_566283.1|  [L=313]
Description: hypothetical protein Mbur_1630 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   43.7   0.1    2.8e-07   29.7   0.1    2.1  2  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   3.2e-06     0.058       4      57 ..       2      56 ..       1      94 [. 0.87
   2 !   29.7   0.1   1.5e-11   2.8e-07     183     350 ..     121     279 ..     108     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-06
                                  HHHHHHHHHHHTTT---TT-EEEEEEETT-HHHH.HHHHHHHHHTT-SEEEEEEE CS
                 Peptidase_M29  4 klekyAellvkvglnlqkgqevvinaevealela.rlvaeeaykagakkvvvews 57
                                  +l+k A++++++++  +kg++v+i +++ + +++ +++++ a++ag + + ++++
  gi|91773591|ref|YP_566283.1|  2 ELKKSADMVINTCMGAKKGETVLIVTDTCTDKMIsEALYDSAVDAGCEAILLTME 56
                                  689***********************998877763789********999887766 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.5e-11
                                   HHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS---SSS----SBSS---EEE-EEEEEEEEEEE CS
                 Peptidase_M29 183 aaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWiggaektkkgiefvaNiPteevftaPdkrgvnGvvr 263
                                   a++e++   +++  ++L+    ke+++++++gtdL +++ eg  W++ ++   +++  ++N+P +e+++aP+  +vnG+ +
  gi|91773591|ref|YP_566283.1| 121 ANYEDIGILADELLETLKG--SKEVRITTEKGTDLVLDV-EGCEWMADTGMC-HEKGTTSNLPAGEMYIAPK--NVNGKAV 195
                                   5667777777777778877..899***************.**********97.788899************7..6****** PP

                                   -SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHT.TSSSGGGSEEEEE---TTSHHHHHT-----HHHHHT..TS CS
                 Peptidase_M29 264 atkPlsysGnliegirltFedGkvveakAekGeevLkkll.etDegarrLGEvALvpndspisqsgilfyntLfDen..as 341
                                    +  +   G l + + +++++  +v+++  +G e L++++ ++ ++ r + E+ ++ n    ++   l+  +L De+  ++
  gi|91773591|ref|YP_566283.1| 196 IDGSMGGIGLLDKPLVIEIRNRSAVSFEG-EGAEKLEAMVeNVGADGRNIAELGIGINP--AAR---LIGVILEDEKvgGT 270
                                   ****************************8.79999999994578999********9987..667...99************ PP

                                   -EEEEE--- CS
                 Peptidase_M29 342 cHlAlGaay 350
                                   +H+AlG+  
  gi|91773591|ref|YP_566283.1| 271 IHIALGDNS 279
                                   ******865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.59
# Mc/sec: 1587.75
//
Query:       gi|91773592|ref|YP_566284.1|  [L=160]
Description: 3-isopropylmalate dehydratase small subunit [Methanococcoides burtonii DSM 6242]
Scores for 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-18   64.8   0.0    1.3e-17   64.4   0.0    1.2  1  Aconitase_C    Aconitase C-terminal domain
     0.0064   16.1   0.2      0.092   12.4   0.2    2.1  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   1.4e-21   1.3e-17      73     130 ..      49     105 ..      29     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.4e-21
                                   T--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                   Aconitase_C  73 gaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                   + ++vv++ +nfG+GSSRehA+ al+   i  via+SF+rIf +n+i+ g+  le +e
  gi|91773592|ref|YP_566284.1|  49 ENDIVVAG-NNFGCGSSREHAPIALKGSKIGCVIAKSFARIFFRNAINIGVALLECPE 105
                                   66677766.******************************************9998775 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 !   12.4   0.2     1e-05     0.092      92     157 ..      76     142 ..      42     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1e-05
                                   E--EEEEEEE-HHHHHHHHHTT-EEEE-.--TT--TT-EEEEETTTTEEEE.TT--EEEE---S-TCH CS
                 Aconitase_2_N  92 aggvvlGgkiaPiFfntvedsGalpiea.dvskletGdvieikpkegkikk.eegevvsefklkpetl 157
                                   + g v+  + a iFf  + + G   +e+ + +k+e Gd ++++ ++g i++  +ge  ++  l p+ +
  gi|91773592|ref|YP_566284.1|  76 KIGCVIAKSFARIFFRNAINIGVALLECpETDKIEDGDELTVDIASGIIENlTKGEKYQAIPL-PDFV 142
                                   3467788899*****988888887788747899****************99666665555444.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 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:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1061.43
//
Query:       gi|91773593|ref|YP_566285.1|  [L=375]
Description: 3-isopropylmalate dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-91  305.1   0.0    7.3e-91  304.9   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 !  304.9   0.0     4e-95   7.3e-91       1     347 [.       5     367 ..       5     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 304.9 bits;  conditional E-value: 4e-95
                                   EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS.SSSSS CS
                        Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk.ekevr 80 
                                   ki++l+gdgiGpe++++ +kv++aa ek g ++++ e+  G+  + etge ++e+tl+ + ++d++ lg++g    + +v 
  gi|91773593|ref|YP_566285.1|   5 KIPVLPGDGIGPEIITEGKKVIDAAGEKFGFDVDWIEYPQGADHYLETGELISEDTLKELSAYDAIYLGSIGDDRiAPGVL 85 
                                   79**********************************************************************999767777 PP

                                   HHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET.................. CS
                        Iso_dh  81 pengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg.................. 143
                                    +  Lla r  +d + nlrp+k++  ++v +plk++++ ++d+ +vRe+t++ Y+g+   +k+                  
  gi|91773593|ref|YP_566285.1|  86 EKGILLAARFYFDQYINLRPIKLL--EGVWCPLKDKTPADIDFTVVRENTEDFYIGIGGRAKTgaskdllevsrtlysakf 164
                                   666899******************..89999**************************99999899**************** PP

                                   ....TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHH CS
                        Iso_dh 144 ....sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvD 219
                                       ++ +ee a+++ ++s+e+++r++ ++f+lA+k+ +k+v +vdKanvl+    +wr++++ +a+ + pd++ +  +vD
  gi|91773593|ref|YP_566285.1| 165 gldiETDSEEIAYQIGMISKEGTQRVIDYSFDLAEKS-DKHVSSVDKANVLSDIYgFWREEFNTIAA-KHPDVKTDLNYVD 243
                                   **9755789****************************.9************98877**********9.************* PP

                                   HHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHH CS
                        Iso_dh 220 saamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalm 300
                                   +++m  vk+p+ fd++vt+N+fGDi+ D+ a++ G+lGl+p+ +++++++ +fE++HGsap++ g +k+Npia+i + +++
  gi|91773593|ref|YP_566285.1| 244 AITMWFVKNPEWFDIVVTPNMFGDIITDLGAMVQGGLGLAPGGNINPNGTSMFEPIHGSAPKYKGLNKVNPIATIWAGSML 324
                                   ********************************************************************************* PP

                                   HHHTTT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHH CS
                        Iso_dh 301 LryslgleeaAdkiekAvekvlea.givTkDlageaakevstsefgda 347
                                   ++  lg++eaAd+i +A+ek++ + ++ T+D++g++    +ts++g +
  gi|91773593|ref|YP_566285.1| 325 IEQ-LGEKEAADAIVSAIEKNILEaKVQTYDMGGSS----TTSDVGSD 367
                                   ***.***************997665*********99....88888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2401.95
//
Query:       gi|91773594|ref|YP_566286.1|  [L=94]
Description: ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   38.9   0.2    8.8e-10   38.8   0.2    1.0  1  AAA_15        AAA ATPase domain
    8.6e-06   25.8   0.0    9.9e-06   25.6   0.0    1.1  1  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.3e-05   23.4   0.6    8.2e-05   23.2   0.6    1.3  1  AAA_23        AAA domain
    0.00018   21.0   0.0    0.00018   21.0   0.0    1.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00033   21.2   0.0    0.00033   21.2   0.0    1.2  1  ABC_tran      ABC transporter
     0.0005   20.0   0.0    0.00056   19.9   0.0    1.1  1  NACHT         NACHT domain
    0.00057   19.9   0.1     0.0008   19.4   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
    0.00088   19.0   0.0     0.0012   18.6   0.0    1.2  1  AAA_29        P-loop containing region of AAA domain
     0.0017   18.8   0.0     0.0017   18.8   0.0    1.1  1  AAA_16        AAA ATPase domain
     0.0046   17.2   0.0     0.0053   17.0   0.0    1.2  1  AAA_22        AAA domain
      0.006   16.2   0.0      0.006   16.2   0.0    1.1  1  AAA_27        AAA domain
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.011   16.1   0.0    1.2  1  AAA           ATPase family associated with various cellular 
       0.02   14.8   0.0      0.025   14.5   0.0    1.2  1  RsgA_GTPase   RsgA GTPase
      0.022   14.3   0.0      0.026   14.1   0.0    1.1  1  AAA_7         P-loop containing dynein motor region
      0.029   13.6   0.0      0.029   13.6   0.0    1.1  1  NB-ARC        NB-ARC domain
      0.048   13.7   0.0      0.057   13.4   0.0    1.2  1  AAA_14        AAA domain
       0.06   12.7   0.0      0.071   12.5   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.099   12.6   0.0       0.15   12.0   0.0    1.3  1  AAA_5         AAA domain (dynein-related subfamily)
        0.1   12.4   0.0       0.14   12.0   0.0    1.3  1  MukB          MukB N-terminal
        0.1   12.3   0.0       0.13   11.9   0.0    1.1  1  AAA_30        AAA domain
       0.16   11.7   0.0       0.17   11.6   0.0    1.1  1  AAA_11        AAA domain


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.2     1e-12   8.8e-10       1      55 [.       1      72 [.       1      93 [. 0.78

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1e-12
                        AAA_15  1 MkIkkikikN.FRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...............k 55
                                  MkIk+i +kN F+ +++ v+++++e +t+l G+N++GK+ +l++l+ ++  +++                 +
  gi|91773594|ref|YP_566286.1|  1 MKIKRIVVKNlFGTFDHdVSLNIEEHITILHGPNGIGKTVLLKILNSLFRSNYYELyripfsrleiefsdrS 72
                                  *****************9********************************7744336666666665555551 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 !   25.6   0.0   1.2e-08   9.9e-06       1      63 [.      27      77 ..      27      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                  +++l GpNg GK+ LL++l  l+r            s++ ++  ip++  +++++ ++++ ++
  gi|91773594|ref|YP_566286.1| 27 ITILHGPNGIGKTVLLKILNSLFR------------SNYYELYRIPFSRLEIEFSDRSRLLVR 77
                                  7999******************76............777777888888777777777777666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.6   9.6e-08   8.2e-05       7      39 ..      12      45 ..       5      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 9.6e-08
                        AAA_23  7 frsf.rdqeidFskgltlItGpNGaGKTTildAi 39
                                  f+ f +d++++ +  +t+++GpNG GKT +l  +
  gi|91773594|ref|YP_566286.1| 12 FGTFdHDVSLNIEEHITILHGPNGIGKTVLLKIL 45
                                  799977899*******************999866 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 !   21.0   0.0   2.2e-07   0.00018       2      42 ..       3      43 ..       2      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-07
                                  EEEEEEES.ETTEECEEEEEETTSSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  2 lkrleien.FksyagktvilpfsksftaivGpNGSGKsnlld 42
                                  +kr++++n F ++ ++ v+l++++++t++ GpNG GK+ ll 
  gi|91773594|ref|YP_566286.1|  3 IKRIVVKNlFGTF-DHDVSLNIEEHITILHGPNGIGKTVLLK 43
                                  89****9945566.7***********************8876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.9e-07   0.00033       3      36 ..      18      50 ..      16      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.9e-07
                                  EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  3 nvslklkegekvaivGenGaGKStLlkllagllk 36
                                  +vsl+++e +++ + G+nG GK+ Llk+l  l +
  gi|91773594|ref|YP_566286.1| 18 DVSLNIEE-HITILHGPNGIGKTVLLKILNSLFR 50
                                  67777765.688899**************98876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.6e-07   0.00056       2      50 ..      27      73 ..      26      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.6e-07
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-. CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgn 50
                                  + il+G++G+GKT+Ll+ l ++ ++++++   ++ +F     e+s++++
  gi|91773594|ref|YP_566286.1| 27 ITILHGPNGIGKTVLLKILNSLFRSNYYEL--YRIPFSRLEIEFSDRSR 73
                                  579**************9999999999888..68888877777776655 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 !   19.4   0.0   9.4e-07    0.0008      20      68 ..      25      72 ..      19      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.4e-07
                      ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                  ++i  + Gp g+GKt Llk i++ l  +++y +y i++++ +i+  d++
  gi|91773594|ref|YP_566286.1| 25 EHITILHGPNGIGKTVLLK-ILNSLFRSNYYELYRIPFSRLEIEFSDRS 72
                                  579999*********9997.66777788**********99888766665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0012       9      40 ..      12      43 ..       3      55 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                        AAA_29  9 Wgtfdg.htieidlkg.atlltGpsGsGKSTllD 40
                                   gtfd+  +++i+  + +t+l Gp+G GK+ ll 
  gi|91773594|ref|YP_566286.1| 12 FGTFDHdVSLNIE--EhITILHGPNGIGKTVLLK 43
                                  4889886777776..558*************985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     2e-06    0.0017      24      51 ..      25      51 ..       7      90 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-06
                        AAA_16 24 pelvllsGesGvGKsslvrellralekd 51
                                  +++++l+G+ G+GK+ l++ l  +l ++
  gi|91773594|ref|YP_566286.1| 25 EHITILHGPNGIGKTVLLKILN-SLFRS 51
                                  3899**************6555.66655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.2e-06    0.0053       6      30 ..      26      50 ..      23      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.2e-06
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                   i++++G+ G+GKT+ll+ l + + 
  gi|91773594|ref|YP_566286.1| 26 HITILHGPNGIGKTVLLKILNSLFR 50
                                  689***************9998873 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     7e-06     0.006       1      50 [.       1      49 [.       1      90 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7e-06
                        AAA_27  1 MrlerLdLer.yGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                  M+++r+ ++  +G f d+ ++++  e+++++++GpN  GK+ +l+ +++l+
  gi|91773594|ref|YP_566286.1|  1 MKIKRIVVKNlFGTF-DHDVSLN-IEEHITILHGPNGIGKTVLLKILNSLF 49
                                  999999997559999.5556665.4689*************9999887775 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 ?   16.1   0.0   1.3e-05     0.011       2      33 ..      29      63 ..      28      88 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                                  EEESSTTSSHHHHHHHHHHHHT...HEEEEEETTT CS
                           AAA  2 llyGppGtGKTllakavakelg...vefleisgse 33
                                  +l+Gp G+GKT l k + + +     e+++i  s+
  gi|91773594|ref|YP_566286.1| 29 ILHGPNGIGKTVLLKILNSLFRsnyYELYRIPFSR 63
                                  79*************98887751224445555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     3e-05     0.025      92     121 ..      18      47 ..       3      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                                   HHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallp 121
                                   +++ ++++++++l G+ G+GK+ L++ l++
  gi|91773594|ref|YP_566286.1|  18 DVSLNIEEHITILHGPNGIGKTVLLKILNS 47 
                                   56678999****************999876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     3e-05     0.026      33      71 ..      25      63 ..      13      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                         AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekylsltinfsa 71
                                  ++ ++l Gp G GKtv++k l + + ++ y    i fs 
  gi|91773594|ref|YP_566286.1| 25 EHITILHGPNGIGKTVLLKILNSLFRSNYYELYRIPFSR 63
                                  5667899************99999999999999999985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.3e-05     0.029      17      42 ..      22      47 ..       7      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                                  TSCSEEEEEEESTTSSHHHHHHHHCC CS
                        NB-ARC 17 elqslvvalvGmgGvGKttlakqiln 42
                                  +++  +  l+G  G+GKt+l+k  ++
  gi|91773594|ref|YP_566286.1| 22 NIEEHITILHGPNGIGKTVLLKILNS 47
                                  56677899************975443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.7e-05     0.057       3      43 ..      26      61 ..      24      89 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                  +i ++ G+  +GKT+llk l ++l+    +  y++l + ++
  gi|91773594|ref|YP_566286.1| 26 HITILHGPNGIGKTVLLKIL-NSLF----RSNYYELYRIPF 61
                                  799*************8544.4544....233333333333 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   8.3e-05     0.071      22      46 ..      25      49 ..      18      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-05
                  Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsll 46
                                  +H  +l Gp G GKt+l k l+sl+
  gi|91773594|ref|YP_566286.1| 25 EHITILHGPNGIGKTVLLKILNSLF 49
                                  6999****************99987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.15       3      28 ..      29      54 ..      27      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                  EEE--SSSSHHHHHHHGGGGBS--EE CS
                         AAA_5  3 lLvGppGtgKselaerlaaalnreve 28
                                  +L Gp G+gK+ l + l +++++++ 
  gi|91773594|ref|YP_566286.1| 29 ILHGPNGIGKTVLLKILNSLFRSNYY 54
                                  89******************988775 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.14       6      43 ..       3      42 ..       1      56 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                  EEEEEEEEETTEEEE..EE-HHHHHHHHHS--SHHHHHHH CS
                          MukB  6 fksltlinWnGffar..tfdldelvttlsGgnGaGksttm 43
                                  +k +++ n  G f +    +++e++t l G nG Gk+  +
  gi|91773594|ref|YP_566286.1|  3 IKRIVVKNLFGTFDHdvSLNIEEHITILHGPNGIGKTVLL 42
                                  6677778888888772246789**************8654 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   0.00015      0.13      18      45 ..      25      52 ..      19      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                  + +++l+Gp G GKt +lk l+ +++++
  gi|91773594|ref|YP_566286.1| 25 EHITILHGPNGIGKTVLLKILNSLFRSN 52
                                  4599*****************9998876 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    0.0002      0.17      15      42 ..      23      49 ..      17      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                        AAA_11 15 seseitliqGPPGtgKTktivellsqll 42
                                   e++it+++GP G gKT +++++l++l 
  gi|91773594|ref|YP_566286.1| 23 IEEHITILHGPNGIGKT-VLLKILNSLF 49
                                  57889***********9.5666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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):              21  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 583.79
//
Query:       gi|91773595|ref|YP_566287.1|  [L=326]
Description: filamentation induced by cAMP protein Fic [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-24   86.6   0.0    3.7e-24   85.4   0.0    1.6  1  Fic       Fic/DOC family
  ------ inclusion threshold ------
      0.066   13.3   0.1       0.27   11.4   0.0    2.0  2  DUF4852   Domain of unknown function (DUF4852)


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 !   85.4   0.0   4.2e-28   3.7e-24       2      97 .]     178     278 ..     177     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 4.2e-28
                                   -SHHHHHHHHCHS-S------TS--SS-S....T..EEEE---SCCCHHHHHHHHHHHHC.HHT-S-HHHHHHHHHHHHHH CS
                           Fic   2 ltledllelhrlllqdigeeagefrdeev....segklesalappeevpaeleelleyln.elekeeplekaaalhyefek 77 
                                   l+ + +lelh++ +++  + ag++rd+ev    ++g++ +   p  e++ el+el +++n ++e+++pl +aa+lh +fe+
  gi|91773595|ref|YP_566287.1| 178 LSISLILELHEMCFRESKDFAGKLRDVEViirdGRGNIVHQGIPSTEIERELNELTAWYNeNREEIKPLLLAAILHNQFEY 258
                                   78899**************99*****999****99*************************99999**************** PP

                                   H--SSS-HHHHHHHHHHHHH CS
                           Fic  78 iHPFaDGNgRtarlllnllL 97 
                                   iHPF DGNgR++rllln+ L
  gi|91773595|ref|YP_566287.1| 259 IHPFEDGNGRVGRLLLNYAL 278
                                   ****************9976 PP

>> DUF4852  Domain of unknown function (DUF4852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.27      21      75 ..      62     118 ..      50     174 .. 0.86
   2 ?   -1.2   0.0      0.24   2.1e+03      31      57 ..     236     262 ..     224     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                       DUF4852  21 eadeFelqelraearkklekalrdvkleetFtille..arlseYdfdkqkFeiepls 75 
                                   + +e ++  lr++a++ + k l++ k+  +F ++++  ++l+eYd d q+ ++ pl+
  gi|91773595|ref|YP_566287.1|  62 NLNEADISTLRKDAEESILKELDSPKNLLKFSLTRKeiLKLNEYDSDIQIAHLDPLQ 118
                                   6799*****************************99745699********99999984 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.24
                       DUF4852  31 raearkklekalrdvkleetFtillea 57 
                                    +e r++++  l +++l+++F+++ + 
  gi|91773595|ref|YP_566287.1| 236 YNENREEIKPLLLAAILHNQFEYIHPF 262
                                   56788999999999999999*999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1974.75
//
Query:       gi|91773596|ref|YP_566288.1|  [L=75]
Description: hypothetical protein Mbur_1636, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-06   28.1   0.1    1.5e-06   28.0   0.1    1.0  1  HxlR      HxlR-like helix-turn-helix
    0.00017   21.5   0.1     0.0002   21.3   0.1    1.1  1  HTH_45    Winged helix-turn-helix
     0.0038   16.8   0.0     0.0064   16.0   0.0    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.048   13.7   0.0      0.079   13.0   0.0    1.3  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   3.3e-10   1.5e-06      21      85 ..       3      67 ..       1      72 [. 0.89

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.3e-10
                                  HHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS.-EEEEEE-TCGGGGHHHHHHHHHHHHH CS
                          HxlR 21 fselkralpkisqkmLaqrLreLeqdglierevypevP.pkveYsltekGrslepvlqelkkwgee 85
                                  f+el++++ ++   +L +rL+e+ + glie  v    + ++v+ +lt+kG++l p l+e+ k++ee
  gi|91773596|ref|YP_566288.1|  3 FNELEKTV-GVYPDTLNKRLKEMLKYGLIEPIVDVVDGkNRVKHRLTAKGQQLIPTLKEFIKLAEE 67
                                  99***999.88899****************99876655279*******************999987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   4.5e-08    0.0002      34      76 ..      15      65 ..       5      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.5e-08
                        HTH_45 34 kllnkYLdmLvekgli........kkskekYvlTekGlelleklkeleela 76
                                  ++lnk L+ +++ gli         k+  k +lT+kG++l+ +lke+++la
  gi|91773596|ref|YP_566288.1| 15 DTLNKRLKEMLKYGLIepivdvvdGKNRVKHRLTAKGQQLIPTLKEFIKLA 65
                                  6899***********9999999998999*******************9987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0064      18      48 .]       1      31 [.       1      31 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                        HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +s +eL + +g+ p t+n+rlk++ + GlI+
  gi|91773596|ref|YP_566288.1|  1 MSFNELEKTVGVYPDTLNKRLKEMLKYGLIE 31
                                  578888899*********************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.8e-05     0.079      25      55 ..       1      31 [.       1      34 [. 0.95

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20 25 ltaselaerldlskntlsyHLrvLeeagLve 55
                                  ++++el +++++ + tl+++L+++ + gL+e
  gi|91773596|ref|YP_566288.1|  1 MSFNELEKTVGVYPDTLNKRLKEMLKYGLIE 31
                                  799***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 484.64
//
Query:       gi|91773597|ref|YP_566289.1|  [L=103]
Description: hypothetical protein Mbur_1637 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.1   0.1       0.12   12.8   0.1    1.1  1  DSPn      Dual specificity protein phosphatase, N-terminal ha


Domain annotation for each model (and alignments):
>> DSPn  Dual specificity protein phosphatase, N-terminal half
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.9e-06      0.12      26      86 ..       9      68 ..       2      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-06
                          DSPn 26 siddelvYenFyaDFGPlnlaqlyrfcvkvnkkLkskelskkkivhytsadekkranaafL 86
                                  +i ++++Ye+F + +  l+ + +  +   v k++ + +  kk+ v +++  + + ++a+f+
  gi|91773597|ref|YP_566289.1|  9 TIKTDMTYEQFIERYAALKFQKTKGYSSYVGKMIGDISPDKKNHVACSTG-KIHPTKAIFI 68
                                  67788*********************************999999999877.4555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 672.85
//
Query:       gi|91773598|ref|YP_566290.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91773598|ref|YP_566290.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91773598|ref|YP_566290.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91773598|ref|YP_566290.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91773598|ref|YP_566290.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91773598|ref|YP_566290.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91773598|ref|YP_566290.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91773598|ref|YP_566290.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91773598|ref|YP_566290.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2067.10
//
Query:       gi|91773599|ref|YP_566291.1|  [L=269]
Description: hypothetical protein Mbur_1641 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-27   97.4   3.2    1.6e-27   96.9   3.2    1.2  1  UPF0489   UPF0489 domain


Domain annotation for each model (and alignments):
>> UPF0489  UPF0489 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   3.2     9e-32   1.6e-27       2     178 .]      20     180 ..      19     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 9e-32
                       UPF0489   2 vivesHheaLeaiyraigskklpsdlslvHlDaHpDllipkkmsaddvfnallkil.ekl...aeelleelsi.dnwIlpa 77 
                                   +++ +H +aL+a+++a++++ +++d++l+HlD+H+D+    +m++d++ ++++ ++ ++l    + ++e +++ d++I++a
  gi|91773599|ref|YP_566291.1|  20 YFIIDHAAALIAWIKAFNEGIISRDATLFHLDKHTDF----HMNSDNIKKSKTILGmDNLelnDFVTVELCDEnDEFIVNA 96 
                                   56779*******************************7....999******999999999999988889****99******* PP

                       UPF0489  78 vyaghisrvvwikpawaqqitegrkellvgkdresirvdstedyflsdllyvpeeeleelkqlelevleveeaslsekqdl 158
                                   +++g+i++++ ++++++                      s++++ +++++++p++ + ++  ++++++ +e +++s  +++
  gi|91773599|ref|YP_566291.1|  97 MWSGLIKDCISFHHEEG----------------------SYDGILIEENQFAPQKINFKCDGMDHNFYLFEGHDISLIDNI 155
                                   *****************......................9***************************************** PP

                       UPF0489 159 .....ilavleksksfildiDlDyF 178
                                        i++++e+ ++fildiDlD+F
  gi|91773599|ref|YP_566291.1| 156 lnyqeIMNICECGRDFILDIDLDFF 180
                                   ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1742.34
//
Query:       gi|91773600|ref|YP_566292.1|  [L=121]
Description: hypothetical protein Mbur_1642 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-06   27.1   0.1    4.2e-06   26.5   0.0    1.3  1  HxlR      HxlR-like helix-turn-helix
    0.00085   19.3   0.0     0.0011   18.9   0.0    1.3  1  HTH_45    Winged helix-turn-helix
     0.0011   19.0   0.0     0.0016   18.4   0.0    1.3  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.22   11.1   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   9.4e-10   4.2e-06       5      85 ..      33     113 ..      29     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 9.4e-10
                                   TTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS.-EEEEEE-TCGGGGHHHHHHHHHHHH CS
                          HxlR   5 kWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevP.pkveYsltekGrslepvlqelkkwge 84 
                                   k  + il+ l + ++ f+ l++++ ++   +L +rL+e+ +  lie  v    + ++v+ +lt+kG++l p l+e+ k++e
  gi|91773600|ref|YP_566292.1|  33 KHFCDILILLERAPMSFNGLEKTV-GVYPDTLNKRLKEMLKYDLIEPIVDVVDGkNRVKHRLTAKGQQLIPTLKEFIKLAE 112
                                   566679999999***********9.89999****************99866655279*******************99998 PP

                                   H CS
                          HxlR  85 e 85 
                                   e
  gi|91773600|ref|YP_566292.1| 113 E 113
                                   7 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.5e-07    0.0011      34      76 ..      61     111 ..      35     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-07
                        HTH_45  34 kllnkYLdmLvekgli........kkskekYvlTekGlelleklkeleela 76 
                                   ++lnk L+ +++ +li         k+  k +lT+kG++l+ +lke+++la
  gi|91773600|ref|YP_566292.1|  61 DTLNKRLKEMLKYDLIepivdvvdGKNRVKHRLTAKGQQLIPTLKEFIKLA 111
                                   7899***********9999999998999*******************9986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.6e-07    0.0016       4      55 ..      27      77 ..      24      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.6e-07
                                  HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                  +++L  +  ++il +L ++++++++ l +++++ + tl+++L+++ + +L+e
  gi|91773600|ref|YP_566292.1| 27 LKLLYKKHFCDILILL-ERAPMSFNGLEKTVGVYPDTLNKRLKEMLKYDLIE 77
                                  5666667789******.**********************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     5e-05      0.22      11      48 .]      40      77 ..      37      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5e-05
                        HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +L + + +s + L + +g+ p t+n+rlk++ +  lI+
  gi|91773600|ref|YP_566292.1| 40 ILLERAPMSFNGLEKTVGVYPDTLNKRLKEMLKYDLIE 77
                                  4555578888888899*****************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 765.14
//
Query:       gi|91773601|ref|YP_566293.1|  [L=1200]
Description: cell surface protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-72  243.8 166.7    1.4e-38  132.6  52.4    6.9  6  NosD        Periplasmic copper-binding protein (NosD)
    5.4e-55  185.6 176.7      4e-20   72.3  45.6    7.2  8  Beta_helix  Right handed beta helix region
    6.6e-10   38.5   0.3    2.2e-09   36.7   0.0    2.1  2  S-layer     S-layer protein
    6.7e-07   29.3   0.0        1.6    8.9   0.0    5.1  5  BiPBP_C     Penicillin-Binding Protein C-terminus Family
  ------ inclusion threshold ------
        2.4    8.4   7.8       0.18   12.1   1.0    2.7  3  SepZ        SepZ
        2.7    7.9  28.0        1.2    9.0   2.3    5.1  4  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 !   64.9  38.7   2.2e-21   6.5e-18      36     175 ..     117     253 ..      47     256 .. 0.85
   2 !   52.4  26.8   1.4e-17   4.2e-14      17     154 ..     230     361 ..     229     363 .. 0.93
   3 !   40.0  24.8   8.6e-14   2.6e-10      71     174 ..     346     450 ..     343     450 .. 0.93
   4 !  132.6  52.4   4.6e-42   1.4e-38      25     241 .]     437     643 ..     433     643 .. 0.95
   5 ?  -10.2  15.1         6   1.8e+04      17     129 ..     805     931 ..     791    1008 .. 0.73
   6 ?   -1.7   0.4      0.46   1.4e+03      31      77 ..    1088    1112 ..    1058    1155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 2.2e-21
                          NosD  36 nsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnn 116
                                   +  +gi    s++nt+ ++  ++++yG+++ +se+ntie+n ++sn++Gi+l +s+nn l  N++s+n+n G ++s+s+n 
  gi|91773601|ref|YP_566293.1| 117 DADSGI-KIMSDDNTVLNCIAQSNNYGVYVFESENNTIENNSVYSNTEGIYLLYSHNNSLISNNLSSNTNRGAYISNSDNI 196
                                   334444.67899**********************************************5555666666666********** PP

                          NosD 117 tisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsen 175
                                   ++  N+++nn++Gi  + s ++t+ +N+ +sn ++G++ lssse+ ++ nN+  +n+++
  gi|91773601|ref|YP_566293.1| 197 SVLSNVAQNNDYGINWYISGNSTVFNNSATSN-NYGMY-LSSSENCNLDNNTAYGNTNH 253
                                   ********************************.*****.******9999*999999887 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 1.4e-17
                          NosD  17 ngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlen 97 
                                   +g++l++se++ + nn+   + ++  +++ss+n +t+nt  ++ yG++ ++s+s t+ +n+++sn++G++ + ss +tl+n
  gi|91773601|ref|YP_566293.1| 230 YGMYLSSSENCNLDNNTAYGNTNHGIYSDSSGNIFTNNTAYSNIYGLYTTGSSS-TLANNIAYSNKYGFYTTGSS-STLTN 308
                                   79***********9999988888888**************************99.********************.***** PP

                          NosD  98 NtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGil 154
                                   N++ +n++ G+++++ss +t++nNt+  n+n+G+++    ++t+ +N+  +n ++G++
  gi|91773601|ref|YP_566293.1| 309 NIAYSNRY-GFYTTGSS-STLTNNTAYsNTNRGFTIHT--RSTLIDNNAFNN-GYGFW 361
                                   ******88.*****999.67******88********99..788888888888.89987 PP

  == domain 3  score: 40.0 bits;  conditional E-value: 8.6e-14
                          NosD  71 ntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqk 150
                                   +t+ dn +++n++G++++s   n+l+nNt+s+n nyG+++   ++n++++Nt+  n+n+G ++ + ++nt+t+N++++n +
  gi|91773601|ref|YP_566293.1| 346 STLIDNNAFNNGYGFWIESDY-NILTNNTASDNANYGFYIYIGDYNKLTKNTANsNSNYGYYIIG-NYNTLTKNNVSDN-S 423
                                   578899999*********999.*******************************99**********.8************.* PP

                          NosD 151 iGilllssseg...ntiynNyFinnse 174
                                    Gi+l+s++ +   n++ +N+ inns+
  gi|91773601|ref|YP_566293.1| 424 GGIHLTSGGASrgsNLLIQNTIINNSN 450
                                   ****8888755667**********985 PP

  == domain 4  score: 132.6 bits;  conditional E-value: 4.6e-42
                          NosD  25 egseisnneisnsrdgilldnssnntitgntienl.ryGihlensesntiedntlssne.sGialmsssnntlenNtisnn 103
                                   ++  i+n+ i+ns++gi+l++s  n +  n+++n+ ++Gi++++s+ nt+++n++s+n+ +Gi+l+sss++tl+nN++snn
  gi|91773601|ref|YP_566293.1| 437 SNLLIQNTIINNSNYGIYLSYSGINILMYNVVSNNtNTGIYISDSKYNTLTNNVVSNNTnNGIYLTSSSDSTLTNNIVSNN 517
                                   677789************************9999999******************************************** PP

                          NosD 104 enyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllssseg..ntiynNyFinnsenvkydgs 181
                                   +n+Gi+ls+s ++++ +N i  n+n+G++l ns +  + +N+i+++ + Gi+ ++++++   +iynN+++n s++ +yd +
  gi|91773601|ref|YP_566293.1| 518 TNHGIYLSNSIDTKLLYNLIFnNTNTGVYLFNSGGGALANNTIDNS-NDGIY-IDQGTTsqSSIYNNTLLNISNHGAYDIK 596
                                   ********************99************************.*****.8888665599****************** PP

                          NosD 182 nnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgv...iDylplvnps 241
                                   + n+W                + Ny++dy+g D+++DGigD++Y i +++    D+ pl++p+
  gi|91773601|ref|YP_566293.1| 597 GLNSW----------------HSNYYDDYNGIDSNNDGIGDSAYYIAGNDvglRDETPLMQPH 643
                                   *****................89***********************98776789******995 PP

  == domain 5  score: -10.2 bits;  conditional E-value: 6
                          NosD  17 ngiqlensegsei...snneisnsrdgi.....lldnssnntitgn....tienl...ryGihlensesntiedntlssne 82 
                                   +gi+l+  +  +          + + g       ++n + +t ++n    +       + +i+l++ +s  i+d + +s +
  gi|91773601|ref|YP_566293.1| 805 DGITLYTNTSVTTasyY---NGSAQLGThnltvVAENTNRKTSQKNwtwtV---TepsAPSITLSSPSSASISDIEGDSRT 879
                                   56666555444442222...2222222233332333333333333344423...044599999999999999999999988 PP

                          NosD  83 sGialmsssnn..tlenNtisnnen..yGillsdssnntisnNtis.nnnkG 129
                                      ++++  n   +l++Nti+ n+      ++++s++  i n ti  +n +G
  gi|91773601|ref|YP_566293.1| 880 FTTTVDQVVNVtwILDGNTIQTNTSiqTASYYNGSAKVGIHNLTIFaENVNG 931
                                   7777777775547899999999999877779999999999999998666665 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 0.46
                          NosD   31 nneisnsrdgilldnssnntitgntienlryGihlensesntiednt 77  
                                    n+                        +++ y+i+++  + n +++n+
  gi|91773601|ref|YP_566293.1| 1088 NT----------------------SAHEGVYNITIVAENANGASQNK 1112
                                    22......................22333444444444443333333 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1  37.4   6.3e-19   1.9e-15       8     148 ..      96     238 ..      82     239 .. 0.92
   2 !   46.4  31.6   1.2e-15   3.7e-12      22     158 .]     228     354 ..     227     354 .. 0.93
   3 !   55.9  38.2   1.4e-18   4.3e-15       1     151 [.     316     462 ..     316     465 .. 0.94
   4 !   72.3  45.6   1.3e-23     4e-20       7     157 ..     435     583 ..     432     584 .. 0.94
   5 ?   -0.8   5.2      0.41   1.2e+03       9      67 ..     575     629 ..     571     669 .. 0.68
   6 ?   -7.8  10.6         6   1.8e+04      16     146 ..     795     936 ..     783     943 .. 0.47
   7 ?   -9.2  12.2         6   1.8e+04      37     121 ..     895    1001 ..     851    1027 .. 0.49
   8 ?   -3.8   0.6       3.4     1e+04      25      51 ..    1072    1097 ..    1064    1115 .. 0.42

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 6.3e-19
                                   S-E.EEESEEEES-........SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S-- CS
                    Beta_helix   8 ssnvtiknntisns........ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnn 80 
                                   ++++ti+++++++s         ++Gi++ +++n ++ n+  ++ + +G+y+ +s+nnti+nn+++ n+  gi+l +++nn
  gi|91773601|ref|YP_566293.1|  96 TDDCTIDGFNVTGSgtdwnggdADSGIKIMSDDN-TVLNCIAQS-NNYGVYVFESENNTIENNSVYSNT-EGIYLLYSHNN 173
                                   45589999999999********************.888677777.************************.*********** PP

                                   EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-S CS
                    Beta_helix  81 lienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgss 148
                                    +  n+ + n + G y+++s+n+++  N++ nn  +Gi  + s+ n tv+nN++t+n+ +G ++ +s 
  gi|91773601|ref|YP_566293.1| 174 SLISNNLSSNTNRGAYISNSDNISVLSNVAQNND-YGINWYISG-NSTVFNNSATSNN-YGMYLSSSE 238
                                   **********999*********************.*********.************8.***888775 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 1.2e-15
                                   SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S- CS
                    Beta_helix  22 ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssn 102
                                   ++yG yl +s+n+ ++nn+ ++n+ +Giy  + s+n+++nnt + n  +g++++g+s +++ nn  + n+  G+y++  s+
  gi|91773601|ref|YP_566293.1| 228 NNYGMYLSSSENCNLDNNTAYGNTNHGIYSDS-SGNIFTNNTAYSNI-YGLYTTGSS-STLANNIAYSNKY-GFYTT-GSS 303
                                   68****************************96.**************.******999.8889999999976.***98.799 PP

                                   -EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                    Beta_helix 103 ntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                    t++nNi+++n+ +G++ + ss   t tnNt+++n + G+++ ++s+   + nN +
  gi|91773601|ref|YP_566293.1| 304 STLTNNIAYSNR-YGFYTTGSS--STLTNNTAYSNTNRGFTIHTRST--LIDNNAF 354
                                   ************.*********..556*************9998888..9999976 PP

  == domain 3  score: 55.9 bits;  conditional E-value: 1.4e-18
                                   -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                    Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                   +g++ +gss+ t++nnt +++ + G+++ + s+ +i+nn ++n  g+G++i++ ++n+++nnt sdn ++g++++ +++n 
  gi|91773601|ref|YP_566293.1| 316 YGFYTTGSSS-TLTNNTAYSNTNRGFTIHTRST-LIDNNAFNN--GYGFWIES-DYNILTNNTASDNANYGFYIYIGDYNK 391
                                   69999*****.*********************9.*******99..******97.*************************** PP

                                   EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT...---EEES-EEES-SSEEEE-TT-SS-- CS
                    Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdss...snvtvtnNtitnnkgaGiavvgsssnv 151
                                   + +n+ + n+++G+y+   + nt+++N++++n+  Gi++++++    ++   +Nti nn+++Gi++ +s+ n+
  gi|91773601|ref|YP_566293.1| 392 LTKNTANSNSNYGYYII-GNYNTLTKNNVSDNS-GGIHLTSGGasrGSNLLIQNTIINNSNYGIYLSYSGINI 462
                                   ****************9.588999999999***.************777789999999999***999998765 PP

  == domain 4  score: 72.3 bits;  conditional E-value: 1.3e-23
                                   SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EE CS
                    Beta_helix   7 gssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnliennei 87 
                                   ++sn  +  nti n+++yGiyl  s+ +++  n+++nn+ +Giyi+ s++nt++nn++s+n++ gi+l+ +s +++ nn +
  gi|91773601|ref|YP_566293.1| 435 RGSN-LLIQNTIINNSNYGIYLSYSGINILMYNVVSNNTNTGIYISDSKYNTLTNNVVSNNTNNGIYLTSSSDSTLTNNIV 514
                                   5667.66777888889***************************************************************** PP

                                   ES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS.--EEES-E CS
                    Beta_helix  88 tdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss.nvtvrnNt 157
                                   ++n ++Giyl++s ++++ +N i nn++ G+++ +s+ +    nNti+n++  Gi++  + + +  ++nNt
  gi|91773601|ref|YP_566293.1| 515 SNNTNHGIYLSNSIDTKLLYNLIFNNTNTGVYLFNSG-GGALANNTIDNSN-DGIYIDQGTTsQSSIYNNT 583
                                   *************************************.8888******886.***999988899******9 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.41
                                   -E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE-- CS
                    Beta_helix   9 snvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdn 67 
                                   s+ +i nnt+ n++++G y   + n    +n++    ++Gi+ ++ +++  s  +i +n
  gi|91773601|ref|YP_566293.1| 575 SQSSIYNNTLLNISNHGAYDIKGLN-SWHSNYYD--DYNGIDSNN-DGIGDSAYYIAGN 629
                                   3457899999999999988888888.44434444..488888877.4444444444444 PP

  == domain 6  score: -7.8 bits;  conditional E-value: 6
                                   EEEES-..SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---......SEEE-TT--S--EEES-EE CS
                    Beta_helix  16 ntisns..ggyGiylrgssnvvienneiannsgsGiyilgs.snntisnntisdnn......gggialfgasnnliennei 87 
                                   n++s++    +Gi+l+++++v+   ++++++ + G + l + ++nt ++ +   n+       ++  ++ +s++  + ++i
  gi|91773601|ref|YP_566293.1| 795 NQVSDVtwILDGITLYTNTSVTTA-SYYNGSAQLGTHNLTVvAENTNRKTSQK-NWtwtvtePSAPSITLSSPSSASISDI 873
                                   555555444566666666663333.4444433333333333222222222221.113455555555555555555555555 PP

                                   ES-SS-SEE-T.T...-S--EEES-EEESTT..--SEE---TT---EEES-EEES-SSEEEE-TT CS
                    Beta_helix  88 tdnggsGiyln.y...ssnntienNiidnna..gsGividdsssnvtvtnNtitnnkgaGiavvg 146
                                   +  ++  ++++ +   +   ++ +N+i  n+  + + +++ s+ +v ++n ti+  + +G +++ 
  gi|91773601|ref|YP_566293.1| 874 EGDSR-TFTTTvDqvvNVTWILDGNTIQTNTsiQTASYYNGSA-KVGIHNLTIFAENVNGTDQNK 936
                                   55544.3333322333333445777777777633344444444.777777766655556665555 PP

  == domain 7  score: -9.2 bits;  conditional E-value: 6
                                    ES-EEES..-SS-SEEE-TT-S-EEES-EE.......E---..........SEEE-TT--S--EEES-EEES-SS-SEE CS
                    Beta_helix   37 enneian..nsgsGiyilgssnntisnnti.......sdnn..........gggialfgasnnlienneitdnggsGiy 96  
                                    ++n+i+   + ++  y +gs+++ i+n ti       +               +  ++ +s++ ++ ++++  ++  ++
  gi|91773601|ref|YP_566293.1|  895 DGNTIQTntSIQTASYYNGSAKVGIHNLTIfaenvngT--DqnkwtwtvtePPAPSITHSSPSSVSISDVEGDSR-TFT 970 
                                    34444443333333333344555555555533332221..02233444444334444444444444444444433.222 PP

                                    -T.T...-S--EEES-EEESTT..--SEE-- CS
                    Beta_helix   97 ln.y...ssnntienNiidnna..gsGivid 121 
                                    ++ +   +   ++ +N+i  n+  + + +++
  gi|91773601|ref|YP_566293.1|  971 TTvDqvaNVTWILDGNTIQTNTsiQTASYYN 1001
                                    2212322222334556665555433333333 PP

  == domain 8  score: -3.8 bits;  conditional E-value: 3.4
                                    SEEE-SSS-.EEES-EEES-SS-SEEE CS
                    Beta_helix   25 GiylrgssnvvienneiannsgsGiyi 51  
                                    Gi l+++++v+    +++ + ++G+y 
  gi|91773601|ref|YP_566293.1| 1072 GIILYTNTSVTTA-AYYNTSAHEGVYN 1097
                                    4444444442222.2222223333332 PP

>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   7.5e-13   2.2e-09     112     204 ..     663     746 ..     625     760 .. 0.83
   2 ?   -3.9   0.0       1.9   5.6e+03      21      51 ..     820     849 ..     817     854 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7.5e-13
                       S-layer 112 ktlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyvyekdlgdeddvviiavhvdevfrgte 192
                                    t+k+g+ + L egY+l + q+Dv g+kvw+eL+ +g+ +d++v++     s + y   +g +++ +i+  ++d++  ++ 
  gi|91773601|ref|YP_566293.1| 663 FTVKAGTAILLYEGYSLVPLQFDVSGEKVWFELRMNGNRIDDEVLEI---GSYFSY---VG-SQNQLILTGRLDSI--SQA 734
                                   5899******************************************9...777776...33.34456666666666..444 PP

                       S-layer 193 dslvviegifqi 204
                                   d+ + ++  +q+
  gi|91773601|ref|YP_566293.1| 735 DNSMKMDSFYQF 746
                                   555555666655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.9
                       S-layer  21 yydiddglssEsltlelesksdrtieegelv 51 
                                   yy+   +l++ +lt+ +e+ ++r+ ++++ +
  gi|91773601|ref|YP_566293.1| 820 YYNGSAQLGTHNLTVVAEN-TNRKTSQKNWT 849
                                   9999999999999998664.88877777655 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 ?   -0.0   0.0      0.31   9.4e+02      18      55 ..     666     702 ..     664     707 .. 0.83
   2 !    6.7   0.0    0.0025       7.6      31      80 ..     786     837 ..     765     845 .. 0.71
   3 ?    4.7   0.0      0.01        31      41      77 ..     886     924 ..     853     928 .. 0.73
   4 !    8.9   0.0   0.00052       1.6      42      79 ..     976    1015 ..     943    1024 .. 0.80
   5 ?    0.6   0.0      0.19   5.8e+02      40      80 ..    1061    1103 ..    1044    1111 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.31
                       BiPBP_C  18 adGailaldpdipkrqrlqlkarggeaplrWlldgepl 55 
                                   ++G+ + l ++  +  +lq+ ++g +  ++++++g  +
  gi|91773601|ref|YP_566293.1| 666 KAGTAILLYEGY-SLVPLQFDVSGEKVWFELRMNGNRI 702
                                   578888888776.8999********999******9877 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0025
                       BiPBP_C  31 krqrlqlkarggeaplrWlldgeplaetkrgrelawqp...epGrhrLtvvDa 80 
                                   + + +++ + +    ++W+ldg  l + ++  +++      + G+h Ltvv +
  gi|91773601|ref|YP_566293.1| 786 DSRLFTMNVNQV-SDVTWILDGITLYTNTSVTTASYYNgsaQLGTHNLTVVAE 837
                                   444445555554.579*********877777777777778899*******977 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.01
                       BiPBP_C  41 ggeaplrWlldgeplaetkrgrelawqp...epGrhrLtv 77 
                                   +    ++W+ldg  +++ ++ ++++      + G h Lt+
  gi|91773601|ref|YP_566293.1| 886 QV-VNVTWILDGNTIQTNTSIQTASYYNgsaKVGIHNLTI 924
                                   33.489*********7777777777766677888888887 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00052
                       BiPBP_C   42 geaplrWlldgeplaetkrgrelawqp...epGrhrLtvvD 79  
                                      a ++W+ldg  +++ ++ ++++      + G+h Ltv  
  gi|91773601|ref|YP_566293.1|  976 V-ANVTWILDGNTIQTNTSIQTASYYNnsaKTGTHNLTVFA 1015
                                    3.58**********7777777777766688********965 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.19
                       BiPBP_C   40 rggeaplrWlldgeplaetkrgrelawqp...epGrhrLtvvDa 80  
                                    ++  a ++W+ dg  l + ++  ++a      ++G + +t+v +
  gi|91773601|ref|YP_566293.1| 1061 DQV-ANVTWIFDGIILYTNTSVTTAAYYNtsaHEGVYNITIVAE 1103
                                    333.589*******995555544444433367999999999865 PP

>> SepZ  SepZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   5.9e-05      0.18      39      89 ..       4      57 ..       2      66 .. 0.77
   2 ?   -4.1   0.1         6   1.8e+04      54      68 ..      82      96 ..      69     102 .. 0.61
   3 ?   -1.7   0.1       1.2   3.5e+03      18      43 ..     413     438 ..     401     479 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                          SepZ 39 srtvrvlaGvalattalaalGaGiaalcvenssqk.klgl..GiaaGvlGglta 89
                                  +r++rv+aGv++a+  la   a  aa+ v++s    +l++   i    +G +  
  gi|91773601|ref|YP_566293.1|  4 NRALRVFAGVVVAILVLAVGSASAAAITVDDSGGAdYLSIqaAINNASVGDVIE 57
                                  89***************9999999999999998766887622344555666555 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 6
                          SepZ 54 alaalGaGiaalcve 68
                                   + a G+G a+  ++
  gi|91773601|ref|YP_566293.1| 82 LINASGSGTAMTITT 96
                                  455666666665554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.2
                          SepZ  18 tinGnnsvdektGvlkpenGtsrtvr 43 
                                   t++ nn  d++ G+  + +G+sr   
  gi|91773601|ref|YP_566293.1| 413 TLTKNNVSDNSGGIHLTSGGASRGSN 438
                                   77888999999999999999999654 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4     0.024        73      52      66 ..     826     840 ..     786     845 .. 0.76
   2 ?    1.2   1.0      0.11   3.2e+02      11      64 ..     875     928 ..     873     934 .. 0.62
   3 ?    7.7   3.8     0.001       3.1      11      67 ..     964    1020 ..     954    1023 .. 0.75
   4 ?    9.0   2.3    0.0004       1.2      11      70 ..    1051    1110 ..    1048    1111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.024
                                   SSEEEEEEEEEE-SS CS
                           PKD  52 spGeYeVtvtasnav 66 
                                   + G++++tv+a+n+ 
  gi|91773601|ref|YP_566293.1| 826 QLGTHNLTVVAENTN 840
                                   37***********86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                   SEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S..SEEEEEEEEEE- CS
                           PKD  11 gatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls..pGeYeVtvtasn 64 
                                   g + +ft +v+  +nvt+  d +  +  + +s +t+++   s   G +++t  a+n
  gi|91773601|ref|YP_566293.1| 875 GDSRTFTTTVDQVVNVTWILDGN--TIQTNTSIQTASYYNGSakVGIHNLTIFAEN 928
                                   66889*****6666666655544..4555555555555432244788888877777 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.001
                                    SEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S...SEEEEEEEEEE-SS- CS
                           PKD   11 gatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls...pGeYeVtvtasnavg 67  
                                    g + +ft +v+  anvt+  d +     + +s +t+++  ++   +G++++tv a+n+ g
  gi|91773601|ref|YP_566293.1|  964 GDSRTFTTTVDQVANVTWILDGNT--IQTNTSIQTASYY-NNsakTGTHNLTVFAENTNG 1020
                                    78899*****77777777777555..5555555666664.44477************998 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0004
                                    SEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S...SEEEEEEEEEE-SS-EEE CS
                           PKD   11 gatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls...pGeYeVtvtasnavgsat 70  
                                    g +  fta+   ++ ++ +W f+      + ++ t+   Y++   +G Y++t +a+na g+++
  gi|91773601|ref|YP_566293.1| 1051 GDSRSFTATI--DQVANVTWIFDG-IILYTNTSVTTAAYYNTsahEGVYNITIVAENANGASQ 1110
                                    6677899999..566666666666.44666677777777777888**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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):               6  [number of targets reported over threshold]
# CPU time: 0.92u 0.37s 00:00:01.29 Elapsed: 00:00:00.50
# Mc/sec: 7163.92
//
Query:       gi|91773602|ref|YP_566294.1|  [L=416]
Description: hypothetical protein Mbur_1644 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.042   13.8   0.0       0.12   12.3   0.0    1.8  1  Phage_Coat_B  Phage Coat protein B
      0.078   13.0   0.5       0.17   12.0   0.0    1.8  2  DUF4366       Domain of unknown function (DUF4366)


Domain annotation for each model (and alignments):
>> Phage_Coat_B  Phage Coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.3e-05      0.12      33      81 ..     358     406 ..     337     408 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                  Phage_Coat_B  33 pvfaasvidtsavesaitdgksdmkaiggyivgalvilavagliysmlr 81 
                                   p+ +a+  +ts+ +s     +sd      y+vgal i+ +ag  y m r
  gi|91773602|ref|YP_566294.1| 358 PMSTATSEQTSTQDSNGEGKQSDEGISMWYLVGALAIMLIAGGTYLMYR 406
                                   55566666677666665555667666678*****************998 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3      0.62   5.5e+03     119     136 ..       7      25 ..       2      30 .. 0.42
   2 ?   12.0   0.0   1.8e-05      0.17      95     143 ..     356     410 ..     340     413 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.62
                       DUF4366 119 glllvvlavaligg.gaay 136
                                   +++ v+l+ +  g+ ga +
  gi|91773602|ref|YP_566294.1|   7 IVAFVLLMAMCTGVaGATW 25 
                                   2333333334444444444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.8e-05
                       DUF4366  95 eepepekeaepee......peeepekksnnglllvvlavaligggaayyfkvlkp 143
                                   +ep +++++e+++      + ++++++ ++  l+  la++li+gg + ++ ++k+
  gi|91773602|ref|YP_566294.1| 356 TEPMSTATSEQTStqdsngEGKQSDEGISMWYLVGALAIMLIAGGTYLMYRTKKD 410
                                   33333333332222111224444444455888999999******99988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 2251.84
//
Query:       gi|91773603|ref|YP_566295.1|  [L=451]
Description: ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-19   69.4  13.1    8.9e-19   68.4  13.1    1.5  1  AAA_15    AAA ATPase domain
    3.5e-15   56.6   6.7    3.3e-09   37.0   2.1    2.5  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.1e-08   35.6   0.1     0.0047   17.5   0.0    2.6  2  ABC_tran  ABC transporter
    0.00012   22.7   4.0    0.00036   21.1   3.6    2.0  1  AAA_23    AAA domain
    0.00029   20.3   0.1     0.0027   17.2   0.1    2.1  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0027   18.1   0.1      0.012   16.0   0.0    2.2  3  AAA_16    AAA ATPase domain
     0.0027   17.6   0.0     0.0068   16.3   0.0    1.7  1  NACHT     NACHT domain
     0.0038   17.2   0.7     0.0038   17.2   0.7    2.1  2  ATPase_2  ATPase domain predominantly from Archaea
     0.0091   15.9   0.1      0.025   14.5   0.1    1.7  1  HNH_4     HNH endonuclease
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.024   14.4   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.014   15.7   0.3      0.042   14.1   0.0    2.0  2  AAA_22    AAA domain
      0.018   15.5   0.0       0.12   12.9   0.0    2.5  2  AAA       ATPase family associated with various cellular acti
      0.078   12.5   0.0       0.36   10.3   0.0    2.0  2  AAA_7     P-loop containing dynein motor region
      0.081   12.5   0.0       0.14   11.7   0.0    1.4  1  AAA_27    AAA domain


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4  13.1   6.9e-22   8.9e-19       1     369 []       1     430 [.       1     430 [. 0.57

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 6.9e-22
                        AAA_15   1 MkIkkikikN.FRslkdveidlsee..ltvliGkNnsGKSsilealdlFlnnkekkn........................ 54 
                                   MkIk+i +kN F+ +++ +++l+ e  +t+l G+N++GK+ +l++l+ ++  +++                          
  gi|91773603|ref|YP_566295.1|   1 MKIKRIVVKNlFGTFDH-DVPLNTEehITILHGPNGIGKTVLLKILNSLFRSNYYELyripfsrleiefsdrsrllvrkkl 80 
                                   **********9999999.666655556************************774444777777877777777777777444 PP

                        AAA_15  55 ..............kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikd 121
                                                 + ++ +e  +  +++ +++ k+i+I+  f     +   ++ + ++ +k +d+ + ++ ++ k t+++
  gi|91773603|ref|YP_566295.1|  81 hldetepikaensgYRELAFEWLKPTHKKVRYTVKPIDIEEVF-----STLKVEHMIPELEKIDDNTWVHFTTQEKLTSEE 156
                                   3333333333333322222222222222233333333333333.....111111111222222222333333333333333 PP

                        AAA_15 122 kklklkknelsdekisvekkks.....kkelpkekeeklekekeelkidkedlkklikkleeslkkee............. 184
                                    +  ++ ++l +++++     +     ++              +++ i + ++              +             
  gi|91773603|ref|YP_566295.1| 157 VMSLFS-DKLPQKRKD-----EpawlrEVL-------------ASINICFIKT--------------Qrllsisfsqsvet 204
                                   222221.111111111.....122222222.............2222222222..............12222222222344 PP

                        AAA_15 185 ...............elknvlksaiikl.ll.isakRnvsdedsekkssllgklkekileealqekl.............. 234
                                                  el  ++++++ ++  l  s +R++ + + +  s+ l++ +++++ e ++ +               
  gi|91773603|ref|YP_566295.1| 205 errtsvipsvisyshELAGSMQKKLAEYaALsQSLDRTFPSRLLKTDSKHLDTSIKELKVELVKLEDkrkqlidagfidse 285
                                   446666666666666444444444444313314568999986666666666666666666544433366678999999998 PP

                        AAA_15 235 ....eeelteklkeiqeklkeidkklaeelk..........kilkkkidkik.kfnykgkkneeieik.....ddeelpln 295
                                       +    e++ +i+e+ +++ + + e+ k          + ++  i+ i+  f yk+ +  +++ +     +++ l+ +
  gi|91773603|ref|YP_566295.1| 286 gsldI----EEITDIDESNRNFLQLYIEDVKqklsvfndltQRIDLLIKIINcRFLYKKLSISKKDGFvfttaEKMPLSPT 362
                                   65543....5555555555555555555555444477666655555555555566666666666555599999******** PP

                        AAA_15 296 knGsGvqrllllilli.leaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                   k +sG q+ l+l++++ ++ e         +++li+EPE++LH   q+++ + l+ + +     v+i THSp ii
  gi|91773603|ref|YP_566295.1| 363 KLSSGEQQELVLFYELlFHVEP-------EALILIDEPEISLHVLWQQQFLRDLQAITQLAGFDVLIATHSPQII 430
                                   *****88776666655045555.......5******************************999*********998 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 !   21.3   0.1   1.6e-07    0.0002       1      62 [.      27      76 ..      27      81 .. 0.79
   2 !   37.0   2.1   2.6e-12   3.3e-09     219     302 ..     338     430 ..     219     431 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefei 62
                                  +++l GpNg GK+ LL++l  l+r            s++ ++  ip++  +++++ ++++ +
  gi|91773603|ref|YP_566295.1| 27 ITILHGPNGIGKTVLLKILNSLFR------------SNYYELYRIPFSRLEIEFSDRSRLLV 76
                                  79999*****************76............67777777777777777777666665 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 2.6e-12
                        AAA_21 219 r........gvvflengdgqelparelSdGtkrll.alltallralkkgsllliDEpEngLHPkllrrll...ellkelsr 287
                                   +        + + +      +l++++lS+G ++ l  ++ +l+   ++ +l+liDEpE +LH  ++  +l   + + +l+ 
  gi|91773603|ref|YP_566295.1| 338 YkklsiskkDGFVFTTAEKMPLSPTKLSSGEQQELvLFYELLFHVEPE-ALILIDEPEISLHVLWQQQFLrdlQAITQLAG 417
                                   1455555555555555556689999*****999874777777777777.*********************76666666655 PP

                        AAA_21 288 ngaQviltTHSplll 302
                                       v+++THSp ++
  gi|91773603|ref|YP_566295.1| 418 --FDVLIATHSPQII 430
                                   ..**********987 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   3.6e-06    0.0047      11      74 ..      25      86 ..      17     235 .. 0.72
   2 !   15.7   0.0   1.3e-05     0.016      37     135 ..     283     393 ..     275     394 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                                  TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTS CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpel 74
                                   +++ + G+nG GK+ Llk+l  l + +  e+     ++++ e+e+++++   + ++ +l+++ 
  gi|91773603|ref|YP_566295.1| 25 EHITILHGPNGIGKTVLLKILNSLFRSNYYEL--YRIPFSRLEIEFSDRSRLLVRKKLHLDETE 86
                                  4677899**************99987543333..444555555555555555555554444444 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                                   -SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGG CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  37 pteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltvren........esdeeiekalsklglkelkdtvvksspss 108
                                   + eG++ ++  +d++e ++++l+  i+ ++q+ ++f++lt r              +   + +k g + ++++++  sp++
  gi|91773603|ref|YP_566295.1| 283 DSEGSLDIEeITDIDESNRNFLQLYIEDVKQKLSVFNDLTQRIDllikiincRFLYKKLSISKKDGFVFTTAEKMPLSPTK 363
                                   5789999997899999***********************8776689775555333344455555555558888888899** PP

                                   S-HHHHHHHHHHHHHH...HTSSEEEEEST CS
                                   xxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                      ABC_tran 109 LSgGqkqrvalarall...kkpkllllDEp 135
                                   LS G++q ++l   ll   +   l+l+DEp
  gi|91773603|ref|YP_566295.1| 364 LSSGEQQELVLFYELLfhvEPEALILIDEP 393
                                   ********9998776523256779999*99 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   3.6   2.8e-07   0.00036       7     194 ..      12     275 ..       5     334 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-07
                        AAA_23   7 frsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese.................. 68 
                                   f+ f +d+ ++ +  +t+++GpNG GKT +l  +   +     +l r     f + ++e++++                  
  gi|91773603|ref|YP_566295.1|  12 FGTFdHDVPLNTEEHITILHGPNGIGKTVLLKILNSLFRSNYYELYR---IPFSRLEIEFSDRsrllvrkklhldetepik 89 
                                   688866777999**********************9999887777776...5678888888888777777777777777877 PP

                        AAA_23  69 gkvkayveltfenkdgrytrsiererelskkkgkttkka......klelleideleqfisellgskkiilnli.lflgqer 142
                                   +++++y el fe  + + +++++++ + ++ +++    +      +le++++++   f++++   +++ ++l+ + l+q+r
  gi|91773603|ref|YP_566295.1|  90 AENSGYRELAFEWLKPT-HKKVRYTVKPIDIEEVFSTLKvehmipELEKIDDNTWVHFTTQEKLTSEEVMSLFsDKLPQKR 169
                                   77778888886554443.244555444444333222222335555677777777777777766666665544414566666 PP

                        AAA_23 143 .............feefelkdkke....................................rleelekeleeledekkllek 174
                                                          +                                       +++k+l e  +  + l++
  gi|91773603|ref|YP_566295.1| 170 kdepawlrevlasI---------NicfiktqrllsisfsqsveterrtsvipsvisysheLAGSMQKKLAEYAALSQSLDR 241
                                   44443333333330.........1344444444444455555566777788888888885334466666666666666666 PP

                        AAA_23 175 l..............eqekekekeleeleeelee 194
                                                    +ke + el +le++ ++
  gi|91773603|ref|YP_566295.1| 242 TfpsrllktdskhldTSIKELKVELVKLEDKRKQ 275
                                   6666665555555553333333344444433333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.1e-06    0.0027       2     172 ..       3     398 ..       2     445 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                                   EEEEEEES.ETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEE CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   2 lkrleien.FksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaevei 81 
                                   +kr++++n F ++ ++ v l+ ++++t++ GpNG GK+ ll  +  ++  +++ +l +  +s+l  +  + +s    + ++
  gi|91773603|ref|YP_566295.1|   3 IKRIVVKNlFGTF-DHDVPLNTEEHITILHGPNGIGKTVLLKILNSLFR-SNYYELYRIPFSRLEIE-FSDRSRLLVRKKL 80 
                                   899***9945566.7***********************99987755554.45556666666666444.2333333334444 PP

                                   EEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                         SMC_N  82 tfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske........................... 135
                                   ++d+++    +++   ++  +  +  + +++   k +  +ev + l+ +++ +e                           
  gi|91773603|ref|YP_566295.1|  81 HLDETEPIKAENSGYRELAFEWLKPTHKKVRYTVKPIDIEEVFSTLKVEHMIPElekiddntwvhfttqekltseevmslf 161
                                   445554443333333444444444444455555555555556555555555555666666666666666666666777777 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773603|ref|YP_566295.1| 162 sdklpqkrkdepawlrevlasinicfiktqrllsisfsqsveterrtsvipsvisyshelagsmqkklaeyaalsqsldrt 242
                                   777777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|91773603|ref|YP_566295.1| 243 fpsrllktdskhldtsikelkvelvkledkrkqlidagfidsegsldieeitdidesnrnflqlyiedvkqklsvfndltq 323
                                   777777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                   .......................................CS-HHHHHHHHH..HHHHHHHCCS--SEEEECTTTTTS- CS
                                   .......................................xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 .......................................lLSgGektLval..aLlfAiqkvkpaplyllDeidaaLD 172
                                                                           LS Ge++ + l   L   + +v+p++l l+De +  L 
  gi|91773603|ref|YP_566295.1| 324 ridllikiincrflykklsiskkdgfvfttaekmplsptKLSSGEQQELVLfyEL---LFHVEPEALILIDEPEISLH 398
                                   7777777777777777777777777777777777777666666665432220122...34566666666666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.2e-06     0.012      23      52 ..      24      52 ..       8     162 .. 0.79
   2 ?   -1.5   0.0       2.2   2.8e+03     104     104 ..     258     258 ..     174     326 .. 0.56
   3 ?   -2.7   0.0       5.1   6.6e+03      85     113 ..     389     417 ..     377     428 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.2e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekdg 52
                                  ++++++l+G+ G+GK+ l++ l  +l +++
  gi|91773603|ref|YP_566295.1| 24 EEHITILHGPNGIGKTVLLKILN-SLFRSN 52
                                  4489***************6555.666553 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                        AAA_16 104 a 104
                                   +
  gi|91773603|ref|YP_566295.1| 258 S 258
                                   1 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.1
                        AAA_16  85 lldeaesaeleawrekleealaavpelag 113
                                   l de+e +++  w++++++ l+a+ +lag
  gi|91773603|ref|YP_566295.1| 389 LIDEPEISLHVLWQQQFLRDLQAITQLAG 417
                                   55667777888888888888887777665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.3e-06    0.0068       2      51 ..      27      74 ..      26     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.3e-06
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.. CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna 51
                                  + il+G++G+GKT+Ll+ l ++ ++++++   ++ +F     e+s++++ 
  gi|91773603|ref|YP_566295.1| 27 ITILHGPNGIGKTVLLKILNSLFRSNYYEL--YRIPFSRLEIEFSDRSRL 74
                                  579**************9999999999888..789998877777777655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.7   2.9e-06    0.0038      19      71 ..      24      78 ..      21     267 .. 0.73
   2 ?   -0.5   0.2      0.74   9.5e+02      52     112 ..     242     314 ..     223     341 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                      ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie....e 71
                                  +++i  + Gp g+GKt Llk i++ l  +++y +y i++++ +i+  d++ +    +
  gi|91773603|ref|YP_566295.1| 24 EEHITILHGPNGIGKTVLLK-ILNSLFRSNYYELYRIPFSRLEIEFSDRS-RllvrK 78
                                  5689999*********9997.66777788**********99999888777.222221 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.74
                      ATPase_2  52 iyyialreesiskldefie.........eeeekkklekalgiavpkaeleeilk...eksklvfkaielllek 112
                                    + + l + ++++ld++i+         e + k+ ++  + +  ++  +eei +   ++++ ++ +ie++++k
  gi|91773603|ref|YP_566295.1| 242 TFPSRLLKTDSKHLDTSIKelkvelvklEDKRKQLIDAGFIDSEGSLDIEEITDideSNRNFLQLYIEDVKQK 314
                                   5555555666666666666443333332222222233333333333333333333223333333344433333 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     2e-05     0.025       3      36 ..     112     143 ..     111     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                                   SSSSB--GGGGGG...SEEEESSTTTT---BSGG CS
                         HNH_4   3 YsgekIsiedlsdtkeydiDHilPrsrskdDsvs 36 
                                   Y+ ++I+ie+++  + + ++H++P     dD  +
  gi|91773603|ref|YP_566295.1| 112 YTVKPIDIEEVF--STLKVEHMIPELEKIDDNTW 143
                                   9***********..59**********99999876 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 ?   14.4   0.0   1.9e-05     0.024      10      40 ..      13      43 ..       3      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                        AAA_29 10 gtfdghtieidlkg.atlltGpsGsGKSTllD 40
                                  gtfd h++++++++ +t+l Gp+G GK+ ll 
  gi|91773603|ref|YP_566295.1| 13 GTFD-HDVPLNTEEhITILHGPNGIGKTVLLK 43
                                  6666.5789998899*************9985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.3e-05     0.042       5      30 ..      25      50 ..      22     170 .. 0.85
   2 ?   -2.3   0.1       3.8   4.9e+03      93     116 ..     386     413 ..     363     426 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                  + i++++G+ G+GKT+ll+ l + + 
  gi|91773603|ref|YP_566295.1| 25 EHITILHGPNGIGKTVLLKILNSLFR 50
                                  6799***************9988873 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.8
                        AAA_22  93 elliiDEaqh.lr...seealeeLrsll 116
                                   +l++iDE +  l    +++ l++L  + 
  gi|91773603|ref|YP_566295.1| 386 ALILIDEPEIsLHvlwQQQFLRDLQAIT 413
                                   6788888776663333366666665544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-05      0.12       2      33 ..      29      63 ..      28     173 .. 0.78
   2 ?   -1.5   0.0       2.5   3.2e+03      86     116 ..     402     431 ..     374     434 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                                  EEESSTTSSHHHHHHHHHHHHT...HEEEEEETTT CS
                           AAA  2 llyGppGtGKTllakavakelg...vefleisgse 33
                                  +l+Gp G+GKT l k + + +     e+++i  s+
  gi|91773603|ref|YP_566295.1| 29 ILHGPNGIGKTVLLKILNSLFRsnyYELYRIPFSR 63
                                  79*************98877751224444444444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                                   HHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                           AAA  86 vnqLlteldgvkkkeskvivigatnrpdkld 116
                                   ++q+l+ l+  ++  + + v++at++p+ + 
  gi|91773603|ref|YP_566295.1| 402 QQQFLRDLQAITQLAG-FDVLIATHSPQIIH 431
                                   6788888888888644.88899998888775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00028      0.36      32      70 ..      24      62 ..      19      68 .. 0.88
   2 ?   -1.5   0.1       1.2   1.5e+03      60      92 ..     139     171 ..     125     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                  +++ ++l Gp G GKtv++k l + + ++ y    i fs
  gi|91773603|ref|YP_566295.1| 24 EEHITILHGPNGIGKTVLLKILNSLFRSNYYELYRIPFS 62
                                  6777899*************9999999999999999998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                         AAA_7  60 ekylsltinfsaqtsanqlqdiiesklekrrkg 92 
                                   ++ + ++++ + + +++++++++ +kl ++rk+
  gi|91773603|ref|YP_566295.1| 139 DDNTWVHFTTQEKLTSEEVMSLFSDKLPQKRKD 171
                                   45566778888899999********99999985 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.14       1      50 [.       1      49 [.       1      69 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                        AAA_27  1 MrlerLdLer.yGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                  M+++r+ ++  +G f d+ + ++ +e+++++++GpN  GK+ +l+ +++l+
  gi|91773603|ref|YP_566295.1|  1 MKIKRIVVKNlFGTF-DHDVPLN-TEEHITILHGPNGIGKTVLLKILNSLF 49
                                  999999997559999.7899**9.7999*************9999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 2623.82
//
Query:       gi|91773604|ref|YP_566296.1|  [L=285]
Description: hypothetical protein Mbur_1646 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-42  145.2   0.1    3.9e-42  144.8   0.1    1.1  1  DUF4435   Protein of unknown function (DUF4435)


Domain annotation for each model (and alignments):
>> DUF4435  Protein of unknown function (DUF4435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.1   2.2e-46   3.9e-42       1     229 [.      22     237 ..      22     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 2.2e-46
                       DUF4435   1 rkivlyvEgyDdekfyrtlldelendkeyfellggkkkvlkivkllekeelgrdvlaiVDrDf...dylkqnkilnnprif 78 
                                   r+ vl++Eg+ d ++y++++d  ++++++++ ++gk++ +k+v+ l k+++ + +l+iVD+Df   d +++    ++++++
  gi|91773604|ref|YP_566296.1|  22 RGSVLIIEGSTDMRLYQRFVD--DKRCKVIP-ANGKENAIKVVQIL-KRSKIEGILTIVDADFwkvDGIRN----ESSDVL 94 
                                   6789******6655*******..********.**************.****************77776554....8***** PP

                       DUF4435  79 vtyaYaIENflcyaesLhkvlvevltlndrdyktifdlfeqfleelseiiiplflwnvlfyrkklekdiklslslqevdls 159
                                   vt+++++E++l+ +e+L+++l+e+ t +++    +  l++ +++ l+++++pl l+  l++    + + klsl++++vd++
  gi|91773604|ref|YP_566296.1|  95 VTDTHDLETMLIASEALERLLEEF-TSPYK----VEALHMPIRQLLLYTAMPLGLFRWLSS----SGKDKLSLRFKDVDFD 166
                                   ************************.99**7....88999***********99888664443....346799********** PP

                       DUF4435 160 siekitleeikvenkieelkeefpdkieeekeeikkelrkl..nqqdlklyiqGhflfefvvslileivkee 229
                                   ++++++  +i++++ i+e+k +++ +   ++++i+k+l+k+  +++d +++++Gh+++e+++  ++ei+ ++
  gi|91773604|ref|YP_566296.1| 167 HFMEVQPLSINIKHLIREVKVNSHGDS-LNERAIRKKLMKMlnEDHDPWQICSGHDVVEILAFGLREIFGNS 237
                                   ***********************9977.458*********995559**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1730.40
//
Query:       gi|91773605|ref|YP_566297.1|  [L=324]
Description: hypothetical protein Mbur_1647 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-92  307.7   0.6    5.8e-92  307.3   0.6    1.2  1  NRD1_2          NrpR regulatory domains NRD1 and 2
    1.7e-29  101.5   0.5    3.7e-29  100.5   0.5    1.6  1  HTH_12          Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
       0.21   11.3   0.0       0.47   10.2   0.0    1.5  2  Ribosomal_S19e  Ribosomal protein S19e


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 !  307.3   0.6   9.7e-96   5.8e-92       1     237 [.      85     322 ..      85     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 307.3 bits;  conditional E-value: 9.7e-96
                                   ---HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE.........EEEEE CS
                        NRD1_2   1 vgfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek.elevpegkvgiat 80 
                                   +gfvi++ieel+y++++dp +++G+VivNls++dk+d+++al+++k + + g+++s+ +ki+ee+++ ++ vpeg+vgiat
  gi|91773605|ref|YP_566297.1|  85 LGFVITRIEELIYNTNYDPISKEGNVIVNLSTLDKNDFDNALDVMKYAASGGMCISPNIKIFEEDSDsGVYVPEGSVGIAT 165
                                   69******************************************************************************* PP

                                   E-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEEEEETT CS
                        NRD1_2  81 vCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlReipvs 161
                                   vCSit+dgvLl+nGIpvkp yGG+le+e++ pv+F +lIsY+gtsidP+++f+ ++ Tsvl+v++tg+g+ilAn+R+ip s
  gi|91773605|ref|YP_566297.1| 166 VCSITYDGVLLRNGIPVKPVYGGILEMEHNDPVQFRDLISYSGTSIDPVKIFMIRHATSVLDVLDTGNGRILANIRTIPSS 246
                                   ********************************************************************************* PP

                                   THHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEGGGSE CS
                        NRD1_2 162 arekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidiselk 237
                                   a +k++e+l++l+++g+  v++ig +  +++g+pvee+  gi v  G+n+i a++eagi+v+++++s+++d++ ++
  gi|91773605|ref|YP_566297.1| 247 AVDKAQEVLHQLEASGLGNVMNIGSSAYDLCGAPVEEGLSGILVGVGVNMISAVEEAGIPVSTSPVSTVLDYKVMS 322
                                   *************************************************************************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 !  100.5   0.5   6.3e-33   3.7e-29       1      66 []      11      76 ..      11      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 6.3e-33
                        HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                  +eI+++++esdkpiga++ia+eL+ rgy++geravRy+Lr+l+erg+t+++gy+gr++t  G +eL
  gi|91773605|ref|YP_566297.1| 11 IEIMRVISESDKPIGARNIADELQSRGYNLGERAVRYHLRILDERGFTEKHGYNGRTITTFGRKEL 76
                                  79**********************************************************999987 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   7.8e-05      0.47      93     129 ..      42      78 ..      25      81 .. 0.89
   2 ?   -3.8   0.0       1.6   9.3e+03      97     108 ..     252     263 ..     247     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.8e-05
                                   HHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S- CS
                Ribosomal_S19e  93 gsvirkilqqLeklglvkkekkkgrrltkkGqrlldr 129
                                   ++ +r+ l+ L++ g+ +k+  +gr++t  G++ ld 
  gi|91773605|ref|YP_566297.1|  42 ERAVRYHLRILDERGFTEKHGYNGRTITTFGRKELDD 78 
                                   56799************888899************97 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.6
                                   SSS--SSS---S CS
                Ribosomal_S19e  97 rkilqqLeklgl 108
                                   +++l+qLe+ gl
  gi|91773605|ref|YP_566297.1| 252 QEVLHQLEASGL 263
                                   689999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1878.10
//
Query:       gi|91773606|ref|YP_566298.1|  [L=559]
Description: 2-octaprenylphenol hydroxylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-37  127.1   0.1      8e-37  126.0   0.1    1.6  1  ABC1           ABC1 family
    3.1e-07   30.0   0.1    6.2e-07   29.0   0.1    1.4  1  Pkinase        Protein kinase domain
    8.5e-05   22.6   0.1    0.00075   19.5   0.1    2.1  2  APH            Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.037   14.3   0.0    1.6  1  SWIRM-assoc_3  SWIRM-associated domain at the C-terminal
      0.043   13.1   0.2       0.12   11.6   0.0    1.9  3  Pkinase_Tyr    Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.1   2.2e-40     8e-37       1     119 []     117     236 ..     117     236 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 2.2e-40
                          ABC1   1 eelgkkleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelr.ldleelv 80 
                                   ee+gkk+e+iF +fd+  iAaASi+qVhrAkl +g eV+vKvqrpg++k i sDl++l+ +a  +++ ++e + ++  e+v
  gi|91773606|ref|YP_566298.1| 117 EEFGKKIEDIFLSFDSSSIAAASIGQVHRAKLLDGTEVVVKVQRPGIRKIIGSDLDILYSIAGFAEEHVEEAKlYSPVEVV 197
                                   689**********************************************************************9******* PP

                          ABC1  81 defskslleEldferEAknaekfrenfaklkevkvPkvy 119
                                   de+ +s+  E+d+++EA+n e+fr+nf++ +++ +P+vy
  gi|91773606|ref|YP_566298.1| 198 DEVYHSIHAEMDYTQEARNIERFRRNFENEPDIVIPNVY 236
                                   *************************************98 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   1.7e-10   6.2e-07      56     153 ..     225     322 ..     196     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.7e-10
                                   S.CTTB--EEEEEEESSEEEEEEE--TTEBHHHHHH......HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGE CS
                       Pkinase  56 k.hpnivrlyevfeekdelylvleyveggeladlle......rkgslseeeakkiakqilegleylHskgiiHrDlKpeNi 129
                                   +  p iv    ++e +++++l +ey++g + +++ +      ++ +++e+ +k ++kq       +++ g++H D+ + N+
  gi|91773606|ref|YP_566298.1| 225 EnEPDIVIPNVYWEYSTRRVLTMEYIDGVKCDNFKTleemglDRYKIAENGTKAFMKQ-------IFEDGFFHADMHSGNV 298
                                   346777777788889************9996665554234445555666666666655.......6789************ PP

                                   EEETTTEEEE-SGTTSEESSSSCS CS
                       Pkinase 130 LidekgelKitDFGlakelesssk 153
                                   Li e+g + + DFG++  ++++ k
  gi|91773606|ref|YP_566298.1| 299 LILEDGRICLLDFGMVGSISNEVK 322
                                   *****************9999875 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.14     5e+02      32      84 ..     209     257 ..     150     272 .. 0.80
   2 !   19.5   0.1   2.1e-07   0.00075     167     197 ..     287     315 ..     278     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                                   S-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                           APH  32 raaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllr 84 
                                   ++ +e+r++ ++ r++++ +   +P v++     e + ++++ +ey++g   ++
  gi|91773606|ref|YP_566298.1| 209 DYTQEARNIERFRRNFENEPDiVIPNVYW-----EYSTRRVLTMEYIDGVKCDN 257
                                   56667777777777877665569******.....7777789999**99988887 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.1e-07
                                   EEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                           APH 167 vllHgDlhpgNllvdpddgrvtGviDfedag 197
                                   ++ H D h+gN+l+  +dgr+ +++Df+++g
  gi|91773606|ref|YP_566298.1| 287 GFFHADMHSGNVLIL-EDGRI-CLLDFGMVG 315
                                   789************.99**9.******987 PP

>> SWIRM-assoc_3  SWIRM-associated domain at the C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.037      15      59 ..      94     137 ..      90     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                 SWIRM-assoc_3  15 eeFskikdevPaalveaHvknveaaaektgkv.dpavgLeksGiag 59 
                                   eeF+k+++evP+  +++ ++ ve++   ++k+ d  +  ++s ia 
  gi|91773606|ref|YP_566298.1|  94 EEFAKLQNEVPSFCFDEVERIVEEEF--GKKIeDIFLSFDSSSIAA 137
                                   9****************999999998..444404446777777776 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.88   3.2e+03       7      38 ..     135     161 ..     132     166 .. 0.78
   2 ?   11.6   0.0   3.5e-05      0.12     116     156 ..     280     320 ..     186     331 .. 0.86
   3 ?   -3.9   0.0       1.9   6.8e+03      75     107 ..     424     456 ..     411     471 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.88
                                   EEEESSEEEEEEEEETTTTSSEEEEEEEEEST CS
                   Pkinase_Tyr   7 lGeGafGkVvegtlkgekekkevkVavKtlke 38 
                                   +++ + G+V++++l      + ++V+vK+ + 
  gi|91773606|ref|YP_566298.1| 135 IAAASIGQVHRAKLL-----DGTEVVVKVQRP 161
                                   667778999999999.....788999998766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.5e-05
                                   HHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTS CS
                   Pkinase_Tyr 116 meyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekd 156
                                   m+ + +  + H d+ + NvL+ e+  + + DfG+  +i+++
  gi|91773606|ref|YP_566298.1| 280 MKQIFEDGFFHADMHSGNVLILEDGRICLLDFGMVGSISNE 320
                                   6666778899************************9999554 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.9
                                   SEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHH CS
                   Pkinase_Tyr  75 pllivteyvkgGdLlkfLrkkekekltlkdlls 107
                                   ++ +v e  ++G +++ L+ k+ ++  ++dl +
  gi|91773606|ref|YP_566298.1| 424 NVTVVAEPYAKGIMHNRLKPKQIAESLYSDLWQ 456
                                   467888888888888888877544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3466.72
//
Query:       gi|91773607|ref|YP_566299.1|  [L=128]
Description: hypothetical protein Mbur_1649 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-10   41.3   5.3    3.5e-08   33.5   5.3    2.1  1  Phasin           Poly(hydroxyalcanoate) granule associated pr
    4.4e-05   23.9   2.9    4.4e-05   23.9   2.9    1.9  2  BMFP             Membrane fusogenic activity
     0.0019   17.4   0.1     0.0032   16.6   0.1    1.3  1  PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subuni
  ------ inclusion threshold ------
       0.01   16.1   0.7        3.6    7.9   0.0    2.5  2  Sun2_CC2         SUN2 coiled coil domain 2
      0.016   14.8   0.4      0.018   14.5   0.4    1.0  1  ECH_2            Enoyl-CoA hydratase/isomerase
       0.13   12.7   0.4       0.17   12.3   0.4    1.4  1  DUF4094          Domain of unknown function (DUF4094)
       0.36   11.2   0.4       0.36   11.2   0.4    2.9  3  TSC22            TSC-22/dip/bun family
        0.5   11.0   2.8       0.79   10.4   0.6    1.9  2  DUF883           Bacterial protein of unknown function (DUF88
          1    9.9   7.0         19    5.8   7.0    2.1  1  PRESAN           Plasmodium RESA N-terminal
        1.2    9.2   8.2        2.4    8.2   2.7    2.5  2  DUF2680          Protein of unknown function (DUF2680)


Domain annotation for each model (and alignments):
>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   5.3   1.9e-11   3.5e-08      16     123 ..      31     123 ..      24     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.9e-11
                        Phasin  16 rqiWLAGLGafakvqeeGsklfeaLvkeGeklekktkkvaeekleevresvkskveevkekaeeqwdklekafdervakaL 96 
                                   ++  L GLG +a ++e+ ++l+++Lv++Ge  ++++kk +e+ +e+ +               +q +  e a+ e+v+++ 
  gi|91773607|ref|YP_566299.1|  31 KKLGLFGLGMYAITEEKVDELVKNLVEDGEFNKEEGKKFVEDLVEKQK---------------QQQKDFEAAVSEKVQDVF 96 
                                   667788************************999999988877665544...............566789************ PP

                        Phasin  97 srlgvpsredveaLsarvdeLtkelek 123
                                    + +++++e+++aL++++d L++ l++
  gi|91773607|ref|YP_566299.1|  97 GKADLATKEEIDALHKKIDDLETLLKE 123
                                   **********************99886 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.3     6e+03      61      70 ..      44      53 ..      40      58 .. 0.56
   2 !   23.9   2.9   2.4e-08   4.4e-05      12      56 ..      68     112 ..      64     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.3
                          BMFP 61 trekleaLea 70
                                  t ek+++L +
  gi|91773607|ref|YP_566299.1| 44 TEEKVDELVK 53
                                  5555555544 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.4e-08
                          BMFP  12 kkvgdalpaaagvreeieknvravlqealsklDLVtREEFdvqre 56 
                                   k v+d +++ ++ ++++e++v + +q ++ k DL t+EE d++++
  gi|91773607|ref|YP_566299.1|  68 KFVEDLVEKQKQQQKDFEAAVSEKVQDVFGKADLATKEEIDALHK 112
                                   7788999999999****************************9987 PP

>> PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.8e-06    0.0032     270     310 ..      81     121 ..      59     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
               PHA_synth_III_E 270 qmalkaemqrlveevlealnlPtRsEldtlhkriqelrrev 310
                                   q ++ a+ ++ v +v+++ +l t+ E+d+lhk+i +l+  +
  gi|91773607|ref|YP_566299.1|  81 QKDFEAAVSEKVQDVFGKADLATKEEIDALHKKIDDLETLL 121
                                   4567778899999***********************98655 PP

>> Sun2_CC2  SUN2 coiled coil domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.002       3.6      39      54 ..      39      54 ..      32      56 .. 0.90
   2 ?    5.8   0.6    0.0087        16      11      37 ..      68      94 ..      65     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                      Sun2_CC2 39 GvtgvTeeqVhrIVnr 54
                                  G+ ++Tee+V + V++
  gi|91773607|ref|YP_566299.1| 39 GMYAITEEKVDELVKN 54
                                  999*********9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0087
                      Sun2_CC2 11 kILaklaeeqgksardaaasvgvaLqk 37
                                  k  + l+e+q+++++d  a v + +q 
  gi|91773607|ref|YP_566299.1| 68 KFVEDLVEKQKQQQKDFEAAVSEKVQD 94
                                  667899****************99985 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4     1e-05     0.018     165     244 ..      36     116 ..      26     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                                   TTS--EE--GGGHHHHHHHHHTT........--------......----SHHHHHHHHHHHT.-S..-TTTHHHHHH.T.. CS
                         ECH_2 165 aglathyvpseklealeeaLaelessdeeaveevleelaeeaeeeeeeselaekreaidrlfsad..sveeiveaLekaea 243
                                   +gl    + +ek+++l ++L e  + ++e+ ++++e+l e+++++++++e a   e+++++f++     +e ++aL+k+ +
  gi|91773607|ref|YP_566299.1|  36 FGLGMYAITEEKVDELVKNLVEDGEFNKEEGKKFVEDLVEKQKQQQKDFEAA-VSEKVQDVFGKAdlATKEEIDALHKKID 115
                                   6899999***************98888999********99999988877776.899******8875667888899986433 PP

                                   - CS
                         ECH_2 244 e 244
                                   +
  gi|91773607|ref|YP_566299.1| 116 D 116
                                   3 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   9.7e-05      0.17      36      83 ..      75     122 ..      36     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.7e-05
                       DUF4094  36 eelklvsedcdskdaesrskdilg.evskthkaiqtLdktissLemeLa 83 
                                   e++k  ++d++     ++ +d++g     t+++i +L k+i+ Le+ L 
  gi|91773607|ref|YP_566299.1|  75 EKQKQQQKDFEAAV-SEKVQDVFGkADLATKEEIDALHKKIDDLETLLK 122
                                   33333455555433.33356999977789****************9876 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.1      0.65   1.2e+03       9      23 ..      40      55 ..      39      82 .. 0.71
   2 ?   -0.4   0.1      0.82   1.5e+03      23      35 ..      70      82 ..      63      93 .. 0.59
   3 ?   11.2   0.4    0.0002      0.36      10      29 ..     101     120 ..     100     128 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.65
                         TSC22  9 mfAVrEe.VevLkekI 23
                                  m+A+ Ee V++L ++ 
  gi|91773607|ref|YP_566299.1| 40 MYAITEEkVDELVKNL 55
                                  7887665488774433 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.82
                         TSC22 23 IkeLeernselee 35
                                  + +L+e+ ++ ++
  gi|91773607|ref|YP_566299.1| 70 VEDLVEKQKQQQK 82
                                  4455555444443 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0002
                         TSC22  10 fAVrEeVevLkekIkeLeer 29 
                                   +A++Ee++ L +kI +Le  
  gi|91773607|ref|YP_566299.1| 101 LATKEEIDALHKKIDDLETL 120
                                   699**************975 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00044      0.79      12      66 ..      46     100 ..      42     106 .. 0.93
   2 ?    0.6   0.1      0.51   9.1e+02       7      23 ..     110     126 ..     103     128 .] 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                        DUF883  12 adleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaad 66 
                                   ++++el+k+  ++++ + ee ++ +e+ +e+ +++ +d e av e+++++  +ad
  gi|91773607|ref|YP_566299.1|  46 EKVDELVKNLVEDGEFNKEEGKKFVEDLVEKQKQQQKDFEAAVSEKVQDVFGKAD 100
                                   6899*********************************************999988 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.51
                        DUF883   7 leslladleellkeaad 23 
                                   l++ ++dle llke+ +
  gi|91773607|ref|YP_566299.1| 110 LHKKIDDLETLLKEKMK 126
                                   44556666666666544 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   7.0     0.011        19      38     120 ..      41     123 ..       8     128 .] 0.58

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-SEE.EHHHHHHHHHHHHHHHHHH CS
                        PRESAN  38 yknmikkLsnyleelakkynipeeykkklwkeckneitkelkklekeynknfynllkkkkl.sidefkefinsyrklwkkl 117
                                   y  +++k  +++++l +  ++++e+ kk+ ++  ++ ++ +k++e   +++ ++ + k +l +++e++ + +++++  ++l
  gi|91773607|ref|YP_566299.1|  41 YAITEEKVDELVKNLVEDGEFNKEEGKKFVEDLVEKQKQQQKDFEAAVSEKVQDVFGKADLaTKEEIDAL-HKKIDDLETL 120
                                   4444555555555555555557777777788888888888888888888888888877777455555444.4444444444 PP

                                   HHH CS
                        PRESAN 118 lkk 120
                                   lk+
  gi|91773607|ref|YP_566299.1| 121 LKE 123
                                   443 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.7    0.0013       2.4      21      54 ..      49      82 ..      41      87 .. 0.83
   2 ?    3.6   0.3     0.037        66       6      20 ..     104     118 ..     103     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                       DUF2680 21 KqivdKyVeaGllTkeqgekikkniDkrlkylke 54
                                   ++v+ +Ve G++ ke g+k ++ + +++k++++
  gi|91773607|ref|YP_566299.1| 49 DELVKNLVEDGEFNKEEGKKFVEDLVEKQKQQQK 82
                                  689****************999887777766665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.037
                       DUF2680   6 kkeleaLyqqiaelr 20 
                                   k+e++aL+++i +l+
  gi|91773607|ref|YP_566299.1| 104 KEEIDALHKKIDDLE 118
                                   789*******98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2519  (0.140499); expected 358.6 (0.02)
Passed bias filter:                     1006  (0.0561102); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 804.64
//
Query:       gi|91773608|ref|YP_566300.1|  [L=372]
Description: transposase, IS891/IS1136/IS1341 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-26   92.0   1.0    8.3e-26   90.6   1.0    1.7  1  OrfB_IS605      Probable transposase
    2.8e-19   68.8   0.8      7e-19   67.5   0.8    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      1e-18   66.5   1.0    2.3e-18   65.4   1.0    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
      0.004   17.3   4.0     0.0099   16.0   4.0    1.6  1  zf-piccolo      Piccolo Zn-finger


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   1.0   1.9e-29   8.3e-26      14     117 ..     178     278 ..     166     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 1.9e-29
                    OrfB_IS605  14 kgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhk 94 
                                   +  +++giD+G+ n+a +++++   +++++++l++   +++  ++++++k+++skn+ k +  +a+lh+k++++r+++lhk
  gi|91773608|ref|YP_566300.1| 178 EDRTTLGIDVGLTNFAILSNGE---KINNPKHLRNSMDRMKILQKRMSKKQSGSKNRNKSRHNVAKLHEKIRNQRNDFLHK 255
                                   56789*****************...******************************************************** PP

                    OrfB_IS605  95 lathliktlkevgvetLnvgnmk 117
                                   ++++li ++++++ve Lnv +m 
  gi|91773608|ref|YP_566300.1| 256 TTSKLISENQAIAVESLNVSGML 278
                                   *********************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.8   1.6e-22     7e-19       1      68 [.     292     361 ..     292     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.6e-22
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                   ++++ +qleyka +y +++ ++ ++  +Sk C++Cg  n++ +l++r + Cp+C++e+drD+nAaiN+ k
  gi|91773608|ref|YP_566300.1| 292 WSEFFRQLEYKADWYRKTLLKIGQFEpSSKLCNVCGFHNNKmTLKDRDWCCPECNTEHDRDINAAINVKK 361
                                   99*****************************************************************976 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 !   65.4   1.0   5.2e-22   2.3e-18       1      46 [.       1      45 [.       1      46 [. 0.96

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 5.2e-22
                HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeeg 46
                                  M lkaykyrlyP + Q e l +++G++Rf YN+aL+++++aye ++
  gi|91773608|ref|YP_566300.1|  1 M-LKAYKYRLYPSESQSEILMKHIGACRFTYNWALEQKNKAYEVNK 45
                                  8.****************************************9776 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.0   2.2e-06    0.0099      28      56 ..     320     348 ..     316     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                    zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQtq 56 
                                   +++Cn+CGF  +  + + ++W c +C t+
  gi|91773608|ref|YP_566300.1| 320 SKLCNVCGFHNNKMTLKDRDWCCPECNTE 348
                                   789********99999**********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1541  (0.0859501); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2644.45
//
Query:       gi|91773609|ref|YP_566301.1|  [L=573]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-50  169.7   0.0    4.4e-24   85.6   0.0    2.6  2  ABC_tran      ABC transporter
    6.9e-10   39.2   6.8     0.0073   16.2   1.2    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.3e-07   30.4   0.2     0.0073   16.2   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
    5.5e-06   26.5   1.4      0.023   14.9   0.1    4.1  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
    1.2e-05   25.0   5.7      0.018   14.8   1.1    2.7  3  AAA_29        P-loop containing region of AAA domain
    0.00011   22.5   3.2       0.31   11.3   0.1    3.8  3  AAA_22        AAA domain
     0.0002   21.1   0.2       0.33   10.6   0.1    2.4  2  AAA_30        AAA domain
    0.00023   21.0   0.7       0.39   10.4   0.3    2.3  2  PRK           Phosphoribulokinase / Uridine kinase family
    0.00028   21.3   0.1       0.31   11.4   0.0    2.5  2  AAA_16        AAA ATPase domain
    0.00035   20.5   1.7       0.27   11.1   0.6    2.4  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
    0.00055   19.7   0.8        1.1    8.9   0.2    2.5  2  AAA_24        AAA domain
    0.00056   20.5   0.4      0.075   13.6   0.2    2.8  2  AAA_18        AAA domain
    0.00071   19.5   1.6          1    9.2   0.9    2.6  2  NACHT         NACHT domain
    0.00081   19.7   0.0       0.44   10.8   0.0    2.7  2  AAA_28        AAA domain
    0.00094   19.4   0.5       0.84    9.8   0.1    2.7  2  AAA_33        AAA domain
     0.0012   18.6   1.0       0.14   11.8   0.0    2.5  2  AAA_15        AAA ATPase domain
     0.0012   18.8   0.6        2.9    7.8   0.0    3.2  3  ATPase_2      ATPase domain predominantly from Archaea
     0.0018   17.7   1.4      0.091   12.2   0.0    3.4  4  TniB          Bacterial TniB protein
     0.0031   17.5   0.3        1.1    9.3   0.0    2.4  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
     0.0039   17.1   0.0        1.1    9.1   0.0    2.5  2  Rad17         Rad17 P-loop domain
     0.0049   16.1   1.0       0.84    8.8   0.2    2.4  2  NB-ARC        NB-ARC domain
     0.0052   16.5   0.6        3.1    7.5   0.1    2.5  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0055   16.3   1.3       0.37   10.3   0.1    2.3  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0089   15.5   2.1        2.8    7.3   0.1    2.6  2  Pox_A32       Poxvirus A32 protein
      0.009   15.6   1.5        7.8    6.0   0.0    3.5  4  AAA_25        AAA domain
     0.0099   15.3   0.8        1.7    8.0   0.0    2.7  2  PhoH          PhoH-like protein
  ------ inclusion threshold ------
       0.01   16.3   0.3         17    5.9   0.1    4.0  3  AAA           ATPase family associated with various cellular 
      0.012   16.1   8.8      0.058   13.9   0.9    2.5  2  AAA_23        AAA domain
      0.017   14.3   0.3        1.2    8.2   0.0    2.2  2  G-alpha       G-protein alpha subunit
      0.025   14.4   0.5        3.3    7.5   0.2    2.4  2  dNK           Deoxynucleoside kinase
      0.028   13.3   1.2        3.7    6.3   0.1    2.2  2  DLIC          Dynein light intermediate chain (DLIC)
      0.031   14.2   1.3       0.57   10.1   0.1    2.5  2  NTPase_1      NTPase
      0.041   13.8   0.1        9.8    6.1   0.0    2.4  2  APS_kinase    Adenylylsulphate kinase
      0.056   12.5   0.1        2.3    7.2   0.0    2.3  2  T2SSE         Type II/IV secretion system protein
      0.066   12.5   0.1        4.8    6.4   0.0    2.4  2  Zeta_toxin    Zeta toxin
      0.087   13.2   0.1         22    5.4   0.1    2.5  2  AAA_19        AAA domain
        0.1   12.3   0.1         23    4.7   0.0    2.9  3  IstB_IS21     IstB-like ATP binding protein
       0.11   12.2   0.0        7.4    6.2   0.0    2.2  2  VirE          Virulence-associated protein E
       0.18   11.9   1.6         11    6.2   0.2    2.6  2  MMR_HSR1      50S ribosome-binding GTPase
       0.19   11.0   1.2       0.51    9.5   0.1    2.0  2  KAP_NTPase    KAP family P-loop domain
       0.19   12.1   0.6         25    5.3   0.0    2.4  2  RNA_helicase  RNA helicase
       0.22   11.7   0.2         22    5.3   0.0    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase
       0.23   10.8   1.0          9    5.6   0.1    2.5  2  ATPase        KaiC
        9.8    6.3   6.5         15    5.6   1.1    3.0  3  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.0   1.1e-26   4.4e-24       1     136 [.      21     180 ..      21     181 .. 0.88
   2 !   81.6   0.0   1.8e-25   7.5e-23       2     136 ..     285     490 ..     284     491 .. 0.80

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 1.1e-26
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS.--S-TTSBH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqe.pqlfpeltv 76 
                                   l+ +s+++  ge+++i+G++G+GK+tLlk+l g +  ++G+i++dg  ++e    +  + l ++ ++  q    l+ +  +
  gi|91773609|ref|YP_566301.1|  21 LNGISFDVADGEILGITGKSGSGKTTLLKILRGAEPFNNGSIEIDGSIITElsgaEGAKLLGRSTAIHLQRnFGLWAGP-A 100
                                   789************************************************9999888888888888888766666666.4 PP

                                   HHH.....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  77 ren.....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    en                      +de  e+ ++ l+l++l+++ + +s s LSgG+kqr+ +ar l+ +p+llllDEp 
  gi|91773609|ref|YP_566301.1| 101 IENiirrlniqygghegmpepdapFYDELYERSMAYLRLVGLEHKAL-HSSSVLSGGEKQRLIIARQLAAQPRLLLLDEPV 180
                                   45568889999999999987777655666999999999999999998.778*****************************6 PP

  == domain 2  score: 81.6 bits;  conditional E-value: 1.8e-25
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.....B-HHHCCHCEEEE-SS--S-TTSBH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.....qeleslrkeigvlpqepqlfpeltv 76 
                                   k+ sl +++ge+v ++G++GaGK+t+lk++ gl +p+eG++ +  + ++ +     +++ +l k+i++++qe +l p++tv
  gi|91773609|ref|YP_566301.1| 285 KDQSLVINKGEIVSFIGSSGAGKTTFLKIMEGLKEPKEGSVSYLhDGEWVNissfaRQRMELWKKISIMHQEFSLSPHSTV 365
                                   678999***********************************65443344334667788999999***************** PP

                                   HHH..................................................................HHHTCHHHHHHH CS
                                   xxx..................................................................xxxxxxxxxxxx RF
                      ABC_tran  77 ren..................................................................esdeeiekalsk 91 
                                   r++                                                                  +           
  gi|91773609|ref|YP_566301.1| 366 RRQigfrlsmkmhgalefarqkaqelgisdemldkiyilpdmgeiertntlnsmrlsmdvysklfpvipN----------- 435
                                   ******9999999999999888888888887777777777777776666666666666665555555541........... PP

                                   STTGG..............TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  92 lglke..............lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                      l  +++++ ++++SgG+ +r  +a al+++p++l+lDEp+
  gi|91773609|ref|YP_566301.1| 436 ----TdvdkyaipvfealdLSLDILDKTTYQISGGEHVRAYIALALATEPEFLMLDEPF 490
                                   ....0344444444444446669999999*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2   1.8e-05    0.0073       3      44 ..      35      64 ..      33      84 .. 0.71
   2 ?    5.4   0.1     0.033        14     233     300 ..     149     214 ..     102     216 .. 0.81
   3 !   11.6   0.0   0.00045      0.18       4      24 ..     299     319 ..     296     342 .. 0.82
   4 ?    6.5   0.0     0.016       6.5     249     298 ..     473     522 ..     461     527 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-05
                        AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44
                                  +++G+ gsGK++LL++l+++            e+ ++g+i +
  gi|91773609|ref|YP_566301.1| 35 GITGKSGSGKTTLLKILRGA------------EPFNNGSIEI 64
                                  79***************988............3333333333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.033
                        AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                   +++ lS G k+   +++  l+a +  +lll+DEp +   P    ++++++ k++ r ++ +i+++H p+
  gi|91773609|ref|YP_566301.1| 149 SSSVLSGGEKQR-LIIARQLAAQP--RLLLLDEPVTMTGPDTKQEIMDVIlKLKDRLNIPIIVVSHLPE 214
                                   667889999999.88888888777..********99999999999998887777779999999999776 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00045
                        AAA_21   4 liGpNgsGKSnLLdaldllar 24 
                                   +iG  g+GK+++L+++++l+ 
  gi|91773609|ref|YP_566301.1| 299 FIGSSGAGKTTFLKIMEGLKE 319
                                   8*****************974 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.016
                        AAA_21 249 tallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                    al+ a ++  +l +DEp   L+P  lr +   l ++++r g+ ++l++H 
  gi|91773609|ref|YP_566301.1| 473 IALALATEP-EFLMLDEPFGDLDPVTLRDVTNSLkRINARFGTTIVLVSHH 522
                                   233333333.9********************9996666669*********7 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00042      0.17      96     128 ..      27      60 ..      10      67 .. 0.79
   2 !   16.2   0.0   1.8e-05    0.0073      71     131 ..     265     326 ..     199     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00042
                                   HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S CS
                   RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktg 128
                                    ++d ++  + G+SG GK+tL++ l++ +  + g
  gi|91773609|ref|YP_566301.1|  27 DVADgEILGITGKSGSGKTTLLKILRGAEPFNNG 60 
                                   4555488999***************998766655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.8e-05
                                   HHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase  71 elealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                   + e++  +++l+++ +  ++++ + ++++ +++ ++G+SG+GK+t+++ + + +e k g+vs
  gi|91773609|ref|YP_566301.1| 265 RAENISKRLVLMRVGEVLNIKDQSLVINKgEIVSFIGSSGAGKTTFLKIMEGLKEPKEGSVS 326
                                   5566666677777777777777777777779*****************99998888887777 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.036        15      25      49 ..     145     169 ..     126     196 .. 0.75
   2 !   14.9   0.1   5.6e-05     0.023      27      89 ..     457     506 ..     450     507 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.036
                       SbcCD_C  25 elsrssgtlSGGekqflaylalaaa 49 
                                   +  +ss+ lSGGekq l+    +aa
  gi|91773609|ref|YP_566301.1| 145 KALHSSSVLSGGEKQRLIIARQLAA 169
                                   556788999*****98876554444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.6e-05
                       SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   ++ + + SGGe+ + ay+ala+a            + +++++LDE F+ lD+ +++ + + l+
  gi|91773609|ref|YP_566301.1| 457 DKTTYQISGGEH-VRAYIALALA------------TEPEFLMLDEPFGDLDPVTLRDVTNSLK 506
                                   677888999999.9999999843............3589***************999988775 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 !   14.8   1.1   4.3e-05     0.018      18      46 ..      27      51 ..      19      63 .. 0.70
   2 ?   -2.1   0.0       8.4   3.4e+03      12      37 ..      57      85 ..      50      87 .. 0.72
   3 !   11.6   0.1   0.00043      0.18      14      39 ..     286     311 ..     280     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-05
                        AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqalL 46
                                  ++   g +  +tG+sGsGK+Tll     +L
  gi|91773609|ref|YP_566301.1| 27 DVAD-GeILGITGKSGSGKTTLL----KIL 51
                                  4442.34778************9....555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.4
                        AAA_29 12 fdghtieidlkg..atlltGpsGs...GKST 37
                                  f++ +ieid  g  +t l+G+ G+   G ST
  gi|91773609|ref|YP_566301.1| 57 FNNGSIEID--GsiITELSGAEGAkllGRST 85
                                  666677887..43588899999875556666 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00043
                        AAA_29  14 ghtieidlkgatlltGpsGsGKSTll 39 
                                   ++++ i+  +++ ++G sG+GK+T+l
  gi|91773609|ref|YP_566301.1| 286 DQSLVINKGEIVSFIGSSGAGKTTFL 311
                                   567778855599************98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00075      0.31       7      26 ..      33      52 ..      29      67 .. 0.86
   2 ?    2.6   0.1      0.37   1.5e+02      60     128 ..     136     209 ..     127     219 .. 0.73
   3 ?    6.6   0.0     0.022       8.9       6      25 ..     295     314 ..     291     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00075
                        AAA_22  7 ilvvtGesGtGKTtllrrll 26
                                  il +tG sG+GKTtll+ l+
  gi|91773609|ref|YP_566301.1| 33 ILGITGKSGSGKTTLLKILR 52
                                  7779************9776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.37
                        AAA_22  60 llralglelkaerlsseell.ealeqalrarav...ielliiDEaqhlr...s.eealeeLrsllnlsrkgvqliLv 128
                                    lr +gle+ka  +ss+ l     ++ + ar+    ++ll++DE   ++   + +e++  + +l +  r ++++i+v
  gi|91773609|ref|YP_566301.1| 136 YLRLVGLEHKA-LHSSSVLSgGEKQRLIIARQLaaqPRLLLLDEPVTMTgpdTkQEIMDVILKLKD--RLNIPIIVV 209
                                   57888888998.88888888888888888888888999******8888665415555555555555..555666655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.022
                        AAA_22   6 gilvvtGesGtGKTtllrrl 25 
                                    i+  +G sG+GKTt l+ +
  gi|91773609|ref|YP_566301.1| 295 EIVSFIGSSGAGKTTFLKIM 314
                                   577889*********99865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00082      0.33      20      41 ..      33      54 ..      27      97 .. 0.82
   2 !    7.9   0.0    0.0054       2.2      17      49 ..     293     325 ..     287     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00082
                        AAA_30 20 vavltGpAGtGKttalkalrea 41
                                  +  +tG  G+GKtt+lk lr a
  gi|91773609|ref|YP_566301.1| 33 ILGITGKSGSGKTTLLKILRGA 54
                                  6789*************99876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0054
                        AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrv 49 
                                   +  ++   G  G+GKtt lk ++ + e ++g+v
  gi|91773609|ref|YP_566301.1| 293 KGEIVSFIGSSGAGKTTFLKIMEGLKEPKEGSV 325
                                   44578889************9988877775555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.3   0.00095      0.39       1      20 [.      33      52 ..      33      75 .. 0.84
   2 !    8.7   0.0    0.0032       1.3       1      24 [.     296     318 ..     296     355 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00095
                           PRK  1 vIgvagsSGaGkttvarkle 20
                                  ++g++g+SG+Gktt+ + l+
  gi|91773609|ref|YP_566301.1| 33 ILGITGKSGSGKTTLLKILR 52
                                  78************987665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0032
                           PRK   1 vIgvagsSGaGkttvarklekifg 24 
                                   +++  gsSGaGktt+ + +e + +
  gi|91773609|ref|YP_566301.1| 296 IVSFIGSSGAGKTTFLKIMEGL-K 318
                                   67889**********9876643.3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00075      0.31      19      45 ..      28      52 ..      15      69 .. 0.82
   2 ?    7.2   0.0     0.015         6      23      42 ..     293     312 ..     282     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00075
                        AAA_16 19 vrsgrpelvllsGesGvGKsslvrell 45
                                  v++g  e++ ++G sG+GK++l++ l+
  gi|91773609|ref|YP_566301.1| 28 VADG--EILGITGKSGSGKTTLLKILR 52
                                  4555..7999************97655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.015
                        AAA_16  23 rpelvllsGesGvGKsslvr 42 
                                    +e+v ++G sG GK++ ++
  gi|91773609|ref|YP_566301.1| 293 KGEIVSFIGSSGAGKTTFLK 312
                                   4589*************993 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.6   0.00067      0.27       1      18 [.      33      50 ..      33      54 .. 0.90
   2 !    8.0   0.0    0.0062       2.5       1      18 [.     296     313 ..     296     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00067
                          MobB  1 vlgivgksgsGKTtLlek 18
                                  +lgi+gksgsGKTtLl+ 
  gi|91773609|ref|YP_566301.1| 33 ILGITGKSGSGKTTLLKI 50
                                  799************985 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0062
                          MobB   1 vlgivgksgsGKTtLlek 18 
                                   +++++g sg+GKTt+l+ 
  gi|91773609|ref|YP_566301.1| 296 IVSFIGSSGAGKTTFLKI 313
                                   689************974 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.2    0.0027       1.1       6      22 ..      35      51 ..      31      66 .. 0.85
   2 !    8.5   0.0    0.0036       1.5       8      29 ..     300     319 ..     294     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0027
                        AAA_24  6 liyGpsgiGKTtlakel 22
                                   i+G+sg+GKTtl+k l
  gi|91773609|ref|YP_566301.1| 35 GITGKSGSGKTTLLKIL 51
                                  699**********9987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0036
                        AAA_24   8 yGpsgiGKTtlakelgpkplfi 29 
                                   +G+sg+GKTt++k +  + l  
  gi|91773609|ref|YP_566301.1| 300 IGSSGAGKTTFLKIM--EGLKE 319
                                   8************99..33444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   0.00018     0.075       2      22 ..      35      55 ..      34      76 .. 0.80
   2 ?    3.9   0.0      0.18        75       4      18 ..     300     314 ..     297     358 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00018
                        AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                  ++tG++G+GKttl k L+  +
  gi|91773609|ref|YP_566301.1| 35 GITGKSGSGKTTLLKILRGAE 55
                                  59***************7554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.18
                        AAA_18   4 tGtpGvGKttlakeL 18 
                                    G +G+GKtt+ k  
  gi|91773609|ref|YP_566301.1| 300 IGSSGAGKTTFLKIM 314
                                   6999*******9987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.9    0.0026         1       5      18 ..      36      49 ..      32      53 .. 0.86
   2 !    8.2   0.0    0.0052       2.1       3      29 ..     297     322 ..     295     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0026
                                  EEC-TTTCHHHHHH CS
                         NACHT  5 lqGeaGsGKTtLlq 18
                                  ++G++GsGKTtLl+
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLK 49
                                  89**********98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0052
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegkl 29 
                                   v   G +G GKTt+l k+++ ++e+k 
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFL-KIMEGLKEPKE 322
                                   5678**********9.58999988875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0011      0.44       4     155 ..      36     209 ..      34     214 .. 0.63
   2 ?    5.9   0.0     0.034        14       2      20 ..     297     315 ..     296     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                        AAA_28   4 itGgestGKTtlleaLa.....ar.....gypvvpE.aareileeklakgedalp.....wvedllafaervleeqleeea 68 
                                   itG +++GKTtll+ L      ++     + ++++E ++ e  + +++++  +l+     w+  +++  +r+l+ q+  ++
  gi|91773609|ref|YP_566301.1|  36 ITGKSGSGKTTLLKILRgaepfNNgsieiDGSIITElSGAEGAKLLGRSTAIHLQrnfglWAGPAIENIIRRLNIQYGGHE 116
                                   89**************96444322433332223433134444444455555555544444444778888888888888888 PP

                        AAA_28  69 aaaankvlfcDrglldtlaYarayggeaeaelea..aarekrydlvfllppap...ei..dddgeRredleereaiderlr 142
                                      +++  f+D  +  ++aY+r  g e +++l +   +   + ++ ++ +  +    +   d  +   +++  ++i ++++
  gi|91773609|ref|YP_566301.1| 117 GMPEPDAPFYDELYERSMAYLRLVGLE-HKALHSssVLSGGEKQRLIIARQLAaqpRLllLDEPVTMTGPDTKQEIMDVIL 196
                                   888888889999999999999888888.77666543222333333444444333442233577777777778888888888 PP

                        AAA_28 143 ealrelgipviiv 155
                                   ++ ++l+ip+i+v
  gi|91773609|ref|YP_566301.1| 197 KLKDRLNIPIIVV 209
                                   8888888888777 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.034
                        AAA_28   2 ivitGgestGKTtlleaLa 20 
                                   + ++G +++GKTt l+ ++
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFLKIME 315
                                   569**********998765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.016       6.5       5      19 ..      37      51 ..      33      65 .. 0.85
   2 !    9.8   0.1    0.0021      0.84       2      17 ..     297     312 ..     296     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.016
                        AAA_33  5 vGlpGsGKstlaerl 19
                                   G +GsGK+tl++ l
  gi|91773609|ref|YP_566301.1| 37 TGKSGSGKTTLLKIL 51
                                  69*********9865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0021
                        AAA_33   2 vllvGlpGsGKstlae 17 
                                   v ++G +G+GK+t+++
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFLK 312
                                   789***********87 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.034        14      28      61 ..      36      65 ..      22     271 .. 0.84
   2 !   11.8   0.0   0.00035      0.14      16      55 ..     286     334 ..     283     425 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.034
                        AAA_15 28 liGkNnsGKSsilealdlFlnnkekknkkvikie 61
                                  + Gk +sGK+++l++l       e++n+  i i+
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKIL----RGAEPFNNGSIEID 65
                                  67999**********9....55566664444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00035
                        AAA_15  16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.........k 55 
                                   d ++ +++  +  +iG  ++GK+++l++++ +++ ke  +         +
  gi|91773609|ref|YP_566301.1| 286 DQSLVINKGeIVSFIGSSGAGKTTFLKIMEGLKEPKE-GSvsylhdgewV 334
                                   5555555556999*****************9999882.223444455551 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.015       5.9      21      38 ..      32      49 ..      16      52 .. 0.88
   2 ?    0.4   0.0       1.3   5.2e+02      97     131 ..     182     216 ..     122     248 .. 0.78
   3 !    7.8   0.0     0.007       2.9      21      78 ..     295     346 ..     281     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                      ATPase_2 21 eiyfiYGpegsGKtaLlk 38
                                  ei+ i+G  gsGKt+Llk
  gi|91773609|ref|YP_566301.1| 32 EILGITGKSGSGKTTLLK 49
                                  7888************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                      ATPase_2  97 eksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                    +  + ++ i +++ k+k++   +ii++  l+++ 
  gi|91773609|ref|YP_566301.1| 182 MTGPDTKQEIMDVILKLKDRLNIPIIVVSHLPEVH 216
                                   567888999999********999999998887776 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.007
                      ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkl 78 
                                   ei+   G+ g GKt++lk +   +e k+  v y+ + + ++is++ +       + +l
  gi|91773609|ref|YP_566301.1| 295 EIVSFIGSSGAGKTTFLKIMEGLKEPKEGSVSYLHDGEWVNISSFARQ------RMEL 346
                                   566667***********977777788888**************99987......3333 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.85   3.5e+02      39      54 ..      35      50 ..      30      64 .. 0.81
   2 !   12.2   0.0   0.00022     0.091     108     161 ..     159     210 ..     121     223 .. 0.80
   3 ?   -1.9   0.1       4.5   1.8e+03      39      54 ..     298     313 ..     292     324 .. 0.78
   4 ?    0.8   0.0      0.68   2.8e+02     117     160 ..     478     519 ..     452     526 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.85
                          TniB 39 llvGdsnnGKtmivek 54
                                   + G+s  GKt++++ 
  gi|91773609|ref|YP_566301.1| 35 GITGKSGSGKTTLLKI 50
                                  589*********9985 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                          TniB 108 eqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvG 161
                                   ++ +++   + ++r+L++DE   +  g  ++++e++ ++ +L+++l+ipi++v 
  gi|91773609|ref|YP_566301.1| 159 QRLIIARQLAAQPRLLLLDEPVTMT-G-PDTKQEIMDVILKLKDRLNIPIIVVS 210
                                   444555555789********98877.5.55667899***************985 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.5
                          TniB  39 llvGdsnnGKtmivek 54 
                                    ++G s  GKt+ ++ 
  gi|91773609|ref|YP_566301.1| 298 SFIGSSGAGKTTFLKI 313
                                   5799*******98875 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.68
                          TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                   +++++ L++DE    l     + r ++n+lk+++ ++  +ivlv
  gi|91773609|ref|YP_566301.1| 478 ATEPEFLMLDEPFGDL--DPVTLRDVTNSLKRINARFGTTIVLV 519
                                   5667778888754444..56778999***************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 ?    5.9   0.0      0.03        12      19      39 ..      31      51 ..      12      58 .. 0.80
   2 !    9.3   0.0    0.0027       1.1      18      39 ..     291     314 ..     273     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                                  TEEEEEEESTTSSHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                  g+++ ++G+ G+GKTtl + l
  gi|91773609|ref|YP_566301.1| 31 GEILGITGKSGSGKTTLLKIL 51
                                  677889***********9865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
                                   H..TEEEEEEESTTSSHHHHHHHH CS
                          TsaE  18 l..gdvilLeGdLGaGKTtlvrgl 39 
                                   +  g+++ + G  GaGKTt+ + +
  gi|91773609|ref|YP_566301.1| 291 InkGEIVSFIGSSGAGKTTFLKIM 314
                                   1347789*************9854 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0028       1.1      40      65 ..      26      51 ..      14      57 .. 0.84
   2 ?    5.3   0.0      0.04        16      36      66 ..     285     315 ..     270     358 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                         Rad17 40 LesrkkriLLisGPsGCgkstvvkvL 65
                                   + +  +iL i+G sG gk+t +k+L
  gi|91773609|ref|YP_566301.1| 26 FDVADGEILGITGKSGSGKTTLLKIL 51
                                  55566789*****************9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.04
                         Rad17  36 kadvLesrkkriLLisGPsGCgkstvvkvLs 66 
                                   k ++L  +k +i+   G sG gk+t +k++ 
  gi|91773609|ref|YP_566301.1| 285 KDQSLVINKGEIVSFIGSSGAGKTTFLKIME 315
                                   567787888899999*************985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.2    0.0021      0.84      21      38 ..      32      49 ..      18      55 .. 0.86
   2 ?    5.6   0.0     0.019       7.7      21      39 ..     295     313 ..     280     384 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0021
                                  EEEEEEESTTSSHHHHHH CS
                        NB-ARC 21 lvvalvGmgGvGKttlak 38
                                   ++++ G+ G+GKttl+k
  gi|91773609|ref|YP_566301.1| 32 EILGITGKSGSGKTTLLK 49
                                  499*************86 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
                                   EEEEEEESTTSSHHHHHHH CS
                        NB-ARC  21 lvvalvGmgGvGKttlakq 39 
                                    +v++ G  G GKtt +k 
  gi|91773609|ref|YP_566301.1| 295 EIVSFIGSSGAGKTTFLKI 313
                                   49*************9863 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   0.1    0.0075       3.1       6      24 ..      36      54 ..      32      62 .. 0.88
   2 ?    6.6   0.1     0.015         6       4      23 ..     297     316 ..     294     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0075
                     PduV-EutP  6 liGkvgsGKttLtqalkge 24
                                  + Gk+gsGKttL + l+g 
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKILRGA 54
                                  569************9986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                     PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                   + +iG++g+GKtt  + ++g
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFLKIMEG 316
                                   679**********9998887 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00092      0.37       2      19 ..      33      50 ..      32      67 .. 0.87
   2 ?    4.7   0.1     0.051        21       4      19 ..     298     313 ..     295     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00092
                                  EEEEEESTTCCHHHHHHH CS
                          cobW  2 vtvltGflGsGKTtLlnh 19
                                  ++++tG  GsGKTtLl+ 
  gi|91773609|ref|YP_566301.1| 33 ILGITGKSGSGKTTLLKI 50
                                  5789************85 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.051
                                   EEEESTTCCHHHHHHH CS
                          cobW   4 vltGflGsGKTtLlnh 19 
                                    + G+ G+GKTt+l+ 
  gi|91773609|ref|YP_566301.1| 298 SFIGSSGAGKTTFLKI 313
                                   567999*******975 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.3    0.0082       3.4      16      33 ..      34      51 ..      29      54 .. 0.87
   2 !    7.3   0.1    0.0069       2.8      16      31 ..     297     312 ..     283     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0082
                       Pox_A32 16 lalvGgsGsGktvyLlsL 33
                                  l ++G+sGsGkt+ L+ L
  gi|91773609|ref|YP_566301.1| 34 LGITGKSGSGKTTLLKIL 51
                                  5699*********99865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0069
                       Pox_A32  16 lalvGgsGsGktvyLl 31 
                                   + ++G sG+Gkt++L+
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFLK 312
                                   569************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0       0.1        41      32      50 ..      30      48 ..      15      51 .. 0.85
   2 ?   -2.8   0.0       9.7   3.9e+03     166     189 ..     189     212 ..     162     213 .. 0.67
   3 ?    6.0   0.0     0.019       7.8      29      50 ..     290     311 ..     284     314 .. 0.92
   4 ?    2.5   0.0      0.23        95     167     188 ..     500     521 ..     493     523 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                        AAA_25 32 agelallaGapgtGKttla 50
                                   ge+  ++G +g+GKttl+
  gi|91773609|ref|YP_566301.1| 30 DGEILGITGKSGSGKTTLL 48
                                  57777899*********96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.7
                        AAA_25 166 galvealeriarrtgaavllvhHv 189
                                   +++++ + ++++r+++ +++v H+
  gi|91773609|ref|YP_566301.1| 189 QEIMDVILKLKDRLNIPIIVVSHL 212
                                   566777778888889999999886 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.019
                        AAA_25  29 llpagelallaGapgtGKttla 50 
                                   ++ +ge++ ++G +g+GKtt++
  gi|91773609|ref|YP_566301.1| 290 VINKGEIVSFIGSSGAGKTTFL 311
                                   6899****************96 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.23
                        AAA_25 167 alvealeriarrtgaavllvhH 188
                                    + + l+ri +r+g +++lv H
  gi|91773609|ref|YP_566301.1| 500 DVTNSLKRINARFGTTIVLVSH 521
                                   57789***********999998 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.037        15      18      46 ..      30      59 ..      16      83 .. 0.78
   2 !    8.0   0.0    0.0043       1.7      15      49 ..     290     325 ..     283     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.037
                                  H-SEEEEE--TTSSTTH.HHHHHHHHHHHT CS
                          PhoH 18 kndivfaiGpaGtGKty.lavalavealkk 46
                                  + +i+ ++G++G+GKt  l +  ++e +++
  gi|91773609|ref|YP_566301.1| 30 DGEILGITGKSGSGKTTlLKILRGAEPFNN 59
                                  557999*********851556666666655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0043
                                   HHHH-SEEEEE--TTSSTT.HHHHHHHHHHHHTTS- CS
                          PhoH  15 alkkndivfaiGpaGtGKt.ylavalavealkkkkv 49 
                                   +++k +iv  iG++G+GKt +l ++ +++  k+++v
  gi|91773609|ref|YP_566301.1| 290 VINKGEIVSFIGSSGAGKTtFLKIMEGLKEPKEGSV 325
                                   578999************648888888888777766 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 ?    5.9   0.1     0.041        17       3      35 ..      36      70 ..      34      92 .. 0.72
   2 ?    2.4   0.0      0.47   1.9e+02      30      98 ..     143     204 ..     128     254 .. 0.72
   3 ?    2.6   0.0      0.41   1.7e+02       3      17 ..     299     313 ..     297     343 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.041
                                  EESSTTSSHHHHHHHHHHH..HTHEEEEEETTTCS CS
                           AAA  3 lyGppGtGKTllakavake..lgvefleisgsell 35
                                  ++G  G GKT+l k +     ++   +ei+gs ++
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKILRGAepFNNGSIEIDGSIIT 70
                                  689***********997663345556777776666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.47
                                   ETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                           AAA  30 sgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                   + + l s+ v  + +k r +++  ++ a +p  l++DE   +++ +       ++++++++l+  d+++ 
  gi|91773609|ref|YP_566301.1| 143 EHKALHSSSVLSGGEKQRLIIA--RQLAaQPRLLLLDEPVTMTGPD------TKQEIMDVILKLKDRLNI 204
                                   5555666667777777777774..4555568999999988887766......666667766666666544 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.41
                                   EESSTTSSHHHHHHH CS
                           AAA   3 lyGppGtGKTllaka 17 
                                   ++G  G GKT++ k 
  gi|91773609|ref|YP_566301.1| 299 FIGSSGAGKTTFLKI 313
                                   89*********9885 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   0.00014     0.058      13      40 ..      24      52 ..      16      54 .. 0.76
   2 ?    6.5   0.9     0.026        11      12      37 ..     286     312 ..     272     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                        AAA_23 13 qeidF.skgltlItGpNGaGKTTildAik 40
                                   ++d  +  +  ItG+ G+GKTT+l  ++
  gi|91773609|ref|YP_566301.1| 24 ISFDVaDGEILGITGKSGSGKTTLLKILR 52
                                  444446667889*************9876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.026
                        AAA_23  12 dqeidFsk.gltlItGpNGaGKTTild 37 
                                   dq++  +k  ++ ++G  GaGKTT+l 
  gi|91773609|ref|YP_566301.1| 286 DQSLVINKgEIVSFIGSSGAGKTTFLK 312
                                   55555555258889**********996 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.055        22      28      44 ..      36      52 ..      24      70 .. 0.85
   2 ?    8.2   0.0    0.0029       1.2      26      50 ..     297     321 ..     282     425 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.055
                                  EEESTTSSHHHHHHHHH CS
                       G-alpha 28 llGqseSGKsTilkqlk 44
                                  + G+s+SGK+T+lk l+
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKILR 52
                                  579**********9877 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                                   EEEEESTTSSHHHHHHHHHHHCS-- CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkg 50 
                                   + ++G+s+ GK+T+lk ++ l++++
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFLKIMEGLKEPK 321
                                   5689***************999877 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0082       3.3       3      22 ..      36      55 ..      34      63 .. 0.85
   2 ?    4.8   0.0     0.055        23       5      22 ..     301     318 ..     297     360 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0082
                                  EEESTTSSHHHHHHHHHCCS CS
                           dNK  3 veGnIgaGKstlvklLskkl 22
                                  + G+ g+GK+tl+k+L+ + 
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKILRGAE 55
                                  88999***********8665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.055
                                   ESTTSSHHHHHHHHHCCS CS
                           dNK   5 GnIgaGKstlvklLskkl 22 
                                   G  gaGK+t++k+++   
  gi|91773609|ref|YP_566301.1| 301 GSSGAGKTTFLKIMEGLK 318
                                   7779********998544 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.016       6.4      30      55 ..      36      61 ..      27      63 .. 0.86
   2 ?    6.3   0.1     0.009       3.7      25      55 ..     294     324 ..     278     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                          DLIC 30 vlGedgsGkttliaklqGveeekkGr 55
                                  + G++gsGkttl+  l+G+e  + G+
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKILRGAEPFNNGS 61
                                  6799****************888775 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.009
                          DLIC  25 gksvlvlGedgsGkttliaklqGveeekkGr 55 
                                   g  v  +G +g+Gktt++  + G+ e+k G+
  gi|91773609|ref|YP_566301.1| 294 GEIVSFIGSSGAGKTTFLKIMEGLKEPKEGS 324
                                   4456789*********************997 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0014      0.57       3      19 ..      35      51 ..      33      83 .. 0.71
   2 ?    2.3   0.1      0.35   1.4e+02       6      24 ..     301     318 ..     297     324 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                                  EEE--TTSSHHHHHHHH CS
                      NTPase_1  3 fiTGppGvGKtTlvkkv 19
                                   iTG++G+GKtTl+k +
  gi|91773609|ref|YP_566301.1| 35 GITGKSGSGKTTLLKIL 51
                                  69***********8754 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.35
                                   --TTSSHHHHHHHHHHHH. CS
                      NTPase_1   6 GppGvGKtTlvkkvlellk 24 
                                   G++G GKtT++ k++e lk
  gi|91773609|ref|YP_566301.1| 301 GSSGAGKTTFL-KIMEGLK 318
                                   899******97.5666665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.04        16       3      22 ..      32      51 ..      30      69 .. 0.85
   2 ?    6.1   0.0     0.024       9.8       2      41 ..     294     334 ..     293     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.04
                                  EEEEEESSTTSSHHHHHHHH CS
                    APS_kinase  3 vvvwltGlsgsGKstianal 22
                                   ++ +tG sgsGK+t+ + l
  gi|91773609|ref|YP_566301.1| 32 EILGITGKSGSGKTTLLKIL 51
                                  56779**********97766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.024
                                   -EEEEEESSTTSSHHHHHHHHHHHHH.HTT--EEEEEHHHH CS
                    APS_kinase   2 gvvvwltGlsgsGKstianalekkLv.ekgisvylLdGdnv 41 
                                   g +v + G sg+GK+t  + +e   + ++g   yl dG+ v
  gi|91773609|ref|YP_566301.1| 294 GEIVSFIGSSGAGKTTFLKIMEGLKEpKEGSVSYLHDGEWV 334
                                   678999**********9998885443145577778888866 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 ?    7.2   0.0    0.0057       2.3     129     149 ..      31      51 ..       4      62 .. 0.81
   2 ?    2.8   0.0      0.13        51     131     151 ..     295     316 ..     265     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0057
                         T2SSE 129 rglilvsGgTgsGKttllyal 149
                                     ++ ++G  gsGKttll +l
  gi|91773609|ref|YP_566301.1|  31 GEILGITGKSGSGKTTLLKIL 51 
                                   455559***********9875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                         T2SSE 131 lil.vsGgTgsGKttllyallk 151
                                    i+ + G  g GKtt+l ++  
  gi|91773609|ref|YP_566301.1| 295 EIVsFIGSSGAGKTTFLKIMEG 316
                                   4332569**********87654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.012       4.8      21      51 ..      36      66 ..      32     107 .. 0.82
   2 ?    3.5   0.0     0.089        36      23      38 ..     301     316 ..     290     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                    Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldp 51
                                  + G +G+GK++l++ l+ +   +++ +++d+
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKILRGAEPFNNGSIEIDG 66
                                  6799***********9998877888888886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.089
                    Zeta_toxin  23 GqpGAGKselaellkd 38 
                                   G++GAGK++ ++ ++ 
  gi|91773609|ref|YP_566301.1| 301 GSSGAGKTTFLKIMEG 316
                                   99*******9998875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.054        22       9      28 ..      30      49 ..      24      55 .. 0.85
   2 ?    5.0   0.0     0.068        28       9      37 ..     293     320 ..     287     424 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.054
                        AAA_19  9 kekvllvtaGpGtGKTrvlk 28
                                    ++l +t+  G+GKT++lk
  gi|91773609|ref|YP_566301.1| 30 DGEILGITGKSGSGKTTLLK 49
                                  567889***********997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.068
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvel 37 
                                   k +++  ++  G GKT+ lk i++ l+e 
  gi|91773609|ref|YP_566301.1| 293 KGEIVSFIGSSGAGKTTFLK-IMEGLKEP 320
                                   56778899*********997.45555554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.097        40      32      63 ..      15      47 ..       5      60 .. 0.83
   2 ?   -1.2   0.0       3.7   1.5e+03     103     160 ..     165     221 ..     153     224 .. 0.65
   3 ?    4.7   0.0     0.056        23      44      65 ..     291     312 ..     255     355 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.097
                     IstB_IS21 32 krkvkeLatlsf.iekkenivllGpsGvGKshl 63
                                  ++k++ L + sf +++ e + ++G sG GK+ l
  gi|91773609|ref|YP_566301.1| 15 ENKIRILNGISFdVADGEILGITGKSGSGKTTL 47
                                  667888888888788899999*********987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.7
                     IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewdevlgd 160
                                    +  ++++ll+lD+  + +   + ++++++vi k  +r  i i    ++ e ++ l+d
  gi|91773609|ref|YP_566301.1| 165 RQLAAQPRLLLLDEPVTMT-GPDTKQEIMDVILKLKDRLNIPIIVVSHLPEVHAYLAD 221
                                   4455678999999976665.55666777888888888776655555555566666665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.056
                     IstB_IS21  44 iekkenivllGpsGvGKshlai 65 
                                   i+k e + ++G sG+GK+ +  
  gi|91773609|ref|YP_566301.1| 291 INKGEIVSFIGSSGAGKTTFLK 312
                                   77889999*********85543 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.018       7.4      53      85 ..      32      65 ..      22      75 .. 0.83
   2 ?    3.5   0.0      0.12        51      29      73 ..     266     316 ..     261     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                          VirE 53 fvlvLvGkqgsgKstflekl.geewftdslksve 85
                                  ++l ++Gk gsgK+t+l++l g e f + + + +
  gi|91773609|ref|YP_566301.1| 32 EILGITGKSGSGKTTLLKILrGAEPFNNGSIEID 65
                                  577899**************99998887766555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                          VirE  29 travsklflvaavarvl....eP.giKfDfvlvLvGkqgsgKstflekl.g 73 
                                   ++++sk+++   v+ vl    +   i   +++   G+ g gK+tfl+++ g
  gi|91773609|ref|YP_566301.1| 266 AENISKRLVLMRVGEVLnikdQSlVINKGEIVSFIGSSGAGKTTFLKIMeG 316
                                   56777888888888888443311356677899999************9944 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   0.2     0.027        11       3      22 ..      35      54 ..      33      65 .. 0.86
   2 ?    4.3   0.1       0.1        42       2      19 ..     297     314 ..     296     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                                  EEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                  +i G++ +GK+tL++ l g+
  gi|91773609|ref|YP_566301.1| 35 GITGKSGSGKTTLLKILRGA 54
                                  89************998765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                                   EEEEESTTSSHHHHHHHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinal 19 
                                   v ++G + +GK+t+++ +
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFLKIM 314
                                   789***********9865 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0013      0.51      18      41 ..      29      52 ..      17      69 .. 0.88
   2 ?   -0.7   0.1       1.6   6.6e+02      30      41 ..     304     315 ..     292     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                    KAP_NTPase 18 atpivvgLygkWGsGKssllnkle 41
                                  a++ ++g++gk GsGK++ll+ l+
  gi|91773609|ref|YP_566301.1| 29 ADGEILGITGKSGSGKTTLLKILR 52
                                  567789***************998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                    KAP_NTPase  30 GsGKssllnkle 41 
                                   G+GK+++l+ +e
  gi|91773609|ref|YP_566301.1| 304 GAGKTTFLKIME 315
                                   9*******9876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.096        39       3      18 ..      36      51 ..      34      57 .. 0.89
   2 ?    5.3   0.0     0.062        25       3      34 ..     299     325 ..     297     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.096
                  RNA_helicase  3 lyGpsgeGKStlakeL 18
                                  ++G+sg GK+tl k L
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKIL 51
                                  78**********9876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.062
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkdsv 34 
                                   + G+sg GK+t+ k      ++ lk++k++sv
  gi|91773609|ref|YP_566301.1| 299 FIGSSGAGKTTFLKI-----MEGLKEPKEGSV 325
                                   78**********998.....444455555555 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 ?    4.1   0.1      0.13        53       4      19 ..      36      51 ..      34      75 .. 0.84
   2 ?    5.3   0.0     0.055        22       2      17 ..     297     312 ..     296     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                                  EESSTTSSHHHHHHCH CS
                           Roc  4 lvGdsgvGKtsllkrf 19
                                  + G+sg+GKt+llk +
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLLKIL 51
                                  679*********9866 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.055
                                   EEEESSTTSSHHHHHH CS
                           Roc   2 vvlvGdsgvGKtsllk 17 
                                   v ++G sg+GKt++lk
  gi|91773609|ref|YP_566301.1| 297 VSFIGSSGAGKTTFLK 312
                                   568**********986 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.022         9      18      35 ..      30      47 ..      19      60 .. 0.88
   2 ?    3.2   0.1      0.12        48      16      35 ..     291     310 ..     286     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.022
                        ATPase 18 egrvvlitGepGtGKtif 35
                                  +g++  itG++G+GKt++
  gi|91773609|ref|YP_566301.1| 30 DGEILGITGKSGSGKTTL 47
                                  678999**********97 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                        ATPase  16 ipegrvvlitGepGtGKtif 35 
                                   i +g++v   G++G+GKt+f
  gi|91773609|ref|YP_566301.1| 291 INKGEIVSFIGSSGAGKTTF 310
                                   568999************99 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 ?    5.6   1.1     0.038        15       4      16 ..      36      48 ..      33      53 .. 0.85
   2 ?   -2.0   0.0       8.5   3.5e+03      86     114 ..     184     214 ..     179     220 .. 0.73
   3 ?    2.0   0.2      0.48     2e+02       6      15 ..     301     310 ..     296     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.038
                                  EESSTTSSHHHHH CS
                                  xxxxxxxxxxxxx RF
                          CbiA  4 astkGGvGKTtla 16
                                  + +k+G+GKTtl+
  gi|91773609|ref|YP_566301.1| 36 ITGKSGSGKTTLL 48
                                  679********96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.5
                                   S...-TTCHHHHHHHHHHCTS-EEE..EEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                          CbiA  86 geneetllkealeelkqrygvpvlg..vipr 114
                                   g+++++++++ + +lk r+++p++    +p+
  gi|91773609|ref|YP_566301.1| 184 GPDTKQEIMDVILKLKDRLNIPIIVvsHLPE 214
                                   5668899999999999999888875445555 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.48
                                   SSTTSSHHHH CS
                                   xxxxxxxxxx RF
                          CbiA   6 tkGGvGKTtl 15 
                                   +++G+GKTt+
  gi|91773609|ref|YP_566301.1| 301 GSSGAGKTTF 310
                                   79*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3546.68
//
Query:       gi|91773610|ref|YP_566302.1|  [L=247]
Description: geranylgeranylglyceryl phosphate synthase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-65  220.9   1.4    1.7e-65  220.7   1.4    1.0  1  PcrB            PcrB family
    5.5e-05   22.7   0.5    0.00023   20.7   0.1    2.0  2  His_biosynth    Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.13   11.7   0.5       0.23   10.8   0.5    1.4  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


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 !  220.7   1.4   2.8e-69   1.7e-65       3     224 ..      10     243 ..       8     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 2.8e-69
                                   GGGTS...EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TT CS
                          PcrB   3 ileer...hltklDPeeenpdEiveiv...iesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvvry 74 
                                   i e +   hlt++DP  + p+ ++ei+   + +gtDa++igGs+   +v ld+t+ ++k+   +++P +l+p+n  gv+ +
  gi|91773610|ref|YP_566302.1|  10 IAEREgtvHLTLIDPASQSPEAAAEIAkaaVAGGTDAILIGGSTgavGVALDQTLIKIKEQ--VDVPTILFPGNAGGVSTH 88 
                                   55555778**********9996665555549************9988899****9999998..****************** PP

                                   SSEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT- CS
                          PcrB  75 aDalFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllgl 154
                                   aDa+F+msllns + ++i++ +  g+  v k    +e++ ++Y++ eP+++v++v++ak +++nk++iaa++ la k++g+
  gi|91773610|ref|YP_566302.1|  89 ADAIFFMSLLNSRDINYIITNQVMGAPVVYKSG--IEPISMAYIISEPGGTVGWVGDAKlIPRNKPEIAAAYSLAGKYMGM 167
                                   *****************************9999..********************************************** PP

                                   SEEEEE-.TTSSS-H..HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..HCHHHHHHH CS
                          PcrB 155 rliYlEa.sGaledv..eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd..erkidaile 224
                                    + YlEa sGa  ++  e + a+k +l +++livGGGir++ +Ak  + a AD+iv+G++vee d   +ki++i+ 
  gi|91773610|ref|YP_566302.1| 168 HYTYLEAgSGADRPItpETIGAVKHVLGDNKLIVGGGIRDGKTAKICADAgADMIVTGTIVEETDdvRKKIEEIVS 243
                                   *************99989999******************************************9966678888876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.076   4.5e+02     177     205 ..      57      90 ..      32     112 .. 0.77
   2 !   20.7   0.1   3.8e-08   0.00023      58     118 ..     180     241 ..     144     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.076
                                   ---HHH.HHHHHHHHSSEEEE....ESS--SHHH CS
                  His_biosynth 177 Gpdlel.tkelaeavkipvia....sGGvgsled 205
                                   G+ l++ + +++e+v++p+i     +GGv++ +d
  gi|91773610|ref|YP_566302.1|  57 GVALDQtLIKIKEQVDVPTILfpgnAGGVSTHAD 90 
                                   5566544778888899988864444777777666 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.8e-08
                                   HHHHHHHHHHHHHH-S.SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHH CS
                  His_biosynth  58 reanldlveeiaeevf.ipvqvGGGIrsledveelleagadkviigtaavknpelikelaek 118
                                   r++  + + ++ + +   ++ vGGGIr+ ++++   +agad ++ gt + +  ++ k++ e 
  gi|91773610|ref|YP_566302.1| 180 RPITPETIGAVKHVLGdNKLIVGGGIRDGKTAKICADAGADMIVTGTIVEETDDVRKKIEEI 241
                                   5555555555555554489*****************************99999998888775 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   3.8e-05      0.23     166     197 ..     196     228 ..     182     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
                                   --EEEEESS--T.TTCHHHHHHT--EEEESHHH CS
                Ribul_P_3_epim 166 dlkievDGGvkl.dnieqiaeagadvlVagsav 197
                                   d k+ v GG+++ ++++  a+agad++V+g+ v
  gi|91773610|ref|YP_566302.1| 196 DNKLIVGGGIRDgKTAKICADAGADMIVTGTIV 228
                                   57899*****98355566689*********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1752.21
//
Query:       gi|91773611|ref|YP_566303.1|  [L=49]
Description: 50S ribosomal protein L40e [Methanococcoides burtonii DSM 6242]
Scores for complete 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   31.9   6.5      1e-07   31.8   6.5    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0035   17.3   0.7     0.0038   17.2   0.7    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.013   15.2   1.4      0.021   14.5   1.4    1.4  1  zinc_ribbon_2   zinc-ribbon domain
      0.014   15.0   6.1      0.014   15.0   6.1    1.8  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.13   11.6   5.2       0.11   11.8   3.9    1.5  1  zf-RanBP        Zn-finger in Ran binding protein and others
       0.33   11.2   3.6       0.71   10.1   0.2    2.1  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
        1.8    8.5   6.1       0.31   11.0   1.4    1.9  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !   31.8   6.5   3.9e-11     1e-07      14      48 ..      12      43 ..       7      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.9e-11
                Ribosomal_L40e 14 cdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKK 48
                                   +K+iC kC Ar  +rAt Cr  kCg +n lr K 
  gi|91773611|ref|YP_566303.1| 12 LNKKICMKCSARNAVRATRCR--KCGYTN-LRVKN 43
                                  69*******************..9***97.55554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.7   1.5e-06    0.0038      28      49 .]      14      35 ..       2      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                           DZR 28 edrCpsCgekvdpearfCpeCG 49
                                  ++ C++C++ +  +a+ C +CG
  gi|91773611|ref|YP_566303.1| 14 KKICMKCSARNAVRATRCRKCG 35
                                  6778888888888888888887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.4   8.4e-06     0.021       2      21 ..      17      36 ..      15      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.4e-06
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                  C +C a +  +a+ C +CG+
  gi|91773611|ref|YP_566303.1| 17 CMKCSARNAVRATRCRKCGY 36
                                  *******************8 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   3.9e+03      26      31 ..      10      15 ..       9      15 .. 0.82
   2 ?   15.0   6.1   5.5e-06     0.014       2      25 ..      16      36 ..      16      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                                  ---B-- CS
                DNA_RNApol_7kD 26 RilYKk 31
                                  Ril Kk
  gi|91773611|ref|YP_566303.1| 10 RILNKK 15
                                  999887 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.5e-06
                                  B-SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGh 25
                                  iC++C+a++ ++++   RC++CG+
  gi|91773611|ref|YP_566303.1| 16 ICMKCSARNAVRAT---RCRKCGY 36
                                  8************9...******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 ?   11.8   3.9   4.4e-05      0.11       6      25 ..      16      35 ..      16      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.4e-05
                                  E-SSS--EEESSSSB-TTT- CS
                      zf-RanBP  6 dCskClvqNfawstkCvaCq 25
                                  +C kC+++N   +t+C  C+
  gi|91773611|ref|YP_566303.1| 16 ICMKCSARNAVRATRCRKCG 35
                                  59**************9996 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 ?    3.2   0.3     0.039        99       2      10 ..      17      25 ..      16      30 .. 0.80
   2 ?   10.1   0.2   0.00028      0.71      37      46 ..      30      39 ..      23      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.039
                zinc_ribbon_13  2 CpKCgntea 10
                                  C+KC  ++a
  gi|91773611|ref|YP_566303.1| 17 CMKCSARNA 25
                                  ****98876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00028
                zinc_ribbon_13 37 sCknCgYtel 46
                                   C++CgYt+l
  gi|91773611|ref|YP_566303.1| 30 RCRKCGYTNL 39
                                  6888888876 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.12   3.2e+02      27      35 ..      16      24 ..      14      26 .. 0.78
   2 ?   11.0   1.4   0.00012      0.31       6      18 ..      23      35 ..      22      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.12
                       DUF35_N 27 vCphCgsdd 35
                                  +C +C +++
  gi|91773611|ref|YP_566303.1| 16 ICMKCSARN 24
                                  799997765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                       DUF35_N  6 egrLvgqrCpdCG 18
                                  ++ ++++rC++CG
  gi|91773611|ref|YP_566303.1| 23 RNAVRATRCRKCG 35
                                  77899*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 324.38
//
Query:       gi|91773612|ref|YP_566304.1|  [L=473]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-104  348.3   0.0   4.1e-104  347.8   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    1.2e-40  138.7   0.4    2.1e-40  138.0   0.4    1.4  1  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
      0.046   14.0   0.2      0.093   13.0   0.2    1.4  1  zf-Di19    Drought induced 19 protein (Di19), zinc-binding


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 !  347.8   0.0  6.9e-108  4.1e-104       1     269 [.       9     286 ..       9     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 347.8 bits;  conditional E-value: 6.9e-108
                                   EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TC CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyfy 80 
                                   +++GlE+H+ql++ ++K+F+++st+ +++epn++v++v+++lPG+lPv+nk+ave+aik+++alnce+ e+++f+RKny+y
  gi|91773612|ref|YP_566304.1|   9 VMVGLEVHVQLNNlNTKMFCGCSTQYHDSEPNTHVCPVCMGLPGALPVINKRAVESAIKIGMALNCEVVEQTQFHRKNYYY 89 
                                   58*********998*********8878889*************************************************** PP

                                   TTCTTSEEEEESSS.SEEEEEEEE.....TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEEEEE-STB-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N  81 pdlpkgyQitqkeeplakeGslel.....ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiEivtepdlrs 152
                                   pdlpkg+Q+tq++ p++ +G++ +     e+ vri+r+h+EeD +k vh    ++++ +l+d+nR+G++LiEiv+epd+rs
  gi|91773612|ref|YP_566304.1|  90 PDLPKGFQTTQYDFPIVGNGKVVIegedgEHVVRITRAHMEEDPGKLVHigsiDKSKGTLIDYNRSGMALIEIVSEPDMRS 170
                                   ***********************9999988899*****************99978889*********************** PP

                                   HHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                        GatB_N 153 peearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiell.... 229
                                   p+ear++++klr++l +l+v +g++ eGs+R+D+NvSv         g+r E+Kn++s k  e+ai yei rq +ll    
  gi|91773612|ref|YP_566304.1| 171 PKEARRYLDKLRNILDYLDVFNGDL-EGSMRVDANVSVMG-------GQRAEVKNISSHKGAERAILYEIMRQKNLLrrgg 243
                                   *************************.7************4.......49******************************** PP

                                   ...-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--H CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 230 ...qeTrkfdedkgetvslRskeeaedYryfpepdlppleise 269
                                       eTr+fde++g t+s+R+ke ++dYryfpepdl+p+++s+
  gi|91773612|ref|YP_566304.1| 244 evvMETRHFDEARGVTISMRTKEGEHDYRYFPEPDLVPMRVSD 286
                                   ***************************************9986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   0.4   3.6e-44   2.1e-40       3     147 ..     329     470 ..     327     471 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 3.6e-44
                                   HHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHC CS
                     GatB_Yqey   3 feevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiieek 83 
                                   f evv++  +++ a +w+++ l geln+++l++++  +t +++ +++kl+ e+k+++++a +v++++l++g++p e+++ek
  gi|91773612|ref|YP_566304.1| 329 FYEVVAAAVEPRVAGTWVADVLKGELNYRDLSVDS--FTTDDIIQIIKLVVEDKVTEQSAVDVIRTILDDGGTPMEVVTEK 407
                                   556777778**************************..9******************************************* PP

                                   TXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHH CS
                     GatB_Yqey  84 gLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkek 147
                                   gL +++  + ++++v e+iaen++av+dy +g ek+l+flvGqvMkktkG+ad+++++ell   
  gi|91773612|ref|YP_566304.1| 408 GLLKVKG-DVVTEAVSETIAENEAAVQDYLGGAEKSLNFLVGQVMKKTKGRADARQARELLVAA 470
                                   ******7.9***************************************************9765 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.5e-05     0.093      12      39 ..      22      49 ..      18      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                       zf-Di19 12 ltvkeLveHvedeHrveskevvCPvCae 39
                                  l++k ++   ++ H +e + +vCPvC  
  gi|91773612|ref|YP_566304.1| 22 LNTKMFCGCSTQYHDSEPNTHVCPVCMG 49
                                  6677788888899*************74 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3045.18
//
Query:       gi|91773613|ref|YP_566305.1|  [L=475]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-155  519.0   0.1   1.3e-155  518.8   0.1    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 !  518.8   0.1  7.2e-160  1.3e-155       1     450 [.      21     453 ..      21     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 518.8 bits;  conditional E-value: 7.2e-160
                                   HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS- CS
                       Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekD 81 
                                   e++ ++l+ i++  +++n  +t++++ al +A+ +dk +      gpL+GvPi++KDni++kg+ tt++sk+le+y++++D
  gi|91773613|ref|YP_566305.1|  21 EVTASYLELIDK--SSIN-GYTCTSDGALDTAKMVDKGEV----AGPLAGVPIAIKDNISTKGLATTCSSKILEGYVPPYD 94 
                                   677888887777..8999.9****************9875....9************************************ PP

                                   -HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHH CS
                       Amidase  82 atvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsf 162
                                   a+v+erLk+aGavi+gkTnmdefamg+ste+s++g t NPwd +r+pGGSSGGsAA+vAag +p+++G+DtGGS+R+PA+f
  gi|91773613|ref|YP_566305.1|  95 AHVIERLKEAGAVIIGKTNMDEFAMGTSTESSCYGVTLNPWDHERVPGGSSGGSAAVVAAGEAPISLGSDTGGSVRCPAAF 175
                                   ********************************************************************************* PP

                                   CTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEE CS
                       Amidase 163 cglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvv 243
                                   cg+vGlKPtyg vSr+g++++++sl+++Gp+a++ved+a++++vi g+d +dsts +   ++ d +++l  + kgl+iGv+
  gi|91773613|ref|YP_566305.1| 176 CGVVGLKPTYGAVSRYGLISYANSLEQIGPMATCVEDIAAVMDVIGGYDARDSTSID---KKIDHQAALIDDVKGLKIGVP 253
                                   ********************************************************9...5688999999999******** PP

                                   GGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SCCCCCCCHH CS
                       Amidase 244 kedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvryerlsetkvlsellpks 324
                                    e++ + +d   ++av +a+ + ee+ +  ++v++p+ ++al++yy+i+++eassnlar++g ry + ++ ++++ + +k+
  gi|91773613|ref|YP_566305.1| 254 DEYFGEGVDSGTENAVWDAINKYEEMDASWEKVSMPNTKYALAAYYTIAMSEASSNLARFDGTRYGPRNDGENWHVMASKT 334
                                   ********************************************************************************* PP

                                   HHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGC CS
                       Amidase 325 raellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynl 405
                                   rae++g+ev+rri lg+yalsa++++kyylka +vr+l++++f++af  +Dvl++Pt+p pa+++ge+    +++++ y++
  gi|91773613|ref|YP_566305.1| 335 RAENFGKEVQRRILLGTYALSAGYQDKYYLKALQVRTLVKQDFDRAFANFDVLMAPTMPLPAFKIGEMV---EDPLSQYLI 412
                                   ********************************************************************8...69******* PP

                                   CTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                       Amidase 406 ldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetl 450
                                   ++ t   vp+nlag p +svp+g s+ glPvG+q+ig++f+e++l
  gi|91773613|ref|YP_566305.1| 413 DVNT---VPMNLAGVPCISVPCGSSD-GLPVGLQIIGNHFDEAAL 453
                                   ****...****************985.***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3258.52
//
Query:       gi|91773614|ref|YP_566306.1|  [L=93]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit C [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-19   70.6   0.2    1.4e-19   70.1   0.2    1.2  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 !   70.1   0.2   7.7e-24   1.4e-19       4      61 ..      21      88 ..      18      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 7.7e-24
                                  HHHHHHHHHHHHHHHHHTTCGCS--TT----S.......-EB-S--.....HHHHHTT-SSEETTEEE CS
                   Glu-tRNAGln  4 eEleklakelnsildyveqLqevdttgveplthp.....vlReDev.....reelLknApetedgyfv 61
                                  +E+e++a +l+s+ldy+ qL+evdt+gvep++h+     v+ReD+v     ++++L+n  e +dgy++
  gi|91773614|ref|YP_566306.1| 21 AEAEDYAVKLSSVLDYFGQLDEVDTEGVEPTYHVadimnVFREDVVkpsldQKDVLANTAEEKDGYIK 88
                                  79******************************************9789**8888************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 700.91
//
Query:       gi|91773615|ref|YP_566307.1|  [L=134]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-17   62.3   0.0    4.5e-17   62.0   0.0    1.1  1  Putative_PNPOx  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 !   62.0   0.0   2.5e-21   4.5e-17       1      86 [.       4      89 ..       4      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 2.5e-21
                                  HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEEE CS
                Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtael 83
                                  l+e +++++++ +++ +AT+++ G Pnv+p++++ + ++ +i++a n + ++l n+ enp+v+++++ ++++ +++i+G +el
  gi|91773615|ref|YP_566307.1|  4 LTEDMKAAFNTIQVFPVATASKGGIPNVVPIGFVSLIDDSTIWIADNFMQKTLLNIIENPKVSIYIWGPKTNGSFQIKGDVEL 86
                                  6899******************************************************************************9 PP

                                  ESC CS
                Putative_PNPOx 84 vsd 86
                                   + 
  gi|91773615|ref|YP_566307.1| 87 KTS 89
                                  765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 992.47
//
Query:       gi|91773616|ref|YP_566308.1|  [L=253]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   36.2   0.1    8.9e-09   35.3   0.1    1.5  1  HTH_20    Helix-turn-helix domain
    1.4e-06   28.0   0.2    3.2e-06   26.9   0.1    1.7  2  HTH_5     Bacterial regulatory protein, arsR family
    0.00092   19.1   0.0     0.0017   18.3   0.0    1.4  1  HTH_45    Winged helix-turn-helix
     0.0023   18.1   0.1     0.0048   17.0   0.1    1.6  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.024   14.2   0.2      0.069   12.7   0.1    1.8  2  HTH_24    Winged helix-turn-helix DNA-binding
       0.03   14.4   0.5       0.72   10.0   0.0    2.7  2  CtsR_C    CtsR C-terminal dimerization domain
      0.035   14.3   0.0      0.082   13.1   0.0    1.6  1  Rio2_N    Rio2, N-terminal
      0.035   14.1   0.1       0.18   11.8   0.0    2.0  2  BLACT_WH  Beta-lactamase associated winged helix domain
       0.12   12.2   0.2       0.35   10.7   0.1    1.8  2  HTH_IclR  IclR helix-turn-helix 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 !   35.3   0.1   4.5e-12   8.9e-09       7      60 ..     171     223 ..     162     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4.5e-12
                                   HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                   L++ vR  il+aL  +eg++++el ++ +l+  +l +HL++L+  g ++++ e+
  gi|91773616|ref|YP_566308.1| 171 LSSSVRVQILKAL-YEEGRSFTELSKLTELRGGNLLFHLEKLQNRGMIRQRSER 223
                                   899**********.***********************************99886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   1.6e-09   3.2e-06       2      46 ..     174     218 ..     173     219 .. 0.95
   2 ?   -3.4   0.0       4.7   9.3e+03      18      32 ..     239     253 .]     238     253 .] 0.74

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.6e-09
                                   HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                   + R++ILk+L e+ ++++el++ ++l  +++  HL kL + G+++
  gi|91773616|ref|YP_566308.1| 174 SVRVQILKALYEEGRSFTELSKLTELRGGNLLFHLEKLQNRGMIR 218
                                   68***************************************9985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.7
                                   HHHHHHHHTS-HHHH CS
                         HTH_5  18 vcelaeelglsqstv 32 
                                   + el+ +lgl+ s++
  gi|91773616|ref|YP_566308.1| 239 IAELVGKLGLNYSKI 253
                                   568888899887765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.6e-07    0.0017       7      72 ..     175     242 ..     172     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.6e-07
                        HTH_45   7 IiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikk..skekYvlTekGlelleklkel 72 
                                   + ++IL+a+ e++ + T++ +  +L   +l   L++L+++g+i++  + ++Y++  +G e l+++ el
  gi|91773616|ref|YP_566308.1| 175 VRVQILKALYEEGRSFTELSKLTELRGGNLLFHLEKLQNRGMIRQrsERGEYQISVQGYEALNSIAEL 242
                                   5689***************************************5534889*************99875 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.4e-06    0.0048       1      47 [.     175     220 ..     175     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                        HTH_34   1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd 47 
                                   vR ++l  L+++   +f+el++ +e+  gnL  hl+kL++ g i  +
  gi|91773616|ref|YP_566308.1| 175 VRVQILKALYEE-GRSFTELSKLTELRGGNLLFHLEKLQNRGMIRQR 220
                                   799999999975.568**************************98643 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 ?   12.7   0.1   3.5e-05     0.069       7      48 .]     178     218 ..     174     218 .. 0.92
   2 ?   -2.9   0.0       2.6   5.2e+03      19      30 ..     238     249 ..     237     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                        HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   +IL++L+++ + s +eL++ + l  ++++ +l++L++ G I+
  gi|91773616|ref|YP_566308.1| 178 QILKALYEE-GRSFTELSKLTELRGGNLLFHLEKLQNRGMIR 218
                                   899****95.559***************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                        HTH_24  19 sqreLAerlglS 30 
                                   s++eL  +lgl 
  gi|91773616|ref|YP_566308.1| 238 SIAELVGKLGLN 249
                                   677888888875 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 ?   10.0   0.0   0.00036      0.72       7      33 ..     161     187 ..     153     188 .. 0.89
   2 ?    1.6   0.1      0.16   3.1e+02      25      39 ..     207     221 ..     205     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00036
                        CtsR_C   7 eilinsigdsiseqdaeaiiqrLleeg 33 
                                   e + ++igd +s++   +i++ L+eeg
  gi|91773616|ref|YP_566308.1| 161 EDVSSLIGDPLSSSVRVQILKALYEEG 187
                                   668899*******************97 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                        CtsR_C  25 iiqrLleegliterE 39 
                                   ++++L+++g+i +r 
  gi|91773616|ref|YP_566308.1| 207 HLEKLQNRGMIRQRS 221
                                   5899********996 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.1e-05     0.082      27      74 ..     190     236 ..     184     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
                        Rio2_N  27 telieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyL 74 
                                   +++++++++l+ +++  +l++l ++++i++++     Y+++ +Gy +L
  gi|91773616|ref|YP_566308.1| 190 FTELSKLTELRGGNLLFHLEKLQNRGMIRQRSE-RGEYQISVQGYEAL 236
                                   678999**********************99754.455********988 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.1   2.2e+03      26      37 ..     177     188 ..     177     189 .. 0.86
   2 ?   11.8   0.0   8.9e-05      0.18      24      43 ..     203     222 ..     201     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                      BLACT_WH  26 lahLeKLeeeGk 37 
                                   +++L+ L eeG+
  gi|91773616|ref|YP_566308.1| 177 VQILKALYEEGR 188
                                   589999999998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.9e-05
                      BLACT_WH  24 gvlahLeKLeeeGkVkregd 43 
                                   ++l hLeKL+++G +++ ++
  gi|91773616|ref|YP_566308.1| 203 NLLFHLEKLQNRGMIRQRSE 222
                                   8999************9875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00018      0.35       6      51 ..     177     220 ..     175     221 .. 0.95
   2 ?   -2.9   0.0       3.1   6.1e+03      20      31 ..     238     249 ..     234     252 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR   6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                   ++iL+al e+++   ++el++ t l   +   +L  L+++G+++q 
  gi|91773616|ref|YP_566308.1| 177 VQILKALYEEGRS--FTELSKLTELRGGNLLFHLEKLQNRGMIRQR 220
                                   69**********6..*****************************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                                   BHHHHHHHHTS- CS
                      HTH_IclR  20 tlselArrtglp 31 
                                   +++el  ++gl+
  gi|91773616|ref|YP_566308.1| 238 SIAELVGKLGLN 249
                                   567777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      835  (0.0465726); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1669.40
//
Query:       gi|91773617|ref|YP_566309.1|  [L=281]
Description: hypothetical protein Mbur_1659 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-18   66.0  39.6    3.2e-12   46.8  15.8    2.1  2  EamA      EamA-like transporter family
    0.00039   20.0   0.8    0.00087   18.9   0.8    1.6  1  SLC35F    Solute carrier family 35
  ------ inclusion threshold ------
       0.19   11.0   8.5      0.044   13.1   4.6    1.9  2  TPT       Triose-phosphate Transporter family
       0.37   10.2   4.6          2    7.7   0.9    2.3  2  TssN      Type VI secretion system, TssN
       0.38   10.8   7.6       0.52   10.3   0.7    2.7  2  TMEM234   Putative transmembrane family 234


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5  15.8   3.4e-09   1.2e-05       3     136 ..       8     138 ..       6     139 .. 0.92
   2 !   46.8  15.8     9e-16   3.2e-12       6     136 ..     153     280 ..     150     281 .] 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.4e-09
                          EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllff 83 
                                    ill l++a +w+++ +    ++++++ + ++ ++  ++ ill i+a ++ +++  +   ++++ ++ g +++ l+ ++++
  gi|91773617|ref|YP_566309.1|   8 VILLGLASAAVWGAADFGGGFASKRTNEYYVVILMQAVGLILLPILAIVFSEQF--PQGGGIFWGFVAG-VAGSLGLVVLY 85 
                                   689*****************************9999999999999999999999..8888888866666.7888999**** PP

                          EamA  84 yalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    al+ ++ ++++++++++ v   ++  +l    ++++q+ g+v++l++ +li+
  gi|91773617|ref|YP_566309.1|  86 RALSQGKMGVVAPVSAIVTVALPVIYGALKEGLPSVYQMTGFVVALVAMWLIS 138
                                   ********************9999999999999*****************997 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 9e-16
                          EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyal 86 
                                   l lla + ++i f+  ++++++   + lt+     + i  l+ia l+++k+  +++++ l l++l+ +  + ++l+f  a 
  gi|91773617|ref|YP_566309.1| 153 LPLLAGVGFGIFFISVDMFSEDAVFWPLTVAKA-SSVITILLIAILTGSKN--IPVRGALPLIILAGIFDAGGNLFFALAS 230
                                   557888888888888888766666665555443.33344444444444444..8999999999999999************ PP

                          EamA  87 kktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   + + + +a+++ sl P+ t++l++++l+e+l l q++g+vl+l++v++i+
  gi|91773617|ref|YP_566309.1| 231 QVGRVDIATVVASLYPASTVLLAWIFLKERLALNQWMGVVLALVAVVFIS 280
                                   ************************************************97 PP

>> SLC35F  Solute carrier family 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.8   2.4e-07   0.00087      77     143 ..     213     279 ..     201     281 .] 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-07
                        SLC35F  77 lllalvdveanylvvkayqytsltsvqlldcfaipvvlvlswlflkvryrlvkiigvvvcilGvvll 143
                                   +l +++d  +n +   a q   +  ++++ +   +  ++l+w+flk r  l + +gvv+ ++ vv +
  gi|91773617|ref|YP_566309.1| 213 ILAGIFDAGGNLFFALASQVGRVDIATVVASLYPASTVLLAWIFLKERLALNQWMGVVLALVAVVFI 279
                                   56689**************************99999*************************999875 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       0.4   1.4e+03     141     153 ..     121     133 ..      84     143 .. 0.57
   2 ?   13.1   4.6   1.2e-05     0.044      31     134 ..     179     278 ..     166     281 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                           TPT 141 sFnligfisAlis 153
                                    ++++gf+ Al++
  gi|91773617|ref|YP_566309.1| 121 VYQMTGFVVALVA 133
                                   3555666655554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.2e-05
                           TPT  31 Pltvsavqllvgsvlilvlwalglkkrpkisse.flkailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsr 110
                                   Pltv+ ++ +++++l     ++ l+  ++i ++  l  i+  +++ + g+++  ++ +   V  + +v ++ P+ tv+l+ 
  gi|91773617|ref|YP_566309.1| 179 PLTVAKASSVITILL-----IAILTGSKNIPVRgALPLIILAGIFDAGGNLFFALASQVGRVDIATVVASLYPASTVLLAW 254
                                   555555444433333.....3344445568888789999999*************************************** PP

                           TPT 111 lllgeklsllvylsLlpivgGval 134
                                   ++l+e+l l+ ++ ++  ++ v+ 
  gi|91773617|ref|YP_566309.1| 255 IFLKERLALNQWMGVVLALVAVVF 278
                                   **********99988877776665 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9   0.00057         2      25      92 ..      28      96 ..       5     115 .. 0.70
   2 ?    3.6   0.1      0.01        37      68     151 ..     121     204 ..     117     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00057
                          TssN 25 nkllkkkkliiyiLlaglvlalpgllgf.lknefvpygyillqilylllGilhlylllkkffkelkekk 92
                                  ++ ++  +++++iL+ ++ l l+ +l++ ++ +f   g i+  +++ + G+l l++l++ + +      
  gi|91773617|ref|YP_566309.1| 28 FASKRTNEYYVVILMQAVGLILLPILAIvFSEQFPQGGGIFWGFVAGVAGSLGLVVLYRALSQGKMGVV 96
                                  566777889999999999998888888867778888899999999999999999999998877665544 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.01
                          TssN  68 lylllGilhlylllkkffkelkekkilfeilltlivillglvlfvlvfnllselq.ygvwaatsllvfiipllflktykal 147
                                   +y ++G++ + +++  + +  ++ +i  + +++ + + +g+ +f++ ++++se   + ++ + + ++ +i +l++ +    
  gi|91773617|ref|YP_566309.1| 121 VYQMTGFVVALVAMWLISSSDDNGDIRRQDIVLPLLAGVGFGIFFISVDMFSEDAvFWPLTV-AKASSVITILLIAILTGS 200
                                   67788999888888888888888888999999999999**************9984444433.334444445555555555 PP

                          TssN 148 lsIP 151
                                    +IP
  gi|91773617|ref|YP_566309.1| 201 KNIP 204
                                   5555 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.7     0.016        56      56     115 ..      79     137 ..      69     138 .. 0.85
   2 ?   10.3   0.7   0.00015      0.52      60     115 ..     224     279 ..     210     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                       TMEM234  56 sgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                   +g v+ + +l++ ++ ++ p++  +++++ v+ + +l+e + +  +++g ++ +v++ l+
  gi|91773617|ref|YP_566309.1|  79 LGLVVLYRALSQGKMGVVAPVSAIVTVALPVIYG-ALKEGLPSVYQMTGFVVALVAMWLI 137
                                   57799999**************999999999998.5899999999999999888887775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
                       TMEM234  60 lfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                   lff+l +++    +  ++ sl  + Tvl +++  ++ l  ++++g++l +v+++ +
  gi|91773617|ref|YP_566309.1| 224 LFFALASQVGRVDIATVVASLYPASTVLLAWIFLKERLALNQWMGVVLALVAVVFI 279
                                   4555544444333445778*****************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); 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:                         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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2068.62
//
Query:       gi|91773618|ref|YP_566310.1|  [L=562]
Description: hydroxylamine reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.7e-178  594.5   0.1     2e-178  594.3   0.1    1.0  1  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.3   0.1  1.1e-182    2e-178       1     510 [.       1     558 [.       1     559 [. 0.97

  Alignments for each domain:
  == domain 1  score: 594.3 bits;  conditional E-value: 1.1e-182
                                   -EE-SST....CT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHC......HHHHHHHHHCHTSTTTB-SH CS
                                   xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                      Prismane   1 mfCrqCe....ngpCritknkrGvCGkdadtavardlliavlkgaaahaaharel......adtliakalfktltnvnfdd 71 
                                   m+C+qCe    ++ C+      G+CGk+a++a+++d l+++lkg+a ++++are       +d++ +kalf+t+tn+nf++
  gi|91773618|ref|YP_566310.1|   1 MYCYQCEetinGQSCTKA----GACGKTANVADLQDQLTYILKGIAYYNQKARENgikdknVDSFLMKALFSTVTNTNFSS 77 
                                   89********999***99....*********************************************************** PP

                                   HHHHHHHHHHHCHHHCC.........................................SSHHHHHHHHCCHHHCGGGS-SS CS
                                   xxxxxxxxxxxxxxxxx.........................................xxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane  72 ekklkrlaealgieeel.........................................kdieelaakvaevaledlskeen 111
                                   +++ k+++e + ++e++                                         +      + +++++++ l+++ n
  gi|91773618|ref|YP_566310.1|  78 SDFNKFINEGISLRESIkknlttrkinlgktkdmsfgekvkttlgvshpetrftipeaA--IINTEALKTASVGVLNTQ-N 155
                                   *****************************************************987432..333345566679999977.8 PP

                                   HHHHHHHCCCHHHHHHH..HHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 112 edirslkellpkglkgl..yaehaivlgyadeevveflaktlaglesdpld...llskalrlGlldlkgmelldeantslf 187
                                   edirsl+ell++glkgl  ya+ha vlgy+de++ ef +k+la++ +d+l+   l+ ++l++G++ +++m+lld+ants++
  gi|91773618|ref|YP_566310.1| 156 EDIRSLRELLVYGLKGLaaYAHHAEVLGYTDETLSEFAEKALASTLDDSLSvddLVGLVLECGKYGVNVMALLDKANTSTY 236
                                   *************************************************9999**************************** PP

                                   -----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHHHHHCCEEEEECSSGGGHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 188 GtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalklkyrhlvgnvGnawqqeka 268
                                   G+Pep  tev lg++  + ++Il+sGHdl+d+e+ll+ teg+g++vythgemLp+++++a+k ky+h+vgn+G +w+++k 
  gi|91773618|ref|YP_566310.1| 237 GNPEP--TEVFLGTR-DN-PGILISGHDLKDMEQLLKRTEGTGVDVYTHGEMLPANYYPAFK-KYDHFVGNYGGSWWNQKN 312
                                   *****..********.66.9******************************************.****************** PP

                                   HHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE--CTTCHHHHHHHHHHHHCCHCCTTCGG.-...... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                      Prismane 269 eftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhieeeekadkdaseiiekAielakareekkve...... 343
                                   ef+ ++++i+++tnC+vpp++s    y +r++tts v++ g+khi+++e+  kd+s+i+e+Ai+++++++ ++ +      
  gi|91773618|ref|YP_566310.1| 313 EFETFNGPILMTTNCLVPPKNS----YINRVYTTSVVGFDGVKHIDAKEDGTKDFSAIVEQAIACQPPKQLEDGTivggfa 389
                                   *******************777....********************999999*****************99777799**** PP

                                   ...........HHHHHTTSS-EEEEE-B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHCE CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 344 ...........idaiksGtIkgvvlvvGCdnakkgrdyytelakelikrdvlvltaGCakyalnklglgtieaaelagegi 413
                                              i+a+k+G+I ++++++GCd+++k+rdyyt++a++l ++  ++ltaGCaky++nkl+lg+i       +gi
  gi|91773618|ref|YP_566310.1| 390 haavlsvadkvIEAVKAGKITRFIVMAGCDGRHKERDYYTKFAEAL-PESAVILTAGCAKYRYNKLNLGDI-------DGI 462
                                   **********************************************.************************.......59* PP

                                   ESEEEEESCCCHHHHHHHHHHHHHHTTS.SGGGSSEEEEECC--SHHHHHHHHHHHHTT-.CEEECSS-TTTT-HHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                      Prismane 414 PrvLdvGsCvdnyrivvialklaealgv.dindLplaalalewyeqKAvailltllalGi.nihlgptlpafgspnvlkvl 492
                                   PrvLd+G+C+d+y++vvia+klaea+g+ dindLp+ +++++wyeqKAv +ll+ll+lG+ ni lgptlpaf+spnvl+vl
  gi|91773618|ref|YP_566310.1| 463 PRVLDAGQCNDSYSLVVIAQKLAEAFGLeDINDLPV-SYNIAWYEQKAVLVLLALLHLGVkNITLGPTLPAFVSPNVLNVL 542
                                   ***************************99*******.******************************************** PP

                                   HCHHHHHHCEEEECHCHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                      Prismane 493 vedfedriggivtveedp 510
                                   ve+f  +i++ +tveed+
  gi|91773618|ref|YP_566310.1| 543 VENF--NIAPNTTVEEDL 558
                                   ****..***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3698.68
//
Query:       gi|91773619|ref|YP_566311.1|  [L=116]
Description: hypothetical protein Mbur_1661 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.1   3.0        1.2    9.3   3.0    2.0  1  DUF2371   Uncharacterised conserved protein (DUF2371)


Domain annotation for each model (and alignments):
>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.0   6.8e-05       1.2      42     118 ..      14     107 ..       5     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 6.8e-05
                       DUF2371  42 lvlllGllvllvGiamavlgywpkk.................aklaseekssssstaessseklgllarfleqylysdklk 105
                                   l+l+   l  ++G am +l y + +                   +  +   +s++++++++  +g++++++   +    l 
  gi|91773619|ref|YP_566311.1|  14 LLLITATLFTMIGTAMVLLDYNYYNglqylatalaffttayiI-KVGKVDLDSATDNNHTQIMAGFMITVVALTITFVALS 93 
                                   5566778899************99999*****99999987642.3333445555556666777899999999999999999 PP

                       DUF2371 106 vlGPl.imGiGifl 118
                                   + G +  +Gi +f+
  gi|91773619|ref|YP_566311.1|  94 IKGLFwAVGITVFI 107
                                   99976345666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 875.90
//
Query:       gi|91773620|ref|YP_566312.1|  [L=327]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-13   50.8   1.2    3.2e-13   50.4   0.4    1.6  2  Radical_SAM  Radical SAM superfamily
     0.0016   16.5   0.0     0.0022   16.0   0.0    1.1  1  TssR         Type VI secretion system, TssR


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.4   3.6e-17   3.2e-13       1     162 [.      94     248 ..      94     253 .. 0.79
   2 ?   -2.7   0.0      0.76   6.8e+03     124     140 ..     279     295 ..     272     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3.6e-17
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.TTHHHHHHHHHHTC..CCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.pdfvellerlakla..vpg 77 
                                   ++ t+ C ++C+fC++p+       g+++++eei e++ ++    g  k + +++g      +++ ++le + + +  +  
  gi|91773620|ref|YP_566312.1|  94 INMTEKCIYDCKFCPVPK-----LNGKVKTIEEITELIGKA-NASGkMKAISITSGVDESTeKELDRALEVIDAVKhyNVP 168
                                   578999***********6.....8*****************.677778888888775555313333333333333355666 PP

                                   EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                   Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGend 157
                                   i +++ + +        +rl+ +gvd +  ++e+ d   +++ + + +++e +l+al+ + e  +k+ v+ + +++ Ge+d
  gi|91773620|ref|YP_566312.1| 169 IGVAIYATPDSN-----KRLKAAGVDEIKYNVETMDRPIYREVC-GDQDLEPILDALREAVEMFGKNkVCANFIIGLGETD 243
                                   666666666666.....********************9666666.99****************777799999999999*** PP

                                   HHHHH CS
                                   xxxxx RF
                   Radical_SAM 158 eelee 162
                                   e +e 
  gi|91773620|ref|YP_566312.1| 244 ESVER 248
                                   *9886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.76
                                   TSHHHHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxx RF
                   Radical_SAM 124 ghtfeevlealeklrea 140
                                   +++ e++l+++++lre+
  gi|91773620|ref|YP_566312.1| 279 RPSKERLLKLTKLLREV 295
                                   46778999999999886 PP

>> TssR  Type VI secretion system, TssR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.5e-07    0.0022     337     422 ..     163     246 ..     155     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-07
                          TssR 337 rktsvkfGavvykddrgnkkpgtsslstdykkllsfLekeakskraeseskeepvwealkkalellknqknetNlivliGe 417
                                   + ++v +G+ +y++ ++nk       + ++k+ ++++++ + ++ + +++  ep+ +al++a+e+++++k   N+i+ +Ge
  gi|91773620|ref|YP_566312.1| 163 KHYNVPIGVAIYATPDSNKRLKAAGVD-EIKYNVETMDRPIYREVCGDQDL-EPILDALREAVEMFGKNKVCANFIIGLGE 241
                                   678999*******99999999999988.**************988877666.69*************************** PP

                          TssR 418 tgnns 422
                                   t ++ 
  gi|91773620|ref|YP_566312.1| 242 TDESV 246
                                   *9844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2214.47
//
Query:       gi|91773621|ref|YP_566313.1|  [L=109]
Description: hypothetical protein Mbur_1663 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 765.41
//
Query:       gi|91773622|ref|YP_566314.1|  [L=131]
Description: thioredoxin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  101.5   0.1    2.7e-29  101.2   0.1    1.1  1  Thioredoxin    Thioredoxin
    1.1e-06   28.9   0.0     0.0024   18.2   0.0    2.4  2  Thioredoxin_8  Thioredoxin-like
    1.1e-06   29.0   0.3    4.3e-05   23.9   0.3    2.2  1  Thioredoxin_2  Thioredoxin-like domain
    2.4e-06   27.1   0.0    3.2e-06   26.7   0.0    1.3  1  OST3_OST6      OST3 / OST6 family, transporter family
    3.6e-05   23.6   0.2    6.5e-05   22.7   0.1    1.4  1  Thioredoxin_9  Thioredoxin
    0.00029   20.8   0.1    0.00036   20.5   0.1    1.3  1  Thioredoxin_6  Thioredoxin-like domain
     0.0031   17.4   0.1      0.039   13.9   0.0    2.1  2  AhpC-TSA       AhpC/TSA family
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.032   13.9   0.1    1.8  1  Redoxin        Redoxin
      0.013   15.3   0.0      0.021   14.7   0.0    1.3  1  TraF           F plasmid transfer operon protein
       0.03   14.3   0.0      0.065   13.2   0.0    1.5  2  HyaE           Hydrogenase-1 expression protein HyaE
      0.042   13.5   0.1      0.081   12.6   0.0    1.5  1  Thioredoxin_5  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 !  101.2   0.1   1.6e-32   2.7e-29       3     102 ..      29     127 ..      27     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 1.6e-32
                                   EESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                   Thioredoxin   3 lvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                   +++t+++F+e +ak     +++++A+wCg+C++l P +++la+e+++k+++ k+++den+ +a+++++++iPt+++fkng+
  gi|91773622|ref|YP_566314.1|  29 IHVTDADFNEFIAK-YPITVIDCWAEWCGPCRKLIPIIDALAKEYQGKIVFGKLNTDENQMVARNFNITAIPTILVFKNGN 108
                                   6799**********.9***************************************************************** PP

                                   EEEEEESS-HHHHHHHHHH CS
                   Thioredoxin  84 evkkyegarekeklaaflk 102
                                   ++ +++ga +ke+l+++l+
  gi|91773622|ref|YP_566314.1| 109 AATQIVGALQKEQLVEHLN 127
                                   ***************9987 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0024       3      44 ..      45      84 ..      42      89 .. 0.77
   2 !   10.0   0.1    0.0005      0.82      67      91 ..      82     106 ..      77     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                                  EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S CS
                 Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsld 44
                                  ++++ ++a+wc pc++ +p +++l ++++   k+++  ++ d
  gi|91773622|ref|YP_566314.1| 45 ITVIDCWAEWCGPCRKLIPIIDALAKEYQ--GKIVFGKLNTD 84
                                  7899************************8..44444333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0005
                                   -TT-HHHHTT-S--TT-SEEEEE-T CS
                 Thioredoxin_8  67 ddkkrnklkkkynvkaiPtlvvldk 91 
                                   + ++++ +++++n++aiPt++v ++
  gi|91773622|ref|YP_566314.1|  82 NTDENQMVARNFNITAIPTILVFKN 106
                                   66788999***********877654 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.3   2.7e-08   4.3e-05       9     108 ..      47     125 ..      41     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.7e-08
                 Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt.ivfld 88 
                                   +++ ++++C+ C+kl   ++ l    +      ++ +  +++ ++ +           +en+ +ar +++++ Pt +vf +
  gi|91773622|ref|YP_566314.1|  47 VIDCWAEWCGPCRKLIPIIDAL---AKE-----YQGK--IVFGKLNT-----------DENQMVARNFNITAIPTiLVFKN 106
                                   5666677777777777766666...222.....3333..33333333...........455679***********667999 PP

                 Thioredoxin_2  89 gkeivarlpGyvpaeeleal 108
                                   g+  +++++G++++e+l + 
  gi|91773622|ref|YP_566314.1| 107 GN-AATQIVGALQKEQLVEH 125
                                   99.999**********9876 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 !   26.7   0.0     2e-09   3.2e-06      13     107 ..      28     109 ..      17     131 .] 0.70

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2e-09
                     OST3_OST6  13 viklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklgl 93 
                                    i+++d++++e+++    y + v+ +       C +Cr++ p ++++ak ++ +       ++F+k++ de++ v + +++
  gi|91773622|ref|YP_566314.1|  28 PIHVTDADFNEFIA---KYPITVI-DCW--AEWCGPCRKLIPIIDALAKEYQGK-------IVFGKLNTDENQMVARNFNI 95 
                                   56666666666664...3333332.222..356*****************9988.......9******************* PP

                     OST3_OST6  94 nsaPhlllfppkkg 107
                                   + +P +l+f+  + 
  gi|91773622|ref|YP_566314.1|  96 TAIPTILVFKNGNA 109
                                   *********98332 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1     4e-08   6.5e-05      49     108 ..      51     108 ..      32     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4e-08
                                   --TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT- CS
                 Thioredoxin_9  49 tedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeeg 108
                                    ++wCg ++  +P+++++a e++ +i +  l  den+ + +++      aiPt+++++++ 
  gi|91773622|ref|YP_566314.1|  51 WAEWCGPCRKLIPIIDALAkEYQGKIVFGKLNTDENQMVARNFNI---TAIPTILVFKNGN 108
                                   579**************99678889****************9955...9*****9998763 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.2e-07   0.00036     113     183 ..      61     131 .]      29     131 .] 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEESSSS-EEEET..TSS--HHHHHHHHH CS
                 Thioredoxin_6 113 lkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivdsashkykypp..kdefspeklkeFlk 183
                                   l  +i ++ake+++ki f  +++++++ + + ++++  ++P+i ++++ +  ++     ++e  +e+l +F++
  gi|91773622|ref|YP_566314.1|  61 LIPIIDALAKEYQGKIVFGKLNTDENQMVARNFNIT--AIPTILVFKNGNAATQIVGalQKEQLVEHLNKFIQ 131
                                   5568999**************************999..********988877666644677777888888886 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.4e-05     0.039      26      57 ..      44      74 ..      18      80 .. 0.81
   2 ?    1.4   0.0      0.17   2.8e+02      88     115 ..      83     104 ..      79     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                  SEEEEEEESTST-CCHHHHHHHHHHCHHHCCC CS
                      AhpC-TSA 26 kpvvlffypkdwcpvCttelpalaklyeefke 57
                                   ++v+ ++++ wc +C++ +p + +l++e++ 
  gi|91773622|ref|YP_566314.1| 44 PITVIDCWAE-WCGPCRKLIPIIDALAKEYQG 74
                                  579*******.******************995 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.17
                                   E-TTSHHHHHTT-EETTTTECSCEEEEE CS
                      AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvi 115
                                    De++ va+++++       a+++  v+
  gi|91773622|ref|YP_566314.1|  83 TDENQMVARNFNIT------AIPTILVF 104
                                   6999*******999......77777766 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     2e-05     0.032      31      75 ..      46      88 ..      16     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                                  EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH CS
                       Redoxin 31 vvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf 75
                                  +v+  ++  +c++C++ +p ++ la+++  k + +  +++d+++ 
  gi|91773622|ref|YP_566314.1| 46 TVIDCWAE-WCGPCRKLIPIIDALAKEYQGK-IVFGKLNTDENQM 88
                                  68999999.*****************96554.5555666666666 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-05     0.021     141     210 ..      55     115 ..      50     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                          TraF 141 cpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpva 210
                                   c+ c++++pi++a+a++y+ ++++ +++   +++++          +++++ +P++++++  +  + +v+
  gi|91773622|ref|YP_566314.1|  55 CGPCRKLIPIIDALAKEYQGKIVFGKLNTDENQMVAR---------NFNITAIPTILVFKNGNAATQIVG 115
                                   999***************9999887766666666888.........9*************9998888887 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.8   4.5e+03      16      31 ..      33      48 ..      22      54 .. 0.68
   2 ?   13.2   0.0     4e-05     0.065      50     100 ..      65     114 ..      55     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.8
                                  CCCHHHHHHHHSEEEE CS
                          HyaE 16 adtlddflkaagdavl 31
                                  +++ ++f+++ +++v+
  gi|91773622|ref|YP_566314.1| 33 DADFNEFIAKYPITVI 48
                                  4556666666666654 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4e-05
                                   HHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEE CS
                          HyaE  50 lpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvla 100
                                   +  l k+++       ++ +++++++a++f+++  P++l++++g+    + 
  gi|91773622|ref|YP_566314.1|  65 IDALAKEYQGKIVFGKLN-TDENQMVARNFNITAIPTILVFKNGNAATQIV 114
                                   555667776666666666.7888999*****************99776664 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     5e-05     0.081     130     171 ..      68     109 ..      64     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                 Thioredoxin_5 130 fkeDlesklakkafqcD..lklakemgvtevPtlvffneneeee 171
                                   + + ++ k++  ++++D  + +a+++++t +Pt+ +f +   ++
  gi|91773622|ref|YP_566314.1|  68 LAKEYQGKIVFGKLNTDenQMVARNFNITAIPTILVFKNG--NA 109
                                   556666777766777665588***************9833..23 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 851.22
//
Query:       gi|91773623|ref|YP_566315.1|  [L=478]
Description: hypothetical protein Mbur_1671 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-233  774.1   3.5   3.8e-233  773.9   3.5    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 !  773.9   3.5  2.1e-237  3.8e-233       1     449 []      24     476 ..      24     476 .. 0.99

  Alignments for each domain:
  == domain 1  score: 773.9 bits;  conditional E-value: 2.1e-237
                       DUF2114   1 eyyivasvelGntttkciltatnletgktyllnktvkmtrdvrkpkegeevfgktlagveltresvaelvrdtlleslkka 81 
                                   +++ivasve+Gntttkciltatn+++gktyl++ktvkmtrdvr+pke+e++fg+tl+g+eltresv+elv++tl+e++kka
  gi|91773623|ref|YP_566315.1|  24 PFFIVASVEVGNTTTKCILTATNMDEGKTYLVTKTVKMTRDVRPPKEKETIFGRTLNGIELTRESVSELVKNTLIEAVKKA 104
                                   79******************************************************************************* PP

                       DUF2114  82 kldieedldfvvrstGvvagfdspeevgelikaladGCleagvppkkmtpamskenlpeklrkyslldkvvfdGavasvvp 162
                                   +ldi++d++fvvrstGvvagfd+peevge+ikaladGCl agvppk+mtp+m ++n+pek+rk+s+ldkv+fdGavasv+p
  gi|91773623|ref|YP_566315.1| 105 NLDIKTDINFVVRSTGVVAGFDTPEEVGEFIKALADGCLLAGVPPKNMTPPMGIDNIPEKFRKHSKLDKVFFDGAVASVLP 185
                                   ********************************************************************************* PP

                       DUF2114 163 PkgktgvevvanemegeLvtaGikegakwtdvdfrnPcisidfGttLdGrivndeePyaktvgnfcGlaGaipdaivrGtg 243
                                   P+g+tgve+vanemegeL+taGikegakw+dvdfrnPc+s+dfGttLdGri++++ePyakt+gnfcG+aGaipda+++Gtg
  gi|91773623|ref|YP_566315.1| 186 PTGATGVEIVANEMEGELATAGIKEGAKWVDVDFRNPCMSMDFGTTLDGRIISPDEPYAKTIGNFCGFAGAIPDAMIKGTG 266
                                   ********************************************************************************* PP

                       DUF2114 244 lvdkklgaaldlfkekkkk....kkkkkkikeyaekihelidiekvPkdrerfGtvPvdakaaeeagvvliGcdvgengsd 320
                                    vdkk+g+ald+fk+ +        k k+i+eya+k+ e+i+iekvP++r+r+G+vPv+++aa+e++vvliGcdvg ngsd
  gi|91773623|ref|YP_566315.1| 267 SVDKKVGTALDVFKDIHIDkltlLLKGKNIHEYAKKALEYIKIEKVPENRNRYGSVPVNPTAAKEINVVLIGCDVGVNGSD 347
                                   *************9866555666899******************************************************* PP

                       DUF2114 321 lekleeigaeilekeglkvllavldevsakivkrlievaveeglveektaiGitGragitGkkpelilekieelglyddke 401
                                   ++kl++igaei++k glkvl+av+dev+a++++rl++va+eeglv ++t+iGitGragi+G+k++l l+++++lgl++++e
  gi|91773623|ref|YP_566315.1| 348 FDKLSDIGAEIYDKFGLKVLFAVIDEVMAQVIYRLVNVAKEEGLVFPETTIGITGRAGISGDKAKLALKYLDKLGLHERIE 428
                                   ********************************************************************************* PP

                       DUF2114 402 envvfvddgLarGaavmarCmnslGtpknPlGGvrggkCilkkriklq 449
                                   envvfvddgLarGaavmarCmnslGt+ nPlGG++gg+Cil++riklq
  gi|91773623|ref|YP_566315.1| 429 ENVVFVDDGLARGAAVMARCMNSLGTTFNPLGGHHGGRCILGNRIKLQ 476
                                   **********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); 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: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3686.24
//
Query:       gi|91773624|ref|YP_566316.1|  [L=223]
Description: hypothetical protein Mbur_1672 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-66  221.6   0.0    9.6e-66  221.5   0.0    1.0  1  DUF166    Domain of unknown function
     0.0086   16.2   0.0      0.019   15.1   0.0    1.6  1  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 !  221.5   0.0   1.1e-69   9.6e-66       2     219 ..       6     217 ..       5     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 1.1e-69
                        DUF166   2 vltsgeyGervvenilnepdferslivavvevpeeldefiedpeelLpe......lkeaDiviaytlhpDlllelaekake 76 
                                   v+ +g+yG+r++e+++ ++d+e    v+v+evpe+l+e+i++p+e+++e      +++aDi+i+y+lhpD++ ++a++a e
  gi|91773624|ref|YP_566316.1|   6 VIVRGKYGRRLIETVRFRSDLE----VIVAEVPEHLPELIDEPDEFFSEldfngkVFDADIIITYSLHPDITPQIAKMAGE 82 
                                   899*******************....******************************************************* PP

                        DUF166  77 kkvkalivpaeapkaglrkelkekleelgievavpkpfCsleeegkpkideFleefGkPelevevkdgkikkVeVlrsapC 157
                                   ++v+alivp  a k + ++el++ + ++gi ++v++++C++   ++p+id+F++ fG+P l+v vkdgki+kV+V+r+apC
  gi|91773624|ref|YP_566316.1|  83 AGVGALIVPGGAAK-APIRELDDISLKYGIFIEVDDICCNIG--SDPSIDAFTSFFGNPVLDVGVKDGKISKVNVIRGAPC 160
                                   **************.**************************6..6************************************ PP

                        DUF166 158 GstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                   Gstw +a+ l+G++ve a  kag+ +++YpC+A+++     +++++h+++++hk+a+++A+k
  gi|91773624|ref|YP_566316.1| 161 GSTWRMADALVGNAVEGAGAKAGLLISQYPCRAVRG-----NMGGIHESSELHKKAIDDAIK 217
                                   ************************************.....9******************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 !   15.1   0.0   2.1e-06     0.019       8     120 ..       8     113 ..       2     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-06
                                   TTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S.-HHHHHHHHHHH CS
                        DapB_N   8 asGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFT.tpeavlenlkla 87 
                                   ++G+ G++++++v+ ++dle+  a   ++       + el++ ++ +++ + d++  + +ad++i ++ +p+ + + +k+a
  gi|91773624|ref|YP_566316.1|   8 VRGKYGRRLIETVRFRSDLEVIVAEVPEH-------LPELID-EPDEFFSELDFNGKVFDADIIITYSlHPDITPQIAKMA 80 
                                   479*****************998866655.......445444.48889999999999999********99*********** PP

                                   HHTT-EEEE--SS--HHHHHHHHHHTTTSEEEE CS
                        DapB_N  88 lekgvklViGTTGlseeelaeleelakkigvvi 120
                                    e+gv + i   G  ++ + el++++ k g++i
  gi|91773624|ref|YP_566316.1|  81 GEAGVGALIVPGGAAKAPIRELDDISLKYGIFI 113
                                   *************************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.41
# Mc/sec: 1627.17
//
Query:       gi|91773625|ref|YP_566317.1|  [L=201]
Description: thymidylate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-41  141.9   0.0      2e-41  141.7   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    4.5e-06   26.7   0.0    7.4e-06   26.0   0.0    1.3  1  dNK              Deoxynucleoside kinase
    0.00039   21.0   0.0      0.001   19.6   0.0    1.8  1  AAA_18           AAA domain
    0.00069   19.8   0.0      0.002   18.3   0.0    1.9  1  AAA_33           AAA domain
     0.0032   17.7   0.0     0.0048   17.2   0.0    1.4  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.033   14.5   0.0    1.4  1  CKS              Cyclin-dependent kinase regulatory subunit
      0.064   13.0   0.3        5.3    6.7   0.1    2.4  2  AAA_24           AAA domain
      0.097   12.7   0.0          2    8.5   0.0    2.6  3  KorB             KorB domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   0.0   8.8e-45     2e-41       1     184 [.       8     190 ..       8     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 8.8e-45
                                   EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT- CS
               Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgk 81 
                                   +EG+DG+GK+t++++l ++   +   +v+t+ep+++ iG+ + ++++   + +e++e++lf+ad+++h++++i pa+++gk
  gi|91773625|ref|YP_566317.1|   8 LEGIDGSGKSTITRFLNSHPAFAN--AVFTKEPTTSWIGDAVYKAIQ--SDTDELAELMLFTADHADHISTLIRPAIEEGK 84 
                                   6***************99866555..7*******************9..9999**************************** PP

                                   EEEEES-HHHHHHHHHT..TTTTT..CHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHH CS
               Thymidylate_kin  82 tvivdRylfSslaYqga..kegvd..ldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrer 158
                                   +vi+dRy +S +aYqg+  ke+++  +++++ +++  +  Pdlt+l+d+dp+va++R++kr+e  ++++e+ d l+ vre+
  gi|91773625|ref|YP_566317.1|  85 IVISDRYSDSRYAYQGVtlKERMEepMEWIQMIHRGWTIIPDLTLLFDIDPAVAVQRCGKRGE--QTKFEKTDLLKGVREN 163
                                   ****************94444443224455555555444************************..9*************** PP

                                   HHHHHH.TTSTEEEEETTS-HHHHHHH CS
               Thymidylate_kin 159 ylelak.ederiliidasksieevhee 184
                                   yl+la+ e+er+++id+ + ++e++++
  gi|91773625|ref|YP_566317.1| 164 YLKLAEkEPERFVVIDTDRDLKEIEKD 190
                                   **********************99987 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.3e-09   7.4e-06       1     202 [.       6     198 ..       6     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.3e-09
                                   EEEEESTTSSHHHHHHHHHCCST...CEEEE-HHHHCCSSSSHHHHHHHHSHHHHHHHH..HHHHHHHHHHHHHCHHSSS- CS
                           dNK   1 ivveGnIgaGKstlvklLskklg...vkvfeEpvdkwtnvqknlLekfYkdpsrwsfal..qtyvllsrlkqqlealatkq 76 
                                   i++eG  g+GKst++ +L+ +      ++ +Ep   w  +   + + +  d  +++  +        +    +  a+++++
  gi|91773625|ref|YP_566317.1|   6 ITLEGIDGSGKSTITRFLNSHPAfanAVFTKEPTTSW--IGDAVYKAIQSDTDELAELMlfTADHADHISTLIRPAIEEGK 84 
                                   789****************986633367889******..666777777777777774430033334444444444449999 PP

                                   EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHH..HHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHH CS
                           dNK  77 vvvleRsiysdryiFakalaekgtlseeelkiykelldnll..eelakpdlliYLkasletclerikkRgreeekkieldY 155
                                   +v+ +R  ysd        a +g+  +e ++   e+ +++   +++  pdl    ++++ + ++r  kRg++  k  ++d 
  gi|91773625|ref|YP_566317.1|  85 IVISDR--YSDS-----RYAYQGVTLKERMEEPMEWIQMIHrgWTII-PDLTLLFDIDPAVAVQRCGKRGEQT-KFEKTDL 156
                                   999999..7777.....334456666666666667776666444455.9*********************998.5568999 PP

                                   HHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHHHHHHHHH CS
                           dNK 156 lekLhekyeewlkklnevpvlvidveeldlvaeeekredvveevkel 202
                                   l+ + e+y +  +k +    +vid ++ dl    e ++dv+++++++
  gi|91773625|ref|YP_566317.1| 157 LKGVRENYLKLAEK-EPERFVVIDTDR-DLK---EIEKDVLQAITSI 198
                                   *********99988.777799******.655...5555666666655 PP

>> AAA_18  AAA 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     0.001       1      86 [.       6      94 ..       6     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.6e-07
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss........aleegk 75
                                  I l G+ G+GK+t+++ L+++       + v+++ ++ +++  +a+ +  + d+d l++l+     +++        a eegk
  gi|91773625|ref|YP_566317.1|  6 ITLEGIDGSGKSTITRFLNSHP---AFANAVFTK-EPTTSWIGDAVYKAIQSDTDELAELMLFTADHADhistlirpAIEEGK 84
                                  899***************9983...444444444.566666666455555555555555555555555455566664444444 PP

                        AAA_18 76 nlvidghlael 86
                                    vi+++ ++ 
  gi|91773625|ref|YP_566317.1| 85 I-VISDRYSDS 94
                                  4.666655555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.8e-07     0.002       1     127 [.       5     152 ..       5     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.8e-07
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg...avllssdt..lrr.rlfg...tdqqsktdytrvldrlyqilnelarkalsagrn 72 
                                   l+ l G  GsGKst  + l  + +   av+  ++t  ++  ++++   +d + + ++  ++ +  ++++ l+r a ++g+ 
  gi|91773625|ref|YP_566317.1|   5 LITLEGIDGSGKSTITRFLNSHPAfanAVFTKEPTtsWIGdAVYKaiqSDTDELAELMLFTADHADHISTLIRPAIEEGKI 85 
                                   68899************9976666989999999999944423333333555556667778888999999************ PP

                        AAA_33  73 vildat..........nlsrrer...arflklarr..lgvpvrivvvetdeetlkeRlakRaangddrse 127
                                   vi d               ++++   ++++++ +r     p++ + ++ d++++ +R  kR +++  ++e
  gi|91773625|ref|YP_566317.1|  86 VISDRYsdsryayqgvT-LKERMeepMEWIQMIHRgwTIIPDLTLLFDIDPAVAVQRCGKRGEQT--KFE 152
                                   ***76656566666442.2222244478888877422345799******************9974..333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-06    0.0048       2     127 ..       6     145 ..       5     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                        AAA_28   2 ivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedalpwv.edllafaervleeqleeeaaa.aankvl 76 
                                   i + G  ++GK+t+++ L+++    + +  +E+ +  + +   k  +   ++ ++l+ f +   ++     + a +++k++
  gi|91773625|ref|YP_566317.1|   6 ITLEGIDGSGKSTITRFLNSHpafaNAVFTKEPTTSWIGDAVYKAIQSDTDElAELMLFTADHADHISTLIRPAiEEGKIV 86 
                                   6678889*************9987555555************8877754555577788877755544444455689***** PP

                        AAA_28  77 fcDrglldtlaYarayggeaeae...leaaarekry...dlvfllppapei..dddgeR 127
                                   ++Dr +   +aY  +  +e+++e   + + + +      dl +l++ +p +  ++ g R
  gi|91773625|ref|YP_566317.1|  87 ISDRYSDSRYAYQGVTLKERMEEpmeWIQMIHRGWTiipDLTLLFDIDPAVavQRCGKR 145
                                   ************96665553333222555444333245577888887775543555555 PP

>> CKS  Cyclin-dependent kinase regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.5e-05     0.033       2      27 ..      86     111 ..      85     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                           CKS   2 eYSdkyeddeyeYRhViLpkellkki 27 
                                     Sd+y+d++y Y  V+L + + + +
  gi|91773625|ref|YP_566317.1|  86 VISDRYSDSRYAYQGVTLKERMEEPM 111
                                   67*****************9887755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0024       5.3       5      97 ..       6      92 ..       2     119 .. 0.70
   2 ?    4.3   0.0     0.013        29      22      49 ..     168     198 ..     153     201 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0024
                        AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtideleelclaevir 87
                                  i + G  g+GK+t+ + l  +p+f +       +  + ++      +++++++++ +ela++     D +d++  l++  + +
  gi|91773625|ref|YP_566317.1|  6 ITLEGIDGSGKSTITRFLNSHPAFANAVFTKEPTTSWIGD------AVYKAIQSDTDELAELMLFTADHADHISTLIRPAIEE 82
                                  7788999******999998889887655533444444444......5677777778888888888888888888888877777 PP

                        AAA_24 88 qnekaesked 97
                                   + + +++ +
  gi|91773625|ref|YP_566317.1| 83 GKIVISDRYS 92
                                  7777777644 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.013
                        AAA_24  22 l...gpkplfidtekGlksldadkfpdiesw 49 
                                   +   ++++++idt++ lk+++ d ++ i+s+
  gi|91773625|ref|YP_566317.1| 168 AekePERFVVIDTDRDLKEIEKDVLQAITSI 198
                                   144489**************99999988876 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.25   5.5e+02      65      85 ..       5      25 ..       3      29 .. 0.86
   2 ?    8.5   0.0   0.00089         2      32      73 ..      42      83 ..      32      89 .. 0.88
   3 ?   -2.2   0.0       1.9   4.3e+03      50      71 ..     126     147 ..     122     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                          KorB 65 fvaengeagltrsavrrflks 85
                                  ++   g++g+ +s+++rfl+s
  gi|91773625|ref|YP_566317.1|  5 LITLEGIDGSGKSTITRFLNS 25
                                  56778999***********98 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00089
                          KorB 32 ylrelydseviadirtLyeLrraaekhpaevrafvaengeag 73
                                  ++ +++ + +++d++ L eL  +  +h ++++++++ + e+g
  gi|91773625|ref|YP_566317.1| 42 WIGDAVYKAIQSDTDELAELMLFTADHADHISTLIRPAIEEG 83
                                  778888889*************************98776665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                          KorB  50 eLrraaekhpaevrafvaenge 71 
                                   +L  +++++pa + + + + ge
  gi|91773625|ref|YP_566317.1| 126 DLTLLFDIDPAVAVQRCGKRGE 147
                                   7888888888876666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1364.72
//
Query:       gi|91773626|ref|YP_566318.1|  [L=95]
Description: hypothetical protein Mbur_1674 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 738.21
//
Query:       gi|91773627|ref|YP_566319.1|  [L=235]
Description: histidine biosynthesis [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-27   96.7   0.0    1.7e-27   96.4   0.0    1.1  1  His_biosynth  Histidine biosynthesis protein


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 !   96.4   0.0   9.3e-32   1.7e-27       3     228 ..       5     229 ..       3     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 9.3e-32
                                   EEEEEEETTEEEEECTTCS........TCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTH..HHHHHHHHHHHHH-S CS
                  His_biosynth   3 ipalDlkdGkvVrlvkGdr........fqelryagdpvelakryeeegadelhvvDldaakegr..eanldlveeiaeevf 73 
                                   +++ D+ + ++V+   Gdr         ++     dpv +    +e    e++++Dl+  +     ++n  +++ + e   
  gi|91773627|ref|YP_566319.1|   5 VFVFDVYNRNAVHAQGGDRqkyrpvheISNVCTTSDPVGI---VRELRPAEVYIADLNRLQGRGdpNINFGVIRGVSEL-- 80 
                                   57899*******9999999333333222222233344444...45668899******9998544114566899999999.. PP

                                   SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHH CS
                  His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelak 154
                                    + +++ GI+s+edv  +l + a+ +++gt+++ + + i++++ +++s +i v+iD ++g +++ +        d++e++k
  gi|91773627|ref|YP_566319.1|  81 SQTMLDPGISSFEDVSGVLGL-AEHLVLGTETA-SLDSITKISAAYPS-QINVSIDKKNG-NILSSDPLMP--KDPLEIVK 155
                                   999*****************9.*********87.57799999******.*******9999.7777766666..9******* PP

                                   HHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                  His_biosynth 155 kleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                    l+ l++++i++ d+d +Gt sG+d ++++ +a+  +++v+ +GGv+++ed+++l++ g+++++v++ l++g++
  gi|91773627|ref|YP_566319.1| 156 VLNGLEINDIIFLDMDMVGTSSGFDAQFLSLIADISDHNVLLGGGVRDVEDIRQLEAIGIKGALVATGLHNGSI 229
                                   ***********************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1801.64
//
Query:       gi|91773628|ref|YP_566320.1|  [L=230]
Description: hypothetical protein Mbur_1676 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-86  288.4   0.0    4.7e-86  288.2   0.0    1.0  1  4HFCP_synth  4-HFC-P synthase
    0.00085   19.1   0.0      0.041   13.6   0.0    2.4  2  QRPTase_C    Quinolinate phosphoribosyl transferase, C-termin
  ------ inclusion threshold ------
      0.097   12.2   0.0        1.3    8.5   0.0    2.0  2  EAL          EAL domain


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 !  288.2   0.0   7.9e-90   4.7e-86       1     228 []       3     227 ..       3     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 288.2 bits;  conditional E-value: 7.9e-90
                                   EEE--SSHHHHHHHHHHT-SEEEE--GGG-TT----HHHHHHHHHHS-TTSEEEEEEEEE-S-HHHHHHHHHHHHHTT-SE CS
                   4HFCP_synth   1 LLvSvrnleEaelalaggadiiDvKnPaeGsLGalfpevireivevvpgsvpvSaaiGdlpekpgtvslaalgaaaagvdy 81 
                                   LLvS++n+eEa +al+ggadiiDvKnP+eGsLGa+ p+virei+++v+g+ p+Saa+Gd+ +kpgt++laa+gaaaag+dy
  gi|91773628|ref|YP_566320.1|   3 LLVSPINTEEAVAALNGGADIIDVKNPKEGSLGANYPWVIREIRDAVEGKRPISAALGDFSYKPGTAALAAYGAAAAGADY 83 
                                   8******************************************************************************** PP

                                   EEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGGHHHHHHHHT-SEEEEE-SS-SS--HHHHS CS
                   4HFCP_synth  82 vKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsplellelaaeagaagvmlDTadKdgkslldfl 162
                                   vK+Gl+++++ee+a+e+l+ +v++vk+   + +vva++y+D+er++s++p  l+++  +ag+ +vm+DT  Kdg+s+++f+
  gi|91773628|ref|YP_566320.1|  84 VKIGLYDITTEEQAYEMLTGIVESVKD--MDVTVVACGYSDHERINSINPKLLPAIGEKAGVGLVMVDTGLKDGRSTFEFM 162
                                   *************************99..5569************************************************ PP

                                   -HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGBTTSSTTSSB-HHHHHHHH CS
                   4HFCP_synth 163 seeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavCeegdRngkidaelveklk 228
                                   +ee+l efv++a++ gl+ta+AG++k++d+paLk+++p i+GvRg+vC +gdR+++i++elvekl+
  gi|91773628|ref|YP_566320.1| 163 TEEDLIEFVNDAHSRGLETAIAGTIKFDDIPALKRIQPTIVGVRGIVC-GGDRSTSIKQELVEKLR 227
                                   ************************************************.**************985 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.013        76      85     112 ..       5      32 ..       1      59 [. 0.78
   2 !   13.6   0.0   6.9e-06     0.041      26     148 ..      65     199 ..      62     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.013
                                   EEESSHHHHHHHHHHT-SEEEEES--HH CS
                     QRPTase_C  85 vevesleeleevleaeadiimLDnfsve 112
                                   v   + ee+ ++l+ +adii + n++  
  gi|91773628|ref|YP_566320.1|   5 VSPINTEEAVAALNGGADIIDVKNPKEG 32 
                                   5556899*************99999654 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.9e-06
                                   -TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTTSE...EEEEESSHHHHHHHHH.HT-S CS
                     QRPTase_C  26 tPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdkevk...ievevesleeleevle.aead 102
                                    Pg+++l+ y + ++G+d  ++gL+d+ +  +++ +++g ive vk ++  v          ++  + + l ++ e a++ 
  gi|91773628|ref|YP_566320.1|  65 KPGTAALAAYGAAAAGADYVKIGLYDITTEEQAYEMLTG-IVESVKDMDVTVVACGYsdhERINSINPKLLPAIGEkAGVG 144
                                   6*************************9998888877777.99999998877633321122344444444444443367799 PP

                                   EEEEES-...........-HHHHHHHHHHH.HHHSTTSEEEEESS--TTTHHHHHCTT CS
                     QRPTase_C 103 iimLDnf...........sveelkkaveel.keknkrvlievSGgvtlenveeyaksg 148
                                   ++m+D+            +    ++ +e + +++ + +++  +G ++ +++ ++++++
  gi|91773628|ref|YP_566320.1| 145 LVMVDTGlkdgrstfefmT---EEDLIEFVnDAHSRGLETAIAGTIKFDDIPALKRIQ 199
                                   9****99888887764433...44455555245555599999********99998876 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00022       1.3     170     212 ..      80     119 ..      55     129 .. 0.82
   2 ?    1.7   0.0     0.026   1.6e+02     133     174 ..     164     203 ..     150     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00022
                                   --SEEEE-HHHHTTTTTSCHHHHHHHHCHHHHCCCT-EEEE-S CS
                           EAL 170 ppdiiKldrslladleedeeaqalvkalialakelgikvvaeg 212
                                     d++K+     +d++++e+a ++++++++ +k+++++vva g
  gi|91773628|ref|YP_566320.1|  80 GADYVKIGL---YDITTEEQAYEMLTGIVESVKDMDVTVVACG 119
                                   567777775...566679***********************77 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.026
                                   HHHHH.HHHHHHHCTT-EEEEEEETSSTCCCHHHCCC--SEE CS
                           EAL 133 lealqeevlarLralGirialddfgtgysslsylarlppdii 174
                                   +e+l +e +++ +++G   a+++   +++++  l+r++p+i+
  gi|91773628|ref|YP_566320.1| 164 EEDL-IEFVNDAHSRGLETAIAGT-IKFDDIPALKRIQPTIV 203
                                   3444.59999************98.88***********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1421.01
//
Query:       gi|91773629|ref|YP_566321.1|  [L=736]
Description: AAA family ATPase, CDC48 subfamily protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-97  323.0   0.0    2.2e-48  164.0   0.0    2.4  2  AAA              ATPase family associated with various cellul
    1.1e-32  111.6   0.5    4.7e-16   58.3   0.1    2.7  2  AAA_lid_3        AAA+ lid domain
    2.4e-26   91.7   0.5    7.1e-25   87.0   0.7    2.9  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.5e-14   54.1   0.0      6e-07   29.3   0.0    3.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.6e-14   54.4   0.0    1.7e-06   28.3   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.2e-14   53.7   0.1    0.00023   21.6   0.0    4.3  3  AAA_16           AAA ATPase domain
    1.5e-13   50.3   0.3    3.9e-13   49.0   0.3    1.7  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    4.4e-11   42.6   0.0    8.3e-05   21.9   0.0    2.6  2  TIP49            TIP49 P-loop domain
    6.3e-11   42.7   0.2     0.0019   18.5   0.0    3.7  3  AAA_22           AAA domain
    5.8e-10   39.5   0.0    0.00072   19.7   0.0    2.5  2  AAA_33           AAA domain
    3.4e-09   36.8   0.0    0.00062   19.8   0.0    2.5  2  AAA_14           AAA domain
    3.7e-09   36.7   1.7     0.0015   18.5   0.2    4.2  2  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-08   34.9   0.0     0.0057   17.2   0.0    2.8  2  AAA_18           AAA domain
    9.6e-08   31.7   0.1       0.01   15.2   0.1    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.3e-07   30.7   0.0      0.016   15.0   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    3.8e-07   30.5   0.0      0.026   14.8   0.0    2.7  2  AAA_28           AAA domain
    3.8e-07   30.3   0.1       0.42   10.5   0.0    3.9  4  ATPase_2         ATPase domain predominantly from Archaea
    7.9e-07   29.0   0.0      0.014   15.1   0.0    2.6  2  AAA_24           AAA domain
    8.8e-07   29.3   0.0      0.068   13.6   0.0    2.6  2  RNA_helicase     RNA helicase
    1.3e-06   28.2   0.1       0.15   11.7   0.0    3.5  3  Sigma54_activat  Sigma-54 interaction domain
      2e-06   27.5   0.0      0.038   13.5   0.0    2.8  2  AAA_7            P-loop containing dynein motor region
    2.5e-06   27.2   3.9       0.31   10.6   0.5    4.1  3  AAA_25           AAA domain
    4.8e-06   25.9   0.0      0.064   12.4   0.0    2.8  3  DUF815           Protein of unknown function (DUF815)
    8.6e-06   25.8   0.2       0.99    9.3   0.0    4.1  4  NACHT            NACHT domain
    2.1e-05   24.5   0.0       0.39   10.7   0.1    2.8  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    2.2e-05   23.8   0.0       0.23   10.7   0.0    2.6  2  Zeta_toxin       Zeta toxin
    2.6e-05   24.1   0.0       0.15   11.9   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    2.9e-05   24.4   0.6       0.19   12.0   0.0    2.9  2  AAA_19           AAA domain
    4.6e-05   23.9   0.0       0.25   11.8   0.0    2.6  2  ABC_tran         ABC transporter
    7.7e-05   21.9   0.1       0.21   10.6   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0001   21.8   0.3       0.41   10.1   0.0    2.8  2  PhoH             PhoH-like protein
    0.00011   22.0   0.0       0.72    9.5   0.0    2.7  2  AAA_30           AAA domain
    0.00035   20.0   0.3        1.7    7.9   0.0    3.3  3  ATPase           KaiC
    0.00038   19.9   0.0       0.68    9.3   0.0    3.8  4  TniB             Bacterial TniB protein
    0.00046   19.9   0.0       0.61    9.7   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    0.00051   20.2   0.0       0.85    9.7   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00062   20.2   0.1        2.1    8.7   0.0    3.2  3  AAA_17           AAA domain
    0.00068   19.5   0.4        1.5    8.6   0.0    2.6  2  AAA_11           AAA domain
     0.0007   18.9   0.0       0.96    8.6   0.0    2.6  2  NB-ARC           NB-ARC domain
     0.0013   18.0   0.0        1.3    8.2   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.002   18.0   0.0        3.1    7.6   0.0    3.2  2  Bac_DnaA         Bacterial dnaA  protein
     0.0039   16.9   0.8        5.8    6.6   0.0    4.1  5  Guanylate_kin    Guanylate kinase
     0.0056   16.6   0.2        6.2    6.7   0.0    3.3  3  NTPase_1         NTPase
     0.0084   16.3   0.2        6.1    6.9   0.0    2.8  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0089   16.0   0.2       0.55   10.3   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
     0.0093   14.9   0.0        3.3    6.5   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
     0.0098   15.8   0.0        1.4    8.8   0.0    2.6  2  Rad17            Rad17 P-loop domain
  ------ inclusion threshold ------
      0.015   15.1   0.1        4.8    6.9   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
      0.031   14.4   0.4        5.9    7.0   0.0    2.8  2  SKI              Shikimate kinase
      0.042   13.1   0.3        1.5    8.0   0.1    3.0  3  KAP_NTPase       KAP family P-loop domain
      0.045   13.1   0.1         14    5.0   0.0    2.8  3  IPT              Isopentenyl transferase
      0.052   13.1   0.0       0.38   10.4   0.0    2.6  1  VASP_tetra       VASP tetramerisation domain
      0.098   11.7   0.0         11    5.1   0.0    3.1  4  MCM              MCM P-loop domain
       0.14   11.9   0.0        1.9    8.2   0.0    2.1  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.0   0.0   6.6e-51   2.2e-48       1     131 [.     213     342 ..     213     343 .. 0.98
   2 !  156.7   0.0   1.2e-48     4e-46       1     131 [.     485     615 ..     485     616 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 6.6e-51
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   vllyGppGtGKT++akava+e++++f+ isg+e++sky gese+k+re+f+ea+++  p+i+fiDE+d++a++r++   e+
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEANFIPISGPEIISKYYGESEQKLREIFEEAEKEG-PTIIFIDELDSIAPKRDDVVGEV 292
                                   79*****************************************************98.*********************** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   e+rvv+qLlt +dg++++ +kvivi+atnrp+++d+al+r gRfdr+iei+
  gi|91773629|ref|YP_566321.1| 293 ERRVVAQLLTLMDGLTSR-GKVIVIAATNRPNSIDQALRRgGRFDREIEIG 342
                                   *****************6.77***************************986 PP

  == domain 2  score: 156.7 bits;  conditional E-value: 1.2e-48
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsese 80 
                                   +ll+GppGtGKTllakava+e++++f++i+g+ellskyvgesek +re+f++ak+ a p+++f+DE+d+++++r  gs+++
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEANFISIKGPELLSKYVGESEKAVRETFRKAKQAA-PTVVFFDELDSMVPKRgMGSDQQ 564
                                   69******************************************************9.****************99999** PP

                                   HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +ervv+q+lte+dg ++ ++ +++++atnrpd +dpallr gRfdr i+++
  gi|91773629|ref|YP_566321.1| 565 ATERVVSQILTEIDGIEELKD-IVIVAATNRPDIIDPALLRpGRFDRLIYVR 615
                                   ******************755.**************************9985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   3.1e-16     1e-13       2      40 ..     366     404 ..     365     425 .. 0.77
   2 !   58.3   0.1   1.4e-18   4.7e-16       1      37 [.     638     674 ..     638     684 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 3.1e-16
                     AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                   ++l+++A  T+G++GADla+lc+eAa++Alrr ++ i+ 
  gi|91773629|ref|YP_566321.1| 366 LNLENIADITHGFVGADLASLCKEAAMHALRRMLPLISI 404
                                   69******************************6554332 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 1.4e-18
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                   dv l+eLAe+TeGy+GAD++a+creAa+++lr+ i  
  gi|91773629|ref|YP_566321.1| 638 DVKLEELAELTEGYVGADIEAICREAAMMTLREIIRP 674
                                   8********************************8875 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 !   87.0   0.7   2.1e-27   7.1e-25       2      82 ..       7      87 ..       6      89 .. 0.98
   2 ?    0.6   0.0         2   6.6e+02      19      38 ..     408     427 ..     407     446 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 2.1e-27
                                  EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                       CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                   rVaea+++d+grgi+r+  + m+ ++ ++gd++ei++k++T+a v+pa  +degk+iIr+dg++R na+v+i+d VtV++
  gi|91773629|ref|YP_566321.1|  7 VRVAEANHRDAGRGIARLPNALMQTIDARSGDIIEIRNKKNTYARVYPAGLDDEGKNIIRIDGNLRGNARVGIDDPVTVKR 87
                                  69*****************************************************************************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2
                                   E-HHHHHHHTS-TTSEEEEE CS
                       CDC48_N  19 idpedmeelglepgdvveie 38 
                                   i pe me l++ + d++e +
  gi|91773629|ref|YP_566321.1| 408 IPPEIMETLEVTETDFIEAH 427
                                   789**************986 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.8e-09     6e-07      35     104 ..     212     289 ..     206     335 .. 0.82
   2 !   21.1   0.0   6.4e-07   0.00021      35      69 ..     484     518 ..     474     555 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.8e-09
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevl 104
                                    vllyGpPG Gkt +ak +a+e ++++   sgP +      e ++ l  ++ + e++   ++fide+  ++++ ++v+
  gi|91773629|ref|YP_566321.1| 212 GVLLYGPPGTGKTMIAKAVASESEANFIPISGPEIiskyygESEQKLREIFEEAEKEgpTIIFIDELDSIAPKRDDVV 289
                                   59*******************************8744444445678999998887763469******99998887775 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 6.4e-07
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                    +ll+GpPG Gkt lak +a+e ++++ +  gP l
  gi|91773629|ref|YP_566321.1| 484 GILLFGPPGTGKTLLAKAVANESEANFISIKGPEL 518
                                   58**************************9999976 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.2e-09   1.7e-06       6     105 ..     213     306 ..     208     327 .. 0.88
   2 !   23.5   0.0   1.4e-07   4.8e-05       6     102 ..     485     576 ..     481     581 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.2e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   +ll gp g+Gkt++aka+a+  ++    ++i +   e++     + + ++++  ++   +ae++G  i+++DE+d i+pk 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEA----NFIPISGPEIIS----KYYGESEQKLREIFEEAEKEGptIIFIDELDSIAPKr 285
                                   6899****************9985....************....***********************************75 PP

                                   ---------HHHHHHHHHHHH- CS
                         AAA_2  84 essgadvSregVqrdLLqileg 105
                                   +    +v r  V+  LL +++g
  gi|91773629|ref|YP_566321.1| 286 DDVVGEVER-RVVAQLLTLMDG 306
                                   555555555.578889999998 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.4e-07
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp g+Gkt+laka+a+  ++    ++i +   ell     + + ++++  ++   +a++    +v++DE+d   pk 
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEA----NFISIKGPELLS----KYVGESEKAVRETFRKAKQAAptVVFFDELDSMVPKr 557
                                   7899****************9985....************....66666666667777777777799*************6 PP

                                   ---------HHHHHHHHHH CS
                         AAA_2  84 essgadvSregVqrdLLqi 102
                                   +  + +   e V+  +L  
  gi|91773629|ref|YP_566321.1| 558 GMGSDQQATERVVSQILTE 576
                                   4444445666676666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     7e-07   0.00023      24     139 ..     210     315 ..     200     316 .. 0.66
   2 !   19.3   0.0   3.6e-06    0.0012      20      63 ..     478     518 ..     472     529 .. 0.80
   3 ?    2.8   0.0       0.4   1.3e+02     123     145 ..     530     551 ..     525     578 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7e-07
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawreklee 103
                                   p  vll+G++G+GK+ ++++++ + e++   f+     +      y+    q l r e++++ + e        + ++l++
  gi|91773629|ref|YP_566321.1| 210 PKGVLLYGPPGTGKTMIAKAVASESEAN---FIPISGPEI--ISKYYGeSEQKL-R-EIFEEAEKE---GPTIIFIDELDS 280
                                   489*******************877777...655555555..224444366666.5.777776666...233344444444 PP

                        AAA_16 104 alaavpelagaeasrllellkrllallsrderplvl 139
                                    +   +++ g+ ++r+ ++l  l++ l+++++ +++
  gi|91773629|ref|YP_566321.1| 281 IAPKRDDVVGEVERRVVAQLLTLMDGLTSRGK-VIV 315
                                   44455666666669999999999966666577.433 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 3.6e-06
                        AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                   ++  p+ +ll G++G+GK+ l+++++++ e++   f++ k  +l
  gi|91773629|ref|YP_566321.1| 478 NTTPPRGILLFGPPGTGKTLLAKAVANESEAN---FISIKGPEL 518
                                   444569********************988877...777776655 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.4
                        AAA_16 123 lkrllallsrderplvlvlDdlq 145
                                   +++ ++++++ + p+v+++D+l+
  gi|91773629|ref|YP_566321.1| 530 VRETFRKAKQ-AAPTVVFFDELD 551
                                   6677889999.889********9 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 !   49.0   0.3   1.2e-15   3.9e-13      10      58 ..     113     161 ..     106     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.2e-15
                                   HHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEE CS
                       CDC48_2  10 lkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielg 58 
                                   +  +++grpv kG+++++e+ ++++ +vV+ t+P gpv++t+tT+ie+ 
  gi|91773629|ref|YP_566321.1| 113 VHLSLEGRPVDKGQRIRVENINNPLIFVVKATKPHGPVVVTRTTKIEIV 161
                                   66789******************************************85 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.4e-06    0.0018      51      97 ..     211     255 ..     207     268 .. 0.85
   2 !   21.9   0.0   2.5e-07   8.3e-05      51     106 ..     483     537 ..     475     541 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                   ++vLl Gp+gtGkt +a a++ e   +  f+ +sg e+ s     +e
  gi|91773629|ref|YP_566321.1| 211 KGVLLYGPPGTGKTMIAKAVASES--EANFIPISGPEIISKYYGESE 255
                                   89*******************985..689*********997666555 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.5e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                   r++Ll Gp+gtGkt la a+++e   +  f++++g e+ s  v  +e ++ +++rk+
  gi|91773629|ref|YP_566321.1| 483 RGILLFGPPGTGKTLLAKAVANES--EANFISIKGPELLSKYVGESEkAVRETFRKA 537
                                   89********************95..689**************99985688999998 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   5.9e-06     0.002       8      60 ..     213     265 ..     208     268 .. 0.83
   2 ?    3.9   0.0      0.18        61      72     118 ..     252     306 ..     245     321 .. 0.69
   3 !   18.5   0.0   5.6e-06    0.0019       8      43 ..     485     519 ..     480     578 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.9e-06
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrel 60 
                                   ++++G++GtGKT+ ++ ++++  e++++   +pe++ +++  s+ +++++++e 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASES-EANFIPISGPEIIsKYYGESEQKLREIFEEA 265
                                   689*****************97.4555555899999899999999999998875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.18
                        AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnl 118
                                   + s++ l+e +e+a ++  +  ++ iDE + +   +         +++ +L +l++ 
  gi|91773629|ref|YP_566321.1| 252 GESEQKLREIFEEAEKEGPT--IIFIDELDSIApkRddvvgeveRRVVAQLLTLMDG 306
                                   46778888888888888888..*********98752444555556666666666664 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 5.6e-06
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                   ++++G++GtGKT+l++ ++++ + ++++  ++pe++
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESE-ANFISIKGPELL 519
                                   89******************974.333333444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.2e-06   0.00072       2      82 ..     213     323 ..     213     346 .. 0.80
   2 !   17.2   0.0   1.3e-05    0.0043       2      46 ..     485     531 ..     485     620 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.2e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvl 52 
                                   vll G+pG+GK+  a+ ++ +    ++ +s ++++++++g+ +q+++                               +v+
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEanFIPISGPEIISKYYGESEQKLReifeeaekegptiifideldsiapkrddVVGEVE 293
                                   7899***************999988999************88887777888888888889999999888887654333466 PP

                        AAA_33  53 drlyqilnelarkalsagrnvildatnlsr 82 
                                    r+ ++l  l +   s+g+ +++ atn+ +
  gi|91773629|ref|YP_566321.1| 294 RRVVAQLLTLMDGLTSRGKVIVIAATNRPN 323
                                   677777778887777777778888888754 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.3e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                   +ll G+pG+GK+ la+ ++++    ++ +  ++l+++++g+ ++  +
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEanFISIKGPELLSKYVGESEKAVR 531
                                   6899***************9999888888899988888885444333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.9e-06   0.00062       5      76 ..     213     281 ..     210     330 .. 0.77
   2 !   14.3   0.0   9.1e-05      0.03       5      75 ..     485     552 ..     482     587 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-06
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT+++k +++e+     +++ i+  +   k + ++e+ l++i+e++++e+ t++f+DE   +
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESE---ANFIPISGPEIISKYYGESEQKLREIFEEAEKEGPTIIFIDELDSI 281
                                   7899***************9999...999999999988877777665556666655566*********9887 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.1e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqe 75 
                                   +++ G+  +GKT l+k +++e+     +++ i+  +   k   ++ek  ++ ++k+k+   t++f+DE   
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESE---ANFISIKGPELLSKYVGESEKAVRETFRKAKQAAPTVVFFDELDS 552
                                   6889***************8888...88888888777666666665555444444455699*******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 !   18.5   0.2   4.6e-06    0.0015       1     135 [.     212     330 ..     212     332 .. 0.63
   2 !   13.4   0.1   0.00018     0.059       2      23 ..     485     506 ..     484     604 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.6e-06
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--. CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae. 78 
                                   +vlL GppGtgK+++a+ +a+  ++++  + +++      ++ ++    g+ + +  ++ ++a+   + i+++DE++ +  
  gi|91773629|ref|YP_566321.1| 212 GVLLYGPPGTGKTMIAKAVASESEANFIPISGPE------IISKYY---GESEQKLREIFEEAEkeGPTIIFIDELDSIAp 283
                                   59******************99999999888887......444444...44444445555566555667888888887762 PP

                                   ..HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  79 ..sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                     ++v++++ +    + l l++g +  ++        + via++n+++    ++++alr
  gi|91773629|ref|YP_566321.1| 284 krDDVVGEVERRVVAQLLTLMDGLTSRGK--------VIVIAATNRPN----SIDQALR 330
                                   22344444433333333333333333322........77777777777....6777776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00018
                                   EEEE--SSSSHHHHHHHGGGGB CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                   +lL GppGtgK+ la+ +a   
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANES 506
                                   89**************998755 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.7e-05    0.0057       1      81 [.     213     318 ..     213     342 .. 0.69
   2 !   14.8   0.0   9.2e-05      0.03       1      25 [.     485     516 ..     485     591 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl..gf...................gvnlrdvakenglllevdpe.......aldeskrld 53 
                                   +ll G+pG+GKt +ak+++++   +f                    +++ + a ++g+ + + +e         d   +++
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESeaNFipisgpeiiskyygeseqkLREIFEEAEKEGPTIIFIDEldsiapkRDDVVGEVE 293
                                   799***************555434559999998888888888666555555555555555555556666655555566666 PP

                        AAA_18  54 edkldklldaleenssaleegknlvidg 81 
                                   + ++++ll+++++  s    gk++vi  
  gi|91773629|ref|YP_566321.1| 294 RRVVAQLLTLMDGLTS---RGKVIVIAA 318
                                   6666666666666644...677777765 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 9.2e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl..gf.....g 25 
                                   Ill G+pG+GKt lak+++++   +f      
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESeaNFisikgP 516
                                   99****************77742222544441 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     3e-05      0.01      25      43 ..     213     231 ..     210     235 .. 0.91
   2 !   13.5   0.0    0.0001     0.034      25      43 ..     485     503 ..     480     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKtm+ak+++
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVA 231
                                   79*************9875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0001
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKt+lak+++
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVA 503
                                   89*************9875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00019     0.061      48      70 ..     211     233 ..     200     241 .. 0.87
   2 !   15.0   0.0   4.7e-05     0.016      49      71 ..     484     506 ..     473     550 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                     IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                   ++++l Gp+G+GK+ +a a++ e
  gi|91773629|ref|YP_566321.1| 211 KGVLLYGPPGTGKTMIAKAVASE 233
                                   6899***************9976 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.7e-05
                     IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                   +i+l+Gp+G+GK+ la a++ e 
  gi|91773629|ref|YP_566321.1| 484 GILLFGPPGTGKTLLAKAVANES 506
                                   799***************99876 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   7.8e-05     0.026       2      49 ..     213     261 ..     212     277 .. 0.73
   2 !   12.9   0.0   0.00029     0.096       2      37 ..     485     525 ..     484     549 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.8e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                   + + G+++tGKT +++a a++ + + +p ++ ei+++ + + e++l++ 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASEsEANFIPISGPEIISKYYGESEQKLREI 261
                                   6799***************765666666666666666666555555554 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00029
                        AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareilee 37 
                                   i ++G+++tGKT l++a a++   ++  +  pE   +++ e
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANEseaNFISIkgPELLSKYVGE 525
                                   789****************7654444333477777666655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.025       8.3      20      45 ..     210     235 ..     200     241 .. 0.83
   2 !    8.3   0.0    0.0057       1.9     101     164 ..     253     318 ..     238     338 .. 0.76
   3 !   10.5   0.0    0.0013      0.42      14      68 ..     476     529 ..     471     590 .. 0.55
   4 ?    0.7   0.0       1.2     4e+02     103     131 ..     520     554 ..     508     628 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.025
                      ATPase_2  20 neiyfiYGpegsGKtaLlkeiienle 45 
                                    + +++YGp g GKt + k +++++e
  gi|91773629|ref|YP_566321.1| 210 PKGVLLYGPPGTGKTMIAKAVASESE 235
                                   556899***********999998875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0057
                      ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqkli....dlglngaellvkeLlnliesltkekhlcvvicl 164
                                   + ++++ +++e+ +k+g   ii+iDel  +     d+  + ++ +v++Ll+l++ lt++ +++v+  +
  gi|91773629|ref|YP_566321.1| 253 ESEQKLREIFEEAEKEGP-TIIFIDELDSIApkrdDVVGEVERRVVAQLLTLMDGLTSRGKVIVIA-A 318
                                   457888888888888876.799*****99972222444448899***********99999887764.3 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0013
                      ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68 
                                    l+++p + ++++Gp g GKt L k +++++e  ++  i   +l +++  + ++ 
  gi|91773629|ref|YP_566321.1| 476 ALNTTPPRGILLFGPPGTGKTLLAKAVANESEA-NFISIKGPELLSKYVGESEKA 529
                                   56778888899**********999999998843.544444333333333333333 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.2
                      ATPase_2 103 fkaielllekikkkgkk......iiiiiDelqkli 131
                                    k++ +  ++++++ +k       ++++Del  ++
  gi|91773629|ref|YP_566321.1| 520 SKYVGESEKAVRETFRKakqaapTVVFFDELDSMV 554
                                   45555555555554444444677899****98876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.2e-05     0.014       5      77 ..     213     281 ..     210     294 .. 0.73
   2 !   11.1   0.0   0.00072      0.24       5      29 ..     485     511 ..     482     567 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-05
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                   +l+yGp+g+GKT++ak    + ++ fi + +   ++  + +   es +++++ ++e ++e +   +++iD +d +
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVasESEANFIPISG--PEIISKYYG--ESEQKLREIFEEAEKEGP--TIIFIDELDSI 281
                                   89**************998877777777666..333333333..477888888888777777..56888887765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00072
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi 29 
                                   il++Gp+g+GKT lak    + ++ fi
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVanESEANFI 511
                                   89*************998664444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00028     0.095       1      27 [.     213     245 ..     213     320 .. 0.72
   2 !   13.6   0.0   0.00021     0.068       1      38 [.     485     525 ..     485     580 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00028
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......k 27 
                                   ++lyGp+g+GK+++ak +a++ + ++      +
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEANFipisgpE 245
                                   689**************9998887765554332 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00021
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsvysrn 38 
                                   i+l+Gp+g+GK++lak +a++ + ++   k ++  s y+++
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEANFisiKGPELLSKYVGE 525
                                   689**************888887666444333333333333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00046      0.15      23      48 ..     211     236 ..     203     251 .. 0.84
   2 ?   -0.4   0.0       2.4   8.1e+02      88     143 ..     261     321 ..     248     335 .. 0.56
   3 !   11.6   0.0    0.0005      0.17      23      56 ..     483     513 ..     469     599 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00046
                                   S-EEEECSTTSSHHHHHHHHHHHSTT CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                                     vl+ G  GtGK+++a+a+ ++s+ 
  gi|91773629|ref|YP_566321.1| 211 KGVLLYGPPGTGKTMIAKAVASESEA 236
                                   569****************9988774 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.4
                                   HHHHTTT...SEEEEETGGGS-HHHHHHHHHHHHHSEEESBT...SSSEEE--EEEEEEESS CS
               Sigma54_activat  88 lfekadg...GtlfLDeigelplelQekLlrvlqegevervG...sskeikvdvriiaatne 143
                                    fe+a++    ++f+De+ ++ ++    +   ++++ v ++    +  + + +v +iaatn+
  gi|91773629|ref|YP_566321.1| 261 IFEEAEKegpTIIFIDELDSIAPKRDD-VVGEVERRVVAQLLtlmDGLTSRGKVIVIAATNR 321
                                   566665422247788888887776543.3344455554444311123345556666666665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0005
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                     +l+ G  GtGK+lla+a+ ++s+   ++f+++
  gi|91773629|ref|YP_566321.1| 483 RGILLFGPPGTGKTLLAKAVANESE---ANFISI 513
                                   569*****************99887...556665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00011     0.038      33      63 ..     210     239 ..     200     281 .. 0.86
   2 !   10.7   0.0   0.00082      0.27      33      62 ..     482     510 ..     470     517 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekyl 63 
                                    k vll+Gp GtGKt+i+k + ++ +  +++
  gi|91773629|ref|YP_566321.1| 210 PKGVLLYGPPGTGKTMIAKAVASESE-ANFI 239
                                   5789***************9988877.5555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00082
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkldkeky 62 
                                    + +ll Gp GtGKt+++k + ++ +  ++
  gi|91773629|ref|YP_566321.1| 482 PRGILLFGPPGTGKTLLAKAVANESE-ANF 510
                                   5679***************9998877.555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0021      0.71      36      54 ..     213     231 ..     206     234 .. 0.87
   2 ?    4.3   0.0      0.08        27     128     175 ..     256     303 ..     249     320 .. 0.83
   3 !   10.6   0.5   0.00095      0.31      36     148 ..     485     588 ..     483     589 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   +ll+G+pgtGKt++a  +a
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVA 231
                                   69***********997665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.08
                        AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeri 175
                                   ++++++ +++e+ eg+  + iD l+++ +   +   +v +++v++l  +
  gi|91773629|ref|YP_566321.1| 256 QKLREIFEEAEK-EGPTIIFIDELDSIAPKRDDVVGEVeRRVVAQLLTL 303
                                   67889999****.**************9997777777768888887665 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00095
                        AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVly..vsaEdsedelrrRlravgealrddarllvldlagvesl 114
                                   +ll+G+pgtGKt la  +a +     ++       +g+ l+  +++E   + +r+ +r++ +a+  +  +++  l+++  +
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESE--ANFIS----IKGPELLskYVGESE-KAVRETFRKAKQAA--PTVVFFDELDSM--V 554
                                   68**********98765443322..23333....233333311223333.36788888888887..788888888887..6 PP

                        AAA_25 115 pLfakdrggtlltadvdaleaaieevegvrlvvi 148
                                   p + +++++++++++v ++  +i+ +e+++ +vi
  gi|91773629|ref|YP_566321.1| 555 PKRGMGSDQQATERVVSQILTEIDGIEELKDIVI 588
                                   6677888888899999999999999998877776 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00089       0.3      54     116 ..     211     278 ..     205     336 .. 0.65
   2 ?   -2.4   0.0       6.5   2.1e+03      62     109 ..     379     423 ..     374     426 .. 0.76
   3 !   12.4   0.0   0.00019     0.064      21      82 ..     441     511 ..     421     553 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00089
                        DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli..evek....edlkelpklvellrerperfilfvDDL 116
                                   + vLL+G  GtGK  + ka+ +e +++ + +   e+      e+ ++l +++e+ + ++   i+f+D L
  gi|91773629|ref|YP_566321.1| 211 KGVLLYGPPGTGKTMIAKAVASESEANFIPISgpEIISkyygESEQKLREIFEEAE-KEGPTIIFIDEL 278
                                   679*******************9999885442223332000133444444444433.334578888877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                        DUF815  62 rGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperf 109
                                    G+   sl+k +  ++ ++ L li +e+e     p+++e+l+ +++ f
  gi|91773629|ref|YP_566321.1| 379 VGADLASLCKEAAMHALRRMLPLISIEEE---IPPEIMETLEVTETDF 423
                                   566678999999999999*******9987...4567777776666666 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00019
                        DUF815  21 evdevklddLvgidkqkealvente.......qf..leglpannvLLwGarGtGKSslvkallneyaeegL 82 
                                   e+ +v+++d+ g++k k++l+e +e        f  l+ +p + +LL+G  GtGK  l ka+ ne +++ +
  gi|91773629|ref|YP_566321.1| 441 EIPHVRWEDIGGLNKVKQELIEAVEwplkypeMFtaLNTTPPRGILLFGPPGTGKTLLAKAVANESEANFI 511
                                   56678899999999999999988763332222232256677788********************9988764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.003      0.99       3      23 ..     213     233 ..     211     240 .. 0.89
   2 ?    2.4   0.0      0.41   1.3e+02      57     139 ..     246     329 ..     236     342 .. 0.73
   3 ?    7.4   0.0     0.012       3.8       3      23 ..     485     505 ..     483     512 .. 0.88
   4 ?    0.8   0.0       1.2   4.1e+02      57     115 ..     518     576 ..     515     597 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   v+l G++G GKT+ ++ +a++
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASE 233
                                   799*************99986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.41
                                   HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCCHHH CS
                         NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpralrd 134
                                   ++ + + e++++ +e + + +e +  + + +D lD ++ + +    + +++v   L +l+ + l ++ ++++++ +++ + 
  gi|91773629|ref|YP_566321.1| 246 IISKYYGESEQKLRE-IFEEAEKEGPTIIFIDELDSIAPKRDDvvgEVERRVVAQLLTLMDG-LTSRGKVIVIAATNRPNS 324
                                   677777888888888.445567778888999*******988889995555555555588888.777777777777766666 PP

                                   HCTTS CS
                         NACHT 135 leeql 139
                                   + + l
  gi|91773629|ref|YP_566321.1| 325 IDQAL 329
                                   66655 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.012
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   ++l G++G GKT L++ +a +
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANE 505
                                   7899************99876 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.2
                                   HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..........HHHHHCT CS
                         NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.kekqpvrtlLselirk 115
                                   ll +   e++++v+e +   ++++  ++  +D lD +v + g  +++q+++++ s+++++
  gi|91773629|ref|YP_566321.1| 518 LLSKYVGESEKAVRETFR-KAKQAAPTVVFFDELDSMVPKRGMgSDQQATERVVSQILTE 576
                                   666667777777877333.35677777788999999998877777777777777666654 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    0.0015      0.48      20      51 ..     211     244 ..     188     261 .. 0.77
   2 ?   -0.9   0.0       4.6   1.5e+03      80     106 ..     447     473 ..     444     483 .. 0.72
   3 !   10.7   0.1    0.0012      0.39      21      51 ..     480     516 ..     453     531 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                                   EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                   + +lL+G+ G+GKT++++++a++ + +  +++ P
  gi|91773629|ref|YP_566321.1| 211 KGVLLYGPPGTGKTMIAKAVASESEANfiPISGP 244
                                   459******************9998876667766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.6
                                   HHHCTTCCCCSTSCEEEEETGGGGCCC CS
                          TsaE  80 leelgleeyleeeavvlvEWpekleel 106
                                   +e++g  + +++e + +vEWp k+ e+
  gi|91773629|ref|YP_566321.1| 447 WEDIGGLNKVKQELIEAVEWPLKYPEM 473
                                   5666666667666799*****987655 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0012
                                   E....EEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  21 v....ilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                   +    ilL G+ G+GKT l++++a++ + +  ++k P
  gi|91773629|ref|YP_566321.1| 480 TpprgILLFGPPGTGKTLLAKAVANESEANfiSIKGP 516
                                   144449*******************998877777776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00071      0.23      15      50 ..     209     242 ..     200     250 .. 0.87
   2 !   10.2   0.0   0.00099      0.33      15      51 ..     481     515 ..     472     539 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00071
                    Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                    Pk +ll G pG GK+ +a++++ e   + n++ ++
  gi|91773629|ref|YP_566321.1| 209 PPKGVLLYGPPGTGKTMIAKAVASES--EANFIPIS 242
                                   6999********************98..78887765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00099
                    Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                    P  ill G pG GK+ la+++++e   + n++ +++
  gi|91773629|ref|YP_566321.1| 481 PPRGILLFGPPGTGKTLLAKAVANES--EANFISIKG 515
                                   58889********************8..899999876 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 !    9.7   0.0    0.0022      0.75       2      30 ..     213     241 ..     212     323 .. 0.86
   2 !   11.9   0.0   0.00045      0.15       2     110 ..     485     593 ..     484     604 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0022
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                   vll g PG++kt+++ka+a+  +++f  i
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEANFIPI 241
                                   7999****************999988655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00045
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsal 82 
                                   +ll g PG++ktll+ka+a+  +++f  i+  p+ll   +  +e   +  ++f+  k      +++ de++   pk     
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEANFISIK-GPELLSKYVGESEKAVR--ETFRKAKQ-AAPTVVFFDELDSMVPKRGMGS 561
                                   78999*********************9997.68888655433332222..23332222.2345677777777777654444 PP

                         AAA_3  83 leameerqv....tvegethklpepflvlatq 110
                                    +   er v    t  +   +l++  +v at+
  gi|91773629|ref|YP_566321.1| 562 DQQATERVVsqilTEIDGIEELKDIVIVAATN 593
                                   44444443310013334445566666666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0051       1.7      12      32 ..     212     232 ..     208     241 .. 0.82
   2 !   12.0   0.0   0.00058      0.19       5      75 ..     477     547 ..     474     597 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0051
                        AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                    +l+ ++pGtGKT + k++ +
  gi|91773629|ref|YP_566321.1| 212 GVLLYGPPGTGKTMIAKAVAS 232
                                   5899*********99887655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00058
                        AAA_19   5 vealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                   +++++ + +l+ ++pGtGKT + k++ ++ +++      + ll  + g + k +re  ++++++a T+  +
  gi|91773629|ref|YP_566321.1| 477 LNTTPPRGILLFGPPGTGKTLLAKAVANESEANFISIKGPELLSKYVGESEKAVRETFRKAKQAAPTVVFF 547
                                   556777889***********988887777666654444666777788888888888888888888887766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0046       1.5       8      46 ..     207     243 ..     204     322 .. 0.77
   2 !   11.8   0.0   0.00076      0.25      14      95 ..     485     580 ..     476     593 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0046
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldg 46 
                                   + + + v + G+ G+GK+ ++k++a +++     i + g
  gi|91773629|ref|YP_566321.1| 207 VDPPKGVLLYGPPGTGKTMIAKAVASESEA--NFIPISG 243
                                   666677899***************999864..4444454 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00076
                                   EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHHHH........... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                      ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvren........... 79 
                                   + ++G+ G+GK+ L+k++a++++  +  i ++g +l +    ++++ +r+ ++  +q     p++   ++           
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESE--ANFISIKGPELLSkyvgESEKAVRETFRKAKQA---APTVVFFDEldsmvpkrgmg 560
                                   6799****************986..678888988888844444444444444444444...44443333344455556765 PP

                                   ....HHHTCHHHHHHHSTTG CS
                                   ....xxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ....esdeeiekalsklglk 95 
                                       + ++ ++++l++++ +
  gi|91773629|ref|YP_566321.1| 561 sdqqATERVVSQILTEIDGI 580
                                   54433333366666665555 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00064      0.21     117     136 ..     213     232 ..     209     236 .. 0.90
   2 !    8.8   0.0    0.0023      0.77     116     137 ..     484     505 ..     473     508 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00064
                     Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                   v++yGp+ tGkt++a+a a 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVAS 232
                                   89***************986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                     Parvo_NS1 116 tvwfyGpantGktnlaeaIaka 137
                                    ++++Gp+ tGkt la+a a+ 
  gi|91773629|ref|YP_566321.1| 484 GILLFGPPGTGKTLLAKAVANE 505
                                   48899*************9985 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0035       1.2      22      41 ..     213     232 ..     207     238 .. 0.87
   2 !   10.1   0.0    0.0012      0.41      23      41 ..     486     504 ..     472     515 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0035
                                   EEEE--TTSSTTHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalav 41 
                                   v   Gp GtGKt++a a+a 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVAS 232
                                   6789***********99986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                                   EEE--TTSSTTHHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavalav 41 
                                     +Gp GtGKt+la a+a 
  gi|91773629|ref|YP_566321.1| 486 LLFGPPGTGKTLLAKAVAN 504
                                   679***********99985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0023      0.77      21      43 ..     213     235 ..     201     243 .. 0.84
   2 !    9.5   0.0    0.0022      0.72      11      44 ..     475     508 ..     471     550 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0023
                        AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                   ++l Gp+GtGKt++ ka++   e
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESE 235
                                   6789************9987555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0022
                        AAA_30  11 ealltsgdrvavltGpAGtGKttalkalreawea 44 
                                   +al t++ r  +l Gp+GtGKt + ka+++  ea
  gi|91773629|ref|YP_566321.1| 475 TALNTTPPRGILLFGPPGTGKTLLAKAVANESEA 508
                                   56666666778899************99876665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0064       2.1      19      38 ..     210     229 ..     200     243 .. 0.81
   2 ?    0.1   0.0       1.3   4.3e+02     110     153 ..     260     306 ..     238     324 .. 0.63
   3 !    7.9   0.0    0.0051       1.7      21      38 ..     484     501 ..     480     587 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0064
                        ATPase  19 grvvlitGepGtGKtifalq 38 
                                    + vl++G pGtGKt++a+ 
  gi|91773629|ref|YP_566321.1| 210 PKGVLLYGPPGTGKTMIAKA 229
                                   5679************9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                        ATPase 110 elaeaikeikakrvviDsitglayeeke...avaReilrqlvrvlkk 153
                                   e+ e  ++ + + + iD ++++a + ++   +v R+ + ql++ + +
  gi|91773629|ref|YP_566321.1| 260 EIFEEAEKEGPTIIFIDELDSIAPKRDDvvgEVERRVVAQLLTLMDG 306
                                   22233334445788888888883333331113457777777777765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0051
                        ATPase  21 vvlitGepGtGKtifalq 38 
                                    +l+ G pGtGKt++a+ 
  gi|91773629|ref|YP_566321.1| 484 GILLFGPPGTGKTLLAKA 501
                                   5899***********986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0021      0.68      26      59 ..     201     234 ..     192     242 .. 0.83
   2 ?    5.2   0.0     0.038        13      28      60 ..     475     507 ..     458     517 .. 0.81
   3 ?   -1.7   0.0       4.8   1.6e+03     107     142 ..     529     566 ..     513     577 .. 0.67
   4 ?   -1.9   0.0       5.7   1.9e+03      64     149 ..     617     702 ..     607     707 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                          TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                   L+++   + ++ +ll+G++ +GKtmi++  a++ 
  gi|91773629|ref|YP_566321.1| 201 LFDKLGVDPPKGVLLYGPPGTGKTMIAKAVASES 234
                                   666667777899***************9877665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.038
                          TniB  28 eypkrkrmpnlllvGdsnnGKtmivekFarlhp 60 
                                   ++ + + ++ +ll+G++ +GKt +++  a++ +
  gi|91773629|ref|YP_566321.1| 475 TALNTTPPRGILLFGPPGTGKTLLAKAVANESE 507
                                   5555666789**************998877665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.8
                          TniB 107 leqqvlrllrelkvrvLiiDEihnll..agsarkqref 142
                                   + +++ r  ++  + v+ +DE+++++  +g  ++q+++
  gi|91773629|ref|YP_566321.1| 529 AVRETFRKAKQAAPTVVFFDELDSMVpkRGMGSDQQAT 566
                                   34444555566778999999999996335666666655 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.7
                          TniB  64 dedaekvpvlvvqappkpdekrlyaaiLealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqrefln 144
                                     ++e+ ++l +++  kp  ++   + L++l + +   +  +  +++++ +lre+    +  DE+ + ++  + ++ +f  
  gi|91773629|ref|YP_566321.1| 617 PDKEERAKILDIHLSGKPIAEDVKLEELAELTEGYVGADIEAICREAAMMTLREIIRPGMTKDEVYETVKNVVIQRSHFST 697
                                   455667778888888888888888888888888887777778888888899999888888899999999999999999999 PP

                          TniB 145 alksL 149
                                   a+k+ 
  gi|91773629|ref|YP_566321.1| 698 AIKRV 702
                                   99975 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 !    9.7   0.0    0.0018      0.61      18      67 ..     214     269 ..     211     323 .. 0.75
   2 !    7.6   0.0    0.0079       2.6      17      49 ..     485     559 ..     480     598 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                                   EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHHSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpegt 67 
                                   l+ g  g+Gkt+i+++++ +s+++        ii    Ge +++++e++ee ++++
  gi|91773629|ref|YP_566321.1| 214 LLYGPPGTGKTMIAKAVASESEANfipisGpEIISKYYGESEQKLREIFEEAEKEG 269
                                   678999**************98889999835999999**************99954 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0079
                                   EEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE...........................................E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........................................x RF
                   ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsddaiiyvg...........................................i 49 
                                   +l++g  g+Gkt ++++++++s+++  i + g                                           +
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEAN-FISIKGpellskyvgesekavretfrkakqaaptvvffdeldsmvpkrgM 559
                                   5799*****************9777.33233356666663344444444444444444444444444444444443 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    0.0026      0.85      24      52 ..     213     241 ..     207     286 .. 0.65
   2 ?    7.8   0.0      0.01       3.5      24      48 ..     485     509 ..     476     560 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0026
                                   EEEEEETT--HHHHHHCC--TTS-EE--S CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleif 52 
                                   v+l G++G+gk+++A++ +++s+ +  + 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEANFIPI 241
                                   9******************9999876554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.01
                                   EEEEEETT--HHHHHHCC--TTS-E CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                   ++l G++G+gk+l A++ +++s+ +
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEAN 509
                                   799****************998864 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       8.7   2.9e+03      62      84 ..      85     107 ..      39     129 .. 0.65
   2 ?    7.6   0.0     0.014       4.7       1      25 [.     216     242 ..     216     289 .. 0.70
   3 !    8.7   0.0    0.0064       2.1       1      50 [.     488     538 ..     488     595 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 8.7
                                   HHHHHHHHHSSEEEEEE-SEEEE CS
                        AAA_17  62 aekiaeeakkkgvlvdghprike 84 
                                    ++i e++++k  l  +hp+++e
  gi|91773629|ref|YP_566321.1|  85 VKRILEKDAEKITLAPTHPVLNE 107
                                   34556666666666666665533 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.014
                                   EE-TTSSHHHHHHHHHHHH..TEEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklveky..gfthls 25 
                                   +G+PG GK+ +++ ++ +   +f  +s
  gi|91773629|ref|YP_566321.1| 216 YGPPGTGKTMIAKAVASESeaNFIPIS 242
                                   7***********999976522555555 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0064
                                   EE-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHHHHHTTTSHSSHHHHCTSH CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsa..Gdllreeakrgglakardemrklp 50 
                                   +G+PG GK+ +++ ++ + +  ++s    +ll + + +++ +  r+ +rk++
  gi|91773629|ref|YP_566321.1| 488 FGPPGTGKTLLAKAVANESEANFISIkgPELLSKYVGESE-KAVRETFRKAK 538
                                   6***********9999887555555440455544444433.34566666654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0048       1.6      20      40 ..     213     233 ..     196     270 .. 0.81
   2 !    8.6   0.0    0.0044       1.5      20      71 ..     485     534 ..     472     568 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0048
                        AAA_11  20 tliqGPPGtgKTktivellsq 40 
                                   +l+ GPPGtgKT    ++ s+
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASE 233
                                   6999********776666555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0044
                        AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriL..vCapSNaAvDell 71 
                                    l+ GPPGtgKT    ++ ++       +    ++p++L  + ++S++Av e+ 
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESE----ANFISIKGPELLskYVGESEKAVRETF 534
                                   4889********98888888883....222333333333224555555555554 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    0.0029      0.96      22      44 ..     212     234 ..     199     238 .. 0.81
   2 !    7.3   0.0     0.007       2.3      23      44 ..     485     506 ..     476     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                                   EEEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  22 vvalvGmgGvGKttlakqilnks 44 
                                    v l+G +G GKt +ak + ++s
  gi|91773629|ref|YP_566321.1| 212 GVLLYGPPGTGKTMIAKAVASES 234
                                   4789***************9984 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.007
                                   EEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                   + l G +G GKt lak + n+s
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANES 506
                                   6689**************9994 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0066       2.2       4      25 ..     213     234 ..     210     279 .. 0.80
   2 !    8.2   0.0    0.0039       1.3       6      44 ..     487     518 ..     483     570 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0066
                       DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                   vl  G +GtGKt+++ +++ e 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASES 234
                                   6789***********9999887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                       DUF2075   6 VtGvaGtGKtvvllnllaeleddeeertavylsvNhplv 44 
                                     G +GtGKt+++ ++++e        +a+++s  +p++
  gi|91773629|ref|YP_566321.1| 487 LFGPPGTGKTLLAKAVANES-------EANFISIKGPEL 518
                                   5699***********99998.......444444444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.023       7.6      37     146 ..     213     327 ..     208     360 .. 0.60
   2 !    7.6   0.0    0.0093       3.1      37      66 ..     485     514 ..     478     663 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT.-SEEEEE-GGGGTT-H... CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrk.vDvLliDDiqflagke... 113
                                   +++yg+ G Gkt + ka++ e ++n+     + +++ e +++     ++k  e f e  ++   ++ iD++  +a k    
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEANF-----IPISGPEIISKYYGESEQKLREIFEEAEKEgPTIIFIDELDSIAPKRddv 288
                                   799*********99999988766654.....34455555555544444444444444444313344555555555543111 PP

                                   ......HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS CS
                      Bac_DnaA 114 ......ktqeelfhtfnalleegkqvvlssDrsPkelee 146
                                         ++  +l+++++ l+  gk +v+++   P+++++
  gi|91773629|ref|YP_566321.1| 289 vgeverRVVAQLLTLMDGLTSRGKVIVIAATNRPNSIDQ 327
                                   111111345567777777777788888888777777655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0093
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                   ++++g+ G Gkt L ka++ne ++n+ + +
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEANFISIK 514
                                   799****************99888776544 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.017       5.8       4      31 ..     212     239 ..     210     246 .. 0.85
   2 ?    1.1   0.0      0.84   2.8e+02      76      94 ..     248     266 ..     242     279 .. 0.84
   3 ?    3.8   0.0      0.12        41       3      30 ..     483     510 ..     481     517 .. 0.87
   4 ?   -1.9   0.0       6.9   2.3e+03      76      96 ..     520     540 ..     513     551 .. 0.83
   5 ?   -1.7   0.0       6.1     2e+03     111     164 ..     538     589 ..     533     594 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                                   EEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg 31 
                                    v l gp g+Gk ++ ka+ se + +f 
  gi|91773629|ref|YP_566321.1| 212 GVLLYGPPGTGKTMIAKAVASESEANFI 239
                                   6899***************999998884 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.84
                                   TEEEEEEHHHHHHHHHTTS CS
                 Guanylate_kin  76 gnlygtsveaieevlekgk 94 
                                   +++yg+s ++ +e++e++ 
  gi|91773629|ref|YP_566321.1| 248 SKYYGESEQKLREIFEEAE 266
                                   689************9876 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.12
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                   r + l gp g+Gk  l ka+ +e + +f
  gi|91773629|ref|YP_566321.1| 483 RGILLFGPPGTGKTLLAKAVANESEANF 510
                                   6799****************99988887 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 6.9
                                   TEEEEEEHHHHHHHHHTTSEE CS
                 Guanylate_kin  76 gnlygtsveaieevlekgkiv 96 
                                   +++ g+s +a++e + k+k++
  gi|91773629|ref|YP_566321.1| 520 SKYVGESEKAVRETFRKAKQA 540
                                   578899999999999999985 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 6.1
                                   TTTTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHHHH.HHHHHHHGGG.C.SSEEEE CS
                 Guanylate_kin 111 aelspiivFikppslkelqrrlksrgkeqeeklakrl.aaaekelqey.e.fdvviv 164
                                   ++ +p +vF      +el+ ++ +rg  + ++  +r+ +++  e+    e  d+viv
  gi|91773629|ref|YP_566321.1| 538 KQAAPTVVFF-----DELDSMVPKRGMGSDQQATERVvSQILTEIDGIeElKDIVIV 589
                                   5777888888.....777777878888888777777525667777766446666665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.035        11       2      31 ..     213     242 ..     212     246 .. 0.81
   2 ?   -2.0   0.0       8.9   2.9e+03      82     104 ..     255     278 ..     245     304 .. 0.74
   3 ?    6.7   0.0     0.019       6.2       2      32 ..     485     515 ..     484     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.035
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                   v++ GppG+GKt + k v+++ + + ++++
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEANFIPIS 242
                                   6788***********999988766656655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.9
                                   HHHHHHHHHHHH.HHH-EEEE--- CS
                      NTPase_1  82 eelalealrkal.seadviviDEi 104
                                   e+   e++++a  +++ +i iDE 
  gi|91773629|ref|YP_566321.1| 255 EQKLREIFEEAEkEGPTIIFIDEL 278
                                   556666666666456669999996 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.019
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                   +++ GppG+GKt l k v+++ + + ++++G
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVANESEANFISIKG 515
                                   6788**************9998777777776 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.018       6.1       8      55 ..     219     267 ..     215     315 .. 0.75
   2 ?    6.3   0.0     0.029       9.7       8      60 ..     491     544 ..     485     591 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersr 55 
                                    G+g++ i++a+A + + +f+    +e ++k  g se+++ e ++e+++
  gi|91773629|ref|YP_566321.1| 219 PGTGKTMIAKAVASESEANFIPISGPEIISKYYGESEQKLrEIFEEAEK 267
                                   59************************************99666666333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.029
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersrlssfl 60 
                                    G+g++ +++a+A++ + +f++ + +e ++k  g se+ v e++ +++ ++ ++
  gi|91773629|ref|YP_566321.1| 491 PGTGKTLLAKAVANESEANFISIKGPELLSKYVGESEKAVrETFRKAKQAAPTV 544
                                   69***********************************99976666633322222 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 ?    2.6   0.0       0.4   1.3e+02      18      44 ..     407     433 ..     402     437 .. 0.80
   2 !   10.3   0.0    0.0017      0.55      22      55 ..     683     716 ..     661     721 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.4
                        Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                   +ip++ +   +vt +Df++a ++  p+
  gi|91773629|ref|YP_566321.1| 407 EIPPEIMETLEVTETDFIEAHRNIEPS 433
                                   5775555555************99998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0017
                        Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekhee 55 
                                   + +++  +++++f  a+k++r + s +++++++e
  gi|91773629|ref|YP_566321.1| 683 ETVKNVVIQRSHFSTAIKRVRASTSLDEMKRYDE 716
                                   556667899**********************987 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.01       3.3      58      78 ..     206     226 ..     176     234 .. 0.87
   2 ?    5.5   0.0     0.021       6.9      58      79 ..     478     499 ..     453     506 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                   AFG1_ATPase  58 svepvrglYlwGgvGrGKtyl 78 
                                    v p++g+ l+G+ G GKt++
  gi|91773629|ref|YP_566321.1| 206 GVDPPKGVLLYGPPGTGKTMI 226
                                   468*****************8 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                   AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                   +++p+rg+ l G+ G GKt l 
  gi|91773629|ref|YP_566321.1| 478 NTTPPRGILLFGPPGTGKTLLA 499
                                   578****************985 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.12        39      48      74 ..     213     239 ..     203     278 .. 0.81
   2 !    8.8   0.0    0.0043       1.4      39     115 ..     476     553 ..     456     576 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                         Rad17  48 LLisGPsGCgkstvvkvLskelgiklr 74 
                                   +L+ GP+G gk+ + k ++ e   +++
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEANFI 239
                                   6899**********9999988776665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0043
                         Rad17  39 vLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslke.pdnqksdfkgltekesrflsqiesfkeleLk 115
                                    L+  + r +L+ GP+G gk+   k ++ e   +++    p +l +     ++ ++  + k ++  + +  f el  +
  gi|91773629|ref|YP_566321.1| 476 ALNTTPPRGILLFGPPGTGKTLLAKAVANESEANFISIKGPELLSKyVGESEKAVRETFRKAKQAAPTVVFFDELDSM 553
                                   5677777878899*******************9999999998875514447778888888888889999999998655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.014       4.8       4      27 ..     216     239 ..     213     243 .. 0.89
   2 ?    5.6   0.0     0.034        11       3      28 ..     487     512 ..     485     514 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
                                   E-STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                    GP g+GK  +a+a+a++ +++++
  gi|91773629|ref|YP_566321.1| 216 YGPPGTGKTMIAKAVASESEANFI 239
                                   6****************9999886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.034
                                   EE-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                   + GP g+GK  +a+a+a++ ++++++
  gi|91773629|ref|YP_566321.1| 487 LFGPPGTGKTLLAKAVANESEANFIS 512
                                   56*****************9999875 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     0.018       5.9       1      43 [.     219     266 ..     219     269 .. 0.74
   2 ?    4.7   0.0     0.089        30       1      23 [.     491     513 ..     491     541 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.018
                                   TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT...S-HHHHHHHHH CS
                           SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg...ksiaeifeeeg 43 
                                   +G+GK+ ++k++A + + +fi +   e+i+k  g   ++ +eifee  
  gi|91773629|ref|YP_566321.1| 219 PGTGKTMIAKAVASESEANFIPIsgPEIISKYYGeseQKLREIFEEAE 266
                                   69******************9763356777776644456777777655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.089
                                   TTSSHHHHHHHHHHHHTSEEEEH CS
                           SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                   +G+GK+ ++k++A++ + +fi +
  gi|91773629|ref|YP_566321.1| 491 PGTGKTLLAKAVANESEANFISI 513
                                   69***************999865 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 ?   -0.0   0.0       1.2   4.1e+02      19      43 ..     209     233 ..     196     241 .. 0.80
   2 ?    8.0   0.1    0.0046       1.5     159     201 ..     256     297 ..     244     339 .. 0.63
   3 ?   -0.8   0.0       2.1     7e+02     170     189 ..     536     557 ..     519     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.2
                    KAP_NTPase  19 tpivvgLygkWGsGKssllnklede 43 
                                   +p  v Lyg+ G+GK+ + + + +e
  gi|91773629|ref|YP_566321.1| 209 PPKGVLLYGPPGTGKTMIAKAVASE 233
                                   566689**********998877766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0046
                    KAP_NTPase 159 elladmektLdalqkrlVvviDdLDrceteevlqlleavkllf 201
                                   ++l +++++ ++ + + +++iD+LD++ +++   + e+ + ++
  gi|91773629|ref|YP_566321.1| 256 QKLREIFEEAEK-EGPTIIFIDELDSIAPKRDDVVGEVERRVV 297
                                   345555555555.8999**********9999766666554443 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.1
                    KAP_NTPase 170 a..lqkrlVvviDdLDrcetee 189
                                   +  +  + Vv+ D+LD+  +++
  gi|91773629|ref|YP_566321.1| 536 KakQAAPTVVFFDELDSMVPKR 557
                                   44567889********987765 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.2   2.4e+03      59      94 ..     115     151 ..     104     162 .. 0.82
   2 ?    4.6   0.0     0.053        18       5      28 ..     214     237 ..     211     242 .. 0.86
   3 ?    5.0   0.0     0.041        14       5      31 ..     486     512 ..     483     527 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.2
                           IPT  59 iylddrslseGv.idaeeanerLikevesykdeegli 94 
                                   + l+ r++++G  i  e+ n+ Li +v++ k ++ ++
  gi|91773629|ref|YP_566321.1| 115 LSLEGRPVDKGQrIRVENINNPLIFVVKATKPHGPVV 151
                                   4577899999955999***********9999987776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.053
                           IPT   5 lifGatttGKtaeaiklaketgap 28 
                                   l++G+ +tGKt  a ++a e  a 
  gi|91773629|ref|YP_566321.1| 214 LLYGPPGTGKTMIAKAVASESEAN 237
                                   89****************987765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.041
                           IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                   l+fG+ +tGKt  a ++a+e  a  i+
  gi|91773629|ref|YP_566321.1| 486 LLFGPPGTGKTLLAKAVANESEANFIS 512
                                   89*****************99988877 PP

>> VASP_tetra  VASP tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0011      0.38      19      30 ..     453     464 ..     452     469 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                    VASP_tetra  19 LqKvKeEIIeAi 30 
                                   L+KvK+E+IeA+
  gi|91773629|ref|YP_566321.1| 453 LNKVKQELIEAV 464
                                   89*********8 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.21        71      60      83 ..     213     236 ..     209     245 .. 0.85
   2 ?   -2.4   0.0         6     2e+03     124     144 ..     272     292 ..     269     320 .. 0.78
   3 ?    5.1   0.0     0.032        11      60      91 ..     485     515 ..     477     553 .. 0.87
   4 ?   -2.0   0.0       4.7   1.6e+03      10      38 ..     561     589 ..     557     593 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.21
                                   EEEEESSTSTHHHHHHHHHHHSSS CS
                           MCM  60 vllvgdpgtaKsqlLkyveklapr 83 
                                   vll g pgt+K+ + k+v++ ++ 
  gi|91773629|ref|YP_566321.1| 213 VLLYGPPGTGKTMIAKAVASESEA 236
                                   89***************9976654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                                   EEEEESGGGSTCHHHHHHHHH CS
                           MCM 124 vcciDefdkmkeedrsalhEa 144
                                   ++ iDe+d +  +  +++ E+
  gi|91773629|ref|YP_566321.1| 272 IIFIDELDSIAPKRDDVVGEV 292
                                   789999999998666655554 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.032
                                   EEEEESSTSTHHHHHHHHHHHSSSEEEEESSS CS
                           MCM  60 vllvgdpgtaKsqlLkyveklapravytsgkg 91 
                                   +ll g pgt+K+ l k+v+ + ++a+++s+kg
  gi|91773629|ref|YP_566321.1| 485 ILLFGPPGTGKTLLAKAVA-NESEANFISIKG 515
                                   8***********9999998.566778888876 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.7
                                   TSSTHHHHHHHHSSTTSSS-HHHHHHHHH CS
                           MCM  10 kekdiieklvksiapsiyghedvkkaill 38 
                                   ++++ +e++v++i  +i g e+ k  +++
  gi|91773629|ref|YP_566321.1| 561 SDQQATERVVSQILTEIDGIEELKDIVIV 589
                                   6788999**************99987766 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.73   2.4e+02       5      70 ..     217     277 ..     213     280 .. 0.66
   2 ?    8.2   0.0    0.0057       1.9       3      70 ..     487     549 ..     485     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.73
               Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                   G pG GK+ + + ++++s  ++ +++   e++++   +++++  + ++++++         i+++DE
  gi|91773629|ref|YP_566321.1| 217 GPPGTGKTMIAKAVASESeANFIPISG-PEIISKYYGESEQKLREIFEEAEKEGP-----TIIFIDE 277
                                   78*******999999987766666666.666666665555555555555555432.....3666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0057
               Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                     G pG GK+ l + ++++s  ++ +++   ell++ + ++++   +t++++ +a+       ++++DE
  gi|91773629|ref|YP_566321.1| 487 LFGPPGTGKTLLAKAVANESeANFISIKG-PELLSKYVGESEKAVRETFRKAKQAAPT-----VVFFDE 549
                                   5688*****************88888988.9*******99999999999998888753.....899999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.93u 0.31s 00:00:01.24 Elapsed: 00:00:00.51
# Mc/sec: 4332.20
//
Query:       gi|91773630|ref|YP_566322.1|  [L=230]
Description: hypothetical protein Mbur_1678 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-94  313.2   0.2    7.1e-94  313.0   0.2    1.0  1  PIN_5     PINc domain ribonuclease
  ------ inclusion threshold ------
       0.09   13.0   0.0       0.21   11.8   0.0    1.6  1  DUF2795   Protein of unknown function (DUF2795)
       0.14   12.4   0.0       0.31   11.4   0.0    1.5  1  Cul7      Mouse development and cellular proliferation protei


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 !  313.0   0.2   1.2e-97   7.1e-94       1     206 []       4     220 ..       4     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 313.0 bits;  conditional E-value: 1.2e-97
                         PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyip.psvykElkeflkreeveeeviakldtwlvkks 80 
                                   rfvlDT+altd ++re l+ e+l+++++++ldliae+rl+l+iscy+p psvykEl+ef+k++++++e+ia++dtwlvkk+
  gi|91773630|ref|YP_566322.1|   4 RFVLDTTALTDLQTREMLEIEDLCQGMRAILDLIAESRLHLQISCYVPfPSVYKELHEFAKNNGCDDEIIAMIDTWLVKKT 84 
                                   8******************************************************************************** PP

                         PIN_5  81 pdryevkipaeilyeyveevrerinkGlrvaEeavreaaeeseklekee..........eeeevgelikklRekYrealRk 151
                                   pdr+evkip++i++eyv+++rerinkG+ vaEea+rea+ ++ ++e+e           ++e++g ++ k+R+kYr+alR+
  gi|91773630|ref|YP_566322.1|  85 PDRHEVKIPSHIFHEYVSYMRERINKGMTVAEEAIREASIQCLSIESEIedtrkvedntDREVIGPIVGKFRNKYRSALRY 165
                                   ******************************************999422235677788889********************* PP

                         PIN_5 152 GilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeylk 206
                                   GilDsa+D+dvllLAkELdaavv+sD Gi+kwae+lG+r+v+a++fp++lkeyl+
  gi|91773630|ref|YP_566322.1| 166 GILDSAPDIDVLLLAKELDAAVVASDYGIQKWAEQLGVRFVPANTFPMMLKEYLR 220
                                   *****************************************************95 PP

>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.6e-05      0.21       4      30 ..      50      76 ..      50      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                       DUF2795  4 adyPatKdeLveyArrngApdevleaL 30
                                  +++P   +eL e+A++ng +de++  +
  gi|91773630|ref|YP_566322.1| 50 VPFPSVYKELHEFAKNNGCDDEIIAMI 76
                                  68999999***************9876 PP

>> Cul7  Mouse development and cellular proliferation protein Cullin-7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.2e-05      0.31       8      24 ..      98     114 ..      95     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
                          Cul7   8 deYaeYvrenlkpGMrV 24 
                                    eY++Y+re++++GM+V
  gi|91773630|ref|YP_566322.1|  98 HEYVSYMRERINKGMTV 114
                                   58**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1614.70
//
Query:       gi|91773631|ref|YP_566323.1|  [L=281]
Description: prenyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-43  148.4  18.3    3.2e-43  147.9  18.3    1.2  1  UbiA           UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9  18.3   1.8e-47   3.2e-43      11     247 ..      34     270 ..      13     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 1.8e-47
                          UbiA  11 laaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpl 91 
                                   ++ + s++l+   l++++++l+++a+n+lNdyfD+eiD+   ++p RP++sG+is k al f+++l+i g+ l+ +l+npl
  gi|91773631|ref|YP_566323.1|  34 ASPYVSLSLFDTSLIFAIVFLVTGAGNGLNDYFDIEIDKV--NKPSRPIPSGKISLKSALYFSLFLFITGITLA-FLVNPL 111
                                   33444455588888999999********************..********************************.****** PP

                          UbiA  92 tallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDr 172
                                   + +++l++ +++++Y +  lKr++++g+  +g   g  +l+g a+++     ++++l+l+  l t+a  +++d++d+ gD+
  gi|91773631|ref|YP_566323.1| 112 CGIIALFNSMVLILYAQ-SLKRTPFFGNASVGYLTGSTFLFGGAVFGMAGLQALVVLFLLATLATIAREIVKDVEDIVGDK 191
                                   ****************6.***************************99998888899999999******************* PP

                          UbiA 173 kagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraarlvrrrdakkaakff...l 247
                                   k g +tlp+++G+k+a +++a++ + ++la ++ +l   l+  yl++++++ +++l+  ++++ ++da++ +k+f   +
  gi|91773631|ref|YP_566323.1| 192 KDGARTLPILIGAKKASYIAAAFGFTAMLAsPVPYLQSILNEQYLFVVAIADIFFLIAVYQILGKKDAARSSKLFkfaM 270
                                   ******************855555555555799****************************************995433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1921.77
//
Query:       gi|91773632|ref|YP_566324.1|  [L=306]
Description: quinolinate synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-118  395.7   7.3   1.3e-118  395.5   7.3    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 !  395.5   7.3  7.5e-123  1.3e-118       2     299 .]      10     301 ..       9     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 395.5 bits;  conditional E-value: 7.5e-123
                                   HHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT---HHH CS
                          NadA   2 eikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleagCsla 82 
                                   +i++lkke+navilaH Y +de+q+iadfvGDSl L+++a +++aevivfcGV+FMae+a iLspek+vl+pd++a+C++a
  gi|91773632|ref|YP_566324.1|  10 KINSLKKERNAVILAHCYARDEVQDIADFVGDSLGLSQEAVDQDAEVIVFCGVSFMAESAFILSPEKTVLMPDADADCPMA 90 
                                   89******************************************************************************* PP

                                   CT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH.SEEEEESSS CS
                          NadA  83 dmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklgekkiilwkg 163
                                    m++  ++++lk+++pda+vv+YvN+ a++Ka++di+cTS+nav+vv++l+++k++f+PD+nL++yvak++ +k+ii w+g
  gi|91773632|ref|YP_566324.1|  91 AMVDVISLRKLKAQHPDAMVVCYVNTRADIKAECDICCTSANAVEVVNSLDSDKVIFVPDKNLAAYVAKHT-DKTIIPWNG 170
                                   **********************************************************************9.668****** PP

                                   S-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TTSEE CS
                          NadA 164 aCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglverlkkeapekef 244
                                   +C++H+++ ae+v+ + ++hp+a++++HPEc++ev+e+ad+v ST++++++vk+s+++efi+ Te+g++++l++e+p+k+f
  gi|91773632|ref|YP_566324.1| 171 YCPTHNQILAEDVDLAMNKHPGAELMAHPECRSEVLEKADHVFSTTGMLDHVKSSDNNEFIVSTEQGILHQLETENPNKKF 251
                                   ********************************************************************************* PP

                                   E.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHHH CS
                          NadA 245 ialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalermle 299
                                   + +s+     + C++Mk+i+l+++l++Le++e+  ++v+++++ +Ak+al+rmle
  gi|91773632|ref|YP_566324.1| 252 YPVSK----FTFCPDMKMIDLSSVLRCLENMET-VVTVPKDIQVRAKRALDRMLE 301
                                   *5543....478*******************99.9******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2073.30
//
Query:       gi|91773633|ref|YP_566325.1|  [L=271]
Description: L-aspartate dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-36  125.1   0.7    1.9e-36  124.3   0.7    1.4  1  DUF108           Domain of unknown function DUF108
    1.6e-24   86.8   0.1    2.9e-24   86.0   0.1    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    3.5e-06   27.1   0.3    6.2e-06   26.3   0.3    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    7.3e-06   26.4   0.3    1.6e-05   25.3   0.1    1.6  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    2.6e-05   24.7   0.1    6.3e-05   23.5   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00079   20.3   0.1     0.0028   18.5   0.1    1.8  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0047   16.3   0.1     0.0096   15.3   0.1    1.7  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.046   13.7   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.026   14.7   0.1      0.043   14.0   0.1    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.082   12.8   0.1       0.15   12.0   0.1    1.5  1  Rossmann-like    Rossmann-like domain
       0.14   12.4   2.1       0.29   11.4   2.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


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 !  124.3   0.7   1.2e-39   1.9e-36       2      89 .]     170     257 ..     169     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 1.2e-39
                                   SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEEEEEH CS
                        DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenPktsa 82 
                                   + +tvlFeG a+ea+k+fP nvNvaa+l++a++gfd++kv+++a+p+l++nihei+veG+fg f+++ven+p p+nPkts+
  gi|91773633|ref|YP_566325.1| 170 KGKTVLFEGMASEAVKAFPSNVNVAASLSIAGIGFDKTKVKIIANPALTRNIHEITVEGEFGMFTTRVENVPAPSNPKTSY 250
                                   689****************************************************************************** PP

                                   HHHHHHH CS
                        DUF108  83 laalsvi 89 
                                   laals+i
  gi|91773633|ref|YP_566325.1| 251 LAALSAI 257
                                   *****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 !   86.0   0.1   1.8e-27   2.9e-24       1     117 []       8     121 ..       8     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.8e-27
                                   --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHH CS
                 NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaL 80 
                                   G+GaiG++++++++++    e+el+av+dr+ + + + +++l ++ +++l++ ++++   +d+vVEcas++av ++v+  L
  gi|91773633|ref|YP_566325.1|   8 GCGAIGTELCKAIDSGHI--EVELYAVYDRHeQSIINLKEQLKNTDPKVLEIVEMVK--HVDLVVECASQQAVYDVVPTTL 84 
                                   9****************6..8**********8888888*******************..********************** PP

                                   HTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                 NAD_binding_3  81 kagkdvvtankgaladealyeeLreaaeangakiyve 117
                                    a++dv++ ++ga+ad++l ++ ++ a++ g+kiy++
  gi|91773633|ref|YP_566325.1|  85 HAKCDVMVISVGAFADKKLLDTTFDIAKEYGCKIYFP 121
                                   ***********************************97 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   3.8e-09   6.2e-06       2      99 ..       3      96 ..       2     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.8e-09
                                  EEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHHHH CS
                        DapB_N  2 kvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpeavlen 83
                                  k++v+G+ G +G+e++ka+++ + ++el a++dr+e+++++       +l++++ +v  ++ e+++++d +++  + +av+++
  gi|91773633|ref|YP_566325.1|  3 KIGVFGC-GAIGTELCKAIDSgHIEVELYAVYDRHEQSIIN----LKEQLKNTDPKVL-EIVEMVKHVDLVVECASQQAVYDV 79
                                  9******.************9789**********9954442....2335567777776.78889999**************** PP

                                  HHHHHHTT-EE.EE--S CS
                        DapB_N 84 lklalekgvkl.ViGTT 99
                                  + + l ++ ++ Vi   
  gi|91773633|ref|YP_566325.1| 80 VPTTLHAKCDVmVISVG 96
                                  ***99998765144444 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 !   25.3   0.1   9.8e-09   1.6e-05       1      95 [.       3      94 ..       3     115 .. 0.83
   2 ?   -2.3   0.0       3.5   5.6e+03      50      82 ..     154     187 ..     134     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.8e-09
                                  EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHH CS
                Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskel 82
                                  k+++ G  G++G+el + +++ h evel +++ + ++   +l+e  k    ++d kv +   e +k+vd+v+ ++++++  ++
  gi|91773633|ref|YP_566325.1|  3 KIGVFG-CGAIGTELCKAIDSgHIEVELYAVYDRHEQSIINLKEQLK----NTDPKVLE-IVEMVKHVDLVVECASQQAVYDV 79
                                  689999.9*************************99944444444444....45555555.46788****************** PP

                                  HHHHHHTTS..EEEE CS
                Semialdhyde_dh 83 apklaeagv..kviD 95
                                  +p+ ++a++   vi+
  gi|91773633|ref|YP_566325.1| 80 VPTTLHAKCdvMVIS 94
                                  ****99999556665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                                   TTECEBEEE.GGGGGCTT-SEEEE-SCHHHHHHH CS
                Semialdhyde_dh  50 egkdlkved.vdeeelkevdivflalpagvskel 82 
                                   eg+ + v++ +d +++k+  ++f  + +++ k++
  gi|91773633|ref|YP_566325.1| 154 EGAPYIVQNnIDLDSIKGKTVLFEGMASEAVKAF 187
                                   4444555665788888888888877777776665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   3.8e-08   6.3e-05       1      96 [.       3      97 ..       3      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.8e-08
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCG CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlavkpedveevlsela 82
                                  kig+ G+G +g  l + ++ +g  + e++ + +r+++++  l+e+l+  + +  +  e++++ d vv +   ++v +v+    
  gi|91773633|ref|YP_566325.1|  3 KIGVFGCGAIGTELCK-AIDSGHIEVELYAVYDRHEQSIINLKEQLKnTDPKVLEIVEMVKHVDLVVECASQQAVYDVVPTT- 83
                                  79*************9.899998778888899***********9999866666779**********************9988. PP

                                  HHHHTTSEEEEESS CS
                 F420_oxidored 83 kdalkgklvisvla 96
                                   +a+ + +visv a
  gi|91773633|ref|YP_566325.1| 84 LHAKCDVMVISVGA 97
                                  89999999*99976 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.7e-06    0.0028       1      91 [.       2      92 ..       2      92 .. 0.89
   2 ?   -1.7   0.0       3.1     5e+03      43      76 ..     111     150 ..     101     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                                  EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                  GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpeidavivatpngtheelaka 81
                                  l+++++G+G ig++  +++   + + e+ a++d+++++  ++ e+++     + ++ e+++  ++d+v+ +   +  ++++  
  gi|91773633|ref|YP_566325.1|  2 LKIGVFGCGAIGTELCKAIDSGHIEVELYAVYDRHEQSIINLKEQLKNTdpKVLEIVEMVK--HVDLVVECASQQAVYDVVPT 82
                                  589*************8888887777****************9999988566666778888..99****************** PP

                                  HHHTT-EEEE CS
                  GFO_IDH_MocA 82 aleagkhvll 91
                                   l a+++v++
  gi|91773633|ref|YP_566325.1| 83 TLHAKCDVMV 92
                                  ******9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                   HHHTTHE.EESS.....HHHHHTCTTESEEEE-S-GGGHH CS
                  GFO_IDH_MocA  43 aesfgve.aysd.....leelladpeidavivatpngthe 76 
                                   a+++g++  + +     l+ l++ +++ +++v+  +++h 
  gi|91773633|ref|YP_566325.1| 111 AKEYGCKiYFPSgaivgLDGLKSASAASIYSVTLTTQKHP 150
                                   6666666544445555577888888888888888888885 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 !   15.3   0.1   5.9e-06    0.0096      38      96 ..       3      68 ..       1      97 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.9e-06
                                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.......CHHHHTCEECSHHHHHHH-SEEE CS
                  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee.......eeeelgvelvsleellaesDivs 96
                                  ++G++G+G+IG+++ k + +  ++v  y ++ ++e+       + +++  ++ ++ e++++ D v+
  gi|91773633|ref|YP_566325.1|  3 KIGVFGCGAIGTELCKAIDSGHIEVELYAVYDRHEQsiinlkeQLKNTDPKVLEIVEMVKHVDLVV 68
                                  79*****************99999999888888776666665455666667778888888888876 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.8e-05     0.046       1      80 [.       3      83 ..       3     100 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                  -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H...HHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HH CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvree...elieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsq 80
                                  ki+v+G G+ Gt l k++ +   ev l++  +   + i +++e+ +n+   p++    ++v   dl   ++  + +  vvP+ 
  gi|91773633|ref|YP_566325.1|  3 KIGVFGCGAIGTELCKAIDSGHIEVELYAVYDrheQSIINLKEQLKNT--DPKVLEIVEMVKHVDLVVECASQQAVYDVVPTT 83
                                  79********************99999976552113333444444443..355444445555566666666677777777765 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 ?   14.0   0.1   2.6e-05     0.043       1      74 [.       3      81 ..       3     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                  EEEEE--SHHHHHHHHHHHHTT-EE...EEE-SSHHHHHHHHHTTEEE-SSHH...HHHHHCSEEEE-SSSHHHHHHHHH CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykv...avynrtkekveelvaegakaaesie...elvasldvvitmvkagkavdevie 74
                                  kig+ G G +G+++++ + +  ++v   avy+r+++++ +l ++  ++  ++    e+v+++d+v+ + ++ +av +v+ 
  gi|91773633|ref|YP_566325.1|  3 KIGVFGCGAIGTELCKAIDSGHIEVelyAVYDRHEQSIINLKEQLKNTDPKVLeivEMVKHVDLVVECASQ-QAVYDVVP 81
                                  79*******************99994445788888888888777644444444000444444555555444.33433333 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     9e-05      0.15      11      85 ..       2      80 ..       1     103 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9e-05
                 Rossmann-like 11 lsvGiisaGrvGtalgaaleraghvvvgisaisaasre...raerrlPdv..pvlevedvaaraellllavPdaelpglv 85
                                  l++G+ + G +Gt l +a++  gh+ v ++a+ +  ++     +++l ++  +vle+ +++++ +l++ +     + ++v
  gi|91773633|ref|YP_566325.1|  2 LKIGVFGCGAIGTELCKAIDS-GHIEVELYAVYDRHEQsiiNLKEQLKNTdpKVLEIVEMVKHVDLVVECASQQAVYDVV 80
                                  89*****************85.676666666665554411155677766532799***********99776665555555 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   2.1   0.00018      0.29       1     101 [.       4      95 ..       4     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGG CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppis 81 
                                   + ++G+G++G  + + +   +   +  +v dr++++  +l++        + + +  ++ + +++++k+ dlvv ++ +  
  gi|91773633|ref|YP_566325.1|   4 IGVFGCGAIGTELCKAIDSGHIEVELYAVYDRHEQSIINLKE--------QLKNTDPKVLE-IVEMVKHVDLVVECASQQA 75 
                                   6799*********99998754332366777777777666654........34455566667.899**************** PP

                                   HHHHHHHHHHHT-EEEESS- CS
               Sacchrp_dh_NADP  82 sldvlkaCietgvhyvdtsi 101
                                     dv+ + + ++++++ +s+
  gi|91773633|ref|YP_566325.1|  76 VYDVVPTTLHAKCDVMVISV 95 
                                   ****9999999999988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2236.20
//
Query:       gi|91773634|ref|YP_566326.1|  [L=274]
Description: nicotinate-nucleotide pyrophosphorylase [carboxylating] [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-56  190.8   1.4    2.1e-56  190.3   1.4    1.2  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    2.1e-23   82.2   0.0    4.1e-23   81.2   0.0    1.5  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
     0.0057   16.1   0.4      0.011   15.1   0.3    1.6  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.022   14.1   0.5      0.045   13.1   0.5    1.5  1  TMP-TENI        Thiamine monophosphate synthase
      0.025   13.8   0.1      0.042   13.0   0.1    1.3  1  ALAD            Delta-aminolevulinic acid dehydratase
      0.039   13.8   1.0       0.12   12.1   0.5    1.9  2  KDGP_aldolase   KDGP aldolase
      0.041   13.7   0.5       0.08   12.7   0.5    1.5  1  PRAI            N-(5'phosphoribosyl)anthranilate (PRA) isomer


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 !  190.3   1.4   8.1e-60   2.1e-56       1     169 []     102     272 ..     102     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 8.1e-60
                                   HHHHHHHHHHHHHCT.SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTT CS
                     QRPTase_C   1 iAtltarmveaaksa.kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdke 80 
                                   iAt t+++ve +++   v++++TRkttPg+r++ek A+ +GGgd hr++Lsd+++ikdnh++++g +++a++s++e ++++
  gi|91773634|ref|YP_566326.1| 102 IATNTREYVETVRQYsDVKVAGTRKTTPGIRKFEKLAIIAGGGDPHRFDLSDTIMIKDNHVNMMG-LENAINSAKELAGFT 181
                                   9**************9*************************************************.*************** PP

                                   SEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-SEEEECHHCH CS
                     QRPTase_C  81 vkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvdvisvgalth 159
                                    ki veves+e++  ++++++diim+Dn+s+ ++ k+ve lk+ + r   ++evSGg+   n++eyak+gvdvisvg+l+h
  gi|91773634|ref|YP_566326.1| 182 QKIDVEVESVENAILAAKMGVDIIMFDNMSPGQVIKVVEALKNEDLRnsAILEVSGGIDISNISEYAKTGVDVISVGSLVH 262
                                   *****************************************99998888******************************** PP

                                   TB----EEEE CS
                     QRPTase_C 160 svkalDislk 169
                                   +++++D+sl+
  gi|91773634|ref|YP_566326.1| 263 KSQWIDVSLE 272
                                   ********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 !   81.2   0.0   1.6e-26   4.1e-23       2      89 .]      16     100 ..      15     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1.6e-26
                                   TT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHH CS
                     QRPTase_N   2 grgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaL 82 
                                   g+ D+    ++ +ek++ka ++ k+++++aG+++a+++f+++ gl  ++++kDG+++ +gd++lei+Gna ++l+aER++L
  gi|91773634|ref|YP_566326.1|  16 GANDISC--TLVPEKEIKAIVFVKQDCIIAGIPIAKRIFDYF-GLDSSAKYKDGDQLGSGDTILEISGNAVSVLRAERIVL 93 
                                   5678999..888999***************************.************************************** PP

                                   HHHHHHH CS
                     QRPTase_N  83 nllqrlS 89 
                                   n+l +lS
  gi|91773634|ref|YP_566326.1|  94 NFLGHLS 100
                                   *****98 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   4.4e-06     0.011     154     197 ..     220     261 ..     201     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-06
                                   HHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                Ribul_P_3_epim 154 kkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                   +++++       +  +ev GG++  ni++ a+ g+dv+ +gs v
  gi|91773634|ref|YP_566326.1| 220 EALKNEDL--RNSAILEVSGGIDISNISEYAKTGVDVISVGSLV 261
                                   33333222..267889*************************977 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   1.8e-05     0.045      69     179 ..     152     259 ..     131     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                      TMP-TENI  69 alavgadgvHlgq..ddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelae 147
                                      + ++  H+     + ++++a+el g    i + v+s e+a  a+++g+d i++  + p +  k  e+l  e l++ a 
  gi|91773634|ref|YP_566326.1| 152 SDTIMIKDNHVNMmgLENAINSAKELAGFTQKIDVEVESVENAILAAKMGVDIIMFDNMSPGQVIKVVEALKNEDLRNSAI 232
                                   555555556666622334688999999999999999***********************9999999999999998887554 PP

                      TMP-TENI 148 aleiPvvaiGGitlenvaevleagadgvavvs 179
                                        + + GGi+ +n+ e +++g+d ++v s
  gi|91773634|ref|YP_566326.1| 233 -----LEVSGGIDISNISEYAKTGVDVISVGS 259
                                   .....4578*******************9976 PP

>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.6e-05     0.042     144     187 ..     191     234 ..     176     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHCT-SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB- CS
                          ALAD 144 akvavsqaeaGadivapSdmmDgrvaaireaLdeagfeevails 187
                                   ++ a+  a+ G+di+   +m  g+v ++ eaL+++++++ ail 
  gi|91773634|ref|YP_566326.1| 191 VENAILAAKMGVDIIMFDNMSPGQVIKVVEALKNEDLRNSAILE 234
                                   57899**********************************99985 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.31   8.1e+02      57      87 ..     136     164 ..      88     182 .. 0.65
   2 ?   12.1   0.5   4.8e-05      0.12     131     198 ..     184     251 ..     166     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.31
                                   -EEEE-STT-GGGHHHHHHHCCCH--SEE-- CS
                 KDGP_aldolase  57 aisvGLGaGdpeqskmvaeiskklqpqhinq 87 
                                    +++  G+Gdp+++    +i   ++++h+n 
  gi|91773634|ref|YP_566326.1| 136 KLAIIAGGGDPHRFDLSDTI--MIKDNHVNM 164
                                   44555677888777766666..356667764 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.8e-05
                                   S--EEE.HHHHHHHHHHCT--EEEE---TTTTTHHHHHHHHHHHHHCT-EEEEBSS--TTTHHHHHHHH CS
                 KDGP_aldolase 131 ekaivs.vetaiallkdmggssvkffpmeGlkrleelaavakaaakkgltlePtGGidldnfeeivqia 198
                                    +++v+ ve+ai l ++mg++ + f  m   +  + ++a+ +   +++ +le +GGid+ n++e  ++ 
  gi|91773634|ref|YP_566326.1| 184 IDVEVEsVENAI-LAAKMGVDIIMFDNMSPGQVIKVVEALKNEDLRNSAILEVSGGIDISNISEYAKTG 251
                                   344443144555.7899*********************************************9977665 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 ?   12.7   0.5   3.1e-05      0.08      96     175 ..     180     256 ..     162     269 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                                   TTSEEEEEEE-SSS--S-SSTT-SEEEEESSS-SSSXXXXG.GGGTTSXX...TTEEEESSXXTTTHHHHHT.TXXSEEEE CS
                          PRAI  96 vikalkvaesvdevkearradhvdllllDsgaGGtGelldw.sliskllks..lkviLAGGLtpeNvaeaiklegvlgvDv 173
                                     +++ v+ +  e  +++++  vd++++D+     G+ +   +++++ +      + + GG++++N++e +k    +gvDv
  gi|91773634|ref|YP_566326.1| 180 FTQKIDVEVESVENAILAAKMGVDIIMFDNMSP--GQVIKVvEALKNEDLRnsAILEVSGGIDISNISEYAK----TGVDV 254
                                   45555555444467888899999******8666..555542144444444423555679*************....67776 PP

                                   XG CS
                          PRAI 174 ss 175
                                    s
  gi|91773634|ref|YP_566326.1| 255 IS 256
                                   44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1936.01
//
Query:       gi|91773635|ref|YP_566327.1|  [L=420]
Description: hypothetical protein Mbur_1683 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   36.5   2.6    3.8e-05   23.9   0.0    3.0  3  DUF11            Domain of unknown function DUF11
    1.1e-06   27.8   3.6     0.0062   15.4   0.8    2.5  2  BatD             Oxygen tolerance
    2.3e-06   27.1   2.9      0.038   13.4   0.2    2.7  2  TRAP_beta        Translocon-associated protein beta (TRAPB)
    1.7e-05   25.0   5.2       0.12   12.7   0.1    3.7  3  CARDB            CARDB
    0.00011   22.4   0.7        3.2    8.0   0.1    3.5  3  bMG10            Bacterial Alpha-2-macroglobulin MG10 domain
     0.0022   18.2   0.5        2.1    8.7   0.0    3.1  3  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
     0.0048   15.8   0.2      0.056   12.3   0.1    2.0  2  Integrin_alpha2  Integrin alpha
  ------ inclusion threshold ------
       0.04   13.4   1.0        0.7    9.3   0.1    2.4  2  Peptidase_A4     Peptidase A4 family
      0.058   13.5   8.0       0.97    9.6   2.0    3.4  2  Cupredoxin_1     Cupredoxin-like domain
      0.092   13.3   2.6       0.31   11.6   0.1    2.6  3  PLAT             PLAT/LH2 domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       6.5   1.2e+04      13      24 ..      89     100 ..      86     114 .. 0.54
   2 !   23.9   0.0   2.1e-08   3.8e-05       1      51 [.     142     192 ..     142     234 .. 0.76
   3 !   11.6   0.0   0.00014      0.25       8      46 ..     271     309 ..     254     328 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.5
                         DUF11  13 GdtvtytltvtN 24 
                                   G+t+++tl    
  gi|91773635|ref|YP_566327.1|  89 GETIEVTLLSVG 100
                                   666676665443 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.1e-08
                         DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                   +tK v++ +v+ G+ vt  +t++N g  +a++v+ +D+ P+g+ +++    
  gi|91773635|ref|YP_566327.1| 142 ITKEVSSYTVDQGEVVTIKVTARNKGDGKATEVRFSDPKPTGFILQEILLE 192
                                   79****************************************988876665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00014
                         DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglayv 46 
                                     v+  d+v++t+  +N g + angv +    P+g +y 
  gi|91773635|ref|YP_566327.1| 271 NSVKRNDEVEVTINIKNEGDSYANGVALIIHIPEGIEYK 309
                                   468889********************9988888888875 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   3.5e-06    0.0062      95     219 ..      96     228 ..      86     253 .. 0.67
   2 !   12.3   0.1     3e-05     0.054       7      91 ..     259     351 ..     254     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                          BatD  95 tievdgktyksnpitikVlk..........seasqsssaisdedlflraevskksvYvqeqvlvtlklytrvnvnledgkl 165
                                    ++v+g+t+  + ++i++++          ++ +++++  +  +l ++ evs+ +v  +e v++++    + +++  ++++
  gi|91773635|ref|YP_566327.1|  96 LLSVGGGTLPQATVSITITDddniylkqevDGGHEKATYPGTPSLEITKEVSSYTVDQGEVVTIKVTARNKGDGKATEVRF 176
                                   566788888888888888778888886554323333333333449999999988877777655555554443344445555 PP

                          BatD 166 ..pdlegflveelglpekkqyeetvnGrryrvvelrryalfPqksGkltIpplefd 219
                                     p+ +gf+++e+    +++ + t++  +y++ ++  y l ++ +G+++ +p + +
  gi|91773635|ref|YP_566327.1| 177 sdPKPTGFILQEIL--LEETGQMTID--KYETRTIFLYKLQANEAGTFEFQPTRAS 228
                                   77999999999999..4455666665..5666666678899999999998887766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3e-05
                          BatD   7 aaaaeftasvdknevevgetfrLtftvngasgepdfsapslekdfevlsg....sqssstqiinGksss.......ssskt 76 
                                   +a+ ef++s+ +n v+ ++++++t+ ++++ g++  +   +     + +g    +++s+++iinG  +        +++k 
  gi|91773635|ref|YP_566327.1| 259 VAELEFSTSIESNSVKRNDEVEVTINIKNE-GDSYAN--GVALIIHIPEGieykGSNSNIEIINGMPKVylesfglNQEKE 336
                                   67899*************************.422222..221133333446666888999999997654111111123455 PP

                          BatD  77 wtytLapkkeGtltI 91 
                                   +++ ++pk+ Gt+tI
  gi|91773635|ref|YP_566327.1| 337 IKFLIKPKELGTYTI 351
                                   999999999999999 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 !   13.4   0.2   2.1e-05     0.038      20     109 ..     140     229 ..     128     246 .. 0.70
   2 !   13.2   0.3   2.4e-05     0.044      11     103 ..     253     352 ..     245     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                     TRAP_beta  20 vlvkKkilnrllvegedltveytiyNvGssaAldVslvD...dsfpeeaFevvsgslsakwerlapgenvshsfvvepkks 97 
                                   + + K++ +  + +ge +t+++t  N G+ +A++V+++D   ++f  ++  +++++ ++++++ +  + +   + +++   
  gi|91773635|ref|YP_566327.1| 140 LEITKEVSSYTVDQGEVVTIKVTARNKGDGKATEVRFSDpkpTGFILQE-ILLEETGQMTIDKYETRTIF--LYKLQANEA 217
                                   56789999999999*************************6444553333.23444555555555544443..334566666 PP

                     TRAP_beta  98 gsfngtaavvtY 109
                                   g f+++++  +Y
  gi|91773635|ref|YP_566327.1| 218 GTFEFQPTRASY 229
                                   666666666666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.4e-05
                     TRAP_beta  11 laqedasarvlvkKkilnrllvegedltveytiyNvGssaAldVslv...Ddsf....peeaFevvsgslsakwerlapge 84 
                                    +++++ a++ ++ +i +++++ + ++ v+++i N G+s A  V l     +++    ++++ e+++g+ ++  e+   ++
  gi|91773635|ref|YP_566327.1| 253 GKNAKKVAELEFSTSIESNSVKRNDEVEVTINIKNEGDSYANGVALIihiPEGIeykgSNSNIEIINGMPKVYLESFGLNQ 333
                                   567788999999999**************************9999853332444324478889999999999999999999 PP

                     TRAP_beta  85 nvshsfvvepkksgsfngt 103
                                   + + +f ++pk  g + +t
  gi|91773635|ref|YP_566327.1| 334 EKEIKFLIKPKELGTYTIT 352
                                   9999999999998888765 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.23   4.1e+02      46      87 ..      89     128 ..      58     132 .. 0.64
   2 !   12.7   0.1   6.5e-05      0.12       1      39 [.     137     175 ..     137     178 .. 0.93
   3 !   10.8   0.5   0.00024      0.43       4      41 ..     262     299 ..     259     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.23
                                   TEEEEEEEESEE-CTEEE..EEEEEEE-S-S-CEEEEEEEESTT CS
                         CARDB  46 gelvgtvtvpsLaagest..tvsftwtteategevtltvvvDpd 87 
                                   g   +t++v+ L+ g+ t  + ++++t++    +++l+  vD +
  gi|91773635|ref|YP_566327.1|  89 G---ETIEVTLLSVGGGTlpQATVSITIT-DDDNIYLKQEVDGG 128
                                   2...4455555555544411555555555.77888888888865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.5e-05
                                   S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEE CS
                         CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatk 39 
                                   tp L++t++++  ++ +ge +ti+vt +N+G++++++++
  gi|91773635|ref|YP_566327.1| 137 TPSLEITKEVSSYTVDQGEVVTIKVTARNKGDGKATEVR 175
                                   689******************************999875 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00024
                                   EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEE CS
                         CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkva 41 
                                   L+ +++++ +++  ++e+++t+++kN+G+ ++  + + 
  gi|91773635|ref|YP_566327.1| 262 LEFSTSIESNSVKRNDEVEVTINIKNEGDSYANGVALI 299
                                   6667788899999*****************99887765 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 !    8.0   0.1    0.0018       3.2      21      71 ..     146     201 ..     123     207 .. 0.80
   2 ?    5.2   0.0     0.013        23     102     124 ..     206     228 ..     197     232 .. 0.86
   3 !    6.1   0.0    0.0067        12      19      65 ..     267     317 ..     250     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                         bMG10  21 a...klkvGdkvrvrltvttpr..dleyvaledplPAGlepvnpslgtesesaeey 71 
                                       ++ +G++v++++t + +   + ++v  +dp P G+ + +  l+++ ++  ++
  gi|91773635|ref|YP_566327.1| 146 VssyTVDQGEVVTIKVTARNKGdgKATEVRFSDPKPTGFILQEILLEETGQMTIDK 201
                                   033489************966523679************99999999988876655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                         bMG10 102 ytfeylvravtpGtfsvppakae 124
                                   + f y+++a+ +Gtf   p++a+
  gi|91773635|ref|YP_566327.1| 206 TIFLYKLQANEAGTFEFQPTRAS 228
                                   5688****************986 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0067
                         bMG10  19 sda..klkvGdkvrvrltvttprdl..eyvaledplPAGlepvnpslgtes 65 
                                   s +  ++k+ d+v+v+++++ + d   + val   +P G+e   ++++ e 
  gi|91773635|ref|YP_566327.1| 267 SIEsnSVKRNDEVEVTINIKNEGDSyaNGVALIIHIPEGIEYKGSNSNIEI 317
                                   333547**************7765534789999999999998888776665 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.3   4.2e+03       4      28 ..      89     113 ..      87     115 .. 0.70
   2 !    8.7   0.0    0.0012       2.1       2      33 ..     152     183 ..     151     185 .. 0.89
   3 !    6.1   0.0    0.0072        13       3      33 ..     275     305 ..     273     314 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                   NPCBM_assoc   4 Getvtltltvtndgtaaatnvslsl 28 
                                   Get ++tl  + +gt +   vs+++
  gi|91773635|ref|YP_566327.1|  89 GETIEVTLLSVGGGTLPQATVSITI 113
                                   7777777777777777777777765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                   NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeG 33 
                                   ++Ge vt+++t+ n+g+  at+v++s   P G
  gi|91773635|ref|YP_566327.1| 152 DQGEVVTIKVTARNKGDGKATEVRFSDPKPTG 183
                                   79**********************99766665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0072
                   NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeG 33 
                                   + ++v++t+ ++n+g++ a +v l +  PeG
  gi|91773635|ref|YP_566327.1| 275 RNDEVEVTINIKNEGDSYANGVALIIHIPEG 305
                                   66899************************99 PP

>> Integrin_alpha2  Integrin alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.072   1.3e+02     191     365 ..     148     171 ..     119     183 .. 0.67
   2 !   12.3   0.1   3.1e-05     0.056     194     232 ..     273     312 ..     242     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.072
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Integrin_alpha2 191 ylvLgdekdltlevtvsNkgesAYeaeLlvtipegleysgvksdekkeasstCeqkkstktelvdcdlGnPmkrgtevtvq 271
                                   ++++ + + +t++vt++Nkg+                                                            
  gi|91773635|ref|YP_566327.1| 148 SYTVDQGEVVTIKVTARNKGD------------------------------------------------------------ 168
                                   344545555666666666665............................................................ PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXX CS
               Integrin_alpha2 272 lrlstssleksekelefelevnstnkeqeekdnkvelnvkvvaeaklslsGvskpeqvfyggevkgesamesedeiGseVe 352
                                                                                                                    
  gi|91773635|ref|YP_566327.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                                   XXXXXXXXXXXXX CS
               Integrin_alpha2 353 htyeiqNkGpstv 365
                                              ++
  gi|91773635|ref|YP_566327.1| 169 ----------GKA 171
                                   ..........444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.1e-05
                                   XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX CS
               Integrin_alpha2 194 LgdekdltlevtvsNkge.sAYeaeLlvtipegleysgvk 232
                                   ++++++++++++++N+g+  A    L+++ipeg+ey g +
  gi|91773635|ref|YP_566327.1| 273 VKRNDEVEVTINIKNEGDsYANGVALIIHIPEGIEYKGSN 312
                                   5677899999999999995588899999999999999876 PP

>> Peptidase_A4  Peptidase A4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00039       0.7      76     115 ..     131     172 ..      88     177 .. 0.83
   2 ?    2.4   0.1     0.052        93      84     110 ..     263     289 ..     233     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00039
                  Peptidase_A4  76 dawyewyP..ayavdfsglavsaGDsvtvtvtatsatsgtvt 115
                                   +a y   P  +++ ++s+ +v +G++vt++vta ++  g++t
  gi|91773635|ref|YP_566327.1| 131 KATYPGTPslEITKEVSSYTVDQGEVVTIKVTARNKGDGKAT 172
                                   455666678888899999******************999876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.052
                  Peptidase_A4  84 ayavdfsglavsaGDsvtvtvtatsat 110
                                   + ++++++ +v+  D+v+vt++++++ 
  gi|91773635|ref|YP_566327.1| 263 EFSTSIESNSVKRNDEVEVTINIKNEG 289
                                   5688999999************99876 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4     0.016        29      33      90 ..     145     222 ..     104     231 .. 0.66
   2 ?    9.6   2.0   0.00054      0.97      14      97 ..     251     358 ..     240     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                  Cupredoxin_1  33 ePskievkagekvklkiknkdkt...peefesed............lgee..kvlapgkttti...tiaplkpGeYef 90 
                                   e s+ +v +ge v++k++++ k    ++e+ + d            l+e    ++++ +t ti   ++++ ++G++ef
  gi|91773635|ref|YP_566327.1| 145 EVSSYTVDQGEVVTIKVTARNKGdgkATEVRFSDpkptgfilqeilLEETgqMTIDKYETRTIflyKLQANEAGTFEF 222
                                   567889999999999987766664443777777766666555556544433356666666666222334445566666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00054
                  Cupredoxin_1  14 kaaaaaektveitvkdggfePskievkagekvklkiknkdkt....................peefesed.....lgeekv 69 
                                   ++ ++a+k+ e++++ +++e ++++ + + +v+++ikn++++                     +++e+ +       e+  
  gi|91773635|ref|YP_566327.1| 251 DTGKNAKKVAELEFS-TSIESNSVKRNDEVEVTINIKNEGDSyangvaliihipegieykgsNSNIEIINgmpkvYLESFG 330
                                   455788899999997.99999999999***************999999999999998888765777777777775334478 PP

                  Cupredoxin_1  70 lapgktttitiaplkpGeYeftcdmhmd 97 
                                   l+++k+ ++ i+p++ G+Y++t d+  +
  gi|91773635|ref|YP_566327.1| 331 LNQEKEIKFLIKPKELGTYTITTDYSYQ 358
                                   9999999999************998764 PP

>> PLAT  PLAT/LH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00017      0.31      11      97 ..      99     198 ..      91     206 .. 0.84
   2 ?    0.5   0.2      0.48   8.7e+02      19      59 ..     247     288 ..     242     350 .. 0.59
   3 ?   -0.9   0.0       1.3   2.3e+03      19      62 ..     324     348 ..     304     369 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                   TT.CEEEEEEEEEEESSEEEEEEEEEEE.TTSEEETTT-EEEEEEEESS-.....ECSEEEEEEEEECSSS.......... CS
                          PLAT  11 egagtdanvyislygkngesasleltld.tsgpdfergatdsFkvdtdvd.....lGallkinlhwensgv.......... 75 
                                    g gt ++ ++s+  ++++ ++l+++ d  + +   +g t s +++ +v+      G++ +i+++  n+g           
  gi|91773635|ref|YP_566327.1|  99 VGGGTLPQATVSITITDDDNIYLKQEVDgGHEKATYPG-TPSLEITKEVSsytvdQGEVVTIKVTARNKGDgkatevrfsd 178
                                   5889************************7776766777.*******8886688889************999********** PP

                                   .S-E.EEEEEEEEEEETTTSSEEE CS
                          PLAT  76 .sde.wflksitvekpgetgqkvt 97 
                                    ++  + l+ i +e   etg ++t
  gi|91773635|ref|YP_566327.1| 179 pKPTgFILQEILLE---ETG-QMT 198
                                   95556********4...555.444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.48
                                   EEEEEEESSEEEEEEEEEEE.TTSEEETTT-EEEEEEEESS- CS
                          PLAT  19 vyislygkngesasleltld.tsgpdfergatdsFkvdtdvd 59 
                                   ++++  gkn ++  +  +      ++++r+ + + +++ +++
  gi|91773635|ref|YP_566327.1| 247 ITVTDTGKNAKKVAELEFSTsIESNSVKRNDEVEVTINIKNE 288
                                   666777777766544444433555777777777777776664 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                                   EEEEEEESSEEEEEEEEEEETTSEEE..TTT-EEEEEEEESS-ECS CS
                          PLAT  19 vyislygkngesasleltldtsgpdf..ergatdsFkvdtdvdlGa 62 
                                   vy+                    ++f   + ++ +F+++ ++ lG 
  gi|91773635|ref|YP_566327.1| 324 VYL--------------------ESFglNQEKEIKFLIKPKE-LGT 348
                                   333....................4443344455555555443.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2895.08
//
Query:       gi|91773636|ref|YP_566328.1|  [L=368]
Description: tubulin/FtsZ, GTPase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-34  118.2   0.3    1.3e-33  116.9   0.3    1.7  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    8.5e-06   25.2   0.0    1.7e-05   24.2   0.0    1.6  1  Tubulin_2  Tubulin like
  ------ inclusion threshold ------
       0.18   11.8   0.0       0.26   11.2   0.0    1.4  1  GHL15      Hypothetical glycosyl hydrolase family 15


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 !  116.9   0.3   2.1e-37   1.3e-33       1     195 [.       3     182 ..       3     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 2.1e-37
                                   EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEES...BHHHHHTS-GS......EEEE- CS
                       Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidt...dpqvlneikagselfnpnklll 78 
                                   +i+++g GqcGn+i++++ +   +++g    ++++ +f+s+++ ++ +  ++ai+t   d ++l+ +ka+      +++++
  gi|91773636|ref|YP_566328.1|   3 NILIVGNGQCGNRILDAINK---EAFGG---KSKFAKFYSQQKYKSKV-ETIAINTainDLKELSFTKAK------DRMHI 70 
                                   699*****************...44443...589*******9888877.889***966666777777777......99999 PP

                                   -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--G CS
                       Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPse 159
                                        + +g+g+++++gk++ ee++ +i++++e+  +++  f+++s +GGTGS+++p +++ +ke+ ++ +v++vvvlP++
  gi|91773636|ref|YP_566328.1|  71 ----PHLHGVGANRTLGKSVFEENKSHIMRNIEERGNFDVGFVITSASGGTGSSFTPPLIKEIKEN-HDFPVYAVVVLPFR 146
                                   ....889***********************************************************.8************9 PP

                                   G.G-HHHHHHHHHHHHHHHHT.-SEEEEEEHHHHHCC CS
                       Tubulin 160 fsevvvepynailalkeliee.sdavividNdaLlki 195
                                   + e++++ +na+++lke++++ +d +i+ dN+ L++i
  gi|91773636|ref|YP_566328.1| 147 E-EGTLYLQNAAFCLKEIRDSgVDGIILADNQFLKQI 182
                                   9.******************99************998 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.8e-09   1.7e-05      78     226 ..      44     165 ..       5     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.8e-09
                     Tubulin_2  78 vdrilrnllreetasaypsieeWlppeleelrkapeseGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnv 158
                                   v++i  n+       a ++++e    +++ +  +p  +G G +Rt+G+ ++ +n + i+++++++ +   g          
  gi|91773636|ref|YP_566328.1|  44 VETIAINT-------AINDLKELSFTKAKDRMHIPHLHGVGANRTLGKSVFEENKSHIMRNIEERGNFDVG---------- 107
                                   33333333.......2345666666677777778888*************************997655444.......... PP

                     Tubulin_2 159 fVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna 226
                                   fV++S +GGTGS+   +++   ++i ++ +    ++++v+lP       e+g+ + +Na+  LkE+  
  gi|91773636|ref|YP_566328.1| 108 FVITSASGGTGSSFTPPLI---KEIKENHDF--PVYAVVVLPFR-----EEGTLYLQNAAFCLKEIRD 165
                                   **************99965...555556665..78*******86.....5689999999999999976 PP

>> GHL15  Hypothetical glycosyl hydrolase family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.4e-05      0.26      78     178 ..     157     251 ..     154     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                         GHL15  78 ksalnelrdsgiDGv.faDndvktlsyysldlplsgvaeiidaklregldellkelkealkegkllvgniaesr.alsyld 156
                                   +++l+e+rdsg+DG+ +aDn +   ++++  +  + +++ i+  ++ +  +ll +l +++    ++v+     + + s   
  gi|91773636|ref|YP_566328.1| 157 AFCLKEIRDSGVDGIiLADNQFL--KQIG--GNVQSAYNTINDMIARRILFLLDALDSEM----MMVTDLGDFKtVMSGGA 229
                                   68************737888887..4444..77787777668889999999999999999....66666555443566666 PP

                         GHL15 157 gamiEnfaesgegkeslltmde 178
                                   g    +f+e+++g + ++t+++
  gi|91773636|ref|YP_566328.1| 230 GLATIGFYEAEKGMNIKTTIQK 251
                                   6677777777766666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2780.95
//
Query:       gi|91773637|ref|YP_566329.1|  [L=147]
Description: hypothetical protein Mbur_1685 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-18   65.2   0.1      7e-18   65.0   0.1    1.0  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.27   11.1   0.0    1.2  1  DSPc      Dual specificity phosphatase, catalytic 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 !   65.0   0.1   7.8e-22     7e-18       1     106 [.      10     125 ..      10     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 7.8e-22
                                   TEEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEECTTT...........EE-S-EEEEEEEEEEEETT.. CS
                        DUF296   1 rphvlrlepGediveaieefarkrgiraacvlsaiGavsnvtrladgee...........kllgrfeilslsGtilpdg.. 68 
                                   r++ +r+++Ged++ ++e +a k++i++a++ + +Gav++v+ l+ g++           + ++++e++++ G+i+ ++  
  gi|91773637|ref|YP_566329.1|  10 RVFTVRIDTGEDLLRELEGIATKEEIKSAVF-TLLGAVAKVN-LVVGPKenaippetmwvNHTEPYEVIGV-GNIFMEEgt 87 
                                   6899***************************.**********.777777688887777665559*******.999984458 PP

                                   ..EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE-C CS
                        DUF296  69 ..lHlhvslagedgqvvgGhlaegplvaattvevvvaefe 106
                                     +Hlh +++++  +v  G+l+ g+  a+ ++ev+++e++
  gi|91773637|ref|YP_566329.1|  88 pkIHLHTAAGRG-DNVNVGCLR-GESAAFMVLEVFIMEIN 125
                                   99*********8.99*******.99************986 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     3e-05      0.27      66     110 ..      92     136 ..      82     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3e-05
                                   HHHHHHTT-EEEEEESSSSSHHHHHHHHHHHHHHTSCHHHHHHHH CS
                          DSPc  66 idkakqkgkkvlVHCqaGisRSatliiaYlmktknlslneayefl 110
                                   +++a+ +g +v V C  G s   ++   ++m+ +++++  a++  
  gi|91773637|ref|YP_566329.1|  92 LHTAAGRGDNVNVGCLRGESAAFMVLEVFIMEINGMEAMRAFDAA 136
                                   578999**************9999999***********9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1119.06
//
Query:       gi|91773638|ref|YP_566330.1|  [L=121]
Description: hypothetical protein Mbur_1686 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-05   23.5   1.2      5e-05   23.1   0.0    1.8  3  TrmB             Sugar-specific transcriptional regulator Trm
      0.005   16.5   0.0     0.0065   16.1   0.0    1.3  1  SMC_ScpB         Segregation and condensation complex subunit
      0.005   16.7   0.0     0.0079   16.1   0.0    1.3  1  MarR_2           MarR family
     0.0064   16.4   0.1      0.013   15.4   0.0    1.6  2  HTH_37           Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.7   0.2       0.39   10.6   0.0    2.4  2  HTH_5            Bacterial regulatory protein, arsR family
      0.027   14.4   0.0      0.036   13.9   0.0    1.2  1  BsuBI_PstI_RE_N  BsuBI/PstI restriction endonuclease HTH doma


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.7e-08     5e-05       1      63 [.      16      85 ..      16      90 .. 0.88
   2 ?   -2.8   0.1         2   6.1e+03       6      14 ..      95     103 ..      95     105 .. 0.79
   3 ?   -2.6   0.1       1.8   5.3e+03      39      47 ..     112     120 ..     106     121 .] 0.67

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.7e-08
                                  HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                          TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63
                                  Lq ++ s  Ea   + L++  +++ +ei +++g+ ++ v  ++r L ++G+Ve + ++       p +Y 
  gi|91773638|ref|YP_566330.1| 16 LQSINVSRIEALSIACLVNGRELSSQEIENATGLRQPEVSVAMRPLCERGWVEEKNEKrtkcrgrPAKYY 85
                                  6777888889999999***************************************999777777777776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                                   HHHHCCCHC CS
                          TrmB   6 LseyEakvY 14 
                                   L+eyE+++ 
  gi|91773638|ref|YP_566330.1|  95 LKEYESDIL 103
                                   799999875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.8
                                   HHHHHHHHH CS
                          TrmB  39 vYevLrsLe 47 
                                   v ++Lr+L+
  gi|91773638|ref|YP_566330.1| 112 VVKSLRNLV 120
                                   556777776 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 !   16.1   0.0   2.2e-06    0.0065      83     146 ..      21      92 ..       8     105 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                      SMC_ScpB  83 qaaletLai..Iaykqpvtraeiee...iRGvnsdsvvrtLlerglieekgrkee..pgrpil.YgtTekFl 146
                                    + +e L+i   +    ++++eie+   +R  +++ ++r L erg++eek++k++   grp+  Y++   F 
  gi|91773638|ref|YP_566330.1|  21 VSRIEALSIacLVNGRELSSQEIENatgLRQPEVSVAMRPLCERGWVEEKNEKRTkcRGRPAKyYSLNMDFT 92 
                                   5555555541144455788999988222455669999************99988866899998345555555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.6e-06    0.0079      19      54 ..      35      70 ..      21      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.6e-06
                                  TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  gr+l+ +e++ ++gl ++ vs + + L ++G+ve++
  gi|91773638|ref|YP_566330.1| 35 GRELSSQEIENATGLRQPEVSVAMRPLCERGWVEEK 70
                                  5579*****************************987 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   0.0   4.5e-06     0.013      19      53 ..      25      59 ..       9      64 .. 0.88
   2 ?   -2.9   0.0       2.3   6.8e+03      50      61 ..     101     112 ..     100     120 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.5e-06
                                  HHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHT CS
                        HTH_37 19 lalaiaeliekrelsqseaaqllgiaqPkvsrllr 53
                                   al ia l  +rels +e+ +++g  qP+vs  +r
  gi|91773638|ref|YP_566330.1| 25 EALSIACLVNGRELSSQEIENATGLRQPEVSVAMR 59
                                  5788999************************8776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                                   HHHTT--TT--H CS
                        HTH_37  50 rllrgklsrfsl 61 
                                   ++l+++ +r+++
  gi|91773638|ref|YP_566330.1| 101 DILKENEKRLEV 112
                                   566666666654 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.39       7      34 ..      29      56 ..      25      69 .. 0.83
   2 ?    2.9   0.1     0.033        98       1      12 [.     106     117 ..     106     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                  HHHHHTTSSEEHHHHHHHHTS-HHHHHH CS
                         HTH_5  7 ILklLaegelcvcelaeelglsqstvSh 34
                                  I +l++ +el++ e+ +++gl q+ vS 
  gi|91773638|ref|YP_566330.1| 29 IACLVNGRELSSQEIENATGLRQPEVSV 56
                                  6688899*******************96 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.033
                                   SHHHHHHHHHHT CS
                         HTH_5   1 dptRlkILklLa 12 
                                   +++Rl+++k+L+
  gi|91773638|ref|YP_566330.1| 106 NEKRLEVVKSLR 117
                                   589********8 PP

>> BsuBI_PstI_RE_N  BsuBI/PstI restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.036      80     128 ..      58     106 ..      55     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
               BsuBI_PstI_RE_N  80 lhqlvqaglvvensdkpgratnspkarYaleaeflellktfgtaaWees 128
                                   ++ l + g v+e+++k ++    p++ Y+l+ +f+e+lk+++++  +e+
  gi|91773638|ref|YP_566330.1|  58 MRPLCERGWVEEKNEKRTKCRGRPAKYYSLNMDFTEILKEYESDILKEN 106
                                   7889999**********************************99866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 947.86
//
Query:       gi|91773639|ref|YP_566331.1|  [L=425]
Description: phosphopyruvate hydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-117  389.6   0.5   1.4e-116  388.9   0.5    1.3  1  Enolase_C  Enolase, C-terminal TIM barrel domain
      2e-59  199.5   0.1    3.8e-59  198.5   0.1    1.5  1  Enolase_N  Enolase, N-terminal domain
    8.4e-07   28.8   0.0    1.3e-06   28.1   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.055   12.6   0.0       0.11   11.7   0.0    1.4  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.9   0.5  3.1e-120  1.4e-116       2     287 ..     147     422 ..     146     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 388.9 bits;  conditional E-value: 3.1e-120
                                   -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHH CS
                     Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkea 82 
                                   + lPvP++nvinGG+hagn+l++qefmi+P ga++f++alr+Gae+yh l +vl++kyg satnvG eGG+aP ++++++a
  gi|91773639|ref|YP_566331.1| 147 FALPVPTMNVINGGKHAGNDLSIQEFMIQPKGADTFSNALRMGAETYHALGKVLEDKYGASATNVGYEGGYAPPISTTADA 227
                                   579****************************************************************************** PP

                                   HHHHHHHHHHCT-TC.TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT- CS
                     Enolase_C  83 ldliveaiekaGykg.kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldedd 162
                                   ld +v+aie+aGy++ +++i+ld a+sef+  + +ky +d+++        l+ ++l+d+y +l++ yPi+siedp+ e+ 
  gi|91773639|ref|YP_566331.1| 228 LDALVSAIEEAGYTEsEISIGLDSAASEFF--DGDKYFIDGNK--------LAPAELVDYYLDLIETYPILSIEDPFHEES 298
                                   *************998**************..5569*999877........99**************************** PP

                                   HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S-- CS
                     Enolase_C 163 weawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGetedt 243
                                   +e ++ lt+e  d + ivGddl+vtn++rl+++ie +aanalllkvnqiG+++es++a++la+++gy+vvvshrs etedt
  gi|91773639|ref|YP_566331.1| 299 FEDFAALTSEAWDTI-IVGDDLFVTNVNRLAKGIEMEAANALLLKVNQIGTISESFDAANLAQRNGYSVVVSHRSAETEDT 378
                                   ********9998655.9**************************************************************** PP

                                   HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE CS
                     Enolase_C 244 tiadlavglsaGqiktGaparserlakynqllrieeelgekaky 287
                                   +iad++v++    iktGaparser akynqllriee+lg++a+y
  gi|91773639|ref|YP_566331.1| 379 MIADISVAIGGDLIKTGAPARSERTAKYNQLLRIEEDLGDAARY 422
                                   ******************************************99 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.1   8.6e-63   3.8e-59       1     131 []      12     141 ..      12     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 8.6e-63
                                   EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBT CS
                     Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldv 81 
                                   I+kv+areildSrGnpTvev+++t  g +gra+vpsGaStg++ealelrD+d +ry+gkgv+kav+n+n++++++l+g+d+
  gi|91773639|ref|YP_566331.1|  12 IQKVHAREILDSRGNPTVEVDIYTGCG-FGRASVPSGASTGSNEALELRDKDADRYNGKGVLKAVDNINKTLSKELLGMDA 91 
                                   89**********************988.8**************************************************** PP

                                   T-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                     Enolase_N  82 tdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                   ++q+eiD+l+i+lDgtenk+++GaNail++S+A+akaaA+++++ lyryl
  gi|91773639|ref|YP_566331.1|  92 RNQREIDELMIALDGTENKKTFGANAILGISMATAKAAADSLGIALYRYL 141
                                   *************************************************8 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0     3e-10   1.3e-06      43     156 ..     258     370 ..     244     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3e-10
                                   TTSTSEEEEE-TTTSBHHHHHH.HHHHHGGGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSS.HHHHHHHHHHT CS
                      MR_MLE_C  43 pgddvdlmvDanqawdlatAir.vareleeldllwlEEPvppeddleglaelrara.sipiaagEslys.radfrelleag 120
                                   +gd  + ++D n    +a+ +  ++  +e + +l +E+P++  ++ e+ a+l+++a ++ i+++    + + ++++ +e +
  gi|91773639|ref|YP_566331.1| 258 DGD--KYFIDGNKL-APAELVDyYLDLIETYPILSIEDPFHE-ESFEDFAALTSEAwDTIIVGDDLFVTnVNRLAKGIEME 334
                                   556..666677766.34444440445555599*********9.67********98887878887765555*********** PP

                                   SESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                      MR_MLE_C 121 avdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                   a+ ++ ++v+++g i+e+ + a+la+ +g+ v++ +
  gi|91773639|ref|YP_566331.1| 335 AANALLLKVNQIGTISESFDAANLAQRNGYSVVVSH 370
                                   ******************************987655 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 ?   11.7   0.0   2.4e-05      0.11     132     214 ..     304     387 ..     272     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                        MAAL_C 132 klkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvh 211
                                   +l++++ +  +v D+ +  +++ + + ++ eaa+++ +k+  +G+i+++ +a   ++++g  + +   + et+ +  + + 
  gi|91773639|ref|YP_566331.1| 304 ALTSEAWDTIIVGDDlFVTNVNRLAKGIEMEAANALLLKVNQIGTISESFDAANLAQRNGYSVVVSHRSAETEDTMIADIS 384
                                   4566677777888773566678899999********************************************987555554 PP

                        MAAL_C 212 val 214
                                   va+
  gi|91773639|ref|YP_566331.1| 385 VAI 387
                                   444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3049.48
//
Query:       gi|91773640|ref|YP_566332.1|  [L=910]
Description: replicative DNA polymerase I [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-112  377.1   0.0   1.4e-112  376.7   0.0    1.1  1  DNA_pol_B       DNA polymerase family B
    8.1e-53  179.7   0.0    1.1e-52  179.2   0.0    1.2  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
  ------ inclusion threshold ------
      0.015   14.2   0.1      0.066   12.1   0.0    1.9  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral
        0.1   12.3   0.0       0.25   11.0   0.0    1.6  2  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex


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 !  376.7   0.0  3.2e-116  1.4e-112       3     457 ..     393     854 ..     391     856 .. 0.91

  Alignments for each domain:
  == domain 1  score: 376.7 bits;  conditional E-value: 3.2e-116
                                   HHHHHHS-HHHHHHHHHHHHHHHTTBE-B-.....----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT CS
                     DNA_pol_B   3 lsrvledgqqirveslLlrlakeegfilpd.....rtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahN 78 
                                   l+ ++++gq   ve +Ll+++ ++g+++        ++ ++k++e+ +G+ VleP+kgl++ +v+vlD++SLYP i++ahN
  gi|91773640|ref|YP_566332.1| 393 LQDTVSGGQTNMVEHILLTEFGKQGRVMSTkpdeeTSSFRRKQNEDLKGGAVLEPEKGLHK-NVIVLDYKSLYPTIMMAHN 472
                                   567899**********************986666533333444446*************96.689**************** PP

                                   -STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHH CS
                     DNA_pol_B  79 lcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlal 159
                                   lcytt+v   +  +     d   +v  +p++ efvk++v +g++p++L++ll+kR + kk +k+++de e ++ld+ Qlal
  gi|91773640|ref|YP_566332.1| 473 LCYTTVVPPGKYPE-----D---KVIRSPSKGEFVKPEVFKGIVPSVLESLLDKRIETKKLMKQASDEGEYQVLDATQLAL 545
                                   *******9998733.....3...588899999************************************************* PP

                                   HHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT.....SSGGGT-SS.............T-EEEEEBS CS
                     DNA_pol_B 160 KvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekk..aellskllalpe.ea.....eee..klkviYGDT 230
                                   K++ Ns+YG+ G+a  rl++l++A+svT+iGR ++ +t+++v ++  +  l++  a+ + e+     +++  kl+v YGDT
  gi|91773640|ref|YP_566332.1| 546 KILLNSFYGYSGYARARLYSLQMANSVTSIGRGNIARTQDIVCNRigTVILRDNKAYLRdEVdelkdDDKavKLSVAYGDT 626
                                   ********************************************9854455554444443555555423369********* PP

                                   SEEEEE-..........S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTS...EE CS
                     DNA_pol_B 231 DSvfiel..........kvkdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskan...kl 298
                                   DSvf+++          +v ++e+++ +gk++a++v+   +++p++lefe++ k++lLi+KK+Ya  ++e + + +   ++
  gi|91773640|ref|YP_566332.1| 627 DSVFVHCkndqdlefeeGVFSLEDSALVGKKVASIVTA-SLPDPMELEFEATAKRVLLIAKKRYAQWIFE-PANGGwtdSI 705
                                   ****************999******************9.99*****************************.5555557569 PP

                                   EEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHH.HHHHTT-S-GGGG-EEEEESS.CCCSSG CS
                     DNA_pol_B 299 liKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvl.eeleenkvplekfvlskelskepenyks 378
                                    +KG+++vRrd+c+l++++ ++vlel+lk+     ++e  +e ++ ++++v+  ++++ +  +e++vl+k++sk+p++yk+
  gi|91773640|ref|YP_566332.1| 706 KVKGLETVRRDWCELTSKMLNRVLELVLKE----GDIEGSVEHVRTLVDRVRnLDVAKDSDLFEDLVLTKNFSKSPSSYKN 782
                                   ******************************....**************99997799999999******************* PP

                                   CCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHHHT CS
                     DNA_pol_B 379 knlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarlle 457
                                   k+ phl+v++ +++r + +p +g+ri++vi++          l  +raedp+yv+e+n+ +d++yY++ q+l++v+r+l+
  gi|91773640|ref|YP_566332.1| 783 KQ-PHLTVVENIQRRTGVRPAIGERIPFVIIAGR-------GLFVDRAEDPDYVRENNVLLDVDYYIQkQMLPPVERILS 854
                                   *9.******************************5.......59**********************************986 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 !  179.2   0.0   2.5e-56   1.1e-52       2     337 .]      25     327 ..      24     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 2.5e-56
                                   ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHH CS
                DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnel 82 
                                   +e+g+svc+ v gf+pyfY++a+   +l+++ ee+ke +e+        +++e+v++ + +gy+++++ +lkv++ +p ++
  gi|91773640|ref|YP_566332.1|  25 SEDGESVCCLVPGFEPYFYLSAS--GDLQKLGEEIKEQFEGV-------KTFEIVERFEPIGYQETKKHMLKVTTYDPGNV 96 
                                   689********************..66656777777777666.......45779************999************ PP

                                   HHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEE..EETTTSCEETTTCCS-EEE CS
                DNA_pol_B_exo1  83 kkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveid..cdvddliakpkesepplrv 161
                                   ++ir+ + +   +  +ye+d+ +  rflid++++g++w s +      e+ + n ++ +d  ++ +++  ++k ++  l+ 
  gi|91773640|ref|YP_566332.1|  97 PEIRDDVASMLGVNAIYETDILFRNRFLIDKGFKGMDWVSTQ-----MEESVPNGKIICDrtIRTSHISEVQKIANSSLKY 172
                                   *******9988899************************9998.....66666666666661145677777777788***** PP

                                   EEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHHH CS
                DNA_pol_B_exo1 162 lsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsEkelL 242
                                   ++FDIec  ++g +p+++    p+i++s++++     + +++++++++e +            ++  + +v   ++E +lL
  gi|91773640|ref|YP_566332.1| 173 MAFDIECLPHDGGMPTPDV--SPVIMVSFAFEPAY--KGHKTLVLVMKEVE------------GV--DEDVEMLPDESDLL 235
                                   *******************..**********6655..578889********............77..6688899******* PP

                                   HHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEE.EEEECEEEETTSEEEEHHHH CS
                DNA_pol_B_exo1 243 qaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfs.kqarekvkisgrihlDlyrv 322
                                   ++f+e++++ydPdvitgYNi++FD+pYi +R+k l + + s+++        + +  +++   +r+ v i+gr+++D +++
  gi|91773640|ref|YP_566332.1| 236 NRFFEIFRDYDPDVITGYNINDFDVPYITDRVK-LLNESGSNINSA---VGRDSRALSYRkVVTRTMVPIPGRVVVDSLPL 312
                                   *********************************.444455665544...4444455555545578**************** PP

                                   HHHHSSSSG-SHHHH CS
                DNA_pol_B_exo1 323 vkrklklpsYkLnav 337
                                   ++++++l+ Y+L +v
  gi|91773640|ref|YP_566332.1| 313 IRQQFSLKRYTLRNV 327
                                   ************987 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 ?   12.1   0.0   1.5e-05     0.066     125     252 ..     344     477 ..     327     496 .. 0.65
   2 ?   -1.7   0.0      0.23     1e+03     371     383 ..     542     554 ..     513     559 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                   DNA_pol_B_2 125 lwkekeekkydivketleYckqDvlvlaklllklkesideff..easinifkrpTisslalaifkqilyrkkkk....ell 199
                                   ++++ +++ ++i+k  ++Y + D ++  +lll lk  +d+++  +    i    T+s+   ++ + il  ++ k    +  
  gi|91773640|ref|YP_566332.1| 344 MEEHWNDSGEKIRK-FIDYSRRDSELALELLLDLKL-LDKYIalSRVSGILLQDTVSGGQTNMVEHILLTEFGKqgrvMST 422
                                   55555555556655.566666666666666665554.44444432223355556666666666666665444444555666 PP

                   DNA_pol_B_2 200 apskeldkyiRka...yrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthypmPygk 252
                                   +p++e  ++ Rk    + GG + +p   + + +n+ v D +SlYP++m+   + y++
  gi|91773640|ref|YP_566332.1| 423 KPDEETSSFRRKQnedLKGGAVlEPE--KGLHKNVIVLDYKSLYPTIMMAHNLCYTT 477
                                   666666666665333399****7777..5578****************987777665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.23
                   DNA_pol_B_2 371 rsiaKlllNsLYG 383
                                   +   K+llNs YG
  gi|91773640|ref|YP_566332.1| 542 QLALKILLNSFYG 554
                                   5667********9 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 ?   11.0   0.0   5.6e-05      0.25      36      71 ..     230     266 ..     194     296 .. 0.85
   2 ?   -3.4   0.0       1.4   6.4e+03     135     162 ..     336     365 ..     315     366 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.6e-05
                DNA_pol_B_exo2  36 sekelikkffegvekkkpqlVs.fngrgfDlpvleyr 71 
                                   +e++l+++ffe+++ + p +++ +n + fD+p ++ r
  gi|91773640|ref|YP_566332.1| 230 DESDLLNRFFEIFRDYDPDVITgYNINDFDVPYITDR 266
                                   599***************98855*********98766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
                DNA_pol_B_exo2 135 KlgvdGskVaelyqe..gklkeireYcetD 162
                                   Kl+vd+++  e +++  +k+++  +Y + D
  gi|91773640|ref|YP_566332.1| 336 KLDVDAADMEEHWNDsgEKIRKFIDYSRRD 365
                                   777788877777765223566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (910 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 6152.25
//
Query:       gi|91773641|ref|YP_566333.1|  [L=181]
Description: hypothetical protein Mbur_1689 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   20.7   0.1     0.0006   20.2   0.1    1.2  1  DUF4367   Domain of unknown function (DUF4367)


Domain annotation for each model (and alignments):
>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   3.3e-08    0.0006       3      99 ..      43     167 ..      41     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-08
                       DUF4367   3 eptylPeGy.............kfkktnisedsesalleYkdengelisfsiskqskeesqklsidteda........eve 62 
                                    ++ +PeG+             k++    ++  +     Y  ++ +++++ i++ s +++++l ++ + +         ++
  gi|91773641|ref|YP_566333.1|  43 ILETVPEGFeylgvhavdldtvKTSYADVEGIVNASEGIYNLDSIDYFIIAIEMDSSASAEELITQFKATftplavgeRFT 123
                                   56789999999999999999998888888888888888886699999999999********99999999999********* PP

                       DUF4367  63 kieingikatyyekedge.......yvlvwedegvvytlsgnis 99 
                                   ++++n+++at+++k  +        y+ +w++e++v+ + gn +
  gi|91773641|ref|YP_566333.1| 124 DVSFNEHDATLVTKYITAggeevprYQYIWNNENFVFLVKGNTD 167
                                   ***********99655558889******************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1066.19
//
Query:       gi|91773642|ref|YP_566334.1|  [L=677]
Description: S-layer-related protein [Methanococcoides burtonii DSM 6242]
Scores for 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-156  516.9  26.3    1.5e-82  276.5   7.8    2.9  3  S-layer    S-layer protein
    5.1e-10   39.0   1.8    5.1e-10   39.0   1.8    2.0  2  PGF-CTERM  PGF-CTERM motif
     0.0077   16.5   0.0        7.6    6.9   0.0    3.5  3  FHA_2      FHA domain
  ------ inclusion threshold ------
       0.08   13.7   0.1       0.08   13.7   0.1    5.0  5  Big_9      Bacterial Ig domain


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.8  10.5   1.4e-79   6.3e-76      12     258 .]      52     298 ..      40     298 .. 0.94
   2 !  276.5   7.8   3.3e-86   1.5e-82       8     258 .]     333     582 ..     326     582 .. 0.96
   3 ?  -10.3  10.9         4   1.8e+04     151     174 ..     603     628 ..     594     647 .. 0.47

  Alignments for each domain:
  == domain 1  score: 254.8 bits;  conditional E-value: 1.4e-79
                       S-layer  12 wtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgs......YevigflaekYfagydns 86 
                                    t ++F++f+ydiddg++sE++ + + s + ++i eg+l+Y+++ ++++f +e w +      +++igflae+Y+++ d++
  gi|91773642|ref|YP_566334.1|  52 TTFTDFAAFFYDIDDGIGSEKIDIITAS-TTDKIPEGDLIYTSNLQTVSFSYEGWADspvdntFDKIGFLAEEYVPI-DED 130
                                   566799*****************97655.999********************99998899999**************.788 PP

                       S-layer  87 aetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska..dsty 165
                                   +           + Lsk+++d+de++t+++g++l+L++g+++++kqiDvdg+kvwleLtkdg+++d++v +++++  +s++
  gi|91773642|ref|YP_566334.1| 131 P-----------SILSKLILDDDEKYTMRVGQTLDLGDGFAITPKQIDVDGNKVWLELTKDGKFLDDDVFNAENSldNSSW 200
                                   8...........89**********************************************************999*9**** PP

                       S-layer 166 vyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvsen.....eiemenddsitLs 241
                                    y++++g+edd+vi+ vhv+evf+g++dsl++ieg+++isd+++e+e++defgk+e++s++       +i m+ +++itLs
  gi|91773642|ref|YP_566334.1| 201 DYDTTVGGEDDIVIMRVHVNEVFQGQVDSLAIIEGMWLISDEAMELETDDEFGKFEITSLTAGpvgtgQIVMKTTEDITLS 281
                                   **********************************************************98876566669************ PP

                       S-layer 242 rdktieimddlkfkvaD 258
                                   +d++iei++d+ +k+aD
  gi|91773642|ref|YP_566334.1| 282 KDSSIEITEDIMIKTAD 298
                                   ****************8 PP

  == domain 2  score: 276.5 bits;  conditional E-value: 3.3e-86
                       S-layer   8 eeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgs......YevigflaekYfag 82 
                                   ++ +wta +F+gfyydid+++ssE+lt+ +e +++rti+eg+l+Y ++ +++++++e w +      +++igf+ae+Y+++
  gi|91773642|ref|YP_566334.1| 333 STESWTAASFAGFYYDIDEDISSETLTAIVEGATNRTIAEGNLTYVSQLQSVSYTYEGWADspvdnsFDKIGFFAEEYVPI 413
                                   4567***************************99***********************99998899999************** PP

                       S-layer  83 ydnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.. 161
                                    d+++           + Lsk+++d+de++t+++g++l+L++g+++++kqiDvdg+kvwleLtkdg+++d++v +++++  
  gi|91773642|ref|YP_566334.1| 414 -DQDP-----------SILSKLILDDDEKYTMRVGQTLDLGDGFAITPKQIDVDGNKVWLELTKDGKFLDDDVFDTTGNmv 482
                                   .8888...........8***********************************************************999** PP

                       S-layer 162 dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvsen...eiemenddsit 239
                                   +s++ y +++g+edd+vi+ vhv+evf+g++dsl+++eg+++isd+++eie++defgk+ev+ +++     i+m++++sit
  gi|91773642|ref|YP_566334.1| 483 NSSWDYGTTVGGEDDIVIMRVHVNEVFQGQVDSLAILEGMWLISDEAMEIEDDDEFGKLEVTGITTGptgAITMDSTESIT 563
                                   ****************************************************************9876669********** PP

                       S-layer 240 LsrdktieimddlkfkvaD 258
                                   L+ d+t ei++ ++fkvaD
  gi|91773642|ref|YP_566334.1| 564 LTADSTKEIAEGMSFKVAD 582
                                   ******************9 PP

  == domain 3  score: -10.3 bits;  conditional E-value: 4
                       S-layer 151 vdskvissska..dstyvyekdlgde 174
                                   vd++v+  ++   d++ v+++d+   
  gi|91773642|ref|YP_566334.1| 603 VDDDVVVDDDVvvDDDVVVDDDVVVD 628
                                   44444444222333333333333222 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   2.2         2   8.9e+03       6      14 ..       5      13 ..       5      14 .. 0.81
   2 !   39.0   1.8   1.1e-13   5.1e-10       2      22 ..     656     676 ..     655     677 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                     PGF-CTERM  6 avlAlaGLL 14
                                  +++A+a+L 
  gi|91773642|ref|YP_566334.1|  5 IAIAIAALM 13
                                  689999995 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 1.1e-13
                     PGF-CTERM   2 PGFGavlAlaGLLaaalLaRR 22 
                                   PGF+av+A+aGLLa+a+++RR
  gi|91773642|ref|YP_566334.1| 656 PGFEAVFAIAGLLAVAYFVRR 676
                                   ********************* PP

>> FHA_2  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.047   2.1e+02      59      85 ..     129     155 ..     124     159 .. 0.90
   2 !    6.9   0.0    0.0017       7.6      36      89 ..     239     292 ..     212     296 .. 0.88
   3 ?    2.5   0.0     0.039   1.7e+02      59      85 ..     415     441 ..     408     445 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.047
                         FHA_2  59 anpssvngkklkknesvelkegqtlel 85 
                                    +ps + + +l  +e+++++ gqtl l
  gi|91773642|ref|YP_566334.1| 129 EDPSILSKLILDDDEKYTMRVGQTLDL 155
                                   579999******************987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0017
                         FHA_2  36 cSrnqvelkadlekklvkvkqlGanpssvngkklkknesvelkegqtlelleek 89 
                                   +S + +el+ d e  + +++ l a p + +++++k  e ++l++++++e++e+ 
  gi|91773642|ref|YP_566334.1| 239 ISDEAMELETDDEFGKFEITSLTAGPVGTGQIVMKTTEDITLSKDSSIEITEDI 292
                                   5778899*******************************************9875 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.039
                         FHA_2  59 anpssvngkklkknesvelkegqtlel 85 
                                   ++ps + + +l  +e+++++ gqtl l
  gi|91773642|ref|YP_566334.1| 415 QDPSILSKLILDDDEKYTMRVGQTLDL 441
                                   68999*******************987 PP

>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.7       2.1   9.6e+03      90      90 .]      69      69 ..      23     104 .. 0.54
   2 ?   -0.6   0.0      0.52   2.3e+03      36      79 ..     250     290 ..     212     301 .. 0.56
   3 ?    0.9   0.9      0.17   7.8e+02      13      70 ..     323     378 ..     311     401 .. 0.49
   4 ?   13.7   0.1   1.8e-05      0.08      32      89 ..     528     584 ..     492     585 .. 0.79
   5 ?   -5.2  14.4         4   1.8e+04      11      39 ..     614     642 ..     596     653 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                         Big_9 90 g 90
                                  g
  gi|91773642|ref|YP_566334.1| 69 G 69
                                  1 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.52
                         Big_9  36 pdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtd 79 
                                    +  + ++tslt+    + + G+++++++  +t + +++   t+
  gi|91773642|ref|YP_566334.1| 250 DEFGKFEITSLTA---GPVGTGQIVMKTTEDITLSKDSSIEITE 290
                                   3334444444433...3344455555555555555555544444 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.17
                         Big_9  13 daPvavddsvtvtedsv...la..ndtdpdgdaltvtsltvtlvtapanGtvtinadgtltyt 70 
                                     P a+ + +++++ ++        d+d d ++ t+t+    +v +++n t+   a g+lty 
  gi|91773642|ref|YP_566334.1| 323 ATPDASITGISTESWTAasfAGfyYDIDEDISSETLTA----IVEGATNRTI---AEGNLTYV 378
                                   34444444455554333333332234444444444333....3444444333...23344443 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 1.8e-05
                         Big_9  32 ndtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDgs 89 
                                    +  +++d +++ +l vt+ t++  G +t++++ ++t t+++     +  +++v D++
  gi|91773642|ref|YP_566334.1| 528 EAMEIEDD-DEFGKLEVTGITTGPTGAITMDSTESITLTADSTKEIAEGMSFKVADSA 584
                                   44455555.56899*****************************************975 PP

  == domain 5  score: -5.2 bits;  conditional E-value: 4
                         Big_9  11 vndaPvavddsvtvtedsvlandtdpdgd 39 
                                   v d  v+vdd+v v+ d+v++ d+ +d+d
  gi|91773642|ref|YP_566334.1| 614 VVDDDVVVDDDVVVDDDEVVDDDVVVDDD 642
                                   34444555555556666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4646.67
//
Query:       gi|91773643|ref|YP_566335.1|  [L=259]
Description: KaiC [Methanococcoides burtonii DSM 6242]
Scores for complete 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-72  241.7   0.4    6.9e-72  241.5   0.4    1.0  1  ATPase    KaiC
     0.0054   16.3   0.0      0.056   13.0   0.0    2.0  1  AAA_25    AAA domain
  ------ inclusion threshold ------
      0.067   12.4   0.0      0.099   11.9   0.0    1.4  1  Rad51     Rad51
      0.068   12.5   0.0       0.14   11.4   0.0    1.7  1  DnaB_C    DnaB-like helicase C terminal domain
      0.092   12.7   0.0       0.17   11.9   0.0    1.5  1  ResIII    Type III restriction enzyme, res subunit


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 !  241.5   0.4   1.9e-75   6.9e-72       1     230 [.      19     253 ..      19     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.5 bits;  conditional E-value: 1.9e-75
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   vktgI+g+De++ gGi ++r++l++G++G+GKt f+ q++++g+ kyge+g++v++ee++e++ren+ +++wdl++le+eg
  gi|91773643|ref|YP_566335.1|  19 VKTGIPGFDELCGGGIIRDRSYLVSGTSGAGKTNFSVQYIYNGITKYGENGIIVATEERPEQIRENVMKFDWDLQALEDEG 99 
                                   79******************************************************************************* PP

                        ATPase  82 klaiidasesaeesaee.....kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgv 156
                                   kl+iida +++++++++      + +d++++++++    +ei+akr +iDs t++  y +++a++R +l +l ++l+ +g+
  gi|91773643|ref|YP_566335.1| 100 KLVIIDACSTKIGIPSQekyvdVRPFDTRSMMDQIIATQEEINAKRALIDSTTSIsFYLQDPAKIRVELLKLSTTLEVIGL 180
                                   *************999999999999******************************************************** PP

                        ATPase 157 TailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvleek 230
                                   T+++++e+ + e++  ++g+e f+ dg++vL++   ++ ++Rt+ei kmRg++hskk hp++It+eg ++++++
  gi|91773643|ref|YP_566335.1| 181 TSLMTCEIVD-ERSPARFGIETFVTDGTFVLHYAMHNNVRTRTMEIFKMRGSDHSKKLHPYDITSEGFVIHPHE 253
                                   *******755.59999******************************************************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.6e-05     0.056      11     107 ..      15     105 ..       6     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                        AAA_25  11 svadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlr 91 
                                   +++++++ +p  + l++g ++++   l+ G +g+GKt + ++  +   t     g       + ++v++E++ +++r+ + 
  gi|91773643|ref|YP_566335.1|  15 EINRVKTGIPGFDELCGGGIIRDRSYLVSGTSGAGKTNFSVQYIYNGITKY---G------ENGIIVATEERPEQIRENVM 86 
                                   6788999999999****999**********************999998855...3......36688888888888887665 PP

                        AAA_25  92 avg...ealrddarllvld 107
                                   +     +al+d ++l ++d
  gi|91773643|ref|YP_566335.1|  87 KFDwdlQALEDEGKLVIID 105
                                   5331124445566666555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.8e-05     0.099      10      56 ..      10      56 ..       2     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                  HHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                         Rad51 10 lekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                  ++   e+ ++ tG   +Del gGGi       + G +++Gkt ++ +
  gi|91773643|ref|YP_566335.1| 10 ISMEDEINRVKTGIPGFDELCGGGIIRDRSYLVSGTSGAGKTNFSVQ 56
                                  556789999********************9*************9987 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 ?   11.4   0.0     4e-05      0.14       2      68 ..      19      86 ..      18     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                                  BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHH CS
                                  xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRll 68
                                  ++tg   +D+l + G+ +   +++ + ++ Gkt + ++ + n  +k+  + +++  e   eq+ + ++
  gi|91773643|ref|YP_566335.1| 19 VKTGIPGFDELCGgGIIRDRSYLVSGTSGAGKTNFSVQYIYNGITKYGENGIIVATEERPEQIRENVM 86
                                  678999999988626889999********************988888878777788888888766655 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 ?   11.9   0.0   4.6e-05      0.17      23      77 ..      36      88 ..       9     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                                  TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                        ResIII 23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkf 77
                                  rd+ +l+  + G+GKT  +++ i++  +k++e+   ++v +++  eq +e+++kf
  gi|91773643|ref|YP_566335.1| 36 RDRSYLVSGTSGAGKTNFSVQYIYNGITKYGENG--IIVATEERPEQIRENVMKF 88
                                  78899************************99643..4455666677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1848.35
//
Query:       gi|91773644|ref|YP_566336.1|  [L=894]
Description: cation transporter, P-type ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-52  176.7   5.3    3.2e-52  176.7   5.3    4.1  4  E1-E2_ATPase     E1-E2 ATPase
    3.8e-37  127.8  13.3    3.8e-37  127.8  13.3    2.1  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    9.6e-26   91.4   3.4    2.9e-24   86.5   3.4    2.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    5.3e-22   77.7   0.0      1e-21   76.8   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
    6.1e-14   51.5   0.1    6.1e-14   51.5   0.1    2.2  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    8.1e-05   23.1   0.0    0.00042   20.8   0.0    2.2  1  HAD              haloacid dehalogenase-like hydrolase
     0.0011   18.8   0.5      0.046   13.5   0.3    2.3  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
        9.2    6.7  10.5        6.3    7.2   1.0    3.2  2  DUF2663          Protein of unknown function (DUF2663)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.8     0.024        55     116     157 ..      49      90 ..      34      94 .. 0.66
   2 !  176.7   5.3   1.4e-55   3.2e-52       2     181 .]     110     289 ..     109     289 .. 0.99
   3 ?    0.6   0.1      0.16   3.5e+02      91     137 ..     666     713 ..     661     743 .. 0.77
   4 ?    3.8   1.9     0.017        37     113     175 ..     763     826 ..     741     829 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                  E1-E2_ATPase 116 dklgkvlvpvvlliallvflialllgkslaeallralallva 157
                                   + l ++++ ++++++l++++i l++ + +++ ++ +l+ +v+
  gi|91773644|ref|YP_566336.1|  49 KVLLRQFTNFIVWVLLAAAAISLMIDEVVNFGVIIFLVAFVI 90 
                                   456677777777888888888877777777444444433333 PP

  == domain 2  score: 176.7 bits;  conditional E-value: 1.4e-55
                                   SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-G-TTEE-TT-EEEE-EE CS
                  E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvekekgdmvfsGtvvvsgea 81 
                                   + ++t++v+rdgt+ e++++++v+GD++++++gd+v+aD+ ++e    +vdesa+TGEs  +ek  g  +fsGt++v g++
  gi|91773644|ref|YP_566336.1| 110 MVQSTTHVVRDGTVAEVPSRDIVVGDVLVMETGDKVAADAFVFEIMGlKVDESAITGESFSIEKGIGGLIFSGTQIVHGKC 190
                                   67899**************************************************************************** PP

                                   EEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TT CS
                  E1-E2_ATPase  82 kavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPca 162
                                   kavVtatg++t+lg ia++++e  +  tplq+k+++l+k+l++++l+++ l+f++ + +g +l e+l+ alal+vaa+P++
  gi|91773644|ref|YP_566336.1| 191 KAVVTATGMQTQLGGIASMIQED-EVMTPLQQKINELSKHLAIIALVASGLTFVLGYATGAPLEEMLIIALALAVAAVPEG 270
                                   **********************9.9******************************************************** PP

                                   HHHHHHHHHHHHHHHHHHT CS
                  E1-E2_ATPase 163 Lplavplalalgarrlakk 181
                                   Lpl+++++la+g+  +ak+
  gi|91773644|ref|YP_566336.1| 271 LPLTMTITLAYGMHHMAKH 289
                                   *****************97 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.16
                                   TSTTTTTSTTS--------HHHHHHHHHHHH.HHHHHHHHHHHHHHS- CS
                  E1-E2_ATPase  91 dtelgkiarlveeakskktplqkkldklgkv.lvpvvlliallvflia 137
                                   d  +g+i+++v++ +    +++k+ + l++  ++ ++l+++ +++l +
  gi|91773644|ref|YP_566336.1| 666 DDNFGTIVEAVKRGRTIYENIEKFTTYLVSRnFTEIILIMLGITLLGF 713
                                   667999********9999999999998887758888777777776644 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.....HHHHH.HHHHHHHHS-TTHHHHHHHHHHHHH CS
                  E1-E2_ATPase 113 kkldklgkvlvpvvlliallvflialllgksla.....eallr.alallvaaiPcaLplavplalalga 175
                                   ++l+ ++++ ++++++++l+++l  ++     +     ++l++ +++ ++ +iP  +  +++  l++g+
  gi|91773644|ref|YP_566336.1| 763 RNLTLVVSIAALMGVVCFLVFLLSDPV-----NdlekaRTLTFaTIVSMILFIPFVFRSLTSSFLSVGV 826
                                   333333444444444444444444444.....44555588888688899999*********99999997 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3      0.85   1.9e+03      56      71 ..      78      93 ..      53     118 .. 0.60
   2 !  127.8  13.3   1.7e-40   3.8e-37       2     182 .]     716     886 ..     715     886 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.85
               Cation_ATPase_C 56 iqgllqalvtllvffl 71
                                    g++++lv++++ + 
  gi|91773644|ref|YP_566336.1| 78 NFGVIIFLVAFVIVLG 93
                                  3344444444444443 PP

  == domain 2  score: 127.8 bits;  conditional E-value: 1.7e-40
               Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgiseke 82 
                                    pl a+qiL+in++ +++pa+aL+l+p   ++m + Prk+ e++++++ l+ ++ +++l+++v++lvf+l    +   + e
  gi|91773644|ref|YP_566336.1| 716 VPLLALQILFINMFDEVMPAIALGLDPVRNEVMYEAPRKPGENILNRRNLTLVVSIAALMGVVCFLVFLLSDPVN---DLE 793
                                   59******************************************************************8888744...333 PP

               Cation_ATPase_C  83 nklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsleewl 163
                                         +a+t++F t+v + +f  ++ rs++ s+++ +g+f+nkl+ll+++ ++ll+++++yv +l+++f+++plsl++w+
  gi|91773644|ref|YP_566336.1| 794 ------KARTLTFATIVSMILFIPFVFRSLTSSFLS-VGVFTNKLMLLGVASTFLLTMVVMYVRPLGQLFDLVPLSLMDWF 867
                                   ......2*************************9999.**************************99**************** PP

               Cation_ATPase_C 164 ialllalvvllvdelvKll 182
                                   i +  a+++++++elvK++
  gi|91773644|ref|YP_566336.1| 868 IPISAAFLTMVLAELVKKI 886
                                   *****************86 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   3.4   1.3e-27   2.9e-24       2     210 .]     306     643 ..     305     643 .. 0.78

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.3e-27
                                   SEEEEESBTTTBCHHHHHHHHHHHH.......................CHHHHHHHHHH.....................H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxx.....................x RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.......................alalaaaletg.....................s 38 
                                   ++++ Dk+GTLt+ e+ ve+++v                         ++++++al t                      s
  gi|91773644|ref|YP_566336.1| 306 TVICTDKTGTLTKNEMTVEKLFVNGqffdvtgigyepegvllkddveaDVSENKALGTLlkgislcnnaslvqrhgvwevS 386
                                   5899******************************************997777777777788888888899999999***** PP

                                   HCHHHHHH.HHHHHHH.........HHHHHHHHHETTTE...................HHHHTHHHHHHHH.......... CS
                                   xxxxxxxx.xxxxxxx.........xxxxxxxxxxxxxx...................xxxxxxxxxxxxx.......... RF
                     Hydrolase  39 ehpigkal.vaaakar.........sgaltgfatfigrg...................ayaigkpewltal.......... 80 
                                     p    l vaaaka           ++++++                          a+++g pe++ +           
  gi|91773644|ref|YP_566336.1| 387 GDPTEVSLiVAAAKAGlwkddleveYEKVHEI------MftserklmttvhetpggrlAFCKGAPEFVLDRcvsierddgv 461
                                   ****9999999999998776664442222222......1333444777777777778999999999998886644444444 PP

                                   ......HCHHHHHHHHHHHHHHCHHHHHH.............................TTHHHHHHHHHHTHHBHTTHHHH CS
                                   ......xxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  81 ......dippdlgaaigsaqsqgrtvall.............................qaralavftiadplkvkpeaaea 126
                                         di   l++              +                             +   l+++++ dp  v++ea++ 
  gi|91773644|ref|YP_566336.1| 462 hdlsaaDIKGILDE--------------NnglagsayrvlgvsyrklsdgmavedsekDLIFLGLVAMIDP--VRKEAKDS 526
                                   44444444444444..............155555555556666***********999888999999999**..******** PP

                                   HHHHHHTTEEEEEEESSEHHHHHHHHHHTT............GGGE.SEEEEHHCES....................STTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxx.xxxxxxxxxx....................xxxx RF
                     Hydrolase 127 vasLkaagievvlltgdnpetaeraanqlG............ddyf.daviasdiet....................vakp 174
                                   +   k+agi+vv++tgdn+eta+++ +++G            d+++  ++ +++i++                     a +
  gi|91773644|ref|YP_566336.1| 527 IDLCKRAGIRVVMITGDNEETAKAIGKKIGlvadyhgsldgmDEKLrGIIKDGSITGsellslddgefdrlvegisvYARV 607
                                   *******************************87777775555333333333333333777777777777777777777777 PP

                                   SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 175 spegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    pe+k+++++ Lq +++ vam GDgvnDa+al++A+
  gi|91773644|ref|YP_566336.1| 608 MPEQKLRIVKALQNRGHVVAMTGDGVNDAPALKRAD 643
                                   **********************************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   4.5e-25     1e-21       2      90 ..     370     454 ..     369     455 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 4.5e-25
                 Cation_ATPase   2 lcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApe 82 
                                   lcN+a++   + +++++++G++tE++L+v+a+k+gl +++l+ e++kv+ei F+s+rK m++v+++   ++ ++++KGApe
  gi|91773644|ref|YP_566336.1| 370 LCNNASL--VQRHGVWEVSGDPTEVSLIVAAAKAGLWKDDLEVEYEKVHEIMFTSERKLMTTVHETP--GGRLAFCKGAPE 446
                                   8******..9*******************************************************76..************ PP

                 Cation_ATPase  83 iilkrCth 90 
                                    +l+rC +
  gi|91773644|ref|YP_566336.1| 447 FVLDRCVS 454
                                   ******76 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 !   51.5   0.1   2.7e-17   6.1e-14       5      69 .]       7      70 ..       4      70 .. 0.96
   2 ?   -3.8   0.4         5   1.1e+04      52      68 ..      74      90 ..      72      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.7e-17
               Cation_ATPase_N  5 sleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                  ++e v+++ + ++ +GL++ ++++rl+  G Nel+ek + +  + ll+qftn++v++Ll+aa++s
  gi|91773644|ref|YP_566336.1|  7 DIESVFAEVG-SSRSGLSETDVKKRLQLSGFNELQEKARITPAKVLLRQFTNFIVWVLLAAAAIS 70
                                  6799999**9.9***************************************************98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5
               Cation_ATPase_N 52 kqftnplvilLlvaalv 68
                                  +++ n+ vi+ lva ++
  gi|91773644|ref|YP_566336.1| 74 DEVVNFGVIIFLVAFVI 90
                                  56779999*****9876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.9e-07   0.00042      53     188 .]     486     640 ..     455     640 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                           HAD  53 glaelleallagls.eelaaelerfv.aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg.adevlat 130
                                    l   +++l  g++ e+ +++l  ++  ++i p   + +a++ ++ +++aG+rvv+++g +++ ++++ ++ g + +  ++
  gi|91773644|ref|YP_566336.1| 486 VLGVSYRKLSDGMAvEDSEKDLIFLGlVAMIDPV--RKEAKDSIDLCKRAGIRVVMITGDNEETAKAIGKKIGlVADYHGS 564
                                   5555566666677766666666666644445554..46***********************************63333333 PP

                           HAD 131 elevdd.rltgelglegkpvrgegkv..........................aalrewlaaegegidlee.......vvay 177
                                    l+  d +l g   + ++++ g++ +                          +                +       vva 
  gi|91773644|ref|YP_566336.1| 565 -LDGMDeKLRGI--IKDGSITGSELLslddgefdrlvegisvyarvmpeqklRI---V-----------KalqnrghVVAM 628
                                   .33333555555..5555555544445555555444444433333333311111...1...........122222227777 PP

                           HAD 178 .GDspsDlpllr 188
                                    GD+++D p+l+
  gi|91773644|ref|YP_566336.1| 629 tGDGVNDAPALK 640
                                   899999999986 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.031        70      16      65 ..     519     565 ..     514     588 .. 0.83
   2 !   13.5   0.3   2.1e-05     0.046     196     253 ..     616     674 ..     612     676 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.031
                                   --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTE CS
                   Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGal 65 
                                   + +++k+ i  +k +gi vv  TG + ++++ + +++g    v  ++G+l
  gi|91773644|ref|YP_566336.1| 519 VRKEAKDSIDLCKRAGIRVVMITGDNEETAKAIGKKIG---LVADYHGSL 565
                                   568899****************************9999...446666655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.1e-05
                                   HHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTHHHH CS
                   Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedGVak 253
                                   +k l+     v+  GDg ND + L++a++g+ mg  +++ +k+ + ++ ++ n + +++
  gi|91773644|ref|YP_566336.1| 616 VKALQNRGHVVAMTGDGVNDAPALKRADIGISMGiKGTDVAKESSLMILQDDNFGTIVE 674
                                   55666666678888*******************96678888888888888877677665 PP

>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.0    0.0028       6.3      17      79 ..      41     104 ..      32     112 .. 0.73
   2 ?    2.2   2.7       0.1   2.3e+02      19      60 ..     766     812 ..     752     851 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0028
                       DUF2663  17 krllllsl.lallvlllfliyvlikssslssllsallessvlllllllvallyvavkllkkKae 79 
                                    + + + + + l  ++ f+++vl  + ++s ++  +++  v+++l+ +v++l ++ ++  +Ka 
  gi|91773644|ref|YP_566336.1|  41 EKARITPAkVLLRQFTNFIVWVLLAAAAISLMIDEVVNFGVIIFLVAFVIVLGFVQEYKAEKAM 104
                                   4444444304556677788899888999999999999999999999999999888888666654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                       DUF2663  19 llllsllallvlllfliyvlik.....ssslssllsallessvllll 60 
                                   +l++s++al+ +++fl+++l+      +++ +  ++++++  +++ +
  gi|91773644|ref|YP_566336.1| 766 TLVVSIAALMGVVCFLVFLLSDpvndlEKARTLTFATIVSMILFIPF 812
                                   45677888888888888887777665433333333333332222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 5927.58
//
Query:       gi|91773645|ref|YP_566337.1|  [L=148]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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   59.8   0.0    3.2e-16   59.3   0.0    1.2  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
    1.8e-08   34.5   0.0    2.2e-08   34.2   0.0    1.1  1  Pyridox_ox_2     Pyridoxamine 5'-phosphate oxidase
    3.4e-07   30.0   0.0      4e-07   29.7   0.0    1.1  1  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
      0.046   13.7   0.0      0.098   12.6   0.0    1.6  1  Pyrid_oxidase_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 !   59.3   0.0   7.1e-20   3.2e-16       2      87 ..       8      95 ..       7      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 7.1e-20
                                  HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT....GSEEEEEEEE CS
                Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde....lgrgvrieGt 80
                                  +e + e l+++++  lAT++++G P v  ++++   g  + +f t + +rk+rn+e+np+va+++++d+    + +g+++eG+
  gi|91773645|ref|YP_566337.1|  8 KERISEYLKKHPFLNLATISPEGNPMVHSMGFA-SSGP-IVYFGTGNTTRKFRNIEQNPNVAFTVDEDGpdvmNITGIQMEGK 88
                                  68899****************************.5555.5******************************************* PP

                                  EEEESCH CS
                Putative_PNPOx 81 aelvsdg 87
                                  a +v+d+
  gi|91773645|ref|YP_566337.1| 89 ASFVTDE 95
                                  *****98 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 !   34.2   0.0   4.9e-12   2.2e-08       3     110 ..       9     110 ..       8     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4.9e-12
                                   HHHHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEEEEE CS
                  Pyridox_ox_2   3 eeilalLdegevgrlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnslnyrS 81 
                                   e i + L++++++ la+   +g+p++  + ++  g  +yf +  ++r+++ ++++p v+++v e dg +       +n + 
  gi|91773645|ref|YP_566337.1|   9 ERISEYLKKHPFLNLATISpEGNPMVHSMGFASSGPIVYFGTGNTTRKFRNIEQNPnVAFTVDE-DGPD------VMNITG 82 
                                   5678999**********996677******************************8889******9.8833......34645* PP

                                   EEEEEEEEEE--HHHHHHHCCCHHHHHST CS
                  Pyridox_ox_2  82 VvvrGraeevtdeeekaealellvekivp 110
                                   +++ G+a+ vtde+e  ++++l+vek+ p
  gi|91773645|ref|YP_566337.1|  83 IQMEGKASFVTDEAELGQIFQLMVEKF-P 110
                                   ************************998.5 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0     9e-11     4e-07      28     123 ..      29     132 ..       6     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9e-11
                 Pyrid_ox_like  28 ksrPMatq.kveedgd.lwfltkkdsdkvkeirkdsqvnlafsdes....kkkyvsvsGtaevvedrakieelWspvvkaw 102
                                   +  PM ++   + +g  ++f t ++++k ++i+++++v +++ +      + + ++++G+a++v+d+a + + ++ +v+++
  gi|91773645|ref|YP_566337.1|  29 EGNPMVHSmGFASSGPiVYFGTGNTTRKFRNIEQNPNVAFTVDEDGpdvmNITGIQMEGKASFVTDEAELGQIFQLMVEKF 109
                                   456664431455556516999*********************87541111345578899********************95 PP

                 Pyrid_ox_like 103 ..fpegkddpnltlikvtpeeae 123
                                     ++e  ++p+ ++ikv+p++a 
  gi|91773645|ref|YP_566337.1| 110 pfMAELPNNPDNVMIKVEPTKAF 132
                                   449999*************9996 PP

>> Pyrid_oxidase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.2e-05     0.098      20     160 ..      21     143 ..      13     148 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                   EEEEEE--SGGGTTSEEEEEEE-BSSSTT---S--EEEE-TTSHHHHHHHH--EEEEEEEGGGSSHHHHHT--TTSTTS-E CS
               Pyrid_oxidase_2  20 gtlsTisttkdiegapfanvvsisdgaaddstGnpylllvdidstaqniqknsklsltiseeqtptckkkkvdpesptcar 100
                                    +l+Tis     eg p++  + ++     +s   +y+   +    ++ni++n+++ +t+ e   +            +   
  gi|91773645|ref|YP_566337.1|  21 LNLATISP----EGNPMVHSMGFA-----SSGPIVYFGTGNTTRKFRNIEQNPNVAFTVDEDGPDVM----------NITG 82 
                                   56666766....677765555444.....5666777778889999*************987655533..........4667 PP

                                   EEEEEEEEE--.TTTHHHHHHHHHHH-GGGGGS-GG...G--EEEEEEEEEEEEE-S...SSS- CS
               Pyrid_oxidase_2 101 vsltGklekve.seekklaekcllsrHpdakkWlpgnsihkshfvkLeveeiylvgg...FGdr 160
                                   +++ Gk   v+ + e   + + ++++ p + + +++    +  ++k e ++ +++++   FG r
  gi|91773645|ref|YP_566337.1|  83 IQMEGKASFVTdEAELGQIFQLMVEKFPFMAELPNN---PDNVMIKVEPTKAFFLDYaveFGFR 143
                                   899999999986777777999999999999999999...8889999999999999985566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1062.92
//
Query:       gi|91773646|ref|YP_566338.1|  [L=431]
Description: PAS sensor protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-52  175.2   4.9    6.2e-17   61.7   0.2    3.2  3  PAS_3     PAS fold
    3.1e-16   59.4   3.5    6.5e-06   26.1   0.0    4.0  3  PAS       PAS fold
    5.4e-14   52.3   2.6    0.00016   21.9   0.0    3.3  3  PAS_9     PAS domain
    4.9e-11   42.8   0.1     0.0006   19.9   0.0    3.7  4  PAS_11    PAS domain
    1.3e-08   35.0   0.2      0.035   14.4   0.0    3.4  3  PAS_4     PAS fold
     0.0039   17.4   0.4         31    5.0   0.0    3.6  3  DUF3823   Protein of unknown function (DUF3823) N-terminal do
     0.0058   16.6   0.0       0.31   11.0   0.0    2.9  3  DUF4265   Domain of unknown function (DUF4265)
  ------ inclusion threshold ------
       0.16   11.7   0.2        4.5    7.1   0.0    2.6  3  VanY      D-alanyl-D-alanine carboxypeptidase
       0.31   11.7   6.2          4    8.1   0.1    4.1  4  LAMTOR    Late endosomal/lysosomal adaptor and MAPK and MTOR 
          1    9.1   3.7         11    5.7   0.1    3.1  3  NdhS      NAD(P)H dehydrogenase subunit S


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.2   3.4e-20   6.2e-17       3      89 .]      56     142 ..      54     142 .. 0.95
   2 !   58.9   0.1   2.5e-19   4.5e-16       3      89 .]     189     275 ..     187     275 .. 0.97
   3 !   55.8   0.1   2.4e-18   4.3e-15       3      89 .]     334     420 ..     332     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.4e-20
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   yvs++v ++ Gy+ e++++    ++d+v+ eD+e+v+++l+++  +g+  +++eyRi+  +G++rwv++r++  rdeng +
  gi|91773646|ref|YP_566338.1|  56 YVSANVTQL-GYTVEDFISGRLLYADIVYGEDLEQVERSLEKSRVEGKsFFDQEYRIVLESGDIRWVDERTYLQRDENGIV 135
                                   899999998.**********************************8888688****************************** PP

                         PAS_3  83 vrvigva 89 
                                   ++++g++
  gi|91773646|ref|YP_566338.1| 136 THYQGTI 142
                                   *****96 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 2.5e-19
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   y+s++v+++ Gys+e++      + dl+h +D + v+++l++  ++g  +y++eyR+++k Ge  wv +++++ rd ng++
  gi|91773646|ref|YP_566338.1| 189 YASPNVSRL-GYSAEDFVLGRIIYGDLIHQDDYNTVKDELDQRSEEGYdDYTQEYRLLTKAGELLWVNEKTFIKRDVNGNV 268
                                   899***999.**********9***************************9******************************** PP

                         PAS_3  83 vrvigva 89 
                                   ++++g++
  gi|91773646|ref|YP_566338.1| 269 THFQGIV 275
                                   *****96 PP

  == domain 3  score: 55.8 bits;  conditional E-value: 2.4e-18
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +vs+++   +Gy+ +++l+    + +++h +D+++v+ +l ++ ++g+  +  eyRi++++G++rwve+++++ r+++gk+
  gi|91773646|ref|YP_566338.1| 334 FVSDNIT-HFGYDVDDFLSGDILYGNIIHADDLPEVQLELSDICNEGGkMFVKEYRILTRSGDIRWVEEQTFIQRNDEGKV 413
                                   5667774.56**********88899*******************9999677****************************** PP

                         PAS_3  83 vrvigva 89 
                                   + ++gv+
  gi|91773646|ref|YP_566338.1| 414 TDYQGVI 420
                                   *****96 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   1.8e-06    0.0032       3     113 .]      28     145 ..      26     145 .. 0.86
   2 !   26.1   0.0   3.6e-09   6.5e-06       2     113 .]     164     278 ..     163     278 .. 0.92
   3 !   14.0   0.0     2e-05     0.037      33     113 .]     341     423 ..     338     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                   HHHHHHHSSSEEEEEE.....TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCC CS
                           PAS   3 lraileslpdpifvvD.....edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrage 76 
                                   l++i++++p+  f++      e  + ++  +a  ++lG++  + ++g+ l+ +i+  +d  ++ + le+ + +g+++ ++e
  gi|91773646|ref|YP_566338.1|  28 LERIIDHSPVIAFLWTadntpEEKWPVEYVSANVTQLGYTVeDFISGRLLYADIVYGEDLeQVERSLEKSRVEGKSFFDQE 108
                                   5778888777777777434444556666667777899****77799***********99999******************* PP

                                   EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                    ++ l  g +++++ r+   rd+ g ++++ g++ di
  gi|91773646|ref|YP_566338.1| 109 YRIVLESGDIRWVDERTYLQRDENGIVTHYQGTIFDI 145
                                   ********************************99776 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 3.6e-09
                                   HHHHHHHHSSSEEEEEETTSBEE..EECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEE CS
                           PAS   2 dlraileslpdpifvvDedgril..yvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageis 78 
                                   dl+ i++++ +++f++++d  +   y++++  +l G+s+ + vlg+ ++++++++dd+ +++++l q+ e+g +  ++e +
  gi|91773646|ref|YP_566338.1| 164 DLEDIINNSSTMVFLWRADEFWPadYASPNVSRL-GYSAeDFVLGRIIYGDLIHQDDYnTVKDELDQRSEEGYDDYTQEYR 243
                                   6788999999999999988887444999999886.7887699*************************************** PP

                                   EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                   + ++ g+  ++   +   rd  g++++f g+++di
  gi|91773646|ref|YP_566338.1| 244 LLTKAGELLWVNEKTFIKRDVNGNVTHFQGIVQDI 278
                                   **********************************8 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 2e-05
                                   HHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           PAS  33 llGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlr 111
                                    +G++  + ++g  l++ i++ dd  e++ +l+  +++g +   +e ++ +r g ++++e ++   r+ +g+++ + gv++
  gi|91773646|ref|YP_566338.1| 341 HFGYDVdDFLSGDILYGNIIHADDLpEVQLELSDICNEGGKMFVKEYRILTRSGDIRWVEEQTFIQRNDEGKVTDYQGVIQ 421
                                   7999998899**************9******************************************************** PP

                                   ES CS
                           PAS 112 di 113
                                   di
  gi|91773646|ref|YP_566338.1| 422 DI 423
                                   *8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.8e-06    0.0087      12     104 .]      53     147 ..      38     147 .. 0.81
   2 !   21.9   0.0   8.7e-08   0.00016      10     104 .]     183     280 ..     173     280 .. 0.79
   3 !   12.8   0.2   6.1e-05      0.11      19     104 .]     338     425 ..     321     425 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.8e-06
                         PAS_9  12 rilyaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltaspvkd 87 
                                   +++y++  + +l Gy+ e+++  +  + d++    e+ e +++ le  r    +++++e+ ++ ++g   wv+ + +  +d
  gi|91773646|ref|YP_566338.1|  53 PVEYVSANVTQL-GYTVEDFISGRllYADIV--YGEDLEQVERSLEKSRVegkSFFDQEYRIVLESGDIRWVDERTYLQRD 130
                                   567999999999.******999988778888..444444444444444446778*******************999999** PP

                         PAS_9  88 ddgelvgiivilrDite 104
                                   ++g ++++ +++ Dit+
  gi|91773646|ref|YP_566338.1| 131 ENGIVTHYQGTIFDITD 147
                                   ****************6 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 8.7e-08
                         PAS_9  10 dgril.yaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltasp 84 
                                   ++    ya++ + rl Gys+e+++  +  + dl+  ++++ +++++ l+q ++     +++e+ l +k ge +wv+ + + 
  gi|91773646|ref|YP_566338.1| 183 EFWPAdYASPNVSRL-GYSAEDFVLGRiiYGDLI--HQDDYNTVKDELDQRSEegyDDYTQEYRLLTKAGELLWVNEKTFI 260
                                   554555999999999.***999555555778888..666666666666666666999*****************9988777 PP

                         PAS_9  85 vkdddgelvgiivilrDite 104
                                    +d +g+++++ +i++Dit+
  gi|91773646|ref|YP_566338.1| 261 KRDVNGNVTHFQGIVQDITK 280
                                   7888**************95 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 6.1e-05
                         PAS_9  19 aalrllGyspeevlgks..itdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgi 95 
                                       + Gy+ +++l  +  + +++  ++ pe + +l+++ ++g  k + +e+ + +++g   wv+   +  ++d+g+++ +
  gi|91773646|ref|YP_566338.1| 338 NITHF-GYDVDDFLSGDilYGNIIhaDDLPEVQLELSDICNEGG-KMFVKEYRILTRSGDIRWVEEQTFIQRNDEGKVTDY 416
                                   55544.8999999988865566669999999************9.99******************777677799******* PP

                         PAS_9  96 ivilrDite 104
                                    ++++Dite
  gi|91773646|ref|YP_566338.1| 417 QGVIQDITE 425
                                   ********8 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   1.9e+02      38      94 ..      76     132 ..      60     143 .. 0.80
   2 !   19.9   0.0   3.4e-07    0.0006      35     107 ..     205     278 ..     194     284 .. 0.83
   3 ?    0.5   0.0      0.35   6.4e+02      18      62 ..     272     311 ..     261     313 .. 0.74
   4 !   15.5   0.0   7.6e-06     0.014      40     100 ..     356     416 ..     347     427 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                        PAS_11  38 rsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqk 94 
                                   +++ d++  +dl+++++ l++   + + +  + yR+ l+++++ +v  +++l ++++
  gi|91773646|ref|YP_566338.1|  76 LLYADIVYGEDLEQVERSLEKSRVEGKSFFDQEYRIVLESGDIRWVDERTYLQRDEN 132
                                   345589999999999999999996666777778********9999999988888766 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.4e-07
                        PAS_11  35 lvgrsiy.dLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneqdfimathtl 107
                                   ++gr+iy dL+h++d  t+k+ l +  ++  +  ++ yRL ++ ++ ++v+ k+ ++++ + n ++f  +++ +
  gi|91773646|ref|YP_566338.1| 205 VLGRIIYgDLIHQDDYNTVKDELDQRSEEGYDDYTQEYRLLTKAGELLWVNEKTFIKRDVNGNVTHFQGIVQDI 278
                                   456666659******************7777888888**********************999999987666655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.35
                        PAS_11  18 DtsaLrasfslglekeelvgrsi.ydLchpqdlstlkshlreviss 62 
                                           +++ ++k++++++ +  +L++++dl + k++l+ ++++
  gi|91773646|ref|YP_566338.1| 272 QG------IVQDITKQKVSEIALdEALVKQNDLLSRKQALETIVNH 311
                                   44......77888888888877635799***********9999965 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 7.6e-06
                        PAS_11  40 iydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneqdf 100
                                   + +++h +dl +++  l+++ ++ g+     yR+ ++++++ +v  ++ + +n + + +d+
  gi|91773646|ref|YP_566338.1| 356 YGNIIHADDLPEVQLELSDICNEGGKMFVKEYRILTRSGDIRWVEEQTFIQRNDEGKVTDY 416
                                   55899***********************************999999888888877776665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     2e-05     0.035      17     109 ..      54     149 ..      32     150 .. 0.80
   2 ?    4.4   0.0     0.025        45      20     109 ..     190     282 ..     170     283 .. 0.70
   3 !   12.8   0.0   5.9e-05      0.11      70     109 ..     388     427 ..     378     428 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                         PAS_4  17 vlyaNaaaaelfgappeell.Gktla.ellpeedaarleralrrvlegeepiefleelll..pgeerhyelrllPlrdesG 93 
                                   v+y++a+  + +g++ e+++ G+ l+ +++  ed +++er l++   ++++ +++e++    +g+ r+++ r +  rde+G
  gi|91773646|ref|YP_566338.1|  54 VEYVSANVTQ-LGYTVEDFIsGRLLYaDIVYGEDLEQVERSLEKSRVEGKSFFDQEYRIVleSGDIRWVDERTYLQRDENG 133
                                   6788888777.5555555541666669999999*********99988888888777766679***********999***** PP

                         PAS_4  94 evigvlvisrDiTerr 109
                                    v ++ +++ DiT+++
  gi|91773646|ref|YP_566338.1| 134 IVTHYQGTIFDITDQK 149
                                   *************987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.025
                         PAS_4  20 aNaaaaelfgappeellGktla.ellpeedaarleralrrvl.egeepiefleelll.pgeerhyelrllPlrdesGevig 97 
                                   a+++  +l+  + + +lG+  + +l  ++d   + + l++   eg + ++++  ll+  ge  +++   +  rd +G v +
  gi|91773646|ref|YP_566338.1| 190 ASPNVSRLGYSAEDFVLGRIIYgDLIHQDDYNTVKDELDQRSeEGYDDYTQEYRLLTkAGELLWVNEKTFIKRDVNGNVTH 270
                                   5555555555555555666666666666666666555444440444555555555559999999999999999******** PP

                         PAS_4  98 vlvisrDiTerr 109
                                   + +i++DiT ++
  gi|91773646|ref|YP_566338.1| 271 FQGIVQDITKQK 282
                                   *********876 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 5.9e-05
                         PAS_4  70 eelllpgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                    +l+++g+ r++e + +  r+++G+v ++ ++++DiTer+
  gi|91773646|ref|YP_566338.1| 388 RILTRSGDIRWVEEQTFIQRNDEGKVTDYQGVIQDITERK 427
                                   456679**********999********************7 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 ?    5.0   0.0     0.017        31      52      71 ..     103     125 ..     101     152 .. 0.77
   2 ?    4.0   0.0     0.035        63      54      85 ..     238     269 ..     237     274 .. 0.88
   3 ?    4.2   0.0     0.029        53      52      77 ..     381     405 ..     379     419 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                                   EE-SEEEEEEE-TT-SSB-...T CS
                       DUF3823  52 llFdGeYklvlkegegpfv...k 71 
                                    +Fd eY++vl++g+  +v   +
  gi|91773646|ref|YP_566338.1| 103 SFFDQEYRIVLESGDIRWVderT 125
                                   68****************94440 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.035
                                   -SEEEEEEE-TT-SSB-TT---EEEEESSSEE CS
                       DUF3823  54 FdGeYklvlkegegpfvkavdtievelkgntk 85 
                                   +  eY+l++k ge  +v+++  i+ +++gn++
  gi|91773646|ref|YP_566338.1| 238 YTQEYRLLTKAGELLWVNEKTFIKRDVNGNVT 269
                                   5679*************88888999****987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.029
                                   EE-SEEEEEEE-TT-SSB-TT---EE CS
                       DUF3823  52 llFdGeYklvlkegegpfvkavdtie 77 
                                   ++F  eY++++++g+  +v +++t  
  gi|91773646|ref|YP_566338.1| 381 KMFVKEYRILTRSGDIRWV-EEQTFI 405
                                   89*****************.555543 PP

>> DUF4265  Domain of unknown function (DUF4265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00017      0.31      57     113 ..      43     102 ..      22     105 .. 0.80
   2 ?    1.1   0.0      0.21   3.7e+02      86     113 ..     208     235 ..     187     238 .. 0.75
   3 ?   -0.0   0.0      0.46   8.2e+02      69     112 ..     335     379 ..     301     385 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                       DUF4265  57 lvdekaelge..sevreeLealgceveglsa.kllavdvpadvdleaikelLaeleeegv 113
                                    +d++ e++   + v +++++lg +ve +   +ll  d+    dle++++ L++ + eg+
  gi|91773646|ref|YP_566338.1|  43 TADNTPEEKWpvEYVSANVTQLGYTVEDFISgRLLYADIVYGEDLEQVERSLEKSRVEGK 102
                                   45555554448899*************99888**********************998886 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.21
                       DUF4265  86 kllavdvpadvdleaikelLaeleeegv 113
                                   +++  d   ++d++++k+ L++++eeg 
  gi|91773646|ref|YP_566338.1| 208 RIIYGDLIHQDDYNTVKDELDQRSEEGY 235
                                   55555677889***********999985 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.46
                       DUF4265  69 vreeLealgceveglsa.kllavdvpadvdleaikelLaeleeeg 112
                                   v ++++ +g +v+ +   ++l  ++   +dl +++  L ++ +eg
  gi|91773646|ref|YP_566338.1| 335 VSDNITHFGYDVDDFLSgDILYGNIIHADDLPEVQLELSDICNEG 379
                                   566666677777666666677777777777777766666654444 PP

>> VanY  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.9   5.2e+03      96     124 ..      41      69 ..      36      71 .. 0.70
   2 ?    7.1   0.0    0.0025       4.5      63     110 ..     133     180 ..     121     189 .. 0.86
   3 ?    1.7   0.0      0.11   2.1e+02      61     110 ..     264     320 ..     222     336 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.9
                                   HHHHHHGGGGTEEESS-TTGHHHHSS--- CS
                          VanY  96 kwlqknaakygFvlrypkgkeqetgvsyE 124
                                    w ++n ++  + + y + + ++ g++ E
  gi|91773646|ref|YP_566338.1|  41 LWTADNTPEEKWPVEYVSANVTQLGYTVE 69 
                                   57777777777777777777777777766 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0025
                                   TT-GGGGTSEEEEEEGGGTT.--SCGGGHCHHHHHHHHHGGGGTEEES CS
                          VanY  63 GaSeHhtGlaiDisdkeaeetkleesfeetkafkwlqknaakygFvlr 110
                                   G   H  G+ +Di+d++++e+  e++++++k  + + +n+  + F +r
  gi|91773646|ref|YP_566338.1| 133 GIVTHYQGTIFDITDQKNNEMLCEKALKKQKDLEDIINNSSTMVFLWR 180
                                   7778************99987669999999999999999998888876 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.11
                                   -TTT-GGGGTSEEEEEEGGGTT.--.......SCGGGHCHHHHHHHHHGGGGTEEES CS
                          VanY  61 lpGaSeHhtGlaiDisdkeaeetkl.......eesfeetkafkwlqknaakygFvlr 110
                                   + G+  H  G+  Di++++ +e  l       ++ +++++a + + ++++ + F ++
  gi|91773646|ref|YP_566338.1| 264 VNGNVTHFQGIVQDITKQKVSEIALdealvkqNDLLSRKQALETIVNHSPVVAFLWK 320
                                   578899************999988866666655556666666777777766666665 PP

>> LAMTOR  Late endosomal/lysosomal adaptor and MAPK and MTOR activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1       0.1   1.8e+02      26      47 ..      11      32 ..       2      34 .. 0.80
   2 ?    8.1   0.1    0.0022         4      15      52 ..     135     174 ..     122     176 .. 0.78
   3 ?    0.8   0.1      0.43   7.8e+02      33      48 ..     295     310 ..     284     312 .. 0.87
   4 ?   -2.3   0.0         4   7.2e+03      39      49 ..     368     378 ..     364     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
                        LAMTOR 26 qqqeqespekltdeqeaLnkIv 47
                                  ++ e++  ek++d++e L++I+
  gi|91773646|ref|YP_566338.1| 11 NRSEKSPLEKVLDRKEILERII 32
                                  677888899************7 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0022
                        LAMTOR  15 g..nysrgydnslqqqeqespekltdeqeaLnkIvqetsd 52 
                                      ++++ +d   q+++++  ek ++ q+ L++I+++ s+
  gi|91773646|ref|YP_566338.1| 135 VthYQGTIFDITDQKNNEMLCEKALKKQKDLEDIINNSST 174
                                   2346688899999***********************9876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.43
                        LAMTOR  33 pekltdeqeaLnkIvq 48 
                                   ++ l+ +++aL+ Iv+
  gi|91773646|ref|YP_566338.1| 295 QNDLLSRKQALETIVN 310
                                   5677899********8 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4
                        LAMTOR  39 eqeaLnkIvqe 49 
                                    q +L++I++e
  gi|91773646|ref|YP_566338.1| 368 VQLELSDICNE 378
                                   5889*****96 PP

>> NdhS  NAD(P)H dehydrogenase subunit S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.66   1.2e+03      12      30 ..     131     149 ..     129     151 .. 0.82
   2 ?    5.7   0.1    0.0063        11      17      31 ..     269     283 ..     261     286 .. 0.85
   3 ?    2.5   0.1     0.063   1.1e+02      17      30 ..     414     427 ..     403     429 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.66
                          NdhS  12 pkdiYygfeGlvQrvsdgk 30 
                                   ++ i   ++G +  ++d+k
  gi|91773646|ref|YP_566338.1| 131 ENGIVTHYQGTIFDITDQK 149
                                   5667789*****9999987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0063
                          NdhS  17 ygfeGlvQrvsdgka 31 
                                     f+G+vQ ++ +k+
  gi|91773646|ref|YP_566338.1| 269 THFQGIVQDITKQKV 283
                                   57**********998 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.063
                          NdhS  17 ygfeGlvQrvsdgk 30 
                                     ++G++Q +++ k
  gi|91773646|ref|YP_566338.1| 414 TDYQGVIQDITERK 427
                                   67********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.62
# Mc/sec: 2091.77
//
Query:       gi|91773647|ref|YP_566339.1|  [L=390]
Description: sodium/hydrogen exchanger [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  207.7  53.4      3e-61  207.3  53.4    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
        1.4    8.3  14.4      0.025   14.0   4.0    2.9  3  AveC_like       Spirocyclase AveC-like


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 !  207.3  53.4   3.4e-65     3e-61       2     375 ..       8     375 ..       4     378 .. 0.92

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 3.4e-65
                                   HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHC.TCGCCTGCCTHHHHHH CS
                Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGl.eldlrelrknlksill 81 
                                   +l++lla l+g +++r + p+i+g+++ G++lG  +    ++s e+l++l+e g i+llF aG+ e+++r+l++   ++ +
  gi|91773647|ref|YP_566339.1|   8 LLILLLAKLFGEIFERAGFPSILGELLSGMVLGILLIH--QES-EILKFLAEMGAIFLLFTAGYkEVHIRDLKESSAKASV 85 
                                   3444445555559**********************999..898.*******************978*************** PP

                                   HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHH CS
                Na_H_Exchanger  82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavl 162
                                   + l+++l+++ + G+++++   + +++le++++g+++s+t+++vv++il ++  ++++ g+++l  ++++D+++++ll+++
  gi|91773647|ref|YP_566339.1|  86 VTLVQILVAFSF-GVAIGV--YFHLSVLESIFIGVAFSPTSIGVVVRILIDMDYLSSKPGSMMLTSAIFDDIIGIFLLSIV 163
                                   ************.*****8..589********************************************************* PP

                                   HHHTX..XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHH CS
                Na_H_Exchanger 163 lalak..eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilga 241
                                   +++a+  +  +g+  l+ ll+ +++va++++l ++v++ l+  i ++  + +e+ +++v+++al++a+lae++g+++++ga
  gi|91773647|ref|YP_566339.1| 164 VTMATyeQFPSGVQVLIILLKMVAFVAIMFFLRKWVFSRLFDQIHKM--HVKESIFAFVIVIALFSAYLAEVFGLHAVIGA 242
                                   ******99999999999*****************************9..******************************** PP

                                   HHHHHHHHHHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSS CS
                Na_H_Exchanger 242 flaGlvlseyefsnk..lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllgl 320
                                   f+ G++ls++++++   ++ k+  +++g+f+p+fF+++G+sl++  l       ++ +l++v+ llg++l++fl +rl+g+
  gi|91773647|ref|YP_566339.1| 243 FIGGVMLSDVSHAKIehVQSKVTGLAYGFFVPIFFAFIGISLNIGTL---QTIGLFSVLVVVLALLGKLLGGFLGCRLIGF 320
                                   ********6666662226666**************************...5566666666666669*************** PP

                                   XHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHH CS
                Na_H_Exchanger 321 slrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlsl 375
                                   +  ++li+g+g  +r  v l+l+++g+  g++  e++++++++v ++++v +l l
  gi|91773647|ref|YP_566339.1| 321 DNYDSLIFGVGVMPRAGVELVLISIGKEMGIIGDEVFSAIVLMVAVSIFVSPLLL 375
                                   *************************************************555444 PP

>> AveC_like  Spirocyclase AveC-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2     0.064   5.7e+02     178     209 ..      74     105 ..      57     119 .. 0.64
   2 ?   14.0   4.0   2.8e-06     0.025     137     216 ..     166     243 ..     143     253 .. 0.89
   3 ?   -0.8   0.2     0.091   8.2e+02      87     132 ..     283     329 ..     260     334 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.064
                     AveC_like 178 drlrkgrakqalvrflavvavvnaayflygaa 209
                                     l+++ ak+++v+++ ++++++  +++   +
  gi|91773647|ref|YP_566339.1|  74 RDLKESSAKASVVTLVQILVAFSFGVAIGVYF 105
                                   55666666666777766666665433332223 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.8e-06
                     AveC_like 137 aGtkyQfP.iYealavglvmvalavllyfrDdrGrtvvekgadrlrkgrakqalvrflavvavvnaayflygaaylvvklv 216
                                     t+ QfP   + l++ l mva+ ++++f     + v  ++ d+++k  +k+++  f+ v+a+++a ++ +++ ++v+ ++
  gi|91773647|ref|YP_566339.1| 166 MATYEQFPsGVQVLIILLKMVAFVAIMFFL---RKWVFSRLFDQIHKMHVKESIFAFVIVIALFSAYLAEVFGLHAVIGAF 243
                                   56888***9899*************99975...57899**************************************99765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.091
                     AveC_like  87 karwplisplrLiavvlvigfvldlilealvlvr.lGlyiYsqvips 132
                                   +   + +++++L  v++v+  +l  +l +++++r +G++ Y   i +
  gi|91773647|ref|YP_566339.1| 283 SLNIGTLQTIGLFSVLVVVLALLGKLLGGFLGCRlIGFDNYDSLIFG 329
                                   44567788889999999999888888888888874588888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2581.01
//
Query:       gi|91773648|ref|YP_566340.1|  [L=163]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-22   79.9   3.2    3.3e-11   43.4   0.4    2.2  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 !   43.4   0.4   1.9e-15   3.3e-11       1      55 [.      26      80 ..      26      82 .. 0.93
   2 !   37.2   0.1   1.6e-13   2.9e-09       2      55 ..     104     156 ..     103     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.9e-15
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                  ++d+mt+d+vt+++++++ ++l+++ +++++ +PVV+ed+ lvG + +  +l+ l
  gi|91773648|ref|YP_566340.1| 26 IKDFMTKDLVTISENDSIDQVLDTFDKYHFHTYPVVNEDNVLVGTIDQNIILKIL 80
                                  68***********************9888*****************998888876 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 1.6e-13
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   + im + +v+++p++tl + ++++ +++++r+++V edg lvG++ + D+++ +
  gi|91773648|ref|YP_566340.1| 104 KTIMIPHPVSISPNETLCDTADMILKHKIDRFCIV-EDGILVGMICKPDIIKEV 156
                                   679********************88**********.9**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1131.85
//
Query:       gi|91773649|ref|YP_566341.1|  [L=440]
Description: cobalt ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-32  113.5   0.0    1.8e-32  112.7   0.0    1.4  1  ABC_tran     ABC transporter
    4.7e-12   46.3   1.1    1.1e-06   28.6   0.0    2.6  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.8e-07   29.8   0.1    1.1e-06   28.3   0.1    1.6  1  SMC_N        RecF/RecN/SMC N terminal domain
    8.2e-05   22.5   1.2     0.0016   18.3   0.1    2.2  2  AAA_15       AAA ATPase domain
     0.0015   18.3   0.3      0.003   17.2   0.3    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.037   13.9   0.1    1.6  1  RsgA_GTPase  RsgA GTPase
      0.019   15.4   0.6       0.04   14.4   0.4    1.6  1  AAA_23       AAA domain
        0.1   12.1   0.1       0.23   11.0   0.1    1.5  1  AAA_7        P-loop containing dynein motor region
       0.11   12.5   0.0        0.3   11.2   0.0    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
       0.21   10.8   0.1        0.5    9.6   0.0    1.5  2  DUF2813      Protein of unknown function (DUF2813)


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 !  112.7   0.0   9.9e-36   1.8e-32       1     136 [.      19     166 ..      19     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 9.9e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpeltvr 77 
                                   lk +++k+k+g+k+a+vG+nG+GKStL++ll g lkp+eG++++ gk++++  ++l++ rk++g+++q+  +q+f  + v+
  gi|91773649|ref|YP_566341.1|  19 LKGIDVKIKKGKKIAFVGKNGSGKSTLFMLLNGTLKPKEGTVHFHGKPMEYdsKSLREIRKSVGIVFQNsdDQIFAPT-VY 98 
                                   7899***********************************************9999**************888888887.66 PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   +              e de +ek l+ +g++e+++++     ++LSgGqk+rva+a +   +p++++lDEp 
  gi|91773649|ref|YP_566341.1|  99 QDvgfgptnlghskeEVDELVEKTLEYIGITEFRNKPP----HHLSGGQKKRVAIAGVCSMEPEVMILDEPL 166
                                   667********765444445999999******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 !   15.7   0.2   5.5e-06    0.0098       3      21 ..      33      51 ..      32     100 .. 0.73
   2 !   28.6   0.0   6.4e-10   1.1e-06     230     301 ..     132     200 ..      96     201 .. 0.85
   3 ?   -3.0   0.0       2.7   4.9e+03     165     196 ..     244     275 ..     230     289 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                        AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                  +++G+NgsGKS+L+ +l +
  gi|91773649|ref|YP_566341.1| 33 AFVGKNGSGKSTLFMLLNG 51
                                  68*************9954 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 6.4e-10
                        AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                   ++ p+++lS G+k+  a++  +   +    + ++DEp ++L+P    ++l+ll+el++n++  i++TH+ +l
  gi|91773649|ref|YP_566341.1| 132 RNKPPHHLSGGQKKRVAIAGVCSMEP---EVMILDEPLANLDPVGADEILDLLNELNQNNTTMIISTHDVEL 200
                                   55589*******************99...9**************************************9776 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.7
                        AAA_21 165 rigllnifadyfgfakekrllqrlvrslklve 196
                                   +i +    +++++ +k ++ + +lv+slk++e
  gi|91773649|ref|YP_566341.1| 244 EIYNELERRNLATRNKFPKSVPELVHSLKPPE 275
                                   44444555566666666666666666666655 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 !   28.3   0.1   5.9e-10   1.1e-06      27     200 ..      32     199 ..      14     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.9e-10
                                   EEEEESTTSSHHHHHHHHHHHCTT.TTT.TTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  27 taivGpNGSGKsnlldAilFvLGersak.klrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrk 106
                                    a vG+NGSGKs l+  +  +L  ++ + ++  + +     + +++ +  + +v i+f+n+d+++   +    +     + 
  gi|91773649|ref|YP_566341.1|  32 IAFVGKNGSGKSTLFMLLNGTLKPKEGTvHFHGKPM----EYDSKSLREIRKSVGIVFQNSDDQIFAPTVYQDVGFGPTNL 108
                                   5679*********99888777765544113333333....3346666667789***********88888888899999999 PP

                                   SEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 107 geseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                   g+s+ ++++   +  e+  + e  +  ++ LSgG+k+ va+a +    +++p+ +++lDe  a+LD     ++ +ll+e +
  gi|91773649|ref|YP_566341.1| 109 GHSKEEVDELVEKTLEYIGITEFRNKPPHHLSGGQKKRVAIAGV---CSMEPE-VMILDEPLANLDPVGADEILDLLNELN 185
                                   999*****9999999999999999999**************977...556676.5699********************998 PP

                                   TT.SEEEEE-SSHH CS
                                   xx.xxxxxxxxxxx RF
                         SMC_N 188 kn.aQfivislree 200
                                   +n + +i+ +++ e
  gi|91773649|ref|YP_566341.1| 186 QNnTTMIISTHDVE 199
                                   88355555555544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   8.6e-07    0.0016      15      83 ..      20      85 ..      17     132 .. 0.71
   2 ?    3.1   0.1     0.036        64     325     365 ..     158     197 ..     154     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.6e-07
                        AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83
                                  k +++++++     ++GkN+sGKS++ ++l+  l+ k    + ++ +  + +e+  +  ++++  + + f
  gi|91773649|ref|YP_566341.1| 20 KGIDVKIKKGkKIAFVGKNGSGKSTLFMLLNGTLKPK----EGTVHFHGKPMEYDSKSLREIRKSVGIVF 85
                                  5566666666699*****************8777777....55555555555555555555555555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.036
                        AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    + +++EP a+L p    ++ +ll el ++n    ii+TH 
  gi|91773649|ref|YP_566341.1| 158 EVMILDEPLANLDPVGADEILDLLNELNQNNT-TMIISTHD 197
                                   567899********************988886.9******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 !   17.2   0.3   1.7e-06     0.003      16      39 ..      23      46 ..      16      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                        AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                  +++i+ kg  + ++G++GsGKSTl+
  gi|91773649|ref|YP_566341.1| 23 DVKIK-KGkKIAFVGKNGSGKSTLF 46
                                  67777.44599************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.1e-05     0.037      88     130 ..      17      60 ..       3      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                                   TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                   ++l+ +  ++k+ k +++vG+ G GKStL   l+++l+ k g v
  gi|91773649|ref|YP_566341.1|  17 QALKGIDVKIKKgKKIAFVGKNGSGKSTLFMLLNGTLKPKEGTV 60 
                                   566777788888799***************99999887766655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   2.3e-05      0.04      22      42 ..      32      52 ..      15     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                        AAA_23 22 tlItGpNGaGKTTildAikla 42
                                   +++G+NG+GK+T++  +   
  gi|91773649|ref|YP_566341.1| 32 IAFVGKNGSGKSTLFMLLNGT 52
                                  579***********9877655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00013      0.23      28      62 ..      24      58 ..      16      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                         AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldkeky 62
                                    +k++k++ +vG+ G+GK+++ + l  +l++++ 
  gi|91773649|ref|YP_566341.1| 24 VKIKKGKKIAFVGKNGSGKSTLFMLLNGTLKPKEG 58
                                  56899****************99988888876665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017       0.3       1      22 [.      31      52 ..      31      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                  EEEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  1 evaivGrpNvGKStLinaltge 22
                                  ++a+vG+  +GKStL+  l g+
  gi|91773649|ref|YP_566341.1| 31 KIAFVGKNGSGKSTLFMLLNGT 52
                                  69**************988765 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00028       0.5      23      83 ..      30      90 ..      19     102 .. 0.89
   2 ?   -2.6   0.1       1.4   2.5e+03     286     312 ..     159     185 ..     154     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                       DUF2813 23 entvLiGENaWGKSSLldALslilnvekelyqFtlkDFhvdeseeeeqekhlqlvltfkee 83
                                  ++ +++G N  GKS L+  L   l++++   +F+ k    d+++ +e +k++ +v+  +++
  gi|91773649|ref|YP_566341.1| 30 KKIAFVGKNGSGKSTLFMLLNGTLKPKEGTVHFHGKPMEYDSKSLREIRKSVGIVFQNSDD 90
                                  57789**********************************9*99999999999999986655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                       DUF2813 286 illlEdpearLHPtmlaiaWellellP 312
                                   +++l++p a+L P+    + +ll+ l 
  gi|91773649|ref|YP_566341.1| 159 VMILDEPLANLDPVGADEILDLLNELN 185
                                   8999*********99999988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2617.32
//
Query:       gi|91773650|ref|YP_566342.1|  [L=260]
Description: cobalt ABC transporter CbiQ, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-39  134.4  11.6    6.8e-39  133.7  11.6    1.2  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
          5    7.6  12.1        1.5    9.3   5.3    2.7  2  DUF4212   Domain of unknown function (DUF4212)


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 !  133.7  11.6   7.5e-43   6.8e-39      12     211 ..      21     221 ..      11     224 .. 0.96

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 7.5e-43
                                   HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE.......EECTTEEE.. CS
                          CbiQ  12 vkliwlfllllalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillfqlittegefvfaggg.q 89 
                                   +k +++ + +l+ v +++++ +  i+  + ++ +  +++  ++++ +l+ p  f ll+++i++f++ + ++ f f++++ +
  gi|91773650|ref|YP_566342.1|  21 LKIAIVGFGVLVGVSSQSFIPPFAIALCMSFTTVYFGKTslKFYLTILSAPAVFVLLSVIIIAFFFGSGTEIFGFNIFNyH 101
                                   67888888999999999999999999999999999999999***********************9999************* PP

                                   ..E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT CS
                          CbiQ  90 isitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikqAqklRlgd 170
                                   +++++ Gl  +ll++ R+l+ +s+l++lalTTp+ el+s l+  + P+ +++i + +yR+if++le +  ik+Aq+ Rlg+
  gi|91773650|ref|YP_566342.1| 102 LGVNTGGLDMALLVFSRTLSGMSCLFFLALTTPMVELFSVLKATKLPDSFIEISMMMYRYIFVFLEVAWGIKYAQTVRLGY 182
                                   ********************************************************************************* PP

                                   S..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                          CbiQ 171 sklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                   +   +r  l+sl++l  +lf+r+++++e++ ++m aR+Y+g
  gi|91773650|ref|YP_566342.1| 183 K--DWRTALNSLAMLSTTLFIRSWEQGEKIFISMSARCYDG 221
                                   *..*************************************9 PP

>> DUF4212  Domain of unknown function (DUF4212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.3   0.00016       1.5      14      64 ..      29      80 ..      15      87 .. 0.82
   2 ?    1.4   0.5     0.048   4.3e+02      56      71 ..     243     258 ..     239     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                       DUF4212 14 ilLviWfvvsfg..lgillaeelntirtflgfplgFwfaaqgsilvfvvlifv 64
                                   +Lv     sf+  ++i l  ++ t+  f+   l F+++   ++ vfv+l ++
  gi|91773650|ref|YP_566342.1| 29 GVLVGVSSQSFIppFAIALCMSFTTV-YFGKTSLKFYLTILSAPAVFVLLSVI 80
                                  45666666678888899999******.6*********************9886 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.048
                       DUF4212  56 lvfvvlifvYalrmdr 71 
                                   + +vvl+++Y  r++ 
  gi|91773650|ref|YP_566342.1| 243 YFAVVLVLWYLTRINS 258
                                   6789999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1543.93
//
Query:       gi|91773651|ref|YP_566343.1|  [L=99]
Description: cobalt transport binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   88.2   0.9    7.6e-25   86.7   0.9    1.6  1  CbiN      Cobalt transport protein component CbiN


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 !   86.7   0.9   4.2e-29   7.6e-25       3      67 .]       5      79 ..       4      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 4.2e-29
                          CbiN  3 lllllvvllavvplflv....kgaeFgGaDdqaeevIeeiapdyep.....wfepl.weppsGEiESlLFalQAA 67
                                  +++ ++v+l++++++++    +++eFgGaD+qa +vI+ei++dy+p     w++++ +epp+GE+ESlLF+lQAA
  gi|91773651|ref|YP_566343.1|  5 VIFGVIVVLFMASFMYGiaanPDSEFGGADGQAGDVITEIDSDYQPwtedsWINSIkFEPPGGETESLLFGLQAA 79
                                  57899***********999999999*********************8888888999******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 628.87
//
Query:       gi|91773652|ref|YP_566344.1|  [L=231]
Description: cobalt transport protein CbiM [Methanococcoides burtonii DSM 6242]
Scores for 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-52  179.0  22.1    1.2e-52  178.8  22.1    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 !  178.8  22.1   6.5e-57   1.2e-52       1     206 [.       2     210 ..       2     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 6.5e-57
                          CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaaiLlGp 79 
                                   Hi +g+L+++++ ++++ +++++ ++++rl+k ++e+r  +plla+++afif+++++++p  +g+s+H++g+++aaiL+Gp
  gi|91773652|ref|YP_566344.1|   2 HIFEGFLPSPWWQLWFVFSIPVIFFGMYRLNKLVSEKRelLPLLAVAGAFIFVLSSLKMPSVTGSSSHPTGTGMAAILFGP 82 
                                   9********************************9988889***************************************** PP

                          CbiM  80 waaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaallvalel 160
                                   ++a++  ++vll qa+++++GG+t+LGaN+ +m++ig+++ay++y++  +    + +  + +fla++++ +++++++a +l
  gi|91773652|ref|YP_566344.1|  83 AIAAVLSLIVLLYQAIFLAHGGLTTLGANVASMGIIGPVFAYVIYKAGMKA---NINFYVVVFLATAFADWATYVVTATQL 160
                                   **********************************************76444...6899*********************** PP

                          CbiM 161 alsgleas.....lsltaalaamllvhlpvgilEgviTaaivkalkkvrpe 206
                                   al+  + +     +sl+a+l +++++++p++i+Eg++Ta+i+k++ +v+++
  gi|91773652|ref|YP_566344.1| 161 ALAFPA-EvggvaASLKAFLLVFATTQVPLAIMEGALTALIFKYIIQVKSD 210
                                   ***554.34789999999999999***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1454.83
//
Query:       gi|91773653|ref|YP_566345.1|  [L=340]
Description: cobalt-precorrin-6A synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  170.4   3.4    6.5e-50  169.8   3.4    1.3  1  CbiD         CbiD
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.19   11.8   0.0    1.5  1  sCache_like  Single Cache-like
       0.13   12.6   0.2       0.46   10.9   0.0    1.9  2  Rep_fac-A_3  Replication factor A protein 3


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 !  169.8   3.4   1.1e-53   6.5e-50       1     242 [.      45     273 ..      45     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 1.1e-53
                          CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee.aavikdaGddpDvTngaeivaeve.. 78 
                                   l++GyTtG++A+ AakaA+l l  ++++++v++ +p g +++++++     + + +av+ +   + D+T+g+e va+    
  gi|91773653|ref|YP_566345.1|  45 LKRGYTTGTTATVAAKAAVLSL--KKEIDHVSVPTPVGLRAHMDVKAK---DGHaVAVKLNNDHESDITRGLEFVARAVes 120
                                   589*******************..8889****************6543...334266777777789********9997779 PP

                          CbiD  79 eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleea.kegvevtisvpeGeelAkkTlNprlGivgGiSi 158
                                   ++i+i++GeG+G+vt+ gL+ + g +AInp p ++i e+v e++ee   +g++v+is+p+G+e+Ak+TlN r+G++gGiSi
  gi|91773653|ref|YP_566345.1| 121 DKITITAGEGIGIVTRGGLQSKKGYPAINPRPMQQIMEAVVEAVEEIgIKGASVEISLPRGAEIAKQTLNGRIGVEGGISI 201
                                   88******************************************999877******************************* PP

                          CbiD 159 LGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvsnfvgealeeaaekgvkkvll 239
                                   LGTtG vep+ +  +l +++++l      +  ++vl+tG++g ++ +    +p+ ++v  +  + e +e a+     kv +
  gi|91773653|ref|YP_566345.1| 202 LGTTGFVEPWND--HLGEMKSDLIR----DAAKVVLTTGRIGIRYSTM--LFPDYTVVLAGSRISEFMESAT----GKVAI 270
                                   *********864..45555555554....4556***********9987..6899999999988888888775....34555 PP

                          CbiD 240 vgh 242
                                   +g 
  gi|91773653|ref|YP_566345.1| 271 CGL 273
                                   555 PP

>> sCache_like  Single Cache-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.2e-05      0.19      40      62 ..     316     338 ..     285     340 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                                   HHHHT-EEEEEETTS-EEEETTS CS
                   sCache_like  40 sekldaritivdadgkvlydtgq 62 
                                   ++  +ari++vd+dg+vl d+g+
  gi|91773653|ref|YP_566345.1| 316 EKGKGARIVVVDRDGTVLMDSGE 338
                                   344579***************98 PP

>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.7e-05      0.46      38      76 ..      87     125 ..      81     134 .. 0.86
   2 ?   -2.7   0.0       1.3   7.8e+03      57      78 ..     152     173 ..     146     176 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.7e-05
                                   EE-TTS-EEEEEESS--SS---SEEEEEEEE-TTS-EEE CS
                   Rep_fac-A_3  38 lqstdggsvtvrlsedstleiskwvEvvGkvsddlgirl 76 
                                   ++++dg+ v v+l++d + +i++ +E+v ++ + ++i +
  gi|91773653|ref|YP_566345.1|  87 VKAKDGHAVAVKLNNDHESDITRGLEFVARAVESDKITI 125
                                   67899**************************99666633 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                   ---SEEEEEEEE-TTS-EEEEE CS
                   Rep_fac-A_3  57 eiskwvEvvGkvsddlgirlds 78 
                                    +++++E v  + ++ gi  +s
  gi|91773653|ref|YP_566345.1| 152 PMQQIMEAVVEAVEEIGIKGAS 173
                                   4566777777777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2357.03
//
Query:       gi|91773654|ref|YP_566346.1|  [L=603]
Description: DNA mismatch repair protein MutL [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  124.2   0.0    3.5e-36  123.5   0.0    1.3  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    2.4e-36  124.7   0.0    4.4e-36  123.8   0.0    1.4  1  MutL_C          MutL C terminal dimerisation domain
    7.8e-12   45.2   0.2    2.1e-11   43.8   0.2    1.7  2  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.9e-09   38.0   0.0    5.9e-09   36.4   0.0    1.9  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0   7.8e-40   3.5e-36       3     118 ..     216     331 ..     214     332 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 7.8e-40
                                   HHHHHHHHCCEEEEEEEETTEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEEEEEES CS
                DNA_mis_repair   3 avlgkevaenlleiekeeeqlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvLnleid 83 
                                    +lg ++a++++++e +++ ++i+G+iskpe++rs +d+qf+f+NgR v+s+++++a+r +Y +l+pkgrypv+vL le+d
  gi|91773654|ref|YP_566346.1| 216 YLLGVDIAKKIVPVEFRSDIVNISGYISKPEVTRSGTDQQFFFINGRGVSSTSISNAVRLGYYNLIPKGRYPVAVLDLELD 296
                                   57899**************************************************************************** PP

                                   SGGEE-TSSTT----EETTHHCHHHHHHHHHHHHH CS
                DNA_mis_repair  84 peevDvNvhPtKreVrfqdeeevieaieealkeal 118
                                    +evDvNvhP+Kr Vr+++e+ev +a+  a+++al
  gi|91773654|ref|YP_566346.1| 297 LREVDVNVHPAKRYVRLSHEREVSDAVILAVENAL 331
                                   *******************************9998 PP

>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   9.9e-40   4.4e-36       4     144 ..     418     556 ..     416     558 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 9.9e-40
                                   EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHCT-EEE CS
                        MutL_C   4 kalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLaklGfele 84 
                                   +++gqv++ yi++e e g+++vDqhaAher++ye+++    +     Q+L++P+ l+l+++e  ll+e+  +L+++Gf ++
  gi|91773654|ref|YP_566346.1| 418 RIVGQVNELYIIVEFEGGIMIVDQHAAHERVMYEQIRDGNSS---GWQELITPVMLDLTSKEKVLLDEYIPLLEEMGFAIS 495
                                   579**********************************87777...89********************************** PP

                                   E-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS.-H-HCCHHHHHHHHCTTSSSSSS CS
                        MutL_C  85 efgpnslivravPallrqqnleelirelleelaekgk.esleekleellatmachssvkag 144
                                   efgpns++v+++P+ll++ + +eli++++ ++ + gk ++ +   + l++tmac++++kag
  gi|91773654|ref|YP_566346.1| 496 EFGPNSFVVTSIPSLLGKLENTELIHDIIMDVLSSGKvKRDTGMFDSLCKTMACRAAIKAG 556
                                   *************************************855799****************97 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 !   43.8   0.2   4.8e-15   2.1e-11       4     101 ..      30     127 ..      26     142 .. 0.80
   2 ?   -3.7   0.0       2.2     1e+04      41      57 ..     260     276 ..     260     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4.8e-15
                   HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeak....rkstslGkkGiGlklA 80 
                                    +++ elvdN++dA a+++ +ev      t+ i+++D+G+Gm++e+ + a++ + +sk a+    ++  +lG +G    l+
  gi|91773654|ref|YP_566346.1|  30 ASVVKELVDNAIDAGATEIRVEVVAA--GTELITVTDNGSGMPREDAILAFTKHGTSKIAQiedlEEVLTLGFRGEA--LS 106
                                   689**********************7..4799***************999987777777663322345558888755..99 PP

                   HATPase_c_3  81 slslgkkltvitkkegesstl 101
                                   s+   +++ ++t+++ e   +
  gi|91773654|ref|YP_566346.1| 107 SIAAVARVYLTTRQKKEIAGT 127
                                   999999999999988776644 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
                   HATPase_c_3  41 dGkGmseeelknalrla 57 
                                   +G G+s   + na rl+
  gi|91773654|ref|YP_566346.1| 260 NGRGVSSTSISNAVRLG 276
                                   899*****999999886 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 !   36.4   0.0   1.3e-12   5.9e-09       5      63 ..      28      83 ..      24     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.3e-12
                                  HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH CS
                     HATPase_c  5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq 63
                                  r   ++++lvdNa+++   a+ei+ve+ a  ++  i+v+DnG G+p+ed  + f+k+ +
  gi|91773654|ref|YP_566346.1| 28 RPASVVKELVDNAIDA--GATEIRVEVVAA-GTELITVTDNGSGMPREDAILAFTKHGT 83
                                  56689**********6..799999999954.599********************98888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3848.54
//
Query:       gi|91773655|ref|YP_566347.1|  [L=887]
Description: DNA mismatch repair protein MutS [Methanococcoides burtonii DSM 6242]
Scores for complete 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-85  284.0   0.2    1.1e-84  283.2   0.2    1.4  1  MutS_V    MutS domain V
    2.7e-43  146.8   0.0    6.7e-43  145.5   0.0    1.7  1  MutS_I    MutS domain I
    5.7e-42  144.1   0.2    1.4e-41  142.8   0.0    1.8  2  MutS_III  MutS domain III
    2.3e-30  104.8   0.3    1.1e-29  102.6   0.1    2.2  2  MutS_IV   MutS family domain IV
    6.5e-26   91.2   0.0    4.5e-25   88.5   0.0    2.3  2  MutS_II   MutS domain II
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.053   13.1   0.0    1.4  1  AAA_27    AAA domain
      0.061   13.1   0.0       0.13   12.1   0.0    1.6  1  AAA_29    P-loop containing region of 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 !  283.2   0.2   4.3e-88   1.1e-84       1     188 []     622     811 ..     622     811 .. 0.97

  Alignments for each domain:
  == domain 1  score: 283.2 bits;  conditional E-value: 4.3e-88
                                   EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSEE CS
                        MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatekslv 81 
                                   llitGpnmaGksty+rqv+liv++aq Gsfvpa++a+i+ivd++ftRvga Ddla+g+stFmvEm+E+a+il+nat kslv
  gi|91773655|ref|YP_566347.1| 622 LLITGPNMAGKSTYMRQVSLIVIMAQAGSFVPASHASIGIVDRVFTRVGAFDDLASGQSTFMVEMVELANILNNATPKSLV 702
                                   58******************************************************************************* PP

                                   EEESTS-SS-HHHHHHHHHHHHHHHHHT..T--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEEES--SS CS
                        MutS_V  82 ilDElGRGtstydGlaialavaeyllek..ikaktlfatHyheltklaekleevknlhlavkeeeedivflykvkegaaek 160
                                   +lDE+GRGtstydG++ia+av+ey+++k  +  ++lfatHyh+lt+++++l++vkn+h+avke+ +d+vfl+k+ +ga++k
  gi|91773655|ref|YP_566347.1| 703 LLDEIGRGTSTYDGYSIAKAVVEYIHNKgrVGVRSLFATHYHQLTNISSSLKRVKNYHIAVKEDGDDLVFLRKIVPGATDK 783
                                   **************************872256799********************************************** PP

                                   --HHHHHHHTT--HHHHHHHHHHHHHTT CS
                        MutS_V 161 syGikvaklaglPesvverArevlkele 188
                                   syGi+va+lag+P++v +rA+evl+++e
  gi|91773655|ref|YP_566347.1| 784 SYGIHVARLAGVPHKVTQRAKEVLQDIE 811
                                   ***********************99875 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.0   2.6e-46   6.7e-43       1     112 [.       5     117 ..       5     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 2.6e-46
                                   HHHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC..EEEEEEEHHHHHHHHHHHHHTT-EE CS
                        MutS_I   1 tplmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkksseke.ipmagvPehalekylrkLvekgykV 80 
                                   tp mkqy + kk++ da++ffr+GdfYe fgeDA+i+a+eleitlt+r+k+ e e +p ag+P+hal++yl +L++kgykV
  gi|91773655|ref|YP_566347.1|   5 TPAMKQYYDAKKQHSDALIFFRMGDFYESFGEDAKIIAKELEITLTTRGKDIEGEkMPLAGIPYHALDNYLPRLIKKGYKV 85 
                                   89**********************************************98877777************************* PP

                                   EEEEE-S-HHHHS.S--EEEEEEEBTTC-TTS CS
                        MutS_I  81 avveqtetpaekkgvvkrevvrviTpGtltde 112
                                   a++eq e+p+++kg++kr vvrv+TpGt +d 
  gi|91773655|ref|YP_566347.1|  86 AICEQLEDPKKAKGIIKRGVVRVVTPGTAIDT 117
                                   ****************************9985 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       5.2   1.3e+04      99     120 ..     187     208 ..     161     224 .. 0.53
   2 !  142.8   0.0   5.6e-45   1.4e-41       2     191 .]     276     570 ..     275     570 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.2
                                   HHHHHHHHHHTTTTT---SSTH CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                      MutS_III  99 allealkaleelvallekekla 120
                                   +l+e lk+l+ lv+  ++e  +
  gi|91773655|ref|YP_566347.1| 187 RLVERLKELNVLVQGFKDEAFD 208
                                   2555666655555555554443 PP

  == domain 2  score: 142.8 bits;  conditional E-value: 5.6e-45
                                   HHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT---HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                      MutS_III   2 TlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrrlpDle 81 
                                   TlrnLei++n rg++++ s+l+vld T T+mG RlL++wll+Pl+++++I++Rlda e+  ++++lr ++r+ l  ++D+e
  gi|91773655|ref|YP_566347.1| 276 TLRNLEIVKNVRGEGNDTSILKVLDDTNTPMGGRLLQKWLLKPLINVDSIDHRLDALEClANDTMLRFDVRSHLSFVKDIE 356
                                   9*********99998899*****************************************88999***************** PP

                                   HHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH...........HHHH...HHHHHHB-SS--SSGGGS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxx...xxxxxxxxxxxxxxxxxxxx RF
                      MutS_III  82 Rllsrislgkakardlkallealkaleelvallekeklaesee...........esla...elleeaideeplalekeged 148
                                   Rl+ r+ +g+++ardl al ++l +++++v+ ++++    +e            e+l+   +l+++ai++ep+ + +eg+ 
  gi|91773655|ref|YP_566347.1| 357 RLIGRVVYGNSNARDLIALKRSLGSVPQIVESMGDDP--GCEMlinirdgllgfEQLEnivKLIDDAIVDEPPVSVREGGM 435
                                   ******************************9996553..3555999*99999995555566******************** PP

                                   B-T.............................................................................. CS
                                   xxx.............................................................................. RF
                      MutS_III 149 lra.............................................................................. 151
                                   +r                                                                               
  gi|91773655|ref|YP_566347.1| 436 IRSgynekldelkgmstggktwiasfqqkerdrtgikslkvgynrvfgyyieitksniaqipddyirkqtmrnaerfytpe 516
                                   ********************************************************************************* PP

                                   ..............HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                   ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MutS_III 152 ..............iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                 i+ale+elf e+ +++++++++l+r+a ++ +LD+ +SlA
  gi|91773655|ref|YP_566347.1| 517 lkewedvilsadekITALENELFTEITSRIASHASDLQRIAVLIGQLDCTASLA 570
                                   **************9**************************************9 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.96   2.5e+03      54      91 ..     167     204 ..     163     205 .. 0.75
   2 !  102.6   0.1   4.2e-33   1.1e-29       1      91 [.     439     529 ..     439     530 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.96
                                   CCTTT.--SEEEEEECTCEEEEECCCHHHHHHHHHHHHH CS
                       MutS_IV  54 eakkv.pkefirlqtlknseryttaelkkleaelleaee 91 
                                   ea +  p+e i+  t+++ er  +++lk+l+  ++ +++
  gi|91773655|ref|YP_566347.1| 167 EAARMrPSECIISRTMFSDER-LVERLKELNVLVQGFKD 204
                                   444443779999999999999.57999999999888776 PP

  == domain 2  score: 102.6 bits;  conditional E-value: 4.2e-33
                                   TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECCCHHH CS
                       MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknseryttaelkk 81 
                                   g++e+Ldel+ + ++ ++++++ ++ker ++gikslkv+yn+v+Gyy+e+t+s+  ++p+++ir+qt+ n+er++t+elk+
  gi|91773655|ref|YP_566347.1| 439 GYNEKLDELKGMSTGGKTWIASFQQKERDRTGIKSLKVGYNRVFGYYIEITKSNIAQIPDDYIRKQTMRNAERFYTPELKE 519
                                   89******************************************************************************* PP

                                   HHHHHHHHHH CS
                       MutS_IV  82 leaelleaee 91 
                                    e+ +l+a e
  gi|91773655|ref|YP_566347.1| 520 WEDVILSADE 529
                                   ***9999876 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.0   1.8e-28   4.5e-25       1     136 [.     126     258 ..     126     259 .. 0.96
   2 ?   -0.8   0.0      0.65   1.7e+03      44      79 ..     328     363 ..     327     373 .. 0.87

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1.8e-28
                                   -EEEEEEEETTTSEEEEEEEETTTTEEEEEEEEE...-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEEE CS
                       MutS_II   1 nylaAisekregrrvGlafiDlstgefvvsefed...feeleaeLsrlsPkElllpedlsestaeeessklrelrsrvgvr 78 
                                   nyl++is    +  +G++f+D+stgef +++f+d   ++++++e +r  P+E++++ +  ++  e  +++l+el   v+ +
  gi|91773655|ref|YP_566347.1| 126 NYLMSISG--GDGDYGVSFLDVSTGEFLTTQFADkspYDRIASEAARMRPSECIISRTMFSD--ERLVERLKELNVLVQGF 202
                                   8******8..7777********************************************9988..569************** PP

                                   SCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCCSCCCCT-C CS
                       MutS_II  79 etvefesekaserleedfsvedldgfglekekklalaAlgalisYleetqkekelshl 136
                                   +++ f+++++++ le++f+v +l+g+g+  ++++a +++ga+++Y+  tq++ el+h+
  gi|91773655|ref|YP_566347.1| 203 KDEAFDVDSSRKLLERHFNVSTLEGMGC-AGLPYATSSAGAALDYALTTQMR-ELGHV 258
                                   ****************************.***********************.**997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                                   HH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEEES CS
                       MutS_II  44 rlsPkElllpedlsestaeeessklrelrsrvgvre 79 
                                   rl + E+l++++ +  +++ ++s ++++ + +g++ 
  gi|91773655|ref|YP_566347.1| 328 RLDALECLANDTMLRFDVRSHLSFVKDIERLIGRVV 363
                                   78999***********99999999999999888875 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   2.1e-05     0.053      22      47 ..     615     640 ..     605     644 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                        AAA_27  22 saeeadlhliyGpNEAGKstalrAis 47 
                                   +  ++++ li GpN AGKst +r +s
  gi|91773655|ref|YP_566347.1| 615 DCVDEQFLLITGPNMAGKSTYMRQVS 640
                                   344789***************99765 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 ?   12.1   0.0   4.9e-05      0.13      22      58 ..     619     655 ..     605     658 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                        AAA_29  22 kgatlltGpsGsGKSTllDAiqalLvpakkvrfNkaa 58 
                                   +++ l+tGp+ +GKST +  ++ + + a+  +f  a+
  gi|91773655|ref|YP_566347.1| 619 EQFLLITGPNMAGKSTYMRQVSLIVIMAQAGSFVPAS 655
                                   3489************987776666655556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (887 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.66
# Mc/sec: 4064.58
//
Query:       gi|91773656|ref|YP_566348.1|  [L=128]
Description: hypothetical protein Mbur_1705 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.0  12.2       0.37   10.8   1.7    3.3  3  DUF2108   Predicted membrane protein (DUF2108)
      0.084   12.4   0.2      0.084   12.4   0.2    1.8  2  DUF3959   Protein of unknown function (DUF3959)
       0.94    9.3   2.9        1.5    8.7   2.9    1.5  1  DUF2637   Protein of unknown function (DUF2637)
        1.6    9.0   5.8       0.66   10.2   3.3    1.6  1  Pox_A14   Poxvirus virion envelope protein A14
        2.6    8.3   6.3       0.23   11.7   0.7    2.1  2  DUF2530   Protein of unknown function (DUF2530)


Domain annotation for each model (and alignments):
>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.017        61      24      48 ..       4      27 ..       1      29 [. 0.83
   2 ?    5.1   0.3    0.0062        22      29      46 ..      41      58 ..      32      61 .. 0.90
   3 ?   10.8   1.7    0.0001      0.37      27      62 ..      83     117 ..      70     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.017
                       DUF2108 24 ldKlimlalleaGlillivakgYLD 48
                                  + K+++++l+   li++iv++ ++D
  gi|91773656|ref|YP_566348.1|  4 YLKMVIFGLIV-WLIPFIVSFAFVD 27
                                  56888899885.59*******9998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0062
                       DUF2108 29 mlalleaGlillivakgY 46
                                  ++ ++++G+++++ a +Y
  gi|91773656|ref|YP_566348.1| 41 SITIVTGGIVGVLLAIQY 58
                                  5789***********999 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0001
                       DUF2108  27 limlalleaGlillivakgYLDVaiavallePvsti 62 
                                    i l+l+ +G++++ v+++++D+ +   l +P+ ti
  gi|91773656|ref|YP_566348.1|  83 AIDLSLVYSGFFPMTVTQYFTDIGMRY-LGMPIYTI 117
                                   5889*******************9854.66777766 PP

>> DUF3959  Protein of unknown function (DUF3959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   2.3e-05     0.084     101     150 ..       8      58 ..       4      73 .. 0.86
   2 ?   -0.3   0.6      0.17   6.2e+02      14      60 ..      80     124 ..      66     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                       DUF3959 101 alwgallwdikevqslavlgrlmnlltteklylll.lvagfllggllantl 150
                                    ++g ++w i  + s+a ++r  n+l +e ++  + +v+g ++g lla ++
  gi|91773656|ref|YP_566348.1|   8 VIFGLIVWLIPFIVSFAFVDRNGNFLIAETFFKSItIVTGGIVGVLLAIQY 58 
                                   5799**************************997652788********9765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.17
                       DUF3959  14 kqiplelslflggllfftslgsyytkktssricswlaytifitlllg 60 
                                    +++++lsl+  g++ +t +  y+t  +  r +    yti + ++l+
  gi|91773656|ref|YP_566348.1|  80 INLAIDLSLVYSGFFPMT-VTQYFTD-IGMRYLGMPIYTIGMGYILM 124
                                   456778888888865444.5566664.66677777778887777765 PP

>> DUF2637  Protein of unknown function (DUF2637)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.9   0.00041       1.5       4      20 ..       8      24 ..       6      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00041
                       DUF2637  4 aifvlivaviafvlSFa 20
                                  +if+liv++i+f++SFa
  gi|91773656|ref|YP_566348.1|  8 VIFGLIVWLIPFIVSFA 24
                                  89**************8 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.3   0.00018      0.66       9      60 ..       2      56 ..       1      64 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                       Pox_A14  9 nyystvliaGiiLLilaci..fafvdfskststtdkawralsivs.Filgivill 60
                                  n+y +++i+G+i+  +  i  fafvd   +   +++ +++++iv+  i+g+++ +
  gi|91773656|ref|YP_566348.1|  2 NKYLKMVIFGLIVWLIPFIvsFAFVDRNGNFLIAETFFKSITIVTgGIVGVLLAI 56
                                  678888999987655555425888888888878*********9973588877665 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   6.5e-05      0.23      15      54 ..       6      53 ..       1      59 [. 0.80
   2 ?   -0.8   0.6      0.52   1.9e+03      33      33 ..      93      93 ..      65     127 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                       DUF2530 15 pvivvgtllWlvalvvllvvgdales........wlpvclaGlvvGll 54
                                   +++ g ++Wl+ ++v +++ d+  +           + ++G +vG+l
  gi|91773656|ref|YP_566348.1|  6 KMVIFGLIVWLIPFIVSFAFVDRNGNfliaetffKSITIVTGGIVGVL 53
                                  6899**************999988877777766556677778888876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.52
                       DUF2530 33 v 33
                                  +
  gi|91773656|ref|YP_566348.1| 93 F 93
                                  0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 749.71
//
Query:       gi|91773657|ref|YP_566349.1|  [L=158]
Description: hypothetical protein Mbur_1706 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   89.9   0.3    1.7e-25   89.5   0.3    1.1  1  DUF4231         Protein of unknown function (DUF4231)
    2.5e-10   40.3   2.0    3.2e-10   40.0   2.0    1.1  1  SLATT_1         SMODS and SLOG-associating 2TM effector domai
     0.0022   18.1   0.0     0.0029   17.7   0.0    1.1  1  HisKA_7TM       N-terminal 7TM region of histidine kinase
  ------ inclusion threshold ------
      0.011   15.7   0.4      0.017   15.1   0.4    1.2  1  DUF3754         Protein of unknown function (DUF3754)
      0.084   12.3   0.1       0.59    9.5   0.0    2.0  2  ArenaCapSnatch  Arenavirus cap snatching domain


Domain annotation for each model (and alignments):
>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.3   4.7e-29   1.7e-25       2     103 ..      23     125 ..      22     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 4.7e-29
                       DUF4231   2 qlswyekkasrakrrfrllrlitivlgallpilvs.sklgagvsvlkiltallsalvailaaleeffrykerWrryRstaE 81 
                                   + swy++ka ++k+r+  ++ i++++++l+p++++ s+++++v+++k++++l ++lva+  a+e++f+yke+W++yRst++
  gi|91773657|ref|YP_566349.1|  23 YRSWYDNKAVKMKKRYQQTQAIAAIGAVLVPVINNvSIEAQDVDLAKLSVTLTGILVALAIAFEGIFHYKEQWKNYRSTEQ 103
                                   679*********************************9******************************************** PP

                       DUF4231  82 sLktekwlflakagpYsdnksh 103
                                    L+t+k lf+ + g Ys+ ++ 
  gi|91773657|ref|YP_566349.1| 104 YLETQKQLFVHRIGDYSELDED 125
                                   *****************98875 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   2.0   8.9e-14   3.2e-10       1     119 [.      15     143 ..      15     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 8.9e-14
                       SLATT_1   1 YlreRveeqldwYrkkaeeneraakrwrlllillellalllaalr.afgelsv..dlvgvlaavaaallaWlelkqyeela 78 
                                   Yl++R+e+ ++wY +ka ++++++++++++ ++  +l  ++  ++  ++++++    v ++  ++a  +a+  +  y+e+ 
  gi|91773657|ref|YP_566349.1|  15 YLKNRLEQYRSWYDNKAVKMKKRYQQTQAIAAIGAVLVPVINNVSiEAQDVDLakLSVTLTGILVALAIAFEGIFHYKEQW 95 
                                   9****************************9999999999998888566666666455666667788889999********* PP

                       SLATT_1  79 aaYslaaeeLeiiraalea.......eateeewaklVadaEeaisreh 119
                                   ++Y  +++ Le++++ + +        ++++ ++ lV++ E+ai++e+
  gi|91773657|ref|YP_566349.1|  96 KNYRSTEQYLETQKQLFVHrigdyseLDEDSAFKLLVNRIESAIAEEN 143
                                   **************999988999998889999*************998 PP

>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     8e-07    0.0029     156     213 ..      33      86 ..      27      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8e-07
                     HisKA_7TM 156 rssg.lyrrqalllligllvPwlanllyllglsplpgidltplafaltglllaiaifry 213
                                   ++++  + +qa++ + ++lvP++ n+ +       +++dl  l+++ltg+l+a+ai   
  gi|91773657|ref|YP_566349.1|  33 KMKKrYQQTQAIAAIGAVLVPVINNVSIEA-----QDVDLAKLSVTLTGILVALAIAFE 86 
                                   555514456************998877766.....7*******************9755 PP

>> DUF3754  Protein of unknown function (DUF3754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.4   4.8e-06     0.017      50     121 ..      29     100 ..      29     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.8e-06
                       DUF3754  50 ntkvsfrlkdklllgvpaivglvavllkllkaeklknklssliaaliavlalggfafrqyvkyknkkiryqk 121
                                   n+ v+++ + + + +++ai+++++ +++ ++ e+ + +l +l  +l+ +l   ++af  ++ yk+++++y +
  gi|91773657|ref|YP_566349.1|  29 NKAVKMKKRYQQTQAIAAIGAVLVPVINNVSIEAQDVDLAKLSVTLTGILVALAIAFEGIFHYKEQWKNYRS 100
                                   57788888888899999****99999998899999999********************************75 PP

>> ArenaCapSnatch  Arenavirus cap snatching domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.094   3.4e+02     119     142 ..      33      56 ..       7      65 .. 0.76
   2 ?    9.5   0.0   0.00017      0.59       5      64 ..      88     149 ..      85     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.094
                                   HHHHHHTTHHHHHHTT-EEEEEEE CS
                ArenaCapSnatch 119 dlkkleqlkedlksagitlvpvvd 142
                                    +kk  q  + +++ g  lvpv++
  gi|91773657|ref|YP_566349.1|  33 KMKKRYQQTQAIAAIGAVLVPVIN 56 
                                   467777788889999999999997 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHHHS---GGGHHHHHHHHT--SHHHHHHH..HHHHHHHHHHHHHHHHTTSEE-T CS
                ArenaCapSnatch   5 iselkdlvrkyiedderlsrqklaflsqteprmllle..Glkllsrlievdsaeksgcehns 64 
                                   i   k+  ++y + ++ l  qk+ f+ +    + l e   +kll + ie   ae+++ ++n 
  gi|91773657|ref|YP_566349.1|  88 IFHYKEQWKNYRSTEQYLETQKQLFVHRIGDYSELDEdsAFKLLVNRIESAIAEENAVTLNI 149
                                   5567888999999****************99999988446******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1343  (0.0749066); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 961.15
//
Query:       gi|91773658|ref|YP_566350.1|  [L=1403]
Description: A-macroglobulin like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-81  271.4   0.0    1.3e-80  270.8   0.0    1.2  1  TED_complement   A-macroglobulin TED domain
      5e-28   96.8   0.2    2.9e-26   91.1   0.0    3.8  4  A2M              Alpha-2-macroglobulin family
    3.1e-23   82.7   3.3      3e-21   76.2   0.6    3.9  3  A2M_BRD          Alpha-2-macroglobulin bait region domain
    1.1e-18   67.5   0.0    4.1e-14   52.8   0.0    4.1  3  MG2              MG2 domain
    3.1e-17   63.0   0.0    1.2e-16   61.1   0.0    2.1  1  A2M_recep        A-macroglobulin receptor binding domain
    1.4e-11   44.5   0.1    4.8e-11   42.8   0.1    1.9  1  MG3              Macroglobulin domain MG3
    1.3e-07   31.7   0.8    3.5e-05   23.9   0.0    4.2  4  MG4              Macroglobulin domain MG4
      1e-06   28.1   1.0     0.0035   16.5   0.1    3.2  3  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
     0.0036   17.2   0.1      0.017   15.0   0.1    2.3  1  GYD              GYD domain
  ------ inclusion threshold ------
       0.17   11.7   5.8       0.37   10.6   0.0    3.4  3  fn3_3            Polysaccharide lyase family 4, domain II
       0.18   12.1   1.0         23    5.4   0.1    2.7  2  DUF4124          Domain of unknown function (DUF4124)


Domain annotation for each model (and alignments):
>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.8   0.0     8e-84   1.3e-80      11     311 ..     900    1193 ..     892    1195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 270.8 bits;  conditional E-value: 8e-84
                                    TTTTSTTHHHHHSSS--SSHHHHGGGTHHHHHHHHHHHHTTGTTTSHHHHHHHHHHHHHHHHHTCBETTSEBBSSS..S CS
                TED_complement   11 aiktvpenlesLlrlPygcgEqnmvllapnvyvlkYLekteqltkeikkkaleklekgyqrqlsykkadgsysafgkds 89  
                                    +++++ +++++Ll +PygcgEqnm+l+  +v vl+YL++t q ++e++ kal+++ +gyqr+l+++++dgs+safg+ +
  gi|91773658|ref|YP_566350.1|  900 IVAQTISGVDDLLGMPYGCGEQNMMLFSTDVEVLRYLKATGQQNPEVQAKALTFITTGYQRELTFMHSDGSFSAFGESD 978 
                                    3444566*********************************************************************778 PP

                                    S-BEHHHHHHHHHHHHHCHHHST--HHHHHHHHHHHHTTB-TTS-B--SS-SS-TTCSSSTHCHHHHHHHHHHHHHHHH CS
                TED_complement   90 segstWLtAfvlkvlaqakefifideeeiseslewLlseQkedGsFkeegsllnrkmkggvekevtLtAyvliaLleak 168 
                                     egs WLt+fvl  ++ a++  +ide+ ++e+ ew+ s QkedGs++ +g +++++m ggv+++++LtAyv++aL e+ 
  gi|91773658|ref|YP_566350.1|  979 GEGSLWLTSFVLSQFSGARDLTTIDENIVREAAEWIGSYQKEDGSWEAVGFVIHEDMMGGVSGTYALTAYVTLALDEY- 1056
                                    *****************************************************************************8. PP

                                    TTCSHHHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-THHHHHHHHHHHTTEEEETTEEEE--TTSSSGG CS
                TED_complement  169 eilelkkkvelsiskAleyLeekqaeelesvyalAilaYalalakseekaeellksLkaeakeegnsvyWeedekskee 247 
                                              +++++A +yLe+ + ++++++yalAi + al+  +s + a e +++L ++ake++n vyW+ d  + e+
  gi|91773658|ref|YP_566350.1| 1057 -----GYAAPIVMENARSYLEA-ELDKQDDPYALAIGTLALQKLESDR-ADESMEKLLELAKEDENGVYWGYDDVMPEP 1128
                                    .....667889***********.********************99999.9***********************999988 PP

                                    GTSS..-B----HHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHTHTSTSSSSSHHHHHHHHHHHH CS
                TED_complement  248 ekle..lkekasslevettaYaLLallsekdleladkivkWLtkqrnsaGGFsStqDtvvaLqaLs 311 
                                     ++     +  ss +vettaYa Lal++ +d   a++ +kW+++qrns+GGFsStqDtv+a  aL 
  gi|91773658|ref|YP_566350.1| 1129 YEYGgyGFHPISSKNVETTAYATLALIETND-PRASSSLKWIAAQRNSNGGFSSTQDTVMAFRALM 1193
                                    777786447789*****************99.5677789*************************96 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5   2.5e+03      10      63 ..     105     157 ..     102     159 .. 0.68
   2 ?   -2.3   0.0       2.6   4.2e+03       5      38 ..     197     232 ..     195     242 .. 0.67
   3 !   91.1   0.0   1.8e-29   2.9e-26       1      92 []     707     796 ..     707     796 .. 0.98
   4 ?   -0.1   0.0      0.53   8.6e+02      28      52 ..    1023    1047 ..    1018    1054 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                                   C...CEEEEEEEEESSSC.EEEEEEEEEETTTEEEEEEEEEEEE--SEEEEEE-- CS
                           A2M  10 tdasgkaslsftlPDsiT.tWrvtavalsedkglgvaeplevrvfkpffvdlnlP 63 
                                   t++sg++  +f++PD    ++ +ta    ++   g++++++v    p+f+++  P
  gi|91773658|ref|YP_566350.1| 105 TSESGNNVAKFDVPDVEEgSYTLTATPSGAE--SGFTTTVKVMQNNPIFIETDKP 157
                                   5578999999999996543777777766666..4555554577777777777665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                                   EEEEEC...CEEEEEEEEESSSC..EEEEEEEEEET CS
                           A2M   5 edvlvtdasgkaslsftlPDsiT..tWrvtavalse 38 
                                   +d lvt++ g a +++ l  ++   tW+v a + s 
  gi|91773658|ref|YP_566350.1| 197 KDDLVTNEYGVAFFDLPLASELNlgTWKVKATSGSS 232
                                   56666666666666666666544449***9998776 PP

  == domain 3  score: 91.1 bits;  conditional E-value: 1.8e-29
                                   ECCEEEEEEC...CEEEEEEEEESSSCEEEEEEEEEETTTEEEEEEEEEEEE--SEEEEEE--SEEETTSEEEEEEEEEE- CS
                           A2M   1 twlWedvlvtdasgkaslsftlPDsiTtWrvtavalsedkglgvaeplevrvfkpffvdlnlPysvrrgeqveikavvfNy 81 
                                   tw+W ++ +td++g a+l+++ PDsiT+Wr++av+  ++ g+g++e+  ++vf++ff+d+ lPy v+rge++ +++ v+Ny
  gi|91773658|ref|YP_566350.1| 707 TWIWMPEILTDDNGLATLDLNAPDSITKWRLHAVSSGPE-GIGISEA-GLTVFQDFFIDPDLPYAVIRGEEFPVQVQVYNY 785
                                   8**************************************.*******.********************************* PP

                                   SSS-EEEEEEE CS
                           A2M  82 ldkeikvrvel 92 
                                   ld +++v+++l
  gi|91773658|ref|YP_566350.1| 786 LDMPQNVKLTL 796
                                   *******9875 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.53
                                    EEEEEEEEEETTTEEEEEEEEEEEE CS
                           A2M   28 tWrvtavalsedkglgvaeplevrv 52  
                                    +W++ ++ ++ed+  gv+ ++ +++
  gi|91773658|ref|YP_566350.1| 1023 SWEAVGFVIHEDMMGGVSGTYALTA 1047
                                    8***********9999998877665 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.049        79       3      26 ..     152     184 ..     150     290 .. 0.57
   2 !   76.2   0.6   1.9e-24     3e-21       5     140 .]     464     589 ..     459     589 .. 0.89
   3 ?   -0.1   0.0      0.68   1.1e+03       5      43 ..    1278    1351 ..    1274    1401 .. 0.42

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.049
                                   EEESSSS--TTSEEEEEEE-SS-.........E CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.........x RF
                       A2M_BRD   3 ispdkeeykvGetakltvkstfa.........t 26 
                                   i++dk  yk+G+ + +++ s  +         t
  gi|91773658|ref|YP_566350.1| 152 IETDKPIYKPGQIIHVRLLSLNNnlipvvqntT 184
                                   789***************997666654322221 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 1.9e-24
                                   ESSSS--TTSEEEEEEE-SS-EE-TT-.....BSS-----.-S...S....-EEEEEE--TT-----EEEEEE..E--CEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       A2M_BRD   5 pdkeeykvGetakltvkstfatverdstl.ylvlsrgnivssgekveeidsstsfsfpvtadmaPnarvvvyyirrdgevv 84 
                                     ++  +vG+ + ++v st      ++t  y v+++g++v s +     ++++++++ vt++m+P+a+vv+y+i++++ev 
  gi|91773658|ref|YP_566350.1| 464 VSEGIPEVGDVISFKVYSTN-----AGTVfYDVFANGRTVYSAT-----SDEPQINILVTPQMSPSAKVVAYLINPNNEVS 534
                                   5667899***********98.....45445*********97884.....4568**************************** PP

                                   EEEEE----.-GGGB-EEEEE.EE...-SSSEEEEEEE..ET-EEEEEEEEHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       A2M_BRD  85 adsvqlpvekdfenklsvsle.synetrPgeevtlkvkaspgslvalaaVDksvlll 140
                                   ads++++v+  f+ ++++s   + + + Pg+ v++++ a ++s ++l++VD+sv++l
  gi|91773658|ref|YP_566350.1| 535 ADSLPFDVK--FSTQVDLSTGfDEEMVAPGDAVSVELDAGTKSMIGLSIVDESVYAL 589
                                   *********..9999999987667789************9***************97 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.68
                                    ESSSS--TTSEEEEEEE-SS-.................................EE-TT-......BSS----- CS
                                    xxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxx..xxxxxxxxxx RF
                       A2M_BRD    5 pdkeeykvGetakltvkstfa.................................tverdstl..ylvlsrgniv 43  
                                     d++ ++v++ +k+ v+ +++                                 + ++d+t+  y++  r+ i+
  gi|91773658|ref|YP_566350.1| 1278 YDSTDVEVDDVVKVDVRLKYNgmpgirgviessgmmivdiavptgftpvgssleALKEDGTItrYEIAGRKIIL 1351
                                    55556666666666666666554444444444444444444444443444443322233322345555555553 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.023        37      34      96 .]      84     144 ..      55     144 .. 0.76
   2 !   52.8   0.0   2.5e-17   4.1e-14       2      96 .]     150     240 ..     149     240 .. 0.96
   3 ?    4.6   0.0     0.028        46      12      72 ..     370     431 ..     369     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.023
                                   EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-EEEEEEEE CS
                           MG2  34 lplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaeeslssgsfrV 96 
                                   + ++ t++++ g  +   + at+e+g    +f++p+  + G+y++++ + s +es ++++++V
  gi|91773658|ref|YP_566350.1|  84 RGVEYTLTSAAGDIIPLVKAATSESGNNVAKFDVPD-VEEGSYTLTA-TPSGAESGFTTTVKV 144
                                   35677999999999999*****************96.789*******.778888888888877 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 2.5e-17
                                   EEEEES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEE CS
                           MG2   2 afvytDRglYrPgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsa 82 
                                   +f+ tD+++Y+Pg+ ++++ l+++++l ++ + +++++i d++g ++++ +l+t+e g+a ++++l ++  lG+++v++  
  gi|91773658|ref|YP_566350.1| 150 IFIETDKPIYKPGQIIHVRLLSLNNNLIPVVQ-NTTVEIADAKGVKIYKDDLVTNEYGVAFFDLPLASELNLGTWKVKA-- 227
                                   6899**************************99.**********************************************.. PP

                                   CSTTT-EEEEEEEE CS
                           MG2  83 dsaeeslssgsfrV 96 
                                    + ++s+s+ ++rV
  gi|91773658|ref|YP_566350.1| 228 -TSGSSMSEVDIRV 240
                                   .8888888888887 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.028
                                   -TT-EEEEEEEEESTTCSB---.EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT-- CS
                           MG2  12 rPgetVslkallrdetlqglak.lplkltirdpdgkevkelplatdetggaesefalpeaak 72 
                                   +Pg  +++  +++d+ +++l+k   l +++rd++ +  + ++  t+etg+a +++++pe+a 
  gi|91773658|ref|YP_566350.1| 370 KPGMPLQVLLVTKDPGGEPLEKeVTLVANFRDDNYNYEEIKETYTTETGIALVTLEIPEDAV 431
                                   57777788888899999***998888889999999999999999***************985 PP

>> A2M_recep  A-macroglobulin receptor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   7.6e-20   1.2e-16       1      90 [.    1310    1395 ..    1310    1396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 7.6e-20
                     A2M_recep    1 sgmavvevkllsGfvpdeedlkklvkgeeelikkveleddgkvilYldkvsekeeecvsfraeqefkVanlqpalvkvy 79  
                                    sgm++v++ +++Gf+p+ ++l++l  +e+++i ++e   ++k+ilY+d++ + ee ++s++++  f+V+ +     ++y
  gi|91773658|ref|YP_566350.1| 1310 SGMMIVDIAVPTGFTPVGSSLEAL--KEDGTITRYE-IAGRKIILYIDEMMPGEEMEFSLNMRAMFPVKAM-VQESSAY 1384
                                    79*******************876..45799*****.77*********98889***************655.555689* PP

                     A2M_recep   80 dYyeperratt 90  
                                     Yy+pe +a++
  gi|91773658|ref|YP_566350.1| 1385 SYYNPEVKAEV 1395
                                    ******99975 PP

>> MG3  Macroglobulin domain MG3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   2.9e-14   4.8e-11       1      76 [.     242     313 ..     242     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.9e-14
                                   -----SEEEEEE.EEEE-STT--EEEEEEEEETTS-B---EEEEEEEE..E-SSS-EEE---EEEE-BTTEEEEEE CS
                           MG3   1 eyVLPkFeVkvevPkvitvedeelqvsvcAkYtyGkpVkGkvkvtlclkqkdkkkkkeeeqiekelekdGcgsasv 76 
                                   +yVLPkF+ + ++ k   + de ++ +v+A+Y++Gk V+G+v+v+  + ++  +++ +    +  + kdG++++++
  gi|91773658|ref|YP_566350.1| 242 KYVLPKFDLETSTEKSWFLADEPITGTVSANYFFGKVVEGTVEVKASR-YVGVWEEYS---TSTATLKDGNVEFTL 313
                                   7***********************************************.554444444...5677889**999997 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.38   6.2e+02       8      69 ..     157     219 ..     150     248 .. 0.65
   2 !   23.9   0.0   2.2e-08   3.5e-05       7      78 ..     366     440 ..     360     450 .. 0.80
   3 ?    1.6   0.0       0.2   3.2e+02      49      73 ..     713     737 ..     706     745 .. 0.86
   4 ?   -3.0   0.1       5.3   8.7e+03      16      39 ..     776     798 ..     772     846 .. 0.54

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.38
                           MG4   8 kffKpGlPfsikVlvkdpdgs.paknvpVkiealkseteekeslttdedGtakfsintpedak 69 
                                   + +KpG   ++++l  + +    ++n +V i+  k  + +k+ l t+e G+a f + ++++ +
  gi|91773658|ref|YP_566350.1| 157 PIYKPGQIIHVRLLSLNNNLIpVVQNTTVEIADAKGVKIYKDDLVTNEYGVAFFDLPLASELN 219
                                   466777544444333333222135677788877454467889999999999999887766555 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.2e-08
                           MG4   7 pkffKpGlPfsikVlvkdpdgspaknvpVkiealk...seteekeslttdedGtakfsintpedaksltitvktk 78 
                                   ++ +KpG+P ++ +  kdp g+p++++   ++ ++    + ee ++++t e G+a +++++peda s+++ +  +
  gi|91773658|ref|YP_566350.1| 366 SNSIKPGMPLQVLLVTKDPGGEPLEKEVTLVANFRddnYNYEEIKETYTTETGIALVTLEIPEDAVSVELSAASE 440
                                   6789********************98755555545555445666667788***************9999987665 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.2
                           MG4  49 slttdedGtakfsintpedakslti 73 
                                   ++ td++G+a + +n p++ ++  +
  gi|91773658|ref|YP_566350.1| 713 EILTDDNGLATLDLNAPDSITKWRL 737
                                   5789*************99888766 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 5.3
                           MG4  16 fsikVlvkdpdgspaknvpVkiea 39 
                                   f ++V+v ++++ p +nv ++++ 
  gi|91773658|ref|YP_566350.1| 776 FPVQVQVYNYLDMP-QNVKLTLSG 798
                                   56778888877777.444444444 PP

>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0089        14      35      91 ..     596     652 ..     581     671 .. 0.81
   2 !   16.5   0.1   2.2e-06    0.0035     184     274 ..     980    1071 ..     927    1081 .. 0.71
   3 ?    3.8   0.0     0.015        25     243     290 ..    1141    1185 ..    1082    1207 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0089
                                   TT-B-S--GGGGT-TTS---BB-SSSS-TT--BHHHHHHHHHHHTT---STHHHHHH CS
               SQHop_cyclase_C  35 ekqvlvkGdWkvkrpevepgGwafefaneyyPdvddtavvvlalkrvrlkeekkkee 91 
                                    kqv ++ + +  +p ve+   +f ++ + y  +dd++++vla  ++++ +++++++
  gi|91773658|ref|YP_566350.1| 596 LKQVFDELEIRFMEPRVEAHPQYFGYQTTAYDVLDDAGMIVLASGSLEIPRSQTNDA 652
                                   567777777788899999999*********************998888776655543 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.2e-06
                                    SSHHHHHHHHHHHHHHTT..--TTSHHHHHHHHHHHTT--TTSSBB--GGGGT-GGGTT-SSBBHHHHHHHHHHHHHTT CS
               SQHop_cyclase_C  184 vnyiyGtwsvlsalaavg..edleepvirkavdWlksvqnedGGWGesaesykdpklagkgestasqtaWallallaag 260 
                                       ++ t  vls ++ ++  +  +e+++r+a++W+ s q+edG W e++    +++++g  + t + ta+ +lal   g
  gi|91773658|ref|YP_566350.1|  980 EGSLWLTSFVLSQFSGARdlTTIDENIVREAAEWIGSYQKEDGSW-EAVGFVIHEDMMGGVSGTYALTAYVTLALDEYG 1057
                                    555666667777766665334578999******************.66667778889999999***********98887 PP

                                    GGGSHHHHHHHHHH CS
               SQHop_cyclase_C  261 eveseavkrGiayl 274 
                                     +    ++   +yl
  gi|91773658|ref|YP_566350.1| 1058 YAAPIVMENARSYL 1071
                                    76665555555555 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.015
                                    SBBHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHH--TTS-----S-- CS
               SQHop_cyclase_C  243 estasqtaWallallaageveseavkrGiaylletqkedGtWeeeayt 290 
                                    +   + ta+a+lal+ +++   + ++  ++++ ++++++G ++ ++ t
  gi|91773658|ref|YP_566350.1| 1141 SKNVETTAYATLALIETND---PRASSSLKWIAAQRNSNGGFSSTQDT 1185
                                    3344455566665554433...33334455555555555555555444 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.1e-05     0.017      34      83 ..    1213    1260 ..    1185    1262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                           GYD   34 GgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetlraft 83  
                                    G++++ l +t  +yDvv+i+E+p  e ++ l ++l++sG ++ +++r f+
  gi|91773658|ref|YP_566350.1| 1213 GVEIKGLRITSENYDVVNIIEVP--EGVEVLEMELSGSGELNYQLVRRFN 1260
                                    999********************..6666679999999999999998876 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 ?   10.6   0.0   0.00023      0.37      35      68 ..     109     145 ..     102     150 .. 0.80
   2 ?   -2.6   0.2       2.9   4.8e+03      50      71 ..     268     289 ..     267     291 .. 0.83
   3 ?    2.0   0.3      0.11   1.8e+02      44      54 ..    1040    1050 ..    1039    1063 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                         fn3_3  35 g....sftipnVkpGtYrltvYadglfgdykqdsvtVt 68 
                                   g    +f +p+V +G+Y+lt+  +g +  + +++v+V 
  gi|91773658|ref|YP_566350.1| 109 GnnvaKFDVPDVEEGSYTLTATPSGAESGF-TTTVKVM 145
                                   444449******************999888.7888886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                         fn3_3  50 tvYadglfgdykqdsvtVtagk 71 
                                   tv a+ +fg+ ++ +v+V+a +
  gi|91773658|ref|YP_566350.1| 268 TVSANYFFGKVVEGTVEVKASR 289
                                   56788899999999****9975 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.11
                         fn3_3   44 pGtYrltvYad 54  
                                     GtY+lt+Y++
  gi|91773658|ref|YP_566350.1| 1040 SGTYALTAYVT 1050
                                    6********96 PP

>> DUF4124  Domain of unknown function (DUF4124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.014        23      20      51 ..     493     521 ..     484     525 .. 0.81
   2 ?    4.4   0.1     0.029        48      18      51 ..     814     847 ..     814     851 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                       DUF4124  20 anGvvhysdqPppdgkqaeqvetapppsaaap 51 
                                   anG+++ys +    ++ + ++ + p+ s++a 
  gi|91773658|ref|YP_566350.1| 493 ANGRTVYSATS---DEPQINILVTPQMSPSAK 521
                                   8**********...777777777777777765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.029
                       DUF4124  18 vDanGvvhysdqPppdgkqaeqvetapppsaaap 51 
                                   vDan v+h s +  p+++++++ve   +++++a 
  gi|91773658|ref|YP_566350.1| 814 VDANSVTHVSFTIRPTRVGVQTVELTGQTTEKAD 847
                                   89**********************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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):              11  [number of targets reported over threshold]
# CPU time: 0.96u 0.33s 00:00:01.29 Elapsed: 00:00:00.54
# Mc/sec: 7833.89
//
Query:       gi|91773659|ref|YP_566351.1|  [L=185]
Description: hypothetical protein Mbur_1709 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.6   0.0      0.078   12.7   0.0    1.3  1  PYC_OADA  Conserved carboxylase domain
       0.24   12.0   1.4       0.55   10.8   1.4    1.6  1  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


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 ?   12.7   0.0   8.7e-06     0.078      63     116 ..     103     156 ..      99     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-06
                                   HH........TS.TTSS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S CS
                      PYC_OADA  63 lnklteedvleegrykdipdsvvdllkGelGkppggfpeelvkkvlkgeepits 116
                                    ++++e+ +l   +++ i++s+ +++ G +Gk p+  ++e+vk++ +++e  ++
  gi|91773659|ref|YP_566351.1| 103 HFSINETVILMLRKDTLINESMFRVVSGSYGKHPVSDKDEIVKAIEFENEIDEE 156
                                   55666677777778999****************************987665444 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 ?   10.8   1.4   6.1e-05      0.55       1      16 [.      16      31 ..      16      31 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.1e-05
                        LPAM_1  1 MKKillalgalllLsG 16
                                  MK +ll++ ++l+L++
  gi|91773659|ref|YP_566351.1| 16 MKQTLLLIILVLILTS 31
                                  **************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1327.72
//
Query:       gi|91773660|ref|YP_566352.1|  [L=304]
Description: peptidase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-05   24.9   4.1        0.4   11.3   0.1    4.1  3  PepSY     Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.022     4e+02       2      18 ..      51      67 ..      50     113 .. 0.44
   2 !   10.7   0.2   3.3e-05      0.59       1      59 [.     124     198 ..     124     201 .. 0.65
   3 !   11.3   0.1   2.2e-05       0.4      31      60 ..     265     297 ..     232     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.022
                                  S-HHHHHHHHHHHSTTE CS
                         PepSY  2 iseeqAlaiAlaavpgk 18
                                  +++e+A+ai   ++p+ 
  gi|91773660|ref|YP_566352.1| 51 VTLEEAKAIMISENPEL 67
                                  67777777766655532 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.3e-05
                                   SS-HHHHHHHHHHH..........STTE.EEEEEEEEEE.TTEEEEEEEEE.......EE.TTEEEEEEEETTT--E CS
                         PepSY   1 kiseeqAlaiAlaa..........vpgk.iieieleded.dgrlvYevelst......aepegpeyevfiDAkTGkv 59 
                                   k+see+A++iA +            ++  + +++le+ + d  + Y +++ +      + ++g  +   ++ +TG+v
  gi|91773660|ref|YP_566352.1| 124 KVSEEEAVEIAGKYveakfspeqlKEVQlEAVNYLEPVAdDLPGFYHIKYNRiingisSLSDGVIMR--VNSETGDV 198
                                   79*********66622222222222333344444444436888888888888888888888888888..88888887 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 2.2e-05
                                   EEEEEEEEE....EE.TTEEEEEEEETTT--EE CS
                         PepSY  31 rlvYevelst...aepegpeyevfiDAkTGkvl 60 
                                   +lv+  ++++   + ++    +vfiDA+TG+vl
  gi|91773660|ref|YP_566352.1| 265 HLVWWMQFTDsnlGLDKSLPGIVFIDANTGTVL 297
                                   556666666556544555556899********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2013.80
//
Query:       gi|91773661|ref|YP_566353.1|  [L=142]
Description: hypothetical protein Mbur_1711 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.027   14.9   0.2       0.07   13.6   0.1    1.6  2  DUF1831     Putative amino acid metabolism
       0.04   14.0   0.8      0.099   12.7   0.4    1.8  2  CHU_C       C-terminal domain of CHU protein family
      0.088   13.0   0.1       0.78    9.9   0.0    2.1  2  Sm_like     Sm_like domain
       0.13   12.5   0.0       0.26   11.5   0.0    1.5  1  HCMV_UL124  Family of unknown function
       0.15   11.9   0.1       0.23   11.3   0.1    1.2  1  DUF5337     Family of unknown function (DUF5337)


Domain annotation for each model (and alignments):
>> DUF1831  Putative amino acid metabolism
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.85   3.1e+03      81      97 ..      57      73 ..      43      75 .. 0.65
   2 ?   13.6   0.1   1.9e-05      0.07      36     101 ..      76     141 ..      70     142 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.85
                                  B--S-GGG--HHHHHHH CS
                       DUF1831 81 kvniFknekakelvekf 97
                                  +v+iF++  a+  v+ +
  gi|91773661|ref|YP_566353.1| 57 TVEIFNSTGASIFVDAY 73
                                  57777777776666665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.9e-05
                                   TTS-EEEEEEES-SSTT--SEEEEEEE-TTSS-EEEEEEETTSSSB--S-GGG--HHHHHHHHHHH CS
                       DUF1831  36 kaGnfelersLepespsneglkLkitinkdlkgfklsvtdanglkkvniFknekakelvekfefll 101
                                   ++G+f  + s+ +e++  +++  k ++++d+++  + ++da+ + ++ +++++++ke   +f + +
  gi|91773661|ref|YP_566353.1|  76 NSGQFMKSPSIIDETNDGDTYIYKAILENDMNETYIFTVDADAAASITVYNDSENKEAYINFGYTI 141
                                   799****************************************************99988888765 PP

>> CHU_C  C-terminal domain of CHU protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   2.8e-05     0.099      17      78 ..      43     108 ..      42     122 .. 0.67
   2 ?    0.0   0.1      0.25   9.1e+02      14      35 ..     106     126 ..      95     131 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                         CHU_C  17 vfkiegieky.pnnsleifnrwGqlVyekknyknewdGtskgk.....eklpeGtYfYvlkleegeke 78 
                                   +f++++ + y +++++eifn  G +++    + n+  G+  ++     e     tY+Y   le++ +e
  gi|91773661|ref|YP_566353.1|  43 FFTMKNKDIYsHKITVEIFNSTGASIFVDAYTLNS--GQFMKSpsiidETNDGDTYIYKAILENDMNE 108
                                   5788887756256**************87655432..3333223455344444588887777555554 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.25
                         CHU_C  14 knDvfkiegiekypnnsleifn 35 
                                   +n+++  + ++   ++s++++n
  gi|91773661|ref|YP_566353.1| 106 MNETYIFT-VDADAAASITVYN 126
                                   44444333.3333556666666 PP

>> Sm_like  Sm_like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.17   6.1e+02      62      71 ..      43      52 ..      32      60 .. 0.82
   2 ?    9.9   0.0   0.00022      0.78       6      40 ..      92     126 ..      87     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
                       Sm_like 62 ffilrekdil 71
                                  ff +++kdi 
  gi|91773661|ref|YP_566353.1| 43 FFTMKNKDIY 52
                                  8999999996 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                       Sm_like   6 nGeevlgkavltedegetlvfiqdPvvvqvvtkel 40 
                                   +G+  + ka+l +d +et +f  d  +   +t   
  gi|91773661|ref|YP_566353.1|  92 DGDTYIYKAILENDMNETYIFTVDADAAASITVYN 126
                                   6888999**************98876555554333 PP

>> HCMV_UL124  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.3e-05      0.26      60      99 ..      11      50 ..       7      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.3e-05
                    HCMV_UL124 60 lcgtlvvvgivlclslastvrskelpsdhepleaweqgsd 99
                                  l   lv+ g+ ++l ++st+r   l   hepl    +  d
  gi|91773661|ref|YP_566353.1| 11 LFTILVITGLFFALIVTSTIRYDILKEKHEPLFFTMKNKD 50
                                  56789**************************976655555 PP

>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.5e-05      0.23      41      65 ..       6      30 ..       4      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.5e-05
                       DUF5337 41 nRyalLfdLaAlAaliwalvvtyql 65
                                  +R  +Lf + ++ +l++al+vt  +
  gi|91773661|ref|YP_566353.1|  6 QRWIMLFTILVITGLFFALIVTSTI 30
                                  6999*****************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1053.19
//
Query:       gi|91773662|ref|YP_566354.1|  [L=422]
Description: hypothetical protein Mbur_1712 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   61.0   3.5    3.1e-16   60.1   3.5    1.4  1  Reprolysin_5     Metallo-peptidase family M12
      6e-09   36.5   0.8    1.7e-08   35.0   0.2    2.0  2  Reprolysin_3     Metallo-peptidase family M12B Reprolysin-lik
    4.1e-07   30.3   0.0    7.9e-07   29.4   0.0    1.5  1  Pep_M12B_propep  Reprolysin family propeptide
    7.4e-06   25.8   4.0    1.8e-05   24.5   4.0    1.7  1  Reprolysin_4     Metallo-peptidase family M12B Reprolysin-lik
    0.00058   19.8   0.7     0.0016   18.4   0.7    1.8  1  Reprolysin_2     Metallo-peptidase family M12B Reprolysin-lik
     0.0016   18.3   0.0     0.0028   17.6   0.0    1.3  1  Reprolysin       Reprolysin (M12B) family zinc metalloproteas
  ------ inclusion threshold ------
      0.011   15.6   0.4       0.24   11.3   0.0    2.3  2  PTSIIA_gutA      PTS system glucitol/sorbitol-specific IIA co
       0.18   11.9   1.4       0.47   10.6   1.4    1.8  1  ETRAMP           Malarial early transcribed membrane protein 


Domain annotation for each model (and alignments):
>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   3.5   1.4e-19   3.1e-16       4     165 ..     221     375 ..     218     419 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.4e-19
                  Reprolysin_5   4 tvallvaaDcsfvaafggdaaaqanivnlvnrasnvyeres.nislglanvtildeedpstaseasstgdaselLnefqsa 83 
                                    + +l+a+D +f +++ ++    + i+n++ +++ ++ ++  +++l+l ++   ++  ++         d  +lL+efq++
  gi|91773662|ref|YP_566354.1| 221 SIYVLAAYDTEFSNKY-SS--PGTEIYNMFSQTKTAFSEPYiGVNLVLDGYYYMNSLTST---------DRIDLLDEFQDE 289
                                   566889**********.55..689*********8888887789*********99999995.........579********* PP

                  Reprolysin_5  84 ssalrgqqnddlailflmtnfsgg.vGlAwlgqlcnsgsagsvstrveksnsvvvstatevqvvaHElGHnfGavHDcdss 163
                                   +s++r++qn dla+l++ ++f+g  +G++  ++++ns+ a ++ +  + + ++++  ++  + +aHElGHnf a HD  ++
  gi|91773662|ref|YP_566354.1| 290 ASSQRDSQNSDLAFLYSGKDFDGSyIGRSTGYNSGNSDYAYAIGQMKSEVSYQAT-FSQRSILTAHELGHNFAATHDEGAT 369
                                   ***************************************9999988555556655.6788999**************9876 PP

                  Reprolysin_5 164 s....e 165
                                        +
  gi|91773662|ref|YP_566354.1| 370 WtewfT 375
                                   555662 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   3.4e+03      41      75 ..      31      65 ..      15      95 .. 0.68
   2 !   35.0   0.2   7.6e-12   1.7e-08       7     124 .]     246     365 ..     241     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                  Reprolysin_3 41 kdatealdelaevtaeaergqagyDlvhlftarde 75
                                  kd   ++de  + ++ +  +++++ +  ++++ d 
  gi|91773662|ref|YP_566354.1| 31 KDTYISMDECFQTIEVTTSQKKNVEISDAIKKYDT 65
                                  44455555555555555566777777766666554 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 7.6e-12
                  Reprolysin_3   7 lvnranqiye.rdlgirlqlvaiiitdkasdpytkkdatealdelaevtaeaergqagyDlvhlftarde.sgvgGlAyvg 85 
                                   ++++  +++    +g++l l ++ ++++     t++d+ + lde+++  + + r++++ Dl+ l +++d+ +++ G    +
  gi|91773662|ref|YP_566354.1| 246 MFSQTKTAFSePYIGVNLVLDGYYYMNSL----TSTDRIDLLDEFQDEASSQ-RDSQNSDLAFLYSGKDFdGSYIGRSTGY 321
                                   55555566664445566666677777775....7777888999999998888.9****************97777776665 PP

                  Reprolysin_3  86 svcnsskk..agvnsgssvlgk.vga..dtvaHEiGHnfganHt 124
                                   +  ns+++   g+++++  +++ +++  + +aHE+GHnf a H+
  gi|91773662|ref|YP_566354.1| 322 NSGNSDYAyaIGQMKSEVSYQAtFSQrsILTAHELGHNFAATHD 365
                                   55555555447777777555552444899**************7 PP

>> Pep_M12B_propep  Reprolysin family propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.5e-10   7.9e-07      31     140 .]      73     180 ..      29     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.5e-10
               Pep_M12B_propep  31 eeekeerlsyrlkafgkefhLnLepnsellapgftvethredgeereespqeeehCyYqGevrgeegssvalstCsG.lrG 110
                                    ++++++ s ++ + g ef ++Lep    + +++ +    e+g +++e++ +     Y+G+v g+++s v +++ +  + G
  gi|91773662|ref|YP_566354.1|  73 FKKQADKGSINIALAGDEFNVDLEPA-VWVNRDLKAYCNDENG-KVKEMKMD-PIYQYTGHVAGDPNSIVCFTLDDDvVLG 150
                                   333379999****************9.99*******9666655.45554443.3479*****************997369* PP

               Pep_M12B_propep 111 virteneeYfIePleeeeeeeeekkpHvvY 140
                                    i++++e+Y+Ie +    ++++++ + ++Y
  gi|91773662|ref|YP_566354.1| 151 WIEINDEQYVIEQVGWIADKNTKEVTYIIY 180
                                   *************98445555555666666 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 !   24.5   4.0   7.9e-09   1.8e-05      26     154 ..     240     367 ..     219     417 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.9e-09
                  Reprolysin_4  26 raainalvtvlnevYg.rdlnvrLelisdqdviytdsetdsfaadisgedlgnsslatltstrdskdyDlaallrdtrasq 105
                                    ++i+++   +  +++   ++v+L l +   +++ +s td         dl ++ +    s+rds++ Dla l      ++
  gi|91773662|ref|YP_566354.1| 240 GTEIYNMFSQTKTAFSePYIGVNLVLDGYYYMNSLTS-TDRI-------DLLDEFQDEASSQRDSQNSDLAFLYSGKDFDG 312
                                   4788999999999998778999998887766666554.4555.......55566666677777888888877776665555 PP

                  Reprolysin_4 106 qnvgvawvgalcls..arq..nkka.sgvaasrdeydi.fAHEiGHtfGaaHdls 154
                                      g +  +  + s  a+   ++k+   ++a+ ++ +i  AHE GH+f a Hd  
  gi|91773662|ref|YP_566354.1| 313 SYIGRSTGYNSGNSdyAYAigQMKSeVSYQATFSQRSIlTAHELGHNFAATHDEG 367
                                   5566666666555534333324444233344355669999************965 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 !   18.4   0.7   7.1e-07    0.0016      70     144 ..     297     367 ..     268     399 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.1e-07
                  Reprolysin_2  70 kdydlahlvllgtfsggvlGLa..yvgqicqkeassrktntglsttansgsaveetkeidvvaHEvGHaFGatHdnd 144
                                   ++ dla+l   ++f g+ +G    y ++     +   ++++ +s    ++ +   ++   + aHE+GH+F atHd  
  gi|91773662|ref|YP_566354.1| 297 QNSDLAFLYSGKDFDGSYIGRStgYNSGNSDYAYAIGQMKSEVS----YQATF--SQRSILTAHELGHNFAATHDEG 367
                                   56666666666666666666430022222222222211222222....32222..5666669*************86 PP

>> Reprolysin  Reprolysin (M12B) family zinc metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06    0.0028      63     150 ..     276     367 ..     268     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                   -SSHHHHHHHHHHHHHHCTTTS-..SEEEEEESS--STTSSEEE-TT-TTSTSTSEEEEE--S..SSHHHH...HHHHHHH CS
                    Reprolysin  63 skdaeetLeeflkwkeellkkrkkhdaaqLlsgkefekktvGaayvgglCskeksggvaedkk..knleal...avilaqe 138
                                   s+d  ++L+ef +  ++++ ++ + d a+L sgk+f ++++G ++  +  +++++ ++ + k+  +   ++   +++ a+e
  gi|91773662|ref|YP_566354.1| 276 STDRIDLLDEFQDEASSQRDSQ-NSDLAFLYSGKDFDGSYIGRSTGYNSGNSDYAYAIGQMKSevSYQATFsqrSILTAHE 355
                                   5566788999988888877755.59*********************************99887422223332226678*** PP

                                   HHHHCT---GHH CS
                    Reprolysin 139 LghnlGlthdee 150
                                   Lghn+  thde 
  gi|91773662|ref|YP_566354.1| 356 LGHNFAATHDEG 367
                                   **********97 PP

>> PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2     0.089     2e+02      36      63 ..      46      74 ..      38      78 .. 0.84
   2 ?   11.3   0.0   0.00011      0.24      55      81 ..     152     178 ..     144     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.089
                                  TCEEEE-T..GG----TT-EEEETTEEEE CS
                   PTSIIA_gutA 36 ysviheve.elkeeikkgdtltigeqeyk 63
                                  +   ++++ e +++ikk dt++i+ + +k
  gi|91773662|ref|YP_566354.1| 46 VTTSQKKNvEISDAIKKYDTVKIDAKAFK 74
                                  55667777799**************9987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                                   EEETTEEEEEEEE-TTHHHHHHHHS-E CS
                   PTSIIA_gutA  55 ltigeqeykitaVGevanknLkelGHv 81 
                                   ++i++++y i++VG +a kn ke+  +
  gi|91773662|ref|YP_566354.1| 152 IEINDEQYVIEQVGWIADKNTKEVTYI 178
                                   79******************9998665 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.4   0.00021      0.47       5      61 ..       6      59 ..       1      88 [. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                        ETRAMP  5 kvllffafLlavnlltpeslcdevnkkkekakkaikkiddkiekkkkkkKliiisti 61
                                   +++++++Ll+v ++  ++++ e+nk   +   ++++  ++ie  +++kK++ is +
  gi|91773662|ref|YP_566354.1|  6 TIASILMVLLIVGVVLTPLVSAESNK---DTYISMDECFQTIEVTTSQKKNVEISDA 59
                                  46899*******************96...5555555555555555555555555533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2798.94
//
Query:       gi|91773663|ref|YP_566355.1|  [L=186]
Description: NADPH-dependent FMN reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-28   98.0   0.0      5e-28   97.8   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    8.8e-13   48.4   0.0    1.1e-12   48.1   0.0    1.1  1  Flavodoxin_2  Flavodoxin-like fold
    0.00028   21.1   0.0    0.00059   20.1   0.0    1.5  2  Flavodoxin_5  Flavodoxin domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0   8.4e-32     5e-28       1     125 [.       2     132 ..       2     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 8.4e-32
                                   -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                       FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaadali 77 
                                   mk+l+i+GS+rk++nt+ +++ ++e ++e+gae+e i +++l  ++c    lc+     +++ +dd+ ++++k+++ada++
  gi|91773663|ref|YP_566355.1|   2 MKVLAIIGSPRKNGNTDVVVQKVLEGAAEKGAETESIYINELdFKGCqgcGLCNVMA--DCKLKDDMTDVYKKLEEADAFV 80 
                                   9**********************************************9876666554..578******************* PP

                                   EEEEECTTCE-HHHHHHHHCHT-.....SSCHCCTT-EEEEEEE-SSTTTTH CS
                       FMN_red  78 ivtPeYngsysgllKnalDrlsr....trgkkelrgKpvalvavgggrrggl 125
                                   +++P+Y+ +++g++ ++lDr+ +    + +++   gK ++lv + g+ +g +
  gi|91773663|ref|YP_566355.1|  81 FGSPIYFNQFTGQMRSFLDRCYAlvdaELKPRLPVGKNAVLVRAQGDPNGPM 132
                                   *********************7799887777777788888888888888754 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   1.8e-16   1.1e-12       1     192 [.       2     178 ..       2     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.8e-16
                                   -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHC.......C.HHHHTTC.HHHHHHHH CS
                  Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaa.......k.layeekp.adveseqi 72 
                                   mk+L i ++pr+ + ++  + q+++e+++++g +e + + ++++        d+++         +a+   +  d  ++  
  gi|91773663|ref|YP_566355.1|   2 MKVLAIIGSPRK-NGNTDVVVQKVLEGAAEKG-AETESIYINEL--------DFKGcqgcglcNvMADC--KlKDDMTDVY 70 
                                   9***********.6999***************.99999999997........66666656433233333..3344444446 PP

                                   HHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S-HHH CS
                  Flavodoxin_2  73 ekllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgpeesyqerglegaamde 153
                                   +kl++ada v+++P+++  +  ++  ++Dr +    a       ++  ++  gk a+++ + G p         +g   d 
  gi|91773663|ref|YP_566355.1|  71 KKLEEADAFVFGSPIYFNQFTGQMRSFLDRCYALVDAE---L--KP--RLPVGKNAVLVRAQGDP---------NGPMYDN 135
                                   ******************************96665544...1..23..5555*************.........4433477 PP

                                   HHHHHHHHH.HHTT-EEEEEEEEESCT...CCCH.HHHHHHHHH CS
                  Flavodoxin_2 154 llpplrgil.gfiGikdvepvlvegva...gaed.eealaeale 192
                                   +   ++ il  f+G+++ + +++ g +   +  + +++l ++++
  gi|91773663|ref|YP_566355.1| 136 VFDDFEEILkMFFGMTVTDKIVAAGFDlpgS-VRkDKELMDKAK 178
                                   7777999996799*********999998752.333444444444 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.9   1.1e+04       8      29 ..      14      35 ..      13      43 .. 0.68
   2 !   20.1   0.0   9.8e-08   0.00059      31      69 ..      66     101 ..      55     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.9
                  Flavodoxin_5  8 dGqTkkiaeriaeelreegelv 29
                                   G+T  +++++ e  +e+g+++
  gi|91773663|ref|YP_566355.1| 14 NGNTDVVVQKVLEGAAEKGAET 35
                                  5777777777777777666655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 9.8e-08
                  Flavodoxin_5  31 vedvekesedlesydavvigasvyygkllpelakFvekh 69 
                                   ++d     ++le++da+v+g+++y +++ +++++F+++ 
  gi|91773663|ref|YP_566355.1|  66 MTD---VYKKLEEADAFVFGSPIYFNQFTGQMRSFLDRC 101
                                   333...4589*************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 1085.90
//
Query:       gi|91773664|ref|YP_566356.1|  [L=68]
Description: hypothetical protein Mbur_1714 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0007   20.0   2.0     0.0021   18.4   0.3    1.9  2  HEPN_Apea  Apea-like HEPN
  ------ inclusion threshold ------
      0.064   13.2   0.1      0.064   13.2   0.1    1.1  1  DUF2118    Uncharacterized protein conserved in archaea (DUF2


Domain annotation for each model (and alignments):
>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   2.4e-07    0.0021      75      95 ..       3      23 ..       1      34 [. 0.79
   2 ?    2.3   0.1     0.025   2.2e+02      49      79 ..      32      63 ..      21      65 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-07
                     HEPN_Apea 75 kikklYdlRSkivHggkikkk 95
                                  +i+k+Y+ RS++vH gk+ ++
  gi|91773664|ref|YP_566356.1|  3 NISKIYNARSNVVHKGKMIYD 23
                                  699*************98744 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.025
                     HEPN_Apea 49 eitekislrsnayl.kedkeerkelkkkikkl 79
                                  ei+ k +++++++l ++++e + ++kk+i+k+
  gi|91773664|ref|YP_566356.1| 32 EIAGKYARQVLKHLiYQNSEHKGDFKKFISKI 63
                                  35555555555444455688888899988876 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 ?   13.2   0.1   7.2e-06     0.064      25      69 ..       2      46 ..       1      62 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-06
                       DUF2118 25 eevekfadkveekklkgkvvYeelldeivdvleekvtrdviivlp 69
                                  e++ k+ +  ++   kgk +Y++ +de +d ++ k  r+v+ +l 
  gi|91773664|ref|YP_566356.1|  2 ENISKIYNARSNVVHKGKMIYDVNADENIDEIAGKYARQVLKHLI 46
                                  566778888888999**********************99987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 447.48
//
Query:       gi|91773665|ref|YP_566357.1|  [L=333]
Description: hypothetical protein Mbur_1715 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0056   17.1   0.2     0.0056   17.1   0.2    2.9  3  HEPN_Apea  Apea-like HEPN


Domain annotation for each model (and alignments):
>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   2.8    0.0088   1.6e+02      14      76 ..      18      86 ..       2      97 .. 0.57
   2 ?   -1.1   0.0      0.15   2.7e+03      52      52 ..     154     154 ..      88     235 .. 0.63
   3 !   17.1   0.2   3.1e-07    0.0056       3      62 ..     270     328 ..     268     333 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0088
                     HEPN_Apea 14 lewfgeaireeddedaildlvialEaldll.......ldkkeeitekislrsn.aylkedkeerkelkkki 76
                                  +e +++ i++++++d  ++++ ++++ +++       + + +e +  i + +n ++++e  ++ k++kk+i
  gi|91773665|ref|YP_566357.1| 18 VEILHKLITSDKNNDDAINYIPSINFKFNTvikplgcE-SAKEFKSIINEILNfNKFNE-VYSTKYVKKEI 86
                                  44455555555666667777777777755578887752.32334444433333477766.55556666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.15
                     HEPN_Apea  52 e 52 
                                    
  gi|91773665|ref|YP_566357.1| 154 F 154
                                   1 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 3.1e-07
                     HEPN_Apea   3 ltkfekrlkralewfgeaireeddedaildlvialEaldll.ldkkeeitekislrsnayl 62 
                                   ++k  +++k++l+w++  ++e+  + ++l++ ++lE+ ++l +++ +e++ ++s r+ a l
  gi|91773665|ref|YP_566357.1| 270 NNKITNIVKQCLHWLEIGLNEDLQSAKLLHFTTILESTLKLpSES-TELKQRVSDRC-ALL 328
                                   6788899*************7777899***********7776655.55********9.877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1059  (0.0590663); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2309.21
//
Query:       gi|91773666|ref|YP_566358.1|  [L=263]
Description: ABC transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-24   85.8  22.7    4.2e-24   85.2  22.7    1.3  1  ABC2_membrane    ABC-2 type transporter
    3.5e-10   39.5  33.3    4.9e-10   39.1  33.3    1.2  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 !   85.2  22.7   4.6e-28   4.2e-24       6     208 ..      19     226 ..      16     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 4.6e-28
                 ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.....pgllffsvlflafsaltsvapvferergv 81 
                                   +++r+   + ++  l+ll ++++pll+++ +g+  g   ++ dg+ +     p l+  sv++ af+ ++  + v+++ +++
  gi|91773666|ref|YP_566358.1|  19 VWRRNKDVFMKNAKLNLLPPFVEPLLYLFAMGFGLGMFIEEIDGVPYakfiaPALISVSVMYGAFFECSYGSYVRMYYQKT 99 
                                   5677777999**************************533555555447899****************************** PP

                 ABC2_membrane  82 lerelvsplyslsayvlakvlvelpvsllqalifll.ivyf.lvgldlsrfflflllllltalaasslgllisalapsfed 160
                                   ++   ++pl s  +++++ +l+ +++s++ a++++  i++f l+ ++ s  +l++++++l +l++ +lg++i+a++p++  
  gi|91773666|ref|YP_566358.1| 100 FDAIIATPL-SIEDVIIGELLWGATRSTISATLMIPvIALFgLLTFPHS--LLIIPFAFLAGLLFACLGMCIAAVTPNIMS 177
                                   *********.************************994444433455554..****************************** PP

                 ABC2_membrane 161 asqlaslvllpllllsGffipidsmpkwlqwiay.lnPltyavealrsn 208
                                   ++  ++l+++p++l+sG f+p++ +p+ +q+ia  ++Plt++v ++r+ 
  gi|91773666|ref|YP_566358.1| 178 INYPIMLFITPMFLFSGTFFPLNVLPEIVQYIALaILPLTHVVMIIRAL 226
                                   *************************999999765389*******99986 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 !   39.1  33.3   5.4e-14   4.9e-10     159     343 ..      65     253 ..      42     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.4e-14
               ABC2_membrane_3 159 vasflvgliliilifitasf..iavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllil.ll.afglgipf 235
                                   +a f++++++ ++++++a+f     s+v+   +++   ++ +++s    +++ +l+ ++ + +++ l++ ++ +fg  ++f
  gi|91773666|ref|YP_566358.1|  65 YAKFIAPALISVSVMYGAFFecSYGSYVRMYYQKTFDAIIATPLSIEDVIIGELLWGATRSTISATLMIpVIaLFG-LLTF 144
                                   678999999999999998874334489**************************************99985456899.8999 PP

               ABC2_membrane_3 236 gnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwi.fsiiPffapglgllr 315
                                    +++l++ + +l gl++++lg+ + +++ n  + +  i+++i ++++f+g +fpl+ lp+++++i + i+P++++ + +  
  gi|91773666|ref|YP_566358.1| 145 PHSLLIIPFAFLAGLLFACLGMCIAAVTPNIMSINYPIMLFITPMFLFSGTFFPLNVLPEIVQYIaLAILPLTHVVMIIRA 225
                                   9******************************99988899999989999999999*********9736699*********** PP

               ABC2_membrane_3 316 litgdplweillsliilalfavvyllla 343
                                   l +g+p+ e+l +l++ ++ +++ ++++
  gi|91773666|ref|YP_566358.1| 226 LTFGTPGLELLFNLAWIVGVCAIGFVVS 253
                                   *******************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1725.43
//
Query:       gi|91773667|ref|YP_566359.1|  [L=305]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-33  114.8   0.0    1.5e-32  113.0   0.0    1.8  2  ABC_tran  ABC transporter
    1.8e-13   51.0   0.0    4.8e-06   26.6   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00011   22.1   0.0      0.051   13.3   0.0    2.2  2  AAA_15    AAA ATPase domain
     0.0017   17.8   0.0      0.093   12.2   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
     0.0018   18.8   0.9     0.0034   17.9   0.9    1.6  1  AAA_23    AAA domain
     0.0033   18.1   0.1       0.01   16.6   0.0    1.9  2  DUF4162   Domain of unknown function (DUF4162)
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.027   13.7   0.0    1.4  1  G-alpha   G-protein alpha subunit
      0.013   15.1   0.0      0.024   14.2   0.0    1.3  1  AAA_27    AAA domain
      0.045   14.0   0.7       0.73   10.1   0.7    2.4  1  AAA_22    AAA domain
      0.064   11.9   0.0        0.1   11.2   0.0    1.3  1  AAA_13    AAA domain
       0.13   11.9   0.0       0.42   10.3   0.0    1.8  2  AAA_30    AAA domain
       0.15   12.3   0.0        1.3    9.3   0.0    2.2  1  SbcCD_C   Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0     1e-35   1.5e-32       2     136 ..      24     166 ..      23     167 .. 0.97
   2 ?   -0.8   0.0       1.3     2e+03      34      52 ..     208     235 ..     200     295 .. 0.47

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 1e-35
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   + v ++++ege+ +++G+nGaGK+t ++l+   +  t+G++++ g d+++   ++ + ++gv+pqe++l+p+ tv+en   
  gi|91773667|ref|YP_566359.1|  24 DSVAFSVNEGELFGFLGPNGAGKTTTMRLIQCISPMTSGTLEVFGMDVNS-HQREIKFKMGVVPQENNLDPDFTVYENlfv 103
                                   7899**********************************************.7788899*********************** PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             e+++++e++l+ + l+e++dt      +sLSgG+k+r++lar+l++kp+ll+lDEpt
  gi|91773667|ref|YP_566359.1| 104 fsryfdipedEAKKRVEELLKFVHLEEKRDTMT----ESLSGGMKRRLVLARSLINKPRLLILDEPT 166
                                   ********9999999************999998....*****************************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                                   SS--SEEEEEETTCEGGG.........B CS
                                   xxxxxxxxxxxxxxxxxx.........x RF
                      ABC_tran  34 llkpteGeilldgkdlke.........q 52 
                                   l+  ++G+il++g +++           
  gi|91773667|ref|YP_566359.1| 208 LVIMDNGKILVEGSPTDLiqkyigsaiV 235
                                   5566778887777766653233332222 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   0.0   4.6e-08   6.9e-05       2      83 ..      36     102 ..      35     118 .. 0.87
   2 !   26.6   0.0   3.2e-09   4.8e-06     180     298 ..     114     197 ..     108     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.6e-08
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersq 82 
                                    ++ GpNg+GK++ +++++++              s+  + +   +  d ++   +++f    ++ q+++ +  ++++++ 
  gi|91773667|ref|YP_566359.1|  36 FGFLGPNGAGKTTTMRLIQCI--------------SPMTSGTLEVFGMDVNSHQREIKFKMG-VVPQENNLDPDFTVYENL 101
                                   5789****************9..............6888999********************.***************999 PP

                        AAA_21  83 v 83 
                                   +
  gi|91773667|ref|YP_566359.1| 102 F 102
                                   9 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 3.2e-09
                        AAA_21 180 kekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsl 260
                                   + k+++++l++ ++l e ++++++                                +lS G+kr l l+ +l+  +   +l
  gi|91773667|ref|YP_566359.1| 114 EAKKRVEELLKFVHLEEKRDTMTE--------------------------------SLSGGMKRRLVLARSLINKP---RL 159
                                   556666666666666666666664................................78******955555555444...** PP

                        AAA_21 261 lliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   l++DEp  gL+P+  +  ++ lk l++ g+ ++ltTH 
  gi|91773667|ref|YP_566359.1| 160 LILDEPTVGLDPQSRHLMWDKLKGLKKQGVTIVLTTHY 197
                                   ************9999999999999999*********6 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0034       5.1      25      45 ..      35      55 ..      24      81 .. 0.86
   2 !   13.3   0.0   3.4e-05     0.051     287     364 ..     124     196 ..      70     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
                        AAA_15 25 ltvliGkNnsGKSsilealdl 45
                                  l  + G+N++GK++ +++++ 
  gi|91773667|ref|YP_566359.1| 35 LFGFLGPNGAGKTTTMRLIQC 55
                                  55689************9975 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.4e-05
                        AAA_15 287 k.....ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviit 362
                                   k     ++ ++  +  + G++r l+l+  ++++         + +l+++EP + L pq    ++++lk l +++   +++t
  gi|91773667|ref|YP_566359.1| 124 KfvhleEKRDTMTESLSGGMKRRLVLARSLINK---------PRLLILDEPTVGLDPQSRHLMWDKLKGLKKQGV-TIVLT 194
                                   145566777777777788888877776555444.........456*****************************7.9**** PP

                        AAA_15 363 TH 364
                                   TH
  gi|91773667|ref|YP_566359.1| 195 TH 196
                                   ** 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     0.023        35      29      42 ..      38      51 ..      20      65 .. 0.84
   2 !   12.2   0.0   6.2e-05     0.093     120     209 ..     116     205 ..      74     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.023
                                  EEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxx RF
                         SMC_N 29 ivGpNGSGKsnlld 42
                                   +GpNG+GK+  + 
  gi|91773667|ref|YP_566359.1| 38 FLGPNGAGKTTTMR 51
                                  57*******98776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.2e-05
                                   HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE CS
                                   xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 120 kkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv 194
                                   kk v+ell+ ++++++      +LSgG k      L++A   +++  l +lDe    LD + ++ + + lk  +   Q + 
  gi|91773667|ref|YP_566359.1| 116 KKRVEELLKFVHLEEKrdtmteSLSGGMKR----RLVLARSLINKPRLLILDEPTVGLDPQSRHLMWDKLKGLK--KQGVT 190
                                   45566666666665555555559****987....7899999999999************************999..56666 PP

                                   E-SSHHHCCC-SCEE CS
                                   xxxxxxxxxxxxxxx RF
                         SMC_N 195 islreemlekadklv 209
                                   i l+++ le+a++l+
  gi|91773667|ref|YP_566359.1| 191 IVLTTHYLEEASQLC 205
                                   666777777776654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.9   2.3e-06    0.0034      15      40 ..      26      54 ..      15     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-06
                        AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                  + F   +  l+ + GpNGaGKTT ++ i+
  gi|91773667|ref|YP_566359.1| 26 VAFsvnEGELFGFLGPNGAGKTTTMRLIQ 54
                                  4555555679*************998876 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       7.2   1.1e+04      58      75 ..     120     137 ..     110     137 .. 0.69
   2 !   16.6   0.0   6.7e-06      0.01       1      80 [.     220     298 ..     220     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.2
                                   ----EEEEEEEE---HHH CS
                       DUF4162  58 tsgveirsFeeeePsLnd 75 
                                   ++ ++ +++ee++ ++ +
  gi|91773667|ref|YP_566359.1| 120 EELLKFVHLEEKRDTMTE 137
                                   445667788888888865 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.7e-06
                                   E-HHHHHTTS.-SSEEEEE-------..--.-EEEE-TTS-EEEEE--.---------------EEEEEEEE---HHHHHH CS
                       DUF4162   1 GtleeiKrsy.gknrieveadaeelleepg.veeveeeggelelkled.eeaanellkaltsgveirsFeeeePsLndIFi 78 
                                   G++ ++ ++y g+ ++e e+d++ l  ++g   + e  g+++++  ++ +e+  ++l+++    +++s++ + ++L+d+F+
  gi|91773667|ref|YP_566359.1| 220 GSPTDLIQKYiGSAIVETENDPAILSCLEGhKATYEVLGDNVQIYTDNlQETTDHILSEC----KLKSVTARAATLEDVFL 296
                                   6777777788799999999999999999**55555888999*******999999999999....9**************** PP

                                   HH CS
                       DUF4162  79 ek 80 
                                   ++
  gi|91773667|ref|YP_566359.1| 297 KL 298
                                   97 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.027      28     171 ..      38     273 ..      35     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                   EEESTTSSHHHHHHHHHHHCS--..........--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT................ CS
                       G-alpha  28 llGqseSGKsTilkqlkllykkg..........fseeelatwraviqlnivrsiktilealesleselsesf......... 89 
                                   +lG ++ GK+T+++ ++++   +          +                 ++ + i +++    +e + ++         
  gi|91773667|ref|YP_566359.1|  38 FLGPNGAGKTTTMRLIQCISPMTsgtlevfgmdV----------------NSHQREIKFKMGVVPQENNLDPdftvyenlf 102
                                   799**************99955434455544441................3333444444443322222222235555555 PP

                                   ........HHHC-SS-SCCCS-HCHHHH..................................................... CS
                       G-alpha  90 ........elqelkerldplkkveasliaklssateee........................................... 119
                                            ++e k+r+++l+k+ +   ++ + +++                                             
  gi|91773667|ref|YP_566359.1| 103 vfsryfdiPEDEAKKRVEELLKFVHLEEKRDTMTES-Lsggmkrrlvlarslinkprllildeptvgldpqsrhlmwdklk 182
                                   555555556667777777776666654333222222.24777888888888888888888877777777777777777777 PP

                                   .......................................HHCCHHC-HCHHHHHHHHCCSHHHHHHHC.CGCCTT--.TTH CS
                       G-alpha 120 .......................................qeiefnpraevgedikaLwndpgiqelye.rrnkikle.dna 159
                                                                           ++ ++  + +g +i++  ndp+i +++e ++  ++++ dn+
  gi|91773667|ref|YP_566359.1| 183 glkkqgvtivltthyleeasqlcdrlvimdngkilvegsPTDLIQ--KYIGSAIVETENDPAILSCLEgHKATYEVLgDNV 261
                                   777777666665555555555555555555444444443333333..36666****************7667888555*** PP

                                   HHHHCTHHHHCS CS
                       G-alpha 160 eyFlddlerits 171
                                   +++ d+l++ t+
  gi|91773667|ref|YP_566359.1| 262 QIYTDNLQETTD 273
                                   ******998775 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.024      10      46 ..      16      53 ..      14      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                        AAA_27 10 ryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAi 46
                                   +G+ft   s++fs +e +l   +GpN AGK+t++r i
  gi|91773667|ref|YP_566359.1| 16 EFGEFTAVdSVAFSVNEGELFGFLGPNGAGKTTTMRLI 53
                                  79***98549************************9866 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7   0.00049      0.73      12      99 ..      40     164 ..      34     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                        AAA_22  12 GesGtGKTtllrrlleqldeeakaee.................................erpevv..fvtlpsstsskdll 57 
                                   G+ G+GKTt++r ++   +  +   e                                 e+  v+  ++++p+++  k+  
  gi|91773667|ref|YP_566359.1|  40 GPNGAGKTTTMRLIQCISPMTSGTLEvfgmdvnshqreikfkmgvvpqennldpdftvyENLFVFsrYFDIPEDE-AKKRV 119
                                   999********9999887655554448999999999999999999999999976666644444448899999998.77777 PP

                        AAA_22  58 rellralglelkaerlsseell.ealeqalrarav...ielliiDE 99 
                                   +ell++++le k+    +e l   + ++ + ar+    ++lli+DE
  gi|91773667|ref|YP_566359.1| 120 EELLKFVHLEEKR-DTMTESLSgGMKRRLVLARSLinkPRLLILDE 164
                                   9999999999999.55555555577777778877789999999999 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     7e-05       0.1      23      71 ..      40     103 ..      36     127 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7e-05
                        AAA_13  23 GwNGaGKTtLSrllrslelgetepkfangsi............eitnge.............eldirVfNrdFv 71 
                                   G NGaGKTt  rl+++++       +++g++            e                   +d  V+ + Fv
  gi|91773667|ref|YP_566359.1|  40 GPNGAGKTTTMRLIQCIS------PMTSGTLevfgmdvnshqrE----IkfkmgvvpqennlDPDFTVYENLFV 103
                                   99**************94......33444443345544444441....04444444455555455555555444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00028      0.42      20      41 ..      35      56 ..      23      83 .. 0.80
   2 ?   -2.1   0.0       1.8   2.6e+03      81      98 ..     144     166 ..     114     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                        AAA_30 20 vavltGpAGtGKttalkalrea 41
                                  +    Gp G+GKtt+++ ++ +
  gi|91773667|ref|YP_566359.1| 35 LFGFLGPNGAGKTTTMRLIQCI 56
                                  66678************99765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                        AAA_30  81 k.....grarlepgtllivDEag 98 
                                   k     +r  +++ +lli DE  
  gi|91773667|ref|YP_566359.1| 144 KrrlvlARSLINKPRLLILDEPT 166
                                   14445544556666889999865 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00088       1.3      62      86 ..     155     179 ..     123     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00088
                       SbcCD_C  62 palrlvfLDEAFsklDeesiatlle 86 
                                   +++rl++LDE   +lD++s++ + +
  gi|91773667|ref|YP_566359.1| 155 NKPRLLILDEPTVGLDPQSRHLMWD 179
                                   579***************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1851.23
//
Query:       gi|91773668|ref|YP_566360.1|  [L=589]
Description: hypothetical protein Mbur_1718 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.025   14.5   2.7        7.4    6.6   0.0    2.8  2  Sec20           Sec20
      0.028   13.7   2.5      0.058   12.7   2.5    1.4  1  DUF4805         Domain of unknown function (DUF4805)
      0.034   14.2   7.3      0.036   14.1   3.7    2.5  2  Laminin_II      Laminin Domain II
      0.037   12.0   3.0      0.035   12.1   0.4    1.9  2  Prominin        Prominin
      0.047   13.7   0.4      0.047   13.7   0.4    3.7  4  DUF1664         Protein of unknown function (DUF1664)
      0.051   14.1   0.2        1.3    9.6   0.1    2.6  2  Tox-REase-5     Restriction endonuclease fold toxin 5
       0.13   12.3  11.3      0.033   14.2   3.5    3.0  3  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.29   11.0   7.7       0.45   10.4   0.4    3.3  3  CK2S            Casein Kinase 2 substrate
        0.3   10.7  14.0        1.7    8.3   0.2    3.5  3  YkyA            Putative cell-wall binding lipoprotein
       0.55   10.7   9.2        6.6    7.3   1.0    3.6  3  Spectrin        Spectrin repeat
       0.81   10.3   6.0        1.5    9.5   0.9    2.9  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
       0.95    9.9   5.4         11    6.5   0.4    2.8  2  DUF4140         N-terminal domain of unknown function (DUF414
       0.99    9.8   7.6        0.2   12.0   1.2    3.1  3  CLZ             C-terminal leucine zipper domain of cyclic nu
        1.1    9.5  11.0        1.6    8.9   1.7    3.8  4  COG5            Golgi transport complex subunit 5
        1.4    9.2  13.6         15    5.9   7.1    4.2  4  DUF948          Bacterial protein of unknown function (DUF948
        3.8    7.4   9.3       0.99    9.2   0.5    3.6  3  DASH_Duo1       DASH complex subunit Duo1
        7.7    6.9  11.0        1.2    9.5   2.5    3.2  3  Muted           Organelle biogenesis, Muted-like protein
        9.6    6.1  18.7        0.2   11.6   1.9    3.3  4  DASH_Spc19      Spc19


Domain annotation for each model (and alignments):
>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0074       7.4       4      64 ..     143     201 ..     140     211 .. 0.72
   2 ?    6.4   1.0    0.0086       8.6      23      64 ..     509     548 ..     487     556 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0074
                         Sec20   4 kqiTeslraisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkkler 64 
                                    +iTe l +   +l  ++ + +e le l++  + l  +ee +k+v+d ++ +++l+k +++
  gi|91773668|ref|YP_566360.1| 143 AEITEVLYQEPGVLTTGIYNAKEVLERLNTIEQPL--IEEILKSVDDNFEVTEELLKEVKK 201
                                   68999999999999999999999999999877655..455555555555555555555544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0086
                         Sec20  23 qSeenleeldastkslekleeeykqvedvlsrskklvkkler 64 
                                   + ++nle+l  +tk+le+l++++ + +++ls++++ ++++++
  gi|91773668|ref|YP_566360.1| 509 NLNNNLETL--NTKVLETLNDNLEESKSTLSKANDTMETVQK 548
                                   446677777..589******************9999988887 PP

>> DUF4805  Domain of unknown function (DUF4805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.5   5.8e-05     0.058     130     196 ..     332     397 ..     321     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                       DUF4805 130 ssrrssslrGvrlkssavesereekveqrtqksayptppststltttanssssGprekrryrrsqss 196
                                   + rr   + G+ l+++++++++   ++++   s+ pt  sts++  t ++ss+Gp + +r  r++ s
  gi|91773668|ref|YP_566360.1| 332 ARRRNMNISGATLEDKNISDNQPPAPNMNFSSSTGPTG-STSSTGPTGSTSSTGPADPKRSTRADRS 397
                                   5689999***************999*999999999996.788888899999****998887776654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.64   6.4e+02      12      51 ..     163     200 ..     135     210 .. 0.65
   2 ?   14.1   3.7   3.7e-05     0.036       5      69 ..     485     551 ..     482     561 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.64
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdan 51 
                                   akevle l+ ++q l  ++e l++++++ e t+e++k+ +
  gi|91773668|ref|YP_566360.1| 163 AKEVLERLNTIEQPL--IEEILKSVDDNFEVTEELLKEVK 200
                                   556666666666554..33445555555555555555444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.7e-05
                                   XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX--TTT CS
                    Laminin_II   5 aaeanetakevleqlap.lsqnlentkeklseinrsveet.nekvkdankairdArrsvkkLeklap 69 
                                   ++e+ne++++v  + +p +++ l+n++++l+++n++v et n+++++++ ++  A++ + +++k + 
  gi|91773668|ref|YP_566360.1| 485 LDEVNEILENVRTDQQPrINNVLDNLNNNLETLNTKVLETlNDNLEESKSTLSKANDTMETVQKALS 551
                                   799********9998875888899************977658999***************9998765 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.17   1.7e+02     339     377 ..     163     201 ..      47     256 .. 0.61
   2 ?   12.1   0.4   3.5e-05     0.035     314     419 ..     481     561 ..     442     581 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.17
                      Prominin 339 vkeglarlneipekvknqtaevvpdlkkalakgreqikk 377
                                   +ke l+rln+i++ + +++ + v d ++  ++  +++kk
  gi|91773668|ref|YP_566360.1| 163 AKEVLERLNTIEQPLIEEILKSVDDNFEVTEELLKEVKK 201
                                   345555555555555555555554333333332222222 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.5e-05
                      Prominin 314 l.dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisd 393
                                   + ++l++v+e+le++++  + +++++  + +++l+++++kv +++++ +++ k++l+k+++++++++k++           
  gi|91773668|ref|YP_566360.1| 481 IpQALDEVNEILENVRTDQQPRINNVLDNLNNNLETLNTKVLETLNDNLEESKSTLSKANDTMETVQKAL----------- 550
                                   3345555555555555555555555555555555555555555555555555555555555555555555........... PP

                      Prominin 394 lenterssktfddvvekyekyrwlig 419
                                                    ++ + ++i 
  gi|91773668|ref|YP_566360.1| 551 ---------------SILDFDTKYIK 561
                                   ...............44444444444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.1   3.1e+03      47     103 ..      47     103 ..      31     108 .. 0.49
   2 ?   -0.2   0.2         1   9.9e+02      56      91 ..     169     201 ..     154     214 .. 0.57
   3 ?    0.1   0.2      0.81     8e+02      44      83 ..     242     281 ..     236     306 .. 0.80
   4 ?   13.7   0.4   4.7e-05     0.047      46     117 ..     481     557 ..     470     563 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                       DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                   ++ ++++ e+l++  ++ ++ i     +  +  e+  e ke +++++ + +++g+++
  gi|91773668|ref|YP_566360.1|  47 GTTIQSLGEELKSFLKETEELITIRRLSPRDEDELWDEEKERLDDLKAEKKRLGDEL 103
                                   444444444444444444333333333333334444444444444444444444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                       DUF1664  56 slaatkrhLssri.drvdkkldeqkeiskeikeevte 91 
                                    l++  + L ++i ++vd++ + ++e+ ke+k    +
  gi|91773668|ref|YP_566360.1| 169 RLNTIEQPLIEEIlKSVDDNFEVTEELLKEVK----K 201
                                   44444444444432345555554444444443....3 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.81
                       DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeisk 83 
                                   ++v + + +v++++ a k +++  + ++++k+++   +  
  gi|91773668|ref|YP_566360.1| 242 KEVVSGIHTVMDDMPAKKFEFTGSMIHMNRKMNSDHVVDD 281
                                   5677889999999999999999999999999998776655 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 4.7e-05
                       DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqke.....iskeikeevtevredlseigedvesvkeavegleskl 117
                                   + + l++v e l++++ + + ri++v ++l+++ e     + + ++++++e ++ ls+ ++ +e+v++a + l+   
  gi|91773668|ref|YP_566360.1| 481 IPQALDEVNEILENVRTDQQPRINNVLDNLNNNLEtlntkVLETLNDNLEESKSTLSKANDTMETVQKALSILDFDT 557
                                   56789999999999999999999998888887665111115677899999999999999999999999999988655 PP

>> Tox-REase-5  Restriction endonuclease fold toxin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.48   4.8e+02      32      46 ..     187     201 ..     172     206 .. 0.87
   2 ?    9.6   0.1    0.0013       1.3       7      62 ..     418     471 ..     409     504 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.48
                   Tox-REase-5  32 DGfksaeclllEaKa 46 
                                   D+f+  e+ll+E+K+
  gi|91773668|ref|YP_566360.1| 187 DNFEVTEELLKEVKK 201
                                   9************96 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                   Tox-REase-5   7 qitgvpkgteyrvkseewelldvdfDGfksaeclllEaKagYdqffdkkep.klkks 62 
                                   + tg++ +++ +++s+    l+++fDG++ + +ll+     Yd+ + k e  k+  +
  gi|91773668|ref|YP_566360.1| 418 KFTGANMQPHGARISA---SLATKFDGYQRNYDLLKAQASYYDHQLLKLERkKMRFT 471
                                   5677777775533333...3469******9999999888888865555444133333 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.9   3.9e+03      42      62 ..      45      65 ..      38      73 .. 0.54
   2 ?    1.1   0.2      0.37   3.7e+02      17      72 ..     124     177 ..     115     202 .. 0.43
   3 ?   14.2   3.5   3.3e-05     0.033      43     118 ..     481     553 ..     461     565 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.9
                  Baculo_PEP_C 42 aietqLnalsedlksllaeld 62
                                   i t++++l e+lks l+e +
  gi|91773668|ref|YP_566360.1| 45 VIGTTIQSLGEELKSFLKETE 65
                                  344455555555555544433 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                  Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqL.nalsedlksllaeldtrldtlltnL 72 
                                   d+ nvL++   + + i a++++ ++++  q  + l++ + +  +e+ +rl+t  + L
  gi|91773668|ref|YP_566360.1| 124 DMDNVLKQF-QLIARI-AAVNAEITEVLYQEpGVLTTGIYN-AKEVLERLNTIEQPL 177
                                   455555555.112222.333333333222220122222222.333333444444333 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.3e-05
                  Baculo_PEP_C  43 ietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnllqalnnl 118
                                   i + L++++e l+++ ++++ r++++l+nL++ l +l+   ++ L++ln +l +  s +   n t++ + +al  l
  gi|91773668|ref|YP_566360.1| 481 IPQALDEVNEILENVRTDQQPRINNVLDNLNNNLETLN---TKVLETLNDNLEESKSTLSKANDTMETVQKALSIL 553
                                   556678888888888888888*****************...55577777777777777777777777766666655 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         3     3e+03      70      93 ..      48      71 ..      43      90 .. 0.77
   2 ?    3.8   0.3     0.049        49      46      86 ..     161     203 ..     122     233 .. 0.82
   3 ?   10.4   0.4   0.00045      0.45      50     105 ..     485     541 ..     439     552 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                          CK2S 70 evlakLrekleelqkvrdsleklv 93
                                  + +++L e+l+++ k +++l  ++
  gi|91773668|ref|YP_566360.1| 48 TTIQSLGEELKSFLKETEELITIR 71
                                  678899999999999888876665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.049
                          CK2S  46 ygtp..lrdfpdlqerLrekqlealeevlakLrekleelqkvr 86 
                                   y++   l+++  +++ L+e++l++++  ++  +e l+e++k+ 
  gi|91773668|ref|YP_566360.1| 161 YNAKevLERLNTIEQPLIEEILKSVDDNFEVTEELLKEVKKLF 203
                                   4444559***********************9999999999875 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00045
                          CK2S  50 lrdfpdlqerLrekqlealeevlakLrekleelq.kvrdsleklvrdalqlyeekad 105
                                   l+++ ++ e++r  q+  + +vl++L++ le+l+ kv ++l+  ++++ +++ + +d
  gi|91773668|ref|YP_566360.1| 485 LDEVNEILENVRTDQQPRINNVLDNLNNNLETLNtKVLETLNDNLEESKSTLSKAND 541
                                   88999999*************************934555565555444444443333 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.12   1.2e+02      50      97 ..      55     102 ..      36     113 .. 0.68
   2 ?    8.3   0.2    0.0017       1.7      22      68 ..     162     208 ..     155     214 .. 0.90
   3 ?    6.2   2.7    0.0073       7.3      26     116 ..     459     549 ..     449     561 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.12
                          YkyA  50 dkikklsdealenveeReellekekesieeakeefekikeeieeiede 97 
                                   +++k+  +e  e++  R+     e e  +e ke ++++k+e + + de
  gi|91773668|ref|YP_566360.1|  55 EELKSFLKETEELITIRRLSPRDEDELWDEEKERLDDLKAEKKRLGDE 102
                                   456667777777777777777777777777777777777776666554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
                          YkyA  22 eqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeRee 68 
                                   ++ e L++l   eq l eei++   d+f+  ++l +e+ ++   Re+
  gi|91773668|ref|YP_566360.1| 162 NAKEVLERLNTIEQPLIEEILKSVDDNFEVTEELLKEVKKLFVTREK 208
                                   6788999**************988888**************999997 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0073
                          YkyA  26 kLtelekkeqelyeeiielgmdefdkikklsdealenvee.Reellekekesieeakeefekikeeieei...edeelkke 102
                                   +L +le+k++    ei++ +      i +  de+ e++e+ R+++    ++++++ ++++e++++++ e+   + ee k+ 
  gi|91773668|ref|YP_566360.1| 459 QLLKLERKKMRFTHEIVD-K---PGVIPQALDEVNEILENvRTDQQPRINNVLDNLNNNLETLNTKVLETlndNLEESKST 535
                                   666666666666666664.2...2334444444444443324444444444666666666666555444333334455666 PP

                          YkyA 103 aeelieameeryea 116
                                   +++ +++me+ ++a
  gi|91773668|ref|YP_566360.1| 536 LSKANDTMETVQKA 549
                                   66666666655554 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.0    0.0066       6.6      11      60 ..      55     106 ..      49     110 .. 0.90
   2 ?   -0.3   0.1       1.5   1.5e+03      53      69 ..     163     179 ..     123     204 .. 0.58
   3 ?    6.3   0.2     0.014        14      39      98 ..     463     523 ..     457     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0066
                                   HHHHHHHHHHHHHHCCSSC.SSSHHHHHHHHH.HHHHHHHHHHHHHHHHHHH CS
                      Spectrin  11 deleeWieekeellssedl.gkdleevqallk.khkaleaelaaqqervkal 60 
                                   +el++ ++e+eel++ ++l ++d +e+++ +k ++++l+ae +   +++k+l
  gi|91773668|ref|YP_566360.1|  55 EELKSFLKETEELITIRRLsPRDEDELWDEEKeRLDDLKAEKKRLGDELKSL 106
                                   899*****************************99999999999888888876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHH CS
                      Spectrin  53 qqervkalnelaeklld 69 
                                   ++e +++ln++++ l++
  gi|91773668|ref|YP_566360.1| 163 AKEVLERLNTIEQPLIE 179
                                   34444444444444433 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  39 llkkhkaleaelaaqqervkalnelaekl.ldeghsaseeieerleelnerWeeLkelaae 98 
                                   l++k  ++ +e+ ++ + + +  +  +++ ++   +++++i++ l++ln++ e L +++ e
  gi|91773668|ref|YP_566360.1| 463 LERKKMRFTHEIVDKPGVIPQALDEVNEIlENVRTDQQPRINNVLDNLNNNLETLNTKVLE 523
                                   56677788888888888887776555555388889******************99988765 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 ?    2.1   0.4       0.3     3e+02      77      99 .]      77      99 ..      46     108 .. 0.50
   2 ?    9.5   0.9    0.0015       1.5      25      81 ..     492     549 ..     480     555 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.3
                HIP1_clath_bdg 77 sseqsgeqlssqlaaLqaEkesL 99
                                  ++ +  ++ +++l++L+aEk++L
  gi|91773668|ref|YP_566360.1| 77 DEDELWDEEKERLDDLKAEKKRL 99
                                  33333344445555555555544 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0015
                HIP1_clath_bdg  25 verekkeleeelerlkeeaerkle.eqkeelekLkreleakraelarlkssLesseqs 81 
                                   +e+++ + + +++++ ++ +++le   ++ le+L+ +le+++  l++++ ++e+ +++
  gi|91773668|ref|YP_566360.1| 492 LENVRTDQQPRINNVLDNLNNNLEtLNTKVLETLNDNLEESKSTLSKANDTMETVQKA 549
                                   5666667777777777777777774567788999999999999999999999887765 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.041        41      55      91 ..      71     106 ..      62     107 .. 0.76
   2 ?    6.5   0.4     0.011        11      55      98 .]     498     553 ..     482     553 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.041
                       DUF4140  55 ervpnreaeeeelkalraeleeledelaaledelaaa 91 
                                   +r   r+++e   ++ +++l+ l++e+++l del+++
  gi|91773668|ref|YP_566360.1|  71 RRLSPRDEDEL-WDEEKERLDDLKAEKKRLGDELKSL 106
                                   44444444443.89999*************9999875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                       DUF4140  55 ervpnreaeee...........e.lkalraeleeledelaaledelaaaearlafl 98 
                                   +++p+ +++ +           + l++l++ lee + +l++++d+++++++ l++l
  gi|91773668|ref|YP_566360.1| 498 DQQPRINNVLDnlnnnletlntKvLETLNDNLEESKSTLSKANDTMETVQKALSIL 553
                                   44444444444566666666665599*************************99886 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.9   2.9e+03      20      56 ..      30      66 ..      27      69 .. 0.80
   2 ?   -1.3   0.1         3     3e+03      37      56 ..      86     105 ..      74     107 .. 0.64
   3 ?   12.0   1.2    0.0002       0.2      16      66 ..     486     541 ..     481     546 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.9
                           CLZ 20 akagaeqkeleekverLessLeaLqtrlarLlaeyes 56
                                  ++ag+ ++++   +  + +++++L   l+ +l+e e+
  gi|91773668|ref|YP_566360.1| 30 EDAGDAAEQAGLAIAVIGTTIQSLGEELKSFLKETEE 66
                                  5677778888888889999999999999999999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3
                           CLZ  37 essLeaLqtrlarLlaeyes 56 
                                   +++L+ L+   +rL +e++s
  gi|91773668|ref|YP_566360.1|  86 KERLDDLKAEKKRLGDELKS 105
                                   45677777777777666655 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.0002
                           CLZ  16 Dee...aakag.aeqkeleekverLessLeaLqtrl.arLlaeyessqrkLkqRit 66 
                                   De     ++ + ++q  +++ +++L+++Le+L+t++ + L +++e+s+++L +   
  gi|91773668|ref|YP_566360.1| 486 DEVneiLENVRtDQQPRINNVLDNLNNNLETLNTKVlETLNDNLEESKSTLSKAND 541
                                   555444333344788899*****************625666789999999987655 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.18   1.7e+02      22      94 ..      30     102 ..      21     105 .. 0.87
   2 ?   -1.7   0.0       3.1     3e+03      67      80 ..     163     176 ..     125     204 .. 0.56
   3 ?    2.0   0.1      0.21   2.1e+02       6      26 ..     397     417 ..     396     431 .. 0.83
   4 ?    8.9   1.7    0.0016       1.6      31     125 ..     461     552 ..     432     560 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.18
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-T CS
                          COG5  22 nnnddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlksk 94 
                                   +++ d+ + +  +++ +   iq l ++l++ +++ ++ ++ +  + + ++++ +e k++l++L+a  +rl  +
  gi|91773668|ref|YP_566360.1|  30 EDAGDAAEQAGLAIAVIGTTIQSLGEELKSFLKETEELITIRRLSPRDEDELWDEEKERLDDLKAEKKRLGDE 102
                                   66677777888888899999*************999999999999999999**************99999765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                   XXXXXXXXXXXXXX CS
                          COG5  67 skslssvlselkss 80 
                                    k+  + l+++++ 
  gi|91773668|ref|YP_566360.1| 163 AKEVLERLNTIEQP 176
                                   33333333333322 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.21
                                   XXXXXXXXXXXXXXXXXXXXX CS
                          COG5   6 pdFdpksfanallkatnnndd 26 
                                   +dF+++sfa++ +k ++++++
  gi|91773668|ref|YP_566360.1| 397 SDFNAHSFASENMKFQMDKEQ 417
                                   79*********9996666654 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0016
                                   XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHH.HHHHHHHHH CS
                          COG5  31 lstplkrlnydiqeldkr.lrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepye.eaeklqsal 109
                                   l+ ++k++ +  + +dk  +  +  ++ +e+le++++ ++       ++  l++L++ +e l++kvle  + ++e+++s+l
  gi|91773668|ref|YP_566360.1| 461 LKLERKKMRFTHEIVDKPgVIPQALDEVNEILENVRTDQQP-----RINNVLDNLNNNLETLNTKVLETLNdNLEESKSTL 536
                                   55555555555555555324455556666666666555443.....34444555555555555555554432455555555 PP

                                   HHHHHHHHHHHHHHHH CS
                          COG5 110 krlhqtldLlrralrf 125
                                   ++  +t+++  +al +
  gi|91773668|ref|YP_566360.1| 537 SKANDTMETVQKALSI 552
                                   5555555555444443 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 ?    2.7   0.0      0.16   1.6e+02      33      54 ..      48      69 ..      32     106 .. 0.78
   2 ?    0.5   0.1      0.75   7.4e+02      35      57 ..     178     200 ..     133     209 .. 0.54
   3 ?    2.9   1.1      0.13   1.3e+02      28      71 ..     485     518 ..     460     523 .. 0.57
   4 ?    5.9   7.1     0.015        15      24      70 ..     503     553 ..     481     561 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                        DUF948 33 atieelekqvdpilkevedlla 54
                                  +ti++l++++++ lke+e+l++
  gi|91773668|ref|YP_566360.1| 48 TTIQSLGEELKSFLKETEELIT 69
                                  6788888888888888888765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.75
                        DUF948  35 ieelekqvdpilkevedllakvn 57 
                                   iee+ k vd   + +e+ll++v+
  gi|91773668|ref|YP_566360.1| 178 IEEILKSVDDNFEVTEELLKEVK 200
                                   22222222222222222222222 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.13
                        DUF948  28 ldeaaatieelekqvdpilkevedllakvne........lledvneklekvd 71 
                                   lde+++ +e+++                  +        +l+++n+ le+++
  gi|91773668|ref|YP_566360.1| 485 LDEVNEILENVR------------------TdqqprinnVLDNLNNNLETLN 518
                                   444444444444..................4333333334444444444433 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.015
                        DUF948  24 lkktldeaaatieele....kqvdpilkevedllakvnelledvneklekv 70 
                                   ++++ld++++ +e+l+    + ++  l+e++ +l+k+n+++e v++ l  +
  gi|91773668|ref|YP_566360.1| 503 INNVLDNLNNNLETLNtkvlETLNDNLEESKSTLSKANDTMETVQKALSIL 553
                                   567888888888888866666667777888889999999888888877655 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.5   3.5e+03      23      39 ..     182     198 ..     164     203 .. 0.46
   2 ?    1.6   1.1      0.23   2.3e+02      11      27 ..     502     518 ..     482     524 .. 0.57
   3 ?    9.2   0.5   0.00099      0.99       7      37 ..     520     550 ..     518     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.5
                     DASH_Duo1  23 Lkkaksniervketves 39 
                                   Lk++ +n e  +e +++
  gi|91773668|ref|YP_566360.1| 182 LKSVDDNFEVTEELLKE 198
                                   23333444433333333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.23
                     DASH_Duo1  11 kinevienviesLkkak 27 
                                   +in+v++n++++L++ +
  gi|91773668|ref|YP_566360.1| 502 RINNVLDNLNNNLETLN 518
                                   35555555555555544 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00099
                     DASH_Duo1   7 eqLrkinevienviesLkkaksniervketv 37 
                                   + L+++n+ +e ++++L ka++ +e+v++++
  gi|91773668|ref|YP_566360.1| 520 KVLETLNDNLEESKSTLSKANDTMETVQKAL 550
                                   579999999***************9999875 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.6   1.6e+03      62      84 ..      52      73 ..      38     106 .. 0.43
   2 ?    1.0   0.1       0.5   4.9e+02      43      75 ..     165     197 ..     120     252 .. 0.58
   3 ?    9.5   2.5    0.0012       1.2      40      86 ..     502     548 ..     481     556 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                         Muted 62 smkenLselnkkleaalekverl 84
                                  s+ e+L++++k+ e++  +++rl
  gi|91773668|ref|YP_566360.1| 52 SLGEELKSFLKETEELI-TIRRL 73
                                  44444444444422222.22222 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.5
                         Muted  43 nikklvnelkeqllpkclesmkenLselnkkle 75 
                                   ++ + +n +++ l++++l+s+++n + +++ l+
  gi|91773668|ref|YP_566360.1| 165 EVLERLNTIEQPLIEEILKSVDDNFEVTEELLK 197
                                   333333333334444444444333333332222 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0012
                         Muted  40 lLenikklvnelkeqllpkclesmkenLselnkkleaalekverllq 86 
                                   +++n+  ++n+  e+l+ k+le++++nL+e ++ l +a++++e++++
  gi|91773668|ref|YP_566360.1| 502 RINNVLDNLNNNLETLNTKVLETLNDNLEESKSTLSKANDTMETVQK 548
                                   34444455555555555556666666666666666666666666665 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.4     0.013        13     132     157 .]      81     106 ..      51     106 .. 0.78
   2 ?   -1.1   0.2       1.5   1.5e+03      50      80 ..     170     200 ..     168     229 .. 0.79
   3 ?   -3.0   0.1         6     6e+03     138     147 ..     458     467 ..     407     474 .. 0.59
   4 ?   11.6   1.9    0.0002       0.2      50     108 ..     488     547 ..     479     554 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    DASH_Spc19 132 ltkeelerlkkLkqkKerLkytlerL 157
                                   l  ee+erl +Lk++K+rL  +l+ L
  gi|91773668|ref|YP_566360.1|  81 LWDEEKERLDDLKAEKKRLGDELKSL 106
                                   678999**************999865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                    DASH_Spc19  50 leaakaslaeeiePqieellekaekelekle 80 
                                   l++ ++ l+eei  ++++++e +e+ l++ +
  gi|91773668|ref|YP_566360.1| 170 LNTIEQPLIEEILKSVDDNFEVTEELLKEVK 200
                                   6777888999999999999999998877654 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6
                                   XXXXXXXXXX CS
                    DASH_Spc19 138 erlkkLkqkK 147
                                   ++l kL +kK
  gi|91773668|ref|YP_566360.1| 458 HQLLKLERKK 467
                                   3444444444 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHH......HHH CS
                    DASH_Spc19  50 leaakaslaeeiePqieellekaekeleklerr.eetLkaklelqegrlsnaesskkeee 108
                                   +++  ++++ + +P i++ l+ ++++le l+++  etL+ +le  ++ ls+a+++ ++ +
  gi|91773668|ref|YP_566360.1| 488 VNEILENVRTDQQPRINNVLDNLNNNLETLNTKvLETLNDNLEESKSTLSKANDTMETVQ 547
                                   6666788999********************999569***************877666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1436  (0.0800937); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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):              18  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.43
# Mc/sec: 4133.12
//
Query:       gi|91773669|ref|YP_566361.1|  [L=65]
Description: XRE family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-15   56.7   0.1      2e-15   56.6   0.1    1.0  1  HTH_3           Helix-turn-helix
    3.8e-09   36.4   0.2      4e-09   36.4   0.2    1.0  1  HTH_19          Helix-turn-helix domain
      4e-06   27.2   0.0    4.4e-06   27.0   0.0    1.0  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    6.8e-06   26.3   0.0    7.3e-06   26.2   0.0    1.1  1  HTH_31          Helix-turn-helix domain
     0.0023   17.7   0.2     0.0028   17.5   0.2    1.2  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.019   14.9   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.015   14.8   0.1      0.025   14.1   0.1    1.4  1  Sigma70_r4      Sigma-70, region 4
      0.047   13.6   0.1       0.07   13.1   0.1    1.3  1  HTH_11          HTH domain
       0.08   12.7   0.0       0.16   11.8   0.0    1.6  1  MerR            MerR family regulatory protein
       0.12   12.2   0.0       0.16   11.8   0.0    1.3  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


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 !   56.6   0.1   1.1e-18     2e-15       1      54 [.       5      58 ..       5      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.1e-18
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                  +kelR   +l+qeeLA+k+Gv r ti  +E+G+ nPsl+ ++ +ak+++ ++++
  gi|91773669|ref|YP_566361.1|  5 IKELRARYDLTQEELAKKVGVRRETILFLEKGKYNPSLKLAYTIAKVFDSTIED 58
                                  8************************************************99986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.2   2.2e-12     4e-09       3      60 ..       4      60 ..       3      65 .] 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.2e-12
                        HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                  r+ke+R  + ltqeela+++g++r  i  +E+gk+ +ps +l + ia+ ++ ++e  +
  gi|91773669|ref|YP_566361.1|  4 RIKELRARYDLTQEELAKKVGVRRETILFLEKGKY-NPSLKLAYTIAKVFDSTIEDVF 60
                                  9*********************************9.*************998877655 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 !   27.0   0.0   2.4e-09   4.4e-06       1      61 [.       4      63 ..       4      65 .] 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.4e-09
                        HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleye 61
                                  +++el a  ++t+ eLa+++g+ + t+  l kgk  ++sl+   +i+++++ t++D +++ 
  gi|91773669|ref|YP_566361.1|  4 RIKELRARYDLTQEELAKKVGVRRETILFLEKGK-YNPSLKLAYTIAKVFDSTIEDVFILD 63
                                  799******************************9.6*********************9876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.1e-09   7.3e-06       5      51 ..       4      49 ..       3      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.1e-09
                        HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51
                                  + ++lR+r  L+qee+A+ +gv + t+  lE G+  +ps+     +a
  gi|91773669|ref|YP_566361.1|  4 RIKELRARYDLTQEELAKKVGVRRETILFLEKGKY-NPSLKLAYTIA 49
                                  6789*******************************.6*987655555 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   1.5e-06    0.0028       2      37 ..       5      40 ..       4      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                  HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TT CS
                        HTH_25  2 LraaRearglsleevaketkIrkdylealEeddfda 37
                                   ++ R +  l+ ee+ak+  +r +++  lE+++++ 
  gi|91773669|ref|YP_566361.1|  5 IKELRARYDLTQEELAKKVGVRRETILFLEKGKYNP 40
                                  68999****************************986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.1e-05     0.019      20      38 ..      12      30 ..       2      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                  EEHHHHHHHHHTTSSHHHH CS
                     HTH_Crp_2 20 lpltqeelAsmlGltretv 38
                                   +ltqeelA  +G++ret+
  gi|91773669|ref|YP_566361.1| 12 YDLTQEELAKKVGVRRETI 30
                                  589**************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.4e-05     0.025      15      37 ..       8      30 ..       4      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                  HHHTTT--HHHHHHHHTS-HHHH CS
                    Sigma70_r4 15 lrfgeglTleEIgerlgiSrerV 37
                                  lr   +lT+eE++++ g+ re++
  gi|91773669|ref|YP_566361.1|  8 LRARYDLTQEELAKKVGVRRETI 30
                                  666789***************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.9e-05      0.07       6      32 ..       5      30 ..       2      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                        HTH_11  6 lelLleargpisgeeLAeeLnvSrrtv 32
                                  ++ L +ar +++ eeLA++ +v r t+
  gi|91773669|ref|YP_566361.1|  5 IKEL-RARYDLTQEELAKKVGVRRETI 30
                                  5678.99****************9998 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.9e-05      0.16       4      21 ..      18      35 ..       4      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                                  HHHHHHTTTHHHHHHHHH CS
                          MerR  4 evAeltGvsprtLRyYEr 21
                                  e+A+++Gv   t+ ++E+
  gi|91773669|ref|YP_566361.1| 18 ELAKKVGVRRETILFLEK 35
                                  88**************97 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.1e-05      0.16      10      45 ..      15      50 ..      10      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.1e-05
                YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpaervpeIek 45
                                  +q +LA+++gv ++++ ++ kgk + + +   +I k
  gi|91773669|ref|YP_566361.1| 15 TQEELAKKVGVRRETILFLEKGKYNPSLKLAYTIAK 50
                                  599***************999988777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 468.54
//
Query:       gi|91773670|ref|YP_566362.1|  [L=130]
Description: hypothetical protein Mbur_1720 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   33.2   0.9    7.3e-08   32.5   0.9    1.4  1  DUF2178          Predicted membrane protein (DUF2178)
     0.0012   17.7   2.1     0.0017   17.2   2.1    1.3  1  TRP              Transient receptor potential (TRP) ion chann
  ------ inclusion threshold ------
       0.14   12.0   5.6       0.15   12.0   0.7    2.0  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.9   1.2e-11   7.3e-08       5      77 ..      16      91 ..      12     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.2e-11
                       DUF2178  5 vavialvglgiwaaignvllaviavaaGvllaillkkkve...evveDERlariaekAsrktlqillfliallgvv 77
                                  ++ + ++gl +w  +   + a+++++a +l++++l   ++     + DER++ri+ekA + ++ il++ ia+l ++
  gi|91773670|ref|YP_566362.1| 16 ILGMLVLGLILWQFQFYGGSAALIIIASILTVMFLHTATKpqeYFIRDERSVRINEKAGYHAFWILVMCIAILTMM 91
                                  45556677777776677788999999**********999999889********************99999988765 PP

>> TRP  Transient receptor potential (TRP) ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.1   2.8e-07    0.0017     201     268 ..       9      76 ..       6     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-07
                           TRP 201 allrlilifffqllvlclfeft.qrdsaavvvlAvillalflgvllffafrvlitarkskrlhknpayl 268
                                   +l  l+li+++ +l l l++f  ++ saa +++A+il ++fl + +    +++i+ ++s+r+ +++ y+
  gi|91773670|ref|YP_566362.1|   9 TLRGLALILGMLVLGLILWQFQfYGGSAALIIIASILTVMFLHT-ATKPQEYFIRDERSVRINEKAGYH 76 
                                   6777899**************889******************77.777788888888888887776665 PP

>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7   2.4e-05      0.15     123     169 ..       6      52 ..       3      58 .. 0.86
   2 ?    2.7   0.4     0.017     1e+02     149     179 ..      73     106 ..      66     108 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
               Peptidase_M48_N 123 dklkslllalviglpllaallwiiewggeyfylylwlfllvfslllm 169
                                   dk     lal++g+++l ++lw ++ +g +  l++++ +l +++l +
  gi|91773670|ref|YP_566362.1|   6 DKYTLRGLALILGMLVLGLILWQFQFYGGSAALIIIASILTVMFLHT 52 
                                   67777789******************999999999999999888765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.017
               Peptidase_M48_N 149 ggeyfylylwlf...llvfslllmtiyPtlIaPL 179
                                   +g + +++l++    l+++  +  ++y  + aPL
  gi|91773670|ref|YP_566362.1|  73 AGYHAFWILVMCiaiLTMMDWFTEILYKDVSAPL 106
                                   4444443333330003333345556666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 895.41
//
Query:       gi|91773671|ref|YP_566363.1|  [L=128]
Description: hypothetical protein Mbur_1721 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-06   28.6   2.5      2e-06   27.9   2.5    1.4  1  DUF2178          Predicted membrane protein (DUF2178)
     0.0017   17.8   0.9      0.002   17.5   0.9    1.1  1  Polysacc_synt    Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.62   10.5   6.5         15    6.1   0.2    3.1  3  FeoB_associated  FeoB-associated Cys-rich membrane protein
        5.8    6.4   7.3       0.66    9.5   0.7    2.1  2  4HB_MCP_1        Four helix bundle sensory module for signal 
        9.7    6.2   9.1         18    5.4   0.7    2.7  2  PLDc_N           Phospholipase_D-nuclease N-terminal


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   2.5   5.6e-10     2e-06      24      84 ..      37     100 ..      27     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.6e-10
                       DUF2178  24 laviavaaGvllaillkkkve.evveDERlariaekAsrktlqi..llfliallgvvlivlksd 84 
                                   + ++ ++  ++l++++++k   e   DER+++++ kA+r t+ +  l++l +l+g +l++ k +
  gi|91773671|ref|YP_566363.1|  37 IIGMEIGSLIALIYIIRRKKSgEPEHDERTEKVTGKAARSTIIVlmLVLLTILGGDLLSLIKLE 100
                                   55666777899*****999988**********************65455555555555555544 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.9   5.7e-07     0.002      62     130 ..      54     122 ..      19     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.7e-07
                 Polysacc_synt  62 reiakyrek..kelvslillnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrg 130
                                   r ++ +      e++ + + ++  +++++++l+ll+ l  ++l+l  l  +  +++++  ll++++ f++ 
  gi|91773671|ref|YP_566363.1|  54 RKKSGE--PehDERTEKVTGKAARSTIIVLMLVLLTILGGDLLSLIKLEAIEMLAIIIPILLISMVGFVSY 122
                                   233333..1458***************************************99999999999999999875 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.022        79      15      27 ..      46      58 ..      34      61 .. 0.63
   2 ?    3.0   0.5      0.04   1.4e+02       2      12 ..      77      87 ..      76      98 .. 0.71
   3 ?    6.1   0.2    0.0042        15       3      22 ..     107     126 ..     105     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.022
               FeoB_associated 15 fvirrlikkkkkG 27
                                   +++++i++kk+G
  gi|91773671|ref|YP_566363.1| 46 IALIYIIRRKKSG 58
                                  2466677777777 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.04
               FeoB_associated  2 tiIVgliiaaa 12
                                  tiIV+ ++++ 
  gi|91773671|ref|YP_566363.1| 77 TIIVLMLVLLT 87
                                  89999999863 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0042
               FeoB_associated   3 iIVgliiaaavafvirrlik 22 
                                   iI+ +++++ v+fv +++ k
  gi|91773671|ref|YP_566363.1| 107 IIIPILLISMVGFVSYYNSK 126
                                   8999**********999876 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.3      0.12   4.3e+02      11      33 ..      78     102 ..      76     105 .. 0.80
   2 ?    9.5   0.7   0.00018      0.66      10      31 ..     105     126 ..     104     128 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                     4HB_MCP_1  11 lflllallliivG..vvGlyslkki 33 
                                   +++l+++ll+i+G  +++l++l+ i
  gi|91773671|ref|YP_566363.1|  78 IIVLMLVLLTILGgdLLSLIKLEAI 102
                                   5889999999999888888888765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00018
                     4HB_MCP_1  10 llflllallliivGvvGlyslk 31 
                                   l++++ +ll+ +vG+v++y+ k
  gi|91773671|ref|YP_566363.1| 105 LAIIIPILLISMVGFVSYYNSK 126
                                   789*****************87 PP

>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.7    0.0051        18       3      17 ..      44      57 ..      42      91 .. 0.70
   2 ?    0.9   6.1      0.12   4.3e+02      19      38 ..     104     123 ..      78     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0051
                        PLDc_N  3 wiialidiirdrnps 17
                                  ++iali+iir+ + s
  gi|91773671|ref|YP_566363.1| 44 SLIALIYIIRR-KKS 57
                                  689*******4.333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                        PLDc_N  19 klaWllvilflPvlGailYl 38 
                                    la ++ il++  +G++ Y+
  gi|91773671|ref|YP_566363.1| 104 MLAIIIPILLISMVGFVSYY 123
                                   67889*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 962.29
//
Query:       gi|91773672|ref|YP_566364.1|  [L=401]
Description: hypothetical protein Mbur_1722 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-13   48.2   1.1    9.7e-13   47.7   1.1    1.2  1  DUF2254   Predicted membrane protein (DUF2254)
     0.0033   17.9   1.6         17    6.4   0.0    4.6  4  HEAT_PBS  PBS lyase HEAT-like repeat


Domain annotation for each model (and alignments):
>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   1.1   1.1e-16   9.7e-13      41     173 ..       6     144 ..       1     158 [. 0.85

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-16
                       DUF2254  41 gaeaaralLstiagsmltvagfvfSitvvalqlassqfsPRllrnfmrdrvtqvvLGtfigtfvYsllvlrairteee... 118
                                   ++++ar +Ls+++ s+ +v+++v+++ +va+ql ++++s R++  + + +   + ++++  t+++ l ++  i+t++    
  gi|91773672|ref|YP_566364.1|   6 NPDNARYMLSALIQSLAAVVAIVITLSLVAIQLSAQSYSSRVIDVYRKTPDIWILISIYTTTIFFGLGTIKIIGTNTLpin 86 
                                   799***********************************************************************8865876 PP

                       DUF2254 119 ...vpqlsvlvalllaivsvllLiyFihhlarsiqvsnviarveeelrkai...learede 173
                                        +  ++ +++l +++ ++Li +i ++  +++ s +++ ++e++ +        ++ e
  gi|91773672|ref|YP_566364.1|  87 glfSLESFIFGTYFLGFFCFICLIPYIWNTLALLNPSVIVQLLAEDITEDKiskT--ED-E 144
                                   6654447788899*****************************9999766542321..22.1 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 !    5.0   0.0    0.0057        51       4      17 ..     246     259 ..     245     261 .. 0.86
   2 ?   -0.5   0.0      0.32   2.9e+03       5      15 ..     270     280 ..     268     289 .. 0.77
   3 !    6.4   0.0    0.0019        17       4      17 ..     315     328 ..     314     330 .. 0.90
   4 ?    1.2   0.0     0.092   8.2e+02       5      24 ..     339     358 ..     337     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0057
                                   HHHHHHHHCTSGGG CS
                      HEAT_PBS   4 aAakaLgqlgdeea 17 
                                   +A+ aLgq+g + a
  gi|91773672|ref|YP_566364.1| 246 YAVMALGQIGGKTA 259
                                   79********8655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.32
                                   HHHHHHHCTSG CS
                      HEAT_PBS   5 AakaLgqlgde 15 
                                    + +Lg++g +
  gi|91773672|ref|YP_566364.1| 270 VIIGLGAIGEK 280
                                   5789****985 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0019
                                   HHHHHHHHCTSGGG CS
                      HEAT_PBS   4 aAakaLgqlgdeea 17 
                                   +A+ aLgq+g ++a
  gi|91773672|ref|YP_566364.1| 315 YAVMALGQIGEKAA 328
                                   79********9887 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.092
                                   HHHHHHHCTSGGGHHHHHHH CS
                      HEAT_PBS   5 AakaLgqlgdeeaipaLlea 24 
                                    + aLg+ g ++a   L +a
  gi|91773672|ref|YP_566364.1| 339 VIIALGKTGEKAAENKLEWA 358
                                   678*******9998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2874.83
//
Query:       gi|91773673|ref|YP_566365.1|  [L=238]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  199.5   0.0    4.5e-59  199.2   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.16   11.4   0.0    1.3  1  TPALS          TIR- and PNP-associating SLOG family
       0.15   10.9   0.0       0.24   10.3   0.0    1.2  1  Lyase_8_N      Polysaccharide lyase family 8, N terminal alph


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 !  199.2   0.0   7.5e-63   4.5e-59       2     191 ..      12     230 ..      11     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 7.5e-63
                                   HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S.......... CS
                 DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene.......... 72 
                                   +ai+a ++G++  ++D+++re+e+d++i A++vtp++v++m+r+++Glicva+++e+ ++L+Lp++++             
  gi|91773673|ref|YP_566365.1|  12 KAIKAAQNGEMFFIYDSDSREGETDFVITASSVTPDDVRWMRRDGGGLICVAIDSENSKKLGLPFISD--Vlrdeakanpa 90 
                                   79****************************************************************96..33356789999 PP

                                   ............STT---BB--EEESST-SSS-SHHHHHHHHHHHH-.T...........T--GGGEEEEEEEEEEEE-TT CS
                 DHBP_synthase  73 ............dkhktaftvsvdaaegttTGIsaaDRalTirklad.p...........kakpedfrrPGhvfplrareg 129
                                                  +++f+++v+++ +t+TGI ++DRalTi++l + +           +   ++fr+PGhv +lra+++
  gi|91773673|ref|YP_566365.1|  91 lgntvekggdlaYDTRSSFSIWVNHR-KTRTGIPDNDRALTINELSNiTekcmkgedvifG---SEFRTPGHVALLRAADH 167
                                   9********9995568**********.9*******************62567766654332...9**************** PP

                                   GGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TT.SCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                 DHBP_synthase 130 gvleRrghTEaavdLarlaglkpaavicellndd.gtmarrdeleefakkhglkiitiedlie 191
                                    v +R+g+TE+++++a++a+++pa v+ce+l+d+ g+++++++++e+a+ hgl +++++++++
  gi|91773673|ref|YP_566365.1| 168 LVHDRKGQTELSIAIAKMADVTPAMVVCEMLDDSnGRALSKKDAKEYAELHGLVFLEGQEIVD 230
                                   ***********************99******998899***********************996 PP

>> TPALS  TIR- and PNP-associating SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.16      11     108 ..      28     135 ..      19     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                         TPALS  11 SiskeaskaaverAhelvralvkellkaggnlV.vpvdaeptredglpltfdw.........liweaikenlasrpadasg 81 
                                   S s+e +++ v +A   + + v+ + + gg+l+ v +d e  ++ glp   d           + ++++++ +  + d+++
  gi|91773673|ref|YP_566365.1|  28 SDSREGETDFVITASSVTPDDVRWMRRDGGGLIcVAIDSENSKKLGLPFISDVlrdeakanpALGNTVEKGGDL-AYDTRS 107
                                   55666677777777777777777777888887548899999999********9555554444333333333222.346689 PP

                         TPALS  82 plavvvshhkteeqipeerreL.wdrLr 108
                                   ++ + v+h kt++ ip++ r+L +++L+
  gi|91773673|ref|YP_566365.1| 108 SFSIWVNHRKTRTGIPDNDRALtINELS 135
                                   ********************99557776 PP

>> Lyase_8_N  Polysaccharide lyase family 8, N terminal alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   3.9e-05      0.24     269     294 ..     190     215 ..     178     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.9e-05
                                   GGEETTEE-GGGSGGGGGSCCCTCHH CS
                     Lyase_8_N 269 plivkgemmdmvrGRsiSRaneqnke 294
                                   p +v  em+d+ +GR+ S ++++++ 
  gi|91773673|ref|YP_566365.1| 190 PAMVVCEMLDDSNGRALSKKDAKEYA 215
                                   899******************99773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1925.17
//
Query:       gi|91773674|ref|YP_566366.1|  [L=223]
Description: winged helix-turn-helix domain-containing protein/riboflavin kinase [Methanococcoides burtonii DSM 6242]
Scores for 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-45  153.2   0.0    4.3e-45  152.7   0.0    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120
  ------ inclusion threshold ------
      0.062   13.1   0.0       0.12   12.2   0.0    1.4  1  FtsK_gamma      Ftsk gamma domain
      0.063   13.2   0.0       0.11   12.4   0.0    1.3  1  MarR            MarR family


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.7   0.0   7.2e-49   4.3e-45       1     121 []      96     216 ..      96     216 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 7.2e-49
                                   EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEECCEE CS
                CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypakiekik 81 
                                   V++GlgeG+yy+ ++gy +qfeeklgf+pypGTLNv+l+++s ++ k+ ++ + i+i+gf+d++rtfg++++y +++e+++
  gi|91773674|ref|YP_566366.1|  96 VITGLGEGQYYIAQDGYGSQFEEKLGFKPYPGTLNVRLTSHSADILKRKSQKNIIPISGFTDGQRTFGGCNCYFVEVEGVR 176
                                   89******************************************************************************* PP

                                   EEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                CTP-dep_RFKase  82 aavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                   +avv+per+hy++d+lEii+p++LR++lel+dgdev++ +
  gi|91773674|ref|YP_566366.1| 177 GAVVTPERSHYPHDLLEIISPVHLRKTLELNDGDEVKIMI 216
                                   *************************************976 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     2e-05      0.12      19      49 ..      21      51 ..      16      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                    FtsK_gamma 19 kaStSllQRrlriGYnRAarlidqLeeeGiV 49
                                  k+S S + R  + G + Aar++ qLeeeG +
  gi|91773674|ref|YP_566366.1| 21 KISSSEFTRYTSTGSKTAARILKQLEEEGSI 51
                                  7899*************************87 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05      0.11      19      54 ..      23      58 ..       8      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT CS
                          MarR 19 svseLakklgvskstvtrvldrLekkGlieRskspe 54
                                  s se  +  ++ + t+ r+l++Le++G i+R   pe
  gi|91773674|ref|YP_566366.1| 23 SSSEFTRYTSTGSKTAARILKQLEEEGSIDRLIIPE 58
                                  555777777777889****************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1627.28
//
Query:       gi|91773675|ref|YP_566367.1|  [L=292]
Description: Ion transport protein [Methanococcoides burtonii DSM 6242]
Scores for 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-33  113.4  20.4    1.2e-32  113.1  20.4    1.1  1  Ion_trans      Ion transport protein
    2.3e-14   53.1   4.5    2.3e-14   53.1   4.5    2.6  3  Ion_trans_2    Ion channel
     0.0062   16.5   0.2     0.0094   16.0   0.2    1.3  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.022   13.5  14.7       0.36    9.4  14.7    2.1  1  PKD_channel    Polycystin cation channel
      0.022   14.5   3.6      0.039   13.7   3.6    1.4  1  zinc_ribbon_2  zinc-ribbon domain
      0.072   13.6   0.3       0.13   12.8   0.3    1.4  1  zf-CHY         CHY zinc finger
       0.17   12.1   0.8       0.29   11.3   0.8    1.3  1  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
       0.19   11.2   4.9       0.68    9.4   4.9    1.8  1  zf-ribbon_3    zinc-ribbon domain
        0.3   10.7   1.4        2.2    7.9   0.2    2.1  2  pEK499_p136    HEPN pEK499 p136
        1.2    8.9   4.7        5.2    6.9   4.8    2.0  2  zf-CCHC_4      Zinc knuckle


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 !  113.1  20.4   6.5e-36   1.2e-32       2     238 ..      35     246 ..      34     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 6.5e-36
                                   HHHHHHHHHHHHHHHHHHHCCCSSSSHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCHSHHHHHHHHHHHHHH CS
                     Ion_trans   2 svfelfilllillncvflaletyfpedelektileilelvftaiftlemllkilalgllikkrYlrdpwnilDflvvlpsl 82 
                                   ++f++  +l+i+l++++++l++ +  ++   + l ++e++ft++ft+e ll++++ +   k rY ++++ i+D+l+++p++
  gi|91773675|ref|YP_566367.1|  35 KYFDITLILTIILSVIVVMLDSVHSISSIHHQKLYMAEIIFTILFTIEYLLRMICVKS--KVRYATSFFGIIDLLAIIPTY 113
                                   69******************9998886666699*************************..********************* PP

                                   HHH....HHHHHHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCC CS
                     Ion_trans  83 lsl....vlseesllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlllllvvlfifaligvqlfkgklrek 159
                                   ls+        + ll+++v+rl+r++r+lkl+++l    +lv+al++s k++  + + +l +++i +++++ +        
  gi|91773675|ref|YP_566367.1| 114 LSFffpgS---QYLLIIRVFRLLRIFRVLKLVQYLTEADMLVQALKDSSKKITVFTFTVLNLVLILGSLMYVIE------- 184
                                   ***75431...669********************************************************9999....... PP

                                   CCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 160 necaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNlliaviadnfq 238
                                           ++   ++ F++++ +++w+++++tt+g+gd++++t  ++       ++++++l ++ +++++ ++i++++ 
  gi|91773675|ref|YP_566367.1| 185 --------GE---QNGFTSIPRSVFWAITTLTTVGYGDLVPVTPLGQ------AMASVVMLLGYSIIAVPTGIITHSII 246
                                   ........22...334888****************************......**********************9875 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.4      0.46   8.3e+02      48      71 ..      31      54 ..      27      62 .. 0.57
   2 ?   -2.3   4.0       2.5   4.5e+03       2      34 ..      40      73 ..      39     116 .. 0.65
   3 !   53.1   4.5   1.3e-17   2.3e-14       2      76 ..     169     244 ..     168     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.46
                                  -----HHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2 48 tdagrlftivyillGlalfalfla 71
                                  t++g++f i +il+ ++ +++++ 
  gi|91773675|ref|YP_566367.1| 31 TPIGKYFDITLILTIILSVIVVML 54
                                  555666665555555555555444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                  HHHHTCHHHHHHHHT.......T---HHH.HHHHHHH CS
                   Ion_trans_2  2 vlllvlifgaviysl...eegwekwsfld.alYfsfv 34
                                  +l+l++i+++++++l   +   +  s+ +  lY++ +
  gi|91773675|ref|YP_566367.1| 40 TLILTIILSVIVVMLdsvH---SISSIHHqKLYMAEI 73
                                  6788888888888883331...122222235555422 PP

  == domain 3  score: 53.1 bits;  conditional E-value: 1.3e-17
                                   HHHHTCHHHHHHHHT......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2   2 vlllvlifgaviysl..eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkv 76 
                                   vl lvli+g+++y +  e +    s+  +++++++tltT+GYGd+vp+t++g++++ v++llG++++a+ + +++  
  gi|91773675|ref|YP_566367.1| 169 VLNLVLILGSLMYVIegE-QNGFTSIPRSVFWAITTLTTVGYGDLVPVTPLGQAMASVVMLLGYSIIAVPTGIITHS 244
                                   56789**********852.334579999****************************************998888765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   5.3e-06    0.0094      28      49 .]     267     289 ..     244     292 .] 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.3e-06
                           DZR  28 edrCpsCgek.vdpearfCpeCG 49 
                                   +++C +Cg +  d +a fC++CG
  gi|91773675|ref|YP_566367.1| 267 NIACHNCGLQgHDIDAYFCKNCG 289
                                   56777777777777777777777 PP

>> PKD_channel  Polycystin cation channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  14.7    0.0002      0.36     211     401 ..      41     224 ..      36     251 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SSS----HHHH CS
                   PKD_channel 211 lllievvfvvfvlyfvveeilkirkerasylrsvwnlldlaivvlsvvlivlailrevlakkllkkveaekeefldFreva 291
                                   l+l  ++ v++v++ +v+ i  i+++ + y+ ++   + + i  l  ++ v + +r+ +    +  ++a   ++l+F  + 
  gi|91773675|ref|YP_566367.1|  41 LILTIILSVIVVMLDSVHSISSIHHQ-KLYMAEIIFTILFTIEYLLRMICVKSKVRYATSFFGIIDLLAIIPTYLSFFFP- 119
                                   44545555555555666666666666.44444433233333433333333444444443333333344667778887665. PP

                                   HHHHHHHHHHHHHHHHHHHGGGGG------------------------HHHHHHHHHHHHHHHHHHSSSS-STTSSHHHHH CS
                   PKD_channel 292 qldqllriilavlvflttlkllkvlrfnktlslltktlaralkdvlgfalvivilflayaqlgvllfGtqasnfsnlvksi 372
                                      +++  i+ v  +l + ++lk++++  +  +l ++l++++k++  f++ ++ l+l  + l++++ G+q + f  + +s+
  gi|91773675|ref|YP_566367.1| 120 --GSQYLLIIRVFRLLRIFRVLKLVQYLTEADMLVQALKDSSKKITVFTFTVLNLVLILGSLMYVIEGEQ-NGFTSIPRSV 197
                                   ..456777777888899999999999999***************************************97.57******** PP

                                   HHHHHHHTT---HHHHHHH-TTHHHHHHH CS
                   PKD_channel 373 ltlfrlilgdfqytelesgnrvLGpllll 401
                                   +   +++l  ++y +l  +   LG  + +
  gi|91773675|ref|YP_566367.1| 198 FWA-ITTLTTVGYGDLVPV-TPLGQAMAS 224
                                   *99.788889999987432.334444444 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.6   2.2e-05     0.039       2      23 .]     270     292 .]     269     292 .] 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                 zinc_ribbon_2   2 CpnCGaelqd.nakFCpyCGtpl 23 
                                   C nCG +  d +a FC +CG++l
  gi|91773675|ref|YP_566367.1| 270 CHNCGLQGHDiDAYFCKNCGAKL 292
                                   ********877**********97 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   7.1e-05      0.13      49      74 ..     262     290 ..     240     291 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                        zf-CHY  49 teqekavlCkkCkk...efaeyfCpiCkl 74 
                                   +    +++C++C+    ++++yfC++C +
  gi|91773675|ref|YP_566367.1| 262 KDVALNIACHNCGLqghDIDAYFCKNCGA 290
                                   22356789****776669*********75 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   0.00016      0.29      10      32 ..     269     291 ..     262     292 .] 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                  NOB1_Zn_bind  10 rChaCfkvtkdmtkkFCpkCGnk 32 
                                    Ch C    +d +  FC++CG k
  gi|91773675|ref|YP_566367.1| 269 ACHNCGLQGHDIDAYFCKNCGAK 291
                                   7********************75 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.9   0.00038      0.68       3      26 .]     268     292 .]     266     292 .] 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00038
                   zf-ribbon_3   3 vrCPnCGap.lssddnvCpyCGtkl 26 
                                   + C nCG +  + d+ +C++CG+kl
  gi|91773675|ref|YP_566367.1| 268 IACHNCGLQgHDIDAYFCKNCGAKL 292
                                   67999**8556***********997 PP

>> pEK499_p136  HEPN pEK499 p136
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0012       2.2      33      62 ..      35      65 ..      22      86 .. 0.71
   2 ?    1.5   0.0      0.11     2e+02      32      62 ..     155     195 ..     134     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                   pEK499_p136 33 ekynlTlllnsllGlivlpke..rlfkkalls 62
                                  + ++ Tl+l  +l++iv++     ++ +++  
  gi|91773675|ref|YP_566367.1| 35 KYFDITLILTIILSVIVVMLDsvHSI-SSIHH 65
                                  789***************98843233.34444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                   pEK499_p136  32 e.......ekynlTll.lnsllGlivlpke...rlfkkalls 62 
                                           +++ +T+l l  +lG++++  e   + f ++++ 
  gi|91773675|ref|YP_566367.1| 155 LkdsskkiTVFTFTVLnLVLILGSLMYVIEgeqNGF-TSIPR 195
                                   123345669999998878889999999888666666.66665 PP

>> zf-CCHC_4  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.8    0.0029       5.2      30      47 ..     266     285 ..     265     288 .. 0.86
   2 ?   -0.4   0.3      0.54   9.6e+02      33      38 ..     284     289 ..     282     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0029
                     zf-CCHC_4  30 LrsfCyiCgvlGHsdk..rC 47 
                                   L ++C +Cg+ GH+++  +C
  gi|91773675|ref|YP_566367.1| 266 LNIACHNCGLQGHDIDayFC 285
                                   7899**********986666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.54
                     zf-CCHC_4  33 fCyiCg 38 
                                   fC +Cg
  gi|91773675|ref|YP_566367.1| 284 FCKNCG 289
                                   9****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2103.33
//
Query:       gi|91773676|ref|YP_566368.1|  [L=526]
Description: hypothetical protein Mbur_1726 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0017   17.0   0.4     0.0025   16.5   0.4    1.2  1  Herpes_LAMP2  Herpesvirus Latent membrane protein 2
  ------ inclusion threshold ------
      0.015   15.1   0.7      0.069   13.0   0.0    2.3  3  DUF4307       Domain of unknown function (DUF4307)
      0.034   13.6   1.4      0.054   12.9   1.4    1.3  1  Ceramidase    Ceramidase


Domain annotation for each model (and alignments):
>> Herpes_LAMP2  Herpesvirus Latent membrane protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   4.2e-07    0.0025     273     370 ..      70     163 ..      43     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.2e-07
                  Herpes_LAMP2 273 iilllvclillyclyvwqsfnkaslvtGilflilawshaGgcvklvllltdGltrGvlsglicvivllstlqallvfylyk 353
                                     +llv   ll+ + +wqs ++ ++   + f+i++ + + +  +l+ l        + s++i ++++l  + a +   ly+
  gi|91773676|ref|YP_566368.1|  70 DSILLVFFTLLWAVTIWQSSKRRAMNHNLSFIIASVAFTISASHLINLHD----PIIFSVVIAIATILGYGAASITRNLYN 146
                                   3467788899***********************************99875....458999********************* PP

                  Herpes_LAMP2 354 ekklvavnsvtrrlriy 370
                                   ek    ++++  +   y
  gi|91773676|ref|YP_566368.1| 147 EKIAYRFDEMMGKITSY 163
                                   *9888888776666555 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.33     2e+03      11      31 ..      72      92 ..      68     104 .. 0.71
   2 ?   13.0   0.0   1.2e-05     0.069      16      88 ..     136     215 ..     120     227 .. 0.71
   3 ?   -3.8   0.0       1.9   1.1e+04      55      67 ..     241     253 ..     234     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.33
                       DUF4307 11 vlvvvalalvawigysqgsad 31
                                  +l+v +++l+a++++++++ +
  gi|91773676|ref|YP_566368.1| 72 ILLVFFTLLWAVTIWQSSKRR 92
                                  678888888999888884443 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.2e-05
                       DUF4307  16 alalvawigysq....gsadvsaevvgfevvddstvevtfeVtrddgs...pavCiVrAldedgaevGrrevlvpagder 88 
                                   ++a ++  +y++    + +++ ++ ++++ v++s+ ++t +V+ + ++   + +C+Vr  ded  + G  +++v a++  
  gi|91773676|ref|YP_566368.1| 136 GAASITRNLYNEkiayRFDEMMGKITSYDLVEASSKNITRDVDDPLSAavdSIRCAVRNHDEDSFKKGLDKITVSAKNLM 215
                                   333344444444443445678899*******************99877556789********************988433 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.9
                       DUF4307  55 rddgspavCiVrA 67 
                                   ++d+++ +C+V++
  gi|91773676|ref|YP_566368.1| 241 SRDETATECVVHS 253
                                   4566688999986 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   9.1e-06     0.054      84     148 ..      70     135 ..      31     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                    Ceramidase  84 Delsmiyatalvlyavfsekksrstrvllgvlltalavvvtllylv.lkepvlhqvafalltvlvl 148
                                   D + +++ t+l ++ + + +k+r +++ l+++++++a+++++ +l+ l++p++++v+ a++t+l +
  gi|91773676|ref|YP_566368.1|  70 DSILLVFFTLLWAVTIWQSSKRRAMNHNLSFIIASVAFTISASHLInLHDPIIFSVVIAIATILGY 135
                                   55555566666666666668888999********************99***********9988643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3711.80
//
Query:       gi|91773677|ref|YP_566369.1|  [L=95]
Description: hypothetical protein Mbur_1727 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 624.21
//
Query:       gi|91773678|ref|YP_566370.1|  [L=297]
Description: formylmethanofuran--tetrahydromethanopterin formyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-65  217.7   1.0    6.7e-65  217.7   1.0    1.4  2  FTR_C     FTR, proximal lobe
    4.8e-63  211.3   0.8    9.8e-63  210.3   0.1    1.8  2  FTR       Formylmethanofuran-tetrahydromethanopterin formyltr


Domain annotation for each model (and alignments):
>> FTR_C  FTR, proximal lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.1   9.5e+03      18      37 ..      21      40 ..       8      42 .. 0.69
   2 !  217.7   1.0   7.4e-69   6.7e-65       1     149 []     147     296 ..     147     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                                  EEEEEEESSHHHHHHHHHHH CS
                         FTR_C 18 gnllilaedqeaaleaaeaa 37
                                  + +li+a++++ a  aa++a
  gi|91773678|ref|YP_566370.1| 21 SRILITAATKRWATVAAQEA 40
                                  56778888888888887776 PP

  == domain 2  score: 217.7 bits;  conditional E-value: 7.4e-69
                                   EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-.S-TT-SEEE-GGG-TT CS
                         FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgs.kykflkastNeafcpt 80 
                                   g+fl+e++lg+v+++aGgn++i++++q+++l+aae+av+ai +v+g+itpFpGgiv+sgSK g+ kykflka++Ne+fcp+
  gi|91773678|ref|YP_566370.1| 147 GDFLVEDTLGAVTAIAGGNFFIFGDTQMTTLTAAENAVDAIGAVDGTITPFPGGIVASGSKAGAnKYKFLKATANEKFCPS 227
                                   8***************************************************************9**************** PP

                                   STT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGGG CS
                         FTR_C  81 lkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLkel 149
                                   +k+kve se+p+dv++v+EiVi+gld e++a+a+++gi+aav+v+g++ki+AgNygG+LG++kf+L++l
  gi|91773678|ref|YP_566370.1| 228 IKDKVEGSEIPADVNCVYEIVINGLDFESIAKATEMGIRAAVAVPGIKKITAGNYGGSLGPHKFNLHDL 296
                                   *******************************************************************97 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.3   0.1   1.1e-66   9.8e-63       1     142 []       1     144 [.       1     144 [. 0.98
   2 ?   -1.3   0.1      0.21   1.9e+03      25      59 ..     177     213 ..     167     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 1.1e-66
                                   -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEEESSH CS
                           FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailifaask 81 
                                   +e+ngveiedtfaEaF+ik++r++iTaatk+wa+ aa+eatgf+tsvigc+aEagie++ +++etpDgRpGv+i+++++  
  gi|91773678|ref|YP_566370.1|   1 MELNGVEIEDTFAEAFPIKISRILITAATKRWATVAAQEATGFGTSVIGCPAEAGIEKYADASETPDGRPGVYIQFCTFGF 81 
                                   89******************************************************************************* PP

                                   HHHHHHHHHHHHHHTTTSTT-EEEE--..GG-SEEHHHHHHGGGTT--EEEEETTEEEEEEEE CS
                           FTR  82 kklekqlleRigqcvLtapttavfngl..aeekiklgkklrffgDgyeiekelggrkvwriPv 142
                                   k+le+qlleR+gqc+Ltapttavfngl  ae+++++g+kl++f+Dg e+e+e+ggrk++ iP+
  gi|91773678|ref|YP_566370.1|  82 KSLEEQLLERVGQCILTAPTTAVFNGLpdAEKQFDTGRKLKYFADGTESETEVGGRKMHVIPM 144
                                   ***************************7666*******************************6 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.21
                                   EE-SSHHHHHHHHH..HHHSS-S-TTTSS-EEEESEE CS
                           FTR  25 iTaatkkwakeaat..eatgfatsvigceaEagierv 59 
                                   +Taa++++  + a   ++t f++ +++ +  ag +++
  gi|91773678|ref|YP_566370.1| 177 LTAAENAVDAIGAVdgTITPFPGGIVASGSKAGANKY 213
                                   5666666555555412577889999998888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2120.67
//
Query:       gi|91773679|ref|YP_566371.1|  [L=172]
Description: lipoprotein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-12   48.4   0.0    1.4e-12   48.1   0.0    1.1  1  Transglut_core  Transglutaminase-like superfamily


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 !   48.1   0.0   7.7e-17   1.4e-12      11     112 .]       3     101 ..       1     101 [. 0.91

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 7.7e-17
                Transglut_core  11 akdplekakaiyewvrknveys.aprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsgeeekeqsva 90 
                                    ++p e  k+  ewvr+n+  s +   +p + +a++vle+g G+c   ++l++allRa+ ipa + ++ ls ++    +++
  gi|91773679|ref|YP_566371.1|   3 SDEPVEITKRCFEWVRDNIYHShDHCLNPITLKASEVLEAGTGYCYAKSHLLAALLRANSIPAGLYYQRLSRDN----NGE 79 
                                   67899999**************77778888888************************************99764....488 PP

                Transglut_core  91 sedaHawvevylegygWvplDp 112
                                   +   H  + +yl++  W+++D+
  gi|91773679|ref|YP_566371.1|  80 PFCLHDLNAIYLPDISWYRIDA 101
                                   8999***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1418.89
//
Query:       gi|91773680|ref|YP_566372.1|  [L=461]
Description: TraB family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-32  111.7   0.0    9.2e-32  111.0   0.0    1.2  1  TraB      TraB family


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.0   5.1e-36   9.2e-32       9     252 ..      64     281 ..      59     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 5.1e-36
                          TraB   9 gttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd...tdeatqkelaklkllpdgktlsdllseelyarlqk 86 
                                   +++++++GT+Hvs+ksv ++++++e+  ek+d v+vEl++ ++   + e + ++l+ +++l+ g+++  +l + l+a +qk
  gi|91773680|ref|YP_566372.1|  64 PSEIIIVGTAHVSEKSVNEVTSAIEN--EKPDIVAVELCQGRYdslKGEVKDSDLPIKDILS-GGKIYYFLVHLLLAYVQK 141
                                   5679**********************..9***********9997888888888888899999.****************** PP

                          TraB  87 alakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsllss.lpdeeqlea 166
                                   ++ + ++++      +P  +a+++++++  ++++g + +lvDr+++ t++r + +++ +E++  +++l+ss l    +++ 
  gi|91773680|ref|YP_566372.1| 142 KIGD-EMGV------QP--GAEMITAIDV-AEANGAKVALVDRDIQLTLQRFWSKMSIFEKFNMLVALVSSaLGIGGSKNI 212
                                   ****.9***......**..9********8.5899999999*****************************654888888887 PP

                          TraB 167 leetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkep.gsvfvaVGagHlaG 246
                                     + +     ++d++++l++              e+++++p+   vl+deR+++ a ++ +l +++ +++ ++ GagH  G
  gi|91773680|ref|YP_566372.1| 213 DIDNI---T-DQDMVTTLIN--------------ELRKASPNAATVLIDERDAYIAGNLLRLANGGnKKIIAVLGAGHKQG 275
                                   77555...3.5789******..............**************************9887778*************9 PP

                          TraB 247 edgvla 252
                                    +++l+
  gi|91773680|ref|YP_566372.1| 276 VEKYLK 281
                                   998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3353.32
//
Query:       gi|91773681|ref|YP_566373.1|  [L=366]
Description: peptidase M50 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   80.1   2.7    1.7e-10   41.2   0.2    2.3  2  CBS             CBS domain
    5.7e-17   61.8   6.7    1.8e-09   37.3   0.8    3.1  2  Peptidase_M50   Peptidase family M50
    0.00044   20.0   1.1    0.00044   20.0   1.1    2.2  2  Peptidase_M50B  Peptidase M50B-like
  ------ inclusion threshold ------
        3.1    7.6   7.8        1.7    8.4   0.2    2.3  2  FA_desaturase   Fatty acid desaturase


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.2   1.7e-13   7.7e-10       1      55 [.     245     298 ..     245     300 .. 0.88
   2 !   41.2   0.2   3.8e-14   1.7e-10       1      53 [.     307     359 ..     307     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.7e-13
                                   HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+d+m++dv++v p++t+ e+ +  + ek++ ++PV+ e + l Gi+t +D+ r++
  gi|91773681|ref|YP_566373.1| 245 VKDVMSKDVIFVEPSMTIDELTQFmF-EKKHMGYPVM-ERNTLKGIITFTDVRRVM 298
                                   89**********************55.55544*****.5666**********9987 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 3.8e-14
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllr 53 
                                   V+d mt+dvvt+p +++ ++a++lm + + ++r++V+de g + Gi++++Dl+ 
  gi|91773681|ref|YP_566373.1| 307 VSDAMTHDVVTIPLEANAADAFKLM-SFNkIGRVLVIDEGGSVTGILSRTDLMH 359
                                   8999*********************.7666********999***********86 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   1.0   1.9e-09   8.3e-06       3     106 ..      57     125 ..      55     129 .. 0.88
   2 !   37.3   0.8   3.9e-13   1.8e-09     181     250 .]     136     202 ..     124     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.9e-09
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkks 83 
                                    lll+++vv+HElGH ++A++ gvk+                      i+l+ +GG+ +m++                 ++
  gi|91773681|ref|YP_566373.1|  57 TLLLFVCVVLHELGHSYLAQKYGVKITD--------------------ITLFLIGGVSSMEEVP---------------RD 102
                                   689***********************88....................888889**99999988...............56 PP

                                   XXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  84 pwqrllivlAGplanfilailvf 106
                                   p q++ +++AGpl+ fi++  ++
  gi|91773681|ref|YP_566373.1| 103 PSQEAKMAFAGPLVSFIIGTSLL 125
                                   889999********999987665 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 3.9e-13
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 181 seaaeaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglalllll 250
                                   +   e+ +s ++q+l +i++ Lg++NLlP +++DGg++l+a +    rk   ++++ +a  vg ++ +ll
  gi|91773681|ref|YP_566373.1| 136 ATFGENVVSRIIQMLGYINIVLGMFNLLPAFPMDGGRILRAWFA---RKMNYVQATHTAASVGKMFAFLL 202
                                   4556777889******************************9855...77899999999999998888765 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.1   9.7e-08   0.00044      20      95 ..      59     135 ..      46     187 .. 0.80
   2 ?    0.2   0.6      0.11   4.8e+02      89     128 ..     186     225 ..     170     241 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.7e-08
                Peptidase_M50B  20 fkllvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg..pgglgqiltllaGYlgpallGlllillsasgkarl 95 
                                   +  + v++HElGH   a   G ++++i+l+   +Gv+ ++   +   + + +++aG+l + ++G  l+l+ +    ++
  gi|91773681|ref|YP_566373.1|  59 LLFVCVVLHELGHSYLAQKYGVKITDITLFLI-GGVSSMEEvpRDPSQEAKMAFAGPLVSFIIGTSLLLINFVLADTF 135
                                   4556799**********************985.788888888777778899**************9999877655544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                Peptidase_M50B  89 asgkarlllvllvllllvllllvrnlfglvlllllgalll 128
                                   ++++++++++ ++++ll +l lv n+ + +l+++++ + +
  gi|91773681|ref|YP_566373.1| 186 QATHTAASVGKMFAFLLGFLGLVSNPWNPWLIFIAIFVYM 225
                                   5556666777666666666666666555544444433333 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00039       1.7       3      34 ..      47      76 ..      44      97 .. 0.54
   2 ?    1.6   3.0     0.045     2e+02     122     175 ..     178     225 ..     110     234 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00039
                 FA_desaturase  3 wlalllalllglf.llgitg.slaHeaaHgalfk 34
                                  +l++    ll+l+ +l++ + ++ He++H +l +
  gi|91773681|ref|YP_566373.1| 47 FLGY----LLALVtTLLLFVcVVLHELGHSYLAQ 76
                                  3444....45555443333449*******87772 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.045
                 FA_desaturase 122 arrrapsksrrrkwrllawlllllaw...lglwlalllllglall...lwlvplllllfl 175
                                   ++r+           ++ +   ++++    +++l++l+l +   +    wl+++++++ +
  gi|91773681|ref|YP_566373.1| 178 FARKM---------NYVQATHTAASVgkmFAFLLGFLGLVS---NpwnPWLIFIAIFVYM 225
                                   22222.........222222222222112333333333333...2334777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2534.93
//
Query:       gi|91773682|ref|YP_566374.1|  [L=379]
Description: L-tyrosine decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-31  109.5   0.0    2.9e-31  108.6   0.0    1.4  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    6.7e-09   35.4   0.0    9.3e-07   28.3   0.0    2.4  1  Aminotran_1_2    Aminotransferase class I and II
      2e-08   33.6   0.0    4.7e-08   32.4   0.0    1.5  2  Aminotran_5      Aminotransferase class-V
    3.1e-05   23.4   0.0    4.7e-05   22.8   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  108.6   0.0   6.4e-35   2.9e-31      62     356 ..      46     310 ..      22     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 6.4e-35
                                   HHHT-BTSSTTTSHHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHH CS
                 Pyridoxal_deC  62 dainkngftweesPaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaei 142
                                   + i  n+ +    P + +le  vl + +++l+  +     e  g l++g++es++ a        i+ m++  ++      
  gi|91773682|ref|YP_566374.1|  46 QFIESNMGDPGLFPGTFNLEKQVLAMFGKMLHHKNSP---EKAGYLTTGGTESNIQA--------IRSMHNFRHD------ 109
                                   567777778888899****************998433...457***********976........4666666656...... PP

                                   HCCEEEEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHH CS
                 Pyridoxal_deC 143 ldklvlytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdi 223
                                     +++++  + ah s +k+a++ g+++r   ld+  k+  ++ + +i   +++  ++   v ++Gtt  g+ d ++el +i
  gi|91773682|ref|YP_566374.1| 110 ISRPNIVMPESAHFSFDKVANLSGIEIRKASLDKLLKVDLDSVRSLI---DKN--TI-GLVGIAGTTEFGQLDPINELSKI 184
                                   679******************************86666666655555...444..55.6788******************* PP

                                   HHHCT-EEEEE-TTGGGGGGSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTT CS
                 Pyridoxal_deC 224 cekydlwlHvDAAyaGsaficpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLeheds 301
                                     + ++ lH+DAA++G  f+ p++      ++++e + S+t+ phK+ l ++  + l++k+ e   ++l+++  YL  +  
  gi|91773682|ref|YP_566374.1| 185 AIEKGIFLHIDAAFGG--FVIPFMDIdytYDFRLEGVTSMTIDPHKMALSTIPSGGLLFKEPEYF-ECLEIHTPYLSVN-- 260
                                   ****************..*****976677********************************9986.7999*******33.. PP

                                   TTSEECCCGSSSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                 Pyridoxal_deC 302 dvaadlgtkaiplsr.rvrilklwfvlralGveglqnqirksvelakyleklirkd 356
                                         +++ +   r    ++  + v++ lG++g+++++  ++ + k+l +  +k 
  gi|91773682|ref|YP_566374.1| 261 ------KQYSLTGTRsGAGVASTYAVMKHLGRKGYKKVVSDCMSVTKKLVDGAEKL 310
                                   ......3567777776788999**************************99988775 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   2.1e-10   9.3e-07      49     243 ..      64     284 ..      56     374 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.1e-10
                                   HHHHHHHHHC..TCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-....EEEEEESS-THHHHHHHHTTSEEEEEEBE CS
                 Aminotran_1_2  49 leealakflg..rseklklkreaavvvgsGagaliealifllklnpgd....eilvpdptyasyknilrlsggevvryply 123
                                   le+++   +g   ++k +   +a  ++++G+ ++i+a+  +  ++++d    +i++p+  + s++++++lsg+e+++ +l+
  gi|91773682|ref|YP_566374.1|  64 LEKQVLAMFGkmLHHKNSP-EKAGYLTTGGTESNIQAIRSMH-NFRHDisrpNIVMPESAHFSFDKVANLSGIEIRKASLD 142
                                   6666666666432222222.2235788888888888888877.6777744445**************************99 PP

                                   ETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH. CS
                 Aminotran_1_2 124 seedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat. 203
                                     +  ++dl+++  +++++      t +++        G++ + +el k+   a +++++l +D a++gfv   +d   t 
  gi|91773682|ref|YP_566374.1| 143 --KLLKVDLDSVRSLIDKN------TIGLVGIAGTTEFGQLDPINELSKI---AIEKGIFLHIDAAFGGFVIPFMDIDYTy 212
                                   ..****************4......3344444444568************...9999***************955433335 PP

                                   ...........................HGGSTTSTT...EEEEE.ESSSTTSSGGG-EEEEEEEH.HHHHHH CS
                 Aminotran_1_2 204 ...........................ranveeepn...llivg.slsKafGlaGeRvGyilgna.avvsql 243
                                                              +++  e+ +   +++ + s+ K ++l+G R G+ +++  av ++l
  gi|91773682|ref|YP_566374.1| 213 dfrlegvtsmtidphkmalstipsgglLFKEPEYFEcleIHTPYlSVNKQYSLTGTRSGAGVASTyAVMKHL 284
                                   455555555555555444444444444333333444443333222444555555555555444222333333 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0     1e-11   4.7e-08      65     177 ..      87     197 ..      74     214 .. 0.85
   2 ?   -2.3   0.0      0.38   1.7e+03     250     296 ..     266     312 ..     238     342 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1e-11
                                   EEESSHHHHHHHHHHHCCCC..-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEE CS
                   Aminotran_5  65 iftsGtteainlvalslars..lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklv 143
                                   + t G+te++  +++s+ +      + +iv+ e+ h +      ++a+  g+++++++ld+  ++dld +++l++++t  +
  gi|91773682|ref|YP_566374.1|  87 YLTTGGTESNIQAIRSMHNFrhDISRPNIVMPESAHFSFD----KVANLSGIEIRKASLDKLLKVDLDSVRSLIDKNTIGL 163
                                   5689999987777777755443334567888877777765....99999****************************9999 PP

                                   EEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                   Aminotran_5 144 aithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                      +  ++ G ++p++e+ k+a +kg+++++Daa
  gi|91773682|ref|YP_566374.1| 164 VGIAGTTEFGQLDPINELSKIAIEKGIFLHIDAA 197
                                   9999*****************************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.38
                                   .SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTT CS
                   Aminotran_5 250 aGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpg 296
                                    GT   ag+ +  a++++l + g++++ +   + +++l+++ ++l+ 
  gi|91773682|ref|YP_566374.1| 266 TGTRSGAGVASTYAVMKHLGRKGYKKVVSDCMSVTKKLVDGAEKLGI 312
                                   48888888888888888888888888888777777777776666555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0     1e-08   4.7e-05      52     169 ..      82     197 ..      43     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1e-08
                                   E......ES-HHHHHHHHH.....HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S CS
               Beta_elim_lyase  52 f......vpqGtaAnsill.....killqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikev 121
                                   +      ++ Gt +n  ++       +  + +++++ e ah+ fd   +   l+g++ r++  ++  k+dl++++++i++ 
  gi|91773682|ref|YP_566374.1|  82 PekagylTTGGTESNIQAIrsmhnFRHDISRPNIVMPESAHFSFDKVAN---LSGIEIRKASLDKLLKVDLDSVRSLIDK- 158
                                   144444488888888888743332112224578999999******8766...5999************************. PP

                                   -TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
               Beta_elim_lyase 122 gaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       + i+l+ ++ T++   Gq   l+ ++e+++ia ++gi lh+D+A
  gi|91773682|ref|YP_566374.1| 159 ----NTIGLVGIAGTTEF--GQ---LDPINELSKIAIEKGIFLHIDAA 197
                                   ....589**********8..76...68889999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2520.33
//
Query:       gi|91773683|ref|YP_566375.1|  [L=411]
Description: cell division control protein 6 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   80.3   0.4    1.7e-22   79.1   0.4    1.6  1  Cdc6_C           CDC6, C terminal winged helix domain
    6.7e-12   45.9   0.0    1.4e-11   44.8   0.0    1.4  1  AAA_22           AAA domain
    6.6e-09   36.4   0.2    1.6e-07   31.9   0.0    2.6  2  AAA_16           AAA ATPase domain
    3.3e-08   34.0   0.1    7.8e-08   32.8   0.1    1.6  1  AAA              ATPase family associated with various cellul
    7.5e-07   28.7   0.0    1.4e-06   27.9   0.0    1.4  1  TniB             Bacterial TniB protein
    2.2e-05   24.5   1.0    8.5e-05   22.6   1.0    1.9  1  ATPase_2         ATPase domain predominantly from Archaea
    3.7e-05   23.7   0.0    9.7e-05   22.3   0.0    1.7  2  NACHT            NACHT domain
    0.00042   20.1   0.3       0.79    9.5   0.0    2.7  3  DEAD             DEAD/DEAH box helicase
    0.00056   19.7   0.0     0.0014   18.4   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
    0.00071   18.9   0.1       0.87    8.8   0.1    2.2  2  KAP_NTPase       KAP family P-loop domain
    0.00088   19.0   0.0      0.076   12.7   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0055   16.0   0.0     0.0074   15.6   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0063   16.1   0.0      0.018   14.6   0.0    1.7  1  AAA_25           AAA domain
     0.0095   15.7   0.2      0.019   14.7   0.2    1.5  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.014   16.0   0.1      0.048   14.2   0.0    2.0  2  AAA_18           AAA domain
      0.025   13.8   0.1      0.099   11.8   0.0    1.9  2  DUF815           Protein of unknown function (DUF815)
      0.046   13.5   0.1       0.45   10.2   0.0    2.4  3  IstB_IS21        IstB-like ATP binding protein
      0.048   14.0   0.5       0.13   12.6   0.5    1.8  1  AAA_assoc_2      AAA C-terminal domain
      0.059   12.6   0.4       0.27   10.5   0.0    2.1  3  Zeta_toxin       Zeta toxin
      0.075   12.4   0.1          1    8.6   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.084   12.9   0.2        0.3   11.0   0.1    2.0  2  ResIII           Type III restriction enzyme, res subunit
      0.086   12.8   0.0       0.17   11.9   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.092   12.6   0.2       0.41   10.4   0.2    1.9  1  Bac_DnaA         Bacterial dnaA  protein
      0.097   12.8   0.3        1.4    9.0   0.3    2.3  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.11   12.0   0.0       0.18   11.3   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.12   12.7   0.0       0.31   11.4   0.0    1.7  1  RNA_helicase     RNA helicase
       0.14   11.0   0.0       0.25   10.2   0.0    1.3  1  Kinesin          Kinesin motor domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.4   2.6e-25   1.7e-22       1      82 [.     307     386 ..     307     388 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.6e-25
                                   HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHH CS
                        Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddv 81 
                                   L++++ l + +g + vttgevy+vY++lC s ++d ltqr+v dl+seL+mlgil++ ++skGr +grt++i L+v+ +  
  gi|91773683|ref|YP_566375.1| 307 LYSVMVLRD-NGHRNVTTGEVYNVYRQLCISVDMDILTQRRVTDLISELDMLGILNAVVVSKGR-YGRTKEIVLSVPIEST 385
                                   899998888.*****************************************************9.***********99876 PP

                                   H CS
                        Cdc6_C  82 l 82 
                                   +
  gi|91773683|ref|YP_566375.1| 386 R 386
                                   5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   2.1e-14   1.4e-11       4     129 ..      57     183 ..      54     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.1e-14
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                   t + ++++G +GtGKT ++r +  +l++ ++  + + +v++ ++ +  ++  ll +l++++g++    +  ++++++++ +
  gi|91773683|ref|YP_566375.1|  57 TPSNILIYGKTGTGKTAVARYVGIELERKSEDLDVPCSVLYLNCEVIDTQYRLLANLAKQFGEDIPMTGWPTDQVFSKFKE 137
                                   56789*********************76555555999999*************************99899999999***** PP

                        AAA_22  85 alraravielliiDEaqhlr..seealeeLrsl.lnlsrkgvqliLvG 129
                                   a+++++ + ++i+DE+++l    +++l +L+++  +   k+ +l ++G
  gi|91773683|ref|YP_566375.1| 138 AIDSKKQVIMIILDEIDKLVkkGDDVLYNLSRInTD--LKNAKLSMIG 183
                                   *******9**********986549999999555244..6777766666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.4e-10   1.6e-07       2     160 ..      35     169 ..      34     182 .. 0.62
   2 ?   -2.1   0.0       6.7   4.4e+03      86      94 ..     258     266 ..     202     305 .. 0.52

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.4e-10
                        AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysalaqa 75 
                                   l+ R e+++ L+++l ++ +g++ +++l++G  G+GK++++r +  +le++       + +l+ +c+    ++ y    ++
  gi|91773683|ref|YP_566375.1|  35 LPHRTEQVNNLATILVSALRGDTpSNILIYGKTGTGKTAVARYVGIELERKsedldvPCSVLYLNCEVI--DTQY----RL 109
                                   788********9999999999988********************9988888565543344455555555..2222....22 PP

                        AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqlla 156
                                   l +  l +q +++        w++                  +++ ++k+++   s+++  + ++lD+++++     ++l+
  gi|91773683|ref|YP_566375.1| 110 L-A-NLAKQFGED---IPMTGWPT-----------------DQVFSKFKEAI--DSKKQV-IMIILDEIDKLVKKGDDVLY 165
                                   2.1.222222222...11222222.................34444444444..222233.77777777777666666666 PP

                        AAA_16 157 aLlr 160
                                   +L r
  gi|91773683|ref|YP_566375.1| 166 NLSR 169
                                   6665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.7
                        AAA_16  86 ldeaesael 94 
                                   +    + el
  gi|91773683|ref|YP_566375.1| 258 DLLRVAGEL 266
                                   222222222 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 !   32.8   0.1   1.2e-10   7.8e-08       1     113 [.      61     192 ..      61     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.2e-10
                                   EEEESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSS................STTHHHHHHHHHHHHHHHT CS
                           AAA   1 vllyGppGtGKTllakavakelgve.........fleisgsellsk................yvgesekkirelfkeakek 56 
                                   +l+yG  GtGKT++a+ v  el+++         +l +++  +  +                + g   +++   fkea  +
  gi|91773683|ref|YP_566375.1|  61 ILIYGKTGTGKTAVARYVGIELERKsedldvpcsVLYLNCEVIDTQyrllanlakqfgedipMTGWPTDQVFSKFKEAIDS 141
                                   699******************964333333444455555555554478888889999999998888888888888887544 PP

                                   S.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GG CS
                           AAA  57 a.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pd 113
                                   + +   +++DEid+l+k+         ++v+  L +   ++k+  +k+ +ig++n+    d
  gi|91773683|ref|YP_566375.1| 142 KkQVIMIILDEIDKLVKKG--------DDVLYNLSRINTDLKN--AKLSMIGISNDlkfTD 192
                                   424589999********99........8899999998888888..689******9955444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     2e-09   1.4e-06      20     133 ..      42     158 ..      34     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2e-09
                          TniB  20 lerLee.LleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplk 99 
                                   +++L+  L+++ + + ++n+l++G++ +GKt++++    + +++++  +  + vl++++    ++ rl a++ +++g+++ 
  gi|91773683|ref|YP_566375.1|  42 VNNLATiLVSALRGDTPSNILIYGKTGTGKTAVARYVGIELERKSEDLDVPCSVLYLNCEVIDTQYRLLANLAKQFGEDIP 122
                                   455544155666777789*************987665555555555557799***************************98 PP

                          TniB 100 ara.rvskleqqvlrllr.elkvrvLiiDEihnlla 133
                                    +   +++  ++  + ++ + +v ++i+DEi++l++
  gi|91773683|ref|YP_566375.1| 123 MTGwPTDQVFSKFKEAIDsKKQVIMIILDEIDKLVK 158
                                   7743777888888888762678999*******9974 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 !   22.6   1.0   1.3e-07   8.5e-05      12     151 ..      50     173 ..      38     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-07
                      ATPase_2  12 eeilerepneiyfiYGpegsGKtaLlkeiienledkdk.....yviyyialreesiskldefieeeeekkklekalgiavp 87 
                                    + l+ ++ + ++iYG  g GKta+ + +  +le k++       + y + + +++++            +l+k++g+++p
  gi|91773683|ref|YP_566375.1|  50 VSALRGDTPSNILIYGKTGTGKTAVARYVGIELERKSEdldvpCSVLYLNCEVIDTQYRLL--------ANLAKQFGEDIP 122
                                   456778889999***************9966665555446666455666676666554444........47999999**99 PP

                      ATPase_2  88 kaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnlies 151
                                    +             ++ +++++e+i  k++ i ii+De+ kl+    ++  +++++L ++  +
  gi|91773683|ref|YP_566375.1| 123 MTGW---------PTDQVFSKFKEAIDSKKQVIMIILDEIDKLV----KKGDDVLYNLSRINTD 173
                                   9777.........55899999999**999999************....6778888888776555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.2   4.8e+03     105     149 ..       6      52 ..       2      56 .. 0.63
   2 !   22.3   0.0   1.5e-07   9.7e-05       3      99 ..      61     162 ..      59     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.2
                                   ....HHHHHCTTTTT--EEEE..EEECCCHHHHCTTSSCE..EEEE- CS
                         NACHT 105 vrtlLselirkkllpeaslll..tvrpralrdleeqleeaivleveg 149
                                   +  l+++l++ ++l +++ +l  + +p++l++  eq+   + + v +
  gi|91773683|ref|YP_566375.1|   6 LGGLFEDLLQSESLFKNKEVLrpSYTPDSLPHRTEQVNNLATILVSA 52 
                                   55677888888777777655544667777777666666665555555 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.5e-07
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C....CHHHHCC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse....vwavlle 78 
                                   +++ G+ G GKT+ ++ +  ++ ++  + +  + v++l++  + ++ +    la++  ++ p  + p ++    + + + +
  gi|91773683|ref|YP_566375.1|  61 ILIYGKTGTGKTAVARYVGIELERKSEDLDVPCSVLYLNCEVIDTQYRLlANLAKQFGEDIPMTGWPTDQvfskFKEAIDS 141
                                   799********************999999989*************988888899999999998888888866644455667 PP

                                   SCCCEEEEEE-STT-SS-TCH CS
                         NACHT  79 lperlLlilDglDelvtdlgq 99 
                                    ++ +++ilD +D+lv++ + 
  gi|91773683|ref|YP_566375.1| 142 KKQVIMIILDEIDKLVKKGDD 162
                                   777788*********986555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0037       2.4      15      33 ..      59      77 ..      40      97 .. 0.80
   2 !    9.5   0.0    0.0012      0.79     119     166 ..     142     185 ..     124     192 .. 0.75
   3 ?   -3.0   0.0       7.8   5.2e+03      68      95 ..     331     355 ..     323     379 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0037
                                  CEEEEEESTTSSHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxx RF
                          DEAD 15 gdvlvaaeTGsGKTlafli 33
                                   ++l+ ++TG+GKT+++  
  gi|91773683|ref|YP_566375.1| 59 SNILIYGKTGTGKTAVARY 77
                                  699************9865 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                                   CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlS 166
                                    +qv +++lDE+d+l ++  +d++   l+++++  ++ kl+  +i +S
  gi|91773683|ref|YP_566375.1| 142 KKQVIMIILDEIDKLVKK--GDDVLYNLSRINTDLKNAKLS--MIGIS 185
                                   47999************9..566666678886666665544..66655 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.8
                                   HHHTTTSTSEEEEEETTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  68 kkfkkyidlrvlliiggvaardqlskld 95 
                                   ++++  +d+    i+++ + +d +s+ld
  gi|91773683|ref|YP_566375.1| 331 RQLCISVDM---DILTQRRVTDLISELD 355
                                   444444332...2234444444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.1e-06    0.0014      20      59 ..      56     101 ..      37     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                                   TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS......-EEEEETT CS
               Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkek......pfvavnca 59 
                                   +t++++li G++GtGK+ +ar +  + +rk++      +++ +nc 
  gi|91773683|ref|YP_566375.1|  56 DTPSNILIYGKTGTGKTAVARYVGIELERKSEdldvpcSVLYLNCE 101
                                   5679*****************9977666665522222234455555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0019       1.3       3      36 ..      40      74 ..      38      91 .. 0.84
   2 !    8.8   0.1    0.0013      0.87     158     187 ..     129     158 ..      92     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                    KAP_NTPase  3 lyasaladilseptl..atpivvgLygkWGsGKssl 36
                                     ++la+il++  l   tp+ + +ygk G+GK+++
  gi|91773683|ref|YP_566375.1| 40 EQVNNLATILVSA-LrgDTPSNILIYGKTGTGKTAV 74
                                  5679*******54.6689****************87 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                    KAP_NTPase 158 eelladmektLdalqkrlVvviDdLDrcet 187
                                   +++++++++++d +++ + +++D++D + +
  gi|91773683|ref|YP_566375.1| 129 DQVFSKFKEAIDSKKQVIMIILDEIDKLVK 158
                                   6689**********************9865 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 !   12.7   0.0   0.00012     0.076      17      60 ..      43      85 ..      26      94 .. 0.74
   2 ?    3.4   0.0     0.084        56      54     106 ..     114     166 ..     107     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                        RuvB_N 17 eklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                  ++l+ ++  +  r+++   +l+yG  G Gkt++a+ +  el+ k
  gi|91773683|ref|YP_566375.1| 43 NNLATIL-VSALRGDTPSNILIYGKTGTGKTAVARYVGIELERK 85
                                  4444333.344799999********************9999866 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.084
                        RuvB_N  54 akelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                                   ak++g ++ +t  P+ +  + +   + + ++  ++ +dei +l ++ ++vly+
  gi|91773683|ref|YP_566375.1| 114 AKQFGEDIPMTGWPTDQVFSKFKEAIDSKKQVIMIILDEIDKLVKKGDDVLYN 166
                                   5556666666666666666666666666666677889***************6 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05    0.0074       3     106 ..      60     162 ..      58     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                       DUF2075   3 vvlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinn.lsefkka 80 
                                    +l+ G++GtGKt v+  +  el  ++++++    +l+ N + +++ ++ la+ +  k+++e++        + +s+fk+a
  gi|91773683|ref|YP_566375.1|  60 NILIYGKTGTGKTAVARYVGIELerKSEDLDVPCSVLYLNCEVIDTQYRLLANLA--KQFGEDIPMTGWPTDQvFSKFKEA 138
                                   689****************99996667778888899*************999888..778887776665444404433555 PP

                       DUF2075  81 eekkeepkedvvivDEAhrlltksdq 106
                                   ++  +++++ ++i DE  +l +k+d 
  gi|91773683|ref|YP_566375.1| 139 ID--SKKQVIMIILDEIDKLVKKGDD 162
                                   54..5567888999999999987764 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05     0.018      36     155 ..      61     157 ..      54     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                        AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagveslpL 116
                                   +l++G +gtGKt++a  +++++ + ++ l+     +  Vly+++E     ++ Rl a ++++ + ++ + + +++      
  gi|91773683|ref|YP_566375.1|  61 ILIYGKTGTGKTAVARYVGIELERKSEDLD----VPCSVLYLNCEVID--TQYRLLANLAKQ-FGEDIPMTGWPT------ 128
                                   799********************9887667....578********998..999999999886.667776665544...... PP

                        AAA_25 117 fakdrggtlltadvdaleaaieevegvrlvviDplsral 155
                                             ++++ +  +ai++ ++v ++++D +++++
  gi|91773683|ref|YP_566375.1| 129 ----------DQVFSKFKEAIDSKKQVIMIILDEIDKLV 157
                                   ..........57888888899998889999999888755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   2.8e-05     0.019       3      80 ..      59     159 ..      57     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-05
                        AAA_24   3 lkiliyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie............swedfldevve 58 
                                    +iliyG+ g+GKT +a+               + ++l++++e    +++ + + ++               +++ ++++e
  gi|91773683|ref|YP_566375.1|  59 SNILIYGKTGTGKTAVARYVgielerksedldvPCSVLYLNCEV--IDTQYRLLANLAkqfgedipmtgwPTDQVFSKFKE 137
                                   589***************99999988888888888888887776..22233333333345566666886666777777777 PP

                        AAA_24  59 laaeladyktlviDtideleel 80 
                                     + +++   +++D id+l++ 
  gi|91773683|ref|YP_566375.1| 138 AIDSKKQVIMIILDEIDKLVKK 159
                                   7888888999999999998875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.3e-05     0.048       1      69 [.      61     140 ..      61     168 .. 0.60
   2 ?   -1.5   0.0       5.3   3.5e+03      46      69 ..     281     304 ..     259     350 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.3e-05
                        AAA_18   1 IlltGtpGvGKttlakeL.....skrlgf.........gvnlrdvakenglllevdpe.aldeskrldedkldklldalee 66 
                                   Il+ G+ G+GKt +a+++     +              +  l++ + + +++l  + + ++ e   +  + +d+++++++e
  gi|91773683|ref|YP_566375.1|  61 ILIYGKTGTGKTAVARYVgieleR----KsedldvpcsVLYLNCEVIDTQYRLLANLAkQFGEDIPMTGWPTDQVFSKFKE 137
                                   99***************9655542....02333557774444444443333333333334666666666666666666666 PP

                        AAA_18  67 nss 69 
                                   +++
  gi|91773683|ref|YP_566375.1| 138 AID 140
                                   665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.3
                        AAA_18  46 ldeskrldedkldklldaleenss 69 
                                    + ++++++d+  +++++l  +s+
  gi|91773683|ref|YP_566375.1| 281 RRAQEKIEIDRIVEVVRTLPTQSK 304
                                   344445555555555555555444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015     0.099      35      78 ..      40      83 ..      27     115 .. 0.82
   2 ?   -1.2   0.2       1.3   8.8e+02      84     120 ..     156     192 ..     143     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                        DUF815 35 kqkealventeqfleglpannvLLwGarGtGKSslvkallneya 78
                                  +q ++l +     l+g + +n+L++G+ GtGK ++ + +  e++
  gi|91773683|ref|YP_566375.1| 40 EQVNNLATILVSALRGDTPSNILIYGKTGTGKTAVARYVGIELE 83
                                  555666666677789999****************9998776665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                        DUF815  84 lievekedlkelpklvellrerperfilfvDDLsFee 120
                                   l++   + l +l+++ + l++++  +i    DL F++
  gi|91773683|ref|YP_566375.1| 156 LVKKGDDVLYNLSRINTDLKNAKLSMIGISNDLKFTD 192
                                   555566779999*********************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 ?   10.2   0.0   0.00068      0.45      46      73 ..      57      84 ..      26     107 .. 0.84
   2 ?   -0.0   0.2      0.95   6.3e+02      98     120 ..     134     156 ..     128     194 .. 0.73
   3 ?   -2.4   0.0       5.2   3.5e+03       3      26 ..     169     192 ..     166     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00068
                     IstB_IS21 46 kkenivllGpsGvGKshlaialgveavr 73
                                  +  ni++ G +G+GK+ +a  +g e  r
  gi|91773683|ref|YP_566375.1| 57 TPSNILIYGKTGTGKTAVARYVGIELER 84
                                  568***************9998887655 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.95
                     IstB_IS21  98 klaralkrllkvdllilDdlgll 120
                                   k+++a+++  +v ++ilD++  l
  gi|91773683|ref|YP_566375.1| 134 KFKEAIDSKKQVIMIILDEIDKL 156
                                   67788888888888899988644 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.2
                     IstB_IS21   3 rletrlrlaklpaqktledidfra 26 
                                   r++t l++akl +    +d++f+ 
  gi|91773683|ref|YP_566375.1| 169 RINTDLKNAKLSMIGISNDLKFTD 192
                                   7899999****9998888888875 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 ?   12.6   0.5    0.0002      0.13      15      56 ..     245     285 ..     223     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                                   XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                   AAA_assoc_2  15 laeladGDaRkaLnlLElaaeaaeakegkieitledleealq 56 
                                    a+  +GDaR+aL lL +a e ae+ +++  + +e++++a +
  gi|91773683|ref|YP_566375.1| 245 FAAQEHGDARRALDLLRVAGELAER-DNQSYVAEENVRRAQE 285
                                   556668**************99987.8888888888887654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00041      0.27      12      42 ..      54      84 ..      43      90 .. 0.84
   2 ?   -2.7   0.0       4.6     3e+03      33      54 ..     132     153 ..     130     162 .. 0.80
   3 ?   -1.4   0.0       1.8   1.2e+03     158     186 ..     268     297 ..     254     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                    Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdeler 42
                                  ++++P  il+ G +G GK+++a+++  eler
  gi|91773683|ref|YP_566375.1| 54 RGDTPSNILIYGKTGTGKTAVARYVGIELER 84
                                  6799*******************99888864 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.6
                    Zeta_toxin  33 aellkdelerqgnvvrldpDdl 54 
                                    +++k++++++++v+ +  D++
  gi|91773683|ref|YP_566375.1| 132 FSKFKEAIDSKKQVIMIILDEI 153
                                   6788888888999999998886 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                    Zeta_toxin 158 ehdeafeglresvealeeekqldrvk.ikd 186
                                   e d++ + ++e+v++ +e+  +dr++ +++
  gi|91773683|ref|YP_566375.1| 268 ERDNQSYVAEENVRRAQEKIEIDRIVeVVR 297
                                   567888888899999888889998887764 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0016         1      35      54 ..      53      73 ..      33      77 .. 0.80
   2 ?    0.9   0.0      0.37   2.4e+02     136     171 ..     133     176 ..     119     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                                  GGGS-..SEEEE--TTSSHHH CS
                  FtsK_SpoIIIE 35 lkkma.shllvaGatgsGKSt 54
                                  l++ + s++l+ G tg+GK+ 
  gi|91773683|ref|YP_566375.1| 53 LRGDTpSNILIYGKTGTGKTA 73
                                  4444459************96 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.37
                                   HHHHHHHHTT---B-TT-.......................... CS
                  FtsK_SpoIIIE 136 geiaedpldifgdvflvlDnyddlaaene........ritsLsn 171
                                   ++++e+++  +++++++lD+ d+l +++          +t L+n
  gi|91773683|ref|YP_566375.1| 133 SKFKEAIDSKKQVIMIILDEIDKLVKKGDdvlynlsrINTDLKN 176
                                   6789999999999*************999777666633445555 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   0.1   0.00046       0.3       8      45 ..      41      80 ..      34     174 .. 0.73
   2 ?   -2.6   0.0       7.1   4.7e+03     125     146 ..     301     322 ..     264     343 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                                  HHHHHHHHT.......TTSEEEEEESTTSTHHHHH.HHHH CS
                        ResIII  8 Qeeaienll.eklkskrdkrglikmaTGtGKTlva.akli 45
                                  Q + +  +l ++l  +   ++li   TGtGKT va +  i
  gi|91773683|ref|YP_566375.1| 41 QVNNLATILvSALRGDTPSNILIYGKTGTGKTAVArYVGI 80
                                  33333333345555588889**************944444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.1
                                   ..HHHTTT-SEEEEETGGGTTS CS
                        ResIII 125 seellrdrfdviiiDEaHrlga 146
                                   ++++l+ ++ +++ D  Hr   
  gi|91773683|ref|YP_566375.1| 301 TQSKLSLYSVMVLRDNGHRNVT 322
                                   3445555556788888888665 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   0.0   0.00025      0.17       4      44 ..      39      83 ..      36      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                                  HHHHHHHHHHHHHCH.TEE...EEEEESTTSSHHHHHHHHHHHTT CS
                          TsaE  4 eeetealgkklakal.gdv...ilLeGdLGaGKTtlvrglakalg 44
                                  +e++++l++ l +al gd+   il++G+ G+GKT+ +r +  +l+
  gi|91773683|ref|YP_566375.1| 39 TEQVNNLATILVSALrGDTpsnILIYGKTGTGKTAVARYVGIELE 83
                                  6788999999999888444455***************99877665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00062      0.41      24      73 ..      48     101 ..      35     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                                   HHHHHSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-....EEEEEHH CS
                      Bac_DnaA  24 lkvaeapgkkynPlfiygevGlGktHLlkaignevlenapelr....vvYltae 73 
                                     v+   g +   ++iyg++G Gkt + + +g e+++++++l     v+Yl+ e
  gi|91773683|ref|YP_566375.1|  48 ILVSALRGDTPSNILIYGKTGTGKTAVARYVGIELERKSEDLDvpcsVLYLNCE 101
                                   45555555656679**********************999987511115676665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3    0.0022       1.4       4      87 ..      59     160 ..      56     173 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                                   --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHH.HHHTTT-HHHHTTS............. CS
                         AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrl.igappgyvgaeegG............. 70 
                                   ++il+ g+tg+Gkt +a+ +   l+ +k++ l +     +l      ++++      ++     ++ G             
  gi|91773683|ref|YP_566375.1|  59 SNILIYGKTGTGKTAVARYVGIELE-RKSEDLDVPCSVLYLN----CEVIDTQyRLLANLA---KQFGedipmtgwptdqv 131
                                   6888888888888888888877777.5666666666666666....333322201222222...22222224555677777 PP

                                   ...............EEEEETGGG-------- CS
                         AAA_2  71 ...............ivllDEidKihpkessg 87 
                                                  ++ lDEidK  +k   g
  gi|91773683|ref|YP_566375.1| 132 fskfkeaidskkqviMIILDEIDKLVKK---G 160
                                   7777777777777778999*****9994...2 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.18      34      58 ..      59      83 ..      39     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                         AAA_7 34 kpvllvGptGtGKtviikdllkkld 58
                                   ++l++G+tGtGKt++++ +  +l+
  gi|91773683|ref|YP_566375.1| 59 SNILIYGKTGTGKTAVARYVGIELE 83
                                  689*************988766666 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   0.00047      0.31       1      27 [.      61      87 ..      61     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklk 27
                                  i++yG++g+GK+ +a+++  +l++k++
  gi|91773683|ref|YP_566375.1| 61 ILIYGKTGTGKTAVARYVGIELERKSE 87
                                  789**************9999998774 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00037      0.25      44      89 ..      21      72 ..      11      74 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                                  EESEEEETTS-......HHHHHHHHHHHHHHHHHTT.SEEEEEEEESTTSSHH CS
                       Kinesin 44 kFdkvfdeeat......qeevyeetakplvesvleG.ynatifaYGqtgsGKT 89
                                  k ++v+ ++ t       +e  +++ + ++ s+l+G   + i+ YG+tg+GKT
  gi|91773683|ref|YP_566375.1| 21 KNKEVLRPSYTpdslphRTEQVNNL-ATILVSALRGdTPSNILIYGKTGTGKT 72
                                  5555555555555555333333443.566667777724588***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 2979.13
//
Query:       gi|91773684|ref|YP_566376.1|  [L=184]
Description: peptidase S26B, signal peptidase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   24.5   0.2    4.1e-05   23.5   0.2    1.6  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   2.3e-09   4.1e-05       2      45 ..      51     112 ..      50     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.3e-09
                                   XXSSTTCCTXXTTXEEEEECTS................---TTSEEEEEETTCE..-EEEEE CS
                 Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs................epkrGdivvfrlpgee..eayiKr 45 
                                   v+++SMep +++Gd+i+++  +                   +Gd++  r +g+e  + +i+r
  gi|91773684|ref|YP_566376.1|  51 VESGSMEPHMQIGDIIFIKSIDraqiitnndtstehikFKMQGDVILYRPHGQEgvTPIIHR 112
                                   89*****************8888999999999999998888999999999999988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1335.57
//
Query:       gi|91773685|ref|YP_566377.1|  [L=316]
Description: tRNA-modifying enzyme [Methanococcoides burtonii DSM 6242]
Scores for complete 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   81.0   0.0    1.2e-22   80.0   0.0    1.6  1  Wyosine_form  Wyosine base formation
    1.3e-16   61.4   0.2    6.8e-16   59.1   0.2    2.0  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
        0.1   13.7   0.0       0.52   11.4   0.0    2.0  2  SOXp          SOX transcription factor


Domain annotation for each model (and alignments):
>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   2.1e-26   1.2e-22       1      63 []     247     308 ..     247     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 2.1e-26
                                   HHT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                  Wyosine_form   1 kaepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                   ka+pd++EvKay+++G+sr rL ++++P h+ev++fak+l+g+++ Y+++++ + Sr+vll++
  gi|91773685|ref|YP_566377.1| 247 KADPDYIEVKAYMHLGYSRGRLPREAMPAHDEVLEFAKELAGHIG-YSVADDVEVSRIVLLSK 308
                                   699******************************************.**************985 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.2   1.1e-19   6.8e-16       2     157 ..      69     235 ..      68     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.1e-19
                                   EEESEESS--TTTSCCTT......................HHHHHHHHHHHHHHHHHHHHHHHH............HTTSE CS
                                   xxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxx............xxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpet......................vrregrgrslsveeileevkelka............ekgvk 48 
                                   ++t  Cn+rC +C+rp+                       +  ++                  +            +  ++
  gi|91773685|ref|YP_566377.1|  69 TPTLRCNQRCLHCWRPTEvevslpnnwdspveivgssikaQ--RKLITG--------------FghsaprerwieaNEPKH 133
                                   7899************9888887776666666665554321..222222..............122222222222133388 PP

                                   EEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                   Radical_SAM  49 evilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtf 127
                                   + i+++gep+lyp + el+e++      g++++v++ngt+p     e + + ++ +++++l+a+d+e++ k +    +  +
  gi|91773685|ref|YP_566377.1| 134 VAISLSGEPTLYPYLPELVEEYESQ---GFSTFVVSNGTVP-----EMMEKIEPSQLYMSLDAPDKETYEKVCLpkSPALW 206
                                   88888*******************8...************8.....666666669************66666645566777 PP

                                   HHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 128 eevlealeklreagikrvvdrivglpGend 157
                                   +++ ++le+l  ++ +   +ri++++G n+
  gi|91773685|ref|YP_566377.1| 207 DKINRSLEILGTKNNR-KAIRITLIKGLNM 235
                                   8888999999888777.8*********997 PP

>> SOXp  SOX transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.7e-05      0.52       8      24 ..      19      35 ..      17      55 .. 0.85
   2 ?   -1.1   0.0       0.7   4.2e+03      46      61 ..     246     267 ..     215     287 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.7e-05
                          SOXp  8 KTLlKkdkysLpgglla 24
                                   TLlKk+kysL+g   a
  gi|91773685|ref|YP_566377.1| 19 ETLLKKQKYSLAGTHSA 35
                                  59***********8765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.7
                          SOXp  46 d....gyahmNGyangaYs..s 61 
                                   +    +y ++  y+  +Ys   
  gi|91773685|ref|YP_566377.1| 246 EkadpDYIEVKAYMHLGYSrgR 267
                                   2333578888888888886442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2190.74
//
Query:       gi|91773686|ref|YP_566378.1|  [L=414]
Description: peptide chain release factor 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-41  140.1   0.0    8.7e-41  139.4   0.0    1.4  1  eRF1_2          eRF1 domain 2
      4e-32  111.0   0.1    1.1e-31  109.7   0.0    1.7  2  eRF1_3          eRF1 domain 3
    8.9e-13   48.7   0.1    1.3e-12   48.1   0.1    1.3  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    2.4e-12   47.3   0.0    4.2e-12   46.5   0.0    1.3  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    2.9e-12   46.7   0.0    5.5e-12   45.8   0.0    1.5  1  eRF1_1          eRF1 domain 1
    0.00024   20.9   1.2       0.69    9.8   0.1    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
  ------ inclusion threshold ------
       0.03   14.3   0.1      0.059   13.4   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.08   13.5   0.0       0.19   12.3   0.0    1.6  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
       0.12   12.5   4.2       0.37   10.9   1.6    2.5  2  Zn-ribbon_8     Zinc ribbon domain
        1.6    9.2   3.6        8.6    6.9   0.1    3.1  3  zf-IS66         zinc-finger binding domain of transposase IS6


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 !  139.4   0.0   4.9e-44   8.7e-41       2     133 .]     140     271 ..     139     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 4.9e-44
                                   EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEE CS
                        eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiil 82 
                                   +gl+vld++eAt+gll+g+++e  ++++++vP+K+++Ggqsa+rf+ lr  +++ f+k++++aa++ fl v++++ +g+++
  gi|91773686|ref|YP_566378.1| 140 YGLLVLDRREATVGLLTGKQIEAFRNLTSTVPGKQRKGGQSAHRFQQLRLIAIHDFYKRIGDAASEVFLAVEQKDFEGVLI 220
                                   8******************************************************************************** PP

                                   EESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                        eRF1_2  83 agpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                   +gp+++keef  ++++++e +kkv++l+dv+y++esgl+e++++a+e+l+d
  gi|91773686|ref|YP_566378.1| 221 GGPSPTKEEFEAGNFFHHEIEKKVLDLFDVAYTDESGLSELVNAASERLED 271
                                   ***********************************************9987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.8   8.7e+03       7      39 ..      39      71 ..       5      76 .. 0.65
   2 !  109.7   0.0   5.9e-35   1.1e-31       2     112 ..     275     411 ..     274     412 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.8
                                  HHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EE CS
                        eRF1_3  7 lleefleelakdtgkavYGveevlkalemgAve 39
                                   +++++++l+++  +a   + +  k +  gA++
  gi|91773686|ref|YP_566378.1| 39 QISDVVSQLRNEHSQASNIKSKLTKTNVQGAID 71
                                  445555555555555555555555555555555 PP

  == domain 2  score: 109.7 bits;  conditional E-value: 5.9e-35
                                   HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS.......................- CS
                        eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv.......................k 59 
                                   + ekkl+++f++el  d+gka+YG+++v++ l +gAv+ LL+se+l+  r t+k++                        +
  gi|91773686|ref|YP_566378.1| 275 MVEKKLMQQFFRELVSDSGKATYGEDNVRENLIIGAVDILLISEDLRAVRETVKCTScdyeqktsrefkpgdsssptgncP 355
                                   679************************************************9888778*********************** PP

                                   HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                        eRF1_3  60 etgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                   ++g+ le+ e   ++++l e ++++g++ve+is+++eeG ql+kafgG++aiLR++
  gi|91773686|ref|YP_566378.1| 356 KCGSYLEITEkvdVVDQLSEICDQMGTRVEFISTDFEEGSQLLKAFGGVVAILRFN 411
                                   ***9999988888******************************************7 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.1   7.4e-16   1.3e-12       2     123 ..     126     251 ..     126     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 7.4e-16
                baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellak 82 
                                   +l+pL + l+e + yg++++dr++a +    + ++e  + +++ vpg++++gg+ s +rfq+ +   ++ ++k++++++ +
  gi|91773686|ref|YP_566378.1| 126 FLTPLEDMLKEAKTYGLLVLDRREATVGLLTGKQIEAFRNLTSTVPGKQRKGGQ-SAHRFQQLRLIAIHDFYKRIGDAASE 205
                                   799***************************************************.*********************99999 PP

                baeRF_family10  83 ll...eergverlvlgGdeeetaall..drlpkalrarvvgtlplp 123
                                   ++   e++++e +++gG+   +++++  + ++ +++++v + +++ 
  gi|91773686|ref|YP_566378.1| 206 VFlavEQKDFEGVLIGGPSPTKEEFEagNFFHHEIEKKVLDLFDVA 251
                                   873336677*********8888777622467777777777666655 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   2.4e-15   4.2e-12       4     123 ..     142     264 ..     139     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.4e-15
                       acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae....vvlg 80 
                                   +++l+rr + +vg++ g++++a+++ t+ v g+ ++GG+S  Rf++ r   + + ++++ +aa +++ + +++    v++g
  gi|91773686|ref|YP_566378.1| 142 LLVLDRREA-TVGLLTGKQIEAFRNLTSTVPGKQRKGGQSAHRFQQLRLIAIHDFYKRIGDAASEVFLAVEQKdfegVLIG 221
                                   58999***9.*********************************************************7777767889**** PP

                       acVLRF1  81 GdrslvaevledarlaplatlareelldvpdprravLedavrr 123
                                   G+  + +e+++ +  ++  + ++ +l+dv+  +++ L + v+ 
  gi|91773686|ref|YP_566378.1| 222 GPSPTKEEFEAGNFFHHEIEKKVLDLFDVAYTDESGLSELVNA 264
                                   **********997755555555556778877778888777765 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   3.1e-15   5.5e-12       7     128 ..      21     133 ..      13     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 3.1e-15
                                   CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT..SSEEEEEE CS
                        eRF1_1   7 dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd..agvlrisG 85 
                                     +++g+++++L++++d++++++   +++++s+++++++k ++         ++v+ ++ + + ++++ +   +g++ ++G
  gi|91773686|ref|YP_566378.1|  21 GKKGRGTELISLYIPPDKQISDVVSQLRNEHSQASNIKSKLTK---------TNVQGAIDSIMSRLRYGTVpeNGIVYFTG 92 
                                   67899************************************88.........9***************98777******** PP

                                   EEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                        eRF1_1  86 kvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                    v  + +   ++++ t  +e+++p+ +++++ ++sf l +L+++
  gi|91773686|ref|YP_566378.1|  93 AVDVGAN---KTNMETTIVEPPQPIITYRYHcDSSFFLTPLEDM 133
                                   *****99...99*****************999*********998 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00044      0.79      11      34 ..     314     339 ..     312     341 .. 0.68
   2 !    9.8   0.1   0.00038      0.69       4      19 ..     354     369 ..     354     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00044
                                   EEEEECSCCCE..EEESSSS-EEESS CS
                RNA_POL_M_15KD  11 Llpkedkegkn..feCrqCgYeepad 34 
                                   Ll+ ed   ++  + C +C+Ye+ ++
  gi|91773686|ref|YP_566378.1| 314 LLISEDLRAVRetVKCTSCDYEQKTS 339
                                   444455444444899*******9765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                                   ESTTTSBEEEEECSCC CS
                RNA_POL_M_15KD   4 CpkCgNlLlpkedkeg 19 
                                   CpkCg+ L+++e++ +
  gi|91773686|ref|YP_566378.1| 354 CPKCGSYLEITEKVDV 369
                                   ***********99866 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 ?   13.4   0.1   3.3e-05     0.059      65      95 ..     321     360 ..     274     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                                   EEE--EEEETTTS-EEECHHHHH..........S-TTTSSS CS
                          HypA  65 eevpvkvrCreCgkefeleekal..........rCpkCgsa 95 
                                   + v+ +v+C++C++e +++++ +          +CpkCgs 
  gi|91773686|ref|YP_566378.1| 321 RAVRETVKCTSCDYEQKTSRE-FkpgdsssptgNCPKCGSY 360
                                   5678899******99997754.34577899999******95 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 ?   12.3   0.0    0.0001      0.19      41     130 ..     164     256 ..     159     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                baeRF_family12  41 regssdrpGrsssggagrsameetdfkeq.eeerFakeladeLkk...rakegkferlvlvappetlgelr..khlhkevk 115
                                   r+++s+ pG+++ gg++++   +++   + + ++F+k++ d+  +   ++++++fe + + +p +t +e++  + +h e++
  gi|91773686|ref|YP_566378.1| 164 RNLTSTVPGKQRKGGQSAH---RFQQLRLiAIHDFYKRIGDAASEvflAVEQKDFEGVLIGGPSPTKEEFEagNFFHHEIE 241
                                   6788899999888888822...333334558999***998877775558999******************933469****9 PP

                baeRF_family12 116 krlvgeiaknltkhp 130
                                   k++   ++  +t+++
  gi|91773686|ref|YP_566378.1| 242 KKVLDLFDVAYTDES 256
                                   999988888888775 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.28     5e+02       3      10 ..     116     123 ..     116     136 .. 0.90
   2 ?   10.9   1.6   0.00021      0.37       7      34 ..     328     359 ..     326     365 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.28
                   Zn-ribbon_8   3 iYeYrCee 10 
                                   +Y Y+C++
  gi|91773686|ref|YP_566378.1| 116 TYRYHCDS 123
                                   7*****86 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
                   Zn-ribbon_8   7 rCeeCghefe...vlqsisdaplta.CPeCgs 34 
                                   +C++C+ e     ++ + + +++t  CP+Cgs
  gi|91773686|ref|YP_566378.1| 328 KCTSCDYEQKtsrEFKPGDSSSPTGnCPKCGS 359
                                   8*****88886666666554446778*****9 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       5.5   9.8e+03      27      33 ..     110     116 ..     101     121 .. 0.60
   2 ?    1.9   0.1      0.16   2.9e+02      35      46 .]     322     333 ..     320     333 .. 0.86
   3 ?    6.9   0.1    0.0048       8.6       3      19 ..     353     367 ..     351     374 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.5
                       zf-IS66  27 PakfrVi 33 
                                   P++++++
  gi|91773686|ref|YP_566378.1| 110 PPQPIIT 116
                                   5555554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                       zf-IS66  35 hirpkyaCpcCe 46 
                                    +r++++C +C+
  gi|91773686|ref|YP_566378.1| 322 AVRETVKCTSCD 333
                                   68*********6 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0048
                       zf-IS66   3 tCpcCGgllkpigedrv 19 
                                   +Cp+CG+ l +i e+ v
  gi|91773686|ref|YP_566378.1| 353 NCPKCGSYL-EITEK-V 367
                                   7******54.66665.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2752.98
//
Query:       gi|91773687|ref|YP_566379.1|  [L=567]
Description: arginyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-38  131.8   0.2    7.4e-38  130.4   0.2    1.6  2  tRNA-synt_1d     tRNA synthetases class I (R)
    2.6e-32  111.5   0.1    4.8e-32  110.6   0.1    1.5  1  DALR_1           DALR anticodon binding domain
    3.1e-13   50.1   0.0    1.1e-12   48.4   0.0    2.0  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    2.5e-05   23.4   0.0      0.067   12.1   0.0    2.2  2  tRNA-synt_1f     tRNA synthetases class I (K)
    0.00039   19.9   0.1    0.00075   18.9   0.1    1.5  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
    0.00054   18.8   0.4      0.099   11.4   0.1    3.0  3  tRNA-synt_1g     tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.034   14.1   0.1      0.083   12.9   0.1    1.6  1  NTase_sub_bind   Nucleotidyltransferase substrate binding pro
      0.068   11.4   0.0       0.11   10.8   0.0    1.2  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.2   3.3e-41   7.4e-38      20     349 .]     112     433 ..      95     433 .. 0.90
   2 ?   -1.8   0.0      0.53   1.2e+03     118     151 ..     523     556 ..     513     563 .. 0.81

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 3.3e-41
                                   -EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS-----SCCCH CS
                  tRNA-synt_1d  20 kkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqelqdLeaf 100
                                    +++++++s n   ++hvGh+r  iiGd++ r+l  +Gydv    +v D G+q  ++   l   + ++  ++++   + ++
  gi|91773687|ref|YP_566379.1| 112 GRILLEHTSANPNGPLHVGHIRNSIIGDTLGRILKRAGYDVELHYYVNDMGRQIAIVSWALGYFEFDE--SSKPDHAIADV 190
                                   57999*************************************************99888887665555..3577788999* PP

                                   HHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC..CCCCCHHHHHHHHH CS
                  tRNA-synt_1d 101 ykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGes..lykeslneivkelk 178
                                   y +a+ +++   +   +  + ++ +++gd  + + + + vd++    +++ ++++v+  e   es  +    +  i++e+k
  gi|91773687|ref|YP_566379.1| 191 YIKANAELNAHPEKVAEIDKLMQLVEKGDAATIETFDKAVDLAVSGIKETLKKMNVAHDEfPKESsfIRSGDVSRIIEEIK 271
                                   ********999888889999***********999999*********************99844554667789********* PP

                                   CTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSS CS
                  tRNA-synt_1d 179 kkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyv 259
                                   + g  + ++Galvv l+++g +  +v+q+ DG+ lytt+D+a   +  + ++ad+++ v  +  +l   q+ + l+ ig  
  gi|91773687|ref|YP_566379.1| 272 ATGRTEIDNGALVVNLQDYGFKKTLVIQRTDGTSLYTTRDLAY--HEWKGERADRIIDVFGADHKLISGQLKATLNAIGK- 349
                                   *****************************************86..567889***************************95. PP

                                   TTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCCTS- CS
                  tRNA-synt_1d 260 peskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekvaeavgvgaikyaDlskn 340
                                      k+ e   f  v    + +++tr+G+ +  +dlLd+   +a + +  + +d  ++ d +  vae vg+ga++y  ++  
  gi|91773687|ref|YP_566379.1| 350 ---KEPEFVIFEFV-SLPEGSMSTRSGKFISADDLLDQIKTQAYEEVDKRRPD--MPDDFKATVAEIVGIGAVRYDIVKVS 424
                                   ...34445556666.446779********************************..********************999888 PP

                                   TTS-EE--H CS
                  tRNA-synt_1d 341 rindyifdw 349
                                     +  +fdw
  gi|91773687|ref|YP_566379.1| 425 PEKSTVFDW 433
                                   888888888 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.53
                                   HHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1d 118 arnyvvkLqsgdedirklwkllvditrtelqkly 151
                                    + +v  L+++de++r  +  lvd +r  l ++ 
  gi|91773687|ref|YP_566379.1| 523 FYRFVSVLNAEDEQLRSSRIALVDCARMVLANTL 556
                                   5789999**********99999999887666555 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.1   2.1e-35   4.8e-32       1     119 []     447     567 .]     447     567 .] 0.97

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 2.1e-35
                                   HHHHHHHHHHHHHHTTCTTCCCCHCCHCC..S-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHC CS
                        DALR_1   1 vqyahaRiksilrkaeeegekleeealal..leeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnke 79 
                                   +qy+haR++sil+ka++eg  ++ee   +  l e++e  L+k++a f ++l ++a+el+ph+ a y+ eLa++f++fY+ +
  gi|91773687|ref|YP_566379.1| 447 IQYSHARACSILQKAKDEGLWSSEEPINTtlLVEDSEVSLIKKMAMFDNMLDQCAKELRPHTFAIYARELADAFNQFYRFV 527
                                   7******************9988888777879999********************************************** PP

                                   TSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                        DALR_1  80 rvlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                   +vl++e+e+l+ +R+aLv+++r vLan+Ld LG+ ape m
  gi|91773687|ref|YP_566379.1| 528 SVLNAEDEQLRSSRIALVDCARMVLANTLDTLGLGAPESM 567
                                   **************************************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 !   48.4   0.0   4.7e-16   1.1e-12       2      83 ..       8      84 ..       7      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 4.7e-16
                                  HHHHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT.EEE CS
               Arg_tRNA_synt_N  2 elkeaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagpGFiN 82
                                  ++++++++a+++a   ++e +++++     ++++D+++ +a++la+ +k++P+++Ae+ia ++  +++  +ekve+ gp ++N
  gi|91773687|ref|YP_566379.1|  8 QVTSILNDAVSSA---GFEADDMELGP---SQHADLSSRIAFRLASVAKQSPKDVAEKIAGEIVIPKGsfVEKVEALGP-YLN 83
                                  6889999999999...56777889985...9*******************************99999889*********.*** PP

                                  E CS
               Arg_tRNA_synt_N 83 f 83
                                  +
  gi|91773687|ref|YP_566379.1| 84 I 84
                                  9 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00024      0.54      29      71 ..     119     161 ..      97     165 .. 0.87
   2 !   12.1   0.0     3e-05     0.067     237     302 ..     326     387 ..     207     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00024
                  tRNA-synt_1f  29 sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                   + + p G++H+G +r+ + +d + r l++ g +v+l ++++dm
  gi|91773687|ref|YP_566379.1| 119 TSANPNGPLHVGHIRNSIIGDTLGRILKRAGYDVELHYYVNDM 161
                                   67789**********************************9999 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3e-05
                  tRNA-synt_1f 237 fEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwlevaepe 302
                                   +  +G Dh     S ++++ + + +g ++Pe v++e+++l +g  ms  +G++++ +d+l+ ++++
  gi|91773687|ref|YP_566379.1| 326 IDVFGADHKL--ISGQLKATL-NAIGKKEPEFVIFEFVSLPEG-SMSTRSGKFISADDLLDQIKTQ 387
                                   5678999988..444544443.6779****************9.9***************988876 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 !   18.9   0.1   3.4e-07   0.00075      23      94 ..     127     202 ..     120     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.4e-07
                                   -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-..............HHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks..............vkelaekfieefkkdlea 89 
                                    h+Gh R+ ++ D l ril+ +gYdv++   v D+  +i   + + + +              v          + k+ ++
  gi|91773687|ref|YP_566379.1| 127 LHVGHIRNSIIGDTLGRILKRAGYDVELHYYVNDMGRQIAIVSWALGYFefdesskpdhaiadV----------YIKANAE 197
                                   7***************************999999998876555554444223222222222220..........3333333 PP

                                   TT--- CS
                  tRNA-synt_1e  90 Lnvlk 94 
                                   Ln ++
  gi|91773687|ref|YP_566379.1| 198 LNAHP 202
                                   33332 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   4.4e-05     0.099      10      40 ..     123     153 ..     115     171 .. 0.88
   2 ?    0.4   0.0     0.095   2.1e+02      64     111 ..     227     274 ..     184     287 .. 0.81
   3 ?    3.0   0.0     0.015        34     301     348 ..     341     387 ..     305     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                                   -SS---HHHHHHHHHHHHHHHHHHHTT-EEE CS
                  tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevl 40 
                                   +ng+lH+Gh+++ i++D + R  +  g++v 
  gi|91773687|ref|YP_566379.1| 123 PNGPLHVGHIRNSIIGDTLGRILKRAGYDVE 153
                                   69**************************984 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.095
                                   HHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT CS
                  tRNA-synt_1g  64 eelvekvheeikelfkklnisfdkygrttseehkelvqeifkklkekg 111
                                   ++ v+ + + ike++kk+n+++d++ + +s   +  v++i++++k+ g
  gi|91773687|ref|YP_566379.1| 227 DKAVDLAVSGIKETLKKMNVAHDEFPKESSFIRSGDVSRIIEEIKATG 274
                                   566777788899*************99999888888888888888776 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.015
                                   HHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HH CS
                  tRNA-synt_1g 301 PaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldad 348
                                    a+l++ + k p+ v   e++ + ++ +S+  g ++ a+++l++++++
  gi|91773687|ref|YP_566379.1| 341 KATLNAIGKKEPEFV-IFEFVSLPEGSMSTRSGKFISADDLLDQIKTQ 387
                                   567777777777766.579************************99876 PP

>> NTase_sub_bind  Nucleotidyltransferase substrate binding protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.7e-05     0.083       6      81 ..     191     271 ..     188     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHHHHHHHHH-.HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCTTT.HHHHHHHHHTTS-S-HH CS
                NTase_sub_bind   6 lekAlasLeeavelsrd.dplsdler...dgvIqrFEftyElawkllkryleeegisaeavsp.rdliReaaeagliedge 81 
                                   + kA a+L+  +e++++ d+l +l++   +++I+ F+ +++la+  +k+ l++ ++++++  +  + iR +   ++ie+++
  gi|91773687|ref|YP_566379.1| 191 YIKANAELNAHPEKVAEiDKLMQLVEkgdAATIETFDKAVDLAVSGIKETLKKMNVAHDEFPKeSSFIRSGDVSRIIEEIK 271
                                   889999***9999998885666665512267**********************9999999876699999999999999876 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.7e-05      0.11      33      65 ..     122     154 ..     109     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                   tRNA-synt_1  33 yvtGslHiGhalaktlkdivirykrmkGkevly 65 
                                   + +G lH+Gh+ ++++ d++ r+ +  G++v+ 
  gi|91773687|ref|YP_566379.1| 122 NPNGPLHVGHIRNSIIGDTLGRILKRAGYDVEL 154
                                   679***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3811.99
//
Query:       gi|91773688|ref|YP_566380.1|  [L=93]
Description: hypothetical protein Mbur_1740 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-25   88.3   0.6    3.9e-25   87.9   0.6    1.2  1  DUF1294   Protein of unknown function (DUF1294)
  ------ inclusion threshold ------
      0.076   13.0   0.0      0.097   12.7   0.0    1.1  1  Rib       Rib/alpha-like repeat


Domain annotation for each model (and alignments):
>> DUF1294  Protein of unknown function (DUF1294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.6   4.3e-29   3.9e-25       1      55 []      15      69 ..      15      69 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 4.3e-29
                       DUF1294  1 nlitfllygiDKrkAkkkkwRipEktLlllallgGslGallgmrlfrHKtkkksF 55
                                  n+++f l++ DK+kA+k+k+RipEktL+++allgGs+G ++gm+ frHKt++++F
  gi|91773688|ref|YP_566380.1| 15 NIYSFWLMYSDKKKAIKNKYRIPEKTLFTWALLGGSIGSIMGMQKFRHKTRHQTF 69
                                  99***************************************************99 PP

>> Rib  Rib/alpha-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.097      10      30 ..      25      45 ..      22      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                           Rib 10 datdgikNksdlPdGTkytWk 30
                                  d+++ ikNk  +P+ T +tW 
  gi|91773688|ref|YP_566380.1| 25 DKKKAIKNKYRIPEKTLFTWA 45
                                  78899***************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 715.08
//
Query:       gi|91773689|ref|YP_566381.1|  [L=559]
Description: hypothetical protein Mbur_1741 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-05   21.8   2.1     0.0078   15.0   0.1    3.7  4  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    0.00012   22.3   0.0     0.0035   17.6   0.0    3.2  3  ANAPC4_WD40      Anaphase-promoting complex subunit 4 WD40 do
     0.0015   18.4   1.7        2.1    8.4   0.0    3.9  4  PD40             WD40-like Beta Propeller Repeat
  ------ inclusion threshold ------
      0.016   13.9   0.2        0.7    8.5   0.1    2.4  2  Pectate_lyase22  Oligogalacturonate lyase
      0.075   12.8   0.1        0.2   11.4   0.1    1.7  1  DUF2286          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> 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 ?   -0.9   0.0      0.15   5.2e+02      46     120 ..     180     196 ..     147     224 .. 0.72
   2 !   15.0   0.1   2.2e-06    0.0078      22      80 ..     252     313 ..     238     341 .. 0.79
   3 !    6.2   0.1     0.001       3.6      26      60 ..     299     334 ..     295     378 .. 0.76
   4 ?   -2.3   0.0      0.39   1.4e+03      53      59 ..     464     470 ..     417     497 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.15
                                   SEEEEESSTTEEEEEETTEEEEESTTTSEEEECES-STTTEEESB--HHHHHHTSSSSBEEEE-TTSSEEEEEEE CS
                       DPPIV_N  46 qlakwSPagdklafvrnnnLyvrelatgkeiqlTsdgsagifnGvadWvyeEEvlgsnsavwWspdgsrlaylrf 120
                                   +                                                          a  Ws +g + ay+++
  gi|91773689|ref|YP_566381.1| 180 T----------------------------------------------------------APVWSHSGAYFAYMEL 196
                                   3..........................................................4455555555555554 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.2e-06
                                   TTEEEEEETTT..EECEEEETTTT.BSEEEEESSTTEEEEEET.TEEEEESTTTSEEEECES CS
                       DPPIV_N  22 taeyyiydlet..neveelspgeeklqlakwSPagdklafvrn.nnLyvrelatgkeiqlTs 80 
                                   +++++iydle+  n v +l++++++++ ++wSP+g+k++f++n  n+ + ++++++  q+ s
  gi|91773689|ref|YP_566381.1| 252 PGNLIIYDLEEntNLVFNLPDDTADVENMEWSPDGEKIVFIQNiCNIIIVDIEKRELNQIYS 313
                                   678999***9866788999999*******************994599888887777766654 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.001
                                   EEEETTTEECEEEETT.TT.BSEEEEESSTTEEEEE CS
                       DPPIV_N  26 yiydletneveelspg.eeklqlakwSPagdklafv 60 
                                   +i+d+e++e++++ +  +    +a+wSP+++kl+f 
  gi|91773689|ref|YP_566381.1| 299 IIVDIEKRELNQIYSAeHVGMYDAQWSPDSNKLIFY 334
                                   678888888888888844455678888888888884 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.39
                                   STTEEEE CS
                       DPPIV_N  53 agdklaf 59 
                                   +g++l f
  gi|91773689|ref|YP_566381.1| 464 KGTDLLF 470
                                   2333444 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.34   1.2e+03      37      53 ..     113     129 ..      91     134 .. 0.64
   2 ?   -1.5   0.0      0.91   3.3e+03      30      54 ..     168     192 ..     152     217 .. 0.67
   3 !   17.6   0.0   9.9e-07    0.0035       2      79 ..     239     315 ..     238     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.34
                   ANAPC4_WD40  37 edsevrsLaWkpdgklL 53 
                                   +++ v ++ W+pdg+ +
  gi|91773689|ref|YP_566381.1| 113 NNKPVFNVIWNPDGSQM 129
                                   45566667777777655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.91
                   ANAPC4_WD40  30 wtleedkedsevrsLaWkpdgklLa 54 
                                   w+ ++ + +++v++  W+++g  +a
  gi|91773689|ref|YP_566381.1| 168 WGESSYSGSKSVTAPVWSHSGAYFA 192
                                   3335555666777777777777766 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 9.9e-07
                   ANAPC4_WD40   2 swcptmDLiAlatedgellvfRl..ngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                   +++pt D iA  +  g+l+++ l  n + v++l  +++   v++++W+pdg+ +++  +  ++ ++d+e+ ++ + +s++
  gi|91773689|ref|YP_566381.1| 239 KYSPTEDKIAALM-PGNLIIYDLeeNTNLVFNL--PDDTADVENMEWSPDGEKIVFIQNICNIIIVDIEKRELNQIYSAE 315
                                   89*****999665.5777777775688999999..899999*****************************9987777665 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   5.9e+03      16      23 ..     122     129 ..     118     131 .. 0.77
   2 ?    1.1   0.1      0.11   4.1e+02      11      25 ..     179     193 ..     174     194 .. 0.78
   3 !    8.4   0.0   0.00058       2.1      16      25 ..     282     291 ..     282     294 .. 0.93
   4 !    5.1   0.1    0.0064        23      16      26 ..     324     334 ..     320     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                                   E-TTSSEE CS
                          PD40  16 fSPDGkrl 23 
                                   + PDG+ +
  gi|91773689|ref|YP_566381.1| 122 WNPDGSQM 129
                                   77***987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                                   EEEEEE-TTSSEEEE CS
                          PD40  11 egaPsfSPDGkrlaF 25 
                                    +aP +S  G ++a+
  gi|91773689|ref|YP_566381.1| 179 VTAPVWSHSGAYFAY 193
                                   589*****9977776 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00058
                                   E-TTSSEEEE CS
                          PD40  16 fSPDGkrlaF 25 
                                   +SPDG +++F
  gi|91773689|ref|YP_566381.1| 282 WSPDGEKIVF 291
                                   *********9 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.0064
                                   E-TTSSEEEEE CS
                          PD40  16 fSPDGkrlaFs 26 
                                   +SPD ++l+F+
  gi|91773689|ref|YP_566381.1| 324 WSPDSNKLIFY 334
                                   **********6 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0    0.0096        35     217     267 ..     152     206 ..     139     230 .. 0.75
   2 ?    8.5   0.1   0.00019       0.7      58     144 ..     253     336 ..     244     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0096
               Pectate_lyase22 217 rmwlinedgsnlrkvk....ehaegescthevwvpdgsalayvsylkgsterviy 267
                                    +++ n +gs++++v     +++  +s+t  vw   g+ +ay+   k +  rv  
  gi|91773689|ref|YP_566381.1| 152 ALYIANANGSDVKRVAwgesSYSGSKSVTAPVWSHSGAYFAYMELSKERMYRVTS 206
                                   4789999*****9995333256677899999999999988888777766666544 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00019
               Pectate_lyase22  58 gprnyylldlntqqavqltegkgdntfggflssdddalfyvknernlmrvdletleetviyqvdeewvgygtwvansdctk 138
                                   g+   y l+ nt+   +l + + d       s+d + + +++n  n++ vd+e  e + iy+ ++  +    w  +s   k
  gi|91773689|ref|YP_566381.1| 253 GNLIIYDLEENTNLVFNLPDDTADVENME-WSPDGEKIVFIQNICNIIIVDIEKRELNQIYSAEHVGMYDAQWSPDS--NK 330
                                   56666777777777777777777765444.59999999999999999999999999999998765444445555444..45 PP

               Pectate_lyase22 139 lvgiei 144
                                   l+  ei
  gi|91773689|ref|YP_566381.1| 331 LIFYEI 336
                                   555555 PP

>> DUF2286  Uncharacterized protein conserved in archaea (DUF2286)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.5e-05       0.2      40      92 ..     205     260 ..     200     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                       DUF2286  40 eesDfivlrdklelelklplkpelydklk...elslsregneaivklPvyvisfdn 92 
                                   ++s +i++  +++l+ + +l+pe+++  +   +++ s +++++ + +P  +i++d 
  gi|91773689|ref|YP_566381.1| 205 TSSQLIIMSSDMQLTQQVELDPEMIELESdpsNFKYSPTEDKIAALMPGNLIIYDL 260
                                   6899*********************98651226777******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4004.10
//
Query:       gi|91773690|ref|YP_566382.1|  [L=450]
Description: proteinase inhibitor I4, serpin [Methanococcoides burtonii DSM 6242]
Scores for 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-116  387.2   1.5   1.1e-115  387.0   1.5    1.0  1  Serpin    Serpin (serine protease inhibitor)


Domain annotation for each model (and alignments):
>> Serpin  Serpin (serine protease inhibitor)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.0   1.5    6e-120  1.1e-115       2     371 .]      76     448 ..      75     448 .. 0.95

  Alignments for each domain:
  == domain 1  score: 387.0 bits;  conditional E-value: 6e-120
                                   HHHHHHHHHHHHHHHHSTTSSEEE-HHHHHHHHHHHHHTB-HHHHHHHHHHHTGCCHCHHHHHHHHHHHHHHHCSSGGTSE CS
                        Serpin   2 antkfaldlfkalskekpskNiifSPlsistaLallllGakgetaeellevLglnesdeeelhealekllsrlneseekdk 82 
                                   an++f++d++++l+ +    Ni+fSP+si+ta+a++++Ga+++t+ee++ v+ ++  +++ l+++ +++++ +n+ +++++
  gi|91773690|ref|YP_566382.1|  76 ANNAFSFDMYNNLATDG---NIVFSPYSIFTAMAICYNGAESTTQEEIAYVFYYP-LSKPVLEKSSKEMMNIINS-DDDNN 151
                                   79*************99...********************************996.889999*************.9**** PP

                                   EEEEEEEEEEETTSEB-HHHHHHHHHHHS-EEEEE-TTTHHH.HHHHHHHHHHHHTTTSSSSSSSTTSS-TTECEEEEEEE CS
                        Serpin  83 elkianglfvekglklkeeflklakklykaevesvdfkddee.arkkINswvekqTngkIkdllsegsidsdtrlvlvNai 162
                                   +lk+an+l+v+++++l+e+f+ ++k +y+ +v++vdf++++e +r+ IN+wv+++Tn+kIkdl+++++++sdt ++++Nai
  gi|91773690|ref|YP_566382.1| 152 DLKTANALWVRENYPLNERFVGNSKIYYDGKVTNVDFRNEPErSRDIINEWVATKTNEKIKDLVPDDMVTSDTAMIITNAI 232
                                   ********************************************************************************* PP

                                   EEEEEBSS--BGGGEEEEEEE..SSSSEEEEEEEEEEEEEEEEEEETTTTEEEEEEEBGG.SEEEEEEEESSTTTHHHHHH CS
                        Serpin 163 yFkGkWeepFqpeatreekFy..vnegekvkvpmMsqegkfkyaedeelnakvlelpYkg.nlsmlillPdeekgleelek 240
                                   yFkGkW ++F+ e+t++e Fy   +++e ++++mM+++++f y+e++  +ak++elpYkg +l m+i+lP+ e+++e++e+
  gi|91773690|ref|YP_566382.1| 233 YFKGKWLNEFDVEETQKELFYnsSSNEEGTPIDMMYTKQYFSYGENK--DAKIVELPYKGdDLCMYIVLPE-ENNIENFES 310
                                   *********************866666677*************9978..***********9*********6.567****** PP

                                   HHSHHHHHHHHHHGEEEEEEEEEEEE-EEEEEEEEHHHHHHHTTHCGGGSTTTB.BTTTB......SSSSEEEEEEEEEEE CS
                        Serpin 241 kltaerleewlsklkmkkekeevslPkfkieesidlkevLqklGlkdlFseneadlsgis......kkeplfvsevlhkaf 315
                                   ++  +++++++s++++ +e  ++ lPkfk++++ +l ++L+ +Gl ++F+ ++ad+sgi+      ++  l + +v+h+af
  gi|91773690|ref|YP_566382.1| 311 RFRLSDYNNLKSSMESGNEV-RIWLPKFKFDTKAKLSDTLKTMGLVEAFT-GNADFSGIFdiqkvpEDYALWLHDVVHQAF 389
                                   **************965433.89***************************.*********9999987799*********** PP

                                   EEESSSEEEEEEEEE...ECCTTCS-SSCEEEEECSEEEEEEEETTTTEEEEEEEESSC CS
                        Serpin 316 ievnEeGteaaaata...vatllskksspvefkvdrPFlflireektgliLFlGkvvnP 371
                                   i+v+EeGtea+aata   v + l  + + +efkvd+PF+f+i++++tg+iLF+Gkv nP
  gi|91773690|ref|YP_566382.1| 390 IDVQEEGTEATAATAieaVDSCLPLPGEVMEFKVDHPFMFFIEDKRTGCILFMGKVENP 448
                                   ***************886577889999*****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3042.12
//
Query:       gi|91773691|ref|YP_566383.1|  [L=186]
Description: hypothetical protein Mbur_1743 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1331.35
//
Query:       gi|91773692|ref|YP_566384.1|  [L=214]
Description: transglutaminase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-12   46.8   0.2    5.5e-12   46.1   0.2    1.3  1  Transglut_core  Transglutaminase-like superfamily


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 !   46.1   0.2   3.1e-16   5.5e-12      10     112 .]      51     154 ..      45     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 3.1e-16
                Transglut_core  10 gakdplekakaiyewvrknveysaprrtpgsrdaeavle...tgk......GncedfaslfvallRalGipaRvvtgylsg 81 
                                   + ++p+e a++i ++v k + y+++   ++s++a++++    t +      G+c ++a+l  a  RalGip++  +    +
  gi|91773692|ref|YP_566384.1|  51 NSTTPYETANQITDYVYKVMHYDDEAFLDRSYTASDLWIinhT-NasgyyiGVCDEYATLSNAFNRALGIPSKQYYLNMTN 130
                                   5789*******************77777777776665554332.1345599*********************987655555 PP

                Transglut_core  82 eeekeqsvasedaHawvevylegygWvplDp 112
                                            ++ aH ++e++  g+ W++ Dp
  gi|91773692|ref|YP_566384.1| 131 S------SGNRSAHEMAEIWD-GQEWIHSDP 154
                                   4......899***********.********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1600.64
//
Query:       gi|91773693|ref|YP_566385.1|  [L=300]
Description: hypothetical protein Mbur_1745 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2471.10
//
Query:       gi|91773694|ref|YP_566386.1|  [L=159]
Description: hypothetical protein Mbur_1746 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   19.5   0.6        1.9    9.2   0.1    2.2  2  TTR-52    Transthyretin-like family


Domain annotation for each model (and alignments):
>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00011       1.9      14      56 ..      51     102 ..      44     108 .. 0.72
   2 !    8.8   0.1   0.00015       2.6      11      52 ..     111     153 ..     106     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                                   -EEEEEE.HHHH.TS--EEEEEE--TTSEEEEE.......EEE---.S--EE CS
                        TTR-52  14 vkVkLwe.kdtl.dpddlldetkTdedGnFels.......gseneltsidPy 56 
                                    kVkL+   d + ++ ++++e +Td+ G F+++        +++e  ++ Py
  gi|91773694|ref|YP_566386.1|  51 QKVKLYVaPDAGdNTGEIYAEYTTDDPGDFDVKtgvisvlKDTEESFTVSPY 102
                                   57888873455556778899999*********97666666555566677777 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00015
                                   GSS-EEEEEEHHHHTS--EE.EEEE--TTSEEEEEEEE---.S CS
                        TTR-52  11 aknvkVkLwekdtldpddll.detkTdedGnFelsgsenelts 52 
                                   a   +V +w++dtl  dd+l d  kT ++G +  s s+ +lt+
  gi|91773694|ref|YP_566386.1| 111 ADSLHVLVWDDDTLSGDDKLfDAYKTVSSGVYVWSNSNVKLTT 153
                                   56789*********66666515566*****9999988777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1039.85
//
Query:       gi|91773695|ref|YP_566387.1|  [L=208]
Description: hypothetical protein Mbur_1747 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1493.49
//
Query:       gi|91773696|ref|YP_566388.1|  [L=430]
Description: peptidase M28 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   90.3   0.0    1.8e-25   89.8   0.0    1.2  1  Peptidase_M28    Peptidase family M28
  ------ inclusion threshold ------
      0.081   12.6   0.0       0.13   12.0   0.0    1.3  1  Peptidase_M20    Peptidase family M20/M25/M40
        0.1   12.6   0.3       0.23   11.5   0.3    1.6  1  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0     3e-29   1.8e-25       1     196 [.     115     298 ..     115     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 3e-29
                                   EEEEEESTTCE.SEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHH CS
                 Peptidase_M28   1 Nviatlegkat.devlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSka 80 
                                   N+i+  +g++  ++ +++++HyD+  +  +p   GAdD A gvaa Le+ar+l++   +++r+v f++f  E    +G++ 
  gi|91773696|ref|YP_566388.1| 115 NIIGVKRGTNLeNQIIIVCSHYDTART--SP---GADDAALGVAATLEIARLLQD--YELNRTVYFMVFP-EHSQPIGADM 187
                                   788888888876779************..**...********************9..78********995.999******* PP

                                   HHHHHC.CCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--E CS
                 Peptidase_M28  81 fakakp.elkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkagvpv 160
                                   +++ +p  +++i  ++ lD +g g++  ++ + +++s+ l + ++ +a++ + ++++++         sDh+pf+++++p+
  gi|91773696|ref|YP_566388.1| 188 WIEMHPdLKNNITGLICLDQIGYGNNLQIS-YIPQTSW-LADIVQLSANESNISVSKHMGL----IAFSDHTPFIQNNIPA 262
                                   **96676999****************9996.5555555.6777787777777754444433....334************* PP

                                   EEECTSSS-TTTTSTTSSGGGB-HHHHHHHHHHHHH CS
                 Peptidase_M28 161 ldlaetgfpevyHtprDtldnidkdtlariaelvle 196
                                   + l+e +f++  H+p Dt++ i+ + +++ +e++ e
  gi|91773696|ref|YP_566388.1| 263 VELIESEFTPFHHKPGDTIETINFSLAENATEIAVE 298
                                   ************************999999988766 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 ?   12.0   0.0   2.1e-05      0.13      33      83 ..     143     190 ..     135     326 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                   TTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20  33 rGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakalle 83 
                                   +Gadd   gv+a le++r l+d    +++t+ ++++p+   +  Ga   +e
  gi|91773696|ref|YP_566388.1| 143 PGADDAALGVAATLEIARLLQDYE--LNRTVYFMVFPEHS-QPIGADMWIE 190
                                   7*****************999987..699*******9544.3377766666 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   3.8e-05      0.23      11      40 ..     402     430 .]     402     430 .] 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Gram_pos_anchor  11 kTGengnifltaaGllallggllLlvkrRK 40 
                                   +TG +++++l ++++l++++ ++L+ kr K
  gi|91773696|ref|YP_566388.1| 402 DTG-SKTYGLGFFAILLIILVVVLRSKRNK 430
                                   699.********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2746.69
//
Query:       gi|91773697|ref|YP_566389.1|  [L=289]
Description: hypothetical protein Mbur_1749 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   15.2   0.1       0.29   10.8   0.0    2.1  2  Peptidase_M24  Metallopeptidase family M24
      0.067   13.5   0.7        0.2   12.0   0.1    2.0  2  DUF1947        Domain of unknown function (DUF1947)


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 ?    2.2   0.0     0.014   1.2e+02      16      48 ..      56      91 ..      41     129 .. 0.59
   2 ?   10.8   0.0   3.3e-05      0.29      57      93 ..     187     223 ..     184     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.014
                                  HHHHHHH...TTCBHHHHHHHHHHHHHHHTTTCEES CS
                 Peptidase_M24 16 avleaik...pgvterelaaeieattlkrhgargla 48
                                  ++ + i    pg +e++ ++ +e+++ k+++a+  +
  gi|91773697|ref|YP_566389.1| 56 KMSKTITpdtPGLSEKDFEDYVEKMKQKYGEAGVFG 91
                                  3334466444699**********8743433333223 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.3e-05
                                   GGGGSTTTBCSSSB--TTEEEEEEEEEEETTEEEEEE CS
                 Peptidase_M24  57 enaavlhytpndrvlkegdlvlidagaeydgyasDit 93 
                                    n+++l y+p+ + + ++d+v + +ga+y+g  + i+
  gi|91773697|ref|YP_566389.1| 187 SNYDLLVYSPDADIIGDEDIVTVSLGAVYQGVSCAIS 223
                                   69999**************************988776 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.2e-05       0.2       5      32 ..      68      93 ..      67     101 .. 0.89
   2 ?   -1.3   0.1      0.32   2.9e+03      24      54 ..     112     142 ..     104     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                                  --HHHHHHHHHHHHTTT---TT--..-E CS
                       DUF1947  5 LSkKeakeileklkekyisislesdkiE 32
                                  LS+K+++++ ek+k+ky ++ + +  iE
  gi|91773697|ref|YP_566389.1| 68 LSEKDFEDYVEKMKQKYGEAGVFG--IE 93
                                  8****************9999887..54 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.32
                                   -TT--..-EEEE-SS-EEEEETTEEEEEESS CS
                       DUF1947  24 islesdkiEieeekkeklYlingvpilfeee 54 
                                   i+  ++ +E++ + + ++   ++  +l++ +
  gi|91773697|ref|YP_566389.1| 112 INSWTEYLEVKDSNGIVMASSDNLVALYKLD 142
                                   5555555999999999888888888888744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2350.49
//
Query:       gi|91773698|ref|YP_566390.1|  [L=79]
Description: hypothetical protein Mbur_1750 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 548.40
//
Query:       gi|91773699|ref|YP_566391.1|  [L=135]
Description: inorganic pyrophosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   33.8   0.1    3.4e-08   33.5   0.1    1.1  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   1.9e-12   3.4e-08       3      92 ..       5      85 ..       3      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.9e-12
                                  EEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEE.EEEEEEEEE CS
               Pyrophosphatase  3 vEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvev.kvlGvlami 84
                                  +E p+ s  Ky+   +     ++rvlf+    ++nYGfi++T+ d     Dg   D++vlg +   +g++v+     Gv++ +
  gi|91773699|ref|YP_566391.1|  5 IETPKFSFFKYQKVDD----EYKRVLFSPIPTIFNYGFIEETMGD-----DGMEEDAIVLGPRL-PQGTLVKLtNAGGVVRFV 77
                                  6777777777765444....478999*******************.....***********776.678766651677899*** PP

                                  ETTEEEEE CS
               Pyrophosphatase 85 DegetDdK 92
                                  D++ +DdK
  gi|91773699|ref|YP_566391.1| 78 DDSVQDDK 85
                                  *9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1013.36
//
Query:       gi|91773700|ref|YP_566392.1|  [L=333]
Description: hypothetical protein Mbur_1752 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00028   20.4   8.6      0.025   14.0   1.2    2.2  2  IMD       IRSp53/MIM homology domain


Domain annotation for each model (and alignments):
>> IMD  IRSp53/MIM homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.1   1.5e-05      0.27      98     131 ..       8      41 ..       3      63 .. 0.88
   2 !   14.0   1.2   1.4e-06     0.025      71     146 ..      94     170 ..      84     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                           IMD  98 kvlnqldkdyakEykkkraelkKkssellklqkK 131
                                   + +n+++++y++E ++++ el++++ +l k+q  
  gi|91773700|ref|YP_566392.1|   8 RSINAAHRKYEREAQRRQRELERQQKQLEKMQEI 41 
                                   789****************************975 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHCC.CS-CHHHHHHHH CS
                           IMD  71 eskLeelvkalhdsLlnpleekveedkkvlnqldkdyakEykkkraelkKkssellklqkKakk.gkddlkvqldel 146
                                   ++kL ++ + + d++l+++e k +   + ++++++  +kEy++  +  ++  ++   ++  +++   +d++  ld +
  gi|91773700|ref|YP_566392.1|  94 QTKLDKFRSGFFDKILKRVESKRDTLTQNVEEARQADEKEYRESLQVYEQEYADWATIRELSDRiLSGDTEAYLDAI 170
                                   89******************************************999999999988888877764445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2007  (0.111942); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
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 0.27s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 2461.89
//
Query:       gi|91773701|ref|YP_566393.1|  [L=344]
Description: cobalamin synthesis protein, P47K [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  133.9   1.2    6.9e-39  133.2   1.2    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0005   19.1   3.3      0.013   14.5   0.2    2.4  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00081   19.1   0.6     0.0021   17.7   0.6    1.7  1  SRP54            SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.019   15.0   0.7      0.019   15.0   0.7    2.0  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.029   14.2   2.8          1    9.1   0.1    2.6  3  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.029   14.3   0.4       0.07   13.0   0.4    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
       0.11   12.6   0.0        1.1    9.3   0.0    2.4  2  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.14   11.4   0.2       0.45    9.8   0.2    1.8  1  Zeta_toxin       Zeta toxin
       0.15   11.3   0.7       0.27   10.5   0.1    1.7  2  DUF1611          Domain of unknown function (DUF1611_C) P-loo
        3.5    7.4   7.5        7.1    6.3   0.1    2.9  3  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   1.2   3.8e-42   6.9e-39       2     176 ..       3     178 ..       2     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 3.8e-42
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeere 80 
                                   +++++GflGsGKTt l +l       g k+a+ivNe+ge+++D++ l++tg  + el+ GciCctl+  +  +l++l ++ 
  gi|91773701|ref|YP_566393.1|   3 IMIIGGFLGSGKTTTLLKLGkhLSDTGHKIAIIVNEIGEIGLDGDTLSSTGIVTEELTSGCICCTLKISMEYTLSNLSDEF 83 
                                   689**************9997777899*****************************************************9 PP

                                   TT-SEEEEEECTTTTHHHHHTTSHHHHH..CCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..H CS
                          cobW  81 erldviliEttGlaePapvafteeelks..dltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeall 159
                                    ++dvi+iE tG+a P ++   +  l +  +l    +v +vD++++++e +++++ ++ q++ ad+l +nK+D +++e+ +
  gi|91773701|ref|YP_566393.1|  84 -HPDVIIIEPTGIAFPRQI-KDDIALMKieNLSFAPIVNIVDGTRFNTEIKQTPKFIQTQIEDADILCINKVDIAEKEK-V 161
                                   .8*****************.44555554237888889****************************************95.5 PP

                                   HHHHHHHHHHHTTS-EE CS
                          cobW 160 ekleerlrqlnpeakvl 176
                                   +++++ l+ lnpea+v+
  gi|91773701|ref|YP_566393.1| 162 AEVRNFLEGLNPEAEVI 178
                                   **************997 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 !   14.5   0.2   7.3e-06     0.013      34      63 ..       6      35 ..       2      41 .. 0.92
   2 !    4.8   0.3    0.0065        12     166     190 ..     142     166 ..      77     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.3e-06
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavl 63
                                  + G+ G+Gk t++ +lg +l + G+++a++
  gi|91773701|ref|YP_566393.1|  6 IGGFLGSGKTTTLLKLGKHLSDTGHKIAII 35
                                  67999************************8 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0065
                                   HHH-SEEEEE---HHHHHHHHHHHH CS
                          MeaB 166 leiaDiivvnkaDkkeaekaarelr 190
                                   +e aDi+ +nk D +e ek+a+  +
  gi|91773701|ref|YP_566393.1| 142 IEDADILCINKVDIAEKEKVAEVRN 166
                                   788**********999888876544 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.6   1.2e-06    0.0021       3      35 ..       3      35 ..       1      39 [. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllv 35
                                  ++++ G+ G+GKTttl KL ++l++ g+k++++
  gi|91773701|ref|YP_566393.1|  3 IMIIGGFLGSGKTTTLLKLGKHLSDTGHKIAII 35
                                  5667799***********************997 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.7   1.1e-05     0.019       1      33 [.       3      35 ..       3      37 .. 0.92
   2 ?   -0.5   0.1      0.69   1.2e+03     110     110 ..     245     245 ..     122     337 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                  EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllv 33
                                  i+i+++  G+GKTt++++L++ l++ g++++ +
  gi|91773701|ref|YP_566393.1|  3 IMIIGGFLGSGKTTTLLKLGKHLSDTGHKIAII 35
                                  68888888*********************9976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.69
                                   E CS
                                   x RF
                          CbiA 110 g 110
                                    
  gi|91773701|ref|YP_566393.1| 245 T 245
                                   1 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 ?    9.1   0.1   0.00056         1       3      30 ..       8      35 ..       5      37 .. 0.86
   2 ?    5.0   0.1    0.0099        18     126     211 ..     118     196 ..      67     220 .. 0.63
   3 ?   -2.6   0.0       2.1   3.8e+03     196     235 ..     265     304 ..     227     309 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00056
                    ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvavv 30
                                  G  GsGKtt   +l ++l+++g ++a++
  gi|91773701|ref|YP_566393.1|  8 GFLGSGKTTTLLKLGKHLSDTGHKIAII 35
                                  677******************9998764 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0099
                    ATP_bind_1 126 vvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek.lekeleffedvealslllekeeekykklaeaia 205
                                   +v++vD +r ++ +k   +      +  ++e   + ++nk+D+++++   +  +f+e ++   +++e   +      e+  
  gi|91773701|ref|YP_566393.1| 118 IVNIVDGTRFNTEIKQTPK-----FIQTQIEDADILCINKVDIAEKEkVAEVRNFLEGLNPEAEVIEFSAKE---ADEKFQ 190
                                   4666666666664444444.....445588888899999999987553333333333333333333333333...333333 PP

                    ATP_bind_1 206 elleef 211
                                   +l+++ 
  gi|91773701|ref|YP_566393.1| 191 RLIDLL 196
                                   333333 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                    ATP_bind_1 196 kykklaeaiaelleefalvlrflplssekeesiedllsli 235
                                   + ++ +  ++++++  + ++++   +++++e + ++ls++
  gi|91773701|ref|YP_566393.1| 265 ALEYPETLMKASITSSESIPNIEFFETKSKECTLKFLSAV 304
                                   3344445555566666666666666666666666666655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   3.9e-05      0.07       2      36 ..       4      38 ..       3      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKha 36
                                  + i g+ gsGKTt l kl ++l++ g ++++i  +
  gi|91773701|ref|YP_566393.1|  4 MIIGGFLGSGKTTTLLKLGKHLSDTGHKIAIIVNE 38
                                  5677999***********************99665 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 ?    9.3   0.0    0.0006       1.1       6      84 ..      11      93 ..       8     139 .. 0.80
   2 ?    0.3   0.0      0.37   6.7e+02      58      78 ..     237     259 ..     198     275 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0006
               Glyco_trans_4_2  6 anlssvhtlrlakeLakrgyeVhvitpkkga....kdeleaegihvhrlkvdrkgpleylkaf.klkklikkikPDvvhahya 83
                                  +  + + +l+l k L++ g+++++i ++ g+     d l + gi   +l++++      +++  +l +l +++ PDv+ ++++
  gi|91773701|ref|YP_566393.1| 11 GSGKTTTLLKLGKHLSDTGHKIAIIVNEIGEigldGDTLSSTGIVTEELTSGCICCTLKISMEyTLSNLSDEFHPDVI-IIEP 92
                                  55566778999****************77664444566778899999999776665555666559************9.4555 PP

               Glyco_trans_4_2 84 k 84
                                  +
  gi|91773701|ref|YP_566393.1| 93 T 93
                                  5 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
               Glyco_trans_4_2  58 leyl.k.afklkklikkikPDvv 78 
                                    +y+   + ++ k ikk++PD v
  gi|91773701|ref|YP_566393.1| 237 EKYAiDvLTSIGKQIKKLNPDFV 259
                                   33321433477788888888877 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00025      0.45      17      49 ..       2      34 ..       2      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                    Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgnvvrl 49
                                  k++++gG  G+GK++++ +l + l  +g  + +
  gi|91773701|ref|YP_566393.1|  2 KIMIIGGFLGSGKTTTLLKLGKHLSDTGHKIAI 34
                                  5789***************99999866665555 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00015      0.27      14      94 ..       2      91 ..       1      98 [. 0.76
   2 ?   -3.0   0.1       2.1   3.7e+03     160     184 ..     147     171 ..     128     186 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                       DUF1611 14 rvlvvGTdcavGKrttaleleealeerGlkaafv..aTgqtgi...liagegvvldavvvdfvaGav....eglvkkaaeeee 87
                                  +++++G     GK tt l+l + l + G k+a++    g++g+     +  g+v + + +  ++ ++    e++  ++ +e +
  gi|91773701|ref|YP_566393.1|  2 KIMIIGGFLGSGKTTTLLKLGKHLSDTGHKIAIIvnEIGEIGLdgdTLSSTGIVTEELTSGCICCTLkismEYTLSNLSDEFH 84
                                  57888888899*******************99983346787774334588888888888888888752222556666677889 PP

                       DUF1611 88 pdlilve 94
                                  pd+i++e
  gi|91773701|ref|YP_566393.1| 85 PDVIIIE 91
                                  9999988 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                       DUF1611 160 gislNtknlseeeakealeeleeel 184
                                    +++N+ ++ e+e  ++++++ e l
  gi|91773701|ref|YP_566393.1| 147 ILCINKVDIAEKEKVAEVRNFLEGL 171
                                   4677777777777666666655544 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.014        25      19      41 ..       3      25 ..       1      57 [. 0.84
   2 ?    6.3   0.1     0.004       7.1     196     223 ..      61      90 ..      51      91 .. 0.83
   3 ?   -0.9   0.2      0.66   1.2e+03     149     150 ..     187     194 ..     118     257 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                        AAA_11 19 itliqGPPGtgKTktivellsql 41
                                  i +i G  G+gKT+t+++l ++l
  gi|91773701|ref|YP_566393.1|  3 IMIIGGFLGSGKTTTLLKLGKHL 25
                                  56788889***********9998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.004
                        AAA_11 196 aeivltTlsgagsklleklakkf..dvviI 223
                                   + ++++Tl ++ + +l++l ++f  dv+iI
  gi|91773701|ref|YP_566393.1|  61 SGCICCTLKISMEYTLSNLSDEFhpDVIII 90 
                                   568****************99663367776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.66
                        AAA_11 149 k......e 150
                                   +      +
  gi|91773701|ref|YP_566393.1| 187 EkfqrliD 194
                                   12222220 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2254.72
//
Query:       gi|91773702|ref|YP_566394.1|  [L=346]
Description: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0011   18.3   0.1        1.9    7.7   0.0    2.8  2  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0   0.00017       3.1       6     248 ..       9     233 ..       4     259 .. 0.61
   2 !    7.7   0.0   0.00011       1.9     273     320 ..     287     334 ..     260     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00017
                                   -SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTE.E--SS--EE CS
                   Meth_synt_2   6 iGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgf.aftkngwvq 85 
                                   iGSfP  ++v    +e+ ++++s+ ++ +++ + i ++ +++ ++gv v+   ++  +dm e f   ++     ++   v+
  gi|91773702|ref|YP_566394.1|   9 IGSFPLPEDV---TKEWMANAFSKRDSDEQLFNIIGSAFKQKLDAGVQVATYPQF--QDMNEQFLSIIKDPkCVEEPFKVK 84 
                                   6777766554...346666777777777777777777776666666666665555..666666655554442222222222 PP

                                   EETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-.BEEEEE-HHHHHHTSEE-..TTS-HHHHHHHHHHHHHHHHHHH CS
                   Meth_synt_2  86 sygsrcvrppiivgdvsrpaamtvkesalaqsltdkp.vkglltGpvtilnwsfvr..ddvdraeaaaqialalrdevkdL 163
                                           + i+  d++ ++a ++k     + + +kp v+  +tGp  +    f        +++ a+ i   + +++k  
  gi|91773702|ref|YP_566394.1|  85 EDS-----ARILELDILEKTAAQYK-----EETGNKPdVRVCVTGPLELYLKDFGGtqYTDILDTLAVSIDRFISKAIKSA 155
                                   222.....22344444444443333.....344555568888899888765555442133447788888888889999999 PP

                                   HHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS.-TTSEEEEEES-S--CCCHHHHHTT--SEEEESBSS CS
                   Meth_synt_2 164 eaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaa.addtqvhtHlCyselndilsaiaaldvDvitieasr 243
                                   ++  i  i iDep +  G+  ++  ++a     v+a  l+t+ a ++d++v  Hl ++   +i  a +  ++ vi +e + 
  gi|91773702|ref|YP_566394.1| 156 KNFTIRTISIDEPSI--GINPQVMFEDAE---LVKALSLSTAYAgKQDVDVEIHLHSPLHYKI--ACDTPNINVIGVESAA 229
                                   999999999999977..555555444444...4777777777663567777777766666666..5666666666666666 PP

                                   S-SSG CS
                   Meth_synt_2 244 sdeel 248
                                   ++ + 
  gi|91773702|ref|YP_566394.1| 230 NP-SY 233
                                   65.55 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00011
                                   --THHHHHHHHHCHHCTS-STSB-BB-SS-STTS-HHHHHHHHHHHHH CS
                   Meth_synt_2 273 vpsmeeiaalikkaldvapkerlwvnPdCGLktrkreearaalknmvd 320
                                   +++ e ia+++++a  +      +v PdCG+   +++e   +l n v+
  gi|91773702|ref|YP_566394.1| 287 METPEIIAKRLEDAYSIFGDRIKYVGPDCGVGSWPTQEIACQLLNNVE 334
                                   67778899999999988855556*************999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2224.08
//
Query:       gi|91773703|ref|YP_566395.1|  [L=247]
Description: ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-46  158.4   0.1    3.5e-46  157.4   0.1    1.4  1  ATPase     KaiC
    1.9e-07   30.8   0.0     0.0012   18.5   0.0    2.1  2  AAA_25     AAA domain
    2.8e-05   23.6   0.0    4.9e-05   22.8   0.0    1.3  1  DnaB_C     DnaB-like helicase C terminal domain
     0.0035   17.1   0.3       0.64    9.7   0.3    2.7  1  AAA_24     AAA domain
     0.0084   16.4   0.1      0.053   13.8   0.1    2.0  1  AAA_22     AAA domain
  ------ inclusion threshold ------
      0.047   12.9   0.3        3.5    6.8   0.1    2.0  2  Rad51      Rad51
      0.066   12.9   0.0       0.15   11.8   0.0    1.5  1  IstB_IS21  IstB-like ATP binding protein
      0.067   13.2   0.0       0.12   12.5   0.0    1.5  1  AAA_14     AAA domain
       0.14   12.6   0.6       0.32   11.4   0.6    1.9  1  AAA        ATPase family associated with various cellular act


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 !  157.4   0.1   1.8e-49   3.5e-46       1     227 [.       3     243 ..       3     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 1.8e-49
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   +++gIeglD+i++gG+  +rv+l++G pG GKt+f++qFl +ga   ge g++vt+ e+++++++++++  +++  l +  
  gi|91773703|ref|YP_566395.1|   3 IPSGIEGLDDIIQGGLVADRVYLLSGPPGGGKTTFGMQFLSQGATF-GEVGLYVTLLESPQNVINDMSNYAMNVATLIKMK 82 
                                   699****************************************887.********************************** PP

                        ATPase  82 klaiidasesaeesaee..................kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaRei 143
                                   kl + d+   +e    +                   +  ++  + +e+a +++e+++kr+viDs +++   ++++++  ++
  gi|91773703|ref|YP_566395.1|  83 KLLFADLGPRMEYGYIDdlhevinsdyevgyssveGEAPSPAMVFKEIAAYVSEYNVKRLVIDSMSAIrFSTKDHSLEEKE 163
                                   *******999887665568999********999854556777889***********************98999999999** PP

                        ATPase 144 lrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegi 224
                                   + +++r lk+lg+T+i+ se+    +  + y  e+f++ gv+ L++ ++ ++++R ++++kmRgtkh+ ++++ e t++g 
  gi|91773703|ref|YP_566395.1| 164 MGRFIRNLKNLGCTTIILSEM----TDPNSYSTEQFAAHGVLFLHNFLYGKKMTRAVQVIKMRGTKHHCDMMEVEFTDKGL 240
                                   ********************5....45578999***********************************************9 PP

                        ATPase 225 kvl 227
                                    + 
  gi|91773703|ref|YP_566395.1| 241 AIK 243
                                   986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.9e-07    0.0012      19      58 ..       7      46 ..       2      65 .. 0.87
   2 !   10.5   0.0   0.00017      0.33     127     185 ..     124     180 ..      85     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.9e-07
                        AAA_25 19 ppprrwlvkgllpagelallaGapgtGKttlaldlalava 58
                                  ++ ++++++g l+a+ + ll G+pg GKtt+ ++     a
  gi|91773703|ref|YP_566395.1|  7 IEGLDDIIQGGLVADRVYLLSGPPGGGKTTFGMQFLSQGA 46
                                  677899***999********************99887666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00017
                        AAA_25 127 tadvdaleaaieevegvrlvviDplsralgg...densnsdvgalvealeriarrtgaavll 185
                                   + ++++++a + e ++v+ +viD++s++       + +++++g+++ +l+++    g+++++
  gi|91773703|ref|YP_566395.1| 124 AMVFKEIAAYVSE-YNVKRLVIDSMSAIRFStkdHSLEEKEMGRFIRNLKNL----GCTTII 180
                                   4568999******.77***********8888553444455579999988887....777765 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.4e-08   4.9e-05       2     164 ..       3     174 ..       2     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.4e-08
                                   BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHH...HHHHHHHHHTXXHHH CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                        DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeql...vqRllsseaeidskk 78 
                                   +++g + LD++++ Gl    ++++ + p+ Gkt++ +++ ++ a+  +++  v  le +++ +    +  +   + i++kk
  gi|91773703|ref|YP_566395.1|   3 IPSGIEGLDDIIQgGLVADRVYLLSGPPGGGKTTFGMQFLSQGATFGEVGLYVTLLESPQNVIndmSNYAMNVATLIKMKK 83 
                                   78999****98762799999**********************999899999999999998766332555666777889999 PP

                                   HHHTTSX.H...HHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTSCS.SSCCCHHH CS
                                   xxxxxxx.x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                        DnaB_C  79 lrtgklk.e...edweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmegsee.kenreqev 154
                                   l  ++l  +     +++l+e i++  e+     +  a +++ + +++  + +e +++ +viD +  ++ s++ ++ +e+e+
  gi|91773703|ref|YP_566395.1|  84 LLFADLGpRmeyGYIDDLHEVINSDYEVGYSSVEGEAPSPAMVFKEIAAYVSEYNVKRLVIDSMSAIRFSTKdHSLEEKEM 164
                                   977666533111334444444444444444444444557777777788888899**************8754355778889 PP

                                   HHHHHHHHHH CS
                                   xxxxxxxxxx RF
                        DnaB_C 155 seisrsLkal 164
                                    +  r+Lk+l
  gi|91773703|ref|YP_566395.1| 165 GRFIRNLKNL 174
                                   9999998876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.3   0.00032      0.64       4      23 ..      23      49 ..      20     196 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00032
                        AAA_24  4 kiliyGpsgiGKTtlakel.......g 23
                                   +l+ Gp+g GKTt+  ++       g
  gi|91773703|ref|YP_566395.1| 23 VYLLSGPPGGGKTTFGMQFlsqgatfG 49
                                  568889999999999988865544442 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   2.7e-05     0.053       6     127 ..      22     181 ..      19     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...............................erpevvfvtlpsst...s 52 
                                   ++ ++ G++G GKTt   ++l+q                                        + ++++f +l   +    
  gi|91773703|ref|YP_566395.1|  22 RVYLLSGPPGGGKTTFGMQFLSQGA---T--FgevglyvtllespqnvindmsnyamnvatliKMKKLLFADLGPRMeygY 97 
                                   67899*****************962...2..23467799999766666655555555444444333334555555444544 PP

                        AAA_22  53 skdllrellralglelka...erlsseellealeqalraravielliiDEaqhlr...s......eealeeLrsllnlsrk 121
                                    +dl + + ++++++ ++   e  s   +++ ++ +++++ v + l+iD +  +r   +      +e+ +++r+l n    
  gi|91773703|ref|YP_566395.1|  98 IDDLHEVINSDYEVGYSSvegEAPSPAMVFKEIAAYVSEYNV-KRLVIDSMSAIRfstKdhsleeKEMGRFIRNLKN--LG 175
                                   455555555555555555997777777778************.*********9988651556777888888888888..55 PP

                        AAA_22 122 gvqliL 127
                                    +++iL
  gi|91773703|ref|YP_566395.1| 176 CTTIIL 181
                                   555555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0018       3.5      18      57 ..       2      41 ..       1      49 [. 0.93
   2 ?    4.8   0.0    0.0074        15     118     227 ..     124     225 ..      61     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0018
                                  EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                         Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                  ++  G + lD++++GG+ +  +  + G  + Gkt + +++
  gi|91773703|ref|YP_566395.1|  2 RIPSGIEGLDDIIQGGLVADRVYLLSGPPGGGKTTFGMQF 41
                                  6788999*****************************9985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0074
                                   HHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.----- CS
                         Rad51 118 eellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfs 198
                                   + + +++aa ++e +++ l++Ds+ a     fs ++  +  ++++g+++r+L++l      + +i  ++++   ++++ f+
  gi|91773703|ref|YP_566395.1| 124 AMVFKEIAAYVSEYNVKRLVIDSMSAI---RFSTKDH-SLEEKEMGRFIRNLKNLG----CTTIILSEMTDPNSYSTEQFA 196
                                   45677999999************9875...4777765.555778999999999985....445555566666666666666 PP

                                   -------HHHHHHHH-SEEEEEEE-STTE CS
                         Rad51 199 adpkkPigGlvlahasttRlalrkgkgee 227
                                   a         + ++++t  ++++k +g++
  gi|91773703|ref|YP_566395.1| 197 AHGVLFLHNFLYGKKMTRAVQVIKMRGTK 225
                                   66666555555666666566666666655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.3e-05      0.15      50     139 ..      24     110 ..      10     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                     IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqaeaell 130
                                    +l Gp+G GK+ + + +  ++++ g   l+v++ +  +++   ++  ++a ++++l+k++ l+  dlg   ++     +l
  gi|91773703|ref|YP_566395.1|  24 YLLSGPPGGGKTTFGMQFLSQGATFGEVGLYVTLLESPQNV--INDMSNYAMNVATLIKMKKLLFADLGP-RMEYGYIDDL 101
                                   5799***************************9987766665..456678999999999999999999996.5777888888 PP

                     IstB_IS21 131 feviekrye 139
                                    evi++ ye
  gi|91773703|ref|YP_566395.1| 102 HEVINSDYE 110
                                   999988887 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.8e-05      0.12       3     105 ..      22     151 ..      20     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklke.......ekktylflDE 72 
                                   ++++++G+   GKTt+  q++++  +  e  ly++l + ++  ++d +    ++ +li+ k  +       ++++y ++D 
  gi|91773703|ref|YP_566395.1|  22 RVYLLSGPPGGGKTTFGMQFLSQGATFGEVGLYVTLLESPQNVINDMSnyamNVATLIKMK--KllfadlgPRMEYGYIDD 100
                                   7999*****************9988667888999977766644443322223233333322..133345667999999999 PP

                        AAA_14  73 iqev...................pewekalkslvdegknldvivtGSnskll 105
                                    +ev                     ++k +  +v e+ n++ +v  S s + 
  gi|91773703|ref|YP_566395.1| 101 LHEVinsdyevgyssvegeapspAMVFKEIAAYVSEY-NVKRLVIDSMSAIR 151
                                   9999777777777777777766655666666666666.66666666666555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00016      0.32       2      21 ..      25      44 ..      24     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                  EEESSTTSSHHHHHHHHHHH CS
                           AAA  2 llyGppGtGKTllakavake 21
                                  ll+GppG GKT++  +  ++
  gi|91773703|ref|YP_566395.1| 25 LLSGPPGGGKTTFGMQFLSQ 44
                                  9***********98777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 1707.51
//
Query:       gi|91773704|ref|YP_566396.1|  [L=161]
Description: hypothetical protein Mbur_1756 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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       0.14   11.8   0.0    1.1  1  GH131_N   Glycoside hydrolase 131 catalytic N-terminal domain


Domain annotation for each model (and alignments):
>> GH131_N  Glycoside hydrolase 131 catalytic N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.8e-06      0.14     169     243 ..      22      95 ..      10      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-06
                       GH131_N 169 kgtwhNFavevdfdastlqvyyStgeapLkkvtepiandtsggggefhfgllklplanqsdvvhdGiqesgiqeg 243
                                   +++ +N ++ev+++++    ++ +   +Lk  ++++   ++ +  ++h+g +k ++a ++    d++q+++ +eg
  gi|91773704|ref|YP_566396.1|  22 EDKSYNLGLEVGYNKHSEIGWVNESLVKLKTLSKNLGLGDVISA-QYHYGKQKGAIAREKGLKIDAFQKAERNEG 95 
                                   46679************999*********************888.*************99999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1136.67
//
Query:       gi|91773705|ref|YP_566397.1|  [L=345]
Description: elongation factor Tu domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-07   31.0   0.2    2.6e-06   27.7   0.1    2.5  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    2.2e-05   24.1   0.1     0.0052   16.3   0.0    2.3  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0091   15.7   0.5      0.033   13.9   0.2    2.0  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
      0.012   15.8   0.3      0.022   15.0   0.3    1.4  1  AAA_28        AAA domain
      0.015   15.0   0.7      0.026   14.2   0.7    1.4  1  AAA_24        AAA domain
      0.048   13.1   0.2        1.2    8.5   0.1    2.3  2  Arf           ADP-ribosylation factor family
      0.076   13.0   0.0       0.16   12.0   0.0    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.14   12.7   0.1       0.27   11.8   0.1    1.5  1  AAA_18        AAA domain
       0.18   11.3   0.8       0.37   10.2   0.2    1.9  2  SRPRB         Signal recognition particle receptor beta subun
       0.18   12.0   0.2       0.42   10.8   0.2    1.6  1  Roc           Ras of Complex, Roc, domain of DAPkinase


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 !   27.7   0.1   1.5e-09   2.6e-06       2      73 ..     183     248 ..     182     249 .. 0.96
   2 ?    0.0   0.0      0.63   1.1e+03      33      63 ..     288     318 ..     279     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.5e-09
                                   EEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   2 tvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                    v+lg+v +G+++  d++     +t+k+    +i+s++ +  d ++a aga++G+ ++ +  +d +++G +l
  gi|91773705|ref|YP_566397.1| 183 CVVLGVVDQGIINAKDKLIA--FPTDKQ---IEIRSIQLHDVDAKTAPAGARVGLALKNVQSKD-VERGFVL 248
                                   599*****************..999999...*********************************.*****99 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.63
                                   EEEEEEEEETEEESEEETTSEEEEEEEESSC CS
                   GTP_EFTU_D2  33 trissletfhededeavaganaGvivaikgl 63 
                                    r+ +++++ e+++    +a + + + + +l
  gi|91773705|ref|YP_566397.1| 288 MRVEKILVNGEEVKRTTTEAECMLTLSGSKL 318
                                   6899999999999999999999998887666 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.3    0.0061        11       5      24 ..       3      22 ..       1      29 [. 0.86
   2 !   16.3   0.0   2.9e-06    0.0052      61     190 ..      33     151 ..      22     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0061
                                  EEEEEESTTSSHHHHHHHHH CS
                      GTP_EFTU  5 nigiighvDhGKtTLtdrLl 24
                                  +i+iig   +GKtTL  +L 
  gi|91773705|ref|YP_566397.1|  3 KIIIIGSEKSGKTTLAAKLG 22
                                  799*************9986 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.9e-06
                                   EEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST....H CS
                      GTP_EFTU  61 isleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl....k 136
                                     +   ++ + ++ iD+ G    +k + +gl+  D+avl +   eG    + e +  +  +g +  i++++K D      +
  gi|91773705|ref|YP_566397.1|  33 YDFA--KSGKVLTTIDATGYPTAIKPMMAGLNLSDIAVLCIPP-EGLDLYSGECIIALDLLGYKhGIIVLTKSDTSypfaI 110
                                   3444..888999****************************985.6*******************99********9974444 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                      GTP_EFTU 137 aelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                   +elke ++++ +           + e    + + + +S  + eg+++l e++++
  gi|91773705|ref|YP_566397.1| 111 EELKEKITKLTTGT---------ALE----NWEYISVSTTSFEGMEELKEMIFD 151
                                   44444444433222.........222....456777777777888877777765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   1.9e-05     0.033       1      23 [.       1      23 [.       1      64 [. 0.90
   2 ?   -0.7   0.0      0.58     1e+03      95     141 ..      98     149 ..      90     151 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                     PduV-EutP  1 mkkilliGkvgsGKttLtqalkg 23
                                  m ki++iG+ +sGKttL+ +l +
  gi|91773705|ref|YP_566397.1|  1 MTKIIIIGSEKSGKTTLAAKLGK 23
                                  89****************99966 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.58
                     PduV-EutP  95 iitkidlaedeenieaveelLks...aGae...kifevsavekegieellkyl 141
                                   ++tk d++    +ie  +e++++     a    + ++vs+++ eg+eel++++
  gi|91773705|ref|YP_566397.1|  98 VLTKSDTS-YPFAIEELKEKITKlttGTALenwEYISVSTTSFEGMEELKEMI 149
                                   55666665.44444444444333110222211134678999999999998876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   1.2e-05     0.022       1      24 [.       3      26 ..       3      33 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                        AAA_28  1 kivitGgestGKTtlleaLaargy 24
                                  ki+i+G e +GKTtl+++L ++g+
  gi|91773705|ref|YP_566397.1|  3 KIIIIGSEKSGKTTLAAKLGKKGT 26
                                  79*****************99987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   1.5e-05     0.026       4      29 ..       3      28 ..       1      54 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                        AAA_24  4 kiliyGpsgiGKTtlakelgpkplfi 29
                                  ki+i+G++++GKTtla++lg+k  + 
  gi|91773705|ref|YP_566397.1|  3 KIIIIGSEKSGKTTLAAKLGKKGTVA 28
                                  99*****************5554444 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00068       1.2      15      39 ..       2      26 ..       1      37 [. 0.86
   2 ?    2.2   0.0     0.059     1e+02     119     171 ..      96     149 ..      84     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00068
                                  EEEEEEESTTSSHHHHHHHHHHSSC CS
                           Arf 15 lrilllGLDnaGKtTilkklkleel 39
                                  ++i+++G +++GKtT+  kl ++ +
  gi|91773705|ref|YP_566397.1|  2 TKIIIIGSEKSGKTTLAAKLGKKGT 26
                                  59****************9987655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.059
                                   EEEEE-TTSTTSS-HHHHHHHTT.GGGSSSSSSEEEEEEBTTTTBTHHHHHHHH CS
                           Arf 119 lvlaNKqDlpealseeelrellg.leelkgkrkleiqkcsavkgeglkeglewl 171
                                   +++  K D++     eel+e+++ l++ ++ +++e +++s+++ eg++e  e +
  gi|91773705|ref|YP_566397.1|  96 IIVLTKSDTSYPFAIEELKEKITkLTTGTALENWEYISVSTTSFEGMEELKEMI 149
                                   788999999999999999988751555557889999999999999999877665 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 ?   12.0   0.0   9.1e-05      0.16      55     102 ..      92     151 ..      85     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                  MMR_HSR1_Xtn  55 YipclyvlNKiDlisleeldelare............pnsvviSaekelnldeLkekiwe 102
                                   Y++ ++vl K D+     ++el+++             +++ +S+ +  +++eLke+i++
  gi|91773705|ref|YP_566397.1|  92 YKHGIIVLTKSDTSYPFAIEELKEKitklttgtalenWEYISVSTTSFEGMEELKEMIFD 151
                                   9999*********65555555555445568888886558899999999**********97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00015      0.27       1      41 [.       4      45 ..       4      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllev 41
                                  I++ G   +GKttla  L k++ +  +   d ak +  l++ 
  gi|91773705|ref|YP_566397.1|  4 IIIIGSEKSGKTTLAAKLGKKGTVaDFTMYDFAKSGKVLTTI 45
                                  99******************9644766666666665555555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2    0.0002      0.37       5      28 ..       3      26 ..       1      49 [. 0.82
   2 ?   -2.7   0.0       1.8   3.3e+03      90     123 ..     301     334 ..     299     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                  EEEEE-STTSSHHHHHHHHHHSS- CS
                         SRPRB  5 avllvGlsdsGKTslftrLttdsv 28
                                  +++++G  +sGKT+l  +L ++ +
  gi|91773705|ref|YP_566397.1|  3 KIIIIGSEKSGKTTLAAKLGKKGT 26
                                  79****************988743 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TT CS
                         SRPRB  90 kevkevAEllyeilliteklkdavdiliACnKqe 123
                                   k+ ++ AE + ++   + ++ ++ d +i Cn +e
  gi|91773705|ref|YP_566397.1| 301 KRTTTEAECMLTLSGSKLLAYNGSDRFIICNLDE 334
                                   6778889999999999999999999999999665 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 ?   10.8   0.2   0.00024      0.42       1      21 [.       3      23 ..       3      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                                  EEEEESSTTSSHHHHHHCHCT CS
                           Roc  1 KvvlvGdsgvGKtsllkrfve 21
                                  K++++G +++GKt+l+ ++ +
  gi|91773705|ref|YP_566397.1|  3 KIIIIGSEKSGKTTLAAKLGK 23
                                  9**************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2379.81
//
Query:       gi|91773706|ref|YP_566398.1|  [L=317]
Description: ATP dependent DNA ligase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-41  140.3   0.0    5.2e-41  139.6   0.0    1.4  1  Lig_C           Ligase Pab1020 C-terminal region
    2.8e-15   57.0   0.0    4.4e-15   56.4   0.0    1.3  1  RNA_ligase      RNA ligase
    2.4e-07   30.6   0.0    1.7e-05   24.5   0.0    2.3  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
  ------ inclusion threshold ------
      0.094   12.1   0.0          6    6.2   0.0    2.1  2  ZnuA            Zinc-uptake complex component A periplasmic


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 !  139.6   0.0   1.2e-44   5.2e-41       1     125 []     191     315 ..     191     315 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 1.2e-44
                                   HHCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHHHH CS
                         Lig_C   1 vafsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeenieell 81 
                                   +af+++++ grd+lfsRv+Re+fqave+ee+ +++ +r+ +LG+siL+pm+++i ++ ++ ++++e+++r+ + e++ +++
  gi|91773706|ref|YP_566398.1| 191 HAFKFYNDAGRDYLFSRVVREGFQAVEWEETGDDIDKRCLQLGRSILYPMIDSIVNIGNGVRLADEVQMRLSNLETVSKFK 271
                                   79******************************************************************************* PP

                                   HHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT- CS
                         Lig_C  82 ehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeGg 125
                                   e+Lrr+g++a+++e+e  ++e++vk+kk+++st+dk+ s+++G+
  gi|91773706|ref|YP_566398.1| 272 EYLRRQGIDAIFSEPEVVGDEFIVKIKKLNKSTNDKTLSMWKGE 315
                                   ******************************************96 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   9.7e-19   4.4e-15       2     148 ..      25     172 ..      24     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 9.7e-19
                                   EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH........ECCEEEEEEEES....S CS
                    RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkekla......neelilyGElig...hs 71 
                                   +v v+EK++G n+ri++v++ + +++R++++ p  +++        +a+++      +      ++el+l+GE++g   + 
  gi|91773706|ref|YP_566398.1|  25 TVCVEEKMNGFNVRIVTVDGkIIAITRGGYVcP--YST-------ERAQKFL-----NidffeeHPELVLHGEMVGpdnP- 90 
                                   799***************555**********54..222.......2222222.....2223446788*********8752. PP

                                   S......TTSS.EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS.HHHHHCCC...HHHHTC--EEEE CS
                    RNA_ligase  72 i....kygglpkefyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl.aaeellel..llskgnkrEGlVi 143
                                   +     y+    e++vFdi    +k+++  l+  e+++la+++g  +v++++e++++ a   + e+  +   +   EG++i
  gi|91773706|ref|YP_566398.1|  91 YipkkIYNVESLELFVFDIR---HKHSGIPLPLHERRQLAEEYGftQVRLFGEFPKEeAPLRISEIirE-LGKIEHEGVII 167
                                   23443555555599999999...888*************************999987766666666431.67779****** PP

                                   EESSS CS
                    RNA_ligase 144 kpese 148
                                   k++ +
  gi|91773706|ref|YP_566398.1| 168 KDPMM 172
                                   *6644 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 !   24.5   0.0   3.8e-09   1.7e-05       9     189 ..      15     172 ..       8     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.8e-09
                                   CHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTC CS
                DNA_ligase_A_M   9 siekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketge 89 
                                   +ie  ++ +  +++ vE+K++G  +++   ++k+  ++R +   +++ ++  k+l+  f+++  +++l GE+v  d+    
  gi|91773706|ref|YP_566398.1|  15 AIEAHFSDV--ETVCVEEKMNGFNVRIVTVDGKIIAITRGGYVCPYSTERAQKFLNIDFFEEHPELVLHGEMVGPDNP--- 90 
                                   566667775..5677***********************************************9***********4443... PP

                                   BEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHHHH CS
                DNA_ligase_A_M  90 ilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveeleel 170
                                    +p++         ++v       +l lfvFDi    + s + +pl+eRr+l ee+    ++   + e  + +    + e+
  gi|91773706|ref|YP_566398.1|  91 YIPKKI--------YNV------ESLELFVFDIR--HKHSGIPLPLHERRQLAEEYG--FTQVRLFGEFPKEEAPLRISEI 153
                                   444433........322......3579******8..66678**************98..344444667777788899**** PP

                                   HHHHHHTTECEEEEEETT- CS
                DNA_ligase_A_M 171 leeaiseglEGlvvKnpds 189
                                   ++e  + ++EG+++K+p+ 
  gi|91773706|ref|YP_566398.1| 154 IRELGKIEHEGVIIKDPMM 172
                                   ****************975 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0072        32     165     196 ..     125     159 ..     122     200 .. 0.81
   2 ?    6.2   0.0    0.0013         6     184     218 ..     264     299 ..     245     312 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0072
                                   HHHHHTT-EEEEEE.SSSSS..HHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxx RF
                          ZnuA 165 ylarayglevagia.giste..aaqiaalieeike 196
                                    la++yg++++ ++ ++ +e  + +i+++i+e+ +
  gi|91773706|ref|YP_566398.1| 125 QLAEEYGFTQVRLFgEFPKEeaPLRISEIIRELGK 159
                                   599***********666666999999999988755 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHTT-SEEEEET.TS-THHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                          ZnuA 184 aaqiaalieeikeagvkaifvep.laspklaetlae 218
                                    +++++++e ++ +g+ aif+ep ++ ++ + ++++
  gi|91773706|ref|YP_566398.1| 264 LETVSKFKEYLRRQGIDAIFSEPeVVGDEFIVKIKK 299
                                   6899*******************6667777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2024.59
//
Query:       gi|91773707|ref|YP_566399.1|  [L=258]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  136.9  13.2    1.5e-13   51.0   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 !   32.8   0.5   3.9e-12   7.1e-08       1      54 [.       3      54 ..       3      56 .. 0.89
   2 !   26.1   0.1     5e-10     9e-06       6      52 ..      75     119 ..      69     122 .. 0.87
   3 !   51.0   0.4   8.3e-18   1.5e-13       2      53 ..     129     179 ..     128     182 .. 0.95
   4 !   34.3   0.1   1.4e-12   2.5e-08       1      55 [.     202     256 ..     202     258 .] 0.96

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.9e-12
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                  V+dim  ++ +++  +t++ al+ m++k+ +rl  V  d+kl+Gi+t+r l + 
  gi|91773707|ref|YP_566399.1|  3 VKDIMVQPI-SIDKADTISHALDVMEKKATRRL-LVKHDDKLIGILTMRGLTKE 54
                                  899998877.***************8888****.8889999********98776 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 5e-10
                                   BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                           CBS   6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                   ++d+v v pd+++ +al lm  k+ +++ +V e++k++G vt   +l
  gi|91773707|ref|YP_566399.1|  75 SDDFVKVLPDMDVDDALTLM-AKN-RGIIIVSENEKILGWVTPNEVL 119
                                   7899****************.777.7998899999*******98776 PP

  == domain 3  score: 51.0 bits;  conditional E-value: 8.3e-18
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                   ++im++d++tv+p + ++ +  ++ +k+++r+PV+ edgkl+Givt+ D+++
  gi|91773707|ref|YP_566399.1| 129 AEIMNKDPITVHPGDRVSHIRHIILDKDIGRFPVI-EDGKLIGIVTEQDIAK 179
                                   79*********************88**********.9*************97 PP

  == domain 4  score: 34.3 bits;  conditional E-value: 1.4e-12
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+dim r v tv  +t ++++  +m ++++++lPVV+ +g  vG +t+r +++a 
  gi|91773707|ref|YP_566399.1| 202 VEDIMKRGVKTVQSNTLMSDVTAMMLKEKIGGLPVVNLEGDMVGFITRRNIISAF 256
                                   89***********************9999***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1695.87
//
Query:       gi|91773708|ref|YP_566400.1|  [L=279]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-44  147.8  20.3    8.9e-13   48.5   0.8    4.1  4  CBS        CBS domain
  ------ inclusion threshold ------
      0.037   13.8   1.5        3.8    7.3   0.0    3.1  3  PduV-EutP  Ethanolamine utilisation - propanediol utilisation
      0.045   13.7   0.2         22    5.0   0.0    3.6  4  GCV_T_C    Glycine cleavage T-protein C-terminal barrel domai
       0.18   11.9   0.1       0.78    9.9   0.0    2.0  3  TMEM223    Transmembrane protein 223
       0.25   11.6   3.5         38    4.7   0.0    4.0  4  IF3_N      Translation initiation factor IF-3, N-terminal dom


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 !   40.6   0.5   7.1e-14   2.5e-10       1      51 [.       3      52 ..       3      57 .. 0.92
   2 !   48.5   0.8   2.5e-16   8.9e-13       3      55 ..      75     126 ..      73     128 .. 0.93
   3 !   30.1   0.4   1.4e-10     5e-07       2      53 ..     136     187 ..     135     190 .. 0.89
   4 !   41.3   0.9   4.4e-14   1.6e-10       1      54 [.     226     278 ..     225     279 .] 0.95

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 7.1e-14
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51
                                  V+dim+++v +  p+++++ a +lm ++++s + VV e +k vGivt++Dl
  gi|91773708|ref|YP_566400.1|  3 VSDIMSSPVYVMEPEEPVSHARKLMLRHKISTIVVV-EGNKMVGIVTKSDL 52
                                  89*******************************778.6778*********9 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 2.5e-16
                                   HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    imt+d+vt++ d+++++a  lm++++++ +PVV ++g+lvGivt+ D++r +
  gi|91773708|ref|YP_566400.1|  75 MIMTEDPVTIYKDASVSQATALMVDNDINNIPVV-NNGELVGIVTRVDVVRCM 126
                                   58********************************.5*************9865 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 1.4e-10
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                   g+imt d+++v+   tl  ++++m+ ++vs l V+d++g+ vG +t r l+ 
  gi|91773708|ref|YP_566400.1| 136 GEIMTADPIFVHRHHTLNHVVDEMEINKVSKLIVTDDSGEAVGFITTRELAL 187
                                   89**********************5344****888************99975 PP

  == domain 4  score: 41.3 bits;  conditional E-value: 4.4e-14
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   ++d+m++ + +++  +++ +a+++m++k+++++P+  e++++vGiv+++D++ra
  gi|91773708|ref|YP_566400.1| 226 AEDVMSDIFAVLDVGDDITKAAKIMVDKNITGIPIA-ENNEIVGIVSRTDIMRA 278
                                   469********************************9.8999***********97 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   0.0     0.022        79      91     104 ..      42      55 ..      33      65 .. 0.79
   2 ?    7.3   0.0    0.0011       3.8      89     124 ..     110     145 ..      90     166 .. 0.83
   3 ?    0.4   0.1      0.14   4.9e+02      89     102 ..     263     276 ..     225     279 .] 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.022
                     PduV-EutP  91 eviGiitkidlaed 104
                                   +++Gi+tk dl + 
  gi|91773708|ref|YP_566400.1|  42 KMVGIVTKSDLGRR 55 
                                   689*******9854 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                     PduV-EutP  89 nkeviGiitkidlaedeenieaveelLksaGaekif 124
                                   n e++Gi+t++d+++ ++++ + ++l + + a+ if
  gi|91773708|ref|YP_566400.1| 110 NGELVGIVTRVDVVRCMSELPVKKNLGEIMTADPIF 145
                                   5689**********9999999888877777777777 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.14
                     PduV-EutP  89 nkeviGiitkidla 102
                                   n e++Gi+ ++d++
  gi|91773708|ref|YP_566400.1| 263 NNEIVGIVSRTDIM 276
                                   6799****999986 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 ?    5.0   0.0    0.0062        22      21      41 ..      37      57 ..      16      59 .. 0.80
   2 ?    3.6   0.0     0.017        61      19      34 ..     105     120 ..      93     123 .. 0.86
   3 ?   -1.0   0.0      0.48   1.7e+03      23      33 ..     172     182 ..     156     187 .. 0.77
   4 ?   -1.3   0.0      0.58   2.1e+03      18      33 ..     257     272 ..     247     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0062
                       GCV_T_C 21 ilrdgevvGhvTSgaysptlg 41
                                  +++++++vG vT +  + +l 
  gi|91773708|ref|YP_566400.1| 37 VVEGNKMVGIVTKSDLGRRLA 57
                                  45789*********9998875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
                       GCV_T_C  19 epilrdgevvGhvTSg 34 
                                    p++++ge vG vT++
  gi|91773708|ref|YP_566400.1| 105 IPVVNNGELVGIVTRV 120
                                   58999*********87 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.48
                       GCV_T_C  23 rdgevvGhvTS 33 
                                   ++ge vG++T+
  gi|91773708|ref|YP_566400.1| 172 DSGEAVGFITT 182
                                   37899***996 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.58
                       GCV_T_C  18 gepilrdgevvGhvTS 33 
                                   g pi +++e+vG v++
  gi|91773708|ref|YP_566400.1| 257 GIPIAENNEIVGIVSR 272
                                   5578899999**9976 PP

>> TMEM223  Transmembrane protein 223
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00022      0.78      80     125 ..      26      77 ..      20      88 .. 0.77
   2 ?   -2.3   0.0       1.2   4.4e+03      77     105 ..      93     121 ..      83     139 .. 0.75
   3 ?   -1.9   0.0      0.89   3.2e+03      86     134 ..     164     217 ..     160     224 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                       TMEM223  80 lfplRsvkkvvllkggktveivTyapfgkkrs......fevplkqvsckqsr 125
                                   l+ + +++++v+ +g+k+v ivT + +g++        +++p+++v +k   
  gi|91773708|ref|YP_566400.1|  26 LMLRHKISTIVVVEGNKMVGIVTKSDLGRRLAqaepmwRRRPIDKVPVKMIM 77 
                                   566889**********************885555666677777777666544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                       TMEM223  77 lgllfplRsvkkvvllkggktveivTyap 105
                                   ++ l+    ++++ + ++g+ v ivT   
  gi|91773708|ref|YP_566400.1|  93 ATALMVDNDINNIPVVNNGELVGIVTRVD 121
                                   55666667789999999999999998655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.89
                       TMEM223  86 vkkvvllk.ggktveivTyapfgkk....rsfevplkqvsckqsrseaksqipl 134
                                   v+k++++  +g+ v + T   +  +    ++ + p k++ ++++++ + ++i+ 
  gi|91773708|ref|YP_566400.1| 164 VSKLIVTDdSGEAVGFITTRELALHvltdNEGQLPSKNIKMARRAEPSGEKIYR 217
                                   566665555677777666665554433334477777777777777777776664 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 ?    0.7   0.0      0.19   6.6e+02      10      31 ..      35      55 ..      30      61 .. 0.67
   2 ?    2.8   0.0      0.04   1.4e+02       8      34 ..     103     128 ..      98     135 .. 0.84
   3 ?    4.7   0.0     0.011        38       8      39 ..     165     197 ..     158     222 .. 0.68
   4 ?    0.8   0.1      0.17   6.1e+02      13      32 ..     260     279 .]     239     279 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.19
                                  EEEE-SSS-.EEEEEEHHHHHHH CS
                         IF3_N 10 vrlvdedGe.qlGvistreAlrl 31
                                  + +v  +G+ ++G++++++  r+
  gi|91773708|ref|YP_566400.1| 35 IVVV--EGNkMVGIVTKSDLGRR 55
                                  5555..444288***99987665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.04
                                   SEEEEE-SSS-EEEEEEHHHHHHHHHH CS
                         IF3_N   8 revrlvdedGeqlGvistreAlrlaee 34 
                                   +++ +v ++Ge +G++++ +++r + e
  gi|91773708|ref|YP_566400.1| 103 NNIPVV-NNGELVGIVTRVDVVRCMSE 128
                                   567788.679***********999887 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.011
                                   SEEEEE-SSS-EEEEEEHHH.HHHHHHHHTSEE CS
                         IF3_N   8 revrlvdedGeqlGvistre.AlrlaeekgldL 39 
                                   ++  + d+ Ge +G i+tre Al    +++ +L
  gi|91773708|ref|YP_566400.1| 165 SKLIVTDDSGEAVGFITTRElALHVLTDNEGQL 197
                                   566677777*****8888774777766666555 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.17
                                   E-SSS-EEEEEEHHHHHHHH CS
                         IF3_N  13 vdedGeqlGvistreAlrla 32 
                                   + e++e +G++s+ +++r a
  gi|91773708|ref|YP_566400.1| 260 IAENNEIVGIVSRTDIMRAA 279
                                   45778899*****9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1914.23
//
Query:       gi|91773709|ref|YP_566401.1|  [L=315]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-52  175.0   2.5    1.2e-13   51.3   0.0    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 !   43.5   0.2   1.8e-15   3.2e-11       4      55 ..      46      98 ..      41     100 .. 0.88
   2 !   43.3   0.0     2e-15   3.6e-11       2      54 ..     123     175 ..     122     178 .. 0.95
   3 !   34.0   0.0   1.7e-12     3e-08       5      54 ..     189     237 ..     184     239 .. 0.93
   4 !   51.3   0.0   6.6e-18   1.2e-13       2      56 ..     261     314 ..     260     315 .] 0.95

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.8e-15
                                  HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                           CBS  4 imtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55
                                  + t+ v+t+pp+t + +a+++m+ek+++++P++  + +k+ Gi+t  D++++l
  gi|91773709|ref|YP_566401.1| 46 VATKHVITIPPTTKIIDAIKIMTEKKFRHIPITnAGTNKIEGIITSFDIIDFL 98
                                  57899****************************544559************98 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 2e-15
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   ++im + vv+++ + +++ea+elm ++++++lPVVd+ ++++Gi t++D l +
  gi|91773709|ref|YP_566401.1| 123 SSIMQPHVVSIHSTGNIKEAFELMLKHNIGSLPVVDSTDHVCGICTEKDFLTF 175
                                   789***********************************************987 PP

  == domain 3  score: 34.0 bits;  conditional E-value: 1.7e-12
                                   SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   m+++v  ++ d+ ++ea++ m++++++rlPVV + g l+G+v  + ++++
  gi|91773709|ref|YP_566401.1| 189 MSKKVEKASSDMKIGEAAKVMVKNNFRRLPVV-KKGILIGVVNASAIMNF 237
                                   9*******************************.8*********9999876 PP

  == domain 4  score: 51.3 bits;  conditional E-value: 6.6e-18
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   +++ ++dvv  + dt+l+ea  lm ++gv++lP++ ++gkl+Gi+t+rD+lra++
  gi|91773709|ref|YP_566401.1| 261 SSLVSKDVVWTTSDTDLGEASSLMLKHGVGSLPII-DNGKLCGIITERDVLRAIA 314
                                   67889******************************.6****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2149.82
//
Query:       gi|91773710|ref|YP_566402.1|  [L=258]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  157.6   9.3    4.7e-13   49.4   0.4    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.022   14.8   0.7        3.9    7.6   0.0    3.4  3  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   4.3e-14   3.8e-10       1      53 [.       3      55 ..       3      57 .. 0.94
   2 !   28.9   0.1   1.3e-10   1.2e-06       8      53 ..      71     118 ..      65     122 .. 0.88
   3 !   43.0   0.0   5.3e-15   4.7e-11       2      54 ..     131     183 ..     129     184 .. 0.94
   4 !   49.4   0.4   5.3e-17   4.7e-13       1      54 [.     204     256 ..     203     258 .] 0.94

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 4.3e-14
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                  V +im++d v+v++ +++  a +lmr++ +++lPV+d +gk vGi+ + D+l+
  gi|91773710|ref|YP_566402.1|  3 VNEIMSKDAVCVKEHDNMTHARQLMRDHFLRGLPVTDANGKMVGILKDQDILN 55
                                  679**********************77669*********************96 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 1.3e-10
                                   SCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                           CBS   8 dvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53 
                                   d + ++p t++ +a++l++e+gv+r P+V  + + ++vGi++ +D+l 
  gi|91773710|ref|YP_566402.1|  71 DCPLITPKTDIMDAARLIIESGVGRCPIVrsETEREIVGILSNSDILA 118
                                   567899***********99**********8755667**********97 PP

  == domain 3  score: 43.0 bits;  conditional E-value: 5.3e-15
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   +d+mt+d+++++p + l ++  ++  +++s+lPVV + ++l G++t rD++r+
  gi|91773710|ref|YP_566402.1| 131 ADVMTTDIISCNPHDLLTKIWPILLTSNYSGLPVVTNADELQGMITIRDIIRF 183
                                   69*********************88999******977889***********97 PP

  == domain 4  score: 49.4 bits;  conditional E-value: 5.3e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   V  im+++  tv  dt+++e++e+m +++v+rl VV +dgk++Giv+++D+lra
  gi|91773710|ref|YP_566402.1| 204 VDKIMSTPAYTVLSDTSVKECVEKMLHYDVGRLTVV-NDGKVIGIVSRTDILRA 256
                                   5579*********************9999*******.5***************8 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00044       3.9       4      27 ..      27      50 ..      25      58 .. 0.87
   2 ?    2.2   0.0     0.021   1.9e+02       7      25 ..     157     175 ..     153     184 .. 0.80
   3 ?    0.8   0.2      0.06   5.4e+02       8      27 ..     232     252 ..     226     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00044
                                  CCS---TT-EEEETTSSEEEEEEE CS
                           PRC  4 frasdliGkeVytedGeklGkVkD 27
                                  +r + l+G++V + +G+ +G +kD
  gi|91773710|ref|YP_566402.1| 27 MRDHFLRGLPVTDANGKMVGILKD 50
                                  567789**************9977 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.021
                                   ---TT-EEEETTSSEEEEE CS
                           PRC   7 sdliGkeVytedGeklGkV 25 
                                   s+  G++V+t+ +e  G +
  gi|91773710|ref|YP_566402.1| 157 SNYSGLPVVTNADELQGMI 175
                                   7889********9998877 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.06
                                   --TT-EEEETTSSEEEEE..EE CS
                           PRC   8 dliGkeVytedGeklGkV..kD 27 
                                   d+  ++V+++ G+ +G V  +D
  gi|91773710|ref|YP_566402.1| 232 DVGRLTVVND-GKVIGIVsrTD 252
                                   6667788887.8****995555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1917.37
//
Query:       gi|91773711|ref|YP_566403.1|  [L=200]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-19   70.5   6.9    4.4e-11   43.1   0.2    2.5  2  CBS       CBS domain
     0.0045   16.9   0.7     0.0093   15.9   0.7    1.5  1  DeoRC     DeoR C terminal sensor 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 !   29.5   2.1   8.4e-11   7.5e-07       1      52 [.      24      74 ..      24      83 .. 0.94
   2 !   43.1   0.2   4.9e-15   4.4e-11       2      54 ..      90     141 ..      89     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8.4e-11
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                                  V++imt+dv+ ++ ++t  e+++ m e +++++ ++ ++g+  Gi+t+rD +
  gi|91773711|ref|YP_566403.1| 24 VHEIMTKDVFILDVTSTTLEVAKAMDEQNIDSV-IITKYGEATGIITERDMV 74
                                  89***********************9999****.7779************75 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 4.9e-15
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   ++im+++++tv+p+t + +a e+m++ +++rl V+++   +vG+vt+rD+l +
  gi|91773711|ref|YP_566403.1|  90 EEIMSSPILTVKPNTGVIKASEMMVKFHIRRLAVTNGKA-IVGLVTDRDILTV 141
                                   79***********************999****9996444.**********976 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.7     1e-06    0.0093       6      54 ..      16      65 ..      13      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                         DeoRC  6 KrrIAkaAaeliedgdtifldaGtTtlelaraLaekk.nltvvTnslnva 54
                                  K+ +   A+  i  +d+ +ld  +Ttle+a+a++e++ + +++T   +  
  gi|91773711|ref|YP_566403.1| 16 KETLKDVAVHEIMTKDVFILDVTSTTLEVAKAMDEQNiDSVIITKYGEAT 65
                                  56666789999*************************98889999866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1464.98
//
Query:       gi|91773712|ref|YP_566404.1|  [L=373]
Description: replication factor A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-22   76.9   5.6    2.9e-08   33.6   0.7    3.4  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.5e-15   57.5   1.8    4.7e-06   26.5   0.1    3.1  3  CDC24_OB3        Cell division control protein 24, OB domain 
    3.3e-07   30.1   3.0       0.12   12.3   0.3    3.4  3  REPA_OB_2        Replication protein A OB domain
      0.004   17.0   0.1        2.5    8.0   0.0    2.6  3  POT1PC           ssDNA-binding domain of telomere protection 
     0.0043   16.8   0.1        5.3    6.8   0.0    3.1  3  Rep_fac-A_C      Replication factor-A C terminal domain
     0.0087   15.8   0.0        5.5    6.7   0.0    2.6  2  DUF5088          Domain of unknown function (DUF5088)
  ------ inclusion threshold ------
      0.041   14.1   0.3       0.64   10.3   0.1    3.1  3  DUF3127          Domain of unknown function (DUF3127)
       0.17   12.2   0.2        7.8    6.9   0.1    2.9  3  DUF2889          Protein of unknown function (DUF2889)


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.7   1.3e-11   2.9e-08       1      72 [.      70     149 ..      70     172 .. 0.83
   2 !   28.1   0.1   6.7e-10   1.5e-06       3      69 ..     181     256 ..     179     260 .. 0.85
   3 !   16.2   0.0   3.5e-06    0.0079       2      68 ..     289     362 ..     288     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.3e-11
                                   EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTT.S-TTSEEEEEEEEEECTTSSEEEEEEE CS
               tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaen.lkeGdvvrvtGrvkrrpggelelkvee 72 
                                   V+++++vtsi         d+ +g+v ++++ D+tg+i+++l++e a+ +++  +++Gd++++tG+ k  + g  e+++ +
  gi|91773712|ref|YP_566404.1|  70 VSFVAKVTSILdvrefnrnDGTIGRVGTVKVADETGSIKLTLWDERADIIKNGsIEVGDCLEITGYAKDGYSG-TEINIGK 149
                                   7889999999999999999*************************444444433699*****************.7776654 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 6.7e-10
                                   EEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTS.SEEEE CS
               tRNA_anti-codon   3 vaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpgg.elelk 69 
                                   + G++ +is        d++ g+v++i + D+tg+i+v+l++ e+ +   +l  +d v++  G+ ++ +   ++e++
  gi|91773712|ref|YP_566404.1| 181 ISGKLLDISdvrnfqkkDGNPGRVMNILIGDETGKIRVTLWD-EKVDSTTSLNLDDAVEIInGYARTNNFSqQVEVQ 256
                                   667777777777888999************************.******************9*99999433235554 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 3.5e-06
                                   EEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEE CS
               tRNA_anti-codon   2 tvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelel 68 
                                   +++G v+           d+ ++ v++i + D+tgri++ l+  +   l ++l++++ +++   + k+ ++  +el
  gi|91773712|ref|YP_566404.1| 289 SIKGFVSGLGelrefekdDGTSNMVSNIYVSDDTGRIRIALWG-DHALLVDELDIETPIEIIdTYSKSGYED-IEL 362
                                   788999999899999999999999*******************.9999999999999998874444444554.665 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 !   23.2   0.1   2.1e-08   4.8e-05       1      69 [.      62     134 ..      62     143 .. 0.83
   2 !   26.5   0.1   2.1e-09   4.7e-06       1      68 [.     171     240 ..     171     268 .. 0.75
   3 !    5.8   0.0    0.0045        10      21      51 ..     304     333 ..     288     344 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.1e-08
                     CDC24_OB3   1 DLrekmlnvtLlGrvvai..freknsek.kkmdryslrieDttGaidatlweeagklhfk.rlrvGhlvllsg 69 
                                   D+ ++  nv+ +++v+ i  +re n ++ +  ++  ++++D+tG+i++tlw+e +  +++ +++vG+++ ++g
  gi|91773712|ref|YP_566404.1|  62 DITAEIGNVSFVAKVTSIldVREFNRNDgTIGRVGTVKVADETGSIKLTLWDERADIIKNgSIEVGDCLEITG 134
                                   6778888***********884444444444555569*****************999999999****9987765 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.1e-09
                     CDC24_OB3   1 DLrekmlnvtLlGrvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvlls 68 
                                   D+++ m+++ + G++ +i     f++k++ +  ++   ++ i D+tG+i++tlw+e + +  + l++ + v + 
  gi|91773712|ref|YP_566404.1| 171 DIKDGMSDINISGKLLDIsdvrnFQKKDG-NpGRVM--NILIGDETGKIRVTLWDEKVDSTTS-LNLDDAVEII 240
                                   89****************99766544444.434444..8*****************9988887.8887777544 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0045
                     CDC24_OB3  21 eknsekkkmdryslrieDttGaidatlweea 51 
                                   ek++++ +m  +++ + D+tG i+++lw   
  gi|91773712|ref|YP_566404.1| 304 EKDDGTSNMV-SNIYVSDDTGRIRIALWGDH 333
                                   5666665666.8****************765 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 !    8.6   0.1   0.00075       1.7      16      85 ..      73     143 ..      51     155 .. 0.71
   2 !   12.3   0.3   5.5e-05      0.12      13      65 ..     179     229 ..     166     260 .. 0.77
   3 !    8.1   0.0    0.0011       2.4      17      94 ..     292     369 ..     281     373 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00075
                     REPA_OB_2  16 igvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe...sseepvvalkgvkvsdFggr 85 
                                   ++ v+s+ +v+e+++ +++   +  ++++ De+g s+++tlW+++a+ ++    +  + + + g     ++g 
  gi|91773712|ref|YP_566404.1|  73 VAKVTSILDVREFNRNDGT-IGRVGTVKVADETG-SIKLTLWDERADIIKngsIEVGDCLEITGYAKDGYSGT 143
                                   5567777777777776666.45556899999998.7********99988743334455555555555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.5e-05
                     REPA_OB_2  13 vDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe 65 
                                   + + g + ++++v+++++k+++ + +  ++ + De+g +++vtlW+++ ++ +
  gi|91773712|ref|YP_566404.1| 179 INISGKLLDISDVRNFQKKDGN-PGRVMNILIGDETG-KIRVTLWDEKVDSTT 229
                                   6677888899*********999.9999********99.59******9666544 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0011
                     REPA_OB_2  17 gvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe..sseepvvalkgvkvsdFggrslsllssst 94 
                                   g v+ ++e++e+ + +++ +    ++ + D++g+ ++++lWg++a  ++    e p+ ++     s ++  +ls  + ++
  gi|91773712|ref|YP_566404.1| 292 GFVSGLGELREFEKDDGT-SNMVSNIYVSDDTGR-IRIALWGDHALLVDelDIETPIEIIDTYSKSGYEDIELSAGNRTR 369
                                   556666677776666555.6667899******96.9*******9988775546677777777777777666666666655 PP

>> POT1PC  ssDNA-binding domain of telomere protection protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0011       2.5      78     103 ..     106     132 ..      93     141 .. 0.93
   2 !    6.1   0.0    0.0041       9.1      79     120 ..     216     256 ..     208     275 .. 0.85
   3 ?   -3.6   0.0         4     9e+03      79      92 ..     325     338 ..     324     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                   EEEEEE-HHHHHHHTTT.--TT-EEEE CS
                        POT1PC  78 tlqitlydehaefaren.lkpgdfvrL 103
                                   ++++tl+de a+++++  +++gd++ +
  gi|91773712|ref|YP_566404.1| 106 SIKLTLWDERADIIKNGsIEVGDCLEI 132
                                   7899********************988 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0041
                                   EEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.-EEEE CS
                        POT1PC  79 lqitlydehaefarenlkpgdfvrLrNvhiklgrkgsklegf 120
                                   + +tl+de +++  + l+ +d v + N  ++ ++ ++++e +
  gi|91773712|ref|YP_566404.1| 216 IRVTLWDEKVDSTTS-LNLDDAVEIINGYARTNNFSQQVEVQ 256
                                   68*************.***********988888877766654 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4
                                   EEEEE-HHHHHHHT CS
                        POT1PC  79 lqitlydehaefar 92 
                                   + i l+++ha ++ 
  gi|91773712|ref|YP_566404.1| 325 IRIALWGDHALLVD 338
                                   6799*****97765 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 !    5.4   0.0    0.0062        14      57      79 ..      97     119 ..      94     128 .. 0.90
   2 !    6.8   0.0    0.0023       5.3      55      90 ..     204     239 ..     199     275 .. 0.73
   3 ?    0.0   0.0      0.28   6.3e+02      53      76 ..     311     334 ..     304     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0062
                                   EEEEE-SS-EEEEEEEHHHHHHH CS
                   Rep_fac-A_C  57 sikvsDstgqlwvtlFneaaekl 79 
                                   ++kv+D+tg++ +tl++e a  +
  gi|91773712|ref|YP_566404.1|  97 TVKVADETGSIKLTLWDERADII 119
                                   589****************9876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                                   EEEEEEE-SS-EEEEEEEHHHHHHHHSS-HHHHHHH CS
                   Rep_fac-A_C  55 ilsikvsDstgqlwvtlFneaaekllglsaeelkkl 90 
                                   +++i + D+tg+++vtl++e+  +   l+ ++  ++
  gi|91773712|ref|YP_566404.1| 204 VMNILIGDETGKIRVTLWDEKVDSTTSLNLDDAVEI 239
                                   6899****************9877666655555555 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.28
                                   EEEEEEEEE-SS-EEEEEEEHHHH CS
                   Rep_fac-A_C  53 ryilsikvsDstgqlwvtlFneaa 76 
                                   +++ +i vsD tg++++ l+ ++a
  gi|91773712|ref|YP_566404.1| 311 NMVSNIYVSDDTGRIRIALWGDHA 334
                                   5667899***********999987 PP

>> DUF5088  Domain of unknown function (DUF5088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0025       5.5      29      62 ..     103     138 ..      97     172 .. 0.84
   2 !    6.6   0.0    0.0025       5.7      20      73 ..     203     257 ..     183     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0025
                       DUF5088  29 saglvkvvvWke..alrkysslkvGDiivikkfrkk 62 
                                   ++g +k+ +W e  ++ k  s++vGD++ i+++ k 
  gi|91773712|ref|YP_566404.1| 103 ETGSIKLTLWDEraDIIKNGSIEVGDCLEITGYAKD 138
                                   5677999***8744789****************765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0025
                       DUF5088  20 lfffiilstsaglvkvvvWkealrkysslkvGDii.vikkfrkkkkiealskidr 73 
                                     + i++  ++g ++v +W e++    sl+  D++ +i+++ + ++ +++  +++
  gi|91773712|ref|YP_566404.1| 203 RVMNILIGDETGKIRVTLWDEKVDSTTSLNLDDAVeIINGYARTNNFSQQVEVQI 257
                                   5567888889999*********************944678888777777766665 PP

>> DUF3127  Domain of unknown function (DUF3127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.1   2.5e+03      38      52 ..     106     120 ..      72     133 .. 0.57
   2 ?   10.3   0.1   0.00028      0.64       2      62 ..     181     239 ..     180     275 .. 0.88
   3 ?   -1.0   0.0      0.98   2.2e+03      38      62 ..     324     348 ..     317     353 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                       DUF3127  38 kiclevvgdkideld 52 
                                   +i+l+++++++d ++
  gi|91773712|ref|YP_566404.1| 106 SIKLTLWDERADIIK 120
                                   466666666666554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00028
                       DUF3127   2 itGkiikilptqegssknG.efkkrefvleteeqYpkkiclevvgdkideldklqvgdevkv 62 
                                   i+Gk+  i +++++++k G + +  ++++  e     ki ++++++k+d++ +l+ +d v++
  gi|91773712|ref|YP_566404.1| 181 ISGKLLDISDVRNFQKKDGnPGRVMNILIGDE---TGKIRVTLWDEKVDSTTSLNLDDAVEI 239
                                   89***************996666666666554...579**********************98 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.98
                       DUF3127  38 kiclevvgdkideldklqvgdevkv 62 
                                   +i + ++gd + ++d+l ++  +++
  gi|91773712|ref|YP_566404.1| 324 RIRIALWGDHALLVDELDIETPIEI 348
                                   57899******99999999888876 PP

>> DUF2889  Protein of unknown function (DUF2889)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.034        77      76     106 ..       3      33 ..       2      39 .. 0.91
   2 ?    6.9   0.1    0.0035       7.8      25      71 ..      25      72 ..      24      81 .. 0.81
   3 ?   -2.2   0.0       2.2   4.9e+03      20      32 ..     217     229 ..     203     260 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.034
                       DUF2889  76 eaaasyqkLvGltigrgfrravrerlggveG 106
                                   e+++ y+kL G+    +fr++v e++ +++G
  gi|91773712|ref|YP_566404.1|   3 EITEIYNKLGGIISEDDFRKRVDEKVDQMSG 33 
                                   678899********************99887 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0035
                       DUF2889 25 Dskaedvelaek.elkagepvHelrlrltvddtltiveaeaemealPy 71
                                  D+k+++++   + ++ a  + H+l ++ tv+d ++i++++ae+ ++ +
  gi|91773712|ref|YP_566404.1| 25 DEKVDQMSGLCDmKTAAMLVAHDLGVTDTVKDIIKIKDITAEIGNVSF 72
                                  566666655555567788899*********************998877 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.2
                       DUF2889  20 eaelrDskaedve 32 
                                   + +l D+k+++++
  gi|91773712|ref|YP_566404.1| 217 RVTLWDEKVDSTT 229
                                   5555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.43
# Mc/sec: 2625.55
//
Query:       gi|91773713|ref|YP_566405.1|  [L=216]
Description: RNA 2'-phosphotransferase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   96.3   0.0    2.5e-27   96.1   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 !   96.1   0.0   1.4e-31   2.5e-27       2     181 .]      38     203 ..      37     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1.4e-31
                     PTS_2-RNA   2 revqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslkvtleeikevVesndKqRFelveleelliranqghsi 82 
                                   re++l++ +s  LRh +++ gL+++e+G+v+++ l +    + + +t e++ +++es+ K R+e   +++  ira  ghs+
  gi|91773713|ref|YP_566405.1|  38 REERLGRFISGALRHFPDDVGLTMDEQGWVNMDLLCDIMDRRYKWATRERLISLIESDLKTRYE---IKGSKIRARYGHSV 115
                                   7999*****************************998866555555*******************...66678********5 PP

                     PTS_2-RNA  83 kkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisg.mrksaevliyidveka 162
                                   +   +   +l+ +e+  elp  +++g + ++++ +l ++g+ +m+++++hl+t+  +  ++ s  + +++ v++ +dv++a
  gi|91773713|ref|YP_566405.1| 116 N---V---ELDYLET--ELPY-LYYGVSQEEVDMLL-DTGIAPMRQRYVHLSTSYGK--AIESAsVHTENPVVLEVDVDEA 184
                                   2...2...3899866..5676.**************.99**************9753..344440556888********** PP

                     PTS_2-RNA 163 ladgikfyvsengviLteG 181
                                    ++g++f++ +++++Lt+G
  gi|91773713|ref|YP_566405.1| 185 QNNGLHFMLVNDDIVLTDG 203
                                   *****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1686.64
//
Query:       gi|91773714|ref|YP_566406.1|  [L=331]
Description: RNA 3'-terminal-phosphate cyclase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-81  272.8   0.0    1.8e-81  272.6   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    7.6e-14   52.1   0.0    1.5e-13   51.1   0.0    1.5  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.6   0.0     2e-85   1.8e-81       1     222 []       8     319 ..       8     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 272.6 bits;  conditional E-value: 2e-85
                                   STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikageyevd 81 
                                   +gegGgqi+R+a+aLsa+tgk+ +I+nIR+ R++PGL+aqh++a+ ++a +++a+veg +igst++ F P+ei++g+y++d
  gi|91773714|ref|YP_566406.1|   8 YGEGGGQIVRNAIALSAVTGKATSIKNIRKDRPNPGLSAQHVKAIGIAALLCDAKVEGIKIGSTNIAFFPQEIRGGKYTID 88 
                                   69******************************************************************************* PP

                                   EESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC  82 igtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGevelev 162
                                   igtAGsi+lllq+++p++ +++++++l++kGgT+vs+aps+dylk+v+l++l+++g +++++++ krG+yp+GgG v++ +
  gi|91773714|ref|YP_566406.1|  89 IGTAGSIALLLQCIMPIATYSNTNIKLEIKGGTDVSWAPSIDYLKNVTLSALSKMG-YRCNIDILKRGYYPRGGGIVNAII 168
                                   ********************************************************.8*********************** PP

                                   E-.-S---EB....................................................................... CS
                                   xxxxxxxxxx....................................................................... RF
                           RTC 163 epskklkpie....................................................................... 172
                                   eps +l p +                                                                       
  gi|91773714|ref|YP_566406.1| 169 EPS-HLVPDRfseergtirgishcsnlpehvaqrqadkakailenaghecsietcrtdftstgsgitlycgmkgsfvpgkr 248
                                   *97.55555566********************************************************************* PP

                                   ......................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHHHHHSS-EEEE CS
                                   ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC 173 ......................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvieqflgvkfkv 222
                                                         + vD hl+dqli+++ La+g ++++v+e+++ht+t+i+v+e+fl+vkfk+
  gi|91773714|ref|YP_566406.1| 249 gttaekvgndaatslldelltpSSVDIHLADQLIPYLGLAEG-GSFTVKEISPHTKTNIWVTEKFLDVKFKI 319
                                   *****************************************9.67*************************97 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 !   51.1   0.0   1.7e-17   1.5e-13       9     102 ..     185     267 ..     181     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.7e-17
                                   EEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-TT--HHH CS
                    RTC_insert   9 irGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgekgvpped 89 
                                   irG++++++++ +va+r++++a+++L+++++++ i+t      ++   s G+gi+L +  +      g+ + g++g+++e+
  gi|91773714|ref|YP_566406.1| 185 IRGISHCSNLPEHVAQRQADKAKAILENAGHECSIETC-----RTDFTSTGSGITLYCGMK------GSFVPGKRGTTAEK 254
                                   9****************************999996655.....4556799**********5......456779******** PP

                                   HHHHHHHHHHHHH CS
                    RTC_insert  90 vGeeaaeeLleei 102
                                   vG +aa  Ll+e+
  gi|91773714|ref|YP_566406.1| 255 VGNDAATSLLDEL 267
                                   ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2051.13
//
Query:       gi|91773715|ref|YP_566407.1|  [L=453]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-51  172.9   1.9    1.1e-50  172.6   1.4    1.4  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    3.3e-19   69.2   3.6    5.7e-17   62.0   0.8    3.2  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    3.2e-14   52.9   0.1    1.6e-08   34.2   0.0    2.2  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    7.4e-14   51.9   0.3      2e-13   50.5   0.0    1.8  1  Pyr_redox_dim    Pyridine nucleotide-disulphide oxidoreductas
    1.6e-07   30.4   4.4       0.02   13.6   0.1    3.5  4  HI0933_like      HI0933-like protein
    3.3e-07   29.7   5.0     0.0052   15.9   0.1    3.1  3  Lycopene_cycl    Lycopene cyclase protein
    4.9e-07   29.2   0.0    0.00013   21.2   0.0    2.2  2  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
    1.1e-06   28.6  13.1     0.0017   18.0   0.8    3.7  4  DAO              FAD dependent oxidoreductase
    3.1e-06   27.3   4.2     0.0061   16.8   0.2    2.6  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
      5e-06   25.9   9.3    0.00017   20.8   0.1    2.8  3  FAD_binding_2    FAD binding domain
      1e-05   24.9   1.6     0.0094   15.2   0.0    2.7  2  Thi4             Thi4 family
    1.9e-05   24.3   0.2     0.0015   18.2   0.1    2.5  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00071   18.8  10.6      0.048   12.7   2.8    3.3  3  GIDA             Glucose inhibited division protein A
    0.00086   19.3   4.4        1.2    9.1   0.0    3.4  3  NAD_binding_9    FAD-NAD(P)-binding
     0.0014   18.5   3.0     0.0021   18.0   0.6    2.3  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0022   17.3   3.3       0.16   11.2   1.1    2.3  2  FAD_binding_3    FAD binding domain
     0.0024   18.3   0.2        3.7    8.1   0.1    2.5  2  NAD_binding_7    Putative NAD(P)-binding
     0.0045   17.2   0.5        0.5   10.7   0.1    2.6  2  TrkA_N           TrkA-N domain
     0.0046   16.3   0.2      0.073   12.4   0.1    2.1  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.029   14.6   1.5        7.8    6.8   0.1    3.0  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.033   14.3   2.1      0.066   13.3   0.3    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.054   12.9   0.2        0.1   12.0   0.2    1.4  1  ThiF             ThiF family
      0.096   13.3   2.8          1   10.0   0.3    3.0  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
        0.1   12.6   0.2        2.1    8.3   0.0    2.3  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.21   10.4   3.5       0.63    8.8   0.0    2.6  3  Trp_halogenase   Tryptophan halogenase
       0.25   10.6   9.7        1.1    8.5   0.3    3.0  3  FAD_oxidored     FAD dependent oxidoreductase
        1.1    8.5   5.5       0.21   10.8   1.9    1.6  2  Malic_M          Malic enzyme, NAD 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 !  172.6   1.4   1.6e-53   1.1e-50       1     294 []       7     311 ..       7     311 .. 0.92
   2 ?   -3.2   0.0       5.9   3.9e+03     269     278 ..     331     340 ..     330     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 172.6 bits;  conditional E-value: 1.6e-53
                                   CSEEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCCHCCTCE CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq.agakvtlvelegtclnggcllskallgvaedaeias....evvkklnqgielllgeevv 76 
                                   +d+++iGgG+AGla+a+++++ + + v++++++ ++ +  c ++ +l+g  +d + +     e ++k+  gi+  l++e++
  gi|91773715|ref|YP_566407.1|   7 YDLAIIGGGAAGLATATHVKRcSDLSVIVISKDSHISYSECGIPFKLAGKVHDFDSLIvktpEFFDKM--GIDIALETEAL 85 
                                   689******************88********************9999988888886668998555555..577777777** PP

                                   EEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCT...TC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx...xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                   Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gip...Gvaenvgklvrtldsaealklkllp.krivvvGgGy 152
                                   +id  ++++kle      + +i +dkl++AtG+++r++ +++   G+ ++v++l +tl++  +++ +ll  + +v++G+G+
  gi|91773715|ref|YP_566407.1|  86 SIDILNRTIKLE------NYDILFDKLIIATGGKQRIPqPLQkyiGM-DGVFTL-QTLADGMKIETALLSaETVVIIGAGA 158
                                   ***********4......357*****************977766688.666666.***************999******** PP

                                   HHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 153 iGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvv 232
                                   iGvE+Aa +ak g ++tl+ +++ +l r  d+++++++ e+l+  Gv++++g+++ +i+g++  +e vl +ge+i+ad v+
  gi|91773715|ref|YP_566407.1| 159 IGVEIAAGIAKRGIDTTLINRGPAILsRLIDPDMAEIVSEYLKSVGVTLVTGNVPDTIEGKEG-VESVLISGERIPADIVI 238
                                   **************************************************************8.99*************** PP

                                   E-S-EEES-HHCSHCCT-EEEETTEEE--TTSBE....S.STTEEE-GGGC.......TECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 233 vavGvrpstelleeklglelderggivvdeflrt....n.vpgiyaiGDva.......ggkggpelaqaAvqqG 294
                                   +++G+ p+ el+ ek+g+ + e ggi v+++l++    n  ++i+a GD++       ++k+ ++la+aA  ++
  gi|91773715|ref|YP_566407.1| 239 ISTGILPDVELA-EKAGISTGELGGIIVNQHLQVfvdgNfSTDIFAGGDCCeitdfitNKKTLVQLAPAARHMA 311
                                   ************.********************9778777899***************************9886 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.9
                                   TTEEE-GGGC CS
                                   xxxxxxxxxx RF
                   Pyr_redox_2 269 pgiyaiGDva 278
                                   p+iy++GD  
  gi|91773715|ref|YP_566407.1| 331 PSIYVAGDLL 340
                                   789****986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.048        32       2      33 ..       9      41 ..       8      47 .. 0.79
   2 ?    0.3   0.0       1.6   1.1e+03      50      67 ..      71      88 ..      66      99 .. 0.80
   3 !   62.0   0.8   8.6e-20   5.7e-17       2      78 ..     151     227 ..     150     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.048
                                  EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversdk 33
                                  ++++GgG  gl  A+  ++    +V v+   ++
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVKRCSdLSVIVISKDSH 41
                                  68************9999966257777776655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                                  HHHTTEEEECSEEEEEEE CS
                     Pyr_redox 50 lekngievllntkveeie 67
                                  + k+gi++ l+t++ +i+
  gi|91773715|ref|YP_566407.1| 71 FDKMGIDIALETEALSID 88
                                  5789*********99998 PP

  == domain 3  score: 62.0 bits;  conditional E-value: 8.6e-20
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                   vv++G+G ig+E A+ +a+ g ++t++ r++ +l rl+D+++++i+ e+l+  g+++++++++  ieg+e  vesv +
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRGIDTTLINRGPAILsRLIDPDMAEIVSEYLKSVGVTLVTGNVPDTIEGKEG-VESVLI 227
                                   9******************************************************************9997.999987 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   0.1   5.7e-06    0.0038       2      32 ..      11      41 ..      10      46 .. 0.90
   2 !   34.2   0.0   2.5e-11   1.6e-08      96     291 ..      76     267 ..      66     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-06
                   Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgni 32
                                  IiG+G+aGla+a+++k++   +++++ k+++
  gi|91773715|ref|YP_566407.1| 11 IIGGGAAGLATATHVKRCSDLSVIVISKDSH 41
                                  9*****************999*****99865 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.5e-11
                   Pyr_redox_3  96 lpiklfeeVesvkkedegfevetsketyeAkkviiAtGefd.kP....nklnipGeeklvkhyskvk.efhkyagqkvvVi 170
                                   ++i l++e  s++  ++  +++ ++ ++  +k+iiAtG  + +P    ++ ++ G   l++    +k e + ++ + vv+i
  gi|91773715|ref|YP_566407.1|  76 IDIALETEALSIDILNR--TIKLENYDILFDKLIIATGGKQrIPqplqKYIGMDGVFTLQTLADGMKiETALLSAETVVII 154
                                   55555555555555443..45556667777889999976542452122344555555555555555556668899****** PP

                   Pyr_redox_3 171 GgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvkted 251
                                   G++  +v++A  ++++g + t++ rg  i +        + pd+ + + e++k+  +++++ +  + i+ ke  ++    +
  gi|91773715|ref|YP_566407.1| 155 GAGAIGVEIAAGIAKRGIDTTLINRGPAILS------RLIDPDMAEIVSEYLKSVGVTLVTGNVPDTIEGKEG-VESVLIS 228
                                   **************************96655......58**************9669*****99999998765.5555556 PP

                   Pyr_redox_3 252 gkkvevkddvvlatGykpdlsflkkslfeldedgrpvlte 291
                                   g+++ + d v++ tG  pd+++ +k+++++ e g + +++
  gi|91773715|ref|YP_566407.1| 229 GERIPA-DIVIISTGILPDVELAEKAGISTGELGGIIVNQ 267
                                   678775.888999**************9998888777776 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 !   50.5   0.0     3e-16     2e-13       8     105 ..     338     434 ..     332     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3e-16
                                   SSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHHHHHHHTT CS
                 Pyr_redox_dim   8 dpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqelavaikag 86 
                                   d+ ++svGlt + A+a+   i +++ + + +++a +y+  +++++Kl++    +++ Ga+i+G  g++e+i+ la++ik++
  gi|91773715|ref|YP_566407.1| 338 DLLIGSVGLTSKRARAED--IYIITGYATGTTKASYYPGsSDIHIKLIFSD--DRLTGAQIIGkSGVKERIDSLAFMIKKK 414
                                   6789**************..99*****************9*********87..9*********76899************* PP

                                   SBHH.HHHTSBSSSSSTGGG CS
                 Pyr_redox_dim  87 ltve.dladtihihPtlsea 105
                                   +t+e +l  + +++P++s +
  gi|91773715|ref|YP_566407.1| 415 ATIEeMLSIETCYAPPVSTV 434
                                   ****7799999999999954 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   2.9e-05      0.02       2      34 ..       8      41 ..       7      44 .. 0.85
   2 ?    4.1   0.0     0.024        16     120     165 ..      72     113 ..      63     118 .. 0.83
   3 !   11.7   1.0   0.00012     0.077       2      38 ..     150     186 ..     149     188 .. 0.92
   4 ?   -3.2   0.0       3.9   2.6e+03     118     163 ..     199     242 ..     192     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                                  SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisa.akrgkrVlllekakk 34
                                  d+++iGgGaAGl +A ++ +  + +V+++ k ++
  gi|91773715|ref|YP_566407.1|  8 DLAIIGGGAAGLATATHVkRCSDLSVIVISKDSH 41
                                  899**************95557899999988765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.024
                                   HHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like 120 keagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                   ++ g+++ lete  s++  +    ++k+ ++  +  dkl++AtGG+
  gi|91773715|ref|YP_566407.1|  72 DKMGIDIALETEALSIDILNR---TIKL-ENYDILFDKLIIATGGK 113
                                   678999999999999966444...5888.8899************8 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00012
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38 
                                   +v++iG+Ga G+  A+ +akrg +++l++++++++++
  gi|91773715|ref|YP_566407.1| 150 TVVIIGAGAIGVEIAAGIAKRGIDTTLINRGPAILSR 186
                                   69****************************9998876 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 3.9
                                   HHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 118 elkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                    lk+ gv+l + +   ++ + ++g+ +v + s+e++ ad ++++tG
  gi|91773715|ref|YP_566407.1| 199 YLKSVGVTLVTGNVPDTI-EGKEGVESVLI-SGERIPADIVIISTG 242
                                   566677777766655555.45666677778.899999999999998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.9e-06    0.0052       1      31 [.       8      37 ..       8      46 .. 0.87
   2 !   10.4   1.3   0.00035      0.24       2      37 ..     151     184 ..     150     187 .. 0.94
   3 ?    3.4   0.0     0.047        31      88     141 ..     191     243 ..     185     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.9e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                  D+++iG+G+Agl+ A ++ +   +l+v++i 
  gi|91773715|ref|YP_566407.1|  8 DLAIIGGGAAGLATATHV-KRCSDLSVIVIS 37
                                  9*****************.8889*****994 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                   vv+iGaG+ g+ +Aa +  ak g+  +li+ +p +l
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGI--AKRGIDTTLINRGPAIL 184
                                   8****************..***********999875 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.047
                 Lycopene_cycl  88 rlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdargl 141
                                   +++e + e l + gv+l+ + v    e ++  +  vl  g++i+a +v+ ++g+
  gi|91773715|ref|YP_566407.1| 191 DMAEIVSEYLKSVGVTLVTGNVPDTIEGKE-GVESVLISGERIPADIVIISTGI 243
                                   6888888999999*********76655555.36667778899**********95 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 !    5.9   0.0    0.0091         6       2      39 ..       6      42 ..       5      46 .. 0.90
   2 !   21.2   0.0     2e-07   0.00013     147     215 ..     101     172 ..      76     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0091
                   K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalflerqpef 39
                                   +Dl++iG G++ L+ a +++  + +l+++++ + ++ 
  gi|91773715|ref|YP_566407.1|  6 KYDLAIIGGGAAGLATATHVKRCS-DLSVIVISKDSHI 42
                                  59*********************9.9999999988776 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2e-07
                   K_oxygenase 147 learnlvlgvGtepkiPevleklegkervvHsseylerkee...llakkriaVvGsGqSaaeifedllrrqk 215
                                   +   +l++++G++  iP+ l+k+ g + v+  ++++  ++    ll++++++++G+G  + ei+  +++r  
  gi|91773715|ref|YP_566407.1| 101 ILFDKLIIATGGKQRIPQPLQKYIGMDGVFTLQTLADGMKIetaLLSAETVVIIGAGAIGVEIAAGIAKRGI 172
                                   55679*******************9999999887766553355699*******************9999854 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.8   2.5e-06    0.0017       1      33 [.       8      43 ..       8      58 .. 0.87
   2 ?   -1.1   0.0       1.7   1.1e+03     157     203 ..      72     113 ..      62     124 .. 0.72
   3 !   10.9   4.0   0.00036      0.24       2      30 ..     151     181 ..     150     185 .. 0.93
   4 ?    2.7   0.0      0.12        77     156     206 ..     200     248 ..     190     271 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-06
                                  EEEEECTSHHHHHHHHHHHHT.T...EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarr.g...Vtllekgdiag 33
                                  d++iiGGG +Gl+tA +  +r     V+++ k++ ++
  gi|91773715|ref|YP_566407.1|  8 DLAIIGGGAAGLATATHV-KRcSdlsVIVISKDSHIS 43
                                  789***************.6645699******97765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                                   HHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                           DAO 157 ealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                    + G++i ++te+ +++       ++ + ++  +   +d++++a+G  
  gi|91773715|ref|YP_566407.1|  72 DKMGIDIALETEALSIDIL---NRTI-KLENyDIL--FDKLIIATGGK 113
                                   67899**********9543...3444.22333454..69999999965 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00036
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                   vviiG+G iG+ +A   a+rg  +tl+ +g+
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRGidTTLINRGP 181
                                   9**************************9984 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.12
                                   HHHTT-EEEESECEEE.EEEEETCEEEEE....EECTEEEEEEEEEEE--GGGHH.H CS
                           DAO 156 aealGveilegtevtg.leeedgkvwgve....rttpgendaadavVnaaGawsd.l 206
                                   +++ Gv++++g +v + +e    k  gve        ge+  ad v++++G+  d +
  gi|91773715|ref|YP_566407.1| 200 LKSVGVTLVTG-NVPDtIEG---K-EGVEsvliS---GERIPADIVIISTGILPDvE 248
                                   67789******.77774633...2.555543233...77756699******876654 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   9.3e-06    0.0061       1      32 [.      11      43 ..      11      57 .. 0.94
   2 !   11.3   0.6   0.00046      0.31       1      29 [.     153     181 ..     153     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.3e-06
                                  EE--SHHHHHHHHHHHC.CTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLak.agfdvlllekrdrlG 32
                                  I+G+G++Gl++A + ++  +++v ++ k ++++
  gi|91773715|ref|YP_566407.1| 11 IIGGGAAGLATATHVKRcSDLSVIVISKDSHIS 43
                                  9***************956*********99986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00046
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                   I+GaG+ G  +A+ +ak+g+d +l+ +++
  gi|91773715|ref|YP_566407.1| 153 IIGAGAIGVEIAAGIAKRGIDTTLINRGP 181
                                   9***********************99887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.5e-07   0.00017       1      44 [.       8      48 ..       8      62 .. 0.84
   2 !    8.6   2.2    0.0013      0.86       2      33 ..     151     182 ..     150     187 .. 0.94
   3 ?   -1.3   0.1       1.4     9e+02     372     401 ..     259     287 ..     254     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                                  SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGGG--S- CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavvekeqefggatawsqGg 44
                                  D+ +iG+G+AGLa A+  +++   +v+v++k +    ++ +s+ g
  gi|91773715|ref|YP_566407.1|  8 DLAIIGGGAAGLATATHVKRCSDlSVIVISKDS----HISYSECG 48
                                  899*****************6665*******98....46666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                   v++iG+G+ G   A+ +a++G ++++++ +++
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRGIDTTLINRGPA 182
                                   9**************************99986 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.4
                                   ES-EEEBETTSBESTTEEESSBTEEE-STC CS
                 FAD_binding_2 372 tmgGvetdengrvldadgqpipGLYAaGev 401
                                    +gG+ ++++++v   dg+   + +A G +
  gi|91773715|ref|YP_566407.1| 259 ELGGIIVNQHLQV-FVDGNFSTDIFAGGDC 287
                                   589**********.7788888888887766 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05    0.0094      17      83 ..       6      77 ..       1      89 [. 0.70
   2 !    7.7   0.6    0.0029       1.9      19      49 ..     150     179 ..     139     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES..SSS-...-TTTTTTSTT..BSEEEEETTTHHHHHHTT-- CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer..svsp...GGGawlGGql..fsaivvrkpakelLdelgik 83
                                  + D++i+G+G++GL++a  + +  dl v+++ +  ++s+   G    l G++  f+ ++v+ p  e+ d +gi 
  gi|91773715|ref|YP_566407.1|  6 KYDLAIIGGGAAGLATATHVKRCSDLSVIVISKdsHISYsecGIPFKLAGKVhdFDSLIVKTP--EFFDKMGID 77
                                  679****************************65225654211333456665444777777766..567777665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0029
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                          Thi4  19 DvvivGaGssGLtaayylakkpdlkvailer 49 
                                    vvi+GaG+ G+  a  +ak+ ++ +++++r
  gi|91773715|ref|YP_566407.1| 150 TVVIIGAGAIGVEIAAGIAKR-GIDTTLINR 179
                                   69*******************.999999876 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.057        38       2      47 ..      10      55 ..       9     100 .. 0.81
   2 !   18.2   0.1   2.2e-06    0.0015       1      33 [.     151     184 ..     151     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.057
                                  EEES-SHHHHHHHHHHHH.HTHCEEEE-SCHHHHHHHHHCEEEEETT CS
                          ApbA  2 ailGaGaiGsllaakLak.agadvtlilrsrrlealkknGlrltseg 47
                                  ai+G Ga G   a + ++     v++i ++ ++   ++ G+ ++  g
  gi|91773715|ref|YP_566407.1| 10 AIIGGGAAGLATATHVKRcSDLSVIVISKDSHIS-YSECGIPFKLAG 55
                                  8***************999999999999999775.788888777776 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.2e-06
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HH CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rl 33 
                                   ++i+GaGaiG  +aa +ak g d tli+r++  l
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRGIDTTLINRGPaIL 184
                                   68***************************99544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0048       3.2       1      28 [.       8      36 ..       8      65 .. 0.75
   2 !   12.7   2.8   7.3e-05     0.048       1      29 [.     150     178 ..     150     187 .. 0.91
   3 ?    3.7   0.1     0.042        28      98     152 ..     193     244 ..     177     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0048
                                  CEEEE-SSHHHHHHHHHHHHTT.--EEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlG.akvlLi 28
                                  d+ +iGgG AG++ A +++r   ++v+ i
  gi|91773715|ref|YP_566407.1|  8 DLAIIGGGAAGLATATHVKRCSdLSVIVI 36
                                  5789*************999751444443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.3e-05
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLit 29 
                                   +v++iG+G  G+e A+ +a++G++++Li 
  gi|91773715|ref|YP_566407.1| 150 TVVIIGAGAIGVEIAAGIAKRGIDTTLIN 178
                                   59*************************94 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.042
                                   HHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-B CS
                          GIDA  98 skevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtfl 152
                                   ++ v e+l++   +++++++v + i  ++ v+ v+  +ge i a++v+i+tG  l
  gi|91773715|ref|YP_566407.1| 193 AEIVSEYLKS-VGVTLVTGNVPDTIEGKEGVESVL-ISGERIPADIVIISTGI-L 244
                                   4566777777.8899******99976566666665.57999***********7.4 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 !    8.0   0.1    0.0039       2.6       1      31 [.      10      36 ..      10      45 .. 0.78
   2 ?    1.4   1.3      0.44   2.9e+02       1      20 [.     152     171 ..     152     191 .. 0.85
   3 !    9.1   0.0    0.0018       1.2     105     154 ..     193     242 ..     182     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlf 31
                                  ai+G+G++Gla+++++ + +    +l++ ++
  gi|91773715|ref|YP_566407.1| 10 AIIGGGAAGLATATHVKRCS----DLSVIVI 36
                                  8**************87774....5666555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.44
                 NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                   +i+GaG+ G+ +++ +++r 
  gi|91773715|ref|YP_566407.1| 152 VIIGAGAIGVEIAAGIAKRG 171
                                   7************9999884 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0018
                 NAD_binding_9 105 eellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                   +e+++++ ++v v++++++v d  e ++g++ +l +g+++ ad V++ +G
  gi|91773715|ref|YP_566407.1| 193 AEIVSEYLKSVGVTLVTGNVPDTIEGKEGVESVLISGERIPADIVIISTG 242
                                   567788888999*************************************9 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 ?   -0.5   0.1       1.4   9.5e+02       2      30 ..       9      38 ..       8      45 .. 0.78
   2 !   18.0   0.6   3.2e-06    0.0021       1      38 [.     150     187 ..     150     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                                  EEEE--SCCHHHHHHHHHHT.T-EEEEE-S CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasa.gleVvlvdi 30
                                  +a+iG G  G   a+ + +  +l+V ++  
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVKRCsDLSVIVISK 38
                                  699*******99998877654777777765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.2e-06
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                                   +v +iGaG +G +iaa +a++g++++l+++ +++l + 
  gi|91773715|ref|YP_566407.1| 150 TVVIIGAGAIGVEIAAGIAKRGIDTTLINRGPAILSRL 187
                                   589**************************999988775 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0093       6.2       2      33 ..       7      39 ..       6      49 .. 0.72
   2 !   11.2   1.1   0.00024      0.16       3      32 ..     150     179 ..     148     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0093
                                  EEEEEE--SHHHHHHHHHHHHT.THHEEEEESS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea.Gvrvvlvekr 33
                                  +d +I+G+G aGl +a+  ++    +v+++ k 
  gi|91773715|ref|YP_566407.1|  7 YDLAIIGGGAAGLATATHVKRCsDLSVIVISKD 39
                                  6789***********987766412346666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00024
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                   +V+I+GaG  G+  a   +++G++++l+++
  gi|91773715|ref|YP_566407.1| 150 TVVIIGAGAIGVEIAAGIAKRGIDTTLINR 179
                                   699*************************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 !    7.9   0.0    0.0064       4.2      10      41 ..       9      41 ..       2     112 .. 0.79
   2 !    8.1   0.1    0.0055       3.7       6      39 ..     147     180 ..     144     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0064
                 NAD_binding_7 10 vlvvGgGevAarkvrklleag.akvtvvapevk 41
                                    ++GgG  ++  + ++ +++   v+v++++++
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVKRCSdLSVIVISKDSH 41
                                  67*****************76599******963 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0055
                 NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvape 39 
                                   + ++v+++G+G ++ + +  +++ g + t++   
  gi|91773715|ref|YP_566407.1| 147 SAETVVIIGAGAIGVEIAAGIAKRGIDTTLINRG 180
                                   6789**************************7655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.065        43       2      31 ..      10      40 ..       9      65 .. 0.77
   2 !   10.7   0.1   0.00075       0.5       1      39 [.     151     189 ..     151     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.065
                                  EEES-SHHHHHHHHHHHH.TTEEEEEEESSH CS
                        TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkde 31
                                  +iiG G  G + a  +++ +  +v+vi kd 
  gi|91773715|ref|YP_566407.1| 10 AIIGGGAAGLATATHVKRcSDLSVIVISKDS 40
                                  79**************996554477777764 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00075
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelre 39 
                                   ++iiG+G +G ++a  + ++g+d ++i + ++ + +l +
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRGIDTTLINRGPAILSRLID 189
                                   79*****************9989****999998888876 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 ?    1.6   0.0      0.23   1.5e+02      35      68 ..       5      39 ..       1      64 [. 0.82
   2 !   12.4   0.1   0.00011     0.073      30      68 ..     142     180 ..     129     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                                  TTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSS CS
                  2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlk.afgmkviaydrs 68
                                  ++  ++iiG G+ G a+a  +k   ++ vi++++ 
  gi|91773715|ref|YP_566407.1|  5 RKYDLAIIGGGAAGLATATHVKrCSDLSVIVISKD 39
                                  566799************99995667788877655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                                   SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                  2-Hacid_dh_C  30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                                       ls +tv iiG+G+IG ++a  +++ g++ + ++r 
  gi|91773715|ref|YP_566407.1| 142 ETALLSAETVVIIGAGAIGVEIAAGIAKRGIDTTLINRG 180
                                   5567899****************9999999988888775 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.026        17       2      33 ..      10      39 ..       9      45 .. 0.92
   2 ?   -2.2   0.0         7   4.7e+03      71     101 ..      61      91 ..      53     101 .. 0.70
   3 ?    6.8   0.1     0.012       7.8       1      32 [.     151     179 ..     151     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                                  EEE--SHHHHHHHHHHHCTCCT-GEEEEEESS CS
               Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrs 33
                                   iiG+G+ G a+a  ++r +d+   ++v++++
  gi|91773715|ref|YP_566407.1| 10 AIIGGGAAGLATATHVKRCSDL--SVIVISKD 39
                                  69********************..99999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7
                                   SEEEE-SSGGGHHHHHHHHHHHT-EEEESS- CS
               Sacchrp_dh_NADP  71 dlvvnlsppissldvlkaCietgvhyvdtsi 101
                                   d ++  +p +++   +++++et ++ +d+ +
  gi|91773715|ref|YP_566407.1|  61 DSLIVKTPEFFDKMGIDIALETEALSIDILN 91 
                                   5566667778888889999999999999655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.012
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEES CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadr 32 
                                   v+iiGaG++G  +a  +a+++ +  + t++ r
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRG-I--DTTLINR 179
                                   89*************999987.3..4555555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.7   3.1e+03      15      35 ..       9      29 ..       3      39 .. 0.72
   2 ?   13.3   0.3   9.9e-05     0.066      10      48 ..     146     183 ..     138     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.7
                                  EEEES-SHHHHHHHHHHHCCT CS
                  Shikimate_DH 15 vlliGaGemaelvakhLlakg 35
                                    +iG G  +  +a+h  + +
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVKRCS 29
                                  679999999999999986543 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.9e-05
                                   .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHH CS
                  Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtler 48 
                                   l+ ++v++iGaG ++ ++a  ++++g++  + +NR  + 
  gi|91773715|ref|YP_566407.1| 146 LSAETVVIIGAGAIGVEIAAGIAKRGID-TTLINRGPAI 183
                                   7889***********************9.8889997665 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00015       0.1      16      43 ..     146     173 ..     132     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                   HHTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  16 LrdskvllvGaGglGsellknLalsGvg 43 
                                   L++ +v+++GaG++G e++  +a+ G+ 
  gi|91773715|ref|YP_566407.1| 146 LSAETVVIIGAGAIGVEIAAGIAKRGID 173
                                   56689******************99986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.41   2.7e+02       2      31 ..       9      36 ..       8      44 .. 0.77
   2 ?   10.0   0.3    0.0015         1       2      37 ..     151     182 ..     150     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.41
                                  EEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                 F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivva 31
                                  ++iiG+G  g a a  + ++   + +++v+
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVKRCS--DLSVIVI 36
                                  79********99999888886..4555545 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0015
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCC CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpe 37 
                                   + iiGaG +g  +a g++++g    + +++ +r p 
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRG---IDTTLI-NRGPA 182
                                   78*******************...666656.66665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.26   1.7e+02       2      22 ..       9      29 ..       8      44 .. 0.79
   2 ?    8.3   0.0    0.0032       2.1       2      38 ..     151     187 ..     150     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.26
                                  EEEE--SHHHHHHHHHHHTTT CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaeng 22
                                   a++G+G+ G a A+++++  
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVKRCS 29
                                  59************9998754 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0032
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHH CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieei 38 
                                   + ++GaG+ G  +A+ +a++g +++l+ r ++ + ++
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRGIDTTLINRGPAILSRL 187
                                   89********************999999988666554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00094      0.63       2      34 ..       9      39 ..       8      73 .. 0.88
   2 ?   -3.1   2.3       3.8   2.5e+03       2      31 ..     151     177 ..     150     180 .. 0.81
   3 ?    1.3   0.0      0.18   1.2e+02     157     208 ..     193     242 ..     189     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00094
                                  EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlvese 34
                                  + i+GGG aG  +A+++++    +l+v ++ ++
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVKRCS--DLSVIVISKD 39
                                  68*****************99..6888888775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEE CS
                Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlv 31 
                                   +vi+G+G  G   Aa +ak +   ++ tl+
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRG---IDTTLI 177
                                   9*********99999998877...555555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SG CS
                Trp_halogenase 157 akfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsG 208
                                   a++  ++ ++ Gvt v g+v + +++ ++ ves+ + +g+++ ad++i  +G
  gi|91773715|ref|YP_566407.1| 193 AEIVSEYLKSVGVTLVTGNVPD-TIEGKEGVESVLI-SGERIPADIVIISTG 242
                                   78888999999*********66.5788889***999.7888******98887 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3    0.0017       1.1       1      33 [.       8      41 ..       8      42 .. 0.89
   2 ?    2.8   3.5      0.09        59       2      32 ..     151     181 ..     150     183 .. 0.94
   3 ?    1.6   0.0      0.21   1.4e+02      90     155 ..     193     256 ..     185     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAar.aGakvlLveergv 33
                                  D+ ++GGg+aG+a A   +r ++ +v++++++ +
  gi|91773715|ref|YP_566407.1|  8 DLAIIGGGAAGLATATHVKRcSDLSVIVISKDSH 41
                                  899***************9967889999998877 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.09
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                   vv++G+g+ Gv  A   a++G  + L+++ +
  gi|91773715|ref|YP_566407.1| 151 VVIIGAGAIGVEIAAGIAKRGIDTTLINRGP 181
                                   9**************************9987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.21
                  FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg...dGdlaalaGvp 155
                                   ++++ e l+  gvt++++ +++ +e ++  +esv +     +++i A+++i +Tg   d +la++aG++
  gi|91773715|ref|YP_566407.1| 193 AEIVSEYLKSVGVTLVTGNVPDTIEGKE-GVESVLIS----GERIPADIVIISTGilpDVELAEKAGIS 256
                                   46777888999**************986.8******5....89********999866677777777775 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 ?   -3.6   0.1       7.8   5.2e+03      28      45 ..       9      26 ..       6      30 .. 0.77
   2 ?   10.8   1.9   0.00031      0.21       5      47 ..     128     170 ..     124     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.8
                                  EEEEC-SHHHHHHHHHHH CS
                       Malic_M 28 ivvlGaGsagiGiaeqiv 45
                                  + ++G+G+ag+  a ++ 
  gi|91773715|ref|YP_566407.1|  9 LAIIGGGAAGLATATHVK 26
                                  568999999998887776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHH CS
                       Malic_M   5 aavalagllaalkitgkklseqkivvlGaGsagiGiaeqivea 47 
                                   ++ +l +l+ ++ki+   ls +++v++GaG+ g+ ia  i++ 
  gi|91773715|ref|YP_566407.1| 128 GVFTLQTLADGMKIETALLSAETVVIIGAGAIGVEIAAGIAKR 170
                                   5678999***************************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2953.49
//
Query:       gi|91773716|ref|YP_566408.1|  [L=104]
Description: hypothetical protein Mbur_1768 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 680.27
//
Query:       gi|91773717|ref|YP_566409.1|  [L=475]
Description: DNA primase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-12   48.2   0.2    3.6e-12   46.6   0.2    2.0  1  Toprim_4  Toprim domain
    2.6e-06   27.8   0.0    6.6e-06   26.5   0.0    1.7  1  Toprim_2  Toprim-like
      0.006   16.8   0.1      0.025   14.8   0.1    2.1  1  Toprim    Toprim domain
  ------ inclusion threshold ------
       0.11   13.2   0.0        6.5    7.4   0.0    2.6  2  DUF5499   Family of unknown function (DUF5499)
        5.4    7.1  13.1          2    8.5   7.5    2.7  2  DUF1388   Repeat of unknown function (DUF1388)


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 !   46.6   0.2     1e-15   3.6e-12       2      76 ..     172     255 ..     171     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1e-15
                      Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGeatae 72 
                                   +i++VEg+aDvl+l ++gikn++ v g+++ p++ ++++k+kt +++++    ++ ++ke++++ d D+     +G+ + +
  gi|91773717|ref|YP_566409.1| 172 AIVVVEGRADVLNLLRYGIKNTICVGGTNV-PPEVAELTKKKTvTAFTDgdrgGKLIIKELLQVADIDYiarapDGKSVED 251
                                   79****************************.************999999****9**************9888888888877 PP

                      Toprim_4  73 rlae 76 
                                    + +
  gi|91773717|ref|YP_566409.1| 252 LVQR 255
                                   7666 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.8e-09   6.6e-06       1      85 [.     174     248 ..     174     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.8e-09
                      Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvrekirelp 81 
                                   vv+Eg  D+l l+++gik   n + +gGt+++++ ++l +++   +v   +D D+ G+  +k+l +++      + i++ p
  gi|91773717|ref|YP_566409.1| 174 VVVEGRADVLNLLRYGIK---NTICVGGTNVPPEVAELTKKK---TVTAFTDGDRGGKLIIKELLQVAD-I---DYIARAP 244
                                   79***************9...********8888888877777...79999***********99998884.2...3455566 PP

                      Toprim_2  82 egkD 85 
                                   +gk 
  gi|91773717|ref|YP_566409.1| 245 DGKS 248
                                   6665 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     7e-06     0.025       2      91 ..     173     240 ..     172     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7e-06
                                   EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHH CS
                        Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawe 82 
                                   +v+vEg +d+ ++ ++   g ++++ + G+ +  e                    +el  + + +   tD+Dr G+ i +e
  gi|91773717|ref|YP_566409.1| 173 IVVVEGRADVLNLLRY---GIKNTICVGGTNVPPEV-------------------AEL-TKKKTVTAFTDGDRGGKLIIKE 230
                                   89**************...9*********9998887...................444.477899999************* PP

                                   HHHHHT.HHH CS
                        Toprim  83 llevlk.ell 91 
                                   ll+v++ +++
  gi|91773717|ref|YP_566409.1| 231 LLQVADiDYI 240
                                   **99985544 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.052   1.9e+02       7      26 ..     145     164 ..     141     188 .. 0.82
   2 ?    7.4   0.0    0.0018       6.5       3      39 ..     225     260 ..     223     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.052
                       DUF5499   7 rkdlkvrdydyfgkrkapdg 26 
                                   r+ +++ + +y+gk k p g
  gi|91773717|ref|YP_566409.1| 145 RQSVRIEEMQYYGKNKIPCG 164
                                   7789999**********987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                       DUF5499   3 ktyrrkdlkvrdydyfgkrkapdgvshkdmve.nifrs 39 
                                   k   ++ l+v d dy+   +apdg s +d+v+ +i+rs
  gi|91773717|ref|YP_566409.1| 225 KLIIKELLQVADIDYIA--RAPDGKSVEDLVQrEIVRS 260
                                   555667799******97..69*********97357787 PP

>> DUF1388  Repeat of unknown function (DUF1388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.5   0.00055         2       3      26 ..     348     371 ..     347     374 .. 0.74
   2 ?    0.6   0.3      0.16   5.7e+02       4       9 ..     461     466 ..     461     467 .. 0.37

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00055
                       DUF1388   3 EAKSPaeaKSPgeaKSPgeaKSPv 26 
                                   E +SP e +SP e +SP e + P 
  gi|91773717|ref|YP_566409.1| 348 ETRSPRETRSPRETRSPRETREPK 371
                                   568888888888888888877665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                       DUF1388   4 AKSPae 9  
                                   AKSPa+
  gi|91773717|ref|YP_566409.1| 461 AKSPAS 466
                                   344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3032.14
//
Query:       gi|91773718|ref|YP_566410.1|  [L=173]
Description: SSU ribosomal protein S18P alanine acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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    2.8e-16   59.8   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.3e-14   53.4   0.1    2.8e-14   53.2   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    9.2e-11   42.0   0.0    1.5e-10   41.4   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.8e-07   29.4   0.0      1e-06   28.6   0.0    1.3  1  FR47             FR47-like protein
    0.00036   20.7   0.4    0.00052   20.2   0.4    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0017   19.0   0.1     0.0035   18.0   0.1    1.6  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0078   16.3   0.0      0.036   14.1   0.0    1.8  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.037   13.7   0.0       0.18   11.5   0.0    1.9  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.062   12.8   0.1       0.13   11.7   0.1    1.5  1  Acetyltransf_15  Putative acetyl-transferase
      0.087   13.0   0.0       0.16   12.2   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   1.6e-19   2.8e-16      20     117 .]      28     120 ..       8     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.6e-19
                                   HHHH.HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE CS
                Acetyltransf_1  20 seee.feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivl 99 
                                   ++++ f+e     +eg+lva  d ++iGf++++       +++ i slaV++e+++ G+G++Ll+ +++ ++++gik   l
  gi|91773718|ref|YP_566410.1|  28 FVYMnFYEM---KDEGFLVATMDSNIIGFVMGYRSET---NEGRIFSLAVKKEWQNIGVGKKLLNSILDLFKDKGIKSATL 102
                                   222246666...8999*******************99...9***********************************999** PP

                                   EEETTEHHHHHHHHH.TTE CS
                Acetyltransf_1 100 aveedndaairlYek.lGF 117
                                   +v+ +nd+ai +Y + + F
  gi|91773718|ref|YP_566410.1| 103 EVRISNDKAIQMY-RnMDF 120
                                   *************.65877 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1   1.5e-17   2.8e-14      27     127 .]      35     143 ..      12     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.5e-17
               Acetyltransf_10  27 eegealllvaeeggkivGvi...el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfY 101
                                   e ++  +lva+ + +i+G++   +  +++++i  l+V++e++  G+gk+Ll+ +++ ++++gik  +l+v+ s+ +a+++Y
  gi|91773718|ref|YP_566410.1|  35 EMKDEGFLVATMDSNIIGFVmgyRSeTNEGRIFSLAVKKEWQNIGVGKKLLNSILDLFKDKGIKSaTLEVRISNdKAIQMY 115
                                   44677799999999******8554445555********************************************9****** PP

               Acetyltransf_10 102 eklGFkav..geeqeenGirfvpMekel 127
                                   +++ F a+  ++  + +G + + M+k+l
  gi|91773718|ref|YP_566410.1| 116 RNMDFIACwiEQDYYSDGESGIIMKKQL 143
                                   ********999*************9986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   8.2e-14   1.5e-10       3      75 ..      39     121 ..      37     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 8.2e-14
                                   EEEEEEEETTEEEEEEEEEEES...TCTEE...EEE-GGGTTSSHHHHHHHHTT.....SEEEEE.EEEE..THHHHHHHH CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslld...aeitr...laVdpeyrgkGiGraLleaae.....kgiile.qlel..naekaikfY 69 
                                   + ++Va  d +i+Gf+  ++++   +   r   laV++e+++ G+G++Ll+ +      kgi+ + +le+  +++kai++Y
  gi|91773718|ref|YP_566410.1|  39 EGFLVATMDSNIIGFVMGYRSEtneG---RifsLAVKKEWQNIGVGKKLLNSILdlfkdKGIK-SaTLEVriSNDKAIQMY 115
                                   6799*************999995544...3455******************512345557855.33333344555****** PP

                                   HHTTEE CS
                Acetyltransf_7  70 eklGFe 75 
                                   + + F+
  gi|91773718|ref|YP_566410.1| 116 RNMDFI 121
                                   ***996 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   5.6e-10     1e-06      18      81 ..      60     124 ..      50     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.6e-10
                                   E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEEE CS
                          FR47  18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfekie 81 
                                   + + g +++l v++e ++ G g++l +++      +g++ ++l v++sN+++i++y  + f + +
  gi|91773718|ref|YP_566410.1|  60 ETNEGRIFSLAVKKEWQNIGVGKKLLNSILDLFKDKGIKsATLEVRISNDKAIQMYRNMDFIACW 124
                                   55679*******************************97626899*****************9874 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.4   2.9e-07   0.00052      47     145 ..      36     131 ..       3     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                Acetyltransf_4  47 ekeyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensi 126
                                   +k   flva  + +i+G   +   +    ++  + s  ++ +  ++ g+g++l++++ + +k  +i++ + e+  +n+++i
  gi|91773718|ref|YP_566410.1|  36 MKDEGFLVATmDSNIIGFVMGYRSE---TNEGRIFSLAVK-KEWQNIGVGKKLLNSILDLFKDKGIKSATLEVRISNDKAI 112
                                   3444455666566666665544222...245556666675.89******************************99****** PP

                Acetyltransf_4 127 qfhkalGFelvgifkkcik 145
                                   q++ ++ F    i+++++ 
  gi|91773718|ref|YP_566410.1| 113 QMYRNMDFIACWIEQDYYS 131
                                   ******9988877777766 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.9e-06    0.0035      44     137 ..      25     120 ..       1     121 [. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                Acetyltransf_3  44 a....waeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvav 120
                                   +    + + +e ++ g+++ + d+++iG+v+ ++ e +++   +++ +++++++ G+++  ++++l+++ ++ g++    +
  gi|91773718|ref|YP_566410.1|  25 HnpfvYMNFYEMKDEGFLVATMDSNIIGFVMGYRSETNEG-RIFSLAVKKEWQNIGVGKKLLNSILDLF-KDKGIKSATLE 103
                                   2455666677778999***9899989****8888888775.56667777777677*************9.8888**99999 PP

                Acetyltransf_3 121 idkeNeaSirvleklGf 137
                                   +  +N + i+ ++ + f
  gi|91773718|ref|YP_566410.1| 104 VRISNDKAIQMYRNMDF 120
                                   99999999998888776 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0     2e-05     0.036       3     125 ..       4     120 ..       3     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                   EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-C CS
                Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavap 83 
                                   r+  + d+++vl++  +aF ++++ +    +   + ++++ +l+a  +  ++g ++ ++ e       ++ + + + av+ 
  gi|91773718|ref|YP_566410.1|   4 RKFMPRDFEQVLAIEMEAFTEHNPFV----YMNFYEMKDEGFLVATMDSNIIGFVMGYRSE-------TNEGRIFSLAVKK 73 
                                   66667788888888888888888875....3345566666777777777777777777665.......556789999**** PP

                                   CGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT- CS
                Acetyltransf_9  84 ehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGy 125
                                   e ++ gv +kLl+  l+  +++g++ ++l        +i++Yr +++
  gi|91773718|ref|YP_566410.1|  74 EWQNIGVGKKLLNSILDLFKDKGIKSATLEVrisndKAIQMYRNMDF 120
                                   ***********************999999877655555677777765 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.9e-05      0.18      54     137 ..      26     120 ..      21     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-05
                                   EEEEEEEEEEGGGCGGGGCS............---TT-EEEEEEES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE-- CS
                Acetyltransf_8  54 epvgyfeiYwakedelaeyy............daepgdrGiHllig.eaeargkglttallralvhylfadprtrrvvvEP 121
                                   +p+ y+ +Y++k++    +             +  +   G  + ++ ++e  + g++++ll+++++ lf+d+++++  +E 
  gi|91773718|ref|YP_566410.1|  26 NPFVYMNFYEMKDEGFLVATmdsniigfvmgyR-SETNEGRIFSLAvKKEWQNIGVGKKLLNSILD-LFKDKGIKSATLEV 104
                                   566666666666664322223354554444431.233333333333256667899********998.79999********* PP

                                   BTT-HHHHHHHHHTT- CS
                Acetyltransf_8 122 dvrNerairllekaGf 137
                                   +++N +ai++++++ f
  gi|91773718|ref|YP_566410.1| 105 RISNDKAIQMYRNMDF 120
                                   ***********99987 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.1e-05      0.13      64     146 ..      38     129 ..      19     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
               Acetyltransf_15  64 s.................silieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnis 127
                                   +                  ++ e n   i++l v++++++ G+ kklL+ +l+ +    k + ++  +L +  +    +++
  gi|91773718|ref|YP_566410.1|  38 DegflvatmdsniigfvmGYRSETNEGRIFSLAVKKEWQNIGVGKKLLNSILDLF----KDKGIKSATLEVRISN---DKA 111
                                   4455555555555555557777888889**********************96666....5555555555554322...356 PP

               Acetyltransf_15 128 falYyslgFrkglfvksgP 146
                                    ++Y+++ F  +++++++ 
  gi|91773718|ref|YP_566410.1| 112 IQMYRNMDFI-ACWIEQDY 129
                                   6677777776.45565555 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.7e-05      0.16      10      59 ..      49      98 ..      34     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
               Acetyltransf_CG 10 eevafl.eYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglk 59
                                  + ++f+  Y+ +++++  +    V++e +  G++kkL +++ld  +++g k
  gi|91773718|ref|YP_566410.1| 49 NIIGFVmGYR-SETNEGRIFSLAVKKEWQNIGVGKKLLNSILDLFKDKGIK 98
                                  4566654898.88899999**************************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1440.99
//
Query:       gi|91773719|ref|YP_566411.1|  [L=615]
Description: tRNA-guanine transglycosylases, various specificities [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-61  206.3   0.7      4e-61  205.4   0.7    1.5  1  DUF5591   Domain of unknown function (DUF5591)
    1.9e-18   66.4   0.0    2.3e-17   62.9   0.0    2.4  2  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    8.2e-14   51.5   0.1    3.4e-13   49.5   0.0    1.9  2  TGT       Queuine tRNA-ribosyltransferase
    2.4e-13   49.8   0.1    5.6e-13   48.7   0.1    1.6  1  PUA       PUA domain


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 !  205.4   0.7   8.8e-65     4e-61       1     153 [.     308     458 ..     308     459 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 8.8e-65
                                   X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT----------- CS
                       DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdiav 81 
                                   v+rf++r++erY+ppe +++lvL+PcsakkPys s+sh+kf+++++k+++ vheviltsPlG++Prele +YPaa+Yd++v
  gi|91773719|ref|YP_566411.1| 308 VVRFAKRIQERYTPPE-SEILVLFPCSAKKPYSISNSHNKFIKSLGKYRKFVHEVILTSPLGIIPRELEMTYPAAHYDAVV 387
                                   89*************7.**************************************************************** PP

                                   -----HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHH CS
                       DUF5591  82 tgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknLkea 153
                                   tg+w++eei++v+ +l++yl+k+ky++v+ahle++yrei+e v+e+l++e+iyt+ ++++ s +sl+nLk++
  gi|91773719|ref|YP_566411.1| 388 TGYWDAEEIKWVSACLRDYLSKHKYSHVVAHLEGAYREICEIVSEQLSIEFIYTS-TGNVSSYDSLDNLKKT 458
                                   *******************************************************.9*************97 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 ?    0.6   0.0      0.14   6.2e+02      27      54 ..      53      83 ..      15      85 .. 0.78
   2 !   62.9   0.0   5.1e-21   2.3e-17       2      69 ..     477     542 ..     476     544 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                        TGT_C2 27 trs.atgrirqvlv..dgerlatlraqdgrl 54
                                   +  a+ rir+++   ++e +  l  qd +l
  gi|91773719|ref|YP_566411.1| 53 SIEeAEERIRKIREevGDETIIILPHQDLTL 83
                                  4444999*****9977788888888887665 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 5.1e-21
                        TGT_C2   2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslp 69 
                                   ++r+iadYqFG gag+ ++p+d++i+  a    +qv++++e++at+ +q+g+l L+++G r+l +s +
  gi|91773719|ref|YP_566411.1| 477 MMRSIADYQFGPGAGKLIVPDDAKIK--APFPKHQVFIGKEQIATMIPQYGILALTVAGIRLLSNSEE 542
                                   689***********************..***********************************99866 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   7.5e-17   3.4e-13     190     346 ..     118     264 ..     109     267 .. 0.91
   2 ?   -1.5   0.0      0.24   1.1e+03     152     216 ..     396     464 ..     394     477 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 7.5e-17
                                   -SEEEE-SSSSSS.HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEET CS
                           TGT 190 fdgyaigGlsvge.ekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnl 269
                                   +d y+ +G    e + +++le +  ++ ++  d  +yl    tP + + +v lG+D++d + ++ ++  + ++t+ g++ l
  gi|91773719|ref|YP_566411.1| 118 ADLYVMEGAGSLEgNARKFLERLIDLKGSVAPDTAIYLPNLCTPANAAMLVYLGIDIVDDTKAIIAGCSDIYMTTAGKYFL 198
                                   578999997655559999***********************************************************9999 PP

                                   TSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           TGT 270 knakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefar 346
                                      +++e   p    C C +C   t ++l+ + k+++   a L++ HN  ++  ++  +Re I++g++ e++e  +r
  gi|91773719|ref|YP_566411.1| 199 D--SMTEL--P----CRCEACAPITIEELRAMPKADR---AELISRHNRNMLEAEIVLARERIRSGNLREYIEGQCR 264
                                   7..44444..7....******99**************...*******************************997665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.24
                                   HHHHHHHHHHH......SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHHHHHGG CS
                           TGT 152 lrwldrcleah......qalfgivqGglyedlreesaeelakrdfdgyaigGlsvgeekeellevveavte 216
                                   ++w+  cl+ +      +++++  +G  y++  e   e+l +++f     g +s +++ ++l ++v+ ++ 
  gi|91773719|ref|YP_566411.1| 396 IKWVSACLRDYlskhkySHVVAHLEG-AYREICEIVSEQL-SIEFIYTSTGNVSSYDSLDNLKKTVSDIVA 464
                                   68999999655566675558888888.5666888877877.667765566669999999999999987765 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   1.2e-16   5.6e-13      17      73 ..     557     611 ..     549     612 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.2e-16
                                   -EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA  17 asLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                    sLlapGvv +++++++gd+V i     ++++vG+a++s+ee+    +g++v++++v
  gi|91773719|ref|YP_566411.1| 557 GSLLAPGVVAADKNIRPGDEVMITGS--KAIGVGRAMMSGEEMVGSSRGVAVDLRHV 611
                                   49*******************88888..***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3952.24
//
Query:       gi|91773720|ref|YP_566412.1|  [L=457]
Description: D-lactate dehydrogenase (cytochrome) [Methanococcoides burtonii DSM 6242]
Scores for 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-60  202.4   0.1    1.2e-59  202.0   0.1    1.1  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    4.3e-43  146.4   0.4    9.5e-43  145.3   0.1    1.7  2  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.1   1.3e-63   1.2e-59       2     249 ..     213     454 ..     212     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 1.3e-63
                                   -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHH CS
                 FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeelea 82 
                                   p ar+v+l++f++ + a kav+++ ++giip+a+e++d++a+++v+++++      ++ +a+l++e++g + ++++ee++ 
  gi|91773720|ref|YP_566412.1| 213 PHARSVILASFDNTTLAGKAVVKVLSSGIIPSACEILDSTAIKAVRSFDPS--VELSDVGAILMIEVDGME-NAVREEAA- 289
                                   8899***********************************************..99****************.99999999. PP

                                   HHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEEEE CS
                 FAD-oxidase_C  83 lveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglevvlf 163
                                   lv +++e+ + a   va++ ae e+lwkaR+ + + ++++  k+  +++ eD+ vP+++l+ +++ ++ l ++++++++++
  gi|91773720|ref|YP_566412.1| 290 LVGKACEELASAI-KVAESGAESENLWKARRLVGAAISKIDVKRTRIYVGEDIGVPIKELPGMLEYVRSLSEEFDIHIMTY 369
                                   ********99995.******************************************************************* PP

                                   EEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH-TT-- CS
                 FAD-oxidase_C 164 gHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPkgi 244
                                   gH+gdgnlh  +++d+ +e+e e+a++++d++ ++a+++gG++s+EHGvG++++ y+e e  ++ l++mr+iK++lDPkgi
  gi|91773720|ref|YP_566412.1| 370 GHIGDGNLHTGMAIDMLSEEELETAHAVADRIYRRAISVGGTVSAEHGVGKARAMYMELEH-PTSLEIMRQIKKTLDPKGI 449
                                   *********************************************************9998.77***************** PP

                                   BSTT- CS
                 FAD-oxidase_C 245 LNPgk 249
                                   LNPgk
  gi|91773720|ref|YP_566412.1| 450 LNPGK 454
                                   ****9 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3   0.1   1.1e-46   9.5e-43       1     139 []      37     176 ..      37     176 .. 0.98
   2 ?   -3.1   0.0      0.64   5.8e+03      98     106 ..     406     414 ..     387     430 .. 0.65

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 1.1e-46
                                   EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                 FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                   p+ vvrp+++e+va++++la+  ++pv++rG+Gs+l+g+av  +gg+vld+  +++il+id ++ ++tve+Gv+ ++l++a
  gi|91773720|ref|YP_566412.1|  37 PDFVVRPATTEQVADVVKLADMSNTPVVARGAGSGLCGGAVpVEGGIVLDMCSMDHILDIDIDNLQITVEPGVVHEKLNKA 117
                                   899**********************************999999********99**************************** PP

                                   HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                 FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                   l+++g++++++pgs   +t+GG++a+n++G ++ kyG++r++vl levv+adG++v+++
  gi|91773720|ref|YP_566412.1| 118 LEPYGFFFPPDPGSTAMCTIGGLMANNGSGIRCVKYGTTRNYVLDLEVVMADGRIVHTG 176
                                   ********************************************************985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.64
                                   SBHHHTTTT CS
                 FAD_binding_4  98 gtvGGaiat 106
                                    +vGG+++ 
  gi|91773720|ref|YP_566412.1| 406 ISVGGTVSA 414
                                   466666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2713.13
//
Query:       gi|91773721|ref|YP_566413.1|  [L=356]
Description: hypothetical protein Mbur_1774 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-28   98.9   9.4    3.6e-15   55.9   0.1    2.7  3  CCG          Cysteine-rich domain
    5.5e-12   45.9   3.7    5.5e-12   45.9   3.7    2.4  2  Fer4_8       4Fe-4S dicluster domain
    1.8e-09   38.0   4.9    1.8e-09   38.0   4.9    2.7  4  Fer4_17      4Fe-4S dicluster domain
    3.5e-08   33.9   5.5    3.5e-08   33.9   5.5    2.4  2  Fer4_7       4Fe-4S dicluster domain
    1.4e-05   24.7  20.8     0.0012   18.6   2.9    2.9  2  Fer4         4Fe-4S binding domain
    2.1e-05   24.6  22.8    0.00037   20.5  13.1    3.3  4  Fer4_10      4Fe-4S dicluster domain
    0.00016   21.6  17.4     0.0029   17.6   2.6    3.4  3  Fer4_2       4Fe-4S binding domain
    0.00084   19.7   1.2    0.00084   19.7   1.2    3.5  3  Fer4_4       4Fe-4S binding domain
     0.0013   18.9  12.4     0.0013   18.9  12.4    3.5  4  Fer4_9       4Fe-4S dicluster domain
     0.0017   18.6   3.2       0.53   10.5   0.1    2.6  2  Fer4_18      4Fe-4S dicluster domain
     0.0047   17.8  15.5      0.013   16.4  12.8    2.9  3  Fer4_16      4Fe-4S double cluster binding domain
     0.0052   16.9  15.4       0.11   12.6   1.0    3.8  4  Fer4_21      4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.033   14.7  12.2       0.34   11.5   0.6    2.9  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
        2.6    8.9   8.1        2.9    8.7   0.7    2.7  2  Fer4_15      4Fe-4S single cluster domain
        3.8    7.5   5.0         12    5.9   0.1    2.9  3  Thioredoxin  Thioredoxin


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   0.5       8.8   1.1e+04      75      82 ..      60      67 ..      53      71 .. 0.64
   2 !   55.9   0.1   3.1e-18   3.6e-15       1      85 []     135     214 ..     135     214 .. 0.96
   3 !   49.2   0.4   3.9e-16   4.7e-13       1      84 [.     246     330 ..     246     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.8
                           CCG 75 tacpgCll 82
                                  ++c +C l
  gi|91773721|ref|YP_566413.1| 60 NTCTTCGL 67
                                  45555543 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 3.1e-18
                           CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCl 81 
                                   ++yf+gC l+ ++ +e+  ++  l++ +gv++     e CCG++  r+g++  a +l ++n+e++e+tga  iv+ c+gC+
  gi|91773721|ref|YP_566413.1| 135 YVYFVGC-LGSYRFRETALKTYDLIKDMGVTVLSD--EVCCGSPLLRTGFD--ADELIRHNLEQIEKTGAHTIVASCAGCY 210
                                   68*****.*************************55..*************9..89************************** PP

                           CCG  82 lqlk 85 
                                   +++k
  gi|91773721|ref|YP_566413.1| 211 NTFK 214
                                   *985 PP

  == domain 3  score: 49.2 bits;  conditional E-value: 3.9e-16
                           CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadaivtac 77 
                                   v+y+d+Chl+ra+   + +rk++ ++   ++ e+ ++ e+++CCG ggg++   + l+ ++ak+++  + + ++d++vt c
  gi|91773721|ref|YP_566413.1| 246 VTYHDPCHLGRANrvFDPPRKLIIAV--CDLKEMRTNrENAKCCGGGGGVRKGYPeLSASIAKKRIMDVPD-NVDYMVTCC 323
                                   89***********9999999999999..45567777778*****998876655444***************.7******** PP

                           CCG  78 pgCllql 84 
                                   p C ++l
  gi|91773721|ref|YP_566413.1| 324 PLCRTNL 330
                                   ***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 !   45.9   3.7   4.6e-15   5.5e-12       3      64 ..      10      75 ..       8      76 .. 0.82
   2 ?   -0.6   0.1       1.6   1.9e+03      44      55 ..     197     210 ..     168     211 .. 0.64

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 4.6e-15
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaae........dvqeeqvleeeealwsCttcgaCtevCpvg 64
                                   kC++CgaC+s Cpv+++++ +++++rg+           dv e++     +++++Cttcg C++ Cp g
  gi|91773721|ref|YP_566413.1| 10 LKCVRCGACRSICPVFEEFGWESFSTRGRMLLakgisngmDVDESM----IDSINTCTTCGLCEQMCPAG 75
                                  69*****************999999999977766665554333333....699***************86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                        Fer4_8  44 e..eealwsCttcg 55 
                                   +  ++++ sC +c 
  gi|91773721|ref|YP_566413.1| 197 TgaHTIVASCAGCY 210
                                   13378899999985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   4.9   1.5e-12   1.8e-09       1      59 [.      11      75 ..      11      77 .. 0.80
   2 ?   -0.9   0.0       2.1   2.5e+03      32      49 ..     192     209 ..     172     211 .. 0.67
   3 ?   -2.5   0.1       6.8   8.2e+03      33      47 ..     273     287 ..     251     291 .. 0.59
   4 ?   -2.7   0.4       7.8   9.3e+03      12      17 ..     323     328 ..     319     337 .. 0.57

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.5e-12
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl.....glleeaeke.ekaslCieCgeCerkCPqg 59
                                  +C +Cg+C+  Cp +e+ ++e  +++ ++ l     + ++  e + + +++C++Cg+Ce+ CP+g
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICPVFEEFGWESFSTRGRMLLakgisNGMDVDESMiDSINTCTTCGLCEQMCPAG 75
                                  6****************9999888888876666443333333344679***************87 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                       Fer4_17  32 glleeaekeekaslCieC 49 
                                   +++e++ + + + +C++C
  gi|91773721|ref|YP_566413.1| 192 EQIEKTGAHTIVASCAGC 209
                                   445555445677888888 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.8
                       Fer4_17  33 lleeaekeekaslCi 47 
                                   +l+e+ ++++  +C+
  gi|91773721|ref|YP_566413.1| 273 DLKEMRTNRENAKCC 287
                                   445555566666665 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 7.8
                       Fer4_17  12 Cpsyea 17 
                                   Cp ++ 
  gi|91773721|ref|YP_566413.1| 323 CPLCRT 328
                                   444443 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   5.5   2.9e-11   3.5e-08       1      52 []      11      76 ..      11      76 .. 0.72
   2 ?   -1.4   0.0       3.1   3.7e+03      35      43 ..     203     211 ..     181     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.9e-11
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt.............ekveid.pekClgCgaCvavCPtga 52
                                  +C+ CgaC + Cpv     +e+ + +g+             ++  id  ++C++Cg C++ CP+ga
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICPVFEEFGWESFSTRGRmllakgisngmdvDESMIDsINTCTTCGLCEQMCPAGA 76
                                  7************88877778777775545554445443432224443678*************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                        Fer4_7  35 pekClgCga 43 
                                     +C gC++
  gi|91773721|ref|YP_566413.1| 203 VASCAGCYN 211
                                   467888875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.1     4e-06    0.0048       7      20 ..      11      24 ..      10      25 .. 0.96
   2 !   18.6   2.9   9.9e-07    0.0012       7      22 ..      61      76 ..      58      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4e-06
                                  TSSS-THHHHHSTT CS
                          Fer4  7 kCigCGaCvevCPv 20
                                  kC++CGaC ++CPv
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICPV 24
                                  8************8 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 9.9e-07
                                  TSSS-THHHHHSTTTE CS
                          Fer4  7 kCigCGaCvevCPvgA 22
                                   C+ CG+C+++CP gA
  gi|91773721|ref|YP_566413.1| 61 TCTTCGLCEQMCPAGA 76
                                  6**************9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  13.1   3.1e-07   0.00037       8      56 .]      11      73 ..       5      73 .. 0.81
   2 !   17.2   2.1   3.3e-06     0.004       6      26 ..      59      79 ..      54      99 .. 0.72
   3 ?   -1.1   0.0       1.8   2.2e+03      39      49 ..     200     210 ..     187     213 .. 0.65
   4 ?   -3.2   0.2       7.9   9.5e+03      44      48 ..     322     326 ..     309     332 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.1e-07
                       Fer4_10  8 tCirCgkCvkaCPadl..............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +C+rCg+C++ CP+                 ++g ++  + +e   + +  Ct+cg C + CP
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICPVFEefgwesfstrgrmlLAKGISNGMDVDESMIDSINTCTTCGLCEQMCP 73
                                  7*************77***********998444444455555555556888***********9 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.3e-06
                       Fer4_10  6 ddtCirCgkCvkaCPadltsv 26
                                   +tC+ Cg C ++CPa ++ +
  gi|91773721|ref|YP_566413.1| 59 INTCTTCGLCEQMCPAGAKPS 79
                                  579*************55333 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.8
                       Fer4_10  39 rkkvekCtgcg 49 
                                   ++ v +C gc 
  gi|91773721|ref|YP_566413.1| 200 HTIVASCAGCY 210
                                   44666777775 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 7.9
                       Fer4_10  44 kCtgc 48 
                                    C+ c
  gi|91773721|ref|YP_566413.1| 322 CCPLC 326
                                   33333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.6   2.5e-06    0.0029       9      21 ..      11      23 ..       4      24 .. 0.92
   2 !   11.4   2.8   0.00023      0.27       8      22 .]      60      74 ..      55      74 .. 0.92
   3 ?   -0.8   0.1       1.8   2.1e+03       8      14 ..     204     210 ..     199     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.5e-06
                        Fer4_2  9 rCigCgaCvsaCP 21
                                  +C++CgaC+s CP
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICP 23
                                  8************ PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00023
                        Fer4_2  8 drCigCgaCvsaCPa 22
                                  ++C+ Cg C + CPa
  gi|91773721|ref|YP_566413.1| 60 NTCTTCGLCEQMCPA 74
                                  58************8 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.8
                        Fer4_2   8 drCigCg 14 
                                   ++C gC 
  gi|91773721|ref|YP_566413.1| 204 ASCAGCY 210
                                   6799995 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.2   7.1e-07   0.00084       3      15 ..      11      23 ..       5      34 .. 0.91
   2 !   10.2   2.1   0.00075       0.9       2      16 ..      60      74 ..      59      81 .. 0.91
   3 ?   -1.5   0.2       4.3   5.1e+03       3       7 ..     205     209 ..     204     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.1e-07
                        Fer4_4  3 rCigCgsCvaaCP 15
                                  +C++Cg+C+++CP
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICP 23
                                  6************ PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00075
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  ++C+ Cg C+  CP 
  gi|91773721|ref|YP_566413.1| 60 NTCTTCGLCEQMCPA 74
                                  68************6 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.3
                        Fer4_4   3 rCigC 7  
                                   +C gC
  gi|91773721|ref|YP_566413.1| 205 SCAGC 209
                                   57777 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   3.0   0.00022      0.26      34      47 ..      10      23 ..       1      26 [. 0.75
   2 !   18.9  12.4     1e-06    0.0013       1      50 [.      11      76 ..      11      77 .. 0.69
   3 ?   -1.4   0.0       2.3   2.7e+03      35      39 ..     205     209 ..     182     212 .. 0.66
   4 ?   -2.3   0.3       4.5   5.4e+03       8      19 ..     322     333 ..     319     341 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                        Fer4_9 34 eaCigCgaCveaCp 47
                                   +C+ CgaC  +Cp
  gi|91773721|ref|YP_566413.1| 10 LKCVRCGACRSICP 23
                                  57999999999999 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1e-06
                        Fer4_9  1 kCtgCgaCveaC.........pagvvvedaaerkarlraase...............eaCigCgaCveaCpkga 50
                                  kC++CgaC + C                  + +  r+  a+                + C++Cg C++ Cp ga
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICpvfeefgweS--------FSTRGRMLLAKGisngmdvdesmidsiNTCTTCGLCEQMCPAGA 76
                                  7***********6555555552........44444443333344455555677777789************985 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.3
                        Fer4_9  35 aCigC 39 
                                   +C gC
  gi|91773721|ref|YP_566413.1| 205 SCAGC 209
                                   46666 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.5
                        Fer4_9   8 CveaCpagvvve 19 
                                   C + C +++ + 
  gi|91773721|ref|YP_566413.1| 322 CCPLCRTNLEQA 333
                                   666676666555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.6    0.0032       3.8      53      73 ..       4      24 ..       1      28 [. 0.83
   2 !   10.5   0.1   0.00044      0.53      49      75 ..      50      76 ..      35      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                       Fer4_18 53 rkekgagdcidcescvkvcPt 73
                                   k+++  +c+ c++c ++cP+
  gi|91773721|ref|YP_566413.1|  4 DKQRSILKCVRCGACRSICPV 24
                                  46777889************7 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00044
                       Fer4_18 49 ekeerkekgagdcidcescvkvcPtgi 75
                                  +++e   ++ + c++c+ c ++cP g 
  gi|91773721|ref|YP_566413.1| 50 DVDESMIDSINTCTTCGLCEQMCPAGA 76
                                  45667778999*************985 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  12.8   1.1e-05     0.013       1      66 [.      11      74 ..      11      75 .. 0.74
   2 !   13.1   2.8   0.00012      0.14       1      20 [.      61      80 ..      61      91 .. 0.82
   3 ?   -2.2   0.1       7.1   8.5e+03      50      60 ..     199     209 ..     185     212 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                  +C++Cg+C ++CP+    +   +++ +r  +  ++   +++  de   ++ + +t C+ C+++CPa
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICPVFEEFGW--ESFSTRGRMLLAKGISNGMDVDESMIDSINTCTTCGLCEQMCPA 74
                                  5************8443333..4555555555445556778888888888899************8 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00012
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C+tCg C ++CP++a  ++
  gi|91773721|ref|YP_566413.1| 61 TCTTCGLCEQMCPAGAKPSD 80
                                  5************9996655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.1
                       Fer4_16  50 kqeaitgCdiC 60 
                                    ++ ++ C+ C
  gi|91773721|ref|YP_566413.1| 199 AHTIVASCAGC 209
                                   34555667666 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.7   0.00015      0.18      40      53 ..      11      24 ..       3      28 .. 0.88
   2 !   12.6   1.0   9.6e-05      0.11      39      53 ..      60      74 ..      46      77 .. 0.81
   3 ?    0.3   0.1      0.68   8.1e+02      30      44 ..     195     209 ..     182     213 .. 0.75
   4 ?   -2.5   0.1       4.9   5.8e+03      42      47 ..     321     326 ..     305     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                       Fer4_21 40 eCvGCnlCssvCPv 53
                                  +Cv C  C s+CPv
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICPV 24
                                  7************9 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.6e-05
                       Fer4_21 39 deCvGCnlCssvCPv 53
                                  ++C+ C lC ++CP 
  gi|91773721|ref|YP_566413.1| 60 NTCTTCGLCEQMCPA 74
                                  689**********94 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.68
                       Fer4_21  30 aktvlkvvedeCvGC 44 
                                   +kt ++++  +C GC
  gi|91773721|ref|YP_566413.1| 195 EKTGAHTIVASCAGC 209
                                   566777788899999 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 4.9
                       Fer4_21  42 vGCnlC 47 
                                   + C lC
  gi|91773721|ref|YP_566413.1| 321 TCCPLC 326
                                   445555 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 ?   10.5   1.2   0.00059      0.71       5      19 ..      11      24 ..      10      30 .. 0.87
   2 ?   11.5   0.6   0.00029      0.34       4      18 ..      60      74 ..      56      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00059
                       Fer4_13  5 tCiacgaCvelaPdv 19
                                  +C+ cgaC++++P v
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICP-V 24
                                  7************.4 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00029
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  +tC+ cg+C +++P 
  gi|91773721|ref|YP_566413.1| 60 NTCTTCGLCEQMCPA 74
                                  69************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 ?    2.9   1.6      0.15   1.8e+02       7      24 ..      11      27 ..      10      58 .. 0.85
   2 ?    8.7   0.7    0.0024       2.9       6      31 ..      60      91 ..      55     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                       Fer4_15  7 aCigcglCvaeapevfel 24
                                  +C  cg+C   +p vfe+
  gi|91773721|ref|YP_566413.1| 11 KCVRCGACRSICP-VFEE 27
                                  6***********9.7765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                       Fer4_15  6 daCigcglCvaea......pevfeldedglas 31
                                  ++C+ cglC + +      ++vfe+  ++l s
  gi|91773721|ref|YP_566413.1| 60 NTCTTCGLCEQMCpagakpSDVFEELRRDLVS 91
                                  69***********9999988999998888755 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1      0.01        12      30      44 ..      15      29 ..      12      54 .. 0.86
   2 ?    2.4   0.3      0.13   1.5e+02      28      49 ..      63      84 ..      60     106 .. 0.73
   3 ?   -1.8   0.1       2.6   3.1e+03      23      34 ..     316     327 ..     305     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.01
                                  SHHHHCHHHHHHHHH CS
                   Thioredoxin 30 CghCkalaPelekla 44
                                  Cg C+++ P++e++ 
  gi|91773721|ref|YP_566413.1| 15 CGACRSICPVFEEFG 29
                                  ************985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                                  TTSHHHHCHHHHHHHHHHHCTT CS
                   Thioredoxin 28 pwCghCkalaPeleklaeelkd 49
                                  + Cg C ++ P  +k ++ +++
  gi|91773721|ref|YP_566413.1| 63 TTCGLCEQMCPAGAKPSDVFEE 84
                                  78*********98887766665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.6
                                   EEEE-TTSHHHH CS
                   Thioredoxin  23 veFyApwCghCk 34 
                                   v+++ + C+ C+
  gi|91773721|ref|YP_566413.1| 316 VDYMVTCCPLCR 327
                                   89999******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2068.10
//
Query:       gi|91773722|ref|YP_566414.1|  [L=510]
Description: PAS/PAC sensor hybrid histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-22   79.6   0.2    3.9e-22   78.5   0.2    1.6  1  Response_reg     Response regulator receiver domain
    7.6e-19   68.3   0.0    1.9e-18   67.0   0.0    1.6  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    4.6e-16   58.6   0.5    1.7e-15   56.8   0.5    2.0  1  HisKA            His Kinase A (phospho-acceptor) domain
    6.9e-09   35.7   0.0    1.9e-08   34.3   0.0    1.8  1  PAS              PAS fold
    2.1e-08   34.3   0.2    7.2e-08   32.6   0.2    1.9  1  PAS_9            PAS domain
    6.8e-07   29.5   0.0    1.4e-06   28.5   0.0    1.6  1  PAS_4            PAS fold
    0.00064   20.0   0.1     0.0018   18.5   0.0    1.8  1  PAS_3            PAS fold
      0.001   18.7   0.1     0.0024   17.5   0.1    1.6  1  PAS_12           UPF0242 C-terminal PAS-like domain
     0.0041   17.1   0.0      0.011   15.7   0.0    1.7  1  PAS_8            PAS domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.031   14.1   0.0    1.6  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
      0.027   14.6   0.0      0.065   13.4   0.0    1.6  1  PAS_11           PAS domain
      0.032   13.1   2.6      0.038   12.9   2.6    1.2  1  LMBR1            LMBR1-like membrane protein
      0.054   12.7   2.8      0.056   12.7   1.0    1.8  2  Glyco_transf_15  Glycolipid 2-alpha-mannosyltransferase
        0.1   12.5   5.5        3.3    7.6   0.3    2.2  2  PBECR5           phage-Barnase-EndoU-ColicinE5/D-RelE like nu


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 !   78.5   0.2   3.1e-25   3.9e-22       1     111 [.       8     118 ..       8     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 3.1e-25
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +li+d++  ++ell+ +l  ++y ev +a +g + le++ +e++d+illDi++p+++G+el+k +++++  + +p+i+lt+
  gi|91773722|ref|YP_566414.1|   8 ILIIDNEIFNVELLEAILS-SDY-EVIKAYSGYKGLEIATTESPDIILLDIMIPDITGHELCKILKNDErtRLIPIIMLTS 86 
                                   8*****************9.99*.9999*************************************99995566******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    +e++++++ l+ gaddfl Kp++  e+ +++
  gi|91773722|ref|YP_566414.1|  87 LTEKKEKIKSLEEGADDFLNKPVNYLEISSRV 118
                                   ***********************988887776 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 !   67.0   0.0   1.5e-21   1.9e-18       4     109 ..     393     499 ..     390     501 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1.5e-21
                                   HHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHHHH CS
                     HATPase_c   4 krLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsivkk 83 
                                   k ++ ++ +l+dNa+k+++++++i++  + +++d++i ++D+G+Gip ++l ++f    +  d+ +  ++   +Gl i+kk
  gi|91773722|ref|YP_566414.1| 393 KYIESVLMHLLDNAIKYTPSGKSISLIASEENGDIHIIIKDTGKGIPTDMLTHIFSEVPEeGDECDLCYSNQDYGLIICKK 473
                                   5677899**********8899999998885559**********************98777557777779************ PP

                                   HHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  84 lvelmgGeiwvesepgrGttftftlp 109
                                   ++e ++G+iw++se ++Gt+++++lp
  gi|91773722|ref|YP_566414.1| 474 IIEAHRGSIWINSEVNHGTEIHVKLP 499
                                   ***********************998 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 !   56.8   0.5   1.3e-18   1.7e-15       1      66 [.     276     343 ..     276     344 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.3e-18
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH..HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaL..kregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                   ++ +fla++ HELrtPL +i+g++e+L  +r g+l+e++k+  e+++++++rl+hl+e l   s +++
  gi|91773722|ref|YP_566414.1| 276 MKDEFLANINHELRTPLISIKGFSELLynERLGNLNERQKRTMESVVRNSERLQHLIESLFYVSEMQN 343
                                   689************************64444****************************99988875 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   1.5e-11   1.9e-08       7      85 ..     142     223 ..     137     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.5e-11
                                   HHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC...TTS CS
                           PAS   7 leslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl...rdg 84 
                                   l+++ + i+++++d++i+++N++ + ++G++ +++ gks +dli e+ ++ +++ l++ l+ + e+  +  ++ +    dg
  gi|91773722|ref|YP_566414.1| 142 LDAAGSIIVIINKDTEIVFANKKSCNIFGWEKKDIRGKSWIDLIQENGRESRKQDLHNILSGKAEPPEYYERLIVtknADG 222
                                   78999********************************************9*******999999888777777777666555 PP

                                   S CS
                           PAS  85 r 85 
                                   +
  gi|91773722|ref|YP_566414.1| 223 T 223
                                   5 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.2   5.6e-11   7.2e-08       3     104 .]     148     255 ..     146     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.6e-11
                         PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkng.etfwvll 80 
                                    i+i+n+d +i++aN++ ++++G  ++++ gks+ dl+   + ++++++l+++l  + ++++ +e  +++kn  +tf  ++
  gi|91773722|ref|YP_566414.1| 148 IIVIINKDTEIVFANKKSCNIFGWEKKDIRGKSWIDLIqeNGRESRKQDLHNILSGKAEPPEYYERLIVTKNAdGTFSERI 228
                                   577899********************************9999999999999999999996666666666666635555335 PP

                         PAS_9  81 ta...spvkdddgelvgiivilrDite 104
                                    +   + +kd++g+++gii   ++ te
  gi|91773722|ref|YP_566414.1| 229 ILwhdVILKDSEGNITGIIRSGENTTE 255
                                   55554888999*****99877777665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.1e-09   1.4e-06       1     109 [.     142     257 ..     142     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee....daarleralrrvlegeepiefleelll... 74 
                                   ld+   +++++++d  +++aN+ ++ +fg++ ++++Gk++ +l  e      +++l+++l   +e  e +e+l++++    
  gi|91773722|ref|YP_566414.1| 142 LDAAGSIIVIINKDTEIVFANKKSCNIFGWEKKDIRGKSWIDLIQENgresRKQDLHNILSGKAEPPEYYERLIVTKNadg 222
                                   57778899999*******************************999996666666666666666666777777777777977 PP

                         PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                     +er+++++ + l+d++G + g++  +  +Ter+
  gi|91773722|ref|YP_566414.1| 223 TFSERIILWHDVILKDSEGNITGIIRSGENTTERK 257
                                   779******************************98 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-06    0.0018       1      85 [.     158     246 ..     158     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                         PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge....pyegeyRirrkdG..eyrwveararvi 75 
                                   i++++++ ++i+G+++ +++gk  sw+dl+    re  +++l+++l++++     ye  +  +++dG  + r + ++ +++
  gi|91773722|ref|YP_566414.1| 158 IVFANKKSCNIFGWEKKDIRGK--SWIDLIQENGRESRKQDLHNILSGKAeppeYYERLIVTKNADGtfSERIILWHDVIL 236
                                   5899******************..**********************66664221334446666777733357777777777 PP

                         PAS_3  76 rdengkpvrv 85 
                                   +d++g+++ +
  gi|91773722|ref|YP_566414.1| 237 KDSEGNITGI 246
                                   7777777665 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 !   17.5   0.1   1.8e-06    0.0024      20     108 ..      99     199 ..      85     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                        PAS_12  20 tgansftneksrfrdlsldnya.ldlRrLfDsLrsEnl.........gailvysqkenkllfaNaqirallGwssdkfl.q 89 
                                   +ga+ f n+   + ++s    + l +++L +++ +E++         g+i+v  +k+  ++faN+++ ++ Gw++ ++  +
  gi|91773722|ref|YP_566414.1|  99 EGADDFLNKPVNYLEISSRVRSlLKIKHLQENIIQEKNqayqyldaaGSIIVIINKDTEIVFANKKSCNIFGWEKKDIRgK 179
                                   6778888888888888777655257788888877775322233333389**************************999735 PP

                        PAS_12  90 dfseivqe.gleeWkralak 108
                                   +  +++qe g e+ k++l +
  gi|91773722|ref|YP_566414.1| 180 SWIDLIQEnGRESRKQDLHN 199
                                   67888886356666777755 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.6e-06     0.011       9      49 ..     144     185 ..     137     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.6e-06
                         PAS_8   9 sspdgiavvdlgdrivdvNqaalellGys.adlkgellgqll 49 
                                   ++   i++++ ++ iv++N++ + ++G++ +d++g+   +l+
  gi|91773722|ref|YP_566414.1| 144 AAGSIIVIINKDTEIVFANKKSCNIFGWEkKDIRGKSWIDLI 185
                                   55555777887778***************9999998875444 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 ?   14.1   0.0   2.4e-05     0.031       4      53 ..     396     446 ..     392     456 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                   HATPase_c_3   4 ekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelkna 53 
                                   e++l+ l+dN++    + +++++ +++++  +  i i+D GkG++ + l   
  gi|91773722|ref|YP_566414.1| 396 ESVLMHLLDNAIKytPSGKSISLIASEEN-GDIHIIIKDTGKGIPTDMLTHI 446
                                   789********875588899999999975.699***********99987765 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.1e-05     0.065      13      75 ..     157     216 ..     147     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                        PAS_11  13 kIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrl 75 
                                    I+  ++   ++    g+ek+++ g+s+ dL++++ +++ k+ l++++s + e  + + RL++
  gi|91773722|ref|YP_566414.1| 157 EIVFANK---KSCNIFGWEKKDIRGKSWIDLIQENGRESRKQDLHNILSGKAEPPEYYERLIV 216
                                   5666666...5556679*******************************666666666667766 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.6     3e-05     0.038     218     312 ..     251     346 ..      87     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                         LMBR1 218 eaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks....nenkteeslaklekqlikalqkrertekqw 294
                                   e++ e +++ +e++k+++++ +s+   k+ +e l ++++e+++ l s    +e    e+l +l+++++++++  +r+++++
  gi|91773722|ref|YP_566414.1| 251 ENTTERKNIEEELSKANEKLHSSH---KMKDEFLANINHELRTPLISikgfSELLYNERLGNLNERQKRTMESVVRNSERL 328
                                   34466677899999******9999...9***************999998865555889*********************** PP

                         LMBR1 295 krllekalelediiknks 312
                                   ++l+e  + + ++ ++  
  gi|91773722|ref|YP_566414.1| 329 QHLIESLFYVSEMQNETI 346
                                   *******99999887654 PP

>> Glyco_transf_15  Glycolipid 2-alpha-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.1   1.4e+03     211     241 ..      86     116 ..      82     147 .. 0.70
   2 ?   12.7   1.0   4.4e-05     0.056      37     112 ..     297     371 ..     250     397 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
               Glyco_transf_15 211 slkeieetiktlWdstkkflkenkefieekn 241
                                   sl+e++e ik+l +   +fl++  +++e ++
  gi|91773722|ref|YP_566414.1|  86 SLTEKKEKIKSLEEGADDFLNKPVNYLEISS 116
                                   7778888888888888888888777766443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.4e-05
               Glyco_transf_15  37 efkpkslvnrgrkPiedene..............nAtllalvrn.selakilrsikkvekrFnkkfnYpyvfindepftek 102
                                   +f+                e              + t+ ++vrn + l+++++s+  v +  n+  +Y + f+n +++ e+
  gi|91773722|ref|YP_566414.1| 297 GFS----------------EllynerlgnlnerqKRTMESVVRNsERLQHLIESLFYVSEMQNETIKYTFSFLNIKNILET 361
                                   222................02222233444445599********555******************************9999 PP

               Glyco_transf_15 103 fkekieklve 112
                                    k+++   ++
  gi|91773722|ref|YP_566414.1| 362 LKKDMFPQID 371
                                   9998866655 PP

>> PBECR5  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0026       3.3     102     179 ..      92     165 ..      84     206 .. 0.72
   2 ?    7.1   0.9    0.0037       4.8     131     236 ..     258     376 ..     239     383 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0026
                        PBECR5 102 dkieqlsrelaegafaraaslsqgqdmkdqltsegsekeLaekllndeavkaaYLadkGeevevayvekektfteeqv 179
                                   +ki+ l + + +   ++ +      +++  ++s   +k+L e++ +++  +++YL + G  +  ++++ e +f++++ 
  gi|91773722|ref|YP_566414.1|  92 EKIKSLEEGADDFLNKPVNY----LEISSRVRSLLKIKHLQENIIQEKNQAYQYLDAAGSIIVIINKDTEIVFANKKS 165
                                   55666666664444444454....48888999****************************999988888779988765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0037
                        PBECR5 131 qltsegsekeLaekllndeavkaaYLadkGeevevayvekektftee.qvevlekltdalgddeee............... 195
                                   ++++e s+++  ekl  ++ +k  +La+  +e++   +   k f e   +e+l +l+++ +++ e                
  gi|91773722|ref|YP_566414.1| 258 NIEEELSKAN--EKLHSSHKMKDEFLANINHELRTPLISI-KGFSELlYNERLGNLNERQKRTMESvvrnserlqhliesl 335
                                   4555555554..7999999999999999999999977775.4666651467788888886655555778777788889999 PP

                        PBECR5 196 ..geelaekiieekaeiakseakdrketekdkmedkidvnvlk 236
                                     + e+++++i+  +     ++k+++et k++m+ +id + l+
  gi|91773722|ref|YP_566414.1| 336 fyVSEMQNETIKYTFSFL--NIKNILETLKKDMFPQIDHKGLE 376
                                   998899999998888888..48899999999999999777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 2972.88
//
Query:       gi|91773723|ref|YP_566415.1|  [L=622]
Description: hypothetical protein Mbur_1776 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-127  425.4   0.0   1.5e-127  424.9   0.0    1.2  1  Radical_SAM_N  Radical SAM N-terminal
    2.8e-28   99.1   0.0    4.8e-28   98.4   0.0    1.4  1  DUF3362        Domain of unknown function (DUF3362)
    7.6e-16   58.9   0.4    2.1e-15   57.5   0.3    1.8  2  Radical_SAM    Radical SAM superfamily
    0.00014   21.8   0.0        0.2   11.7   0.0    3.0  3  B12-binding    B12 binding domain
  ------ inclusion threshold ------
      0.082   12.9   0.0       0.18   11.9   0.0    1.5  1  DUF523         Protein of unknown function (DUF523)


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 !  424.9   0.0  4.3e-131  1.5e-127       1     298 []      16     319 ..      16     319 .. 0.96

  Alignments for each domain:
  == domain 1  score: 424.9 bits;  conditional E-value: 4.3e-131
                 Radical_SAM_N   1 flpvsrkemeergwdelDvilvsgDaYvDhpsfgaaligrlLeaeGfrvgiiaqPdwksaedfkklGkPrlffgvsaGnlD 81 
                                   flp+  k++++rgwd+lD+i+v+gDaYvDhp fga++igr+Le++Gf+vgiiaqP+w++++df+klGkPrlff+v++Gn D
  gi|91773723|ref|YP_566415.1|  16 FLPMDIKDIKSRGWDQLDIIIVTGDAYVDHPGFGATIIGRVLEDAGFKVGIIAQPNWEDTKDFTKLGKPRLFFAVTSGNTD 96 
                                   9******************************************************************************** PP

                 Radical_SAM_N  82 smvnkytaekklrsdDaytpggkagkRPdravivYsnlireaykdvpvvlGgiEaSLRriahYDywsdkvrrsilldskad 162
                                   smv++yt + k r +D+y+pggk g RP rav+vYsn+++++y+dvp+++GgiEaSLRr+a++D+ws kvr+sil+d+ ad
  gi|91773723|ref|YP_566415.1|  97 SMVSNYTPALKPRPKDMYSPGGKPGLRPSRAVVVYSNRLKQTYPDVPIIIGGIEASLRRFAEFDHWSGKVRQSILADAPAD 177
                                   ********************************************************************************* PP

                 Radical_SAM_N 163 llvyGmgeraiveiakrlakgeeveelkdirgtavllkkea..kakek.....evielpsyeevkedkklyaeafrlleee 236
                                   llvyGmge ++ eia+rl++ge+++++++i+gt+++l+ ++  +ake+      ++e+psy+ev++dk +ya+af+l++++
  gi|91773723|ref|YP_566415.1| 178 LLVYGMGELQTPEIARRLDSGEDIRNINEIPGTTWKLEVKKwkEAKENdqipfPYVEMPSYNEVSKDKPTYAKAFKLMYDQ 258
                                   ***********************************88853322112212344589************************** PP

                 Radical_SAM_N 237 tnplnakalvqkhgdravvlnppalplsteelDevyelpyarkahpsykkkkipalemikfS 298
                                   ++p+++ +lvq h ++++v+npp+++ls++elD+vy+lpy+r+ hpsy k+ +pale++++S
  gi|91773723|ref|YP_566415.1| 259 QDPVRGITLVQPHPKTTIVQNPPMRQLSQKELDHVYDLPYTRREHPSY-KEPVPALETVRVS 319
                                   ************************************************.59*********98 PP

>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.0   1.3e-31   4.8e-28       1      86 [.     533     613 ..     533     621 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.3e-31
                       DUF3362   1 dqVqtFyPsPmatattmYhtgknpltkvkreeesvdvvrgekerrlhkAllrYhdpknwpllreALkkmGredLiGngkkh 81 
                                   +qVq+F P+Pm+ at+m+htg++p t       +v+v+ + +e+++++A+++Y+dpkn+ l+ e Lk++ r+dLiGn  ++
  gi|91773723|ref|YP_566415.1| 533 EQVQDFIPTPMTAATCMFHTGLDPFT-----GKPVYVATSRREKNIQRAMMHYRDPKNYGLIFEGLKNADRQDLIGNTWNC 608
                                   7*************************.....99************************************************ PP

                       DUF3362  82 Liptf 86 
                                   Lip  
  gi|91773723|ref|YP_566415.1| 609 LIPRK 613
                                   ***76 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.2     8e+03      92     115 ..      19      42 ..      10      83 .. 0.70
   2 !   57.5   0.3   5.9e-19   2.1e-15       2     167 .]     321     525 ..     320     525 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                                   HHHHHHHHTT-SEEEEEEBSSSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  92 eklerllelgvdrvslgleaadde 115
                                     ++ ++ +g+d++ + + ++d  
  gi|91773723|ref|YP_566415.1|  19 MDIKDIKSRGWDQLDIIIVTGDAY 42 
                                   567777777777777666555544 PP

  == domain 2  score: 57.5 bits;  conditional E-value: 5.9e-19
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEESSTGGGS.................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.................... RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg..vkevilgggeplly.................... 60 
                                   ++ rgC + CsfCa+ ++  +++   s+s+++il+e++ l  ++   ++++i +gg p+++                    
  gi|91773723|ref|YP_566415.1| 321 TTHRGCFGSCSFCAIAQH--QGRMITSRSIDSILREAELLT-RMKefKGNIIGVGG-PSANmyamkcknwenkgackdklc 397
                                   6789*************8..********************5.66664666666666.************************ PP

                                   .............TTHHHHHHHHHHTCCCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  61 .............pdfvellerlaklavpgiritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmn 122
                                                ++ +e l++l++   p+++ ++++ g++ d     +e++ +l +++   ++ +  e++++  v + m 
  gi|91773723|ref|YP_566415.1| 398 lypepcpsmdtshKENIEMLRQLREM--PEVKRVFVSYGVRYDlalqdPEYITELCQYHvSGQLKIAPEHFSKS-VTDCM- 474
                                   *************9999********9..9******************************99*************.*****. PP

                                   CTSHHHHHHHHHHHHHHTTSET.......EEEEEEEBTTTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 123 rghtfeevlealeklreagikr.......vvdrivglpGendeeleellell 167
                                   +++++e + +  ++++e + kr       v++ + g+p  +++ + el+e++
  gi|91773723|ref|YP_566415.1| 475 KKPGREVFEKFAKIFKETN-KRlnkdqylVTFLMSGHPACTMDNMIELAEYI 525
                                   6677777777777777774.333667999***************99999875 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   5.5e-05       0.2       4      54 ..      37      86 ..      34     118 .. 0.75
   2 !    6.6   0.0    0.0021       7.7      72      93 ..     132     153 ..     124     161 .. 0.84
   3 ?   -2.3   0.0       1.2   4.3e+03      42      92 ..     356     377 ..     338     385 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                   B12-binding  4 llatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdv 54
                                  + + ++ d++ +G+ ++ ++l+dagf+V ++ a+ + ed+ +  +  kp++
  gi|91773723|ref|YP_566415.1| 37 VTGDAYVDHPGFGATIIGRVLEDAGFKVGII-AQPNWEDTKDFTKLGKPRL 86
                                  6677889*********************998.5555577766666666665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0021
                   B12-binding  72 vellkrirprvkvvvGGahpsl 93 
                                    ++lk+  p+v++++GG+ +sl
  gi|91773723|ref|YP_566415.1| 132 SNRLKQTYPDVPIIIGGIEASL 153
                                   46799*************9887 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                   B12-binding  42 divaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahps 92 
                                   +++ +++++k                             + ++ vGG+ ++
  gi|91773723|ref|YP_566415.1| 356 ELLTRMKEFK-----------------------------GNIIGVGGPSAN 377
                                   3333333333.............................346666665543 PP

>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.9e-05      0.18      54     105 ..     466     518 ..     435     541 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-05
                        DUF523  54 aelakr.vlkkegedvtealekgaeealeelkeeeikgailkekSPSCGveki 105
                                      + + ++kk g++v e+++k+ +e+ ++l++ +  +  l+++ P+C ++++
  gi|91773723|ref|YP_566415.1| 466 FSKSVTdCMKKPGREVFEKFAKIFKETNKRLNKDQYLVTFLMSGHPACTMDNM 518
                                   33333348999***************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3920.37
//
Query:       gi|91773724|ref|YP_566416.1|  [L=211]
Description: beta-lactamase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  112.2   0.1    3.5e-32  112.0   0.1    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    9.6e-09   35.0   0.2    1.3e-08   34.6   0.2    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.4e-05   25.0   0.1    2.4e-05   24.3   0.1    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
    0.00024   20.6   0.1    0.00047   19.6   0.1    1.4  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 !  112.0   0.1   7.9e-36   3.5e-32       3     197 .]      10     188 ..       8     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 7.9e-36
                                   CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                   Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                   p  +nsyli   ++ iLiD+G++t++  ++    +++ +p++++ +ilTH+H+DH+++++ ++e  ++p+++++++a al+
  gi|91773724|ref|YP_566416.1|  10 PYASNSYLI---NEKILIDPGMDTDQLIQKI---KEHTQPENIELIILTHSHFDHCAAAKAVAEICNAPIAIHKDDAQALK 84 
                                   5689*****...7****************97...*********************************************** PP

                                   CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHHCCCCCC. CS
                   Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.agetgridlt 163
                                     e+  +  +    ++++++d+++  e+++ +   + ++l+v+++pgh++g+++++ ++ k lf+GD+++ +g +gr+d+ 
  gi|91773724|ref|YP_566416.1|  85 SKEESVSILFS---APAPDIDPDILYENGDIIKISETESLEVIHTPGHTPGGISLYEPSSKSLFSGDTVFpNGGIGRTDF- 161
                                   ****7766666...69******************************************************9999999999. PP

                                   TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 164 lrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                           +++ +k+  s++kl +l++ +l+pgH
  gi|91773724|ref|YP_566416.1| 162 -------TGGSLDKLSVSIEKLTELDVITLYPGH 188
                                   .......999999999999*************** 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 !   34.6   0.2     3e-12   1.3e-08       2      75 ..      21      88 ..      20     162 .. 0.63

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3e-12
                                  EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCG CS
                 Lactamase_B_2  2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfv 75
                                   iLiD+g d+ q      q+ +   +++ i++++lth+H+DH+a +  ++e+++  +p+  +k+ ++ l+++  
  gi|91773724|ref|YP_566416.1| 21 KILIDPGMDTDQLI----QKIKEHTQPENIELIILTHSHFDHCAAAKAVAEICN--APIAIHKDDAQALKSKEE 88
                                  69*******65442....22334556889**********************998..566666666666665533 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 !   24.3   0.1   5.5e-09   2.4e-05      12      68 ..      18      78 ..      10     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.5e-09
                 Lactamase_B_3 12 letagarilvDPf.......kanlgyeppaeeaDlvlisqaledHahlet.lkqlaenvkvleeg 68
                                  +   + +il+DP+       + +++   ++e+++l+++++++ dH+++++ ++++ + +  ++++
  gi|91773724|ref|YP_566416.1| 18 I---NEKILIDPGmdtdqliQ-KIKEHTQPENIELIILTHSHFDHCAAAKaVAEICNAPIAIHKD 78
                                  5...468******77765421.67777778****************8764144543333334433 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.1e-07   0.00047       6      53 ..      19      63 ..      17      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-07
                 Lactamase_B_6  6 nvkiLlDvGwdeskvslesalkelekvi..ptvdliLLshatlehlGaya 53
                                  n kiL+D+G+d       + +++++++   ++++li+L+h+  +h +a  
  gi|91773724|ref|YP_566416.1| 19 NEKILIDPGMDTD-----QLIQKIKEHTqpENIELIILTHSHFDHCAAAK 63
                                  569********85.....56888888864479*************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1293.22
//
Query:       gi|91773725|ref|YP_566417.1|  [L=281]
Description: TatD-related deoxyribonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-69  234.5   0.2    1.5e-69  234.3   0.2    1.0  1  TatD_DNase  TatD related DNase
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.18   11.7   0.0    1.2  1  PXA         PXA domain


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 !  234.3   0.2   1.6e-73   1.5e-69       1     254 [.      35     279 ..      35     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.3 bits;  conditional E-value: 1.6e-73
                                   EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH.HHH CS
                    TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel.kel 80 
                                   iD+HcHld+++f++dr++++era++agv ++v+ g+++k+++a+l+la++y+  +y+++G+ P  v +  +++ + +  +l
  gi|91773725|ref|YP_566417.1|  35 IDSHCHLDFPKFNRDRDKTIERAHNAGVVKMVNSGIDLKTNQATLALANEYDF-IYPTIGLSPLIVSHYGNEVANSIlLQL 114
                                   8***************************************************9.**********99999777776651555 PP

                                   HHCCCTSEEEEEEEEEET.-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S- CS
                    TatD_DNase  81 anvkhskvvaiGeiGLDy.ysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgs 160
                                    +++ +++v+iGe GLDy y++e++++e+q++ F++ +++A+++++ lviH r+aeed+ e++k+++    kvv+H++ gs
  gi|91773725|ref|YP_566417.1| 115 -ELHAEQAVGIGEAGLDYhYYKEDKEREHQKQYFRKVIEIAEKYEKTLVIHGREAEEDCFEMVKDLD----KVVFHCYGGS 190
                                   .99999************779********************************************84....79******** PP

                                   HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHH CS
                    TatD_DNase 161 aeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltlee 241
                                   +e+a+++ + gyyis++ +++f  ++++++++++vpl+++LiETD+Pyl+p   r+ rnepa+v   + ++ae+k+ ++e+
  gi|91773725|ref|YP_566417.1| 191 IETAARINDAGYYISIPTIVCF--SEHHKKIAENVPLNKMLIETDSPYLSP---RKGRNEPAFVLDNLSVIAEAKGTDIET 266
                                   **********************..789************************...789************************ PP

                                   HHHHHHHHHHHHH CS
                    TatD_DNase 242 laeitaeNakrlf 254
                                   +a++t  N+k++f
  gi|91773725|ref|YP_566417.1| 267 IANATFRNTKKIF 279
                                   ***********99 PP

>> PXA  PXA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05      0.18      37     132 ..       4     152 ..       2     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                           PXA  37 vrsilrsviralanrlkkvDlaqllltrlldlltshl....rdyrqaeekvkskkae..................eesdld 95 
                                   +++++  ++ ++++ +++++++ + ++++l++++sh+      +++ ++k+ +   +                  ++ +l+
  gi|91773725|ref|YP_566417.1|   4 IYNVISIALTSIEALVTAINML-FNIRSMLKVIDSHChldfPKFNRDRDKTIE---RahnagvvkmvnsgidlktNQATLA 80 
                                   7889999999999999999977.556***********6555333333333333...244588889999*****99888888 PP

                           PXA  96 laakffalephpalsavlrd...................................ieeskeaelaylrslve 132
                                   la+++    p ++ls+++ +                                   +++++e +++y+r+++e
  gi|91773725|ref|YP_566417.1|  81 LANEYDFIYPTIGLSPLIVShygnevansillqlelhaeqavgigeagldyhyykEDKEREHQKQYFRKVIE 152
                                   888888877777777666667777777777777777777888888899999997777778889******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2086.48
//
Query:       gi|91773726|ref|YP_566418.1|  [L=418]
Description: hypothetical protein Mbur_1779 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2666.49
//
Query:       gi|91773727|ref|YP_566419.1|  [L=79]
Description: hypothetical protein Mbur_1780 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.7   1.3      0.021   14.5   1.3    1.2  1  RPW8      Arabidopsis broad-spectrum mildew resistance protei
      0.041   12.6   1.1      0.048   12.4   1.1    1.0  1  Rabaptin  Rabaptin
       0.16   11.9   2.5       0.91    9.5   2.3    2.0  2  NitrOD1   Nitrosopumilus output domain 1


Domain annotation for each model (and alignments):
>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.3   3.4e-06     0.021      94     138 ..      23      67 ..       3      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-06
                          RPW8  94 yrYkkklkeLekslrkfvqvelqvqqvrdikellakmkelntkld 138
                                    rY+ +++e++ ++ + ++ +++ + ++d+ke+ a +  ++  +d
  gi|91773727|ref|YP_566419.1|  23 IRYEDQIEEIDRKVQEAINDNVKFDLCQDRKEIQARLDTTKACID 67 
                                   58*********************************9998887776 PP

>> Rabaptin  Rabaptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.1   8.1e-06     0.048     163     224 ..       5      67 ..       3      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-06
                      Rabaptin 163 edemkkaqedaeklrsvvmpmekeiaalkekltea.edkikeleaskvkelnhyleaekscrt 224
                                   ++em  a + +ekl+  v+  e +i  +  k+ ea +d++k       ke++  l++ k+c  
  gi|91773727|ref|YP_566419.1|   5 NQEMYDAAKKSEKLKWDVIRYEDQIEEIDRKVQEAiNDNVKFDLCQDRKEIQARLDTTKACID 67 
                                   789******************************996789998889999*************65 PP

>> NitrOD1  Nitrosopumilus output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.028   1.7e+02      55      66 ..       4      15 ..       1      19 [. 0.87
   2 ?    9.5   2.3   0.00015      0.91      36      68 .]      13      45 ..       5      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.028
                       NitrOD1 55 inqklveaikke 66
                                  inq++ +a kk 
  gi|91773727|ref|YP_566419.1|  4 INQEMYDAAKKS 15
                                  9*********97 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00015
                       NitrOD1 36 kvceiverdvsisGdeieqinqklveaikkeik 68
                                  k+ e ++ dv    d+ie+i++k+ eai  ++k
  gi|91773727|ref|YP_566419.1| 13 KKSEKLKWDVIRYEDQIEEIDRKVQEAINDNVK 45
                                  56677888888899**************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1540  (0.0858944); expected 358.6 (0.02)
Passed bias filter:                      875  (0.0488036); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 508.99
//
Query:       gi|91773728|ref|YP_566420.1|  [L=442]
Description: 2-isopropylmalate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  211.1   5.1      4e-62  210.2   5.1    1.5  1  HMGL-like   HMGL-like
    4.9e-32  110.6   1.5      1e-31  109.6   1.5    1.6  1  LeuA_dimer  LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
      0.049   14.1   0.0       0.75   10.2   0.0    2.3  2  DUF5541     Family of unknown function (DUF5541)


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 !  210.2   5.1   6.7e-66     4e-62      53     264 .]       2     208 ..       1     208 [. 0.98

  Alignments for each domain:
  == domain 1  score: 210.2 bits;  conditional E-value: 6.7e-66
                                   HHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ET CS
                     HMGL-like  53 evvraiakavkkarilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdv 133
                                   e+vr+ia+a+ ++++++l+r   kd++a ++    ag+ ++h+f++ts++++ + +kk+reev++++++av++++++g+++
  gi|91773728|ref|YP_566420.1|   2 ESVRNIANAGLTSEVCGLARVLTKDLDACID----AGVGMIHTFVSTSDIQRIHTIKKSREEVVEMSVNAVQYIKDHGMRC 78 
                                   89*****************************....********************************************** PP

                                   TT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHH CS
                     HMGL-like 134 elsledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAve 214
                                    +s++da+rtdl++l+ev+ a+e+aG+++in++DtvG++ P+ +++lis+l ++++  +++ +HcHnd+GlAvan+l+A+e
  gi|91773728|ref|YP_566420.1|  79 MFSAMDATRTDLDYLIEVYRAVEDAGCDIINVPDTVGIIAPSGMYRLISKLDKEMN--IPIDTHCHNDFGLAVANSLMAIE 157
                                   ********************************************************..*********************** PP

                                   TT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                     HMGL-like 215 aGadrvdgtvnGlGeraGnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                   aGa++  +tvnGlGeraGna+l e v+ l+    ++t ++++ + ++a++v
  gi|91773728|ref|YP_566420.1| 158 AGASQAQVTVNGLGERAGNADLAETVMSLHSIYgAKTSINTEYIVETARMV 208
                                   *****************************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 !  109.6   1.5   1.7e-35     1e-31       2     133 .]     306     440 ..     305     440 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.7e-35
                                   XXXXXXXXXXXXXXXXXX..--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T-EE CS
                    LeuA_dimer   2 vtdedlealvkdelleae..erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..dikL 78 
                                   +td dl++++ d l+++e    + l++++v++g+ ++sta+vk+   +g+e ++s +G GpvdA+l+A++ ++g+  ++++
  gi|91773728|ref|YP_566420.1| 306 ITDSDLYTIAFDILGKPEgmPAIDLKEVSVMTGNITTSTAVVKALF-NGKECVTSNVGIGPVDAALKAVETLIGQhaKVTI 385
                                   8***************997789************************.****************************7777** PP

                                   EEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHHS CS
                    LeuA_dimer  79 ldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrll 133
                                    d++++a+t+g+da+aev + +++d+g++v+++++++div AS++Al+ a+n+ll
  gi|91773728|ref|YP_566420.1| 386 HDFRIEAVTGGSDALAEVVIGVQNDNGRIVTARAANADIVLASVEALVTAINMLL 440
                                   ***********************999**************************985 PP

>> DUF5541  Family of unknown function (DUF5541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00013      0.75      73     100 ..     214     240 ..     183     245 .. 0.86
   2 ?    1.0   0.0     0.091   5.4e+02      65     103 ..     356     394 ..     335     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                       DUF5541  73 gpippatpvvdgnhfqhpagdchpygil 100
                                     ipp +pvv  n f h +g  h +g+l
  gi|91773728|ref|YP_566420.1| 214 VQIPPHMPVVGENAFAHESG-IHTHGVL 240
                                   469**************998.6888887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.091
                       DUF5541  65 eqsnhagmgpippatpvvdgnhfqhpagdchpygilclq 103
                                     +   g+gp+  a+  v+    qh     h + i ++ 
  gi|91773728|ref|YP_566420.1| 356 CVTSNVGIGPVDAALKAVETLIGQHAKVTIHDFRIEAVT 394
                                   456678**************999*999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2965.31
//
Query:       gi|91773729|ref|YP_566421.1|  [L=247]
Description: UbiA prenyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-31  107.4  11.3      9e-31  107.1  11.3    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        2.2    8.0  15.9        2.5    7.8   3.7    3.3  2  DUF21     Cyclin M transmembrane N-terminal domain


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 !  107.1  11.3     1e-34     9e-31      21     201 ..      40     216 ..      16     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 1e-34
                          UbiA  21 lllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllall 101
                                    l++ ++ ++l+ + +  +NdyfD++iD  ++r ++RP+v G is+ +al +a+v+++l+++ + l+l+ +  +++ +++l
  gi|91773729|ref|YP_566421.1|  40 YLIAGTVSIFLFMG-SFSINDYFDHKIDIVNNR-KDRPIVIGTISRSKALNIATVCFFLAFFTS-LFLGVFPSIFIGFNIL 117
                                   44555555555554.5589***********855.9*****************************.**************** PP

                          UbiA 102 lyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvv 182
                                   l++vY+   lK++ ll++++++ +f   +l+g  +v + ++ l+ +++++ fl+ +a+ ++ d+ d+ gD + +ikt++  
  gi|91773729|ref|YP_566421.1| 118 LAIVYS-SHLKKVLLLKNITIAYCFMATILFGTIIVDNRIDQLVGFYMIMAFLVGFAFEIMADISDMIGDMQHNIKTIASF 197
                                   ******.69************************************************************************ PP

                          UbiA 183 lGrkaarillalllavlll 201
                                   + +++a++++ ++ + ++l
  gi|91773729|ref|YP_566421.1| 198 HSPRVAAFVSSFFFISIFL 216
                                   ****999953333333333 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 ?    7.8   3.7   0.00028       2.5      48     107 ..       3     110 ..       1     132 [. 0.77
   2 ?    2.3   6.2     0.014   1.2e+02     106     135 ..     192     221 ..     114     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00028
                         DUF21  48 nperlLstlligntlvnillsalatalfvellae............................................... 81 
                                   ++  +L+ + +gn+l  ++++++a++l vel+++                                               
  gi|91773729|ref|YP_566421.1|   3 QLRPYLALTRFGNSLFGTFSVSIAGVLSVELIGNeidyliagtvsiflfmgsfsindyfdhkidivnnrkdrpivigtisr 83 
                                   56679999************************9888888887777777777777788888888888888888888888876 PP

                         DUF21  82 .galavviatvivtllilvfgEilPks 107
                                    +al ++ + +++ +++ +f  ++P +
  gi|91773729|ref|YP_566421.1|  84 sKALNIATVCFFLAFFTSLFLGVFPSI 110
                                   555555555567777777887777765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.014
                         DUF21 106 kslalkyaekialalapplrvlmvllyPlv 135
                                   k++a  ++ ++a++++ ++ + ++l+ Pl 
  gi|91773729|ref|YP_566421.1| 192 KTIASFHSPRVAAFVSSFFFISIFLFDPLP 221
                                   99*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1831.26
//
Query:       gi|91773730|ref|YP_566422.1|  [L=475]
Description: dihydrolipoamide dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-46  158.7   0.0    2.6e-46  158.2   0.0    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.7e-18   66.9   0.0    3.6e-18   65.8   0.0    1.6  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    1.9e-15   57.2   0.0    4.9e-15   55.8   0.0    1.8  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.8e-10   40.6   0.0    2.7e-10   40.0   0.0    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    5.2e-06   25.8   0.0      0.022   13.9   0.0    2.8  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.031   14.2   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.026   13.9   0.0      0.044   13.2   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.066   12.5   0.0       0.14   11.4   0.0    1.6  1  Thi4           Thi4 family
      0.066   13.7   0.0       0.13   12.7   0.0    1.5  1  NAD_binding_7  Putative NAD(P)-binding
       0.14   11.8   0.0        3.6    7.2   0.0    2.3  2  ApbA           Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.2   0.0   1.4e-49   2.6e-46       1     282 [.       4     313 ..       4     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 1.4e-49
                                   CSEEEE--SHHHHHHHHHHHHH.TS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqa.gakvtlve...legtclnggcllskallgvaedaeias.................... 57 
                                   +d++viG+G +   ++l ++q+ ++k+++++    +g cl++gc++sk ll  ae  +++                     
  gi|91773730|ref|YP_566422.1|   4 YDLIVIGSGSGMNYVSLIIQQYpEMKIAVIDkdkPGGICLTRGCIPSKMLLYPAELVREIGkanrfgidaeiksidfkfvm 84 
                                   689******************66*******99999****************9999988888899**999544444444333 PP

                                   .HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC....................TCEEEEEESEEEE---EEE-BCTCT CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 .evvkklnqgielllgeevvkidpgkkkvklekkke....................gdeekiaydklvlAtGssprdlgip 117
                                    +                  +id++ + ++   +++                      ee i+ + ++l +Gs+p +++++
  gi|91773730|ref|YP_566422.1|  85 eR---------------MRSSIDKDIEMIHH-GLSSdpnldyyehvakfvepyvleIGEELITSKMIFLSIGSKPMIPPVK 149
                                   31...............34555555533333.22223555566666666778888855689******************** PP

                                   TC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 118 GvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGv 198
                                   G+     + +++l+s+  l+l  lpk+++++GgGyi+ E+  +++ +g++vt++ + +r++ + ++e+s+ +++++ +  v
  gi|91773730|ref|YP_566422.1| 150 GL-----DDISYLTSDTVLELTTLPKSLAIIGGGYIAAEYGHFFSAMGSKVTIIGRSPRIVDNEEPEISELARKKMAR-YV 224
                                   **.....33489****************************************************************99.6* PP

                                   EEEESCEEEEEEETTEEEEEEETTSCE.....EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 199 evklgtsvkeidgngeklevvledgee.....idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiya 273
                                   ++ + ++v ei + g++ + v +d ++     i +d v+va+G++p+t++l  ek g+e+derg+i+v+++l+t++ +++a
  gi|91773730|ref|YP_566422.1| 225 DIITDHEVSEIHPSGRQKKIVAKDRNSenemeILVDEVLVATGRSPNTDILHpEKGGIETDERGWIKVNDHLETTCSNVWA 305
                                   ***************95556666655556777************************************************* PP

                                   -GGGCTECC CS
                                   xxxxxxxxx RF
                   Pyr_redox_2 274 iGDvaggkg 282
                                    GD   g++
  gi|91773730|ref|YP_566422.1| 306 FGDAN-GQY 313
                                   ***76.444 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 !   65.8   0.0     2e-21   3.6e-18       1     109 [.     343     454 ..     343     455 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2e-21
                                   BEEEEESSSEEEEEES-HHHHHHHHSG..EEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHH CS
                 Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagie..ikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqel 79 
                                   +p ++f+ pe+a vG++e  A ++++e  i++g  +f+++g+ +a++ ++ fvK++   + + +lGahi+Gp+a+ li++l
  gi|91773730|ref|YP_566422.1| 343 VPYAIFSYPEIAGVGIGESAAIEQYGEdnISIGFHRFEDTGKGMAMGLDSYFVKVILGDSGNTLLGAHIIGPQASILIHQL 423
                                   799****************************************************************************** PP

                                   HHHHHTTSBHH.HHHTSBSSSSSTGGGGHCH CS
                 Pyr_redox_dim  80 avaikagltve.dladtihihPtlsealkea 109
                                    ++++   +    + + + ihP+lse++k a
  gi|91773730|ref|YP_566422.1| 424 ITLMNTPGSNVgPVVNGMDIHPSLSEVVKRA 454
                                   ***9997766659*************99976 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   2.8e-18   4.9e-15       2      79 ..     172     247 ..     171     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 2.8e-18
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                   ++++GgGyi+ E++ +++++g+kVt++ rs+++  ++++e+s++ ++k+ +  ++++++++v ei+ s+++ ++++ k
  gi|91773730|ref|YP_566422.1| 172 LAIIGGGYIAAEYGHFFSAMGSKVTIIGRSPRIVDNEEPEISELARKKMARY-VDIITDHEVSEIHPSGRQ-KKIVAK 247
                                   79************************************************99.*************88886.567766 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 !   40.0   0.0   1.5e-13   2.7e-10     107     302 ..     114     304 ..     109     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.5e-13
                   Pyr_redox_3 107 vkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhys.kvkefhkyagqkvvViGgknSavDaAlelvrk 186
                                   v+k  e +++e  +e +++k +++++G   kP  + ++G ++ +  +s +v e+  +  + +++iGg+  a+++   + ++
  gi|91773730|ref|YP_566422.1| 114 VAKFVEPYVLEIGEELITSKMIFLSIGS--KPMIPPVKGLDDISYLTSdTVLEL-TTLPKSLAIIGGGYIAAEYGHFFSAM 191
                                   6677777889999999***********9..***********8554444044455.455899******************** PP

                   Pyr_redox_3 187 gaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvev....kddvvl 263
                                   g++Vt++ r+  i ++e   + +++   +++++++     +++++++ev ei+ + ++ k+ ++d ++ ++     d+v++
  gi|91773730|ref|YP_566422.1| 192 GSKVTIIGRSPRIVDNE---EPEISELARKKMARY-----VDIITDHEVSEIHPSGRQKKIVAKDRNSENEmeilVDEVLV 264
                                   **********9888875...445777888888776.....56778888888887766666654443332222335799999 PP

                   Pyr_redox_3 264 atGykpdlsflkk..slfeldedgrpvlteeteetnvpglf 302
                                   atG +p++++l+    ++e+de g+++++++ e t  ++++
  gi|91773730|ref|YP_566422.1| 265 ATGRSPNTDILHPekGGIETDERGWIKVNDHLETT-CSNVW 304
                                   ***********98889*************987655.66665 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.41   7.4e+02       3      35 ..       4      35 ..       2      38 .. 0.51
   2 !   13.9   0.0   1.2e-05     0.022     146     231 ..     129     207 ..     119     216 .. 0.80
   3 !    8.4   0.0   0.00057         1     293     339 ..     222     267 ..     211     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.41
                   K_oxygenase  3 lDligiGiGp..snLsLailleevkkelkalfler 35
                                  +Dli iG G     +sL+i  ++ + e+k+ ++++
  gi|91773730|ref|YP_566422.1|  4 YDLIVIGSGSgmNYVSLII--QQYP-EMKIAVIDK 35
                                  7888887765103344444..3333.456666655 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                   K_oxygenase 146 elearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelklvtrse 226
                                    ++++ + l++G++p iP+v + l+ +   + s+++le +     +k++a++G+G  aae  +   +  +  +++++ rs+
  gi|91773730|ref|YP_566422.1| 129 LITSKMIFLSIGSKPMIPPV-KGLD-DISYLTSDTVLELT---TLPKSLAIIGGGYIAAEYGHFFSAMGS--KVTIIGRSP 202
                                   567899************97.5577.58899999999887...7899*************7666555544..788888887 PP

                   K_oxygenase 227 alepl 231
                                   ++   
  gi|91773730|ref|YP_566422.1| 203 RIVDN 207
                                   77655 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00057
                   K_oxygenase 293 erlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                   + + +++++ev +++ +g+ + ++  ++++s++e ++ vd v++ATG
  gi|91773730|ref|YP_566422.1| 222 RYVDIITDHEVSEIHPSGR-QKKIVAKDRNSENEMEILVDEVLVATG 267
                                   34899*************6.99************************9 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05     0.031       2      71 ..     172     239 ..     171     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisftt 71 
                                   +a+iG G + a+  + f + g +V+++ +s++++++ + +i++ l++ + ++ ++   +++ +++i+++ 
  gi|91773730|ref|YP_566422.1| 172 LAIIGGGYIAAEYGHFFSAMGSKVTIIGRSPRIVDNEEPEISE-LARKKMARYVD-IITDHEVSEIHPSG 239
                                   69***************************************98.44433333333.44445555555554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.044      37      97 ..     170     229 ..     157     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                   SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE CS
                  2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivsl 97 
                                   k ++iiG G I+ +  + ++a+g kv+++ rs++  +  ee +++    +++ +  Di++ 
  gi|91773730|ref|YP_566422.1| 170 KSLAIIGGGYIAAEYGHFFSAMGSKVTIIGRSPRIVD-NEEPEISELARKKMARYVDIITD 229
                                   789*****************************99776.66667777888888888888875 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.9e-05      0.14      17      69 ..       3      54 ..       1      71 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEE CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivv 69
                                  e D++++G+Gs     + ++ + p++k+a++++   pGG     G + s++++
  gi|91773730|ref|YP_566422.1|  3 EYDLIVIGSGSGMNYVSLIIQQYPEMKIAVIDKD-KPGGICLTRGCIPSKMLL 54
                                  78********7655666666666********987.678777777777777765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.5e-05      0.13       8      55 ..     170     220 ..     165     274 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                 NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev...keeleelvklaeeel 55 
                                   k+  ++GgG +Aa+  + + + g kvt++        +e +e+ +la++++
  gi|91773730|ref|YP_566422.1| 170 KSLAIIGGGYIAAEYGHFFSAMGSKVTIIGRSPrivDNEEPEISELARKKM 220
                                   6778************************96553334233334444444443 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.002       3.6       2      33 ..     173     204 ..     172     236 .. 0.89
   2 ?    2.1   0.0     0.077   1.4e+02      93     117 ..     429     453 ..     418     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                                   EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHH CS
                          ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrrl 33 
                                   ai+G G i   +++  ++ g +vt+i+rs+r+
  gi|91773730|ref|YP_566422.1| 173 AIIGGGYIAAEYGHFFSAMGSKVTIIGRSPRI 204
                                   8****************************954 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.077
                                   CTCEEEEEESSSSCHHHHHTTTSTT CS
                          ApbA  93 dpntvvlllqNGlgheeelrealpk 117
                                   +p ++v ++ NG++ +  l e +++
  gi|91773730|ref|YP_566422.1| 429 TPGSNVGPVVNGMDIHPSLSEVVKR 453
                                   68899**************999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        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: 00:00:00.43
# Mc/sec: 3300.06
//
Query:       gi|91773731|ref|YP_566423.1|  [L=471]
Description: sodium/glutamate symporter [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-12   47.4  17.0    5.8e-11   41.7  10.4    2.4  2  Glt_symporter  Sodium/glutamate symporter
  ------ inclusion threshold ------
        1.4    8.8   7.6       0.71    9.7   2.1    3.2  2  CoxIIa         Cytochrome c oxidase subunit IIa family


Domain annotation for each model (and alignments):
>> Glt_symporter  Sodium/glutamate symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.5   4.8e-05      0.43       8      45 ..       9      46 ..       4      58 .. 0.90
   2 !   41.7  10.4   6.5e-15   5.8e-11     103     321 ..     121     366 ..      83     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 4.8e-05
                 Glt_symporter  8 tlvvailvlllGkalvkkvkfLkkfniPepvvgGliva 45
                                  +++v  ++lllGk +    + ++k+ iP++++gG+++ 
  gi|91773731|ref|YP_566423.1|  9 SFLVLGVILLLGKWIRVMSPPIQKLFIPSSLIGGFLAL 46
                                  67788899***************************864 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 6.5e-15
                 Glt_symporter 103 liviqnlvGvslasllgldpllGl..laGs...islsGGhGtaaawakvladkyglqnalevalacatfGlvlGGliGgPv 178
                                   ++  q + G+ la++l l p++G+  +aG+   is++GGhGtaa  + ++++  g+++a+++al  at+G+++G ++G  +
  gi|91773731|ref|YP_566423.1| 121 IAWGQYVFGI-LAAILILTPFFGMdpMAGAlleISFEGGHGTAAGMSATFEEL-GFSDATDLALGLATVGILFGVILGIVL 199
                                   5556777887.56677889999987789975558*****************99.*************************** PP

                 Glt_symporter 179 akfLikrnk...lkeekeedtkeevleea...fekekekrkit.akslle....tlaliliclvvgkylsalv...ke... 242
                                     + ++  k   lk++++    +e+ +++   f+  +++ kit   + +e     +a + +++ +g+ + +++   ++   
  gi|91773731|ref|YP_566423.1| 200 LNYGVRSGKtsvLKDQSQLS-LSETYQKGiidFDARESAGKITtRPESIEplslHFAYVGVAIGIGYLILQALiwiEAitw 279
                                   ****9987733322222222.223333331113344444444414455651111567799999999876553312222322 PP

                 Glt_symporter 243 .......talelPtfvlalfvgvilrnllellklkk.veekavdvlgdvsLslfLalalmslkllelaklalpllvillvq 315
                                          +  +lP f la++ g+il+  l+++  +  ++ + +  +   sL + ++ a+ +l l+ + +  +p++++ +v 
  gi|91773731|ref|YP_566423.1| 280 gqatgiyLLAHLPLFPLAMIGGIILQMFLDKFDPYYtLDRDLMMRIQGLSLDILITSAIATLSLTVIGNNLMPFVILATVG 360
                                   334233223479*****************9998665277778889**********************99999999888887 PP

                 Glt_symporter 316 vvvlvl 321
                                   +v  ++
  gi|91773731|ref|YP_566423.1| 361 IVWNLI 366
                                   765433 PP

>> CoxIIa  Cytochrome c oxidase subunit IIa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.14   1.3e+03       6      16 ..     129     139 ..     128     141 .. 0.83
   2 ?    9.7   2.1   7.9e-05      0.71      11      27 ..     449     467 ..     447     469 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHH CS
                        CoxIIa   6 GaLavivvLta 16 
                                   G La i++Lt 
  gi|91773731|ref|YP_566423.1| 129 GILAAILILTP 139
                                   77999999995 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 7.9e-05
                                   HHHHHHHHHHHH..HHHHH CS
                        CoxIIa  11 ivvLtatILvFW..fgvFy 27 
                                   i+++t  I+vFW  +gvFy
  gi|91773731|ref|YP_566423.1| 449 ILIMTSVIMVFWagLGVFY 467
                                   89**********6557998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2941.83
//
Query:       gi|91773732|ref|YP_566424.1|  [L=116]
Description: nascent polypeptide-associated complex protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-18   64.5   2.2    8.5e-18   64.1   2.2    1.2  1  NAC         NAC domain
     0.0066   16.2   0.1      0.012   15.4   0.1    1.4  1  UBA_4       UBA-like domain
  ------ inclusion threshold ------
      0.046   13.5   0.1       0.16   11.8   0.0    1.8  2  HTH_10      HTH DNA binding domain
       0.13   12.6   0.0        2.9    8.3   0.0    2.8  3  E3_binding  e3 binding domain


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   2.2   1.9e-21   8.5e-18       1      56 [.      12      70 ..      12      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.9e-21
                           NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                  + K+++++k++g+   +i+g+e+V+ir++d k +vf++++V    ++g +ty+v+G++ee
  gi|91773732|ref|YP_566424.1| 12 PAKVKQMMKQMGIniDQIEGVEQVIIRTAD-KDIVFNDADVSimNAQGVDTYQVVGTPEE 70
                                  579***************************.***********99**************98 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.8e-06     0.012      11      33 ..      89     111 ..      80     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-06
                         UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                                   TG++ee A + L+++n+dL  Ai
  gi|91773732|ref|YP_566424.1|  89 TGVSEEAALESLKSANGDLAEAI 111
                                   9********************98 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.46   2.1e+03      25      35 ..      14      24 ..      12      30 .. 0.81
   2 ?   11.8   0.0   3.5e-05      0.16      28      52 ..      84     108 ..      80     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.46
                        HTH_10 25 tlkeLAkelGI 35
                                  ++k++ k++GI
  gi|91773732|ref|YP_566424.1| 14 KVKQMMKQMGI 24
                                  67888999999 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.5e-05
                        HTH_10  28 eLAkelGIskstlsehLrkaeskli 52 
                                    +A++ G+s+ +++e L++a   l+
  gi|91773732|ref|YP_566424.1|  84 LVAEQTGVSEEAALESLKSANGDLA 108
                                   58******************88775 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00065       2.9       7      23 ..      15      31 ..      14      37 .. 0.94
   2 ?    0.3   0.0      0.21   9.2e+02      11      24 ..      54      67 ..      52      68 .. 0.85
   3 ?   -1.1   0.0      0.56   2.5e+03       7      16 ..      82      91 ..      82     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00065
                                  HHHHHHHCT--TTTS-- CS
                    E3_binding  7 aRklAkelGidLsdvkG 23
                                  ++ + k++Gi+++++ G
  gi|91773732|ref|YP_566424.1| 15 VKQMMKQMGINIDQIEG 31
                                  899************88 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.21
                                  HHHCT--TTTS--- CS
                    E3_binding 11 AkelGidLsdvkGt 24
                                   + +G+d  +v+Gt
  gi|91773732|ref|YP_566424.1| 54 MNAQGVDTYQVVGT 67
                                  5678****9***98 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.56
                                  HHHHHHHCT- CS
                    E3_binding  7 aRklAkelGi 16
                                  +R  A++ G+
  gi|91773732|ref|YP_566424.1| 82 VRLVAEQTGV 91
                                  7889999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 834.75
//
Query:       gi|91773733|ref|YP_566425.1|  [L=107]
Description: HesB/YadR/YfhF [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-15   55.0   0.1    9.6e-15   54.7   0.1    1.0  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 !   54.7   0.1   5.3e-19   9.6e-15       3     108 ..       2     100 ..       1     102 [. 0.97

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 5.3e-19
                                   EEE-HHHHHHHHHHHHCTTEC...EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS. CS
                   Fe-S_biosyn   3 itlteaAaeklkkllaedkke...lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvfld 80 
                                   i++t+ Aa +lk+ll++++k+   lr++v   g       Cs g +y + l de  +e+d++++s+++k+++ ++ +++l 
  gi|91773733|ref|YP_566425.1|   2 IEITDIAATELKALLETEEKKdhaLRIFVAGMG-------CS-GVQYGMALDDEI-KEDDITVTSKDIKIVIGPDISEQL- 72 
                                   99***************99999**********9.......**.************.************************. PP

                                   TTEEEEEEEETTEEEEEEETCCEEEEEE CS
                   Fe-S_biosyn  81 eglvldfvedlgtlgLksdngilddnvg 108
                                   e+ ++d+ +++g+ g+  dn+ +++ +g
  gi|91773733|ref|YP_566425.1|  73 EEATVDYIDTDGGKGFIIDNPSVNSGCG 100
                                   99**********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 719.95
//
Query:       gi|91773734|ref|YP_566426.1|  [L=393]
Description: hypothetical protein Mbur_1788 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2750.02
//
Query:       gi|91773735|ref|YP_566427.1|  [L=254]
Description: hypothetical protein Mbur_1789 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-30  103.7   0.1    1.2e-29  103.4   0.1    1.1  1  ATPase    KaiC
    0.00021   20.6   0.0     0.0063   15.7   0.0    2.0  2  PAXNEB    PAXNEB protein
  ------ inclusion threshold ------
      0.045   13.3   0.1      0.082   12.4   0.1    1.4  1  DUF3201   Protein of unknown function (DUF3201)


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 !  103.4   0.1   1.9e-33   1.2e-29       1     226 [.      13     247 ..      13     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.9e-33
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   v+tg+  lD  l gG+p g+++l+  epG+   +fa+qF++ g+++  e + + + e p +++ e++k++Gw++ek  +eg
  gi|91773735|ref|YP_566427.1|  13 VPTGVVSLDVQLGGGVPPGTTILLLAEPGSSAEVFAQQFIYGGLKN-HEDVYYFSAEHPIQEIVEDMKNFGWNIEKQIDEG 92 
                                   79*****************************************999.********************************** PP

                        ATPase  82 klaiidasesaeesaee..........kdkedleelieelaeaikeika..krvviDsitgl..ayeekeavaReilrqlv 148
                                   k+ +ida++ +  ++            ++ +     +++l+ a  + +    r v+Dsi+ +  +ye ++     ++   +
  gi|91773735|ref|YP_566427.1|  93 KVDFIDAYTARVCNILPknaacnlsakDYLKLNTDTMNQLKAAATKERKgsYRGVVDSISYFlrSYELSSVIEAIEIISSI 173
                                   **********9876544567888755422222223444555544433323489********95334444333333344444 PP

                        ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikv 226
                                     l +  +  +++      ++ + ++ ++  ++dgvi  + +e  +e++R++ i+kmRg     k++ ++It++gi+ 
  gi|91773735|ref|YP_566427.1| 174 GKLTNAVQLVMMTDG---MHDPIVENTLKG-VCDGVIEFRMRERGSEIERSILIRKMRGMIPPDKTISYNITNKGIEL 247
                                   444444444555555...7899********.*********************************************97 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-06    0.0063      18      82 ..      12      75 ..       6      81 .. 0.81
   2 !    3.0   0.0    0.0077        46     184     303 ..     121     229 ..      76     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                        PAXNEB 18 ltStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewl 82
                                   + tG+ sLD  LgGG+p G+ +l+ ++   + a+v ++ F+  G+ ++ +v++ s+++  +e++
  gi|91773735|ref|YP_566427.1| 12 RVPTGVVSLDVQLGGGVPPGTTILLLAE-PGSSAEVFAQQFIYGGLKNHEDVYYFSAEHPIQEIV 75
                                  577*****************87666544.345599***********99999*9999977666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0077
                        PAXNEB 184 yssllnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliars 264
                                   y +l ++  ++lk+   ++   k   R v+ s+   l       + + +++++ + ++ ++ + +n+v l+ +   ++  +
  gi|91773735|ref|YP_566427.1| 121 YLKLNTDTMNQLKAAATKER--KGSYRGVVDSISYFLR------SYELSSVIEAIEIISSIGKLTNAVQLVMMTDGMH--D 191
                                   55555555555555222222..2356666666655544......5678889999999999999999999999999999..9 PP

                        PAXNEB 265 sslvrkieqlvDtvieLesfag.seketepalkseeyqGl 303
                                   + + + ++ ++D+vie    ++ se e +  ++  ++ G+
  gi|91773735|ref|YP_566427.1| 192 PIVENTLKGVCDGVIEFRMRERgSEIERSILIR--KMRGM 229
                                   99999**********987666666666665555..66666 PP

>> DUF3201  Protein of unknown function (DUF3201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.4e-05     0.082      91     125 ..      45      78 ..      41     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                   HH-SEEEEESS-TTT-EEEE..TTS---HHHHHHH CS
                       DUF3201  91 eafeklfiygaedfledvynclresplseevidri 125
                                   e f + fiyg  +  edvy    e+p+ e v + +
  gi|91773735|ref|YP_566427.1|  45 EVFAQQFIYGGLKNHEDVYYFSAEHPIQEIV-EDM 78 
                                   6899***********************7644.433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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 0.32s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1689.32
//
Query:       gi|91773736|ref|YP_566428.1|  [L=121]
Description: phosphoribosyl-AMP cyclohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-36  123.6   0.5    2.6e-36  123.3   0.5    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase
  ------ inclusion threshold ------
      0.077   13.2   0.1       0.14   12.4   0.1    1.5  1  DUF5514   Family of unknown function (DUF5514)


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3   0.5   2.9e-40   2.6e-36       1      74 []      29     102 ..      29     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 2.9e-40
                                   EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                        PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                   m+a+mn+ealekt+etg a+y+Srsr+klWkKGe+Sg++qkv+e+ +DcD Da++lk++q+g aCHtg++sCFy
  gi|91773736|ref|YP_566428.1|  29 MFAFMNREALEKTIETGIAHYWSRSRQKLWKKGESSGHMQKVHELLIDCDMDAIILKISQEGGACHTGYRSCFY 102
                                   9************************************************************************7 PP

>> DUF5514  Family of unknown function (DUF5514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.6e-05      0.14      72     112 ..      47      87 ..      31     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                       DUF5514  72 akkyritefelwkkhegdstydkgfgiviegsmdnpilkfk 112
                                   a+ +  +  +lwkk e     +k   ++i+  md  ilk+ 
  gi|91773736|ref|YP_566428.1|  47 AHYWSRSRQKLWKKGESSGHMQKVHELLIDCDMDAIILKIS 87 
                                   4455566789****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 717.41
//
Query:       gi|91773737|ref|YP_566429.1|  [L=618]
Description: ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-12   46.8   0.2    3.1e-12   46.1   0.2    1.3  1  T2SSE     Type II/IV secretion system protein
      8e-06   26.4   0.0    2.5e-05   24.8   0.0    1.9  2  PIN       PIN domain
      2e-05   24.3   0.3      7e-05   22.6   0.3    2.0  1  KH_1      KH domain
  ------ inclusion threshold ------
       0.03   13.7   0.2       0.12   11.7   0.0    2.1  2  ATPase    KaiC
      0.039   13.8   0.6       0.13   12.2   0.6    1.9  1  KH_4      KH domain
      0.042   14.2   0.0       0.17   12.2   0.0    2.1  2  AAA_16    AAA ATPase domain
      0.052   14.3   0.0       0.16   12.7   0.0    2.0  1  PIN_3     PIN domain
      0.094   12.5   0.0       0.26   11.1   0.0    1.7  1  AAA_29    P-loop containing region of AAA domain
       0.13   12.8   0.0       0.53   10.8   0.0    2.0  2  AAA_18    AAA domain
       0.17   12.0   0.0       0.57   10.3   0.0    1.9  2  AAA_33    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 !   46.1   0.2   1.7e-15   3.1e-12      46     245 ..     188     378 ..     154     404 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.7e-15
                         T2SSE  46 alerlisriaalakld...iseerplqdarlpekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevl 122
                                   +l+++i+++   a++d     e ++     l+ + +r+ ++++P + + e  ++R   +++++ldd+    +lke+   +l
  gi|91773737|ref|YP_566429.1| 188 ELKQIIRELLERARADdesFTEMSLKGATVLQIRDMRIAISTPPFSDDvEITAVR--PVASVSLDDYYLGDELKER---IL 263
                                   45555555544444331102233333333455899*************999****..4566789***998877765...55 PP

                         T2SSE 123 rkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqlega..nqvqlnakkakvtfadllraaLRlrPD 201
                                   ++       ilvsG+ g GK+t+   +  ++++++  + t+E p+ +q+ ++  ++  l+       +++    +L  rPD
  gi|91773737|ref|YP_566429.1| 264 AQR-----GILVSGPPGAGKSTFGAGVAIFLHENNYVVKTMESPRDLQVPNEitQYAPLEG-----SMEKTADVLLLVRPD 334
                                   555.....8***************999999999999999*********9543113333443.....456666667889*** PP

                         T2SSE 202 rimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeq 245
                                     +  E+R +  +ei   +     g ++ +Han a++a++rL  
  gi|91773737|ref|YP_566429.1| 335 YTIYDEVRKTRDFEIFADMRLAGVGMIGVVHANRAIDAVQRLIG 378
                                   ***************77666666666***************964 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.4e-08   2.5e-05       1     120 [.       9     123 ..       9     125 .. 0.80
   2 ?   -2.9   0.0       5.3   9.5e+03       3      15 ..     489     501 ..     487     505 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.4e-08
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHH CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaee 80 
                                   iv DTsv+i+ + +e         +e+  el++s++ +aEl   ++r+++  +k  +++++l++ +++  +    ++   +
  gi|91773737|ref|YP_566429.1|   9 IVPDTSVIIDGFLSEMVE---SGKYEG-IELFISEAMVAELESQANRGLDIGNKGLDELKQLQEmAREGMLDMSFTGKIPT 85 
                                   688*********555533...456666.99*****************6666666555555555537777777777888888 PP

                                   HHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                           PIN  81 aaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                   a+e +  +  +++Da+i ++A+  +++ + t D+  ++va
  gi|91773737|ref|YP_566429.1|  86 AEERMYAK-AGTIDAIIRSCAEDLDATFV-TGDKVQYDVA 123
                                   88888887.9****************999.****988887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.3
                                   E-HHHHHHHHTTS CS
                           PIN   3 lDTsvliallrge 15 
                                    DTs+++++l +e
  gi|91773737|ref|YP_566429.1| 489 SDTSAVVKVLGSE 501
                                   5******999766 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.3   3.9e-08     7e-05       4      40 ..     495     532 ..     492     544 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.9e-08
                                   EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT CS
                          KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sed 40 
                                   ++v  s ++++IGk G +I eI++  g++I+v + +e+
  gi|91773737|ref|YP_566429.1| 495 VKVLGSEISKVIGKSGVTIDEIEKIVGVHIDVRElDEK 532
                                   66777889****************99*****9865544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.8e-05      0.12      10      37 ..     256     283 ..     252     306 .. 0.85
   2 ?   -2.7   0.1       1.7   3.1e+03     101     131 ..     488     519 ..     471     524 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                        ATPase  10 eilkgGipegrvvlitGepGtGKtifal 37 
                                   + lk+ i  +r +l++G pG+GK++f++
  gi|91773737|ref|YP_566429.1| 256 DELKERILAQRGILVSGPPGAGKSTFGA 283
                                   445789999*****************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                        ATPase 101 kedleelieelaeaike.ikakrvviDsitgl 131
                                    +d++++++ l + i++ i+ + v iD i+ +
  gi|91773737|ref|YP_566429.1| 488 LSDTSAVVKVLGSEISKvIGKSGVTIDEIEKI 519
                                   56777778888777765256688899999876 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   7.2e-05      0.13      18      58 ..     483     520 ..     468     528 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-05
                          KH_4  18 vevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylv 58 
                                   v+v++    ++++  ++v g+++ +vIGk G t+d +  +v
  gi|91773737|ref|YP_566429.1| 483 VDVEML---SDTSAVVKVLGSEISKVIGKSGVTIDEIEKIV 520
                                   344443...4577889999***************9776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         2   3.6e+03       6      24 ..     186     205 ..     161     224 .. 0.74
   2 ?   12.2   0.0   9.6e-05      0.17      21     145 ..     264     399 ..     254     428 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                        AAA_16   6 eeeleqL.lsalervrsgrp 24 
                                    +el+q+ +++ler+r++++
  gi|91773737|ref|YP_566429.1| 186 SHELKQIiRELLERARADDE 205
                                   45555555666666655554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.6e-05
                        AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqllde........... 88 
                                   ++  + +l+sG++G GKs+    ++  l +++ ++ + +  ++l         ++q++  e+ +++ +d            
  gi|91773737|ref|YP_566429.1| 264 AQ--RGILVSGPPGAGKSTFGAGVAIFLHENNYVVkTMESPRDL----QVPNeITQYAPLEGSMEKTADVlllvrpdytiy 338
                                   44..68*************8877775555553333333333333....222224444444444444444422222233333 PP

                        AAA_16  89 aesaeleawrekleealaavpelagaeasrllellkrllallsrderp....lvlvlDdlq 145
                                   +e ++ +++  + + +la v+ +   +a+r  ++++rl+ + + +  p    +v+++D  +
  gi|91773737|ref|YP_566429.1| 339 DEVRKTRDFEIFADMRLAGVGMIGVVHANRAIDAVQRLIGRVELGVIPqvvdTVIFIDKGE 399
                                   2222222222222233334444444444666666666665555433333333666666555 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.9e-05      0.16       1      69 [.       8      69 ..       8     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                         PIN_3  1 rvvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaalla 69
                                  r+v Dt+v++d++l        +++  + + i+l++s++++ Ele  + r l+  ++ l+ + k+++++
  gi|91773737|ref|YP_566429.1|  8 RIVPDTSVIIDGFL------SEMVESGKYEGIELFISEAMVAELESQANRGLDIGNKGLD-ELKQLQEM 69
                                  89************......57899999999**************999888776654444.44444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.26      20      38 ..     264     281 ..     247     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                        AAA_29  20 dlkgatlltGpsGsGKSTl 38 
                                    ++g +l++Gp G+GKST+
  gi|91773737|ref|YP_566429.1| 264 AQRG-ILVSGPPGAGKSTF 281
                                   4466.9************7 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.4     6e+03      75      88 ..      13      26 ..       5      35 .. 0.80
   2 ?   10.8   0.0   0.00029      0.53       1      15 [.     268     282 ..     268     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.4
                        AAA_18 75 knlvidghlaeles 88
                                   +++idg+l+e+++
  gi|91773737|ref|YP_566429.1| 13 TSVIIDGFLSEMVE 26
                                  568*******9986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00029
                        AAA_18   1 IlltGtpGvGKttla 15 
                                   Il++G+pG+GK+t++
  gi|91773737|ref|YP_566429.1| 268 ILVSGPPGAGKSTFG 282
                                   99***********97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4   7.2e+03      75      97 ..     108     130 ..      85     133 .. 0.74
   2 ?   10.3   0.0   0.00032      0.57       2      20 ..     268     286 ..     268     329 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                        AAA_33  75 ldatnlsrrerarflklarrlgv 97 
                                   ldat+++ ++ +  +++a+ ++v
  gi|91773737|ref|YP_566429.1| 108 LDATFVTGDKVQYDVAVAKGMDV 130
                                   49999998888888888886666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00032
                        AAA_33   2 vllvGlpGsGKstlaerll 20 
                                   +l+ G+pG+GKst+  +++
  gi|91773737|ref|YP_566429.1| 268 ILVSGPPGAGKSTFGAGVA 286
                                   5789**********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.76u 0.27s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3666.68
//
Query:       gi|91773738|ref|YP_566430.1|  [L=98]
Description: cobalt transport protein CbiN [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-18   65.4   0.2      4e-18   65.1   0.2    1.1  1  PDGLE     PDGLE domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.014   15.3   0.0    1.5  2  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> PDGLE  PDGLE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.2   4.5e-22     4e-18       2      88 ..      15      93 ..      14      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 4.5e-22
                         PDGLE  2 aalliggvlswfASanPdGLEwsiekvagtaeleasgdlhealaeiqektalLpDYsfkgaeekkagtsvAgivGvlltlala 84
                                  +a+li +++ ++AS++PdGLE+++ekv g++      ++ e +++    ++++pDY+++g+ +  +g++vA+++G++ +la++
  gi|91773738|ref|YP_566430.1| 15 LAILISILAPFLASSDPDGLESAAEKVIGEE------RFAELEETEATIDSPMPDYAIEGKGK--LGEIVAICLGTIGILAIS 89
                                  79*************************9984......3445555555558***********99..9***************** PP

                         PDGLE 85 glig 88
                                  +++g
  gi|91773738|ref|YP_566430.1| 90 FGLG 93
                                  *998 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.6e-06     0.014      21      41 ..      11      31 ..       2      49 .. 0.81
   2 ?   -3.7   0.9       1.4   1.2e+04      24      29 ..      81      86 ..      75      90 .. 0.43

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                        OppC_N 21 villlllliaifaPliaPydp 41
                                  ++l+l +li+i+aP++a  dp
  gi|91773738|ref|YP_566430.1| 11 IVLALAILISILAPFLASSDP 31
                                  78999999*********8887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                        OppC_N 24 llllli 29
                                   ++ ++
  gi|91773738|ref|YP_566430.1| 81 GTIGIL 86
                                  333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 606.77
//
Query:       gi|91773739|ref|YP_566431.1|  [L=218]
Description: cobalt transport protein CbiM [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-54  182.5  21.0    9.9e-54  182.3  21.0    1.0  1  CbiM           Cobalt uptake substrate-specific transmembrane
     0.0097   15.9   5.4     0.0097   15.9   5.4    2.4  2  Na_Ca_ex       Sodium/calcium exchanger protein
  ------ inclusion threshold ------
       0.35   11.3  13.8      0.043   14.2   6.3    2.6  2  Peptidase_A24  Type IV leader peptidase family


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 !  182.3  21.0   1.7e-57   9.9e-54       1     207 []       2     204 ..       2     204 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.3 bits;  conditional E-value: 1.7e-57
                          CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLlG.pw 80 
                                   Hipd +++++ +l+++a+a++++ ++lr++r+++d+ ++p la+l+a ifa+q +nipi  gts+H++ga+l+ai+lG p 
  gi|91773739|ref|YP_566431.1|   2 HIPDSFMPLSQALVYWAIAIPFIFMSLRWARRDMDDMKIPILAALSAGIFAIQALNIPIGMGTSGHMVGAALVAIILGsPF 82 
                                   ********************************************************************************* PP

                          CbiM  81 aaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaallvalela 161
                                   a++l++++vll+q ++f+dGGit++GaNilnm+vi  +++y+ + +l+++   +  ++++af++a+l+++++++++a+e++
  gi|91773739|ref|YP_566431.1|  83 AGVLVLTLVLLVQGIVFADGGITVMGANILNMGVISGFIGYYGFVALRKR---NIDIKISAFIGAWLGLFISSIATAIEMS 160
                                   *********************************************99777...678************************* PP

                          CbiM 162 lsgleaslsltaalaamllvhlpvgil.EgviTaaivkalkkvrpel 207
                                   ++g+   ++l   + am ++h+++gi+ Eg+iTa+++ a++k+rp+l
  gi|91773739|ref|YP_566431.1| 161 IAGT---FPLVPGIVAMGTFHFVIGIIgEGLITAIAIGAIAKARPDL 204
                                   **77...5****************8888*****************97 PP

>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   5.2      0.54   3.2e+03      69      89 ..      66      86 ..       6     104 .. 0.53
   2 !   15.9   5.4   1.6e-06    0.0097      70     146 ..     105     181 ..     102     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.54
                                  HHHHHHHHHHHHTHHHHHHHH CS
                      Na_Ca_ex 69 gnvlGsnifnlllviGliali 89
                                  g ++G++++ + l+ ++++++
  gi|91773739|ref|YP_566431.1| 66 GHMVGAALVAIILGSPFAGVL 86
                                  344444444444444444433 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.6e-06
                                   HHHHHHHHHHHTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  70 nvlGsnifnlllviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalyl 146
                                   +v+G+ni+n++++ G+i+++g +  +++++++++++++ + l l+++ ++  + +++ g+  ++ g+v ++++ +++
  gi|91773739|ref|YP_566431.1| 105 TVMGANILNMGVISGFIGYYGFVALRKRNIDIKISAFIGAWLGLFISSIATAIEMSIAGTFPLVPGIVAMGTFHFVI 181
                                   799*****************99999999*9****999999999999999988888889**********999998776 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.0     0.095   5.7e+02      13      57 ..      33      75 ..       8      87 .. 0.49
   2 ?   14.2   6.3   7.2e-06     0.043      24     105 ..      88     165 ..      85     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.095
                 Peptidase_A24 13 iDldtrtlpdeltlpllllgvlfaqllllglpnlaqavlgalvga 57
                                   D+d +++p    l+  ++ + +   + +g+ +   +++ga+++a
  gi|91773739|ref|YP_566431.1| 33 RDMDDMKIPILAALSAGIFAIQAL-NIPIGMGTS-GHMVGAALVA 75
                                  455555555433333222222222.112222222.2222332222 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.2e-06
                 Peptidase_A24  24 ltlpllllgvlfa..qllllglpnlaqavlgalvgalvlllislvdeqamGgGDvklaavlgaflgwerlllavlvaillg 102
                                   ltl+ll+ g++fa   ++ +g++ l+  v+++++g+  +++  l +++     D+k+ a +ga+lg++   +a+ + + ++
  gi|91773739|ref|YP_566431.1|  88 LTLVLLVQGIVFAdgGITVMGANILNMGVISGFIGYYGFVA--LRKRNI----DIKISAFIGAWLGLFISSIATAIEMSIA 162
                                   89***********9977789*********************..777776....****************999999988666 PP

                 Peptidase_A24 103 avl 105
                                   + +
  gi|91773739|ref|YP_566431.1| 163 GTF 165
                                   554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1412.96
//
Query:       gi|91773740|ref|YP_566432.1|  [L=284]
Description: cobalt ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-33  114.8   0.0      6e-33  114.3   0.0    1.3  1  ABC_tran      ABC transporter
    2.2e-15   57.3   0.8    1.2e-09   38.4   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.1e-12   44.9   0.0    1.5e-11   44.2   0.0    1.3  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00075   19.2   0.2     0.0019   17.9   0.2    1.7  1  AAA_29        P-loop containing region of AAA domain
     0.0026   18.3   0.0     0.0035   17.9   0.0    1.3  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.011   15.9   0.0       0.19   12.0   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.013   15.5   0.3      0.024   14.7   0.3    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.032   14.5   0.1      0.056   13.7   0.1    1.4  1  AAA_28        AAA domain
      0.035   13.5   0.0      0.061   12.7   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.054   14.0   0.3        0.3   11.6   0.2    2.2  3  AAA_18        AAA domain
      0.058   13.3   0.3       0.14   12.1   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
       0.06   13.1   0.1       0.26   10.9   0.2    1.8  2  AAA_15        AAA ATPase domain
      0.072   12.2   0.0      0.072   12.2   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.099   12.8   0.0       0.22   11.7   0.0    1.6  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   4.7e-36     6e-33       1     137 []      25     171 ..      25     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 4.7e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren 79 
                                   l+ ++l++++gek+ai+G nGaGKStL+k l g l+p +G++l++g+ ++++++ ++rk +g+++q+  +q+f+ + v+e 
  gi|91773740|ref|YP_566432.1|  25 LDGIDLSIYPGEKIAILGANGAGKSTLFKHLNGILSPSSGNVLIKGDTISKKTIYKARKTVGIVFQNpdDQIFSPT-VEED 104
                                   6899***************************************************************777777777.9999 PP

                                   .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                e +e+i   l+ ++l++++++      ++LSgGqk+ va+a +l+ +p++++lDEpta
  gi|91773740|ref|YP_566432.1| 105 vafgpinmglseeEVEERIRSSLELVNLSGFEKRAP----HHLSGGQKKLVAIAGVLAMQPEVVVLDEPTA 171
                                   9********987777777888888888888888887....*****************************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 !   16.7   0.6   3.8e-06    0.0049       3      56 ..      39      95 ..      38     110 .. 0.74
   2 !   38.4   0.0   9.5e-13   1.2e-09     228     301 ..     134     205 ..     105     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                        AAA_21  3 vliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkipslldlydpei 56
                                  ++ G+Ng+GKS+L++ l ++ +    +  ++g+t+++  + + rk  +  + + +++
  gi|91773740|ref|YP_566432.1| 39 AILGANGAGKSTLFKHLNGILSPssgNVLIKGDTISKKTIYKARKTVGIVFQNPDDQ 95
                                  799**************9998777776666666666666666666666666655555 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 9.5e-13
                        AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                   +  ++ +++lS G+k+l a++  l+ ++    ++++DEp +gL+P   ++++ ++ k + + g  v+l+TH+  +
  gi|91773740|ref|YP_566432.1| 134 GFEKRAPHHLSGGQKKLVAIAGVLAMQP---EVVVLDEPTAGLDPLNAAKVMNIIeKMNLELGMTVVLSTHDVDI 205
                                   4457889*******************99...9***********************74444489********9765 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 !   44.2   0.0   1.2e-14   1.5e-11      27     189 ..      38     191 ..      20     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.2e-14
                                   EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkg 107
                                    ai+G+NG+GKs l+  +  +L+ +s + l      d i+k  +     + +v i+f+n+d+++   + e  +    ++ g
  gi|91773740|ref|YP_566432.1|  38 IAILGANGAGKSTLFKHLNGILSPSSGNVL---IKGDTISK--KTIYKARKTVGIVFQNPDDQIFSPTVEEDVAFGPINMG 113
                                   68****************999997666332...33344444..3333445579**********9999999999999999** PP

                                   EEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 108 eseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                    se +++++  ++ e+ +l   ++  ++ LSgG+k+Lva+a ++A+q      +++lDe  a LD  n +kv +++++ + 
  gi|91773740|ref|YP_566432.1| 114 LSEEEVEERIRSSLELVNLSGFEKRAPHHLSGGQKKLVAIAGVLAMQP----EVVVLDEPTAGLDPLNAAKVMNIIEKMNL 190
                                   *******************************************99874....3789********************98775 PP

                                   T CS
                                   x RF
                         SMC_N 189 n 189
                                   +
  gi|91773740|ref|YP_566432.1| 191 E 191
                                   5 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.5e-06    0.0019      16      50 ..      29      63 ..      23      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  +++i + + + + G++G+GKSTl+  ++ +L p++
  gi|91773740|ref|YP_566432.1| 29 DLSIYPGEKIAILGANGAGKSTLFKHLNGILSPSS 63
                                  56677777899*************99999998876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.8e-06    0.0035      23      46 ..      39      62 ..      21     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                        AAA_23 23 lItGpNGaGKTTildAiklaLyge 46
                                  +I G NGaGK+T++  +  +L   
  gi|91773740|ref|YP_566432.1| 39 AILGANGAGKSTLFKHLNGILSPS 62
                                  8**************999998763 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 ?   12.0   0.0   0.00015      0.19      63      89 ..     160     186 ..     133     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                       SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                   ++++v+LDE  ++lD+ ++a++++++e
  gi|91773740|ref|YP_566432.1| 160 QPEVVVLDEPTAGLDPLNAAKVMNIIE 186
                                   4789********************987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   1.9e-05     0.024       1      22 [.      37      58 ..      37     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                  EEEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  1 evaivGrpNvGKStLinaltge 22
                                  ++ai+G   +GKStL++ l g 
  gi|91773740|ref|YP_566432.1| 37 KIAILGANGAGKSTLFKHLNGI 58
                                  69****************9874 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.4e-05     0.056       1      20 [.      37      56 ..      37      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                        AAA_28  1 kivitGgestGKTtlleaLa 20
                                  ki+i+G+ ++GK+tl ++L+
  gi|91773740|ref|YP_566432.1| 37 KIAILGANGAGKSTLFKHLN 56
                                  79***************996 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   4.7e-05     0.061      17      58 ..      30      71 ..      19      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                  Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealeva 58
                                  +++  g ++ ++G+ G+GK+ l k l+++l+p s +  ++  
  gi|91773740|ref|YP_566432.1| 30 LSIYPGEKIAILGANGAGKSTLFKHLNGILSPSSGNVLIKGD 71
                                  55556678999********************99877666554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00024       0.3       1      22 [.      38      59 ..      38      85 .. 0.70
   2 ?   -2.9   0.0       7.4   9.5e+03      96     112 ..     106     125 ..      80     129 .. 0.66
   3 ?   -1.2   0.0       2.2   2.8e+03      57      89 ..     178     208 ..     148     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                        AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                  I++ G+ G+GK+tl k+L+  l
  gi|91773740|ref|YP_566432.1| 38 IAILGANGAGKSTLFKHLNGIL 59
                                  89****************5443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.4
                        AAA_18  96 k...vvLtaspeelleRlek 112
                                       + + +s+ee  eR++ 
  gi|91773740|ref|YP_566432.1| 106 AfgpINMGLSEEEVEERIRS 125
                                   23447777888888888875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.2
                        AAA_18  57 ldklldaleenssaleegknlvidghlaelese 89 
                                    +k+++++e+ +  le g ++v++ h ++ +++
  gi|91773740|ref|YP_566432.1| 178 AAKVMNIIEKMN--LELGMTVVLSTHDVDIIPA 208
                                   456677777765..4778888888888776665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.14      89     123 ..      24      59 ..       4      80 .. 0.74
   2 ?   -2.9   0.0       4.3   5.5e+03      34      60 ..     246     272 ..     237     279 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                   THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                   +l+ +   +   + ++++G  G+GKStL ++l++ l
  gi|91773740|ref|YP_566432.1|  24 ALDGIDLSIYPgEKIAILGANGAGKSTLFKHLNGIL 59 
                                   55555544444478899**************98755 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                                   HHHHHHHHHHHTT-EEEEEEE-GGG-- CS
                   RsgA_GTPase  34 lldrfLvlaeekgiepvivlnKiDlle 60 
                                   ++  +  l++e+gi++ i ++ +D  +
  gi|91773740|ref|YP_566432.1| 246 RIAEVFELLQEEGIDVQIQITPVDAKD 272
                                   556666677888888888888888655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2    0.0002      0.26      20      73 ..      29      81 ..      23     137 .. 0.72
   2 ?   -0.2   0.0       0.5   6.4e+02     325     369 .]     162     206 ..     143     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                        AAA_15 20 dlsee...ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenise 73
                                  dls +      + G+N++GKS++ + l+ +l+ + +     + i+ + ++++  ++ 
  gi|91773740|ref|YP_566432.1| 29 DLSIYpgeKIAILGANGAGKSTLFKHLNGILSPS-S---GNVLIKGDTISKKTIYKA 81
                                  4444455588999*******************99.3...334444444444433333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.5
                        AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                    +++++EP a L p +   +++ + ++  +  + v+++TH   ii
  gi|91773740|ref|YP_566432.1| 162 EVVVLDEPTAGLDPLNAAKVMNIIEKMNLELGMTVVLSTHDVDII 206
                                   678999999999999999999999999999999*******87776 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.6e-05     0.072      25      78 ..      37      88 ..      14     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                                  EEEEEESTTSSHHHHHHHHHHHCS----HHHHHCCHHHHHHHHHHHHHHHHHHH CS
                       G-alpha 25 kllllGqseSGKsTilkqlkllykkgfseeelatwraviqlnivrsiktileal 78
                                  k+ +lG+++ GKsT++k+l  +  ++  +    +  + i ++++ ++++ + ++
  gi|91773740|ref|YP_566432.1| 37 KIAILGANGAGKSTLFKHLNGILSPSSGNV--LIKGDTISKKTIYKARKTVGIV 88
                                  899*****************8887776655..3333444444444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.22       4      40 ..      40      80 ..      38     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                        AAA_33  4 lvGlpGsGKstlaerl...lkklg.avllssdtlrrrlfgt 40
                                  + G++G+GKstl ++l   l +    vl+  dt++++  ++
  gi|91773740|ref|YP_566432.1| 40 ILGANGAGKSTLFKHLngiLSPSSgNVLIKGDTISKKTIYK 80
                                  679************96654443379999999999855443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1698.85
//
Query:       gi|91773741|ref|YP_566433.1|  [L=270]
Description: cobalt ABC transporter CbiQ, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  120.7   8.9      9e-35  120.3   8.9    1.2  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 !  120.3   8.9     5e-39     9e-35       3     213 ..      16     239 ..      14     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 5e-39
                                   CCCCS-HHHHHHHHHHHHHHHHHS-H.....HHHHHHHHHHHHHHHHTTS---...HHHHHHHCCCHCHHHHHHHHHHE.. CS
                          CbiQ   3 svlhrldprvkliwlfllllalvlap.....nlvtlliiiallllllllvilp...rvlaqalilpllflllgllillfql 75 
                                   s++hrld r k ++l+++++ +  +p     n++ ll++ ++l++l+ ++ l     +   +++lp+++ l+ ++ +++q 
  gi|91773741|ref|YP_566433.1|  16 SPIHRLDGRIKILALLSIVFYVAALPrlddsNMIKLLVLESYLFVLIIIARLNlfyVLVRLVAVLPFGLGLAVFQPFIRQP 96 
                                   89*****************99999871222244555555555555555555556643344455678888888888888876 PP

                                   .....EECTTEEE......E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHH CS
                          CbiQ  76 ittegefvfaggg...qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflL 153
                                   +   ++f++ + +    ++it+eGl +g++l+ R+l++++  + l+ T ++++++ s +rlgvP+e++l+l+ + R++f++
  gi|91773741|ref|YP_566433.1|  97 FI--ETFTVYPVSlplGLTITYEGLDFGMTLMARFLVCVTSIIVLSSTMKMNDFVVSARRLGVPKEFVLLLTMMVRYLFVF 175
                                   64..4555555555588**************************************************************** PP

                                   HHHHHHHHHHHHHTTTTS.....SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS... CS
                          CbiQ 154 leevqrikqAqklRlgds...klgirrslrslgkliaalflralkraervalAmeaRGYtg.se 213
                                      ++ri+ Aq++Rl+d+   + ++++ l ++g +i +lf+++++++er++++m  RGY+  ++
  gi|91773741|ref|YP_566433.1| 176 WSVLKRIRVAQQSRLFDIwnkNVPRKWILEQVGNTISSLFVQSYEQGERTYISMLCRGYSNdNS 239
                                   *******************76777777889*****************************98555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1698.11
//
Query:       gi|91773742|ref|YP_566434.1|  [L=431]
Description: UDP-glucose 6-dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-63  211.5   0.2      1e-62  211.0   0.2    1.2  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    6.3e-38  128.9   0.0    1.2e-37  128.0   0.0    1.5  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    6.7e-31  106.8   0.0      6e-30  103.8   0.0    2.4  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      6e-05   23.6   0.0        0.2   12.3   0.0    3.3  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    6.3e-05   22.9   0.0    0.00019   21.4   0.0    1.8  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    6.9e-05   22.9   0.0    0.00016   21.7   0.0    1.8  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00049   20.2   0.3      0.019   15.1   0.0    3.2  4  DpaA_N          Dipicolinate synthase subunit A N-terminal do
     0.0006   20.3   0.0      0.002   18.6   0.0    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0016   18.6   0.1       0.45   10.7   0.0    2.7  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0018   19.1   0.0       0.01   16.7   0.0    2.2  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
     0.0082   15.5   0.3        0.5    9.7   0.0    2.7  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.014   15.0   0.1      0.033   13.8   0.1    1.7  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.014   14.6   0.0      0.026   13.7   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.015   14.6   0.0      0.032   13.5   0.0    1.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.12   12.3   0.1       0.33   10.8   0.0    1.8  2  Rossmann-like   Rossmann-like domain
       0.14   12.4   0.0       0.41   10.9   0.0    1.9  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
       0.22   10.8   0.1       0.37   10.0   0.1    1.3  1  FAD_binding_3   FAD binding domain
       0.36   11.1   1.2        0.8   10.0   0.2    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like 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 !  211.0   0.2   1.1e-65     1e-62       1     186 [.       1     188 [.       1     189 [. 0.96

  Alignments for each domain:
  == domain 1  score: 211.0 bits;  conditional E-value: 1.1e-65
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEE CS
                UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvif 81 
                                   mk+s+iG+GYvG v+aa++ae+ghevi++Dide kv+++n g  pi e+gLe l++k++ +++l +t+d++ a++++d+ f
  gi|91773742|ref|YP_566434.1|   1 MKVSIIGSGYVGSVSAACFAELGHEVICIDIDEMKVRMINDGIPPIWEEGLEGLMQKHA-EKNLIATSDYDYAIQNSDISF 80 
                                   89*********************************************************.7******************** PP

                                   E-----B-TTTTCB-THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEEE------T CS
                UDPG_MGDP_dh_N  82 iaVgTPskkkgkaaDlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvvsnPEflre 158
                                   i+VgTPs++   ++Dl+ v +a++s++ a+ k    ++vvvkSTv++gt+e++v ++lee+s k+ g+df++++nPEflre
  gi|91773742|ref|YP_566434.1|  81 ICVGTPSNE-HGNIDLSIVGNACKSLGMAMAKkdgFHIVVVKSTVVPGTTEDVVLHLLEEHSCKTaGKDFGLAMNPEFLRE 160
                                   *********.7777*************9998878889*************************9999*************** PP

                                   TSHHHHHHS-S-EEEEESSCHHHHHHHH CS
                UDPG_MGDP_dh_N 159 gsavkdllnpdrvviGveekkaeaalee 186
                                   g+av+d++npd++v+G+ + ++ a+++e
  gi|91773742|ref|YP_566434.1| 161 GKAVYDFMNPDKIVVGGIDGRTIALVSE 188
                                   ****************998888776665 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 !  128.0   0.0   1.2e-40   1.2e-37       1      93 [.     203     295 ..     203     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 1.2e-40
                  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgle 81 
                                   +tAE+iK+++N+flatkIsf+Ne++n+c++lgid+ eV++avg+d ri+++fl+ g+G+GGsc+pkDv+aL+ +a+el++ 
  gi|91773742|ref|YP_566434.1| 203 RTAEMIKYVNNSFLATKISFSNEVGNICKRLGIDTYEVMKAVGKDFRISEHFLNSGAGFGGSCFPKDVRALIGKAKELDYY 283
                                   69******************************************************************************* PP

                  UDPG_MGDP_dh  82 aelleavrevNe 93 
                                   + lle+v+evN+
  gi|91773742|ref|YP_566434.1| 284 PALLESVVEVND 295
                                   ***********7 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 ?   -0.2   0.0       1.3   1.3e+03      51      84 ..      60      95 ..      27     105 .. 0.72
   2 !  103.8   0.0     6e-33     6e-30       1     105 []     318     417 ..     318     417 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                                  BTCCEEES-CHHHHTT-SE..EEE-S--GGGGGS-H CS
                UDPG_MGDP_dh_C 51 ekgvevvdsleealkgada..iviltehdefkeldl 84
                                  ek++  +++ + a++++d+  i++ t+ +e  ++dl
  gi|91773742|ref|YP_566434.1| 60 EKNLIATSDYDYAIQNSDIsfICVGTPSNEHGNIDL 95
                                  678888888888999888722555566677766666 PP

  == domain 2  score: 103.8 bits;  conditional E-value: 6e-33
                                   EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGG CS
                UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefke 81 
                                   a+lGlafK+dtdD+ReS+++ +i++Lle+ga v++yDP+++e  ++     +++++++s e+al+gada++i+te+ ef++
  gi|91773742|ref|YP_566434.1| 318 AVLGLAFKNDTDDIRESRSIPVIRKLLEKGALVTAYDPMASEHMKAV---FEDITYCESSEDALNGADACLIMTEWTEFRK 395
                                   89****************************************99998...779**************************** PP

                                   S-HHHHHHCCSS-EEEESSS-CCC CS
                UDPG_MGDP_dh_C  82 ldlaklkelmkpavvfDgrnvldp 105
                                   ld     + mk +vv+Dgr+++dp
  gi|91773742|ref|YP_566434.1| 396 LDS--EFSGMKSKVVIDGRKMIDP 417
                                   864..56779**********9996 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0    0.0002       0.2       1      71 [.       2      85 ..       2      91 .. 0.91
   2 ?   -1.5   0.0       4.1     4e+03      23      55 ..     167     201 ..     148     228 .. 0.47
   3 !    7.1   0.0    0.0083       8.3      16      93 ..     341     410 ..     338     411 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.................-EEECECHHHHHHH-SEEE CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.................vkvtavdneeaaeeadvvv 66
                                  k+ iiG+G +g+  a  +++ g   he++ + + ++ k++ + + +                    + ++d+  a++++d+ +
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELG---HEVICI-DIDEMKVRMINDGIPpiweegleglmqkhaekNLIATSDYDYAIQNSDISF 80
                                  689*******************...****88.***********999999************9986677779999999****** PP

                                  E-S-H CS
                 F420_oxidored 67 lavkp 71
                                  ++v +
  gi|91773742|ref|YP_566434.1| 81 ICVGT 85
                                  *9965 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.1
                                   S.-GGCEEEEE..ESSCCCHHHHHHHHC-EEECECH CS
                 F420_oxidored  23 a.qpheivvan..srnpekaeelaeelgvkvtavdn 55 
                                   + +p +ivv++   r+   + el ++l+ +vt+ +n
  gi|91773742|ref|YP_566434.1| 167 FmNPDKIVVGGidGRTIALVSELYRDLECEVTS-TN 201
                                   256667776521134444444444444444443.22 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0083
                                   HHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                 F420_oxidored  16 sgllaagaqpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                   ++ll++g     ++     +p   e++++ ++ ++ ++ + e+a++ ad  ++   ++ + ++ se   +  k k+vi+
  gi|91773742|ref|YP_566434.1| 341 RKLLEKG---ALVT---AYDPMASEHMKAVFEdITYCE-SSEDALNGADACLIMTEWTEFRKLDSEF--SGMKSKVVID 410
                                   5566666...3333...345555566666666567777.9***************************..999*****98 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.9e-07   0.00019       1      56 [.       2      56 ..       2      80 .. 0.76
   2 ?   -2.5   0.0       4.2   4.2e+03      55      80 ..     356     382 ..     334     385 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56
                                  kv +iG+G +G+  aa fa+ g+eV  +di+e +++  ++ i   +e+  e g ++
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEMKVRMINDGIPPIWEEGLE-GLMQ 56
                                  699*****************************9999988888776555433.3333 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                   S-HHHHCCCHHCEEEES-HHHHH.C-S CS
                       3HCDH_N  55 lkeeeveaalarisfttdleeav.dad 80 
                                   +  e+++a+++ i++ ++ e+a  +ad
  gi|91773742|ref|YP_566434.1| 356 MASEHMKAVFEDITYCESSEDALnGAD 382
                                   336777778888888888877776666 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 !   21.7   0.0   1.6e-07   0.00016       1      79 [.       2      85 ..       2     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                                  -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH.....SSBTTTBTT----TTEEEES-HHHHHTT--EEEE--- CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeinee.....henvkyLpgiklpenlvattdlaealkgadiivlvvP 78
                                  k++++G+G  G+  A+ +ae ghev  +  +e  ++ in+      +e  + L + + ++nl at+d + a++++di ++ v 
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEMKVRMINDGippiwEEGLEGLMQKHAEKNLIATSDYDYAIQNSDISFICVG 84
                                  79*************************************863333378889999999*******************9888774 PP

                                  H CS
                NAD_Gly3P_dh_N 79 s 79
                                  +
  gi|91773742|ref|YP_566434.1| 85 T 85
                                  4 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 ?   -2.4   0.0       5.1   5.1e+03      29      53 ..      53      77 ..      17      97 .. 0.56
   2 ?   -0.3   0.1       1.1   1.1e+03       4      21 ..     174     192 ..     171     221 .. 0.79
   3 ?    0.7   0.0      0.54   5.4e+02      67     116 .]     192     241 ..     183     241 .. 0.83
   4 !   15.1   0.0   1.9e-05     0.019      10      57 ..     335     386 ..     333     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                                  S-TSSS-BTTEEEE-GGGS-GGG-S CS
                        DpaA_N 29 gleleekiegvekaesleealedad 53
                                  gl +++  +++  +++ + a++++d
  gi|91773742|ref|YP_566434.1| 53 GLMQKHAEKNLIATSDYDYAIQNSD 77
                                  3344455555555555555555555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                   EESB.-HHHHHHHHHHHHT CS
                        DpaA_N   4 viGG.DaRqlylarkLaek 21 
                                   v+GG D R ++l+ +L ++
  gi|91773742|ref|YP_566434.1| 174 VVGGiDGRTIALVSELYRD 192
                                   7888899****99999876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.54
                                   EE-BSS-SS-EE-HHHHHTS-TT-EEEESS--HHHHHHHHHCT-EEEEGG CS
                        DpaA_N  67 eintpfseeklsleelleklkkgqllfgGiippelkelaeekgielvdlm 116
                                   +++++++++  + +e++++++++ l     +++e+ +++++ gi ++++m
  gi|91773742|ref|YP_566434.1| 192 DLECEVTSTNPRTAEMIKYVNNSFLATKISFSNEVGNICKRLGIDTYEVM 241
                                   5677778888888899999999988777888999**********999987 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHHTT-EEEEES-....TSSS-BTTEEEE-GGGS-GGG-SEEE- CS
                        DpaA_N  10 RqlylarkLaekgakvslygl....eleekiegvekaesleealedadviil 57 
                                   R + ++rkL ekga v++y      +++  +e+++ +es e+al+ ad+++ 
  gi|91773742|ref|YP_566434.1| 335 RSIPVIRKLLEKGALVTAYDPmaseHMKAVFEDITYCESSEDALNGADACLI 386
                                   8999***************6667788999*******************9876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     2e-06     0.002       1      51 [.       2      52 ..       2      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHH CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqekle 51
                                  kv ++G+Gy+g   A+ +aelg++V +++  ++  r++++ +  i++e le
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEMKVRMINDGIPPIWEEGLE 52
                                  578*************************99877778888888877777665 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 ?    5.4   0.0      0.02        19       1      63 [.       2      83 ..       2     143 .. 0.72
   2 !   10.7   0.0   0.00046      0.45      14      63 ..     339     388 ..     337     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.02
                                  EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...................EEE-SSHHHHHHHCSEEEE-S CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...................akaaesieelvasldvvitmv 63
                                  k+ +iG G  Gs  a  +++ g++v++++ ++ kv+ + +                     + a+++   ++++ d+ +++v
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEMKVRMINDGIppiweegleglmqkhaeknLIATSDYDYAIQNSDISFICV 83
                                  5789*************************99988876554335555555555555555554444555555555555555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00046
                                   HHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-S CS
                 NAD_binding_2  14 malnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmv 63 
                                    +++ll++g  v++y+  +++  ++v e ++ +es e++++++d+ ++m 
  gi|91773742|ref|YP_566434.1| 339 VIRKLLEKGALVTAYDPMASEHMKAVFEDITYCESSEDALNGADACLIMT 388
                                   6789************99999999999****************9999985 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     1e-05      0.01       1      82 [.       1      97 [.       1     105 [. 0.77
   2 ?   -1.3   0.0       3.8   3.8e+03      27      70 ..     348     388 ..     316     394 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                                  EEEEEETTSHHHHHHHHHHHHTTTTE........EEEEEECSSHHHHHHH.......HHHTTHEEESSHHHHHTCTTESEEEE CS
                  GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrle........evvalldpdaeraeav.......aesfgveaysdleelladpeidaviv 68
                                  ++v iiG+G++gs  ++ + e  ++         +v  + d  ++  e+         ++ ++ a sd+++  ++++i +++v
  gi|91773742|ref|YP_566434.1|  1 MKVSIIGSGYVGSVSAACFAELGHEVicididemKVRMINDGIPPIWEEGleglmqkHAEKNLIATSDYDYAIQNSDISFICV 83
                                  5899***********97777775555888888886666666666666665666654445555559999*************** PP

                                  -S-GGGHHHHHHHH CS
                  GFO_IDH_MocA 69 atpngtheelakaa 82
                                  +tp+++h ++ + +
  gi|91773742|ref|YP_566434.1| 84 GTPSNEHGNIDLSI 97
                                  *******9986665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.8
                                   EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S CS
                  GFO_IDH_MocA  27 evvalldpdaeraeavaesfgveaysdleelladpeidavivat 70 
                                    +v ++dp a+++ + a   ++  +++ e+ l+   +da++++t
  gi|91773742|ref|YP_566434.1| 348 ALVTAYDPMASEHMK-AVFEDITYCESSEDALN--GADACLIMT 388
                                   555555555554444.34444555555566666..567777766 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 !    9.7   0.0    0.0005       0.5      38      70 ..       2      34 ..       1      45 [. 0.89
   2 ?   -3.3   0.0       4.8   4.8e+03      76     106 ..      60      89 ..      54      90 .. 0.63
   3 ?    3.0   0.0     0.058        58      51     102 ..     339     391 ..     337     409 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                  +v iiG G +G+  a +++++g +vi++d  + 
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEM 34
                                  799*************************98766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                                   HHHTCEECSHHHHHHH-SEEEE-S--STTTT CS
                  2-Hacid_dh_C  76 eelgvelvsleellaesDivslhlpltpetr 106
                                   e++ +   + + ++++sDi s  +  tp+++
  gi|91773742|ref|YP_566434.1|  60 EKNLIATSDYDYAIQNSDI-SFICVGTPSNE 89 
                                   4445567788899999995.55555666665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.058
                                   HHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--S CS
                  2-Hacid_dh_C  51 vakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlplt 102
                                   v+++l + g+ v+ayd+  ++  ++  + ++++ s e++l+ +D   +++  t
  gi|91773742|ref|YP_566434.1| 339 VIRKLLEKGALVTAYDPMASEHMKAVFEDITYCeSSEDALNGADACLIMTEWT 391
                                   67788888999*******99888777777755549999******988776655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.3e-05     0.033       2      38 ..       4      41 ..       3     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                                  EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                          ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38
                                   i+G+G +Gs+ aa+ a+ g++v++i+ ++ ++  +++
  gi|91773742|ref|YP_566434.1|  4 SIIGSGYVGSVSAACFAELGHEVICIDIDEmKVRMIND 41
                                  79************************999877776664 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.026     144     182 ..       2      40 ..       1      66 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                   EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllrald 182
                                   ++ ++G+Gy+G++ Aa +a+lg+ev  ++  +  +r+ +
  gi|91773742|ref|YP_566434.1|   2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEMKVRMIN 40 
                                   5789********************998886544445544 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05     0.032      30      69 ..       2      41 ..       1      73 [. 0.88
   2 ?   -3.7   0.0       5.9   5.9e+03      55      85 ..     196     226 ..     183     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                  kv +iG G +G  ++a  ++lg +V  +D+++ + + +++
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEMKVRMIND 41
                                  89*****************************999887776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.9
                                   EEEESSHHHHHHHHHTTTCECEEHCHHHHHH CS
                   AlaDh_PNT_C  55 tvlDvrparleqleslgakfvevlksqeell 85 
                                   +v+ ++p+++e ++ ++++f+ ++ s ++++
  gi|91773742|ref|YP_566434.1| 196 EVTSTNPRTAEMIKYVNNSFLATKISFSNEV 226
                                   4556677777777777777777766655555 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033      0.33      12      40 ..       2      30 ..       1      70 [. 0.89
   2 ?   -2.3   0.0       3.7   3.7e+03       8      37 ..      90     118 ..      84     126 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                 Rossmann-like 12 svGiisaGrvGtalgaaleraghvvvgis 40
                                  +v ii++G vG++ +a ++  gh v+ i 
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICID 30
                                  899**********************9875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.7
                 Rossmann-like   8 sarlsvGiisaGrvGtalgaalerag.hvvv 37 
                                   ++ +++ i+  G+   +lg+a+++ +  ++v
  gi|91773742|ref|YP_566434.1|  90 HGNIDLSIV--GNACKSLGMAMAKKDgFHIV 118
                                   555555555..56667788888876533333 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00041      0.41       4      43 ..     206     245 ..     204     292 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                NAD_binding_11   4 qavKlvnnlllainlaaasEalvlaekaGldpekvlevin 43 
                                   + +K vnn  la+++    E+  +++++G+d  +v++++ 
  gi|91773742|ref|YP_566434.1| 206 EMIKYVNNSFLATKISFSNEVGNICKRLGIDTYEVMKAVG 245
                                   689******************************9999985 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00037      0.37       3      36 ..       2      35 ..       1      39 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                  +V I+G+G +G ++a   +e G +v++++  + +
  gi|91773742|ref|YP_566434.1|  2 KVSIIGSGYVGSVSAACFAELGHEVICIDIDEMK 35
                                  799*************************976655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2    0.0008       0.8       1      27 [.       5      31 ..       5      33 .. 0.94
   2 ?   -2.9   0.0       8.3   8.3e+03       3      11 ..     258     266 ..     258     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0008
                                  EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                  I+G+G  G+v A+  a+ g++v +++ 
  gi|91773742|ref|YP_566434.1|  5 IIGSGYVGSVSAACFAELGHEVICIDI 31
                                  9*********************99995 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.3
                                   --SHHHHHH CS
                 NAD_binding_8   3 GaGlsGlva 11 
                                   GaG++G+++
  gi|91773742|ref|YP_566434.1| 258 GAGFGGSCF 266
                                   899999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2602.83
//
Query:       gi|91773743|ref|YP_566435.1|  [L=140]
Description: hypothetical protein Mbur_1797 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.1   4.1      0.089   12.7   4.1    1.1  1  DUF2723   Protein of unknown function (DUF2723)


Domain annotation for each model (and alignments):
>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.1     5e-06     0.089      30     140 ..      21     133 ..       7     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-06
                       DUF2723  30 fslladaekvalrvnllsalssaltilflfltitlllr...........skakkiailgaglvgalafafsdtfWfsavea 99 
                                   f++           n l+ ++++ t+ ++  t+ ++++           + +  ++ lga+++ + a    ++fW + v +
  gi|91773743|ref|YP_566435.1|  21 FEI---------INNELTLMLTGSTMALIGGTVYKVIDtvfifngqfrnKFEALVIFLGAMVITGWATLSVQSFWAEIVTQ 92 
                                   333.........3334444444444444444444444466666668874444445567799999999999*********** PP

                       DUF2723 100 eVYalsslftalvlwlilkweeeadekrsdrwlvliaylig 140
                                     +++  l+ a+++  ++ ++++  +++      +i+y ig
  gi|91773743|ref|YP_566435.1|  93 LNFSMFDLIGAALIIGMIAVNNTVPNWKYLDPKSVIVYGIG 133
                                   **************999999998887665544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 797.18
//
Query:       gi|91773744|ref|YP_566436.1|  [L=118]
Description: hypothetical protein Mbur_1798 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.06   13.5   8.0        1.2    9.3   0.5    2.3  2  Fun_ATP-synt_8  Fungal ATP synthase protein 8 (A6L)


Domain annotation for each model (and alignments):
>> Fun_ATP-synt_8  Fungal ATP synthase protein 8 (A6L)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5   6.9e-05       1.2       9      37 ..      14      42 ..       7      50 .. 0.80
   2 ?    7.6   1.9   0.00023       4.2       5      31 ..      70      98 ..      69     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 6.9e-05
                                  HHHHHHHHHHHHHHHHHHHHHTHHHHHHH CS
                Fun_ATP-synt_8  9 FvNqltfgfliltvllylfskyiLPrllr 37
                                  F+  ++ g+ ++ ++l   sky+LP +  
  gi|91773744|ref|YP_566436.1| 14 FTFAIFMGMKAFLTILAYRSKYLLPSVYT 42
                                  5667888888888889999******9865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00023
                                  -SSTHHHHHHHHHH..HHHHHHHHHHHTH CS
                Fun_ATP-synt_8  5 VPFYFvNqltfgfl..iltvllylfskyi 31
                                  VPF  +N ++ g+    +tvl+ lfs ++
  gi|91773744|ref|YP_566436.1| 70 VPFISINVISPGITwdWITVLISLFSLFV 98
                                  9*********9998446*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 736.00
//
Query:       gi|91773745|ref|YP_566437.1|  [L=202]
Description: imidazole glycerol phosphate synthase subunit HisH [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-19   70.4   0.0    1.9e-19   70.2   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
      3e-09   37.0   0.0    2.3e-08   34.1   0.0    1.9  1  SNO            SNO glutamine amidotransferase family
    7.8e-07   29.1   0.0    1.2e-06   28.4   0.0    1.3  1  Peptidase_C26  Peptidase C26
    1.3e-06   28.1   0.1    6.5e-06   25.9   0.0    1.8  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
       0.05   13.4   0.0      0.077   12.8   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0   5.4e-23   1.9e-19       2     186 ..       6     198 ..       5     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 5.4e-23
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEE CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGI 77 
                                   +iD++ ++ +++ + l ++g++v + +    a+ i     n+dgi++ +G+g+ +     +   ++ i+ +  +++P+LGI
  gi|91773745|ref|YP_566437.1|   6 IIDYGLGNLRSVQKGLEHAGAEVLISKDP--AD-I----GNADGIIL-PGVGAFSdamknIVPFLDPITDYVASGKPLLGI 78 
                                   89********************9999944..33.3....37899988.57888888767755555566666667******* PP

                                   THHHHHHHHHTTT............EEE.....EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTT CS
                        GATase  78 CLGmQllaiefgr............kvv.....kekekehhggtmrlgddetallyglknevierhrHryevnpkelepag 141
                                   CLGmQ+l+  + +            +vv     +  + +++g+++   ++++  ++g ++   +++ H+y v+      + 
  gi|91773745|ref|YP_566437.1|  79 CLGMQMLMTRSEEggltegldlvpgNVVrfprsEL-KVPQMGWNSLKIEHDHPFYEGVSDGAFVYFVHSYYVDT-----DS 153
                                   ********999998899999888887779999455.5*******988888889999*****************8.....44 PP

                                   EEEEEEEETTEEEEEEEEETT.TEEEESSBTTSTTSTTHHHHHHHH CS
                        GATase 142 levtakseddeelmeiiekkn.pfvgvQFHPEststpegpellfnf 186
                                    +++a ++ +  +++ + ++  +++g+QFHPE++   +  ++l nf
  gi|91773745|ref|YP_566437.1| 154 SHMLASCDYGIDFAASVVNSAgNVIGTQFHPEKSGDIG-LKMLTNF 198
                                   45667777777677666666647*********876554.7777776 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   6.3e-12   2.3e-08       6     186 ..      12     202 .]      10     202 .] 0.68

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 6.3e-12
                                   SSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-S..S-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCE CS
                           SNO   6 GaveehveaikkclaenktvkrkedlaevdaliiPG..GestamskliertglyedllefvknsekvvlGtCaGlillske 84 
                                   G+++  ++ +++++ae +  k++ d+ + d++i+PG    s am+ ++    +++++ ++v+ + k++lG C G+ +l  +
  gi|91773745|ref|YP_566437.1|  12 GNLRSVQKGLEHAGAEVLISKDPADIGNADGIILPGvgAFSDAMKNIV---PFLDPITDYVASG-KPLLGICLGMQMLMTR 88 
                                   5667777889*************************8323477787776...6999*******99.**********887766 PP

                                   ETTB.SS-SS--CCEEEETTT........T-SCCGEEEEEEEE.TTTCSEEEEEESS--EEEEE-.TTTCEEEEECT.TEE CS
                           SNO  85 lene.lvktlellkvkvkrna........fGrqvdsfekeldf.knliekftavfiraPvieeilddeavkvlyeld.gei 154
                                    e+  l + l+l+  +v r           G      e++  f +++ +     f+ + +++   +       y  d    
  gi|91773745|ref|YP_566437.1|  89 SEEGgLTEGLDLVPGNVVRFPrselkvpqMGWNSLKIEHDHPFyEGVSDGAFVYFVHSYYVDTDSSHMLASCDYGIDfAAS 169
                                   655559999***987777643001100002222222333333312233444555566666665555555555555554355 PP

                                   EEEEETTEEEESS-GGGSTT.HCHHHHHHHHHH CS
                           SNO 155 vvakqkkilatsfhPelaed.dirvhdyfveev 186
                                   vv   +++++t fhPe + d + ++   fv+++
  gi|91773745|ref|YP_566437.1| 170 VVNSAGNVIGTQFHPEKSGDiGLKMLTNFVDMC 202
                                   666689**********99764788888888875 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   3.5e-10   1.2e-06     100     216 .]      67     185 ..      62     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.5e-10
                 Peptidase_C26 100 aalergvPilgiCrGlqllnv.alGGtlyqdieeqsgltdhreheq....saashavkvekgsllaellgseeievnslHh 175
                                     +++g+P+lgiC+G+q+l      G l + ++ ++g++     ++    +    ++k+e++  ++e ++ + + v  +H+
  gi|91773745|ref|YP_566437.1|  67 DYVASGKPLLGICLGMQMLMTrSEEGGLTEGLDLVPGNVVRFPRSElkvpQMGWNSLKIEHDHPFYEGVS-DGAFVYFVHS 146
                                   567899***********8766156799******9888874444442445677799*************99.8899****** PP

                 Peptidase_C26 176 qaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                     +++ ++  ++ A ++ g+  a ++ ++   v+g Q+HPE
  gi|91773745|ref|YP_566437.1| 147 YYVDTDSS--HMLASCDYGIDFAASVVNSAGNVIGTQFHPE 185
                                   ***98655..5678999999999999**99**********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 !   25.9   0.0   1.8e-09   6.5e-06      26     113 ..      27     103 ..       8     124 .. 0.78
   2 ?    0.0   0.0      0.15   5.4e+02     172     188 ..     169     183 ..     143     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.8e-09
                      GATase_3  26 rvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageve 106
                                   +v +++    ++g+ ad +ilpG        a+++   + + i++++++g+p+lgiC G+qmL ++ e+  g        e
  gi|91773745|ref|YP_566437.1|  27 EVLISK-DPADIGN-ADGIILPGVGAFS--DAMKNIVPFLDPITDYVASGKPLLGICLGMQMLMTRSEEG-G------LTE 96 
                                   444444.6778877.********87655..55566677**************************996653.2......456 PP

                      GATase_3 107 glglLdi 113
                                   gl+l++ 
  gi|91773745|ref|YP_566437.1|  97 GLDLVPG 103
                                   6666665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.15
                      GATase_3 172 GavkksedgnvlGtYlH 188
                                    +v  ++ gnv+Gt +H
  gi|91773745|ref|YP_566437.1| 169 SVV--NSAGNVIGTQFH 183
                                   566..6799*****999 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 ?   12.8   0.0   2.2e-05     0.077      56     109 ..      34      87 ..      12      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                   GCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                     DJ-1_PfpI  56 dvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaa 109
                                    ++ ++ D ++lpG  a ++ +++   +++ + + + +gk++  IC g q+L+ 
  gi|91773745|ref|YP_566437.1|  34 PADIGNADGIILPGVGAFSDAMKNIVPFLDPITDYVASGKPLLGICLGMQMLMT 87 
                                   4556788*******9999********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1279.94
//
Query:       gi|91773746|ref|YP_566438.1|  [L=440]
Description: AIR synthase related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-19   69.5   2.4    8.1e-19   68.3   2.4    1.7  1  AIRS_C    AIR synthase related protein, C-terminal domain
    3.3e-07   30.9   0.4    9.2e-07   29.4   0.4    1.9  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 !   68.3   2.4     9e-23   8.1e-19       1     154 [.     229     380 ..     229     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 9e-23
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHHHHHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGGLlgalaem 79 
                                   ++Gdv+++ ++ G g ++t++   + ++         ++d+    + +++++al+a+  +++v+a++DvT+GG+ g+++e+
  gi|91773746|ref|YP_566438.1| 229 QVGDVILMSEGAGGGTVSTAALYYGMHD---------VVDETINIKFLEACEALIASglTKHVHAMTDVTNGGIRGDAKEI 300
                                   68****************8988866544.........67777777************************************ PP

                                   HHTTTEEEEEECG......THHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEEE CS
                        AIRS_C  80 apasgvgaeidld......kvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsvi 154
                                    + +gv++++d++      ++++++ le+ +  +l  +   llv++ppe a+++++++++ g+ +  vIGe++++ + +++
  gi|91773746|ref|YP_566438.1| 301 SRTAGVKLVFDESkmrplvNPKVLEMLEKLEIDYLGVSLDALLVIAPPEYAEQIIQVVKDVGV-DIDVIGEIVEGSGAEIV 380
                                   *************9888888888888864444455588888**********************.8*********9987766 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 !   29.4   0.4     1e-10   9.2e-07       5      91 ..     118     216 ..      79     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1e-10
                                   EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEEEE CS
                          AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGdts 79 
                                   ++vt+d+  + +   p+   G  ++ + l+D++amG rP+all  + +       ++ + ++g+    e  g+plv+G t 
  gi|91773746|ref|YP_566438.1| 118 IIVTIDGIHSRLSDFPFLA-GFHVARASLRDVYAMGSRPVALLSDIHVAddgdvaKIFDHIAGITTVSELTGIPLVTGSTL 197
                                   5888886666666556555.********************9999999889**9998888899****************998 PP

                                   EESS.......EEEEEEEE CS
                          AIRS  80 fsne.......ptisvtav 91 
                                   +  +       +t  v+av
  gi|91773746|ref|YP_566438.1| 198 RIGGdmdigerMTGGVGAV 216
                                   6533444444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2798.07
//
Query:       gi|91773747|ref|YP_566439.1|  [L=437]
Description: nodulation efficiency protein NfeD [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-13   49.9   0.5    1.2e-12   48.0   0.1    2.2  2  NfeD          NfeD-like C-terminal, partner-binding
      1e-09   38.6   0.4    1.6e-09   37.9   0.4    1.2  1  CLP_protease  Clp protease


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.71   6.3e+03      47      58 ..      93     105 ..      71     132 .. 0.54
   2 !   48.0   0.1   1.3e-16   1.2e-12       3      84 .]     350     431 ..     347     431 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.71
                                   EEEEETT.EEEEE CS
                          NfeD  47 GrvkvdG.eeWsa 58 
                                   G v  +G + Wsa
  gi|91773747|ref|YP_566439.1|  93 GYVYPGGtKAWSA 105
                                   5555555444554 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.3e-16
                                   XXXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSSE CS
                          NfeD   3 avvsvlllvllrplllkklkkkekktnaealiGkegvvledi..g.tGrvkvdGeeWsarsegeiekgerVrVveveGltl 80 
                                   +v+++l+++++++ +l  ++kk+   + e+ iG+ + ++edi  g +G vk++Ge+W+a+ e+ei+ g++V++++v+G   
  gi|91773747|ref|YP_566439.1| 350 IVMGILFVFVFYK-VLEVRHKKPV-IG-EDPIGEMANAIEDIkaGeEGFVKYKGEYWKAKVEEEISDGDKVEITDVQGPLF 427
                                   4555566666665.6665666554.45.459***********98568*******************************999 PP

                                   EEEE CS
                          NfeD  81 iVep 84 
                                   +V++
  gi|91773747|ref|YP_566439.1| 428 TVKK 431
                                   9987 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.4   1.8e-13   1.6e-09      29     179 ..      43     192 ..      25     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.8e-13
                                   HHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE..EE.EETHHHHHHHTS-TTGEEEETT CS
                  CLP_protease  29 vankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticl..Gl.aaSmgslllaagekgkRfalpn 106
                                   va++++   l L ++++ + + + +n+pGG v+++l I +++     +v+ ++   G+ a S+g+l+l++ +    ++ pn
  gi|91773747|ref|YP_566439.1|  43 VADDLVIDALQLAEQNEYEALIITLNTPGGGVDETLKIIEAIDRSDIPVIGYVYpgGTkAWSAGTLILIGTDIA--AMSPN 121
                                   455555555566677888899***********************99999887777443488**********999..799** PP

                                   EEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE- CS
                  CLP_protease 107 arimihqPlggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLidevi 179
                                   + i   qP++   +  + i  e +++++    l+++ ak+ g+++ + ek ++ +  l+ eeA+e G+i+ v 
  gi|91773747|ref|YP_566439.1| 122 TIIGSAQPVSVSPQGIEPI--EDDKIVNALVALAKTKAKQHGRNETTAEKFITENLNLNDEEALEAGIIEYVA 192
                                   **********998866655..5679********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2635.33
//
Query:       gi|91773748|ref|YP_566440.1|  [L=252]
Description: SPFH domain-containing protein/band 7 family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  125.4   3.0      4e-36  124.7   3.0    1.3  1  Band_7          SPFH domain / Band 7 family
     0.0005   19.8   0.5     0.0013   18.5   0.1    1.9  2  Band_7_1        SPFH domain-Band 7 family
  ------ inclusion threshold ------
      0.043   13.3   0.0       0.06   12.8   0.0    1.2  1  Glyco_hydro_80  Glycosyl hydrolase family 80 of chitosanase A


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   3.0   6.6e-40     4e-36       2     177 ..      23     192 ..      22     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.7 bits;  conditional E-value: 6.6e-40
                        Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaav 82 
                                   +++e e+ v++r G+ls+v++pGl +i+P+++sv+++++rv+t+dv++ + v+tkD++ v +d++++yrv  +++++v++v
  gi|91773748|ref|YP_566440.1|  23 MVKEYERVVIFRLGRLSGVKGPGLFLIIPIIDSVVKIDLRVVTIDVPK-QAVITKDNVTVAVDAVIYYRV-LKPAAAVTEV 101
                                   799*********************************************.*********************.********** PP

                        Band_7  83 eresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaa 163
                                       +n++     + + +lr vi++ +l+++ls+r+ +++++++ l +  + +G+ v+ v+++d+++ ++  +a+a+ ++a
  gi|91773748|ref|YP_566440.1| 102 ----ENYKFATAMLSQTTLRDVIGQIELDDVLSKRDTINKDIQELLDASTDPWGIKVTAVTLRDVSIDETMLRAIAKQAEA 178
                                   ....99999999999****************************************************************** PP

                        Band_7 164 eaeaqaeiaraeae 177
                                   e+e++a+i  +e+e
  gi|91773748|ref|YP_566440.1| 179 EREKRARIILSEGE 192
                                   ********999986 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.1e-07    0.0013     145     209 ..     116     178 ..      94     180 .. 0.85
   2 ?   -1.8   0.0      0.34     2e+03     142     168 ..     218     244 ..     203     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-07
                      Band_7_1 145 lsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                   l dv++  +i + d+ +k +++ + ++e l+++ +  G+++++++++++s++e + +a+ k+a++
  gi|91773748|ref|YP_566440.1| 116 LRDVIG--QIELDDVLSKRDTINKDIQELLDASTDPWGIKVTAVTLRDVSIDETMLRAIAKQAEA 178
                                   455554..57778999*********************************************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.34
                      Band_7_1 142 vtrlsdvlaeskipvldlaakseelae 168
                                    +++++v  e+++ v+  ++++ e+a+
  gi|91773748|ref|YP_566440.1| 218 FQTIAEVAREKNLIVISTSSNTAEIAA 244
                                   567889999999999999999998876 PP

>> Glyco_hydro_80  Glycosyl hydrolase family 80 of chitosanase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05      0.06     108     149 ..     146     187 ..     116     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                   HHHHHHHHHH---GGGEEEETTEEEESTTS-TT-HHHHHHHH CS
                Glyco_hydro_80 108 dmknwgvqvtgiaaadlkaddtrldpypnlsrsdskkraalt 149
                                       wg++vt ++  d+  d+t l    +++ ++++kra + 
  gi|91773748|ref|YP_566440.1| 146 STDPWGIKVTAVTLRDVSIDETMLRAIAKQAEAEREKRARII 187
                                   3456**********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1655.61
//
Query:       gi|91773749|ref|YP_566441.1|  [L=707]
Description: phosphoesterase, RecJ-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-10   39.2  11.2    6.5e-10   39.2  11.2    2.0  1  DnaJ_CXXCXGXG    DnaJ central domain
    8.3e-09   35.3   0.0    2.1e-08   34.0   0.0    1.7  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.9e-05   24.8   0.3    4.3e-05   23.7   0.3    1.6  1  DHH              DHH family
     0.0007   19.9   0.3     0.0007   19.9   0.3    2.0  2  S1               S1 RNA binding domain
    0.00098   19.3   0.0     0.0026   17.9   0.0    1.7  1  tRNA_anti_2      OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.033   14.7   1.1      0.033   14.7   1.1    2.4  3  zf-CHY           CHY zinc finger
       0.37   11.0   5.1       0.26   11.5   0.3    2.7  2  Prok-RING_2      Prokaryotic RING finger family 2
       0.64   10.0  24.7       0.17   11.9   6.7    3.4  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        1.4    8.9  17.8        3.8    7.6   0.8    4.2  4  HypA             Hydrogenase/urease nickel incorporation, met
        4.3    7.0  13.0        0.8    9.3   1.0    2.9  1  TackOD1          Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2  11.2   3.6e-13   6.5e-10       1      67 []       5      75 ..       5      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.6e-13
                 DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvree......qktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67
                                  C++C G+g +  ++++C++CkGsG++++       q+ +++f  +  s C++C+G+G++   +++C++C+Gkg
  gi|91773749|ref|YP_566441.1|  5 CNECGGKGYEVLSTEKCPECKGSGKIKSVnlmdlsQNDVKNFL-NEGSVCSKCGGSGEIE-VRKQCPACSGKG 75
                                  ********98888999********7544435554333366666.4588**********65.6679******97 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.2e-11   2.1e-08       1      74 [.     211     281 ..     211     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.2e-11
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
               tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                   V+++G+v+++  +++++   +++ D+ g i + +f ++ t+ + +++ ++++ +tG+v++r ++ l+l v +++
  gi|91773749|ref|YP_566441.1| 211 VKIEGEVIQV--KQTAGPTIFTISDEDGLISCAAFESAGTRAFPEIDADMIITATGEVTSRGDR-LQLEVRSMK 281
                                   89********..****************************************************.***999886 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   2.4e-08   4.3e-05       7      61 ..     344     455 ..     340     500 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.4e-08
                                   ECSSSHHHHHHHHHHHH.......................................................CECS--TCG CS
                                   xxxxxxxxxxxxxxxxx.......................................................xxxxxxxxx RF
                           DHH   7 hknpDtDsigSaialan.......................................................llvDhneks 32 
                                    ++ D+D++++a+a+++                                                       ++vD+++++
  gi|91773749|ref|YP_566441.1| 344 RHHADADGMTAAVAIEKailpmirevngpdaeyhyykrapskapfyelpdvtkdisfaledaarhgqklplvVMVDNGSTE 424
                                   5789*************88888888888888888888888888888888887777777777777777777777******** PP

                                   GCGCCH..HCCCSEEEEEEE-S---SS---S CS
                                   xxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  33 qavege..akeeaedviiiDHHrlgeefetl 61 
                                   ++v +   a+  + d++++DHH + e ++++
  gi|91773749|ref|YP_566441.1| 425 EDVPAMrqAQVYGIDMVVVDHHHPDEIVDQY 455
                                   99987655788899*********98633333 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3   3.9e-07    0.0007       2      68 ..     118     175 ..     117     192 .. 0.85
   2 ?   -3.5   0.1       7.5   1.3e+04       8      16 ..     213     221 ..     210     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.9e-07
                                   STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTT CS
                            S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrr 68 
                                   +e+g+ + ++V +  ++G+fV+l  + +g+++ s+l  +         l ++ +v v+v ++++d +
  gi|91773749|ref|YP_566441.1| 118 LEVGKMYLAKVNNHADFGVFVDLNSNLRGLIHSSNLNIK---------LEEKAPVIVQVKEIRRDGK 175
                                   68999********************************88.........6666666666666666655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.5
                                   EEEEEEEEE CS
                            S1   8 veGeVtsvt 16 
                                   +eGeV++v 
  gi|91773749|ref|YP_566441.1| 213 IEGEVIQVK 221
                                   577777775 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 !   17.9   0.0   1.4e-06    0.0026      20      94 ..     209     280 ..     194     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                   tRNA_anti_2  20 kavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyqlivedi 94 
                                   k v ++Ge+ ++k ++ g + ft++De+  is++ f+s+ ++   +++ +m + ++g+++   +  ++ql v+++
  gi|91773749|ref|YP_566441.1| 209 KLVKIEGEVIQVK-QTAGPTIFTISDEDGLISCAAFESAGTRAFPEIDADMIITATGEVTS--RGDRLQLEVRSM 280
                                   5589********5.469********************887665445777777777777663..333567777665 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5      0.56     1e+03      56      73 ..       4      25 ..       2      32 .. 0.66
   2 ?   14.7   1.1   1.9e-05     0.033      21      73 ..      20      84 ..      16      86 .. 0.82
   3 ?   -2.0   0.1       2.9   5.2e+03      43      61 ..      96     114 ..      92     125 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.56
                        zf-CHY 56 lCkkCkk...efaey....fCpiCk 73
                                  +C++C+    e        +Cp Ck
  gi|91773749|ref|YP_566441.1|  4 ECNECGGkgyE---VlsteKCPECK 25
                                  68899773441...23333699887 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                        zf-CHY 21 aCreCH..........eeledhelerlevkevlcllCeteq..ekavlCkkCkkefaeyfCpiCk 73
                                  +C eC            +l++++++++  +  +c++C      e+ ++C +C+ + a+y C++C+
  gi|91773749|ref|YP_566441.1| 20 KCPECKgsgkiksvnlMDLSQNDVKNFLNEGSVCSKCGGSGeiEVRKQCPACSGKGASYRCDVCD 84
                                  588888888888877744778889999899999****88763366778****************8 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.9
                        zf-CHY  43 lcllCeteqekavlCkkCk 61 
                                    c+ C + + ++vl ++C+
  gi|91773749|ref|YP_566441.1|  96 ACIACGKIEIVHVLDNSCN 114
                                   3555555555555544454 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 ?    0.6   0.6      0.37   6.6e+02       9      29 ..      52      72 ..      48      77 .. 0.86
   2 ?   11.5   0.3   0.00015      0.26       6      40 ..      76     117 ..      72     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.37
                   Prok-RING_2  9 vcdlcatahplaglrqcvlcG 29
                                  vc  c  ++ +   +qc  c 
  gi|91773749|ref|YP_566441.1| 52 VCSKCGGSGEIEVRKQCPACS 72
                                  899999*****9999**9985 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                   Prok-RING_2   6 sqyvcdlcat..ahplaglrqcvlcGrWac.....dacWkde 40 
                                   + y cd+c+   a+p+ g   c+ cG+        ++c +de
  gi|91773749|ref|YP_566441.1|  76 ASYRCDVCDKpiAGPIDGKEACIACGKIEIvhvldNSCNQDE 117
                                   679*****973369************9754333346777777 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 ?    8.7   0.6   0.00093       1.7      11      24 ..      19      32 ..      16      37 .. 0.83
   2 ?   11.9   6.7   9.3e-05      0.17      12      40 ..      52      75 ..      47      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00093
                                  EE-TTTTTTSEETT CS
                     Anti-TRAP 11 tkCdaCngsGkiep 24
                                  +kC++C+gsGki++
  gi|91773749|ref|YP_566441.1| 19 EKCPECKGSGKIKS 32
                                  68999999999987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.3e-05
                                  E-TTTTTTSEETTE......E-TTTTTSS CS
                     Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkg 40
                                   C +C gsG+ie        +CP+CsGkg
  gi|91773749|ref|YP_566441.1| 52 VCSKCGGSGEIEVR-----KQCPACSGKG 75
                                  6***********99.....79*******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 ?    7.6   0.8    0.0021       3.8      72      96 ..       4      28 ..       1      44 [. 0.75
   2 ?    6.1   2.2    0.0059        11      72      96 ..      52      75 ..      45      78 .. 0.83
   3 ?    3.8   0.9     0.032        57      69     100 ..      76     108 ..      74     120 .. 0.75
   4 ?   -0.3   0.0      0.59   1.1e+03      29      68 ..     565     604 ..     547     614 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                                  EETTTS-EEECHHHHHS-TTTSSS- CS
                          HypA 72 rCreCgkefeleekalrCpkCgsad 96
                                  +C+eCg ++ +  ++++Cp+C++++
  gi|91773749|ref|YP_566441.1|  4 ECNECGGKGYEVLSTEKCPECKGSG 28
                                  7****988775544679****9863 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0059
                                  EETTTS-EEECHHHHHS-TTTSSS- CS
                          HypA 72 rCreCgkefeleekalrCpkCgsad 96
                                   C++Cg ++e+e +  +Cp+C++++
  gi|91773749|ref|YP_566441.1| 52 VCSKCGGSGEIEVR-KQCPACSGKG 75
                                  7*********8865.68****9875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.032
                                   -EEEETTTS-EEECHHH.HHS-TTTSSS-EEEE CS
                          HypA  69 vkvrCreCgkefeleek.alrCpkCgsadveiv 100
                                   +++rC++C+k +    + ++ C +Cg+ ++  v
  gi|91773749|ref|YP_566441.1|  76 ASYRCDVCDKPIAGPIDgKEACIACGKIEIVHV 108
                                   6789*****999955455788*****9876555 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.59
                                   EEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE- CS
                          HypA  29 vkvevGelsgvepeaLefafellaegtvlegaeLeieevp 68 
                                   vk+ + + + +  e+L  ++  ++++++ + a+L++ +v+
  gi|91773749|ref|YP_566441.1| 565 VKLLCEQANAMISEQLDACMPNVKSEDLPNTAVLNVLDVE 604
                                   7777788899999***********9999999999876665 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0   0.00045       0.8      67      94 ..      44      72 ..      39      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00045
                       TackOD1 67 eelvdrirlCpsCk.sghlnvrevCpkCk 94
                                  ++++++  +C++C  sg+++vr+ Cp C+
  gi|91773749|ref|YP_566441.1| 44 KNFLNEGSVCSKCGgSGEIEVRKQCPACS 72
                                  57888999*****6478***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4435.82
//
Query:       gi|91773750|ref|YP_566442.1|  [L=203]
Description: orotate phosphoribosyltransferase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-20   72.9   0.4    3.3e-20   72.2   0.4    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
    0.00013   22.0   1.7    0.00041   20.4   1.4    1.9  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
     0.0021   18.1   0.1      0.013   15.6   0.1    2.2  2  HTH_7           Helix-turn-helix domain of resolvase
     0.0043   16.6   0.4      0.012   15.1   0.3    1.7  2  PRTase_2        Phosphoribosyl transferase
      0.005   16.3   0.0     0.0065   15.9   0.0    1.3  1  UPRTase         Uracil phosphoribosyltransferase
     0.0077   15.8   0.0      0.057   13.0   0.0    2.3  2  GerE            Bacterial regulatory proteins, luxR family
  ------ inclusion threshold ------
      0.051   13.5   0.1       0.14   12.1   0.1    1.7  1  HTH_11          HTH domain
       0.11   12.7   0.3       0.95    9.7   0.0    2.5  3  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.11   12.3   0.0        2.8    7.9   0.0    2.4  2  HTH_23          Homeodomain-like domain
       0.11   12.6   0.2       0.87    9.7   0.0    2.1  2  DUF1335         Protein of unknown function (DUF1335)
       0.14   12.1   0.0        0.5   10.4   0.0    1.9  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.14   11.7   0.0       0.33   10.5   0.0    1.6  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 !   72.2   0.4   2.2e-23   3.3e-20      12     128 ..      72     184 ..      64     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.2e-23
                                   EEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEE CS
                  Pribosyltran  12 ldavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVli 92 
                                   ++a +++  e+le  ++  d+v+gi   G+p+a+ +a eLe+ +a+      +++++++  + s    r+ +d++gkk++i
  gi|91773750|ref|YP_566442.1|  72 SQALCDMVIEKLERTQQDADLVIGIGLSGIPIATMMAEELEIDFAIFHDYDDQKGKTNQRGIFS----RNFADVEGKKCII 148
                                   556666777777777899***********************99999888888877777776543....6************ PP

                                   E-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HH CS
                  Pribosyltran  93 VDDildtGgTllaalelLkekgpeevriavlvdkpa 128
                                   VDD++++G T++ ++e L+e+g++ + +av+vdk+ 
  gi|91773750|ref|YP_566442.1| 149 VDDVVSSGATVTDVAEQLREVGATPIAVAVIVDKMN 184
                                   *********************************975 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4   2.1e+03      18      41 ..     104     127 ..     100     139 .. 0.76
   2 !   20.4   1.4   2.8e-07   0.00041      79     136 ..     139     196 ..     130     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                                   HHHHHHHTT-EEEEE--------- CS
                Pribosyl_synth  18 atsyaerlrlglavihGeqkeaea 41 
                                   at  ae l +  a+ h  + ++ +
  gi|91773750|ref|YP_566442.1| 104 ATMMAEELEIDFAIFHDYDDQKGK 127
                                   788999999999999976555444 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.8e-07
                                   S--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS- CS
                Pribosyl_synth  79 GdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesai 136
                                    dv+G+  iivdd++    ++ + ae l+e Ga  i v +    + +d  +++  s++
  gi|91773750|ref|YP_566442.1| 139 ADVEGKKCIIVDDVVSSGATVTDVAEQLREVGATPIAVAVIVDKMNADMIANVPMSSL 196
                                   69***********************************999988888888777777665 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 !   15.6   0.1   8.7e-06     0.013      11      38 ..       8      35 ..       2      35 .. 0.89
   2 ?   -1.1   0.0       1.4     2e+03      19      31 ..     154     166 ..     153     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.7e-06
                                  HGGGGSSTTTT--STTTSSSS---SSSS CS
                         HTH_7 11 inrvvkLleeGisiskIAkevnisRsTv 38
                                  i  +v+L ++G    +IA e+n+sR+Tv
  gi|91773750|ref|YP_566442.1|  8 ILKAVELQSNGLVTGQIANELNVSRETV 35
                                  667999999**99**************8 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                   TTT--STTTSSSS CS
                         HTH_7  19 eeGisiskIAkev 31 
                                   ++G +++++A+++
  gi|91773750|ref|YP_566442.1| 154 SSGATVTDVAEQL 166
                                   57999*****985 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.77   1.1e+03      33      81 ..      69     117 ..      61     135 .. 0.73
   2 !   15.1   0.3   8.3e-06     0.012     121     165 ..     143     186 ..     126     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.77
                      PRTase_2  33 reagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadaleeealy 81 
                                   r + +aL +++ e+ +++ ++  lvig+    + ++  +a++le +  +
  gi|91773750|ref|YP_566442.1|  69 RCISQALCDMVIEKLERTQQDADLVIGIGLSGIPIATMMAEELEIDFAI 117
                                   5566777777777766777777788888888888888888877655555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.3e-06
                      PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryvvvslvdwrsee 165
                                    k+ ++vDD +s+G t+++++++l+e   ++ ++v+ +vd ++++
  gi|91773750|ref|YP_566442.1| 143 GKKCIIVDDVVSSGATVTDVAEQLREVG-ATPIAVAVIVDKMNAD 186
                                   46789*******************9864.5678899999988776 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.4e-06    0.0065     117     160 ..     139     180 ..      81     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.4e-06
                       UPRTase 117 kkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvl 160
                                   ++++ ++ +++D v+++G+++ ++ ++L+e g     I v+ ++
  gi|91773750|ref|YP_566442.1| 139 ADVEGKKCIIVDDVVSSGATVTDVAEQLREVG--ATPIAVAVIV 180
                                   5678899***********************55..5566665554 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.8e-05     0.057      15      35 ..      16      36 ..       9      44 .. 0.86
   2 ?   -0.5   0.0      0.62   9.3e+02      14      27 ..     153     166 ..     151     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                                  CTTS-HHHHHHHHTS-HHHHH CS
                          GerE 15 aeGksnkeIAeelniSekTVk 35
                                   +G+ + +IA eln+S +TV+
  gi|91773750|ref|YP_566442.1| 16 SNGLVTGQIANELNVSRETVT 36
                                  68999***************7 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.62
                                   HCTTS-HHHHHHHH CS
                          GerE  14 laeGksnkeIAeel 27 
                                   + +G +++++Ae+l
  gi|91773750|ref|YP_566442.1| 153 VSSGATVTDVAEQL 166
                                   56899*******98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.6e-05      0.14       5      32 ..       8      35 ..       5      36 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-05
                        HTH_11  5 ilelLleargp.isgeeLAeeLnvSrrtv 32
                                  il+ + e +++ +   ++A eLnvSr tv
  gi|91773750|ref|YP_566442.1|  8 ILKAV-ELQSNgLVTGQIANELNVSRETV 35
                                  66665.44444466778***********9 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 ?    9.7   0.0   0.00063      0.95      13      45 ..       8      41 ..       3      46 .. 0.80
   2 ?   -2.4   0.0       3.7   5.6e+03      24      34 ..     103     113 ..      99     114 .. 0.74
   3 ?   -0.8   0.0       1.2   1.8e+03      36      48 ..     156     168 ..     153     173 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                                  HHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHH CS
                Fe_dep_repress 13 IYtlse.ekkvvktkdlaerLnvspssVsemlkk 45
                                  I+++ e +++   t ++a +Lnvs  +V+  l +
  gi|91773750|ref|YP_566442.1|  8 ILKAVElQSNGLVTGQIANELNVSRETVTWLLTR 41
                                  666667666677799*************977766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                                   -HHHHHHHHTS CS
                Fe_dep_repress  24 ktkdlaerLnv 34 
                                     +++ae+L++
  gi|91773750|ref|YP_566442.1| 103 IATMMAEELEI 113
                                   56889999987 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHH CS
                Fe_dep_repress  36 pssVsemlkkLek 48 
                                   +++V+   + L++
  gi|91773750|ref|YP_566442.1| 156 GATVTDVAEQLRE 168
                                   4555555555544 PP

>> HTH_23  Homeodomain-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       2.8      21      35 ..      22      36 ..       7      41 .. 0.81
   2 ?    1.6   0.0      0.17   2.5e+02      11      27 ..     149     166 ..     142     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                        HTH_23 21 reIAreLgvsrrTvy 35
                                   +IA eL+vsr Tv 
  gi|91773750|ref|YP_566442.1| 22 GQIANELNVSRETVT 36
                                  59***********95 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                        HTH_23  11 llllae.GlsvreIAreL 27 
                                   +  +   G++v+++A++L
  gi|91773750|ref|YP_566442.1| 149 VDDVVSsGATVTDVAEQL 166
                                   5555557*********98 PP

>> DUF1335  Protein of unknown function (DUF1335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00058      0.87       9      43 ..      67     101 ..      63     113 .. 0.86
   2 ?    0.4   0.0      0.43   6.4e+02      24      54 ..     143     171 ..     133     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
                       DUF1335   9 lyrilterlsnaavkkkdylivstdfliGlGfsae 43 
                                     r +++ l +++++k ++    +d++iG+G+s  
  gi|91773750|ref|YP_566442.1|  67 RLRCISQALCDMVIEKLERTQQDADLVIGIGLSGI 101
                                   4689****************************975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.43
                       DUF1335  24 kkdylivstdfliGlGfsaenvtkklksmes 54 
                                    k+++iv  d ++  G + ++v ++l  ++ 
  gi|91773750|ref|YP_566442.1| 143 GKKCIIV--DDVVSSGATVTDVAEQLREVGA 171
                                   4555555..5567888888888888887764 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 ?   10.4   0.0   0.00034       0.5      26      47 ..      23      44 ..      13      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                                  HHHHHTTSSHHHHHHHHHHHHH CS
                     HTH_Crp_2 26 elAsmlGltretvsrilseLkr 47
                                  ++A+ l+++retv+ +l++ k+
  gi|91773750|ref|YP_566442.1| 23 QIANELNVSRETVTWLLTRSKK 44
                                  8*************99998666 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00022      0.33      24      38 ..      22      36 ..       6      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                  HHHHHHHTS-HHHHH CS
                    Sigma70_r4 24 eEIgerlgiSrerVr 38
                                   +I+++l++Sre+V 
  gi|91773750|ref|YP_566442.1| 22 GQIANELNVSRETVT 36
                                  58***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1276.14
//
Query:       gi|91773751|ref|YP_566443.1|  [L=159]
Description: hypothetical protein Mbur_1807 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-11   44.0   0.1      4e-11   43.3   0.1    1.4  1  PIN_6           PIN domain of ribonuclease
     0.0049   16.8   1.5     0.0089   15.9   1.5    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
     0.0078   16.2   0.6      0.014   15.4   0.2    1.6  2  zinc-ribbons_6  zinc-ribbons
     0.0081   16.5   0.0      0.011   16.1   0.0    1.3  1  PIN_4           PIN domain
  ------ inclusion threshold ------
      0.016   14.6   0.7       0.13   11.6   0.1    2.1  2  PIN_5           PINc domain ribonuclease
      0.032   14.3   0.1       0.05   13.7   0.1    1.3  1  Fer4_11         4Fe-4S dicluster domain
      0.082   13.3   0.1       0.17   12.3   0.1    1.5  1  C6_DPF          Cysteine-rich domain
        0.2   11.5   0.5        0.2   11.5   0.5    2.2  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.57   10.3   4.0       0.62   10.2   2.0    2.1  2  Zn-ribbon_8     Zinc ribbon domain
        1.3    9.3   4.1        1.1    9.5   1.7    1.9  2  DUF2072         Zn-ribbon containing protein


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 !   43.3   0.1   2.2e-14     4e-11       3      87 ..       6      87 ..       4      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.2e-14
                         PIN_6  3 lDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellpl.elevrePspesvkkvtefakktGDlsvLSktDievlA 84
                                   D++ +i      ++   + ++t+p+V +E++ ++a  r+e++ + + ++++P+p+  k v ++akkt D++ LS+tDi++l 
  gi|91773751|ref|YP_566443.1|  6 TDSAVFIYG----YDGDTSLFITVPSVKEEMKSREAMMRFEIACEtGTRIETPDPQVRKEVLSIAKKTRDVEELSSTDIDILT 84
                                  677777755....77778889*********************99779**********************************98 PP

                         PIN_6 85 Lty 87
                                   ++
  gi|91773751|ref|YP_566443.1| 85 KAL 87
                                  776 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.5   4.9e-06    0.0089       4      28 ..     128     149 ..     126     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                   Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgt 28 
                                   gkkC++C ++++e+dD   Cp+Cg+
  gi|91773751|ref|YP_566443.1| 128 GKKCTACYRKFDEGDD---CPVCGS 149
                                   79**************...888885 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.5   6.2e+03      14      14 ..      36      36 ..      26      52 .. 0.50
   2 !   15.4   0.2   7.8e-06     0.014      17      43 ..     129     155 ..     115     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                                  S CS
                zinc-ribbons_6 14 g 14
                                  +
  gi|91773751|ref|YP_566443.1| 36 E 36
                                  3 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.8e-06
                                   EE-TTT--EEEEEEE-SSS-S---EEE CS
                zinc-ribbons_6  17 yhCeaCqedlkkealCpeCeqelevlk 43 
                                    +C aC +++++   Cp C++ l++++
  gi|91773751|ref|YP_566443.1| 129 KKCTACYRKFDEGDDCPVCGSLLKKVR 155
                                   48********************99887 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.9e-06     0.011      65     127 ..      60     113 ..       9     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.9e-06
                         PIN_4  65 sgrlkvqtsaeelpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                   ++ l + +++ +++    e +++D  Il  ale+ke+      vL+++D  +++ A++lgie+
  gi|91773751|ref|YP_566443.1|  60 KEVLSIAKKTRDVE----ELSSTDIDILTKALEYKETG-----VLLTDDYAVQNMASVLGIEV 113
                                   22333333333333....35699999999999999998.....******************97 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.13   2.3e+02      43      59 ..      19      36 ..      15      65 .. 0.67
   2 ?   11.6   0.1   7.3e-05      0.13     156     201 ..      76     125 ..      67     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                         PIN_5 43 iscyip.psvykElkefl 59
                                   s++i+ psv +E+k+  
  gi|91773751|ref|YP_566443.1| 19 TSLFITvPSVKEEMKSRE 36
                                  578888899999987533 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.3e-05
                         PIN_5 156 saeDldvllLAkELd..aavvssDeGikkwaeklGlrl..veakkfpkvl 201
                                   s+ D+d+l  A E +  ++++++D  ++++a+ lG+++  ++ kk+++vl
  gi|91773751|ref|YP_566443.1|  76 SSTDIDILTKALEYKetGVLLTDDYAVQNMASVLGIEVkpINQKKIKDVL 125
                                   789********9986447899**************865337777776665 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.8e-05      0.05      29      86 ..      88     147 ..      74     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                       Fer4_11  29 kdeetGaVlldektkkeevrev..veacPykivrkneetgkvekCdmcldrveaGl.lpac 86 
                                   + +etG+ l+d+ +++ ++ +v  +e+ P +  + ++     +kC+ c+ + ++G  +p+c
  gi|91773751|ref|YP_566443.1|  88 EYKETGVLLTDDYAVQ-NMASVlgIEVKPINQKKIKDVLVWGKKCTACYRKFDEGDdCPVC 147
                                   4578999999999998.55555236899************************999636777 PP

>> C6_DPF  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.4e-05      0.17      35      68 ..     113     146 ..      74     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-05
                        C6_DPF  35 kDPfseekeekilvlGakCslCekavCvdeeCsl 68 
                                     P +++k +++lv G kC++C ++   +++C +
  gi|91773751|ref|YP_566443.1| 113 VKPINQKKIKDVLVWGKKCTACYRKFDEGDDCPV 146
                                   3455555659**************9999999965 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       0.4   7.1e+02      21      32 ..     130     141 ..     118     142 .. 0.76
   2 ?   11.5   0.5   0.00011       0.2      18      37 ..     140     159 .]     135     159 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.4
                                   E-TTT--EE-HH CS
                 Rad50_zn_hook  21 cCPlCgReldee 32 
                                   +C  C R++de 
  gi|91773751|ref|YP_566443.1| 130 KCTACYRKFDEG 141
                                   777799***985 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                                   -SEE-TTT--EE-HHHHHHH CS
                 Rad50_zn_hook  18 akgcCPlCgReldeehrseL 37 
                                   ++++CP+Cg+ l   ++++L
  gi|91773751|ref|YP_566443.1| 140 EGDDCPVCGSLLKKVRKRKL 159
                                   3459*******999998776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.2   5.8e+03       4      15 ..      41      51 ..      38      57 .. 0.65
   2 ?   10.2   2.0   0.00034      0.62       7      39 ..     130     154 ..     130     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.2
                   Zn-ribbon_8  4 YeYrCeeCghef 15
                                  +e  Ce  g++ 
  gi|91773751|ref|YP_566443.1| 41 FEIACET-GTRI 51
                                  5666776.5554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00034
                   Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgsevrrv 39 
                                   +C++C ++f++          +CP Cgs +++v
  gi|91773751|ref|YP_566443.1| 130 KCTACYRKFDE--------GDDCPVCGSLLKKV 154
                                   69999999982........234******99986 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   0.0       0.7   1.2e+03      54      73 ..      56      75 ..      21     106 .. 0.58
   2 ?    9.5   1.7    0.0006       1.1       3      27 ..     130     149 ..     128     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.7
                       DUF2072 54 eeeieevldaeeteeeklek 73
                                   ++++evl +++++++ +e 
  gi|91773751|ref|YP_566443.1| 56 PQVRKEVLSIAKKTRDVEEL 75
                                  22355555555555554443 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0006
                       DUF2072   3 kCtkCekvfedgskeilkGCpsCGg 27 
                                   kCt C + f++g++     Cp+CG 
  gi|91773751|ref|YP_566443.1| 130 KCTACYRKFDEGDD-----CPVCGS 149
                                   9*************.....*****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1030.79
//
Query:       gi|91773752|ref|YP_566444.1|  [L=454]
Description: circadian clock protein KaiC [Methanococcoides burtonii DSM 6242]
Scores for complete 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-79  265.8   6.6    2.9e-42  144.6   4.3    2.1  2  ATPase           KaiC
    3.2e-11   43.2   3.1    4.6e-05   23.0   0.0    2.4  2  RecA             recA bacterial DNA recombination protein
    4.7e-10   39.4   0.1    0.00073   19.2   0.0    3.5  4  AAA_25           AAA domain
    1.3e-08   34.5   0.5     0.0007   19.0   0.0    2.6  2  DnaB_C           DnaB-like helicase C terminal domain
    5.3e-08   33.4   0.1    0.00024   21.5   0.0    2.3  2  AAA_16           AAA ATPase domain
    6.8e-08   32.9   0.0     0.0016   18.7   0.0    2.4  2  AAA_22           AAA domain
    1.9e-06   27.7   0.4      0.016   14.8   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    6.9e-06   25.9   0.9        0.1   12.3   0.1    2.9  2  AAA_24           AAA domain
    8.5e-06   25.8   0.1    0.00016   21.7   0.0    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
    1.3e-05   24.9   0.3       0.13   11.9   0.1    2.3  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    2.1e-05   24.6   0.1        0.1   12.6   0.0    3.1  2  AAA_14           AAA domain
    2.4e-05   23.2   1.2       0.59    8.7   0.0    3.9  4  GvpD             GvpD gas vesicle protein
    2.5e-05   23.5   0.3      0.012   14.7   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
    2.6e-05   24.6   1.5       0.16   12.4   0.1    2.7  2  AAA              ATPase family associated with various cellul
      5e-05   22.7   0.9      0.024   13.9   0.0    2.3  2  Zeta_toxin       Zeta toxin
    5.2e-05   22.6   0.2      0.064   12.5   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00016   22.2   2.5       0.17   12.5   0.1    2.8  2  AAA_18           AAA domain
    0.00016   21.0   1.1       0.14   11.4   0.0    2.4  2  Rad51            Rad51
    0.00035   20.1   2.2        0.1   12.1   0.0    3.0  3  AAA_7            P-loop containing dynein motor region
    0.00037   20.2   0.7       0.13   11.9   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    0.00038   20.4   0.4      0.049   13.6   0.0    2.5  2  NACHT            NACHT domain
    0.00078   19.8   0.0       0.27   11.5   0.0    2.4  2  AAA_19           AAA domain
    0.00093   18.9   9.4      0.048   13.4   0.3    2.7  2  AAA_29           P-loop containing region of AAA domain
     0.0011   18.3   0.6      0.046   12.9   0.0    2.3  2  NB-ARC           NB-ARC domain
     0.0015   18.5   0.1       0.13   12.2   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
     0.0024   18.0   0.2       0.36   11.0   0.0    2.3  2  AAA_33           AAA domain
     0.0031   17.3   0.7       0.71    9.6   0.0    2.3  2  AAA_30           AAA domain
     0.0037   17.1   0.1        1.1    9.2   0.0    2.7  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0039   16.7   0.7      0.023   14.2   0.0    2.2  2  PhoH             PhoH-like protein
      0.005   17.4   4.0        1.3    9.5   0.0    2.6  2  ABC_tran         ABC transporter
     0.0062   16.3   0.1        1.5    8.5   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
     0.0066   16.5   0.8          1    9.4   0.0    2.5  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
  ------ inclusion threshold ------
      0.013   15.4   0.1        2.7    7.9   0.0    2.4  2  NTPase_1         NTPase
      0.018   14.3   0.1       0.13   11.4   0.0    2.1  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.018   14.3   1.6       0.25   10.5   0.1    2.3  2  TIP49            TIP49 P-loop domain
       0.02   15.1   0.1        9.5    6.5   0.0    2.5  2  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.02   14.7   0.2        1.6    8.4   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.02   14.6   0.5        1.5    8.5   0.0    2.5  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.022   14.8   0.4        3.1    7.8   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.025   14.5   1.6          5    7.0   0.0    2.7  3  APS_kinase       Adenylylsulphate kinase
      0.026   13.9   0.2       0.24   10.8   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.027   14.4   0.3        3.1    7.7   0.1    2.5  2  RsgA_GTPase      RsgA GTPase
      0.032   14.6   0.2        2.7    8.4   0.0    2.6  2  RNA_helicase     RNA helicase
       0.04   13.5   0.5        2.1    7.9   0.0    2.5  2  SRP54            SRP54-type protein, GTPase domain
      0.042   13.6   0.7       0.21   11.3   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
      0.043   14.1   2.8        5.4    7.2   0.1    2.8  2  AAA_28           AAA domain
      0.055   12.9   0.2       0.85    9.0   0.0    2.3  2  SRPRB            Signal recognition particle receptor beta su
      0.077   12.7   2.2        5.1    6.8   0.0    3.4  3  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.08   12.7   1.5       0.57    9.9   0.1    2.4  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.084   12.6   0.2          3    7.5   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.095   11.6   0.3        6.9    5.5   0.1    2.3  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.12   11.8   0.0        8.1    5.8   0.0    2.3  2  TniB             Bacterial TniB protein
       0.12   11.5   1.1        6.1    5.9   0.0    2.3  2  G-alpha          G-protein alpha subunit
       0.18   11.1   2.7        1.8    7.8   0.1    2.8  3  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.25   11.4   0.7        1.6    8.7   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
       0.45   11.0  10.7        1.5    9.3   0.1    2.9  3  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.0   8.3e-38   2.7e-35       3     229 ..       6     222 ..       4     224 .. 0.94
   2 !  144.6   4.3     9e-45   2.9e-42       1     228 [.     236     450 ..     236     453 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 8.3e-38
                        ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvt.veepaedlrenakslGwdlekleeegk 82 
                                   + I  lD+ilkgG+p+ +++li+G +G+GKt++a+q +++  ek  e +++vt ++ep + + + +++l      l ++g 
  gi|91773752|ref|YP_566444.1|   6 SEIDALDTILKGGFPKPSAILIAGPAGSGKTTLAMQSIFSASEK-KEVCMYVTsLNEPITMVNKFMSKLNFYNISLLSSGT 85 
                                   67999*********************************999777.*******8478888999999******999******* PP

                        ATPase  83 laiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvse 163
                                   +++i + +++         + +  ++ +l+e i++ik  r+viD+it++  + +e+  R+    l+ ++kk++   i + e
  gi|91773752|ref|YP_566444.1|  86 MNYIPIGTESL-------DKGIYTFMWNLEESIEKIKPDRIVIDPITTIGSTLDEEAKRRFYYDLFLRMKKWDALVIATGE 159
                                   ****9999864.......689****************************8899999999999*************999999 PP

                        ATPase 164 kssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                      +e++  + ++++ ++dgvi L ++e+++++v +le++k+Rg +  + + pf Iteegi+ + +
  gi|91773752|ref|YP_566444.1| 160 F--TEDELLKSDLSH-VADGVIYLSNDENNKRRVHHLEVLKLRGQGYISGKQPFSITEEGIVLHRQ 222
                                   5..7779********.*********************************************98765 PP

  == domain 2  score: 144.6 bits;  conditional E-value: 9e-45
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   v+tgIeglD ++ +G+ +g+++li+G +G+GKt+++ qF+ +ga+  +epg++v++ e++ + + na+s+G+d++++ ++g
  gi|91773752|ref|YP_566444.1| 236 VSTGIEGLDIMTGNGVIRGTSTLISGCSGAGKTTIGTQFIAEGAKA-EEPGMIVSFIESEGQTIANASSIGHDIRDFVSSG 315
                                   78*****************************************999.********************************** PP

                        ATPase  82 klaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvs 162
                                    + +i +s+s           ++ e + +l+++ik+ ++kr+ iD +++++  +++  a++ +r l ++++ +gvT+i+ +
  gi|91773752|ref|YP_566444.1| 316 VIKVIFTSMSCL---------EAGEHAINLRSIIKKENIKRIFIDDVNVFSDLMTPLDAKDHIRLLSEMFRSNGVTSIFAQ 387
                                   999998888864.........4778899***************************************************98 PP

                        ATPase 163 ekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvle 228
                                       +++ +g ++ve + +d  + L lke+e+++ +tl ++kmRg++h++ +  feI e g+ ++ 
  gi|91773752|ref|YP_566444.1| 388 R---TDNINGIQNVEDYGMDASVLLSLKEEENHIDKTLTVIKMRGSSHDTGIRQFEIRETGVDIML 450
                                   8...7788999***************************************************9985 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.4e-07   4.6e-05      34      88 ..       4      57 ..       1      73 [. 0.90
   2 !   19.3   1.5   1.9e-06   0.00062      31     110 ..     233     313 ..     216     360 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.4e-07
                                  E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                          RecA 34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafid 88
                                  +ss   ald+ l  GG+pk   i i Gp  sGkttla++ i +a +k  v+ ++ 
  gi|91773752|ref|YP_566444.1|  4 MSSEIDALDTILK-GGFPKPSAILIAGPAGSGKTTLAMQSIFSASEKKEVCMYVT 57
                                  6777778998887.*************************************9985 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.9e-06
                                   --EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT...T--EEEEESS----HHHHHHTT--GGG- CS
                          RecA  31 vetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkk...ggvaafidaehaldpkyakklGvdidel 108
                                    + +s+G  +ldi  G  G+ +G  + i G   +Gktt+  + iae  k+   g +++fi++e     + a  +G di ++
  gi|91773752|ref|YP_566444.1| 233 TDRVSTGIEGLDIMTG-NGVIRGTSTLISGCSGAGKTTIGTQFIAEGAKAeepGMIVSFIESEGQT-IANASSIGHDIRDF 311
                                   5789************.6789***********************9876653337899*****9764.56688888888876 PP

                                   EE CS
                          RecA 109 lv 110
                                   + 
  gi|91773752|ref|YP_566444.1| 312 VS 313
                                   53 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.3e-06   0.00073      16      61 ..       5      50 ..       1      67 [. 0.85
   2 ?    5.5   0.0     0.034        11     129     164 ..     103     138 ..      77     158 .. 0.78
   3 ?   -2.4   0.0       9.3     3e+03      56      91 ..     154     191 ..     150     196 .. 0.68
   4 !   10.4   0.0    0.0011      0.34      28      60 ..     250     281 ..     225     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-06
                        AAA_25 16 aapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGk 61
                                   +++  ++ ++kg  p+ + +l+aG+ g+GKttla++  ++ ++ k
  gi|91773752|ref|YP_566444.1|  5 SSEIDALDTILKGGFPKPSAILIAGPAGSGKTTLAMQSIFSASEKK 50
                                  5678889999**999*********************9888776655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.034
                        AAA_25 129 dvdaleaaieevegvrlvviDplsralgg.densnsd 164
                                   ++ +le+ ie+++ ++ +viDp++ + +  de++++ 
  gi|91773752|ref|YP_566444.1| 103 FMWNLEESIEKIK-PDRIVIDPITTIGSTlDEEAKRR 138
                                   566899*****87.**********9988888887765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.3
                        AAA_25  56 avatGkpwlg......pvapeqgkVlyvsaEdsedelrrRlr 91 
                                    +atG+ +++      ++ +    V+y+s+++++   +rR++
  gi|91773752|ref|YP_566444.1| 154 VIATGE-FTEdellksDLSHVADGVIYLSNDENN---KRRVH 191
                                   556555.444455557666788889999999988...66665 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0011
                        AAA_25  28 gllpagelallaGapgtGKttlaldlalavatG 60 
                                   g+ ++g+ +l+ G +g+GKtt+ ++  ++ a+ 
  gi|91773752|ref|YP_566444.1| 250 GV-IRGTSTLISGCSGAGKTTIGTQFIAEGAKA 281
                                   45.59*******************999988854 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-06    0.0007       3      85 ..       5      87 ..       4     155 .. 0.72
   2 !   13.1   0.3   0.00014     0.044       2      62 ..     236     297 ..     235     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                                  XSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTS CS
                                  xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  3 stgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgkl 84
                                  s++ + LD++++ G+ k   i+iA+ ++ Gkt+la++ + +a +k+++ + v sl+ +  ++v++++s+    + + l +g++
  gi|91773752|ref|YP_566444.1|  5 SSEIDALDTILKgGFPKPSAILIAGPAGSGKTTLAMQSIFSASEKKEVCMYVTSLNEP-ITMVNKFMSKLNFYNISLLSSGTM 86
                                  5678899987752799999********************9999988888888999865.457777777776666666666665 PP

                                  X CS
                                  x RF
                        DnaB_C 85 k 85
                                  +
  gi|91773752|ref|YP_566444.1| 87 N 87
                                  5 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                                   BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHH CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C   2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeq 62 
                                   +stg + LD +t +G+ +g+ ++i ++++ Gkt++ ++++++ a+ e+ +++v  +e + ++
  gi|91773752|ref|YP_566444.1| 236 VSTGIEGLDIMTgNGVIRGTSTLISGCSGAGKTTIGTQFIAEGAKAEEPGMIVSFIESEGQT 297
                                   789******99946************************999888766644444445554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.4e-07   0.00024       8      52 ..       7      51 ..       5      72 .. 0.76
   2 !    9.5   0.1    0.0038       1.2      24      46 ..     254     276 ..     245     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.4e-07
                        AAA_16  8 eleqLlsalervrsgrpelvllsGesGvGKsslv.rellralekdg 52
                                  e+++L ++l+    + p+++l+ G++G+GK++l+ ++++ a ek++
  gi|91773752|ref|YP_566444.1|  7 EIDALDTILKGGF-PKPSAILIAGPAGSGKTTLAmQSIFSASEKKE 51
                                  6777777776444.445*****************899997666664 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0038
                        AAA_16  24 pelvllsGesGvGKsslvrellr 46 
                                   + ++l+sG sG GK+++ +++  
  gi|91773752|ref|YP_566444.1| 254 GTSTLISGCSGAGKTTIGTQFIA 276
                                   3799*************988875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00072      0.23       6      29 ..      23      46 ..      21      85 .. 0.71
   2 !   18.7   0.0     5e-06    0.0016       6     128 ..     255     386 ..     252     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00072
                        AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                  + +++ G++G+GKTtl+ +   ++
  gi|91773752|ref|YP_566444.1| 23 SAILIAGPAGSGKTTLAMQSIFSA 46
                                  6799***********986554444 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 5e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelkaerlsseellealeq 84 
                                   +++++ G+sG+GKTt   ++  +    akaee++  v f++  ++t  + +++ +++  ++ ++  +   +s  +lea e+
  gi|91773752|ref|YP_566444.1| 255 TSTLISGCSGAGKTTIGTQFIAEG---AKAEEPGMIVSFIESEGQTiaNASSIGHDIRDFVSSGVIKVIFTSMSCLEAGEH 332
                                   7899*****************995...677777777779999999999999999999999999999988999999999999 PP

                        AAA_22  85 alrarav.....ielliiDEaqhlrs........eealeeLrsllnlsrkgvqliLv 128
                                   a++ r+      i+ + iD++  + s        +++++ L++++   + gv+ i++
  gi|91773752|ref|YP_566444.1| 333 AINLRSIikkenIKRIFIDDVNVF-SdlmtpldaKDHIRLLSEMFR--SNGVTSIFA 386
                                   999999999999999*****9999.444556666888888877777..888877775 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 !   14.8   0.0   5.1e-05     0.016       5      48 ..       8      57 ..       5     189 .. 0.85
   2 !   11.0   0.3   0.00075      0.24       1      58 [.     239     300 ..     239     356 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-05
                                  HHHHS-EBTT-.....EEEEEESTTSSHHHHH.HHHHHHSSTSSEEEEEE CS
                                  xxxxxxxxxxx.....xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  5 lDalfpivqGq.....rtlipgafgvGktvis.qslskqsnsddaiiyvg 48
                                  +Dal +i +G+      +li g +g Gkt+++ qs+   s++++++ yv 
  gi|91773752|ref|YP_566444.1|  8 IDALDTILKGGfpkpsAILIAGPAGSGKTTLAmQSIFSASEKKEVCMYVT 57
                                  8999999999755554799************99******99999999996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00075
                                   SSHHHHHHS..-EBTT-EEEEEESTTSSHHHHH.HHHHHHSSTSS.EEEEEEESEEHHHHHH CS
                                   xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   1 GirvlDalf..pivqGqrtlipgafgvGktvis.qslskqsnsdd.aiiyvgiGergnevae 58 
                                   Gi+ lD ++   +++G  tli g +g Gkt+i  q +++ +++++  +i+  i   g+++a+
  gi|91773752|ref|YP_566444.1| 239 GIEGLDIMTgnGVIRGTSTLISGCSGAGKTTIGtQFIAEGAKAEEpGMIVSFIESEGQTIAN 300
                                   66777777622589******************967777777777677777777666666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00032       0.1       4      84 ..      24     134 ..      21     139 .. 0.51
   2 !   11.2   0.1   0.00071      0.23       3      82 ..     255     361 ..     253     370 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00032
                        AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.swedfldevvel........................ 59 
                                    ili Gp+g+GKTtla +     +f   ek    ++++ ++++   +++f++++++                         
  gi|91773752|ref|YP_566444.1|  24 AILIAGPAGSGKTTLAMQS----IFSASEKKEVCMYVTSLNEPItMVNKFMSKLNFYnisllssgtmnyipigtesldkgi 100
                                   699*************988....4444444333333333332211333333333333444444444444455555555555 PP

                        AAA_24  60 .........aaeladyktlviDtideleelclae 84 
                                            + e+ + + +viD i+ + +  ++e
  gi|91773752|ref|YP_566444.1| 101 ytfmwnleeSIEKIKPDRIVIDPITTIGSTLDEE 134
                                   5555555443333333556666666665555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00071
                        AAA_24   3 lkiliyGpsgiGKTtlakel..........gpkplfidtekGlksldadkfpdie...swedfldevvel........... 59 
                                    + li G sg+GKTt+ +++          g  + fi  e+ + +     + di+   s         +            
  gi|91773752|ref|YP_566444.1| 255 TSTLISGCSGAGKTTIGTQFiaegakaeepGMIVSFIESEGQTIANASSIGHDIRdfvS---------SGvikviftsmsc 326
                                   67899****************99999764333444445554333333333333333331.........2244455566677 PP

                        AAA_24  60 ............aaeladyktlviDtideleelcl 82 
                                                 +++++k ++iD ++ + +l++
  gi|91773752|ref|YP_566444.1| 327 leagehainlrsIIKKENIKRIFIDDVNVFSDLMT 361
                                   77778888888977888899999999999988775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.9e-07   0.00016       7      68 ..       7      69 ..       5     149 .. 0.75
   2 ?    1.7   0.0      0.61     2e+02      24      67 ..     258     303 ..     252     379 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.9e-07
                      ATPase_2  7 elkeleeilerepnei..yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                  e++ l +il+ +  ++  ++i Gp gsGKt+L +++i   ++k++  +y+++l+e  i+ +++f
  gi|91773752|ref|YP_566444.1|  7 EIDALDTILKGGFPKPsaILIAGPAGSGKTTLAMQSIFSASEKKEVCMYVTSLNEP-ITMVNKF 69
                                  7888888888885544228999******************9*99999999999763.4455555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.61
                      ATPase_2  24 fiYGpegsGKtaLlkeiienledkdk..yviyyialreesisklde 67 
                                   +i G  g GKt++  ++i +  + ++   ++ +i+ +++ i+++++
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFIAEGAKAEEpgMIVSFIESEGQTIANASS 303
                                   6889999******999999876655544333334445555555554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00075      0.24       2      28 ..      24      51 ..      23      83 .. 0.83
   2 !   11.9   0.1    0.0004      0.13       3      90 ..     257     352 ..     255     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00075
                                  EEEEEESTTCCHHHHHHHHH.CT--SS- CS
                          cobW  2 vtvltGflGsGKTtLlnhll.enraglk 28
                                  +++++G+ GsGKTtL  + + + +++++
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAMQSIfSASEKKE 51
                                  5789***********8877765555554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0004
                                   EEEEESTTCCHHHHHHHHH.....CT--SS-EEEEESS-SSCHCCCCCCHCCCT......EEEETTTTECCHCTT-HHHHH CS
                          cobW   3 tvltGflGsGKTtLlnhll.....enraglklavivNefgevsiDaellretgve.....ivelenGciCctlredllkel 73 
                                   t+++G  G+GKTt+ ++ +     +++ g+ +  i+ e + +  +a+ + ++        ++++    + c  + +   +l
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIaegakAEEPGMIVSFIESEGQ-TIANASSIGHDIRDfvssgVIKVIFTSMSCLEAGEHAINL 336
                                   789***************9966655556666666777766.55555555444222555669999999999999999999** PP

                                   HHHHHHHTT-SEEEEEE CS
                          cobW  74 ealeereerldviliEt 90 
                                   +++ ++e ++ +i+i  
  gi|91773752|ref|YP_566444.1| 337 RSIIKKE-NIKRIFIDD 352
                                   ****999.899999976 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   0.00032       0.1       4      50 ..      24      70 ..      21      95 .. 0.77
   2 !    8.5   0.0     0.006       1.9       5      49 ..     257     301 ..     253     366 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00032
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50
                                  +++i G+  +GKTtl+ q i +   kke ++y++  +e+ ++ +++ 
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAMQSIFSASEKKEVCMYVTSLNEPITMVNKFM 70
                                  799************99988777779999999998888887766664 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.006
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                    +i+G+  +GKTt+  q+i e    +e  + +++ + + +++a+ 
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIAEGAKAEEPGMIVSFIESEGQTIANA 301
                                   689****************99886666677777777666555554 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0054       1.7      12      54 ..      24      67 ..      17      86 .. 0.84
   2 !    8.7   0.0    0.0019      0.59     159     207 ..     167     214 ..     153     234 .. 0.83
   3 ?    1.6   0.1      0.25        80      10      32 ..     254     276 ..     247     310 .. 0.78
   4 ?    1.3   0.0      0.33     1e+02     163     205 ..     400     441 ..     372     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0054
                          GvpD 12 tllikGaPGtGktlftlrgldvlrresdv.lyvstrvddetvse 54
                                  ++li G  G+Gkt+++++ + + +++++v +yv++  +  t+ +
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAMQSIFSASEKKEVcMYVTSLNEPITMVN 67
                                  689*****************999999998569988766666555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                          GvpD 159 nsrleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftlad 207
                                   +s l +++dGv+ l   e++  r + +l + klrG    +  qPf++++
  gi|91773752|ref|YP_566444.1| 167 KSDLSHVADGVIYLSNDENN-KRRVHHLEVLKLRGQGYISGKQPFSITE 214
                                   68899*********877774.4666789999****9877779***9975 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.25
                          GvpD  10 GktllikGaPGtGktlftlrgld 32 
                                   G + li G  G+Gkt+   +++ 
  gi|91773752|ref|YP_566444.1| 254 GTSTLISGCSGAGKTTIGTQFIA 276
                                   8999************9888875 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.33
                          GvpD 163 eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftl 205
                                   +y +d  v l +ke+    + + l++ k+rG + +  ++ f +
  gi|91773752|ref|YP_566444.1| 400 DYGMDASVLLSLKEE-ENHIDKTLTVIKMRGSSHDTGIRQFEI 441
                                   6889999******99.678999*********998877777766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.8e-05     0.012     116     156 ..       9      49 ..       1      58 [. 0.73
   2 ?    6.6   0.1     0.011       3.4      93     152 ..     217     277 ..     183     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                         T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                   ++++ +l+    +   il++G+ gsGKttl+   +    ++
  gi|91773752|ref|YP_566444.1|   9 DALDTILKGGFPKPSAILIAGPAGSGKTTLAMQSIFSASEK 49 
                                   5667777777778889*************996655444444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                         T2SSE  93 lviRkksakeltlddlgaeealkekiaevlr.kavrerglilvsGgTgsGKttllyallke 152
                                   +v+ +++  e+++ ++  + ++  +  +++  + v +  + l+sG  g GKtt+    ++e
  gi|91773752|ref|YP_566444.1| 217 IVLHRQELTEMEIPHFTDRVSTGIEGLDIMTgNGVIRGTSTLISGCSGAGKTTIGTQFIAE 277
                                   55555666666666665555555444444441457777899************87666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2    0.0015      0.47       1      23 [.      25      47 ..      25     180 .. 0.61
   2 !   12.4   0.1   0.00051      0.16       2      70 ..     258     356 ..     257     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                                  EEEESSTTSSHHHHHHHHHHHHT CS
                           AAA  1 vllyGppGtGKTllakavakelg 23
                                  +l+ Gp G GKT+la + + +++
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQSIFSAS 47
                                  699***********976655542 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00051
                                   EEESSTTSSHHHHHHHHHHH.HT.......HEEEEEETTTCSSS..........................STTHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavake.lg.......vefleisgsellsk..........................yvgesekkire 48 
                                   l++G  G GKT++  + + e ++       v+f+e +g ++ +                             ge + ++r 
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFIAEgAKaeepgmiVSFIESEGQTIANAssighdirdfvssgvikviftsmsclEAGEHAINLRS 338
                                   789**********99988885333333344779999999999778999999999999999999999988778888888888 PP

                                   HHHHHHHTSTSEEEEEETGGGH CS
                           AAA  49 lfkeakekakpsilfiDEidal 70 
                                   ++k+   ++  + +fiD++  +
  gi|91773752|ref|YP_566444.1| 339 IIKK---EN-IKRIFIDDVNVF 356
                                   8865...33.466****99765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   7.6e-05     0.024      14      37 ..      20      43 ..       9      65 .. 0.83
   2 ?    6.9   0.2      0.01       3.3      18      41 ..     256     279 ..     249     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.6e-05
                    Zeta_toxin 14 erPklillgGqpGAGKselaellk 37
                                   +P +il++G  G+GK++la  + 
  gi|91773752|ref|YP_566444.1| 20 PKPSAILIAGPAGSGKTTLAMQSI 43
                                  79*****************97765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                    Zeta_toxin  18 lillgGqpGAGKselaellkdele 41 
                                   + l++G +GAGK+++ + + +e +
  gi|91773752|ref|YP_566444.1| 256 STLISGCSGAGKTTIGTQFIAEGA 279
                                   679************999988865 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0    0.0002     0.064       3      39 ..      24      58 ..      22      78 .. 0.75
   2 !    7.8   0.1    0.0054       1.7       5      25 ..     258     278 ..     255     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                       DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsv 39
                                   +l+ G aG+GKt ++++ ++ +  +e+++   y++ 
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAMQSIFSA--SEKKEVCMYVTS 58
                                  689***************99999..666655555543 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0054
                       DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                                   l++G +G+GKt ++ +++ae 
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFIAEG 278
                                   89**************99987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00052      0.17       1      15 [.      25      39 ..      25      52 .. 0.95
   2 !    9.0   0.6    0.0062         2       2      18 ..     258     274 ..     258     415 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00052
                        AAA_18  1 IlltGtpGvGKttla 15
                                  Il++G++G+GKttla
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLA 39
                                  99***********98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0062
                        AAA_18   2 lltGtpGvGKttlakeL 18 
                                   l++G++G+GKtt++   
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQF 274
                                   699**********8765 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00044      0.14      23      56 ..       8      41 ..       1      51 [. 0.89
   2 !    7.6   0.6    0.0061         2      13      57 ..     221     274 ..     202     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                                  -HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                         Rad51 23 skklDelLgGGietgsiteifGefrsGktqlcht 56
                                    +lD++L+GG++  s   i G  +sGkt l+++
  gi|91773752|ref|YP_566444.1|  8 IDALDTILKGGFPKPSAILIAGPAGSGKTTLAMQ 41
                                  5689****************************98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0061
                                   HHSS-E.........E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                         Rad51  13 rsellq.........lttGskklDelLgGGietgsiteifGefrsGktqlchtl 57 
                                   r+el +         ++tG + lD + g G+  g+ t i G +++Gkt +  ++
  gi|91773752|ref|YP_566444.1| 221 RQELTEmeiphftdrVSTGIEGLDIMTGNGVIRGTSTLISGCSGAGKTTIGTQF 274
                                   5555555666666669********************************998875 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      71 ..      22      61 ..       9      76 .. 0.76
   2 ?    6.0   0.1     0.024       7.7      32      60 ..     253     281 ..     243     302 .. 0.72
   3 ?   -0.4   0.0       2.2     7e+02     104     112 ..     348     356 ..     341     399 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                         AAA_7 33 kkpvllvGptGtGKtviikd.llkkldkekylsltinfsa 71
                                     +l+ Gp+G+GKt+++++ ++++ +k+++ + + +++ 
  gi|91773752|ref|YP_566444.1| 22 PSAILIAGPAGSGKTTLAMQsIFSASEKKEVCMYVTSLNE 61
                                  5679************999878888887777666666654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                         AAA_7  32 nkkpvllvGptGtGKtviikdllkkldke 60 
                                   ++ ++l+ G +G GKt+i ++++ +  k 
  gi|91773752|ref|YP_566444.1| 253 RGTSTLISGCSGAGKTTIGTQFIAEGAKA 281
                                   57789**************9966654433 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.2
                         AAA_7 104 vFvDDlnmp 112
                                   +F+DD+n+ 
  gi|91773752|ref|YP_566444.1| 348 IFIDDVNVF 356
                                   89****974 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00041      0.13      16      51 ..      16      52 ..       1      71 [. 0.73
   2 ?    6.1   0.1     0.026       8.4      23      54 ..     255     286 ..     245     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00041
                                  HHHCTSSS-EEEECSTTSSHHHHH.HHHHHHSTTTTS CS
               Sigma54_activat 16 kkvaktdlsvlitGesGtGKella.raiheaskrkek 51
                                  k   ++++ +li G  G+GK++la ++i++as++ke 
  gi|91773752|ref|YP_566444.1| 16 KGGFPKPSAILIAGPAGSGKTTLAmQSIFSASEKKEV 52
                                  444567799************9994578888887764 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.026
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfv 54 
                                   +s+li G sG+GK+++ ++  ++  ++e+p +
  gi|91773752|ref|YP_566444.1| 255 TSTLISGCSGAGKTTIGTQFIAEGAKAEEPGM 286
                                   689*************9998888887777655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00015     0.049       3      25 ..      25      47 ..      23      58 .. 0.78
   2 ?    4.7   0.1     0.078        25       4      38 ..     258     290 ..     255     391 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00015
                                  EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                  +++ G+aGsGKTtL+ + ++ + 
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQSIFSAS 47
                                  89************976555544 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.078
                                   EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEE CS
                         NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklvF 38 
                                   ++ G +G GKTt   +++ + a+ + p+  + ++F
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFIAEGAKAEEPG--MIVSF 290
                                   799*********9999998888888777..34444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00085      0.27      11      49 ..      23      57 ..      14     160 .. 0.84
   2 ?    6.1   0.0     0.039        13      10      38 ..     254     282 ..     248     385 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00085
                        AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillva 49
                                  + +l+ +++G+GKT++ ++ +  + e ++v    ++ v+
  gi|91773752|ref|YP_566444.1| 23 SAILIAGPAGSGKTTLAMQSIFSASEKKEV----CMYVT 57
                                  456677778*******99999988888865....44444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.039
                        AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelg 38 
                                    +  l+ +  G GKT++ ++ +a+  +++
  gi|91773752|ref|YP_566444.1| 254 GTSTLISGCSGAGKTTIGTQFIAEGAKAE 282
                                   5678999**********999998877666 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 !   13.4   0.3   0.00015     0.048      24      50 ..      24      48 ..      18      52 .. 0.81
   2 !    8.9   2.5    0.0037       1.2      22      38 ..     253     270 ..     248     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                        AAA_29 24 atlltGpsGsGKSTllDAiqalLvpak 50
                                  a+l++Gp GsGK+Tl  A+q ++ +++
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTL--AMQSIFSASE 48
                                  58************9..6888877765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0037
                        AAA_29  22 kg.atlltGpsGsGKSTl 38 
                                   +g +tl++G sG+GK+T+
  gi|91773752|ref|YP_566444.1| 253 RGtSTLISGCSGAGKTTI 270
                                   4668*************8 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00014     0.046      18      46 ..      20      49 ..       5      59 .. 0.73
   2 ?    3.1   0.2      0.14        45      25      42 ..     259     276 ..     252     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                  SCSEEEEEEESTTSSHHHHH.HHHCCSHCC CS
                        NB-ARC 18 lqslvvalvGmgGvGKttla.kqilnksde 46
                                  ++   + + G +G+GKttla ++i++ s++
  gi|91773752|ref|YP_566444.1| 20 PKPSAILIAGPAGSGKTTLAmQSIFSASEK 49
                                  5555789************83557777544 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                                   EEESTTSSHHHHHHHHCC CS
                        NB-ARC  25 lvGmgGvGKttlakqiln 42 
                                   ++G  G GKtt+ +q + 
  gi|91773752|ref|YP_566444.1| 259 ISGCSGAGKTTIGTQFIA 276
                                   89**********998765 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 !   12.2   0.0   0.00042      0.13       9      53 ..       8      51 ..       1     145 [. 0.83
   2 ?    4.4   0.0       0.1        33      27      51 ..     257     281 ..     231     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00042
                                  HHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                        ResIII  9 eeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgk 53
                                  ++a++ +l+     +   +li+ + G+GKT +a++ i + ++k++
  gi|91773752|ref|YP_566444.1|  8 IDALDTILKGGF-PKPSAILIAGPAGSGKTTLAMQSIFSASEKKE 51
                                  556666665555.88899******************999998743 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.1
                                   EEEEESTTSTHHHHHHHHHHHH-S. CS
                        ResIII  27 glikmaTGtGKTlvaaklierllkk 51 
                                    li    G+GKT + +++i++ +k+
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIAEGAKA 281
                                   6788889************987775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0011      0.36       2      19 ..      25      42 ..      25      77 .. 0.82
   2 ?    4.8   0.1     0.089        29       3      20 ..     258     275 ..     257     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                        AAA_33  2 vllvGlpGsGKstlaerl 19
                                  +l+ G++GsGK+tla + 
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQS 42
                                  5789***********985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.089
                        AAA_33   3 llvGlpGsGKstlaerll 20 
                                   l+ G +G+GK+t  ++ +
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFI 275
                                   5679********988765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0022      0.71      21      44 ..      25      49 ..      18      63 .. 0.74
   2 ?    5.7   0.3     0.034        11      21      45 ..     257     282 ..     250     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0022
                        AAA_30 21 avltGpAGtGKtta.lkalreawea 44
                                   ++ GpAG+GKtt+ ++++  a e+
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLaMQSIFSASEK 49
                                  5799********9625655555554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.034
                        AAA_30  21 avltGpAGtGKttalkal.reaweaa 45 
                                   +++ G  G+GKtt+ ++  +e ++a+
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFiAEGAKAE 282
                                   6899*********9887646655555 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 ?    5.1   0.0     0.061        20       2      20 ..      25      43 ..      24      55 .. 0.82
   2 !    9.2   0.0    0.0034       1.1       4      65 ..     259     324 ..     257     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.061
                          MobB  2 lgivgksgsGKTtLlekli 20
                                  + i+g  gsGKTtL  + i
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQSI 43
                                  6799**********98876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0034
                          MobB   4 ivgksgsGKTtLleklipelkar...glrvgtiKhahhgfd.vdkpgkDsyrhrkAGAkevlvask 65 
                                   i g+sg+GKTt+ ++ i+e ++    g+ v+ i  + + +    + g D   + ++G  +v+ +s 
  gi|91773752|ref|YP_566444.1| 259 ISGCSGAGKTTIGTQFIAEGAKAeepGMIVSFIESEGQTIAnASSIGHDIRDFVSSGVIKVIFTSM 324
                                   789**************9865432338999999988888764777788888888888888877765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.1e-05     0.023      21      50 ..      24      53 ..       9      77 .. 0.87
   2 ?   -0.1   0.3       1.7   5.3e+02      22      42 ..     257     277 ..     249     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.1e-05
                                  EEEEE--TTSSTTHHHHHHHHHHHHTTS-S CS
                          PhoH 21 ivfaiGpaGtGKtylavalavealkkkkvk 50
                                   + ++GpaG+GKt la++  ++a +kk+v 
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAMQSIFSASEKKEVC 53
                                  57899**************99999999875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                                   EEEE--TTSSTTHHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalave 42 
                                   + + G +G+GKt + ++  +e
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIAE 277
                                   678899******998876555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0042       1.3      10      29 ..      21      40 ..      15      71 .. 0.85
   2 ?    7.6   0.9     0.016       5.2      10      30 ..     253     273 ..     249     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0042
                                  TTSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 10 egekvaivGenGaGKStLlk 29
                                  + + + i G+ G+GK+tL++
  gi|91773752|ref|YP_566444.1| 21 KPSAILIAGPAGSGKTTLAM 40
                                  556789***********974 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.016
                                   TTSEEEEEESTTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  10 egekvaivGenGaGKStLlkl 30 
                                   +g+ + i G +GaGK+t+   
  gi|91773752|ref|YP_566444.1| 253 RGTSTLISGCSGAGKTTIGTQ 273
                                   789999***********9554 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 !    8.5   0.0    0.0048       1.5      48      81 ..      23      56 ..       5      68 .. 0.81
   2 ?    5.3   0.0     0.047        15      41      82 ..     248     292 ..     225     311 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0048
                     IstB_IS21 48 enivllGpsGvGKshlaialgveavraglsvlfv 81
                                   +i++ Gp+G GK+ la+    +a ++    ++v
  gi|91773752|ref|YP_566444.1| 23 SAILIAGPAGSGKTTLAMQSIFSASEKKEVCMYV 56
                                  5799*************97777777666666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.047
                     IstB_IS21  41 lsfiekkenivllGpsGvGKshlaial...gveavraglsvlfvr 82 
                                   ++ + +  + ++ G sG+GK+ + + +   g +a + g+ v+f+ 
  gi|91773752|ref|YP_566444.1| 248 GNGVIRGTSTLISGCSGAGKTTIGTQFiaeGAKAEEPGMIVSFIE 292
                                   555667778899**********98654222777777888888875 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 !    9.4   0.0    0.0032         1       5      33 ..      28      55 ..      25     156 .. 0.88
   2 ?    4.7   0.6     0.095        31       3      19 ..     258     274 ..     256     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0032
                                  ESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  5 stkGGvGKTtlaanLaralarrglrVllv 33
                                  ++  G+GKTtla  ++++ ++ +++V ++
  gi|91773752|ref|YP_566444.1| 28 AGPAGSGKTTLAMQSIFSASE-KKEVCMY 55
                                  45569***************9.9999986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.095
                                   EEESSTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          CbiA   3 iastkGGvGKTtlaanL 19 
                                   ++s+ +G+GKTt+ + +
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQF 274
                                   68999*******97766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0083       2.7       2      18 ..      25      41 ..      24      55 .. 0.79
   2 ?    5.2   0.1     0.058        19       3      51 ..     258     310 ..     256     354 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0083
                                  EEEE--TTSSHHHHHHH CS
                      NTPase_1  2 vfiTGppGvGKtTlvkk 18
                                  ++i Gp G+GKtTl  +
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQ 41
                                  89***********9754 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.058
                                   EEE--TTSSHHHHHHHHHHH.H.....GGGEEEEEEEEE-.------EEEEEE CS
                      NTPase_1   3 fiTGppGvGKtTlvkkvlel.lkss..gvkvgGfyteevr.eggrrigFkivd 51 
                                   +i+G +G GKtT+  + + +  k +  g+ v+ +  e  +  + + ig +i d
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFIAEgAKAEepGMIVSFIESEGQTiANASSIGHDIRD 310
                                   799**********7765544033221144444333333334455555666655 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0004      0.13      26      62 ..      25      61 ..      14      74 .. 0.84
   2 ?   -0.2   0.0       1.4   4.5e+02      26      51 ..     257     285 ..     253     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                  EEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-GGG CS
                          DAP3 26 lvltGekgsGKSvlLlqalayAlekgwvvlhvpeaed 62
                                  +++ G  gsGK++l +q++  A ek+ v + v + ++
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQSIFSASEKKEVCMYVTSLNE 61
                                  6899**********************99999887655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                                   EEEE-SSSSSTTTTHHHHHHHGGGS...- CS
                          DAP3  26 lvltGekgsGKSvlLlqalayAlek...g 51 
                                    +++G  g GK++  +q +a ++++   g
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIAEGAKAeepG 285
                                   6799*************999988774444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00077      0.25      52      71 ..      24      43 ..      14      59 .. 0.79
   2 ?    2.5   0.2       0.2        66      45      67 ..     249     271 ..     235     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00077
                                  XXXXXXXXXXXXXXXXXXXX CS
                         TIP49 52 avLlaGpsgtGktalaiais 71
                                  a+L+aGp+g+Gkt la+   
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAMQSI 43
                                  8***************9754 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.2
                                   XXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  45 ekklaGravLlaGpsgtGktala 67 
                                   ++ + G + L++G sg+Gkt + 
  gi|91773752|ref|YP_566444.1| 249 NGVIRGTSTLISGCSGAGKTTIG 271
                                   5678899*************996 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.03       9.5       2      29 ..      25      52 ..      24      79 .. 0.69
   2 ?    6.1   0.0     0.038        12       4      44 ..     259     298 ..     257     313 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.03
                                  EEEESSTTSSHHHHHHCHCT-CCC-EEE CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkfsekek 29
                                  +++ G +g+GKt+l+ + + +  ++ke 
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQSIFSASEKKEV 52
                                  7899**********98887555544443 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.038
                                   EESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGS CS
                           Roc   4 lvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtki 44 
                                   + G sg+GKt++ ++f+ +  + +e + + v+f+++e ++i
  gi|91773752|ref|YP_566444.1| 259 ISGCSGAGKTTIGTQFIAEGAKAEE-PGMIVSFIESEGQTI 298
                                   56899************88776655.445577777665554 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0     0.005       1.6       1      39 [.      25      59 ..      25      89 .. 0.65
   2 ?    4.1   0.2      0.11        34       1      20 [.     257     276 ..     257     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.005
               Viral_helicase1  1 ivvhGvpGcGKStli.rkllrtsliltvnrptaelltegk 39
                                  i+++G +G+GK+tl  +++++      + ++ ++++  ++
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAmQSIFSA-----SEKKEVCMYVTSL 59
                                  6899*********851445544.....3344455555544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
               Viral_helicase1   1 ivvhGvpGcGKStlirkllr 20 
                                   ++++G+ G+GK+t+  +++ 
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIA 276
                                   589**********8777665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0047       1.5       2      48 ..      25      73 ..      24     116 .. 0.68
   2 ?    3.7   0.1      0.14        43       4      19 ..     259     274 ..     258     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0047
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaei....egdsflrldraekdl 48
                                  I +ag+ G+Gktt+a  +++if   ++k + +        +++++++  +l
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLA--MQSIFSASEKKEVCMyvtsLNEPITMVNKFMSKL 73
                                  679**********86..7888887777755443332222344445555555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
                           PRK   4 vagsSGaGkttvarkl 19 
                                   ++g SGaGktt+  ++
  gi|91773752|ref|YP_566444.1| 259 ISGCSGAGKTTIGTQF 274
                                   7899*******98877 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0097       3.1      20      39 ..      23      42 ..       2      60 .. 0.70
   2 ?    4.6   0.1     0.099        32      19      41 ..     254     276 ..     232     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0097
                                  EEEEEEESTTSSHHHHHHHH CS
                          TsaE 20 dvilLeGdLGaGKTtlvrgl 39
                                  ++il+ G+ G+GKTtl+ + 
  gi|91773752|ref|YP_566444.1| 23 SAILIAGPAGSGKTTLAMQS 42
                                  4699***********97543 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.099
                                   TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglak 41 
                                   g+  l++G  GaGKTt+  ++++
  gi|91773752|ref|YP_566444.1| 254 GTSTLISGCSGAGKTTIGTQFIA 276
                                   4557899999******9555443 PP

>> APS_kinase  Adenylylsulphate kinase
   #    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      21 ..      22      41 ..      21      58 .. 0.82
   2 ?    5.8   0.1     0.035        11       2      22 ..     254     274 ..     253     289 .. 0.84
   3 ?   -2.0   0.0       9.4     3e+03      72     107 ..     313     350 ..     291     375 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.016
                                  -EEEEEESSTTSSHHHHHHH CS
                    APS_kinase  2 gvvvwltGlsgsGKstiana 21
                                  +  ++++G +gsGK+t+a++
  gi|91773752|ref|YP_566444.1| 22 PSAILIAGPAGSGKTTLAMQ 41
                                  67899*************86 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.035
                                   -EEEEEESSTTSSHHHHHHHH CS
                    APS_kinase   2 gvvvwltGlsgsGKstianal 22 
                                   g+  +++G sg+GK+ti +++
  gi|91773752|ref|YP_566444.1| 254 GTSTLISGCSGAGKTTIGTQF 274
                                   666789***********8765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 9.4
                                   HTT-E.EEEE----SHHHHH..HHHHHHHCHTEEEEEEE CS
                    APS_kinase  72 dagli.vlvafisPyreeRe..aarelleealkfievfv 107
                                    +g+i v+ + +s  ++  +  + r++++++ ++  +f+
  gi|91773752|ref|YP_566444.1| 313 SSGVIkVIFTSMSCLEAGEHaiNLRSIIKKE-NIKRIFI 350
                                   5555423334444444332211234444432.3333333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00075      0.24      25      55 ..      25      53 ..      16      79 .. 0.80
   2 ?    0.4   0.0       1.1   3.5e+02      25      41 ..     257     273 ..     251     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00075
                  Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeeal 55
                                  +l++Gp+GsGKt la  ++s++++ +++e+ 
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLA--MQSIFSASEKKEVC 53
                                  899***********8..68899888888864 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                  Mg_chelatase  25 lllvGppGsGKtmlakr 41 
                                    l+ G +G+GKt + ++
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQ 273
                                   6899********99765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.11        37     100     116 ..      23      39 ..       2      54 .. 0.77
   2 ?    7.7   0.1    0.0095       3.1      95     119 ..     250     274 ..     211     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                                   SEEEEECSTTSSHHHHH CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLi 116
                                   + ++++G+ G GK+tL 
  gi|91773752|ref|YP_566444.1|  23 SAILIAGPAGSGKTTLA 39 
                                   56789**********96 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0095
                                   HHCTTSEEEEECSTTSSHHHHHHHH CS
                   RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinal 119
                                    ++++  +++ G SG+GK+t+  ++
  gi|91773752|ref|YP_566444.1| 250 GVIRGTSTLISGCSGAGKTTIGTQF 274
                                   4789999*************96655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0083       2.7       1      25 [.      25      46 ..      25      75 .. 0.76
   2 ?    3.6   0.1      0.26        83       2      23 ..     258     279 ..     257     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0083
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                  i++ Gp+g GK+tla +   ++ ++
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQ---SIFSA 46
                                  6899**********998...33333 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.26
                  RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                                   +++G sg GK+t+ ++++++ +
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFIAEGA 279
                                   589**********999988765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0066       2.1       2      20 ..      23      41 ..      22      58 .. 0.69
   2 ?    3.4   0.1      0.16        53       4      21 ..     257     274 ..     255     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0066
                                  EEEEEEESTTSSHHHHHHH CS
                         SRP54  2 nvillvGlqGaGKTttlaK 20
                                  + il++G+ G+GKTt + +
  gi|91773752|ref|YP_566444.1| 23 SAILIAGPAGSGKTTLAMQ 41
                                  689***********97643 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.16
                                   EEEEESTTSSHHHHHHHH CS
                         SRP54   4 illvGlqGaGKTttlaKL 21 
                                   +l+ G  GaGKTt  ++ 
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQF 274
                                   6899*********86655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00067      0.21       8      57 ..      11      60 ..       7     165 .. 0.79
   2 ?    0.2   0.3       1.8   5.6e+02      12      31 ..     252     271 ..     245     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00067
                                  HHHHHTT.....CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSH CS
                                  xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  8 iplilgg.....gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtr 57
                                  +++il+g       +l+a++ GsGKT+ ++  ++++      +++  +++v+ + 
  gi|91773752|ref|YP_566444.1| 11 LDTILKGgfpkpSAILIAGPAGSGKTTLAMQSIFSAS-----EKKEVCMYVTSLN 60
                                  5566655455557899*************99999555.....3444555555544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.8
                                   HTTCEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          DEAD  12 lgggdvlvaaeTGsGKTlaf 31 
                                   ++g + l+++  G+GKT++ 
  gi|91773752|ref|YP_566444.1| 252 IRGTSTLISGCSGAGKTTIG 271
                                   567889999********975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.036        11       2      16 ..      25      39 ..      24      50 .. 0.91
   2 ?    7.2   0.1     0.017       5.4       3      22 ..     258     277 ..     256     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.036
                        AAA_28  2 ivitGgestGKTtll 16
                                  i i G+ ++GKTtl+
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLA 39
                                  89***********98 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.017
                        AAA_28   3 vitGgestGKTtlleaLaar 22 
                                    i+G++++GKTt+  ++ a+
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQFIAE 277
                                   69**********98776655 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 ?    9.0   0.0    0.0027      0.85       4      30 ..      23      49 ..      21      75 .. 0.64
   2 ?    1.2   0.0      0.69   2.2e+02       6      26 ..     257     277 ..     253     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0027
                                  -EEEEE-STTSSHHHHHHHHHHSS--- CS
                         SRPRB  4 pavllvGlsdsGKTslftrLttdsvkk 30
                                   a+l++G+  sGKT+l  +    + +k
  gi|91773752|ref|YP_566444.1| 23 SAILIAGPAGSGKTTLAMQSIFSASEK 49
                                  589***********9976654443333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.69
                                   EEEE-STTSSHHHHHHHHHHS CS
                         SRPRB   6 vllvGlsdsGKTslftrLttd 26 
                                    l+ G s +GKT++ t+   +
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIAE 277
                                   6999*********99988766 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.016       5.1       3      24 ..      24      46 ..      22     101 .. 0.70
   2 ?    0.3   0.1       1.7   5.4e+02       5      19 ..     258     272 ..     255     283 .. 0.79
   3 ?    2.5   0.0      0.35   1.1e+02     104     140 ..     365     401 ..     358     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                     PduV-EutP  3 killiGkvgsGKttLt.qalkge 24
                                   il+ G+ gsGKttL+ q++   
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAmQSIFSA 46
                                  58999**********63555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.7
                     PduV-EutP   5 lliGkvgsGKttLtq 19 
                                   l+ G +g+GKtt+  
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGT 272
                                   67799*******854 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.35
                     PduV-EutP 104 deenieaveelLksaGaekifevsavekegieellky 140
                                    +++i+   e+++s G+++if   + + +gi+++ +y
  gi|91773752|ref|YP_566444.1| 365 AKDHIRLLSEMFRSNGVTSIFAQRTDNINGIQNVEDY 401
                                   468899999*************999999999999876 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 ?    9.9   0.1    0.0018      0.57       1      18 [.      27      44 ..      27      61 .. 0.65
   2 ?    1.4   0.2      0.73   2.3e+02       1      15 [.     259     273 ..     259     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0018
                    ATP_bind_1  1 vvGpaGsGKttfvgalse 18
                                  ++GpaGsGKtt+  + + 
  gi|91773752|ref|YP_566444.1| 27 IAGPAGSGKTTLAMQSIF 44
                                  79*********9543332 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.73
                    ATP_bind_1   1 vvGpaGsGKttfvga 15 
                                   + G+ G+GKtt+  +
  gi|91773752|ref|YP_566444.1| 259 ISGCSGAGKTTIGTQ 273
                                   579********8655 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 ?    7.5   0.0    0.0095         3      35      51 ..      24      40 ..      19      66 .. 0.81
   2 ?    2.2   0.1      0.41   1.3e+02      36      56 ..     257     278 ..     242     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0095
                        RuvB_N 35 hvllyGpPGlGkttlak 51
                                   +l++Gp G Gkttla+
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAM 40
                                  589************96 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.41
                        RuvB_N  36 vllyGpPGlGkttla.kiiake 56 
                                   +l++G  G Gktt+  + ia+ 
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGtQFIAEG 278
                                   699**********962566665 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 ?    3.9   0.0     0.065        21      17      42 ..      24      49 ..      21      57 .. 0.77
   2 ?    5.5   0.1     0.021       6.9      18      48 ..     257     288 ..     253     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.065
                 TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairar 42
                                   ili+G +GsGKt+ + + + ++ ++
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTLAMQSIFSASEK 49
                                  589**********9877666555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                 TrwB_AAD_bind  18 ilivGttGsGKtqalekllra.irargdraiv 48 
                                   +li G  G+GKt+  ++++++ ++a +  +iv
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFIAEgAKAEEPGMIV 288
                                   89***************997527777778887 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      0.13        41      34      54 ..      21      41 ..       2      67 .. 0.81
   2 ?    5.8   0.0     0.025       8.1      33      61 ..     252     280 ..     241     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                          TniB 34 rmpnlllvGdsnnGKtmivek 54
                                  +++ +l++G+   GKt+++ +
  gi|91773752|ref|YP_566444.1| 21 KPSAILIAGPAGSGKTTLAMQ 41
                                  56789************9754 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.025
                          TniB  33 krmpnlllvGdsnnGKtmivekFarlhpp 61 
                                    r  + l+ G s  GKt+i  +F ++  +
  gi|91773752|ref|YP_566444.1| 252 IRGTSTLISGCSGAGKTTIGTQFIAEGAK 280
                                   577899*****************876555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.019       6.1      23      54 ..      22      47 ..       2     208 .. 0.67
   2 ?    4.5   0.3     0.051        16      26      44 ..     257     275 ..     245     447 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.019
                                  EEEEEEEESTTSSHHHHHHHHHHHCS----HH CS
                       G-alpha 23 evkllllGqseSGKsTilkqlkllykkgfsee 54
                                  +  +l+ G ++SGK+T+   ++ ++    s +
  gi|91773752|ref|YP_566444.1| 22 PSAILIAGPAGSGKTTLA--MQSIF----SAS 47
                                  4579*************5..44444....333 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.051
                                   EEEEESTTSSHHHHHHHHH CS
                       G-alpha  26 llllGqseSGKsTilkqlk 44 
                                    l+ G+s+ GK+Ti  q+ 
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTIGTQFI 275
                                   6899**********99986 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0057       1.8      39      63 ..      22      46 ..      14      57 .. 0.83
   2 ?    2.3   0.1      0.27        87      41      64 ..     256     279 ..     225     306 .. 0.83
   3 ?   -2.2   0.0       6.5   2.1e+03     121     133 ..     374     386 ..     334     432 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0057
                                  -.SEEEE--TTSSHHHHHHHHHHHH CS
                  FtsK_SpoIIIE 39 ashllvaGatgsGKStalntLilSl 63
                                  +s +l+aG  gsGK+t  +  i S+
  gi|91773752|ref|YP_566444.1| 22 PSAILIAGPAGSGKTTLAMQSIFSA 46
                                  4569************998877776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.27
                                   SEEEE--TTSSHHHHHHHHHHHHH CS
                  FtsK_SpoIIIE  41 hllvaGatgsGKStalntLilSla 64 
                                    +l+ G +g GK+t    +i+  a
  gi|91773752|ref|YP_566444.1| 256 STLISGCSGAGKTTIGTQFIAEGA 279
                                   589***********9888887655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.5
                                   HHHHHTT-SSHHH CS
                  FtsK_SpoIIIE 121 alfreagvrsiaa 133
                                   ++fr+ gv si a
  gi|91773752|ref|YP_566444.1| 374 EMFRSNGVTSIFA 386
                                   3333333333333 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     0.005       1.6       2      19 ..      25      42 ..      24      61 .. 0.81
   2 ?   -0.7   0.0         4   1.3e+03       3      19 ..     258     274 ..     256     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.005
                                  EEEE--SSSSHHHHHHHG CS
                         AAA_5  2 vlLvGppGtgKselaerl 19
                                  +l+ Gp G+gK++la++ 
  gi|91773752|ref|YP_566444.1| 25 ILIAGPAGSGKTTLAMQS 42
                                  6899***********985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4
                                   EEE--SSSSHHHHHHHG CS
                         AAA_5   3 lLvGppGtgKselaerl 19 
                                   l+ G +G gK+++  ++
  gi|91773752|ref|YP_566444.1| 258 LISGCSGAGKTTIGTQF 274
                                   7889********98765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0046       1.5      21      35 ..      24      38 ..      15      43 .. 0.87
   2 ?    4.2   4.3      0.17        54      22      35 ..     257     270 ..     248     272 .. 0.93
   3 ?   -1.3   0.0       8.4   2.7e+03      57      85 ..     347     382 ..     297     430 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0046
                        AAA_23 21 ltlItGpNGaGKTTi 35
                                    lI Gp G+GKTT+
  gi|91773752|ref|YP_566444.1| 24 AILIAGPAGSGKTTL 38
                                  679***********9 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.17
                        AAA_23  22 tlItGpNGaGKTTi 35 
                                   tlI+G  GaGKTTi
  gi|91773752|ref|YP_566444.1| 257 TLISGCSGAGKTTI 270
                                   9************9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 8.4
                        AAA_23  57 gfeksdveiese....gkvkayvelt...fenkdgr 85 
                                   +++ +dv+++s+     + k  ++l    f++++ +
  gi|91773752|ref|YP_566444.1| 347 RIFIDDVNVFSDlmtpLDAKDHIRLLsemFRSNGVT 382
                                   333444443333333322222233333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 2766.89
//
Query:       gi|91773753|ref|YP_566445.1|  [L=263]
Description: NAD synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-84  282.3   0.0    2.6e-84  282.1   0.0    1.0  1  NAD_synthase   NAD synthase
    1.6e-07   30.4   0.0    7.5e-06   25.0   0.1    2.1  2  tRNA_Me_trans  tRNA methyl transferase
    1.4e-05   24.7   0.0    3.5e-05   23.4   0.0    1.6  2  QueC           Queuosine biosynthesis protein QueC
    0.00048   19.9   0.0     0.0005   19.8   0.0    1.1  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
       0.13   11.8   0.0        0.2   11.2   0.0    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.1   0.0   7.3e-88   2.6e-84       5     242 .]      10     249 ..       6     249 .. 0.97

  Alignments for each domain:
  == domain 1  score: 282.1 bits;  conditional E-value: 7.3e-88
                                   HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHH CS
                  NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpiv 85 
                                   + df+  +++ +g +g+v+G+SGG+DS+lva+l+v+alg envl++ +P+  ++++++eda ++ae lgi++k+i+i++++
  gi|91773753|ref|YP_566445.1|  10 IIDFIGTKLEGTGIEGAVVGISGGIDSALVAYLSVEALGAENVLGIHMPEASTPKSEIEDASKVAEALGIDFKVINITNVL 90 
                                   679****************************************************************************** PP

                                   HHHHHHHHHHH..-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHHHHHH CS
                  NAD_synthase  86 rafeqelkeak..edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevkeLak 164
                                   ++++ ++ +    +  ++gNlkaRiRm +ly++an+++++v+gTgnksE+++GyfTkyGDg++d++pi++l+Ktev+e++k
  gi|91773753|ref|YP_566445.1|  91 EVYRTAMPDIDgaSAHVDGNLKARIRMSMLYYYANMFGRVVMGTGNKSEILLGYFTKYGDGGVDIEPIGDLYKTEVREMSK 171
                                   *****88776666899***************************************************************** PP

                                   HTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGGSSS CS
                  NAD_synthase 165 elnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklvkksehKrklp 242
                                    l+vPe++l+k+PsA+L++gqtDe++Lg++Y+++D++L+ +  ++ +e ++ ++++p e+++ i  +v+++ hKr++p
  gi|91773753|ref|YP_566445.1| 172 MLGVPESILEKAPSAGLWEGQTDEDDLGVTYETIDKVLQPILAGEGQERVHLKLGVPMEEISSILLRVRSNLHKRTTP 249
                                   ***************************************9999999999**************************987 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   2.1e-09   7.5e-06       4      72 ..      27      88 ..      24      97 .. 0.85
   2 !    3.4   0.0    0.0077        28     167     195 ..     157     187 ..     154     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.1e-09
                 tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                  vv++SgG+DS+++a+l  e+    +v g+++   ++          +++++da++vae lgi ++v+++++
  gi|91773753|ref|YP_566445.1| 27 VVGISGGIDSALVAYLSVEALgaENVLGIHMPEAST---------PKSEIEDASKVAEALGIDFKVINITN 88
                                  89*************988875458999**9976554.........45789****************99875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0077
                 tRNA_Me_trans 167 PlgeltKeevrkiAkeagla..vaekkdSqg 195
                                   P+g+l K+evr++ k  g++  + ek  S g
  gi|91773753|ref|YP_566445.1| 157 PIGDLYKTEVREMSKMLGVPesILEKAPSAG 187
                                   9**************9998766777777766 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   9.9e-09   3.5e-05       2      72 ..      26      97 ..      25     114 .. 0.88
   2 ?   -2.2   0.0      0.67   2.4e+03     157     176 ..     157     176 ..     152     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.9e-09
                                  EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG CS
                          QueC  2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaL 72
                                  avv +SGG+DS+ v++l  ++   ++v  +++   +  k+e+e a+k+a++lg+ + k+++++ + e+ ++a+
  gi|91773753|ref|YP_566445.1| 26 AVVGISGGIDSALVAYLSVEALgaENVLGIHMPEASTPKSEIEDASKVAEALGI-DFKVINITNVLEVYRTAM 97
                                  89**************999886457899999999999*****************.******998888777765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.67
                                   TTTT--HHHHHHHHHHTTHH CS
                          QueC 157 PlidlsKaeivklgkelgvp 176
                                   P+ dl K+e+ +++k lgvp
  gi|91773753|ref|YP_566445.1| 157 PIGDLYKTEVREMSKMLGVP 176
                                   999999*******9999987 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.4e-07    0.0005      24     123 ..      30     132 ..      26     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-07
                  Asn_synthase  24 LSGGlDSSliaalaarqsksplktFsigfee..kgsdeakyakevaehlgtehtelvlte.....eelldalpdviyhlee 97 
                                   +SGG+DS+l+a+l  + +    +   i++ e     +e++ a +vae+lg++   + +t+     + ++  ++ +  h++ 
  gi|91773753|ref|YP_566445.1|  30 ISGGIDSALVAYLSVEALG-AENVLGIHMPEasTPKSEIEDASKVAEALGIDFKVINITNvlevyRTAMPDIDGASAHVDG 109
                                   7***************997.7788888884446999****************66665555211112333346666667777 PP

                  Asn_synthase  98 pfadrsaiplyllsrlakrkgvkvvL 123
                                    + +r  +++++   +a +++ +vv+
  gi|91773753|ref|YP_566445.1| 110 NLKARIRMSMLY--YYA-NMFGRVVM 132
                                   655555555544..444.44555555 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.5e-05       0.2       6      57 ..      26      78 ..      22     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                          ThiI  6 vlaLlSgGiDSpVaaylllkR.Gc.rvvlvhlknepgtseeaiekveklaella 57
                                  +++ +SgGiDS   ayl ++  G  +v  +h+  e  t++ +ie   k+ae l 
  gi|91773753|ref|YP_566445.1| 26 AVVGISGGIDSALVAYLSVEAlGAeNVLGIHMP-EASTPKSEIEDASKVAEALG 78
                                  45669************9874476256678885.77788888888888877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1574.55
//
Query:       gi|91773754|ref|YP_566446.1|  [L=431]
Description: nucleic acid binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-38  129.4   0.0    1.3e-37  128.4   0.0    1.5  1  DUF1743          Domain of unknown function (DUF1743)
    0.00013   21.8   1.9    0.00033   20.5   1.9    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0012   18.8   1.9     0.0036   17.3   1.9    1.8  1  DZR              Double zinc ribbon
     0.0017   18.1   0.7     0.0032   17.2   0.7    1.4  1  Rep_fac-A_C      Replication factor-A C terminal domain
     0.0042   17.4   0.3     0.0096   16.2   0.3    1.6  1  C1_2             C1 domain
     0.0073   16.2   1.7      0.015   15.1   1.7    1.5  1  C1_1             Phorbol esters/diacylglycerol binding domain
  ------ inclusion threshold ------
      0.012   15.6   0.5      0.012   15.6   0.5    1.7  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.021   14.4   1.1        4.6    6.9   0.1    3.0  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.057   13.4   1.4       0.19   11.7   1.4    1.9  1  zinc-ribbons_6   zinc-ribbons
      0.083   12.6   4.6       0.31   10.8   4.6    2.1  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.12   12.1   3.1        8.9    6.2   0.2    2.9  2  zinc_ribbon_2    zinc-ribbon domain
       0.13   13.0   0.0       0.31   11.8   0.0    1.5  1  CoA_binding      CoA binding domain
       0.15   12.2   2.2          7    6.9   0.1    3.0  3  Zn-ribbon_8      Zinc ribbon domain
       0.33   11.5   3.3          1   10.0   3.3    1.8  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.47   10.5   3.1        1.4    8.9   3.1    1.9  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.6    8.4   6.0        4.6    7.0   6.0    1.7  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   1.1e-40   1.3e-37       1     116 []     140     255 ..     140     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 1.1e-40
                                   TTHHHHHHHHHH-..-TT.S-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEE CS
                       DUF1743   1 grgiiGAtaalganiale.dstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGi 79 
                                   grg+iGA+aa+ga ++l  d+tyE+laYre+++wg +r+vde+sv++ad +typ+t+d+vD++++ vv+ Ph+ dpvlfG+
  gi|91773754|ref|YP_566446.1| 140 GRGLIGALAACGAMLNLGwDHTYEYLAYREKDAWGtKRQVDEDSVRKADIATYPNTWDTVDIANNAVVCIPHAGDPVLFGV 220
                                   89***********8888799************************************************************* PP

                                   EES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                       DUF1743  80 rgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                   rg+  e +  + ++i s  e++e+ a++ t qgtd h
  gi|91773754|ref|YP_566446.1| 221 RGNGIEPVTITSQMISS--EPVERHAIYMTDQGTDLH 255
                                   *****************..***************977 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.9     3e-07   0.00033      30      57 ..     356     383 ..     344     385 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3e-07
                OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfead 57 
                                   tCseCg+k+k a +g+ ++C++Cg++ad
  gi|91773754|ref|YP_566446.1| 356 TCSECGKKMKSAGKGQGYRCKKCGTKAD 383
                                   8************************998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.9   3.2e-06    0.0036      11      40 ..     353     384 ..     347     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                           DZR  11 darfCseCgtklkavaa..edrCpsCgekvdp 40 
                                    + +CseCg+k+k++ +   +rC +Cg+k+d+
  gi|91773754|ref|YP_566446.1| 353 VNPTCSECGKKMKSAGKgqGYRCKKCGTKADS 384
                                   5669*********888899*********9986 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 !   17.2   0.7   2.9e-06    0.0032       8      50 ..     344     385 ..     339     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                                   EEEEETTTTEEEB--STT---B-EEETTTE.EEETTTTEEESS- CS
                   Rep_fac-A_C   8 vsfikkdnlvYkACpsedCnkKvveeedge.wrCekCdkeveep 50 
                                   +s +++ + v + C+  +C kK+ ++++g+ +rC+kC ++ ++ 
  gi|91773754|ref|YP_566446.1| 344 ISLVQEHESVNPTCS--ECGKKMKSAGKGQgYRCKKCGTKADSA 385
                                   66778889999****..*********88777******9987765 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   8.6e-06    0.0096      10      43 ..     347     383 ..     337     385 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.6e-06
                          C1_2  10 skgedssesfnCsaCgrk....idgff..YsCseCdfslh 43 
                                   + +e +s + +Cs Cg+k    ++     Y+C++C  + +
  gi|91773754|ref|YP_566446.1| 347 V-QEHESVNPTCSECGKKmksaGK--GqgYRCKKCGTKAD 383
                                   4.677888899*******874444..356******88776 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.7   1.4e-05     0.015      13      37 ..     356     381 ..     348     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                   B-TTT-SB--S.SSS-EEEETTT--E CS
                          C1_1  13 fCkhCgeflwg.kekqglkCswCkll 37 
                                   +C++Cg+ ++  +  qg++C+ C+ +
  gi|91773754|ref|YP_566446.1| 356 TCSECGKKMKSaGKGQGYRCKKCGTK 381
                                   7********999***********976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.7   9.8e+03       7      20 ..      69      82 ..      66     121 .. 0.59
   2 ?   15.6   0.5   1.1e-05     0.012      60      95 ..     344     381 ..     324     392 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.7
                                  HHHHHHHHHHHHCC CS
                          HypA  7 aesivevveeeake 20
                                  +e++++ v+e a+ 
  gi|91773754|ref|YP_566446.1| 69 MEHVISRVNELAQL 82
                                  55555555555532 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.1e-05
                                   -EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS CS
                          HypA  60 aeLeieevpvkvrCreCgkefeleek..alrCpkCgsa 95 
                                    +L  e+++v+ +C+eCgk+++++ k   +rC+kCg++
  gi|91773754|ref|YP_566446.1| 344 ISLVQEHESVNPTCSECGKKMKSAGKgqGYRCKKCGTK 381
                                   4566899999************88754588*****986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0041       4.6       4      14 ..     356     366 ..     354     370 .. 0.86
   2 ?    5.1   0.1     0.015        17       2      17 ..     372     387 ..     371     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                        zf_UBZ   4 lCerCgkeipe 14 
                                   +C++Cgk++ +
  gi|91773754|ref|YP_566446.1| 356 TCSECGKKMKS 366
                                   7*******987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                        zf_UBZ   2 tylCerCgkeipesel 17 
                                    y C++Cg++  ++el
  gi|91773754|ref|YP_566446.1| 372 GYRCKKCGTKADSAEL 387
                                   699*****99888876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017      0.19       2      28 ..     356     384 ..     355     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                   --SSS-S--EE-S..SEEE-TTT--EEEE CS
                zinc-ribbons_6   2 kCpeCqqelekrg..eqyhCeaCqedlkk 28 
                                   +C eC +++++ g  + y+C++C ++ + 
  gi|91773754|ref|YP_566446.1| 356 TCSECGKKMKSAGkgQGYRCKKCGTKADS 384
                                   6*********5544599******987665 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.6   0.00028      0.31       2      26 ..     356     381 ..     356     382 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                                   B-SSS--B--.--SSS----SSS--- CS
                DNA_RNApol_7kD   2 iCgeCgaevs.lkkgdpiRCkeCGhR 26 
                                   +C eCg++++   kg   RCk+CG +
  gi|91773754|ref|YP_566446.1| 356 TCSECGKKMKsAGKGQGYRCKKCGTK 381
                                   5********999************76 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2    0.0079       8.9      11      22 ..     352     363 ..     348     366 .. 0.63
   2 ?    5.3   0.3     0.015        16       1       8 [.     374     381 ..     374     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0079
                 zinc_ribbon_2  11 dnakFCpyCGtp 22 
                                     ++ C++CG +
  gi|91773754|ref|YP_566446.1| 352 SVNPTCSECGKK 363
                                   556667777654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                 zinc_ribbon_2   1 fCpnCGae 8  
                                   +C++CG++
  gi|91773754|ref|YP_566446.1| 374 RCKKCGTK 381
                                   69999998 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.31       7      72 ..     216     282 ..     213     285 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                                   EEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC..TTTEEEEES-H CS
                   CoA_binding   7 iviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt..evdvavitvPa 72 
                                   ++ G+ g+gi+ ++ ++++++ + ++   +  ++ gt+ + +pv   +++++e +   ++v+v t P+
  gi|91773754|ref|YP_566446.1| 216 VLFGVRGNGIEPVTITSQMISSEPVERHAIYMTDQGTDLHLIPVE-RIADIKEMHsySIEVTVSTCPE 282
                                   578********************999999999999**********.*********644*****99997 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   0.0       5.4   6.1e+03      18      31 ..     268     282 ..     264     283 .. 0.67
   2 ?    3.7   0.1     0.062        70      23      36 ..     351     364 ..     342     366 .. 0.73
   3 ?    6.9   0.1    0.0063         7       6      16 ..     373     383 ..     372     393 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.4
                   Zn-ribbon_8  18 lqsis.dapltaCPe 31 
                                   ++s s +    +CPe
  gi|91773754|ref|YP_566446.1| 268 MHSYSiEVTVSTCPE 282
                                   667775555667997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                   Zn-ribbon_8  23 dapltaCPeCgsev 36 
                                   ++ +++C eCg+++
  gi|91773754|ref|YP_566446.1| 351 ESVNPTCSECGKKM 364
                                   55578899999865 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0063
                   Zn-ribbon_8   6 YrCeeCghefe 16 
                                   YrC++Cg++ +
  gi|91773754|ref|YP_566446.1| 373 YRCKKCGTKAD 383
                                   9******9766 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.3    0.0009         1       8      33 ..     357     382 ..     356     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0009
               Zn_ribbon_recom   8 CgeCGspmtrrkrkgkrhyYrCstyr 33 
                                   C eCG++m+  +++ ++++ +C+t+ 
  gi|91773754|ref|YP_566446.1| 357 CSECGKKMKSAGKGQGYRCKKCGTKA 382
                                   ***********998888888888875 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   3.1    0.0013       1.4      19      45 ..     355     380 ..     349     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                 Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrglfqCkeCrk 45 
                                   ++C  Cg++     k+ + ++Ck+C++
  gi|91773754|ref|YP_566446.1| 355 PTCSECGKKMKSAGKG-QGYRCKKCGT 380
                                   89*****994444454.66******86 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.0    0.0041       4.6       6      29 ..     357     380 ..     356     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0041
                 zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                   C+ CG +++ a  g + +C  Cg+
  gi|91773754|ref|YP_566446.1| 357 CSECGKKMKSAGKGQGYRCKKCGT 380
                                   **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2656.02
//
Query:       gi|91773755|ref|YP_566447.1|  [L=323]
Description: hypothetical protein Mbur_1811 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-09   37.4   0.2    9.6e-09   35.2   0.1    2.1  2  HTH_3           Helix-turn-helix
    5.7e-09   35.9   0.1    3.1e-08   33.5   0.0    2.3  2  HTH_19          Helix-turn-helix domain
    1.4e-05   25.3   0.0    2.7e-05   24.4   0.0    1.4  1  HTH_31          Helix-turn-helix domain
     0.0015   18.5   0.1     0.0055   16.6   0.0    2.1  2  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.03   14.2   0.0    1.8  1  HTH_25          Helix-turn-helix domain
      0.023   14.5   0.0       0.05   13.5   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.071   13.2   0.0        0.2   11.8   0.0    1.8  2  GP3_package     DNA-packaging protein gp3
       0.08   13.2   0.1       0.66   10.3   0.0    2.4  2  NUMOD1          NUMOD1 domain
       0.15   11.9   0.1       0.32   10.8   0.1    1.6  1  HTH_38          Helix-turn-helix domain
       0.17   11.7   0.0        0.4   10.5   0.0    1.5  1  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.84   1.5e+03      39      49 ..      60      70 ..      58      75 .. 0.68
   2 !   35.2   0.1   5.3e-12   9.6e-09       1      50 [.     132     181 ..     132     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.84
                                  HHHHHHHHHHT CS
                         HTH_3 39 etlkklakaLg 49
                                  + +k lak+L+
  gi|91773755|ref|YP_566447.1| 60 REMKSLAKYLN 70
                                  56778888887 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 5.3e-12
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50 
                                   lke+R    +s+  LA +lGvsr+tis++E G+   s+++++ l++ L+ 
  gi|91773755|ref|YP_566447.1| 132 LKEARMNVSMSLGALASELGVSRRTISKYEEGQMDASIDIVLHLEEILDM 181
                                   89***************************************999999975 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.7e-11   3.1e-08       1      53 [.     129     180 ..     129     186 .. 0.94
   2 ?   -2.8   0.0       3.8   6.9e+03      39      54 ..     294     309 ..     280     311 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.7e-11
                        HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53 
                                   G+ LkeaR +  +++ +la++lg+sr+ is++E g++ ++s++ +l++ e+l+
  gi|91773755|ref|YP_566447.1| 129 GDVLKEARMNVSMSLGALASELGVSRRTISKYEEGQM-DASIDIVLHLEEILD 180
                                   677**********************************.******999988876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.8
                        HTH_19  39 vpsaelllkiaealgi 54 
                                    +++++l+ ia   ++
  gi|91773755|ref|YP_566447.1| 294 LIERDELNTIADSDDL 309
                                   5678888888866655 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.5e-08   2.7e-05       3      54 ..     129     179 ..     129     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.5e-08
                        HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54 
                                   G+ L+++R    +s+ ++A  lgvs+ t+s++E G+ +  s + +  l ++l
  gi|91773755|ref|YP_566447.1| 129 GDVLKEARMNVSMSLGALASELGVSRRTISKYEEGQMD-ASIDIVLHLEEIL 179
                                   899********************************985.7777666666665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       6.9   1.2e+04      33      43 ..       8      18 ..       7      21 .. 0.58
   2 !   16.6   0.0   3.1e-06    0.0055      16      35 ..     141     160 ..     130     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.9
                        HTH_11 33 rrdIkaLeelg 43
                                  ++ I+ Le +g
  gi|91773755|ref|YP_566447.1|  8 HQIIEVLERAG 18
                                  55566666666 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.1e-06
                        HTH_11  16 isgeeLAeeLnvSrrtvrrd 35 
                                   +s   LA eL+vSrrt+ ++
  gi|91773755|ref|YP_566447.1| 141 MSLGALASELGVSRRTISKY 160
                                   78999************986 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05      0.03       2      37 ..     132     167 ..     131     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TT CS
                        HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfda 37 
                                   L++aR+  ++sl ++a e+ ++ +++ + Ee+++da
  gi|91773755|ref|YP_566447.1| 132 LKEARMNVSMSLGALASELGVSRRTISKYEEGQMDA 167
                                   9*******************************9885 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.8e-05      0.05      11      46 ..     143     178 ..     136     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                YdaS_antitoxin  11 qkaLAealgvsqqaVsqWlkgkkqvpaervpeIeka 46 
                                     aLA +lgvs++++s+  +g+  +++  v+ +e++
  gi|91773755|ref|YP_566447.1| 143 LGALASELGVSRRTISKYEEGQMDASIDIVLHLEEI 178
                                   579***************999988999999999986 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011       0.2      28      77 ..     132     176 ..     102     197 .. 0.78
   2 ?   -3.7   0.0       7.5   1.3e+04      69      84 ..     261     276 ..     250     278 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   EEEEE...EEEE-----HHHHHHHHT--HHHHHHHGG..SHHH.HHHHHHH CS
                   GP3_package  28 lkeakegyevvgdraptvtGLalyLgisrstlkeyekrkrefs.etierik 77 
                                   lkea+       ++++++  La  Lg+sr+t+ +ye+ + + s +++   +
  gi|91773755|ref|YP_566447.1| 132 LKEAR------MNVSMSLGALASELGVSRRTISKYEEGQMDASiDIVLHLE 176
                                   44444......3889**********************88754435555544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.5
                                   HHHHHHHHHHHHHHHH CS
                   GP3_package  69 fsetierikqivenqq 84 
                                    + +++ i++++e+q+
  gi|91773755|ref|YP_566447.1| 261 RAHLMSSISNVIETQS 276
                                   4456677778888775 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.83   1.5e+03      20      27 ..      63      70 ..      62      71 .. 0.86
   2 ?   10.3   0.0   0.00037      0.66      18      36 ..     142     160 ..     141     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.83
                        NUMOD1 20 reAakyLg 27
                                  +++akyL+
  gi|91773755|ref|YP_566447.1| 63 KSLAKYLN 70
                                  799****9 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00037
                        NUMOD1  18 SireAakyLgishntInky 36 
                                   S+ ++a  Lg+s++tI+ky
  gi|91773755|ref|YP_566447.1| 142 SLGALASELGVSRRTISKY 160
                                   78899*************9 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00018      0.32      21      39 ..     141     159 ..     134     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                        HTH_38  21 lslreIArrLgrspsTIsR 39 
                                   +sl + A +Lg+s+ TIs+
  gi|91773755|ref|YP_566447.1| 141 MSLGALASELGVSRRTISK 159
                                   8999*************96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00022       0.4      22      37 ..     145     160 ..     134     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                        HTH_23  22 eIAreLgvsrrTvyrw 37 
                                   + A eLgvsrrT++++
  gi|91773755|ref|YP_566447.1| 145 ALASELGVSRRTISKY 160
                                   6799*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1778.78
//
Query:       gi|91773756|ref|YP_566448.1|  [L=202]
Description: phosphoribosylglycinamide formyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.0    1.7e-52  177.8   0.0    1.0  1  Formyl_trans_N  Formyl transferase
  ------ inclusion threshold ------
      0.099   12.6   0.2         17    5.4   0.2    2.2  2  DUF2824         Protein of unknown function (DUF2824)


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 !  177.8   0.0   1.8e-56   1.7e-52       2     181 .]       4     184 ..       3     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.8 bits;  conditional E-value: 1.8e-56
                                   EEEEEESESSHHHHHHHHHHHHTTSE.CEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-S CS
                Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsle.advvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkad 81 
                                   +i+vl+sg gsnlq ++d+ ++g +  a v +v+s+k +a+ le+ae ++i+   ++ +++  ++ +e+++ e+l ++  +
  gi|91773756|ref|YP_566448.1|   4 NIAVLVSGRGSNLQSIIDNIENGYIPnAAVKVVISDKGDAYALERAEVHDIVPVFVDPSSFGDKKDYENKILEVLGKYDTN 84 
                                   8************************989999************************************************** PP

                                   EEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--H CS
                Formyl_trans_N  82 livlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtk 162
                                   l++lagym++l++ ++ ++r+ i+niHp+LLP+f G++a++++l  G+k++G+t+hfvde++DtG+i++q  v++++ d++
  gi|91773756|ref|YP_566448.1|  85 LVLLAGYMRILGSRIIGKYRNSIMNIHPALLPSFMGLHAQKQTLDYGVKVAGCTVHFVDEGMDTGPIVLQRCVPVLEGDDE 165
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHH CS
                Formyl_trans_N 163 eeleqrvadaehkalveal 181
                                   e+l++r+ ++eh +++ea+
  gi|91773756|ref|YP_566448.1| 166 ESLSERILEQEHIIYPEAV 184
                                   ****************996 PP

>> DUF2824  Protein of unknown function (DUF2824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0018        17       3      69 ..      19      83 ..      17      91 .. 0.87
   2 ?    5.3   0.0     0.002        18      49      83 ..      96     130 ..      86     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0018
                       DUF2824  3 lienidrlieflddkakvgaavengdeYqlkpdavYlgvyeglilvGvvevreienkvvevhavydp 69
                                  +i+ni+    ++ + a  + ++++gd Y l+   v+  v +    + + + ++ enk++ev   yd+
  gi|91773756|ref|YP_566448.1| 19 IIDNIE--NGYIPNAAVKVVISDKGDAYALERAEVHDIVPVFVDPSSFGDKKDYENKILEVLGKYDT 83
                                  689999..788999999999************99998888888888888999999999999888886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.002
                       DUF2824  49 GvvevreienkvvevhavydpgfrGkyaleatkaf 83 
                                   G   + + +n+++++h+  +p f G +a++ t+ +
  gi|91773756|ref|YP_566448.1|  96 GSRIIGKYRNSIMNIHPALLPSFMGLHAQKQTLDY 130
                                   555677899****************9988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 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:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1312.04
//
Query:       gi|91773757|ref|YP_566449.1|  [L=414]
Description: serine hydroxymethyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-170  567.4   0.6   1.5e-170  567.1   0.6    1.0  1  SHMT             Serine hydroxymethyltransferase
    5.3e-10   39.0   0.0    6.8e-10   38.7   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    2.1e-06   27.3   0.3    2.8e-06   26.8   0.3    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00021   20.4   0.1    0.00064   18.8   0.1    1.8  1  Aminotran_5      Aminotransferase class-V
    0.00028   20.3   0.2    0.00093   18.6   0.1    1.8  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0006   18.7   0.1     0.0014   17.4   0.1    1.5  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
  ------ inclusion threshold ------
      0.035   12.7   0.0      0.054   12.0   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !  567.1   0.6  5.8e-174  1.5e-170       1     398 [.       4     379 ..       4     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 567.1 bits;  conditional E-value: 5.8e-174
                                   HHHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT- CS
                          SHMT   1 leesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkl 81 
                                   ++e dpe+a+++  e +rq  +++liasen+ts+av+ea+Gs++tnkyaeGy GkryyGGcefvd++e+la++rak++f++
  gi|91773757|ref|YP_566449.1|   4 ISEIDPEIANALSLEAQRQDFKLNLIASENYTSRAVMEAQGSIMTNKYAEGYSGKRYYGGCEFVDMAEDLAISRAKQIFGA 84 
                                   5789***************************************************************************** PP

                                   STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHH CS
                          SHMT  82 dpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydele 162
                                   +    +vnvqp+sGs an+avy ++++pgd+i+++dl++GGhl+hG++v++     s++l+++v+y+v+++t+++dy+el 
  gi|91773757|ref|YP_566449.1|  85 E----HVNVQPHSGSGANMAVYFSVIKPGDKIMSMDLSHGGHLSHGSPVSF-----SGQLYNIVPYGVSQDTEMLDYNELM 156
                                   *....*******************************************999.....************************* PP

                                   HHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EEEE CS
                          SHMT 163 kkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprgglil 243
                                   + ak+ kP++iv G+saysr+id++ +reiadevgayll+d+ahiaGl+aagv+p+Pf+yad+vtttthktlrGprgg+++
  gi|91773757|ref|YP_566449.1| 157 EIAKKEKPQMIVVGASAYSRIIDFKAFREIADEVGAYLLADVAHIAGLIAAGVHPNPFPYADFVTTTTHKTLRGPRGGMVM 237
                                   ********************************************************************************* PP

                                   EC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-EEG CS
                          SHMT 244 lrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgyklv 324
                                   ++              ee++k in++vfPg+qGGPl+h+iaakava+keal++ fk+ q+q +knakal  al+++ +++v
  gi|91773757|ref|YP_566449.1| 238 CK--------------EEYAKAINKSVFPGIQGGPLMHIIAAKAVAFKEALSDSFKKDQEQTVKNAKALCAALQDREFDIV 304
                                   **..............89*************************************************************** PP

                                   GGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHHTT--HHHHHHHHHH CS
                          SHMT 325 sgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpaltsrgfkeedlekvakf 398
                                   s+Gtdnhl+l++l++ +l+Gk+ae +++k+ i +nknt+P++ + +++tsGlr Gtpa+t+rg+ke+ ++++a+f
  gi|91773757|ref|YP_566449.1| 305 SDGTDNHLMLINLNKYDLTGKDAEVIMSKAGIVINKNTIPFEtRGPFITSGLRAGTPACTTRGMKESAMDEIADF 379
                                   ******************************************99****************************997 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   2.6e-13   6.8e-10      66     356 ..      85     369 ..      30     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.6e-13
                                   TGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHH.....HHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTT CS
                 Aminotran_1_2  66 kreaavvvgsGagaliealifllklnpgdeilvpdptyasykn.....ilrlsggevvryplyseedfhldlealeealke 141
                                   ++  +v+  sG+ga+ ++ + ++k  pgd+i + d++++ +        +      +v+y + s+++  ld ++l e  k+
  gi|91773757|ref|YP_566449.1|  85 EHV-NVQPHSGSGANMAVYFSVIK--PGDKIMSMDLSHGGHLShgspvSFSGQLYNIVPYGV-SQDTEMLDYNELMEIAKK 161
                                   344.9******************9..***********9988651111134444444555553.358889999999996666 PP

                                   HHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSST CS
                 Aminotran_1_2 142 apegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKa 222
                                        k+  +++ +s+++    +++ +  +++   a++ +++l+ D a+ ++   +     +++n  ++ + +++++  K 
  gi|91773757|ref|YP_566449.1| 162 E----KPQMIVVGASAYS---RIIDFKAFREI---ADEVGAYLLADVAHIAGLIAA----GVHPNPFPYAD-FVTTTTHKT 227
                                   3....3445677777777...89*********...*******************92....45888889888.888888887 PP

                                   T.SSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEEC CS
                 Aminotran_1_2 223 f.GlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvla 301
                                   + G  G   G++ ++++++++++k + p++    l+  ++a+a+  ++   +++++ +++  k++k l+++L++ ++++++
  gi|91773757|ref|YP_566449.1| 228 LrGPRG---GMVMCKEEYAKAINKSVFPGIQgGPLMHIIAAKAVAFKEALSDSFKKDQEQTVKNAKALCAALQDREFDIVS 305
                                   645555...**********************555555566777777777788***********************999998 PP

                                   CS.CSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS......TTEEEEEC.TTS-HHHH CS
                 Aminotran_1_2 302 sq.sgmflltdlsae.takelskkLleevgvyvtpgtsftv......pgrlRitv.Aglteeel 356
                                       + ++l  l+++    + ++++  + g+++ ++t++        ++ lR    A++t+ + 
  gi|91773757|ref|YP_566449.1| 306 DGtDNHLMLINLNKYdLTGKDAEVIMSKAGIVINKNTIPFEtrgpfiTSGLRAGTpACTTRGMK 369
                                   8768888888899885333344558888899999999987778888877788888555554444 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.3   1.1e-09   2.8e-06      14     263 ..      47     285 ..      35     344 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.1e-09
                                   HHHHHHCS----CCCT--HHHHHHHH....HHHHHTT-SEE.EEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTH CS
               Beta_elim_lyase  14 msdaqaaamlGdesYgedktvnrLed....avaelfgkeaa.lfvpqGtaAnsillkillqrgeevivtepahihfdetga 89 
                                   m+++ a+   G   Yg+ + v   ed    +++++fg+e++ +  ++G +An   +  ++++g++++  + +h+     g 
  gi|91773757|ref|YP_566449.1|  47 MTNKYAEGYSGKRYYGGCEFVDMAEDlaisRAKQIFGAEHVnVQPHSGSGANMAVYFSVIKPGDKIMSMDLSHGGHLSHGS 127
                                   5555566666666777766665555422226788*****8725788*********************************** PP

                                   HHHCC--EEEEE-EBTT...TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase  90 iaelagvklrdlknkea...GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                   ++ ++g   + ++         +d ++l ++ k+     ek+++i++     +       +   ++ ++ia++ g  l+ D
  gi|91773757|ref|YP_566449.1| 128 PVSFSGQLYNIVPYGVSqdtEMLDYNELMEIAKK-----EKPQMIVVGASAYS------RIIDFKAFREIADEVGAYLLAD 197
                                   ****998444444332222366677777776666.....89*****9998886......67777888899*********** PP

                                   ETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH......................HHHHHHHHHHHHT CS
               Beta_elim_lyase 168 gARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel..................edylaerveqrkylg 230
                                    A +a    + g+++   f y+D vt    K l  + Gg+++ +++ +                  +              
  gi|91773757|ref|YP_566449.1| 198 VAHIAGLI-AAGVHPN-PFPYADFVTTTTHKTLRGPRGGMVMCKEE-YakainksvfpgiqggplmH-------------- 261
                                   ****9866.6777775.699**************************.42444444444444444431.............. PP

                                   ---SSTHHHHH..HHHHHHHHSSTTHHHHHHHH CS
               Beta_elim_lyase 231 gglrqagvlaaleagiraleeglaslerdhkta 263
                                          ++aa   ++   e  + s+++d++ +
  gi|91773757|ref|YP_566449.1| 262 -------IIAA--KAVAFKEALSDSFKKDQEQT 285
                                   .......4444..44433333344444444333 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.5e-07   0.00064      14     228 ..      38     253 ..      29     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.5e-07
                                   HHHHHHHHHHHCTCCSSSS.SSSHHHHHHHHHHHH.HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEE CS
                   Aminotran_5  14 eVldalqeyytdynanvhr.svhhlgkeatkavee.arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeiv 92 
                                   +V++a     t+ +a + + + +  g e+ ++ e+ a ++ +++++ae   ++   sG++ a+ +v  s+   +kpgd+i 
  gi|91773757|ref|YP_566449.1|  38 AVMEAQGSIMTNKYAEGYSgKRYYGGCEFVDMAEDlAISRAKQIFGAEH-VNVQPHSGSG-ANMAVYFSV---IKPGDKIM 113
                                   5666666666666666666444444556666666524466777888886.7777778887.888888888...99***998 PP

                                   EETTSHGGGTHHHHHHHHHHT..EEEEEEEB.ETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT- CS
                   Aminotran_5  93 vteaehhanlvpwqelakrtg..akvkvipl.deegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkga 170
                                     ++ h + l     ++ + g  ++++ + + +++  ld +el + +++k k  +i    ++   i +++++ ++a ++ga
  gi|91773757|ref|YP_566449.1| 114 SMDLSHGGHLSHGSPVS-FSGqlYNIVPYGVsQDTEMLDYNELME-IAKKEKPQMIVVGASAYSRIIDFKAFREIADEVGA 192
                                   77776666665444444.333127777776614455667777754.455555555666666777899************** PP

                                   EEEEE-TTTTTTS---HHHH...TESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.ST CS
                   Aminotran_5 171 lvlvDaaqavghipidvkkl...gvDflafsghK.llgPtGiGvlyvrkellekleplllgg 228
                                   ++l+D a  +g i   v+      +Df++ ++hK l gP G G++++++e+ +++++  ++g
  gi|91773757|ref|YP_566449.1| 193 YLLADVAHIAGLIAAGVHPNpfpYADFVTTTTHKtLRGPRG-GMVMCKEEYAKAINKSVFPG 253
                                   *******999999888876522369*********999****.*********99998776655 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   3.6e-07   0.00093      86     194 ..     137     246 ..      78     277 .. 0.79
   2 ?   -0.3   0.0       0.2   5.1e+02      12      71 ..     272     334 ..     261     343 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.6e-07
                                   EEEEE-B-TTTSSB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSE CS
               DegT_DnrJ_EryC1  86 kpvfvDvdpdtynidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgda 164
                                   + v+  v +dt ++d +++ +   ++     ++ + +y+++ d++a ++ia++ g +++ D Ah  G   +g +   +  a
  gi|91773757|ref|YP_566449.1| 137 NIVPYGVSQDTEMLDYNELMEIAKKEKpqMIVVGASAYSRIIDFKAFREIADEVGAYLLADVAHIAGLIAAGVHPNPFPYA 217
                                   5577788889999998888776665554345566899**********************************9988888888 PP

                                   EEEE-BTTSSS-SSS-EEEEESTHHHHHHH CS
               DegT_DnrJ_EryC1 165 avfSFyptKnlttGeGGavvtndeelaeka 194
                                     +     K+l    GG+v+ ++e +a+ +
  gi|91773757|ref|YP_566449.1| 218 DFVTTTTHKTLRGPRGGMVMCKEE-YAKAI 246
                                   888889999999999999988754.45554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.2
                                   HHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH..TTTT.TT-EEEEESS CS
               DegT_DnrJ_EryC1  12 evlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLra..lgvg.pgdeVIvpsl 71 
                                   e+l   +    +++ + +ka++a l+++    vs Gt+  +++++    +++ ++ eVI+ ++
  gi|91773757|ref|YP_566449.1| 272 EALSDSFKKDQEQTVKNAKALCAALQDREFDIVSDGTDNHLMLINLnkYDLTgKDAEVIMSKA 334
                                   555444444466777778999999999999999999997555444433665569999999876 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 !   17.4   0.1   5.6e-07    0.0014      75     313 ..      78     295 ..      69     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.6e-07
                                   HHHHCT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE---GGGGSHH CS
                      OKR_DC_1  75 aarvfgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiiggidlkefeee 154
                                   a ++fga++  +  +  s++n++v  +v++pgd+++        + h+  ls   Pv ++ +  n   ++ g+ +   ++e
  gi|91773757|ref|YP_566449.1|  78 AKQIFGAEHVNVQPHSGSGANMAVYFSVIKPGDKIMSM-----DLSHGGHLSHGSPVSFSGQlYNI--VPYGVSQ---DTE 148
                                   679********************************965.....466777899999*9999884442..3455555...334 PP

                                   HHH.HHHHHSTTTGSESEEEEESS-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEE CS
                      OKR_DC_1 155 tlk.ekikevpdakaprlavitnsTYdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilv 234
                                   +l  +++ e +++++p+++v+  s Y   + + k   + +++++ ++l D A+++      +  +  +  a+       +v
  gi|91773757|ref|YP_566449.1| 149 MLDyNELMEIAKKEKPQMIVVGASAYS-RIIDFKAFREIADEVGAYLLADVAHIAGLIAAGVHPNPFPY-AD-------FV 220
                                   4432679999999999*******9997.6789*********************9987777777666664.67.......99 PP

                                   EEEHCCCCS--TT-EEEEEES-BT--HHHHHHHHHHTS-SS--HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHH CS
                      OKR_DC_1 235 tqSvHKllaalsqaSlihvkeelivneerlneafmmhattSpsYpllAsldvaakmlegesgrrlleevveraielrke 313
                                   t+ +HK+l +  ++ ++  kee     +++n+         p+  ++A+  va k   + s ++  e++v++a  l  +
  gi|91773757|ref|YP_566449.1| 221 TTTTHKTLRG-PRGGMVMCKEEY---AKAINKSVFPGIQGGPLMHIIAAKAVAFKEALSDSFKKDQEQTVKNAKALCAA 295
                                   9999999999.567788888884...67777777777788999999999999999999999999999999988776655 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 ?   12.0   0.0   2.1e-05     0.054      74     212 ..      92     237 ..      74     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                   SSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHH.....HHHHTHHH...TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS CS
               Cys_Met_Meta_PP  74 ssGmaAiaaailallkaGdeivvsddlYggtqr.....llkkvlkk...lgievkfvdtsdleelekaikentklvylEtp 146
                                    sG +A +a+ ++++k Gd+i+++d  +gg  +      ++  l +    g++ +    +  e +e a ke+ +++ + + 
  gi|91773757|ref|YP_566449.1|  92 HSGSGANMAVYFSVIKPGDKIMSMDLSHGGHLShgspvSFSGQLYNivpYGVSQDTEMLDYNELMEIAKKEKPQMIVVGA- 171
                                   69**********************99998855411111333333321223444433333444455556667888888864. PP

                                   -TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT....-SEEEEETTTTTTCSSS--EEEEE CS
               Cys_Met_Meta_PP 147 tnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklg....aDivvhSaTKylgGhsdvvaGviv 212
                                    +   +++D+++  ++a ++g+ ++ D + +++l+   ++ +    aD v+  + K l G     +G+++
  gi|91773757|ref|YP_566449.1| 172 -SAYSRIIDFKAFREIADEVGAYLLADVAHIAGLIAAGVHPNpfpyADFVTTTTHKTLRGPR---GGMVM 237
                                   .66889*********************99999988877776666679999999999999976...45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 2990.71
//
Query:       gi|91773758|ref|YP_566450.1|  [L=286]
Description: bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-64  214.3   4.9    8.6e-64  213.7   4.9    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    1.5e-39  134.9   0.2    2.4e-39  134.2   0.2    1.3  1  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,
     0.0028   17.7   2.7       0.24   11.4   2.7    2.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
  ------ inclusion threshold ------
      0.016   15.9   2.6       0.12   13.1   0.4    2.7  3  PTS_IIB        PTS system, Lactose/Cellobiose specific IIB su


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 !  213.7   4.9   1.9e-67   8.6e-64       1     158 [.     128     284 ..     128     286 .] 0.99

  Alignments for each domain:
  == domain 1  score: 213.7 bits;  conditional E-value: 1.9e-67
                                   SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSS CS
                 THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitread 81 
                                   hp+n+g+l+ g e l+pctpkg+++ l+e+g+e++gk++v+vG+sn+vgkp+a++L ++natV++ch  tkd++++tr ad
  gi|91773758|ref|YP_566450.1| 128 HPFNMGQLLIGVEELVPCTPKGIIRALEEYGVEIQGKHAVIVGHSNVVGKPMAAMLVNRNATVSICHVFTKDVTKFTRDAD 208
                                   899****************************************************************************** PP

                                   EEEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHHHHC CS
                 THF_DHG_CYH_C  82 ivvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntleaakr 158
                                   i+vva+G+++lik++mvkeg+v+ DvGi++  +gk++GDvdfe+v ++as +tPvpgGVGp+T+a+l++++l++a++
  gi|91773758|ref|YP_566450.1| 209 ILVVATGVKHLIKEDMVKEGSVIFDVGITEE-NGKVYGDVDFENVIKKASRVTPVPGGVGPVTIATLMQHVLMSAQK 284
                                   ******************************9.*****************************************9987 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 !  134.2   0.2   5.4e-43   2.4e-39       1     116 []       9     125 ..       9     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 5.4e-43
                                   E--HHHHHHHHHHHHHHHHHHHHHH.T---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHH CS
                   THF_DHG_CYH   1 lldGkalakeireelkeeveklkek.gvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkliee 80 
                                   ++dG+a+ak++++e+k++ve+l ++ g++p+L +ilvg+dpas++Yvr k+kac +vGi  e  +lped+++eell++i +
  gi|91773758|ref|YP_566450.1|   9 IIDGRAIAKKVEAEVKADVERLVREkGITPGLSAILVGEDPASKMYVRLKHKACGRVGIFAEDQHLPEDITQEELLEAISS 89 
                                   79*******************9985599***************************************************** PP

                                   HHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                   THF_DHG_CYH  81 lneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                   ln++++++Gil+qlPlpkh++e+++++ai+p+KD D
  gi|91773758|ref|YP_566450.1|  90 LNARKDIHGILLQLPLPKHLNEQEAMNAIDPAKDAD 125
                                   **********************************88 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   2.7   5.4e-05      0.24      19     111 ..     159     236 ..     144     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                                   S--TTSEEEEE--SH.HHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHC CS
                 AdoHcyase_NAD  19 vllaGkvavvaGyGd.vGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdiitlehlk 98 
                                   v + Gk av++G+ + vGk  aa l +  a v +  v               + + + +++adi+v +tG k +i+ +++k
  gi|91773758|ref|YP_566450.1| 159 VEIQGKHAVIVGHSNvVGKPMAAMLVNRNATVSICHVF-------------TKDVTKFTRDADILVVATGVKHLIKEDMVK 226
                                   67999999999999845999999999999999887663.............2456677899999999***99999998765 PP

                                   CS-TTEEEEE-SS CS
                 AdoHcyase_NAD  99 kmkddaivcniGh 111
                                      + +++ ++G 
  gi|91773758|ref|YP_566450.1| 227 ---EGSVIFDVGI 236
                                   ...4444444443 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   6.1e+03      29      38 ..      19      30 ..      12      63 .. 0.57
   2 ?    1.7   0.0     0.097   4.4e+02      22      37 ..     152     167 ..     148     169 .. 0.87
   3 ?   13.1   0.4   2.6e-05      0.12      10      90 .]     169     255 ..     168     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                                  EEEEETTEE..G CS
                       PTS_IIB 29 ieaegeagv..e 38
                                  +eae++a v   
  gi|91773758|ref|YP_566450.1| 19 VEAEVKADVerL 30
                                  455555444332 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.097
                                   HHHHHCTEEEEETTEE CS
                       PTS_IIB  22 kaakelgieaegeagv 37 
                                   +a++e g+e++g++ v
  gi|91773758|ref|YP_566450.1| 152 RALEEYGVEIQGKHAV 167
                                   799*********9976 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHHHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSGG...CTHHHHTTSEEEEECTTH....HHCCHC CS
                       PTS_IIB  10 matSlmaaeklekaakelgieaegeagveleaeeiaddaDlvllapqvrv...kdlarfagkpvavinikd....algimd 83 
                                   +++S ++ + +  ++ +++  + + + + +++ + + daD++++a+ v++   +d+ +     +  + i++    ++g  d
  gi|91773758|ref|YP_566450.1| 169 VGHSNVVGKPMAAMLVNRNATVSICHVFTKDVTKFTRDADILVVATGVKHlikEDMVKEGS-VIFDVGITEengkVYGDVD 248
                                   6899999999999999999888888888999******************998777777777.4666666666778899999 PP

                                   HHHHHHH CS
                       PTS_IIB  84 gekvlke 90 
                                    e+v+k+
  gi|91773758|ref|YP_566450.1| 249 FENVIKK 255
                                   9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1658.54
//
Query:       gi|91773759|ref|YP_566451.1|  [L=410]
Description: dihydropteroate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.1      2e-54  184.9   0.1    1.3  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 !  184.9   0.1   1.1e-58     2e-54       1     244 []      21     256 ..      21     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 1.1e-58
                                   EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S CS
                   Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDtt 81 
                                   mg++N++ +sf++g+ + d d+ l++a+km+++GA+i+D+g+ st P a+++ +e e  r++p le l+d++d  is+Dt+
  gi|91773759|ref|YP_566451.1|  21 MGVINLSRESFYKGSVV-DTDSLLDVAHKMIDDGATIIDLGARSTWPLADPITKEVECGRLLPALELLKDNVDAVISVDTV 100
                                   9************8777.*************************************************************** PP

                                   -HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT- CS
                   Pterin_bind  82 kaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeeaGv 162
                                    a++ae+A+++gad+vNdv g+  d  ml +vae+g++ vvm+         + +g+   +++ +   l+  + + ee G+
  gi|91773759|ref|YP_566451.1| 101 FADIAEKAIENGADVVNDVAGFATDGGMLDVVAEHGCPAVVMAAG-------KLPGDPLGMDA-IMHSLDDILIRSEERGI 173
                                   *********************************************.......44445555444.445567788999***** PP

                                   -GGGEEEETTTTSSTTHHHHHHHHHTHHHHH..HTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT-SEE CS
                   Pterin_bind 163 aperillDpgigfgkteehnlellrrldelr..ealevpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaGadiv 241
                                   ++++++lDp ig    e++ ++ l+++d+++  +++e p+l ++Srksf+g+ll ++ a+eR  g++a++a+ +++Ga+i+
  gi|91773759|ref|YP_566451.1| 174 DTDQLILDPAIGKWVPEKSAMYDLETIDQFErlKIFEKPLLAAISRKSFIGDLL-DKPATERLYGSLAAAAIVVQKGAHII 253
                                   ************9666666666666666663115556***************98.56699********************* PP

                                   EES CS
                   Pterin_bind 242 rVh 244
                                   r+h
  gi|91773759|ref|YP_566451.1| 254 RTH 256
                                   **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2397.28
//
Query:       gi|91773760|ref|YP_566452.1|  [L=204]
Description: hypothetical protein Mbur_1816 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-35  120.3   1.1    4.4e-35  119.2   1.1    1.6  1  MTHFR_C   Methylene-tetrahydrofolate reductase C terminal


Domain annotation for each model (and alignments):
>> MTHFR_C  Methylene-tetrahydrofolate reductase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   1.1   2.4e-39   4.4e-35       1      93 [.     108     200 ..     108     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 2.4e-39
                       MTHFR_C   1 ypalntlflgveeevkvleekCkaCgdCvlaetggiCpvsrCakkllnGpCggskngkCevkpekeCaweliyerlkklgk 81 
                                   ypa+nt +lg+ +  kv+++ C++Cg+C +a++ggiCp+++C+k+llnGpCggs +gkCev+pek+Caweliyerl++lg+
  gi|91773760|ref|YP_566452.1| 108 YPANNTDSLGAMTGDKVIHNLCAMCGQCSIADFGGICPTAQCPKELLNGPCGGSMDGKCEVDPEKDCAWELIYERLERLGR 188
                                   799****************************************************************************** PP

                       MTHFR_C  82 lekleeivppkd 93 
                                   l+ lee+ ++kd
  gi|91773760|ref|YP_566452.1| 189 LDLLEEVRDAKD 200
                                   *******99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1221.81
//
Query:       gi|91773761|ref|YP_566453.1|  [L=243]
Description: hypothetical protein Mbur_1817 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-15   56.9   0.0    1.1e-08   34.5   0.0    2.6  2  HTH_24          Winged helix-turn-helix DNA-binding
    1.5e-11   44.0   0.0    0.00021   21.1   0.0    2.6  2  MarR_2          MarR family
    2.5e-11   43.2   0.0      9e-07   28.7   0.0    2.5  2  HTH_5           Bacterial regulatory protein, arsR family
    7.8e-08   32.3   0.0    1.8e-05   24.7   0.0    2.3  2  HTH_20          Helix-turn-helix domain
    5.5e-07   29.4   0.0      0.044   13.7   0.0    2.3  2  MarR            MarR family
    2.6e-06   27.1   0.0      0.064   13.1   0.0    2.3  2  HTH_IclR        IclR helix-turn-helix domain
    1.2e-05   25.4   0.6       0.14   12.4   0.0    2.9  3  B-block_TFIIIC  B-block binding subunit of TFIIIC
    0.00054   19.8   0.0      0.052   13.4   0.0    2.2  2  TFIIE_alpha     TFIIE alpha subunit
     0.0011   19.3   0.0     0.0026   18.1   0.0    1.6  1  FaeA            FaeA-like protein
     0.0037   17.1   0.0        2.6    8.0   0.0    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.024   15.1   0.0        1.5    9.4   0.0    2.3  2  HTH_40          Helix-turn-helix domain
      0.026   14.2   0.0        1.2    8.7   0.0    2.2  2  RP-C            Replication protein C N-terminal domain
      0.092   12.3   0.1       0.69    9.5   0.1    1.9  2  DDRGK           DDRGK 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 !   19.9   0.0   2.9e-07   0.00041       7      41 ..      92     126 ..      87     133 .. 0.94
   2 !   34.5   0.0     8e-12   1.1e-08       1      47 [.     162     208 ..     162     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                        HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrL 41 
                                   +IL ++  np+ +++++ ++lg+ +s+v+++lk L
  gi|91773761|ref|YP_566453.1|  92 RILYYITTNPGSTISDIEKALGMKRSNVRYHLKVL 126
                                   8********************************88 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 8e-12
                        HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                   +++t + IL ++  +p+i++++L +  +l ++tv+++++ + +eGl+
  gi|91773761|ref|YP_566453.1| 162 RNDTGKSILIYILHKPGITNQDLTQTFHLDKGTVHWHINDMYNEGLV 208
                                   68999****************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00021       9      46 ..      92     127 ..      87     140 .. 0.94
   2 !   20.3   0.0   2.8e-07   0.00038      10      56 ..     169     213 ..     167     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                        MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLv 46 
                                   r+L+++  +pg   t+++++++lg+++s+v ++lk L+
  gi|91773761|ref|YP_566453.1|  92 RILYYITTNPG--STISDIEKALGMKRSNVRYHLKVLQ 127
                                   89*********..8*********************996 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.8e-07
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                   +L ++ + pg  +t ++l+++++l+k++v+ +++++   GLv  + +
  gi|91773761|ref|YP_566453.1| 169 ILIYILHKPG--ITNQDLTQTFHLDKGTVHWHINDMYNEGLVDFEND 213
                                   899*******..******************************98854 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 !   28.7   0.0   6.6e-10     9e-07       1      39 [.      87     126 ..      87     128 .. 0.97
   2 !   12.1   0.0   9.9e-05      0.14      16      46 ..     179     209 ..     164     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.6e-10
                                   SHHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHH CS
                         HTH_5   1 dptRlkILklLaege.lcvcelaeelglsqstvShHLkkL 39 
                                   +p+R +IL++   ++  +++++ ++lg+ +s+v++HLk+L
  gi|91773761|ref|YP_566453.1|  87 NPNRDRILYYITTNPgSTISDIEKALGMKRSNVRYHLKVL 126
                                   69999*********************************99 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.9e-05
                                   EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  16 lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                    +  +l+  ++l ++tv  H + ++++GLV+
  gi|91773761|ref|YP_566453.1| 179 ITNQDLTQTFHLDKGTVHWHINDMYNEGLVD 209
                                   57789************************95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.3e-08   1.8e-05       9      49 ..      87     127 ..      85     129 .. 0.96
   2 ?    5.3   0.0     0.015        21      24      55 ..     178     209 ..     167     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.3e-08
                                   -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                        HTH_20   9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLe 49 
                                   +P R ril +++++ g t s++ ++l++++++++yHL+vL+
  gi|91773761|ref|YP_566453.1|  87 NPNRDRILYYITTNPGSTISDIEKALGMKRSNVRYHLKVLQ 127
                                   899************************************95 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                                   TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  24 gltaselaerldlskntlsyHLrvLeeagLve 55 
                                   g t  +l +++ l+k t++ H++ +   gLv+
  gi|91773761|ref|YP_566453.1| 178 GITNQDLTQTFHLDKGTVHWHINDMYNEGLVD 209
                                   6666789999*************999999997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   4.1e-05     0.056       7      50 ..      92     135 ..      87     138 .. 0.90
   2 !   13.7   0.0   3.2e-05     0.044       8      51 ..     169     212 ..     164     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                   +iL+ + ++++ ++s++ k+lg+++s+v   l+ L  ++ i+R 
  gi|91773761|ref|YP_566453.1|  92 RILYYITTNPGSTISDIEKALGMKRSNVRYHLKVLQFNNKITRL 135
                                   79*******************************99999988886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                   iL  + +++++++++L   ++++k+tv   +  ++ +Gl++ + 
  gi|91773761|ref|YP_566453.1| 169 ILIYILHKPGITNQDLTQTFHLDKGTVHWHINDMYNEGLVDFEN 212
                                   8888999*********************************8765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   4.6e-05     0.064       8      43 ..      93     127 ..      92     130 .. 0.90
   2 !   11.8   0.0   0.00011      0.16       8      49 ..     169     209 ..     166     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHH CS
                      HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLv 43 
                                   iL ++++ p+  t+s++ +++g+ +S+v+ +L+ L+
  gi|91773761|ref|YP_566453.1|  93 ILYYITTNPGS-TISDIEKALGMKRSNVRYHLKVLQ 127
                                   88888888886.********************9996 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                   iL ++ + p+  t+++l + ++l k tvh +++ + ++G+v 
  gi|91773761|ref|YP_566453.1| 169 ILIYILHKPG-ITNQDLTQTFHLDKGTVHWHINDMYNEGLVD 209
                                   6666667777.8****************************96 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00061      0.84      18      51 ..     102     135 ..      99     162 .. 0.88
   2 ?   -0.4   0.0      0.99   1.4e+03      25      49 ..     148     172 ..     142     175 .. 0.84
   3 !   12.4   0.0   9.9e-05      0.14      18      48 ..     178     208 ..     174     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00061
                B-block_TFIIIC  18 GitqsdLakeskqdprslfyrlksLekkgLIvkq 51 
                                   G t sd+ k+++++ +++ y+lk+L+ ++ I+++
  gi|91773761|ref|YP_566453.1| 102 GSTISDIEKALGMKRSNVRYHLKVLQFNNKITRL 135
                                   8899**********************99888876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.99
                B-block_TFIIIC  25 akeskqdprslfyrlksLekkgLIv 49 
                                   +k++  +++ +f +++   k+ LI+
  gi|91773761|ref|YP_566453.1| 148 CKYTATEKKIIFFLRNDTGKSILIY 172
                                   899999999***9999888887776 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 9.9e-05
                B-block_TFIIIC  18 GitqsdLakeskqdprslfyrlksLekkgLI 48 
                                   Git +dL +++  d+  ++ +++ + + gL+
  gi|91773761|ref|YP_566453.1| 178 GITNQDLTQTFHLDKGTVHWHINDMYNEGLV 208
                                   9*****************************9 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.028        38      14      51 ..      89     126 ..      77     139 .. 0.79
   2 !   13.4   0.0   3.8e-05     0.052       6      60 ..     157     211 ..     154     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.028
                                   HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHH CS
                   TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidlnelrklLnrL 51 
                                   +   +l  + ++   t  d++k l++++ ++r  L  L
  gi|91773761|ref|YP_566453.1|  89 NRDRILYYITTNPGSTISDIEKALGMKRSNVRYHLKVL 126
                                   566788888888888889**************888766 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.8e-05
                                   HHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                   TFIIE_alpha   6 vvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkyk 60 
                                   +++   ++  + +l  +l k  +t+ dl +  ++d+  +   +n++y+++lv++ 
  gi|91773761|ref|YP_566453.1| 157 IIFFLRNDTGKSILIYILHKPGITNQDLTQTFHLDKGTVHWHINDMYNEGLVDFE 211
                                   666667788899****************************************985 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.9e-06    0.0026       2      50 ..      90     137 ..      89     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                                   HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE-- CS
                          FaeA   2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspv 50 
                                   ++ Il y++  + + + ++i +alg+    +Ry L+ L+   ki r   
  gi|91773761|ref|YP_566453.1|  90 RDRILYYITT-NPGSTISDIEKALGMKRSNVRYHLKVLQFNNKITRLEK 137
                                   589******9.7777779**************************99765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0041       5.7      19      52 ..      99     132 ..      92     154 .. 0.80
   2 !    8.0   0.0    0.0019       2.6      13      63 ..     169     220 ..     163     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                          TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlV 52 
                                   ++  +t+++i ++lg  rs+v   L+ L     +
  gi|91773761|ref|YP_566453.1|  99 TNPGSTISDIEKALGMKRSNVRYHLKVLQFNNKI 132
                                   67889****************9999888765555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                                   HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                          TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                   + +++l +   t +++ +   +++ +v   ++ + + GlV+ e  g++k+Y 
  gi|91773761|ref|YP_566453.1| 169 ILIYILHKPGITNQDLTQTFHLDKGTVHWHINDMYNEGLVDFENdGKYKRYF 220
                                   67889999999******************************99956677885 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.083   1.2e+02      12      33 ..     102     123 ..      95     142 .. 0.88
   2 ?    9.4   0.0    0.0011       1.5       8      61 ..     174     233 ..     170     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.083
                        HTH_40  12 glsieeIAkerglkesTIegHL 33 
                                   g +i +I k  g+k+s +  HL
  gi|91773761|ref|YP_566453.1| 102 GSTISDIEKALGMKRSNVRYHL 123
                                   889******************9 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                        HTH_40   8 lleeglsieeIAkerglkesTIegHLaelieegeeidl.......erlvseeeekeIeeai 61 
                                   l++ g + ++  +  +l ++T+  H+ ++++eg  +d+       + ++++ +e  +++ai
  gi|91773761|ref|YP_566453.1| 174 LHKPGITNQDLTQTFHLDKGTVHWHINDMYNEGL-VDFendgkykRYFINPAIEVDLKKAI 233
                                   667889999999********************97.77744444433335555555555555 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 ?    3.0   0.0     0.049        68      77      95 ..     108     126 ..     103     135 .. 0.86
   2 ?    8.7   0.0   0.00088       1.2      73     113 ..     180     220 ..     178     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.049
                          RP-C  77 LsralglsestlrrhlaaL 95 
                                   + +alg+ +s +r+hl+ L
  gi|91773761|ref|YP_566453.1| 108 IEKALGMKRSNVRYHLKVL 126
                                   5689************998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00088
                          RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirrDspngkRya 113
                                    N++L + + l + t+  h+  + + Gl+       +kRy 
  gi|91773761|ref|YP_566453.1| 180 TNQDLTQTFHLDKGTVHWHINDMYNEGLVDFENDGKYKRYF 220
                                   599*************************************6 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0005      0.69     100     156 ..      89     143 ..      79     158 .. 0.85
   2 ?    0.9   0.0      0.22     3e+02     102     143 ..     167     208 ..     145     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0005
                                   HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE- CS
                         DDRGK 100 lleefinyikekKvvlleelavkfklktqevierikeLeeqgsltGvlDdrGkyiyi 156
                                     ++++ yi ++   ++ ++   +++k ++v+  +k L+ ++++t +  ++Gk + +
  gi|91773761|ref|YP_566453.1|  89 NRDRILYYITTNPGSTISDIEKALGMKRSNVRYHLKVLQFNNKITRL--EKGKLVLL 143
                                   5688999*************************************987..78887765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                                   HHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                         DDRGK 102 eefinyikekKvvlleelavkfklktqevierikeLeeqgsl 143
                                   ++++ yi +k  ++ ++l+  f+l+   v   i+++ ++g +
  gi|91773761|ref|YP_566453.1| 167 KSILIYILHKPGITNQDLTQTFHLDKGTVHWHINDMYNEGLV 208
                                   567778888888889999999999999999999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1483.85
//
Query:       gi|91773762|ref|YP_566454.1|  [L=140]
Description: hypothetical protein Mbur_1818 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 836.40
//
Query:       gi|91773763|ref|YP_566455.1|  [L=269]
Description: hypothetical protein Mbur_1819 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.5   0.1       0.33   11.3   0.0    1.7  2  SH3_15    Mind bomb SH3 repeat domain


Domain annotation for each model (and alignments):
>> SH3_15  Mind bomb SH3 repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.76   1.4e+04      25      36 ..      34      44 ..      29      54 .. 0.78
   2 ?   11.3   0.0   1.9e-05      0.33      30      62 ..      77     116 ..      57     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.76
                        SH3_15 25 gWsgamtlgsvG 36
                                   W  +m l+s G
  gi|91773763|ref|YP_566455.1| 34 TWHSQM-LESNG 44
                                  688888.88877 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 1.9e-05
                        SH3_15  30 m......tlgsvGtVlkvd.adgdlrVkfpgegraWtldP 62 
                                   m      tl+s+Gt++++  +dg + V++ g++  + l+ 
  gi|91773763|ref|YP_566455.1|  77 MidgklkTLKSKGTISGIVnQDGTINVEYSGNNFNFVLNS 116
                                   344446689********8758999*****88888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1859.89
//
Query:       gi|91773764|ref|YP_566456.1|  [L=155]
Description: hypothetical protein Mbur_1820 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.025   14.4   0.2       0.03   14.2   0.2    1.1  1  S1-P1_nuclease  S1/P1 Nuclease


Domain annotation for each model (and alignments):
>> S1-P1_nuclease  S1/P1 Nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.6e-06      0.03      87     202 ..       2     128 ..       1     153 [. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-06
                                   HHHHHHHHHHHCCTT.TTTH..HHHHHHHHHHHHHCTSGGGGEECGGHCCTTT-EEEETTEEEEHHHHHHTHHHHHHHCCT CS
                S1-P1_nuclease  87 vsaienltselkdkkaskaqr.aealkflvHfvGDiHqPLHtagreedrGGNkikvqfegkktnLHsvWDseiiekiseek 166
                                   +++++nl+++++++ + ++++  + + + +H++ D   P+H++g ++  GG  + +     +  LH  + s + ++ ++ +
  gi|91773764|ref|YP_566456.1|   2 IKEVQNLSHNIAKYLSRRYANaHTNFGYASHYLSDPGIPFHSTGATDYLGGFVVALF----NAALHISYESYVADEWTSGY 78 
                                   678999999999998886555378899******************999999766655....679********998887755 PP

                                   SC..........CCHHHHHHHHHHHHH.....CCCHHHCC.........CHHHHHHHHH CS
                S1-P1_nuclease 167 sr.........lsalkeladaleakik.....seevkswe.........klsaeawake 202
                                              +   +++ ++ ++ +k     s      +         +++++ w ++
  gi|91773764|ref|YP_566456.1|  79 DYsyyvtdnsqS---NTV-TDPAQAVKdnaehS-----AQyysyitnemTTNPTGWKTD 128
                                   324555543321...111.11112222111111.....111222333323355555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1025.73
//
Query:       gi|91773765|ref|YP_566457.1|  [L=234]
Description: hypothetical protein Mbur_1821 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1504.33
//
Query:       gi|91773766|ref|YP_566458.1|  [L=195]
Description: hypothetical protein Mbur_1822 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1287.64
//
Query:       gi|91773767|ref|YP_566459.1|  [L=186]
Description: hypothetical protein Mbur_1824, partial [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-06   28.7   0.0      3e-06   27.1   0.0    1.8  1  LolA_like  Outer membrane lipoprotein-sorting protein
  ------ inclusion threshold ------
      0.033   13.9   0.0      0.076   12.7   0.0    1.5  2  LolA       Outer membrane lipoprotein carrier protein LolA


Domain annotation for each model (and alignments):
>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   3.3e-10     3e-06      15     116 ..      84     186 .]      73     186 .] 0.79

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.3e-10
                                   TTT-EEEEESSSTTEEEEEETTTTCEEEE-GGGTTS..ECCTTC.EHHHHC--SCCCEEEEEEEEEEETTEEEEEEEEEES CS
                     LolA_like  15 vkGtafLtlkekdddlWlYlPalkrvrrisssdksq..sfmGsdfsyeDlssrevedythellgeeevggkdcyvleltpk 93 
                                   +kGt + ++ ++ + +W+Y+ ++++v ++  sd  +  ++   +  ++ + + ++   t++llg e+++g+++y leltp 
  gi|91773767|ref|YP_566459.1|  84 DKGTEVIMI-SDREFQWIYDSESETVFKTDISDGLDglKIFEPN-VFAEFLNGTLMGKTASLLGVEDLDGNNAYLLELTPS 162
                                   79*******.77779***********998755555411445555.455555667888899********************* PP

                                   S..TTSSECEEEEEEETTT--EEE CS
                     LolA_like  94 d.aadvsYskivlwvdketylplk 116
                                   + ++++  ++  +wvd++t++p++
  gi|91773767|ref|YP_566459.1| 163 EnNKSSLQGRSMIWVDRDTWMPIR 186
                                   944455578999*********985 PP

>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.5e-06     0.076      29      70 ..      68     112 ..      50     120 .. 0.77
   2 ?   -2.4   0.0      0.36   3.3e+03     106     128 ..     156     180 ..     139     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.5e-06
                                   EEEETTTEEEEEE-TTS...-EEEEEETTEEEEEETTTTEEEEEE CS
                          LolA  29 laikrPgkfrweytsPd...eqlivsdgktvwlydpdleqvties 70 
                                   +  k+P++++  +  Pd   e  ++sd++  w+yd++ e+v  ++
  gi|91773767|ref|YP_566459.1|  68 VIWKKPDLMKTIIRVPDkgtEVIMISDREFQWIYDSESETVFKTD 112
                                   55678888888887776333689******************6655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.36
                                   EEEEEES..SS-SSECEEEEEE.ET CS
                          LolA 106 tltlkpk..akdanlsritigfdkk 128
                                    l+l+p   +k++ + r  i++d++
  gi|91773767|ref|YP_566459.1| 156 LLELTPSenNKSSLQGRSMIWVDRD 180
                                   4566665436677777777887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1175.02
//
Query:       gi|91773768|ref|YP_566460.1|  [L=298]
Description: hypothetical protein Mbur_1825 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.12   12.2   0.1       0.21   11.4   0.1    1.4  1  Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal doma
        0.6   10.1   1.8         26    4.9   0.0    2.3  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.4e-05      0.21      21      66 ..     234     279 ..     223     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
               Glyco_hydro2_C5  21 tvevvDknGnlvpnadnevtfeveGpGelvgvdngdptslesfksn 66 
                                   t+ v+D++Gn++  a++e  f+ eG+  ++g +  ++++ ++ +++
  gi|91773768|ref|YP_566460.1| 234 TIAVIDDDGNVIIYAEDEAYFDEEGNLVIIGNETTQEENGTNKQTP 279
                                   799****************************988777776666655 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4    0.0048        43      21      36 ..       5      20 ..       2      26 .. 0.90
   2 ?    4.9   0.0    0.0029        26      22      40 ..     280     298 .]     274     298 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0048
                                  XXXXXXXXXXXXXXXX CS
               Gram_pos_anchor 21 taaGllallggllLlv 36
                                  +++Gll+++g++++++
  gi|91773768|ref|YP_566460.1|  5 LLLGLLIVVGMIGFGL 20
                                  689**********976 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0029
                                   XXXXXXXXXXXXXXXXXXX CS
               Gram_pos_anchor  22 aaGllallggllLlvkrRK 40 
                                    + +++l+ gllL+ + RK
  gi|91773768|ref|YP_566460.1| 280 GFTSIMLIIGLLLSARSRK 298
                                   56789********999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1836.41
//
Query:       gi|91773769|ref|YP_566461.1|  [L=204]
Description: hypothetical protein Mbur_1827 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  120.4   1.2    4.3e-35  119.2   1.2    1.6  1  MTHFR_C   Methylene-tetrahydrofolate reductase C terminal


Domain annotation for each model (and alignments):
>> MTHFR_C  Methylene-tetrahydrofolate reductase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   1.2   2.4e-39   4.3e-35       1      93 [.     108     200 ..     108     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 2.4e-39
                       MTHFR_C   1 ypalntlflgveeevkvleekCkaCgdCvlaetggiCpvsrCakkllnGpCggskngkCevkpekeCaweliyerlkklgk 81 
                                   ypa+nt +lg+ +  kv+++ C++Cg+C++a++ggiCp+++C+k+llnGpCggs +gkCev+pek+Caweliyerl+++g+
  gi|91773769|ref|YP_566461.1| 108 YPANNTESLGAMTGDKVIHHLCAMCGQCTIADFGGICPTAQCPKELLNGPCGGSMDGKCEVDPEKDCAWELIYERLERIGR 188
                                   799****************************************************************************** PP

                       MTHFR_C  82 lekleeivppkd 93 
                                   l+ l+e+ ++kd
  gi|91773769|ref|YP_566461.1| 189 LDLLDEVRDAKD 200
                                   ******999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 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:                        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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1664.82
//
Query:       gi|91773770|ref|YP_566462.1|  [L=363]
Description: hypothetical protein Mbur_1828 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.1   1.1       0.05   13.9   0.1    1.6  2  ATP-synt_E_2  ATP synthase epsilon subunit
       0.05   14.5   0.2       0.12   13.3   0.1    1.5  1  Trypsin_2     Trypsin-like peptidase domain


Domain annotation for each model (and alignments):
>> ATP-synt_E_2  ATP synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.4   1.3e+04      12      25 ..      77      90 ..      71      92 .. 0.52
   2 ?   13.9   0.1   5.6e-06      0.05       3      27 ..     124     146 ..     122     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                  ATP-synt_E_2 12 YlniLkskLdeKKs 25
                                  +l+ +k+++++  +
  gi|91773770|ref|YP_566462.1| 77 WLDTIKESINDSEN 90
                                  34455555555555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.6e-06
                  ATP-synt_E_2   3 eidkstiDKYlniLkskLdeKKsEl 27 
                                   +idkstiDK+ ni+    + KK El
  gi|91773770|ref|YP_566462.1| 124 DIDKSTIDKFYNIIDA--NAKKAEL 146
                                   89***********975..5677775 PP

>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.3e-05      0.12      79     145 ..     266     327 ..     216     331 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                     Trypsin_2  79 ealkggepvyvvGyplggeksgsvssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsdG 145
                                    +++ g++vy+ G  +g +++  v +  +++ +       g+ ++ + +d ++++G SG+p+f   G
  gi|91773770|ref|YP_566462.1| 266 YDPSLGSQVYMSGITSGLTSG-NVKETYINKNSA----TFGTLYDQFVADYPCAGGDSGAPVFTMYG 327
                                   255556699999998888887.888888888888....44444444455555555********9666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2172.87
//
Query:       gi|91773771|ref|YP_566463.1|  [L=244]
Description: hypothetical protein Mbur_1830 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-15   55.3   0.0    5.5e-08   32.2   0.0    2.6  3  HTH_24          Winged helix-turn-helix DNA-binding
    7.5e-09   35.3   0.0    2.4e-05   24.1   0.0    2.4  2  HTH_5           Bacterial regulatory protein, arsR family
    3.1e-08   33.4   0.0     0.0018   18.1   0.0    2.3  2  MarR_2          MarR family
    6.6e-07   29.0   0.0     0.0016   18.2   0.0    2.2  2  HTH_IclR        IclR helix-turn-helix domain
    3.7e-06   26.9   0.0    0.00016   21.7   0.0    2.2  2  HTH_20          Helix-turn-helix domain
    1.2e-05   25.2   0.0       0.07   13.1   0.0    2.2  2  MarR            MarR family
    0.00022   21.1   0.0       0.83    9.6   0.0    2.2  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0018   18.6   0.0      0.014   15.7   0.1    2.1  2  FaeA            FaeA-like protein
      0.006   16.7   0.5        5.2    7.3   0.3    2.7  3  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.064   13.1   0.0        2.4    8.0   0.0    2.4  2  HTH_10          HTH DNA binding domain
      0.088   12.7   0.0        9.6    6.1   0.0    2.2  2  TFIIE_alpha     TFIIE alpha subunit


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 !   20.4   0.1   1.8e-07   0.00029       7      41 ..      93     127 ..      88     133 .. 0.96
   2 ?    0.4   0.0       0.3   4.9e+02       3      16 ..     153     166 ..     152     170 .. 0.83
   3 !   32.2   0.0   3.4e-11   5.5e-08       1      47 [.     163     209 ..     163     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                        HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrL 41 
                                   +IL ++ +np+ +++++ + lg+ +s+++++lk L
  gi|91773771|ref|YP_566463.1|  93 RILYYITANPGSTITDIEKNLGIKRSNIRYHLKVL 127
                                   7********************************88 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.3
                        HTH_24   3 etdrkILelLqknp 16 
                                   +t++kI+  L+ + 
  gi|91773771|ref|YP_566463.1| 153 DTEKKIIFFLRNDT 166
                                   799*******9985 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 3.4e-11
                        HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                   +++t + IL  +  +p+i++++L  + +l +stv+++++ + +eGl+
  gi|91773771|ref|YP_566463.1| 163 RNDTGKSILISILHEPGITNQDLTHAFDLAKSTVHWYIDDMHNEGLV 209
                                   689999***************************************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 !   24.1   0.0   1.5e-08   2.4e-05       1      39 [.      88     127 ..      88     129 .. 0.96
   2 !    8.9   0.0   0.00083       1.4      16      46 ..     180     210 ..     165     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.5e-08
                                   SHHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHH CS
                         HTH_5   1 dptRlkILklLaege.lcvcelaeelglsqstvShHLkkL 39 
                                   +p R +IL++   ++  +++++ + lg+ +s++++HLk+L
  gi|91773771|ref|YP_566463.1|  88 NPSRDRILYYITANPgSTITDIEKNLGIKRSNIRYHLKVL 127
                                   68999*********************************99 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00083
                                   EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  16 lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                    +  +l+ +++l +stv  +   ++++GLV+
  gi|91773771|ref|YP_566463.1| 180 ITNQDLTHAFDLAKSTVHWYIDDMHNEGLVD 210
                                   57789************************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0018       9      46 ..      93     128 ..      88     131 .. 0.94
   2 !   12.8   0.0   4.9e-05      0.08      10      54 ..     170     212 ..     168     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                        MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLv 46 
                                   r+L+++ ++pg   t++++++ lg+++s++ ++lk L+
  gi|91773771|ref|YP_566463.1|  93 RILYYITANPG--STITDIEKNLGIKRSNIRYHLKVLQ 128
                                   89*********..8********************9986 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.9e-05
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                   +L  + ++pg  +t ++l+ +++l ks+v+  ++++   GLv  +
  gi|91773771|ref|YP_566463.1| 170 ILISILHEPG--ITNQDLTHAFDLAKSTVHWYIDDMHNEGLVDFE 212
                                   7999******..******************************876 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 !    8.6   0.0   0.00095       1.5       8      43 ..      94     128 ..      93     130 .. 0.88
   2 !   18.2   0.0   9.8e-07    0.0016      14      49 ..     176     210 ..     167     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00095
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHH CS
                      HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLv 43 
                                   iL ++++ p+  t++++ +++g+ +S+ + +L+ L+
  gi|91773771|ref|YP_566463.1|  94 ILYYITANPGS-TITDIEKNLGIKRSNIRYHLKVLQ 128
                                   77788888886.*******************99986 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 9.8e-07
                                   TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  14 eapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                   ++p+  t+++l ++++l+kStvh ++  ++++G+v 
  gi|91773771|ref|YP_566463.1| 176 HEPG-ITNQDLTHAFDLAKSTVHWYIDDMHNEGLVD 210
                                   4444.8****************************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 !   21.7   0.0   9.9e-08   0.00016       9      49 ..      88     128 ..      87     129 .. 0.96
   2 ?    3.0   0.0     0.066   1.1e+02      19      60 ..     175     215 ..     170     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.9e-08
                                   -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                        HTH_20   9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLe 49 
                                   +P+R ril +++ + g t +++ + l++++++++yHL+vL+
  gi|91773771|ref|YP_566463.1|  88 NPSRDRILYYITANPGSTITDIEKNLGIKRSNIRYHLKVLQ 128
                                   89999**********************************95 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.066
                                   HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  19 LaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                   L  + g t  +l +++dl+k+t++  ++ +   gLv+ + eg
  gi|91773771|ref|YP_566463.1| 175 L-HEPGITNQDLTHAFDLAKSTVHWYIDDMHNEGLVDFENEG 215
                                   5.67778888999***********999999999999877776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0004      0.65       7      52 ..      93     138 ..      88     141 .. 0.90
   2 !   13.1   0.0   4.3e-05      0.07       7      49 ..     169     211 ..     165     220 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0004
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                   +iL+ +  +++ +++++ k lg+++s++   l+ L  ++ i+R  +
  gi|91773771|ref|YP_566463.1|  93 RILYYITANPGSTITDIEKNLGIKRSNIRYHLKVLQFNNKITRFEK 138
                                   7999999**************************9999999999765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.3e-05
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49 
                                   +iL ++ +++++++++L  ++ + kstv   +d +  +Gl++ 
  gi|91773771|ref|YP_566463.1| 169 SILISILHEPGITNQDLTHAFDLAKSTVHWYIDDMHNEGLVDF 211
                                   699************************************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 !    9.6   0.0   0.00051      0.83      19      66 ..     100     153 ..      93     155 .. 0.82
   2 !    9.5   0.0   0.00056      0.91      13      66 ..     170     223 ..     164     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00051
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE-- CS
                          TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravd 66 
                                   ++  +t+++i ++lg+ rs++   L+ L     ++r ++r      ++ Y+++d
  gi|91773771|ref|YP_566463.1| 100 ANPGSTITDIEKNLGIKRSNIRYHLKVLQFNNKITRFEKRnsvllfKNSYKYTD 153
                                   67889*********************9999999988887777777766666666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00056
                                   HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                          TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66 
                                   + + +l +   t +++ ++ ++ +s+v  ++  + + GlV+ e + +++ + ++
  gi|91773771|ref|YP_566463.1| 170 ILISILHEPGITNQDLTHAFDLAKSTVHWYIDDMHNEGLVDFENEGKYKRCFIN 223
                                   67788999999********************************98877766555 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   8.9e-06     0.014       2      51 ..      91     139 ..      90     143 .. 0.89
   2 ?    0.1   0.0      0.64     1e+03      13      46 ..     177     210 ..     166     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.9e-06
                                   HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--S CS
                          FaeA   2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvr 51 
                                   ++ Il y++  + + + ++i + lg+    +Ry L+ L+   ki r   r
  gi|91773771|ref|YP_566463.1|  91 RDRILYYITA-NPGSTITDIEKNLGIKRSNIRYHLKVLQFNNKITRFEKR 139
                                   588******9.7777779**************************997766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.64
                                   S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                          FaeA  13 kapckTreiAdalglsaYQaRyYLeqLekegkik 46 
                                   + + + +++  a+ l+   +  Y+  ++ eg + 
  gi|91773771|ref|YP_566463.1| 177 EPGITNQDLTHAFDLAKSTVHWYIDDMHNEGLVD 210
                                   3344557999999999999999999999999875 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 !    7.3   0.3    0.0032       5.2      18      51 ..     103     136 ..     100     163 .. 0.86
   2 ?   -0.6   0.0      0.95   1.6e+03      25      48 ..     149     172 ..     137     175 .. 0.78
   3 !    6.4   0.0    0.0063        10      17      48 ..     178     209 ..     170     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
                B-block_TFIIIC  18 GitqsdLakeskqdprslfyrlksLekkgLIvkq 51 
                                   G t +d+ k ++++ +++ y+lk+L+ ++ I++ 
  gi|91773771|ref|YP_566463.1| 103 GSTITDIEKNLGIKRSNIRYHLKVLQFNNKITRF 136
                                   78889999*****************988888775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.95
                B-block_TFIIIC  25 akeskqdprslfyrlksLekkgLI 48 
                                   +k+++ +++ +f +++   k+ LI
  gi|91773771|ref|YP_566463.1| 149 YKYTDTEKKIIFFLRNDTGKSILI 172
                                   789999999999999876666655 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0063
                B-block_TFIIIC  17 sGitqsdLakeskqdprslfyrlksLekkgLI 48 
                                    Git +dL ++++  ++ ++  ++ + + gL+
  gi|91773771|ref|YP_566463.1| 178 PGITNQDLTHAFDLAKSTVHWYIDDMHNEGLV 209
                                   6******************************9 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0015       2.4      25      45 ..     105     125 ..     103     131 .. 0.91
   2 ?    2.2   0.0     0.099   1.6e+02      24      44 ..     180     200 ..     179     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                        HTH_10  25 tlkeLAkelGIskstlsehLr 45 
                                   t+ ++ k lGI++s++ +hL+
  gi|91773771|ref|YP_566463.1| 105 TITDIEKNLGIKRSNIRYHLK 125
                                   788999**************7 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.099
                        HTH_10  24 vtlkeLAkelGIskstlsehL 44 
                                   +t ++L  +++++kst++ ++
  gi|91773771|ref|YP_566463.1| 180 ITNQDLTHAFDLAKSTVHWYI 200
                                   677999***********9776 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.015        25      17      59 ..      93     136 ..      78     163 .. 0.72
   2 ?    6.1   0.0    0.0059       9.6       5      60 ..     157     212 ..     153     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                                   HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHH.HCTSEEE CS
                   TFIIE_alpha  17 lvldvLlekgevteedlakelkidlnelrklLnrLy.earlvky 59 
                                    +l  +  +   t  d++k+l+i++ ++r  L  L+ + ++  +
  gi|91773771|ref|YP_566463.1|  93 RILYYITANPGSTITDIEKNLGIKRSNIRYHLKVLQfNNKITRF 136
                                   6677777777777889*************999888514455444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0059
                                   HHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                   TFIIE_alpha   5 evvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkyk 60 
                                    +++   ++  + +l ++l +  +t+ dl +   + +  +   + ++ +++lv++ 
  gi|91773771|ref|YP_566463.1| 157 KIIFFLRNDTGKSILISILHEPGITNQDLTHAFDLAKSTVHWYIDDMHNEGLVDFE 212
                                   5666677788899****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1590.67
//
Query:       gi|91773772|ref|YP_566464.1|  [L=140]
Description: hypothetical protein Mbur_1831 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 953.30
//
Query:       gi|91773773|ref|YP_566465.1|  [L=134]
Description: hypothetical protein Mbur_1832 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 896.72
//
Query:       gi|91773774|ref|YP_566466.1|  [L=528]
Description: hypothetical protein Mbur_1833 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-05   25.0   6.2        2.2    8.3   0.0    5.5  5  PD40         WD40-like Beta Propeller Repeat
    0.00013   22.2   0.1     0.0018   18.5   0.0    3.1  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
     0.0019   17.0   4.1       0.71    8.6   0.0    4.7  6  DPPIV_N      Dipeptidyl peptidase IV (DPP IV) N-terminal regi


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.011        66      16      23 ..      69      76 ..      65      77 .. 0.86
   2 !    4.7   0.1    0.0051        30       6      25 ..     120     139 ..     117     140 .. 0.86
   3 !    8.3   0.0   0.00036       2.2      16      25 ..     227     236 ..     227     239 .. 0.94
   4 !    6.7   0.0    0.0012       6.9      16      30 ..     269     283 ..     264     296 .. 0.72
   5 ?   -1.4   0.1       0.4   2.4e+03       8      24 ..     438     454 ..     432     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                                  E-TTSSEE CS
                          PD40 16 fSPDGkrl 23
                                  +SPDG+ +
  gi|91773774|ref|YP_566466.1| 69 WSPDGSNM 76
                                  *****976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0051
                                   SSSS.EEEEEE-TTSSEEEE CS
                          PD40   6 ntpgnegaPsfSPDGkrlaF 25 
                                   n+ ++ + P +S  G ++a+
  gi|91773774|ref|YP_566466.1| 120 NGGQIVTTPVWSQSGDYFAY 139
                                   666799************98 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00036
                                   E-TTSSEEEE CS
                          PD40  16 fSPDGkrlaF 25 
                                   +SPDG +++F
  gi|91773774|ref|YP_566466.1| 227 WSPDGEKIVF 236
                                   *********9 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0012
                                   E-TTSSEEEEEEECT CS
                          PD40  16 fSPDGkrlaFsSdRg 30 
                                   +SPD k+l F   +g
  gi|91773774|ref|YP_566466.1| 269 WSPDSKKLLFFEKKG 283
                                   **********76666 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.4
                                   SS.EEEEEE-TTSSEEE CS
                          PD40   8 pgnegaPsfSPDGkrla 24 
                                   ++n g +s+ P G+ +a
  gi|91773774|ref|YP_566466.1| 438 SKNSGRISLAPSGRFIA 454
                                   55899999*****9987 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.2   1.3e+04      39      52 ..      62      75 ..      58      78 .. 0.76
   2 ?   -1.9   0.0      0.74   4.4e+03      35      54 ..     119     138 ..      99     177 .. 0.65
   3 !   18.5   0.0     3e-07    0.0018       2      73 ..     184     254 ..     183     277 .. 0.91
   4 ?   -2.7   0.0       1.3   7.8e+03      42      60 ..     316     334 ..     306     344 .. 0.75
   5 ?   -2.6   0.0       1.1   6.9e+03      58      71 ..     417     430 ..     397     458 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                   ANAPC4_WD40 39 sevrsLaWkpdgkl 52
                                  s v ++ W+pdg+ 
  gi|91773774|ref|YP_566466.1| 62 SLVFDVLWSPDGSN 75
                                  5677889***9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.74
                   ANAPC4_WD40  35 dkedsevrsLaWkpdgklLa 54 
                                   ++ ++ v+   W+++g  +a
  gi|91773774|ref|YP_566466.1| 119 SNGGQIVTTPVWSQSGDYFA 138
                                   34555555556666665554 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 3e-07
                   ANAPC4_WD40   2 swcptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvv 73 
                                   +w+p+ + iA    +g++ v+ l+ +  +++e +++  +v++++W+pdg+ +++  ++  v  ld+e+ ++ 
  gi|91773774|ref|YP_566466.1| 184 KWSPKENKIAA-IVSGKITVYDLDEKTDFSFEMPDDTVRVEDMEWSPDGEKIVFLQNNHDVITLDIENRELN 254
                                   69999999985.4579***************************************************99875 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.3
                   ANAPC4_WD40  42 rsLaWkpdgklLavaysdg 60 
                                   + ++W pd + L v    g
  gi|91773774|ref|YP_566466.1| 316 KVIQWYPDSERLLVKKRHG 334
                                   5588999999888876555 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 1.1
                   ANAPC4_WD40  58 sdgevrlldaesgk 71 
                                   +d+e+++l+ ++ +
  gi|91773774|ref|YP_566466.1| 417 KDNEISVLNTSTHD 430
                                   55666665555444 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 ?   -2.9   0.0      0.37   2.2e+03      44     113 ..      63      74 ..      37      78 .. 0.56
   2 ?   -0.9   0.0      0.09   5.4e+02     107     128 ..     129     150 ..     123     156 .. 0.76
   3 !    8.6   0.0   0.00012      0.71      42      63 ..     219     240 ..     188     256 .. 0.69
   4 !    4.3   0.0    0.0023        14     100     120 ..     261     281 ..     253     300 .. 0.85
   5 ?   -3.5   0.0      0.54   3.2e+03     102     117 ..     314     329 ..     312     339 .. 0.75
   6 ?   -1.7   0.0      0.16   9.6e+02      53      75 ..     409     433 ..     384     446 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.37
                                   .BSEEEEESSTTEEEEEETTEEEEESTTTSEEEECES-STTTEEESB--HHHHHHTSSSSBEEEE-TTSS CS
                       DPPIV_N  44 klqlakwSPagdklafvrnnnLyvrelatgkeiqlTsdgsagifnGvadWvyeEEvlgsnsavwWspdgs 113
                                    + ++ wSP+g                                                          s
  gi|91773774|ref|YP_566466.1|  63 LVFDVLWSPDG----------------------------------------------------------S 74 
                                   44444444443..........................................................3 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.09
                                   EE-TTSSEEEEEEEECTTS-EE CS
                       DPPIV_N 107 wWspdgsrlaylrfdeseVpei 128
                                    Ws +g++ ayl++ e + ++i
  gi|91773774|ref|YP_566466.1| 129 VWSQSGDYFAYLELLEGSMHKI 150
                                   6999999999998877666655 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00012
                                   TT.BSEEEEESSTTEEEEEETT CS
                       DPPIV_N  42 eeklqlakwSPagdklafvrnn 63 
                                   + ++++++wSP+g+k++f +nn
  gi|91773774|ref|YP_566466.1| 219 TVRVEDMEWSPDGEKIVFLQNN 240
                                   5667777888888888887776 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.0023
                                   SSSSBEEEE-TTSSEEEEEEE CS
                       DPPIV_N 100 lgsnsavwWspdgsrlaylrf 120
                                   + +  +  Wspd+++l++++ 
  gi|91773774|ref|YP_566466.1| 261 FVAMYGAQWSPDSKKLLFFEK 281
                                   66778999**********975 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 0.54
                                   SSBEEEE-TTSSEEEE CS
                       DPPIV_N 102 snsavwWspdgsrlay 117
                                   s++ + W pd++rl++
  gi|91773774|ref|YP_566466.1| 314 SSKVIQWYPDSERLLV 329
                                   5677888888888875 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 0.16
                                   STTEEEEEETTEEEEESTTTS..EE CS
                       DPPIV_N  53 agdklafvrnnnLyvrelatg..ke 75 
                                   +g++l fv++n++ v +++t   + 
  gi|91773774|ref|YP_566466.1| 409 KGTDLLFVKDNEISVLNTSTHdtRD 433
                                   5777888888888777777664444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 3181.69
//
Query:       gi|91773775|ref|YP_566467.1|  [L=307]
Description: ABC efflux pump, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-36  125.4  19.0    4.7e-35  121.3  19.0    2.0  1  ABC2_membrane_2  ABC-2 family transporter protein
      9e-10   38.2  16.3      9e-10   38.2  16.3    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein
    7.7e-07   29.2  18.9    7.7e-07   29.2  18.9    2.1  2  ABC2_membrane_4  ABC-2 family transporter protein
     0.0069   15.8  27.5     0.0057   16.1  24.0    2.0  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
      0.032   13.8  28.4       0.11   12.0  24.1    2.9  2  ABC2_membrane_5  ABC-2 family transporter protein
        5.8    6.8  27.4      0.039   13.9   6.4    2.9  4  Fig1             Ca2+ regulator and membrane fusion protein F


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3  19.0   1.6e-38   4.7e-35       2     288 .]      15     302 ..      14     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 1.6e-38
               ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstima 82 
                                   +ia+kEf+d + s r++ l++++ +i     ++k++ +  ++ + +i+  +     v+                   + +a
  gi|91773775|ref|YP_566467.1|  15 VIAQKEFADNMWSSRLIMLMLVFTVI----VFSKSYVTIIGA-ESNIFRGLFI--DVA-------------------QVIA 69 
                                   69************************....555555444444.4444444333..222...................38** PP

               ABC2_membrane_2  83 vlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledll 162
                                   +++p++++++g+da ++E+e+g+l +lL++P +Rd i++gK +g ++  la ++ + ++tv+      +a+g +++  +l 
  gi|91773775|ref|YP_566467.1|  70 LFLPFMGIVLGFDAMTKERESGSLNVLLTHPLYRDNIIAGKTLGAMVT-LAlVVFLSIVTVVG--TRLVASGAEFSSLMLN 147
                                   ***********************************************9.77566666666444..5566889999999999 PP

               ABC2_membrane_2 163 llvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp........qeindfls 234
                                   +lv++++l+ l++  f+alg+l S++++++++++ + +++++vl ++++++  + a++ ag+++          e+n +++
  gi|91773775|ref|YP_566467.1| 148 RLVIFTILTYLYLsIFMALGILGSIITKNATKSLIYNIAIWLVLCVAFGMIFTTTASIIAGHKPLdltdndnfLELNADIQ 228
                                   9999999999999999***************************************************************** PP

               ABC2_membrane_2 235 llsptsayntllneilagsdlna....................lgstatnllilllllavllvlgyvlFkrkDl 288
                                    lspt++y  +++ +++ s+l                          +tn++il + ++ l+++++ +F r+D+
  gi|91773775|ref|YP_566467.1| 229 KLSPTHHYAMAVSGVPSLSPLGVsserptvrgifdtehtleqwWNELWTNVIILTITPVFLMIMAFMAFLRQDI 302
                                   *******************988799****************888889*************************96 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 ?   -1.9   2.3      0.46   1.4e+03     205     223 ..      25      43 ..      20      72 .. 0.57
   2 !   38.2  16.3     3e-13     9e-10     160     344 ..      57     294 ..      43     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.46
               ABC2_membrane_3 205 ywlskilgdflvyllqlll 223
                                   +w s++++++lv+ ++++ 
  gi|91773775|ref|YP_566467.1|  25 MWSSRLIMLMLVFTVIVFS 43 
                                   6888888888888888753 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 3e-13
               ABC2_membrane_3 160 asflvg.liliilifitasfiav...siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl..... 231
                                    + l++ ++ +i++f++++ i+    ++ +E+es+ + ++l+ ++ +  ++ +k lg ++  +l+++l ++ ++g+     
  gi|91773775|ref|YP_566467.1|  57 FRGLFIdVAQVIALFLPFMGIVLgfdAMTKERESGSLNVLLTHPLYRDNIIAGKTLGAMVTLALVVFLSIVTVVGTrlvas 137
                                   4444444666677777777777733467******************************************98777778888 PP

               ABC2_membrane_3 232 .....gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp....ledlp......... 294
                                        +++ + l+++ +l  l++ ++ alg l s ++kn+++  i  ++++l+l+++fg++f+    +  ++         
  gi|91773775|ref|YP_566467.1| 138 gaefsSLMLNRLVIFTILTYLYLSIFMALGILGSIITKNATKSLIYNIAIWLVLCVAFGMIFTttasI--IAghkpldltd 216
                                   8886555555556666*********************************************9977442..33556666666 PP

               ABC2_membrane_3 295 .....salkwifsiiPffapglgllrli........tgdplwe....................illsliilalfavvylll 342
                                        +  + i  + P+++++++   ++        +     e                    +++++iil ++ v+++++
  gi|91773775|ref|YP_566467.1| 217 ndnflELNADIQKLSPTHHYAMAVSGVPslsplgvsS-----ErptvrgifdtehtleqwwneLWTNVIILTITPVFLMIM 292
                                   7744444445*****************9788844440.....256666666677777777778***************999 PP

               ABC2_membrane_3 343 al 344
                                   a+
  gi|91773775|ref|YP_566467.1| 293 AF 294
                                   86 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 !   29.2  18.9   2.6e-10   7.7e-07      17     177 ..      27     193 ..      18     209 .. 0.73
   2 ?   -0.1   0.1      0.25   7.5e+02      53      70 ..     280     295 ..     257     303 .. 0.49

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.6e-10
               ABC2_membrane_4  17 llvlaallvpllall.yfnllgktgldpaefys.lsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtkll 95 
                                    + l++l++++++++    +++  g++ + f   +  +   + l+lp++ ++++   +++E++++ l+ Llt P  r +++
  gi|91773775|ref|YP_566467.1|  27 SSRLIMLMLVFTVIVfSKSYVTIIGAESNIFRGlFIDVAQVIALFLPFMGIVLGFDAMTKERESGSLNVLLTHPLYRDNII 107
                                   455555555554333133344444444333333233344456789************************************ PP

               ABC2_membrane_4  96 laKli...vllllsvllmlvtflitvlfallsgfvg.fsvklvlellkkclelgllvffavlpiialvllkksyvlplilt 172
                                   ++K +   v+l l+v+l++vt++ t l+a  + f++ +   lv++++  +l l +++++ +l  i+  +++ks ++ +++ 
  gi|91773775|ref|YP_566467.1| 108 AGKTLgamVTLALVVFLSIVTVVGTRLVASGAEFSSlMLNRLVIFTILTYLYLSIFMALGILGSIITKNATKSLIYNIAIW 188
                                   ***862225556666667777777777766666665344556889999999999999999999999999*******99999 PP

               ABC2_membrane_4 173 lvyti 177
                                   lv+ +
  gi|91773775|ref|YP_566467.1| 189 LVLCV 193
                                   99865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.25
               ABC2_membrane_4  53 gftlllllplilgiiasy 70 
                                    +   ++ p+ l i+a +
  gi|91773775|ref|YP_566467.1| 280 IIL--TITPVFLMIMAFM 295
                                   211..2222222222222 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  24.0   1.9e-06    0.0057       3     182 ..      13     201 ..      11     206 .. 0.81
   2 ?    0.8   0.1     0.092   2.8e+02      13      41 ..     270     298 ..     249     305 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                 ABC2_membrane   3 ikallkrefl.qrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr......pgllffsvlflafsaltsvapvfe 76 
                                   ++++ ++ef  ++w ++ l++l+ +++ ++++  + t++g   n   ++ r      + +++ ++ f+++++ + + ++ e
  gi|91773775|ref|YP_566467.1|  13 VFVIAQKEFAdNMWSSR-LIMLMLVFTVIVFSKSYVTIIGAESN---IF-RglfidvAQVIALFLPFMGIVLGFDA-MTKE 87 
                                   67899999998888888.5559999999***********93323...22.23455669999999999997777777.**** PP

                 ABC2_membrane  77 rergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv....gldls.....rfflflllllltalaasslg 148
                                   re g+l+ +l++pl  +  ++++k+l+ ++  +l++++ +++v+ +     g + s     r ++f +l++l++ ++++lg
  gi|91773775|ref|YP_566467.1|  88 RESGSLNVLLTHPL-YRDNIIAGKTLGAMVTLALVVFLSIVTVVGTRlvasGAEFSslmlnRLVIFTILTYLYLSIFMALG 167
                                   **************.899*******99988888888887776666411234555556666688****************** PP

                 ABC2_membrane 149 llisalapsfedasqlaslvllpllllsGffipi 182
                                   +l s++++++    ++  ++ l+l +  G+++++
  gi|91773775|ref|YP_566467.1| 168 ILGSIITKNATKSLIYNIAIWLVLCVAFGMIFTT 201
                                   *****************99999999999988875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.092
                 ABC2_membrane  13 qrwrdpslgllwrliqplllalvfgtvfg 41 
                                   q+w    ++++  +i+p++l+++   +f 
  gi|91773775|ref|YP_566467.1| 270 QWWNELWTNVIILTITPVFLMIMAFMAFL 298
                                   45555555555555555555555555554 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  24.1   3.8e-05      0.11      36     170 ..      64     205 ..      19     221 .. 0.70
   2 ?    0.7   0.1      0.11   3.2e+02      38      54 ..     280     296 ..     266     305 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
               ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.....v 111
                                   v+ +++++ +++ i+l + ++ +++ s++  +llt P+ r +i++ K l++ +  ++++++++++++   l+ +      +
  gi|91773775|ref|YP_566467.1|  64 VAQVIALFLPFMGIVLGFDAMTKERESGSLNVLLTHPLYRDNIIAGKTLGAMVTLALVVFLSIVTVVGTRLVASGaefssL 144
                                   455677888899999999*****************************9999888888888888877664444444344442 PP

               ABC2_membrane_5 112 tisevllsiliglvialiflaivlPl.....yfkfgvekgrivliiiifgiifllvaifsl.skl 170
                                       +l+ ++i+ ++++++l+i++ l     ++   + k+ i++i+i++++++ +  if +  ++
  gi|91773775|ref|YP_566467.1| 145 ----MLNRLVIFTILTYLYLSIFMALgilgsIITKNATKSLIYNIAIWLVLCVAFGMIFTTtASI 205
                                   ....4444444444444444444444111113444567777899999999999777666642444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
               ABC2_membrane_5  38 lifsilslvisiililt 54 
                                   +i++i +++++i+  + 
  gi|91773775|ref|YP_566467.1| 280 IILTITPVFLMIMAFMA 296
                                   22333333333332222 PP

>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.4   0.00063       1.9      69     131 ..      18      80 ..       7      86 .. 0.74
   2 ?   13.9   6.4   1.3e-05     0.039      56     152 ..      86     186 ..      78     194 .. 0.87
   3 ?    4.5   2.9    0.0098        29      81     141 ..     145     204 ..     136     209 .. 0.64
   4 ?   -4.5   2.3       5.8   1.7e+04     169     186 ..     276     293 ..     275     299 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00063
                          Fig1  69 akkfsdnvvhpyllmvaiiLtlllfllllyfpl.gseipllPfkskavskvalvlsflllllwl 131
                                    k+f+dn+  ++l+m  +++t+++f    y++  g+e +++ +    v +v+ ++ +++ ++++
  gi|91773775|ref|YP_566467.1|  18 QKEFADNMWSSRLIMLMLVFTVIVFSKS-YVTIiGAESNIFRGLFIDVAQVIALFLPFMGIVLG 80 
                                   468**********************988.54444777777777777777777777666655555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                          Fig1  56 skstsdplnlvelakkfsdnvvhpyllmvaiiLtlllfllllyfpl....gseipllPfkskavskvalvlsflllllwlv 132
                                   ++ +s +ln + +    +dn++  + l + + L+l++fl ++++ +     s +++  +   ++  +++++   l++++++
  gi|91773775|ref|YP_566467.1|  86 KERESGSLNVLLTHPLYRDNIIAGKTLGAMVTLALVVFLSIVTVVGtrlvASGAEFSSLMLNRLVIFTILTYLYLSIFMAL 166
                                   4555569**********************************9998888887778888888888889999999999****** PP

                          Fig1 133 galwqhvassaastlveeas 152
                                   g+l + ++ +a+++l+ +++
  gi|91773775|ref|YP_566467.1| 167 GILGSIITKNATKSLIYNIA 186
                                   *************9998766 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0098
                          Fig1  81 llmvaiiLtlllfllllyfpl....gseipllPfkskavskvalvlsflllllwlvgalwqhvas 141
                                   +l   +i+t+l  l l+ f +    gs+i + +      +++++ +++ l+l +++g++++++as
  gi|91773775|ref|YP_566467.1| 145 MLNRLVIFTILTYLYLSIFMAlgilGSIITKNA-----TKSLIYNIAIWLVLCVAFGMIFTTTAS 204
                                   455567888888888887775433333333333.....566666666677777888888888776 PP

  == domain 4  score: -4.5 bits;  conditional E-value: 5.8
                          Fig1 169 Wfafaflllvclglwvli 186
                                   W+ +++l+++ + l+++ 
  gi|91773775|ref|YP_566467.1| 276 WTNVIILTITPVFLMIMA 293
                                   555555555444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1846.10
//
Query:       gi|91773776|ref|YP_566468.1|  [L=289]
Description: hypothetical protein Mbur_1835 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-35  123.4  18.8    6.7e-35  120.8  18.8    1.8  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.5e-09   37.5  22.8    2.4e-09   36.8  22.9    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
      7e-07   29.4  17.9      7e-07   29.4  17.9    2.8  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.054   13.9   0.4      0.054   13.9   0.4    2.8  3  Curto_V3         Curtovirus V3 protein
      0.069   12.7  27.1      0.036   13.6  21.6    2.8  2  ABC2_membrane_5  ABC-2 family transporter protein
        3.4    7.2  11.1        0.2   11.2   1.2    2.5  3  L6_membrane      L6 membrane protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8  18.8   2.2e-38   6.7e-35       2     288 .]       8     287 ..       7     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 2.2e-38
               ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstima 82 
                                   +ia+kE++d++r+  fl+l + + li   + ++  +++s++ ea ++  ++ ++                       ++++
  gi|91773776|ref|YP_566468.1|   8 VIAQKEVSDHLRDSGFLVLLATYTLI---VFASTYMYGSMKHEASSLLLSSINV-----------------------QMIS 62 
                                   69************************...5555566666655555544444443.......................3799 PP

               ABC2_membrane_2  83 vlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledll 162
                                   +++p+ ++++g+da+++E+ +g+l +lL++Pv+Rd i++gK++g++++  a i+ +++++v     +   +g+ +   +l+
  gi|91773776|ref|YP_566468.1|  63 LFGPLSGIVLGFDAVVRERKSGSLNVLLTHPVFRDNIIAGKLLGSMLVLAAiIVFSVFVSV---GTLLIFYGVGIGQTELI 140
                                   ************************************************4444444444443...3355678999999**** PP

               ABC2_membrane_2 163 llvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp..qeindflsllspts 240
                                   +++v+++l++l+v  fl++++l+S+ +++++ ++++ ++++++  il++ vl +v  +l+g +    + i+++ls  + ++
  gi|91773776|ref|YP_566468.1| 141 RIAVFTILTFLYVsIFLGIAVLVSTMVKDATDSLTYNVVIWLFIGILFGAVLKAVVVILTGDTSNegALITQLLSVSPLHH 221
                                   ******************************************************999999988866555666665555555 PP

               ABC2_membrane_2 241 ayntllneilagsdlna....................lgstatnllilllllavllvlgyvlFkrkDl 288
                                   + +++l+ +  + +                       l  ++ n+++l++ ++vl++ ++  F r+D+
  gi|91773776|ref|YP_566468.1| 222 YAEAVLGKLDLSFG--GfnsdpviggifdtgytltrcLKEFWMNIVVLIVTPVVLFIAAFITFLRRDI 287
                                   55555555533222..13358*********************************************96 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 !   36.8  22.9   7.9e-13   2.4e-09     168     344 ..      59     279 ..      21     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 7.9e-13
               ABC2_membrane_3 168 liilifitasfiav...siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill.....l..afglgipfgnl 238
                                    +i++f ++s i+    ++v+E++s+ + ++l+ +v +  ++ +k+lg++lv + ++++ ++     l  ++g+gi  ++l
  gi|91773776|ref|YP_566468.1|  59 QMISLFGPLSGIVLgfdAVVRERKSGSLNVLLTHPVFRDNIIAGKLLGSMLVLAAIIVFSVFvsvgtLliFYGVGIGQTEL 139
                                   3666666677666644467**************************************999873333313355547888888 PP

               ABC2_membrane_3 239 ..glll.llfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.......ledlp...salkwifsiiPf 306
                                     ++++ +l +l+  +++ ++ l+s+++k++++  +  ++++l ++g+++g ++       + d +     + +++s+ P+
  gi|91773776|ref|YP_566468.1| 140 irIAVFtILTFLYVSIFLGIAVLVSTMVKDATDSLTYNVVIWL-FIGILFGAVLkavvvilTGDTSnegALITQLLSVSPL 219
                                   343455799999999****************999887666666.66666666555555554333337778899******** PP

               ABC2_membrane_3 307 fapglgllrli...tgdplwe...................illsliilalfavvylllal 344
                                   ++++++ l  +   +g  +++                   +++++++l+++ vv++++a+
  gi|91773776|ref|YP_566468.1| 220 HHYAEAVLGKLdlsFGGFNSDpviggifdtgytltrclkeFWMNIVVLIVTPVVLFIAAF 279
                                   *****9865555557663333788899999999999**********************98 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 !   29.4  17.9   2.3e-10     7e-07      17     174 ..      24     179 ..      18     187 .. 0.67
   2 ?    1.8   8.7     0.066     2e+02     100     159 ..     143     199 ..     140     217 .. 0.67
   3 ?    1.7   0.2     0.075   2.2e+02     134     160 ..     253     278 ..     239     286 .. 0.46

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.3e-10
               ABC2_membrane_4  17 llvlaallvpllallyfnllgktgldpaefyslsvfgft.lllllplilgiiasylifrEeqndtlknLltiPvsrtklll 96 
                                   l++la+ ++ ++a +y++  g+ + ++a+  +ls+++++ + l+ pl  ++++   + rE++++ l+ Llt Pv r ++++
  gi|91773776|ref|YP_566468.1|  24 LVLLATYTLIVFASTYMY--GSMK-HEASSLLLSSINVQmISLFGPLSGIVLGFDAVVRERKSGSLNVLLTHPVFRDNIIA 101
                                   334444445455555543..3344.444444444444441668888888889999************************** PP

               ABC2_membrane_4  97 aKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvlpliltlv 174
                                   +Kl+  +l+ +++++++++++v + l++ +vg+  + ++++ + +++++l+v +++  +++++++ k    +l+ ++v
  gi|91773776|ref|YP_566468.1| 102 GKLLGSMLVLAAIIVFSVFVSVGTLLIFYGVGIGQTELIRIAVFTILTFLYVSIFLGIAVLVSTMVKDATDSLTYNVV 179
                                   ********9999999999999999999999998877777665555555555554444444445555544444444433 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.066
               ABC2_membrane_4 100 ivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialv 159
                                   +v  +l++l++ +++ i+vl+   s++v+  +++++++++++l +g+l  +++ +++++ 
  gi|91773776|ref|YP_566468.1| 143 AVFTILTFLYVSIFLGIAVLV---STMVKDATDSLTYNVVIWLFIGILFGAVLKAVVVIL 199
                                   455556666666655555555...667777788999999999999998877666665553 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.075
               ABC2_membrane_4 134 vlellkkclelgllvffavlpi.ialvl 160
                                   ++++lk++ + ++ v+ +v+p+ +++++
  gi|91773776|ref|YP_566468.1| 253 LTRCLKEFWMNIV-VL-IVTPVvLFIAA 278
                                   4444444442222.22.23333133332 PP

>> Curto_V3  Curtovirus V3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.8e-05     0.054       7      68 ..      23      84 ..      18      88 .. 0.93
   2 ?   -0.8   0.5      0.67     2e+03      11      27 ..     114     132 ..     108     172 .. 0.65
   3 ?   -0.0   0.1      0.39   1.2e+03       7      24 ..     181     198 ..     177     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                      Curto_V3  7 wlfllfvfsillqsginfygtfqserisaklsslasridelflklqqvvyaryrvsrdrvvd 68
                                  +l ll  +++++ + + +yg+++ e  s  lss+  ++  lf  l  +v     v r+r + 
  gi|91773776|ref|YP_566468.1| 23 FLVLLATYTLIVFASTYMYGSMKHEASSLLLSSINVQMISLFGPLSGIVLGFDAVVRERKSG 84
                                  6889999******************************************9999999999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.67
                      Curto_V3  11 lfvfsillqsgi..nfygt 27 
                                   ++vfs+++  g+   fyg 
  gi|91773776|ref|YP_566468.1| 114 IIVFSVFVSVGTllIFYGV 132
                                   6789999998873358875 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.39
                      Curto_V3   7 wlfllfvfsillqsginf 24 
                                   wlf+ ++f  +l++ + +
  gi|91773776|ref|YP_566468.1| 181 WLFIGILFGAVLKAVVVI 198
                                   ********9999986654 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  21.6   1.2e-05     0.036      34     173 ..      55     200 ..      24     219 .. 0.72
   2 ?   -0.3   0.2      0.22   6.6e+02     120     132 ..     264     277 ..     248     287 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
               ABC2_membrane_5  34 dsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavl.ikgn... 110
                                   +  + ++s++ ++  i+l + ++  ++ks++  +llt Pv r +i++ K l++ ++ ++ i++++++++   l ++g    
  gi|91773776|ref|YP_566468.1|  55 SINVQMISLFGPLSGIVLGFDAVVRERKSGSLNVLLTHPVFRDNIIAGKLLGSMLVLAAIIVFSVFVSVGTLLiFYGVgig 135
                                   4445667777888888888899999************************99888877777777666654433322222333 PP

               ABC2_membrane_5 111 ..vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifslsklels 173
                                       i+ ++++il +l +++++++ vl+ +    +  + +++++i+++i +l+ a+++   ++l+
  gi|91773776|ref|YP_566468.1| 136 qtELIRIAVFTILTFLYVSIFLGIAVLVSTMVKDATDSLTYNVVIWLFIGILFGAVLKAVVVILT 200
                                   33556677777777777777777788888888888888889999999999999999987554444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
               ABC2_membrane_5 120 iliglvia.lifla 132
                                   i++ +v   ++f+a
  gi|91773776|ref|YP_566468.1| 264 IVVLIVTPvVLFIA 277
                                   22222211011111 PP

>> L6_membrane  L6 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.023        70      56     105 ..      21      73 ..      11      79 .. 0.74
   2 ?   -3.5   0.5       2.2   6.5e+03     155     167 ..     112     124 ..     102     130 .. 0.55
   3 ?   11.2   1.2   6.8e-05       0.2       8      74 ..     141     204 ..     135     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.023
                   L6_membrane  56 gGllvllpaivilllgkkrac...scgnrckmllsillavlgvlGalyclvvs 105
                                   +G+lvll++ ++++ + +      + + +   l+si + +++++G l  +v+ 
  gi|91773776|ref|YP_566468.1|  21 SGFLVLLATYTLIVFASTYMYgsmKHEASSLLLSSINVQMISLFGPLSGIVLG 73 
                                   899***99999999888885454344555566677888999999988777765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                   L6_membrane 155 whltlFsiLllvs 167
                                     +++Fs+ + v+
  gi|91773776|ref|YP_566468.1| 112 AAIIVFSVFVSVG 124
                                   3344555555554 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 6.8e-05
                   L6_membrane   8 kclGlsLlplallsivaNilllfpngkteylkeekiskevwlfgGilGgGllvllpaivilllgkkr 74 
                                   ++  +++l+++ +si + i  l+ ++ ++++++      +wlf Gil g +l     +v++l+g ++
  gi|91773776|ref|YP_566468.1| 141 RIAVFTILTFLYVSIFLGIAVLVSTMVKDATDSLTYNVVIWLFIGILFGAVLKA---VVVILTGDTS 204
                                   66779999*********************99988889999*********98755...6666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1759.95
//
Query:       gi|91773777|ref|YP_566469.1|  [L=402]
Description: hypothetical protein Mbur_1836 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-09   36.9   0.5      0.031   14.5   0.0    4.1  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
    0.00054   20.2   0.3       0.91    9.9   0.0    3.8  3  DUF11        Domain of unknown function DUF11
    0.00057   20.1   1.8      0.014   15.6   0.1    2.9  2  CARDB        CARDB
     0.0024   18.1   2.5       0.22   11.7   0.3    3.4  3  FixG_C       IG-like fold at C-terminal of FixG, putative oxi
  ------ inclusion threshold ------
      0.043   13.9   0.0          1    9.5   0.1    3.1  2  Fn3-like     Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.59   2.1e+03      42      60 ..      39      57 ..      23      63 .. 0.66
   2 ?    3.0   0.0     0.034   1.2e+02      56      74 ..     106     124 ..     100     127 .. 0.85
   3 !   14.2   0.0   1.1e-05     0.039       5      76 ..     165     242 ..     161     245 .. 0.79
   4 !   14.5   0.0   8.5e-06     0.031       2      67 ..     281     346 ..     280     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.59
                   NPCBM_assoc 42 asaaslapGetveatvkVt 60
                                   +++ + pG+tve+ +++ 
  gi|91773777|ref|YP_566469.1| 39 ITGKVVLPGDTVEFPITIE 57
                                  3444888899988887776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.034
                   NPCBM_assoc  56 tvkVtppagaaaGdyevta 74 
                                    ++V+pp ++ +G y++ a
  gi|91773777|ref|YP_566469.1| 106 ILRVKPPIDTPNGAYTIWA 124
                                   578************9965 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.1e-05
                   NPCBM_assoc   5 etvtltltvtndgtaaatnvslslslPeGWtvvevspasaa......slapGetveatvkVtppagaaaGdyevtaka 76 
                                   ++v++ +t+ nd +  +t+    ++ P++W v+  +  +++      s+a+++++ + vkV+p+++   G+y+v + +
  gi|91773777|ref|YP_566469.1| 165 DPVEFYVTLENDYDHRVTADINVVEKPDNWDVEFLEEGNGKyritktSIAANDKQNFIVKVRPSTNSSDGTYPVIVDV 242
                                   67778888888887776665555888*****76666666555555889**************************8876 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 8.5e-06
                   NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaa 67 
                                   +pG++ ++ + + n+g++++ nv+l++++ +G t    s   +++l+pGe+ e  v++++ a++  
  gi|91773777|ref|YP_566469.1| 281 NPGSSREIVVNLRNSGDRTLNNVELKIQGVSGITTFVRSFGAIDELEPGESREIPVEIKVRADTSS 346
                                   79********************************6666777788***************9999875 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.061   2.2e+02       8      22 ..      42      56 ..      34      74 .. 0.79
   2 ?    3.5   0.1     0.025        89       9      30 ..     160     181 ..     141     258 .. 0.81
   3 !    9.9   0.0   0.00026      0.91       9      85 ..     279     347 ..     270     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.061
                         DUF11  8 sevrpGdtvtytltv 22
                                  + v pGdtv++ +t 
  gi|91773777|ref|YP_566469.1| 42 KVVLPGDTVEFPITI 56
                                  4799*********97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.025
                         DUF11   9 evrpGdtvtytltvtNtgpasa 30 
                                   e rp d v++ +t+ N +    
  gi|91773777|ref|YP_566469.1| 160 ETRPNDPVEFYVTLENDYDHRV 181
                                   57999***********987654 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00026
                         DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrvtrtaasg 85 
                                   +++pG   + ++ ++N+g +++n+v ++    +g+++++   +       +++  +Le+ges+ + ++++v++ ++s+
  gi|91773777|ref|YP_566469.1| 279 NLNPGSSREIVVNLRNSGDRTLNNVELKI---QGVSGITTFVR------SFGAiDELEPGESREIPVEIKVRADTSSD 347
                                   6899999999*****************97...55555555544......344469*******9988888877776654 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.049   1.8e+02       5      85 ..     151     241 ..     147     246 .. 0.53
   2 !   15.6   0.1     4e-06     0.014       8      89 ..     273     362 ..     267     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.049
                                   EE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEE..............SEE-CTEEEEEEEEEE CS
                         CARDB   5 tvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtv..............psLaagesttvsftwt 70 
                                    + +  +  e+ +++ ++++vt++N      ++++v+  ++  ++ ++++v              +s+aa+++ +  +++ 
  gi|91773777|ref|YP_566469.1| 151 DIYSDMPGLETRPNDPVEFYVTLEND-----YDHRVTADINVVEKpDNWDVefleegngkyritkTSIAANDKQNFIVKVR 226
                                   55555555666666666666666665.....33333333333333466777444444444444446666666666666666 PP

                                   -S-S-CEEEEEEEES CS
                         CARDB  71 teategevtltvvvD 85 
                                   +++++++ t+ v vD
  gi|91773777|ref|YP_566469.1| 227 PSTNSSDGTYPVIVD 241
                                   665555555555555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4e-06
                                   EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEE.ETTEEE...EEEEESEE-CTEEEEEEEEEE-S....-S-CEEEE CS
                         CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvaly.ldgelv...gtvtvpsLaagesttvsftwtte....ategevtl 80 
                                    +++  ++++g++ +i v+++N+G+ +  ++++++  ++g ++   +   + +L++ges+++ + ++++      ++e+ +
  gi|91773777|ref|YP_566469.1| 273 PESKSINLNPGSSREIVVNLRNSGDRTLNNVELKIQgVSGITTfvrSFGAIDELEPGESREIPVEIKVRadtsSDTKEILM 353
                                   5667778999**********************9996588888888877789************999999654444466667 PP

                                   EEEESTT-S CS
                         CARDB  81 tvvvDpdne 89 
                                   ++v D+  +
  gi|91773777|ref|YP_566469.1| 354 RAVSDEAES 362
                                   777777665 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.02        70      41     102 ..     175     243 ..     164     260 .. 0.52
   2 ?    1.7   0.0     0.082   2.9e+02      58      85 ..     268     294 ..     251     308 .. 0.70
   3 !   11.7   0.3   6.1e-05      0.22      39     109 ..     292     364 ..     289     372 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.02
                                   E-SSS-EEEEEEEES-S...S-EE.......E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEE.EEEEEEE CS
                        FixG_C  41 Nktekprrytlsveglp...glel......agraekeitvapgekrkvpvfvrvpaealkkkst.pitfkvt 102
                                   N  +++ + +++v ++p   ++e+      + ++ +++++a++ k++++v vr  +++  +++t p+ + v 
  gi|91773777|ref|YP_566469.1| 175 NDYDHRVTADINVVEKPdnwDVEFleegngK-YRITKTSIAANDKQNFIVKVRPSTNS--SDGTyPVIVDVA 243
                                   3333334444444432222323334332211.23456778888877777777766665..556668888885 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.082
                                   S-EE.E.S--EEEE-TT-EEEEEEEEEE CS
                        FixG_C  58 glelagraekeitvapgekrkvpvfvrv 85 
                                    l++  +++k+i++ pg++r+++v +r 
  gi|91773777|ref|YP_566469.1| 268 MLTIF-PESKSINLNPGSSREIVVNLRN 294
                                   55553.46899***********999985 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 6.1e-05
                                   EEE-SSS-EE.EEEEEES-SS-EE.E.S--EE.EE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE.EGGGTEE CS
                        FixG_C  39 ilNktekprr.ytlsveglpglelagraekei.tvapgekrkvpvfvrvpaealkkkstpitfkvt.dddeket 109
                                   ++N  +++ + ++l+++g  g++   r+   i +++pge+r++pv ++v+a+  ++++++i +++  d++e+e 
  gi|91773777|ref|YP_566469.1| 292 LRNSGDRTLNnVELKIQGVSGITTFVRSFGAIdELEPGESREIPVEIKVRADT-SSDTKEILMRAVsDEAESED 364
                                   66666666555999999999999855444444279**************9987.77788999998633333332 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.23   8.1e+02      27      42 ..     278     293 ..     274     299 .. 0.86
   2 ?    9.5   0.1   0.00028         1      22      51 ..     318     348 ..     303     375 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                                   EEE-TT-EEEEEEEEE CS
                      Fn3-like  27 veLapGesktvtftld 42 
                                   ++L+pG s+++ ++l 
  gi|91773777|ref|YP_566469.1| 278 INLNPGSSREIVVNLR 293
                                   689********99986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00028
                                   EEEEEEE.E-TT-EEEEEEEEECGGG-EEET CS
                      Fn3-like  22 kgFekve.LapGesktvtftldrkdlsvwde 51 
                                   + F  ++ L+pGes+++ +++++++  + d+
  gi|91773777|ref|YP_566469.1| 318 RSFGAIDeLEPGESREIPVEIKVRADTSSDT 348
                                   67888888**************977555454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2605.07
//
Query:       gi|91773778|ref|YP_566470.1|  [L=327]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-26   92.9   0.0    5.5e-26   91.7   0.0    1.6  2  ABC_tran  ABC transporter
    2.1e-13   50.8   0.1    2.6e-08   34.0   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    6.8e-06   26.0   0.0       0.12   12.1   0.0    2.2  2  AAA_15    AAA ATPase domain
    0.00071   20.1   0.4     0.0013   19.3   0.4    1.7  1  AAA_23    AAA domain
     0.0031   17.9   0.8      0.054   13.9   0.8    2.5  1  AAA       ATPase family associated with various cellular acti
      0.007   17.1   0.3      0.026   15.2   0.1    2.1  2  DUF4162   Domain of unknown function (DUF4162)
  ------ inclusion threshold ------
      0.027   14.2   0.1      0.068   12.9   0.1    1.7  2  AAA_30    AAA domain
      0.039   13.6   0.1       0.11   12.1   0.1    1.7  1  SRP54     SRP54-type protein, GTPase domain
      0.041   14.2   0.3        0.3   11.4   0.3    2.2  1  AAA_22    AAA domain
      0.052   13.5   0.1       0.81    9.6   0.0    2.3  2  Rad17     Rad17 P-loop domain
       0.11   12.3   0.3       0.22   11.3   0.3    1.5  1  AAA_29    P-loop containing region of AAA domain
       0.15   11.5   0.1         13    5.2   0.0    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   3.7e-29   5.5e-26       2     137 .]      38     181 ..      37     181 .. 0.96
   2 ?   -2.0   0.0       3.1   4.6e+03      54      79 ..     216     240 ..     192     317 .. 0.58

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 3.7e-29
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   + +sl++k+ge+ ++vG+nGaGK+t +k+l+gll+pt+G+ ++ g d+ + e+   r+  gvlp+ + + ++lt+r+n   
  gi|91773778|ref|YP_566470.1|  38 DSLSLDVKKGEVFGFVGPNGAGKTTTMKMLIGLLEPTSGTGKVAGFDIVR-EIINIREVTGVLPEPAGFYDNLTARQNlrf 117
                                   789***********************************************.99999************************* PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                             +++++i ++l+ +gl++  d+++      +S G+ +r  la+al+++p +l+lDEpt+
  gi|91773778|ref|YP_566470.1| 118 yaklynietgTREKRIVELLEMVGLNGAIDQKI----GGFSTGMLKRFGLAQALINEPGILFLDEPTS 181
                                   *******99988999999999999999888888....*****************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                                   HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  54 leslrkeigvlpqepqlfpeltvren 79 
                                    e+  ++i+v+++ + l  ++ v+e 
  gi|91773778|ref|YP_566470.1| 216 VEEICNRIAVIEKGKLLAVGT-VEEL 240
                                   455555555555443333333.4333 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 !   14.5   0.2   1.6e-05     0.023       2      24 ..      50      72 ..      49     138 .. 0.68
   2 !   34.0   0.0   1.7e-11   2.6e-08     234     300 ..     150     214 ..     143     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                   +++GpNg+GK++ ++ l +l  
  gi|91773778|ref|YP_566470.1| 50 FGFVGPNGAGKTTTMKMLIGLLE 72
                                  679*************9988863 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.7e-11
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                   +  +S G+++ ++l+ al+  +   ++l++DEp +g++Pk      +l+k+lsr n++ ++l++HS +
  gi|91773778|ref|YP_566470.1| 150 IGGFSTGMLKRFGLAQALINEP---GILFLDEPTSGIDPKGAQMMRDLIKKLSReNDVTIFLSSHSMS 214
                                   5679***************999...**************555555566688888889*********76 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.7e-05      0.12      21      48 ..      44      72 ..      36     114 .. 0.82
   2 !   11.9   0.0   9.1e-05      0.14     322     365 ..     169     212 ..     157     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                        AAA_15 21 lsee.ltvliGkNnsGKSsilealdlFln 48
                                  +++  +  ++G+N++GK++ +++l  +l+
  gi|91773778|ref|YP_566470.1| 44 VKKGeVFGFVGPNGAGKTTTMKMLIGLLE 72
                                  555456779**************987776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.1e-05
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   +++ il+++EP   + p+  +++ +l+k+l+++n+  +++++HS
  gi|91773778|ref|YP_566470.1| 169 NEPGILFLDEPTSGIDPKGAQMMRDLIKKLSRENDVTIFLSSHS 212
                                   6789***************************************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.4   8.6e-07    0.0013      16     127 ..      43     152 ..      16     272 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.6e-07
                        AAA_23  16 dF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.veltfenkdgrytrsierer 94 
                                   d  +  ++ ++GpNGaGKTT +  +   L   t+++++  g +++++ ++i   + v +  + +  + + +   +++++  
  gi|91773778|ref|YP_566470.1|  43 DVkKGEVFGFVGPNGAGKTTTMKMLIGLLE-PTSGTGKVAGFDIVREIINIREVTGVLPEpAGFYDNLTAR---QNLRFYA 119
                                   44333699**************98865554.4566666666677777777655544433322222222222...3466666 PP

                        AAA_23  95 elskkkgkttkkaklelleideleqfisellgs 127
                                   +l+  ++ t+ k + elle+  l+  i++++g 
  gi|91773778|ref|YP_566470.1| 120 KLYNIETGTREKRIVELLEMVGLNGAIDQKIGG 152
                                   666666666666666666666666666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.8   3.6e-05     0.054       3     120 ..      52     221 ..      50     230 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                                   EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS............................................ CS
                           AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk............................................ 37 
                                   ++Gp G GKT+++k ++  l+  +   ++ g +++ +                                            
  gi|91773778|ref|YP_566470.1|  52 FVGPNGAGKTTTMKMLIGLLEptSGTGKVAGFDIVREiinirevtgvlpepagfydnltarqnlrfyaklynietgtrekr 132
                                   79*****************85322233333333333333333333344555555555555555556666666655555555 PP

                                   ................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSS CS
                           AAA  38 ................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkes 101
                                                    +g  +  + + f  a++   +p ilf+DE  + +  +       + +++  L+++l+++++   
  gi|91773778|ref|YP_566470.1| 133 ivellemvglngaidqKIGGFSTGMLKRFGLAQALInEPGILFLDEPTSGIDPK-------GAQMMRDLIKKLSREND--- 203
                                   555666666555555577777777777787777666889999999988887777.......55666666666665544... PP

                                   TEEEEEEESSGGGSTHHHH CS
                           AAA 102 kvivigatnrpdkldpall 120
                                    v++ + +++++++++   
  gi|91773778|ref|YP_566470.1| 204 -VTIFLSSHSMSEVEEICN 221
                                   .888888888888876555 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.8   8.6e+03      52      65 ..     193     206 ..     184     228 .. 0.60
   2 !   15.2   0.1   1.7e-05     0.026       1      80 [.     235     324 ..     235     325 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.8
                                   ----------EEEE CS
                       DUF4162  52 ellkaltsgveirs 65 
                                   +l+k+l++  +++ 
  gi|91773778|ref|YP_566470.1| 193 DLIKKLSRENDVTI 206
                                   55555544444433 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-05
                                   E-HHHHHTTS-SS...EEEEE.......-------..---EEEE-TTS-EEEEE-------------.----EEEEEEEE- CS
                       DUF4162   1 GtleeiKrsygkn...rieve.......adaeelleepgveeveeeggelelkledeeaanellkal.tsgveirsFeeee 70 
                                   Gt+ee+ +  +++   ++ +e         a++l+e++gv+e + ++g l ++ +    + e+ k +   ++++ +Fee +
  gi|91773778|ref|YP_566470.1| 235 GTVEELQDMVREKegvQYILEisdfplqYAADKLNEIDGVFETRIRDGVLHVHADA-GMRAEIAKSIkLMDGTVSRFEEDR 314
                                   66666666664431113335565777555599***************999999997.59********66************ PP

                                   --HHHHHHHH CS
                       DUF4162  71 PsLndIFiek 80 
                                     L+ +F+++
  gi|91773778|ref|YP_566470.1| 315 MDLQKVFLKL 324
                                   *******986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.6e-05     0.068      19      49 ..      48      80 ..      40     103 .. 0.83
   2 ?   -2.9   0.0       3.1   4.7e+03      86     115 ..     168     201 ..     108     208 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g.grv 49
                                   v   +Gp G+GKtt++k l  ++e   g g+v
  gi|91773778|ref|YP_566470.1| 48 EVFGFVGPNGAGKTTTMKMLIGLLEPTsGtGKV 80
                                  477889*************99988876444455 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                        AAA_30  86 lepgtllivDEagmv....dtkqlaallkaaeka 115
                                   +++  +l  DE        +++++++l+k+++++
  gi|91773778|ref|YP_566470.1| 168 INEPGILFLDEPTSGidpkGAQMMRDLIKKLSRE 201
                                   4444555555533332444566666777666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.5e-05      0.11       4      39 ..      50      85 ..      48      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.5e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  + +vG++GaGKTtt+  L  ll+    +  ++  D+
  gi|91773778|ref|YP_566470.1| 50 FGFVGPNGAGKTTTMKMLIGLLEPTSGTGKVAGFDI 85
                                  569***********9988777776655555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3    0.0002       0.3      11      30 ..      53      72 ..      45     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                        AAA_22 11 tGesGtGKTtllrrlleqld 30
                                  +G+ G+GKTt++++l   l+
  gi|91773778|ref|YP_566470.1| 53 VGPNGAGKTTTMKMLIGLLE 72
                                  8*************998775 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00054      0.81      35      66 ..      37      68 ..      30      75 .. 0.85
   2 ?    1.6   0.0      0.15   2.3e+02     115     160 ..     280     325 ..     226     327 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00054
                         Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                  +++ +L+ +k ++    GP G gk+t++k+L 
  gi|91773778|ref|YP_566470.1| 37 VDSLSLDVKKGEVFGFVGPNGAGKTTTMKMLI 68
                                  5667788888889999*************995 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                         Rad17 115 kdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevirkyl 160
                                   +d    +    G  ++  k++ l++   ++f+ d   l++v +k +
  gi|91773778|ref|YP_566470.1| 280 RDGVLHVHADAGMRAEIAKSIKLMDGTVSRFEEDRMDLQKVFLKLI 325
                                   5555555556778888899999*************99**9999876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00015      0.22      17      49 ..      42      74 ..      36      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  ++++  +++ ++Gp+G+GK+T +  ++ lL p+
  gi|91773778|ref|YP_566470.1| 42 LDVKKGEVFGFVGPNGAGKTTTMKMLIGLLEPT 74
                                  5666444899***********997777777765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0086        13      28      42 ..      51      65 ..      38      73 .. 0.81
   2 ?    4.1   0.0     0.018        27     149     209 ..     161     221 ..     111     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0086
                                  EEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxx RF
                         SMC_N 28 aivGpNGSGKsnlld 42
                                    vGpNG+GK+  + 
  gi|91773778|ref|YP_566470.1| 51 GFVGPNGAGKTTTMK 65
                                  469*******98775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                                   HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                   + +A   ++   + +lDe  + +D k  + + +l+k+ s +  + +   ++ m e  + + 
  gi|91773778|ref|YP_566470.1| 161 FGLAQALINEPGILFLDEPTSGIDPKGAQMMRDLIKKLSRENDVTIFLSSHSMSEVEEICN 221
                                   556666677778899*********************9887766555544444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2043.66
//
Query:       gi|91773779|ref|YP_566471.1|  [L=361]
Description: hypothetical protein Mbur_1838 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.4   0.2       0.25   10.1   0.0    2.0  2  FbpA      Fibronectin-binding protein A N-terminus (FbpA)


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 ?   -0.7   0.1     0.025   4.5e+02     199     285 ..      62     148 ..      37     151 .. 0.63
   2 ?   10.1   0.0   1.4e-05      0.25     224     294 ..     214     281 ..     205     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.025
                                   TXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX....XX..EE.....XSSSEESSXXTTXX.SSXXXX CS
                          FbpA 199 Glspllaeelleragldketsakelseedlerlyealqelleeleeekfep..qlvlkeekpeefsvvplkslselekesf 277
                                   Glsp    e+++++g+ +e +++e ++e   rl e  ++l +e+ + ++ p  ++++   + +++ v+ +++ +  e+e++
  gi|91773779|ref|YP_566471.1|  62 GLSPS-EHEVIASVGILPEFNTEEQKKEWTLRLEELNERLKDEMVSSHMYPygEVLTCGYNSNGYLVILFEN-KTIEQETM 140
                                   56654.467777777777776666666666666666666666666666666543333333555555553333.45666777 PP

                                   SXHHHHHH CS
                          FbpA 278 dslseald 285
                                   d++ + +d
  gi|91773779|ref|YP_566471.1| 141 DEIYTYVD 148
                                   76666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 1.4e-05
                                   ........HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX- CS
                          FbpA 224 seedlerlyealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaer 294
                                   ++e+ ++  + l+++l e++ +++ep + ++  + +e+sv+  +   + +k+++d+++ ++d+ Y+  +e+
  gi|91773779|ref|YP_566471.1| 214 TDEQRSDFGKDLMDILYEVR-TEMEPYM-YNG-QVVEYSVFGSSVEVGINKNETDNVQMLCDDVYRIFDEE 281
                                   78899999999********9.7899988.455.6*******987767******************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2274.39
//
Query:       gi|91773780|ref|YP_566472.1|  [L=93]
Description: hypothetical protein Mbur_1839 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-12   46.4   0.3    2.6e-12   46.4   0.3    2.3  2  PLDc_N    Phospholipase_D-nuclease N-terminal
    0.00038   20.7   0.8    0.00051   20.3   0.4    1.5  1  DUF2516   Protein of unknown function (DUF2516)
  ------ inclusion threshold ------
       0.17   10.6   1.9       0.19   10.4   1.9    1.1  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   5.8       1.2   7.4e+03      24      37 ..      12      26 ..       3      30 .. 0.60
   2 !   46.4   0.3   4.4e-16   2.6e-12       1      40 [.      34      80 ..      34      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                        PLDc_N 24 lvilflP.vlGailY 37
                                   +i+f+  ++G +l+
  gi|91773780|ref|YP_566472.1| 12 GLIIFFTiLIGQLLW 26
                                  444444436666666 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 4.4e-16
                        PLDc_N  1 ilwiialidiirdrnpss........klaWllvilflPvlGailYllf 40
                                  ++wi++l+d+++ rn++         kl+W+lv++fl+++Ga+lY+ +
  gi|91773780|ref|YP_566472.1| 34 VFWIFMLCDCLQ-RNTEDfpskgdneKLIWALVLIFLNFIGAVLYYYL 80
                                  79**********.555555579***********************987 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   8.5e-08   0.00051       6      58 ..      23      75 ..      18      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.5e-08
                       DUF2516  6 lvllllalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlll 58
                                   +l+ +  +++v+ ++ l d+l r  + F+  g + K +W+++l+   +++ +
  gi|91773780|ref|YP_566472.1| 23 QLLWGIIAIATVFWIFMLCDCLQRNTEDFPSKGDNEKLIWALVLIFLNFIGAV 75
                                  5789999999*********************************9987777766 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.9   3.3e-05      0.19     380     435 ..      16      82 ..       2      93 .] 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.3e-05
                       DUF2207 380 lkklsalglgliilglilillallllvll.....................lvfllilllillliaiivlllfsrllg 435
                                   ++++ +  l+++i++++           +                      +  li++l+l+++++i ++l+++l++
  gi|91773780|ref|YP_566472.1|  16 FFTILIGQLLWGIIAIAT----------VfwifmlcdclqrntedfpskgDNEKLIWALVLIFLNFIGAVLYYYLVR 82 
                                   223333333333333333..........24556666666***********888888888888888888888777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 601.23
//
Query:       gi|91773781|ref|YP_566473.1|  [L=501]
Description: hypothetical protein Mbur_1840 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-28   97.3   0.0    2.1e-27   95.8   0.0    1.9  1  AAA_14        AAA domain
    1.2e-11   44.8   0.1    2.4e-11   43.8   0.1    1.6  1  DUF4143       Domain of unknown function (DUF4143)
    0.00071   19.6   0.0     0.0016   18.4   0.0    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0024   18.2   0.0       0.11   12.8   0.0    2.3  2  AAA_22        AAA domain
     0.0031   17.9   0.0      0.011   16.2   0.0    2.0  1  RNA_helicase  RNA helicase
  ------ inclusion threshold ------
      0.022   15.2   0.0       0.06   13.8   0.0    1.8  1  AAA           ATPase family associated with various cellular 
      0.024   14.6   0.1       0.19   11.6   0.0    2.6  2  NACHT         NACHT domain
      0.037   13.8   0.0      0.074   12.8   0.0    1.5  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.088   13.3   1.3       0.41   11.1   0.0    2.7  3  DUF234        Archaea bacterial proteins of unknown function
       0.11   13.0   0.0        2.1    8.9   0.0    2.5  2  ABC_tran      ABC transporter
       0.13   12.3   0.1       0.28   11.2   0.1    1.5  1  HTH_11        HTH domain
       0.21   12.0   0.0       0.39   11.1   0.0    1.5  1  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   1.4e-30   2.1e-27       3     130 ..      60     196 ..      58     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 1.4e-30
                        AAA_14   3 kilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelileklke..ekktylflDEiqevpew 79 
                                   k+++++G+R+vGKTtl+k+li++ll   +++si+y+++d  +++k+  + ++++ +++  ++   +++ylflDEi+ v++w
  gi|91773781|ref|YP_566473.1|  60 KVYTLRGPRQVGKTTLCKTLIQDLLteNDPKSIFYYSCDLVSNEKEL-F-DVIHQYMDWSSAfdLNRKYLFLDEISSVKNW 138
                                   899************************9************9997755.6.477778876333457899************* PP

                        AAA_14  80 ekalkslvdeg..knldvivtGSnskllskeiatslagrva......eielyplsfaEf 130
                                   ek lk+l+d+   kn  +++tGS+s +++k i+ +l gr        +  l p++faEf
  gi|91773781|ref|YP_566473.1| 139 EKGLKHLIDTAalKNTSIMLTGSHSIDIKKSIE-RLPGRRGesnetiDKILLPMKFAEF 196
                                   *********88899**************88665.66666655888777889*******9 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   1.6e-14   2.4e-11       3     121 ..     322     458 ..     242     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.6e-14
                                   xxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                       DUF4143   3 Dirklagvrdpeelrk........glverlppwsespnskkrlrkspKlyfvDtGLlvallgldkeelleds......... 66 
                                   Di+ ++ +       k        ++++ l++  + +++    rk  K+y  D++++++l +++++++   +         
  gi|91773781|ref|YP_566473.1| 322 DISSHNTIS------KyvqslessFVLNILYAL-DLNKKIPSFRKEKKIYPQDPFIFHSLRSWTSASVNYFEssleylssp 395
                                   555555553......133345568899999999.666677779*********************9997666699******* PP

                                   xxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  67 enkGallEnlVaqeLlky.........sekegaklyyyrdkngaEvDfvielkggkivpiEvKs 121
                                   enk +l+E++V ++++++           + + +l+y+r k g+EvD+v++ k++++  iE K+
  gi|91773781|ref|YP_566473.1| 396 ENKSKLVESVVQSHFVRFmyntfpsdiF-SPEEHLFYWRGKGGKEVDYVLKSKDNELLSIELKY 458
                                   *****************9*****98852.44799******99*********************8 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0016      14      61 ..      53     101 ..      48     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                      ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdk.yviyyialrees 61 
                                   + + + +++y + Gp+++GKt+L k +i+ l+  ++ + i+y++   +s
  gi|91773781|ref|YP_566473.1|  53 YFKFDCDKVYTLRGPRQVGKTTLCKTLIQDLLTENDpKSIFYYSCDLVS 101
                                   5566778999999******************555554888888766544 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   7.4e-05      0.11       7      59 ..      61     109 ..      58     115 .. 0.75
   2 ?    4.4   0.0     0.029        43      74     133 ..     102     164 ..      98     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-05
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllre 59 
                                   + ++ G+  +GKTtl+++l + l  e    + +++++++ +   ++ k+l+  
  gi|91773781|ref|YP_566473.1|  61 VYTLRGPRQVGKTTLCKTLIQDLLTE----NDPKSIFYYSCDLVSNEKELFDV 109
                                   56788****************99543....34555558888877777777665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.029
                        AAA_22  74 sseellealeqalrarav....ielliiDEaqhlrs..eealeeLrsllnlsrkgvqliLvGtpel 133
                                   +++el++ ++q+++  ++    ++ l +DE+  + +  e+ l++L + +    k++++ L G +++
  gi|91773781|ref|YP_566473.1| 102 NEKELFDVIHQYMDWSSAfdlnRKYLFLDEISSV-KnwEKGLKHLIDTAA--LKNTSIMLTGSHSI 164
                                   567777777777777777888999**********.667999999999999..**********9987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     7e-06     0.011       3      34 ..      64      93 ..      62     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7e-06
                  RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsv 34
                                  l Gp+++GK+tl+k+L+++ll++  ++k + +
  gi|91773781|ref|YP_566473.1| 64 LRGPRQVGKTTLCKTLIQDLLTEN-DPK-SIF 93
                                  78*******************766.222.222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     4e-05      0.06       3      70 ..      64     135 ..      62     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                                   EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGH CS
                           AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidal 70 
                                   l Gp  +GKT+l+k ++++l       +++  s+  + +   +e  + i+++++  ++   + + lf+DEi ++
  gi|91773781|ref|YP_566473.1|  64 LRGPRQVGKTTLCKTLIQDLltendPKSIFYYSCDLVSN--EKELFDVIHQYMDWSSAFDlNRKYLFLDEISSV 135
                                   78*****************96654313355555543332..255555555555553333355789999999887 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   0.00013      0.19       4      66 ..      63     118 ..      60     177 .. 0.79
   2 ?   -2.6   0.0       2.9   4.4e+03     103     123 ..     295     314 ..     284     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                   EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS-- CS
                         NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepa 66 
                                    l+G+  +GKTtL + l++++ ++++p+     +F+ s+  +s ++    l d++++ +++++
  gi|91773781|ref|YP_566473.1|  63 TLRGPRQVGKTTLCKTLIQDLLTENDPK----SIFYYSCDLVSNEK---ELFDVIHQYMDWSS 118
                                   67888889*****************999....48999999999986...67888887766655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                                   ......HHHHHCTTTTT--EE CS
                         NACHT 103 qpvrtlLselirkkllpeasl 123
                                    +v++ Ls+l++k l +++s+
  gi|91773781|ref|YP_566473.1| 295 IAVKQILSSLFQK-LTTNVSW 314
                                   5678899999999.5555554 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     5e-05     0.074       1      32 [.      66      99 ..      66     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgr.kpv.yvDlDv 32
                                  Gp+++GK+Tl+++L++ +l ++  k + y  +D+
  gi|91773781|ref|YP_566473.1| 66 GPRQVGKTTLCKTLIQDLLTENDpKSIfYYSCDL 99
                                  99****************9887435554777775 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.6   2.4e+03      58      70 ..      18      30 ..       5      47 .. 0.77
   2 ?   -2.9   0.0       6.6   9.8e+03      29      50 ..     298     319 ..     292     337 .. 0.60
   3 ?   11.1   0.0   0.00027      0.41      60      92 ..     428     463 ..     385     470 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                        DUF234 58 tkvGrwWkkeeei 70
                                  ++   wWk+ +ei
  gi|91773781|ref|YP_566473.1| 18 SRQNPWWKNASEI 30
                                  4556688888887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.6
                        DUF234  29 neyvgkvFEelvrelllelnka 50 
                                   ++ +++ F +l+ ++ ++   +
  gi|91773781|ref|YP_566473.1| 298 KQILSSLFQKLTTNVSWQSLVN 319
                                   5667777777777777744332 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00027
                        DUF234  60 vGrwW..kkeeeiDivaldeeekkalfgEvKwkn..s 92 
                                      +W  k ++e+D v  ++++ ++l +E K++n  +
  gi|91773781|ref|YP_566473.1| 428 HLFYWrgKGGKEVDYVLKSKDN-ELLSIELKYQNklQ 463
                                   45599555889*****988888.5**********433 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0014       2.1       6      36 ..      54      84 ..      51     196 .. 0.90
   2 ?    1.5   0.0      0.26   3.8e+02      52      98 ..     352     398 ..     301     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                                  EEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  6 lklkegekvaivGenGaGKStLlkllagllk 36
                                  +k+  ++++ + G+   GK+tL+k+l++ l 
  gi|91773781|ref|YP_566473.1| 54 FKFDCDKVYTLRGPRQVGKTTLCKTLIQDLL 84
                                  7889999*******************98765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                                   B-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCHHHHHHHSTTGGTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  52 qeleslrkeigvlpqepqlfpeltvrenesdeeiekalsklglkelk 98 
                                   ++++s+rke +++pq+p++f  l+  +++s + +e  l+ l+ +e k
  gi|91773781|ref|YP_566473.1| 352 KKIPSFRKEKKIYPQDPFIFHSLRSWTSASVNYFESSLEYLSSPENK 398
                                   688999***********999999877775555555555555555543 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.28       3      43 ..     298     340 ..     297     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                        HTH_11   3 lqilelLleargp.isgeeLAeeLnv.SrrtvrrdIkaLeelg 43 
                                   +qil  L+++  + +s + L  e+++ S  t+ +++++Le++ 
  gi|91773781|ref|YP_566473.1| 298 KQILSSLFQKLTTnVSWQSLVNETDIsSHNTISKYVQSLESSF 340
                                   68888888888888************99************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.39      28      99 ..      63     140 ..      55     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                        AAA_16  28 llsGesGvGKsslvrellralekd...ggif.lrgkcdqlesa.....ipysalaqalareellrqlldeaesaeleawre 99 
                                    l+G++ vGK++l ++l + l ++   + if  +++ +++e++       y  + +a+   +l r+ l  +e +++  w +
  gi|91773781|ref|YP_566473.1|  63 TLRGPRQVGKTTLCKTLIQDLLTEndpKSIFyYSCDLVSNEKElfdviHQYMDWSSAF---DLNRKYLFLDEISSVKNWEK 140
                                   689***********99999888887775444466666666444555534444488887...34444444444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3352.27
//
Query:       gi|91773782|ref|YP_566474.1|  [L=953]
Description: HsdR family type I site-specific deoxyribonuclease [Methanococcoides burtonii DSM 6242]
Scores for complete 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-62  210.7   4.0    2.2e-62  210.7   4.0    2.4  3  SWI2_SNF2    SWI2/SNF2 ATPase
    4.8e-61  206.7  27.5    4.8e-61  206.7  27.5    3.6  2  EcoR124_C    Type I restriction and modification enzyme - sub
    1.8e-39  135.7   4.9    1.8e-39  135.7   4.9    3.8  4  HSDR_N       Type I restriction enzyme R protein N terminus (
    1.5e-36  125.9   1.9    1.5e-36  125.9   1.9    2.9  3  ResIII       Type III restriction enzyme, res subunit
    1.9e-10   40.8   0.8    1.3e-09   38.1   0.6    2.4  2  DEAD         DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.45   10.9   0.1       0.45   10.9   0.1    3.8  5  Helicase_C   Helicase conserved C-terminal domain
       0.47   10.6   7.9      0.084   13.0   1.3    3.2  3  T3SchapCesA  Type III secretion system filament chaperone Ces
       0.65   10.0   2.7        4.1    7.5   0.3    2.8  2  Ubiquitin_3  Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.4     3e+03      61     100 ..       9      50 ..       8      80 .. 0.63
   2 !  210.7   4.0   9.6e-66   2.2e-62       1     218 [.     242     469 ..     242     475 .. 0.92
   3 ?   -2.4   0.3       1.4     3e+03     104     146 ..     817     857 ..     758     872 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                     SWI2_SNF2  61 LdkQlsktfakageek...pkqaesrkeLkellekesekiift 100
                                   L++Ql +++ ++g +    +++ae  ++Lk +l +++++i+f+
  gi|91773782|ref|YP_566474.1|   9 LEEQLVGQLCELGYSLvriKDEAELIANLKGQL-EKHNEIVFS 50 
                                   678888888877544300033555555666666.447777775 PP

  == domain 2  score: 210.7 bits;  conditional E-value: 9.6e-66
                     SWI2_SNF2   1 qQyravekavervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageekpkqae 81 
                                   +Q++ave++++rvk++ +k+ +iWHt+GSGK+lt++++++ l++   + +kvv+v+DRkdLd Q++k+f+++++   + ++
  gi|91773782|ref|YP_566474.1| 242 YQFYAVEALIDRVKHS-HKNAYIWHTTGSGKTLTSFKASQILTK-LPTVKKVVFVVDRKDLDYQTTKEFNSFSKGCIDGTD 320
                                   7*************96.9**************************.999*************************99999*** PP

                     SWI2_SNF2  82 srkeLkellekesekiifttiqKfe....eeek..eklevlsereniivlvDEaHRsqygelakklrkalpnaafigFTGT 156
                                   ++k+L+++l ++++ +i+ttiqK++    + ++  ek+e+l++++ i++++DE+HRsq+ge++k+++++++n +++gFTGT
  gi|91773782|ref|YP_566474.1| 321 NTKQLVKQL-SDDTALIVTTIQKLNvaisK-KQylEKMEQLRDQR-IVFIFDECHRSQFGETHKRINQFFKNPQMFGFTGT 398
                                   *********.6699**********976631.22457789999988.*********************************** PP

                     SWI2_SNF2 157 Pilkkd........kktkevFgeyidkYtikeaveDgavvp..ilYesrlaklelkeeekldeefeeiteel 218
                                   Pi++++        ++tk+ Fge+++kY i++a++D++v++  ++Y +r++++e +e++ +d e+e+i +++
  gi|91773782|ref|YP_566474.1| 399 PIFAENaiknesgrRTTKDLFGECLHKYVITDAIADENVLKfsVEYVGRYKQKEGRETS-IDIEVEDIDTNE 469
                                   ***9777777888799************************999************9988.*******98665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                     SWI2_SNF2 104 KfeeeekeklevlsereniivlvDEaHRsqygelakklrkalp 146
                                   Kf++++  ++++++++   ++      Rs+++ ++k +++ lp
  gi|91773782|ref|YP_566474.1| 817 KFDAQK--DVDQVEKEISRVLSSESTLRSKKELIEKFIQENLP 857
                                   343322..24444443333333333345555555555555555 PP

>> EcoR124_C  Type I restriction and modification enzyme - subunit R C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -10.4  15.1         8   1.8e+04     150     195 ..     566     616 ..     349     674 .. 0.71
   2 !  206.7  27.5   2.1e-64   4.8e-61       1     258 []     690     946 ..     690     946 .. 0.95

  Alignments for each domain:
  == domain 1  score: -10.4 bits;  conditional E-value: 8
                                   XXXXXXXXXXXXXXXXX..XXX...XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     EcoR124_C 150 lrskkdlieefindlkk..kle...ddkedieeefeefknkekekeleeli 195
                                   ++  ++ ++e+i+d++k  +++   +d++++ +++++  +k kek ++ li
  gi|91773782|ref|YP_566474.1| 566 SKHSREKLDEYIEDYNKlfNSKfstKDSQSFYNYYNDISKKVKEKKIDILI 616
                                   445555666666666665522244555666666666666666666666555 PP

  == domain 2  score: 206.7 bits;  conditional E-value: 2.1e-64
                                   XX--HHHHHHHHHHHHHHHHHHH--SHHHHHT--SHHHHHHHHHHHHHHHHHHHHHCTSTT-..-S..S-HHHHHHHHHHH CS
                     EcoR124_C   1 vlvkpyeevvekfkdavkeLkelfpdpesvdslkseeekkeFiklFrellrllnalksYdefdede.glteqefedyrskY 80 
                                   ++++pye++++kf++ +++L+ ++p++esv+ l se+e+ eFi +Fre++r+ln+ k + +f++++  +teq fedy+skY
  gi|91773782|ref|YP_566474.1| 690 IIMQPYEDYIAKFDEKYDALQRITPTVESVNTLSSENEELEFITTFREIMRILNITKAFADFKWSDlSMTEQLFEDYKSKY 770
                                   699**************************************************************989************* PP

                                   HCH-XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     EcoR124_C  81 ldiydelke.kekekesildDidFeleliksdeInydYIleLiekylkkkeeddkeereeiekalrssaelrskkdlieef 160
                                   ld+yd++k+ ++kek sil+D+dFeleli++deIn++YI++L+ +++ + ++d +++ +ei ++l+s+++lrskk+lie+f
  gi|91773782|ref|YP_566474.1| 771 LDLYDKVKSdHQKEKVSILEDVDFELELIHRDEINVNYIIQLLIQLKFDAQKDVDQVEKEISRVLSSESTLRSKKELIEKF 851
                                   **********999************************************8666666666********************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXX CS
                     EcoR124_C 161 indlkkkleddkedieeefeefknkekekeleelieeegldeealkkfikeilkrgkfdalgteilklllspkklglkerr 241
                                   i+++ ++++ +++++ eef++f+n+e++k++e+l+++e l+ee ++k i+++l+ ++ ++l +eil+l+ ++ ++++ +r+
  gi|91773782|ref|YP_566474.1| 852 IQENLPDIH-TSDSVSEEFDQFWNNEQQKAFEQLVKDEVLSEERTQKLIENYLYAEQ-EPLLDEILELI-EGAQPSVLKRK 929
                                   ******655.667********************************************.59****77766.999999999** PP

                                   XXXXXXXXXXXXXXXXX CS
                     EcoR124_C 242 kkkkkvmeklrellkkf 258
                                   k   ++ ek+++++++f
  gi|91773782|ref|YP_566474.1| 930 KIGARILEKIKDFIDTF 946
                                   **************997 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   4.9     8e-43   1.8e-39       2     192 ..       4     186 ..       3     188 .. 0.86
   2 ?   -1.9   0.1       1.2   2.8e+03      96     131 ..     576     619 ..     504     631 .. 0.63
   3 ?    0.2   0.2      0.27     6e+02      39      99 ..     723     790 ..     703     818 .. 0.53
   4 ?    0.9   1.4      0.17   3.8e+02      11      86 ..     808     892 ..     801     904 .. 0.66

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 8e-43
                                   SSHHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH....-HHHHHHHH..TT--HH.H CS
                        HSDR_N   2 lsEaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgaln....ikkltkrla..lsdgnk.e 75 
                                   +sEa le++l+ +l  elGy+                + +k+e  l +nl++ql++ n    +++++k+    ls+g + e
  gi|91773782|ref|YP_566474.1|   4 QSEAVLEEQLVGQLC-ELGYSL---------------VRIKDEAELIANLKGQLEKHNeivfSDNEFKKVMnlLSKGSVfE 68 
                                   89**99996666655.*****9...............67789999*****************6666666555755555514 PP

                                   HHHHHHTS.-EEEETS-EEEEESS-SSSGGGS-EEEEE----SSSS---EEEEEEETTEEEEEEEE--TT.-HHHHHHHHT CS
                        HSDR_N  76 fyellkeg.kvkfkegrkknikLiDkknlenNrfqvvnQvtvtgnqkrrpDivlfvnglplvviElKrpg.tieeAinQik 154
                                   + + l+e  ++ +++g + + ++++++++++N++qv++Qv ++g+ k+r+D++l+vnglplv+iElKr+g +++eA+nQi+
  gi|91773782|ref|YP_566474.1|  69 KAKNLREKqHILRDNGDDLYFDFLNTEHWCQNEYQVTHQVAMEGKYKNRYDVTLLVNGLPLVQIELKRRGlELKEAFNQIQ 149
                                   444444443555559******************************************************99********** PP

                                   SS---.---SSSGGGGG--EEEEE-SS-EEEEE--SSS CS
                        HSDR_N 155 ryrkeksdvsipqlfrYlqfgvisngketrfyaktkrr 192
                                   ry+k+ s+ s   lf+Y+q++visng++t++ya+++++
  gi|91773782|ref|YP_566474.1| 150 RYQKH-SFGSHAALFQYIQIFVISNGVNTKYYANNRKQ 186
                                   ***88.7999************************9886 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                   ESS-SSSGGGS-EEEEE----S........SSS---EEEEEEET CS
                        HSDR_N  96 kLiDkknlenNrfqvvnQvtvt........gnqkrrpDivlfvn 131
                                    + D+++l n +f+     ++         + +++++Di++ vn
  gi|91773782|ref|YP_566474.1| 576 YIEDYNKLFNSKFSTKDSQSFYnyyndiskKVKEKKIDILIVVN 619
                                   34455555555555543222223555555566677777777777 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.27
                                   ----SHHHHHHHHHHHHHHHH-HHHHHHHH.............TT--HHHHHHHHHTS-EEEE.TS-EEEEESS- CS
                        HSDR_N  39 rkskaevaleknlreqlgalnikkltkrla.............lsdgnkefyellkegkvkfk.egrkknikLiD 99 
                                    ++ +e    + +re +  lni k +++++               ++  + y+++       k +++k+++ ++ 
  gi|91773782|ref|YP_566474.1| 723 SSENEELEFITTFREIMRILNITKAFADFKwsdlsmteqlfedYKSKYLDLYDKV-------KsDHQKEKVSILE 790
                                   4455566667778888888886666666666543321111112222222222222.......2445555554432 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.17
                                   HHHHHHHHTT-EE................----SHHHHHHHHHHHHHHHH......-HHHHHHHH...TT--HHHHHHHHH CS
                        HSDR_N  11 lidellrelGyqvlskkdveiegrrpe.vrkskaevaleknlreqlgaln......ikkltkrla...lsdgnkefyellk 81 
                                    i++ll +l +++++       +++   v +s++    +k+l e++ + n      +++++++++    +++ k+f +l+k
  gi|91773782|ref|YP_566474.1| 808 YIIQLLIQLKFDAQKDV--DQVEKEISrVLSSESTLRSKKELIEKFIQENlpdihtSDSVSEEFDqfwNNEQQKAFEQLVK 886
                                   67788877777775433..32222223566777777777888888888888888897777777777768888888888888 PP

                                   TS.-EE CS
                        HSDR_N  82 eg.kvk 86 
                                   ++   +
  gi|91773782|ref|YP_566474.1| 887 DEvLSE 892
                                   886655 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 !  125.9   1.9   6.8e-40   1.5e-36       2     170 ..     237     400 ..     236     401 .. 0.91
   2 ?   -2.9   1.3       2.6   5.7e+03      76      93 ..     594     611 ..     528     661 .. 0.60
   3 ?   -3.6   1.4       4.2   9.5e+03     118     118 ..     820     820 ..     756     889 .. 0.50

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 6.8e-40
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   + lr+yQ  a+e+l++ +k + +k+++i+++TG+GKTl+++k+ + l+k    +k++f+v+rk+l  qt +ef++f++ + 
  gi|91773782|ref|YP_566474.1| 237 MVLRPYQFYAVEALIDRVK-HSHKNAYIWHTTGSGKTLTSFKASQILTKLPTVKKVVFVVDRKDLDYQTTKEFNSFSKGCI 316
                                   679***************9.***********************************************************96 PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH.........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEE CS
                        ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseee.eeeseellrdrfdviiiDEaHrlgakkswreilekfkeavl 162
                                   +  g++ +++  k+    s+++ ++vttiq+l+ +++++   e+ e+lrd+  v+i+DE+Hr++  +++++i++ fk+  +
  gi|91773782|ref|YP_566474.1| 317 D--GTDNTKQLVKQ---LSDDTALIVTTIQKLNVAISKKqYLEKMEQLRDQRIVFIFDECHRSQFGETHKRINQFFKNPQM 392
                                   3..33333333333...68999***********999777577889999********************************* PP

                                   EEEESS-S CS
                        ResIII 163 lglTATpe 170
                                   +g+T+Tp 
  gi|91773782|ref|YP_566474.1| 393 FGFTGTPI 400
                                   ******95 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                                   GGTGG....GEEEESSS- CS
                        ResIII  76 kflseaykeigkkvsgdk 93 
                                   + + ++y++i+kkv+++k
  gi|91773782|ref|YP_566474.1| 594 QSFYNYYNDISKKVKEKK 611
                                   222222222333333333 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.2
                                   H CS
                        ResIII 118 s 118
                                    
  gi|91773782|ref|YP_566474.1| 820 A 820
                                   0 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.33   7.5e+02     100     135 ..     205     237 ..     161     257 .. 0.70
   2 !   38.1   0.6   5.8e-13   1.3e-09      13     146 ..     257     387 ..     240     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.33
                                   EEEEEHHHHHHHHHCTSSHCTTE..EEEEEETHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                          DEAD 100 ivvgtpgrlddllstgklnlsqv..rflVlDEadrlld 135
                                   i+ g +  ++d ++     ls++  r++Vl Ea+++l 
  gi|91773782|ref|YP_566474.1| 205 ILNGFTRDFLDPCN-----LSKMicRYIVLNEAQKILM 237
                                   44444444444333.....4443349*******99875 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 5.8e-13
                                   TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlsk 93 
                                   + ++  +   TGsGKTl  ++ + qi++  k  t +k+++v+  + L  qt +++++f k       +i g +++++ +++
  gi|91773782|ref|YP_566474.1| 257 SHKNAYIWHTTGSGKTLT-SFKASQILT--KLPTVKKVVFVVDRKDLDYQTTKEFNSFSKG------CIDGTDNTKQLVKQ 328
                                   5578889999******99.889999996..69****************************6......567899999999** PP

                                   HHTTCSEEEEEHHHHHHHH.HCTSSH....CTTEEE.EEEETHHHHHHTTTHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxx....xxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  94 ldngvdivvgtpgrlddll.stgkln....lsqvrf.lVlDEadrlldqgfsdfinril 146
                                   l+ ++ ++v+t ++l   + ++++l+    l++ r+ +++DE++r +  +  + in+ +
  gi|91773782|ref|YP_566474.1| 329 LSDDTALIVTTIQKLNVAIsKKQYLEkmeqLRDQRIvFIFDECHRSQFGETHKRINQFF 387
                                   *889************9884444455644444445449******976554444444433 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 ?   -1.4   0.1       1.4     3e+03      40      54 ..     337     351 ..     279     369 .. 0.50
   2 ?   -1.9   0.0       1.8   4.1e+03      10      54 ..     488     539 ..     475     557 .. 0.61
   3 ?   10.9   0.1    0.0002      0.45      25     110 ..     569     654 ..     553     655 .. 0.81
   4 ?   -0.4   0.0      0.65   1.5e+03      10      46 ..     655     692 ..     653     737 .. 0.84
   5 ?   -3.2   0.0       4.8   1.1e+04      43      62 ..     832     851 ..     805     865 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                                   TSTEEEESTTSTHHH CS
                    Helicase_C  40 gikvavlhgelpqne 54 
                                     ++ +l+  +++++
  gi|91773782|ref|YP_566474.1| 337 VTTIQKLNVAISKKQ 351
                                   233344444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                   H..HHTTTTSEEEEEESSHHHHHH.HHHHHHHT.....TSTEEEESTTSTHHH CS
                    Helicase_C  10 l..kleeeggkilifvntidrlek.vklllekk.....gikvavlhgelpqne 54 
                                      k+++++ +++  v +i++l +  ++l++kk     ++k+a++ +  ++ne
  gi|91773782|ref|YP_566474.1| 488 HsrKTHNREFTAIFTVSSIKTLINyYDILQRKKaegkhDLKIATIFS-YTANE 539
                                   25555666667777778888663345666555455555677777776.44444 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0002
                                   SHHHHHHHHHH...HHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHH CS
                    Helicase_C  25 tidrlekvkll...lekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiq 102
                                   ++++l+  +++   ++ ++ k+ + +++   n  ++i ++ +++++d+Li  ++  +G d p +n+ i +d   +++ +iq
  gi|91773782|ref|YP_566474.1| 569 SREKLD--EYIedyNKLFNSKFSTKDSQSFYNYYNDISKKVKEKKIDILIVVNMFLTGFDSPFLNT-IYVDKNLKYHGLIQ 646
                                   555666..4442213444888888888888899999**************************8887.67899999****** PP

                                   HHTTSSST CS
                    Helicase_C 103 riGRtgRa 110
                                   +  Rt R+
  gi|91773782|ref|YP_566474.1| 647 AYSRTNRI 654
                                   *****996 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.65
                                   HHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEE CS
                    Helicase_C  10 lkleeeggkilifvntidrlek.vklllekkgikvavl 46 
                                   l++++++g+++ f n ++  +  ++l+ ++++i+v+++
  gi|91773782|ref|YP_566474.1| 655 LNEQKSQGNVVAFRNLKKATDAaITLFSNTEAIEVIIM 692
                                   56789999999999999977767788877777777665 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 4.8
                                   EEEESTTSTHHHHHHHHHHH CS
                    Helicase_C  43 vavlhgelpqnereeileqf 62 
                                   + vl +e + ++++e +e+f
  gi|91773782|ref|YP_566474.1| 832 SRVLSSESTLRSKKELIEKF 851
                                   33455555555566666666 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       1.1   2.4e+03      13      67 ..     300     355 ..     288     365 .. 0.74
   2 ?   -3.5   0.0       5.4   1.2e+04      48      63 ..     566     581 ..     551     589 .. 0.65
   3 ?   13.0   1.3   3.8e-05     0.084       9      79 ..     844     919 ..     838     943 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                   T3SchapCesA  13 ldkkirseieaikk.iiaefdvvkesvnilsekaktdpqaaeklnkliegytygee 67 
                                   ld +   e ++  k  i   d  k+ v++ls+ +     + +kln  i    y e+
  gi|91773782|ref|YP_566474.1| 300 LDYQTTKEFNSFSKgCIDGTDNTKQLVKQLSDDTALIVTTIQKLNVAISKKQYLEK 355
                                   55566666666544267788999999999999998888888999988887777665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.4
                   T3SchapCesA  48 dpqaaeklnkliegyt 63 
                                   +  + ekl+  ie y 
  gi|91773782|ref|YP_566474.1| 566 SKHSREKLDEYIEDYN 581
                                   4456677777777774 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 3.8e-05
                   T3SchapCesA   9 nkelldkkirs...eieaikkiiaefdvvkes..vnilsekaktdpqaaeklnkliegytygeerklydsalskie 79 
                                   +kel++k i+    +i +   +  efd   ++   + + +  k +  + e+ +klie y y e+  l d  l  ie
  gi|91773782|ref|YP_566474.1| 844 KKELIEKFIQEnlpDIHTSDSVSEEFDQFWNNeqQKAFEQLVKDEVLSEERTQKLIENYLYAEQEPLLDEILELIE 919
                                   699999999972224677778999***9865511556667789999999******************999988776 PP

>> Ubiquitin_3  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3    0.0018       4.1      10      44 ..     808     842 ..     803     868 .. 0.81
   2 ?    1.4   0.2      0.14   3.1e+02      43      63 ..     870     890 ..     848     914 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                                   ..CCEEEEEEE-TTSBHHHHHHHHHHHTT-TS-EE CS
                   Ubiquitin_3  10 valqspvtkkfrktDtvdfiekelkkllsieketR 44 
                                     +q  ++ kf     vd++eke+ ++ls e   R
  gi|91773782|ref|YP_566474.1| 808 YIIQLLIQLKFDAQKDVDQVEKEISRVLSSESTLR 842
                                   457888999*******************9865544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                                   EEEEEEETTTEEEE---TTSB CS
                   Ubiquitin_3  43 tRLWkkgssegrelLtkpdit 63 
                                    + W+  +++++e+L k ++ 
  gi|91773782|ref|YP_566474.1| 870 DQFWNNEQQKAFEQLVKDEVL 890
                                   578************998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (953 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1455  (0.0811534); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.87u 0.34s 00:00:01.21 Elapsed: 00:00:00.55
# Mc/sec: 5207.87
//
Query:       gi|91773783|ref|YP_566475.1|  [L=391]
Description: restriction modification system DNA specificity subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-28   99.1  18.3    1.4e-21   77.5   0.4    2.7  2  Methylase_S  Type I restriction modification DNA specificity 
     0.0095   14.9   0.1      0.015   14.3   0.1    1.2  1  Herpes_UL31  Herpesvirus UL31-like protein
  ------ inclusion threshold ------
      0.061   13.4   2.2        2.2    8.4   0.4    2.5  2  DUF2443      Protein of unknown function (DUF2443)


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  11.7   3.2e-09   1.9e-05       2     167 ..      15     193 ..      14     194 .. 0.67
   2 !   77.5   0.4   2.3e-25   1.4e-21       3     163 ..     220     374 ..     219     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.2e-09
                                   TT-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HH.HCCT............EE-HHHHCCTT---B-TT-EEEE-SSS CS
                   Methylase_S   2 edwevvkLgdvfeikkgktpkkkelkengkypyirag.ilnn............kvvkdglgykkkyilpkgdilissrat 69 
                                   e+we++kLg+vf i+ +++  +   ++ ++y +     ++++            ++++ +l   +++++++++  + +   
  gi|91773783|ref|YP_566475.1|  15 EEWEEKKLGEVF-IEVNEKVGQ---RNLETYSITAGQgFVSQkekfgrdisgqqNAKYTALQVNQFAYNKGNSKKYKY--G 89 
                                   89**********.644444433...44444444444445555554444455554444444444444444455555554..7 PP

                                   TT-EEEESS-BEE-TTEEEEEESTTT--.....HHHHHHHHHHCHHHHHHH.CCSSTTT---HHHHCC-EEEE--HHHHHH CS
                   Methylase_S  70 iGkvayrdkkyylnqsvivlipknkkki.....neflylylllklkklksl.svgstqpkltkenlkkikIplPpleeQkk 144
                                   + + +  dk + + + +i++++++++       + f+ +yl + l++++s   +  +  +++k+ + ++kI +P  +eQ+k
  gi|91773783|ref|YP_566475.1|  90 CVYLNTTDKQIAVPNVFISFKLIDNEMSsvfyaKLFENHYLDKGLRQIISSsARMDGLLNVNKKYFFQLKIIVPTTPEQHK 170
                                   88888888899999999999998754444555555555555555555555437888999********************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                   Methylase_S 145 IakiLsqldntielekkikneie 167
                                   Ia +L+++d++++  kk+k+ +e
  gi|91773783|ref|YP_566475.1| 171 IAIFLTSVDEKLQALKKKKELLE 193
                                   **********7777777777777 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 2.3e-25
                                   T-EEEEHHHHEEE.EE-----TT.GGTTT--E..EEE-HHHCCTEE-HHHHCCTT---B-TT-EEEE-SSSTT-EEEESS- CS
                   Methylase_S   3 dwevvkLgdvfei.kkgktpkkk.elkengky..pyiragilnnkvvkdglgykkkyilpkgdilissratiGkvayrdkk 79 
                                   dwe++kLgd+f+i  +g ++k+k  + + g y  p+++++ +++    +  gy++ y + ++ ++++ r+  G++  r ++
  gi|91773783|ref|YP_566475.1| 220 DWEEKKLGDIFDIkAGGDIDKSKvSDIKTGLYryPIYSNSEKEK----GLFGYSNSYSISEKCLTVTGRGRLGIAHARFEN 296
                                   8************777777777796666665555******8888....********************************* PP

                                   BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHHHHHHHH CS
                   Methylase_S  80 yylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldntielek 160
                                   +y   ++ vlipk           ++ ++ ++l++ + +++ p+lt ++++++k++ P+  eQ+kIa++Ls++d    +e+
  gi|91773783|ref|YP_566475.1| 297 FYPIVRLLVLIPKI-----PANVVFYENIINQLNFAIESTGVPQLTSPQISSYKVHYPSFTEQEKIADFLSSIDG--SIEN 370
                                   ************85.....788999**************************************************..5555 PP

                                   .HHH CS
                   Methylase_S 161 .kik 163
                                    +++
  gi|91773783|ref|YP_566475.1| 371 vGKQ 374
                                   4333 PP

>> Herpes_UL31  Herpesvirus UL31-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.5e-06     0.015     179     249 ..     128     199 ..     102     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-06
                                   EE-HHHHHHHHHHTTTEEEEEEEETTEEE.EEEEC------------HHHHHHHHHCS---CCHHHHHHHCH CS
                   Herpes_UL31 179 HlseklirqlldnlegYkvvadvvkdtfv.lsvlceaateassvkidvediyekvadlditdelkeeyerlk 249
                                   H   k +rq++  +      ++v k+ f  l++++++++e+++++i  + + ek+++l+ + el e+y+++ 
  gi|91773783|ref|YP_566475.1| 128 HYLDKGLRQIISSSARMDGLLNVNKKYFFqLKIIVPTTPEQHKIAIFLTSVDEKLQALKKKKELLEQYKKGA 199
                                   66678899999999999999***99876549**************************************975 PP

>> DUF2443  Protein of unknown function (DUF2443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.4   0.00036       2.2       6      76 ..     131     199 ..     124     201 .. 0.70
   2 ?    4.0   0.1    0.0084        50      51      77 ..     360     386 ..     353     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00036
                                   HHHHHHHHHHHHHHHHHHHHHT--HHHHHHHHTTSS---TTS-HH.HHHHHHHHHHHHHHHHHHHHHHHGGG CS
                       DUF2443   6 dkilkdiedskeeielLLklakislvdyilikrGsldmPesldva.fltqideevekLkeaidaLnkikkel 76 
                                   dk l++i  s + ++ LL++ k     +  +k      Pe+ ++a flt +de+++ Lk++ + L ++kk+ 
  gi|91773783|ref|YP_566475.1| 131 DKGLRQIISSSARMDGLLNVNKKY---FFQLKIIVPTTPEQHKIAiFLTSVDEKLQALKKKKELLEQYKKGA 199
                                   555666666666666666665543...4445555556687777652789********************975 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0084
                                   HHHHHHHHHHHHHHHHHHHHHHHGGG- CS
                       DUF2443  51 fltqideevekLkeaidaLnkikkelL 77 
                                   fl+ id  +e++ ++i+a    kk+lL
  gi|91773783|ref|YP_566475.1| 360 FLSSIDGSIENVGKQIEASQEWKKGLL 386
                                   7899********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2276.86
//
Query:       gi|91773784|ref|YP_566476.1|  [L=554]
Description: type I restriction-modification system, M subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-111  373.1   0.0   1.4e-111  372.7   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
    4.2e-18   66.3   1.2    6.8e-17   62.4   1.2    2.7  1  HsdM_N           HsdM N-terminal domain
    7.1e-07   28.9   0.0    8.4e-06   25.4   0.0    2.1  2  MTS              Methyltransferase small domain
    5.7e-05   23.6   0.0    0.00021   21.8   0.0    2.0  2  Eco57I           Eco57I restriction-modification methylase
     0.0019   17.9   0.0      0.018   14.7   0.0    2.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0022   17.8   0.1      0.011   15.6   0.0    2.2  2  N6-adenineMlase  Probable N6-adenine methyltransferase
  ------ inclusion threshold ------
       0.01   15.7   0.0       0.02   14.7   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
      0.012   15.0   0.0      0.022   14.2   0.0    1.3  1  AviRa            RRNA methyltransferase AviRa
      0.025   15.3   0.0       0.15   12.8   0.0    2.3  2  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.7   0.0  7.2e-115  1.4e-111       3     311 ..     213     516 ..     211     517 .. 0.96

  Alignments for each domain:
  == domain 1  score: 372.7 bits;  conditional E-value: 7.2e-115
                      N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivell..epksgesvyDpacGsggllvqaekvlkeedgktkelsiy 81 
                                    d+lGd+YEyl+++fa+ +gk++Gef+TP++vs+++++l+   +k+ +svyDp cGsg+ll+ +++ ++          +y
  gi|91773784|ref|YP_566476.1| 213 LDVLGDAYEYLIGQFASGAGKKAGEFYTPQQVSTILAKLVttGKKRLRSVYDPTCGSGSLLLRVAREVE------DVSAFY 287
                                   59**************************************664455569*****************984......55679* PP

                      N6_Mtase  82 GqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkew.kektlekderfrea..vapks 159
                                   Gqe+n+tty+La+mN++lh+++y k++i+++dtle p++   ++f+++vaNppf+++ w ++    +derf+++  +apks
  gi|91773784|ref|YP_566476.1| 288 GQELNRTTYNLARMNMILHNVHYRKFDIKQEDTLEYPQHL-GMQFEAIVANPPFSAQ-WsANPLFSSDERFSQYgkLAPKS 366
                                   ****************************************.****************.98899999*******99****** PP

                      N6_Mtase 160 nadlafllhiieslkpkGraavvlangvLfrggkegkIrkalve.kdlveavialpeklFyntsiptcilvlkkekaerkg 239
                                   +ad+af++h+i++l+++G +a+vl++gvLfrg++eg+Ir+ l+e k++++avi lp ++Fy+tsiptc+lv+kk ++ + +
  gi|91773784|ref|YP_566476.1| 367 KADYAFVQHMIHHLAENGSMAIVLPHGVLFRGAAEGHIRQFLIEeKNYLDAVIGLPANVFYGTSIPTCVLVFKKCRE-NPD 446
                                   ******************************************973689****************************5.99* PP

                      N6_Mtase 240 kvlfidaseefkkkdrkknklteediekildtykekskevdkfskvveleeiaendynlnvgryveteeeee 311
                                   ++lfidas++++k  + +n+l++ di+ki+dty+++ ke++k+s+v++l+ei+endynln++ryv+t eeee
  gi|91773784|ref|YP_566476.1| 447 DILFIDASQDYEKV-KTQNQLRPCDIDKIVDTYRNR-KEIEKYSHVASLDEIKENDYNLNIPRYVDTFEEEE 516
                                   **************.8********************.******************************99987 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   1.2   3.4e-20   6.8e-17       1     136 [.       9     200 ..       9     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 3.4e-20
                                   HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC..................--....--------.... CS
                        HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereekllee........yken...al..eeleeklkskeafy 68 
                                   le++lw++a++LRgk++a e+++yilg++F+K+l+++ e + +++l+         +++    ++  e+ +e   +k +++
  gi|91773784|ref|YP_566476.1|   9 LEQQLWNIANELRGKMNADEFRDYILGFIFYKYLSNKIEIYADEILKPdgiafkdiKEDTelgKEfiEAISEASVEKLGYF 89 
                                   89*******************************************999999988763333344222333444444447888 PP

                                   S-CCCSHHH....................................HHHS.....--HHHHHHHHHHCHHHHCT--S..... CS
                        HsdM_N  69 ipeelrWke....................................lakk.....kdddelgenlnkafpaleelnk..... 103
                                   +++   ++e                                             ++   ++e+l+ +++ +++++      
  gi|91773784|ref|YP_566476.1|  90 LKPSELFSEvarrgsssysassgssnysnsslsvepfvtgqnamaV--AessygDEF--ILEDLQGILNNIQSSTMgtese 166
                                   8887777775555555555566666666677666776666555543..155655555..8999999999999987776655 PP

                                   .THHHHHHHS.......S-----SSHHHHHHHHHH CS
                        HsdM_N 104 .slkgvfmkd.dfnafalgeitkkspalLskviek 136
                                    +++++f+ d d+n+++lg++   ++al+skv+ +
  gi|91773784|ref|YP_566476.1| 167 dDFENLFE-DmDLNSSKLGKTPAARNALISKVLSH 200
                                   45999996.88*********************987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   4.2e-09   8.4e-06      26     112 ..     251     345 ..     242     353 .. 0.84
   2 ?    0.8   0.0      0.16   3.1e+02     117     139 ..     368     390 ..     359     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.2e-09
                                   HCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTST..TS-E CS
                           MTS  26 tlpke..lsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle...vevvasdvleeve..ekkf 98 
                                    +++   + ++v D  cG G l + +a+e ++++     + +    ++a+ n+  ++++    ++ ++d le  +   ++f
  gi|91773784|ref|YP_566476.1| 251 LVTTGkkRLRSVYDPTCGSGSLLLRVAREVEDVSaFYGQELNRTTYNLARMNMILHNVHyrkFDIKQEDTLEYPQhlGMQF 331
                                   43333335567*********************9989999*****************999989999*****997774469** PP

                                   EEEEE---STTTCH CS
                           MTS  99 dlivsNPPfhagka 112
                                   ++iv NPPf a+  
  gi|91773784|ref|YP_566476.1| 332 EAIVANPPFSAQWS 345
                                   *********98865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHEEEEEEEEEEE CS
                           MTS 117 vaeeliaeAkeaLkegGeLliVa 139
                                   +  +++++  ++L+e+G++ iV 
  gi|91773784|ref|YP_566476.1| 368 ADYAFVQHMIHHLAENGSMAIVL 390
                                   55678888899**********97 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.1   8.2e+03      70      96 ..      78     104 ..      66     109 .. 0.74
   2 !   21.8   0.0     1e-07   0.00021       1     102 [.     329     440 ..     329     444 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.1
                        Eco57I  70 lkdkklkklvefedskevFkdveikgg 96 
                                   +++ +++kl +f + +e F++v+ +g+
  gi|91773784|ref|YP_566476.1|  78 ISEASVEKLGYFLKPSELFSEVARRGS 104
                                   456788999999999999999987766 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1e-07
                        Eco57I   1 mkfdviiGNPPYqeseakkelkaleek..........akdiyqkFvekalkle.dkylaliiparflasgkglkefrekll 70 
                                   m+f++i+ NPP+  + + + l +  e+          +k+ y   ++   +l+ ++ +a+++p+  l +g    ++r++l+
  gi|91773784|ref|YP_566476.1| 329 MQFEAIVANPPFSAQWSANPLFSSDERfsqygklapkSKADYAFVQHMIHHLAeNGSMAIVLPHGVLFRGAAEGHIRQFLI 409
                                   9************9998887777777799999**9976666765566667788788999*****9999999********** PP

                        Eco57I  71 kdkklkklvefedskevFkdveikggilvflk 102
                                   ++k++   v    ++ vF +++i +++lvf k
  gi|91773784|ref|YP_566476.1| 410 EEKNYLDAVIGLPAN-VFYGTSIPTCVLVFKK 440
                                   ***999999888887.*************987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.3e-06     0.018      23     132 ..     253     341 ..     243     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.3e-06
                                   HTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-G. CS
                       UPF0020  23 lagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvg. 102
                                    +g k+ ++ +DP CGsG++l+  a  ++++                         +yg +l+r   + ar N    +v  
  gi|91773784|ref|YP_566476.1| 253 TTGKKRLRSVYDPTCGSGSLLLRVAREVEDVS-----------------------AFYGQELNRTTYNLARMNMILHNVHy 310
                                   578889999**************999999999.......................48999999999999999987777752 PP

                                   GGEEEEE--GGG--.STTS---EEEE----- CS
                       UPF0020 103 dliefsqadaakLr.lkegevdvivtnpPYG 132
                                    + +++q d  + + +   ++++iv+npP+ 
  gi|91773784|ref|YP_566476.1| 311 RKFDIKQEDTLEYPqHLGMQFEAIVANPPFS 341
                                   5678888888888854444899999999986 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.5e-06     0.011      64      99 ..     304     344 ..     298     393 .. 0.80
   2 ?   -1.8   0.0       1.2   2.4e+03      37      64 ..     506     537 ..     492     542 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
               N6-adenineMlase  64 lygeekfvfYdlnnpe..elpeelkgkfdviviDPPF...l 99 
                                   ++++ +++ +d+++++  e p++l ++f+ iv+ PPF    
  gi|91773784|ref|YP_566476.1| 304 ILHNVHYRKFDIKQEDtlEYPQHLGMQFEAIVANPPFsaqW 344
                                   567788********9977788****************5441 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
               N6-adenineMlase  37 Psvyealkkek....kkekvlLleiDkrFeal 64 
                                   P+   ++++e+    +  +++Lle+D++ +++
  gi|91773784|ref|YP_566476.1| 506 PRYVDTFEEEEpidiDAVAASLLELDEKMSKI 537
                                   555566666666777668899*****998554 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     1e-05      0.02       6      84 ..     261     340 ..     256     424 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdieeleklledekfDlilsnevl 84 
                                   +v+D+ CG+G l+++ a+e+ + + ++G + + +  +lAr n   +++    +  +q+d  e +++l   +f  i++n ++
  gi|91773784|ref|YP_566476.1| 261 SVYDPTCGSGSLLLRVAREVEDVSAFYGQELNRTTYNLARMNMILHNVHyrKFDIKQEDTLEYPQHLG-MQFEAIVANPPF 340
                                   79***************99999999***9999999999999655443332266666666666665555.89****999444 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.022      48     101 ..     253     305 ..     242     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                         AviRa  48 kkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLsL 101
                                   +++++   ++yDp CG++ Ll  ++    + +++ ++ + ++++ +la+ N+ L
  gi|91773784|ref|YP_566476.1| 253 TTGKKRLRSVYDPTCGSGSLLLRVAR-EVEDVSAFYGQELNRTTYNLARMNMIL 305
                                   455556679***********999875.67899*******************977 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.4e-05      0.15       1      71 [.     262     337 ..     262     352 .. 0.83
   2 ?   -1.9   0.0       2.8   5.6e+03      61      80 ..     364     383 ..     353     396 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-05
                                   EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTT.TEEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedg.sfDlvvss 71 
                                   v d  cG+G l+l++a+++   + ++g +++ +  + ar ++  +++   ++++ q d  ++p++ g +f ++v++
  gi|91773784|ref|YP_566476.1| 262 VYDPTCGSGSLLLRVAREVeDVSAFYGQELNRTTYNLARMNMILHNVhyrKFDIKQEDTLEYPQHLGmQFEAIVAN 337
                                   56889**************54899***************9998877777888888999988987665699999994 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                                   STTTEEEEEEESTGGGSSHH CS
               Methyltransf_25  61 edgsfDlvvssgalhhlsde 80 
                                   ++++ D+ ++++++hhl ++
  gi|91773784|ref|YP_566476.1| 364 PKSKADYAFVQHMIHHLAEN 383
                                   45577777776667776643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3324.95
//
Query:       gi|91773785|ref|YP_566477.1|  [L=96]
Description: hypothetical protein Mbur_1844 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-10   39.1   0.8    5.2e-10   39.1   0.8    2.2  2  PLDc_N    Phospholipase_D-nuclease N-terminal
    0.00023   21.4   1.6    0.00023   21.4   1.6    2.0  2  DUF2516   Protein of unknown function (DUF2516)
  ------ inclusion threshold ------
        1.4    8.6   9.5       0.28   10.8   3.6    1.9  2  DUF4131   Domain of unknown function (DUF4131)
        3.3    7.9  10.0         21    5.3  10.0    1.9  1  VKOR      Vitamin K epoxide reductase family


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.4      0.92   4.1e+03      19      26 ..      28      35 ..       9      38 .. 0.55
   2 !   39.1   0.8   1.2e-13   5.2e-10       1      40 [.      39      85 ..      39      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.92
                        PLDc_N 19 klaWllvi 26
                                   l+W ++ 
  gi|91773785|ref|YP_566477.1| 28 QLLWGIIA 35
                                  45555555 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1.2e-13
                        PLDc_N  1 ilwiialidiirdrnpss........klaWllvilflPvlGailYllf 40
                                  ++w+++l+d+++ rn           kl+W lv++fl ++Ga+lY+ +
  gi|91773785|ref|YP_566477.1| 39 LFWVFMLFDCLQ-RNADDfphkgdtdKLIWSLVLIFLTFIGAVLYYYL 85
                                  58**********.555555589999********************987 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.9     0.058   2.6e+02      45      78 ..       8      40 ..       3      42 .. 0.51
   2 !   21.4   1.6   5.1e-08   0.00023       7      58 ..      29      80 ..      24      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.058
                       DUF2516 45 Wlailgvallvlll.glfgalsllgliavvaalvY 78
                                  W+++ g+ +++++l  +++  +ll+ i ++a+ ++
  gi|91773785|ref|YP_566477.1|  8 WTIV-GLMVFFTILvFTYHIGQLLWGIIAIAI-LF 40
                                  7654.444444444234566666666555544.34 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 5.1e-08
                       DUF2516  7 vllllalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlll 58
                                  +l+ +  +++++ ++ l+d+l r ad F+  g   K +W ++l+  ++++ +
  gi|91773785|ref|YP_566477.1| 29 LLWGIIAIAILFWVFMLFDCLQRNADDFPHKGDTDKLIWSLVLIFLTFIGAV 80
                                  6788889999999******************************999999887 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.6   6.2e-05      0.28       7      62 ..       8      59 ..       3      70 .. 0.80
   2 ?    4.7   4.3    0.0048        22       7      50 ..      33      84 ..      30      95 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                       DUF4131  7 lvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsql 62
                                  + +++l++++++l + +       + l++++++++l+++++++  +q+na+d+++ 
  gi|91773785|ref|YP_566477.1|  8 WTIVGLMVFFTILVFTY----HIGQLLWGIIAIAILFWVFMLFDCLQRNADDFPHK 59
                                  55666666666666665....578899*************************9985 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0048
                       DUF4131  7 lvllalllllllllllllrr........rprrrvllllllllllallgfalr 50
                                  ++++a+l+++++l  +l+r+         + + ++ l+l++l +++++++++
  gi|91773785|ref|YP_566477.1| 33 IIAIAILFWVFMLFDCLQRNaddfphkgDTDKLIWSLVLIFLTFIGAVLYYY 84
                                  3334444444444433333377777765444444555555544444444444 PP

>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  10.0    0.0048        21      58     104 ..      30      95 ..       2      96 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0048
                                   HHHHHHHHHHHHHHHS-....................HHHHHHHHHHHHHHHHHHHHHHHHTTS-- CS
                          VKOR  58 llGllayalvlllalapl...................lwlllllgslagvvfslyLiylslfviga 104
                                   l+G++a a+++++ ++                       l+l++++++g+v   yL+ +++ ++ +
  gi|91773785|ref|YP_566477.1|  30 LWGIIAIAILFWVFMLFDclqrnaddfphkgdtdkliWSLVLIFLTFIGAVLYYYLVRIQVREVDQ 95 
                                   77888877777776655589999*********9999433455666669*********999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 540.04
//
Query:       gi|91773786|ref|YP_566478.1|  [L=82]
Description: hypothetical protein Mbur_1845 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0072   16.4   3.0        1.4    9.0   0.2    2.3  2  Col_cuticle_N    Nematode cuticle collagen N-terminal domain
  ------ inclusion threshold ------
       0.12   11.5   7.0       0.13   11.4   7.0    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.15   12.0   3.9       0.34   10.9   1.0    2.2  2  Gram_pos_anchor  LPXTG cell wall anchor motif
       0.16   12.2   8.3       0.32   11.2   0.3    2.2  2  DUF347           Repeat of Unknown Function (DUF347)
       0.96    9.2   5.9       0.27   11.0   1.2    2.1  2  PMP1_2           ATPase proteolipid family


Domain annotation for each model (and alignments):
>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.3    0.0009       3.2       9      29 ..      22      42 ..      21      44 .. 0.89
   2 !    9.0   0.2   0.00039       1.4       2      26 ..      57      81 ..      56      82 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0009
                 Col_cuticle_N  9 vailsslitlpsiyndiqsfq 29
                                   a++++l+++ ++y ++  f+
  gi|91773786|ref|YP_566478.1| 22 SALFGLLLVVTILYYYMEYFY 42
                                  69**************98775 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00039
                 Col_cuticle_N  2 vavalStvailsslitlpsiyndiq 26
                                  ++++l ++ai++++ ++ +++ +++
  gi|91773786|ref|YP_566478.1| 57 IGSVLFGLAIIAMIAFILLLFRKVN 81
                                  6788999****************99 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   7.0   3.6e-05      0.13     213     265 ..      22      79 ..       5      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
               ABC2_membrane_3 213 dflvyllqlllilllafglgipfg.nlglll....llfllfglayialgyllsslfkn 265
                                   ++l +ll ++ il+++  +++p + +l+++l    + ++lfgla+ia+++++  lf++
  gi|91773786|ref|YP_566478.1|  22 SALFGLLLVVTILYYYMEYFYPNKyDLLFMLtgqiIGSVLFGLAIIAMIAFILLLFRK 79 
                                   44444444444444433324566679999888999*********************86 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.057     2e+02      21      32 ..      23      34 ..      18      38 .. 0.72
   2 ?   10.9   1.0   9.5e-05      0.34      18      43 .]      57      82 .]      52      82 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.057
                                  XXXXXXXXXXXX CS
               Gram_pos_anchor 21 taaGllallggl 32
                                   ++Gll++++ l
  gi|91773786|ref|YP_566478.1| 23 ALFGLLLVVTIL 34
                                  678888887766 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.5e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXX. CS
               Gram_pos_anchor 18 ifltaaGllallggllLlvkrRKkek 43
                                  i+  ++Gl++++  +++l+  RK++k
  gi|91773786|ref|YP_566478.1| 57 IGSVLFGLAIIAMIAFILLLFRKVNK 82
                                  667899*9999999999999999986 PP

>> DUF347  Repeat of Unknown Function (DUF347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3     9e-05      0.32      30      48 ..      20      38 ..      12      40 .. 0.88
   2 ?    4.2   2.8     0.014        49      27      47 ..      54      74 ..      48      79 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9e-05
                        DUF347 30 vgaaifgalllvvvlaqfl 48
                                   ++a+fg+ll+v++l++++
  gi|91773786|ref|YP_566478.1| 20 YASALFGLLLVVTILYYYM 38
                                  579**************96 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                        DUF347 27 gyavgaaifgalllvvvlaqf 47
                                  g  +g+++fg+++++++++ +
  gi|91773786|ref|YP_566478.1| 54 GQIIGSVLFGLAIIAMIAFIL 74
                                  556788888888887776544 PP

>> PMP1_2  ATPase proteolipid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.15   5.2e+02      24      30 ..      29      35 ..      23      38 .. 0.79
   2 ?   11.0   1.2   7.4e-05      0.27       9      32 ..      54      79 ..      48      82 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                        PMP1_2 24 ivltilY 30
                                  +v tilY
  gi|91773786|ref|YP_566478.1| 29 LVVTILY 35
                                  6899999 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.4e-05
                        PMP1_2  9 GviLvFvLvGLACvAivltil..YRk 32
                                  G i+  vL GLA +A++  il  +Rk
  gi|91773786|ref|YP_566478.1| 54 GQIIGSVLFGLAIIAMIAFILllFRK 79
                                  667788***********988522676 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 530.47
//
Query:       gi|91773787|ref|YP_566479.1|  [L=262]
Description: hypothetical protein Mbur_1846 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 1454.34
//
Query:       gi|91773788|ref|YP_566480.1|  [L=294]
Description: methylenetetrahydrofolate reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-36  123.9   0.0    8.5e-36  123.7   0.0    1.0  1  MTHFR           Methylenetetrahydrofolate reductase
  ------ inclusion threshold ------
      0.045   13.8   0.1       0.11   12.5   0.1    1.7  1  Hydrolase_like  HAD-hyrolase-like
       0.15   11.4   0.0       0.44    9.9   0.0    1.9  1  AP_endonuc_2    Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7   0.0   1.4e-39   8.5e-36       2     285 ..       5     288 ..       4     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 1.4e-39
                                   HHHHHT.SS-EEEEEE---SSHHHHHHHHHHHHHHGGGG-SEEEE---CCCTTHHHHHHHHHHHHHHH-S-EEEEEESTTS CS
                         MTHFR   2 leqaleegkalisfEffpPkteegernLleridrleevkplfvdvTwgaggstaeltssiakviqqelgleailhlTctda 82 
                                   +++ l+++++++++E+ pPk+++   +L ++ + +     + +++T++ ++ + +++ +++ ++  + g e+i++lTc+d+
  gi|91773788|ref|YP_566480.1|   5 FNDVLNSDRFIVTAEVAPPKGTDISATLEDA-ELIR-GLVDAINITDNQRA-VMRMSPIAVGKLLMDAGHEVIVQLTCRDR 82 
                                   57788999****************9999775.4444.34479*********.99*************************** PP

                                   -HHHHHHHHHHHHHCT--EEEEE--S--TT-GG.C---S----SHHHHHHHHHHHHC..GGSEEEEEE-TT--T...T-S- CS
                         MTHFR  83 skeeldkalekakelGirnilALrGDppkdedk.weekeeefkyaldLvrlireeyg..dlfdigvaaYPevhp...eaks 157
                                   ++  l++++  a +lGi+n+  ++GD   ++d+  ++ +++++  ++L +li + +g  d+    +a+ P   +   ++ +
  gi|91773788|ref|YP_566480.1|  83 NRLALQSDILAASALGIENLCVMTGDYTTKGDHvGAKAVYDLD-SVQLLSLITKMMGgsDMAGNELAGAPSFTVgavSNTD 162
                                   *********************************7777788866.6777777777554337888899999976665557777 PP

                                   HHHHHH..HHHHHHHCT--EEEEEE-S-HHHHHHHHHHHHHCT-SS-EEEEE---SSHHHHHHHHHHH.T----HHHHCCC CS
                         MTHFR 158 leadlk..ylkeKvdaGAdfiitQlffdvdkflkfveqvreagidipiipgimpiksykslkrlakls.kvkiPqelldrl 235
                                   + + ++  +lk+K++aGA fi+tQ ++dv++f  f + + ++g ++ +++gi+p++s+++++++++   ++++ +el++r+
  gi|91773788|ref|YP_566480.1| 163 VTKRMQmlKLKKKINAGARFIQTQAVYDVESFKDFSDLMGQIGPNVLVLAGIIPLRSAAMAHFMNNNIpGIRVGDELIKRM 243
                                   76655411789*****************************************************98766************ PP

                                   TCHCT-HHHHHHHHHHHHHHHHHHHHHCT--EEEEE-TT--HHHHHHHHH CS
                         MTHFR 236 eeikdddeavkkigielavemvkkllaegvkglHlytlnkekaileileq 285
                                   e++kd  ++    g e+a e + +l +   +g+Hl+ +     ++ +le+
  gi|91773788|ref|YP_566480.1| 244 ENAKDPIQE----GLEIAAESILELRDLC-RGIHLMPIGGHGNTQRLLEM 288
                                   *66654444....5555566665554444.56999988777777766665 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.9e-05      0.11      31      57 ..      87     113 ..      86     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                   TTTHHHHHHHCT-EEEEESSSSS-TTT CS
                Hydrolase_like  31 latDiagAnnaGwksvLVltGvtrped 57 
                                   l +Di++A + G++ + V tG ++ + 
  gi|91773788|ref|YP_566480.1|  87 LQSDILAASALGIENLCVMTGDYTTKG 113
                                   679*******************88743 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 ?    9.9   0.0   7.4e-05      0.44      59     100 ..      56     113 ..      17     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.4e-05
                                   C............HTTCS......HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTS CS
                  AP_endonuc_2  59 d............erear......reesvdalkraielaaaLGapllvlhpGtagagpkg 100
                                   +             ++++      r++ + al++ i +a+aLG+++l +++G+  +  kg
  gi|91773788|ref|YP_566480.1|  56 RmspiavgkllmdAGHEVivqltcRDRNRLALQSDILAASALGIENLCVMTGD--YTTKG 113
                                   2455555555555333334555566677************************5..33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1881.44
//
Query:       gi|91773789|ref|YP_566481.1|  [L=415]
Description: thiamine biosynthesis protein ThiC [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     3e-146  487.5   0.8   3.4e-146  487.3   0.8    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 !  487.3   0.8  1.9e-150  3.4e-146       1     417 [.       4     408 ..       4     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 487.3 bits;  conditional E-value: 1.9e-150
                  ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEveKl 81 
                                   tq+e+a++g+it+eme+vae+e++ +e+v+++va+G++vi+ +      pvaiG+g++tk+n+n+Gts+++ d ++E+eK+
  gi|91773789|ref|YP_566481.1|   4 TQVEYAKNGTITPEMEYVAEHESIYVETVMSRVADGSLVIMVRDGC--PPVAIGRGAKTKINVNLGTSSASIDPDAELEKV 82 
                                   89**************************************987654..4******************************** PP

                  ThiC_Rad_SAM  82 kvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdfltiHagvt 162
                                   k+a+k+gadt+ dLs+ggdi++ir+ +++++++p++tvp+Yqa++  e  +++++++++l+ +++q+++Gv+ + +H+ v+
  gi|91773789|ref|YP_566481.1|  83 KIAEKYGADTITDLSMGGDISAIRKIVFDNTTLPITTVPVYQAVV--ECGMKDTSSDDVLSYLKKQVDEGVSSVVVHC-VE 160
                                   ********************************************7..6799***************************.** PP

                  ThiC_Rad_SAM 163 lellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlaelivl 243
                                   +++le+lk ++R++g+vS+gGs+++  ml+ + enp++e+fde+l+ilk+ dv+lSlg+++R+G+++D  d+ q++e+ ++
  gi|91773789|ref|YP_566481.1| 161 KQMLEKLKGTGRIMGMVSKGGSFTSVLMLKDGCENPYLENFDEVLSILKKNDVVLSLGNTMRSGCVHDVCDNPQMMEIRTN 241
                                   ********************************************************************************* PP

                  ThiC_Rad_SAM 244 gelvkrareagvqvmveG.PGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGadllCyv 323
                                   ++l+k+a+eagvqv++eG  GHv+ ++i  ++++++ l++  P++v Gpl+tD+++gYDhi++a+Ga++a+ +Gad+lCy+
  gi|91773789|ref|YP_566481.1| 242 AKLAKQANEAGVQVIIEGmGGHVQANDIVPHIQAHRALSD-FPLFVAGPLPTDVGMGYDHISGAVGASIASGNGADYLCYI 321
                                   ******************889************9999876.9*************************************** PP

                  ThiC_Rad_SAM 324 tpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelaldpekareireeklpeeeeaC 404
                                   tpaEHl+lP+ e+v+eG+ia+kiaah++d +k   +  erdk l++ R+++dwe q++laldp+k + +   + p     C
  gi|91773789|ref|YP_566481.1| 322 TPAEHLSLPTPEQVREGLIAFKIAAHIGDSMKY--GLDERDKLLADRRANFDWEGQMALALDPDKPKGMCPMTGP-----C 395
                                   ********************************8..899*******************************998775.....* PP

                  ThiC_Rad_SAM 405 smCgekCavkive 417
                                   smCge+Ca+ki++
  gi|91773789|ref|YP_566481.1| 396 SMCGEYCAIKIMA 408
                                   **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2434.20
//
Query:       gi|91773790|ref|YP_566482.1|  [L=257]
Description: coenzyme F420-0 gamma-glutamyl ligase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  198.2   0.0    1.5e-58  198.0   0.0    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   0.0   8.4e-63   1.5e-58       1     244 []      11     228 ..      11     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 8.4e-63
                                   -..-----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H......... CS
                   F420_ligase   1 giktplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsl 81 
                                   gi+t li  gdd++++++++++k+g+ led+Di+v++e++va+aeg++v+l+++ p++ Aee+a ++  +dp         
  gi|91773790|ref|YP_566482.1|  11 GIRTSLIGVGDDMVKVLCDALEKHGVFLEDRDILVLAESAVATAEGRLVNLSSVVPGKIAEELAGNY-CLDP--------- 81 
                                   89*****************************************************************.****......... PP

                                   .........HHHHHHHHTEEEEEE-...S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHH CS
                   F420_ligase  82 iLkalakatrkvevvlsepsdevgn...qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklk 159
                                            r++e+vl e+++++g      ++ +         G+l  nagid sn++eg+++llP+d+++sa++i+k ++
  gi|91773790|ref|YP_566482.1|  82 ---------REMELVLCECDEVIGGvpgAALTLT--------NGTLSPNAGIDGSNAPEGHVVLLPKDAQRSAADIRKGIE 145
                                   .........***************9776555555........5************************************** PP

                                   HHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EE CS
                   F420_ligase 160 ertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGsadegtPvv 240
                                   e   ++v+V+i   D+++++++l++++va+gtsg+ +++d rg++dl+gk+l++t +av+d+l s+a+L++G+ade++P+v
  gi|91773790|ref|YP_566482.1| 146 EYSACHVGVII--GDSRTQPLRLGCMGVALGTSGMVPVEDARGSHDLFGKPLHITRKAVADNLVSAAQLLMGEADECIPCV 224
                                   ***********..******************************************************************** PP

                                   EEES CS
                   F420_ligase 241 lvrg 244
                                   l+rg
  gi|91773790|ref|YP_566482.1| 225 LIRG 228
                                   ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1507.18
//
Query:       gi|91773791|ref|YP_566483.1|  [L=156]
Description: hypothetical protein Mbur_1850 [Methanococcoides burtonii DSM 6242]
Scores for complete 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    1.6e-06   27.6   4.3    1.2  1  YdjM       LexA-binding, inner membrane-associated putative h
     0.0001   22.1  10.5      0.075   12.7   0.2    2.1  2  DUF4184    Domain of unknown function (DUF4184)
  ------ inclusion threshold ------
       0.55    9.9   2.8         10    5.8   0.1    2.3  2  Kinocilin  Kinocilin protein


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   4.3   2.7e-10   1.6e-06      42     135 ..      22     124 ..      12     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.7e-10
                          YdjM  42 iDhpsstlgrklgllskklaklvgH...RgftHSllflallalvlllllrlfgrsa......lrlglllllgvlsHlllDl 113
                                   iD+ ++ l++ +  +++++  + gH    g +H+++++ +lal+l+++l  ++ +       +++ l+ l+g++sH++lD+
  gi|91773791|ref|YP_566483.1|  22 IDIIAVLLASVVIDIRATIYLFLGHeplHGPFHTFIGATVLALLLSYVLSYIFYRLgmniemKHIILGSLIGAWSHVFLDS 102
                                   56666666666666666666699998888*******************999998889998987778889999********* PP

                          YdjM 114 ltkyGvpllwPfskkkvrlsll 135
                                   +    +  +wP+ ++  +  + 
  gi|91773791|ref|YP_566483.1| 103 FLYTDIIPFWPMMSNPLFGAIS 124
                                   ************8766665554 PP

>> DUF4184  Domain of unknown function (DUF4184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   6.1   1.8e-05      0.11       1      73 [.       1      77 [.       1      85 [. 0.89
   2 !   12.7   0.2   1.3e-05     0.075     104     146 ..      85     125 ..      79     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                       DUF4184  1 MPfTlsHpaavlplkllkrkrlslsaLviGslaPDveyf....lrlkakstltHtllglllvdlplalllalvfhlv 73
                                  MPfT  H+  ++ l ++ +k++++ a  + s++ D+       l+ ++ +   Ht++g+ +++l+l+++l ++f+ +
  gi|91773791|ref|YP_566483.1|  1 MPFTPFHLGPAFLLGMVFKKKIDIIAVLLASVVIDIRATiylfLGHEPLHGPFHTFIGATVLALLLSYVLSYIFYRL 77
                                  *******988888888*******************98654445888999999*********************9865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.3e-05
                       DUF4184 104 vvvvsaliGaatHvlwDsfTHedgwfvrlipvlqssvagdvpl 146
                                    +++  liGa +Hv++Dsf  +d  ++  +p++++ ++g+++ 
  gi|91773791|ref|YP_566483.1|  85 HIILGSLIGAWSHVFLDSFLYTD--IIPFWPMMSNPLFGAISS 125
                                   568899*************8877..456677777777555553 PP

>> Kinocilin  Kinocilin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3    0.0039        23      43      74 ..      55      89 ..      23      96 .. 0.82
   2 ?    5.8   0.1    0.0017        10      43      64 ..     133     154 ..     123     156 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0039
                     Kinocilin 43 ifigaaglglll...laypflkarfnldrilpaig 74
                                   figa+ l lll   l+y f +  +n++     +g
  gi|91773791|ref|YP_566483.1| 55 TFIGATVLALLLsyvLSYIFYRLGMNIEMKHIILG 89
                                  59******998544489999999888875444444 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0017
                     Kinocilin  43 ifigaaglgllllaypflkarf 64 
                                   ++ g aglg++ + y f + ++
  gi|91773791|ref|YP_566483.1| 133 VLSGMAGLGIFAFNYMFCNQKL 154
                                   56799************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1069.46
//
Query:       gi|91773792|ref|YP_566484.1|  [L=89]
Description: thioredoxin-related [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-22   77.8   0.0    5.5e-22   77.7   0.0    1.0  1  Thioredoxin    Thioredoxin
    3.7e-09   37.0   0.1    1.3e-08   35.3   0.1    1.7  1  Thioredoxin_2  Thioredoxin-like domain
    6.5e-07   29.6   0.0     0.0015   18.8   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    6.2e-06   26.0   0.0    7.4e-06   25.8   0.0    1.1  1  Thioredoxin_9  Thioredoxin
      2e-05   24.7   0.0    3.3e-05   24.0   0.0    1.4  1  Glutaredoxin   Glutaredoxin
    6.1e-05   23.0   0.1    6.6e-05   22.9   0.1    1.1  1  Thioredoxin_3  Thioredoxin domain
    8.8e-05   22.2   0.2      0.055   13.2   0.0    2.0  2  Redoxin        Redoxin
    0.00018   21.2   0.0    0.00021   21.0   0.0    1.1  1  KaiB           KaiB domain
    0.00069   19.5   0.0    0.00088   19.2   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0012   18.0   0.0     0.0013   17.9   0.0    1.0  1  Calsequestrin  Calsequestrin
     0.0034   17.3   0.1      0.022   14.7   0.1    1.9  1  AhpC-TSA       AhpC/TSA family
     0.0065   16.3   0.1      0.032   14.0   0.0    1.8  2  DSBA           DSBA-like thioredoxin domain
     0.0082   16.3   0.0      0.014   15.6   0.0    1.4  1  Thioredoxin_7  Thioredoxin-like
  ------ inclusion threshold ------
      0.017   15.5   0.0       0.02   15.3   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
      0.019   14.9   0.0      0.021   14.8   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
       0.13   12.4   0.1       0.19   11.9   0.0    1.3  1  Thioredoxin_4  Thioredoxin
       0.21   11.5   0.0       0.21   11.5   0.0    1.1  1  Thioredoxin_6  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   5.2e-25   5.5e-22      19     101 ..       3      85 ..       1      87 [. 0.96

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 5.2e-25
                                   SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHH CS
                   Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaa 99 
                                   + v+++F+A+wCg+C+  +P le+l  el dkv +  vdvd+n+ la ky+v+++Ptl++ k+g+ vk+y+g  +++ l+a
  gi|91773792|ref|YP_566484.1|   3 NVVIMDFTATWCGPCQIQKPILEQLEGELGDKVEFKMVDVDQNNALAGKYGVSAVPTLIIEKDGEVVKRYTGVTSADVLRA 83 
                                   57999**********************************************************************999998 PP

                                   HH CS
                   Thioredoxin 100 fl 101
                                    l
  gi|91773792|ref|YP_566484.1|  84 EL 85 
                                   77 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   1.2e-11   1.3e-08       8     108 ..       5      84 ..       2      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.2e-11
                 Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv.fl 87 
                                   v+++ft+++C+ C+  k  l++l   +       l++++e+k+v++++++              la kygv+++Pt++   
  gi|91773792|ref|YP_566484.1|   5 VIMDFTATWCGPCQIQKPILEQL---EGE-----LGDKVEFKMVDVDQNNA-------------LAGKYGVSAVPTLIiEK 64 
                                   899***********999988888...445.....99**********99986.............579*********66266 PP

                 Thioredoxin_2  88 dgkeivarlpGyvpaeeleal 108
                                   dg+ +v r++G ++a+ l+a 
  gi|91773792|ref|YP_566484.1|  65 DGE-VVKRYTGVTSADVLRAE 84 
                                   666.***********999876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06    0.0015       3      46 ..       4      45 ..       2      47 .. 0.90
   2 !   11.8   0.0   0.00022      0.23      68      95 .]      42      68 ..      39      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                  EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS- CS
                 Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkk 46
                                  vv++ f a+wc pc+   p l +l+ +l   +kve+  v +d++
  gi|91773792|ref|YP_566484.1|  4 VVIMDFTATWCGPCQIQKPILEQLEGELG--DKVEFKMVDVDQN 45
                                  89**************************9..8888888888875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
                                  TT-HHHHTT-S--TT-SEEEEE-TT-BE CS
                 Thioredoxin_8 68 dkkrnklkkkynvkaiPtlvvldkngev 95
                                   +++n+l+ ky+v+a+Ptl ++ k+gev
  gi|91773792|ref|YP_566484.1| 42 VDQNNALAGKYGVSAVPTL-IIEKDGEV 68
                                  46799*************5.67888876 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0     7e-09   7.4e-06      46     111 ..       7      69 ..       2      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7e-09
                                   EEE--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EE CS
                 Thioredoxin_9  46 lvltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeel 111
                                   + +t+ wCg +++  P+l+++  el +++e+k++  d+n+ l  +y   g  a+Ptlii  ++ge++
  gi|91773792|ref|YP_566484.1|   7 MDFTATWCGPCQIQKPILEQLEgELGDKVEFKMVDVDQNNALAGKY---GVSAVPTLIIE-KDGEVV 69 
                                   5589*****************98999********************...99*****9974.555555 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.1e-08   3.3e-05       4      57 ..       9      66 ..       4      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.1e-08
                                  EESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEE..TT CS
                  Glutaredoxin  4 ftkptCpyCkkakrlLkelg......vkfeeidvdkdeeireelkelsgvrtvPqvfi..dg 57
                                  ft ++C+ C+  k +L++l       v+f+++dvd++     +l  + gv++vP++ i  dg
  gi|91773792|ref|YP_566484.1|  9 FTATWCGPCQIQKPILEQLEgelgdkVEFKMVDVDQN----NALAGKYGVSAVPTLIIekDG 66
                                  889*************9999999999**********9....5555555*********94455 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   6.3e-08   6.6e-05      10      70 ..      14      80 ..       3      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.3e-08
                                  STTCHHHHHHHHHHCHCCT..CECEEECCTTHHHH.HHCT-SSSSEEECT..TCEE..EESS---CCH CS
                 Thioredoxin_3 10 CakCpklekavkeaaaekg..ikaevekvtdfeei.ekygVmsvPalvid..gkvv..vsGkvpseee 70
                                  C  C+  + +++++  e+g  +++++++v +++ +  kygV +vP+l+i+  g+vv  ++G v s + 
  gi|91773792|ref|YP_566484.1| 14 CGPCQIQKPILEQLEGELGdkVEFKMVDVDQNNALaGKYGVSAVPTLIIEkdGEVVkrYTG-VTSADV 80
                                  788887777777777777545999*****9999999*************877887533677.666655 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.2e-05     0.055      31      67 ..       4      39 ..       2      49 .. 0.70
   2 !    9.1   0.1   0.00097         1      91     139 ..      42      81 ..      33      89 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                                  EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEE CS
                       Redoxin 31 vvvnfvpgafcPtCsaehpyleklaellkekgvdvva 67
                                  vv+  +++++c++C+ + p le+l+ +l++k v++ +
  gi|91773792|ref|YP_566484.1|  4 VVIMDFTATWCGPCQIQKPILEQLEGELGDK-VEFKM 39
                                  444444455***************8776665.55544 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00097
                                   E-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.S CS
                       Redoxin  91 sDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.e 139
                                   +D++ a++ ++G+          + p + +i +dg vv++++++ + +  
  gi|91773792|ref|YP_566484.1|  42 VDQNNALAGKYGVS---------AVP-TLIIEKDGEVVKRYTGVTSADvL 81 
                                   68999999999966.........555.5689************9886554 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.9e-07   0.00021      18      56 ..      24      61 ..      17      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.9e-07
                                  HHHHCCCHCTTTEEEEEEETTTSHCHHCCTCEESCCCCC CS
                          KaiB 18 lkkleeedlgfqyeLqvvdvleqPelaeedrlvatPaLi 56
                                  l++le  +lg ++e ++vdv ++  la ++ + a+P+Li
  gi|91773792|ref|YP_566484.1| 24 LEQLE-GELGDKVEFKMVDVDQNNALAGKYGVSAVPTLI 61
                                  44444.459*****************************8 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.3e-07   0.00088     132     219 ..       5      81 ..       2      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.3e-07
                          TraF 132 gLlfFyrgkcpyceaqapilqafadkyg..levraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpva 210
                                    ++ F +  c+ c+ q pil++++ + g   e ++V+vd++    l+          ++gv+ +P+l++ +   ++vv   
  gi|91773792|ref|YP_566484.1|   5 VIMDFTATWCGPCQIQKPILEQLEGELGdkVEFKMVDVDQNNA--LAG---------KYGVSAVPTLIIEKD--GEVVKRY 72 
                                   566788999*****************97225557788888866..777.........*********987544..4666666 PP

                          TraF 211 aGllsldel 219
                                    G++s+d l
  gi|91773792|ref|YP_566484.1|  73 TGVTSADVL 81 
                                   777777766 PP

>> Calsequestrin  Calsequestrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.2e-06    0.0013      80     141 ..      22      83 ..      15      89 .] 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHHHCCCCTEEEEEEETTTTHHHHHCCT--STTEEEEEETTCEE.EE-S--SHHHHHH CS
                 Calsequestrin  80 lvlelvaqvledkdvgfvlvdakkeaklakklgldevdslyvlkgdevi.eydgefaadvlve 141
                                    +le     l dk v f +vd +++ +la k g++ v +l + k  ev+  y g  +advl  
  gi|91773792|ref|YP_566484.1|  22 PILEQLEGELGDK-VEFKMVDVDQNNALAGKYGVSAVPTLIIEKDGEVVkRYTGVTSADVLRA 83 
                                   5666666666665.99**************************997776626********9965 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.1e-05     0.022      27     102 ..       4      76 ..       2      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                                   EEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H...SSEEEE-TTSHHHHHTT-EE CS
                      AhpC-TSA  27 pvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes..lnfpllsDeegkvakaygvlk 102
                                   +v+  f+++ wc +C+ + p l++l  e+   +ve  +v vd+     + + k++     +l+  ++g+v+k+y  ++
  gi|91773792|ref|YP_566484.1|   4 VVIMDFTAT-WCGPCQIQKPILEQLEGELG-DKVEFKMVDVDQNN---ALAGKYGvsAVPTLIIEKDGEVVKRYTGVT 76 
                                   566677777.*******************9.57999999999887...555555543444677788888888887665 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.14   1.5e+02       8      34 ..      12      39 ..       5      43 .. 0.78
   2 !   14.0   0.0     3e-05     0.032     152     192 ..      41      85 ..      25      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.14
                                  TTBHHHHHHHHHHHHHHHHC.CTEEEEE CS
                          DSBA  8 vlCPyCylgkerleklaars.pdvkvvl 34
                                    C+ C + k+ le+l+    ++v++++
  gi|91773792|ref|YP_566484.1| 12 TWCGPCQIQKPILEQLEGELgDKVEFKM 39
                                  57**************999944488776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHHH CS
                          DSBA 152 avrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtladal 192
                                   +v++n a+a ++gv+ vPt ++  dg+  +  +G+++ d l+ +l
  gi|91773792|ref|YP_566484.1|  41 DVDQNNALAGKYGVSAVPTLIIekDGEvvKRYTGVTSADVLRAEL 85 
                                   799*******************87776777899****99999877 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05     0.014      20      79 ..       5      61 ..       2      63 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                  EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---...SSEEE CS
                 Thioredoxin_7 20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqg...vPvva 79
                                  v+ +f+a+wc++Cq ++  +++ e     l +k+ +  vdv++++a  +++   g   vP+++
  gi|91773792|ref|YP_566484.1|  5 VIMDFTATWCGPCQIQKPILEQLEGE---LGDKVEFKMVDVDQNNALAGKY---GvsaVPTLI 61
                                  5669**********999988887543...6788888888888888844332...233488776 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.9e-05      0.02       8      57 ..      12      64 ..       6      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                                  TT-HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCTT.TTEEEECT CS
                        DUF836  8 pgChlCeqakekLkelkleeg..leleviDIakdeeleakYgle.ipvlaleg 57
                                    C+ C+  k +L++l+ e g  +e + +D+++++ l  kYg+  +p l +e+
  gi|91773792|ref|YP_566484.1| 12 TWCGPCQIQKPILEQLEGELGdkVEFKMVDVDQNNALAGKYGVSaVPTLIIEK 64
                                  56999**9999999987777667*******************85388888887 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     2e-05     0.021      60     102 ..      34      75 ..      20      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                                   S-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEESS CS
                          HyaE  60 alraavvadreqeealaerfgvlktPsllflrdgeylgvlaki 102
                                     +  +v   +q++ala ++gv+ +P+l++ +dge++    ++
  gi|91773792|ref|YP_566484.1|  34 KVEFKMVD-VDQNNALAGKYGVSAVPTLIIEKDGEVVKRYTGV 75 
                                   55555554.99***********************998766665 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.19     125     153 ..      41      71 ..      20      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHHHHT--SS-EEEE..TTEEE-T CS
                 Thioredoxin_4 125 lveaeskeakkagiestPtfii..ngekvee 153
                                   +v ++ + a k g++++Pt+ii  +ge+v++
  gi|91773792|ref|YP_566484.1|  41 DVDQNNALAGKYGVSAVPTLIIekDGEVVKR 71 
                                   5667777789************988988754 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.21     114     164 ..      21      67 ..       5      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEESSSS- CS
                 Thioredoxin_6 114 kkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivdsashk 164
                                   k ++e+++ e+ dk+ f  +d+++++ +   +g+s  ++P+++ ++ ++++
  gi|91773792|ref|YP_566484.1|  21 KPILEQLEGELGDKVEFKMVDVDQNNALAGKYGVS--AVPTLI-IE-KDGE 67 
                                   4578999999*************************..*****9.66.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 612.63
//
Query:       gi|91773793|ref|YP_566485.1|  [L=337]
Description: mRNA 3-end processing factor [Methanococcoides burtonii DSM 6242]
Scores for 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-06   25.3   0.2    3.9e-05   23.2   0.1    1.8  2  Lactamase_B_2  Beta-lactamase superfamily domain
      0.001   19.1   0.2       0.46   10.5   0.0    2.4  2  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0055   16.6   0.1      0.012   15.5   0.1    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.21   11.5   0.0    2.5  3  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 !   23.2   0.1   8.8e-09   3.9e-05      27     169 ..      49     163 ..      39     183 .. 0.82
   2 ?   -0.9   0.0      0.21   9.5e+02     178     200 ..     280     302 ..     270     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.8e-09
                                   -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEE CS
                 Lactamase_B_2  27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleita 107
                                   + p+ da l+thaH DH     +l  l+      + ++++++ le + +++++++        ++ g+s++++  g+++++
  gi|91773793|ref|YP_566485.1|  49 KQPQPDAYLVTHAHSDHNGKSAMLSDLS------VSTEKTAKALEIRHDRDFKGRT-------VACGDSIDIN--GVTVKT 114
                                   34899*************7777777743......3689999999999776666665.......*********9..889999 PP

                                   EEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SST CS
                 Lactamase_B_2 108 tparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayed 169
                                    +  h++g         +  +++ + g r++ +gD++  +      l ++d+l+ ++++ + 
  gi|91773793|ref|YP_566485.1| 115 YQTGHTAGA--------VGFYWVNDVGTRILVTGDVKDAS-----ALPKCDVLITEANYGDH 163
                                   999999999........999*****************444.....68899999999986555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.21
                                   ---STSHHHHCTTSSSSEEEEES CS
                 Lactamase_B_2 178 HltpeeaveaaadlgakrlvliH 200
                                   Hl+ ++ +++++d++++ +++ H
  gi|91773793|ref|YP_566485.1| 280 HLDANGLAKMVEDIDPELTIVYH 302
                                   88889999999999999988888 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0001      0.46      41      59 ..      49      67 ..      40      77 .. 0.85
   2 !    6.4   0.0    0.0018       7.9     120     151 ..     111     142 ..      78     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                  GGGGEEEEE-SBSSHHHHT CS
                   Lactamase_B 41 kpkdvdavilTHlHlDHiG 59
                                  k+ ++da ++TH+H+DH G
  gi|91773793|ref|YP_566485.1| 49 KQPQPDAYLVTHAHSDHNG 67
                                  67799999*********88 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
                                   EEEEEHECTTSTSCCEEEEEETTCCEEEECTT CS
                   Lactamase_B 120 rralyvtggpghghghgvveygggkvlftGDa 151
                                    + +y+tg+ +   g + v + g ++l+tGD+
  gi|91773793|ref|YP_566485.1| 111 TVKTYQTGHTAGAVGFYWVNDVGTRILVTGDV 142
                                   56789**************************7 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.7e-06     0.012      29     134 ..      45     156 ..      24     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                 Lactamase_B_3  29 gyeppaeeaDlvlisqaledHahletlkq.l.......aenvkvlee...........geslevg.gleiravatshdavg 89 
                                    + ++++++D+ l+++a++dH+   ++ + l       a       +           g ++++g +++i++v+ ++  + 
  gi|91773793|ref|YP_566485.1|  45 RLPNKQPQPDAYLVTHAHSDHNGKSAMLSdLsvstektA-------KaleirhdrdfkGRTVACGdSIDINGVTVKTY-QT 117
                                   4567789**************977665550466664430.......03333444444444455544666666666663.34 PP

                 Lactamase_B_3  90 gsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvlt 134
                                   g++ g    + +++ g +i+  G++          +l + Dv++t
  gi|91773793|ref|YP_566485.1| 118 GHTAGAVGFYWVNDVGTRILVTGDVKD------ASALPKCDVLIT 156
                                   666665444555556888888888875......455556677665 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.1   4.6e+02      13      29 ..      59      75 ..      50      78 .. 0.79
   2 ?   -3.3   0.0         2   8.8e+03      35      47 ..     136     148 ..     136     149 .. 0.88
   3 ?   11.5   0.0   4.7e-05      0.21      13      51 ..     277     315 ..     274     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.1
                         RMMBL 13 fSgHadknellelirkl 29
                                    +H+d+n+   +++ l
  gi|91773793|ref|YP_566485.1| 59 THAHSDHNGKSAMLSDL 75
                                  78******988888765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                         RMMBL  35 ilvHGeeeatsal 47 
                                   ilv G+ + +sal
  gi|91773793|ref|YP_566485.1| 136 ILVTGDVKDASAL 148
                                   79****9999987 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 4.7e-05
                         RMMBL  13 fSgHadknellelirklkprnvilvHGeeeatsalarll 51 
                                   +S H d n+l ++++ + p+  i+ H + e  +++a++l
  gi|91773793|ref|YP_566485.1| 277 VSDHLDANGLAKMVEDIDPELTIVYHPSGERPEKFASYL 315
                                   899***********************8888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2043.90
//
Query:       gi|91773794|ref|YP_566486.1|  [L=129]
Description: hypothetical protein Mbur_1853 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 997.96
//
Query:       gi|91773795|ref|YP_566487.1|  [L=589]
Description: ATPase RIL [Methanococcoides burtonii DSM 6242]
Scores for complete 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  140.5   0.0    9.5e-23   81.2   0.0    2.4  2  ABC_tran      ABC transporter
    5.5e-13   48.9   7.4     0.0002   20.8   0.0    4.2  4  SMC_N         RecF/RecN/SMC N terminal domain
    2.1e-12   46.6   3.0    4.3e-12   45.7   3.0    1.5  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    3.6e-10   40.1   5.1     0.0094   15.8   0.1    4.3  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.9e-07   30.6   3.7    1.9e-07   30.6   3.7    2.4  2  Fer4          4Fe-4S binding domain
    1.6e-06   28.5   0.0     0.0004   20.7   0.0    2.5  2  AAA_22        AAA domain
    1.7e-06   28.1   0.0      0.096   12.6   0.0    2.5  2  Rad17         Rad17 P-loop domain
    1.9e-05   25.2   0.8       0.17   12.3   0.0    2.4  2  AAA_23        AAA domain
    2.7e-05   24.6   0.0      0.085   13.2   0.0    3.2  3  AAA_16        AAA ATPase domain
    9.5e-05   22.3   2.6    9.5e-05   22.3   2.6    2.4  2  Fer4_6        4Fe-4S binding domain
    0.00011   22.1   0.5      0.049   13.5   0.0    2.3  2  RsgA_GTPase   RsgA GTPase
    0.00013   22.3   0.0       0.24   11.8   0.0    2.6  2  RNA_helicase  RNA helicase
    0.00018   21.6   6.8    0.00032   20.8   6.8    1.4  1  Fer4_21       4Fe-4S dicluster domain
    0.00022   21.0   0.1       0.18   11.5   0.0    2.4  2  AAA_24        AAA domain
    0.00058   19.9   9.9     0.0028   17.7   1.0    2.5  2  Fer4_10       4Fe-4S dicluster domain
    0.00065   19.5   3.4       0.67    9.6   0.4    3.2  3  AAA_15        AAA ATPase domain
    0.00072   19.3   3.1       0.73    9.6   0.2    2.4  2  AAA_29        P-loop containing region of AAA domain
    0.00097   19.3   7.5     0.0019   18.3   7.5    1.5  1  Fer4_9        4Fe-4S dicluster domain
      0.001   19.1   1.2      0.001   19.1   1.2    2.4  2  Fer4_2        4Fe-4S binding domain
     0.0047   17.4   0.0       0.44   11.0   0.0    2.6  2  AAA           ATPase family associated with various cellular 
     0.0055   17.3   1.6     0.0055   17.3   1.6    2.3  3  Fer4_7        4Fe-4S dicluster domain
     0.0088   15.9   0.0        3.8    7.3   0.0    2.5  2  dNK           Deoxynucleoside kinase
     0.0091   15.6   0.7        3.1    7.3   0.0    3.6  4  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.013   15.5   0.2       0.86    9.5   0.0    2.4  2  NACHT         NACHT domain
      0.017   15.7   0.1          9    6.9   0.0    3.1  3  AAA_18        AAA domain
      0.026   14.5   0.0         16    5.5   0.0    3.0  3  AAA_5         AAA domain (dynein-related subfamily)
      0.028   14.5   1.9        3.6    7.6   0.1    3.5  3  AAA_14        AAA domain
      0.031   14.0   0.0        3.3    7.4   0.0    2.3  2  VirE          Virulence-associated protein E
      0.033   14.4   0.0         13    6.1   0.0    2.9  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.046   13.9   1.5        1.7    8.8   0.0    3.2  3  AAA_33        AAA domain
      0.047   13.8   0.4       0.98    9.5   0.1    2.7  2  MMR_HSR1      50S ribosome-binding GTPase
      0.048   14.2   1.9      0.048   14.2   1.9    2.4  2  Fer4_4        4Fe-4S binding domain
      0.071   13.2   0.9         18    5.3   0.0    2.9  3  DUF87         Helicase HerA, central domain
      0.099   13.1   0.3      0.099   13.1   0.3    2.2  2  Fer4_8        4Fe-4S dicluster domain
        0.1   11.6   1.2        2.5    7.0   0.1    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.12   12.3   2.6        4.8    7.1   0.0    3.4  4  NTPase_1      NTPase
       0.12   11.5   0.1        1.3    8.2   0.0    2.2  2  NB-ARC        NB-ARC domain
       0.17   12.1   0.7         19    5.5   0.0    2.8  2  AAA_28        AAA domain
       0.42   10.8   3.0       0.82    9.8   3.0    1.4  1  Fer4_11       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   6.6e-18   3.1e-15      11     134 ..      96     233 ..      92     235 .. 0.75
   2 !   81.2   0.0   2.1e-25   9.5e-23       5     137 .]     355     478 ..     351     478 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 6.6e-18
                                   TSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.........EETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGei.........lldgkdlke..qeleslrkeigvlpqepqlfpeltvren. 79 
                                   g++++i+G+nG GKSt +++l+g l p+ Ge          ++ g+ + +  ++    + +++  pq   + p+  ++++ 
  gi|91773795|ref|YP_566487.1|  96 GKVTGILGPNGIGKSTSVQILSGALVPNFGEDigdwdtvleHYAGTGMYDyfKNVVDGKIKVSQKPQYVDMIPKAFNGKTr 176
                                   99*************************999984555555555555555555544444444444444444444444333336 PP

                                   ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                   ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                         +++  ++++++kl+l ++ ++++     +LSgG+ qrva+a++ +++++++++DE
  gi|91773795|ref|YP_566487.1| 177 dllegtDERGVMDELVEKLDLGHIINRNI----GELSGGELQRVAIAACAARDADFYFFDE 233
                                   77765444445************999999....***************************9 PP

  == domain 2  score: 81.2 bits;  conditional E-value: 2.1e-25
                                   EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvrenesdeei 85 
                                   s +lkege+++ivG+nG GKSt++k+lag+++p+eGe++ +  ++   + +    ++  + q  q+ + +t r+ + +   
  gi|91773795|ref|YP_566487.1| 355 SGSLKEGEVIGIVGPNGIGKSTFVKILAGEVEPDEGELESE-VSI---SYKPQYIKVDSFMQVRQFLRSIT-RRFDTSYYE 430
                                   7799*********************************9222.222...33444555555555555555553.333555556 PP

                                   HHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  86 ekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   +++++ l+l+ l d+ +    + LSgG+ qrva+a++l k+++l++lDEp+a
  gi|91773795|ref|YP_566487.1| 431 AEIIKPLQLEPLFDKML----NDLSGGELQRVAIAACLSKDADLYILDEPSA 478
                                   67888899999889999....*****************************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 ?    5.9   0.1     0.017       7.8      25      40 ..      97     112 ..      87     120 .. 0.85
   2 !   20.8   0.0   4.4e-07    0.0002     135     211 ..     206     278 ..     149     283 .. 0.84
   3 !    7.2   0.2    0.0068       3.1      26      42 ..     363     379 ..     351     382 .. 0.84
   4 !   16.4   0.0     1e-05    0.0048     136     202 ..     449     513 ..     393     527 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                                   SEEEEEESTTSSHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnl 40 
                                   ++t i+GpNG GKs  
  gi|91773795|ref|YP_566487.1|  97 KVTGILGPNGIGKSTS 112
                                   6899*********975 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4.4e-07
                                   TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                    +LSgGe + va+a      +++ a +y++Dei   LD  ++ + ++l++   k+  ++v+ ++  +l   + +v+v
  gi|91773795|ref|YP_566487.1| 206 GELSGGELQRVAIAAC----AARDADFYFFDEISPYLDIYQRINSSKLIQDLAKDKAVLVVEHDLAILDMLSDVVQV 278
                                   479****999998766....678999***********************************9998888877777776 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0068
                                   EEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                         SMC_N  26 ftaivGpNGSGKsnlld 42 
                                   +  ivGpNG GKs ++ 
  gi|91773795|ref|YP_566487.1| 363 VIGIVGPNGIGKSTFVK 379
                                   678**********9875 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 1e-05
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreeml 202
                                    LSgGe + va+a  +     k a ly+lDe  a+LD ++++   + +k+  +n     +v+ ++  m+
  gi|91773795|ref|YP_566487.1| 449 DLSGGELQRVAIAACL----SKDADLYILDEPSAHLDVEQRSLATKAIKRFAENngKTAMVVDHDIYMI 513
                                   79****9999998776....58899************************87666335566666665555 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   3.0   9.3e-15   4.3e-12       1      34 [.       1      31 [.       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 9.3e-15
                                  --EEEES---------TTHHHHHTTSEEEESS-- CS
                           RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgk 34
                                  mr+Ai ++d+C+P++C++ +c+++cp   vrtg 
  gi|91773795|ref|YP_566487.1|  1 MRIAILNKDRCQPRRCSH-ECEKYCPR--VRTGY 31
                                  9*****************.********..***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 !   10.3   0.5   0.00096      0.44       1      23 [.      98     120 ..      98     145 .. 0.80
   2 ?    4.2   0.0     0.068        31     220     271 ..     191     239 ..     164     270 .. 0.71
   3 !   15.8   0.1   2.1e-05    0.0094       2      40 ..     364     396 ..     363     405 .. 0.82
   4 !    9.6   0.0    0.0016      0.72     235     288 ..     448     498 ..     384     514 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00096
                        AAA_21   1 lnvliGpNgsGKSnLLdaldlla 23 
                                   ++++ GpNg GKS+  ++l+++ 
  gi|91773795|ref|YP_566487.1|  98 VTGILGPNGIGKSTSVQILSGAL 120
                                   699***********999998874 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.068
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLH 271
                                    v  l+ g+  ++++ elS G ++  a+++  +r++   +++++DE+   L+
  gi|91773795|ref|YP_566487.1| 191 LVEKLDLGHIINRNIGELSGGELQRVAIAACAARDA---DFYFFDEISPYLD 239
                                   4555666788889999*******9967777777766...9******976666 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.1e-05
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40 
                                    +++GpNg GKS++ ++l      +++ve++  el + +
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKIL------AGEVEPDEGELESEV 396
                                   68****************......777777777766555 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0016
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrn 288
                                   ++lS G ++  a+++ l  ++   +l+++DEp ++L+ +  +   + +k+ ++n
  gi|91773795|ref|YP_566487.1| 448 NDLSGGELQRVAIAACLSKDA---DLYILDEPSAHLDVEQRSLATKAIKRFAEN 498
                                   456999998855555555544...9*************5554444777666554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4      0.78   3.6e+02      13      19 ..      19      25 ..      18      27 .. 0.87
   2 !   30.6   3.7   4.2e-10   1.9e-07       2      23 ..      43      64 ..      42      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.78
                                  HHHHHST CS
                          Fer4 13 aCvevCP 19
                                  +C++ CP
  gi|91773795|ref|YP_566487.1| 19 ECEKYCP 25
                                  6****** PP

  == domain 2  score: 30.6 bits;  conditional E-value: 4.2e-10
                                  EEETTTSSS-THHHHHSTTTEE CS
                          Fer4  2 videekCigCGaCvevCPvgAI 23
                                  +i ee+C+gCG+Cv+ CP+ AI
  gi|91773795|ref|YP_566487.1| 43 IISEELCVGCGICVNKCPFSAI 64
                                  799******************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.054        25       9      25 ..     100     116 ..      94     135 .. 0.86
   2 !   20.7   0.0   8.7e-07    0.0004       6      99 ..     362     475 ..     357     506 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.054
                        AAA_22   9 vvtGesGtGKTtllrrl 25 
                                    + G+ G+GK+t+++ l
  gi|91773795|ref|YP_566487.1| 100 GILGPNGIGKSTSVQIL 116
                                   588**********9866 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 8.7e-07
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevv....fvtlpsstsskdllrellralglelka....erlssee 77 
                                    ++ ++G+ G+GK+t ++ l+ + + ++   e e +++     ++++ s +  +++lr + r ++ +  +    ++l++e 
  gi|91773795|ref|YP_566487.1| 362 EVIGIVGPNGIGKSTFVKILAGEVEPDEGELEsE-VSISykpqYIKVDSFMQVRQFLRSITRRFDTSYYEaeiiKPLQLEP 441
                                   56779*****************986544433342.333358999999******************99999*********** PP

                        AAA_22  78 llealeqalrarav............ielliiDE 99 
                                   l++++ + l+                  l i+DE
  gi|91773795|ref|YP_566487.1| 442 LFDKMLNDLSGGELqrvaiaaclskdADLYILDE 475
                                   **77777776665545565555555556666666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00021     0.097      50      76 ..     101     127 ..      92     134 .. 0.86
   2 !   12.6   0.0   0.00021     0.096      46      82 ..     362     398 ..     350     433 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                         Rad17  50 isGPsGCgkstvvkvLskelgiklrew 76 
                                   i GP G gkst v++Ls  l++++ e 
  gi|91773795|ref|YP_566487.1| 101 ILGPNGIGKSTSVQILSGALVPNFGED 127
                                   88*****************99988765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00021
                         Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvsl 82 
                                   +++ i GP G gkst vk+L+ e  ++  e    vs+
  gi|91773795|ref|YP_566487.1| 362 EVIGIVGPNGIGKSTFVKILAGEVEPDEGELESEVSI 398
                                   57789****************9988877666655554 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   0.00038      0.17      20      44 ..      97     121 ..      93     209 .. 0.83
   2 !   10.8   0.3    0.0011      0.51      21      37 ..     363     379 ..     347     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00038
                        AAA_23  20 gltlItGpNGaGKTTildAiklaLy 44 
                                   ++t I GpNG GK+T ++ +  aL 
  gi|91773795|ref|YP_566487.1|  97 KVTGILGPNGIGKSTSVQILSGALV 121
                                   6899***********9999988885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                        AAA_23  21 ltlItGpNGaGKTTild 37 
                                   +  I+GpNG GK+T++ 
  gi|91773795|ref|YP_566487.1| 363 VIGIVGPNGIGKSTFVK 379
                                   678***********976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.022        10      28      48 ..     100     120 ..      86     182 .. 0.86
   2 ?    0.8   0.0       1.2   5.7e+02      64     103 ..     232     270 ..     211     313 .. 0.76
   3 !   13.2   0.0   0.00018     0.085      23     141 ..     360     506 ..     351     509 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                        AAA_16  28 llsGesGvGKsslvrellral 48 
                                    + G+ G+GKs+ v+ l  al
  gi|91773795|ref|YP_566487.1| 100 GILGPNGIGKSTSVQILSGAL 120
                                   589***********8776555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                        AAA_16  64 esaipysalaqalareellrqlldeaesaeleawreklee 103
                                   ++  py+ + q +  ++l+++l+ +++   +e++ + +++
  gi|91773795|ref|YP_566487.1| 232 DEISPYLDIYQRINSSKLIQDLAKDKAVLVVEHDLA-ILD 270
                                   33489999**************99966644444444.444 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00018
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekd........................ggiflrgkcdqlesaipy.sa.laqala 77 
                                   ++e++ ++G+ G+GKs+ v+ l+ ++e d                           flr  ++++  +++y  a +++ l 
  gi|91773795|ref|YP_566487.1| 360 EGEVIGIVGPNGIGKSTFVKILAGEVEPDegelesevsisykpqyikvdsfmqVRQFLRSITRRF--DTSYyEAeIIKPLQ 438
                                   348899******************99999888877776666666555555553233333333333..23344334677666 PP

                        AAA_16  78 reellrqlldeaesaeleawrekleeala..........avpelagaeasrllellkrllallsrderplvlvl 141
                                    e l+ ++l++++  el++   ++ + l+          ++++l+ +++s    ++kr++   +++++ + +v+
  gi|91773795|ref|YP_566487.1| 439 LEPLFDKMLNDLSGGELQRV--AIAACLSkdadlyildePSAHLDVEQRSLATKAIKRFA---ENNGK-TAMVV 506
                                   77777777777444444333..33333335566766655555555554444444444444...44343.55555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.8      0.15        68       5      20 ..       7      25 ..       6      32 .. 0.85
   2 !   22.3   2.6   2.1e-07   9.5e-05       2      24 .]      42      64 ..      41      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.15
                        Fer4_6  5 dpdkCi..gCgd.CvrvCP 20
                                  ++d+C    C   C++ CP
  gi|91773795|ref|YP_566487.1|  7 NKDRCQprRCSHeCEKYCP 25
                                  689999777*777*****9 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 2.1e-07
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  + i +++C+gCg Cv+ CP+ ai
  gi|91773795|ref|YP_566487.1| 42 AIISEELCVGCGICVNKCPFSAI 64
                                  56889***************998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.016       7.4      99     122 ..      96     119 ..      87     130 .. 0.85
   2 !   13.5   0.0   0.00011     0.049      96     131 ..     357     393 ..     329     398 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                                   TSEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                   +k++ ++G+ G+GKSt +  l + 
  gi|91773795|ref|YP_566487.1|  96 GKVTGILGPNGIGKSTSVQILSGA 119
                                   588999**********99988876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00011
                                   HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                    lk+ +++ +vG+ G+GKSt+++ l++e e   ge+ 
  gi|91773795|ref|YP_566487.1| 357 SLKEgEVIGIVGPNGIGKSTFVKILAGEVEPDEGELE 393
                                   455558999******************9887777665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0      0.01       4.7       3      27 ..     101     125 ..     100     154 .. 0.80
   2 !   11.8   0.0   0.00053      0.24       3      25 ..     366     388 ..     364     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkklk 27 
                                   + Gp+g+GKSt ++ L+ al  +++
  gi|91773795|ref|YP_566487.1| 101 ILGPNGIGKSTSVQILSGALVPNFG 125
                                   67*************9999886664 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00053
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkk 25 
                                   ++Gp+g+GKSt++k La +++ +
  gi|91773795|ref|YP_566487.1| 366 IVGPNGIGKSTFVKILAGEVEPD 388
                                   89**************9998833 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   6.8     7e-07   0.00032       3      57 ..       6      64 ..       4      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7e-07
                       Fer4_21  3 idedkCi..gCg.kCliaCed..tshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                  +++d+C    C  +C + C+   t+++ i + ++ ++ + e+ CvGC +C++ CP   +i
  gi|91773795|ref|YP_566487.1|  6 LNKDRCQprRCShECEKYCPRvrTGYETIVFGDDGKAIISEELCVGCGICVNKCPF-SAI 64
                                  5666663224532588888744489******99999999****************7.554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0089       4.1       5      28 ..      99     121 ..      96     150 .. 0.84
   2 !   11.5   0.0   0.00038      0.18       4      22 ..     363     381 ..     360     434 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0089
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplf 28 
                                     i Gp+giGK+t++  l   +l+
  gi|91773795|ref|YP_566487.1|  99 TGILGPNGIGKSTSVQIL-SGALV 121
                                   6799*********99887.55555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00038
                        AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                    i i+Gp+giGK+t++k l
  gi|91773795|ref|YP_566487.1| 363 VIGIVGPNGIGKSTFVKIL 381
                                   689*************988 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3  12.1    0.0003      0.14       2      56 .]       4      60 ..       3      60 .. 0.80
   2 !   17.7   1.0   6.1e-06    0.0028       2      24 ..      42      68 ..      41      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
                       Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +++++d+C   rC  +C k CP   t+++++ + ++++a+    e C gcg Cv +CP
  gi|91773795|ref|YP_566487.1|  4 AILNKDRCqpRRCShECEKYCPRVRTGYETIVFGDDGKAIIS-EELCVGCGICVNKCP 60
                                  57899***7779*99********6677777777666665544.688***********9 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 6.1e-06
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl....t 24
                                  ++i ++ C++Cg Cv+ CP+++     
  gi|91773795|ref|YP_566487.1| 42 AIISEELCVGCGICVNKCPFSAimiiG 68
                                  78999**************96544440 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.038        17      23      43 ..      97     116 ..      94     123 .. 0.89
   2 !    9.6   0.4    0.0015      0.67      25      43 ..     363     381 ..     355     384 .. 0.87
   3 ?    3.6   0.0     0.098        45     322     368 ..     466     512 ..     459     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                        AAA_15  23 eeltvliGkNnsGKSsileal 43 
                                   + +t + G+N++GKS+ +++l
  gi|91773795|ref|YP_566487.1|  97 K-VTGILGPNGIGKSTSVQIL 116
                                   5.78899*********99998 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                        AAA_15  25 ltvliGkNnsGKSsileal 43 
                                   +  ++G+N++GKS+++++l
  gi|91773795|ref|YP_566487.1| 363 VIGIVGPNGIGKSTFVKIL 381
                                   6669*************98 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.098
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                   ++ ++++++EP ahL  ++ +   k++k+ a++n +  ++  H  ++
  gi|91773795|ref|YP_566487.1| 466 KDADLYILDEPSAHLDVEQRSLATKAIKRFAENNGKTAMVVDHDIYM 512
                                   6789*****************************98766666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.3    0.0016      0.74      23      48 ..      96     122 ..      89     125 .. 0.80
   2 !    9.6   0.2    0.0016      0.73      24      39 ..     363     378 ..     352     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                        AAA_29  23 g.atlltGpsGsGKSTllDAiqalLvp 48 
                                   g +t + Gp+G GKST +  ++  Lvp
  gi|91773795|ref|YP_566487.1|  96 GkVTGILGPNGIGKSTSVQILSGALVP 122
                                   44788***********98777777777 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                        AAA_29  24 atlltGpsGsGKSTll 39 
                                   ++ ++Gp+G GKST++
  gi|91773795|ref|YP_566487.1| 363 VIGIVGPNGIGKSTFV 378
                                   7779**********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 !   18.3   7.5   4.1e-06    0.0019       6      51 .]      14      64 ..       9      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.1e-06
                        Fer4_9  6 gaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkgai 51
                                  ++C + C++   + + + +++    +++     e C+gCg Cv++Cp  ai
  gi|91773795|ref|YP_566487.1| 14 RRCSHECEKYCPRVRTGYETIVFGDDGKaiiseELCVGCGICVNKCPFSAI 64
                                  3688888888888888888888777766788889*************8876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.0      0.42   1.9e+02       5      21 ..       6      25 ..       2      26 .. 0.77
   2 !   19.1   1.2   2.2e-06     0.001       4      21 ..      43      60 ..      40      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.42
                        Fer4_2  5 vdtdrC.i.gCg.aCvsaCP 21
                                   + drC   +C+  C + CP
  gi|91773795|ref|YP_566487.1|  6 LNKDRCqPrRCShECEKYCP 25
                                  68899974379779*****9 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.2e-06
                        Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                   + ++ C+gCg+Cv+ CP
  gi|91773795|ref|YP_566487.1| 43 IISEELCVGCGICVNKCP 60
                                  56799************* PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0       0.2        92       4      22 ..     102     120 ..     100     150 .. 0.86
   2 !   11.0   0.0   0.00095      0.44       3      23 ..     366     386 ..     364     431 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.2
                                   ESSTTSSHHHHHHHHHHHH CS
                           AAA   4 yGppGtGKTllakavakel 22 
                                    Gp G+GK++ ++ +   l
  gi|91773795|ref|YP_566487.1| 102 LGPNGIGKSTSVQILSGAL 120
                                   7**********99987765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00095
                                   EESSTTSSHHHHHHHHHHHHT CS
                           AAA   3 lyGppGtGKTllakavakelg 23 
                                   ++Gp G+GK++++k +a e++
  gi|91773795|ref|YP_566487.1| 366 IVGPNGIGKSTFVKILAGEVE 386
                                   68****************974 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   3.5       3.3   1.5e+03      35      49 ..       8      25 ..       2      27 .. 0.71
   2 !    9.8  12.8    0.0025       1.2       5      52 .]      16      63 ..      10      63 .. 0.70
   3 !   17.3   1.6   1.2e-05    0.0055       2      19 ..      49      66 ..      48      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.3
                        Fer4_7 35 pekCl..gCga.CvavCP 49
                                   ++C+   C + C++ CP
  gi|91773795|ref|YP_566487.1|  8 KDRCQprRCSHeCEKYCP 25
                                  677764467777999999 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0025
                        Fer4_7  5 C.gaCvaaCp.....vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  C + C+++Cp     +++i + +        k+ i++e C+gCg Cv+ CP+ a
  gi|91773795|ref|YP_566487.1| 16 CsHECEKYCPrvrtgYETIVFGD------DGKAIISEELCVGCGICVNKCPFSA 63
                                  53489999994332233333322......358999****************976 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 1.2e-05
                        Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                  C+gCg Cv+ Cp +ai++
  gi|91773795|ref|YP_566487.1| 49 CVGCGICVNKCPFSAIMI 66
                                  **************9986 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0084       3.8       4      39 ..     102     136 ..     100     161 .. 0.85
   2 ?    5.9   0.0     0.022        10       1      23 [.     364     386 ..     364     439 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0084
                                   EESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSS CS
                           dNK   4 eGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqk 39 
                                    G+ g GKst v++Ls +l v+ f E + +w  v +
  gi|91773795|ref|YP_566487.1| 102 LGPNGIGKSTSVQILSGAL-VPNFGEDIGDWDTVLE 136
                                   58889**************.***********66554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                                   EEEEESTTSSHHHHHHHHHCCST CS
                           dNK   1 ivveGnIgaGKstlvklLskklg 23 
                                   i + G+ g GKst+vk+L+ +++
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKILAGEVE 386
                                   5688999***********98765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.85   3.9e+02      33      53 ..      96     116 ..      94     127 .. 0.82
   2 ?    2.4   0.1      0.22     1e+02      80     155 ..     207     276 ..     205     279 .. 0.73
   3 !    7.3   0.0    0.0068       3.1      28      54 ..     356     382 ..     354     406 .. 0.87
   4 ?   -0.8   0.0       2.1   9.6e+02     143     188 ..     468     508 ..     439     509 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.85
                        AAA_25  33 gelallaGapgtGKttlaldl 53 
                                   g+++ + G+ g GK+t +  l
  gi|91773795|ref|YP_566487.1|  96 GKVTGILGPNGIGKSTSVQIL 116
                                   6677889*********87655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                        AAA_25  80 EdsedelrrRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsral 155
                                   E s  el+r + a+++a+  da+ ++ d       l++++ ++ ++l++   ++ +  + e    +l ++D+ls ++
  gi|91773795|ref|YP_566487.1| 207 ELSGGELQRVAIAACAAR--DADFYFFDE--IsPYLDIYQRINSSKLIQDLAKDKAVLVVE---HDLAILDMLSDVV 276
                                   667789999999999996..455555553..225699999999999997776665555555...5999****99876 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0068
                        AAA_25  28 gllpagelallaGapgtGKttlaldla 54 
                                   g l +ge++ ++G+ g GK+t++  la
  gi|91773795|ref|YP_566487.1| 356 GSLKEGEVIGIVGPNGIGKSTFVKILA 382
                                   56889****************987666 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.1
                        AAA_25 143 vrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                   ++l ++D  s+ l+ +       + + +a++r+a++ g + ++v H
  gi|91773795|ref|YP_566487.1| 468 ADLYILDEPSAHLDVEQR-----SLATKAIKRFAENNGKTAMVVDH 508
                                   444444444433322222.....33445566666666666666666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3      0.14        63       5      20 ..     101     116 ..      97     121 .. 0.82
   2 ?    9.5   0.0    0.0019      0.86       2      25 ..     363     386 ..     362     420 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                                   EEC-TTTCHHHHHHHH CS
                         NACHT   5 lqGeaGsGKTtLlqkl 20 
                                   + G++G+GK+t +q l
  gi|91773795|ref|YP_566487.1| 101 ILGPNGIGKSTSVQIL 116
                                   89*********99866 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0019
                                   CEEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawa 25 
                                   ++ + G++G+GK+t+++ la +  
  gi|91773795|ref|YP_566487.1| 363 VIGIVGPNGIGKSTFVKILAGEVE 386
                                   56799************9987765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.11        49       3      25 ..     101     132 ..     100     195 .. 0.76
   2 ?    6.9   0.0      0.02         9       1      20 [.     364     383 ..     364     425 .. 0.85
   3 ?    0.2   0.0       2.2     1e+03      33     118 ..     466     573 ..     442     583 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                        AAA_18   3 ltGtpGvGKttlakeLskrl.gf........g 25 
                                   + G+ G GK+t  + Ls  l  +         
  gi|91773795|ref|YP_566487.1| 101 ILGPNGIGKSTSVQILSGALvPNfgedigdwD 132
                                   89**************9888644544444432 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.02
                        AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                                   I++ G+ G GK+t+ k L+ 
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKILAG 383
                                   89***************964 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.2
                        AAA_18  33 kenglllevdpealdeskrldedkldklldaleenss.............aleegknlvidghlaeleseaakdikk.... 96 
                                   k+ +l++ ++p      +++++    k+++ + en+              ++ ++  +v++g +a +  +           
  gi|91773795|ref|YP_566487.1| 466 KDADLYILDEPS--AHLDVEQRSLATKAIKRFAENNGktamvvdhdiymiDMLSERLIVFEGEPAVFGIAHPPSSMQkgmn 544
                                   566666666666..6666666667777777777777777655555555554445555555555544443333322224556 PP

                        AAA_18  97 .......vvLtaspeelleRlekRgyeea 118
                                          +  + ++e+ + R++k + + +
  gi|91773795|ref|YP_566487.1| 545 kflsdlgITFRRDEETIRPRVNKKDSRLD 573
                                   66777777777777777777777765554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.047        22       4      23 ..     101     120 ..     100     127 .. 0.87
   2 ?   -1.2   0.0       4.2   1.9e+03      51      75 ..     212     235 ..     200     244 .. 0.75
   3 ?    5.5   0.0     0.035        16       4      22 ..     366     384 ..     364     445 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.047
                                   EE--SSSSHHHHHHHGGGGB CS
                         AAA_5   4 LvGppGtgKselaerlaaal 23 
                                   ++Gp G+gKs+ ++ l+ al
  gi|91773795|ref|YP_566487.1| 101 ILGPNGIGKSTSVQILSGAL 120
                                   58**************9998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.2
                                   ......--------G-SEEEEESGG CS
                         AAA_5  51 ttslvdsplvraaregeilvlDEve 75 
                                   + ++v  ++  aar ++ +++DE+ 
  gi|91773795|ref|YP_566487.1| 212 ELQRVAIAAC-AARDADFYFFDEIS 235
                                   4455555555.999*********96 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.035
                                   EE--SSSSHHHHHHHGGGG CS
                         AAA_5   4 LvGppGtgKselaerlaaa 22 
                                   +vGp G+gKs++++ la  
  gi|91773795|ref|YP_566487.1| 366 IVGPNGIGKSTFVKILAGE 384
                                   69***********999865 PP

>> AAA_14  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        67       3      21 ..      97     115 ..      95     126 .. 0.83
   2 ?    0.4   0.0       1.4   6.2e+02      64      85 ..     225     246 ..     189     260 .. 0.80
   3 ?    7.6   0.1    0.0079       3.6       3      27 ..     362     386 ..     360     506 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                        AAA_14   3 kilvitGaRrvGKTtllkq 21 
                                   k+  i G+  +GK+t ++ 
  gi|91773795|ref|YP_566487.1|  97 KVTGILGPNGIGKSTSVQI 115
                                   7899***********9864 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.4
                        AAA_14  64 kktylflDEiqevpewekalks 85 
                                   +  + f+DEi+ + ++++ ++s
  gi|91773795|ref|YP_566487.1| 225 DADFYFFDEISPYLDIYQRINS 246
                                   56789*****999888777765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0079
                        AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                   +++ i+G+  +GK+t++k l+ e  
  gi|91773795|ref|YP_566487.1| 362 EVIGIVGPNGIGKSTFVKILAGEVE 386
                                   7899*************99987655 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.07        32      50      75 ..      94     119 ..      87     136 .. 0.81
   2 ?    7.4   0.0    0.0072       3.3      49      75 ..     358     384 ..     340     395 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.07
                          VirE  50 KfDfvlvLvGkqgsgKstfleklgee 75 
                                   ++  v+ + G+ g+gKst++++l+++
  gi|91773795|ref|YP_566487.1|  94 QVGKVTGILGPNGIGKSTSVQILSGA 119
                                   566788899**************776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                          VirE  49 iKfDfvlvLvGkqgsgKstfleklgee 75 
                                    K  +v+ +vG+ g+gKstf+++l++e
  gi|91773795|ref|YP_566487.1| 358 LKEGEVIGIVGPNGIGKSTFVKILAGE 384
                                   57778999****************654 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.029        13      26      48 ..     201     223 ..     188     230 .. 0.83
   2 ?    4.7   0.0      0.08        37      25      82 ..     442     486 ..     421     494 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.029
                       SbcCD_C  26 lsrssgtlSGGekqflaylalaa 48 
                                   ++r++g+lSGGe q +a  a aa
  gi|91773795|ref|YP_566487.1| 201 INRNIGELSGGELQRVAIAACAA 223
                                   6799*********8887776665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.08
                       SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesia 82 
                                    ++++ + lSGGe q +a  a        +s+      + +l +LDE  + lD e ++
  gi|91773795|ref|YP_566487.1| 442 LFDKMLNDLSGGELQRVAIAA-------CLSK------DADLYILDEPSAHLDVEQRS 486
                                   577888899999996543332.......2222......23556666666666666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.49   2.2e+02       5      17 ..     102     114 ..      98     123 .. 0.82
   2 ?    8.8   0.0    0.0036       1.7       2      20 ..     364     382 ..     363     394 .. 0.86
   3 ?   -1.1   0.0       4.1   1.9e+03     102     123 ..     552     573 ..     540     581 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.49
                        AAA_33   5 vGlpGsGKstlae 17 
                                    G++G GKst ++
  gi|91773795|ref|YP_566487.1| 102 LGPNGIGKSTSVQ 114
                                   6*********887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                        AAA_33   2 vllvGlpGsGKstlaerll 20 
                                   + +vG++G GKst+++ l+
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKILA 382
                                   6689***********9876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.1
                        AAA_33 102 vvvetdeetlkeRlakRaangd 123
                                   ++++ deet++ R+ k+  + d
  gi|91773795|ref|YP_566487.1| 552 ITFRRDEETIRPRVNKKDSRLD 573
                                   678899*******999987544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.69   3.2e+02       3      22 ..     100     119 ..      98     134 .. 0.85
   2 ?    9.5   0.1    0.0021      0.98       2      22 ..     364     384 ..     363     514 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.69
                                   EEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                   +i+G    GKSt ++ l+g+
  gi|91773795|ref|YP_566487.1| 100 GILGPNGIGKSTSVQILSGA 119
                                   799*********99988876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0021
                                   EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                   ++ivG    GKSt+++ l ge
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKILAGE 384
                                   89****************996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.5      0.18        84       1      15 [.       8      25 ..       8      35 .. 0.85
   2 ?   14.2   1.9    0.0001     0.048       2      16 ..      47      61 ..      46      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.18
                        Fer4_4  1 qerCi..gCg.sCvaaCP 15
                                  ++rC+  +C   C+ +CP
  gi|91773795|ref|YP_566487.1|  8 KDRCQprRCShECEKYCP 25
                                  689966699988****** PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.0001
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  e C+gCg Cv+ CP+
  gi|91773795|ref|YP_566487.1| 47 ELCVGCGICVNKCPF 61
                                  67************6 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.05        23      26      48 ..      99     121 ..      94     128 .. 0.85
   2 ?    5.3   0.0     0.039        18      26      44 ..     364     382 ..     362     387 .. 0.89
   3 ?   -2.2   0.0       7.9   3.6e+03     137     181 ..     437     501 ..     413     522 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.05
                         DUF87  26 lAilgsTGsGKSntvavLleell 48 
                                   ++ilg  G GKS+ v +L   l+
  gi|91773795|ref|YP_566487.1|  99 TGILGPNGIGKSTSVQILSGALV 121
                                   79**************9976665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.039
                         DUF87  26 lAilgsTGsGKSntvavLl 44 
                                   ++i+g  G GKS++v++L 
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKILA 382
                                   6899************996 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.9
                         DUF87 137 lssdepveklleelk....................kekeelrklknqaiarlldkledllrkggs 181
                                   l+ + ++ k+l++l                     + +e++ +l+ ++++   ++++++ +++g+
  gi|91773795|ref|YP_566487.1| 437 LQLEPLFDKMLNDLSggelqrvaiaaclskdadlyILDEPSAHLDVEQRSLATKAIKRFAENNGK 501
                                   55566666666666633333333333333333333333333333333333333344444333333 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.6       3.5   1.6e+03      10      62 ..      19      25 ..       9      42 .. 0.67
   2 ?   13.1   0.3   0.00022     0.099       5      18 ..      49      62 ..      45      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.5
                        Fer4_8 10 aCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62
                                                                                 C++ Cp
  gi|91773795|ref|YP_566487.1| 19 E----------------------------------------------CEKYCP 25
                                  3..............................................444444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00022
                        Fer4_8  5 CieCgaCqsaCpvl 18
                                  C++Cg C ++Cp+ 
  gi|91773795|ref|YP_566487.1| 49 CVGCGICVNKCPFS 62
                                  999********964 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.082        38      30      53 ..      97     120 ..      90     128 .. 0.84
   2 ?    7.0   0.1    0.0054       2.5      29      52 ..     361     384 ..     351     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.082
                                   EEEEEEE-TTSSHHHHHHHHHHHH CS
                          MeaB  30 qvvGltGvPGaGkstlvealglel 53 
                                   +v G+ G  G Gkst v+ l   l
  gi|91773795|ref|YP_566487.1|  97 KVTGILGPNGIGKSTSVQILSGAL 120
                                   57899************9987766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0054
                                   SEEEEEEE-TTSSHHHHHHHHHHH CS
                          MeaB  29 aqvvGltGvPGaGkstlvealgle 52 
                                    +v+G+ G  G Gkst+v+ l+ e
  gi|91773795|ref|YP_566487.1| 361 GEVIGIVGPNGIGKSTFVKILAGE 384
                                   579***************988755 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.17        80       4      23 ..     101     120 ..      98     124 .. 0.84
   2 ?   -1.4   0.0       4.1   1.9e+03      84     134 ..     216     265 ..     209     278 .. 0.64
   3 ?    7.1   0.0      0.01       4.8       2      23 ..     364     385 ..     363     392 .. 0.85
   4 ?   -2.2   0.0       7.1   3.3e+03      85     103 ..     459     475 ..     449     513 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                                   EE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   4 iTGppGvGKtTlvkkvlell 23 
                                   i Gp G+GK+T v+ ++ +l
  gi|91773795|ref|YP_566487.1| 101 ILGPNGIGKSTSVQILSGAL 120
                                   669*********99887766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.1
                                   HHHHHHHHHHHHH-EEEE---ST.TGGG-HHHHHHHHHHHTTTSEEEEE--S CS
                      NTPase_1  84 lalealrkalseadviviDEiGk.mElkskkfkeaveevLksekpvlavihr 134
                                   +a++a   a ++ad +  DEi + +    +  ++++ + L+++k vl+v h 
  gi|91773795|ref|YP_566487.1| 216 VAIAAC--AARDADFYFFDEISPyLDIYQRINSSKLIQDLAKDKAVLVVEHD 265
                                   444444..55889999999998734444444455677777777777777665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.01
                                   EEEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                   + i Gp G+GK+T+vk ++ ++
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKILAGEV 385
                                   6799***********9887766 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 7.1
                                   HHHHHHHHHHHH-EEEE-- CS
                      NTPase_1  85 alealrkalseadviviDE 103
                                   a++a     ++ad++++DE
  gi|91773795|ref|YP_566487.1| 459 AIAACL--SKDADLYILDE 475
                                   444443..37889999998 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.56   2.6e+02      22      36 ..      98     112 ..      91     127 .. 0.85
   2 ?    8.2   0.0    0.0028       1.3      21      58 ..     362     406 ..     355     475 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.56
                                   EEEEEESTTSSHHHH CS
                        NB-ARC  22 vvalvGmgGvGKttl 36 
                                   v ++ G  G+GK+t 
  gi|91773795|ref|YP_566487.1|  98 VTGILGPNGIGKSTS 112
                                   6799*********94 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0028
                                   EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE.......E CS
                        NB-ARC  21 lvvalvGmgGvGKttlakqilnksdevegrFdsvawv.......v 58 
                                    v+++vG  G+GK+t +k    + +  eg+ +s + +        
  gi|91773795|ref|YP_566487.1| 362 EVIGIVGPNGIGKSTFVKILAGEVEPDEGELESEVSIsykpqyiK 406
                                   399************988766665555556655555544444442 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.11        50       4      21 ..     101     118 ..      99     141 .. 0.82
   2 ?    5.5   0.0     0.041        19       2      20 ..     364     382 ..     363     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                        AAA_28   4 itGgestGKTtlleaLaa 21 
                                   i+G+ + GK+t ++ L+ 
  gi|91773795|ref|YP_566487.1| 101 ILGPNGIGKSTSVQILSG 118
                                   89************9984 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.041
                        AAA_28   2 ivitGgestGKTtlleaLa 20 
                                   i i+G+ + GK+t ++ La
  gi|91773795|ref|YP_566487.1| 364 IGIVGPNGIGKSTFVKILA 382
                                   5699*************99 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.0    0.0018      0.82       6      59 ..      12      64 ..       9      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                       Fer4_11  6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykiv 59
                                   p+ C h  e+ C ++   +  +   ++G  ++ e+ +  ++  +v+ cP++++
  gi|91773795|ref|YP_566487.1| 12 QPRRCSHECEKYCPRVRTGYETIVFGDDGKAIISEELCV-GCGICVNKCPFSAI 64
                                  699****99*******99998888889***********7.***********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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):              39  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 3944.22
//
Query:       gi|91773796|ref|YP_566488.1|  [L=96]
Description: hypothetical protein Mbur_1855 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        4.2    6.9   6.1        6.1    6.3   6.1    1.3  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 ?    6.3   6.1   0.00034       6.1       7      48 ..       3      46 ..       1      50 [. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00034
                                  HHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHH..HHHCHHHHH CS
                    MS_channel  7 liivvgilivlsllgvnvsallavlGalglalg..lalkdlisn 48
                                  +ii+  + ++  +l vn s+l+a+l +lg+ lg  l++ ++  +
  gi|91773796|ref|YP_566488.1|  3 VIIFGLLSTIVLYLLVNYSSLVAGLVLLGIPLGtmLVSPNIATG 46
                                  5666667789999****************988622555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 661.22
//
Query:       gi|91773797|ref|YP_566489.1|  [L=600]
Description: hypothetical protein Mbur_1856 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-10   39.5   0.3    3.2e-05   24.1   0.0    3.3  3  DUF11      Domain of unknown function DUF11
    1.9e-06   27.0   2.8     0.0015   17.4   0.4    2.8  2  BatD       Oxygen tolerance
    1.3e-05   25.4   2.3       0.16   12.2   0.0    3.9  4  CARDB      CARDB
    9.9e-05   22.5   0.2        0.9    9.7   0.0    3.7  3  bMG10      Bacterial Alpha-2-macroglobulin MG10 domain
     0.0016   17.8   1.1       0.03   13.7   0.2    2.9  3  TRAP_beta  Translocon-associated protein beta (TRAPB)
  ------ inclusion threshold ------
      0.012   15.8   0.7         23    5.2   0.0    4.0  2  Top6b_C    Type 2 DNA topoisomerase 6 subunit B C-terminal do
       0.13   13.3   0.5         74    4.5   0.0    3.5  4  CS         CS domain
       0.17   12.2   1.6       0.19   12.0   0.0    1.9  2  Orf78      Orf78 (ac78)
       0.32    9.7   3.0        8.4    5.0   0.2    2.4  3  Gryzun     Gryzun, putative trafficking through Golgi
        8.8    6.1   8.1         10    5.8   1.3    2.3  2  DUF4750    Domain of unknown function (DUF4750)


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 ?    5.1   0.5     0.016        28      12      37 ..     226     251 ..     220     314 .. 0.77
   2 !    6.2   0.0    0.0069        12      18      82 ..     343     399 ..     323     407 .. 0.79
   3 !   24.1   0.0   1.8e-08   3.2e-05       1      88 [.     436     515 ..     436     518 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                         DUF11  12 pGdtvtytltvtNtgpasangvvvtD 37 
                                   p ++ ++++ v+N g+ +a g++vt 
  gi|91773797|ref|YP_566489.1| 226 PNEEPVFNILVKNEGTIPARGMTVTS 251
                                   567889*****************996 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0069
                         DUF11  18 ytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrta 82 
                                   +tl   N+      +v+v+D+ P+++  v   ++      ++++  +  g+s+t++++v++t+ +
  gi|91773797|ref|YP_566489.1| 343 FTLLIFNNASIGH-EVTVNDPIPPSFLPVDIAST------QWNF-FIGSGKSKTITYSVIPTAPG 399
                                   6777777766666.9**********999998888......5554.66789999999999988765 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 1.8e-08
                         DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrt 81 
                                   + K v+ +++  G++v+ t+  +N g+++a +v  t   P+g+++vs++ s       +  g +  ge+ ++ +t+ ++ +
  gi|91773797|ref|YP_566489.1| 436 VEKDVSLTDIYTGEEVDITINIRNVGTRDA-TVSFTENIPTGFEFVSGQRS-------WE-GHIGVGEEEQIVYTMFAKEE 507
                                   578999999*********************.********************.......33.78889999999999999988 PP

                         DUF11  82 aasga.lt 88 
                                   a+ ++ +t
  gi|91773797|ref|YP_566489.1| 508 ATYELpVT 515
                                   87665555 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   8.3e-07    0.0015      59     152 ..     374     457 ..     362     466 .. 0.88
   2 !   15.7   0.3   2.9e-06    0.0052      13     115 ..     437     545 ..     434     597 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.3e-07
                          BatD  59 ssstqiinGkssssssktwtytLapkkeGtltIpaatievdgktyksnpitikVlkseasqsssaisdedlflraevskks 139
                                   s++++++ G  +s   kt+ty+++p+ +G+++I +a +     +  s+  t  V  +++++ + ++++  l ++ +vs + 
  gi|91773797|ref|YP_566489.1| 374 STQWNFFIGSGKS---KTITYSVIPTAPGNFEILPAFA-----NWYSQGETYSV--NSEESGEITVNGTMLEVEKDVSLTD 444
                                   5677666666666...579****************999.....88899999999..7789999999999************ PP

                          BatD 140 vYvqeqvlvtlkl 152
                                   +Y +e v +t+ +
  gi|91773797|ref|YP_566489.1| 445 IYTGEEVDITINI 457
                                   *******999987 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.9e-06
                          BatD  13 tasvdknevevgetfrLtftvngasgepdfsap...slekdfevlsgsqssstqiinGkssssssktwtytLapkkeGtlt 90 
                                   +  v+ + + +ge++ +t+ + +  g  d +++   +++++fe++sg++s   +i  G+ +     ++ yt+ +k+e t++
  gi|91773797|ref|YP_566489.1| 437 EKDVSLTDIYTGEEVDITINIRNV-GTRDATVSfteNIPTGFEFVSGQRSWEGHIGVGEEE-----QIVYTMFAKEEATYE 511
                                   567888999*************99.555555442246777*****9985555544444433.....39************* PP

                          BatD  91 Ipaatievd.....gktyksnpitikVlk....s 115
                                   +p  ++ ++     ++t +s+p+++ V +    +
  gi|91773797|ref|YP_566489.1| 512 LPVTKVAFEdesgtKGTFESKPMRLYVYSfgpiD 545
                                   ******9852222246788999999887666542 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.95   1.7e+03      34      68 ..      70     105 ..      66     128 .. 0.63
   2 !    9.6   0.2   0.00059       1.1      13      85 ..     222     298 ..     210     309 .. 0.79
   3 ?   -1.6   0.0       1.8   3.3e+03      58      79 ..     382     402 ..     380     408 .. 0.83
   4 !   12.2   0.0     9e-05      0.16       4      40 ..     434     470 ..     432     516 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.95
                                   -EEEEEEEEEETTEEEEEEEE.SEE-CTEEEEEEEE CS
                         CARDB  34 asgatkvalyldgelvgtvtv.psLaagesttvsft 68 
                                   ++++ +v +y+dge ++t+   + L+++  ++++++
  gi|91773797|ref|YP_566489.1|  70 SEYSATVLFYVDGEFKETFFAdADLNNEFLYDENLK 105
                                   567889999999999866544455555555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00059
                                   SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEES CS
                         CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLaagesttvsftwtte..ategevtltvvvD 85 
                                    + f++ee  +++ vkN+Gt+ ++ ++v+  +   +   +++++p L+ +++    +  t++   t  +v+++v v+
  gi|91773797|ref|YP_566489.1| 222 MTYFPNEEPVFNILVKNEGTIPARGMTVTSSATNAQIetDSFEIPILDTSNYQITPVILTIPetPTGTDVEISVLVE 298
                                   5678899999***************999999888887789999****999999888888888433445555666665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.8
                                   -CTEEEEEEEEEE-S-S-CEEE CS
                         CARDB  58 aagesttvsftwtteategevt 79 
                                    +g+s+t+++++ ++ ++g+ +
  gi|91773797|ref|YP_566489.1| 382 GSGKSKTITYSVIPT-APGNFE 402
                                   689999999999998.999877 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 9e-05
                                   EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                         CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkv 40 
                                   L+v++ ++ ++ ++gee+ it++++N Gt +++ + +
  gi|91773797|ref|YP_566489.1| 434 LEVEKDVSLTDIYTGEEVDITINIRNVGTRDATVSFT 470
                                   7888999999********************9875544 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 ?    1.9   0.0      0.14   2.4e+02      38      61 ..     351     374 ..     323     379 .. 0.73
   2 !    6.1   0.0    0.0065        12     101     123 ..     386     408 ..     375     411 .. 0.88
   3 !    9.7   0.0    0.0005       0.9      15      89 ..     439     507 ..     427     537 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.14
                         bMG10  38 prdleyvaledplPAGlepvnpsl 61 
                                    +  ++v ++dp+P  + pv+ ++
  gi|91773797|ref|YP_566489.1| 351 ASIGHEVTVNDPIPPSFLPVDIAS 374
                                   334499**************9776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0065
                         bMG10 101 tytfeylvravtpGtfsvppaka 123
                                   + t++y v  ++pG+f + pa a
  gi|91773797|ref|YP_566489.1| 386 SKTITYSVIPTAPGNFEILPAFA 408
                                   5789*****************87 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0005
                         bMG10  15 evsksdaklkvGdkvrvrltvt.tprdleyvaledplPAGlepvnpslgtesesaeeyewleeltefsyreirddr 89 
                                   +vs +   + +G++v ++++++ + ++   v   + +P G+e v  + + e   + ++e      ++ y+ + +++
  gi|91773797|ref|YP_566489.1| 439 DVSLT--DIYTGEEVDITINIRnVGTRDATVSFTENIPTGFEFVSGQRSWEGHIGVGEE-----EQIVYTMFAKEE 507
                                   23333..699************55666699************99876665555555554.....344444444444 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 ?   -3.7   0.0       3.6   6.5e+03      27      53 ..     118     144 ..     117     146 .. 0.77
   2 ?    1.5   0.0     0.097   1.7e+02      83     110 ..     384     411 ..     372     431 .. 0.76
   3 !   13.7   0.2   1.7e-05      0.03      19     147 ..     433     561 ..     416     597 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.6
                     TRAP_beta  27 lnrllvegedltveytiyNvGssaAld 53 
                                   l+++  e e + +   i+N+G  + ++
  gi|91773797|ref|YP_566489.1| 118 LEMYIHEYELVWIPERIINIGVGESYE 144
                                   5677777777888889*****988876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.097
                     TRAP_beta  83 genvshsfvvepkksgsfngtaavvtYr 110
                                   g++ + ++ v+p+++g+f++ +a  ++ 
  gi|91773797|ref|YP_566489.1| 384 GKSKTITYSVIPTAPGNFEILPAFANWY 411
                                   666677899*************998873 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 1.7e-05
                     TRAP_beta  19 rvlvkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepkksgs 99 
                                   ++ v+K +       ge++ ++++i NvG+  A+ Vs++++   +  Fe+vsg+ s +   +  ge+ + ++++ +k +  
  gi|91773797|ref|YP_566489.1| 433 MLEVEKDVSLTDIYTGEEVDITINIRNVGTRDAT-VSFTENI--PTGFEFVSGQRSWE-GHIGVGEEEQIVYTMFAKEEAT 509
                                   5566777766667789****************97.****983..678******98755.3799999999999999999999 PP

                     TRAP_beta 100 fngtaavvtYresekgaelqlalssepgegdilaerevekkfslh.......led 147
                                   ++   + v +++ e+g++    + s+p+ +++ +  +++   + +       +++
  gi|91773797|ref|YP_566489.1| 510 YELPVTKVAFED-ESGTK--GTFESKPMRLYVYSFGPIDSSKDQGieyqpltMKE 561
                                   999999999933.33233..22335555555444444443333333344445333 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 ?    5.2   0.0     0.013        23      75      95 ..     375     395 ..     371     404 .. 0.85
   2 ?    4.8   0.5     0.017        30      29      99 ..     449     508 ..     423     522 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                                   E-EEE---TT-EEEE----SS CS
                       Top6b_C  75 lkWelsvsageskvleYsvds 95 
                                    +W+  +++g+sk+++Ysv  
  gi|91773797|ref|YP_566489.1| 375 TQWNFFIGSGKSKTITYSVIP 395
                                   58****************965 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                                   S-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE---TT-EEEE----SS-GGG CS
                       Top6b_C  29 dgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWelsvsageskvleYsvdseaee 99 
                                   ++v+++++++N +++ ++++ +e +p+  e +s +             We +++ ge++++ Y++ +++e+
  gi|91773797|ref|YP_566489.1| 449 EEVDITINIRNVGTRDATVSFTENIPTGFEFVSGQ-----------RSWEGHIGVGEEEQIVYTMFAKEEA 508
                                   56888889999999999988888888766555522...........3455555555555555555555555 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.8   6.7e+03      53      65 ..      62      74 ..      30      76 .. 0.73
   2 ?   -2.0   0.0       4.4   7.8e+03      15      42 ..     241     269 ..     241     277 .. 0.76
   3 ?    4.4   0.0     0.043        77       8      65 ..     287     345 ..     285     348 .. 0.77
   4 ?    4.5   0.0     0.041        74       8      35 ..     447     472 ..     447     481 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.8
                                  SS-BETTTEEEEE CS
                            CS 53 fgpIdpeesswti 65
                                  +++I pe+s ++ 
  gi|91773797|ref|YP_566489.1| 62 LHEIRPEDSEYSA 74
                                  5899999999876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.4
                                   EEE-TTCTTTTTCEEEEEETTEEEEEE.T CS
                            CS  15 tiyvkkvnikkkdvkvefkerslkvki.g 42 
                                   ti++ +++++++  + +++++s+++ i +
  gi|91773797|ref|YP_566489.1| 241 TIPARGMTVTSSATNAQIETDSFEIPIlD 269
                                   68888888899999999999998887753 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.043
                                   ETTEEEEEEE-TTCTTTTTCEEEE.....EETTEEEEEETSCEEEEECEBSS-BETTTEEEEE CS
                            CS   8 tldeVvvtiyvkkvnikkkdvkve.....fkerslkvkigkeklliegeLfgpIdpeesswti 65 
                                   t ++V++++ v++++ k+++ + +     f e ++ ++    k +++ +L ++Id+ e  +t+
  gi|91773797|ref|YP_566489.1| 287 TGTDVEISVLVEGYDYKGNNYQTStnavtFVEPYIAIS----KTYDDSQLQEEIDVPEIFFTL 345
                                   6689**************99999944444444446666....566676799999998887775 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.041
                                   ETTEEEEEEE-TTCTTTTTCEEEEEETT CS
                            CS   8 tldeVvvtiyvkkvnikkkdvkvefker 35 
                                   t +eV++ti++ +v   ++d +v+f+e+
  gi|91773797|ref|YP_566489.1| 447 TGEEVDITINIRNV--GTRDATVSFTEN 472
                                   5689*********9..899999998876 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.4       5.7     1e+04      78      87 ..      14      23 ..       6      29 .. 0.53
   2 ?   12.0   0.0   0.00011      0.19      56      97 ..     556     597 ..     500     600 .] 0.71

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.7
                         Orf78 78 vllyviyYfv 87
                                  vl  +i++f+
  gi|91773797|ref|YP_566489.1| 14 VLTVIIVFFL 23
                                  2333333333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                         Orf78  56 aaekaqalnillisllavvcvlvllyviyYfvilrerqkssv 97 
                                     + +++   l+ s+++++cvl  + +i+Y  i+r+++++ +
  gi|91773797|ref|YP_566489.1| 556 PLTMKENILFLISSFITILCVLSTIPLIVYLYISRQQSNRRK 597
                                   334455556667788999999999999********9887655 PP

>> Gryzun  Gryzun, putative trafficking through Golgi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0047       8.4     182     219 ..     200     239 ..     159     248 .. 0.83
   2 ?   -3.0   0.0       1.2   2.2e+03     259     323 ..     257     320 ..     247     322 .. 0.66
   3 ?    4.4   0.1     0.007        13     198     271 ..     439     518 ..     409     538 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0047
                        Gryzun 182 taikilP.kP..PkleiklpelkeqYYtnEkieLeleieNe 219
                                   t i+ilP +P  P l++++++l  +Y+ nE+ ++++ ++Ne
  gi|91773797|ref|YP_566489.1| 200 T-ITILPyQPgkPALNLEIQDLDMTYFPNEEPVFNILVKNE 239
                                   4.666653333389**************************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                        Gryzun 259 ekeeslpklgklessastelsivltetedpleyeleikasYhlvsdletpiiktlsvklslvnpF 323
                                   + e+++ ++  l++s+ + ++++lt  e+p+  ++ei++  +   d +   ++t +  +++v+p+
  gi|91773797|ref|YP_566489.1| 257 QIETDSFEIPILDTSNYQITPVILTIPETPTGTDVEISVLVEG-YDYKGNNYQTSTNAVTFVEPY 320
                                   3333333588899999999999999999999999999986543.355556666666666666665 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.007
                        Gryzun 198 pelkeqYYtnEkieLeleieNeEdeeaevklevrl.......lGesesalkisvldeeeeaeeaeeeeekeeslpklgkle 271
                                       +  Yt E+++++++i+N    +a+v+   ++       +G+++ + +i v +ee+   +  ++ee++ +lp ++k++
  gi|91773797|ref|YP_566489.1| 439 DVSLTDIYTGEEVDITINIRNVGTRDATVSFTENIptgfefvSGQRSWEGHIGVGEEEQIVYTMFAKEEATYELP-VTKVA 518
                                   5556778**********************9988887777777777777777777554444444446666666666.66655 PP

>> DUF4750  Domain of unknown function (DUF4750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.8     0.025        44       7      24 ..       8      25 ..       5      27 .. 0.84
   2 ?    5.8   1.3    0.0058        10       3      25 ..     560     582 ..     558     586 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.025
                       DUF4750  7 lfvlrlllalliVlllil 24
                                  + + r +l+++iV++l++
  gi|91773797|ref|YP_566489.1|  8 MHLNRAVLTVIIVFFLMC 25
                                  556689**********98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0058
                       DUF4750   3 eevllfvlrlllalliVlllill 25 
                                   +e  lf+++ ++++l+Vl++i l
  gi|91773797|ref|YP_566489.1| 560 KENILFLISSFITILCVLSTIPL 582
                                   56789**************9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4067.17
//
Query:       gi|91773798|ref|YP_566490.1|  [L=273]
Description: imidazole glycerol phosphate synthase subunit HisF [Methanococcoides burtonii DSM 6242]
Scores for complete 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-88  295.1   0.4    3.6e-88  294.9   0.4    1.0  1  His_biosynth  Histidine biosynthesis protein
      1e-06   28.3   0.2     0.0025   17.2   0.1    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
    1.3e-06   28.0   0.2    0.00033   20.1   0.1    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    3.4e-06   26.4   0.0    0.00024   20.3   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    5.7e-06   25.9   0.1     0.0033   16.9   0.0    2.2  2  NMO           Nitronate monooxygenase
    1.5e-05   24.4   0.1       0.01   15.2   0.0    2.3  2  TMP-TENI      Thiamine monophosphate synthase
    3.7e-05   23.1   0.1     0.0022   17.3   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
    0.00025   20.2   0.6       0.15   11.0   0.1    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0054   16.2   0.2      0.017   14.6   0.1    1.8  2  PcrB          PcrB family
  ------ inclusion threshold ------
       0.27   11.3   3.0         13    6.0   0.0    3.8  4  Sigma70_r3    Sigma-70 region 3


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 !  294.9   0.4     2e-91   3.6e-88       1     229 []       5     256 ..       5     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 294.9 bits;  conditional E-value: 2e-91
                                   EEEEEEEE....ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEE CS
                  His_biosynth   1 riipalDl....kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvq 77 
                                   riip+lD+      G vV   kG++f +l+ agdpv+lakry+e+gadel+++D++a++egr++++d++e++a+evfip++
  gi|91773798|ref|YP_566490.1|   5 RIIPCLDVtldaSGGTVV---KGVEFVDLKKAGDPVDLAKRYNEQGADELVFLDITASHEGRSTMIDVIERTANEVFIPLT 82 
                                   8*******9886677777...************************************************************ PP

                                   EESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.....C................EEEE CS
                  His_biosynth  78 vGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.....g................ykva 137
                                   vGGGI+s+edv+++l+agadkv+++taavknpe+i+e+++ fgsq+iv aiD++r     +                y+v+
  gi|91773798|ref|YP_566490.1|  83 VGGGINSVEDVRQILRAGADKVSVNTAAVKNPEFIREASNIFGSQCIVTAIDCKRnldveNnqdktileledgtlawYEVV 163
                                   *******************************************************6666515677788888899******* PP

                                   ETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEE CS
                  His_biosynth 138 ikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.dav 217
                                   i+g+re tgld+v++akk+eelg geillt+++rdGt +G+d+++tk+l+e+++ip+iasGGvg++e++++ + +g+ da 
  gi|91773798|ref|YP_566490.1| 164 IYGGREPTGLDTVQWAKKVEELGSGEILLTSMNRDGTYDGFDIPITKKLSEELDIPIIASGGVGNPEHMYKGFVDGKaDAG 244
                                   *************************************************************************99999*** PP

                                   EESHHHHTTSS- CS
                  His_biosynth 218 ivgsalyegelt 229
                                   +++s++++ge+t
  gi|91773798|ref|YP_566490.1| 245 LAASIFHFGEYT 256
                                   *********986 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.4e-06    0.0025     134     217 ..      37     120 ..       4     134 .. 0.78
   2 !    9.2   0.0   0.00038      0.67     136     194 ..     178     236 ..     170     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHHHTT-SEBEEBSSSTTS----S-H.HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                          ThiG 134 lvlarrleevGcaavmPlaapiGsglGllnk.ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                   + la+r +e G+  ++ l     s +G +++  +++   +e+ +P+ v  Gi s +d+ q +  Gad v +nta  +  + 
  gi|91773798|ref|YP_566490.1|  37 VDLAKRYNEQGADELVFLDI-TASHEGRSTMiDVIERTANEVFIPLTVGGGINSVEDVRQILRAGADKVSVNTAAVKNPEF 116
                                   44788888888888776643.4566776665156788888999******************************98877666 PP

                                   HHHH CS
                          ThiG 214 vamA 217
                                   ++ A
  gi|91773798|ref|YP_566490.1| 117 IREA 120
                                   6555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00038
                                   HHHHHHHTT-SEBE.EBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHH CS
                          ThiG 136 larrleevGcaavm.PlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqam 194
                                    a+++ee+G   ++       G+  G   +   k + ee+++P+i   G+g+p++  + +
  gi|91773798|ref|YP_566490.1| 178 WAKKVEELGSGEILlTSMNRDGTYDGFDIPI-TKKLSEELDIPIIASGGVGNPEHMYKGF 236
                                   6888888887655414455678888877665.57899*****************987765 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 !   20.1   0.1   1.9e-07   0.00033     126     169 ..      65     108 ..      64     111 .. 0.92
   2 !    5.7   0.0    0.0048       8.5     130     156 ..     208     234 ..     203     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                                   GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                  G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                   ++ +vi+++ +e+ ip+  GG i++ edv+++l+aGa+ vs+ +
  gi|91773798|ref|YP_566490.1|  65 TMIDVIERTANEVFIPLTVGGGINSVEDVRQILRAGADKVSVNT 108
                                   5789*************************************876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0048
                                   HHCTSTTS...EEEEESS--SHHHHHH CS
                  G3P_antiterm 130 vikeikkelkipiiaGGLietkedvee 156
                                   ++k++++el+ipiia+G + + e++ +
  gi|91773798|ref|YP_566490.1| 208 ITKKLSEELDIPIIASGGVGNPEHMYK 234
                                   7899*************9999988765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07   0.00024     141     228 ..      37     123 ..      27     152 .. 0.78
   2 ?    4.1   0.0     0.012        21     139     198 ..     174     232 ..     167     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                   HHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTT CS
                           Dus 141 lelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPw 221
                                   ++lak+ +++Ga++l+    t+ ++ +    ++ I+   ++v ip+ + G+I ++ed+++il+  Gad v +  +a +nP 
  gi|91773798|ref|YP_566490.1|  37 VDLAKRYNEQGADELVFLDITASHEGR-STMIDVIERTANEVFIPLTVGGGINSVEDVRQILRA-GADKVSVNTAAVKNPE 115
                                   566666666666666655555544444.345778888889999********************9.**************** PP

                                   HHHH.HHH CS
                           Dus 222 lfae.sta 228
                                   +++e s+ 
  gi|91773798|ref|YP_566490.1| 116 FIREaSNI 123
                                   *9985544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                                   .HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHH CS
                           Dus 139 nalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaeda 198
                                   ++++ ak+ve+ G  ++ +    r   y g  d+   k++ +++ ip+ia G++ ++e +
  gi|91773798|ref|YP_566490.1| 174 DTVQWAKKVEELGSGEILLTSMNRDGTYDG-FDIPITKKLSEELDIPIIASGGVGNPEHM 232
                                   678888888888888888866666666655.6788889****************999876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-06    0.0033     170     224 ..      60     109 ..      35     116 .. 0.76
   2 !    7.2   0.0    0.0017         3     184     214 ..     208     238 ..     171     268 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                           NMO 170 hqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                   h+G ++      + ++++ ++ v iP+   GGi+  ++v  +L++GA  v + t+
  gi|91773798|ref|YP_566490.1|  60 HEG-RS----TMIDVIERTANEVFIPLTVGGGINSVEDVRQILRAGADKVSVNTA 109
                                   555.33....35778888888888****************************998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0017
                           NMO 184 LvpqvldavdiPviAaGGiidrrgvaaaLal 214
                                   + ++  + +diP+iA GG+ + + +   +  
  gi|91773798|ref|YP_566490.1| 208 ITKKLSEELDIPIIASGGVGNPEHMYKGFVD 238
                                   5667788899********9887766555555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.6e-06      0.01     109     180 ..      40     109 ..      35     110 .. 0.84
   2 !    7.0   0.0    0.0018       3.3     120     160 ..     185     227 ..     171     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.6e-06
                      TMP-TENI 109 aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitl.envaevleagadgvavvsa 180
                                   a++ +++gad +++  i  T+++++++   ++ ++++a+++ iP+ + GGi+  e+v ++l+agad v+v +a
  gi|91773798|ref|YP_566490.1|  40 AKRYNEQGADELVFLDI--TASHEGRS-TMIDVIERTANEVFIPLTVGGGINSvEDVRQILRAGADKVSVNTA 109
                                   67777888888888888..88888874.45899******************95499************99765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                      TMP-TENI 120 igvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGit 160
                                   +g G i  T+   d   +  ++   k+l+e+l iP++a GG+ 
  gi|91773798|ref|YP_566490.1| 185 LGSGEILLTSMNRDGtyDGFDIPITKKLSEELDIPIIASGGVG 227
                                   6778888887777764556667789****************96 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.2e-06    0.0022     230     282 ..      66     116 ..      61     122 .. 0.83
   2 ?    3.7   0.0     0.017        30     237     255 ..     212     228 ..     206     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTC CS
                        DHO_dh 230 alkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpk 282
                                    + vi + ++++   ip+   GGi+s eD+   ++aGA  v v ta v++  +
  gi|91773798|ref|YP_566490.1|  66 MIDVIERTANEVF--IPLTVGGGINSVEDVRQILRAGADKVSVNTAAVKNPEF 116
                                   5666777777777..999999*************************9887655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.017
                                   HHHHTTT.S-EEEESS--S CS
                        DHO_dh 237 lykrlkkeipiIgvGGies 255
                                   l+++l+  ipiI++GG+  
  gi|91773798|ref|YP_566490.1| 212 LSEELD--IPIIASGGVGN 228
                                   555666..********965 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   8.3e-05      0.15     109     172 ..      40     106 ..      29     110 .. 0.68
   2 !    7.6   0.0   0.00092       1.6     200     229 ..     210     239 ..     185     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.3e-05
                                   HHHHHHTT-SEEE.EE-..STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE CS
                                   xxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 109 vkalveagvdvlv.vds..ahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkv 172
                                   +k+  e+g+d lv +d+  +h   +++++++++  ++v     ++G + + e ++++++agad v v
  gi|91773798|ref|YP_566490.1|  40 AKRYNEQGADELVfLDItaSHEGRSTMIDVIERTANEVFIPLTVGGGINSVEDVRQILRAGADKVSV 106
                                   5566677777544256511444456677777777766643336899999999999999999999877 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00092
                                   HHHHCTCT-EEEEES---SHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 200 aeaakkagvpviaDGGikysgdivkAlaaG 229
                                    +  ++ ++p+ia GG+ + +++ k ++ G
  gi|91773798|ref|YP_566490.1| 210 KKLSEELDIPIIASGGVGNPEHMYKGFVDG 239
                                   5678899******************98877 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   9.6e-06     0.017     181     215 ..      79     114 ..      50     123 .. 0.72
   2 ?   -1.1   0.0       0.6   1.1e+03     171     197 ..     209     234 ..     160     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.6e-06
                                   SEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                          PcrB 181 arlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                   + l vGGGi+s E+ +++++a AD + v ++  +++
  gi|91773798|ref|YP_566490.1|  79 IPLTVGGGINSVEDVRQILRAgADKVSVNTAAVKNP 114
                                   4578*********************99888766665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                                   HHHHHHHHSSSEEEEESS--SHHHHHH CS
                          PcrB 171 vialkkklekarlivGGGirsaEkAke 197
                                   +++l+  l+ + +i  GG+ ++E+ ++
  gi|91773798|ref|YP_566490.1| 209 TKKLSEELD-IPIIASGGVGNPEHMYK 234
                                   444444443.55677777777777655 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   1.9e+02      46      70 ..      50      74 ..      46      77 .. 0.86
   2 ?    6.0   0.0    0.0071        13      33      55 ..      89     111 ..      88     115 .. 0.89
   3 ?   -1.1   0.1       1.2   2.1e+03      52      68 ..     139     154 ..     138     157 .. 0.82
   4 ?   -0.2   0.0      0.59   1.1e+03      33      48 ..     256     271 ..     253     273 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                                  XXEETTXBSSSSTTXBSTTTXBXSS CS
                    Sigma70_r3 46 epvSldlpvgeeedtelgdlledde 70
                                  e v ld+ +++e+ +++ d++e++ 
  gi|91773798|ref|YP_566490.1| 50 ELVFLDITASHEGRSTMIDVIERTA 74
                                  66889*****************984 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0071
                                   XHHHHHHHHHHHXXXEETTXBSS CS
                    Sigma70_r3  33 seekVrevleaarepvSldlpvg 55 
                                   s+e+Vr++l+a  + vS+++ + 
  gi|91773798|ref|YP_566490.1|  89 SVEDVRQILRAGADKVSVNTAAV 111
                                   79****************99765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.2
                                   XBSSSSTTXBSTTTXBX CS
                    Sigma70_r3  52 lpvgeeedtelgdlled 68 
                                   l+v +++d+++ + led
  gi|91773798|ref|YP_566490.1| 139 LDVENNQDKTILE-LED 154
                                   789999***9999.777 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.59
                                   XHHHHHHHHHHHXXXE CS
                    Sigma70_r3  33 seekVrevleaarepv 48 
                                   ++ +V+e+l+a + pv
  gi|91773798|ref|YP_566490.1| 256 TVRDVKEALRAKNIPV 271
                                   899*******999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1806.57
//
Query:       gi|91773799|ref|YP_566491.1|  [L=95]
Description: MazG nucleotide pyrophosphohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-15   56.5   0.0    2.9e-15   56.2   0.0    1.1  1  MazG          MazG nucleotide pyrophosphohydrolase domain
    5.6e-05   23.5   0.1    6.9e-05   23.2   0.1    1.2  1  PRA-PH        Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
      0.014   15.7   0.1      0.022   15.0   0.1    1.2  1  MazG-like     MazG-like family
       0.05   13.4   3.0      0.083   12.7   3.0    1.3  1  Cys_rich_KTR  Cysteine-rich KTR


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   6.5e-19   2.9e-15       5      71 ..      25      84 ..      22      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 6.5e-19
                                  HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH-G CS
                          MazG  5 tllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetileKlerRhp 71
                                  +++++l+eEvgE+aeaI+++d+++l+eEL+D++ ++  lan+    ++idle+++   leK+   +p
  gi|91773799|ref|YP_566491.1| 25 ATTLWLVEEVGELAEAIRRNDMENLREELADCFAWIGALANL----YDIDLEKAF---LEKYPLVCP 84
                                  5789*************************************9....*********...888876666 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.5e-08   6.9e-05      30      76 ..      29      75 ..       4      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.5e-08
                                  HHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHHHH CS
                        PRA-PH 30 ligEEavElleaasegdlaeladelaDllYvtygllvllGidldavf 76
                                  +++EE+ El ea  ++d+++l +elaD +  + +l+ l++idl++ f
  gi|91773799|ref|YP_566491.1| 29 WLVEEVGELAEAIRRNDMENLREELADCFAWIGALANLYDIDLEKAF 75
                                  789*************************99999999999***99877 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   4.9e-06     0.022      15      58 ..      30      73 ..      28      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.9e-06
                     MazG-like 15 llksveelfkallkgseeeildeLAdviiylylLAdrlGidfee 58
                                  l+++v+el +a+ +++ e++ +eLAd ++    LA+  +id+e+
  gi|91773799|ref|YP_566491.1| 30 LVEEVGELAEAIRRNDMENLREELADCFAWIGALANLYDIDLEK 73
                                  678999****999****************************997 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.0   1.9e-05     0.083      19      38 ..      72      91 ..      70      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                  Cys_rich_KTR 19 edTvLknfpLfCPKCkqetl 38
                                  e+  L+++pL CP C+++  
  gi|91773799|ref|YP_566491.1| 72 EKAFLEKYPLVCPTCRKNPC 91
                                  5678************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 580.19
//
Query:       gi|91773800|ref|YP_566492.1|  [L=319]
Description: hypothetical protein Mbur_1859 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-05   24.7   1.2    2.7e-05   24.0   1.2    1.4  1  PGF-CTERM  PGF-CTERM motif
  ------ inclusion threshold ------
      0.089   12.9   0.0        1.2    9.2   0.0    2.3  2  NGP1NT     NGP1NT (NUC091) domain
      0.095   12.1   0.0       0.14   11.6   0.0    1.3  1  COE1_DBD   Transcription factor COE1 DNA-binding domain


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   1.2   4.5e-09   2.7e-05       1      23 []     296     318 ..     296     318 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.5e-09
                     PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                   tPGF +++Ala +L+a+ + RRr
  gi|91773800|ref|YP_566492.1| 296 TPGFTILFALASILSAVIIRRRR 318
                                   9****************999998 PP

>> NGP1NT  NGP1NT (NUC091) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00021       1.2      59      90 ..     181     212 ..     170     222 .. 0.82
   2 ?    0.8   0.0     0.088   5.2e+02      81     102 ..     261     282 ..     251     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00021
                        NGP1NT  59 ekvkdpysvllkrnklPmsLledkakkkkvkl 90 
                                   ++ +d y+vl+k++++  sLl dka +++ ++
  gi|91773800|ref|YP_566492.1| 181 RALSDDYRVLIKAREMDASLLADKAWTNTGSI 212
                                   6789*******************998755544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.088
                        NGP1NT  81 dkakkkkvklletesfeetFgp 102
                                   dk++  ++k++++e+fe++F +
  gi|91773800|ref|YP_566492.1| 261 DKDTVVQKKVIDAEDFERIFVD 282
                                   4455567999*********976 PP

>> COE1_DBD  Transcription factor COE1 DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.3e-05      0.14      45      81 ..      64     100 ..      33     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                      COE1_DBD  45 nlrksnffhfvlalydrqgqavevertafvdfvekdk 81 
                                    +  sn   ++l +yd+++  +++er  f+ fve+  
  gi|91773800|ref|YP_566492.1|  64 RFADSNNVSILLKVYDKDTGFLDMERDVFIGFVENGD 100
                                   566799999*************************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1987.45
//
Query:       gi|91773801|ref|YP_566493.1|  [L=78]
Description: hypothetical protein Mbur_1860 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.6   5.6      0.015   14.5   5.6    1.1  1  NKAIN     Na,K-Atpase Interacting protein


Domain annotation for each model (and alignments):
>> NKAIN  Na,K-Atpase Interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.6   8.6e-07     0.015       8      52 ..      25      69 ..      18      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.6e-07
                         NKAIN  8 ctllalcllqlvavlerqvfdflGyqwapilvnffhiivvilGlf 52
                                  +++l+l+++ql + +er ++ ++ +q++pi+  f+++ v++l ++
  gi|91773801|ref|YP_566493.1| 25 MIFLILSAFQLYISIERIIYTWFEHQYVPIVRSFVNLAVLVLSVY 69
                                  5788999**********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 511.46
//
Query:       gi|91773802|ref|YP_566494.1|  [L=810]
Description: peptidase U32 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-119  394.8   0.0    8.6e-85  283.6   0.0    2.2  2  Peptidase_U32  Peptidase family U32
    3.5e-24   85.5   0.0    6.5e-24   84.6   0.0    1.5  1  DUF3656        Collagenase
  ------ inclusion threshold ------
      0.042   14.2   0.1         30    5.0   0.0    3.2  4  Radical_SAM    Radical SAM superfamily
       0.11   11.9   1.9         10    5.5   0.0    3.6  4  PEP_mutase     Phosphoenolpyruvate phosphomutase


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 !  283.6   0.0   1.9e-88   8.6e-85       1     230 [.      76     299 ..      76     301 .. 0.97
   2 !  109.0   0.1   4.3e-35   1.9e-31       1     204 [.     599     794 ..     599     803 .. 0.91

  Alignments for each domain:
  == domain 1  score: 283.6 bits;  conditional E-value: 1.9e-88
                 Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikek 81 
                                   ++k++++l +l e+g+davivqD+g+l+la++++p+l++h+Stq++++nse+v fl+elG++rvvlaRE+s++ei++++ k
  gi|91773802|ref|YP_566494.1|  76 MKKAANMLCFLSECGADAVIVQDLGLLHLAKDIVPDLPIHASTQMTVHNSEGVLFLEELGVKRVVLAREMSIDEIRQVRGK 156
                                   68899999************************************************************************* PP

                 Peptidase_U32  82 vpdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkdlclieel 162
                                   + ++elE+f+hGalc++ysG+cllss+++grs+nrg+caqpcr++y+l+  +   + e       g yllspkdl+  + l
  gi|91773802|ref|YP_566494.1| 157 T-NIELETFIHGALCISYSGQCLLSSVIGGRSGNRGQCAQPCRKSYELLGYDGAVSTE-------GPYLLSPKDLNSKDVL 229
                                   *.*********************************************98888776666.......67************** PP

                 Peptidase_U32 163 pelleaGvdslKIeGRmkspeyvatvvrvYreaidallagr..eevkeelkeeleklanrgltsgfllgr 230
                                   p+l+eaGv+s+KIeGRmk+peyva vv +Yr++id++ +++  ++v+++   +le+l+nrg+t+++l g 
  gi|91773802|ref|YP_566494.1| 230 PQLIEAGVSSFKIEGRMKRPEYVAGVVGIYRKLIDRYFDDPdaYFVSKDESLALEQLFNRGFTDAYLKGS 299
                                   ******************************************************************9876 PP

  == domain 2  score: 109.0 bits;  conditional E-value: 4.3e-35
                 Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikek 81 
                                   ++++r+++  +++l+vd+v+v+ +g  +la      l++ +++ +n+ n+++ + +k+lGa  vvl+ E+s++++++++e 
  gi|91773802|ref|YP_566494.1| 599 MDAVRELFGLAKKLEVDGVVVSNYGTYHLAMGF--GLPVVADSPMNVFNVRSYAAMKKLGAASVVLSPEMSIAQVEEVAEC 677
                                   67899999999******************7766..*********************************************9 PP

                 Peptidase_U32  82 vpdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrl.dyrlieekekgeeepieedekgt.yllspkdlclie 160
                                        +E+ vhG   v++s+ c+l  +l++    ++ c q c + d +l++e +   +  ++ d+  + ++l++k+lcl+ 
  gi|91773802|ref|YP_566494.1| 678 G---PVECIVHGRQDVMVSRYCMLGDLLGN----KDGCIQVCEEeDFELVDELDYYFPLLVDSDC--RmHVLNSKELCLLG 749
                                   9...6**********************665....89********999999999866555555544..449*********** PP

                 Peptidase_U32 161 elpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagr.e 204
                                   +++ +l aGv++++Ie R+ + + va+v+  Yr ++d   agr +
  gi|91773802|ref|YP_566494.1| 750 NMDIILRAGVAAIRIEARTMDVDLVAKVTHRYRGVLDGKKAGRcK 794
                                   *************************************99999844 PP

>> DUF3656  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.0   1.4e-27   6.5e-24       1     106 [.     388     507 ..     388     508 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1.4e-27
                       DUF3656   1 vyrtsdkklteelekslek.seerkipvdlelaakegeplkltvtde............leeAkkrplteenirkqLsklG 68 
                                   ++rt d++l+++l++++++ ++ rk+pv++++ +  g+ + l+++d             +e A+k+p+++e+i+kqL klG
  gi|91773802|ref|YP_566494.1| 388 IFRTMDRALMDSLKRTFTSsKPVRKVPVSIKADVVAGSSIVLEMEDGdgnrvsvlsdyvVEVAQKKPTDKEQIEKQLLKLG 468
                                   79******************************999999******977999******************************* PP

                       DUF3656  69 gtpFeleeieidld.glfiPvseLnelRRealekLeear 106
                                   ++ Fe+++i++++  ++fiP+++Ln++R +a++ L +ar
  gi|91773802|ref|YP_566494.1| 469 NSVFEASSIDVNITgEVFIPIKQLNDVRNNAVSLLGAAR 507
                                   ************98466****************999887 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.13   5.9e+02     101     147 ..      24      67 ..       3      83 .. 0.60
   2 ?    5.0   0.0    0.0066        30      30     121 ..      45     154 ..      37     166 .. 0.72
   3 ?    4.9   0.0    0.0069        31      40     100 ..     545     605 ..     526     620 .. 0.75
   4 ?   -1.2   0.0      0.53   2.4e+03      28      55 ..     661     688 ..     653     784 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.13
                                   T-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                   Radical_SAM 101 gvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvd 147
                                   g d v+lg++a+  +     + ++ t+ee+ ea+++++ +g+k+ v++
  gi|91773802|ref|YP_566494.1|  24 GADAVYLGAKALGAR----AFAGNFTLEEIGEAVDYAHLRGVKVfVTV 67 
                                   444444444444444....44466778888888888888888864333 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0066
                                   HHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.....................CCTEEEEEEECSSCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxx RF
                   Radical_SAM  30 sveeileevkelkaekgvkevilgggepllypdfvellerlakla.....................vpgiritvetngtlp 89 
                                   ++eei e v++++  +gvk+++ +  +   +  + +++ +l+ l                      vp++ i+ +t  t++
  gi|91773802|ref|YP_566494.1|  45 TLEEIGEAVDYAH-LRGVKVFVTV-NTLVKDMQMKKAANMLCFLSecgadavivqdlgllhlakdiVPDLPIHASTQMTVH 123
                                   7889999999985.5443333333.222222334444444444447777778888888888888999************** PP

                                   GHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  90 deeklerllelgvdrvslgleaaddekvlklm 121
                                   + e +  l elgv rv l  e   de +++  
  gi|91773802|ref|YP_566494.1| 124 NSEGVLFLEELGVKRVVLAREMSIDE-IRQVR 154
                                   ****************9998888888.77766 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0069
                                   HHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHT CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  40 elk.aekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllel 100
                                   +l  a  g+  v+ +gge +  +++++l e+ a ++++g+r+ v ++ ++  e+ +++ +el
  gi|91773802|ref|YP_566494.1| 545 RLNaAIEGGADVLYVGGEFFRGRKYIDLEEAVAICKDNGRRVYVNSSRIVS-EDDMDAVREL 605
                                   34334446888999999999999999999999999999**********998.6666665554 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.53
                                   HHHHHHHHHHHHHHHHHTT.SEEEEEESS CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                   Radical_SAM  28 slsveeileevkelkaekg.vkevilggg 55 
                                   +ls+e+ +++v+e+ ae g v+ ++ g +
  gi|91773802|ref|YP_566494.1| 661 VLSPEMSIAQVEEV-AECGpVECIVHGRQ 688
                                   68999999999999.78885555554444 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.013        59     125     224 ..      48     146 ..      19     158 .. 0.71
   2 ?   -2.6   0.0      0.67     3e+03      90     107 ..     228     245 ..     221     254 .. 0.80
   3 ?    5.5   0.0    0.0023        10     157     177 ..     541     561 ..     497     601 .. 0.87
   4 ?   -1.1   0.0      0.23     1e+03      31     215 ..     658     681 ..     634     692 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.013
                    PEP_mutase 125 kiaaaraaaeeagfvinARtdalllsagagleeaieRaraYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvpl.kgtl 204
                                    i +a++ a   g+ ++  + +l+  ++ ++++a + +    e GAd+v+v  l   +  +++v  +++     ++ +++ 
  gi|91773802|ref|YP_566494.1|  48 EIGEAVDYAHLRGVKVFVTVNTLV--KDMQMKKAANMLCFLSECGADAVIVQDLGLLHLAKDIVPDLPIHASTQMTvHNSE 126
                                   556666666666666666666766..777788888888888999****999977655555566655553333333224457 PP

                    PEP_mutase 205 svaelaelGvarislgnhll 224
                                    v  l+elGv+r++l+ ++ 
  gi|91773802|ref|YP_566494.1| 127 GVLFLEELGVKRVVLAREMS 146
                                   7888**********998875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.67
                    PEP_mutase  90 tvrrliaaGvvgvniEDk 107
                                     ++li+aGv+ + iE +
  gi|91773802|ref|YP_566494.1| 228 VLPQLIEAGVSSFKIEGR 245
                                   56899**********977 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0023
                    PEP_mutase 157 eaieRaraYaeAGAdgvfvpg 177
                                   ++++R++a  e GAd+++v g
  gi|91773802|ref|YP_566494.1| 541 DTLKRLNAAIEGGADVLYVGG 561
                                   79***************9976 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.23
                    PEP_mutase  31 kalatsSlavaaslGvpDgeelpleellaavraiaevvslPlivDledGygespeevaetvrrliaaGvvgvniEDkkknd 111
                                                                                                                    
  gi|91773802|ref|YP_566494.1| 658 AS------------------------------------------------------------------------------- 659
                                   11............................................................................... PP

                    PEP_mutase 112 aerqlldieefaekiaaaraaaeeagfvinARtdalllsagagleeaieRaraYaeAGAdgvfvpglqkdaeiaelvaavd 192
                                                                                                                    
  gi|91773802|ref|YP_566494.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                    PEP_mutase 193 vplnvvplkgtlsvaelaelG.va 215
                                     +++ p+ +  +v+e+ae G v+
  gi|91773802|ref|YP_566494.1| 660 --VVLSPEMSIAQVEEVAECGpVE 681
                                   ..1111222224555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (810 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 4826.73
//
Query:       gi|91773803|ref|YP_566495.1|  [L=122]
Description: deoxynucleoside 5'-monophosphate N-glycosidase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-06   28.5   0.0    1.4e-06   28.4   0.0    1.0  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   7.7e-11   1.4e-06       2     102 ..       4     100 ..       3     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.7e-11
                                   EEESGGGCSCCCHHHHHHHHHHHHTTTTEEE-CCTT-TT.....--SSHHHHHHHHHHHHHC-SEEEEE--SSSSSS--HH CS
               Nuc_deoxyrib_tr   2 YLAgplvFrpdakalaarlkallaengldglaPldneaelel.paeetaraiyeadialirqaDavianldpfrgpeaDsG 81 
                                   +L g++   ++    ++ + + l+++g+++l     + e e  ++  t+ +iye+d+++++ ++++ia +++     +  G
  gi|91773803|ref|YP_566495.1|   4 FLSGSIRGGRQMLPTYQFICRFLRNKGHEVLSWHVADSEVEGkESLLTETQIYERDMSFLQDSECMIAEVSM-----PSIG 79 
                                   66666666666777777888889999998886664455555558999*************************.....99** PP

                                   HHHHHHHHHHCT-EEEEE-S- CS
               Nuc_deoxyrib_tr  82 tafEvGyavalgkpvlayttd 102
                                   + +Ev  a+  g+pv+++   
  gi|91773803|ref|YP_566495.1|  80 VGYEVCSAIKKGIPVMCVHMP 100
                                   ****************99654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 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:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 774.84
//
Query:       gi|91773804|ref|YP_566496.1|  [L=81]
Description: hypothetical protein Mbur_1863 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  24.9    1.5e-10   41.1  24.9    1.1  1  BofA      SigmaK-factor processing regulatory protein BofA
  ------ inclusion threshold ------
       0.75    9.7  16.5       0.11   12.4  10.4    1.9  2  YqhR      Conserved membrane protein YqhR


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 !   41.1  24.9   1.7e-14   1.5e-10       2      74 ..       7      76 ..       6      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.7e-14
                          BofA  2 gilllllvikllkkplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillkl 74
                                  ++l++++++ +l+k lk + ++++n+vlG+v+L+++     v+g+ i++ ++t+l++++ G+ G++lL+ll +
  gi|91773804|ref|YP_566496.1|  7 IVLVAIIAAFILYKVLKSIKNMVVNTVLGIVILLVAK---FVLGINIAFTWVTILVCALAGVVGALLLVLLAY 76
                                  789999*******************************...779****************************87 PP

>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  10.4   1.2e-05      0.11      73     114 ..       5      46 ..       1      58 [. 0.89
   2 ?    1.0   1.1      0.04   3.6e+02      21      38 ..      60      77 ..      48      81 .] 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                          YqhR  73 vligvvsigvallyyvllkkikslwagilyGvvlwllvfyvl 114
                                   ++i +v+i +a++ y +lk ik++ +  + G+v+ l+  +vl
  gi|91773804|ref|YP_566496.1|   5 LIIVLVAIIAAFILYKVLKSIKNMVVNTVLGIVILLVAKFVL 46 
                                   578899*****************************9998887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.04
                          YqhR 21 vviiGfvGGvlWsllayl 38
                                  +++ G vG +l  llayl
  gi|91773804|ref|YP_566496.1| 60 CALAGVVGALLLVLLAYL 77
                                  345677777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1777  (0.0991132); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 518.59
//
Query:       gi|91773805|ref|YP_566497.1|  [L=221]
Description: hypothetical protein Mbur_1864 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.9   0.0    2.1e-21   76.4   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
      5e-19   68.8   0.0    8.7e-19   68.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.2e-13   49.4   0.0    5.6e-13   49.0   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.4e-12   48.2   0.0    2.1e-12   47.6   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    8.2e-12   45.2   0.0    1.1e-11   44.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.8e-06   27.5   0.0    2.1e-06   27.2   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00015   21.2   0.0    0.00022   20.6   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0029   17.2   0.0     0.0041   16.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
     0.0038   16.8   0.0     0.0052   16.4   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0065   16.0   0.0      0.025   14.0   0.0    1.9  2  CheR             CheR methyltransferase, SAM binding domain
     0.0093   15.4   0.0      0.011   15.2   0.0    1.2  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.095   12.7   0.0        5.3    7.1   0.0    2.4  2  Caf4             CCR4-associated factor 4
        0.1   12.4   0.0       0.38   10.6   0.0    1.9  1  Methyltransf_8   Hypothetical methyltransferase
       0.12   10.9   0.0       0.12   10.9   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   1.6e-24   2.1e-21       1      95 [.      43     138 ..      43     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 1.6e-24
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edpek 79 
                                   Ld+G+G+Gr++ +l +++ +++g+D+s+++l+++ke   +++ +     a++++lpf++nsfD++v++ vl+h+  +++e 
  gi|91773805|ref|YP_566497.1|  43 LDAGSGNGRHLLPLSNYY-NCIGIDVSTKALTASKEYLAKRDREAHHSTASITDLPFQNNSFDAIVCFGVLQHLlrKERET 122
                                   8**************555.************9999988888875566999******************************* PP

                                   HHHHHHHHEEEEEEEE CS
               Methyltransf_11  80 alkeiaRvLkpgGllv 95 
                                   a  e+ R+LkpgG+++
  gi|91773805|ref|YP_566497.1| 123 AACEFERILKPGGMIF 138
                                   *************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   6.8e-22   8.7e-19       1      97 []      42     135 ..      42     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 6.8e-22
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   +Ld+G G+Gr++l l++    ++ +g+D+s ++l a +e +++++ +++  +++++dlpf+++sfD++v++g+l+hl +++
  gi|91773805|ref|YP_566497.1|  42 ILDAGSGNGRHLLPLSNY---YNCIGIDVSTKALTASKEYLAKRDREAHHSTASITDLPFQNNSFDAIVCFGVLQHLLRKE 119
                                   8***************88...79******************99999************************988***999** PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                   +e+a  e+ r+LkpgG
  gi|91773805|ref|YP_566497.1| 120 RETAACEFERILKPGG 135
                                   ***************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   4.4e-16   5.6e-13      19     155 ..      35     179 ..      19     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.4e-16
               Methyltransf_23  19 klraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlrevleh 94 
                                   + +++gr+Ld G G G+ l  l+ + ++++g+D s +a    +      ++ a+++ +   + ++++++fd Iv++ vl h
  gi|91773805|ref|YP_566497.1|  35 RIPEKGRILDAGSGNGRHLLPLSNY-YNCIGIDVSTKALTASKeylakRDREAHHSTASITDLPFQNNSFDAIVCFGVLQH 114
                                   456899**********877777555.8********87666555999999999999999999******************** PP

               Methyltransf_23  95 vpd..ppellrqiatllkpgGylllseplasl..kedrllldwlylvpagrhisffsarslkell 155
                                   +     + +   + ++lkpgG ++l++++ ++  +  + +++ ++ ++ g   ++f+ ++lk l+
  gi|91773805|ref|YP_566497.1| 115 LLRkeRETAACEFERILKPGGMIFLEVFGINDmrYGGEEVEEHTFVRQSGIIYHYFTKEELKSLF 179
                                   *96225577888999************98887778999999999999996666********9997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   1.6e-15   2.1e-12       1      99 []      43     137 ..      43     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.6e-15
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl.. 79 
                                   L+ G+G+G+ l +l ++    + +g+D+s++a+++ ke lakr++  +++ +   +dl  +   +sfD++v+++vl+hl  
  gi|91773805|ref|YP_566497.1|  43 LDAGSGNGRHLLPLSNY---YNCIGIDVSTKALTASKEYLAKRDR-EAHHSTASITDLPFQN--NSFDAIVCFGVLQHLlr 117
                                   899***********999...99***********777777777775.5566666666665443..6***************9 PP

               Methyltransf_12  80 kdirevldnirklLkpgGrl 99 
                                   k+++ +  ++ + LkpgG++
  gi|91773805|ref|YP_566497.1| 118 KERETAACEFERILKPGGMI 137
                                   99999999**********86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   8.7e-15   1.1e-11       5     113 ..      40     143 ..      37     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 8.7e-15
               Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevln 85 
                                    r+lD+G+G+G+ ++ l        + +GiD s +a++ ++e ++k   + ++ + ++i++l+  ++ ++fD i++++vl+
  gi|91773805|ref|YP_566497.1|  40 GRILDAGSGNGRHLLPLSNY----YNCIGIDVSTKALTASKEYLAKRDRE-AHHSTASITDLP--FQNNSFDAIVCFGVLQ 113
                                   589***************54....349***************99999986.99999*******..***************5 PP

               Methyltransf_31  86 aladpdkile..eiervlkpggilliedpr 113
                                   +l  ++      e er lkpgg + +e + 
  gi|91773805|ref|YP_566497.1| 114 HLLRKERETAacEFERILKPGGMIFLEVFG 143
                                   544443332235**********99887766 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.6e-09   2.1e-06      65     186 ..      41     161 ..      31     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.6e-09
                                   EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-.EEEEES-GGG-----SEEEEES-GGGTSGGG CS
                          CMAS  65 tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerk.vevklldyedldekvdrvvsvgafehvgken 144
                                   ++Ld G G G  +    + y  + +g+ +S++    +k+ ++++d e +  + +++d    ++ +d++v +g+++h+  ++
  gi|91773805|ref|YP_566497.1|  41 RILDAGSGNGRHLLPLSNYY--NCIGIDVSTKALTASKEYLAKRDREAHhSTASITDLPFQNNSFDAIVCFGVLQHLLRKE 119
                                   79**********99998887..68********************9875515566777766677****************99 PP

                                   HHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHH CS
                          CMAS 145 ydtffkklkkllkedGllllhtitslhkkelaerglklkfid 186
                                    +t   +++++lk++G++ l+   + + +   e+  + +f++
  gi|91773805|ref|YP_566497.1| 120 RETAACEFERILKPGGMIFLEVFGINDMRYGGEEVEEHTFVR 161
                                   9*******************9999888877776666666665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.7e-07   0.00022      52     150 ..      43     138 ..      19     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                                   EEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-... CS
               Ubie_methyltran  52 lDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnv... 129
                                   lD  +G g   + ls+     ++ +++D++ + L  +++ l ++   + ++ +a+  +Lpf+++sfD + v fG+      
  gi|91773805|ref|YP_566497.1|  43 LDAGSGNGRHLLPLSN----YYNCIGIDVSTKALTASKEYLAKRD-REAHHSTASITDLPFQNNSFDAI-VCFGVLQHllr 117
                                   5555555555444443....3467899*******99999887765.4678899999***********97.89998664233 PP

                                   S-HHHHHHHHHHHEEEEEEEE CS
               Ubie_methyltran 130 tDklkaLkeayrvlkpGGrlv 150
                                    ++++a  e  r+lkpGG ++
  gi|91773805|ref|YP_566497.1| 118 KERETAACEFERILKPGGMIF 138
                                   68899*************875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.2e-06    0.0041       6      88 ..      31     115 ..      27     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-06
                          MetW   6 liaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaec....vakGlsviqgdldkdlenfedksfdyvvls 82 
                                   +i   i+++ r+ld G+G+G  l  l +    +  G+++++++++++     ++  + ++  +      f+++sfd +v  
  gi|91773805|ref|YP_566497.1|  31 AIRSRIPEKGRILDAGSGNGRHLLPLSN--YYNCIGIDVSTKALTASkeylAKRDREAHHSTASITDLPFQNNSFDAIVCF 109
                                   68889***************99999977..5677888888888776522223466777787777666689*******9998 PP

                          MetW  83 qtlqat 88 
                                     lq +
  gi|91773805|ref|YP_566497.1| 110 GVLQHL 115
                                   888875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     4e-06    0.0052      30     103 ..      35     108 ..      18     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4e-06
                                   C..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE CS
                           MTS  30 e..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivs 103
                                   +  ++g++lD G+G+G   + l +     +   +dv+++Al+++ke l++ + e++  + ++++  +++++fd+iv+
  gi|91773805|ref|YP_566497.1|  35 RipEKGRILDAGSGNGRHLLPLSN---YYNCIGIDVSTKALTASKEYLAKRDREAHHSTASITDlPFQNNSFDAIVC 108
                                   4446899********986555555...5556799*******************97777666665267899******8 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         1   1.3e+03      65      82 ..      60      77 ..      31      86 .. 0.72
   2 !   14.0   0.0     2e-05     0.025     134     173 ..     100     139 ..      87     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1
                                  EEEEEEESSCHHHHHHHH CS
                          CheR 65 vkilAtDidlkvlekAka 82
                                  ++ +++D+++k+l++ k+
  gi|91773805|ref|YP_566497.1| 60 YNCIGIDVSTKALTASKE 77
                                  455677777777776665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2e-05
                                   G--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                          CheR 134 lgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                    +++D i+c  vl  + ++++e+   +f + lkpgg+++l
  gi|91773805|ref|YP_566497.1| 100 NNSFDAIVCFGVLQHLLRKERETAACEFERILKPGGMIFL 139
                                   468***********************************97 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.6e-06     0.011      28     129 ..      36     136 ..      13     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                                   CS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-.EEEEEEESSGGG CS
                          TehB  28 ivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklder.ydfilstvvlmf 107
                                   i + g++ld g g+gr  l ls + y+   +d   ++++  +e   k + +  + ++  i ++ ++++ +d i+   vl  
  gi|91773805|ref|YP_566497.1|  36 IPEKGRILDAGSGNGRHLLPLS-NYYNCIGIDVSTKALTASKEYLAKRDRE-AHHSTASITDLPFQNNsFDAIVCFGVLQH 114
                                   456689***********99997.5699999999999999999988888877.677888999999986549*****999999 PP

                                   S-GGGHHHHHHHHHHTEEEEEE CS
                          TehB 108 leaeripsiienmqectkvggy 129
                                   l ++   +   ++++  k+gg 
  gi|91773805|ref|YP_566497.1| 115 LLRKERETAACEFERILKPGGM 136
                                   9888888888888888888885 PP

>> Caf4  CCR4-associated factor 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0042       5.3       9      27 ..      97     115 ..      91     122 .. 0.87
   2 ?    2.9   0.0     0.084   1.1e+02      40      51 ..     172     183 ..     169     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                          Caf4   9 sfqnnyaDsattfkiLahL 27 
                                    fqnn  D+   f +L hL
  gi|91773805|ref|YP_566497.1|  97 PFQNNSFDAIVCFGVLQHL 115
                                   6*****************8 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.084
                          Caf4  40 kkqLPsLfeGfk 51 
                                   k++L sLf Gf 
  gi|91773805|ref|YP_566497.1| 172 KEELKSLFCGFT 183
                                   899********6 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.38     108     156 ..      88     139 ..      17     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                                   EEES-TTS-S--TT-EEEEEEE..S.---SS-HHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_8 108 vvacdlakvPledesvdvavfc..l.slmgtnladflkeanrvlkvGGllkv 156
                                     +  ++ +P +++s d +v+   l  l+ ++ ++   e +r+lk+GG++++
  gi|91773805|ref|YP_566497.1|  88 HSTASITDLPFQNNSFDAIVCFgvLqHLLRKERETAACEFERILKPGGMIFL 139
                                   44567899*********66543222235667777888999********9864 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     9e-05      0.12     164     223 ..      85     145 ..      44     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9e-05
               Methyltransf_29 164 pailavlgtkrlpyPsrsfdlihCsrCridwteed.gilllevdRvlRpgGyfvlsappvy 223
                                    a  +  + + lp+  +sfd i C   + +  +++  +   e +R+l+pgG   l    ++
  gi|91773805|ref|YP_566497.1|  85 EAHHSTASITDLPFQNNSFDAIVCFGVLQHLLRKErETAACEFERILKPGGMIFLEVFGIN 145
                                   56667777889**************9999987665267889**********9877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1370.15
//
Query:       gi|91773806|ref|YP_566498.1|  [L=528]
Description: lysyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-125  418.6   0.0   2.7e-125  418.1   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)
    6.8e-09   34.9   0.0    0.00018   20.4   0.0    2.3  2  tRNA-synt_1g  tRNA synthetases class I (M)
    2.9e-06   26.9   0.0      0.057   12.7   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.082   12.2   0.0        6.7    5.9   0.0    2.2  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)
       0.29   11.6   0.0       0.29   11.6   0.0    3.2  5  zf-IS66       zinc-finger binding domain of transposase IS66


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 !  418.1   0.0  7.4e-129  2.7e-125       1     351 [.       5     341 ..       5     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 418.1 bits;  conditional E-value: 7.4e-129
                  tRNA-synt_1f   1 kaWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenl 81 
                                   ++Wad++ae+   ++       ++++v++Gi+pSG+iHiGn+rev+tad+ +ra+++ g e ++i+i+D++D+lRkv+++l
  gi|91773806|ref|YP_566498.1|   5 THWADVIAEEAA-KN------GNKHLVSTGITPSGHIHIGNMREVVTADAAYRAMNDAGLESEFIYIADNFDPLRKVYPFL 78 
                                   589999999988.22......3679******************************************************** PP

                  tRNA-synt_1f  82 pekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeilekyr 162
                                   pe+ +++++gkp+++iP+p g+++syaehf  +++e L++lgi+ ++++a elYksg++ eaik al +r++i++il+++ 
  gi|91773806|ref|YP_566498.1|  79 PES-YAEHVGKPISEIPCPCGECKSYAEHFLTPFLEGLEKLGIHPKVYRADELYKSGRFVEAIKAALIKRDDIAKILKEVS 158
                                   ***.***************************************************************************** PP

                  tRNA-synt_1f 163 geereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkD 243
                                   g++   ++sp++p+c++c++++t++v+ +da++e++ Y+c +cG++++v++ +g gKL+W+vdw+++W++l+V++Ep+GkD
  gi|91773806|ref|YP_566498.1| 159 GKDVLPEWSPFNPICQECKKINTATVTGFDADAETVDYEC-SCGHSGTVSMIGG-GKLTWRVDWPAKWKMLNVTVEPFGKD 237
                                   ****************************************.**********997.************************** PP

                  tRNA-synt_1f 244 haaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldl 323
                                   ha+ GgS+d++++i+ ei++ e+P+++vYe+i+l ++++mssS+G+v++++d+l+v++pevlr+li+r+kP+k++k+d+ +
  gi|91773806|ref|YP_566498.1| 238 HASRGGSYDTGKRIVrEIFDHEPPQPIVYEWIMLGQKGAMSSSSGVVVSISDMLKVVPPEVLRYLIMRTKPEKHIKFDPAQ 318
                                   ********************************************************************************* PP

                  tRNA-synt_1f 324 eilrlvdeYdklerkyfaeqeeeeekek 351
                                    +l lvdeY++l+ +        e  +k
  gi|91773806|ref|YP_566498.1| 319 PLLTLVDEYERLNSNTE-----IEGLNK 341
                                   ***********998764.....344444 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 !   12.1   0.1   1.7e-05     0.061      10      47 ..      30      67 ..      22      69 .. 0.83
   2 !   20.4   0.0   4.9e-08   0.00018     317     362 ..     265     311 ..     252     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                                  -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE-- CS
                  tRNA-synt_1g 10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDe 47
                                  ++g++H+G+++ev+ aD+ +R     g e  f+   D+
  gi|91773806|ref|YP_566498.1| 30 PSGHIHIGNMREVVTADAAYRAMNDAGLESEFIYIADN 67
                                  6899*******************999999888876665 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4.9e-08
                                   EE--EEE.--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
                  tRNA-synt_1g 317 aheyltv.egkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                                   + e++++ + + +S+S gvvv ++++l+ +++++lRY +++++pek+
  gi|91773806|ref|YP_566498.1| 265 VYEWIMLgQKGAMSSSSGVVVSISDMLKVVPPEVLRYLIMRTKPEKH 311
                                   556665515567****************************9999864 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 !   12.7   0.0   1.6e-05     0.057       6      52 ..      17      63 ..      12     141 .. 0.85
   2 !   11.8   0.0   3.1e-05      0.11     251     292 ..     274     315 ..     259     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                  BTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                  tRNA-synt_1e  6 eekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvq 52
                                  ++++ +l + G+t   ++h+G+ R++v+ D   r ++++g + +f+ 
  gi|91773806|ref|YP_566498.1| 17 KNGNKHLVSTGITPSGHIHIGNMREVVTADAAYRAMNDAGLESEFIY 63
                                  5556677789*****************************99988874 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.1e-05
                                   TBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE- CS
                  tRNA-synt_1e 251 gekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfk 292
                                   +  ms s + +++i d+lk + p++lR+l++ ++ +++++f+
  gi|91773806|ref|YP_566498.1| 274 KGAMSSSSGVVVSISDMLKVVPPEVLRYLIMRTKPEKHIKFD 315
                                   346****************************99998888885 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 ?    5.9   0.0    0.0019       6.7       6      23 ..      22      39 ..      17      66 .. 0.81
   2 ?    4.0   0.0    0.0073        26     148     258 ..     226     334 ..     222     350 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0019
                                  -EEEEEEETSSS-BGGGH CS
                  tRNA-synt_1b  6 lrvysGidPTgklHlGyl 23
                                    v +Gi P+g +H+G++
  gi|91773806|ref|YP_566498.1| 22 HLVSTGITPSGHIHIGNM 39
                                  55889***********87 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0073
                                   HTCHSEEEEEGGGH...HHHHHHHHHHHHHHHHSTTSS-EEEEET.-BBSTTSSSBTTCETTCGC-BTTCCHHHH.HHHHH CS
                  tRNA-synt_1b 148 llkadlvpgGsDQk...qnielgrdlarrfnkkevfkkpegltvp.lltgldGekKmSKSagnsaIfLddekesv.kkkiq 223
                                   +l+++++p G+D     +    g  ++r++ +    ++p++++ + ++ g +G   mS+S+g  ++ ++d  + v  ++ +
  gi|91773806|ref|YP_566498.1| 226 MLNVTVEPFGKDHAsrgGSYDTGKRIVREIFDH---EPPQPIVYEwIMLGQKGA--MSSSSGV-VVSISDMLKVVpPEVLR 300
                                   566677777777542224567888999998888...89999999999*******..*******.9*999988764257777 PP

                                   HCHCSTTC.SHHHHHHHHHTHHHCHHHHHHHHCCSE CS
                  tRNA-synt_1b 224 kavtdsde.evekllklktelsnelierleavsgkk 258
                                   + + + +  +  k+ + ++ l+   ++++e +++++
  gi|91773806|ref|YP_566498.1| 301 YLIMRTKPeKHIKFDPAQPLLTL--VDEYERLNSNT 334
                                   76544443355666666666665..55565555555 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 ?   -1.6   0.2       1.1   3.8e+03       2       9 ..      95     102 ..      94     125 .. 0.72
   2 ?   -2.0   0.4       1.4   5.2e+03       3      25 ..     172     196 ..     171     198 .. 0.67
   3 ?   -1.8   0.1       1.2   4.4e+03       4      17 ..     198     212 ..     195     222 .. 0.55
   4 ?   11.6   0.0   8.1e-05      0.29      14      36 ..     247     269 ..     242     272 .. 0.88
   5 ?   -4.0   0.0         5   1.8e+04      19      30 ..     287     298 ..     285     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                       zf-IS66   2 rtCpcCGg 9  
                                   + C +C +
  gi|91773806|ref|YP_566498.1|  95 CPCGECKS 102
                                   45666654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldi 25 
                                   +C +C +    +  g d+  e++d+
  gi|91773806|ref|YP_566498.1| 172 ICQECKKiNtATVTGFDADAETVDY 196
                                   6888887656666666666677666 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                       zf-IS66   4 CpcCGg.llkpiged 17 
                                   C+c+++ +++ ig+ 
  gi|91773806|ref|YP_566498.1| 198 CSCGHSgTVSMIGGG 212
                                   554444445556665 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 8.1e-05
                       zf-IS66  14 igedrvreeldipPakfrViehi 36 
                                    g++ vre++d  P++++V e+i
  gi|91773806|ref|YP_566498.1| 247 TGKRIVREIFDHEPPQPIVYEWI 269
                                   58888****************98 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 5
                       zf-IS66  19 vreeldipPakf 30 
                                   ++  l+++P+++
  gi|91773806|ref|YP_566498.1| 287 ISDMLKVVPPEV 298
                                   677888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 3779.29
//
Query:       gi|91773807|ref|YP_566499.1|  [L=319]
Description: hypothetical protein Mbur_1866 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.9e-11   42.0   0.2    2.2e-10   40.9   0.2    1.6  1  HEPN_Swt1   Swt1-like HEPN
    0.00048   20.2   3.4          1    9.6   0.0    2.7  2  HNH         HNH endonuclease
  ------ inclusion threshold ------
      0.013   15.6   0.2      0.059   13.5   0.0    2.2  3  CxC7        CxC7 like cysteine cluster associated with KDZ tr
      0.052   13.5   0.1       0.34   10.9   0.0    2.3  2  DUF2556     Protein of unknown function (DUF2556)
      0.074   13.4   0.1        1.8    8.9   0.1    2.5  1  DUF2004     Protein of unknown function (DUF2004)
      0.078   13.7   0.3       0.18   12.5   0.3    1.6  1  FYDLN_acid  Protein of unknown function (FYDLN_acid)
       0.16   11.9   3.7       0.22   11.4   1.1    2.6  3  HNH_5       HNH endonuclease


Domain annotation for each model (and alignments):
>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.2   8.7e-14   2.2e-10       4     116 .]     191     317 ..     189     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 8.7e-14
                     HEPN_Swt1   4 dlLeegLrpfverelskaygedwweevea...........slekdeeek.......kesekeiskldvqdllrvitenWke 66 
                                   +++e++Lr f+++++++++ge+++++++            +  +d   +        ++++++ + d++d  r+i +nW +
  gi|91773807|ref|YP_566499.1| 191 YCIENSLRLFIDKRFKEEHGENYLDKIAIvrglsdklknrK--AD---EekhkwlsLRGGNDLFYFDLEDFSRLIERNW-S 265
                                   699*******************9999887787877554222..22...123456877799*******************.6 PP

                     HEPN_Swt1  67 vFkkklsrae..rslaseLrevRNkwaHqesfstddayraldtierllrais 116
                                   vF+k++++ +   + ++e+ + RN +aH++ +  d+        +++l++is
  gi|91773807|ref|YP_566499.1| 266 VFEKDFPELHwiTAKITEIAKCRNLIAHNSYVGHDEKVLLSLYYKQILKQIS 317
                                   6*******9999*******************999998888888888888886 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   3.5    0.0015       3.9      25      42 ..      97     114 ..      81     119 .. 0.81
   2 !    9.6   0.0    0.0004         1       8      36 ..     143     171 ..     140     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                           HNH  25 ggaddieNlqllCksCHn 42 
                                   ++  d++Nl  +C++C++
  gi|91773807|ref|YP_566499.1|  97 EKYYDYNNLNVVCPTCNQ 114
                                   56689************8 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0004
                           HNH   8 fhksealevdHiipisqggaddieNlqll 36 
                                   f+ s+ l v Hi+++ q++++   Nl+++
  gi|91773807|ref|YP_566499.1| 143 FKLSQGLSVEHIVSKIQEDTTVTKNLEAI 171
                                   5666889*******************987 PP

>> CxC7  CxC7 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.4   3.6e+03      21      28 ..     108     115 ..      95     121 .. 0.79
   2 ?   -3.6   0.0       5.2   1.3e+04      13      30 ..     118     135 ..     116     140 .. 0.61
   3 ?   13.5   0.0   2.3e-05     0.059       1      52 [.     263     312 ..     263     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                          CxC7  21 ecsecgdi 28 
                                    c+ c++ 
  gi|91773807|ref|YP_566499.1| 108 VCPTCNQF 115
                                   59999975 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.2
                          CxC7  13 frvPfsliecsecgdifk 30 
                                   + +   l++c++    +k
  gi|91773807|ref|YP_566499.1| 118 NNILRKLTKCANELGYYK 135
                                   556666777876555555 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 2.3e-05
                          CxC7   1 nWsrfsedykkefrvPfsliecsecgdifkdspvGyvGdGrkGvlrgfysti 52 
                                   nWs f  d+ + + +   ++e ++c +        yvG+  k  l  +y +i
  gi|91773807|ref|YP_566499.1| 263 NWSVFEKDFPELHWITAKITEIAKCRNLIAHN--SYVGHDEKVLLSLYYKQI 312
                                   8************************9988766..7**************876 PP

>> DUF2556  Protein of unknown function (DUF2556)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.75   1.9e+03      35      43 ..      83      91 ..      67      93 .. 0.69
   2 ?   10.9   0.0   0.00013      0.34      23      40 ..     274     291 ..     259     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.75
                       DUF2556 35 kCRnmnsvn 43
                                   CR  +s+n
  gi|91773807|ref|YP_566499.1| 83 ICRRHDSIN 91
                                  599999999 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                       DUF2556  23 mqwielltteidkCRnmn 40 
                                   ++wi    tei kCRn+ 
  gi|91773807|ref|YP_566499.1| 274 LHWITAKITEIAKCRNLI 291
                                   79**************85 PP

>> DUF2004  Protein of unknown function (DUF2004)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00071       1.8       2     100 ..      48     165 ..      47     169 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00071
                                   SHHHHHHHHHHHHHHHTT---EEEEEEEE......................S--HHHHHHHHHHHHHHHS-HHHHHHHH.. CS
                       DUF2004   2 ldeearkaladylknekdtvtkyidfHvd......................elgpeieeellekddlsklteeellkklkL 60 
                                   +d +++++l+d ++n+ +   ++i++ +d                        +++ ++ + +  +  +  e+++l+kl  
  gi|91773807|ref|YP_566499.1|  48 YDSDINQFLRDAYENDPESIADFINYLIDslprhiicrrhdsincalynekYYDYNNLNVVCP--TCNQFLENNILRKL-- 124
                                   788999**********9999*********7777777766666666555433222222221111..12233333333333.. PP

                                   ...................HGGGGT-------.-EEE-SSS-S- CS
                       DUF2004  61 vrigllpdeea....rfavldfklepdftdellvveldeegdvq 100
                                      +  + e      ++  ++fkl++ ++ e++v +++e+ +v+
  gi|91773807|ref|YP_566499.1| 125 ---TKCANELGyyksEEGFFEFKLSQGLSVEHIVSKIQEDTTVT 165
                                   ...22222222333344566677777777777666666666665 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   7.1e-05      0.18      12      41 ..      92     121 ..      90     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.1e-05
                    FYDLN_acid  12 CpscgakFYDLnkdPivcpkcgeefepeev 41 
                                   C   ++k+YD n+  +vcp c++  e + +
  gi|91773807|ref|YP_566499.1|  92 CALYNEKYYDYNNLNVVCPTCNQFLENNIL 121
                                   666789***************998887766 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.6   6.7e+03       8      21 ..      24      37 ..      22      39 .. 0.72
   2 ?   11.4   1.1   8.7e-05      0.22      28      53 ..     101     126 ..      99     129 .. 0.89
   3 ?   -1.2   0.0      0.75   1.9e+03      11      20 ..     147     156 ..     144     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.6
                         HNH_5  8 iaekelseeHIiPe 21
                                  ia+++l  eHI ++
  gi|91773807|ref|YP_566499.1| 24 IADSSLLGEHIPHN 37
                                  56677778999776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.7e-05
                         HNH_5  28 tisnlvtlCkkCNqkkgqkvdaalsk 53 
                                   + +nl ++C +CNq + +++ ++l+k
  gi|91773807|ref|YP_566499.1| 101 DYNNLNVVCPTCNQFLENNILRKLTK 126
                                   679999**************999986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.75
                         HNH_5  11 kelseeHIiP 20 
                                   + ls eHI+ 
  gi|91773807|ref|YP_566499.1| 147 QGLSVEHIVS 156
                                   57899***85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2272.55
//
Query:       gi|91773808|ref|YP_566500.1|  [L=349]
Description: Orn/DAP/Arg decarboxylase 2 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   55.4   0.0    7.4e-15   55.0   0.0    1.2  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
      0.001   19.3   0.0     0.0013   18.9   0.0    1.5  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   8.2e-19   7.4e-15      56     247 .]      62     243 ..      18     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 8.2e-19
                                   HCTTTGGGEEEEESS--HHHHHHHHHCTHTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSS CS
                 Orn_Arg_deC_N  56 aagvsperiifanpckqreelryalekgvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKF 132
                                   ++  + +r+ f +++ + e +r++ ekg++ + vdn+  l+ l  ++++      +llR k+  ++++ +     ++   F
  gi|91773808|ref|YP_566500.1|  62 KHTEDMSRVLFLAQAWTPEMIRELYEKGIRSFAVDNEFDLDTLLSTVDDtdwkITLLLRLKL--KEHSIRT----ERYFVF 136
                                   45567799***********************************9999998877888888887..4444444....45699* PP

                                   SEEHCHHHHHHHHHHHHTTEEEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSST CS
                 Orn_Arg_deC_N 133 GaaleeavealleaakeenlqlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplk 213
                                   G++ ++  + + ++  ++n++ +Gv+fH   +  +  +++  +e+al+          +++iL++GGG+ +ey +++ ++ 
  gi|91773808|ref|YP_566500.1| 137 GMSSDTINKRIAQLKGNKNIEKLGVHFHRKTQNVNEWKIQPEIEDALTE-----GTLEAIDILNIGGGLPSEYANTNVDV- 211
                                   ****99999**********************************998753.....3334799*************643333. PP

                                   HHHHHHHHHHHHHHHHHTSSS-EEEE--SHHHHG CS
                 Orn_Arg_deC_N 214 leeiaekirealeeafpgdkevtiiaEpGRalva 247
                                   ++ i + i+e  e +  ++ke+++++EpGR+++a
  gi|91773808|ref|YP_566500.1| 212 INGIFRRISELREWL--HEKEIKLMIEPGRFISA 243
                                   466666666666555..6799**********986 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 !   18.9   0.0   1.5e-07    0.0013       6      98 .]     244     329 ..      27     329 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-07
                                   GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-E.ESBT...T-SCEEC.EEEEEEEE-SSSSTT-EEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC   6 eagvLvtrViavkesekkkfvivdaGmndllrpalygsfhei.pvke...eeaekeeeeeeevdvvGptCesgDvlakdre 82 
                                    ag Lv+++++v +    + +iv+a++        y+s +++  v      e+e  +++ e++ v G t  s+D +  +++
  gi|91773808|ref|YP_566500.1| 244 PAGKLVSHITGVYD----NNIIVNASV--------YNSDMDAiLVPVklrIEGEVGNDSGEPYVVKGCTPCSMDLFRYRVY 312
                                   68899999999994....469******........888876644433678334445557789******************* PP

                                   EEE.--TT-EEEESS-S CS
                                   xxx.xxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC  83 lpe.levGdllafedaG 98 
                                   l++ +++Gd l+f +aG
  gi|91773808|ref|YP_566500.1| 313 LKDePKIGDELVFINAG 329
                                   **9************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.40
# Mc/sec: 2625.14
//
Query:       gi|91773809|ref|YP_566501.1|  [L=324]
Description: deoxyhypusine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-98  329.0   0.5    2.6e-98  328.8   0.5    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 !  328.8   0.5  1.5e-102   2.6e-98       1     285 [.      17     298 ..      17     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 328.8 bits;  conditional E-value: 1.5e-102
                            DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkk 81 
                                   el++sye igfq+ +l++a d++ km k++++++fl++tsn+++sGlr+++a+l++ ++ dvivtT gg+eeD++ka+g++
  gi|91773809|ref|YP_566501.1|  17 ELVDSYEFIGFQSVELQRASDVIVKM-KKDSAKVFLTFTSNMVTSGLRGFFAQLIDLGVADVIVTTVGGLEEDIMKATGED 96 
                                   69************************.67789************************************************* PP

                            DS  82 tylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSilywAykndip 162
                                   + +g+f++dd eL+e+ginR+gnll++ e+y +fe+ v +il++l e+q++w++s++++e+G  ++de+Sily+A+kn++p
  gi|91773809|ref|YP_566501.1|  97 FQIGSFHTDDVELHEQGINRVGNLLIKTESYMNFESLVDKILKELYEKQNRWAVSDMLREIGLMLDDESSILYQAAKNNVP 177
                                   ********************************************************************************* PP

                            DS 163 vfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlmrngadyavyitta 243
                                   +fcpa+tDg++G++l lf+  +e+ ++++d+vkD+ ++   + + ++ g+i lGG+++Khh++ ++l++ ga+yavy+tta
  gi|91773809|ref|YP_566501.1| 178 IFCPAITDGAFGFHLYLFQ--QEHPDFIVDVVKDFGNILFASSHDDRKGVIALGGSISKHHAILSTLLNGGAEYAVYMTTA 256
                                   *************999999..57778******************************************************* PP

                            DS 244 qefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlv 285
                                   +   Gs+sga+++Ea+Swgk+k+e++ ++v++D++i++PL +
  gi|91773809|ref|YP_566501.1| 257 HRTSGSMSGANTNEAKSWGKVKDESDVATVIGDVSITFPLAM 298
                                   ***************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2088.77
//
Query:       gi|91773810|ref|YP_566502.1|  [L=247]
Description: hypothetical protein Mbur_1869 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-46  158.1   5.0    4.6e-46  157.8   5.0    1.1  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   5.0   2.6e-50   4.6e-46       1     200 []      44     244 ..      44     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 2.6e-50
                         SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysyengknkitgye 81 
                                   I+ +Gsae +v+pD+a+++++v  ++++ +ea+ e+a+ m++vl+ lk lg+++kdi+ts +s++p y+y +g ++i+gy 
  gi|91773810|ref|YP_566502.1|  44 IQMSGSAEEKVVPDTASISIGVVIDADTSKEASVENAAIMATVLQELKDLGLEDKDIRTSYVSVYPIYNY-DGVRTIEGYS 123
                                   789*********************************************99*******************9.9********* PP

                         SIMPL  82 asqsltvkfrdldklgevldaavka.aneingvsfslsde..delrdeareeAvkdArakAealAkalgvklgkv..vsis 157
                                   as+s+++ +++l+ l++++d+ ++a an+i+gvsfs+sde  +elr+e+++eAv+dA  kAe lA++lgv++ +v   sis
  gi|91773810|ref|YP_566502.1| 124 ASNSVEIITTNLELLSDIVDKSAAAgANQIGGVSFSVSDEmqKELREELIDEAVADASSKAELLADSLGVRIVGVqaSSIS 204
                                   **************************************9999999***************************988444554 PP

                         SIMPL 158 esgsnpyappapamaaaaaaaasaatpfepgeievtasVtvvf 200
                                   +   + +++   + a++a+ +  ++tp+ +ge +v++sV+v++
  gi|91773810|ref|YP_566502.1| 205 D---GFSSRVFFDVAEEAMDMGGSSTPIMSGESTVSMSVHVTY 244
                                   4...2233445556666666999******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1640.89
//
Query:       gi|91773811|ref|YP_566503.1|  [L=180]
Description: pyruvoyl-dependent arginine decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for 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-61  204.8   0.0    7.8e-61  204.6   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.6   0.0   4.4e-65   7.8e-61       1     162 []       2     179 ..       2     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 4.4e-65
                      PvlArgDC   1 vPkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrlia 81 
                                   +Pkk+f++kG+g +k++lasF+lAL+dAgIe+fNLv+vSSilPp+++ivs++egl+el pG+iv++vma++++nep+r+ia
  gi|91773811|ref|YP_566503.1|   2 IPKKAFVVKGTGVHKDKLASFELALRDAGIEKFNLVTVSSILPPNCSIVSRKEGLEELAPGQIVYCVMAKNQTNEPERMIA 82 
                                   7******************************************************************************** PP

                      PvlArgDC  82 aavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrgl................leekiietkeievaave 146
                                   aa+g a+p d++ +Gyi+E+++fge+e++a+ +ae+laa+mlatt+g+                ++++i++t++++   ++
  gi|91773811|ref|YP_566503.1|  83 AAIGNAVPVDSNDYGYISEHHSFGEDERTAGIYAEDLAATMLATTLGIefdadsawgerervykASGHIFDTVHYCRCVKG 163
                                   **************************************************************98888************** PP

                      PvlArgDC 147 akvekygtvlaaavfv 162
                                   ++++ ++tv++ +vfv
  gi|91773811|ref|YP_566503.1| 164 DENGLWTTVVVSMVFV 179
                                   **************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1334.83
//
Query:       gi|91773812|ref|YP_566504.1|  [L=226]
Description: iron dependent repressor [Methanococcoides burtonii DSM 6242]
Scores for 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-19   67.3   0.1    1.7e-18   66.5   0.1    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      8e-17   61.1   0.0    1.2e-15   57.3   0.0    2.5  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    1.4e-12   47.6   0.2    2.8e-12   46.7   0.1    1.6  1  FeoA            FeoA domain
    1.8e-06   27.9   0.1    5.6e-06   26.2   0.0    1.8  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    5.1e-06   26.3   0.0    1.4e-05   24.9   0.0    1.7  1  MarR_2          MarR family
    2.7e-05   23.6   0.0    5.9e-05   22.5   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    7.2e-05   22.6   0.0    0.00015   21.6   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    9.5e-05   22.2   0.0    0.00026   20.9   0.0    1.7  1  MarR            MarR family
    0.00017   21.3   0.0    0.00033   20.4   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    0.00093   19.7   0.0     0.0019   18.7   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
     0.0024   17.5   0.0     0.0047   16.6   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
     0.0034   17.7   0.0      0.032   14.6   0.0    2.3  2  Rrf2            Transcriptional regulator
     0.0037   17.0   0.0     0.0077   16.0   0.0    1.4  1  LexA_DNA_bind   LexA DNA binding domain
     0.0051   16.7   0.0      0.012   15.5   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.024   14.3   0.0      0.058   13.1   0.0    1.6  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.038   14.4   0.0      0.082   13.3   0.0    1.6  1  FaeA            FaeA-like protein
       0.04   13.9   0.1        0.6   10.1   0.0    2.3  2  HTH_36          Helix-turn-helix domain
      0.058   13.7   0.0       0.13   12.5   0.0    1.6  1  KORA            TrfB plasmid transcriptional repressor
      0.064   13.2   0.0       0.18   11.8   0.0    1.8  1  HTH_11          HTH domain
       0.13   12.4   0.1        0.3   11.2   0.1    1.6  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.13   12.4   0.2        7.3    6.8   0.0    2.2  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.14   12.6   0.2       0.35   11.3   0.2    1.6  1  MFMR_assoc      Disordered region downstream of MFMR


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.1   2.1e-21   1.7e-18       1      60 []       1      61 [.       1      61 [. 0.96

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 2.1e-21
                                  X--HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                Fe_dep_repress  1 dLvestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                  ++ +++E+YLetI +l +  + +vk+kd+ae+L+ s +sVsem++kL+++G+v++e+y g+
  gi|91773812|ref|YP_566504.1|  1 MTGDRIEEYLETIDSLVKsRGTPVKNKDIAEELGFSQASVSEMVQKLADEGLVIHEPYHGV 61
                                  6789**************78889***********************************997 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 !   57.3   0.0   1.4e-18   1.2e-15       1      60 [.      64     123 ..      64     134 .. 0.92
   2 ?    0.4   0.0      0.85     7e+02      41      66 ..     198     223 ..     194     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.4e-18
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.S CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpe 60 
                                   T +G    +++ r+h ++e+f++dvl +++e ah+eA+ lEh +s+ ++e ++++lg+ +
  gi|91773812|ref|YP_566504.1|  64 TNRGVLQVNSIRRKHHVIETFFSDVLALEPEVAHNEACGLEHTVSDLVVESMCNYLGNNN 123
                                   7888899999***********************************************865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.85
                                   GGGS-HHHHHHHHHHCT-.SB-TTS- CS
                 Fe_dep_repr_C  41 EhalseelierldellgfpeecPhgd 66 
                                   E al  e+++++   lg  ++ P+g+
  gi|91773812|ref|YP_566504.1| 198 EIALGNEIAKKIFVRLGMRKRYPRGN 223
                                   66788889999999999999999887 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.1   3.5e-15   2.8e-12       1      73 [.     142     212 ..     142     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 3.5e-15
                                   EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                          FeoA   1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73 
                                   v+L+dlkeG+ g+++ +  + +  + rL ++G+  G+ iev  r++ +g +++  ++t++aLg e+A++I+V+
  gi|91773812|ref|YP_566504.1| 142 VSLADLKEGDFGTVVMMTLS-DSSKGRLSSLGMITGENIEVK-RKQKQGSTSILTRGTEIALGNEIAKKIFVR 212
                                   68***************876.7799*****************.56678************************8 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   6.9e-09   5.6e-06      20      66 ..      22      70 ..       6      71 .. 0.85
   2 ?   -1.8   0.0       3.8   3.1e+03      44      61 ..     167     183 ..     166     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.9e-09
                                  EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.EE.EEES-HHHHH CS
                     HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrg.rr.irildleaLr 66
                                   p+ ++++A+ lG ++ +vs + ++L +egl+  + ++ ++++++  L+
  gi|91773812|ref|YP_566504.1| 22 TPVKNKDIAEELGFSQASVSEMVQKLADEGLVIHEpYHgVELTNRGVLQ 70
                                  5999***************************985434449999998775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.8
                                   HHHHTTSEEETEEEEES- CS
                     HTH_Crp_2  44 eLkreglisrgrririld 61 
                                   +L+  g+i+ ++ i+++ 
  gi|91773812|ref|YP_566504.1| 167 RLSSLGMITGEN-IEVKR 183
                                   789999999887.99876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.7e-08   1.4e-05      25      55 ..      27      57 ..      16      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                                  HHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 25 gelarrlglsksavsrilkrLvaaGLverrp 55
                                  +++a++lg s+++vs ++++L + GLv  +p
  gi|91773812|ref|YP_566504.1| 27 KDIAEELGFSQASVSEMVQKLADEGLVIHEP 57
                                  79*************************8775 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   7.3e-08   5.9e-05      19      47 ..      25      53 ..      21      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.3e-08
                        HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   ++++Ae+lg S++ v++ +++L +eGl+
  gi|91773812|ref|YP_566504.1| 25 KNKDIAEELGFSQASVSEMVQKLADEGLV 53
                                  69*************************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.8e-07   0.00015      22      55 ..      23      56 ..      15      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-07
                                  CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVere 55
                                  p + ++iaeelg ++++v e++++L d GlV  e
  gi|91773812|ref|YP_566504.1| 23 PVKNKDIAEELGFSQASVSEMVQKLADEGLVIHE 56
                                  67789**************************877 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.2e-07   0.00026      17      47 ..      23      53 ..      15      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-07
                                  TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR 17 plsvseLakklgvskstvtrvldrLekkGli 47
                                  p +++++a+ lg s+++v++++ +L ++Gl+
  gi|91773812|ref|YP_566504.1| 23 PVKNKDIAEELGFSQASVSEMVQKLADEGLV 53
                                  57899*************************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 !   20.4   0.0   4.1e-07   0.00033      14      48 ..      19      53 ..      15      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.1e-07
                                  TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                  +++ +++++++A+++g + ++v+ ++q L  +G+v
  gi|91773812|ref|YP_566504.1| 19 SRGTPVKNKDIAEELGFSQASVSEMVQKLADEGLV 53
                                  566789****************************9 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.3e-06    0.0019      11      50 ..      12      55 ..       8      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-06
                        HTH_27 11 lir....hrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                  +i      r+ ++k +d+++ l ++++++s+++ kL   GLv +
  gi|91773812|ref|YP_566504.1| 12 TIDslvkSRGTPVKNKDIAEELGFSQASVSEMVQKLADEGLVIH 55
                                  555555578888999***************************44 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.7e-06    0.0047      12      62 ..      12      61 ..       2      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                                  HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                          GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                   I s + + G++  + +++a+e+g+s  +v e  ++L+ eglv+ ++  G+
  gi|91773812|ref|YP_566504.1| 12 TIDSLVKSRGTPV-KNKDIAEELGFSQASVSEMVQKLADEGLVIHEPYHGV 61
                                  5777777788999.999**************************98887665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.9e-05     0.032      21      55 ..      19      53 ..      10      59 .. 0.90
   2 ?   -0.2   0.0       1.6   1.3e+03       6      30 ..     149     173 ..     146     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                                  STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglv 55
                                  ++++pv+ ++iae+ + s+  ++ +++kL+ +glv
  gi|91773812|ref|YP_566504.1| 19 SRGTPVKNKDIAEELGFSQASVSEMVQKLADEGLV 53
                                  45678*****************************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHSSTCC-B-HHH CS
                          Rrf2   6 kteyalhallyLakeeeeepvssee 30 
                                   ++++++ +++ L+  ++++  s+  
  gi|91773812|ref|YP_566504.1| 149 EGDFGTVVMMTLSDSSKGRLSSLGM 173
                                   6789999999999999998555554 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 !   16.0   0.0   9.4e-06    0.0077       8      57 ..       6      54 ..       3      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.4e-06
                                  HHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                 LexA_DNA_bind  8 QrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyie 57
                                   +e l+ i + ++++g p   ++ia++lg++  ++v e  ++L+  G++ 
  gi|91773812|ref|YP_566504.1|  6 IEEYLETIDSLVKSRGTPVKNKDIAEELGFS-QASVSEMVQKLADEGLVI 54
                                  568899************************7.99***********99985 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 !   15.5   0.0   1.4e-05     0.012      17      45 ..      25      53 ..      13      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLV 45
                                  +  ++aeelg sq+ vS+   kL ++GLV
  gi|91773812|ref|YP_566504.1| 25 KNKDIAEELGFSQASVSEMVQKLADEGLV 53
                                  678*************************9 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.1e-05     0.058       8      55 ..       8      55 ..       3      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-05
                  HrcA_DNA-bdg  8 eilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                  e l+++ +l + ++++vK ++iAe l+  +  v  ++q L   gLv  
  gi|91773812|ref|YP_566504.1|  8 EYLETIDSLVKSRGTPVKNKDIAEELGFSQASVSEMVQKLADEGLVIH 55
                                  5677888899999***************************99999976 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0    0.0001     0.082       5      45 ..       6      53 ..       2      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                  HHHHHHH........S----HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                          FaeA  5 Ileylnsi.......kapckTreiAdalglsaYQaRyYLeqLekegki 45
                                  I eyl  i       ++p+k ++iA+ lg s+  +    ++L  eg +
  gi|91773812|ref|YP_566504.1|  6 IEEYLETIdslvksrGTPVKNKDIAEELGFSQASVSEMVQKLADEGLV 53
                                  5567777777799989***************99999999999999877 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00074       0.6      27      54 ..      25      52 ..      15      53 .. 0.91
   2 ?    1.1   0.1      0.48   3.9e+02       9      26 ..     110     128 ..     108     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00074
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                   ++++a+ lg s  +vs  +++L++ G+
  gi|91773812|ref|YP_566504.1| 25 KNKDIAEELGFSQASVSEMVQKLADEGL 52
                                  599*********************9987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.48
                        HTH_36   9 lllgslasfankngg.cfp 26 
                                   l+  s++ + ++n++ c p
  gi|91773812|ref|YP_566504.1| 110 LVVESMCNYLGNNNIdCKP 128
                                   6777999999999998855 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   0.00016      0.13      32      56 ..      24      48 ..      14      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                          KORA 32 kkqadvatelgltkqavsqavkrvw 56
                                  +k +d+a+elg ++  vs++v++  
  gi|91773812|ref|YP_566504.1| 24 VKNKDIAEELGFSQASVSEMVQKLA 48
                                  4789******************975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.18       9      46 ..      16      54 ..       2      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                        HTH_11  9 Lleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                  L ++rg+ +  +++AeeL+ S + v   +++L + g+ I
  gi|91773812|ref|YP_566504.1| 16 LVKSRGTpVKNKDIAEELGFSQASVSEMVQKLADEGLVI 54
                                  56889999************************9999655 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00037       0.3      26      77 ..      27      78 ..      15      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                       DUF2250 26 ksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhH 77
                                  k ia+el  ++  v+e+++kL + GL+ +   + +  t++   + +  +++H
  gi|91773812|ref|YP_566504.1| 27 KDIAEELGFSQASVSEMVQKLADEGLVIHEPYHGVELTNRGVLQVNSIRRKH 78
                                  889************************9999999999988776655555444 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 ?    6.8   0.0     0.009       7.3      20      54 ..      25      59 ..      12      85 .. 0.79
   2 ?    3.4   0.1       0.1        85      42      67 ..     168     193 ..     164     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.009
                B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsii 54
                                    +d+a e++ +  s+   +++L + gL+   ++ 
  gi|91773812|ref|YP_566504.1| 25 KNKDIAEELGFSQASVSEMVQKLADEGLVIHEPYH 59
                                  568999***********************998886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.1
                B-block_TFIIIC  42 LekkgLIvkqsiidsatkksistsll 67 
                                   L++ g I++ +i    ++k+ sts+l
  gi|91773812|ref|YP_566504.1| 168 LSSLGMITGENIEVKRKQKQGSTSIL 193
                                   8999********55556667788887 PP

>> MFMR_assoc  Disordered region downstream of MFMR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00043      0.35       7      39 ..     163     195 ..     159     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                    MFMR_assoc   7 rskgslgslnmitgknneegkssegsangalsq 39 
                                    skg l+sl mitg+n e  +++++++ ++l +
  gi|91773812|ref|YP_566504.1| 163 SSKGRLSSLGMITGENIEVKRKQKQGSTSILTR 195
                                   59***************9888888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1338.85
//
Query:       gi|91773813|ref|YP_566505.1|  [L=658]
Description: ferrous iron transport protein B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-58  195.3   0.1    6.9e-58  194.6   0.1    1.3  1  FeoB_N       Ferrous iron transport protein B
    1.4e-25   89.7  25.3    1.5e-14   54.2   7.5    3.1  4  Gate         Nucleoside recognition
    7.2e-19   67.9   0.0    1.4e-18   67.0   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    6.6e-13   48.1   0.1    6.6e-13   48.1   0.1    2.8  2  FeoB_C       Ferrous iron transport protein B C terminus
    0.00068   19.7   0.7       0.41   10.7   0.0    2.4  2  Dynamin_N    Dynamin family
    0.00071   19.0   0.0     0.0012   18.3   0.0    1.3  1  AIG1         AIG1 family
     0.0037   16.7   0.0      0.007   15.8   0.0    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
  ------ inclusion threshold ------
      0.038   14.5   0.1      0.097   13.2   0.1    1.7  1  FeoB_Cyto    FeoB cytosolic helical domain
      0.051   13.3   0.2       0.17   11.7   0.0    1.8  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.077   12.5   0.0       0.27   10.8   0.0    1.8  1  GTP_EFTU     Elongation factor Tu GTP binding domain
       0.16   11.9   0.2         14    5.6   0.0    2.4  2  RsgA_GTPase  RsgA GTPase


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 !  194.6   0.1   4.2e-61   6.9e-58       2     150 ..      25     173 ..      24     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.6 bits;  conditional E-value: 4.2e-61
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvv 82 
                                   t+a+vGnp vGk+++f +ltg+   v+N+pG+tve ++g++++ +k++++vDlPGiYsl a +e+ekv++++ll+e pd++
  gi|91773813|ref|YP_566505.1|  25 TIAFVGNPSVGKSAFFSRLTGVGVVVANYPGTTVELTHGSVNVGSKKLDVVDLPGIYSLGASTEDEKVSKRYLLREYPDAI 105
                                   89******************************************************************************* PP

                                   EEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHH CS
                        FeoB_N  83 vnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegie 150
                                   +nvvdat+lernL+Ltlqlle+++p+v+aln +d+a++ gieid++kLse+Lgvpvv+t+a+k+ g+e
  gi|91773813|ref|YP_566505.1| 106 INVVDATRLERNLFLTLQLLEFNIPMVVALNQMDAAKEMGIEIDIEKLSEILGVPVVPTIATKGFGLE 173
                                   ***************************************************************99987 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       9.2   1.5e+04      38      61 ..     125     146 ..     120     148 .. 0.74
   2 ?   -3.6   0.2       7.9   1.3e+04      87      94 ..     311     318 ..     296     336 .. 0.54
   3 !   47.4   2.6   1.2e-15     2e-12       4     111 ..     369     461 ..     366     462 .. 0.95
   4 !   54.2   7.5   9.4e-18   1.5e-14       2     111 ..     525     630 ..     524     631 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.2
                          Gate  38 lgqeldwkatvslltgfaakevvv 61 
                                   l   ++ +++v+l    aake+++
  gi|91773813|ref|YP_566505.1| 125 LE--FNIPMVVALNQMDAAKEMGI 146
                                   55..88888888888888888877 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.9
                          Gate  87 afllfvll 94 
                                    + +fv++
  gi|91773813|ref|YP_566505.1| 311 LLTFFVVF 318
                                   22222222 PP

  == domain 3  score: 47.4 bits;  conditional E-value: 1.2e-15
                          Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpks 84 
                                   a+p+i+++ ++++++++s++l r+++ll+   ++ g  l+++a+++l++g++   ++v+++++++         + +t ++
  gi|91773813|ref|YP_566505.1| 369 AIPYIAVFYVILSLFEDSGYLTRASFLLDNWTHKVG--LHGRAIIPLILGMG---CNVPAIMSTR---------TLNTVRE 435
                                   99**********************************..**************...*********9.........******* PP

                          Gate  85 alafllfvllytpcvatlavivrelgs 111
                                   + ++ ++++l tpc a++++i++ +g+
  gi|91773813|ref|YP_566505.1| 436 KRIASVLIAL-TPCSARTVIIIGLVGT 461
                                   9999999999.69**********9997 PP

  == domain 4  score: 54.2 bits;  conditional E-value: 9.4e-18
                          Gate   2 lkagpiillasiliwflssssllgrigkllepv.faplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdt 81 
                                   + a+p+++++s+l++++ s ++l+ + +++epv +  lg  l+  a+++l++g++ ke+++++l++l      +  +   t
  gi|91773813|ref|YP_566505.1| 525 YVAFPLLVAGSALLGLIDSLGVLDVFQNAVEPVsVGLLG--LPAFAATALIFGILRKEMALQILAVLA---GTANFALVLT 600
                                   679******************************9999**..***********************9994...556667999* PP

                          Gate  82 pksalafllfvllytpcvatlavivrelgs 111
                                   p + ++f +++++y+pcvat+a+++ elg+
  gi|91773813|ref|YP_566505.1| 601 PLQMYSFAVITTIYIPCVATIAILKNELGW 630
                                   ****************************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 !   67.0   0.0   8.6e-22   1.4e-18       2     113 ..      26     136 ..      25     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 8.6e-22
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS.HHHHHH.HHHHHHHHHHCTSEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie.gaseek.glgkaflaleeadlil 80 
                                   +a+vG+p vGKS ++++ltg  + v+++pgtT + ++g v+++ k++ +vD+pG+++ gas+e  +++k++l  e  d+i+
  gi|91773813|ref|YP_566505.1|  26 IAFVGNPSVGKSAFFSRLTGVGVVVANYPGTTVELTHGSVNVGSKKLDVVDLPGIYSlGASTEDeKVSKRYLLREYPDAII 106
                                   89***************************************999**********98775555555999999965557**** PP

                                   EEEETTTTCSHHH...HHHHHHHHHHTTSEEEEEEE CS
                      MMR_HSR1  81 lvvdaseeklkpl...deeleelleeakkplilvln 113
                                    vvda+ + l+++     +l e     ++p++++ln
  gi|91773813|ref|YP_566505.1| 107 NVVDAT-R-LERNlflTLQLLE----FNIPMVVALN 136
                                   ****77.3.4333000233344....4588888887 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.8       5.2   8.5e+03       4      13 ..     309     318 ..     303     325 .. 0.47
   2 !   48.1   0.1   4.1e-16   6.6e-13       2      53 .]     469     519 ..     468     519 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.2
                        FeoB_C   4 lYllgilval 13 
                                     ll ++v++
  gi|91773813|ref|YP_566505.1| 309 ALLLTFFVVF 318
                                   2334444444 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 4.1e-16
                        FeoB_C   2 fslYllgilvallvalllkkttlkgepspfvmELPpYrlPslknvliktweR 53 
                                   +s+Y+l ++++++++++l k  l+ge+++++mE+ p+r+P+ + ++ ktw R
  gi|91773813|ref|YP_566505.1| 469 ISIYVLELVIIFATGWVLGKG-LPGERTGLIMEMAPLRKPDRRATFQKTWLR 519
                                   79******************8.****************************87 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.3    0.0035       5.8       1      27 [.      26      52 ..      26      62 .. 0.81
   2 !   10.7   0.0   0.00025      0.41     100     140 ..      69     113 ..      59     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0035
                                  EEEEEBTTTTHHHHHHHHHTS--S--- CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprg 27
                                  ia+vG+ S GKS++   L+g  + +  
  gi|91773813|ref|YP_566505.1| 26 IAFVGNPSVGKSAFFSRLTGVGVVVAN 52
                                  89*****************99876554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00025
                                   S-SEEEEE---B-S..SSGTTSHHHHHHH..STTEEEEEEEETTS CS
                     Dynamin_N 100 vkgltlvDlPGlds..vnkrdqelvkeyi..kkadiilavtsanh 140
                                    k+l +vDlPG+ s    ++d+++ k+y+  +  d+i+ v++a  
  gi|91773813|ref|YP_566505.1|  69 SKKLDVVDLPGIYSlgASTEDEKVSKRYLlrEYPDAIINVVDATR 113
                                   578999********76778888*******87778*******9975 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   7.1e-07    0.0012       2      98 ..      25     116 ..      24     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.1e-07
                                   EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT CS
                          AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllsee 82 
                                   ti  vG   +GkSa    + g  +   ++   + t + ++ s  +  kk++V+D Pg+ +l +s++   +++++++ll e 
  gi|91773813|ref|YP_566505.1|  25 TIAFVGNPSVGKSAFFSRLTGVGVVVANY--PGTTVELTHGSVNVGSKKLDVVDLPGIYSLGASTE--DEKVSKRYLLREY 101
                                   67889999999999999999988888885..6777888899999999****************999..6789999999988 PP

                                   -ESEEEEEEETTB-SH CS
                          AIG1  83 gihalllvlslgrfte 98 
                                    ++a++ v++++r+++
  gi|91773813|ref|YP_566505.1| 102 -PDAIINVVDATRLER 116
                                   .9*******9999875 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.3e-06     0.007       5      95 ..      25     121 ..      22     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.3e-06
                                   EEEEE-STTSSHHHHHHHHHHS.S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG.EE....EE CS
                         SRPRB   5 avllvGlsdsGKTslftrLttd.svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkakss.lk....gl 79 
                                   ++ +vG    GK ++f rLt    v   +     ++++   +   +kl+++D+PG  +l     ++ + k+  l+    ++
  gi|91773813|ref|YP_566505.1|  25 TIAFVGNPSVGKSAFFSRLTGVgVVVANYPGTTVELTHGSVNVGSKKLDVVDLPGIYSLGASTEDEKVSKRYlLReypdAI 105
                                   6889***************97536677777778888888889999**************987777766665533333338* PP

                                   EEEEETTS-HHHHHHH CS
                         SRPRB  80 vfvvDStidpkevkev 95 
                                   + vvD+t  ++++  +
  gi|91773813|ref|YP_566505.1| 106 INVVDATRLERNLFLT 121
                                   *******999988655 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     6e-05     0.097      32      89 ..     218     278 ..     194     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6e-05
                     FeoB_Cyto  32 lklLegDeelleelkedpelraev....eearkeleaelgedledvIvdarykfiegilrev 89 
                                   ++ Le+Dee+ +     p +++ +    e + + +e+ +g +++d Iv ++y+ +  i+++v
  gi|91773813|ref|YP_566505.1| 218 VRALERDEEFVKLSCR-PHDADLLlitsESITDDIEKAHGMSISDTIVRDLYGEAGYIVDSV 278
                                   6789*****9997776.444444445668999**********************99999877 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.82   1.3e+03       2      17 ..      29      44 ..      28      54 .. 0.89
   2 ?   11.7   0.0    0.0001      0.17      90     180 ..      69     153 ..      45     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.82
                    ATP_bind_1  2 vGpaGsGKttfvgals 17
                                  vG +++GK+ f ++l+
  gi|91773813|ref|YP_566505.1| 29 VGNPSVGKSAFFSRLT 44
                                  89*********99886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0001
                    ATP_bind_1  90 eddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllk 170
                                   ++++ ++D PG   l    e+ +   + L +e++  ++++vD++rl+          +    +l+ ++P+vv+ln++D +k
  gi|91773813|ref|YP_566505.1|  69 SKKLDVVDLPGIYSLGASTEDEKVSKRYLLREYPDAIINVVDATRLERNL-------FLTLQLLEFNIPMVVALNQMDAAK 142
                                   67778888888888888888888777778888999999999999998833.......33346899**************88 PP

                    ATP_bind_1 171 ek.lekeleff 180
                                   e   e ++e +
  gi|91773813|ref|YP_566505.1| 143 EMgIEIDIEKL 153
                                   55555555544 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.27      53     179 ..      55     170 ..      52     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                   TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHH........HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEE CS
                      GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirg........lrvlDgavlvvdaveGvepqteevlrlalkegvpi 125
                                   g T++ ++ s++    ++++ ++D PG  +    ++           +  D  + vvda+    ++   +  ++l+ ++p+
  gi|91773813|ref|YP_566505.1|  55 GTTVELTHGSVN--VGSKKLDVVDLPGIYSLGASTEDEkvskryllREYPDAIINVVDAT--RLERNLFLTLQLLEFNIPM 131
                                   667777777777..8888888888888777666555544444555345679999999999..566777888999******* PP

                                   EEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTB CS
                      GTP_EFTU 126 ivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkge 179
                                   +v++N mD + +  ++  +e++++ l                 vpvv++ a kg+
  gi|91773813|ref|YP_566505.1| 132 VVALNQMDAAkEMGIEIDIEKLSEIL----------------GVPVVPTIATKGF 170
                                   *********94334444444444443................2455555555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.029        47     100     122 ..      24      46 ..      11      86 .. 0.69
   2 ?    5.6   0.0    0.0085        14      33      90 ..     112     172 ..     105     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.029
                                   SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe 122
                                    t+++vG+  vGKS++  +l++ 
  gi|91773813|ref|YP_566505.1|  24 MTIAFVGNPSVGKSAFFSRLTGV 46 
                                   6889*************999885 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0085
                                   HHHHHHHHH...HHHTT-EEEEEEE-GGG--HHHHHH.HHHHHHHHTTSEEEE--TTTHTTH CS
                   RsgA_GTPase  33 nlldrfLvl...aeekgiepvivlnKiDlleeeeele.elkeelealgyevllvsaktkegl 90 
                                    +l+r L+l   + e +i++v++ln +D ++e+  +e ++++  e lg++v+ + a+++ gl
  gi|91773813|ref|YP_566505.1| 112 TRLERNLFLtlqLLEFNIPMVVALNQMDAAKEMG-IEiDIEKLSEILGVPVVPTIATKGFGL 172
                                   56666665411145789****************9.551455555667999988877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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):              11  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3945.39
//
Query:       gi|91773814|ref|YP_566506.1|  [L=72]
Description: hypothetical protein Mbur_1873 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 497.76
//
Query:       gi|91773815|ref|YP_566507.1|  [L=266]
Description: hypothetical protein Mbur_1874 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-50  168.7   0.6    9.1e-50  168.1   0.6    1.2  1  TPD       Protein of unknown function TPD sequence-motif


Domain annotation for each model (and alignments):
>> TPD  Protein of unknown function TPD sequence-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.1   0.6   5.1e-54   9.1e-50       2     135 ..     112     244 ..     111     245 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 5.1e-54
                           TPD   2 dkrlakevkeaieedsvyspladairssvGeeyEellekllkekgiafkteedlrekgldktPDvkLevpvavegkvvnWi 82 
                                   d+rla e++ea+++d+++sp+a+a + ++G+++E++++k+l+++++ ++teedlr++g++ktPD+ L++p+ v+++ v Wi
  gi|91773815|ref|YP_566507.1| 112 DRRLASEIEEATSSDHFFSPKAHALQVVKGQMGEDIISKWLDHHQLGYSTEEDLRAMGMQKTPDFFLDKPLYVDDTEVGWI 192
                                   89******************************************************************************* PP

                           TPD  83 esKalfgdeeehkkylkkQlssYvnrfGpGlviYwfGyvdelesekgvlikde 135
                                   esKa+fgde+eh++y+kkQ+++Y++++G+G+viYw+G++d+le e g li+d+
  gi|91773815|ref|YP_566507.1| 193 ESKAMFGDEREHSHYYKKQFQHYEREYGTGMVIYWYGHIDTLEFE-GNLIRDH 244
                                   *******************************************99.8888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1963.17
//
Query:       gi|91773816|ref|YP_566508.1|  [L=237]
Description: DNA-3-methyladenine glycosylase III [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   64.6   0.0    2.4e-17   63.3   0.0    1.6  2  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.32   5.7e+03      19      40 ..      27      48 ..      23      53 .. 0.54
   2 !   63.3   0.0   1.3e-21   2.4e-17       1      99 [.      65     199 ..      65     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.32
                                  HHHHHHHSHCSHHHHHHSHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD 19 erlferfgfptpedladadeek 40
                                  e+lf++++    +d+ ++  ek
  gi|91773816|ref|YP_566508.1| 27 EHLFKEMKNERIHDIYKVLLEK 48
                                  4555555555555555555555 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 1.3e-21
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   ++ail+qqt++ +++++ie l++    ++pe+la+ad e ++++ir++Gfyr+Kak++k++A  ++               
  gi|91773816|ref|YP_566508.1|  65 IGAILTQQTKWTNVEKAIEGLKRYD-LIEPEKLARADLELIEKIIRCCGFYRQKAKRLKDIAGFFAregiddvlsmpttel 144
                                   789*******************997.8****************************************************** PP

                                   .......................S-SSS--TTSHHHHHHHHHHTTSSSS.TTHHHHH CS
                                   .......................xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       HhH-GPD  67 .......................gkpdvlivvDvhvrrilkrlrsikek.ktkkkve 99 
                                                          +k  + +v D ++ r++k +++  +  + +++ e
  gi|91773816|ref|YP_566508.1| 145 rnlmlslrgvgnetadsivlyaaNK--PKFVIDAYTTRMMKCIGIEGNYlQLQEMFE 199
                                   *********************7655..55999*********9987766555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1778.99
//
Query:       gi|91773817|ref|YP_566509.1|  [L=160]
Description: hypothetical protein Mbur_1876 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.5   0.8      0.074   13.1   0.8    1.2  1  Cnd1      non-SMC mitotic condensation complex subunit 1


Domain annotation for each model (and alignments):
>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   4.1e-06     0.074      45     102 ..      93     152 ..      89     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-06
                          Cnd1  45 vakL..ilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllpdiis 102
                                   v+++  i++++v e++    +++ ++D+n+++v+ a+a+ +e ++k++  ++ +l di  
  gi|91773817|ref|YP_566509.1|  93 VTHVteIKETVVMESKDTTVIESHVSDPNAEIVNEAVASKEETNKKDKIDMMMNLEDISE 152
                                   777777899999999999****************************98888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1502  (0.0837749); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1041.89
//
Query:       gi|91773818|ref|YP_566510.1|  [L=282]
Description: ribose-phosphate pyrophosphokinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-26   91.5   0.1    1.4e-24   86.3   0.0    2.2  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    2.5e-21   75.9   0.2    4.5e-21   75.0   0.2    1.4  1  Pribosyltran    Phosphoribosyl transferase domain
    3.9e-07   30.3   0.6    3.9e-07   30.3   0.6    1.7  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    1.1e-06   28.2   0.0    2.3e-06   27.2   0.0    1.5  1  UPRTase         Uracil phosphoribosyltransferase
     0.0007   19.1   0.1      0.005   16.4   0.1    2.1  2  PRTase_2        Phosphoribosyl transferase


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 !   86.3   0.0   3.8e-28   1.4e-24       1     113 [.       1     109 [.       1     111 [. 0.95
   2 ?    3.3   0.0     0.021        76       7      58 ..     159     211 ..     153     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3.8e-28
                Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakr 81 
                                   +ki+ag +s+ La+++a++l++e + ++ +rf+dgE++ +i e++  +dv iiqs+ ++   +l+ ll +ida++   a +
  gi|91773818|ref|YP_566510.1|   1 MKIIAGPASQLLASRVARELNMEPTLCEFNRFPDGEVYTRILEDIV-DDVTIIQSTPTD--ADLVSLLQLIDACE--DAPT 76 
                                   89******************************************97.69******9877..79***********7..999* PP

                Pribosyltran_N  82 itaViPylgysrqdrk.ksrepisaklvaklLe 113
                                   it+ViPy+gy+rqd++ +s e+isa+ +a+ ++
  gi|91773818|ref|YP_566510.1|  77 ITVVIPYMGYARQDKAfRSGESISARAIARTIH 109
                                   *****************************9876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.021
                Pribosyltran_N   7 ssskeLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqslsk 58 
                                   + +  Lae+ a+ +g+e    + +r + + + ++ ++ +v gk++++i ++ +
  gi|91773818|ref|YP_566510.1| 159 KGAITLAESAAADVGIEYDYLEKTRHSGDTVTIKTKNiDVTGKEIILIDDMIA 211
                                   5567899999****************9999999999889*********99874 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.2   1.3e-24   4.5e-21      14     124 ..     135     237 ..     123     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.3e-24
                                   EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE- CS
                  Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVD 94 
                                   ++ +l+ +++++ + + ++++++++g++++a   a  ++++++y++k+++++d+ +  +        + +d+ gk ++++D
  gi|91773818|ref|YP_566510.1| 135 DASHLIGNYIRSLGLEDPLIIAPDKGAITLAESAAADVGIEYDYLEKTRHSGDTVTIKT--------KNIDVTGKEIILID 207
                                   7889***************************************************9998........899*********** PP

                                   SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                  Pribosyltran  95 DildtGgTllaalelLkekgpeevriavlv 124
                                   D+++tGgT+ + ++lL+++g++ v ia+++
  gi|91773818|ref|YP_566510.1| 208 DMIATGGTMAESIKLLRSQGAKDVYIACVH 237
                                   ***********************9999998 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.3   4.6e+03      88      98 ..      41      51 ..      35      58 .. 0.76
   2 !   30.3   0.6   1.1e-10   3.9e-07      80     147 ..     197     264 ..     188     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                  EEEEEE-S-HH CS
                Pribosyl_synth 88 ivddliddves 98
                                  i++d++ddv+ 
  gi|91773818|ref|YP_566510.1| 41 ILEDIVDDVTI 51
                                  68899999875 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 1.1e-10
                                   --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS-- CS
                Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiph 147
                                   dv+G+  i++dd+i    ++ ++ ++l+ +Ga  +y+ + h +l+++   +l ++ ++e++ ++t+ +
  gi|91773818|ref|YP_566510.1| 197 DVTGKEIILIDDMIATGGTMAESIKLLRSQGAKDVYIACVHPVLTKNGVLRLYNAGVHEIIASDTLEK 264
                                   9*************************************************************999866 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   6.5e-10   2.3e-06     120     171 ..     199     250 ..     176     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.5e-10
                       UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlae 171
                                   + ++++l+D +iaTGg++a+ i+lL+++g++   I ++  +  ++gv rl +
  gi|91773818|ref|YP_566510.1| 199 TGKEIILIDDMIATGGTMAESIKLLRSQGAKDVYIACVHPVLTKNGVLRLYN 250
                                   6678***********************************9******988865 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.085     3e+02      57      89 ..     154     186 ..     131     194 .. 0.81
   2 !   16.4   0.1   1.4e-06     0.005     114     154 ..     193     233 ..     176     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.085
                      PRTase_2  57 vigfAEtAtaLghgvadaleeealylhtTRekv 89 
                                   +i+    A++L+++ a+ +  e+ yl+ TR++ 
  gi|91773818|ref|YP_566510.1| 154 IIAPDKGAITLAESAAADVGIEYDYLEKTRHSG 186
                                   5556667999999999999889********986 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.4e-06
                      PRTase_2 114 deellaaakelvLvDDEistGktalnliralqeklprkryv 154
                                   ++++  + ke++L+DD i+tG t+++ i+ l+++  ++ y+
  gi|91773818|ref|YP_566510.1| 193 TKNIDVTGKEIILIDDMIATGGTMAESIKLLRSQGAKDVYI 233
                                   3444445689*********************9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2146.43
//
Query:       gi|91773819|ref|YP_566511.1|  [L=159]
Description: molybdenum cofactor biosynthesis protein MoaC [Methanococcoides burtonii DSM 6242]
Scores for complete 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-49  166.8   3.5      3e-49  166.6   3.5    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 !  166.6   3.5   1.7e-53     3e-49       1     134 [.      14     152 ..      14     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 1.7e-53
                                   E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTTT CS
                          MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeeee 81 
                                   mvd+s+k+++ r A+A+g++kl++et+e+i++++++kG+vla+ar a+i+a+K+t++lip+cH++p+t+v+ve+e+   ++
  gi|91773819|ref|YP_566511.1|  14 MVDISNKDTVVRYATASGKIKLHDETVEKIRSGDVEKGNVLATARTAAILAVKRTPDLIPMCHQIPITSVDVEFEIG--KS 92 
                                   9*************************************************************************987..79 PP

                                   EEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                          MoaC  82 sveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                    v+ +++vk  g+tGvemEALt+vsva+lt++DmvK+++k+       + ie++++++K 
  gi|91773819|ref|YP_566511.1|  93 DVTANVEVKSVGRTGVEMEALTGVSVALLTIWDMVKSAEKDntgnypsTAIENIHVIRKV 152
                                   9***************************************99***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1271.38
//
Query:       gi|91773820|ref|YP_566512.1|  [L=62]
Description: hypothetical protein Mbur_1879 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 401.67
//
Query:       gi|91773821|ref|YP_566513.1|  [L=481]
Description: YjeF-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-47  161.9   4.4    2.7e-47  161.3   4.4    1.3  1  Carb_kinase  Carbohydrate kinase
    8.8e-41  139.6   1.2    4.2e-40  137.4   0.2    2.1  2  YjeF_N       YjeF-related protein N-terminus
      8e-05   22.1   0.2    0.00023   20.6   0.2    1.8  1  HK           Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.3   4.4   4.5e-51   2.7e-47       2     243 ..     244     477 ..     243     478 .. 0.93

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 4.5e-51
                                   EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEEE-TT- CS
                   Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavviGpGL 77 
                                   l+igG   y+GA+ l+a aalr+ga++v+va+  + +  + s +p++iv+ l+     +e++ +i ++ e  d+vviG+GL
  gi|91773821|ref|YP_566513.1| 244 LIIGG-GPYSGAPALTAMAALRAGADIVTVAAPANVADIIASFSPNIIVKALSsnilCKEDMgTITKLIESHDVVVIGMGL 323
                                   78888.9*************************999999***************9999567777899999************ PP

                                   SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEE CS
                   Carb_kinase  78 grdekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavv 158
                                   gr e++k  + ++      +v DAd+L+ ++       +  e+i+TPh++E++ L +          e   e++++ n+++
  gi|91773821|ref|YP_566513.1| 324 GRAEQTKDTVSKIIPLCTKVVADADALYGIDLP---VPKGIEMIITPHAGEYNALGGNGK-------EDTLEFSKRNNVTI 394
                                   **************99999***********995...455679*************99988.......3345688999**** PP

                                   EEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCHHHH CS
                   Carb_kinase 159 llkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlatels 239
                                   llkg +d i + ++ + in +g++++++GG+GDvLaG+ gal+a +  +++aa+ aa+++gaa+d+a+e+ g g+lat+++
  gi|91773821|ref|YP_566513.1| 395 LLKGREDHISN-GKRIAINRNGNPGMTVGGTGDVLAGIAGALFATAC-KMDAACGAAYINGAAGDLAFERMGSGLLATDII 473
                                   *********99.*********************************99.99******************************* PP

                                   HHHC CS
                   Carb_kinase 240 kiip 243
                                   + i+
  gi|91773821|ref|YP_566513.1| 474 DMIT 477
                                   9986 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 !  137.4   0.2     7e-44   4.2e-40       3     171 .]      25     192 ..      23     192 .. 0.92
   2 ?    0.9   0.1     0.061   3.7e+02      28      58 ..     242     272 ..     221     357 .. 0.69

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 7e-44
                        YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegak.Vtv.llleeeekldedaeralellkka 81 
                                   +Lmenag+a+a+ +r+++    ++ +vl+++G+gnnGgd+++aArhLa   a  + + l+ + ++ ++eda +++ ll+++
  gi|91773821|ref|YP_566513.1|  25 QLMENAGAAIAHEVRERV----QKGNVLIVAGRGNNGGDAFVAARHLAYDPAItINIaLIGSASQIRSEDAINNYGLLEHC 101
                                   8*****************....8999*********************6666554777666677779*************** PP

                        YjeF_N  82 ggkvveekpeedleekls..apvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkad 160
                                   +++ + e  + ++ +++    ++d+++DAllG+g+ g+l+e+ a++i+ +n+s+ pv+avD+PSG+d+d G+ +   v+ad
  gi|91773821|ref|YP_566513.1| 102 RINALIEITDPQKLKEMGwlDNADIIVDALLGTGITGKLKETEATIIDLINDSNVPVIAVDVPSGFDPDGGEFE-RSVRAD 181
                                   ***9998888888777779*******************************************************.89**** PP

                        YjeF_N 161 vtvtfgapkrg 171
                                   vt+tf+ +k+g
  gi|91773821|ref|YP_566513.1| 182 VTLTFHRMKKG 192
                                   *********87 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.061
                        YjeF_N  28 kvlvlvGsgnnGgdglaaArhLaqegak.Vtv 58 
                                   k+l++ G+  +G+ +l a + L ++ga+ Vtv
  gi|91773821|ref|YP_566513.1| 242 KILIIGGGPYSGAPALTAMAAL-RAGADiVTV 272
                                   5677777778999999988888.666664666 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   3.9e-08   0.00023     146     243 ..     385     479 ..     375     481 .] 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.9e-08
                                   HHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHH CS
                            HK 146 kvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaars 226
                                   +  ++ +v++++ G+ D +s+gk+++  +nG++ ++ + ++G +l+ + +a  a    k++aa  a  +   Ag   a + 
  gi|91773821|ref|YP_566513.1| 385 EFSKRNNVTILLKGREDHISNGKRIAINRNGNPGMT-VGGTGDVLAGIAGALFATA-CKMDAACGAAYINGAAG-DLAFER 462
                                   566788999*************************97.9********9999998865.45677788877777777.666777 PP

                                   HTTHHHHHHHHHHHHH- CS
                            HK 227 egsgsFqvelldalsql 243
                                    gsg   + ++d ++++
  gi|91773821|ref|YP_566513.1| 463 MGSGLLATDIIDMITEV 479
                                   89999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3439.54
//
Query:       gi|91773822|ref|YP_566514.1|  [L=498]
Description: TrkA-N [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-22   80.5   0.3    2.3e-22   79.4   0.3    1.6  1  TrkA_N           TrkA-N domain
    5.6e-14   52.2   1.3    5.4e-13   49.0   0.3    2.6  3  DHH              DHH family
    6.7e-13   49.2   0.7    5.3e-12   46.3   0.0    2.6  3  DHHA1            DHHA1 domain
     0.0027   18.3   0.0     0.0065   17.0   0.0    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0031   17.1   0.0     0.0052   16.4   0.0    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0033   16.9   0.0     0.0081   15.6   0.0    1.7  2  Epimerase        NAD dependent epimerase/dehydratase family
     0.0036   17.4   0.0       0.01   15.9   0.0    1.7  1  TyeA             TyeA
     0.0044   16.4   0.0     0.0086   15.5   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.015   15.8   0.0       0.46   11.1   0.0    3.0  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.021   15.1   0.0       0.04   14.2   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.032   13.9   0.0      0.056   13.1   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.041   14.3   0.0       0.11   12.9   0.0    1.7  1  NAD_binding_7    Putative NAD(P)-binding
      0.078   13.5   0.0       0.22   12.0   0.0    1.9  1  XdhC_C           XdhC Rossmann domain
       0.13   11.5   0.0       0.22   10.7   0.0    1.3  1  FAD_binding_3    FAD binding domain
       0.13   11.7   0.0       0.28   10.6   0.0    1.5  1  adh_short        short chain dehydrogenase


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 !   79.4   0.3     2e-25   2.3e-22       1     116 []      29     145 ..      29     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2e-25
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                   ++i+G G +G ++a+eL+e ++ d +++dkd ++ve+lre+ ++++ gd +d+ev +++++++  +v+++ +d+ean  a+
  gi|91773822|ref|YP_566514.1|  29 YLILGSGSIGFAVAKELRElDK-DLIIVDKDSQKVETLREDAYQAIAGDISDPEVYKQLNLKELTGVLVLSSDNEANKKAL 108
                                   68*****************777.8********************************************************* PP

                                   HHHHHHTSS.SEEEEEESSGGGHHHHHHHTTSEEEEH CS
                        TrkA_N  81 llakelnpk.kkiiaraqdpehaellkklgadvvisp 116
                                   +++ +l  + ++++ara+d+ + + ++ lgad v++p
  gi|91773822|ref|YP_566514.1| 109 EIISTLGINdAYCVARASDAINLQEMEALGADLVLMP 145
                                   ***99987779**********************9987 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.58   6.9e+02      30      61 ..      36      65 ..      28      90 .. 0.79
   2 !   49.0   0.3   4.5e-16   5.4e-13       4     101 .]     183     324 ..     180     324 .. 0.81
   3 ?   -1.8   0.0         3   3.6e+03      16      38 ..     340     362 ..     334     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.58
                                  TCGGCGCCHHCCCSEEEEEEE-S---SS---S CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH 30 eksqavegeakeeaedviiiDHHrlgeefetl 61
                                  +   av++e++e ++d+ii+D   ++  +etl
  gi|91773822|ref|YP_566514.1| 36 SIGFAVAKELRELDKDLIIVDKDSQK--VETL 65
                                  55667888999**********87775..5554 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 4.5e-16
                                   EE-ECSSSHHHHHHHHHHHHC...............................................ECS--TCGGCGCC CS
                                   xxxxxxxxxxxxxxxxxxxxx...............................................xxxxxxxxxxxxx RF
                           DHH   4 ivghknpDtDsigSaialanl...............................................lvDhneksqaveg 37 
                                   iv h npD D+i Sa+al+++                                               +vD+  +      
  gi|91773822|ref|YP_566514.1| 183 IVVHDNPDPDAISSALALQKIaesfdvrssilyhgeighqenkafvnllgidlnrmeehslsdftdiaMVDCAVPGANNML 263
                                   667*****************6666666666666677777777777777777777777777777777779999999888754 PP

                                   HHCCCSEEE.EEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  38 eakeeaedv.iiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                      ++++++ i++DHH lg + e  a+++ ++++vg+ a+i++++l+e ++ei+k +a++ll gi
  gi|91773822|ref|YP_566514.1| 264 ---SPGMHLgIVLDHHPLG-DSEIDADFVDIRPNVGASATILTKYLQELNIEIDKVLATALLYGI 324
                                   ...6666653889******.8888889999*********************************98 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3
                                   HHHHHHHHCECS--TCGGCGCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  16 gSaialanllvDhneksqavege 38 
                                    Sa a+ + l Dh++ +q + + 
  gi|91773822|ref|YP_566514.1| 340 LSAAAYLYPLADHEILDQLERPS 362
                                   47999999999**9999988774 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.3   1.6e+03      50      96 ..     102     131 ..      42     136 .. 0.54
   2 ?   -1.7   0.0       3.1   3.7e+03      28      59 ..     160     197 ..     146     212 .. 0.63
   3 !   46.3   0.0   4.4e-15   5.3e-12      39     124 ..     381     469 ..     352     483 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                   CHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSHSS-H CS
                         DHHA1  50 ewdagalgiaadklksklkkpvivfvakeegdkvkvsarskkdgvda 96 
                                   e++++al              +i+ +++ +   ++++ar+++  +++
  gi|91773822|ref|YP_566514.1| 102 EANKKAL--------------EIISTLGIN--DAYCVARASD-AINL 131
                                   3333333..............333333333..2455555555.5555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                   HHHHHTCEEEC.......TCEEEEEECHCCHHHHHHHHH CS
                         DHHA1  28 eellekaeevk.......gvkvlvaevgeewdagalgia 59 
                                   +e++++  +++       g+ ++++   ++ d++a+ +a
  gi|91773822|ref|YP_566514.1| 160 AEVVHRGNKLSqwfkdmsGKALAIVVH-DNPDPDAISSA 197
                                   455555544445555554555555555.77777777766 PP

  == domain 3  score: 46.3 bits;  conditional E-value: 4.4e-15
                                   TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH.SS-HHHHHHHHHHHTTCCE.EEETC CS
                         DHHA1  39 gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd.gvdagelakeaaaklgggG.GGHdl 116
                                     ++l+++vg   d++al +aad+l+s   +  +  +v++  +d++ +s+rs+ d ++++ge++++   ++g +  GGH +
  gi|91773822|ref|YP_566514.1| 381 IGSYLLTNVGVIRDRDALPQAADYLLS--LEgISTSIVFGVSDDRIFISGRSN-DiRINLGEVLRR---AFGEKAaGGHSN 455
                                   4678888998*****************..444444444444445*********.55**********...66666679**** PP

                                   EEEEEEE......H CS
                         DHHA1 117 AaGagip......a 124
                                   AaGa+ip      +
  gi|91773822|ref|YP_566514.1| 456 AAGAQIPlgvfsdI 469
                                   *******4444442 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.5e-06    0.0065       4      50 ..      31      73 ..      28     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.5e-06
                                  EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EE CS
                 F420_oxidored  4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkv 50
                                  i+G+G++g+a+a+ l + +   ++++++ +++ +k+e l+e+++  +
  gi|91773822|ref|YP_566514.1| 31 ILGSGSIGFAVAKELRELD---KDLIIV-DKDSQKVETLREDAYQAI 73
                                  89*****************...999988.**********99887333 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.4e-06    0.0052       5      46 ..      31      72 ..      28     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.4e-06
                                  EE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS CS
                UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi 46
                                  ++G+G +G   a  l e+ +++i+vD+d++kv++l+++  + 
  gi|91773822|ref|YP_566514.1| 31 ILGSGSIGFAVAKELRELDKDLIIVDKDSQKVETLREDAYQA 72
                                  89**********************************998765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   6.8e-06    0.0081       5      59 ..      33      86 ..      29     126 .. 0.84
   2 ?   -4.0   0.0       6.9   8.2e+03      54      88 ..     179     214 ..     176     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-06
                                  TTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHH CS
                     Epimerase  5 GatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerl 59
                                  G +G iG a++k+l e + ++i +d++s++ +t r++  + + +d+ d++  ++l
  gi|91773822|ref|YP_566514.1| 33 G-SGSIGFAVAKELRELDKDLIIVDKDSQKVETLREDAYQAIAGDISDPEVYKQL 86
                                  4.6*********************************************9876665 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.9
                                   HHHHHHHHHH.T-SEEEE--S---HHHHHHSHHHHH CS
                     Epimerase  54 salerlfkee.qpdavihlAavggvaassedpadfi 88 
                                   +al+ +++++ +pda+  + a + +a+s++ ++ ++
  gi|91773822|ref|YP_566514.1| 179 KALAIVVHDNpDPDAISSALALQKIAESFDVRSSIL 214
                                   566777777779999999988888888887776655 PP

>> TyeA  TyeA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.7e-06      0.01      48      72 ..     459     483 ..     454     487 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.7e-06
                                   GGS-GGGSS-HHHHHHHHHHHHHHH CS
                          TyeA  48 relPlkvFadeeqRqklLaaaqeAl 72 
                                   +++Pl+vF+d ++Rq+lL  ++eA+
  gi|91773822|ref|YP_566514.1| 459 AQIPLGVFSDIKDRQTLLRLVNEAV 483
                                   68*********************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 !   15.5   0.0   7.2e-06    0.0086      30      77 ..      20      67 ..       6      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.2e-06
                                  SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                  2-Hacid_dh_C 30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77
                                  + k+ ++ t  i+G G+IG avak l++++ ++i++d+  +k e+ +e
  gi|91773822|ref|YP_566514.1| 20 PDKKWQNPTYLILGSGSIGFAVAKELRELDKDLIIVDKDSQKVETLRE 67
                                  5667789999****************************9998775444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.46       3      41 ..      30      68 ..      28      93 .. 0.83
   2 ?   -1.3   0.0       2.8   3.3e+03      24      45 ..     159     180 ..     149     185 .. 0.72
   3 ?    0.5   0.0      0.78   9.3e+02      42      57 ..     297     312 ..     285     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                                  EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHH CS
                     Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDee 41
                                  +++G+G ig  +A++l+el k+  +v+  ++    l e+
  gi|91773822|ref|YP_566514.1| 30 LILGSGSIGFAVAKELRELDKDLIIVDKDSQKVETLRED 68
                                  79***********************99887766555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                                   EEEEEESSSSSSTTSSHHHHHH CS
                     Pyr_redox  24 kVtvversdkllrllDeeaski 45 
                                   +  vv+r++kl + + ++ +k+
  gi|91773822|ref|YP_566514.1| 159 RAEVVHRGNKLSQWFKDMSGKA 180
                                   7889*****9998877766665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.78
                                   HHHHHHHHHHHTTEEE CS
                     Pyr_redox  42 askilqeklekngiev 57 
                                    ++il+++l++++ie+
  gi|91773822|ref|YP_566514.1| 297 SATILTKYLQELNIEI 312
                                   5789**********97 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-05      0.04       2      75 ..      30      96 ..      29     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                                  EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE CS
               Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvn 75
                                  li+G+Gs+G ava++l + ++   +++++d++ +k+e l    ++   +aia d++++e   ++l lke + v+ 
  gi|91773822|ref|YP_566514.1| 30 LILGSGSIGFAVAKELRELDK---DLIIVDKDSQKVETL----REDAYQAIAGDISDPEV-YKQLnLKELTGVLV 96
                                  89**************98765...69*********7777....56678888888888886.77776777644444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-05     0.056       2      43 ..      30      72 ..      29     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                                  EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEE CS
                          ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrl 43
                                  +ilG+G+iG  +a +L +   d ++++++  ++e+l+++ ++ 
  gi|91773822|ref|YP_566514.1| 30 LILGSGSIGFAVAKELRELDKDLIIVDKDSqKVETLREDAYQA 72
                                  8**********************************99988765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.2e-05      0.11       7      85 ..      26     114 ..      23     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                 NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele....elvklaeeelekd...........legadlviaatddr 72 
                                   + + l+ G G+++   ++ l e ++++++v++++ +++e    + ++++      d           l++   v++  +d+
  gi|91773822|ref|YP_566514.1|  26 NPTYLILGSGSIGFAVAKELRELDKDLIIVDKDS-QKVEtlreDAYQAIAG----DisdpevykqlnLKELTGVLVLSSDN 101
                                   6689*****************************3.3344222233333333....233345555556888999999999** PP

                 NAD_binding_7  73 elneriaeaakar 85 
                                   e n++  e + + 
  gi|91773822|ref|YP_566514.1| 102 EANKKALEIISTL 114
                                   ***9988877655 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.22       2      66 ..      30     113 ..      29     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                   EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE......................-EEEE--S-HHHHHHH CS
                        XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade......................tavvvlthdhklDaea 60 
                                   +i+G g ++ a+a+ +++l+ ++++vd++++   +e + e  +                      t v+vl+ d +  ++a
  gi|91773822|ref|YP_566514.1|  30 LILGSGSIGFAVAKELRELDKDLIIVDKDSQK--VETLRED-AyqaiagdisdpevykqlnlkelTGVLVLSSDNEANKKA 107
                                   79***************************963..3333311.123566778888888889999999999999999999999 PP

                                   HHHHSS CS
                        XdhC_C  61 leaalr 66 
                                   le + +
  gi|91773822|ref|YP_566514.1| 108 LEIIST 113
                                   998764 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.22       5      42 ..      30      67 ..      27      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                                  EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS- CS
                 FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpra 42
                                  lI G+G  G+  a++L+e   + ++v+k s++v++ r 
  gi|91773822|ref|YP_566514.1| 30 LILGSGSIGFAVAKELRELDKDLIIVDKDSQKVETLRE 67
                                  89******************************999885 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.28       8      67 ..      33      86 ..      28      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                  TTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHH CS
                     adh_short  8 assGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreeveal 67
                                  +s+ IG a+akel + + ++++vd+ ++k+e++ +        + ai++D++d e  ++l
  gi|91773822|ref|YP_566514.1| 33 GSGSIGFAVAKELRELDKDLIIVDKDSQKVETLREDA------YQAIAGDISDPEVYKQL 86
                                  4568**********************99996665553......56899999998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3650.32
//
Query:       gi|91773823|ref|YP_566515.1|  [L=236]
Description: hypothetical protein Mbur_1882 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-09   38.2   5.2    1.4e-08   35.3   5.2    2.2  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 !   35.3   5.2   7.8e-13   1.4e-08       2      84 ..      39     158 ..      38     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 7.8e-13
                      CxxCxxCC   2 CkeCgaCCk....elkvklteedlerlkaaevaeeeeeskkiak.................................adgr 45 
                                   C +Cg+CC+    +++v lt  d++ l++ + ++  +     ++                                 ++g+
  gi|91773823|ref|YP_566515.1|  39 CSMCGKCCRrscgDNRVFLTSSDIRSLQECSLDDAVFPMLPDIQdvpfedalheyaqelevdsqgryhtfgwmlkrkVNGN 119
                                   ************999999999999999999996555544333336999999999999************************ PP

                      CxxCxxCC  46 Cvfldeetk.lCkiYeeRpkicrlfpasekeellaraetC 84 
                                   C f+ e+   +C iY +Rp  c ++p+   +  + ++++C
  gi|91773823|ref|YP_566515.1| 120 CSFIGEDGSnRCGIYDRRPMLCGTYPFY-IKCGKLLTSEC 158
                                   *****98667*****************5.55555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1446.66
//
Query:       gi|91773824|ref|YP_566516.1|  [L=428]
Description: 3-isopropylmalate dehydratase large subunit [Methanococcoides burtonii DSM 6242]
Scores for 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-94  315.9   0.3      5e-92  309.3   0.3    2.1  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.038   12.7   0.0      0.059   12.1   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.3   0.3   5.6e-96     5e-92      12     461 .]      26     420 ..      13     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: 309.3 bits;  conditional E-value: 5.6e-96
                     Aconitase  12 egiayv...pdrvllqdvtgvqalvdl.aaareav....rrlggtlatidhlvpvdlvidhsvgaeealeknledefernk 84 
                                    g ++v    dr +++d+tg+ a+ ++ + +r++     +++++ + + dh+vp+d                   +++  +
  gi|91773824|ref|YP_566516.1|  26 AG-DFVlanIDRAMTHDITGPLAVDGFyDIMRDKEekkvWDPSKIVIVFDHQVPAD-------------------SLNA-S 85 
                                   33.3333447****************976676555000144444444555555555...................2222.2 PP

                     Aconitase  85 eryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipk 165
                                    +  +L+++ak+ gi  +++ +G++Hqv++E+g + pg ++vg+DSHT+ +g lG++ +GvG++++ av++  +l++++p+
  gi|91773824|ref|YP_566516.1|  86 ANHIMLRKFAKEQGILNYDVYEGVCHQVMPEMGHVRPGDLIVGSDSHTCAYGSLGAFSTGVGSTDMSAVFASGKLWFRVPE 166
                                   34467999************************************************************************* PP

                     Aconitase 166 vvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLka 246
                                   +++++ +Gkl+++v +kDl+l++ig ++++g+   + E++G+++e L++ +r+Ti+NMa+E+G ++g+++ d++t +YLk 
  gi|91773824|ref|YP_566516.1| 167 TIRFEANGKLPKHVYSKDLILHMIGDVGAEGARYMAAEYAGSAIEGLTISERMTISNMAIEMGGKAGIIEADKTTEAYLK- 246
                                   ********************************************************************************. PP

                     Aconitase 247 tgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekeaaekaleyk 327
                                    +r ++        + + ++  ++dedaey++  + ++s+lep+va p++++++ p+ ++v                    
  gi|91773824|ref|YP_566516.1| 247 -ERIPDY-------EFDPYW--KSDEDAEYAEFHDYNVSDLEPQVACPHNVDNVKPV-SEV-------------------- 296
                                   .774444.......346688..799*******************************9.333.................... PP

                     Aconitase 328 lkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevv 408
                                          + +kvd++++gSCTN++ ed++++a+++      +  v+++v++++ P+S+    ++ ++G+ e++++aG+ v 
  gi|91773824|ref|YP_566516.1| 297 -------EGTKVDQVFVGSCTNGRFEDIKIVAEMMG-----DEPVAKDVRLLIIPASRTEYMKVLRAGYVEQFMEAGAIVE 365
                                   .......345799***********************.....889************************************* PP

                     Aconitase 409 gagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                   ++ C++C+g   + l +ge+++ +sNRNF+gR+g p++  yL SP+ ++a+Al+G
  gi|91773824|ref|YP_566516.1| 366 APCCGPCMGgSFGLLGDGEVGLATSNRNFKGREGsPDSFVYLSSPATAAASALTG 420
                                   *********8889999*****************8677777*************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.6e-06     0.059     286     357 ..     296     369 ..     283     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.6e-06
                        DUF521 286 akeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtC 357
                                    + +kvd v++G c    +e+++ +ae++ ++ ++++v+l+++ +sr+ + ++ r+g+ve+  +aG+ v + +C
  gi|91773824|ref|YP_566516.1| 296 VEGTKVDQVFVGsCTNGRFEDIKIVAEMMGDEPVAKDVRLLIIpASRTEYMKVLRAGYVEQFMEAGAIVEAPCC 369
                                   5678999999996778899**********999999999986653889999*****************7766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2494.72
//
Query:       gi|91773825|ref|YP_566517.1|  [L=148]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-22   79.8   7.7    2.4e-13   50.3   0.7    2.1  2  CBS             CBS domain
  ------ inclusion threshold ------
      0.048   14.1   0.1       0.56   10.7   0.1    2.2  2  Ribosomal_L9_C  Ribosomal protein L9, C-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 !   33.5   1.2   4.7e-12   4.2e-08       1      55 [.      22      76 ..      22      78 .. 0.93
   2 !   50.3   0.7   2.6e-17   2.4e-13       1      55 [.      86     145 ..      86     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.7e-12
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllral 55
                                  V+d+mtr vvtvp +++  e+++ m++ +vs + V +++ g++ G++++ D+l  +
  gi|91773825|ref|YP_566517.1| 22 VKDVMTRGVVTVPFESNAVEIAKVMADQNVSTV-VaIEDGGEIFGVISDIDILGRM 76
                                  89****************************999.8788888************876 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 2.6e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTT...BEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV..dedg...klvGivtlrDllral 55 
                                   V+d+m++ v tv+p++t+++++++m++k+v+rl V+  ++ g   +++Gi++ +D+++ l
  gi|91773825|ref|YP_566517.1|  86 VEDLMSDSVETVSPNATVHDVADMMADKRVHRLIVMseESVGasyRPIGIISSSDIIKEL 145
                                   89*******************************5557766667778***********987 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 ?   10.7   0.1   6.2e-05      0.56       3      49 ..      39      83 ..      37      97 .. 0.82
   2 ?    1.3   0.0     0.055   4.9e+02      19      41 ..     123     145 ..     102     148 .] 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.2e-05
                                  HHHHHHHHSS..-EEEE--B-TT-BBSS---HHHHHHHHHHHT---- CS
                Ribosomal_L9_C  3 aealaekLeakvkvtikakagedgklFGsVtakdIaealkkklgiei 49
                                  a ++a+ +++  +v   +   ++g++FG ++  dI   +k+k + e+
  gi|91773825|ref|YP_566517.1| 39 AVEIAKVMAD-QNVSTVVAIEDGGEIFGVISDIDILGRMKDK-NWEL 83
                                  7788888984.45577777789**************999998.6665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.055
                                   E--B-TT-BBSS---HHHHHHHH CS
                Ribosomal_L9_C  19 kakagedgklFGsVtakdIaeal 41 
                                   +  +g++ +  G ++++dI+++l
  gi|91773825|ref|YP_566517.1| 123 EESVGASYRPIGIISSSDIIKEL 145
                                   55678888889999*****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 937.21
//
Query:       gi|91773826|ref|YP_566518.1|  [L=99]
Description: phosphoribosyl-ATP pyrophosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-16   59.9   0.2    2.9e-16   59.7   0.2    1.1  1  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase
    9.4e-07   28.9   1.6    1.4e-06   28.3   1.1    1.6  2  MazG      MazG nucleotide pyrophosphohydrolase domain


Domain annotation for each model (and alignments):
>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.2   3.2e-20   2.9e-16       2      82 ..      10      97 ..       9      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.2e-20
                                  HHHHHHCT----SS----.-HHHHHH......HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHHHHH CS
                        PRA-PH  2 kefhrligerkpetPeas.taelasl......raaligEEavElleaasegdlaeladelaDllYvtygllvllGidldavfe 77
                                  +e+ ++i +rk++  e+s   +l+++      +++++gEE +E++ a++++d+ae+++e  Dll++++++l++ +i+ld++ e
  gi|91773826|ref|YP_566518.1| 10 NEVFDVIMDRKNNPVEGSyVCSLLDHrkginkILEKVGEETAETILAVKDNDRAEIIYETSDLLFHLLVMLAATDITLDDIAE 92
                                  56778899999999999999999999999999*************************************************** PP

                                  HHHHH CS
                        PRA-PH 78 evhra 82
                                  e +++
  gi|91773826|ref|YP_566518.1| 93 EMKKR 97
                                  *9987 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.57   5.1e+03      15      23 ..      10      18 ..       9      24 .. 0.64
   2 !   28.3   1.1   1.6e-10   1.4e-06       5      63 ..      41      95 ..      37      99 .] 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.57
                                  HHHHHHHHT CS
                          MazG 15 gEvaeaIkk 23
                                   Ev+++I  
  gi|91773826|ref|YP_566518.1| 10 NEVFDVIMD 18
                                  477777754 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.6e-10
                                  HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH CS
                          MazG  5 tllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetil 63
                                   +l+ + eE+ E + a+k +dr e+  E  D+L+++l +       ++i+l+d+ae++ 
  gi|91773826|ref|YP_566518.1| 41 KILEKVGEETAETILAVKDNDRAEIIYETSDLLFHLLVMLAA----TDITLDDIAEEMK 95
                                  6788999******************************99996....*********8864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 655.79
//
Query:       gi|91773827|ref|YP_566519.1|  [L=291]
Description: hypothetical protein Mbur_1886 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-35  119.8   0.2      8e-35  118.4   0.2    1.8  1  HrcA_DNA-bdg   Winged helix-turn-helix transcription represso
    3.1e-21   75.6   7.9    5.6e-12   45.9   1.2    2.6  3  CBS            CBS domain
      1e-07   32.2   0.1    2.4e-07   31.0   0.1    1.5  1  Rrf2           Transcriptional regulator
    3.7e-07   30.0   0.1    8.1e-07   28.9   0.1    1.6  1  HTH_11         HTH domain
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.056   13.3   0.0    2.0  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.024   14.3   0.7       0.23   11.2   0.0    2.7  4  Sigma70_r4_2   Sigma-70, region 4
      0.053   13.1   0.2       0.11   12.1   0.1    1.5  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus
      0.069   13.0   0.0       0.13   12.1   0.0    1.5  1  HTH_IclR       IclR 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 !  118.4   0.2   3.6e-38     8e-35       1      77 [.       2      78 ..       2      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 3.6e-38
                  HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqt 77
                                  eLt++qkei+ +Li+l+r+k +avKgeeiAe+++rn+GtvRNq+qsLk lgLvegvpGPkGGY+ t +ayeal+++ 
  gi|91773827|ref|YP_566519.1|  2 ELTPIQKEIIIELINLQRQKASAVKGEEIAELIDRNPGTVRNQMQSLKMLGLVEGVPGPKGGYRATGDAYEALNVTA 78
                                  69***********************************************************************9976 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         8   1.8e+04      30      44 ..     139     150 ..     137     150 .. 0.78
   2 !   33.6   0.0   1.7e-11   3.9e-08       1      51 [.     173     222 ..     173     227 .. 0.91
   3 !   45.9   1.2   2.5e-15   5.6e-12       1      55 [.     235     288 ..     235     290 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8
                                   SSEEEEEETTTBEEE CS
                           CBS  30 vsrlPVVdedgklvG 44 
                                   v+rl +V   g++vG
  gi|91773827|ref|YP_566519.1| 139 VNRL-IV--RGEVVG 150
                                   6788.88..788888 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 1.7e-11
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                   V+++  +d ++v p+ t+ ea+++++ +++++ PV +++gk+vG+vt +D+
  gi|91773827|ref|YP_566519.1| 173 VKHYIKKDTISVEPNYTIQEAARIFITNKIHGAPV-EDNGKIVGMVTFMDI 222
                                   566778999***************98888******.68************8 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 2.5e-15
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   ++dimt++v+t++ d++l++a+ l+ e++++rl +V  dg + G+++++D+l  l
  gi|91773827|ref|YP_566519.1| 235 IKDIMTKNVITIDGDSSLSDAVHLFNEHNIGRL-IVTIDGIPRGMISKTDVLHEL 288
                                   68************************9******.66689*************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   1.1e-10   2.4e-07      14      69 ..      14      68 ..       6      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.1e-10
                                  HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESS CS
                          Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLak 69
                                  l+ L++++ +  v+ eeiae  + +p  ++  ++ L+  glv+ v G++GGyr + 
  gi|91773827|ref|YP_566519.1| 14 LINLQRQKASA-VKGEEIAELIDRNPGTVRNQMQSLKMLGLVEGVPGPKGGYRATG 68
                                  66777777766.****************************************9665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   3.6e-10   8.1e-07       9      55 .]      18      65 ..       8      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.6e-10
                        HTH_11  9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                   +++ + + gee+Ae +++   tvr+ +++L++lg  +e++pg+  GYr
  gi|91773827|ref|YP_566519.1| 18 QRQKASAVKGEEIAELIDRNPGTVRNQMQSLKMLG-LVEGVPGPkgGYR 65
                                  3455566****************************.***********97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.5e-05     0.056      23      64 ..      25      66 ..      12      69 .. 0.91
   2 ?   -2.9   0.0         3   6.7e+03      28      44 ..     162     178 ..     161     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                  CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                          TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                   + +eiae +++   +v + ++sL+  GlVe ++g +  Yra
  gi|91773827|ref|YP_566519.1| 25 VKGEEIAELIDRNPGTVRNQMQSLKMLGLVEGVPGPKGGYRA 66
                                  6789*****************************999988887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                                   HCCCTTSSCHCHHHHHH CS
                          TrmB  28 iaeelgvprskvYevLr 44 
                                   i e++ +p+ +v  +++
  gi|91773827|ref|YP_566519.1| 162 ITEMVSLPKKSVKHYIK 178
                                   88999999999987765 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 ?   -0.5   0.0      0.44   9.9e+02      10      20 ..       2      12 ..       1      14 [. 0.89
   2 ?   11.2   0.0    0.0001      0.23      30      48 ..      28      46 ..      24      48 .. 0.92
   3 ?   -3.0   0.0       2.7     6e+03      38      48 ..     168     178 ..     164     179 .. 0.76
   4 ?   -2.8   0.0       2.3   5.1e+03      27      36 ..     188     197 ..     187     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.44
                                  TS-HHHHHHHH CS
                  Sigma70_r4_2 10 eLperqreifl 20
                                  eL+++q+ei++
  gi|91773827|ref|YP_566519.1|  2 ELTPIQKEIII 12
                                  79*******86 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0001
                                  HHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2 30 kEIAellgisegtVksrls 48
                                  +EIAel++ ++gtV+++++
  gi|91773827|ref|YP_566519.1| 28 EEIAELIDRNPGTVRNQMQ 46
                                  8***************986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.7
                                   --HHHHHHHHH CS
                  Sigma70_r4_2  38 isegtVksrls 48 
                                   ++ ++Vk++++
  gi|91773827|ref|YP_566519.1| 168 LPKKSVKHYIK 178
                                   67899999987 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.3
                                   --HHHHHHHH CS
                  Sigma70_r4_2  27 lsykEIAell 36 
                                   ++++E+A+++
  gi|91773827|ref|YP_566519.1| 188 YTIQEAARIF 197
                                   7999***985 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 ?   12.1   0.1   4.9e-05      0.11      83     136 ..      81     138 ..      49     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                                   EETTEEEEEE--EEEEEEE-HHHHHHHHH....TT-EEEE---TT--TT-EEEEETTT CS
                 Aconitase_2_N  83 dipyvPnkraggvvlGgkiaPiFfntved....sGalpieadvskletGdvieikpke 136
                                   +   vP  ++ ++v G+++a i f+tv       G + +  ++++++ Gd +++ p+ 
  gi|91773827|ref|YP_566519.1|  81 KEAEVPIYKNETIVNGATVAEISFTTVRHpdlcNGRIKVLGNIKAFNSGDRVQVGPTP 138
                                   45679**********************86334479******************97653 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 ?   12.1   0.0   5.9e-05      0.13      19      49 ..      25      55 ..      11      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                                  -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyve 49
                                  ++  e+A+ ++ ++ tv++ +q+L  lG+ve
  gi|91773827|ref|YP_566519.1| 25 VKGEEIAELIDRNPGTVRNQMQSLKMLGLVE 55
                                  5668**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1929.30
//
Query:       gi|91773828|ref|YP_566520.1|  [L=356]
Description: GTP-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  161.0   0.7    5.2e-47  159.8   0.0    1.7  2  NOG1_N     NOG1 N-terminal helical domain
    2.6e-22   78.3   0.3    6.3e-22   77.1   0.3    1.7  1  NOG1       Nucleolar GTP-binding protein 1 (NOG1)
    5.2e-19   68.4   0.0    1.8e-18   66.7   0.0    2.0  2  MMR_HSR1   50S ribosome-binding GTPase
    3.7e-10   39.5   0.0      9e-10   38.3   0.0    1.7  2  FeoB_N     Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.015   15.0   0.1       0.37   10.5   0.0    2.3  2  AAA_24     AAA domain
      0.098   12.6   0.0       0.43   10.5   0.0    1.9  2  Sushi_2    Beta-2-glycoprotein-1 fifth domain
       0.11   11.9   0.5         12    5.3   0.0    2.2  2  KTI12      Chromatin associated protein KTI12
       0.58   10.2   3.4        4.4    7.3   0.0    2.7  3  Dynamin_N  Dynamin family


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.8   0.0   2.3e-50   5.2e-47       1     159 [.       3     156 ..       3     156 .. 0.95
   2 ?   -1.3   0.1      0.85   1.9e+03      17      46 ..     307     335 ..     295     351 .. 0.49

  Alignments for each domain:
  == domain 1  score: 159.8 bits;  conditional E-value: 2.3e-50
                        NOG1_N   1 Fekiptvptseelidkalrrakraa.kttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldv 80 
                                   Feki tvpts+elidka+rra ra+  +t+++k+ ++++    +++++t  n+lsd+L++iv++fPn+d+l  Fy el+d+
  gi|91773828|ref|YP_566520.1|   3 FEKIHTVPTSDELIDKAFRRAARAKaGKTVRDKDGAMKA---HESMIMTSGNILSDNLANIVRRFPNFDDLSNFYFELTDI 80 
                                   9**********************9854555666777655...999************************************ PP

                        NOG1_N  81 lvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpai 159
                                   +v++d l+ +L++ +wa+++i +i++eyv+k++k++d+    + r+eafgr+asv+  ++k+l fL+d+r+ +rk+p++
  gi|91773828|ref|YP_566520.1|  81 VVGIDDLRLALGSADWASNKIHEISREYVGKIRKSKDPV---KTRKEAFGRMASVIGTINKHLLFLNDARNIMRKFPDV 156
                                   *************************************88...99*********************************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.85
                        NOG1_N  17 alrrakraakttkkkkneikrlrnlearkv 46 
                                   ++ ++     +tkk+ +e+k + ++ ark+
  gi|91773828|ref|YP_566520.1| 307 IVDKLVEMVIETKKE-KEAKEAAEVAARKL 335
                                   444444444333332.33333333333333 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 !   77.1   0.3   2.8e-25   6.3e-22       2      58 .]     227     282 ..     226     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 2.8e-25
                          NOG1   2 IEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                   +E+qAi+A+khl+++vlF+lD+se+cgy++++Q +Ll+e+ ++f+  pv+vv+nK+D
  gi|91773828|ref|YP_566520.1| 227 VELQAITAIKHLDAVVLFILDASETCGYEIADQKRLLDEVVANFE-MPVYVVANKCD 282
                                   8********************************************.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 ?   -3.0   0.0       3.4   7.6e+03      23      42 ..     111     130 ..      98     143 .. 0.71
   2 !   66.7   0.0   8.1e-22   1.8e-18       2     114 .]     162     280 ..     161     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.4
                                   TEEESSSTTSSSSEEEEEEE CS
                      MMR_HSR1  23 kaivsdkpgtTrdinegrvk 42 
                                   k + s+ p +Tr+  +gr++
  gi|91773828|ref|YP_566520.1| 111 KIRKSKDPVKTRKEAFGRMA 130
                                   45667788888888777765 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 8.1e-22
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCT.SEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleea.dli 79 
                                   ++++G+pNvGKS++++  tg++ +v+++p+tT+ +  g+++ + ++++++DtpGl++  ++++++ + +a+ a++    ++
  gi|91773828|ref|YP_566520.1| 162 IVVAGYPNVGKSSFVSMATGARPEVASYPFTTKGVLIGHFERGYDRYQVIDTPGLLDrpMSERNNVELQAITAIKHLdAVV 242
                                   89**************************************97779*********996544444446666677766663679 PP

                                   EEEEETT....TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  80 llvvdas....eeklkpldeeleelleeakkplilvlnk 114
                                   l+++das      +++++++ l e+  + + p+ +v+nk
  gi|91773828|ref|YP_566520.1| 243 LFILDASetcgY-EIADQKRLLDEVVANFEMPVYVVANK 280
                                   9999*9954431.45555555555555566899999997 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.9   6.5e+03      31      46 ..      28      43 ..      28      47 .. 0.78
   2 !   38.3   0.0     4e-13     9e-10       2      90 ..     161     250 ..     160     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.9
                                  TTSSSEEEEEEEEETT CS
                        FeoB_N 31 pGvtvekkegklklkg 46
                                  +G+tv  k g++k ++
  gi|91773828|ref|YP_566520.1| 28 AGKTVRDKDGAMKAHE 43
                                  599*****99999654 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 4e-13
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..CTSSS CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..eeepd 80 
                                   t++++G pnvGk++++   tga+ +v+ +p +t     g+++   ++++++D PG  +  ++se ++v  + ++  ++   
  gi|91773828|ref|YP_566520.1| 161 TIVVAGYPNVGKSSFVSMATGARPEVASYPFTTKGVLIGHFERGYDRYQVIDTPGLLD-RPMSERNNVELQAITaiKHLDA 240
                                   699***************************************888**********987.7899999999888873233345 PP

                                   EEEEEEEGGG CS
                        FeoB_N  81 vvvnvvdatn 90 
                                   vv+ ++da++
  gi|91773828|ref|YP_566520.1| 241 VVLFILDASE 250
                                   6678999986 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   0.00016      0.37       3      44 ..     160     214 ..     158     218 .. 0.82
   2 ?    1.2   0.1      0.11   2.5e+02     147     176 ..     291     320 ..     260     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                        AAA_24   3 lkiliyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfp 44 
                                     i++ G + +GK+++++++             ++ +l+  +e+G+++ ++++ p
  gi|91773828|ref|YP_566520.1| 160 PTIVVAGYPNVGKSSFVSMAtgarpevasypftTKGVLIGHFERGYDRYQVIDTP 214
                                   579*****************98877777777766667777999999998888765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                        AAA_24 147 rlepklgkktanelkeevDlvlranlkred 176
                                   ++  k++  t+++l ++vD ++++ +++++
  gi|91773828|ref|YP_566520.1| 291 FVDAKMSTATGENLDSIVDKLVEMVIETKK 320
                                   677899999999999999999999998765 PP

>> Sushi_2  Beta-2-glycoprotein-1 fifth domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00019      0.43      20      54 ..     225     259 ..     221     273 .. 0.85
   2 ?   -1.3   0.0      0.95   2.1e+03      49      65 ..     275     291 ..     268     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                       Sushi_2  20 vkiedllknrvlHgekvsffCknkekkCsytveaq 54 
                                    ++e +    ++H + v +f  ++ ++C+y+ + q
  gi|91773828|ref|YP_566520.1| 225 NNVELQAITAIKHLDAVVLFILDASETCGYEIADQ 259
                                   55666667889*******************98765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.95
                       Sushi_2  49 ytveaqCvdgklkiPeC 65 
                                   y v+++C    +kiP+ 
  gi|91773828|ref|YP_566520.1| 275 YVVANKCDHDLFKIPDF 291
                                   89999999999999985 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0082        18       2      18 ..     160     176 ..     160     182 .. 0.88
   2 ?    5.3   0.0    0.0052        12     127     182 ..     260     328 ..     224     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0082
                                   .EEEEE--TTSSHHHHH CS
                         KTI12   2 pLvvltGlPssGKstra 18 
                                   p +v+ G+P +GKs+++
  gi|91773828|ref|YP_566520.1| 160 PTIVVAGYPNVGKSSFV 176
                                   679***********986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0052
                                   HHHHHHHHHH---TT..SS-GGGS-SEEEE..TTS---H..........HHHHHHHHHHHTS--SSSTT CS
                         KTI12 127 kelldaLiqRyeePd..sknrWDsPlftvls.aeeklpl..........deilkaliekkklkpnqatl 182
                                   k lld+++  +e P    +n+ D+ lf++    + k+++          d++++++ie kk+k++++  
  gi|91773828|ref|YP_566520.1| 260 KRLLDEVVANFEMPVyvVANKCDHDLFKIPDfVDAKMSTatgenldsivDKLVEMVIETKKEKEAKEAA 328
                                   6799999999999963368999*****999884444444456666444455555556655555544433 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.038        85       1      22 [.     162     183 ..     162     203 .. 0.79
   2 ?    7.3   0.0     0.002       4.4     102     160 ..     207     272 ..     200     281 .. 0.66
   3 ?   -3.0   0.2         3   6.7e+03      41      60 ..     319     338 ..     308     353 .. 0.42

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.038
                                   EEEEEBTTTTHHHHHHHHHTS- CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlged 22 
                                   i+v G  + GKSS++   +g++
  gi|91773828|ref|YP_566520.1| 162 IVVAGYPNVGKSSFVSMATGAR 183
                                   8999**********98877776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                                   SEEEEE---B-SSSGTTS.....HHHHHHH.STTEEEEEEEETTS-C..CC-CHHHHHHHHSTTBTT CS
                     Dynamin_N 102 gltlvDlPGldsvnkrdq.....elvkeyi.kkadiilavtsanhdl..snsealflarevdpkgkr 160
                                   ++ ++D+PGl +++  +      + + ++i +  +++l++++a+  +    +++++l +ev  + + 
  gi|91773828|ref|YP_566520.1| 207 RYQVIDTPGLLDRPMSERnnvelQAI-TAIkHLDAVVLFILDASETCgyEIADQKRLLDEVVANFEM 272
                                   5678******9988888766653333.4453667778889999885411455777777776666666 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3
                                   CCT---CCS...SSEEEET- CS
                     Dynamin_N  41 geeeeaseravkeelkekek 60 
                                   ++e+ea+e+a+ +  k  e+
  gi|91773828|ref|YP_566520.1| 319 KKEKEAKEAAEVAARKLSEE 338
                                   33333232222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2147.88
//
Query:       gi|91773829|ref|YP_566521.1|  [L=370]
Description: aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  225.2   0.0    1.6e-66  225.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.6e-10   39.8   0.1    5.1e-10   38.9   0.0    1.5  2  Aminotran_5      Aminotransferase class-V
    8.8e-10   38.4   0.0    1.7e-09   37.5   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.5e-08   33.6   0.0    2.2e-08   33.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    6.1e-05   22.4   0.0     0.0001   21.7   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.039   12.6   0.1       0.15   10.6   0.1    1.9  1  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 !  225.0   0.0   5.2e-70   1.6e-66       2     361 ..      28     364 ..      27     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 5.2e-70
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   d +nLg +++++d    t+ ++++a+++  + +++++ y+   g  el+eal + ++++++ ++ ++  ++v+sGa++++e
  gi|91773829|ref|YP_566521.1|  28 DAVNLGLGQPDFD----TPGHIRQAAID--AINEGFTGYTYGAGIVELREALSQKFREQNGFEVSPD-GIIVTSGASEALE 101
                                   579**********....***********..*************************************.************* PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                   ++i++l ++pgdei+++dp + sy+  +  +gg+vv +pl   +d ++  e++ e ++       ktk ++v+sp NPtG 
  gi|91773829|ref|YP_566521.1| 102 IAIAAL-IDPGDEIIISDPGFVSYNALAGFMGGKVVGVPLG--DDLTMRPENVMESITP------KTKAVIVNSPCNPTGG 173
                                   ******.********************************99..***************9......**************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlr 244
                                   v+++ ++++ +++a+ + + l++De+Y++f ++ +     ++ ++  +n+++v+ +sK ++++G+RvGy+++++++ +q+ 
  gi|91773829|ref|YP_566521.1| 174 VLSKSDIKAYAEIADDNDITLISDEVYEHFLYEGEH----VSPAKFTDNVITVNAFSKTYAMTGWRVGYTAASQEYTNQML 250
                                   *********************************653....666777778******************************** PP

                                   HHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHH CS
                 Aminotran_1_2 245 klsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskk 323
                                   k+++ +     s++q+a++aa+  +++   ++  mr+++++rr++l+++ ++lg ++ a++++++++  ++++  +e++ k
  gi|91773829|ref|YP_566521.1| 251 KVHQYVQAcaNSIAQKAALAATTGPQD---FVYMMRDEFKSRRDVLVEGVNALGMECEAPKGAFYMFPKVENS--TEVATK 326
                                   ***98877779**************97...9****************************************99..9***** PP

                                   HHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                 Aminotran_1_2 324 Lleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                   L+ + gv+v+pgt f++   g +R+++ +++ +e++++++
  gi|91773829|ref|YP_566521.1| 327 LVAN-GVVVVPGTAFGKngDGYIRMSY-ATSMDEIKRALK 364
                                   ****.************9999******.999999999986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   1.7e-13   5.1e-10      59     175 ..      86     197 ..      46     201 .. 0.84
   2 ?   -3.7   0.1       1.4   4.2e+03      22      55 ..     225     259 ..     212     268 .. 0.58

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.7e-13
                                   STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TT CS
                   Aminotran_5  59 eseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnek 139
                                   +  + ii+tsG++ea+++++ +l   ++pgdei++++ +  +      +la + g kv+ +pl ++ +++++++ + +++k
  gi|91773829|ref|YP_566521.1|  86 S-PDGIIVTSGASEALEIAIAAL---IDPGDEIIISDPGFVSYN----ALAGFMGGKVVGVPLGDDLTMRPENVMESITPK 158
                                   4.489******************...9***********988877....8999***************************** PP

                                   EEEEEEESBETTTTEB-...-HHHHHHHHHHTT-EEEEE CS
                   Aminotran_5 140 tklvaithvsnvtGtiq...pveeigklakkkgalvlvD 175
                                   tk+v+++   n tG +    ++++ +++a ++++ ++ D
  gi|91773829|ref|YP_566521.1| 159 TKAVIVNSPCNPTGGVLsksDIKAYAEIADDNDITLISD 197
                                   *************99761114555555555666666665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                                   HHHCTCCSSSS.SSSHHHHHHHHHHHHHHHHHHHH CS
                   Aminotran_5  22 yytdynanvhr.svhhlgkeatkaveearekvael 55 
                                   +++ y+  + r +   +++e t+++ ++++ v++ 
  gi|91773829|ref|YP_566521.1| 225 FSKTYAMTGWRvGYTAASQEYTNQMLKVHQYVQAC 259
                                   44445555555445555666666666666666554 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 !   37.5   0.0   5.7e-13   1.7e-09      41     144 ..      90     197 ..      46     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 5.7e-13
                                   EEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-.. CS
               DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh.. 119
                                    i +s +++Al++a+ al ++pgde+I+   +Fv+  + +  +g k+v v    d++++ p+++ + it++tka+++    
  gi|91773829|ref|YP_566521.1|  90 IIVTSGASEALEIAIAAL-IDPGDEIIISDPGFVSYNALAGFMGGKVVGVPLG-DDLTMRPENVMESITPKTKAVIVNSpc 168
                                   356666789******998.99*****************************887.9********************975433 PP

                                   ..GGGB--..-HHHHHHHHHHCT-EEEEE CS
               DegT_DnrJ_EryC1 120 ..lyGqva..dmdalkaiaakhglkvieD 144
                                     + G  +  d++a  +ia++ ++ +i+D
  gi|91773829|ref|YP_566521.1| 169 npTGGVLSksDIKAYAEIADDNDITLISD 197
                                   3355665567*****************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 !   33.1   0.0   7.3e-12   2.2e-08      65     175 ..      84     199 ..      44     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 7.3e-12
                                   HT-SEEEEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEE CS
               Cys_Met_Meta_PP  65 eggeaalavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvyl 143
                                   e +  +++v+sG + A++ ai al+  Gdei++sd  + + ++l   +  k +g+      t  +e++ + i+++tk+v +
  gi|91773829|ref|YP_566521.1|  84 EVSPDGIIVTSGASeALEIAIAALIDPGDEIIISDPGFVSYNALAGFMGGKvVGVPLGDDLTMRPENVMESITPKTKAVIV 164
                                   4456789999998769999*******************988888888777756666666667899**************** PP

                                   ESS-TTT...T----HHHHHHHHHHTT-EEEEEGT CS
               Cys_Met_Meta_PP 144 Etptnpl...lkvvDiekiaklakkagvlvvvDnt 175
                                    +p np+   l+  Di++ a++a +++++++ D +
  gi|91773829|ref|YP_566521.1| 165 NSPCNPTggvLSKSDIKAYAEIADDNDITLISDEV 199
                                   ******93334557****************99976 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.5e-08    0.0001      36     167 ..      72     197 ..      43     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.5e-08
                                   HHHHHHHHHTT-S...EEEEES-H.HHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HH CS
               Beta_elim_lyase  36 rLedavaelfgke...aalfvpqG.taAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdle 112
                                   +L ++++e  g+e    ++ v++G   A +i++++l+ +g+e+i+++p+ +      a+a + g k++ ++  ++ +m +e
  gi|91773829|ref|YP_566521.1|  72 ALSQKFREQNGFEvspDGIIVTSGaSEALEIAIAALIDPGDEIIISDPGFVSY---NALAGFMGGKVVGVPLGDDLTMRPE 149
                                   456666666666633346778888346889999***************96655...45566677779999988889***** PP

                                   HHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase 113 kleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                   ++ + i++      k+k++++   +n   G v+s   +++ a+ia++++i+l+ D
  gi|91773829|ref|YP_566521.1| 150 NVMESITP------KTKAVIVNSPCNP-TGGVLSKSDIKAYAEIADDNDITLISD 197
                                   ******99......5889999999996.788*********************988 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   5.1e-05      0.15     183     235 ..     149     200 ..     142     370 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.1e-05
                                   HHHHCHTCCCEEEEEE-S.CETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TT CS
                   Aminotran_3 183 ealekkkkdevaAvivEp.iqgegGvvvaspeflaklrelckkhdvllivDEvq 235
                                   e++ + +++++ Aviv       gGv  +s+  +++ +e+++++d+ li DEv 
  gi|91773829|ref|YP_566521.1| 149 ENVMESITPKTKAVIVNSpCNPTGGVLSKSD--IKAYAEIADDNDITLISDEVY 200
                                   56677888899999998669*****998877..68899**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2352.13
//
Query:       gi|91773830|ref|YP_566522.1|  [L=202]
Description: hexulose-6-phosphate isomerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   61.9   0.1    2.3e-16   59.8   0.0    1.8  2  SIS       SIS domain
    0.00043   20.3   1.8       0.06   13.4   0.1    2.2  2  SIS_2     SIS domain
  ------ inclusion threshold ------
       0.11   11.4   0.0        5.9    5.8   0.0    2.3  2  DUF4788   Domain of unknown function (DUF4788)


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 !   59.8   0.0   3.9e-20   2.3e-16       2     106 ..      42     140 ..      41     149 .. 0.95
   2 ?   -0.5   0.0      0.17     1e+03      80      95 ..     180     195 ..     170     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.9e-20
                                   HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                           SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                   + +a++++v+GaG+s+ ++k +a+ l+++g + ++v ++++      + + ++d+v+ is sgetk+  ++ +  k  gak
  gi|91773830|ref|YP_566522.1|  42 ILEADSVFVMGAGRSGLVGKAFAMRLMHLGLKSYVVGESTT------PAVHPEDVVVTISGSGETKSISNLGKITKDIGAK 116
                                   56899*********************************999......99******************************** PP

                                   EEEEESSTTSHHHHHSSEEEEEEE CS
                           SIS  83 iiaITdskgsplareadlalyina 106
                                   +i++T++++s+l + +d+a++i  
  gi|91773830|ref|YP_566522.1| 117 LITVTSNPNSTLGNLSDVAMEIKG 140
                                   ********************9976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                                   TSEEEEEESSTTSHHH CS
                           SIS  80 gakiiaITdskgspla 95 
                                    a+ii+IT+ +++ l 
  gi|91773830|ref|YP_566522.1| 180 IAEIISITGASEDDLK 195
                                   5789****99998875 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0012       7.4      15      59 ..      24      69 ..      12      83 .. 0.76
   2 !   13.4   0.1     1e-05      0.06     101     138 .]      85     122 ..      75     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0012
                                  HHSHHHHHH.HHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT- CS
                         SIS_2 15 etqaeaiek.aaeliadslenggkvlvfGsGhSaalaeelaaragg 59
                                  e+ ae ++k  ++ + +++ +   v+v+G+G S +  + +a r+  
  gi|91773830|ref|YP_566522.1| 24 ESVAEDLDKeSIRNMISTILEADSVFVMGAGRSGLVGKAFAMRLMH 69
                                  44455554325688999999999************99999999875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1e-05
                                   --TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                         SIS_2 101 lkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                   ++p+Dv + iS sG+ +++ ++ +  k++g+k+i +ts
  gi|91773830|ref|YP_566522.1|  85 VHPEDVVVTISGSGETKSISNLGKITKDIGAKLITVTS 122
                                   79**********************************98 PP

>> DUF4788  Domain of unknown function (DUF4788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0   0.00099       5.9     125     159 ..       8      53 ..       5      58 .. 0.69
   2 ?    3.1   0.0    0.0064        38     142     167 ..      79     104 ..      68     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00099
                       DUF4788 125 kcedldkeee.secsr...........scrnldksinpqDimFvlgd 159
                                   kce+l + ++ ++              s+rn+ ++i + D +Fv+g 
  gi|91773830|ref|YP_566522.1|   8 KCEHLISSMQlIAH-HlesvaedldkeSIRNMISTILEADSVFVMGA 53 
                                   55555555553222.2345555666669*****************96 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0064
                       DUF4788 142 rnldksinpqDimFvlgdsqrcpias 167
                                   ++  ++++p+D++ +++ s ++++ s
  gi|91773830|ref|YP_566522.1|  79 ESTTPAVHPEDVVVTISGSGETKSIS 104
                                   567889***********999886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1270.98
//
Query:       gi|91773831|ref|YP_566523.1|  [L=170]
Description: hypothetical protein Mbur_1890 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   15.9   0.0      0.015   14.7   0.0    1.5  1  DUF4941   Domain of unknown function (DUF4941)


Domain annotation for each model (and alignments):
>> DUF4941  Domain of unknown function (DUF4941)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   8.3e-07     0.015      67     104 ..      99     136 ..      94     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.3e-07
                       DUF4941  67 lFgidyikegntlklaemivediseigeiievvyeGen 104
                                   +F+i++  +   ++lae i+ed+++++  i++ ++G +
  gi|91773831|ref|YP_566523.1|  99 MFNIPFYSNKALYYLAESIIEDLKKDDVHIDIYWNGDD 136
                                   8***********************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1110.85
//
Query:       gi|91773832|ref|YP_566524.1|  [L=119]
Description: hypothetical protein Mbur_1891 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-46  154.1   0.6    1.1e-45  153.8   0.6    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 !  153.8   0.6   6.1e-50   1.1e-45       1     105 []      14     117 ..      14     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 6.1e-50
                       DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkeseerl 81 
                                   l+km+++ek+r+i+d+vk gki+vlE+gLtpeeea+lie+tm+ i+pd+F+Gie+e+yp++++ ++ll+kl++k+  ++rl
  gi|91773832|ref|YP_566524.1|  14 LAKMQPVEKVRFIIDEVKGGKILVLERGLTPEEEASLIEMTMTLIEPDDFAGIEMESYPSQTD-NSLLGKLFKKNVVRTRL 93 
                                   689*********************************************************999.***************** PP

                       DUF2073  82 tvigPanqlktlkkdkdlisalvs 105
                                   tvigPan+lktlkkd+d+isalvs
  gi|91773832|ref|YP_566524.1|  94 TVIGPANKLKTLKKDRDMISALVS 117
                                   **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 787.70
//
Query:       gi|91773833|ref|YP_566525.1|  [L=207]
Description: small GTP-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   61.7   0.0    8.6e-17   61.3   0.0    1.2  1  MMR_HSR1      50S ribosome-binding GTPase
    1.7e-15   57.1   0.5    1.3e-06   28.1   0.1    2.9  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    3.4e-07   30.3   0.1      0.029   14.3   0.0    2.1  2  RsgA_GTPase   RsgA GTPase
      5e-07   29.3   0.0     0.0089   15.5   0.0    2.3  2  Arf           ADP-ribosylation factor family
      2e-05   24.8   0.0     0.0074   16.5   0.0    2.2  2  Roc           Ras of Complex, Roc, domain of DAPkinase
    0.00015   21.3   0.4     0.0032   17.0   0.4    2.6  1  FeoB_N        Ferrous iron transport protein B
    0.00036   20.2   0.0      0.025   14.2   0.0    2.3  2  Ras           Ras family
     0.0008   18.8   0.0     0.0012   18.2   0.0    1.2  1  Septin        Septin
    0.00092   19.0   0.0     0.0023   17.7   0.0    1.9  1  AAA_24        AAA domain
     0.0011   18.4   0.0      0.045   13.2   0.0    2.3  2  SRPRB         Signal recognition particle receptor beta subun
     0.0049   16.5   0.0        1.6    8.3   0.0    2.2  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0086   16.6   0.0       0.02   15.4   0.0    1.7  1  AAA_18        AAA domain
     0.0094   15.9   0.0      0.013   15.5   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0095   16.4   0.0      0.013   16.0   0.0    1.3  1  ABC_tran      ABC transporter
     0.0097   16.3   0.1      0.028   14.8   0.1    2.0  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.017   15.5   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.013   14.7   0.0      0.023   13.9   0.0    1.3  1  NB-ARC        NB-ARC domain
       0.02   14.8   0.0      0.034   14.1   0.0    1.6  1  ATPase_2      ATPase domain predominantly from Archaea
      0.021   14.7   0.0       0.04   13.8   0.0    1.4  1  NTPase_1      NTPase
      0.032   14.2   0.0       0.13   12.2   0.0    2.0  1  NACHT         NACHT domain
      0.035   14.2   0.0        5.5    7.0   0.0    2.3  2  Dynamin_N     Dynamin family
      0.036   13.2   0.0      0.058   12.5   0.0    1.3  1  Parvo_NS1     Parvovirus non-structural protein NS1
      0.036   13.8   0.1       0.25   11.2   0.0    2.3  2  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
       0.04   14.3   0.0       0.08   13.3   0.0    1.5  1  RNA_helicase  RNA helicase
      0.095   11.5   0.0       0.13   11.1   0.0    1.2  1  PPV_E1_C      Papillomavirus helicase
       0.12   12.0   0.0       0.25   10.9   0.0    1.6  1  AAA_25        AAA domain
       0.18   11.1   0.0       0.34   10.2   0.0    1.6  1  AIG1          AIG1 family


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   1.3e-19   8.6e-17       1     114 []      21     164 ..      21     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.3e-19
                                   EEEEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSEEEEEEE...ETT..EEEEEEECGGC.............S. CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.....kaivsdkpgtTrdinegrvk...lkg..keielvDtpGl.............i. 57 
                                   +++i+G pN+GK+tL n+++++        vs+++  Tr  ++++      +g   ++ ++DtpGl             + 
  gi|91773833|ref|YP_566525.1|  21 RIGIYGPPNAGKTTLANRILRDwtgdaMGSVSHIAHETRRARRREGVtiqSNGgsISLDIIDTPGLatkidfhefmelgMn 101
                                   69*****************984433224588888888888866653223333324679*******8777776666554413 PP

                                   ..S...HHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  58 ..e...gaseek.glgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                     e   +a+e   g+ +a++ le+ d ++lv+da+e+ +++++ ++   +e ++ pl++v+nk
  gi|91773833|ref|YP_566525.1| 102 eaEskrRAKEATeGVIEAVKWLENLDGVILVMDATEDPYTQVNVTVIGNMEARNLPLLIVANK 164
                                   331333222222578888887889*********9999************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 !   28.1   0.1     2e-09   1.3e-06       3      93 ..      19     102 ..      17     116 .. 0.83
   2 !   25.0   0.0   1.8e-08   1.2e-05      91     188 ..     123     202 ..     113     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2e-09
                                   EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESS...S CS
                      GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPG...H 80 
                                      igi g  ++GKtTL  r+l +   +++ +  +    +  t+ + r+ g+Ti+s+  s++       + +iDtPG    
  gi|91773833|ref|YP_566525.1|  19 NARIGIYGPPNAGKTTLANRILRDWTGDAMGSVSH---IAHETRRARRREGVTIQSNGGSIS-------LDIIDTPGlatK 89 
                                   5789*******************999988855444...45899***************9999.......********4444 PP

                                   GGGHHHHHHHHHT CS
                      GTP_EFTU  81 vdFskevirglrv 93 
                                   +dF + ++ g++ 
  gi|91773833|ref|YP_566525.1|  90 IDFHEFMELGMNE 102
                                   5788877777765 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.8e-08
                                   HHT-SEEEEEEETTTBSTHHHH.HHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEE CS
                      GTP_EFTU  91 lrvlDgavlvvdaveGvepqte.evlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpv 170
                                   l+ lDg++lv+da+e++ +q + +v+  + ++++p+ ++ NK D ++++   i e+  q                    p+
  gi|91773833|ref|YP_566525.1| 123 LENLDGVILVMDATEDPYTQVNvTVIGNMEARNLPLLIVANKTDLPESSATSIREAFPQ-------------------HPM 184
                                   7889************999975499********************98877766665542...................467 PP

                                   EEEBTTTTBTHHHHHHHH CS
                      GTP_EFTU 171 vfgSalkgegvktlleal 188
                                   v +Sal+g++++t+ + +
  gi|91773833|ref|YP_566525.1| 185 VAISALEGKNIDTFYDEV 202
                                   777777777777777766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.4e-05     0.029     103     162 ..      23      87 ..       8      92 .. 0.74
   2 !   14.2   0.0   4.6e-05     0.031      14      97 ..     124     202 ..     105     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                                   EEECSTTSSHHHHHHHHCT.T-----S--------------SEEEEEETTTEE....EESS-SSS CS
                   RsgA_GTPase 103 vlvGqSGvGKStLinallp.elelktgevseklgrGkhTTtavellelaeggl....liDtPGfr 162
                                    + G+  +GK+tL n++l   +  ++g+vs+  ++ +   ++  +   ++gg     +iDtPG+ 
  gi|91773833|ref|YP_566525.1|  23 GIYGPPNAGKTTLANRILRdWTGDAMGSVSHIAHETRRARRREGVTIQSNGGSisldIIDTPGLA 87 
                                   5789999*********998345788999999888888876666655555555423338*****86 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.6e-05
                                   ES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHH CS
                   RsgA_GTPase  14 aNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelk 94 
                                    N+d +++v+ ++e+ +++  +  ++  +e+++++++iv nK+Dl e++   ++++e++ +   +++++sa +++++++  
  gi|91773833|ref|YP_566525.1| 124 ENLDGVILVMDATEDPYTQVNV-TVIGNMEARNLPLLIVANKTDLPESSA--TSIREAFPQH--PMVAISALEGKNIDTFY 199
                                   699*******999666655555.5899******************99988..6666666665..77777777788877766 PP

                                   HHC CS
                   RsgA_GTPase  95 ell 97 
                                   +++
  gi|91773833|ref|YP_566525.1| 200 DEV 202
                                   665 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0002      0.13       2      37 ..       8      42 ..       7      59 .. 0.86
   2 !   15.5   0.0   1.3e-05    0.0089      78     136 ..     122     175 ..     119     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                  HHHHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHS CS
                           Arf  2 lsilaklklkkkelrilllGLDnaGKtTilkklkle 37
                                  ++ +++l++ kk++ri + G  naGKtT+ +++  +
  gi|91773833|ref|YP_566525.1|  8 KKFFKRLFN-KKNARIGIYGPPNAGKTTLANRILRD 42
                                  678889999.9******************9998765 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
                                   GCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHH CS
                           Arf  78 YfektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeel 136
                                   ++e+ d+vi v+D+++    +       +++ + e ++ +ll++aNK Dlpe+  +  +
  gi|91773833|ref|YP_566525.1| 122 WLENLDGVILVMDATEDPYTQVN----VTVIGNMEARNLPLLIVANKTDLPESSAT-SI 175
                                   67899999999999987543333....356778899***************97544.44 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 !   16.5   0.0   1.1e-05    0.0074       2      66 ..      22      86 ..      21     103 .. 0.90
   2 ?    6.3   0.0     0.016        11      78     120 .]     124     167 ..     116     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                                  EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq 66
                                  + + G  ++GKt+l++r+++d   +   s   +   t+++ + +gv+ +++  +++l+i Dt G 
  gi|91773833|ref|YP_566525.1| 22 IGIYGPPNAGKTTLANRILRDWTGDAMGSVSHIAHETRRARRREGVTIQSNGGSISLDIIDTPGL 86
                                  56789******************************99999999****9999***********985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                                   CTSCEEEEEEEGHHHHCHHHHHHHHHHH.CSSS-EEEEEE-TTT CS
                           Roc  78 reaalailvydsrssenlkeWlkelkkv.agkspvilvgnkiDl 120
                                   ++ + +ilv+d++++   +  ++ + ++ a++ p+++v+nk+Dl
  gi|91773833|ref|YP_566525.1| 124 ENLDGVILVMDATEDPYTQVNVTVIGNMeARNLPLLIVANKTDL 167
                                   566789999**9999888888999988724567*********95 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   4.9e-06    0.0032       3     154 ..      22     200 ..      20     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                                   EEEEESTTSSHHHHHHHHHT..TSEEEEESTTSSSE......EEEEEEEETT..EEEEEEE----......SSS....... CS
                        FeoB_N   3 valvGnpnvGkttlfnaltg..akqkvgNwpGvtve......kkegklklkg..keveivDlPGi......Ysl....... 60 
                                   + + G pn+Gkttl n++    +   +g  + ++ e      ++ ++++ +g   +++i+D PG       +         
  gi|91773833|ref|YP_566525.1|  22 IGIYGPPNAGKTTLANRILRdwTGDAMGSVSHIAHEtrrarrREGVTIQSNGgsISLDIIDTPGLatkidfH-Efmelgmn 101
                                   7789************996412223344444443330001103333444444335689******95555542.05666877 PP

                                   ......SSSSHHHHHHHHHHHCTSSSEEEEEEEGGG...HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHH CS
                        FeoB_N  61 ......sayseeekvardflleeepdvvvnvvdatn...lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLse 132
                                          a    e v + +   e+ d v+ v+dat+    + n++++ ++   ++p++++ n++d  e++ ++i ++    
  gi|91773833|ref|YP_566525.1| 102 eaeskrRAKEATEGVIEAVKWLENLDGVILVMDATEdpyTQVNVTVIGNMEARNLPLLIVANKTDLPESSATSIREAF--- 179
                                   7655443344445566666668999*********974435667777778888889*************9999997653... PP

                                   HHTS-EEEEBTTTTBTHHHHHH CS
                        FeoB_N 133 kLgvpvvktsakkkegieellk 154
                                     + p+v++sa ++++i+++ +
  gi|91773833|ref|YP_566525.1| 180 -PQHPMVAISALEGKNIDTFYD 200
                                   .456889999999999888766 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.061        41       6      57 ..      26      85 ..      21     105 .. 0.62
   2 !   14.2   0.0   3.7e-05     0.025      70     158 ..     124     204 ..     118     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.061
                                  ESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET........TEEEEEEEEEETT CS
                           Ras  6 GdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd........gkevkleiwDTAG 57
                                  G  + GKt+l +r  +d   + + s  +++  t++ + +        g +++l+i DT G
  gi|91773833|ref|YP_566525.1| 26 GPPNAGKTTLANRILRDWTGDAMGSVSHIAHETRRARRRegvtiqsnGGSISLDIIDTPG 85
                                  6677788888888777666555544444443333222222233334489999*****988 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.7e-05
                                   TTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHH CS
                           Ras  70 rdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenve 150
                                   ++ +g++lv d t+ + +++v+  v+ i ++  +n+p+++v+nK+Dl e+ a s +e+       + + + +SA + +n++
  gi|91773833|ref|YP_566525.1| 124 ENLDGVILVMDATE-DPYTQVN--VTVIGNMEARNLPLLIVANKTDLPESSATSIREAF-----PQHPMVAISALEGKNID 196
                                   67788888888764.6788887..334555556789************98887777765.....45788999********9 PP

                                   HHHHHHHH CS
                           Ras 151 eafeellr 158
                                   + ++e+++
  gi|91773833|ref|YP_566525.1| 197 TFYDEVAK 204
                                   99999987 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.8e-06    0.0012       9      81 ..      24      95 ..      18     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                  EEEBTTSSCCCCCCTTSSSS------------------S-E.EEEEEEEETTCEEEEEEEE---BSSSSSHHCC CS
                        Septin  9 vvGesglGkttlintlfetdlieeekleeasekkkktveik.kkkvvieedgvklnltviDtpgfGdavdnsks 81
                                  + G    Gkttl n ++++   ++      s+ +++t + + ++ v+i+ +g  + l +iDtpg   ++d ++ 
  gi|91773833|ref|YP_566525.1| 24 IYGPPNAGKTTLANRILRDWTGDAMGSV--SHIAHETRRARrREGVTIQSNGGSISLDIIDTPGLATKIDFHEF 95
                                  5688899*********998888875433..33333344443288999*******************99998765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.5e-06    0.0023       2      22 ..      19      39 ..      18     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                        AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                  +++i iyGp+ +GKTtla+++
  gi|91773833|ref|YP_566525.1| 19 NARIGIYGPPNAGKTTLANRI 39
                                  799***************987 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.8e-05     0.045       4      58 ..      20      85 ..      17      97 .. 0.67
   2 ?    2.8   0.0       0.1        67      67     127 ..     117     170 ..     111     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                                  -EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG..............GGTT-SEEEETT CS
                         SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSqessaalkv...........ksekgskltliDfPG 58
                                   ++ + G+ ++GKT+l +r++ d + +++ S+   a +             ++    +l++iD PG
  gi|91773833|ref|YP_566525.1| 20 ARIGIYGPPNAGKTTLANRILRDWTGDAMGSVSHIAHETRrarrregvtiqSNGGSISLDIIDTPG 85
                                  567799*****************7777776664333332212444555553334445677777777 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.1
                                   HHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT- CS
                         SRPRB  67 leklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelfla 127
                                   +e +k  ++l g++ v+D+t dp    +v        +i  ++  ++++li  nK +l  +
  gi|91773833|ref|YP_566525.1| 117 IEAVKWLENLDGVILVMDATEDPYTQVNV-------TVIGNMEARNLPLLIVANKTDLPES 170
                                   56677778888888888888888655443.......3333334556778888888887654 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0024       1.6       3      26 ..      22      45 ..      20      77 .. 0.84
   2 !    6.4   0.0    0.0092       6.1     110     157 ..     124     172 ..     102     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                                  EEEEESTTCCHHHHHHHHHCT--S CS
                          cobW  3 tvltGflGsGKTtLlnhllenrag 26
                                  +++ G++ +GKTtL n++l++  g
  gi|91773833|ref|YP_566525.1| 22 IGIYGPPNAGKTTLANRILRDWTG 45
                                  57899*************976554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0092
                                   CCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSS...EEEEE-HHHHCHC. CS
                          cobW 110 ltldavvavvDaknleaeeekieekaedqlaaad...llvlnKtDlldeea 157
                                    +ld+v+ v+Da++  +  ++ + ++   ++a +   l+v nKtDl +++a
  gi|91773833|ref|YP_566525.1| 124 ENLDGVILVMDATE--DPYTQVNVTVIGNMEARNlplLIVANKTDLPESSA 172
                                   6799********44..6677777777777777663336999****988873 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     3e-05      0.02       1      80 [.      22     134 ..      22     149 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-05
                        AAA_18   1 IlltGtpGvGKttlakeL.................skrlgf...............gvnlrdvakenglllevdpe..... 44 
                                   I++ G+p +GKttla+++                 +                    g ++ d++   gl +  d +     
  gi|91773833|ref|YP_566525.1|  22 IGIYGPPNAGKTTLANRIlrdwtgdamgsvshiahE----TrrarrregvtiqsngGSISLDIIDTPGLATKIDFHefmel 98 
                                   89**************99666665544444444440....04444444447777776666666666666666665556666 PP

                        AAA_18  45 .....aldeskrldedkldklldaleenssaleegknlvid 80 
                                        + ++  ++ ++ + ++++ le+ +     g  lv+d
  gi|91773833|ref|YP_566525.1|  99 gmneaESKRRAKEATEGVIEAVKWLENLD-----GVILVMD 134
                                   66666666666666666677777777765.....3555555 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 !   15.5   0.0     2e-05     0.013      53     102 ..     153     204 ..      99     207 .] 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                  MMR_HSR1_Xtn  53 rvYipclyvlNKiDlisleeldelar..epnsvviSaekelnldeLkekiwe 102
                                      +p l+v NK+Dl + + ++  +   ++ +v iSa +++n+d+  +++ +
  gi|91773833|ref|YP_566525.1| 153 ARNLPLLIVANKTDLPESSATSIREAfpQHPMVAISALEGKNIDTFYDEVAK 204
                                   466899*********5555444333322568999***********9998865 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-05     0.013       9      66 ..      17      70 ..      14     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
                                  ETTSEEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGGB-HHHCCHCEEEE-S CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  9 kegekvaivGenGaGKStLlkllagllkp.teGeilldgkdlkeqeleslrkeigvlpq 66
                                  k++ +++i G+  aGK+tL++ +++  +  ++G++     ++ +++ +++r++ gv  q
  gi|91773833|ref|YP_566525.1| 17 KKNARIGIYGPPNAGKTTLANRILRDWTGdAMGSV----SHIAHET-RRARRREGVTIQ 70
                                  57889****************99998776578888....4444433.333333333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   4.2e-05     0.028       3      23 ..      24      44 ..      22     173 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
                                  EESSTTSSHHHHHHHHHHHHT CS
                           AAA  3 lyGppGtGKTllakavakelg 23
                                  +yGpp  GKT+la+ + +++ 
  gi|91773833|ref|YP_566525.1| 24 IYGPPNAGKTTLANRILRDWT 44
                                  7***************99963 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   0.0   2.5e-05     0.017      28      91 ..      23     105 ..       8     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                        AAA_16  28 llsGesGvGKsslvrellralekd..................ggiflrgkcdqlesa.........ipy....sa.laqal 76 
                                    ++G++  GK++l++++lr +++d                  +             +         i++     + la+ +
  gi|91773833|ref|YP_566525.1|  23 GIYGPPNAGKTTLANRILRDWTGDamgsvshiahetrrarrrE-------------GvtiqsnggsISLdiidTPgLATKI 90 
                                   59**********************6544433333333222222.............1222222223111223233355555 PP

                        AAA_16  77 areellrqlldeaes 91 
                                   +++e+++   +eaes
  gi|91773833|ref|YP_566525.1|  91 DFHEFMELGMNEAES 105
                                   554444444444333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.4e-05     0.023       6      43 ..       8      42 ..       4      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                                  HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                  +k  ++L++k++     ++++G +  GKttla+ il++
  gi|91773833|ref|YP_566525.1|  8 KKFFKRLFNKKNAR---IGIYGPPNAGKTTLANRILRD 42
                                  56778999888887...******************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 ?   14.1   0.0   5.1e-05     0.034      20      44 ..      19      43 ..       8     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
                      ATPase_2 20 neiyfiYGpegsGKtaLlkeiienl 44
                                  n  + iYGp + GKt+L ++i+   
  gi|91773833|ref|YP_566525.1| 19 NARIGIYGPPNAGKTTLANRILRDW 43
                                  55567***************98766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     6e-05      0.04       2      50 ..      22      70 ..      21      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                                  EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkiv 50
                                  + i Gpp  GKtTl +++l+    + +     +++e r+  rr g +i 
  gi|91773833|ref|YP_566525.1| 22 IGIYGPPNAGKTTLANRILRDWTGDAMGSVSHIAHETRRARRREGVTIQ 70
                                  7899******************999999999999*********998875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.13       5      47 ..      24      63 ..      20     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                  EEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTT CS
                         NACHT  5 lqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsr 47
                                  + G++  GKTtL+ ++ ++w  +   ++     + ++ r+ +r
  gi|91773833|ref|YP_566525.1| 24 IYGPPNAGKTTLANRILRDWTGDAMGSVS---HIAHETRRARR 63
                                  7899999*************988766632...44444444444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.029        20       1      20 [.      22      41 ..      22      46 .. 0.89
   2 ?    7.0   0.0    0.0083       5.5     103     166 ..      78     163 ..      51     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.029
                                  EEEEEBTTTTHHHHHHHHHT CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                  i + G  ++GK++++n +l+
  gi|91773833|ref|YP_566525.1| 22 IGIYGPPNAGKTTLANRILR 41
                                  6788999**********996 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0083
                                   EEEEE---B-SSSGTTS......................HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTE CS
                     Dynamin_N 103 ltlvDlPGldsvnkrdq......................elvkeyikkadiilavtsanhdlsnsealflarevdpkgkrt 161
                                   l ++D+PGl    + ++                        + + +++ d +++v++a  d  ++ +  +  +++ ++   
  gi|91773833|ref|YP_566525.1|  78 LDIIDTPGLATKIDFHEfmelgmneaeskrrakeategvIEAVKWLENLDGVILVMDATEDPYTQVNVTVIGNMEARNLPL 158
                                   789*******99999999999999999999999888866334455688888888888888766666666666666666666 PP

                                   EEEEE CS
                     Dynamin_N 162 ivvlt 166
                                   ++v +
  gi|91773833|ref|YP_566525.1| 159 LIVAN 163
                                   66655 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   8.8e-05     0.058     106     135 ..      10      40 ..       4      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.8e-05
                     Parvo_NS1 106 wlskqlgkrnt.vwfyGpantGktnlaeaIa 135
                                   ++++ + k+n+ +++yGp+n Gkt la+ I 
  gi|91773833|ref|YP_566525.1|  10 FFKRLFNKKNArIGIYGPPNAGKTTLANRIL 40 
                                   5667778888769***************886 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 ?   11.2   0.0   0.00037      0.25       6      58 .]     119     166 ..     117     166 .. 0.86
   2 ?   -1.2   0.0       2.6   1.7e+03      40      53 ..     174     187 ..     172     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                          NOG1   6 AiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                   A+  L++l++++l ++D++e+ +++++  + ++ +++++  n p+++v+nK+D
  gi|91773833|ref|YP_566525.1| 119 AVKWLENLDGVIL-VMDATEDPYTQVN--VTVIGNMEAR--NLPLLIVANKTD 166
                                   7888999999998.89*****998776..7888888888..79********99 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                          NOG1  40 eikelfankpvivv 53 
                                   +i+e f++ p++ +
  gi|91773833|ref|YP_566525.1| 174 SIREAFPQHPMVAI 187
                                   89*****9999865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012      0.08       3      25 ..      24      46 ..      22      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                  RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                  +yGp++ GK+tla+++ ++++++
  gi|91773833|ref|YP_566525.1| 24 IYGPPNAGKTTLANRILRDWTGD 46
                                  8***************9998854 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.13     249     295 ..       4      52 ..       1      58 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                      PPV_E1_C 249 ltalkefLkg.vPkknc.lvllGppntGkslfamslikfLkGkvlsfvn 295
                                   + ++k+f+k    kkn+ + ++Gppn+Gk+++a+ +++  +G  +  v+
  gi|91773833|ref|YP_566525.1|   4 MGSFKKFFKRlFNKKNArIGIYGPPNAGKTTLANRILRDWTGDAMGSVS 52 
                                   56778887762578887477**************999988887766555 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   0.00038      0.25      34      97 ..      20      72 ..      13     136 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                        AAA_25 34 elallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97
                                  + + ++G+p +GKttla  +  +++  +          g V  ++ E ++   rrR   + + +
  gi|91773833|ref|YP_566525.1| 20 ARIGIYGPPNAGKTTLANRILRDWTG-D--------AMGSVSHIAHETRR--ARRREGVTIQSN 72
                                  56668*************99999994.4........23567777766666..444444444444 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00052      0.34       6      64 ..      25      91 ..      20     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00052
                                  ESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETT........EEEEEEE--SCCCTTC CS
                          AIG1  6 vGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdg........kkinViDTPglfdlsv 64
                                   G   +Gk + +N il++   +   s + + ++ ++++r++           ++++iDTPgl    +
  gi|91773833|ref|YP_566525.1| 25 YGPPNAGKTTLANRILRDWTGDAMGSVSHIAHETRRARRREGVtiqsnggsISLDIIDTPGLATKID 91
                                  5777899999999999998866666666665555444332211122223557899******965444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1303.07
//
Query:       gi|91773834|ref|YP_566526.1|  [L=203]
Description: protein-L-isoaspartate O-methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-71  239.3   0.1    3.8e-71  239.2   0.1    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    3.2e-12   46.5   0.0    4.2e-12   46.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.3e-07   32.2   0.0    2.4e-07   31.3   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    2.1e-06   27.1   0.0      3e-06   26.6   0.0    1.2  1  Methyltransf_3   O-methyltransferase
    8.7e-06   25.0   0.0    1.3e-05   24.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    4.6e-05   24.0   0.0    8.7e-05   23.1   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      6e-05   22.8   0.0    7.9e-05   22.5   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00015   21.4   0.0    0.00022   21.0   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00016   21.1   0.0     0.0002   20.8   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00036   19.7   0.0     0.0005   19.2   0.0    1.2  1  Fibrillarin      Fibrillarin
     0.0008   19.0   0.0     0.0013   18.4   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00089   20.3   0.0     0.0015   19.5   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
     0.0028   17.5   0.0     0.0037   17.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0057   16.0   0.0     0.0074   15.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.017   14.6   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
      0.016   15.2   0.0      0.019   14.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.036   13.8   0.2      0.053   13.2   0.2    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.12   13.1   0.0       0.19   12.5   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
       0.12   12.9   0.0        0.2   12.2   0.0    1.4  1  POTRA            Surface antigen variable number repeat
       0.15   11.7   0.0       0.21   11.2   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020


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 !  239.2   0.1   4.3e-74   3.8e-71       6     208 ..       1     200 [.       1     202 [. 0.99

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 4.3e-74
                                   HHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSH CS
                          PCMT   6 lieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGy 86 
                                   +i+ lk++g  ++++v++a+++v+R+ f+pe ++++aY d+pl+igy++tiSaphmva++++ll++++g+ +Le+GsGsGy
  gi|91773834|ref|YP_566526.1|   1 MIRALKANG--TDQRVLNAMKKVPRHLFLPEDMQSFAYADTPLPIGYDQTISAPHMVAIMCDLLKITEGMTILEIGSGSGY 79 
                                   68999****..9********************************************************************* PP

                                   HHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEEEE CS
                          PCMT  87 ltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLkeGG 167
                                   ++av+a+l ge+g+v ++eri+elv+ a++nl++ +++nv+vv+ DG  G +e+aPYd+i v+  ape+P +l +QL + G
  gi|91773834|ref|YP_566526.1|  80 NAAVMAELAGENGKVYTVERIPELVDLARNNLERAGYSNVTVVHDDGSCGLPEHAPYDRIAVTSVAPEVPPPLREQLSKNG 160
                                   ********************************************************************************* PP

                                   EEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCC CS
                          PCMT 168 rlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdk 208
                                   ++v+Pvg ++ Q+l +v+k+++g+++ k + ev+fvpl +k
  gi|91773834|ref|YP_566526.1| 161 IMVIPVG-TQYQTLVVVKKDSKGNITHKAMGEVIFVPLIGK 200
                                   *******.99****************************876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   4.6e-15   4.2e-12       2      80 ..      65     141 ..      64     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.6e-15
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                   ++g+++l++G+G+G+ + ++ae++g++++v+ +++ +e + lAr+n+++ g++nv++ + d    l+++   +++D i  
  gi|91773834|ref|YP_566526.1|  65 TEGMTILEIGSGSGYNAAVMAELAGENGKVYTVERIPELVDLARNNLERAGYSNVTVVHDDGSCgLPEH---APYDRIAV 141
                                   689**********************************************************99999976...78887655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.7e-10   2.4e-07       1      80 [.      70     151 ..      70     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.7e-10
                                   EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEESTGGGSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvssgalhhls 78 
                                   +L++G G+G +++ +a+  g ++kv+ v+  +e+++ ar+++e++g+ nv++v+ d +  lp e++ +D + ++ +   ++
  gi|91773834|ref|YP_566526.1|  70 ILEIGSGSGYNAAVMAELAGeNGKVYTVERIPELVDLARNNLERAGYsNVTVVHDDGSCgLP-EHAPYDRIAVTSVAPEVP 149
                                   8****************99669***********************99**********76366.667999998854455555 PP

                                   HH CS
               Methyltransf_25  79 de 80 
                                   ++
  gi|91773834|ref|YP_566526.1| 150 PP 151
                                   55 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.4e-09     3e-06      42      99 ..      61     118 ..      43     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.4e-09
                                   HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GG CS
                Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvae 99 
                                   L+k+++   +leiG   Gy +  +a    e+Gk+ +++  +e +++a++ +++ag+ +
  gi|91773834|ref|YP_566526.1|  61 LLKITEGMTILEIGSGSGYNAAVMAELAGENGKVYTVERIPELVDLARNNLERAGYSN 118
                                   89*****************************************************975 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.5e-08   1.3e-05      24      85 ..      60     126 ..      48     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.5e-08
                                   HHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                        RrnaAD  24 dklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                                   d l+++e +t+leig+G G   + +a+ a    +v  +E  ++L+ l +++l+   +++++vvh D+
  gi|91773834|ref|YP_566526.1|  60 DLLKITEGMTILEIGSGSGYNAAVMAELAgenGKVYTVERIPELVDLARNNLEraGYSNVTVVHDDG 126
                                   668999***********************99889999****************999*********96 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   9.7e-08   8.7e-05       1      70 [.      71     144 ..      71     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.7e-08
                                   EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEEES- CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvssev 70 
                                   L++G+G+G++a+ +a+ +   ++v++v+  +e+++la+++ +++g  +v++v+ d +   +++ + +D + +++v
  gi|91773834|ref|YP_566526.1|  71 LEIGSGSGYNAAVMAELAgenGKVYTVERIPELVDLARNNLERAGYsNVTVVHDDGS-CGLPEhAPYDRIAVTSV 144
                                   89*************7666899***********************998888888776.44544245666665555 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   8.8e-08   7.9e-05      29     100 ..      55     125 ..      45     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.8e-08
                         GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrD 100
                                   ++++   L++++G  ++e G Gsg  +  +a   +  G+++t+e   + ++ ar+++++ + s+ vtv h D
  gi|91773834|ref|YP_566526.1|  55 VAIMCDLLKITEGMTILEIGSGSGYNAAVMAELAGENGKVYTVERIPELVDLARNNLERAGYSN-VTVVHDD 125
                                   56777889***************************************************99876.5555555 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 !   21.0   0.0   2.4e-07   0.00022       3      71 ..      61     129 ..      59     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                                   HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCC CS
               Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarki 71 
                                   lL+  e+ til++ ++ G   + +ael  ++g+v+ v++  e ++   +nl+r g  n++v++ D++  
  gi|91773834|ref|YP_566526.1|  61 LLKITEGMTILEIGSGSGYNAAVMAELAGENGKVYTVERIPELVDLARNNLERAGYSNVTVVHDDGSCG 129
                                   6889999**********************************************************9854 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.3e-07    0.0002      41     108 ..      60     127 ..      53     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.3e-07
                                   HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
               Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanae 108
                                   +l    +g ++l++ +G+g  a+ +++ +ge+gkv  ++  +++++ +++ l++ g++n+  ++ ++ 
  gi|91773834|ref|YP_566526.1|  60 DLLKITEGMTILEIGSGSGYNAAVMAELAGENGKVYTVERIPELVDLARNNLERAGYSNVTVVHDDGS 127
                                   455667999******************************************************99875 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.6e-07    0.0005      64     107 ..      60     103 ..      51     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.6e-07
                                   S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                   Fibrillarin  64 kelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                   + l+i +g  +L +G++sG  ++ ++++ ge+g+vy+ve  p  
  gi|91773834|ref|YP_566526.1|  60 DLLKITEGMTILEIGSGSGYNAAVMAELAGENGKVYTVERIPEL 103
                                   456899*********************************98865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06    0.0013      23     101 ..      58     139 ..      54     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                                   HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEE CS
                           MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdl 100
                                   + + l+ ++  ++l +G+G G+ +a++a+   e+  v  v+   + +++a++nle+ + + v+vv+ d+   ++ ++ +d 
  gi|91773834|ref|YP_566526.1|  58 MCDLLKITEGMTILEIGSGSGYNAAVMAELAGENGkVYTVERIPELVDLARNNLERAGYSnVTVVHDDGSCGLPeHAPYDR 138
                                   556666667789****************99988766**********************999*******9988872345666 PP

                                   E CS
                           MTS 101 i 101
                                   i
  gi|91773834|ref|YP_566526.1| 139 I 139
                                   6 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.7e-06    0.0015       1      63 [.      71     131 ..      71     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-06
               Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaee....aaalareaglddrvrlikadseeala 63 
                                   +EiG+ sG+ ++++++++ +ng+  +++v+  p   e    a++++++ag+++ v+++++d +  l+
  gi|91773834|ref|YP_566526.1|  71 LEIGSGSGYNAAVMAELAGENGK--VYTVERIP---ElvdlARNNLERAGYSN-VTVVHDDGSCGLP 131
                                   7********************96..********...42334667777788887.5666655544444 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   4.1e-06    0.0037      21      95 ..      65     148 ..      52     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.1e-06
               Methyltransf_23  21 raggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                    +g+ +L+iG G+G+++ v++e  g   +v+ v+  pe+v++a+         +    ++d     +  ++ + +d I  +
  gi|91773834|ref|YP_566526.1|  65 TEGMTILEIGSGSGYNAAVMAELaGEngKVYTVERIPELVDLARnnleragysNVTVVHDDGS---CGLPEHAPYDRIAVT 142
                                   56889***************6642545699999999999999987777766654444444433...555566666666655 PP

               Methyltransf_23  90 evlehv 95 
                                    v   v
  gi|91773834|ref|YP_566526.1| 143 SVAPEV 148
                                   555555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   8.3e-06    0.0074      52     131 ..      56     139 ..      46     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.3e-06
                                   HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..-- CS
                          CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kv 128
                                    ++++ l++ +Gmt+L+iG G G+ +  ++e  +   kv  +    e   la++++++++ ++ + v+  +   l+e  ++
  gi|91773834|ref|YP_566526.1|  56 AIMCDLLKITEGMTILEIGSGSGYNAAVMAELAGenGKVYTVERIPELVDLARNNLERAGYSNVTVVHDDGSCGLPEhaPY 136
                                   6789*******************9887777654411456666556677777777777777777666666666666666666 PP

                                   SEE CS
                          CMAS 129 drv 131
                                   dr+
  gi|91773834|ref|YP_566526.1| 137 DRI 139
                                   665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.9e-05     0.017       3      64 ..      68     130 ..      66     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                   EEEEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 
                                    ++leiG+G+G     +A+   ++ ++  +E   ++v+ + ++ e+ +++N+ +++ d    l
  gi|91773834|ref|YP_566526.1|  68 MTILEIGSGSGYNAAVMAELAGENgKVYTVERIPELVDLARNNLERAGYSNVTVVHDDGSCGL 130
                                   5789*******999999998877636889**************************99986555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.2e-05     0.019      11      78 ..      56     116 ..      47     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
               Methyltransf_32  11 elvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78 
                                   ++  +ll    k ++ +t++++G+G gY + v+a   +  + kv+ ++   elv+ a++  e+ g  +
  gi|91773834|ref|YP_566526.1|  56 AIMCDLL----KITEGMTILEIGSGSGYNAAVMAE-LAGENGKVYTVERIPELVDLARNNLERAG--Y 116
                                   3333333....447899*****************9.44479**************9999999888..4 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   5.9e-05     0.053      46      93 ..      66     115 ..      54     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
               Methyltransf_16  46 sklsvlELGsGtGlvGlavaell.peakvi.ltDleellellkknielnk 93 
                                   +++++lE+GsG+G    ++ael+ ++ kv+ +  ++el++l ++n+e ++
  gi|91773834|ref|YP_566526.1|  66 EGMTILEIGSGSGYNAAVMAELAgENGKVYtVERIPELVDLARNNLERAG 115
                                   6789***********9999999778899972566899********99855 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00021      0.19       1      75 [.      71     144 ..      71     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
               Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnv 75 
                                   LeiG+G+G ++++++e   ++ +++ v+  p+ ++ a++ l + +  n+++v+ +  +   l++ + +D + + +v
  gi|91773834|ref|YP_566526.1|  71 LEIGSGSGYNAAVMAELAgENGKVYTVERIPELVDLARNNLERAGYSNVTVVHDD-GSC-GLPEHAPYDRIAVTSV 144
                                   8***************999***************888888888887555544433.332.2333467777766666 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022       0.2      21      58 ..      85     122 ..      61     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                   TTTSSSTTSBHCHHHHHHHHHHHHHHHHCTT-EE.EEE CS
                         POTRA  21 relelkegdvynpekleadkealksryanlGyfdasVq 58 
                                   +el    g+vy+ e++ + ++  ++++++ Gy +++V+
  gi|91773834|ref|YP_566526.1|  85 AELAGENGKVYTVERIPELVDLARNNLERAGYSNVTVV 122
                                   44544679************************997774 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.21      75     126 ..      90     140 ..      61     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                   HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEE CS
                       UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdviv 126
                                   ++ k+y ++ ++++v+ ar+N+e+ag ++   + +   + L+ +++ +d i+
  gi|91773834|ref|YP_566526.1|  90 ENGKVYTVERIPELVDLARNNLERAGYSNVTVVHDDGSCGLP-EHAPYDRIA 140
                                   56679******************************99*****.777999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1313.50
//
Query:       gi|91773835|ref|YP_566527.1|  [L=215]
Description: hypothetical protein Mbur_1895 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00037   20.5   1.2    0.00076   19.5   1.2    1.4  1  Elf1             Transcription elongation factor Elf1 like
     0.0012   19.2   0.9     0.0023   18.3   0.9    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.017   15.0   1.3      0.047   13.6   1.3    1.8  1  zinc_ribbon_4    zinc-ribbon domain
       0.08   12.4   0.9       0.15   11.5   0.9    1.4  1  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
       0.13   12.3   3.2       0.26   11.3   1.5    2.2  3  HypA             Hydrogenase/urease nickel incorporation, met
       0.19   11.7   0.9       0.53   10.3   0.1    2.2  2  CAT_RBD          CAT RNA binding domain
       0.41   10.9   0.2       0.41   10.9   0.2    2.6  3  zf-RING_7        C4-type zinc ribbon domain
       0.75   10.1   3.2        1.1    9.6   0.4    2.2  2  zf-LITAF-like    LITAF-like zinc ribbon domain
        2.3    8.2   5.9         11    6.0   5.9    2.0  1  Prok-RING_1      Prokaryotic RING finger family 1
        3.3    7.5   6.5        9.6    6.0   1.1    2.6  2  zf-CSL           CSL zinc finger


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.2   4.2e-07   0.00076      23      60 ..       8      45 ..       4      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.2e-07
                          Elf1 23 dCpfCnheksvevkldkkekiaevsCkvCgesfetkvn 60
                                  +Cp+C+ ++sve ++ +  ++ +v+C+ Cg+  +t ++
  gi|91773835|ref|YP_566527.1|  8 ECPVCSPKESVEHEVLRAGQNPVVQCQECGAVHTTVIE 45
                                  7*****************************99888776 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 !   18.3   0.9   1.3e-06    0.0023       3      43 ..       6      45 ..       4      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
               Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCgastpwfki 43
                                  +  CP C  ++ +e++ +++    ++v+C++Cga+++++ +
  gi|91773835|ref|YP_566527.1|  6 IVECPVCSPKESVEHEVLRAG-QNPVVQCQECGAVHTTVIE 45
                                  568******999999988886.466*********5554443 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.3   2.6e-05     0.047       2      34 ..       6      39 ..       6      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                 zinc_ribbon_4  2 kitCpsCkakyeiddeklpakgv.kvrCskCghv 34
                                  +++Cp C+ k +++ e l+a+    v+C  Cg+v
  gi|91773835|ref|YP_566527.1|  6 IVECPVCSPKESVEHEVLRAGQNpVVQCQECGAV 39
                                  69*****************88877********87 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   8.1e-05      0.15      12      44 ..       9      41 ..       8      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.1e-05
                   Vps36-NZF-N 12 CpICsfsNevpsnfdpnastplPpClaCGvkpd 44
                                  Cp+Cs + +v+ ++    ++p+  C+ CG   +
  gi|91773835|ref|YP_566527.1|  9 CPVCSPKESVEHEVLRAGQNPVVQCQECGAVHT 41
                                  *************9989999*********7655 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   1.5   0.00015      0.26      67     110 ..       3      54 ..       1      56 [. 0.78
   2 ?   -0.5   0.0      0.67   1.2e+03      29      29 ..     129     129 ..      91     173 .. 0.51
   3 ?   -1.1   0.0       1.1   1.9e+03      21      37 ..     160     176 ..     144     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                   E--EEEETTTS-EEECHHHHH.........S-TTTSSS-EEEEESSSEEEEEE CS
                          HypA  67 vpvkvrCreCgkefeleekal.........rCpkCgsadveivsGeellvksi 110
                                   ++v v+C +C+ + ++e++ +         +C++Cg+ ++++++ +   v+++
  gi|91773835|ref|YP_566527.1|   3 EEVIVECPVCSPKESVEHE-VlragqnpvvQCQECGAVHTTVIEEKKPIVTKV 54 
                                   67899*****988776653.1245678888************99888777765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.67
                                   E CS
                          HypA  29 v 29 
                                   +
  gi|91773835|ref|YP_566527.1| 129 I 129
                                   2 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                                   TT..EEEEEEEEEETTC CS
                          HypA  21 aaarkvtkvkvevGels 37 
                                    ++ ++tk+k++ G+++
  gi|91773835|ref|YP_566527.1| 160 GKTFHITKIKIRGGSFQ 176
                                   33446777777777766 PP

>> CAT_RBD  CAT RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.8   6.8e+03      35      47 ..     102     114 ..     101     114 .. 0.83
   2 ?   10.3   0.1    0.0003      0.53      30      55 ..     174     199 ..     171     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.8
                                   TTSEEETTTSSEE CS
                       CAT_RBD  35 kgdeideekieKv 47 
                                   +g ++d ++++K+
  gi|91773835|ref|YP_566527.1| 102 EGRRVDRQEVDKI 114
                                   5889999999997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0003
                                   TTT--TTSEEETTTSSEEEEE-SHCH CS
                       CAT_RBD  30 GFgkkkgdeideekieKvFvlkdeee 55 
                                    F+ +kgd++ ++ i+++++++++++
  gi|91773835|ref|YP_566527.1| 174 SFQSRKGDRVAAKYIKRIYSIDKRKQ 199
                                   7********************99875 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4      0.36   6.4e+02      21      29 ..       4      12 ..       1      13 [. 0.79
   2 ?   10.9   0.2   0.00023      0.41      16      31 ..      21      38 ..      17      39 .. 0.71
   3 ?   -2.8   0.0       4.4   7.9e+03       9      23 ..     106     125 ..     105     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.36
                                  TB-EE-TTT CS
                     zf-RING_7 21 devvtCpeC 29
                                  +++v Cp C
  gi|91773835|ref|YP_566527.1|  4 EVIVECPVC 12
                                  679****99 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00023
                                  HH.CCS.TB-EE-TTT-- CS
                     zf-RING_7 16 el.rag.devvtCpeCGR 31
                                  e+ rag + vv+C eCG+
  gi|91773835|ref|YP_566527.1| 21 EVlRAGqNPVVQCQECGA 38
                                  562555666********7 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.4
                                   --CCHHHHH.....CCSTB- CS
                     zf-RING_7   9 lppqvlsel.....ragdev 23 
                                   ++ q++ ++     ra+dev
  gi|91773835|ref|YP_566527.1| 106 VDRQEVDKIdtiwgRATDEV 125
                                   67788877766666777765 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 ?    0.5   0.1      0.41   7.4e+02       6      12 ..       7      13 ..       2      21 .. 0.71
   2 ?    9.6   0.4   0.00059       1.1       6      30 ..      31      55 ..      27      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.41
                 zf-LITAF-like  6 vdCpaCq 12
                                  v+Cp C+
  gi|91773835|ref|YP_566527.1|  7 VECPVCS 13
                                  6777776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00059
                 zf-LITAF-like  6 vdCpaCqqrvvTsveyksgkltwll 30
                                  v+C+ C++  +T++e+k+  +t ++
  gi|91773835|ref|YP_566527.1| 31 VQCQECGAVHTTVIEEKKPIVTKVI 55
                                  89**************998887655 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.9    0.0064        11       6      30 ..       8      40 ..       3      43 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0064
                   Prok-RING_1  6 kCpvCgkelkee........dDiVvCpeCgtpy 30
                                  +CpvC+ + + e        + +V+C eCg+++
  gi|91773835|ref|YP_566527.1|  8 ECPVCSPKESVEhevlragqNPVVQCQECGAVH 40
                                  7999975433333377777789*********97 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.1    0.0054       9.6      41      51 ..       3      13 ..       1      21 [. 0.82
   2 ?    4.0   0.4     0.022        40      40      50 ..      26      36 ..      14      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0054
                                  .--EEEETTSS CS
                        zf-CSL 41 aevvvqCssCS 51
                                   ev+v+C+ CS
  gi|91773835|ref|YP_566527.1|  3 EEVIVECPVCS 13
                                  49********* PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                                  ..--EEEETTS CS
                        zf-CSL 40 gaevvvqCssC 50
                                  g + vvqC++C
  gi|91773835|ref|YP_566527.1| 26 GQNPVVQCQEC 36
                                  5788******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1438.54
//
Query:       gi|91773836|ref|YP_566528.1|  [L=289]
Description: agmatinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-79  265.8   0.0    5.2e-79  265.7   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.7   0.0   2.9e-83   5.2e-79       2     277 ..      18     280 ..      17     283 .. 0.95

  Alignments for each domain:
  == domain 1  score: 265.7 bits;  conditional E-value: 2.9e-83
                                   EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHH CS
                      Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaeilk 81 
                                   + +++GvPfd + s+r+G+r +P+air+a+a++e+   yn   ++  +e++ +d+g+ +  +   ++vl++++  v +i++
  gi|91773836|ref|YP_566528.1|  18 SYVIFGVPFDRTSSFRAGSRWAPDAIRSATANFES---YNSFYDIdISEIPAHDAGNFEAGA-LVDDVLDELYLDVINIVD 94 
                                   579*******************************8...6776777799**********9987.8888************** PP

                                   TTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCS CS
                      Arginase  82 agklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdn 162
                                   +gklpi++GG+Hs++l++++a+a+++g+++gv+ +DAH+Dlr++  eg +++h+++ r+++ e+++  +++v iGirs  +
  gi|91773836|ref|YP_566528.1|  95 DGKLPIMIGGEHSLTLPCMKACAKHAGEDFGVVVLDAHFDLRDEF-EGMKYNHACVSRHIL-EEVT--ENYVSIGIRSGPK 171
                                   *******************************************88.***************.6666..59*********** PP

                                   HHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHC CS
                      Arginase 163 eeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelae 243
                                   ee+++ake ++r++t ++++e+g+k + +ei+e+++  ++++y+S+D+D+lDpa+aPG+Gtpep Glt+ ++++++re+a 
  gi|91773836|ref|YP_566528.1| 172 EEWDYAKENNVRYYTPEDVTEKGIKGLTNEIREYLD--CENIYISLDMDALDPAFAPGVGTPEPFGLTSVQVRDIIREFAP 250
                                   ***********************************5..89***************************************77 PP

                                   HSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                      Arginase 244 klnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       +g+Dv+E++P++d+ + qta+l+a+ +re+
  gi|91773836|ref|YP_566528.1| 251 --IARGFDVMEISPEYDS-G-QTAILGAKYIREF 280
                                   ..68*************9.6.9**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1909.02
//
Query:       gi|91773837|ref|YP_566529.1|  [L=127]
Description: translation initiation factor IF-5A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-08   34.9   0.5    2.8e-08   33.7   0.5    1.6  1  eIF-5a       Eukaryotic elongation factor 5A hypusine, DNA-bi
    4.1e-05   23.5   0.1    6.6e-05   22.9   0.1    1.4  1  EFP_N        Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.018   14.2   0.1       0.02   14.0   0.1    1.1  1  Cas_St_Csn2  CRISPR-associated protein Csn2 subfamily St
      0.024   14.9   0.4       0.23   11.8   0.1    2.2  2  DUF1947      Domain of unknown function (DUF1947)


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 !   33.7   0.5   6.2e-12   2.8e-08       1      65 [.      68     124 ..      68     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 6.2e-12
                                   --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEE CS
                        eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeeki 65 
                                   +V+rk +q+++I+ +   +Lmd ++++t+e l +p     ++ k++ +egkd  +t+++amG+ ki
  gi|91773837|ref|YP_566529.1|  68 IVERKSAQVLSISSN-IAQLMDmETYTTFE-LTIP-----EDYKDRVTEGKD--ITYIEAMGKMKI 124
                                   69**********988.**************.****.....8999********..********9987 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 !   22.9   0.1   1.5e-08   6.6e-05       2      33 ..       7      38 ..       6      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                                  GGG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                         EFP_N  2 aselkkGlvieidgklyvVlefehvkpGkGqa 33
                                  ++elk G  +  d++++v+++++ +kpGk ++
  gi|91773837|ref|YP_566529.1|  7 VKELKEGKYVLADDEPCVIKSIQKSKPGKHGS 38
                                  689*************************8653 PP

>> Cas_St_Csn2  CRISPR-associated protein Csn2 subfamily St
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.5e-06      0.02     216     257 ..      54      95 ..      41     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                                   EEEEEE--SSS-----TTTGGGEEEESSSEEE---HHHHHHH CS
                   Cas_St_Csn2 216 itiiltlslegYvkideekieginiindevyqlpdlefvkef 257
                                    +ii  +s + Yv i e k+  +  i+ ++ ql d+e   +f
  gi|91773837|ref|YP_566529.1|  54 RSIISSVSAKTYVPIVERKSAQVLSISSNIAQLMDMETYTTF 95 
                                   579999*******************************98776 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.2e-05      0.23      29      52 ..       3      26 ..       1      33 [. 0.85
   2 ?    1.0   0.0      0.12   5.3e+02      24      47 ..      60      82 ..      51      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                                  ..-EEEE-SS-EEEEETTEEEEEE CS
                       DUF1947 29 dkiEieeekkeklYlingvpilfe 52
                                  +++E++e k+ k+ l ++ p++++
  gi|91773837|ref|YP_566529.1|  3 QQVEVKELKEGKYVLADDEPCVIK 26
                                  45********************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                                  -TT--....-EEEE-SS-EEEEETTE CS
                       DUF1947 24 islesdk..iEieeekkeklYlingv 47
                                  +s    k  + i e+k++ ++ i++ 
  gi|91773837|ref|YP_566529.1| 60 VSA---KtyVPIVERKSAQVLSISSN 82
                                  333...33499999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 844.90
//
Query:       gi|91773838|ref|YP_566530.1|  [L=231]
Description: peptidase M10A and M12B, matrixin and adamalysin [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-16   58.1   0.0    1.2e-15   57.7   0.0    1.1  1  Peptidase_M10  Matrixin
    8.1e-05   21.7   0.0    0.00012   21.1   0.0    1.3  1  Peptidase_M66  Peptidase M66
     0.0001   22.8   0.0    0.00014   22.4   0.0    1.3  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
     0.0039   16.8   0.0     0.0049   16.5   0.0    1.2  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase
     0.0089   15.7   0.0      0.017   14.8   0.0    1.4  1  Astacin        Astacin (Peptidase family M12A)
       0.01   15.1   0.0      0.014   14.7   0.0    1.1  1  DUF4953        Met-zincin
  ------ inclusion threshold ------
      0.016   15.8   0.4          5    7.9   0.0    2.4  2  DUF3139        Protein of unknown function (DUF3139)
       0.02   14.5   0.0      0.026   14.2   0.0    1.2  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
      0.028   13.0   0.0      0.041   12.5   0.0    1.1  1  Metallopep     Putative peptidase family
      0.037   14.0   0.0      0.062   13.3   0.0    1.3  1  Peptidase_M54  Peptidase family M54
      0.051   13.7   0.0       0.07   13.3   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12
       0.09   12.7   0.0       0.12   12.3   0.0    1.2  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-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 !   57.7   0.0   8.3e-19   1.2e-15       2     143 ..      37     184 ..      36     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 8.3e-19
                                   TSSSEEEEEESSSX.TTSXHHHHHHHHHHHHHHHHTTS......SSEEEEESSSCESEEEEEESSSSSSSSSXBSSSSESE CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M10   2 wekknltyrilnet.pdleeeevrkairrAfkvwsevt......plkFtevkkgeadikieFgrgehgdgypfdgkggvla 75 
                                   w+++ +t  i++ + p   +++ rkai +A + w++        + +F+ +++ +adi + + +  ++     dg  g+  
  gi|91773838|ref|YP_566530.1|  37 WDHSPITVYIDDVNtPPHYSHTYRKAIVDATEYWETGGngklyyEPDFEIIDSPDADIYVMWVETMEEVTGAEDGVAGYCR 117
                                   8999999999887635589999*************9886655555678888****************************** PP

                                   EEBSSSSTTTTEEEEETTS-EESSTS-.SSSEEHHHHHHHHHHHHTTBESXSSTTSTTSSSCTXTTTX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M10  76 hafapgeglggdihfdddeqWtlgeekveqgvslflVaaHEiGHalGLeHssdkdalmyplykeekkv 143
                                    +   g+ ++++i ++  ++  l+ ++    ++++++a+HE+GHalGL+Hs+dk+++myp y+++++v
  gi|91773838|ref|YP_566530.1| 118 PEISAGRFIRASIVLEVGDKRGLSWQQ-YGDANMEQIAIHELGHALGLDHSNDKKDIMYPSYEQRDNV 184
                                   ****************99988888655.7899******************************976665 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.2e-08   0.00012     187     223 ..     145     179 ..     122     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.2e-08
                 Peptidase_M66 187 tgdatltgefiHEqGHalGLpHylageaaskgsyp.ya 223
                                    gda+++++ iHE+GHalGL H  + ++++   yp y+
  gi|91773838|ref|YP_566530.1| 145 YGDANMEQIAIHELGHALGLDH--SNDKKD-IMYPsYE 179
                                   589*******************..554444.2444254 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 !   22.4   0.0   9.1e-08   0.00014      59     124 .]      87     167 ..      44     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.1e-08
                  Reprolysin_3  59 rgqagyDlvhlftarde......sgvgGlAyv.............gsvcnsskkagvnsgssvlgk.vgadtvaHEiGHnf 119
                                   +++ ++D+ ++  ++ e      +gv+G                 + v ++++k g+++++  +g+  + + ++HE+GH +
  gi|91773838|ref|YP_566530.1|  87 IDSPDADIYVMWVETMEevtgaeDGVAG---YcrpeisagrfiraSIVLEVGDKRGLSWQQ--YGDaNMEQIAIHELGHAL 162
                                   5667777777766554457744444444...334488888888888889999999****99..5664788*********** PP

                  Reprolysin_3 120 ganHt 124
                                   g++H+
  gi|91773838|ref|YP_566530.1| 163 GLDHS 167
                                   ****6 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 !   16.5   0.0   3.3e-06    0.0049     122     151 ..     139     168 ..      83     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
                 Peptidase_M57 122 gtglesysvdvnehvithelGhtvGlRhsD 151
                                   g ++++y+ + +e +  helGh++Gl hs+
  gi|91773838|ref|YP_566530.1| 139 GLSWQQYGDANMEQIAIHELGHALGLDHSN 168
                                   568999999*******************95 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.017      79     101 ..     150     172 ..     124     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                   SHHHHHHHHHHHHTB--GGGSTT CS
                       Astacin  79 klgiivHElmHalGffHeqsRtd 101
                                      i++HEl+HalG+ H + ++d
  gi|91773838|ref|YP_566530.1| 150 MEQIAIHELGHALGLDHSNDKKD 172
                                   45799************998877 PP

>> DUF4953  Met-zincin
   #    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       9      29 ..     146     166 ..     141     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.1e-06
                       DUF4953   9 mgallrfvvaHEvGhtLGLrh 29 
                                     a +++++ HE Gh+LGL+h
  gi|91773838|ref|YP_566530.1| 146 GDANMEQIAIHELGHALGLDH 166
                                   56789**************** PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0033         5       3      37 ..       2      40 ..       1      79 [. 0.78
   2 ?    6.1   0.2     0.012        17       2      40 ..     191     230 ..     190     231 .] 0.56

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0033
                       DUF3139  3 kiiiililliillvivkvflglvgskpikkylan....k 37
                                  ki+i+++++++l+  +++  g+ g+k++ +++++     
  gi|91773838|ref|YP_566530.1|  2 KIKITILSILLLCTLIIPAHGFLGEKEYPRFFDEpwdhS 40
                                  67777777777777767777999*****99998755554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                       DUF3139   2 kkiiiililliillvivkvfl...glvgskpikkylankkld 40 
                                   k + ii+ +++i + +   +l   +l ++k+i k l  k+++
  gi|91773838|ref|YP_566530.1| 191 KTYPIIIAIVLIAIGV-LGYLgtgWLRYHKKI-KSLEDKHIK 230
                                   5566777777666665.466668545555555.445556655 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 ?   14.2   0.0   1.7e-05     0.026     134     156 ..     147     171 ..      85     186 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                  Reprolysin_4 134 d.ey.difAHEiGHtfGaaHdlsde 156
                                   d +  +i  HE GH +G++H+ +++
  gi|91773838|ref|YP_566530.1| 147 DaNMeQIAIHELGHALGLDHSNDKK 171
                                   234457888***********98754 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.7e-05     0.041     319     344 ..     155     182 ..     153     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                    Metallopep 319 lHEiGHllglpHqed..Gvmlrdydaln 344
                                   +HE+GH+lgl H +d   +m  +y + +
  gi|91773838|ref|YP_566530.1| 155 IHELGHALGLDHSNDkkDIMYPSYEQRD 182
                                   8************99889**99998655 PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.1e-05     0.062     150     175 ..     155     181 ..     148     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHTT----S-.TSTTS--SSHH CS
                 Peptidase_M54 150 lhelGhlyGLshCke.dCvmnfsndlk 175
                                   +helGh +GL h ++ + +m +s + +
  gi|91773838|ref|YP_566530.1| 155 IHELGHALGLDHSNDkKDIMYPSYEQR 181
                                   7**************889999987655 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.7e-05      0.07     135     162 ..     143     170 ..      98     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                  Reprolysin_5 135 vvvstatevqvvaHElGHnfGavHDcds 162
                                   + +++a+  q+  HElGH++G  H  d+
  gi|91773838|ref|YP_566530.1| 143 QQYGDANMEQIAIHELGHALGLDHSNDK 170
                                   45678888999*************7664 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     8e-05      0.12      80     147 ..     102     175 ..      81     186 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                  Reprolysin_2  80 lgtfsggvlGLayvgqicqkeassrk...........tntglsttansgsaveetkeidvvaHEvGHaFGatHdndgs... 146
                                   +++++g++ G a   + c  e s  +            + gls  +++g+a+      ++  HE+GHa G  H nd +   
  gi|91773838|ref|YP_566530.1| 102 MEEVTGAEDGVA---GYCRPEISAGRfirasivlevgDKRGLS-WQQYGDANM----EQIAIHELGHALGLDHSNDKKdim 174
                                   455555555544...3343333333334455555555567888.899999994....67888***********99966444 PP

                  Reprolysin_2 147 s 147
                                   +
  gi|91773838|ref|YP_566530.1| 175 Y 175
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1529.44
//
Query:       gi|91773839|ref|YP_566531.1|  [L=462]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-27   93.9   1.7    4.5e-27   93.9   1.7    2.6  3  HisKA_2       Histidine kinase
    1.1e-26   93.1   1.3    2.7e-26   91.9   1.3    1.7  1  Response_reg  Response regulator receiver domain
    7.4e-11   42.6   0.8    2.3e-10   41.0   0.8    1.9  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    9.6e-10   38.7   0.0    1.9e-09   37.7   0.0    1.6  1  PAS_4         PAS fold
    3.7e-06   27.6   0.6      1e-05   26.1   0.2    1.9  2  HWE_HK        HWE histidine kinase
    4.5e-06   26.6   0.0    8.7e-06   25.7   0.0    1.5  1  HATPase_c_2   Histidine kinase-like ATPase domain
    7.5e-06   26.1   0.6    3.9e-05   23.9   0.1    2.4  2  PAS_9         PAS domain
     0.0016   18.4   0.0     0.0044   17.0   0.0    1.8  1  PAS           PAS fold
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.064   13.1   0.0    1.5  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
      0.084   13.2   0.0       0.24   11.7   0.0    1.7  1  PAS_3         PAS fold


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3   2.4e+03      60      60 ..     114     114 ..      82     141 .. 0.49
   2 ?   -2.4   0.0       2.9   5.1e+03      12      37 ..     240     265 ..     234     266 .. 0.79
   3 !   93.9   1.7   2.5e-30   4.5e-27       1      74 [.     271     344 ..     271     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                       HisKA_2  60 d 60 
                                   +
  gi|91773839|ref|YP_566531.1| 114 E 114
                                   3 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                       HisKA_2  12 visslLslqarkakdeevkealresq 37 
                                    i+++Ls   + ++ ++v+eal e++
  gi|91773839|ref|YP_566531.1| 240 KITGMLSSGEDITERKRVEEALIETE 265
                                   58899999999999999999998765 PP

  == domain 3  score: 93.9 bits;  conditional E-value: 2.5e-30
                       HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfk 74 
                                   EihHR+kNnLq+i+slL+l+a++++d++v +a++es++R+ si++ heeLy+s+d+++v f++y +++++ l +
  gi|91773839|ref|YP_566531.1| 271 EIHHRIKNNLQIIASLLDLEASNFTDPQVINAFKESRDRIHSISIAHEELYRSRDMTNVAFQDYAKDVTNYLYQ 344
                                   9********************************************************************99987 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   1.3   1.5e-29   2.7e-26       1     111 [.       9     119 ..       9     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.5e-29
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +l+vdDd++++el++ +l   +y e+  a  gkeale+l+++++dl+llD++mp+m+G+e++ +++e+   + +pvii++a
  gi|91773839|ref|YP_566531.1|   9 ILVVDDDQKNVELMEAYLS-PDY-ETIPAYRGKEALEILEKDEIDLVLLDVMMPDMKGYEVCIKLKEDIktQFIPVIIVSA 87 
                                   8*****************9.999.77789************************************99884455******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    s ++d++++l+agad+fl+Kp+d+ eL++++
  gi|91773839|ref|YP_566531.1|  88 LSRKKDRIQGLEAGADEFLTKPVDQIELKTRV 119
                                   *****************************998 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.8   1.3e-13   2.3e-10       4     109 ..     370     460 ..     367     462 .] 0.83

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.3e-13
                                   HHHHHHHHHHHHHHHHHHS..TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHH CS
                     HATPase_c   4 krLrqiisnlvdNavkfat..kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivk 82 
                                   ++L  i+++l+ N  k+a    +g+i++  ++++d++++ v DnGiGi ke+     ++               lG+ +v+
  gi|91773839|ref|YP_566531.1| 370 IHLGLILNELIVNCFKYAFpdGKGNISIVFHRKDDQFTLIVADNGIGIQKEIEI---GN------------TKTLGMQLVN 435
                                   57888************773455566666665669***************9888...33............4459****** PP

                                   HHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  83 klvelmgGeiwvesepgrGttftftlp 109
                                   +lv+++gG+i+++ +   Gt++t+t++
  gi|91773839|ref|YP_566531.1| 436 ELVKQIGGNIHIDRSN--GTKVTITFK 460
                                   ************8888..***999987 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   1.1e-12   1.9e-09       1     110 []     143     256 ..     143     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.1e-12
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelll.....p 75 
                                   +d   ++l+v+dpd ++  +N+ ++++++++  +l+G  ++  ++pe+ ++   ++  r ++g+  i+ le         +
  gi|91773839|ref|YP_566531.1| 143 FDTADVMLIVIDPDHKIKLINKKGCKIMACEEMTLIGTDFFnTMVPERFRESGIEDFYRFISGN--ISGLENFEApllrlD 221
                                   677889***********************************77*****8888888888888875..555554444455689 PP

                         PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                   geer+++++ + l++ +G++ g l  + DiTer+r
  gi|91773839|ref|YP_566531.1| 222 GEERIVNWHNTLLKNKNGKITGMLSSGEDITERKR 256
                                   *********************************97 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         3   5.3e+03      35      64 ..      92     121 ..      87     132 .. 0.69
   2 !   26.1   0.2   5.8e-09     1e-05       1      52 [.     271     324 ..     271     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3
                                   HHHHHHHHHHHHHHHHCTTS-EEHHHHHHH CS
                        HWE_HK  35 sgRLqALsaahdllsreewagaeLaellee 64 
                                   ++R+q L a  d + ++   ++eL+  +++
  gi|91773839|ref|YP_566531.1|  92 KDRIQGLEAGADEFLTKPVDQIELKTRVKS 121
                                   578888887777766666666666655554 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 5.8e-09
                                   HHHHHHHHHHHHHHHHHHHHSSSXS-HH..HHHHHHHHHHHHHHHHHHHHHHCT CS
                        HWE_HK   1 ElnHRvKNlLavvqsiarqtlrsaesle..efaeklsgRLqALsaahdllsree 52 
                                   E++HR+KN L ++ s+    +++ ++++  ++ ++ ++R++++s ah+ l r++
  gi|91773839|ref|YP_566531.1| 271 EIHHRIKNNLQIIASLLDLEASNFTDPQviNAFKESRDRIHSISIAHEELYRSR 324
                                   89******************999888872234567789*********9988876 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   4.9e-09   8.7e-06      22     124 ..     362     458 ..     348     459 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.9e-09
                   HATPase_c_2  22 aglseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGl 102
                                     ls +++ ++ l ++E+++N++++a ++++ g +++ + ++++++t+ vaD+G g + e           e + +  +G+
  gi|91773839|ref|YP_566531.1| 362 TLLSVDRAIHLGLILNELIVNCFKYAFPDGK-GNISIVFHRKDDQFTLIVADNGIGIQKEI----------EIGNTKTLGM 431
                                   568889999*******************999.************************77764..........5556677999 PP

                   HATPase_c_2 103 alikglvDev..ey...dgegnvvtms 124
                                    l+++lv ++  ++   + +g++vt++
  gi|91773839|ref|YP_566531.1| 432 QLVNELVKQIggNIhidRSNGTKVTIT 458
                                   999999999987445577789999887 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   2.1e-08   3.9e-05       4     104 .]     149     253 ..     146     253 .. 0.83
   2 ?   -1.3   0.0       1.5   2.6e+03      59      77 ..     426     456 ..     398     460 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.1e-08
                         PAS_9   4 ili.dnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                   +li ++pd++i  +N++ ++++   +  ++g+++++++    + +++ e++ +++    +  +++e  l r +ge+  v+ 
  gi|91773839|ref|YP_566531.1| 149 MLIvIDPDHKIKLINKKGCKIMACEEMTLIGTDFFNTMvpeRFRESGIEDFYRFISGNISGLENFEAPLLRLDGEERIVNW 229
                                   444477***999*********8877777**********555555555555555555555599******************* PP

                         PAS_9  81 taspvkdddgelvgiivilrDite 104
                                   + + +k+++g+++g+++  +Dite
  gi|91773839|ref|YP_566531.1| 230 HNTLLKNKNGKITGMLSSGEDITE 253
                                   ***********************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                         PAS_9  59 k............kerevevvlirkngetfw 77 
                                   +            k+  +++++ r+ng+++ 
  gi|91773839|ref|YP_566531.1| 426 TktlgmqlvnelvKQIGGNIHIDRSNGTKVT 456
                                   4444555555566788899999999998875 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.4e-06    0.0044       8     113 .]     144     251 ..     140     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                                   HHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.....HHHHHHHHHHHHTT-ECCCCEEEECTT CS
                           PAS   8 eslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.....elaelleqlleqgeesrageisfklrd 83 
                                   ++++++ +v+D d++i ++N++ +++   ++  ++g  ++  +++e  +     ++++ ++ +++  e+++a    ++l d
  gi|91773839|ref|YP_566531.1| 144 DTADVMLIVIDPDHKIKLINKKGCKIMACEEMTLIGTDFFNTMVPERFResgieDFYRFISGNISGLENFEA--PLLRL-D 221
                                   799*******************************************99899999999999999999999999..55577.9 PP

                                   SSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  84 grpihlevraspvrdaggeilgflgvlrdi 113
                                   g+++ +  +++ + ++ g+i+g l  + di
  gi|91773839|ref|YP_566531.1| 222 GEERIVNWHNTLLKNKNGKITGMLSSGEDI 251
                                   9******************99999888886 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 ?   13.1   0.0   3.6e-05     0.064       8      52 ..     377     425 ..     372     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                   HATPase_c_3   8 aelvdNsld....AdaenvkievnknrgktgeivieDdGkGmsee.elkn 52 
                                    el+ N++         n++i++++++ ++ ++ + D+G G+++e e+ n
  gi|91773839|ref|YP_566531.1| 377 NELIVNCFKyafpDGKGNISIVFHRKD-DQFTLIVADNGIGIQKEiEIGN 425
                                   678888887544344568*******86.89*************9977765 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.24       5      86 ..     163     245 ..     160     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                         PAS_3   5 serveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.py.egeyRirrkdGeyrwveararvirdengkp 82 
                                   +++ ++i+  ++  l+g+  ++ + + pe  re   e++ + ++++   + ++e  ++r dGe r v ++ + ++++ngk+
  gi|91773839|ref|YP_566531.1| 163 NKKGCKIMACEEMTLIGT--DFFNTMVPERfRESGIEDFYRFISGNIsGLeNFEAPLLRLDGEERIVNWHNTLLKNKNGKI 241
                                   666778888888899999..99999999999************88886566999*************************** PP

                         PAS_3  83 vrvi 86 
                                   + ++
  gi|91773839|ref|YP_566531.1| 242 TGML 245
                                   9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2876.58
//
Query:       gi|91773840|ref|YP_566532.1|  [L=266]
Description: nuclease (SNase-like) [Methanococcoides burtonii DSM 6242]
Scores for complete 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   80.6   0.1    2.5e-22   79.4   0.0    1.6  2  SNase            Staphylococcal nuclease homologue
    1.1e-07   31.7   0.1    2.3e-07   30.7   0.1    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.8e-05   24.9   0.1    7.1e-05   22.9   0.0    1.9  2  tRNA_anti_2      OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.039   13.6   0.3        1.1    8.8   0.0    2.4  2  tRNA_anti-like   tRNA_anti-like


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 !   79.4   0.0   5.5e-26   2.5e-22       1     107 [.      61     160 ..      61     161 .. 0.97
   2 ?   -2.6   0.0       1.8   7.9e+03      51      61 ..     176     186 ..     172     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 5.5e-26
                                   EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S.SBSTTSEEEEEEEETTEEHHHHHHHTTSSEE--- CS
                         SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk.kkDkygrllayvylnkknineeLvkeGlArvyev 80 
                                   +vrL+g+d+Pe        +p+ +eAk+++ ++vl  kv+ le+d  ++D ygrll yv+++++++n+eLv  GlA+  ++
  gi|91773840|ref|YP_566532.1|  61 RVRLIGVDTPEAG------EPYYSEAKQYMVHRVL-GKVIGLEKDVsETDVYGRLLRYVWVENEMVNKELVLSGLAF-SKA 133
                                   79***********......****************.99999999999******************************.889 PP

                                   BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                         SNase  81 yekneekkkellkaeeeAkkkrkglWs 107
                                   y++ +++++ + +ae  Akk+ +glWs
  gi|91773840|ref|YP_566532.1| 134 YSPDTHYQDIFDSAEVVAKKNGVGLWS 160
                                   99999*********************8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                                   TSEEEEEEEET CS
                         SNase  51 ygrllayvyln 61 
                                    gr++++v++ 
  gi|91773840|ref|YP_566532.1| 176 AGRYIGQVITV 186
                                   599***99875 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 !   30.7   0.1   5.1e-11   2.3e-07       2      71 ..     185     257 ..     184     264 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.1e-11
                                   EEEEEEEEEEEEEETTEEEEEEEETT.EEEEEEEETHHHHHHHTTS-...TTSEEEEEEEEEECTTSSEEEEEE CS
               tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgt.griqvvlfreeatklaenlk...eGdvvrvtGrvkrrpggelelkve 71 
                                   tv+G ++++ +++ +++if+   D   g ++vv++++  +++ ++     eG++v vtG+v +++++ +e++ve
  gi|91773840|ref|YP_566532.1| 185 TVEGTIVQTTKKDDAGIIFLNFHDPYeGYFTVVIWSDYWDRFSQDPVvmyEGKHVLVTGKVIEYKEN-PEIIVE 257
                                   89**********************************99999999988899*****************.999987 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 ?   -1.4   0.0      0.63   2.8e+03      19      31 ..     109     121 ..      95     132 .. 0.74
   2 !   22.9   0.0   1.6e-08   7.1e-05      20      84 ..     182     251 ..     172     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.63
                   tRNA_anti_2  19 kkavwvrGeisnl 31 
                                    + vwv+ e  n 
  gi|91773840|ref|YP_566532.1| 109 LRYVWVENEMVNK 121
                                   4679999999887 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.6e-08
                   tRNA_anti_2  20 kavwvrGeisnlkrka.sghvYftLkD.ekakisavifrsraaklkft...ledGmkVlvkgrlsvYepr 84 
                                   + ++v+G i + ++k+  g ++++  D  +    +vi++  +++ + +   + +G++Vlv+g++  Y+++
  gi|91773840|ref|YP_566532.1| 182 QVITVEGTIVQTTKKDdAGIIFLNFHDpYEGYFTVVIWSDYWDRFSQDpvvMYEGKHVLVTGKVIEYKEN 251
                                   5689********86555**********98899*******99999996655589***********999876 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00025       1.1      83     100 ..     178     195 ..     175     209 .. 0.81
   2 ?    2.3   0.0     0.025   1.1e+02      74     100 ..     227     250 ..     215     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                                   HHTT-EEEEEEEEEEEEE CS
                tRNA_anti-like  83 kYkGkiieVeGvvsdikk 100
                                   +Y G++i+VeG++++++k
  gi|91773840|ref|YP_566532.1| 178 RYIGQVITVEGTIVQTTK 195
                                   7*************9966 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.025
                                   HH-HHHHHHHHTT-EEEEEEEEEEEEE CS
                tRNA_anti-like  74 dkNevkadkkYkGkiieVeGvvsdikk 100
                                   ++++v     Y Gk ++V+G v + k+
  gi|91773840|ref|YP_566532.1| 227 SQDPV---VMYEGKHVLVTGKVIEYKE 250
                                   55555...36**********7776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1539.47
//
Query:       gi|91773841|ref|YP_566533.1|  [L=266]
Description: haloacid dehalogenase-like hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   63.0   0.1    4.8e-16   59.7   0.1    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    8.3e-08   32.3   0.1      0.016   14.9   0.1    2.5  3  Hydrolase_3     haloacid dehalogenase-like hydrolase
     0.0027   17.8   0.1      0.011   15.9   0.1    1.9  1  HAD_2           Haloacid dehalogenase-like hydrolase
     0.0093   16.0   0.1      0.018   15.1   0.1    1.4  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.056   13.6   0.0       0.41   10.8   0.0    2.2  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   1.3e-19   4.8e-16       4     210 .]       7     229 ..       5     229 .. 0.57

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.3e-19
                                   EEEESBTTTBCHHHHHHH........HHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.................HHHHHH CS
                                   xxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxx RF
                     Hydrolase   4 vvfDkdGTLttgepsved........vivsaalalaaaletgsehpigkalvaaakar.................sgaltg 59 
                                   vvfD  GTL++  ++ +d         i+s                    lva+ k+r                 s  +++
  gi|91773841|ref|YP_566533.1|   7 VVFDSAGTLLHMYRVAKDmgsgqiitGIDST------------------GLVAQRKGRalivlhtepsvvlsadhSMRVSD 69 
                                   6666666666666444443333322222222..................23333333332222222222222222222222 PP

                                   HHHETTTE.................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH.................... CS
                                   xxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                     Hydrolase  60 fatfigrg.................ayaigkpewltaldippdlgaaigsaqsqgrtvall.................... 103
                                   f    +                   a                                                       
  gi|91773841|ref|YP_566533.1|  70 FID--E-YgvtiaiscasdpfsvdeA----------------------------------Ydiikgselrisdilqvvdmv 113
                                   222..1.1232332233333333331..................................022222222222222333333 PP

                                   .................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHH CS
                                   .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 104 .................qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasd 167
                                                     +++   + ++   +++ ++++++++L  +g++v++++gd+ ++ e +a+ l           +
  gi|91773841|ref|YP_566533.1| 114 kaqcpnifyvaagiivdRNDYSVPYVLSTGGRLFHDTKDTIEKLEVRGVDVYIASGDSMRNLEQLAKCLS--------IPI 186
                                   33344444445555555446667777777888************************************99........444 PP

                                   CESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 168 ietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   + ++  +  + k+++i eL+gk e+v+mVGDg+nD+ al+aA+
  gi|91773841|ref|YP_566533.1| 187 DRVFDIATTREKERIILELKGKYEKVLMVGDGMNDILALRAAD 229
                                   4449999***********************************8 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1     4e+03      68      91 ..      90     113 ..      58     133 .. 0.50
   2 !   14.6   0.0   5.6e-06      0.02      12      54 ..     142     184 ..     139     191 .. 0.87
   3 !   14.9   0.1   4.5e-06     0.016     198     241 ..     204     251 ..     198     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                                   CTTTEEEEE--B-HHHHHHHHHHH CS
                   Hydrolase_3  68 dekgkilykstiskedvkeiikll 91 
                                   de   i++ s++  +d+ ++++ +
  gi|91773841|ref|YP_566533.1|  90 DEAYDIIKGSELRISDILQVVDMV 113
                                   344444444444444444444444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.6e-06
                                   TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                   Hydrolase_3  12 sdkkisektkeaikklkekgikvviATGRslravlpvleelgl 54 
                                    ++++ + tk++i+kl+ +g+ v iA+G s+r+++++++ l +
  gi|91773841|ref|YP_566533.1| 142 TGGRLFHDTKDTIEKLEVRGVDVYIASGDSMRNLEQLAKCLSI 184
                                   56677789*****************************997775 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 4.5e-06
                                   HCT--GGGEEEEESSGGGHHHHHHSSEEEEE....TTS-HHHHHHSSE CS
                   Hydrolase_3 198 elnisleeviafGDgeNDieMLeaaglgvAm....gnaseevkkaAdy 241
                                   el+ + e+v+ +GDg+NDi  L aa++gv+     +n  e++ + A+ 
  gi|91773841|ref|YP_566533.1| 204 ELKGKYEKVLMVGDGMNDILALRAADIGVMTiqqgDNRPEKLVNSANV 251
                                   6777889**********************8533333445555555555 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     3e-06     0.011      80     176 ..     146     233 ..     127     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                         HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekle..qlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyv 158
                                   ++ + k+++e+L+ +g+ + i++  s +++e+  +   + i+++Fd   t e+           e+++ +lk k e+v++v
  gi|91773841|ref|YP_566533.1| 146 LFHDTKDTIEKLEVRGVDVYIASGDSMRNLEQLAKclSIPIDRVFDIATTREK-----------ERIILELKGKYEKVLMV 215
                                   789999*****************998888887766114556666766554443...........67788999********* PP

                         HAD_2 159 GDsptDieaakkagikvi 176
                                   GD  +Di a ++a i v+
  gi|91773841|ref|YP_566533.1| 216 GDGMNDILALRAADIGVM 233
                                   *********999998765 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     5e-06     0.018      19      74 ..     207     258 ..     185     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                                   --GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                Hydrolase_like  19 sdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                    + e+vlm+GD    Di++ ++a +  + + +G +rpe+l     ++++++d++ e
  gi|91773841|ref|YP_566533.1| 207 GKYEKVLMVGDG-MNDILALRAADIGVMTIQQGDNRPEKLV---NSANVIIDHIGE 258
                                   45789*******.************************9876...678888888776 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.24   8.7e+02       1      15 [.       7      21 ..       7      65 .. 0.83
   2 ?   10.8   0.0   0.00012      0.41       8      56 ..     139     184 ..     138     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                                  EEEESTTTSEETTEE CS
                   Hydrolase_6  1 flfDidGvLwrgdka 15
                                  ++fD  G+L++ +++
  gi|91773841|ref|YP_566533.1|  7 VVFDSAGTLLHMYRV 21
                                  689999999987665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                                   TSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT- CS
                   Hydrolase_6   8 vLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgv 56 
                                   vL  g++++   +++++ l+ +g++v++ +  s ++ e++ak l    +
  gi|91773841|ref|YP_566533.1| 139 VLSTGGRLFHDTKDTIEKLEVRGVDVYIASGDSMRNLEQLAKCL---SI 184
                                   78999******************************988777655...44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1515.14
//
Query:       gi|91773842|ref|YP_566534.1|  [L=538]
Description: ABC transporter, fused ATPase subunits [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-49  167.5   0.0    2.7e-23   83.0   0.0    2.3  2  ABC_tran      ABC transporter
    2.4e-06   27.1   0.5     0.0037   16.7   0.2    3.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    4.6e-05   23.4   0.3       0.15   12.0   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
    8.1e-05   22.4   0.1       0.26   11.0   0.0    2.4  2  PRK           Phosphoribulokinase / Uridine kinase family
    0.00035   21.1   0.1       0.66   10.5   0.0    3.1  3  AAA_18        AAA domain
    0.00054   20.4   0.1       0.22   11.9   0.0    2.6  2  AAA_16        AAA ATPase domain
    0.00068   19.5   0.1        1.8    8.3   0.0    3.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0008   19.1   0.9        1.1    9.1   0.2    2.4  2  AAA_29        P-loop containing region of AAA domain
     0.0011   18.7   0.2      0.056   13.2   0.0    3.0  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0016   18.9   2.6      0.077   13.5   0.2    2.3  2  AAA_23        AAA domain
     0.0024   18.1   0.6       0.79   10.0   0.0    2.7  2  AAA_22        AAA domain
     0.0026   17.7   0.1        2.1    8.2   0.0    2.9  3  MobB          Molybdopterin guanine dinucleotide synthesis pr
     0.0032   17.2   1.3        4.7    6.9   0.0    3.3  3  IstB_IS21     IstB-like ATP binding protein
     0.0037   17.0   0.6        0.5   10.1   0.0    2.6  2  AAA_30        AAA domain
     0.0052   16.1   0.2        0.3   10.3   0.1    2.5  2  Zeta_toxin    Zeta toxin
  ------ inclusion threshold ------
      0.011   15.4   0.0        1.5    8.4   0.0    2.3  2  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
      0.019   15.1   0.0        6.7    6.9   0.0    2.7  2  AAA_33        AAA domain
      0.028   14.4   0.2        9.9    6.2   0.0    2.5  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.03   13.7   2.5        1.2    8.4   0.0    3.0  3  ATPase        KaiC
      0.038   14.1   1.3        2.5    8.2   0.1    3.3  3  MMR_HSR1      50S ribosome-binding GTPase
      0.045   12.9   0.9        1.3    8.1   0.0    2.7  3  NB-ARC        NB-ARC domain
      0.075   13.3   0.8         11    6.2   0.1    3.0  2  AAA_28        AAA domain
      0.094   11.9   1.0        4.7    6.3   0.0    2.6  2  PIF1          PIF1-like helicase
       0.14   12.1   0.1        0.3   11.0   0.1    1.5  1  Tnp_DNA_bind  Transposase DNA-binding
       0.31   11.1   1.1        2.5    8.1   0.6    2.7  3  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
       0.35   10.6   1.2         22    4.7   0.3    2.5  2  AAA_24        AAA domain
        4.3    6.9   6.1         24    4.5   0.0    3.5  4  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   6.5e-26   4.3e-23       1     136 [.      20     203 ..      20     204 .. 0.76
   2 !   83.0   0.0   4.1e-26   2.7e-23       2     136 ..     308     462 ..     307     463 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 6.5e-26
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE..................................EET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..................................xxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei..................................lld 45 
                                   lkn++l+++ege+++i+G++GaGK+ L+ +l g ++    +G+i                                     
  gi|91773842|ref|YP_566534.1|  20 LKNINLNINEGEVIGILGRSGAGKTILMHALRGAEEYenISGSIiyhlarcdqcghidppskvgepcrlcnheymkafD-- 98 
                                   79*****************************9866554499***99999999999889998888888766665555441.. PP

                                   TCEGGG.........B-HHHCCHCEEEE-SS.--S-TTSBHHHH.............HHHTCHHHHHHHSTTGGTTCBGES CS
                                   xxxxxx.........xxxxxxxxxxxxxxxx.xxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  46 gkdlke.........qeleslrkeigvlpqe.pqlfpeltvren.............esdeeiekalsklglkelkdtvvk 103
                                                  +e++s++k+i+++ q    l  + +v  n             ++   +++a++ l+++ l ++ + 
  gi|91773842|ref|YP_566534.1|  99 -----AdfvalsqhdHERRSVSKRIAIMLQRtFALYGDDQVVANvmnslkeigytgpDA---MSRAMELLEDVRLSHRLM- 170
                                   .....033334445567788889999888884444444457777898777777744444...555555555555555555. PP

                                   TTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 104 sspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   + ++ LSgG+kqrv+lar l+++p lll+DEpt
  gi|91773842|ref|YP_566534.1| 171 HVARDLSGGEKQRVVLARQLVRNPMLLLADEPT 203
                                   444*****************************9 PP

  == domain 2  score: 83.0 bits;  conditional E-value: 4.1e-26
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......B-HHHCCHCEEEE-SS--S-TTSB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......qeleslrkeigvlpqepqlfpelt 75 
                                   +++s+++kege+ ++ G +GaGK+t  ++l+g + pt+G i+++ g+++ +      +++ ++ k +g+l+qe  l  + +
  gi|91773842|ref|YP_566534.1| 308 NDISFDVKEGEIFGLAGTSGAGKTTTSEMLMGIVAPTKGVIQVRvGDEWVDmtipgpDNRGRATKYMGILHQEYGLYTHRS 388
                                   89******************************************99999999***************************** PP

                                   HHHH.............HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxx.............xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  76 vren.............esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   + +n             +  +++ k l + g +e ++++++ + +  +S+G++ rvala++l+k+p+++++DEpt
  gi|91773842|ref|YP_566534.1| 389 IIDNltesigidlpyelA-VRKAIKTLITTGFSEeKAKSILPKMADDISEGERHRVALAQILMKEPTIIVMDEPT 462
                                   999999999999977532.23344444444444315555555556*****************************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 !   16.7   0.2   5.6e-06    0.0037       7     205 ..      14     242 ..       8     254 .. 0.74
   2 ?    5.9   0.0     0.012       7.8     136     208 ..     434     504 ..     287     515 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.6e-06
                                   EESETTEECEEEEEETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.........BTTCSSTTEE CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx RF
                         SMC_N   7 ienFksyagktvilpfsk.sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.........skekasvkka 77 
                                    +n+k ++  ++ l++++ ++  i+G+ G+GK+ l+ A+    G ++++++  + + +l            sk ++    +
  gi|91773842|ref|YP_566534.1|  14 YDNVKVLK--NINLNINEgEVIGILGRSGAGKTILMHAL---RGAEEYENISGSIIYHLARCdqcghidppSKVGEPCRLC 89 
                                   56666663..45555544146778999999999999998...588888888888888887765554443333333333333 PP

                                   EEEEEEEETTEE....SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT................... CS
                                   xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                         SMC_N  78 eveitfdnedkk....lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske................... 135
                                   + e + +  d++    ++ ++e+ s+s+r+    + ++++ g +   ++v++ l++ g +                     
  gi|91773842|ref|YP_566534.1|  90 NHEYM-KAFDADfvalSQHDHERRSVSKRIAIMLQRTFALYGDDQVVANVMNSLKEIGYTGPdamsramelledvrlshrl 169
                                   33332.33333355555666667888888888888889999999999999999999998877899999999999999999* PP

                                   .....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                         SMC_N 136 .....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                         LSgGek+     +++A q v+   l l De    LD +   +v ++++++ k+  + ++++s+ +e++ek 
  gi|91773842|ref|YP_566534.1| 170 mhvarDLSGGEKQ----RVVLARQLVRNPMLLLADEPTGTLDPRTADIVHDVIEKAVKTynMTMVITSHWSEVIEKL 242
                                   ****9*******9....56788899999999999********************87765338899999999999986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadkl 208
                                    +S Ge+  vala ++    +k   + ++De    +D     +v + + +++++    f+++s++ ++l+++   
  gi|91773842|ref|YP_566534.1| 434 DISEGERHRVALAQIL----MKEPTIIVMDEPTGTMDPITKIEVTRSILKARDEmgDTFVIVSHDMDFLHEVCDR 504
                                   6899999999999884....5556799**********9888888777666666534579999**99999887433 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   0.00022      0.15      81     124 ..      11      55 ..       4      65 .. 0.80
   2 !    8.9   0.1    0.0019       1.3      88     121 ..     305     339 ..     287     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                   E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                   ++  ++ + l++++ ++++ +++ ++G SG+GK+ L+ al++ +e
  gi|91773842|ref|YP_566534.1|  11 TITYDNVKVLKNINLNINEgEVIGILGRSGAGKTILMHALRGAEE 55 
                                   555566677888888888879999****************99755 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                                   TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   +++++++  +k+ ++  l+G SG+GK+t  ++l++
  gi|91773842|ref|YP_566534.1| 305 HAVNDISFDVKEgEIFGLAGTSGAGKTTTSEMLMG 339
                                   56788888888889999***********9888876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    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       1      24 [.      32      55 ..      32      81 .. 0.80
   2 !   11.0   0.0    0.0004      0.26       1      24 [.     319     342 ..     319     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                           PRK  1 vIgvagsSGaGkttvarklekifg 24
                                  vIg+ g SGaGkt ++++l+ + +
  gi|91773842|ref|YP_566534.1| 32 VIGILGRSGAGKTILMHALRGAEE 55
                                  8***************99986655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0004
                           PRK   1 vIgvagsSGaGkttvarklekifg 24 
                                   + g+ag SGaGktt+++ l  i++
  gi|91773842|ref|YP_566534.1| 319 IFGLAGTSGAGKTTTSEMLMGIVA 342
                                   679**************9998887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.012         8       1      33 [.      33      69 ..      33     115 .. 0.84
   2 ?   -1.6   0.0       5.7   3.8e+03      25      91 ..     184     243 ..     164     250 .. 0.55
   3 !   10.5   0.0     0.001      0.66       3      18 ..     322     337 ..     321     391 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf....gvnlrdvak 33
                                  I++ G +G+GKt l ++L+  +++    g ++ ++a+
  gi|91773842|ref|YP_566534.1| 33 IGILGRSGAGKTILMHALRGAEEYenisGSIIYHLAR 69
                                  89****************7666665567666666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.7
                        AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaa 91 
                                   +v  r+++++ +lll ++p      +    d ++ ++++  + +     + + vi +h +e ++  a
  gi|91773842|ref|YP_566534.1| 184 VVLARQLVRNPMLLLADEPT--GTLDPRTADIVHDVIEKAVKTY-----NMTMVITSHWSEVIEKLA 243
                                   66667777777777777777..2222223333333333333333.....366788888777766554 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.001
                        AAA_18   3 ltGtpGvGKttlakeL 18 
                                   l+Gt+G+GKtt ++ L
  gi|91773842|ref|YP_566534.1| 322 LAGTSGAGKTTTSEML 337
                                   89***********999 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00033      0.22      22      63 ..      28      73 ..      18     190 .. 0.77
   2 ?    5.9   0.1     0.022        15      25      52 ..     318     345 ..     304     460 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                        AAA_16 22 grpelvllsGesGvGKsslvrellralekd...g.giflrgkcdql 63
                                  +++e++ + G sG GK+ l+ +l+ a e +   g +i+  ++cdq+
  gi|91773842|ref|YP_566534.1| 28 NEGEVIGILGRSGAGKTILMHALRGAEEYEnisGsIIYHLARCDQC 73
                                  5668899****************986666688854888*******9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                        AAA_16  25 elvllsGesGvGKsslvrellralekdg 52 
                                   e+  l G sG GK++  ++l+  +  ++
  gi|91773842|ref|YP_566534.1| 318 EIFGLAGTSGAGKTTTSEMLMGIVAPTK 345
                                   677899**********999996666553 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0074       4.9       2      22 ..      33      53 ..      32      71 .. 0.81
   2 ?   -2.4   0.0       4.9   3.3e+03     259     297 ..     195     234 ..     172     239 .. 0.63
   3 ?    1.2   0.0       0.4   2.7e+02       2      51 ..     320     363 ..     319     395 .. 0.85
   4 !    8.3   0.0    0.0026       1.8     173     298 ..     358     494 ..     354     499 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0074
                        AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                   ++ G+ g+GK+ L+ al+++
  gi|91773842|ref|YP_566534.1| 33 IGILGRSGAGKTILMHALRGA 53
                                  5799**************876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.9
                        AAA_21 259 sllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                    lll DEp   L+P+    + ++++++ +  +   ++t+H
  gi|91773842|ref|YP_566534.1| 195 MLLLADEPTGTLDPRTADIVHDVIEKAVKtYNMTMVITSH 234
                                   5677799999999965555558886665557777788888 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.4
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51 
                                    +l G  g+GK++  + l      ++ v +++ + + ++g  +++  +++
  gi|91773842|ref|YP_566534.1| 320 FGLAGTSGAGKTTTSEML------MGIVAPTKGVIQVRVGDEWVDMTIPG 363
                                   67999********99999......88889999999888888888877765 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0026
                        AAA_21 173 adyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.............gvvflengdgqelparelSdG 240
                                   ++++++++++++++++++ l++    ++   + ++l +s+  +l+++             g+  ++ ++  +  a+++S+G
  gi|91773842|ref|YP_566534.1| 358 DMTIPGPDNRGRATKYMGILHQEYGLYTHRSIIDNLTESIGIDLPYElavrkaiktlittGFSEEKAKSILPKMADDISEG 438
                                   566777888888888888888888888888888888888888888888888888888776667777777777778888*** PP

                        AAA_21 241 tkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTHS 298
                                    ++  al+ +l   +   ++++ DEp   ++P    +++r++l+  +e  +    +++++H+
  gi|91773842|ref|YP_566534.1| 439 ERHRVALAQILMKEP---TIIVMDEPTGTMDPitkiEVTRSILKARDEMGD---TFVIVSHD 494
                                   ****99999999988...**************9999999999987666655...67777776 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 !    8.1   0.0    0.0032       2.1      17      42 ..      25      50 ..      15      52 .. 0.79
   2 !    9.1   0.2    0.0016       1.1      14      38 ..     306     333 ..     297     347 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0032
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAi 42
                                  ++i++ +++ + G+sG+GK+ l+ A+
  gi|91773842|ref|YP_566534.1| 25 LNINEGEVIGILGRSGAGKTILMHAL 50
                                  5566455889**********999886 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                        AAA_29  14 g.htieidlkg..atlltGpsGsGKSTl 38 
                                     ++i++d+k+  ++ l+G+sG+GK+T 
  gi|91773842|ref|YP_566534.1| 306 AvNDISFDVKEgeIFGLAGTSGAGKTTT 333
                                   5455666665556999**********95 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   8.4e-05     0.056       6      90 ..      35     124 ..      31     129 .. 0.76
   2 ?   -1.4   0.1       2.7   1.8e+03      51      99 ..     223     274 ..     218     280 .. 0.77
   3 ?    1.4   0.0      0.36   2.4e+02       6      23 ..     322     339 ..     318     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.4e-05
                     PduV-EutP   6 liGkvgsGKttLtqalkg....eelkYkktqaiefsdev..iDtPGeylenrklysalivtsaeadvialvqdateeesvf 80 
                                   ++G++g+GKt L++al+g    e+++ +    +   d++  iD P +  e  +l +   + +++ad +al q+ +e++   
  gi|91773842|ref|YP_566534.1|  35 ILGRSGAGKTILMHALRGaeeyENISGSIIYHLARCDQCghIDPPSKVGEPCRLCNHEYMKAFDADFVALSQHDHERR-SV 114
                                   79****************76663444444444444455455****************************988765554.55 PP

                     PduV-EutP  81 ppgfasvfnk 90 
                                   ++ +a ++++
  gi|91773842|ref|YP_566534.1| 115 SKRIAIMLQR 124
                                   7777777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                     PduV-EutP  51 rklysalivtsaeadvialvqdat...eeesvfppgfasvfnkeviGiitki 99 
                                   +++  ++++ts+ ++vi  + d     e   ++++g  + ++ke +G++  i
  gi|91773842|ref|YP_566534.1| 223 KTYNMTMVITSHWSEVIEKLADKAiilEDGVIISEGEPCKVAKEFMGMVPSI 274
                                   6678889999999999988877432227778899999999999999998766 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.36
                     PduV-EutP   6 liGkvgsGKttLtqalkg 23 
                                   l G++g+GKtt ++ l g
  gi|91773842|ref|YP_566534.1| 322 LAGTSGAGKTTTSEMLMG 339
                                   679********9888765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   0.00012     0.077       2      42 ..      12      53 ..      11      60 .. 0.85
   2 ?    5.3   0.2     0.037        24      15      35 ..     310     333 ..     303     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                        AAA_23  2 LkienfrsfrdqeidFsk.gltlItGpNGaGKTTildAikla 42
                                  ++  n++ +++ +++ +   +  I G  GaGKT ++ A++ a
  gi|91773842|ref|YP_566534.1| 12 ITYDNVKVLKNINLNINEgEVIGILGRSGAGKTILMHALRGA 53
                                  6677888889988899552799****************9865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.037
                        AAA_23  15 idF...skgltlItGpNGaGKTTi 35 
                                   i F   +  ++ + G  GaGKTT 
  gi|91773842|ref|YP_566534.1| 310 ISFdvkEGEIFGLAGTSGAGKTTT 333
                                   5555566689*************6 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0012      0.79       7      51 ..      32      82 ..      27     126 .. 0.78
   2 ?    5.4   0.7     0.031        20      10      26 ..     322     338 ..     314     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsst 51
                                  ++ + G sG+GKT l+  l+    e++++         +++++ ++++ps+ 
  gi|91773842|ref|YP_566534.1| 32 VIGILGRSGAGKTILMHALRGAE-EYENISGsiiyhlaRCDQCGHIDPPSKV 82
                                  56689**************9985.6666666788888766666688888765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.031
                        AAA_22  10 vtGesGtGKTtllrrll 26 
                                   + G sG+GKTt+ ++l+
  gi|91773842|ref|YP_566534.1| 322 LAGTSGAGKTTTSEMLM 338
                                   779*********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 !    8.2   0.0    0.0032       2.1       1      22 [.      32      53 ..      32      73 .. 0.80
   2 ?    6.3   0.0     0.013       8.6       1      23 [.     319     341 ..     319     366 .. 0.83
   3 ?   -2.8   0.0       8.4   5.6e+03     103     116 ..     467     480 ..     465     490 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0032
                          MobB  1 vlgivgksgsGKTtLleklipe 22
                                  v+gi g+sg+GKT L++ l  +
  gi|91773842|ref|YP_566534.1| 32 VIGILGRSGAGKTILMHALRGA 53
                                  799*************998655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                          MobB   1 vlgivgksgsGKTtLleklipel 23 
                                   ++g++g+sg+GKTt  e l+ ++
  gi|91773842|ref|YP_566534.1| 319 IFGLAGTSGAGKTTTSEMLMGIV 341
                                   689***********999887665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.4
                          MobB 103 alpkievlraelgk 116
                                   ++ kiev r+ l+ 
  gi|91773842|ref|YP_566534.1| 467 PITKIEVTRSILKA 480
                                   689*****986654 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 !    6.9   0.0    0.0071       4.7      44      67 ..      27      50 ..      11      66 .. 0.83
   2 ?    5.7   0.1     0.017        11     102     158 ..     186     239 ..     163     249 .. 0.72
   3 ?    1.4   0.0      0.34   2.2e+02      35      63 ..     304     333 ..     289     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0071
                     IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                  i++ e i +lG sG+GK+ l  al
  gi|91773842|ref|YP_566534.1| 27 INEGEVIGILGRSGAGKTILMHAL 50
                                  78889999************9998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                     IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekryerrs..iiitsnlpfaewdevl 158
                                    +++l++  +l+l d  + +ld   a  + +viek++++    ++its     +w+ev+
  gi|91773842|ref|YP_566534.1| 186 LARQLVRNPMLLLADEPTGTLDPRTADIVHDVIEKAVKTYNmtMVITS-----HWSEVI 239
                                   56889999999999999******************9998651155665.....344443 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.34
                     IstB_IS21  35 vkeLatlsf.iekkenivllGpsGvGKshl 63 
                                   ++++   sf +++ e + l G sG+GK+  
  gi|91773842|ref|YP_566534.1| 304 IHAVNDISFdVKEGEIFGLAGTSGAGKTTT 333
                                   556666666577888899*********965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00075       0.5      19      45 ..      31      57 ..      23      69 .. 0.79
   2 ?    4.1   0.3     0.051        34      20      41 ..     319     340 ..     312     354 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00075
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaa 45
                                   v  + G+ G+GKt ++ alr a e +
  gi|91773842|ref|YP_566534.1| 31 EVIGILGRSGAGKTILMHALRGAEEYE 57
                                  488899**************9876654 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.051
                        AAA_30  20 vavltGpAGtGKttalkalrea 41 
                                   +  l G  G+GKtt+ + l  +
  gi|91773842|ref|YP_566534.1| 319 IFGLAGTSGAGKTTTSEMLMGI 340
                                   66789*********98777655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.089        59      21      39 ..      35      53 ..      19      60 .. 0.79
   2 !   10.3   0.1   0.00045       0.3      21      49 ..     322     350 ..     310     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.089
                    Zeta_toxin 21 lgGqpGAGKselaellkde 39
                                  + G +GAGK+ l+++l+ +
  gi|91773842|ref|YP_566534.1| 35 ILGRSGAGKTILMHALRGA 53
                                  55899*********99876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00045
                    Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrl 49 
                                   l+G +GAGK++++e+l   ++++++v+++
  gi|91773842|ref|YP_566534.1| 322 LAGTSGAGKTTTSEMLMGIVAPTKGVIQV 350
                                   9***************9999999999987 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 ?    8.4   0.0    0.0023       1.5      10      49 ..      26     129 ..      17     251 .. 0.66
   2 ?    5.2   0.0     0.022        14       6      51 ..     309     354 ..     305     520 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                                   -EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS..S.EEEEEE....................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.xxxxxx....................................... RF
                   ATP-synt_ab  10 pivqGqrtlipgafgvGktvisqslskqsnsd..d.aiiyvg....................................... 48 
                                    i +G+ ++i+g +g Gkt ++++l    + +  +  iiy +                                       
  gi|91773842|ref|YP_566534.1|  26 NINEGEVIGILGRSGAGKTILMHALRGAEEYEniSgSIIYHLarcdqcghidppskvgepcrlcnheymkafdadfvalsq 106
                                   57899*****************99976655443423777766666666666666665555555555555555555555555 PP

                                   ......................E CS
                                   ......................x RF
                   ATP-synt_ab  49 ......................i 49 
                                                          
  gi|91773842|ref|YP_566534.1| 107 hdherrsvskriaimlqrtfalY 129
                                   55555555555555555555550 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                                   HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   6 DalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGe 51 
                                   D  f + +G+  ++ g +g Gkt+ s++l+     ++ +i v +G 
  gi|91773842|ref|YP_566534.1| 309 DISFDVKEGEIFGLAGTSGAGKTTTSEMLMGIVAPTKGVIQVRVGD 354
                                   77788899999*****************998876666777777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.023        16       4      35 ..      35      66 ..      32     174 .. 0.75
   2 ?    6.9   0.0      0.01       6.7       4      20 ..     322     338 ..     319     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.023
                        AAA_33  4 lvGlpGsGKstlaerllkklgavllssdtlrr 35
                                  + G +G+GK+ l + l  ++ ++ +s  +++ 
  gi|91773842|ref|YP_566534.1| 35 ILGRSGAGKTILMHALRGAEEYENISGSIIYH 66
                                  6799************9999999998877544 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                        AAA_33   4 lvGlpGsGKstlaerll 20 
                                   l G +G+GK+t +e l+
  gi|91773842|ref|YP_566534.1| 322 LAGTSGAGKTTTSEMLM 338
                                   579**********9986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.015       9.9      18      42 ..      27      53 ..      13      69 .. 0.74
   2 ?    5.5   0.1     0.024        16      19      40 ..     317     338 ..     295     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                                  H..TEEEEEEESTTSSHHHHHHHHHHH CS
                          TsaE 18 l..gdvilLeGdLGaGKTtlvrglaka 42
                                  +  g+vi + G  GaGKT l+++l  a
  gi|91773842|ref|YP_566534.1| 27 IneGEVIGILGRSGAGKTILMHALRGA 53
                                  2448899999***********998655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                                   TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrgla 40 
                                   g+++ L G  GaGKTt +  l+
  gi|91773842|ref|YP_566534.1| 317 GEIFGLAGTSGAGKTTTSEMLM 338
                                   67799***********887665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0018       1.2      16      46 ..      27      55 ..      17      60 .. 0.82
   2 ?   -2.1   0.1         3     2e+03     149     176 ..     220     247 ..     209     258 .. 0.62
   3 ?    3.7   0.1      0.05        33      17      37 ..     315     335 ..     304     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
                        ATPase 16 ipegrvvlitGepGtGKtifalqFlikgaek 46
                                  i eg+v+ i G +G+GKti+    +++gae+
  gi|91773842|ref|YP_566534.1| 27 INEGEVIGILGRSGAGKTILM--HALRGAEE 55
                                  7899***************96..45666666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                        ATPase 149 rvlkklgvTailvsekssseeaaggygv 176
                                   + +k +++T +++s  s+  e+    ++
  gi|91773842|ref|YP_566534.1| 220 KAVKTYNMTMVITSHWSEVIEKLADKAI 247
                                   3458888888888887775555444444 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.05
                        ATPase  17 pegrvvlitGepGtGKtifal 37 
                                    eg++  ++G++G+GKt+ ++
  gi|91773842|ref|YP_566534.1| 315 KEGEIFGLAGTSGAGKTTTSE 335
                                   5789999**********9886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0037       2.5       2      22 ..      33      53 ..      32      64 .. 0.85
   2 ?    2.6   0.0      0.21   1.4e+02       3      22 ..     321     340 ..     319     360 .. 0.81
   3 ?   -1.7   0.0       4.5     3e+03      19      39 ..     449     470 ..     442     526 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0037
                                  EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                  ++i+Gr+ +GK+ L+ al g+
  gi|91773842|ref|YP_566534.1| 33 IGILGRSGAGKTILMHALRGA 53
                                  89****************886 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.21
                                   EEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                   +++G + +GK+t    l+g 
  gi|91773842|ref|YP_566534.1| 321 GLAGTSGAGKTTTSEMLMGI 340
                                   799*********99999884 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.5
                                   HHTS.TEEESSSTTSSSSEEEE CS
                      MMR_HSR1  19 ltge.kaivsdkpgtTrdineg 39 
                                   l++e + iv d+p  T d++++
  gi|91773842|ref|YP_566534.1| 449 LMKEpTIIVMDEPTGTMDPITK 470
                                   5555556777777777777544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.002       1.3      17      39 ..      29      49 ..      14      64 .. 0.80
   2 ?    2.0   0.1      0.14        96      19      37 ..     318     334 ..     304     358 .. 0.85
   3 ?   -2.4   0.0       3.1   2.1e+03      81     110 ..     433     459 ..     414     475 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.002
                                  TSCSEEEEEEESTTSSHHHHHHH CS
                        NB-ARC 17 elqslvvalvGmgGvGKttlakq 39
                                  e +  v+++ G+ G GKt+l++ 
  gi|91773842|ref|YP_566534.1| 29 EGE--VIGILGRSGAGKTILMHA 49
                                  444..9**************975 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                                   CSEEEEEEESTTSSHHHHH CS
                        NB-ARC  19 qslvvalvGmgGvGKttla 37 
                                   +  + +l G  G GKtt +
  gi|91773842|ref|YP_566534.1| 318 E--IFGLAGTSGAGKTTTS 334
                                   3..889**********965 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.1
                                   TTSSSS-STTSHHHHHHHHCCCTTEEEEEE CS
                        NB-ARC  81 ddleekeeveslkrklvrlLltkrfllvlD 110
                                   dd++   e+e     l ++L +  +++v+D
  gi|91773842|ref|YP_566534.1| 433 DDIS---EGERHRVALAQILMKEPTIIVMD 459
                                   3333...34445688999999999999999 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.082        54       3      24 ..      34      56 ..      32      68 .. 0.81
   2 ?    6.2   0.1     0.016        11       4      19 ..     322     337 ..     320     359 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.082
                        AAA_28  3 vitGgestGKTtlleaLa.argy 24
                                   i+G +++GKT l+ aL  a++y
  gi|91773842|ref|YP_566534.1| 34 GILGRSGAGKTILMHALRgAEEY 56
                                  58999************843344 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.016
                        AAA_28   4 itGgestGKTtlleaL 19 
                                   + G++++GKTt++e L
  gi|91773842|ref|YP_566534.1| 322 LAGTSGAGKTTTSEML 337
                                   67***********988 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0071       4.7       4      43 ..      14      51 ..      11      64 .. 0.85
   2 ?    3.5   0.1     0.049        33       9      51 ..     303     345 ..     294     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0071
                                  HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHH CS
                          PIF1  4 eeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkall 43
                                   +  kv+++i   ++ ++g+++ + G +G+gKt+l +al 
  gi|91773842|ref|YP_566534.1| 14 YDNVKVLKNI--NLNINEGEVIGILGRSGAGKTILMHALR 51
                                  5667888888..77889******************99986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.049
                                   HHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                          PIF1   9 vfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklrsegk 51 
                                   v++a+ +  ++ ++g++f + G +G+gKt   + l+ ++ ++ k
  gi|91773842|ref|YP_566534.1| 303 VIHAVNDISFDvKEGEIFGLAGTSGAGKTTTSEMLMGIVAPT-K 345
                                   5555554444448999999**********9988888877765.3 PP

>> Tnp_DNA_bind  Transposase DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00046       0.3      12      39 ..     160     187 ..     156     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                  Tnp_DNA_bind  12 LgDkRltkRlvklaeslaekpgasiPqa 39 
                                   L D Rl++Rl+++a++l+   +++++ a
  gi|91773842|ref|YP_566534.1| 160 LEDVRLSHRLMHVARDLSGGEKQRVVLA 187
                                   79****************9999998766 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.1   1.4e+03       6      18 ..      37      49 ..      35      58 .. 0.82
   2 ?   -1.8   0.0       4.5     3e+03      54      69 ..     137     166 ..      92     254 .. 0.60
   3 ?    8.1   0.6    0.0038       2.5       5      24 ..     323     342 ..     319     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                                  SSTTSSHHHHHHH CS
                                  xxxxxxxxxxxxx RF
                          CbiA  6 tkGGvGKTtlaan 18
                                  + +G+GKT l  +
  gi|91773842|ref|YP_566534.1| 37 GRSGAGKTILMHA 49
                                  679*****98655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                                   H..............CCHCCCHHHHHHCHC CS
                                   x..............xxxxxxxxxxxxxxx RF
                          CbiA  54 p..............dlkrllellealgkk 69 
                                   +               ++r  elle+++ +
  gi|91773842|ref|YP_566534.1| 137 NvmnslkeigytgpdAMSRAMELLEDVRLS 166
                                   144444444444444344444444444433 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0038
                                   ESSTTSSHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          CbiA   5 stkGGvGKTtlaanLarala 24 
                                   ++++G+GKTt++  L+ + a
  gi|91773842|ref|YP_566534.1| 323 AGTSGAGKTTTSEMLMGIVA 342
                                   799*********99998776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.054        36       4      22 ..      32      50 ..      29      56 .. 0.85
   2 ?    4.7   0.3     0.033        22       6      22 ..     321     337 ..     317     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.054
                        AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   i i G sg+GKT l+  l
  gi|91773842|ref|YP_566534.1| 32 VIGILGRSGAGKTILMHAL 50
                                  689**********998765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.033
                        AAA_24   6 liyGpsgiGKTtlakel 22 
                                    + G sg+GKTt+  +l
  gi|91773842|ref|YP_566534.1| 321 GLAGTSGAGKTTTSEML 337
                                   589*********99877 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 ?    4.5   0.0     0.036        24       2      21 ..      32      51 ..      31      64 .. 0.80
   2 ?    1.4   0.1      0.32   2.1e+02      89     148 ..     201     256 ..     168     295 .. 0.80
   3 ?    2.2   0.3      0.18   1.2e+02       3      16 ..     320     333 ..     318     352 .. 0.82
   4 ?   -3.5   0.0       9.8   6.5e+03      85     106 ..     455     478 ..     440     496 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.036
                                  EEEEEESTTCCHHHHHHHHH CS
                          cobW  2 vtvltGflGsGKTtLlnhll 21
                                  v+++ G  G+GKT L+ +l 
  gi|91773842|ref|YP_566534.1| 32 VIGILGRSGAGKTILMHALR 51
                                  6889999*******998775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                                   EECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE CS
                          cobW  89 EttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvln 148
                                   E tG ++P +  + ++ ++++++   + +v+ +    + +e ie++a++ +   d ++++
  gi|91773842|ref|YP_566534.1| 201 EPTGTLDPRTADIVHDVIEKAVKTYNMTMVITS----HWSEVIEKLADKAIILEDGVIIS 256
                                   899999999997779999999999999999988....44677777777777777777776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.18
                                   EEEEESTTCCHHHH CS
                          cobW   3 tvltGflGsGKTtL 16 
                                   ++l+G  G+GKTt 
  gi|91773842|ref|YP_566534.1| 320 FGLAGTSGAGKTTT 333
                                   6799********96 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 9.8
                                   EEEE.EECTTTTHHHH.HTTSHHH CS
                          cobW  85 vili.EttGlaePapv.afteeel 106
                                   +i+  E tG ++P +   +t + l
  gi|91773842|ref|YP_566534.1| 455 IIVMdEPTGTMDPITKiEVTRSIL 478
                                   333348889888887632223333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.78u 0.38s 00:00:01.16 Elapsed: 00:00:00.56
# Mc/sec: 2889.35
//
Query:       gi|91773843|ref|YP_566535.1|  [L=521]
Description: hypothetical protein Mbur_1903 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0035   17.6   0.0         24    5.2   0.0    4.3  5  Pro_isomerase   Cyclophilin type peptidyl-prolyl cis-trans is
  ------ inclusion threshold ------
      0.036   14.2   0.0        7.3    6.7   0.0    2.3  2  Dehydratase_SU  Dehydratase small subunit


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 ?    0.1   0.0       0.1     9e+02       4      21 ..      63      79 ..      61      91 .. 0.79
   2 ?    3.1   0.0     0.011     1e+02     124     140 ..     160     176 ..     149     186 .. 0.89
   3 ?    2.2   0.0     0.021   1.9e+02      12      38 ..     214     239 ..     211     250 .. 0.91
   4 ?   -2.5   0.0      0.63   5.7e+03     121     140 ..     296     315 ..     284     324 .. 0.78
   5 !    5.2   0.0    0.0027        24      11      45 ..     387     432 ..     380     475 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.1
                 Pro_isomerase  4 ietsskGrivieLfadka 21
                                  ++ts kG+++ieL+++++
  gi|91773843|ref|YP_566535.1| 63 VKTS-KGEFKIELNGESV 79
                                  6895.*********9875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                 Pro_isomerase 124 FGkVveGmdvvekiekv 140
                                   FGk+++G++v++++ ++
  gi|91773843|ref|YP_566535.1| 160 FGKIISGTNVLKELGSG 176
                                   ************99876 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.021
                 Pro_isomerase  12 ivieLfadkaPktvenFlklvkegfYd 38 
                                   +++eL++++ P+ +e F +l+++g++d
  gi|91773843|ref|YP_566535.1| 214 VEVELNPET-PEGAEHFFALIRDGTFD 239
                                   689999998.**************987 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.63
                 Pro_isomerase 121 ytvFGkVveGmdvvekiekv 140
                                   + v G++ +G+++v+  e++
  gi|91773843|ref|YP_566535.1| 296 HSVIGHLSHGLELVQMAEAG 315
                                   78999999999999977765 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0027
                 Pro_isomerase  11 rivieLfadkaPktvenFlklvkeg...........fYdgttFhRv 45 
                                    + ieL++d aPkt + F++ ++ +           +Y++t ++++
  gi|91773843|ref|YP_566535.1| 387 LVSIELYDDLAPKTLDFFRHAIDLQfkpvgalpvmmTYENTYIFKA 432
                                   5789***************999866666666666667777776666 PP

>> Dehydratase_SU  Dehydratase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00082       7.3      49      92 ..     354     399 ..     335     402 .. 0.80
   2 ?    5.0   0.0    0.0026        24      20      58 ..     435     473 ..     423     480 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00082
                Dehydratase_SU  49 LelqaqiAesagrkqlaknlrRaaElvkvpderil..eiYnalrPy 92 
                                   +e  a + ++   ++++   +R+ E++ vpd +++  e+Y+ l P+
  gi|91773843|ref|YP_566535.1| 354 VEKDAVVVKQDPPHSIDVMRQRSVEVIGVPDSKLVsiELYDDLAPK 399
                                   666777888888888888899************962267**99996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0026
                Dehydratase_SU  20 tgksldditlekvlsgkvkaedlritpetLelqaqiAes 58 
                                    ++++++i  e+v +gkv+a d+ +t+++ +  + +  +
  gi|91773843|ref|YP_566535.1| 435 AAEKYKEIMPENVPEGKVNAGDIGVTNQAAKRHGMVGVK 473
                                   567899*********************999888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2934.40
//
Query:       gi|91773844|ref|YP_566536.1|  [L=144]
Description: hypothetical protein Mbur_1904 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-41  139.0   0.0    4.9e-41  138.6   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 !  138.6   0.0   2.7e-45   4.9e-41       2     103 .]      13     114 ..      12     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 2.7e-45
                       DUF2102   2 vvieseaevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRakr.gga 81 
                                   vvi+se+ ++p++ v+kvye+e+++tiketCfG++v+g++e+v kvve++r++d+n+ifvkeRgf+pg e rCRa r gg+
  gi|91773844|ref|YP_566536.1|  13 VVISSES-ILPTDAVMKVYESEDSITIKETCFGTMVNGPREAVLKVVETLRSMDHNHIFVKERGFKPGAEVRCRAGRgGGP 92 
                                   7888887.*********************************************************************99** PP

                       DUF2102  82 RpGfhqlekEvelleliskaLe 103
                                   RpGfh+l++Ev++l++i++aL+
  gi|91773844|ref|YP_566536.1|  93 RPGFHFLREEVNMLPMIGRALD 114
                                   ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 957.69
//
Query:       gi|91773845|ref|YP_566537.1|  [L=151]
Description: hypothetical protein Mbur_1905 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-65  218.6   0.0    3.5e-65  218.4   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 !  218.4   0.0     2e-69   3.5e-65       1     143 []       2     144 ..       2     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.4 bits;  conditional E-value: 2e-69
                       DUF2112   1 mkvaviPdnsliladlverfgheplslakeikekvktaeldspplniteedpkkGlkyaavevPsGvrGRlsligplieea 81 
                                   +kv+++P+nslil+d+verfghepl+++++ike ++t ++dspplnit+e pk+GlkyaavevP+GvrGR+sligp+i+ a
  gi|91773845|ref|YP_566537.1|   2 AKVIIYPTNSLILSDMVERFGHEPLAMMEKIKEIINTIGVDSPPLNITPEGPKHGLKYAAVEVPAGVRGRMSLIGPMIDFA 82 
                                   59******************************************************************************* PP

                       DUF2112  82 eaaiiveeadilfgcvGCartnelvkalirkkdiPileleyPkseeeaielvkkineFLksl 143
                                   ea iiv +++++fgc+GCartnel+k+lir+kdiPile++yP++ee+++++v+ki++FLksl
  gi|91773845|ref|YP_566537.1|  83 EAGIIVGDSSFSFGCMGCARTNELTKFLIREKDIPILEIQYPHTEEDGQDFVYKIADFLKSL 144
                                   ***********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 988.61
//
Query:       gi|91773846|ref|YP_566538.1|  [L=414]
Description: CoA enzyme activase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-59  202.1   4.2    1.6e-59  201.6   4.2    1.2  1  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.019   14.5   0.5        1.3    8.5   0.5    2.4  1  FGGY_N         FGGY family of carbohydrate kinases, N-termina
      0.019   14.6   0.0        5.5    6.6   0.0    2.4  2  Peptidase_M22  Glycoprotease family
      0.041   14.3   0.6       0.34   11.4   0.6    2.4  1  FtsA           Cell division protein FtsA
      0.075   12.7   0.5      0.075   12.7   0.5    1.9  2  Hydant_A_N     Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.6   4.2   4.5e-63   1.6e-59       2     267 .]     155     408 ..     154     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 4.5e-63
                                   EEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTTBS CS
                   BcrAD_BadFG   2 GiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlpekfe 82 
                                   GiD+GsTttkav+m++++ v   ++ + + les++         +al++al+++g++++di+ +  ++tgyGr  ++e+f+
  gi|91773846|ref|YP_566538.1| 155 GIDSGSTTTKAVVMKDNEIVGEGWVPTIKVLESAE---------TALQQALDQSGLKKEDIQAI--GTTGYGRFLVGEHFK 224
                                   9****************999999999999999886.........9*****************88..*************** PP

                                   EEE-..HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT--TTTHHHHH CS
                   BcrAD_BadFG  83 keiirseilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmglreldgla 160
                                   ++ +++ei+++++Gav+l+++++   tv+digG+d+k+i +++g++  f+m++ ca+ +Gr+l+++a++l++++ el++la
  gi|91773846|ref|YP_566538.1| 225 ADLVQEEITMNSKGAVYLADKQKgpaTVIDIGGMDNKAISVQDGIPGMFTMGGICAGASGRFLEMTAKRLGVEITELGDLA 305
                                   ********************************************************************************* PP

                                   TT--.S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.... CS
                   BcrAD_BadFG 161 ekat.kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvakneaavkelrklv 240
                                    k++ ++  +ns+c vf  + l++ l++g + ed+ a +++++ +++ +++ ++ +v++ ++l+GG +  +++ k+l +l+
  gi|91773846|ref|YP_566538.1| 306 IKGMgENVEMNSYCIVFGIQSLVNSLAKGSSPEDVAAAACHSVVEQIFEQQLQEVEVKEPLILVGGSSLIAGVPKALGDLL 386
                                   ****7779*********************************************************************6666 PP

                                   .HHHH-S-EE--GGGGGHHHHHHHHHH CS
                   BcrAD_BadFG 241 kenygevkininpdsiytgalGAalfA 267
                                   k      ++ ++p+s+  ga+GAal+A
  gi|91773846|ref|YP_566538.1| 387 K-----IDVIVPPHSQLIGAVGAALLA 408
                                   6.....555679*************98 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 ?    8.5   0.5   0.00037       1.3      47      79 ..     183     215 ..     152     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00037
                                   HHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-S CS
                        FGGY_N  47 eiwqalaeairkvleqagisekqikaIgisgqr 79 
                                   +++++   a++++l+q+g+++++i+aIg +g +
  gi|91773846|ref|YP_566538.1| 183 KVLESAETALQQALDQSGLKKEDIQAIGTTGYG 215
                                   467788889999999999999999999999876 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0032        11      31      57 ..     186     212 ..     166     214 .. 0.85
   2 ?    6.6   0.0    0.0015       5.5     161     260 ..     304     396 ..     243     406 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0032
                                   HHHHHHHHHHHHHHTSTGGGEEEEEEE CS
                 Peptidase_M22  31 erllplieealaeaglsledldaIavt 57 
                                   e    ++++al+++gl++ed++aI  t
  gi|91773846|ref|YP_566538.1| 186 ESAETALQQALDQSGLKKEDIQAIGTT 212
                                   5667889*****************877 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0015
                                   HHCTC..S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHH CS
                 Peptidase_M22 161 lakeg..kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakelvilGGvaankr 238
                                   la +g  +++e     ++  ++  G+++ v ++++  + ed+aa+  ++vv++   + e+ l++ ++ke +il  v++ ++
  gi|91773846|ref|YP_566538.1| 304 LAIKGmgENVE-----MNSYCIVFGIQSLVNSLAKGsSPEDVAAAACHSVVEQ---IFEQQLQEVEVKEPLIL--VGGSSL 374
                                   44445444455.....3333567788888888774444**********99998...55556678999998888..777777 PP

                                   HHHCHCCHHHHTTSEEEXXXHH CS
                 Peptidase_M22 239 LrealeeeaeelglkliiPplk 260
                                   +    +++ + l++++i+Pp++
  gi|91773846|ref|YP_566538.1| 375 IAGVPKALGDLLKIDVIVPPHS 396
                                   7777765555689999999965 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   9.5e-05      0.34       1      35 [.     154     186 ..     154     403 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                                   EEEEE-SSSEEEEEEETTEEEE...EEEES--HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                          FtsA   1 alvDiGagktdvavaedgalvh...lrvigvggngitk 35 
                                   a++D G+++t+++v++d+++v    +   ++    + +
  gi|91773846|ref|YP_566538.1| 154 AGIDSGSTTTKAVVMKDNEIVGegwV---PT--IKVLE 186
                                   79***************998884442...22..22333 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 ?   12.7   0.5   2.1e-05     0.075       3      65 ..     155     212 ..     153     221 .. 0.76
   2 ?   -1.6   0.1      0.51   1.8e+03     151     173 ..     338     360 ..     325     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                    Hydant_A_N   3 gIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTT 65 
                                   gID G+T T av+++++ e v    +++   +v e   +al+++l++s+ ++++i+++  GTT
  gi|91773846|ref|YP_566538.1| 155 GIDSGSTTTKAVVMKDN-EIVGEGWVPTI--KVLESAETALQQALDQSGLKKEDIQAI--GTT 212
                                   9**************88.76777777776..667777777777777777777777654..555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.51
                    Hydant_A_N 151 esiavvllhSylnpehElrvaei 173
                                   e +a +  hS++    E++ +e+
  gi|91773846|ref|YP_566538.1| 338 EDVAAAACHSVVEQIFEQQLQEV 360
                                   55788999999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2623.29
//
Query:       gi|91773847|ref|YP_566539.1|  [L=197]
Description: hypothetical protein Mbur_1907 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-63  211.7   2.1    5.9e-63  211.6   2.1    1.0  1  DUF2113      Uncharacterized protein conserved in archaea (DU
  ------ inclusion threshold ------
      0.078   12.4   0.1       0.29   10.5   0.0    1.8  2  vATP-synt_E  ATP synthase (E/31 kDa) subunit


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 !  211.6   2.1   6.5e-67   5.9e-63       1     184 [.       7     192 ..       7     193 .. 0.99

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 6.5e-67
                       DUF2113   1 fevectdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspiklgdvaeveedkeegkvkikied 81 
                                   f+ve+t +++a+aYe+i++di+++l + r+i+r+kv i+pe++lF++++llr+ ++pik g+++++e d+e+ kv+i+++d
  gi|91773847|ref|YP_566539.1|   7 FTVETTVPSEAAAYESILKDIISELAFSRTIGRIKVRIRPEDSLFMMVILLRRGLPPIKAGEISDTEFDREHAKVVITVRD 87 
                                   79******************************************************************************* PP

                       DUF2113  82 EtylpelLkkLwekygrenveqpdRfeiiiesdedl..eeleelvVaDpkeelkkkvidaliriaPEGfrvrkealednsf 160
                                   E+ +p++L++Lwe++gr+nv qp+R+ i+++sd ++  + ++el+V+Dp+++++++++d++ir +PEGfr+r+++l+  +f
  gi|91773847|ref|YP_566539.1|  88 EKTIPQFLDRLWEQFGRQNVIQPERNIIEVASDLEIvdKFIAELIVDDPEKTIRERLADMAIRATPEGFRIRYHSLDSGKF 168
                                   *********************************99999******************************************* PP

                       DUF2113 161 vfvAseetlkeewieeakelkeel 184
                                   vfvAse+t++++wi+ea+ +++el
  gi|91773847|ref|YP_566539.1| 169 VFVASEDTMQQDWIDEANVMMKEL 192
                                   *********************998 PP

>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.2e-05      0.29      87     124 ..      12      49 ..      10      56 .. 0.92
   2 ?   -0.9   0.1       0.1   9.2e+02     112     130 ..     109     127 ..      68     150 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.2e-05
                                   HHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCH CS
                   vATP-synt_E  87 eveedkdeYkellkkLivqalvkleepevivrarkeDa 124
                                   +v+++  +Y+++lk++i + +++   +++ vr r eD 
  gi|91773847|ref|YP_566539.1|  12 TVPSEAAAYESILKDIISELAFSRTIGRIKVRIRPEDS 49 
                                   5788899****************************995 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.1
                                   SSCEEEEECCCCHHCCCCT CS
                   vATP-synt_E 112 epevivrarkeDaelveea 130
                                   +pe  +   + D e+v++ 
  gi|91773847|ref|YP_566539.1| 109 QPERNIIEVASDLEIVDKF 127
                                   3333333334444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 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:                        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 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1219.13
//
Query:       gi|91773848|ref|YP_566540.1|  [L=310]
Description: hypothetical protein Mbur_1908 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-124  414.6   0.3   1.7e-124  414.3   0.3    1.1  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 !  414.3   0.3  9.3e-129  1.7e-124       1     271 []       5     274 ..       5     274 .. 0.99

  Alignments for each domain:
  == domain 1  score: 414.3 bits;  conditional E-value: 9.3e-129
                         MCR_C   1 lepltyeGGvykhdellelieDlGGyilqknvialevvltllvPkedvelieelakellgklteaPlagteiavvsptLar 81 
                                   lep++yeGG++kh+++lel+eDlGGy++qk+ +++e++l++l+Pk+dv+l+e+++ +llgklt+aPl+gte+avvsptLa+
  gi|91773848|ref|YP_566540.1|   5 LEPYIYEGGIHKHSLILELLEDLGGYLVQKTPASTEITLVMLIPKKDVHLVEDVCIKLLGKLTSAPLTGTEVAVVSPTLAS 85 
                                   689****************************************************************************** PP

                         MCR_C  82 hhlPhsaCDvaeylrraGaktnmiGlarGvgkriaqikeeekrlinehDlavfvlGnfkdCikkkkeklfedievPvvvtg 162
                                   hhlPhsaCD+aeylrr Ga+tnmiGlarG+g+r+a  +++e+rlinehD+avf++G fkdCi +kk+klfe+ie+P+vvtg
  gi|91773848|ref|YP_566540.1|  86 HHLPHSACDIAEYLRRGGANTNMIGLARGMGRRVALSADYERRLINEHDVAVFSFGIFKDCIINKKPKLFEGIEIPIVVTG 166
                                   ********************************************************************************* PP

                         MCR_C 163 gPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldkkreelakDpllvsparvkkeieeqveeieevl 243
                                   gP ++++ee++ga+ yvgg+Gr+ahr+rk+ e++a+d l+e+v+e+++ kre++akDpl+v par++ke++eqv+ i +vl
  gi|91773848|ref|YP_566540.1| 167 GP-DIRTEEISGADIYVGGIGRVAHRMRKGPELDAMDVLNEKVGEIVNLKRESIAKDPLAVLPARLMKEVQEQVPVILSVL 246
                                   **.9***************************************************************************** PP

                         MCR_C 244 sPapitlqldglrvklpydeyaekieev 271
                                   +Papitlqldg+r+klpyd+y++++ ++
  gi|91773848|ref|YP_566540.1| 247 TPAPITLQLDGMRIKLPYDRYRDAVGNI 274
                                   ************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1903.14
//
Query:       gi|91773849|ref|YP_566541.1|  [L=149]
Description: alkylhydroperoxidase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-13   50.7   0.1    2.2e-13   50.1   0.1    1.3  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 !   50.1   0.1   1.2e-17   2.2e-13      13      76 ..      55     118 ..      50     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.2e-17
                                   HHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHH CS
                           CMD  13 alla.reggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaa 76 
                                   +++    ++Ldpk+ eLi ++vs a++c++C+++H+r A + G+++eei +++ +a a +   ++
  gi|91773849|ref|YP_566541.1|  55 SIMReF-ERLDPKTIELICIGVSSALRCDHCMNMHIRVANRLGLSKEEIFDAVLIAGAISNASVL 118
                                   556544.45********************************************999888765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 966.01
//
Query:       gi|91773850|ref|YP_566542.1|  [L=299]
Description: hypothetical protein Mbur_1910 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-98  327.5  25.5    8.7e-98  327.3  25.5    1.0  1  SPP              Signal-peptide peptidase, presenilin asparty
    2.7e-07   30.4  12.4    4.4e-07   29.7  12.4    1.3  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 !  327.3  25.5  9.7e-102   8.7e-98       2     282 ..      19     294 ..      18     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 327.3 bits;  conditional E-value: 9.7e-102
                           SPP   2 alfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvflvlls 82 
                                   +l+++vqv al+la p+++ ++qa e+P+ + ns +yi ++l ft  +l++ik+++k++i++ i+++v+a+ify f  +l 
  gi|91773850|ref|YP_566542.1|  19 GLILIVQVIALILASPMDELGMQAVENPESTANSFYYIGFILAFTFLLLLAIKRNMKWVIQLTILLAVGATIFYGFYPILY 99 
                                   79*******************************************999********************************* PP

                           SPP  83 ivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvyktkhmial 163
                                   ++ +   l  ++ +++a al+++ly++peWyvid++G+i++  +sa+fGis+g+lpa+vll +lavydaisvyktkhmi l
  gi|91773850|ref|YP_566542.1| 100 MLGISETLSSTVGIILAAALTIILYKFPEWYVIDIIGIIIGAAASAIFGISFGILPAIVLLSLLAVYDAISVYKTKHMIDL 180
                                   **9****************************************************************************** PP

                           SPP 164 aegvvdlklPillvvPetlaysfveeafeeaeeaearnvlfiGlGdavlPsilvvsaavfleshilaglelavllalaGtl 244
                                   aegv+dlklPil+++P++ +ysf+++++++++e++a   +f+GlGdav+P++lvvsa+vf      + +++++l+a++Gtl
  gi|91773850|ref|YP_566542.1| 181 AEGVMDLKLPILFIIPKKRNYSFIKDGMKKEGEKDA---FFMGLGDAVMPTVLVVSANVFIAHT--GFISYPALGAVIGTL 256
                                   *********************************666...*********************9985..45************* PP

                           SPP 245 vGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaag 282
                                    G++ l+i+v++g+p+aGlP+lnsG i G++ g+l +g
  gi|91773850|ref|YP_566542.1| 257 AGFIGLTIFVMKGKPQAGLPFLNSGVILGYIAGALLSG 294
                                   **********************************9886 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7  12.4   4.9e-11   4.4e-07      51     203 ..      57     234 ..       8     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.9e-11
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....................XXXXXXXXXXXXX------S--XXXXXX CS
                Peptidase_A22B  51 lgvvalasllsplvtrlflkkvelakvklefla....................ielkaaeivalllsiviavlwllkrhwi 111
                                     + a+++ll  +++r + k v + +                           i+ + ++ v ++l+ +++++ + +++w 
  gi|91773850|ref|YP_566542.1|  57 GFILAFTFLLLLAIKRNM-KWVIQLT------IllavgatifygfypilymlgISETLSSTVGIILAAALTIILYKFPEWY 130
                                   333344444444443221.1111111......0222222444455556667667778888899999999************ PP

                                   XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX.......XXXXXXX CS
                Peptidase_A22B 112 lndilglalailviellrlp.slkvgalLLvglflYDifwVFgtdvmvevAk...eldiPillklPq.......lsneiee 181
                                   + di+g+ +  +  ++  +   +  + +LL+ l +YD   V+ t+ m+ +A+   +l++Pil+ +P+       ++ + +e
  gi|91773850|ref|YP_566542.1| 131 VIDIIGIIIGAAASAIFGISfGILPAIVLLSLLAVYDAISVYKTKHMIDLAEgvmDLKLPILFIIPKkrnysfiKDGMKKE 211
                                   ******9987777777666523445678899999******************99999**********77665532223333 PP

                                   .XXXXXXXXXXXXXXXXXXXXXX CS
                Peptidase_A22B 182 .askfsiLGlGDivlPGlliall 203
                                    +++   +GlGD v+P +l+  +
  gi|91773850|ref|YP_566542.1| 212 gEKDAFFMGLGDAVMPTVLVVSA 234
                                   13445679**********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1780.05
//
Query:       gi|91773851|ref|YP_566543.1|  [L=107]
Description: hypothetical protein Mbur_1911 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0063   16.7   1.9     0.0091   16.1   1.9    1.2  1  DUF5446          Family of unknown function (DUF5446)
  ------ inclusion threshold ------
      0.027   14.5   0.1      0.033   14.2   0.1    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.028   14.3   0.0      0.031   14.2   0.0    1.1  1  PapD_N           Pili and flagellar-assembly chaperone, PapD 
      0.089   13.4   3.7        1.1   10.0   3.7    2.0  1  DUF3139          Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.9     2e-06    0.0091      14      53 ..      58      97 ..      53     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                       DUF5446 14 LeeiEeeltevEkelseavneteaekeekeeerldllekE 53
                                  L  iE+ l+e E++l   v+  e  + +k +e+++++++ 
  gi|91773851|ref|YP_566543.1| 58 LRRIEKTLDEKERSLRINVQSIESSMDKKMNEVISVVDEA 97
                                  678**********************************985 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 ?   14.2   0.1   7.3e-06     0.033      45     110 ..       7      77 ..       6      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.3e-06
               Phage_holin_3_6  45 vlallalllllvalalala.a...lwlaalivaavllvlagvlalvglk.klkkakplpertieelkedva 110
                                   v+ ++++++ +v+   +l+ +   ++ + +i+ a+++v a++++++ +  +l++ ++++++  ++l+ +v+
  gi|91773851|ref|YP_566543.1|   7 VFSIVMVVSSFVLTYEWLGrFkysSANSLIILSAIVMVGALAAMILSVDiRLRRIEKTLDEKERSLRINVQ 77 
                                   55566666666666788877788455555558888888887777777777999988888888888888877 PP

>> PapD_N  Pili and flagellar-assembly chaperone, PapD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.8e-06     0.031      47     120 ..      29     103 ..      11     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.8e-06
                                   SSCS.SEEEESSEEEE-TTEEEEEEE.EE...SS---SSS-EEEEEEEEEE-----.TCEEEEEEEEEEEEEEEEEE CS
                        PapD_N  47 kakaspfvvtPPlfrlepgeeqvlRi.vt..agkklpkdrEslfwlnvkeiPpkkkkkekknklqlalrsriklfyr 120
                                    ++a+ ++++  ++ + + +  +l + ++  + +k  +++E   ++nv+ i ++ +  +k n++  ++   + +f r
  gi|91773851|ref|YP_566543.1|  29 YSSANSLIILSAIVMVGALAAMILSVdIRlrRIEKTLDEKERSLRINVQSIESSMD--KKMNEVISVVDEAMDVFNR 103
                                   456668999999999999999988888554477888999**************774..6789998888988888866 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.7   0.00024       1.1       5      67 ..      35      90 ..       5      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                       DUF3139  5 iiililliillvivkvflglvgskpikkylankkldkyl.qekgykeddIksikpkydskkgsy 67
                                  +iil+ ++++ + ++    ++ s+ i       +++k+l +++   + +++si++++d k+++ 
  gi|91773851|ref|YP_566543.1| 35 LIILSAIVMVGALAA----MILSVDI----RLRRIEKTLdEKERSLRINVQSIESSMDKKMNEV 90
                                  344444444444444....4445555....3499*****656667899*************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 695.65
//
Query:       gi|91773852|ref|YP_566544.1|  [L=104]
Description: hypothetical protein Mbur_1912 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 654.09
//
Query:       gi|91773853|ref|YP_566545.1|  [L=338]
Description: flap endonuclease-1 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-27   96.2   0.0      2e-27   95.3   0.0    1.4  1  XPG_I       XPG I-region
    2.2e-21   76.2   0.0      4e-21   75.4   0.0    1.4  1  XPG_N       XPG N-terminal domain
     0.0019   18.8   0.0     0.0048   17.5   0.0    1.7  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold


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 !   95.3   0.0   3.4e-31     2e-27       2      94 .]     141     236 ..     140     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 3.4e-31
                                   HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHHHHT- CS
                         XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlkelgl 79 
                                   lmgipyv+Ap+E+EAq++y+++kg++d++ s+D+D++lFGap+v+rnl+ ++k+k    + ++++k+ev++l + l elg+
  gi|91773853|ref|YP_566545.1| 141 LMGIPYVKAPSEGEAQASYMVQKGDADYIGSQDYDSFLFGAPQVVRNLTiTGKRKLPkkNIYVDVKPEVLSLVDSLGELGI 221
                                   8***********************************************975554444668999****************** PP

                                   -HHHHHHHHHHHCET CS
                         XPG_I  80 treqlidlaillgcD 94 
                                   tr+qlid+a+++g+D
  gi|91773853|ref|YP_566545.1| 222 TRQQLIDIAMCVGTD 236
                                   *************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   6.7e-25     4e-21      20     100 ..      15     100 ..       8     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 6.7e-25
                                   EGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHHHHHHHH CS
                         XPG_N  20 siealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkkeelekrs 95 
                                   +i  l++k++aiDa+  ly+fl  +r+++g+ l+      tshl g+++rl  l++ g+kPifVFdgk+pd+k+++l+kr+
  gi|91773853|ref|YP_566545.1|  15 EIAGLSNKVVAIDAYNTLYQFLSIIRQRDGTPLKDsrgqiTSHLSGILYRLTSLIEAGVKPIFVFDGKPPDFKSDTLAKRH 95 
                                   67889*****************************99********************************************* PP

                                   HHHHH CS
                         XPG_N  96 errqe 100
                                   e r++
  gi|91773853|ref|YP_566545.1|  96 EVRES 100
                                   *9986 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 !   17.5   0.0     8e-07    0.0048       4      49 ..     224     267 ..     221     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8e-07
                    5_3_exonuc   4 eqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenld 49 
                                   +q+id++  vG  +D   G + iG+k A kL+ke+g+++ +l++l 
  gi|91773853|ref|YP_566545.1| 224 QQLIDIAMCVG--TDYNTGLENIGPKRALKLVKEHGDIKVVLKELG 267
                                   67777777777..46668*************************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2120.65
//
Query:       gi|91773854|ref|YP_566546.1|  [L=518]
Description: phosphoglyceromutase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-85  284.5   0.1    6.4e-85  284.0   0.1    1.2  1  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    5.4e-82  274.9   0.1    6.4e-82  274.7   0.1    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    0.00046   19.7   0.0      0.001   18.6   0.0    1.6  1  AP_endonuc_2   Xylose isomerase-like TIM barrel
    0.00081   19.1   0.0     0.0012   18.5   0.0    1.3  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
     0.0072   15.7   0.0      0.019   14.3   0.0    1.9  2  Sulfatase      Sulfatase
  ------ inclusion threshold ------
      0.017   15.2   0.1      0.032   14.3   0.1    1.4  1  PglZ           PglZ domain
       0.12   12.6   0.5        1.6    9.0   0.1    2.4  3  PHP            PHP domain
       0.18   11.1   0.5        1.9    7.7   0.2    2.3  3  Baculo_E56     Baculoviral E56 protein, specific to ODV envel


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 !  284.0   0.1   2.9e-88   6.4e-85       1     215 []      84     301 ..      84     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 284.0 bits;  conditional E-value: 2.9e-88
                                   HHHHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT-HHH CS
                        iPGM_N   1 inkaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapksale 81 
                                   in++i +g++f+n++lk+aie+ak++g+alHl+GL+S GgVHSh++hl al+e+ak+eg++++++haflDGRD++p+ ale
  gi|91773854|ref|YP_566546.1|  84 INRDIGNGDFFKNPVLKQAIENAKAQGSALHLMGLFSYGGVHSHMKHLRALIEFAKDEGITEIFIHAFLDGRDVSPRAALE 164
                                   899****************************************************************************** PP

                                   HHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG---EEE.... CS
                        iPGM_N  82 yleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefveptviae.e 161
                                    ++e  e++++l+vgkia+vsGRyyaMDRd+rw+r+e ay+a+++g+g   ++ +v+ai+e y +ge+Def++ptvi++ +
  gi|91773854|ref|YP_566546.1| 165 DMKEHVEYCNNLSVGKIATVSGRYYAMDRDNRWDRTEDAYNAITRGDGVYYSKGPVDAISEGYGRGENDEFIKPTVIVDeN 245
                                   **********************************************99887778************************999 PP

                                   TCCGGS--TT-EEEE----CCCCHHHHHHHHSTTHHCC...--TT-EEEESS-S-T CS
                        iPGM_N 162 gkkegtikdgDaviffNFRaDRareltraltdkefkefe..kakklklvtmteYde 215
                                   g++ g+++++D+viffNFR+DRar+lt a++++ef++fe  ++ k+++v+mteYde
  gi|91773854|ref|YP_566546.1| 246 GRPIGRMNENDTVIFFNFRPDRARQLTYAFVNDEFDNFErkSHPKVHFVCMTEYDE 301
                                   ********************************9*****876667889*******96 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.7   0.1   2.8e-85   6.4e-82       2     248 .]       7     505 ..       6     505 .. 0.98

  Alignments for each domain:
  == domain 1  score: 274.7 bits;  conditional E-value: 2.8e-85
                                   EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                 Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel............... 67 
                                   +++l +lDG+G++p+ e naih A+tP+ld L +++P++ l++a+g++vglpe++mgnsevgHl++               
  gi|91773854|ref|YP_566546.1|   7 PFLLTILDGWGYSPEVEGNAIHAANTPNLDDLLETYPNT-LLSASGEDVGLPEGQMGNSEVGHLNIgagrvvyqdltrinr 86 
                                   57899**********************************.9**************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|91773854|ref|YP_566546.1|  87 digngdffknpvlkqaienakaqgsalhlmglfsyggvhshmkhlraliefakdegiteifihafldgrdvspraaledmk 167
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|91773854|ref|YP_566546.1| 168 ehveycnnlsvgkiatvsgryyamdrdnrwdrtedaynaitrgdgvyyskgpvdaisegygrgendefikptvivdengrp 248
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|91773854|ref|YP_566546.1| 249 igrmnendtviffnfrpdrarqltyafvndefdnferkshpkvhfvcmteydeklevpiafpseelkntlgevlskegikq 329
                                   ********************************************************************************* PP

                                   HHHHTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  68 lrisetvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldailsgkfdlvvvniknaDmvGHt 148
                                   lri+et+k+ahvtff+ngg++++ ++ eer+ ips++v+t+dl+pem+a+ev+e++++ i sgk+d++v+n++n+DmvGH+
  gi|91773854|ref|YP_566546.1| 330 LRIAETEKYAHVTFFFNGGVEKQNEG-EERCLIPSPKVATYDLKPEMSAYEVTEELIERIGSGKYDVIVLNLANMDMVGHS 409
                                   *************************9.****************************************************** PP

                                   T-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS............-----EEEEEESTT----S--SSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme 149 gdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk....qplTsHtlepVPilivgkglapdkvkega 225
                                   g +ea+++a+e +D +v++i+ ai++v+g  +v+ADHgnae+mv+  +    q +T+Ht +pV +++v ++ +        
  gi|91773854|ref|YP_566546.1| 410 GIMEAAVKAVEVVDDCVGKIITAIKEVGGEAMVMADHGNAEKMVEFCNnterQCYTAHTSNPVRCIYVTQEKRV------- 483
                                   *******************************************985445678*****************98554....... PP

                                   HHHTT-TTEEEEGGGHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme 226 kfrekggLanvaatllnllglea 248
                                    + +kg L++va+t+l+++g+e+
  gi|91773854|ref|YP_566546.1| 484 -ELQKGRLSDVAPTILKIMGIEK 505
                                   .4569**************9985 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 !   18.6   0.0   4.6e-07     0.001      28     116 ..     129     207 ..     103     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.6e-07
                                   HHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHH CS
                  AP_endonuc_2  28 eelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawer 108
                                   + lr+l + +++ g++   +++f +  ++      a+    ++++k+++e+++ L +  + + +G   +++  +++ +w+r
  gi|91773854|ref|YP_566546.1| 129 KHLRALIEFAKDEGITEIFIHAFLDGRDVSP---RAA----LEDMKEHVEYCNNLSVGKIATVSG---RYYAMDRDNRWDR 199
                                   468999999*******999999999999776...466....************************...99*********** PP

                                   HHHHHHHH CS
                  AP_endonuc_2 109 laeslnel 116
                                     ++ n++
  gi|91773854|ref|YP_566546.1| 200 TEDAYNAI 207
                                   99888876 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.5e-07    0.0012     166     235 ..     380     449 ..     298     480 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.5e-07
                                   HHHCT......SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---E CS
                  Phosphodiest 166 lekel......ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGma 235
                                   +++el      +k+d+++++l + D vgH+ G+  ++  +a++ vD+++g+++ a++e         ++++DHG a
  gi|91773854|ref|YP_566546.1| 380 VTEELierigsGKYDVIVLNLANMDMVGHS-GI-MEAAVKAVEVVDDCVGKIITAIKEV----GGEAMVMADHGNA 449
                                   444445566779*****************5.44.4566799*****************9....556699*****65 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2   4.5e+03       4      33 ..       9      39 ..       8      41 .. 0.63
   2 !   14.3   0.0   8.6e-06     0.019     209     309 .]     410     503 ..     283     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                                  EEEEESSE-TT.GSGGGTTTSCSSHHHHHHH CS
                     Sulfatase  4 vliladdlgag.dlglyggktattpnldrla 33
                                  +l ++d +g++  ++ +  + a+tpnld+l 
  gi|91773854|ref|YP_566546.1|  9 LLTILDGWGYSpEVEGNAIHAANTPNLDDLL 39
                                  56677777775444444445566****9875 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.6e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEE CS
                     Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekaprv 289
                                     +ea   +ve vDd++g+++ a+  +++  +++v  ++Dhg +   + + +  + + ++y  +t  P    +  + ++ v
  gi|91773854|ref|YP_566546.1| 410 GIMEAAVKAVEVVDDCVGKIITAI--KEVGGEAMV--MADHGNAE--KMVEFCNNTERQCYTAHTSNPVRCIYVTQEKR-V 483
                                   67899999****************..666666665..79****65..67888888888**********87777777777.8 PP

                                   ECSEEEGGGHHHHHHHHTTE CS
                     Sulfatase 290 seelvshiDlfptildlagi 309
                                   + +   ++D++ptil+ +gi
  gi|91773854|ref|YP_566546.1| 484 ELQKGRLSDVAPTILKIMGI 503
                                   88888899**********97 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.4e-05     0.032     110     169 ..     391     448 ..     352     452 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                          PglZ 110 kdkevvyivhnkvDalgdkasteqksfeaveeslkelkelvkslleengykvlltaDHGf 169
                                   ++++v+++ + + D++g++ + e ++ +ave     + ++++ + e  g + +++aDHG+
  gi|91773854|ref|YP_566546.1| 391 GKYDVIVLNLANMDMVGHSGIMEAAV-KAVEVVDDCVGKIITAIKEV-GGEAMVMADHGN 448
                                   68999999999*******77766554.56666666788888888898.999********7 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.3   6.8e+02      93     119 ..     131     169 ..      63     215 .. 0.65
   2 ?    0.9   0.0      0.23   5.1e+02      22     119 ..     136     169 ..     112     352 .. 0.56
   3 ?    9.0   0.1   0.00069       1.6      13      50 ..     424     459 ..     417     470 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.3
                                   H............HHHHHHHHH..........HHHHHHS CS
                                   x............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  93 l............lkllskaylegfyrkpridkellekh 119
                                   l            ++ +++a+l+g+   pr   e +++h
  gi|91773854|ref|YP_566546.1| 131 LraliefakdegiTEIFIHAFLDGRDVSPRAALEDMKEH 169
                                   133344444444467777777777777777777777776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
                                   HHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE..................E....EHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  22 kkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddsekerpshltllaknqeGyknllkllskayl 102
                                   + ak+ g+ +i                                                                +++a+l
  gi|91773854|ref|YP_566546.1| 136 EFAKDEGITEI----------------------------------------------------------------FIHAFL 152
                                   44444444443................................................................344444 PP

                                   ..........HHHHHHS CS
                                   xxxxxxxxxxxxxxxxx RF
                           PHP 103 egfyrkpridkellekh 119
                                   +g+   pr   e +++h
  gi|91773854|ref|YP_566546.1| 153 DGRDVSPRAALEDMKEH 169
                                   44444444444444443 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00069
                                   S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  13 galsieelvkkakelglkaiaiTDhgnlfgyvefykaa 50 
                                   + +   +++ + ke g +a+ + Dhgn+ ++vef ++ 
  gi|91773854|ref|YP_566546.1| 424 DCV--GKIITAIKEVGGEAMVMADHGNAEKMVEFCNNT 459
                                   555..899**************************9987 PP

>> Baculo_E56  Baculoviral E56 protein, specific to ODV envelope
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.13     3e+02      98     143 ..     170     219 ..     155     227 .. 0.70
   2 ?   -3.3   0.0       1.9   4.2e+03      62     100 ..     330     369 ..     316     372 .. 0.75
   3 ?    7.7   0.2   0.00083       1.9     102     166 ..     404     470 ..     399     481 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                    Baculo_E56  98 atylkglGyatllavsv.ylvl...kaadlvqdivealnrtGGsyyvrGk 143
                                    +y + l  + +++vs+ y+ +   +  d  +d  +a+ r  G yy++G 
  gi|91773854|ref|YP_566546.1| 170 VEYCNNLSVGKIATVSGrYYAMdrdNRWDRTEDAYNAITRGDGVYYSKGP 219
                                   56666666666666665244442223456788999************995 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                    Baculo_E56  62 lhikqtrknavktsfPetdv.rtreGvenalaknPrlaty 100
                                   l i++t k a  t f +  v +++eG e+ l   P++aty
  gi|91773854|ref|YP_566546.1| 330 LRIAETEKYAHVTFFFNGGVeKQNEGEERCLIPSPKVATY 369
                                   5667777777767666666636778999999999999999 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00083
                    Baculo_E56 102 kglGyatllavsvylvlkaadlvqdivealnrtGGsyyvrGkngGd..nvdacllkyrscgvdqsla 166
                                     +G + ++ ++v  v  + d v +i+ a+ + GG   v  + g     v+ c    r c + ++ +
  gi|91773854|ref|YP_566546.1| 404 DMVGHSGIMEAAVKAVEVVDDCVGKIITAIKEVGGEAMVMADHGNAekMVEFCNNTERQCYTAHTSN 470
                                   556788888888988888999***************99998877654479**********9866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2835.93
//
Query:       gi|91773855|ref|YP_566547.1|  [L=414]
Description: hypothetical protein Mbur_1915 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-31  108.2   5.8    6.4e-31  108.2   5.8    2.4  2  MacB_PCD   MacB-like periplasmic core domain
    2.8e-13   50.1   6.5    2.8e-13   50.1   6.5    3.1  3  FtsX       FtsX-like permease family


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   5.8   7.1e-35   6.4e-31       1     194 [.      21     245 ..      21     246 .. 0.73
   2 ?   -3.7   7.1       1.5   1.3e+04       5      38 ..     282     315 ..     278     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 7.1e-35
                      MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlg.nlvtvtpgk.........gsges..............lsdpdv 57 
                                   s+lt++Gi+iGva+v++iv+lg+++++sv+s+++d++ +++t+tpg+         g   +              l+d d+
  gi|91773855|ref|YP_566547.1|  21 SWLTIIGIVIGVASVVSIVALGDAMTESVESSFEDMDlTIITITPGYsgaqssmgpG---RgggggtaatidedeLTDKDI 98 
                                   79**********************************823667888877666655551...045556666666666777777 PP

                      MacB_PCD  58 ealrrevp.veavapvv....tvrgggsgeeevtvvgvdpdyfk.vfglklaeGrffteadlrggpnvvvigeelaerlf. 131
                                    alr +++ +e +  ++     v ++g+ + + +v+gvd++  k    ++ ++Gr ++++    +++v+vig+++a++lf 
  gi|91773855|ref|YP_566547.1|  99 MALR-SIEeIEYMYGQIsgkaDVEFTGE-TATLSVTGVDTQVWKyTSEMDYESGRALEPS----DKYVAVIGYNVANELFd 173
                                   7664.34558877777655442222222.34489***9985555334443367***9886....688************** PP

                      MacB_PCD 132 ...pvGdtirl..kpftVvGvledppgsgsalgddavylplttl.......qrrs.....itvrlkdgadleaaaaelek 194
                                       v+++i++  k+++VvG+led  g++    ++av++p+ ++       +        i+++++d + +e+a +e+e+
  gi|91773855|ref|YP_566547.1| 174 qpiGVNRVITIegKSVRVVGILED--GES----NNAVIMPIDAAinviedaE--KdvygsIVIKVEDEEVVESAVEEIER 245
                                   *877******************77..433....789****554433333332..044556******************96 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.5
                      MacB_PCD   5 vLGiaiGvaaviaivslgeglqasvlsqisdlgn 38 
                                    LG + Gv  +++ v++ +++  sv +  ++ g+
  gi|91773855|ref|YP_566547.1| 282 FLGAIAGVSLLVGAVGIANTMFTSVMEKTKEIGT 315
                                   589999***************9999888776653 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.6    0.0026        23      28      69 ..      23      63 ..      19      68 .. 0.70
   2 ?    1.4   0.2     0.052   4.6e+02      23      46 ..     278     301 ..     268     309 .. 0.56
   3 !   50.1   6.5   3.2e-17   2.8e-13       2      96 .]     311     407 ..     310     407 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0026
                          FtsX 28 itlvalviGlglgllaaqllsdvllssvfsselkisidlitv 69
                                  +t++++viG +++++ + +l d + +sv ss  ++ + +it+
  gi|91773855|ref|YP_566547.1| 23 LTIIGIVIG-VASVVSIVALGDAMTESVESSFEDMDLTIITI 63
                                  789999999.66777777778888888887555555555554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.052
                          FtsX  23 teillitlvalviGlglgllaaql 46 
                                   + +++++++a v+ l+ ++ +a+ 
  gi|91773855|ref|YP_566547.1| 278 SMTFFLGAIAGVSLLVGAVGIANT 301
                                   445555555555555545555544 PP

  == domain 3  score: 50.1 bits;  conditional E-value: 3.2e-17
                          FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs..selkisidlitvliiivllllla 80 
                                   +eig+++a+G+k+++++ ++++ ++l+++v+ ++G++lg +++ ++  + + + +   ++ +  ++++ ++++i+l++l+ 
  gi|91773855|ref|YP_566547.1| 311 KEIGTMKAIGAKNGDIMMIFVMNSALVGFVGGFLGIVLGEIVSRIVIPMSGLQIGRtaTSSATGLSPELMILGIGLAMLIG 391
                                   8********************************************99999999886779********************** PP

                          FtsX  81 llagllsiskilkkep 96 
                                   +++g+++++ ++k++p
  gi|91773855|ref|YP_566547.1| 392 VISGVIPAYSASKMKP 407
                                   *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2722.11
//
Query:       gi|91773856|ref|YP_566548.1|  [L=433]
Description: hypothetical protein Mbur_1916 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   44.7   1.5     0.0097   16.1   0.0    4.1  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    3.1e-06   27.4   9.0     0.0086   16.4   0.0    4.8  3  DUF11            Domain of unknown function DUF11
    4.1e-06   27.0  15.7      0.059   13.6   0.1    4.5  4  CARDB            CARDB
     0.0045   16.9   0.9       0.01   15.7   0.2    2.1  2  Gram_pos_anchor  LPXTG cell wall anchor motif
     0.0052   16.8   0.1      0.091   12.8   0.0    2.8  3  DUF2393          Protein of unknown function (DUF2393)
  ------ inclusion threshold ------
      0.011   16.2   0.1         18    5.9   0.0    4.0  4  MG2              MG2 domain
      0.052   13.1   6.9       0.27   10.8   0.3    2.8  2  DUF4998          Domain of unknown function


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00022      0.57       2      29 ..      42      69 ..      41      73 .. 0.92
   2 ?   -3.8   0.0       6.3   1.6e+04      50      60 ..     128     138 ..     122     140 .. 0.66
   3 !   16.1   0.0   3.8e-06    0.0097       9      77 ..     163     233 ..     159     235 .. 0.91
   4 !   14.2   0.1   1.5e-05     0.038       6      64 ..     267     325 ..     262     329 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                   NPCBM_assoc  2 epGetvtltltvtndgtaaatnvslsls 29
                                  +pGet ++tl+v ndg++ +++v ++++
  gi|91773856|ref|YP_566548.1| 42 RPGETMEITLSVRNDGNSDLEDVTVTIK 69
                                  79*********************99876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.3
                   NPCBM_assoc  50 GetveatvkVt 60 
                                   G t ++tv++ 
  gi|91773856|ref|YP_566548.1| 128 GGTITTTVNID 138
                                   66667777664 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 3.8e-06
                   NPCBM_assoc   9 ltltvtndgtaaatnvslslslPeGWt..vvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                   l++ vtn+g+++++n  +s +  +G    v +  ++ +a l++Ge++++  +V +  +a++G y++ + ++
  gi|91773856|ref|YP_566548.1| 163 LEFIVTNTGNSPLKNMVISWDEESGVIlpVYSDNTKYIAYLDAGESATVSYTVMADVNAIPGLYQLDIYLS 233
                                   67889****************999988889999999999**************************988776 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 1.5e-05
                   NPCBM_assoc   6 tvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppag 64 
                                   + ++ l+v+n g+  a +v++s+   +G tv+ +s + +  l+ G+++ + ++V  +a+
  gi|91773856|ref|YP_566548.1| 267 SGEVSLSVANVGNNEAYSVKVSIPEQDGYTVTGSSSTIVGNLEKGDYTITSFNVVQSAN 325
                                   56899*************************************************98887 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.4e-06    0.0086       7      36 ..      38      67 ..      24      72 .. 0.91
   2 !    9.1   0.3    0.0006       1.5      21      84 ..     166     223 ..     149     229 .. 0.79
   3 ?    2.4   1.2     0.078     2e+02      17      77 ..     269     321 ..     260     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-06
                         DUF11  7 ksevrpGdtvtytltvtNtgpasangvvvt 36
                                  + ++rpG+t++ tl v+N g++++++v+vt
  gi|91773856|ref|YP_566548.1| 38 PDPARPGETMEITLSVRNDGNSDLEDVTVT 67
                                  4589************************98 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0006
                         DUF11  21 tvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaas 84 
                                   +vtNtg+++++++v++    +g+ +   s        + ++  L agesat+s+tv + + a  
  gi|91773856|ref|YP_566548.1| 166 IVTNTGNSPLKNMVISWDEESGVILPVYSDN------TKYIAYLDAGESATVSYTVMADVNAIP 223
                                   6899999999999998656677776666666......33447899***********99887765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.078
                         DUF11  17 tytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvr 77 
                                   ++ l v N g++ a+ v+v+ +   g + v++s+s       t vg+Le g  +  sf v 
  gi|91773856|ref|YP_566548.1| 269 EVSLSVANVGNNEAYSVKVSIPEQDGYT-VTGSSS-------TIVGNLEKGDYTITSFNVV 321
                                   6788999999999988888764434444.333333.......3447777777666666654 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   2.3e-05     0.059       8      42 ..      34      68 ..      26     142 .. 0.83
   2 !    9.5   0.3   0.00045       1.1      13      81 ..     153     229 ..     146     246 .. 0.74
   3 !   12.3   1.2     6e-05      0.15      20      72 ..     267     323 ..     250     337 .. 0.84
   4 ?   -1.7   0.2       1.3   3.5e+03      11      50 ..     367     406 ..     356     422 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                  EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEE CS
                         CARDB  8 ntlnpseafvgeentitvtvkNqGtaasgatkval 42
                                   ++np++a +ge+++it++v+N G+ + ++++v++
  gi|91773856|ref|YP_566548.1| 34 LNQNPDPARPGETMEITLSVRNDGNSDLEDVTVTI 68
                                  57899************************999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00045
                                   SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE......EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEE CS
                         CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelv......gtvtvpsLaagesttvsftwtte..ategevtlt 81 
                                   s+    +e  +++ v+N+G+   +++ ++   +  +       +t +++ L+ages+tvs+t+ ++  a +g ++l 
  gi|91773856|ref|YP_566548.1| 153 SNIDIATEEPLEFIVTNTGNSPLKNMVISWDEESGVIlpvysdNTKYIAYLDAGESATVSYTVMADvnAIPGLYQLD 229
                                   5555666677788899999888888777766555555678888999*****************99965555666655 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 6e-05
                                   EEEEEEEEEE-SSS-EEEEEEEEEE.TTEEE...EEEEESEE-CTEEEEEEEEEE-S CS
                         CARDB  20 entitvtvkNqGtaasgatkvalyl.dgelv...gtvtvpsLaagesttvsftwtte 72 
                                   + +++++v+N G+ +++++kv++   dg +v   ++++v +L+ g++t  sf+++ +
  gi|91773856|ref|YP_566548.1| 267 SGEVSLSVANVGNNEAYSVKVSIPEqDGYTVtgsSSTIVGNLEKGDYTITSFNVVQS 323
                                   568999****************97526677799999999***********9998765 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.3
                                   C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEE CS
                         CARDB  11 npseafvgeentitvtvkNqGtaasgatkvalyldgelvg 50 
                                   + + ++v++++ i++t   +G+ +    k +   +g++++
  gi|91773856|ref|YP_566548.1| 367 TGQRLSVEKNVDISFTSGATGENDVAYAKNRNASSGTSTT 406
                                   5566666666666666666666666666666666666644 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         4     1e+04      13      24 ..     206     217 ..     205     217 .. 0.88
   2 !   15.7   0.2   4.1e-06      0.01      13      42 ..     402     430 ..     400     431 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4
                                   XXXXXXXXXXXX CS
               Gram_pos_anchor  13 GengnifltaaG 24 
                                   Ge+++ ++t+++
  gi|91773856|ref|YP_566548.1| 206 GESATVSYTVMA 217
                                   999999999986 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.1e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Gram_pos_anchor  13 GengnifltaaGllallggllLlvkrRKke 42 
                                   G++ +++l++++ ++++g++++++kr+ ke
  gi|91773856|ref|YP_566548.1| 402 GTSTTTYLLILA-AIVAGAAVVYKKRKDKE 430
                                   755666666666.67777777777777665 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.5e-05     0.091      21      87 ..       5      71 ..       1     102 [. 0.73
   2 ?   -0.1   0.0      0.32   8.2e+02      65      83 ..     163     181 ..     142     184 .. 0.75
   3 ?   -1.7   0.0      0.99   2.5e+03     109     131 ..     243     265 ..     239     291 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                       DUF2393 21 liflsllilflapfvvhliidkylkkaeltilsqkrllyteafvvdgtitNeGkftikeCkleiklv 87
                                  ++++ +++++++++ + + +d  + + +  +    +    e++ ++++++N+G+ ++  ++++ik  
  gi|91773856|ref|YP_566548.1|  5 ILLILFVCITAGSASAAVYVDSSMITVDMLNQNPDPARPGETMEITLSVRNDGNSDLEDVTVTIKPE 71
                                  3344455555556666666677766888888888889999************************964 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                       DUF2393  65 vdgtitNeGkftikeCkle 83 
                                   +++ +tN+G+ ++k+ +++
  gi|91773856|ref|YP_566548.1| 163 LEFIVTNTGNSPLKNMVIS 181
                                   6789********9998875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.99
                       DUF2393 109 sevikedlkpgeskeFrviidyf 131
                                   +++ k++l  g +++F v++ + 
  gi|91773856|ref|YP_566548.1| 243 EITTKAGLFVGGETDFDVSFSES 265
                                   56667777777777777766543 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.018        45      12      49 ..      42      79 ..      41     137 .. 0.87
   2 ?   -2.2   0.0       2.2   5.7e+03      34      53 ..     116     135 ..      85     154 .. 0.66
   3 ?   -0.3   0.0      0.58   1.5e+03      25      60 ..     152     187 ..     140     192 .. 0.83
   4 ?    5.9   0.0     0.007        18      16      87 ..     210     281 ..     201     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                                  -TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEE CS
                           MG2 12 rPgetVslkallrdetlqglaklplkltirdpdgkevk 49
                                  rPget +++  +r++  + l++  ++++ + p +k++ 
  gi|91773856|ref|YP_566548.1| 42 RPGETMEITLSVRNDGNSDLEDVTVTIKPEYPFSKVTG 79
                                  9**************99999998888887777777665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                                   EEEEEEEE-TTSSEEEEEEE CS
                           MG2  34 lplkltirdpdgkevkelpl 53 
                                   ++l ++++d++++ + ++++
  gi|91773856|ref|YP_566548.1| 116 YELDIVVTDSENGGTITTTV 135
                                   55555666655554444444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.58
                                   STTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTE CS
                           MG2  25 detlqglaklplkltirdpdgkevkelplatdetgg 60 
                                   +++   +++ pl++ ++++++   k++ + +de++g
  gi|91773856|ref|YP_566548.1| 152 KSNIDIATEEPLEFIVTNTGNSPLKNMVISWDEESG 187
                                   4677778889****************9999998765 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.007
                                   EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--.TT--SEEEEEEEEECSTTT CS
                           MG2  16 tVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalp.eaaklGeysvelsadsaee 87 
                                   tVs+++++ +++  gl +l + l+++d d+++ + ++ ++  + g e++f+++ +++  Ge s+++ + +++e
  gi|91773856|ref|YP_566548.1| 210 TVSYTVMADVNAIPGLYQLDIYLSFEDYDSNTNEITT-KAGLFVGGETDFDVSfSESASGEVSLSVANVGNNE 281
                                   7999999999999999999999999999988766555.66667777777777645666788777773333333 PP

>> DUF4998  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00011      0.27      79     121 ..     109     151 ..      76     231 .. 0.78
   2 ?    4.1   2.3     0.012        30      55     147 ..     279     374 ..     194     409 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                       DUF4998  79 dnLeEgsytFsivtydkkgnsSlksevtgevYGdsYqasltnr 121
                                   ++ +E  y+++iv +d+++   + ++v  +v G++Y++ +t  
  gi|91773856|ref|YP_566548.1| 109 NDAPEDLYELDIVVTDSENGGTITTTVNIDVRGKEYAQIVTIT 151
                                   3479********************************9976533 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                       DUF4998  55 nnkkdsvevpverke...gvdtveviidnLeEgsytFsivtydkkgnsSlksevtgevYGdsYqasltnrslksvelekke 132
                                   nn++ sv+v + +++    + + ++i+ nLe g yt+  +++ ++ n  + ++   e  G+  ++    rs ++++ ++ +
  gi|91773856|ref|YP_566548.1| 279 NNEAYSVKVSIPEQDgytVTGSSSTIVGNLEKGDYTITSFNVVQSANVAIDENSDDEKTGTG-ENIPAGRSASRSSGNELT 358
                                   566689999998888433467789************99999988888888877776666654.444456666666666666 PP

                       DUF4998 133 ltinwskveqea.lvk 147
                                   + i++ +++ +   v+
  gi|91773856|ref|YP_566548.1| 359 TIIEYTDSTGQRlSVE 374
                                   6666666666664444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2841.10
//
Query:       gi|91773857|ref|YP_566549.1|  [L=286]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-31  108.4   0.1    8.1e-31  107.4   0.0    1.6  1  ABC_tran     ABC transporter
    1.2e-09   37.9   0.1    3.4e-08   33.2   0.1    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.6e-06   28.2   0.6      0.012   15.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00015   21.4   0.0     0.0003   20.5   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00082   19.9   1.2     0.0018   18.8   0.0    2.1  2  AAA_23       AAA domain
     0.0015   18.5   0.0     0.0024   17.8   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0093   16.0   0.2      0.042   13.9   0.0    2.1  3  AAA_14       AAA domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.029   14.8   0.0    1.6  1  AAA_16       AAA ATPase domain
      0.034   13.9   0.0       0.16   11.7   0.0    1.9  2  AAA_30       AAA domain
      0.045   12.4   0.1       0.86    8.2   0.0    2.1  2  AAA_13       AAA domain
      0.047   14.2   0.0        0.9   10.1   0.0    2.3  2  AAA_18       AAA domain
      0.048   13.6   0.2        0.3   11.0   0.2    2.2  1  ATPase_2     ATPase domain predominantly from Archaea
      0.056   13.7   0.0       0.16   12.2   0.0    1.7  2  AAA_22       AAA domain
       0.06   13.3   0.1        0.2   11.6   0.1    1.9  1  TTRAP        Putative tranposon-transfer assisting protein
      0.064   13.2   0.5         12    5.7   0.1    2.3  2  NTPase_1     NTPase
       0.13   12.3   0.6       0.37   10.9   0.6    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
       0.14   11.9   0.0        1.7    8.4   0.0    2.1  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 !  107.4   0.0   7.6e-34   8.1e-31       1     136 [.      77     225 ..      77     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 7.6e-34
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                   lknv+l+++ ge v+i+G++G+GKSt+++l+  l  p +G i+ld++d+++    +  ++  ++ig+++q+ +l p+l+  
  gi|91773857|ref|YP_566549.1|  77 LKNVDLDIYSGEFVVILGPSGSGKSTMMNLIGCLDVPSKGIIRLDNQDISTlkesNLAQIRGQSIGFIFQQFNLIPTLNSL 157
                                   79*************************************************9996667778899***************99 PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   en              ++++ +++l+ +gl ++ ++      s+LSgGq+qrva+ar+l+ +p+++l+DEpt
  gi|91773857|ref|YP_566549.1| 158 ENvmlplefqevdpdIAKKRGKELLEIVGLGDKLTNLP----SQLSGGQRQRVAIARSLAIDPPIILADEPT 225
                                   99*****9999888878888889999999888666665....*****************************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 !   33.2   0.1   3.2e-11   3.4e-08      23     213 ..      86     272 ..      71     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.2e-11
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                   s +f +i+Gp GSGKs +++ i  +L   s+  +r ++ +d+ +  +++ a++   ++  +f++ +   ++ ++  +++  
  gi|91773857|ref|YP_566549.1|  86 SGEFVVILGPSGSGKSTMMNLI-GCLDVPSKGIIRLDN-QDISTLkESNLAQIRGQSIGFIFQQFNLI-PTLNSLENVMLP 163
                                   56799***************99.899987765566554.44433325677888888999999999887.555554555555 PP

                                   EETTSEEEEEETTEEE-H.HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 103 vkrkgeseykingkevtk.kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                   ++ ++  +  i +k+ ++  e+  l  +    +++LSgG+++ va+a  +Ai      p+ l De   +LD k  + + e+
  gi|91773857|ref|YP_566549.1| 164 LEFQEV-DPDIAKKRGKElLEIVGLGDKLTNLPSQLSGGQRQRVAIARSLAID----PPIILADEPTGNLDSKTGTYILEF 239
                                   554444.456766666665899999999999999*****************96....5*********************** PP

                                   HH..HHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                   xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 183 lk..eksknaQfivislreemlekadklvgvtk 213
                                   l+  ++++n  +i++++++e ++ adk+v ++ 
  gi|91773857|ref|YP_566549.1| 240 LNemHQKENKTIIIVTHDTEPVQYADKIVYIRD 272
                                   *9444566799****************998865 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00031      0.33       1      25 [.      89     112 ..      89     152 .. 0.66
   2 !   15.4   0.0   1.2e-05     0.012     234     299 ..     195     258 ..     163     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarl 25 
                                   + v+ Gp gsGKS+ + ++ +l ++
  gi|91773857|ref|YP_566549.1|  89 FVVILGPSGSGKSTMMNLIGCL-DV 112
                                   689*************999888.33 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.2e-05
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                   +++lS G+++  a++ +l+ ++   +++l DEp  +L+ k  + +le+l+e ++ ++  +i++TH++
  gi|91773857|ref|YP_566549.1| 195 PSQLSGGQRQRVAIARSLAIDP---PIILADEPTGNLDSKTGTYILEFLNEMHQkENKTIIIVTHDT 258
                                   568899**99999999999999...************************888887**********96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.9e-07    0.0003      14      46 ..      76     111 ..      63     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.9e-07
                        AAA_29  14 g.htieidlkg..atlltGpsGsGKSTllDAiqalL 46 
                                     + +++d  +  ++++ GpsGsGKST++  i  l 
  gi|91773857|ref|YP_566549.1|  76 AlKNVDLDIYSgeFVVILGPSGSGKSTMMNLIGCLD 111
                                   444444443322699*************97665555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-06    0.0018       8      39 ..      65     107 ..      57     109 .. 0.78
   2 ?   -0.9   0.4       1.9     2e+03     102     102 ..     175     175 ..     121     283 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                        AAA_23   8 rsfrdqeidF...........skgltlItGpNGaGKTTildAi 39 
                                   + ++  ei+F           s  +++I Gp G+GK+T ++ i
  gi|91773857|ref|YP_566549.1|  65 KTYQMGEIEFdalknvdldiySGEFVVILGPSGSGKSTMMNLI 107
                                   556666777777777777778889***************9987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                        AAA_23 102 k 102
                                   k
  gi|91773857|ref|YP_566549.1| 175 K 175
                                   1 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06    0.0024      97     119 ..      85     107 ..      33     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                   CTTSEEEEECSTTSSHHHHHHHH CS
                   RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinal 119
                                    +++++v++G+SG GKSt++n +
  gi|91773857|ref|YP_566549.1|  85 YSGEFVVILGPSGSGKSTMMNLI 107
                                   45699****************87 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     4e-05     0.042       3      50 ..      88     134 ..      86     153 .. 0.81
   2 ?   -3.2   0.0       7.7   8.2e+03     121     130 ..     160     169 ..     155     169 .. 0.82
   3 ?   -1.6   0.1       2.4   2.6e+03      21      43 ..     238     261 ..     231     282 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50 
                                   + +vi G+  +GK+t+++ +   l v+++ i+ ++ +d ++ k+++ +
  gi|91773857|ref|YP_566549.1|  88 EFVVILGPSGSGKSTMMNLIG-CLDVPSKGIIRLDNQDISTLKESNLA 134
                                   689*************96665.5558********99999998877654 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.7
                        AAA_14 121 elyplsfaEf 130
                                    + pl+f+E+
  gi|91773857|ref|YP_566549.1| 160 VMLPLEFQEV 169
                                   699****995 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                        AAA_14  21 qlikell.vkkesilyinldderd 43 
                                   ++++e    +++ i+ ++ d+e+ 
  gi|91773857|ref|YP_566549.1| 238 EFLNEMHqKENKTIIIVTHDTEPV 261
                                   343333334455666666666555 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   2.7e-05     0.029      23      44 ..      86     107 ..      68     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                        AAA_16  23 rpelvllsGesGvGKsslvrel 44 
                                   ++e v++ G+sG+GKs++++ +
  gi|91773857|ref|YP_566549.1|  86 SGEFVVILGPSGSGKSTMMNLI 107
                                   4589*************99876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.16      17      38 ..      87     107 ..      80     112 .. 0.86
   2 ?   -0.9   0.0       1.1   1.2e+03      32      55 ..     234     257 ..     232     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                        AAA_30  17 gdrvavltGpAGtGKttalkal 38 
                                   g  ++v+ Gp G+GK+t+++ +
  gi|91773857|ref|YP_566549.1|  87 G-EFVVILGPSGSGKSTMMNLI 107
                                   4.3899*************876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                        AAA_30  32 ttalkalreaweaaggrviglApt 55 
                                   t++l+ l+e+++++++++i++++ 
  gi|91773857|ref|YP_566549.1| 234 TYILEFLNEMHQKENKTIIIVTHD 257
                                   889999999999999999998876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.053        56      20      40 ..      91     111 ..      82     149 .. 0.85
   2 ?    8.2   0.0   0.00081      0.86     526     578 ..     215     265 ..     206     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.053
                        AAA_13  20 liYGwNGaGKTtLSrllrsle 40 
                                   +i G  G+GK+t+ +l+ +l 
  gi|91773857|ref|YP_566549.1|  91 VILGPSGSGKSTMMNLIGCLD 111
                                   7999************99984 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00081
                        AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                      i+  D P   LDs+   ++  ++++    +k+ k ++i TH +e  ++++
  gi|91773857|ref|YP_566549.1| 215 DPPIILADEPTGNLDSKTGTYILEFLNEMH--QKENKTIIIVTHDTEPVQYAD 265
                                   5689**********************9997..8999********998666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00086       0.9       1      18 [.      90     107 ..      90     152 .. 0.84
   2 ?    1.6   0.0      0.35   3.7e+02      59      93 ..     235     267 ..     211     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00086
                        AAA_18   1 IlltGtpGvGKttlakeL 18 
                                   +++ G++G+GK+t+ + +
  gi|91773857|ref|YP_566549.1|  90 VVILGPSGSGKSTMMNLI 107
                                   789**********98776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.35
                        AAA_18  59 klldaleenssaleegknlvidghlaeleseaakd 93 
                                   ++l+ l+e   ++ e+k+++i  h  e++++a+k+
  gi|91773857|ref|YP_566549.1| 235 YILEFLNEM--HQKENKTIIIVTHDTEPVQYADKI 267
                                   455555555..45899************9999886 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 ?   11.0   0.2   0.00028       0.3      20      40 ..      87     107 ..      71     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                      ATPase_2  20 neiyfiYGpegsGKtaLlkei 40 
                                    e+++i Gp gsGK+++++ i
  gi|91773857|ref|YP_566549.1|  87 GEFVVILGPSGSGKSTMMNLI 107
                                   5799************99854 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.16       5      24 ..      87     106 ..      83     125 .. 0.90
   2 ?   -2.4   0.0       5.1   5.4e+03      93     104 ..     217     229 ..     180     259 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                        AAA_22   5 agilvvtGesGtGKTtllrr 24 
                                     ++v+ G+sG+GK+t ++ 
  gi|91773857|ref|YP_566549.1|  87 GEFVVILGPSGSGKSTMMNL 106
                                   6799************9975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                        AAA_22  93 elliiDEaqh.lr 104
                                   ++++ DE    l+
  gi|91773857|ref|YP_566549.1| 217 PIILADEPTGnLD 229
                                   4455554333343 PP

>> TTRAP  Putative tranposon-transfer assisting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00019       0.2      11      59 ..      28      78 ..      26      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                  HH--.SHHHHHHHHHHHS.TTTS.-HHHHHHHHHHHHHHTT--HHHHHHHS CS
                         TTRAP 11 iyne.gtRkelieelkaa.lkyleddelreLaestlaKLkaltDaefaele 59
                                  +++e + R e+ie+++ + +  +++d+   +  s + K  ++ + ef++l+
  gi|91773857|ref|YP_566549.1| 28 CFHEnKKRDETIENMNGTeRVEMQEDNTPLIKLSNVWKTYQMGEIEFDALK 78
                                  56663799**********888997777777778889***********9985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.012        13       2      19 ..      90     107 ..      89     119 .. 0.83
   2 ?    5.7   0.1     0.012        12      98     161 ..     218     284 ..     201     286 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                                   EEEE--TTSSHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkv 19 
                                   v+i Gp+G+GK+T+++ +
  gi|91773857|ref|YP_566549.1|  90 VVILGPSGSGKSTMMNLI 107
                                   6899**********9866 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                                   EEEE--.-STTGGG-HHHH.HHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TTTTT CS
                      NTPase_1  98 viviDE.iGkmElkskkfk.eaveevLk.sekpvlavihrrkdlalveeirerkdvkvfevteenrd 161
                                   +i+ DE  G++  k+ +++ e ++e+ + ++k +++v h +++ +  ++i   +d+++ ++  +n++
  gi|91773857|ref|YP_566549.1| 218 IILADEpTGNLDSKTGTYIlEFLNEMHQkENKTIIIVTHDTEPVQYADKIVYIRDGQIEKIEYKNKM 284
                                   5666665577776665554156667766799999***************************999986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00035      0.37       2      19 ..      90     107 ..      89     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                   EEEEESTTSSHHHHHHHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinal 19 
                                   v+i+G + +GKSt++n +
  gi|91773857|ref|YP_566549.1|  90 VVILGPSGSGKSTMMNLI 107
                                   89**************87 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    0.0016       1.7      44      68 ..      84     108 ..      64     117 .. 0.81
   2 ?    1.2   0.0      0.26   2.7e+02     112     155 ..     218     264 ..     189     269 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                     IstB_IS21  44 iekkenivllGpsGvGKshlaialg 68 
                                   i + e +v+lGpsG GKs +   +g
  gi|91773857|ref|YP_566549.1|  84 IYSGEFVVILGPSGSGKSTMMNLIG 108
                                   5567889***********8876655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.26
                     IstB_IS21 112 lilDdlgllpldqaeaellfeviekryerrs...iiitsnlpfaewd 155
                                   +il d  + +ld++  ++++e +++  +++    ii+t + +  ++ 
  gi|91773857|ref|YP_566549.1| 218 IILADEPTGNLDSKTGTYILEFLNEMHQKENktiIIVTHDTEPVQYA 264
                                   778888889999**********9988765422226677777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 1553.11
//
Query:       gi|91773858|ref|YP_566550.1|  [L=263]
Description: hypothetical protein Mbur_1918 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   28.1   0.0    1.6e-06   27.5   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00011   22.0   0.0    0.00021   21.1   0.0    1.4  1  MarR             MarR family
     0.0002   21.2   0.0    0.00035   20.4   0.0    1.4  1  MarR_2           MarR family
    0.00026   20.8   0.0    0.00056   19.8   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00029   20.9   0.0    0.00085   19.5   0.0    1.7  1  HTH_34           Winged helix DNA-binding domain
     0.0021   18.3   0.0     0.0039   17.4   0.0    1.5  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0024   16.7   0.3     0.0033   16.3   0.3    1.1  1  REJ              REJ domain
     0.0043   16.5   1.8     0.0066   15.9   1.8    1.4  1  DUF5305          Family of unknown function (DUF5305)
     0.0049   17.2   0.0     0.0092   16.3   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
     0.0055   17.2   0.1      0.011   16.2   0.1    1.5  1  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.046   13.7   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.037   13.9   0.0      0.063   13.2   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
      0.058   13.2   0.0      0.093   12.6   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
      0.058   13.4   0.1       0.12   12.4   0.1    1.6  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
      0.073   12.5   0.0       0.13   11.6   0.0    1.4  1  GpcrRhopsn4      Rhodopsin-like GPCR transmembrane domain
      0.083   12.1   0.0       0.11   11.7   0.0    1.1  1  Zip              ZIP Zinc transporter
       0.16   12.0   0.2       0.27   11.3   0.2    1.3  1  FeoC             FeoC like transcriptional regulator


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 !   27.5   0.0   1.5e-09   1.6e-06       7      47 ..     202     243 ..     200     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.5e-09
                        HTH_24   7 kILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                   kI + Lq  + r++q++L  +++ S + v+  l+ Le++G++
  gi|91773858|ref|YP_566550.1| 202 KIVKMLQSnDDRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWV 243
                                   899*****7778****************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     2e-07   0.00021      16      51 ..     212     247 ..     202     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                                   TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                   + +++++L +k+  s + v+ +l  LekkG+++++k
  gi|91773858|ref|YP_566550.1| 212 DRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDKRK 247
                                   45******************************9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.3e-07   0.00035      16      56 ..     209     248 ..     202     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.3e-07
                                   CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                    +++r +t+++l  + ++s + vs +l++L+++G+v +r+ 
  gi|91773858|ref|YP_566550.1| 209 SNDDR-MTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDKRKE 248
                                   56665.9*****************************99964 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.3e-07   0.00056      20      58 ..     211     249 ..     200     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.3e-07
                                   HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                    +++t +++ ++++ ++ kv  +L+ Le+kG+V+++k+ 
  gi|91773858|ref|YP_566550.1| 211 DDRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDKRKEG 249
                                   568999*****************************9975 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.1e-07   0.00085       5      52 ..     203     251 ..     201     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.1e-07
                        HTH_34   5 vlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkg 52 
                                   ++ +L s +d+++ ++l++++  ++g+ s  l+ Lek+g++  +ke +g
  gi|91773858|ref|YP_566550.1| 203 IVKMLQSnDDRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDKRKEGRG 251
                                   78899997899******************************99998665 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.7e-06    0.0039       1      74 [.      27      97 ..      27     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
               CarboxypepD_reg  1 tisGrVtd.asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatreevtltagqt 74
                                  ti+G V    + +p  +a +++     +t ++    + G ++l+ lppg+y++t+ s++  +   ++ev lt  ++
  gi|91773858|ref|YP_566550.1| 27 TIHGVVYEwDTFEPTDNAYIEIN----TTPTQSIVPQYGIYSLE-LPPGNYQITAtSYKENKLEYSTEVPLTITDN 97
                                  7999999956899**********....788999999*******7.**********644444444445555554433 PP

>> REJ  REJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   3.2e-06    0.0033      11      79 ..      29      95 ..      22     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.2e-06
                           REJ 11 ekllynWtvfeltsgngnqentrklnttepqltippsfLpygtyvflltvslsgepsleatdiikvrve 79
                                  + + y+W +fe t++   ++nt++ +   pq+ i +  Lp g+y+++  ++  +e++le ++ + +++ 
  gi|91773858|ref|YP_566550.1| 29 HGVVYEWDTFEPTDNAYIEINTTPTQSIVPQYGIYSLELPPGNYQIT--ATSYKENKLEYSTEVPLTIT 95
                                  7789****************************************996..55666667787777777765 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.8   6.2e-06    0.0066      68     148 ..      80     159 ..      39     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.2e-06
                       DUF5305  68 esieesktsrlpipl.teqtyeikkdetdeengeitetvtvkespslaegilliilgllaliglvvlirriiftsskaeky 147
                                   ++++ ++++++p+++ +++ty i+  +     ++i e+ +++++p++  g + i+++ll +i+l+v+i   i +++k++k+
  gi|91773858|ref|YP_566550.1|  80 KENKLEYSTEVPLTItDNGTYVIDL-LLMPVYSDIVESDENEKHPTTQAGTISIVFYLLLAIILMVAIEK-ITSNTKKDKK 158
                                   5667778999999997778888886.5559999**************99888888888888888888766.6666665554 PP

                       DUF5305 148 e 148
                                   +
  gi|91773858|ref|YP_566550.1| 159 R 159
                                   4 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.8e-06    0.0092      23      60 ..     215     252 ..     198     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-06
                                   HHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
               Penicillinase_R  23 vveeleeekelaysTVktllrrLvkKgllsrekegraf 60 
                                    ++ l ++ + ++  V  +l+ L+kKg+++++kegr  
  gi|91773858|ref|YP_566550.1| 215 TQKDLRSKIDYSEGKVSMMLNDLEKKGWVDKRKEGRGN 252
                                   456677778888999********************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 !   16.2   0.1   1.1e-05     0.011      14      58 ..     209     250 ..     202     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                        HTH_27  14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58 
                                    +++r++++dl+ + +++   +s +l+ L++kG+v +    +++r
  gi|91773858|ref|YP_566550.1| 209 SNDDRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDKR---KEGR 250
                                   5799*******************************333...3344 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 ?   13.7   0.0   4.3e-05     0.046      21      60 ..     213     257 ..     200     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE..EEES CS
                     HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.r..grr..iril 60 
                                   ++tq++l s +  +   vs +l++L+++g+++ r  gr+  i ++
  gi|91773858|ref|YP_566550.1| 213 RMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDkRkeGRGniIFLK 257
                                   799999999999999*****************7433354644455 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     6e-05     0.063       6      47 .]     202     245 ..     201     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6e-05
                                   HHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   6 kILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                   kI+k+L++    ++  +l  +++ s+++vS+ L+ L++ G V+k
  gi|91773858|ref|YP_566550.1| 202 KIVKMLQSndDRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDK 245
                                   79******8666***************************98875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.8e-05     0.093       8      50 ..     203     245 ..     202     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.8e-05
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                   i ++l + + ++t ++l  +++ +  +v+ +L+ L++ G+v +
  gi|91773858|ref|YP_566550.1| 203 IVKMLQSNDDRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDK 245
                                   67889999*********************************86 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 ?   12.4   0.1   0.00012      0.12       1      59 [.      28      83 ..      28     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
               CarbopepD_reg_2  1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqe 59
                                  i+G V++ +t ep   a + ++ t ++ +  + G ++l+ lp+g+y+++++  +yk+ +
  gi|91773858|ref|YP_566550.1| 28 IHGVVYEWDTFEPTDNAYIEINTTPTQSIVPQYGIYSLE-LPPGNYQITAT--SYKENK 83
                                  78************************************6.9*****77654..555543 PP

>> GpcrRhopsn4  Rhodopsin-like GPCR transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.13     147     208 ..     101     161 ..      78     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                   GpcrRhopsn4 147 vlqvilvileekfefdsaskihsyeslaGylllalrivlaiyFlyglrntikkekskkkkqF 208
                                   v++++l+ +++  +++s ++     + aG++ ++ +++lai +++++ ++   +k+ kk+ +
  gi|91773858|ref|YP_566550.1| 101 VIDLLLMPVYSD-IVESDENEKHPTTQAGTISIVFYLLLAIILMVAIEKITSNTKKDKKRHY 161
                                   555666666455.77777777778899**********************7655555555554 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.11      60     128 ..     109     181 ..     103     236 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                           Zip  60 alealeesqleeehth.....plagllvllGflllllveklltmivekksshkektpkkasssssesaakksvs 128
                                   ++  + es+++e+h+      ++  +++ll+++l+  +ek++++ ++  ++++ ++p+ + +++s+++ +++v+
  gi|91773858|ref|YP_566550.1| 109 VYSDIVESDENEKHPTtqagtISIVFYLLLAIILMVAIEKITSNTKKD-KKRHYIEPEIEITEYSAPEHVEEVP 181
                                   444444555554444455788***********************9988.6666666666666666555555443 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00026      0.27      11      50 ..     210     249 ..     200     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                          FeoC  11 ergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50 
                                   +  r   k+L  + + s+  +  mL+ +++kG v k++++
  gi|91773858|ref|YP_566550.1| 210 NDDRMTQKDLRSKIDYSEGKVSMMLNDLEKKGWVDKRKEG 249
                                   45688889999*************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1404  (0.0783089); expected 358.6 (0.02)
Passed bias filter:                      959  (0.0534888); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1706.90
//
Query:       gi|91773859|ref|YP_566551.1|  [L=307]
Description: hypothetical protein Mbur_1919 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.6   1.3       0.14   12.5   0.0    3.4  3  DUF4969   Domain of unknown function (DUF4969)
     0.0061   16.6   3.2      0.037   14.1   0.5    2.2  2  YqeY      Yqey-like protein


Domain annotation for each model (and alignments):
>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   1.5e-05      0.14       3      30 ..       2      29 ..       1      54 [. 0.81
   2 ?    1.5   0.1     0.044   3.9e+02      25      40 ..     132     147 ..     124     155 .. 0.84
   3 ?    1.0   0.1     0.059   5.3e+02      39      62 ..     202     226 ..     177     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                       DUF4969  3 kRgllLvsvLvlFillavaCsdsednee 30
                                  k+ l ++ +L+ Fill+  C+d +dn +
  gi|91773859|ref|YP_566551.1|  2 KKVLGITLALLTFILLTSGCADRQDNLQ 29
                                  66778899**************999953 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.044
                       DUF4969  25 sedneesveiilkeie 40 
                                   s++ne+s  i++++ e
  gi|91773859|ref|YP_566551.1| 132 SQNNENSQTISTEQRE 147
                                   78**********9977 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.059
                       DUF4969  39 ielsvddpi.klvdengeatvevdv 62 
                                   + lsv++ +  ++den++   + ++
  gi|91773859|ref|YP_566551.1| 202 MTLSVQNAVvTIMDENNDKIFSIEG 226
                                   4566766651567899887766665 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.011     1e+02      41      67 ..      67      93 ..      59     111 .. 0.76
   2 !   14.1   0.5   4.1e-06     0.037      36      97 ..     113     173 ..     105     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.011
                                  --HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YqeY 41 lsdeevlkvlakevkqRresieefeka 67
                                  ++d+++++++++ + + + ++  fe+ 
  gi|91773859|ref|YP_566551.1| 67 VDDQDIVNIIDRDIERSEGALYYFETE 93
                                  79************9999998888764 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.1e-06
                                   HTTSS--HHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHGGGS-----HHHHH CS
                          YqeY  36 derkelsdeevlkvlakevkqRresieefekagRedlaekekaEievleeYlPeqlseeeie 97 
                                   + rk+l+++++ k l+ e+ q +e  ++ ++ +Re l ++  +E+++++e lP+  ++++i 
  gi|91773859|ref|YP_566551.1| 113 EFRKHLENAKMHKALSDELSQNNENSQTISTEQREYLFNAI-KELRIIHELLPQIFNDKQIM 173
                                   45779******************************999876.79***********9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2154.18
//
Query:       gi|91773860|ref|YP_566552.1|  [L=255]
Description: hypothetical protein Mbur_1920 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0039   16.7   1.0      0.006   16.1   1.0    1.3  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 !   16.1   1.0   3.3e-07     0.006     112     173 ..     157     224 ..     149     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-07
                       DUF2031 112 klinelrkeleev...kkeldnkrnseLaiqpiedkritkkdenssvSeeedfkqLeneenvle...e 173
                                   +li+ + k +e +   k +ld++ n+e++ + i++++++ +d ++ +S  ed +++++  + l+   e
  gi|91773860|ref|YP_566552.1| 157 RLITSFDKRIERLeilKENLDEIGNDEITGELIDEHIVQLEDAKELISSAEDNEEINEVMESLSpifE 224
                                   6777777766544333999************************************9998877775542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1780.96
//
Query:       gi|91773861|ref|YP_566553.1|  [L=851]
Description: Toll-interleukin receptor [Methanococcoides burtonii DSM 6242]
Scores for complete 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-13   49.4   0.0    5.2e-12   46.4   0.0    2.5  2  TIR_2            TIR domain
    2.8e-07   30.5   0.7    3.8e-06   26.8   0.1    2.6  2  TIR              TIR domain
    6.6e-06   26.2   1.4    6.6e-06   26.2   1.4    3.6  4  ATPase_2         ATPase domain predominantly from Archaea
    0.00022   21.2   0.3    0.00022   21.2   0.3    3.7  3  AAA_14           AAA domain
    0.00031   21.2   0.6     0.0044   17.4   0.0    3.0  3  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
       0.01   15.8   0.3       0.03   14.2   0.0    2.0  2  NTPase_1         NTPase
      0.013   15.0   0.1      0.034   13.7   0.1    1.7  1  AAA_7            P-loop containing dynein motor region
      0.013   15.8   0.1      0.071   13.4   0.1    2.2  1  AAA_22           AAA domain
      0.016   14.9   0.2      0.073   12.7   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
      0.032   14.4   0.4       0.12   12.6   0.1    2.3  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.041   13.1   0.1      0.041   13.1   0.1    2.2  3  NB-ARC           NB-ARC domain
      0.063   13.8   5.5      0.078   13.5   0.1    3.4  4  AAA_18           AAA domain
       0.11   11.7   0.0        4.5    6.5   0.0    2.5  2  Zeta_toxin       Zeta toxin
       0.13   12.6   0.1       0.13   12.6   0.1    3.1  4  RNA_helicase     RNA helicase


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 !   46.4   0.0   4.1e-15   5.2e-12       1      92 [.       9     103 ..       9     138 .. 0.84
   2 ?   -1.1   0.0       2.2   2.8e+03      18      65 ..     240     259 ..     223     310 .. 0.51

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4.1e-15
                         TIR_2   1 VFiSyssedkewaeklaea...Leaag.irvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreeleaale 77 
                                   VFiSys++d++ +  ++++   L+ +  i+ w+dr +++pged++++i+  ++++d++ +++s ++l+s++c++e + a+e
  gi|91773861|ref|YP_566553.1|   9 VFISYSHQDEHHINLFKTHispLKTNDlIEEWYDR-EIVPGEDFQNQIDCNLDNADIICLFISAHFLASKSCMAEKKKAME 88 
                                   9********98777777662225555547789999.8*******************************************9 PP

                         TIR_2  78 aaeegkkrlipvlle 92 
                                   ++ +++  ++p++l 
  gi|91773861|ref|YP_566553.1|  89 LKDNNGISVVPIILS 103
                                   87777788****998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                         TIR_2  18 eaLeaagir.vwldrwdlkpgedweeeieeaiessdvvlvvlspayles 65 
                                   ++L+++++  v++++ ++                             +s
  gi|91773861|ref|YP_566553.1| 240 SDLRSKNYVpVYVSEDKI-----------------------------SS 259
                                   344333333223333222.............................22 PP

>> TIR  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1     3e-09   3.8e-06      30      99 ..      35     102 ..       8     106 .. 0.79
   2 ?    0.8   0.1      0.29   3.7e+02      65     106 ..     519     558 ..     517     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3e-09
                                   TTSEEEESSTT--SSS-HHHHHHHHHHCSSEEEEEE-TTHHHHCCCCHHHHHHHCHHH-CTSTCEEEEEC CS
                           TIR  30 kgiklfiddrdlepGeaiadelksaIkkSrrlivvlSknyasskwcleElekilecalvekgqkvilify 99 
                                     i+    dr+++pGe+  ++++ +  +  ++   +S +++ sk c+ E +k++e+++ ++g+ v++i +
  gi|91773861|ref|YP_566553.1|  35 DLIEEWY-DREIVPGEDFQNQIDCNLDNADIICLFISAHFLASKSCMAEKKKAMELKD-NNGISVVPIIL 102
                                   4444455.5*************************************************.*********87 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.29
                                   E-TTHHHHCCCCHHHHHHHCHHH-CTSTCEEEEECSS-HCCC CS
                           TIR  65 lSknyasskwcleElekilecalvekgqkvilifyevdpedv 106
                                   lS n+ +sk +++E   i+++ +v+ + + i if++  ++++
  gi|91773861|ref|YP_566553.1| 519 LSDNMENSK-VIDEITNIIDNLHVD-ENAYIAIFLTHHSKNS 558
                                   788888888.**********99955.5566788887776655 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 ?   -2.5   0.1         3   3.9e+03      97     128 ..     157     188 ..     117     195 .. 0.67
   2 !   26.2   1.4   5.2e-09   6.6e-06      23     152 ..     221     342 ..     217     376 .. 0.75
   3 ?    0.4   1.2       0.4   5.1e+02      65     169 ..     523     556 ..     491     627 .. 0.60
   4 ?   -0.3   0.1      0.67   8.5e+02     126     159 ..     668     701 ..     608     706 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3
                      ATPase_2  97 eksklvfkaielllekikkkgkkiiiiiDelq 128
                                     +k+ ++ i+++    k   +k  ii+D+++
  gi|91773861|ref|YP_566553.1| 157 VVKKEFESWIQDVAILTKAHSQKTNIILDDIF 188
                                   33455566777777777778888888888877 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 5.2e-09
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvf 103
                                   +++ G  +sGKt++ k+i + l++k++  +y+++ + +s+ k++++         ++k ++++ + a ++ei    ++++ 
  gi|91773861|ref|YP_566553.1| 221 IVLAGEDQSGKTTICKKIFSDLRSKNYVPVYVSEDKISSLGKTSNK---------ISKSFSEQYQDAHIDEI---DKNKII 289
                                   5778999********************99**987666666666666.........55555555555555555...444445 PP

                      ATPase_2 104 kaielllekikkkgkk........iiiiiDelqklidlglngaellvkeLlnliesl 152
                                     i+++  +i+k++           ii++D+++ l    ++ +e l+++++n+  + 
  gi|91773861|ref|YP_566553.1| 290 PIIDNFHHAINKQKHIenlseyshCIIVVDDIFGLN---IK-DETLISSFMNFRIRE 342
                                   5555555555555443455555669*********99...44.79*******997665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.4
                      ATPase_2  65 ldefieeeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeL 145
                                   ++++    +                                                                   +++e+
  gi|91773861|ref|YP_566553.1| 523 MENS----K-------------------------------------------------------------------VIDEI 532
                                   4443....3...................................................................44444 PP

                      ATPase_2 146 lnliesltkekhlcvviclsSegl 169
                                    n+i++l  ++++ ++i l+  + 
  gi|91773861|ref|YP_566553.1| 533 TNIIDNLHVDENAYIAIFLTHHSK 556
                                   444444444444444444443332 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.67
                      ATPase_2 126 elqklidlglngaellvkeLlnliesltkekhlc 159
                                   +l +l  +g+n +  l+++L++li + t++++++
  gi|91773861|ref|YP_566553.1| 668 DLENLLCVGMNVHLRLLSNLFELINNETEQEKMV 701
                                   5666667788888899999999999999888765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.27   3.5e+02      54      82 ..     169     196 ..     134     203 .. 0.68
   2 !   21.2   0.3   1.8e-07   0.00022       5      89 ..     221     311 ..     219     319 .. 0.75
   3 ?   -0.8   1.4       1.1   1.4e+03      51      77 ..     509     536 ..     424     579 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.27
                        AAA_14  54 elileklkeekktylflDEiqevpeweka 82 
                                    +il k++ ++kt ++lD i   pe+ek+
  gi|91773861|ref|YP_566553.1| 169 VAILTKAH-SQKTNIILDDIFVWPELEKF 196
                                   34555544.48999******999998875 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.8e-07
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke.......ekktylflDEiqevpe 78 
                                   +v+ G  ++GKTt++k+++++l  k+   +y++ d+ +   ++ + k+ + + e++++       ++k + ++D  +++ +
  gi|91773861|ref|YP_566553.1| 221 IVLAGEDQSGKTTICKKIFSDLRSKNYVPVYVSEDKISSLGKTSN-KISKSFSEQYQDahideidKNKIIPIIDNFHHAIN 300
                                   6788999************99995556667777777777555533.56777777754456667877788889999999999 PP

                        AAA_14  79 wekalkslvde 89 
                                    +k++ +l + 
  gi|91773861|ref|YP_566553.1| 301 KQKHIENLSEY 311
                                   99999888765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                        AAA_14  51 kllelilek.lkeekktylflDEiqevp 77 
                                    ++ ++ +k l+++ ++  ++DEi ++ 
  gi|91773861|ref|YP_566553.1| 509 YFYYFFVAKyLSDNMENSKVIDEITNII 536
                                   3444455553344455556788888773 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 !   17.4   0.0   3.4e-06    0.0044       2      74 ..     222     302 ..     221     314 .. 0.77
   2 ?   -0.8   0.0       1.5   1.9e+03      50      70 ..     305     324 ..     293     338 .. 0.71
   3 ?   -0.1   0.0      0.92   1.2e+03      79     112 ..     522     555 ..     515     577 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                                   EEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.......TSEEEEEETGGGHHHHH CS
                           AAA   2 llyGppGtGKTllakavakelg.vefleisgsellskyvgesekkirelfkeakeka.......kpsilfiDEidalaksr 74 
                                   +l G    GKT+++k + ++l   +++ + +se   + +g++++ki++ f+e  + a       ++ i +iD+++  ++++
  gi|91773861|ref|YP_566553.1| 222 VLAGEDQSGKTTICKKIFSDLRsKNYVPVYVSEDKISSLGKTSNKISKSFSEQYQDAhideidkNKIIPIIDNFHHAINKQ 302
                                   7899999*************953556666666666568999*******999987777778887444666888888877777 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                                   HHHHHHTSTSEEEEEETGGGH CS
                           AAA  50 fkeakekakpsilfiDEidal 70 
                                   +++++e + ++i+++D+i  l
  gi|91773861|ref|YP_566553.1| 305 IENLSEYS-HCIIVVDDIFGL 324
                                   34444454.9*******9665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.92
                                   CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                           AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrp 112
                                   + e+++v++++ + +d++  +e+  i i  t++ 
  gi|91773861|ref|YP_566553.1| 522 NMENSKVIDEITNIIDNLHVDENAYIAIFLTHHS 555
                                   6678899999999999999999999999999874 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       7.2   9.3e+03      70     104 ..     151     187 ..     141     187 .. 0.62
   2 ?   14.2   0.0   2.3e-05      0.03       1      28 [.     220     247 ..     220     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.2
                                   EETTEEE-HHHHHHHH..HHHHHHHHHHH-EEEE--- CS
                      NTPase_1  70 rvgkyvvdvesfeela..lealrkalseadviviDEi 104
                                   r+ k  v  ++fe+ +  +++l+ka s++  i++D i
  gi|91773861|ref|YP_566553.1| 151 RIVKQLVVKKEFESWIqdVAILTKAHSQKTNIILDDI 187
                                   4444444447777765335667888877777888876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.3e-05
                                   EEEEE--TTSSHHHHHHHHHHHH...GG CS
                      NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgv 28 
                                   k+++ G+ ++GKtT++kk+ + l+s+++
  gi|91773861|ref|YP_566553.1| 220 KIVLAGEDQSGKTTICKKIFSDLRSKNY 247
                                   689*********************9997 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   0.1   2.6e-05     0.034      18     109 ..     204     295 ..     199     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                         AAA_7  18 dtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpg 98 
                                   +tv+  yll+ +l  +k ++l G+  +GKt+i+k++++ l +++y+++ ++  +  s  ++ + i +++  + ++      
  gi|91773861|ref|YP_566553.1| 204 KTVSSGYLLDNFLGFSK-IVLAGEDQSGKTTICKKIFSDLRSKNYVPVYVSEDKISSLGKTSNKISKSFSEQYQDAHIDEI 283
                                   57888899999888776.6679****************************9999999888888888877766665554443 PP

                         AAA_7  99 .gkklvvFvDDl 109
                                    ++k++  +D++
  gi|91773861|ref|YP_566553.1| 284 dKNKIIPIIDNF 295
                                   033455556655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.5e-05     0.071       8     100 ..     221     321 ..     219     343 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst......sskdllrellralglelka..erlsseelle 80 
                                   +v+ Ge  +GKTt ++++++ l         ++ +v v++++++      +s ++ + + +++++ + +    ++   +++
  gi|91773861|ref|YP_566553.1| 221 IVLAGEDQSGKTTICKKIFSDLR--------SKNYVPVYVSEDKisslgkTSNKISKSFSEQYQDAHIDeiDKNKIIPIID 293
                                   7899*****************94........77777777777775533345555555555555544444533333333336 PP

                        AAA_22  81 aleqalrarav........ielliiDEa 100
                                    +++a+++++         + ++++D++
  gi|91773861|ref|YP_566553.1| 294 NFHHAINKQKHienlseysHCIIVVDDI 321
                                   6666666666566666666666666665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05     0.073       3      53 ..     225     276 ..     223     310 .. 0.87
   2 ?   -1.7   0.1       1.5     2e+03      31      57 ..     600     626 ..     544     642 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH.TCS--- CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll.keeele 53 
                                   G D +GKtt+++++ + l+++ +  v   e++ +++G++ +++ + ++e+++
  gi|91773861|ref|YP_566553.1| 225 GEDQSGKTTICKKIFSDLRSKNYVPVYVSEDKISSLGKTSNKISKsFSEQYQ 276
                                   789********************97777888889999998888776555554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                   SSSTTSHHHHHHHHHHHTCS---HHHH CS
               Thymidylate_kin  31 repggteiGekirelllkeeeleeqte 57 
                                   +++g+t+  +   e+l+++ ele+++e
  gi|91773861|ref|YP_566553.1| 600 FPSGNTRPEKERAEILNQQDELEQYQE 626
                                   333333333333333333333333333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.5e-05      0.12       1      31 [.     220     250 ..     220     278 .. 0.80
   2 ?   -3.6   0.0       9.4   1.2e+04     101     118 ..     802     819 ..     779     820 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                                   EEEEESSTTSSHHHHHHCHCT-CCC-EEETT CS
                           Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekst 31 
                                   K+vl G+ ++GKt+++k++ +d  s+++ + 
  gi|91773861|ref|YP_566553.1| 220 KIVLAGEDQSGKTTICKKIFSDLRSKNYVPV 250
                                   9*******************99999887654 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.4
                                   HHHHHCSSS-EEEEEE-T CS
                           Roc 101 elkkvagkspvilvgnki 118
                                   +++kva+k++ ++v+n++
  gi|91773861|ref|YP_566553.1| 802 DFSKVAKKAIKLMVANHC 819
                                   567788888889999986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       1.9   2.5e+03      87     113 ..     163     188 ..     126     197 .. 0.54
   2 ?   13.1   0.1   3.2e-05     0.041      23     114 ..     221     323 ..     210     337 .. 0.71
   3 ?   -3.7   0.0       4.3   5.5e+03      61      83 ..     693     715 ..     690     723 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                                   -STTSHHHHHHHHCCCTTEEEEEEEE- CS
                        NB-ARC  87 eeveslkrklvrlLltkrfllvlDDVw 113
                                   e+       +     ++++ ++lDD++
  gi|91773861|ref|YP_566553.1| 163 ESWI-QDVAILTKAHSQKTNIILDDIF 188
                                   2222.3333333334446777777764 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.2e-05
                                   EEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS............ CS
                        NB-ARC  23 valvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeves............ 91 
                                   + l G   +GKtt+ k+i+++   ++++  + ++v+  k ++  +  ++i k +s++ +d ++ e  ++            
  gi|91773861|ref|YP_566553.1| 221 IVLAGEDQSGKTTICKKIFSD---LRSKNYVPVYVSEDKISSLGKTSNKISKSFSEQYQDAHIDEIDKNkiipiidnfhha 298
                                   66888899*************...555444666664444555556666666666666544444443333556677777777 PP

                                   ..HHHHHHHHCCCTTEEEEEEEE-S CS
                        NB-ARC  92 ..lkrklvrlLltkrfllvlDDVwe 114
                                     +++++ +l +    ++v DD++ 
  gi|91773861|ref|YP_566553.1| 299 inKQKHIENLSEYSHCIIVVDDIFG 323
                                   76888899988888********975 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.3
                                   SXXHHHHHHHXXHHHHHCCCTTS CS
                        NB-ARC  61 ktdkseeiletilkeLslseddl 83 
                                   ++ ++e+++++i+++L++ eddl
  gi|91773861|ref|YP_566553.1| 693 NETEQEKMVDFIVERLNQLEDDL 715
                                   56678888888888887777664 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      0.51   6.6e+02      56      91 ..     154     196 ..     123     201 .. 0.74
   2 ?   13.5   0.1   6.1e-05     0.078       1      70 [.     221     307 ..     221     334 .. 0.54
   3 ?   -2.0   0.1         4   5.1e+03      15      59 ..     516     567 ..     493     602 .. 0.50
   4 ?   -2.1   0.1       4.1   5.2e+03      46      66 ..     615     635 ..     578     686 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.51
                        AAA_18  56 kldklldaleenss.......aleegknlvidghlaeleseaa 91 
                                   k+ ++ +++e +++       a  +  n+++d++ +++e e++
  gi|91773861|ref|YP_566553.1| 154 KQLVVKKEFESWIQdvailtkAHSQKTNIILDDIFVWPELEKF 196
                                   44467777777777788888877888999*****999998876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.1e-05
                        AAA_18   1 IlltGtpGvGKttlakeL....skrlgf......gvnlrdvakenglllevdpe..aldeskrldedkldklldaleenss 69 
                                   I+l+G   +GKtt++k +    +++ ++       ++++++ k ++     + e  +    +++d++k   ++d+++ +++
  gi|91773861|ref|YP_566553.1| 221 IVLAGEDQSGKTTICKKIfsdlRSK-NYvpvyvsEDKISSLGKTSNKISKSFSEqyQDAHIDEIDKNKIIPIIDNFHHAIN 300
                                   899***************6444333.2356555533333333333222222222233333555555555555555555554 PP

                        AAA_18  70 ......a 70 
                                         +
  gi|91773861|ref|YP_566553.1| 301 kqkhieN 307
                                   5555553 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4
                        AAA_18  15 akeLskrlgf......gvnlrdvakenglllevdpe........aldeskrldedkldk 59 
                                   ak+Ls+ +++       +n++d++         d++         ++++  + ++  ++
  gi|91773861|ref|YP_566553.1| 516 AKYLSDNMENskvideITNIIDNLHV-------DENayiaifltHHSKNSTIFKKIEMV 567
                                   45554444222433332222221111.......11111122222334444444444444 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.1
                        AAA_18  46 ldeskrldedkldklldalee 66 
                                   l+++++l++ + ++l+++  +
  gi|91773861|ref|YP_566553.1| 615 LNQQDELEQYQENNLQEEDVN 635
                                   333333333333333333333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.064        82      76     108 ..     158     192 ..     140     210 .. 0.77
   2 ?    6.5   0.0    0.0035       4.5      19      49 ..     221     250 ..     219     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.064
                    Zeta_toxin  76 tqkdaselve..kllqeaiengyniivegtlrspd 108
                                   ++k+   + +   +l++a++++ nii++  +  p+
  gi|91773861|ref|YP_566553.1| 158 VKKEFESWIQdvAILTKAHSQKTNIILDDIFVWPE 192
                                   566666666622469************98776555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0035
                    Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrl 49 
                                   i+l+G   +GK+++ +++  +l+  +n+v +
  gi|91773861|ref|YP_566553.1| 221 IVLAGEDQSGKTTICKKIFSDLR-SKNYVPV 250
                                   79********************5.6666644 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       9.9   1.3e+04      42      94 ..      35      85 ..      27      88 .. 0.69
   2 ?   12.6   0.1    0.0001      0.13       1      63 [.     221     300 ..     221     330 .. 0.74
   3 ?   -2.7   0.0       6.1   7.8e+03      58      79 ..     454     476 ..     430     487 .. 0.66
   4 ?   -2.1   0.1       3.9     5e+03      51     100 ..     787     836 ..     759     842 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.9
                  RNA_helicase 42 dfwdgYtgqevvvidDfgqvkdeenps.dlaelirlvsstpyplnmasleekgt 94
                                  d  + + + e+v  +Df ++ d    + d a++i l+ s+++   +  ++ek++
  gi|91773861|ref|YP_566553.1| 35 DLIEEWYDREIVPGEDFQNQIDC---NlDNADIICLFISAHFLASKSCMAEKKK 85
                                  55556666777777888888877...6677777777777777777777777765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0001
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl................klkkkdsvysrnpeddfwdgYtgqevv.vidDfgqvkd 63 
                                   i+l G+ + GK+t++k++ ++l +k                  ++k ++ +s + +d + d  ++++++ +id f    +
  gi|91773861|ref|YP_566553.1| 221 IVLAGEDQSGKTTICKKIFSDLRSKNyvpvyvsedkisslgkTSNKISKSFSEQYQDAHIDEIDKNKIIpIIDNFHHAIN 300
                                   7899*******************888899888888888877655555666677778888888886665524444544444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.1
                  RNA_helicase  58 fgqvkdee.npsdlaelirlvss 79 
                                   ++ +k++e +p+++ae+++l s 
  gi|91773861|ref|YP_566553.1| 454 IYDRKKKElSPDEFAEFMELYSE 476
                                   55566666678888998888764 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.9
                  RNA_helicase  51 evvvidDfgqvkdee.npsdlaelirlvsstpyplnmasleekgtlftSkv 100
                                   + + id+f++   +    +  +  i+l+  +++ +++    e    ++Sk+
  gi|91773861|ref|YP_566553.1| 787 KNLQIDEFSKGIRDDdFSKVAKKAIKLMVANHCSVHKIGARER-QRIQSKF 836
                                   5567777777765553455888888888888888888888876.4666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1388  (0.0774165); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 5490.66
//
Query:       gi|91773862|ref|YP_566554.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91773862|ref|YP_566554.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91773862|ref|YP_566554.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91773862|ref|YP_566554.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91773862|ref|YP_566554.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91773862|ref|YP_566554.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91773862|ref|YP_566554.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91773862|ref|YP_566554.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91773862|ref|YP_566554.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2117.39
//
Query:       gi|91773863|ref|YP_566555.1|  [L=291]
Description: methyltransferase type 12 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-12   47.0   0.0    5.7e-12   46.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      1e-09   38.5   0.0    1.4e-09   38.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.9e-08   33.7   0.0    2.8e-08   33.2   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    6.1e-08   33.3   0.0      1e-07   32.6   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    6.2e-08   33.2   0.0    1.5e-07   32.0   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.1e-07   31.8   0.0      2e-07   30.9   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    7.4e-06   25.9   0.0    1.2e-05   25.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-05   24.6   0.0    2.2e-05   23.9   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.6e-05   24.7   0.2    2.7e-05   24.0   0.2    1.3  1  Methyltransf_16  Lysine methyltransferase
    1.9e-05   24.1   0.0    2.7e-05   23.6   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
    4.4e-05   23.2   0.0    6.4e-05   22.7   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00017   21.1   0.0    0.00028   20.5   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00023   20.6   0.0    0.00038   19.8   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00086   18.8   1.3     0.0016   17.9   0.0    1.8  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.001   18.8   0.0     0.0016   18.1   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0012   18.0   0.0     0.0018   17.4   0.0    1.3  1  Fibrillarin      Fibrillarin
     0.0028   17.4   0.0     0.0076   16.0   0.0    1.7  1  Met_10           Met-10+ like-protein
     0.0034   16.5   0.0     0.0051   16.0   0.0    1.3  1  DREV             DREV methyltransferase
     0.0068   15.4   0.0       0.01   14.8   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.007   16.3   0.0      0.011   15.7   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.016   14.6   0.0       0.03   13.7   0.0    1.4  1  TehB             Tellurite resistance protein TehB
      0.047   13.2   0.0      0.073   12.5   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
       0.05   13.7   0.0      0.076   13.1   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
      0.053   12.8   0.0        0.2   10.9   0.0    1.8  2  Methyltransf_2   O-methyltransferase domain
      0.067   12.8   0.0       0.14   11.7   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   7.9e-15   5.7e-12       1      92 [.      75     164 ..      75     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 7.9e-15
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS..SSTTTEEEEEEESTGGGSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp..fedgsfDlvvssgalhhls 78 
                                   vLd+G G+G l++ ++kr+   +v++v++s++m+   +e++ee ++ n++++++  ed++  +  g+fDlv++s++l+   
  gi|91773863|ref|YP_566555.1|  75 VLDIGSGPGALAIPISKRV--REVVAVEPSDGMMSVLQENIEELDIsNINCIHKGWEDINidELGGKFDLVIASYSLN--- 150
                                   9*****************9..9*******************998889***********76326789*******97755... PP

                                   HHHHHHHHHHHHHH CS
               Methyltransf_25  79 dedlekalkeiarv 92 
                                    +d+++++++i +v
  gi|91773863|ref|YP_566555.1| 151 VPDIRQTFEKIQSV 164
                                   589*****999876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0     2e-12   1.4e-09      19     108 ..      67     164 ..      46     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2e-12
               Methyltransf_23  19 k.lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                     l++++rvLdiG G G l+  +++++ +v++v++s+ + + ++         ++ + +k  +  ++++e  gkfdl++++
  gi|91773863|ref|YP_566555.1|  67 LdLKSDSRVLDIGSGPGALAIPISKRVREVVAVEPSDGMMSVLQenieeldisNINCIHKGWE-DINIDELGGKFDLVIAS 146
                                   2379999******************************9999999********99999999999.9**************** PP

               Methyltransf_23  90 evlehvpdppellrqiatl 108
                                   ++l+ vpd   ++ +i++ 
  gi|91773863|ref|YP_566555.1| 147 YSLN-VPDIRQTFEKIQSV 164
                                   ***5.88888888888874 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   3.9e-11   2.8e-08      19      83 ..      60     126 ..      54     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.9e-11
                                   HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S CS
                        RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhq 83 
                                   i++ l++l+l+ +  vl+ig+G+G+l  ++ kr+++vv++E    ++ +lq++++  + ++++ +h+
  gi|91773863|ref|YP_566555.1|  60 IEQTLSELDLKSDSRVLDIGSGPGALAIPISKRVREVVAVEPSDGMMSVLQENIEelDISNINCIHK 126
                                   678899**********************************************999877888888886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   1.4e-10     1e-07       1      91 [.      76     163 ..      76     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.4e-10
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   L+iG+G G+l+ ++ ++    e+++v++s  ++   +e + + +  n n+++   +d+  ++ g++fDlv+as  l++ +d
  gi|91773863|ref|YP_566555.1|  76 LDIGSGPGALAIPISKR--VREVVAVEPSDGMMSVLQENIEELDISNINCIHKGWEDINIDELGGKFDLVIASYSLNV-PD 153
                                   8****************..********************************99988888888889************9.8* PP

               Methyltransf_12  82 irevldnirk 91 
                                   ir+++++i +
  gi|91773863|ref|YP_566555.1| 154 IRQTFEKIQS 163
                                   *****99976 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.1e-10   1.5e-07       1      85 [.      76     162 ..      76     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.1e-10
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T..T-EEEEEEES-CCC-CCHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfed..nsfDlvvssevlhhvedpe 78 
                                   Ld+G+G G+la ++ kr+++vv+v++s+ m+ + +e+++e ++ ++++++   e++++ +  ++fDlv++s +l+ v+d +
  gi|91773863|ref|YP_566555.1|  76 LDIGSGPGALAIPISKRVREVVAVEPSDGMMSVLQENIEELDIsNINCIHKGWEDINIDElgGKFDLVIASYSLN-VPDIR 155
                                   8*****************************************9************99988778********9986.55777 PP

                                   HHHHHHH CS
               Methyltransf_11  79 kalkeia 85 
                                   +++++i 
  gi|91773863|ref|YP_566555.1| 156 QTFEKIQ 162
                                   7777765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.8e-10     2e-07       2     102 ..      70     166 ..      69     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.8e-10
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsn 81 
                                   +++ rvlD+G+G G+l++ + +++++   vv ++ s  + ++ +en ++l ++n++  +  +e+++ + l   kfDl+++ 
  gi|91773863|ref|YP_566555.1|  70 KSDSRVLDIGSGPGALAIPISKRVRE---VVAVEPSDGMMSVLQENIEELDISNINCIHKGWEDINIDeLG-GKFDLVIAS 146
                                   7899*****************99986...***********************************9966666.9*******9 PP

               Methyltransf_31  82 evlnaladpdkileeiervlk 102
                                     l  ++d  +++e+i++v +
  gi|91773863|ref|YP_566555.1| 147 YSL-NVPDIRQTFEKIQSVSS 166
                                   999.79999999999998865 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 !   25.2   0.0   1.6e-08   1.2e-05      67     130 ..      65     125 ..      50     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.6e-08
                                   HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEE CS
                          PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvv 130
                                     l+lk  +rvL++GsG G l+  +++ v+e   vv++e +  +++  ++n+++ld++n+  ++
  gi|91773863|ref|YP_566555.1|  65 SELDLKSDSRVLDIGSGPGALAIPISKRVRE---VVAVEPSDGMMSVLQENIEELDISNINCIH 125
                                   4577******************999998886...56**********************998765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     3e-08   2.2e-05      46     142 ..      70     164 ..      56     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3e-08
                                   --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-..T-EEEEEEES CS
               Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed..dsfDvvtvsf 124
                                   k+ ++vlD+ +G g la+ +s+ v+e   vv ++ ++ m++v ++ ++e   +ni+ ++   e+++ ++  + fD+v  s+
  gi|91773863|ref|YP_566555.1|  70 KSDSRVLDIGSGPGALAIPISKRVRE---VVAVEPSDGMMSVLQENIEELDISNINCIHKGWEDINIDElgGKFDLVIASY 147
                                   56789******************996...78888999************************999999888799******** PP

                                   -GGG-S-HHHHHHHHHHH CS
               Ubie_methyltran 125 GlrnvtDklkaLkeayrv 142
                                    l nv+D+ ++++++  v
  gi|91773863|ref|YP_566555.1| 148 SL-NVPDIRQTFEKIQSV 164
                                   *9.9*****999988776 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   3.8e-08   2.7e-05       7     127 ..      23     146 ..      19     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.8e-08
               Methyltransf_16   7 Lkieedtgesigrk.vWdaavvlvkylekklake........lganelsklsvlELGsGtGlvGlavaellpeakviltDl 78 
                                   +++ ++ +   +++ +W++   +  y e+  +k+        ++ +  s+ +vl++GsG G   + + +   +  v +   
  gi|91773863|ref|YP_566555.1|  23 MRLYNEVEGTLAKVdIWESKENARRYWEMSQNKGagrieqtlSELDLKSDSRVLDIGSGPGALAIPISKR-VREVVAVEPS 102
                                   566666666666544**************8888899999987667778999*****************99.5666888888 PP

               Methyltransf_16  79 eellellkknielnknalkskvkvevLdWgeeleedllekeevDlilaa 127
                                   + ++ +l++nie    +  s+++     W e+++ d l   ++Dl++a+
  gi|91773863|ref|YP_566555.1| 103 DGMMSVLQENIEE---LDISNINCIHKGW-EDINIDELGG-KFDLVIAS 146
                                   89**********9...45789999999**.6677777755.69****98 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.7e-08   2.7e-05      48     121 ..      70     145 ..      60     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.7e-08
                                   CC-..EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC...TTTTT-EEEEEE CS
                          GidB  48 krd.kviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee...kqeeekydvvts 121
                                   k d +v+D+GsG+G  +ip++  +   +++ +e++   ++ L+e +eel+++n++ +++  e+    +   k+d+v++
  gi|91773863|ref|YP_566555.1|  70 KSDsRVLDIGSGPGALAIPIS--KRVREVVAVEPSDGMMSVLQENIEELDISNINCIHKGWEDiniDELGGKFDLVIA 145
                                   33326*********9888865..66677889****************************9999765555678888875 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   8.9e-08   6.4e-05      42     117 ..      72     143 ..      61     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.9e-08
                                   C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                 Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                   ++rvLD+ +G Gal++  +S  ++++v+ve ++ ++++l+en+eel++++   ++k  +  ++++l   +++fd+v
  gi|91773863|ref|YP_566555.1|  72 DSRVLDIGSGPGALAI-PISKRVREVVAVEPSDGMMSVLQENIEELDISNINCIHKGWEDINIDEL---GGKFDLV 143
                                   679*************.69****************************9983223333333333333...5567776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.8e-07   0.00028      24     102 ..      64     144 ..      57     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.8e-07
                                   HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTSTTS-EEE CS
                           MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleeveekkfdl 100
                                   l+ l+ + + +vlD+G+G G+l++ + k+  e  v++v+ +   + + +en+e+ +++    ++  ++d+  +   +kfdl
  gi|91773863|ref|YP_566555.1|  64 LSELDLKSDSRVLDIGSGPGALAIPISKRVRE--VVAVEPSDGMMSVLQENIEELDISnincIHKGWEDINIDELGGKFDL 142
                                   56777778899*****************9998..89999999999999999998888875577777888876666699999 PP

                                   EE CS
                           MTS 101 iv 102
                                   ++
  gi|91773863|ref|YP_566555.1| 143 VI 144
                                   98 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.3e-07   0.00038      50     131 ..      59     143 ..      45     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.3e-07
                                   HHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.... CS
                          CMAS  50 KldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.... 126
                                   +++ +l  l+lk  +++LdiG G G+l++   +r   +vv++  S+  + + +++++eld+++ + ++ +++ed++     
  gi|91773863|ref|YP_566555.1|  59 RIEQTLSELDLKSDSRVLDIGSGPGALAIPISKR-VREVVAVEPSDGMMSVLQENIEELDISNINCIH-KGWEDINIdelg 137
                                   678999***********************99999.679**********************98877665.799998643355 PP

                                   .--SEE CS
                          CMAS 127 .kvdrv 131
                                    k+d v
  gi|91773863|ref|YP_566555.1| 138 gKFDLV 143
                                   566655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.6       1.2   8.9e+02      91     105 ..       9      23 ..       3      51 .. 0.76
   2 !   17.9   0.0   2.3e-06    0.0016     159     232 ..      69     145 ..      59     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                          PrmA  91 eveeedWaeewkkyy 105
                                   ++++ dW + wk++ 
  gi|91773863|ref|YP_566555.1|   9 NLNNIDWNDVWKEQM 23 
                                   688999999999875 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.3e-06
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk....eekadviva 232
                                   +k++++vlD+G G G Lai  +k   ++vvav   +  ++v +eN+e  ++++   ++   e ++     +k+d+++a
  gi|91773863|ref|YP_566555.1|  69 LKSDSRVLDIGSGPGALAIPISK-RVREVVAVEPSDGMMSVLQENIEELDISNINCIHKGWEDINidelGGKFDLVIA 145
                                   57788****************99.6899********************999996657765444433456789999998 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.3e-06    0.0016       4      83 ..      67     143 ..      64     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-06
                                   H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEE CS
               Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDri 83 
                                   L+++ + ++lD+ ++PG+    i    k   +vvAv+ ++  ++ ++en++ L + n+ +++     i+ +  g +fD +
  gi|91773863|ref|YP_566555.1|  67 LDLKSDSRVLDIGSGPGALAIPI---SKRVREVVAVEPSDGMMSVLQENIEELDISNINCIHKGWEDINIDELGGKFDLV 143
                                   88999************866555...567899******************************999988877777788866 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.5e-06    0.0018      40     112 ..      41     110 ..      12     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.5e-06
                                   ETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH CS
                   Fibrillarin  40 veeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli 112
                                   ++e+  R W+  + K a+ i + l+el +k++s+vL +G++ G  +  +s  v     v ave s+ ++  l 
  gi|91773863|ref|YP_566555.1|  41 SKENARRYWEMSQNKGAGRIEQTLSELDLKSDSRVLDIGSGPGALAIPISKRVR---EVVAVEPSDGMMSVLQ 110
                                   3444679*************************************9999999888...7889999888887665 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05    0.0076      94     151 ..      64     120 ..      20     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                                   HHTT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                        Met_10  94 lakl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                   l +l  + + +V+d+  G G +aipi+k  + ++v+a++     +  l+eni+  ++++
  gi|91773863|ref|YP_566555.1|  64 LSELdLKSDSRVLDIGSGPGALAIPISK--RVREVVAVEPSDGMMSVLQENIEELDISN 120
                                   33334567889*****************..99********************9777765 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     7e-06    0.0051      93     134 ..      70     111 ..      58     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7e-06
                          DREV  93 qedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkk 134
                                   + d ++ld+G+G G ++  +++ + ev a e s  m+  l+ 
  gi|91773863|ref|YP_566555.1|  70 KSDSRVLDIGSGPGALAIPISKRVREVVAVEPSDGMMSVLQE 111
                                   4689********************************998875 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.4e-05      0.01     201     257 ..      71     127 ..      53     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
               tRNA_U5-meth_tr 201 skgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirls 257
                                   s++ +l++  G G ++++++++++ v+a e +   +++ q ni++  i n++ i   
  gi|91773863|ref|YP_566555.1|  71 SDSRVLDIGSGPGALAIPISKRVREVVAVEPSDGMMSVLQENIEELDISNINCIHKG 127
                                   5667899999*****************************************998765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05     0.011      13      76 ..      70     129 ..      58     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
               Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGle 76 
                                   +++srv+DiG+  g l+i +   +++++v+a++ ++g ++  +enie+ ++++ i+++  +G e
  gi|91773863|ref|YP_566555.1|  70 KSDSRVLDIGSGPGALAIPIS--KRVREVVAVEPSDGMMSVLQENIEELDISN-INCI-HKGWE 129
                                   5678**************997..68999********************99964.6653.45555 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.1e-05      0.03      27     104 ..      68     148 ..      45     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                                   CCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHH...HTT-TTEEEEE--GGG----S-EEEEEEESS CS
                          TehB  27 kivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeike...kenlknistalydineaklderydfilstvv 104
                                   ++ + ++vld+g g g  ++ +s    +v a++  +  ++ l+e +e   + n++ i+    din  +l  ++d+++++  
  gi|91773863|ref|YP_566555.1|  68 DLKSDSRVLDIGSGPGALAIPISKRVREVVAVEPSDGMMSVLQENIEeldISNINCIHKGWEDINIDELGGKFDLVIASYS 148
                                   5567899****************************999999998765122678888999999***999*9****9998755 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001     0.073       4      57 ..      74     125 ..      71     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEE CS
                Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilr 57 
                                    vl+iG+G G + + ++k+    +++++E +  ++  + ++ie+l+++N+++++
  gi|91773863|ref|YP_566555.1|  74 RVLDIGSGPGALAIPISKRV--REVVAVEPSDGMMSVLQENIEELDISNINCIH 125
                                   689**************997..5689**************************97 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.076       7     110 ..      58     162 ..      52     169 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHHTTEEEECS-CCCSSHHHHHCH CS
                          FtsJ   7 yKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvttiqgditdpetiekike 81 
                                     +++ +++ + +k + +v+D+g++PG+ +  +++r+     vvav    +      ++++ + + + +  ++  ++   +
  gi|91773863|ref|YP_566555.1|  58 GRIEQTLSELD-LKSDSRVLDIGSGPGALAIPISKRV---REVVAVEPSDGmmsvlqENIEELDISNINCIHKGWEDINID 134
                                   55667778888.88999*******************8...46****99665333333233333333444444444443334 PP

                                   CHHHSSEEEEEE--S-SS-CHHHHHHHHH CS
                          FtsJ  82 alserkvdlvvsDgapdvsgvhdldeylq 110
                                    l+  k+dlv++  + +v  ++++ e +q
  gi|91773863|ref|YP_566555.1| 135 ELG-GKFDLVIASYSLNVPDIRQTFEKIQ 162
                                   443.699***9999999988877777665 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029       0.2      15      82 ..      24      91 ..      13      99 .. 0.86
   2 ?   -1.0   0.0       1.2   8.7e+02      14      40 ..     203     229 ..     189     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                  ..HHHHHS--HHHHHTSSHHHHHHHHHHHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHH CS
                Methyltransf_2 15 iifkkafGislfeaikrdeeerakfnkglqessslvakkvleafdleglkslvDvGGGtGalakaivs 82
                                  ++++++ G+ +   i +++e  +++ +  q++     ++ l + dl++ ++++D+G G Gala  i++
  gi|91773863|ref|YP_566555.1| 24 RLYNEVEGTLAKVDIWESKENARRYWEMSQNKGAGRIEQTLSELDLKSDSRVLDIGSGPGALAIPISK 91
                                  68999999998888888999999999999999999***************************988776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                   -..HHHHHS--HHHHHTSSHHHHHHHH CS
                Methyltransf_2  14 qiifkkafGislfeaikrdeeerakfn 40 
                                   +++++  +G+++f  ++  +  r +  
  gi|91773863|ref|YP_566555.1| 203 NVMYNVLYGMGIFPNMEVFPMQRSMTF 229
                                   478888888888876665555554444 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.14       3      78 ..      74     146 ..      72     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                    +lD+ sG G  +i + +  ++v+a+e +   + + q+N e  ++s +i +++  ++++         k+dlv++S
  gi|91773863|ref|YP_566555.1|  74 RVLDIGSGPGALAIPISKRVREVVAVEPSDGMMSVLQENIEELDIS-NINCIHKGWEDINIDELGG--KFDLVIAS 146
                                   68*****************************************997.6999999998864443333..34777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2221.82
//
Query:       gi|91773864|ref|YP_566556.1|  [L=455]
Description: MATE efflux family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-56  189.7  47.9    8.2e-32  110.1  17.9    2.6  3  MatE             MatE
    2.7e-14   53.5  23.7    8.7e-12   45.3  14.9    4.7  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
      0.059   13.7   0.1         12    6.2   0.0    2.5  2  DDE_Tnp_1_5      Transposase DDE domain


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1  17.9   1.4e-35   8.2e-32       1     161 []      23     187 ..      23     187 .. 0.96
   2 ?   -2.8   0.3      0.75   4.5e+03      32      42 ..     206     216 ..     191     225 .. 0.48
   3 !   90.5  16.5   1.4e-29   8.5e-26      10     158 ..     257     407 ..     249     410 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.4e-35
                          MatE   1 Pialenllesllslidtllvgrl.gskal...AavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                   P+ + ++++ l+sl+dt++vg+  g++++   A+++ia++i ++++ ++l ++++ +++++++lGak  +ra  al  ++ 
  gi|91773864|ref|YP_566556.1|  23 PATIGMIVQALYSLVDTIFVGQAlGPESVqgiAGITIAFPIQMIIMGIALTIGIGSASIISRSLGAKIHERADIALGNAIT 103
                                   899*******************9966554333************************************************* PP

                          MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnipl 158
                                   + l+ls+++++l+++++e++l++f+++e+++++a +y +i+++g++++a++++l++i+r+ g+++v++  ++is+ lni+l
  gi|91773864|ref|YP_566556.1| 104 AILALSVVMTILGIVYIEPLLRMFGATETIMPFAYDYTKIILYGTIFFAFSMTLNNIVRAEGNARVAMLTMVISAGLNIIL 184
                                   ********************************************************************************* PP

                          MatE 159 nyl 161
                                   +++
  gi|91773864|ref|YP_566556.1| 185 DPI 187
                                   986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.75
                          MatE  32 sialsilsllf 42 
                                   s + s l+ll+
  gi|91773864|ref|YP_566556.1| 206 SQVVSALFLLY 216
                                   22223333333 PP

  == domain 3  score: 90.5 bits;  conditional E-value: 1.4e-29
                          MatE  10 sllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiall 89 
                                   sl+ ++++ +++ + g+  +A+ +i++++++++f++++g+  +l+++vg ++Gakn+ r+  ++  ++++++l+s++ +ll
  gi|91773864|ref|YP_566556.1| 257 SLMVIVINNVLAVYgGDIPIAVFGIVNRLFMFTFMPMIGIVQGLQPIVGFNYGAKNYARVISSTALAMKITTLVSIAGFLL 337
                                   566677777777788****************************************************************** PP

                          MatE  90 vllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipl 158
                                   +++f+ q++s+ft+d+e++e++k  +ri+ l +p+ ++q+v ++i+++ gk+k+++++s+++  l+ ipl
  gi|91773864|ref|YP_566556.1| 338 LFIFPTQLFSIFTTDQELIEAGKAAMRIMSLALPLVGFQIVGASIYQTLGKAKPAFFLSISRQvLFLIPL 407
                                   **************************************************************97777776 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 ?   -4.3   9.4         3   1.8e+04      54     111 ..      66     120 ..      24     135 .. 0.61
   2 !   45.3  14.9   1.5e-15   8.7e-12       3      85 ..     142     227 ..     140     282 .. 0.84
   3 ?   -3.7   4.4       1.9   1.2e+04     108     108 ..     299     299 ..     246     346 .. 0.47
   4 !   21.5   1.5   3.2e-08   0.00019       1      83 [.     362     445 ..     362     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 3
               Polysacc_synt_C  54 givGaaiatvlallvvavln.lyalrrllgiklellrrllkpllaalvmgivvylllll 111
                                    i+G+a+ + ++ + ++       ++ +  i l   + +  +l++++vm i+  +++++
  gi|91773864|ref|YP_566556.1|  66 IIMGIALTIGIGSASIISRSlGAKIHERADIAL--GNAITAILALSVVMTIL--GIVYI 120
                                   355555555555444444332334444444444..45555677777777777..33333 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 1.5e-15
               Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavlnlyalrr.l 80 
                                    i+ +++if+++s++l++i  + g ++ a++ +vi+a +++il  ++i    +gi Gaaiatv++++v+a+++ly+  +  
  gi|91773864|ref|YP_566556.1| 142 KIILYGTIFFAFSMTLNNIVRAEGNARVAMLTMVISAGLNIILDPIFIfgLNMGIKGAAIATVISQVVSALFLLYYFAKgM 222
                                   578899******************************************87799*******************988877734 PP

               Polysacc_synt_C  81 lgikl 85 
                                     +++
  gi|91773864|ref|YP_566556.1| 223 SSFNF 227
                                   44555 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.9
               Polysacc_synt_C 108 l 108
                                    
  gi|91773864|ref|YP_566556.1| 299 G 299
                                   2 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 3.2e-08
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrrl 80 
                                   +++i++l++++ ++++v++si q lg++k a+  ++   ++ li  +l +  +f + G+ +a  l+  +++++ +++l ++
  gi|91773864|ref|YP_566556.1| 362 AMRIMSLALPLVGFQIVGASIYQTLGKAKPAFFLSISRQVLFLIPLVLILpRFFELQGVWMAFPLSDGLSFLVTFVMLAKE 442
                                   589****************************999998777655555555515669************************99 PP

               Polysacc_synt_C  81 lgi 83 
                                   + +
  gi|91773864|ref|YP_566556.1| 443 YSL 445
                                   875 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.006        36      45      68 ..      15      39 ..       7      45 .. 0.85
   2 ?    6.2   0.0    0.0021        12      35      80 ..     273     318 ..     265     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.006
                   DDE_Tnp_1_5 45 kvlfklplRqlqGf.vqsllklagl 68
                                  kvlfkl+l ++ G+ vq+l +l++ 
  gi|91773864|ref|YP_566556.1| 15 KVLFKLSLPATIGMiVQALYSLVDT 39
                                  89***********835999999875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0021
                   DDE_Tnp_1_5  35 daaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystlsr 80 
                                   d+ i ++ +v +lf +++  + G+vq l  ++g+++ + +y+ +++
  gi|91773864|ref|YP_566556.1| 273 DIPIAVFGIVNRLFMFTFMPMIGIVQGLQPIVGFNYGAKNYARVIS 318
                                   7889999**********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3169.98
//
Query:       gi|91773865|ref|YP_566557.1|  [L=307]
Description: prenyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   60.9   8.3    1.7e-16   60.3   8.3    1.3  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.055   12.4   0.4       0.11   11.4   0.4    1.6  1  DUF3488   Domain of unknown function (DUF3488)


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 !   60.3   8.3   1.9e-20   1.7e-16      21     246 ..      62     288 ..      31     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.9e-20
                          UbiA  21 lllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllall 101
                                     +l ++g+ l+  ++++l++ +D e+Da   ++ +   +++ i     l+++++++++g+    +l+   ++ll++l l+
  gi|91773865|ref|YP_566557.1|  62 CNILSCIGGGLVVYSVYTLDRALDSEEDAV--NRSELTGARRDIA----LFVSLLTFLMGAY---FLFRDGLLLLAFLPLM 133
                                   5678889999********************..8677755555554....6666666666665...5688889999999999 PP

                          UbiA 102 lyvvYt.......g.lrlKrrtllgtvvggiafg..lppllgwaavtgslsllalllalavflltwaialandlrdregDr 172
                                    +++Y+       + l lK    ++++v+g+++g  ++ ++gw+a  +s  l+++ ++l +++  +    ++d++d++gD+
  gi|91773865|ref|YP_566557.1| 134 TGFLYSkgikvgkHhLKLKGGLGVKNLVVGTTWGafIAGIAGWYA--ES-MLPVFGVFLYFGIKLFVNSSVYDFKDIKGDA 211
                                   9*****999999978999999899**********66666677777..55.3677777777777777777778********* PP

                          UbiA 173 kagiktlpvvlGrkaaril...lalllavlllallllllalllllylllalllaalallraarlvrrrdakkaakff 246
                                    agiktlpv lG++++r +   ++l+   ll +l++++l ++ ++ l+++++++++++ r a  v ++++++  k++
  gi|91773865|ref|YP_566557.1| 212 LAGIKTLPVSLGEQRTRDIllsIHLFSHSLLSILIITGLVAYEPMVLVYSFVSGLVCIDRFAAPVENESKNRLYKRL 288
                                   ******************87654444444444488888899999999999999988888877777776666665554 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   1.2e-05      0.11      92     137 ..      99     144 ..      94     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.2e-05
                       DUF3488  92 srRDalvllllgffllatsflfsqsllfalylllalllllaalval 137
                                   +rRD+ + + l  fl+ + flf+ +ll++++l l++ +l    +++
  gi|91773865|ref|YP_566557.1|  99 ARRDIALFVSLLTFLMGAYFLFRDGLLLLAFLPLMTGFLYSKGIKV 144
                                   79******************************99998887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2309.72
//
Query:       gi|91773866|ref|YP_566558.1|  [L=261]
Description: hypothetical protein Mbur_1927 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-23   80.2   0.1    1.9e-22   79.2   0.1    1.6  1  DUF1724        Domain of unknown function (DUF1724)
    0.00077   19.3   0.0     0.0014   18.5   0.0    1.3  1  MarR_2         MarR family
     0.0014   18.4   0.0     0.0026   17.6   0.0    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
     0.0045   16.9   0.0       0.01   15.7   0.0    1.5  1  MarR           MarR family
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.11   12.5   0.0    2.3  2  HTH_45         Winged helix-turn-helix
      0.025   14.5   0.0      0.051   13.5   0.0    1.5  1  HTH_11         HTH domain
      0.052   13.4   1.5        2.6    7.9   0.3    2.4  2  Transcrip_act  Transcriptional activator
      0.066   13.3   0.0       0.12   12.5   0.0    1.3  1  HTH_20         Helix-turn-helix domain
       0.13   12.1   0.0       0.32   10.9   0.0    1.6  2  PTSIIA_gutA    PTS system glucitol/sorbitol-specific IIA comp


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 !   79.2   0.1   9.5e-26   1.9e-22       1      62 []     197     257 ..     197     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 9.5e-26
                       DUF1724   1 tklyvydeeikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlkrSep 62 
                                   tkly++de   +++++vtD+f+s+slf+k+g yd + dli +d++A+kWG+eLF +Y++++++
  gi|91773866|ref|YP_566558.1| 197 TKLYLIDEA--KVAFVVTDRFFSMSLFFKNGAYDPQnDLIGNDNAAIKWGKELFGHYKEKAKE 257
                                   689***994..9************************************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.8e-07    0.0014       9      52 ..      18      58 ..      12      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.8e-07
                                  HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  ++L+++  +p+   t +e+ +++++s + +s ++k+++a  ++ 
  gi|91773866|ref|YP_566558.1| 18 DLLFFIEEEPR---TLSEIREHFNVSSPEISPRIKEMEASNFIY 58
                                  89********6...*************************99885 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0026       2      46 ..      14      58 ..      13      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  ++R ++L++ +e++++ +e+ e++++s + +S   k ++ +++++
  gi|91773866|ref|YP_566558.1| 14 EKRKDLLFFIEEEPRTLSEIREHFNVSSPEISPRIKEMEASNFIY 58
                                  89******************************9888888888876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.2e-06      0.01      15      49 ..      25      59 ..      18      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.2e-06
                                  STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  ++p ++se+ ++++vs++ ++  ++++e  ++i++
  gi|91773866|ref|YP_566558.1| 25 EEPRTLSEIREHFNVSSPEISPRIKEMEASNFIYK 59
                                  567799***************************86 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05      0.11      10      64 ..      18      72 ..      16      84 .. 0.88
   2 ?    0.1   0.1       0.4   7.9e+02      21      60 ..     197     213 ..     161     218 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                        HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGle 64
                                  d+L  i+e+  + ++i  + n s   ++  ++ +   ++i k+++kY++T  G+ 
  gi|91773866|ref|YP_566558.1| 18 DLLFFIEEEPRTLSEIREHFNVSSPEISPRIKEMEASNFIYKDGKKYYITPIGRV 72
                                  6777888888999999999999999*************************99975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.4
                        HTH_45  21 kkTkimykanLsykllnkYLdmLvekglikkskekYvlTe 60 
                                   +k                         li++ k  +v+T+
  gi|91773866|ref|YP_566558.1| 197 TKL-----------------------YLIDEAKVAFVVTD 213
                                   222.......................24566666666665 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   2.6e-05     0.051       5      55 .]      19      66 ..      15      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                        HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                                  +l ++ e ++p + +e+ e++nvS   +  +Ik++e++   I+++ +++Y+
  gi|91773866|ref|YP_566558.1| 19 LLFFI-E-EEPRTLSEIREHFNVSSPEISPRIKEMEASN-FIYKDGKKYYI 66
                                  44444.4.4558**************************8.99999999885 PP

>> Transcrip_act  Transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.019        39      46      72 ..      13      39 ..       9      53 .. 0.82
   2 ?    7.9   0.3    0.0013       2.6      99     128 ..     173     203 ..     169     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                 Transcrip_act 46 rekveaqLgrveeetkrLaeireeLea 72
                                   ek +  L ++eee + L+eire +++
  gi|91773866|ref|YP_566558.1| 13 SEKRKDLLFFIEEEPRTLSEIREHFNV 39
                                  5777788999*************9876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
                 Transcrip_act  99 gqscqkk.ekeykealeafneknkekaqlvs 128
                                   ++++  k   eyk+ale++ + ++ k  l+ 
  gi|91773866|ref|YP_566558.1| 173 TKNVFEKvKNEYKDALETYMNSENTKLYLID 203
                                   55555441679*********99999999885 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.9e-05      0.12      12      54 ..      16      57 ..       6      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                                  HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                        HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                  R ++l  + ++e++t+se+ e + +s  ++s +++++e   ++
  gi|91773866|ref|YP_566558.1| 16 RKDLLFFI-EEEPRTLSEIREHFNVSSPEISPRIKEMEASNFI 57
                                  66666667.99**************************987765 PP

>> PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.32      20      78 ..      17      80 ..       8     101 .. 0.78
   2 ?   -3.8   0.0       5.9   1.2e+04      89     108 ..     162     181 ..     158     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                  -EEEEE-TTS-HHHHTTCEEEE-T......GG----TT-EEEETTEEEEEEEE-TTHHHHHHHH CS
                   PTSIIA_gutA 20 kmlIlFgeeapdeLadysviheve.....elkeeikkgdtltigeqeykitaVGevanknLkel 78
                                  k l +F ee p +L+++    +v+     +  +e+++ + +  ++++y it +G+va+  Lk l
  gi|91773866|ref|YP_566558.1| 17 KDLLFFIEEEPRTLSEIREHFNVSspeisPRIKEMEASNFIYKDGKKYYITPIGRVASGHLKPL 80
                                  6688999999999999887777765423346778888999999***************999876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.9
                                   -SGG-TTEEEEES-S----- CS
                   PTSIIA_gutA  89 keaelpgaiylegkelpelk 108
                                   +e+++p a+ l+++ ++++k
  gi|91773866|ref|YP_566558.1| 162 TESNIPTALVLTKNVFEKVK 181
                                   67778888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1854.50
//
Query:       gi|91773867|ref|YP_566559.1|  [L=538]
Description: phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-98  330.2   0.0    1.5e-98  329.9   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    1.1e-26   92.8   0.0    2.3e-26   91.8   0.0    1.6  1  MGS              MGS-like domain
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.24   11.6   0.0    1.6  1  TGT_C2           Patch-forming domain C2 of tRNA-guanine tran


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 !  329.9   0.0  2.5e-102   1.5e-98       1     294 [.     134     449 ..     134     451 .. 0.93

  Alignments for each domain:
  == domain 1  score: 329.9 bits;  conditional E-value: 2.5e-102
                                   HHHTTTT-EEE-SGGGHHHHHHHHHC.T.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS..E...EEEEEEEEESSSS CS
               AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkk.gevsletrkklaakaFahtaaYDaaiaeylskqlp..etlklslekkqkLrYGe 78 
                                   AAKN+ksVtvv+dp+dY e+l+el++ g+vs +tr+kla+k+F+ ta+YD+ i +ylsk+l   ++l++++++ +kLrYGe
  gi|91773867|ref|YP_566559.1| 134 AAKNYKSVTVVSDPEDYGEILKELRSsGTVSDTTREKLAVKVFRYTANYDSNIDTYLSKTLLdeDVLRMNFTEGTKLRYGE 214
                                   9*************************99*****************************99944336999************* PP

                                   STTS-EEEEE-TT..STTHHH-EEEESS---HHHHHHHHHHHHHHCTS....EEEEEEETTEEEEEEEESSHHHHHHHHHC CS
               AICARFT_IMPCHas  79 NphQkaalyeeee..eeglakaeqlqGkelsynNllDadaalelvkef....aavaivKHanpcGvAvgetlaeAyekAla 153
                                   N+hQ+a++y++e+     l++a+ql+GkelsynN++Dad+al+++ke+     avaivKH+npcG+A+g+tl eA+e+A++
  gi|91773867|ref|YP_566559.1| 215 NWHQDATFYKDETivGPALSNAKQLHGKELSYNNYVDADNALQTIKEVgnrnPAVAIVKHNNPCGLATGNTLCEALEHAWD 295
                                   *********99889988999**************************9976543999************************* PP

                                   CSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTS.SS-EEEE-SS...-.....EEEEETTEEEEE CS
               AICARFT_IMPCHas 154 aDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkk.knlrvlelke...e.....elrsvsgglLvq 225
                                   +DpvSaFG+ii++n+ +d e ae +k +f+e+i+Ap+fe++ale+l++k +nlr+lel++   +     +++ v gg+L q
  gi|91773867|ref|YP_566559.1| 296 GDPVSAFGSIICTNTVFDLESAEFLKGKFVEIILAPGFEHDALEYLEDKsSNLRLLELPQfneAfdtetTYKYVIGGMLKQ 376
                                   **********************************************99999*******997651566779999******** PP

                                   E--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTE.....EEEEE-SSSSHHHHHH.HHH CS
               AICARFT_IMPCHas 226 erdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgq.....tvgiGaGqmsRvdsar.lAv 294
                                   +r+    e  ++++vt+++  ee+    +f++ ++k +kSN+++la + +     ++++GaGq++Rvds+r lA+
  gi|91773867|ref|YP_566559.1| 377 TRNIGLYE--KWDCVTETAYPEEKRGLSEFCICACKSTKSNSVTLAYEYKdgcyvMIAMGAGQPNRVDSIRkLAA 449
                                   ***76655..6*******9899999999******************9776666889*************984565 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   3.8e-30   2.3e-26       1      95 []      14     129 ..      14     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 3.8e-30
                                   THHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH..................HHHHHHHTTSCC. CS
                           MGS   1 glvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv..................eildaikngeid. 62 
                                   g+v++a+ l++l++e+++TgGTak+l++agi+ ++v+e+tg++e++ggrv                  e++ + +++ i+ 
  gi|91773867|ref|YP_566559.1|  14 GIVDFARGLEQLNIEIISTGGTAKMLRDAGIETIDVSEVTGFPEMMGGRVktlhpkihggllcmrgdpEHMGEAEKESIKl 94 
                                   69******************************************************************9999999999999 PP

                                   ..EEEEE--THHHHHHCHHHHHHHHHHHTTSHEES CS
                           MGS  63 ..lvintlypfkatvakdgykirraaenidIplpt 95 
                                     lv ++lypf+ tv+k+g+++++a+enidI++pt
  gi|91773867|ref|YP_566559.1|  95 idLVAVNLYPFEITVSKEGVNLDEAIENIDIGGPT 129
                                   99*******************************98 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 ?   11.6   0.0     4e-05      0.24      15      48 ..     483     522 ..     481     531 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                        TGT_C2  15 agdaLfpedvtitrsatgrirqvlv......dgerlatlr 48 
                                   a da+fp d +i +s + +ir++l       d+e +at +
  gi|91773867|ref|YP_566559.1| 483 ASDAFFPFDDSIIYSDESKIRYILSpggsirDDEVIATAN 522
                                   789**********************999999999999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3936.75
//
Query:       gi|91773868|ref|YP_566560.1|  [L=633]
Description: hypothetical protein Mbur_1929 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.0    2.5e-43  148.1   0.0    1.3  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
    1.5e-18   66.5   0.4    5.2e-18   64.8   0.1    2.0  2  PUA          PUA domain
    2.5e-08   33.4  26.1    6.8e-06   25.7   4.3    3.0  3  Fer4         4Fe-4S binding domain
      2e-06   27.8  15.8      2e-06   27.8  15.8    2.4  1  Fer4_9       4Fe-4S dicluster domain
    3.2e-06   26.9  12.3     0.0016   18.4   2.3    3.0  2  Fer4_2       4Fe-4S binding domain
    6.9e-06   26.1  14.8    6.9e-06   26.1  14.8    2.1  1  Fer4_10      4Fe-4S dicluster domain
    2.1e-05   25.0  16.0    2.1e-05   25.0  16.0    2.4  1  Fer4_7       4Fe-4S dicluster domain
    0.00012   22.0   3.3    0.00012   22.0   3.3    2.8  2  Fer4_6       4Fe-4S binding domain
    0.00019   21.8  12.3      0.017   15.5   2.4    3.3  3  Fer4_8       4Fe-4S dicluster domain
    0.00053   20.1   7.8    0.00053   20.1   7.8    2.2  2  Fer4_18      4Fe-4S dicluster domain
     0.0019   18.7  12.4      0.063   13.8   0.8    3.1  3  Fer4_17      4Fe-4S dicluster domain
     0.0028   18.0   3.6     0.0028   18.0   3.6    3.7  3  Fer4_4       4Fe-4S binding domain
     0.0038   17.3  18.5     0.0038   17.3  18.5    3.2  3  Fer4_21      4Fe-4S dicluster domain
     0.0079   17.1   5.6     0.0079   17.1   5.6    3.0  2  Fer4_3       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.064   13.5   0.0       0.13   12.5   0.0    1.5  1  UPF0113      UPF0113 PUA domain
          1    9.9  15.5       0.61   10.7   4.3    2.7  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
        6.4    7.8  24.5       0.52   11.3   2.4    3.1  3  Fer4_16      4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   2.4e-46   2.5e-43       2     173 ..     250     422 ..     249     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 2.4e-46
                                   EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHCHH CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyeeaa 82 
                                   + vs+sgGkdsl++l+L+++++++ +++f+dtg efpetie v+e++e+y+  l + +  e ++e++  ++ +s   ++ +
  gi|91773868|ref|YP_566560.1| 250 VSVSYSGGKDSLAVLQLVSECLDDYELLFADTGLEFPETIENVKEIVEHYQRPLRTKDVGEAFWESVGDFGPPSVEARW-C 329
                                   579***********************************************999**************************.* PP

                                   HHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CCCCT CS
                   PAPS_reduct  83 eriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpLydq 161
                                   ++++K+ p+ + ++++  d  ++++G+R++es++ra+ + v+++ +  +++   P+ +Wt  +vw yi ++++pyn +y++
  gi|91773868|ref|YP_566560.1| 330 CKVCKLGPISQIINDNyeDGCLTFIGQRKYESAARANSERVWKNPWVGNQIGASPIQDWTAMHVWLYIFKTGVPYNVMYER 410
                                   *************9995566699********************************************************** PP

                                   T-SS--BCTTB- CS
                   PAPS_reduct 162 gfrsiGcvpctg 173
                                   gf++iGc+ c++
  gi|91773868|ref|YP_566560.1| 411 GFDRIGCWLCPS 422
                                   **********86 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   4.9e-21   5.2e-18       1      71 [.     130     200 ..     130     201 .. 0.98
   2 ?   -1.9   0.0       3.3   3.5e+03      25      43 ..     532     550 ..     528     581 .. 0.50

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 4.9e-21
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                   g vv+d gAv ++l+gas+l+pG+++++ +++  d+ ++++++ge++avG+a++s+ ++ + k+g++v+++
  gi|91773868|ref|YP_566560.1| 130 GWVVLDSGAVSFILKGASVLVPGIIDADPQIQVSDETVVLTPEGEIIAVGRARMSGPDMIEHKKGVGVKNR 200
                                   689****************************************************************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                                   EEEETT--TTSEEEEEETT CS
                           PUA  25 vevegdfeegdvVaivded 43 
                                   +++ g++   + Va v+++
  gi|91773868|ref|YP_566560.1| 532 LRAAGKVAYIEGVASVNHE 550
                                   5555555444444444332 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.9       7.7   8.1e+03       9      14 ..     415     420 ..     415     420 .. 0.89
   2 !   20.1   6.2   3.7e-07   0.00039       7      24 .]     588     605 ..     583     605 .. 0.94
   3 !   25.7   4.3   6.5e-09   6.8e-06       3      20 ..     612     629 ..     610     630 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.7
                                   SS-THH CS
                          Fer4   9 igCGaC 14 
                                   igC +C
  gi|91773868|ref|YP_566560.1| 415 IGCWLC 420
                                   899999 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.7e-07
                                   TSSS-THHHHHSTTTEEE CS
                          Fer4   7 kCigCGaCvevCPvgAIt 24 
                                   kC+gCG Cv  CP ++It
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCPKNCIT 605
                                   9***************97 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 6.5e-09
                                   EETTTSSS-THHHHHSTT CS
                          Fer4   3 ideekCigCGaCvevCPv 20 
                                   i+ +kCi+CGaCve+CPv
  gi|91773868|ref|YP_566560.1| 612 IISSKCIHCGACVEICPV 629
                                   7899*************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8  15.8   1.9e-09     2e-06       1      48 [.     588     629 ..     588     631 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.9e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                   kC+gCg Cv +Cp++ ++ ++++ +++       +Ci+CgaCve+Cp 
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCPKNCITIEDGKAIISS------KCIHCGACVEICPV 629
                                   7**************************8......7***********95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.6   0.00011      0.11       8      21 ..     587     600 ..     580     601 .. 0.88
   2 !   18.4   2.3   1.6e-06    0.0016       6      21 ..     613     628 ..     610     629 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                    +C+gCg Cv  CP
  gi|91773868|ref|YP_566560.1| 587 LKCMGCGVCVGKCP 600
                                   69***********9 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.6e-06
                        Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                    + +Ci+CgaCv  CP
  gi|91773868|ref|YP_566560.1| 613 ISSKCIHCGACVEICP 628
                                   5789************ PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1  14.8   6.6e-09   6.9e-06       5      56 .]     585     628 ..     581     628 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.6e-09
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    + +C++Cg Cv  CP         + +++e+ + + ++kC++cgaCve+CP
  gi|91773868|ref|YP_566560.1| 585 RSLKCMGCGVCVGKCPK--------NCITIEDGKAIISSKCIHCGACVEICP 628
                                   5679*************........99999999999***************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 !   25.0  16.0     2e-08   2.1e-05       1      50 [.     588     629 ..     588     630 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                   +C+gCg Cv  Cp ++i++++          +i ++kC++CgaCv+ CP+
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCPKNCITIEDG--------KAIISSKCIHCGACVEICPV 629
                                   7******************775........36899**************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 ?    3.6   6.4     0.075        79       8      24 .]     588     604 ..     584     604 .. 0.90
   2 !   22.0   3.3   1.1e-07   0.00012       4      20 ..     612     628 ..     611     631 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.075
                        Fer4_6   8 kCigCgdCvrvCPegai 24 
                                   kC gCg Cv  CP + i
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCPKNCI 604
                                   8************8765 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-07
                        Fer4_6   4 idpdkCigCgdCvrvCP 20 
                                   i  +kCi+Cg+Cv +CP
  gi|91773868|ref|YP_566560.1| 612 IISSKCIHCGACVEICP 628
                                   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 ?   -2.7   0.0       7.9   8.3e+03      51      55 ..     330     334 ..     309     375 .. 0.69
   2 !   11.4   0.7   0.00033      0.35      49      63 ..     587     601 ..     550     608 .. 0.72
   3 !   15.5   2.4   1.6e-05     0.017       3      19 ..     615     631 ..     613     632 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.9
                        Fer4_8  51 Cttcg 55 
                                   C  c+
  gi|91773868|ref|YP_566560.1| 330 CKVCK 334
                                   22222 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00033
                        Fer4_8  49 wsCttcgaCtevCpv 63 
                                    +C++cg C+ +Cp+
  gi|91773868|ref|YP_566560.1| 587 LKCMGCGVCVGKCPK 601
                                   456666666666665 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.6e-05
                        Fer4_8   3 ekCieCgaCqsaCpvlr 19 
                                   +kCi+CgaC + Cpv++
  gi|91773868|ref|YP_566560.1| 615 SKCIHCGACVEICPVVK 631
                                   79************986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.3   3.5e+03      59      85 ..      27      52 ..      23      58 .. 0.79
   2 !   20.1   7.8   5.1e-07   0.00053      39      98 ..     567     630 ..     542     631 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                       Fer4_18 59 gdcidcescvkvcPtgidirkGlqlec 85
                                    c +  + v+v P g dir  +q++ 
  gi|91773868|ref|YP_566560.1| 27 CSCGNTTTKVEVTPPG-DIRPAFQYDI 52
                                  5677788889999998.9**9999875 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.1e-07
                       Fer4_18  39 grkkekkalkekeerkekgagdcidcescvkvcPtg.idirkGlql...eciscllcidacdkv 98 
                                   ++++ +++ +++ er+ + + +c+ c++cv  cP + i i +G  +   +ci c+ c++ c  v
  gi|91773868|ref|YP_566560.1| 567 NDENDAREFMTRIERAVRRSLKCMGCGVCVGKCPKNcITIEDGKAIissKCIHCGACVEICPVV 630
                                   344445566667777888999*************85499**997654449***********765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       8.9   9.4e+03       8      14 ..     329     335 ..     326     371 .. 0.57
   2 !   13.8   0.8   5.9e-05     0.063      41      59 ..     584     602 ..     547     604 .. 0.73
   3 !   11.9   0.9   0.00024      0.26      45      57 ..     616     628 ..     605     631 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.9
                       Fer4_17   8 ClpeCps 14 
                                   C ++C  
  gi|91773868|ref|YP_566560.1| 329 CCKVCKL 335
                                   5555664 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.9e-05
                       Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                   ++  +C++Cg C+ kCP++
  gi|91773868|ref|YP_566560.1| 584 RRSLKCMGCGVCVGKCPKN 602
                                   57789***********987 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00024
                       Fer4_17  45 lCieCgeCerkCP 57 
                                   +Ci+Cg C++ CP
  gi|91773868|ref|YP_566560.1| 616 KCIHCGACVEICP 628
                                   5555555555555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7       4.4   4.7e+03       2       8 ..      13      19 ..      12      27 .. 0.80
   2 !   11.5   3.5   0.00034      0.36       3      16 ..     588     601 ..     586     602 .. 0.91
   3 !   18.0   3.6   2.7e-06    0.0028       2      16 ..     615     629 ..     614     631 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.4
                        Fer4_4  2 erCigCg 8 
                                   +C +C 
  gi|91773868|ref|YP_566560.1| 13 HWCKDCN 19
                                  6999996 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00034
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +C gCg+Cv  CP 
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCPK 601
                                   7************6 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.7e-06
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++Ci+Cg+Cv +CP+
  gi|91773868|ref|YP_566560.1| 615 SKCIHCGACVEICPV 629
                                   69************5 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.9   4.1e+03      19      33 ..     232     246 ..     228     252 .. 0.82
   2 !   11.7   6.1   0.00021      0.22      38      58 ..     586     605 ..     573     606 .. 0.83
   3 !   17.3  18.5   3.6e-06    0.0038       7      54 ..     588     630 ..     582     632 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.9
                       Fer4_21  19 edtshqaieidaktv 33 
                                   ed++hq i+ ++ktv
  gi|91773868|ref|YP_566560.1| 232 EDKAHQFIKHTSKTV 246
                                   799*****9998876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00021
                       Fer4_21  38 edeCvGCnlCssvCPvedcie 58 
                                   + +C+GC +C+  CP ++ci+
  gi|91773868|ref|YP_566560.1| 586 SLKCMGCGVCVGKCP-KNCIT 605
                                   569************.7***8 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 3.6e-06
                       Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPve 54 
                                   kC+gCg C+  C+    ++i+i++ +   +++++C+ C  C+++CPv 
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCP---KNCITIEDGKA--IISSKCIHCGACVEICPVV 630
                                   8************...59**9986665..89***************95 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  11.6       1.1   1.1e+03       1      14 [.     589     602 ..     589     603 .. 0.95
   2 !   17.1   5.6   7.5e-06    0.0079       1      13 [.     617     629 ..     617     631 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+gCg Cv  CP++
  gi|91773868|ref|YP_566560.1| 589 CMGCGVCVGKCPKN 602
                                   ************98 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.5e-06
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C++CgaCve CPv
  gi|91773868|ref|YP_566560.1| 617 CIHCGACVEICPV 629
                                   ************6 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.13       2      60 ..     132     193 ..     131     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                       UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspg 60 
                                   vv++  a + +L G  vl  +i+  +++++ ++  vVl  +ge++++G++r ++      ++
  gi|91773868|ref|YP_566560.1| 132 VVLDSGAVSFILKGASVLVPGIIDADPQIQVSDETVVLTPEGEIIAVGRARMSGpdMiEHKK 193
                                   45666666667889************************************998875333444 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   3.4     0.059        63       5      18 ..     588     601 ..     586     613 .. 0.86
   2 ?   10.7   4.3   0.00058      0.61       4      18 ..     615     629 ..     612     630 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.059
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                   +C++cg+Cv  +P+
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCPK 601
                                   7************7 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00058
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                   ++Ci cgaCve++P 
  gi|91773868|ref|YP_566560.1| 615 SKCIHCGACVEICPV 629
                                   69************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 ?   11.3   2.4    0.0005      0.52      36      67 .]     570     602 ..     552     602 .. 0.73
   2 ?    6.6   8.4     0.014        15       1      20 [.     588     607 ..     588     617 .. 0.80
   3 ?    8.9   4.6    0.0028       2.9       1      14 [.     616     629 ..     616     632 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0005
                       Fer4_16  36 aekkdlaedeekck.kqeaitgCdiCqdvCPan 67 
                                   ++ +++ +++e+   +  +++gC++C+  CP n
  gi|91773868|ref|YP_566560.1| 570 NDAREFMTRIERAVrRSLKCMGCGVCVGKCPKN 602
                                   55566666666665355789***********87 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C +Cg C+  CP n+i+ +
  gi|91773868|ref|YP_566560.1| 588 KCMGCGVCVGKCPKNCITIE 607
                                   5***************9966 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0028
                       Fer4_16   1 rCgtCgkCaevCPt 14 
                                   +C+ Cg+C+e+CP+
  gi|91773868|ref|YP_566560.1| 616 KCIHCGACVEICPV 629
                                   599*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4305.91
//
Query:       gi|91773869|ref|YP_566561.1|  [L=272]
Description: hypothetical protein Mbur_1930 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-11   43.8   3.1    1.3e-09   38.3   0.2    2.4  2  Cas_Cas4    Domain of unknown function DUF83
    1.1e-05   25.5   0.7    0.00012   22.1   0.7    2.0  1  PDDEXK_1    PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.049   13.2   1.6       0.12   12.0   0.4    2.2  2  VASP_tetra  VASP tetramerisation domain


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 !    6.1   0.2    0.0018        11       3      37 ..      13      44 ..      11     106 .. 0.62
   2 !   38.3   0.2   2.2e-13   1.3e-09      63     161 ..     160     262 ..     118     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0018
                      Cas_Cas4  3 tkiqyyliCkrklwlisheitleensetvelGkll 37
                                  +++  yl C+r++++ ++e tl  n   ++ G + 
  gi|91773869|ref|YP_566561.1| 13 SELLLYLKCPRQVYYTYREQTLMPN---ISSGYIE 44
                                  677789************9887766...4444444 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 2.2e-13
                      Cas_Cas4  63 ekeklvvvEvKkskkkee....aaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeiis 138
                                   ++ek+v+  ++ +k  e+    +++l + +  +l+e + g +++ G++ey ke k ++v++ +e+r+++ k+ +++++i +
  gi|91773869|ref|YP_566561.1| 160 YNEKMVPLTIRTGKCPEKgvwgNDRLHIAALSMLVEeNVGETVEFGFVEYAKEGKIRKVKVRPEDRRQVLKIRDRVDKIKD 240
                                   666666666666655433111134777888888999899999************************************999 PP

                      Cas_Cas4 139 sekppkvkkkkiCkkCayaelCl 161
                                     + p+ k+ kiC++C ++++C 
  gi|91773869|ref|YP_566561.1| 241 G-YLPERKEGKICEHCNFTQFCT 262
                                   8.9*******************6 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 !   22.1   0.7   1.9e-08   0.00012       2     254 ..      10     261 ..       9     262 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.9e-08
                      PDDEXK_1   2 lSvsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefye.......wkkldke.dleelleeaveelwpell 74 
                                   + vs+l  +l+Cp++ +++y ++    + +++   G + H +l+e+         + k++ke  leel+ ++++++ +el+
  gi|91773869|ref|YP_566561.1|  10 ANVSELLLYLKCPRQVYYTYREQT-LMPNISS---GYIEHMMLKELAMgyadvvkKAKPTKEsILEELS-AEFKRVKDELD 85 
                                   579***************999997.3567777...***********99*97776655555554555555.66666666655 PP

                      PDDEXK_1  75 leeeilessarlrylaeklkevleklverlaeeleakrg.frpvalelefg.............gekvrLkGriDrvddke 141
                                   +  +  +++ +++ +  ++k+v+  l + +a+    ++  ++  + e+                +e+++L+G+   + + +
  gi|91773869|ref|YP_566561.1|  86 FIYSTELKNVQFNVIETAQKNVFDLL-DDIAT--NISDAiIKSNKDEV--IqsivhhrtepvlhSERLKLTGIPSAIVQYN 161
                                   55555445555555555554444433.22222..22222222222221..12234555667785599***********888 PP

                      PDDEXK_1 142 gelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleall 222
                                   ++++ +   tg+ p ++    + +++l  ++  ++++e+        +++ + +++   +  +e++++k++  +e+++++l
  gi|91773869|ref|YP_566561.1| 162 EKMVPLTIRTGKCP-EKGV--WGNDRLHIAALSMLVEEN--------VGETVEFGF--VEYAKEGKIRKVKVRPEDRRQVL 229
                                   889999999***66.4444..788888888888888888........444444444..22357888888888888887777 PP

                      PDDEXK_1 223 qeleelaeeilagefparpskk.CeyCpyksvC 254
                                   + +++++++i++g  p r + k Ce+C + + C
  gi|91773869|ref|YP_566561.1| 230 K-IRDRVDKIKDGYLPERKEGKiCEHCNFTQFC 261
                                   5.677779999998888888788********** PP

>> VASP_tetra  VASP tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4     2e-05      0.12       8      26 ..      66      84 ..      65      87 .. 0.95
   2 ?   -1.9   0.0      0.42   2.5e+03      23      31 ..     127     135 ..     126     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                    VASP_tetra  8 KqEILeEvrkELqKvKeEI 26
                                  K+ ILeE+  E++ vK+E+
  gi|91773869|ref|YP_566561.1| 66 KESILEELSAEFKRVKDEL 84
                                  899**************95 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.42
                    VASP_tetra  23 KeEIIeAir 31 
                                   K+E+I  i+
  gi|91773869|ref|YP_566561.1| 127 KDEVIQSIV 135
                                   99***9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2052.54
//
Query:       gi|91773870|ref|YP_566562.1|  [L=246]
Description: XRE family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-06   28.0   0.0    5.8e-06   26.3   0.0    2.0  1  HTH_3     Helix-turn-helix
    0.00024   21.0   0.0     0.0012   18.9   0.0    2.2  3  HTH_19    Helix-turn-helix domain
  ------ inclusion threshold ------
       0.04   14.3   0.0      0.089   13.1   0.0    1.5  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 !   26.3   0.0   9.8e-10   5.8e-06       1      48 [.      32      80 ..      32      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 9.8e-10
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                  lk++R+   + q++L+ +l vs+s is++E+G + +P   ++ k+  aL
  gi|91773870|ref|YP_566562.1| 32 LKKWRLNFEIAQTDLSGYLKVSPSVISDYESGrRKSPGTLIVSKIVAAL 80
                                  89******************************88888888888887776 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.9e-07    0.0012       1      50 [.      29      78 ..      29      88 .. 0.88
   2 ?   -1.0   0.0      0.32   1.9e+03      23      46 ..      82     109 ..      77     115 .. 0.66
   3 ?   -2.5   0.0      0.88   5.2e+03      15      29 ..     229     242 ..     213     246 .] 0.59

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-07
                        HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                  Ge Lk+ R ++ + q +l++ l++s+s is +E+g+++ p+   + ki+ 
  gi|91773870|ref|YP_566562.1| 29 GEALKKWRLNFEIAQTDLSGYLKVSPSVISDYESGRRKSPGTLIVSKIVA 78
                                  99*********************************999**9877766544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.32
                        HTH_19  23 gis....rskisaiEngkkdvpsaelll 46 
                                   +i+      ki+ +E+  + +p+a+ ++
  gi|91773870|ref|YP_566562.1|  82 DIDtskgGQKIHSYEGMLYADPGAKAVY 109
                                   4444477899999997666677766665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.88
                        HTH_19  15 qeelaerlgisrski 29 
                                   ++el+e l+   s++
  gi|91773870|ref|YP_566562.1| 229 IDELVEVLKK-YSQY 242
                                   3444443333.4444 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   1.5e-05     0.089       3      42 ..      29      68 ..      29      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                        HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrp 42
                                  G+ L+ +R    + q+++ + l vs+s +s++E+Grr  p
  gi|91773870|ref|YP_566562.1| 29 GEALKKWRLNFEIAQTDLSGYLKVSPSVISDYESGRRKSP 68
                                  667777888888889999999****************855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1478.44
//
Query:       gi|91773871|ref|YP_566563.1|  [L=349]
Description: hypothetical protein Mbur_1932 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   41.5   0.0    3.2e-10   40.0   0.0    1.8  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    1.8e-05   24.5   0.0    0.00032   20.4   0.0    2.1  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    0.00028   20.8   0.4    0.00037   20.4   0.4    1.2  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
  ------ inclusion threshold ------
      0.019   14.3   0.6      0.035   13.5   0.6    1.3  1  Thiolase_N      Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   7.1e-14   3.2e-10       1      82 [.     221     302 ..     221     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 7.1e-14
                                   HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GG..GB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEET CS
                 ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpee..kvvvnldeyGntsaasiplaLdeaveegklkpgdlvllvgfGa 79 
                                   +ek g +p+d d+ v+hq n ++   vak lg+++e  k    +  +Gnt + s ++ ++  ++  + kpgd++  ++fG 
  gi|91773871|ref|YP_566563.1| 221 MEKMGTKPSDYDYAVFHQPNGKFPSRVAKMLGFTKEqiKPGLVVPWLGNTYSGSCMMGIAATLD--QAKPGDRIFATAFGS 299
                                   57899*******************************444456679*******************..89************* PP

                                   TTE CS
                 ACP_syn_III_C  80 Glt 82 
                                   G  
  gi|91773871|ref|YP_566563.1| 300 GAG 302
                                   975 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 ?    1.4   0.0     0.044     2e+02      68      82 ..     229     243 ..     209     253 .. 0.75
   2 !   20.4   0.0   7.2e-08   0.00032     139     219 ..     253     327 ..     246     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.044
                                   GG-SEEEE--SSHHH CS
                HMG_CoA_synt_C  68 ddfdyvifhsPfckl 82 
                                    d+dy +fh P  k+
  gi|91773871|ref|YP_566563.1| 229 SDYDYAVFHQPNGKF 243
                                   689********9986 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 7.2e-08
                                   HHHHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHH.HHTTTT CS
                HMG_CoA_synt_C 139 lfkkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsild.iakvld 218
                                   ++k+++kp l+vp   Gn Y  s    +a+ l    ++   g ri + ++GsG     fs+rv+++ +e  ++d   kvld
  gi|91773871|ref|YP_566563.1| 253 FTKEQIKPGLVVPW-LGNTYSGSCMMGIAATL----DQAKPGDRIFATAFGSGAGGDAFSFRVTDKIDE--VRDaAPKVLD 326
                                   68999*****9995.8****************....566679**********************99887..6664556666 PP

                                   H CS
                HMG_CoA_synt_C 219 l 219
                                   l
  gi|91773871|ref|YP_566563.1| 327 L 327
                                   5 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   8.3e-08   0.00037       4     172 ..       2     167 ..       1     169 [. 0.91

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.3e-08
                HMG_CoA_synt_N   4 dvgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgtet 84 
                                    vgi++   y+p   ++  ++ +  g +a   + gl   + +  +  ed  ++++   +  + r+++d + ig +  g+e+
  gi|91773871|ref|YP_566563.1|   2 SVGIVSYGAYIPKFRIKVEDIARVWGDDADILSAGLMVYEKSVPDLDEDTATIAVEAARSAVLRNNIDAKRIGAVYTGSES 82 
                                   59******************************************************************************* PP

                HMG_CoA_synt_N  85 iidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna.rptggaga 164
                                        k   +++ + +e      +   d   ac  gtaa+  ++  + s + d   a  +  d++  + g+a   t  ag 
  gi|91773871|ref|YP_566563.1|  83 HPYAVKPTSTIVAEAIEA--TPVLTAADFEFACKAGTAAMQACMGLVGSGMVDLGMA--IGADVSQGAPGDAlEYTAAAGG 159
                                   999999999999888887..455688999***********************97666..5789999999988356999999 PP

                HMG_CoA_synt_N 165 valligpd 172
                                   v+ +ig +
  gi|91773871|ref|YP_566563.1| 160 VSYIIGNK 167
                                   99999976 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   7.8e-06     0.035      25     112 ..      53     140 ..      43     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-06
                                   HHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHS CS
                    Thiolase_N  25 eLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaagead 105
                                    ++ ea+++++ ++++d++ +  v+ G   +  + +  +  +a +++     +a   + +c  g +a+ ++++ + +g +d
  gi|91773871|ref|YP_566563.1|  53 TIAVEAARSAVLRNNIDAKRIGAVYTGSESHPYAVKPTSTIVAEAIEATPVLTAADFEFACKAGTAAMQACMGLVGSGMVD 133
                                   577789999*******************9999998888888888888888899999************************* PP

                                   EEEEEEE CS
                    Thiolase_N 106 vvvagGv 112
                                     +a+G+
  gi|91773871|ref|YP_566563.1| 134 LGMAIGA 140
                                   *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 2033.36
//
Query:       gi|91773872|ref|YP_566564.1|  [L=390]
Description: acetyl-CoA acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-23   83.2   5.2    6.3e-23   81.5   5.2    1.9  1  Thiolase_N       Thiolase, N-terminal domain
      3e-11   43.1   1.5      4e-10   39.4   1.3    2.5  1  Thiolase_C       Thiolase, C-terminal domain
    8.2e-08   32.1   7.5    3.8e-06   26.7   7.5    2.6  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
     0.0012   18.9   0.3       0.36   10.8   0.1    3.1  2  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 !   81.5   5.2   1.4e-26   6.3e-23       1     259 [.       4     226 ..       4     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 1.4e-26
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-..TTSE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagip..eevp 77 
                                   v+i++ + t++g+    + d s +++  ea+ +++e+ g++ e++d ++vGn+  + + +q  i   +a  +g++   ++p
  gi|91773872|ref|YP_566564.1|   4 VAIIGVKNTNFGE----MWDRSFRDIVVEAGVGAIEDSGISGEKLDGMYVGNMSGGqFVEQEhIGALIADYSGLSldLHIP 80 
                                   78999999***99....9999*******************************9987766666455555555554411599* PP

                                   EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHH CS
                    Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGlt 158
                                   +++v+ +c+Sg  a  +a+ ++a+g+ d v+a GvE+m++++  ++++  + +   d++ ++++  +           ++ 
  gi|91773872|ref|YP_566564.1|  81 STRVEAACASGGLAFRQAVMAVASGHEDLVMAAGVEKMTDVSATAASA--ALAAAADREWEGIMGAT------FPGLYAMI 153
                                   *****************************************9998744..44555556666666444......33367899 PP

                                   HHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS- CS
                    Thiolase_N 159 aenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtv 239
                                   a++  ++y+ + e+++++Avk+hq+++ ++ a+ +k+ i              + d+ ++s ++a++L+            
  gi|91773872|ref|YP_566564.1| 154 AKMHMHQYGTTSEQLAAVAVKNHQNGSMNPIAQ-YKSRI--------------TIDNVLNSIMVADPLHIF---------- 209
                                   *********************************.99999..............89***************9.......... PP

                                   BTTSB--BEEEEEEEEEEEH CS
                    Thiolase_N 240 tAgnasqisDGaaavllmse 259
                                      ++s+i+DGa+a++l+++
  gi|91773872|ref|YP_566564.1| 210 ---DCSPITDGASALVLAPA 226
                                   ...**************875 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   1.3   8.9e-14     4e-10      23     106 ..     262     363 ..     239     384 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 8.9e-14
                                   HHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTH CS
                    Thiolase_C  23 gPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGas 85 
                                   + + a k++ + a +t +didl+E+++ F+   + ++++l++ +                    vN  GG  a GHP+Ga+
  gi|91773872|ref|YP_566564.1| 262 ASVVAGKRAYEMAKMTPADIDLVEVHDCFTIAEICAIEDLGFVKkglggkmtedgetaiggkIPVNTSGGLKACGHPVGAT 342
                                   45788999**********************************999***************87789**************** PP

                                   HHHHHHHHHHHHHHCTTSEEE CS
                    Thiolase_C  86 GaRivvtllselkkeggklgv 106
                                   G +++v ++++l+ + g   v
  gi|91773872|ref|YP_566564.1| 343 GIKQLVEVTQQLRGDSGPRQV 363
                                   ************987664444 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 !   26.7   7.5   8.5e-10   3.8e-06     145     221 ..      58     134 ..      16     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 8.5e-10
                                   HHHHHSTTHHHHHHHHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB- CS
                 ketoacyl-synt 145 avgavlanviagrisyalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaaglls 221
                                   + +  + + ia    ++l+l+ ps  v++AC+S+  a  +av+++ sg+ d++ a Gve ++  +a+a+ +a+++ +
  gi|91773872|ref|YP_566564.1|  58 VEQEHIGALIADYSGLSLDLHIPSTRVEAACASGGLAFRQAVMAVASGHEDLVMAAGVEKMTDVSATAASAALAAAA 134
                                   33334666777777788**********************************************99999988888544 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 !   10.8   0.1   8.1e-05      0.36      28      52 ..     265     289 ..     239     294 .. 0.82
   2 !    4.6   0.0    0.0068        31      87     114 ..     335     362 ..     329     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.1e-05
                                   HHHHHHHHHHT--GGGEEEEE-SS- CS
               Ketoacyl-synt_C  28 raiekalaeagvdpedvdyveahgt 52 
                                    a ++a+++a+++p+d+d+ve h+ 
  gi|91773872|ref|YP_566564.1| 265 VAGKRAYEMAKMTPADIDLVEVHDC 289
                                   45689******************86 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0068
                                   H-B-GGGHHHHHHHHHHHHHHHTEE--B CS
               Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkhgvippt 114
                                    GH  +A G+ +l+ v ++l+ +  p +
  gi|91773872|ref|YP_566564.1| 335 CGHPVGATGIKQLVEVTQQLRGDSGPRQ 362
                                   7******************998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2517.05
//
Query:       gi|91773873|ref|YP_566565.1|  [L=133]
Description: hypothetical protein Mbur_1934 [Methanococcoides burtonii DSM 6242]
Scores for 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   66.1   0.1    2.9e-18   65.6   0.1    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    3.2e-11   42.9   1.4    4.5e-11   42.4   1.4    1.3  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.031   14.2   0.2      0.036   13.9   0.2    1.1  1  FdhE            Protein involved in formate dehydrogenase for
      0.045   13.7   0.3      0.069   13.1   0.3    1.3  1  zinc-ribbons_6  zinc-ribbons
      0.098   13.2   0.4       0.16   12.5   0.4    1.3  1  Sar8_2          Sar8.2 family
       0.38   10.8   4.5          1    9.4   4.6    1.7  1  CxC5            CxC5 like cysteine cluster associated with KD


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 !   65.6   0.1   9.7e-22   2.9e-18       5      65 .]      50     109 ..      47     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 9.7e-22
                                   -GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                 OB_aCoA_assoc   5 sgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                   +g G+v+++t++h a++gf+ +aPy+++++eLdeg+r ++++v+ dp ev iGm V+ vfr
  gi|91773873|ref|YP_566565.1|  50 AGPGKVVTYTIIHTAAEGFEMQAPYALAIIELDEGPRFTSQVVC-DPKEVSIGMWVKPVFR 109
                                   789****************************************5.677899********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 !   42.4   1.4   1.5e-14   4.5e-11       5      33 ..      12      40 ..       8      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.5e-14
                       DUF35_N  5 aegrLvgqrCpdCGtvqfPPravCphCgs 33
                                   ++ +vg++C+ C+t+++PPr+vCp+C++
  gi|91773873|ref|YP_566565.1| 12 NRYNIVGTHCKTCDTHYYPPRNVCPKCRR 40
                                  6999***********************86 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.2e-05     0.036     181     225 ..       2      49 ..       1      59 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                   EEEE-------EEE....EEETTT--EEE--TTS-TTT---SS-EEE-- CS
                          FdhE 181 svvriggeaeglRy....lhCslCeteWhvvRvkCsnCeetkelaylsl 225
                                   sv r++  ++  Ry     hC +C t++   R  C +C  + +++  ++
  gi|91773873|ref|YP_566565.1|   2 SVARFWR-KQINRYnivgTHCKTCDTHYYPPRNVCPKCRRHGDIEAYKF 49 
                                   5556666.666677544469*********************99987766 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.3e-05     0.069      15      37 ..      17      40 ..       6      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                                  SEEE-TTT--EE.EEEEE-SSS-S CS
                zinc-ribbons_6 15 eqyhCeaCqedl.kkealCpeCeq 37
                                    +hC++C++++    ++Cp+C+ 
  gi|91773873|ref|YP_566565.1| 17 VGTHCKTCDTHYyPPRNVCPKCRR 40
                                  568******97615799*****86 PP

>> Sar8_2  Sar8.2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   5.3e-05      0.16      64      92 ..       9      38 ..       2      40 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                        Sar8_2 64 kaakvkyivgkackickcknq.icskcpkc 92
                                  k  +  +ivg  ck+c + +    + cpkc
  gi|91773873|ref|YP_566565.1|  9 KQINRYNIVGTHCKTCDTHYYpPRNVCPKC 38
                                  5556678***********875145778888 PP

>> CxC5  CxC5 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.6   0.00035         1      45      67 ..      15      37 ..       4      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00035
                          CxC5 45 wvlslyCpkCktrYypdyyvhdg 67
                                   ++ ++C++C t+Yyp + v  +
  gi|91773873|ref|YP_566565.1| 15 NIVGTHCKTCDTHYYPPRNVCPK 37
                                  57889***********9998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 858.72
//
Query:       gi|91773874|ref|YP_566566.1|  [L=171]
Description: adenylate cyclase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-33  114.9   1.6    4.4e-33  114.7   1.6    1.0  1  CYTH      CYTH domain


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   1.6   2.5e-37   4.4e-33       1     179 []       1     165 [.       1     165 [. 0.88

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 2.5e-37
                                   EEEEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEE.EEEEEECSSST...E CS
                          CYTH   1 miEvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgee.ltlKgpgvdge...r 77 
                                   miE+E+K++ ++a  +d   r  +l+a++++t+   d+Yy++p+rd+a+tdeaLR+R  + dg + +t+Kg ++d+    r
  gi|91773874|ref|YP_566566.1|   1 MIEIEIKVRAEHALVKD---RVIKLGAQKVRTEDHVDVYYNSPHRDFAKTDEALRLR--SVDGGTrMTYKGKKLDEVsktR 76 
                                   89********5444444...4669*********************************..7889999*******99844455 PP

                                   EEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHH CS
                          CYTH  78 eevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedeeevkeaae 158
                                            eE+e p++   +a  +l++lg+ + ++vkk+R +yk++++++++D ve+l ge+vE+El ++++ e  + +e
  gi|91773874|ref|YP_566566.1|  77 ---------EEFETPVD-GVAARGILNALGFFESGVVKKTRDIYKFDEITICFDNVEGL-GEFVEVELVADSDIE--AHRE 144
                                   .........55555555.4445679**********************************.********9999888..7789 PP

                                   HHHHHHHHTTEEGGGBSCSHH CS
                          CYTH 159 kllallrelglssaskirrsy 179
                                    l+++l+ +g+++++ ir+sy
  gi|91773874|ref|YP_566566.1| 145 RLFEFLESMGIKKEDSIRTSY 165
                                   99*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1060.51
//
Query:       gi|91773875|ref|YP_566567.1|  [L=684]
Description: methionyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-148  493.7   0.1   4.3e-148  493.2   0.1    1.2  1  tRNA-synt_1g    tRNA synthetases class I (M)
    2.4e-26   91.7   0.5    6.3e-26   90.3   0.5    1.8  1  tRNA_bind       Putative tRNA binding domain
      7e-20   70.8   0.0    7.1e-10   37.8   0.0    4.1  3  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    4.2e-19   69.0   4.9      8e-19   68.1   4.9    1.5  1  Anticodon_1     Anticodon-binding domain of tRNA
    1.8e-13   50.5   0.4      2e-09   37.2   0.0    2.7  3  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
     0.0019   17.2   0.0       0.17   10.8   0.0    2.5  2  tRNA-synt_1f    tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.028   14.1   0.8      0.063   12.9   0.8    1.5  1  TackOD1         Thaumarchaeal output domain 1
        1.7    8.7   9.2        5.2    7.1   8.7    2.0  1  zinc-ribbons_6  zinc-ribbons
        3.7    7.6  11.1        1.3    9.1   3.7    2.4  2  DZR             Double zinc ribbon


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 !  493.2   0.1  2.2e-151  4.3e-148       1     391 []      10     396 ..      10     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 493.2 bits;  conditional E-value: 2.2e-151
                                   EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHT CS
                  tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkkl 81 
                                   vlvt++lpYangk H+Ghl+++++aDif+R  +++g+ev+fvcg+D+hGtpi  +Ae+ ++tp e+++ +h++++e+fkk+
  gi|91773875|ref|YP_566567.1|  10 VLVTCGLPYANGKAHVGHLRTYVPADIFTRSLKKTGQEVTFVCGSDTHGTPIVFNAEELKTTPTEIIKVYHKHFDEIFKKM 90 
                                   69******************************************************************************* PP

                                   T---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.-TTSSB-E. CS
                  tRNA-synt_1g  82 nisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.eecgkklep 161
                                   ++  d++g+t++ ++++ + ei++kl e+g++y k+ie +ycp+++r lpdryv+gtCP+ck +eargd+c + cgk+lep
  gi|91773875|ref|YP_566567.1|  91 GVMLDAFGTTDDPTNHNRTTEIVSKLIENGYVYPKTIEIAYCPSCDRSLPDRYVKGTCPHCK-KEARGDECdQGCGKHLEP 170
                                   **************************************************************.77******889******* PP

                                   ...............EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EETTECC CS
                  tRNA-synt_1g 162 telinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvPgaek 242
                                    el+ p ++ ++  +e+k++eh+ffkls+f+++l e++  e    + n++++++ w+k++L+d++i+r ldwGi++Pg+e+
  gi|91773875|ref|YP_566567.1| 171 GELEHPACTTCNGPAEYKQQEHFFFKLSQFKDFLLEYL--EGLGGTLNARNYALGWVKQELTDWCITRSLDWGIKFPGHED 249
                                   **************************************..4446999********************************** PP

                                   EEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE--EEE CS
                  tRNA-synt_1g 243 kvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillgaelklpkkvvaheyltv 323
                                    v+YVW+dA+igYi++t+e+a  + ++e+w+++W  +++ +++hfig dii++H+ifwPa+l+ga++++p++vva++++++
  gi|91773875|ref|YP_566567.1| 250 LVVYVWVDAPIGYIAFTEEWA--EANNESWEKFW--KDDGSIIHFIGGDIIYHHCIFWPAMLKGAGYNQPDAVVASGMVKI 326
                                   ********************9..5569*******..579****************************************** PP

                                   --------------H.HHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
                  tRNA-synt_1g 324 egkKlSkSrgvvvka.kealer.ldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                                   e++ +SkSrg+vv++ +++l++ +++dllRYyla+ ++++k+l+fsw+ f+++vN+eL++ +gn+++R+l
  gi|91773875|ref|YP_566567.1| 327 EDRTFSKSRGYVVWVdEDYLDHgFHQDLLRYYLASYTSHTKELNFSWKVFQDKVNTELVGVFGNFLYRTL 396
                                   **************96789*************************************************85 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.5   3.2e-29   6.3e-26       1      95 [.     588     681 ..     588     682 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.2e-29
                                   EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESSC CS
                     tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldeke 81 
                                   +r+G++++ae +++++kLl+l+vd+Geee rqiv+g+k+  epe+l++k+v+v+ nl p+kl GveS+GM+l+  + + ++
  gi|91773875|ref|YP_566567.1| 588 IRIGTIVSAEAIKKSKKLLKLQVDLGEEETRQIVAGLKESHEPEQLIGKQVAVLTNLAPAKLCGVESNGMVLAGVD-AADN 667
                                   79*************************************************************************5.9999 PP

                                   EEEEEESST--TTC CS
                     tRNA_bind  82 vgilelpadveaGe 95 
                                     +l++++++++G+
  gi|91773875|ref|YP_566567.1| 668 AILLQPEKETNPGT 681
                                   ************97 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   3.6e-13   7.1e-10      25     175 ..      10     141 ..       2     147 .. 0.87
   2 !   23.1   0.0   9.6e-09   1.9e-05     353     438 ..     166     251 ..     159     289 .. 0.76
   3 ?    2.2   0.0     0.021        41     550     602 .]     318     372 ..     299     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 3.6e-13
                   tRNA-synt_1  25 filvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvr 105
                                     ++ g Py++G+ H+Gh  + +  di +r+ + +G+ev++v G D++G +i  + e+                  +    
  gi|91773875|ref|YP_566567.1|  10 VLVTCGLPYANGKAHVGHLRTYVPADIFTRSLKKTGQEVTFVCGSDTHGTPIVFNAEEL-----------------KTTPT 73 
                                   5677899********************************************97665543.................34446 PP

                   tRNA-synt_1 106 ewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalse 175
                                   e+ + y+++  + +k++Gv++D      T d+  ++ ++e+  +l+++g +y  +  + +++++  +l +
  gi|91773875|ref|YP_566567.1|  74 EIIKVYHKHFDEIFKKMGVMLDA--FGTTDDPTNHNRTTEIVSKLIENGYVYPKTIEIAYCPSCDRSLPD 141
                                   7888999999**********993..456888999999***************************998866 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 9.6e-09
                   tRNA-synt_1 353 lkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhripl 433
                                    + e+ e++ p c   + p +y+ +e  f ++++++d +l+ +e    + + ++       ++  dWci R++ WG + p 
  gi|91773875|ref|YP_566567.1| 166 KHLEPGELEHPACTTCNGPAEYKQQEHFFFKLSQFKDFLLEYLEGLGGTLNARNYALGWVKQELTDWCITRSLDWGIKFPG 246
                                   6778889999**********************************99999988877777666789*************9996 PP

                   tRNA-synt_1 434 fvske 438
                                   + +  
  gi|91773875|ref|YP_566567.1| 247 HEDLV 251
                                   55444 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.021
                   tRNA-synt_1 550 vlvhglvrdeeGrKmSKslgNvi..dpldvikkygadalRltli.lsdvgrdinls 602
                                   v+ +g+v  e+ r  SKs g v+  d +++ +    d lR++l+ +++ ++++n+s
  gi|91773875|ref|YP_566567.1| 318 VVASGMVKIED-RTFSKSRGYVVwvDEDYLDHGFHQDLLRYYLAsYTSHTKELNFS 372
                                   66677776554.899*****9863256666667789********9******99986 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   4.9     4e-22     8e-19       2     146 ..     413     560 ..     412     569 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 4e-22
                   Anticodon_1   2 rwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrllaPfm 81 
                                   + il e+n +++ ++ea+e+y+f+k a+ ++ +   ++ ++y+++++p+   ++++++  ++ ++++ + ++l+ l++P++
  gi|91773875|ref|YP_566567.1| 413 QDILDEINTTIENAKEAMENYEFKKYADTVMAL--ASYGNTYFQSNEPWKLIKENKEAcGEIVKNCAQITKALCLLFEPIL 491
                                   679*****************************8..899**************99988866688****************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpekaeel....ekele......eeevellkeivkairklrselkikpss 146
                                   P  +Ee+w    +++g +++++  ++ e+  el    ++  e      e+  +   e ++ai ++r ++ i++ +
  gi|91773875|ref|YP_566567.1| 492 PEKMEEAW----KQIGMETDVHETNYMEAT-ELvksgTTL-EkpsilfEKIEDEKTEEMEAISAARVKEAIAKEN 560
                                   ********....**************9733.343565222.2366888666666666699999999999998765 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 !   37.2   0.0     1e-12     2e-09      14     125 ..      13     126 ..       3     145 .. 0.87
   2 !   10.5   0.0   0.00014      0.28     241     296 ..     318     376 ..     286     381 .. 0.76
   3 ?   -1.8   0.1      0.78   1.6e+03      76     110 ..     533     570 ..     416     579 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1e-12
                                   EEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT-- CS
                  tRNA-synt_1e  14 vCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvl 93 
                                   +CG p +  ++h+Gh R++v  Di+ r l+++g +v+fv         i+ +a+e +++ +e+ + + ++f + +++++v 
  gi|91773875|ref|YP_566567.1|  13 TCGlPYANGKAHVGHLRTYVPADIFTRSLKKTGQEVTFVCGSDTHGTPIVFNAEELKTTPTEIIKVYHKHFDEIFKKMGVM 93 
                                   67734567899****************************998888899*******************************98 PP

                                   --SB.--BGGGGHHHHHHHHHHHHHTTSEEE-T CS
                  tRNA-synt_1e  94 kptl.eprvsekvdeiielvekliekgyaYavs 125
                                      + ++    + +   e+v klie+gy Y+ +
  gi|91773875|ref|YP_566567.1|  94 LDAFgTTDDPTNHNRTTEIVSKLIENGYVYPKT 126
                                   76551555667778999*************987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                                   EEEE--EEETTBE--TTTT---BHH.HHHTT.S-HHHHHHHHHSS.-TTS-EEE-HHHH CS
                  tRNA-synt_1e 241 flhnghlkiegekmsksLknfitik.dvlkk.fdprqlRllllsa.hyrsqldfkeell 296
                                    + +g++kie++  sks + ++ +  d l + f++  lR++l+s   + ++l+f+ + +
  gi|91773875|ref|YP_566567.1| 318 VVASGMVKIEDRTFSKSRGYVVWVDeDYLDHgFHQDLLRYYLASYtSHTKELNFSWKVF 376
                                   5679******************997256754489999*****98526788999987665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.78
                                   HHHHHHHHHHHHHHT...T----SB--BGGGGHHHHHH CS
                  tRNA-synt_1e  76 aekfieefkkdleaL...nvlkptleprvsekvdeiie 110
                                    ek+++e ++++ea+    v+++ ++   +e+v+e+ e
  gi|91773875|ref|YP_566567.1| 533 FEKIEDEKTEEMEAIsaaRVKEAIAKENGTEEVEEVKE 570
                                   33344444444443311156667777777777776655 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   8.4e-05      0.17      24      70 ..       9      56 ..       2      59 .. 0.86
   2 ?    3.5   0.0     0.014        27     263     325 ..     312     375 ..     306     381 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.4e-05
                  tRNA-synt_1f 24 evvvesGis.pSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                   v+v  G+  + G+ H+G lr  + ad+  r+l+k g+ev +++ sD+
  gi|91773875|ref|YP_566567.1|  9 PVLVTCGLPyANGKAHVGHLRTYVPADIFTRSLKKTGQEVTFVCGSDT 56
                                  667777775257********************************9997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                  tRNA-synt_1f 263 geaPekvvYelillkggekmssSkGnvltled.wlev.aepevlrflilrrkPkkakkldldlei 325
                                   +++P  vv   +   +++  s+S+G v+ +++  l+   ++++lr+++++    + k+l+++ ++
  gi|91773875|ref|YP_566567.1| 312 YNQPDAVVASGMVKIEDRTFSKSRGYVVWVDEdYLDHgFHQDLLRYYLAS-YTSHTKELNFSWKV 375
                                   56666655544444444599*******999652665527999*****999.66777777776554 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   3.2e-05     0.063     132     177 ..     115     160 ..     106     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                       TackOD1 132 kLrhiGvDYdrplevykCnsCkslfsepevkarClsCekesesddl 177
                                   kL + G  Y + +e+  C sC+++  +  vk +C +C+ke + d++
  gi|91773875|ref|YP_566567.1| 115 KLIENGYVYPKTIEIAYCPSCDRSLPDRYVKGTCPHCKKEARGDEC 160
                                   78889999*******************************9998876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.7    0.0026       5.2       2      40 ..     131     169 ..     130     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0026
                                   --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S--- CS
                zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqele 40 
                                   +Cp+C++ l  r  + +C +C+++ +   + + C+++le
  gi|91773875|ref|YP_566567.1| 131 YCPSCDRSLPDRYVKGTCPHCKKEARGDECDQGCGKHLE 169
                                   8***********************998887788999998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.7   0.00065       1.3      13      38 ..     130     155 ..     124     161 .. 0.83
   2 ?    3.4  11.6     0.039        77       1      48 [.     132     181 ..     132     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00065
                           DZR  13 rfCseCgtklkavaaedrCpsCgekv 38 
                                    +C+ C  +l+    + +Cp+C++++
  gi|91773875|ref|YP_566567.1| 130 AYCPSCDRSLPDRYVKGTCPHCKKEA 155
                                   699****99998888999***99876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.039
                           DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrCps.Cgekvdpe...arfCpeC 48 
                                   Cp+C + lp++    +C++C+++ +     d C++ Cg+ ++p+   +  C  C
  gi|91773875|ref|YP_566567.1| 132 CPSCDRSLPDRYVkgTCPHCKKEAR----GDECDQgCGKHLEPGeleHPACTTC 181
                                   9*********988789*******99....6888755887776641114446666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 4041.69
//
Query:       gi|91773876|ref|YP_566568.1|  [L=410]
Description: signal peptide peptidase A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-43  148.0   0.1    2.8e-43  147.5   0.1    1.2  1  Peptidase_S49  Peptidase family S49
    0.00032   20.6   0.7     0.0055   16.6   0.1    2.3  2  CLP_protease   Clp protease
    0.00097   19.0   0.3     0.0048   16.7   0.1    2.2  3  Ligase_CoA     CoA-ligase


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   0.1   4.7e-47   2.8e-43       3     152 ..     213     362 ..     211     364 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 4.7e-47
                                   HHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS--HH CS
                 Peptidase_S49   3 kkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrreltee 83 
                                   ++ + Pvv+s+++vaaS++Yy+++ ad ivanpst +gsiGvi   +n ++++d  g+e+ v k G++k+++   r lt e
  gi|91773876|ref|YP_566568.1| 213 QDMGVPVVISMGDVAASAAYYISAPADLIVANPSTTTGSIGVISVYTNRSEFYDEEGIEFYVSKLGSFKDVGGDWRGLTSE 293
                                   57799**************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCH CS
                 Peptidase_S49  84 ereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelak 152
                                   e+e++ + + ++y+ F+++Va+nRn+++++v++iA+gr++ g++A+k gLvdelg++ da++ ++el +
  gi|91773876|ref|YP_566568.1| 294 EKEYVDNVVLDVYDLFITSVAENRNMTKSEVKDIADGRIYIGKEAQKIGLVDELGNFYDAIDAAAELGG 362
                                   ****************************************************************99765 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   9.3e-07    0.0055      28      95 ..     167     237 ..     158     249 .. 0.81
   2 ?    1.9   0.1     0.029   1.7e+02     142     178 ..     312     347 ..     292     349 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.3e-07
                                   HHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEE.EEETHHHHHHHT CS
                  CLP_protease  28 evankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlG.laaSmgslllaa 95 
                                   ++++++++ L  +   d+ k i+l +ns GGs  a+ +I   ++ +      ++i +G +aaS++  + a 
  gi|91773876|ref|YP_566568.1| 167 ATSEDVCNSLRKATDDDSVKAIVLRVNSGGGSPVAAEEIVTEIKRVqdMGVPVVISMGdVAASAAYYISAP 237
                                   578999************************************99984323345777875677777777665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.029
                                   HHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE CS
                  CLP_protease 142 ilakhtgqslekiekdldrdtflsaeeAveyGLidev 178
                                    +a++ +++ ++++ d+   ++   +eA++ GL+de 
  gi|91773876|ref|YP_566568.1| 312 SVAENRNMTKSEVK-DIADGRIYIGKEAQKIGLVDEL 347
                                   56666666666665.45555666689*********96 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         2   1.2e+04      39      50 ..      78      89 ..      72      92 .. 0.81
   2 ?   -1.8   0.0       0.4   2.4e+03      68      82 ..     140     154 ..     138     158 .. 0.86
   3 !   16.7   0.1     8e-07    0.0048      59     110 ..     170     220 ..     167     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2
                                  EEE-TSS--... CS
                    Ligase_CoA 39 iidlGddaftkG 50
                                   +d+Gd + + G
  gi|91773876|ref|YP_566568.1| 78 YVDVGDKRVPYG 89
                                  69****998876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.4
                                   HHS-TT-SEEEEEEE CS
                    Ligase_CoA  68 laadpevkvilldiv 82 
                                   ++ d++v+vi ++++
  gi|91773876|ref|YP_566568.1| 140 YTTDDKVAVIYVQGF 154
                                   789*******99987 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 8e-07
                                   HHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S- CS
                    Ligase_CoA  59 tkriealkklaadpevkvilldivlGygahedpaaellkaikeakaegrelp 110
                                   +++ + l+k + d++vk+i+l +  G g +   a+e++ +ik+++++g +++
  gi|91773876|ref|YP_566568.1| 170 EDVCNSLRKATDDDSVKAIVLRVNSG-GGSPVAAEEIVTEIKRVQDMGVPVV 220
                                   5678899*******************.******************8776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2787.20
//
Query:       gi|91773877|ref|YP_566569.1|  [L=321]
Description: translation initiation factor IF-2B subunit delta [Methanococcoides burtonii DSM 6242]
Scores for complete 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-87  291.5   4.0    6.3e-87  291.3   4.0    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.3   4.0   3.5e-91   6.3e-87       1     282 []      28     302 ..      28     302 .. 0.99

  Alignments for each domain:
  == domain 1  score: 291.3 bits;  conditional E-value: 3.5e-91
                                   SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHH CS
                         IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakkslie 81 
                                   ++rG+ +ia aa+ +l++++ ++k ++ +++ +++ +a++ L+++rPtavsl na++  ++     +  ++v+ea++++++
  gi|91773877|ref|YP_566569.1|  28 EIRGAGRIAEAASAALRDYVLRIKVTNIKDFNKKVDEAANILIQTRPTAVSLPNAVQLTKR-----HTATEVSEAREEILR 103
                                   589**********************************************************.....999************ PP

                                   HHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXEEE CS
                         IF-2B  82 kikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagipvt 162
                                   +++++++++ +a ek+g+i+a++i+dgd+i+T+cns ++l+v+ +a +++k+++Vi++EsrPr qG  t+keL+++gip+t
  gi|91773877|ref|YP_566569.1| 104 NADRFLEQAGQALEKMGEIGAKRIHDGDVIMTHCNSHAALSVITTAFEQGKDISVIATESRPRRQGLITIKELNDHGIPTT 184
                                   ********************************************************************************* PP

                                   EEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHH CS
                         IF-2B 163 litdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeell 243
                                   li+dsav+y+m+  vd+vivGAd+i+ nGa++nk+GTs+lA++A+e++ ++l vae++kfs+++  ++ i ieer pee++
  gi|91773877|ref|YP_566569.1| 185 LIVDSAVRYCMKD-VDTVIVGADAITINGALVNKVGTSQLALAANEARKNLLCVAETFKFSPKTIQGDMIDIEERSPEEVI 264
                                   *************.******************************************************************* PP

                                   EETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                         IF-2B 244 nitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                     +     + ++kv npafD+tP+e+I++iITevG++pp
  gi|91773877|ref|YP_566569.1| 265 DSDILAGMP-NVKVKNPAFDITPAEYIDMIITEVGAFPP 302
                                   ***999988.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2245.30
//
Query:       gi|91773878|ref|YP_566570.1|  [L=79]
Description: hypothetical protein Mbur_1939 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 602.60
//
Query:       gi|91773879|ref|YP_566571.1|  [L=454]
Description: aldehyde dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-138  460.1   0.0   7.4e-138  459.9   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.9   0.0  4.1e-142  7.4e-138       8     461 ..       3     450 ..       1     451 [. 0.97

  Alignments for each domain:
  == domain 1  score: 459.9 bits;  conditional E-value: 4.1e-142
                                   EEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH CS
                        Aldedh   8 tievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara 88 
                                   ++ +inPa+g+v ++++  ++++vd +++++ e f+ w++l+  eRa +++++a++l+++k+elae++t+e+Gkp+++a a
  gi|91773879|ref|YP_566571.1|   3 KMTSINPANGTVNGEFEFHSPDEVDLILKRSSESFQYWSSLKGVERAVYIENVAKVLRSDKQELAETITMEMGKPIRQALA 83 
                                   6899***************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHH CS
                        Aldedh  89 eveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetpls 168
                                   eve+++++++ +a+ +   le +v++   +  a++ +eP+G v+aI PWNfPl  ++ ++ + la GNt+vlK +  +p++
  gi|91773879|ref|YP_566571.1|  84 EVEKCASMFDHFATNICSlLEPDVVKE--SPSAFISYEPMGAVLAIKPWNFPLWQVLSAASHILAGGNTMVLKHSGYVPMC 162
                                   ***************988577799777..5799************************************************ PP

                                   HHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSH CS
                        Aldedh 169 alllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaD 249
                                   al +  +fe+ag+P+gv++ v  +g  +++ l++ pe+++vsftG+ + g+++a+ a++n+k+++lElGG +p+ivledaD
  gi|91773879|ref|YP_566571.1| 163 ALNIESVFEKAGFPEGVFQTVLVDGP-TASSLISRPEIAAVSFTGGLSAGQNVAEVAGRNMKKCVLELGGSDPFIVLEDAD 242
                                   ***********************997.66677888********************************************** PP

                                   HHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHT CS
                        Aldedh 250 ldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakee 330
                                   ++ka++a v+g f+n+GQ+Ci+ +r+++++s++def++++ve ++klk+gdpld dtd+GPl++ +q++ +e ++ +a++ 
  gi|91773879|ref|YP_566571.1| 243 IEKAAKAGVAGRFLNTGQTCISSKRFIIESSVVDEFTSAFVENTRKLKIGDPLDADTDLGPLVRDKQVSLLEHQIYNAISM 323
                                   ********************************************************************************* PP

                                   TSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHH CS
                        Aldedh 331 gaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdleraer 411
                                   gak+ lGg    + + +gy+++P+vl+nv+  m++++eE+FGPV+++i++++e ea+++aN+te+GL+a++++ d ++a  
  gi|91773879|ref|YP_566571.1| 324 GAKVELGG---GKVEGDGYYFSPVVLSNVSLYMQVMKEETFGPVAPIISVETESEALDVANATEFGLGASIWSGDKDKASL 401
                                   ******99...78899***************************************************************** PP

                                   HHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEE CS
                        Aldedh 412 vaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevkt 461
                                   +a++++ G v++N   + +a+  pfgGvk+Sg+Gre ++ g+ e++++++
  gi|91773879|ref|YP_566571.1| 402 LASQVQSGVVGVNGFFKPEADL-PFGGVKKSGIGRELSRFGFYEFMNIRS 450
                                   ***************9999999.***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2906.12
//
Query:       gi|91773880|ref|YP_566572.1|  [L=479]
Description: hypothetical protein Mbur_1941 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-65  218.3   0.0    9.6e-65  217.9   0.0    1.2  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase
  ------ inclusion threshold ------
       0.17   11.5   0.0       0.37   10.4   0.0    1.5  1  MmcB-like       DNA repair protein MmcB-like


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 !  217.9   0.0   1.1e-68   9.6e-65       3     204 ..      84     280 ..      82     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.9 bits;  conditional E-value: 1.1e-68
                                   ---SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS----- CS
                tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPtelk 83 
                                    d+dl+if+S+H+s++g++lLT+H+tGn+g+a++GG p+el++aaP +l+ llr++++++ +  +f+v++E tHHGP++l+
  gi|91773880|ref|YP_566572.1|  84 LDCDLLIFASKHKSADGRRLLTAHFTGNPGSADFGGYPGELSMAAPFALRCLLRNMAELS-ESIGFDVSMESTHHGPSDLD 163
                                   689*********************************************************.99****************** PP

                                   S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG--HHH CS
                tRNA_deacylase  84 vPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyaleelkeev 164
                                   vPs+++EiGS+e eW d+da+++va+++l++ +     ++v +g+GGgHYa r+++lvl +++++Gh +++y+l+ ++ ++
  gi|91773880|ref|YP_566572.1| 164 VPSVYAEIGSSEVEWVDQDAGDIVARSILSVRSGF---CPVGIGFGGGHYAARQSELVLGSDISFGHNFPNYQLQFVDVDM 241
                                   *******************************6666...******************************************* PP

                                   HHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                tRNA_deacylase 165 ikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                   +++a+e+s gad+++ d+k+++s++k++i+el++e g++v
  gi|91773880|ref|YP_566572.1| 242 FRKAVERS-GADLVYCDRKAMSSDEKKRINELADEFGLDV 280
                                   ********.**************************99987 PP

>> MmcB-like  DNA repair protein MmcB-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   4.2e-05      0.37      34      89 ..      39      95 ..      25      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.2e-05
                     MmcB-like 34 pelsLasGrraDlvalskkgeiwiieiks.sveDfrtDrkWpeyrahcDrlffavee 89
                                   e+s++ G   Dl a+ + g+  iie+    +    +Drk +e    cD l fa ++
  gi|91773880|ref|YP_566572.1| 39 VEMSVPGGIFDDLSAVYQSGNFYIIEVTEhHIYQDGIDRKIEEAGLDCDLLIFASKH 95
                                  5899999*******************9752688889******************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3268.30
//
Query:       gi|91773881|ref|YP_566573.1|  [L=368]
Description: cell division protein FtsZ [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-41  143.2   0.2    1.7e-41  142.6   0.2    1.3  1  Tubulin         Tubulin/FtsZ family, GTPase domain
      4e-35  120.0   0.4    1.3e-34  118.4   0.4    1.9  1  FtsZ_C          FtsZ family, C-terminal domain
  ------ inclusion threshold ------
       0.02   14.8   2.4      0.039   13.9   0.2    2.2  2  NAD_binding_10  NAD(P)H-binding
        1.2    8.3   4.3       0.93    8.6   2.1    1.9  2  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.6   0.2   3.8e-45   1.7e-41       1     196 [.      43     203 ..      43     204 .. 0.98

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 3.8e-45
                                   EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                       Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                   +i+v+g+G++G++ ++++ +    e gi             +g +e +    a++td+q+l +++++      +k+l+g +
  gi|91773881|ref|YP_566573.1|  43 NIKVVGCGGGGSNSAQRMQQ----E-GI-------------KG-AEVV----AVNTDAQHLLNVTTE------RKILIGRK 94 
                                   699*****************....8.**.............78.7777....***************......******** PP

                                   CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G CS
                       Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefse 162
                                   +++++gag+ p++g+ aa e+ +e+r  ve++d+   +fita+lgGGTG+G +pv++e++++   +al+++vv+lP++  e
  gi|91773881|ref|YP_566573.1|  95 KTRGLGAGSLPQIGEDAALESIDEVRSIVEGSDM---VFITAGLGGGTGTGSAPVVAEAARDA--GALTIAVVTLPFSV-E 169
                                   **********************************...**************************..**************.* PP

                                   -HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                       Tubulin 163 vvvepynailalkelieesdavividNdaLlkil 196
                                   + v+ +na+ +l++l++ +d+viv++Nd+Ll+++
  gi|91773881|ref|YP_566573.1| 170 GHVRRENAEAGLERLRDVADTVIVVPNDKLLEVV 203
                                   ******************************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 !  118.4   0.4   2.8e-38   1.3e-34       1      94 [.     251     344 ..     251     345 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2.8e-38
                                   EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT- CS
                        FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavideel 81 
                                   GvAm+g+Gea+ge++a e++++a++spLLdvd+sgA+++lvn+ gg+d+t+ E+e+v++++++++d++a++i+Ga++d++l
  gi|91773881|ref|YP_566573.1| 251 GVAMIGLGEADGENKAVESVQKALRSPLLDVDISGATSALVNVVGGPDMTIAEAESVVQEVYSRIDPNARLIWGAQVDPDL 331
                                   99******************************************************************************* PP

                                   -SEEEEEEEEES- CS
                        FtsZ_C  82 edeirvtvvatgl 94 
                                   e ++r++ v+tg+
  gi|91773881|ref|YP_566573.1| 332 EHSVRTMLVVTGV 344
                                   ************8 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.16   7.3e+02      40      79 ..      15      62 ..       4      91 .. 0.47
   2 ?   13.9   0.2   8.6e-06     0.039      46      98 ..     111     164 ..     106     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                                  TCEEEE--TT-CCHHHHHHT........T-SEEEES---TCCHHHHHH CS
                NAD_binding_10 40 glevvegdvtdvedlaealk........gadaVvsalggggkdeegak 79
                                  ++++ +g v+++ed+ + l+        ++ +V + +gg+++ +++ +
  gi|91773881|ref|YP_566573.1| 15 ETQIRSGGVSQSEDINAELEamlkdlqtNIKVVGCGGGGSNSAQRMQQ 62
                                  344444444444444444443333332255555555555555444422 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.6e-06
                                   --TT-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEEE CS
                NAD_binding_10  46 gdvtdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvsa 98 
                                   + +++ +++++ ++g d V++++g gg++ +g a  +++aa+ ag   + +v+ 
  gi|91773881|ref|YP_566573.1| 111 AALESIDEVRSIVEGSDMVFITAGLGGGTGTGsAPVVAEAARDAGALTIAVVTL 164
                                   568999****************98777755555889999******999888875 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.39   1.7e+03       2      11 ..      46      55 ..      23      66 .. 0.69
   2 ?    8.6   2.1   0.00021      0.93     153     182 ..     124     153 ..      87     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.39
                     Tubulin_2  2 viGLGGtGgk 11
                                  v+G+GG G++
  gi|91773881|ref|YP_566573.1| 46 VVGCGGGGSN 55
                                  4666666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00021
                     Tubulin_2 153 eeglnvfVvgSLaGGTGSGiflDvayllrk 182
                                   e++  vf+  +L GGTG G++  va   r+
  gi|91773881|ref|YP_566573.1| 124 EGSDMVFITAGLGGGTGTGSAPVVAEAARD 153
                                   33468**************99877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2686.02
//
Query:       gi|91773882|ref|YP_566574.1|  [L=69]
Description: preprotein translocase subunit SecE [Methanococcoides burtonii DSM 6242]
Scores for complete 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-06   26.6   0.6    4.6e-06   26.4   0.6    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.6   2.6e-10   4.6e-06       4      49 ..      19      64 ..      16      69 .] 0.89

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-10
                                  HHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SecE  4 fkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsk 49
                                  +k   + lk   +P+r+E+l +++v  ++++++g+++fl+ ++++ 
  gi|91773882|ref|YP_566574.1| 19 LKSYLRVLKLSKKPSREEFLMISKVAGAGILVIGFVGFLIYVLLTE 64
                                  677788999*******************************988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 551.56
//
Query:       gi|91773883|ref|YP_566575.1|  [L=154]
Description: transcription antitermination protein NusG [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-26   90.6   0.2    6.3e-26   90.1   0.2    1.3  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    5.1e-07   29.4   1.0    8.1e-06   25.6   0.3    2.5  2  KOW       KOW motif
  ------ inclusion threshold ------
       0.13   12.8   0.0          4    8.0   0.0    2.5  1  NusG      Transcription termination factor nusG


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 !   90.1   0.2   1.1e-29   6.3e-26       2      84 .]       7      85 ..       6      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 1.1e-29
                      Spt5-NGN  2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEvedll 84
                                  i+ vk+ta+qEr+va++l++     akkenl+I+S++apdelkGy+++E++++ ave+a++++p++r+vv+g+++i+E+e++l
  gi|91773883|ref|YP_566575.1|  7 IFVVKTTANQERSVAAMLAQV----AKKENLDIRSIIAPDELKGYVLLESSDSGAVEQAIQTVPHARTVVKGQSTIAEIEHFL 85
                                  9*****************998....99******************************************************98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.3   1.4e-09   8.1e-06       2      32 .]      97     127 ..      96     127 .. 0.91
   2 ?    1.9   0.0     0.041   2.4e+02       1       9 [.     140     148 ..     140     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-09
                                   TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                           KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                   G + +V+sGp+kG++++V++vd+  + ++v+
  gi|91773883|ref|YP_566575.1|  97 GAIIEVTSGPFKGEKARVKRVDEGHEEITVE 127
                                   8899******************998888876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.041
                                   TTSEEEESS CS
                           KOW   1 pGdhVkVvs 9  
                                   +Gd+V++++
  gi|91773883|ref|YP_566575.1| 140 RGDTVRILR 148
                                   69****986 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00067         4       5      75 ..       9      72 ..       6      98 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00067
                                  EEEE-TTTHHHHHHHH...HHHCT-...EEE-SCEEEEEEETTEEECSSTTEEEEEE---CHHHHHHHCSTTEEEE- CS
                                  xxxxxxxxxxxxxxxx...xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          NusG  5 vlqvepgkekkvkenL...leeegl...evivPaeekveirqgkkkklfpgyifikadmndkllmairktpgVtgfv 75
                                  v+++  ++e++v+  L   +++e+l   ++i P               ++gy++++ +++     ai+++p+   +v
  gi|91773883|ref|YP_566575.1|  9 VVKTTANQERSVAAMLaqvAKKENLdirSIIAP-------------DELKGYVLLESSDSGAVEQAIQTVPHARTVV 72
                                  555555555555555555544555433333333.............3355666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 00:00:00.45
# Mc/sec: 1037.45
//
Query:       gi|91773884|ref|YP_566576.1|  [L=161]
Description: 50S ribosomal protein L11P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-26   92.1   1.9    4.4e-26   90.5   0.8    2.0  2  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    9.1e-22   77.3   1.0      3e-21   75.7   0.8    1.8  2  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.8   4.9e-30   4.4e-26       5      64 ..       2      61 ..       1      62 [. 0.97
   2 ?    0.1   0.0     0.081   7.3e+02      43      60 ..     119     136 ..     116     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 4.9e-30
               Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrs 64
                                  ++vv+  +p+GkA+p+PplGpaLGplG+nik++++++n++Tkd++g+++pVk+ v++d+s
  gi|91773884|ref|YP_566576.1|  2 ASVVEALIPGGKANPGPPLGPALGPLGVNIKDVIEKINEKTKDYNGMQVPVKVIVNDDKS 61
                                  68999******************************************************8 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.081
               Ribosomal_L11_N  43 kaTkdkkglripVkitvy 60 
                                   +a k+ +g+ +p+ +t++
  gi|91773884|ref|YP_566576.1| 119 AAIKEVMGTCVPMGVTIE 136
                                   6778899999*****993 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.18   1.6e+03      31      56 ..      30      56 ..      12      66 .. 0.73
   2 !   75.7   0.8   3.4e-25     3e-21       2      70 .]      68     135 ..      67     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.18
                                  EHHHHHHHHHHHGGGHT.XS.SHHHHH CS
                 Ribosomal_L11 31 slkqvyeIAkiKksdln.aalsleaav 56
                                   +k+v+e    K +d n ++++++ +v
  gi|91773884|ref|YP_566576.1| 30 NIKDVIEKINEKTKDYNgMQVPVKVIV 56
                                  566777766677777776666666555 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 3.4e-25
                                   --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                 Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                   tPpts+l++k+++iekgsg++g+ +vG++ ++qv +IA++Kk+d  ++ sl+aa+k+++gt+  mG+++
  gi|91773884|ref|YP_566576.1|  68 TPPTSALILKELNIEKGSGESGTVVVGNLEIAQVAKIARMKKDDILSY-SLKAAIKEVMGTCVPMGVTI 135
                                   9*****************************************998899.******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1133.86
//
Query:       gi|91773885|ref|YP_566577.1|  [L=213]
Description: 50S ribosomal protein L1P [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  160.5   0.1    5.3e-47  160.2   0.1    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.2   0.1     3e-51   5.3e-47       6     203 ..      19     207 ..      10     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 3e-51
                                   -SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHH CS
                  Ribosomal_L1   6 kkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfea 86 
                                   ++kf es +ia+nl+++++ ++++r+ ++i Lp++lgk++ki++++k++      +ak+ag  + +++ +++k+  +++ +
  gi|91773885|ref|YP_566577.1|  19 ERKFSESLDIAINLKNLDMSQPKNRVDEEIILPNGLGKTMKIAVFAKGEVGL---NAKDAG-CDYILTEEDIKELGEDKSK 95 
                                   689*************************************************...9*****.99999************** PP

                                   HHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSS CS
                  Ribosomal_L1  87 krkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsft 167
                                    r+l++e+d+f+a+ ++m +++k+LG ++g+r+kmP+p   +    ++v+  +++ ++ +v +r++++ +++v vG+ +++
  gi|91773885|ref|YP_566577.1|  96 ARSLANECDFFIAEVQYMAQIGKALGAILGPRGKMPVPL--T--PDKNVADLINSTKN-SVRIRSKDKLTFHVSVGRRDMD 171
                                   ***************************************..3..4679**********.********************** PP

                                   HHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                  Ribosomal_L1 168 aeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                    e+laeNie+v+  l+ +++k++ n+ks+y++ttm+
  gi|91773885|ref|YP_566577.1| 172 VEKLAENIETVLGRLEHSLEKGKHNLKSVYVTTTMG 207
                                   ***********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1443.19
//
Query:       gi|91773886|ref|YP_566578.1|  [L=337]
Description: acidic ribosomal protein P0 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-24   85.3   2.0    1.4e-23   82.9   0.0    2.5  3  Ribosomal_L10  Ribosomal protein L10
    1.7e-17   63.2   0.1    3.6e-17   62.1   0.1    1.5  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    2.7e-05   24.7  14.1    0.00013   22.5  14.1    2.2  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.051   12.8   0.1      0.073   12.3   0.1    1.3  1  GLE1           GLE1-like protein


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   3.2e-27   1.4e-23       3      98 ..      11     106 ..       9     107 .. 0.96
   2 ?   -3.2   0.1       2.1   9.6e+03      55      66 ..     240     251 ..     238     258 .. 0.82
   3 ?    1.3   0.0     0.087   3.9e+02      56      96 ..     275     313 ..     266     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 3.2e-27
                                   CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS..SSCGCCSSSEEEE CS
                 Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeee.klkellkgpvalv 82 
                                   +++K++ ++e+k l+++y  + v+ +eg++++qlq +R++l++  a lkv++n+l+rrAl++++++  k+++++  ++al+
  gi|91773886|ref|YP_566578.1|  11 PQWKKDEIEEIKSLIESYPLFGVIGIEGIPAKQLQSMRRDLKDF-AVLKVCRNSLTRRALDQSSDDVkKMDDYIDVQTALI 90 
                                   79*****************************************9.********************9756************ PP

                                   EESS-TCHHHHCCCCC CS
                 Ribosomal_L10  83 ftnedpvalakvleef 98 
                                   ft+++p++l+k+le+ 
  gi|91773886|ref|YP_566578.1|  91 FTKQNPFKLYKLLEKS 106
                                   *************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.1
                                   CCCCCCCCHCCT CS
                 Ribosomal_L10  55 ntlmrrAleetg 66 
                                   ntl+ +A+ +++
  gi|91773886|ref|YP_566578.1| 240 NTLLAKAASDSR 251
                                   899999988765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.087
                                   CCCCCCCHCCTSS.SSCGCCSSSEEEEEESS-TCHHHHCCC CS
                 Ribosomal_L10  56 tlmrrAleetgeeeklkellkgpvalvftnedpvalakvle 96 
                                   ++m +A + ++ ++ l++ lk   + + +   + a+ +v+e
  gi|91773886|ref|YP_566578.1| 275 KMMAIASAASSNDDALDDELKEALGAASS--AVSAVEEVVE 313
                                   79999999999986799999998887766..5555556555 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   8.1e-21   3.6e-17       2      71 .]     113     182 ..     113     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 8.1e-21
                  RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                   +aG +At+d+i+++gp++  Pg+i   ++ +g+p+ ++ Gk+v++e + v+k+Ge+++++ a++L +L+i
  gi|91773886|ref|YP_566578.1| 113 KAGMVATSDIIVEKGPTSFPPGPILGDMQGAGIPAAIDGGKVVIKETKAVAKAGEVVSQKLAAMLTRLEI 182
                                   89******************************************************************98 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  14.1   2.8e-08   0.00013       1      88 []     233     336 ..     233     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.8e-08
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..................XXXXXXXXXXXXXXXX CS
                 Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaakla..................aaaaaaaaaaaaaaaa 63 
                                   +pta ni+++l +a  +  +++v++ v +    di  ll+++++k+                   +a +aa +a+ a ++ 
  gi|91773886|ref|YP_566578.1| 233 YPTAMNINTLLAKAASDSRNVAVNATVYEPGIMDI--LLGKAYSKMMaiasaassnddalddelkEALGAASSAVSAVEEV 311
                                   69**************9999999888776665554..677777776667777777**********9999************ PP

                                   XXXXXXXXXXXX.XX--SS--.STTT CS
                 Ribosomal_60s  64 aaaeekkkeeeeeEeedddmG.fgLF 88 
                                    +++e+ keeee Ee+d + G ++LF
  gi|91773886|ref|YP_566578.1| 312 VEEQEEVKEEEE-EESDMASGlGALF 336
                                   *99999999999.8*******99**9 PP

>> GLE1  GLE1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05     0.073      78     156 ..     212     304 ..     166     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                          GLE1  78 flAkalvsqaetevsakpeaAfplArvavgllseh...............pelgdlllArlvkkCpylvpfypakkegqst 143
                                    + +++v+ a++ + ++ +aA+p A+ + +ll++                p ++d+ll++ ++k + +     + +++  +
  gi|91773886|ref|YP_566578.1| 212 QIFSNFVQAAQQAFNMSVNAAYPTAMNINTLLAKAasdsrnvavnatvyePGIMDILLGKAYSKMMAIASA-ASSNDDALD 291
                                   57899*****************************77****************************9987777.666667778 PP

                          GLE1 144 eeyrkrlGykrsd 156
                                    e +++lG   s 
  gi|91773886|ref|YP_566578.1| 292 DELKEALGAASSA 304
                                   8889998877544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1392  (0.0776396); expected 358.6 (0.02)
Passed bias filter:                      864  (0.0481901); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2553.05
//
Query:       gi|91773887|ref|YP_566579.1|  [L=100]
Description: 50S ribosomal protein L12P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-15   55.5  17.3    7.5e-15   55.3  17.3    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein


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 !   55.3  17.3   4.2e-19   7.5e-15       2      88 .]      17      99 ..      16      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 4.2e-19
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--S.S- CS
                 Ribosomal_60s  2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedd.dm 83
                                  +t+e++ +vl+aag+ev+++r+k+lv+ale++diee++a++a +       aaa +aa  a+ aaee ++ee ++Eee+  ++
  gi|91773887|ref|YP_566579.1| 17 ITEESVSAVLSAAGTEVNESRAKALVAALEDVDIEEAMATAAFA------PAAAVVAAPVAETAAEEVPAEENKAEEEESgMA 93
                                  9****************************************633......333344444444444444444444433333388 PP

                                  -.STTT CS
                 Ribosomal_60s 84 G.fgLF 88
                                  G ++LF
  gi|91773887|ref|YP_566579.1| 94 GlGALF 99
                                  888998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 807.12
//
Query:       gi|91773888|ref|YP_566580.1|  [L=340]
Description: hypothetical protein Mbur_1949 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        9.5    6.0  49.3      0.013   15.4  28.5    2.3  2  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 ?   15.4  28.5   7.2e-07     0.013       4     167 ..      86     252 ..      84     260 .. 0.56
   2 ?   -7.0  20.7         1   1.8e+04      50     106 ..     248     303 ..     245     320 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.2e-07
                       DUF4013   4 llliiaivlslvllGYlvrvlrdtirgddelPefd...dwgkllvdGlkafvvslvYllipliialltllvalaslaagds 81 
                                   ++++i+i+++++l+GY+ +v+  ++ ++ +  +++      k l+ Gl +f+v lv+ ++ l i+l++ l +++ +  ++s
  gi|91773888|ref|YP_566580.1|  86 IAAFIIILVLVLLFGYFASVMDLVLVESVTKNDVRfreYSAKFLRMGLDLFIVRLVLRIVYLGIFLMAALPLIMQIVHNPS 166
                                   67788888889***********666665553333333255789999**********8877777733333333333333333 PP

                       DUF4013  82 aa.gallvlallglllall..lvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvigivl 159
                                   ++ + ll++    l+++++  +++ +++  +++l++ +a++ +tg +++     ++++  +++ ++++++++  +v++++ 
  gi|91773888|ref|YP_566580.1| 167 TNlLPLLIASSPSLIVVIIalSIISSIINSFIVLCIPIAMYSYTGFIESL---ERVIANFRRDWKQMFVYWLGRMVLWALG 244
                                   33144444444444444442245555554444444888888888866665...3344434455545555555444444444 PP

                       DUF4013 160 sllaillv 167
                                   s+++++lv
  gi|91773888|ref|YP_566580.1| 245 SIAVVILV 252
                                   44444433 PP

  == domain 2  score: -7.0 bits;  conditional E-value: 1
                       DUF4013  50 afvvslvYlliplii..alltllvalaslaagdsaagallvlallglllalllvlllll 106
                                   ++++ lv++lip+++  +   + +++  ++++  + +a +++a ++++ ++ll+l++++
  gi|91773888|ref|YP_566580.1| 248 VVILVLVLILIPILLfsI---IDAVIYFVLSMIIGEAAWIIIAPIAFIEIILLMLISIM 303
                                   567777788999999332...22222222222222233333333333333332222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1216  (0.0678231); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 2241.52
//
Query:       gi|91773889|ref|YP_566581.1|  [L=522]
Description: DEAD/DEAH box helicase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-52  177.6   0.1    5.5e-52  176.1   0.0    1.7  2  DEAD           DEAD/DEAH box helicase
      3e-31  108.0   0.1    1.6e-28   99.3   0.0    2.6  3  Helicase_C     Helicase conserved C-terminal domain
    1.6e-09   38.0   0.0      3e-09   37.1   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
    0.00038   19.7   0.1    0.00061   19.1   0.1    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
     0.0049   16.8   0.0       0.01   15.7   0.0    1.5  1  Helicase_RecD  Helicase
      0.009   15.7   0.0       0.02   14.7   0.0    1.5  1  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.014   14.2   0.8        3.1    6.5   0.1    3.4  3  UTP25          Utp25, U3 small nucleolar RNA-associated SSU p
      0.017   14.5   0.0      0.057   12.8   0.0    1.9  2  CMS1           U3-containing 90S pre-ribosomal complex subuni
      0.021   14.6   0.1      0.039   13.7   0.1    1.4  1  PRAI           N-(5'phosphoribosyl)anthranilate (PRA) isomera
      0.054   13.5   0.1       0.17   11.8   0.0    1.8  2  Flavi_DEAD     Flavivirus DEAD domain
      0.067   12.7   0.1      0.093   12.2   0.1    1.3  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
       0.15   12.4   0.1       0.28   11.5   0.0    1.5  2  AAA_19         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.1   0.0   3.7e-55   5.5e-52       1     174 [.      26     188 ..      26     190 .. 0.97
   2 ?   -1.4   0.0       1.1   1.7e+03      69     104 ..     255     294 ..     228     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 176.1 bits;  conditional E-value: 3.7e-55
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   t+iQ+ aiplil+g+d+++ a+TGsGKTlaf   ++q++   ++ +g +al+++PtreLaeq+ n lk+f  + +lrv  i
  gi|91773889|ref|YP_566581.1|  26 TEIQKMAIPLILEGKDIIGGAATGSGKTLAFGCGIIQKI---EKGNGIRALVLTPTRELAEQVQNSLKEFSRHKQLRVAPI 103
                                   79*************************************...68*****************************99****** PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                   +ggva + q+++l +++d+vv+tpgrl+d++++g+++l +v++lVlDEadr+ld+gf d++++i+ ++       +++rq+
  gi|91773889|ref|YP_566581.1| 104 YGGVAINPQIRQL-ERADVVVATPGRLLDHIERGTIDLGDVEILVLDEADRMLDMGFIDDVEEIIDEC-------PSDRQT 176
                                   *************.9*****************************************************.......67889* PP

                                   EEEESSBSHHHH CS
                                   xxxxxxxxxxxx RF
                          DEAD 163 ivlSATlpkdvk 174
                                   +++SAT++kd++
  gi|91773889|ref|YP_566581.1| 177 MMFSATVSKDIQ 188
                                   ********9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                   HHTTTSTSEEEEEETTSSHHHHHHHH...H.TTCSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxx RF
                          DEAD  69 kfkkyidlrvlliiggvaardqlskl...d.ngvdivvgt 104
                                   k + + d+ + +i gg+++ + +s+l   + ++++ +v t
  gi|91773889|ref|YP_566581.1| 255 KNLRKNDIDAIAIHGGHTQAKRKSTLskfHsSNAHALVCT 294
                                   3334456677888888888777777732222447777766 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.011        17      12      62 ..      65     119 ..      55     152 .. 0.78
   2 ?   -2.5   0.0       4.3   6.4e+03      11      35 ..     168     190 ..     160     210 .. 0.64
   3 !   99.3   0.0     1e-31   1.6e-28       2     111 .]     224     332 ..     223     332 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                                   HTTTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                    Helicase_C  12 leeeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileqf 62 
                                   ++ +g ++l+ ++t++ +e+    +k + ++k+++va+++g    n +++ le+ 
  gi|91773889|ref|YP_566581.1|  65 EKGNGIRALVLTPTRELAEQvqnsLKEFSRHKQLRVAPIYGGVAINPQIRQLERA 119
                                   56778899********77665456666666669********99999998888876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                                   HHTTTTSEEEEEESSHH.HHHHHHHH CS
                    Helicase_C  11 kleeeggkilifvntid.rlekvkll 35 
                                   ++  +++++++f+ t++ +++   +l
  gi|91773889|ref|YP_566581.1| 168 DECPSDRQTMMFSATVSkDIQ---YL 190
                                   444677889999999886553...33 PP

  == domain 3  score: 99.3 bits;  conditional E-value: 1e-31
                                   HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                    Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                   k++ l++ll ++e+ g +++f+nt+++++ v+  l+k++i ++++hg  +q +r+ +l++f + + + L++tdva+rG+di
  gi|91773889|ref|YP_566581.1| 224 KFSLLVHLL-KSEKSGLVMVFCNTRSNVDFVQKNLRKNDIDAIAIHGGHTQAKRKSTLSKFHSSNAHALVCTDVAARGLDI 303
                                   677889999.899***************88666668889***********************99999************** PP

                                   TTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRag 111
                                   p v++V nfd+p+++++y++riGRt+Rag
  gi|91773889|ref|YP_566581.1| 304 PHVSHVYNFDIPDDPSEYVHRIGRTARAG 332
                                   ***************************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 !   37.1   0.0     2e-12     3e-09      30     169 ..      45     183 ..      13     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2e-12
                                   EESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEE CS
                        ResIII  30 kmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvt 109
                                    +aTG+GKTl   + +i+++ k +++ ++l+l p+++l eq ++ +k+f+  ++ ++  ++ g   +++ ++ + ++++v+
  gi|91773889|ref|YP_566581.1|  45 GAATGSGKTLAFgCGIIQKIEKGNGI-RALVLTPTRELAEQVQNSLKEFSRHKQLRVAPIYGGVAINPQIRQLERADVVVA 124
                                   579*********88888888876555.**************************999888888888888788899******* PP

                                   EHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT-.--SEEEEEESS- CS
                        ResIII 110 tiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekf.keavllglTATp 169
                                   t  +l  ++     e+ + + +  ++++ DEa r+ ++   + ++ei++ + ++   + ++AT 
  gi|91773889|ref|YP_566581.1| 125 TPGRLLDHI-----ERGTIDLGDVEILVLDEADRMLDMgfiDDVEEIIDECpSDRQTMMFSATV 183
                                   *********.....88888889999************96666888876665366888999**97 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 !   19.1   0.1   4.1e-07   0.00061      22     129 ..     201     310 ..     194     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.1e-07
                 ERCC3_RAD25_C  22 efykeylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkp.....yiyGetseaerlki 97 
                                    f k y+++++ k+  + v    kf+ + +L+k   +++  ++vf++    +  + k+l+k+      i+G  ++a+r++ 
  gi|91773889|ref|YP_566581.1| 201 VFAKAYVDSDKLKQVYIDVPKKMKFSLLVHLLK--SEKSGLVMVFCNTRSNVDFVQKNLRKNdidaiAIHGGHTQAKRKST 279
                                   688899999988888777777777777777765..577889*****977777766666665422222789*********** PP

                 ERCC3_RAD25_C  98 lqkfkknpkvntiflskvgDtsiDlPeanvli 129
                                   l+kf++++  ++++   v+   +D+P+ + + 
  gi|91773889|ref|YP_566581.1| 280 LSKFHSSN-AHALVCTDVAARGLDIPHVSHVY 310
                                   ****8775.66778899*********987665 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     7e-06      0.01       4     100 ..      46     152 ..      45     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7e-06
                 Helicase_RecD   4 AdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke...........eekkkkaekaelrvr 72 
                                   A+ G GK+ a G  + + i++g+  + lv  p++e ++++ ++l++  ++ +l+            + ++ ++ ++ +++ 
  gi|91773889|ref|YP_566581.1|  46 AATGSGKTLAFGCGIIQKIEKGNgIRALVLTPTRELAEQVQNSLKEFSRHKQLRVapiyggvainpQIRQLERADVVVATP 126
                                   788******************999********************8887777777788999999955444555555566666 PP

                 Helicase_RecD  73 kqrieyiapdellklkeqadllvvDEAA 100
                                   ++ +++i+  ++     + ++lv DEA 
  gi|91773889|ref|YP_566581.1| 127 GRLLDHIERGTIDLG--DVEILVLDEAD 152
                                   999999998887774..57*******95 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05      0.02       6      98 ..      29     152 ..      25     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                        AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalk.alreaweaa.ggrviglAptgkaAkvLa..................... 63 
                                   Q+ a+  +l+++d   +  ++ G+GKt a + ++ + +e+  g r ++l+pt + A++++                     
  gi|91773889|ref|YP_566581.1|  29 QKMAIPLILEGKD--IIGGAATGSGKTLAFGcGIIQKIEKGnGIRALVLTPTRELAEQVQnslkefsrhkqlrvapiyggv 107
                                   8888888888886..4444555******99744577777776******************555555555555555555444 PP

                        AAA_30  64 .........eelgieastiakllkrlk.grarlepgtllivDEag 98 
                                            e +++  +t  +ll+  + g+ +l + ++l+ DEa 
  gi|91773889|ref|YP_566581.1| 108 ainpqirqlERADVVVATPGRLLDHIErGTIDLGDVEILVLDEAD 152
                                   444444444455555555566665555766777777899999985 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.56   8.3e+02      78     102 ..      72      96 ..      70     100 .. 0.86
   2 ?    2.7   0.0     0.029        43     158     216 ..     115     168 ..     112     172 .. 0.77
   3 ?    6.5   0.1     0.002       3.1     246     293 ..     174     220 ..     166     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.56
                         UTP25  78 vLillptreaalevvelllklleae 102
                                    L+l ptre a +v ++l +++ ++
  gi|91773889|ref|YP_566581.1|  72 ALVLTPTRELAEQVQNSLKEFSRHK 96 
                                   69***********999999998876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.029
                         UTP25 158 kfyssdiiiaSPlglrliieeedkkkrdtdfLsSiEvlivdqadvl.emQnwehvetvlk 216
                                   ++ ++d+++a P  l   ie     +   d L  +E+l++d+ad +  m  ++ ve++++
  gi|91773889|ref|YP_566581.1| 115 QLERADVVVATPGRLLDHIE-----RGTID-LGDVEILVLDEADRMlDMGFIDDVEEIID 168
                                   67889999999999888888.....33344.899*********96526777888888876 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.002
                         UTP25 246 RQtlvfssyetpeinslfnskleNlaGkvkvkkvvkggslekvglkvr 293
                                   RQt++fs+  + +i+ l +++++N   kv  k+ v + +l++v + v 
  gi|91773889|ref|YP_566581.1| 174 RQTMMFSATVSKDIQYLSSKYMNN-PSKVFAKAYVDSDKLKQVYIDVP 220
                                   999999999999999998666655.56777777776667777766664 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.8e-05     0.057     128     210 ..      71     151 ..      57     188 .. 0.82
   2 ?   -2.6   0.0       1.8   2.7e+03     107     128 ..     363     384 ..     336     385 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                          CMS1 128 elLvltlaalRaaDlaralkklq.tkdskvakLFakhikleesvtylkksrigiavGtpgRildLleeeslsvdeLkrivl 207
                                   + Lvlt +   a  +  +lk++  +k+ +va +++  + ++ ++  l ++   + v tpgR+ld +e +++ + +++ +vl
  gi|91773889|ref|YP_566581.1|  71 RALVLTPTRELAEQVQNSLKEFSrHKQLRVAPIYGG-VAINPQIRQLERA--DVVVATPGRLLDHIERGTIDLGDVEILVL 148
                                   5688888888899999999999659999******95.8899999988765..56677********************9999 PP

                          CMS1 208 Das 210
                                   D +
  gi|91773889|ref|YP_566581.1| 149 DEA 151
                                   864 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                          CMS1 107 leelsefakklvksaksngsPe 128
                                    e l+ef++ l+ks  s g P+
  gi|91773889|ref|YP_566581.1| 363 REDLPEFERVLIKSEDSGGRPT 384
                                   4789999999999999999996 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 ?   13.7   0.1   2.6e-05     0.039      12      90 ..     201     280 ..     192     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--EEEEEESSS..-HHHHHHHHHHCTECEEEE-CGG.-HHHHHHH CS
                          PRAI  12 vkaavkagadelglifaesskrevseeqaqellekvpaklVGVfvNq..pieevlriaqelgldvvQLHGdedeqeyeell 90 
                                   v a + ++ d+l+++  ++ +++++   +  ll++ +  lV Vf N   ++++v++ +++ ++d++ +HG  ++ + +++l
  gi|91773889|ref|YP_566581.1| 201 VFAKAYVDSDKLKQVYIDV-PKKMKFSLLVHLLKSEKSGLVMVFCNTrsNVDFVQKNLRKNDIDAIAIHGGHTQAKRKSTL 280
                                   5555555666777777777.6677777777777777788*******63379*******************99544444444 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.17      13      56 ..      48      92 ..      40     102 .. 0.86
   2 ?   -2.6   0.0       3.3   4.9e+03      73     115 ..     261     299 ..     243     302 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                  TTS-TTTTHHHHHHHHHHH.TT--EEEEESSHHHHHHHHHHTTTS CS
                    Flavi_DEAD 13 PGaGktrkvlpelvkeaie.rrlrtlvLaPtrvvlaemeealkgl 56
                                   G+Gkt  +   ++++  + + +r+lvL+Ptr  ++ ++++lk+ 
  gi|91773889|ref|YP_566581.1| 48 TGSGKTLAFGCGIIQKIEKgNGIRALVLTPTRELAEQVQNSLKEF 92
                                  699*****999999998763679******************9975 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.3
                                   -SEEEEEHHHHHHHHHHT------SEEEEETTT--SHHHHHHH CS
                    Flavi_DEAD  73 elvdvmchatftkrllspvrkknyeliimDeahflDPasiaar 115
                                   ++  ++ h  +t+ +    rk     +   +ah l  + +aar
  gi|91773889|ref|YP_566581.1| 261 DIDAIAIHGGHTQAK----RKSTLSKFHSSNAHALVCTDVAAR 299
                                   444444444444332....222222222334555555555555 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.2e-05     0.093       5      68 ..      29      94 ..      26     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                                  HHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH..H CS
                 UvrD-helicase  5 qreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee..a 68
                                  q+ ai     g++i+  A+ GsGKT      i+++i+++  +  r lv+T T+  ae  ++ ++e  +
  gi|91773889|ref|YP_566581.1| 29 QKMAIPLilEGKDIIGGAATGSGKTLAFGCGIIQKIEKG--NGIRALVLTPTRELAEQVQNSLKEfsR 94
                                  55566555456777778999*******************..788899***999888888777777331 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.28      15      68 ..      42      95 ..      29     205 .. 0.72
   2 ?   -3.2   0.0       6.6   9.8e+03      43      74 ..     238     269 ..     222     292 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                        AAA_19 15 vtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae 68
                                  +++G+ tG  ++l   + +++++++ +  + l++++t+  a++++++l+++ ++
  gi|91773889|ref|YP_566581.1| 42 IIGGAATGSGKTLAFGCGIIQKIEKGNGIRALVLTPTRELAEQVQNSLKEFSRH 95
                                  556665555555556666666666667789***************999766554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.6
                        AAA_19  43 eeillvaftgrAakelrerlaalgaeatTiHr 74 
                                     +++ + t+  ++ ++++l++ + +a  iH+
  gi|91773889|ref|YP_566581.1| 238 GLVMVFCNTRSNVDFVQKNLRKNDIDAIAIHG 269
                                   44566677777777777777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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):              12  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 3000.60
//
Query:       gi|91773890|ref|YP_566582.1|  [L=326]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   55.9   0.0    1.9e-14   54.4   0.0    1.7  2  Radical_SAM    Radical SAM superfamily
    2.5e-05   24.1   0.2    4.4e-05   23.3   0.2    1.4  1  DUF3463        Domain of unknown function (DUF3463)
  ------ inclusion threshold ------
      0.034   14.2   0.3        9.6    6.3   0.0    2.4  2  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
       0.26   11.5   0.1       0.26   11.5   0.1    2.4  3  Fer4_12        4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   4.3e-18   1.9e-14       6     166 ..      34     177 ..      31     178 .. 0.95
   2 ?   -2.0   0.0      0.92   4.1e+03     112     143 ..     196     228 ..     192     239 .. 0.65

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 4.3e-18
                                   EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                    Cn+ C+fC  ++     ++g+++s+++i + ++ ++ + g+++      epll++d+ ++l+ ++ l   g+ ++++tng
  gi|91773890|ref|YP_566582.1|  34 RCNMSCKFCEYWK-----DPGQEMSLDSIFKMLEDAR-SFGIGVYNAWTVEPLLRDDLPQILKFAKDL---GMITSLITNG 105
                                   7***********6.....9*****************6.999**************************9...********** PP

                                   SCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  87 tlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                                    l+ e+ ++ l++  +d++s++++ + +    k + rg +++ +l+++ + +++ +k+   +  ++ G n +++eel++l
  gi|91773890|ref|YP_566582.1| 106 KLL-EKRIDDLKD--LDYLSVSVDGTKSY---KEI-RGVDLDVLLNSIMNVKDK-LKNPLLMNCVISGKNLDDIEELVQL 177
                                   ***.*********..89***********9...899.99****************.8887889999999********9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.92
                                   SSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSE CS
                                   xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 112 addekvlklmn..rghtfeevlealeklreagik 143
                                   +dd+ v   m+   ++ + ++++ +  +++ g +
  gi|91773890|ref|YP_566582.1| 196 IDDD-VWASMGirEMDKYRRTIDRVIEMKKQGYP 228
                                   5666.66666555666777777777777777777 PP

>> DUF3463  Domain of unknown function (DUF3463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   9.8e-09   4.4e-05      19     129 ..     207     320 ..     185     325 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.8e-09
                       DUF3463  19 lerektkelfrkilelkkkkyklnesplyldflag.kqeykCtpWg.nptrnvlGwqkPCYllee...gyaktfkelleet 94 
                                    e++k ++ + +++e+kk++y +++s  yl ++ + k++++C      + ++v G  + C +  e   + ++ +++++++ 
  gi|91773890|ref|YP_566582.1| 207 REMDKYRRTIDRVIEMKKQGYPIINSISYLSMIRDlKKRFNCHVNNfILDVTVDGSIENCRVHREplgNINEGIATVWKRS 287
                                   356788999**************************666****9876156899*********99772223344445677666 PP

                       DUF3463  95 dwekygkgkdpkCanCmvhsgyEasavsdtvksll 129
                                     ++ +    ++C+ C    + E+s++ d++ +++
  gi|91773890|ref|YP_566582.1| 288 RSQQDE--VTKNCEGCFFFGYVENSMMYDMNLEVM 320
                                   666655..6678**************999887665 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0028        12      54      85 ..     145     176 ..     119     184 .. 0.87
   2 ?    6.3   0.0    0.0021       9.6      31      90 ..     190     252 ..     179     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0028
                 Nit_Regul_Hom  54 aikiikdlseeavlintvvdeekvekikeele 85 
                                   +i  +kd  ++ +l+n+v++ +++++i+e ++
  gi|91773890|ref|YP_566582.1| 145 SIMNVKDKLKNPLLMNCVISGKNLDDIEELVQ 176
                                   46679999*******************99875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0021
                 Nit_Regul_Hom  31 lieYkGlsPqewkgfllee..dpesaikiikdlseeav.lintvvdeekvekikeeleeklkd 90 
                                   ++e+kG+  + w+++ ++e      +i+ + ++ +++  +in++    +++++k++++ ++++
  gi|91773890|ref|YP_566582.1| 190 MYEFKGIDDDVWASMGIREmdKYRRTIDRVIEMKKQGYpIINSISYLSMIRDLKKRFNCHVNN 252
                                   68***************9732456789988888888754899999999999999998877765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.9e-05      0.26      13     118 ..      33     128 ..      22     135 .. 0.70
   2 ?   -2.1   0.0      0.95   4.3e+03     111     121 ..     255     265 ..     216     274 .. 0.70
   3 ?   -3.6   0.6       2.7   1.2e+04      18      23 ..     297     302 ..     295     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                       Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytg 93 
                                   s+Cn+sCk+C   e w+ + g+e++ + + +++ed+    i        EPll   +++l +++k  k  ++  + ++++g
  gi|91773890|ref|YP_566582.1|  33 SRCNMSCKFC---EYWK-DPGQEMSLDSIFKMLEDARSFGIGVYNAWTVEPLL---RDDLPQILKFAKDLGM-ITSLITNG 105
                                   79*******6...5665.45666666666666666644444444556679999...6666666666666666.67899*** PP

                       Fer4_12  94 ytleelskkekeellkeidvlvdGk 118
                                     le+  +    + l+++ v vdG 
  gi|91773890|ref|YP_566582.1| 106 KLLEKRID--DLKDLDYLSVSVDGT 128
                                   ***99985..355599999999996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.95
                       Fer4_12 111 idvlvdGkfee 121
                                   +dv+vdG  e+
  gi|91773890|ref|YP_566582.1| 255 LDVTVDGSIEN 265
                                   67888887765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.7
                       Fer4_12  18 sCkgCf 23 
                                   +C+gCf
  gi|91773890|ref|YP_566582.1| 297 NCEGCF 302
                                   8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2203.01
//
Query:       gi|91773891|ref|YP_566583.1|  [L=638]
Description: Na+/solute symporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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  35.3    1.8e-33  116.0  35.3    1.3  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0  35.3   9.8e-38   1.8e-33       1     406 []      35     433 ..      35     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 9.8e-38
                           SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylskRfkg 81 
                                   ++lagr+++ + +g s aas + a+ ++ + G  ++ G++ ++  +   +l+ll++ ++++++ n+  +T +++l++R+ +
  gi|91773891|ref|YP_566583.1|  35 FWLAGRKIGTIGIGFSSAASWLTAGGILAVIGFFMLLGMGSIWGFVAPNILALLIIAIFVKKFKNLPSITQAELLEQRYSS 115
                                   89**************************************99999999999****************************98 PP

                           SSF  82 krilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvgalill 162
                                      +  + +++++++i +++ +d+ g a  ++   G++   a l++a+++  Y+ +GGl Avv+td++q v + + al ++
  gi|91773891|ref|YP_566583.1| 116 AI-RAPVGIIITIVMILFAV-ADIKGFALVLQIFYGVDPIYAALIVALAVSAYVTLGGLSAVVWTDVVQFVFLSIFALAMA 194
                                   76.999****9999999886.7****************999999*************************988766555555 PP

                           SSF 163 iivllevGgleslveklkeaapkv....vdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakdakailkgvl 239
                                   ++++ ++    s    + +a+  +    +d  +p     +  p  +l++  +++ G +  +   +++ aakd+ ++++g++
  gi|91773891|ref|YP_566583.1| 195 FLAIGAAT---SGSADISSASDLIsnvsTDWWNPFI---IGIP-MVLIFVFAIIPGWITEQDPWQKVWAAKDSTSARNGLV 268
                                   55555555...4444444444433000355555443...3334.4455568888899999*******************99 PP

                           SSF 240 kltivlilvligmisiilfaiklagavp..kavg..tevgvsniaypeLvvkllpnllaGlllavmlAaimstltslllsa 316
                                    +  ++ +v+       + ai l    p   a+g    +g ++ a+ + +v+ + + + Gl      Aa ms  ++   s+
  gi|91773891|ref|YP_566583.1| 269 LGSFLVTVVFTA---CAFIAIGLNSLYPeiSAMGfpMGMGLAEPALLTFIVETFSPAVIGLCAIGLAAASMSCADTFATSG 346
                                   998888777776...6677777777777665555114567899*****************9876677789*********** PP

                           SSF 317 ssaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillalfwkrvneq 397
                                   +s +++D+Y+++++   a+ k+++ + r+ vl +++ a +       +g+l+ +++a+ ++ +  +  ++ +l+wkr++++
  gi|91773891|ref|YP_566583.1| 347 ASCVSRDIYQRFVKPD-ATMKQMLTINRLSVLFIVAAATVSSFFI--NGILDAIHIATFIASASYFFPLMGGLYWKRATKE 424
                                   *************999.7888888888887777766666554443..459******************************* PP

                           SSF 398 GAlagliiG 406
                                   GAlagli+G
  gi|91773891|ref|YP_566583.1| 425 GALAGLILG 433
                                   *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1134  (0.0632495); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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):               1  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 3920.50
//
Query:       gi|91773892|ref|YP_566584.1|  [L=315]
Description: hypothetical protein Mbur_1953 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.8   0.5      0.032   13.0   0.5    1.5  1  DUF2206   Predicted membrane protein (DUF2206)


Domain annotation for each model (and alignments):
>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.8e-06     0.032     216     282 ..       6      81 ..       3     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-06
                       DUF2206 216 klkiisvflvvllLfnsGfiyeivkdsptsialdetldya.......lfndsevtgakWlsksaseektiy..sdk 282
                                   +l i +v++ +l +++sG i+e+v  s  s a++et+dy+       + +  +++  ++  + + +++++y  sd 
  gi|91773892|ref|YP_566584.1|   6 RLAITMVLVFILAIMSSGCINELVPVSDNSNAISETFDYElevfpssVDKSDDLNTTTFYLTRNGTTNVVYmvSDT 81 
                                   678999**********************************986666544555666666665666666666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2201.95
//
Query:       gi|91773893|ref|YP_566585.1|  [L=248]
Description: beta-lactamase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-30  106.2   0.7      2e-30  105.9   0.7    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.3e-20   72.9   1.2    4.7e-20   72.4   1.2    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    9.3e-08   32.1   1.1    1.8e-07   31.2   1.1    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.068   13.3   0.0       0.12   12.5   0.0    1.3  1  V-ATPase_H_C   V-ATPase subunit H
      0.078   11.9   0.1       0.11   11.5   0.1    1.1  1  DDR            Diol dehydratase reactivase ATPase-like 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 !  105.9   0.7   5.4e-34     2e-30       3     201 .]      49     223 ..      48     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 5.4e-34
                                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTT CS
                 Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeep 83 
                                   +LiD++pd+r+q+lr+         l++id+V++th+HyDH++g+  + + ++ ++++y+  ++l+++ +      + ++ 
  gi|91773893|ref|YP_566585.1|  49 VLIDTSPDMREQMLRKG--------LKHIDGVIWTHGHYDHYTGFGEFHRVQY-NVDVYGVTETLDYILDYV---SFLRP- 116
                                   8***********87776........99***********************887.59**96666666666654...44444. PP

                                   TEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.---HHHHHHHCT-SEEEEE CS
                 Lactamase_B_2  84 avnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yipeeigerlggadlllld 163
                                     ++h++ +++sfel   gle+t+++++h  ++       +++G++i +g+k+v+ +gDt   ipe+  e ++ +d+ ++d
  gi|91773893|ref|YP_566585.1| 117 --KRHDIPLNTSFELI--GLEFTLFEVNHPPAK-------KAVGVMICEGDKKVVISGDTDeNIPEKSIEIIQSPDIFIVD 186
                                   ..588**********5..89**********999.......9*******************857899999************ PP

                                   -S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 164 itayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                   + + +d  +     H++ +ea+e+a++++akr+v++Hi
  gi|91773893|ref|YP_566585.1| 187 AIIPHDVGFH-VKKHMDAKEAMEIAEKINAKRVVMTHI 223
                                   **99999987.8*************************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 !   72.4   1.2   1.3e-23   4.7e-20       7     197 .]      38     222 ..      34     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.3e-23
                                   EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                   Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87 
                                   +s+lie d+g +LiDt  + +++++       ++++k +d vi TH+H+DH+ g g++ +   ++ ++   e+  ++ +++
  gi|91773893|ref|YP_566585.1|  38 FSILIESDEGKVLIDTSPDMREQML-------RKGLKHIDGVIWTHGHYDHYTGFGEFHRVQYNVDVYGVTETLDYILDYV 111
                                   799*********************6.......89*************************9887777777777777777777 PP

                                   HHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC...... CS
                   Lactamase_B  88 ddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl...... 162
                                    + +++          +++++     ++++++  +++v + p+  ++++ ++ g++kv+++GD+  + ++ +i+       
  gi|91773893|ref|YP_566585.1| 112 SFLRPK----------RHDIPLNTSFELIGLEFTLFEVNHPPAKKAVGVMICEGDKKVVISGDTDENIPEKSIEIiqspdi 182
                                   665554..........6899999***************************************************9999999 PP

                                   .........TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 163 ........tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                              g++v ++ da++++   + +++ +a+++v++H
  gi|91773893|ref|YP_566585.1| 183 fivdaiipHDVGFHVKKHMDAKEAM---EIAEKINAKRVVMTH 222
                                   9999655555555555555555555...455566777777766 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   1.1   5.1e-11   1.8e-07       9     163 .]      39     222 ..      38     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.1e-11
                 Lactamase_B_3   9 sflletagarilvDPfka..nlgyeppaeeaDlvlisqaledHahl.etlkqlaenvkvlee................... 67 
                                   s+l+e+++ ++l+D      ++ +++  +++D v+ ++++ dH++   +  +++ nv+v                      
  gi|91773893|ref|YP_566585.1|  39 SILIESDEGKVLIDTSPDmrEQMLRKGLKHIDGVIWTHGHYDHYTGfGEFHRVQYNVDVYGVtetldyildyvsflrpkrh 119
                                   789***********77555567777777****************9624566664444444444455555556666665644 PP

                 Lactamase_B_3  68 ....geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvgg...... 138
                                         s+e+ gle++ ++ +h     ++ ++ +g ++ +++ +++  G+++ ++ +++++ ++ +D++++  +       
  gi|91773893|ref|YP_566585.1| 120 diplNTSFELIGLEFTLFEVNH-----PPAKKAVGVMICEGDKKVVISGDTDENIPEKSIEIIQSPDIFIVDAIIphdvgf 195
                                   4444455666677777666666.....66677788899999*****************************9988789999* PP

                 Lactamase_B_3 139 ..pltlgqeealelakrLkpklvlPmh 163
                                     ++ ++++ea+e+a+++++k v+ +h
  gi|91773893|ref|YP_566585.1| 196 hvKKHMDAKEAMEIAEKINAKRVVMTH 222
                                   9999********************998 PP

>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05      0.12      48      97 ..     174     226 ..     162     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                  V-ATPase_H_C  48 iklleeskd.ktvlavalnDigelvkllpegkkvl...eklkaKekimellehe 97 
                                   i++++ s d   v a++ +D+g  vk + + k+ +   ek++aK ++m++++h 
  gi|91773893|ref|YP_566585.1| 174 IEIIQ-SPDiFIVDAIIPHDVGFHVKKHMDAKEAMeiaEKINAKRVVMTHISHY 226
                                   56663.44423678999********99876666555559***********9985 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 ?   11.5   0.1     3e-05      0.11      44     102 ..     168     226 ..     155     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                           DDR  44 eltekkvedikikDllavdtlvpqkvkgglAgefslekavglaamvktdklqmqkiaee 102
                                   ++ ek++e i+  D++ vd+++p++v   + + + + +a+ +a+ ++++++ m++i++ 
  gi|91773893|ref|YP_566585.1| 168 NIPEKSIEIIQSPDIFIVDAIIPHDVGFHVKKHMDAKEAMEIAEKINAKRVVMTHISHY 226
                                   5667788889999******************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1932.50
//
Query:       gi|91773894|ref|YP_566586.1|  [L=430]
Description: AAA ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-36  124.1   0.0    1.6e-35  122.4   0.0    1.9  1  AAA              ATPase family associated with various cellul
    6.1e-09   35.5   0.0    1.6e-08   34.2   0.0    1.7  1  AAA_lid_3        AAA+ lid domain
    1.6e-07   31.4   0.1      4e-06   26.9   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
    7.5e-05   22.0   0.0    0.00014   21.1   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
    0.00022   21.8   0.0    0.00063   20.3   0.0    1.9  1  AAA_18           AAA domain
    0.00027   21.4   0.3      0.012   16.0   0.3    2.9  1  AAA_16           AAA ATPase domain
     0.0003   20.9   0.0    0.00064   19.9   0.0    1.6  1  AAA_33           AAA domain
    0.00083   19.6   0.3      0.064   13.5   0.0    2.8  3  AAA_22           AAA domain
    0.00084   19.1   0.0     0.0016   18.2   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00093   18.5   0.0     0.0018   17.5   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.001   19.2   0.0      0.043   13.9   0.0    2.8  2  SKI              Shikimate kinase
     0.0018   18.7   0.2      0.088   13.2   0.0    2.6  2  AAA_17           AAA domain
     0.0023   18.2   0.0     0.0051   17.1   0.0    1.7  1  AAA_28           AAA domain
     0.0026   17.9   0.1     0.0092   16.1   0.0    2.0  2  AAA_2            AAA domain (Cdc48 subfamily)
     0.0042   16.5   0.0     0.0092   15.4   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0047   16.7   0.0       0.01   15.6   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0057   16.4   0.0      0.011   15.5   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
     0.0076   15.8   0.1      0.018   14.6   0.1    1.6  1  AAA_7            P-loop containing dynein motor region
     0.0084   15.8   0.0      0.016   14.9   0.0    1.5  1  AAA_24           AAA domain
     0.0091   15.8   0.1      0.039   13.8   0.1    1.9  2  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.055   13.2   0.0    1.7  1  Cytidylate_kin   Cytidylate kinase
      0.047   13.1   0.1        9.3    5.6   0.0    2.4  2  TniB             Bacterial TniB protein
      0.048   13.7   0.0      0.094   12.7   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      0.092   12.3   0.0       0.17   11.5   0.0    1.4  1  RE_AspBHI_N      Restriction endonuclease AspBHI N-terminal
       0.13   12.4   0.0       0.26   11.4   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.16   12.4   0.0       0.31   11.4   0.0    1.6  1  RNA_helicase     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 !  122.4   0.0   2.3e-38   1.6e-35       1     131 [.     214     342 ..     214     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 2.3e-38
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   +l++GppGtGKT++aka+ + l+++f+e+ +s ++++y+ge++k+i  +f+ ak+ + p+ilfiDE+d +ak+r ++e+  
  gi|91773894|ref|YP_566586.1| 214 ILMVGPPGTGKTSVAKAMSERLSIPFVEVRLSMITDQYLGETAKNIDRVFTLAKRLS-PCILFIDEFDFVAKTRASDEHAA 293
                                   699*****************************************************9.****************99***** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                    +r+vn+Ll+++d  +  ++ v++++atn+p++ld+a   +Rfd+++ ++
  gi|91773894|ref|YP_566586.1| 294 LKRAVNTLLKAIDSISLTNDGVLLMAATNHPRMLDSAAW-RRFDEIMDFP 342
                                   ***************************************.7*****9997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.4e-11   1.6e-08       1      43 [.     363     405 ..     363     407 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.4e-11
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                   d+d +e+A +TeGySG Dl  ++re++l+Al + +  it++d+
  gi|91773894|ref|YP_566586.1| 363 DFDNAEIAPLTEGYSGSDLRMVIRESVLNALVEERMIITQDDL 405
                                   677799***********************************97 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.41   2.8e+02      77     134 ..     140     197 ..     136     200 .. 0.78
   2 !   26.9   0.0   5.7e-09     4e-06       2     138 .]     214     335 ..     213     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.41
                                   --HHHHHHHHHHHHSSEEE..-SSSEEE---.......-EEEEEESS--.-TT-TTHHH CS
                         AAA_5  77 aesevlnsLlslleerrllleeggelvkakndd.llerfrviatanpldrslnelspal 134
                                   +++e+++sL+s ++e++   e++ +lv+  +++ +++++r + ++++++ + +++ +a+
  gi|91773894|ref|YP_566586.1| 140 VDREWIESLISEISEEEGG-EDMLKLVQIIAPEdIAQPMRYMVLTEDQKEEIEKIVKAI 197
                                   569999*****99999999.777777777777779999999999999986666666665 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 5.7e-09
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HHH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraesev 81 
                                   +l+vGppGtgK+++a+ ++++l  ++++v l+       ++ ++   ++t++  d +++ a r +++il++DE++ + +  
  gi|91773894|ref|YP_566586.1| 214 ILMVGPPGTGKTSVAKAMSERLSIPFVEVRLSM------ITDQYL--GETAKNIDRVFTLAKRlSPCILFIDEFDFVAKTR 286
                                   79***************************9987......444555..45557899999988889***********999988 PP

                                   HHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  82 lnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   ++  +  l +    l +    ++  nd+    + ++a++n ++     l++a ++Rf
  gi|91773894|ref|YP_566586.1| 287 ASDEHAALKRAVNTLLKAIDSISLTNDG----VLLMAATNHPR----MLDSAAWRRF 335
                                   8888899999888888888888888887....89999998888....7778888877 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     2e-07   0.00014      55     155 ..     213     327 ..     163     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                        DUF815  55 nvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr...erperfilfvDDLsFeeeeeey..... 125
                                   ++L++G  GtGK s+ ka+ ++++     +rl  ++ + l e  k ++ +    +r   +ilf+D   F ++ ++      
  gi|91773894|ref|YP_566586.1| 213 KILMVGPPGTGKTSVAKAMSERLSIPFveVRLSMITDQYLGETAKNIDRVFtlaKRLSPCILFIDEFDFVAKTRASdehaa 293
                                   79********************99887779999999999998888877765111555669*******99765433322323 PP

                        DUF815 126 ..ksLksvLeG..sleakpenvliyaTsNrRhLl 155
                                     +++ ++L    s++ + + vl+ a +N+  +l
  gi|91773894|ref|YP_566586.1| 294 lkRAVNTLLKAidSISLTNDGVLLMAATNHPRML 327
                                   3344445554333677788888888888886666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.2e-07   0.00063       1      37 [.     214     252 ..     214     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.2e-07
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........gvnlrdvakengl 37 
                                   Il  G+pG+GKt++ak+ s+rl +                      +l
  gi|91773894|ref|YP_566586.1| 214 ILMVGPPGTGKTSVAKAMSERLSIpfvevrlsmitD---------QYL 252
                                   7889*****************977875444444441.........333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.8e-05     0.012      27     144 ..     214     405 ..     188     408 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-05
                        AAA_16  27 vllsGesGvGKsslvrellralekd....ggiflrgkcdql..esa..........ipysa.laqalareellrqlldeae 90 
                                   +l +G++G+GK+s++++  ++l+      +   l+  +dq+  e+a           ++s+ ++ +  + +++++  + +e
  gi|91773894|ref|YP_566586.1| 214 ILMVGPPGTGKTSVAKAMSERLSIPfvevR---LSMITDQYlgETAknidrvftlaKRLSPcILFID-EFDFVAKTRASDE 290
                                   7899****************9998844440...3333333332112111111111122233122222.2233333333333 PP

                        AAA_16  91 saeleawrekleeala..............................................................avp 109
                                    a+l ++  +l++a+                                                               ++p
  gi|91773894|ref|YP_566586.1| 291 HAALKRAVNTLLKAIDsisltndgvllmaatnhprmldsaawrrfdeimdfplpnekmrkaildivtkeiegdfdnaeIAP 371
                                   344444444444444477777777777777777777777777777777777777777777766666666655554442222 PP

                        AAA_16 110 elagaea....srllellkrll.allsrderplvlvlDdl 144
                                         +    s+l+ ++++ + + l + er  +++ Ddl
  gi|91773894|ref|YP_566586.1| 372 LT----EgysgSDLRMVIRESVlNALVE-ER-MIITQDDL 405
                                   22....2333477777777777333333.55.77777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.3e-07   0.00064       2      91 ..     214     338 ..     214     359 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.3e-07
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvl 52 
                                   +l+vG+pG+GK+ +a+ + ++l   +v ++   + +++ g+  +++                             d   +l
  gi|91773894|ref|YP_566586.1| 214 ILMVGPPGTGKTSVAKAMSERLSipFVEVRLSMITDQYLGETAKNIDrvftlakrlspcilfidefdfvaktrasDEHAAL 294
                                   79********************99866666666555555544443333444444444445555555544444443444566 PP

                        AAA_33  53 drlyqilnelarkalsagrnvil.dat....nlsrrerarflkl 91 
                                   +r+ ++l + +++    + +v+l  at    +l+ ++++rf+++
  gi|91773894|ref|YP_566586.1| 295 KRAVNTLLKAIDSISLTNDGVLLmAATnhprMLDSAAWRRFDEI 338
                                   66666666666655555555555233455566666666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.7   3.9e+03      42      64 ..     125     149 ..      94     169 .. 0.41
   2 !   13.5   0.0   9.3e-05     0.064       8      45 ..     214     242 ..     211     261 .. 0.84
   3 ?    3.0   0.0      0.17   1.1e+02      87     112 ..     267     301 ..     248     323 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.7
                        AAA_22  42 vv.fvtlpsstsskdl.lrellral 64 
                                   ++ + ++ +st++k++ ++++ + +
  gi|91773894|ref|YP_566586.1| 125 TAnYKKALASTGPKEVdREWIESLI 149
                                   2222233333444444344444333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.3e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45 
                                   ++ +G++GtGKT +++ + e+l         + ++v+v
  gi|91773894|ref|YP_566586.1| 214 ILMVGPPGTGKTSVAKAMSERL---------SIPFVEV 242
                                   6789***************999.........5555555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.17
                        AAA_22  87 raravielliiDEaqhlr....s......eealeeL 112
                                   ++ + + +l iDE++++     s      ++a+++L
  gi|91773894|ref|YP_566586.1| 267 KRLS-PCILFIDEFDFVAktraSdehaalKRAVNTL 301
                                   3333.599********98764425555555555555 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 !   18.2   0.0   2.3e-06    0.0016      15      97 ..     186     283 ..     175     338 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                        RuvB_N  15 vkeklkifieaakkree.......aldhvllyGpPGlGkttlakiiakelg.....vklkitsgPvl.ekagdlaallt.. 80 
                                    ke+++ +++a + re+        +  +l++GpPG Gkt++ak +++ l      v+l + +   l e a+++  ++t  
  gi|91773894|ref|YP_566586.1| 186 QKEEIEKIVKAIQYREHlkkiglyDIGKILMVGPPGTGKTSVAKAMSERLSipfveVRLSMITDQYLgETAKNIDRVFTla 266
                                   56666666666666654222221135689******************9987222113333334333323444444443300 PP

                        RuvB_N  81 nleekdvlfideihrls 97 
                                   +  +  +lfide   ++
  gi|91773894|ref|YP_566586.1| 267 KRLSPCILFIDEFDFVA 283
                                   33334588888876555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.6e-06    0.0018      52      88 ..     213     247 ..     187     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88 
                                    +L++Gp+gtGkt++a a+s+ l+  +pfv +  s +
  gi|91773894|ref|YP_566586.1| 213 KILMVGPPGTGKTSVAKAMSERLS--IPFVEVRLSMI 247
                                   489********************9..***99887765 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.31   2.2e+02      14      29 ..      69      84 ..      65     103 .. 0.85
   2 !   13.9   0.0   6.2e-05     0.043       1      23 [.     220     242 ..     220     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.31
                                  HHHTSEEEEHHHHHHH CS
                           SKI 14 kklglefiDlDeliek 29
                                  + l+l+fiD+Del +k
  gi|91773894|ref|YP_566586.1| 69 QVLSLPFIDIDELTSK 84
                                  789********99776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.2e-05
                                   TTSSHHHHHHHHHHHHTSEEEEH CS
                           SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                   +G+GK++v+k+++++l+++f+++
  gi|91773894|ref|YP_566586.1| 220 PGTGKTSVAKAMSERLSIPFVEV 242
                                   69******************985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.23   1.6e+02      40      74 ..     126     161 ..     116     195 .. 0.78
   2 !   13.2   0.0   0.00013     0.088       1      25 [.     217     241 ..     217     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                                   HSSHHHHC.TSHHHHHHHHHHHHHHHHHHHHHSSEE CS
                        AAA_17  40 akardemr.klpleekkelqkeaaekiaeeakkkgv 74 
                                   a+ +++++ ++p+e+++e+ + ++ +i ee++ +++
  gi|91773894|ref|YP_566586.1| 126 ANYKKALAsTGPKEVDREWIESLISEISEEEGGEDM 161
                                   444555554789****************99865554 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                                   EE-TTSSHHHHHHHHHHHHTEEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                   +G+PG GK+ +++ + e++ +++++
  gi|91773894|ref|YP_566586.1| 217 VGPPGTGKTSVAKAMSERLSIPFVE 241
                                   7*********************998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.5e-06    0.0051       1      43 [.     213     256 ..     213     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.5e-06
                        AAA_28   1 kivitGgestGKTtlleaLaar.gypvvpEaareileeklakge 43 
                                   ki ++G+++tGKT++++a+++r  +p v+    +i+++ l ++ 
  gi|91773894|ref|YP_566586.1| 213 KILMVGPPGTGKTSVAKAMSERlSIPFVEVRLSMITDQYLGETA 256
                                   6999*****************98899886555555555554444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         9   6.2e+03      75      81 ..     188     194 ..     140     200 .. 0.66
   2 !   16.1   0.0   1.3e-05    0.0092       3     109 ..     211     311 ..     209     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9
                                   ETGGG-- CS
                         AAA_2  75 DEidKih 81 
                                   +Ei+Ki 
  gi|91773894|ref|YP_566586.1| 188 EEIEKIV 194
                                   3555554 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.3e-05
                                   ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG---- CS
                         AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihpk 83 
                                   i++il++gp g+Gkt +aka++e l++    +++ +  s ++   +     ++ i       ++    i+++DE d ++++
  gi|91773894|ref|YP_566586.1| 211 IGKILMVGPPGTGKTSVAKAMSERLSI----PFVEVRLSMITD--QYLGETAKNIDRVFTLAKRLSPCILFIDEFDFVAKT 285
                                   789**********************98....666666666655..33333333334444444455567************9 PP

                                   ---------HHHHHHHHHHHH--EE- CS
                         AAA_2  84 essgadvSregVqrdLLqileggtlt 109
                                   + s +    +  ++ LL+ ++   lt
  gi|91773894|ref|YP_566586.1| 286 RASDEHAALKRAVNTLLKAIDSISLT 311
                                   88888888888889999999987766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05    0.0092      24      45 ..     213     234 ..     193     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                  Mg_chelatase  24 nlllvGppGsGKtmlakrlpsl 45 
                                   ++l+vGppG+GKt +ak++++ 
  gi|91773894|ref|YP_566586.1| 213 KILMVGPPGTGKTSVAKAMSER 234
                                   79***************99865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.5e-05      0.01      49     124 ..     213     286 ..     182     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                     IstB_IS21  49 nivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldq 124
                                    i+++Gp+G+GK+ +a a++ +     ++v+   ++d     ++a++ +++ + +krl  + +l +D++ ++   +
  gi|91773894|ref|YP_566586.1| 213 KILMVGPPGTGKTSVAKAMSERLSIPFVEVRLSMITDQYL-GETAKNIDRVFTLAKRL-SPCILFIDEFDFVAKTR 286
                                   689****************998877777777777766433.36677777777666665.45577778877665554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05     0.011      10      65 ..     198     251 ..     187     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHCTSS.S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTC CS
               Sigma54_activat  10 elleqikkvaktd.lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeel 65 
                                   + +e++kk+  +d  ++l++G  GtGK+ +a+a+   s+r + pfv+v  + i+++ 
  gi|91773894|ref|YP_566586.1| 198 QYREHLKKIGLYDiGKILMVGPPGTGKTSVAKAM---SERLSIPFVEVRLSMITDQY 251
                                   5667788888888669****************98...56677899999888877765 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   0.1   2.6e-05     0.018      35      75 ..     213     245 ..     194     293 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                         AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsa 75 
                                   ++l+vGp GtGKt+++k + ++l+        i f     +
  gi|91773894|ref|YP_566586.1| 213 KILMVGPPGTGKTSVAKAMSERLS--------IPFVEVRLS 245
                                   69****************999998........233222223 PP

>> AAA_24  AAA 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     0.016       4      30 ..     213     238 ..     212     333 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                        AAA_24   4 kiliyGpsgiGKTtlakelgpkplfid 30 
                                   kil++Gp+g+GKT++ak +  + l i 
  gi|91773894|ref|YP_566586.1| 213 KILMVGPPGTGKTSVAKAM-SERLSIP 238
                                   89****************9.6655554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.51   3.5e+02      60     120 ..     135     193 ..     109     208 .. 0.67
   2 !   13.8   0.1   5.6e-05     0.039       4      42 ..     184     236 ..     181     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.51
                        AAA_11  60 CapSNaAvD.ellerllrglldsegekykpkivRvgneeeriseavksvsleekvekrleke 120
                                   ++p +  vD e +e l++++ ++eg +  +k+v + ++e +i + ++ + l e +++++ek 
  gi|91773894|ref|YP_566586.1| 135 TGPKE--VDrEWIESLISEISEEEGGEDMLKLVQIIAPE-DIAQPMRYMVLTEDQKEEIEKI 193
                                   44433..33245666666699999999999999999999.7888888888877777777653 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.6e-05
                        AAA_11   4 dsqreaiksalsese..............itliqGPPGtgKTktivellsqll 42 
                                   ++q+e i+++++  +                l+ GPPGtgKT++  ++ ++l 
  gi|91773894|ref|YP_566586.1| 184 EDQKEEIEKIVKAIQyrehlkkiglydigKILMVGPPGTGKTSVAKAMSERLS 236
                                   56666665555555555556666777777789************999988884 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.9e-05     0.055       4      28 ..     217     241 ..     214     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                                   E-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                    GP g+GK sva+a++e+l++ +++
  gi|91773894|ref|YP_566586.1| 217 VGPPGTGKTSVAKAMSERLSIPFVE 241
                                   59******************99876 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      0.02        13      36      55 ..     212     231 ..     186     239 .. 0.84
   2 ?    5.6   0.0     0.013       9.3     104     143 ..     255     294 ..     244     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.02
                          TniB  36 pnlllvGdsnnGKtmivekF 55 
                                    ++l+vG++ +GKt++++  
  gi|91773894|ref|YP_566586.1| 212 GKILMVGPPGTGKTSVAKAM 231
                                   579************99865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.013
                          TniB 104 vskleqqvlrllrelkvrvLiiDEihnllagsarkqrefl 143
                                   ++k  ++v +l ++l++ +L iDE++ + + +a++ +++l
  gi|91773894|ref|YP_566586.1| 255 TAKNIDRVFTLAKRLSPCILFIDEFDFVAKTRASDEHAAL 294
                                   566778899999****************999998877655 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   0.00014     0.094       3      49 ..     181     236 ..     179     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                   EE-HHHHHHHHHHT......TTS..........EEEEEESTTSTHHHHHHHHHHHH- CS
                        ResIII   3 elreyQeeaienlleklkskrdk..........rglikmaTGtGKTlvaaklierll 49 
                                    l e Q+e ie+++++++  r++          ++l++ + GtGKT va ++ erl+
  gi|91773894|ref|YP_566586.1| 181 VLTEDQKEEIEKIVKAIQY-REHlkkiglydigKILMVGPPGTGKTSVAKAMSERLS 236
                                   68899*********99984.4444455566666***************999888876 PP

>> RE_AspBHI_N  Restriction endonuclease AspBHI N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.17     125     168 ..     110     153 ..     100     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                   CCSEEEEEEEETTEEEEEEEEEEEEBS-SEE-HHHHHCCCTCGG CS
                   RE_AspBHI_N 125 eedlvaqwkekegerfqNYraeftiLdvkevsleWiekraeaee 168
                                   +  l   ++ek++ ++ NY+  ++    kev++eWie++ ++ +
  gi|91773894|ref|YP_566586.1| 110 NPVLAYYYEEKKSYETANYKKALASTGPKEVDREWIESLISEIS 153
                                   55566777889999************************988654 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   0.00037      0.26      11      78 ..     200     279 ..     192     305 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                                   HHHHHHHH.T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..............HHHHHHTTTSEEEEE CS
               Sigma54_activ_2  11 kerLeqaa.qsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp..............ldlleqakggtLylk 76 
                                   +e+L+++  +    ++++G++G+gk++vA+++++  +    +fv+ rl+ ++                l +++++ +L++ 
  gi|91773894|ref|YP_566586.1| 200 REHLKKIGlYDIGKILMVGPPGTGKTSVAKAMSERLSI---PFVEVRLSMITdqylgetaknidrvFTLAKRLSPCILFID 277
                                   677777775666689****************9875443...5555555544432333333333333333333466666666 PP

                                   E- CS
               Sigma54_activ_2  77 di 78 
                                   ++
  gi|91773894|ref|YP_566586.1| 278 EF 279
                                   65 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      0.31       1      23 [.     214     236 ..     214     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                   i+++Gp+g+GK+++ak ++++l+
  gi|91773894|ref|YP_566586.1| 214 ILMVGPPGTGKTSVAKAMSERLS 236
                                   6799*************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 3251.15
//
Query:       gi|91773895|ref|YP_566587.1|  [L=187]
Description: hypothetical protein Mbur_1956 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00014   22.1   1.4    0.00025   21.3   1.4    1.4  1  DUF1922          Domain of unknown function (DUF1922)
     0.0074   16.4   0.3      0.018   15.1   0.1    1.8  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.023   14.2   0.1      0.049   13.1   0.1    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.042   13.5   1.2      0.099   12.4   1.2    1.6  1  Ribosomal_S27e   Ribosomal protein S27
      0.045   13.2   0.1      0.059   12.9   0.1    1.2  1  LuxQ-periplasm   LuxQ, periplasmic
      0.048   14.1   0.2      0.089   13.2   0.2    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.51   10.2   3.5        8.8    6.2   0.1    2.6  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        1.5    9.6   5.7        5.1    7.9   5.6    2.1  1  MRNIP            MRN-interacting protein


Domain annotation for each model (and alignments):
>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.4   1.1e-07   0.00025      12      64 ..      19      72 ..       7      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                  EEEETT-SEEEET.TTEEEE--SSS-BS--SSHHHHHHHHHHHSS---S-TTSS CS
                       DUF1922 12 lYakegaktrkCv.CGktikvkerrilkkaedaeeAselVrklqeekyGltafk 64
                                  l   ++akt kC  CG ++++++ r++++ ed eeA  +  k+q +  G ++ +
  gi|91773895|ref|YP_566587.1| 19 LIEDKDAKTTKCQlCGTNLHIRKLRVFHTGEDIEEARAVRTKVQAQLLGEKQST 72
                                  6667899999**55**********************999999**9999987755 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   8.1e-06     0.018       1      36 [.       2      37 ..       2      42 .. 0.78
   2 ?   -3.7   0.0       6.1   1.4e+04      28      31 ..      78      81 ..      73      87 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.1e-06
                   Zn-ribbon_8  1 MPiYeYr.CeeCghefevlqsisdapltaCPeCgsev 36
                                  MP+Y    C +C +    +   +da+ t+C  Cg ++
  gi|91773895|ref|YP_566587.1|  2 MPVYSVIaCPKCRKSAQLIE-DKDAKTTKCQLCGTNL 37
                                  9***9988*****7777666.45666666*****965 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.1
                   Zn-ribbon_8 28 aCPe 31
                                  +CP+
  gi|91773895|ref|YP_566587.1| 78 KCPT 81
                                  5885 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.2e-05     0.049       2      27 ..       9      35 ..       8      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                                  EETTTTCEE.CHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgstn.lveDpergelvCtdCGl 27
                                   CP+C  +  l+eD +  ++ C  CG+
  gi|91773895|ref|YP_566587.1|  9 ACPKCRKSAqLIEDKDAKTTKCQLCGT 35
                                  5****997769**************96 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.2   4.4e-05     0.099       8      36 ..       8      37 ..       4      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                                  EE-TTTS-.EEEEESS-SS-EEESSSTCEE CS
                Ribosomal_S27e  8 vkCpdCen.etvvFshaatvvkCisCgkvL 36
                                  + Cp+C +  + + ++ a+  kC+ Cg+ L
  gi|91773895|ref|YP_566587.1|  8 IACPKCRKsAQLIEDKDAKTTKCQLCGTNL 37
                                  78****873699***************987 PP

>> LuxQ-periplasm  LuxQ, periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.7e-05     0.059      15      80 ..      73     138 ..      60     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHTT-CCCHHHHHHHHHHCCCCCS-SEEEEEET CS
                LuxQ-periplasm  15 qtssliqnlfdsrLsiLqihqdssaknealaealssgdeealdafflsvdqkepsntpdlrfissq 80 
                                     s l    f  +Ls+L   +d ++ ++++ +a++ +d +++++ + +v  k+ +   d+r i ++
  gi|91773895|ref|YP_566587.1|  73 TMSNLKCPTFGEELSSLSTPRDDASISKTIDKAFKPNDPSEIKTPIENVRRKKNNAEKDMRSILEN 138
                                   444444557999*************************************************88654 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     4e-05     0.089       5      50 ..       9      54 ..       6      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
               Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga.....stpwfkiaedeaea 50
                                   CP C + a l+++++ +     +  C+ Cg          f++ ed +ea
  gi|91773895|ref|YP_566587.1|  9 ACPKCRKSAQLIEDKDAK-----TTKCQLCGTnlhirKLRVFHTGEDIEEA 54
                                  6*************9998.....89**99**97776644445566665555 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 ?    4.4   0.1     0.014        32       2       9 ..       8      15 ..       7      23 .. 0.75
   2 ?    6.2   0.1    0.0039       8.8       3      15 ..      29      41 ..      27      44 .. 0.89
   3 ?   -3.9   0.0       5.5   1.2e+04       3       8 ..      78      83 ..      78      87 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                                  EE-SSS-- CS
                zf-C4_Topoisom  2 ekCPkCgg 9 
                                  + CPkC++
  gi|91773895|ref|YP_566587.1|  8 IACPKCRK 15
                                  57****93 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0039
                                  E-SSS--EEEEEE CS
                zf-C4_Topoisom  3 kCPkCggdLvlkr 15
                                  kC  Cg +L++++
  gi|91773895|ref|YP_566587.1| 29 KCQLCGTNLHIRK 41
                                  9**********97 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 5.5
                                  E-SSS- CS
                zf-C4_Topoisom  3 kCPkCg 8 
                                  kCP  g
  gi|91773895|ref|YP_566587.1| 78 KCPTFG 83
                                  799755 PP

>> MRNIP  MRN-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.6    0.0023       5.1       1      56 [.       7      69 ..       7     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                         MRNIP  1 vlrCysCetf.qvkqvkKskkwkCkvCnekqslkk..vygsg....sgkdcrqlVqklnlkkg 56
                                  v+ C +C+   q    k +k+ kC++C++   ++k  v+  g    +++ +r++Vq+  l ++
  gi|91773895|ref|YP_566587.1|  7 VIACPKCRKSaQLIEDKDAKTTKCQLCGTNLHIRKlrVFHTGedieEARAVRTKVQAQLLGEK 69
                                  689****98736666666999************982244433111134456777765444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1233.77
//
Query:       gi|91773896|ref|YP_566588.1|  [L=139]
Description: SSU ribosomal protein S18P alanine acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.3   0.0    1.5e-13   51.0   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.4e-11   44.6   0.0    1.9e-11   44.2   0.0    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      3e-11   43.3   0.0    3.8e-11   43.0   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00087   19.5   0.0     0.0015   18.7   0.0    1.5  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0026   17.8   0.0      0.098   12.7   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0048   16.7   0.0     0.0087   15.9   0.0    1.4  1  Acetyltransf_18  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.026   14.5   0.0    1.4  1  FR47             FR47-like protein
      0.043   14.5   0.0      0.054   14.2   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.057   13.4   0.0       0.15   12.1   0.0    1.7  2  Acetyltransf_13  ESCO1/2 acetyl-transferase
       0.11   12.7   0.0       0.14   12.3   0.0    1.2  1  Acetyltransf_6   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 !   51.0   0.0   8.2e-17   1.5e-13       4     117 .]      13     117 ..      10     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 8.2e-17
                                   HHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHH CS
                Acetyltransf_1   4 lvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlea 84 
                                   +v+l+++sf +p+  ++++    +   +++g++v  edg + G++ l  i d     a++ s+a++p++r++++Gs Ll+ 
  gi|91773896|ref|YP_566588.1|  13 VVDLENLSFAEPWDLRTFRS---Y--VHHPGFIVFDEDGSICGYVILVVIAD----DAHLASIAIHPKHRRRNIGSCLLDS 84 
                                   56666666555555555555...3..467799999*****************....8************************ PP

                                   HHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  85 leerareegikkivlaveedndaairlYeklGF 117
                                   ++  a+ + +  + l+v+e n+ a+ +Y   GF
  gi|91773896|ref|YP_566588.1|  85 CMLLAKTNSFPLVRLEVREKNKTAQDFYLANGF 117
                                   **********99****************87888 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.1e-14   1.9e-11       5      75 ..      39     118 ..      33     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.1e-14
                                   EEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEE....EE..EEEETHHHHHHHHHHT CS
                Acetyltransf_7   5 vfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea.....aekgii....le..qlelnaekaikfYekl 72 
                                   ++V ++dg i+G+++l++++  a++  +a++p++r++ iG+ Ll+      +    +    l+  +++ ++++a++fY  +
  gi|91773896|ref|YP_566588.1|  39 FIVFDEDGSICGYVILVVIAddAHLASIAIHPKHRRRNIGSCLLDScmllaK----TnsfpLVrlEVREKNKTAQDFYLAN 115
                                   6778889**********9998777777******************4344421....122232212222333489******* PP

                                   TEE CS
                Acetyltransf_7  73 GFe 75 
                                   GFe
  gi|91773896|ref|YP_566588.1| 116 GFE 118
                                   **8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   2.1e-14   3.8e-11      33     109 ..      39     120 ..      19     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 2.1e-14
               Acetyltransf_10  33 llvaeeggkivGvi...elrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFka 108
                                   ++v++e+g+i+G++    + d+ h++ ++++p++r++ ig+ Ll+ +   a+++   l +l+v++++ +a++fY   GF+a
  gi|91773896|ref|YP_566588.1|  39 FIVFDEDGSICGYVilvVIADDAHLASIAIHPKHRRRNIGSCLLDSCMLLAKTNSFPLvRLEVREKNkTAQDFYLANGFEA 119
                                   7899*********9874449999***************************999988889*********************9 PP

               Acetyltransf_10 109 v 109
                                   v
  gi|91773896|ref|YP_566588.1| 120 V 120
                                   7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.5e-07    0.0015      52     144 ..      39     127 ..       2     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.5e-07
                Acetyltransf_4  52 flvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhka 131
                                   f v++ ++ i Gy  l+ + +     + + s+ + + + + + +g+ l+d+++  +k +++     e+  +n+ +++f+ a
  gi|91773896|ref|YP_566588.1|  39 FIVFDeDGSICGYVILVVIAD----DAHLASIAI-HPKHRRRNIGSCLLDSCMLLAKTNSFPLVRLEVREKNKTAQDFYLA 114
                                   667777***********8888....555666667.46789***************************************** PP

                Acetyltransf_4 132 lGFelvgifkkci 144
                                    GFe v+i  +++
  gi|91773896|ref|YP_566588.1| 115 NGFEAVAIIPDYY 127
                                   ******9987776 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.4e-05     0.098       2     110 ..       2      97 ..       1     120 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                                   EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE- CS
                Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVava 82 
                                   ir++t +dl++v++l + +F++  + +      fr ++ +  +++  ++g + g + l+         + + a ++++a +
  gi|91773896|ref|YP_566588.1|   2 IRTATRSDLPAVVDLENLSFAEPWDLR-----TFRSYVHHPGFIVFDEDGSICGYVILVV--------IADDAHLASIAIH 69 
                                   899999999999999999999988873.....5677777777777777888888776653........3445788999999 PP

                                   CCGTTS-HHHHHHHHHHHHHHHTT--EE CS
                Acetyltransf_9  83 pehrgrgvlskLlaraleemreegqpls 110
                                   p+hr+r + s Ll+  +  ++ +  pl+
  gi|91773896|ref|YP_566588.1|  70 PKHRRRNIGSCLLDSCMLLAKTNSFPLV 97 
                                   9999999999999887766666666665 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.9e-06    0.0087      29     103 ..      40     121 ..      28     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
               Acetyltransf_18  29 vvveedgeivGyglarktrkglkiGPlvAe....neeiAeaLlkalvanaeg...kkvridvpeenkalielleklgfkev 102
                                   +v +edg+i+Gy +++ + ++  +  +  +     ++i  +Ll++++  a+    + vr+ v e+nk+++++    gf+ v
  gi|91773896|ref|YP_566588.1|  40 IVFDEDGSICGYVILVVIADDAHLASIAIHpkhrRRNIGSCLLDSCMLLAKTnsfPLVRLEVREKNKTAQDFYLANGFEAV 120
                                   8999***************9999999876422226789*****99876555522478*********************988 PP

               Acetyltransf_18 103 f 103
                                   +
  gi|91773896|ref|YP_566588.1| 121 A 121
                                   6 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.5e-05     0.026      20      79 ..      59     119 ..      47     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                                   TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE..EEEETT-HHHHHHHHHHT-EE CS
                          FR47  20 dggelgalqvlpehrrrGlgsrlvkalakeiaergktvl..lvvvasNtpsirlyeklGfek 79 
                                   d+  l ++ ++p+hrrr  gs l  +    +a+ +  +l  l v+++N++++ +y + Gfe+
  gi|91773896|ref|YP_566588.1|  59 DDAHLASIAIHPKHRRRNIGSCLLDSCM-LLAKTNSFPLvrLEVREKNKTAQDFYLANGFEA 119
                                   678899*****************99975.5677666665125799***********999986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-05     0.054      37     138 .]      30     118 ..       1     118 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                Acetyltransf_3  37 aeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelg.ymlapsfwgkGyateavralleyafeelgler 116
                                    ++++         +   g++++++d+++ G+v l  + ++   a+l  + ++p+++++ +++  + +++ +a ++   + 
  gi|91773896|ref|YP_566588.1|  30 FRSYVH--------HP--GFIVFDEDGSICGYVILVVIADD---AHLAsIAIHPKHRRRNIGSCLLDSCMLLA-KTNSFPL 96 
                                   333333........23..499*9988878*******99998...5555499********************99.66669** PP

                Acetyltransf_3 117 lvavidkeNeaSirvleklGfe 138
                                   ++ ++ ++N+  +  +   Gfe
  gi|91773896|ref|YP_566588.1|  97 VRLEVREKNKTAQDFYLANGFE 118
                                   *************999999996 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.9   3.3e+03      55      69 .]      28      42 ..      11      42 .. 0.64
   2 ?   12.1   0.0   8.2e-05      0.15      11      29 ..      67      85 ..      63      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.9
               Acetyltransf_13 55 klarkyfgtedflvY 69
                                  + +r+y+ +++f v+
  gi|91773896|ref|YP_566588.1| 28 RTFRSYVHHPGFIVF 42
                                  446777777777776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.2e-05
               Acetyltransf_13 11 WvssshRrkgiAtkLldaa 29
                                   ++++hRr++i ++Lld+ 
  gi|91773896|ref|YP_566588.1| 67 AIHPKHRRRNIGSCLLDSC 85
                                  579**************75 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.8e-05      0.14      49     124 ..      21      90 ..       6     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-05
                Acetyltransf_6  49 fadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweliedaa 124
                                   fa+p+  + +r++++++       + v   dg + +++++++  d +++  ++++p +++  +g +ll  ++  a+
  gi|91773896|ref|YP_566588.1|  21 FAEPWDLRTFRSYVHHP------GFIVFDEDGSICGYVILVVIADDAHLASIAIHPKHRRRNIGSCLLDSCMLLAK 90 
                                   899999999****9999......3788888**************************************99986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1035.14
//
Query:       gi|91773897|ref|YP_566589.1|  [L=395]
Description: translation-associated GTPase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-31  108.3   0.2    6.5e-31  107.2   0.1    1.6  2  MMR_HSR1_C    GTPase of unknown function C-terminal
    1.1e-19   70.6   0.0    3.8e-19   68.8   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
      5e-14   52.1   0.0    1.5e-13   50.5   0.0    1.8  2  TGS           TGS domain
    1.3e-08   34.6   2.5      5e-07   29.4   0.1    2.8  3  FeoB_N        Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.011   15.8   0.2      0.029   14.4   0.0    1.8  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.22    9.9   0.3       0.45    8.8   0.1    1.5  2  BcsB          Bacterial cellulose synthase subunit


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 ?   -3.5   0.0       5.2   1.6e+04      65      91 ..     152     178 ..     144     183 .. 0.65
   2 !  107.2   0.1   2.2e-34   6.5e-31       1     112 []     220     325 ..     220     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.2
                    MMR_HSR1_C  65 eldekqkkaLekirdlvlkrygsTGVq 91 
                                   +l++k +++  k+++ v ++  + GV+
  gi|91773897|ref|YP_566589.1| 152 KLSRKIRAEGMKMEQAVSDQLLGAGVN 178
                                   466666666666677777777777765 PP

  == domain 2  score: 107.2 bits;  conditional E-value: 2.2e-34
                    MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlv 81 
                                   a+NK+D+ a++en+++l+e +    +vvp+sAaaElaLr+aak+++i+Y+pgd+ fei  d   +++e+qk+ L+++++++
  gi|91773897|ref|YP_566589.1| 220 AANKIDV-APAENVKALEELDI---MVVPTSAAAELALRSAAKNNIISYNPGDMGFEIISD---KVSEAQKNGLQSLKEMI 293
                                   89*****.************88...7********************************999...69*************87 PP

                    MMR_HSR1_C  82 .lkrygsTGVqealnaavfelldlivVYPVed 112
                                       +g+ G+qe++n+avf+ll+livVYPVed
  gi|91773897|ref|YP_566589.1| 294 tTLGTGGAGIQECINRAVFDLLELIVVYPVED 325
                                   333569999*********************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 !   68.8   0.0   1.3e-22   3.8e-19       2      87 ..       5     122 ..       4     151 .. 0.75
   2 ?   -1.5   0.0      0.88   2.6e+03      90     114 .]     198     223 ..     143     223 .. 0.58

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.3e-22
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE........ETTEE...............EEEEECGGCSSH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk........lkgke...............ielvDtpGlieg 59 
                                   ++++G+pN+GKSt+++a t + ++++++p+tT++ n+g           +   +               ie++D++Gl+ +
  gi|91773897|ref|YP_566589.1|   5 IGLAGKPNAGKSTFFKAATLADVEIANYPFTTINANKGVTYvravcpctE---RdkrcgncqdgiryvpIEIIDVAGLVPD 82 
                                   89************************************777444444431...0334444555555555********9999 PP

                                   HHHHHHHHHHHHHHHC.TSEEEEEEETT...........T CS
                      MMR_HSR1  60 aseekglgkaflalee.adlillvvdas...........e 87 
                                   a+ ++glg++fl+  + a++i++v+das            
  gi|91773897|ref|YP_566589.1|  83 AHMGRGLGNTFLDELRqAQAIIHVIDASggtdiegnpvdI 122
                                   ************977669********99665554444330 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.88
                                   SHHHHHHHHHHHHH...TTSEEEEEEES CS
                      MMR_HSR1  90 lkpldeeleellee...akkplilvlnk 114
                                   +   de++++l e     +kp+++++nk
  gi|91773897|ref|YP_566589.1| 198 W--TDEDMAKLCETiraITKPTMIAANK 223
                                   2..3344444433333477888888887 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.3   9.8e+03      29      41 ..     167     179 ..     163     195 .. 0.73
   2 !   50.5   0.0   5.1e-17   1.5e-13       6      59 ..     338     391 ..     332     392 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.3
                                   THHHHEEEEEECS CS
                           TGS  29 slakkfiyAlVnG 41 
                                    + +++++A Vn 
  gi|91773897|ref|YP_566589.1| 167 AVSDQLLGAGVNE 179
                                   5678899999997 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 5.1e-17
                                   TTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                           TGS   6 PdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                   Pd+ +  +++g+t+ D+Ay++h++++++f+yA   +  +r g +h L++gdvv+Iv
  gi|91773897|ref|YP_566589.1| 338 PDAFL--MKKGSTPHDLAYRVHTDIGNRFLYAVDGKtkMRLGEKHDLQNGDVVKIV 391
                                   44444..99***********************8888999****************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 !   29.4   0.1   1.7e-10     5e-07       2      43 ..       4      45 ..       3      50 .. 0.92
   2 ?   -3.0   0.0       1.5   4.6e+03      78      89 ..      99     110 ..      92     111 .. 0.82
   3 !    4.2   0.1    0.0092        28     100     147 ..     209     251 ..     201     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.7e-10
                                  EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEE CS
                        FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklk 43
                                  t+ l+G+pn+Gk+t+f a t a+ +++N+p +t++ ++g + 
  gi|91773897|ref|YP_566589.1|  4 TIGLAGKPNAGKSTFFKAATLADVEIANYPFTTINANKGVTY 45
                                  799********************************9999765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                                   SSSEEEEEEEGG CS
                        FeoB_N  78 epdvvvnvvdat 89 
                                   +++++++v+da+
  gi|91773897|ref|YP_566589.1|  99 QAQAIIHVIDAS 110
                                   6789999*9996 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0092
                                   HHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTB CS
                        FeoB_N 100 qllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkke 147
                                    +  +++p+++a n+id+a ++++    k+L e+L++ vv+tsa+ + 
  gi|91773897|ref|YP_566589.1| 209 TIRAITKPTMIAANKIDVAPAENV----KAL-EELDIMVVPTSAAAEL 251
                                   56678899***********99865....556.4699*****9998765 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.6e-06     0.029      42      93 ..     200     253 ..     162     262 .. 0.83
   2 ?   -3.1   0.0       2.6   7.7e+03      85     100 ..     278     293 ..     275     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.6e-06
                  MMR_HSR1_Xtn  42 vDdlidvieg.nrvYipclyvlNKiDlisleeldelarep.nsvviSaekelnl 93 
                                    +d+    e      +p++++ NKiD +  e++++l++ +  +v++Sa+ el l
  gi|91773897|ref|YP_566589.1| 200 DEDMAKLCETiRAITKPTMIAANKIDVAPAENVKALEELDiMVVPTSAAAELAL 253
                                   556666665523356799********************7648999***999877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.6
                  MMR_HSR1_Xtn  85 iSaekelnldeLkeki 100
                                   +S +++ +l++Lke+i
  gi|91773897|ref|YP_566589.1| 278 VSEAQKNGLQSLKEMI 293
                                   6788889999999987 PP

>> BcsB  Bacterial cellulose synthase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00015      0.45     481     547 ..     198     264 ..     195     295 .. 0.83
   2 ?   -2.3   0.0      0.36   1.1e+03     326     349 ..     335     358 ..     331     363 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00015
                          BcsB 481 ptaaelsallnllgrmGaqtgypalrvtvadaadaesladkdlLvigslesqpllarlekslpllld 547
                                    t+++++ l +++ ++++ t  +a +++va a+++++l++ d++v+ +   ++l+ r+++++++   
  gi|91773897|ref|YP_566589.1| 198 WTDEDMAKLCETIRAITKPTMIAANKIDVAPAENVKALEELDIMVVPTSAAAELALRSAAKNNIISY 264
                                   678999999*************************************************998876543 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.36
                          BcsB 326 rlPpDlflwrgegiplqlryryta 349
                                   r+ pD fl ++++ p +l yr+ +
  gi|91773897|ref|YP_566589.1| 335 RMLPDAFLMKKGSTPHDLAYRVHT 358
                                   789******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2700.34
//
Query:       gi|91773898|ref|YP_566590.1|  [L=500]
Description: thermosome subunit, group II chaperonin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-166  554.7  20.3   1.9e-166  554.5  20.3    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.5  20.3  1.1e-170  1.9e-166      17     490 ..       1     476 [.       1     477 [. 0.98

  Alignments for each domain:
  == domain 1  score: 554.5 bits;  conditional E-value: 1.1e-170
                                   EEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHH CS
                    Cpn60_TCP1  17 mlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyeka 97 
                                   mlv+++g++v+TnDGatilke++i+hPaak++ve++++qd evGDGTtt+++L geLl++ae+li +gvh t i egy++a
  gi|91773898|ref|YP_566590.1|   1 MLVDSMGDIVITNDGATILKEMDIQHPAAKMIVEVSKTQDAEVGDGTTTAAVLSGELLSKAEELIMKGVHSTIISEGYRHA 81 
                                   9******************************************************************************** PP

                                   HHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS...EECSCCCEECCCCEECE CS
                    Cpn60_TCP1  98 lekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene...keldlgrikvvkieggs 174
                                   +ek+ e+L+ i+++i  + +d+ +L+k+a t++++k  ++ +e+ls+l+v+Av +++ee+e   k   l++ik++k  ggs
  gi|91773898|ref|YP_566590.1|  82 AEKCREILETITIAI--SPDDEAALIKIAGTAITGKGAEAYKEKLSALTVKAVrSIVEEEEdglKVNVLENIKIEKRAGGS 160
                                   ***********5555..5679********************************888888888977777888********** PP

                                   CTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECE CS
                    Cpn60_TCP1 175 ledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnv 255
                                   ++dsel++Glv+dk+ ++p+mp+k+enak+lll++++e+ kte++++++++++ +++ ++++eek+++e+ ek+i+sg+nv
  gi|91773898|ref|YP_566590.1| 161 IDDSELIDGLVIDKERSHPNMPEKVENAKILLLSCPVEFRKTEVDSEIKITSPGQMQLFLDQEEKMMREMAEKVIASGANV 241
                                   ********************************************************************************* PP

                                   EEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSX CS
                    Cpn60_TCP1 256 vvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigsekttiieevksgki 336
                                   v+cqkgidd+a+ + +k+gi a+rrvkk+dl+rl+k+tGat++++l+++t e++Gta+ vee+++   k+t++++++++k+
  gi|91773898|ref|YP_566590.1| 242 VFCQKGIDDMAQYYIEKAGIYAVRRVKKSDLKRLSKVTGATIIQDLDQITTEDVGTAGLVEEKEVRGGKMTYVTGCQNSKA 322
                                   ********************************************************************************* PP

                                   EEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHH CS
                    Cpn60_TCP1 337 atillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaieafakALevipktLa 417
                                   +t+ll g t++v+d +  a++dAl+vv  +ied+kvv+GGG++e+el+ +l+eya++++g+eqla+ +fa+ALevip +La
  gi|91773898|ref|YP_566590.1| 323 VTVLLHGGTEHVVDSLDHALNDALHVVGVVIEDGKVVVGGGSSEVELSLRLSEYASTLKGREQLAVSKFAEALEVIPVALA 403
                                   ********************************************************************************* PP

                                   HHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                    Cpn60_TCP1 418 eNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiikak 490
                                   eNaGldpi+++ +lr++h+kg+k++g++v +ge++d++e+ v++pl++k+qa+++A+ea  +iLrid+++  k
  gi|91773898|ref|YP_566590.1| 404 ENAGLDPIDIMVELRSQHEKGNKNAGLNVYTGEVVDMWENDVIEPLRIKTQAINAAMEATVMILRIDDVVASK 476
                                   **********************************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3604.46
//
Query:       gi|91773899|ref|YP_566591.1|  [L=187]
Description: BioY protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  134.2  23.1      4e-39  133.8  23.1    1.1  1  BioY      BioY family
  ------ inclusion threshold ------
      0.045   13.9   0.2      0.045   13.9   0.2    2.4  3  Pox_A9    A9 protein conserved region
        2.6    7.9  12.7         12    5.7  12.7    1.9  1  DUF4271   Domain of unknown function (DUF4271)


Domain annotation for each model (and alignments):
>> BioY  BioY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.8  23.1   6.7e-43     4e-39       2     132 ..      45     184 ..      44     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 6.7e-43
                          BioY   2 gpvpitlqtlavllaglllgprrgalavllYlllGalglPvfag.ggGlavllgptgGYllGFlvaalvvgll.....kk. 75 
                                   gp+p+tlq+++vl+ag++lg+++g +++++Y+llG++glPvf++ g+Gl+v+lgptgGYl+GF++aa+++g+l     ++ 
  gi|91773899|ref|YP_566591.1|  45 GPIPFTLQMVFVLMAGAMLGSKWGGISMIVYVLLGIAGLPVFSNgGSGLGVILGPTGGYLIGFIAAAFIIGYLfemngSNn 125
                                   79******************************************66***************************99986335 PP

                          BioY  76 laelllallagllviyalGvlwlalv..lslaaalaagvlpfipgdlvkavlaallaka 132
                                   l +  l + +g++vi+++G++ l++v  +s+++a+++g+lpfi++ +vk+++a+ +a++
  gi|91773899|ref|YP_566591.1| 126 LLKNGLFVTIGSVVIFCFGLAHLMIVadMSFMQAVTVGFLPFILPGIVKIAVATGIATK 184
                                   7888888888***************9899**************************9987 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.8       1.5   8.8e+03      31      43 ..      51      63 ..      49      64 .. 0.76
   2 ?   13.9   0.2   7.5e-06     0.045      30      50 ..      69      89 ..      67      91 .. 0.91
   3 ?   -1.6   0.5      0.52   3.1e+03      30      46 ..     135     150 ..     113     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                        Pox_A9 31 isMvmyLvlGvaL 43
                                  + Mv  L+ G +L
  gi|91773899|ref|YP_566591.1| 51 LQMVFVLMAGAML 63
                                  5699999988766 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.5e-06
                        Pox_A9 30 iisMvmyLvlGvaLlyissnd 50
                                   isM++y +lG+a l ++sn+
  gi|91773899|ref|YP_566591.1| 69 GISMIVYVLLGIAGLPVFSNG 89
                                  59*************999986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.52
                        Pox_A9  30 iisMvmyLvlGvaLlyi 46 
                                   i s v++   G+a l i
  gi|91773899|ref|YP_566591.1| 135 IGSVVIF-CFGLAHLMI 150
                                   3444444.567776666 PP

>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.7     0.002        12      62     169 ..      70     174 ..       2     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.002
                       DUF4271  62 lglllylllsefgslfgsylassllllliiflilllylllKlllykllgwlFfdkkkirqwifsylsylsllglllfplvl 142
                                   +++++y+ll   g    s   +    l++i++ + +yl+  + +  ++g+lF++   +++  + ++ ++   +++ f l+ 
  gi|91773899|ref|YP_566591.1|  70 ISMIVYVLLGIAGLPVFS---NGGSGLGVILGPTGGYLIGFIAAAFIIGYLFEMNGSNNLLKNGLFVTIGSVVIFCFGLAH 147
                                   455555555553333333...8899999***************************************************** PP

                       DUF4271 143 llvyfplssqillililiillliklll 169
                                   l++  ++s+  +++++++ ++l  ++ 
  gi|91773899|ref|YP_566591.1| 148 LMIVADMSFMQAVTVGFLPFILPGIVK 174
                                   ******************999866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1334.96
//
Query:       gi|91773900|ref|YP_566592.1|  [L=269]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-25   89.6   0.0    4.1e-25   88.9   0.0    1.3  1  ABC_tran     ABC transporter
    1.6e-09   37.5   0.4    0.00026   20.5   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    4.8e-09   36.5   0.1      0.002   18.0   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.1e-05   24.2   0.1    3.9e-05   23.3   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00013   22.2   0.1    0.00064   20.0   0.1    1.9  1  AAA_22       AAA domain
    0.00057   19.7   0.0    0.00065   19.5   0.0    1.2  1  AAA_15       AAA ATPase domain
    0.00066   19.6   0.0     0.0012   18.8   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
    0.00069   20.2   0.2     0.0011   19.5   0.2    1.3  1  AAA_23       AAA domain
     0.0022   18.4   0.0     0.0045   17.4   0.0    1.4  1  AAA_16       AAA ATPase domain
     0.0039   16.8   0.0        1.2    8.7   0.0    2.5  3  AAA_25       AAA domain
     0.0084   15.5   0.2       0.29   10.5   0.0    2.1  2  TniB         Bacterial TniB protein
  ------ inclusion threshold ------
       0.01   15.6   0.2      0.051   13.3   0.2    1.9  1  AAA_30       AAA domain
      0.013   15.5   0.4        2.2    8.1   0.1    2.2  2  NTPase_1     NTPase
      0.021   15.2   0.1       0.38   11.2   0.1    2.2  1  AAA          ATPase family associated with various cellular a
      0.042   13.5   0.1        2.5    7.7   0.0    2.0  2  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.054   13.2   0.2        1.2    8.9   0.0    2.1  2  AAA_24       AAA domain
      0.079   11.7   0.0        0.1   11.3   0.0    1.1  1  Herpes_UL21  Herpesvirus UL21
       0.11   12.6   0.1       0.44   10.6   0.0    1.9  2  AAA_5        AAA domain (dynein-related subfamily)
       0.13   12.0   0.1       0.25   11.1   0.1    1.4  2  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.14   12.7   0.1        3.7    8.1   0.0    2.2  2  AAA_18       AAA domain
       0.15   11.4   0.5          5    6.4   0.0    2.2  2  ATPase       KaiC
       0.17   11.7   0.1       0.38   10.5   0.0    1.6  2  DEAD         DEAD/DEAH box helicase
       0.18   11.7   0.0       0.33   10.8   0.0    1.4  1  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   5.2e-28   4.1e-25       1     137 []      18     165 ..      18     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 5.2e-28
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-T.TSBHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfp.eltvren 79 
                                   l+++++ +++g+ + i+G+nG+GKStL++ + gllkp  G + + g d+ + +++ + r+ +g+++q+p+ +  + tv+e 
  gi|91773900|ref|YP_566592.1|  18 LEEIDIRIEKGSFTTILGDNGSGKSTLIRHMNGLLKPSVGVVSVCGMDTASsTDIWEIRQTVGMVFQDPHSQAvGATVEED 98 
                                   678999**************************************9777777699**************6655416779999 PP

                                   .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                e + ++++a++++gl++l+   +      LSgGq q+ a+a +l+ +p++l++DE t+
  gi|91773900|ref|YP_566592.1|  99 vafgpenlalendEIRIRVTNAIANVGLEGLEGYLL----MYLSGGQLQKTAIAGVLAMAPEILIFDEVTS 165
                                   ********9987777777*****************9....9***************************985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.2e-05    0.0095      20      42 ..      23      46 ..      10      54 .. 0.79
   2 !   20.5   0.0   3.3e-07   0.00026     136     207 ..     136     204 ..      65     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                  EETTS.SEEEEEESTTSSHHHHHH CS
                                  xxxxx.xxxxxxxxxxxxxxxxxx RF
                         SMC_N 20 lpfsk.sftaivGpNGSGKsnlld 42
                                  ++++k sft i+G NGSGKs l+ 
  gi|91773900|ref|YP_566592.1| 23 IRIEKgSFTTILGDNGSGKSTLIR 46
                                  5554427*************9986 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.3e-07
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE.E-SSHHHCCC-SC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv.islreemlekadk 207
                                   +LSgG+ + +a+a ++A+    p  + ++De+ + LD   ++++ +++++ +k+   +v ++++ e    ad+
  gi|91773900|ref|YP_566592.1| 136 YLSGGQLQKTAIAGVLAMA---P-EILIFDEVTSMLDSDSRSQIIDIVRQLNKRGKTVVyVTHHMEEALFADR 204
                                   7**************9985...3.4889**********************99995554426666665555555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.1e-06    0.0063       1      22 [.      30      51 ..      30      74 .. 0.89
   2 !   18.0   0.0   2.6e-06     0.002     237     298 ..     137     195 ..     129     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.1e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                  ++ + G+NgsGKS+L++ + +l
  gi|91773900|ref|YP_566592.1| 30 FTTILGDNGSGKSTLIRHMNGL 51
                                  799*************988777 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.6e-06
                        AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   lS G+++  a++  l+ a+    +l++DE+ + L+    + +++++++l+++g  v+ +TH 
  gi|91773900|ref|YP_566592.1| 137 LSGGQLQKTAIAGVLAMAP---EILIFDEVTSMLDSDSRSQIIDIVRQLNKRGKTVVYVTHH 195
                                   5999999988888888888...9**************************************6 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1     5e-08   3.9e-05      16      49 ..      22      55 ..      16      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5e-08
                        AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49
                                  +i+i+ kg +t + G++GsGKSTl+  ++ lL p+
  gi|91773900|ref|YP_566592.1| 22 DIRIE-KGsFTTILGDNGSGKSTLIRHMNGLLKPS 55
                                  46676.4559***************8888888775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   8.2e-07   0.00064       4     117 ..      27     183 ..      23     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.2e-07
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelka........... 70 
                                   + +++++ G  G+GK+tl+r +   l+       ++++vv    ++ +sst+  ++++ +   ++++++            
  gi|91773900|ref|YP_566592.1|  27 KGSFTTILGDNGSGKSTLIRHMNGLLK-------PSVGVVsvcGMDTASSTDIWEIRQTVGMVFQDPHSQavgatveedva 100
                                   7899*********************95.......47777755577777777777788888888888888888888888888 PP

                        AAA_22  71 ..................................erlsseellealeqalrarav.......ielliiDEaqh.lr..see 107
                                                                       ls  +l         ++a        +e+li DE+   l+  s  
  gi|91773900|ref|YP_566592.1| 101 fgpenlalendeirirvtnaianvgleglegyllMYLSGGQLQ--------KTAIagvlamaPEILIFDEVTSmLDsdSRS 173
                                   8888888888888888888887766644433333223333333........222244445555788888888855455466 PP

                        AAA_22 108 aleeLrslln 117
                                   ++ ++++ ln
  gi|91773900|ref|YP_566592.1| 174 QIIDIVRQLN 183
                                   6666666666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.3e-07   0.00065      14      50 ..      18      55 ..      16     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.3e-07
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                  l++++i +++  +t++ G N+sGKS++++ ++ +l+ +
  gi|91773900|ref|YP_566592.1| 18 LEEIDIRIEKGsFTTILGDNGSGKSTLIRHMNGLLKPS 55
                                  677788888879*****************999999876 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   1.5e-06    0.0012      87     150 ..      15      76 ..       5      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                                   HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEET CS
                   RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellela 150
                                   ++ lee+  ++++ ++++++G  G GKStLi ++++ l+ ++g vs     G  T  ++ + e+ 
  gi|91773900|ref|YP_566592.1|  15 NKVLEEIDIRIEKgSFTTILGDNGSGKSTLIRHMNGLLKPSVGVVSV---CGMDTASSTDIWEIR 76 
                                   467888888888889***************************99997...588888777777766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.5e-06    0.0011      14      39 ..      20      48 ..       2      52 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                        AAA_23 14 eidF...skgltlItGpNGaGKTTildAi 39
                                  eid    +  +t I G+NG+GK+T+++ +
  gi|91773900|ref|YP_566592.1| 20 EIDIrieKGSFTTILGDNGSGKSTLIRHM 48
                                  455555444699*************9865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.8e-06    0.0045      24     152 ..      28     204 ..      16     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.8e-06
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                   ++ + + G+ G+GKs+l+r+    l+ + + +++    +  s++    + q+     ++++ +++a  a +e++ ++ +e+
  gi|91773900|ref|YP_566592.1|  28 GSFTTILGDNGSGKSTLIRHMNGLLKPS-VGVVSVCGMDTASSTDIWEIRQTV-G-MVFQDPHSQAVGATVEEDVAFGPEN 105
                                   367889****************877777.555555555543444443333333.3.3444444444444444444444444 PP

                        AAA_16 105 la...................................................avpelagaeasrllellkrllallsrde 134
                                   la                                                   + +e+++ + s+ + ++ +++++l +++
  gi|91773900|ref|YP_566592.1| 106 LAlendeirirvtnaianvgleglegyllmylsggqlqktaiagvlamapeilIFDEVTSMLDSDSRSQIIDIVRQLNKRG 186
                                   446666666666666888888888888888888888888888877777777777777777777888888888887777778 PP

                        AAA_16 135 rplvlvlDdlqwadeasl 152
                                   +++v v  +++ a +a++
  gi|91773900|ref|YP_566592.1| 187 KTVVYVTHHMEEALFADR 204
                                   888888777777766665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0015       1.2      29      50 ..      24      45 ..      17      49 .. 0.88
   2 ?   -2.9   0.0       5.3   4.2e+03     142     162 ..      78      98 ..      72     104 .. 0.74
   3 ?    5.5   0.0     0.015        11     137     189 ..     150     196 ..     105     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                        AAA_25 29 llpagelallaGapgtGKttla 50
                                   + +g+++ + G+ g+GK+tl 
  gi|91773900|ref|YP_566592.1| 24 RIEKGSFTTILGDNGSGKSTLI 45
                                  5789****************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.3
                        AAA_25 142 gvrlvviDplsralggdensn 162
                                    v++v  Dp s+a+g+  +++
  gi|91773900|ref|YP_566592.1|  78 TVGMVFQDPHSQAVGATVEED 98 
                                   489999999999999965544 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.015
                        AAA_25 137 ieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhHv 189
                                   + +++ ++ +++D ++++l+ d+      +++++ ++++ +r +  v ++hH 
  gi|91773900|ref|YP_566592.1| 150 VLAMA-PEILIFDEVTSMLDSDSR-----SQIIDIVRQLNKRGKTVVYVTHHM 196
                                   34434.899999999999999888.....789999999998999999999996 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.079        62      38      55 ..      31      48 ..      16      57 .. 0.86
   2 !   10.5   0.0   0.00037      0.29     107     152 ..     142     185 ..     136     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.079
                          TniB 38 lllvGdsnnGKtmivekF 55
                                    ++Gd   GK++++++ 
  gi|91773900|ref|YP_566592.1| 31 TTILGDNGSGKSTLIRHM 48
                                  5799***********986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00037
                          TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgne 152
                                   l++ +++   ++ +++Li+DE+ ++l   ++++ +++ ++++L+ +
  gi|91773900|ref|YP_566592.1| 142 LQKTAIAGVLAMAPEILIFDEVTSML--DSDSRSQIIDIVRQLNKR 185
                                   56666777778999************..667788899999999765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   6.6e-05     0.051      18     120 ..      28     190 ..      21     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-05
                        AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g......................grviglAptgkaAkvLaeelgieastiak 75 
                                     ++++ G  G+GK+t++++++ +++ + g                      g v+   +++++ ++++e++ +       
  gi|91773900|ref|YP_566592.1|  28 GSFTTILGDNGSGKSTLIRHMNGLLKPSvGvvsvcgmdtasstdiweirqtvGMVFQDPHSQAVGATVEEDVAFG------ 102
                                   4588999*******************9966555555444444444444322222222222222223333444443...... PP

                        AAA_30  76 llkrlk.............................................grarlepgtllivDEa.gmvdtkqlaallk 110
                                                                                      g +   + ++li DE+ +m+d+++  ++++
  gi|91773900|ref|YP_566592.1| 103 -----PenlalendeirirvtnaianvgleglegyllmylsggqlqktaiaG-VLAMAPEILIFDEVtSMLDSDSRSQIID 177
                                   .....03444444444577778888888889999999999999999998753.3444559999999537887777666666 PP

                        AAA_30 111 aaek...agakvi 120
                                   ++++   +g +v+
  gi|91773900|ref|YP_566592.1| 178 IVRQlnkRGKTVV 190
                                   6655211455555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0029       2.2       4      36 ..      33      67 ..      31      78 .. 0.83
   2 ?    5.5   0.0     0.019        15      94     141 ..     153     202 ..     131     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                                  EE--TTSSHHHHHHHHHHHH.....GGGEEEEEEE CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGfyte 36
                                  i G  G+GK+Tl++ +  llk s   v+v+G+ t 
  gi|91773900|ref|YP_566592.1| 33 ILGDNGSGKSTLIRHMNGLLKPSvgVVSVCGMDTA 67
                                  6699****************977534678887765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                                   HHH-EEEE---STT.GGG-.HHHHHHHHHHHTTTSEEEEE--SS--SHHH CS
                      NTPase_1  94 seadviviDEiGkm.Elks.kkfkeaveevLksekpvlavihrrkdlalv 141
                                     +++++ DE+ +m    s  ++++ v+++ k++k v+ v h+ ++  + 
  gi|91773900|ref|YP_566592.1| 153 MAPEILIFDEVTSMlDSDSrSQIIDIVRQLNKRGKTVVYVTHHMEEALFA 202
                                   467899*****999433441467778888888*********998655555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00049      0.38       4      90 ..      34     183 ..      31     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00049
                                   ESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS............................................. CS
                           AAA   4 yGppGtGKTllakavakelg..vefleisgsellsk............................................. 37 
                                    G  G GK++l++ +   l+  v ++++ g++  s+                                             
  gi|91773900|ref|YP_566592.1|  34 LGDNGSGKSTLIRHMNGLLKpsVGVVSVCGMDTASStdiweirqtvgmvfqdphsqavgatveedvafgpenlalendeir 114
                                   688899999999998888864467788888888866788888888888888888888888888888888888888888888 PP

                                   ....................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                           AAA  38 ....................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLl 90 
                                                       +   + +  +  ++ + ++a p il++DE+ ++  s+   ++++  ++v qL 
  gi|91773900|ref|YP_566592.1| 115 irvtnaianvgleglegyllMYLSGGQLQKTAIAGVLAMA-PEILIFDEVTSMLDSD---SRSQIIDIVRQLN 183
                                   8888888888888888888533444444444444455555.9***********9999...5556666666664 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0032       2.5      11      60 ..      25      73 ..      14     122 .. 0.84
   2 ?    4.1   0.0     0.039        31      13      80 ..     141     213 ..     130     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                                  EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevl 60
                                  i +G  t i+g++g Gk+++++++    + + + ++  +G  + + ++++
  gi|91773900|ref|YP_566592.1| 25 IEKGSFTTILGDNGSGKSTLIRHMNGLLKPS-VGVVSVCGMDTASSTDIW 73
                                  779999***************8888776555.888888988777666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                                   TT-EEEEEESTTSSHHHHH.HHHHHHSSTS...S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  13 qGqrtlipgafgvGktvis.qslskqsnsd...d.aiiyvgiGergnevaevleefpegtimkrtvlvantsn 80 
                                   q q+t+i g   +    ++ ++++   +sd   + + i+    +rg++v  v ++++e+   +r++l+ n s 
  gi|91773900|ref|YP_566592.1| 141 QLQKTAIAGVLAMAPEILIfDEVTSMLDSDsrsQiIDIVRQLNKRGKTVVYVTHHMEEALFADRVILLENGSI 213
                                   557777777777666665555555554444443457789999************************9998775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0015       1.2       6      24 ..      32      54 ..      29      86 .. 0.81
   2 ?    2.3   0.0      0.16   1.2e+02     109     134 ..     173     198 ..     169     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                        AAA_24  6 liyGpsgiGKTtlakel....gp 24
                                   i G++g+GK+tl++++    +p
  gi|91773900|ref|YP_566592.1| 32 TILGDNGSGKSTLIRHMngllKP 54
                                  699*************9666544 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.16
                        AAA_24 109 eefrrllkklqelrknvifiahektr 134
                                    ++++++++l++ +k+v+ + h  ++
  gi|91773900|ref|YP_566592.1| 173 SQIIDIVRQLNKRGKTVVYVTHHMEE 198
                                   56788999999999977766665554 PP

>> Herpes_UL21  Herpesvirus UL21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013       0.1      46     104 ..     156     216 ..     133     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                   -EEEEEEEE--SSTT--HHHHHHHHHHHHHT-----..------EEHHHHHTTSTT.-SSG CS
                   Herpes_UL21  46 eiakfGlvvrGvgpddrsvaayvrseLrrrGlkwav..ssdedevflDsvalLaadsvase 104
                                   ei  f  v      d+rs    + + L++rG++ ++     e+ +f D+v lL+++s+ s+
  gi|91773900|ref|YP_566592.1| 156 EILIFDEVTSMLDSDSRSQIIDIVRQLNKRGKTVVYvtHHMEEALFADRVILLENGSIESD 216
                                   55556666666667888877777889******987611556999************99887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00056      0.44       4      34 ..      33      64 ..      31      93 .. 0.73
   2 ?   -0.9   0.0       1.9   1.5e+03      66      77 ..     155     166 ..     139     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                                  EE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                         AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltr 34
                                  ++G+ G+gKs+l++++  +l  +  ++  +  
  gi|91773900|ref|YP_566592.1| 33 ILGDNGSGKSTLIRHMNGLLkPSVGVVSVCGM 64
                                  68******************533333334444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                                   -SEEEEESGGG- CS
                         AAA_5  66 geilvlDEvera 77 
                                   +eil++DEv+ +
  gi|91773900|ref|YP_566592.1| 155 PEILIFDEVTSM 166
                                   678888888754 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00032      0.25       1      38 [.      33      70 ..      33      82 .. 0.87
   2 ?   -3.5   0.0       9.2   7.1e+03     112     127 ..     176     191 ..     168     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaee 38
                                  ++G  GsGK+t+++ ++ +l+ +   v v  +D+A+++
  gi|91773900|ref|YP_566592.1| 33 ILGDNGSGKSTLIRHMNGLLKPSVGVVSVCGMDTASST 70
                                  68999***************999899999999999875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.2
                    ATP_bind_1 112 akiveeLesefalvvv 127
                                     iv++L++++++vv 
  gi|91773900|ref|YP_566592.1| 176 IDIVRQLNKRGKTVVY 191
                                   5688889888887764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0047       3.7       3      22 ..      33      52 ..      32     101 .. 0.68
   2 ?    2.4   0.0      0.27   2.1e+02      50      92 ..     165     205 ..     152     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0047
                        AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                  + G  G+GK+tl ++ + +l
  gi|91773900|ref|YP_566592.1| 33 ILGDNGSGKSTLIRHMNGLL 52
                                  7899**********986665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                        AAA_18  50 krldedkldklldaleenssaleegknlvidghlaeleseaak 92 
                                     ld d + +++d++++ ++  +   ++++  h++e ++++++
  gi|91773900|ref|YP_566592.1| 165 SMLDSDSRSQIIDIVRQLNK--RGKTVVYVTHHMEEALFADRV 205
                                   56788899999999999987..555555999999999888766 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0064         5      14      37 ..      23      46 ..      12     105 .. 0.86
   2 ?    3.4   0.1     0.054        42     121     165 ..     156     196 ..     141     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0064
                        ATPase 14 gGipegrvvlitGepGtGKtifal 37
                                    i +g+ + i G+ G+GK+++  
  gi|91773900|ref|YP_566592.1| 23 IRIEKGSFTTILGDNGSGKSTLIR 46
                                  57899***************9865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.054
                        ATPase 121 krvviDsitglayeekeavaReilrqlvrvlkklgvTailvseks 165
                                   + ++ D +t++     ++  R+++  +vr+l+k+g T + v+   
  gi|91773900|ref|YP_566592.1| 156 EILIFDEVTSM----LDSDSRSQIIDIVRQLNKRGKTVVYVTHHM 196
                                   66677888877....445579999999999999999999888754 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.3   4.9e+03      18      29 ..      32      43 ..      19      45 .. 0.73
   2 ?   10.5   0.0   0.00049      0.38     123     152 ..     156     185 ..     130     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.3
                                  EEEESTTSSHHH CS
                                  xxxxxxxxxxxx RF
                          DEAD 18 lvaaeTGsGKTl 29
                                   + ++ GsGK++
  gi|91773900|ref|YP_566592.1| 32 TILGDNGSGKST 43
                                  56678899*986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00049
                                   EEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 123 rflVlDEadrlldqgfsdfinrilnqlpqi 152
                                   ++l++DE+  +ld++ + +i  i++ql++ 
  gi|91773900|ref|YP_566592.1| 156 EILIFDEVTSMLDSDSRSQIIDIVRQLNKR 185
                                   78*************************543 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.33       4      21 ..      32      49 ..      29      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                                  EEEC-TTTCHHHHHHHHH CS
                         NACHT  4 ilqGeaGsGKTtLlqkla 21
                                   + G++GsGK+tL++++ 
  gi|91773900|ref|YP_566592.1| 32 TILGDNGSGKSTLIRHMN 49
                                  689***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1641.90
//
Query:       gi|91773901|ref|YP_566593.1|  [L=268]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-27   95.1   0.0    8.2e-27   94.4   0.0    1.3  1  ABC_tran         ABC transporter
    1.6e-09   38.0   3.6    2.3e-06   27.6   0.2    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0004   20.7   0.0     0.0015   18.8   0.0    1.8  1  AAA_22           AAA domain
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.022   14.5   0.1    1.5  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.011   15.2   0.2       0.22   10.9   0.2    2.2  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.014   15.0   0.1      0.022   14.4   0.1    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.014   15.9   0.2      0.069   13.7   0.1    2.0  2  AAA_18           AAA domain
      0.017   14.1   0.4      0.029   13.3   0.4    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.025   14.5   0.1      0.045   13.7   0.1    1.5  1  NTPase_1         NTPase
      0.025   14.3   0.3       0.05   13.4   0.3    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.041   14.0   0.1      0.074   13.1   0.1    1.4  1  tRNA_lig_kinase  tRNA ligase kinase domain
      0.059   12.7   0.0      0.093   12.1   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.074   12.8   0.0      0.092   12.5   0.0    1.3  1  AAA_30           AAA domain
        0.1   12.5   0.8       0.38   10.6   0.2    2.0  2  MobB             Molybdopterin guanine dinucleotide synthesis
       0.14   11.0   0.1        0.2   10.5   0.1    1.2  1  Spore_IV_A       Stage IV sporulation protein A (spore_IV_A)
       0.15   12.5   0.1       0.21   12.1   0.1    1.2  1  AAA_23           AAA domain
       0.15   11.2   0.8       0.25   10.5   0.4    1.5  2  NB-ARC           NB-ARC domain
       0.23   11.4   0.3       0.43   10.6   0.3    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.26   11.2   0.8       0.45   10.4   0.5    1.5  2  RsgA_GTPase      RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   8.7e-30   8.2e-27       1     137 []      18     162 ..      18     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 8.7e-30
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren 79 
                                   lk+v++++ +ge v+i+G+ G+GK+tL+k l gll p +G++++dg  +++   +++ +++gvl+q+  +qlf ++ v e 
  gi|91773901|ref|YP_566593.1|  18 LKDVTFSVGKGEFVGIIGKVGCGKTTLIKHLNGLLVPLSGNVTVDGLASSK---KEVCRKVGVLFQQpsKQLFCKT-VFED 94 
                                   79*******************************************999988...899999*******877888877.8888 PP

                                   .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                e +  +++a++k+gl+    ++++ssp sLSgG+ + vala +l + p+ l+lDEpt+
  gi|91773901|ref|YP_566593.1|  95 iaygpsnfgmkgdELEHCVHDAIEKVGLSS---DILGSSPFSLSGGEMRLVALAGVLSSSPDYLVLDEPTS 162
                                   9*****999876666666999999999777...9***********************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.4   0.00021       0.2       1      22 [.      30      51 ..      30      71 .. 0.86
   2 !   27.6   0.2   2.4e-09   2.3e-06     233     298 ..     130     192 ..     107     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                        AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                  + ++iG+ g+GK++L++ l +l
  gi|91773901|ref|YP_566593.1| 30 FVGIIGKVGCGKTTLIKHLNGL 51
                                  678**************99888 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.4e-09
                        AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   ++++lS G  rl al+  l + +   + l++DEp +gL     ++l++ l++l++ng+ v+l++H 
  gi|91773901|ref|YP_566593.1| 130 SPFSLSGGEMRLVALAGVLSSSP---DYLVLDEPTSGLSTFYKEHLFKTLELLRQNGVGVVLVSHH 192
                                   5789*****************99...77*************************************7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.6e-06    0.0015       7     128 ..      30     189 ..      26     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka................ 70 
                                   ++ ++G +G+GKTtl++ l   l          p    vt+ ++  s k+++r++   ++++ k                 
  gi|91773901|ref|YP_566593.1|  30 FVGIIGKVGCGKTTLIKHLNGLL---------VPLSGNVTVDGLAsSKKEVCRKVGVLFQQPSKQlfcktvfediaygpsn 101
                                   5669******************9.........4444456666665568888888888888877777787777777777778 PP

                        AAA_22  71 ...erlsseell.ealeqalrarav.........................ielliiDEaqh.lrs...eealeeLrsllnl 118
                                      +++++e+++ +a+e+   + +                          +  l++DE    l s   +e+l +  +ll  
  gi|91773901|ref|YP_566593.1| 102 fgmKGDELEHCVhDAIEKVGLSSDIlgsspfslsggemrlvalagvlsssPDYLVLDEPTSgL-StfyKEHLFKTLELLR- 180
                                   999777777777666666666555555555555555555555555555555577777777766.4444444333345566. PP

                        AAA_22 119 srkgvqliLv 128
                                    + gv ++Lv
  gi|91773901|ref|YP_566593.1| 181 -QNGVGVVLV 189
                                   .666666665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.3e-05     0.022       6      24 ..      33      51 ..      29      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                     PduV-EutP  6 liGkvgsGKttLtqalkge 24
                                  +iGkvg+GKttL ++l+g 
  gi|91773901|ref|YP_566593.1| 33 IIGKVGCGKTTLIKHLNGL 51
                                  79**************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 ?   10.9   0.2   0.00023      0.22      25     208 ..      29     203 ..      18     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                   SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                   +f  i+G+ G+GK+ l+  +  +L   s     + +++ l +    +++    +v ++f++++k+l      +++  + + 
  gi|91773901|ref|YP_566593.1|  29 EFVGIIGKVGCGKTTLIKHLNGLLVPLSG----NVTVDGLAS----SKKEVCRKVGVLFQQPSKQLF-----CKTVFEDIA 96 
                                   57778888888888887777555553222....223333333....233333467777777777733.....333444455 PP

                                   TSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 106 kgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                    g s++ ++g e + + v++ +e++g+s++       +LSgGe  Lvala +++    +p    +lDe  + L   + + +
  gi|91773901|ref|YP_566593.1|  97 YGPSNFGMKGDELE-HCVHDAIEKVGLSSDilgsspfSLSGGEMRLVALAGVLSS---SPD-YLVLDEPTSGLSTFYKEHL 172
                                   56677888887765.56888888888888888888889***********988653...343.3467888888888888888 PP

                                   HHHHHHHCTT.SEEEEE-SS.HHHCCC-SCE CS
                                   xxxxxxxxxx.xxxxxxxxx.xxxxxxxxxx RF
                         SMC_N 180 aellkekskn.aQfivislr.eemlekadkl 208
                                    + l+  ++n + ++ +s++ e++l  adk+
  gi|91773901|ref|YP_566593.1| 173 FKTLELLRQNgVGVVLVSHHlEDVLGVADKI 203
                                   7777766665444444444315556666665 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 ?   14.4   0.1   2.4e-05     0.022       6      34 ..      20      48 ..      17      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                                  HHHS-EBTT-EEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqsl 34
                                  D+ f++++G+ ++i+g+ g+Gkt+++++l
  gi|91773901|ref|YP_566593.1| 20 DVTFSVGKGEFVGIIGKVGCGKTTLIKHL 48
                                  889**********************9876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   7.3e-05     0.069       1      33 [.      31      60 ..      31      87 .. 0.76
   2 ?   -0.5   0.0       1.8   1.7e+03      63     105 ..     178     219 ..     159     226 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvak 33
                                  +++ G+ G+GKttl k+L+ +l   v l+ +++
  gi|91773901|ref|YP_566593.1| 31 VGIIGKVGCGKTTLIKHLNGLL---VPLSGNVT 60
                                  689***************8775...44444444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                        AAA_18  63 aleenssaleegknlvidghlaeleseaakdikk.....vvLtaspee 105
                                   +l++n       ++++++ hl++ +  a+k+ ++     vv + spee
  gi|91773901|ref|YP_566593.1| 178 LLRQNG-----VGVVLVSHHLEDVLGVADKI-VYlnegaVVFEGSPEE 219
                                   444432.....35556666666666555554.4346666666666665 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 ?   13.3   0.4   3.1e-05     0.029      17      55 ..      16      54 ..       8      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                                  HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHC CS
                          MeaB 17 ellerllakaGraqvvGltGvPGaGkstlvealglelrr 55
                                  ++l+ ++ + G+ + vG+ G  G Gk tl+++l   l+ 
  gi|91773901|ref|YP_566593.1| 16 TILKDVTFSVGKGEFVGIIGKVGCGKTTLIKHLNGLLVP 54
                                  68999999************************9887765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.8e-05     0.045       3      63 ..      32      89 ..      30     128 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                                  EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-.------EEEEEET.T--EEEEEET CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr.eggrrigFkivdlasgeegiLarv 63
                                   i G+ G GKtTl+k +  ll    v+++G +t +   + ++ ++ k+  l ++  ++L  +
  gi|91773901|ref|YP_566593.1| 32 GIIGKVGCGKTTLIKHLNGLL----VPLSGNVTVDGLaSSKKEVCRKVGVLFQQPSKQLFCK 89
                                  688****************99....6666655555443555666666655555555555444 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 ?   13.4   0.3   5.3e-05      0.05      16      50 ..      22      56 ..      16      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  t+++   +++ ++G+ G GK+Tl+  ++ lLvp +
  gi|91773901|ref|YP_566593.1| 22 TFSVGKGEFVGIIGKVGCGKTTLIKHLNGLLVPLS 56
                                  55665444888****************99999965 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.8e-05     0.074       5      55 ..      34      84 ..      30      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.8e-05
                                  E--TTSSHHHHHHHHHHH-TT.SEEEEGGGS-TT-SS-HHHHHHHTTSSTT- CS
               tRNA_lig_kinase  5 iatiGCGkttvaltlenlfge.WghvqnDnitgkdkkklvkealellkkdes 55
                                  i  +GCGktt  + l+ l     g v  D +++ +kk++++++  l+++  +
  gi|91773901|ref|YP_566593.1| 34 IGKVGCGKTTLIKHLNGLLVPlSGNVTVDGLAS-SKKEVCRKVGVLFQQPSK 84
                                  6789************98766599999999998.666777776666655544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.9e-05     0.093      27      53 ..      33      59 ..      19     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.9e-05
                  Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseee 53
                                  ++G  G+GKt l+k l++ll pls + 
  gi|91773901|ref|YP_566593.1| 33 IIGKVGCGKTTLIKHLNGLLVPLSGNV 59
                                  79********************98764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.8e-05     0.092      19      58 ..      29      70 ..      21     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.8e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g.grviglAptgka 58
                                   ++ + G  G GKtt++k+l+ ++    g  +v glA+++k 
  gi|91773901|ref|YP_566593.1| 29 EFVGIIGKVGCGKTTLIKHLNGLLVPLsGnVTVDGLASSKKE 70
                                  478899**************9998877545888899999875 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2    0.0004      0.38       2      23 ..      31      52 ..      30      61 .. 0.85
   2 ?   -0.6   0.0       1.2   1.2e+03      18      39 ..     174     195 ..     164     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                          MobB  2 lgivgksgsGKTtLleklipel 23
                                  +gi+gk g+GKTtL+++l   l
  gi|91773901|ref|YP_566593.1| 31 VGIIGKVGCGKTTLIKHLNGLL 52
                                  79**************996655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                          MobB  18 klipelkarglrvgtiKhahhg 39 
                                   k ++ l+++g+ v ++ h+ ++
  gi|91773901|ref|YP_566593.1| 174 KTLELLRQNGVGVVLVSHHLED 195
                                   5667788888888888887655 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 ?   10.5   0.1   0.00021       0.2       4      42 ..      15      53 ..      12      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                    Spore_IV_A  4 ldiykdiaertngdiyigvvGpvRtGKStfikrfmellv 42
                                  l i+kd++   +   ++g++G v +GK t+ik++  llv
  gi|91773901|ref|YP_566593.1| 15 LTILKDVTFSVGKGEFVGIIGKVGCGKTTLIKHLNGLLV 53
                                  6789999988888889****************9866655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00022      0.21      11      42 ..      19      51 ..      13      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                        AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAikla 42
                                  +d+++  +k  ++ I+G+ G+GKTT++  +   
  gi|91773901|ref|YP_566593.1| 19 KDVTFSVGKgEFVGIIGKVGCGKTTLIKHLNGL 51
                                  56666676624778*************887655 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   0.4   0.00026      0.25      21      40 ..      29      48 ..      16      55 .. 0.88
   2 ?   -3.9   0.0       6.4     6e+03     154     174 ..      73      93 ..      63      97 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                  EEEEEEESTTSSHHHHHHHH CS
                        NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                   +v++ G+ G+GKttl+k+ 
  gi|91773901|ref|YP_566593.1| 29 EFVGIIGKVGCGKTTLIKHL 48
                                  489*************9875 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.4
                                   EEESS--HHHHHHHHHHCCTS CS
                        NB-ARC 154 ievelLekdeawellenkvfe 174
                                    +v +L ++ + +l+++ vfe
  gi|91773901|ref|YP_566593.1|  73 RKVGVLFQQPSKQLFCKTVFE 93 
                                   456666677777788888776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00045      0.43      19      39 ..      28      48 ..      12      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00045
                                  TEEEEEEESTTSSHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                  g+++ + G++G+GKTtl+++l
  gi|91773901|ref|YP_566593.1| 28 GEFVGIIGKVGCGKTTLIKHL 48
                                  6779999************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00048      0.45      98     121 ..      27      50 ..       9      66 .. 0.81
   2 ?   -3.6   0.0       9.9   9.3e+03      68      85 ..     175     192 ..     168     213 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                                   TTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallp 121
                                   k++++ ++G+ G GK+tLi++l++
  gi|91773901|ref|YP_566593.1|  27 KGEFVGIIGKVGCGKTTLIKHLNG 50 
                                   4488899**************987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.9
                                   HHHHHHHTTSEEEE--TT CS
                   RsgA_GTPase  68 lkeelealgyevllvsak 85 
                                   + e l++ g+ v+lvs +
  gi|91773901|ref|YP_566593.1| 175 TLELLRQNGVGVVLVSHH 192
                                   445556666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1589.52
//
Query:       gi|91773902|ref|YP_566594.1|  [L=255]
Description: cobalt ABC transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-33  115.1   6.0    4.4e-33  114.7   6.0    1.1  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   6.0   2.5e-37   4.4e-33       2     213 ..      12     224 ..      11     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 2.5e-37
                                   SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE.......EE CS
                          CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlittegef 82 
                                   ks+lhrldprvk + +++l+++++ +++l  l  ++++ll++ l  i  + l+ + +++ l++++ +++l+  ++ teg+ 
  gi|91773902|ref|YP_566594.1|  12 KSFLHRLDPRVKIFSVMCLSILIFRSSALTDL--LVFALLFIGLTIIAGSGLSGIRSVRPLLPIFVFIFLIH-SFFTEGAA 89 
                                   89*****************9999999998888..666777777777777789999999**************.6668**** PP

                                   CTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--H..........HHHHHHHHHHHHHHHH CS
                          CbiQ  83 vfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPl..........elalillLayRfiflL 153
                                   +f+    +s t+eG+l+g l++ R++ l++  +ll+ TT p+ +t+++er+++Pl          e+a++++La+ f++ L
  gi|91773902|ref|YP_566594.1|  90 LFDSQ--FSPTDEGVLKGSLVTARFVLLILYSSLLTSTTRPAVITAGIERILRPLplrwvgvtsfEIATMMSLALYFVPHL 168
                                   *9875..59************************************************************************ PP

                                   HHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.. CS
                          CbiQ 154 leevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtgse 213
                                   l  +++ k++q +R+ ++     + +  +  l+++++  ++++a++v  Ame R+Y+g +
  gi|91773902|ref|YP_566594.1| 169 LWYARQVKDSQLSRGSRY---GHNPIYGTLSLAIPVLKGSMRMADDVVMAMEGRCYQG-N 224
                                   ******************...566699999****************************.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1879.37
//
Query:       gi|91773903|ref|YP_566595.1|  [L=120]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-15   57.2   0.7    1.1e-15   57.2   0.7    1.7  2  HTH_5          Bacterial regulatory protein, arsR family
      1e-08   35.1   0.5      1e-08   35.1   0.5    1.8  2  HTH_20         Helix-turn-helix domain
    8.3e-05   22.4   0.8    0.00017   21.4   0.2    1.8  2  MarR_2         MarR family
    0.00073   19.7   0.1     0.0013   18.8   0.1    1.4  1  HTH_34         Winged helix DNA-binding domain
     0.0046   16.7   0.0     0.0077   16.0   0.0    1.4  1  Arg_repressor  Arginine repressor, DNA binding domain
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.029   14.3   0.1    1.4  1  HTH_1          Bacterial regulatory helix-turn-helix protein,
      0.019   14.8   0.0      0.035   14.0   0.0    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.024   15.2   0.1      0.042   14.4   0.1    1.4  1  HTH_27         Winged helix DNA-binding domain
      0.028   14.5   0.0      0.047   13.7   0.0    1.4  1  Cro            Cro
      0.047   13.5   1.1      0.061   13.1   0.3    1.7  2  HTH_IclR       IclR helix-turn-helix domain
      0.091   12.6   0.1       0.13   12.2   0.1    1.2  1  HxlR           HxlR-like helix-turn-helix
      0.099   12.3   0.0       0.11   12.1   0.0    1.2  1  DUF4423        Domain of unknown function (DUF4423)


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 !   57.2   0.7   7.4e-19   1.1e-15       4      46 ..      45      87 ..      42      88 .. 0.96
   2 ?   -2.1   0.0       2.5   3.8e+03      24      29 ..     107     112 ..      99     115 .. 0.58

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 7.4e-19
                                  HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  Rl I++lL e+ +cvcel ++lg++qs++Sh L+ Lr+++LV+
  gi|91773903|ref|YP_566595.1| 45 RLTIMYLLLEKDMCVCELERALGMTQSAISHNLRTLRQLDLVR 87
                                  9*****************************************6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                                   HHTS-H CS
                         HTH_5  24 elglsq 29 
                                    l+ls+
  gi|91773903|ref|YP_566595.1| 107 LLELSR 112
                                   345555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.5   6.8e-12     1e-08       2      61 .]      35      93 ..      34      93 .. 0.97
   2 ?   -1.7   0.1       2.1   3.2e+03      42      50 ..     101     109 ..      98     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.8e-12
                                  HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                        HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                  +i++AL ++ R+ i+ +L  ++ +++ el ++l+++++ +s++Lr+L++ +Lv+v++ gr
  gi|91773903|ref|YP_566595.1| 35 NIFHALRSEPRLTIMYLL-LEKDMCVCELERALGMTQSAISHNLRTLRQLDLVRVRKDGR 93
                                  6999**************.**************************************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                                   HHHHHHHHH CS
                        HTH_20  42 syHLrvLee 50 
                                   + H+r+L e
  gi|91773903|ref|YP_566595.1| 101 DEHVRALLE 109
                                   679999987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   1.1e-07   0.00017      20      56 ..      45      91 ..      31      93 .. 0.79
   2 ?   -1.9   0.0       2.1   3.2e+03       7      17 ..     103     113 ..     101     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                  S..........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 20 r..........dltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  r          d+ v el+r+lg+++sa+s  l+ L +  Lv+ r++
  gi|91773903|ref|YP_566595.1| 45 RltimylllekDMCVCELERALGMTQSAISHNLRTLRQLDLVRVRKD 91
                                  4566666666668888***************************9985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                   HHHHHHHHHCT CS
                        MarR_2   7 qarvLaaLgrr 17 
                                   + r+L++L r+
  gi|91773903|ref|YP_566595.1| 103 HVRALLELSRS 113
                                   67899999886 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   8.8e-07    0.0013       2      49 ..      45      91 ..      45      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.8e-07
                        HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                  Rl ++  L+ ++ ++  el  al++t++++s +l++L + + + v+k+
  gi|91773903|ref|YP_566595.1| 45 RLTIMY-LLLEKDMCVCELERALGMTQSAISHNLRTLRQLDLVRVRKD 91
                                  677775.5556668899***************************9997 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 !   16.0   0.0   5.2e-06    0.0077      35      67 ..      67     102 ..      47     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.2e-06
                                   ---HHHHH...HHHHHHT-EEEETTSTSEEEE-B-S CS
                 Arg_repressor  35 dvtQatvS...RdLkelglvkvraengeyvYvlpae 67 
                                     tQ+ +S   R L+ l lv+vr+++  +vY++++e
  gi|91773903|ref|YP_566595.1|  67 GMTQSAIShnlRTLRQLDLVRVRKDGRFAVYSVADE 102
                                   5799999977788999*****************998 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.9e-05     0.029      21      39 ..      64      82 ..      64      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                  HHHTS-HHHHHHHHHHHHH CS
                         HTH_1 21 eeLglsqpavsrqikrLEe 39
                                  ++Lg++q+a+s+ +++L++
  gi|91773903|ref|YP_566595.1| 64 RALGMTQSAISHNLRTLRQ 82
                                  68***************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.4e-05     0.035      16      65 ..      50     100 ..      48     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE- CS
                          TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYrav 65 
                                   +Ll ++ + + e+ ++lg  +s +   Lr L + +lV+++k gr  +Y+++
  gi|91773903|ref|YP_566595.1|  50 YLLLEKDMCVCELERALGMTQSAISHNLRTLRQLDLVRVRKdGRFAVYSVA 100
                                   68889999999*****************************94456688776 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 ?   14.4   0.1   2.8e-05     0.042      23      65 ..      61     100 ..      54     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                        HTH_27  23 dlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65 
                                   +l ++l +++s+is +l+ L   +Lv   + ++d+r   +++ 
  gi|91773903|ref|YP_566595.1|  61 ELERALGMTQSAISHNLRTLRQLDLV---RVRKDGRFAVYSVA 100
                                   57789*********************...66677887777765 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.1e-05     0.047      20      47 ..      64      92 ..      61     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                                  HHHTS-HHHHHHHHHCT-EEEE.EEETTS CS
                           Cro 20 kdlgvkqsaIsKAlkakRnIyl.ivdedG 47
                                  ++lg++qsaIs  l+  R++ l  v +dG
  gi|91773903|ref|YP_566595.1| 64 RALGMTQSAISHNLRTLRQLDLvRVRKDG 92
                                  68*****************9751578898 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   4.1e-05     0.061      19      49 ..      57      87 ..      29      90 .. 0.80
   2 ?   -2.4   0.0         3   4.4e+03      27      37 ..     107     117 ..     105     120 .] 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
                                  -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyve 49
                                  + + el r++g++ S+ ++ L+tL +l +v+
  gi|91773903|ref|YP_566595.1| 57 MCVCELERALGMTQSAISHNLRTLRQLDLVR 87
                                  6677999**********************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                                   HHTS-HHHHHH CS
                      HTH_IclR  27 rtglpkStvhR 37 
                                    + l++S v +
  gi|91773903|ref|YP_566595.1| 107 LLELSRSHVMG 117
                                   56788887765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.5e-05      0.13       8      50 ..      46      87 ..      41     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                                  HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEE CS
                          HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglie 50
                                  l i++ ll++ +   el+ral +++q+ ++++Lr L q  l+ 
  gi|91773903|ref|YP_566595.1| 46 LTIMYLLLEKDMCVCELERAL-GMTQSAISHNLRTLRQLDLVR 87
                                  579999***************.89*************998885 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.6e-05      0.11      35      78 ..      55      96 ..      25     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                       DUF4423 35 fkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78
                                  ++  + el+++l+  ++++ +++ l++L +l+l++  +dg++ +
  gi|91773903|ref|YP_566595.1| 55 KDMCVCELERALG--MTQSAISHNLRTLRQLDLVRVRKDGRFAV 96
                                  4456899******..************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 802.67
//
Query:       gi|91773904|ref|YP_566596.1|  [L=378]
Description: hypothetical protein Mbur_1966 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-48  165.2  11.1    2.6e-48  164.7  11.1    1.2  1  ArsP_1         Predicted permease
  ------ inclusion threshold ------
       0.37   10.4   2.0        0.9    9.1   2.0    1.6  1  AIRC           AIR carboxylase
        1.3    8.0  13.0       0.22   10.5   8.8    1.8  2  Acyl_transf_3  Acyltransferase family


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 !  164.7  11.1   4.3e-52   2.6e-48      13     292 ..      22     328 ..      10     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 4.3e-52
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1  13 lleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkGaplgaavaFlva 92 
                                   l ea + L+lgf ++g++ vfv+ eki+++Lg ++ ++ s+l a+l+G+ lp+Csc++vP a +l k+Ga  ga+++Fl++
  gi|91773904|ref|YP_566596.1|  22 LAEAAPYLLLGFGVAGILHVFVPDEKIMQYLGhSAGKFRSVLNASLIGVPLPLCSCGVVPAALSLKKRGATNGATLSFLIS 102
                                   67899**************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.................. RF
                        ArsP_1  93 aPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarev.aeaglek.................. 154
                                    P + +  i++t++ll   ++++r ++++i+a+v+g+    l+  ++++ ++ e+ +  ++ +                  
  gi|91773904|ref|YP_566596.1| 103 TPQTGVDSIAITYALLDPIMTIFRPIATFITALVAGIADDLLRSPRDVSGKDVEKiPTTNILEmaslptpssslssscscn 183
                                   **************************************9999988888877765514444444****************** PP

                                   ......xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1 155 ......ltlkpklealka..faknevkewlelgkyLiiGvaiagviqaflpesvllsllggnsvsssllamligvvlyvcs 227
                                          + + +++++    + +  v+ ++ +   LiiG+++ag+i+  +pe+ + s lgg ++ s lla ++g++ly+c+
  gi|91773904|ref|YP_566596.1| 184 scgpngTEDADTFSGRVIsgIRYAYVELLGDISYWLIIGIILAGIITYMVPEDLVGSHLGG-GLVSMLLALVVGIPLYICA 263
                                   ****9966667777655455888888888*****************************776.57789************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1 228 lgevpfiaalfesglalGsalAfLlagpllslpellillkvlkkklvavllglvvvsvvlaglvi 292
                                   ++  p++a+l+++g++ G a  fLlagp+ +  ++ ++lk+l+k+   v+l+ ++v +v+ g+++
  gi|91773904|ref|YP_566596.1| 264 TASTPLAAVLIAKGMSPGAAFVFLLAGPATNAATITMVLKYLGKRSTGVYLASIAVCAVAGGILL 328
                                   ************************************************************99986 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.0   0.00015       0.9      66     124 ..     240     300 ..     238     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00015
                                   --HHHHHHHHSSS-EEEEEE--..STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHH CS
                          AIRC  66 ahLpgvvaslttlPVigvPvks..kalkgldsllSivqmPsgvpvatvaigkaknAallAa 124
                                   +hL+g + s+    V+g+P+    +a + l ++l    m +g++ + + +g a+nAa +++
  gi|91773904|ref|YP_566596.1| 240 SHLGGGLVSMLLALVVGIPLYIcaTASTPLAAVLIAKGMSPGAAFVFLLAGPATNAATITM 300
                                   69*****************985336788999**************************9876 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.33     2e+03     258     290 ..      24      53 ..      11      56 .. 0.55
   2 ?   10.5   8.8   3.7e-05      0.22     191     312 ..     212     328 ..     196     371 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.33
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 258 aslllvslgimllllllfalpsrsafkllrylg 290
                                    ++++++lg+ +  +l++  p+ +   +++ylg
  gi|91773904|ref|YP_566596.1|  24 EAAPYLLLGFGVAGILHVFVPDEK---IMQYLG 53 
                                   444555555555555555555555...566665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 3.7e-05
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 191 lplpsvla.llfflfGalladaddrdrnlsrglkislllsllllalillalfgqtdggglvasvliqsaslllvslgimll 270
                                   l++ s+++ +  +l+G++ ++  +    + +g  ++ +l++l++ ++l  +++ +       + l+    +  +s g++++
  gi|91773904|ref|YP_566596.1| 212 LGDISYWLiIGIILAGIITYMVPEDLVGSHLGGGLVSMLLALVVGIPLYICATAS-------TPLAAVLIAKGMSPGAAFV 285
                                   4444555536666777777777766666666666666666666666666666666.......6777788888899999999 PP

                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 271 llllfalpsrsafk.llrylgkiSygiYliHlpllmllqkllr 312
                                   +ll+   ++   +  +l+ylgk S g+Yl+ + +  + + +l 
  gi|91773904|ref|YP_566596.1| 286 FLLAGPATNAATITmVLKYLGKRSTGVYLASIAVCAVAGGILL 328
                                   999999999988889***************9555554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2642.67
//
Query:       gi|91773905|ref|YP_566597.1|  [L=639]
Description: hydantoinase/oxoprolinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-33  116.5   3.6      2e-32  112.6   1.8    2.9  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    3.3e-33  114.9   5.4      3e-29  102.0   1.1    3.2  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    1.2e-05   24.1   0.6      0.021   13.5   0.1    2.2  2  MutL            MutL protein
     0.0019   17.8   1.3      0.038   13.5   0.0    2.5  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
       0.11   13.0   1.2       0.81   10.1   0.2    2.5  2  FtsA            Cell division protein FtsA
       0.16   11.4   0.5       0.37   10.2   0.5    1.5  1  Ppx-GppA        Ppx/GppA phosphatase family


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 ?    0.5   0.0     0.095   2.8e+02      82     100 ..       5      23 ..       2      40 .. 0.79
   2 !  112.6   1.8   6.8e-36     2e-32       1     286 [.     179     543 ..     179     548 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.095
                Hydantoinase_A  82 ItfDmGGTstDvslikdge 100
                                   +++D GGT tD+ l++d  
  gi|91773905|ref|YP_566597.1|   5 LGIDAGGTYTDAVLLRDSD 23 
                                   578*********9999754 PP

  == domain 2  score: 112.6 bits;  conditional E-value: 6.8e-36
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   r++ta +nA l p+ ++++  ve+ +  +g+ a+++++++dG+++ ++ a +kp+e i SGPa+++vga+    l+g++ +
  gi|91773905|ref|YP_566597.1| 179 RAVTAFLNAQLIPVTEKFMTTVEEYISSKGIDAKVFMLKCDGSVIGIQSALEKPIESIFSGPAGSLVGASF---LTGNDTC 256
                                   899*******************************************************************9...******* PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpe....sagadpgp.... 153
                                    ++D+GGTstD+s+ik+g +e+s +  + +g k+r++a++++t ++gG+s ++v++ +++++gp+     ++a+  +    
  gi|91773905|ref|YP_566597.1| 257 AVIDVGGTSTDISVIKNGVPEMSESGAVvGGWKTRVKAIKMETSAMGGDSDVWVKD-NSVNIGPRrvipLCRAADLYpgfl 336
                                   **********************99887769**********************8888.8999**973333233333335669 PP

                Hydantoinase_A 154 ...........................................................................acyrkG 159
                                                                                                              +     
  gi|91773905|ref|YP_566597.1| 337 dqlrtnpmpskgllginfqptkfyirtgydpidispqemdvfryisdeptsirelhsrmkkypsskhldsllqkrLIQTI- 416
                                   99999999999999999999999999999999999999999999999999999999999999999999988664322222. PP

                Hydantoinase_A 160 gteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlk.veevAegilsvavenm.anavrkl..sver 236
                                       t TDa  vLG  ++        g  +l + l rr + e a  ++++ ++++A +++s   e + + ++rk+  +++ 
  gi|91773905|ref|YP_566597.1| 417 --GFTPTDALHVLGDYTEHTVEASEIGSKYLGS-LCRRDAVEFASFVKQEfAKNMASNLMSFFLEGIpKTEIRKIfdIESP 494
                                   ..4699999999999999877755556655554.55666666777776666889999999988887734466666443344 PP

                Hydantoinase_A 237 gldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAd 286
                                    + + +  +v +GG+     + l   l+  ++ivp+y+ v +a G+++A+
  gi|91773905|ref|YP_566597.1| 495 AKFKVDIPVVLIGGPVIAYLEDLQSILDA-EIIVPEYSNVGNATGALAAK 543
                                   44445677788888888888888777775.58888888999999998886 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 !  102.0   1.1     1e-32     3e-29       2     176 ..       5     158 ..       4     160 .. 0.91
   2 !   10.5   0.2   0.00012      0.36       3      31 ..     258     300 ..     257     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 1e-32
                    Hydant_A_N   2 igIDvGGTfTDavaldekeee.vavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaL 81 
                                   +gID+GGT+TDav+l++ +e+ v + K+l+t  ++  gir+a++   e+     ++i+vv ++TT+ tN +le++g +v+L
  gi|91773905|ref|YP_566597.1|   5 LGIDAGGTYTDAVLLRDSDEViVSSNKALTTYPDPLGGIRNAIDGIDEKYL---NDIKVVSVSTTLSTNSILEGTGFPVGL 82 
                                   79*************99885515678*******************988755...69************************* PP

                    Hydant_A_N  82 ittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhSyl 162
                                   i    ++                     ++++e  v+v+++++++g    +lde++vr+ ++++k++ v ++av++++S +
  gi|91773905|ref|YP_566597.1|  83 ILVGNYELNQ------------------ELPTEHYVQVEGGHDYNGIPTASLDEDAVRQFAESVKDR-VAAFAVSSYFSIR 144
                                   *999887543..................45677889*****************************99.************* PP

                    Hydant_A_N 163 npehElrvaeiare 176
                                   n ehElrv+ei++e
  gi|91773905|ref|YP_566597.1| 145 NHEHELRVKEIIKE 158
                                   ************98 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00012
                    Hydant_A_N   3 gIDvGGTfTDavaldeke..............eevavlKllst 31 
                                    IDvGGT TD+ +++++               ++v+++K+ ++
  gi|91773905|ref|YP_566597.1| 258 VIDVGGTSTDISVIKNGVpemsesgavvggwkTRVKAIKMETS 300
                                   69************95547788887777777766777777776 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   6.9e-06     0.021       2      64 ..       5      64 ..       4      76 .. 0.80
   2 !    9.0   0.1   0.00015      0.46     222     273 ..     234     280 ..     211     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-06
                          MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgkt.evdevl 64
                                  l iD G t+T ++l+++++  e ++ + +a+Tt    d l G+++a++ + ek  +  +v  v 
  gi|91773905|ref|YP_566597.1|  5 LGIDAGGTYTDAVLLRDSD--EVIVSSNKALTTYP--DPLGGIRNAIDGIDEKYLNDiKVVSVS 64
                                  569**************66..*************5..99***********99965334333333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00015
                          MutL 222 aeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                   + i   Pa  l ++++l    ++    + v+DvGG++Td+  + +g pe+++
  gi|91773905|ref|YP_566597.1| 234 ESIFSGPAGSLVGASFLTG--ND---TCAVIDVGGTSTDISVIKNGVPEMSE 280
                                   5677788888999999988..33...689***********999999888776 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   1.3e-05     0.038       1      24 [.       5      28 ..       5     147 .. 0.90
   2 ?    2.6   0.4     0.027        80       3      30 ..     259     293 ..     244     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                  EEEEE-SSEEEEEEEETTTEEEEE CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgr 24
                                  +GiD G+T t avl++++ ev+  
  gi|91773905|ref|YP_566597.1|  5 LGIDAGGTYTDAVLLRDSDEVIVS 28
                                  8*******************8765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.027
                                   EEE-SSEEEEEEEE.......TTTEEEEEEEE--T CS
                   BcrAD_BadFG   3 iDgGsTttkavlmd.......ekgevlgrgitnsa 30 
                                   iD+G+T+t   +++       e+g v+g ++t  +
  gi|91773905|ref|YP_566597.1| 259 IDVGGTSTDISVIKngvpemsESGAVVGGWKTRVK 293
                                   78888888887777777777777777777777655 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.24     7e+02       2      19 ..       6      23 ..       5      52 .. 0.83
   2 ?   10.1   0.2   0.00027      0.81       1      22 [.     257     278 ..     257     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.24
                                  EEEE-SSSEEEEEEETTE CS
                                  xxxxxxxxxxxxxxxxxx RF
                          FtsA  2 lvDiGagktdvavaedga 19
                                  ++D G++ td+++++d+ 
  gi|91773905|ref|YP_566597.1|  6 GIDAGGTYTDAVLLRDSD 23
                                  79***********99854 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00027
                                   EEEEE-SSSEEEEEEETTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA   1 alvDiGagktdvavaedgalvh 22 
                                   a++D+G+++td++v+++g +  
  gi|91773905|ref|YP_566597.1| 257 AVIDVGGTSTDISVIKNGVPEM 278
                                   79***************97655 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00012      0.37     114     139 ..     256     281 ..     243     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                                   EEEEEEETTEEEEEEEETTEEEEEEE CS
                      Ppx-GppA 114 glviDiGGGStElvlgeekevsklvS 139
                                     viD+GG St+++++++  +++++S
  gi|91773905|ref|YP_566597.1| 256 CAVIDVGGTSTDISVIKNGVPEMSES 281
                                   469***************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 4718.51
//
Query:       gi|91773906|ref|YP_566598.1|  [L=62]
Description: hypothetical protein Mbur_1968 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 423.50
//
Query:       gi|91773907|ref|YP_566599.1|  [L=379]
Description: fructose-bisphosphate aldolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-30  107.1   0.1    1.4e-30  106.8   0.1    1.0  1  F_bP_aldolase   Fructose-bisphosphate aldolase class-II
    7.5e-09   34.8   0.0    1.2e-08   34.1   0.0    1.2  1  Tagatose_6_P_K  Tagatose 6 phosphate kinase


Domain annotation for each model (and alignments):
>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.1   1.5e-34   1.4e-30      15     256 ..      23     306 ..      12     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.5e-34
                                   --EEEEE--SHHHHHHHHHHHHHHTS-EEEEE-HHHHHHHH-.....HHHHHHHHHHHHHHHHT...-E.EEEEE--.--G CS
                 F_bP_aldolase  15 yavgafnvtnletvkavleaaeeaksPvIlqlsegaaakyag.....gaealaelvraaaeaykkasvp.valhlDH.gak 88 
                                   + ++  n      +k++++aa+e+++P+Il+l++++ +  +g        a+ ++ r+aa++++        lh DH g k
  gi|91773907|ref|YP_566599.1|  23 TIIMTANPRIALVTKGIMRAAKEMDAPLILELARSECN-LEGgyaglTPAAISKITRDAAKELE---FDmWSLHADHiGIK 99 
                                   556666666777899*********************95.4455787777788899999999554...66269*****6555 PP

                                   ..........HHHHHHHHHH....S-SEEEE--TTS..........-HHHHHHHHHHHHHHHHH....TT-EEEEE----- CS
                 F_bP_aldolase  89 ..........leglkkaiea....gfsSvMiDgSel..........pleeNialtkevveraha....lgvsvEaElGrig 141
                                              + +          g++S  iD+S+l          +l++Ni+ t ++   ++      +  +E+E+G+ig
  gi|91773907|ref|YP_566599.1| 100 kgtdedieatKKLVD----GqieaGYTSFAIDASHLfnfqggnlreELANNIDATTKIGLHIKRgmgdKEYGLEVEVGEIG 176
                                   677677433333333....35555**********8888888888889******99998554443322266**********9 PP

                                   ------TT-TTTS--HHHHHHHHHHHH.....-EEEE--SS---SS.--SS........--THHHHHHHHHH......--S CS
                 F_bP_aldolase 142 geedgvvaeeklyTdpeeaeefveetg.....vdalAvaiGnvHGv.ykpk.pk.....Ldferlkeiqkav......vpl 204
                                    e++    + +++T+peea++f+++++      ++lA+a G++HG  y+++ ++      d+e   ++++a+      v +
  gi|91773907|ref|YP_566599.1| 177 REDE----HGRVLTRPEEAVTFIKALNengvyPHFLAIANGSAHGNtYDTNgNRieqvsVDIEQTVAVAQALkdnnldVRI 253
                                   6554....357********************99************966666522556779999999999999999988889 PP

                                   EE-SGTTS-HHHHHHHHHTT.EEEEEE-HHHHHHHHHHHHHGGE-HHH-HHHH CS
                 F_bP_aldolase 205 VlHGgsgvpdeeirkaiklG.vvKiNidtdlrlaytkavkkekenkkydprkl 256
                                   + HG +g+p++ i++++ +G +vK N++t +++ +++ +k ++++   d  ++
  gi|91773907|ref|YP_566599.1| 254 AQHGITGTPRDLIHNHFPHGdIVKGNVATFYQNIVWDLFKVYEPELYKDLWDW 306
                                   ***********************************999977754432333333 PP

>> Tagatose_6_P_K  Tagatose 6 phosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.3e-12   1.2e-08      25     130 ..      34     133 ..      21     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-12
                                   HHHHHHHHHHHHS-S-EEEEEETTTS-TT-TTTT--HHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGTTS-HHHHHHH CS
                Tagatose_6_P_K  25 lvieaaleqakekesavLiEatsNqvnqfGGYtGmtpadFrefvleiaeevglpkerlilGGDHLGPnawkklpaeeAmak 105
                                   lv +  +++ake ++++++E     +n +GGY+G+tpa   ++  + a+e++++  +  l  DH+G +    + ++e ++ 
  gi|91773907|ref|YP_566599.1|  34 LVTKGIMRAAKEMDAPLILELARSECNLEGGYAGLTPAAISKITRDAAKELEFDMWS--LHADHIGIK----KGTDEDIEA 108
                                   6788899*******************************************9998765..779****64....667788999 PP

                                   HHHHHHHHHTTT--EEEE---B--S CS
                Tagatose_6_P_K 106 aeelvaayvaagfkKiHlDasmsca 130
                                   +++lv+  ++ag++   +Das   +
  gi|91773907|ref|YP_566599.1| 109 TKKLVDGQIEAGYTSFAIDASHLFN 133
                                   9********************7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2501.65
//
Query:       gi|91773908|ref|YP_566600.1|  [L=209]
Description: hypothetical protein Mbur_1970 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-32  113.3  14.7    1.2e-32  112.9  14.7    1.0  1  Yip1      Yip1 domain
    0.00075   19.3  19.2    0.00098   18.9  19.2    1.3  1  DUF1282   Protein of unknown function (DUF1282)
  ------ inclusion threshold ------
      0.012   15.2   9.2      0.012   15.2   9.2    2.1  2  DUF1189   Protein of unknown function (DUF1189)
        6.3    6.1   6.2        8.7    5.6   6.2    1.3  1  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9  14.7   2.8e-36   1.2e-32       1     171 [.       8     199 ..       8     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 2.8e-36
                          Yip1   1 llldPrevfrrlkkeppilrapdlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllglllla 81 
                                   +l dP+++f++ +k++  ++ p+l+++++ +l++++++++++ +++ ++++  +++++ + l++ai+g+++g+++++++++
  gi|91773908|ref|YP_566600.1|   8 ILKDPNSFFEEKIKSEVEFKTPLLIMIFIGVLAAISATVMTQSIMSAMPEE--MAMFGIIGLVAAIAGAFIGVFITWVIYT 86 
                                   578********9999998888888888888888888888885555555555..9*************************** PP

                          Yip1  82 lllhliakllggkgsfkqtlsvvgyallPlilgaliaillllllgt.......................llllvgllaliW 139
                                    +++l++ ++gg+g+fk+tl++v+y+++P+i+ ++ +i+++                             +++vg+++++W
  gi|91773908|ref|YP_566600.1|  87 IIFYLLSSVFGGEGDFKRTLEFVAYGFIPTIINSITSIYVISKIFStidmttvdpiainetlladptmqMITVVGIIINLW 167
                                   **************************************998877779********************************** PP

                          Yip1 140 slvllylglkaahnlskkkallaalillllli 171
                                   s+ ++  gl +a n++ k+a++a++i++ + i
  gi|91773908|ref|YP_566600.1| 168 SANIWRYGLVHARNMTVKNATIAVMIPIGISI 199
                                   **************************887765 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9  19.2   2.2e-07   0.00098      16     137 ..      23     170 ..       8     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-07
                       DUF1282  16 eetgkvlyivlillllliglvvfiystfqvlseiltkqankltlas..sliisvvfylal...gvlvlayliklmgrtyds 91 
                                   e   k + +++i +     +v++ +s +++  +i++ +++++ ++   +l+ ++++++++   ++++ + +++l ++++++
  gi|91773908|ref|YP_566600.1|  23 EVEFKTPLLIMIFI-----GVLAAISATVMTQSIMSAMPEEMAMFGiiGLVAAIAGAFIGvfiTWVIYTIIFYLLSSVFGG 98 
                                   44444443333333.....555666666666777776555555555668888888888889999***************** PP

                       DUF1282  92 qhsyskifafaayalvplflgglalgl..sllllva........................lvslllllyvvv 137
                                   +  ++ ++ f+ay ++p ++  + +++  s ++ ++                        +v+ ++ l+++ 
  gi|91773908|ref|YP_566600.1|  99 EGDFKRTLEFVAYGFIPTIINSITSIYviSKIFSTIdmttvdpiainetlladptmqmitVVGIIINLWSAN 170
                                   ********************9987654114555555888888888888888888888888777777777765 PP

>> DUF1189  Protein of unknown function (DUF1189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.3      0.17   7.7e+02     138     164 ..      15      39 ..       1      52 [. 0.40
   2 ?   15.2   9.2   2.6e-06     0.012     147     222 ..      52     126 ..      42     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                       DUF1189 138 ltkedlreflssvksilkiilvliliv 164
                                   + +e++++ + ++k+ + +i+++i ++
  gi|91773908|ref|YP_566600.1|  15 FFEEKIKSEV-EFKT-PLLIMIFIGVL 39 
                                   3444444444.2222.22222222222 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.6e-06
                       DUF1189 147 lssvksilkiilvlilivlflvsllltlidalilaliglilarilkiklsYkqlfkisvyalTlPtilnaileiln 222
                                   +s + + + ++ ++ l++++   +++++i+ +i+++i ++l+++++ +  +k  + +++y++ +Pti+n i +i  
  gi|91773908|ref|YP_566600.1|  52 MSAMPEEMAMFGIIGLVAAIAGAFIGVFITWVIYTIIFYLLSSVFGGEGDFKRTLEFVAYGF-IPTIINSITSIYV 126
                                   345566677888888999999****************************************9.9******999876 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.2    0.0019       8.7      18      68 ..      31      87 ..      19     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0019
                       DUF4407 18 avvlltallAalsgayAlytvlkspll..........lallvGllwgllIfnlDRfivssi 68
                                   +++++++lAa+s+++  ++++++             +    +++ g++I  +  +++ +i
  gi|91773908|ref|YP_566600.1| 31 LIMIFIGVLAAISATVMTQSIMSAMPEemamfgiiglV----AAIAGAFIGVFITWVIYTI 87
                                  6899*******************999988888855552....3444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1331  (0.0742373); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1517.48
//
Query:       gi|91773909|ref|YP_566601.1|  [L=107]
Description: hypothetical protein Mbur_1971 [Methanococcoides burtonii DSM 6242]
Scores for 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-20   70.5   0.1    1.2e-19   70.2   0.1    1.1  1  DUF167    Uncharacterised ACR, YggU family COG1872


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   6.8e-24   1.2e-19       1      76 [.      15      89 ..      15      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 6.8e-24
                                  EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                        DUF167  1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                  g+ ++++v+Pg+kk +++  +++++re++++++++++++GkAN +li+++a+ +++ +++v i sG+ks++K+v i
  gi|91773909|ref|YP_566601.1| 15 GIAIDLEVTPGSKKACFP-AGYNQWRERIEIKLTSAAQKGKANGQLIEIVADFFNIGQREVIIGSGAKSSKKTVII 89
                                  5789**************.8899***************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 664.66
//
Query:       gi|91773910|ref|YP_566602.1|  [L=416]
Description: glutamate dehydrogenase (NAD/NADP) [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-69  233.6   4.7    3.2e-69  233.4   3.0    1.8  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
      6e-55  184.7   0.0      1e-54  183.9   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0059   16.0   0.1       0.01   15.2   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.17     1e+03     173     187 ..     105     119 ..     103     135 .. 0.65
   2 !  233.4   3.0   5.3e-73   3.2e-69       1     243 []     180     413 ..     180     413 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.17
                                   THHHHHHHHHHHHHH CS
                 ELFV_dehydrog 173 aGGVtvSslEmlqnl 187
                                   +GGV++   Em+q+ 
  gi|91773910|ref|YP_566602.1| 105 KGGVICNPKEMSQSE 119
                                   566766666666653 PP

  == domain 2  score: 233.4 bits;  conditional E-value: 5.3e-73
                                   T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-HHHHH CS
                 ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldieell 80 
                                   GGsl+r +aT++G +y+v+e++ +++l+ l++++vai+G+Gn g +a  l++el g kvvavsDs+G  ++ +G++ e+ +
  gi|91773910|ref|YP_566602.1| 180 GGSLGRGDATARGGLYAVREAAAEIGLE-LKDATVAIQGYGNAGYFAGTLCEELfGCKVVAVSDSRGGAVNMNGISAEAAQ 259
                                   9***********************9999.************************99************************** PP

                                   HHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHHT CS
                 ELFV_dehydrog  81 elkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeileea 161
                                   e+k++++sv  ++     ++e i+ne ++lel+vdil+P+A++ +i+ ena+ +ik  +k+v+E AN+ptt+eA+e+l ++
  gi|91773910|ref|YP_566602.1| 260 EHKKATGSVVGLA-----GTEPISNE-DILELDVDILIPAALEHVITHENAD-NIK--AKIVAELANGPTTPEADEMLFQK 331
                                   *************.....4699***7.*************************.***..*********************** PP

                                   T-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHHC CS
                 ELFV_dehydrog 162 gvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiagfekvaeamkaq 242
                                   gv ++pd+++N GGVtvS++Em+qn+ ++ w+ e+v+++l+++m+++++av+e+ ++y+++++++a+++++++v+eam ++
  gi|91773910|ref|YP_566602.1| 332 GVHLIPDFLCNGGGVTVSYFEMVQNFYMYRWSIERVHNRLDAKMTNAYHAVLEASKQYNVNMRTAAYVVAVNRVVEAMADR 412
                                   *******************************************************************************99 PP

                                   T CS
                 ELFV_dehydrog 243 G 243
                                   G
  gi|91773910|ref|YP_566602.1| 413 G 413
                                   8 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.0   1.7e-58     1e-54       1     129 [.      34     161 ..      34     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 1.7e-58
                                   -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GGG CS
               ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpkk 81 
                                   p r ++v++p+++d+G+++v++g+r+q+++a gP+kGGiRfhp+ + d+vkaLaa+mt+K+a++d+p+GG+kggv+++pk+
  gi|91773910|ref|YP_566602.1|  34 PMREMHVSLPIRMDDGSIKVFQGFRVQYNDAKGPTKGGIRFHPDETVDTVKALAAWMTWKCAVMDIPLGGGKGGVICNPKE 114
                                   678899*************************************************************************** PP

                                   S-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
               ELFV_dehydrog_N  82 lseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                   +s++eler+ r+++++++  ++Gp++DvpApDv+t+++ maw++de++
  gi|91773910|ref|YP_566602.1| 115 MSQSELERLSRKYISSIS-MIVGPDKDVPAPDVYTNPQMMAWMMDEFS 161
                                   ******************.9**************************97 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 !   15.2   0.1   1.7e-06      0.01      14      70 ..     186     245 ..     177     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-06
                                   HHHHHHTTCC..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHH CS
                  2-Hacid_dh_C  14 adeevregew..ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskk 70 
                                   +d+  r g +  ++ +a  g el++ tv+i G+G+ G  +  +++  fg+kv+a++ s+ 
  gi|91773910|ref|YP_566602.1| 186 GDATARGGLYavREAAAEIGLELKDATVAIQGYGNAGYFAGTLCEeLFGCKVVAVSDSRG 245
                                   555566665565667788999***********************988********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2532.58
//
Query:       gi|91773911|ref|YP_566603.1|  [L=242]
Description: reduced coenzyme F420:NADP oxidoreductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-18   66.2   0.9    4.9e-18   65.5   0.9    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.002   17.8   0.2     0.0043   16.7   0.2    1.5  2  ApbA            Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.023   14.7   0.1      0.035   14.1   0.1    1.2  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.04   13.5   0.6      0.081   12.5   0.6    1.5  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


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 !   65.5   0.9   1.1e-21   4.9e-18       1      97 []       2     102 ..       2     102 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.1e-21
                                   EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S-H CS
                 F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlavkp 71 
                                   ki+i+ G+Gn+g+++a+++ +     h++v++ srn eka   aee+           k++++ n+ aa+ adv+++a+++
  gi|91773911|ref|YP_566603.1|   2 KIAILgGTGNIGRGFALRWGQM----HDVVIG-SRNSEKAITVAEEYTrilsergfdSKIEGMGNKSAAKVADVIIIAIRY 77 
                                   7******************999....9***88.************************************************ PP

                                   HHHHHHHHHCGHHHHTTSEEEEESSS CS
                 F420_oxidored  72 edveevlselakdalkgklvisvlag 97 
                                   e+v++v++ + +  lk+++v+sv+++
  gi|91773911|ref|YP_566603.1|  78 EQVSSVIELI-APVLKDQVVVSVVVP 102
                                   *******999.999*********986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   9.6e-07    0.0043       2     100 ..       4      98 ..       3     103 .. 0.79
   2 ?   -2.5   0.0      0.82   3.7e+03      62      83 ..     124     145 ..     100     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.6e-07
                                   EEE.S-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCH.SCCCCS-ESEEEE-SSGG CS
                          ApbA   2 ail.GaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsae.ekselepidlvivtvKay 79 
                                   ail G+G iG+ +a +  +  +dv++  r+  ++ ++ ++  r+ se+g     ++ +++   +ks ++ +d++i+++   
  gi|91773911|ref|YP_566603.1|   4 AILgGTGNIGRGFALRWGQ-MHDVVIGSRNSeKAITVAEEYTRILSERG-----FDSKIEGMgNKSAAKVADVIIIAIRYE 78 
                                   555268*******999966.89999999999788889999999999993.....3333333334455799*********** PP

                                   GHHHHHHHHGGGECTCEEEEE CS
                          ApbA  80 qteealeeikplldpntvvll 100
                                   q+ +++e i+p+l+++ vv++
  gi|91773911|ref|YP_566603.1|  79 QVSSVIELIAPVLKDQ-VVVS 98 
                                   ***************9.5554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.82
                                   SCCCCS-ESEEEE-SSGGGHHH CS
                          ApbA  62 ekselepidlvivtvKayqtee 83 
                                   +++++ ++d++  t++a   ++
  gi|91773911|ref|YP_566603.1| 124 ASKSDYNADYFCYTTPAAGSAA 145
                                   4456677777777777665544 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.8e-06     0.035       1     101 [.       2      98 ..       2     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-06
                                   -EEEE-.-SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HH CS
                NAD_Gly3P_dh_N   1 kiavlG.aGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsq 80 
                                   kia+lG +G+ G  +A   ++  h+v++ +r++e  ++i  ++e ++ L +  ++++++   + ++a+k ad+i++++  +
  gi|91773911|ref|YP_566603.1|   2 KIAILGgTGNIGRGFALRWGQM-HDVVIGSRNSE--KAITVAEEYTRILSERGFDSKIEGMGN-KSAAKVADVIIIAIRYE 78 
                                   79999736********999876.58988888776..5688889999************99877.788999*********** PP

                                   HHHHHHHHHCCC--TT-EEEE CS
                NAD_Gly3P_dh_N  81 alrevlkklkgllkkkailvs 101
                                    + +v++ ++++lk+++ +vs
  gi|91773911|ref|YP_566603.1|  79 QVSSVIELIAPVLKDQV-VVS 98 
                                   ***********996655.444 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   1.8e-05     0.081       6      92 ..       2      98 ..       1     116 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                  -EEEES.-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHH.......TT-....EEEEHHHHHHT-SEEEE-S-HHHHHHH CS
                          IlvN  6 kiaviG.yGsqGhaqalnlrdsgldvvvglregsksvkkAke.......egf....evltvaeavkkadvvmiliPDelqkev 76
                                  kia++G  G+ G+  al    +  dvv+g r+++k ++ A+e       +gf    e +  + a+k adv++i i  e+ ++v
  gi|91773911|ref|YP_566603.1|  2 KIAILGgTGNIGRGFALRWG-QMHDVVIGSRNSEKAITVAEEytrilseRGFdskiEGMGNKSAAKVADVIIIAIRYEQVSSV 83
                                  78888537888887776543.345999999999987777765222222256622224577899******************** PP

                                  HHHHTGGG--TT-EEE CS
                          IlvN 77 yeeeiepnlkegkala 92
                                  + e i+p lk++ +++
  gi|91773911|ref|YP_566603.1| 84 I-ELIAPVLKDQVVVS 98
                                  9.89*****9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1590.06
//
Query:       gi|91773912|ref|YP_566604.1|  [L=442]
Description: L-glutamine synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-132  439.5   0.0   9.3e-132  439.2   0.0    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    3.5e-33  113.2   0.1    6.5e-33  112.3   0.1    1.5  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
    0.00042   20.1   0.0     0.0037   17.1   0.0    2.2  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 !  439.2   0.0  1.6e-135  9.3e-132       2     345 .]     106     438 ..     105     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 439.2 bits;  conditional E-value: 1.6e-135
                                   T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHHH CS
                    Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreiveal 82 
                                   +dPR++lk+++++++e+G++++vgpElEFflf++++ k+            ++ p++ g+yf++ap+d aed+rr+iv +l
  gi|91773912|ref|YP_566604.1| 106 GDPRYTLKKVMKEAKEMGFSLNVGPELEFFLFERHDGKA------------TTIPHDFGRYFEFAPADLAEDIRRDIVLTL 174
                                   79*******************************998855............4568899*********************** PP

                                   HHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTEE CS
                    Gln-synt_C  83 ealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgkn 163
                                    +lg+e+eashhEva gQ+Ei++k+ dal++aDnv+tfK+v++++A+ +gl+atFmpKp++g+nGsgmHv+lSl+ k+g+n
  gi|91773912|ref|YP_566604.1| 175 MDLGFEIEASHHEVAFGQHEIDFKYGDALTTADNVTTFKYVTRTIAKLNGLHATFMPKPIFGENGSGMHVNLSLS-KNGEN 254
                                   ***************************************************************************.***** PP

                                   SSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-TSGGCSTEEEECE CS
                    Gln-synt_C 164 lfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipaskekakrvElRlp 244
                                   +f+d+d+++++s+ ar+figGllkh+ka+ta+ +p +nSYkRlvpgyeaPv++aw+  NRs l+Ripa+++k++rvElR+p
  gi|91773912|ref|YP_566604.1| 255 IFYDADGDMQISDEARYFIGGLLKHVKAITAISNPLINSYKRLVPGYEAPVYIAWSGANRSSLIRIPAARGKGTRVELRSP 335
                                   ********************************************************************************* PP

                                   BTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-HHHHHHHH CS
                    Gln-synt_C 245 dasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeedellkevlgeevieayl 323
                                   d+s+NPY+++Aa+laAgldGi+nk++pg++ e++++el+++     gie+lP++l+++ + l++dellke+lg +v ++ l
  gi|91773912|ref|YP_566604.1| 336 DPSCNPYITFAAVLAAGLDGIRNKIDPGDNREENIFELTDKGLrdFGIETLPSTLNDSAKYLADDELLKEALGAHVHNSVL 416
                                   ****************************************988889*********************************** PP

                                   HHHHHCHHHHHCT--HHHHHHH CS
                    Gln-synt_C 324 alkraEleeleeevsdwelery 345
                                   +l +aE+++++ +v+dwe+ery
  gi|91773912|ref|YP_566604.1| 417 SLAKAEWDSYRIQVHDWEIERY 438
                                   ********************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 !  112.3   0.1   1.1e-36   6.5e-33       1      83 []      17      99 ..      17      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 1.1e-36
                                  T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEEEEEEE- CS
                    Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarvicdvyd 82
                                  +vkf++lqFtDi+g +k+v+ip++++ e+al+ g+sFDGSsiegf++i+eSDm+LkPd+s+++i+P++++k  +ar+icd+y 
  gi|91773912|ref|YP_566604.1| 17 NVKFIRLQFTDIQGVVKDVEIPVTQI-EKALSVGISFDGSSIEGFVRINESDMVLKPDTSSFAILPWNQKKgVVARMICDIYL 98
                                  79************************.*******************************************************8 PP

                                  T CS
                    Gln-synt_N 83 p 83
                                  p
  gi|91773912|ref|YP_566604.1| 99 P 99
                                  6 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 !   17.1   0.0   6.3e-07    0.0037       4     107 .]       7     104 ..       4     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.3e-07
                                   .......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE-GGG-E CS
                  Gln-synt_N_2   4 eavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvpdPasav 84 
                                   e v++ +e+++v++i++ ++d +Gv++   +p +++e+ L  Gi +    ++++    i+e+       ++ L pd +s+ 
  gi|91773912|ref|YP_566604.1|   7 EDVLKAIENNNVKFIRLQFTDIQGVVKDVEIPVTQIEKALSVGISFD--GSSIEGFVRINES-------DMVLKPDTSSFA 78 
                                   6799999*********************************9999875..4566667777776.......567999999999 PP

                                   EE---SS...TTSEEEEEE-TTS-B- CS
                  Gln-synt_N_2  85 alpyaPd...aaallgdlvevdgtPy 107
                                    lp   +   +a ++ d++  dgtP+
  gi|91773912|ref|YP_566604.1|  79 ILPWNQKkgvVARMICDIYLPDGTPF 104
                                   99875442225669999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2704.32
//
Query:       gi|91773913|ref|YP_566605.1|  [L=1367]
Description: hypothetical protein Mbur_1976 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-109  361.1  47.3    4.1e-28   98.4   2.8    5.8  6  Laminin_G_3  Concanavalin A-like lectin/glucanases superfamil
    1.1e-16   61.5   2.1    1.1e-16   61.5   2.1    2.4  2  Pilin_N      Archaeal Type IV pilin, N-terminal
    3.6e-14   53.4  15.5    9.9e-06   26.2   0.2    6.1  6  Laminin_G_2  Laminin G domain
    1.2e-06   28.8   5.2       0.44   10.8   0.0    5.4  6  Laminin_G_1  Laminin G domain
    3.4e-05   23.6   6.2       0.27   10.9   0.3    3.7  3  Pentaxin     Pentaxin family
    4.1e-05   23.2  15.5       0.12   11.9   0.5    5.6  5  Sialidase    Sialidase, N-terminal domain
  ------ inclusion threshold ------
      0.055   13.3   0.1        1.4    8.8   0.0    3.5  3  DUF4183      Domain of unknown function (DUF4183)


Domain annotation for each model (and alignments):
>> Laminin_G_3  Concanavalin A-like lectin/glucanases superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   2.8   1.6e-31   4.1e-28       4     152 .]     214     367 ..     211     367 .. 0.88
   2 !   92.2   4.1   1.3e-29   3.4e-26       1     151 [.     421     573 ..     421     574 .. 0.89
   3 !   92.6   3.2     1e-29   2.7e-26       2     151 ..     636     796 ..     635     797 .. 0.91
   4 ?    4.2   0.2     0.017        44      35     110 ..     816     905 ..     807     929 .. 0.69
   5 !   96.4   6.7   6.7e-31   1.7e-27       1     151 [.    1030    1179 ..    1030    1180 .. 0.87
   6 ?   -3.8   0.0         5   1.3e+04      90     110 ..    1333    1353 ..    1331    1361 .. 0.65

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.6e-31
                   Laminin_G_3   4 sdyvtlpd.aslp.tssfTvsaWvkpdslpsaaqiiis.sssdg.rgfelgl.dgsgrlrfsvnagngaeesvtsgasvpa 79 
                                   sd v++++  sl+  s++T++aWvk+   p++   + +  ++dg ++++l+  +g++r++f+vn+++ ++++++s+++ ++
  gi|91773913|ref|YP_566605.1| 214 SDVVRVENsISLNpKSEITLEAWVKWAIDPNDGENWANiLNKDGeDQYQLQHtYGNNRFEFAVNTDD-GRDWISSTTAPQK 293
                                   6778886656675599************9999999888845555569***9868999*******997.7889999999999 PP

                   Laminin_G_3  80 geWtHvavtyd..ggtlrlYvNGvevgsatltggllsatsgplviGrdpggddpfdGlidevriynralsaaeIa 152
                                   + W+Hv+++y+  ++++ +YvNGv+  sa++ g++   +s+p+ iG    +d+ f+G idev++yn+ l++++I+
  gi|91773913|ref|YP_566605.1| 294 EIWYHVVGVYSsyDQEIAIYVNGVKERSAVHEGDIA-ISSAPFLIGEHLISDRSFNGIIDEVWVYNTRLTDEQIK 367
                                   ***********88899*************9999955.599*********88**********************96 PP

  == domain 2  score: 92.2 bits;  conditional E-value: 1.3e-29
                   Laminin_G_3   1 dggsdyvtlpdaslptssfTvsaWvkpdslpsaaqiiis...sssdg.rgfelgldgsgrlrfsvnagngaeesvtsgasv 77 
                                   dg++d+v+++++ + +  f+vsaW+k + ++ ++ +iis   ss  +  +++++ld ++ l+++ +++  a + v+s+ +v
  gi|91773913|ref|YP_566605.1| 421 DGSNDHVSVDSSIIENYPFSVSAWIKNSGSNKDE-VIISmadSSA-TnAYYGMYLDKTKGLTIAAKNT--ALKEVSSTVDV 497
                                   799****************************965.5555585444.458**************99977..59********* PP

                   Laminin_G_3  78 pageWtHvavtydggt.lrlYvNGvevgsatltggllsatsgplviGrdp..ggddpfdGlidevriynralsaaeI 151
                                   ++g W++v++++ +    +lYv+Gv+ g+ t t +++s + + + iGr +    + +f+G ide  i +r+lsa+eI
  gi|91773913|ref|YP_566605.1| 498 TDGNWHYVVGVFASAIdRKLYVDGVLNGTDTRTVPFNS-DFDRWNIGRWAdkTPSAYFNGVIDEASITDRELSASEI 573
                                   *************8877**************9999886.567799**9985445**********************9 PP

  == domain 3  score: 92.6 bits;  conditional E-value: 1e-29
                   Laminin_G_3   2 ggsdyvtlpd.aslp.tssfTvsaWvkpdslpsaaqiiis...sssdgrgfelgldgsgrlrfsvnagngaeesvtsgasv 77 
                                   + + yv ++d +sl+ +++ ++ +W+k++s  ++a+i+++   +s++++ ++l++d++ ++++ ++++ g+ ++vts +++
  gi|91773913|ref|YP_566605.1| 636 DRTEYVVVNDnSSLDlSTEGSIDTWIKLNSHIANAGIVHKgdrKSKSDKAYSLEFDNDEHVSLVLYNSSGSFQQVTSVTKL 716
                                   56889***99788999***********************9876443337******************************** PP

                   Laminin_G_3  78 pageWtHvavtydggtlrlYvNGvevgsatltggllsatsgplviGrdp...gg...ddpfdGlidevriynralsaaeI 151
                                   ++++W+H+++t++++++ +Y+NG ++ s+++t g+ ++t+g+l+iG++    +g   ++ +dG+idev + n+ ++  +I
  gi|91773913|ref|YP_566605.1| 717 ELDKWYHLTGTWNSSSIEVYINGILDRSEQNTIGAVRNTDGTLQIGAKItqnDGankKYGLDGTIDEVYLSNKKMTLFDI 796
                                   **********************************************9976652256699999************998776 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.017
                   Laminin_G_3  35 qiiis.sssdg....rgfelgldgsgrlrfsvnagngaeesvtsgasvpageWtHvavtyd.........ggtlrlYvNGv 101
                                   qii++  +++g     g+  + +g+++ ++++++++++ e+ +s +   ++  t  ++ ++         + +++lY+NG 
  gi|91773913|ref|YP_566605.1| 816 QIIFNkPNKGGvikdGGYISFTNGNDHRHVRIDGTKYDLETGDSVKLEVVNDQTSATISMNdvssqisdfDLNVKLYINGD 896
                                   4455442222344433777777777788888888888888888777666677788888888776555444455******** PP

                   Laminin_G_3 102 evgsatltg 110
                                   ++ +  +t+
  gi|91773913|ref|YP_566605.1| 897 LKDTGRVTS 905
                                   *99987765 PP

  == domain 5  score: 96.4 bits;  conditional E-value: 6.7e-31
                   Laminin_G_3    1 dggsdyvtlpd.aslp.tssfTvsaWvkpdslpsaaqiiissssdgrgfelgldgsgrlrfsvnagngaeesvt.sgas 76  
                                    dg++d+v +p+ ++++ t+s+T  aWv+ d +++    i+++++   g++lgld  + +  sv+ ++++++s++ +++ 
  gi|91773913|ref|YP_566605.1| 1030 DGTNDHVFVPNsSDFKfTDSITMMAWVNSDVSNT--AKIVQKGDW-GGYGLGLDIWNGWGASVYFDGSGSQSLRwGSGV 1105
                                    799******99888999****************9..446623444.5******98888888887777788888845555 PP

                   Laminin_G_3   77 vpageWtHvavtydggtlrlYvNGvevgsatltggllsatsgplviGrdpggddpfdGlidevriynralsaaeI 151 
                                     + g+W+Hva+tydg+ +rlYv+G ev+ at++g+l+  +s++++iG+d  ++++fdG+idev +++ al+  eI
  gi|91773913|ref|YP_566605.1| 1106 PENGRWYHVAFTYDGSAMRLYVDGREVNNATVSGDLK-VNSKDIYIGSDGVTQKFFDGKIDEVGVHQNALTGNEI 1179
                                    566*******************************966.69999******999*********************99 PP

  == domain 6  score: -3.8 bits;  conditional E-value: 5
                   Laminin_G_3   90 dggtlrlYvNGvevgsatltg 110 
                                    +g++l++ +NG+ + + +  +
  gi|91773913|ref|YP_566605.1| 1333 SGNSLSIIINGNGRRTVESYN 1353
                                    377799999998777764433 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   2.1   4.2e-20   1.1e-16       1      80 [.      15      89 ..      15      90 .. 0.97
   2 ?   -2.8   0.0         5   1.3e+04      41      73 ..     458     487 ..     441     493 .. 0.65

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 4.2e-20
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivlnseg 80
                                  ++VS V+G+i+m+ai+vI++++iaa+vl++ + +++ p++++  ++d +a+t    v+++h gG+++d +d++++ln +g
  gi|91773913|ref|YP_566605.1| 15 DGVSVVVGEIMMTAIVVIAVSFIAASVLSY-EGPSDVPNVDVIGWVDVGADT----VNFRHTGGETVDGQDIRLNLNLNG 89
                                  69****************************.9*******************9....*******************99886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                       Pilin_N  41 sievkidssastgknavslehkgGdsidtkdlk 73 
                                   s+    dssa+++++ ++l +  G +i+ k+++
  gi|91773913|ref|YP_566605.1| 458 SM---ADSSATNAYYGMYLDKTKGLTIAAKNTA 487
                                   33...4444444444499999999999888776 PP

>> Laminin_G_2  Laminin G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.15   3.9e+02      34      77 ..      59     102 ..      54     136 .. 0.83
   2 !    5.8   0.0    0.0076        20      28     123 ..     270     356 ..     252     359 .. 0.74
   3 ?    3.8   0.0     0.031        80      38      82 ..     486     530 ..     453     570 .. 0.66
   4 !   20.7   0.6   1.8e-07   0.00047      14     125 ..     676     788 ..     665     789 .. 0.85
   5 ?   -0.1   0.1      0.51   1.3e+03      47      78 ..     851     882 ..     828     907 .. 0.56
   6 !   26.2   0.2   3.9e-09   9.9e-06      34     123 ..    1090    1169 ..    1064    1172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                                   EESSS-EEEEE-SSSS-ESSSSEEEEEEECTTEEEEEECTS--C CS
                   Laminin_G_2  34 ynlgsgdtellssgkklndgewHsveverkgknltlsvDggets 77 
                                   +++g ++++++++g +  dg+  +++++ +g++++ls  + ++ 
  gi|91773913|ref|YP_566605.1|  59 VDVGADTVNFRHTGGETVDGQDIRLNLNLNGSAIKLSSQEIQSI 102
                                   789999999999977777***************99998666554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0076
                                   TEEEEEEESSS-EEEEE-SSSS-ESSSSEEEEEEEC..TTEEEEEECTS--CCCE-CSS.......S.EEES--TTHHHHC CS
                   Laminin_G_2  28 gklvltynlgsgdtellssgkklndgewHsveverk..gknltlsvDggetseanepgesqgldleeslylGGlepeepet 106
                                   ++ ++ +n+ +g+  ++s ++      w +v   ++  ++++ + v+g ++++a  +g+     +++++ +G +       
  gi|91773913|ref|YP_566605.1| 270 NRFEFAVNTDDGRDWISS-TTAPQKEIWYHVVGVYSsyDQEIAIYVNGVKERSAVHEGDIAI--SSAPFLIGEH------- 340
                                   445555555555555555.44446666777777766689***********999998888775..**********....... PP

                                   CTTTS-B-CEEEEEEEE CS
                   Laminin_G_2 107 aspvtegFvGcirdlrl 123
                                      + ++F+G i+++ +
  gi|91773913|ref|YP_566605.1| 341 -LISDRSFNGIIDEVWV 356
                                   .999********99986 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.031
                                   S-EEEEE-SSSS-ESSSSEEEEEEEC.TTEEEEEECTS--CCCE-C CS
                   Laminin_G_2  38 sgdtellssgkklndgewHsveverk.gknltlsvDggetseanep 82 
                                   +  +e++s + +++dg+wH v          +l vDg  + + +++
  gi|91773913|ref|YP_566605.1| 486 TALKEVSS-TVDVTDGNWHYVVGVFAsAIDRKLYVDGVLNGTDTRT 530
                                   44455555.999*******876444326666677777665555555 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 1.8e-07
                                   EE...STTEEEEEEEE.TTEEEEEEESSS-EEEEE-SSSS-ESSSSEEEEEEECTTEEEEEECTS--CCCE-CSS...... CS
                   Laminin_G_2  14 gd...eksdflalelk.dgklvltynlgsgdtellssgkklndgewHsveverkgknltlsvDggetseanepgesqgldl 90 
                                   gd   +++   +le++ d +++l++  +sg+ + ++s +kl  ++w +++ +++ +++++ ++g   ++++++    + ++
  gi|91773913|ref|YP_566605.1| 676 GDrksKSDKAYSLEFDnDEHVSLVLYNSSGSFQQVTSVTKLELDKWYHLTGTWNSSSIEVYINGILDRSEQNTIGAVR-NT 755
                                   5555444555789999889999987777777777777****************************9999999988888.** PP

                                   .S.EEES--TTHHHHCCTTTS-B-CEEEEEEEECC CS
                   Laminin_G_2  91 eeslylGGlepeepetaspvtegFvGcirdlrlng 125
                                   +++l++G+    ++++ ++ + g++G i++++l++
  gi|91773913|ref|YP_566605.1| 756 DGTLQIGAK--ITQNDGANKKYGLDGTIDEVYLSN 788
                                   *********..999999**************9986 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.51
                                   SSS-ESSSSEEEEEEECTTEEEEEECTS--CC CS
                   Laminin_G_2  47 gkklndgewHsveverkgknltlsvDggetse 78 
                                   + +l  g+  ++ev  +++++t+s+++ +++ 
  gi|91773913|ref|YP_566605.1| 851 KYDLETGDSVKLEVVNDQTSATISMNDVSSQI 882
                                   45555555555555555555555555544333 PP

  == domain 6  score: 26.2 bits;  conditional E-value: 3.9e-09
                                    EESSS-EEEEE-SSSS-.ESSSSEEEEEEECTTEEEEEECTS--CCCE-CSS.......S.EEES--TTHHHHCCTTTS CS
                   Laminin_G_2   34 ynlgsgdtellssgkkl.ndgewHsveverkgknltlsvDggetseanepgesqgldleeslylGGlepeepetaspvt 111 
                                    y  gsg+++l++ g+ +  +g+w +v ++++g++++l vDg+e++ a+ +g+ +    ++++y+G           +++
  gi|91773913|ref|YP_566605.1| 1090 YFDGSGSQSLRW-GSGVpENGRWYHVAFTYDGSAMRLYVDGREVNNATVSGDLKV--NSKDIYIGSD--------GVTQ 1157
                                    55599*******.555559*******************************99996..999*****99........9999 PP

                                    -B-CEEEEEEEE CS
                   Laminin_G_2  112 egFvGcirdlrl 123 
                                    + F+G i+++ +
  gi|91773913|ref|YP_566605.1| 1158 KFFDGKIDEVGV 1169
                                    999999998866 PP

>> Laminin_G_1  Laminin G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.9   9.9e+03      44      76 ..      68     101 ..      59     139 .. 0.68
   2 ?   -0.9   0.0      0.69   1.8e+03     112     129 ..     343     360 ..     330     362 .. 0.85
   3 ?    0.2   0.0      0.32   8.3e+02      42      59 ..     488     506 ..     455     530 .. 0.79
   4 !   10.2   0.2   0.00026      0.66      32     130 ..     697     791 ..     668     792 .. 0.82
   5 ?    4.0   0.0     0.021        53      28      76 ..     831     880 ..     830     917 .. 0.82
   6 !   10.8   0.0   0.00017      0.44      38      99 ..    1093    1152 ..    1086    1168 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.9
                                   EEEEEE.TTSSS-EEEEEEEETTEEEEEETTSC- CS
                   Laminin_G_1  44 vvsgqk.lndGkwhkvevernkrsgtlsvdgeer 76 
                                    +++     dG+  ++ ++ n++ + ls ++ ++
  gi|91773913|ref|YP_566605.1|  68 FRHTGGeTVDGQDIRLNLNLNGSAIKLSSQEIQS 101
                                   4555444778999999999999988888766665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.69
                                   CCSB-EEEEEEEEETTEE CS
                   Laminin_G_1 112 istsfkGcirdvsvnnkq 129
                                   + +sf+G+i +v+v n+ 
  gi|91773913|ref|YP_566605.1| 343 SDRSFNGIIDEVWVYNTR 360
                                   6789*********98876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.32
                                   EEEEEEEE.TTSSS-EEEE CS
                   Laminin_G_1  42 avvvsgqk.lndGkwhkve 59 
                                      vs++  + dG+wh v+
  gi|91773913|ref|YP_566605.1| 488 LKEVSSTVdVTDGNWHYVV 506
                                   444444444*******885 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00026
                                   EEEEESSS-.EEEEEEEEETTSSS-EEEEEEEETTEEEEEETTSC-EEEES-TT-SSSEEECSEEEESSSSGSTCCCSCCC CS
                   Laminin_G_1  32 evsldlgsg.aavvvsgqklndGkwhkvevernkrsgtlsvdgeervtgesplgatttlnvnkklyvGGlpdekvkkeala 111
                                   ++ l ++sg    v+s +kl+  kw++++ + n +s+ + ++g  + + e+++   +  n+++ l +G      +++  ++
  gi|91773913|ref|YP_566605.1| 697 SLVLYNSSGsFQQVTSVTKLELDKWYHLTGTWNSSSIEVYINGILD-RSEQNTIGAV-RNTDGTLQIGAK---ITQNDGAN 772
                                   5555566663455666667***************************.7777776666.799998888863...47999999 PP

                                   CCSB-EEEEEEEEETTEEG CS
                   Laminin_G_1 112 istsfkGcirdvsvnnkql 130
                                    + +++G i +v+++nk++
  gi|91773913|ref|YP_566605.1| 773 KKYGLDGTIDEVYLSNKKM 791
                                   9999************987 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.021
                                   TTEEEEEEESSS-EEEEEEEEE.TTSSS-EEEEEEEETTEEEEEETTSC- CS
                   Laminin_G_1  28 dGrlevsldlgsgaavvvsgqk.lndGkwhkvevernkrsgtlsvdgeer 76 
                                   +G +++   + ++ + + +++  l++G   k+ev+  ++s+t+s ++ ++
  gi|91773913|ref|YP_566605.1| 831 GGYISFTNGNDHRHVRIDGTKYdLETGDSVKLEVVNDQTSATISMNDVSS 880
                                   57777777777888888888889*********************999877 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00017
                                    SS-EEEEEEEEE.TTSSS-EEEEEEEETTEEEEEETTSC-EEEES-TT-SSSEEECSE.EEESS CS
                   Laminin_G_1   38 gsgaavvvsgqk.lndGkwhkvevernkrsgtlsvdgeervtgesplgatttlnvnkk.lyvGG 99  
                                    gsg+ +++ g+   ++G+w++v  ++ ++ + l vdg+e+ + ++++g   +l+vn k +y+G+
  gi|91773913|ref|YP_566605.1| 1093 GSGSQSLRWGSGvPENGRWYHVAFTYDGSAMRLYVDGREV-NNATVSG---DLKVNSKdIYIGS 1152
                                    556666777777679*************************.3333333...4455544499996 PP

>> Pentaxin  Pentaxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.3    0.0001      0.27      73     166 ..     284     369 ..     227     387 .. 0.76
   2 !   10.0   0.2    0.0002       0.5      77     169 ..     708     802 ..     679     810 .. 0.71
   3 ?    3.5   0.0      0.02        51      83     173 ..    1109    1190 ..    1096    1203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                                   EEEEE-SS-SSSEEEEEEEEETTTTEEEEEETTEEEEEEE-STT--B-SSEEEEESS-BSCTTCTCSGGGB--EEEEEEEE CS
                      Pentaxin  73 evlvkvseekvepvhvCasWesssGivelwvdGkplvkkslkkgytvgaeasiilGqeqDsyGGkfdasqslvGelsdlnl 153
                                    + +++ ++k  + hv   ++s + ++ ++v+G      + + ++++   + +i        G +   ++s+ G + ++ +
  gi|91773913|ref|YP_566605.1| 284 WISSTTAPQKEIWYHVVGVYSSYDQEIAIYVNGVKERSAVHEGDIAISSAPFLI--------GEHLISDRSFNGIIDEVWV 356
                                   344566788889*********************555555555555565555444........6678889************ PP

                                   ESS---HHHHHHH CS
                      Pentaxin 154 WdyvLspeeiktv 166
                                   +++ L+ e+ik  
  gi|91773913|ref|YP_566605.1| 357 YNTRLTDEQIKAR 369
                                   **********975 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                                   E-SS-SS.....SEEEEEEEEETTTTEEEEEETTEEEEEEE-STT--B-SSEEEEESS-BSCTTCTCSGGGB--EEEEEEE CS
                      Pentaxin  77 kvseekv.....epvhvCasWesssGivelwvdGkplvkkslkkgytvgaeasiilGqeqDsyGGkfdasqslvGelsdln 152
                                   +++ + +     ++ h+  +W+sss  +e++++G +   + +  g + +++  + +G    +  G  +++  l G + +++
  gi|91773913|ref|YP_566605.1| 708 QQVTSVTkleldKWYHLTGTWNSSS--IEVYINGILDRSEQNTIGAVRNTDGTLQIGAKITQNDG-ANKKYGLDGTIDEVY 785
                                   3333222233469**********98..899****7777776766766667777777877766666.488999999999999 PP

                                   EESS---HHHHHHHHHT CS
                      Pentaxin 153 lWdyvLspeeiktvykg 169
                                   l +  ++  +i++ y+ 
  gi|91773913|ref|YP_566605.1| 786 LSNKKMTLFDIRSRYEM 802
                                   99999988888877765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.02
                                    SSEEEEEEEEETTTTEEEEEETTEEEEEEE-STT--B-SSEEEEESS-BSCTTCTCSGGG.B--EEEEEEEEESS---H CS
                      Pentaxin   83 vepvhvCasWesssGivelwvdGkplvkkslkkgytvgaeasiilGqeqDsyGGkfdasq.slvGelsdlnlWdyvLsp 160 
                                     ++ hv  +++ s   + l+vdG+ + + +   +  v+          +D y G+   +q  + G++ ++ + + +L+ 
  gi|91773913|ref|YP_566605.1| 1109 GRWYHVAFTYDGS--AMRLYVDGREVNNATVSGDLKVN---------SKDIYIGSDGVTQkFFDGKIDEVGVHQNALTG 1176
                                    5667777776655..35677777555544444444443.........34444444444441478*************** PP

                                    HHHHHHHHT-S.-- CS
                      Pentaxin  161 eeiktvykgat.ls 173 
                                    +ei  +y+++  ++
  gi|91773913|ref|YP_566605.1| 1177 NEIYEIYNSSRpVT 1190
                                    ******99876455 PP

>> Sialidase  Sialidase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00087       2.2     161     189 .]     346     374 ..     297     374 .. 0.75
   2 !    7.2   0.4    0.0013       3.3      50     184 ..     456     576 ..     441     581 .. 0.76
   3 !   11.9   0.5   4.6e-05      0.12     117     186 ..     731     801 ..     680     804 .. 0.79
   4 ?    2.4   0.1     0.037        95      93     146 ..     862     916 ..     828     941 .. 0.64
   5 ?   -0.3   0.1      0.26   6.6e+02     158     184 ..    1156    1182 ..    1115    1187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00087
                     Sialidase 161 lakgsidelsvyNkalsdeevskksqetk 189
                                    ++g ide+ vyN  l+de+++ +  ++k
  gi|91773913|ref|YP_566605.1| 346 SFNGIIDEVWVYNTRLTDEQIKARHDLNK 374
                                   689*******************9988876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                     Sialidase  50 LfgvSnskkkdeYFslfvrnsevglElRdskkkqnyqssrealvklkkdqknsatentvklkaelkdkryklyvNGvieev 130
                                   ++++++s + + Y+ +++   + gl +  +k+    + s    v +  +++  ++  + +  ++      klyv Gv++ +
  gi|91773913|ref|YP_566605.1| 456 IISMADSSATNAYYGMYLD-KTKGLTIA-AKNTALKEVSST--VDVTDGNWHYVV-GVFASAID-----RKLYVDGVLNGT 526
                                   6788889999999999985.45566664.333333444444..789999988766.46666777.....68********** PP

                     Sialidase 131 setsdkFikniedvdkatiGatnRegkeeylakgsidelsvyNkalsdeevskk 184
                                     ++  F ++    d+  iG+   +    y ++g ide s+  + ls  e+ + 
  gi|91773913|ref|YP_566605.1| 527 DTRTVPFNSD---FDRWNIGRWADKTPSAY-FNGVIDEASITDRELSASEIMNN 576
                                   9999999775...68999**9998888777.89************999998765 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 4.6e-05
                     Sialidase 117 kryklyvNGvieevsetsdkFikniedvdkatiGa..tnReg.keeylakgsidelsvyNkalsdeevskksq 186
                                     +++y+NG++++ ++ +   ++n ++    +iGa  t+  g +++y+ +g ide+ + Nk ++  ++ ++ +
  gi|91773913|ref|YP_566605.1| 731 SSIEVYINGILDRSEQNTIGAVRNTDGT--LQIGAkiTQNDGaNKKYGLDGTIDEVYLSNKKMTLFDIRSRYE 801
                                   56789****9998766665557777764..577764477777899****************999777777665 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.037
                     Sialidase  93 vklkkdqkns.atentvklkaelkdkryklyvNGvieevsetsdkFikniedvdk 146
                                   +++ +dq     + n v  ++   d ++kly+NG ++ +   +  + + + d  +
  gi|91773913|ref|YP_566605.1| 862 LEVVNDQTSAtISMNDVSSQISDFDLNVKLYINGDLKDTGRVTSIYANPMSDFSS 916
                                   444444443313345555555558899*******999888777777777777665 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.26
                     Sialidase  158 eeylakgsidelsvyNkalsdeevskk 184 
                                    ++  ++g+ide+ v+ +al+ +e+ ++
  gi|91773913|ref|YP_566605.1| 1156 TQKFFDGKIDEVGVHQNALTGNEIYEI 1182
                                    5556899*************9999776 PP

>> DUF4183  Domain of unknown function (DUF4183)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.2   5.7e+03      36      42 ..     311     317 ..     304     334 .. 0.78
   2 ?    8.8   0.0   0.00053       1.4      23      49 ..     722     747 ..     717     769 .. 0.78
   3 ?   -2.4   0.0       1.7   4.3e+03      35      41 ..     889     895 ..     875     900 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.2
                       DUF4183  36 nlYINGv 42 
                                    +Y+NGv
  gi|91773913|ref|YP_566605.1| 311 AIYVNGV 317
                                   68****9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00053
                       DUF4183  23 talpailtpnsyfnlYINGvLQessly 49 
                                   + l+++  ++s++ +YING+L  s+  
  gi|91773913|ref|YP_566605.1| 722 YHLTGT-WNSSSIEVYINGILDRSEQN 747
                                   566776.578***********877655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.7
                       DUF4183  35 fnlYING 41 
                                   + lYING
  gi|91773913|ref|YP_566605.1| 889 VKLYING 895
                                   579***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.54
# Mc/sec: 7683.38
//
Query:       gi|91773914|ref|YP_566606.1|  [L=187]
Description: hypothetical protein Mbur_1977 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.041   12.9   0.4        4.7    6.2   0.1    2.1  2  BPL_N       Biotin-protein ligase, N terminal
      0.099   12.7   0.0       0.16   12.0   0.0    1.2  1  Phage_coat  Phage PP7 coat protein


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 ?    6.2   0.1   0.00052       4.7      45      90 ..      36      84 ..      27      84 .. 0.81
   2 ?    5.1   0.0    0.0011       9.8     184     223 ..     131     171 ..     107     186 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00052
                         BPL_N 45 PWastcallVlPgG.aDlpYvrelng..egnrkikeyVekGGkylGlCA 90
                                  P    c  +V+P G a+ +Y++ + g  +  + ++++V +GG  + ++A
  gi|91773914|ref|YP_566606.1| 36 PFLPPCKCVVIPTGfANPAYTKICPGieNNDKSFEKFVLAGGILVVFGA 84
                                  677789******994567799999962155578*********9988876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0011
                         BPL_N 184 ArYa..eeldvdsgeakkaAvvlckvgeGkalLtgvhpEfal 223
                                     Y+  + + v ++++++a  v+ ++g+G ++ t++h Ef+ 
  gi|91773914|ref|YP_566606.1| 131 GYYSetDGTVVIENSEGNAVLVVKEIGDGLVIATTIH-EFPS 171
                                   3444322233333334557777778888888888777.5554 PP

>> Phage_coat  Phage PP7 coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.8e-05      0.16      78     121 ..     107     151 ..      99     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                                   EEEEEEEEEEEEEETTS-HHHH.HHHHHHHHHHHHSHHHHHHHHH CS
                    Phage_coat  78 vrytqvwshdvtivansteasr.kslydltkslvvtatvedlvvn 121
                                   v   qvwsh+v+ +a+  e+      y  t   vv  ++e   v 
  gi|91773914|ref|YP_566606.1| 107 VGLVQVWSHEVSCIADVRESVEcDGYYSETDGTVVIENSEGNAVL 151
                                   6789************99986526788999999998888876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1131.27
//
Query:       gi|91773915|ref|YP_566607.1|  [L=92]
Description: hypothetical protein Mbur_1978 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-34  117.4   0.2    2.9e-34  117.3   0.2    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 !  117.3   0.2   1.6e-38   2.9e-34       1      88 []       1      88 [.       1      88 [. 0.99

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 1.6e-38
                                  B---HHH--S-SS-EEESSHHHHHHHHTTSEEEEES--EEESSS---SS----EEEE--S-EEEE---SS-EEEEE-SS-GGG CS
                       DUF1894  1 maCleklkyeillkeasfkeceeyikkkakevyevepgykilgvrliGvppipvgideekilfpytkPCyGtfvlkvkeseee 83
                                  maC+++++yeillk+a+++ece++ikk+++evy+v++gyk++g++l G + ip+gi++++++f+++kPC G+++l++++++e+
  gi|91773915|ref|YP_566607.1|  1 MACINDIPYEILLKGATPQECEDFIKKECDEVYHVKGGYKLHGIMLRGGDSIPIGIKGDDLIFQFIKPCSGLYILRYSDAKED 83
                                  89********************************************************************************* PP

                                  HHHHH CS
                       DUF1894 84 ieklr 88
                                  ie+lr
  gi|91773915|ref|YP_566607.1| 84 IEQLR 88
                                  ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 606.64
//
Query:       gi|91773916|ref|YP_566608.1|  [L=333]
Description: phosphoribosylaminoimidazole synthetase [Methanococcoides burtonii DSM 6242]
Scores for 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-17   63.8   0.0    3.9e-17   62.8   0.0    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
    3.8e-14   53.1   0.4    6.4e-14   52.4   0.4    1.4  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 !   62.8   0.0   4.3e-21   3.9e-17       3     149 ..     173     324 ..     171     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 4.3e-21
                                   TEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.......TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                        AIRS_C   3 GdvliltgslGlggagtslkrkileeegldds.......avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                   Gdvl++++s G++++g+ l+r i++e+g  +        +  +gd+ll pt+iy   +   ++ +v++++++Tg GLl  l
  gi|91773916|ref|YP_566608.1| 173 GDVLVGIPSNGVHSNGYTLVRDIIKESGHSYHedfsyntETTIGDELLIPTRIYMEVLDVIKECDVHGLAHITGSGLLK-L 252
                                   9***************************8877******7777************998877779***********99995.5 PP

                                   HHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                        AIRS_C  77 aemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                   +++    g+g+ ++ +     if+ l+     ++lem++++n+G +++++ pe++++  a+++  g    +++G++++++
  gi|91773916|ref|YP_566608.1| 253 KRV---TGLGFDFTDPiePGNIFKFLQeegnvDDLEMYRTFNMGMGFLIILPEADAEKAAEMT--G---GKIVGKIVESG 324
                                   555...5677888777775556666666679***********************955555555..3...36899999874 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   7.2e-18   6.4e-14       4      94 .]      56     159 ..      23     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 7.2e-18
                                   EEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEE CS
                          AIRS   4 avvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvg 75 
                                   a++++td+++++vl+++       +G  ++a+n++Dl+a GA+P+ ++++lal+      ++++ +gl ++ae   +++vg
  gi|91773916|ref|YP_566608.1|  56 ALAMATDGVGSKVLIANEMKrwntVGIDCIAMNVNDLLAIGAEPISFVDYLALEkhsddFASQIGEGLVKGAEISRMSIVG 136
                                   5799***********664335788**********************************999******************** PP

                                   EEEEEESS....EEEEEEEEEEE CS
                          AIRS  76 Gdtsfsne....ptisvtavGlv 94 
                                   G+t+  +e    + ++ t++G+v
  gi|91773916|ref|YP_566608.1| 137 GETATLPEivngFDLAGTCLGMV 159
                                   ****9999888999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2253.26
//
Query:       gi|91773917|ref|YP_566609.1|  [L=469]
Description: aspartate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-46  158.9   0.5    1.6e-46  158.9   0.5    1.6  2  AA_kinase  Amino acid kinase family
    1.3e-27   95.3   3.7    1.8e-14   53.2   0.0    3.4  3  ACT_7      ACT domain
    1.5e-21   75.8   4.3    2.6e-11   43.1   0.0    2.9  3  ACT        ACT domain
  ------ inclusion threshold ------
      0.026   14.5   0.2       0.22   11.5   0.1    2.4  3  ACT_6      ACT domain
       0.11   12.9   0.8         11    6.5   0.1    2.5  2  MCM_lid    MCM AAA-lid domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.5   4.5e-50   1.6e-46       1     241 []       1     289 [.       1     289 [. 0.86
   2 ?   -1.9   0.1      0.56     2e+03      50      50 ..     364     364 ..     297     442 .. 0.58

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 4.5e-50
                                   TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC..............E.. CS
                     AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa..........glrstl 70 
                                   +r V+K+GG+s++d+++  +r++a+ +  +ke g ++v ++++ g++tdg+l+ +++ s++++ +          +     
  gi|91773917|ref|YP_566609.1|   1 MRYVMKFGGTSIADGKK--IRHVAQLLIGYKEGGDQVVAITSAlGGVTDGILTNAAEASQKGKVSqvkefmaelaK----- 74 
                                   789**************..***********************************4444444444234344444440..... PP

                                   HHHHHHHHH...............................................HHHHHHHHHHHHHHHHTTHGEEEE- CS
                     AA_kinase  71 eeagevatr...............................................dalaslgerlvaallaaglpavgls 104
                                           +                                               d++ s gerl   +++  ++++g++
  gi|91773917|ref|YP_566609.1|  75 --------KhydaisdaidneriadevietidiridelekaligicylgeltprsiDYISSYGERLAVPIISGSIRSMGID 147
                                   ........24444455555666666777779999*********************************************** PP

                                   GGGTCEECCCE......HHHTTTCEEECCHHHHHH....HTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSS CS
                     AA_kinase 105 aaaldateagr....degsdgnvesvdaeaieell....eagvvpvltgfigldeege...lgrgssDtiaallAealgAd 174
                                   +++++  eag+    ++g++++++  + ++i+e +    e+  +pv+tgfi+ d +g    lgrg+sD +a+l+++a++Ad
  gi|91773917|ref|YP_566609.1| 148 SKPFTGGEAGIntteNYGNARPLK-KSYAQIKEVVgplvEN-SIPVVTGFIAEDKNGIittLGRGGSDFTASLIGAAIQAD 226
                                   ************996555555544.4455555555443155.8************************************** PP

                                   EEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                     AA_kinase 175 kliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                                   +++++++V+G+++ dpk+vp a  +++is+ ea+e    l+++G+kv+hp+a+++a  +gipv+++n
  gi|91773917|ref|YP_566609.1| 227 EIWLWKEVHGIMTTDPKIVPEASTISQISYIEAME----LSYFGAKVLHPRAIEPAIIHGIPVRVKN 289
                                   ***********************************....**************************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.56
                                   H CS
                     AA_kinase  50 l 50 
                                    
  gi|91773917|ref|YP_566609.1| 364 S 364
                                   2 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.11   3.9e+02      24      38 ..     177     191 ..     173     193 .. 0.89
   2 !   39.6   0.8   9.1e-14   3.3e-10       4      64 ..     318     380 ..     315     381 .. 0.95
   3 !   53.2   0.0   5.1e-18   1.8e-14       3      65 .]     394     458 ..     392     458 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
                                   HHHHHHHHHTTT--- CS
                         ACT_7  24 vaklaspLaeagIsi 38 
                                   ++++++pL e+ I++
  gi|91773917|ref|YP_566609.1| 177 IKEVVGPLVENSIPV 191
                                   689**********98 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 9.1e-14
                                   EEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                         ACT_7   4 dgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                   ++++++++ g+g+ + ++G +ak+++ La+ag++i +iS   ++  +++++++++l++A++ L+
  gi|91773917|ref|YP_566609.1| 318 RNVAAINICGAGMVG-AIGTAAKIFTTLANAGVNIIMISqssSEANMSLVIEQSHLKRAIKSLE 380
                                   6899*********88.********************************************9996 PP

  == domain 3  score: 53.2 bits;  conditional E-value: 5.1e-18
                                   EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                         ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                   ++++ ++ vvg+g+++ ++G++ k++++L +++I++ +iS   +++ ++++V+eed+e+Av++Lh+
  gi|91773917|ref|YP_566609.1| 394 DEDVCVVAVVGAGMDG-SPGVAGKIFGALGKEKINVIMISqgsSQHNISFVVKEEDAEEAVKVLHR 458
                                   578889**********.************************************************6 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       2.7   9.7e+03      41      57 ..      90     106 ..      83     108 .. 0.45
   2 !   33.5   0.2     7e-12   2.5e-08      11      62 ..     334     379 ..     327     382 .. 0.89
   3 !   43.1   0.0   7.3e-15   2.6e-11       3      65 ..     403     459 ..     401     461 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                                   CEEEEEEEEEEHHHHHH CS
                           ACT  41 agivfvvivvdeedlee 57 
                                   a++v+ +i +  ++le+
  gi|91773917|ref|YP_566609.1|  90 ADEVIETIDIRIDELEK 106
                                   33444444444444443 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 7e-12
                                   TTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHH CS
                           ACT  11 PGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevleal 62 
                                    G++a++f++la++g+Ni++i+q+ss      ++++ +v+++++l+ +++ l
  gi|91773917|ref|YP_566609.1| 334 IGTAAKIFTTLANAGVNIIMISQSSS------EANMSLVIEQSHLKRAIKSL 379
                                   59************************......88999999999999998877 PP

  == domain 3  score: 43.1 bits;  conditional E-value: 7.3e-15
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                   +  g+ + PG+++++fgal++  iN+++i+q+ss       +++ +vv eed+ee+++ l++ 
  gi|91773917|ref|YP_566609.1| 403 VGAGMDGSPGVAGKIFGALGKEKINVIMISQGSS------QHNISFVVKEEDAEEAVKVLHRE 459
                                   66788999**************************......99999999999999999999876 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.3   1.5e+04      10      27 ..     198     215 ..     194     221 .. 0.60
   2 ?   11.5   0.1   6.1e-05      0.22      14      61 ..     335     382 ..     324     386 .. 0.87
   3 ?   -0.9   0.0      0.46   1.6e+03      12      45 ..     410     443 ..     404     460 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.3
                         ACT_6  10 pdrpGltasLtsvlaefg 27 
                                   +d+ G++  L +  ++f 
  gi|91773917|ref|YP_566609.1| 198 EDKNGIITTLGRGGSDFT 215
                                   577777776665544444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.1e-05
                         ACT_6  14 GltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarleka 61 
                                   G  a+++ +la  gvni+ i q+  + ++sL++  s  ++a++ le a
  gi|91773917|ref|YP_566609.1| 335 GTAAKIFTTLANAGVNIIMISQSSSEANMSLVIEQSHLKRAIKSLEHA 382
                                   7889***************************99777667777666655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.46
                         ACT_6  12 rpGltasLtsvlaefgvnilDieqavihgrlsLg 45 
                                    pG+  +++++l + ++n++ i q     + s++
  gi|91773917|ref|YP_566609.1| 410 SPGVAGKIFGALGKEKINVIMISQGSSQHNISFV 443
                                   5999999999999999999999997776666665 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.015        54      55      85 ..     351     381 ..     340     383 .. 0.91
   2 ?    6.5   0.1     0.003        11      55      84 ..     428     457 ..     426     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHHHTSSSE-HHHHHHHHHHHHH CS
                       MCM_lid  55 liRLseAlAklrlsevvteedveeairllke 85 
                                   +i +s++++  ++s v+++++ ++ai+ l++
  gi|91773917|ref|YP_566609.1| 351 IIMISQSSSEANMSLVIEQSHLKRAIKSLEH 381
                                   899***********************97765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.003
                                   HHHHHHHHHHHHTSSSE-HHHHHHHHHHHH CS
                       MCM_lid  55 liRLseAlAklrlsevvteedveeairllk 84 
                                   +i +s+ +++ ++s vv+eed+eea+++l+
  gi|91773917|ref|YP_566609.1| 428 VIMISQGSSQHNISFVVKEEDAEEAVKVLH 457
                                   68899999*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2832.25
//
Query:       gi|91773918|ref|YP_566610.1|  [L=405]
Description: hypothetical protein Mbur_1981 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   41.8  27.7    3.3e-06   26.4   9.3    2.9  3  S-layer   S-layer protein
    8.1e-05   22.0   1.0    0.00074   19.0   0.0    2.8  3  TcfC      E-set like domain
    0.00086   19.6   0.7       0.06   13.7   0.1    2.9  2  PA-IIL    Fucose-binding lectin II (PA-IIL)
     0.0022   19.0   0.1     0.0075   17.3   0.1    1.9  1  CopC      CopC domain
  ------ inclusion threshold ------
      0.038   14.0   0.7      0.038   14.0   0.7    2.3  3  CE2_N     Carbohydrate esterase 2 N-terminal
      0.056   13.7   0.6       0.57   10.5   0.1    2.4  2  DUF5599   Domain of unknown function (DUF5599)
       0.58   10.2   4.0        3.3    7.7   0.0    3.3  4  PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA syste


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 !   25.7   3.7     2e-09   5.1e-06     111     173 ..      35      98 ..      30     126 .. 0.74
   2 !   26.4   9.3   1.3e-09   3.3e-06      98     225 ..     135     257 ..     123     282 .. 0.83
   3 ?   -1.2   2.1      0.33   8.5e+02     150     220 ..     279     356 ..     253     358 .. 0.51

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2e-09
                       S-layer 111 ektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.dstyvyekdlgd 173
                                   e++++ g++l+L++gY+l+i +i+ ++  vw+e+ +dg+ v +   + +++   +y+ + + +d
  gi|91773918|ref|YP_566610.1|  35 ESVINIGTKLTLDQGYTLHIVDINENDGDVWVEVLRDGKVVKDGDGTGQEDdPFEYILTVEAED 98 
                                   678999***********************************98654443333334443333333 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.3e-09
                       S-layer  98 dekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyvyekdlgdeddvv 178
                                   +ekL+ +li + +++++  g++l+Leeg++l+ ++ D + + + ++L+k+g+ v + + +  ++ + +   k +++e   +
  gi|91773918|ref|YP_566610.1| 135 EEKLNDLLIYD-DSRSIDIGDELNLEEGFSLKASNYDDEEETITITLEKNGHLVKE-I-NDMEKGEIFSHYKAVNGEI-TT 211
                                   68999999976.7889************************************9975.5.55588999*9999999965.55 PP

                       S-layer 179 iiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksv 225
                                   i++  + + f +te+  v+++ + q +d ++e + + +++ +  + v
  gi|91773918|ref|YP_566610.1| 212 IVIATIYDFFDSTET-TVFLKEVTQREDVIIENNVEITVEGLAGNVV 257
                                   556678889999988.899***9999999888777766666655555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.33
                       S-layer 150 evdskvissska..dsty.vyekdlgd.eddvviiavhvdevfrgtedslvviegifq....isddvleieegdefgkm 220
                                    vd++ i+++k+  + +y  +++++   + +v+i +v+ d    ++eds  ++e        i ++ l++e+  ++++m
  gi|91773918|ref|YP_566610.1| 279 YVDDELIDTRKEvdEGKYpAVTEEMDAgKHEVTITIVSEDGSV-SSEDSSFTVEKSNSitetIKETSLDVENMSKIDEM 356
                                   3688888887777755552233344330233444444444433.44444445554333000144445666666666665 PP

>> TcfC  E-set 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   6.8e+02      15      25 ..      66      76 ..      54      78 .. 0.81
   2 ?   -1.1   0.1      0.54   1.4e+03      47      66 ..     244     264 ..     244     266 .. 0.85
   3 !   19.0   0.0   2.9e-07   0.00074      10      67 ..     271     329 ..     260     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.27
                          TcfC 15 veiyRdgqLls 25
                                  ve++Rdg++++
  gi|91773918|ref|YP_566610.1| 66 VEVLRDGKVVK 76
                                  78999998875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.54
                          TcfC  47 eveirvye.ngqvvrteqqkf 66 
                                   +vei v + +g+vvr++++ +
  gi|91773918|ref|YP_566610.1| 244 NVEITVEGlAGNVVRENERAI 264
                                   69999999999***9988766 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 2.9e-07
                          TcfC  10 pragrveiyRdgqLlstq.nvnaGnqeidtssLPsGiYeveirvyengqvvrteqqkft 67 
                                   + a+++ +y d++L++t+ +v+ G     t+++  G  ev+i ++++++ v++e + ft
  gi|91773918|ref|YP_566610.1| 271 NDASEIKVYVDDELIDTRkEVDEGKYPAVTEEMDAGKHEVTITIVSEDGSVSSEDSSFT 329
                                   6789***********98626**************************9999999888776 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 ?    3.1   0.0     0.044   1.1e+02      48      95 ..      55     103 ..      40     110 .. 0.72
   2 !   13.7   0.1   2.3e-05      0.06      12      73 ..     265     327 ..     255     349 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.044
                                   EEEE-TTSEEEEEEEETTEE-EEEEEEEEETTT.EEEEEEEEESSSSSS CS
                        PA-IIL  48 kvlnsgsGkvrvevsanGkpsklrsaqvtlekk.lnfaivgsedgtdnd 95 
                                     +n   G v vev  +Gk  k    + + ++   ++ +v +ed+ d+d
  gi|91773918|ref|YP_566610.1|  55 VDINENDGDVWVEVLRDGKVVKDGDGTGQEDDPfEYILTVEAEDDDDED 103
                                   5578899************988766665555542455667777776665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                                   EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEEEEE-TTSEEEEEEEE.TTEE-EEEEE CS
                        PA-IIL  12 tafanaaeqqtikvyiddelkatftgkgtrdkvlgtkvlnsgsGkvrvevsa.nGkpsklrsa 73 
                                   + +   ++  +ikvy+ddel +t ++    + +  t+ +++g+ +v +++++ +G  s+ +s+
  gi|91773918|ref|YP_566610.1| 265 IYYELDNDASEIKVYVDDELIDTRKEVDEGKYPAVTEEMDAGKHEVTITIVSeDGSVSSEDSS 327
                                   44555567789****************9999999**************876516776665554 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.9e-06    0.0075      33      92 .]     274     330 ..     252     330 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                          CopC  33 skvkvtdpdgkeevetvdaktveaelkvplpelaaGtYtVewrvvsaDGHpvsGsfsFtv 92 
                                   s++kv+  d+   + +++++ +e ++ +  +e++aG+++V+ ++vs+DG   s++ sFtv
  gi|91773918|ref|YP_566610.1| 274 SEIKVYVDDE---LIDTRKEVDEGKYPAVTEEMDAGKHEVTITIVSEDGSVSSEDSSFTV 330
                                   7788887776...223344444444444444666************************98 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 ?   -2.2   0.1       1.6   4.1e+03      38      57 ..      58      77 ..      41      85 .. 0.70
   2 ?   -2.2   0.0       1.6     4e+03      51      77 ..     171     197 ..     166     212 .. 0.75
   3 ?   14.0   0.7   1.5e-05     0.038      37      99 ..     260     329 ..     221     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                                  ..SSS-EEEEEEETTS--EE CS
                         CE2_N 38 kedkgknrlaviiDgkrvkd 57
                                  +e++g+ +++v+ Dgk vkd
  gi|91773918|ref|YP_566610.1| 58 NENDGDVWVEVLRDGKVVKD 77
                                  35789999999999998776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                                   TTS--EEEEE-SS-EEEEEEEEEEEEE CS
                         CE2_N  51 Dgkrvkdlkldgeektytlaeglepge 77 
                                   D++++++++l+++++ ++ +++ e+ge
  gi|91773918|ref|YP_566610.1| 171 DEEETITITLEKNGHLVKEINDMEKGE 197
                                   556677777777777676666666665 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.5e-05
                                   E.........SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE-S-GGG--EEEEEEE CS
                         CE2_N  37 d.......kedkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlvkrtEaeagkteflgfv 99 
                                   +       + d++ ++++v++D++ + + k  +e+k   + e+  +g+h+v+++  +E    + e   f+
  gi|91773918|ref|YP_566610.1| 260 NeraiiyyELDNDASEIKVYVDDELIDTRKEVDEGKYPAVTEEMDAGKHEVTITIVSEDGSVSSEDSSFT 329
                                   455555556678999**********8777777777757788999**********9999766555555555 PP

>> DUF5599  Domain of unknown function (DUF5599)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.25   6.5e+02      34      63 ..     150     180 ..     126     200 .. 0.68
   2 ?   10.5   0.1   0.00022      0.57      15      91 ..     260     331 ..     256     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                       DUF5599  34 lvvGDelrlkykgse.aeeWegeghvvkltd 63 
                                   + +GDel l+   s  a++++ e + +++t 
  gi|91773918|ref|YP_566610.1| 150 IDIGDELNLEEGFSLkASNYDDEEETITITL 180
                                   5578888887655543455555444444443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00022
                       DUF5599  15 nkkrlasFvlpkldsgelrlvvGDelrlkykgseaeeWegeghvvkltdssseevtleLrssskkaPtevttgFtve 91 
                                   n++ ++++ l + d +e+++ v Del+   k  ++ ++ +   v++ +d  ++evt+ + s+  +     ++ Ftve
  gi|91773918|ref|YP_566610.1| 260 NERAIIYYELDN-DASEIKVYVDDELIDTRKEVDEGKYPA---VTEEMDAGKHEVTITIVSE-DGSVSSEDSSFTVE 331
                                   889999****99.777**********98777777766655...5556666789****99887.77778888899987 PP

>> PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0013       3.3      48      84 ..      43      79 ..      32      86 .. 0.85
   2 ?   -2.5   0.0       1.8   4.7e+03     121     139 ..      88     106 ..      81     108 .. 0.80
   3 ?    1.8   0.2     0.089   2.3e+02      43      75 ..     149     181 ..     135     190 .. 0.83
   4 ?   -2.8   0.1       2.2   5.7e+03      65      88 ..     332     354 ..     326     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                                  HHHT...TT--EEEEEEEETTEEEEEECCGTEEEEES CS
                      PHD_like 48 kelldrgyklepeieeekdgevytltldelevyvegs 84
                                  k  ld+gy+l +++++e+dg+v+   l + +v+ +g+
  gi|91773918|ref|YP_566610.1| 43 KLTLDQGYTLHIVDINENDGDVWVEVLRDGKVVKDGD 79
                                  5678********************9999999998875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                                   HHHHHHHHHSSSHHHHHTT CS
                      PHD_like 121 ypYllrvllcedidevkel 139
                                   + Y+l v   +d+de k +
  gi|91773918|ref|YP_566610.1|  88 FEYILTVEAEDDDDEDKDY 106
                                   7799999999998887766 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.089
                                   EHHHHHHHT....TT--EEEEEEEETTEEEEEEC CS
                      PHD_like  43 stdllkell.drgyklepeieeekdgevytltld 75 
                                   s+d+ +el  ++g++l++    ++++++ t+tl+
  gi|91773918|ref|YP_566610.1| 149 SIDIGDELNlEEGFSLKASNYDDEEETI-TITLE 181
                                   56777887559******99988888888.99886 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.2
                                   EETTEEEEEECCGTEEEEESSHHH CS
                      PHD_like  65 kdgevytltldelevyvegstkee 88 
                                   k +++ t t++e+ + ve+ +k++
  gi|91773918|ref|YP_566610.1| 332 KSNSI-TETIKETSLDVENMSKID 354
                                   44555.889999999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2429.85
//
Query:       gi|91773919|ref|YP_566611.1|  [L=401]
Description: cofactor-independent phosphoglycerate mutase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-57  192.4   0.0    7.6e-57  191.9   0.0    1.2  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
    1.3e-41  142.6   0.0    1.5e-41  142.4   0.0    1.0  1  Metalloenzyme    Metalloenzyme superfamily
     0.0017   18.0   0.2     0.0038   16.9   0.0    1.5  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
  ------ inclusion threshold ------
       0.11   11.4   1.5       0.51    9.2   0.3    2.0  2  Alk_phosphatase  Alkaline phosphatase


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 !  191.9   0.0   1.7e-60   7.6e-57       2     170 .]      38     200 ..      37     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 1.7e-60
                                   HTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG-.- CS
                  PhosphMutase   2 kkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragrist 82 
                                   k+G  Gl+ +vpeg++pgSdvAn+s++Gydp+ yy+GR+plEA+++G+ l+ +dvafRcnl+t+  +dg+i+d++ag+i++
  gi|91773919|ref|YP_566611.1|  38 KNGLAGLAINVPEGYSPGSDVANMSVMGYDPALYYSGRAPLEAASMGIPLEVNDVAFRCNLITI--RDGLITDHSAGHITS 116
                                   7899************************************************************..59************* PP

                                   TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE..--S-B--S--..SSTTS------BS.SGGGHHHHHHHHHHHHH CS
                  PhosphMutase  83 eeakeLikalneel..eegvevkfypgveyrhllvl..lsdkitdtdpphdkegkeikellplkseeaketaellneliek 159
                                   eea+eLi+a++ el  e    +kfypg++yrhllv   +  +  d++pphd+ + ei++++p +    ++ +++l +lie 
  gi|91773919|ref|YP_566611.1| 117 EEARELIEAVDAELgsE---GLKFYPGISYRHLLVAsnGLGANADCTPPHDVIDGEINDHMP-R----GDGSDVLGKLIEG 189
                                   **************766...9*****************555569******************.7....99*********** PP

                                   HHHHHHHSHHH CS
                  PhosphMutase 160 sqeiLedhpvN 170
                                   s  iLe hp+N
  gi|91773919|ref|YP_566611.1| 190 SIPILEGHPIN 200
                                   **********9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.0   3.3e-45   1.5e-41       1     247 [.       1     396 [.       1     397 [. 0.95

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 3.3e-45
                                   -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........... CS
                                   xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                 Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........... 67 
                                   +k+++++ DG+++ p +el++   ++ A+tP++d+++k+       +  g+a  +pe+ +++s+v+++++           
  gi|91773919|ref|YP_566611.1|   1 MKYIILIGDGMADHPLEELGGmtaLQKANTPNMDQMTKN-------GLAGLAINVPEGYSPGSDVANMSVmgydpalyysg 74 
                                   5789***************99999***************.......89********************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|91773919|ref|YP_566611.1|  75 rapleaasmgiplevndvafrcnlitirdglitdhsaghitseearelieavdaelgseglkfypgisyrhllvasnglga 155
                                   ********************************************************************************* PP

                                   ..............................................HHHHTT-----EEEEEEEE-S---SSHHHHHT--E CS
                                   ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  68 ..............................................lrisetvkfahvtffwnggrsgyfnpleereeips 102
                                                                                 +rise++++++ ++fw++g  ++f ++e+ +++ +
  gi|91773919|ref|YP_566611.1| 156 nadctpphdvidgeindhmprgdgsdvlgkliegsipileghpineKRISEGKNPGNSVWFWGQGYAPSFRTFEDLYGLTG 236
                                   ********************************************************************************* PP

                                   EEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHH CS
                                   xxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme 103 dtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDe 163
                                    ++ ++dl                    + ++++v +ae a+  + ++  d+vvv+++ +D++GH gd+ea+ +aie++De
  gi|91773919|ref|YP_566611.1| 237 SVISAVDLimglgiyagldvievpgatgYLDTNYVGKAEFAMASL-KD-KDFVVVHVEAPDEAGHMGDIEAKLQAIEDFDE 315
                                   *********************************************.55.7******************************9 PP

                                   .HHHHHHTTS-T..TTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S--SSHHHHT....T-TTEEEE CS
                                   .xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                 Metalloenzyme 164 .avkeildaieq..vdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvkegakfre....kggLanva 237
                                     v+ +l a ++  +d ++vv++DH+++  + +        Ht epVP++++++  + d+v   ++f e    kg+L+ v+
  gi|91773919|ref|YP_566611.1| 316 kVVGTVLRAAREsdEDYTIVVLPDHPTPIALRT--------HTSEPVPFVMYSTL-E-DEVDDVETFDEdamkKGSLGIVR 386
                                   7899****99872246799**************........***********984.3.445555555555555******** PP

                                   GGGHHHHHHH CS
                                   xxxxxxxxxx RF
                 Metalloenzyme 238 atllnllgle 247
                                   +  l +l++e
  gi|91773919|ref|YP_566611.1| 387 GCDLVQLMME 396
                                   9999999887 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3     6e+03      16      32 ..      27      41 ..      19      45 .. 0.77
   2 !   16.9   0.0   8.4e-07    0.0038     165     232 ..     276     340 ..     245     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                  HHGSTSHHHHHHHHHSE CS
                  Phosphodiest 16 rlaellpnlaaLakegv 32
                                  +    +pn++++ k+g+
  gi|91773919|ref|YP_566611.1| 27 K--ANTPNMDQMTKNGL 41
                                  3..58999999999997 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.4e-07
                                   HHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHH.HHHHHHHHHHHHTTGTTTEEEEEEES- CS
                  Phosphodiest 165 vlekelekpdlllvyleetDtvgHkfGpdspevedalrrvD.kaigdLlealderglsaetniilvSDH 232
                                   +++++l++ d+++v++e++D +gH  G d ++ ++a+++ D k++g  l+a++e   +++++i+++ DH
  gi|91773919|ref|YP_566611.1| 276 FAMASLKDKDFVVVHVEAPDEAGH-MG-DIEAKLQAIEDFDeKVVGTVLRAARES--DEDYTIVVLPDH 340
                                   334444999***************.55.66778999*****44689999999999..***********9 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.037   1.7e+02       5      17 ..       4      16 ..       2      42 .. 0.78
   2 ?    9.2   0.3   0.00011      0.51     260     324 ..     292     358 ..     274     382 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.037
                                  EEEEETT-SHHHH CS
               Alk_phosphatase  5 illigDGmgvstv 17
                                  i+ligDGm++  +
  gi|91773919|ref|YP_566611.1|  4 IILIGDGMADHPL 16
                                  99******98655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00011
                                   TCHHHHHHTTTHHHHHHHHHHHHHH.HHHHHHHCHH.CTTEEEEEEESSEESEEEESTTSTT..TTS CS
               Alk_phosphatase 260 srIDhaaHendavgalsEvvefdeA.vkaalefakk.eketlvvvTaDHshvfsfggyttrgesvlg 324
                                      D+a+H +d+  +l+ + +fde  v ++l +a++ +++  +vv  DH + + +  +t ++   + 
  gi|91773919|ref|YP_566611.1| 292 EAPDEAGHMGDIEAKLQAIEDFDEKvVGTVLRAAREsDEDYTIVVLPDHPTPIALRTHTSEPVPFVM 358
                                   5569******************986167888888777888899999*****9999998888654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 3262.75
//
Query:       gi|91773920|ref|YP_566612.1|  [L=153]
Description: heat shock protein Hsp20 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-22   79.1   2.8    2.6e-22   78.9   2.8    1.1  1  HSP20       Hsp20/alpha crystallin family
    2.4e-11   43.0   0.0    3.4e-11   42.5   0.0    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00017   22.6   0.6    0.00026   21.9   0.6    1.3  1  CS          CS domain
  ------ inclusion threshold ------
      0.026   14.6   3.0        2.1    8.5   0.4    2.4  2  FKBP26_C    FKBP26_C-terminal
      0.079   13.0   0.1       0.44   10.6   0.1    2.0  2  GvpH        GvpH
       0.11   12.9   0.0       0.16   12.5   0.0    1.2  1  DUF2718     Protein of unknown function (DUF2718)


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 !   78.9   2.8   8.7e-26   2.6e-22       1      99 [.      53     152 ..      53     153 .] 0.92

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.7e-26
                                   E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEEEETT CS
                         HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkaslkdG 79 
                                   dikee+++  v+ d+pg++ke+++++v++n + +++e +  +e e+e ++ ker++++Fsr+  LP  v ++ vka+l+ G
  gi|91773920|ref|YP_566612.1|  53 DIKEEDNNVIVTTDLPGIDKEDVEISVNNNILEIHAEFKkeSESEKEGYVQKERTYSSFSRSAVLPSVVSDEGVKAKLEAG 133
                                   79**********************************9886677788889999***************************** PP

                                   EEEEEEEBSS--..------ CS
                         HSP20  80 vLtvtvpkkepekkkkerki 99 
                                   vLt+t+pk+++e+k +++ki
  gi|91773920|ref|YP_566612.1| 134 VLTITLPKTKAEEK-TKIKI 152
                                   ***********976.55555 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 !   42.5   0.0   1.1e-14   3.4e-11       1      63 []      58     139 ..      58     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.1e-14
                    ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedgvLeI 61 
                                   d++++++ dLP++dke++++s +++ L I+++                    +f+R+ +LPsv++++ v +Ak+e gvL+I
  gi|91773920|ref|YP_566612.1|  58 DNNVIVTTDLPGIDKEDVEISVNNNILEIHAEfkkesesekegyvqkertysSFSRSAVLPSVVSDEGV-KAKLEAGVLTI 137
                                   67899**************************************************************99.*********** PP

                    ArsA_HSP20  62 rF 63 
                                   ++
  gi|91773920|ref|YP_566612.1| 138 TL 139
                                   96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.6   8.8e-08   0.00026       7      76 .]      56     141 ..      51     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.8e-08
                                   EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE..TS.CEEEEECE..................BSS-BETTTEEEEEE CS
                            CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki..gk.eklliege..................LfgpIdpeesswtie 66 
                                   +++++V+vt  ++++  +k+dv+++ +++ l+++   +k  +    ++                  L + +  e  + ++e
  gi|91773920|ref|YP_566612.1|  56 EEDNNVIVTTDLPGI--DKEDVEISVNNNILEIHAefKKeSES---EKegyvqkertyssfsrsavLPSVVSDEGVKAKLE 131
                                   7899**********9..*****************954442333...22577****************************** PP

                                   TTEEEEEEEB CS
                            CS  67 skkveitLkK 76 
                                   +  + itL K
  gi|91773920|ref|YP_566612.1| 132 AGVLTITLPK 141
                                   ********98 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4    0.0007       2.1       6      33 ..      60      87 ..      55      91 .. 0.86
   2 ?    6.4   0.1    0.0031       9.4      19      37 ..     124     142 ..     115     153 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0007
                                  HHHHHHH-TT--..--EEEEETTEEEEE CS
                      FKBP26_C  6 kelIkryiPnidlekfkieiedktvtIe 33
                                    ++   +P id+e+++i++++++++I 
  gi|91773920|ref|YP_566612.1| 60 NVIVTTDLPGIDKEDVEISVNNNILEIH 87
                                  5688889****************99985 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0031
                                   .--EEEEETTEEEEE--TT CS
                      FKBP26_C  19 ekfkieiedktvtIelpee 37 
                                   e +k ++e +++tI+lp++
  gi|91773920|ref|YP_566612.1| 124 EGVKAKLEAGVLTITLPKT 142
                                   67999************97 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00015      0.44      99     123 ..      57      81 ..      52      98 .. 0.82
   2 ?    0.1   0.0      0.25   7.4e+02     107     131 ..     115     138 ..     105     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                          GvpH  99 dsdelvvvadlpGvtdedvdvalet 123
                                   + ++++v +dlpG+  edv+++++ 
  gi|91773920|ref|YP_566612.1|  57 EDNNVIVTTDLPGIDKEDVEISVNN 81 
                                   456788889************9983 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.25
                          GvpH 107 adlpGvtded.vdvaletdeqaltlr 131
                                   a lp v  ++ v + le   + lt++
  gi|91773920|ref|YP_566612.1| 115 AVLPSVVSDEgVKAKLE--AGVLTIT 138
                                   66888765555999999..6777775 PP

>> DUF2718  Protein of unknown function (DUF2718)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.3e-05      0.16      44      87 ..      51      95 ..      36     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                       DUF2718 44 lpdpkkdddavivpddlppepkekikek.dngagvvekaikteen 87
                                  l+d k +d+ viv  dlp + ke ++ + +n+  +++   k e +
  gi|91773920|ref|YP_566612.1| 51 LMDIKEEDNNVIVTTDLPGIDKEDVEISvNNNILEIHAEFKKESE 95
                                  4678999****************9986614455567776666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.51
# Mc/sec: 897.92
//
Query:       gi|91773921|ref|YP_566613.1|  [L=251]
Description: F420-0--gamma-glutamyl ligase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-58  198.1   2.2    1.8e-58  197.8   2.2    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 !  197.8   2.2     1e-62   1.8e-58       4     244 .]       9     218 ..       8     218 .. 0.99

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 1e-62
                                   -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H............ CS
                   F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsliLk 84 
                                   +plikegd++a++++e+ +      e++D++v+++++vak+e  ++  + i pse+A  +a+k+ ++dp            
  gi|91773921|ref|YP_566613.1|   9 LPLIKEGDNIAAMICERTQ-----PESHDVIVIASTIVAKSEAATILKDAIIPSERAVAMAKKC-GTDP------------ 71 
                                   79****************9.....89**************************************.****............ PP

                                   ......HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHHHHHS CS
                   F420_ligase  85 alakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklkertg 163
                                         + v+vvl+++ + + +  +l++e+         G++  nagid+snv++++ + +P+dpd sa++i  +++e +g
  gi|91773921|ref|YP_566613.1|  72 ------ALVQVVLDNSVEQIVEfpVLLVEN-------LNGHVSINAGIDDSNVDDRYFLHMPHDPDGSAKSIGLHIAELCG 139
                                   ......9***********999999999999.......99****************************************** PP

                                   ---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EEEEES CS
                   F420_ligase 164 kdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGsadegtPvvlvrg 244
                                   kdv+V+i  +D++gr+++ ++++va+g++g+++++d+rg+kdl+gk l++t++av+de++s+a+L++G+a  +tPvv+vrg
  gi|91773921|ref|YP_566613.1| 140 KDVSVII--TDTNGRAFKIGQTGVAVGVYGVHPIKDWRGEKDLFGKVLEITEEAVADEIASAANLLMGEAAGSTPVVIVRG 218
                                   *******..***********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1491.63
//
Query:       gi|91773922|ref|YP_566614.1|  [L=151]
Description: CMP/dCMP deaminase, zinc-binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  100.1   3.8      1e-28   99.2   3.8    1.4  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.2e-19   70.4   1.0    1.8e-19   69.9   1.0    1.2  1  MafB19-deam      MafB19-like deaminase
     0.0011   18.9   0.6     0.0014   18.6   0.6    1.3  1  APOBEC_N         APOBEC-like N-terminal domain
     0.0029   17.7   1.6     0.0053   16.8   0.7    1.7  2  Bd3614-deam      Bd3614-like deaminase
      0.008   15.8   0.1      0.011   15.4   0.1    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.021   14.9   0.1    1.3  1  XOO_2897-deam    Xanthomonas XOO_2897-like deaminase
      0.097   12.7   0.6       0.13   12.3   0.6    1.2  1  NAD1             Novel AID APOBEC clade 1
        0.1   12.7   0.3       0.16   12.1   0.3    1.2  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
        1.5    8.8   7.1       0.88    9.5   4.4    2.1  2  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)


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 !   99.2   3.8     5e-32     1e-28       3     100 ..       7     125 ..       5     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 5e-32
                                   HHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.......................TTB-HHHHHHH CS
               dCMP_cyt_deam_1   3 kdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.......................ktiHAEvnAil 60 
                                    de++le+a  ++k++ +c + kVGaviv+n++i+stgyng p + +                       + +HAE+nAi+
  gi|91773922|ref|YP_566614.1|   7 IDEYFLEIASVVSKRS-TCLRNKVGAVIVRNKRILSTGYNGAPSNMEhcleigcirqqnniasgtrhekcRAVHAEQNAII 86 
                                   689*************.**************************9999********************************** PP

                                   HHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
               dCMP_cyt_deam_1  61 kaaknggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                   +aa   g+++ gat+y+t++PC  Cak+ii+s+i kvv+ 
  gi|91773922|ref|YP_566614.1|  87 QAALH-GVSIGGATVYCTHQPCILCAKMIINSNITKVVYS 125
                                   ***88.899*****************************97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   1.0     9e-23   1.8e-19       4     106 ..       8     131 ..       6     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 9e-23
                   MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsn.......................ekelnakataHaEiaalqqA 61 
                                   +++f ++++ v+k++ +   k+gaviv +k+++ +g+n                        +  ++    HaE +a+ qA
  gi|91773922|ref|YP_566614.1|   8 DEYFLEIASVVSKRSTCLRNKVGAVIVRNKRILSTGYNgapsnmehcleigcirqqnniasGTRHEKCRAVHAEQNAIIQA 88 
                                   689999*************************************************9999984445677788********** PP

                   MafB19-deam  62 akklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks 106
                                   a  + s+   +at+y t++pC  Ca++i+++++ k+vy +++p++
  gi|91773922|ref|YP_566614.1|  89 ALHGVSI--GGATVYCTHQPCILCAKMIINSNITKVVYSTSYPDT 131
                                   6666555..********************************9997 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 !   18.6   0.6     7e-07    0.0014      19      94 ..      53     116 ..      15     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7e-07
                                   EEEEEEEEESSSEEEEEEEEEEE-..SSTBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHH CS
                      APOBEC_N  19 lcyeVkrssgkrklskkGvLrnqsgaaaskHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaa 94 
                                    c+e+ + ++++ +  +G  r +++     HaE+    +i +++l    +    t+Y++ +PC      Ca+++ +
  gi|91773922|ref|YP_566614.1|  53 HCLEIGCIRQQNNI-ASGT-RHEKCR--AVHAEQN---AIIQAALH-GVSIGGATVYCTHQPCIL----CAKMIIN 116
                                   57788887777766.7777.667766..79***99...44445555.7999**************....****986 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.9   1.8e+03      33      45 ..      76      88 ..      62      97 .. 0.75
   2 !   16.8   0.7   2.7e-06    0.0053      77     112 ..      97     125 ..      87     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.9
                   Bd3614-deam 33 kvLHAEvnLlapl 45
                                  + +HAE n ++++
  gi|91773922|ref|YP_566614.1| 76 RAVHAEQNAIIQA 88
                                  5689999977654 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.7e-06
                   Bd3614-deam  77 garllvtlqcCkmCAalvvaaadapgrevllkvvYl 112
                                   ga+++ t+q+C +CA ++++          +kvvY+
  gi|91773922|ref|YP_566614.1|  97 GATVYCTHQPCILCAKMIINSNI-------TKVVYS 125
                                   89****************98654.......455554 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 !   15.4   0.1   5.6e-06     0.011      89     140 ..      54     105 ..      52     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.6e-06
                                   -CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES- CS
               Methyltr_RsmB-F  89 CsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCs 140
                                   C   g ir+++++    + +   +++  q+++++aa++ +  gG  vY+T  
  gi|91773922|ref|YP_566614.1|  54 CLEIGCIRQQNNIASGTRHEKCRAVHAEQNAIIQAALHGVSIGGATVYCTHQ 105
                                   777899*********99********************************954 PP

>> XOO_2897-deam  Xanthomonas XOO_2897-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.1e-05     0.021      22      88 ..      71     132 ..      60     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                 XOO_2897-deam  22 rsskggvmHsEekllqqleeagvepakvlelytErepClpgneCakllkeslkevevthsvdygkea 88 
                                   r+ k +  H+E++ + q++ +gv+ +    +y   +pC     Cak++ +s    +v +s +y +++
  gi|91773922|ref|YP_566614.1|  71 RHEKCRAVHAEQNAIIQAALHGVSIGGA-TVYCTHQPC---ILCAKMIINSNI-TKVVYSTSYPDTD 132
                                   56677888************99998875.6********...******988765.6666666666655 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   6.7e-05      0.13      33      91 ..      61     116 ..      41     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                          NAD1  33 kssssllkGvlenesk.cHaEllflnkikslklldpsqkykvtwylswSPCseCasklae 91 
                                   ++++++  G  +++ + +HaE+  + +    +l +  ++   t+y+++ PC  Ca+ +++
  gi|91773922|ref|YP_566614.1|  61 RQQNNIASGTRHEKCRaVHAEQNAIIQA---AL-HGVSIGGATVYCTHQPCILCAKMIIN 116
                                   456666666666633324***9875555...44.66689999*************99976 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   7.9e-05      0.16      15      62 ..      71     116 ..      57     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                         SNAD4  15 gvlknkke.haEllflekikseldpsqeyrvtwylswsPCaeCaekiae 62 
                                   +  ++++  haE + + +    l+       t+y +  PC  Ca+ i++
  gi|91773922|ref|YP_566614.1|  71 R-HEKCRAvHAEQNAIIQA--ALHGVSIGGATVYCTHQPCILCAKMIIN 116
                                   2.2333337****999888..7888888999**************9986 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 ?   -4.1   0.0       7.8   1.6e+04      24      28 ..      23      27 ..      22      29 .. 0.62
   2 ?    9.5   4.4   0.00044      0.88      12      34 ..      83     118 ..      54     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 7.8
                                  HHHHH CS
                      zf-C3HC4 24 kCirk 28
                                  +C+r+
  gi|91773922|ref|YP_566614.1| 23 TCLRN 27
                                  57665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00044
                                   E...............E-TTS--B-CHHHHHHHHCTS CS
                      zf-C3HC4  12 n..............elleCkHsfCskCirkilksrk 34 
                                   n               +  C+H+ C  C + i++ ++
  gi|91773922|ref|YP_566614.1|  83 NaiiqaalhgvsiggATVYCTHQPCILCAKMIIN-SN 118
                                   4455555566666667899**************9.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 961.46
//
Query:       gi|91773923|ref|YP_566615.1|  [L=300]
Description: preprotein translocase subunit SecF [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-36  124.4  13.5    5.5e-36  123.7  13.5    1.3  1  SecD_SecF  Protein export membrane protein
    0.00017   19.8  11.1    0.00025   19.3  11.1    1.2  1  Patched    Patched family
     0.0068   15.9   0.0      0.014   14.8   0.0    1.6  1  Sec_GG     SecD/SecF GG Motif


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 !  123.7  13.5   9.2e-40   5.5e-36       6     187 ..     105     290 ..     100     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 9.2e-40
                                   T--SSS-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HH CS
                     SecD_SecF   6 lkevdkdaekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdla 85 
                                    k++ ++++ ++++ +g+ ++kel+++a++al +++++++++v+l+F+  v++ a+++ +++D+ i++g++ l+gie++l 
  gi|91773923|ref|YP_566615.1| 105 EKAITSKYSSVEIKQIGALYGKELQTQALIALCLSFIGMALVVFLIFRTAVPSLAVVLsAFSDIAIAIGFMNLVGIELSLG 185
                                   45566689999******************************************9999879********************* PP

                                   HHHHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHH.....HHHHHHHHHHHHTTTTHHHH CS
                     SecD_SecF  86 tvaalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslt.....tllvvvallllggdslkdfa 161
                                   tvaalL++iGYSv++++++++rv ++ r + ++++ +++ +++++t t t+++ ++     t+ ++v+  +   + l+d+a
  gi|91773923|ref|YP_566615.1| 186 TVAALLMLIGYSVDSDILLTTRVLKR-RGSPDENIGRAMHTGITMTTT-TLAALVVmyvvsTFSYLVTSSVSQINLLSDIA 264
                                   *************************9.67799***********99988.77777764444466666666666669****** PP

                                   HHHHHHTSTTTTTHHHHHHHHHHHHH CS
                     SecD_SecF 162 lallvGlivgtyssifiasplllllk 187
                                   ++l++Gl+++ ++++++++++l +  
  gi|91773923|ref|YP_566615.1| 265 IVLIFGLAADLMNTWLLNTGILRWHV 290
                                   **********************9865 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3  11.1   4.1e-08   0.00025     654     777 ..     127     245 ..     118     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.1e-08
                       Patched 654 tilpstiqnivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiaya 734
                                   +++++++  + l+++ m++v +l+    + +l+++ls  s     iGf+ l g++L   ++++++m iG+svd     + +
  gi|91773923|ref|YP_566615.1| 127 ELQTQALIALCLSFIGMALVVFLIFRTAVPSLAVVLSAFSDIAIAIGFMNLVGIELSLGTVAALLMLIGYSVDSDILLTTR 207
                                   68889999999************99999999999999999777789*********************************** PP

                       Patched 735 fvrsekddakeRvvealealgwPvvqgalSTilgvlvLlfvds 777
                                     + ++ +++e + +a+ + g  +    + T+++++v+++v +
  gi|91773923|ref|YP_566615.1| 208 VLKRRG-SPDENIGRAMHT-GITMT---TTTLAALVVMYVVST 245
                                   999999.999999999987.55554...456666666666654 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.4e-06     0.014       4      27 ..      43      66 ..      40      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-06
                                  HHC--EE-TTTS-EEEEEEEE-TT CS
                        Sec_GG  4 ftkGlNLGlDFtGGthielqfdqp 27
                                  ++ +++LG +F GGt+i  +++ +
  gi|91773923|ref|YP_566615.1| 43 TGAPVKLGMEFEGGTMIAFETQES 66
                                  67799************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1940.43
//
Query:       gi|91773924|ref|YP_566616.1|  [L=564]
Description: preprotein translocase subunit SecD [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-14   53.0  10.3    5.3e-14   52.0  10.3    1.4  1  SecD_SecF   Protein export membrane protein
  ------ inclusion threshold ------
      0.029   13.8   0.0      0.079   12.5   0.0    1.8  1  Sec_GG      SecD/SecF GG Motif
       0.04   14.0   2.5       0.11   12.7   2.5    1.7  1  Podoplanin  Podoplanin
       0.05   12.5  17.0      0.097   11.6  17.0    1.4  1  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 !   52.0  10.3   1.2e-17   5.3e-14      20     173 ..     396     546 ..     385     555 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.2e-17
                                   EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH.HHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSH CS
                     SecD_SecF  20 tvgpsvskelaekavlallialvliliyvalrFewr.valaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvn 99 
                                    v++ ++ +++++++la l+al++++ +v+ r++++ + l  + + +  vi+++g+  +++ ++dla++a+++  iG  ++
  gi|91773924|ref|YP_566616.1| 396 QVDAALGAQFKRQVALAGLFALLAVAAVVFRRYHQKeILLPMVGTSICEVIMILGFAGAVNWQLDLAAIAGIIAAIGTGID 476
                                   6999****************************98761556667779*********************************** PP

                                   HHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTT CS
                     SecD_SecF 100 dtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgty 173
                                     v+++d v  + +     + +++  + +++ +    ++ +tt++++  l+++g ++l++fa++ +vG+++g++
  gi|91773924|ref|YP_566616.1| 477 HLVIITDEVLYEGK----LPSTKVYMERITKAFAIIFAAAATTMIAMSPLVIMGFGALRGFAITTIVGVLIGVL 546
                                   *********99844....566666666777777777779999999***************************96 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05     0.079       8      25 ..      44      61 ..      44      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                  -EE-TTTS-EEEEEEEE- CS
                        Sec_GG  8 lNLGlDFtGGthielqfd 25
                                  lN+GlD+ GG+ i+++ +
  gi|91773924|ref|YP_566616.1| 44 LNYGLDLEGGSWIQIKLQ 61
                                  8**********9888877 PP

>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.5   2.4e-05      0.11     125     155 ..     532     562 ..     529     564 .] 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Podoplanin 125 GLatvtLvgiivGvllaigfiggiiivvvrk 155
                                   G a+ t+vg+++Gvl+a  + g +i vv+ k
  gi|91773924|ref|YP_566616.1| 532 GFAITTIVGVLIGVLIARPVYGKVIKVVLDK 562
                                   8999************************977 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  17.0   2.2e-05     0.097     145     293 ..     406     550 ..     362     559 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                          MMPL 145 lklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvl.liavGtDYallLvs 224
                                    + + +++l  +l++ ++v+r      ++l +v++s+      ++il ++ +++ +   ++++ ++ +i++G+D  ++++ 
  gi|91773924|ref|YP_566616.1| 406 KRQVALAGLFALLAVAAVVFRRYHQKEILLPMVGTSICEV---IMILGFAGAVNWQLDLAAIAGIIaAIGTGIDHLVIITD 483
                                   34456677778888999999999999*******9998654...45577777777777777776555279******999887 PP

                          MMPL 225 RyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlT 293
                                       e +  +++   +++ ++++   ++aa++t +iam  Lv++ +++l++++++  +Gvl+ vli++ 
  gi|91773924|ref|YP_566616.1| 484 EVLYEGKLPSTK--VYMERITKAFAIIFAAAATTMIAMSPLVIMGFGALRGFAITTIVGVLIGVLIARP 550
                                   666655555555..788899999999****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 3160.50
//
Query:       gi|91773925|ref|YP_566617.1|  [L=341]
Description: replication factor C small subunit 2 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-12   45.0   0.0    1.7e-11   44.1   0.0    1.4  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
    3.5e-10   40.2   0.2    7.1e-10   39.2   0.2    1.5  1  Rep_fac_C        Replication factor C C-terminal domain
    2.6e-09   37.6   0.0      1e-08   35.7   0.0    2.0  2  AAA              ATPase family associated with various cellul
    5.7e-05   23.2   0.0    0.00031   20.8   0.0    2.0  1  AAA_14           AAA domain
    0.00099   19.1   0.0     0.0018   18.2   0.0    1.4  1  Rad17            Rad17 P-loop domain
     0.0098   16.2   0.3      0.055   13.8   0.0    2.2  2  AAA_assoc_2      AAA C-terminal domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.066   13.6   0.0    2.0  1  AAA_16           AAA ATPase domain
      0.017   14.9   0.0        4.3    7.1   0.0    3.1  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.043   13.5   0.0      0.096   12.4   0.0    1.6  1  AAA_24           AAA domain
       0.09   13.1   0.0       0.48   10.7   0.0    2.1  2  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> 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 !   44.1   0.0   9.7e-15   1.7e-11       6     159 ..      24     183 ..      19     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 9.7e-15
               DNA_pol3_delta2   6 lkilskalksgrlahayLfeGdegigkkelalnlakallceeknetk....pcgecksckkieqgkhpDvivieteekers 82 
                                   ++ l + + sg+l h ++f+G+ ++gk ++a++la +l  e  +++     + +  ++ k+    +   v++i+t++  ++
  gi|91773925|ref|YP_566617.1|  24 VNSLVHLVGSGNLPH-LVFHGPVNSGKSSTAFALAYELYGEYYENNFtyfnASDFFDQGKRYLVRDKRFVHIIGTDDP-KK 102
                                   666777777888888.68**********************99877656444444445555555555555777788877.44 PP

               DNA_pol3_delta2  83 ikldqi...relieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkf 159
                                   i    i   +e+i+e+  ++   + +kii i+++e +++ A+ al +++E   +   fiL t++++kl+ ++rSR  el f
  gi|91773925|ref|YP_566617.1| 103 IYSSVIsifKEVINEFAGMGSLdADYKIIFIDNVESLETGAQHALRRIMEKYTRTCRFILSTTQPSKLIAPLRSRGLELFF 183
                                   444333111577777776665549***************************************************999877 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 !   39.2   0.2     4e-13   7.1e-10       5      86 ..     257     337 ..     254     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 4e-13
                                   HHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHHHHHH CS
                     Rep_fac_C   5 eieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlqlsal 85 
                                    ++e+ +a+ + d+ +a+k +++ll+e+G+ ++++l+qlh vv+e+ +++ ++   i  +++++++ +++ a+++++l+ l
  gi|91773925|ref|YP_566617.1| 257 NVTELHNAAIEHDVLKARKLIDTLLIEEGFTGDEVLQQLHSVVVESGRVEGEVAKAIC-RIADTDAMVIDSANPRIHLEKL 336
                                   577888888889*********************************8546666666666.5*******************99 PP

                                   H CS
                     Rep_fac_C  86 l 86 
                                   +
  gi|91773925|ref|YP_566617.1| 337 V 337
                                   7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   5.7e-12     1e-08       2     123 ..      40     177 ..      39     184 .. 0.79
   2 ?   -2.0   0.0       2.5   4.5e+03      10      31 ..     238     263 ..     235     284 .. 0.53

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.7e-12
                                   EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS..........................STTHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellsk..........................yvgesekkirelfk 51 
                                   +++Gp   GK+++a a+a el     + +f  +++s+++++                          +++  ++ i+e+  
  gi|91773925|ref|YP_566617.1|  40 VFHGPVNSGKSSTAFALAYELygeyyENNFTYFNASDFFDQgkrylvrdkrfvhiigtddpkkiyssVISIFKEVINEFAG 120
                                   79******************95444448899999999997789**********9998887777555333333333333332 PP

                                   HHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTT CS
                           AAA  52 eakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgR 123
                                             + +i+fiD++++l +             + +L + ++++++   ++ +i+ t++p+kl  +l+ +R
  gi|91773925|ref|YP_566617.1| 121 M----GsldaDYKIIFIDNVESLETGA-----------QHALRRIMEKYTR---TCRFILSTTQPSKLIAPLR-SR 177
                                   2....1455456***********7777...........*************...69*****************.77 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                                   SHHHHHHHHHHHH....THEEEEEET CS
                           AAA  10 GKTllakavakel....gvefleisg 31 
                                   GKT++ + + +e+    + ++ e+  
  gi|91773925|ref|YP_566617.1| 238 GKTITGEILYEEAlgdvSKNVTELHN 263
                                   67777766666643222233333333 PP

>> AAA_14  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   0.00031       5     102 ..      39     167 ..      37     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                        AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderd..................kkladpe....kllelileklk 61 
                                   lv  G+  +GK+  ++ l++el+    ++++ y+n  d  d                  +   dp+    +++++++e ++
  gi|91773925|ref|YP_566617.1|  39 LVFHGPVNSGKSSTAFALAYELYgeYYENNFTYFNASDFFDqgkrylvrdkrfvhiigtD---DPKkiysSVISIFKEVIN 116
                                   6778999*****************9999*******9997776666666665555553330...333333333444444333 PP

                        AAA_14  62 e........ekktylflDEiqevpe.wekalkslvdeg.knldvivtGSns 102
                                   e         + +++f+D +  +++ +++al+++++++ + +++i++  + 
  gi|91773925|ref|YP_566617.1| 117 EfagmgsldADYKIIFIDNVESLETgAQHALRRIMEKYtRTCRFILSTTQP 167
                                   37778898878889********9754999*******997889999987665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     1e-06    0.0018       6     164 ..       2     159 ..       1     167 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                         Rad17   6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepd 86 
                                   n+lW  ky+P+k+e++    + ++ + + + +  L++     L+  GP   gks +   L+ el  ++ e+ n + ++ +d
  gi|91773925|ref|YP_566617.1|   2 NDLWTVKYRPQKLEDIVGNGESVNSLVHLVGSGNLPH-----LVFHGPVNSGKSSTAFALAYELYGEYYEN-NFTYFNASD 76 
                                   689**************99999999999999999987.....599*******************9999997.777888888 PP

                         Rad17  87 nqksdfkgltekesrf.............lsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalre 154
                                   +  +  + l+  ++rf              s i  fke+ ++  ++  +      l +d k+i+++++ +   +  +alr 
  gi|91773925|ref|YP_566617.1|  77 FFDQGKRYLV-RDKRFvhiigtddpkkiySSVISIFKEV-IN--EFAGMG----SLDADYKIIFIDNVESLETGAQHALRR 149
                                   8555544444.4455767788887888878999999999.32..333344....6889*********************** PP

                         Rad17 155 virkylrsse 164
                                   ++ ky r+ +
  gi|91773925|ref|YP_566617.1| 150 IMEKYTRTCR 159
                                   ****988765 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.1e-05     0.055       2      41 ..     201     249 ..     200     281 .. 0.75
   2 ?   -0.4   0.0      0.85   1.5e+03       7      23 ..     305     321 ..     301     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                                   XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........X CS
                   AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaaeak.........e 41 
                                   +++++++dd ++al+ +a+G + kaL +L++a+ ++  k         e
  gi|91773925|ref|YP_566617.1| 201 KEAISISDDGYDALLYYAGGNVSKALLTLQFAVMNHPGKtitgeilyeE 249
                                   56899***************************99987654444444440 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.85
                                   XXXXXXXXXXXXXXXXX CS
                   AAA_assoc_2   7 leddalealaeladGDa 23 
                                   +e ++ +a++++ad Da
  gi|91773925|ref|YP_566617.1| 305 VEGEVAKAICRIADTDA 321
                                   678999**********8 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   3.7e-05     0.066      12     160 ..      24     152 ..      19     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-05
                        AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalareellrqlldeae 90 
                                   ++s+++ v sg  + ++++G+  +GKss + +l+ +l ++  +  f++ ++ ++     +++  ++l r++ +  +     
  gi|91773925|ref|YP_566617.1|  24 VNSLVHLVGSGNLPHLVFHGPVNSGKSSTAFALAYELYGEyyENNFTYFNASDF-----FDQGKRYLVRDKRFVHIIGT-- 97 
                                   6788999999999*****************777766666633122233333333.....22233334444444444433.. PP

                        AAA_16  91 saeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlr 160
                                        ++++k+ +++           s + e++++++   s d++  ++++D+++ ++++ +++l+ +++
  gi|91773925|ref|YP_566617.1|  98 -----DDPKKIYSSVI----------SIFKEVINEFAGMGSLDADYKIIFIDNVESLETGAQHALRRIME 152
                                   .....56677777777..........99999999999666666888999999999999999999998876 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 ?    7.1   0.0    0.0024       4.3       2      58 ..      10      61 ..       9      68 .. 0.85
   2 ?    3.8   0.1     0.024        43      83     112 ..     126     155 ..      92     164 .. 0.85
   3 ?   -1.3   0.0       0.9   1.6e+03     136     152 ..     161     177 ..     156     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0024
                        RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelg 58
                                  rP++le+ +g  +  ++l  ++ +      +l h++++Gp   Gk++ a  +a el 
  gi|91773925|ref|YP_566617.1| 10 RPQKLEDIVGNGESVNSLVHLVGS-----GNLPHLVFHGPVNSGKSSTAFALAYELY 61
                                  899999999999888888766655.....4699********************9986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                        RuvB_N  83 eekdvlfideihrlsraveevlysamedfr 112
                                    + +++fid++  l++ ++  l   me ++
  gi|91773925|ref|YP_566617.1| 126 ADYKIIFIDNVESLETGAQHALRRIMEKYT 155
                                   46789*********************9985 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.9
                        RuvB_N 136 vgattragllssPlrdr 152
                                   + +tt+ + l +Plr+r
  gi|91773925|ref|YP_566617.1| 161 ILSTTQPSKLIAPLRSR 177
                                   6689***********98 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.3e-05     0.096       6      90 ..      40     152 ..      37     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                        AAA_24   6 liyGpsgiGKTtlakel.........gpkplfi...dtek.Glksl.dadkfpdie...........swedfldevvel.. 59 
                                   +  Gp  +GK+++a  l         ++++ ++   d+++ G + l  +++f+ i             +  f++ ++e+  
  gi|91773925|ref|YP_566617.1|  40 VFHGPVNSGKSSTAFALayelygeyyENNFTYFnasDFFDqGKRYLvRDKRFVHIIgtddpkkiyssVISIFKEVINEFag 120
                                   566888889998888887788888877777777777554435554314555666666666666677533444444444466 PP

                        AAA_24  60 .aaeladyktlviDtideleelclaevirqne 90 
                                       +adyk+++iD+++ le  + + ++r  e
  gi|91773925|ref|YP_566617.1| 121 mGSLDADYKIIFIDNVESLETGAQHALRRIME 152
                                   69999***************999988877555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.48       7      89 ..      38     158 ..      35     168 .. 0.70
   2 ?   -2.9   0.0       4.2   7.5e+03      74      99 ..     257     284 ..     234     297 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...........erpevv.....fvtlpsstsskdllrellralglelka. 70 
                                   +lv +G++ +GK+ ++  l+++l  e++ ++           ++++++     fv + +  ++k++++ + +++++  ++ 
  gi|91773925|ref|YP_566617.1|  38 HLVFHGPVNSGKSSTAFALAYELYGEYYENNftyfnasdffdQGKRYLvrdkrFVHIIGTDDPKKIYSSVISIFKEVINEf 118
                                   7899******************97777776689999999998444444445555555566667888888888888777776 PP

                        AAA_22  71 .....................erlsseellealeqalrar 89 
                                                        e++ +++l++ +e++ r++
  gi|91773925|ref|YP_566617.1| 119 agmgsldadykiifidnveslETGAQHALRRIMEKYTRTC 158
                                   6666666666666666666655555555555555555554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.2
                        AAA_22  74 sseell.ealeqalrarav.ielliiDE 99 
                                   +  el  +a+e+ + ++++ i  l+i+E
  gi|91773925|ref|YP_566617.1| 257 NVTELHnAAIEHDVLKARKlIDTLLIEE 284
                                   4444444566666666666555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1967.78
//
Query:       gi|91773926|ref|YP_566618.1|  [L=548]
Description: ELP3 family histone acetyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-26   91.7   0.0    4.8e-26   90.6   0.0    1.6  1  Radical_SAM_C    Radical_SAM C-terminal domain
      3e-17   63.5   0.0    8.1e-17   62.1   0.0    1.7  1  Radical_SAM      Radical SAM superfamily
    0.00011   22.2   0.0     0.0003   20.7   0.0    1.7  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00037   20.7   0.0    0.00079   19.7   0.0    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.017   15.5   0.1      0.034   14.6   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   1.3e-29   4.8e-26       1      81 [.     315     395 ..     315     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 1.3e-29
                 Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlreliekrlk 81 
                                   pd +K+yp+lv++gTeL++++  gey+ l  ee+++l+adi+++lp+++r +R+++dip++++ ag++++n r+l+++rl+
  gi|91773926|ref|YP_566618.1| 315 PDYLKIYPTLVTEGTELYDMWSGGEYEALGDEEAIELLADIKAILPKWVRMQRIQRDIPSPQIFAGVKKSNVRQLAKERLE 395
                                   89***************************************************************************9996 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   2.3e-20   8.1e-17       7     155 ..      92     295 ..      87     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.3e-20
                                   ESS-.-TTTSCCTT..................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.TTHHHHH CS
                                   xxxx.xxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Radical_SAM   7 Cnlr.CsfCarpet..................vrregrgrslsveeileevkelkaekgvkevilgggeplly.pdfvell 67 
                                   C+++ C+ C+ + +                    ++++  ++ v   l ++k + ++ ++ e+i++gg+ + +  d++e++
  gi|91773926|ref|YP_566618.1|  92 CPHGvCIPCPGGPKssfnspqsymgqepatmrAMQYEYDPYRIVSGRLSQLKHIGHDVDKAELIVMGGTFSSRaIDYQEWY 172
                                   888889999999999999999999999999998888888888888899999999999998888888888888878999999 PP

                                   HHHHHTC.................................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSS CS
                                   xxxxxxx.................................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  68 erlakla.................................vpgiritvetngtlpd...eeklerllelgvdrvslgleaa 112
                                    +++ +a                                  + +r+t +t +t+pd    ++++r+l+lg + v++g++++
  gi|91773926|ref|YP_566618.1| 173 TKRCLEAmndfsgtqwredikvigdvvpyvtvedvqraneTAIVRNTGITFETRPDwtnTDHVDRMLDLGATKVEIGVQSV 253
                                   99999999999999999999999999999999999999998899999999999999889********************** PP

                                   SHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 113 ddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                    d+ vl++m+rgh++++ +++ + lr++ +k+ +++++ lpG 
  gi|91773926|ref|YP_566618.1| 254 YDF-VLERMRRGHSVQDSVDSNRVLRDSALKVGFHMMPHLPGM 295
                                   ***.**********************************99996 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.4e-08    0.0003      58     109 ..     490     540 ..     483     545 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.4e-08
               Acetyltransf_10  58 fVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkav 109
                                   +V  +++++G+g++Lle++e  a+++g+  ++++ +    +++Y+k+G+ + 
  gi|91773926|ref|YP_566618.1| 490 AVGMDWQHRGYGAELLENAEILAKDAGYL-KVSIISGIGVRQYYRKFGYYRD 540
                                   67889******************999888.*******************765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.2e-07   0.00079      42     117 .]     449     537 ..     414     537 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.2e-07
                                   TEEEEEEEEEEEET....TSTTEEEEEEEEE............SGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEH CS
                Acetyltransf_1  42 geliGfisllkipd....ekggvayieslaV............speyrgkGlGsaLlealeerareegikkivlaveednd 106
                                   + liGf++l+  +     e ++ a +++l+V              +++++G+G +Lle +e  a++ g+ k+ +    +  
  gi|91773926|ref|YP_566618.1| 449 DILIGFLRLRFPNTphreELQDAALVRELHVygsmvpvgkgavGMDWQHRGYGAELLENAEILAKDAGYLKVSI---ISGI 526
                                   4499999999998877763334444444444444445555555**************************88766...6899 PP

                                   HHHHHHHHTTE CS
                Acetyltransf_1 107 aairlYeklGF 117
                                   + + +Y+k+G+
  gi|91773926|ref|YP_566618.1| 527 GVRQYYRKFGY 537
                                   9*****88**8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.6e-06     0.034      31      74 ..     490     537 ..     444     539 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.6e-06
                                   EE-GGGTTSSHHHHHHH.HTT....SEEEEEEEEE.THH.....HHHHHHHHTTE CS
                Acetyltransf_7  31 aVdpeyrgkGiGraLle.aae....kgiileqlel.nae.....kaikfYeklGF 74 
                                   aV  +++ +G+G +Lle a++     g+      l + +       +++Y+k+G+
  gi|91773926|ref|YP_566618.1| 490 AVGMDWQHRGYGAELLEnAEIlakdAGY------LkV-SiisgiGVRQYYRKFGY 537
                                   67889***********965324434442......211.1122334456******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3264.48
//
Query:       gi|91773927|ref|YP_566619.1|  [L=115]
Description: hypothetical protein Mbur_1990 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-05   24.5   0.0      3e-05   23.8   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.17   11.9   0.0    1.4  1  FeoC      FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.4e-09     3e-05      16      63 ..      60     107 ..      59     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.4e-09
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                          TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63 
                                   aL +lg+atade+a +++ +r+   ++L++L+++G V ++++ +k+Y 
  gi|91773927|ref|YP_566619.1|  60 ALFELGSATADELAGKTNKERAVESNYLNQLVRMGHVVKNRSGRKVYF 107
                                   899****************************************99995 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.17       9      49 ..      61     101 ..      53     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                          FeoC   9 leergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaa 49 
                                   l e g++  +eL+ + + + +     L+q+vr+G+v k   
  gi|91773927|ref|YP_566619.1|  61 LFELGSATADELAGKTNKERAVESNYLNQLVRMGHVVKNRS 101
                                   55678999999***99999988899***********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 683.45
//
Query:       gi|91773928|ref|YP_566620.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-22   76.9   0.0    1.8e-21   75.9   0.0    1.5  1  DUF772       Transposase domain (DUF772)
    1.8e-16   60.4   2.1    5.5e-16   58.9   2.1    1.8  1  DDE_Tnp_1    Transposase DDE domain
     0.0038   17.4   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.037   13.7   0.0      0.067   12.9   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   5.1e-25   1.8e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.1e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+++    +++++e
  gi|91773928|ref|YP_566620.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERIAQsgkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   2.1   1.5e-19   5.5e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.5e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91773928|ref|YP_566620.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91773928|ref|YP_566620.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91773928|ref|YP_566620.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91773928|ref|YP_566620.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91773928|ref|YP_566620.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91773928|ref|YP_566620.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.067      72     132 ..     213     276 ..     160     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91773928|ref|YP_566620.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1778.38
//
Query:       gi|91773929|ref|YP_566621.1|  [L=250]
Description: chromosome partitioning ATPase protein-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-13   51.3   0.0    2.7e-13   50.2   0.0    1.6  2  AAA_31       AAA domain
    6.2e-12   45.5   1.6    2.2e-09   37.2   1.6    3.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    5.9e-10   39.3   0.0    8.2e-10   38.8   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.8e-06   27.5   0.0    0.00016   21.0   0.0    2.1  2  MipZ         ATPase MipZ
    5.8e-05   22.7   0.0    0.00051   19.6   0.0    2.0  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    0.00023   20.6   0.0     0.0013   18.1   0.0    1.9  2  VirC1        VirC1 protein
      0.009   15.7   0.0       0.83    9.2   0.0    2.2  2  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.027   13.9   0.0    1.4  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.038   13.8   0.1      0.086   12.6   0.0    1.5  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.048   12.6   0.1       0.74    8.7   0.1    2.2  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.14   11.7   0.6       0.94    9.0   0.1    2.0  2  AAA_25       AAA domain
       0.18   10.9   0.2       0.55    9.4   0.0    1.9  3  ArsA_ATPase  Anion-transporting ATPase


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.8e-16   2.7e-13       3     164 ..       4     173 ..       2     184 .. 0.72
   2 ?   -3.3   0.0       4.7     7e+03     132     155 ..     213     236 ..     205     248 .. 0.61

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.8e-16
                        AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenl.. 81 
                                   +Ia+  +KGG GKT  ++nla+a a+ gk v l D+D  a +++++ + +  +++ +++v+  ++ + ++++  + e+   
  gi|91773929|ref|YP_566621.1|   4 TIAVHSYKGGSGKTSFAINLASAYASVGKSVCLLDVDLKAPSSFNYLLPE--AKRWVNDVFEGRYGVMDVVMDVSKEMGta 82 
                                   79******************************************988744..44556666545555555555333222222 PP

                        AAA_31  82 ...dlipssidLaeaeielvelekkeeilkellekvkde.....YDyiiiDcpPsLglltenaLvasdsviipvqaeayal 154
                                      d+  s+ d+ ++ +   + +k ++   ++l + k +      D++i+D+   ++   +na++++d v+++ ++ a   
  gi|91773929|ref|YP_566621.1|  83 gafDVGYSNPDILAVRDVSSKDRKWQSKALKFLMNAKRDlsnigIDVVILDTGAGVDFTSVNAIAVADHVVMVGKPGASRQ 163
                                   345677777776655554443333333322333333332233358****************************99999989 PP

                        AAA_31 155 eGleqllkti 164
                                   + ++q++k i
  gi|91773929|ref|YP_566621.1| 164 RAIDQVVKGI 173
                                   9999888766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.7
                        AAA_31 132 ltenaLvasdsviipvqaea.yale 155
                                   +++ a+   ++v++ +++e+ ++ +
  gi|91773929|ref|YP_566621.1| 213 MCDVAVRCDNEVLVLTEPEHsFS-K 236
                                   55566666677888887776333.3 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   1.6   1.5e-12   2.2e-09       5     241 ..       4     241 ..       1     246 [. 0.56

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.5e-12
                          ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee...............ekpeqsekkliPvea 70 
                                   +iav S KGG GK+++a+nlA a a+ g++v+llD+D+  ps  + l  e                + ++  +k++    a
  gi|91773929|ref|YP_566621.1|   4 TIAVHSYKGGSGKTSFAINLASAYASVGKSVCLLDVDLKAPSSFNYLLPEAkrwvndvfegrygvmDVVMDVSKEMGTAGA 84 
                                   69***************************************9877776666234434443333332111111222222222 PP

                          ParA  71 kgikvmSigflle..sedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttp... 145
                                    ++     ++l     +++   w++  + k++ +  +d +   +D++i+D+  G      t ++ +   + +v+V  p   
  gi|91773929|ref|YP_566621.1|  85 FDVGYSNPDILAVrdVSSKDRKWQSKAL-KFLMNAKRDLSNIGIDVVILDTGAGV---DFTSVNAIaVADHVVMVGKPgas 161
                                   2222222222222002222233433322.23333344555566888888885553...34444444144677788887222 PP

                          ParA 146 qevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplv 226
                                   ++ a+++v k+i +  +   k  ++veNm +   ++     +        ++  ++++p+l++ip   +++  +d+   lv
  gi|91773929|ref|YP_566621.1| 162 RQRAIDQVVKGIYIPLE---KNCSIVENMGHANNST-----D-------LSYEGQFDLPVLASIPCMCDVAVRCDNEV-LV 226
                                   34455556666555544...4456788887655432.....2.......23445677888888888888888888777.55 PP

                          ParA 227 lkepeseaakaleei 241
                                   l+epe++ +k++ + 
  gi|91773929|ref|YP_566621.1| 227 LTEPEHSFSKNIFNA 241
                                   566666666655554 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 !   38.8   0.0   5.5e-13   8.2e-10       1      55 [.       5     133 ..       5     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5.5e-13
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   ia+ s kGG+GKT++a+nLa a a  g+ V l+D+D  a++++    l ++ ++                           
  gi|91773929|ref|YP_566621.1|   5 IAVHSYKGGSGKTSFAINLASAYASVGKSVCLLDVDLKAPSSFN--YLLPEAKRwvndvfegrygvmdvvmdvskemgtag 83 
                                   7999*************************************983..22222222445555566666666666666666666 PP

                                   .................................................C CS
                                   .................................................x RF
                          CbiA  55 .................................................d 55 
                                                                                    d
  gi|91773929|ref|YP_566621.1|  84 afdvgysnpdilavrdvsskdrkwqskalkflmnakrdlsnigidvvilD 133
                                   66666666666666666666555555555555555555555555555550 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.1e-07   0.00016       3      48 ..       5      50 ..       3      61 .. 0.89
   2 ?    4.4   0.0     0.013        19      64     126 ..      91     153 ..      75     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                  EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH CS
                          MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl 48
                                  i +   kGGsGk+  a+ +a a ++ G++v  +d+dl+  ++  yl
  gi|91773929|ref|YP_566621.1|  5 IAVHSYKGGSGKTSFAINLASAYASVGKSVCLLDVDLKAPSSFNYL 50
                                  667788********************************99988886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
                                   --EEE-SSS-HHHHTTS-HHHHHHHHHHHHHHHHH.H-SEEEEE--SS--HHHHHHHHT-SEEE CS
                          MipZ  64 lpealalseaeeaeveeeeeaevaeleelvadlea.eldfividtPGsdsalsrlahsladtlv 126
                                    p++la++++++++ + +++a  + l+++ +dl++  +d++++dt    +  s  a ++ad +v
  gi|91773929|ref|YP_566621.1|  91 NPDILAVRDVSSKDRKWQSKAL-KFLMNAKRDLSNiGIDVVILDTGAGVDFTSVNAIAVADHVV 153
                                   5666666666665555444444.566677777665379*******999999999999****998 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.4e-07   0.00051       3     150 ..       4     161 ..       1     173 [. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.4e-07
                      CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwaraeldga.pwrqaaleyapgldll 82 
                                   ++a++  +GG G+ts +  La a  ++g+sv ++D+  +     +Fn  + +++ w++  ++g+    + ++++ +++   
  gi|91773929|ref|YP_566621.1|   4 TIAVHSYKGGSGKTSFAINLASAYASVGKSVCLLDVDLKAP--SSFNYLLPEAKRWVNDVFEGRyGVMDVVMDVSKEMGTA 82 
                                   5899999***************************9866654..56666666888999999887635788888888887653 PP

                      CBP_BcsQ  83 P.f..Gelnveekenlqqlaek........aeallaalkelk.eqyrwillDlpagasaltrellaladlvllvvepdan 150
                                     f  G  ++ +  +++ + +k         + l++a + l+    + ++lD  ag + +  +++a+ad+v++v +p a+
  gi|91773929|ref|YP_566621.1|  83 GaFdvGY-SNPDILAVRDVSSKdrkwqskaLKFLMNAKRDLSnIGIDVVILDTGAGVDFTSVNAIAVADHVVMVGKPGAS 161
                                   2121022.222333344444440000000134444455555556789999999999999999999999999999998776 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.5e-07    0.0013       4      43 ..       5      44 ..       1      49 [. 0.90
   2 ?   -0.1   0.0      0.32   4.8e+02      67     110 ..     110     153 ..     104     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.5e-07
                         VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                  i++ s+kGG+Gkt+  + l sa as gk v+l++ d   P
  gi|91773929|ref|YP_566621.1|  5 IAVHSYKGGSGKTSFAINLASAYASVGKSVCLLDVDLKAP 44
                                  6788******************************997766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                         VirC1  67 delplleaayeeaegeGfdyaladtrgGsselnntiiassdlll 110
                                   + l  l +a ++    G d+++ dt  G        ia +d ++
  gi|91773929|ref|YP_566621.1| 110 KALKFLMNAKRDLSNIGIDVVILDTGAGVDFTSVNAIAVADHVV 153
                                   5677888899999999*********9998655444555555444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00056      0.83      11      61 ..      13      63 ..       7      87 .. 0.82
   2 ?    4.4   0.0     0.017        26      62      99 ..     105     143 ..      94     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00056
                                  TSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE CS
                         SRP54 11 GaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik 61
                                  G+GKT+ +  La  + + gk+v+l  +D   ++ ++ L   a++   +v++
  gi|91773929|ref|YP_566621.1| 13 GSGKTSFAINLASAYASVGKSVCLLDVDLKAPSSFNYLLPEAKRWVNDVFE 63
                                  9***************************99999888888777776666666 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.017
                                   SSTTSCHHHHHHHHHHHHHHTTSSEEEEEE.--SSTTHH CS
                         SRP54  62 kkeeadpaavakeavekakeekidvvlvDT.aGrlqndk 99 
                                   +k ++++ +++ +a +   + +idvv++DT aG   +  
  gi|91773929|ref|YP_566621.1| 105 RKWQSKALKFLMNAKRDLSNIGIDVVILDTgAGVDFTSV 143
                                   5667889999999999999**********9666655555 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.027       8      61 ..      11      64 ..       4      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                     Fer4_NifH  8 kGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlre 61
                                  kGG+Gk+  + nl++a a+ gk v ++  D ka s    l   a++ v d+++ 
  gi|91773929|ref|YP_566621.1| 11 KGGSGKTSFAINLASAYASVGKSVCLLDVDLKAPSSFNYLLPEAKRWVNDVFEG 64
                                  9********************************998766666666666666655 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05     0.086       4      33 ..      13      42 ..      11      49 .. 0.92
   2 ?   -3.3   0.0       4.4   6.6e+03     127     140 ..     144     159 ..     131     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                        CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                   sGK+++a +L+   ++ g++++++D+D+ 
  gi|91773929|ref|YP_566621.1| 13 GSGKTSFAINLASAYASVGKSVCLLDVDLK 42
                                  69**************************86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.4
                        CLP1_P 127 ealep.dvvvvldq.e 140
                                   +a+ + d+vv++++  
  gi|91773929|ref|YP_566621.1| 144 NAIAVaDHVVMVGKpG 159
                                   4444447888777632 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 ?    1.6   0.0     0.073   1.1e+02      39      71 ..      13      45 ..       6      58 .. 0.88
   2 ?    8.7   0.1    0.0005      0.74     118     155 ..     123     161 ..      96     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.073
                                  TSSHHHHHHHHHHHHHCTT--EEEEEE------ CS
                          MeaB 39 GaGkstlvealglelrrrGkrvavlavDPsspf 71
                                  G+Gk  +  +l+  +++ Gk v +l vD  +p 
  gi|91773929|ref|YP_566621.1| 13 GSGKTSFAINLASAYASVGKSVCLLDVDLKAPS 45
                                  99*************************966554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0005
                                   HHTT-SEEEEEE.ESSTTHHHHHHTT-SEEEEEEESSTT CS
                          MeaB 118 eaaGfDvvliet.vGvGqsevdvaevvdtfvvlllpeaG 155
                                     +G Dvv+++t  Gv    v+ ++v+d++v++  p+a 
  gi|91773929|ref|YP_566621.1| 123 SNIGIDVVILDTgAGVDFTSVNAIAVADHVVMVGKPGAS 161
                                   678********96699999*************9888775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00063      0.94      42      61 ..      12      32 ..       9      46 .. 0.88
   2 ?    1.0   0.1      0.18   2.7e+02     134     161 ..     119     145 ..      53     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00063
                        AAA_25 42 pgtGKttlaldlalava.tGk 61
                                  +g+GKt +a++la a+a  Gk
  gi|91773929|ref|YP_566621.1| 12 GGSGKTSFAINLASAYAsVGK 32
                                  8***************96565 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                        AAA_25 134 eaaieevegvrlvviDplsralggdens 161
                                    +++  + g+++v++D+ + +   + n+
  gi|91773929|ref|YP_566621.1| 119 KRDLSNI-GIDVVILDTGAGVDFTSVNA 145
                                   5566665.699*****988777776665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00037      0.55       7      38 ..       9      40 ..       3      54 .. 0.90
   2 ?   -3.7   0.0       3.5   5.3e+03     119     132 ..     121     134 ..     114     136 .. 0.69
   3 ?   -2.5   0.0       1.5   2.2e+03      30      45 ..     222     236 ..     211     244 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00037
                                  EESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  7 gGKGGVGKttvsaatavklsekgkkvllistD 38
                                  + KGG GKt+ +  +a   +  gk+v l+ +D
  gi|91773929|ref|YP_566621.1|  9 SYKGGSGKTSFAINLASAYASVGKSVCLLDVD 40
                                  66*************************99887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.5
                                   HHHCSSSSEEEEES CS
                   ArsA_ATPase 119 yvkeeeydvvvlDt 132
                                    +++   dvv+lDt
  gi|91773929|ref|YP_566621.1| 121 DLSNIGIDVVILDT 134
                                   55555679999998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.5
                                   S-EEEEE-STTTHHHH CS
                   ArsA_ATPase  30 kkvllistDPAhslsD 45 
                                   ++ +l+ t P hs s 
  gi|91773929|ref|YP_566621.1| 222 NE-VLVLTEPEHSFSK 236
                                   34.4555899999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1471.66
//
Query:       gi|91773930|ref|YP_566622.1|  [L=266]
Description: hypothetical protein Mbur_1993 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-05   24.3   0.3     0.0031   17.1   0.0    2.6  2  ATP-synt_J  ATP synthase j chain
  ------ inclusion threshold ------
      0.013   15.4  14.6       0.03   14.3  14.5    1.7  1  Trep_Strep  Hypothetical bacterial integral membrane protein 


Domain annotation for each model (and alignments):
>> ATP-synt_J  ATP synthase j chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.1    0.0027        24      10      32 ..      91     115 ..      85     116 .. 0.74
   2 !   17.1   0.0   3.4e-07    0.0031      14      39 ..     214     239 ..     206     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0027
                                   SHHHHHH..HHHHHHHHHHHHHHST CS
                    ATP-synt_J  10 mwPFfaa..glivlygvnkaqnamm 32 
                                   + PFf+a  ++++  ++ k ++a+m
  gi|91773930|ref|YP_566622.1|  91 LTPFFVAmaSVVTGLCITKREKAAM 115
                                   78***96437788888888887776 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.4e-07
                                   HHHHHHHHHHHHHHHHHSTTSSSSSS CS
                    ATP-synt_J  14 faaglivlygvnkaqnammnsdEfkn 39 
                                   faa++iv+ ++ ++q+ +m+s+ f+n
  gi|91773930|ref|YP_566622.1| 214 FAAAAIVYLLIIALQSTLMESETFQN 239
                                   89**********************98 PP

>> Trep_Strep  Hypothetical bacterial integral membrane protein (Trep_Strep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3  14.5   3.3e-06      0.03      27     169 ..      84     222 ..      64     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-06
                    Trep_Strep  27 ispvlmlllpaivallagivymllvakvpkfgailimglllgllllltGhgwlvlllaiiggliaeliaksggykskkkni 107
                                   +  +++ll+p++v  +a++v  l+++k +k  +il ++l+lg +++  G  ++  +++ i  +++ +++   +y++k++n 
  gi|91773930|ref|YP_566622.1|  84 TPDMFHLLTPFFV-AMASVVTGLCITKREKAAMILFSILILGWYITPLGREVFYYPWFHI-IVLGSFVLFHHKYHDKRGNF 162
                                   2344555555555.56789999****************************8888888888.799***************** PP

                    Trep_Strep 108 lsyavfslwllgsilplllmkdaylaslaergmsaeyidtlvalitpwmlvvlliltivgal 169
                                     +a++++++l  il   l + +++a +    ++ ++ ++++a+++ + + +++++++++ l
  gi|91773930|ref|YP_566622.1| 163 YTFAFLLFSTLIAILADHL-AGSITAAIL-YDITPQMFTSVIAIYPIERITLAFAAAAIVYL 222
                                   **99999999999998888.455555554.57888999999999987777777777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1944.74
//
Query:       gi|91773931|ref|YP_566623.1|  [L=396]
Description: bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-70  236.8   0.2      1e-70  236.8   0.2    1.5  2  Fae             Formaldehyde-activating enzyme (Fae)
    1.6e-23   83.5   2.0    5.4e-23   81.8   1.7    2.0  2  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    2.8e-06   26.9   1.2    6.3e-06   25.7   1.2    1.7  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
       0.03   13.8   4.2      0.098   12.1   0.5    2.2  2  PcrB            PcrB family
      0.056   13.2   0.8       0.13   12.1   0.4    1.8  2  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter


Domain annotation for each model (and alignments):
>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.8   0.2   2.8e-74     1e-70       1     159 []       4     162 ..       4     162 .. 0.99
   2 ?   -3.7   0.2       2.8   9.9e+03      85     134 ..     248     254 ..     242     275 .. 0.48

  Alignments for each domain:
  == domain 1  score: 236.8 bits;  conditional E-value: 2.8e-74
                           Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfGpaQa 81 
                                   +GEal+ge +e+Ah+dl+iG+k+gpvg+Afa+ +++ s+ghtp+l+v+rpnl++kP+tl+v+kvt+k ++qa+++fGpaQa
  gi|91773931|ref|YP_566623.1|   4 IGEALIGEAPELAHVDLMIGDKEGPVGQAFATGMTQLSAGHTPVLSVIRPNLPTKPSTLIVPKVTVKGMDQASQIFGPAQA 84 
                                   8******************************************************************************** PP

                           Fae  82 avakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdkakhpfv 159
                                   av+kavadaveeg+ipke+a+dlvii+svfi+p+a d+++iy+yny AtklA+krAl+++P+id+vl+ekd+a+h+++
  gi|91773931|ref|YP_566623.1|  85 AVSKAVADAVEEGLIPKEKAEDLVIIASVFIHPQAVDYNRIYRYNYGATKLALKRALDGFPDIDTVLHEKDRAAHAVM 162
                                   ***************************************************************************975 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.8
                           Fae  85 kavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAi 134
                                   +                                           At  Ai
  gi|91773931|ref|YP_566623.1| 248 D-------------------------------------------ATADAI 254
                                   3...........................................333333 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 ?   -1.2   0.0      0.35   1.2e+03     114     156 ..      59      99 ..      29     116 .. 0.71
   2 !   81.8   1.7   1.5e-26   5.4e-23       2     224 ..     174     377 ..     173     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.35
                                   .EEEEEESTSSGGHHHHHH.HSHHHHHHHHHHHHHHHTTESEEE CS
                     OMPdecase 114 rgllilaqmsskgnlmlqe.kgytqacveaarehkaedfvmGfv 156
                                   +  li+ +++ kg  +  +  g +qa+v +a +++ e    G++
  gi|91773931|ref|YP_566623.1|  59 PSTLIVPKVTVKGMDQASQiFGPAQAAVSKAVADAVE---EGLI 99 
                                   6778999999999988888548888888887776655...3444 PP

  == domain 2  score: 81.8 bits;  conditional E-value: 1.5e-26
                                   EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHHHST CS
                     OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqatag 79 
                                    L++alD ++   +l +++++ +  +++l+ +++l++++g     +++++++r+    + i++D+K+ D Gn +++++   
  gi|91773931|ref|YP_566623.1| 174 YLQVALDNPNLPVILNIIKQLPKsDHLILEAGTPLIKRYG-----VDVISKIREVRpdAFIVADLKTLDTGNLEARMV--- 246
                                   69*********************9****************.....**********999********************... PP

                                   CHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTTESEEECCC CS
                     OMPdecase  80 sarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkaedfvmGfvaqe 159
                                      +++ ad++ v+a+a  a++ +++e+a k+g     + + +++++  ++ e+  +  ++ve  r+   e        + 
  gi|91773931|ref|YP_566623.1| 247 ---ADATADAIVVSALAPIATLNKVIEEAHKTG--IYAVMDTLNTPDPVAVLEQlDVLPDVVELHRAIDIE--------GT 314
                                   ...69***************************8..8899999***********778888888888888844........33 PP

                                   HTH..HHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                     OMPdecase 160 tln..ateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                   +++  ++e    + + +++  ++   ++++g++ +t+ ++ g agadi++vGR+I++++d +++a r
  gi|91773931|ref|YP_566623.1| 315 AHAwgSIEG--IKALAVKRSSKV-LVAVAGGVRVDTISDALG-AGADILVVGRAITNSKDVRQAADR 377
                                   333223333..489999999999.****************99.99*******************998 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.2   1.7e-09   6.3e-06      76     197 ..     246     365 ..     212     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                                   HHHCT-SEEEEE-S.T-TTHHHHHHHHHHTTSEEEE.EE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHH CS
                Ribul_P_3_epim  76 faeagasiisvHaE.alehlkrtiqeikeaGakagl.vlnpatplealeyllekldlvllmsvePgfgGQkFipevlekik 154
                                    a+a a+ i+v a   + +l+++i+e +++G+ a +  ln   p+ +le+l + l  v+ +    + +G +     +e ik
  gi|91773931|ref|YP_566623.1| 246 VADATADAIVVSALaPIATLNKVIEEAHKTGIYAVMdTLNTPDPVAVLEQL-DVLPDVVELHRAIDIEGTAHAWGSIEGIK 325
                                   5778888888877646899999*********99887579999999999986.55555555667789999887666665555 PP

                                   HHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                Ribul_P_3_epim 155 kvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                      +l+ +++ ++ + v GGv++d+i+ +  agad+lV+g+a+
  gi|91773931|ref|YP_566623.1| 326 ---ALAVKRSSKVLVAVAGGVRVDTISDALGAGADILVVGRAI 365
                                   ...555666779*****************************98 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.019        67      23      76 ..     243     297 ..     234     303 .. 0.78
   2 ?   12.1   0.5   2.7e-05     0.098     162     217 ..     315     371 ..     304     382 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.019
                                   HHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSS CS
                          PcrB  23 veiviesgtDavmigGsq.svtldntvrllkkvsriklPivlepsnvegvvryaD 76 
                                   +++v++  +Da++++    ++tl+++++  +k   + +   l   ++ +v +++D
  gi|91773931|ref|YP_566623.1| 243 ARMVADATADAIVVSALApIATLNKVIEEAHKTGIYAVMDTLNTPDPVAVLEQLD 297
                                   5678999999*99999888999999988888887777777777777777766666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.7e-05
                                   TTSSS-HHHHHHH.HHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHC CS
                          PcrB 162 sGaledveevial.kkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekder 217
                                   + a + +e ++al +k+ +k  + v GG+r   +      a AD++vvG ++ ++++ 
  gi|91773931|ref|YP_566623.1| 315 AHAWGSIEGIKALaVKRSSKVLVAVAGGVRVDTISDALG-AgADILVVGRAITNSKDV 371
                                   5577888989887357777888889****9877666555.55************9943 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.66   2.4e+03      92     122 ..     242     273 ..     214     299 .. 0.67
   2 ?   12.1   0.4   3.5e-05      0.13     121     162 ..     328     369 ..     254     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.66
                                   HHHHHHHHT-SEEEEES--H.HHHHHHHHHHH CS
                     QRPTase_C  92 eleevleaeadiimLDnfsv.eelkkaveelk 122
                                   e++ v+ a ad i +  + +  +l+k++ee +
  gi|91773931|ref|YP_566623.1| 242 EARMVADATADAIVVSALAPiATLNKVIEEAH 273
                                   45666667777777777766566777776554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.5e-05
                                   HHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB- CS
                     QRPTase_C 121 lkeknkrvlievSGgvtlenveeyaksgvdvisvgalthsvk 162
                                     ++  +vl+ v+Ggv  +++++    g d++ vg +++++k
  gi|91773931|ref|YP_566623.1| 328 AVKRSSKVLVAVAGGVRVDTISDALGAGADILVVGRAITNSK 369
                                   2356667****************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2577.74
//
Query:       gi|91773932|ref|YP_566624.1|  [L=221]
Description: triosephosphate isomerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-10   40.0   0.0    3.7e-10   39.6   0.0    1.2  1  TIM       Triosephosphate isomerase
    6.2e-05   22.4   1.0    0.00033   20.0   0.6    2.0  2  ThiG      Thiazole biosynthesis protein ThiG
      0.003   17.0   3.4      0.003   17.0   3.4    1.6  2  NMO       Nitronate monooxygenase


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 !   39.6   0.0   6.2e-14   3.7e-10       3     125 ..       5     122 ..       3     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 6.2e-14
                                   EEEE-TBTS..-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHHH CS
                           TIM   3 iagNwKmnk..tleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlkd 81 
                                   i+ N K++   t e a  +++++k+  + + +e++iap+f+ + +v+++++   + +++q ++    G+fTG   a+ +kd
  gi|91773932|ref|YP_566624.1|   5 IVLNLKTYLegTGEGAVRIARACKEVGEASGIEIAIAPQFCDIYRVASQVD---VPVYSQHLDGVGAGSFTGHAFAKCIKD 82 
                                   677888776446677777788888888889***************999986...9************************** PP

                                   TT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE-- CS
                           TIM  82 lgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGE 125
                                   +g+  ++i HsE+r  + +    +++ v aa+ +gl++i+C  +
  gi|91773932|ref|YP_566624.1|  83 AGAVGTLINHSECRLKLAD----IEASVTAAKGEGLRTIICTNN 122
                                   **************98765....7788999***********876 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.073   4.3e+02      74      99 ..      16      41 ..      14      49 .. 0.84
   2 !   20.0   0.6   5.6e-08   0.00033     175     215 ..     172     212 ..     145     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.073
                                  SHHHHHHHHHHHHHTTS-SEEEE--B CS
                          ThiG 74 taeeAvriarlarevletdliklEvi 99
                                  t e Avriar  +ev e + i + + 
  gi|91773932|ref|YP_566624.1| 16 TGEGAVRIARACKEVGEASGIEIAIA 41
                                  56889*********999998888775 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.6e-08
                                   SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                          ThiG 175 kvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                    v v+  AGi + +d  +a+elG  +vll++ + +akdp a
  gi|91773932|ref|YP_566624.1| 172 AVKVLCGAGISKGEDLKAAIELGSVGVLLASGIVKAKDPKA 212
                                   688999********************************975 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.18   1.1e+03      18      40 ..      67      89 ..      52     104 .. 0.87
   2 !   17.0   3.4   4.9e-07     0.003     128     233 ..     105     212 ..      94     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.18
                           NMO 18 gmggiskarLaaavsnaGgLGvl 40
                                  g+g  ++ ++a  + +aG+ G l
  gi|91773932|ref|YP_566624.1| 67 GAGSFTGHAFAKCIKDAGAVGTL 89
                                  78899999999999999999987 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.9e-07
                           NMO 128 vvarlkeagvvliptissvkearkvearGaDalivqGpeaGGh.qGtpevgd....kglfaLvpqvldavdiPviAaGGii 203
                                    v + k  g+  i+ +  +    +++a+G+D + v+ pe  G  ++ ++++d    +g +a v+++  av+  v+   Gi 
  gi|91773932|ref|YP_566624.1| 105 SVTAAKGEGLRTIICTNNIATTAAAAALGPDYVAVEPPELIGSgIP-VSKADpevvTGSVAAVERIDPAVK--VLCGAGIS 182
                                   566777788889999999999999*************997554155.444443345666677777777666..79999*** PP

                           NMO 204 drrgvaaaLalGAsgvqigtrfLltkesda 233
                                   ++++++aa+ lG  gv +++  + +k+ +a
  gi|91773932|ref|YP_566624.1| 183 KGEDLKAAIELGSVGVLLASGIVKAKDPKA 212
                                   ********************9999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1578.95
//
Query:       gi|91773933|ref|YP_566625.1|  [L=130]
Description: hypothetical protein Mbur_1996 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 958.39
//
Query:       gi|91773934|ref|YP_566626.1|  [L=437]
Description: prephenate dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-59  200.8   0.0    2.4e-59  200.4   0.0    1.1  1  PDH             Prephenate dehydrogenase
    9.4e-13   48.6   0.0      2e-12   47.5   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    2.5e-09   37.6   0.1    8.5e-09   35.9   0.0    2.0  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    2.2e-07   30.4   0.1    4.4e-07   29.4   0.1    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.4e-05   24.0   0.1    8.3e-05   22.2   0.0    1.8  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    0.00012   22.1   1.5      0.017   15.1   0.1    2.8  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0011   19.1   0.1     0.0089   16.1   0.0    2.2  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0021   18.4   0.2     0.0088   16.4   0.0    2.1  2  FDX-ACB         Ferredoxin-fold anticodon binding domain
     0.0052   17.6   0.1      0.031   15.1   0.0    2.2  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
     0.0099   15.5   0.0      0.026   14.1   0.0    1.7  1  NmrA            NmrA-like family
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.059   13.3   0.0    2.2  2  KR              KR domain
       0.02   15.0   0.0      0.066   13.3   0.0    1.9  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do
      0.023   14.2   0.0      0.037   13.5   0.0    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
      0.027   15.0   0.0      0.059   13.9   0.0    1.6  1  CoA_binding_2   CoA binding domain
      0.029   14.3   0.1        2.3    8.1   0.0    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.052   14.2   0.1       0.14   12.8   0.1    1.8  1  CoA_binding     CoA binding domain
      0.054   13.6   0.4       0.14   12.3   0.1    1.8  2  DapB_N          Dihydrodipicolinate reductase, N-terminus
        0.3   10.4   2.8        2.3    7.5   0.4    2.7  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


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 !  200.4   0.0   2.5e-62   2.4e-59       5     257 ..      20     263 ..      16     264 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 2.5e-62
                                   HHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHH CS
                           PDH   5 lrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekv 85 
                                      +g +v v g ++++e a   +++g++++ + d +a+++ div++ vP++ +++v++e ap++k + l++D++s+K+++
  gi|91773934|ref|YP_566626.1|  20 FTDHGYEVVVWGSSQKTEIA---KQMGVEFASDLD-NAIRTSDIVIITVPIDITADVIRETAPKMKAGSLLMDLTSIKAEP 96 
                                   55678888888877666554...467*******98.********************************************* PP

                                   HHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHH CS
                           PDH  86 vreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvva 166
                                   vr+++e  ++g+++ g+hPm+G+        +   +++++vi+ Pt+   ++++ ++++l+ee ga+++ ++peeHD+ v+
  gi|91773934|ref|YP_566626.1|  97 VRAMRETAPDGVEILGTHPMFGP--------SIPTLQGQIVIMSPTKGRSEKWFPIMRNLFEENGAHIEIIKPEEHDKFVS 169
                                   ***********************........999*********************************************** PP

                                   HHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                           PDH 167 vvshlphvvaialaatlkekkndekeirklasggfrdvt....RiaksnPelwadilleNkeavlealdkfikelkklkel 243
                                   vv++l+h+++i + +t k    d  ++r++ s+ ++ +     Ri ++nP+l+a+i+++N++ vl+++++fi e++ l+e+
  gi|91773934|ref|YP_566626.1| 170 VVQGLTHFAYITIGNTFKSLDFDVSMSRRFMSPVYEIMVdfvgRILGQNPYLYAHIQMQNEQ-VLKVHETFISECNILSEI 249
                                   **************************************999********************9.****************** PP

                                   HHTT-HHHHHHHHH CS
                           PDH 244 ienedaeeLvellk 257
                                   ++++d e + + + 
  gi|91773934|ref|YP_566626.1| 250 VREQDIEAFCNKMT 263
                                   *********99886 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 !   47.5   0.0     2e-15     2e-12       6     153 ..       8     156 ..       4     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2e-15
                                   --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EE CS
                 NAD_binding_2   6 GlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdil 86 
                                   G+G+MG+ + + ++++gy+v+v+  + +k+e + + g++ a+++ +++++ d+vi+ v+  + + +vi++ ++++k+g++l
  gi|91773934|ref|YP_566626.1|   8 GTGEMGKWFTKFFTDHGYEVVVWGSS-QKTEIAKQMGVEFASDLDNAIRTSDIVIITVPI-DITADVIRETAPKMKAGSLL 86 
                                   99*********************966.99******************************8.78999*************** PP

                                   EE-S---HHHHHHHHHHHHHTT-EEEEE.EEESHHHHHHHT-EEEEE...EE-HHHHHHHHHHHHHHEEEE CS
                 NAD_binding_2  87 idgstsspedtrelakelkekglkflda.PVSGGeegAekGtLsimv...GGseeafervkpvleaigakv 153
                                   +d +++++e  r +  e +  g+++l++ P  G      +G++ im    G se+ f+ +++++e+ ga++
  gi|91773934|ref|YP_566626.1|  87 MDLTSIKAEPVRAMR-ETAPDGVEILGThPMFGPSIPTLQGQIVIMSptkGRSEKWFPIMRNLFEENGAHI 156
                                   *******99887765.56889*****977*************99997222456777888999999988876 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 !   35.9   0.0   8.5e-12   8.5e-09       4      95 ..       5      90 ..       2      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 8.5e-12
                                  EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHH CS
                 F420_oxidored  4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakda 85
                                  ii G+G+mg+ +++ ++ +g   +e+vv +s+++   +e+a+++gv+  + d   a++ +d+v+++v+   +++v++e a++ 
  gi|91773934|ref|YP_566626.1|  5 IIgGTGEMGKWFTKFFTDHG---YEVVVWGSSQK---TEIAKQMGVEFAS-DLDNAIRTSDIVIITVPIDITADVIRETAPKM 80
                                  899*****************...****8744433...588999****999.******************************** PP

                                  HTTSEEEEES CS
                 F420_oxidored 86 lkgklvisvl 95
                                  ++g+l+ + +
  gi|91773934|ref|YP_566626.1| 81 KAGSLLMDLT 90
                                  ***9999876 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 !   29.4   0.1   4.4e-10   4.4e-07      39     123 ..       4      86 ..       1      90 [. 0.84

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.4e-10
                                   EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCST CS
                  2-Hacid_dh_C  39 vGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltpetrhlinaeelakmk 118
                                   + i G+G++G+ + k ++  g +v+++  s+k+e  ++++gve++ +l++++++sDiv++++p+ + t ++i + +  kmk
  gi|91773934|ref|YP_566626.1|   4 LIIGGTGEMGKWFTKFFTDHGYEVVVWGSSQKTEI-AKQMGVEFAsDLDNAIRTSDIVIITVPI-DITADVIRE-TAPKMK 81 
                                   56789*************************98666.9*****99989****************6.566666654.446777 PP

                                   TTEEE CS
                  2-Hacid_dh_C 119 kgail 123
                                    g++l
  gi|91773934|ref|YP_566626.1|  82 AGSLL 86 
                                   77766 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 !   22.2   0.0   8.3e-08   8.3e-05       7      91 ..       4      86 ..       1      91 [. 0.86
   2 ?   -1.6   0.0       1.7   1.7e+03      50      83 ..     349     382 ..     333     392 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.3e-08
                                  EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE.EHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT CS
                          IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl.tvaeavkkadvvmiliPDelqkevyeeeiepnlkeg 88
                                  + + G G  G+  ++ + d g +vvv   +++  ++ Ak+ g+e + ++++a++++d+v+i +P  + ++v+ +e +p++k+g
  gi|91773934|ref|YP_566626.1|  4 LIIGGTGEMGKWFTKFFTDHGYEVVVWGSSQK--TEIAKQMGVEFAsDLDNAIRTSDIVIITVPIDITADVI-RETAPKMKAG 83
                                  445589******************99766665..78999999997526999*********************.7789*****9 PP

                                  -EE CS
                          IlvN 89 kal 91
                                  + l
  gi|91773934|ref|YP_566626.1| 84 SLL 86
                                  987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                                   EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGG CS
                          IlvN  50 evltvaeavkkadvvmiliPDelqkevyeeeiep 83 
                                   +  +v+++ +    + +l+P  + ++v+e+ i +
  gi|91773934|ref|YP_566626.1| 349 KDWKVKNLLHPKRDISVLLPSGADASVFEKVIDN 382
                                   5556666666666689999999999999888765 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 ?    5.4   0.2     0.017        17       6      33 ..       8      35 ..       2      43 .. 0.84
   2 !   15.1   0.1   1.7e-05     0.017      56     103 ..      43      90 ..      37     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                                  --SHHHHHHHHHHHTTT--EEEE-S-HH CS
                NAD_Gly3P_dh_N  6 GaGswGtalAkvlaenghevrlwvreee 33
                                  G+G  G  + k ++++g ev++w+ +++
  gi|91773934|ref|YP_566626.1|  8 GTGEMGKWFTKFFTDHGYEVVVWGSSQK 35
                                  78*********************99875 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.7e-05
                                   TEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE-- CS
                NAD_Gly3P_dh_N  56 nlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsli 103
                                    +++ +dl++a++ +di+++ vP  ++++v+++ ++++k+   l+ l+
  gi|91773934|ref|YP_566626.1|  43 GVEFASDLDNAIRTSDIVIITVPIDITADVIRETAPKMKAGSLLMDLT 90 
                                   58899********************************99988877665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     9e-06    0.0089      14      83 ..       2      64 ..       1      91 [. 0.78
   2 ?    0.2   0.0       0.7   6.9e+02      50      86 ..     256     289 ..     247     310 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9e-06
                                  EEEEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                  Shikimate_DH 14 kvlli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83
                                  k+l+i G+Gem++  +k + ++g++ vvv + ++    e+a++++ e       ++l+++++ +d+vi+ +
  gi|91773934|ref|YP_566626.1|  2 KMLIIgGTGEMGKWFTKFFTDHGYE-VVVWGSSQ--KTEIAKQMGVE-----FASDLDNAIRTSDIVIITV 64
                                  67888359****************9.88888665..479*****555.....679************9865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.7
                                   HHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                  Shikimate_DH  50 kelaeelkgeeiealkleelkellaeadvvisatase 86 
                                   +++++++ ++   a ++++  ++l+++d +i a  se
  gi|91773934|ref|YP_566626.1| 256 EAFCNKMTEA---AAHFKDTPSALHRSDKLINAKISE 289
                                   5677777666...999999999999999999987665 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       5.8   5.8e+03      69      85 ..     227     243 ..     223     265 .. 0.76
   2 !   16.4   0.0   8.8e-06    0.0088       7      66 ..     360     415 ..     358     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.8
                                   --HHHHHHHHHHHHHHH CS
                       FDX-ACB  69 Ltdeevnaaiekvveal 85 
                                   +++e+v +++e++++++
  gi|91773934|ref|YP_566626.1| 227 MQNEQVLKVHETFISEC 243
                                   67788888888777664 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.8e-06
                                   EEEEEEEEESSS-HHHHHHHHHHHH-TTEEEEEEEEEEESTTS-SSEEEEEEEEEE--SS CS
                       FDX-ACB   7 erDlalvvdekveaaelleavreaagellesvqlfDvYrgkklaegkkSlalrltlqske 66 
                                   +rD+++++++   a+ +++++ + +   + s +++D+Y g +   ++ S ++r+t+ +++
  gi|91773934|ref|YP_566626.1| 360 KRDISVLLPSGADASVFEKVIDNDE--RIASTEIIDTYSGIS--DNRLSATFRITILEES 415
                                   69*******************9987..9***********966..9*********986554 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 !   15.1   0.0   3.1e-05     0.031       2      78 ..       2      72 ..       1      83 [. 0.76
   2 ?   -0.7   0.0       2.4   2.4e+03      26      55 ..     276     308 ..     234     328 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                                  EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                  GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78
                                  +++iiG+ G +g+++ + + ++  ++evv ++ +++    ++a+++gve+ sdl++  +    d+vi+++p +  +++
  gi|91773934|ref|YP_566626.1|  2 KMLIIGGtGEMGKWFTKFFTDH--GYEVV-VWGSSQ--KTEIAKQMGVEFASDLDNAIR--TSDIVIITVPIDITADV 72
                                  67788777*******9666666..88888.444433..35578****************..77999999987655555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                                   E.EEEEEECSSHHHHHHHHHHTTHE..EESSHH CS
                  GFO_IDH_MocA  26 e.evvalldpdaeraeavaesfgve..aysdle 55 
                                   + +   l++ + ++ e++ +s gve   y++++
  gi|91773934|ref|YP_566626.1| 276 LhRSDKLINAKISEFEEMIASVGVErgLYHNYS 308
                                   136666777777777777777777777666643 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.6e-05     0.026       2      73 ..       4      65 ..       3      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                  EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                          NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                  l+iG+TG++Gk ++++++++g++v +    +k+e ak+    Gve+ +        l++a++++d v+++++
  gi|91773934|ref|YP_566626.1|  4 LIIGGTGEMGKWFTKFFTDHGYEVVVWGSSQKTEIAKQ---MGVEFAS-------DLDNAIRTSDIVIITVP 65
                                  89**********************99988888888875...4777643.......25556666666666665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.9e-05     0.059       3      63 ..       3      69 ..       2      83 .. 0.68
   2 ?   -2.9   0.0       5.4   5.3e+03      80     102 ..     169     191 ..     151     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                                  EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHH........HHHHHHHTT-EEEE----TT CS
                            KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedska........liaelealgaevevvaaDvs 63
                                   li+GG+G +G+ ++++  ++g + +v  s ++  +e +k+        l ++++ +++ + +v++D++
  gi|91773934|ref|YP_566626.1|  3 MLIIGGTGEMGKWFTKFFTDHGYEVVVWGSSQK--TEIAKQmgvefasdLDNAIRTSDIVIITVPIDIT 69
                                  59********************99888877774..3333321222222244445555566666666665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.4
                                   S---EEEE---------TTT--H CS
                            KR  80 ppikGvihaAgvlrdklleemta 102
                                   + ++G  h A ++  +++++++ 
  gi|91773934|ref|YP_566626.1| 169 SVVQGLTHFAYITIGNTFKSLDF 191
                                   67899999999988888887765 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 ?   13.3   0.0   6.7e-05     0.066      16      61 ..      18      66 ..       3      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                                  HHHHHTT-EEEEES-...TSSS-BTTEEEE-GGGS-GGG-SEEE--TT- CS
                        DpaA_N 16 rkLaekgakvslygl...eleekiegvekaesleealedadviilPvpg 61
                                  + ++++g++v ++g     +  k  gve a++l+ a++++d++i  vp+
  gi|91773934|ref|YP_566626.1| 18 KFFTDHGYEVVVWGSsqkTEIAKQMGVEFASDLDNAIRTSDIVIITVPI 66
                                  678899*********87666678889******************99884 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.7e-05     0.037       1      35 [.       3      37 ..       3      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                  EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTT CS
                     Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssas 35
                                  +l++G+tG +G+ ++k + ++gyev+++ + ++++
  gi|91773934|ref|YP_566626.1|  3 MLIIGGTGEMGKWFTKFFTDHGYEVVVWGSSQKTE 37
                                  69**********************99999884443 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.9e-05     0.059      14     107 ..      11     112 ..       2     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-05
                                   SHHHHHHHHHHHHT--EEEESSS-.SEETTEES----T.......T--EEEE-S-HHHHGGGHHHH.HHH--SEEEE-TT- CS
                 CoA_binding_2  14 kfgykvlryllehglpvvpVnpke.eeilgekvyaslae.d..pepvdlvdvftppeatpeivkea.lalgakavwlqpgs 89 
                                     g   ++++ +hg++vv+    + +ei  +  ++  ++ d    + d+v + +p ++t+++++e   +++a ++ + + s
  gi|91773934|ref|YP_566626.1|  11 EMGKWFTKFFTDHGYEVVVWGSSQkTEIAKQMGVEFASDlDnaIRTSDIVIITVPIDITADVIRETaPKMKAGSLLMDLTS 91 
                                   567777899999*****999777667887776444444333358999******************956669********** PP

                                   --HHHHHHHHH...TT-EEE. CS
                 CoA_binding_2  90 edeeaaelaee...agirvvg 107
                                    ++e +++++e   +g++++g
  gi|91773934|ref|YP_566626.1|  92 IKAEPVRAMREtapDGVEILG 112
                                   *99999999997777777765 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 ?    8.1   0.0    0.0023       2.3       6      33 ..       8      35 ..       2      43 .. 0.84
   2 ?    4.5   0.0     0.029        29      66     143 ..      43     121 ..      31     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                                  --SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                       3HCDH_N  6 GaGtmGagiaavfasagleVvlvdisee 33
                                  G+G mG+  ++ f  +g+eVv+   s++
  gi|91773934|ref|YP_566626.1|  8 GTGEMGKWFTKFFTDHGYEVVVWGSSQK 35
                                  67*******************9988765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.029
                                   CEEEES-HHHHH.C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--S..SS-HHHHCCCSSSGGGEEEEEE-SSTTT CS
                       3HCDH_N  66 risfttdleeav.dadlviEavvEnlelKrkvfaelekiakpdailasnTS..slsiselaealkrperviglHFfnPppl 143
                                    ++f++dl++a+   d+vi +v+  +++ ++v++e +  +k+ ++l   TS  + +++++ e+  +  +++g+H++  p +
  gi|91773934|ref|YP_566626.1|  43 GVEFASDLDNAIrTSDIVIITVP--IDITADVIRETAPKMKAGSLLMDLTSikAEPVRAMRETAPDGVEILGTHPMFGPSI 121
                                   5899********9******9998..77789*****************9999444689999999999999*****9876655 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00014      0.14       5      83 ..       2      77 ..       1      86 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                  EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHH CS
                   CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelv 83
                                  k+++iG +g+ ++  ++f+ + +y++++ +  + + +  +  g++   ++d+++ +   d+ +itvP +  ++++ e +
  gi|91773934|ref|YP_566626.1|  2 KMLIIGGTGEMGKWFTKFFTDHGYEVVVWGSSQKTEI-AKQMGVEFASDLDNAIRT--SDIVIITVPIDITADVIRETA 77
                                  6899999999999999999999999876655555555.555688888899999999..*****************9975 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014      0.14       1      72 [.       1      61 [.       1      82 [. 0.81
   2 ?   -3.0   0.0       7.6   7.5e+03      41      72 ..     252     283 ..     236     295 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEE CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvli 72
                                  +k +++G +G mGk  +k  ++  ++e+v   ++++           +++  ++gv++ +dl+++++ +d++i
  gi|91773934|ref|YP_566626.1|  1 MKMLIIGGTGEMGKWFTKFFTD-HGYEVVVWGSSQK-----------TEIAkQMGVEFASDLDNAIRTSDIVI 61
                                  7999****************99.8999988877777...........22333899*************99665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.6
                                   TTBHHHHSSSS--S-BEBSSHHHHHHH-SEEE CS
                        DapB_N  41 gkdagellglgklgvavtddleevlekadvli 72 
                                   ++d+  ++++ +   a ++d  ++l  +d li
  gi|91773934|ref|YP_566626.1| 252 EQDIEAFCNKMTEAAAHFKDTPSALHRSDKLI 283
                                   34666666666555555555555555555554 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 ?    7.5   0.4    0.0023       2.3      83     128 ..      48      90 ..      31     112 .. 0.81
   2 ?    2.1   0.0       0.1     1e+02     130     159 ..     151     180 ..     148     186 .. 0.90
   3 ?   -3.3   0.0       4.4   4.4e+03      76      99 ..     264     297 ..     229     300 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                                   HHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETT CS
                   AlaDh_PNT_C  83 ellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvA 128
                                   + l++a++++d+vi tv i    ++ ++ +e+  +Mk gs ++D+ 
  gi|91773934|ref|YP_566626.1|  48 SDLDNAIRTSDIVIITVPID--ITADVI-RETAPKMKAGSLLMDLT 90 
                                   568899********997765..455555.677899*********96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                                   GGT-SBTT--TBBTTSEEEEETTEEEEEBS CS
                   AlaDh_PNT_C 130 dqGGnvetsrltthgepvveekgvvhygva 159
                                   ++G  +e +++ +h++ v +++g +h ++ 
  gi|91773934|ref|YP_566626.1| 151 ENGAHIEIIKPEEHDKFVSVVQGLTHFAYI 180
                                   6899***99*****************9875 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.4
                                   EE..........HCHHHHHHHHHHHH-SEEEE-- CS
                   AlaDh_PNT_C  76 ev..........lksqeellaeavkeadvvigtv 99 
                                   e+          l+++ +l++ +++e + +i +v
  gi|91773934|ref|YP_566626.1| 264 EAaahfkdtpsaLHRSDKLINAKISEFEEMIASV 297
                                   2233333334445666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2997.82
//
Query:       gi|91773935|ref|YP_566627.1|  [L=269]
Description: shikimate dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   93.7   0.0    1.7e-26   92.3   0.0    1.8  1  Shikimate_dh_N  Shikimate dehydrogenase substrate binding dom
    1.7e-14   53.3   0.2    3.1e-14   52.4   0.2    1.5  1  SDH_C           Shikimate 5'-dehydrogenase C-terminal domain
    7.8e-12   45.4   0.1    1.3e-11   44.7   0.1    1.4  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    6.5e-05   23.4   0.3    0.00013   22.5   0.3    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00017   21.1   1.7    0.00064   19.2   1.7    1.9  1  adh_short       short chain dehydrogenase
    0.00042   19.7   0.4    0.00095   18.6   0.1    1.7  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0029   18.0   0.0     0.0044   17.4   0.0    1.4  1  NAD_binding_7   Putative NAD(P)-binding
     0.0034   17.0   0.1     0.0077   15.8   0.1    1.6  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.004   16.5   0.5     0.0063   15.8   0.5    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.012   15.7   0.7      0.018   15.1   0.7    1.3  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
      0.018   14.9   0.3       0.03   14.2   0.3    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.029   14.0   0.1      0.045   13.4   0.1    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.033   13.7   0.2      0.052   13.1   0.2    1.3  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
      0.039   13.0   0.6      0.061   12.4   0.6    1.3  1  FAD_binding_2   FAD binding domain
      0.049   12.9   0.0       0.52    9.6   0.0    2.1  2  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
      0.054   12.7   0.1       0.07   12.4   0.1    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


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 !   92.3   0.0   1.5e-29   1.7e-26       1      83 []       7      88 ..       7      88 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1.5e-29
                                  EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SEE CS
                Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNti 83
                                  v+G+pi+hSlSP++hn+af+al+++++y+af+ve+++le+a+++++a g+ Gln T+P+Ke++++++d +++ A++igA+Nti
  gi|91773935|ref|YP_566627.1|  7 VLGDPIEHSLSPIMHNSAFEALDMDCTYHAFRVEKNDLENALQGAKAMGFGGLNLTVPLKETALKFVD-ADSLAAKIGAINTI 88
                                  79*****************************************************************9.9************8 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.2   2.8e-17   3.1e-14       4      31 .]     237     264 ..     234     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.8e-17
                                   HHHHHHHHHHHHHHS----HHHHHHHHH CS
                         SDH_C   4 MLveQgaeqFelWTGrepPvevMreall 31 
                                   MLv+Qgae+F++WTG+epP++vM+++++
  gi|91773935|ref|YP_566627.1| 237 MLVYQGAEAFRIWTGKEPPINVMKKTVM 264
                                   *************************985 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.1   1.2e-14   1.3e-11       9      84 ..     114     186 ..     104     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.2e-14
                                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84 
                                   ++k+k+vl++GaG  a+ +a  ++++g++ v +aNRt era +la e++++  +   l+ +++ l+++d++i  t 
  gi|91773935|ref|YP_566627.1| 114 DIKDKNVLILGAGGAARAIAFTFAEAGAN-VNIANRTPERAMQLAAEIGDA--KGYGLDIVDNGLEDIDILINTTT 186
                                   799*************************9.******************877..8999***************9885 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   1.1e-07   0.00013       3      47 ..     121     161 ..     119     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                                   EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                 F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47 
                                    i+GaG  ++a+a  +++ag    ++ +a +r+pe+a +la+e+g
  gi|91773935|ref|YP_566627.1| 121 LILGAGGAARAIAFTFAEAG---ANVNIA-NRTPERAMQLAAEIG 161
                                   599*****************...****88.************998 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.7   5.7e-07   0.00064       1      58 [.     118     170 ..     118     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.7e-07
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TT CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDv 58 
                                   k vl+ Ga+ G  raia ++a++Ga+v +++r++e++ ++a+e+++    a  + +D+
  gi|91773935|ref|YP_566627.1| 118 KNVLILGAG-GAARAIAFTFAEAGANVNIANRTPERAMQLAAEIGD----AKGYGLDI 170
                                   6899***98.**********************************98....45555555 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       1.6   1.8e+03      95     113 ..      59      77 ..      24      81 .. 0.53
   2 !   18.6   0.1   8.5e-07   0.00095      28     100 ..     109     186 ..      92     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.6
                                   EEE-S--STTTTTSBSHHH CS
                  2-Hacid_dh_C  95 vslhlpltpetrhlinaee 113
                                   + l++pl++   ++++a++
  gi|91773935|ref|YP_566627.1|  59 LNLTVPLKETALKFVDADS 77 
                                   3345555555555555555 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 8.5e-07
                                   CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.....CHHHHTCEECSHHHHHHH-SEEEE-S- CS
                  2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.....eeeelgvelvsleellaesDivslhlp 100
                                   +  g ++++k v i+G+G  ++a+a ++++ g++v + +r++++         +++g+ l+ +++ l++ Di+++++ 
  gi|91773935|ref|YP_566627.1| 109 EDEGVDIKDKNVLILGAGGAARAIAFTFAEAGANVNIANRTPERAMqlaaeIGDAKGYGLDIVDNGLEDIDILINTTT 186
                                   567889***********************************9976644433334456666777777777777776554 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 !   17.4   0.0   3.9e-06    0.0044       3      45 ..     113     155 ..     112     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-06
                 NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele 45 
                                   +d+k+k+vl+ G+G  A   + +++eaga+v +   + +++++
  gi|91773935|ref|YP_566627.1| 113 VDIKDKNVLILGAGGAARAIAFTFAEAGANVNIANRTPERAMQ 155
                                   689*****************************97777433333 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 !   15.8   0.1   6.8e-06    0.0077       2      48 ..     115     161 ..     114     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.8e-06
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeeg 48 
                                   +k+k++ ++G G  ++a a  + ++g +v +++r+ ++ ++ A e g
  gi|91773935|ref|YP_566627.1| 115 IKDKNVLILGAGGAARAIAFTFAEAGANVNIANRTPERAMQLAAEIG 161
                                   89*********************************999999887755 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   5.6e-06    0.0063      24     115 ..     114     202 ..     105     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.6e-06
                                   TCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-SEEEE---B.T CS
                   AlaDh_PNT_C  24 pgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellaeavkeadvvigtvli.p 102
                                     ++  +vl++G+G a  + + t ++ ga+V + +  p+r+ ql + +g      +    + +++ +++ d++i t  +  
  gi|91773935|ref|YP_566627.1| 114 D-IKDKNVLILGAGGAARAIAFTFAEAGANVNIANRTPERAMQLAAeIGDA----KGYGLDIVDNGLEDIDILINTTTVgL 189
                                   4.77889**********9999999*******************99865555....6778889999999*****98888845 PP

                                   TSS---SC-HHHH CS
                   AlaDh_PNT_C 103 GkkaPkLvteemv 115
                                   G++  +Lvt+e +
  gi|91773935|ref|YP_566627.1| 190 GNSNGTLVTAEQM 202
                                   8899999998865 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 ?   15.1   0.7   1.6e-05     0.018      19      87 ..     113     190 ..      94     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                   S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCT.....T-EE--HHHCTTT-SEEEE-S....S CS
                 AdoHcyase_NAD  19 vllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaame.....Gfevvtleevvkkadivvttt....G 87 
                                   v +  k++++ G G   +  a ++ ++Ga v +++  P  a+q a e     G+ +  +++ +++ di++ tt    G
  gi|91773935|ref|YP_566627.1| 113 VDIKDKNVLILGAGGAARAIAFTFAEAGANVNIANRTPERAMQLAAEigdakGYGLDIVDNGLEDIDILINTTtvglG 190
                                   55788**************************************8765445559****************987734333 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   0.3   2.7e-05      0.03       2      43 ..     120     161 ..     119     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekie 43 
                                   v ++GaG   + ia  fa+ag +V++ ++++e++ + +++i 
  gi|91773935|ref|YP_566627.1| 120 VLILGAGGAARAIAFTFAEAGANVNIANRTPERAMQLAAEIG 161
                                   889***************************999988887775 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     4e-05     0.045       1      39 [.     120     159 ..     120     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHH CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkkn 39 
                                   ++ilGaG+  + +a + a+aga+v + +r++ r+++l  +
  gi|91773935|ref|YP_566627.1| 120 VLILGAGGAARAIAFTFAEAGANVNIANRTPeRAMQLAAE 159
                                   68*****************************999987765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   4.6e-05     0.052       4      53 ..     126     173 ..     124     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                                   TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.EEE--TTSH CS
                  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.vlecDVtde 53 
                                    g +raiA ++ae+Ga+v ++++  e+   + +la+e+g +  + +D+ d+
  gi|91773935|ref|YP_566627.1| 126 GGAARAIAFTFAEAGANVNIANRTPER---AMQLAAEIGDAkGYGLDIVDN 173
                                   5789******************99998...888899988663688888765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   5.4e-05     0.061       2      40 ..     120     158 ..     119     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggataw 40 
                                   v++ G+G+A  a A + aeaG++v + + ++e+  ++a+
  gi|91773935|ref|YP_566627.1| 120 VLILGAGGAARAIAFTFAEAGANVNIANRTPERAMQLAA 158
                                   9*****************************998877775 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00046      0.52      22      71 ..     103     151 ..      99     184 .. 0.87
   2 ?    1.1   0.0       0.2   2.2e+02      89     118 ..     193     221 ..     170     242 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                                   HHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSC CS
                 THF_DHG_CYH_C  22 gvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktk 71 
                                   g  + ++++g+++++k+v+++G++    +++a+ ++e++a V ++++  +
  gi|91773935|ref|YP_566627.1| 103 GAKRTIEDEGVDIKDKNVLILGAGGA-ARAIAFTFAEAGANVNIANRTPE 151
                                   55677999***************986.799*************9987654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                                   -TT-B-GGGS-TT-EEEE---EEC-TTEEE CS
                 THF_DHG_CYH_C  89 kpelikaemvkegavviDvGinrvekgklv 118
                                   +  l++ae+++++ +v D+ +n +  +kl+
  gi|91773935|ref|YP_566627.1| 193 NGTLVTAEQMHSDLAVFDIVYNPL-MTKLL 221
                                   346999999********9999988.44444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.3e-05      0.07     158     201 ..     111     154 ..      91     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                   Pyr_redox_3 158 efhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiek 201
                                   e  ++++++v++ G++  a  +A+ ++++ga+V+++ r+ e+  
  gi|91773935|ref|YP_566627.1| 111 EGVDIKDKNVLILGAGGAARAIAFTFAEAGANVNIANRTPERAM 154
                                   444899********************************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 00:00:00.47
# Mc/sec: 1727.29
//
Query:       gi|91773936|ref|YP_566628.1|  [L=233]
Description: 3-dehydroquinate dehydratase [Methanococcoides burtonii DSM 6242]
Scores for 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-55  186.8   1.0    8.1e-55  186.5   1.0    1.0  1  DHquinase_I   Type I 3-dehydroquinase
    0.00098   18.7   0.2        1.2    8.6   0.1    2.3  2  HMGL-like     HMGL-like
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.12   11.7   0.0    1.3  1  Dehalogenase  Reductive dehalogenase subunit


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 !  186.5   1.0   1.4e-58   8.1e-55      11     228 ..      22     228 ..      14     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 1.4e-58
                                   HHHHHHHHHTT.S-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT- CS
                   DHquinase_I  11 eilaelesgke.kaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielga 90 
                                   e l++++ ++e +aD++E+R Dll  t++ ++ ++ l+ l+ t++lp+i+t r +++gg++ +++ee ++ ll+ +++l  
  gi|91773936|ref|YP_566628.1|  22 EPLQQCKTAAEhGADILEIRFDLLGITTS-KEAANLLRMLKGTTSLPCIATNRLQSQGGNW-EGTEENRIALLEDIMHL-T 99 
                                   4456666666666***********77755.88999999999999****************9.9***************8.8 PP

                                   SEEEEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHH CS
                   DHquinase_I  91 dyvDvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsltse 171
                                   d vD+El e++e+  +r++++++e++   I+S+hdfe+tp++e+lk++l + ++ gaDi+K+avm+++++Dvl+ll++t e
  gi|91773936|ref|YP_566628.1| 100 DAVDIEL-ETDEQLRDRIVKKAKEESKTTIISSHDFERTPDKETLKSILDHSHDAGADIAKLAVMPENMQDVLNLLEVTLE 179
                                   *******.77877666999999999999***************************************************63 PP

                                   HHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHH CS
                   DHquinase_I 172 akeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelrei 228
                                   +        +++++mG+lGk +Ri+++++Gs +t+as+++a   apGql++++l+++
  gi|91773936|ref|YP_566628.1| 180 V------DDVCTISMGKLGKHTRIIAPLYGSKLTYASVSDA--VAPGQLKVEDLKKA 228
                                   3......57****************************6655..***********997 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0003       1.8     149     189 ..      24      65 ..      16      72 .. 0.88
   2 !    8.6   0.1   0.00021       1.2     102     178 ..      96     168 ..      81     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0003
                                   HHHHHHHHHHT-SEEEEE.ETTS---HHHHHHHHHHHHHHS- CS
                     HMGL-like 149 aevveaaeeaGatrinia.DtvGvltPneaaelisalkervk 189
                                   ++++++a+e Ga++++i  D +G++t +eaa+l++ lk  ++
  gi|91773936|ref|YP_566628.1|  24 LQQCKTAAEHGADILEIRfDLLGITTSKEAANLLRMLKGTTS 65 
                                   799**************77*****************997665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00021
                                   HHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--.HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHH CS
                     HMGL-like 102 lhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtd.leflaevveaaeeaGatriniaDtvGvltPneaa 178
                                   +hl   + ++ e   +  +++vk a++  k + +s  d+ rt+  e+l  +++   +aGa++ ++a +     P++++
  gi|91773936|ref|YP_566628.1|  96 MHLTDAVDIELETDEQLRDRIVKKAKEESKTTIISSHDFERTPdKETLKSILDHSHDAGADIAKLAVM-----PENMQ 168
                                   55555666666666777899*********************962578899************999754.....44444 PP

>> Dehalogenase  Reductive dehalogenase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05      0.12     117     164 ..      80     126 ..      14     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                  Dehalogenase 117 kWeGTpEenlrmlraalrffGasdvgvleldektkklifakdkkgkki 164
                                    WeGT+E+ +++l   +++  a d+  le de++++ i++k k++ k 
  gi|91773936|ref|YP_566628.1|  80 NWEGTEENRIALLEDIMHLTDAVDIE-LETDEQLRDRIVKKAKEESKT 126
                                   7************************8.589999999999986666333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1641.62
//
Query:       gi|91773937|ref|YP_566629.1|  [L=384]
Description: 3-dehydroquinate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-150  498.5   3.3   9.7e-150  498.3   3.3    1.0  1  DHQS      3-dehydroquinate synthase II
  ------ inclusion threshold ------
      0.023   14.8   0.0          6    7.0   0.0    2.5  2  OapA      Opacity-associated protein A LysM-like domain
      0.061   12.7   0.1       0.21   11.0   0.0    1.8  2  Aldolase  KDPG and KHG aldolase


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 !  498.3   3.3  1.6e-153  9.7e-150       1     352 []       8     384 .]       8     384 .] 0.97

  Alignments for each domain:
  == domain 1  score: 498.3 bits;  conditional E-value: 1.6e-153
                          DHQS   1 kevwikadeeeweerkelvtaaleagvdavlveeedaekvkelgkikviakeed.....davlvgkd.............. 62 
                                   k++wikad+++we++k+++t++le+g+++vlv+++++ekv+elg+i+v+a++ d     d+v+vgk               
  gi|91773937|ref|YP_566629.1|   8 KTIWIKADKGHWEAHKDRITTGLESGANCVLVNSDEVEKVRELGDIQVAAFTYDdksgaDIVVVGKGgegdgtkplspdpv 88 
                                   79*************************************************9555899999****99************** PP

                          DHQS  63 .......dleklkka....kkvaalveikskeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavksae 132
                                           + +         +v+a+v i++k++ee+aae++ke+d++i+ ++dw+vIPlEnliAalq++++kiia+v++++
  gi|91773937|ref|YP_566629.1|  89 gsldmitAI-R---LkekgLTVGAYVVIQNKKYEEFAAEIGKECDFLIIVGTDWKVIPLENLIAALQDSDVKIIAGVRDQD 165
                                   *99655222.2...2244699************************************************************ PP

                          DHQS 133 eAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvGsssr 213
                                   eAklalet+E+G++gvll+++d+++ik++++++e++  e+l+L++ +vtkve vgmgdRvcvDtc++m++geGmLvGs+++
  gi|91773937|ref|YP_566629.1| 166 EAKLALETMEHGSEGVLLDSDDPNTIKATVAVAERSGIEDLKLVPGKVTKVEAVGMGDRVCVDTCNMMTKGEGMLVGSQAS 246
                                   ********************************************************************************* PP

                          DHQS 214 glfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRPlllveaea 294
                                   g+fLvhsE++espYvasRPFRVNAGavhaYv+v g++T+YLseL++Gdev++v++ Gk+r+ +vGRvKiE+RPl+lveae+
  gi|91773937|ref|YP_566629.1| 247 GMFLVHSESEESPYVASRPFRVNAGAVHAYVKV-GDRTRYLSELSSGDEVTIVNAGGKQRTGIVGRVKIERRPLMLVEAEV 326
                                   *********************************.*********************************************** PP

                          DHQS 295 egkkvstilQnaetirlvtedgkaisvteLkeGdevlvyleekaRHfGikieEtiiEk 352
                                   +g+ ++ ilQnaeti+lv+ +g++isv++Lk+G+ev+vy+e +aRHfG+k+eEtiiEk
  gi|91773937|ref|YP_566629.1| 327 NGEIIKNILQNAETIKLVDINGEPISVADLKPGNEVMVYYEGGARHFGMKVEETIIEK 384
                                   *********************************************************8 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 ?    7.0   0.0     0.001         6      23      53 ..     269     299 ..     263     320 .. 0.76
   2 ?    5.1   0.0    0.0042        25      20      54 ..     333     367 ..     330     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.001
                          OapA  23 plsdvnalakveGadkplSnlksGqkvrikl 53 
                                   +   v+a +kv  + + lS+l sG++v+i  
  gi|91773937|ref|YP_566629.1| 269 NAGAVHAYVKVGDRTRYLSELSSGDEVTIVN 299
                                   566799*********************9953 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0042
                          OapA  20 nnLplsdvnalakveGadkplSnlksGqkvrikln 54 
                                   n L+ ++  +l+ ++G+  ++++lk G++v +  +
  gi|91773937|ref|YP_566629.1| 333 NILQNAETIKLVDINGEPISVADLKPGNEVMVYYE 367
                                   6678889999*******************988665 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.5e-05      0.21      46     119 ..      90     172 ..      86     181 .. 0.83
   2 ?   -2.6   0.0      0.51     3e+03     114     133 ..     195     214 ..     189     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.5e-05
                                   HHHHHHHHHHH-TTSEEEEES--SHHHHHH.HHHCT..-SEEEESS--......HHHHHHHHHTTS-EEEEESSHHHHHHH CS
                      Aldolase  46 aldairvlrkerpdllvgaGtvlnaeqlae.akeaG..aqfvvsPGlt......adllkaavdlkipllPGvstpseimla 117
                                   +ld+i ++r + ++l vga  v+++++ +e a+e G  ++f++  G        ++l+ a++d++++++ Gv    e +la
  gi|91773937|ref|YP_566629.1|  90 SLDMITAIRLKEKGLTVGAYVVIQNKKYEEfAAEIGkeCDFLIIVGTDwkviplENLIAALQDSDVKIIAGVRDQDEAKLA 170
                                   6899*******************99998873566665699***999863333336788999**************999999 PP

                                   HH CS
                      Aldolase 118 ld 119
                                   l+
  gi|91773937|ref|YP_566629.1| 171 LE 172
                                   87 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.51
                                   HHHHHHTT--EEEETTTTTT CS
                      Aldolase 114 imlaldlGlkrlklfPaeas 133
                                   + +a   G++ lkl P +++
  gi|91773937|ref|YP_566629.1| 195 VAVAERSGIEDLKLVPGKVT 214
                                   56677788888888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2559.13
//
Query:       gi|91773938|ref|YP_566630.1|  [L=285]
Description: fructose-bisphosphate aldolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-65  218.6   0.2    1.1e-64  218.3   0.2    1.1  1  DeoC       DeoC/LacD family aldolase
     0.0044   16.4   1.6      0.038   13.3   0.2    2.4  2  ThiG       Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.012   15.7   0.3        2.3    8.3   0.0    2.8  3  PA         PA domain
      0.021   14.4   0.1      0.036   13.7   0.1    1.4  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


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 !  218.3   0.2   2.4e-68   1.1e-64       2     235 .]      42     257 ..      41     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 2.4e-68
                                   EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEET CS
                          DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvde 82 
                                   vi+++D++ + +++ +       +d++  +++++++ga+a+l+++g++ +++++y++d++l+v+++++t l ++++++v+ 
  gi|91773938|ref|YP_566630.1|  42 VIIPMDHGMSDGPIRGV------IDIADSINKVAEGGANAILMQKGMVNHGHRGYGHDVGLIVHMSASTALGPDPNDKVL- 115
                                   89***************......9*******************************************************9. PP

                                   TCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTCC CS
                          DeoC  83 vasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsael 163
                                   v++veea+++GAdav+++v++   gse+e+++l++++ v+e+c+e+g+pl+ ++y+r+++i++ + dp+ va+Aarv+ael
  gi|91773938|ref|YP_566630.1| 116 VCKVEEAMKMGADAVSIHVNI---GSETEAEQLKKLGSVAEQCDEWGIPLLSMMYPRGKNISNPH-DPQMVAHAARVGAEL 192
                                   *********************...*****************************************.*************** PP

                                   T-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
                          DeoC 164 GaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsGRaifqk 235
                                   G+D+iK+ ++        +d+++fkdv++++pvp vv++GG+   ++++fle+++ A+ eaga Gv++GR++fq+
  gi|91773938|ref|YP_566630.1| 193 GSDVIKTVYT--------GDVDSFKDVVNGCPVP-VVIAGGPkteTDQEFLEMISGAM-EAGARGVAIGRNVFQH 257
                                   **********........****************.********9999***********.**************97 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.027   1.2e+02     190     209 ..     119     138 ..     115     152 .. 0.81
   2 !   13.3   0.2   8.5e-06     0.038     168     225 ..     209     272 ..     177     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.027
                                   HHHHHHTT-SEEEESHHHHT CS
                          ThiG 190 aaqamelGadavllntavae 209
                                   + +am++Gadav +   + +
  gi|91773938|ref|YP_566630.1| 119 VEEAMKMGADAVSIHVNIGS 138
                                   678*********98877765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.5e-06
                                   HHHHHH-SS-BEEES---SHHH......HHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                          ThiG 168 kiiieeakvPvivDAGigspsd......aaqamelGadavllntavaeakdpvamArafklave 225
                                   k +++ + vPv++  G  + +d      +  ame Ga +v +   v +  dpv+m ra+++ v+
  gi|91773938|ref|YP_566630.1| 209 KDVVNGCPVPVVIAGGPKTETDqeflemISGAMEAGARGVAIGRNVFQHPDPVKMTRAITQVVH 272
                                   55677778999998888777663333334679**************************998875 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.41   1.8e+03      36      53 ..      62      79 ..      40     101 .. 0.74
   2 ?    8.3   0.0    0.0005       2.3      22      81 ..     108     165 ..      89     173 .. 0.71
   3 ?    4.1   0.0      0.01        46      34      54 ..     232     252 ..     199     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.41
                            PA 36 aeKarnAqaaGAagviiv 53
                                  a+ ++ +++ GA ++++ 
  gi|91773938|ref|YP_566630.1| 62 ADSINKVAEGGANAILMQ 79
                                  666778888899888765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0005
                            PA  22 vdvkGkivLvqrtfaeKarnAqaaGAagviiv....ndgelgaatgasgnegepdgitiPavgv 81 
                                    d + k++++      K++ A + GA +v i     +++e +   + + ++++ d+++iP  + 
  gi|91773938|ref|YP_566630.1| 108 PDPNDKVLVC------KVEEAMKMGADAVSIHvnigSETEAEQLKKLGSVAEQCDEWGIPLLSM 165
                                   4678899***......*************99977664444444444455556666788887655 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.01
                            PA  34 tfaeKarnAqaaGAagviivn 54 
                                   +f e +  A +aGA gv i +
  gi|91773938|ref|YP_566630.1| 232 EFLEMISGAMEAGARGVAIGR 252
                                   67888999*********8874 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   8.1e-06     0.036      83     224 ..     123     266 ..     115     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.1e-06
                                   HHTTESEEEEEGTGHHHH....HHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCC CS
                     OMPdecase  83 ikewadivtvhavaGkas....vkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqe 159
                                    k +ad+v +h+  G+++    +k+l  +ae++++ g+ +l +m   g+        + ++v +a++  ae    G  + +
  gi|91773938|ref|YP_566630.1| 123 MKMGADAVSIHVNIGSETeaeqLKKLGSVAEQCDEWGIPLLSMMYPRGKNISNP--HDPQMVAHAARVGAE---LGSDVIK 198
                                   678899999999988765444477777777777788999999999999988777..566666666666657...5777777 PP

                                   HTHHHHHHTTCSCEEEHHHTT.....EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                     OMPdecase 160 tlnateedaddfihltpgigl.....eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                   t      d d f+ ++ g+ +         +  +q+  ++   + +aga  + +GR +++ +dpv+ +++
  gi|91773938|ref|YP_566630.1| 199 TVY--TGDVDSFKDVVNGCPVpvviaGGPKTETDQEFLEMISGAMEAGARGVAIGRNVFQHPDPVKMTRA 266
                                   755..34458**********966643222223344444444456679******************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1802.00
//
Query:       gi|91773939|ref|YP_566631.1|  [L=189]
Description: GMP synthase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-39  135.3   0.0    2.3e-39  135.1   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    5.2e-12   46.0   3.9    2.2e-10   40.7   2.1    2.9  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.031   14.1   0.0       0.06   13.1   0.0    1.5  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.1   0.0   3.9e-43   2.3e-39       2     188 ..       8     184 ..       7     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.1 bits;  conditional E-value: 3.9e-43
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQ 82 
                                   +i+ny ++ + +++ ++ l++++++v +++s e il   ++pdgi++sgGp    v+ + e ++     +iPiLGICLG+Q
  gi|91773939|ref|YP_566631.1|   8 VINNYGQFCHLIHRTVRDLDMDTKIVANTTSVEDIL--DEEPDGIILSGGPSMERVGSCQEYVES---IDIPILGICLGHQ 83 
                                   799****************************99995..79*************999999888876...579********** PP

                                   HHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTT CS
                        GATase  83 llaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknp 163
                                   l+a+ fg+++   k  ++     ++ + e ++l+gl+++  ++ +H +ev+    +p++++ +a+s d +e+++++++++p
  gi|91773939|ref|YP_566631.1|  84 LIAQTFGGHTGAGKLGGYAAIDVEVIE-EDDILKGLGPRTSVWASHADEVTV---LPDEFIHLARS-DVCEIEAMRHEERP 159
                                   **************9999999999999.67*********************9...*******9999.778*********** PP

                                   EEEESSBTTSTTSTTHHHHHHHHHH CS
                        GATase 164 fvgvQFHPEststpegpellfnfli 188
                                   ++gvQ+HPE+ +t +g+el+ nf+ 
  gi|91773939|ref|YP_566631.1| 160 IYGVQWHPEVAHTDKGEELFMNFFK 184
                                   **********************985 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.042   2.5e+02      48      70 ..      35      58 ..      30      66 .. 0.76
   2 !   40.7   2.1   3.6e-14   2.2e-10     105     216 .]      72     168 ..      63     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.042
                 Peptidase_C26 48 deedvkaild.kldgllltGgqdv 70
                                  ++++v++ild + dg++l+Gg+ +
  gi|91773939|ref|YP_566631.1| 35 NTTSVEDILDeEPDGIILSGGPSM 58
                                  5667777776257********865 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 3.6e-14
                 Peptidase_C26 105 gvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavk.vekgsllaellgseeievnslHhqaikelaee 184
                                   ++PilgiC+G+ql++ ++GG++        g         +a + +v+ +e++ +l+ l    +++v   H   ++ l +e
  gi|91773939|ref|YP_566631.1|  72 DIPILGICLGHQLIAQTFGGHTGAGKLG--G---------YA-AIDVEvIEEDDILKGLGP--RTSVWASHADEVTVLPDE 138
                                   79******************87654331..1.........22.334441678888888877..999*************** PP

                 Peptidase_C26 185 lrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   +   A+++   iEa+++ee+  +++gvQwHPE
  gi|91773939|ref|YP_566631.1| 139 FIHLARSDVCEIEAMRHEER--PIYGVQWHPE 168
                                   *****************994..6********9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05      0.06      48     110 ..      32      88 ..      20     117 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                   EE-.SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                     DJ-1_PfpI  48 vtv.daslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                   +++ ++s++d+ ++e D ++l GG +  er+  +         + + + ++  IC g ql a++
  gi|91773939|ref|YP_566631.1|  32 IVAnTTSVEDILDEEPDGIILSGGPS-MERVGSC------QEYVESIDIPILGICLGHQLIAQT 88 
                                   444157899***************99.6666655......444456689999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1379.20
//
Query:       gi|91773940|ref|YP_566632.1|  [L=462]
Description: Ig-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-10   41.0   7.4    5.2e-10   39.2   7.4    2.1  1  Big_1            Bacterial Ig-like domain (group 1)
    5.8e-06   26.4   5.5    5.8e-06   26.4   5.5    2.9  3  Big_3_5          Bacterial Ig-like domain (group 3)
    4.1e-05   23.8   3.2    9.9e-05   22.6   3.2    1.6  1  Invasin_D3       Invasin, domain 3
     0.0049   17.1   2.1      0.016   15.5   2.1    1.9  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> 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 !   39.2   7.4   1.2e-13   5.2e-10       5      64 .]     350     411 ..     347     411 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.2e-13
                         Big_1   5 dtntltatvkDangnpvagatVtfsvsggals..assgtTdanGkatvtltstkagtvtvtA 64 
                                   +++++tatv+D ng +v g+ V+f++ +g ++  ++ + Td nG+a++++ts+  gt  + A
  gi|91773940|ref|YP_566632.1| 350 ESHEVTATVQDDNGAAVTGTMVHFEIASGPNAgtTADVLTDTNGEASFSFTSQSVGTDVIVA 411
                                   6799************************666667**********************988866 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.092   4.1e+02      22      56 ..      37      72 ..      25      85 .. 0.60
   2 ?   -0.9   0.0      0.43   1.9e+03       5      38 ..      91     128 ..      87     159 .. 0.66
   3 !   26.4   5.5   1.3e-09   5.8e-06       6      67 ..     348     413 ..     343     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.092
                                  TTS--EEEEEE...TTEE-SS-EE--TTSEEEEEEE-S CS
                       Big_3_5 22 gtptGtVtftd...ggttlgtavllsanGtAtltvsal 56
                                  ++p+G V   +    +t+l ++v+++ +G+ +l++ ++
  gi|91773940|ref|YP_566632.1| 37 ENPSGPVMNSVmsvASTSL-APVVTE-TGKISLSIDGY 72
                                  5666666655422255555.556444.89999988763 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.43
                                   ETTSEEEEEEE--CCCCTTS--EEEEEE.....TTEE-S CS
                       Big_3_5   5 tagqtvtltatVtaasggtptGtVtftd.....ggttlg 38 
                                   t+ +++ lta++ ++ ++ p G Vt+       +++++g
  gi|91773940|ref|YP_566632.1|  91 TVRSAYLLTASLWSG-NEIPDGGVTLAGfpvnwDDVVIG 128
                                   555666677777777.77788888876433334444444 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 1.3e-09
                                   TTSEEEEEEE--CCCCTTS--E.EEEEETTEE-...SS-EE--TTSEEEEEEE-SS-EEEEEEEEE CS
                       Big_3_5   6 agqtvtltatVtaasggtptGt.Vtftdggttl...gtavllsanGtAtltvsalaaGthsitAtY 67 
                                    g++ ++tatV++ +g+++tGt V f + + +     + vl+++nG A++++++ ++Gt  i+A++
  gi|91773940|ref|YP_566632.1| 348 LGESHEVTATVQDDNGAAVTGTmVHFEIASGPNagtTADVLTDTNGEASFSFTSQSVGTDVIVASF 413
                                   69999****************74778875544321134677778********************98 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   3.2   2.2e-08   9.9e-05      10      82 ..     340     415 ..     336     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.2e-08
                    Invasin_D3  10 spasivAdGkststltvtlkDangnpvsgltvtfstt...sagtlsavtdngdGtytatLtattagtatitptvnG 82 
                                   sp+s++ +  ++  +t+t++D+ng +v+g  v+f      +agt+ +v ++ +G  +  +t++++gt  i ++  +
  gi|91773940|ref|YP_566632.1| 340 SPDSAINNLGESHEVTATVQDDNGAAVTGTMVHFEIAsgpNAGTTADVLTDTNGEASFSFTSQSVGTDVIVASFFN 415
                                   67788888778889*********************87566777999999*****************9888887643 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.1   3.5e-06     0.016       2      60 ..     354     417 ..     353     429 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.5e-06
               CarboxypepD_reg   2 isGrVtdasgapiagatVtvtna...dtgtvastttdadGafrlrglpp..gtysvtvsapGya 60 
                                   ++ +V d +ga+++g  V ++ a   + gt+a + td++G+ ++++  +  gt  +++s+ + +
  gi|91773940|ref|YP_566632.1| 354 VTATVQDDNGAAVTGTMVHFEIAsgpNAGTTADVLTDTNGEASFSFTSQsvGTDVIVASFFNSQ 417
                                   6789**************976541114589***********99999888889999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3147.29
//
Query:       gi|91773941|ref|YP_566633.1|  [L=576]
Description: RNA-directed DNA polymerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-42  145.7   0.1    3.1e-42  144.6   0.0    1.6  2  RVT_1            Reverse transcriptase (RNA-dependent DNA pol
    7.4e-28   96.6   2.2    7.4e-28   96.6   2.2    1.9  2  RVT_N            N-terminal domain of reverse transcriptase
    3.4e-24   84.7   6.4    8.9e-24   83.4   6.4    1.8  1  GIIM             Group II intron, maturase-specific domain
  ------ inclusion threshold ------
      0.012   15.6   3.5       0.12   12.3   0.5    3.7  3  Intron_maturas2  Type II intron maturase
       0.12   12.6   3.4       0.25   11.6   3.4    1.6  1  HNH              HNH endonuclease


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   0.0   8.7e-46   3.1e-42       1     222 []     129     350 ..     129     350 .. 0.95
   2 ?   -3.3   0.0       1.4     5e+03      94     136 ..     453     497 ..     444     498 .. 0.63

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 8.7e-46
                                   EE-TT.S-EEE......-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEBCCGCC CS
                         RVT_1   1 ipKkgpgsyRpisllsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaFd 81 
                                   i K g ++ Rp++++++ ++a+++l+a +L +++e + +++++gfr+ rst+da  ++  +++kk +a+++l+ D+k++Fd
  gi|91773941|ref|YP_566633.1| 129 IEKYGSDKKRPLGIPTMYDRAMQALYALALDPIAEVTADKRSFGFRKFRSTHDACSQIFGTISKKDSAQCILEGDIKGCFD 209
                                   56777899************************************************************************* PP

                                   CSBB-GGGGGGG-EEET..........................TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T...... CS
                         RVT_1  82 svpleellrkltafkvptklinliksflstrsfsvrv.ngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra... 158
                                   ++++++l+  +     +++   ++k+fl    +++ v ++   + +++k+g+pqG+++SP+l+n++++ ++  l+ ++   
  gi|91773941|ref|YP_566633.1| 210 NISHQWLIDNIPM---DKS---ILKQFL----KAGFVyEN---SLFPTKAGTPQGGIISPILANMTLDGIEGVLADKYhrg 277
                                   ********99888...534...899999....56666355...89*******************************99*** PP

                                   ...............TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE.....ESSEEETTEEE CS
                         RVT_1 159 ............kgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlftvkseevkyLGvtl 222
                                                +v+++rYaDD+++++k+ke ++e+ e ++++l + gl++++eKt +++     + +++LG ++
  gi|91773941|ref|YP_566633.1| 278 vsgkittrqrakHKVNFVRYADDFIVTAKTKEIAEEAKELIKNFLTDRGLELSDEKTLITH---IDDGFDFLGWNV 350
                                   ************************************************************9...89*******875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                   -EEET...........................TEEEEESB--ST- CS
                         RVT_1  94 afkvptklinliksflstrsfsvrvnge..eskgryekkglpqGs 136
                                    f++ +++++l+++ +  r   ++++++  + +++++++ l qGs
  gi|91773941|ref|YP_566633.1| 453 VFSTMKNQLKLMSDKMIVRNPQIKLDKNpyTDTEYFVERKLNQGS 497
                                   456666667777666666666666633335777888888888887 PP

>> RVT_N  N-terminal domain of reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   2.2   2.1e-31   7.4e-28       1      83 []      33     114 ..      33     114 .. 0.99
   2 ?   -3.3   0.0       3.2   1.1e+04      49      58 ..     365     372 ..     360     388 .. 0.53

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 2.1e-31
                         RVT_N   1 WkeidWkkvekkVfkLqkrIykAsqegdikkvkkLqklLtkSlsakllAvrrVtqdnkgkktagvDgvksltpkerlelve 81 
                                   W+ i+W++ve++V+++q rI+kA+ +++++ vk+L +lLt+S++akllAvr+V   nkg++tag+Dg+ ++tp +++++++
  gi|91773941|ref|YP_566633.1|  33 WNFINWSSVESHVNRIQVRITKAVINKNWNLVKRLSYLLTHSHYAKLLAVRKVIR-NKGRRTAGIDGEFWSTPVSKVNAAR 112
                                   *******************************************************.**********************998 PP

                         RVT_N  82 eL 83 
                                   +L
  gi|91773941|ref|YP_566633.1| 113 SL 114
                                   76 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                         RVT_N  49 AvrrVtqdnk 58 
                                   ++++Vt+  k
  gi|91773941|ref|YP_566633.1| 365 SIKKVTE--K 372
                                   4555555..2 PP

>> GIIM  Group II intron, maturase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   6.4   2.5e-27   8.9e-24       1      80 []     366     444 ..     366     444 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2.5e-27
                          GIIM   1 vkrlkrkireltkrsskgvsleelirklnpilrGWanYyrlgvakrvfskldhyirrrLrrwllrkhkkkkrrralrkyw 80 
                                   +k++++ki++++ ++ k++++e+li klnpi++GW nY++ + +k++fs +d  i++ L++w++r+h+ k+r ++++kyw
  gi|91773941|ref|YP_566633.1| 366 IKKVTEKISNTI-KDGKTWTQEDLISKLNPIITGWSNYHQGVASKETFSLIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 444
                                   6999********.7779**************************************************************9 PP

>> Intron_maturas2  Type II intron maturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.19   6.7e+02      68     103 ..      61      90 ..      49     125 .. 0.68
   2 ?   -0.4   0.0      0.29     1e+03       4      32 ..     216     249 ..     213     261 .. 0.76
   3 ?   12.3   0.5   3.4e-05      0.12      38     103 ..     383     444 ..     356     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.19
               Intron_maturas2  68 krlrerikyilrkscvkTLArKlklktvrkvikkfG 103
                                    +l++r+ y+l +s         kl  vrkvi+  G
  gi|91773941|ref|YP_566633.1|  61 WNLVKRLSYLLTHSH------YAKLLAVRKVIRNKG 90 
                                   466677777777664......344445555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.29
               Intron_maturas2   4 lvlnaPir.kiikkLakagfvktkk....ekgkP 32 
                                   l+ n+P++ +i k+  kagfv +++    + g P
  gi|91773941|ref|YP_566633.1| 216 LIDNIPMDkSILKQFLKAGFVYENSlfptKAGTP 249
                                   566899973588999******9986665555555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.4e-05
               Intron_maturas2  38 widledrdIllrykaiirgllnYYsfadnkkrlrerikyilrkscvkTLArKlklktvrkvikkfG 103
                                   w+   + d++ + + ii g +nY++++  k+++  +i + + + + k   r++ +k +  + +k+ 
  gi|91773941|ref|YP_566633.1| 383 WT---QEDLISKLNPIITGWSNYHQGVASKETFS-LIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 444
                                   44...457899**********************9.***9998888887777777777776666665 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.4   6.9e-05      0.25      23      46 ..     534     561 ..     515     562 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.9e-05
                           HNH  23 sq..ggadd..ieNlqllCksCHnkkhd 46 
                                   ++  g++dd  i Nl+ ++  CH++ h+
  gi|91773941|ref|YP_566633.1| 534 HHknGNHDDngITNLVYAHVYCHRQYHA 561
                                   44437777799**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4041.09
//
Query:       gi|91773942|ref|YP_566634.1|  [L=435]
Description: hypothetical protein Mbur_2006 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.033   14.9   2.9       0.04   14.7   0.2    2.5  3  GPI-anchored     Ser-Thr-rich glycosyl-phosphatidyl-inositol-
      0.052   13.5   0.1       0.11   12.5   0.1    1.5  1  Gram_pos_anchor  LPXTG cell wall anchor motif
      0.093   12.6   0.1       0.43   10.5   0.0    2.2  3  Deltameth_res    Deltamethrin resistance


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 ?   14.7   0.2   6.8e-06      0.04      22      81 ..     125     187 ..     111     195 .. 0.78
   2 ?   -2.6   0.0       1.6   9.6e+03      15      38 ..     255     279 ..     242     286 .. 0.61
   3 ?   -2.3   0.1       1.3   7.8e+03      25      53 ..     329     358 ..     318     371 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.8e-06
                  GPI-anchored  22 sgtdpgtvtlvLcagss...nnlksvktiasgiknsdgsytwtvpaslesggaYflqivsesn 81 
                                   s+  +g+++++L  +++   ++++ + t +s+i+ +dgsy++  ++s  ++g++ l+i  e++
  gi|91773942|ref|YP_566634.1| 125 SNVPKGSYSIKLTGNAQpakTSVDMKITATSEIPVKDGSYEFRYSTSSMPEGNFKLTIDGETK 187
                                   444569*******999974333444455599999999********************996666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                  GPI-anchored  15 vtitWkdsg.tdpgtvtlvLcagss 38 
                                   + i++++s  + + ++t+ +++++s
  gi|91773942|ref|YP_566634.1| 255 TYIKFTSSVtARSVPITIEILKETS 279
                                   4466666552333677777766666 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.3
                  GPI-anchored  25 dpgtvtlvLcagssnnlksv.ktiasgikn 53 
                                   dp  v+++ ++ +s++ ++v +t +++ ++
  gi|91773942|ref|YP_566634.1| 329 DPHRVSIMHYNSGSDQWETVpTTYIKTLDG 358
                                   566777777776664433332555555554 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.8e-05      0.11      17      41 ..     410     434 ..     410     435 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXX CS
               Gram_pos_anchor  17 nifltaaGllallggllLlvkrRKk 41 
                                   n+++++aG+++l+g+l ++ k++ k
  gi|91773942|ref|YP_566634.1| 410 NLVTLIAGITILTGSLIFYRKKHIK 434
                                   7899**************9999765 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.5   9.2e+03       2      15 ..     156     169 ..     155     170 .. 0.81
   2 ?   -3.9   0.0       2.2   1.3e+04       6      11 ..     174     179 ..     173     180 .. 0.87
   3 ?   10.5   0.0   7.3e-05      0.43      20      41 ..     408     430 ..     394     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.5
                 Deltameth_res   2 DlPvPeGdwkeqys 15 
                                   ++Pv  G+++  ys
  gi|91773942|ref|YP_566634.1| 156 EIPVKDGSYEFRYS 169
                                   89999999987775 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.2
                 Deltameth_res   6 PeGdwk 11 
                                   PeG++k
  gi|91773942|ref|YP_566634.1| 174 PEGNFK 179
                                   9***98 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 7.3e-05
                 Deltameth_res  20 kYNav.LaaGiviligTialake 41 
                                    YN v L+aGi+il g++++ ++
  gi|91773942|ref|YP_566634.1| 408 SYNLVtLIAGITILTGSLIFYRK 430
                                   6***99************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3148.72
//
Query:       gi|91773943|ref|YP_566635.1|  [L=373]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.008   16.2   0.0      0.035   14.1   0.0    2.1  2  DUF772    Transposase domain (DUF772)
  ------ inclusion threshold ------
      0.026   14.1   0.1      0.057   12.9   0.1    1.5  1  DUF4283   Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.9e-06     0.035       5      70 ..      62     130 ..      61     133 .. 0.81
   2 ?   -3.1   0.0      0.96   8.6e+03      21      37 ..     310     326 ..     309     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                        DUF772   5 yppelmlkllllqylyglSdreleeal.renlsfrwflgldleedpvpdhstlsrfRk.rlee..lerlf 70 
                                   y +  m+kl++++ + +lS ++++  l +e +++  f + +    ++p+++tl +f k rl++  l++++
  gi|91773943|ref|YP_566635.1|  62 YKVSSMIKLIVVKCYRNLSFEKTISTLtKEEAQLLSFEDNNGI-MNLPSPATLHHFVKyRLGKtgLDEVM 130
                                   67889*************9999998772566667777664433.89*****************9977776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.96
                        DUF772  21 glSdreleealrenlsf 37 
                                   ++S r  +e++++++ +
  gi|91773943|ref|YP_566635.1| 310 DYSHRGECERVHNHIKW 326
                                   568888999***99998 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.3e-06     0.057      13      54 ..     241     286 ..     234     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-06
                       DUF4283  13 lvgrfsgkk....pslsalrrvlakaWklkggvkikelgdglflfr 54 
                                   ++++fs++k      ++++ ++++k+Wkl+g +++k+ ++ +fl++
  gi|91773943|ref|YP_566635.1| 241 VIAYFSDSKvqyeGMMERIDHWVNKMWKLGGSIHMKYEEKLHFLYE 286
                                   788887777344334567899**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 3111.04
//
Query:       gi|91773944|ref|YP_566636.1|  [L=291]
Description: hypothetical protein Mbur_2008 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-112  374.0   0.1   5.9e-112  373.8   0.1    1.0  1  DUF1616         Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
      0.017   14.4   0.1       0.03   13.6   0.1    1.3  1  Chordopox_A33R  Chordopoxvirus A33R protein
      0.076   13.2   0.9        1.4    9.1   0.0    2.5  2  DUF872          Eukaryotic protein of unknown function (DUF87
        1.9    8.6   4.6       0.36   10.9   0.3    1.9  2  DUF3671         Protein of unknown function
        2.9    8.0   8.1        4.2    7.5   2.7    2.7  2  DUF4870         Domain of unknown function (DUF4870)


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 !  373.8   0.1  1.7e-115  5.9e-112       1     293 []      11     287 ..      11     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 373.8 bits;  conditional E-value: 1.7e-115
                       DUF1616   1 vlvlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtpwgi 81 
                                   v+ ++ll++ +il+p l++t++R++lglp+vLflPGY liaaLFP+++d+dgieR+aLSfglSia+vpligl+ln+tpwgi
  gi|91773944|ref|YP_566636.1|  11 VVSMVLLTCGFILIPQLSDTAIRTILGLPMVLFLPGYSLIAALFPNRDDLDGIERVALSFGLSIAVVPLIGLGLNYTPWGI 91 
                                   57899**************************************************************************** PP

                       DUF1616  82 rlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldkalnvlLvvsivlavaalgyavva 162
                                   rl pil+sls+ft+ +++vA++rR++lpe e+fsvp++++++s+k el++k++++ld++l+++Lv+si++++++l+y+vv+
  gi|91773944|ref|YP_566636.1|  92 RLLPILISLSFFTIGMCVVALLRRRTLPEGEEFSVPFASTYHSMKGELSKKPDNKLDRVLSIILVLSIIASIVTLIYVVVT 172
                                   ***************************************************999*************************** PP

                       DUF1616 163 PkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrrevtl 243
                                   PkegekfTe+y+lg dg   +a++ypt++t+ges +vivg++NhE+e ++Y+++++l++  ++      ++   ++  ++l
  gi|91773944|ref|YP_566636.1| 173 PKEGEKFTEFYILGIDG---MADGYPTNFTLGESGNVIVGVVNHEYEVTDYSLRLFLEN--NS------SSVAYEQLYMSL 242
                                   *****************...*************************************98..44......345689****** PP

                       DUF1616 244 adnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                   ++netwe+el++ pe  ge+++l+flLYkd      +++ +yr+lhlw++
  gi|91773944|ref|YP_566636.1| 243 EHNETWEEELSFMPEVVGEDMKLQFLLYKD-----GNMTVPYRDLHLWID 287
                                   ******************************.....*************96 PP

>> Chordopox_A33R  Chordopoxvirus A33R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.3e-06      0.03      28      61 ..     138     171 ..     121     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-06
                Chordopox_A33R  28 klkkktkkkkskclsillrvaiitsilsllaiat 61 
                                    l kk  +k  ++lsi+l ++ii+si++l+ +  
  gi|91773944|ref|YP_566636.1| 138 ELSKKPDNKLDRVLSIILVLSIIASIVTLIYVVV 171
                                   48899999*********************98865 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 ?    1.7   0.4     0.077   2.8e+02      54      90 ..      11      46 ..       5      56 .. 0.54
   2 ?    9.1   0.0   0.00038       1.4      47      84 ..     150     187 ..     123     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.077
                        DUF872 54 llGlvLlllgvvilvepseGvssavflvlGlllfiPG 90
                                  ++ +vLl+ g+ il+ + + +     l l ++lf+PG
  gi|91773944|ref|YP_566636.1| 11 VVSMVLLTCGF-ILIPQLSDTAIRTILGLPMVLFLPG 46
                                  33344444443.3333334444444466666777777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00038
                        DUF872  47 laallLlllGlvLlllgvvilvepseGvssavflvlGl 84 
                                   +++++L+l  ++ +++ ++++v+p+eG++ + f++lG+
  gi|91773944|ref|YP_566636.1| 150 VLSIILVLSIIASIVTLIYVVVTPKEGEKFTEFYILGI 187
                                   57888888888899999*******************98 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.5      0.97   3.5e+03      48      61 ..      10      23 ..       7      54 .. 0.70
   2 ?   10.9   0.3   9.9e-05      0.36      46     109 ..      94     171 ..      87     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.97
                       DUF3671 48 lilpvllpligliv 61
                                  +++ ++l ++g+i+
  gi|91773944|ref|YP_566636.1| 10 IVVSMVLLTCGFIL 23
                                  55555555555553 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.9e-05
                       DUF3671  46 lllilpvllpliglivpilfeaksk..............kslkkkelevlatsieklytiffiilvviillvliYili 109
                                   l++++ + +++ig+ v++l   +                +s+k +  ++ +++++ +  i+++ +++  +++liY+++
  gi|91773944|ref|YP_566636.1|  94 LPILISLSFFTIGMCVVALLRRRTLpegeefsvpfastyHSMKGELSKKPDNKLDRVLSIILVLSIIASIVTLIYVVV 171
                                   5677888899999999988554443899********888777777777788888888888888889999999***987 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.7    0.0012       4.2      45     106 ..      65     129 ..       8     131 .. 0.81
   2 ?    2.5   0.3     0.041   1.5e+02      75     102 ..     153     180 ..     146     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                       DUF4870  45 kealNFqislliysiilivlsllvligf.lllllllllllnlvlviiaaika...negeeyryplt 106
                                   + al F +s+ ++ +i++ l   + +g+ ll++l+ l  + + ++++a ++     egee++ p+ 
  gi|91773944|ref|YP_566636.1|  65 RVALSFGLSIAVVPLIGLGL-NYTPWGIrLLPILISLSFFTIGMCVVALLRRrtlPEGEEFSVPFA 129
                                   55788999999887777777.4666677668999***************99855568999999985 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.041
                       DUF4870  75 lllllllllnlvlviiaaikanegeeyr 102
                                   ++l+l +++++v  i+ ++  +ege+++
  gi|91773944|ref|YP_566636.1| 153 IILVLSIIASIVTLIYVVVTPKEGEKFT 180
                                   4555556666666666666667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2029.97
//
Query:       gi|91773945|ref|YP_566637.1|  [L=271]
Description: abortive infection protein [Methanococcoides burtonii DSM 6242]
Scores for 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-17   61.1   7.3    9.7e-17   61.1   7.3    2.5  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.8   7.3         1   1.8e+04      13      13 ..      67      67 ..      19     157 .. 0.61
   2 !   61.1   7.3   5.4e-21   9.7e-17       3      91 ..     171     261 ..     169     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: -5.8 bits;  conditional E-value: 1
                                  H CS
                          CPBP 13 l 13
                                  +
  gi|91773945|ref|YP_566637.1| 67 V 67
                                  1 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 5.4e-21
                                   TTHHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG..HHH.HHHHHHHHHHHHHHHHHTT-HH CS
                          CPBP   3 nlllvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn..gps.vllaalaGlvlgylylktgsll 80 
                                   nll + ++++++++++EE++fR++l+++l++  ++   ++++silFg++H  +    + +l++a+aGlvlgy+y +++sl+
  gi|91773945|ref|YP_566637.1| 171 NLLKISIVMIIFVGFFEEIIFRSILQTKLESMIGKYQGLFLASILFGVMHSGYgtL-YeMLFTAFAGLVLGYMYQRSRSLF 250
                                   66788899************************55589*************999633.36********************** PP

                                   HHHHHHHHHHH CS
                          CPBP  81 aaillHallnl 91 
                                    + ++H+++n+
  gi|91773945|ref|YP_566637.1| 251 LVSITHGFVNV 261
                                   **********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1863.87
//
Query:       gi|91773946|ref|YP_566638.1|  [L=83]
Description: hypothetical protein Mbur_2010 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 684.36
//
Query:       gi|91773947|ref|YP_566639.1|  [L=606]
Description: hypothetical protein Mbur_2011 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.9   0.1       0.25   11.7   0.0    2.5  2  DUF4969   Domain of unknown function (DUF4969)


Domain annotation for each model (and alignments):
>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.4e-05      0.25       7      49 ..      10      52 ..       5      74 .. 0.81
   2 ?   -0.7   0.0       0.1   1.8e+03      48      68 ..     469     489 ..     458     495 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                       DUF4969  7 lLvsvLvlFillavaCsdsedneesveiilkeielsvddpikl 49
                                  l+   L+ F++++v  +++ ++e   ei++ e  +s  d   +
  gi|91773947|ref|YP_566639.1| 10 LILALLITFSFITVVSANTTNDEYIMEISIGEQHVSFADHDDP 52
                                  33345788**********9999999*******99998775554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.1
                       DUF4969  48 klvdengeatv..evdvdPkskl 68 
                                      den+ + v  e+ ++P   +
  gi|91773947|ref|YP_566639.1| 469 YWYDENNTTWVplEGSGNP--SF 489
                                   5679****99844566666..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4118.91
//
Query:       gi|91773948|ref|YP_566640.1|  [L=249]
Description: hypothetical protein Mbur_2013 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-06   25.8   0.0    8.8e-05   22.6   0.0    2.0  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.9e-09   8.8e-05      94     178 ..      90     198 ..      23     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.9e-09
                        AbiEii  94 f.ggyarqkikieigfreavppaerreippyleel........ggpafevpvysleellaeKllalldrgrdrsr...... 159
                                   +  +  ++++ i++++r  + p+e ++++ +++ l         ++++e+ v ++++ll  Kl a+ dr+ + ++      
  gi|91773948|ref|YP_566640.1|  90 VkKETEAGPVIIDFATRQKPFPFEGKDMSLDFSILngntetrqIRGGIEMAVPNRATLLVLKLKAVWDRNYRIAHgtsddi 170
                                   24667788999******************************************************9955555555777777 PP

                        AbiEii 160 .......aRDlyDlalLle..aeldaea 178
                                          ++D+ D+ +L++  ++ ++ +
  gi|91773948|ref|YP_566640.1| 171 ewetgklIKDYADVLALIDpdHGGEQIE 198
                                   7888888***********9876665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1889.29
//
Query:       gi|91773949|ref|YP_566641.1|  [L=343]
Description: hypothetical protein Mbur_2014 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   12.1   0.0      0.095   11.5   0.0    1.3  1  BRO1      BRO1-like domain


Domain annotation for each model (and alignments):
>> BRO1  BRO1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.3e-06     0.095     317     352 ..      49      84 ..      14     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          BRO1 317 aekDNdlIYheevPsesslpeikkaslvkaipleee 352
                                   + +DNd+IY+ e+ s+++++ i +++l + + l++e
  gi|91773949|ref|YP_566641.1|  49 LLEDNDTIYLIEIKSKATIDTIARMNLLRDLWLQNE 84 
                                   558*************************99888332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2569.15
//
Query:       gi|91773950|ref|YP_566642.1|  [L=298]
Description: endonuclease IV [Methanococcoides burtonii DSM 6242]
Scores for complete 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   54.4   0.0    1.3e-14   54.1   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 !   54.1   0.0   7.3e-19   1.3e-14       2     203 ..      48     253 ..      47     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 7.3e-19
                                   HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaL 82 
                                   +++a++G  ++El +  +v ++   +e+++ +r+ ++e ++ ++++ +++ + ++ e+e      +sv+++ + +++ a +
  gi|91773950|ref|YP_566642.1|  48 RRIAQLGLGCMELEFVRGVRMK---EETAANVRQTAEEENVALSVHAPYYINLNSAEEEK---ITASVQRIYESARIGALC 122
                                   689******************9...59***************************998544...4669************** PP

                                   TBSEEEEEBCCGBCTTTSGHH...HHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEE CS
                  AP_endonuc_2  83 GapllvlhpGtagagpkgsee...eawerlaeslneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgvcl 160
                                   Ga  +v+hp    ++++ s +   e +  l e+l   +   e  +v l  Et+ +++++   ee++ +  a++   v  c+
  gi|91773950|ref|YP_566642.1| 123 GASSIVFHPA---YYQGHSSKkvmEKVTGLLEGLTSGLSD-EGIDVVLRPETTGKATQFGSLEETLMMATAIEG--VMPCI 197
                                   **********...455555551246666666666666666.555699**********99988***********8..***** PP

                                   EHHHHHHH.......TTTHHHHHHHHHGG.......EEEEEE.EESSTTTTSSTTEE CS
                  AP_endonuc_2 161 DtgHllia.......eedvddalraladr.......ikhvHikDakgdlgagrdrhv 203
                                   D++Hl+++        e ++++l+ +++          h Hi+ +   +++g+ +h+
  gi|91773950|ref|YP_566642.1| 198 DFSHLHARscgeyntIEEFRSVLESVESAlgregleNMHCHISGIAY-GNKGEKNHL 253
                                   ********999888877777777777777777886667777766666.555666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1917.30
//
Query:       gi|91773951|ref|YP_566643.1|  [L=372]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   85.1   1.7    2.8e-23   81.6   1.3    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.1e-11   44.1   0.1    4.4e-11   43.1   0.1    1.5  1  OrfB_IS605      Probable transposase
    0.00012   22.3   1.4    0.00026   21.2   1.4    1.5  1  C1_2            C1 domain
     0.0021   17.9   0.8     0.0046   16.8   0.8    1.5  1  C1_1            Phorbol esters/diacylglycerol binding domain 
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.036   14.1   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.059   13.3   0.4        0.1   12.5   0.4    1.4  1  DUF4202         Domain of unknown function (DUF4202)
       0.07   13.0   0.6       0.36   10.6   0.0    2.4  3  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
      0.076   12.9   1.5        3.1    7.8   0.1    2.7  2  zinc_ribbon_4   zinc-ribbon domain
      0.077   13.2   1.4       0.19   12.0   0.7    1.9  2  IBR             IBR domain, a half RING-finger domain
       0.08   13.0   0.7       0.19   11.8   0.7    1.6  1  DZR             Double zinc ribbon
        0.2   11.4   4.9        1.7    8.4   0.3    2.4  2  zf-C2H2_11      zinc-finger C2H2-type
       0.28   10.9   6.1       0.42   10.4   1.0    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.33   10.7   5.5        1.3    8.7   5.5    2.0  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.36   11.0   2.2        8.1    6.7   0.1    2.7  3  Zn-ribbon_8     Zinc ribbon domain
        1.8    8.1   4.0        9.9    5.7   0.5    2.6  2  zf-ribbon_3     zinc-ribbon domain
        2.3    8.1   6.7         27    4.7   0.9    2.5  2  zinc_ribbon_2   zinc-ribbon domain
        2.6    8.0   4.1         16    5.5   0.3    2.4  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.39   4.1e+02      10      39 ..      95     125 ..      94     139 .. 0.83
   2 !   81.6   1.3   2.7e-26   2.8e-23       1      68 [.     280     347 ..     280     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.39
                OrfB_Zn_ribbon  10 ykakeyGikveevnpay.TSktCseCgsknk 39 
                                   y a +y + v+++   y + +  s +g++n 
  gi|91773951|ref|YP_566643.1|  95 YSAIRYNKRVVTIHMQYnSATIASIHGRVNI 125
                                   77899999******99967777888888775 PP

  == domain 2  score: 81.6 bits;  conditional E-value: 2.7e-26
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                   f++l+++++yka+   ++v+ v+p+y+S++Cs+Cg++ k +++g  ++C+nCgf++++D+nAa+Ni++
  gi|91773951|ref|YP_566643.1| 280 FYQLEQFIRYKAEAVAKQVVSVDPRYSSQKCSKCGHIYKGNRDGSSYRCRNCGFQIHADLNAARNIAQ 347
                                   899***************************************************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.1   4.1e-14   4.4e-11       3     102 ..     158     248 ..     156     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 4.1e-14
                    OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrk 83 
                                    v++++e+pkp gn+ +giD Gi n a+++++     +++  ++k++  ++a  ++elqsk  ks     a+r l++++rk
  gi|91773951|ref|YP_566643.1| 158 HVTLRTESPKPVGNTILGIDRGIVNVAVCSNNV----FFNTSSIKNTRAKYAYLRKELQSKGTKS-----AKRLLKKISRK 229
                                   5788899*************************9....77777*******************6666.....8********** PP

                    OrfB_IS605  84 rsrrrkhllhklathlikt 102
                                    +r+++++ h +a+++++ 
  gi|91773951|ref|YP_566643.1| 230 ERRFVTDVNHCIAKDIVNM 248
                                   ****************985 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.4   2.5e-07   0.00026      13      44 ..     302     337 ..     294     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.5e-07
                          C1_2  13 edssesfnCsaCgrkidgff....YsCseCdfslhv 44 
                                   +++++s +Cs Cg+  +g++    Y+C  C f++h 
  gi|91773951|ref|YP_566643.1| 302 DPRYSSQKCSKCGHIYKGNRdgssYRCRNCGFQIHA 337
                                   478999*********666666678***********7 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 !   16.8   0.8   4.4e-06    0.0046      10      40 ..     306     337 ..     301     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.4e-06
                                   S--B-TTT-SB--S.SSS-EEEETTT--EE-C CS
                          C1_1  10 qptfCkhCgeflwg.kekqglkCswCkllvHk 40 
                                   ++++C++Cg + +g      ++C++C++ +H 
  gi|91773951|ref|YP_566643.1| 306 SSQKCSKCGHIYKGnRDGSSYRCRNCGFQIHA 337
                                   789****************************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 ?   14.1   0.1   3.4e-05     0.036      53      94 ..     290     333 ..     234     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                                   CC.TTTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSS CS
                          HypA  53 egtvlegaeLeieevpvkvrCreCgkefeleek..alrCpkCgs 94 
                                   + +++++ +++++    + +C++Cg+ ++ +++  ++rC +Cg 
  gi|91773951|ref|YP_566643.1| 290 KAEAVAKQVVSVDPRYSSQKCSKCGHIYKGNRDgsSYRCRNCGF 333
                                   555567788899999999***********76645699*****95 PP

>> DUF4202  Domain of unknown function (DUF4202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   9.8e-05       0.1      68     146 ..     195     274 ..     191     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.8e-05
                       DUF4202  68 ssYpegragYlkWRtelkkrqAelaaelleeagyde.eeiervaalvrkeelkrdeetqlLEDvacLvFLedqfeeFakk 146
                                   ss +++ra Y   R+el++   + a++ll++ + +e   +  v++ ++k+ ++   ++ +LED   +   +++ ++F++k
  gi|91773951|ref|YP_566643.1| 195 SSIKNTRAKYAYLRKELQSKGTKSAKRLLKKISRKErRFVTDVNHCIAKDIVNMPFDVIALEDLTSIRVQKRKGKNFNRK 274
                                   67889*************************999866156899************9********99887777777777766 PP

>> 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 ?   -2.4   0.0       3.5   3.7e+03      58      84 ..      93     119 ..      69     134 .. 0.54
   2 ?   10.6   0.0   0.00034      0.36     100     153 ..     178     232 ..     146     236 .. 0.89
   3 ?   -0.9   0.0       1.2   1.3e+03      88     116 ..     277     307 ..     273     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                Topo-VIb_trans  58 ekaeilRfaNrvPLlydegadvitkav 84 
                                   +  + +R+  rv  ++ + + +++ ++
  gi|91773951|ref|YP_566643.1|  93 QPYSAIRYNKRVVTIHMQYNSATIASI 119
                                   222455555555544444444444443 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                Topo-VIb_trans 100 pvvvlvhvastkvPfkseg.KeaiadveeiekeiklalqevarkLkkylskkeke 153
                                   + +v v v+s +v f++ + K++ a++  ++ke+++   + a++L k++s+ke++
  gi|91773951|ref|YP_566643.1| 178 RGIVNVAVCSNNVFFNTSSiKNTRAKYAYLRKELQSKGTKSAKRLLKKISRKERR 232
                                   56789**********7666599999************99999999999**99985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.2
                Topo-VIb_trans  88 nwkrYkleq..pedpvvvlvhvastkvPfks 116
                                   nw+ Y+leq    +  +v  +v+s+   ++s
  gi|91773951|ref|YP_566643.1| 277 NWSFYQLEQfiRYKAEAVAKQVVSVDPRYSS 307
                                   8999***997756677888888888777766 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0029       3.1      27      35 ..     309     317 ..     300     318 .. 0.81
   2 ?    3.5   0.1     0.064        68      23      34 ..     323     334 ..     320     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                 zinc_ribbon_4  27 rCskCghvF 35 
                                   +CskCgh+ 
  gi|91773951|ref|YP_566643.1| 309 KCSKCGHIY 317
                                   9******85 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.064
                 zinc_ribbon_4  23 gvkvrCskCghv 34 
                                   g++ rC +Cg  
  gi|91773951|ref|YP_566643.1| 323 GSSYRCRNCGFQ 334
                                   778899999965 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 ?   -2.4   0.0       5.6   5.9e+03      18      34 ..      86     102 ..      79     110 .. 0.72
   2 ?   12.0   0.7   0.00018      0.19       3      47 ..     289     334 ..     287     338 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.6
                           IBR  18 lkwCprpdCeaiiekse 34 
                                   lk Cp+++  ++i+ ++
  gi|91773951|ref|YP_566643.1|  86 LKTCPESQPYSAIRYNK 102
                                   78899877767766665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00018
                           IBR   3 yeklklkksles.dpn..lkwCprpdCeaiieksegcksvtCskCgfe 47 
                                   y+  + +k++ s dp    ++C   +C++i++ + + +s +C++Cgf+
  gi|91773951|ref|YP_566643.1| 289 YKAEAVAKQVVSvDPRysSQKCS--KCGHIYKGNRDGSSYRCRNCGFQ 334
                                   555555555444477766899*9..********99977779*****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00018      0.19      12      43 ..     307     340 ..     301     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                           DZR  12 arfCseCgtklkavaa..edrCpsCgekvdpear 43 
                                   ++ Cs+Cg+  k   +  ++rC +Cg +++++ +
  gi|91773951|ref|YP_566643.1| 307 SQKCSKCGHIYKGNRDgsSYRCRNCGFQIHADLN 340
                                   678******999766699********99887765 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 ?    4.6   0.6     0.026        28       3      12 ..     306     315 ..     305     318 .. 0.86
   2 ?    8.4   0.3    0.0016       1.7       1      11 [.     322     332 ..     322     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.026
                    zf-C2H2_11   3 stcqCleCGl 12 
                                   s+++C +CG 
  gi|91773951|ref|YP_566643.1| 306 SSQKCSKCGH 315
                                   89*******6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
                    zf-C2H2_11   1 destcqCleCG 11 
                                   d s+++C+ CG
  gi|91773951|ref|YP_566643.1| 322 DGSSYRCRNCG 332
                                   78********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 ?    2.9   0.4     0.089        94       3       9 ..     310     316 ..     309     319 .. 0.81
   2 ?   10.4   1.0    0.0004      0.42       1      10 [.     326     335 ..     326     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.089
                  Rubredoxin_2   3 CsqCGfe 9  
                                   Cs+CG+ 
  gi|91773951|ref|YP_566643.1| 310 CSKCGHI 316
                                   9***996 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0004
                  Rubredoxin_2   1 YvCsqCGfes 10 
                                   Y+C++CGf+ 
  gi|91773951|ref|YP_566643.1| 326 YRCRNCGFQI 335
                                   9*******96 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.7      0.18   1.9e+02      19      25 ..     309     315 ..     302     321 .. 0.87
   2 ?    8.7   5.5    0.0013       1.3       2      27 ..     309     335 ..     308     336 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                                   --SSS-- CS
                DNA_RNApol_7kD  19 RCkeCGh 25 
                                   +C +CGh
  gi|91773951|ref|YP_566643.1| 309 KCSKCGH 315
                                   7999999 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                                   B-SSS--B--.--SSS----SSS---- CS
                DNA_RNApol_7kD   2 iCgeCgaevs.lkkgdpiRCkeCGhRi 27 
                                   +C +Cg+  +  + g + RC++CG+ i
  gi|91773951|ref|YP_566643.1| 309 KCSKCGHIYKgNRDGSSYRCRNCGFQI 335
                                   699999999989999**********87 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         8   8.5e+03      26      31 ..      86      91 ..      79      93 .. 0.73
   2 ?    3.1   0.1       0.1   1.1e+02       7      15 ..     309     317 ..     303     324 .. 0.83
   3 ?    6.7   0.1    0.0077       8.1       6      14 ..     326     334 ..     325     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8
                   Zn-ribbon_8 26 ltaCPe 31
                                  l++CPe
  gi|91773951|ref|YP_566643.1| 86 LKTCPE 91
                                  678*97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                   Zn-ribbon_8   7 rCeeCghef 15 
                                   +C +Cgh +
  gi|91773951|ref|YP_566643.1| 309 KCSKCGHIY 317
                                   699999976 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0077
                   Zn-ribbon_8   6 YrCeeCghe 14 
                                   YrC++Cg +
  gi|91773951|ref|YP_566643.1| 326 YRCRNCGFQ 334
                                   *******65 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5    0.0094       9.9       3      11 ..     308     316 ..     306     320 .. 0.81
   2 ?    2.8   0.2     0.081        86      19      26 .]     328     335 ..     326     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0094
                   zf-ribbon_3   3 vrCPnCGap 11 
                                   ++C++CG++
  gi|91773951|ref|YP_566643.1| 308 QKCSKCGHI 316
                                   589999985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.081
                   zf-ribbon_3  19 CpyCGtkl 26 
                                   C +CG ++
  gi|91773951|ref|YP_566643.1| 328 CRNCGFQI 335
                                   99999876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.9     0.025        27       1      21 [.     309     315 ..     306     316 .. 0.62
   2 ?    3.0   6.8     0.082        86       1      22 [.     309     334 ..     309     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                   +              C++CG+
  gi|91773951|ref|YP_566643.1| 309 K--------------CSKCGH 315
                                   3..............555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.082
                 zinc_ribbon_2   1 fCpnCG...aelqdnakF.CpyCGtp 22 
                                   +C++CG   + + d++ + C +CG+ 
  gi|91773951|ref|YP_566643.1| 309 KCSKCGhiyKGNRDGSSYrCRNCGFQ 334
                                   79999933335667777799999975 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.015        16      12      21 ..     308     317 ..     308     317 .. 0.89
   2 ?    3.5   0.4     0.063        67      13      21 ..     327     335 ..     326     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                       DUF35_N  12 qrCpdCGtvq 21 
                                   q+C++CG+ +
  gi|91773951|ref|YP_566643.1| 308 QKCSKCGHIY 317
                                   9******975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.063
                       DUF35_N  13 rCpdCGtvq 21 
                                   rC++CG  +
  gi|91773951|ref|YP_566643.1| 327 RCRNCGFQI 335
                                   9*****866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2504.52
//
Query:       gi|91773952|ref|YP_566644.1|  [L=115]
Description: hypothetical protein Mbur_2017 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 778.65
//
Query:       gi|91773953|ref|YP_566645.1|  [L=391]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-41  140.4   2.7    1.2e-23   83.8   0.1    2.2  2  Glycos_transf_2  Glycosyl transferase family 2
    8.9e-11   42.1   3.1    1.1e-06   28.7   0.1    2.4  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.1e-09   38.7   0.1    9.5e-05   22.8   0.0    2.4  2  Glyco_tranf_2_4  Glycosyl transferase family 2
    3.5e-09   36.5   0.2    5.6e-05   22.7   0.0    2.1  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.061   12.9   0.2       0.15   11.6   0.0    1.6  2  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.4   5.5e-19     2e-15       3     118 ..       6     115 ..       4     149 .. 0.93
   2 !   83.8   0.1   3.3e-27   1.2e-23       2     166 ..     200     360 ..     199     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 5.5e-19
                                   EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS.. CS
               Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd.. 81 
                                    ip+yN e  +++ +++     +y+ +++ivvDDgS+D t+ i+ +      + rvir+  n Gka+al ++++aa+    
  gi|91773953|ref|YP_566645.1|   6 AIPAYNAEVHIKNIIKRT----KYYVDHVIVVDDGSSDATAHIATNM-----GARVIRHGDNLGKAAALATAFEAAKKLnp 77 
                                   59***********99944....566**********************.....9*************************99* PP

                                   .EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEE CS
               Glycos_transf_2  82 .yilflDaDdepdpdwleklvealekdgadvvlgqrpr 118
                                    +++++ a   ++pd+++ ++++    +advv g+   
  gi|91773953|ref|YP_566645.1|  78 aVLVTIYANGFHNPDDIPSILKPVLSKDADVVNGAYIS 115
                                   ********************************998766 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 3.3e-27
                                   EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS. CS
               Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd. 81 
                                   vv+p+yNeek++++t+e + +      ++i+v++D+StD+t++++e l  +dprv vi++e n+G ++al +g ++a  + 
  gi|91773953|ref|YP_566645.1| 200 VVVPAYNEEKLIKNTVEGIPQY----VDRIYVINDASTDNTAKVIETL--NDPRVVVITHETNKGVGAALINGYKKALREn 274
                                   8****************76666....**********************..69***************************99 PP

                                   ..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEE.EECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCC CS
               Glycos_transf_2  82 ..yilflDaDdepdpdwleklvealekdgadvvlgqrpr.ifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaa 159
                                     +++++  Dd+++pd l kl+ ++ +++ad   g+r   i+++ +  +++k    n  l + ++ +s ++++++   +++
  gi|91773953|ref|YP_566645.1| 275 mdVVAVMAGDDQMNPDQLYKLIIPIIEGRADYTKGNRLMdIEYHIGMSKWRKV--GNAVLTILTKIGSGYWHIMDPQNGYT 353
                                   *********************************99985313333333333333..46788888888888888888888888 PP

                                   EEEEHHH CS
               Glycos_transf_2 160 llrreal 166
                                   +++++al
  gi|91773953|ref|YP_566645.1| 354 AISKDAL 360
                                   8888877 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 !   13.6   0.3   1.3e-05     0.047       7     120 ..       6     109 ..       2     118 .. 0.76
   2 !   28.7   0.1   3.2e-10   1.1e-06       3     107 ..     197     294 ..     194     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
               Glyco_tranf_2_3   7 lVptfneedvlgevlesllaqe.yprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealrav 86 
                                   ++p++n+    +  + ++++ + y  ++v+vv+d+s+++t+  a         ++ rv++  +nlg   k+ al+ a++a+
  gi|91773953|ref|YP_566645.1|   6 AIPAYNA----EVHIKNIIKRTkYYVDHVIVVDDGSSDATAHIATN-------MGARVIRHGDNLG---KAAALATAFEAA 72 
                                   5666666....334666675543899***************98875.......6779997777777...888999999999 PP

               Glyco_tranf_2_3  87 k...sdlvllvDdDtvvePdtlkrllqffltpkvgav 120
                                   k   +++++ + +     Pd ++++l  +l++++++v
  gi|91773953|ref|YP_566645.1|  73 KklnPAVLVTIYANGFHNPDDIPSILKPVLSKDADVV 109
                                   9887888888888888888888888877777777776 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.2e-10
               Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                   ++ v+Vp++nee+ + +++e +  +    ++++v+ d s++ t++v+e     l d rv+v++ + n g++++   +n+  
  gi|91773953|ref|YP_566645.1| 197 RIGVVVPAYNEEKLIKNTVEGIPQY---VDRIYVINDASTDNTAKVIET----LNDPRVVVITHETNKGVGAAL--INGYK 268
                                   588*******************996...99*****************85....788899999998888875443..45555 PP

               Glyco_tranf_2_3  84 ravk..sdlvllvDdDtvvePdtlkr 107
                                   +a +   d+v+++ +D+   Pd l +
  gi|91773953|ref|YP_566645.1| 269 KALRenMDVVAVMAGDDQMNPDQLYK 294
                                   55444499***********9997654 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 !   13.6   0.0   2.1e-05     0.074       3      48 ..      12      55 ..      10      81 .. 0.69
   2 !   22.8   0.0   2.7e-08   9.5e-05       1      51 [.     205     256 ..     205     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
               Glyco_tranf_2_4  3 eadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhv 48
                                  ++  +++ ++  + + +d+++v+d++s+D t++i  ++  ++++++
  gi|91773953|ref|YP_566645.1| 12 AEVHIKNIIKRTKYY-VDHVIVVDDGSSDATAHIATNMG-ARVIRH 55
                                  555566666666555.9*****************99973.344444 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.7e-08
               Glyco_tranf_2_4   1 rneadiLpeflahhlalgfdrilvydndstDgtrailkel..pevkllhvdks 51 
                                   +ne+++++++++ + ++ +dri+v+++ stD+t+++++ l  p+v +++++++
  gi|91773953|ref|YP_566645.1| 205 YNEEKLIKNTVEGIPQY-VDRIYVINDASTDNTAKVIETLndPRVVVITHETN 256
                                   69**************9.*******************9983355666666643 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 !   12.0   0.1   2.9e-05       0.1       4     108 ..       7     103 ..       2     155 .. 0.66
   2 !   22.7   0.0   1.6e-08   5.6e-05       2     103 ..     200     296 ..     199     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
               Glyco_tranf_2_2   4 iplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa...skae 81 
                                   ip ++ e +  i++ ++ ++kyy    ++ivvddgSs+ +++   ++ +   +    d+     ++aaa    +   +k +
  gi|91773953|ref|YP_566645.1|   7 IPAYNAEVH--IKNIIK-RTKYY--VDHVIVVDDGSSDATAHIATNMGARVIRHG--DN----LGKAAALATAFeaaKKLN 76 
                                   566666655..777665.56665..3369**********9998887765433222..22....233333333330003444 PP

               Glyco_tranf_2_2  82 sdlvlFlDaDcfissDkfekilkliti 108
                                     +++ + a+ f  +D +  ilk + +
  gi|91773953|ref|YP_566645.1|  77 PAVLVTIYANGFHNPDDIPSILKPVLS 103
                                   566777777777777777777765555 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.6e-08
               Glyco_tranf_2_2   2 vviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska.. 80 
                                   vv+p +++e+   i+++v  + +y     ++ v++d S+++++++++++ d +  v   +e  +  + +aa   G +ka  
  gi|91773953|ref|YP_566645.1| 200 VVVPAYNEEKL--IKNTVEGIPQY---VDRIYVINDASTDNTAKVIETLNDPRVVVI-THE--TNKGVGAALINGYKKAlr 272
                                   899***99999..***********...66899*********************9998.777..556888888899999944 PP

               Glyco_tranf_2_2  81 .esdlvlFlDaDcfissDkfekil 103
                                    + d+v  + +D+ + +D++ k++
  gi|91773953|ref|YP_566645.1| 273 eNMDVVAVMAGDDQMNPDQLYKLI 296
                                   34689**************99864 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.65   2.3e+03      85     136 ..      60      82 ..      26     118 .. 0.60
   2 ?   11.6   0.0   4.2e-05      0.15      18     116 ..     195     288 ..     193     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.65
                                   BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEE CS
               NTP_transferase  85 gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvt 136
                                   g A A+a a e +                             ++ + +++vt
  gi|91773953|ref|YP_566645.1|  60 GKAAALATAFEAA-----------------------------KKLNPAVLVT 82 
                                   3333333333333.............................3333333333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.2e-05
                                   TTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHT CS
               NTP_transferase  18 rtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelle 98 
                                   rt+    vp +++e+li+ t++ +  + +++ i+v+++      ++ +++ ++ +  v +++ + +kg   A++ + + + 
  gi|91773953|ref|YP_566645.1| 195 RTRIGVVVPAYNEEKLIKNTVEGIP-QYVDR-IYVINDASTDNTAKVIETLNDPR--VVVITHETNKGVGAALINGYKKAL 271
                                   5666667999************998.57888.99****************99755..99********************** PP

                                   TSSE..EEEEETTEEEES CS
               NTP_transferase  99 deksdelvlvLggDhlik 116
                                   +e+  ++v v++gD  ++
  gi|91773953|ref|YP_566645.1| 272 REN-MDVVAVMAGDDQMN 288
                                   999.58899998886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2721.37
//
Query:       gi|91773954|ref|YP_566646.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91773954|ref|YP_566646.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91773954|ref|YP_566646.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91773954|ref|YP_566646.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91773954|ref|YP_566646.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91773954|ref|YP_566646.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91773954|ref|YP_566646.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91773954|ref|YP_566646.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91773954|ref|YP_566646.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2190.50
//
Query:       gi|91773955|ref|YP_566647.1|  [L=153]
Description: dolichyl-phosphate beta-D-mannosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0092   16.2   7.9      0.015   15.5   7.9    1.4  1  DUF2304    Uncharacterized conserved protein (DUF2304)
  ------ inclusion threshold ------
       0.16   11.7   3.4       0.19   11.4   3.4    1.2  1  Claudin_2  PMP-22/EMP/MP20/Claudin tight junction


Domain annotation for each model (and alignments):
>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   7.9   1.7e-06     0.015      11      91 ..      56     138 ..      47     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                       DUF2304  11 vllllliirlvrkkk..lkleysllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvilfslslklskl 89 
                                   ++l+  ++++++ k+  +++   +l+ +l+++li + ++ ++ +v+a+l G+  +tn ++l +++fl  + f l++++ ++
  gi|91773955|ref|YP_566647.1|  56 AMLFKSFLWRLKTKYmvMSFHPLVLFYILSMFLIPFGIIFGLSMVIASLAGFTVQTNYVLLDALIFLSGMQFLLFAMFFDM 136
                                   5555555555555551146677899999************************************************99999 PP

                       DUF2304  90 ee 91 
                                   +e
  gi|91773955|ref|YP_566647.1| 137 QE 138
                                   87 PP

>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.4   2.2e-05      0.19      85     150 ..      72     140 ..      41     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.2e-05
                     Claudin_2  85 llalarfvqvlliLslvlivlavvlgllallkqsvlllkaagilfl.....lagvlgllavvvfiesvkkv 150
                                    +++++ v  + iLs++li  ++++gl+ ++ + +++ + + +++l     l+g+  +l  ++f+ + +++
  gi|91773955|ref|YP_566647.1|  72 VMSFHPLVL-FYILSMFLIPFGIIFGLSMVIASLAGFTVQTNYVLLdalifLSGM-QFLLFAMFFDMQESD 140
                                   566666666.99***********************99999988888888855555.555566666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1325.44
//
Query:       gi|91773956|ref|YP_566648.1|  [L=347]
Description: hypothetical protein Mbur_2021 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-25   89.2   2.3    3.2e-25   88.9   2.3    1.0  1  DUF354           Protein of unknown function (DUF354)
    0.00015   21.8   0.2    0.00034   20.7   0.1    1.7  2  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.072   13.1   0.0        0.2   11.6   0.0    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   2.3   5.4e-29   3.2e-25       1     319 [.       1     315 [.       1     344 [. 0.80

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 5.4e-29
                        DUF354   1 ldvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvtlkekliesakrvinlskliae 81 
                                   ++v id+    hv++f+++i  +ek+G evl+t rd      l++ yn+ +  +Gk G    + + e  kr +++ k+  +
  gi|91773956|ref|YP_566648.1|   1 MKVLIDIGHPAHVHFFKNIILGLEKNGHEVLVTSRDKDVAIDLLDAYNIPYIPVGKIGSGKFDLIKEWIKRDYDILKIAKK 81 
                                   5899*********************************9999**********************999*************** PP

                        DUF354  82 vkpdvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeGtsevinv 162
                                    +pd+ +      +   a  l+  +    d e  +++  +t p++d i  p        k+ G +  ri+ y+  s  ++ 
  gi|91773956|ref|YP_566648.1|  82 FNPDLLMGMLNPCVAHSAKLLGKKCFIFNDSEVVNSTALITYPFSDVIFTPSNF----SKDAGKKQVRINGYKEHSY-LHS 157
                                   *****99888777777777788888778899******************99865....4678999899999998875.689 PP

                        DUF354 163 qsyeideeilkdlnlkledektilmrpepslasyldadchkdvltki..veklkdridilviprdeeqkeiyeevdnvivi 241
                                   + ++ d  i+++l++ + ++k ilmr    +a +   +   d+ tki  v+ l++++++ +    e   e+ e++  + ++
  gi|91773956|ref|YP_566648.1| 158 NHFNPDPSIFDNLDIGI-NDKFILMRFVAWKAGHDVKQKGFDLETKIryVKALEKYAKVFISSETELPPEL-EDYR-IKIP 235
                                   99************555.6799******988887666666788888766999******9997766665554.6666.5555 PP

                        DUF354 242 ketvdalsllkrsdlviGaGGtmnreaallGipvvsc..ypqkllsvdkyliek..dlmirstdvdeivntalrllvdkle 318
                                    e  d   +++ +dl++G   tm  eaallG+p+v c  + ++    +   +e+  +l+++ ++ de +n a+ +++d   
  gi|91773956|ref|YP_566648.1| 236 SE--DIHNFVYYADLLVGDSQTMTTEAALLGTPAVRCnsFVGENDMANFVELENkyGLIFNFNNYDEAMNKAIEIIQDPNI 314
                                   55..6667799**************************4334555444444455533789999**********999876432 PP

                        DUF354 319 k 319
                                   k
  gi|91773956|ref|YP_566648.1| 315 K 315
                                   2 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 !   20.7   0.1   5.6e-08   0.00034      12     101 ..      15     106 ..       2     152 .. 0.73
   2 ?   -2.7   0.0      0.93   5.6e+03      58      68 ..     203     214 ..     182     233 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.6e-08
               Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvdrkgpleylk.a....fklkklikkikPDvvhahyakpy 86 
                                   + ++++ +L k+g+eV v +++k+   d l a++i  +++ +  +g++ ++k        + k+ kk++PD++  +  + +
  gi|91773956|ref|YP_566648.1|  15 FFKNIILGLEKNGHEVLVTSRDKDVaIDLLDAYNIPYIPVGKIGSGKFDLIKeWikrdYDILKIAKKFNPDLLMGMLNPCV 95 
                                   4567899**************7776699999999999999544444554444322333599************77764444 PP

               Glyco_trans_4_2  87 gllgslaarlsgvip 101
                                   +  ++l+ +    + 
  gi|91773956|ref|YP_566648.1|  96 AHSAKLLGK----KC 106
                                   444444433....33 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.93
               Glyco_trans_4_2  58 leylkaf.klkk 68 
                                   + y+ka+ k++k
  gi|91773956|ref|YP_566648.1| 203 IRYVKALeKYAK 214
                                   222222222222 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.4e-05       0.2       9      98 ..      17     105 ..      13     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                Glyco_transf_4   9 leLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflr.....rlrrllkrekpDvvHahspaal 84 
                                    +++ +L ++GheV v +++ d +++    + +++p++p  + +  +++l   +     ++ +++k+++pD++     +++
  gi|91773956|ref|YP_566648.1|  17 KNIILGLEKNGHEVLVTSRDKDVAIDLL--DAYNIPYIPVGKIGSGKFDLIKEWikrdyDILKIAKKFNPDLLMGMLNPCV 95 
                                   577889***********99999998888..556666666655555555443332222337999*********944432222 PP

                Glyco_transf_4  85 gaallalrrrlgip 98 
                                      ++ +++ lg++
  gi|91773956|ref|YP_566648.1|  96 ---AHSAKL-LGKK 105
                                   ...222232.4544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2447.34
//
Query:       gi|91773957|ref|YP_566649.1|  [L=357]
Description: UDP-N-acetylglucosamine 2-epimerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-117  391.1   0.0   4.2e-117  390.9   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
    2.3e-05   23.7   0.5    2.9e-05   23.3   0.5    1.2  1  DUF354           Protein of unknown function (DUF354)
     0.0093   16.0   0.0      0.017   15.2   0.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.026   14.5   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4


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 !  390.9   0.0  9.3e-121  4.2e-117       9     343 ..      27     348 ..      21     352 .. 0.95

  Alignments for each domain:
  == domain 1  score: 390.9 bits;  conditional E-value: 9.3e-121
                                   .EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHHHHHHHHHH CS
                   Epimerase_2   9 lelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtnetlagalaAfk 89 
                                    +++l++tGqH+d++m++++feel+i++pdy+l+ +s+s++ +tg++l+++eevl  e+pDlvl +GDtn+tlagalaA+k
  gi|91773957|ref|YP_566649.1|  27 HHEVLIHTGQHYDHKMNQVFFEELNIPEPDYFLEIGSGSHGYQTGEMLKKIEEVLIIEQPDLVLTYGDTNSTLAGALAASK 107
                                   4689***************************************************************************** PP

                                   TT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHHHHHHHHHHH...T CS
                   Epimerase_2  90 lripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDalllskeeieeklk 170
                                   l+i++aHve GlRsfd+t  mpeEinR+++d++sd++f+pte+a +nL +eg+  +++f +G+++ D++ ++k+ +e+   
  gi|91773957|ref|YP_566649.1| 108 LHIKTAHVESGLRSFDKT--MPEEINRIVTDHCSDILFCPTENAVNNLKNEGI-TDNVFLTGDVMADSVIYNKDIAEK--- 182
                                   ******************..*********************************.678*****************9994... PP

                                   -HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH..HHHHHH-.TTEEEE- CS
                   Epimerase_2 171 aseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl..leeleel.envtlie 246
                                   +s+il++  l++k+y+l+t+Hr++n+d+p++l++i++a+++l++     vv+pvh  prt+k l  ++ +++l + v+lie
  gi|91773957|ref|YP_566649.1| 183 QSTILNDlnLESKNYLLATVHRASNTDNPKNLQNIVDAFSKLDDL----VVFPVH--PRTKKLLkeYNLYDKLaSSVKLIE 257
                                   5699999999*********************************98....9*****..*******88778888877****** PP

                                   ---HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT-..--.... CS
                   Epimerase_2 247 plgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklledkkelekma 327
                                   p+g+ldf++l++n+k++ltdSgGiq+Ea++l++p+++lRe+te+ e+ve g+nvlvg dk++Iv+a+++l          +
  gi|91773957|ref|YP_566649.1| 258 PVGFLDFIKLMNNSKMILTDSGGIQKEAYILKIPCITLRENTEWMETVEDGWNVLVGVDKSRIVNAIDELNPV------SK 332
                                   **********************************************************************944......45 PP

                                   ..--TT-SS-HHHHHH CS
                   Epimerase_2 328 naknpYgdGkaseriv 343
                                   n+ + +g+G as++i+
  gi|91773957|ref|YP_566649.1| 333 NHDDRFGNGTASKKII 348
                                   56779**********8 PP

>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.5   6.5e-09   2.9e-05     119     277 ..     131     294 ..     100     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.5e-09
                        DUF354 119 nkltlpladeii.kpividendlkktGadpnrirryeG..tsevinvqsyeideeilkdlnlkledektilmrpepslasy 196
                                   n++    + +i+  p     n+lk+ G   n     +    s + n +  e +  il+dln  le ++ +l       as 
  gi|91773957|ref|YP_566649.1| 131 NRIVTDHCSDILfCPTENAVNNLKNEGITDNVFLTGDVmaDSVIYNKDIAEKQSTILNDLN--LESKNYLLA-TVH-RASN 207
                                   5655555655542678888899999998877665333300333444444788888999999..555555444.444.5777 PP

                        DUF354 197 ldadchkdvltkiveklkdridilviprdeeqkeiyeevd.......nviviket..vdalsllkrsdlviGaGGtmnrea 268
                                    d     + l +iv+ + +  d++v+p + + k++ +e++       +v +i +   +d + l+++s +++   G +++ea
  gi|91773957|ref|YP_566649.1| 208 TDN---PKNLQNIVDAFSKLDDLVVFPVHPRTKKLLKEYNlydklasSVKLIEPVgfLDFIKLMNNSKMILTDSGGIQKEA 285
                                   776...456999*************9988888888777763333322233443323369999******************* PP

                        DUF354 269 allGipvvs 277
                                    +l ip ++
  gi|91773957|ref|YP_566649.1| 286 YILKIPCIT 294
                                   ******997 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.8e-06     0.017      16     118 ..      19     128 ..       2     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-06
               Glyco_trans_4_2  16 lakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd........rkgpleyl..kaf.klkklikkikPDvvhahyakp 85 
                                   + +eL+k ++eV + t +     + +++++ + +l+++         +g+ +y    ++ k+ +++  ++PD+v ++  + 
  gi|91773957|ref|YP_566649.1|  19 VSRELRKTHHEVLIHTGQHY---DHKMNQVFFEELNIPepdyfleiGSGSHGYQtgEMLkKIEEVLIIEQPDLVLTYGDTN 96 
                                   4789********99887655...4457778899998888899988655599998543555******************999 PP

               Glyco_trans_4_2  86 ygllgslaarlsgvipvvlsvwGldvlkfpkks 118
                                     l+g+laa ++  i+++    Gl  +++  + 
  gi|91773957|ref|YP_566649.1|  97 STLAGALAASKLH-IKTAHVESGLRSFDKTMPE 128
                                   9*********998.9997777777777766555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.8e-06     0.026      12     153 ..      20     157 ..      18     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.8e-06
                Glyco_transf_4  12 araLarrGheVtvvtpgddgpleeev....elvvrvprvp.lpllkrllrslaflrrlrrllkrekpDvv.Hahspaalga 86 
                                   +r+L++  heV + t ++ ++  ++v     ++ ++ ++  + +    +++  +l+++ ++l  e+pD+v  + +  + +a
  gi|91773957|ref|YP_566649.1|  20 SRELRKTHHEVLIHTGQHYDHKMNQVffeeLNIPEPDYFLeIGSGSHGYQTGEMLKKIEEVLIIEQPDLVlTYGDTNSTLA 100
                                   799***********99999999888888865555555554234455667778889999999**9******75556677778 PP

                Glyco_transf_4  87 allalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeatadelreryg 153
                                   ++la+ + l+i++ +   gl          ++ + + +++ r +  + +d +++++e + ++l+   g
  gi|91773957|ref|YP_566649.1| 101 GALAASK-LHIKTAHVESGLR---------SFDKTMPEEINRIVtDHCSDILFCPTENAVNNLKN-EG 157
                                   8777776.7777655444443.........44444444444444345566777777777777766.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2485.81
//
Query:       gi|91773958|ref|YP_566650.1|  [L=401]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-35  120.5   0.0    1.2e-34  119.3   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    1.4e-26   93.6   0.0    2.6e-26   92.7   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.8e-09   35.9   0.1    1.1e-08   35.3   0.1    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.2e-08   34.4   0.0    4.2e-08   33.5   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0052   16.5   0.1     0.0091   15.7   0.1    1.4  1  Glyco_transf_5   Starch synthase catalytic domain
  ------ inclusion threshold ------
      0.018   15.5   0.0      0.027   14.9   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      0.022   14.8   0.7       0.15   12.1   0.3    2.3  2  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 ?   -2.9   0.0       1.6   4.2e+03      68      97 ..      24      54 ..      16      58 .. 0.66
   2 !  119.3   0.0   4.8e-38   1.2e-34       5     167 ..     212     373 ..     208     378 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                                  HHCTTCGGGEEECCHSSSHHHHHHC.ESEEE CS
               Glycos_transf_1 68 elelsdnviflgevsredleellkn.adifv 97
                                  ++ ++dn+++ g   +++le+l+k+  +ifv
  gi|91773958|ref|YP_566650.1| 24 SYPNEDNTFIGGSFIKNQLESLKKHfDNIFV 54
                                  5666667666666667888888888555555 PP

  == domain 2  score: 119.3 bits;  conditional E-value: 4.8e-38
                                   HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
               Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsred 85 
                                    r kl+++++kkii+s+g l ++Kg+++li+a++ + k+ +++v + i Gng+ ++ l+k++  l+l++nv+++g+v +e 
  gi|91773958|ref|YP_566650.1| 212 CRGKLNLPKNKKIIFSLGGLIERKGFNYLIDAIKFVTKK-QKDVLCFIGGNGPLKDALQKQIIDLNLQNNVKLVGFVTDEL 291
                                   578999****************************99998.***************************************** PP

                                   HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHH CS
               Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlg 166
                                   l  +++++difvlps sEg ++v  E + +g+p + + +gg++e++++ + Gllv+p+n ++lae+i+ +l++e +r+++ 
  gi|91773958|ref|YP_566650.1| 292 LSIWINSCDIFVLPSLSEGNPTVMFECLGCGKPYVGTGVGGVPEIITSDKYGLLVEPGNSQDLAEKIIIALNKEWDRDAIL 372
                                   ***********************************************************************9996666655 PP

                                   H CS
               Glycos_transf_1 167 e 167
                                   e
  gi|91773958|ref|YP_566650.1| 373 E 373
                                   5 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0     1e-29   2.6e-26       2     132 ..     223     362 ..     222     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1e-29
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHH.T.T-T.TEEEE---TH..HHHHHHH-SE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleela.a.gleerveftGfved..laellaaadv 75 
                                   ++i  +G l  ++kg+ +l++a++ + kk + v + i G+gp + ++l++++ + +l+++v+++Gfv+d  l+ +++++d+
  gi|91773958|ref|YP_566650.1| 223 KIIFSLGGLI-ERKGFNYLIDAIKFVTKKqKdVLCFIGGNGPlK-DALQKQIiDlNLQNNVKLVGFVTDelLSIWINSCDI 301
                                   6788999995.56**************77435988888899955.69999884599***********5558********** PP

                                   EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                   fv+Ps  eg + ++ E + +g+p V t vgg++e++   + gllv+pg++++lae+i+  l
  gi|91773958|ref|YP_566650.1| 302 FVLPSlsEGNPTVMFECLGCGKPYVGTGVGGVPEIItsDKYGLLVEPGNSQDLAEKIIIAL 362
                                   ************************************97799****************9776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   4.3e-12   1.1e-08      38     165 ..      79     199 ..      47     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4.3e-12
                Glyco_transf_4  38 elvvrvprvplpllkrllrslaflrrl.rrllkre..kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkar 115
                                   ++v+ ++++++p+++ +++ + +++++  +++k+e  k+D++Hah+ ++  +    l+ ++++p+++t+H  +e       
  gi|91773958|ref|YP_566650.1|  79 INVYFPRSYYIPIFYFNKILIDNRLHVvEKIIKNEnlKFDLIHAHFTWPSAYISTSLKEKYHVPTITTIHENAE------W 153
                                   45666677777777777777777666515666666***********9999888888888**************5......5 PP

                Glyco_transf_4 116 lkplsrllralerrllrradrviavSeatadelrerygvppekitVipnG 165
                                   l ++  ++  l + + r++d +i v  +    l e y+   +++  ipnG
  gi|91773958|ref|YP_566650.1| 154 LVKEAGINSSLINNAWRNSDVLIRVNSKDLPILSE-YN---KNVISIPNG 199
                                   56666777777777888999999888888888888.77...678888887 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 !   33.5   0.0   1.6e-11   4.2e-08       1      82 [.     301     379 ..     301     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.6e-11
               Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervla 79 
                                   i++ ps se++ +++fE+++cG + + +   g++e++t +k ++l+e  + ++laeki  +l+ + +r+ai e   ++   
  gi|91773958|ref|YP_566650.1| 301 IFVLPSLSEGNPTVMFECLGCGKPYVGTGVGGVPEIITSDKYGLLVEpgNSQDLAEKIIIALNKEWDRDAILEYSDRF--- 378
                                   5678999*******************************************************9999999886544444... PP

               Glyco_trans_1_2  80 eht 82 
                                     t
  gi|91773958|ref|YP_566650.1| 379 --T 379
                                   ..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 !   15.7   0.1   3.6e-06    0.0091      37     171 ..      19     149 ..      12     166 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                Glyco_transf_5  37 rvilPrygaikeek.......keleevaelskaaedevevevekvkvaklkk.dgvdvyfldnpe.ffdreglYgdkgedy 108
                                    vi P+y++ +++        ++le+++   k++++ + ++   +++ kl k + ++ y  dn + +f r ++Y +    +
  gi|91773958|ref|YP_566650.1|  19 LVIAPSYPNEDNTFiggsfikNQLESLK---KHFDNIFVISPVLFSFNKLDKdKLCNNYRYDNINvYFPR-SYYIP---IF 92 
                                   5677777655555556653333333332...233332222223334444444213333444444322221.23322...33 PP

                Glyco_transf_5 109 ednaerfalfsraalelleklgwkpdvihah.DWhtalvpallkelykerglfkkiktvftiHN 171
                                     n+  +    +++ +++++ + k+d+ihah  W +a +   lke y       +++t+ tiH 
  gi|91773958|ref|YP_566650.1|  93 YFNKILIDNRLHVVEKIIKNENLKFDLIHAHfTWPSAYISTSLKEKY-------HVPTITTIHE 149
                                   355555555556777777774559*******88*************9.......4********7 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.027      70     113 ..     113     159 ..      98     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
               Glyco_trans_4_4  70 rrerpdvvhahs.ptaglaarlarrrrgiplvvtlhg..lllrrgsg 113
                                   +  ++d++hah  ++++++   ++ + ++p + t+h+   +l++++g
  gi|91773958|ref|YP_566650.1| 113 ENLKFDLIHAHFtWPSAYISTSLKEKYHVPTITTIHEnaEWLVKEAG 159
                                   5679*******98*******9999899*********63333444434 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   5.9e-05      0.15      67     108 ..     107     149 ..      36     157 .. 0.73
   2 ?   -0.2   0.0      0.36   9.1e+02      33      63 ..     178     210 ..     163     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
               Glyco_trans_4_2  67 kklikk..ikPDvvhahyakpygllgslaarlsgvipvvlsvwG 108
                                    k+ik   +k+D++hah ++p +++ + ++ +   +p+++++++
  gi|91773958|ref|YP_566650.1| 107 EKIIKNenLKFDLIHAHFTWPSAYISTSLKEKYH-VPTITTIHE 149
                                   6777652269***********9998888866665.999999995 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
               Glyco_trans_4_2  33 kkga.kdeleaegihvhrlkvdrkgpleylk.a 63 
                                    +++   +l +++ +v++++++ +++++y+  +
  gi|91773958|ref|YP_566650.1| 178 VNSKdLPILSEYNKNVISIPNGFSSKFKYIDkM 210
                                   334335678888999999999999999999425 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2418.12
//
Query:       gi|91773959|ref|YP_566651.1|  [L=317]
Description: NAD-dependent epimerase/dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-51  175.5   0.0    1.5e-51  175.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.4e-45  154.9   0.0      4e-45  154.7   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.1e-23   83.7   0.1    1.4e-23   83.3   0.1    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.8e-19   67.9   0.1    9.2e-18   64.4   0.1    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.5e-13   50.5   0.0    1.9e-13   50.1   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    3.9e-11   43.2   0.0    5.8e-11   42.6   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    5.8e-11   42.1   0.9    2.3e-08   33.5   0.9    2.7  1  NAD_binding_4    Male sterility protein
    1.1e-06   28.3   0.0    7.6e-06   25.5   0.0    2.3  1  adh_short        short chain dehydrogenase
    0.00016   21.3   0.0     0.0003   20.4   0.0    1.4  1  NmrA             NmrA-like family
    0.00025   21.0   0.1     0.0011   18.9   0.1    1.9  1  KR               KR domain
  ------ inclusion threshold ------
        0.1   13.2   0.1        1.5    9.4   0.0    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


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 !  175.2   0.0   9.1e-55   1.5e-51       1     241 []       8     243 ..       8     243 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 9.1e-55
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                   il+tG++GfiGs++v++l + g +vi++d+lss++ +  +++l     +++++dl+d ++++++++  ++d+v+h+Aa  +
  gi|91773959|ref|YP_566651.1|   8 ILITGGAGFIGSHVVDKLINIGNRVIVFDNLSSGNLEYIDQHLdnpnfTFINGDLLDTDKITKACH--NIDCVYHIAANPD 86 
                                   8******************************888888888888**********************9..9************ PP

                                   HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHH CS
                     Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveaya 157
                                   v+  +++ +  +++n+  t+nllea+rk+++++++f s+s+vYG+   +p+ e+   gpl p s Y+a+Kl  e l+++y 
  gi|91773959|ref|YP_566651.1|  87 VRLGFSNTKVHFDQNITATYNLLEAMRKNNIRNIVFTSTSTVYGEASIIPTPENY--GPLVPISLYGASKLSCEALITSYC 165
                                   ********************************************99999977777..9*********************** PP

                                   HHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEE CS
                     Epimerase 158 aqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiy 238
                                   ++++++  i+r  n++G+r    + +++i+ +i+k++++ +++ +lgdg++   +l+++ +++ail+v+++  + d+ +i+
  gi|91773959|ref|YP_566651.1| 166 HTFNMRSWIFRFANIIGER----STHGIIFDFIKKLHNNPDQLEILGDGQQSKSYLHISACIDAILFVVNK--SLDDVNIF 240
                                   *******************....99**************9*******************************..667789** PP

                                   EES CS
                     Epimerase 239 niG 241
                                   niG
  gi|91773959|ref|YP_566651.1| 241 NIG 243
                                   **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 !  154.7   0.0   2.5e-48     4e-45       1     267 [.       9     262 ..       9     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 2.5e-48
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   LiTG+aGfiGs+++++L++ g +v++++++ss  n++ i++  +      ++n+++++gDl D+++++++ +++  d vy+
  gi|91773959|ref|YP_566651.1|   9 LITGGAGFIGSHVVDKLINIGNRVIVFDNLSS-GNLEYIDQHLD------NPNFTFINGDLLDTDKITKACHNI--DCVYH 80 
                                   9***********************99988766.58888887665......468****************99876..9**** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPYaaaKlyad 161
                                    AA   V+  f++ +  ++ n+++t++LLea+r+ +++    ++++Sts+vYG+++ +p  E+  p+ P s Y+a+Kl+++
  gi|91773959|ref|YP_566651.1|  81 IAANPDVRLGFSNTKVHFDQNITATYNLLEAMRKNNIR---NIVFTSTSTVYGEASIIPTPENyGPLVPISLYGASKLSCE 158
                                   **********************************9886...5889**************998868**************** PP

                                   HHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC..S CS
                 GDP_Man_Dehyd 162 wivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq..d 240
                                    ++++y +++++   + ++ n  + r         i +++ + +++  +  +lG++++ ++++h++  ++a+  ++++  d
  gi|91773959|ref|YP_566651.1| 159 ALITSYCHTFNMRSWIFRFANIIGERS----THGIIFDFIKKLHNNPDQLEILGDGQQSKSYLHISACIDAILFVVNKslD 235
                                   ************************995....4567999999999999888889********************99998344 PP

                                   S---EEE-TT-EEECHHCHHCCHHCCC CS
                 GDP_Man_Dehyd 241 kpedyviatgethsvrefvelaflelg 267
                                     + ++i++ +t +  ++  + ++e+g
  gi|91773959|ref|YP_566651.1| 236 DVNIFNIGSEDTINSTQIGMIVVEEMG 262
                                   444555666666665555555555555 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 !   83.3   0.1   8.6e-27   1.4e-23       1     224 [.       9     225 ..       9     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 8.6e-27
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlaslvdv 79 
                                   ++tGgaGF+G+++v +L+++++   v v+D   s +l    +++++ +  +i+gD++d+dk+++a++++d+v h+a+  dv
  gi|91773959|ref|YP_566651.1|   9 LITGGAGFIGSHVVDKLINIGN--RVIVFDNLSSGNLEYIDQHLDNPNftFINGDLLDTDKITKACHNIDCVYHIAANPDV 87 
                                   69*******************6..999***88887776555556555556******************************* PP

                     3Beta_HSD  80 ag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlk 159
                                   +    +++   + n+  T n+lea +k+++r +v+tS+  v g+      i+   E  + + ++ + y  sK   E+l+ +
  gi|91773959|ref|YP_566651.1|  88 RLgFSNTKVHFDQNITATYNLLEAMRKNNIRNIVFTSTSTVYGE----ASIIPTPE-NYGPLVPISLYGASKLSCEALITS 163
                                   972555566789*******************************9....55554555.567899****************98 PP

                     3Beta_HSD 160 aNgrtlknggrlyTcaLRpagiyGegdkl..lvpllkqlaklglalfkigdeevlsdrvYvgNvawa 224
                                             ++     R a i Ge+++   ++ ++k+l ++  +l  +gd ++ +++       +a
  gi|91773959|ref|YP_566651.1| 164 YCH-----TFNMRSWIFRFANIIGERSTHgiIFDFIKKLHNNPDQLEILGDGQQSKSYLHISACIDA 225
                                   777.....34678888999999999987533778899999998888888888887777666555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.1   5.7e-21   9.2e-18       1     263 [.       8     272 ..       8     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 5.7e-21
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +l+tG++G iGs++v+++++   + i+  + +  +l  i+++l    ++ ++    + + gd+ d+++++ka++  ++d+v
  gi|91773959|ref|YP_566651.1|   8 ILITGGAGFIGSHVVDKLINIGNRVIVFDNLSSGNLEYIDQHL----DNPNF----TFINGDLLDTDKITKACH--NIDCV 78 
                                   89******************99877776677888999999998....34444....3468*************9..***** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG...............SS--SHHHHHHHHHHH CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA...............vnPtnvmGatKrlaek 147
                                   +h AA   V l  +n+   +++N+++t n++ea  +++++++v+ St                    P++++Ga+K+ +e 
  gi|91773959|ref|YP_566651.1|  79 YHIAANPDVRLGFSNTKVHFDQNITATYNLLEAMRKNNIRNIVFTSTSTVygeasiiptpenygpLVPISLYGASKLSCEA 159
                                   ***********************************************8642222322222222223589************ PP

                                   HHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEE.S-TT-EEEEE-HHHHHHHHHHHHHH--SS- CS
               Polysacc_synt_2 148 llqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtv.TdpemtRyfmtieeavqLvlqalalakgge 224
                                   l++++ ++    +++  + Rf N++g  S   +i  F k+++++ +++ +  d +  + ++ i+  ++ +l  ++++   +
  gi|91773959|ref|YP_566651.1| 160 LITSYCHTF---NMRSWIFRFANIIGerSTHGIIFDFIKKLHNNpDQLEIlGDGQQSKSYLHISACIDAILFVVNKS-LDD 236
                                   **9999888...899999*******9444445777788777777677776357778888888888888888766554.567 PP

                                   EEEE--.-EEEHHHHHHHH..........SSSS-EEE-- CS
               Polysacc_synt_2 225 ifvldmGepvkivdlakalielsgleekkeedieikitG 263
                                   + + ++G   +i      +i + ++  +   ++e ++tG
  gi|91773959|ref|YP_566651.1| 237 VNIFNIGSEDTINSTQIGMIVVEEMGLE---NVEFTYTG 272
                                   7777888877777777777655554333...35555555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   1.2e-16   1.9e-13       3     234 ..       8     264 ..       6     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.2e-16
                                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE------ CS
                 RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAyta 63 
                                   il+tG+ G +Gs+++++l + g  v+ +++                     + dl d ++++++ ++   d+v++ AA  +
  gi|91773959|ref|YP_566651.1|   8 ILITGGAGFIGSHVVDKLINIGNRVIVFDNLssgnleyidqhldnpnftfiNGDLLDTDKITKACHN--IDCVYHIAANPD 86 
                                   8*********************9***99776799*******************************99..567********* PP

                                   HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHHHHHHH-S. CS
                 RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEqavlaagk. 141
                                   v    s+ +  +  n +a+ +l ea ++ ++  +++ St  V+  +   p  e+  +  P+++YG++Kl  E  + ++++ 
  gi|91773959|ref|YP_566651.1|  87 VRLGFSNTKVHFDQNITATYNLLEAMRKNNIrNIVFTSTSTVYGEASIIPtPENYGPLVPISLYGASKLSCEALITSYCHt 167
                                   *****************************984599********9998888445567899*****************96543 PP

                                   ...SEEEEEE-SEESS.SSS-HHHHHHHHH.HH-SEEEEESS-EE--EEHH..HHHHHHHHHHHHCHH.GGG-EEEE---B CS
                 RmlD_sub_bind 142 ...kalivRtswvyge.kgknfvktmlrla.kereelkvvaDqlgsPTsar..dlAevllqllekaaeekelagvyHlane 215
                                      + +i+R++ + ge + +  ++ +++++ ++ ++l++  D + s ++ +     +++l +++k++   ++  ++ +++e
  gi|91773959|ref|YP_566651.1| 168 fnmRSWIFRFANIIGErSTHGIIFDFIKKLhNNPDQLEILGDGQQSKSYLHisACIDAILFVVNKSL---DDVNIFNIGSE 245
                                   333899********99556677776666553899******997777665430033355555555555...46888999999 PP

                                   S-EEHHHHHHHHHHHHCHT CS
                 RmlD_sub_bind 216 getswlefArailkeagad 234
                                   ++++  +++  +++e+g +
  gi|91773959|ref|YP_566651.1| 246 DTINSTQIGMIVVEEMGLE 264
                                   9988888888888888765 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 !   42.6   0.0   3.6e-14   5.8e-11       1     104 [.      12     131 ..      12     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.6e-14
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETT.....HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.....peklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk... 73 
                                   G+ G +G+++v++l++ g  +v ++  n      e +++  ++++ + + gd++d++++++a+ ++d V+  +++ +    
  gi|91773959|ref|YP_566651.1|  12 GGAGFIGSHVVDKLINIG-NRVIVF-DNlssgnLEYIDQHLDNPNFTFINGDLLDTDKITKACHNIDCVYHIAANPDVrlg 90 
                                   99***************6.566554.54221225666666699**************************999976666667 PP

                                   ........HHHH..HHHHHHHHHHCT--EEEEEEETTTTSG CS
                NAD_binding_10  74 ........deeg..aknivdaakeagvkRfvlvsaigvgde 104
                                           d+++  + n+++a+++++++ +v+ s+  v+ e
  gi|91773959|ref|YP_566651.1|  91 fsntkvhfDQNItaTYNLLEAMRKNNIRNIVFTSTSTVYGE 131
                                   65445555444488**********************99975 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.9   1.4e-11   2.3e-08       1     214 [.      10     189 ..      10     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.4e-11
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHH CS
                 NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedl 81 
                                   +TG+ GF+G++++ kL++  +  ++++    +sg   +e +     ++ l          + ++++GDl      L+ +++
  gi|91773959|ref|YP_566651.1|  10 ITGGAGFIGSHVVDKLINIGN--RVIVFDNLSSG--NLEYI-----DQHLD-------NPNFTFINGDL------LDTDKI 68 
                                   8****************9998..78877666666..34444.....33333.......456799****9......7788** PP

                                   HHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H...... CS
                 NAD_binding_4  82 qelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekee 159
                                    + ++++d+++h+aA+ ++     ++k+ ++ N+++t ++le  +k +    +++ ST++v+ge +  +            
  gi|91773959|ref|YP_566651.1|  69 TKACHNIDCVYHIAANPDVRLgfsNTKVHFDQNITATYNLLEAMRKNNIR-NIVFTSTSTVYGEAS--I------------ 134
                                   ***************97776433488889*************99977666.9*************9..3............ PP

                                   HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST- CS
                 NAD_binding_4 160 kldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGw 214
                                      + e          Y  sK   E l+ ++ +  +++  i+R  +i+g +s+ G+
  gi|91773959|ref|YP_566651.1| 135 -IPTPENYGPLVPISLYGASKLSCEALITSYCHTFNMRSWIFRFANIIGeRSTHGI 189
                                   .567777777777889****************999*************94444476 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   4.7e-09   7.6e-06       2     118 ..       7     111 ..       6     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.7e-09
                                   EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                     adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                   v+l+tG+++ IG  ++++l++ G +v+v+d+ ++   e +++  + + ++++i++D+ d +++ ++  ++       d+++
  gi|91773959|ref|YP_566651.1|   7 VILITGGAGFIGSHVVDKLINIGNRVIVFDNLSSGNLEYIDQHLD-NPNFTFINGDLLDTDKITKACHNI-------DCVY 79 
                                   89**************************88766655555555554.378**********99988887665.......6666 PP

                                   E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHH CS
                     adh_short  83 nNAGitgsgpfselseeewervievNltgvflltra 118
                                   + A+     p  +l  ++++  ++ N+t++++l +a
  gi|91773959|ref|YP_566651.1|  80 HIAAN----PDVRLGFSNTKVHFDQNITATYNLLEA 111
                                   66655....455555555556666666666665554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.9e-07    0.0003       1     101 [.       8     124 ..       8     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S...-SHHH.HHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                          NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt...ksela.kslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                   Il++G++G +G++vv+ l++ g++v +   ++   + e + ++l +   ++++gdl d + + +a ++ d v+   +    
  gi|91773959|ref|YP_566651.1|   8 ILITGGAGFIGSHVVDKLINIGNRVIVF-DNLssgNLEYIdQHLDNPNFTFINGDLLDTDKITKACHNIDCVYHIAANPdv 87 
                                   89*********************98654.34445644555145555555777********************987764356 PP

                                   ...........S-HHHHHHHHHHHHHHHS-SEEEEEE CS
                          NmrA  76 ...........skeiedgkklvdAakeaGvkhfiySs 101
                                              +++i    +l +A  +  ++++++ s
  gi|91773959|ref|YP_566651.1|  88 rlgfsntkvhfDQNITATYNLLEAMRKNNIRNIVFTS 124
                                   6777777777777777777777777777777777766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   6.6e-07    0.0011       2     143 ..       7     131 ..       6     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.6e-07
                                   EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                            KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                   + litGG+G +G ++++ l++ g+r +v+   s+ + e     i++  + + + ++++ D+ d d+++++ ++i+      
  gi|91773959|ref|YP_566651.1|   7 VILITGGAGFIGSHVVDKLINIGNRVIVFDNLSSGNLE----YIDQHLD-NPNFTFINGDLLDTDKITKACHNID------ 76 
                                   679*************************9877743333....3333222.5689999999999999998887765...... PP

                                   -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH-- CS
                            KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgs 143
                                     v+h A   + +l  + t+ +++q     ++++ nL e+++++++  +v f+S ++++g+
  gi|91773959|ref|YP_566651.1|  77 -CVYHIAANPDVRLGFSNTKVHFDQ----NITATYNLLEAMRKNNIRNIV-FTSTSTVYGE 131
                                   .899999887777766666666665....567899999999999998865.6677777776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00093       1.5       6      33 ..      13      40 ..       8      52 .. 0.84
   2 ?    0.8   0.0      0.46   7.5e+02      41      68 ..     103     130 ..      88     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00093
                                  CSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                     Pyr_redox  6 GgGyiglElAgalaelgkkVtvversdk 33
                                  G+G+ig  +   l ++g++V v+++ + 
  gi|91773959|ref|YP_566651.1| 13 GAGFIGSHVVDKLINIGNRVIVFDNLSS 40
                                  99*********************98765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                                   HHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                     Pyr_redox  41 easkilqeklekngievllntkveeieg 68 
                                   +a  +l e ++kn+i+ +  t++  + g
  gi|91773959|ref|YP_566651.1| 103 TATYNLLEAMRKNNIRNIVFTSTSTVYG 130
                                   46678899*******9888777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 1829.59
//
Query:       gi|91773960|ref|YP_566652.1|  [L=513]
Description: hypothetical protein Mbur_2026 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2886.85
//
Query:       gi|91773961|ref|YP_566653.1|  [L=360]
Description: glycosyl transferase, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  102.9   0.1    3.4e-29  101.6   0.1    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    2.4e-20   73.3   0.0    3.7e-20   72.7   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    9.6e-14   51.7   0.0    7.7e-13   48.8   0.0    2.3  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-09   38.5   0.0    2.4e-09   37.5   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00027   21.4   0.0     0.0014   19.1   0.0    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.017   15.1   1.0       0.24   11.4   0.1    2.9  3  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 ?   -2.1   0.0      0.79   2.4e+03      89     111 ..     121     148 ..     118     150 .. 0.75
   2 !  101.6   0.1   1.1e-32   3.4e-29      20     171 ..     187     334 ..     165     335 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.79
                                   HHHCESEEEEEESS.....BSS-HHHHH CS
               Glycos_transf_1  89 llknadifvlpsis.....EgfGivllE 111
                                   ll+ +d++ + s s     E fG+   E
  gi|91773961|ref|YP_566653.1| 121 LLNGCDCITFVSKSlkkenERFGLIFNE 148
                                   6667888888777778999999997666 PP

  == domain 2  score: 101.6 bits;  conditional E-value: 1.1e-32
                                   EESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEE CS
               Glycos_transf_1  20 svgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlps 100
                                   ++++  k Kg + lika+++l  +  p++ lv+ G+g+  +e+k  +ee +ls+nvif+g++s  d    l +++i+ + s
  gi|91773961|ref|YP_566653.1| 187 FMSNKLKAKGSTILIKALKHLLNK-YPQTILVLTGDGAFSNEVKLFVEEVGLSENVIFTGHLS--DPFVPLAICNIYTHIS 264
                                   55556678*************988.**************************************..99999*********** PP

                                   SSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
               Glycos_transf_1 101 isEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                     +g +++llEAma g+p+ a+n+gg++e + +g +G+lv+p    ++ e+i+ l+ +++ + ++g+na++
  gi|91773961|ref|YP_566653.1| 265 LADGVPLALLEAMAMGKPIMATNIGGIPEAIDNGINGILVEPC-ENQIYEGIEYLILNSDVATKMGYNAKQ 334
                                   *******************************************.99***********************97 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 !   72.7   0.0   1.2e-23   3.7e-20       5     131 ..     183     318 ..     179     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1.2e-23
                                   EEES--.-G.G.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH-SEEEE CS
               Glyco_trans_1_4   5 lfvGrl.ee.nvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaadvfva 78 
                                   l  G + ++ + kg  +l++a+++l++k +   lv+ Gdg    +e++  ++  gl+e+v+ftG+++d    la ++++  
  gi|91773961|ref|YP_566653.1| 183 LAQGFMsNKlKAKGSTILIKALKHLLNKyPqTILVLTGDGAfS-NEVKLFVEevGLSENVIFTGHLSDPFVPLAICNIYTH 262
                                   555666444788**********99998864699*******976.4888666669************999999********9 PP

                                   --..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHH CS
               Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrL 131
                                    s   g++l+llEama+g+p+ at++ggi+e++  g ng+lv+p  ++++ e i+ L
  gi|91773961|ref|YP_566653.1| 263 ISlaDGVPLALLEAMAMGKPIMATNIGGIPEAIdnGINGILVEPC-ENQIYEGIEYL 318
                                   99988******************************9******975.66777777666 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   2.6e-16   7.7e-13       3     167 ..      17     157 ..      15     160 .. 0.77
   2 ?   -2.5   0.0       1.5   4.5e+03      86     141 ..     271     322 ..     259     325 .. 0.61

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.6e-16
                Glyco_transf_4   3 GverhvleLaraLarrGh.eVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspa 82 
                                   Gv +++  L+ ++  r + +V+v+  ++++ + ++                  ++ + f+++    lk+ +pD++H+++ +
  gi|91773961|ref|YP_566653.1|  17 GVKTYLTSLVDEFNNRDYlDVSVIFKSGKDYENYH----------------IEGNKIVFVFKTFLNLKQLNPDIIHSQGTW 81 
                                   55555555555555555445555554433333333................445667777777888999*********988 PP

                Glyco_transf_4  83 algaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVip 163
                                   ++++ + a ++ +g +lV+t+H+           ++l+ + r + + ll+ +d+++ vS+++++e ++ +g+  +  ++ +
  gi|91773961|ref|YP_566653.1|  82 YCLLPGYAYKKLYGTKLVHTFHSQP--------FGKLKLVGRIFFQTLLNGCDCITFVSKSLKKENER-FGLIFNEYAITY 153
                                   888888888889*************........5889999999999*******************999.998888888888 PP

                Glyco_transf_4 164 nGvD 167
                                    Gv+
  gi|91773961|ref|YP_566653.1| 154 AGVN 157
                                   8887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                Glyco_transf_4  86 aallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavS 141
                                   +all +++  g+p+ +t  g  +       ++   +l++ +e++++     +i +S
  gi|91773961|ref|YP_566653.1| 271 LALLEAMA-MGKPIMATNIGGIP---EAIDNGINGILVEPCENQIYEGIEYLILNS 322
                                   45555554.88888888766663...455566666677777777776666666666 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 !   37.5   0.0     8e-13   2.4e-09       4      90 ..     262     349 ..     255     351 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 8e-13
               Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaehty 83 
                                   ++s ++++ l l+Ea+a+G +++++ + g++e +++g  +il+e  ++++ e i+yl+ n + + +++ +a++ v +++t+
  gi|91773961|ref|YP_566653.1| 262 HISLADGVPLALLEAMAMGKPIMATNIGGIPEAIDNGINGILVEpCENQIYEGIEYLILNSDVATKMGYNAKQTVSNKFTW 342
                                   56667889999********************************************************************** PP

               Glyco_trans_1_2  84 dhraeql 90 
                                   +++a+ +
  gi|91773961|ref|YP_566653.1| 343 KNAANVF 349
                                   ***9866 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 ?   -0.5   0.0      0.49   1.5e+03       1      26 [.      16      43 ..      16      58 .. 0.79
   2 !   19.1   0.0   4.7e-07    0.0014      63     148 ..      61     143 ..      56     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.49
               Glyco_trans_4_4  1 gGigryvaelaraLaarGh.eVtvlt.p 26
                                  gG+++y   l+ ++  r + +V v+  +
  gi|91773961|ref|YP_566653.1| 16 GGVKTYLTSLVDEFNNRDYlDVSVIFkS 43
                                  8**************9987799998743 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 4.7e-07
               Glyco_trans_4_4  63 lrrllrqrrerpdvvhahs.ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeae 142
                                   ++ +l  ++ +pd++h+++ ++  l++ + +   g++lv+t+h+  + +    v+r++    ++ll+++d+++ vs ++ +
  gi|91773961|ref|YP_566653.1|  61 FKTFLNLKQLNPDIIHSQGtWYCLLPGYAYKKLYGTKLVHTFHSQPFGKL-KLVGRIF---FQTLLNGCDCITFVSKSLKK 137
                                   5666767999*********999999999999899**********877544.4444444...5789999***9999999988 PP

               Glyco_trans_4_4 143 elralg 148
                                   e +++g
  gi|91773961|ref|YP_566653.1| 138 ENERFG 143
                                   877776 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 ?   11.4   0.1   8.2e-05      0.24      70     137 ..      67     130 ..      12     132 .. 0.77
   2 ?   -3.0   0.0       2.3   6.7e+03     118     136 ..     164     182 ..     151     185 .. 0.72
   3 ?   -3.3   0.0       2.8   8.2e+03      88     113 ..     200     225 ..     192     232 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-05
               Glyco_trans_4_2  70 ikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksklkklllklalkkatkvis 137
                                   +k+++PD++h + ++   l g++ ++l g  ++v +++      f+k + + ++ ++++l+  +++++
  gi|91773961|ref|YP_566653.1|  67 LKQLNPDIIHSQGTWYCLLPGYAYKKLYG-TKLVHTFHSQ---PFGKLKLVGRIFFQTLLNGCDCITF 130
                                   7999***********88999999999999.***9999932...2222222567777777777777776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
               Glyco_trans_4_2 118 sklkklllklalkkatkvi 136
                                   +++ ++ +k++lk+++ v+
  gi|91773961|ref|YP_566653.1| 164 KQIAEFSEKYNLKSSNYVL 182
                                   3466778999999988886 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.8
               Glyco_trans_4_2  88 llgslaarlsgvipvvlsvwGldvlk 113
                                   l+ +l  +l+++++++l  +G + ++
  gi|91773961|ref|YP_566653.1| 200 LIKALKHLLNKYPQTILVLTGDGAFS 225
                                   34444445677777777766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2218.73
//
Query:       gi|91773962|ref|YP_566654.1|  [L=423]
Description: polysaccharide biosynthesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  24.0    4.4e-30  105.0  24.0    2.6  3  Polysacc_synt    Polysaccharide biosynthesis protein
    3.7e-27   95.3  18.5    6.1e-27   94.6  18.5    1.3  1  Polysacc_synt_3  Polysaccharide biosynthesis protein
    3.2e-18   65.9  32.3    1.5e-09   37.7  12.2    2.6  2  MatE             MatE
    2.9e-13   50.1  51.9    2.7e-11   43.7   9.6    4.8  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.2e-08   34.0  32.2    2.8e-08   32.8  32.0    1.6  1  MurJ             Lipid II flippase MurJ
  ------ inclusion threshold ------
       0.16   11.6   0.1       0.92    9.1   0.0    2.1  2  Catalase_C       C-terminal domain found in long catalases


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 !  105.0  24.0   1.5e-33   4.4e-30       3     273 ..      11     285 ..       9     286 .. 0.91
   2 ?   -0.8   0.6      0.27     8e+02     170     224 ..     306     360 ..     293     376 .. 0.60
   3 ?   -2.8   6.4       1.1   3.2e+03     162     191 ..     380     417 ..     310     422 .. 0.76

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.5e-33
                 Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek....kelvsli.l 78 
                                   k+v + ++s  ++ l  ++ +++l   lgp g Gl++l+++i+++ + ++ +G++aal+++ia+y+++    ke vs++ +
  gi|91773962|ref|YP_566654.1|  11 KDVQWSFISLATASLSHLLLRIVLGKELGPSGLGLYTLVFTIYMFGMQFAAFGIGAALTKYIAQYSDDegkiKEFVSSGvI 91 
                                   667777777777888899**************************************************9999777666516 PP

                 Polysacc_synt  79 lnvllvllvlvllfllllliaa.flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvli 158
                                    ++++++ + +ll+ll++lia  f++ p+   l+ i a+ ++ +++++ ++ g ++g++rm+++a+ ++ +++s++il+++
  gi|91773962|ref|YP_566654.1|  92 GSLISGSAMGILLYLLSPLIAInFFDMPAMEELLKITAICFP-FIAIQKVVIGTLNGQRRMQAFALVNITQNVSVAILSIA 171
                                   688899999***********779*******************.*************************************9 PP

                 Polysacc_synt 159 avflfld.ivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsillglllga 238
                                   +v+ f+  +++a++g+v+ +++ gi+s+++ ++   p+  i+ +   +e+  f++++++   ++l++ +ids++ g + + 
  gi|91773962|ref|YP_566654.1| 172 LVLFFKMdVTGAIIGYVAPTILIGILSIYLAKHDIQPSLFIS-KTVLKEISWFGFYVVLANSIGLINMQIDSLMVGHFMDE 251
                                   99999988************************5555555555.9999********************************** PP

                 Polysacc_synt 239 eavGiYnaayqllvaisgllapivtaalfPvfsel 273
                                   ++vG+Y +a  + +   +ll   v++++ Pv++++
  gi|91773962|ref|YP_566654.1| 252 TEVGYYAVA-IIFMQGVILLPQVVQRVTTPVMAKY 285
                                   *****9876.4667777888888899999999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                 Polysacc_synt 170 vlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslailly 224
                                    +g+++ +++ ++++ +++ ++f+ +f    + +   l+ +s+   i+s++++l+
  gi|91773962|ref|YP_566654.1| 306 FGGILFISVIIAVFGNYLIITIFTEEFLPAYRPMLILLVGYSICAPIGSVGNTLS 360
                                   4555555555555555555556665555444556666666666666666666665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.1
                 Polysacc_synt 162 lfld........ivaavlgavlaalvggivslavlrkk 191
                                   ++l         i +a+ ++++++++++++ l++++k+
  gi|91773962|ref|YP_566654.1| 380 TMLNlilipnygIIGAASATSISQIITLLIHLLFIKKY 417
                                   33333333334688889999999999999888888866 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6  18.5     2e-30   6.1e-27       6     291 ..      38     335 ..      33     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 2e-30
               Polysacc_synt_3   6 LspedFGvvaialvvislanlfvdmGlssaliqke...dltee....dlstvftfnlvlgllialvlfllaplias.fynq 78 
                                   L p+  G+++++++++ +   f+ +G++ al +     +++e      +s+    +l++g ++ ++l+ll+plia  f+++
  gi|91773962|ref|YP_566654.1|  38 LGPSGLGLYTLVFTIYMFGMQFAAFGIGAALTKYIaqySDDEGkikeFVSSGVIGSLISGSAMGILLYLLSPLIAInFFDM 118
                                   89***************************9965432113333334446677777789999999************76**** PP

               Polysacc_synt_3  79 pelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAll.glgvwALvigtllssllslvllw 158
                                   p ++++l+++a+ + + ++++v   +l+ + + ++++ ++++ +v  +i++i+l+l+  + v   +ig ++  +l+ +l++
  gi|91773962|ref|YP_566654.1| 119 PAMEELLKITAICFPFIAIQKVVIGTLNGQRRMQAFALVNITQNVSVAILSIALVLFfKMDVTGAIIGYVAPTILIGILSI 199
                                   *****************************************************99752689***************99999 PP

               Polysacc_synt_3 159 laskwr..prlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsviakVlf 237
                                   + +k+   p+l +s ++lke+ +fg +++l+n +  +++++d+l++G +++++++G+Y+va  +++ ++  + +v+++V++
  gi|91773962|ref|YP_566654.1| 200 YLAKHDiqPSLFISKTVLKEISWFGFYVVLANSIGLINMQIDSLMVGHFMDETEVGYYAVAIIFMQGVI-LLPQVVQRVTT 279
                                   8887763388889*************************************************9988765.89********* PP

               Polysacc_synt_3 238 PalSrl..qddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                   P++++   ++d +++r+l++ ++  +   +l i v++av+ ++l+ +++++++l+a
  gi|91773962|ref|YP_566654.1| 280 PVMAKYygKNDFESIRKLIKSTMVKTFGGILFISVIIAVFGNYLIITIFTEEFLPA 335
                                   ****98668999999999987665555555559*******************9986 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6  12.2   9.4e-12   2.8e-08       3     157 ..      17     167 ..      16     172 .. 0.92
   2 !   37.7  12.2   4.9e-13   1.5e-09      13     161 .]     238     385 ..     227     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 9.4e-12
                          MatE   3 alenllesllslidtllvgrl.gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglillll 81 
                                   +++ ++ sl+ l++ +++g+  g++ l+ ++++++i ++ +   ++g+++alt  ++q+  + +  ++ke +  g+i +l+
  gi|91773962|ref|YP_566654.1|  17 FISLATASLSHLLLRIVLGKElGPSGLGLYTLVFTIYMFGMQfAAFGIGAALTKYIAQY--SDDEGKIKEFVSSGVIGSLI 95 
                                   6788889999999999999878******************99899**************..57778*************** PP

                          MatE  82 lsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnip 157
                                    + ++ +l++l+s+ i+  f + ++     +++l+i++++ p++a+q v  g+l+g+ ++ + + +++  ++  ++
  gi|91773962|ref|YP_566654.1|  96 SGSAMGILLYLLSPLIAINFFDMPA----MEELLKITAICFPFIAIQKVVIGTLNGQRRMQAFALVNITQNVSVAI 167
                                   *****************99988886....799***********************************998855444 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 4.9e-13
                          MatE  13 slidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvll 92 
                                     id+l+vg++ ++++++ +++a+ + + +++++  +   +t+++++++G+++f+ +++ +  +++ +++  l+i++++ +
  gi|91773962|ref|YP_566654.1| 238 MQIDSLMVGHFmDETEVGYYAVAIIFMQGVILLPQVVQRVTTPVMAKYYGKNDFESIRKLIKSTMVKTFGGILFISVIIAV 318
                                   679*******************************************************************99999999999 PP

                          MatE  93 fseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161
                                   f ++++  + ++e     a r ++il++g+ + a+     ++l ++gk+ +++ ++++++l n +ln +
  gi|91773962|ref|YP_566654.1| 319 FGNYLIITIFTEE--FLPAYRPMLILLVGYSICAPIGSVGNTLSSVGKVNIVFKMTALCALMNTMLNLI 385
                                   9998776665555..45678888899999999999******************************9975 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   5.0     0.031        92      26     109 ..      11     108 ..       4     121 .. 0.66
   2 !   16.7  13.8     2e-06    0.0059       1     134 [.     124     263 ..     124     272 .. 0.72
   3 ?    1.1   2.9      0.13   3.8e+02      78     119 ..     295     331 ..     291     352 .. 0.60
   4 !   43.7   9.6   9.1e-15   2.7e-11      14      81 ..     351     418 ..     338     422 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.031
               Polysacc_synt_C  26 grqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl..............ellrrll 92 
                                   + +++ +++l+ + l +l+l ++l  ++g  G  + t++  + ++ +++ a      +                 +   ++
  gi|91773962|ref|YP_566654.1|  11 KDVQWSFISLATASLSHLLLRIVLGKELGPSGLGLYTLVFTIYMFGMQFAAFGIGAALTKyiaqysddegkikeFVSSGVI 91 
                                   566788999999999999999999999999999999999999999988654332222222223334666544433333344 PP

               Polysacc_synt_C  93 kpllaalvmgivvylll 109
                                     l+++ +mgi++yll 
  gi|91773962|ref|YP_566654.1|  92 GSLISGSAMGILLYLLS 108
                                   77777777777766333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2e-06
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavlnlyalrr 79 
                                   +L i a+ ++f++++ v+ + L+g  r ++++++++   +   il++ l+ +f   ++Ga+i+ v+  +++ +l +y++++
  gi|91773962|ref|YP_566654.1| 124 LLKITAICFPFIAIQKVVIGTLNGQRRMQAFALVNITQNVSVAILSIALVLFFkmDVTGAIIGYVAPTILIGILSIYLAKH 204
                                   5899**********************************************6662257************************ PP

               Polysacc_synt_C  80 llgikl....ellrrll...kpllaalvmgivvylllllllgllllaalalllavlvgalvY 134
                                    ++ +l    ++l+ +     ++++a  +g++ + + +l++g++++   ++ ++  + a+++
  gi|91773962|ref|YP_566654.1| 205 DIQPSLfiskTVLKEISwfgFYVVLANSIGLINMQIDSLMVGHFMD---ETEVGYYAVAIIF 263
                                   ******6665223333112244444444444444444444444444...3444444444444 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.13
               Polysacc_synt_C  78 rrllgiklellrrllkpllaalvmgivvylllllllglllla 119
                                   r+l++  +  ++++  +l++++++++     ++l++++++ +
  gi|91773962|ref|YP_566654.1| 295 RKLIKSTM--VKTFGGILFISVIIAVF---GNYLIITIFTEE 331
                                   55555555..88888999999999999...455554444443 PP

  == domain 4  score: 43.7 bits;  conditional E-value: 9.1e-15
               Polysacc_synt_C  14 lstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrll 81 
                                    +  +++ L ++g++ i++k ++++al++  lnl+lip +gi+Gaa at ++++++++++l ++++++
  gi|91773962|ref|YP_566654.1| 351 PIGSVGNTLSSVGKVNIVFKMTALCALMNTMLNLILIPNYGIIGAASATSISQIITLLIHLLFIKKYV 418
                                   344567889********************************************************986 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8  32.0   9.4e-12   2.8e-08      43     403 ..      73     417 ..      54     422 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 9.4e-12
                          MurJ  43 eakkkdeekaaefv.rkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLn 122
                                    ++++de k +efv + v++ li   ++ +l+ +l +++ i+++++++ ee l       +i++    ++ +  v+ ++Ln
  gi|91773962|ref|YP_566654.1|  73 AQYSDDEGKIKEFVsSGVIGSLISGSAMGILLYLLSPLIAINFFDMPAMEELL-------KITAICFPFIAIQKVVIGTLN 146
                                   33334555555555156899998888888888899999999999999955555.......55555555678899******* PP

                          MurJ 123 arkkFfapafsPvllNvsv.Iltlll.lanklgeeailaLaiGvliGgvlq.llvqlpalkkaglllkprfafrdeglkkf 200
                                    + +  a+a+  +  Nvsv Il+++l l  k++       + G +iG v+  +l+ +  ++ a+   +p +   +  lk++
  gi|91773962|ref|YP_566654.1| 147 GQRRMQAFALVNITQNVSVaILSIALvLFFKMD-------VTGAIIGYVAPtILIGILSIYLAKHDIQPSLFISKTVLKEI 220
                                   *****************8657776541445555.......46888888885145666666666666668888889999999 PP

                          MurJ 201 lklllptllgvsvsqlnllvdtalA.sflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsq 280
                                       +  +l++s+ ++n ++d  +   f++e+ v ++a    i++  + l+   +  v  P +++ + ++d +++r+l++ 
  gi|91773962|ref|YP_566654.1| 221 SWFGFYVVLANSIGLINMQIDSLMVgHFMDETEVGYYAV-AIIFMQGVILLPQVVQRVTTPVMAKYYGKNDFESIRKLIKS 300
                                   999999**************9876505566666665554.46667777788889999************************ PP

                          MurJ 281 airltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislis 361
                                   ++  t+  ++ +s++++v++++++ ++f   +F + + + +  +L +y++  +  ++ + l+    + + ++  +k++ + 
  gi|91773962|ref|YP_566654.1| 301 TMVKTFGGILFISVIIAVFGNYLIITIF-TEEFLP-AYRPMLILLVGYSICAPIGSVGNTLS----SVGKVNIVFKMTALC 375
                                   ****************************.334444.34445556666766666666666666....66************* PP

                          MurJ 362 lvlnillsllllpplgvvglalatslsaliglvllyvllrkr 403
                                   + +n++l+l+l+p++g +g a ats+s +i l++ +++++k 
  gi|91773962|ref|YP_566654.1| 376 ALMNTMLNLILIPNYGIIGAASATSISQIITLLIHLLFIKKY 417
                                   ******************************999999999885 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.24   7.1e+02      90     123 ..      47      80 ..      40      97 .. 0.80
   2 ?    9.1   0.0   0.00031      0.92      55     117 ..     307     367 ..     274     415 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.24
                    Catalase_C  90 qllldayrhgKpigalGsgaealkaagisaeepG 123
                                   +l+  +y +g  ++a+G ga++ k +   ++++G
  gi|91773962|ref|YP_566654.1|  47 TLVFTIYMFGMQFAAFGIGAALTKYIAQYSDDEG 80 
                                   789999*************999886666665555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00031
                    Catalase_C  55 daveFDaivvadgaeslfsakataasslfpagrplqllldayrhgKpigalGsgaealkaagi 117
                                    +++F ++++a   + l+   +  +++  pa rp+ +ll  y+ + pig +G+  + + +++i
  gi|91773962|ref|YP_566654.1| 307 GGILFISVIIAVFGNYLII--TIFTEEFLPAYRPMLILLVGYSICAPIGSVGNTLSSVGKVNI 367
                                   4577777888776666663..36788999***********************98777765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2710.02
//
Query:       gi|91773963|ref|YP_566655.1|  [L=472]
Description: UDP-glucose/GDP-mannose dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  119.5   0.0    2.8e-34  118.4   0.0    1.6  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.4e-21   76.9   0.0    3.1e-21   75.8   0.0    1.6  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    1.4e-19   70.1   0.0    3.2e-19   68.9   0.0    1.6  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
       0.16   12.1   0.3         14    5.8   0.0    3.1  4  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy


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 !  118.4   0.0   6.2e-38   2.8e-34       2     184 ..      17     208 ..      16     211 .. 0.94
   2 ?   -0.1   0.0      0.13   5.7e+02     100     132 ..     204     238 ..     200     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 6.2e-38
                                   EEEEE--STTHHHHHHHHHHCT..SEEEEE-S-HH....HHHHHCTTS-SS..--TTHHHHHHHHCHTTTEEEES-HHHHH CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeig..hevigvDidee....kvdklnsgkipi..yepgLeelvkkavesgrlsfttdvekav 74 
                                   ki v+G+GYvG++ aa++a +    +v+g   +++    k+d++n+g++p+  +epgLe+l++k++ s++++ t d+++ +
  gi|91773963|ref|YP_566655.1|  17 KIGVLGMGYVGIPAAALFADVDkfEKVLGFQRNSAssgyKIDMINAGESPLkgEEPGLEDLLRKVTGSNKFECTPDFSR-I 96 
                                   8******************9887789****9998655559*********99556************************9.* PP

                                   HC-SEEEE-----B-T.TTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEEE-- CS
                UDPG_MGDP_dh_N  75 eeadvifiaVgTPskk.kgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvvsnP 153
                                   +e d++ +a+ TP+++ ++  +D  ++ + +r+++++l  g++vv++ST+ +gt++ ++k+ilee+s    g+df +++ P
  gi|91773963|ref|YP_566655.1|  97 AEMDAVTLAIQTPFENpTDLIPDFGALIEGIRNVGRYLTPGTLVVLESTITPGTTNGMAKEILEEESGLIaGEDFALAHAP 177
                                   ***************989999********************************************999878********** PP

                                   ----TTSHHHHHHS-S-EEEEESSCHHHHHH CS
                UDPG_MGDP_dh_N 154 EflregsavkdllnpdrvviGveekkaeaal 184
                                   E++  g  ++++++ dr+v+G +++++e a+
  gi|91773963|ref|YP_566655.1| 178 ERVMVGRLLRNIQEHDRIVGGIDNTSTERAI 208
                                   *************************999544 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHCEEEEEE-S---..TTHHHHCH CS
                UDPG_MGDP_dh_N 100 vesaarsiaealkkgkvvvvkSTvp..vgtaeelv 132
                                    e+a++  +++l kgk++ + ST +   +tae++ 
  gi|91773963|ref|YP_566655.1| 204 TERAIELYSPVLTKGKIIPMTSTAAevTKTAENTF 238
                                   6788999999*************852256666655 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 !   75.8   0.0     7e-25   3.1e-21       1     105 []     355     453 ..     355     453 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 7e-25
                                   EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGG CS
                UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefke 81 
                                   a+lG+af +d+dD R+ p+  +++ L e+gaev+i+DP+v +          +v++ ++l+  ++gad+i ilt h+++ +
  gi|91773963|ref|YP_566655.1| 355 AMLGWAFINDSDDARNPPSEPLYDLLIEAGAEVRIHDPHVLDY--------PNVTIEKDLNAVVDGADVIAILTGHSDYFK 427
                                   79***************************************94........5899************************** PP

                                   S-HHHHHHCC..SS-EEEESSS-CCC CS
                UDPG_MGDP_dh_C  82 ldlaklkelm..kpavvfDgrnvldp 105
                                   l+ a++k +m   ++v++Dgrnv+dp
  gi|91773963|ref|YP_566655.1| 428 LNPADIKTTMgkDKPVIIDGRNVVDP 453
                                   ***********9999*********96 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 !   68.9   0.0   7.1e-23   3.2e-19       2      73 ..     227     300 ..     226     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 7.1e-23
                  UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldpr..igpkflkpglGvGGsclpkDvkaLva 73 
                                   +AE++K a+N+f++++I+ +N+la +ce++gi+  +V+ ++ + +   i++++l+pg+GvGG+cl kD++ L +
  gi|91773963|ref|YP_566655.1| 227 AAEVTKTAENTFRDLQIAAANQLALYCESMGINFYDVRAGIDSLKGegITRAILYPGAGVGGHCLTKDTYHLER 300
                                   79***************************************9987667999*******************9976 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 ?    2.5   0.1     0.034   1.5e+02       1      33 [.      17      51 ..      17      63 .. 0.84
   2 ?    5.8   0.0    0.0031        14      73     108 ..     127     162 ..     116     168 .. 0.81
   3 ?   -1.9   0.0      0.74   3.3e+03      81      86 ..     216     221 ..     180     261 .. 0.56
   4 ?   -2.8   0.0       1.4   6.1e+03      44      84 ..     401     441 ..     380     452 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.034
                                  EEEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHH CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnl..lkagykvavynrtke 33
                                  kig++G+G  G + a  +  +++  kv +++r+++
  gi|91773963|ref|YP_566655.1| 17 KIGVLGMGYVGIPAAALFadVDKFEKVLGFQRNSA 51
                                  79***********9999855577788988888865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0031
                                   HHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT CS
                 NAD_binding_2  73 iegllealkkgdilidgstsspedtrelakelkekg 108
                                   i+++ ++l +g++++  st+ p +t+ +ake+ e++
  gi|91773963|ref|YP_566655.1| 127 IRNVGRYLTPGTLVVLESTITPGTTNGMAKEILEEE 162
                                   45588999**********************986655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.74
                                   -TT-EE CS
                 NAD_binding_2  81 kkgdil 86 
                                    kg+i+
  gi|91773963|ref|YP_566655.1| 216 TKGKII 221
                                   333322 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.4
                                   EE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT- CS
                 NAD_binding_2  44 kaaesieelvasldvvitmvkagkavdeviegllealkkgd 84 
                                   ++ ++++++v+++dv+ ++  +++  +    +++ ++ k++
  gi|91773963|ref|YP_566655.1| 401 TIEKDLNAVVDGADVIAILTGHSDYFKLNPADIKTTMGKDK 441
                                   55566667777777777776666666655555666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3067.21
//
Query:       gi|91773964|ref|YP_566656.1|  [L=310]
Description: oxidoreductase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-28   98.0   0.2    1.3e-27   96.9   0.1    1.6  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00018   21.5   0.0    0.00034   20.6   0.0    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
      0.002   18.6   0.1     0.0045   17.4   0.1    1.7  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.015   15.4   0.5      0.046   13.8   0.5    2.0  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
      0.039   14.6   0.0       0.09   13.5   0.0    1.6  1  CoA_binding     CoA binding domain
      0.055   13.5   0.2       0.44   10.6   0.0    2.2  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.074   13.2   0.1       0.14   12.4   0.1    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
        0.1   13.2   0.0       0.26   11.9   0.0    1.8  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.12   12.8   0.1       0.32   11.4   0.1    1.8  1  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD


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 !   96.9   0.1   6.8e-31   1.3e-27       1     120 []       2     119 ..       2     119 .. 0.96
   2 ?   -3.0   0.0       6.5   1.3e+04      14      35 ..     198     217 ..     187     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 6.8e-31
                                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelaka 81 
                                   lrv++iG+G +g +h+r ++e  ++ e+v++ d+d++r ++++++++ e ++d+ +ll  ++ dav++++p+++h++++++
  gi|91773964|ref|YP_566656.1|   2 LRVGVIGTGAMGVNHIRIYHEM-EDVELVGISDIDEKRVKELSDKYETEHFTDYMRLLG-KDLDAVSIVVPTKLHKQVCLD 80 
                                   69**************555555.***********************************9.77******************* PP

                                   HHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                  GFO_IDH_MocA  82 aleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                   aleag +vl+EKP+a+t+e a+ ++++a+ ++k +++g+
  gi|91773964|ref|YP_566656.1|  81 ALEAGTNVLVEKPIADTPENADIMIKAAKAANKALMIGH 119
                                   ***********************************9987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.5
                                   HHHHHHHHTTTTEEEEEEECSS CS
                  GFO_IDH_MocA  14 khlrplnesqrleevvalldpd 35 
                                   +h+ +++ +  ++++++l+d++
  gi|91773964|ref|YP_566656.1| 198 DHA-SIHLR-FDHDLTGLVDTN 217
                                   343.33333.455888888876 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.7e-07   0.00034       1      68 [.     131     188 ..     131     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                                   HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEE CS
                GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaal 68 
                                   Ke I++g lG++vs++     tr+  ++ +r +     + Gv  d+g+HdiD+  +L G +  +v a+
  gi|91773964|ref|YP_566656.1| 131 KEIIDEGLLGKIVSIS-----TRRVGPYNPRIR-----DVGVILDIGVHDIDIISYLYGLEVNKVHAI 188
                                   899************7.....999999999999.....67*******************888887665 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 !   17.4   0.1   2.3e-06    0.0045       1      93 [.       3      88 ..       3     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                  EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHH CS
                Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskela 83
                                  +v+++G tG++G + +r+ +e  +velv ++  +++  k+l+++++      +  ++d+     k++d v   +p + +k++ 
  gi|91773964|ref|YP_566656.1|  3 RVGVIG-TGAMGVNHIRIYHEMEDVELVGISDIDEKRVKELSDKYE------TEHFTDYMRLLGKDLDAVSIVVPTKLHKQVC 78
                                  79****.**********************99999977777777755......5556664444447888888888999999999 PP

                                  HHHHHTTSEE CS
                Semialdhyde_dh 84 pklaeagvkv 93
                                   +++eag+ v
  gi|91773964|ref|YP_566656.1| 79 LDALEAGTNV 88
                                  9999999876 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   2.3e-05     0.046       2      40 ..       3      40 ..       2     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                                  EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTT CS
                        DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkesele 40
                                  +v+v+G  G mG + ++  +e ed+elv+  d +e++++
  gi|91773964|ref|YP_566656.1|  3 RVGVIGT-GAMGVNHIRIYHEMEDVELVGISDIDEKRVK 40
                                  8*****8.**********************999874333 PP

>> CoA_binding  CoA binding 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      0.09       5      91 ..       3      90 ..       1      92 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-05
                                  EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.T.TTEEEEES-HHHHHHHHHHHHHT CS
                   CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt.e.vdvavitvPaesaqeavdelvea 85
                                  +v+viG g +g       +e+ +++++ + +++++ v +  +  +   + ++ +  + +  d+  i+vP +  ++++++++ea
  gi|91773964|ref|YP_566656.1|  3 RVGVIGTGAMGVNHIRIYHEMEDVELVGISDIDEKRVKELSDKYETE-HFTDYMRLLgKdLDAVSIVVPTKLHKQVCLDALEA 84
                                  79*********************************988888877777.777777777524*********************** PP

                                  T-SEEE CS
                   CoA_binding 86 gikgiv 91
                                  g ++ v
  gi|91773964|ref|YP_566656.1| 85 GTNVLV 90
                                  *98765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00022      0.44      14      81 ..       3      70 ..       1      86 [. 0.80
   2 ?    1.0   0.1      0.21   4.1e+02      69      99 ..      94     124 ..      56     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                  EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
                  Shikimate_DH 14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81
                                  +v +iG+G m+   ++  ++   v+ v +   + +r+kel +++++e   +  +  l + l+++ +v+ 
  gi|91773964|ref|YP_566656.1|  3 RVGVIGTGAMGVNHIRIYHEMeDVELVGISDIDEKRVKELSDKYETE-HFTDYMRLLGKDLDAVSIVVP 70
                                  799*************999865899999****************766.445556666667777777665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.21
                                   HHHHHHT-SEEEE-SSSSS-SB-HHHHHCCH CS
                  Shikimate_DH  69 lkellaeadvvisataseepilekeeveeal 99 
                                   + +  ++ad++i a ++ +  l  +++e+ +
  gi|91773964|ref|YP_566656.1|  94 IADTPENADIMIKAAKAANKALMIGHIERFN 124
                                   55566899******99999999988888876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.9e-05      0.14       1      75 [.       3      81 ..       3     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                                  EEEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHTT.EEE-SSHHHHH.HHCSEEEE-SSSHHHHHHHHHS CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnl..lkagykvavynrtkekveelvaeg.akaaesieelv.asldvvitmvkagkavdevieg 75
                                  ++g+iG+G MG n ++    ++    v + + ++++v+el ++   + +++   l+ ++ld+v ++v+ + + + +++ 
  gi|91773964|ref|YP_566656.1|  3 RVGVIGTGAMGVNHIRIYheMEDVELVGISDIDEKRVKELSDKYeTEHFTDYMRLLgKDLDAVSIVVPTKLHKQVCLDA 81
                                  58**********99887732344445667789999*****99965667776665542677***9999998776655555 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 ?   11.9   0.0   0.00013      0.26       1      81 [.       3      81 ..       3      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81
                                  ++g+iG+G mg   ++   +   + + +  +++ ++++++el ++++ + ++     + ++ d v + v+++ +++v+ ++
  gi|91773964|ref|YP_566656.1|  3 RVGVIGTGAMGVNHIRIYHEME-DVELVG-ISDIDEKRVKELSDKYETEHFTDYMRLLGKDLDAVSIVVPTKLHKQVCLDA 81
                                  69*************9555554.555555.66***************9999955556667999999999999999998655 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00016      0.32       2      48 ..       3      49 ..       2      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                  EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHHHEETT CS
                       Gp_dh_N  2 kvainGfGRIGrlvlralleekelevvaindltdletlayllkyDsv 48
                                  +v++ G G +G + +r+  e +++e+v i d+ + +  +   ky++ 
  gi|91773964|ref|YP_566656.1|  3 RVGVIGTGAMGVNHIRIYHEMEDVELVGISDIDEKRVKELSDKYETE 49
                                  89*****************************8776666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1825.42
//
Query:       gi|91773965|ref|YP_566657.1|  [L=163]
Description: phosphopantetheine adenylyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-12   45.5   0.0    9.4e-12   45.3   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.13   11.5   0.1        0.4    9.8   0.0    1.7  2  Pantoate_ligase  Pantoate-beta-alanine ligase
       0.14   12.0   0.1       0.28   11.1   0.1    1.5  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   1.6e-15   9.4e-12       2     141 ..      15     150 ..      14     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.6e-15
                                   EEE--TT--HHHHHHHHHHHHHSSES.EEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
               CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleed.livgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                   +gGtF ++H GH++l+++a++l + d + +g++s e + +k++ + + ++R + l +++++   ++ +++ ++  +++ ++
  gi|91773965|ref|YP_566657.1|  15 VGGTFEFLHDGHMALIRKAFELAKGDvVDIGLTSEEMAGRKNRIIPDIATRKKSLTAFIKELG-FPEEKYNIQT-LKDPYG 93 
                                   69************************999************999999***********88877.9999999997.555555 PP

                                   TT....EEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
               CTP_transf_like  82 pd....klylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                   +       ylv++ ++l  + + +e+++  g++++ +vs++       +  +++  +iSst+i 
  gi|91773965|ref|YP_566657.1|  94 STleedYEYLVVSPETLPVARKINEIRKTNGKREIKIVSIN-------YVMAEDDLPISSTRIE 150
                                   52323244******************************999.......77778888******96 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   6.8e-05       0.4      28      51 ..      18      41 ..       7      46 .. 0.79
   2 ?   -1.3   0.0      0.17   9.9e+02     162     181 ..     127     146 ..      89     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.8e-05
                                  E-SS-GHHHHHHHHHHHHHSSEEE CS
               Pantoate_ligase 28 TmGaLHeGHlsLvkaakeendvvv 51
                                  T   LH+GH++L+++a e ++  v
  gi|91773965|ref|YP_566657.1| 18 TFEFLHDGHMALIRKAFELAKGDV 41
                                  6668************88665544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.17
                                   SSEEEEEEEEBETTSEBTTG CS
               Pantoate_ligase 162 pveivavpivReedgLAlSS 181
                                   +++iv+++ v +ed L +SS
  gi|91773965|ref|YP_566657.1| 127 EIKIVSINYVMAEDDLPISS 146
                                   56777777777777777776 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.7e-05      0.28      13      36 ..      17      40 ..       8      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                       FAD_syn 13 GnFDGvHlGHqallkkaveaakek 36
                                  G F  +H GH al++ka e+ak +
  gi|91773965|ref|YP_566657.1| 17 GTFEFLHDGHMALIRKAFELAKGD 40
                                  89999***************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1090.01
//
Query:       gi|91773966|ref|YP_566658.1|  [L=180]
Description: membrane-bound metal-dependent hydrolase [Methanococcoides burtonii DSM 6242]
Scores for 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-17   60.9   8.8    1.1e-16   60.6   8.8    1.1  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
        1.6    8.9   8.6       0.64   10.1   0.1    2.7  3  MASE2     MASE2 domain


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   8.8   1.2e-20   1.1e-16       1     147 [.       1     148 [.       1     174 [. 0.76

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 1.2e-20
                          YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPD.iD..hpsstlgrklgllskklaklvgHRgftHSllflal 78 
                                   M  + H+ l++a++l++  l ++ ++++ + ++++gAllPD iD  ++++++ + +++           R f H++lf+++
  gi|91773966|ref|YP_566658.1|   1 MFIIGHLGLTLAIFLVISLLVPSIRNMIDYRFVAVGALLPDlIDkpIGRLFFEEIFAN----------GRIFAHTFLFVLV 71 
                                   77889******************999******************88888888888877..........9************ PP

                          YdjM  79 lalvlllllrlfgrsalrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltll..........s 147
                                   l ++++++++  + +  +  ++l ++ ++Hll D +++ +  +lwP+ ++++  +++    +  l  +          s
  gi|91773966|ref|YP_566658.1|  72 LFAMGAIIHKYHKEN-GTGMIILSIASFMHLLQDRMWTVPQTFLWPIMGWEFPHGTTYGGFSHYLS-VvtansfapevS 148
                                   *99999999998888.6666669999*********************9866665555443333222.234445555441 PP

>> MASE2  MASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6    0.0064        57       7      40 ..       6      39 ..       1      42 [. 0.91
   2 ?   -3.5   0.2       1.3   1.2e+04      13      18 ..      67      72 ..      59      79 .. 0.45
   3 ?   10.1   0.1   7.2e-05      0.64       9      48 ..      87     122 ..      82     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0064
                         MASE2  7 vlGlllgaliiaaglleqhfslalllllvlnall 40
                                   lGl+l+ + +++ l+   ++++ + +++++all
  gi|91773966|ref|YP_566658.1|  6 HLGLTLAIFLVISLLVPSIRNMIDYRFVAVGALL 39
                                  59***********************999999986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.3
                         MASE2 13 galiia 18
                                   ++ ++
  gi|91773966|ref|YP_566658.1| 67 LFVLVL 72
                                  332222 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 7.2e-05
                         MASE2   9 GlllgaliiaaglleqhfslalllllvlnallwPhlayll 48 
                                   G++++ l+ia+ ++  +      ++ v+  +lwP++ + +
  gi|91773966|ref|YP_566658.1|  87 GTGMIILSIASFMHLLQDR----MWTVPQTFLWPIMGWEF 122
                                   6777888888888887777....9***********98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1125.82
//
Query:       gi|91773967|ref|YP_566659.1|  [L=325]
Description: DNA repair and recombination protein RadA [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-84  283.0   0.0    2.3e-84  282.7   0.0    1.1  1  Rad51            Rad51
    6.7e-12   45.8   0.6    2.6e-11   44.0   0.4    2.2  2  HHH_5            Helix-hairpin-helix domain
    1.1e-11   44.7   0.3    7.1e-10   38.8   0.0    2.3  2  RecA             recA bacterial DNA recombination protein
    7.4e-08   32.0   0.1    1.1e-07   31.4   0.1    1.3  1  ATPase           KaiC
    1.7e-06   27.8   0.0    2.5e-06   27.2   0.0    1.3  1  AAA_25           AAA domain
      3e-06   27.2   0.3    7.9e-06   25.9   0.3    1.6  1  HHH_2            Helix-hairpin-helix motif
     0.0014   18.4   0.0     0.0033   17.2   0.0    1.7  1  AAA_24           AAA domain
     0.0022   17.8   0.0     0.0067   16.2   0.0    1.8  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0088   16.3   0.0      0.019   15.2   0.0    1.6  1  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
       0.01   15.7   0.3        1.2    9.1   0.4    2.6  2  HHH              Helix-hairpin-helix motif
      0.011   16.0   0.0       0.02   15.2   0.0    1.5  1  AAA_22           AAA domain
      0.024   15.0   0.1       0.11   12.9   0.1    2.0  1  AAA              ATPase family associated with various cellul
      0.034   14.1   0.1       0.15   12.0   0.1    2.0  1  NACHT            NACHT domain
      0.037   13.6   0.0        0.4   10.2   0.0    2.1  2  CobU             Cobinamide kinase / cobinamide phosphate gua
       0.12   12.5   0.0       0.21   11.6   0.0    1.4  1  RNA_pol_RpbG     DNA-directed RNA polymerase, subunit G
       0.12   13.0   0.0       0.41   11.2   0.0    1.8  1  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.7   0.0   2.1e-87   2.3e-84       2     254 ..      65     324 ..      64     325 .] 0.93

  Alignments for each domain:
  == domain 1  score: 282.7 bits;  conditional E-value: 2.1e-87
                                   S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS- CS
                         Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegt 82 
                                   gf ++  +le+r+ + +l+tG++++De++gGGiet+site++Gef+sGktq++h+l+v vqlp e+gG  g ++ idte t
  gi|91773967|ref|YP_566659.1|  65 GFETGDLVLERRKLVGKLSTGCTEFDEMMGGGIETQSITEMYGEFGSGKTQIAHQLAVNVQLPPEQGGLGGSVIMIDTENT 145
                                   6888888999999999***************************************************************** PP

                                   --GGGGHHHH....HHT..T--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-.....EEEEEEETTTGGGCH----- CS
                         Rad51  83 frperlveia....ery..kldkeevlenvayaRaytiehqeellqqaaallaedk.....fallivDsvtalyRtdfsgr 152
                                   frper+ ++     +++  + d+ee l+n+ +aRa++++hq  l+++a +l +e k     ++llivDs+ta++R+++ gr
  gi|91773967|ref|YP_566659.1| 146 FRPERIAQMVkgisDKHgiEYDPEEFLKNIHVARAFNSNHQILLVDSANELANELKntempVKLLIVDSLTAHFRAEYIGR 226
                                   *******988778777744789**********************9966554443221112279****************** PP

                                   --THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEE CS
                         Rad51 153 gelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvv 233
                                   g la+Rqqkl+k+l+++ ++ d  +++vv+tnqv++++d+    f +dp+kPigG++l+h++t Rl++rk kge+Rivk+v
  gi|91773967|ref|YP_566659.1| 227 GTLADRQQKLNKHLHEILRFGDLSNACVVVTNQVMSKPDA----FFGDPTKPIGGHILGHTATFRLYIRKSKGEKRIVKLV 303
                                   ****************************************....99*********************************** PP

                                   S-SSS-S-EEEEEEETTEEE- CS
                         Rad51 234 dsPnlpeleavfaigeeGied 254
                                   dsPnlp+ ea ++++++Gi d
  gi|91773967|ref|YP_566659.1| 304 DSPNLPDGEALISVTTDGIGD 324
                                   *******************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 !   44.0   0.4   2.3e-14   2.6e-11       3      56 ..       5      58 ..       3      59 .. 0.96
   2 ?   -2.3   0.0       6.4   7.2e+03      35      46 ..     149     161 ..     147     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.3e-14
                                  HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                         HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                  +L +++ +Gp+tA +l +aG++++e++a a+++eLa    iG+ tA +ii +++
  gi|91773967|ref|YP_566659.1|  5 LLEDLDHVGPATAQKLKDAGFTTIEAIAVASPAELANSAEIGESTAAKIINAAR 58
                                  578999********************************************9998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.4
                                   HHHHT.STTS-HH CS
                         HHH_5  35 eeLak.ipGiGkk 46 
                                   e++a+ ++Gi+ k
  gi|91773967|ref|YP_566659.1| 149 ERIAQmVKGISDK 161
                                   6677757888776 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.3     6e+03     131     158 ..      27      53 ..      24      61 .. 0.66
   2 !   38.8   0.0   6.3e-13   7.1e-10      29     225 ..      77     296 ..      66     305 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.3
                                   --SEEEEE-TTT---STT---------- CS
                          RecA 131 aidlivvdsvaalvpkaeieGemgdskv 158
                                   +i+ i v s a l   aei Ge + +k+
  gi|91773967|ref|YP_566659.1|  27 TIEAIAVASPAELANSAEI-GESTAAKI 53 
                                   5777888888888888888.44444444 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 6.3e-13
                                   ----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HT...T--EEEEESS----HHH...... CS
                          RecA  29 lkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kk...ggvaafidaehaldpky...... 97 
                                   + v  +s+G   +d  +G GG+    i+e+yG   sGkt +a ++ +++q   ++   gg + +id+e ++ p+       
  gi|91773967|ref|YP_566659.1|  77 KLVGKLSTGCTEFDEMMG-GGIETQSITEMYGEFGSGKTQIAHQLAVNVQlppEQgglGGSVIMIDTENTFRPERiaqmvk 156
                                   568899************.***********************999999985442322267899********9975111111 PP

                                   ..HHHTT--GG......G-EEE--SSH.......HHHHHHHHHHHTTT.--SEEEEE-TTT---STT-.----------HH CS
                          RecA  98 ..akklGvdid......ellvsqpdtG.......eqaleiadalvrsg.aidlivvdsvaalvpkaei.eGemgdskvglq 161
                                     + k G++ d      ++ v++  +        ++a e+a+ l ++   + l++vds++a      i  G ++d +    
  gi|91773967|ref|YP_566659.1| 157 giSDKHGIEYDpeeflkNIHVARAFNSnhqillvDSANELANELKNTEmPVKLLIVDSLTAHFRAEYIgRGTLADRQQK-- 235
                                   1134567764333222267777765541111111446677777877652699******999875444433556665544.. PP

                                   HHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES-- CS
                          RecA 162 arlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieei 225
                                      + + l  +    + sn+ v+  nq+  k    fg+p    GG+ l   a+ rl +r+++  
  gi|91773967|ref|YP_566659.1| 236 ---LNKHLHEILRFGDLSNACVVVTNQVMSKPDAFFGDPTKPIGGHILGHTATFRLYIRKSKGE 296
                                   ...4566667766777889999*************************************98755 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1     1e-10   1.1e-07       2     131 ..      83     218 ..      82     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1e-10
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgae.....kygepgvfvtveepa......edlrenakslG 71 
                                   +tg  ++De++ gGi  ++++ ++Ge G+GKt +a q +++          g  ++++ +e +       + ++    + G
  gi|91773967|ref|YP_566659.1|  83 STGCTEFDEMMGGGIETQSITEMYGEFGSGKTQIAHQLAVNVQLppeqgGLGGSVIMIDTENTFrperiaQMVKGISDKHG 163
                                   79**************************************95431111135778899999988777666333333333566 PP

                        ATPase  72 wdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl 131
                                   ++ +  e   ++ +  a++s++++      ++++el++el++   e+ +k +++Ds+t++
  gi|91773967|ref|YP_566659.1| 164 IEYDPEEFLKNIHVARAFNSNHQIL---LVDSANELANELKN--TEMPVKLLIVDSLTAH 218
                                   6665555555577888887776644...69999999999998..59999********998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.3e-09   2.5e-06      24     156 ..      91     220 ..      73     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.3e-09
                        AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarll 104
                                     ++g +  ++++  +G  g+GKt +a +la+ v +  p  g      g V+++++E++    ++R++++ + ++d+ +  
  gi|91773967|ref|YP_566659.1|  91 EMMGGGIETQSITEMYGEFGSGKTQIAHQLAVNVQL-PPEQGG---LGGSVIMIDTENTF--RPERIAQMVKGISDKHGIE 165
                                   566777888999999*******************95.333343...58***********8..79**********5555555 PP

                        AAA_25 105 vldlagv.eslpLfak.drggtl.ltadvdaleaaieeveg.vrlvviDplsralg 156
                                       +++ ++++++ +  +++++ l    ++l+++++ +e  v+l+++D+l++ ++
  gi|91773967|ref|YP_566659.1| 166 YDP-EEFlKNIHVARAfNSNHQIlLVDSANELANELKNTEMpVKLLIVDSLTAHFR 220
                                   444.45556666654423444445455569********8778*********98766 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.3   7.1e-09   7.9e-06      10      54 ..      11      56 ..       9      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.1e-09
                         HHH_2 10 hVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivef 54
                                  hVG +tA++L  + F +++a++ as  eL++  +iGe +A++i++ 
  gi|91773967|ref|YP_566659.1| 11 HVGPATAQKLKDAgFTTIEAIAVASPAELANSAEIGESTAAKIINA 56
                                  9*********9755*****************************986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     3e-06    0.0033       7      79 ..     105     198 ..     102     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3e-06
                        AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie...........swedfldevvelaael 63 
                                   +yG+ g+GKT +a +l             g ++++idte+ +    + ++ ++              e+fl+ +   +a +
  gi|91773967|ref|YP_566659.1| 105 MYGEFGSGKTQIAHQLavnvqlppeqgglGGSVIMIDTENTF---RPERIAQMVkgisdkhgieyDPEEFLKNIHVARAFN 182
                                   6***************************************55...566655555577899999998888999999989999 PP

                        AAA_24  64 adyktlviDtidelee 79 
                                   ++ ++l +D+++el +
  gi|91773967|ref|YP_566659.1| 183 SNHQILLVDSANELAN 198
                                   9999999999888765 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     6e-06    0.0067       9      42 ..      12      46 ..      10      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
               DNA_pol_lambd_f  9 VGpktAkkwyakGirtledlra.krakLtreqqiG 42
                                  VGp+tA+k+ ++G++t+e +    +a+L ++  iG
  gi|91773967|ref|YP_566659.1| 12 VGPATAQKLKDAGFTTIEAIAVaSPAELANSAEIG 46
                                  9******************9887778888888887 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-05     0.019       8      45 ..       6      43 ..       3      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                          Cdd1  8 lqdiPniGkalaedlvelGirsveelkgedpeelyekl 45
                                  l+d+  +G+a+a++l + G++++e ++  +p+el +  
  gi|91773967|ref|YP_566659.1|  6 LEDLDHVGPATAQKLKDAGFTTIEAIAVASPAELANSA 43
                                  78999****************************98765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.049        55      15      28 ..       8      21 ..       5      23 .. 0.76
   2 ?    9.1   0.4    0.0011       1.2       2      29 ..      28      55 ..      27      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.049
                                  TSTT-SHHHHHHHH CS
                           HHH 15 alPGVGpktAeaIl 28
                                  +l  VGp+tA++  
  gi|91773967|ref|YP_566659.1|  8 DLDHVGPATAQKLK 21
                                  56669******976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                                  HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                           HHH  2 leglipasreeLlalPGVGpktAeaIls 29
                                  +e++  as++eL+    +G++tA +I++
  gi|91773967|ref|YP_566659.1| 28 IEAIAVASPAELANSAEIGESTAAKIIN 55
                                  78999********************985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.7e-05      0.02       4     104 ..      99     197 ..      97     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseell..eal 82 
                                   t++i+  +Ge G+GKT  + +l+ + +  +++   + +v+ ++  +   ++ +++++  + +  + +   + ee+l   ++
  gi|91773967|ref|YP_566659.1|  99 TQSITEMYGEFGSGKTQIAHQLAVNVQLPPEQGGLGGSVIMIDTENTFRPERIAQMVKGISDKHGIE--YDPEEFLknIHV 177
                                   7899999******************988888888****************************87777..555555515566 PP

                        AAA_22  83 eqalraravielliiDEaqhlr 104
                                   ++a+++ +   +l++D a  l 
  gi|91773967|ref|YP_566659.1| 178 ARAFNSNHQ--ILLVDSANELA 197
                                   666666666..99999999983 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.8e-05      0.11       3      98 ..     105     248 ..     104     269 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-05
                                   EESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSS..................................... CS
                           AAA   3 lyGppGtGKTllakavakelgve.........fleisgsellsk..................................... 37 
                                   +yG  G GKT +a+++a +++ +         ++ i+  + +                                       
  gi|91773967|ref|YP_566659.1| 105 MYGEFGSGKTQIAHQLAVNVQLPpeqgglggsVIMIDTENTFRPeriaqmvkgisdkhgieydpeeflknihvarafnsnh 185
                                   69*****************75444444555556666666666223555555555555543333333333333333333343 PP

                                   ..STTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTT CS
                           AAA  38 ..yvgesekkirelfkeakekakp.silfiDEidalaksr..sgseseeeervvnqLlteldgvkk 98 
                                     ++ +s++++++ +k+ +    p + l++D + a ++++   +++  ++++ +n+ l+e+ ++ +
  gi|91773967|ref|YP_566659.1| 186 qiLLVDSANELANELKNTE---MPvKLLIVDSLTAHFRAEyiGRGTLADRQQKLNKHLHEILRFGD 248
                                   3333333333333333322...23366666666666666665444444455555555555555555 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   0.00013      0.15       6     115 ..     106     217 ..     102     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                   EC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C....CHHHHCCSCCC CS
                         NACHT   6 qGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse....vwavllelper 82 
                                    Ge GsGKT  +++la+  + +  ++g    v+++    + r++++  + + + ++   + +p  e    + + ++ + + 
  gi|91773967|ref|YP_566659.1| 106 YGEFGSGKTQIAHQLAVNVQLPPEQGGLGGSVIMIDTENTFRPERIAQMVKGISDKHGIEYDPE-EflknIHVARAFNSNH 185
                                   799*****************99999998899999999999999888788888877655444444.3353333444444555 PP

                                   EEEEEE-STT-SS-TCH.........HHHHHCT CS
                         NACHT  83 lLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                     l++D+++el+++l++ ++ pv+ l+ + +++
  gi|91773967|ref|YP_566659.1| 186 QILLVDSANELANELKN-TEMPVKLLIVDSLTA 217
                                   56889*******99999.555555555555544 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.26   2.9e+02       5      22 ..     107     124 ..     104     153 .. 0.88
   2 ?   10.2   0.0   0.00035       0.4      56     127 ..     189     261 ..     164     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.26
                          CobU   5 GgarSGKSefAeklaees 22 
                                   G   SGK ++A +la + 
  gi|91773967|ref|YP_566659.1| 107 GEFGSGKTQIAHQLAVNV 124
                                   6778**********9765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00035
                          CobU  56 tveepldlaealkeeek.kevvLvDcltlwltnlllee.eaekveekleeeveellealkelkatvvlVsnEvg 127
                                   +v++ ++la+ lk++e   + ++vD+lt         + + ++ ++kl+++++e+l+   +l++ +v+V+n v 
  gi|91773967|ref|YP_566659.1| 189 LVDSANELANELKNTEMpVKLLIVDSLTAHFRAEYIGRgTLADRQQKLNKHLHEILRF-GDLSNACVVVTNQVM 261
                                   57778899****99888899********988766665404445888999999998875.56788999****985 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.21      14      91 ..     170     249 ..     163     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                  RNA_pol_RpbG  14 sklkdlkivkikcqneeiel.Diisel.nifkeed.kveviisrekPeyldgkdFcghGylvtekeeenkiitliSlfGll 91 
                                   + lk+++++++ + n++i l D ++el n +k+ +  v++ i  +   +    +++g+G+l+ ++++ nk +  i  fG l
  gi|91773967|ref|YP_566659.1| 170 EFLKNIHVARAFNSNHQILLvDSANELaNELKNTEmPVKLLIVDSLTAHFR-AEYIGRGTLADRQQKLNKHLHEILRFGDL 249
                                   5699******99999987644**9999445666652599999999888888.8****************999999888755 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00037      0.41       5      90 ..     107     223 ..     105     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                        AAA_18   5 GtpGvGKttlakeLskrlgf.........................gvnlrdvakenglllevdpe..aldeskrldedkld 58 
                                   G  G+GKt++a+ L+   ++                          + ++ +  ++g++++ +++   ++  + ++ + + 
  gi|91773967|ref|YP_566659.1| 107 GEFGSGKTQIAHQLAVNVQLppeqgglggsvimidtentfrperiAQMVKGISDKHGIEYDPEEFlkNIHVARAFNSNHQI 187
                                   668***********7664447777777666777777777777777666777777777777777776544444444444444 PP

                        AAA_18  59 klldaleenss....aleegknlvidghlaelesea 90 
                                    l+d  +e ++    +++  k l++d++ a+++ e+
  gi|91773967|ref|YP_566659.1| 188 LLVDSANELANelknTEMPVKLLIVDSLTAHFRAEY 223
                                   44444444444777678899999********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1830.21
//
Query:       gi|91773968|ref|YP_566660.1|  [L=226]
Description: phosphoglycolate phosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-29  103.0   2.5    1.4e-18   67.5   0.9    2.1  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
      6e-10   39.8   1.3    0.00026   21.4   0.1    3.1  3  Hydrolase    haloacid dehalogenase-like hydrolase
    2.6e-09   37.0   0.1    7.5e-08   32.2   0.0    2.0  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
     0.0011   19.5   2.4        5.6    7.3   0.0    3.4  4  HAD          haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.056   13.5   0.9       0.35   10.9   0.9    2.2  1  HAD_2        Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   1.6e-12   5.8e-09       1      69 [.       6      73 ..       6     119 .. 0.80
   2 !   67.5   0.9     4e-22   1.4e-18     147     246 ..     111     208 ..      80     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.6e-12
                                  EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE..ECT CS
                   Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali..dde 69
                                  i++D+DGT+ n d ++     ++ k+++e ++ v+++TG++l  v+  ++ +g++ +via NG++i   + 
  gi|91773968|ref|YP_566660.1|  6 IVIDIDGTITNPDRSL---DLDVAKRFRELNVPVILSTGNPLCYVHAAAKLIGISGIVIAENGGVIstGFD 73
                                  89*************9...578888999999***********************************43333 PP

  == domain 2  score: 67.5 bits;  conditional E-value: 4e-22
                                   EES-HHHHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEE CS
                   Hydrolase_3 147 ilkdkekldelekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvA 227
                                   +l+ +  +++l+++l+++   +++i++ +++ + i +  ++Kgt+l k+a+ +++++ + +a+GD+ ND eM+++ag+g+A
  gi|91773968|ref|YP_566660.1| 111 VLNRDVAVEDLRSTLSENGI-DIEIID-TGYAIHIKSTAMNKGTGLLKVAELMGLEPTDYLAIGDSCNDAEMMQVAGFGIA 189
                                   55555556666667766643.445554.56899************************************************ PP

                                   ETTS-HHHHHHSSEEE--G CS
                   Hydrolase_3 228 mgnaseevkkaAdyvtksn 246
                                   ++na+  ++kaA+++tk  
  gi|91773968|ref|YP_566660.1| 190 VANADSDAIKAARHITKAS 208
                                   ****************976 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00024      0.87       2      19 ..       4      21 ..       3      26 .. 0.86
   2 !    6.3   0.0    0.0029        10     127     161 ..      26      61 ..      22      90 .. 0.73
   3 !   21.4   0.1   7.1e-08   0.00026     145     210 .]     118     185 ..      78     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                                  SEEEEESBTTTBCHHHHH CS
                                  xxxxxxxxxxxxxxxxxx RF
                     Hydrolase  2 ktvvfDkdGTLttgepsv 19
                                  k++v+D+dGT+t+  +s+
  gi|91773968|ref|YP_566660.1|  4 KAIVIDIDGTITNPDRSL 21
                                  9***********987665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0029
                                   HHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                     Hydrolase 127 vasLkaagievvlltgdnpetaeraanqlG.ddyfd 161
                                    +++++ +++v+l tg+    +++aa+ +G   ++ 
  gi|91773968|ref|YP_566660.1|  26 AKRFRELNVPVILSTGNPLCYVHAAAKLIGiSGIVI 61 
                                   56789999*9999999999***********433332 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 7.1e-08
                                   HHHHHHHHHHTT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 145 petaeraanqlG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    e  ++++++ G   +++d  +a+ i+  a  +  g++++++ ++ +p + +++GD+ nDa++++ Ag
  gi|91773968|ref|YP_566660.1| 118 VEDLRSTLSENGidIEIIDTGYAIHIKSTAMNKGTGLLKVAELMGLEPTDYLAIGDSCNDAEMMQVAG 185
                                   55566667777764555577788888889999********************************9997 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.019        70       3      44 ..       4      42 ..       2      61 .. 0.73
   2 !   32.2   0.0   2.1e-11   7.5e-08     133     243 ..     118     218 ..     106     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.019
                                  EEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS CS
                          S6PP  3 lllvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGR 44
                                  +++v+d+D+t++++d++   +  +  +   + +v ++++TG 
  gi|91773968|ref|YP_566660.1|  4 KAIVIDIDGTITNPDRSLDLDVAKRFR---ELNVPVILSTGN 42
                                  579*********887765444444444...577777777775 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 2.1e-11
                                   HHHHHHHHHTTTS-EEEEEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHH CS
                          S6PP 133 lkeleqlLekreldvkviyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeel 213
                                   +++l+ +L+++++d+++i   g ++ +   + +kg  l   a+ ++le+   l  Gds nD+e+++    g+ V+na++  
  gi|91773968|ref|YP_566660.1| 118 VEDLRSTLSENGIDIEII-DTGYAIHIKSTAMNKGTGLLKVAELMGLEPTDYLAIGDSCNDAEMMQVAGFGIAVANADSD- 196
                                   6899***********986.899********************************************************99. PP

                                   HHHHHHH--TTE..EE-SS-THHHHHHHHH CS
                          S6PP 214 lqwllenakeneriylaeercaaGilegla 243
                                      + ++a++       +++  +G le+++
  gi|91773968|ref|YP_566660.1| 197 ---AIKAARHIT-----KASFGKGALEAIE 218
                                   ...455555544.....5556666666666 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.3    0.0096        34       1      16 [.       6      21 ..       6      31 .. 0.73
   2 !    6.5   0.0    0.0029        10      98     154 ..      30      84 ..      23     105 .. 0.68
   3 !    7.3   0.0    0.0016       5.6     145     188 .]     135     182 ..      99     182 .. 0.64
   4 ?   -3.6   0.0       3.4   1.2e+04      83      97 ..     206     220 ..     191     224 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0096
                           HAD  1 alfDfDgTLldgdsle 16
                                  ++ D+DgT+++ d   
  gi|91773968|ref|YP_566660.1|  6 IVIDIDGTITNPDRSL 21
                                  688********96544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0029
                           HAD  98 raaGdrvvvvSgglrplvepllaelgadevlat.elevdd.rltgelglegkpvrgegk 154
                                   r+ +++v++ +g++  +v++ +++ g    ++   +++++ +++ +   +  +  g++ 
  gi|91773968|ref|YP_566660.1|  30 RELNVPVILSTGNPLCYVHAAAKLIG----ISGiVIAENGgVISTGFDSPSIIADGKEE 84 
                                   48899*********************....55524444557665553444444444443 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0016
                           HAD 145 egkpvrgegkvaalre....wlaaegegidleevvayGDspsDlpllr 188
                                   +++  + + k +a ++       ae  g+++ +  a+GDs +D ++++
  gi|91773968|ref|YP_566660.1| 135 IDTGYAIHIKSTAMNKgtglLKVAELMGLEPTDYLAIGDSCNDAEMMQ 182
                                   3333333444444444555555666778888889************96 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 3.4
                           HAD  83 pklldpgalellaah 97 
                                   ++ +  gale+++ +
  gi|91773968|ref|YP_566660.1| 206 KASFGKGALEAIEYA 220
                                   222324566665554 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   9.8e-05      0.35     134     174 ..     150     187 ..       6     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.8e-05
                         HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsptDieaakkagik 174
                                   k    + ++k+ e ++l++ + + +GDs +D e  + ag  
  gi|91773968|ref|YP_566660.1| 150 K---GTGLLKVAELMGLEPTDYLAIGDSCNDAEMMQVAGFG 187
                                   4...678999**************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1405.87
//
Query:       gi|91773969|ref|YP_566661.1|  [L=90]
Description: PRC-barrel protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-12   45.0   0.7      1e-11   44.7   0.7    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 !   44.7   0.7   5.7e-16     1e-11       3      74 ..       4      79 ..       2      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 5.7e-16
                                  ECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT..........-EEEEEGG.CEECCCTEEEETT CS
                           PRC  3 efrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi.....gekevliPfdlavkigkdriivda 74
                                   ++a +l +k+V+ +dG++lG+++++v++ k+g+++ l+++   +l+      ++ ++++ fd av+++kd+i+vd 
  gi|91773969|ref|YP_566661.1|  4 KVFAKNLSNKQVMATDGTELGVLNNIVMENKTGELEDLIIKPDIGLDTskyqkDGQYIIVSFD-AVSAIKDYIVVDK 79
                                  67899*************************************876666***************.***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 590.34
//
Query:       gi|91773970|ref|YP_566662.1|  [L=738]
Description: AAA family ATPase, CDC48 subfamily protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-98  326.8   0.1    1.9e-48  164.2   0.0    2.5  2  AAA              ATPase family associated with various cellul
    2.4e-32  110.5   4.1    5.3e-17   61.3   1.4    3.0  2  AAA_lid_3        AAA+ lid domain
    9.7e-29   99.4   0.1    3.4e-28   97.6   0.1    2.0  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    6.7e-16   58.5   0.1    3.7e-07   30.2   0.0    3.3  2  AAA_5            AAA domain (dynein-related subfamily)
    3.6e-15   56.0   0.1    6.5e-07   29.2   0.0    3.3  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.2e-15   56.0   0.0      6e-06   26.5   0.0    2.8  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.7e-14   52.3   0.1    1.6e-13   50.2   0.1    2.1  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    9.7e-14   52.1   0.0    7.1e-05   23.2   0.0    3.9  2  AAA_16           AAA ATPase domain
    2.4e-11   44.0   0.8     0.0058   16.9   0.0    4.5  4  AAA_22           AAA domain
    2.1e-10   40.7   0.0    6.2e-05   23.0   0.0    2.7  2  AAA_14           AAA domain
    7.1e-09   35.3   0.2    0.00015   21.1   0.0    3.0  3  TIP49            TIP49 P-loop domain
    2.8e-08   33.7   0.0     0.0059   16.3   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    4.6e-08   33.7   0.0      0.018   15.6   0.0    2.8  2  AAA_18           AAA domain
    8.7e-08   32.4   0.0     0.0033   17.6   0.0    2.4  2  AAA_33           AAA domain
    1.4e-07   31.2   0.0     0.0049   16.4   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    3.1e-07   30.3   0.1      0.048   13.4   0.0    3.7  2  Sigma54_activat  Sigma-54 interaction domain
    4.7e-07   29.4   0.4      0.015   14.7   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.3e-06   28.0   0.9      0.011   15.1   0.0    3.6  3  ATPase           KaiC
    1.3e-06   28.1   1.7       0.17   11.4   0.0    3.7  3  AAA_25           AAA domain
    2.3e-06   28.0   0.0      0.059   13.8   0.0    2.6  2  RNA_helicase     RNA helicase
    2.9e-06   26.7   0.0      0.042   13.1   0.0    2.5  2  Zeta_toxin       Zeta toxin
    3.7e-06   26.8   0.1       0.11   12.2   0.0    2.6  2  AAA_24           AAA domain
    5.6e-06   26.3   0.0      0.088   12.6   0.0    2.5  2  Bac_DnaA         Bacterial dnaA  protein
    6.7e-06   26.4   0.0      0.029   14.6   0.0    2.5  2  AAA_28           AAA domain
    1.4e-05   24.6   0.0       0.14   11.4   0.0    2.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    2.4e-05   23.9   0.0       0.32   10.4   0.0    2.8  2  PhoH             PhoH-like protein
      3e-05   23.3   0.2       0.18   10.9   0.1    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
      3e-05   24.0   0.2       0.23   11.4   0.0    3.6  2  ATPase_2         ATPase domain predominantly from Archaea
    6.9e-05   23.4   0.0          1    9.9   0.0    3.3  3  ABC_tran         ABC transporter
    0.00012   22.1   0.0       0.65   10.0   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00012   21.4   0.0       0.36   10.0   0.0    2.7  2  NB-ARC           NB-ARC domain
    0.00014   21.7   0.1       0.34   10.8   0.0    2.9  2  AAA_3            ATPase family associated with various cellul
    0.00015   22.2   0.2       0.39   11.1   0.0    3.6  2  AAA_17           AAA domain
    0.00016   21.6   0.0       0.23   11.2   0.0    2.4  2  AAA_11           AAA domain
    0.00019   21.3   0.3       0.54   10.3   0.1    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
    0.00026   21.3   0.8        1.1    9.6   0.0    3.0  2  AAA_19           AAA domain
    0.00029   20.6   0.0       0.65    9.7   0.0    2.6  2  AAA_30           AAA domain
    0.00038   19.7   0.0       0.55    9.3   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
    0.00091   19.3   0.0        1.1    9.2   0.0    2.9  2  ResIII           Type III restriction enzyme, res subunit
     0.0011   19.0   0.1          3    7.8   0.0    3.2  3  NACHT            NACHT domain
     0.0011   19.1   0.0        1.4    9.0   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0018   18.2   0.8        3.8    7.4   0.0    3.5  3  NTPase_1         NTPase
     0.0023   17.4   0.0        3.9    6.8   0.0    3.6  3  TniB             Bacterial TniB protein
     0.0037   17.0   0.2        5.2    6.7   0.0    3.3  3  Cytidylate_kin   Cytidylate kinase
     0.0044   16.7   0.0        1.5    8.4   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0057   15.7   0.0       0.33   10.0   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
     0.0091   15.7   0.8        9.9    5.8   0.0    4.4  5  Guanylate_kin    Guanylate kinase
     0.0098   15.2   0.0        7.7    5.7   0.0    3.0  3  KAP_NTPase       KAP family P-loop domain
  ------ inclusion threshold ------
      0.016   14.6   0.2       0.85    9.0   0.0    2.7  2  IPT              Isopentenyl transferase
      0.022   14.4   0.0        1.2    8.7   0.0    2.7  2  Zot              Zonular occludens toxin (Zot)
      0.033   13.1   0.0        1.5    7.6   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
       0.04   13.8   1.1        2.3    8.1   0.0    3.3  4  Rad17            Rad17 P-loop domain
      0.092   12.6   0.0         12    5.7   0.0    2.4  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.096   12.8   0.1         15    5.7   0.0    2.6  2  SKI              Shikimate kinase
       0.12   12.6   0.5         14    5.9   0.0    2.5  2  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.14   11.3   0.0         18    4.4   0.0    2.2  2  DAP3             Mitochondrial ribosomal death-associated pro


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 !  160.3   0.0   9.6e-50   3.1e-47       1     131 [.     225     354 ..     225     355 .. 0.98
   2 !  164.2   0.0   6.1e-51   1.9e-48       1     130 [.     498     628 ..     498     630 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 9.6e-50
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   v+lyGppGtGKTl+akava+e+ ++fl + g+e++  + gese+++r++f+ea e+a psi+fiDEid++a++r++ + e+
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESRANFLYVAGPEIMGRFYGESEERLRKIFEEAAENA-PSIIFIDEIDSIAPKRENVTGEV 304
                                   79******************************************************9.*********************** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   e+rvv+qLlt +dg++++ ++++vi+atnr d++dpal+r gRfdr+iei+
  gi|91773970|ref|YP_566662.1| 305 ERRVVAQLLTLMDGMEER-GQIVVIAATNRLDSIDPALRRpGRFDREIEIG 354
                                   *****************7.56***************************996 PP

  == domain 2  score: 164.2 bits;  conditional E-value: 6.1e-51
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgses 79 
                                   +llyGppGtGKTl+a+ava+e++++f++i+g+++lsk+vgesek +r++fk+a++ + p+i+f+DEid++a++r  ++++ 
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISIKGPQMLSKFVGESEKAVRDTFKKARQVS-PCIIFFDEIDSIATTRiaDSETG 577
                                   69******************************************************9.*****************988999 PP

                                   HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                           AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                   +++++vvnqLlteldg++  ++ v+vi+atnrpd++dpal+r gRfdr + +
  gi|91773970|ref|YP_566662.1| 578 RSSQQVVNQLLTELDGLEPLKE-VVVIAATNRPDMIDPALMRsGRFDRLVLV 628
                                   9******************865.************************98876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   1.5e-15   4.9e-13       1      42 [.     377     418 ..     377     438 .. 0.79
   2 !   61.3   1.4   1.7e-19   5.3e-17       2      44 ..     653     697 ..     652     701 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.5e-15
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                                   dvdl++LA  T+G++GADl +l++eA+++Alrr ++ei+ ++
  gi|91773970|ref|YP_566662.1| 377 DVDLEHLATYTQGFVGADLLSLVQEASMRALRRILPEINLDE 418
                                   9********************************655554433 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 1.7e-19
                     AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfe 44 
                                   v+++ LA++TeGy+GAD++a+creAa+lAlr++++  ++++++f 
  gi|91773970|ref|YP_566662.1| 653 VSIQSLAAMTEGYVGADIEAVCREAAMLALREDFDaeSVKERHFL 697
                                   99*********************************744*****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 !   97.6   0.1   1.1e-30   3.4e-28       2      84 ..       6      88 ..       5      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 1.1e-30
                                  EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
                       CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                                   +V++a + d grgi+r+dp+++ +l+l+pgd+vei+gk+kT+a+vw+a+++d+g+gi r+dg+tR+nagv+iG+++++++ae
  gi|91773970|ref|YP_566662.1|  6 IKVEKAHPIDFGRGIIRLDPSTLLSLQLSPGDIVEIVGKKKTAAKVWRADRQDWGQGIGRIDGFTRQNAGVGIGERIHIQRAE 88
                                  69******************************************************************************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 !   30.2   0.0   1.2e-09   3.7e-07       1     136 [.     224     343 ..     224     344 .. 0.75
   2 !   24.5   0.0   6.9e-08   2.2e-05       2     135 ..     498     617 ..     497     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.2e-09
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--H. CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraes. 79 
                                   +v+L GppGtgK+ +a+ +a   +++++yv++++      + gr    ++ +++  +++ +aa+  ++i+++DE++ + + 
  gi|91773970|ref|YP_566662.1| 224 GVILYGPPGTGKTLIAKAVANESRANFLYVAGPE------IMGRFY--GESEERLRKIFEEAAEnAPSIIFIDEIDSIAPk 296
                                   59*******************************9......555555..5556777788888888789*********88751 PP

                                   ..HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                         AAA_5  80 ..evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                     +v++++ +          ++ +l++  ++    ++ via++n+ld    +++palr+
  gi|91773970|ref|YP_566662.1| 297 reNVTGEVERRVVA------QLLTLMDGMEE--RGQIVVIAATNRLD----SIDPALRR 343
                                   11444444444444......55555554442..2239**********....99999997 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6.9e-08
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HHH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraesev 81 
                                   +lL GppGtgK+ +a+ +a   n+++  + +++ ++  +++g+ e      + v   +++a + +++i+++DE++ + +  
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISIKGPQMLS--KFVGESE------KAVRDTFKKARQvSPCIIFFDEIDSIATTR 570
                                   89*******************************665..6899998......4555566655557***********999554 PP

                                   HHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  82 lnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                   ++   +  + +++    ++el + ++   l+++ via++n++d     ++pal 
  gi|91773970|ref|YP_566662.1| 571 IADSETGRSSQQVVNQLLTELDGLEP---LKEVVVIAATNRPD----MIDPALM 617
                                   44444555555555455555555555...56699999999999....7777775 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0     2e-09   6.5e-07      31     103 ..     220     300 ..     197     342 .. 0.86
   2 !   22.5   0.0   2.3e-07   7.5e-05      34      69 ..     496     531 ..     489     569 .. 0.81
   3 ?   -0.7   0.0       3.4   1.1e+03      22      58 ..     611     648 ..     592     702 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2e-09
                        RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                   e+   v+lyGpPG Gkt +ak +a+e  +++   +gP +      e +  l  ++ +  e+   ++fidei  ++++ e+v
  gi|91773970|ref|YP_566662.1| 220 EPPKGVILYGPPGTGKTLIAKAVANESRANFLYVAGPEImgrfygESEERLRKIFEEAAENapSIIFIDEIDSIAPKRENV 300
                                   566779*******************************995555555677899999888765337********999988876 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.3e-07
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                     +llyGpPG Gkt +a+ +a+e ++++ +  gP +
  gi|91773970|ref|YP_566662.1| 496 KGILLYGPPGTGKTLIAQAVANEANANFISIKGPQM 531
                                   569**************************9999976 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.4
                        RuvB_N  22 fieaakkreealdhvllyGpPGl.Gkttlakiiakelg 58 
                                   +i+ a +r+   d ++l+G   + G+ ++ +i ++e+ 
  gi|91773970|ref|YP_566662.1| 611 MIDPALMRSGRFDRLVLVGNSTIqGRESIFNIHTREMP 648
                                   46667778888888888887765477788888777774 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.9e-08     6e-06       7     105 ..     226     318 ..     221     326 .. 0.88
   2 !   26.2   0.0   2.3e-08   7.4e-06       6     105 ..     498     593 ..     494     595 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.9e-08
                                   EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----.- CS
                         AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk.e 84 
                                   +l gp g+Gkt++aka+a+  ++    ++  +   e++     + + ++++  ++   +a+e+   i+++DEid i+pk e
  gi|91773970|ref|YP_566662.1| 226 ILYGPPGTGKTLIAKAVANESRA----NFLYVAGPEIMG----RFYGESEERLRKIFEEAAENApsIIFIDEIDSIAPKrE 298
                                   6779***************9996....9***********....99999999999999999999999************988 PP

                                   --------HHHHHHHHHHHH- CS
                         AAA_2  85 ssgadvSregVqrdLLqileg 105
                                   + + +v r  V+  LL +++g
  gi|91773970|ref|YP_566662.1| 299 NVTGEVERR-VVAQLLTLMDG 318
                                   888888776.77778999997 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 2.3e-08
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp g+Gkt++a+a+a+  ++    ++i +   ++l     + + ++++  ++  ++a +    i+++DEid i+ + 
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANA----NFISIKGPQMLS----KFVGESEKAVRDTFKKARQVSpcIIFFDEIDSIATTr 570
                                   7999******************96....999999998888....55555555556666666666688************99 PP

                                   .---------HHHHHHHHHHHH- CS
                         AAA_2  84 .essgadvSregVqrdLLqileg 105
                                      s+   S++ V++ LL  l+g
  gi|91773970|ref|YP_566662.1| 571 iADSETGRSSQQVVNQLLTELDG 593
                                   99999999*********987776 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   0.1     5e-16   1.6e-13       2      64 .]     107     177 ..     106     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5e-16
                                   .SCCCCHHHHCCCTTEEE-TTEEEEECCT.......CCCEEEEEEEECCCC.SCEEECTSCCEEESTTCCE CS
                       CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefk.......gqeiklvVvstePkg.pvgitetTeielgtkpvev 64 
                                   + g+  a +k+++l+rp+++Gd+++++ +       +q+i+lv+ + eP + + +++e+Teiel++kpve+
  gi|91773970|ref|YP_566662.1| 107 FGGNINAIIKHNILKRPFVVGDVIPITSSmtqtapgNQAIPLVAIESEPEEgILIVSENTEIELRQKPVEG 177
                                   7899888*******************9977999999***************788***************95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.2e-07   7.1e-05      17     139 ..     215     327 ..     192     337 .. 0.71
   2 !   21.9   0.0   5.6e-07   0.00018      23      63 ..     494     531 ..     487     603 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.2e-07
                        AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                   +r++   p  v+l+G++G+GK+ ++++++++ +++   fl+    +      +  +     +e+l +  +++ae+a    +
  gi|91773970|ref|YP_566662.1| 215 QRLNVEPPKGVILYGPPGTGKTLIAKAVANESRAN---FLYVAGPEI-----MGRFYGES-EERLRKIFEEAAENAPSIIF 286
                                   4444334499*******************988877...777777777.....22233333.43444444444555666666 PP

                        AAA_16  98 rekleealaavpelagaeasrllellkrllallsrderplvl 139
                                    +++++ +    +++g+ ++r+ ++l  l++ ++++++ +v+
  gi|91773970|ref|YP_566662.1| 287 IDEIDSIAPKRENVTGEVERRVVAQLLTLMDGMEERGQ-IVV 327
                                   67777777788888888889999999999999998777.554 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 5.6e-07
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    p  +ll+G++G+GK+ ++++++++++++   f++ k  q 
  gi|91773970|ref|YP_566662.1| 494 APKGILLYGPPGTGKTLIAQAVANEANAN---FISIKGPQM 531
                                   5689********************99999...888888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0    0.0001     0.032       8      44 ..     225     252 ..     220     261 .. 0.83
   2 ?    7.1   0.0     0.019       6.2      72     128 ..     264     328 ..     253     337 .. 0.72
   3 !   16.9   0.0   1.8e-05    0.0058       8      45 ..     498     526 ..     492     603 .. 0.81
   4 ?   -1.1   0.0       6.8   2.2e+03      37      75 ..     690     731 ..     673     738 .] 0.56

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.0001
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvf 44 
                                   ++++G++GtGKT+ ++ ++++          r+ +++
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANES---------RANFLY 252
                                   689****************997.........555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.019
                        AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLv 128
                                   + s+e+l++ +e+a++++    ++ iDE++ +   +         +++ +L +l++  +   q++++
  gi|91773970|ref|YP_566662.1| 264 GESEERLRKIFEEAAENAPS--IIFIDEIDSIApkRenvtgeveRRVVAQLLTLMDGMEERGQIVVI 328
                                   56889999999999999988..**********87624555667777777887887774444444444 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.8e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45 
                                   ++++G++GtGKT+ ++ +++++         ++ ++++
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEA---------NANFISI 526
                                   89*******************9.........4444444 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 6.8
                        AAA_22  37 e.erpevv....fvtlpsstsskdllrellralglelkaerlss 75 
                                     ++++++    +v+++  ++ +++++++  +l+ ++++  +++
  gi|91773970|ref|YP_566662.1| 690 SvKERHFLaaieKVKPTITEDMAEFYSKIQDKLKGGTHK--QET 731
                                   253333443334455555557788888888888877777..443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.9e-07   6.2e-05       5      88 ..     225     317 ..     222     352 .. 0.72
   2 !   14.7   0.0   7.1e-05     0.023       5      78 ..     498     568 ..     494     596 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.9e-07
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev......... 76 
                                   +++ G+  +GKT ++k +++e+     ++ly++  +   + + ++e+ l+ i+e++ e+  +++f+DEi  +         
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESR---ANFLYVAGPEIMGRFYGESEERLRKIFEEAAENAPSIIFIDEIDSIapkrenvtg 302
                                   899****************9999...*******9998876666555445555555445599*********99655555555 PP

                        AAA_14  77 ...pewekalkslvd 88 
                                      +++   l  l+d
  gi|91773970|ref|YP_566662.1| 303 eveRRVVAQLLTLMD 317
                                   555555555555555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.1e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpe 78 
                                   +++ G+  +GKT +++ +++e      +++ i+  +   k   ++ek  +  ++k+++    ++f+DEi  + +
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEAN---ANFISIKGPQMLSKFVGESEKAVRDTFKKARQVSPCIIFFDEIDSIAT 568
                                   7899**********999997777...7777777777666554455544544444444447799******98854 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00062       0.2      51      88 ..     223     258 ..     216     279 .. 0.84
   2 ?   -1.9   0.0       4.5   1.4e+03     263     288 ..     267     291 ..     256     293 .. 0.71
   3 !   21.1   0.0   4.8e-07   0.00015      47     106 ..     492     550 ..     485     555 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00062
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88 
                                   ++v+l Gp+gtGkt +a a+++e      f  ++g e+
  gi|91773970|ref|YP_566662.1| 223 KGVILYGPPGTGKTLIAKAVANESR--ANFLYVAGPEI 258
                                   899******************9954..66777777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.5
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 263 nkkvakyveegkaeivpGvlfiDevh 288
                                   ++ + k  e + ae  p ++fiDe+ 
  gi|91773970|ref|YP_566662.1| 267 EERLRKIFE-EAAENAPSIIFIDEID 291
                                   555555554.579999********85 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 4.8e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                         TIP49  47 klaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                     a +++Ll Gp+gtGkt +a a+++e +    f++++g ++ s  v  +e ++ ++++k+
  gi|91773970|ref|YP_566662.1| 492 IKAPKGILLYGPPGTGKTLIAQAVANEAN--ANFISIKGPQMLSKFVGESEkAVRDTFKKA 550
                                   45779*********************987..78***********99998884566778877 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 !   14.9   0.0   5.1e-05     0.016      45      71 ..     220     246 ..     206     329 .. 0.81
   2 !   16.3   0.0   1.9e-05    0.0059      45      76 ..     493     524 ..     488     561 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.1e-05
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgvea 71 
                                   e  ++++l Gp+G+GK+ +a a++ e 
  gi|91773970|ref|YP_566662.1| 220 EPPKGVILYGPPGTGKTLIAKAVANES 246
                                   556789****************99875 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.9e-05
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavragl 76 
                                   ++ ++i+l Gp+G+GK+ +a a++ ea ++ +
  gi|91773970|ref|YP_566662.1| 493 KAPKGILLYGPPGTGKTLIAQAVANEANANFI 524
                                   667899******************99977655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.5e-05     0.024       1      64 [.     225     316 ..     225     335 .. 0.61
   2 !   15.6   0.0   5.6e-05     0.018       1      35 [.     498     550 ..     498     608 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.5e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe.......aldeskrld 53 
                                   ++l G+pG+GKt +ak+++++  ++                     +++ + a+en +++ + +e         + + +++
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESrANflyvagpeimgrfygeseerLRKIFEEAAENAPSIIFIDEidsiapkRENVTGEVE 305
                                   79****************776433347777777777777777666555555555555555555554444444334444444 PP

                        AAA_18  54 edkldklldal 64 
                                   + ++++ll+++
  gi|91773970|ref|YP_566662.1| 306 RRVVAQLLTLM 316
                                   44444444444 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.6e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvaken 35 
                                   Ill G+pG+GKt +a++++++  ++                    +rd++k+ 
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEAnANfisikgpqmlskfvgesEKAVRDTFKKA 550
                                   99****************88863225777777666666666644555555444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     1e-05    0.0033       2      80 ..     225     333 ..     225     391 .. 0.73
   2 !   12.5   0.0   0.00038      0.12       2      43 ..     498     541 ..     498     591 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvl 52 
                                   v+l G+pG+GK+  a+ ++++    +  ++ ++++ r +g+ +++++                               +v+
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESRanFLYVAGPEIMGRFYGESEERLRkifeeaaenapsiifideidsiapkrenVTGEVE 305
                                   7899***************999988999***********988888887777777777788888888777776554333466 PP

                        AAA_33  53 drlyqilnelarkalsagrnvildatnl 80 
                                    r+ ++l  l + + ++g+ v++ atn+
  gi|91773970|ref|YP_566662.1| 306 RRVVAQLLTLMDGMEERGQIVVIAATNR 333
                                   6666677777777777777777777776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00038
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqq 43 
                                   +ll G+pG+GK+  a+ ++++    ++ +  ++++++ +g+ ++
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANanFISIKGPQMLSKFVGESEK 541
                                   6789***************9988777777788877777774444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0    0.0004      0.13      27      58 ..     216     247 ..     209     257 .. 0.81
   2 !   16.4   0.0   1.5e-05    0.0049      25      64 ..     487     525 ..     483     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                         AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkld 58 
                                   +l ++  k v+l+Gp GtGKt+i+k + ++  
  gi|91773970|ref|YP_566662.1| 216 RLNVEPPKGVILYGPPGTGKTLIAKAVANESR 247
                                   566777899****************9888765 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.5e-05
                         AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                   ++e+ +k+ k +ll+Gp GtGKt+i++ + ++ +  +++s
  gi|91773970|ref|YP_566662.1| 487 IIEMGIKAPKGILLYGPPGTGKTLIAQAVANEAN-ANFIS 525
                                   678889999*******************999998.44433 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00096      0.31      23      48 ..     223     248 ..     208     336 .. 0.90
   2 !   13.4   0.0   0.00015     0.048      15      56 ..     488     526 ..     477     570 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00096
                                   S-EEEECSTTSSHHHHHHHHHHHSTT CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                                     v++ G  GtGK+l+a+a+ ++s+ 
  gi|91773970|ref|YP_566662.1| 223 KGVILYGPPGTGKTLIAKAVANESRA 248
                                   6799****************998864 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00015
                                   HHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
               Sigma54_activat  15 ikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                   i++ +k +  +l+ G  GtGK+l+a+a+ ++    +++f+++
  gi|91773970|ref|YP_566662.1| 488 IEMGIKAPKGILLYGPPGTGKTLIAQAVANEA---NANFISI 526
                                   6666788899*****************97654...4566665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00028      0.09      25      42 ..     225     242 ..     221     245 .. 0.90
   2 !   14.7   0.1   4.8e-05     0.015      13      43 ..     486     516 ..     481     521 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                  Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                   ++l+GppG+GKt++ak++
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAV 242
                                   79*************987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.8e-05
                  Mg_chelatase  13 raleiaaaGgHnlllvGppGsGKtmlakrlp 43 
                                   r +e+ +     +ll+GppG+GKt++a++++
  gi|91773970|ref|YP_566662.1| 486 RIIEMGIKAPKGILLYGPPGTGKTLIAQAVA 516
                                   5666667777789**************9875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.019         6      22      39 ..     225     242 ..     221     259 .. 0.81
   2 ?    2.7   0.0      0.21        68     120     154 ..     282     319 ..     261     334 .. 0.63
   3 !   15.1   0.0   3.4e-05     0.011       9      38 ..     485     514 ..     481     547 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                        ATPase  22 vlitGepGtGKtifalqF 39 
                                   v ++G pGtGKt++a+  
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAV 242
                                   6789**********9865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                        ATPase 120 akrvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                    + + iD i+++    ++ + +v R+ + ql++ + ++
  gi|91773970|ref|YP_566662.1| 282 PSIIFIDEIDSIapkRENVTGEVERRVVAQLLTLMDGM 319
                                   36667777776632144555677899999999998665 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.4e-05
                        ATPase   9 DeilkgGipegrvvlitGepGtGKtifalq 38 
                                   D+i++ Gi   + +l++G pGtGKt++a+ 
  gi|91773970|ref|YP_566662.1| 485 DRIIEMGIKAPKGILLYGPPGTGKTLIAQA 514
                                   999************************985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0078       2.5      36      51 ..     225     240 ..     221     246 .. 0.87
   2 ?    6.0   0.1     0.025         8     128     176 ..     268     316 ..     243     330 .. 0.85
   3 !   11.4   0.0   0.00054      0.17      14      54 ..     476     516 ..     467     519 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0078
                        AAA_25  36 allaGapgtGKttlal 51 
                                   ++l+G+pgtGKt +a 
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAK 240
                                   69**********9985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.025
                        AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                   + ++++ +++ e + +  + iD ++++ +  en   +v +++v++l  + 
  gi|91773970|ref|YP_566662.1| 268 ERLRKIFEEAAE-NAPSIIFIDEIDSIAPKRENVTGEVeRRVVAQLLTLM 316
                                   456677788888.66**********************99*****997765 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00054
                        AAA_25  14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldla 54 
                                   ++++p+++++ +++  + a + +ll+G+pgtGKt +a  +a
  gi|91773970|ref|YP_566662.1| 476 AVEWPLKHPDRIIEMGIKAPKGILLYGPPGTGKTLIAQAVA 516
                                   56677788888888666888899************998766 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   0.00093       0.3       1      23 [.     225     247 ..     225     270 .. 0.84
   2 !   13.8   0.0   0.00018     0.059       1      30 [.     498     527 ..     498     585 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00093
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                   ++lyGp+g+GK+++ak +a++  
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESR 247
                                   689**************888755 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00018
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkk 30 
                                   i+lyGp+g+GK+++a+ +a++   ++ ++k
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISIK 527
                                   789**************9999887763333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0006      0.19      13      47 ..     219     251 ..     210     282 .. 0.86
   2 !   13.1   0.0   0.00013     0.042      14      51 ..     493     528 ..     485     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                    Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnvv 47 
                                    e Pk ++l G pG GK+ +a+++++e   + n++
  gi|91773970|ref|YP_566662.1| 219 VEPPKGVILYGPPGTGKTLIAKAVANES--RANFL 251
                                   688***********************98..56655 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00013
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                   + Pk ill G pG GK+ +a+++++e   + n++ +++
  gi|91773970|ref|YP_566662.1| 493 KAPKGILLYGPPGTGKTLIAQAVANEA--NANFISIKG 528
                                   78************************8..999999986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00036      0.11       5      29 ..     225     253 ..     222     301 .. 0.65
   2 !   11.6   0.1   0.00052      0.17       4      22 ..     497     515 ..     494     566 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00036
                        AAA_24   5 iliyGpsgiGKTtlakel....gpkplfi 29 
                                   +++yGp+g+GKT +ak        ++l++
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVanesRANFLYV 253
                                   789************99976555555554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00052
                        AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                    il+yGp+g+GKT +a   
  gi|91773970|ref|YP_566662.1| 497 GILLYGPPGTGKTLIAQAV 515
                                   699**********999877 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00027     0.088      37     179 ..     225     367 ..     218     391 .. 0.69
   2 !   10.9   0.0   0.00091      0.29      36      94 ..     497     550 ..     485     613 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00027
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT-HH.. CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagkek.. 114
                                   +++yg+ G Gkt + ka++ne +     +  +Y+ + e + ++    +++  + f e   ++  ++ iD+i  +a k +  
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESR-----ANFLYVAGPEIMGRFYGESEERLRKIFEEAAENApSIIFIDEIDSIAPKREnv 300
                                   789*********99999998765.....5579*****************9999**999986537899*******9886422 PP

                                   ...HHHHHHHHHHHH...HTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHH CS
                      Bac_DnaA 115 ...tqeelfhtfnal...leegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkki 179
                                      ++  ++  + +l   +ee  q+v+ +    ++l++++  lr   +    ++i  pd + rl++l+  i
  gi|91773970|ref|YP_566662.1| 301 tgeVERRVVAQLLTLmdgMEERGQIVVIAA--TNRLDSIDPALRRPGRFDREIEIGVPDSDDRLEVLQ--I 367
                                   111233333333333122345556666553..468899999888644444456666677777887775..4 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00091
                                   -EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHH CS
                      Bac_DnaA  36 PlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkek 94 
                                    +++yg+ G Gkt + +a++ne+ +n+ + +   + + +F+ e  ka+r    ++fk+ 
  gi|91773970|ref|YP_566662.1| 497 GILLYGPPGTGKTLIAQAVANEANANFISIKGPQMLS-KFVGESEKAVR----DTFKKA 550
                                   589******************9999987766554443.34444444444....445443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.1e-05     0.029       2      48 ..     225     276 ..     224     311 .. 0.82
   2 !    9.3   0.0     0.004       1.3       2      23 ..     498     520 ..     497     556 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.1e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpw 48 
                                   +++ G+++tGKT +++a a++   ++ +v  pE++ +++ e  ++ +++ ++
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANEsraNFLYVagPEIMGRFYGESEERLRKIFEE 276
                                   789****************665677776668999999998888777766655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.004
                        AAA_28   2 ivitGgestGKTtlleaLaar.g 23 
                                   i + G+++tGKT +++a a++ +
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEaN 520
                                   7899**************96543 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00043      0.14       4      64 ..     225     278 ..     222     306 .. 0.73
   2 !   10.8   0.0   0.00066      0.21       4      25 ..     498     519 ..     495     581 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeaf 64 
                                   v+  G +GtGKt+++ ++++e        +a++l+v +p+++   + + +++  +k ++ea+
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANES-------RANFLYVAGPEIMgRFYGESEERL-RKIFEEAA 278
                                   6789*************99998.......888888888876634555555555.44454444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00066
                       DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                   +l  G +GtGKt+++ ++++e+
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEA 519
                                   6789***************998 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0     0.001      0.32      21      42 ..     224     245 ..     209     252 .. 0.83
   2 !   10.2   0.0    0.0011      0.36      22      43 ..     498     519 ..     485     526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                                   EEEEE--TTSSTTHHHHHHHHH CS
                          PhoH  21 ivfaiGpaGtGKtylavalave 42 
                                    v+  Gp GtGKt++a a+a e
  gi|91773970|ref|YP_566662.1| 224 GVILYGPPGTGKTLIAKAVANE 245
                                   58899***********999865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                   EEEE--TTSSTTHHHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                   +   Gp GtGKt++a a+a ea
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEA 519
                                   6789*************99776 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.001      0.33     117     137 ..     225     245 ..     218     249 .. 0.89
   2 !   10.9   0.1   0.00055      0.18     117     136 ..     498     517 ..     495     521 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                     Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                   v +yGp+ tGkt +a+a a+ 
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANE 245
                                   789**************9986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00055
                     Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                   +++yGp+ tGkt +a+a a+
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVAN 517
                                   899**************997 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   0.00071      0.23      10      56 ..     212     254 ..     210     330 .. 0.50
   2 !    7.7   0.0    0.0093         3      23     113 ..     498     591 ..     480     605 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00071
                      ATPase_2  10 eleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyia 56 
                                   e+ + l+ ep + + +YGp g GKt + k ++++++  ++    y a
  gi|91773970|ref|YP_566662.1| 212 EIFQRLNVEPPKGVILYGPPGTGKTLIAKAVANESRA-NF---LYVA 254
                                   56677888999999***********998888888855.32...2222 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0093
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal........giavpkaeleeil 95 
                                   +++YGp g GKt L+ +++ n  + ++  i   ++ +++  + ++ ++     + ++ka          +++ + +  +i 
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKT-LIAQAVANEANANFISIKGPQMLSKFVGESEKAVR-----DTFKKARqvspciifFDEIDSIATTRIA 572
                                   689********9.67777777767776555544444444444444433.....3222222223333554444444444455 PP

                      ATPase_2  96 k.eksklvfkaiellleki 113
                                   + e+ +  ++ +++ll ++
  gi|91773970|ref|YP_566662.1| 573 DsETGRSSQQVVNQLLTEL 591
                                   5555566566666665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       6.2     2e+03       4      19 ..      29      44 ..      27      45 .. 0.92
   2 !    9.3   0.0    0.0047       1.5       6      37 ..     217     248 ..     215     334 .. 0.84
   3 !    9.9   0.0    0.0032         1       4      80 ..     488     579 ..     486     606 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 6.2
                                  EEEEEETTSEEEEEES CS
                                  xxxxxxxxxxxxxxxx RF
                      ABC_tran  4 vslklkegekvaivGe 19
                                  +sl+l++g +v ivG+
  gi|91773970|ref|YP_566662.1| 29 LSLQLSPGDIVEIVGK 44
                                  699************7 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0047
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp 37 
                                   l++++ + v + G+ G+GK+ ++k++a++++ 
  gi|91773970|ref|YP_566662.1| 217 LNVEPPKGVILYGPPGTGKTLIAKAVANESRA 248
                                   6788888999****************998864 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0032
                                   EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.... RF
                      ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.... 79 
                                   +++ +k+ + + + G+ G+GK+ +++++a++ +  +  i ++g ++ ++   +++k ++  +++  q+ p +   ++    
  gi|91773970|ref|YP_566662.1| 488 IEMGIKAPKGILLYGPPGTGKTLIAQAVANEAN--ANFISIKGPQMLSKFVGESEKAVRDTFKKaRQVSPCIIFFDEidsi 566
                                   567888999999*****************9987..5677778777777556666666665555544555554444444555 PP

                                   ............H CS
                                   ............x RF
                      ABC_tran  80 ............e 80 
                                                
  gi|91773970|ref|YP_566662.1| 567 attriadsetgrS 579
                                   5555555555533 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0051       1.6      19      45 ..     222     248 ..     195     258 .. 0.73
   2 !   10.0   0.0     0.002      0.65      20      51 ..     496     529 ..     481     532 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0051
                                   TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgv 45 
                                    + ++L+G+ G+GKT +++++a++   
  gi|91773970|ref|YP_566662.1| 222 PKGVILYGPPGTGKTLIAKAVANESRA 248
                                   4459*****************998765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.002
                                   EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                   + ilL+G+ G+GKT +++++a++ + +  ++k P
  gi|91773970|ref|YP_566662.1| 496 KGILLYGPPGTGKTLIAQAVANEANANfiSIKGP 529
                                   459******************9998876666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0011      0.36       8      44 ..     213     246 ..     209     252 .. 0.77
   2 !    8.2   0.0    0.0038       1.2      23      43 ..     498     518 ..     483     526 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                   HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC   8 viekLlekdelqslvvalvGmgGvGKttlakqilnks 44 
                                   + ++L   + ++   v l+G +G GKt +ak + n+s
  gi|91773970|ref|YP_566662.1| 213 IFQRLN-VEPPK--GVILYGPPGTGKTLIAKAVANES 246
                                   566666.33344..589****************9984 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0038
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   + l+G +G GKt +a+ + n+
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANE 518
                                   779***************998 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0073       2.3       2      30 ..     225     253 ..     224     337 .. 0.78
   2 !   10.8   0.0    0.0011      0.34       2      37 ..     498     532 ..     497     613 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0073
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                   v+l g PG++ktl++ka+a+   ++f  +
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESRANFLYV 253
                                   78999**************9988888655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                   +ll g PG++ktl+++a+a+  +++f  i+  p +l
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISIK-GPQML 532
                                   7999********************998876.34444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.029       9.2       1      22 [.     228     251 ..     228     300 .. 0.82
   2 !   11.1   0.0    0.0012      0.39       1      55 [.     501     556 ..     501     589 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.029
                                   EE-TTSSHHHHHHHHHHHH..TEE CS
                        AAA_17   1 lGgPGsGKgtqceklveky..gft 22 
                                   +G+PG GK+ +++ ++ +   +f 
  gi|91773970|ref|YP_566662.1| 228 YGPPGTGKTLIAKAVANESraNFL 251
                                   7***********999987622444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0012
                                   EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHHHH CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklpleekk 55 
                                   +G+PG GK+ +++ ++ + +  ++s  G  + +    ++ +  rd ++k+ ++  +
  gi|91773970|ref|YP_566662.1| 501 YGPPGTGKTLIAQAVANEANANFISIkGPQMLSKFVGESEKAVRDTFKKARQVSPC 556
                                   7******************9999987777777776666555567777777666555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0081       2.6      20      41 ..     225     246 ..     209     283 .. 0.78
   2 !   11.2   0.0   0.00072      0.23      12      67 ..     490     543 ..     482     588 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0081
                        AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                   +++ GPPGtgKT    ++ ++ 
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANES 246
                                   6899********7766666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00072
                        AAA_11  12 salseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriL..vCapSNaAv 67 
                                     ++ ++  l+ GPPGtgKT    ++ ++++ +        ++p++L    ++S++Av
  gi|91773970|ref|YP_566662.1| 490 MGIKAPKGILLYGPPGTGKTLIAQAVANEANAN----FISIKGPQMLskFVGESEKAV 543
                                   5566667789**********9999999988532....222333333311344444444 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      0.54      18      45 ..     420     447 ..     412     461 .. 0.77
   2 !    8.2   0.0    0.0075       2.4      28      48 ..     690     710 ..     677     717 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0017
                        Vps4_C  18 dipsdkllePpvtlkDflkalkkarptV 45 
                                   +i ++ l +  vt +Df++alk++ p+ 
  gi|91773970|ref|YP_566662.1| 420 EISQEVLEKLVVTAEDFEDALKEVEPSA 447
                                   4555555555****************96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0075
                        Vps4_C  28 pvtlkDflkalkkarptVske 48 
                                   +v+ ++fl+a++k++pt++++
  gi|91773970|ref|YP_566662.1| 690 SVKERHFLAAIEKVKPTITED 710
                                   57889*************986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0068       2.2      11      32 ..     223     244 ..     215     252 .. 0.81
   2 !    9.6   0.0    0.0035       1.1      11      35 ..     496     520 ..     486     609 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0068
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                   k +++ ++pGtGKT + k++ +
  gi|91773970|ref|YP_566662.1| 223 KGVILYGPPGTGKTLIAKAVAN 244
                                   66899*********99887655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0035
                        AAA_19  11 kvllvtaGpGtGKTrvlkhivallv 35 
                                   k +l+ ++pGtGKT + +++ ++++
  gi|91773970|ref|YP_566662.1| 496 KGILLYGPPGTGKTLIAQAVANEAN 520
                                   56899*********99888776655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0     0.002      0.65      20      41 ..     224     245 ..     211     258 .. 0.81
   2 !    7.9   0.0    0.0071       2.3      22      43 ..     499     520 ..     492     532 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.002
                        AAA_30  20 vavltGpAGtGKttalkalrea 41 
                                    ++l Gp+GtGKt + ka+++ 
  gi|91773970|ref|YP_566662.1| 224 GVILYGPPGTGKTLIAKAVANE 245
                                   57999************99865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0071
                        AAA_30  22 vltGpAGtGKttalkalreawe 43 
                                   +l Gp+GtGKt + +a+++ ++
  gi|91773970|ref|YP_566662.1| 499 LLYGPPGTGKTLIAQAVANEAN 520
                                   688***********99977655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0017      0.55      48      84 ..     217     253 ..     197     334 .. 0.74
   2 !    7.6   0.0    0.0058       1.9      53      82 ..     495     524 ..     444     564 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                        DUF815  48 leglpannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                   l+ +p + v+L+G  GtGK  + ka+ ne +++ L +
  gi|91773970|ref|YP_566662.1| 217 LNVEPPKGVILYGPPGTGKTLIAKAVANESRANFLYV 253
                                   56678889*********************99998765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0058
                        DUF815  53 annvLLwGarGtGKSslvkallneyaeegL 82 
                                    + +LL+G  GtGK  + +a+ ne++++ +
  gi|91773970|ref|YP_566662.1| 495 PKGILLYGPPGTGKTLIAQAVANEANANFI 524
                                   3679*******************9988764 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.02       6.5      22      60 ..     220     253 ..     195     330 .. 0.78
   2 !    9.2   0.0    0.0034       1.1       6      49 ..     468     520 ..     464     536 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.02
                                   .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                   +  k +++  + GtGKTl+a +++ + +      +fl +
  gi|91773970|ref|YP_566662.1| 220 EPPKGVILYGPPGTGKTLIAKAVANESRA-----NFLYV 253
                                   6678888999*********9887776665.....55555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHHT...............TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                        ResIII   6 eyQeeaienlleklks.........krdkrglikmaTGtGKTlvaaklierll 49 
                                   +  +e+ie+++  lk+         k  k +l+  + GtGKTl+a +++ +  
  gi|91773970|ref|YP_566662.1| 468 DAKQEIIEAVEWPLKHpdriiemgiKAPKGILLYGPPGTGKTLIAQAVANEAN 520
                                   56678888888888778888888889999****************88887765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.014       4.3       3      24 ..     225     246 ..     223     325 .. 0.87
   2 ?   -0.8   0.0         4   1.3e+03      64     123 ..     265     325 ..     253     354 .. 0.62
   3 !    7.8   0.0    0.0092         3       3      25 ..     498     520 ..     496     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                   vil G++G GKT  ++ +a + 
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANES 246
                                   89**************999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4
                                   S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCTTTTT--EE CS
                         NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirkkllpeasl 123
                                   e++++ ++++++ +e++ ++ + +D +D ++ + ++      +++v   L +l+ + +  +  +
  gi|91773970|ref|YP_566662.1| 265 ESEERLRKIFEEAAENAPSIIF-IDEIDSIAPKRENvtgeV-ERRVVAQLLTLMDG-MEERGQI 325
                                   5566666677777777777776.488888877666666633.33333333355555.4444444 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0092
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                   ++l G++G GKT  +q +a ++ 
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEAN 520
                                   7899**************98875 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.014       4.6      23      49 ..     224     250 ..     210     299 .. 0.70
   2 !    9.0   0.0    0.0045       1.4      23      80 ..     497     565 ..     486     572 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                                   -EEEEEETT--HHHHHHCC--TTS-EE CS
               Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwl 49 
                                    v l G++G+gk+l+A++ +++s  + 
  gi|91773970|ref|YP_566662.1| 224 GVILYGPPGTGKTLIAKAVANESRANF 250
                                   5889***************99887654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0045
                                   -EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H.......HHHHHHT...TTSEEEEEE-TT CS
               Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpw.leifvverlaklp.......ldlleqa...kggtLylkdiad 80 
                                    ++l G++G+gk+l+A++ ++++  + ++i+  + l+k          d++++a   ++ ++++ +i++
  gi|91773970|ref|YP_566662.1| 497 GILLYGPPGTGKTLIAQAVANEANANfISIKGPQMLSKFVgesekavRDTFKKArqvSPCIIFFDEIDS 565
                                   589****************99866531333333333321123333335555553333666777777765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.029       9.4       2      30 ..     225     253 ..     224     270 .. 0.84
   2 ?    0.9   0.1       1.2   3.7e+02      82     118 ..     267     304 ..     259     316 .. 0.69
   3 ?    7.4   0.0     0.012       3.8       2      32 ..     498     528 ..     497     548 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.029
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                   v++ GppG+GKt + k v+++ + + + v
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESRANFLYV 253
                                   7899********99999998876665555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHH CS
                      NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkeav 118
                                   ee   +++++a  + + +i iDEi ++  k +++  +v
  gi|91773970|ref|YP_566662.1| 267 EERLRKIFEEAAeNAPSIIFIDEIDSIAPKRENVTGEV 304
                                   55556666666645667*******77766666655555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.012
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                   +++ GppG+GKt + + v+++ + + ++++G
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISIKG 528
                                   6788****************99888888887 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.044        14      26      59 ..     213     246 ..     200     253 .. 0.82
   2 ?    6.8   0.0     0.012       3.9      17      60 ..     471     520 ..     466     531 .. 0.72
   3 ?    0.1   0.0       1.4   4.6e+02     106     138 ..     541     573 ..     526     587 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.044
                          TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                   ++++ + + ++ ++l+G++ +GKt i++  a++ 
  gi|91773970|ref|YP_566662.1| 213 IFQRLNVEPPKGVILYGPPGTGKTLIAKAVANES 246
                                   5666667778899*************99887765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                          TniB  17 keilerLeeLleypkr......krmpnlllvGdsnnGKtmivekFarlhp 60 
                                   +ei+e  e+ l++p+r      k ++ +ll+G++ +GKt i++  a++ +
  gi|91773970|ref|YP_566662.1| 471 QEIIEAVEWPLKHPDRiiemgiKAPKGILLYGPPGTGKTLIAQAVANEAN 520
                                   566666666666666422222245589**************998877655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                          TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsark 138
                                   k+ +++ +  r++++ ++ +DEi+++ + +  +
  gi|91773970|ref|YP_566662.1| 541 KAVRDTFKKARQVSPCIIFFDEIDSIATTRIAD 573
                                   4455566777899999*********99877655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.032        10       3      27 ..     227     251 ..     225     256 .. 0.88
   2 ?   -0.2   0.0       2.2   7.1e+02     139     181 ..     401     445 ..     387     463 .. 0.72
   3 ?    6.7   0.0     0.016       5.2       3      28 ..     500     525 ..     498     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.032
                                   EE-STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                   + GP g+GK  +a+a+a++  +++l
  gi|91773970|ref|YP_566662.1| 227 LYGPPGTGKTLIAKAVANESRANFL 251
                                   56****************9988876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.2
                                   -HHHHHHHHHHHHHHTT----HHHHHHHH..HHHHHHHHCTSSS- CS
                Cytidylate_kin 139 sveeRakRRlkqlkakgtsvsleellaei..keRDklDkerevgp 181
                                    + +Ra RR+    +   ++  +e+l+++   + D  D  +ev+p
  gi|91773970|ref|YP_566662.1| 401 EASMRALRRILPEINLDEEEISQEVLEKLvvTAEDFEDALKEVEP 445
                                   567899999988777777777777777742267888888888887 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.016
                                   EE-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                   + GP g+GK  +a+a+a++ ++++++
  gi|91773970|ref|YP_566662.1| 500 LYGPPGTGKTLIAQAVANEANANFIS 525
                                   67*******************99986 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 ?    5.7   0.0     0.033        10      18      65 ..     226     279 ..     223     337 .. 0.69
   2 !    8.4   0.0    0.0047       1.5      17      89 ..     498     573 ..     491     617 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                                   EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE........ESEEHHHHHHHHHHCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg........iGergnevaevleefpe 65 
                                   ++ g  g+Gkt i+++++++s+++    yv+         Ge ++ +++++ee  e
  gi|91773970|ref|YP_566662.1| 226 ILYGPPGTGKTLIAKAVANESRAN--FLYVAgpeimgrfYGESEERLRKIFEEAAE 279
                                   578999**************8666..677766777666666666666666666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0047
                                   EEEEESTTSSHHHHHHHHHHHSSTS....SEEEEEE.......ESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsd....daiiyvg.......iGergnevaevleefpegtimkrtvlvantsnepvaar 86 
                                   +l+ g  g+Gkt i+q++++++n++    +     g       +Ge ++ v++ +++    + ++ +++++ + ++ +++r
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANfisiK-----GpqmlskfVGESEKAVRDTFKKA---RQVSPCIIFFDEIDSIATTR 570
                                   578899***************998844441.....24444444555555555443333...33334444444444444444 PP

                                   HHH CS
                                   xxx RF
                   ATP-synt_ab  87 eas 89 
                                   +a 
  gi|91773970|ref|YP_566662.1| 571 IAD 573
                                   443 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 ?    3.2   0.0      0.12        38     126     152 ..     219     245 ..     153     252 .. 0.83
   2 !   10.0   0.0     0.001      0.33     116     156 ..     482     522 ..     418     529 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                         T2SSE 126 vrerglilvsGgTgsGKttllyallke 152
                                   v+  + +++ G+ g+GKt ++ a+ +e
  gi|91773970|ref|YP_566662.1| 219 VEPPKGVILYGPPGTGKTLIAKAVANE 245
                                   5556678999*********99998776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.001
                         T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                   ++ +++++  +++ + il+ G+ g+GKt ++ a+ +e n++
  gi|91773970|ref|YP_566662.1| 482 KHPDRIIEMGIKAPKGILLYGPPGTGKTLIAQAVANEANAN 522
                                   56678999999999********************9998876 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.031       9.9       3      31 ..     223     251 ..     221     257 .. 0.88
   2 ?    0.3   0.0       1.6     5e+02      74      95 ..     258     279 ..     246     297 .. 0.79
   3 ?   -0.0   0.0       1.9     6e+02     146     176 ..     413     444 ..     363     450 .. 0.71
   4 ?    3.1   0.0       0.2        65       3      30 ..     496     523 ..     494     531 .. 0.86
   5 ?   -2.0   0.0       7.5   2.4e+03      76      97 ..     533     557 ..     526     581 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.031
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                 Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                                   + v+l gp g+Gk  + ka+ +e   +f 
  gi|91773970|ref|YP_566662.1| 223 KGVILYGPPGTGKTLIAKAVANESRANFL 251
                                   679*****************999988885 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                                   ETTEEEEEEHHHHHHHHHTTSE CS
                 Guanylate_kin  74 fsgnlygtsveaieevlekgki 95 
                                     g  yg+s e  ++++e++ +
  gi|91773970|ref|YP_566662.1| 258 IMGRFYGESEERLRKIFEEAAE 279
                                   67899***********998765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.9
                                   HHHHHHHHHGGG.CSSEEEEESSHHHHHHHHH CS
                 Guanylate_kin 146 rlaaaekelqey.efdvvivnddleealkklk 176
                                   +++  e+e+++     +v++ +d+e+alk+++
  gi|91773970|ref|YP_566662.1| 413 EINLDEEEISQEvLEKLVVTAEDFEDALKEVE 444
                                   44444444444322358999999999999987 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.2
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                   + + l gp g+Gk  + +a+ +e + +f
  gi|91773970|ref|YP_566662.1| 496 KGILLYGPPGTGKTLIAQAVANEANANF 523
                                   66899***************99998887 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 7.5
                                   TEEEEEEHHHHHHHHHTTSE...EE CS
                 Guanylate_kin  76 gnlygtsveaieevlekgki...vi 97 
                                   ++  g+s +a++  ++k+++   +i
  gi|91773970|ref|YP_566662.1| 533 SKFVGESEKAVRDTFKKARQvspCI 557
                                   5677999999999999999855544 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 ?   -0.4   0.0       1.7   5.5e+02      17      43 ..     219     245 ..     210     251 .. 0.79
   2 ?    5.3   0.0     0.031        10     165     199 ..     274     307 ..     263     329 .. 0.79
   3 ?    5.7   0.0     0.024       7.7      19      93 ..     494     734 ..     481     737 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
                    KAP_NTPase  17 latpivvgLygkWGsGKssllnklede 43 
                                   +++p  v Lyg+ G+GK+ + + + +e
  gi|91773970|ref|YP_566662.1| 219 VEPPKGVILYGPPGTGKTLIAKAVANE 245
                                   56777899**********888777665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.031
                    KAP_NTPase 165 ektLdalqkrlVvviDdLDrceteevlqlleavkl 199
                                   +++ + ++ + +++iD++D++ +++ + + e+ + 
  gi|91773970|ref|YP_566662.1| 274 FEEAA-ENAPSIIFIDEIDSIAPKRENVTGEVERR 307
                                   33333.58999************998888877655 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.024
                    KAP_NTPase  19 tpivvgLygkWGsGKssllnkledelkefa................................................... 48 
                                    p  + Lyg+ G+GK+ + + + +e + +                                                    
  gi|91773970|ref|YP_566662.1| 494 APKGILLYGPPGTGKTLIAQAVANEANANFisikgpqmlskfvgesekavrdtfkkarqvspciiffdeidsiattriads 574
                                   5566899*********99999999999988999999999999999999999999999999999999999999999999999 PP

                    KAP_NTPase  49 ................................................................................. 48 
                                                                                                                    
  gi|91773970|ref|YP_566662.1| 575 etgrssqqvvnqllteldgleplkevvviaatnrpdmidpalmrsgrfdrlvlvgnstiqgresifnihtrempldsevsi 655
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                    KAP_NTPase  49 ...................................kpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkll 93 
                                                                       ++r++ a ++  +++   + +ae+++ ++d l+    +++t+ +
  gi|91773970|ref|YP_566662.1| 656 qslaamtegyvgadieavcreaamlalredfdaesVKERHFLAAIEKVKPTI-TEDMAEFYSKIQDKLKGGTHKQETSSY 734
                                   9999999999999999999999999999999999988999999999999998.556899999999999998888888765 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.26        85       5      25 ..     226     246 ..     223     253 .. 0.87
   2 ?    9.0   0.0    0.0027      0.85       5      58 ..     499     552 ..     496     556 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                           IPT   5 lifGatttGKtaeaiklaket 25 
                                   +++G+ +tGKt  a ++a+e 
  gi|91773970|ref|YP_566662.1| 226 ILYGPPGTGKTLIAKAVANES 246
                                   68***************9986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0027
                           IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqcyselavgsGrpleeelegtrR 58 
                                   l++G+ +tGKt  a ++a+e  a  i++   q  s+    s +++ + +++ r 
  gi|91773970|ref|YP_566662.1| 499 LLYGPPGTGKTLIAQAVANEANANFISIKGPQMLSKFVGESEKAVRDTFKKARQ 552
                                   89*************************999999999988888888888887765 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0039       1.2       4      64 ..     226     291 ..     225     310 .. 0.79
   2 ?    2.6   0.0      0.29        92       4      59 ..     499     559 ..     498     590 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0039
                           Zot   4 lvtGapGsgKts..gavkkdllp.alk..egRkiitnidGlrlerieqvlgekvs.tarliridnpe 64 
                                   + +G+pG+gKt+  +av ++ +  +    +g +i+ +  G   er++++++e+ + ++ +i+id+ +
  gi|91773970|ref|YP_566662.1| 226 ILYGPPGTGKTLiaKAVANESRAnF-LyvAGPEIMGRFYGESEERLRKIFEEAAEnAPSIIFIDEID 291
                                   779********82245766655532.3348**********************9999999***99333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.29
                           Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarlir 59 
                                   l +G+pG+gKt+  +av ++++      +g ++  +  G   ++++  ++++ + ++ +i+
  gi|91773970|ref|YP_566662.1| 499 LLYGPPGTGKTLiaQAVANEANANFIsiKGPQMLSKFVGESEKAVRDTFKKARQvSPCIIF 559
                                   679********72246777666522213566666555555555555555555555555555 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0048       1.5      19      78 ..     180     238 ..     164     245 .. 0.69
   2 ?    2.6   0.0      0.16        50      60      79 ..     493     512 ..     482     522 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0048
                   AFG1_ATPase  19 daaqaeavealdrlteelaaqdlarkssalgklfgrkrksvepvrglYlwGgvGrGKtyl 78 
                                   d+a     e++  l +e+++ +++ +  + ++ ++++  +vep++g+ l+G+ G GKt +
  gi|91773970|ref|YP_566662.1| 180 DTATGITYEDIGGLGDEIQRVREMIELPLKHHEIFQR-LNVEPPKGVILYGPPGTGKTLI 238
                                   5555555555556666666655555544444445544.4899****************76 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                   AFG1_ATPase  60 epvrglYlwGgvGrGKtylm 79 
                                   ++++g+ l+G+ G GKt + 
  gi|91773970|ref|YP_566662.1| 493 KAPKGILLYGPPGTGKTLIA 512
                                   699**************875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.54   1.7e+02      46      69 ..     223     246 ..     211     261 .. 0.81
   2 ?   -1.8   0.0       7.6   2.4e+03     142     178 ..     259     293 ..     245     300 .. 0.69
   3 ?    8.1   0.0    0.0073       2.3      48     117 ..     498     568 ..     481     601 .. 0.79
   4 ?   -1.7   0.1       7.4   2.4e+03       8      30 ..     698     720 ..     691     723 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.54
                         Rad17  46 riLLisGPsGCgkstvvkvLskel 69 
                                   + +++ GP+G gk+ + k ++ e 
  gi|91773970|ref|YP_566662.1| 223 KGVILYGPPGTGKTLIAKAVANES 246
                                   556789********9999988775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.6
                         Rad17 142 Pnkfyrds.dalrevirkylrssealplilviteiesl 178
                                     +fy++s ++lr++  ++       p i+ i ei+s+
  gi|91773970|ref|YP_566662.1| 259 MGRFYGESeERLRKIFEEAAENA---PSIIFIDEIDSI 293
                                   56777777677888777765433...446667777764 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0073
                         Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkeleLkda 117
                                   +L+ GP+G gk+ + + ++ e   +++    p  l +     ++ ++  ++k  +  + i  f e+   ++
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISIKGPQMLSKFVGeSEKAVRDTFKKARQVSPCIIFFDEIDSIAT 568
                                   4678*********************9999999776554332677778888888877888888888865555 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 7.4
                         Rad17   8 lWfekykPekaeelavhkkkiee 30 
                                     +ek kP  +e++a   +ki++
  gi|91773970|ref|YP_566662.1| 698 AAIEKVKPTITEDMAEFYSKIQD 720
                                   5579***********99999986 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0       0.1        33       4      34 ..     225     255 ..     223     331 .. 0.82
   2 ?    5.7   0.0     0.037        12       4      36 ..     498     530 ..     496     556 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                                   EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                           CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                   ++L G + +GK+ +a+a+ + + + +l ++ 
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESRANFLYVAG 255
                                   89*****************999999998765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.037
                                   EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHH CS
                           CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDa 36 
                                   ilL G + +GK+ +a+a+ + +++ ++ ++  +
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISIKGPQ 530
                                   89********************99999887555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.12        37       1      20 [.     231     250 ..     231     254 .. 0.91
   2 ?    5.7   0.0     0.046        15       1      21 [.     504     524 ..     504     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.12
                                   TTSSHHHHHHHHHHHHTSEE CS
                           SKI   1 mGaGKstvGkllAkklglef 20 
                                   +G+GK+ ++k++A++ + +f
  gi|91773970|ref|YP_566662.1| 231 PGTGKTLIAKAVANESRANF 250
                                   69*************99988 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.046
                                   TTSSHHHHHHHHHHHHTSEEE CS
                           SKI   1 mGaGKstvGkllAkklglefi 21 
                                   +G+GK+ +++++A++ + +fi
  gi|91773970|ref|YP_566662.1| 504 PGTGKTLIAQAVANEANANFI 524
                                   69*****************98 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 ?    4.3   0.1      0.13        43       2      28 ..     225     251 ..     224     255 .. 0.87
   2 ?    5.9   0.0     0.043        14       2      30 ..     498     526 ..     497     534 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAll 28 
                                   +i+ G+P +GKt +a ++a +  a +l
  gi|91773970|ref|YP_566662.1| 225 VILYGPPGTGKTLIAKAVANESRANFL 251
                                   899**************9998887776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.043
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                   i++ G+P +GKt +a ++a + +a +++i
  gi|91773970|ref|YP_566662.1| 498 ILLYGPPGTGKTLIAQAVANEANANFISI 526
                                   7889********************99998 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.055        18      19      39 ..     218     238 ..     204     252 .. 0.83
   2 ?    4.3   0.0     0.058        18      25      55 ..     497     526 ..     491     549 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.055
                                   SSS---EEEEE-SSSSSTTTT CS
                          DAP3  19 kkkkvkrlvltGekgsGKSvl 39 
                                   + ++ k ++l+G +g+GK++ 
  gi|91773970|ref|YP_566662.1| 218 NVEPPKGVILYGPPGTGKTLI 238
                                   55678889**********974 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.058
                                   EEEEE-SSSSSTTTTHHHHHHHGGGS--EEE CS
                          DAP3  25 rlvltGekgsGKSvlLlqalayAlekgwvvl 55 
                                    ++l+G +g+GK++ ++qa+a  ++++++ +
  gi|91773970|ref|YP_566662.1| 497 GILLYGPPGTGKTL-IAQAVANEANANFISI 526
                                   5789********85.7899887777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); 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: 0.88u 0.31s 00:00:01.19 Elapsed: 00:00:00.49
# Mc/sec: 4564.11
//
Query:       gi|91773971|ref|YP_566663.1|  [L=299]
Description: NAD-dependent epimerase/dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-59  200.8   0.0    2.8e-59  200.5   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    9.6e-59  199.4   0.0      8e-58  196.4   0.0    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      2e-21   76.2   0.0    2.7e-21   75.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.6e-19   67.9   0.1      3e-17   62.7   0.1    2.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      3e-15   56.1   0.0    6.1e-15   55.1   0.0    1.6  1  RmlD_sub_bind    RmlD substrate binding domain
    3.6e-13   49.3   0.0      2e-11   43.6   0.0    2.5  2  NAD_binding_4    Male sterility protein
    4.4e-11   43.0   0.0    7.1e-11   42.3   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00025   20.7   0.0    0.00058   19.5   0.0    1.6  1  NmrA             NmrA-like family
    0.00033   20.8   0.0    0.00061   19.9   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0022   18.3   0.1     0.0036   17.5   0.1    1.4  1  TrkA_N           TrkA-N domain
     0.0068   16.3   0.1       0.63    9.9   0.1    2.3  1  KR               KR domain
  ------ inclusion threshold ------
       0.12   12.8   0.0        1.6    9.2   0.0    2.3  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
       0.13   12.4   0.1       0.42   10.8   0.0    1.9  2  AAA_lid_10       AAA lid domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.5   0.0     2e-62   2.8e-59       1     240 [.       4     233 ..       4     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 2e-62
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   il+tG++G++Gs+lv+++ e++ ev+ ld++ss  ++   e ++++++d++d  ++ + ++  + d++ih Aa+ +v +s+
  gi|91773971|ref|YP_566663.1|   4 ILITGGAGQVGSYLVDRFHEEN-EVTILDNYSSPTRKDVPEGVSVIKADIRD--DISEHMS--NTDVIIHTAAQISVVRSM 79 
                                   8******************987.9*******999999999999*******98..6788888..89**************** PP

                                   HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT- CS
                     Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqygl 162
                                   ++p   +++n++gtlnlle+ar a+++r++++sS+++YG++ ++p  et    p +p spY+a+Klagek++  y+++ygl
  gi|91773971|ref|YP_566663.1|  80 NEPFFDAQNNIMGTLNLLEEARHANIERFVYFSSAATYGNPLKVPIGETH---PQEPLSPYGASKLAGEKYCIMYNKAYGL 157
                                   **************************************************...99************************** PP

                                   EEEEEEESEEESTTS-TTS.TTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
                     Epimerase 163 naiilrlfnlyGprngege.vsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                                   +++++r+fn+y+pr+ +++  s+vi+++i k+  g  + t++gdg++ Rdf+yv+D+++++ l++ +  + + ge +n 
  gi|91773971|ref|YP_566663.1| 158 PTTCIRPFNIYSPRQDPSNpYSGVISKFIDKVSGGA-SPTIFGDGEQTRDFIYVRDIVDLVDLMISK--RTAIGESFNA 233
                                   **************555555***************9.*****************************9..4456888886 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 !  196.4   0.0   5.8e-61     8e-58       1     330 [.       5     294 ..       5     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 5.8e-61
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   LiTG+aG++Gsyl++++ e+  ev++++++ss ++ +              e ++++k+D++D   + + ++++  d +++
  gi|91773971|ref|YP_566663.1|   5 LITGGAGQVGSYLVDRFHEE-NEVTILDNYSSPTRKDVP------------EGVSVIKADIRD--DISEHMSNT--DVIIH 68 
                                   9****************998.899999999998663322............34689*******..688988888..9**** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadw 162
                                    AAq  V +s+++P   a++n++Gtl+LLe +r++++e   rf+  S++  YG++ +vp+ Et+p +P sPY+a+Kl+ + 
  gi|91773971|ref|YP_566663.1|  69 TAAQISVVRSMNEPFFDAQNNIMGTLNLLEEARHANIE---RFVYFSSAATYGNPLKVPIGETHPQEPLSPYGASKLAGEK 146
                                   ***********************************997...9*************************************** PP

                                   HHHHHHHHH---EEEEEE-EEESTTS-TTSCCC.HHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS- CS
                 GDP_Man_Dehyd 163 ivvnyreayglfavngilfnhesprrgetfvtr.kitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkp 242
                                    ++ y++aygl+++  + fn +spr+ ++ +    i++++ ++  g  ++ ++G+++++Rd+ +v+D+v+ ++lm+ + ++
  gi|91773971|ref|YP_566663.1| 147 YCIMYNKAYGLPTTCIRPFNIYSPRQDPSNPYSgVISKFIDKVSGGASPT-IFGDGEQTRDFIYVRDIVDLVDLMISKRTA 226
                                   ***************************98665538999999999998666.59***********************99886 PP

                                   ..--EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH---- CS
                 GDP_Man_Dehyd 243 ..edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkp 321
                                     e ++ atg++++++e++e+ +   gk+++                      d+k   +g+ +  ++d+ska+ +Lg+ p
  gi|91773971|ref|YP_566663.1| 227 igESFNAATGRSTTINELAEIIIDLFGKELK---------------------ADYKDPLEGDIKHSVADISKAE-KLGFVP 285
                                   6699***************988888877544.....................4444555678888889999987.899999 PP

                                   SS-HHHHHH CS
                 GDP_Man_Dehyd 322 kvsfeelvr 330
                                   kv+++++++
  gi|91773971|ref|YP_566663.1| 286 KVDLRKGLE 294
                                   999888876 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 !   75.8   0.0     2e-24   2.7e-21       1     223 [.       5     215 ..       5     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 2e-24
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                   ++tGgaG +G++lv ++ +++   ev +lD   sp+ ++  + v    vi++D++d  +++e + + dv+ih+a+ + v  
  gi|91773971|ref|YP_566663.1|   5 LITGGAGQVGSYLVDRFHEEN---EVTILDNYSSPTRKDVPEGVS---VIKADIRD--DISEHMSNTDVIIHTAAQISVVR 77 
                                   69**************98877...7*******9999977776665...56****97..79***************999988 PP

                     3Beta_HSD  82 kltedeim.kvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaN 161
                                    ++e  ++ + n+ GT n+le +++a+++++vY Ssa   g+  l+ +i      +++++ + ++y  sK   Ek+ +  N
  gi|91773971|ref|YP_566663.1|  78 SMNEPFFDaQNNIMGTLNLLEEARHANIERFVYFSSAATYGN-PLKVPIG-----ETHPQEPLSPYGASKLAGEKYCIMYN 152
                                   777665542679*************************98887.7777777.....456677889***************** PP

                     3Beta_HSD 162 grtlknggrlyTcaLRpagiyGegdkllvpl......lkqlaklglalfkigdeevlsdrvYvgNvaw 223
                                            l T ++Rp  iy ++++   p       +   +  g +    gd e++ d++Yv  +++
  gi|91773971|ref|YP_566663.1| 153 K---AY--GLPTTCIRPFNIYSPRQDPSNPYsgviskFIDKVSGGASPTIFGDGEQTRDFIYVRDIVD 215
                                   9...44..5*************998765554111000222333466778899999999****998875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.1   2.2e-20     3e-17       1     270 [.       4     281 ..       4     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 2.2e-20
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +l+tG++G +Gs lv+++ ++  +++ +l++            ++++ +  +     ++ +d+rd   +++ ++  + dv+
  gi|91773971|ref|YP_566663.1|   4 ILITGGAGQVGSYLVDRFHEE--NEVTILDNYSSPT-------RKDVPE-GV----SVIKADIRD--DISEHMS--NTDVI 66 
                                   89***************9876..4677777654332.......222333.22....234588987..5899999..99*** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS..............S--SHHHHHHHHHHHH CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv..............nPtnvmGatKrlaekl 148
                                   +h+AA   V    ++p+   ++N++gt n++e a +a+++++v+ S+                  +P + +Ga+K++ ek+
  gi|91773971|ref|YP_566663.1|  67 IHTAAQISVVRSMNEPFFDAQNNIMGTLNLLEEARHANIERFVYFSSAATYgnplkvpigethpqEPLSPYGASKLAGEKY 147
                                   ******99999999999999*************************9864422222222233333378999*********** PP

                                   HHHGGG--SSS--EEEEEEE-EETTGT.......TSSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHHHH.HHHHHH- CS
               Polysacc_synt_2 149 lqalakeseekktkfvvvRfGNVlgSr.......GSviplFkkqikeggpvtv.TdpemtRyfmtieeavqLv.lqalala 220
                                   ++ ++k         +++R  N+   r         vi +F ++++ g + t+  d e tR f+ +++ v+Lv l+  +++
  gi|91773971|ref|YP_566663.1| 148 CIMYNKAY---GLPTTCIRPFNIYSPRqdpsnpySGVISKFIDKVSGGASPTIfGDGEQTRDFIYVRDIVDLVdLMISKRT 225
                                   *****999...6777888988998765332223346************666653899****************66777889 PP

                                   -SS-EEEE--.-EEEHHHHHHHH................SSSS-EEE----TT--S CS
               Polysacc_synt_2 221 kggeifvldmGepvkivdlakalielsgleekk......eedieikitGlRpGEkl 270
                                     ge f    G +++i +la+ +i+l+g+e k+      e+di++++  + + Ekl
  gi|91773971|ref|YP_566663.1| 226 AIGESFNAATGRSTTINELAEIIIDLFGKELKAdykdplEGDIKHSVADISKAEKL 281
                                   99**************************9998877888888888888888887776 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 !   55.1   0.0   4.4e-18   6.1e-15       2     280 ..       3     295 ..       1     299 [] 0.72

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.4e-18
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------HHHH CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAytavDka 67 
                                   +il+tG+ Gq+Gs L+++++ee+ ev+ l++                ++d++d   + e     + dv++++AA   v + 
  gi|91773971|ref|YP_566663.1|   3 RILITGGAGQVGSYLVDRFHEEN-EVTILDNYssptrkdvpegvsviKADIRDD--ISEH--MSNTDVIIHTAAQISVVRS 78 
                                   7*******************998.777775555677666666554444444432..3333..34579************** PP

                                   HHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SE CS
                 RmlD_sub_bind  68 EseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....ka 143
                                    +e+  +++ n  ++ +l e+a+++++  +++ S+   +    k p  e+++++Pl+ YG++KlaGE+    ++k     +
  gi|91773971|ref|YP_566663.1|  79 MNEPFFDAQNNIMGTLNLLEEARHANIeRFVYFSSAATYGNPLKVPIGETHPQEPLSPYGASKLAGEKYCIMYNKayglPT 159
                                   **************************945***************************************9876544111156 PP

                                   EEEEE-SEESS......SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS CS
                 RmlD_sub_bind 144 livRtswvyge......kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyHlaneg 216
                                   + +R   +y+            +++++++++   + +++ D  q++   ++rd+ + +  +++k+++   + + + +a  +
  gi|91773971|ref|YP_566663.1| 160 TCIRPFNIYSPrqdpsnPYSGVISKFIDKVSGGASPTIFGDgeQTRDFIYVRDIVDLVDLMISKRTA---IGESFNAATGR 237
                                   7888888887644333222345667777777777666666655777778888888877777777765...67788888888 PP

                                   -EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS-.--SBE-B--HHHHHCCT----BHHHHHHH CS
                 RmlD_sub_bind 217 etswlefArailkeagadseevkpistaeyptpAk.RPanSvLdtekleatfgiklrewrealke 280
                                   +t+  e+A+ i++ +g++   +k    a+y +p +   ++Sv d +k+e+ + ++  + r++l++
  gi|91773971|ref|YP_566663.1| 238 STTINELAEIIIDLFGKE---LK----ADYKDPLEgDIKHSVADISKAEKLGFVPKVDLRKGLET 295
                                   888888888888877763...22....33444433123555555555555555555555555555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.038        53       1      20 [.       6      25 ..       6      31 .. 0.82
   2 !   43.6   0.0   1.4e-14     2e-11      79     217 ..      54     184 ..      48     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.038
                                  EE-TTSHHHHHHHHHHHHHS CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrtt 20
                                  +TG+ G +G++L+ +  +++
  gi|91773971|ref|YP_566663.1|  6 ITGGAGQVGSYLVDRFHEEN 25
                                  8************9876665 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 1.4e-14
                                   HHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H... CS
                 NAD_binding_4  79 edlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeege 156
                                   +d+ e ++++dviih aA+++++++++e     + N++Gt ++le a+  +    ++++S+a+ +g+  + v         
  gi|91773971|ref|YP_566663.1|  54 DDISEHMSNTDVIIHTAAQISVVRSMNEpffDAQNNIMGTLNLLEEARHANIE-RFVYFSSAATYGNPLK-V--------- 123
                                   5788999*********************5444689*************77666.*******999999993.3......... PP

                                   ...HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-......-SSST---T CS
                 NAD_binding_4 157 keekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg......esktGwing 217
                                            +++ ++    Y  sK ++Ek +  +++  glp++ +Rp +i++      ++ +G+i +
  gi|91773971|ref|YP_566663.1| 124 ------PIGETHPQEPLSPYGASKLAGEKYCIMYNKAYGLPTTCIRPFNIYSprqdpsNPYSGVISK 184
                                   ......466778888899*********************************9777655555555543 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 !   42.3   0.0   5.2e-14   7.1e-11       1     147 [.       8     168 ..       8     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5.2e-14
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHC.HHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC....... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekl.aeleaeeglevvegdvtdvedlaealkgadaVvsalggggk....... 73 
                                   G+ G+vG++lv++  +++  evt+l   ++ + ++++  eg++v+++d+   +d+ e+++++d+++ ++++ +        
  gi|91773971|ref|YP_566663.1|   8 GGAGQVGSYLVDRFHEEN--EVTILDNYSSPTrKDVP--EGVSVIKADIR--DDISEHMSNTDVIIHTAAQISVvrsmnep 82 
                                   99***************5..89988444443313465..8*********9..9*************999555443333344 PP

                                   ..HHHH......HHHHHHHHHHCT--EEEEEEETTTTS.GCGCHHHHHHH.HCCHHHHHHHHHHHHHH....HHSSSEEEE CS
                NAD_binding_10  74 ..deeg......aknivdaakeagvkRfvlvsaigvgd.evpgefgewnk.ellkaylaakraaeell....rasgldwTi 140
                                     d  +      + n+++ a+ a+++Rfv+ s++ ++    + + ge+   e l++y a k a e++     +a gl  T 
  gi|91773971|ref|YP_566663.1|  83 ffD--AqnnimgTLNLLEEARHANIERFVYFSSAATYGnPLKVPIGETHPqEPLSPYGASKLAGEKYCimynKAYGLPTTC 161
                                   442..0457789********************99887514555566655436899999********953433558****** PP

                                   EEE-CEE CS
                NAD_binding_10 141 vrpggLt 147
                                   +rp  + 
  gi|91773971|ref|YP_566663.1| 162 IRPFNIY 168
                                   **97765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.2e-07   0.00058       1     228 [.       4     255 ..       4     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.2e-07
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT........-HHHHHHHHTT-SEEEE--- CS
                          NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdld........dkeslvealkgvdvvfsvtg 73 
                                   Il++G++G+ G+++v+ + +++ +v +l  + +s + k +  +Gv ++k+d+         + +++ +   +  vv s+ +
  gi|91773971|ref|YP_566663.1|   4 ILITGGAGQVGSYLVDRFHEEN-EVTIL-DNYSSPTRKDVP-EGVSVIKADIRddisehmsNTDVIIHTAAQISVVRSMNE 81 
                                   89**************998765.56555.677888888875.7*******9985666555555555555555555555544 PP

                                   GG...S-HHHHHHHHHHHHHHHS-SEEEE.EE---GG........GT.SSS---TTTHHHHHHHHHH....HHCTS-EEEE CS
                          NmrA  74 fy...skeiedgkklvdAakeaGvkhfiy.Sslgddnd.......rsnaeepavphfdsKaeieeyv....ralgipytfv 139
                                    +   +++i    +l + a +a +++f+y Ss +   +       +++ +ep  p  +sK   e+y     +a g+p+t +
  gi|91773971|ref|YP_566663.1|  82 PFfdaQNNIMGTLNLLEEARHANIERFVYfSSAATYGNplkvpigETHPQEPLSPYGASKLAGEKYCimynKAYGLPTTCI 162
                                   3389999*********************84443332221222233688999999999999999998633335669**9999 PP

                                   EE.-EEG.....GG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-H CS
                          NmrA 140 ya.gffm.....enflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsg 214
                                   ++ +++      +n  s +  +++++ + ++ + t+ g+g+    ++  ++Di   v  ++++++++  +  + +g   + 
  gi|91773971|ref|YP_566663.1| 163 RPfNIYSprqdpSNPYSGVISKFIDKVS-GGASPTIFGDGEQTRDFI-YVRDIVDLVDLMISKRTAIGESFNAATGRSTTI 241
                                   9844775333334555555554555555.555999999999888888.999999999999999999999999999999999 PP

                                   HHHHHHHHHHHTS- CS
                          NmrA 215 neivelfekkigkt 228
                                   ne++e++    gk+
  gi|91773971|ref|YP_566663.1| 242 NELAEIIIDLFGKE 255
                                   99999988777776 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.4e-07   0.00061       2     111 ..       3     107 ..       2     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.4e-07
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHHH CS
                        DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpeavle 82 
                                   +++++G +G +G+ +v+  +e++++++   +++++     kd+ e  g++ ++  + dd++e + ++dv+i   +  +v+ 
  gi|91773971|ref|YP_566663.1|   3 RILITGGAGQVGSYLVDRFHEENEVTILDNYSSPT----RKDVPE--GVSVIKADIRDDISEHMSNTDVIIHTAAQISVVR 77 
                                   799****************************9998....788887..666799999***************9998888888 PP

                                   HHHHHHHTT-EEEE--SS-.-HHHHHHHHH CS
                        DapB_N  83 nlklalekgvklViGTTGl.seeelaelee 111
                                    ++  +    + ++GT  l +e+++a++e+
  gi|91773971|ref|YP_566663.1|  78 SMNEPFFDAQNNIMGTLNLlEEARHANIER 107
                                   888877788888888877645556666665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.6e-06    0.0036       5      52 ..       9      55 ..       4     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                                  S-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSH CS
                        TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatde 52
                                  G+G+vG+ l+++++e+++ v++ d+  +  ++   eg+ v+++d  d+
  gi|91773971|ref|YP_566663.1|  9 GAGQVGSYLVDRFHEENE-VTILDNYSSPTRKDVPEGVSVIKADIRDD 55
                                  89*************995.*************************9987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00046      0.63      98     142 ..      77     118 ..       3     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00046
                                   TT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH- CS
                            KR  98 eemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllg 142
                                    +m++  +++  +  + G+ nL e  ++ +++ fv+fSS+a+ +g
  gi|91773971|ref|YP_566663.1|  77 RSMNEPFFDA--QNNIMGTLNLLEEARHANIERFVYFSSAAT-YG 118
                                   4444444443..34578999999999999********99987.45 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 ?    9.2   0.0    0.0012       1.6       2      71 ..       4      67 ..       3      90 .. 0.77
   2 ?    1.3   0.0      0.33   4.6e+02      16      42 ..      94     122 ..      91     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                                  EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEE CS
                Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivf 71
                                  + i G+ G vG+ l+ + +e+ ev+++  +ss     k + e v+    + +  ++d  +e +++ d+++
  gi|91773971|ref|YP_566663.1|  4 ILITGGAGQVGSYLVDRFHEENEVTILDNYSSPT--RKDVPEGVS----VIKADIRDDISEHMSNTDVII 67
                                  7799************************999998..556666655....667777776666667777766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
                                   HHHHHC..TSSEEEEEEEESTTTTTSBHH CS
                Semialdhyde_dh  16 lrlLee..hpevelvvllsssrsaGkkla 42 
                                   l+lLee  h ++e  v +ss+   G++l+
  gi|91773971|ref|YP_566663.1|  94 LNLLEEarHANIERFVYFSSAATYGNPLK 122
                                   68999999999999999999999998876 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.42      15      55 ..      22      62 ..      10      72 .. 0.85
   2 ?   -2.5   0.0       4.3   5.9e+03       4      15 ..      76      87 ..      73     104 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                  ------------------------------------HHHHH CS
                    AAA_lid_10 15 nektgsailieaeeekkqklPenvkkvrlkisddaieiasr 55
                                   e+++ +il + ++ +++ +Pe+v  ++  i dd+ e +s 
  gi|91773971|ref|YP_566663.1| 22 HEENEVTILDNYSSPTRKDVPEGVSVIKADIRDDISEHMSN 62
                                  478999*****************************998875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                                  H----------- CS
                    AAA_lid_10  4 lkglnksffyvn 15
                                  ++++n++ff  +
  gi|91773971|ref|YP_566663.1| 76 VRSMNEPFFDAQ 87
                                  789999999633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 1828.93
//
Query:       gi|91773972|ref|YP_566664.1|  [L=194]
Description: hypothetical protein Mbur_2038 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.6   1.7       0.13   12.6   1.7    1.6  1  NLRC4_HD  NLRC4 helical domain


Domain annotation for each model (and alignments):
>> NLRC4_HD  NLRC4 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.7   7.3e-06      0.13       4      60 ..      19      79 ..      18     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.3e-06
                                  HHHHHHHCTT-SHHHHHCCCHHHHHHCCC--TTCHHHHHHHHHHTTSSSTHHCHCH.......T CS
                      NLRC4_HD  4 dkGlsyLkqinsilkivsrYsnlLlYtcgsstkAgpkivshLlalvdekeslenls.......e 60
                                  +++++yLk i+  l+i+  Ys + lY+c  s    ++  + Ll l+  ke l +         e
  gi|91773972|ref|YP_566664.1| 19 SLSNKYLKFIDIALQITR-YSRFPLYSCRYSKRTYTQ--NQLLTLILFKEYLGEDYrdfvdfvE 79
                                  5799************98.**********99876554..4444444444555443344445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1243.99
//
Query:       gi|91773973|ref|YP_566665.1|  [L=592]
Description: RNA-directed DNA polymerase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  145.6   0.1    3.3e-42  144.5   0.0    1.5  2  RVT_1            Reverse transcriptase (RNA-dependent DNA pol
    7.9e-28   96.5   2.4    7.9e-28   96.5   2.4    1.9  2  RVT_N            N-terminal domain of reverse transcriptase
    3.5e-24   84.6   6.4    9.2e-24   83.3   6.4    1.8  1  GIIM             Group II intron, maturase-specific domain
  ------ inclusion threshold ------
      0.019   14.9   3.5       0.14   12.1   0.5    3.6  3  Intron_maturas2  Type II intron maturase
       0.12   12.5   3.4       0.26   11.5   3.4    1.6  1  HNH              HNH endonuclease


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   0.0   9.3e-46   3.3e-42       1     222 []     145     366 ..     145     366 .. 0.95
   2 ?   -3.3   0.0       1.5   5.2e+03      94     136 ..     469     513 ..     460     514 .. 0.63

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 9.3e-46
                                   EE-TT.S-EEE......-THHHHCTB--.........-------HHHH.............HCCHTS--EEEEEEBCCGCC CS
                         RVT_1   1 ipKkgpgsyRpisllsvdykalnkliakrLkdvlekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaFd 81 
                                   i K g ++ Rp++++++ ++a+++l+a +L +++e + +++++gfr+ rst+da  ++  +++kk +a+++l+ D+k++Fd
  gi|91773973|ref|YP_566665.1| 145 IEKYGSDKKRPLGIPTMYDRAMQALYALALDPIAEVTADKRSFGFRKFRSTHDACSQIFGTISKKDSAQCILEGDIKGCFD 225
                                   56777899************************************************************************* PP

                                   CSBB-GGGGGGG-EEET..........................TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T...... CS
                         RVT_1  82 svpleellrkltafkvptklinliksflstrsfsvrv.ngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra... 158
                                   ++++++l+  +     +++   ++k+fl    +++ v ++   + +++k+g+pqG+++SP+l+n++++ ++  l+ ++   
  gi|91773973|ref|YP_566665.1| 226 NISHQWLIDNIPM---DKS---ILKQFL----KAGFVyEN---SLFPTKAGTPQGGIISPILANMTLDGIEGVLADKYhrg 293
                                   ********99888...534...899999....56666355...89*******************************99*** PP

                                   ...............TEEECTTEEEEEESSHHHHHHHHHHHHHHHHHTT--BEGGG-EEE.....ESSEEETTEEE CS
                         RVT_1 159 ............kgvtllrYaDDililskskeelqelleaveewlkesglkinpeKtklvlftvkseevkyLGvtl 222
                                                +v+++rYaDD+++++k+ke ++e+ e ++++l + gl++++eKt +++     + +++LG ++
  gi|91773973|ref|YP_566665.1| 294 vsgkittrqrakHKVNFVRYADDFIVTAKTKEIAEEAKELIKNFLTDRGLELSDEKTLITH---IDDGFDFLGWNV 366
                                   ************************************************************9...89*******875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                                   -EEET...........................TEEEEESB--ST- CS
                         RVT_1  94 afkvptklinliksflstrsfsvrvnge..eskgryekkglpqGs 136
                                    f++ +++++l+++ +  r   ++++++  + +++++++ l qGs
  gi|91773973|ref|YP_566665.1| 469 VFSTMKNQLKLMSDKMIVRNPQIKLDKNpyTDTEYFVERKLNQGS 513
                                   456666667777666666666666633335777888888888887 PP

>> RVT_N  N-terminal domain of reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   2.4   2.2e-31   7.9e-28       1      83 []      49     130 ..      49     130 .. 0.99
   2 ?   -3.3   0.0       3.3   1.2e+04      49      58 ..     381     388 ..     376     404 .. 0.53

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 2.2e-31
                         RVT_N   1 WkeidWkkvekkVfkLqkrIykAsqegdikkvkkLqklLtkSlsakllAvrrVtqdnkgkktagvDgvksltpkerlelve 81 
                                   W+ i+W++ve++V+++q rI+kA+ +++++ vkkL +lLt+S++akllAvr+V   nkg++tag+Dg+ ++tp +++++++
  gi|91773973|ref|YP_566665.1|  49 WNFINWSSVESHVNRIQVRITKAVINKNWNLVKKLSYLLTHSHYAKLLAVRKVIR-NKGRRTAGIDGEFWSTPVSKVNAAR 128
                                   *******************************************************.**********************998 PP

                         RVT_N  82 eL 83 
                                   +L
  gi|91773973|ref|YP_566665.1| 129 SL 130
                                   76 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.3
                         RVT_N  49 AvrrVtqdnk 58 
                                   ++++Vt+  k
  gi|91773973|ref|YP_566665.1| 381 SIKKVTE--K 388
                                   4555555..2 PP

>> GIIM  Group II intron, maturase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   6.4   2.6e-27   9.2e-24       1      80 []     382     460 ..     382     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 2.6e-27
                          GIIM   1 vkrlkrkireltkrsskgvsleelirklnpilrGWanYyrlgvakrvfskldhyirrrLrrwllrkhkkkkrrralrkyw 80 
                                   +k++++ki++++ ++ k++++e+li klnpi++GW nY++ + +k++fs +d  i++ L++w++r+h+ k+r ++++kyw
  gi|91773973|ref|YP_566665.1| 382 IKKVTEKISNTI-KDGKTWTQEDLISKLNPIITGWSNYHQGVASKETFSLIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 460
                                   6999********.7779**************************************************************9 PP

>> Intron_maturas2  Type II intron maturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.46   1.7e+03      71     106 ..      80     109 ..      70     139 .. 0.63
   2 ?   -0.5   0.0       0.3   1.1e+03       4      32 ..     232     265 ..     229     277 .. 0.76
   3 ?   12.1   0.5   3.9e-05      0.14      38     103 ..     399     460 ..     372     491 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
               Intron_maturas2  71 rerikyilrkscvkTLArKlklktvrkvikkfGkkl 106
                                   ++ +      s ++T  +  kl  vrkvi+  G++ 
  gi|91773973|ref|YP_566665.1|  80 VKKL------SYLLTHSHYAKLLAVRKVIRNKGRRT 109
                                   4444......44455555556666777776666554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
               Intron_maturas2   4 lvlnaPir.kiikkLakagfvktkk....ekgkP 32 
                                   l+ n+P++ +i k+  kagfv +++    + g P
  gi|91773973|ref|YP_566665.1| 232 LIDNIPMDkSILKQFLKAGFVYENSlfptKAGTP 265
                                   566899973588999******9986665555555 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 3.9e-05
               Intron_maturas2  38 widledrdIllrykaiirgllnYYsfadnkkrlrerikyilrkscvkTLArKlklktvrkvikkfG 103
                                   w+   + d++ + + ii g +nY++++  k+++  +i + + + + k   r++ +k +  + +k+ 
  gi|91773973|ref|YP_566665.1| 399 WT---QEDLISKLNPIITGWSNYHQGVASKETFS-LIDFKIWNILWKWAKRRHPMKSRTWIAHKYW 460
                                   44...457899**********************9.**99988888877777777777766666665 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.4   7.2e-05      0.26      23      46 ..     550     577 ..     531     578 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.2e-05
                           HNH  23 sq..ggadd..ieNlqllCksCHnkkhd 46 
                                   ++  g++dd  i Nl+ ++  CH++ h+
  gi|91773973|ref|YP_566665.1| 550 HHknGNHDDngITNLVYAHVYCHRQYHA 577
                                   44437777799**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3911.97
//
Query:       gi|91773974|ref|YP_566666.1|  [L=73]
Description: hypothetical protein Mbur_2040 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.8   0.3      0.037   13.7   0.3    1.1  1  DDE_Tnp_1  Transposase DDE domain
      0.038   13.8   0.0      0.041   13.6   0.0    1.0  1  PSS        Phosphatidyl serine synthase


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   4.1e-06     0.037     166     214 .]       5      52 ..       1      52 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-06
                     DDE_Tnp_1 166 evaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       +y+ R   E+ F+ lkrk+g ++lr+r+++  + ++ ++ + +nl
  gi|91773974|ref|YP_566666.1|   5 FDSKIYSMRNLSETMFSVLKRKYG-ENLRARKYRNQVKEVKFKVILHNL 52 
                                   55679****************999.**************9999999997 PP

>> PSS  Phosphatidyl serine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.6e-06     0.041      31      79 ..      16      64 ..       8      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-06
                           PSS 31 arqllklldpelgkklpeksyaedCsllslenvlekldvfvlaHflGwl 79
                                   ++++++l+ + g++l+ ++y ++ + ++++ +l++ld fv + fl w+
  gi|91773974|ref|YP_566666.1| 16 SETMFSVLKRKYGENLRARKYRNQVKEVKFKVILHNLDRFVKTVFLVWM 64
                                  46788999999********************************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 463.46
//
Query:       gi|91773975|ref|YP_566667.1|  [L=140]
Description: CopG family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for 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-34  115.8   1.5    9.4e-34  115.4   1.5    1.2  1  NikR_C           NikR C terminal nickel binding domain
    6.4e-08   32.3   0.1    1.8e-07   30.8   0.0    1.8  2  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.037   14.1   0.0    1.8  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
      0.072   13.3   0.1       0.38   10.9   0.0    1.9  2  RHH_8            Ribbon-Helix-Helix transcriptional regulator


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   1.5   2.1e-37   9.4e-34       1      76 [.      58     133 ..      58     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 2.1e-37
                                   EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                        NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                   vG+iti+ydh++r+ls+ ++diqh+y+dli+ss+h+hldhdncLevi+ +Ge+e ike+ e+l+alkgVk+vkl++
  gi|91773975|ref|YP_566667.1|  58 VGTITIIYDHTKRGLSNAVADIQHDYSDLIKSSVHIHLDHDNCLEVIIFDGEGELIKEMDERLMALKGVKYVKLNT 133
                                   7*************************************************************************97 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 !   30.8   0.0   4.1e-11   1.8e-07       1      39 []       7      46 ..       7      46 .. 0.97
   2 ?   -2.6   0.2       1.4   6.3e+03       8      13 ..     114     119 ..     111     123 .. 0.50

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.1e-11
                                  EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                         RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyler 39
                                  r+ ++l+++ll ++d +++ rg +SrSe IR+ +r y+ +
  gi|91773975|ref|YP_566667.1|  7 RIGVSLPDNLLNKFDSIIEGRGySSRSEGIRDSIRTYINQ 46
                                  899**********************************976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                   HHHHHH CS
                         RHH_1   8 eeller 13 
                                   +e++er
  gi|91773975|ref|YP_566667.1| 114 KEMDER 119
                                   344444 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.2e-06     0.037      87     117 ..       3      34 ..       1      39 [. 0.87
   2 ?   -1.2   0.0      0.47   2.1e+03      74      83 ..      87      96 ..      71     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-06
               HicB_lk_antitox  87 gkaeriNitlpervlkriDaavkaag.esRSg 117
                                   ++  ri ++lp+++l++ D++++ +g +sRS 
  gi|91773975|ref|YP_566667.1|   3 QELMRIGVSLPDNLLNKFDSIIEGRGySSRSE 34 
                                   56789********************9669997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.47
               HicB_lk_antitox 74 iwalvdvdls 83
                                  i   v++ l+
  gi|91773975|ref|YP_566667.1| 87 IKSSVHIHLD 96
                                  4444444333 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 ?   10.9   0.0   8.5e-05      0.38      15      46 ..      17      48 ..       2      82 .. 0.73
   2 ?    0.2   0.0      0.18   7.9e+02      31      47 ..      84      99 ..      79     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                         RHH_8 15 LgqiDlLveeGfYsnRtDlirtairaqLakhd 46
                                  L + D ++e   Ys+R++ ir +ir+ +++++
  gi|91773975|ref|YP_566667.1| 17 LNKFDSIIEGRGYSSRSEGIRDSIRTYINQYE 48
                                  788999999999**************999885 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                         RHH_8 31 tDlirtairaqLakhdd 47
                                  +Dli+++++ +L+ hd+
  gi|91773975|ref|YP_566667.1| 84 SDLIKSSVHIHLD-HDN 99
                                  89******99996.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1042.56
//
Query:       gi|91773976|ref|YP_566668.1|  [L=238]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-60  205.1   0.2    1.6e-60  204.8   0.2    1.1  1  SAICAR_synt   SAICAR synthetase
  ------ inclusion threshold ------
      0.014   14.5   0.1      0.021   13.9   0.1    1.2  1  FA_synthesis  Fatty acid synthesis protein


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 !  204.8   0.2   1.8e-64   1.6e-60       2     251 ..       6     230 ..       5     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 204.8 bits;  conditional E-value: 1.8e-64
                                   EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSEEEEE CS
                   SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrsmlvk 80 
                                   ly+GK++ +Y++e++++l+ +++D ++Afd+++k+e ++KG ++ q+s+ +fe+le+  i++h++       ++g++mlvk
  gi|91773976|ref|YP_566668.1|   6 LYSGKAKTIYKTENPNELISEFRDSLTAFDGKKKSEATNKGYYNAQISKKIFEMLEEegIKTHYLGM-----VSGNEMLVK 81 
                                   89******************************************************668******65.....9******** PP

                                   -EEEESEEEEEEEE--HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT..-HHHH CS
                   SAICAR_synt  81 klkmlpvEvvvRgyltGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevvealg..teeea 159
                                   k++++ +Ev+ R++++Gs+       ++    ++   ++eg+ ++ep++ + +K++e + D++i+++ +v  +g  t+ee+
  gi|91773976|ref|YP_566668.1|  82 KVDIILIEVIPRNIAAGSI-------TR----KY--PVEEGTVFKEPVLVFDYKSDEFG-DPMINDDIAV-VMGiaTREEI 147
                                   *******************.......55....56..89********************9.*******999.88999***** PP

                                   HHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT-ST CS
                   SAICAR_synt 160 eeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdwlee 240
                                   + i+++al+++++++++++++g +l D+KlEFG+   dge+vLaDe+ + D++Rfwd et       es+DK+++R + ++
  gi|91773976|ref|YP_566668.1| 148 DFIRSMALKINAILKSYLESNGFLLPDFKLEFGRV--DGEIVLADEI-SCDTCRFWDVET------GESMDKDLFRFDKGD 219
                                   **********************************9..7*********.************......9************** PP

                                   HHHHHHHHHHH CS
                   SAICAR_synt 241 veekwkekler 251
                                    +++++++++r
  gi|91773976|ref|YP_566668.1| 220 LSKAYEKVARR 230
                                   *****998875 PP

>> FA_synthesis  Fatty acid synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.3e-06     0.021     189     232 ..      51      95 ..      38     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHHHT-T.TSEEEEEEEGGGCCCTS-SEEE--HHHHHH CS
                  FA_synthesis 189 dlvkqtfellkaie.sieflGnvegrdildgkvdvivcdgftgNv 232
                                   ++ k++fe+l++ + + ++lG v g+++l  kvd+i+++ +  N+
  gi|91773976|ref|YP_566668.1|  51 QISKKIFEMLEEEGiKTHYLGMVSGNEMLVKKVDIILIEVIPRNI 95 
                                   489*******9976799********************98766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1705.85
//
Query:       gi|91773977|ref|YP_566669.1|  [L=476]
Description: amine oxidase [Methanococcoides burtonii DSM 6242]
Scores for 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   71.3   0.0    2.3e-19   70.0   0.0    1.7  1  Amino_oxidase   Flavin containing amine oxidoreductase
    2.9e-18   65.9   0.1    5.8e-18   64.9   0.1    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      6e-11   42.5   0.0    7.5e-08   32.3   0.0    2.4  2  DAO             FAD dependent oxidoreductase
    7.8e-10   38.4   0.7    7.2e-09   35.2   0.8    2.2  3  FAD_binding_2   FAD binding domain
    1.3e-08   34.7   0.0    1.9e-08   34.1   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    1.3e-07   30.7   0.6    3.3e-06   26.1   0.2    2.8  3  HI0933_like     HI0933-like protein
    1.6e-06   27.7   0.7    2.7e-06   26.9   0.7    1.3  1  FAD_binding_3   FAD binding domain
    3.7e-06   26.4   0.0    3.3e-05   23.3   0.0    2.3  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.5e-06   25.2   0.2    1.1e-05   24.2   0.2    1.5  1  GDI             GDP dissociation inhibitor
    1.5e-05   24.4   0.2    2.9e-05   23.4   0.2    1.5  2  Thi4            Thi4 family
    6.5e-05   22.3   0.0      0.002   17.4   0.1    2.6  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    6.7e-05   22.1   0.4    0.00058   19.0   0.1    2.1  2  GIDA            Glucose inhibited division protein A
    0.00016   22.2   1.1    0.00033   21.2   0.4    1.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0084   15.4   0.0      0.013   14.8   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.019   14.0   0.1      0.028   13.5   0.1    1.2  1  Lycopene_cycl   Lycopene cyclase protein
       0.13   11.1   0.0       0.21   10.3   0.0    1.3  1  MCRA            MCRA family
        0.2   10.4   0.7        0.3    9.9   0.7    1.2  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   2.2e-22   2.3e-19       2     365 ..      14     396 ..      13     461 .. 0.70

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.2e-22
                                   HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET.TTHHHHHHHHHTTCCCCEEEESCCGCEEEEET CS
                 Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg.agnpllellkelgledslslpdpgapkrvlsk 81 
                                   +GL aA +L+ +G +V+vlE +d vGG ++++  dGy +++G++ +t  a+ pl +l++   ++ ++++ ++g ++++ + 
  gi|91773977|ref|YP_566669.1|  14 TGLLAALTLSKHGKKVLVLEKQDVVGGNCNSYSVDGYQVDTGPHAITHlAEGPLRRLMDN-YFDYQPVFENYG-QYYIRT- 91 
                                   8***********************************************************.788888899999.666666. PP

                                   TEECCTTEECHHHHHHHHHHHHHHHH.CHHHHHHHHHHHHHHHHH...........HHHCCCCHHHHHHHHHCHHHHHHHH CS
                 Amino_oxidase  82 ggrefpgdlspvpaewealleqgals.aellsleeklrlgleall...........qktldeldldskslaesleelgrre 150
                                         +++ +vp+ +++++ +   +  + l +++ + ++l+              ++ ++ l  d+ ++a++++ +   +
  gi|91773977|ref|YP_566669.1|  92 -----EERFVKVPSTIKEFVTFDVFPkLDRLAITQAITKSLTMASfgidlsdqsvyDSLPANLSKDTYDFANAISYFLSGR 167
                                   .....8889999999999999444445555555555555555555566666655555555555555555555555555555 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE.......................... CS
                 Amino_oxidase 151 pgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllp.......................... 205
                                     + +  +r++  + f + ++ +  f+  +                                                   
  gi|91773977|ref|YP_566669.1| 168 CMKETSAQRVLAGSSFVRDSVTQEQFEEII-----------------------KQestprtesilqsvlpsnlhlslhsri 225
                                   555444555555544444444444444322.......................2222223333333344455555556666 PP

                                   ....................TTHTHHHHHHHHH.TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHH CS
                 Amino_oxidase 206 ....................rgGlsqlpealae.elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvl 265
                                                       r+Gl++l +a+     + ++i+++++V++i +++++ +  +e  ++++aD V+ T     l
  gi|91773977|ref|YP_566669.1| 226 nlsclgrlasnkvslsqgypRKGLKSLLNAILYsLPSTVEIKTGCEVHKIFTDKGKAWG-VEADNTYSADLVIYTGFATSL 305
                                   777799999999999999*9**********999899999*************8888666.6889999********999999 PP

                                   HSSEEESCCSHHHHHHHHHSEEEEEEEEEEEESSGGSGCSTSE.CE.CECCCEEETTTEEEEECC..ECCCSTTTEEEEEE CS
                 Amino_oxidase 266 kailfsPplpdekaeairnlgfgsvnkvilefdrkfwednalg.qg.vlvseltttlgeafissd..fpsrappgkglvll 342
                                       ++  lp    e ++ +    +  + l  dr        + ++ v  +++ ++ ++ ++ ++   ps ap gk+lv +
  gi|91773977|ref|YP_566669.1| 306 P--FLVEDLPASYKEQLDGIVHSKSLTLWLGLDRMM------DeFKyVGSEIWFKGTPYWAMPTSnyDPSLAPKGKQLVGF 378
                                   9..666689889999999997777778999999988......323345555555555555555557788889999999888 PP

                                   EEECHHHHHHHTTS-HHHHHHHH CS
                 Amino_oxidase 343 vyvggdaaneleslsdeelvqav 365
                                   ++++++ ++e       ++++a 
  gi|91773977|ref|YP_566669.1| 379 AFFMDEGNDE-----SRDIKNAY 396
                                   8888666654.....34444444 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 !   64.9   0.1   5.5e-21   5.8e-18       1      66 [.       8      72 ..       8      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 5.5e-21
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHC CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllr 66
                                  +vGaG++Gl+aA +L+k+g++vl+lek+d +GG++ sy+v+g+ vd+g+h+++       +rrl++
  gi|91773977|ref|YP_566669.1|  8 VVGAGVTGLLAALTLSKHGKKVLVLEKQDVVGGNCNSYSVDGYQVDTGPHAITHLA-EGPLRRLMD 72
                                  8***************************************************8864.688888887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   7.1e-11   7.5e-08       1      34 [.       5      40 ..       5     116 .. 0.93
   2 !    7.9   0.0    0.0019         2     161     331 ..     264     444 ..     241     456 .. 0.57

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 7.1e-11
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags 34
                                  dv+++G+G++Gl +A+ L+++g  V++lek+d +g 
  gi|91773977|ref|YP_566669.1|  5 DVIVVGAGVTGLLAALTLSKHGkkVLVLEKQDVVGG 40
                                  8********************99********99994 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0019
                                   -EEEESECEEEEEEEETCEEEEEEECTEEEEEEEE.EEE--GGGHH..HH.HTTCTT....TSEE.EEEEEEEEEE.EECC CS
                           DAO 161 veilegtevtgleeedgkvwgverttpgendaada.vVnaaGawsd..ll.gllkel....dlpi.spvrgqvlvl.kpls 231
                                   vei +g+ev ++  + gk+wgve  ++++   + a +V+ +G  ++  +l +   +l    + ++   v + +l+l   l+
  gi|91773977|ref|YP_566669.1| 264 VEIKTGCEVHKIFTDKGKAWGVE--ADNT---YSAdLVIYTGFATSlpFLvE---DLpasyKEQLdGIVHSKSLTLwLGLD 336
                                   99*********966669*****3..3232...33446666677776553322...44222222221223444444411333 PP

                                   THSTGSGCSEEEEE.....EEETTTTEEEEEE........TTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGG CS
                           DAO 232 eklvspaailpvpe.....tdddgrgvyvtpr........kdgrvlvGgtadeesgdddpevdeedidellealrklfPql 299
                                   + +        +++     +   g+ + ++p+        ++g+ lvG     ++ d+    +++di   +e + + +P++
  gi|91773977|ref|YP_566669.1| 337 RMM-------DEFKyvgseIWFKGTPYWAMPTsnydpslaPKGKQLVGFA---FFMDEG-NDESRDIKNAYETIFRAIPNI 406
                                   311.......1111233333344444455554666666665677777764...354455.777888888888888888886 PP

                                   CG.EE..EEEEEEEE.....ETTSSEEEEEEETEEEEEEE CS
                           DAO 300 gd.vl..rkwaGlrp.....lpdglpligetpgvkglyla 331
                                   +d ++  ++++ + p     + +g +   +tp vkgly+a
  gi|91773977|ref|YP_566669.1| 407 EDrIEmkHQQV-IIPekaavTLNGKFADIRTP-VKGLYVA 444
                                   44355324555.88865432246666666666.8888887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.8   6.8e-12   7.2e-09       1      37 [.       5      41 ..       5      49 .. 0.94
   2 ?   -3.7   0.0       4.3   4.6e+03     141     180 ..     250     288 ..     210     294 .. 0.58
   3 ?   -0.1   0.0      0.37   3.9e+02     389     404 ..     435     450 ..     424     459 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 6.8e-12
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                  DviV+G+G+ GL AAl+++++G+kv+v+ek +++gg+
  gi|91773977|ref|YP_566669.1|  5 DVIVVGAGVTGLLAALTLSKHGKKVLVLEKQDVVGGN 41
                                  9*********************************995 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.3
                                   HHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEE CS
                 FAD_binding_2 141 hallarlvesarkagvdfqerteadeLivedgrvtGavve 180
                                   + ll + + s+    v++ + +e+ ++ +++g++ G+++ 
  gi|91773977|ref|YP_566669.1| 250 KSLLNAILYSL-PSTVEIKTGCEVHKIFTDKGKAWGVEAD 288
                                   33333333333.2336888888888888888888777765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.37
                                   EESSBTEEE-STCEES CS
                 FAD_binding_2 389 gqpipGLYAaGevaag 404
                                    +p++GLY aG ++  
  gi|91773977|ref|YP_566669.1| 435 RTPVKGLYVAGTDTDK 450
                                   56*********99944 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.8e-11   1.9e-08       1      60 [.       5      67 ..       5     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.8e-11
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv...atdignkaeeqvvtgia 60
                                  Dv+VvG+g+ G+ AA++  ++G+kvl++e+++v+GG+  s  v   + d+g++a +++++g  
  gi|91773977|ref|YP_566669.1|  5 DVIVVGAGVTGLLAALTLSKHGKKVLVLEKQDVVGGNCNSYSVdgyQVDTGPHAITHLAEGPL 67
                                  9************************************87765522255555553334444444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.2   3.1e-09   3.3e-06       1      36 [.       4      39 ..       4      43 .. 0.94
   2 ?   -1.3   0.0      0.63   6.7e+02     261     288 ..     103     130 ..      95     202 .. 0.73
   3 ?    1.4   0.0       0.1   1.1e+02     122     163 ..     262     300 ..     232     308 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.1e-09
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  +dviv+G+G  Gl+aA++++k+gk+Vl+lek++ +g
  gi|91773977|ref|YP_566669.1|  4 YDVIVVGAGVTGLLAALTLSKHGKKVLVLEKQDVVG 39
                                  59*****************************98776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.63
                                   T--EEEECSTTS-...HHHHHHHHHHHT CS
                   HI0933_like 261 eetleidllPdldaeelkaalekekeke 288
                                   +e ++ d++P+ld+ ++++a++k+ +  
  gi|91773977|ref|YP_566669.1| 103 KEFVTFDVFPKLDRLAITQAITKSLTMA 130
                                   5678888888888888888888776544 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.1
                                   HT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 122 agvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   + v++++ +ev+++ ++++++  v++  +++++ad + + tG
  gi|91773977|ref|YP_566669.1| 262 STVEIKTGCEVHKIFTDKGKAWGVEA--DNTYSADLV-IYTG 300
                                   579***********999999999998..556666555.5445 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.7   2.6e-09   2.7e-06       2      34 ..       4      36 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.6e-09
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  +dV++VGaG +Gl++al Ls++G +v+++ek++
  gi|91773977|ref|YP_566669.1|  4 YDVIVVGAGVTGLLAALTLSKHGKKVLVLEKQD 36
                                  79****************************986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.1e-08   3.3e-05       1      44 [.       4      46 ..       4     106 .. 0.81
   2 ?   -0.2   0.0      0.43   4.5e+02     198     233 ..     264     298 ..     250     317 .. 0.77
   3 ?   -2.3   0.0         2   2.1e+03     263     287 ..     433     456 ..     408     461 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.1e-08
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllsk 44
                                  +dv+v+G+G+ Gl aaltl+++g kv+++ +++ +++g c  ++
  gi|91773977|ref|YP_566669.1|  4 YDVIVVGAGVTGLLAALTLSKHGKKVLVL-EKQDVVGGNCNSYS 46
                                  69***************************.77777787776554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.43
                                   EEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 198 vevklgtsvkeidgngekle.vvledgeeidadlvvv 233
                                   ve+k+g++v++i  ++   +    e  +++ adlv++
  gi|91773977|ref|YP_566669.1| 264 VEIKTGCEVHKIFTDKG--KaWGVEADNTYSADLVIY 298
                                   89999999999998888..333444444578888875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                                   TSBESSTTEEE-GGGCTECCSS--H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 263 flrtnvpgiyaiGDvaggkggpela 287
                                     rt v+g+y++G  + +k+++  +
  gi|91773977|ref|YP_566669.1| 433 DIRTPVKGLYVAGTDT-DKRSMGVT 456
                                   4589999***999655.45554444 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   1.1e-08   1.1e-05       3      47 ..       2      46 ..       1      58 [. 0.92

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.1e-08
                                  XEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE- CS
                           GDI  3 eeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesaslt 47
                                  ++ydviv+G+G++  + +  ls +gkkvl+l+++d  Gg++ s +
  gi|91773977|ref|YP_566669.1|  2 DKYDVIVVGAGVTGLLAALTLSKHGKKVLVLEKQDVVGGNCNSYS 46
                                  58************999999*******************999876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   2.8e-08   2.9e-05      18      56 ..       4      41 ..       1      45 [. 0.92
   2 ?   -3.9   0.0         6   6.3e+03     209     222 ..     435     448 ..     413     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.8e-08
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                   Dv++vGaG +GL aa +l+k+ + kv++le++  +GG 
  gi|91773977|ref|YP_566669.1|  4 YDVIVVGAGVTGLLAALTLSKH-GKKVLVLEKQDVVGGN 41
                                  6*********************.*********9999985 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6
                                   CEEETTEEE-THHH CS
                          Thi4 209 revvpnlyvaGmev 222
                                   r  v++lyvaG ++
  gi|91773977|ref|YP_566669.1| 435 RTPVKGLYVAGTDT 448
                                   56689999999765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.9e-06     0.002       1      33 [.       7      38 ..       7      54 .. 0.89
   2 ?    1.7   0.0      0.12   1.2e+02     225     276 ..     262     310 ..     235     327 .. 0.66
   3 ?   -2.1   0.0       1.8   1.8e+03     292     305 .]     432     445 ..     410     445 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                  i++GaG  Gl aa++l k+g  ++l+lEk+ ++
  gi|91773977|ref|YP_566669.1|  7 IVVGAGVTGLLAALTLSKHGK-KVLVLEKQDVV 38
                                  89******************9.7*******665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                   Pyr_redox_3 225 ekikvlfnaevkeikek.eeeykvktedgkkvevkddvvlatGykpdlsflkk 276
                                   +++++ +  ev++i ++  + + v++++    + + d v+ tG+  +l fl +
  gi|91773977|ref|YP_566669.1| 262 STVEIKTGCEVHKIFTDkGKAWGVEADN----TYSADLVIYTGFATSLPFLVE 310
                                   4567777777777754404444555555....345788999999999999876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.8
                   Pyr_redox_3 292 eteetnvpglflaG 305
                                   ++  t v+gl++aG
  gi|91773977|ref|YP_566669.1| 432 ADIRTPVKGLYVAG 445
                                   577899******99 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   5.5e-07   0.00058       1      41 [.       5      43 ..       5      73 .. 0.79
   2 ?    0.9   0.0      0.18   1.9e+02     189     249 ..     140     211 ..     119     225 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.5e-07
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSS CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCn 41
                                  dviV+G+G  G+ AAl++++ G kvl + +k d ++   Cn
  gi|91773977|ref|YP_566669.1|  5 DVIVVGAGVTGLLAALTLSKHGKKVLVL-EKQDVVGGN-CN 43
                                  8************************988.666666655.44 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                                   EEEEEE--EEEGGGS-TTTSEEE---....SS-B-.........SSSSSSSTCG----EEEEE-.-HHHHHHHHC CS
                          GIDA 189 rlktgtppridkesidfskleeqsgd....kegee.........fsylnkplnkeqvecfltat.neathkiike 249
                                   + +++ p+ ++k++ df ++++   +    k   e          s++ +++++eq+e+++++  +++t++i+++
  gi|91773977|ref|YP_566669.1| 140 SVYDSLPANLSKDTYDFANAISYFLSgrcmK---EtsaqrvlagSSFVRDSVTQEQFEEIIKQEsTPRTESILQS 211
                                   5667777777777777776544221110111...11223444448999999999999988876515555555554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.4   3.1e-07   0.00033       2      36 ..       6      40 ..       5      47 .. 0.91
   2 ?   -2.4   0.0       7.2   7.6e+03      10      23 ..     268     281 ..     263     287 .. 0.54

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.1e-07
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                  v+vvG+G++gl +A +l+++gkkV v+e +d +  
  gi|91773977|ref|YP_566669.1|  6 VIVVGAGVTGLLAALTLSKHGKKVLVLEKQDVVGG 40
                                  89***************************998875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.2
                                   HHHHHHHHHHHTTS CS
                     Pyr_redox  10 iglElAgalaelgk 23 
                                   +g+E+ +++++ gk
  gi|91773977|ref|YP_566669.1| 268 TGCEVHKIFTDKGK 281
                                   34555555544443 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-05     0.013      30      69 ..       5      44 ..       1      97 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                   v+v+G+Gv Gl A+ t ++ g kV vl+++  +  + +s
  gi|91773977|ref|YP_566669.1|  5 DVIVVGAGVTGLLAALTLSKHGKKVLVLEKQDVVGGNCNS 44
                                  69***************************99887777666 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.7e-05     0.028       1      45 [.       5      46 ..       5      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWs 45
                                  Dv+v+GaG  gl+ A  l  +k g kv+++e  + +  ++n  ++s
  gi|91773977|ref|YP_566669.1|  5 DVIVVGAGVTGLLAALTL--SKHGKKVLVLEKQDVV--GGNCnSYS 46
                                  9*****************..**********887766..55544555 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002      0.21       4      61 ..       6      57 ..       3      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                                  EEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC---- CS
                          MCRA  4 aylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrggre 61
                                  + +vG+G+++L aA+ L ++    g+++ +le+++v+gg ++++  + +Gy + +g +
  gi|91773977|ref|YP_566669.1|  6 VIVVGAGVTGLLAALTLSKH----GKKVLVLEKQDVVGGNCNSY--SVDGYQVDTGPH 57
                                  689************99775....78**************9985..556888877755 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.7   0.00028       0.3       1      36 [.       5      37 ..       5      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00028
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseei 36
                                  ++++vG+G  G laA +l+k++k   +v+++e++++
  gi|91773977|ref|YP_566669.1|  5 DVIVVGAGVTGLLAALTLSKHGK---KVLVLEKQDV 37
                                  699*******************4...5999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3355.35
//
Query:       gi|91773978|ref|YP_566670.1|  [L=228]
Description: hypothetical protein Mbur_2044 [Methanococcoides burtonii DSM 6242]
Scores for 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-51  172.6   5.5    7.9e-51  172.4   5.5    1.0  1  PhoU_div  Protein of unknown function DUF47
     0.0036   17.7   1.4     0.0036   17.7   1.4    2.5  2  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.026   14.7   0.9      0.084   13.1   0.2    1.9  2  DUF1380   Protein of unknown function (DUF1380)
       0.11   11.6   0.2       0.13   11.4   0.2    1.1  1  G-alpha   G-protein alpha subunit


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.4   5.5   1.8e-54   7.9e-51       2     213 ..      10     226 ..       9     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 172.4 bits;  conditional E-value: 1.8e-54
                      PhoU_div   2 lflfgsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedlle 82 
                                   l +f++sp+k+l  h+ k +etv kl ++ +a+   +++ veel +ei+++E+eAD ik+ ir +l ++++lPv  edll+
  gi|91773978|ref|YP_566670.1|  10 LNVFAKSPFKPLCLHASKGVETVRKLDQAVNAYCI-NMPLVEELSHEIDNIEHEADIIKQTIRGQLSSSIMLPVNAEDLLN 89 
                                   679*******************************9.99******************************************* PP

                      PhoU_div  83 lveslDeildvlediamlvtlrkvefpeelkdeflallkktveaiealaevieeleklletalskk......diveeiesl 157
                                   +++ +D+i+dv++++a +++lr+ ++pe +kd++ +l   t++++e +++ +++l+ llet++sk+      ++v++ie++
  gi|91773978|ref|YP_566670.1|  90 FLKPQDSIADVAQEAAYMLSLRQCDMPEGIKDQLCQLSTETLKTVEIYEKLVDSLSELLETSFSKRdveetlALVPQIEEM 170
                                   ****************************************************************99*************** PP

                      PhoU_div 158 EdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisiill 213
                                   E+ +D++++kl+k+ + +e+  + ++v +l+e+++ ++ ++d+ e +adr++ +++
  gi|91773978|ref|YP_566670.1| 171 EHITDLIEKKLVKDIYAHEKELGAVGVFYLIELVRTIADIADKTEHAADRLRTMII 226
                                   ******************************************************98 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4     0.056   2.5e+02      31      72 ..      50      91 ..      27     108 .. 0.53
   2 !   17.7   1.4     8e-07    0.0036       9      88 ..     142     220 ..     133     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.056
                                  HHHHHHHHHHHHHHHHHHHHHH.HH.HGG-SH..HHHHHHHHHHHH CS
                          PhoU 31 ierddeidrlekeierslleal.ak.rqplae..dlrellsllria 72
                                   e+  eid++e+e +    + + ++ +++     + ++   ll+  
  gi|91773978|ref|YP_566670.1| 50 EELSHEIDNIEHEADII-KQTIrGQlSSSIMLpvNAED---LLNFL 91
                                  34466677776666333.22222332222222233333...44444 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 8e-07
                                   HHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   9 eemlddalealeekdtelarevierddeidrlekeierslleal.akrqplaedlrellsllriardlERigDhavniaer 88 
                                    +  +++ ++++++d+e   +++ + +e++ + ++ie++l++ + a++++l++    +++l++++r +  i+D  ++ a+r
  gi|91773978|ref|YP_566670.1| 142 DSLSELLETSFSKRDVEETLALVPQIEEMEHITDLIEKKLVKDIyAHEKELGA--VGVFYLIELVRTIADIADKTEHAADR 220
                                   4444556677**********************************999999988..34567888888888888887777765 PP

>> DUF1380  Protein of unknown function (DUF1380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.27   1.2e+03      61      98 ..      32      70 ..      22      77 .. 0.77
   2 ?   13.1   0.2   1.9e-05     0.084      29     101 ..     138     211 ..     118     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.27
                       DUF1380 61 eqrlesGissaav.melieqvkenrktvtvpadllatll 98
                                    +l++ + +  + m l+e+++++  ++  +ad++++ +
  gi|91773978|ref|YP_566670.1| 32 VRKLDQAVNAYCInMPLVEELSHEIDNIEHEADIIKQTI 70
                                  567888888865438899999999999999999888766 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.9e-05
                       DUF1380  29 pediealadgmeyslseqevravlarlddipeeqrlesGissaavmelieqvkenr.ktvtvpadllatllrta 101
                                   ++ +++l++ +e s+s+++v+  la + +i e +++ + i  ++v+++ ++ ke +   v   ++l+ t+   a
  gi|91773978|ref|YP_566670.1| 138 EKLVDSLSELLETSFSKRDVEETLALVPQIEEMEHITDLIEKKLVKDIYAHEKELGaVGVFYLIELVRTIADIA 211
                                   667899999***************************************99988863033444455555544444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.9e-05      0.13      59     154 ..      66     193 ..      30     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                                   CHHHHHHHHHHHHHHHHHHHHHTT........................................HHHC-SS-SCCCS-HCH CS
                       G-alpha  59 wraviqlnivrsiktilealesleselsesf.................................elqelkerldplkkvea 106
                                   +++ i+ ++ +si + ++a +         +                                 +l +l+ +  +  ++ +
  gi|91773978|ref|YP_566670.1|  66 IKQTIRGQLSSSIMLPVNAEDL--------LnflkpqdsiadvaqeaaymlslrqcdmpegikdQLCQLSTETLKTVEIYE 138
                                   4444444444444444444443........033333334566677777777778888888887766666666666677777 PP

                                   HHH.................HHCCHHC-HCHHHHHHHHCCSHHHHHHHCCGCCTT CS
                       G-alpha 107 sliaklssateee.......qeiefnpraevgedikaLwndpgiqelyerrnkik 154
                                   +l ++ls+  e +       ++  + p++e  e+i +L +++ ++ +y++++++ 
  gi|91773978|ref|YP_566670.1| 139 KLVDSLSELLETSfskrdveETLALVPQIEEMEHITDLIEKKLVKDIYAHEKELG 193
                                   777777777666665544444444555899999****************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1481.53
//
Query:       gi|91773979|ref|YP_566671.1|  [L=346]
Description: phosphate transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-99  331.6  37.5    1.6e-98  329.8  37.5    1.7  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.8  37.5  9.2e-103   1.6e-98       1     337 []      23     334 ..      23     334 .. 0.94

  Alignments for each domain:
  == domain 1  score: 329.8 bits;  conditional E-value: 9.2e-103
                          PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelf...dpselmlgmlaallgaavwll 78 
                                   iGanD ana++tsvgs+al+l+q +++a++fef+Gav++G++V++ti+kgiv ++ +   dp+ +++gmlaa+l+a++w +
  gi|91773979|ref|YP_566671.1|  23 IGANDLANAMGTSVGSGALSLKQVILVAGVFEFVGAVFFGKKVTSTIAKGIVPIDSIkllDPNLVAVGMLAAILAAGFWIT 103
                                   7***************************************************77755577********************* PP

                          PHO4  79 latvlglPvStthslvGaliGaalaa.....egg.eavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklkna 153
                                   +at+++lPvStths+vG+++G++l++       + + ++w  l+kiv swv+sP+lg+++a+++f++++ + l+       
  gi|91773979|ref|YP_566671.1| 104 FATFYNLPVSTTHSIVGSVLGFGLVSayqgiI-TySDINWIVLTKIVGSWVVSPILGAVLAYIIFTIIRLTLLQ------- 176
                                   *************************9885533.34899999******************************663....... PP

                          PHO4 154 lralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykask.evplw 233
                                                           ++++  ++ek f +lq+ +a++++fahG+nDvana+Gpl+a l +++  ++ ++p w
  gi|91773979|ref|YP_566671.1| 177 ------------------------KTDNPYNIEKKFVILQIGTACFIAFAHGSNDVANAVGPLYAGL-NALGFADlTIPAW 232
                                   ........................12567789999****************************8877.4444688899*** PP

                          PHO4 234 vlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresav 314
                                   vl++gg+++++Gl+++G+rvi+t+G+kit+ ltp+rGf+aela+a +v+l s+  lP+StTh+lvg+v+GvGla  + +av
  gi|91773979|ref|YP_566671.1| 233 VLMVGGIGMVIGLATWGYRVIETIGTKITE-LTPTRGFSAELATASVVVLHSYSSLPISTTHTLVGSVIGVGLAG-GLAAV 311
                                   *****************************5.********************************************.79*** PP

                          PHO4 315 nwklvrnivlaWvlTlpvsalls 337
                                   + +++++i+++W++T+p++a++s
  gi|91773979|ref|YP_566671.1| 312 DLSVIGKIAMSWIITVPIAAVTS 334
                                   ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2602.52
//
Query:       gi|91773980|ref|YP_566672.1|  [L=315]
Description: tetratricopeptide protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-28   96.7  11.0      0.012   15.6   0.0    9.1  9  TPR_2            Tetratricopeptide repeat
    1.3e-23   82.9   1.6    2.5e-06   27.5   0.1    5.8  5  TPR_9            Tetratricopeptide repeat
    1.2e-22   78.7  11.1      0.042   13.7   0.2    9.1  9  TPR_1            Tetratricopeptide repeat
    4.7e-21   75.1   6.6     0.0038   17.7   0.2    5.2  5  TPR_19           Tetratricopeptide repeat
    8.5e-20   69.3  14.3    0.00023   21.1   0.0    8.6  9  TPR_8            Tetratricopeptide repeat
    4.6e-17   62.4   0.3    0.00041   20.9   0.2    6.0  7  TPR_16           Tetratricopeptide repeat
    1.1e-14   54.4   0.3     0.0093   16.2   0.1    5.0  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    5.4e-14   51.7   9.7       0.26   12.2   0.0    7.9  9  TPR_14           Tetratricopeptide repeat
      6e-14   52.1  14.2    0.00044   20.5   0.1    6.9  6  TPR_12           Tetratricopeptide repeat
      2e-13   49.8   6.0      0.014   15.1   0.3    7.1  8  TPR_11           TPR repeat
    7.5e-13   47.9   0.0       0.14   12.6   0.0    6.8  7  TPR_17           Tetratricopeptide repeat
    8.6e-10   38.0   6.3      0.038   14.0   0.1    6.6  5  TPR_7            Tetratricopeptide repeat
    1.5e-09   37.4   4.4     0.0033   16.4   1.6    3.9  4  NARP1            NMDA receptor-regulated protein 1
      4e-06   27.1   4.4        9.9    7.1   0.0    6.8  7  TPR_6            Tetratricopeptide repeat
    0.00019   21.4   0.9       0.18   11.9   0.1    4.4  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00026   20.5   1.7    0.00026   20.5   1.7    2.3  4  SNAP             Soluble NSF attachment protein, SNAP
    0.00086   19.8   2.8        1.6    9.2   0.7    3.3  4  BTAD             Bacterial transcriptional activator domain
     0.0014   18.7   3.8        1.9    8.5   0.1    4.3  4  DUF3856          Domain of Unknown Function (DUF3856)
     0.0045   17.4   0.6        5.1    7.5   0.1    3.6  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0066   16.2   4.2      0.087   12.5   0.2    3.2  3  TPR_21           Tetratricopeptide repeat-like domain
     0.0066   16.0   0.6         16    5.1   0.0    4.8  4  HTH_Bact         Helix-turn-helix bacterial domain
     0.0068   15.8   5.3        5.1    6.4   0.2    4.2  3  TPR_MalT         MalT-like TPR region
  ------ inclusion threshold ------
      0.019   15.0   0.4        1.4    8.9   0.0    3.3  3  SRP_TPR_like     Putative TPR-like repeat
      0.041   12.4   0.1      0.063   11.7   0.1    1.3  1  Nic96            Nup93/Nic96
      0.052   12.6   0.1       0.13   11.2   0.0    1.6  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
      0.052   13.0   0.0       0.39   10.1   0.0    2.0  2  DUF1487          Protein of unknown function (DUF1487)
      0.055   12.2   0.0        0.1   11.3   0.0    1.4  1  COPI_C           Coatomer (COPI) alpha subunit C-terminus
      0.096   12.2   0.1         32    4.1   0.0    3.4  3  SHNi-TPR         SHNi-TPR
      0.097   12.4   0.3        8.6    6.0   0.0    2.4  2  YfiO             Outer membrane lipoprotein
       0.15   11.8   0.0       0.48   10.2   0.0    2.0  1  PPR_1            PPR repeat
        0.2   11.6   8.1         11    6.0   0.1    5.8  7  TPR_10           Tetratricopeptide repeat
        1.3    9.2   5.7         70    3.6   0.8    4.5  3  ANAPC5           Anaphase-promoting complex subunit 5


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 !    8.0   0.0    0.0063       3.5      12      33 ..      25      46 ..      22      47 .. 0.85
   2 ?    4.5   0.1     0.082        46       7      30 ..      54      77 ..      49      80 .. 0.83
   3 !    9.5   0.0    0.0021       1.2       2      34 .]      82     114 ..      81     114 .. 0.93
   4 !   15.6   0.0   2.2e-05     0.012       1      33 [.     115     147 ..     115     148 .. 0.96
   5 !   11.3   0.0   0.00053       0.3       3      32 ..     151     180 ..     150     182 .. 0.92
   6 !   13.4   0.1   0.00011     0.062       7      29 ..     189     211 ..     184     212 .. 0.89
   7 ?    6.2   0.2     0.023        13       7      31 ..     216     240 ..     210     243 .. 0.77
   8 !   14.4   0.4   5.5e-05     0.031       4      30 ..     247     273 ..     245     274 .. 0.93
   9 !   15.4   0.1   2.6e-05     0.014       3      34 .]     266     297 ..     265     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0063
                         TPR_2 12 yklgdyeeAleafekAleldPn 33
                                   +  ++++Ale  e+A++++P+
  gi|91773980|ref|YP_566672.1| 25 CRESHLDQALEVVEQAIKHAPD 46
                                  566689***************8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.082
                         TPR_2  7 lGlayyklgdyeeAleafekAlel 30
                                   ++++  l  y++Al+  ++Al+l
  gi|91773980|ref|YP_566672.1| 54 KARILTGLHLYDDALATTNEALAL 77
                                  6778888889************98 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0021
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +al   G++++ ++d+e Ale f    e++P++
  gi|91773980|ref|YP_566672.1|  82 DALKLKGNILAIKDDLEGALEIFTNITEIAPKD 114
                                   588899*************************86 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 2.2e-05
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                   ae ++  G +++++g+ +e +e fe +le+dP 
  gi|91773980|ref|YP_566672.1| 115 AESYFLKGGILAEMGRAQEGIEEFEHSLEIDPS 147
                                   789*****************************6 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00053
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                   ++y  G++++++ +y  A+  fek  el +
  gi|91773980|ref|YP_566672.1| 151 VWYSKGMLLLESERYGAAISTFEKTMELTE 180
                                   7***********************999976 PP

  == domain 6  score: 13.4 bits;  conditional E-value: 0.00011
                         TPR_2   7 lGlayyklgdyeeAleafekAle 29 
                                    G a++klg+ +eA+e+f  A e
  gi|91773980|ref|YP_566672.1| 189 TGIAHRKLGQAKEAIECFHSAAE 211
                                   699***************98876 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.023
                         TPR_2   7 lGlayyklgdyeeAleafekAleld 31 
                                    +l+ ++   ye+Al a e Aleld
  gi|91773980|ref|YP_566672.1| 216 KALVSRNTEPYEKALGAIENALELD 240
                                   55555666669************98 PP

  == domain 8  score: 14.4 bits;  conditional E-value: 5.5e-05
                         TPR_2   4 lynlGlayyklgdyeeAleafekAlel 30 
                                   +  +G+++yklg+ +eA++ +  A el
  gi|91773980|ref|YP_566672.1| 247 WRTRGKLLYKLGHKQEAKAILSNAAEL 273
                                   899****************99999998 PP

  == domain 9  score: 15.4 bits;  conditional E-value: 2.6e-05
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +l n ++++ + ++y++A++ ++  +eldP++
  gi|91773980|ref|YP_566672.1| 266 ILSNAAELCVQEDNYNDAIKTYDMLIELDPED 297
                                   578999************************86 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2    0.0017      0.96       7      51 ..      26      70 ..      22      87 .. 0.74
   2 !   24.4   0.0   4.3e-08   2.4e-05       4      61 ..      90     147 ..      88     151 .. 0.93
   3 ?    7.2   0.0      0.01       5.7       4      57 ..     158     211 ..     155     214 .. 0.88
   4 !   27.5   0.1   4.5e-09   2.5e-06       3      59 ..     217     274 ..     215     277 .. 0.91
   5 !    8.1   0.1    0.0053         3       6      28 ..     275     297 ..     270     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                         TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAlad 51
                                  re + ++al+vve  +  aPd+ + ++  +++l  l  +  Ala 
  gi|91773980|ref|YP_566672.1| 26 RESHLDQALEVVEQAIKHAPDPTHALLIKARILTGLHLYDDALAT 70
                                  788888888888888888888888888888888777777777665 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 4.3e-08
                         TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   i++ ++d e al++   +  +aP+d+e ++  G +la++G+ +++++++e+ l+++p+
  gi|91773980|ref|YP_566672.1|  90 ILAIKDDLEGALEIFTNITEIAPKDAESYFLKGGILAEMGRAQEGIEEFEHSLEIDPS 147
                                   666689*************************************************995 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.01
                         TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                   +++++e++ +a+ + e  + l  d +e ++  G+++ +lG+ ++A++++  +++
  gi|91773980|ref|YP_566672.1| 158 LLLESERYGAAISTFEKTMELTEDFVEPIFFTGIAHRKLGQAKEAIECFHSAAE 211
                                   46889999999999999999999999999999*************999998876 PP

  == domain 4  score: 27.5 bits;  conditional E-value: 4.5e-09
                         TPR_9   3 aia.ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   a+   + e +e+al ++e  l l+   ++ +r RG ll++lG+ ++A a L  +++l+
  gi|91773980|ref|YP_566672.1| 217 ALVsRNTEPYEKALGAIENALELDVANIDMWRTRGKLLYKLGHKQEAKAILSNAAELC 274
                                   5554677889******************************************999998 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0053
                         TPR_9   6 ireedweralavverllllaPdd 28 
                                    +e+++  a++++++l+ l+P+d
  gi|91773980|ref|YP_566672.1| 275 VQEDNYNDAIKTYDMLIELDPED 297
                                   68888999999999999999987 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.058        33      17      33 ..      30      46 ..      23      47 .. 0.90
   2 ?    4.2   0.1     0.076        42       7      30 ..      54      77 ..      50      80 .. 0.84
   3 !   10.3   0.0   0.00088      0.49       2      34 .]      82     114 ..      81     114 .. 0.95
   4 !   10.4   0.0   0.00081      0.45       1      33 [.     115     147 ..     115     148 .. 0.97
   5 !   11.1   0.0    0.0005      0.28       3      30 ..     151     178 ..     151     182 .. 0.91
   6 !   12.9   0.0   0.00013     0.074       8      29 ..     190     211 ..     189     214 .. 0.91
   7 ?    4.9   0.1     0.045        25      17      31 ..     226     240 ..     226     241 .. 0.96
   8 ?    6.0   0.3      0.02        11       3      30 ..     246     273 ..     244     274 .. 0.84
   9 !   13.7   0.2   7.6e-05     0.042       4      34 .]     267     297 ..     265     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.058
                                  HHHHHHHHHHHHHHSTT CS
                         TPR_1 17 ydeAleyyekALelnPn 33
                                  +d+Ale  e+A+++ P+
  gi|91773980|ref|YP_566672.1| 30 LDQALEVVEQAIKHAPD 46
                                  79**************8 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.076
                                  HHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1  7 lGnayfklgkydeAleyyekALel 30
                                  ++ ++  l  yd+Al+  ++AL l
  gi|91773980|ref|YP_566672.1| 54 KARILTGLHLYDDALATTNEALAL 77
                                  6777888999************98 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00088
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +al+ +Gn++  + +++ Ale +    e+ P++
  gi|91773980|ref|YP_566672.1|  82 DALKLKGNILAIKDDLEGALEIFTNITEIAPKD 114
                                   89***************************9986 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00081
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                   a++++ +G ++ ++g+ +e +e +e  Le++P+
  gi|91773980|ref|YP_566672.1| 115 AESYFLKGGILAEMGRAQEGIEEFEHSLEIDPS 147
                                   799*****************************7 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.0005
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                   ++y +G+++++ ++y  A+  +ek  el
  gi|91773980|ref|YP_566672.1| 151 VWYSKGMLLLESERYGAAISTFEKTMEL 178
                                   6**********************98776 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.00013
                                   HHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1   8 GnayfklgkydeAleyyekALe 29 
                                   G a++klg+ +eA+e++  A e
  gi|91773980|ref|YP_566672.1| 190 GIAHRKLGQAKEAIECFHSAAE 211
                                   89***************98866 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.045
                                   HHHHHHHHHHHHHHS CS
                         TPR_1  17 ydeAleyyekALeln 31 
                                   y++Al + e ALel+
  gi|91773980|ref|YP_566672.1| 226 YEKALGAIENALELD 240
                                   9************98 PP

  == domain 8  score: 6.0 bits;  conditional E-value: 0.02
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                    +  +G +++klg  +eA +  + A el
  gi|91773980|ref|YP_566672.1| 246 MWRTRGKLLYKLGHKQEAKAILSNAAEL 273
                                   57889*************9888777776 PP

  == domain 9  score: 13.7 bits;  conditional E-value: 7.6e-05
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   l n + ++ +  +y++A++ y+  +el+P++
  gi|91773980|ref|YP_566672.1| 267 LSNAAELCVQEDNYNDAIKTYDMLIELDPED 297
                                   66778889999******************86 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   2.7e-05     0.015       6      57 ..      29      80 ..      25      90 .. 0.87
   2 !   14.0   0.0   9.9e-05     0.056       5      57 ..      95     147 ..      91     155 .. 0.91
   3 !   13.2   0.0   0.00017     0.097       1      51 [.     159     209 ..     159     212 .. 0.94
   4 !   17.7   0.2   6.8e-06    0.0038       7      49 ..     226     268 ..     225     270 .. 0.96
   5 !   13.9   0.3   0.00011      0.06      31      65 ..     270     304 ..     267     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-05
                        TPR_19  6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                                   +++Al+  eqa++++p+   a+l  A++l  l  +d+A a+ +++++   d
  gi|91773980|ref|YP_566672.1| 29 HLDQALEVVEQAIKHAPDPTHALLIKARILTGLHLYDDALATTNEALALGED 80
                                  689*********************99****************9999887776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.9e-05
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                    d++ Al++++++ + +pk+ae   l   +l ++g+ +e ++  +  +e dp 
  gi|91773980|ref|YP_566672.1|  95 DDLEGALEIFTNITEIAPKDAESYFLKGGILAEMGRAQEGIEEFEHSLEIDPS 147
                                   699*************************************9999999888886 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00017
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                   ll++++y +A++ +e+ ++   +  e      +a+ +lgq +eA+++   +
  gi|91773980|ref|YP_566672.1| 159 LLESERYGAAISTFEKTMELTEDFVEPIFFTGIAHRKLGQAKEAIECFHSA 209
                                   799******************************************997665 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 6.8e-06
                        TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49 
                                   y+ Al + e+al+ d  n + +    ++l++lg+ +eA+a+L+
  gi|91773980|ref|YP_566672.1| 226 YEKALGAIENALELDVANIDMWRTRGKLLYKLGHKQEAKAILS 268
                                   789**************************************96 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 0.00011
                        TPR_19  31 LAeallalgqldeAealLdalpeedpddaryasLl 65 
                                    Ae++++  ++++A+++ d l e dp d+++++++
  gi|91773980|ref|YP_566672.1| 270 AAELCVQEDNYNDAIKTYDMLIELDPEDEDAKKAR 304
                                   69**************************9998665 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.95   5.3e+02      17      33 ..      30      46 ..      14      47 .. 0.86
   2 ?   -1.6   0.0       7.7   4.3e+03       3      28 ..      50      75 ..      48      77 .. 0.78
   3 ?    6.8   0.0     0.016       9.2       6      34 .]      86     114 ..      81     114 .. 0.92
   4 !   21.1   0.0   4.1e-07   0.00023       1      33 [.     115     147 ..     115     148 .. 0.97
   5 !   15.8   0.0     2e-05     0.011       2      32 ..     150     180 ..     149     182 .. 0.90
   6 !    7.6   0.0    0.0088       4.9      10      27 ..     192     209 ..     190     212 .. 0.83
   7 ?    3.6   0.0      0.16        92       1      31 [.     210     240 ..     210     242 .. 0.94
   8 !    7.9   0.3    0.0071         4       6      30 ..     249     273 ..     244     274 .. 0.85
   9 !    9.7   0.1    0.0019       1.1       5      34 .]     268     297 ..     265     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.95
                                  HHHHHHHHHHHHHHHHH CS
                         TPR_8 17 yeeAkeyyekaleldpd 33
                                  +++A e+ e+a++ +pd
  gi|91773980|ref|YP_566672.1| 30 LDQALEVVEQAIKHAPD 46
                                  799*********97776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.7
                                  HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8  3 ayynlgsiylklgdyeeAkeyyekal 28
                                  a++ +++i+  l  y+ A ++ ++al
  gi|91773980|ref|YP_566672.1| 50 ALLIKARILTGLHLYDDALATTNEAL 75
                                  67788999999988999988877776 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.016
                                   HHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   ++g+i+  + d+e A e +   +e++p++
  gi|91773980|ref|YP_566672.1|  86 LKGNILAIKDDLEGALEIFTNITEIAPKD 114
                                   68*************************86 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 4.1e-07
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ae+y+++g i+ ++g+ +e +e +e+ le+dp+
  gi|91773980|ref|YP_566672.1| 115 AESYFLKGGILAEMGRAQEGIEEFEHSLEIDPS 147
                                   79*****************************96 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 2e-05
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                   +++y +g+++l+ ++y +A++++ek  el +
  gi|91773980|ref|YP_566672.1| 150 HVWYSKGMLLLESERYGAAISTFEKTMELTE 180
                                   68***********************888766 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0088
                                   HHHHTT-HHHHHHHHHHH CS
                         TPR_8  10 iylklgdyeeAkeyyeka 27 
                                   +++klg+ +eA+e++  a
  gi|91773980|ref|YP_566672.1| 192 AHRKLGQAKEAIECFHSA 209
                                   789***********9655 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.16
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                   ae++ +++++ ++++ ye+A  ++e aleld
  gi|91773980|ref|YP_566672.1| 210 AEMWELKALVSRNTEPYEKALGAIENALELD 240
                                   789999**********************997 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0071
                                   HHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8   6 nlgsiylklgdyeeAkeyyekalel 30 
                                     g+++ klg ++eAk+ +  a el
  gi|91773980|ref|YP_566672.1| 249 TRGKLLYKLGHKQEAKAILSNAAEL 273
                                   5799*************99888776 PP

  == domain 9  score: 9.7 bits;  conditional E-value: 0.0019
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    n + ++ +  +y+ A+++y   +eldp++
  gi|91773980|ref|YP_566672.1| 268 SNAAELCVQEDNYNDAIKTYDMLIELDPED 297
                                   5789999*********************86 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   7.3e-07   0.00041      11      64 ..      28      78 ..      19      83 .. 0.90
   2 !   10.5   0.1    0.0013      0.74      13      67 ..      64     114 ..      62     115 .. 0.90
   3 !   13.4   0.0   0.00016     0.092      12      65 ..      96     146 ..      86     147 .. 0.90
   4 !   12.0   0.0   0.00044      0.25       3      58 ..     121     173 ..     119     181 .. 0.92
   5 ?    2.3   0.0      0.49   2.7e+02       4      27 ..     190     213 ..     189     223 .. 0.84
   6 ?    4.9   0.1     0.074        41      13      53 ..     226     263 ..     221     272 .. 0.90
   7 ?    7.5   0.0     0.011       6.3       9      44 ..     276     311 ..     267     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.3e-07
                        TPR_16 11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64
                                   + d+A+++ e+a+k +   Pd  +All +++++  +  +++A+a  ++al+ +
  gi|91773980|ref|YP_566672.1| 28 SHLDQALEVVEQAIKHA---PDPTHALLIKARILTGLHLYDDALATTNEALALG 78
                                  679**************...************************9999999654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                        TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   yddA+a  ++al+++    ++ +Al l+g++++ + +l++A++ +    + ap++
  gi|91773980|ref|YP_566672.1|  64 YDDALATTNEALALG----EDIDALKLKGNILAIKDDLEGALEIFTNITEIAPKD 114
                                   9**************....4899*******************9888777888876 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00016
                        TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                   d + A++ ++  ++ +   P +ae+++l+g ++++ gr +e ++ ++  l+ +p
  gi|91773980|ref|YP_566672.1|  96 DLEGALEIFTNITEIA---PKDAESYFLKGGILAEMGRAQEGIEEFEHSLEIDP 146
                                   7899************...************************98887777776 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00044
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyr 58 
                                   ++ ++++ g+ ++ ++ +e  l+ d   P   + ++ +g ++l+  r+ +A+  ++
  gi|91773980|ref|YP_566672.1| 121 KGGILAEMGRAQEGIEEFEHSLEID---PSIEHVWYSKGMLLLESERYGAAISTFE 173
                                   68999********************...************************6665 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.49
                        TPR_16   4 araalragdyddAaaaleaalkrd 27 
                                   + a++++g+  +A++ ++ a +++
  gi|91773980|ref|YP_566672.1| 190 GIAHRKLGQAKEAIECFHSAAEMW 213
                                   568899999999999999999888 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.074
                        TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                   y++A+ a e al++d    ++ +++  +g +++++g  +eA
  gi|91773980|ref|YP_566672.1| 226 YEKALGAIENALELD---VANIDMWRTRGKLLYKLGHKQEA 263
                                   899999*********...99999999999999999999988 PP

  == domain 7  score: 7.5 bits;  conditional E-value: 0.011
                        TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                   +  +y dA++ ++ ++++dp++ da  A+ +   aa
  gi|91773980|ref|YP_566672.1| 276 QEDNYNDAIKTYDMLIELDPEDEDAKKAREEIISAA 311
                                   4558********************999998776665 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 !   13.4   0.0   0.00013      0.07      32      78 ..      23      70 ..       8      74 .. 0.93
   2 !   12.7   0.0   0.00021      0.12       6      82 .]      98     175 ..      83     175 .. 0.92
   3 !    8.3   0.0    0.0046       2.6       3      49 ..     163     209 ..     161     213 .. 0.90
   4 !   16.2   0.1   1.7e-05    0.0093      28      81 ..     215     269 ..     207     270 .. 0.92
   5 ?    2.8   0.0      0.25   1.4e+02      62      80 ..     270     288 ..     269     290 .. 0.87
   6 ?    2.1   0.0      0.41   2.3e+02       3      25 ..     278     300 ..     276     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                  HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                        ANAPC3 32 clylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78
                                  +l++ +  ++A+e++++a k ++    +++++A+ l  L+ y++A+a+
  gi|91773980|ref|YP_566672.1| 23 SLCRESHLDQALEVVEQAiKHAPDPTHALLIKARILTGLHLYDDALAT 70
                                  58999999**********99999999*******************986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00021
                                   HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                        ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                   + A+ ++  + +  ++++e+ +l++  l ++g+ ++ +e ++ + +++++ + ++y ++  ll+ ++y  Ai+++ek+
  gi|91773980|ref|YP_566672.1|  98 EGALEIFTNITEIAPKDAESYFLKGGILAEMGRAQEGIEEFEHSlEIDPSIEHVWYSKGMLLLESERYGAAISTFEKT 175
                                   667777777788889************************************************************985 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0046
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka 49 
                                   ++y  Ai  +e+ ++   +  e +++ + ++ ++gq k+A+e +++a
  gi|91773980|ref|YP_566672.1| 163 ERYGAAISTFEKTMELTEDFVEPIFFTGIAHRKLGQAKEAIECFHSA 209
                                   68999*********988999999******************998876 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  28 llAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   l+Al+  +++ y++A+  +++a +l+  ++  + + ++ l+kL++ +eA a+L++
  gi|91773980|ref|YP_566672.1| 215 LKALVSRNTEPYEKALGAIENAlELDVANIDMWRTRGKLLYKLGHKQEAKAILSN 269
                                   46999999*****************************************999986 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.25
                                   HHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  62 fAqcllkLkkyeeAiaaLe 80 
                                   +A+ +++ ++y++Ai++++
  gi|91773980|ref|YP_566672.1| 270 AAELCVQEDNYNDAIKTYD 288
                                   6899***********9875 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.41
                                   T-HHHHHHHHHHHH.HHH--HHH CS
                        ANAPC3   3 nnyknAiflaerllaaetesped 25 
                                    ny++Ai  ++ l + ++e++++
  gi|91773980|ref|YP_566672.1| 278 DNYNDAIKTYDMLIELDPEDEDA 300
                                   7999******9999999998875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1    0.0015      0.86      15      43 ..      28      56 ..      21      57 .. 0.86
   2 ?    6.4   0.3     0.034        19       3      37 ..      50      84 ..      48      87 .. 0.87
   3 !    8.4   0.0    0.0075       4.2       3      40 ..      83     120 ..      81     123 .. 0.88
   4 ?    6.8   0.0     0.025        14       5      39 ..     119     153 ..     115     159 .. 0.86
   5 ?   -0.6   0.0         6   3.3e+03       3      26 ..     151     174 ..     149     182 .. 0.83
   6 ?    6.3   0.1     0.038        21       8      29 ..     190     211 ..     188     218 .. 0.88
   7 ?    3.4   0.1      0.31   1.8e+02      16      42 ..     225     251 ..     210     254 .. 0.77
   8 ?    5.2   0.0     0.085        48       2      31 ..     245     274 ..     244     277 .. 0.90
   9 !   12.2   0.0   0.00046      0.26       7      38 ..     270     301 ..     265     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0015
                        TPR_14 15 GdpdeAiallrralalaPddaeawlllaq 43
                                    +d+A+++ ++a+++aPd+  a+l  a+
  gi|91773980|ref|YP_566672.1| 28 SHLDQALEVVEQAIKHAPDPTHALLIKAR 56
                                  568****************9999887776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.034
                        TPR_14  3 allalaeallalGdpdeAiallrralalaPddaea 37
                                  all  a++l  l  +d+A+a  ++alal+ d +++
  gi|91773980|ref|YP_566672.1| 50 ALLIKARILTGLHLYDDALATTNEALALGEDIDAL 84
                                  678889999999***************99987665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0075
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                   al++ + +l+  +d+++A++++  + + aP+dae ++l
  gi|91773980|ref|YP_566672.1|  83 ALKLKGNILAIKDDLEGALEIFTNITEIAPKDAESYFL 120
                                   67778999999*********************997766 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.025
                        TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawl 39 
                                    + + +l++ G+ +e i+ ++  l+ +P+ + +w+
  gi|91773980|ref|YP_566672.1| 119 FLKGGILAEMGRAQEGIEEFEHSLEIDPSIEHVWY 153
                                   56678999********************9988885 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 6
                        TPR_14   3 allalaeallalGdpdeAiallrr 26 
                                   +++  + +ll+++++ +Ai  +++
  gi|91773980|ref|YP_566672.1| 151 VWYSKGMLLLESERYGAAISTFEK 174
                                   577888899999999999988875 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.038
                        TPR_14   8 aeallalGdpdeAiallrrala 29 
                                   + a++ lG+ +eAi++++ a +
  gi|91773980|ref|YP_566672.1| 190 GIAHRKLGQAKEAIECFHSAAE 211
                                   57999************99865 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.31
                        TPR_14  16 dpdeAiallrralalaPddaeawllla 42 
                                    +++A+ + + al+l+ ++ + w+  +
  gi|91773980|ref|YP_566672.1| 225 PYEKALGAIENALELDVANIDMWRTRG 251
                                   5799*************9999997665 PP

  == domain 8  score: 5.2 bits;  conditional E-value: 0.085
                        TPR_14   2 eallalaeallalGdpdeAiallrralala 31 
                                   ++++ ++++l+ lG  +eA a+l  a +l+
  gi|91773980|ref|YP_566672.1| 245 DMWRTRGKLLYKLGHKQEAKAILSNAAELC 274
                                   5799*******************9998876 PP

  == domain 9  score: 12.2 bits;  conditional E-value: 0.00046
                        TPR_14   7 laeallalGdpdeAiallrralalaPddaeaw 38 
                                   +ae++ + +++ +Ai+ ++ +++l+P+d++a 
  gi|91773980|ref|YP_566672.1| 270 AAELCVQEDNYNDAIKTYDMLIELDPEDEDAK 301
                                   689999**********************9986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.3    0.0029       1.6      24      74 ..      28      77 ..      12      81 .. 0.63
   2 !   14.5   0.0   5.6e-05     0.031       7      76 ..      85     146 ..      79     147 .. 0.79
   3 !   20.5   0.1   7.9e-07   0.00044       5      76 ..     117     180 ..     113     181 .. 0.90
   4 !   11.9   0.2   0.00037      0.21      10      34 ..     190     214 ..     188     218 .. 0.91
   5 ?    7.1   0.3     0.011       6.4       3      67 ..     210     266 ..     208     268 .. 0.73
   6 ?    6.9   0.1     0.014       7.9       5      32 ..     266     293 ..     262     304 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                        TPR_12 24 ellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                  ++l++ale+++++  ++ p+   +l   +r++  l  y++Al+  +eala+
  gi|91773980|ref|YP_566672.1| 28 SHLDQALEVVEQAI-KHAPDPTHALLIKARILTGLHLYDDALATTNEALAL 77
                                  45566666664442.344666666666666666666777888888887776 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.6e-05
                        TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                      +++l+   +++ Ale++    eia     p+    a++++  g ++ ++gr +e +e +e++l+i++
  gi|91773980|ref|YP_566672.1|  85 KLKGNILAIKDDLEGALEIFTNITEIA-----PK---DAESYFLKGGILAEMGRAQEGIEEFEHSLEIDP 146
                                   456777777777777777777777777.....65...699999999999999999999999999999975 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 7.9e-07
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                   ++   + +l+++gr +e +e +e++lei    +  +h     + +  g+l+++++ry +A++ +e+++++ e
  gi|91773980|ref|YP_566672.1| 117 SYFLKGGILAEMGRAQEGIEEFEHSLEID---PSIEH-----VWYSKGMLLLESERYGAAISTFEKTMELTE 180
                                   5556899**********************...77888.....778***********************9876 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00037
                        TPR_12  10 aavlrrlgrydeAlellekaleiar 34 
                                   + ++r+lg+  eA+e+++ a e+++
  gi|91773980|ref|YP_566672.1| 190 GIAHRKLGQAKEAIECFHSAAEMWE 214
                                   67899******************96 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.011
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                   a ++   a+v r  + y++Al   e ale+   +      + +   r+ g l+++lg+ +eA ++
  gi|91773980|ref|YP_566672.1| 210 AEMWELKALVSRNTEPYEKALGAIENALELD--V------ANIDMWRTRGKLLYKLGHKQEAKAI 266
                                   7788778888888888888888888888887..3......2466777777777777777777665 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.014
                        TPR_12   5 alnnlaavlrrlgrydeAlellekalei 32 
                                   +l+n a+++ +  +y +A++ ++  +e+
  gi|91773980|ref|YP_566672.1| 266 ILSNAAELCVQEDNYNDAIKTYDMLIEL 293
                                   5567777777777777777777766665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.6   8.9e+02      10      25 ..      30      45 ..      24      46 .. 0.80
   2 ?   -1.9   0.1       5.1   2.8e+03      10      23 ..      64      77 ..      64      80 .. 0.82
   3 !    9.5   0.0    0.0013      0.75       1      42 []      88     129 ..      88     129 .. 0.96
   4 ?    4.6   0.0     0.046        26       3      35 ..     124     156 ..     122     162 .. 0.85
   5 ?    1.4   0.0      0.47   2.6e+02       4      29 ..     159     184 ..     156     187 .. 0.86
   6 ?    4.6   0.0     0.047        26       3      20 ..     192     209 ..     190     212 .. 0.84
   7 !   12.3   0.0   0.00018       0.1      10      42 .]     226     258 ..     224     258 .. 0.95
   8 !   15.1   0.3   2.4e-05     0.014       4      30 ..     274     300 ..     271     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.6
                        TPR_11 10 yeeAieaYkkAlkldP 25
                                  +++A+e+ ++A+k  P
  gi|91773980|ref|YP_566672.1| 30 LDQALEVVEQAIKHAP 45
                                  7899999999998555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.1
                        TPR_11 10 yeeAieaYkkAlkl 23
                                  y++A++  ++Al+l
  gi|91773980|ref|YP_566672.1| 64 YDDALATTNEALAL 77
                                  88999998999987 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0013
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G+++  + ++e+A+e + +  ++ P++ae y+  G +++++G
  gi|91773980|ref|YP_566672.1|  88 GNILAIKDDLEGALEIFTNITEIAPKDAESYFLKGGILAEMG 129
                                   99********************************99999887 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.046
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                   ++ e G+  e ie+++  l++dP+   ++y  G
  gi|91773980|ref|YP_566672.1| 124 ILAEMGRAQEGIEEFEHSLEIDPSIEHVWYSKG 156
                                   788999999**************9998888877 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.47
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnae 29 
                                   + e  +y +Ai  ++k  +l++d++e
  gi|91773980|ref|YP_566672.1| 159 LLESERYGAAISTFEKTMELTEDFVE 184
                                   678899**********9999999876 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.047
                        TPR_11   3 ayyeqGkyeeAieaYkkA 20 
                                   a +++G+ +eAie++  A
  gi|91773980|ref|YP_566672.1| 192 AHRKLGQAKEAIECFHSA 209
                                   6799*********98777 PP

  == domain 7  score: 12.3 bits;  conditional E-value: 0.00018
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ye+A+ a ++Al+ld  n + +  +G+++yk+G
  gi|91773980|ref|YP_566672.1| 226 YEKALGAIENALELDVANIDMWRTRGKLLYKLG 258
                                   899999999**********************99 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 2.4e-05
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaea 30 
                                   +++  +y++Ai+ Y   ++ldP++ +a
  gi|91773980|ref|YP_566672.1| 274 CVQEDNYNDAIKTYDMLIELDPEDEDA 300
                                   678899*****************9987 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         2   1.1e+03       3      25 ..      38      60 ..      37      69 .. 0.70
   2 ?    0.2   0.0       2.2   1.2e+03      13      33 ..      81     101 ..      79     102 .. 0.84
   3 !   11.5   0.0   0.00055      0.31       2      31 ..     104     133 ..     103     136 .. 0.88
   4 !   12.6   0.0   0.00025      0.14       2      33 ..     138     169 ..     137     170 .. 0.94
   5 ?    2.2   0.0      0.53   2.9e+02      21      34 .]     191     204 ..     171     224 .. 0.65
   6 !    9.9   0.1    0.0018         1       3      33 ..     234     264 ..     232     265 .. 0.92
   7 ?   -0.4   0.0       3.5   1.9e+03       2      12 ..     287     297 ..     286     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2
                        TPR_17  3 lkaleldPnnadaynnLAelllk 25
                                  ++a+++ P+   a+  +A++l  
  gi|91773980|ref|YP_566672.1| 38 EQAIKHAPDPTHALLIKARILTG 60
                                  789***88877777777777765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.2
                        TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                    da+ +++++l+ + dl+ A+
  gi|91773980|ref|YP_566672.1|  81 IDALKLKGNILAIKDDLEGAL 101
                                   5788889*********99997 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00055
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                   +++  e+ P++a++y++++ +l++ G+ ++
  gi|91773980|ref|YP_566672.1| 104 FTNITEIAPKDAESYFLKGGILAEMGRAQE 133
                                   66778999******************9987 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00025
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   ++ +le+dP+   +++ ++ lll+  +++ A+
  gi|91773980|ref|YP_566672.1| 138 FEHSLEIDPSIEHVWYSKGMLLLESERYGAAI 169
                                   899*************************9997 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.53
                        TPR_17  21 elllknGdlmtArq 34 
                                    +++k+G+ ++A++
  gi|91773980|ref|YP_566672.1| 191 IAHRKLGQAKEAIE 204
                                   55666666666654 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.0018
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   ++aleld  n d +  +++ll+k+G +++A+
  gi|91773980|ref|YP_566672.1| 234 ENALELDVANIDMWRTRGKLLYKLGHKQEAK 264
                                   899999999********************98 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 3.5
                        TPR_17   2 ylkaleldPnn 12 
                                   y   +eldP +
  gi|91773980|ref|YP_566672.1| 287 YDMLIELDPED 297
                                   7789*****98 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.079        45      10      34 ..      25      49 ..      21      51 .. 0.79
   2 ?    0.5   0.0       1.4   8.1e+02       6      33 ..     122     149 ..     113     151 .. 0.68
   3 ?    4.2   0.0     0.096        54       6      31 ..     156     181 ..     151     182 .. 0.80
   4 !    9.7   0.2    0.0016      0.92       6      29 ..     190     213 ..     189     244 .. 0.87
   5 !   14.0   0.1   6.9e-05     0.038       2      35 ..     267     300 ..     266     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.079
                         TPR_7 10 srlGdyeeAielyeqsLaltkdped 34
                                  +r+ + ++A+e+ eq++  + dp++
  gi|91773980|ref|YP_566672.1| 25 CRESHLDQALEVVEQAIKHAPDPTH 49
                                  788999*********6666666665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.4
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                   + +  ++G+ +e ie +e sL+++ + e
  gi|91773980|ref|YP_566672.1| 122 GGILAEMGRAQEGIEEFEHSLEIDPSIE 149
                                   5566666666666788888888887766 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.096
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                   + l  +  +y  Ai+ +e+ ++lt+d
  gi|91773980|ref|YP_566672.1| 156 GMLLLESERYGAAISTFEKTMELTED 181
                                   55677888999********8888876 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0016
                         TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                   + ++++lG+ +eAie++  + +++
  gi|91773980|ref|YP_566672.1| 190 GIAHRKLGQAKEAIECFHSAAEMW 213
                                   679**************9965554 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 6.9e-05
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                   L+n a+l++++ +y +Ai+ y  +++l+ ++eda
  gi|91773980|ref|YP_566672.1| 267 LSNAAELCVQEDNYNDAIKTYDMLIELDPEDEDA 300
                                   799********************77888777775 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   7.1e-05      0.04     207     252 ..      29      74 ..      13      80 .. 0.82
   2 ?    4.8   0.0      0.02        11     207     256 ..      96     145 ..      89     152 .. 0.91
   3 ?    1.8   0.0      0.16        87     207     255 ..     164     212 ..     150     216 .. 0.79
   4 !   16.4   1.6   5.9e-06    0.0033       5      83 ..     211     294 ..     207     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                                   -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                   + ++Ale++++ai+h p  +   l+Karil      ++A ++ +ea
  gi|91773980|ref|YP_566672.1|  29 HLDQALEVVEQAIKHAPDPTHALLIKARILTGLHLYDDALATTNEA 74 
                                   4689*************************98766666666666666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                                   -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                         NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                   + e Ale+  +  e  p+  e y  K+ il  +G  ++ +e  e++ ++D
  gi|91773980|ref|YP_566672.1|  96 DLEGALEIFTNITEIAPKDAESYFLKGGILAEMGRAQEGIEEFEHSLEID 145
                                   567899999999999*****************************998888 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.16
                                   -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                         NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                   ++  A+++ +k +e t  +ve     +  +++ G+ k+A+e+  +a ++
  gi|91773980|ref|YP_566672.1| 164 RYGAAISTFEKTMELTEDFVEPIFFTGIAHRKLGQAKEAIECFHSAAEM 212
                                   4557888888888888888888888888888888888888888877665 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 5.9e-06
                                   HHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT... CS
                         NARP1   5 ellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak... 82 
                                   e+   k+ + ++++ +e+Al  +e++ +  v ++ +  t+++ll kLg+k+eA+a++++  e + ++ +Y +++++     
  gi|91773980|ref|YP_566672.1| 211 EMWELKALVSRNTEPYEKALGAIENALELDVANIDMWRTRGKLLYKLGHKQEAKAILSNAAELCVQEDNYNDAIKTYDmli 291
                                   6666678899999999********9999999999999********************999999999999988887766555 PP

                                   ... CS
                         NARP1  83 ..k 83 
                                     +
  gi|91773980|ref|YP_566672.1| 292 elD 294
                                   332 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       3.2   1.8e+03      15      32 ..      29      46 ..      22      47 .. 0.81
   2 ?    2.2   0.0      0.62   3.5e+02      14      32 ..      95     113 ..      64     114 .. 0.86
   3 ?   -1.5   0.0       9.6   5.4e+03       3      23 ..     118     138 ..     115     140 .. 0.55
   4 ?    0.1   0.0         3   1.7e+03       5      25 ..     154     174 ..     151     177 .. 0.80
   5 ?    6.0   0.0     0.038        21       7      25 ..     190     208 ..     187     211 .. 0.87
   6 ?    5.1   0.1     0.072        40       7      26 ..     251     270 ..     250     273 .. 0.86
   7 ?    7.1   0.0     0.018       9.9       7      32 ..     271     296 ..     269     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 3.2
                                  HHHHHHHHHHHHHHH-TT CS
                         TPR_6 15 dtdkAlealerlikeYPd 32
                                    d+Ale  e+ ik  Pd
  gi|91773980|ref|YP_566672.1| 29 HLDQALEVVEQAIKHAPD 46
                                  679999999999999997 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.62
                                   HHHHHHHHHHHHHHHH-TT CS
                         TPR_6  14 gdtdkAlealerlikeYPd 32 
                                   +d + Ale++ ++ +  P+
  gi|91773980|ref|YP_566672.1|  95 DDLEGALEIFTNITEIAPK 113
                                   5899********9999886 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 9.6
                                   HHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   3 lyklalsyrklgdtdkAleal 23 
                                   +++ +  + ++g++++ +e +
  gi|91773980|ref|YP_566672.1| 118 YFLKGGILAEMGRAQEGIEEF 138
                                   344444444557777777666 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 3
                                   HHHHHHHH.HHHHHHHHHHHHH CS
                         TPR_6   5 klalsyrk.lgdtdkAlealer 25 
                                     ++++++   ++ +A+ ++e+
  gi|91773980|ref|YP_566672.1| 154 SKGMLLLEsE-RYGAAISTFEK 174
                                   5688888856.999******97 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.038
                                   HHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealer 25 
                                   + ++rklg++ +A+e + +
  gi|91773980|ref|YP_566672.1| 190 GIAHRKLGQAKEAIECFHS 208
                                   889***99*******9976 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.072
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerl 26 
                                   +++++klg +++A+++l + 
  gi|91773980|ref|YP_566672.1| 251 GKLLYKLGHKQEAKAILSNA 270
                                   8999**99*******99765 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                   a++  + +++ +A+++++ li+  P+
  gi|91773980|ref|YP_566672.1| 271 AELCVQEDNYNDAIKTYDMLIELDPE 296
                                   667777789*************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 ?    1.0   0.0       0.8   4.5e+02      17      38 ..      30      51 ..      25      57 .. 0.80
   2 ?    1.6   0.0      0.51   2.9e+02       4      22 ..     186     204 ..     184     209 .. 0.83
   3 ?    0.3   0.0       1.4   7.6e+02      17      33 ..     226     242 ..     220     246 .. 0.85
   4 !   11.9   0.1   0.00032      0.18      16      47 ..     279     310 ..     274     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.8
                                  HHHHHHHHHHHHHHTTS-HHHH CS
                    Fis1_TPR_C 17 YseArryvdalLeiEPenrQaq 38
                                   ++A++ v++ +++ P+   a+
  gi|91773980|ref|YP_566672.1| 30 LDQALEVVEQAIKHAPDPTHAL 51
                                  579************9966665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.51
                                   HHHHHHHHHHHT-HHHHHH CS
                    Fis1_TPR_C   4 lYylAlGhyklgeYseArr 22 
                                   +++  ++h klg+ +eA +
  gi|91773980|ref|YP_566672.1| 186 IFFTGIAHRKLGQAKEAIE 204
                                   799*********9888765 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  17 YseArryvdalLeiEPe 33 
                                   Y++A+  ++  Le++  
  gi|91773980|ref|YP_566672.1| 226 YEKALGAIENALELDVA 242
                                   9***********98755 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00032
                                   -HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHH CS
                    Fis1_TPR_C  16 eYseArryvdalLeiEPenrQaqsLkeliedk 47 
                                   +Y++A +  d+l+e++Pe + a++ +e i ++
  gi|91773980|ref|YP_566672.1| 279 NYNDAIKTYDMLIELDPEDEDAKKAREEIISA 310
                                   9*********************9988887665 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       9.4   5.3e+03      86     102 ..      26      42 ..      11      44 .. 0.63
   2 ?   -2.2   0.0         4   2.2e+03     171     183 ..      97     109 ..      83     151 .. 0.56
   3 ?   -0.9   0.0       1.6   8.7e+02     163     180 ..     157     174 ..      97     183 .. 0.71
   4 !   20.5   1.7   4.7e-07   0.00026      30     134 ..     198     303 ..     172     312 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.4
                                   HHT-HHHHHHHHHHHHH CS
                          SNAP  86 kkvspeeAvealekAie 102
                                   ++++ ++A e++e+Ai+
  gi|91773980|ref|YP_566672.1|  26 RESHLDQALEVVEQAIK 42 
                                   44455666666666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4
                                   HHHHHHHHHHHHH CS
                          SNAP 171 yekAieiyekvak 183
                                   +e A+ei++++ +
  gi|91773980|ref|YP_566672.1|  97 LEGALEIFTNITE 109
                                   4455555544432 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                                   HHHHHTT-HHHHHHHHHH CS
                          SNAP 163 elsaelekyekAieiyek 180
                                   +l  e e+y +Ai  +ek
  gi|91773980|ref|YP_566672.1| 157 MLLLESERYGAAISTFEK 174
                                   444556666666666665 PP

  == domain 4  score: 20.5 bits;  conditional E-value: 4.7e-07
                                   HHHHHHHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHH.HHHH.HHHHT-HHHHHHHHHHHHHHHHHTT CS
                          SNAP  30 kaeeAadlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayv.eAak.cykkvspeeAvealekAieiytekg 108
                                   +a+eA +++ +AA+ + l+  +++  e ++ka  + e++ e d a   ++   +k  yk  +++eA + l++A+e+ ++++
  gi|91773980|ref|YP_566672.1| 198 QAKEAIECFHSAAEMWELKALVSRNTEPYEKALGAIENALELDVANIDMWrTRGKlLYKLGHKQEAKAILSNAAELCVQED 278
                                   344555555555555555555555555555555555554444433333330223313444455555555555555555555 PP

                                   -HHHHHHHHHHHHHHHHHTT--HHHH CS
                          SNAP 109 rfrraAklkkeiaelyekelgdlekA 134
                                   + + a k +  + el  ++ +d +kA
  gi|91773980|ref|YP_566672.1| 279 NYNDAIKTYDMLIELDPED-EDAKKA 303
                                   5555555555555555555.555555 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.3   5.2e+03      99      99 ..      49      49 ..      23      85 .. 0.57
   2 !    7.8   0.0    0.0074       4.1      71     125 ..     124     178 ..      92     185 .. 0.89
   3 !    9.2   0.7    0.0028       1.6      15      92 ..     192     274 ..     188     285 .. 0.74
   4 ?    2.6   0.1      0.31   1.7e+02      65      99 ..     267     301 ..     260     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.3
                                  H CS
                          BTAD 99 h 99
                                  h
  gi|91773980|ref|YP_566672.1| 49 H 49
                                  2 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0074
                                   HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                    ++++Gra+e ++e e  ++ +P  E  +      l  s+r ++A+ ++e++++l
  gi|91773980|ref|YP_566672.1| 124 ILAEMGRAQEGIEEFEHSLEIDPSIEHVWYSKGMLLLESERYGAAISTFEKTMEL 178
                                   67899************************9999999**************99986 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0028
                                   HHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT..STTHHHHHH...HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  15 aalaagdpeeaaelleaAlalwrGpaladlea..gewleaere...rleelrlealealaeaelrlGraeealaelealva 90 
                                   a  + g+ +ea+e++  A+++w+ +al   +   +e + +++e   +l+   +++ +++ +++ +lG+ +ea a l+++++
  gi|91773980|ref|YP_566672.1| 192 AHRKLGQAKEAIECFHSAAEMWELKALVSRNTepYEKALGAIEnalELDVANIDMWRTRGKLLYKLGHKQEAKAILSNAAE 272
                                   55667899***************99998766666555555544111566678899999*********88888888877766 PP

                                   HS CS
                          BTAD  91 eh 92 
                                   ++
  gi|91773980|ref|YP_566672.1| 273 LC 274
                                   54 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.31
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHH CS
                          BTAD  65 lealaeaelrlGraeealaelealvaehPlrErlh 99 
                                   l   ae+ ++   +++a+++++ l++++P +E++ 
  gi|91773980|ref|YP_566672.1| 267 LSNAAELCVQEDNYNDAIKTYDMLIELDPEDEDAK 301
                                   566677778888999*****************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 ?    1.9   0.0      0.37   2.1e+02      58      83 ..      49      76 ..      25      85 .. 0.82
   2 ?    0.4   0.0       1.1   6.2e+02     105     128 ..     120     143 ..     113     147 .. 0.84
   3 !    8.5   0.1    0.0035       1.9      99     131 ..     182     214 ..     160     223 .. 0.83
   4 ?    5.2   0.2     0.035        20      67     134 ..     229     298 ..     215     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.37
                                  HHHHHHH..HHHTT-HHHHHHHHHHHHH CS
                       DUF3856 58 haglsea..laklgrydealesadkalr 83
                                  ha l +a  l++l  yd+al ++++al 
  gi|91773980|ref|YP_566672.1| 49 HALLIKAriLTGLHLYDDALATTNEALA 76
                                  5555554226799999999999999985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 105 sravaleelGrkdealkafrmage 128
                                    ++  l+e+Gr +e +++f+ + e
  gi|91773980|ref|YP_566672.1| 120 LKGGILAEMGRAQEGIEEFEHSLE 143
                                   57778999********99998776 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0035
                                   HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                       DUF3856  99 WiaavfsravaleelGrkdealkafrmagemia 131
                                   ++  +f  + a  +lG+ +ea++ f+ a+em +
  gi|91773980|ref|YP_566672.1| 182 FVEPIFFTGIAHRKLGQAKEAIECFHSAAEMWE 214
                                   678899999**********************75 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.035
                                   HTT-HHHHHHHHHHHHHHHHHH--TTSTHH.HHHHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHHHH-- CS
                       DUF3856  67 klgrydealesadkalryfnrrGeleqdeG.klWiaavfsravale.elGrkdealkafrmagemiaerk 134
                                    lg  ++ale     +  +  rG+l    G k+  +a++s a+ l  +  ++++a+k++ m  e+  e +
  gi|91773980|ref|YP_566672.1| 229 ALGAIENALELDVANIDMWRTRGKLLYKLGhKQEAKAILSNAAELCvQEDNYNDAIKTYDMLIELDPEDE 298
                                   4566666666666666778889998766663778889999998885255788999999999999866655 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.47   2.6e+02      73     116 ..      18      61 ..      14      77 .. 0.84
   2 ?    2.7   0.0      0.28   1.6e+02      81     122 ..      93     134 ..      71     140 .. 0.87
   3 ?    0.4   0.1       1.4     8e+02      58     123 ..     198     264 ..     193     273 .. 0.78
   4 !    7.5   0.1    0.0091       5.1      70     112 ..     264     307 ..     261     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.47
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHH CS
               Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleql 116
                                   ++k+ + ++e  +  a+e++++++   p+ + a  +ka++l+ l
  gi|91773980|ref|YP_566672.1|  18 INKVMSLCRESHLDQALEVVEQAIKHAPDPTHALLIKARILTGL 61 
                                   66777778899999***************999999999998866 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.28
                                   HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
               Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                    ++d++ a+e+  ++ +  p++ae   lk  +l ++g+++e 
  gi|91773980|ref|YP_566672.1|  93 IKDDLEGALEIFTNITEIAPKDAESYFLKGGILAEMGRAQEG 134
                                   57899*********************************9985 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.4
                                   HHHHHHHHTTSHHHHHH.HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
               Alkyl_sulf_dimr  58 kakrlvelmGgaekvle.kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                   +ak+ +e++ +a+++ e ka  +++ + y+ a+  ++++++ d  n +  + + + l +lg+++e+ 
  gi|91773980|ref|YP_566672.1| 198 QAKEAIECFHSAAEMWElKALVSRNTEPYEKALGAIENALELDVANIDMWRTRGKLLYKLGHKQEAK 264
                                   5777888887777777623444556677999999999999999999999999999999999998864 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0091
                                   HHHHHHHHHHH.HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHH CS
               Alkyl_sulf_dimr  70 ekvlekakeal.kegdyrwaaellnhlvfadpenaeakelkada 112
                                   +++l++a e + +e++y+ a++  ++l++ dpe+++ak+++ ++
  gi|91773980|ref|YP_566672.1| 264 KAILSNAAELCvQEDNYNDAIKTYDMLIELDPEDEDAKKAREEI 307
                                   5666666666548999*******************999987665 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   0.00016     0.087      89     169 ..      27     104 ..      12     119 .. 0.90
   2 ?   -1.2   0.0       2.5   1.4e+03     151     174 ..     120     143 ..     114     147 .. 0.86
   3 ?    3.2   0.3      0.11        63     125     175 ..     222     273 ..     191     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                        TPR_21  89 agdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaY 169
                                   +  l++A +  e+++++a+d + + l++   ar+l     yd+Al+t +++ + + +  +  l+G+il+ +++l+ A + +
  gi|91773980|ref|YP_566672.1|  27 ESHLDQALEVVEQAIKHAPDPTHALLIK---ARILTGLHLYDDALATTNEALALGEDIDALKLKGNILAIKDDLEGALEIF 104
                                   67899****************9999999...568899999**********************************9997665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                        TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                   l+G il+++g+ +e  ++++++l+
  gi|91773980|ref|YP_566672.1| 120 LKGGILAEMGRAQEGIEEFEHSLE 143
                                   79***********99999998875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.11
                        TPR_21 125 aekkydeAlktLeakkeeafa.alvaelrGDilvaqgkldeAraaYqaAlaa 175
                                   +++ y++Al ++e++ e   a   +   rG +l++ g+++eA+a  ++A + 
  gi|91773980|ref|YP_566672.1| 222 NTEPYEKALGAIENALELDVAnIDMWRTRGKLLYKLGHKQEAKAILSNAAEL 273
                                   5566777777776665544330445678999999999999999988888765 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 ?    5.1   0.0     0.029        16       3      15 ..      31      43 ..      29      46 .. 0.90
   2 ?    0.1   0.0       1.1   6.1e+02       2      15 ..      64      77 ..      63      89 .. 0.83
   3 ?   -0.4   0.0       1.5   8.6e+02      29      48 ..     118     137 ..     118     138 .. 0.92
   4 ?    3.4   0.1       0.1        56       2      22 ..     226     246 ..     225     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.029
                                  HHHHHHHHHHHHH CS
                      HTH_Bact  3 eeaLeqvnkAiei 15
                                  ++aLe+v++Ai+ 
  gi|91773980|ref|YP_566672.1| 31 DQALEVVEQAIKH 43
                                  79*********85 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                  HHHHHHHHHHHHHH CS
                      HTH_Bact  2 YeeaLeqvnkAiei 15
                                  Y+ aL  +n A+++
  gi|91773980|ref|YP_566672.1| 64 YDDALATTNEALAL 77
                                  9*********9986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHTT--HHHHHH CS
                      HTH_Bact  29 yYqkgecleklgfseeeIke 48 
                                   y+ kg  l ++g ++e I+e
  gi|91773980|ref|YP_566672.1| 118 YFLKGGILAEMGRAQEGIEE 137
                                   8889**************98 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHHHHHHHHTTB- CS
                      HTH_Bact   2 YeeaLeqvnkAieiSirinsM 22 
                                   Ye+aL  ++ A+e+ + +  M
  gi|91773980|ref|YP_566672.1| 226 YEKALGAIENALELDVANIDM 246
                                   999999999999998877777 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.2    0.0092       5.1      90     139 ..      24      65 ..      16     115 .. 0.61
   2 ?    5.1   0.1     0.022        12     265     309 ..     195     239 ..     189     243 .. 0.92
   3 ?    3.4   0.1     0.072        40     126     179 ..     248     302 ..     240     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0092
                      TPR_MalT  90 lvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLe 139
                                   l    +L++Ale+ eqa+++a+++  +      +l  + a++l   +  +
  gi|91773980|ref|YP_566672.1|  24 LCRESHLDQALEVVEQAIKHAPDPTHA------LL--IKARILTGLHLYD 65 
                                   555668889999999999988775443......22..2244444444444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.022
                      TPR_MalT 265 rLlkaaeelgrvrslieiliLqalalqaqgreeeAlaaLeqALeL 309
                                   +L +a e+ +   s  e++ L al+   ++  e+Al a+e ALeL
  gi|91773980|ref|YP_566672.1| 195 KLGQAKEAIECFHSAAEMWELKALVSRNTEPYEKALGAIENALEL 239
                                   688888999999999****************************98 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.072
                      TPR_MalT 126 vlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdlee 179
                                   + +++lly  ++ +eA+  l ++ el+ q  + + a++ y +l+++    +d+++
  gi|91773980|ref|YP_566672.1| 248 RTRGKLLYKLGHKQEAKAILSNAAELCVQEdNYNDAIKTYDMLIELDPEDEDAKK 302
                                   6677888888888888888888888777773447777777777666555555555 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 ?    0.1   0.0       1.4     8e+02      22      46 ..      56      80 ..       8     111 .. 0.64
   2 ?    8.9   0.0    0.0026       1.4      19      97 ..     154     232 ..     134     246 .. 0.74
   3 ?    3.3   0.2      0.15        82      28      72 ..     224     271 ..     216     302 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                  SRP_TPR_like 22 valiklekyeeaLkllkkgsalsed 46
                                    l  l  y++aL  ++++ al ed
  gi|91773980|ref|YP_566672.1| 56 RILTGLHLYDDALATTNEALALGED 80
                                  3333444466666655555555444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0026
                  SRP_TPR_like  19 fkvvaliklekyeeaLkllkkgsalsedv...rfEkaYvlYklkkykkalkilkkveaeekvkvlksqvlYrlgsyekAYk 96 
                                   +k + l++ e+y  a++  +k+ +l+ed    +f    ++ kl + k+a + ++++ +   + +lk+ v    + yekA  
  gi|91773980|ref|YP_566672.1| 154 SKGMLLLESERYGAAISTFEKTMELTEDFvepIFFTGIAHRKLGQAKEAIECFHSAAE---MWELKALVSRNTEPYEKALG 231
                                   3788899**************9999998733357777788888888888887776655...57888888888899988865 PP

                  SRP_TPR_like  97 l 97 
                                    
  gi|91773980|ref|YP_566672.1| 232 A 232
                                   5 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                  SRP_TPR_like  28 ekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkve 72 
                                   e ye aL +++++      + d+   +   lYkl + ++a  il+++ 
  gi|91773980|ref|YP_566672.1| 224 EPYEKALGAIENALeldVANIDMWRTRGKLLYKLGHKQEAKAILSNAA 271
                                   667777777776653334456777778888899998888888887654 PP

>> Nic96  Nup93/Nic96
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011     0.063     370     445 ..     215     294 ..     169     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                   HHHHHHHH--.HHHHHEEE-TT....S-EEE-HHHHTGGGGT-SSSSHHHHHHHHHHHHHHHHCT-HHHHHHHHHHTT-HH CS
                         Nic96 370 lrelvletre.falLLGdirsd....GtripGlieerlkliklddeeeflkkiieqaAreaeekgrledAilLydlageyd 445
                                   l+ lv  + e +++ LG i++           + + r kl++   ++++ k+i+ +aA+ + ++ +++dAi+ yd+  e+d
  gi|91773980|ref|YP_566672.1| 215 LKALVSRNTEpYEKALGAIENAleldV-ANIDMWRTRGKLLYKLGHKQEAKAILSNAAELCVQEDNYNDAIKTYDMLIELD 294
                                   455555555557777777776534431.222233445566655567779**************************987765 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.13     164     273 ..      10     120 ..       2     135 .. 0.82
   2 ?   -2.0   0.0       2.4   1.3e+03     258     290 ..     200     232 ..     195     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                   --SSSSHHHHHHHHHHHHHT-HHHHHHHHHHHHTT-GG.GHHHHHHHHHHTT-HH..HHHHHHHHHH-SSS-HHHHHHHHH CS
                         ChAPs 164 ptlvnNyLvetllklvrltkrydralellekLkeeepe.vvillarvllladeEv..davkllneeleeeekdaelLllqa 241
                                   p     +L++ ++ l r + ++d+ale++e+ +++ p+   +ll++  +l+   +  da+ ++ne+l    +d + L+l+ 
  gi|91773980|ref|YP_566672.1|  10 PQELADFLINKVMSLCRES-HLDQALEVVEQAIKHAPDpTHALLIKARILTGLHLydDALATTNEAL-ALGEDIDALKLKG 88 
                                   6778889999999999986.689********999998734566666665555555449********9.78899******** PP

                                   HHHHHSS--HHHHHHHHHHHHH-TT-HHHHHH CS
                         ChAPs 242 efllskkkeelAlevakravksaPsefktWal 273
                                   + l  k++ e Ale+ ++ +++aP + + ++l
  gi|91773980|ref|YP_566672.1|  89 NILAIKDDLEGALEIFTNITEIAPKDAESYFL 120
                                   ************************99887765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                   HHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                         ChAPs 258 kravksaPsefktWalLvkvYikledienALlt 290
                                   k+a+++  s+ + W l + v  + e +e+AL +
  gi|91773980|ref|YP_566672.1| 200 KEAIECFHSAAEMWELKALVSRNTEPYEKALGA 232
                                   555555555555555544444444444444433 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.73   4.1e+02       6      29 ..      20      43 ..      17      60 .. 0.80
   2 ?   10.1   0.0    0.0007      0.39      88     140 ..     175     227 ..     133     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.73
                       DUF1487  6 rlmvifedgDlnsalealveslke 29
                                  ++m +++++ l++ale++ +++k+
  gi|91773980|ref|YP_566672.1| 20 KVMSLCRESHLDQALEVVEQAIKH 43
                                  6899************99998886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0007
                       DUF1487  88 ksesakakasPilVldvthsflgdkptgvvTlhtFrnakEvvkllakeslkfa 140
                                   ++e ++    Pi+ +++ h++lg+   ++  +h   ++ E+ +l+++++ +++
  gi|91773980|ref|YP_566672.1| 175 TMELTEDFVEPIFFTGIAHRKLGQAKEAIECFHSAAEMWELKALVSRNTEPYE 227
                                   4555555678*************************************998886 PP

>> COPI_C  Coatomer (COPI) alpha subunit C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018       0.1     283     329 ..     266     313 ..     258     315 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHHHHTBHHHHHHHHHHHHHH---HHHHHHHHH.HHHHHHH CS
                        COPI_C 283 aLrsAlnlffKlknfktaasfarrLLelgpkeevaqqark.vlqacek 329
                                    L +A +l+    n++ a +   +L+el+p++e a++ar+ +++a+ +
  gi|91773980|ref|YP_566672.1| 266 ILSNAAELCVQEDNYNDAIKTYDMLIELDPEDEDAKKAREeIISAATN 313
                                   4889**********************************9637776654 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.7   2.6e+03      21      30 ..     135     144 ..     133     144 .. 0.75
   2 ?    4.1   0.0     0.056        32      12      30 ..     160     178 ..     158     182 .. 0.85
   3 ?    3.7   0.0     0.078        44       8      23 ..     271     286 ..     271     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.7
                      SHNi-TPR  21 veDlrkaLeL 30 
                                   +e+++ +Le+
  gi|91773980|ref|YP_566672.1| 135 IEEFEHSLEI 144
                                   5788888876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.056
                      SHNi-TPR  12 lEnenFpqAveDlrkaLeL 30 
                                   lE+e++  A++ ++k  eL
  gi|91773980|ref|YP_566672.1| 160 LESERYGAAISTFEKTMEL 178
                                   8*********988876665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.078
                      SHNi-TPR   8 GEislEnenFpqAveD 23 
                                   +E+++  +n+++A++ 
  gi|91773980|ref|YP_566672.1| 271 AELCVQEDNYNDAIKT 286
                                   799**********985 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.015       8.6      61      96 ..     131     175 ..     125     213 .. 0.55
   2 ?    4.0   0.2     0.064        36      11      53 ..     270     312 ..     260     315 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHH-SSSTTHHHHHHHHHH............HHHHHHSHS CS
                          YfiO  61 alasaerFlrlyPthknvdyvlYlrgl............salaqarel 96 
                                   a++ +e+F +     ++++ v+Y +g+            s   ++++ 
  gi|91773980|ref|YP_566672.1| 131 AQEGIEEFEHSLEIDPSIEHVWYSKGMllleserygaaiS---TFEKT 175
                                   6666667777777777777777777765555555553332...22222 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.064
                                   HHHHHHHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHH CS
                          YfiO  11 kgqealqkgdyaeAikklealdsryPfspyaeqaqldliyAyy 53 
                                   +++  +q+++y++Aik  + l +  P  + a++a+ ++i A+ 
  gi|91773980|ref|YP_566672.1| 270 AAELCVQEDNYNDAIKTYDMLIELDPEDEDAKKAREEIISAAT 312
                                   4555689999999999999999999999999999999999875 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00087      0.48      16      32 ..      23      39 ..      21      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00087
                                  HHHHTS-HHHHHHHHHH CS
                         PPR_1 16 GlCkaGrvdeAfelfde 32
                                  +lC++ ++d A+e++++
  gi|91773980|ref|YP_566672.1| 23 SLCRESHLDQALEVVEQ 39
                                  8**************97 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.9   2.7e+03      25      35 ..      30      40 ..      21      46 .. 0.64
   2 ?   -0.2   0.0       1.8   9.9e+02      23      36 ..      62      75 ..      61      80 .. 0.83
   3 ?    2.1   0.0      0.35   1.9e+02      10      31 ..     123     144 ..     122     144 .. 0.90
   4 ?   -2.1   0.0       7.3   4.1e+03       9      32 ..     156     179 ..     156     181 .. 0.74
   5 ?    6.0   0.1      0.02        11       9      33 ..     190     214 ..     190     215 .. 0.96
   6 ?   -1.4   0.0       4.2   2.4e+03      24      37 ..     225     238 ..     223     241 .. 0.71
   7 ?    1.6   0.1      0.49   2.7e+02      10      31 ..     252     273 ..     250     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.9
                        TPR_10 25 leealairrrl 35
                                  l++al++ +++
  gi|91773980|ref|YP_566672.1| 30 LDQALEVVEQA 40
                                  45555554444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                        TPR_10 23 alleealairrrll 36
                                   l+++ala+  ++l
  gi|91773980|ref|YP_566672.1| 62 HLYDDALATTNEAL 75
                                  68999999998887 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.35
                        TPR_10  10 nalrqrgrydeAealleealai 31 
                                    +l ++gr +e  + +e++l+i
  gi|91773980|ref|YP_566672.1| 123 GILAEMGRAQEGIEEFEHSLEI 144
                                   6899***************997 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 7.3
                        TPR_10   9 analrqrgrydeAealleealair 32 
                                   +++l +  ry +A   +e+++++ 
  gi|91773980|ref|YP_566672.1| 156 GMLLLESERYGAAISTFEKTMELT 179
                                   677778888888888788877765 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.02
                        TPR_10   9 analrqrgrydeAealleealairr 33 
                                   ++a+r++g+ +eA + ++ a ++++
  gi|91773980|ref|YP_566672.1| 190 GIAHRKLGQAKEAIECFHSAAEMWE 214
                                   89********************997 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 4.2
                        TPR_10  24 lleealairrrllG 37 
                                   ++e+al + + +l+
  gi|91773980|ref|YP_566672.1| 225 PYEKALGAIENALE 238
                                   67888877777765 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.49
                        TPR_10  10 nalrqrgrydeAealleealai 31 
                                    +l+++g  +eA a+l  a ++
  gi|91773980|ref|YP_566672.1| 252 KLLYKLGHKQEAKAILSNAAEL 273
                                   5799*********998777666 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.2   1.1e+02      37      71 ..      10      44 ..       1      49 [. 0.84
   2 ?    0.2   0.0       1.4   7.9e+02      43      70 ..      50      77 ..      46      82 .. 0.87
   3 ?    3.6   0.8      0.13        70      49      71 ..     252     274 ..     170     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                        ANAPC5 37 kksyqyalLnlaslhadfghneeAvkaleeairlA 71
                                   +++  +l+n ++  ++ +h ++A++ +e ai+ A
  gi|91773980|ref|YP_566672.1| 10 PQELADFLINKVMSLCRESHLDQALEVVEQAIKHA 44
                                  4677888999**********************977 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.4
                        ANAPC5 43 alLnlaslhadfghneeAvkaleeairl 70
                                  alL  a++ + ++ +++A+++ +ea +l
  gi|91773980|ref|YP_566672.1| 50 ALLIKARILTGLHLYDDALATTNEALAL 77
                                  89999999999999*******9999876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.13
                        ANAPC5  49 slhadfghneeAvkaleeairlA 71 
                                    l +++gh++eA + l++a +l 
  gi|91773980|ref|YP_566672.1| 252 KLLYKLGHKQEAKAILSNAAELC 274
                                   56788899999999999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 1794.66
//
Query:       gi|91773981|ref|YP_566673.1|  [L=406]
Description: hypothetical protein Mbur_2047 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-106  355.2   0.0     4e-106  354.8   0.0    1.2  1  Nre_N          Archaeal Nre, N-terminal
    9.8e-41  138.1   0.1    1.7e-40  137.4   0.1    1.4  1  Nre_C          Archaeal Nre, C-terminal
  ------ inclusion threshold ------
       0.15   12.4   0.0       0.28   11.5   0.0    1.4  1  Peptidase_C21  Tymovirus endopeptidase


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 !  354.8   0.0  6.7e-110    4e-106       1     270 []      14     285 ..      14     285 .. 0.99

  Alignments for each domain:
  == domain 1  score: 354.8 bits;  conditional E-value: 6.7e-110
                         Nre_N   1 Lcglkkcpileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppveg..dasvldspekwlglslediik 78 
                                   Lcg++ cpilek+r++ek++++i s+ +++G+spP+vfVGrygYP+V++gp++pp+++  da  l++p++wl+++++dii+
  gi|91773981|ref|YP_566673.1|  14 LCGRPLCPILEKFRSAEKTTTSIsSDGSIFGASPPAVFVGRYGYPQVKAGPMIPPQVDakDAMALEDPKHWLSMDIQDIIS 94 
                                   8*******************9998999*****************************9999********************* PP

                         Nre_N  79 lrlslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkv 158
                                    r++lvr++++++vk+a+ +dklle+ qelals++p+d+e++++k+ +++lkfd+vl+P+Gps++++++++aenpkvp+kv
  gi|91773981|ref|YP_566673.1|  95 ARCQLVRANTTIDVKNANrPDKLLEKSQELALSKSPIDTEAWFTKPLQQDLKFDSVLTPMGPSGTMKDFDIAENPKVPKKV 175
                                   *****************99************************************************************** PP

                         Nre_N 159 eklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfsg 239
                                   ++l +Dtd+ A++av+eL++ ++ +++i+rlLS+GlLG+  +r+lVPTrW+ITA+dd+vgk++++++ dlp i+e+ vfsg
  gi|91773981|ref|YP_566673.1| 176 DHLAYDTDALAKDAVCELFKGDIPTEHITRLLSIGLLGQ--ERKLVPTRWAITATDDMVGKDITDRVIDLPLISEISVFSG 254
                                   **************************************9..**************************************** PP

                         Nre_N 240 eylgNrflviLaPgkwsfelvEawapgslwn 270
                                    ++gN+f ++++P+++s+el+E+w+++s+w+
  gi|91773981|ref|YP_566673.1| 255 GCFGNYFEILMTPRRYSYELLEIWMKSSVWS 285
                                   ******************************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 !  137.4   0.1   2.8e-44   1.7e-40       1     110 []     296     405 ..     296     405 .. 0.99

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 2.8e-44
                         Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevs 81 
                                   e+++g+k+ys++aG+Yyaar+a+le+Leki+rqa+v+++reitpeYwaP+GvW+vRea+r+al++ p++fe++eeal+ ++
  gi|91773981|ref|YP_566673.1| 296 EDINGKKGYSNLAGGYYAARIAALEHLEKIQRQASVFMIREITPEYWAPLGVWVVREAARNALSSIPRTFETIEEALDDMA 376
                                   6789***************************************************************************** PP

                         Nre_C  82 eklklplkkllkkskllkelkkqktLddF 110
                                   +++++p+k++++k k+l++++ q+tLd+F
  gi|91773981|ref|YP_566673.1| 377 TRVRTPSKQWKAKAKMLSDIRFQRTLDSF 405
                                   ***************************99 PP

>> Peptidase_C21  Tymovirus endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.7e-05      0.28      34     103 ..     118     185 ..     106     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                                   TSSHHHHHH---HHHHHHHH.HHHTEEEEEEETTEEEEES-SS-SEEEEEEEE-SSS....-EEEESS--- CS
                 Peptidase_C21  34 lsneevsdlGlstehltala.flyqflvtlrsdelvilfGlldaikaieithttgvPpatvshfalskrll 103
                                   l  e+ ++l ls   + + a f+   +  l+ d      G++ ++k ++i+  + vP   v h+a     l
  gi|91773981|ref|YP_566673.1| 118 L--EKSQELALSKSPIDTEAwFTKPLQQDLKFDSVLTPMGPSGTMKDFDIAENPKVP-KKVDHLAYDTDAL 185
                                   4..77888999988886655367789999****************************.999**99876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2954.11
//
Query:       gi|91773982|ref|YP_566674.1|  [L=119]
Description: hypothetical protein Mbur_2048 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-05   24.2   0.0      4e-05   23.6   0.0    1.3  1  HTH_3           Helix-turn-helix
    0.00036   20.0   0.2    0.00067   19.1   0.0    1.5  2  Sigma70_r4      Sigma-70, region 4
    0.00046   19.7   0.0    0.00085   18.8   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00099   19.5   0.0     0.0016   18.8   0.0    1.3  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.001   19.3   0.1     0.0024   18.1   0.1    1.6  1  KORA            TrfB plasmid transcriptional repressor
     0.0039   17.1   0.0     0.0062   16.5   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0068   16.7   0.1     0.0098   16.2   0.1    1.2  1  HTH_31          Helix-turn-helix domain
     0.0084   16.3   0.0      0.016   15.4   0.0    1.5  1  HTH_17          Helix-turn-helix domain
     0.0091   15.9   0.1      0.015   15.2   0.1    1.3  1  MarR_2          MarR family
     0.0092   15.6   0.1      0.017   14.8   0.1    1.4  1  Sigma70_r4_2    Sigma-70, region 4
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.063   13.1   0.0    1.8  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.021   15.3   0.0      0.028   14.9   0.0    1.2  1  HTH_40          Helix-turn-helix domain
       0.03   14.1   0.0      0.046   13.5   0.0    1.4  1  HTH_23          Homeodomain-like domain
       0.03   14.1   0.0      0.047   13.5   0.0    1.2  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.062   12.9   0.0       0.13   11.8   0.0    1.5  1  GerE            Bacterial regulatory proteins, luxR family
      0.095   12.8   0.0       0.15   12.2   0.0    1.4  1  HTH_7           Helix-turn-helix domain of resolvase
       0.11   12.5   0.0       0.23   11.5   0.0    1.5  1  HTH_29          Winged helix-turn helix
       0.12   12.2   0.0       0.19   11.5   0.0    1.4  1  HTH_8           Bacterial regulatory protein, Fis family


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0     4e-08     4e-05       4      34 ..      24      54 ..      22      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4e-08
                                  HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                         HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGer 34
                                  ++ ++g +q+++A+ lG+sr+++s++ + +r
  gi|91773982|ref|YP_566674.1| 24 MMIEHGCTQQQVADILGLSRAAVSQYVSEKR 54
                                  66799*********************99876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.8e-07   0.00067      18      40 ..      27      49 ..       7      52 .. 0.88
   2 ?   -3.0   0.0       5.3   5.3e+03      27      36 ..      55      64 ..      55      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.8e-07
                                  TTT--HHHHHHHHTS-HHHHHHH CS
                    Sigma70_r4 18 geglTleEIgerlgiSrerVrqi 40
                                  ++g T+++++++lg+Sr +V+q 
  gi|91773982|ref|YP_566674.1| 27 EHGCTQQQVADILGLSRAAVSQY 49
                                  7899*****************95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.3
                                  HHHHTS-HHH CS
                    Sigma70_r4 27 gerlgiSrer 36
                                  g++ g S+e+
  gi|91773982|ref|YP_566674.1| 55 GAEVGFSEET 64
                                  7889999997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.6e-07   0.00085      17      40 ..      29      52 ..      28      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.6e-07
                        HTH_24 17 risqreLAerlglSpstvnrrlkr 40
                                  +++q+++A+ lglS+++v++++ +
  gi|91773982|ref|YP_566674.1| 29 GCTQQQVADILGLSRAAVSQYVSE 52
                                  69*******************975 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 !   18.8   0.0   1.6e-06    0.0016       3      34 ..      22      53 ..      22      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                        HTH_26  3 relmadrgitkseLargtgisaatlsrlvkgk 34
                                  r +m+++g+t++++a  +g+s+a +s +v++k
  gi|91773982|ref|YP_566674.1| 22 RSMMIEHGCTQQQVADILGLSRAAVSQYVSEK 53
                                  679**************************997 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.4e-06    0.0024      23      53 ..      20      51 ..       5      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                          KORA 23 iargvLVeg.kkqadvatelgltkqavsqavk 53
                                   ar +++e+  +q++va+ lgl++ avsq v 
  gi|91773982|ref|YP_566674.1| 20 LARSMMIEHgCTQQQVADILGLSRAAVSQYVS 51
                                  7999***97369*****************985 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 !   16.5   0.0   6.2e-06    0.0062      17      44 ..      25      52 ..       9      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-06
                                  EEEEEHHHHHHHHHTTSSHHHHHHHHHH CS
                     HTH_Crp_2 17 eielpltqeelAsmlGltretvsrilse 44
                                   ie   tq++ A++lGl+r  vs+  se
  gi|91773982|ref|YP_566674.1| 25 MIEHGCTQQQVADILGLSRAAVSQYVSE 52
                                  577789*****************98776 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.9e-06    0.0098       7      40 ..      22      55 ..      18      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.9e-06
                        HTH_31  7 ralReraGLsqeevAerlgvsestlsrlEqGrrg 40
                                  r +  ++G +q++vA+ lg+s++ +s++ + +rg
  gi|91773982|ref|YP_566674.1| 22 RSMMIEHGCTQQQVADILGLSRAAVSQYVSEKRG 55
                                  6677799********************9987775 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.6e-05     0.016       3      26 ..      31      54 ..      30      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                        HTH_17  3 tveEaAelLgvsrstvyrlirrge 26
                                  t +++A++Lg+sr+ v +++++++
  gi|91773982|ref|YP_566674.1| 31 TQQQVADILGLSRAAVSQYVSEKR 54
                                  668*****************9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.5e-05     0.015      20      42 ..      22      50 ..       7      52 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                                  S......EEEHHHHHHHHTSSHHHHHHHH CS
                        MarR_2 20 r......dltvgelarrlglsksavsril 42
                                  r       +t++++a+ lgls++avs+ +
  gi|91773982|ref|YP_566674.1| 22 RsmmiehGCTQQQVADILGLSRAAVSQYV 50
                                  555555548*****************987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.7e-05     0.017      24      48 ..      27      51 ..      23      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                  TS---HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2 24 leglsykEIAellgisegtVksrls 48
                                  ++g++++++A +lg+s ++V +++s
  gi|91773982|ref|YP_566674.1| 27 EHGCTQQQVADILGLSRAAVSQYVS 51
                                  79******************99975 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.3e-05     0.063      10      35 ..      31      56 ..      24      73 .. 0.84
   2 ?   -1.5   0.0       2.3   2.3e+03      28      41 ..     100     112 ..      81     113 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.3e-05
                YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqv 35
                                  +q+++A+ lg s++aVsq ++ k+++
  gi|91773982|ref|YP_566674.1| 31 TQQQVADILGLSRAAVSQYVSEKRGA 56
                                  799*****************999884 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                YdaS_antitoxin  28 Wlkgkkqvpaervp 41 
                                   Wl  k    ae+++
  gi|91773982|ref|YP_566674.1| 100 WLF-KNAPEAEYCI 112
                                   332.2224577876 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.8e-05     0.028       8      65 ..      25      80 ..      21      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                        HTH_40  8 lleeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiekvg 65
                                  ++e g++ +++A++ gl+++ + +++ e  + g e+ +++ ++ee++k  ++ +++++
  gi|91773982|ref|YP_566674.1| 25 MIEHGCTQQQVADILGLSRAAVSQYVSE--KRGAEVGFSEETNEEIRKFATDLVNEMP 80
                                  789*************************..8888899977777776665555555554 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.6e-05     0.046      19      40 ..      31      52 ..       9      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                        HTH_23 19 svreIAreLgvsrrTvyrwlkr 40
                                  +++++A++Lg sr  v+++++ 
  gi|91773982|ref|YP_566674.1| 31 TQQQVADILGLSRAAVSQYVSE 52
                                  89****************9986 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 ?   13.5   0.0   4.7e-05     0.047       5      29 ..      25      49 ..      22      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                                  HHHHHSSHHHHHHHHTS-HHHHHHH CS
                       P22_Cro  5 vikhFGgvekvAkalgvtksAVsqW 29
                                   i+h  ++++vA  lg + +AVsq 
  gi|91773982|ref|YP_566674.1| 25 MIEHGCTQQQVADILGLSRAAVSQY 49
                                  57888899****************8 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   0.0   0.00013      0.13      13      39 ..      25      51 ..      24      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                  HHCTTS-HHHHHHHHTS-HHHHHHHHH CS
                          GerE 13 llaeGksnkeIAeelniSekTVkvhks 39
                                  ++  G + +++A++l++S   V+ ++s
  gi|91773982|ref|YP_566674.1| 25 MIEHGCTQQQVADILGLSRAAVSQYVS 51
                                  7889*******************9987 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 ?   12.2   0.0   0.00015      0.15      17      42 ..      25      50 ..      20      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                  STTTT--STTTSSSS---SSSS--SS CS
                         HTH_7 17 LleeGisiskIAkevnisRsTvYRyl 42
                                  ++e G + +++A+++++sR+ v +y 
  gi|91773982|ref|YP_566674.1| 25 MIEHGCTQQQVADILGLSRAAVSQYV 50
                                  899****************9987776 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.23       7      33 ..      25      50 ..      23      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                        HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwl 33
                                  ++++G+ t +q+A +lglsr  v  ++
  gi|91773982|ref|YP_566674.1| 25 MIEHGC-TQQQVADILGLSRAAVSQYV 50
                                  678899.9**************98876 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.19      14      33 ..      25      44 ..      22      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                  HHHTTT-HHHHHHHHTS-HH CS
                         HTH_8 14 LertgGnkskAArlLGisRr 33
                                  + ++g  ++++A++LG+sR 
  gi|91773982|ref|YP_566674.1| 25 MIEHGCTQQQVADILGLSRA 44
                                  5678889************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 893.00
//
Query:       gi|91773983|ref|YP_566675.1|  [L=102]
Description: translation initiation factor Sui1 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-20   72.4   0.1    3.9e-20   72.1   0.1    1.1  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
      0.013   15.3   0.9      0.017   14.9   0.9    1.2  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 !   72.1   0.1   4.4e-24   3.9e-20       1      76 [.      24      95 ..      24      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4.4e-24
                          SUI1  1 akpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                  ++++i++++ +r+ +K vT+v+g++a++idl++l+  lk+kfac+g+v k++   +++QG++  + + +L++k g+
  gi|91773983|ref|YP_566675.1| 24 EQQRITVKVNRRRYGKEVTVVEGFDANEIDLHELSTYLKSKFACGGTV-KGS--AVELQGNHLSRMKAVLVKK-GF 95
                                  5899*******************************************9.555..8*****************9.87 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   1.8e-06     0.017       2      29 ..       4      30 ..       3      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                           DTW  2 elCerCllpaevclcsslppleklpikv 29
                                  e+C+ C lp+e+c+c+++ + e+++i v
  gi|91773983|ref|YP_566675.1|  4 EMCPVCGLPSELCICEEVAK-EQQRITV 30
                                  68*****************9.7665665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 803.39
//
Query:       gi|91773984|ref|YP_566676.1|  [L=117]
Description: hypothetical protein Mbur_2050 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-25   88.1   0.0    3.5e-25   88.0   0.0    1.0  1  DUF192    Uncharacterized ACR, COG1430


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0     2e-29   3.5e-25       2      94 ..      13     112 ..      12     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 2e-29
                                   EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT........-ECE CS
                        DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq........svry 74 
                                   +v +A++  ++a+GLm+r+s+ ++++m+f+f++ r+ s++M ++ +p+d++fl++d++iv+ ++ l+p+        ++ry
  gi|91773984|ref|YP_566676.1|  13 DVDYAKSMFQQAKGLMFRRSVHDSYAMVFIFSSLRKISLHMLFVPFPIDVLFLNEDKIIVKTTH-LRPWigiadsgeKIRY 92 
                                   6899**********************************************************96.77**988876666*** PP

                                   EEEEETTHHHHHT--TT-EE CS
                        DUF192  75 vLElpaGaakklgikpGdrl 94 
                                   v+Elp+Ga++++g+k+Gd+l
  gi|91773984|ref|YP_566676.1|  93 VIELPSGAISSNGLKVGDHL 112
                                   ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 855.57
//
Query:       gi|91773985|ref|YP_566677.1|  [L=715]
Description: phosphoribosylformylglycinamidine synthase II [Methanococcoides burtonii DSM 6242]
Scores for complete 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-48  162.9   7.2    1.6e-30  106.3   0.6    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
    3.4e-45  152.6   0.9    6.6e-24   84.4   0.0    2.9  3  AIRS            AIR synthase related protein, N-terminal doma
      3e-07   30.9   0.2    1.4e-06   28.7   0.1    2.2  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.29   11.0   0.0    1.7  1  HTH_ParB        HTH domain found in ParB protein


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 !  106.3   0.6   3.6e-34   1.6e-30       1     148 [.     185     334 ..     185     341 .. 0.94
   2 !   59.9   1.0   6.7e-20     3e-16       2     148 ..     553     684 ..     552     689 .. 0.86

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 3.6e-34
                                   STTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                        AIRS_C   1 kpGdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                   k+G++l+l+gs    +Glgga+ +++r + ee++ +d+ + q+gd++ e+  i++ ++++ + g v +++D+++ GL+ga 
  gi|91773985|ref|YP_566677.1| 185 KAGNKLVLIGSttgrDGLGGAS-FASRDLSEEAEAEDRpSIQIGDPFTEKLAIEATLEAIGA-GYVLSCRDLGAAGLAGAS 263
                                   69********************.6667777777777777**********************9.****************** PP

                                   HHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                        AIRS_C  77 aemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                   +ema ++++g+++++dkv +++  ++p+e++++e+++r l+ v+pe+ davlai ++++l+ a+ IGe+t++
  gi|91773985|ref|YP_566677.1| 264 SEMASKGKLGMRLEADKVILREDGMTPYEIMIAESQERILMEVEPENVDAVLAIGKKYDLH-ASMIGELTER 334
                                   ************************************************************6.********97 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 6.7e-20
                                   TTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHH CS
                        AIRS_C   2 pGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaema 80 
                                   +G+++il+g+  + +gg+ ++  +++     ++    +++d+  +  +++   +  ++ g+v aahDv++GGL++al+em+
  gi|91773985|ref|YP_566677.1| 553 EGNTIILVGNtlDEMGGSEYYNMVGLRLNGNVP----KVTDESVK--VVETLINVVRD-GNVVAAHDVSAGGLAVALSEMC 626
                                   8**********************9988888888....45555444..66666666676.********************** PP

                                   HTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                        AIRS_C  81 pasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                   +   +gaeidl    + d+l  + ++l+se+  r +++ +++e+  v+++l++   p  +vIG+v + 
  gi|91773985|ref|YP_566677.1| 627 DS--IGAEIDLT--SVGDNL-RADDVLFSESHARAILVTSSPEK--VKEMLADV--P-HTVIGTVGGN 684
                                   *7..9*******..999999.89************999999999..88888875..4.7999999865 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 !   84.4   0.0   1.5e-27   6.6e-24       1      93 [.      59     172 ..      59     173 .. 0.94
   2 ?   -2.8   0.0       2.4   1.1e+04      55      79 ..     240     264 ..     230     270 .. 0.49
   3 !   66.0   0.0   8.1e-22   3.6e-18       2      93 ..     421     538 ..     420     539 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 1.5e-27
                                   SSSE.........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHH CS
                          AIRS   1 dDaa.........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrgla 63 
                                   dDaa         +++ ++shn+p++v+p+++  a++v+++++D+++mGArP+al++ l ++          +e +++g+a
  gi|91773985|ref|YP_566677.1|  59 DDAAiirfgegwvLAIGMESHNHPSYVDPYNG-SATGVGGIVRDIISMGARPIALMDPLYFGplntpknlyLFEHIIEGIA 138
                                   89996665555555******************.************************************************ PP

                                   HHHHHTT-EEEEEEEEEESS....EEEEEEEEEE CS
                          AIRS  64 eaaeelgvplvgGdtsfsne....ptisvtavGl 93 
                                    +++++gvp+v G+t f+++    p+++v++vGl
  gi|91773985|ref|YP_566677.1| 139 GYGNCIGVPVVRGETYFDESysgnPLVNVVCVGL 172
                                   *****************99899***********8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHTT-EEEEEEEE CS
                          AIRS  55 leevvrglaeaaeelgvplvgGdts 79 
                                   le++ +g    ++ lg++ + G +s
  gi|91773985|ref|YP_566677.1| 240 LEAIGAGYVLSCRDLGAAGLAGASS 264
                                   4444444444555555544444443 PP

  == domain 3  score: 66.0 bits;  conditional E-value: 8.1e-22
                                   SSEE.........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHH CS
                          AIRS   2 Daav.........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglae 64 
                                   Daav         ++++ +++r++l++p+++ G+ ++ +n  +la+ GA+ +al+++l+++         ++++++ gl++
  gi|91773985|ref|YP_566677.1| 421 DAAVlrigdgkglAMSCGCNPRHTLLDPYEG-GKGTLIENSMNLAVKGAEGIALVDCLNFGnperpdiywQFKQAILGLGD 500
                                   8884445555555******************.************************************************* PP

                                   HHHHTT-EEEEEEEEEESS.........EEEEEEEEEE CS
                          AIRS  65 aaeelgvplvgGdtsfsne.........ptisvtavGl 93 
                                   aa+ l +p+vgG++s +ne         pt+s++ +G+
  gi|91773985|ref|YP_566677.1| 501 AARSLSIPVVGGNVSLYNEsgeygtaiaPTPSIGLIGI 538
                                   *****************999*****************8 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 !   28.7   0.1   3.1e-10   1.4e-06      15      49 ..       5      36 ..       1      37 [. 0.85
   2 ?   -1.4   0.0      0.79   3.5e+03       9      22 ..     694     707 ..     691     712 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.1e-10
                FGAR-AT_linker 15 eEidylqeafeklgrnPtdvElemfaqvwSEHCrH 49
                                  ++ + ++e    +gr+P+ vE ++f   wSEHC++
  gi|91773985|ref|YP_566677.1|  5 NDLKIITEE---MGREPNLVEQGCFLNLWSEHCSY 36
                                  556666666...9*********************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.79
                FGAR-AT_linker   9 glaLsdeEidylqe 22 
                                   +l+Ls+eEi+  + 
  gi|91773985|ref|YP_566677.1| 694 DLSLSLEEISDARA 707
                                   699*****987665 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.4e-05      0.29      12      34 ..     649     671 ..     642     673 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                      HTH_ParB  12 iseGHARaLlslkdeelqlqlae 34 
                                    se+HARa+l  +++e+ ++++ 
  gi|91773985|ref|YP_566677.1| 649 FSESHARAILVTSSPEKVKEMLA 671
                                   69***************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 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:                        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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4993.36
//
Query:       gi|91773986|ref|YP_566678.1|  [L=68]
Description: hypothetical protein Mbur_2052 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-05   22.9   0.0     0.0001   22.8   0.0    1.0  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0093   15.8   0.0       0.01   15.7   0.0    1.0  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


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 !   22.8   0.0   1.2e-08    0.0001      36      73 ..      24      62 ..       4      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-08
                                  TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTS CS
                     HATPase_c 36 ddlvisveDnGiGipkedlkklfekfsq.ddstkrgggg 73
                                   +l + v+D GiG++ +d+++lf+ f+q d+s++ ++g 
  gi|91773986|ref|YP_566678.1| 24 YYLDLLVKDAGIGMSSKDIDRLFTLFVQlDSSNTKKYGE 62
                                  577888**********************88888777765 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 !   15.7   0.0   1.1e-06      0.01      13      61 ..       6      53 ..       3      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                   HATPase_c_3 13 NsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatssk 61
                                  Ns +A+  nv i ++ n g   ++ ++D G Gms +++++ ++l  +  
  gi|91773986|ref|YP_566678.1|  6 NSDSAKWGNVVIGAKLN-GYYLDLLVKDAGIGMSSKDIDRLFTLFVQLD 53
                                  88899999999999987.67899*****************887543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 462.52
//
Query:       gi|91773987|ref|YP_566679.1|  [L=115]
Description: hypothetical protein Mbur_2053 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 804.08
//
Query:       gi|91773988|ref|YP_566680.1|  [L=115]
Description: voltage-dependent potassium channel [Methanococcoides burtonii DSM 6242]
Scores for complete 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   60.0   8.1    2.4e-16   59.5   8.1    1.4  1  Ion_trans_2  Ion channel
    1.2e-08   34.6   1.9    1.4e-08   34.3   1.9    1.1  1  Ion_trans    Ion transport protein
  ------ inclusion threshold ------
       0.83    9.5   4.4        4.4    7.1   4.4    1.9  1  IRK          Inward rectifier potassium channel transmembrane
        1.5    9.4   6.1       0.18   12.4   1.1    2.0  2  DUF4405      Domain of unknown function (DUF4405)


Domain annotation for each model (and alignments):
>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   8.1   5.3e-20   2.4e-16       2      73 ..      24      96 ..      13     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 5.3e-20
                                  HHHHTCHHHHHHHHT........T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2  2 vlllvlifgaviysl....eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavl 73
                                  +l l++i+g+++y++    +      ++ d++Y++++tltTiGYGdivp+td+gr+++ +++llG +++++ + ++
  gi|91773988|ref|YP_566680.1| 24 LLSLTIISGVLMYFIegrtGG---FANIPDSIYWAITTLTTIGYGDIVPQTDIGRAVNSIITLLGSSIIIIPIVIV 96
                                  5789999********875333...35****************************************9999877655 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   1.9   3.1e-12   1.4e-08     122     240 ..       9     104 ..       2     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.1e-12
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHH CS
                     Ion_trans 122 alirsvkdllnvlllllvvlfifaligvqlfkgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyat 202
                                    l +s+++++++++ ll + +i +++++ +                    ++  F n++++++w+++++tt+g+gdi+++t
  gi|91773988|ref|YP_566680.1|   9 VLHESFRKIVLFIFTLLSLTIISGVLMYFIE------------------GRTGGFANIPDSIYWAITTLTTIGYGDIVPQT 71 
                                   5668889999999988888888888886666..................33446*************************** PP

                                   HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 203 ldekskvaliyfvifiilgsflllNlliaviadnfqel 240
                                     ++     ++  i+ +lgs +++  ++ vi + +++l
  gi|91773988|ref|YP_566680.1|  72 DIGR-----AVNSIITLLGSSIIIIPIVIVIGEIYNSL 104
                                   ****.....55555555555555555555555555555 PP

>> IRK  Inward rectifier potassium channel transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.4   0.00098       4.4      87     128 ..      50      91 ..       5     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00098
                           IRK  87 sallfslEtqttigyGsrvvteeCpeailllviqsivgllid 128
                                   + + +++ t ttigyG  v++++   a+  +++ +  +++i 
  gi|91773988|ref|YP_566680.1|  50 DSIYWAITTLTTIGYGDIVPQTDIGRAVNSIITLLGSSIIII 91 
                                   6677899***************99999887766555554443 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.1   3.9e-05      0.18       3      34 ..      18      46 ..      17      66 .. 0.75
   2 ?   -1.4   0.3      0.79   3.5e+03       9      21 ..      79      91 ..      76     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                       DUF4405  3 dlllllsflvlaiSGillsfavlpsgrgaywa 34
                                   l+++ +  +++iSG+l++f+   +gr +++a
  gi|91773988|ref|YP_566680.1| 18 VLFIFTLLSLTIISGVLMYFI---EGRTGGFA 46
                                  68899999***********98...56666655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.79
                       DUF4405  9 sflvlaiSGills 21
                                  s+++l+ S+i++ 
  gi|91773988|ref|YP_566680.1| 79 SIITLLGSSIIII 91
                                  5677888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 853.10
//
Query:       gi|91773989|ref|YP_566681.1|  [L=122]
Description: hypothetical protein Mbur_2055 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-10   41.6  15.1    1.2e-10   41.6  15.1    2.0  2  DUF4064          Protein of unknown function (DUF4064)
  ------ inclusion threshold ------
       0.16   12.5   0.4       0.16   12.5   0.4    2.1  2  ATP_synt_H       ATP synthase subunit H


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 !   41.6  15.1   1.3e-14   1.2e-10       2     101 ..       3      96 ..       2      98 .. 0.94
   2 ?   -0.5   2.7      0.16   1.4e+03      60      79 ..      99     118 ..      96     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.3e-14
                       DUF4064   2 rkaeiiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvi..aliaivlgivgal 80 
                                   +k+e i+g+ Gg++g++++ ++++++++++++         + ++++ +s+v ++   +++++g++   li++++gi+g +
  gi|91773989|ref|YP_566681.1|   3 KKTETIFGIAGGSIGVIIAAVIFYVAIINIWPG--------GGTMMYGTSEVFGISDPFVVMMGFGtvTLILGLIGIAGGI 75 
                                   89***************************9999........8999************999988877669************ PP

                       DUF4064  81 llkknkkvsGilfiiaailsl 101
                                   + k++kk++G l+++++il++
  gi|91773989|ref|YP_566681.1|  76 VAKTDKKKGGKLMLASGILGI 96 
                                   *******************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.16
                       DUF4064  60 llivlgvialiaivlgivga 79 
                                   ++++ ++ +l++++ gi+++
  gi|91773989|ref|YP_566681.1|  99 FFWMWMLPGLLLTIGGIIAI 118
                                   56777777777777777765 PP

>> ATP_synt_H  ATP synthase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4     0.073   6.5e+02       6      16 ..      18      28 ..      10      50 .. 0.58
   2 ?   12.5   0.4   1.8e-05      0.16       3      45 ..      60     104 ..      58     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.073
                                  HHHHHHHHTCS CS
                    ATP_synt_H  6 tiifavlgvva 16
                                   ii av+  va
  gi|91773989|ref|YP_566681.1| 18 VIIAAVIFYVA 28
                                  33333332222 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHTCSCSSS-S.TTHH..HHHHHHHHHHHHHHHTCH CS
                    ATP_synt_H   3 lvgtiifavlgvvatfvvpkgenrg..lirvlviltavccWlfWl 45 
                                    ++t+i  ++g+++ +v++  +++g  l+  + il ++ ++ +W+
  gi|91773989|ref|YP_566681.1|  60 GTVTLILGLIGIAGGIVAKTDKKKGgkLMLASGILGIALFFWMWM 104
                                   589************999966555556999**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 889.82
//
Query:       gi|91773990|ref|YP_566682.1|  [L=112]
Description: hypothetical protein Mbur_2056 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-10   38.9   0.0    6.2e-10   38.9   0.0    2.3  2  PLDc_N         Phospholipase_D-nuclease N-terminal
    6.7e-06   26.3   0.2    6.7e-06   26.3   0.2    2.0  2  DUF2516        Protein of unknown function (DUF2516)
    0.00086   19.5   6.7     0.0058   16.9   0.8    2.1  2  DUF4181        Domain of unknown function (DUF4181)
    0.00089   19.5   0.9     0.0011   19.2   0.9    1.1  1  TctB           Tripartite tricarboxylate transporter TctB fam
  ------ inclusion threshold ------
      0.013   14.9   0.4      0.016   14.7   0.4    1.1  1  EBP            Emopamil binding protein
      0.032   14.4   5.2        6.7    6.9   3.0    2.7  3  COX2_TM        Cytochrome C oxidase subunit II, transmembrane
      0.042   12.7   5.8      0.053   12.4   5.8    1.1  1  EcsB           Bacterial ABC transporter protein EcsB
      0.063   12.9   6.6      0.096   12.3   6.6    1.3  1  DUF4153        Domain of unknown function (DUF4153)
      0.079   13.6   0.1       0.16   12.6   0.1    1.6  1  Bcl-2          Apoptosis regulator proteins, Bcl-2 family
       0.11   12.8   0.6       0.14   12.4   0.3    1.5  2  Shisa          Wnt and FGF inhibitory regulator
       0.11   11.8   0.6       0.15   11.3   0.6    1.3  1  MSP1a          Major surface protein 1a (MSP1a)
       0.47   10.1   5.9       0.19   11.3   2.6    1.7  2  DUF4131        Domain of unknown function (DUF4131)
        1.2    8.9   4.0       0.52   10.1   1.2    1.6  2  FA_desaturase  Fatty acid desaturase
        1.2    7.8  10.6         12    4.6  11.0    1.9  1  DUF2207        Predicted membrane protein (DUF2207)
        4.5    7.7   8.8         21    5.5   8.8    1.9  1  MgtE           Divalent cation transporter
        8.6    6.6   9.7        4.2    7.6   5.4    2.0  2  SdpI           SdpI/YhfL protein family


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   4.0       7.4   8.3e+03      20      27 ..      45      52 ..      28      56 .. 0.59
   2 !   38.9   0.0   5.5e-13   6.2e-10       2      42 .]      56     103 ..      55     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.4
                        PLDc_N 20 laWllvil 27
                                  l+W ++ +
  gi|91773990|ref|YP_566682.1| 45 LLWGIIAI 52
                                  34444444 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 5.5e-13
                        PLDc_N   2 lwiialidiirdrnpss........klaWllvilflPvlGailYllfGr 42 
                                   + i++l+d+++ rn++         kl+W +v+++l+++Gai+Y+++ r
  gi|91773990|ref|YP_566682.1|  56 FCIFMLCDCLQ-RNTEDfphkgkheKLIWSIVLIVLNFIGAIMYYFLVR 103
                                   679********.666666799*************************865 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.7      0.76   8.6e+02      64      79 ..      24      39 ..      16      42 .. 0.73
   2 !   26.3   0.2     6e-09   6.7e-06       7      58 ..      45      96 ..      40     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.76
                       DUF2516 64 lsllgliavvaalvYl 79
                                   ++ gl+ ++a+lvY 
  gi|91773990|ref|YP_566682.1| 24 WTVAGLMILIAILVYT 39
                                  5566788888888885 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 6e-09
                       DUF2516  7 vllllalvvlvlslvAlvdalrrradaFeaagkrtKpfWlailgvallvlll 58
                                  +l+ +  +v++++++ l d+l r  + F+  gk+ K +W ++l+v  +++ +
  gi|91773990|ref|YP_566682.1| 45 LLWGIIAIVILFCIFMLCDCLQRNTEDFPHKGKHEKLIWSIVLIVLNFIGAI 96
                                  78889999999********************************998888877 PP

>> DUF4181  Domain of unknown function (DUF4181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.0      0.01        12      23      54 ..      13      42 ..       1      46 [. 0.62
   2 !   16.9   0.8   5.2e-06    0.0058      36      81 ..      47      99 ..      42     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                       DUF4181 23 yekhvnklhkkielilrvlfiifiilsliiil 54
                                  +e +vnk   k e+++++l+i++ il++++++
  gi|91773990|ref|YP_566682.1| 13 GEDKVNKI--KSEWTVAGLMILIAILVYTFYI 42
                                  34455554..5689988999988888888765 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.2e-06
                       DUF4181 36 lilrvlfiifiilsliiilsreyvdii.......ilifvflvvlelfRavmew 81
                                  +++ +++i+f+i++l   l+r++ d+        +++ ++l+vl+++ a+m +
  gi|91773990|ref|YP_566682.1| 47 WGIIAIVILFCIFMLCDCLQRNTEDFPhkgkhekLIWSIVLIVLNFIGAIMYY 99
                                  667789*******************99***********************976 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.9     1e-06    0.0011      52     126 ..      13     100 ..       4     104 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-06
                          TctB  52 gekeekearedwrkllklvlallaalllyalllepl..Gfilata.lflllll...g...........reerkwlkalila 115
                                   ge++  + +++w+ +  ++l+   a+l+y + ++ l  G i+a++ lf++++l               ++e+ ++ ++++ 
  gi|91773990|ref|YP_566682.1|  13 GEDKVNKIKSEWTVAGLMILI---AILVYTFYIGQLlwG-IIAIViLFCIFMLcdcLqrntedfphkgKHEKLIWSIVLIV 89 
                                   444445555556666645555...677777766665447.55555366666667761667888899886667777777777 PP

                          TctB 116 vvlallvyllF 126
                                   + +  ++++ F
  gi|91773990|ref|YP_566682.1|  90 LNFIGAIMYYF 100
                                   76666666655 PP

>> EBP  Emopamil binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   1.4e-05     0.016      88     133 ..      42     102 ..      18     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                           EBP  88 ltvllagplallvvyaia...............kekplrhllqivlataelyGgvlyfate 133
                                   +  ll+g +a++++++i+               k k+ + ++ ivl + +++G ++y++  
  gi|91773990|ref|YP_566682.1|  42 IGQLLWGIIAIVILFCIFmlcdclqrntedfphKGKHEKLIWSIVLIVLNFIGAIMYYFLV 102
                                   445789999999999999**************97789********************9865 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0079       8.9      66      88 ..      19      41 ..       4      42 .. 0.82
   2 ?    6.9   3.0     0.006       6.7      30      79 ..      49      90 ..      43     100 .. 0.69
   3 ?    3.1   0.4     0.093     1e+02      28      54 ..      83     109 ..      76     112 .] 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0079
                       COX2_TM 66 eiEiiWTiiPalililialpSlk 88
                                  +i   WT+   +ili+i ++ + 
  gi|91773990|ref|YP_566682.1| 19 KIKSEWTVAGLMILIAILVYTFY 41
                                  56667**************9996 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.006
                       COX2_TM 30 iltlililVlyilvlilvefrrrknkitakylvhgqeiEiiWTiiPalil 79
                                  i+++++++ +++l+ +l +   + +++++k    g+   +iW i+  ++l
  gi|91773990|ref|YP_566682.1| 49 IIAIVILFCIFMLCDCLQR---NTEDFPHK----GKHEKLIWSIVL-IVL 90
                                  5666677778888888888...56666666....888889999874.333 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.093
                       COX2_TM  28 lliltlililVlyilvlilvefrrrkn 54 
                                     i++++l ++  i+ + lv+ + +++
  gi|91773990|ref|YP_566682.1|  83 WSIVLIVLNFIGAIMYYFLVRIQDNQE 109
                                   456677777788888888887666655 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   5.8   4.8e-05     0.053     106     182 ..      26     100 ..      19     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                          EcsB 106 qllllllvllillPlllettglsiaelllllllllllkllnlllkweelrlqgkkkrridrlirlllnalllyllla 182
                                    + l++l++++++ +++    ++i+++++l+++++l+ +l+   + e + ++gk++++i+ ++ ++ln++ ++++++
  gi|91773990|ref|YP_566682.1|  26 VAGLMILIAILVYTFYIGQLLWGIIAIVILFCIFMLCDCLQR--NTEDFPHKGKHEKLIWSIVLIVLNFIGAIMYYF 100
                                   567888999999999998889999999999999999887665..55788888999999999*****99998666544 PP

>> DUF4153  Domain of unknown function (DUF4153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   6.6   8.6e-05     0.096      21      84 ..      37     104 ..      20     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-05
                       DUF4153  21 sirly..aylf.lfvallfglvffLsllpee.laeeeqskrf.kvLlkfillplviiYlliLylYliki 84 
                                    +++y  + l+ ++ ++++  +f+L  + ++ +++ +++ +  k++++ +l+ l +i  +i+y +l++i
  gi|91773990|ref|YP_566682.1|  37 VYTFYigQLLWgIIAIVILFCIFMLCDCLQRnTEDFPHKGKHeKLIWSIVLIVLNFI-GAIMYYFLVRI 104
                                   223332134446666677777788888888735667777666588888888888888.********998 PP

>> Bcl-2  Apoptosis regulator proteins, Bcl-2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00015      0.16      33      85 ..      32      93 ..       3     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                  HHHHHHHCCTTS--SCHHHHHHHHHHHHHHHHHHHC.........HHHCCHHHHHHHHHHHH CS
                         Bcl-2 33 fakvaeelfsdgelnWgrvvalfafagalaerlvrd.........glpellrrlvellvdyl 85
                                  + +++   f  g+l Wg ++ ++ f+  ++ ++ ++         ++++l+ ++v ++ +++
  gi|91773990|ref|YP_566682.1| 32 LIAILVYTFYIGQLLWGIIAIVILFCIFMLCDCLQRntedfphkgKHEKLIWSIVLIVLNFI 93
                                  556666667778899******************99978888888778888888888888887 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00013      0.14      81     118 ..      22      72 ..       1      91 [. 0.68
   2 ?   -0.7   0.0       1.3   1.5e+03      82      99 ..      81      98 ..      66     104 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                         Shisa  81 d.............iyvpvlivktifivfvivgvvvivcccgclkkkqrek 118
                                   +             +  ++ i++ +  ++ iv+ ++i ++c cl+   ++ 
  gi|91773990|ref|YP_566682.1|  22 SewtvaglmiliaiLVYTFYIGQLLWGIIAIVILFCIFMLCDCLQRNTEDF 72 
                                   23555556666666667788888888888889999********99877654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                         Shisa 82 iyvpvlivktifivfviv 99
                                  ++ ++++++ +fi  ++ 
  gi|91773990|ref|YP_566682.1| 81 LIWSIVLIVLNFIGAIMY 98
                                  677888888888877765 PP

>> MSP1a  Major surface protein 1a (MSP1a)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00013      0.15      22      73 ..      42      98 ..      14     111 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                         MSP1a 22 agqliitiaaLva..avfaiCaCLepal.....aGasgtLiWgCLalvvLLpLlgaaav 73
                                   gql+  i a+v+  ++f +C CL+ +       G    LiW+ + +v+   ++ga+ +
  gi|91773990|ref|YP_566682.1| 42 IGQLLWGIIAIVIlfCIFMLCDCLQRNTedfphKGKHEKLIWSIVLIVL--NFIGAIMY 98
                                  68888888887664479*******987533333699999***9875554..44554443 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.6   0.00017      0.19       8      61 ..      24      74 ..      20      82 .. 0.75
   2 ?    8.2   0.9    0.0016       1.8       9      52 ..      46     102 ..      43     111 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                       DUF4131  8 vllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsq 61
                                  +++a l++l+++l++ +   +  + l++++++ +l+++++++  +q+n++d+++
  gi|91773990|ref|YP_566682.1| 24 WTVAGLMILIAILVYTF---YIGQLLWGIIAIVILFCIFMLCDCLQRNTEDFPH 74
                                  56666666666666663...6678888888888888888999999999998887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                       DUF4131   9 llalllllllllllllrr.............rprrrvllllllllllallgfalrap 52 
                                   l++++++++l++++ l +             +  + ++ ++l++l ++++ +++   
  gi|91773990|ref|YP_566682.1|  46 LWGIIAIVILFCIFMLCDclqrntedfphkgKHEKLIWSIVLIVLNFIGAIMYYFLV 102
                                   444444444444444444445558999999655556666666666555555444444 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.2   0.00046      0.52     126     179 ..      15      61 ..       5      84 .. 0.63
   2 ?   -0.3   0.0      0.69   7.8e+02     136     154 ..      81      99 ..      66     104 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00046
                 FA_desaturase 126 apsksrrrkwrllawlllllawlglwlalllllglalllwlvplllllfllalv 179
                                   +++++++  w++ ++++l++  ++++ ++++ l     lw++ ++++lf++ ++
  gi|91773990|ref|YP_566682.1|  15 DKVNKIKSEWTVAGLMILIA--ILVYTFYIGQL-----LWGIIAIVILFCIFML 61 
                                   45555666677777777777..55555555544.....6666666666665544 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.69
                 FA_desaturase 136 rllawlllllawlglwlal 154
                                    ++ ++l++l+++g++  +
  gi|91773990|ref|YP_566682.1|  81 LIWSIVLIVLNFIGAIMYY 99 
                                   3333333334444443333 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  11.0      0.01        12     373     440 ..      10      71 ..       1     106 [. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                       DUF2207 373 dkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrtee 440
                                   ++kg+ k +k+   ++++++++li+il+  +      ++ l++++i ++i++++++l+  +l+r te+
  gi|91773990|ref|YP_566682.1|  10 KNKGEDKVNKIKSEWTVAGLMILIAILVYTF-----YIGQLLWGIIAIVILFCIFMLC-DCLQRNTED 71 
                                   5666666666666666666666666655443.....4555555555555555555554.677777764 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   8.8     0.019        21      21      81 ..       3      62 ..       1     107 [. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                                  HHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHH CS
                          MgtE 21 talhlgelekk..lkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvlvlla 81
                                  t +h+++ +k     + + +e++v+ l+++i  l+  ++   +g++l  ++++ + +++++l+
  gi|91773990|ref|YP_566682.1|  3 TKIHVKLKNKGedKVNKIKSEWTVAGLMILIAILVYTFY---IGQLLWGIIAIVILFCIFMLC 62
                                  666766443334557778888888777666666666655...444344445555555555554 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.4    0.0037       4.2      33      63 ..      24      60 ..      15      62 .. 0.62
   2 ?    1.2   0.1      0.37   4.2e+02      52      65 ..      84      97 ..      72     102 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                          SdpI 33 wiiaGlilllla......lgavvlvllvlvlllvivp 63
                                  w +aGl++l++       +g++ + ++++v+l++i++
  gi|91773990|ref|YP_566682.1| 24 WTVAGLMILIAIlvytfyIGQLLWGIIAIVILFCIFM 60
                                  7888877666667887665555555555555555554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                          SdpI 52 llvlvlllvivpii 65
                                  ++vl++l +i+ i+
  gi|91773990|ref|YP_566682.1| 84 SIVLIVLNFIGAIM 97
                                  23333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1332  (0.074293); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 773.89
//
Query:       gi|91773991|ref|YP_566683.1|  [L=182]
Description: hypothetical protein Mbur_2057 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.3    5.0  19.0       0.39    8.9  10.3    2.0  2  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  10.3   2.2e-05      0.39     105     184 ..       5      78 ..       1      86 [. 0.79
   2 ?    1.5   1.4    0.0039        70      19      65 ..     122     174 ..     107     180 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 2.2e-05
                       DUF2070 105 vlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfivvvdrplkrnlg 184
                                   ++ l +vf+  + v+ a++ ++ ++++lp++   ll +++l+l+      l   ll++++++++++++ vv++p+ ++++
  gi|91773991|ref|YP_566683.1|   5 IFILGIVFFAFMTVYNAIAYRKNKTSLLPTIFSFLLTLITLLLF------LEQSLLCITILMLAVFLLSVVKYPMISKIQ 78 
                                   55577888888999999999999999999888888888888888......788888888888888888888888877654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.0039
                       DUF2070  19 lliillalligllaflssk......lfgillfglpalvaflltlpvlrilggr 65 
                                   + ++ ++ +igl    +s       + g+l++ +++++++l++ ++ ++l+++
  gi|91773991|ref|YP_566683.1| 122 IYSVSFSTIIGLGLLSMSMlipdygMRGYLVLQMTLIFTVLFYFQMHKTLKKY 174
                                   33333333333332222223344446666666666666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 1505.71
//
Query:       gi|91773992|ref|YP_566684.1|  [L=291]
Description: ABC transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-31  109.8   0.2    2.2e-31  109.2   0.2    1.3  1  ABC_tran    ABC transporter
      1e-15   58.4   1.6    6.8e-11   42.5   0.0    2.3  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.024   14.7   0.0    1.4  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
      0.028   14.3   0.0      0.042   13.8   0.0    1.4  1  Rad17       Rad17 P-loop domain
      0.031   14.0   7.4      0.049   13.3   0.4    2.7  3  AAA_15      AAA ATPase domain
      0.096   12.4   0.1       0.18   11.6   0.1    1.4  1  AAA_29      P-loop containing region of AAA domain
        0.1   12.2   0.2       0.18   11.4   0.2    1.4  1  SRP54       SRP54-type protein, GTPase domain
       0.16   11.7   0.0       0.56    9.9   0.0    1.9  1  AAA_30      AAA domain
       0.17   11.1   0.0       0.29   10.4   0.0    1.3  1  Zeta_toxin  Zeta toxin
       0.89   10.0   7.1        0.2   12.1   1.8    2.3  3  AAA_23      AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.2   1.2e-34   2.2e-31       2     137 .]       2     145 ..       1     145 [. 0.95

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 1.2e-34
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   +n+sl++++ ++++++G+nGaGK+t +kll+gll+pt G+i +dg d+++ e ++ +k +g +pq++++ ++ ++ ++   
  gi|91773992|ref|YP_566684.1|   2 ENISLNVEKESIYGFLGKNGAGKTTTIKLLSGLLTPTDGKIIVDGMDMDS-ESREIKKIMGLVPQDSNFYDDRNALSHmiy 81 
                                   79************************************************.889999*********9999999888889** PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                             e+ ++ +++l+k+gl++ k++ v      +S+G+k+r+ +a+all++pk+l+lDEpt+
  gi|91773992|ref|YP_566684.1|  82 ygrlkglskkEALVQSNALLEKVGLEKEKHKQV----IYFSHGMKKRLGIAQALLNNPKILILDEPTN 145
                                   ******998888889************999999....9*****************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   7.9e-06     0.014       2      24 ..      14      36 ..      13      73 .. 0.73
   2 !   42.5   0.0   3.8e-14   6.8e-11     183     301 ..      61     178 ..      48     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.9e-06
                        AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                   ++ G+Ng+GK++ +++l++l  
  gi|91773992|ref|YP_566684.1| 14 YGFLGKNGAGKTTTIKLLSGLLT 36
                                  5789****************964 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 3.8e-14
                        AAA_21 183 rllqrlvrslklveielsdlgegeeliasvderlrer.....gvvflengdgqelparelSdGtkrllalltallralkkg 258
                                   +l+ + ++ ++++++  +++ +g  +  s +e+l ++      v ++++++ q + +   S G+k+ l+++ all  +   
  gi|91773992|ref|YP_566684.1|  61 GLVPQDSNFYDDRNALSHMIYYGRLKGLSKKEALVQSnalleKVGLEKEKHKQVIYF---SHGMKKRLGIAQALLNNP--- 135
                                   555555555555555555555555555555555555566665555555666666655...99*************999... PP

                        AAA_21 259 sllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                   ++l++DEp ngL+P  +r + ell e+++ g+ +++++H+ l 
  gi|91773992|ref|YP_566684.1| 136 KILILDEPTNGLDPVGIRQIRELLCECNNSGITIFISSHNLLE 178
                                   9***************************************875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-05     0.024       6      55 ..      18     222 ..      16     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH.............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.............................. RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep.............................. 54 
                                   +k G+GKTt+   L  +l     ++++  +D ++++ +i  ++gl+++  +                              
  gi|91773992|ref|YP_566684.1|  18 GKNGAGKTTTIKLLSGLLTPTDGKIIVDGMDMDSESREIkkIMGLVPQDSNfyddrnalshmiyygrlkglskkealvqsn 98 
                                   688****************96666665558888888888889999999999**************9999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|91773992|ref|YP_566684.1|  99 allekvglekekhkqviyfshgmkkrlgiaqallnnpkilildeptngldpvgirqirellcecnnsgitifisshnllei 179
                                   999999999999999999999777777777777777777777777777777766666666666666666666666666666 PP

                                   ..........................................C CS
                                   ..........................................x RF
                          CbiA  55 ..........................................d 55 
                                                                              
  gi|91773992|ref|YP_566684.1| 180 qeicthvgildkgkiiaenkieeirhfesngvitvglynlapK 222
                                   6666666666666666666666666666666666666664444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.3e-05     0.042      38     112 ..       4      85 ..       1     145 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                         Rad17  38 dvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkgltekesrf......lsqiesfke 111
                                    +L+ +k+ i    G  G gk+t++k Ls  l++   +  ++++ + + + + + + gl+ ++s+f      ls +  +  
  gi|91773992|ref|YP_566684.1|   4 ISLNVEKESIYGFLGKNGAGKTTTIKLLSGLLTPTDGKiIVDGMDMDSESREIKKIMGLVPQDSNFyddrnaLSHMIYYGR 84 
                                   57788888899999******************98765516799**999999999********9999666666666655554 PP

                         Rad17 112 l 112
                                   l
  gi|91773992|ref|YP_566684.1|  85 L 85 
                                   4 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   2.7e-05     0.049      16      67 ..       3      51 ..       1      80 [. 0.71
   2 ?    4.3   0.1     0.015        27     299     365 ..     119     175 ..      89     177 .. 0.82
   3 ?   -1.8   0.3       1.1     2e+03     243     278 ..     221     256 ..     193     284 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                        AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedlei 67
                                  ++++++++e +  + GkN++GK++ +++l  +l+ +    + +i ++  d++ 
  gi|91773992|ref|YP_566684.1|  3 NISLNVEKEsIYGFLGKNGAGKTTTIKLLSGLLTPT----DGKIIVDGMDMDS 51
                                  56777777778889****************999988....3333333333333 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                        AAA_15 299 sGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   +G++  l ++  +l+         +++il+++EP + L p   +++ +ll+e  n++   ++i++H+
  gi|91773992|ref|YP_566684.1| 119 HGMKKRLGIAQALLN---------NPKILILDEPTNGLDPVGIRQIRELLCECNNSGI-TIFISSHN 175
                                   555555555555444.........4667****************************99.9******8 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                        AAA_15 243 keiqeklkeidkklaeelkkilkkkidkikkfnykg 278
                                   ++i + ++ +++ +++elk++    i+   k+ +k+
  gi|91773992|ref|YP_566684.1| 221 PKIINLIESLEFVVKTELKSEHVLEIFVNSKGDVKP 256
                                   455555555555555555522222222212222222 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    0.0001      0.18      21      50 ..      10      39 ..       2      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                        AAA_29 21 lkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   ++++ + G++G+GK+T +  ++ lL+p+ 
  gi|91773992|ref|YP_566684.1| 10 KESIYGFLGKNGAGKTTTIKLLSGLLTPTD 39
                                  44477799***********99999999975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2    0.0001      0.18       4      38 ..      14      48 ..      11      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  + ++G +GaGKTtt+  L+ ll+    k+++  +D
  gi|91773992|ref|YP_566684.1| 14 YGFLGKNGAGKTTTIKLLSGLLTPTDGKIIVDGMD 48
                                  5689***********99999998888887776666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00031      0.56      22      50 ..      15      43 ..       6     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                        AAA_30 22 vltGpAGtGKttalkalreaweaaggrvi 50
                                     G  G+GKtt++k l  +++   g++i
  gi|91773992|ref|YP_566684.1| 15 GFLGKNGAGKTTTIKLLSGLLTPTDGKII 43
                                  567999***********999998855554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00016      0.29      23      67 ..      18      62 ..       5      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                    Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilka 67
                                  G  GAGK+++++ll   l+++++ + +d+ d+ +  +e ++i+  
  gi|91773992|ref|YP_566684.1| 18 GKNGAGKTTTIKLLSGLLTPTDGKIIVDGMDMDSESREIKKIMGL 62
                                  899****************99999999999988888888887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.8   0.00011       0.2      19      44 ..      11      36 ..       2      57 .. 0.82
   2 ?   -1.2   0.1       1.4   2.4e+03     167     180 ..      96     109 ..      37     163 .. 0.66
   3 ?   -0.7   0.0      0.93   1.7e+03      56      93 ..     225     276 ..     211     290 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                        AAA_23 19 kgltlItGpNGaGKTTildAiklaLy 44
                                    ++ + G+NGaGKTT +  +   L+
  gi|91773992|ref|YP_566684.1| 11 ESIYGFLGKNGAGKTTTIKLLSGLLT 36
                                  468899***********998887776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                        AAA_23 167 dekkllekleqeke 180
                                   + + llek+  eke
  gi|91773992|ref|YP_566684.1|  96 QSNALLEKVGLEKE 109
                                   22223343322222 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.93
                        AAA_23  56 rgfeksdveiesegkvkayveltfenkdgry..............trsiere 93 
                                   + +e+ ++ +++e k + ++e+ +++k++ +               + ie++
  gi|91773992|ref|YP_566684.1| 225 NLIESLEFVVKTELKSEHVLEIFVNSKGDVKpeinklivenggnvFKLIENS 276
                                   4455555555555555555555555544432222222222222223444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 2437.41
//
Query:       gi|91773993|ref|YP_566685.1|  [L=249]
Description: hypothetical protein Mbur_2059 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-16   59.0  17.0    4.4e-16   59.0  17.0    2.1  2  ABC2_membrane_2  ABC-2 family transporter protein
    7.5e-06   25.3  33.0    7.5e-06   25.3  33.0    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein
    6.6e-05   22.9  18.4    6.6e-05   22.9  18.4    1.8  2  ABC2_membrane_4  ABC-2 family transporter protein
     0.0039   16.8  27.8     0.0039   16.8  27.8    2.7  3  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.1     0.028   1.3e+02     166     207 ..      23      66 ..      20      67 .. 0.79
   2 !   59.0  17.0   9.8e-20   4.4e-16      82     288 .]      65     249 .]      60     249 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.028
               ABC2_membrane_2 166 vasvlllllvvflalglllS..svarssreaaalalglfvvlai 207
                                   +++  ++++++fla+ +  S  s++ +s + +++ l+l++v ++
  gi|91773993|ref|YP_566685.1|  23 LFFGGTFIFLCFLAIHYSASilSLFPNSMNNLTYHLILYFVVLV 66 
                                   5667778878*******999333578999999999999999765 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 9.8e-20
               ABC2_membrane_2  82 avlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledll 162
                                    v++p++++++++d+i+ E+e g+++   sk + R + +lgKf + +++      a++++ +++ ++i  +g+ l+le+ +
  gi|91773993|ref|YP_566685.1|  65 LVIGPFMILVTSFDSISNEMETGSIRYIISK-IDRTSFILGKFFALFIV---FTSAAFVVAVIGQIYIYFSGNGLQLEKSI 141
                                   689***************************9.*****************...999999999******************** PP

               ABC2_membrane_2 163 llvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayn 243
                                      v+s l+l   +f+++++++S++++++++++++a   fv+l  lv i+l+g         +         +l++  +y 
  gi|91773993|ref|YP_566685.1| 142 MWWVFSSLYLG--CFISIFIFVSTLSKNNKTSLTMA---FVFLGSLVFIFLQG-------DDN---------YLKYLTPYF 201
                                   *******8888..**************999999976...55566666677744.......667.........9******** PP

               ABC2_membrane_2 244 tllneilagsdlna...lgstatnllilllllavllvlgyvlFkrkDl 288
                                   ++++ +   s++ +   ++   ++++++l++++++l +++ ++kr+Dl
  gi|91773993|ref|YP_566685.1| 202 YGVKNMGILSGFPDeieYTEVLKSIFAMLIYTTAFLSMSLAALKRRDL 249
                                   ******99999999999******************************7 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   6.4      0.36   1.6e+03     241     284 ..      24      67 ..      18      72 .. 0.67
   2 !   25.3  33.0   1.7e-09   7.5e-06     153     343 ..      48     240 ..      35     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.36
               ABC2_membrane_3 241 ll.llfllfglayialgyllsslfknsetaqilifivilllsgff 284
                                   ++   f++ ++++i  ++ + slf ns +  +  +i+ +   +++
  gi|91773993|ref|YP_566685.1|  24 FFgGTFIFLCFLAIHYSASILSLFPNSMNNLTYHLILYF-VVLVI 67 
                                   344567777999999999999999999887777666666.33333 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.7e-09
               ABC2_membrane_3 153 eeelsnvasflvg...liliilifitasfiav...siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll 227
                                   +++ +n ++ l+    +++i +++i +    +   si +E e++ +  +++  +++++++l+k++++f+v+   ++++ ++
  gi|91773993|ref|YP_566685.1|  48 PNSMNNLTYHLILyfvVLVIGPFMILV----TsfdSISNEMETGSIRYIISK-IDRTSFILGKFFALFIVFTSAAFVVAVI 123
                                   455556666544411133333344444....334489*********998777.******************9998887775 PP

               ABC2_membrane_3 228 .....afgl.gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifs 302
                                        +f+  g++ + ++   +++ l++ ++i+++ ++s+l+kn +t  + + +v+l  s++f++   l+  +++lk+++ 
  gi|91773993|ref|YP_566685.1| 124 gqiyiYFSGnGLQLEKSIMWWVFSSLYLGCFISIFIFVSTLSKNNKTSLT-MAFVFL-GSLVFIF---LQGDDNYLKYLTP 199
                                   553322222445555555555**************************776.444444.4444444...4467777665544 PP

               ABC2_membrane_3 303 iiPffapglgllrli.......tgdplweillsliilalfavvyllla 343
                                   ++    +g+  + ++           + e+l s++++++ + ++l ++
  gi|91773993|ref|YP_566685.1| 200 YF----YGVKNMGILsgfpdeiE---YTEVLKSIFAMLIYTTAFLSMS 240
                                   43....33333344324334322...3579999999999999888776 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  18.4   1.5e-08   6.6e-05      10     175 ..      16     178 ..      14     181 .. 0.79
   2 ?   -0.4   0.1      0.22   9.9e+02     121     151 ..     208     239 ..     201     245 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
               ABC2_membrane_4  10 krskivwllvlaallvpl.lallyfnllgktgldpaefysls...vfgftlllllplilgiiasylifrEeqndtlknLlt 86 
                                   + sk  +l++ +++++   la+ y   ++  +l+p+++  l+    + f +l++ p+++ + +  +i++E + + ++++  
  gi|91773993|ref|YP_566685.1|  16 RGSKNKYLFFGGTFIFLCfLAIHY--SASILSLFPNSMNNLTyhlILYFVVLVIGPFMILVTSFDSISNEMETGSIRYIIS 94 
                                   557777888888887754144444..44557889999988763335567788999***********************987 PP

               ABC2_membrane_4  87 iPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvl 167
                                     + rt+++l+K+++l+++   ++ ++f+++v+ +++  +++ ++ ++ +++++++   l++  +++  i++++l k++ +
  gi|91773993|ref|YP_566685.1|  95 K-IDRTSFILGKFFALFIV---FTSAAFVVAVI-GQIYIYFSGNGLQLEKSIMWWVFSSLYLGCFISIFIFVSTLSKNNKT 170
                                   6.*************9985...55455665555.5777777788888889999999999999988998999********** PP

               ABC2_membrane_4 168 pliltlvy 175
                                   +l++++v+
  gi|91773993|ref|YP_566685.1| 171 SLTMAFVF 178
                                   ******98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.22
               ABC2_membrane_4 121 allsgfvg.fsvklvlellkkclelgllvffa 151
                                   ++lsgf++ ++ + vl++++ +l+++   + +
  gi|91773993|ref|YP_566685.1| 208 GILSGFPDeIEYTEVLKSIFAMLIYTTAFLSM 239
                                   56777765577777777777666554433333 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   3.7     0.038   1.7e+02     146     192 ..      20      66 ..      14      68 .. 0.56
   2 !   16.8  27.8   8.7e-07    0.0039      36     169 ..      60     193 ..      34     213 .. 0.80
   3 ?    3.1   0.8     0.013        60     109     136 ..     215     242 ..     201     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.038
               ABC2_membrane_5 146 grivliiiifgiifllvaifslsklelslidlsnyilliillviill 192
                                    +++++   f++ ++l   +s s l+l+ ++++n++  +il +++l+
  gi|91773993|ref|YP_566685.1|  20 NKYLFFGGTFIFLCFLAIHYSASILSLFPNSMNNLTYHLILYFVVLV 66 
                                   45555555555444555557777777776666666655555555554 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.7e-07
               ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.vtise 115
                                   ++++++++ ++++ ++ + ++s++   ++ +y+++  ++r   +  K++ ++i++++a +++++++ i+ +++gn ++++ 
  gi|91773993|ref|YP_566685.1|  60 LYFVVLVIGPFMILVTSFDSISNEMETGSIRYIIS-KIDRTSFILGKFFALFIVFTSAAFVVAVIGQIYIYFSGNgLQLEK 139
                                   45778888888888889999997777777777766.6***************************************99999 PP

               ABC2_membrane_5 116 vllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifslsk 169
                                   ++++++++ ++   f++i++ +  + ++ k+ + + ++++g  ++++     ++
  gi|91773993|ref|YP_566685.1| 140 SIMWWVFSSLYLGCFISIFIFVSTLSKNNKTSLTMAFVFLGSLVFIFLQGDDNY 193
                                   9999999999999999999999999999****9999999998777775444444 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.013
               ABC2_membrane_5 109 gnvtisevllsiliglvialiflaivlP 136
                                   +++   evl+si+++l+++++fl+++l 
  gi|91773993|ref|YP_566685.1| 215 DEIEYTEVLKSIFAMLIYTTAFLSMSLA 242
                                   4577789*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1594.74
//
Query:       gi|91773994|ref|YP_566686.1|  [L=122]
Description: hypothetical protein Mbur_2060 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2   5.5       0.26   11.1   1.1    2.4  2  IRK       Inward rectifier potassium channel transmembrane do


Domain annotation for each model (and alignments):
>> IRK  Inward rectifier potassium channel transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2    0.0043        77     116     140 ..      23      47 ..      18      49 .. 0.84
   2 ?   11.1   1.1   1.5e-05      0.26      83     126 ..      65     108 ..      55     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0043
                           IRK 116 llviqsivgllidavlvgivlaKla 140
                                   ll i+  +g ++ a+lvgi++ K+a
  gi|91773994|ref|YP_566686.1|  23 LLEIDPTYGGIVGAILVGIIIGKIA 47 
                                   5567778899*************98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1.5e-05
                           IRK  83 ksftsallfslEtqttigyGsrvvteeCpeailllviqsivgll 126
                                      ++++lf+lE +t +gyG  v+       +++ ++ si+g +
  gi|91773994|ref|YP_566686.1|  65 IGWVTTFLFTLEGKTILGYGGGVTGVFLGFILIMTIFYSIIGSI 108
                                   567899**************988777666666777777888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 876.22
//
Query:       gi|91773995|ref|YP_566687.1|  [L=147]
Description: hypothetical protein Mbur_2061 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1168.69
//
Query:       gi|91773996|ref|YP_566688.1|  [L=325]
Description: cytochrome c biogenesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-19   68.6  19.6    6.7e-19   68.6  19.6    1.6  2  DsbD           Cytochrome C biogenesis protein transmembrane 
    1.8e-05   24.7   0.2    3.1e-05   24.0   0.2    1.4  1  Thioredoxin_3  Thioredoxin domain
     0.0015   18.7   0.2     0.0033   17.6   0.2    1.5  1  Glutaredoxin   Glutaredoxin
     0.0025   18.2   0.4     0.0038   17.6   0.4    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.045   13.8   0.1      0.066   13.2   0.1    1.2  1  Thioredoxin    Thioredoxin
       0.15   12.4   2.2       0.43   10.9   1.0    2.2  2  ASFV_L11L      African swine fever virus (ASFV) L11L protein
       0.65    9.8   0.1       0.65    9.8   0.1    4.8  5  LapA_dom       Lipopolysaccharide assembly protein A domain
        1.7    8.3   4.2       0.71    9.5   0.2    2.4  2  DUF3918        Protein of unknown function (DUF3918)
        3.1    6.4   9.1        5.5    5.5   9.1    1.4  1  EMP70          Endomembrane protein 70


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 ?   -2.3   0.1       1.7   3.3e+03      48      70 ..       3      25 ..       2      32 .. 0.79
   2 !   68.6  19.6   3.3e-22   6.7e-19       4     212 ..     128     324 ..     125     325 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                          DsbD 48 lFvlGlslvfvslglsaaflgql 70
                                  +F l +s+ ++s+ +saa+ +q+
  gi|91773996|ref|YP_566688.1|  3 FFFLLFSILLLSIPISAAQPIQI 25
                                  57788999999999999987776 PP

  == domain 2  score: 68.6 bits;  conditional E-value: 3.3e-22
                          DsbD   4 aGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevirrvagl 84 
                                    Gl + +sPC+++++   ls+ +g+s + +         + +a++F +Gl + ++++g++     + l d+ e   +v+g+
  gi|91773996|ref|YP_566688.1| 128 LGLFAGFSPCLMAILGFLLSFTAGTSESARSG-------MERAIVFGVGLMTSYLAIGVGLLVFRKTLPDM-ELFSVVTGI 200
                                   599********************999877766.......6899*************************887.67899**** PP

                          DsbD  85 ivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskeslakgallllvyv 165
                                   ivi +Gl ++g f++++    k  ++  +k+  ++ g + lG++F+l+  PC+ P+l  +l  + +++++   + ll++++
  gi|91773996|ref|YP_566688.1| 201 IVIGIGLYLMGFFSLPM-SLDKYFQNKARKHAGTIGGLFFLGVLFSLVKVPCTVPMLLVLLNKTFTEGTIG-DLALLFAFS 279
                                   **************885.4455555555666666888999*********************9999999554.57899**** PP

                          DsbD 166 lGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvlll 212
                                    G  +pfl +gl+ +  +  +k +++++++++ ++g+ lvllG+ ++
  gi|91773996|ref|YP_566688.1| 280 FGVLTPFLGIGLVGGYTL--SKHVREHKRYLKLISGISLVLLGLWVM 324
                                   ***************777..9**********************9887 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   1.5e-08   3.1e-05       7      61 ..      30      88 ..      22     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.5e-08
                                  SSSSTTCHHHHHHHHHHCHCCT.CEC...EEECCTTHHHHHHCT-SSSSEEECTTCEEE CS
                 Thioredoxin_3  7 gpgCakCpklekavkeaaaekg.ika...evekvtdfeeiekygVmsvPalvidgkvvv 61
                                  ++gC+ C+ +e ++ ++ ++ + +++   +v++++ f++ ++yg + vPa+vi+ + ++
  gi|91773996|ref|YP_566688.1| 30 QTGCHDCEITEPIIDQIEKQYEyVEIvrtDVINTEGFKQWNQYGFIEVPAVVINNETKI 88
                                  789*****999999999999976887888*************************99876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   1.6e-06    0.0033       1      58 [.      25      85 ..      25      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                  EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHH..TSSSSSEEEETTE CS
                  Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde.eireelkels..gvrtvPqvfidgk 58
                                  +++f  ++C +C  +  + ++   ++e++++   +   +e  k+ +  g+  vP v+i+++
  gi|91773996|ref|YP_566688.1| 25 IEYFHQTGCHDCEITEPIIDQIEKQYEYVEIVRTDvINTEGFKQWNqyGFIEVPAVVINNE 85
                                  789***************************999987888889999899**********986 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   1.9e-06    0.0038       3      81 ..      26     102 ..      24     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                                   EEEE-TT-HHHHHHHHHHHHHCCCTT.EEEEEEETTT-CC..CHCCCCT.TTTEEEECTTCGGB.TCCECGCCB-HHHHHH CS
                        DUF836   3 tLyskpgChlCeqakekLkelkleeg.leleviDIakdee..leakYgl.eipvlalegvkktsslleelswrldeeqLaa 79 
                                     +   gCh Ce  + ++ +++++ + +e+++ D+ + e    +++Yg  e+p +++++      ++++ + +++ee+L+ 
  gi|91773996|ref|YP_566688.1|  26 EYFHQTGCHDCEITEPIIDQIEKQYEyVEIVRTDVINTEGfkQWNQYGFiEVPAVVINN------ETKIPKEEITEEKLRL 100
                                   568889*************998888879********888855566999559********......5788888888888876 PP

                                   HH CS
                        DUF836  80 el 81 
                                   ++
  gi|91773996|ref|YP_566688.1| 101 SI 102
                                   55 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.3e-05     0.066      21     101 ..      23     106 ..      16     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                                   EEEE.EE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSH..HHHHHTT-SSSSEEEEEETTE.EEEEEESS-HHHHH CS
                   Thioredoxin  21 vlve.FyApwCghCkalaPeleklaeelkdkvklakvdvdene..dlakkyevegiPtlklfkngk.evkkyegarekekl 97 
                                   + +e F  + C  C   +P ++++ ++++  v +++ dv + e  +  ++y+   +P++++ ++ k   +++++++ + ++
  gi|91773996|ref|YP_566688.1|  23 IQIEyFHQTGCHDCEITEPIIDQIEKQYE-YVEIVRTDVINTEgfKQWNQYGFIEVPAVVINNETKiPKEEITEEKLRLSI 102
                                   5555155677*******************.89999988876662256789999******9999999666667777766777 PP

                                   HHHH CS
                   Thioredoxin  98 aafl 101
                                   +++l
  gi|91773996|ref|YP_566688.1| 103 EKYL 106
                                   7766 PP

>> ASFV_L11L  African swine fever virus (ASFV) L11L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.21   4.3e+02      15      61 ..     182     228 ..     175     236 .. 0.81
   2 ?   10.9   1.0   0.00022      0.43      18      59 ..     219     263 ..     207     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                     ASFV_L11L  15 liflysyfkiklhklitialflgclffilrdfcfppmlwtilqnitl 61 
                                   l+f  +   + l  ++t  + +g  ++++  f +p  l + +qn + 
  gi|91773996|ref|YP_566688.1| 182 LVFRKTLPDMELFSVVTGIIVIGIGLYLMGFFSLPMSLDKYFQNKAR 228
                                   66667777788999999999999999999999999999999998765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                     ASFV_L11L  18 lysyfkiklhkli.ti..alflgclffilrdfcfppmlwtilqni 59 
                                   l  yf+ k  k   ti   +flg lf +++  c  pml   l+++
  gi|91773996|ref|YP_566688.1| 219 LDKYFQNKARKHAgTIggLFFLGVLFSLVKVPCTVPMLLVLLNKT 263
                                   556887777765324421589*****************9999875 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.9      0.24   4.8e+02      19      40 ..     128     149 ..     119     163 .. 0.59
   2 ?   -0.1   0.4      0.41   8.1e+02      24      40 ..     163     179 ..     147     188 .. 0.77
   3 ?    9.8   0.1   0.00033      0.65      24      53 ..     200     229 ..     191     231 .. 0.88
   4 ?   -2.5   0.8       2.3   4.7e+03      27      39 ..     238     246 ..     234     249 .. 0.53
   5 ?    0.8   0.4      0.21   4.3e+02      22      50 ..     273     305 ..     272     312 .. 0.50

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.24
                      LapA_dom  19 LsllllvafgiGallgwllslw 40 
                                   L+l   ++  + a+lg+lls+ 
  gi|91773996|ref|YP_566688.1| 128 LGLFAGFSPCLMAILGFLLSFT 149
                                   5555555555556666666654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.41
                      LapA_dom  24 lvafgiGallgwllslw 40 
                                   +++fg+G++  +l+  +
  gi|91773996|ref|YP_566688.1| 163 AIVFGVGLMTSYLAIGV 179
                                   78999999999998765 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00033
                      LapA_dom  24 lvafgiGallgwllslwsylrlrrelrrlk 53 
                                   ++++giG+ l++++sl++ l +  ++++ k
  gi|91773996|ref|YP_566688.1| 200 IIVIGIGLYLMGFFSLPMSLDKYFQNKARK 229
                                   7999****************9999998876 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.3
                      LapA_dom  27 fgiGallgwllsl 39 
                                   f++G    +l+sl
  gi|91773996|ref|YP_566688.1| 238 FFLG----VLFSL 246
                                   5555....55554 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.21
                      LapA_dom  22 lllvafgiGallgwllsl....wsylrlrrelr 50 
                                    ll+af +G+l  +l       ++  ++ re++
  gi|91773996|ref|YP_566688.1| 273 ALLFAFSFGVLTPFLGIGlvggYTLSKHVREHK 305
                                   567777777765444333211133334444444 PP

>> DUF3918  Protein of unknown function (DUF3918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00036      0.71       4      19 ..     170     185 ..     162     187 .. 0.94
   2 ?   -1.6   0.5       1.1   2.1e+03       5      17 ..     197     209 ..     196     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                       DUF3918   4 lmtSllalGaGaaayq 19 
                                   lmtS la+G+G ++++
  gi|91773996|ref|YP_566688.1| 170 LMTSYLAIGVGLLVFR 185
                                   7************986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                       DUF3918   5 mtSllalGaGaaa 17 
                                   +t ++ +G+G + 
  gi|91773996|ref|YP_566688.1| 197 VTGIIVIGIGLYL 209
                                   678899****875 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.1    0.0028       5.5     265     396 ..     163     299 ..     139     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0028
                         EMP70 265 svlvGsGvqlllmalvtlllallgflspsnrgslltvalllyvllgliaGYvs..arlyktfggekwkkntlltalllpgl 343
                                   +++ G+G+    +a+++ ll + ++l   +  s++t +++++ +  ++ G++s  ++l k+f+++  k+   + +l++ g+
  gi|91773996|ref|YP_566688.1| 163 AIVFGVGLMTSYLAIGVGLLVFRKTLPDMELFSVVT-GIIVIGIGLYLMGFFSlpMSLDKYFQNKARKHAGTIGGLFFLGV 242
                                   678888888888888888888777775555555554.4555566778889999556779****999999999999999999 PP

                         EMP70 344 lflvffl....lnlilwakessgalpfgtlvlllllwflisvPlvliGsllgfkkka 396
                                   lf+++ +      l+++++++ +   +g l ll+++ f++ +P+  iG + g++ ++
  gi|91773996|ref|YP_566688.1| 243 LFSLVKVpctvPMLLVLLNKTFTEGTIGDLALLFAFSFGVLTPFLGIGLVGGYTLSK 299
                                   9998765444467788999999999***********************999998442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2182.71
//
Query:       gi|91773997|ref|YP_566689.1|  [L=391]
Description: hypothetical protein Mbur_2063 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2568.83
//
Query:       gi|91773998|ref|YP_566690.1|  [L=210]
Description: hypothetical protein Mbur_2064 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1438.52
//
Query:       gi|91773999|ref|YP_566691.1|  [L=245]
Description: UbiA prenyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  101.0  13.8    8.2e-29  100.6  13.8    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 !  100.6  13.8   4.6e-33   8.2e-29      22     225 ..       6     205 ..       3     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 4.6e-33
                          UbiA  22 llllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllalll 102
                                   ++l++l++++++++  +lNd+fD+eiD++   +pn +++sG++s k+a+ ++i+l+ ++ll++ + l++ ++l++l+++++
  gi|91773999|ref|YP_566691.1|   6 AILVILTGMMIHSGCDILNDIFDFEIDKI--CKPNGAIASGQMSMKKAWGYMILLFSVALLIA-FKLSLILFLCLLAGIII 83 
                                   578899999********************..********************************.***************** PP

                          UbiA 103 y.vvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlp 180
                                   + ++Y+ + +r+K+++ ++ +  +++f+l  ++ w +++  l++  l++a+ +f+l++++ +++d++d+ gD    i++lp
  gi|91773999|ref|YP_566691.1|  84 GgIMYShPmFRFKDIPGIAMLDMAVCFALESIGLWSVYSP-LTPDSLMVAAYIFVLIFSLTFMKDFKDVAGD----INSLP 159
                                   *******99***********************99999987.699999999999**************99999....9**** PP

                          UbiA 181 vvlGrkaarillalllavllla.llllllalllllylllalllaal 225
                                   +++G ++a+i++ ll +++l+  l++++ +++l+l++l++++l+a 
  gi|91773999|ref|YP_566691.1| 160 LKIGIRRAAIVCSLLAILPLIPlLYAVTKYHYLSLAALIYVVLIAG 205
                                   **********877666666666333333333444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1561.90
//
Query:       gi|91774000|ref|YP_566692.1|  [L=226]
Description: AsnC family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-06   25.7   0.1    2.8e-05   23.6   0.1    2.1  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0018   18.2   0.0     0.0046   16.8   0.0    1.7  1  MarR            MarR family
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.026   14.3   0.0    1.7  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.016   15.3   0.0       0.03   14.5   0.0    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.058   13.5   0.0       0.52   10.4   0.0    2.1  2  HTH_20          Helix-turn-helix domain
       0.13   12.2   0.0       0.28   11.1   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   9.5e-09   2.8e-05       1      47 [.      24      71 ..      24      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.5e-09
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSps.tvnrrlkrLeeeGlI 47
                                  l+etd  IL +L+kn++i+++eLA+ l+   +    ++ +++++eGlI
  gi|91774000|ref|YP_566692.1| 24 LNETDMFILLTLMKNSKITNSELAKILDFKDGnSAAYHTRNMQKEGLI 71
                                  799999*********************976541689999999999999 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-06    0.0046       1      51 [.      24      75 ..      24      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HH.HHHHHHHHHHHTTSEEEEE CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvsks.tvtrvldrLekkGlieRsk 51
                                  l++t + iL +l  +  +++seLak l  + + ++   ++ + k+Gli+R+ 
  gi|91774000|ref|YP_566692.1| 24 LNETDMFILLTLMKNSKITNSELAKILDFKDGnSAAYHTRNMQKEGLIDRYT 75
                                  799**************************9983599**************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 ?   -3.0   0.1       2.3   6.9e+03       1       6 [.       3       8 ..       3       9 .. 0.87
   2 ?   14.3   0.0   8.9e-06     0.026       1      27 [.      24      50 ..      24      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.3
                 HTH_AsnC-type 1 LDeiDr 6
                                 LDe+D+
  gi|91774000|ref|YP_566692.1| 3 LDETDQ 8
                                 8***96 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.9e-06
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAerv 27
                                  L e+D  IL  L+++++i+++eLA+ +
  gi|91774000|ref|YP_566692.1| 24 LNETDMFILLTLMKNSKITNSELAKIL 50
                                  679*********************976 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 ?   14.5   0.0     1e-05      0.03      19      61 ..      41      84 ..      31     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                B-block_TFIIIC 19 itqsdLakesk.qdprslfyrlksLekkgLIvkqsiidsatkks 61
                                  it s+Lak+++ +d++s  y+++ ++k gLI + +i+  ++ ++
  gi|91774000|ref|YP_566692.1| 41 ITNSELAKILDfKDGNSAAYHTRNMQKEGLIDRYTIVPNWKRAG 84
                                  799********************************974444444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.52      15      56 ..      31      73 ..      16      76 .. 0.83
   2 ?    0.5   0.0      0.22   6.6e+02      28      49 ..     197     219 ..     195     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                  HHHHHSTCTTB-HHHHHHHHTS-HHH.HHHHHHHHHHCTTEEE CS
                        HTH_20 15 ilraLaraegltaselaerldlsknt.lsyHLrvLeeagLvev 56
                                  il  L+ +   t sela+ ld ++ + + yH r +++ gL+++
  gi|91774000|ref|YP_566692.1| 31 ILLTLMKNSKITNSELAKILDFKDGNsAAYHTRNMQKEGLIDR 73
                                  6677778888899********666666**************97 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                                   HHHHHHHTS-HHH.HHHHHHHHH CS
                        HTH_20  28 selaerldlsknt.lsyHLrvLe 49 
                                   + l+e+++++ ++  s+ L++L+
  gi|91774000|ref|YP_566692.1| 197 AKLKELFQIPEKEeTSDTLDKLQ 219
                                   56889999999999*******95 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.4e-05      0.28       2      53 ..      19      72 ..      18      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.4e-05
                                  H.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSC.HCHHHHHHHHHHCTSEE CS
                          TrmB  2 q.klGLseyEakvYlaLlklgpatadeiaeelgvpr.skvYevLrsLedkGlVe 53
                                  + + +L+e+++ + l+L+k+ + t +e+a++l+    +++    r++ + Gl++
  gi|91774000|ref|YP_566692.1| 19 SeVSNLNETDMFILLTLMKNSKITNSELAKILDFKDgNSAAYHTRNMQKEGLID 72
                                  55779**************************99753123333346666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1482.82
//
Query:       gi|91774001|ref|YP_566693.1|  [L=392]
Description: aminotransferase, class V [Methanococcoides burtonii DSM 6242]
Scores for complete 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-126  420.7   0.0   5.1e-126  420.6   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    1.2e-08   34.7   0.1    1.8e-08   34.1   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      2e-07   29.9   0.0    2.6e-07   29.5   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00037   19.9   0.0    0.00066   19.1   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
        0.1   11.3   0.0       0.34    9.6   0.0    1.7  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas


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 !  420.6   0.0  1.4e-129  5.1e-126       1     371 []      18     381 ..      18     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.6 bits;  conditional E-value: 1.4e-129
                                   EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHC CS
                   Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsl 81 
                                   iylds Attq+p ++++++++y+ +y+an  r++h+l+ ++t+ +e+ar+ vae++n+ s + +ift+++te+in+v l+l
  gi|91774001|ref|YP_566693.1|  18 IYLDSGATTQTPVQAVNSMNDYFFKYAANHGRGAHRLARQTTDHYEDARDIVAEFLNIGS-DGTIFTKNATESINMVSLGL 97 
                                   8**********************************************************9.******************** PP

                                   CCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHH CS
                   Aminotran_5  82 arslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeig 162
                                     ++++gd++v+t++ehh+nl+pw +l+ ++g++v+v+  d+eg++d+++++++++++t+lv+++hvsnv G + +v++i+
  gi|91774001|ref|YP_566693.1|  98 --KWETGDHVVTTVVEHHSNLLPWMRLR-EQGVEVTVVGSDREGNVDPKDIDEAITDRTRLVSVNHVSNVFGSVRDVKKIT 175
                                   ..59***********************8.77************************************************** PP

                                   HHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEH CS
                   Aminotran_5 163 klakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleettfa 242
                                   ++a+++++l lvD++q++gh+p+d+k++++Df+   ghK llgP+G+Gvl++++   e lep+++gg++v+ v+ e++ ++
  gi|91774001|ref|YP_566693.1| 176 QIAHRSEVLSLVDGSQSAGHMPVDIKNIECDFFITPGHKgLLGPQGTGVLCIKD--PEILEPVYVGGGTVHAVTTESYELE 254
                                   ******************************************************..99*********************** PP

                                   CTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHH CS
                   Aminotran_5 243 eapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaed 323
                                     pskfeaGTpn++giiglg a+ey+++ig+eaiekhekela+ +  rl+++ gv++ygp   + r+++v fn++g++++d
  gi|91774001|ref|YP_566693.1| 255 PYPSKFEAGTPNIPGIIGLGRAVEYVKDIGVEAIEKHEKELAQDTATRLAEIVGVEVYGP---KDRTGVVPFNVQGMNPHD 332
                                   ***********************************************************9...9***************** PP

                                   HHHHHHHT.TEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                   Aminotran_5 324 vatlLdee.gIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                   va++Lde+ +I+vrsG hca+p+++++++egtvRaS+++ynt+eevd l
  gi|91774001|ref|YP_566693.1| 333 VAMILDETrKICVRSGYHCAMPSVDLIGVEGTVRASFALYNTKEEVDSL 381
                                   **********************************************986 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 !   34.1   0.1   5.1e-12   1.8e-08      36     150 ..      75     194 ..      54     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.1e-12
                                   HT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHH...HHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEE CS
               DegT_DnrJ_EryC1  36 lgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatana...vlelgakpvfvDvdpdtynidpaaieaaitertk 113
                                   +g++  i + ++t+++ ++   l+ + gd V+++ +   +   +    +e g ++  v  d    n+dp++i +ait rt+
  gi|91774001|ref|YP_566693.1|  75 IGSDGTIFTKNATESINMVSLGLKWETGDHVVTTVVEHHSNLLPwmrLREQGVEVTVVGSD-REGNVDPKDIDEAITDRTR 154
                                   468888999******99999999999*******9887777766511156667777777777.789***************9 PP

                                   EEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
               DegT_DnrJ_EryC1 114 aIlpVh...lyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                    + + h   ++G v d++++++ia++ ++  + D +++ G
  gi|91774001|ref|YP_566693.1| 155 LVSVNHvsnVFGSVRDVKKITQIAHRSEVLSLVDGSQSAG 194
                                   99987733369*********************99999987 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   7.2e-11   2.6e-07      88     181 ..      99     196 ..      27     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.2e-11
                                   S-TTEEEEEESTSSHHHHHHH.HHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHH CS
               Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrll.kkvlkklgievkfvdt.....sdleelekaikentklvylEtptnpllkvvDiekiakl 162
                                    ++Gd++v++  + +  ++ll    l++ g+ev++v        d++++ +ai+++t+lv +  ++n + +v D++ki+++
  gi|91774001|ref|YP_566693.1|  99 WETGDHVVTT--VVEHHSNLLpWMRLREQGVEVTVVGSdregnVDPKDIDEAITDRTRLVSVNHVSNVFGSVRDVKKITQI 177
                                   4678988865..3344444440455677899999987734444688999******************************** PP

                                   HHHTT-EEEEEGTTTHTTT CS
               Cys_Met_Meta_PP 163 akkagvlvvvDntfaspll 181
                                   a+  +vl +vD + +++ +
  gi|91774001|ref|YP_566693.1| 178 AHRSEVLSLVDGSQSAGHM 196
                                   ***********99998854 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.8e-07   0.00066      94     216 ..     125     243 ..      34     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-07
                                   C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHH CS
               Beta_elim_lyase  94 agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfana 174
                                   +gv+++ + ++++G++d++++ +ai++      +++l+s+    n+      s+  ++++++ia++ ++  ++Dg      
  gi|91774001|ref|YP_566693.1| 125 QGVEVTVVGSDREGNVDPKDIDEAITD------RTRLVSVNHVSNV----FGSVRDVKKITQIAHRSEVLSLVDGSQS--- 192
                                   6888888888888*************9......599*********8....5589999******************754... PP

                                   HHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH............. CS
               Beta_elim_lyase 175 akslgeivkemfsyvDsvtmslkKdllanvG.gvlafrddel..........e 216
                                   a ++ +++k++   +D +   + K+ll + G gvl+++d e+           
  gi|91774001|ref|YP_566693.1| 193 AGHMPVDIKNI--ECDFFITPGHKGLLGPQGtGVLCIKDPEIlepvyvgggtV 243
                                   45667778777..6************************996655555555551 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   9.4e-05      0.34      92     242 ..      92     224 ..      86     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 9.4e-05
                                   HHHHH.HHCC--CCEEEEEETCHHH...HHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTCCCEEEEEECSSTTTT CS
                       SepSecS  92 lsalr.krskakkviwvridekSsl...kavelaGleialvekvlegDelitdvedveeiiekkreevilavlstlsffap 168
                                   + +l+ k   +++v+  +++++S l     ++  G+e+++v   +eg    +d++d++e+i+ +     l+ +  +s   +
  gi|91774001|ref|YP_566693.1|  92 MVSLGlKWETGDHVVTTVVEHHSNLlpwMRLREQGVEVTVVGSDREGN---VDPKDIDEAITDRT---RLVSVNHVSNVFG 166
                                   667776777888999999999986511156778899999999999985...89999999998733...4555666677778 PP

                                   B----HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCC CS
                       SepSecS 169 rspDdvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfi 242
                                    + D vk+i++i +  +v  lv g  +                G ++v +k+++ ++++  G++ + +++ +++
  gi|91774001|ref|YP_566693.1| 167 SVRD-VKKITQIAHRSEVLSLVDGSQSA---------------GHMPVDIKNIECDFFITPGHKGLLGPQGTGV 224
                                   8999.999*9999999999999987665...............7777777777777777777776666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2192.50
//
Query:       gi|91774002|ref|YP_566694.1|  [L=426]
Description: hypothetical protein Mbur_2069 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-88  294.7   0.1    1.3e-87  294.1   0.1    1.2  1  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 !  294.1   0.1   7.2e-92   1.3e-87       1     323 []      71     391 ..      71     391 .. 0.92

  Alignments for each domain:
  == domain 1  score: 294.1 bits;  conditional E-value: 7.2e-92
                          YcaO   1 nGkGateeaArasalgEalErysaegffr........gdekrvrasyrelegegaldpeelglyseeekdaadfvlepfdp 73 
                                   +GkGa+e +Ar+sa++E++Er  ae +           +++ +++s ++ e++++ld ++l l+            ep++ 
  gi|91774002|ref|YP_566694.1|  71 SGKGASEGQARISAMMESFERCLAERVSVnadideeiAADEFIESSDKATEDHELLDVHSLLLF------------EPITS 139
                                   6*********************888555566666665555555566666688888888888888............9**** PP

                          YcaO  74 drpidwvpgwsltdgeevlvPanlvyl.yeppegearlfletsnGlAaGntleeAilhGllEliERdafalawyerlplpr 153
                                   d+ ++w++gw+l++++e++vP n+v++ y++p ++a+lf++++nGlA+Gn +eeAilhGllE+iERda+++  ++r p ++
  gi|91774002|ref|YP_566694.1| 140 DKLVEWTKGWDLLQEKEIYVPSNAVHHpYDSPGMSAKLFRSNTNGLASGNVIEEAILHGLLEVIERDALSISEFNRNPGKE 220
                                   ********************************************************************************9 PP

                          YcaO 154 idla.sdpeirellerlreagievrlldatldlgipvvaavlvd...pk.lllvagaGahldpevAlerAltElaqsrltl 229
                                   + l  +d   +el++++++ag++++l+ +++d+ +++++a  +d   ++ +llv+gaG+hl+pe+A++rA+tE+aqsr  +
  gi|91774002|ref|YP_566694.1| 221 LVLTeNDGLSYELVKKFENAGVQIKLWYLQHDTAVTTILAATDDlelKDaALLVMGAGSHLKPEIAVRRAITEAAQSRVVQ 301
                                   9976477*************************************87633688999************************** PP

                          YcaO 230 isgaredpdfdeeladvatleradreallwlpeaaakrldfllfaewassgdleedletllerlkaagldvlvvdltrpdl 310
                                   i+gared+d+ e++ ++ ++er++r++++w++e+++ +ld     ++ s+++++e+++ +l++l++    ++vvdl+r+++
  gi|91774002|ref|YP_566694.1| 302 IHGAREDTDR-ESFVRQIGYERMKRMNRFWYDEGESITLDQI---NDISASTPAENIDVVLNELRKVADSAIVVDLSRESI 378
                                   **********.8******************999998777775...566789****************************** PP

                          YcaO 311 glpvvkvivPgle 323
                                   g+pvv+vi+Pg+e
  gi|91774002|ref|YP_566694.1| 379 GVPVVRVIIPGFE 391
                                   ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 2363.25
//
Query:       gi|91774003|ref|YP_566695.1|  [L=214]
Description: TfuA-like protein [Methanococcoides burtonii DSM 6242]
Scores for 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-47  157.7   0.0    1.4e-46  157.1   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 !  157.1   0.0     8e-51   1.4e-46       1     120 []      48     165 ..      48     165 .. 0.99

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 8e-51
                          TfuA   1 DGvfeqepavahkEilaalkegvavvGaasmGALRAaElaafGmigvGeiyeayrsgeledDdeVavlhapaelgyealse 81 
                                   DG+f++++avahkEil+a+++g+ vvG++smGALRA+El+ +GmigvG++ye+yr+g+le+DdeVav+++p+  ++e++s 
  gi|91774003|ref|YP_566695.1|  48 DGMFFDRAAVAHKEILHAMNKGIIVVGGCSMGALRASELDVHGMIGVGKVYEWYRDGVLESDDEVAVITNPE--TFEPVSV 126
                                   9**********************************************************************9..9****** PP

                          TfuA  82 alvnlratlkaaveegiiseeeaaallelakelyykert 120
                                   +lvn+r+tl+aa++egii+e+++ +ll++a el+y+ r+
  gi|91774003|ref|YP_566695.1| 127 SLVNIRETLQAACDEGIIDESTRISLLNIAMELHYPLRS 165
                                   ************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 1418.54
//
Query:       gi|91774004|ref|YP_566696.1|  [L=145]
Description: iron dependent repressor [Methanococcoides burtonii DSM 6242]
Scores for complete 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-15   55.5   0.0    8.1e-15   54.7   0.0    1.5  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    1.2e-11   44.6   0.0    1.8e-11   44.1   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    4.1e-05   23.4   0.0    9.7e-05   22.2   0.0    1.6  1  MarR_2          MarR family
    0.00025   20.9   0.0     0.0004   20.3   0.0    1.3  1  MarR            MarR family
    0.00028   21.3   0.0    0.00046   20.6   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
     0.0038   17.1   0.0      0.008   16.0   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.039   13.5   0.0       0.29   10.7   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.047   14.0   0.0      0.072   13.5   0.0    1.3  1  Rrf2            Transcriptional regulator
      0.047   13.5   0.0       0.11   12.3   0.0    1.6  1  HTH_38          Helix-turn-helix domain
      0.061   13.2   0.0       0.44   10.5   0.0    2.3  2  RuvB_C          RuvB C-terminal winged helix domain
      0.066   13.0   0.0       0.14   12.0   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
       0.11   12.5   0.0       0.24   11.4   0.0    1.5  1  HTH_36          Helix-turn-helix domain
       0.11   11.2   0.0       0.15   10.9   0.0    1.1  1  HTH_micro       HTH-like
       0.15   12.0   0.0       0.39   10.6   0.0    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
       0.16   11.9   0.1       0.32   11.0   0.0    1.6  2  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> 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 !   54.7   0.0   6.8e-18   8.1e-15       1      61 [.      67     126 ..      67     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 6.8e-18
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpee 61 
                                   TekG+ +  +++rrhr+l  +L +++g+ +ee ++e+ r+E  +s+++i+ +++ +g+p++
  gi|91774004|ref|YP_566696.1|  67 TEKGKVYTHFILRRHRILSLML-NHYGLTPEESCKEVARFEGFVSKDAIDSICNSMGHPTF 126
                                   9*********************.89**********************************97 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.5e-14   1.8e-11       2      60 .]       9      64 ..       8      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.5e-14
                                  --HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                Fe_dep_repress  2 LvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                  L++++ +YL+    l e+++ v+t+d+++ ++v ps+ ++ + +L++ Gyv++ +y+g+
  gi|91774004|ref|YP_566696.1|  9 LSPKKIEYLKF---LLEKGDNVRTTDISRHMKVDPSTTTKAITELDSTGYVKHIPYRGV 64
                                  55666667775...567889*************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   8.1e-08   9.7e-05       3      53 ..       9      58 ..       6      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.1e-08
                                  --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  l+p     L +L   +++ ++ +++ r++++++s++++++ +L + G+v  
  gi|91774004|ref|YP_566696.1|  9 LSPKKIEYLKFLLEKGDN-VRTTDISRHMKVDPSTTTKAITELDSTGYVKH 58
                                  567777888888888876.9*****************************75 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.3e-07    0.0004       4      48 ..      12      57 ..       9      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.3e-07
                                  HHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  4 tqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                    ++ L  l e+g+  + +++ ++++v++st+t+++++L   G+++
  gi|91774004|ref|YP_566696.1| 12 KKIEYLKFLLEKGDnVRTTDISRHMKVDPSTTTKAITELDSTGYVK 57
                                  5566666666666559***********************9999885 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.8e-07   0.00046       5      68 .]      13      70 ..       9      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.8e-07
                        HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   + +L  + + ++ ++ +d+++ ++v+ s++ +++ +L   G+v++ +++       v+lT+kG
  gi|91774004|ref|YP_566696.1| 13 KIEYLKFLLEKGDNVRTTDISRHMKVDPSTTTKAITELDSTGYVKHIPYR------GVSLTEKG 70
                                  56777788889999******************************777775......99999999 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.7e-06     0.008       5      57 ..       8      61 ..       5      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
                                  HHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB  5 GLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                   Ls   ++  + Ll k ++ ++++i+++ +v+ s+  +++ +L + G+V+ ++ 
  gi|91774004|ref|YP_566696.1|  8 ELSPKKIEYLKFLLeKGDNVRTTDISRHMKVDPSTTTKAITELDSTGYVKHIPY 61
                                  677777788888995566899****************************98865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.29      13      48 .]      21      57 ..      15      57 .. 0.84
   2 ?    0.0   0.0      0.53   6.4e+02       6      21 ..      81      96 ..      79     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                        HTH_24 13 qknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ++++    ++++++  + pst+++ + +L + G++k
  gi|91774004|ref|YP_566696.1| 21 LEKGDnVRTTDISRHMKVDPSTTTKAITELDSTGYVK 57
                                  4444447789*************************97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.53
                        HTH_24  6 rkILelLqknprisqr 21
                                   +IL+l+  + +++  
  gi|91774004|ref|YP_566696.1| 81 HRILSLMLNHYGLTPE 96
                                  6899998886666654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-05     0.072      21      58 ..      23      59 ..      14      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                                  STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  +++  v++++i++++++ ps   k +++L   g+vk +
  gi|91774004|ref|YP_566696.1| 23 KGD-NVRTTDISRHMKVDPSTTTKAITELDSTGYVKHI 59
                                  344.49*****************************975 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.1e-05      0.11       5      36 ..       9      42 ..       6      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.1e-05
                        HTH_38  5 LsleeReeIerllaeGlslr..eIArrLgrspsT 36
                                  Ls+   e +  ll++G ++r  +I r+++++psT
  gi|91774004|ref|YP_566696.1|  9 LSPKKIEYLKFLLEKGDNVRttDISRHMKVDPST 42
                                  888888999999*********************9 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 ?   10.5   0.0   0.00036      0.44       4      44 ..       9      47 ..       6      75 .. 0.81
   2 ?   -0.5   0.0      0.98   1.2e+03      25      46 ..     113     134 ..     104     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                                  --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
                        RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedvi 44
                                  L+++ i+yLk+l e  kg  v+ + ++ +++++ +t ++ i
  gi|91774004|ref|YP_566696.1|  9 LSPKKIEYLKFLLE--KGDNVRTTDISRHMKVDPSTTTKAI 47
                                  78899********9..7****************99987766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.98
                                   -HHHHHHHTT--HHHHHHTTHH CS
                        RuvB_C  25 glktlaailgeeketiedviEP 46 
                                   +++++++ +g ++  i   iE 
  gi|91774004|ref|YP_566696.1| 113 AIDSICNSMGHPTFGICGRIEH 134
                                   6899999999999998888885 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 ?   12.0   0.0   0.00012      0.14       9      50 ..      17      58 ..      15      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                  HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  L++l e +  ++ ++++r+  + +St+   +  L   Gyv+ 
  gi|91774004|ref|YP_566696.1| 17 LKFLLEKGDNVRTTDISRHMKVDPSTTTKAITELDSTGYVKH 58
                                  667778888899****************************86 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.24      27      55 .]      28      56 ..      21      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                     +++++++++ +T  +ai eL  +Gy+
  gi|91774004|ref|YP_566696.1| 28 RTTDISRHMKVDPSTTTKAITELDSTGYV 56
                                  5789***********************96 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.15      97     139 ..      17      59 ..       7      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                     HTH_micro  97 vdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqk 139
                                   + fl+++ d+v + ++  ++++dp ++  +i  L + g+++ +
  gi|91774004|ref|YP_566696.1|  17 LKFLLEKGDNVRTTDISRHMKVDPSTTTKAITELDSTGYVKHI 59 
                                   689************************************9954 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00032      0.39       2      32 ..      11      43 ..      10      57 .. 0.87
   2 ?   -2.5   0.0       4.2     5e+03       4      12 ..      80      88 ..      79      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                                  HHHHHHHHHHTT..SSEEHHHHHHHHTS-HHHH CS
                         HTH_5  2 ptRlkILklLae..gelcvcelaeelglsqstv 32
                                  p++++ Lk+L e   +   +++++++++ +st+
  gi|91774004|ref|YP_566696.1| 11 PKKIEYLKFLLEkgDNVRTTDISRHMKVDPSTT 43
                                  888888999999966699*************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                  HHHHHHHHT CS
                         HTH_5  4 RlkILklLa 12
                                  R +IL+l+ 
  gi|91774004|ref|YP_566696.1| 80 RHRILSLML 88
                                  779999986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.32       6      45 ..      17      55 ..      12      65 .. 0.87
   2 ?   -3.3   0.0       7.6   9.1e+03       1      12 [.      79      90 ..      79      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                        HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                  l++Lle+ +++   +++++++v  +t  + I +L ++g  
  gi|91774004|ref|YP_566696.1| 17 LKFLLEKGDNVRTTDISRHMKVDPSTTTKAITELDSTG-Y 55
                                  899*999999***************************9.3 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.6
                        HTH_11  1 RllqilelLlea 12
                                  R+  il l l++
  gi|91774004|ref|YP_566696.1| 79 RRHRILSLMLNH 90
                                  677888887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 910.13
//
Query:       gi|91774005|ref|YP_566697.1|  [L=281]
Description: NUDIX hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-21   74.4   0.0    3.1e-20   72.6   0.0    1.9  2  NUDIX          NUDIX domain
    2.2e-08   33.6   4.6    3.3e-08   33.0   4.6    1.3  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
    1.1e-05   26.0   0.0      2e-05   25.2   0.0    1.4  1  NUDIX-like     NADH pyrophosphatase-like rudimentary NUDIX do


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 ?   -0.9   0.0      0.26   1.5e+03      99     115 ..      76      96 ..      35     111 .. 0.67
   2 !   72.6   0.0   5.2e-24   3.1e-20       6     117 ..     156     260 ..     151     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.26
                                   T....STTTEEEEEEEEHHHH CS
                         NUDIX  99 n....denevsevrwvpleel 115
                                   +    +e+e+++ +++ l++l
  gi|91774005|ref|YP_566697.1|  76 CfeipEEAEFENMEFLGLNDL 96 
                                   344446788888888888887 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 5.2e-24
                                   EEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                         NUDIX   6 vgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdehei 84 
                                   ++vvl+++++e+L++r++  +f++  + l++G+ve+gEt+e A++RE++EE+G++ ++l ++g         +p++ + ++
  gi|91774005|ref|YP_566697.1| 156 AIVVLIEKEKELLMARSH--HFKEgmYGLVAGFVEAGETIEHAVHREVKEEVGVSIKELSYFG--------SQPWPFPSSL 226
                                   456677777789999877..66665778**************************99*****99........5688888999 PP

                                   EEEEE.EEECSGCSSTSTTTEEEEEEEEHHHH.HH CS
                         NUDIX  85 lyvfl.eevegelepndenevsevrwvpleel.lk 117
                                   ++ f+ + + g++e + +ne+++++w+p++++  +
  gi|91774005|ref|YP_566697.1| 227 MIGFTaAYESGDIEID-TNEIEDAKWFPIDKIpTP 260
                                   999**99999999999.**************9422 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 !   33.0   4.6   5.6e-12   3.3e-08       1      32 []     119     150 ..     119     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 5.6e-12
                 zf-NADH-PPase   1 rthrFCgrCGaptepaeggwarvCpaCglehY 32 
                                   rth++Cg CG+ t+ ++ +++++C +C +  Y
  gi|91774005|ref|YP_566697.1| 119 RTHQYCGLCGSSTHYVPEETGMQCGSCAHLAY 150
                                   89*************************99876 PP

>> NUDIX-like  NADH pyrophosphatase-like rudimentary NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.4e-09     2e-05       2     100 ..      27     115 ..      26     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.4e-09
                    NUDIX-like   2 arfllfrrgrllveseeseeelllpadssaalvgkdseelvfLGldeggapvfAvdvsareeeikeaeeeggafvelRavm 82 
                                   a+++++++ ++lve   +e ++ ++  ++ ++   +s+e++++G++ +  p+ + ++ +++e       e+++f +l+ ++
  gi|91774005|ref|YP_566697.1|  27 ALYFPVQSRKVLVEN-GIETDEYFRHIPERSV--LESTEVIYIGTLGD-IPCHCFEIPEEAE------FENMEFLGLNDLY 97 
                                   68899999*******.9************998..**************.**********999......************* PP

                    NUDIX-like  83 lalsaedaalaaqArall 100
                                     +++e++++  +A ++ 
  gi|91774005|ref|YP_566697.1|  98 GIIDEEMLGITSRAVQMA 115
                                   **************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1708.53
//
Query:       gi|91774006|ref|YP_566698.1|  [L=435]
Description: hypothetical protein Mbur_2073 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-48  164.2  24.3    3.1e-48  164.2  24.3    2.6  2  DUF4010       Domain of unknown function (DUF4010)
    2.1e-21   76.5  12.4    2.1e-21   76.5  12.4    4.3  3  MgtC          MgtC family
  ------ inclusion threshold ------
       0.27   11.0   6.4        3.3    7.5   0.0    2.9  3  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


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 ?   -4.1   8.4       1.8   1.1e+04      57     102 ..      81     126 ..      30     143 .. 0.56
   2 !  164.2  24.3   5.2e-52   3.1e-48       1     210 []     193     401 ..     193     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.8
                       DUF4010  57 aagillAnavmllrvllivavvnpallvalalpllalallallvaa 102
                                    a i +++   + r+ +i + + ++  +al+l +l+++l+a+ + +
  gi|91774006|ref|YP_566698.1|  81 TALIAASCFFLIYRIYMISGKLGMTSSIALFLTYLLGMLVAMGYYL 126
                                   2333444444444555555555544444444444444444444433 PP

  == domain 2  score: 164.2 bits;  conditional E-value: 5.2e-52
                       DUF4010   1 VlisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivavvnp. 80 
                                   Vl+++i+f++Y+ l+ +g++ G+ ++gl+GG++SS+A+t++la  sk++++l ++l++gil++n+ m++ ++li+++v+p 
  gi|91774006|ref|YP_566698.1| 193 VLVMFIGFISYISLKRFGTKGGMSYSGLFGGFISSEATTAALAALSKKQSSLIHALYIGILMSNISMIISNTLIALIVDPt 273
                                   89******************************************************************************7 PP

                       DUF4010  81 .allvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilllakaaqeyfGdaglyalaal 160
                                    +++ a+ +p  +++l+++l+++++ r++    +e+ le+++P+ lk+A+kf+ lf ++l+++ +a e++G++g+y++a l
  gi|91774006|ref|YP_566698.1| 274 gKTMLAM-IPPQLAMLVVILIIIAIRRKSYDIMTEP-LEIGSPFALKPAFKFGTLFSILLVITSLAGEFAGSTGIYITA-L 351
                                   6444444.6777778888888887777777777777.****************************************99.* PP

                       DUF4010 161 sGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalviG 210
                                   +Gl+++ A+++s+a la +g+++ ++aa++ ++a + +tl+K++l++++G
  gi|91774006|ref|YP_566698.1| 352 GGLVSSSAVVASVAALAFTGNVPYTVAAQTAVMAGIISTLNKIMLIRISG 401
                                   *********************************************99876 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5  12.4   3.6e-25   2.1e-21       2     120 ..      26     147 ..      25     148 .. 0.84
   2 ?   -2.6   3.4       1.1   6.8e+03      30      30 ..     225     225 ..     155     302 .. 0.61
   3 ?   -3.0   7.0       1.6   9.3e+03      32      93 ..     357     423 ..     334     427 .. 0.51

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 3.6e-25
                          MgtC   2 llAlllGlliGleRelrek....aaGlRTfaLvalgaalfvllslelaesrvaaqvvsgigflgagvilkekegakvkglT 78 
                                   +l+l++G+liG+eRe++++    +aG+RTfa+v++ +++++++++ + ++ +++ + + i+  +  +i + +  +   g+T
  gi|91774006|ref|YP_566698.1|  26 VLSLMIGILIGIEREHHRQdqevFAGVRTFAIVCICGMVATFVAQLI-DMMILQITTALIAASCFFLIYRIYMISGKLGMT 105
                                   689*************8777899********************5444.55555555555555555555555566689**** PP

                          MgtC  79 TaaslwvtaaiGllvglglyllavvatvlvllllallreler 120
                                   ++++l++t+++G+lv++g+yl a+++ v++++ll+ +++l++
  gi|91774006|ref|YP_566698.1| 106 SSIALFLTYLLGMLVAMGYYLFAIIIGVIITFLLIEKKPLHS 147
                                   ****************************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                          MgtC  30 v 30 
                                   +
  gi|91774006|ref|YP_566698.1| 225 I 225
                                   1 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.6
                          MgtC  32 lgaalfvllslelae.........srvaaqvvsgigflg..agvilkekegakvkglTTaaslwvtaaiGllv 93 
                                     a+++++      +           vaaq++++ g++     ++l + +g+k     +  ++ + a++G++v
  gi|91774006|ref|YP_566698.1| 357 SSAVVASV------AalaftgnvpYTVAAQTAVMAGIIStlNKIMLIRISGSKELYYHSRNTFVLIAIVGTVV 423
                                   22222222......12334557777777775555555554333333344444555555555666666666555 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00055       3.3      33      84 ..      40      91 ..      35     109 .. 0.84
   2 ?   -2.0   0.0      0.44   2.6e+03      18      53 ..     202     237 ..     188     244 .. 0.73
   3 ?    3.9   2.5    0.0071        42      65     130 ..     346     425 ..     328     430 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00055
                  Trp_oprn_chp 33 tvalsGadwapaltalAlvllAaavAvlavrglgrrvvgvllalagagaava 84
                                  + + + +++ + +  +A+v+++++vA+++++ +  +++ + +al++a   + 
  gi|91774006|ref|YP_566698.1| 40 EHHRQDQEVFAGVRTFAIVCICGMVATFVAQLIDMMILQITTALIAASCFFL 91
                                  556677888899999****************999999999999999877665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.44
                  Trp_oprn_chp  18 tWvtvtvsdalggprtvalsGadwapaltalAlvll 53 
                                    +++ + + ++gg +   l G+ +++++t  Al++l
  gi|91774006|ref|YP_566698.1| 202 SYISLKRFGTKGGMSYSGLFGGFISSEATTAALAAL 237
                                   566666677777777788888888888888888877 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0071
                  Trp_oprn_chp  65 lgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaave...lta...........wpvlalaggvlll 130
                                   +  +++g l+  ++++a+vaal+   + + +++a++a ++g+ s+ +++    +++            +++a++g+v+l 
  gi|91774006|ref|YP_566698.1| 346 IYITALGGLVSSSAVVASVAALAFTGNVPYTVAAQTAVMAGIISTLNKIMlirISGskelyyhsrntFVLIAIVGTVVLY 425
                                   55567788888888888888888877777777777766666655555555444222555666666667777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 2568.86
//
Query:       gi|91774007|ref|YP_566699.1|  [L=126]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-21   75.9   0.0    2.7e-21   75.7   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
      0.059   13.1   0.1      0.074   12.8   0.1    1.2  1  Endonuc-PvuII  Restriction endonuclease PvuII
       0.11   12.1   0.0       0.18   11.4   0.0    1.3  1  PrpR_N         Propionate catabolism activator


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 !   75.7   0.0   4.6e-25   2.7e-21       2      94 ..      14     101 ..      13     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 4.6e-25
                                   TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES- CS
                 Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykga 82 
                                   ++ v  hFG+ap+++ y++e+++v+i+en      + + gg+g +++ll+++gvd+v+++++G++ ++ le++gie+++ga
  gi|91774007|ref|YP_566699.1|  14 EDYVELHFGKAPTYTTYDTETETVEIIENT-----SVHMGGKGIPPELLKDAGVDIVLCSGVGQKIVELLEKKGIEIFVGA 89 
                                   678999************************.....777789999************************************* PP

                                   SSBHHHHHHHHH CS
                 Nitro_FeMo-Co  83 ggtveealkevl 94 
                                   ++tv++a++ ++
  gi|91774007|ref|YP_566699.1|  90 DETVKDAIDSWK 101
                                   ********9996 PP

>> Endonuc-PvuII  Restriction endonuclease PvuII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05     0.074      32      78 ..      70     120 ..      57     126 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                 Endonuc-PvuII  32 nGGkllqllillGlrispgreG..ndavda..eGkeyelktvnvelsrsvt 78 
                                    G k+++ll   G++i  g +    da+d+   Gk y+ kt+n+e +  + 
  gi|91774007|ref|YP_566699.1|  70 VGQKIVELLEKKGIEIFVGADEtvKDAIDSwkAGKLYKPKTINIEKDSGLG 120
                                   5889***********9877654238****7447***********9887754 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.18     114     155 ..      56      98 ..      54     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                        PrpR_N 114 elkaegvevvvGdgvvadlAekaGlksvlltsg.kesvrqAie 155
                                    lk++gv++v+++gv ++++e +  k++ +  g +e+v+ Ai+
  gi|91774007|ref|YP_566699.1|  56 LLKDAGVDIVLCSGVGQKIVELLEKKGIEIFVGaDETVKDAID 98 
                                   58999*******9999999999999998888873579999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 852.04
//
Query:       gi|91774008|ref|YP_566700.1|  [L=218]
Description: beta-lactamase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   44.4   0.0    2.2e-11   44.1   0.0    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.8e-09   36.4   0.0    6.2e-09   35.7   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.3e-06   27.9   0.0    1.9e-06   27.4   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.031   14.2   0.0    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   4.9e-15   2.2e-11      11      73 ..      25      85 ..      20     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.9e-15
                                  EEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEET CS
                   Lactamase_B 11 iegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvg 73
                                  ie+d++ iL+DtG+++   ++   +a lg ++++ d ++l+H H+DHiGgl+ + +a +   +
  gi|91774008|ref|YP_566700.1| 25 IETDDKKILFDTGWDGGLLLEN--MATLGMDIREYDILLLSHQHWDHIGGLPAVLNANPKIEV 85
                                  89***************99996..8*****************************999776555 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   0.0   1.4e-12   6.2e-09       2      80 ..      31     105 ..      30     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.4e-12
                                   EEEES--TT...HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                 Lactamase_B_2   2 riLiDagpd...lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                    iL+D+g+d   l+++ + +     l  ++++ d +ll+h+H+DH+ gl+ +    p k+++y  ++ +++l+++++   +
  gi|91774008|ref|YP_566700.1|  31 KILFDTGWDgglLLEN-MAT-----LGMDIREYDILLLSHQHWDHIGGLPAVLNANP-KIEVYTLASFSEKLKKEIQKRTK 104
                                   69*******6644444.333.....5889*************************776.6****999999999998765554 PP

                                   H CS
                 Lactamase_B_2  80 e 80 
                                    
  gi|91774008|ref|YP_566700.1| 105 L 105
                                   4 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 !   27.4   0.0   4.3e-10   1.9e-06       2      69 ..      25      85 ..      24      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.3e-10
                 Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipv 69
                                  +e d+ kiL D Gwd+  +   + ++ l   i + d+ LLsh   +h+G+++ ++++ +     +i+v
  gi|91774008|ref|YP_566700.1| 25 IETDDKKILFDTGWDGGLL--LENMATLGMDIREYDILLLSHQHWDHIGGLPAVLNANP-----KIEV 85
                                  689************9854..4678899999********************98886543.....3444 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     7e-06     0.031       9      50 ..      22      70 ..      20     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-06
                 Lactamase_B_3  9 sflletagarilvDPf.......kanlgyeppaeeaDlvlisqaledHa 50
                                  s  +et++++il D +       ++ ++++ + +e D++l+s++++dH 
  gi|91774008|ref|YP_566700.1| 22 SCSIETDDKKILFDTGwdgglllENMATLGMDIREYDILLLSHQHWDHI 70
                                  56799*********88666655422444455559**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1456.80
//
Query:       gi|91774009|ref|YP_566701.1|  [L=191]
Description: hypothetical protein Mbur_2077 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-52  177.2   2.9    2.2e-52  176.9   2.9    1.1  1  DUF1847   Protein of unknown function (DUF1847)


Domain annotation for each model (and alignments):
>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.9   2.9   1.2e-56   2.2e-52      12     157 .]      21     161 ..      12     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 1.2e-56
                       DUF1847  12 ealeeykdeeekkiakaaaeveaegyakltRveeiiefakrmgykkiGiafCvglleeakalakileakgfevvsviCkvg 92 
                                   ++l+ y + e+ +i+k+a+ +ea++y+++tR+eeii f+k++gy+k+G+afC+gl +eak++ +ile++ ++v sv+Ckv+
  gi|91774009|ref|YP_566701.1|  21 DILADY-KGEDLEIMKVASGIEAKYYMQKTRLEEIILFTKELGYEKVGVAFCIGLEKEAKVFCEILEKH-MTVESVCCKVC 99 
                                   567778.78899******************************************************876.9********** PP

                       DUF1847  93 svdkeelgieeeekvkkkkkeamCnPilQAellneaktdlnvvlGLCvGhDslfikyseapvttL 157
                                   +v+k++ g+++ +   +++ e  CnPi+QA++ln+a+t+ln+ +GLC+GhD+lf+k+seapvtt+
  gi|91774009|ref|YP_566701.1| 100 GVEKDTYGLDKMQ---EENIEVSCNPIAQANILNRAGTQLNIAIGLCLGHDMLFNKHSEAPVTTF 161
                                   *********9987...79*********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1233.77
//
Query:       gi|91774010|ref|YP_566702.1|  [L=275]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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   36.5  12.6    1.1e-05   25.0   3.3    2.6  2  Fer4         4Fe-4S binding domain
    1.7e-08   34.9   6.5    0.00075   20.0   0.9    2.5  2  Fer4_7       4Fe-4S dicluster domain
    4.7e-07   29.9   0.0    6.5e-07   29.5   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.5e-06   26.8  11.0     0.0046   17.0   2.0    2.6  2  Fer4_2       4Fe-4S binding domain
    1.3e-05   24.8   0.0    2.7e-05   23.7   0.0    1.6  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.5e-05   25.3   2.2      0.036   14.5   0.2    2.5  2  Fer4_8       4Fe-4S dicluster domain
    2.8e-05   24.0  12.6      0.023   14.8   2.4    2.5  2  Fer4_6       4Fe-4S binding domain
    0.00011   22.3  12.4    0.00027   21.0  12.4    1.8  1  Fer4_21      4Fe-4S dicluster domain
    0.00014   21.9  12.8    0.00035   20.6  12.8    1.7  1  Fer4_10      4Fe-4S dicluster domain
    0.00044   20.4  13.1     0.0033   17.5  13.4    2.2  2  Fer4_9       4Fe-4S dicluster domain
     0.0012   17.2   0.0     0.0049   15.1   0.0    1.8  2  FTHFS        Formate--tetrahydrofolate ligase
     0.0035   17.7  16.2      0.019   15.4   1.7    2.9  2  Fer4_4       4Fe-4S binding domain
     0.0036   17.2   0.0     0.0053   16.7   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0096   16.8  10.2        0.2   12.6   1.4    2.7  2  Fer4_16      4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.055   13.0   0.0      0.082   12.4   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
       0.11   13.2   4.9        1.4    9.7   0.1    2.7  2  Fer4_15      4Fe-4S single cluster domain
       0.13   12.1   0.0       0.23   11.4   0.0    1.4  1  AAA_31       AAA domain
        1.8    9.2  15.3        7.1    7.3   4.1    2.6  3  Fer4_17      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 !   16.3   1.9   6.4e-06    0.0063       2      23 ..      38      59 ..      37      60 .. 0.93
   2 !   25.0   3.3   1.1e-08   1.1e-05       2      24 .]      64      86 ..      63      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.4e-06
                                  EEETTTSSS-THHHHHSTTTEE CS
                          Fer4  2 videekCigCGaCvevCPvgAI 23
                                  +id e+C  C +C + C ++AI
  gi|91774010|ref|YP_566702.1| 38 KIDLERCNECYNCQNSCNFDAI 59
                                  79***************99999 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.1e-08
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  ++++ kC gCG C+ vC ++AI+
  gi|91774010|ref|YP_566702.1| 64 IVNQHKCEGCGVCEYVCENDAIK 86
                                  69999*****************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.9   7.5e-07   0.00075      26      52 .]      32      58 ..       6      58 .. 0.79
   2 !   17.4   0.5   5.1e-06    0.0051       1      22 [.      69      90 ..      69     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.5e-07
                        Fer4_7 26 kgtekveidpekClgCgaCvavCPtga 52
                                   g++k++id e+C  C++C++ C ++a
  gi|91774010|ref|YP_566702.1| 32 YGMDKAKIDLERCNECYNCQNSCNFDA 58
                                  38899******************9986 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.1e-06
                        Fer4_7  1 rCigCgaCvaaCpvkaieldee 22
                                  +C gCg C+ +C ++ai++  +
  gi|91774010|ref|YP_566702.1| 69 KCEGCGVCEYVCENDAIKMVTK 90
                                  7****************99754 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   6.5e-10   6.5e-07      29     121 ..       4     231 ..       1     238 [. 0.92

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.5e-10
                                   -EEEEEEEESSCCCCHHTTEB-HHHH....................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                          CbiA  29 rVllvDaDpqannlaileglendiep....................................................... 54 
                                   + ++ D+D++++nl++   l+++i +                                                       
  gi|91774010|ref|YP_566702.1|   4 NAVMADCDVDTPNLHL--LLRPKIMEthafygmdkakidlercnecyncqnscnfdaidehlivnqhkcegcgvceyvcen 82 
                                   5689***********5..444444444578888888888999*************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|91774010|ref|YP_566702.1|  83 daikmvtkisgnvfrsatnhgtmvhaelgigeevsgklvsavkersrsialenendllitdsppgtgcpvlatitgahlal 163
                                   ********************************************************************************* PP

                                   ...........CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCC CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...........dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaea 121
                                              dl+r+l++ e++ ++       a v +n++d ++++ + +ea++ +    +++v g++p+  + + a
  gi|91774010|ref|YP_566702.1| 164 ivtepslsgmhDLERVLQVTEHFEIP-------AIVCINKYDINENNSRTIEAFCHER---NIEVAGKLPYYPSTNLA 231
                                   ********999999999999****98.......***********99999999999998...*********97766555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.0   4.6e-06    0.0046       3      20 ..      37      54 ..      35      56 .. 0.91
   2 !   14.4   1.9     3e-05     0.029       2      20 ..      62      80 ..      61      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.6e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                  +++d +rC++C  C+++C
  gi|91774010|ref|YP_566702.1| 37 AKIDLERCNECYNCQNSC 54
                                  789*************** PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3e-05
                        Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                  +  v+  +C gCg C  +C
  gi|91774010|ref|YP_566702.1| 62 HLIVNQHKCEGCGVCEYVC 80
                                  6778999************ 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 !   23.7   0.0   2.7e-08   2.7e-05     111     215 ..     136     228 ..     118     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.7e-08
                          ParA 111 elDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgk 191
                                   e D+Li D PPGtg   l+ +     + a+iVt p    ++d ++ ++++++ +++ +  ++     + ++ ++++e f  
  gi|91774010|ref|YP_566702.1| 136 ENDLLITDSPPGTGCPVLATITGA--HLALIVTEPSLSGMHDLERVLQVTEHFEIPAIVCINKYD--INENNSRTIEAF-- 210
                                   679************999988877..579*************************99887776443..344444444444.. PP

                          ParA 192 gggeklaeelgvpllgeipldpei 215
                                         ++e ++++ g++p  p+ 
  gi|91774010|ref|YP_566702.1| 211 ------CHERNIEVAGKLPYYPST 228
                                   ......445555555555555544 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   0.2   3.6e-05     0.036       2      16 ..      41      55 ..      14      65 .. 0.81
   2 !   10.2   0.1   0.00079      0.79       3      17 ..      68      88 ..      66     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                        Fer4_8  2 lekCieCgaCqsaCp 16
                                  le+C+eC  Cq++C 
  gi|91774010|ref|YP_566702.1| 41 LERCNECYNCQNSCN 55
                                  567777777777774 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00079
                        Fer4_8  3 ekCieCgaCqsaCp......v 17
                                  +kC +Cg C+  C       v
  gi|91774010|ref|YP_566702.1| 68 HKCEGCGVCEYVCEndaikmV 88
                                  688889999888843333332 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.4   2.3e-05     0.023       1      24 []      36      59 ..      36      59 .. 0.93
   2 !   14.3   2.7   3.3e-05     0.033       4      24 .]      65      85 ..      63      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  ++ id ++C+ C++C + C ++ai
  gi|91774010|ref|YP_566702.1| 36 KAKIDLERCNECYNCQNSCNFDAI 59
                                  5789***************99998 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.3e-05
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +++ kC gCg C+ vC  +ai
  gi|91774010|ref|YP_566702.1| 65 VNQHKCEGCGVCEYVCENDAI 85
                                  7999************98887 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  12.4   2.8e-07   0.00027       1      59 []      37      87 ..      37      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.8e-07
                       Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                  A+id ++C +C +C  +C+    +ai+    ++l v +++C GC +C  vC  +d+i+m
  gi|91774010|ref|YP_566702.1| 37 AKIDLERCNECYNCQNSCN---FDAID----EHLIVNQHKCEGCGVCEYVCE-NDAIKM 87
                                  89*****************...89997....68999***************9.799998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  12.8   3.5e-07   0.00035       2      55 ..      37      80 ..      36      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.5e-07
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                  ++id ++C +C +C+++C          +++ ++e+  ++  kC+gcg C  +C
  gi|91774010|ref|YP_566702.1| 37 AKIDLERCNECYNCQNSC----------NFDAIDEHLIVNQHKCEGCGVCEYVC 80
                                  789***************..........8999999999999************* 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  13.4   3.3e-06    0.0033       1      51 []      43      85 ..      43      85 .. 0.90
   2 !   12.1   3.2   0.00017      0.17       1      21 [.      69      89 ..      69     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  +C++C +C+++C+++++ e+   +  +        C gCg C+ +C+++ai
  gi|91774010|ref|YP_566702.1| 43 RCNECYNCQNSCNFDAIDEHLIVNQHK--------CEGCGVCEYVCENDAI 85
                                  5****************9988777655........*************987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                        Fer4_9  1 kCtgCgaCveaCpagvvveda 21
                                  kC gCg C+++C+++++++  
  gi|91774010|ref|YP_566702.1| 69 KCEGCGVCEYVCENDAIKMVT 89
                                  799999999999999887655 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.32   3.2e+02      29      47 ..      29      47 ..      24      56 .. 0.78
   2 !   15.1   0.0     5e-06    0.0049     355     404 ..     171     219 ..     164     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                                  EEEBSTTEEEE-CHHCCTC CS
                         FTHFS 29 lelyGkykakvslkvlerl 47
                                     yG  kak++l+ +++ 
  gi|91774010|ref|YP_566702.1| 29 HAFYGMDKAKIDLERCNEC 47
                                  578**********988765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5e-06
                                   HHHHHHHHHHHHHCTTT--EEEEEE--TT--HHHHHHHHHHHHCTTSEEE CS
                         FTHFS 355 kGlanlekhienvkkfgvpvvvainkfktDteaelelvkelaeakaveva 404
                                   +G+++le+ ++ +++f++p++v+ink++  + ++ ++++++++++++eva
  gi|91774010|ref|YP_566702.1| 171 SGMHDLERVLQVTEHFEIPAIVCINKYDINE-NNSRTIEAFCHERNIEVA 219
                                   69*************************9865.567899999999988876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   3.7    0.0011       1.1       2      15 ..      42      55 ..      41      57 .. 0.89
   2 !   15.4   1.7   1.9e-05     0.019       1      15 [.      67      81 ..      67      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  erC++C  C ++C 
  gi|91774010|ref|YP_566702.1| 42 ERCNECYNCQNSCN 55
                                  9************6 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.9e-05
                        Fer4_4  1 qerCigCgsCvaaCP 15
                                  q +C gCg+C+++C+
  gi|91774010|ref|YP_566702.1| 67 QHKCEGCGVCEYVCE 81
                                  679***********8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.3e-06    0.0053      13      71 ..     153     210 ..     125     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.3e-06
                                   EES--EEEEEEESTTTT--.HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHH CS
                   RsgA_GTPase  13 vaNvdqllivvslkepels.lnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkee 71 
                                    a ++ + + + ++ep+ls ++ l+r+L + e+ +i+ ++++nK D+ e+++  +++++ 
  gi|91774010|ref|YP_566702.1| 153 LATITGAHLALIVTEPSLSgMHDLERVLQVTEHFEIPAIVCINKYDINENNS--RTIEAF 210
                                   56677777777777788873578************************99888..333333 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   2.0    0.0067       6.6       1      20 [.      43      62 ..      43      69 .. 0.88
   2 !   12.6   1.4    0.0002       0.2       1      22 [.      69      90 ..      69     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0067
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  rC +C +C ++C  +ai+e 
  gi|91774010|ref|YP_566702.1| 43 RCNECYNCQNSCNFDAIDEH 62
                                  6***************9986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0002
                       Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                  +C +Cg C  vC  +aik+ ++
  gi|91774010|ref|YP_566702.1| 69 KCEGCGVCEYVCENDAIKMVTK 90
                                  5****************99844 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 ?   12.4   0.0   8.3e-05     0.082      94     147 ..     159     212 ..     151     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                                   -SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHH CS
                      GTP_EFTU  94 lDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevk 147
                                   +++a++v + +   ++  e+vl++    ++p iv+iNK D  +++ + i    +
  gi|91774010|ref|YP_566702.1| 159 AHLALIVTEPSLSGMHDLERVLQVTEHFEIPAIVCINKYDINENNSRTIEAFCH 212
                                   667788888888889999**********************99877776665555 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.6     0.093        93       2      18 ..      38      54 ..      38      62 .. 0.85
   2 ?    9.7   0.1    0.0014       1.4       3      19 ..      65      82 ..      63     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.093
                       Fer4_15  2 vvDrdaCigcglCvaea 18
                                  ++D ++C  c +C   +
  gi|91774010|ref|YP_566702.1| 38 KIDLERCNECYNCQNSC 54
                                  59***********9887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                       Fer4_15  3 vDrdaCigcglCvaea.p 19
                                  v++ +C+gcg+C  ++  
  gi|91774010|ref|YP_566702.1| 65 VNQHKCEGCGVCEYVCeN 82
                                  7899********999951 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.23     113     166 ..     132     185 ..      75     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                        AAA_31 113 kvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktiee 166
                                   ++++e D+ i D pP  g+ +   ++ +   +i+++++   ++ le++l+  e+
  gi|91774010|ref|YP_566702.1| 132 ALENENDLLITDSPPGTGCPVLATITGAHLALIVTEPSLSGMHDLERVLQVTEH 185
                                   578999*******************************88888888887776665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.1    0.0071       7.1      39      57 ..      37      55 ..      10      60 .. 0.76
   2 ?    6.5   3.7     0.013        13      44      59 ..      68      83 ..      58      85 .. 0.82
   3 ?    6.2   3.6     0.016        16       2      58 ..      70      82 ..      69     120 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0071
                       Fer4_17 39 keekaslCieCgeCerkCP 57
                                  ++   ++C+eC +C+ +C 
  gi|91774010|ref|YP_566702.1| 37 AKIDLERCNECYNCQNSCN 55
                                  3357899*********996 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                       Fer4_17 44 slCieCgeCerkCPqg 59
                                  ++C +Cg Ce++C ++
  gi|91774010|ref|YP_566702.1| 68 HKCEGCGVCEYVCEND 83
                                  5799999999999875 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.016
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                  C +Cg C+ +C                                             +
  gi|91774010|ref|YP_566702.1| 70 CEGCGVCEYVCE--------------------------------------------N 82
                                  555555555555............................................4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1772.55
//
Query:       gi|91774011|ref|YP_566703.1|  [L=126]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Methanococcoides burtonii DSM 6242]
Scores for complete 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   72.6   0.2    3.9e-20   72.0   0.0    1.4  2  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.83    9.8   0.0    2.0  2  FeThRed_A      Ferredoxin thioredoxin reductase variable alph


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 !   72.0   0.0   4.3e-24   3.9e-20       2      94 ..      14     101 ..      13     102 .. 0.96
   2 ?   -2.9   0.0         1     9e+03      33      44 ..     111     122 ..     105     125 .. 0.67

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 4.3e-24
                                   TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES- CS
                 Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykga 82 
                                   ++ v qhFG  p+++++++e+++v+iven      ++++gg g +++ll+++gv+++++g+ G++a++ + + gi+v++ga
  gi|91774011|ref|YP_566703.1|  14 DDIVGQHFGMVPTYTVMDIENNSVEIVENT-----SEHKGGVGLPPELLSKAGVNIMLCGGLGQSAVNMFCEYGIDVFVGA 89 
                                   67799*************************.....99999***************************************** PP

                                   SSBHHHHHHHHH CS
                 Nitro_FeMo-Co  83 ggtveealkevl 94 
                                    gtve a+++++
  gi|91774011|ref|YP_566703.1|  90 QGTVETAINDWK 101
                                   *********997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                                   .GCCCTSSCSST CS
                 Nitro_FeMo-Co  33 eeaadaeggggg 44 
                                   e+ ++++g++++
  gi|91774011|ref|YP_566703.1| 111 ENVCQGHGHDED 122
                                   566777777765 PP

>> FeThRed_A  Ferredoxin thioredoxin reductase variable alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.081   7.2e+02      23      42 ..      29      48 ..      20      54 .. 0.81
   2 ?    9.8   0.0   9.3e-05      0.83      28      49 ..      88     110 ..      80     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.081
                                  -EE-TT-EEEEEEE-SEETT CS
                     FeThRed_A 23 aldlkgmeGevvqivtewkG 42
                                   +d+++   e+v++ +e+kG
  gi|91774011|ref|YP_566703.1| 29 VMDIENNSVEIVENTSEHKG 48
                                  47889999999999999988 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 9.3e-05
                                   T-EEEEEEE-SEET.TEE---SS CS
                     FeThRed_A  28 gmeGevvqivtewk.GrkiSanl 49 
                                   g +G+v++ +++wk G+ +S++ 
  gi|91774011|ref|YP_566703.1|  88 GAQGTVETAINDWKeGNLVSPTS 110
                                   899**********99*****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 844.90
//
Query:       gi|91774012|ref|YP_566704.1|  [L=137]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-24   86.6   0.0    1.3e-24   86.3   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 !   86.3   0.0   7.2e-29   1.3e-24       3      94 ..      14     102 ..      12     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 7.2e-29
                                   SCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-S CS
                 Nitro_FeMo-Co   3 srvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykgag 83 
                                   s+ d++FGr+pyF+i++ ++ +++ +en+      aegg+g+k+aq l + +vdv+++g++Gp+a   l+aagi+vy+g +
  gi|91774012|ref|YP_566704.1|  14 SQCDPRFGRCPYFVIVDHDSMSFEALENP---GPLAEGGAGIKAAQALTALNVDVLLTGNMGPNASSVLDAAGIKVYTGIE 91 
                                   6789*************************...999********************************************** PP

                                   SBHHHHHHHHH CS
                 Nitro_FeMo-Co  84 gtveealkevl 94 
                                   gtve+ + +++
  gi|91774012|ref|YP_566704.1|  92 GTVEDTVSQYR 102
                                   *******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 901.64
//
Query:       gi|91774013|ref|YP_566705.1|  [L=265]
Description: bacitracin resistance protein BacA [Methanococcoides burtonii DSM 6242]
Scores for 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-52  179.4  14.7    1.2e-52  179.2  14.7    1.0  1  BacA      Bacitracin resistance protein BacA
  ------ inclusion threshold ------
      0.036   13.9   1.5        6.3    6.7   0.0    2.8  2  PspC      PspC domain


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 !  179.2  14.7   1.4e-56   1.2e-52       1     255 [.       7     257 ..       7     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 1.4e-56
                          BacA   1 aiilGivqGltefLPvSSsGhlilveellgle..kedlllfdvvihlGtllAvlvlfrkdilrllkgllkslkkkkkekee 79 
                                   aiilGivqGl+e+LP+SS+G   lv   + +    +++  +++++hlGtllA +v+fr+d++ ll g+ +++++ ++++++
  gi|91774013|ref|YP_566705.1|   7 AIILGIVQGLAEWLPISSEGMTSLVMVTF-FGrsLSEAIPISIWLHLGTLLAAIVYFREDVKVLLYGVPDYVRSFSRKQPH 86 
                                   79********************9999887.33233335669********************************99999999 PP

                          BacA  80 lrlllliivatipaailglllkdlieellrsp.....lvvaialivtglllllaeklrkkkkksl.edltlkdalliGlaQ 154
                                     ++  ++++t  ++i+gl+l  ++++ ++        v++i+livtg+l  ++++      +sl +   ++d+l+ G+aQ
  gi|91774013|ref|YP_566705.1|  87 DPVISFLLISTALTGIVGLPLLLFVTDNVEISggsatAVIGIMLIVTGILQRTVSRD-----ESLsRVPGMSDSLVSGVAQ 162
                                   999999************999766655443223445599************999954.....33314699*********** PP

                          BacA 155 alAllPGvSRSGaTivaglllglsreaaaefSFllaiPailgagllk.llksaealtasellllvgfvvafvvallaikfl 234
                                   ++A +PG+SRSG+T++a ll++++  +a+++SFl++iPa+l+a +   l+     + + ++  +vg+++af ++l++i+++
  gi|91774013|ref|YP_566705.1| 163 GFAAIPGISRSGITMSALLLRKFDAADAIRLSFLMSIPAVLVAEIGVgLM----GMVELDINSIVGLFFAFAFGLVTIDLF 239
                                   *****************************************999743244....22233455599**************** PP

                          BacA 235 lkllkkkklkvFaiYrivlGl 255
                                   lk++kk +   F++++i lG+
  gi|91774013|ref|YP_566705.1| 240 LKVAKKVD---FSYFCIGLGV 257
                                   ********...7777888876 PP

>> PspC  PspC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0007       6.3       8      27 ..       5      24 ..       1      72 [. 0.79
   2 ?    5.6   0.4    0.0016        14       8      27 ..     153     172 ..     151     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0007
                          PspC  8 dnkvlgGVcaGlAeyfgvdp 27
                                  ++ ++ G+++GlAe + ++ 
  gi|91774013|ref|YP_566705.1|  5 SEAIILGIVQGLAEWLPISS 24
                                  6899**********998865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0016
                          PspC   8 dnkvlgGVcaGlAeyfgvdp 27 
                                   ++ ++ GV++G+A+  g++ 
  gi|91774013|ref|YP_566705.1| 153 SDSLVSGVAQGFAAIPGISR 172
                                   57899********9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1655.65
//
Query:       gi|91774014|ref|YP_566706.1|  [L=344]
Description: methylcobalamin:coenzyme M methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-71  240.7   0.1    2.6e-71  240.6   0.1    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.6   0.1   1.4e-75   2.6e-71       1     346 []       5     342 ..       5     342 .. 0.94

  Alignments for each domain:
  == domain 1  score: 240.6 bits;  conditional E-value: 1.4e-75
                                   ----HHHHHHTT.---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGG CS
                         URO-D   1 tknerllralrg.ekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaea 80 
                                   t+++rl ++l++ ekvdr+P ++   ++++ + +++e  g+ ++e+ +++++ a ++ + + + g++a+ +++di+ eae 
  gi|91774014|ref|YP_566706.1|   5 TPKTRLAAVLNQtEKVDRMPAIC---VTQTGTVEQMEACGIFWPEANYDAKMLAGLAAAGHTEIGFEAIRVPFDITAEAEF 82 
                                   6789999999988**********...888**************************************************** PP

                                   GT-EEEEETTTE.EEEE--S-.....GGGS----GGG..G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT- CS
                         URO-D  81 lGlevefeegeg.Pvvekpvr.taedveklevpddvee.grlpyvleaikllkkelggevpligfvgaPftlasylveGgs 158
                                   +G++++ +++ + P+v ++v+ +++d++  e +d  +  +r++++le+ik++ +e+g e+p+ig +++Pf+la +l+    
  gi|91774014|ref|YP_566706.1|  83 FGCGIKDGTKVQqPSVINHVVnSLDDLKPFEGYDINDSsKRISTILESIKIVADEYGAELPIIGSMIGPFSLAQHLT---- 159
                                   *********9989******999******999999865589*************************************.... PP

                                   SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHHHHHHHH.H-- CS
                         URO-D 159 kgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkrivdevkaegpk 237
                                      ++++++++++ e   ++++++t++ i+y++aqi++gAd + i D  ++ +l+  e +++fv+p+++++v++++a+  +
  gi|91774014|ref|YP_566706.1| 160 --GDSWFMDIMTKEEYGLAIMEFTTEFGIAYANAQIDNGADTLSIIDptASYSLIGGEFYKKFVVPFHAKLVEAMHAR--N 236
                                   ..55666666667777889******************************99**************************8..6 PP

                                   S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S-HHHHHHHHHHHHT.T---SS CS
                         URO-D 238 vpvilfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLl.gspeeiekevkeilekgaggkk 317
                                   vpv+l+++g+++  l+ + ++g+d++s+d++v+ + a+++v +k+ ++GnldP+  L   s e++ +e +++l++  +  +
  gi|91774014|ref|YP_566706.1| 237 VPVVLHVCGDTTDGLAIMESAGVDAISVDQNVNAATAVSKV-EKALIVGNLDPVNCLWnTSVETVTAESERVLKE-LD--G 313
                                   8*********************************8888899.99******************************4.44..4 PP

                                   SEEB-BSS---TTS-HHHHHHHHHHHHT- CS
                         URO-D 318 gyilnlGhgippetppenvkalveavkey 346
                                   +  l++G+gi  +tp ++++a+ve++k+y
  gi|91774014|ref|YP_566706.1| 314 KGLLAPGCGIVSQTPSAHLRAMVEVAKSY 342
                                   4499*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2330.98
//
Query:       gi|91774015|ref|YP_566707.1|  [L=259]
Description: hypothetical protein Mbur_2083 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-06   27.0   0.0    1.2e-05   25.7   0.0    1.6  2  NAD_binding_7    Putative NAD(P)-binding
    1.4e-05   25.0   0.0    2.8e-05   24.1   0.0    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    2.5e-05   24.5   0.1    4.7e-05   23.6   0.1    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00017   21.0   0.0    0.00028   20.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00084   19.9   0.0       0.01   16.4   0.0    2.6  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0012   18.3   0.0      0.023   14.2   0.0    2.2  2  adh_short        short chain dehydrogenase
     0.0016   18.7   0.0     0.0028   17.9   0.0    1.4  1  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.013   14.8   0.0       0.02   14.2   0.0    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.047   12.9   0.0      0.073   12.3   0.0    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.071   12.7   0.0       0.14   11.8   0.0    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
       0.08   13.0   0.0       0.15   12.1   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.085   13.2   0.3        6.3    7.2   0.1    2.3  2  Mur_ligase       Mur ligase family, catalytic domain
      0.092   13.0   0.0       0.18   12.1   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.9   1.1e+04      28      41 ..      94     106 ..      89     122 .. 0.63
   2 !   25.7   0.0   8.4e-09   1.2e-05       3      73 ..     137     208 ..     136     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.9
                 NAD_binding_7  28 eagakvtvvapevk 41 
                                   + ga++ ++a + +
  gi|91774015|ref|YP_566707.1|  94 SDGADILLMADD-H 106
                                   567777777776.3 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 8.4e-09
                 NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeel.ekdlegadlviaatddre 73 
                                   ++   k v+v+G G+v++  +++l+++g +v  ++p+ +e++e+ ++ l  + + ++d +++ +v+ at++++
  gi|91774015|ref|YP_566707.1| 137 IHAGSKDVMVIGLGRVGYAGAEHLVKKGFNVYAYDPN-TEFMEKAIEeLGVNAYdSADHKKFSMVFEATPNAN 208
                                   5667899******************************.8999988875667777569************9976 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.1e-08   2.8e-05       2      56 ..     144     198 ..     143     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.1e-08
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56 
                                   v viG G +G   a+ ++++g++V  +d ++e++eka e++  +    + ++k++
  gi|91774015|ref|YP_566707.1| 144 VMVIGLGRVGYAGAEHLVKKGFNVYAYDPNTEFMEKAIEELGVNAYDSADHKKFS 198
                                   89***************************************99888888777766 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 !   23.6   0.1   3.4e-08   4.7e-05       2      50 ..     144     193 ..     143     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.4e-08
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHH CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvae.gakaaesie 50 
                                   + +iGlG  G   a++l+k+g++v++y+ ++e +e++++e g++a++s+ 
  gi|91774015|ref|YP_566707.1| 144 VMVIGLGRVGYAGAEHLVKKGFNVYAYDPNTEFMEKAIEElGVNAYDSAD 193
                                   679**********************************9994466655544 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 !   20.3   0.0   2.1e-07   0.00028      33      87 ..     138     193 ..     105     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.1e-07
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHH CS
                  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvslee 87 
                                       k v +iGlGr+G a a+ l + g++v+ayd++ +  e + eelgv+  +  +
  gi|91774015|ref|YP_566707.1| 138 HAGSKDVMVIGLGRVGYAGAEHLVKKGFNVYAYDPNTEFMEkAIEELGVNAYDSAD 193
                                   567899*****************************988555467777775555544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.5   7.6e+03      71      88 ..       6      21 ..       4      30 .. 0.68
   2 ?    1.8   0.0      0.26   3.6e+02       5      30 ..     123     146 ..     122     147 .. 0.85
   3 !   16.4   0.0   7.3e-06      0.01       2      52 ..     144     190 ..     143     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.5
                                  HHHHHHHHHHCGHHHHTT CS
                 F420_oxidored 71 pedveevlselakdalkg 88
                                  ped+e++l++l  +++++
  gi|91774015|ref|YP_566707.1|  6 PEDLEDLLNKL--RQSNE 21
                                  78888888888..44443 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                                   ETTSHHHHHHHHHHHHTTS-GGCEEE CS
                 F420_oxidored   5 iGaGnmgealasgllaagaqpheivv 30 
                                   i +G + + +as++++ag   ++++v
  gi|91774015|ref|YP_566707.1| 123 ICTGVIYSEIASRFIHAG--SKDVMV 146
                                   568999999*********..788876 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 7.3e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvta 52 
                                   + +iG G++g a a+ l+++g    +++ a ++n e +e++ eelgv++  
  gi|91774015|ref|YP_566707.1| 144 VMVIGLGRVGYAGAEHLVKKG---FNVY-AYDPNTEFMEKAIEELGVNAYD 190
                                   569******************...****.99***************99866 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.087   1.2e+02     163     188 ..     109     134 ..     106     139 .. 0.87
   2 !   14.2   0.0   1.7e-05     0.023       3      49 ..     144     190 ..     142     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.087
                                   HHHHHGGGTEEEEEEEESSBSSHHHH CS
                     adh_short 163 lakelaptgirvnavaPGlvdTdmak 188
                                   +a+ l++ +i  n +++G++ +++a 
  gi|91774015|ref|YP_566707.1| 109 IAHNLKNGKIAANHICTGVIYSEIAS 134
                                   689999999***********999875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.7e-05
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TS CS
                     adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.ga 49 
                                   v+v+G ++ +G+a a++l+k+G++v+++d + e +e++++el+ +  +
  gi|91774015|ref|YP_566707.1| 144 VMVIGLGR-VGYAGAEHLVKKGFNVYAYDPNTEFMEKAIEELGVNaYD 190
                                   66777764.89*******************************976433 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.1e-06    0.0028       1      45 [.     144     189 ..     144     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEE CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levv 45 
                                   +++iGlGrvG++ ae L ++g +v++ d + e +e++ ee  ++++
  gi|91774015|ref|YP_566707.1| 144 VMVIGLGRVGYAGAEHLVKKGFNVYAYDPNTEFMEKAIEELgVNAY 189
                                   69*****************6656*************9888756655 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05      0.02      30     109 ..     143     234 ..     124     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE...........HCHHHHHHHHHHHH-SEEEE- CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev...........lksqeellaeavkeadvvigt 98 
                                    v+viG G +G + ++  ++ g +V+++D +++ +e+  + lg +  +             + ++++++e + +   +i+t
  gi|91774015|ref|YP_566707.1| 143 DVMVIGLGRVGYAGAEHLVKKGFNVYAYDPNTEFMEKAIEeLGVNAYDSadhkkfsmvfeATPNANTISEGMITDRCLIST 223
                                   69*******************************988754448777555566666776666666666677766666677777 PP

                                   --BTTSS---S CS
                   AlaDh_PNT_C  99 vlipGkkaPkL 109
                                     ip +  + L
  gi|91774015|ref|YP_566707.1| 224 PGIPCALPAEL 234
                                   66666665555 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 ?   12.3   0.0   5.3e-05     0.073       1      36 [.     142     177 ..     142     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtcl 36 
                                   kdv+viG G  G+a a++l ++g++v+ ++ +++++
  gi|91774015|ref|YP_566707.1| 142 KDVMVIGLGRVGYAGAEHLVKKGFNVYAYDPNTEFM 177
                                   69***************************5554443 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 ?   11.8   0.0   9.9e-05      0.14       4      57 ..     141     194 ..     139     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.9e-05
                                   TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHT.T-EEEEHHHH CS
                          IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkee.gfevltvaea 57 
                                   +k + viG G  G a a+ l   g++v  +   +++ ++kA ee g++ ++ a+ 
  gi|91774015|ref|YP_566707.1| 141 SKDVMVIGLGRVGYAGAEHLVKKGFNVY-AYDPNTEFMEKAIEElGVNAYDSADH 194
                                   689***********************96.56666667777765437777776664 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.15       9      43 ..     138     171 ..     131     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEE CS
                  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaN 43 
                                   +  +k v++iG G+++   a+hL++kg++ v    
  gi|91774015|ref|YP_566707.1| 138 HAGSKDVMVIGLGRVGYAGAEHLVKKGFN-VYAYD 171
                                   567899********************998.65555 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0045       6.3       5      55 ..      60     112 ..      58     139 .. 0.81
   2 ?    4.1   0.0     0.043        59      14      43 ..     155     189 ..     135     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0045
                                   ESTTSCCHHHHHHHHHHTTSEEEEEESSHC..HHHTT-EEEES-HGGGGEE-T CS
                    Mur_ligase   5 igidgrgmsagalflalkGykvdGsdfies..lialGaaavvghdaanivvss 55 
                                   ig  ++++ a+ +++ l+Gy +d  d+  +  ++  Ga +++  d+++ ++++
  gi|91774015|ref|YP_566707.1|  60 IGNFSSSLLAITEYFGLEGYITDHPDITGYhqAVSDGADILLMADDHMFIAHN 112
                                   5666889999*********************************9999775444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.043
                                   HHHHHHHHTTSEEEEEESSHC.....HHHTT-EEE CS
                    Mur_ligase  14 agalflalkGykvdGsdfies.....lialGaaav 43 
                                   aga+ l +kG++v   d + +      ++lG++a+
  gi|91774015|ref|YP_566707.1| 155 AGAEHLVKKGFNVYAYDPNTEfmekaIEELGVNAY 189
                                   899***********999999999998889999986 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.18       1      46 [.     144     185 ..     144     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTT CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalg 46 
                                   v++iG G+vG a ae l++++ +  ++   d++ e +e++++++ g
  gi|91774015|ref|YP_566707.1| 144 VMVIGLGRVGYAGAEHLVKKG-F--NVYAYDPNTEFMEKAIEEL-G 185
                                   78*****************98.5..8**************9875.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1626.24
//
Query:       gi|91774016|ref|YP_566708.1|  [L=362]
Description: hypothetical protein Mbur_2084 [Methanococcoides burtonii DSM 6242]
Scores for 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-10   39.6   0.0    9.6e-10   38.3   0.0    1.5  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    2.8e-09   37.2   0.0    4.7e-09   36.5   0.0    1.3  1  ATP-grasp_3      ATP-grasp domain
     0.0002   21.2   0.3       0.14   11.9   0.1    2.8  3  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0025   17.4   0.1     0.0089   15.6   0.1    2.0  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
  ------ inclusion threshold ------
      0.018   14.6   0.7       0.64    9.6   0.3    2.4  2  ATP-grasp_4      ATP-grasp domain
      0.083   13.5   0.0        0.3   11.7   0.0    1.8  2  ATPgrasp_N       ATP-grasp N-terminal domain


Domain annotation for each model (and alignments):
>> 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 !   38.3   0.0   3.2e-13   9.6e-10       3     116 ..     155     276 ..     154     289 .. 0.82
   2 ?   -3.6   0.0       2.9   8.8e+03      24      41 ..     327     344 ..     324     350 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 3.2e-13
                  ATPgrasp_Ter   3 pallvmeyLegpEySvDvlaekgevlaavpRrKe.....kgglq.....elekdeelielaerlaeefgldglvnvQvred 73 
                                   p++lv eyLeg+ +S  v+  +g+  a+v+ +K                 +e+d++  e++ rla+ ++l+g++ v     
  gi|91774016|ref|YP_566708.1| 155 PNMLVEEYLEGNVISLEVIG-DGKHFAVVKETKVhiddtY---DchmitPVEHDPKFREISYRLAQGLNLKGIMDVEAIVS 231
                                   78****************98.5***********9764430...2445559******************************* PP

                  ATPgrasp_Ter  74 edgpkLLEiNpRasGG..lgysalaGvnlpylalklllgleteev 116
                                   e+g+k+LEi +R+ +   +++   +G+nl+ l ++++++  te  
  gi|91774016|ref|YP_566708.1| 232 EKGLKILEIDARFPSQtpIVVYHSSGMNLVALLMQAFTEGVTEIE 276
                                   ************9886114555678**********9999633333 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.9
                  ATPgrasp_Ter  24 kgevlaavpRrKekgglq 41 
                                   ++ v + + R K+  + +
  gi|91774016|ref|YP_566708.1| 327 ENDVFTLISRGKDIESTE 344
                                   677889999999944444 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.6e-12   4.7e-09       5     158 ..     105     244 ..     101     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.6e-12
                                   HHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEEEEE.SSS CS
                   ATP-grasp_3   5 lktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvsllsdgek 85 
                                    ++ + +    +++P        ++++ ++ vKp   + + ++ ++ ++ e+    + + lv e++eG+ +S+++++dg++
  gi|91774016|ref|YP_566708.1| 105 KRSKEYFTSIDIPTP------GDRPSQPPYFVKPPCESSSIGTHIIYDDSELADVGP-NMLVEEYLEGNVISLEVIGDGKH 178
                                   555555555556666......4456677899**************999987776666.56********************* PP

                                   EEEEEEEEEEEET....TEE.EEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS- CS
                   ATP-grasp_3  86 vlvlavnrqliekaekefvy.aGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRl 158
                                   + v+   + +i+       y +  +tp+e  ++ +++e+  ++ + l +l+G++ v+ +++++++ ++E+ +R+
  gi|91774016|ref|YP_566708.1| 179 FAVVKETKVHIDD-----TYdCHMITPVE--HDPKFREISYRLAQGL-NLKGIMDVEAIVSEKGLKILEIDARF 244
                                   ***********97.....45045566666..8999************.*************************8 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 ?   -2.1   0.0       0.9   2.7e+03      84     106 ..       6      28 ..       3      34 .. 0.78
   2 !   11.9   0.1   4.8e-05      0.14      73     112 ..     147     186 ..     135     192 .. 0.84
   3 !    6.0   0.0    0.0029       8.8     161     189 ..     216     244 ..     206     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.9
                                   EEEE---SEEEEEEEEECTTEEE CS
                        GARS_A  84 viEelleGeEvsllalvdgktvk 106
                                   +i  +l+G Ev+ la   g  v+
  gi|91774016|ref|YP_566708.1|   6 LIGGKLQGFEVTYLAKKAGMGVV 28 
                                   5677899****999988887665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.8e-05
                                   S-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BE CS
                        GARS_A  73 kkkfGeagekvviEelleGeEvsllalvdgktvkplplaq 112
                                   + +  + g ++++Ee+leG+ +sl ++ dgk+++ ++ ++
  gi|91774016|ref|YP_566708.1| 147 DSELADVGPNMLVEEYLEGNVISLEVIGDGKHFAVVKETK 186
                                   5566778899**********************99887766 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0029
                                   TT---EEEEEEEEEEETTEEEEEEEESS- CS
                        GARS_A 161 egipfkGvLyaglmlvedgpkvlefnvRf 189
                                   +g + kG++ ++ +++e+g k+le+++Rf
  gi|91774016|ref|YP_566708.1| 216 QGLNLKGIMDVEAIVSEKGLKILEIDARF 244
                                   567899**********************9 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 !   15.6   0.1     3e-06    0.0089      38     113 ..     127     195 ..     121     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-06
                                   SEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-H CS
               Dala_Dala_lig_C  38 pvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeaiegreievavlgneklevsevgeivvkkgfydy 113
                                   p fVKp  e SS+G + +   +el++          ++lvEe++eg+ i   v+g++k  + + +  v  ++ yd 
  gi|91774016|ref|YP_566708.1| 127 PYFVKPPCESSSIGTHIIYDDSELADV-------GPNMLVEEYLEGNVISLEVIGDGKHFAVVKETKVHIDDTYDC 195
                                   89*********************9875.......7889*****************888666655555555677775 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.024        71       4      29 ..     127     152 ..     124     155 .. 0.89
   2 ?    9.6   0.3   0.00022      0.64      54     149 ..     156     241 ..     153     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.024
                   ATP-grasp_4   4 PvviKPsvgffSlGVykinneeewka 29 
                                   P  +KP  +++S+G ++i +++e+ +
  gi|91774016|ref|YP_566708.1| 127 PYFVKPPCESSSIGTHIIYDDSELAD 152
                                   889****************9999875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00022
                   ATP-grasp_4  54 sflvEeyieGeEfavdayfdeeGepvilnilkkefaseedvsdrlyvtsakvieetlealeellkevnallglknfpvHiE 134
                                   ++lvEey+eG+ +++++    +G++   +++k +  + +d+ d+  +t+     e+  ++ e+  ++++ l+lk + + +E
  gi|91774016|ref|YP_566708.1| 156 NMLVEEYLEGNVISLEVIG--DGKH--FAVVKETKVHIDDTYDCHMITPV----EHDPKFREISYRLAQGLNLK-GIMDVE 227
                                   78***************98..4544..45668888999999999999986....56888888888888888886.678999 PP

                   ATP-grasp_4 135 lrvsedg.kiipiEvn 149
                                     vse+g ki+  E+ 
  gi|91774016|ref|YP_566708.1| 228 AIVSEKGlKIL--EID 241
                                   99999985555..444 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 ?   11.7   0.0    0.0001       0.3       4      56 ..      20      69 ..      18      72 .. 0.85
   2 ?   -2.2   0.0       2.1   6.3e+03      31      61 ..     194     224 ..     172     227 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                  HHHTT-EEEEEEETTS----S-TT.EEEEEEE-TTT-HHHHHHHHHHHHHHS- CS
                    ATPgrasp_N  4 AkaLGikvvlvdeedewapeelaelvekfipldlaqdpdaaleavralsrerp 56
                                  Ak+ G+ vvl+d++ +    + +++v+++   d++++p++ +e+ +++ +  p
  gi|91774016|ref|YP_566708.1| 20 AKKAGMGVVLIDKNRKP---LIRNVVDELFCFDITEEPERFIEISKNVDAIIP 69
                                  999*********99944...4466799*****************999876555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                                   EEEEE-TTT-HHHHHHHHHHHHHHS--SEEE CS
                    ATPgrasp_N  31 kfipldlaqdpdaaleavralsrerpvdGiv 61 
                                   ++++++  +++ +  e+ ++l++  ++ Gi+
  gi|91774016|ref|YP_566708.1| 194 DCHMITPVEHDPKFREISYRLAQGLNLKGIM 224
                                   4455555555667777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 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:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2423.34
//
Query:       gi|91774017|ref|YP_566709.1|  [L=350]
Description: biotin synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   44.9   0.6    3.2e-11   43.9   0.3    1.6  2  Radical_SAM   Radical SAM superfamily
    4.3e-07   30.1   0.2    9.1e-07   29.0   0.2    1.5  1  Fer4_14       4Fe-4S single cluster domain
    6.2e-07   29.8   0.2    1.4e-06   28.6   0.1    1.6  1  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.037   13.5   0.0    1.5  2  His_biosynth  Histidine biosynthesis 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 !   43.9   0.3     7e-15   3.2e-11       3     149 ..      67     208 ..      65     211 .. 0.85
   2 ?   -3.0   0.0       1.8   8.2e+03      47      66 ..     328     347 ..     310     348 .. 0.60

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 7e-15
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgiritv 82 
                                   ++  C ++C fC+ ++   +    + l++e+i+++ + lk e  ++ v l++ge  +  +  e l++l++   ++  +  +
  gi|91774017|ref|YP_566709.1|  67 FSTHCKNNCAFCYYNRE--NDIERYRLTLEDIKKICQVLKTEE-IHMVDLTMGEDPYFHNNPERLAELVRTVkEEVGKPIM 144
                                   7788***********95..********************9444.8888888777777766666666666666457778888 PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdri 149
                                   +++g+++  e l +l+e g + ++l  e++d+e + kl    ++fee++++   +++ g   v d+i
  gi|91774017|ref|YP_566709.1| 145 ISPGVVD-NETLMLLKENGANFLALYQETYDKELFGKLR-VEQSFEERINSRNHAKRIGYL-VEDGI 208
                                   8888886.*************************999999.9*********99999999988.77777 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                                   SEEEEEESSTGGGSTTHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  47 vkevilgggepllypdfvel 66 
                                   +  +  +g+ep  ++df++l
  gi|91774017|ref|YP_566709.1| 328 IYRLKTMGMEPAKQSDFEKL 347
                                   44555678888888887766 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.2     2e-10   9.1e-07       2      96 ..      67     156 ..      64     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2e-10
                       Fer4_14   2 fvrlsgCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvlt.GGePLhyenkkellklvkrlkeeype 80 
                                   f     C+ +C +C+ n+e  ++      t e++++i + lk +ei  + + lt G +P  + n + l +lv+ +kee+  
  gi|91774017|ref|YP_566709.1|  67 FS--THCKNNCAFCYyNRE--NDIERYRLTLEDIKKICQVLKTEEI--HMVDLTmGEDPYFHNNPERLAELVRTVKEEV-G 140
                                   33..68*********5555..55555667999999***99999999..5556652667*********************.9 PP

                       Fer4_14  81 kkiwletngtleiele 96 
                                   k+i +  + + +  l+
  gi|91774017|ref|YP_566709.1| 141 KPIMISPGVVDNETLM 156
                                   9**9999988885555 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 !   28.6   0.1   3.1e-10   1.4e-06       9      94 ..      65     149 ..      54     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 3.1e-10
                       Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGE.Pllpenaeallelvkevkeekpekdi 88 
                                   + f + C+ +C++C+ +   + ++    t e +++i++ lk e+i  + l+ GE P  ++n e l+elv+ vkee   k i
  gi|91774017|ref|YP_566709.1|  65 VYFSTHCKNNCAFCYYNRENDIERY-RLTLEDIKKICQVLKTEEIHMVDLTMGEdPYFHNNPERLAELVRTVKEEVG-KPI 143
                                   556889*********8877777665.5678999*****************977549998888**************9.567 PP

                       Fer4_12  89 wlytgy 94 
                                   +++ g+
  gi|91774017|ref|YP_566709.1| 144 MISPGV 149
                                   777665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.2e-06     0.037      41     100 ..     103     167 ..      81     191 .. 0.85
   2 ?   -2.7   0.0      0.72   3.2e+03       5      44 ..     277     319 ..     273     320 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.2e-06
                                   HT-SEEEEEEHHHHC.....TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEE CS
                  His_biosynth  41 egadelhvvDldaak.....egreanldlveeiaeevfipvqvGGGIrsledveelleagadkvi 100
                                    + +e+h+vDl+  +     ++ e+  +lv+++ eev  p+++  G+ + e++  l e+ga+ + 
  gi|91774017|ref|YP_566709.1| 103 LKTEEIHMVDLTMGEdpyfhNNPERLAELVRTVKEEVGKPIMISPGVVDNETLMLLKENGANFLA 167
                                   5679*******9887778878889999*************************9999999998665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.72
                                   EEEE..ETTEEEEECTTCSTCEEEE.TTSHHHHHHHHHHHT-S CS
                  His_biosynth   5 alDl..kdGkvVrlvkGdrfqelry.agdpvelakryeeegad 44 
                                   +lDl   dG v rl +G +  +  + +++ +e + +y++e+a+
  gi|91774017|ref|YP_566709.1| 277 SLDLegIDGMVHRLNSGANVVTSIIsSNSALEGVVNYDREHAE 319
                                   4777667899999999988555544044556777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2237.96
//
Query:       gi|91774018|ref|YP_566710.1|  [L=416]
Description: pyrolysyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-14   51.8   0.0      2e-12   47.1   0.0    2.4  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    3.8e-07   29.5   0.2      1e-05   24.8   0.1    2.7  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    7.7e-07   28.8   0.0    1.2e-06   28.1   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.2e-06   28.7   0.0    3.8e-06   27.0   0.0    1.9  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
     0.0071   15.7   0.0      0.011   15.1   0.0    1.2  1  tRNA-synt_His    Histidyl-tRNA synthetase
  ------ inclusion threshold ------
      0.069   13.7   1.0       0.17   12.4   1.0    1.7  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain


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 !   47.1   0.0   6.8e-16     2e-12      11     238 ..     197     406 ..     191     411 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 6.8e-16
                                   TSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHH CS
                  tRNA-synt_2d  11 ieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavq 91 
                                   +e+ + + l k+ ++i+e+f++ gf e+++p +   f   + + +++d+ +   ++ F +       +e++ LR    +  
  gi|91774018|ref|YP_566710.1| 197 YEEDREDRLGKLERDITEFFVDRGFLEIKSPIM-IPFEYIERMGIDKDDHLN--KQIFRV-------DESMCLRPMLAPCL 267
                                   56667778889999***************9988.889999999999998664..457777.......6799********** PP

                                   HHHH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETT CS
                  tRNA-synt_2d  92 irtl....ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpf 168
                                    ++l    +    pi+i+ ig ++R++++ ++hl eF+ v++  ++++ + +++ ++++e+l++l g e ++  ++     
  gi|91774018|ref|YP_566710.1| 268 YNYLrkldKVLPDPIRIFEIGPCYRKESDGSSHLEEFTMVNFCQMGSGCTRENMEALIDEFLEHL-GIEYEIEADNC---- 343
                                   *999765545568****************************************************.**977776654.... PP

                                   EEEEEEEEEEECCSSSSEEEEEEEEEE-HHHH.HHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT. CS
                  tRNA-synt_2d 169 tePsaevdvylvekkkkwlEllgaGmvrpevl.eavgideevsgfafGlGveRlamlkygieDiRelvend 238
                                   +  +  +d+++     + lEl  a +v p  l ++ g+  +++ ++ G+G+eRl  +++++++iR+  +++
  gi|91774018|ref|YP_566710.1| 344 MVYGDTIDIMH-----GDLELSSA-VVGPIPLdREWGV--NKPWMGAGFGLERLLKVRHNYTNIRRASRSE 406
                                   34466789988.....88999876.7788777257899..9999*********************876665 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 !   24.8   0.1   3.4e-09     1e-05      31     122 ..     211     311 ..     205     346 .. 0.70
   2 ?    1.2   0.0     0.053   1.6e+02     283     307 ..     378     402 ..     371     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.4e-09
                                   HHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT..TEEE..........-E-S-SHHHHHHH..HHCTHSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..........xxxxxxxxxxxxx..xxxxxxxxxxxx RF
                   tRNA-synt_2  31 avrkyleengfieietPiLsksdteegarlFkvksrek.ekeff..........aLtqspqlylell..ivagidrvfqia 98 
                                    + +++ ++gf+ei+ Pi++  +     +   + +  + +k+ f          +L+ +   yl  l  +     r+f+i+
  gi|91774018|ref|YP_566710.1| 211 DITEFFVDRGFLEIKSPIMIPFE---YIERMGIDKDDHlNKQIFrvdesmclrpMLAPCLYNYLRKLdkVLPDPIRIFEIG 288
                                   5889****************994...33333343333334455556666668899999999999887333334679***** PP

                                   EEE--S--BTTB-S-CEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  99 raFRaEdsrtdrhlaEFtqieaem 122
                                   +++R+E+ + + hl+EFt++++  
  gi|91774018|ref|YP_566710.1| 289 PCYRKES-DGSSHLEEFTMVNFCQ 311
                                   *****95.7789999*****8744 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.053
                                   SEEEEEEEHHHHHHHHCT-SSGGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 283 phgGlglGldRlvmlllgsesIrdv 307
                                   p  G g+Gl+Rl+ +  + ++Ir +
  gi|91774018|ref|YP_566710.1| 378 PWMGAGFGLERLLKVRHNYTNIRRA 402
                                   5679*****************9975 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 !   28.1   0.0   4.2e-10   1.2e-06      13     168 ..     200     342 ..     193     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.2e-10
               tRNA_synthFbeta  13 gelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlarg 93 
                                    ++++  kl+r + ++ ++ G+ E+ +  ++  + ++++    d+++++  +    ++  +lR+ L p l + l++  +  
  gi|91774018|ref|YP_566710.1| 200 DREDRLGKLERDITEFFVDRGFLEIKSPIMIPFEYIERMG--IDKDDHLNKQIFRVDESMCLRPMLAPCLYNYLRKLDKVL 278
                                   55778889*******************************6..345555555555567778**********99999877777 PP

               tRNA_synthFbeta  94 nedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepae 168
                                    + +r+FEig +++k+ ++++  ee +++ +  +g+               +++ ++++++le+lgi ++e+e+++
  gi|91774018|ref|YP_566710.1| 279 PDPIRIFEIGPCYRKEsDGSSHLEEFTMVNFCQMGSG-----------CTRENMEALIDEFLEHLGI-EYEIEADN 342
                                   777*************999999***************...........*******************.88877644 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 !   27.0   0.0   1.3e-09   3.8e-06       7     125 ..     253     359 ..     248     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.3e-09
                                   TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikai 87 
                                    d++++L+P+  + +++  r+   +    P+++++i+++yR+E     G   + eF++ +   +++        ++++ +i
  gi|91774018|ref|YP_566710.1| 253 VDESMCLRPMLAPCLYNYLRKL-DKVLPDPIRIFEIGPCYRKESD---GSSHLEEFTMVNFCQMGSGC----TRENMEALI 325
                                   5899*************99976.5544459**************9...544689***98765555544....7899***** PP

                                   HHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  88 sriferlglefraiielmsaksadykdkkefeavsesl 125
                                   ++++e+lg+e + i+ ++    + y+d+ +++  + +l
  gi|91774018|ref|YP_566710.1| 326 DEFLEHLGIE-YEIEADNC---MVYGDTIDIMHGDLEL 359
                                   *********9.77999977...4699999999766555 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.6e-06     0.011      12     117 ..     204     310 ..     196     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHHHHHHHHHTT-EEEE--S...EEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHHHHHHHHHH.TSS CS
                 tRNA-synt_His  12 kieelrrrlldlfeswGYelVspPl...lEyldslltgagedld.qtfklvDqsgrllglRaDiTpqvaRiaahrln.rer 87 
                                   +  +l+r+++++f ++G+ ++++P+   +Ey++ +    + +l+ q+f++     +++ lR+ + p    +  ++ +  + 
  gi|91774018|ref|YP_566710.1| 204 RLGKLERDITEFFVDRGFLEIKSPImipFEYIERMGIDKDDHLNkQIFRVD----ESMCLRPMLAPCLYNYLRKLDKvLPD 280
                                   56789*******************944457777777766666655899987....9******************9999*** PP

                                   -EEEEEEEEEEESS-SSTT--CCEEEEEEE CS
                 tRNA-synt_His  88 plRlcYaGsvlrtrpdglgrsreplQvGaE 117
                                   p R+  +G+++r+++dg +  +e++ v   
  gi|91774018|ref|YP_566710.1| 281 PIRIFEIGPCYRKESDGSSHLEEFTMVNFC 310
                                   *****************9999998766555 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   5.6e-05      0.17      10      56 ..      41      86 ..      40      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-05
               Zn_ribbon_recom 10 eCGspmtrrkrkgkr..hyYrCstyrrkgkkCsnhsireekleeavlee 56
                                  +CG+++t+r+++++r  +  r ++yr+ +k+C      +e+++++v ++
  gi|91774018|ref|YP_566710.1| 41 DCGARFTVRNSRSSRsaRSLRHNKYRKPCKRCR---PADEQIDRFVKKT 86
                                  8*********98666456678788766665565...5888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2728.09
//
Query:       gi|91774019|ref|YP_566711.1|  [L=498]
Description: L-threonine O-3-phosphate decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-51  174.1   0.0    5.8e-51  173.8   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    4.2e-23   81.1  11.0    1.8e-22   79.0  11.5    1.8  2  zf-like          Cysteine-rich small domain
     0.0096   14.5   0.0      0.015   13.9   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.039   13.9   0.0      0.082   12.9   0.0    1.4  1  Prefoldin_2      Prefoldin subunit


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 !  173.8   0.0   1.3e-54   5.8e-51       2     363 .]      40     380 ..      39     380 .. 0.86

  Alignments for each domain:
  == domain 1  score: 173.8 bits;  conditional E-value: 1.3e-54
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                   d+i++++n ++++s     pe     k   ++a g+ ++y++++ + e++ea a flg     +    ++++ g+G+++ i
  gi|91774019|ref|YP_566711.1|  40 DLIDMSANLNPYGSPF-DHPEYCLDLKAlFISARGGMHNYPDNR-YLEYREAAAGFLG-----DGISADNIIPGNGSCETI 113
                                   5677888888887544.3333333333347999***********.*************.....555666************ PP

                                   HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT- CS
                 Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtG 162
                                    +++ ++ +n gd++++p+pt+++y++ +r++g+ +++++          ++  +ealk+       +k+++v++p+NPtG
  gi|91774019|ref|YP_566711.1| 114 RLVAECM-INSGDVVVIPQPTFDEYEQQCRIMGASIRYFE------HDGLMDITDEALKD-------VKILFVCNPNNPTG 180
                                   *******.********************************......34555556677885.......59************ PP

                                   -B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHH CS
                 Aminotran_1_2 163 tvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsq 242
                                   ++++++ + +l++ ++ +  llfvDea+++++  +++    +a+v++  n l++++sl K+f+++G+R+G+ +++ +++++
  gi|91774019|ref|YP_566711.1| 181 KLFSRDSILELAKRCEMNSTLLFVDEAFSELADPTQS----VADVAATNNyLFVLRSLTKNFAIPGIRLGFGVASLEMAKA 257
                                   *********************************9554....9999999999****************************** PP

                                   HHHHHHHHTS...SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH..CH CS
                 Aminotran_1_2 243 lrklsrpfls...ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae..ta 317
                                   l+ +  +++    + ++ aa++++        ++l ++r+ ++++r++l+++L  + g++ l+s  +++l+ d++++  + 
  gi|91774019|ref|YP_566711.1| 258 LNTARLSWNLgsvPDVVGAALLNMEGGCY--SKYLVKSRKMIAEEREYLTERLSGIyGFEPLPSAVNYVLV-DIRELlmDS 335
                                   *9998888874344444444444444333..33********************999********8887766.888887989 PP

                                   HHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                 Aminotran_1_2 318 kelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                   +el   L+ + g++v+ ++sf++     +Ri v   t+ee ++l++a+
  gi|91774019|ref|YP_566711.1| 336 QELTSRLASH-GILVRDCSSFYLldNDYIRIAV--RTREETDRLIQAI 380
                                   999999**99.*************999******..**********997 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   6.1e+03      44      60 ..     343     360 ..     333     374 .. 0.73
   2 !   79.0  11.5   4.1e-26   1.8e-22       7      74 ..     411     479 ..     407     487 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                       zf-like  44 teng.kvkdCskCllvHk 60 
                                    ++g  v+dCs+ +l+ +
  gi|91774019|ref|YP_566711.1| 343 ASHGiLVRDCSSFYLLDN 360
                                   678888999998777655 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 4.1e-26
                       zf-like   7 nkeCeyyPCHktedenClfCyCPlYaledeel.Gefveteng.kvkdCskCllvHkkevadellkklkei 74 
                                   +++CeyyPCH+ ++++C+fC+CP+Y++ed ++ G ++e++ g +v++C+kC+++Hk+ev++e+l+ l+  
  gi|91774019|ref|YP_566711.1| 411 RNTCEYYPCHF-SGQDCTFCFCPFYPCEDPKTgGCWIESTTGsEVWSCEKCNILHKPEVVQEVLHILMSD 479
                                   679********.99***************776488999999*********************99876654 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.3e-06     0.015      86     177 ..     119     209 ..     103     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-06
                                   TTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHT CS
               Cys_Met_Meta_PP  86 allkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakka 166
                                    ++++Gd +v+ +  ++      ++ ++ +g ++++++ + l ++     + +k++++  p np+ k+    +i++lak  
  gi|91774019|ref|YP_566711.1| 119 CMINSGDVVVIPQPTFDEY----EQQCRIMGASIRYFEHDGLMDITDEALKDVKILFVCNPNNPTGKLFSRDSILELAKRC 195
                                   5778888888887666655....55556689999********************************************988 PP

                                   T...-EEEEEGTTT CS
               Cys_Met_Meta_PP 167 g...vlvvvDntfa 177
                                   +   +l++vD +f+
  gi|91774019|ref|YP_566711.1| 196 EmnsTLLFVDEAFS 209
                                   66679******996 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.082      42      87 ..     371     416 ..     366     418 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                   -TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  42 dedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqlek 87 
                                   +e+++  + +Gdvl +  k+ ++e+L+e++e++e  + ++ + +e+
  gi|91774019|ref|YP_566711.1| 371 EETDRLIQAIGDVLTEAGKDYAEERLKETIESAESGMPACRNTCEY 416
                                   567788999*************************999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3290.47
//
Query:       gi|91774020|ref|YP_566712.1|  [L=204]
Description: nucleotidyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-11   45.3   0.0    1.5e-11   44.9   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
    7.1e-05   22.8   0.0     0.0001   22.3   0.0    1.2  1  CTP_transf_3  Cytidylyltransferase
    0.00056   19.7   0.0    0.00075   19.3   0.0    1.1  1  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   2.5e-15   1.5e-11       1     112 [.       3     119 ..       3     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.5e-15
                                   EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH..CHHHHHHTTC.TS-EEE-TTSS-SHHHHH CS
                  NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraag.vdevvvvggd..eevlaalarl.gvrvvededpgkgplasl 76 
                                   a+i+AGG ++R+g  +Ka + l ++pl+ ++ld+l +a+ +++v+v + +  +e ++ ++++ g +v+  + pg + ++ +
  gi|91774020|ref|YP_566712.1|   3 AIIMAGGLAQRLGAeEKACVMLIDRPLISYLLDSLIDAEhIERVFVQTSPysPETESCVRGYyGNDVLILRTPGDNYVGDM 83 
                                   79***********77***********************559******988776777666665567777777789******* PP

                                   HHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHH CS
                  NTP_transf_3  77 aaalraaadadavlvlacDmPlltpelverllaaaa 112
                                     a++ a++  +v++l+ D+Pl+++e++++++++++
  gi|91774020|ref|YP_566712.1|  84 IKAVKDAGSIGPVMILMPDLPLVESEHIDAIVESYE 119
                                   ********************************9986 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.7e-08    0.0001      14     116 ..      17     119 ..       3     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.7e-08
                                   TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES..-HHHHHHHHHTT.SEEEE--TTCSSHHHHHHHHHHHHTTT.TTS CS
                  CTP_transf_3  14 pgKnlldlggkpliayvleaalkskafekvivaTD..seeiknvakefg.asvlvtrsslesdterflevvkaflmsenee 91 
                                   ++K+   l ++pli y+l+ +++++ +e+v+v T+  s e++  +  +    vl +r++  +    + ++vk+  +     
  gi|91774020|ref|YP_566712.1|  17 EEKACVMLIDRPLISYLLDSLIDAEHIERVFVQTSpySPETESCVRGYYgNDVLILRTPGDNYVGDMIKAVKDAGSI---G 94 
                                   5799999***************************977899999998877799*****98666666666666665554...7 PP

                                   EEEEE-TT-TT--HHHHHHHHHHHH CS
                  CTP_transf_3  92 iivnlqGdnPllqeevikkaietlk 116
                                    ++ l  d Pl+++e+i++++e ++
  gi|91774020|ref|YP_566712.1|  95 PVMILMPDLPLVESEHIDAIVESYE 119
                                   7888888**************9987 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-07   0.00075       2     130 ..       2     128 ..       1     135 [. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-07
                                   EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..CCEEEE.E--SSHHH CS
                          IspD   2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..ksiqlv.aGGdeRae 79 
                                    ++i A G  +R++a+ +K+ + l +++l++  +d+l + ++++++ v  s++  e+ + + +   +++ ++   Gd+   
  gi|91774020|ref|YP_566712.1|   2 DAIIMAGGLAQRLGAE-EKACVMLIDRPLISYLLDSLIDAEHIERVFVQTSPYSPETESCVRGYygNDVLILrTPGDNYVG 81 
                                   589***********98.69999******************************99555555554476556555156888766 PP

                                   HHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE- CS
                          IspD  80 sVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgailalpv 130
                                      +++k  +g+   V++     pl+++++i+++++  e      i+a++v
  gi|91774020|ref|YP_566712.1|  82 DMIKAVKD-AGSIGPVMILMPDLPLVESEHIDAIVESYER---CSIPAMSV 128
                                   66666665.4555667777777899999999999999885...77888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 1191.67
//
Query:       gi|91774021|ref|YP_566713.1|  [L=498]
Description: L-threonine O-3-phosphate decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-44  152.7   0.0      2e-44  152.3   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    6.3e-27   93.3   6.3    1.5e-26   92.1   6.3    1.7  1  zf-like          Cysteine-rich small domain
  ------ inclusion threshold ------
      0.037   12.6   0.0      0.056   12.0   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.097   12.6   0.0       0.21   11.6   0.0    1.5  1  DUF1246          Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.0   4.5e-48     2e-44      32     363 .]      68     379 ..      60     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 4.5e-48
                                   HHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHH CS
                 Aminotran_1_2  32 laggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrl 112
                                   +a++ + +y++++ + e+++a  +fl       l  + ++v g+G++++i +++  + ++ gd +l+p pt+++y++ ++ 
  gi|91774021|ref|YP_566713.1|  68 HAMERFGQYPDNR-YLEFRKAAVRFLD----NGLSVD-NIVPGNGSCEIIRLVAESI-VDQGDIVLIPHPTFTEYEQQCNV 141
                                   7889999******.*************....334455.99************99999.9********************** PP

                                   TTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
                 Aminotran_1_2 113 sggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                                   +g+ v+++        + d+ +l +++          k+++v++p+NPtG++ ++e++  l++ + ++n llfvDea+ ++
  gi|91774021|ref|YP_566713.1| 142 AGADVRYIG-------QDDIFDLSDDVLG------SAKILFVCNPNNPTGKLHKREDILSLVKRCVSNNTLLFVDEAFIEL 209
                                   *********.......8899999998887......669******************************************* PP

                                   BSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHH.H CS
                 Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqs.e 273
                                   + ++++  ++  +v + ++l+i++sl K+f+++G R+G+ ++++ ++++l+ +  +++  s+  ++  a+l+ +   +s +
  gi|91774021|ref|YP_566713.1| 210 ADDPSQ--TITDTVVDNDHLFILRSLTKDFAIPGVRLGFGVASKTIANTLNTARLSWNLGSIPEEIGIAMLNMDGGCNSpY 288
                                   **9653..5589***************************************************************9999** PP

                                   HHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECT CS
                 Aminotran_1_2 274 leemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvA 349
                                   l ++r+ +++ r +l++++ ++  +k l+s  +++l+ d+sa+  +  el + L+ + gv+++ ++sf    + ++Ri v 
  gi|91774021|ref|YP_566713.1| 289 LVASRKAIENDRNYLTERISRIrKFKPLPSTVNYILV-DISASslDSVELTQRLAAH-GVLIRDCSSFPSmgEDFVRIAV- 366
                                   *******************999********9998888.6666669999********9.************9*********. PP

                                   TS-HHHHHHHHHHH CS
                 Aminotran_1_2 350 glteeeleelveal 363
                                     ++ee + l +a+
  gi|91774021|ref|YP_566713.1| 367 -RPKEETDILSQAI 379
                                   .9999988887765 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   6.3   3.4e-30   1.5e-26       5      80 ..     408     485 ..     404     487 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 3.4e-30
                       zf-like   5 fsnkeCeyyPCHktedenClfCyCPlYaledeel.Gefveteng.kvkdCskCllvHkkevadellkklkeileelkk 80 
                                     n +C+yyPCH++ed++C++C+CP+Y +ede++ G++v++++g kv++C++C+lvH+k+v++ell+ l+e  ++ ++
  gi|91774021|ref|YP_566713.1| 408 GGNLDCPYYPCHSCEDQDCTLCFCPFYRCEDERTgGKWVDRSSGgKVWSCEDCVLVHDKDVVKELLDVLSEDEDMDRN 485
                                   56889**************************98769*******99***********************9999888775 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 ?   12.0   0.0   1.3e-05     0.056      85     177 ..     116     207 ..      86     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                                   HTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT---...-HHHHHHH CS
               Cys_Met_Meta_PP  85 lallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvv...Diekiakl 162
                                    +++ +Gd +++ +  +       ++ ++  g +v+++ ++d+ +l   +    k++++  p np+ k++   Di +++k 
  gi|91774021|ref|YP_566713.1| 116 ESIVDQGDIVLIPHPTFTE----YEQQCNVAGADVRYIGQDDIFDLSDDVLGSAKILFVCNPNNPTGKLHkreDILSLVKR 192
                                   4567777777777765554....55555668999*******************************9988722256666666 PP

                                   HHHTT-EEEEEGTTT CS
               Cys_Met_Meta_PP 163 akkagvlvvvDntfa 177
                                   + ++++l++vD +f+
  gi|91774021|ref|YP_566713.1| 193 CVSNNTLLFVDEAFI 207
                                   66677******9995 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.7e-05      0.21      40     101 ..      97     158 ..      75     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                                   T-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-HHHHHC-SS-EES-TTHHHHH CS
                       DUF1246  40 videvivldkfkdilkeevqeklreenailvPhgsfveYvgiekieelkvpifGnrkllrwE 101
                                    +d+++  +   +i++   ++ + + + +l+Ph +f+eY    ++    v+++G+ +++   
  gi|91774021|ref|YP_566713.1|  97 SVDNIVPGNGSCEIIRLVAESIVDQGDIVLIPHPTFTEYEQQCNVAGADVRYIGQDDIFDLS 158
                                   5688888888889998887778888899**************************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2877.66
//
Query:       gi|91774022|ref|YP_566714.1|  [L=331]
Description: adenosylcobinamide-phosphate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-94  315.0   0.3    4.7e-94  314.7   0.3    1.2  1  CobD_Cbib  CobD/Cbib protein
  ------ inclusion threshold ------
      0.088   12.1   0.0      0.088   12.1   0.0    1.9  3  AmpE       Regulatory signalling modulator protein AmpE
        2.8    8.6   5.3         32    5.2   0.5    2.5  2  Renin_r    Renin receptor-like 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 !  314.7   0.3   7.9e-98   4.7e-94       1     273 [.      16     303 ..      16     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 314.7 bits;  conditional E-value: 7.9e-98
                     CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla.laall....glvl 76 
                                   l+lA  +Dll+g+p+++lhPvv+ig+li++++k++   ++++++Gv++al+++l+a+ +a+++ll+a l+  +     l++
  gi|91774022|ref|YP_566714.1|  16 LILATGFDLLIGEPPTALHPVVWIGNLIGFFKKKVPA-THKKTYGVVFALIVILFAASIAYVVLLIAnLSF-IpefvVLLI 94 
                                   689******************************9964.6899*******************9999886333.24544679* PP

                     CobD_Cbib  77 ealllkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflll.. 154
                                   ea++lk+t+a+r Lle++++v+ +l kgdl +aR+++sm+V+Rdts+l+e +++++++E+++EN++Dg+++Plfy++++  
  gi|91774022|ref|YP_566714.1|  95 EAYFLKSTFAIRRLLEAAMEVYGELvKGDLVSARKKLSMYVSRDTSQLTEGQVSSSVIETCSENFVDGILSPLFYYVIFgp 175
                                   *************************88***************************************************967 PP

                     CobD_Cbib 155 .glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllal....a............aalriarrda 218
                                    gl+ga+++kav+TlDsmvGY ne+y+++G+++A++DD+ln+iPAR++++++++    +             a+r+a  d 
  gi|91774022|ref|YP_566714.1| 176 yGLIGAYIFKAVSTLDSMVGYMNEKYREIGYFSAKTDDVLNWIPARICVVFIMAgsflSsvllkskgldhmGAFRCASTDC 256
                                   77789***********************************************995555045555555665677******** PP

                     CobD_Cbib 219 rkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedieral 273
                                    ++pSpNsg+p+aa+Ag lgvrL++pn+Y  gk  + p+         +edi++a 
  gi|91774022|ref|YP_566714.1| 257 MTTPSPNSGYPMAAIAGTLGVRLEKPNTYvIGKNLSLPK---------TEDIKKAA 303
                                   *****************************8885444444.........45555554 PP

>> AmpE  Regulatory signalling modulator protein AmpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2      0.77   4.6e+03      44      58 ..      64      78 ..      47     113 .. 0.57
   2 ?   12.1   0.0   1.5e-05     0.088     145     207 ..     164     225 ..     151     233 .. 0.72
   3 ?   -1.8   0.2      0.25   1.5e+03     257     283 ..     301     327 ..     290     328 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.77
                          AmpE 44 llltivamvvvlail 58
                                  l++++ a  + +++l
  gi|91774022|ref|YP_566714.1| 64 LIVILFAASIAYVVL 78
                                  333333333333322 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.5e-05
                          AmpE 145 laplfwfvvagpygpvalvgyavlrayqtwlarrktpleraqsgvdallhvldwipvrlagva 207
                                   l+plf++v+ gpyg +    +  + + ++++   +  ++           vl+wip+r++  +
  gi|91774022|ref|YP_566714.1| 164 LSPLFYYVIFGPYGLIGAYIFKAVSTLDSMVGYMNEKYREIGYFSAKTDDVLNWIPARICV-V 225
                                   89************988777766666666665544444433333444567899****9864.4 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.25
                          AmpE 257 kaavslakkvtlvvvvvvalltiygal 283
                                   kaa  +     +vv++ val+ i   l
  gi|91774022|ref|YP_566714.1| 301 KAAEVIGMSSIFVVIIFVALIYIISNL 327
                                   455555556667788888888887666 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5    0.0054        32      45      78 ..      52      82 ..      44      87 .. 0.66
   2 ?    5.0   0.5    0.0064        38      56      78 ..     307     329 ..     283     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0054
                       Renin_r 45 kkyssdYpaiFniiLwlvvvlvlaliaivvalas 78
                                   + ++ Y ++F++i+ l   ++ ++ ++v+ +a+
  gi|91774022|ref|YP_566714.1| 52 ATHKKTYGVVFALIVIL---FAASIAYVVLLIAN 82
                                  56678999999987554...44455555555544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0064
                       Renin_r  56 niiLwlvvvlvlaliaivvalas 78 
                                    +   +vv++++ali+i+ +l++
  gi|91774022|ref|YP_566714.1| 307 GMSSIFVVIIFVALIYIISNLIN 329
                                   5666799***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1891.73
//
Query:       gi|91774023|ref|YP_566715.1|  [L=195]
Description: hypothetical protein Mbur_2091 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   36.8   0.0    4.3e-09   36.5   0.0    1.2  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 !   36.5   0.0   2.4e-13   4.3e-09      18     141 ..      36     168 ..      25     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.4e-13
                                   --HHHHHHHHHHHTT.............HHHHH.HHH...HHHHHHHHHHHHHHHHHHT.-S-.......HHT-TT--HHH CS
                          PgpA  18 gtvgslaalllallll............lleslslll...llilllflvGiwackktek.elg.......ekDpgeiviDE 75 
                                   +tv+ l++++l+l+              +++   +++   ++++ll++ Gi ++++ ek +l        e D + i+ DE
  gi|91774023|ref|YP_566715.1|  36 ITVDMLVDTALELYAPhpgletreiaeeRFRRELYIAisdANLCLLIYSGILLEREGEKgKLPnisrssyEMDLTFIIADE 116
                                   67777777777777756777777666664444445557788999***************77779***************** PP

                                   HTTHHHHH........TTHHHHHHHHHHHHS--THHHHTSSS.-S---TTHHHHHHHHHHHHHHHH CS
                          PgpA  76 vvgqwiallllpatllalllafilFrlfDivKpgpigwldrklkgglgvmlDDllAgiaaalvlal 141
                                   v+g++ia       ++    +++ F  fD+ Kpg++++l          ++DD+++g+++++   +
  gi|91774023|ref|YP_566715.1| 117 VIGMSIAK------YISGDKGIFEFVRFDKQKPGILSKLGP--------FMDDVIGGLIGGVSANM 168
                                   ********......3344789******************77........9*********9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1142.34
//
Query:       gi|91774024|ref|YP_566716.1|  [L=271]
Description: cobalamin-5'-phosphate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-34  118.8  14.9    4.2e-34  118.5  14.9    1.0  1  CobS      Cobalamin-5-phosphate synthase
  ------ inclusion threshold ------
      0.015   15.4   0.3      0.015   15.4   0.3    3.9  4  YtpI      YtpI-like protein


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 !  118.5  14.9   4.7e-38   4.2e-34       2     203 ..      12     249 ..      11     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 4.7e-38
                          CobS   2 lsflTrlPvp.......elaralaffPlvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDtaDglg 73 
                                   ++fl+++Pv        el +  ++  ++G++lG ++ ++a+l+  +l+ +++a+l++++++++tg +HlDGl D++Dg  
  gi|91774024|ref|YP_566716.1|  12 FGFLSTIPVGmsmegldELVKRSYLQTFAGIVLGSMIgIFAYLTESFLPsTISAVLIMVFIYYITGLNHLDGLGDFGDGAT 92 
                                   89*******86554443334466666899*******988888888887777799999999999*****************9 PP

                          CobS  74 sgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala.................lllapvlsRlaallaiallpyaee 137
                                   ++++ e++++++kD ++G +Gv   vl+l++ +a++++l                  ll+a++ ++ a+l+++a++++ +e
  gi|91774024|ref|YP_566716.1|  93 AHGSLEKKVNALKDMSLGIGGVSYTVLALIALYASISSLQaevlffsdnaaliiaisLLIAEIGAKQAMLTVAAFGKPIHE 173
                                   999******************************9964443344456666666688888899****************9999 PP

                          CobS 138 glgalfaeaqkk......lvllal........avlllllall........laallvalllrrlarrklggvtGDvlGavie 196
                                   glg++++++++       +    +        a        +        + a+++a+++ +++ r+++g++GD++G ++e
  gi|91774024|ref|YP_566716.1| 174 GLGSMIINNTTFpryavsF----VlgalvcvlA--------FgtlgiigyISAIVTAFVILNISIRHFKGINGDCIGTSNE 242
                                   *****99754446653321....1222222111........11223334456666666778888889************** PP

                          CobS 197 ltellvl 203
                                   +++++vl
  gi|91774024|ref|YP_566716.1| 243 IARIIVL 249
                                   *****98 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   1.7e-06     0.015      25      67 ..      31      73 ..      27      85 .. 0.89
   2 ?   -0.9   0.6      0.21   1.8e+03      50      67 ..     135     152 ..     114     167 .. 0.62
   3 ?   -0.5   1.3      0.16   1.4e+03      47      72 ..     180     205 ..     175     224 .. 0.70
   4 ?    0.6   0.8     0.072   6.4e+02      46      77 ..     231     263 ..     220     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-06
                          YtpI 25 lekkllsakasialGlflilfginqllllestvalvvgavflv 67
                                  +++ +l++ a i+lG+++ +f+     +l st+++v  +vf+ 
  gi|91774024|ref|YP_566716.1| 31 VKRSYLQTFAGIVLGSMIGIFAYLTESFLPSTISAVLIMVFIY 73
                                  68999*******************9999*************94 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.21
                          YtpI  50 llllestvalvvgavflv 67 
                                   +l++++  al++++ +l+
  gi|91774024|ref|YP_566716.1| 135 VLFFSDNAALIIAISLLI 152
                                   444555566666665555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.16
                          YtpI  47 inqllllestvalvvgavflvlGlan 72 
                                   in + + + +v++v ga+  vl+++ 
  gi|91774024|ref|YP_566716.1| 180 INNTTFPRYAVSFVLGALVCVLAFGT 205
                                   56666777777888887777766654 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.072
                          YtpI  46 gin.qllllestvalvvgavflvlGlanlfaGi 77 
                                   gin   + +++ +a ++ +  l +++  + +G+
  gi|91774024|ref|YP_566716.1| 231 GINgDCIGTSNEIARIIVLMVLTVAITAVNNGY 263
                                   788888888888999999999999998888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1570.66
//
Query:       gi|91774025|ref|YP_566717.1|  [L=201]
Description: nucleotidyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   44.6   0.0    2.5e-11   44.2   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    3.9e-08   33.5   0.0    6.7e-08   32.7   0.0    1.3  1  CTP_transf_3     Cytidylyltransferase
    3.4e-06   27.0   0.0      5e-06   26.4   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.024   14.5   0.1      0.032   14.1   0.1    1.2  1  DUF3865          Domain of Unknown Function with PDB structur
       0.05   13.4   0.0      0.068   13.0   0.0    1.2  1  DUF2064          Uncharacterized protein conserved in bacteri
       0.09   12.0   0.2       0.17   11.0   0.0    1.6  2  CofC             Guanylyl transferase CofC like
        0.1   12.1   0.0       0.14   11.7   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   9.6e-15   2.5e-11       4     114 ..       1     116 [.       1     129 [. 0.78

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 9.6e-15
                                   EEESS-TTTT.TTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH..CHHHHHHTTC.T..S-EEE-TTSS-SHHHHHH CS
                  NTP_transf_3   4 LAGGrSsRmg.gdKallplggkpllervldalraag.vdevvvvggd..eevlaalarl.g..vrvvededpgkgplasla 77 
                                   +AGG++ R+g g+K+ ++l gkpl+ +v+d+l++++ +++++v++ +  ++ ++ ++++ g  ++ ++    g + ++ + 
  gi|91774025|ref|YP_566717.1|   1 MAGGQGLRLGmGEKPCVELLGKPLISYVIDSLERSSyIERIFVAVSPstPATEELVNEKyGdhIQAIYTN--GDNYVGDMV 79 
                                   59********66********************999768******98855455555544423224444443..667777777 PP

                                   HHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHH CS
                  NTP_transf_3  78 aalraaadadavlvlacDmPlltpelverllaaaaas 114
                                    a+++++ +++v++++ D+P++tp+l++ +++a+++ 
  gi|91774025|ref|YP_566717.1|  80 YAVESSNIQEPVMIIMSDLPMVTPKLIDSIIEAYRDC 116
                                   777777799***********************99754 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.6e-11   6.7e-08      15     124 ..      13     122 ..      10     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.6e-11
                                   TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEE..ES-HHHHHHHHH.TT..SEEEE--TTCSSHHHHHHHHHHHHTTT.TT CS
                  CTP_transf_3  15 gKnlldlggkpliayvleaalkskafekviva..TDseeiknvake.fg..asvlvtrsslesdterflevvkaflmsene 90 
                                   +K+  +l+gkpli yv++ +  s  +e+++va   +   +++++ e +g  ++ + t ++       + ++v a+++s  +
  gi|91774025|ref|YP_566717.1|  13 EKPCVELLGKPLISYVIDSLERSSYIERIFVAvsPSTPATEELVNEkYGdhIQAIYTNGDN-----YVGDMVYAVESSNIQ 88 
                                   799*************************666521567778888765155666666666555.....555555555555333 PP

                                   SEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEE CS
                  CTP_transf_3  91 eiivnlqGdnPllqeevikkaietlkenqedyls 124
                                   e ++ + +d P++ +++i+ +ie++++ ++ ++s
  gi|91774025|ref|YP_566717.1|  89 EPVMIIMSDLPMVTPKLIDSIIEAYRDCGSSSMS 122
                                   57899999******************99986655 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 !   26.4   0.0     2e-09     5e-06       7     120 ..       2     116 ..       1     134 [. 0.81

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2e-09
                                   CTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG...CCEEEE.E--SSHHHHHHH CS
                          IspD   7 AAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld...ksiqlv.aGGdeRaesVln 83 
                                   A G+G R++ g +K  +el g++l++  +d+l  s+ +++i v+vs+   +++e+l  +    +iq +   Gd+     + 
  gi|91774025|ref|YP_566717.1|   2 AGGQGLRLGMG-EKPCVELLGKPLISYVIDSLERSSYIERIFVAVSPST-PATEELVNEkygDHIQAIyTNGDNYVGDMVY 80 
                                   88*******99.5999*******************************99.9999999987776677552567777666666 PP

                                   HHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTT CS
                          IspD  84 glkalegeakfVLvHDaARpllkaadiaellaaaeqs 120
                                   +++  ++ ++ V++  +  p+++++ i+++++a ++ 
  gi|91774025|ref|YP_566717.1|  81 AVES-SNIQEPVMIIMSDLPMVTPKLIDSIIEAYRDC 116
                                   6666.444488999999999*********99999873 PP

>> DUF3865  Domain of Unknown Function with PDB structure (DUF3865)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.3e-05     0.032     108     152 ..      43      93 ..      26     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                       DUF3865 108 ksvkPs.qatsklle.....svksvltketeyvlGavyaieassiPellll 152
                                   ++v Ps +at++l++     +++ ++t++ +yv   vya+e+s i e +++
  gi|91774025|ref|YP_566717.1|  43 VAVSPStPATEELVNekygdHIQAIYTNGDNYVGDMVYAVESSNIQEPVMI 93 
                                   6778873578887743333389***********************986554 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 ?   13.0   0.0   2.7e-05     0.068      30      86 ..      59     113 ..      32     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                                   HH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHHHHT CS
                       DUF2064  30 alakglevlpQqggdlgeRlarafdrafeageepvlliGsDcpqltaalleqAfeaL 86 
                                   + +++++ ++ +g++    + +a+++   +  epv++i sD+p++t++l+++ +ea 
  gi|91774025|ref|YP_566717.1|  59 KYGDHIQAIYTNGDNYVGDMVYAVESS--NIQEPVMIIMSDLPMVTPKLIDSIIEAY 113
                                   555666666666666666799999999..5556*****************9988875 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.6e-05      0.17      87     112 ..      87     112 ..      23     117 .. 0.80
   2 ?   -2.9   0.0       1.2     3e+03     158     180 ..     166     188 ..     161     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.6e-05
                          CofC  87 eekeviiipsdiPlikkedvkdllel 112
                                    +++v+ii+sd+P+++ + ++ ++e 
  gi|91774025|ref|YP_566717.1|  87 IQEPVMIIMSDLPMVTPKLIDSIIEA 112
                                   3689*****************99986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                          CofC 158 glkvkiydsfylsvdinteedlg 180
                                   + + +i d   ++++int +d+ 
  gi|91774025|ref|YP_566717.1| 166 EYHNYILDDPEVALNINTVDDMK 188
                                   55678888888999999999875 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.3e-05      0.14       5      77 ..       1      66 [.       1     123 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                                  E--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
               NTP_transferase  5 LaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77
                                  +aGG+G RL        k+ v  lgk +li +++  l +s++ e i+v  +   +  ee ++e++     +++
  gi|91774025|ref|YP_566717.1|  1 MAGGQGLRLG----MGEKPCVELLGK-PLISYVIDSLERSSYIERIFVAVSPSTPATEELVNEKYGDH--IQA 66
                                  8999999994....789*********.***********988777799988888888888777766333..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1335.18
//
Query:       gi|91774026|ref|YP_566718.1|  [L=123]
Description: hypothetical protein Mbur_2094 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 777.76
//
Query:       gi|91774027|ref|YP_566719.1|  [L=243]
Description: KaiC [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-48  163.3   1.4    6.2e-48  163.2   1.4    1.0  1  ATPase     KaiC
      4e-07   29.0   0.5      7e-07   28.2   0.4    1.4  2  GvpD       GvpD gas vesicle protein
    4.7e-06   26.0   1.1     0.0013   18.1   0.8    2.9  3  Rad51      Rad51
    0.00026   20.4   0.5    0.00046   19.6   0.2    1.8  2  DnaB_C     DnaB-like helicase C terminal domain
     0.0015   18.1   0.0     0.0026   17.3   0.0    1.4  1  AAA_25     AAA domain
     0.0048   16.7   0.0     0.0072   16.2   0.0    1.2  1  MEDS       MEDS: MEthanogen/methylotroph, DcmR Sensory domain
     0.0073   15.5   0.4       0.02   14.0   0.1    1.6  2  PAXNEB     PAXNEB protein
     0.0098   16.3   1.2      0.029   14.8   1.2    2.0  1  AAA        ATPase family associated with various cellular act
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.029   14.6   0.0    1.4  1  AAA_22     AAA domain
      0.021   14.6   0.0      0.033   13.9   0.0    1.3  1  IstB_IS21  IstB-like ATP binding protein
      0.053   12.8   0.1      0.079   12.2   0.1    1.2  1  DUF2075    Uncharacterized conserved protein (DUF2075)
       0.12   12.1   0.6       0.24   11.1   0.6    1.5  1  AAA_24     AAA domain
       0.25   10.8   1.0       0.47    9.9   0.3    1.8  2  AAA_7      P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.2   1.4   4.5e-51   6.2e-48       1     229 [.      10     237 ..      10     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 163.2 bits;  conditional E-value: 4.5e-51
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlekleee 80 
                                   v+tgI glDe+lkgG+ +g++  ++G++GtGKtif+ qFl++g++k ge ++ + + e++++l ++++ s+Gwdl+ l + 
  gi|91774027|ref|YP_566719.1|  10 VSTGIRGLDEMLKGGFFKGTANVVSGKSGTGKTIFGTQFLMEGVNK-GETVMCIITSEESKSLVREMQsSFGWDLDGLVKD 89 
                                   78*****************************************999.99999765555555555555549*********** PP

                        ATPase  81 gklaiidasesaeesaeekdkedleelieelaeai....keikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgv 156
                                   gkl+++d++  + + ++ + + +++eli+++++ i    +e+k  rv iDs++++   +e++ ++R+ ++ ++ v++k++v
  gi|91774027|ref|YP_566719.1|  90 GKLVFVDITDPSLRLQK-SVEIAPMELIKSFKKLIesklEETKPDRVFIDSVEAIfLAIESNYKLRTLIDDVFGVFRKREV 169
                                   ********999876555.55666666666555555111167888***********99************************ PP

                        ATPase 157 TailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                   T++++  +      +g  +  e+ +d vi+L ++ i ++l+Rt+ ++k+Rg+++ +++ +++I+++g  vl++
  gi|91774027|ref|YP_566719.1| 170 TSLITVGV-----MFGLDEMVEYGADSVIKLGREVIGSNLQRTVYVMKLRGSGTINEVRVLNISDSGMAVLPQ 237
                                   *******4.....6889999999***********************************************987 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.22     3e+02     239     259 ..       9      29 ..       7      32 .. 0.88
   2 !   28.2   0.4   5.1e-10     7e-07      10     198 ..      28     220 ..      17     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.22
                          GvpD 239 kfsvglrdldkllseGtdrGs 259
                                   + s+g+r ld++l +G+ +G+
  gi|91774027|ref|YP_566719.1|   9 RVSTGIRGLDEMLKGGFFKGT 29 
                                   689*************98885 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 5.1e-10
                          GvpD  10 GktllikGaPGtGktlftlrgl.dvlrresdvlyv.strvddetvseayfsgeaeld......ktalldllkdpleldldv 82 
                                   G + ++ G+ GtGkt+f  ++l + +++ + v+ + ++   ++ v e+  s   +ld      k  ++d+   +l l+  v
  gi|91774027|ref|YP_566719.1|  28 GTANVVSGKSGTGKTIFGTQFLmEGVNKGETVMCIiTSEESKSLVREMQSSFGWDLDglvkdgKLVFVDITDPSLRLQKSV 108
                                   67789***************9845788888888761556678899***944444444443244666779998889888877 PP

                          GvpD  83 dv.PiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgv.rlvlvlet.aans 160
                                   ++ P+e   ++s+ + +++  + ++   + +ds e ++ ++    +s  +++t+ +d+  + r+ +v  l+ v      ++
  gi|91774027|ref|YP_566719.1| 109 EIaPMEL--IKSFKKLIESKLEETKPDRVFIDSVEAIFLAI----ESNYKLRTLIDDVFGVFRKREVtSLITVGVMfGLDE 183
                                   5536643..789999**98878888889999**66665555....455568888888876666655516888865426799 PP

                          GvpD 161 rleyivdGvvtl..nvkeddrgrlrrdlrleklrGvrign 198
                                    +ey +d v+ l  +v       l+r + + klrG    n
  gi|91774027|ref|YP_566719.1| 184 MVEYGADSVIKLgrEVIGS---NLQRTVYVMKLRGSGTIN 220
                                   9***********8766665...799999999999965544 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.8   9.3e-07    0.0013      18      57 ..       9      48 ..       2      61 .. 0.89
   2 ?    2.1   0.0      0.07        96      70     116 ..      88     139 ..      75     166 .. 0.77
   3 ?    2.9   0.0     0.041        56     175     235 ..     166     230 ..     148     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.3e-07
                                  EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                         Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                  +++tG + lDe+L+GG+  g+   + G +++Gkt +  ++
  gi|91774027|ref|YP_566719.1|  9 RVSTGIRGLDEMLKGGFFKGTANVVSGKSGTGKTIFGTQF 48
                                  499*******************************998775 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.07
                                   -SSEEEEEE.SSS---GGGGHHHH.....HHTT--HHHHGGGEEEEE--STTH CS
                         Rad51  70 gegkavyid.tegtfrperlveia.....erykldkeevlenvayaRaytieh 116
                                    +gk v++d t+ ++r ++ veia     + +k   e+ le+ + +R++  ++
  gi|91774027|ref|YP_566719.1|  88 KDGKLVFVDiTDPSLRLQKSVEIApmeliKSFKKLIESKLEETKPDRVFI-DS 139
                                   57999999988999********9999888888888888889999999884.34 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.041
                                   HH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-ST.....TEEEEEEES- CS
                         Rad51 175 efevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkg.....eeRivkvvds 235
                                   + ev+ +it  v+  +d     + ad+ +  g +v++ + +  +++ k +g     e R++ + ds
  gi|91774027|ref|YP_566719.1| 166 KREVTSLITVGVMFGLDE-MVEYGADSVIKLGREVIGSNLQRTVYVMKLRGsgtinEVRVLNISDS 230
                                   567888999999999999.778999***********************999777777788888877 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   3.3e-07   0.00046       2      69 ..      10      77 ..       9     156 .. 0.82
   2 ?   -2.4   0.0       1.7   2.4e+03     201     242 ..     185     222 ..     181     227 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                                  BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHH CS
                                  xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRlls 69
                                  +stg + LD++++ G+ kg+  ++ +++++Gkt + +++  + ++k ++ ++++  e ++++lv+ + s
  gi|91774027|ref|YP_566719.1| 10 VSTGIRGLDEMLKgGFFKGTANVVSGKSGTGKTIFGTQFLMEGVNKGETVMCIITSE-ESKSLVREMQS 77
                                  789******998537************************998887666444444444.45566666655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                   CCCCXSEEEEEEECCHHHHHHCHHCEEEEEEEEET.TSXXEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                        DnaB_C 201 ieqdADvvlflyrdeyykedseekgkaeiiiaKhR.nGptgtv 242
                                   +e  AD v+ l r+ + ++      + +++++K R +G +++v
  gi|91774027|ref|YP_566719.1| 185 VEYGADSVIKLGREVIGSNL-----QRTVYVMKLRgSGTINEV 222
                                   67778888888886443322.....246677776634566665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0026      19     157 ..      14     146 ..       2     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                        AAA_25  19 ppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg.eal 97 
                                   ++ ++  +kg   +g+ +++ G +gtGKt + ++   + + +G+ +            ++  E+s   l r ++  +  +l
  gi|91774027|ref|YP_566719.1|  14 IRGLDEMLKGGFFKGTANVVSGKSGTGKTIFGTQFLMEGVnKGETV----------MCIITSEESK-SLVREMQSSFgWDL 83 
                                   56667778876689*********************99999666633..........3456667777.56666666553344 PP

                        AAA_25  98 ...rddarllvldlagveslpLfak..drggtlltadvdaleaaieevegvrlvviDplsralgg 157
                                        d++l ++d+ +  sl+L ++  ++ ++l++++ + +e ++ee  +++ v iD++ +++ +
  gi|91774027|ref|YP_566719.1|  84 dglVKDGKLVFVDITD-PSLRLQKSveIAPMELIKSFKKLIESKLEE-TKPDRVFIDSVEAIFLA 146
                                   5558899******977.588887764357777788887777888888.56********9996554 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 !   16.2   0.0   5.2e-06    0.0072      19      95 ..      47     127 ..      45     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-06
                          MEDS  19 pfikaglargekvlyvas.astldelrealrkagldvdaalesgqleildaeety...lrgggfdpermlealrralakal 95 
                                   +f+ +g+++ge v+++++ +++ +++re+ ++ g d+d +++ g+l ++d ++      ++ +  p + ++ +++ ++  l
  gi|91774027|ref|YP_566719.1|  47 QFLMEGVNKGETVMCIITsEESKSLVREMQSSFGWDLDGLVKDGKLVFVDITDPSlrlQKSVEIAPMELIKSFKKLIESKL 127
                                   79*********9988888688999999999999**************9999886644445555666777777777777666 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.5e-05      0.02      19      84 ..      10      74 ..       6      80 .. 0.90
   2 ?   -1.1   0.0      0.57   7.9e+02     185     258 ..     113     177 ..      92     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                        PAXNEB 19 tStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlre 84
                                  +StG++ LD++L GG+  G+  ++  + + + +++    Fl eGv ++ +v+ +  ++++++++re
  gi|91774027|ref|YP_566719.1| 10 VSTGIRGLDEMLKGGFFKGTANVVSGK-SGTGKTIFGTQFLMEGVNKGETVMCIITSEESKSLVRE 74
                                  8***********************976.56668899999***************999999999887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.57
                        PAXNEB 185 ssllnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlpl 258
                                    +l+++ ++l++++  +++      R+ i s     l +     +++ +l +++  + ++ r+ +++ lit+ +
  gi|91774027|ref|YP_566719.1| 113 MELIKSFKKLIESKLEETKP----DRVFIDSVEAIFL-A----IESNYKLRTLIDDVFGVFRKREVTSLITVGV 177
                                   67888888888884444444....4888888887777.2....4677778888888888888888888888865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.2   2.1e-05     0.029       3      74 ..      33     147 ..      31     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                   EESSTTSSHHHHHHHHHHH.....HTHE...................................EEEEETTTCS.SSSTTHH CS
                           AAA   3 lyGppGtGKTllakavake.....lgve...................................fleisgsell.skyvges 42 
                                   ++G  GtGKT++  +   e        +                                   f+ i  ++l+ +k v+ +
  gi|91774027|ref|YP_566719.1|  33 VSGKSGTGKTIFGTQFLMEgvnkgE--TvmciitseeskslvremqssfgwdldglvkdgklvFVDITDPSLRlQKSVEIA 111
                                   789**********999999544440..044444555566667777777888888888888888**********9******* PP

                                   HHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHH CS
                           AAA  43 ekkirelfkeakeka....kpsilfiDEidalaksr 74 
                                   ++++ + fk++ e++    kp  +fiD ++a++ + 
  gi|91774027|ref|YP_566719.1| 112 PMELIKSFKKLIESKleetKPDRVFIDSVEAIFLAI 147
                                   ********9975555589899***********9887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.1e-05     0.029       9     135 ..      32     183 ..      26     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka................... 70 
                                   vv G sGtGKT    ++l++ ++       + e+v + ++s++ sk+l re+ + +g +l++                   
  gi|91774027|ref|YP_566719.1|  32 VVSGKSGTGKTIFGTQFLMEGVN-------KGETVMCIITSEE-SKSLVREMQSSFGWDLDGlvkdgklvfvditdpslrl 104
                                   899****************9986.......8888888888888.899**********999999999999999999988888 PP

                        AAA_22  71 .......erlsseellealeqalraravielliiDEaqhlr.seealeeLrsllnl......srkgvqliLvGtp.elrk 135
                                          +    + + +++e  l++++    + iD ++ ++   e   +Lr+l ++      +r  ++li vG   +l++
  gi|91774027|ref|YP_566719.1| 105 qksveiaPMELIKSFKKLIESKLEETKP-DRVFIDSVEAIFlAIESNYKLRTLIDDvfgvfrKREVTSLITVGVMfGLDE 183
                                   8888885555555555888888888888.888889888877767777777777776677788788888888887666665 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   2.4e-05     0.033      33      93 ..      15      74 ..       4     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                     IstB_IS21 33 rkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkra 93
                                  r ++e+ ++ f +  +n+ + G sG+GK+ + + + +e+v++g  v+ + +++  ++l r+
  gi|91774027|ref|YP_566719.1| 15 RGLDEMLKGGFFKGTANV-VSGKSGTGKTIFGTQFLMEGVNKGETVMCIITSEESKSLVRE 74
                                  556777888888888886.69*************************988877766666554 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.7e-05     0.079       5      47 ..      32      72 ..      29      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.7e-05
                       DUF2075  5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvl 47
                                  +V+G++GtGKt+ + ++l e    ++++t+  ++ +++    +
  gi|91774027|ref|YP_566719.1| 32 VVSGKSGTGKTIFGTQFLMEG--VNKGETVMCIITSEESKSLV 72
                                  8******************99..77777777777666655555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   0.00017      0.24       6      77 ..      32     143 ..      27     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                        AAA_24   6 liyGpsgiGKTtlakel......gpkplfi..................................dtekGlksldadkfpdi 46 
                                   ++ G+sg+GKT + +++      + +++++                                  d               i
  gi|91774027|ref|YP_566719.1|  32 VVSGKSGTGKTIFGTQFlmegvnKGETVMCiitseeskslvremqssfgwdldglvkdgklvfvD---------------I 97 
                                   789**************999999666666668888888887777777777333322222222221...............1 PP

                        AAA_24  47 e................swedfldevvelaaeladyktlviDtidel 77 
                                   +                 ++ f++ ++  + e+ + + ++iD+++ +
  gi|91774027|ref|YP_566719.1|  98 TdpslrlqksveiapmeLIKSFKKLIE-SKLEETKPDRVFIDSVEAI 143
                                   133344555555544423333333333.3555555678888888765 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 ?    9.9   0.3   0.00034      0.47      37      68 ..      32      64 ..      20      81 .. 0.78
   2 ?   -2.7   0.0       2.6   3.7e+03      76      89 ..     117     130 ..     106     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                         AAA_7 37 llvGptGtGKtviikd.llkkldkekylsltin 68
                                  ++ G++GtGKt+  ++ l++ ++k ++++ +i+
  gi|91774027|ref|YP_566719.1| 32 VVSGKSGTGKTIFGTQfLMEGVNKGETVMCIIT 64
                                  689*************89999997776666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                         AAA_7  76 nqlqdiiesklekr 89 
                                   ++++++ieskle  
  gi|91774027|ref|YP_566719.1| 117 KSFKKLIESKLEET 130
                                   56789999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1461.88
//
Query:       gi|91774028|ref|YP_566720.1|  [L=228]
Description: hypothetical protein Mbur_2096 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-18   65.5   0.1      7e-18   65.0   0.1    1.2  1  DUF5591   Domain of unknown function (DUF5591)
  ------ inclusion threshold ------
       0.06   13.1   0.0      0.092   12.5   0.0    1.3  1  DUF508    Domain of unknown function (DUF508)


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 !   65.0   0.1   7.8e-22     7e-18       5     136 ..      31     168 ..      27     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 7.8e-22
                                   HHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---.....SEEEEE-SS-.EEEGGGTT-----------.. CS
                       DUF5591   5 rervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrka..kvheviltsPlGvvPreleevYPaaqYdiav.. 81 
                                   +e vl+ Y+pp+ ++ ++ +Pc ++kPy++s sh+++ + i       ++h+v+ +   G+ Pre+++ YP+++Y   +  
  gi|91774028|ref|YP_566720.1|  31 NEWVLSEYQPPT-RDFCIFVPCAMRKPYHTSPSHKMYDRIIFGILDqeEAHVVVFG-TCGITPREIDTEYPFTDYKFMMgk 109
                                   5678999****8.9*************************99887644477777776.68****************987522 PP

                                   ..-----HHHHHHHHHHHHHHHHHHT..-SEEEE---THHHHHHHHHHTT-SSEEEE-- CS
                       DUF5591  82 ..tgewseeeiefvaellakylektk..yekviahleeeyreiveevaeelgleiiytv 136
                                       + +++ i++ ++ la+ylekt+  y++ ia++ +++r+++e++ e +++e+ +  
  gi|91774028|ref|YP_566720.1| 110 cnVAKIKRDFIKIESKRLARYLEKTRdnYNHRIAYCIGDFRTAMEKAVEMTNIEVSIIP 168
                                   2246889999999**********986225789***************998888877665 PP

>> DUF508  Domain of unknown function (DUF508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05     0.092      93     128 ..     126     163 ..     100     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                        DUF508  93 lcarqlkda..klnPrlsyCiGelnyknskPvlsedlk 128
                                     ar l ++  ++n r++yCiG++     k v   +++
  gi|91774028|ref|YP_566720.1| 126 RLARYLEKTrdNYNHRIAYCIGDFRTAMEKAVEMTNIE 163
                                   568999999889************99999998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1470.11
//
Query:       gi|91774029|ref|YP_566721.1|  [L=124]
Description: transcriptional regulator TrmB [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-17   63.3   0.0      2e-17   62.8   0.0    1.2  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0007   19.5   0.0     0.0011   18.9   0.0    1.3  1  HTH_11     HTH domain
      0.001   18.9   0.0     0.0018   18.2   0.0    1.3  1  MarR       MarR family
     0.0013   18.5   0.0     0.0021   17.9   0.0    1.2  1  MarR_2     MarR family
     0.0015   18.3   0.0     0.0021   17.8   0.0    1.3  1  HTH_IclR   IclR helix-turn-helix domain
     0.0083   15.7   0.0      0.015   14.9   0.0    1.5  1  HTH_24     Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.021   15.3   0.0      0.037   14.5   0.0    1.4  1  HTH_27     Winged helix DNA-binding domain
      0.023   14.7   0.0      0.035   14.1   0.0    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.066   13.1   0.0        0.1   12.5   0.0    1.3  1  HTH_5      Bacterial regulatory protein, arsR 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 !   62.8   0.0     1e-20     2e-17       3      67 ..      22      92 ..      20      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1e-20
                                  HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE--H CS
                          TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravdp 67
                                   lGL+  ++++Y+ Ll++gp+ta+ + e l+++rs++Y++L++L+++GlV+re ++       + Y+avdp
  gi|91774029|ref|YP_566721.1| 22 ILGLKTLDMEAYKFLLANGPMTAENLGEFLNRERSTAYRSLQNLISCGLVYRETKTidiggyFYEYVAVDP 92
                                  69**********************************************************87778999987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.3e-07    0.0011       6      43 ..      33      69 ..      30      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.3e-07
                        HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                  +++L  a+gp+++e L e Ln+ r+t +r ++ L + g
  gi|91774029|ref|YP_566721.1| 33 YKFL-LANGPMTAENLGEFLNRERSTAYRSLQNLISCG 69
                                  5677.67778************************9999 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     9e-07    0.0018      15      53 ..      39      77 ..      36      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9e-07
                                  STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                          MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                  +gp++   L+++l+ ++st+ r l  L+  Gl++R+ ++
  gi|91774029|ref|YP_566721.1| 39 NGPMTAENLGEFLNRERSTAYRSLQNLISCGLVYRETKT 77
                                  79*********************************9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0021      13      55 ..      35      75 ..      28      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                  HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  +L ++++  +t+  l + l+ ++s++ r l+ L + GLv r++
  gi|91774029|ref|YP_566721.1| 35 FLLANGP--MTAENLGEFLNRERSTAYRSLQNLISCGLVYRET 75
                                  5777787..******************************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-06    0.0021      15      51 ..      38      74 ..      35      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                  TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  a++++t   l + +   +St++R Lq L+ +G+v ++
  gi|91774029|ref|YP_566721.1| 38 ANGPMTAENLGEFLNRERSTAYRSLQNLISCGLVYRE 74
                                  57788888888889999*****************985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.5e-06     0.015       4      47 ..      28      71 ..      25      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.5e-06
                        HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +d + ++ L +n+ ++   L e l+  +st  r l++L++ Gl+
  gi|91774029|ref|YP_566721.1| 28 LDMEAYKFLLANGPMTAENLGEFLNRERSTAYRSLQNLISCGLV 71
                                  67777899**********************************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.9e-05     0.037      16      62 ..      39      85 ..      35      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                        HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                                  +++++++ l ++ln+e s++  sl  L+  GLv r+++  d +  ++
  gi|91774029|ref|YP_566721.1| 39 NGPMTAENLGEFLNRERSTAYRSLQNLISCGLVYRETKTIDIGGYFY 85
                                  689999***************************99999888887776 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 ?   14.1   0.0   1.7e-05     0.035      19      58 ..      39      79 ..      18      81 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                                  EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EE CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrgrr.ir 58
                                  + p+t e l+++l+  r+t  r l+ L   gl+ r+++ i 
  gi|91774029|ref|YP_566721.1| 39 NGPMTAENLGEFLNRERSTAYRSLQNLISCGLVYRETKtID 79
                                  449*****************************997532265 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-05       0.1      10      46 ..      36      72 ..      35      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                  HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  lLa+g++++  l e l+  +st  + L  L  +GLV+
  gi|91774029|ref|YP_566721.1| 36 LLANGPMTAENLGEFLNRERSTAYRSLQNLISCGLVY 72
                                  8***********************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 839.34
//
Query:       gi|91774030|ref|YP_566722.1|  [L=126]
Description: hypothetical protein Mbur_2098 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0048   16.8   0.0     0.0057   16.5   0.0    1.1  1  VirJ      Bacterial virulence protein (VirJ)


Domain annotation for each model (and alignments):
>> VirJ  Bacterial virulence protein (VirJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.2e-07    0.0057      69     153 ..      15     102 ..      11     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-07
                          VirJ  69 kvvliGysfGaDvlPaaynkLkaatrdkvklvsllalskkadfeis....vegWlgadeegkadivpelakldakrvvCiy 145
                                   ++ ++Gy+ G D++P+  n  +++  ++++++  + +++   f+i      + ++ + +   + +v +++  ++  ++ iy
  gi|91774030|ref|YP_566722.1|  15 SMFILGYALGKDIMPFENN-TEQSFENQISMTDNFKVENDHVFKIGenviTSKYFNTMSRSFSGTVVDINYCETGNIITIY 94 
                                   57899***********866.57888999***************98422213567777777777899999999999999999 PP

                          VirJ 146 Gkdekdea 153
                                    +  ++++
  gi|91774030|ref|YP_566722.1|  95 NSSTDETK 102
                                   98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 798.63
//
Query:       gi|91774031|ref|YP_566723.1|  [L=391]
Description: aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  234.6   0.0    2.2e-69  234.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.7e-12   47.3   0.2    2.5e-12   46.8   0.2    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.9e-08   33.7   0.0    3.5e-08   32.8   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    1.5e-05   23.7   0.1    2.4e-05   23.0   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.023   13.5   0.0      0.032   12.9   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
      0.054   12.1   0.1      0.066   11.9   0.1    1.1  1  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 !  234.4   0.0   7.3e-73   2.2e-69       2     363 .]      35     384 ..      34     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 234.4 bits;  conditional E-value: 7.3e-73
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   dvi Lg++e+++     t+ ++++a ++  +   + ++y+ + gl el+e+l k + r++++ +++e++++v+ G +++++
  gi|91774031|ref|YP_566723.1|  35 DVITLGVGEPDYV----TPWHIREACIH--SIEYGETSYTSNYGLMELREELSKHYTRRHNVYYEPETEILVTAGVSEGLD 109
                                   89***********....*********98..88999999******************************************* PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                   ++i+++ +npgdei+v +p+y  y +++  +gg  v+   ++e+df+++++++ +a+++      ktk ++++ p+NPtG+
  gi|91774031|ref|YP_566723.1| 110 LAIRAI-VNPGDEIIVVQPSYVAYVPAIIFAGGVPVTLGARPENDFKITADEIRAAITN------KTKAVIINYPNNPTGA 183
                                   ******.9***************************************************......**************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH..HGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavat..ranveeepn.llivgslsKafGlaGeRvGyilgnaavvs 241
                                    +++ +le+++d++ ++n+l ++De+Y+ + ++ +    t   ++   + + +++++++sKa++++G+R++y+l+ +++++
  gi|91774031|ref|YP_566723.1| 184 TMDKSDLEAIADVIVEHNILMISDEVYERLTYEGT---HTcfSSLEGMR-DrTILLNGFSKAYAMTGFRMAYALAPKEIID 260
                                   *********************************65...23322333333.359**************************** PP

                                   HHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH..CHH CS
                 Aminotran_1_2 242 qlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae..tak 318
                                   ++  +++   +  +  +q  + +al++ ++   e+e+m++++++rrk ++ +L+++gl+++ + ++++ +  +s    +a+
  gi|91774031|ref|YP_566723.1| 261 AMMLIHQYTMIcaPITAQIGAIEALRNGEE---EVEKMAREYNRRRKLIVGGLNKIGLDCFNPRGAFYAFPAISSTglSAD 338
                                   *****998887789999999999***9997...9*********************************************** PP

                                   HHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                 Aminotran_1_2 319 elskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                   e+++ Ll+e++v+ +pg++f+    g+lR  + + ++e+++e+++++
  gi|91774031|ref|YP_566723.1| 339 EFAERLLNEYKVVTIPGNIFGDtgDGFLRCAY-AASREDIKEALDRI 384
                                   *********************99999******.99*********998 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.2   8.4e-16   2.5e-12      43     144 ..     100     207 ..      68     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 8.4e-16
                                   EESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T.TTSSB-GGGCGGG--TTEEEEE...EB- CS
               DegT_DnrJ_EryC1  43 avssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp.dtynidpaaieaaitertkaIl...pVh 119
                                    ++  +++l la+ra+ v+pgde+Iv++ ++va + a++ +g +pv +   p +++ i++++i+aait++tka++   p +
  gi|91774031|ref|YP_566723.1| 100 VTAGVSEGLDLAIRAI-VNPGDEIIVVQPSYVAYVPAIIFAGGVPVTLGARPeNDFKITADEIRAAITNKTKAVIinyPNN 179
                                   33444789999**998.99*******************************98368*******************9444456 PP

                                   GGGB--...-HHHHHHHHHHCT-EEEEE CS
               DegT_DnrJ_EryC1 120 lyGqva...dmdalkaiaakhglkvieD 144
                                     G+ +   d++a+ ++  +h++ +i+D
  gi|91774031|ref|YP_566723.1| 180 PTGATMdksDLEAIADVIVEHNILMISD 207
                                   67776523377777777789**999998 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.2e-11   3.5e-08      60     177 ..      94     209 ..      68     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.2e-11
                                   TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEE.EEBETTSCBEGGGHHHH--TT CS
                   Aminotran_5  60 seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkv.ipldeegeldldelekllnek 139
                                    e ei++t G +e++ l+++++   ++pgdei+v++  + a + p+   a   g+ v+  ++ +++ +++ de+++++++k
  gi|91774031|ref|YP_566723.1|  94 PETEILVTAGVSEGLDLAIRAI---VNPGDEIIVVQPSYVAYV-PAIIFA--GGVPVTLgARPENDFKITADEIRAAITNK 168
                                   468*******************...9***************99.776666..688887635888999************** PP

                                   EEEEEEESBETTTTE...B--HHHHHHHHHHTT-EEEEE-T CS
                   Aminotran_5 140 tklvaithvsnvtGt...iqpveeigklakkkgalvlvDaa 177
                                   tk+v+i+  +n tG      ++e+i++++ ++++l++ D +
  gi|91774031|ref|YP_566723.1| 169 TKAVIINYPNNPTGAtmdKSDLEAIADVIVEHNILMISDEV 209
                                   **************942234788899999999999998865 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   8.2e-09   2.4e-05      73     175 ..     100     209 ..      90     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.2e-09
                                   ESSHHH.HHHHHHHTTS-TTEEEEEESTS...SHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TT CS
               Cys_Met_Meta_PP  73 vssGma.AiaaailallkaGdeivvsddl...YggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnp 149
                                   v++G++  +++ai+a+++ Gdei+v +     Y ++  +   v   lg + +   +  ++e+++ai+++tk+v +  p np
  gi|91774031|ref|YP_566723.1| 100 VTAGVSeGLDLAIRAIVNPGDEIIVVQPSyvaYVPAIIFAGGVPVTLGARPENDFKITADEIRAAITNKTKAVIINYPNNP 180
                                   455554257899**********99987650115566666677777788888887778999***************999999 PP

                                   T...T----HHHHHHHHHHTT-EEEEEGT CS
               Cys_Met_Meta_PP 150 l...lkvvDiekiaklakkagvlvvvDnt 175
                                   +   ++  D+e+ia+++ ++++l++ D +
  gi|91774031|ref|YP_566723.1| 181 TgatMDKSDLEAIADVIVEHNILMISDEV 209
                                   633377789***************99976 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 ?   12.9   0.0   1.1e-05     0.032      81     145 ..      94     159 ..      82     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                   -SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE- CS
                      OKR_DC_1  81 adksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiigg 145
                                    +   +v+ G s +    + a+++pgd ++v      +   a++++g +Pv l +  +n + i+  
  gi|91774031|ref|YP_566723.1|  94 PETEILVTAGVSEGLDLAIRAIVNPGDEIIVVQPSYVAYVPAIIFAGGVPVTLGARpENDFKITAD 159
                                   55667899**********************************************9999*9999764 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.2e-05     0.066     183     331 ..     159     313 ..     135     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                                   HHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEE....E CS
                   Aminotran_3 183 ealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspDlmt....l 259
                                    ++++++++++ Avi+       G ++ + + l++++++  +h++l+i DEv   +   G+  +  +++   D ++    +
  gi|91774031|ref|YP_566723.1| 159 DEIRAAITNKTKAVIINYPNNPTGATMDKSD-LEAIADVIVEHNILMISDEVYERLTYEGTHTCFSSLEGMRDRTIllngF 238
                                   4566778888889999888888888876655.899*************************999999997777754433347 PP

                                   -GGGG.TTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHH.HHHHHHHHHH..TTHHHHHHHHHHHHHHHHHHH CS
                   Aminotran_3 260 aKalt.gGlplsavlataevmqalapgshgsTfgGnplacav.alavleiiee..ekllenaqelgaalkegLeel 331
                                   +Ka +  G+ ++ +la++e+ +a+    h  T    p+ + + a+++l+  ee  ek++++ ++ ++ +  gL+++
  gi|91774031|ref|YP_566723.1| 239 SKAYAmTGFRMAYALAPKEIIDAM-MLIHQYTMICAPITAQIgAIEALRNGEEevEKMAREYNRRRKLIVGGLNKI 313
                                   89988357***************9.788999999999998884567888777766788888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2423.87
//
Query:       gi|91774032|ref|YP_566724.1|  [L=163]
Description: AsnC family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-14   53.9   0.1    2.3e-14   53.1   0.1    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    5.6e-08   32.5   0.1    1.8e-07   30.9   0.0    1.8  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.2e-07   31.2   0.4    3.4e-07   29.7   0.2    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0044   16.8   0.1     0.0098   15.6   0.1    1.6  1  DUF4423         Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.023   14.8   0.0      0.047   13.7   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.061   12.9   0.0       0.11   12.1   0.0    1.4  1  HTH_47          winged helix-turn-helix
      0.082   12.9   0.1       0.22   11.5   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.088   13.4   0.2        0.8   10.3   0.0    2.2  2  Phage_rep_O     Bacteriophage replication protein O
        0.1   12.2   0.0       0.15   11.6   0.0    1.2  1  PnpCD_PnpD_N    Hydroquinone 1,2-dioxygenase large subunit N-
       0.12   12.2   0.0       0.12   12.1   0.0    1.3  1  NUSAP           Nucleolar and spindle-associated protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.1   1.3e-17   2.3e-14       1      75 []      70     142 ..      68     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.3e-17
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                   + +sle  +++ +++++e+l ++peV+++  ++G++d+ + v+ +++++   f+ ek+a+ + v++t+t++vl+t
  gi|91774032|ref|YP_566724.1|  70 IKISLE--RKLGYQAIAERLYKFPEVRSVRLLSGEHDIAMTVRGKSMKQVAFFVAEKIATQEQVQSTSTHFVLKT 142
                                   345566..347**************************************************************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 !   30.9   0.0   9.9e-11   1.8e-07       1      42 []       1      42 [.       1      42 [. 0.96
   2 ?   -1.6   0.0       1.4   2.5e+03      20      27 ..      80      87 ..      77      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.9e-11
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                  +De  r ILe+L  daR+s  e+A  +G+++++v + ++ Le
  gi|91774032|ref|YP_566724.1|  1 MDEQTRNILEILSDDARTSPVEIATLTGMTADEVKQKIEYLE 42
                                  89999********************************99997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                 HTH_AsnC-type 20 yaeLAerv 27
                                  y+++Aer+
  gi|91774032|ref|YP_566724.1| 80 YQAIAERL 87
                                  88999986 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 !   29.7   0.2   1.9e-10   3.4e-07       1      48 []       1      48 [.       1      48 [. 0.97
   2 ?   -2.6   0.0       2.3   4.1e+03      20      27 ..      80      87 ..      76      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.9e-10
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +de +r+ILe+L +++r+s  e+A  +g++   v++ ++ Le++ +I+
  gi|91774032|ref|YP_566724.1|  1 MDEQTRNILEILSDDARTSPVEIATLTGMTADEVKQKIEYLEKAKIIR 48
                                  89****************************************999996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                        HTH_24 20 qreLAerl 27
                                  ++ +Aerl
  gi|91774032|ref|YP_566724.1| 80 YQAIAERL 87
                                  67899998 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.5e-06    0.0098      34      72 ..      15      51 ..       6      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                       DUF4423 34 dfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                                  d++ +p e+a  ++  ++a+ev++ +e+L+k+++++k +
  gi|91774032|ref|YP_566724.1| 15 DARTSPVEIATLTG--MTADEVKQKIEYLEKAKIIRKYK 51
                                  5568899*******..*******************9965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.047      13      56 ..       6      49 ..       2      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                  HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  r il  L++++  ++ e+a + +++  ++ + ++ Le+a +++ 
  gi|91774032|ref|YP_566724.1|  6 RNILEILSDDARTSPVEIATLTGMTADEVKQKIEYLEKAKIIRK 49
                                  78*****99999999**************************986 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.9e-05      0.11      32      77 ..       4      48 ..       1      49 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                                  -HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 32 aemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                  +++++l++L+  D ++s ++iA  +g+ +d+v++ ++ L++a++++
  gi|91774032|ref|YP_566724.1|  4 QTRNILEILS-DDARTSPVEIATLTGMTADEVKQKIEYLEKAKIIR 48
                                  5667777776.5889999**************************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 ?   11.5   0.0   0.00012      0.22      25      60 ..      21      54 ..       4      59 .. 0.85
   2 ?   -3.3   0.0         5     9e+03      41      50 ..     139     148 ..     125     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrriril 60
                                   e+A + G+t   v + +  L+++++i++ ++i   
  gi|91774032|ref|YP_566724.1| 21 VEIATLTGMTADEVKQKIEYLEKAKIIRKYKTI--I 54
                                  59**************************76524..3 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5
                                   HHHHHHHTTS CS
                     HTH_Crp_2  41 ilseLkregl 50 
                                   +l+  k++gl
  gi|91774032|ref|YP_566724.1| 139 VLKTYKEDGL 148
                                   4566666666 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00045       0.8      51      83 ..      19      51 ..      13      59 .. 0.87
   2 ?    0.8   0.0      0.43   7.6e+02      24      78 ..      97     125 ..      73     145 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                   Phage_rep_O 51 snsqlveltgisrtkvskalkeLirekviikeg 83
                                  s  ++++ltg++ ++v++ +++L ++k+i k +
  gi|91774032|ref|YP_566724.1| 19 SPVEIATLTGMTADEVKQKIEYLEKAKIIRKYK 51
                                  667899***********************9865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.43
                   Phage_rep_O  24 kltkrqlkillavirktYgfkkksdwisnsqlveltgisrtkvskalkeLirekv 78 
                                   +l   + +i++ v  k+                           k++ ++++ek+
  gi|91774032|ref|YP_566724.1|  97 RLLSGEHDIAMTVRGKS--------------------------MKQVAFFVAEKI 125
                                   44444444444443333..........................334444444444 PP

>> PnpCD_PnpD_N  Hydroquinone 1,2-dioxygenase large subunit N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.15      84     142 ..      24      81 ..      17      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                  PnpCD_PnpD_N  84 gtfngvlkeagvdyieqfetpkimatfkailrdwtnagfdpfaapeetgsafgrkhgdn 142
                                    t+ g+  +   + ie +e  ki+  +k+i+ dw  ag d + a  e   ++ rk g +
  gi|91774032|ref|YP_566724.1|  24 ATLTGMTADEVKQKIEYLEKAKIIRKYKTII-DWDLAGDDYVYAIIEIKISLERKLGYQ 81 
                                   57778888888889***************97.9********999999999999998865 PP

>> NUSAP  Nucleolar and spindle-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.6e-05      0.12     218     267 ..      69     119 ..      16     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.6e-05
                         NUSAP 218 DLkaSLsrpLtYkpHkGkLkpwgdskentalk.esassveshkknyKQpkl 267
                                    +k SL r L+Y++ + +L ++ +++    l+ e+  +++++ k+ KQ  +
  gi|91774032|ref|YP_566724.1|  69 EIKISLERKLGYQAIAERLYKFPEVRSVRLLSgEHDIAMTVRGKSMKQVAF 119
                                   6899************************99999***************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 993.11
//
Query:       gi|91774033|ref|YP_566725.1|  [L=125]
Description: 30S ribosomal protein S8e [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-35  120.2   4.5    7.6e-35  120.1   4.5    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   4.5   4.2e-39   7.6e-35       6     137 .]       4     124 ..       1     124 [. 0.98

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 4.2e-39
                                   XCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEECSSS CS
                 Ribosomal_S8e   6 dskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVkknps 86 
                                   ++++ rk tG+k k+ r krk+elgr+++at++++++ k+v ++gG+rk+r+l+ + anvt+p  ++t    I +V++n++
  gi|91774033|ref|YP_566725.1|   4 QGRSRRKYTGAKLKSARGKRKFELGREPAATHVNDTKRKNVPTHGGNRKVRLLQENIANVTNPADGKTIVSAIETVVDNAA 84 
                                   899****************************************************************************** PP

                                   TCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                 Ribosomal_S8e  87 nneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                   n +yvr++++tKg++i++ +++           A+vtsrPgqdG+vna+l+
  gi|91774033|ref|YP_566725.1|  85 NAHYVRRNIITKGSVIQTAAGN-----------ARVTSRPGQDGVVNAILI 124
                                   **********************...........****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 758.53
//
Query:       gi|91774034|ref|YP_566726.1|  [L=305]
Description: ribonuclease Z [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-21   76.3   0.0    7.9e-19   68.0   0.0    2.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.6e-10   41.4   0.0    8.5e-10   39.0   0.0    2.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
      5e-05   22.9   0.0    0.00011   21.8   0.0    1.5  1  Lactamase_B_4  tRNase Z endonuclease
  ------ inclusion threshold ------
      0.079   12.1   0.0       0.17   11.0   0.0    1.5  1  PDEase_II      cAMP phosphodiesterases class-II
       0.17   12.1   0.1       0.35   11.0   0.1    1.4  1  Nbs1_C         DNA damage repair protein Nbs1


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 !   68.0   0.0   2.2e-22   7.9e-19       3     201 .]      32     267 ..      31     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.2e-22
                                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTCGHHH CS
                 Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanfvyla 78 
                                   i +D+g +  qq++ra         +  +  +++th H+DH+ g++ l +   ++++   l++y+p+ v + ++  +    
  gi|91774034|ref|YP_566726.1|  32 IMFDCGEGAQQQMMRAK------TGMMNLSSIFITHFHADHILGIPGLVQtmsFQGRTepLTIYGPEWVEEFVKILSAIGY 106
                                   89******988888886......56889**********************9885555567******999997777766666 PP

                                   CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C............TCCE-TT....................TSEE CS
                 Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgr............rldrnag....................dtlG 127
                                    + ++++++++l+ g+s++ +  g ++ a    h+ +             r+dr++                     ++ G
  gi|91774034|ref|YP_566726.1| 107 YKLKFEIKAVKLKSGTSVKRD--GYSVIALKTDHNIPSigfalvederpgRFDRDKAialgvpvgplfsklhhggsvEVDG 185
                                   666655777777777777776..7899999999999999999988888884444444333333333333333334443334 PP

                                   EEEE........CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEE CS
                 Lactamase_B_2 128 lrie........gggkrvyyigDtgyipeeigerlggadllllditayeddemir...hmgHltpeeaveaaadlgakrlv 197
                                    +i         ++g++v+y+gDt  + + +++ +g adll++d t+ +d  m +   +  H+t +ea+++a+++g+k+lv
  gi|91774034|ref|YP_566726.1| 186 NIISaedvvgepRPGRTVVYSGDTRPCLDVLEASVG-ADLLIHDSTLADD--MLDwakEAMHSTAGEAAALAKKAGVKKLV 263
                                   44434444446677777***********88876665.*********9999..445568*********************** PP

                                   EESB CS
                 Lactamase_B_2 198 liHi 201
                                   l+Hi
  gi|91774034|ref|YP_566726.1| 264 LTHI 267
                                   ***8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   2.4e-13   8.5e-10       5      91 ..      19     100 ..      15     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.4e-13
                                   SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                   Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                   + +++ +  +g++i++D+G ++++++++     ++ +  +++ +++TH+H+DHi g +glv++  +  + ++++ + +++ 
  gi|91774034|ref|YP_566726.1|  19 NPSAIMLNREGELIMFDCGEGAQQQMMR-----AKTGMMNLSSIFITHFHADHILGIPGLVQTMSFQGRTEPLTIYGPEWV 94 
                                   667888999******************8.....8*****************************999999999999988888 PP

                                   HHHHHH CS
                   Lactamase_B  86 eaddaa 91 
                                   e+    
  gi|91774034|ref|YP_566726.1|  95 EEFVKI 100
                                   875544 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     3e-08   0.00011      11      61 ..      19      67 ..      12      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3e-08
                 Lactamase_B_4 11 sgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssi 61
                                  + + ++L+ + +  +f ++gEg Q+ ++  k+ +  l+siF+t+ +  ++i
  gi|91774034|ref|YP_566726.1| 19 NPSAIMLNREGELIMF-DCGEGAQQQMMRAKTGMMNLSSIFITHFH-ADHI 67
                                  446788988889999*.**************************988.5555 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.6e-05      0.17      78     118 ..      51      92 ..      36      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.6e-05
                                   HHTEEEEE-S---GGGTHHH..HHHGGGGGS-S.--EEEEE-H CS
                     PDEase_II  78 knniksylItHsHLDHvsgl..vinSaefykaqlkkktivGlp 118
                                     n+ s +ItH H DH+ g+  ++   +f+    ++ ti+G +
  gi|91774034|ref|YP_566726.1|  51 MMNLSSIFITHFHADHILGIpgLVQTMSFQGR-TEPLTIYGPE 92 
                                   5579999***********98545666666664.7888888865 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 ?   11.0   0.1   9.7e-05      0.35      23      48 ..     221     246 ..     216     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
                        Nbs1_C  23 GsDLlvheakknseleewlkeaveee 48 
                                   G+DLl h++    ++ +w kea++  
  gi|91774034|ref|YP_566726.1| 221 GADLLIHDSTLADDMLDWAKEAMHST 246
                                   9*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2090.63
//
Query:       gi|91774035|ref|YP_566727.1|  [L=236]
Description: hypothetical protein Mbur_2103 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1717.50
//
Query:       gi|91774036|ref|YP_566728.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.7   0.4    6.3e-67  226.0   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
      9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.2e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00011   22.5   0.3       0.17   12.1   0.2    2.8  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.067   13.8   1.4        0.3   11.7   1.4    2.2  1  BST2             Bone marrow stromal antigen 2
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.7   2.6       0.55   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.36   11.2   6.9       0.52   10.7   4.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
          1   10.1   8.9        7.1    7.4   1.5    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.1    9.0   6.0       0.65   10.7   1.1    2.7  2  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.44   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  226.0   0.0   3.5e-70   6.3e-67       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91774036|ref|YP_566728.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 226.0 bits;  conditional E-value: 3.5e-70
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91774036|ref|YP_566728.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91774036|ref|YP_566728.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierear..ea..eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++r  +   ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91774036|ref|YP_566728.1| 329 SENDN--QLWSKAMNIlLIDVKKSVDQIRgmSGcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **976..*********************964338888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91774036|ref|YP_566728.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.5e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91774036|ref|YP_566728.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7     8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91774036|ref|YP_566728.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.6     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.5   0.0    0.0025       4.5       5      45 ..     249     287 ..     245     290 .. 0.84
   3 !   12.1   0.2   9.3e-05      0.17      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91774036|ref|YP_566728.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91774036|ref|YP_566728.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91774036|ref|YP_566728.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91774036|ref|YP_566728.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00046      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91774036|ref|YP_566728.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91774036|ref|YP_566728.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00031      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    0.9   0.1      0.34   6.2e+02      11      58 ..     392     446 ..     383     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91774036|ref|YP_566728.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91774036|ref|YP_566728.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999888854444440......55555555555555555553 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?   10.7   4.5   0.00029      0.52       2      36 ..     156     213 ..     155     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91774036|ref|YP_566728.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91774036|ref|YP_566728.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCellADvCGC 213
                                   79***************99987555588888888888888887775555444446666 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 ?    3.3   0.1     0.074   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.4   1.5     0.004       7.1       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.0   0.1      0.19   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91774036|ref|YP_566728.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91774036|ref|YP_566728.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91774036|ref|YP_566728.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00036      0.65      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.6   0.3        10   1.8e+04      55      66 ..     154     165 ..     144     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91774036|ref|YP_566728.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                         PLATZ  55 kssseaCetCar 66 
                                   +++ ++C +C++
  gi|91774036|ref|YP_566728.1| 154 RAEIKSCPHCGC 165
                                   334478999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 3260.07
//
Query:       gi|91774037|ref|YP_566729.1|  [L=89]
Description: hypothetical protein Mbur_2105 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   14.6   0.0      0.012   14.6   0.0    1.0  1  Trep_dent_lipo  Treponema clustered lipoprotein (Trep_dent_li


Domain annotation for each model (and alignments):
>> Trep_dent_lipo  Treponema clustered lipoprotein (Trep_dent_lipo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.7e-07     0.012      90     157 ..       5      75 ..       1      88 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.7e-07
                Trep_dent_lipo  90 dkvlnykepekisideLarqkatelvevkkdnkiiyCkqka...taknGkeliydvkykwykiekkflnlk 157
                                   ++  ++++     id+L++ k  ++ ++++ +++++ + ka   t + G +l+ +vk   y+ie++ ++++
  gi|91774037|ref|YP_566729.1|   5 EETDRFECKIVNIIDNLKQWKGVVVEDIDSGGRVYFARVKAegfTKEIGDSLFLSVKELPYDIEEMSIEVH 75 
                                   566789999999*********99999***********9998333467799******999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 595.06
//
Query:       gi|91774038|ref|YP_566730.1|  [L=371]
Description: AAA ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  131.9   0.1    3.7e-38  130.9   0.0    1.6  1  AAA              ATPase family associated with various cellul
    1.2e-07   32.0   0.0    3.2e-07   30.6   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
    3.8e-07   29.6   0.1    1.4e-06   27.8   0.0    2.0  3  TIP49            TIP49 P-loop domain
    7.9e-07   28.8   0.1    1.9e-06   27.6   0.1    1.7  1  AAA_lid_3        AAA+ lid domain
    2.6e-06   27.5   0.1      2e-05   24.6   0.1    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    3.3e-05   24.2   0.6     0.0022   18.3   0.0    2.6  2  AAA_22           AAA domain
    5.5e-05   23.1   0.0    8.8e-05   22.4   0.0    1.3  1  Bac_DnaA         Bacterial dnaA  protein
     0.0001   22.7   0.2     0.0025   18.2   0.2    2.6  1  AAA_16           AAA ATPase domain
    0.00023   21.0   0.0    0.00043   20.0   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
    0.00029   20.6   0.0     0.0012   18.7   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00049   20.4   0.0     0.0016   18.7   0.0    2.0  1  AAA_28           AAA domain
     0.0012   18.2   0.1     0.0028   17.1   0.1    1.7  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0016   18.0   0.0      0.031   13.8   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0029   18.2   0.0     0.0092   16.5   0.0    1.9  1  AAA_18           AAA domain
     0.0041   16.3   0.0      0.009   15.2   0.0    1.6  2  DUF815           Protein of unknown function (DUF815)
     0.0059   16.0   0.0      0.095   12.1   0.0    2.2  2  TniB             Bacterial TniB protein
     0.0061   16.7   0.0      0.012   15.7   0.0    1.6  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.042   14.3   0.0    2.0  2  RNA_helicase     RNA helicase
       0.02   14.6   0.0      0.061   13.0   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
      0.024   14.4   0.0       0.08   12.7   0.0    1.9  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.027   14.2   0.0      0.058   13.1   0.0    1.5  1  AAA_24           AAA domain
      0.043   12.9   0.1      0.077   12.1   0.1    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.043   13.7   0.2       0.21   11.5   0.1    2.0  2  NACHT            NACHT domain
      0.052   13.5   0.0        0.1   12.6   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.082   13.4   0.0       0.22   12.1   0.0    1.7  1  ABC_tran         ABC transporter
      0.087   12.2   0.0       0.17   11.3   0.0    1.5  1  IPT              Isopentenyl transferase
      0.091   12.2   0.0       0.21   11.0   0.0    1.5  1  PhoH             PhoH-like protein
      0.093   12.3   2.0        1.4    8.5   0.2    2.3  2  AAA_25           AAA domain
        0.1   11.6   0.0       0.16   11.0   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.11   12.6   0.0        0.3   11.2   0.0    1.6  1  Torsin           Torsin
       0.16   11.9   0.0       0.36   10.7   0.0    1.6  1  RsgA_GTPase      RsgA GTPase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   0.0   6.4e-41   3.7e-38       1     131 [.     155     283 ..     155     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 6.4e-41
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsese 80 
                                   +l++Gp GtGKT+laka+a++++v++l i++++l+ ++vge++++i++l ++a+e++ p+i+fiDE+da+a +r +++ ++
  gi|91774038|ref|YP_566730.1| 155 ILFFGPSGTGKTMLAKALANKTEVPLLPIKATQLIGEFVGEGSRHIHQLYERAEEMQ-PCIIFIDELDAIALDRrNQELRG 234
                                   69******************************************************9.****************8888999 PP

                                   HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                           AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                   +  ++vn+Llte+dg  ++++ v+ i+atnrp++ldpa++ +Rf+++ie+ 
  gi|91774038|ref|YP_566730.1| 235 DVAEIVNALLTEMDGIVERRG-VCTIAATNRPNSLDPAVR-SRFEEEIEFA 283
                                   *****************9866.******************.*******985 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   5.5e-10   3.2e-07       5     104 ..     154     248 ..     152     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5.5e-10
                                   -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                         AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                   +il+ gp+g+Gkt+lakala+  +v    +l  + a++l+     e + +   + ++ y +aee    i+++DE+d i+  
  gi|91774038|ref|YP_566730.1| 154 NILFFGPSGTGKTMLAKALANKTEV----PLLPIKATQLIG----EFVGEGSRHIHQLYERAEEMQpcIIFIDELDAIALD 226
                                   89********************998....************....77777777888888888888777**********996 PP

                                   ...---------HHHHHHHHHHHH CS
                         AAA_2  84 ...essgadvSregVqrdLLqile 104
                                      ++ + dv   +++++LL  ++
  gi|91774038|ref|YP_566730.1| 227 rrnQELRGDVA--EIVNALLTEMD 248
                                   65555666665..78888887666 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.4e-09   1.4e-06      20      88 ..     118     188 ..      93     207 .. 0.84
   2 ?   -2.0   0.0       2.8   1.6e+03     276     290 ..     209     223 ..     195     264 .. 0.65
   3 ?   -2.5   0.1       3.9   2.3e+03     130     170 ..     287     328 ..     277     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.4e-09
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  20 ekeeeglvGqkkareaagvivelike....kklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88 
                                   + + e +vGq +ar+ + +i ++++e    +k a r +L+ GpsgtGkt la a++++   +vp   ++++++
  gi|91774038|ref|YP_566730.1| 118 DVTFEDVVGQSSARQKCKLIERFLEEpekfGKWAPRNILFFGPSGTGKTMLAKALANKT--EVPLLPIKATQL 188
                                   4455689****************9874333678889*******************9975..699999999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                   XXXXXXXXXXXXXXX CS
                         TIP49 276 eivpGvlfiDevhml 290
                                   e+ p ++fiDe   +
  gi|91774038|ref|YP_566730.1| 209 EMQPCIIFIDELDAI 223
                                   667788888886544 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.9
                                   .-SSS-...TTS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT CS
                         TIP49 130 aenpls.kekkikevkitlktakeekklklgskiaeellkek 170
                                   ++n +   ek+i++  + +k  +++k  kl + +  +   ek
  gi|91774038|ref|YP_566730.1| 287 EQNRYLiIEKNINTFPLPVKDIDMKKIAKLTEGLSGRDIVEK 328
                                   444444478888888899999999998888776655444444 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   3.3e-09   1.9e-06       1      41 [.     307     348 ..     307     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.3e-09
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaa.lcreAallAlrrgikeitme 41 
                                   d+d k++A++TeG SG D+++ + + A + A+  +++ i+ +
  gi|91774038|ref|YP_566730.1| 307 DIDMKKIAKLTEGLSGRDIVEkVLKTALHQAIMNDEEVISHD 348
                                   89*****************777***********999988766 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 !   24.6   0.1   3.5e-08     2e-05       1     138 []     154     276 ..     154     276 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.5e-08
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                   ++l  Gp+GtgK++la+ la  ++ +++ +  t+      l+g+     g+ s++   l++ a+  +++i+++DE++ +  
  gi|91774038|ref|YP_566730.1| 154 NILFFGPSGTGKTMLAKALANKTEVPLLPIKATQ------LIGEFV---GEGSRHIHQLYERAEemQPCIIFIDELDAIA- 224
                                   57899***********************998887......555555...455555599999999899**********555. PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspalrsRf 138
                                     l++ ++ l  +   ++e  +    + d++ er  +  ia++n+++    +l+pa+rsRf
  gi|91774038|ref|YP_566730.1| 225 --LDRRNQELRGD---VAEIVNALLTEMDGIVERrgVCTIAATNRPN----SLDPAVRSRF 276
                                   ..33333222222...2222222222222222223588899999888....9999999998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.8e-06    0.0022       7      29 ..     154     176 ..     151     191 .. 0.84
   2 ?    3.6   0.1      0.13        73      79     105 ..     200     228 ..     180     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-06
                        AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                    ++ +G+sGtGKT+l++ l+++ 
  gi|91774038|ref|YP_566730.1| 154 NILFFGPSGTGKTMLAKALANKT 176
                                   6899****************997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.13
                        AAA_22  79 lealeqalraravielliiDEaqhlr...s 105
                                   +++l++ +++ +   ++ iDE + +    +
  gi|91774038|ref|YP_566730.1| 200 IHQLYERAEEMQP-CIIFIDELDAIAldrR 228
                                   4555666666666.9*********866541 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.5e-07   8.8e-05       1     195 [.     115     314 ..     115     338 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-07
                                   --SS-SGGG----TTTHHHHHHHHHHHHSTTT...S--..EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHH CS
                      Bac_DnaA   1 LnkrytFetFviGasnrlAlaaalkvaeapgk..kynP..lfiygevGlGktHLlkaignevlenapelrvvYltaeeFln 77 
                                   L+++ tFe  v  +s r+  +   +  e+p+k  k+ P  ++++g++G Gkt L ka++n+++       ++ ++a + + 
  gi|91774038|ref|YP_566730.1| 115 LKSDVTFEDVVGQSSARQKCKLIERFLEEPEKfgKWAPrnILFFGPSGTGKTMLAKALANKTEVP-----LLPIKATQLIG 190
                                   5778899999999999999999999999999888888866899**************99987655.....55566666666 PP

                                   HHHHHHHTT-HHHHHHHHT..T-SEEEEE-GGGGTT-HHHHH...HHHHHHHHHHTTT-EEE....EEESS-TTT-SS--H CS
                      Bac_DnaA  78 elvkalrdkkaeefkeklr..kvDvLliDDiqflagkektqe...elfhtfnalleegkqvv....lssDrsPkeleeled 149
                                   e+v      +++++ e+    +  ++ iD++  +a   + qe   ++  ++nall e   +v    +++  + ++ ++l+ 
  gi|91774038|ref|YP_566730.1| 191 EFVGEGSR-HIHQLYERAEemQPCIIFIDELDAIALDRRNQElrgDVAEIVNALLTEMDGIVerrgVCTIAATNRPNSLDP 270
                                   66655433.33344333331144577888888887666655533378899999998888887666666666677778999* PP

                                   HHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT----TTHHHHHH CS
                      Bac_DnaA 150 rlrsrfeaGlvvdieppdletrlailkkkieaeklevpeevlefia 195
                                    +rsrfe  +      pd++ r  i++k+i++  l v++  ++ ia
  gi|91774038|ref|YP_566730.1| 271 AVRSRFEEEIEF--ALPDEQNRYLIIEKNINTFPLPVKDIDMKKIA 314
                                   *******97655..569************99776666655555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   4.3e-06    0.0025      24     107 ..     152     264 ..     135     338 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.3e-06
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql......esa.ipysalaqalareellrqlldeaesaeleaw 97 
                                   p+++l+ G+sG+GK+ l+++l++  e   + +l  k++ql      e + ++  +l + +++ + +    de+++ +l++ 
  gi|91774038|ref|YP_566730.1| 152 PRNILFFGPSGTGKTMLAKALANKTE---VPLLPIKATQLigefvgE-GsRHIHQLYERAEEMQPCIIFIDELDAIALDRR 228
                                   699*******************7333...445666666664433321.223333455555455555555555454444444 PP

                        AAA_16  98 rekleeala..........................a 107
                                    ++l++ +a                           
  gi|91774038|ref|YP_566730.1| 229 NQELRGDVAeivnalltemdgiverrgvctiaatnR 264
                                   444444444444444444445555666655544444 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 !   20.0   0.0   7.5e-07   0.00043      47      71 ..     152     176 ..     107     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.5e-07
                     IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                     ni+++GpsG+GK+ la al+ ++
  gi|91774038|ref|YP_566730.1| 152 PRNILFFGPSGTGKTMLAKALANKT 176
                                   469******************9864 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 !   18.7   0.0     2e-06    0.0012       5      94 ..     120     221 ..     117     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-06
                        RuvB_N   5 sleeyigqekvkeklki...fieaakk.reealdhvllyGpPGlGkttlakiiakelgvkl...kits..gPvl.ekagdl 75 
                                   ++e+ +gq++ ++k k+   f+e  +k  + a   +l++Gp G Gkt lak +a++ +v l   k+t   g  + e ++ +
  gi|91774038|ref|YP_566730.1| 120 TFEDVVGQSSARQKCKLierFLEEPEKfGKWAPRNILFFGPSGTGKTMLAKALANKTEVPLlpiKATQliGEFVgEGSRHI 200
                                   67899999999998876233455554414557889*********************9997511133321122222445555 PP

                        RuvB_N  76 aalltnleekd..vlfideih 94 
                                     l  + ee +  ++fide+ 
  gi|91774038|ref|YP_566730.1| 201 HQLYERAEEMQpcIIFIDELD 221
                                   555555555444466777765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.8e-06    0.0016       1      50 [.     154     205 ..     154     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.8e-06
                        AAA_28   1 kivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv.e 50 
                                   +i ++G+++tGKT l++aLa++ ++p +p  a++++ e   +g +++++  e
  gi|91774038|ref|YP_566730.1| 154 NILFFGPSGTGKTMLAKALANKtEVPLLPIKATQLIGEFVGEGSRHIHQLyE 205
                                   589*****************87677777666666666555555555554433 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   4.8e-06    0.0028      23      43 ..     153     173 ..     120     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.8e-06
                  Mg_chelatase  23 HnlllvGppGsGKtmlakrlp 43 
                                    n+l++Gp+G+GKtmlak+l+
  gi|91774038|ref|YP_566730.1| 153 RNILFFGPSGTGKTMLAKALA 173
                                   59****************996 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   5.4e-05     0.031      34      58 ..     153     177 ..     151     186 .. 0.88
   2 ?    1.4   0.0      0.34     2e+02      99     116 ..     210     227 ..     200     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-05
                         AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                   +++l+ Gp+GtGKt+++k l +k +
  gi|91774038|ref|YP_566730.1| 153 RNILFFGPSGTGKTMLAKALANKTE 177
                                   689***************9988765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.34
                         AAA_7  99 gkklvvFvDDlnmpakek 116
                                    + +++F+D+l+  a ++
  gi|91774038|ref|YP_566730.1| 210 MQPCIIFIDELDAIALDR 227
                                   5679*******9988875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-05    0.0092       1      29 [.     155     198 ..     155     256 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf...............gvnlr 29 
                                   Il  G++G+GKt lak+L++++++               g+ +r
  gi|91774038|ref|YP_566730.1| 155 ILFFGPSGTGKTMLAKALANKTEVpllpikatqligefvGEGSR 198
                                   8999****************987777777777777666633333 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.6e-05     0.009      51     126 ..     150     230 ..     104     264 .. 0.71
   2 ?   -2.8   0.0       4.8   2.8e+03     184     221 ..     274     311 ..     271     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                        DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr...erperfilfvDDLsFeeeeeeyk 126
                                    + +n+L++G  GtGK  l kal n+++     ++  ++  e + e ++ +++l    e+ + +i+f+D L   + +++ +
  gi|91774038|ref|YP_566730.1| 150 WAPRNILFFGPSGTGKTMLAKALANKTEVPLlpIKATQLIGEFVGEGSRHIHQLYeraEEMQPCIIFIDELDAIALDRRNQ 230
                                   34489********************99988755455666666666666666665512234467899999986555555554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                        DUF815 184 dRFGlwlgFykld.qeeYleiveklakklglelekeele 221
                                    RF   + F  +d q++Yl i+ek ++++ l++++ +++
  gi|91774038|ref|YP_566730.1| 274 SRFEEEIEFALPDeQNRYL-IIEKNINTFPLPVKDIDMK 311
                                   5888888888776245555.7777777777777665544 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00016     0.095      11      58 ..     125     175 ..     118     182 .. 0.79
   2 ?    1.4   0.0      0.31   1.8e+02     110     137 ..     202     229 ..     194     281 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                          TniB  11 igyprakeilerLeeLleypk...rkrmpnlllvGdsnnGKtmivekFarl 58 
                                   +g + a++  + +e+ le p+   +  ++n+l++G+s +GKtm+++  a++
  gi|91774038|ref|YP_566730.1| 125 VGQSSARQKCKLIERFLEEPEkfgKWAPRNILFFGPSGTGKTMLAKALANK 175
                                   56677778888888888888743345679***************9987765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                          TniB 110 qvlrllrelkvrvLiiDEihnllagsar 137
                                   q ++  +e+++ ++ iDE++ +   +++
  gi|91774038|ref|YP_566730.1| 202 QLYERAEEMQPCIIFIDELDAIALDRRN 229
                                   556667899999*******998743333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.1e-05     0.012       2      25 ..     155     180 ..     155     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..a 25 
                                   +l+ G++G+GK+ la+ l++k+    
  gi|91774038|ref|YP_566730.1| 155 ILFFGPSGTGKTMLAKALANKTEvpL 180
                                   689****************9988433 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.2e-05     0.042       1      23 [.     155     177 ..     155     241 .. 0.85
   2 ?   -2.1   0.0       8.9   5.2e+03      77      93 ..     296     312 ..     287     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                   i+++Gpsg+GK++lak La++ +
  gi|91774038|ref|YP_566730.1| 155 ILFFGPSGTGKTMLAKALANKTE 177
                                   689***************99876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.9
                  RNA_helicase  77 vsstpyplnmasleekg 93 
                                    + +++pl++++++ k+
  gi|91774038|ref|YP_566730.1| 296 KNINTFPLPVKDIDMKK 312
                                   57889999999999886 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.061      22      46 ..     152     176 ..     126     189 .. 0.78
   2 ?   -1.9   0.0         4   2.3e+03      90     108 ..     208     226 ..     185     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                   SS-EEEECSTTSSHHHHHHHHHHHS CS
               Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                   + ++l  G sGtGK++la+a+ +++
  gi|91774038|ref|YP_566730.1| 152 PRNILFFGPSGTGKTMLAKALANKT 176
                                   4799****************98765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4
                                   HHTTTSEEEEETGGGS-HH CS
               Sigma54_activat  90 ekadgGtlfLDeigelple 108
                                   e+ +  ++f+De+  + l+
  gi|91774038|ref|YP_566730.1| 208 EEMQPCIIFIDELDAIALD 226
                                   4555678999999887766 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   0.00014      0.08       2      25 ..     153     176 ..     152     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkgee 25 
                                   ++il++G++g+GKt L++al +++
  gi|91774038|ref|YP_566730.1| 153 RNILFFGPSGTGKTMLAKALANKT 176
                                   589*****************9853 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.058       3      24 ..     153     174 ..     151     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                        AAA_24   3 lkiliyGpsgiGKTtlakelgp 24 
                                   ++il +Gpsg+GKT+lak l +
  gi|91774038|ref|YP_566730.1| 153 RNILFFGPSGTGKTMLAKALAN 174
                                   6899**************9933 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 ?   12.1   0.1   0.00013     0.077     112     137 ..     151     175 ..     148     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                     Parvo_NS1 112 gkrntvwfyGpantGktnlaeaIaka 137
                                    +rn ++f+Gp  tGkt+la+a+a+ 
  gi|91774038|ref|YP_566730.1| 151 APRN-ILFFGPSGTGKTMLAKALANK 175
                                   5666.899***************986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00036      0.21       3      25 ..     155     177 ..     153     189 .. 0.81
   2 ?   -0.4   0.0       1.7   9.6e+02      75     142 ..     205     279 ..     183     286 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                   ++  G++G GKT+L++ la +  
  gi|91774038|ref|YP_566730.1| 155 ILFFGPSGTGKTMLAKALANKTE 177
                                   6778**************98866 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                                   HHCCSCCCEEEEEE-STT-SS-TCH.................HHHHHCTTTTT--EEEEEEECCCHHH.HCTTSSCE CS
                         NACHT  75 vllelperlLlilDglDelvtdlgq........kekqpvrtlLselirkkllpeasllltvrpralrd.leeqleea 142
                                   +++e  +   + +D lD ++ d ++        +  +++ t + +++++     +++ +t rp++l   +++ +ee+
  gi|91774038|ref|YP_566730.1| 205 ERAEEMQPCIIFIDELDAIALDRRNqelrgdvaEIVNALLTEMDGIVER--RGVCTIAATNRPNSLDPaVRSRFEEE 279
                                   4555666667888888888776665544443222222223333333333..23334445555555543455555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018       0.1      14      45 ..     147     178 ..     128     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                   HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
                          TsaE  14 lakalgdvilLeGdLGaGKTtlvrglakalgv 45 
                                   ++k + + il+ G+ G+GKT+l+++la++ +v
  gi|91774038|ref|YP_566730.1| 147 FGKWAPRNILFFGPSGTGKTMLAKALANKTEV 178
                                   333224469******************99877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00037      0.22      14      35 ..     155     176 ..     147     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
                                   EEEEESTTSSHHHHHHHHTTSS CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  14 vaivGenGaGKStLlkllagll 35 
                                   + ++G++G+GK+ L+k+la+++
  gi|91774038|ref|YP_566730.1| 155 ILFFGPSGTGKTMLAKALANKT 176
                                   6789**************9876 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.17       5      37 ..     156     188 ..     152     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                           IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqc 37 
                                   l fG+ +tGKt  a +la++t +p++ +   q 
  gi|91774038|ref|YP_566730.1| 156 LFFGPSGTGKTMLAKALANKTEVPLLPIKATQL 188
                                   78**********************987766665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037      0.21      23      41 ..     156     174 ..     151     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                   EEE--TTSSTTHHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavalav 41 
                                     +Gp+GtGKt+la ala 
  gi|91774038|ref|YP_566730.1| 156 LFFGPSGTGKTMLAKALAN 174
                                   568***********99985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0024       1.4      36      54 ..     155     173 ..     147     177 .. 0.87
   2 ?    2.7   0.1      0.14        81     130     172 ..     200     243 ..     197     262 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0024
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   +l++G++gtGKt+la  la
  gi|91774038|ref|YP_566730.1| 155 ILFFGPSGTGKTMLAKALA 173
                                   6899***********8887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                        AAA_25 130 vdaleaaieevegvrlvviDplsr.algg.densnsdvgalveal 172
                                   +++l +++ee+ ++  + iD l++ al+  + +   dv+++v+al
  gi|91774038|ref|YP_566730.1| 200 IHQLYERAEEM-QPCIIFIDELDAiALDRrNQELRGDVAEIVNAL 243
                                   78999999995.6**********9544446666677765555554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00028      0.16      80     151 ..      85     174 ..      41     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                         T2SSE  80 lrvvllPvvag.ealviR.kksakeltlddlgaeealk............ekiaevlrkavr....erglilvsGgTgsGK 142
                                   +  v++P++    + +i  + ++k l++  l  + +++            + i+++l+++ +    +  +il+ G+ g+GK
  gi|91774038|ref|YP_566730.1|  85 IIEVVPPASSIgIKTTIViNDEEKVLNIPGLKSDVTFEdvvgqssarqkcKLIERFLEEPEKfgkwAPRNILFFGPSGTGK 165
                                   5555666665553333333455566666666666666666666777777778888888883222223579*********** PP

                         T2SSE 143 ttllyallk 151
                                   t l+ al +
  gi|91774038|ref|YP_566730.1| 166 TMLAKALAN 174
                                   ***999876 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00051       0.3      10      77 ..     107     176 ..     100     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00051
                                   XX.---HHHHHHHHH.HH--S-HHHHHHHHHHHHHHHT-S.S-SS..-EEEEEEE-TTSSHHHHHHHHHHHH CS
                        Torsin  10 krisanleeLekdle.kklfGqhlvkklvvksvkaylene.kpkk..pLvlsfhGwtGtGknfvaeiiaenl 77 
                                   ++   n+ +L++d++ + ++Gq  +++   k ++ +le++ k  k  p  + f G +GtGk  +a+ +a+++
  gi|91774038|ref|YP_566730.1| 107 EK-VLNIPGLKSDVTfEDVVGQSSARQK-CKLIERFLEEPeKFGKwaPRNILFFGPSGTGKTMLAKALANKT 176
                                   44.4789999999974679999999987.589999999984445444889******************9975 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00063      0.36      99     129 ..     152     182 ..     123     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                                   TSEEEEECSTTSSHHHHHHHHCTT-----S- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktge 129
                                    + +++ G+SG GK+ L +al++++e+    
  gi|91774038|ref|YP_566730.1| 152 PRNILFFGPSGTGKTMLAKALANKTEVPLLP 182
                                   56789*****************997765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2465.43
//
Query:       gi|91774039|ref|YP_566731.1|  [L=123]
Description: response regulator receiver protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-31  108.5   0.1    2.2e-31  108.3   0.1    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.1   1.2e-35   2.2e-31       1     111 [.       4     115 ..       4     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.2e-35
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +l+v+D+p+++el+ +lle+ gy ev++aedg  al+++ke k+dlillD+++p+mdGle+l++++e++    +pv++lta
  gi|91774039|ref|YP_566731.1|   4 ILVVEDNPMNMELTVNLLESWGY-EVGQAEDGPIALDKVKEAKYDLILLDMQLPRMDGLEVLSHLKEDSetAGIPVVALTA 83 
                                   8**********************.*****************************************99996777******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                   hs   d  + l+ag  +++sKp+d+ e +k++
  gi|91774039|ref|YP_566731.1|  84 HSMAGDQDKFLDAGCTGYISKPIDIHEFKKRI 115
                                   ***************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 00:00:00.43
# Mc/sec: 864.20
//
Query:       gi|91774040|ref|YP_566732.1|  [L=492]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-27   94.9   0.1    7.7e-27   93.7   0.1    1.7  1  Response_reg  Response regulator receiver domain
    7.4e-20   71.5   0.1    1.5e-19   70.5   0.1    1.5  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
      5e-09   36.4   0.0    8.3e-09   35.7   0.0    1.4  1  PAS_4         PAS fold
    7.4e-09   35.8   0.0    1.8e-08   34.5   0.0    1.7  1  PAS_9         PAS domain
    1.7e-05   24.8   0.0    7.6e-05   22.7   0.0    2.0  2  PAS           PAS fold
    0.00012   22.3   0.0    0.00027   21.2   0.0    1.6  1  PAS_3         PAS fold
      0.009   16.0   0.0      0.032   14.3   0.0    1.9  1  PAS_8         PAS domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.023   14.7   0.0    1.5  1  HATPase_c_2   Histidine kinase-like ATPase domain
      0.056   13.5   0.3       0.18   11.8   0.0    2.0  2  HisKA         His Kinase A (phospho-acceptor) 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 !   93.7   0.1   3.9e-30   7.7e-27       1     111 [.       9     119 ..       9     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 3.9e-30
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +l+vdD+pl++el++ +l   +y e+ +a  g e le++ +e+vdlillDi+mp+++G+e+++ +++++  + +p+i++ta
  gi|91774040|ref|YP_566732.1|   9 ILVVDDEPLNVELMEIYLS-PDY-EIISAYGGVEGLEKVATENVDLILLDIMMPDVSGFEVCESLKADPryQLIPIIMVTA 87 
                                   8*****************9.99*.999****************************************998777******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    s ++d+++ ++agaddflsKp+d+ eL +++
  gi|91774040|ref|YP_566732.1|  88 LSGKDDKIRSIEAGADDFLSKPVDRLELATRV 119
                                   ****************************9987 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 !   70.5   0.1   7.7e-23   1.5e-19       6     109 ..     388     490 ..     384     492 .] 0.92

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 7.7e-23
                                   HHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHH CS
                     HATPase_c   6 LrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkkl 84 
                                   +++++ nl++Navk+++++++i+ve++  +     ++ v D G Gi+ ed  ++f++f +   +k g +gtGlGl+ivk++
  gi|91774040|ref|YP_566732.1| 388 IEEVFFNLLSNAVKYSPENTRITVEME--DigSGWKVMVLDQGFGISDEDKALVFDRFKR--LDKGGIKGTGLGLAIVKRI 464
                                   6799***********99**********..34579999***********************..667788************* PP

                                   HHHTTTEEEEEEET.TTEEEEEEEEE CS
                     HATPase_c  85 velmgGeiwvesep.grGttftftlp 109
                                   v+l+gG++ ++++p ++G+ f++tl 
  gi|91774040|ref|YP_566732.1| 465 VDLHGGKVGLSDNPyEKGSMFWVTLN 490
                                   **********99999********986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   4.2e-12   8.3e-09       2     109 ..     144     255 ..     143     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.2e-12
                         PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll...pgee 78 
                                   d   ++l+v+d+ ++++ +N+ +++++g + +e+lGk +++ +lpe++ +   ++   +l+g+   ++ +e+     +g+e
  gi|91774040|ref|YP_566732.1| 144 DVAGVILVVVDKSQNITLINKKGCDILGGSEDEILGKNWFDtFLPEGHVESSKAIFFSLLDGDSNTYEYTETAIrtlGGGE 224
                                   6677899999******************************7699999****************99988888887899**** PP

                         PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                   r ++++ + + de+G+   +l  + D+Terr
  gi|91774040|ref|YP_566732.1| 225 RLISWHHVLIWDEEGKNTSILSSGEDVTERR 255
                                   *******9999*******************8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   9.1e-12   1.8e-08       5     104 .]     149     253 ..     145     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 9.1e-12
                         PAS_9   5 li..dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkng.etfwvll 80 
                                   ++  ++++ +i+ +N++ +++lG s++e+lgk+++d+f ++ + ++ ++ ++  ++   + +e++ + ir  g ++ ++  
  gi|91774040|ref|YP_566732.1| 149 ILvvVDKSQNITLINKKGCDILGGSEDEILGKNWFDTFLPEGHVESSKAIFFSLLDGdsNTYEYTETAIRTLGgGERLISW 229
                                   3224889999****************************4444444444444444444776777777666666647777778 PP

                         PAS_9  81 taspvkdddgelvgiivilrDite 104
                                   + + ++d++g++++i++  +D+te
  gi|91774040|ref|YP_566732.1| 230 HHVLIWDEEGKNTSILSSGEDVTE 253
                                   88999******************8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.8e-08   7.6e-05      10      61 ..     146     198 ..     134     251 .. 0.79
   2 ?   -0.4   0.0      0.57   1.1e+03      14      62 ..     232     278 ..     230     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
                                   SSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHH CS
                           PAS  10 lpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elael 61 
                                   + +  +vvD++ +i+++N++ +++lG s++e+lgk+ +d + +e +    +++
  gi|91774040|ref|YP_566732.1| 146 AGVILVVVDKSQNITLINKKGCDILGGSEDEILGKNWFDTFLPEGHVeSSKAI 198
                                   778899***********************************999777444444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.57
                                   EEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHH CS
                           PAS  14 ifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaell 62 
                                   ++++De g+ + + ++ e+ +  +  e+  k + +++ +    el++l+
  gi|91774040|ref|YP_566732.1| 232 VLIWDEEGKNTSILSSGEDVTERRSAEAALKRYAEELEHSN--ELKDLF 278
                                   67899999999999999999999999999999999998764..466665 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.4e-07   0.00027       4      85 ..     162     244 ..     159     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
                         PAS_3   4 vserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.py.egeyRirrkdGeyrwveararvirdengk 81 
                                   ++++ ++ilG s++e+lgk  +w d   pe   e  ++ +  +l++++  y  +e  ir+  G+ r ++++++ i+de+gk
  gi|91774040|ref|YP_566732.1| 162 INKKGCDILGGSEDEILGK--NWFDTFLPEGhVESSKAIFFSLLDGDSnTYeYTETAIRTLGGGERLISWHHVLIWDEEGK 240
                                   788999*************..*********9777777788888899999998899*************************9 PP

                         PAS_3  82 pvrv 85 
                                    + +
  gi|91774040|ref|YP_566732.1| 241 NTSI 244
                                   8876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.6e-05     0.032      14      55 ..     150     189 ..     139     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                         PAS_8  14 iavvd.lgdrivdvNqaalellGysadlkgellg.qllpvlrpl 55 
                                   ++vvd  ++ i+ +N++ +++lG    + +e lg ++++ + p+
  gi|91774040|ref|YP_566732.1| 150 LVVVDkSQN-ITLINKKGCDILG-G--SEDEILGkNWFDTFLPE 189
                                   345885555.*************.4..55555568999999887 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.1e-05     0.023      32     110 ..     384     466 ..     327     469 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                   HATPase_c_2  32 irlaveEactNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpe..tlpdpteeepkeslkegGrGlalikgl 108
                                   +   +eE++ N    a +  p + +++v++e+ +   +v v D+G g  d       d+ +  +k+  k  G+Gla++k++
  gi|91774040|ref|YP_566732.1| 384 VDSMIEEVFFNLLSNAVKYSPeNTRITVEMEDIGSGWKVMVLDQGFGiSDEDkaLVFDRFKRLDKGGIKGTGLGLAIVKRI 464
                                   5567899999999988888887899******************9998665551134566666669999************* PP

                   HATPase_c_2 109 vD 110
                                   vD
  gi|91774040|ref|YP_566732.1| 465 VD 466
                                   *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 ?   -3.1   0.1       4.2   8.4e+03      41      58 ..     115     132 ..     100     139 .. 0.70
   2 ?   11.8   0.0   9.2e-05      0.18       3      65 ..     276     338 ..     274     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                                   HHHHHHHHHHHHHHHHHH CS
                         HisKA  41 letiesearrldhlvedl 58 
                                   l+t +++  r+++l ++l
  gi|91774040|ref|YP_566732.1| 115 LATRVRSLLRIRQLNDRL 132
                                   555566677777776665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHH.HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                         HisKA   3 grflagvaHELrtPLsailgnaeaL.kregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                     f+  + H+L +P  +++g++++L kr g+   e  ++l+ i++    l ++++    +++ e
  gi|91774040|ref|YP_566732.1| 276 DLFIDIIRHDLMNPAGSVKGFTDILlKR-GNFEGENLKMLHAIKRANAKLIDMIDSAAAFAKVE 338
                                   5688999*****************8466.56677888899999999999999999877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3209.00
//
Query:       gi|91774041|ref|YP_566733.1|  [L=258]
Description: ribulose-1,5-biphosphate synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-77  258.1   2.1    6.7e-77  257.9   2.1    1.1  1  Thi4           Thi4 family
    1.2e-05   24.9   0.5    1.8e-05   24.3   0.5    1.3  1  FAD_oxidored   FAD dependent oxidoreductase
    2.8e-05   23.5   2.4    0.00022   20.5   0.4    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.9e-05   23.2   0.2    0.00013   22.1   0.2    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    7.4e-05   22.0   4.6    0.00022   20.4   1.7    2.5  3  FAD_binding_2  FAD binding domain
     0.0002   20.7   0.1    0.00026   20.3   0.1    1.2  1  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.011   14.4   2.1      0.018   13.8   2.1    1.3  1  HI0933_like    HI0933-like protein
      0.061   12.6   0.0        0.2   10.9   0.0    1.8  2  Amino_oxidase  Flavin containing amine oxidoreductase
      0.082   12.5   3.2       0.64    9.5   3.2    2.4  1  DAO            FAD dependent oxidoreductase
      0.085   11.9   0.2       0.15   11.1   0.2    1.4  1  Lycopene_cycl  Lycopene cyclase protein
       0.15   11.1   1.2       0.23   10.5   1.2    1.2  1  GIDA           Glucose inhibited division protein A
       0.24   10.5   0.0       0.34   10.0   0.0    1.2  1  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.9   2.1   4.5e-80   6.7e-77       1     235 []       9     239 ..       9     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 257.9 bits;  conditional E-value: 4.5e-80
                                   HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT CS
                          Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelg 81 
                                   srai+e+ ++ +l+y + Dv++vG+G++ L aa+yla++ +lk++i e+++++GGG+w GG++f +ivv+++a ++Lde+g
  gi|91774041|ref|YP_566733.1|   9 SRAIIEEFSKVFLDYTDVDVALVGGGPANLVAAKYLAEA-GLKTVIYEKKLAVGGGMWAGGMMFPRIVVQEDALHILDEFG 88 
                                   89*************************************.***************************************** PP

                                   ---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC..TTTSS.-B-EEEEEE CS
                          Thi4  82 ikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvela..hdtqscvDPlvirak 160
                                   i y++++++++v+++++ + +l+s +   a++ ++n v veD+++re++++ G+vinwt+ve+   h     vDPl ir+k
  gi|91774041|ref|YP_566733.1|  89 ISYHEYENGYYVANSIESVGKLISGATS-AGAEIFNLVNVEDVMIRENDEICGLVINWTAVEIGklH-----VDPLAIRSK 163
                                   ***************************9.*********************************99667.....********* PP

                                   EEEE--GSSSTTTTHHHHHHHHCTTTS.-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
                          Thi4 161 vvvdatGhdgeivavvvkkikleakie.kvkgeksldaekaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                                   vvvd tGh + + ++v++k+  ++  e  v gek+++a+++e+ ++ +t+ev+pnlyvaGm++++v ga+RmGp+f
  gi|91774041|ref|YP_566733.1| 164 VVVDGTGHPAVVCSTVQRKVPGAKLGElGVVGEKPMWADVGEKMLLDTTKEVYPNLYVAGMAANAVAGAPRMGPVF 239
                                   ********************8877654379*********************************************9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   1.2e-08   1.8e-05       1     145 [.      27     171 ..      27     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq.rgga...rlk. 76 
                                   Dv  vGGgpa ++AA   a+aG k+++ e++  +GG + +g+++ +    +e+  +  i +ef    ++ ++g+   + + 
  gi|91774041|ref|YP_566733.1|  27 DVALVGGGPANLVAAKYLAEAGLKTVIYEKKLAVGGGMWAGGMMFPRIVVQED--ALHILDEFGISYHEyENGYyvaN-Si 104
                                   9******************************9999888777766555544333..55677777666655555552321.12 PP

                  FAD_oxidored  77 krskwn..tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.grktirAkvfiDATgd 145
                                   +  + +  +   ++ +++++ +  e +v +  n ++ + + +    ++v++ +      +ir+kv++D+Tg 
  gi|91774041|ref|YP_566733.1| 105 ESVG-KliSGATSAGAEIFNLVNVE-DVMIRENDEICGLVIN---WTAVEIGKLHvDPLAIRSKVVVDGTGH 171
                                   2222.13356666666666555555.7777777777777765...566666555544888888888888876 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.4   1.5e-07   0.00022       2      36 ..      27      65 ..      26     115 .. 0.73
   2 ?    2.9   0.1     0.035        53     113     165 ..     123     185 ..     114     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.5e-07
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....legtcl 36
                                  dv+ +GgGpA l aa++la+ag+k++++e     +g + 
  gi|91774041|ref|YP_566733.1| 27 DVALVGGGPANLVAAKYLAEAGLKTVIYEkklaVGGGMW 65
                                  89**************************66665333332 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.035
                                   BC.TCTTC.....TTBEECCSECHHHHHHCCSS-T....SEEEEES-SHHHHHHHHHHHHH.T CS
                                   xx.xxxxx....xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx.x RF
                   Pyr_redox_2 113 dl.gipGv....aenvgklvrtldsaealklkllp....krivvvGgGyiGvElAaalakl.g 165
                                   +l +++ v    +++ + lv +++ +e  kl+  p     ++vv G G  +v+++ +++k+ g
  gi|91774041|ref|YP_566733.1| 123 NLvNVEDVmireNDEICGLVINWTAVEIGKLHVDPlairSKVVVDGTGHPAVVCSTVQRKVpG 185
                                   444555556777778888999999999999999999999999**************9987644 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2     9e-08   0.00013       2      34 ..      31      63 ..      30      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9e-08
                                  E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                 NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                  vG+G + lvaA +La+ag++ +++ek   +GG 
  gi|91774041|ref|YP_566733.1| 31 VGGGPANLVAAKYLAEAGLKTVIYEKKLAVGGG 63
                                  9**************************999985 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.7   1.5e-07   0.00022       1      46 [.      27      71 ..      27      85 .. 0.92
   2 ?   -1.0   0.0      0.47   7.1e+02     145     180 ..     108     144 ..      93     185 .. 0.73
   3 ?    1.1   0.0      0.11   1.6e+02     385     413 ..     209     236 ..     200     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgid 46
                                  Dv  +G+G A L+AA  +aeaGlk+++ ek+ ++gg   w++G+++
  gi|91774041|ref|YP_566733.1| 27 DVALVGGGPANLVAAKYLAEAGLKTVIYEKKLAVGGG-MWAGGMMF 71
                                  899*****************************97775.69999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.47
                                   HHHHHHHHTCTEEEEESEEEEEEEE.CTTEEEEEEEE CS
                 FAD_binding_2 145 arlvesarkagvdfqerteadeLiv.edgrvtGavve 180
                                     l+ +a +ag ++++  +++++++ e++++ G v++
  gi|91774041|ref|YP_566733.1| 108 GKLISGATSAGAEIFNLVNVEDVMIrENDEICGLVIN 144
                                   5678888889999999999999877356699999887 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.11
                                   STTEEESSBTEEE-STCEESSSSTTS--T CS
                 FAD_binding_2 385 ldadgqpipGLYAaGevaaggvhganrlg 413
                                   ld ++++ p+LY aG +a   v ga r+g
  gi|91774041|ref|YP_566733.1| 209 LDTTKEVYPNLYVAGMAA-NAVAGAPRMG 236
                                   67788999**********.8999988876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.8e-07   0.00026       1      33 [.      25      57 ..      25      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                                  EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                  ++dV+ VG+Gpa l++a+ L+eaG ++v+ ek 
  gi|91774041|ref|YP_566733.1| 25 DVDVALVGGGPANLVAAKYLAEAGLKTVIYEKK 57
                                  689**************************9985 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.1   1.2e-05     0.018       2      36 ..      27      61 ..      26      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  dv+ +GgG+A l aA  +a++g +++++ek+ ++g
  gi|91774041|ref|YP_566733.1| 27 DVALVGGGPANLVAAKYLAEAGLKTVIYEKKLAVG 61
                                  899***************************98887 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013       0.2       4      31 ..      38      65 ..      38      93 .. 0.95
   2 ?   -1.2   0.0      0.62   9.2e+02     411     430 ..     209     227 ..     200     254 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                  HHHHHHHHHTTEEEEEEESSSSSBTTS- CS
                 Amino_oxidase  4 LaaArqLlsaGfdVtvlEardrvGGRir 31
                                  L+aA++L++aG++++++E +  vGG ++
  gi|91774041|ref|YP_566733.1| 38 LVAAKYLAEAGLKTVIYEKKLAVGGGMW 65
                                  89***********************766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.62
                                   HHHHCHHCSTTEEE.SGGGC CS
                 Amino_oxidase 411 dplakpegdprlffAGehts 430
                                    +  k+  +p+l++AG +  
  gi|91774041|ref|YP_566733.1| 209 LDTTKE-VYPNLYVAGMAAN 227
                                   444555.7899999998744 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.2   0.00043      0.64       1      89 [.      27     155 ..      27     255 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00043
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS...STHHSTH..................... CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl...rylpeas..................... 55 
                                   dv+ +GGG + l +A +La++g  ++++ek+  +g      ++g+  + +   +   +a                      
  gi|91774041|ref|YP_566733.1|  27 DVALVGGGPANLVAAKYLAEAGlkTVIYEKKLAVG--GGMWAGGMMFPRIvvqE---DALhildefgisyheyengyyvan 102
                                   8999***************************5555..44444444433332220...211233333344444444445555 PP

                                   ....................HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEE CS
                           DAO  56 ....................elarlslealeelreleeelgididyrrtGllsl 89 
                                                        l+ +    ++e +e+++   i++   + G+l++
  gi|91774041|ref|YP_566733.1| 103 siesvgklisgatsagaeifNLVNVEDVMIRENDEICGL-VINWTAVEIGKLHV 155
                                   555555555555555554443334444444555555554.45555555555555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2    0.0001      0.15       1      30 [.      27      54 ..      27      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                  Dv+++G+GpA+l  A+ l  a++glk v+ 
  gi|91774041|ref|YP_566733.1| 27 DVALVGGGPANLVAAKYL--AEAGLKTVIY 54
                                  9*****************..8889988776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2   0.00015      0.23       1      32 [.      27      58 ..      27      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkl 32
                                  dv  +GgG A + AA  +a++G+k++++ +kl
  gi|91774041|ref|YP_566733.1| 27 DVALVGGGPANLVAAKYLAEAGLKTVIYEKKL 58
                                  7999***********************98776 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 ?   10.0   0.0   0.00023      0.34       3      54 ..      26      78 ..      24      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                   K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpefa...Whpgmllegaelqi 54
                                  +D++ +G Gp+nL  a  l+e+   lk++  e++ +++   W  gm+++   +q 
  gi|91774041|ref|YP_566733.1| 26 VDVALVGGGPANLVAAKYLAEAG--LKTVIYEKKLAVGggmWAGGMMFPRIVVQE 78
                                  69***********9999999999..********98864444********998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); 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:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1699.96
//
Query:       gi|91774042|ref|YP_566734.1|  [L=115]
Description: hypothetical protein Mbur_2110 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  144.2   0.0    1.6e-42  144.0   0.0    1.0  1  DUF356    Protein of unknown function (DUF356)
  ------ inclusion threshold ------
      0.064   12.4   0.0        4.9    6.2   0.0    2.0  2  Memo      Memo-like protein


Domain annotation for each model (and alignments):
>> DUF356  Protein of unknown function (DUF356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0   0.0   1.8e-46   1.6e-42       1     106 []       4     109 ..       4     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 1.8e-46
                        DUF356   1 liliRadnkeKvlnalaDlerygklkiegkPriiepevadkilekvlkeelkkkvkvaalveveedatkaisklrkiHPPa 81 
                                   +++iRa++ +Kv++al+Dle+yg++k+ ++P++iep++ad+il++v +++lk+k+++aalve++++a++aisklrkiHPPa
  gi|91774042|ref|YP_566734.1|   4 FAVIRAEDPNKVKIALHDLEHYGSMKFGSNPKRIEPNYADQILVSVSGVPLKTKCNSAALVELDTNAGAAISKLRKIHPPA 84 
                                   79******************************************************************************* PP

                        DUF356  82 Hvvvvseeydeyeellekleklkel 106
                                   Hvv+vs+++d++eell+++e ++++
  gi|91774042|ref|YP_566734.1|  85 HVVIVSPRHDVFEELLDSSELYPDF 109
                                   ******************9999876 PP

>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0   0.00054       4.9     167     203 ..       9      47 ..       3      57 .. 0.79
   2 ?    4.4   0.0    0.0019        17      51      78 ..      70      98 ..      55     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00054
                          Memo 167 ikdesnlviiSsDlsHygr.rFg.spqeiaesieDrevi 203
                                   ++d++++ i+  Dl Hyg  +Fg +p+ i  +  D++++
  gi|91774042|ref|YP_566734.1|   9 AEDPNKVKIALHDLEHYGSmKFGsNPKRIEPNYADQILV 47 
                                   47888999*********9548995566666666688766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0019
                          Memo 51 aakayaeles.skvervvilGpsHtilgs 78
                                  a++a ++l + + +  vvi+ p H ++++
  gi|91774042|ref|YP_566734.1| 70 AGAAISKLRKiHPPAHVVIVSPRHDVFEE 98
                                  6788999999999***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 753.54
//
Query:       gi|91774043|ref|YP_566735.1|  [L=269]
Description: pyrroline-5-carboxylate reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  137.3   0.7    4.2e-40  136.2   0.7    1.6  1  P5CR_dimer      Pyrroline-5-carboxylate reductase dimerisatio
    9.3e-21   74.2   1.6    6.7e-20   71.5   0.6    2.4  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    2.7e-07   30.9   1.4    9.5e-07   29.1   1.4    1.9  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0002   21.4   5.1    0.00046   20.2   5.1    1.8  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0017   19.2   0.0     0.0039   18.0   0.0    1.6  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.003   16.9   0.0     0.0054   16.1   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0051   16.5   1.4      0.011   15.4   1.4    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA
     0.0058   16.0   0.0     0.0076   15.6   0.0    1.2  1  ThiF            ThiF family
     0.0078   16.3   0.3      0.024   14.8   0.1    1.8  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
     0.0089   16.4   0.3      0.026   15.0   0.3    1.9  1  NAD_binding_7   Putative NAD(P)-binding
     0.0099   16.3   0.5      0.024   15.1   0.5    1.7  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.042   13.7   0.1      0.073   12.9   0.1    1.3  1  ERF             ERF superfamily
      0.058   12.4   0.8       0.08   11.9   0.8    1.3  1  PDH             Prephenate dehydrogenase
       0.36   10.8   1.1       0.77    9.8   1.1    1.6  1  VEK-30          Plasminogen (Pg) ligand in fibrinolytic pathw


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   0.7   3.2e-43   4.2e-40       1     103 []     163     267 ..     163     267 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 3.2e-43
                                   CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHHHHHH CS
                    P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTiaglke 79 
                                   Ek++davt+lsGsgpAy+f +iealad++v++Gl+r++A  laaqtv+Gaak++le++  p+el+d+vtsp+GtTi+g+++
  gi|91774043|ref|YP_566735.1| 163 EKLMDAVTGLSGSGPAYIFPVIEALADGAVHEGLDRANAITLAAQTVLGAAKMVLETGmhPGELKDMVTSPAGTTIRGIHT 243
                                   89****************************************************977779********************* PP

                                   HHHTTHHHHHHHHHHHHHHHHHHH CS
                    P5CR_dimer  80 leegglraavieaveaaakrskel 103
                                   lee+g+raa+++av ++ krskel
  gi|91774043|ref|YP_566735.1| 244 LEESGIRAAFMNAVIESSKRSKEL 267
                                   **********************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 !   71.5   0.6   5.3e-23   6.7e-20       1      97 []       7     100 ..       7     100 .. 0.91
   2 ?    0.8   0.0      0.58   7.4e+02      11      46 ..     184     219 ..     182     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 5.3e-23
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESS.CCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                 F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrn.pekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80 
                                   +ig+iG+G+mge+l++g+laa    +ei++ +s   +  +e l +elg++v++ dn e++ ++dvvvlavkp+ +++vl +
  gi|91774043|ref|YP_566735.1|   7 RIGFIGTGKMGESLIRGILAAH---SEITLNASDVyKPALERLNNELGINVST-DNTETIGDSDVVVLAVKPQILKDVLVA 83 
                                   79*******************9...9998543333144589999*********.*************************** PP

                                   CGHHHHTTSEEEEESSS CS
                 F420_oxidored  81 lakdalkgklvisvlag 97 
                                   ++++  ++klvis++ag
  gi|91774043|ref|YP_566735.1|  84 IKDSITADKLVISIAAG 100
                                   ***************97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHH CS
                 F420_oxidored  11 gealasgllaaga.qpheivvansrnpekaeelaeel 46 
                                   +eala g++++g  +++ i++a  ++   a+++  e 
  gi|91774043|ref|YP_566735.1| 184 IEALADGAVHEGLdRANAITLA-AQTVLGAAKMVLET 219
                                   78999******99888888877.77766666666555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   1.4   7.4e-10   9.5e-07       1      91 [.       7      99 ..       7     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.4e-10
                                  EEEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnl..lkagykvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdevieglleal 80
                                  +igfiG+G+MG+++++ +  +++++++ + ++ k ++e+l +e g+++ ++  e + + dvv++ vk  +  ++v+  +++++
  gi|91774043|ref|YP_566735.1|  7 RIGFIGTGKMGESLIRGIlaAHSEITLNASDVYKPALERLNNElGINVSTDNTETIGDSDVVVLAVKP-QILKDVLVAIKDSI 88
                                  69****************3335566677889999******99967999******************85.99************ PP

                                  -TT-EEEE-S- CS
                 NAD_binding_2 81 kkgdilidgst 91
                                   +++++i  + 
  gi|91774043|ref|YP_566735.1| 89 TADKLVISIAA 99
                                  ******97654 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 !   20.2   5.1   3.6e-07   0.00046      52     147 ..      47     134 ..       7     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.6e-07
                                   ---TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--EEEEES CS
                NAD_Gly3P_dh_N  52 klpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeekvavlsG 132
                                   + +  + ++td +e++ ++d++vl+v  q+l++vl  +k+ +++++ ++s++ G++        ++ie+el+e + +v   
  gi|91774043|ref|YP_566735.1|  47 NNELGINVSTDNTETIGDSDVVVLAVKPQILKDVLVAIKDSITADKLVISIAAGVSV-------TAIEDELNEGTRVVRVM 120
                                   555568899**********************************************77.......66777777776444445 PP

                                   S--HHHHHTT--EEE CS
                NAD_Gly3P_dh_N 133 pslAeEvakgkptav 147
                                   p++A  va+   +av
  gi|91774043|ref|YP_566735.1| 121 PNIAATVAEAA-SAV 134
                                   77777777643.223 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     3e-06    0.0039       2      77 ..       7      79 ..       6      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                                  EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                  GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77
                                  r+++iG+Gk+g+  +r + ++ + e    + d  +++ e++ +++g+++ +d  e     + d+v+ a+ ++  ++
  gi|91774043|ref|YP_566735.1|  7 RIGFIGTGKMGESLIRGILAA-HSEITLNASDVYKPALERLNNELGINVSTDNTETIG--DSDVVVLAVKPQILKD 79
                                  89*************999999.77777779******************9999999999..6799999999876555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.3e-06    0.0054      34     100 ..       3      73 ..       1      79 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.3e-06
                                   GTTSEEEEES-SHHHHHHHHHHHHTT-..EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEEEE-S- CS
                  2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgm..kviaydrskkkee.eeeelgvelv.sleellaesDivslhlp 100
                                   l++k++G iG+G++G+++++ + a      + a d++k + e   +elg+++  +  e + +sD+v+l++ 
  gi|91774043|ref|YP_566735.1|   3 LTEKRIGFIGTGKMGESLIRGILAAHSeiTLNASDVYKPALErLNNELGINVStDNTETIGDSDVVVLAVK 73 
                                   789****************97665555116667788877666667778885555999**********9985 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.4   8.4e-06     0.011      57     141 ..      53     137 ..       8     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.4e-06
                                   EECCHSCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEE CS
                          ApbA  57 alsaeekselepidlvivtvKayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgev 137
                                   ++s+++++ +++ d+v+++vK + ++++l +ik+ ++ +  v+++  G+ +  + +e     rv+  +  + at  +    
  gi|91774043|ref|YP_566735.1|  53 NVSTDNTETIGDSDVVVLAVKPQILKDVLVAIKDSITADKLVISIAAGVSVTAIEDELNEGTRVVRVMPNIAATVAEAASA 133
                                   3333355889**************************************998766555555567777777777776666655 PP

                                   EECS CS
                          ApbA 138 hhag 141
                                     ag
  gi|91774043|ref|YP_566735.1| 134 VCAG 137
                                   5555 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.9e-06    0.0076      58     185 ..      20     157 ..      18     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.9e-06
                                   GGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-CCG.CC...S-HHHHTT-......SEEEEESSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx...xxxxxxxxx......xxxxxxxxxxxxxxxxxx RF
                          ThiF  58 lnRqflfreediGkpKaevaaealqeinpdveveavteritd.et...vleellesv......DlVvdalDniearrlvnr 128
                                   l R +l+ +++i  + ++v + al+++n+++ ++  t++ ++      v+      v      D+ v   D+i+a +lv +
  gi|91774043|ref|YP_566735.1|  20 LIRGILAAHSEITLNASDVYKPALERLNNELGINVSTDNTETiGDsdvVVLA----VkpqilkDVLVAIKDSITADKLVIS 96 
                                   8899***************************998888888664333332223....2334588****************** PP

                                   HHHHHT-EEEEEEEETTEEEEEEEEE......CCS-ECTSS-TGGS.EECCCCEEHHHHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 129 acvkkgiplieagtlgfegqvvviip......gktgcyeCldpsstedptekkvplctsiagn 185
                                   +++  ++  ie + l   ++vv ++p       + +   C   ++ted  e   +++ + +g 
  gi|91774043|ref|YP_566735.1|  97 IAAGVSVTAIE-DELNEGTRVVRVMPniaatvAEAASAVCAGKNATEDDMEVALEMF-QSIGS 157
                                   ******999*9.777777777777665555665666666665566666666666666.55554 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.9e-05     0.024       2      84 ..       7      81 ..       6      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                  EEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEEE-S-HHHHHH CS
                        DapB_N  2 kvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvliDFTtpeavle 82
                                  +++ +G  G+mG+++++ + + +++++l a    k+       a  l  l+ +lg++v++d +e++ ++dv++   +p+ +++
  gi|91774043|ref|YP_566735.1|  7 RIGFIGT-GKMGESLIRGILAaHSEITLNASDVYKP-------A--LERLNnELGINVSTDNTETIGDSDVVVLAVKPQILKD 79
                                  6888997.*********9988345666666655555.......2..23333389*******************9999998887 PP

                                  HH CS
                        DapB_N 83 nl 84
                                  +l
  gi|91774043|ref|YP_566735.1| 80 VL 81
                                  66 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3     2e-05     0.026       4      75 ..       2      78 ..       1     153 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                 NAD_binding_7  4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapev.keeleelvk....la.eeelekdlegadlviaatddreln 75
                                  +l++k++  +G G+++++ +r +l+a  ++t+ a +v k++le +++    ++ +++  + + + d+v+ a++ + l+
  gi|91774043|ref|YP_566735.1|  2 HLTEKRIGFIGTGKMGESLIRGILAAHSEITLNASDVyKPALE-RLNnelgINvSTDNTETIGDSDVVVLAVKPQILK 78
                                  7899********************************8433333.2221222221333456688888888887655554 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.5   1.9e-05     0.024       1     105 [.       7     115 ..       7     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                   EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80 
                                   +++++G tG +G+ l+r +   h e++l +    +  a ++l++       +  ++v++ ++e + + d+v+la+  ++ k
  gi|91774043|ref|YP_566735.1|   7 RIGFIG-TGKMGESLIRGILAaHSEITLNASDVYKP-ALERLNN-------ELGINVSTDNTETIGDSDVVVLAVKPQILK 78 
                                   689***.********997666599887777444444.3333333.......455666666699****************** PP

                                   HHHHHH...HHTTSEEEESSSTTTTST.........T CS
                Semialdhyde_dh  81 elapkl...aeagvkviDlssdfRlkd.........d 105
                                   ++  ++   + a+  vi+ ++   +            
  gi|91774043|ref|YP_566735.1|  79 DVLVAIkdsITADKLVISIAAGVSVTAiedelnegtR 115
                                   9998885556667789998887755545555555555 PP

>> ERF  ERF superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.7e-05     0.073      31     108 ..      77     164 ..      74     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                           ERF  31 ledileaikpvlkehglilkpei.....kstegeteltvevttt.lvdneggeiesvkavapldkak....gmdkaqatGs 101
                                   l+d+l aik  ++ ++l++++        +  + +e+t +v+ + +++++  e +s +++ ++ +++    + ++ q++Gs
  gi|91774043|ref|YP_566735.1|  77 LKDVLVAIKDSITADKLVISIAAgvsvtAIEDELNEGTRVVRVMpNIAATVAEAASAVCAGKNATEDdmevALEMFQSIGS 157
                                   78*********************99998555555555555555526777777777888888888888999999999***** PP

                           ERF 102 aitYakr 108
                                   ait+ ++
  gi|91774043|ref|YP_566735.1| 158 AITIPEK 164
                                   ***9776 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   6.3e-05      0.08      28      98 ..      48     115 ..      29     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                                   HHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--.S--CHHHHHHHHHCC..GC CS
                           PDH  28 lelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvg.svKekvvreleellkegks 98 
                                    elg+    ++  e + + d+vvlav ++ +++vl +++  +  d l++ ++ +v    v ++e+ l+eg++
  gi|91774043|ref|YP_566735.1|  48 NELGINVSTDN-TETIGDSDVVVLAVKPQILKDVLVAIKDSITADKLVISIAaGVS---VTAIEDELNEGTR 115
                                   47888888888.8********************************99998751333...3444455555555 PP

>> VEK-30  Plasminogen (Pg) ligand in fibrinolytic pathway
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.1    0.0006      0.77       3      11 ..      41      49 ..      40      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                        VEK-30  3 aELeRLKNE 11
                                  ++LeRL+NE
  gi|91774043|ref|YP_566735.1| 41 PALERLNNE 49
                                  69******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2088.02
//
Query:       gi|91774044|ref|YP_566736.1|  [L=164]
Description: XRE family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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   34.4   1.3    2.7e-08   33.7   1.3    1.3  1  HTH_3       Helix-turn-helix
    7.2e-07   29.5   0.0    1.2e-06   28.8   0.0    1.3  1  HTH_31      Helix-turn-helix domain
      5e-06   26.5   1.1    8.8e-06   25.7   1.1    1.3  1  HTH_19      Helix-turn-helix domain
    0.00012   21.8   0.4    0.00021   21.1   0.4    1.3  1  HTH_25      Helix-turn-helix domain
  ------ inclusion threshold ------
      0.066   13.1   0.2       0.11   12.3   0.2    1.4  1  zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
       0.13   12.3   0.8       0.21   11.6   0.8    1.3  1  DZR         Double zinc ribbon


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 !   33.7   1.3   9.1e-12   2.7e-08       1      50 [.      84     133 ..      84     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 9.1e-12
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50 
                                   ++e+R+++g++qe LA k+  + s i +iE+Ge  P  ++ kk++kaL+v
  gi|91774044|ref|YP_566736.1|  84 MREAREKRGWTQEVLAIKIKEKASLIKKIERGEITPEDSVRKKIEKALNV 133
                                   59***********************************************8 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0     4e-10   1.2e-06       6      56 ..      84     133 ..      82     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4e-10
                        HTH_31   6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                    r++Re++G++qe +A  +   +s + ++E+G+++ p  +v  ++  al++
  gi|91774044|ref|YP_566736.1|  84 MREAREKRGWTQEVLAIKIKEKASLIKKIERGEIT-PEDSVRKKIEKALNV 133
                                   699*******************************6.****99999999986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.1     3e-09   8.8e-06       5      53 ..      85     132 ..      84     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3e-09
                        HTH_19   5 keaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53 
                                   +eaRe++g+tqe la +++   s i +iE g++ +p+ ++ +ki +al+
  gi|91774044|ref|YP_566736.1|  85 REAREKRGWTQEVLAIKIKEKASLIKKIERGEI-TPEDSVRKKIEKALN 132
                                   89*******************************.**9888777766665 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.4   6.9e-08   0.00021       2      35 ..      84     117 ..      83     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.9e-08
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                        HTH_25   2 LraaRearglsleevaketkIrkdylealEeddf 35 
                                   +r+aRe+rg++ e +a ++k ++++++++E++++
  gi|91774044|ref|YP_566736.1|  84 MREAREKRGWTQEVLAIKIKEKASLIKKIERGEI 117
                                   79*****************************986 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   3.8e-05      0.11       4      32 ..       2      33 ..       1      45 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                                  B-TTTSSS...BS-EEETTEEEEEE-HHHHHH CS
                    zf-C3HC4_3  4 eCviCler...prnvvllpCgHlvlCeeCaek 32
                                  eC iC ++   + + v ++  Hl +C++C++ 
  gi|91774044|ref|YP_566736.1|  2 ECEICGTEikeKPTDVTIDGSHLKVCSKCSQY 33
                                  7****9964333345788***********986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   7.2e-05      0.21      15      37 ..       3      33 ..       2      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-05
                           DZR 15 CseCgtklkavaa........edrCpsCgek 37
                                  C+ Cgt++k+ ++         ++C++C++ 
  gi|91774044|ref|YP_566736.1|  3 CEICGTEIKEKPTdvtidgshLKVCSKCSQY 33
                                  *********9999***************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
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 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1209.04
//
Query:       gi|91774045|ref|YP_566737.1|  [L=426]
Description: proteasome-activating nucleotidase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-45  153.3   0.1    1.1e-44  152.1   0.0    1.7  1  AAA              ATPase family associated with various cellul
    6.5e-16   57.9   0.3    1.4e-15   56.8   0.3    1.6  1  AAA_lid_3        AAA+ lid domain
    5.4e-09   36.2   0.0    2.2e-08   34.2   0.0    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
    2.5e-08   33.8   0.1    4.9e-08   32.8   0.1    1.5  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    1.2e-06   28.7   0.0    3.5e-06   27.2   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
      1e-05   26.0   1.2     0.0022   18.4   0.1    2.7  3  AAA_16           AAA ATPase domain
      4e-05   22.9   0.0    9.5e-05   21.7   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
    5.3e-05   23.0   0.1    0.00018   21.3   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.5e-05   22.8   0.3     0.0059   16.9   0.1    2.4  2  AAA_22           AAA domain
    0.00035   20.9   0.1    0.00087   19.6   0.0    1.7  2  AAA_28           AAA domain
     0.0006   20.4   0.0      0.005   17.4   0.0    2.3  2  AAA_18           AAA domain
     0.0013   18.5   0.1     0.0046   16.7   0.0    1.8  2  IstB_IS21        IstB-like ATP binding protein
     0.0046   16.2   0.0     0.0076   15.5   0.0    1.3  1  TIP49            TIP49 P-loop domain
     0.0072   16.5   0.0      0.014   15.5   0.0    1.6  1  AAA_33           AAA domain
     0.0086   16.5   0.0      0.017   15.5   0.0    1.5  1  RNA_helicase     RNA helicase
     0.0098   15.6   0.1        4.9    7.0   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.1       0.02   14.3   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.011   15.5   0.0       0.19   11.4   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
      0.012   15.7   0.1      0.053   13.6   0.0    1.9  2  AAA_14           AAA domain
      0.024   14.2   0.0      0.056   13.0   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.024   14.0   3.1       0.27   10.6   0.0    2.9  3  ATPase           KaiC
      0.026   14.4   0.0      0.061   13.2   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
       0.05   13.6   0.0        0.2   11.7   0.0    1.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.06   12.8   0.1       0.12   11.8   0.1    1.4  1  PhoH             PhoH-like protein
      0.087   12.5   0.0       0.19   11.4   0.0    1.6  1  AAA_24           AAA domain
       0.11   12.2   0.4        0.3   10.8   0.0    1.9  2  AAA_30           AAA domain
       0.14   11.9   0.8        1.1    9.0   0.0    2.1  2  AAA_11           AAA domain
       0.18   10.9   0.0       0.33   10.0   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
        0.3   10.6   2.4       0.67    9.5   0.2    2.4  3  AAA_25           AAA domain
       0.58   10.4   7.8        6.6    7.0   7.8    2.3  1  HALZ             Homeobox associated leucine zipper
       0.72    9.7   4.2        2.6    7.9   1.7    2.4  2  DivIC            Septum formation initiator
        2.9    8.0   9.2       0.82    9.8   1.9    2.4  2  bZIP_2           Basic region leucine zipper


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.1   0.0   1.9e-47   1.1e-44       1     132 []     206     339 ..     206     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.1 bits;  conditional E-value: 1.9e-47
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgse 78 
                                   vll+GppGtGKTllakava+ ++++f+++ gsel++ky+g+++k +r++f+ a++ka p i+fiDE+da+a +r   ++++
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRTNATFIRVVGSELVQKYIGDGAKLVRDIFEMARKKA-PAIIFIDELDAIAATRlgdTNGA 285
                                   79******************************************************9.*****************988889 PP

                                   CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                           AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                   ++e +r++ qLl+e+dg++++ ++v +i+atnrpd ldpa++r gRfdr+iei+l
  gi|91774045|ref|YP_566737.1| 286 DREVQRTLMQLLAEMDGFDNR-GDVRIIAATNRPDVLDPAIVRpGRFDRIIEIPL 339
                                   9999****************7.66****************************985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.3   2.5e-18   1.4e-15       1      44 [.     361     404 ..     361     405 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.5e-18
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                   dvd+k+LA++TeG SGAD+ a++ eA++lA+r + ++i+m+d+ 
  gi|91774045|ref|YP_566737.1| 361 DVDVKKLASLTEGASGADIGAIVMEAGMLAVRNDSDHIGMSDLL 404
                                   9*****************************************85 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 !   34.2   0.0   3.9e-11   2.2e-08       1     135 [.     205     326 ..     205     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.9e-11
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........---.-----G-SEEEEESGGG--HH CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdspl.vraaregeilvlDEveraese 80 
                                   +vlL GppGtgK+ la+ +a+++n+++  v +++      l++++   +++++lv  ++ +   + ++i+++DE++ +   
  gi|91774045|ref|YP_566737.1| 205 GVLLFGPPGTGKTLLAKAVAHRTNATFIRVVGSE------LVQKYI--GDGAKLVRDIFeMARKKAPAIIFIDELDAIAAT 277
                                   59****************************9986......****99..4555555555505445599*********99999 PP

                                   HHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  81 vlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspalr 135
                                    l+  +    e ++ l+++  +++       +r  +r+ia++n++d     l+pa++
  gi|91774045|ref|YP_566737.1| 278 RLGDTNGADREVQRTLMQLLAEMDGFD----NRgdVRIIAATNRPD----VLDPAIV 326
                                   999999998888888888888886544....3445**********9....7777765 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 !   32.8   0.1   8.8e-11   4.9e-08       1      57 []      92     148 ..      92     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 8.8e-11
                                   EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST.--TTEEEEEETTTTEEEEEE- CS
                Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavprem.LrpgDlVavdkdtgfifEkLP 57 
                                   Va+V+++ dd ++a++ +s++ +++v+++    +++ L pg++V+++++t ++++++P
  gi|91774045|ref|YP_566737.1|  92 VASVVDIFDD-DKALIRSSTGPQFLVNVSQDFEDDDlLVPGARVGLNQQTLAVVDIIP 148
                                   9*********.**********************88879******************99 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   6.3e-09   3.5e-06       6     105 ..     206     299 ..     202     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.3e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                   +ll gp g+Gkt+laka+a   ++    ++ir+  sel +    + + +  +  ++    a ++   i+++DE+d i++++
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRTNA----TFIRVVGSELVQ----KYIGDGAKLVRDIFEMARKKApaIIFIDELDAIAATR 278
                                   5677****************9996....************....77777777777776666666666************96 PP

                                   --------HHHHHHHHHHHH- CS
                         AAA_2  85 ssgadvSregVqrdLLqileg 105
                                       +    +Vqr L+q+l +
  gi|91774045|ref|YP_566737.1| 279 LGDTNGADREVQRTLMQLLAE 299
                                   6666666789********965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         9     5e+03       6      13 ..      72      79 ..      26     106 .. 0.52
   2 !   18.4   0.1   3.9e-06    0.0022      15      56 ..     194     232 ..     192     247 .. 0.78
   3 ?    5.3   0.0     0.041        23     122     154 ..     250     292 ..     245     306 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9
                        AAA_16  6 eeeleqLl 13
                                  e+e+++L+
  gi|91774045|ref|YP_566737.1| 72 ERETHRLQ 79
                                  22222222 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.9e-06
                        AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggifl 56 
                                   a++r+    p  vll G++G+GK+ l+++++++ +++   f+
  gi|91774045|ref|YP_566737.1| 194 AFKRIGITPPKGVLLFGPPGTGKTLLAKAVAHRTNAT---FI 232
                                   566666666799*******************865554...44 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.041
                        AAA_16 122 llkrllallsrderplvlvlDdlq...........wadeaslql 154
                                   l++++++ +++ + p ++++D+l+            ad + +  
  gi|91774045|ref|YP_566737.1| 250 LVRDIFEMARK-KAPAIIFIDELDaiaatrlgdtnGADREVQRT 292
                                   45566677777.778*********66666555555444444433 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.7e-07   9.5e-05      21     116 ..     162     271 ..     150     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-07
                        DUF815  21 evdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegLrli..eveke 90 
                                   + +ev+ +++ g+d+q +++ e +e  +++         +p + vLL+G  GtGK  l ka+ ++++++ +r++  e+ ++
  gi|91774045|ref|YP_566737.1| 162 DSQEVDYSQVGGLDQQIREISESVELPITKpeafkrigiTPPKGVLLFGPPGTGKTLLAKAVAHRTNATFIRVVgsELVQK 242
                                   45667777777777777777776654333311111111156688******************************8889999 PP

                        DUF815  91 dlkelpklvellrerper...filfvDDL 116
                                    + +  klv+ + e++++    i+f+D L
  gi|91774045|ref|YP_566737.1| 243 YIGDGAKLVRDIFEMARKkapAIIFIDEL 271
                                   9***999999887554442338*****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 ?   -2.6   0.0         7   3.9e+03      85     103 ..      67      85 ..      61      97 .. 0.78
   2 !   21.3   0.0   3.2e-07   0.00018      34      96 ..     204     274 ..     179     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7
                        RuvB_N  85 kdvlfideihrlsraveev 103
                                   +++ +  e hrl++++e +
  gi|91774045|ref|YP_566737.1|  67 QKLKYERETHRLQSEIERL 85 
                                   5556667999999999875 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.2e-07
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlek.agdlaalltnl......eekdvlfideihrl 96 
                                     vll+GpPG Gkt lak +a+  ++++ ++  +  ++k  gd a l+ ++      ++  ++fide+  +
  gi|91774045|ref|YP_566737.1| 204 KGVLLFGPPGTGKTLLAKAVAHRTNATFiRVVGSELVQKyIGDGAKLVRDIfemarkKAPAIIFIDELDAI 274
                                   569********************998851665556666634787777665522222133469999998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     1e-05    0.0059       8      41 ..     206     230 ..     202     244 .. 0.84
   2 ?    4.2   0.1     0.087        49      74     106 ..     246     291 ..     227     316 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                   ++++G++GtGKT+l++ ++++          +++
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRT---------NAT 230
                                   589****************997.........444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.087
                        AAA_22  74 sseellealeqalraravielliiDEaqhlr....s..........e 106
                                   +   l++ + + +r++a  +++ iDE + +                 
  gi|91774045|ref|YP_566737.1| 246 DGAKLVRDIFEMARKKAP-AIIFIDELDAIAatrlGdtngadrevqR 291
                                   556666777777777777.9*********966544144444433332 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       9.1   5.1e+03      37      67 ..      52      81 ..      43      97 .. 0.45
   2 !   19.6   0.0   1.5e-06   0.00087       2      55 ..     206     263 ..     205     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.1
                        AAA_28 37 eklakgedalpwvedllafaervleeqleee 67
                                  e++++ e + ++  +  +++++++ ++l+ e
  gi|91774045|ref|YP_566737.1| 52 EQYDQMESDKRYI-ESQKLKYERETHRLQSE 81
                                  4444444433333.22222233333333333 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.5e-06
                        AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpwvedllaf 55 
                                   + ++G+++tGKT l++a a r     ++vv  E + +++ ++++  +d+ +++ ++ a 
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRtnatFIRVVgSELVQKYIGDGAKLVRDIFEMA-RKKAP 263
                                   6799***************6666668899999999999999998888777775.44333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       2.2   1.2e+03      53      84 ..      29      69 ..      13      95 .. 0.62
   2 !   17.4   0.0   8.9e-06     0.005       1      66 [.     206     299 ..     206     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.2
                        AAA_18 53 dedkldklldaleenss.........aleegknlvidghla 84
                                  ded+ ++lld +++  s         +++e +  +i+++  
  gi|91774045|ref|YP_566737.1| 29 DEDFSKYLLDRMKQLESrnnllkeqyDQMESDKRYIESQKL 69
                                  55555555555555544333333333344444446655554 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 8.9e-06
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldeskrld 53 
                                   +ll G+pG+GKt lak+++ r++                      ++ + ++a+++ + + + +e        l +++ +d
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRTNAtfirvvgselvqkyigdgaklVRDIFEMARKKAPAIIFIDEldaiaatRLGDTNGAD 286
                                   799***************999855789888877777777777777777777777777777777777777777333444444 PP

                        AAA_18  54 edkldklldalee 66 
                                   ++++  l+++l e
  gi|91774045|ref|YP_566737.1| 287 REVQRTLMQLLAE 299
                                   4444444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.9   2.7e+03      88     113 ..      67      92 ..      66     100 .. 0.87
   2 !   16.7   0.0   8.3e-06    0.0046      48      73 ..     204     229 ..     199     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.9
                     IstB_IS21  88 eelkrarrdgklaralkrllkvdlli 113
                                   ++lk +r+  +l+++++rl  + l++
  gi|91774045|ref|YP_566737.1|  67 QKLKYERETHRLQSEIERLKSPPLVV 92 
                                   689999999******99999988876 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 8.3e-06
                     IstB_IS21  48 enivllGpsGvGKshlaialgveavr 73 
                                   ++++l+Gp+G+GK+ la a+++++ +
  gi|91774045|ref|YP_566737.1| 204 KGVLLFGPPGTGKTLLAKAVAHRTNA 229
                                   6799****************998655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05    0.0076      51      91 ..     204     242 ..     196     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                   ++vLl Gp+gtGkt la a+++  +    f+ ++gse+ + 
  gi|91774045|ref|YP_566737.1| 204 KGVLLFGPPGTGKTLLAKAVAHRTN--ATFIRVVGSELVQK 242
                                   89*******************9876..78*******98765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.6e-05     0.014       2      32 ..     206     238 ..     206     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt 32 
                                   vll G+pG+GK+ la+ ++ ++   ++++   +
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRTNatFIRVVGSE 238
                                   7899**************988875655555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     3e-05     0.017       1      67 [.     206     263 ..     206     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenp 67 
                                   ++l+Gp+g+GK++lak            ++++ +++r + ++ +++Y g  + ++ D+ ++  ++ p
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKA---------VAHRTNATFIRVVGSELVQKYIGDGAKLVRDIFEMARKKAP 263
                                   689**************.........34667888889999999999999999999999888766533 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 ?    5.9   0.0      0.02        11      21      39 ..     203     220 ..     194     225 .. 0.76
   2 !    7.0   0.0    0.0088       4.9      34      50 ..     399     415 ..     395     421 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                        AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                   +kg +ll Gp G+GK+ l 
  gi|91774045|ref|YP_566737.1| 203 PKG-VLLFGPPGTGKTLLA 220
                                   456.9**********8665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0088
                        AAA_29  34 GKSTllDAiqalLvpak 50 
                                   G S llDA++ ++vp++
  gi|91774045|ref|YP_566737.1| 399 GMSDLLDAVTKVMVPKE 415
                                   6689***********98 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.5e-05      0.02      24      43 ..     205     224 ..     194     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                  Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt+lak+++
  gi|91774045|ref|YP_566737.1| 205 GVLLFGPPGTGKTLLAKAVA 224
                                   589*************9875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034      0.19      23      53 ..     204     231 ..     186     244 .. 0.78
   2 ?    1.4   0.0      0.41   2.3e+02     132     143 ..     306     317 ..     260     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpf 53 
                                     vl+ G  GtGK+lla+a+ ++   +++ f
  gi|91774045|ref|YP_566737.1| 204 KGVLLFGPPGTGKTLLAKAVAHR---TNATF 231
                                   679***************98543...34445 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.41
                                   E--EEEEEEESS CS
               Sigma54_activat 132 kvdvriiaatne 143
                                   + dvriiaatn+
  gi|91774045|ref|YP_566737.1| 306 RGDVRIIAATNR 317
                                   5699******97 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       2.7   1.5e+03      75      92 ..      42      59 ..      21     122 .. 0.55
   2 ?   13.6   0.0   9.5e-05     0.053       5      76 ..     206     274 ..     203     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.7
                        AAA_14 75 evpewekalkslvdegkn 92
                                  ++++  + lk+ +d+ + 
  gi|91774045|ref|YP_566737.1| 42 QLESRNNLLKEQYDQMES 59
                                  333333334444333311 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.5e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT l+k ++++       ++ +   +  +k + d +kl + i+e+++++   ++f+DE   +
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRTN---ATFIRVVGSELVQKYIGDGAKLVRDIFEMARKKAPAIIFIDELDAI 274
                                   7899***********99997766...7788887777777777777789999999976678999*****9877 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 ?   13.0   0.0    0.0001     0.056      34      84 ..     204     246 ..     191     286 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                         AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiies 84 
                                   k vll Gp GtGKt+++k + ++ +         +f     ++ +q+ i +
  gi|91774045|ref|YP_566737.1| 204 KGVLLFGPPGTGKTLLAKAVAHRTN--------ATFIRVVGSELVQKYIGD 246
                                   789***************9988877........344444455555555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.31   1.7e+02      87     142 ..      55     108 ..      31     111 .. 0.71
   2 ?   10.6   0.0   0.00048      0.27      14      37 ..     198     221 ..     169     230 .. 0.75
   3 ?    0.6   0.0      0.52   2.9e+02     102     153 ..     245     299 ..     227     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.31
                        ATPase  87 dasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaRe 142
                                   d +es+++   e++k + e  +++l++ i+++k   +v+ s+  +  ++++a++R+
  gi|91774045|ref|YP_566737.1|  55 DQMESDKR-YIESQKLKYERETHRLQSEIERLKSPPLVVASVVDI-FDDDKALIRS 108
                                   33333333.344888999999999999999999999999999988.7777777775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00048
                        ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                    Gi   + vl+ G pGtGKt++a+
  gi|91774045|ref|YP_566737.1| 198 IGITPPKGVLLFGPPGTGKTLLAK 221
                                   68888899**************97 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.52
                        ATPase 102 edleelieelaeaikeikakrvviDsitgl.aye.e.keavaReilrqlvrvlkk 153
                                    d  +l++++ e+ +++    + iD ++++ a++   ++   Re  r+l++ l++
  gi|91774045|ref|YP_566737.1| 245 GDGAKLVRDIFEMARKKAPAIIFIDELDAIaATRlGdTNGADREVQRTLMQLLAE 299
                                   56678999999999999999*****999996433121233345555555555555 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 ?   13.2   0.0   0.00011     0.061       2      30 ..     206     234 ..     205     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                   vll g PG++ktll+ka+a+  +++f r+
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRTNATFIRV 234
                                   7999**********************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 ?   11.7   0.0   0.00036       0.2      20      59 ..     204     243 ..     176     273 .. 0.76
   2 ?   -1.5   0.0       4.2   2.4e+03      65      83 ..     347     367 ..     341     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                                   EEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                          TsaE  20 dvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59 
                                   + +lL G+ G+GKT l++++a+  + + ++     lv++Y
  gi|91774045|ref|YP_566737.1| 204 KGVLLFGPPGTGKTLLAKAVAHRTNATFIRVVGSELVQKY 243
                                   359*******************998874444444666666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                                   S..EEEEE-TT-SSTHHHHHC CS
                          TsaE  65 g..lyHfDlYRledeeeleel 83 
                                   +  l+H+D+  + ++ ++++l
  gi|91774045|ref|YP_566737.1| 347 TifLIHMDMLNIGSDVDVKKL 367
                                   25699***9999776666554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00022      0.12      22      41 ..     206     225 ..     197     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                   EEEE--TTSSTTHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalav 41 
                                   v  +Gp GtGKt+la a+a 
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAH 225
                                   6789***********99885 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   0.00034      0.19       5      24 ..     206     227 ..     203     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                        AAA_24   5 iliyGpsgiGKTtlakel..gp 24 
                                   +l++Gp+g+GKT lak      
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVahRT 227
                                   89*************9885544 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   0.00053       0.3      20      51 ..     205     236 ..     192     242 .. 0.80
   2 ?   -3.0   0.1       9.1   5.1e+03      92     103 ..     381     392 ..     360     409 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                        AAA_30  20 vavltGpAGtGKttalkalreaweaaggrvig 51 
                                    ++l Gp+GtGKt + ka+++  +a   rv+g
  gi|91774045|ref|YP_566737.1| 205 GVLLFGPPGTGKTLLAKAVAHRTNATFIRVVG 236
                                   57899*************99888877777765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.1
                        AAA_30  92 livDEagmvdtk 103
                                    iv Eagm++ +
  gi|91774045|ref|YP_566737.1| 381 AIVMEAGMLAVR 392
                                   577788888443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2       0.5   2.8e+02     105     167 ..      33      75 ..       2     101 .. 0.43
   2 ?    9.0   0.0    0.0019       1.1      20      42 ..     206     228 ..     189     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.5
                        AAA_11 105 ksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqer 167
                                   +++ l+++ + +++++   ++ +++++ ++ ++                     +k k+e+e 
  gi|91774045|ref|YP_566737.1|  33 SKYLLDRMKQLESRNNLLKEQYDQMESDKRYIE--------------------SQKLKYERET 75 
                                   333333332222222222222222221111111....................1122222222 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
                        AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                   +l+ GPPGtgKT    ++ ++ +
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRTN 228
                                   6899********77777776664 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00058      0.33     117     138 ..     206     227 ..     200     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00058
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                   v+++Gp+ tGkt la+a a+ +
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAHRT 227
                                   899***************9965 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.2   3.5e+03     122     144 ..      67      89 ..      29      92 .. 0.45
   2 ?    9.5   0.2    0.0012      0.67      36      55 ..     206     225 ..     199     231 .. 0.87
   3 ?   -0.1   0.1         1   5.8e+02     130     168 ..     251     292 ..     222     313 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.2
                        AAA_25 122 ggtlltadvdaleaaieevegvr 144
                                   +  + ++++++l+ +ie+ + + 
  gi|91774045|ref|YP_566737.1|  67 QKLKYERETHRLQSEIERLKSPP 89 
                                   22224455555555555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                        AAA_25  36 allaGapgtGKttlaldlal 55 
                                   +ll+G+pgtGKt la  +a+
  gi|91774045|ref|YP_566737.1| 206 VLLFGPPGTGKTLLAKAVAH 225
                                   69************988776 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1
                        AAA_25 130 vdaleaaieevegvrlvviDplsralgg...densnsd.vgal 168
                                   v+++ + +++ + ++ + iD l+++ +    d n ++  v++ 
  gi|91774045|ref|YP_566737.1| 251 VRDIFEMARK-KAPAIIFIDELDAIAATrlgDTNGADReVQRT 292
                                   3444555555.55999999999997666566655553314444 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.8     0.012       6.6       1      39 [.      41      86 ..      41      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                          HALZ  1 KQLErDYdvLKasYdaLksdy.....dsLk..kenekLkaelqeLk 39
                                  KQLE   + LK +Yd++ sd      + Lk  +e ++L++e+++Lk
  gi|91774045|ref|YP_566737.1| 41 KQLESRNNLLKEQYDQMESDKryiesQKLKyeRETHRLQSEIERLK 86
                                  9******************961122144543356679999999998 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.7    0.0047       2.6      33      60 ..      40      67 ..      35      69 .. 0.92
   2 ?    1.6   0.1      0.42   2.3e+02      38      53 ..      73      87 ..      66      95 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0047
                                  HHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                         DivIC 33 laklkaeneeLeaevkdLksdedyieer 60
                                  +++l  +n+ L+++ ++++sd+ yie +
  gi|91774045|ref|YP_566737.1| 40 MKQLESRNNLLKEQYDQMESDKRYIESQ 67
                                  789**********************976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.42
                                  HHHHHHHHHHCC-XXX CS
                         DivIC 38 aeneeLeaevkdLksd 53
                                   e  +L++e+++Lk +
  gi|91774045|ref|YP_566737.1| 73 RETHRLQSEIERLK-S 87
                                  46667888888885.4 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.9    0.0015      0.82      28      52 ..      34      58 ..      32      60 .. 0.90
   2 ?    2.5   0.7      0.29   1.6e+02      28      52 ..      62      86 ..      59      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                                  HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2 28 eeleervkeLeeeNaqLrqkveqLe 52
                                  ++l +r+k+Le++N+ L+++++q+e
  gi|91774045|ref|YP_566737.1| 34 KYLLDRMKQLESRNNLLKEQYDQME 58
                                  57889******************98 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                                  HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2 28 eeleervkeLeeeNaqLrqkveqLe 52
                                  +++e++  + e+e  +L+ ++e L+
  gi|91774045|ref|YP_566737.1| 62 RYIESQKLKYERETHRLQSEIERLK 86
                                  6788888899999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      836  (0.0466284); expected 358.6 (0.02)
Passed Vit filter:                       175  (0.00976072); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 2929.79
//
Query:       gi|91774046|ref|YP_566738.1|  [L=448]
Description: phosphoglucosamine mutase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  137.6   0.6      5e-40  136.4   0.6    1.7  1  PGM_PMM_I        Phosphoglucomutase/phosphomannomutase, alpha
    1.1e-27   96.6   0.0    2.1e-27   95.7   0.0    1.5  1  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha
    1.1e-25   90.1   0.1    2.2e-25   89.1   0.1    1.6  1  PGM_PMM_III      Phosphoglucomutase/phosphomannomutase, alpha
    4.4e-12   46.0   0.0    1.9e-11   44.0   0.0    2.1  1  PGM_PMM_IV       Phosphoglucomutase/phosphomannomutase, C-ter
  ------ inclusion threshold ------
      0.018   13.6   0.0      0.028   13.0   0.0    1.2  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.057   13.4   0.0       0.11   12.5   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
      0.064   11.8   0.0      0.091   11.3   0.0    1.2  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
       0.14   12.9   0.4        8.4    7.2   0.1    3.5  4  Methyltransf_25  Methyltransferase domain
       0.18   11.1   0.0       0.35   10.2   0.0    1.4  1  GidB             rRNA small subunit methyltransferase G


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   0.6   2.5e-43     5e-40       4     136 ..       4     131 ..       1     133 [. 0.96

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 2.5e-43
                                   BBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHH CS
                     PGM_PMM_I   4 fgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsf 84 
                                   fgt+G+Rg+++ + +tp+l+  +++++++y+ +   k++vv+GrDtR s+++l++a++ag++++Gv+vi++g++p+Pa+++
  gi|91774046|ref|YP_566738.1|   4 FGTNGVRGIAN-EYITPQLAIDVAKSLGTYMGS---KGTVVIGRDTRKSGDMLKSAAIAGALSTGVTVIDIGIAPIPAIQY 80 
                                   9**********.55******************9...6******************************************** PP

                                   HHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-E CS
                     PGM_PMM_I  85 airklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeee 136
                                   ++++ +adagi +taSHnp eyngiK++  +G ++s+e e+++e+i+ ++++
  gi|91774046|ref|YP_566738.1|  81 YVKE-HADAGIGVTASHNPREYNGIKLVAGDGSEFSREGEKEVEKIYMSKDF 131
                                   ****.8****************************************988776 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 !   95.7   0.0   1.1e-30   2.1e-27       1     103 []     150     251 ..     150     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.1e-30
                                   .HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGG CS
                    PGM_PMM_II   1 eaYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkke 81 
                                   e+Yi+a+ + vd e i+++++kvv+d++ Gag+ +l+ ll++lg++v  lna+ d++fp ++p+p+e ++l +l+++vk+ 
  gi|91774046|ref|YP_566738.1| 150 EQYINAIINSVDAESIREKRFKVVVDTGCGAGSLTLPFLLQKLGCKVMALNAQIDGTFPWRNPEPTE-DVLTELSDIVKSR 229
                                   58*****************************************************************.************* PP

                                   G-SEEEEE-TTS-BEEEEETTE CS
                    PGM_PMM_II  82 gadlglafDgDaDRlgvvderG 103
                                   gad+g+a DgDaDR +++de+G
  gi|91774046|ref|YP_566738.1| 230 GADMGVAQDGDADRAVFFDENG 251
                                   ********************98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.1   1.1e-28   2.2e-25       2     111 ..     256     361 ..     255     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.1e-28
                                   HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS CS
                   PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeatt 82 
                                    d lla++ak +le+  k+g  +v++v++s+ + +va+++g+kl+ t+vG+ +v+++m e gav+GgE +g++if++++++
  gi|91774046|ref|YP_566738.1| 256 EDVLLAMMAKCILED--KKGD-LVTPVSSSQRMLDVAEEAGVKLHWTAVGSINVARKMMEIGAVFGGEGNGGLIFPEHQYC 333
                                   6999********995..5565.9********************************************************** PP

                                   --HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                   PGM_PMM_III  83 kDGilaallvleilaetgkslselleell 111
                                   +DG++a++++lei+a  g++ls l+e+++
  gi|91774046|ref|YP_566738.1| 334 RDGAMACAKLLEIMAS-GRKLSHLAENVP 361
                                   **************96.89*****96654 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   9.6e-15   1.9e-11      23      68 ..     387     437 ..     352     441 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 9.6e-15
                                   H......HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHH CS
                    PGM_PMM_IV  23 a......sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaee 68 
                                          ++ +g+ki + dG++l +RpSGTep +r+ +Eak+ +++++l ee
  gi|91774046|ref|YP_566738.1| 387 VggelevDTTDGVKIWHNDGWVL-IRPSGTEPIIRIFAEAKTLDRAETLMEE 437
                                   134555599**************.**********************999887 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.028      96     136 ..     147     188 ..     116     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
               Methyltransf_29  96 kgadkYidklaelipli.aaggkvrtvlDvGCgvasfgayll 136
                                   +  ++Yi+ + ++++++   +++ ++v+D+GCg  s++  +l
  gi|91774046|ref|YP_566738.1| 147 NANEQYINAIINSVDAEsIREKRFKVVVDTGCGAGSLTLPFL 188
                                   45689*****9999987467999************9975433 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05      0.11      11      60 ..     155     202 ..     146     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
               Methyltransf_32  11 elvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidak 60 
                                   ++++++ +e+ +e++ + vvD G+G g L+    l  +++++kv++++a+
  gi|91774046|ref|YP_566738.1| 155 AIINSVDAESIREKRFKVVVDTGCGAGSLTLPFLL--QKLGCKVMALNAQ 202
                                   4455555555899999*************988877..3479999998876 PP

>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.6e-05     0.091     269     354 ..      66     151 ..      53     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 269 nvidvnkyplpeiekntkktRriGlGvmgladalaklgipydseealkfarkitelltyyaykaSvelAkergpfplfeks 349
                                    vid+   p+p+i++  k++   G+Gv++ ++    +gi+    ++ +f+r+  + +    + +   +A  + +  lf+ +
  gi|91774046|ref|YP_566738.1|  66 TVIDIGIAPIPAIQYYVKEHADAGIGVTASHNPREYNGIKLVAGDGSEFSREGEKEVEKIYMSKDFAAASWERTGDLFKDT 146
                                   59*************************************************999999998888888888888888888877 PP

                                   XXXXX CS
                                   xxxxx RF
               Ribonuc_red_lgC 350 kyskg 354
                                   ++++ 
  gi|91774046|ref|YP_566738.1| 147 NANEQ 151
                                   77665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.2   4.5e+03      47      80 ..     103     137 ..      76     163 .. 0.67
   2 ?    7.2   0.1    0.0042       8.4       1      26 [.     173     198 ..     173     206 .. 0.75
   3 ?   -1.8   0.0       2.6   5.3e+03      23      41 ..     275     293 ..     259     305 .. 0.75
   4 ?    0.8   0.0       0.4     8e+02       8      35 ..     349     381 ..     347     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.2
                                   TEEEEESBCCGBSS.STTTEEEEEEESTGGGSSHH CS
               Methyltransf_25  47 nvefvqgdaedlpf.edgsfDlvvssgalhhlsde 80 
                                    +++v gd ++++   ++++  +++s  +   s e
  gi|91774046|ref|YP_566738.1| 103 GIKLVAGDGSEFSReGEKEVEKIYMSKDFAAASWE 137
                                   66777777777664144466666665555554444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0042
                                   EEEET-TTSHHHHHHH.CTSTSSEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlala.krlgkakvtg 26 
                                   v+d GcG G ltl ++ ++lg +kv++
  gi|91774046|ref|YP_566738.1| 173 VVDTGCGAGSLTLPFLlQKLG-CKVMA 198
                                   89********99886514445.77766 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.6
                                   EEEEEESSHHHHHHHHHHH CS
               Methyltransf_25  23 kvtgvDiseemleaarera 41 
                                    vt v  s++ml+ a+e  
  gi|91774046|ref|YP_566738.1| 275 LVTPVSSSQRMLDVAEEAG 293
                                   5677888999999998865 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.4
                                   TSHHHHHHHCTS....T.SSEEEEEESSHHHHH CS
               Methyltransf_25   8 tGrltlalakrl....g.kakvtgvDiseemle 35 
                                   +Gr + +la+++    + k kv++ D+ ++m +
  gi|91774046|ref|YP_566738.1| 349 SGRKLSHLAENVptyfNsKTKVHCSDLEPTMEN 381
                                   57778888888655553699********99944 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00018      0.35      14      66 ..     135     187 ..     131     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                                   HHHHHS---S--SHHHHHHHCHHHHHHHGGCS-CCC-.EEEETSTTTTTHHHH CS
                          GidB  14 kwNkkinLtsikepeellerhlldslsvlellkekrdkviDvGsGaGlPGipL 66 
                                    w  + +L + ++ +e +   +++s+ + ++ ++  + v+D G GaG   +p 
  gi|91774046|ref|YP_566738.1| 135 SWERTGDLFKDTNANEQYINAIINSVDAESIREKRFKVVVDTGCGAGSLTLPF 187
                                   68888899*******************99988888856*********766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3153.65
//
Query:       gi|91774047|ref|YP_566739.1|  [L=104]
Description: signal recognition particle protein Srp19 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-20   73.2   0.1    3.2e-20   72.9   0.1    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.1   1.8e-24   3.2e-20       1      92 [.      17      99 ..      17     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.8e-24
                                  EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-..........SS-CHH CS
                         SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklkedgkevnekiknkke 82
                                  vi+P+ ld++++rk GR ++++++ e+P+++e+  a+++l+l+ +ve++k+yPr w+++ Gr+ v+ +          ++k+ 
  gi|91774047|ref|YP_566739.1| 17 VIWPANLDKSRSRKGGRIISRKSSLEAPLLRELTAAAEKLNLNPEVEADKKYPRTWWESsGRILVDNN----------EAKTM 89
                                  7******************************************************88666******85..........56666 PP

                                  HHHHHHHHHH CS
                         SRP19 83 llkkiaellk 92
                                  + +kia+++k
  gi|91774047|ref|YP_566739.1| 90 VARKIAKTIK 99
                                  6666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 841.84
//
Query:       gi|91774048|ref|YP_566740.1|  [L=58]
Description: preprotein translocase subunit SecG [Methanococcoides burtonii DSM 6242]
Scores for complete 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-11   42.1   0.2    6.3e-11   42.1   0.2    1.7  2  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 ?   -3.4   0.4       0.6   1.1e+04       1       6 [.       8      13 ..       8      13 .. 0.85
   2 !   42.1   0.2   3.5e-15   6.3e-11       1      38 [.      14      51 ..      14      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.6
                                  XXXXXX CS
                    Sec61_beta  1 SsaGLl 6 
                                  S++GL+
  gi|91774048|ref|YP_566740.1|  8 SGSGLM 13
                                  789998 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 3.5e-15
                                  XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHT CS
                    Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLh 38
                                  SsaGL+ yy+ d+++i++ Pk+V +++++ ++++++  
  gi|91774048|ref|YP_566740.1| 14 SSAGLMTYYDADKKAIHVQPKTVFIFGAICGIVILAFS 51
                                  9********************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 412.40
//
Query:       gi|91774049|ref|YP_566741.1|  [L=339]
Description: translation initiation factor IF-2B subunit alpha [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.2    6.3e-87  291.4   0.2    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.4   0.2   3.5e-91   6.3e-87       2     282 .]      45     330 ..      44     330 .. 0.99

  Alignments for each domain:
  == domain 1  score: 291.4 bits;  conditional E-value: 3.5e-91
                                   S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHH CS
                         IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliek 82 
                                   vrG+pa+a a+  +++ +++ ++++ +++L ++l+ a+++L+++rPtav+l +a++r+lk   + ++s d++++k+ +i +
  gi|91774049|ref|YP_566741.1|  45 VRGAPALAAAGGFGMALAVTLSSANSMEKLLNDLKVAASTLIATRPTAVNLAWAVNRVLK---ATEDSYDLESIKDIVIFE 122
                                   8***********************************************************...789*************** PP

                                   HHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHHHHH CS
                         IF-2B  83 ikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rltakeL 154
                                   + ++++e+++++++ig+++++l+ dgdt++T+cn++         +l+v+r+a++++k+++Vi++E+rP +qG r t +eL
  gi|91774049|ref|YP_566741.1| 123 AIRIADEDVKINKAIGKYGQKLLDDGDTVMTHCNAGRlacvdwgtALGVIRSAVEKGKEISVIACETRPLNQGgRITTWEL 203
                                   ********************************************************************************* PP

                                   HHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSX CS
                         IF-2B 155 vqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifi 234
                                   +q++ipv+litds+ ++vm++ +vdk ivGAdri+++  ++nkiGT++ +++Ake++ip++v+a+ ++f+++  +++ + i
  gi|91774049|ref|YP_566741.1| 204 MQDNIPVKLITDSMSGHVMRQgMVDKMIVGADRITQDV-VFNKIGTYTHSIVAKEHEIPFYVAAPVSTFDPN-GWEDTVTI 282
                                   *************************************8.*********************************.99999*** PP

                                   XBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                         IF-2B 235 eerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                   e rd++el +i +++ia+++++v+npafD tP e+It++ITe+G+++p
  gi|91774049|ref|YP_566741.1| 283 EQRDADELRYIGDVQIAPKNVDVYNPAFDATPMENITALITEKGIFEP 330
                                   *********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2347.53
//
Query:       gi|91774050|ref|YP_566742.1|  [L=582]
Description: multisensor signal transduction histidine kinase, partial [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  100.3   1.6    1.8e-28   99.2   0.2    2.3  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-16   60.2   0.1    5.3e-16   58.4   0.0    2.0  2  HisKA        His Kinase A (phospho-acceptor) domain
    3.8e-16   59.2   0.9    6.4e-16   58.5   0.3    1.7  2  SBP_bac_3    Bacterial extracellular solute-binding proteins,
    3.2e-10   40.2   0.7    1.3e-09   38.2   0.2    2.3  2  PAS_9        PAS domain
    6.6e-06   26.0   0.0    1.3e-05   25.1   0.0    1.5  1  PAS_8        PAS domain
    1.5e-05   24.8   0.2    4.6e-05   23.3   0.2    1.9  1  HATPase_c_5  GHKL domain
    9.4e-05   22.6   0.0    0.00026   21.2   0.0    1.7  2  PAS_4        PAS fold
    0.00035   20.8   0.0    0.00083   19.6   0.0    1.6  1  PAS_3        PAS fold
    0.00097   19.1   0.0     0.0021   18.0   0.0    1.7  1  PAS          PAS fold
     0.0051   17.0   0.0      0.026   14.7   0.0    2.3  2  PAS_7        PAS fold
  ------ inclusion threshold ------
      0.077   13.0   0.0       0.15   12.0   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain


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 ?   -1.8   0.1       2.6   4.2e+03      16      44 ..     412     436 ..     368     439 .. 0.72
   2 !   99.2   0.2   1.1e-31   1.8e-28       2     111 ..     466     576 ..     465     577 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.6
                                   HHHHHHSTTTEEEEEEEEEETEEEEEEEE CS
                     HATPase_c  16 NavkfatkageieveikaseddlvisveD 44 
                                   N  k+  ++ge+e+e++  e+d+  +veD
  gi|91774050|ref|YP_566742.1| 412 NISKI--ENGEVELELD--EVDIYTTVED 436
                                   33443..5666666666..7777777777 PP

  == domain 2  score: 99.2 bits;  conditional E-value: 1.1e-31
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d  +L+qi+ n+++Na+kf++++++i   ik+ +++l+  ++D G+G++++++ ++f++f+q dd+ + +++gtGlGl+iv
  gi|91774050|ref|YP_566742.1| 466 DRLKLKQILYNILSNAIKFSPENENIIMDIKVIDGKLQTNITDKGKGLSEKEQANIFQPFVQlDDEHSEKQKGTGLGLTIV 546
                                   6778***************9999999777777578********************************************** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlple 111
                                   k++v+l++G+iw++se+g+Gttf ft+pl+
  gi|91774050|ref|YP_566742.1| 547 KRFVQLHKGKIWIDSEEGKGTTFCFTIPLN 576
                                   ***************************986 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 ?   -2.0   0.0       2.4   3.9e+03      33      56 ..     202     225 ..     189     226 .. 0.79
   2 !   58.4   0.0   3.3e-19   5.3e-16       2      67 .]     352     419 ..     351     419 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                                   -HSSCHHHHHHHHHHHHHHHHHHH CS
                         HisKA  33 lteelkeyletiesearrldhlve 56 
                                   l+e++k+  e i+s ++  + +++
  gi|91774050|ref|YP_566742.1| 202 LSEKVKRKTEMIKSASEKYSVIIN 225
                                   789999999999999999999988 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 3.3e-19
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   +++f+ +++HELrtPL++ +g++e++  e  g+l++++k+yl+ ++ ++++l++l++++L +s+ie+g
  gi|91774050|ref|YP_566742.1| 352 QSEFIHNISHELRTPLNSTIGFSEMMITEvlGPLNDKQKKYLNNVKISGKHLLSLINEILNISKIENG 419
                                   799***********************88889***********************************87 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 !   58.5   0.3   3.9e-19   6.4e-16      54     223 ..       2     169 ..       1     171 [. 0.85
   2 ?   -3.5   0.0       3.5   5.8e+03     167     199 ..     202     232 ..     195     240 .. 0.64

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 3.9e-19
                                   HHTTSSSEEESSEB--HHHHTTEEEESESEEE.EEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                     SBP_bac_3  54 lksgkvDiaiaaititpeReekvdFsqpyfsa.gqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk.. 131
                                   l++g++D++i ++ +t+eR ek+d+s+ y+++  ++ +vr++     ++i s  dL gk +  +++  + +++ e++ +  
  gi|91774050|ref|YP_566742.1|   2 LENGEIDLII-TMGYTKERHEKYDLSEEYMVSdWVQTYVRSG-----TEIHSAYDLDGKNISGSKNGISIAWFDEYATRye 76 
                                   89********.7******************994467777744.....4688888****************9*998666586 PP

                                   .TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHH CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3 132 .gaeivefdtleealqaLkngrvdavvadspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelka 211
                                    + e +e+ + +ealq L++g + a v+ ++    + ++ +   + +  e++    ya+a + ++++L +ai+k lae+k 
  gi|91774050|ref|YP_566742.1|  77 iNYEYIETRSTTEALQYLEDGIAYASVVPKTLGTAHENEFDIVGAPI--ESYPIRFYAAASKGNNTDLIQAIDKNLAEMKR 155
                                   66666799***************999999998877666666666666..99999999999999*****************9 PP

                                   TT..HHHHHHHHHH CS
                                   xx..xxxxxxxxxx RF
                     SBP_bac_3 212 dg..tlakisekWf 223
                                   d    +++i+ kW+
  gi|91774050|ref|YP_566742.1| 156 DDnsNYNAIATKWL 169
                                   8622699******8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.5
                                   HHHCCGCCEEEEECGGCECEEEEEEETTTHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3 167 vkknpdkkvvlveeplsseeyaiavrkgdseLr 199
                                   + ++ + k ++   +++se+y ++++kg++  +
  gi|91774050|ref|YP_566742.1| 202 LSEKVKRKTEM--IKSASEKYSVIINKGNDGIV 232
                                   44444444444..67788899999999988766 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.2   8.3e-13   1.3e-09       2     104 .]     229     330 ..     228     330 .. 0.79
   2 ?   -1.5   0.0       1.8   2.9e+03      60      91 ..     419     451 ..     391     457 .. 0.68

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 8.3e-13
                         PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk....kerevevvlirknget 75 
                                   dgi+i  +++  l ++N+ ++++ Gy++++++g+++++ +  +++ e  +  r+++    k      +++e+ li +++  
  gi|91774050|ref|YP_566742.1| 229 DGIVI--EQNDKLkFVNPRFAKMVGYDANDIIGQPFSEYVqnHHKNELTNINRKLW----KsegpADHRYEISLISNENDI 303
                                   89999..4444566**************************5444444444444444....3455699************** PP

                         PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                   ++v+++ + +  +++  +   +++rDite
  gi|91774050|ref|YP_566742.1| 304 IPVEISSTILNYEGKSSIV--SVIRDITE 330
                                   **********777766666..*******8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                         PAS_9  60 kerevevvlirkngetfwvlltaspvkdd.dge 91 
                                    e e e+++++   +   v++ ++p+  + ++e
  gi|91774050|ref|YP_566742.1| 419 GEVELELDEVDIYTTVEDVEMLMAPILAEnKNE 451
                                   456777777777777888999999997773444 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     8e-09   1.3e-05       1      55 [.     218     272 ..     218     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8e-09
                         PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                   e++  +++  +dgi+ +  +++ + +vN++++++ Gy+ +d++g+++ ++++ ++ +
  gi|91774050|ref|YP_566742.1| 218 EKYSVIINKGNDGIV-IEqNDK-LKFVNPRFAKMVGYDaNDIIGQPFSEYVQNHHKN 272
                                   6888999999*****.663556.************************9888777655 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   2.8e-08   4.6e-05       4      98 ..     468     573 ..     465     576 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.8e-08
                   HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek.....kklesskskkeehGiGlk 72 
                                   l l  il n+L NAi  + +    ++ I + ++  +++l  +i+ + +g       ++     +   ++++k++  G+Gl+
  gi|91774050|ref|YP_566742.1| 468 LKLKQILYNILSNAIKFSPE----NENIIMDIKVIDGKLQTNITDKGKGlsekeqaNIfqpfvQLDDEHSEKQKGTGLGLT 544
                                   568899*********88766....45799999999999999999997776655444114334233337789999******* PP

                   HATPase_c_5  73 sireivkkykgnlsieaedg...lFtlsv 98 
                                    +++ v+ +kg+++i+ e+g   +F+ ++
  gi|91774050|ref|YP_566742.1| 545 IVKRFVQLHKGKIWIDSEEGkgtTFCFTI 573
                                   ****************9987555666665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.3     7e+03      30      65 ..     140     174 ..     128     179 .. 0.76
   2 !   21.2   0.0   1.6e-07   0.00026      15     109 ..     237     332 ..     228     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.3
                         PAS_4  30 appeellGktlaellpeedaarleralrrvlegeep 65 
                                    +  ++++k lae+  + d  ++ ++ +++leg+++
  gi|91774050|ref|YP_566742.1| 140 TDLIQAIDKNLAEMKRD-DNSNYNAIATKWLEGKKT 174
                                   56678889999997554.999999999999999876 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.6e-07
                         PAS_4  15 grvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...pgeerhyelrllPlrdes 92 
                                    +  ++N+++a+++g+++ +++G+++ e++  +++ +l ++ r+++++e p++   e  l   + +  ++e++ + l + +
  gi|91774050|ref|YP_566742.1| 237 DKLKFVNPRFAKMVGYDANDIIGQPFSEYVQNHHKNELTNINRKLWKSEGPADHRYEISLisnENDIIPVEISSTIL-NYE 316
                                   566789************************************************99999998777888888888887.899 PP

                         PAS_4  93 GevigvlvisrDiTerr 109
                                   G+   ++ ++rDiTe +
  gi|91774050|ref|YP_566742.1| 317 GK-SSIVSVIRDITEHK 332
                                   99.9999999****976 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.1e-07   0.00083       3      82 ..     241     319 ..     239     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.1e-07
                         PAS_3   3 yvserveeilGyspeellgk.veswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +v++r+ +++Gy++++++g+ ++++ +  h  ++ +++++l+++ ++ ++   e+ ++    +++ ve + +++ + +gk 
  gi|91774050|ref|YP_566742.1| 241 FVNPRFAKMVGYDANDIIGQpFSEYVQNHHKNELTNINRKLWKS-EGPADHRYEISLISNENDIIPVEISSTIL-NYEGKS 319
                                   89******************99********************77.57777888899999999999999999999.666664 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.3e-06    0.0021      19     113 .]     235     328 ..     218     328 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-06
                                   TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-E.CCCCEEEECTTSSEEEEEEEEEEEEE CS
                           PAS  19 edgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgees.rageisfklrdgrpihlevraspvrd 98 
                                    + +  +vN+ ++++ G+++++++g+++++++ + +  el  + ++l ++  ++ + +eis+    + +i++e+  + +  
  gi|91774050|ref|YP_566742.1| 235 QNDKLKFVNPRFAKMVGYDANDIIGQPFSEYVQNHHKNELTNINRKLWKSEGPAdHRYEISLISNENDIIPVEISSTILNY 315
                                   5666668************************98765556666666666555544256777777766666666666554444 PP

                                   TTEEEEEEEEEEEES CS
                           PAS  99 aggeilgflgvlrdi 113
                                   +g+    ++ v+rdi
  gi|91774050|ref|YP_566742.1| 316 EGKS--SIVSVIRDI 328
                                   4443..888888886 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.9   6.4e+03      38      78 ..     120     161 ..     115     166 .. 0.74
   2 !   14.7   0.0   1.6e-05     0.026       8     115 .]     231     336 ..     224     336 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.9
                         PAS_7  38 gvpleel.lrynaergefgagdveaeverrlaaaragkphsf 78 
                                   g+p+e+  +r+ a+  + ++ d  +++++ la++++++++++
  gi|91774050|ref|YP_566742.1| 120 GAPIESYpIRFYAAASKGNNTDLIQAIDKNLAEMKRDDNSNY 161
                                   566555437777777777788888999999999999887766 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.6e-05
                         PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdgrvi 88 
                                   i v+ ++++L ++N r+ ++ ++ ++ + +g p++e ++  ++++  +   ++ ++ +    a ++ + s+  +++d   +
  gi|91774050|ref|YP_566742.1| 231 I-VIEQNDKLKFVNPRFAKMVGYDANDI-IGQPFSEYVQNHHKNELTN---INRKLWKSEGPADHRYEISLISNENDIIPV 306
                                   4.78999*********************.********99775555544...333332333334444444444444455555 PP

                         PAS_7  89 evrgnpl...pdgGfVttytDiTerrraee 115
                                   e+ ++ l    +  +V++  DiTe++++e+
  gi|91774050|ref|YP_566742.1| 307 EISSTILnyeGKSSIVSVIRDITEHKQHEQ 336
                                   6666666443345699*********99986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.1e-05      0.15      39     112 ..     477     553 ..     453     573 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                   HATPase_c_2  39 actNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeep........keslkegGrGlalikglvD 110
                                   +++Na++   +   ++ + + +++ +++l+  ++D+G+g  + e+++   +  p        +e++k  G+Gl ++k++v 
  gi|91774050|ref|YP_566742.1| 477 ILSNAIKFSPE---NENIIMDIKVIDGKLQTNITDKGKGlSEKEQANI-FQ--PfvqlddehSEKQKGTGLGLTIVKRFVQ 551
                                   44555555554...56788999999**************655554432.22..223456877999999**********997 PP

                   HATPase_c_2 111 ev 112
                                     
  gi|91774050|ref|YP_566742.1| 552 LH 553
                                   65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 4138.61
//
Query:       gi|91774051|ref|YP_566743.1|  [L=682]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-32  111.5   0.3    5.9e-31  107.6   0.0    2.1  2  SBP_bac_3    Bacterial extracellular solute-binding proteins,
    3.3e-28   98.4   2.3    1.4e-26   93.2   0.3    2.9  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      2e-17   63.0   0.1      6e-17   61.5   0.1    1.9  1  HisKA        His Kinase A (phospho-acceptor) domain
    2.1e-10   40.8   2.0    3.1e-10   40.2   0.5    2.2  2  PAS_9        PAS domain
    1.8e-07   31.1   0.1    4.6e-07   29.8   0.1    1.7  1  PAS          PAS fold
    4.6e-07   29.7   1.6    4.6e-07   29.7   1.6    3.6  3  HATPase_c_5  GHKL domain
    6.7e-07   29.2   0.0    1.6e-06   28.0   0.0    1.6  1  PAS_8        PAS domain
    2.6e-05   24.4   0.0    5.6e-05   23.4   0.0    1.6  1  PAS_4        PAS fold
     0.0054   16.7   0.0      0.033   14.1   0.0    2.1  2  NMT1         NMT1/THI5 like
     0.0091   16.3   0.0      0.031   14.6   0.0    2.0  1  PAS_3        PAS fold
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.029   14.2   0.0    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.055   13.4   0.0       0.12   12.3   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
       0.21   11.6   2.7       0.29   11.1   0.7    2.3  2  DUF4083      Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   4.3e-34   5.9e-31       1     224 [.      42     262 ..      42     263 .. 0.92
   2 ?    1.9   0.1     0.094   1.3e+02     132     206 ..     538     613 ..     498     615 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 4.3e-34
                                   EEEEE-S-BTTTBEE-TTS-EESHHHHHHHHHHHHCT-EEEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTEEE.ES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                     SBP_bac_3   1 lrvgvdadypPfsykdengeltGfdvdlakaiakrlgvkvefvpvswdelipalksgkvDiaiaaititpeReekvdF.sq 80 
                                   +r+g+ ++y+P  y+d+ng ++Gf+vd+++ ia++ g+++e+vp +w+e i++l+sg++ ++i ++ +t+eR ek+d+ s+
  gi|91774051|ref|YP_566743.1|  42 VRIGI-EEYAPIAYVDDNGFVKGFNVDIIEYIAREEGWEIEYVPSTWSECIDNLESGEINLII-TMIYTEERDEKYDYaSE 120
                                   699**.6********************************************************.799**********8688 PP

                                   ESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC...TSEEEEESSHHHHHHHHHTTSSSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3  81 pyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk...gaeivefdtleealqaLkngrvdavva 158
                                   p+ +   +l++r++  + i si+   dL+g+ +   ++  + +++ke++++   + e++e+++ ++ l+ + +g + av+ 
  gi|91774051|ref|YP_566743.1| 121 PFITDWAQLFIRSN--TGIHSIT---DLEGTIISGITDDQTTTWFKEHAERyelEYELIETNSVSSSLEPIDDGTATAVIL 196
                                   ************44..4555555...*****9999999888889999776689999999********************** PP

                                   EHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHH..TTHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                     SBP_bac_3 159 dspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelka..dgtlakisekWfg 224
                                   ++++ + l k+++ + + +  e+l  e ya+ +  +d+e + +i k l+ +k+  d  ++  ++kWf 
  gi|91774051|ref|YP_566743.1| 197 SRISGNALSKEHGIEGAPI--ESLPIEIYAATLEGNDQEILVTIGKHLEVMKEeeDSFYYTTYDKWFP 262
                                   *******************..******************************972255699******96 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.094
                                   TSEEEE.ESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHH CS
                                   xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3 132 gaeive.fdtleealqaLkngrvdavvadspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkal 206
                                   +++ +e   ++e+ ++++ ++r+  +   +  + +++k++p+++++ +  +  ++++ i v+++++   ++++k +
  gi|91774051|ref|YP_566743.1| 538 QISKNElIFNIENGIEKIYADRIKIISILQNLVDNAIKHSPKNEKIFINITTKDKNLQICVKNKGKGITQEMQKEI 613
                                   334444368999******************************9999999999999999999999999988888876 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 ?    4.0   0.1      0.05        69       5      55 ..     349     402 ..     345     443 .. 0.65
   2 !   93.2   0.3   9.9e-30   1.4e-26       2     110 ..     558     667 ..     557     669 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.05
                                   HHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT CS
                     HATPase_c   5 rLrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlk 55 
                                    ++ +++n + Na+k+   + +++ i+ + ++++++ +   ++nG  ip+e+  
  gi|91774051|ref|YP_566743.1| 349 LIKTLLNNCINNALKNeviTRYEQLIQGRSETEQQYETNFFSHNGENIPVEINS 402
                                   567899999999999855433454444444433344444588999999998766 PP

  == domain 2  score: 93.2 bits;  conditional E-value: 9.9e-30
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d +++  i++nlvdNa+k+++k+++i+++i++++++l+i v++ G+Gi++e++k++f++f+q ++  + ++ gtGlGl+iv
  gi|91774051|ref|YP_566743.1| 558 DRIKIISILQNLVDNAIKHSPKNEKIFINITTKDKNLQICVKNKGKGITQEMQKEIFTPFVQvEKFISKEYRGTGLGLAIV 638
                                   6678889************99**********8778***************************98899999*********** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                   k +v l++G+iw+es  g+ t+f+ft+p+
  gi|91774051|ref|YP_566743.1| 639 KHYVHLHNGKIWIESVLGEETSFIFTIPQ 667
                                   **************************996 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 !   61.5   0.1   4.3e-20     6e-17       1      67 []     443     511 ..     443     511 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 4.3e-20
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   s++ fla+++H+LrtPL+ai+g++++L  e  g+l+e++ +y + i  ++r l+++++d+L +s+ieag
  gi|91774051|ref|YP_566743.1| 443 SKNTFLASMSHDLRTPLNAIIGYSDLLLTEsvGDLNEKQIKYTNNILISGRLLLNIINDILNISKIEAG 511
                                   6899**********************977779***********************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.5   2.2e-13   3.1e-10       2     104 .]     321     422 ..     320     422 .. 0.91
   2 ?   -3.5   0.0         9   1.2e+04      53      73 ..     525     551 ..     517     572 .. 0.48

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.2e-13
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvl 79 
                                   dgi+i+  +  i++aN +++++lGy ++ ++ + + +++ +++  ne + ++ + ++    +e+++e+ +   nge ++v+
  gi|91774051|ref|YP_566743.1| 321 DGIIIV-QNYLIVFANLKFAEMLGYEKDRLIKTLLNNCI-NNALKNEVITRYEQLIQGrseTEQQYETNFFSHNGENIPVE 399
                                   899998.666588**************************.999999999998888888999******************** PP

                         PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                   ++ s ++  +++ v+   i+rDit+
  gi|91774051|ref|YP_566743.1| 400 INSSLIHYRGNRAVM--YIMRDITK 422
                                   ******999888888..9*****95 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9
                         PAS_9  53 aleqgrk......kerevevvlirkng 73 
                                   +l++  +      +    e+++  +ng
  gi|91774051|ref|YP_566743.1| 525 ILKEVNElvktkvQISKNELIFNIENG 551
                                   333333222224444444444444444 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   3.3e-10   4.6e-07       2     113 .]     311     420 ..     310     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.3e-10
                                   HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC. CS
                           PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl. 81 
                                   +++ ++e + d+i++v  +  i+++N +++e+lG++ + ++   l+  i++    e+  ++eql++ ++e +++  +  + 
  gi|91774051|ref|YP_566743.1| 311 KYSVLVEESNDGIIIV-QNYLIVFANLKFAEMLGYEKDRLIKTLLNNCINNALKNEVITRYEQLIQGRSETEQQYETNFFs 390
                                   7999************.*****************************99999866689999999999888877665555556 PP

                                   TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                    +g+ i++e++ s +  +g +   ++ ++rdi
  gi|91774051|ref|YP_566743.1| 391 HNGENIPVEINSSLIHYRGNR--AVMYIMRDI 420
                                   ******************998..899999997 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.58     8e+02       7      20 ..     351     364 ..     346     394 .. 0.66
   2 ?    4.1   0.6     0.032        44      26      52 ..     528     554 ..     518     561 .. 0.81
   3 !   29.7   1.6   3.4e-10   4.6e-07       3      89 ..     559     653 ..     557     665 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.58
                   HATPase_c_5   7 cvilgnlLdNAiea 20 
                                    ++l n ++NA+  
  gi|91774051|ref|YP_566743.1| 351 KTLLNNCINNALKN 364
                                   45666777776654 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.032
                   HATPase_c_5  26 eekrfIrltvrekkksliisieNsyeg 52 
                                   e ++ ++ +v+ +k+ li++ieN +e+
  gi|91774051|ref|YP_566743.1| 528 EVNELVKTKVQISKNELIFNIENGIEK 554
                                   358899*****************9876 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 3.4e-10
                   HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..............ekkklesskskkeehGi 69 
                                   ++ +++il nl dNAi  + k e    +I +++++k+k+l i ++N+ +g              + +k+   +++ +  G+
  gi|91774051|ref|YP_566743.1| 559 RIKIISILQNLVDNAIKHSPKNE----KIFINITTKDKNLQICVKNKGKGitqemqkeiftpfvQVEKF--ISKEYRGTGL 633
                                   56799***********9998866....6888899999**********8887776665444443333444..35678999** PP

                   HATPase_c_5  70 Glksireivkkykgnlsiea 89 
                                   Gl  +++ v+ ++g+++ie 
  gi|91774051|ref|YP_566743.1| 634 GLAIVKHYVHLHNGKIWIES 653
                                   ****************9986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.2e-09   1.6e-06       1      47 [.     310     356 ..     310     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                         PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgq 47 
                                   e++  l+e s+dgi++v ++  iv++N +++e+lGy+ + l+  ll +
  gi|91774051|ref|YP_566743.1| 310 EKYSVLVEESNDGIIIVQNYL-IVFANLKFAEMLGYEkDRLIKTLLNN 356
                                   68999***********98666.***************55555544444 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.1e-08   5.6e-05       2     110 .]     317     425 ..     316     425 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.1e-08
                         PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...pgeer 79 
                                   + ++d+++++  ++ +++aN  +ae++g++ ++l+   l    +  ++ ++ + ++++++g+   e++ e+++   +ge  
  gi|91774051|ref|YP_566743.1| 317 EESNDGIIIV-QNYLIVFANLKFAEMLGYEKDRLIKTLLNNCINNALKNEVITRYEQLIQGRSETEQQYETNFfshNGENI 396
                                   6677777775.567799**************************************************************** PP

                         PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerrr 110
                                   ++e++ + ++  +G  ++v+ i+rDiT r++
  gi|91774051|ref|YP_566743.1| 397 PVEINSSLIH-YRGN-RAVMYIMRDITKRKQ 425
                                   *********6.5787.8***********985 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.4e-05     0.033      76     155 ..     128     203 ..     122     243 .. 0.83
   2 ?   -0.9   0.0      0.96   1.3e+03      54     100 ..     439     486 ..     426     499 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                                   EEEEECCC--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHH CS
                          NMT1  76 glivlkdsgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegve 155
                                   +l+ + ++gi+s++DL+G  i +  ++ + + +k+  + + ++++ +++ +v  +s  +++ +g++ a+i  +  + g+ 
  gi|91774051|ref|YP_566743.1| 128 QLFIRSNTGIHSITDLEGTIISGITDDQTTTWFKEHAERYELEYELIETNSV--SSSLEPIDDGTATAVI--LSRISGNA 203
                                   788999*****************************************99777..55558*****999998..44445555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.96
                                   HHHHHTT--EEEEEEEE-S--EEEEEECCC-.-SSGGGGTTSEEEE-S CS
                          NMT1  54 laarakglpvvsvaallqeplsglivlkdsg.ikspkDLkGkrigyvg 100
                                   +a ++k+  + s    l++pl+++i   d   ++s+ DL+ k+i y++
  gi|91774051|ref|YP_566743.1| 439 VANHSKNTFLASMSHDLRTPLNAIIGYSDLLlTESVGDLNEKQIKYTN 486
                                   556666666777777789999999999999999**********99986 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.2e-05     0.031       2      82 ..     332     412 ..     331     417 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                         PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegey..RirrkdGeyrwveararvirdeng 80 
                                   ++++ ++ e+lGy+++ l+++   + +++     ++v + ++++++++++ e++y   ++  +Ge + ve   + i+++ +
  gi|91774051|ref|YP_566743.1| 332 VFANLKFAEMLGYEKDRLIKT--LLNNCINNALKNEVITRYEQLIQGRSETEQQYetNFFSHNGENIPVEINSSLIHYRGN 410
                                   78999****************..**********************888877766511689999999999999999966655 PP

                         PAS_3  81 kp 82 
                                   + 
  gi|91774051|ref|YP_566743.1| 411 RA 412
                                   54 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 ?   14.2   0.0   2.1e-05     0.029       7      62 ..     566     623 ..     560     644 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                   HATPase_c_3   7 laelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalr.latsske 62 
                                   l  lvdN++  + +n  + i++ +++ k+ +i+++  GkG+++e  k+ ++ + + +k 
  gi|91774051|ref|YP_566743.1| 566 LQNLVDNAIKHSPKNekIFINITTKD-KNLQICVKNKGKGITQEMQKEIFTpFVQVEKF 623
                                   6789*****96666633555555654.689*************9999988624444444 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     9e-05      0.12      42     109 ..     568     642 ..     551     646 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9e-05
                   HATPase_c_2  42 Navehayleap.egpvevrlesdeealtvevaDsGpg.fdpetlpdpteeep........keslkegGrGlalikglv 109
                                   N v  a ++ p ++++ + ++ +++ l+++v+++G+g  +  +++  t   p        + + +  G+Gla++k++v
  gi|91774051|ref|YP_566743.1| 568 NLVDNAIKHSPkNEKIFINITTKDKNLQICVKNKGKGiTQEMQKEIFT---PfvqvekfiSKEYRGTGLGLAIVKHYV 642
                                   555555555555789**********************65555444333...234578899899999*********998 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00021      0.29       5      34 ..     273     302 ..     271     312 .. 0.73
   2 ?   -1.9   0.1       2.5   3.4e+03      21      41 ..     412     429 ..     411     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                       DUF4083   5 liyliivivLilllvfsftlfiRrvvsrsa 34 
                                   +i+ i+ i  +  +++++ l++Rr++++ a
  gi|91774051|ref|YP_566743.1| 273 IIIIIASITTLTVIFIAVNLILRRTIQKRA 302
                                   4566666667778999************55 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                       DUF4083  21 sftlfiRrvvsrsaakkkksk 41 
                                   +++ ++R +  r   k+++++
  gi|91774051|ref|YP_566743.1| 412 AVMYIMRDITKR---KQQEQD 429
                                   68899**99999...445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4480.17
//
Query:       gi|91774052|ref|YP_566744.1|  [L=616]
Description: metal-dependent phosphohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   47.8   0.0    2.9e-12   46.9   0.0    1.5  1  HD        HD domain
     0.0084   15.6   0.0      0.017   14.6   0.0    1.4  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   3.2e-16   2.9e-12       1      87 [.      53     145 ..      53     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 3.2e-16
                                   HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH.......HHH...CTCCHHHHHHHHHHHHHH CS
                            HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk.......eee...fekflaHekvgaeilrev 70 
                                   r+eHsl++++ a  l++++g+ +ed  +l+la+LlHD+G+  f++a e         +      + f++He ++ +i++ev
  gi|91774052|ref|YP_566744.1|  53 RFEHSLGTMHTASLLGRSVGLdNEDIMKLRLAGLLHDVGHSAFSHAVESVlkrdpaiQ-PkmcENCFVDHEAFTKYIISEV 132
                                   79*******************************************9999986665542.05899***************99 PP

                                   HHHHHHHHHHHHHHHHT CS
                            HD  71 ekrlgldledvaklire 87 
                                      ++    ++a+ +r 
  gi|91774052|ref|YP_566744.1| 133 IPEDN----IIARYVRD 145
                                   65552....45555555 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     142 ..      54     102 ..      46     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-06
                                   HHHHHHHHHHHHHHHHHTT-S-H..HHHHHHHHTTTHHHHHHHHHSHHH CS
                          HDOD  96 wehslavAlvarelaeelgledp..eeaflaGLLhdiGklvllsllpee 142
                                    ehsl +  +a  l +++gl+++   ++ laGLLhd+G  ++ ++++  
  gi|91774052|ref|YP_566744.1|  54 FEHSLGTMHTASLLGRSVGLDNEdiMKLRLAGLLHDVGHSAFSHAVESV 102
                                   58******************996568999**********9999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 4469.91
//
Query:       gi|91774053|ref|YP_566745.1|  [L=250]
Description: methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-14   52.8   0.0    4.5e-12   46.2   0.0    2.1  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    2.9e-10   40.1   0.0    4.4e-10   39.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.2e-08   35.5   0.0    3.6e-08   34.0   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    4.7e-08   33.0   0.0      7e-08   32.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.7e-07   31.2   0.0    5.8e-07   30.1   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    3.3e-07   30.0   0.0    4.9e-07   29.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.3e-06   27.7   0.0    1.9e-06   27.1   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.9e-06   27.3   0.0      6e-06   26.3   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0002   20.9   0.1    0.00036   20.1   0.1    1.3  1  MTS              Methyltransferase small domain
     0.0044   16.9   0.0     0.0081   16.0   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
     0.0096   15.9   0.0      0.016   15.2   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.017   14.7   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.013   16.2   0.0      0.024   15.4   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      0.014   14.9   0.0      0.054   13.0   0.0    1.8  2  Methyltransf_4   Putative methyltransferase
      0.016   14.5   0.0      0.032   13.5   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   3.8e-15   4.5e-12      24     177 ..      79     225 ..      57     232 .. 0.90
   2 ?    5.3   0.0     0.011        13     228     246 ..     231     249 ..     222     250 .] 0.84

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.8e-15
                         GCD14  24 lytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvcke 104
                                   +  +Di +i  +  l++   v+++GtGsg l+ ++  ++a   ++ +fe  ++ ae are+ r+ +l+ +v v+  ++  e
  gi|91774053|ref|YP_566745.1|  79 IMPKDIGMILGYTGLNKNDTVLDAGTGSGILAMYLG-SIA--KRVLSFEVRDDFAEVARENIRRAGLD-NVEVRCGNIVDE 155
                                   4568***************************99986.555..589*********************97.699999999988 PP

                         GCD14 105 GfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrty 177
                                      +e+++k D v LD       +p + + l + gg l ++sP +eq     +a++e +f e++t+e   r  
  gi|91774053|ref|YP_566745.1| 156 V--KELDEKFDIVTLDTIDSATIVPYIPSIL-NPGGFLVTYSPFLEQTALIRKAIAEIDFFEVRTIECIERAM 225
                                   6..59************************99.99*********************************988865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                         GCD14 228 llkPvselkghtgyLtfat 246
                                    ++P +  +ghtgy+t a+
  gi|91774053|ref|YP_566745.1| 231 GTRPSTSRVGHTGYITIAR 249
                                   579999**********997 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   3.7e-13   4.4e-10       2     113 ..      94     196 ..      93     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3.7e-13
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgp.kaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                   +k+ +vlD+G+G+G l+  l     +  ++v +++   +  e+Aren ++ gldnve++ g+i +  ++l  dekfD+++ 
  gi|91774053|ref|YP_566745.1|  94 NKNDTVLDAGTGSGILAMYLG----SiAKRVLSFEVRDDFAEVARENIRRAGLDNVEVRCGNIVDeVKEL--DEKFDIVTL 168
                                   7999*********87766655....42456***********************************87765..8*****999 PP

               Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr 113
                                   +     + d++ i   i++ l+pgg l++ +p 
  gi|91774053|ref|YP_566745.1| 169 D-----TIDSATIVPYIPSILNPGGFLVTYSPF 196
                                   5.....779999999999999999999877765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.7   4.4e+03      65      91 ..      47      74 ..      17      78 .. 0.63
   2 !   34.0   0.0     3e-11   3.6e-08       1      72 [.      99     169 ..      99     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.7
                                  EEEEEEEST.GGGSSHHHHHHHHHHHHH CS
               Methyltransf_25 65 fDlvvssga.lhhlsdedlekalkeiar 91
                                     vvs ++   +++ +++++++++++r
  gi|91774053|ref|YP_566745.1| 47 GETVVSHMGqTFVIQLPRMPDFFRHAKR 74
                                  3445554554666777888888888877 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 3e-11
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBSSSTTTEEEEEEES CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgda.edlpfedgsfDlvvssg 72 
                                   vLd+G+G+G l+++l      ++v+ +++ +++ e are+++++gl nve+++g++ +++++ d++fD+v++  
  gi|91774053|ref|YP_566745.1|  99 VLDAGTGSGILAMYLGSIA--KRVLSFEVRDDFAEVARENIRRAGLdNVEVRCGNIvDEVKELDEKFDIVTL-D 169
                                   9**************9885..9**********************************777***********98.3 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   5.8e-11     7e-08      59     132 ..      81     151 ..      72     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.8e-11
                                   HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                          PCMT  59 phmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                   p+ ++++l +  l+k + vL+ G+GsG+l+  l  + +++   +s e   +++e a++n+++ +l+nv v++g 
  gi|91774053|ref|YP_566745.1|  81 PKDIGMILGYTGLNKNDTVLDAGTGSGILAMYLGSIAKRV---LSFEVRDDFAEVARENIRRAGLDNVEVRCGN 151
                                   556789999*******************999999998765...5****************************96 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.8e-10   5.8e-07       1      68 [.     100     169 ..     100     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.8e-10
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC.TSS-TT-EEEEEEE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaek.lpfednsfDlvvss 68 
                                   Ld+G+G+G+la +l + ++rv+ +++ + + ++a+e+++++gl +ve++++++ + ++  d++fD+v++ 
  gi|91774053|ref|YP_566745.1| 100 LDAGTGSGILAMYLGSIAKRVLSFEVRDDFAEVARENIRRAGLdNVEVRCGNIVDeVKELDEKFDIVTLD 169
                                   8**************999***********************************97589999******764 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.1e-10   4.9e-07     160     281 ..      94     217 ..      87     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.1e-10
                          PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk..eekadvivaNILae 237
                                   +++++vlD GtGSGiLa+    + ak+v+   + +   +va+eN+++ ++++ +++  +  + +k  +ek+d++    + +
  gi|91774053|ref|YP_566745.1|  94 NKNDTVLDAGTGSGILAMYLGSI-AKRVLSFEVRDDFAEVARENIRRAGLDNvEVRCGNIVDEVKelDEKFDIVTLDTIDS 173
                                   6789************9876665.899*****988888**********999866665444444434789*****9988877 PP

                          PrmA 238 vlielaedikklvkeggllilSGilkekaeevaealeq..gfelee 281
                                   +   +++ i +++++gg l++     e++  +++a+++  +fe+ +
  gi|91774053|ref|YP_566745.1| 174 A--TIVPYIPSILNPGGFLVTYSPFLEQTALIRKAIAEidFFEVRT 217
                                   5..6789999999****99987777788888888775443666655 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.6e-09   1.9e-06      21      74 ..      86     141 ..      79     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.6e-09
                                   HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..T CS
                        RrnaAD  21 eIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..k 74 
                                    Il  + l++++tvl+ g+G Gil   L  +ak v ++E + ++a++ +++++   
  gi|91774053|ref|YP_566745.1|  86 MILGYTGLNKNDTVLDAGTGSGILAMYLGSIAKRVLSFEVRDDFAEVARENIRraG 141
                                   577778899****************************************9887444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   5.1e-09     6e-06      13      87 ..      94     167 ..      90     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.1e-09
               Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk.eee.vdtvv 87 
                                   +k+++v+D Gt  g+l++yl   ++ak+v+  ++++   e a+eni++agl d++evr+++ ++++k  +e +d+v+
  gi|91774053|ref|YP_566745.1|  94 NKNDTVLDAGTGSGILAMYLG--SIAKRVLSFEVRDDFAEVARENIRRAGL-DNVEVRCGNIVDEVKeLDEkFDIVT 167
                                   6899****************8..799************************9.68**********9994223477665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1     3e-07   0.00036      31     101 ..      95     166 ..      82     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEE CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdli 101
                                   ++++vlD G+G G+l++ l +  ++  v  ++v     e+a+en+++ +l+ vev+  ++++ev+  ++kfd++
  gi|91774053|ref|YP_566745.1|  95 KNDTVLDAGTGSGILAMYLGSIAKR--VLSFEVRDDFAEVARENIRRAGLDnVEVRCGNIVDEVKelDEKFDIV 166
                                   4678****************99888..88999999999**************************9777999987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.8e-06    0.0081      20      87 ..      93     167 ..      74     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.8e-06
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae................kakkaqkdqfdeqeaaepqgkfd 84 
                                   l+++  vLd G+G+Gil+ +l    + v  ++ ++   e a+                ++           e +e ++kfd
  gi|91774053|ref|YP_566745.1|  93 LNKNDTVLDAGTGSGILAMYLGSIAKRVLSFEVRDDFAEVARenirragldnvevrcgNIVD---------EVKELDEKFD 164
                                   79999****************55544444444444333333343344444433322221111.........2334445666 PP

               Methyltransf_23  85 lIv 87 
                                   +++
  gi|91774053|ref|YP_566745.1| 165 IVT 167
                                   665 PP

>> Methyltransf_32  Methyltransferase 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     0.016      24      82 ..      94     145 ..      85     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
               Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrl 82 
                                   +++ tv+D+G G g L+  l +       +v++++++++ +e a++  ++ g  + +++
  gi|91774053|ref|YP_566745.1|  94 NKNDTVLDAGTGSGILAMYLGS----IAKRVLSFEVRDDFAEVARENIRRAG--L-DNV 145
                                   5789******************....789****************9999988..4.444 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-05     0.017       7      94 ..      94     177 ..      90     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87 
                                   ++++t+lD+ ++ G    ++  +   +++v+  ++ +  ++   en++r g+ n+ v ++ +    k l  e+fD + lD 
  gi|91774053|ref|YP_566745.1|  94 NKNDTVLDAGTGSGILAMYLGSI---AKRVLSFEVRDDFAEVARENIRRAGLDNVEVRCGNIVDEVKELD-EKFDIVTLDT 170
                                   6799**********999999999...899********************************998878777.59*******9 PP

                                   --CCGGG CS
               Methyltr_RsmB-F  88 PCsgtgv 94 
                                     s+t+v
  gi|91774053|ref|YP_566745.1| 171 IDSATIV 177
                                   9999987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0     2e-05     0.024       1      72 [.     100     168 ..     100     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvva 72 
                                   L+ G+G+G l+++l      ++++  ++  ++ e a+e +++ +  +n +v+  ++ ++ +  +  ++fD+v++
  gi|91774053|ref|YP_566745.1| 100 LDAGTGSGILAMYLGSI--AKRVLSFEVRDDFAEVARENIRRAGL-DNVEVRCGNIVDEVK--EldEKFDIVTL 168
                                   89************999..**************999999988885.444444444444444..4449****985 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.5e-05     0.054       3      66 ..      97     158 ..      95     172 .. 0.82
   2 ?   -0.7   0.0       0.7   8.3e+02     102     137 ..     179     214 ..     171     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-05
                                   EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHH CS
                Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvlle 66 
                                    +vl+ G+G+G + + l      k +l  E+r +  + + ++i++ +l N+++ +g+ ++ ++e
  gi|91774053|ref|YP_566745.1|  97 DTVLDAGTGSGILAMYLGS--IAKRVLSFEVRDDFAEVARENIRRAGLDNVEVRCGNIVDEVKE 158
                                   5688888888876666665..57999*******************************9766544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.7
                                   HHHHHEEEEEEEEEEESHHHHHHHHHHHHHCSTTEE CS
                Methyltransf_4 102 elarvLkkgGvlelaTDveeyaeemlkvleeeplfe 137
                                    + ++L++gG+l++ + + e +  + k ++e + fe
  gi|91774053|ref|YP_566745.1| 179 YIPSILNPGGFLVTYSPFLEQTALIRKAIAEIDFFE 214
                                   566789999999999998888888888888876665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-05     0.032      51     138 ..      84     172 ..      68     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                   HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-....GGG---- CS
                          CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklld....yedldek 127
                                   + +il+  +l++ +t+Ld G+G G l+++  +    +v++  + ++ a++a++++ +++l ++vev+  +     ++ldek
  gi|91774053|ref|YP_566745.1|  84 IGMILGYTGLNKNDTVLDAGTGSGILAMYLGSI-AKRVLSFEVRDDFAEVARENIRRAGL-DNVEVRCGNivdeVKELDEK 162
                                   668899999***************999986555.669**********************5.67888865411116778889 PP

                                   -SEEEEES-GG CS
                          CMAS 128 vdrvvsvgafe 138
                                   +d +v+++ ++
  gi|91774053|ref|YP_566745.1| 163 FD-IVTLDTID 172
                                   98.66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1739.01
//
Query:       gi|91774054|ref|YP_566746.1|  [L=225]
Description: DNA repair and recombination protein RadB [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-36  123.5   0.2      1e-35  123.2   0.2    1.0  1  Rad51          Rad51
      1e-14   54.5   3.9    6.3e-14   51.9   3.9    1.9  1  ATPase         KaiC
    4.5e-13   49.3   0.1    5.4e-13   49.0   0.1    1.1  1  RecA           recA bacterial DNA recombination protein
    5.5e-08   32.8   0.0    8.1e-08   32.2   0.0    1.3  1  AAA_24         AAA domain
    1.8e-07   31.0   0.1    2.3e-07   30.7   0.1    1.1  1  Zot            Zonular occludens toxin (Zot)
      1e-06   28.5   0.0      2e-06   27.5   0.0    1.5  1  AAA_25         AAA domain
    2.7e-05   23.9   0.0    4.2e-05   23.3   0.0    1.2  1  SRP54          SRP54-type protein, GTPase domain
      3e-05   23.1   0.0    5.4e-05   22.3   0.0    1.4  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    7.1e-05   22.2   0.1    8.6e-05   21.9   0.1    1.1  1  DUF2075        Uncharacterized conserved protein (DUF2075)
     0.0009   18.8   0.1     0.0022   17.6   0.1    1.6  1  CobU           Cobinamide kinase / cobinamide phosphate guany
     0.0011   18.4   0.1     0.0026   17.2   0.1    1.5  1  PhoH           PhoH-like protein
     0.0049   17.4   0.1     0.0074   16.8   0.1    1.5  1  ABC_tran       ABC transporter
     0.0049   16.1   0.0     0.0079   15.4   0.0    1.3  1  ArsA_ATPase    Anion-transporting ATPase
     0.0058   16.0   0.9       0.36   10.1   0.0    2.2  2  DnaB_C         DnaB-like helicase C terminal domain
     0.0062   17.0   0.3      0.014   15.8   0.3    1.5  1  AAA            ATPase family associated with various cellular
     0.0089   15.8   0.0      0.016   15.0   0.0    1.4  1  IstB_IS21      IstB-like ATP binding protein
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.016   15.3   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.011   15.6   0.4      0.018   14.9   0.4    1.4  1  ATPase_2       ATPase domain predominantly from Archaea
      0.013   16.0   0.0      0.018   15.6   0.0    1.3  1  AAA_18         AAA domain
      0.015   15.4   0.3      0.036   14.2   0.3    1.7  1  DUF87          Helicase HerA, central domain
      0.015   14.8   0.0      0.022   14.3   0.0    1.2  1  RVT_1          Reverse transcriptase (RNA-dependent DNA polym
      0.018   14.8   0.5        1.8    8.3   0.1    2.4  2  DEAD           DEAD/DEAH box helicase
      0.044   13.7   0.1      0.056   13.4   0.1    1.3  1  AAA_31         AAA domain
      0.054   12.9   0.1        1.9    7.9   0.0    2.1  2  Pox_A32        Poxvirus A32 protein
      0.061   13.1   0.0       0.15   11.8   0.0    1.6  2  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
      0.064   13.5   0.1        0.1   12.9   0.1    1.4  1  AAA_22         AAA domain
      0.068   13.2   2.4        1.1    9.2   2.3    2.6  1  ResIII         Type III restriction enzyme, res subunit
       0.08   12.7   0.0       0.12   12.1   0.0    1.2  1  AAA_30         AAA domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   0.2   1.6e-38     1e-35      21     252 ..      10     224 ..       3     225 .] 0.92

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 1.6e-38
                                   -S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HHH CS
                         Rad51  21 tGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldkee 101
                                     +k lDelLgGG+e+g +t ifGe +sGkt +c +l++ +          +ka++idteg + ++r  +ia   + + ++
  gi|91774054|ref|YP_566746.1|  10 SSCKPLDELLGGGFESGVVTQIFGEAGSGKTNICLQLAIECVK------KGKKAIFIDTEG-LSADRFKQIA---GENARK 80 
                                   56899******************************99999853......4699*******7.99********...458899 PP

                                   HGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEE CS
                         Rad51 102 vlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvi 182
                                   + +++ +   ++ e+q++ +++ +++++ ++++++ivDs+ta yR +  + +   +  ++l++ +  L+ la + ++ vvi
  gi|91774054|ref|YP_566746.1|  81 IAQDIIIFEPHSFEEQYSAVRE-TEKISTENVGVIIVDSATAYYRFELDDEDSSIRTRRELSNQIGFLHSLARKRDIVVVI 160
                                   9999999999********9986.578999**********************998888899********************* PP

                                   EEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S.-EEEEEEETTEE CS
                         Rad51 183 tnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpe.leavfaigeeGi 252
                                   tnqv +++         ++ kPigG  l h s+t ++l k    +R +k+ +  + pe + + f+i+ +G+
  gi|91774054|ref|YP_566746.1| 161 TNQVYSDIKS-------NSLKPIGGSSLEHISKTIIQLEKTGTGSRRAKIWKHRSRPEgTTCEFTITADGV 224
                                   ******9988.......999********************98889999*********945799*****998 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   3.9   9.9e-17   6.3e-14       7     224 ..      14     224 ..      10     225 .] 0.77

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 9.9e-17
                        ATPase   7 glDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiid 87 
                                    lDe+l gG+ +g v+ i Ge+G+GKt ++lq +i+ ++k g++ +f+ +e  + d  +++   G + +k+ +   ++i +
  gi|91774054|ref|YP_566746.1|  14 PLDELLGGGFESGVVTQIFGEAGSGKTNICLQLAIECVKK-GKKAIFIDTEGLSADRFKQI--AGENARKIAQD--IIIFE 89 
                                   69***********************************999.**********9887766555..599******99..77777 PP

                        ATPase  88 asesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..ayeekeav...aReilrq...lvrvl.kklgvTai 159
                                     + +e+++      +++e     +e i++ ++  +++Ds t++   + ++e+    +R++l +   +++ l +k++++ +
  gi|91774054|ref|YP_566746.1|  90 PHSFEEQYS------AVRE-----TEKISTENVGVIIVDSATAYyrFELDDEDSsirTRRELSNqigFLHSLaRKRDIVVV 159
                                   766655422......2333.....3456677778888888887753222222222236667765222344456999***** PP

                        ATPase 160 lvsekss.....seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegi 224
                                   +++++ s     s + +gg  +e+ i++ +i+L+++   ++  R  +i+k R+ +    + +f+It +g+
  gi|91774054|ref|YP_566746.1| 160 ITNQVYSdiksnSLKPIGGSSLEH-ISKTIIQLEKT---GTGSRRAKIWKHRSRPEG-TTCEFTITADGV 224
                                   ****999999888899********.********955...55667789*****99865.578999999887 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1   8.4e-16   5.4e-13      36     219 ..      10     191 ..       2     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 8.4e-16
                                   -S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--G....GG-EEE- CS
                          RecA  36 sGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdi....dellvsq 112
                                   s    ld  lG GG+  G +++i+G   sGkt ++l++  e+ kkg+ a fid+e     ++ +  G +     +++++ +
  gi|91774054|ref|YP_566746.1|  10 SSCKPLDELLG-GGFESGVVTQIFGEAGSGKTNICLQLAIECVKKGKKAIFIDTEGLSADRFKQIAGENArkiaQDIIIFE 89 
                                   45567999999.*******************************************8777777777777642222678999* PP

                                   -SSHHHHHHHH.HH.HHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE--- CS
                          RecA 113 pdtGeqaleia.da.lvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqire 191
                                   p + e+    + ++  + +  + +i+vds +a   + e++ e  ds++    r +s+ +  l +  +k ++vv+  nq+  
  gi|91774054|ref|YP_566746.1|  90 PHSFEEQYSAVrETeKISTENVGVIIVDSATAYY-RFELDDE--DSSIRT-RRELSNQIGFLHSLARKRDIVVVITNQVYS 166
                                   *99876655441432588899********98874.6777655..666654.5788999*********************99 PP

                                   --------------HHHHHHH-SEEEEE CS
                          RecA 192 kiGvmfgnpetttGGralkfyasvrldv 219
                                    i     +p    GG +l   +   +++
  gi|91774054|ref|YP_566746.1| 167 DIKSNSLKP---IGGSSLEHISKTIIQL 191
                                   886544444...5666666666555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.3e-10   8.1e-08       3      82 ..      27     127 ..      25     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.3e-10
                        AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie............swedfldevvel.aae 62 
                                   +  +i+G++g+GKT ++++l       g+k++fidte+ ++++ + + +++++            s+e+ +++v e  +  
  gi|91774054|ref|YP_566746.1|  27 VVTQIFGEAGSGKTNICLQLaiecvkkGKKAIFIDTEGlSADRFKQIAGENARkiaqdiiifephSFEEQYSAVRETeKIS 107
                                   5679**********************************6666666666666669999999999999999999999994344 PP

                        AAA_24  63 ladyktlviDtideleelcl 82 
                                    ++  ++++D+++  +++ l
  gi|91774054|ref|YP_566746.1| 108 TENVGVIIVDSATAYYRFEL 127
                                   56789*********999755 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   3.6e-10   2.3e-07       7     154 ..      33     193 ..      28     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.6e-10
                           Zot   7 GapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvs..tarliridnpegaetlkefakwatid..kgal 83 
                                   G+ GsgKt   ++  +   +k  + i+ + +Gl  +r++q+ ge+    ++++i  + + ++e+ ++++   +i   + ++
  gi|91774054|ref|YP_566746.1|  33 GEAGSGKTNICLQLAIECVKKGKKAIFIDTEGLSADRFKQIAGENARkiAQDIIIFEPHSFEEQYSAVRETEKISteNVGV 113
                                   99************88888888888888****************999888889988866677777777777775554889* PP

                           Zot  84 lviDEcqeifpvrakegrkd.........pevi.naftehRhlgwDivlltqdiskihk.evralaekavklkrkaaigik 153
                                   +++D +   +  +   +  d          + i      +R+    +v++ q  s i++  ++ + +   ++  k+ i+++
  gi|91774054|ref|YP_566746.1| 114 IIVDSATAYYRFELDDE--DssirtrrelSNQIgFLHSLARKRDIVVVITNQVYSDIKSnSLKPIGGSSLEHISKTIIQLE 192
                                   **********9999963..33688888875556344556788888899999999999752577777777777777777766 PP

                           Zot 154 g 154
                                   +
  gi|91774054|ref|YP_566746.1| 193 K 193
                                   5 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   3.2e-09     2e-06      15     161 ..       8     132 ..       2     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.2e-09
                        AAA_25  15 laapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg 94 
                                   l ++ +p++ l++g    g ++ ++G  g+GKt ++l+la++++ +Gk           k +++++E+     + R++++ 
  gi|91774054|ref|YP_566746.1|   8 LLSSCKPLDELLGGGFESGVVTQIFGEAGSGKTNICLQLAIECVkKGK-----------KAIFIDTEGLS---ADRFKQIA 74 
                                   5566789999999888****************************5665...........89********9...99***988 PP

                        AAA_25  95 ealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg...dens 161
                                    ++   ar  +       ++ +f++ + +++  ++v++ e+  +e  +v+++++D+ ++ ++    de+s
  gi|91774054|ref|YP_566746.1|  75 GEN---ARKIAQ------DIIIFEPHSFEEQY-SAVRETEKISTE--NVGVIIVDSATAYYRFeldDEDS 132
                                   776...344333......46677766666664.566776766666..6***********99996633333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   6.6e-08   4.2e-05       4      92 ..      29     119 ..      27     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.6e-08
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHH.HHHHHTTEEEEESSTTS.CHHHHHHHHHHHHHHT CS
                         SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLk.tlaeklgvpvikkkeea.dpaavakeavekakee 82 
                                   + ++G  G+GKT  + +La  + k+gkk++++ +    a  ++Q++ ++a+k+  ++i  + ++ ++   a ++ ek   e
  gi|91774054|ref|YP_566746.1|  29 TQIFGEAGSGKTNICLQLAIECVKKGKKAIFIDTEGLSADRFKQIAgENARKIAQDIIIFEPHSfEEQYSAVRETEKISTE 109
                                   5689**************************99766666666666653455665555555343443677788889999999* PP

                                   TSSEEEEEE- CS
                         SRP54  83 kidvvlvDTa 92 
                                   ++ v++vD+a
  gi|91774054|ref|YP_566746.1| 110 NVGVIIVDSA 119
                                   ********98 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   8.4e-08   5.4e-05      18      71 ..      29      91 ..      25     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.4e-08
                 TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivlDltGafvsrfyd.........egkdillnPl 71
                                  + i+G +GsGKt+   +l  +  ++g++ai +D++G   +rf +         +++ i+++P+
  gi|91774054|ref|YP_566746.1| 29 TQIFGEAGSGKTNICLQLAIECVKKGKKAIFIDTEGLSADRFKQiagenarkiAQDIIIFEPH 91
                                  5699**************************************998888877755544566665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.3e-07   8.6e-05       5     128 ..      30     159 ..      26     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                       DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekke 85 
                                    + G+aG+GKt + l+l+ e+   +++++a+++   +   +  ++   ++++k   +  + ++ sf +++s   +++ek +
  gi|91774054|ref|YP_566746.1|  30 QIFGEAGSGKTNICLQLAIEC--VKKGKKAIFIDTEGLSADRFKQIAGENARKIAQDIIIFEPHSFEEQYS-AVRETEKIS 107
                                   578******************..99999999988888888888777777777777777788**********.667777788 PP

                       DUF2075  86 epkedvvivDEAhrllt.........ksdqaekqseenqlkelmkrakvvva 128
                                    +++ v+ivD A               ++++e  ++  +l++l ++ ++vv+
  gi|91774054|ref|YP_566746.1| 108 TENVGVIIVDSATAYYRfelddedssIRTRRELSNQIGFLHSLARKRDIVVV 159
                                   8999******998777766676654422222233334555555555554444 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.4e-06    0.0022       3     130 ..      31     168 ..      29     174 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-06
                          CobU   3 vtGgarSGKSefAekla...eeskekvvYiATaeal.De......emaeRiarHrerR.paeWetveepldlaealkeeek 72 
                                   + G a SGK ++  +la    ++++k ++i T     D+      e a++ia+      p+++e  e++++++e+ k +++
  gi|91774054|ref|YP_566746.1|  31 IFGEAGSGKTNICLQLAiecVKKGKKAIFIDTEGLSaDRfkqiagENARKIAQDIIIFePHSFE--EQYSAVRETEKISTE 109
                                   78999**********998877788999****988773333333335555555544333233333..333444443333333 PP

                          CobU  73 .kevvLvDcltlwltnllleeeaekveekleeeveellealkelkatvvlVsnEvglgv 130
                                      v++vD+ t +    l++e+++  +++  +++  +l++l++++  vv+++n v  ++
  gi|91774054|ref|YP_566746.1| 110 nVGVIIVDSATAYYRFELDDEDSSIRTRRELSNQIGFLHSLARKRDIVVVITNQVYSDI 168
                                   4699***************9887765555556666788888889999*******98877 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   4.1e-06    0.0026      21      50 ..      28      57 ..      18      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.1e-06
                                  EEEEE--TTSSTTHHHHHHHHHHHHTTS-S CS
                          PhoH 21 ivfaiGpaGtGKtylavalavealkkkkvk 50
                                  ++ ++G+aG+GKt + ++la+e +kk+k  
  gi|91774054|ref|YP_566746.1| 28 VTQIFGEAGSGKTNICLQLAIECVKKGKKA 57
                                  67899********************98765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.2e-05    0.0074       8      80 ..      23     113 ..      19     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                                   EETTSEEEEEESTTSSHHHHHHHHT.TSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlklla.gllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren....... 79 
                                   ++ g +++i+Ge G+GK+ ++  la + +k+ +  i +d + l+  + ++++ ++ + + q+  +f+ ++ +e+       
  gi|91774054|ref|YP_566746.1|  23 FESGVVTQIFGEAGSGKTNICLQLAiECVKKGKKAIFIDTEGLSAdRFKQIAGENARKIAQDIIIFEPHSFEEQysavret 103
                                   78899*************997666515566677889999888887466777888999999998888888888886555444 PP

                                   .........H CS
                                   .........x RF
                      ABC_tran  80 .........e 80 
                                             
  gi|91774054|ref|YP_566746.1| 104 ekistenvgV 113
                                   4444333330 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05    0.0079       8      88 ..      33     111 ..      28     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                   ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHGGGSCCH CS
                   ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqkeeeall 88 
                                   G  G GKt +   +a+++ +kgkk + i t      +D f+q +g++++k+ + + + E  + +e + a +e+ k  ++ +
  gi|91774054|ref|YP_566746.1|  33 GEAGSGKTNICLQLAIECVKKGKKAIFIDTEGLS--ADRFKQIAGENARKIAQDIIIFEPHSFEEQYSAVRETEKISTENV 111
                                   888*************************998643..7*********************99888888888777777666655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00056      0.36       7      54 ..      13      60 ..       8      84 .. 0.79
   2 ?    5.0   0.5      0.02        13     113     184 ..      92     170 ..      60     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                                  HHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEE CS
                                  xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  7 kdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavf 54
                                  k LD+l++ G+++g ++ i + ++ Gkt ++l++a ++++k k+  +++
  gi|91774054|ref|YP_566746.1| 13 KPLDELLGgGFESGVVTQIFGEAGSGKTNICLQLAIECVKKGKKA-IFI 60
                                  678988752799999********************9988766644.444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                                   CHHHHHHHHHHHHHH..TTEEEEEEEEGGGTB....TSCSSS.CCCHHHHHHHHHHHHHHHHCTSXEEEEEEXSGGGCC CS
                                   xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx....xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 113 tvseirskarrlkke..kglgliviDyLqlme....gseeke.nreqevseisrsLkalakelnvpvialsqLsraves 184
                                   + +e  s +r+++k   +++g+i++D          ++e+++ + ++e+s+    L +la+  ++ v++  q+  +++s
  gi|91774054|ref|YP_566746.1|  92 SFEEQYSAVRETEKIstENVGVIIVDSATAYYrfelDDEDSSiRTRRELSNQIGFLHSLARKRDIVVVITNQVYSDIKS 170
                                   3445555566655445599*******77665523221222332556799999999*************99998777665 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   2.2e-05     0.014       3     113 ..      31     166 ..      30     174 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-05
                                   EESSTTSSHHHHHHHHHHHH.....THE...........EEEEETTTCSSS...........STTHHHHHHHHHHHHHHHT CS
                           AAA   3 lyGppGtGKTllakavakel.....gve...........fleisgsellsk...........yvgesekkirelfkeakek 56 
                                   ++G  G GKT ++ ++a e+     ++            f +i g + + k            ++e+ + +re+ k   e+
  gi|91774054|ref|YP_566746.1|  31 IFGEAGSGKTNICLQLAIECvkkgkKAIfidteglsadrFKQIAGENAR-KiaqdiiifephSFEEQYSAVRETEKISTEN 110
                                   589****************866644222222222222225555555444.3678887777777777777777776554333 PP

                                   STSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESS.GG CS
                           AAA  57 akpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.eskvivigatnr.pd 113
                                       ++++D + a  + +  ++++++ r+  +L +++  + +  +++ iv+++tn+ ++
  gi|91774054|ref|YP_566746.1| 111 --VGVIIVDSATAYYRFE-LDDEDSSIRTRRELSNQIGFLHSLaRKRDIVVVITNQvYS 166
                                   ..69******99998888.5666677777777777766665554334588888887444 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 !   15.0   0.0   2.4e-05     0.016      51      89 ..      30      68 ..      13      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                     IstB_IS21 51 vllGpsGvGKshlaialgveavraglsvlfvrvedLvee 89
                                   ++G +G GK+ +   l+ e v++g++ +f+ +e L + 
  gi|91774054|ref|YP_566746.1| 30 QIFGEAGSGKTNICLQLAIECVKKGKKAIFIDTEGLSAD 68
                                  589*****************************9998654 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   2.5e-05     0.016       8      91 ..      35     171 ..      31     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                                   TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                          CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                    G+GKT +++ La+   ++g++ + +D+   +   +  ++  ++ ++                                  
  gi|91774054|ref|YP_566746.1|  35 AGSGKTNICLQLAIECVKKGKKAIFIDTEGLSADRF--KQIAGENARkiaqdiiifephsfeeqysavretekistenvgv 113
                                   69*************************877755544..4444444446677899999999999999999999999999999 PP

                                   .........................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-T CS
                                   .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .........................dlkrllellealgkkkalllkiagvvlnrvdgeneet 91 
                                                             l+  +++l++l +k     +i+ v+ n v ++  ++
  gi|91774054|ref|YP_566746.1| 114 iivdsatayyrfelddedssirtrrELSNQIGFLHSLARK----RDIVVVITNQVYSDIKSN 171
                                   9999999999999999999998888777777777777777....678888888888774444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.4   2.9e-05     0.018      20      83 ..      26     103 ..      15     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                      ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal.................g 83 
                                     +  i+G  gsGKt +  +++ +  +k+k+ i++ + ++ s +++++     e+++k+++ +                  
  gi|91774054|ref|YP_566746.1|  26 GVVTQIFGEAGSGKTNICLQLAIECVKKGKKAIFI-DTEGLSADRFKQI--AGENARKIAQDIiifephsfeeqysavreT 103
                                   56778****************9999999**99997.5688888888887..556666677776344444444443333330 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   2.9e-05     0.018       3      91 ..      31     128 ..      30     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpealdeskrldedkldklldaleenss........alee 73 
                                   + G +G+GKt ++  L+ ++ +  g + +++ +e+ + + + + a ++ +++ +d        +ee++s        + e+
  gi|91774054|ref|YP_566746.1|  31 IFGEAGSGKTNICLQLAIEC-VkkGKKAIFIDTEGLSADRFKQIAGENARKIAQDIIIFEPHSFEEQYSavretekiSTEN 110
                                   67999***********7775.255999999999977777777779999999999999999999999999999999988899 PP

                        AAA_18  74 gknlvidghlaeleseaa 91 
                                    +++++d+  a +++e +
  gi|91774054|ref|YP_566746.1| 111 VGVIIVDSATAYYRFELD 128
                                   999999999988877765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   5.6e-05     0.036      28     103 ..      31      97 ..      29     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                         DUF87  28 ilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsakdkelkinpwsldpeell 103
                                   i+g++GsGK+n    L  e + kkg + + +D  G  ++ +++   e+++ i ++         i +   ++ee  
  gi|91774054|ref|YP_566746.1|  31 IFGEAGSGKTNICLQLAIECV-KKGKKAIFIDTEGLSADRFKQIAGENARKIAQD--------IIIFEPHSFEEQY 97 
                                   9********************.99********99977777766666666666665........4444444444444 PP

>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05     0.022      35     135 ..      78     177 ..      61     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                                   ...-------HHHH.............HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET................. CS
                         RVT_1  35 ekllsenqpgfrpgrstldavedllkalkkkkkaklllklDlkkaFdsvpleellrkltafkvptklinliksflstrsfs 115
                                     ++ +++  f+p+ s +++   ++++ k  +++  ++ +D   a+ + +l+ +++ + + +  +++i  ++s+ ++r ++
  gi|91774054|ref|YP_566746.1|  78 ARKIAQDIIIFEPH-SFEEQYSAVRETEKISTENVGVIIVDSATAYYRFELDDEDSSIRTRRELSNQIGFLHSLARKRDIV 157
                                   45566677777777.9999998888888899999************************9999999**************** PP

                                   ........TEEEEESB--ST CS
                         RVT_1 116 vrvngeeskgryekkglpqG 135
                                   v ++++  + ++++   p G
  gi|91774054|ref|YP_566746.1| 158 VVITNQVYSDIKSNSLKPIG 177
                                   ***99866777766666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0028       1.8      21      52 ..      33      59 ..      17      63 .. 0.81
   2 ?    4.1   0.0     0.056        36      98     130 ..      83     119 ..      63     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0028
                                  ESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 21 aeTGsGKTlaflipvlqivyetkgktgpkali 52
                                  +e GsGKT + l  ++++v     k+g+ka++
  gi|91774054|ref|YP_566746.1| 33 GEAGSGKTNICLQLAIECV-----KKGKKAIF 59
                                  789***************9.....55556665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.056
                                   CSEEEEEHHHHHHHH....HCTSSHCTTEEEEEEETH CS
                                   xxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx RF
                          DEAD  98 vdivvgtpgrlddll....stgklnlsqvrflVlDEa 130
                                    di++  p  + +      +t+k+++++v ++++D a
  gi|91774054|ref|YP_566746.1|  83 QDIIIFEPHSFEEQYsavrETEKISTENVGVIIVDSA 119
                                   789999998888866677899**************77 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.8e-05     0.056      12      63 ..      36      86 ..      27     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.8e-05
                        AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevl 63
                                  G GKT  +++la    k+gkk + +D    ++  +  +i  +++ k   +++
  gi|91774054|ref|YP_566746.1| 36 GSGKTNICLQLAIECVKKGKKAIFIDTEGLSADRF-KQIAGENARKIAQDII 86
                                  99************************987655544.3444333333333333 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.003       1.9      18      57 ..      31      71 ..      24     117 .. 0.82
   2 ?    3.0   0.1     0.091        58     169     207 ..     132     169 ..     124     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                       Pox_A32 18 lvGgsGsGktvyLlsLlrtlvkky.khifLltpvknseYdk 57
                                  + G++GsGkt   l+L  + vkk  k if+ t   +++ +k
  gi|91774054|ref|YP_566746.1| 31 IFGEAGSGKTNICLQLAIECVKKGkKAIFIDTEGLSADRFK 71
                                  78**************9999999868899888766665555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.091
                       Pox_A32 169 mslkgskkkllkvlnilrsaeqkkrkvliiedsvfsege 207
                                    s++ ++++l + +  l+s  +k+  v++i + v+s+ +
  gi|91774054|ref|YP_566746.1| 132 SSIR-TRRELSNQIGFLHSLARKRDIVVVITNQVYSDIK 169
                                   5677.677899********9977777779******9865 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024      0.15       1      30 [.      33      62 ..      33      64 .. 0.95
   2 ?   -2.9   0.0       7.7   4.9e+03     123     133 ..     103     113 ..      71     137 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDl 30
                                  G+  sGK+ ++  L+ ++++kg+k +++D+
  gi|91774054|ref|YP_566746.1| 33 GEAGSGKTNICLQLAIECVKKGKKAIFIDT 62
                                  7899*************************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.7
                        CLP1_P 123 leliealepdv 133
                                   +e+i++ ++ v
  gi|91774054|ref|YP_566746.1| 103 TEKISTENVGV 113
                                   22233333333 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   0.00016       0.1       9     102 ..      30     121 ..      24     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka.....erlsseelleal 82 
                                    ++Ge+G+GKT  + +l+ + ++       +++ +f++  +++    k+++ e +r++           e++s ee ++a+
  gi|91774054|ref|YP_566746.1|  30 QIFGEAGSGKTNICLQLAIECVKK------GKKAIFIDTEGLSadRFKQIAGENARKIA----QdiiifEPHSFEEQYSAV 100
                                   59***************9998765......99999999999984445555544444444....345558888888888888 PP

                        AAA_22  83 eqalrarav.ielliiDEaqh 102
                                   ++  +     ++++i+D a  
  gi|91774054|ref|YP_566746.1| 101 RETEKISTEnVGVIIVDSATA 121
                                   877666666679999998765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.3    0.0018       1.1      32      84 ..      34      80 ..      28     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                                  STTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                        ResIII 32 aTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke 84
                                  + G+GKT ++++l+ ++ kkgk  k++f+ +++ l     ++fk+++ e++ +
  gi|91774054|ref|YP_566746.1| 34 EAGSGKTNICLQLAIECVKKGK--KAIFI-DTEGLSA---DRFKQIAGENARK 80
                                  57*****************988..77775.5555543...4444444444433 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   0.00019      0.12      19      95 ..      27     117 ..      22     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                        AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk..............grar 85 
                                    v+ + G AG+GKt +  +l+    ++g++ i +  +g  A++ ++ +g +a+ ia+ +   +              ++ +
  gi|91774054|ref|YP_566746.1|  27 VVTQIFGEAGSGKTNICLQLAIECVKKGKKAIFIDTEGLSADRFKQIAGENARKIAQDIIIFEphsfeeqysavretEKIS 107
                                   588899*********99999888888999999999**********999999999998776666666777777777542222 PP

                        AAA_30  86 lepgtllivD 95 
                                    e+  ++ivD
  gi|91774054|ref|YP_566746.1| 108 TENVGVIIVD 117
                                   3333666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 1504.53
//
Query:       gi|91774055|ref|YP_566747.1|  [L=83]
Description: glutaredoxin-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-08   34.4   0.1    2.5e-08   34.0   0.1    1.2  1  Glutaredoxin   Glutaredoxin
    0.00098   19.5   0.1     0.0015   18.9   0.1    1.4  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.053   14.0   0.2       0.08   13.4   0.2    1.2  1  Thioredoxin_2  Thioredoxin-like 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 !   34.0   0.1   4.1e-12   2.5e-08       1      59 [.       4      62 ..       4      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.1e-12
                                  EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH.TSSSSSEEEETTEE CS
                  Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels.gvrtvPqvfidgkh 59
                                  ++++t+ tCp C++ k++Lk++ v f+e d +  +e   el+ +    +t P++ id+++
  gi|91774055|ref|YP_566747.1|  4 IIIYTTETCPKCVQLKKVLKSNDVIFTEADMST-PESLTELRLNGvFTVTAPVLQIDDDF 62
                                  79****************************999.68888887776766999999999987 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.5e-07    0.0015       2      57 ..       4      60 ..       3      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-07
                                  EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHC.....CCCTTTTEEEECT CS
                        DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIakdeelea.....kYgleipvlaleg 57
                                  +++y+++ C+ C q+k++Lk     +++   + D  + e+l +      + ++ pvl +++
  gi|91774055|ref|YP_566747.1|  4 IIIYTTETCPKCVQLKKVLKS----NDVIFTEADMSTPESLTElrlngVFTVTAPVLQIDD 60
                                  99******************3....455667777777666544444558888888888876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.3e-05      0.08       9      33 ..       4      28 ..       3      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                 Thioredoxin_2  9 lvvftdpdCpyCkklkkelkelddv 33
                                  ++++t+++Cp C +lkk+lk++d +
  gi|91774055|ref|YP_566747.1|  4 IIIYTTETCPKCVQLKKVLKSNDVI 28
                                  67899***************99544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 542.22
//
Query:       gi|91774056|ref|YP_566748.1|  [L=795]
Description: ribonucleoside-triphosphate reductase, anaerobic [Methanococcoides burtonii DSM 6242]
Scores for complete 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-153  510.9   0.0   5.7e-153  510.7   0.0    1.0  1  NRDD      Anaerobic ribonucleoside-triphosphate reductase
  ------ inclusion threshold ------
       0.02   15.0   0.1       0.49   10.5   0.2    2.6  2  RapH_N    response regulator aspartate phosphatase H, N termi
       0.11   12.6   0.2       0.29   11.2   0.2    1.7  1  DUF2953   Protein of unknown function (DUF2953)


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 !  510.7   0.0  9.6e-157  5.7e-153       1     561 []     164     789 ..     164     789 .. 0.93

  Alignments for each domain:
  == domain 1  score: 510.7 bits;  conditional E-value: 9.6e-157
                                   .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SSS... CS
                          NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgngv... 78 
                                   enan+ ++++++ ++k a+++ske +l  llp+++a+ h +gd+HiHDl+y+ ++  +C+++dl++++ +Gl+  +g+   
  gi|91774056|ref|YP_566748.1| 164 ENANL-QENAETAHKKKADKISKEQYLL-LLPPKIADLHLNGDLHIHDLEYFGTR-AFCQDWDLRYFFYYGLMP-DGSgak 240
                                   8****.*********************5.************************95.5***************65.777799 PP

                                   ...-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTTS-S..SSS CS
                          NRDD  79 ...srppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynlntlpsrrGa 156
                                      + p+ ++e+a+ +av++l+++q+++aGgq++++f+t+ apf+  +      ++ +kei+q mq+fvy++++++++rG+
  gi|91774056|ref|YP_566748.1| 241 asvAGPAMKAEVAMLHAVKALGSAQTNFAGGQGFYNFLTFCAPFF--E------GKPYKEIEQLMQMFVYEMTQMMVARGG 313
                                   999******************************************..4......67************************* PP

                                   S---EEEEEE.-HH.......................................HHHHHTTTTS-HCH----SEEEEEEEEE CS
                          NRDD 157 QvpFtninlgldtp........................tegrfee..kliikallevmleGdgnkgtpftFPilifklked 211
                                   Q +F++++l  ++p                         +g++e+  +l +ka+++vmleGd++ g+pf+FP++ ++++ d
  gi|91774056|ref|YP_566748.1| 314 QLVFSSVQLSPGVPkmwrdkpvvyrgrvwdgtngtekrVYGDYERevRLGFKAMMNVMLEGDYW-GKPFNFPKPEISIEPD 393
                                   **************************************99999999******************.**************** PP

                                   TETTH...............HHHHHHHHHHTTT--EEE.......EEES--GGGTT-------....-............. CS
                          NRDD 212 fnleeed..........pnydlfklalevtakrgfpyffnlledlepedekevasmgCRlrld....ege........... 267
                                   f +ee++          ++++l+++++e+tak+g+pyf n+l+++++  e  +++++C ++++    + +           
  gi|91774056|ref|YP_566748.1| 394 F-MEEDEmfnranpelpTYDELYTMTFELTAKYGTPYFDNQLPEYRGAGEGISCYQCCAYQFSanadS-Dsefdekmyfne 472
                                   9.888679********99************************99999999*************65431.133555666555 PP

                                   .S---EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-HHH.HTTSS-GE........ CS
                          NRDD 268 .rlggrgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekllakg.lpflmgkgylksr.kkkdeve 345
                                    ++ ++gs++v+++N+pr a++a++d+ek+f++L++l++ a e+++++ k+l+ ++++g +pf++++   +   +kk  ++
  gi|91774056|ref|YP_566748.1| 473 gKHFSMGSWQVISLNCPRAAYLAENDDEKLFSHLKHLMDEAMEVFQTKVKWLKPIIENGrMPFATQQ-PKDPVtGKKGAIA 552
                                   55555**********************************************************7644.33323377889** PP

                                   ......EEEEEEE-HHHHHHHTTEEEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE---TTHHHHHHHHH.... CS
                          NRDD 346 evlkngtltiGfiGlaEalkaltgkkigeseeakefalkvlkhmrekadelkeetglnfsleatPaEslsgrfakldk..k 424
                                     +++ + tiG+iG++E+++++tg++++es++a ++a++++++m  + +el+++ g++++l +tPaE++++rf   d   +
  gi|91774056|ref|YP_566748.1| 553 VDIDSLVFTIGVIGINEMVQYHTGSQMHESRDAFKLAIRAMTEMDIYGKELSRKFGMEIALARTPAETTGQRFSVSDLlhE 633
                                   ***************************************************************************998778 PP

                                   HH..................................HHG-SSSS-TTSSB-HHHHHHHHHHHTGGGTT-S-EEEEBSS--S CS
                          NRDD 425 kf.........geipgvdke...............pyYtNsfhvpvdekislfekikleaefqklttGGailyieldeekk 481
                                   +f         g       +               +yYtN +hvp ++++sl+++i++e+ f ++++GG i++i+++e ++
  gi|91774056|ref|YP_566748.1| 634 EFrdkvisvvkG-------DvkaavegiknthdlpIYYTNGTHVPPGADVSLVDRINIEHVFFPIVDGGDIMHIWMGEGSP 707
                                   996655555551.......1444555566667999********************************************** PP

                                   SHHHHHHHHH.HHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.EEEEEESSSSEEEHHHHHHHHHHHSGG-- CS
                          NRDD 482 npealeklvk.iakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeevevirRitGYlrpvsswnkgkkaElkdRv 559
                                   + + l+++   +a++t++gYf+++++++vC++  +  +g+++ C +Cgs++ +e ++R+tGY++ v  wn++kk+El+dR+
  gi|91774056|ref|YP_566748.1| 708 DAKGLKDFAMnLARNTQLGYFAFTKDMSVCMDDFHmmAGLKDACENCGSDN-IEQLSRVTGYIQAVGGWNAAKKQELEDRK 787
                                   **********9**********************9999***********888.***************************** PP

                                   -B CS
                          NRDD 560 kh 561
                                   ++
  gi|91774056|ref|YP_566748.1| 788 RY 789
                                   98 PP

>> RapH_N  response regulator aspartate phosphatase H, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   8.2e-05      0.49      10      41 ..      81     112 ..      79     113 .. 0.94
   2 ?    1.0   0.0     0.075   4.5e+02      29      50 ..     643     664 ..     641     665 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.2e-05
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHCTS- CS
                        RapH_N  10 klneWYsaIkkrsvekAeelkeeikqeleeme 41 
                                    l+eWY  I + s ++A+ + +e ++ +  m+
  gi|91774056|ref|YP_566748.1|  81 TLSEWYHNISSISKDEAHDVAKETEKRIRGMN 112
                                   699*************************9995 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.075
                                   HHHHHHHHHCTS---HHHHHHH CS
                        RapH_N  29 lkeeikqeleemeedqdvllYY 50 
                                   +k ++k ++e +++ +d+ +YY
  gi|91774056|ref|YP_566748.1| 643 VKGDVKAAVEGIKNTHDLPIYY 664
                                   5889****************** PP

>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.8e-05      0.29      33      49 ..     381     397 ..     377     400 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
                       DUF2953  33 fnikkpeievtPvFnee 49 
                                   fn++kpei+++P+F+ee
  gi|91774056|ref|YP_566748.1| 381 FNFPKPEISIEPDFMEE 397
                                   899***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4947.32
//
Query:       gi|91774057|ref|YP_566749.1|  [L=261]
Description: ribonucleoside-triphosphate reductase, anaerobic-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-19   70.1   0.0    4.4e-19   69.5   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    3.8e-11   43.4   0.0      7e-11   42.5   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    1.1e-07   32.0   0.0    2.2e-07   31.0   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
     0.0084   15.8   0.0       0.02   14.6   0.0    1.6  1  DUF2717      Protein of unknown function (DUF2717)


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 !   69.5   0.0   9.8e-23   4.4e-19       2     158 ..      24     182 ..      23     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 9.8e-23
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                    ++rgC++rC++C+++e      ++ +++v e+++++++ +    v  v+++ggepl++++    l+ +ak+  +++ + +
  gi|91774057|ref|YP_566749.1|  24 LFLRGCPFRCPYCHNYE---ILTVPDMVDVKELEKKIDSSS-LF-VSSVVFSGGEPLAQKNALIHLASYAKK--KDLLVGI 97 
                                   589*************9...6*******************7.44.***************************..7****** PP

                                   EECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHH..HHHHHHT.CTSHH........HHHHHHHHHHHHTTSETEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxx.xxxxx........xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelg.vdrvslgleaadde..kvlklmn.rghtf........eevlealeklreagikrvvdrivg 151
                                    tng+   ++ +e+l + g vd + ++++a+ d+  ++ k ++ + +++        e + +a+ + +++g++    r++ 
  gi|91774057|ref|YP_566749.1|  98 HTNGYY--PDLVEELIDSGlVDKFFIDVKAPLDDpeMCGKAIGyGEYSVvpdppdvlENIRRAISIVTDKGME-YELRTTA 175
                                   ******..69***********************9998888887666666888888889999999999999999.6666666 PP

                                   BTTTSHH CS
                                   xxxxxxx RF
                   Radical_SAM 152 lpGende 158
                                   ++G+  e
  gi|91774057|ref|YP_566749.1| 176 IRGFIGE 182
                                   6665443 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 !   42.5   0.0   1.6e-14     7e-11       7      95 ..      21     103 ..      15     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.6e-14
                       Fer4_12   7 rlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                    ++lf+ gC+++C++C+n e+  +    +++ el+++i    +   ++ ++++GGEPl+  +++al+ l+ + k++ +  +
  gi|91774057|ref|YP_566749.1|  21 SVVLFLRGCPFRCPYCHNYEILTVPDMVDVK-ELEKKID--SSSLFVSSVVFSGGEPLA--QKNALIHLASYAKKKDL-LV 95 
                                   589******************9998777664.6777763..346899************..**************999.67 PP

                       Fer4_12  88 iwlytgyt 95 
                                    + ++gy 
  gi|91774057|ref|YP_566749.1|  96 GIHTNGYY 103
                                   88888886 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   4.8e-11   2.2e-07       2      91 ..      25     103 ..      22     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.8e-11
                       Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                   f+   gC++ C+ C n e    ++    + ++le+ +  ++ s ++ + +v++GGePL  ++k++l++l ++ k++   + 
  gi|91774057|ref|YP_566749.1|  25 FL--RGCPFRCPYCHNYE--ILTVPDMVDVKELEKKI--DSSSLFVSS-VVFSGGEPL--AQKNALIHLASYAKKKD--LL 94 
                                   44..8************9..44555555566666788..677888666.*********..8899*******999998..77 PP

                       Fer4_14  83 iwletngtl 91 
                                   + + tng +
  gi|91774057|ref|YP_566749.1|  95 VGIHTNGYY 103
                                   777888765 PP

>> DUF2717  Protein of unknown function (DUF2717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.4e-06      0.02       3      40 ..     174     210 ..     172     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
                       DUF2717   3 kpikkllknPdDiPdvpraaaeYLqvrfnasYliasGl 40 
                                   + i+ ++ +P+Di +++ ++a YL +   asY+i+ G+
  gi|91774057|ref|YP_566749.1| 174 TAIRGFIGEPEDIAKIASSIAPYLSIS-GASYVIQQGI 210
                                   5789999******************97.79*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1936.70
//
Query:       gi|91774058|ref|YP_566750.1|  [L=283]
Description: hypothetical protein Mbur_2127 [Methanococcoides burtonii DSM 6242]
Scores for 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-65  219.7   0.4    3.7e-65  219.4   0.4    1.1  1  DUF4349          Domain of unknown function (DUF4349)
     0.0069   16.3   0.8       0.39   10.6   0.4    2.2  2  Cauli_AT         Aphid transmission protein
  ------ inclusion threshold ------
      0.024   14.2   0.1      0.035   13.7   0.1    1.2  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.055   13.9   0.3       0.11   12.9   0.3    1.5  1  Snapin_Pallidin  Snapin/Pallidin
      0.087   13.1   0.7       0.75   10.1   0.0    2.4  2  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
        0.3   11.6   1.8        2.6    8.6   0.9    2.7  2  NPV_P10          Nucleopolyhedrovirus P10 protein
        6.9    6.2  10.4         14    5.2  10.4    1.4  1  SKG6             Transmembrane alpha-helix domain


Domain annotation for each model (and alignments):
>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.4   0.4   1.4e-68   3.7e-65       1     211 [.      68     274 ..      68     276 .. 0.97

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 1.4e-68
                       DUF4349   1 rkliytasltlevedvdaavaairelveeagGyvesss.ersgtegdersasltlRvPaarldafldelaelgkvtsrsts 80 
                                   rk+i+t s+++ev+d +++++ i+++++e++Gyv+sss  ++++++d +++s+t+RvP+ +l+++ld++++lgkvts+sts
  gi|91774058|ref|YP_566750.1|  68 RKVITTSSVSIEVKDTTETLDGISDIADEFNGYVSSSSaYTRYGDDDGMYGSITIRVPSSELEKVLDSIGDLGKVTSESTS 148
                                   89************************************99999************************************** PP

                       DUF4349  81 aeDVTeqyvDleaRlkaleasedrllallekaksvedlleiereLsevqaeieslegqlryLdnqvaystvtvtlrepeae 161
                                   a+DVTe+y+D++aRl++le++e+rl ++le +++ve++l +e+eL +v+ eiesl+g+l+yL+++++++t++v+++ep++ 
  gi|91774058|ref|YP_566750.1| 149 ASDVTEEYIDVNARLSNLEKQEKRLGEILEMSTTVEEILDVEKELVRVRGEIESLTGRLNYLNDRIDLATINVDVSEPRNI 229
                                   ********************************************************************************* PP

                       DUF4349 162 teaeeeegegflealsggwnalveflagllvvlgallPwllvlalvlall 211
                                   t      ++g+++als+++++++ +++g++v++g+++P+++++ +v+++l
  gi|91774058|ref|YP_566750.1| 230 TH-----SWGLRDALSDSVRGFIGSVNGIIVFIGVAIPIVIFVSIVGVML 274
                                   96.....479**********************************666655 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.016        40     127     156 ..      63      92 ..      30      99 .. 0.83
   2 !   10.6   0.4   0.00015      0.39      99     162 ..     142     204 ..     121     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                      Cauli_AT 127 tkklaekivtekllkeevkdlderlseird 156
                                   + +++ k+ t   +  evkd+ e+l  i d
  gi|91774058|ref|YP_566750.1|  63 QSSITRKVITTSSVSIEVKDTTETLDGISD 92 
                                   568999*******************99877 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00015
                      Cauli_AT  99 ggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkaii 162
                                   + ++++++++ +e   +++ r ++le++ k+l e ++    + ee+ d++++l ++r ++ ++ 
  gi|91774058|ref|YP_566750.1| 142 VTSESTSASDVTEEYIDVNARLSNLEKQEKRLGEILEMSTTV-EEILDVEKELVRVRGEIESLT 204
                                   33444455556666666777*************988887666.56889*********9998765 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 ?   13.7   0.1   1.4e-05     0.035      83     136 ..     149     204 ..     123     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                 PI3K_P85_iSH2  83 ieklqenleqlksrlkelhsskekLeedlk..qqkeeereleReinalkpellqLq 136
                                    ++++e + ++++rl++l+++ ++L e l+  +++ee + +e+e+ +++ e+ +L+
  gi|91774058|ref|YP_566750.1| 149 ASDVTEEYIDVNARLSNLEKQEKRLGEILEmsTTVEEILDVEKELVRVRGEIESLT 204
                                   56889999*******************876226788899************99987 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   4.5e-05      0.11      23      87 ..     150     215 ..     141     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
               Snapin_Pallidin  23 kelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                   ++++++  +++++l++l ++ k+l e+ e + +++++    k Lv+++ +++sl  rl+ l++R++
  gi|91774058|ref|YP_566750.1| 150 SDVTEEYIDVNARLSNLEKQEKRLGEILEmSTTVEEILDVEKELVRVRGEIESLTGRLNYLNDRID 215
                                   56666666677777777777777777777777********************************85 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.27   6.9e+02      42      56 ..     167     181 ..     158     188 .. 0.57
   2 ?   10.1   0.0   0.00029      0.75      10      28 ..     190     208 ..     184     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.27
               Val_tRNA-synt_C  42 eeekaklaeleeqae 56 
                                   e+++++l e  e+++
  gi|91774058|ref|YP_566750.1| 167 EKQEKRLGEILEMST 181
                                   445555555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00029
               Val_tRNA-synt_C  10 eKeLaklekeiervqkKLa 28 
                                   eKeL ++++eie++ ++L+
  gi|91774058|ref|YP_566750.1| 190 EKELVRVRGEIESLTGRLN 208
                                   9*****************9 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.46   1.2e+03      36      55 ..      79      98 ..      64     104 .. 0.58
   2 ?    8.6   0.9     0.001       2.6      19      67 ..     141     189 ..     128     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.46
                       NPV_P10 36 dvtelnekLdaqsaqLaele 55
                                  +v++ +e Ld++s+  +e++
  gi|91774058|ref|YP_566750.1| 79 EVKDTTETLDGISDIADEFN 98
                                  34445566666666555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.001
                       NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67 
                                   kV++ +++  dv+e+  dv+   ++L++q + L e+ +  +++++iL  
  gi|91774058|ref|YP_566750.1| 141 KVTSESTSASDVTEEYIDVNARLSNLEKQEKRLGEILEMSTTVEEILDV 189
                                   899999999*************************998877777777763 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  10.4    0.0053        14      14      37 ..     257     280 ..     251     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0053
                          SKG6  14 vaVaVPVaViiivLlailifvrRR 37 
                                   ++Va+P+++ + ++++ li+v RR
  gi|91774058|ref|YP_566750.1| 257 IGVAIPIVIFVSIVGVMLILVKRR 280
                                   8********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1834.82
//
Query:       gi|91774059|ref|YP_566751.1|  [L=331]
Description: thiamine-monophosphate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-20   73.8   1.8    2.7e-20   72.8   1.8    1.5  1  AIRS      AIR synthase related protein, N-terminal domain
      2e-07   31.2   0.0    4.1e-07   30.2   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   1.8     3e-24   2.7e-20       1      94 []      38     149 ..      38     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3e-24
                                   SSSEE.........EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHH CS
                          AIRS   1 dDaav.........vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wleev 58 
                                   dD+av         v+ttd     +l  +++f        iG+ a+avnlsD+a+mGA+P+++l +l +        +e++
  gi|91774059|ref|YP_566751.1|  38 DDCAVidisdedclVITTD-----MLHRKTDFpevmsawqIGWMAAAVNLSDVASMGATPVGFLSALGITddmelgFAEDI 113
                                   89995555555555*****.....********************************************************* PP

                                   HHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEEE CS
                          AIRS  59 vrglaeaaeelgvplvgGdtsfsneptisvtavGlv 94 
                                   +rg+ ++a+ ++++++gGd+  ++e+ti+ ta+G v
  gi|91774059|ref|YP_566751.1| 114 ARGMDACASFCDTSVIGGDIDLHDELTITGTALGRV 149
                                   **********************************86 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.6e-11   4.1e-07       2     149 ..     162     303 ..     162     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.6e-11
                                   TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHT CS
                        AIRS_C   2 pGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapa 82 
                                   pGd++ +tg+ G  ga++++ + +++ ++       l  +l+   + ++ ++la   g v+++ D ++ GL+ +l  +a+ 
  gi|91774059|ref|YP_566751.1| 162 PGDLVCVTGNVGSAGAALLALQNGFDISDDL-----LNTLLQPVPRTKEGQLLAST-GCVTSMMDTSD-GLAMSLYDLAET 235
                                   8*********999998866655555555544.....88888888999999999996.***********.8*********** PP

                                   TTEEEEEECGTHHHHHHHH.......HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                        AIRS_C  83 sgvgaeidldkvpifdele.......splemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                   +gvg+ i ++++pi +e+          +  l++     ll++v+p   d+v++++         v+Gevt++ 
  gi|91774059|ref|YP_566751.1| 236 NGVGFIIFAEALPIDNEVIslvgyddALELGLYTGGDFELLFTVSPSTMDKVKSVCY------LNVVGEVTEDT 303
                                   ******************999999944444556688888999999999999999998......68999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2477.04
//
Query:       gi|91774060|ref|YP_566752.1|  [L=1304]
Description: S-layer-like domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-192  636.2  37.4    1.2e-97  326.0  10.8    3.0  3  S-layer         S-layer protein
    0.00048   20.0  10.5      0.003   17.4   0.0    5.3  5  PEGA            PEGA domain
     0.0015   18.9   4.7          1    9.7   0.1    4.4  4  DUF4198         Domain of unknown function (DUF4198)
      0.003   17.5   6.2       0.77    9.6   0.1    3.8  4  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
  ------ inclusion threshold ------
      0.065   13.4   2.7        1.7    8.8   0.2    3.1  2  PrcB_C          PrcB C-terminal
        6.2    7.0   6.2         25    5.0   0.0    4.6  6  Cupredoxin_1    Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.5  14.7   7.7e-99   2.3e-95       2     258 .]     442     695 ..     441     695 .. 0.97
   2 !  326.0  10.8    4e-101   1.2e-97       3     258 .]     718     970 ..     716     970 .. 0.97
   3 ?   -1.5   0.1      0.34     1e+03     180     217 ..    1020    1057 ..     995    1079 .. 0.75

  Alignments for each domain:
  == domain 1  score: 318.5 bits;  conditional E-value: 7.7e-99
                       S-layer   2 eneeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfag 82 
                                   en+ +s+++ w+a ++sgf+yd+++gl+sE++t++  +  dr+i++g+l+Y+ttp+e++fe+ +wgsYevigf+aekYfag
  gi|91774060|ref|YP_566752.1| 442 ENAGQSTKYIWDALSYSGFFYDLESGLGSEKMTMD--D-IDRNIGKGDLEYETTPIETDFEYGAWGSYEVIGFMAEKYFAG 519
                                   57788999**************************8..3.79**************************************** PP

                       S-layer  83 y..dnsa.etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvisssk 160
                                   y  ++s+ ++++ +sl+s+++L+kvlid+d+++ ++sgs l LeegY l++ ++D +gdk++++L+kdg+evd+ v+ss  
  gi|91774060|ref|YP_566752.1| 520 YtaNTSSdVSDKVISLMSKGHLTKVLIDSDDKERVYSGSGLVLEEGYVLNVVEVDKNGDKIFVSLSKDGDEVDEIVVSS-- 598
                                   *8533335788889*****************************************************************.. PP

                       S-layer 161 adstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemenddsitLs 241
                                     +tyvyekdlgd+ddv+iiav++de+f+gte+++v+iegifqisd++ +i++gde+g m+vks+s+++i+men+d+i+L+
  gi|91774060|ref|YP_566752.1| 599 -GDTYVYEKDLGDVDDVPIIAVNFDEIFSGTETNAVFIEGIFQISDKYEDINTGDEYGAMKVKSISSTMIRMENEDTISLD 678
                                   .******************************************************************************** PP

                       S-layer 242 rdktieimddlkfkvaD 258
                                   +++  +im++lkf vaD
  gi|91774060|ref|YP_566752.1| 679 KGDIADIMGKLKFVVAD 695
                                   ****************8 PP

  == domain 2  score: 326.0 bits;  conditional E-value: 4e-101
                       S-layer   3 neeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy 83 
                                   +++e++ l+wt+ nF+gfyy+id+g+++Esl l+   +++rti++++lvY+t+p +++fe++ w++Y+vigf+aekYf+g 
  gi|91774060|ref|YP_566752.1| 718 TIAEDKGLKWTPLNFEGFYYNIDEGIGTESLNLT---YTGRTINDNDLVYTTSPSSVSFEYSGWDNYTVIGFMAEKYFVGF 795
                                   677889999************************9...479***************************************** PP

                       S-layer  84 dnsa...etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska 161
                                    n++    + +  sl+s+++Lskvlid+d++k+++ gssl LeegY+l++ +++ dgdkv++eL+kdg+evd++v+ss   
  gi|91774060|ref|YP_566752.1| 796 PNDPfndGEVSALSLMSQGQLSKVLIDDDDKKSIFGGSSLILEEGYSLDVVEVNKDGDKVFVELSKDGDEVDEQVLSS--- 873
                                   888845556677899***************************************************************... PP

                       S-layer 162 dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemenddsitLsr 242
                                    +ty+y+kdlg++ddv+ii v+++e+f+gte+++v++egifqisd++ e+++gd++gkme+k++s+ +iem+n+dsi+Ls+
  gi|91774060|ref|YP_566752.1| 874 GKTYTYKKDLGEVDDVPIISVNFKEIFSGTETNAVFVEGIFQISDKYEELNTGDDYGKMEIKTISSIKIEMKNKDSISLSK 954
                                   ********************************************************************************* PP

                       S-layer 243 dktieimddlkfkvaD 258
                                   ++++eim+d+kfkvaD
  gi|91774060|ref|YP_566752.1| 955 GDEVEIMGDIKFKVAD 970
                                   ***************9 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.34
                       S-layer  180 iavhvdevfrgtedslvviegifqisddvleieegdef 217 
                                    + v+  ++  gt+d+   ++++f+ + +++   e d++
  gi|91774060|ref|YP_566752.1| 1020 VTVKAGSIVLGTTDNEGEVDYTFHADGTYTITAEKDDY 1057
                                    46777888888888888899999988887655555554 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.7     5e+03      13      25 ..     163     175 ..     163     183 .. 0.84
   2 ?    0.6   0.1      0.18   5.4e+02       6      25 ..     360     379 ..     355     390 .. 0.84
   3 ?    1.6   0.0     0.086   2.6e+02      31      55 ..    1043    1067 ..    1019    1083 .. 0.79
   4 !   17.4   0.0     1e-06     0.003      14      58 ..    1108    1157 ..    1104    1164 .. 0.87
   5 ?    2.2   0.1     0.058   1.7e+02      31      63 ..    1189    1221 ..    1184    1226 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                          PEGA  13 atVyidGkylGkT 25 
                                   a+V+idG ++  T
  gi|91774060|ref|YP_566752.1| 163 ANVSIDGANYTMT 175
                                   789****999766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                          PEGA   6 irSnpeGatVyidGkylGkT 25 
                                   ++++p+ ++V i G ++G +
  gi|91774060|ref|YP_566752.1| 360 VATDPSYMQVNITGTNYGMS 379
                                   89****************65 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.086
                          PEGA   31 leaGnyslrvekeGYedlektvtvt 55  
                                     + G+y+++ ek+ Y + e+  +v 
  gi|91774060|ref|YP_566752.1| 1043 HADGTYTITAEKDDYVTGEASLEVI 1067
                                    578************9988777765 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 1e-06
                          PEGA   14 tVyidGkylGkTP....vtls.leaGnyslrvekeGYedlektvtvtage 58  
                                     V+idGk++G+T     vt++  + G ++++ ekeG+ ++e+ ++v++ e
  gi|91774060|ref|YP_566752.1| 1108 DVTIDGKSIGETDsdgvVTYVlKDIGMHKITAEKEGFLEAEDNIEVKELE 1157
                                    69********997556589998899*********************9655 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.058
                          PEGA   31 leaGnyslrvekeGYedlektvtvtagetvkln 63  
                                     +aG+y+++++    +++++++++  ge ++++
  gi|91774060|ref|YP_566752.1| 1189 KAAGSYTVELVVNDNTTATQEISLGVGESTQVE 1221
                                    679**********************99999886 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.52   1.6e+03     173     207 ..     192     225 ..     139     228 .. 0.66
   2 !    9.7   0.1   0.00035         1     145     210 ..     998    1053 ..     995    1056 .. 0.73
   3 !    6.4   0.0    0.0034        10     156     210 ..    1083    1140 ..    1070    1143 .. 0.73
   4 ?    0.5   0.1      0.22   6.5e+02     144     210 ..    1169    1237 ..    1148    1240 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.52
                       DUF4198 173 yggtryrdapdeikvktdadGvvtftlpkaGlwll 207
                                   y + ++++a++ ++    +dG v++ +++aG++++
  gi|91774060|ref|YP_566752.1| 192 YSNSGFSTATHSYQ-FFASDGTVAVGPSSAGTFVV 225
                                   22335555555544.45678899999999998887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00035
                       DUF4198  145 ydlkageelevqvlldGkPlagaeveveyggtryrdapdeikv.ktdadGvvtftlpkaGlwlleae 210 
                                      + +g++++v+v+ +G    g++v++             i + +td +G+v +t+ + G++ ++ae
  gi|91774060|ref|YP_566752.1|  998 EVVSEGDKITVTVTSRGSLINGVTVKAG-----------SIVLgTTDNEGEVDYTFHADGTYTITAE 1053
                                    5566788888888888888888888863...........3333689999999999999999888886 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0034
                       DUF4198  156 qvlldGkPlagaeveveyggt.ryrdapdeikv..ktdadGvvtftlpkaGlwlleae 210 
                                    +v ++G  ++ + v+ + g++ +++d + + k   +td+dGvvt+ l+  G+  ++ae
  gi|91774060|ref|YP_566752.1| 1083 EVIYEGNLVTFTVVKSIGGDAlEDVDVTIDGKSigETDSDGVVTYVLKDIGMHKITAE 1140
                                    466666666666666555444555555555555779************9999988887 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.22
                       DUF4198  144 pydlkageelevqv..lldGkPlagaeveveyggtryrdapdeikv..ktdadGvvtftlpkaGlwlleae 210 
                                    p ++k+g ++ v +  + +Gk +   +ve++  +  + +a++ei +      + ++++t  ++G++l+++ 
  gi|91774060|ref|YP_566752.1| 1169 PLEVKSGKDVNVILdaVNNGKAAGSYTVELVVND--NTTATQEISLgvGESTQVEFEYTAGEPGTYLVKVD 1237
                                    5555555555554321568999999999977754..67888888887766666689999999999999986 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 !    9.6   0.1   0.00026      0.77      47      98 ..     543     592 ..     525     644 .. 0.86
   2 !    7.7   0.1   0.00098       2.9      46     100 ..     817     869 ..     810     886 .. 0.83
   3 ?   -1.4   0.0      0.61   1.8e+03      39      77 ..     931     971 ..     919     989 .. 0.73
   4 ?   -0.5   0.0      0.32   9.6e+02      35      58 ..    1130    1156 ..    1087    1190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                tRNA-synt_1c_C  47 eiyiereDakrlkpgeevrLkelynikveevekdesgevtelkleydgesle 98 
                                   +++i+ +D +r+  g+ + L e+y+++v ev  d++g+ + ++l+ dg++++
  gi|91774060|ref|YP_566752.1| 543 KVLIDSDDKERVYSGSGLVLEEGYVLNVVEV--DKNGDKIFVSLSKDGDEVD 592
                                   89**************************999..6778888888888887775 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00098
                tRNA-synt_1c_C  46 keiyiereDakrlkpgeevrLkelynikveevekdesgevtelkleydgesleea 100
                                   ++++i+ +D k++  g+ + L e+y + v ev+kd  g+ + ++l+ dg++++e+
  gi|91774060|ref|YP_566752.1| 817 SKVLIDDDDKKSIFGGSSLILEEGYSLDVVEVNKD--GDKVFVELSKDGDEVDEQ 869
                                   589*****************************655..666666688888888765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.61
                tRNA-synt_1c_C  39 trkvpfsk..eiyiereDakrlkpgeevrLkelynikveev 77 
                                   + +++  +  +i ++++D  +l++g+ev +++ + +kv + 
  gi|91774060|ref|YP_566752.1| 931 KMEIKTISsiKIEMKNKDSISLSKGDEVEIMGDIKFKVADS 971
                                   44554444126666788899999******999888888665 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.32
                tRNA-synt_1c_C   35 pelgtrkvpfskeiyiereD...akrl 58  
                                    ++ g++k++ +ke ++e+eD   +k+l
  gi|91774060|ref|YP_566752.1| 1130 KDIGMHKITAEKEGFLEAEDnieVKEL 1156
                                    356777777777777777775444444 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.031        94      11      47 ..     562     594 ..     554     602 .. 0.78
   2 ?    8.8   0.2   0.00058       1.7      13      48 ..     839     871 ..     838     879 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.031
                        PrcB_C  11 ptgGYsievdkvyetenaiyvkttllgPepgeevtqa 47 
                                     +GY ++v +v +++++i v ++    ++g+ev ++
  gi|91774060|ref|YP_566752.1| 562 LEEGYVLNVVEVDKNGDKIFVSLS----KDGDEVDEI 594
                                   568******************998....556666554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00058
                        PrcB_C  13 gGYsievdkvyetenaiyvkttllgPepgeev.tqal 48 
                                   +GYs++v +v ++++++ v+++    ++g+ev +q+l
  gi|91774060|ref|YP_566752.1| 839 EGYSLDVVEVNKDGDKVFVELS----KDGDEVdEQVL 871
                                   7********************9....45555525554 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.7   8.2e+03      31      62 ..     565     597 ..     560     603 .. 0.66
   2 ?   -3.4   0.0       3.6   1.1e+04      81      99 ..     706     723 ..     704     724 .. 0.76
   3 ?   -2.1   0.0       1.4   4.2e+03      30      58 ..     839     868 ..     834     884 .. 0.74
   4 ?   -2.1   0.1       1.4     4e+03      37      55 ..     932     950 ..     930     969 .. 0.74
   5 ?    0.6   0.0       0.2   6.1e+02      19      55 ..    1002    1038 ..     984    1061 .. 0.80
   6 ?    5.0   0.0    0.0084        25      13      54 ..    1186    1227 ..    1177    1252 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                  Cupredoxin_1  31 gfePskievka.gekvklkiknkdktpeefese 62 
                                   g+  +++ev + g k+ + + ++++++ e+++ 
  gi|91774060|ref|YP_566752.1| 565 GYVLNVVEVDKnGDKIFVSLSKDGDEVDEIVVS 597
                                   666677777542567777777777777776654 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
                  Cupredoxin_1  81 aplkpGeYeftcdmhmdak 99 
                                    + +pG+Ye+ + + +d k
  gi|91774060|ref|YP_566752.1| 706 DMSEPGTYELRGTIAED-K 723
                                   6789****998777666.5 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.4
                  Cupredoxin_1  30 ggfePskievka.gekvklkiknkdktpee 58 
                                   +g++ +++ev++ g kv +++ ++++++ e
  gi|91774060|ref|YP_566752.1| 839 EGYSLDVVEVNKdGDKVFVELSKDGDEVDE 868
                                   678888899865378888899888888744 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.4
                  Cupredoxin_1  37 ievkagekvklkiknkdkt 55 
                                   +e+k+  ++k+++knkd+ 
  gi|91774060|ref|YP_566752.1| 932 MEIKTISSIKIEMKNKDSI 950
                                   5777777889999999874 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.2
                  Cupredoxin_1   19 aektveitvkdggfePskievkagekvklkiknkdkt 55  
                                    + +++++tv++ g   + ++vkag  v  + +n+++ 
  gi|91774060|ref|YP_566752.1| 1002 EGDKITVTVTSRGSLINGVTVKAGSIVLGTTDNEGEV 1038
                                    5578999999999999999999998666556666555 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.0084
                  Cupredoxin_1   13 skaaaaaektveitvkdggfePskievkagekvklkiknkdk 54  
                                    ++ +aa++ tve++v+d++   ++i +  ge+++++++ +  
  gi|91774060|ref|YP_566752.1| 1186 NNGKAAGSYTVELVVNDNTTATQEISLGVGESTQVEFEYTAG 1227
                                    56779999**************************99986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); 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):               6  [number of targets reported over threshold]
# CPU time: 0.85u 0.27s 00:00:01.12 Elapsed: 00:00:00.42
# Mc/sec: 9262.13
//
Query:       gi|91774061|ref|YP_566753.1|  [L=167]
Description: XRE family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-06   26.1   0.2      2e-05   24.6   0.0    1.8  2  HTH_3     Helix-turn-helix
  ------ inclusion threshold ------
      0.019   14.5   0.6      0.029   14.0   0.6    1.3  1  PrpR_N    Propionate catabolism activator
       0.12   12.6   0.0       0.28   11.4   0.0    1.8  1  HTH_17    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 !   24.6   0.0   3.3e-09     2e-05       6      48 ..      22      64 ..      17      67 .. 0.89
   2 ?   -2.5   0.0      0.92   5.5e+03      35      44 ..     135     144 ..     134     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.3e-09
                                  HHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHH CS
                         HTH_3  6 kqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaL 48
                                  + l l+  e++e++++++st++++++G r P+++tl  + k+ 
  gi|91774061|ref|YP_566753.1| 22 EDLELTAIEFSEYANIPPSTLYKLMSGNRGPNMRTLRQIVKTI 64
                                  56779999*******************************9975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.92
                                   CSBHHHHHHH CS
                         HTH_3  35 nPsletlkkl 44 
                                   +P++e+++++
  gi|91774061|ref|YP_566753.1| 135 SPTVEKIIRI 144
                                   5999999887 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   4.8e-06     0.029      73     156 ..      75     161 ..      55     166 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-06
                        PrpR_N  73 kialvgfeniikglktlsell.dldieiytin..seeeaeaavkelkaegvevvvGdgvvadlAek.aGlksvlltsgkes 149
                                    ia+++ + +++++++ ++ + ++  +i++++  + eea  a  ++ +eg +++v+  +v+ ++ek + +++  ++  k+s
  gi|91774061|ref|YP_566753.1|  75 FIAVIAARPVLDNINETKRKIgGTLCTIREYSatTMEEAIIAAVRAEREGAKALVCAPIVSPTVEKiIRIPVATIMP-KNS 154
                                   57777777777777777766634333444443003333333334445678888888888887777744555555555.777 PP

                        PrpR_N 150 vrqAiee 156
                                   v +Aie 
  gi|91774061|ref|YP_566753.1| 155 VIEAIEA 161
                                   7777764 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.7e-05      0.28       2      28 ..      26      52 ..      25      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrgelp 28
                                  lt  E++e+ ++ +st+y+l + ++ p
  gi|91774061|ref|YP_566753.1| 26 LTAIEFSEYANIPPSTLYKLMSGNRGP 52
                                  7999****************9765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1208.74
//
Query:       gi|91774062|ref|YP_566754.1|  [L=319]
Description: ABC transporter, substrate-binding protein, aliphatic sulphonates [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  117.5   0.0    1.1e-33  117.0   0.0    1.2  1  NMT1_2          NMT1-like family
    4.1e-14   53.0   0.0    5.7e-14   52.6   0.0    1.2  1  NMT1            NMT1/THI5 like
    3.7e-05   23.5   0.0    4.4e-05   23.2   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0067   15.9   0.0      0.016   14.6   0.0    1.7  2  NMT1_3          NMT1-like family
     0.0099   15.3   0.0      0.027   13.9   0.0    1.7  2  SBP_bac_3       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.029   14.8   0.0      0.055   13.9   0.0    1.4  1  Ppnp            Pyrimidine/purine nucleoside phosphorylase


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 !  117.0   0.0   3.7e-37   1.1e-33       5     237 ..      20     240 ..      16     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 3.7e-37
                        NMT1_2   5 keqlklGfialtdaaplvvakekglfake....Glt.velekqaswaelrdkllagelDaahv.ltpapllidlGiggaka 79 
                                    +++++G+++ t+  + + a e+g+ a+     G+  ++  ++  ++  +  ++ag++D+a+v  +p++++++ G+     
  gi|91774062|ref|YP_566754.1|  20 LTEINIGYQPSTHQISYMTAFENGWWAEDlapfGIMsINEFEFPTGTPEMHSMIAGNIDVAYVgAAPVISALSTGL----- 95 
                                   689*************************99****999***************************************..... PP

                        NMT1_2  80 dmkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldpeadvklvvvp 160
                                   d k++a++n++G  ++l+n+       + ++ +dl       ++lkia+  pg  +d++++ wL  +Gl+p +dv++v++ 
  gi|91774062|ref|YP_566754.1|  96 DAKIVAAVNTQGSNLVLRNE------FKYDGPADL-------EGLKIATFPPGTIQDTIFKEWLVDNGLEPGTDVEVVAMG 163
                                   *******************8......777889888.......79************************************* PP

                        NMT1_2 161 ppqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvkalleAtkw 237
                                   p ++ a+l+ag++dg + + P +   + eg G+ ++ s+e++ dh ++vl+v+ d++ +np++++++vk++++A ++
  gi|91774062|ref|YP_566754.1| 164 PGDATAALAAGKVDGVFLPHPAPTFIEVEGSGRSVVASGEILADHACCVLVVSGDLIRNNPELVEQIVKTHIKAIEY 240
                                   **************************************************************************876 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.9e-17   5.7e-14      34     208 ..      68     240 ..      30     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.9e-17
                                   HHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHH CS
                          NMT1  34 atelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGkrigyvg.spfekallkalla 113
                                    +  + +g+ d++      ++ a + gl+ + vaa++ ++ s+l+ + + + + p+DL+G +i++++ + ++++++k+ l 
  gi|91774062|ref|YP_566754.1|  68 EMHSMIAGNIDVAYVGAAPVISALSTGLDAKIVAAVN-TQGSNLVLRNEFKYDGPADLEGLKIATFPpGTIQDTIFKEWLV 147
                                   3455778****************************99.777889999999**************9887999********** PP

                                   HTT--G.GG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HH CS
                          NMT1 114 kdggdp.sdvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrifaladlgvpdyyslvlitnekllkenpe 193
                                    +g++p  dv++v +g  ++++al++gkvD ++    +  ++e   eg  ++++a  ++   d    vl+++ +l+++npe
  gi|91774062|ref|YP_566754.1| 148 DNGLEPgTDVEVVAMGPGDATAALAAGKVDGVFLPHPAPTFIE--VEGSGRSVVASGEILA-DHACCVLVVSGDLIRNNPE 225
                                   ****88579***********************98888866666..6777777777777776.77779************** PP

                                   HHHHHHHHHHHHHHH CS
                          NMT1 194 lvkkFlrAlkkGyey 208
                                   lv+++++   k++ey
  gi|91774062|ref|YP_566754.1| 226 LVEQIVKTHIKAIEY 240
                                   *******99999887 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 !   23.2   0.0   1.5e-08   4.4e-05      44     165 ..      70     183 ..      59     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.5e-08
                                   HHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHH CS
                Phosphonate-bd  44 ealragqvDiaflgplayvqardqa.gveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsGylvpa 123
                                    ++ ag++D+a++g+ +++ a     +++ +a+        +  s ++ r++ +++  +dL+g +ia   p     +++ +
  gi|91774062|ref|YP_566754.1|  70 HSMIAGNIDVAYVGAAPVISALSTGlDAKIVAAVN------TQGSNLVLRNEFKYDGPADLEGLKIATFPPGTIQDTIF-K 143
                                   5799****************997643555444443......578999*************************9996666.5 PP

                                   HHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEH CS
                Phosphonate-bd 124 alLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsa 165
                                    +Lv ++gl+p++d + v +g  da+ +a+++g++d  +++ 
  gi|91774062|ref|YP_566754.1| 144 EWLV-DNGLEPGTDVEVVAMGPGDAT-AALAAGKVDGVFLPH 183
                                   6797.9**********9999866655.678******988654 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.35     1e+03     149     176 ..      65      92 ..      21     110 .. 0.55
   2 !   14.6   0.0   5.4e-06     0.016      84     175 ..      99     188 ..      80     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.35
                        NMT1_3 149 ygesadalkdgqldgaalvaGvPvsavt 176
                                    ++ +  +  g++d+a + a++ +sa +
  gi|91774062|ref|YP_566754.1|  65 GTPEMHSMIAGNIDVAYVGAAPVISALS 92 
                                   3456677888888888777777777665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.4e-06
                        NMT1_3  84 aitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealgls.ekdlklleelgygesadalkdgqldg 163
                                   ++++++++  +lv++++ + +  adl+g +++  p+g+ +++ + + l   gl+  +d+++   +g+g+++ al+ g++dg
  gi|91774062|ref|YP_566754.1|  99 IVAAVNTQGSNLVLRNEFKYDGPADLEGLKIATFPPGTIQDTIFKEWLVDNGLEpGTDVEV-VAMGPGDATAALAAGKVDG 178
                                   677888899999******************************************6688885.889**************** PP

                        NMT1_3 164 aalvaGvPvsav 175
                                   ++l+  +P+  +
  gi|91774062|ref|YP_566754.1| 179 VFLP--HPAPTF 188
                                   ***9..555555 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 !   13.9   0.0     9e-06     0.027      85     162 ..     106     185 ..      96     233 .. 0.75
   2 ?   -1.8   0.0      0.57   1.7e+03     140     173 ..     222     255 ..     197     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-06
                                   EEEEEEEEETTSHGTCCHSSCGCGTTSEEE.EETTSHHHHHHHHHHHC.......TSEEEEESSHHHHHHHHHTTSSSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3  85 agqvllvrkkdaskissiksladLkgkkvg.vqagstaeellkeelkk.......gaeivefdtleealqaLkngrvdavv 157
                                    g +l+ r ++     +++++adL+g k++    g+ +++++ke+l +       ++e+v      +a++aL++g+vd v+
  gi|91774062|ref|YP_566754.1| 106 QGSNLVLR-NE----FKYDGPADLEGLKIAtFPPGTIQDTIFKEWLVDnglepgtDVEVV-AMGPGDATAALAAGKVDGVF 180
                                   56667777.54....4789999****8888456778888778876666777795444444.46899**************9 PP

                                   EEHHH CS
                                   xxxxx RF
                     SBP_bac_3 158 adspv 162
                                      p+
  gi|91774062|ref|YP_566754.1| 181 LPHPA 185
                                   88776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.57
                                   SHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3 140 tleealqaLkngrvdavvadspvlaylvkknpdk 173
                                   +++e+++++ +  + a+ +d+ ++ +++++ ++k
  gi|91774062|ref|YP_566754.1| 222 NNPELVEQIVKTHIKAIEYDNLNIDDAANTFANK 255
                                   6667777777777777777777777776665555 PP

>> Ppnp  Pyrimidine/purine nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.055      26      58 ..      52      84 ..      37      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                  EEEE-SECEEEEESS-EEEEEEESEEEEEETT- CS
                          Ppnp 26 vGvmlpgeyeFgtsakEvmevvsGelevklpge 58
                                   G+m+  e+eF t+++E+ ++++G+++v   g+
  gi|91774062|ref|YP_566754.1| 52 FGIMSINEFEFPTGTPEMHSMIAGNIDVAYVGA 84
                                  7**************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2362.13
//
Query:       gi|91774063|ref|YP_566755.1|  [L=262]
Description: ABC nitrate/sulfonate/bicarbonate transporter, inner membrane subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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   73.7  12.1    1.5e-20   73.7  12.1    1.6  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   1.3      0.25   4.5e+03      31     124 ..      41      56 ..      18      80 .. 0.49
   2 !   73.7  12.1   8.2e-25   1.5e-20       1     178 [.      81     247 ..      81     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.25
                  BPD_transp_1  31 PsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppii 111
                                   Psf                                                                              
  gi|91774063|ref|YP_566755.1|  41 PSFT----------------------------------------------------------------------------- 44 
                                   3333............................................................................. PP

                  BPD_transp_1 112 tglilafggllgg 124
                                     +++af+ ++ g
  gi|91774063|ref|YP_566755.1|  45 -DVLFAFIKIIEG 56 
                                   .222222222222 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 8.2e-25
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpk 81 
                                   gi++G++++    k ++++l+pli++++ +P+++++++ +       ++g + +++ ++++++a+++v++++ ++++s+pk
  gi|91774063|ref|YP_566755.1|  81 GIPIGVVMG--WFKNVNHALDPLIEIIRPIPPLAWIPFAI------VWFGLTHTSAGFVVFIGAVFPVIINTFDGFKSVPK 153
                                   89*******..9999*************************......9********************************** PP

                  BPD_transp_1  82 dlveaaralGa.srwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlal 161
                                    +veaa++lG+ s   ++r+v+lP+a+p+i++g+++++g  +   v++e++g    ++t+ l   ++  y + ++  vl++
  gi|91774063|ref|YP_566755.1| 154 FYVEAAKVLGCmSSGSLIRHVALPSAMPSIASGIRISMGVGWMCLVAAEMFG----VSTTGLGYKIWWHYYLHQMDFVLVY 230
                                   **********74888999**********************************....5555555555555555554588888 PP

                  BPD_transp_1 162 viavlllnlvadilqrl 178
                                    +++  l l++d l r+
  gi|91774063|ref|YP_566755.1| 231 MLILGFLGLFIDRLFRW 247
                                   88888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1946.51
//
Query:       gi|91774064|ref|YP_566756.1|  [L=252]
Description: ABC nitrate/sulfonate/bicarbonate transporter, ATPase subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  115.1   0.0    5.1e-33  114.5   0.0    1.3  1  ABC_tran      ABC transporter
      6e-09   36.4   1.4    1.2e-07   32.2   0.2    2.9  2  AAA           ATPase family associated with various cellular 
    9.6e-09   35.5   0.0    0.00029   20.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      2e-05   24.6   0.0     0.0099   15.8   0.0    2.2  2  ATPase_2      ATPase domain predominantly from Archaea
    4.3e-05   23.8   0.1    0.00024   21.4   0.1    2.2  1  AAA_22        AAA domain
    9.2e-05   22.4   0.1    0.00021   21.2   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
     0.0003   21.2   0.0     0.0047   17.3   0.0    2.1  2  AAA_16        AAA ATPase domain
    0.00035   20.9   0.1     0.0042   17.3   0.0    2.3  2  AAA_28        AAA domain
    0.00036   20.7   0.0    0.00096   19.3   0.0    1.7  1  AAA_33        AAA domain
    0.00047   19.7   0.0       0.34   10.3   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00049   19.9   0.0     0.0013   18.5   0.0    1.5  2  AAA_15        AAA ATPase domain
     0.0011   18.9   0.0      0.004   17.1   0.0    1.9  2  Rad17         Rad17 P-loop domain
     0.0025   18.4   0.1     0.0062   17.1   0.1    1.7  1  AAA_23        AAA domain
     0.0026   17.5   0.0      0.027   14.2   0.0    2.2  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0045   16.9   0.0      0.012   15.5   0.0    1.7  1  NACHT         NACHT domain
     0.0058   16.3   0.0      0.012   15.3   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0079   15.0   0.2       0.36    9.6   0.0    2.8  2  ABC_ATPase    Predicted ATPase of the ABC class
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.047   13.7   0.0    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.022   14.2   0.0      0.057   12.9   0.0    1.6  2  PhoH          PhoH-like protein
      0.034   14.1   0.1        3.5    7.5   0.0    2.3  2  NTPase_1      NTPase
      0.038   14.4   0.1       0.21   12.0   0.0    2.3  2  RNA_helicase  RNA helicase
      0.039   13.2   0.1      0.095   11.9   0.0    1.6  2  NB-ARC        NB-ARC domain
      0.043   13.9   0.1       0.38   10.8   0.0    2.4  3  AAA_14        AAA domain
      0.059   13.1   0.0       0.16   11.7   0.0    1.7  2  IstB_IS21     IstB-like ATP binding protein
      0.066   13.3   0.1       0.17   12.0   0.1    2.1  1  MMR_HSR1      50S ribosome-binding GTPase
      0.073   12.6   0.0       0.13   11.8   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
      0.077   12.9   0.0        3.4    7.5   0.0    2.2  2  APS_kinase    Adenylylsulphate kinase
      0.088   12.5   0.0       0.35   10.5   0.0    1.8  2  AAA_30        AAA domain
      0.094   12.4   0.1       0.23   11.1   0.0    1.7  2  AAA_24        AAA domain
       0.13   12.2   0.0       0.24   11.4   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.0   8.6e-36   5.1e-33       1     136 [.      24     163 ..      24     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 8.6e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+nv+l++k  e v ++G++G+GK+tLl+++agl++ ++G+i+ldg+d++       ++  g+++qe +lfp  tv +n  
  gi|91774064|ref|YP_566756.1|  24 LDNVDLEIKDKEFVCFIGPSGCGKTTLLRTIAGLERLDKGQITLDGEDITI-----PDSTRGMVFQEYSLFPWRTVIQNit 99 
                                   79*******************************************999988.....99999**************99999* PP

                                   ........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                            +++    +ek+l+ +gl++++++      ++LSgG++qrva+aral+++pk+ll+DEp+
  gi|91774064|ref|YP_566756.1| 100 fgpqmngiSKNKTlevAEKYLNLVGLEQFRNSYP----YELSGGMRQRVAIARALANEPKVLLMDEPF 163
                                   ******9844555223666666666666666555....*****************************6 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 !   32.2   0.2     2e-10   1.2e-07       1     128 [.      37     220 ..      37     224 .. 0.66
   2 ?    0.3   0.1       1.4   8.6e+02      76      98 ..     229     251 ..     221     252 .] 0.81

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2e-10
                                   EEEESSTTSSHHHHHHHHHHH..HTHE...................................................... CS
                           AAA   1 vllyGppGtGKTllakavake..lgve...................................................... 25 
                                   v+++Gp G+GKT+l + +a    l+                                                        
  gi|91774064|ref|YP_566756.1|  37 VCFIGPSGCGKTTLLRTIAGLerLDKGqitldgeditipdstrgmvfqeyslfpwrtviqnitfgpqmngisknktlevae 117
                                   799****************98553333222333334444444555555555555555655666666666666666666666 PP

                                   .EEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTE CS
                           AAA  26 .fleisgsell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskv 103
                                    +l++ g e + ++y  e +  +r+ ++ a++ a +p++l++DE      ++       +++++++Ll+++d+++    ++
  gi|91774064|ref|YP_566756.1| 118 kYLNLVGLEQFrNSYPYELSGGMRQRVAIARALAnEPKVLLMDEPFGALDAQ------TRNTLQKELLQVWDKYQI---TI 189
                                   6555555555546699999999999999999999999*******76666777......799*************99...35 PP

                                   EEEEEESS.....GGGSTHHHHS.TTSSEEE CS
                           AAA 104 ivigatnr.....pdkldpallr.gRfdrki 128
                                   ++++ + +      dk+     r gR++++i
  gi|91774064|ref|YP_566756.1| 190 VFVTHSVDeavflADKIVVMSARpGRVKKVI 220
                                   5555554444444444444444555555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                                   TCCCHHHHHHHHHHHHHHHHTTT CS
                           AAA  76 gseseeeervvnqLlteldgvkk 98 
                                   +++s+e++++ nqLl++l ++++
  gi|91774064|ref|YP_566756.1| 229 ERTSSEANELRNQLLKMLAEERR 251
                                   467899999*******9988765 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   0.0   4.8e-07   0.00029       1      35 [.      36      70 ..      36     114 .. 0.75
   2 !   13.1   0.0   0.00011     0.063     233     298 ..     132     195 ..      92     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.8e-07
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltde 35
                                  + ++iGp g+GK++LL+++ +l rld+ ++ l  e
  gi|91774064|ref|YP_566756.1| 36 FVCFIGPSGCGKTTLLRTIAGLERLDKGQITLDGE 70
                                  5789******************8874444443333 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                        AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTHS 298
                                    ++elS G+++  a++ al+  +   ++ll DEp   L+      l+++ll++ ++ +   + ++++THS
  gi|91774064|ref|YP_566756.1| 132 YPYELSGGMRQRVAIARALANEP---KVLLMDEPFGALDAqtrnTLQKELLQVWDKYQ---ITIVFVTHS 195
                                   5799********99999999888...9*************777777777777775554...6*******9 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-05    0.0099      21     108 ..      35     122 ..      26     129 .. 0.63
   2 !    6.9   0.0     0.009       5.4     121     190 ..     156     223 ..     142     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                      ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie.eeeekkklekalgiavpkaeleeilk.eks 99 
                                   e++   Gp g+GKt+Ll+ i+     +dk  i   + +++ i   ++ +  +e++    + ++++ +   +++ i+k ++ 
  gi|91774064|ref|YP_566756.1|  35 EFVCFIGPSGCGKTTLLRTIAGLE-RLDKGQI-TLDGEDITIPDSTRGMVfQEYSLFPWRTVIQNITFGPQMNGISKnKTL 113
                                   455556************998766.3343333.345555555554444434666666666666666666666666666666 PP

                      ATPase_2 100 klvfkaiel 108
                                   + ++k+++l
  gi|91774064|ref|YP_566756.1| 114 EVAEKYLNL 122
                                   666666665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.009
                      ATPase_2 121 iiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsS..eglfie.rvyneselegrhky.ilvd 190
                                   ++++De + + d + +  + l keLl+++++    +++++v+++ S  e +f+  ++   s + gr+k  i+vd
  gi|91774064|ref|YP_566756.1| 156 VLLMDEPFGALDAQTR--NTLQKELLQVWDK----YQITIVFVTHSvdEAVFLAdKIVVMSARPGRVKKvINVD 223
                                   89*********77766..************9....899999888886688888777888888888887767666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1     4e-07   0.00024       4     128 ..      33     192 ..      29     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4e-07
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...........................erpevv.......fvtlpss 50 
                                   ++ +++ +G+sG+GKTtllr+++     ++ + +                                +        ++  s+
  gi|91774064|ref|YP_566756.1|  33 DKEFVCFIGPSGCGKTTLLRTIAGLERLDKGQITldgeditipdstrgmvfqeyslfpwrtV----IqnitfgpQMNGISK 109
                                   78899*****************9877655555557889999988888888877777654430....233333567777777 PP

                        AAA_22  51 tsskdllrellralglelka..erlsseellealeqalrarav.ielliiDEaqh.lr...seealeeLrsllnlsrkgvq 124
                                   ++  +++++ l+ +gle+ +  ++ +++  +++    +ra a  +++l+ DE    l+   ++++ +eL + ++  +++++
  gi|91774064|ref|YP_566756.1| 110 NKTLEVAEKYLNLVGLEQFRnsYPYELSGGMRQRVAIARALANePKVLLMDEPFGaLDaqtRNTLQKELLQVWD--KYQIT 188
                                   77777788888888877777553333333333333333333336779999995444766433666667777777..88888 PP

                        AAA_22 125 liLv 128
                                   +++v
  gi|91774064|ref|YP_566756.1| 189 IVFV 192
                                   8877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.5e-07   0.00021      86     130 ..      20      65 ..       3      71 .. 0.77
   2 ?   -2.8   0.0       8.8   5.3e+03      21      26 ..     189     194 ..     168     222 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.5e-07
                                   THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                   ++ +l+++  ++kd ++++++G+SG GK+tL+ ++++ ++l  g++
  gi|91774064|ref|YP_566756.1|  20 STLALDNVDLEIKDkEFVCFIGPSGCGKTTLLRTIAGLERLDKGQI 65 
                                   44566778888998799******************99888877776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.8
                                   EEEEST CS
                   RsgA_GTPase  21 ivvslk 26 
                                   iv+ ++
  gi|91774064|ref|YP_566756.1| 189 IVFVTH 194
                                   222222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.8e-06    0.0047      23      45 ..      33      55 ..      20      87 .. 0.83
   2 ?    1.9   0.0      0.42   2.5e+02      56     127 ..     136     246 ..     121     252 .] 0.68

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.8e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                  + e v ++G+sG+GK++l+r+++
  gi|91774064|ref|YP_566756.1| 33 DKEFVCFIGPSGCGKTTLLRTIA 55
                                  558899**************997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.42
                        AAA_16  56 lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala.............................. 106
                                   l+g  +q       +a+a+ala+ e    l de+  a+ ++ r +l+++l                               
  gi|91774064|ref|YP_566756.1| 136 LSGGMRQR------VAIARALAN-EPKVLLMDEPFGALDAQTRNTLQKELLqvwdkyqitivfvthsvdeavfladkivvm 209
                                   55555555......667888844.777777777777777777777777777777777777777888777777777777777 PP

                        AAA_16 107 ................avpelagaeasrllellkrll 127
                                                     +e +++ea+ l+++l ++l
  gi|91774064|ref|YP_566756.1| 210 sarpgrvkkvinvdlpRPRERTSSEANELRNQLLKML 246
                                   7777777777777776666677777777777777776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.1e-06    0.0042       2      37 ..      37      84 ..      36     101 .. 0.70
   2 ?    0.5   0.0       1.1   6.4e+02     132     162 ..     169     198 ..     165     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.1e-06
                        AAA_28  2 ivitGgestGKTtlleaLa..ar.........gyp.vvpEaareilee 37
                                  ++++G++++GKTtll+ +a  +r         g   ++p++ r ++++
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTIAglERldkgqitldGEDiTIPDSTRGMVFQ 84
                                  89**************99966334444333433223456666666655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                        AAA_28 132 eereaiderlrealrelgipviivpsgdvee 162
                                   + r+ +++ l++++++++i ++ v + +v+e
  gi|91774064|ref|YP_566756.1| 169 QTRNTLQKELLQVWDKYQITIVFV-THSVDE 198
                                   568888999999999999999999.877765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.6e-06   0.00096       2     109 ..      37     199 ..      36     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdt.................................................. 32 
                                   v ++G++G+GK+tl++ ++   g ++l++ +                                                  
  gi|91774064|ref|YP_566756.1|  37 VCFIGPSGCGKTTLLRTIA---GLERLDKGQitldgeditipdstrgmvfqeyslfpwrtviqnitfgpqmngisknktle 114
                                   789**************97...55555555555555558999999999999999999999888888888888877777777 PP

                        AAA_33  33 ...lrr.rlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat..nlsrrer....arflklarrlgvpvrivv 103
                                          +l+g +q + +++ +++  ++q++ ++ar  + + + ++ d +   l++++r    +++l+++ ++   +  v+
  gi|91774064|ref|YP_566756.1| 115 vaeK-YlNLVGLEQFRNSYPYELSGGMRQRV-AIARALANEPKVLLMDEPfgALDAQTRntlqKELLQVWDKYQITIVFVT 193
                                   6532.23556666667778888888899888.8887777777777779884435555556666899999997776666666 PP

                        AAA_33 104 vetdee 109
                                    ++de+
  gi|91774064|ref|YP_566756.1| 194 HSVDEA 199
                                   666666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0037       2.2      23      44 ..      33      54 ..      20      57 .. 0.84
   2 !   10.3   0.0   0.00057      0.34     136     203 ..     135     198 ..      58     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                                  TSSEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 23 sksftaivGpNGSGKsnlldAi 44
                                  +k+f + +Gp G+GK+ ll  i
  gi|91774064|ref|YP_566756.1| 33 DKEFVCFIGPSGCGKTTLLRTI 54
                                  57899************99877 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00057
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                   +LSgG ++ va+a  +A    +p+ + l+De   aLD++ ++ + + l +  ++ Q+ ++ +++ + e
  gi|91774064|ref|YP_566756.1| 135 ELSGGMRQRVAIARALAN---EPK-VLLMDEPFGALDAQTRNTLQKELLQVWDKYQITIVFVTHSVDE 198
                                   89*****99999988773...444.679**********************999***988766655433 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.3e-06    0.0013      14      69 ..      24      76 ..      23      82 .. 0.79
   2 ?   -2.1   0.0         4   2.4e+03     322     365 ..     152     195 ..     129     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                  l++v+++++++ + ++iG+ ++GK+++l+ +  +   +    k  i+++ ed+ i +
  gi|91774064|ref|YP_566756.1| 24 LDNVDLEIKDKeFVCFIGPSGCGKTTLLRTIAGLERLD----KGQITLDGEDITIPD 76
                                  678889999888*****************996665544....666777777776665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   +++++ll++EP   L  q  + l k l+ + ++ +  +++ THS
  gi|91774064|ref|YP_566756.1| 152 NEPKVLLMDEPFGALDAQTRNTLQKELLQVWDKYQITIVFVTHS 195
                                   46678888888888888888888888888888887778888888 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.7e-06     0.004      32      66 ..      21      55 ..       8      85 .. 0.85
   2 ?   -1.4   0.0       3.1   1.8e+03      39      75 ..     149     184 ..     141     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.7e-06
                         Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                    +l+   Le + k+ +   GPsGCgk+t ++ ++
  gi|91774064|ref|YP_566756.1| 21 TLALDNVDLEIKDKEFVCFIGPSGCGKTTLLRTIA 55
                                  457888999*9*9*****************99876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                         Rad17  39 vLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75 
                                    L ++  ++LL+  P G   + + + L kel     +
  gi|91774064|ref|YP_566756.1| 149 ALANE-PKVLLMDEPFGALDAQTRNTLQKELLQVWDK 184
                                   55555.4577788888887777777777777554444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     1e-05    0.0062      12      39 ..      26      54 ..      14      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
                        AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAi 39
                                  +++++  +k +++++Gp G+GKTT+l+ i
  gi|91774064|ref|YP_566756.1| 26 NVDLEIkDKEFVCFIGPSGCGKTTLLRTI 54
                                  44455578899***************977 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.5e-05     0.027       4      25 ..      37      58 ..      34      75 .. 0.86
   2 ?    0.6   0.0      0.73   4.4e+02      98     122 ..     103     127 ..      76     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
                     PduV-EutP  4 illiGkvgsGKttLtqalkgee 25
                                  + +iG++g+GKttL +++ g e
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTIAGLE 58
                                  789*************999865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.73
                     PduV-EutP  98 kidlaedeenieaveelLksaGaek 122
                                   +++  ++++ +e++e++L+ +G e+
  gi|91774064|ref|YP_566756.1| 103 QMNGISKNKTLEVAEKYLNLVGLEQ 127
                                   5677778999************987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.1e-05     0.012       3      21 ..      37      55 ..      35      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                  EEEEC-TTTCHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkla 21
                                  v+  G++G+GKTtLl+ +a
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTIA 55
                                  8999*************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 !   15.3   0.0     2e-05     0.012      13      39 ..      25      51 ..      22      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                  d+ ++ei+ k+++ ++GpsG GK+Tll
  gi|91774064|ref|YP_566756.1| 25 DNVDLEIKDKEFVCFIGPSGCGKTTLL 51
                                  66788999899***************8 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 ?    0.3   0.0      0.38   2.3e+02     248     265 ..      38      55 ..      29      58 .. 0.77
   2 !    9.6   0.0   0.00061      0.36     324     413 ..     137     211 ..     128     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.38
                                   EEEE-TTSSHHHHHHHHH CS
                    ABC_ATPase 248 lIvGggfhGKsTLLeAle 265
                                     +G+   GK+TLL+ ++
  gi|91774064|ref|YP_566756.1|  38 CFIGPSGCGKTTLLRTIA 55 
                                   55788888******9985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00061
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyldv 404
                                   SG + q ++i++al ++ k+lL+DE   A     r ++ +                + ++++k++++++ v+ ++++ + +
  gi|91774064|ref|YP_566756.1| 137 SGGMRQRVAIARALANEPKVLLMDEPFGALDAQTRNTLQK---------------ELLQVWDKYQITIVFVTHSVDEAVFL 202
                                   7778888888888888888888888777765555444444...............45577888888888888888888888 PP

                                   -SEEEEEET CS
                    ABC_ATPase 405 Adtvilmee 413
                                   Ad++++m +
  gi|91774064|ref|YP_566756.1| 203 ADKIVVMSA 211
                                   888888865 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 ?   13.7   0.0   7.8e-05     0.047       2      21 ..      37      56 ..      36      71 .. 0.91
   2 ?   -1.4   0.0       3.6   2.2e+03      81      81 ..     170     170 ..     132     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-05
                                  EEEE--SSSSHHHHHHHGGG CS
                         AAA_5  2 vlLvGppGtgKselaerlaa 21
                                  v+ +Gp+G+gK++l + +a 
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTIAG 56
                                  899*************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                                   H CS
                         AAA_5  81 v 81 
                                   +
  gi|91774064|ref|YP_566756.1| 170 T 170
                                   1 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.5e-05     0.057      16      49 ..      31      65 ..      21      67 .. 0.81
   2 ?   -2.3   0.0       4.2   2.5e+03       5      25 ..     171     191 ..     166     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.5e-05
                                  HHH-SEEEEE--TTSSTT.HHHHHHHHHHHHTTS- CS
                          PhoH 16 lkkndivfaiGpaGtGKt.ylavalavealkkkkv 49
                                  +k++++v+ iGp+G+GKt +l + +++e l k+++
  gi|91774064|ref|YP_566756.1| 31 IKDKEFVCFIGPSGCGKTtLLRTIAGLERLDKGQI 65
                                  78999************825667788888888765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                                   -SHHHHHHHHHHHH-SEEEEE CS
                          PhoH   5 ktkeQkeylealkkndivfai 25 
                                   +++ Qke+l++ +k++i++++
  gi|91774064|ref|YP_566756.1| 171 RNTLQKELLQVWDKYQITIVF 191
                                   666777777777777766554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0058       3.5       5      29 ..      40      66 ..      36      72 .. 0.73
   2 ?    4.4   0.0     0.052        31      87     137 ..     145     199 ..     111     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0058
                                  E--TTSSHHHHHHHHH..HHH...GGG CS
                      NTPase_1  5 TGppGvGKtTlvkkvl..ellkssgvk 29
                                   Gp+G GKtTl++ ++  e l++ +++
  gi|91774064|ref|YP_566756.1| 40 IGPSGCGKTTLLRTIAglERLDKGQIT 66
                                  59***********99622455555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.052
                                   HHHHHHH.HHH-EEEE--.-STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS-.- CS
                      NTPase_1  87 ealrkal.seadviviDE.iGkmElksk.kfkeaveevLk.sekpvlavihrrk.d 137
                                   + + +al +e+ v+++DE  G +  +++ ++++++ +v +  +  +++v h  +  
  gi|91774064|ref|YP_566756.1| 145 A-IARALaNEPKVLLMDEpFGALDAQTRnTLQKELLQVWDkYQITIVFVTHSVDeA 199
                                   3.3344448999******88****9875268999******6666777777766532 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00036      0.21       1      19 [.      37      55 ..      37      86 .. 0.88
   2 ?   -1.0   0.0       3.9   2.3e+03      51      88 ..     155     193 ..     150     211 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00036
                  RNA_helicase  1 iwlyGpsgeGKStlakeLa 19
                                  +++ Gpsg+GK+tl +++a
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTIA 55
                                  6899**********99954 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.9
                  RNA_helicase  51 evvvidDfgqvkdeenps.dlaelirlvsstpyplnmas 88 
                                   +v+++d+     d ++ +   +el+++ + +++++    
  gi|91774064|ref|YP_566756.1| 155 KVLLMDEPFGALDAQTRNtLQKELLQVWDKYQITIVFVT 193
                                   555666555555555333366666666666665554433 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016     0.095      17      41 ..      33      55 ..      23      63 .. 0.84
   2 ?   -2.7   0.0       4.5   2.7e+03      67     100 ..     215     246 ..     174     250 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                  TSCSEEEEEEESTTSSHHHHHHHHC CS
                        NB-ARC 17 elqslvvalvGmgGvGKttlakqil 41
                                  + +  +v + G  G+GKttl++ i 
  gi|91774064|ref|YP_566756.1| 33 DKE--FVCFIGPSGCGKTTLLRTIA 55
                                  445..99**************9885 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                                   HHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHC CS
                        NB-ARC  67 eiletilkeLslseddleekeeveslkrklvrlL 100
                                   ++ + i+ +L  +  ++ + e +e l ++l ++L
  gi|91774064|ref|YP_566756.1| 215 RVKKVINVDLP-RPRERTSSEANE-LRNQLLKML 246
                                   44445555552.223333344344.555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00063      0.38       3      27 ..      35      59 ..      33      87 .. 0.77
   2 ?    0.0   0.0       1.4   8.2e+02      63     100 ..     152     195 ..     109     219 .. 0.69
   3 ?   -2.1   0.0       6.2   3.7e+03      31      59 ..     217     245 ..     201     251 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00063
                        AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                  + ++  G+  +GKTtll++++  + 
  gi|91774064|ref|YP_566756.1| 35 EFVCFIGPSGCGKTTLLRTIAGLER 59
                                  567889************9985444 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.4
                        AAA_14  63 ekktylflDE......iqevpewekalkslvdegknldvivtGS 100
                                   ++ ++l++DE      +q  ++++k l ++ d+++   v+vt S
  gi|91774064|ref|YP_566756.1| 152 NEPKVLLMDEpfgaldAQTRNTLQKELLQVWDKYQITIVFVTHS 195
                                   46777888873333334555777777777777776666666665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.2
                        AAA_14  31 esilyinldderdkkladpekllelilek 59 
                                   ++++ ++l ++r++++++ ++l + +l++
  gi|91774064|ref|YP_566756.1| 217 KKVINVDLPRPRERTSSEANELRNQLLKM 245
                                   45666777777776666555555555554 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   0.00027      0.16      44      67 ..      31      54 ..      10      64 .. 0.81
   2 ?   -2.1   0.0       4.6   2.8e+03     108     142 ..     153     189 ..     141     200 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                     IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                  i++ke ++++GpsG GK+ l  ++
  gi|91774064|ref|YP_566756.1| 31 IKDKEFVCFIGPSGCGKTTLLRTI 54
                                  8899**************986655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
                     IstB_IS21 108 kvdllilDd.lgllpldqae..aellfeviekryerrs 142
                                   ++++l++D+ +g l+ +  +  +++l++v + +y+ + 
  gi|91774064|ref|YP_566756.1| 153 EPKVLLMDEpFGALDAQTRNtlQKELLQVWD-KYQITI 189
                                   5577788874455544433211345555543.355444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00028      0.17       2      21 ..      37      56 ..      36     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                  EEEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                  v+++G +  GK+tL++++ g
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTIAG 56
                                  89****************98 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.13      28      58 ..      29      61 ..      21      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                         AAA_7 28 lllknkkpvllvGptGtGKtviikd..llkkld 58
                                  l +k k  v+++Gp+G+GKt+++++   l++ld
  gi|91774064|ref|YP_566756.1| 29 LEIKDKEFVCFIGPSGCGKTTLLRTiaGLERLD 61
                                  56788999**************99843355555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0057       3.4       5      42 ..      37      73 ..      34      86 .. 0.86
   2 ?    3.1   0.0      0.13        80      66     140 ..     146     225 ..     138     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0057
                                  EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHT CS
                    APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvR 42
                                  v + G sg GK+t+ ++++  L++  +  ++LdG+ + 
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTIA-GLERLDKGQITLDGEDIT 73
                                  6789**********99998.899999999*****9885 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                                   HHHHHHHTT-EEEEE----SHHHHHHHHHHHHCH.......TEEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS CS
                    APS_kinase  66 vaklladaglivlvafisPyreeReaarelleea.......lkfievfvdtplevceerDpkglYkkareGeikeftGids 139
                                   +a+ la++  + l+    P+ +   ++r++l+++        ++  vfv  +++++     k +   ar G++k++  +d 
  gi|91774064|ref|YP_566756.1| 146 IARALANEPKVLLMD--EPFGALDAQTRNTLQKEllqvwdkYQITIVFVTHSVDEAVFLADKIVVMSARPGRVKKVINVDL 224
                                   566666666666654..355555555555555544444565788899*******999999999999*******99988886 PP

                                   - CS
                    APS_kinase 140 p 140
                                   p
  gi|91774064|ref|YP_566756.1| 225 P 225
                                   5 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00059      0.35      18      42 ..      34      58 ..      27      68 .. 0.80
   2 ?   -0.9   0.0       1.9   1.1e+03      33      59 ..     173     199 ..     135     221 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00059
                        AAA_30 18 drvavltGpAGtGKttalkalreaw 42
                                  + +++  Gp G GKtt+l++++ + 
  gi|91774064|ref|YP_566756.1| 34 KEFVCFIGPSGCGKTTLLRTIAGLE 58
                                  4588999************998765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                        AAA_30  33 talkalreaweaaggrviglAptgkaA 59 
                                   t+ k+l ++w++ + +++ ++++   A
  gi|91774064|ref|YP_566756.1| 173 TLQKELLQVWDKYQITIVFVTHSVDEA 199
                                   333444555555555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.23       5      22 ..      37      54 ..      34     112 .. 0.79
   2 ?   -2.2   0.0       4.9   2.9e+03     118     133 ..     182     197 ..     162     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                        AAA_24  5 iliyGpsgiGKTtlakel 22
                                  ++ +Gpsg GKTtl++++
  gi|91774064|ref|YP_566756.1| 37 VCFIGPSGCGKTTLLRTI 54
                                  6889***********998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.9
                        AAA_24 118 lqelrk...nvifiahekt 133
                                    +   k   +++f+ h+  
  gi|91774064|ref|YP_566756.1| 182 WD---KyqiTIVFVTHSVD 197
                                   22...24459999999765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0004      0.24      19      40 ..      34      55 ..      14      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                  TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                  ++++++ G+ G+GKTtl r +a
  gi|91774064|ref|YP_566756.1| 34 KEFVCFIGPSGCGKTTLLRTIA 55
                                  678****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 1776.51
//
Query:       gi|91774065|ref|YP_566757.1|  [L=148]
Description: hypothetical protein Mbur_2134 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-07   30.7   0.3    7.4e-07   29.4   0.2    1.7  1  Bactofilin  Polymer-forming cytoskeletal
  ------ inclusion threshold ------
      0.056   13.9   0.0        9.4    6.8   0.0    2.4  2  SCP2        SCP-2 sterol transfer family


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   8.2e-11   7.4e-07       9      93 ..      27     116 ..      19     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 8.2e-11
                    Bactofilin   9 ikGelevegdlri.dG.kveGdieakgklvvgeggkvegnikaeevvvaGt..vkGnveaeekvelkktakveGdika.ks 84 
                                   ++ +++++g++ +  G ++  d+e +g+l++g+++ v+g+ika+++ ++ +  ++Gn+++ + +++ ++ kv G+  + ++
  gi|91774065|ref|YP_566757.1|  27 FENSIKIDGNMIVgPGaNFWNDLEVSGSLQLGKESLVKGDIKASDALISTRceINGNIDVANDLTMLDNVKVGGSAICgNE 107
                                   4455555555555423366678899******************998887554499******************98777589 PP

                    Bactofilin  85 leieegavf 93 
                                   ++i +g+++
  gi|91774065|ref|YP_566757.1| 108 MSIRPGCQV 116
                                   999999987 PP

>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0047        42      76      92 ..      23      39 ..      17      42 .. 0.90
   2 ?    6.8   0.0    0.0011       9.4      67      97 ..      61      91 ..      45      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0047
                                  HHHHHTTSSEEEC-HHH CS
                          SCP2 76 qkafmqgkLkieGDiel 92
                                   kaf+   +ki+G++ +
  gi|91774065|ref|YP_566757.1| 23 RKAFFENSIKIDGNMIV 39
                                  58************976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0011
                                  HHHCTSS-HHHHHHTTSSEEEC-HHHHHHHH CS
                          SCP2 67 elaegklnpqkafmqgkLkieGDielaqkle 97
                                  +l++g ++++ a+ + + +i G+i++a  l 
  gi|91774065|ref|YP_566757.1| 61 SLVKGDIKASDALISTRCEINGNIDVANDLT 91
                                  589999*********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1023.90
//
Query:       gi|91774066|ref|YP_566758.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91774066|ref|YP_566758.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91774066|ref|YP_566758.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91774066|ref|YP_566758.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91774066|ref|YP_566758.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91774066|ref|YP_566758.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91774066|ref|YP_566758.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91774066|ref|YP_566758.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91774066|ref|YP_566758.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2019.78
//
Query:       gi|91774067|ref|YP_566759.1|  [L=234]
Description: hypothetical protein Mbur_2139 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.8      0.025   14.3   0.0    3.8  3  Prenyltrans      Prenyltransferase and squalene oxidase repea
    2.5e-08   33.4   4.2      0.006   15.7   0.7    3.4  2  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
    1.1e-06   27.9   0.5       0.24   10.4   0.0    3.0  3  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
    1.3e-05   24.4   2.4       0.12   11.4   0.2    3.2  3  TED_complement   A-macroglobulin TED domain
     0.0057   16.3   0.1       0.19   11.5   0.1    2.4  2  TPK_B1_binding   Thiamin pyrophosphokinase, vitamin B1 bindin
  ------ inclusion threshold ------
      0.067   12.1   0.0        3.8    6.3   0.0    2.1  2  Cobalamin_bind   Eukaryotic cobalamin-binding protein


Domain annotation for each model (and alignments):
>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1     3e-05     0.089       2      36 ..      72     103 ..      71     105 .. 0.79
   2 !    6.6   0.0    0.0022       6.5       7      20 ..     159     172 ..     155     173 .. 0.88
   3 !   14.3   0.0   8.3e-06     0.025       7      25 ..     198     216 ..     193     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHH CS
                   Prenyltrans   2 dvekavefLlscQnedGGwggrpgsesdtyytywa 36 
                                   d ek+ e+Lls+    G+wg +  ++ dt y+++a
  gi|91774067|ref|YP_566759.1|  72 DLEKCGEWLLSKRENNGSWGND--VY-DTTYALIA 103
                                   789*****************87..55.55555555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0022
                                   HHHHHHHSHTTS-B CS
                   Prenyltrans   7 vefLlscQnedGGw 20 
                                   ++++ls   e+GGw
  gi|91774067|ref|YP_566759.1| 159 ARWILSERAEEGGW 172
                                   79************ PP

  == domain 3  score: 14.3 bits;  conditional E-value: 8.3e-06
                                   HHHHHHHSHTTS-BBSSTT CS
                   Prenyltrans   7 vefLlscQnedGGwggrpg 25 
                                   +++L+s+Qn  G+wg + g
  gi|91774067|ref|YP_566759.1| 198 LNWLISRQNNNGSWGKNEG 216
                                   79*************9855 PP

>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7     2e-06     0.006       5     112 ..      52     174 ..      51     183 .. 0.72
   2 !   14.1   0.1   6.1e-06     0.018     192     230 ..     180     215 ..     173     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                                   HHHHHHHHHHHHHT--TT-HHHHHHHHHHHTT-B-S--GG...............GGT-TTS---BB-SSSS-TT--BHHH CS
               SQHop_cyclase_C   5 WdtalavlalleagveaeeealkkaleWllekqvlvkGdW...............kvkrpevepgGwafefaneyyPdvdd 70 
                                   Wd ++  +a + ++ ++++  l+k+ eWll+k+ +++G W               +++ +e ++  w  e   e +  v  
  gi|91774067|ref|YP_566759.1|  52 WDNSIRETARACSSLASSNFDLEKCGEWLLSKR-ENNGSWgndvydttyalialaEMEIHETKGCKWLVENYGEKWEHVGT 131
                                   777777777777777778888888888888876.45666622222222222211122344566778999999999****** PP

                                   HHHHHHHHTT---.STHHHHHHHHHHHHHHHHHTB-TTSSB-S CS
               SQHop_cyclase_C  71 tavvvlalkrvrl.keekkkeeaiaraveWilglqsknGGwaa 112
                                   t++++++l + ++ +++k+ ++ i+  ++Wil+ ++++GGw  
  gi|91774067|ref|YP_566759.1| 132 TSLIITTLAKQEAlTKDKHFTDFIEERARWILSERAEEGGWKF 174
                                   ********998652677888999******************75 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.1e-06
                                   HHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--G CS
               SQHop_cyclase_C 192 svlsalaavgedleepvirkavdWlksvqnedGGWGesa 230
                                    v++al  vg +   + ++++++Wl s+qn++G WG + 
  gi|91774067|ref|YP_566759.1| 180 LVIQALVIVGLK---EELKQSLNWLISRQNNNGSWGKNE 215
                                   566677766654...56899****************865 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00038       1.1     232     268 ..      73     109 ..      24     114 .. 0.82
   2 !    6.3   0.1    0.0015       4.4      47      71 ..     155     179 ..     137     188 .. 0.76
   3 !   10.4   0.0   8.1e-05      0.24     232     269 ..     194     231 ..     180     234 .] 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00038
               SQHop_cyclase_N 232 lrkaeewilerqeasgglggifpamvnsvlaLrllgy 268
                                   l+k+ ew+l++ e++g++g+ +  + ++++aL+ + +
  gi|91774067|ref|YP_566759.1|  73 LEKCGEWLLSKRENNGSWGNDVYDTTYALIALAEMEI 109
                                   7899999999999999999999999999999986665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0015
               SQHop_cyclase_N  47 eekiakylrsqqredGgWelypggp 71 
                                   +e+ a++++s++ e+GgW+ +  ++
  gi|91774067|ref|YP_566759.1| 155 IEERARWILSERAEEGGWKFISTSN 179
                                   5677899999999999998876654 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 8.1e-05
               SQHop_cyclase_N 232 lrkaeewilerqeasgglggifpamvnsvlaLrllgyd 269
                                   l++  +w+++rq+++g++g     +  + l L +lgy+
  gi|91774067|ref|YP_566759.1| 194 LKQSLNWLISRQNNNGSWGKNEGDITATALSLITLGYA 231
                                   67777888888888888887777777777777777776 PP

>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00079       2.3     283     312 ..      76     106 ..      63     107 .. 0.88
   2 !    4.8   0.1    0.0041        12     277     310 ..     152     185 ..     124     188 .. 0.70
   3 !   11.4   0.2   3.9e-05      0.12     115     138 ..     191     214 ..     180     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00079
                                   HHHHHHHTHTSTSSSSS.HHHHHHHHHHHHH CS
                TED_complement 283 ivkWLtkqrnsaGGFsS.tqDtvvaLqaLse 312
                                     +WL + r+++G +     Dt  aL aL+e
  gi|91774067|ref|YP_566759.1|  76 CGEWLLSKRENNGSWGNdVYDTTYALIALAE 106
                                   568************88689*********97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0041
                                   CHHHHHHHHHHHHTHTSTSSSSSHHHHHHHHHHH CS
                TED_complement 277 leladkivkWLtkqrnsaGGFsStqDtvvaLqaL 310
                                   +++ ++ ++W+ ++r ++GG++      + +qaL
  gi|91774067|ref|YP_566759.1| 152 TDFIEERARWILSERAEEGGWKFISTSNLVIQAL 185
                                   455667799***********98666666666666 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 3.9e-05
                                   HHHHHHHHHHHHTTB-TTS-B--S CS
                TED_complement 115 eeeiseslewLlseQkedGsFkee 138
                                   +ee+++sl+wL+s+Q+++Gs+ ++
  gi|91774067|ref|YP_566759.1| 191 KEELKQSLNWLISRQNNNGSWGKN 214
                                   6899****************9765 PP

>> TPK_B1_binding  Thiamin pyrophosphokinase, vitamin B1 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   6.3e-05      0.19      12      41 ..      95     123 ..      80     141 .. 0.82
   2 ?    2.4   0.0     0.043   1.3e+02      46      56 ..     173     183 ..     151     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.3e-05
                                   B.-EEEEEESSSSEEEEEEESBSS-EEEEE CS
                TPK_B1_binding  12 egkyvgliPlggevtglttkGlkwnledwe 41 
                                   ++++ +li+l +e++  +tkG kw +e++ 
  gi|91774067|ref|YP_566759.1|  95 YDTTYALIAL-AEMEIHETKGCKWLVENYG 123
                                   778899****.8***************995 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.043
                                   CETEEEEEBS. CS
                TPK_B1_binding  46 gllstSNevee 56 
                                   +++stSN v++
  gi|91774067|ref|YP_566759.1| 173 KFISTSNLVIQ 183
                                   589****9984 PP

>> Cobalamin_bind  Eukaryotic cobalamin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0013       3.8     212     251 ..      73     113 ..      61     125 .. 0.85
   2 ?    3.8   0.0    0.0075        22     202     250 ..     145     193 ..     130     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHTB-TTS-BSS.TTTHHHHHHHHTTSSSTTCH CS
                Cobalamin_bind 212 ieslvekilsekkenGliGn.iySTglAlQaLlvsseeeke 251
                                   +e+  e +ls++++nG  Gn +y T  Al aL  ++ +e++
  gi|91774067|ref|YP_566759.1|  73 LEKCGEWLLSKRENNGSWGNdVYDTTYALIALAEMEIHETK 113
                                   56777889***********879**********999988777 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0075
                                   GGGHHHHHHHHHHHHHHHHHTB-TTS-BSSTTTHHHHHHHHTTSSSTTC CS
                Cobalamin_bind 202 eklraeiskaieslvekilsekkenGliGniySTglAlQaLlvsseeek 250
                                    +++++++  ie+  + ilse+ e+G    i  + l +QaL+  + +e+
  gi|91774067|ref|YP_566759.1| 145 LTKDKHFTDFIEERARWILSERAEEGGWKFISTSNLVIQALVIVGLKEE 193
                                   456789999*****************99888888999****98876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); 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:                         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: 00:00:00.40
# Mc/sec: 1762.65
//
Query:       gi|91774068|ref|YP_566760.1|  [L=604]
Description: ribonucleoside-triphosphate reductase, anaerobic [Methanococcoides burtonii DSM 6242]
Scores for complete 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-149  499.5   0.0   1.6e-149  499.3   0.0    1.0  1  NRDD          Anaerobic ribonucleoside-triphosphate reductase
     0.0048   15.3   0.1      0.015   13.7   0.1    1.8  1  DUF3029       Protein of unknown function (DUF3029)
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.017   15.1   0.0    1.3  1  FTA4          Kinetochore complex Fta4 of Sim4 subunit, or CE
       0.17   11.8   0.4       0.55   10.2   0.1    2.0  2  PyrBI_leader  PyrBI operon leader peptide


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 !  499.3   0.0  3.6e-153  1.6e-149       1     561 []      35     596 ..      35     596 .. 0.93

  Alignments for each domain:
  == domain 1  score: 499.3 bits;  conditional E-value: 3.6e-153
                                   .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SSS-B- CS
                          NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgngvsrp 81 
                                   enan+ + s+s++ +++as+++k+yal++l++keva+ah +g iHiHDl + ++  +yC gid++ +l +Glk+ ++ s+p
  gi|91774068|ref|YP_566760.1|  35 ENANT-RFSPSVIDMHVASQIKKRYALENLYSKEVAKAHTKGNIHIHDL-SNPF-KPYCNGIDARIFLLDGLKFPDSRSSP 112
                                   8****.*******************************************.4466.89************************ PP

                                   --SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTTS-S..SSSS---EE CS
                          NRDD  82 pkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynlntlpsrrGaQvpFtn 162
                                   +k+++ a+ +a+ ++    + +aG+qai+ f+++lap ++++      + +++e+ q +q+f++++n    r GaQ+ Ftn
  gi|91774068|ref|YP_566760.1| 113 AKRFDAAIYHAMSFMLHSKHFFAGAQAIDMFNWLLAPHLHYS------DIDEEELLQIVQGFMFQMN-QSNRIGAQSAFTN 186
                                   ***************************************999......9******************.888********** PP

                                   EEEE.-HH................................HHHHHTTTTS-HCH----SEEEEEEEEETETTH.....HHH CS
                          NRDD 163 inlgldtp.................tegrfee..kliikallevmleGdgnkgtpftFPilifklkedfnleeedpnydlf 224
                                   i l +++p                 t++ fe+  + i  a++++  +Gd++ g pftFP ++ ++++d++ e+      l+
  gi|91774068|ref|YP_566760.1| 187 IGLRINCPsslanelavyggefiekTYSCFEKeaRAIYGAFMDIAAKGDAD-GLPFTFPLITTAITKDIDTED-----TLW 261
                                   *************************9999999999****************.*****************9999.....*** PP

                                   HHHHHHHTTT--EEE.......EEES--GGGTT--------.......S---EEEEEEEEEEHHHHHH..HH-HHHHHHHH CS
                          NRDD 225 klalevtakrgfpyffnlledlepedekevasmgCRlrlde....g.erlggrgslgvvtiNlprlaleakgdeekffelL 300
                                   k ++  t+ +g pyf nl++d+ +e+   + +m+CRl   +    +   + g gs ++vt+Nlpr+ale ++++++ff++L
  gi|91774068|ref|YP_566760.1| 262 KRTMYATSSTGAPYFLNLTTDYLEEN--TTQAMCCRLLARHsggvWtAGGMGSGSNKIVTVNLPRIALE-AENRDRFFKRL 339
                                   ******************98655555..479******999533333347788****************8.7789******* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTT..-HHH.HTTSS-GE...............EEEEEEE-HHHHHHHTTEEEE..-HH CS
                          NRDD 301 dellelakealeerrkilekllakg..lpflmgkgylksrkkkdeveevlkng..tltiGfiGlaEalkaltgkkigesee 377
                                   de+le++++al+e ++i+++ l +   lp+l+++              ++++    lt+G +Gl+E+l +ltg+++    e
  gi|91774068|ref|YP_566760.1| 340 DEILEITRKALLEGQEIVRRSLYEWkiLPWLLQRTEN--------DLPYFDHSsrHLTFGTVGLNECLLNLTGQDM---IE 409
                                   ********************99998899997544333........24566666669*****************999...55 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE---TTHHHHHHHHH..HH..............HHG-SSSS-TTSSB-HHH CS
                          NRDD 378 akefalkvlkhmrekadelkeetglnfsleatPaEslsgrfakldkkkfgeipgv.dke...pyYtNsfhvpvdekislfe 454
                                   ++++++++++hm  k++ ++ ++g+++++e+tPaEs+++r+a ld++ +ge  +v   +    yYtNs+hvp+++kisl+e
  gi|91774068|ref|YP_566760.1| 410 QHDLGMEIIRHMLGKIETYSIQDGIEYTFEQTPAESTAHRLATLDRSAYGEKAHVqG-ShdaAYYTNSTHVPYSSKISLAE 489
                                   88***********************************************99887743.33678****************** PP

                                   HHHHHHHHTGGGTT-S-EEEEBSS--SSHHHHHHHHHHHHHTT--EEEEE--EEEETT.--.EESSSB-TTT--BE..EEE CS
                          NRDD 455 kikleaefqklttGGailyieldeekknpealeklvkiakktgigYfsinpkidvCnecgy.kgeiekCpkCgseee.vev 533
                                   +ik+e++f++++tGG+i++i+++e+ ++pe +++l++ ++ t++ Yf+++p+++vC++ +  +g   kCp+C+  e+ v++
  gi|91774068|ref|YP_566760.1| 490 RIKIESRFHPYFTGGTISHIWMGESFPDPEGMSELIEKLSGTDLAYFCFSPDFTVCENRHVsRGMNLKCPVCN--EPaVDH 568
                                   *************************************99*******************8889999999*****..555*** PP

                                   EEESSSSEEEHHHHHHHHHHHSGG---B CS
                          NRDD 534 irRitGYlrpvsswnkgkkaElkdRvkh 561
                                   ++R+tGY+++v++wn+gk++E+++R+++
  gi|91774068|ref|YP_566760.1| 569 VSRVTGYFGHVEQWNPGKQKEYEERHRY 596
                                   *************************988 PP

>> DUF3029  Protein of unknown function (DUF3029)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   3.4e-06     0.015     220     404 ..     310     511 ..     239     539 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-06
                       DUF3029 220 lgGgaytLvRlnLkevakkaksvedfleevlpkvvelmlelidaRikflveeskffes..sfLvk..eg...liekdrfta 293
                                   +g g++ +v +nL ++a +a++++ f++  l++++e++ +++ +  + +v +s +  +   +L +  e+   + +++    
  gi|91774068|ref|YP_566760.1| 310 MGSGSNKIVTVNLPRIALEAENRDRFFK-RLDEILEITRKALLEGQE-IVRRSLYEWKilPWLLQrtENdlpYFDHSSRHL 388
                                   5678999*******************98.578888877777665544.444443321111355441222233456666667 PP

                       DUF3029 294 mfgivglaeavnkllekegk.eeryGkdeeanelge....eileklaelveetkakyce...vt..egrallHaqv.Giss 363
                                    fg vgl e+  +l+ ++   +++ G +   + lg+    +i + ++ + e+t+a+ +    +t  +  +   a v G ++
  gi|91774068|ref|YP_566760.1| 389 TFGTVGLNECLLNLTGQDMIeQHDLGMEIIRHMLGKietySIQDGIEYTFEQTPAESTAhrlATldRSAYGEKAHVqGSHD 469
                                   8*********99999887651567888888777774222256666666666655544321112200223333344313334 PP

                       DUF3029 364 dkevtpgvRipvGeEPelvkhlkasakfHkyfpsG.isdilt 404
                                       t ++ +p+ +  +l++ +k +++fH yf+ G is i+ 
  gi|91774068|ref|YP_566760.1| 470 AAYYTNSTHVPYSSKISLAERIKIESRFHPYFTGGtISHIWM 511
                                   46789****************************994466654 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.7e-06     0.017      43      91 ..      19      68 ..       5     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
                          FTA4 43 ekavddvLaklNhrlkqhnrrvyspqair.hvaeQidklYlea.....edeklei 91
                                  ++ +ddvL++ N +lk+ ++  +sp +i  hva+Qi+k Y  +     e     +
  gi|91774068|ref|YP_566760.1| 19 NELIDDVLYNRNWLLKENANTRFSPSVIDmHVASQIKKRYALEnlyskE-----V 68
                                  5679********************999855*********9887444431.....3 PP

>> PyrBI_leader  PyrBI operon leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00012      0.55      14      28 ..     233     248 ..     231     250 .. 0.83
   2 ?   -3.6   0.0       2.5   1.1e+04      18      27 ..     272     281 ..     270     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                  PyrBI_leader  14 kkDa.GLPFFFPLlty 28 
                                   k Da GLPF FPL+t 
  gi|91774068|ref|YP_566760.1| 233 KGDAdGLPFTFPLITT 248
                                   566669********95 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.5
                  PyrBI_leader  18 GLPFFFPLlt 27 
                                   G P+F  L t
  gi|91774068|ref|YP_566760.1| 272 GAPYFLNLTT 281
                                   89***99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 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:                        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: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4058.54
//
Query:       gi|91774069|ref|YP_566761.1|  [L=278]
Description: chromosome partitioning ATPase protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-99  332.6   1.3    1.6e-99  332.4   1.3    1.0  1  ParA          NUBPL iron-transfer P-loop NTPase
    3.9e-15   56.0   0.0    1.4e-14   54.2   0.0    1.9  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    2.2e-10   40.8   0.4      2e-09   37.6   0.4    2.1  1  AAA_31        AAA domain
    9.3e-10   38.2   0.2    7.7e-09   35.1   0.1    2.1  2  ArsA_ATPase   Anion-transporting ATPase
    1.9e-07   30.7   0.0    2.5e-07   30.3   0.0    1.2  1  MipZ          ATPase MipZ
    1.1e-05   25.1   0.3    0.00024   20.7   0.1    2.1  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    0.00027   20.8   0.7      0.036   13.9   0.1    2.3  2  AAA_26        AAA domain
     0.0014   18.5   0.0     0.0021   18.0   0.0    1.3  1  APS_kinase    Adenylylsulphate kinase
     0.0014   18.2   0.0     0.0023   17.5   0.0    1.3  1  AAA_25        AAA domain
     0.0031   17.0   0.1      0.022   14.2   0.1    2.0  1  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
     0.0032   17.3   0.0       0.01   15.7   0.0    1.8  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.004   16.8   0.1     0.0078   15.9   0.1    1.4  1  SRP54         SRP54-type protein, GTPase domain
     0.0055   15.7   0.2      0.012   14.6   0.1    1.5  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0078   15.5   0.0      0.012   14.9   0.0    1.2  1  VirC1         VirC1 protein
      0.009   15.7   0.0      0.016   14.9   0.0    1.3  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.013   15.4   1.1      0.018   15.0   0.1    1.7  2  RsgA_GTPase   RsgA GTPase
      0.021   14.8   0.1       0.12   12.3   0.0    2.0  2  NTPase_1      NTPase
      0.021   14.1   0.0      0.035   13.4   0.0    1.2  1  Zeta_toxin    Zeta toxin
      0.032   14.4   0.0      0.049   13.8   0.0    1.3  1  AAA_33        AAA domain
      0.038   13.4   0.0      0.053   13.0   0.0    1.2  1  KTI12         Chromatin associated protein KTI12
       0.05   12.8   0.1      0.082   12.1   0.1    1.3  1  NB-ARC        NB-ARC domain
      0.066   13.1   0.0       0.12   12.3   0.0    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.14   11.6   0.0        0.3   10.6   0.0    1.5  1  DUF4916       Domain of unknown function (DUF4916)
       0.14   12.5   0.0       0.26   11.7   0.0    1.5  1  RNA_helicase  RNA helicase
       0.18   12.3   0.0       0.32   11.5   0.0    1.5  1  AAA_18        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 !  332.4   1.3  2.2e-102   1.6e-99       2     245 ..      28     273 ..      27     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: 332.4 bits;  conditional E-value: 2.2e-102
                          ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSigfl 81 
                                   +k++i+v+SgKGGVGKStv++nlA+aLa++g++vgllD Di+Gp ip+++gve+ekp+++ek+++Pv++ +++k+mSig+l
  gi|91774069|ref|YP_566761.1|  28 IKNKIMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIHGPTIPKMFGVENEKPMVNEKGIVPVKVnDNLKIMSIGLL 108
                                   89******************************************************************9899********* PP

                          ParA  82 lesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemfk 161
                                   l+s+d++vvwrGp k++aikq+l++v+wg lDyLiiDlPPGtgDe l++ q + +l+ga++Vttpq+val+ v+k+++++k
  gi|91774069|ref|YP_566761.1| 109 LDSNDSPVVWRGPAKMSAIKQFLEEVDWGVLDYLIIDLPPGTGDEPLSISQLIgNLTGAIVVTTPQDVALTSVRKSLNFAK 189
                                   *****************************************************99************************** PP

                          ParA 162 kvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeia 242
                                    +kv+v+G+veNmsg+vcp+c+ek+++fg+gg++k+ae+++v++lg++p+++e++ a+d+g+ ++  +++se    +++++
  gi|91774069|ref|YP_566761.1| 190 IIKVPVIGMVENMSGIVCPHCDEKIYVFGSGGVAKAAEDFDVKVLGTLPIETEVAAAGDNGHVHIDIKRDSEWYIGFNKVV 270
                                   ************************************************************************999999999 PP

                          ParA 243 ekv 245
                                   ++v
  gi|91774069|ref|YP_566761.1| 271 DAV 273
                                   876 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 !   54.2   0.0   1.9e-17   1.4e-14       1     126 [.      32     251 ..      32     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.9e-17
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i+++s+kGGvGK+t++anLa+ala+rg+ V l+D D  ++     +g+en++                             
  gi|91774069|ref|YP_566761.1|  32 IMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIHGPTIPKMFGVENEKPMvnekgivpvkvndnlkimsigllldsn 112
                                   89***************************************9988888888888999************************ PP

                                   .........................................................................CCHCCCHH CS
                                   .........................................................................xxxxxxxx RF
                          CbiA  55 .........................................................................dlkrllel 62 
                                                                                                            +       
  gi|91774069|ref|YP_566761.1| 113 dspvvwrgpakmsaikqfleevdwgvldyliidlppgtgdeplsisqlignltgaivvttpqdvaltsvrkslN------- 186
                                   **********9999999999999999999999999999999998888888888888888888776653332221....... PP

                                   HHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                   xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  63 lealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                   ++++ k+ ++     ++ g+v    d++  +   + ++++  +++ v+vlg +p  ++va a  +g+
  gi|91774069|ref|YP_566761.1| 187 FAKIIKV-PVIgmvENMSGIVCPHCDEK-IYVFGSGGVAKAAEDFDVKVLGTLPIETEVAAAGDNGH 251
                                   2333322.12244577777777777776.67777788888888888888888888888888887776 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.4   2.8e-12     2e-09       3     167 ..      31     191 ..      29     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 2.8e-12
                        AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevlieeknikeaiiktkvenld 82 
                                    I ++  KGGvGK+T s nlaaala +g+ v l D D  + +    +g+e+++        +++ek i  + +   ++nl+
  gi|91774069|ref|YP_566761.1|  31 KIMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIHGPTIPkMFGVENEK-------PMVNEKGIVPVKV---NDNLK 101
                                   588999*******************************9987654134432222.......2233444444444...67889 PP

                        AAA_31  83 lipssidLaeaeielvelekkeei.lkellekvkde.YDyiiiDcpPsLg..lltenaLvas.dsviipvqaeayaleGle 158
                                   ++   + L + +  +v     +   +k++le+v+    Dy iiD pP  g   l ++ L+      i+++ +++ al  ++
  gi|91774069|ref|YP_566761.1| 102 IMSIGLLLDSNDSPVVWRGPAKMSaIKQFLEEVDWGvLDYLIIDLPPGTGdePLSISQLIGNlTGAIVVTTPQDVALTSVR 182
                                   99999999999998887776654427*******97659*********9873345555555441456888888889999998 PP

                        AAA_31 159 qllktieev 167
                                   + l++ + +
  gi|91774069|ref|YP_566761.1| 183 KSLNFAKII 191
                                   888877665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   1.1e-11   7.7e-09       2      68 ..      31     106 ..      30     116 .. 0.88
   2 ?    0.6   0.0      0.35   2.5e+02     112     137 ..     126     152 ..     120     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.1e-11
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S.TTTHHHHHHTS........--BSS-EEETSSEEEEE-- CS
                   ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD.PAhslsDsfdq........klgkeptkvkeNLsavEid 68 
                                   k+++++GKGGVGK+tvsa +a+ l++ g++v l+  D   + +  +f          + g  p kv++NL ++ i 
  gi|91774069|ref|YP_566761.1|  31 KIMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDiHGPTIPKMFGVenekpmvnEKGIVPVKVNDNLKIMSIG 106
                                   7899***************************999999446899999998788888888888999*******99986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHCSSSSEEEEESBS.CCH CS
                   ArsA_ATPase 112 sfeellkyvkeeeydvvvlDtaP.TGh 137
                                   + +++l++v+    d++++D +P TG+
  gi|91774069|ref|YP_566761.1| 126 AIKQFLEEVDWGVLDYLIIDLPPgTGD 152
                                   66788888888999*******995664 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.4e-10   2.5e-07       3     108 ..      32     147 ..      30     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.4e-10
                                   EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH..HHHHHHHHHHT-.......-----EEE-SSS-H CS
                          MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl..enraataerkgl.......sLplpealalseae 74 
                                   i++   kGG Gkst++  +a aL+++G +v+ +d d+   t+ + +  en + ++++kg+       +L++ ++  l +++
  gi|91774069|ref|YP_566761.1|  32 IMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIHGPTIPKMFgvENEKPMVNEKGIvpvkvndNLKIMSIGLLLDSN 112
                                   677789************************************998633788889999987444333345555555566666 PP

                                   HHHTTS-HHHHHHHHHHHHHHHHH.H-SEEEEE-- CS
                          MipZ  75 eaeveeeeeaevaeleelvadlea.eldfividtP 108
                                    + v     a+++++++ ++++    ld+++id P
  gi|91774069|ref|YP_566761.1| 113 DSPVVWRGPAKMSAIKQFLEEVDWgVLDYLIIDLP 147
                                   66676666777788888888887525799999976 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   3.3e-07   0.00024       3      36 ..      33      66 ..      31     108 .. 0.84
   2 ?    2.6   0.0      0.11        78     176     244 ..     202     273 ..     167     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.3e-07
                     Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGC 36
                                  + + GkGG+Gkst s+nl+aala++g  v ++  
  gi|91774069|ref|YP_566761.1| 33 MVMSGKGGVGKSTVSANLAAALADRGYSVGLLDS 66
                                  5678*********************988866555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                     Fer4_NifH 176 lgGlii...nsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarki 244
                                   ++G+++   +++  + +++ + k ae+ ++kvl ++P + +v  a  + ++ i+ + +se    ++++ +++
  gi|91774069|ref|YP_566761.1| 202 MSGIVCphcDEKIYVFGSGGVAKAAEDFDVKVLGTLPIETEVAAAGDNGHVHIDIKRDSEWYIGFNKVVDAV 273
                                   556665211334444556778889999999999999999999999988888888888877666666665555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   5.1e-05     0.036       2      33 ..      31      62 ..      30      66 .. 0.94
   2 ?    5.1   0.1     0.024        17     132     194 ..     168     243 ..     150     246 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                        AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                  +i+v +   gvGK++vs+ L++al ++g++vg
  gi|91774069|ref|YP_566761.1| 31 KIMVMSGKGGVGKSTVSANLAAALADRGYSVG 62
                                  79***************************998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                        AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk....vrnp..e.........nvetlekksgipvlGvvPylpdl 194
                                   i+V+++++ +++ +  ++++++  +v+v+G++ N     +  p  +          v+++ + + ++vlG++P ++++
  gi|91774069|ref|YP_566761.1| 168 IVVTTPQDVALTSVRKSLNFAKIIKVPVIGMVENMsgivC--PhcDekiyvfgsgGVAKAAEDFDVKVLGTLPIETEV 243
                                   5667777777777777788888778888888877644422..123245566666688888888888999988877765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.9e-06    0.0021       3      60 ..      31      88 ..      29     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                                  EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHH CS
                    APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkeni 60
                                   ++ ++G  g GKst++ +l+ +L ++g+sv lLd d     + k  g ++e+   n 
  gi|91774069|ref|YP_566761.1| 31 KIMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIHGPTIPKMFGVENEKPMVNE 88
                                  57889******************************99776666666666666655555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.2e-06    0.0023      13      60 ..      10      58 ..       2      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.2e-06
                        AAA_25 13 adlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tG 60
                                  + l+++p++++ +     +++++ +  G +g+GK+t+  +la+a+a +G
  gi|91774069|ref|YP_566761.1| 10 SLLNTKPEEPKLVTNLRGIKNKIMVMSGKGGVGKSTVSANLAAALAdRG 58
                                  446667777775555566799999*********************9766 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   3.1e-05     0.022       4      38 ..      33      66 ..      30     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                      CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDl 38
                                  ++++G +GGvG+++++a La al   g+sv ++D 
  gi|91774069|ref|YP_566761.1| 33 MVMSG-KGGVGKSTVSANLAAALADRGYSVGLLDS 66
                                  55666.8***********************99996 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05      0.01       1      33 [.      37      69 ..      37      88 .. 0.91
   2 ?   -2.7   0.0         6   4.3e+03     140     167 ..     175     200 ..     161     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                  G+  +GKST++++L+  ++ +g+++ ++D D+ 
  gi|91774069|ref|YP_566761.1| 37 GKGGVGKSTVSANLAAALADRGYSVGLLDSDIH 69
                                  66789**************************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6
                        CLP1_P 140 eellnelkrdlplskvkvvklpkspgvv 167
                                   +  l +++++l+  + k++k+p++++v 
  gi|91774069|ref|YP_566761.1| 175 DVALTSVRKSLN--FAKIIKVPVIGMVE 200
                                   444444444444..77888888887775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.1e-05    0.0078       2      39 ..      31      68 ..      30      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  +++++ G  G+GK t  a Laa l ++g++v l   D+
  gi|91774069|ref|YP_566761.1| 31 KIMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDI 68
                                  578999**************************998886 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.6e-05     0.012      29      66 ..      30      67 ..      11      74 .. 0.81
   2 ?   -3.4   0.0       5.2   3.7e+03     144     187 ..     140     183 ..     137     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                  SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                   + + + G  G+Gkst+  +l++ l++rG+ v++l  D
  gi|91774069|ref|YP_566761.1| 30 NKIMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSD 67
                                  4556689**************************98765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.2
                                   SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHH CS
                          MeaB 144 dtfvvlllpeaGDelqgikkGileiaDiivvnkaDkkeaekaar 187
                                   d  ++ l p++GDe  +i + i +++  ivv      + + +++
  gi|91774069|ref|YP_566761.1| 140 DYLIIDLPPGTGDEPLSISQLIGNLTGAIVVTTPQDVALTSVRK 183
                                   66666667888888888877777777777666555444444444 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.012       4      41 ..      32      69 ..      29      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                         VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                  i + s kGG Gk+t    l +ala +g  v+l+++d  
  gi|91774069|ref|YP_566761.1| 32 IMVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIH 69
                                  678899****************************9965 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   2.2e-05     0.016       9      51 ..      21      63 ..      14      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                        AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                  +v++l + +++++v+ G  G GK+t+ + l++a++++g++v +
  gi|91774069|ref|YP_566761.1| 21 LVTNLRGIKNKIMVMSGKGGVGKSTVSANLAAALADRGYSVGL 63
                                  67778888999***************************99965 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.5e-05     0.018      96     122 ..      27      53 ..       5      66 .. 0.79
   2 ?   -2.8   0.1         7     5e+03      14      48 ..     162     194 ..     156     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                                   HCTTSEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpe 122
                                    +k+k++v+ G+ GvGKSt+  +l+  
  gi|91774069|ref|YP_566761.1|  27 GIKNKIMVMSGKGGVGKSTVSANLAAA 53 
                                   4688***************99888765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
                                   ES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-E CS
                   RsgA_GTPase  14 aNvdqllivvslkepelslnlldrfLvlaeekgie 48 
                                    N++ +++v++ +  ++ l  + + L +a+  +++
  gi|91774069|ref|YP_566761.1| 162 GNLTGAIVVTTPQ--DVALTSVRKSLNFAKIIKVP 194
                                   5666666666665..77777777777777666655 PP

>> NTPase_1  NTPase
   #    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       3      31 ..      34      62 ..      32      64 .. 0.93
   2 ?   -0.4   0.0       1.3   9.6e+02      75     111 ..     169     203 ..     142     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                  EEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvg 31
                                  +++G+ GvGK+T+  +++ +l+++g++vg
  gi|91774069|ref|YP_566761.1| 34 VMSGKGGVGKSTVSANLAAALADRGYSVG 62
                                  679***********************995 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                                   EE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG- CS
                      NTPase_1  75 vvdvesfeelalealrkalseadviviDEiGkmElks 111
                                   v  v+  +++al ++rk+l+ a +i +  iG  E  s
  gi|91774069|ref|YP_566761.1| 169 V--VTTPQDVALTSVRKSLNFAKIIKVPVIGMVENMS 203
                                   3..4456789999999999999999999999988765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-05     0.035      13      69 ..      27      84 ..      19      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                    Zeta_toxin 13 qerPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRelhPeyeeilkadp 69
                                  + + k+++++G  G GKs++++ l+++l+ +g  v  ld D   + +P+  ++++++p
  gi|91774069|ref|YP_566761.1| 27 GIKNKIMVMSGKGGVGKSTVSANLAAALADRGYSVgLLDSDIHGPTIPKMFGVENEKP 84
                                  567899**********************955555515677777777777776666655 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   6.8e-05     0.049       2      32 ..      33      68 ..      32     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssdt 32
                                  +++ G  G+GKst++ +l+++l+     + ll+sd+
  gi|91774069|ref|YP_566761.1| 33 MVMSGKGGVGKSTVSANLAAALAdrgysVGLLDSDI 68
                                  6899***************99998886656677776 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.3e-05     0.053       4      41 ..      33      70 ..      31     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                                  EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                  +v++G   +GKst++++La al+++++sv ++d++  g
  gi|91774069|ref|YP_566761.1| 33 MVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIHG 70
                                  6899**************************99988665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012     0.082      17      40 ..      27      50 ..      18      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                  TSCSEEEEEEESTTSSHHHHHHHH CS
                        NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                  +++  ++ ++G+gGvGK+t++++ 
  gi|91774069|ref|YP_566761.1| 27 GIKNKIMVMSGKGGVGKSTVSANL 50
                                  66778**************99876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.12       2      40 ..      33      71 ..      32      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgf 40
                                  + + gk g GK t   +l ++l++rg++vg++  + hg 
  gi|91774069|ref|YP_566761.1| 33 MVMSGKGGVGKSTVSANLAAALADRGYSVGLLDSDIHGP 71
                                  678899**************************9999975 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00042       0.3      19      49 ..      84     115 ..      75     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                                   EEEEEE.EEEEEE-TTS-EEEEEEEEEE-TTS CS
                       DUF4916  19 Pilyve.vvPvrvddlgevtevGlllraseeg 49 
                                   P++  + +vPv+v+d+ ++ ++Glll ++++ 
  gi|91774069|ref|YP_566761.1|  84 PMVNEKgIVPVKVNDNLKIMSIGLLLDSNDSP 115
                                   66554338******************998875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00037      0.26       2      25 ..      34      57 ..      33      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                  +++G+ g+GKSt++ +La+al+++
  gi|91774069|ref|YP_566761.1| 34 VMSGKGGVGKSTVSANLAAALADR 57
                                  789*****************9975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00045      0.32       4      25 ..      36      66 ..      33     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00045
                        AAA_18  4 tGtpGvGKttlakeLskrl.gf........g 25
                                  +G+ GvGK+t++ +L+  l           +
  gi|91774069|ref|YP_566761.1| 36 SGKGGVGKSTVSANLAAALaDRgysvglldS 66
                                  6999***********8886333445544442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 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:                       121  (0.00674884); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1792.99
//
Query:       gi|91774070|ref|YP_566762.1|  [L=107]
Description: hypothetical protein Mbur_2142 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-29  102.7   0.0    1.4e-29  102.5   0.0    1.0  1  DUF134        Protein of unknown function  DUF134
    3.6e-06   26.5   0.2    5.2e-06   26.0   0.2    1.2  1  Sigma70_r4_2  Sigma-70, region 4
    6.2e-05   23.0   0.6    7.6e-05   22.7   0.6    1.1  1  Sigma70_ECF   ECF sigma factor
    0.00048   19.9   0.1     0.0016   18.2   0.0    1.9  2  HTH_10        HTH DNA binding domain
    0.00073   19.3   0.1     0.0011   18.7   0.1    1.3  1  HTH_23        Homeodomain-like domain
     0.0025   17.3   0.1     0.0039   16.7   0.1    1.4  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
      0.017   15.2   0.4      0.017   15.2   0.4    1.7  2  HTH_3         Helix-turn-helix
      0.024   14.6   0.4      0.059   13.3   0.5    1.6  2  HTH_1         Bacterial regulatory helix-turn-helix protein, 
       0.11   12.4   0.0       0.16   11.9   0.0    1.4  1  HTH_11        HTH domain


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.0     7e-33   1.4e-29       1      96 [.       1      98 [.       1     100 [. 0.96

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 7e-33
                        DUF134  1 msrkgrprklrdileePkvrifkPeaveetg.k.vaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiaka 81
                                  m+ +grpr++r++  +P +  fkP++v +t+   v ++l+elea+rlvd e l+q+eaa +mGis++++w  l++arkk+a a
  gi|91774070|ref|YP_566762.1|  1 MTCRGRPRNPRRVECNPDILYFKPRGVALTElEvVSLALEELEALRLVDLEGLQQQEAATKMGISRRAFWEDLKNARKKLALA 83
                                  7789**************************96259************************************************ PP

                        DUF134 82 lveGraiilkGGeyk 96
                                  l  G+ai +kGG+y 
  gi|91774070|ref|YP_566762.1| 84 LTTGKAIEIKGGNYV 98
                                  *************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.2   2.6e-09   5.2e-06      13      54 .]      39      80 ..      33      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.6e-09
                                  HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                  Sigma70_r4_2 13 erqreifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                   ++ e++ l +legl ++E+A ++gis ++    l+ ArkkL
  gi|91774070|ref|YP_566762.1| 39 LEELEALRLVDLEGLQQQEAATKMGISRRAFWEDLKNARKKL 80
                                  566699***********************************8 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.6   3.8e-08   7.6e-05     135     183 ..      36      84 ..      27      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
                   Sigma70_ECF 135 sldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawlerel 183
                                   sl  e ++ + l  leGl  +E+A+k+g+s+r+   +l+ aR++l+ +l
  gi|91774070|ref|YP_566762.1|  36 SLALEELEALRLVDLEGLQQQEAATKMGISRRAFWEDLKNARKKLALAL 84 
                                   46667888999999*****************************998665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   2.2e+03      26      29 ..      29      32 ..      21      41 .. 0.57
   2 !   18.2   0.0   8.1e-07    0.0016      27      52 ..      56      81 ..      52      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                        HTH_10 26 lkeL 29
                                  l eL
  gi|91774070|ref|YP_566762.1| 29 LTEL 32
                                  4443 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 8.1e-07
                        HTH_10 27 keLAkelGIskstlsehLrkaeskli 52
                                  +e A ++GIs+ +++e L++a +kl+
  gi|91774070|ref|YP_566762.1| 56 QEAATKMGISRRAFWEDLKNARKKLA 81
                                  6779********************95 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   5.5e-07    0.0011       6      35 ..      40      70 ..      37      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.5e-07
                        HTH_23  6 eRlrilllla.eGlsvreIAreLgvsrrTvy 35
                                  e l++l+l++ eGl ++e+A+++g+srr  +
  gi|91774070|ref|YP_566762.1| 40 EELEALRLVDlEGLQQQEAATKMGISRRAFW 70
                                  6789******55****************876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     2e-06    0.0039       8      35 ..      40      67 ..      35      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-06
                                  HHHHHHHHHHTTT--HHHHHHHHTS-HH CS
                    Sigma70_r4  8 rerevlelrfgeglTleEIgerlgiSre 35
                                  +e e l+l+ +egl ++E + ++giSr 
  gi|91774070|ref|YP_566762.1| 40 EELEALRLVDLEGLQQQEAATKMGISRR 67
                                  68899*********************96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.4   8.5e-06     0.017       1      24 [.      42      67 ..      42      68 .. 0.88
   2 ?   -2.2   0.1       2.3   4.7e+03       1       8 [.      73      80 ..      73      85 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.5e-06
                                  HHHHHH..HTTHHHHHHHHHHTSSHH CS
                         HTH_3  1 lkelRk..qlglsqeeLAeklGvsrs 24
                                  l++lR+    gl+q+e+A k+G+sr+
  gi|91774070|ref|YP_566762.1| 42 LEALRLvdLEGLQQQEAATKMGISRR 67
                                  5678888899**************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                                  HHHHHHHT CS
                         HTH_3  1 lkelRkql 8 
                                  lk +Rk+l
  gi|91774070|ref|YP_566762.1| 73 LKNARKKL 80
                                  67788876 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 ?   -2.1   0.0       1.9   3.8e+03      50      57 ..      24      31 ..      18      32 .. 0.79
   2 ?   13.3   0.5     3e-05     0.059       1      45 [.      39      84 ..      39      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                                  SSEEEE-H CS
                         HTH_1 50 grglrLTe 57
                                   rg+ LTe
  gi|91774070|ref|YP_566762.1| 24 PRGVALTE 31
                                  58999998 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3e-05
                                  HHHHHHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHHHHTS-S CS
                         HTH_1  1 lrqlrlfvavaeeg.sftrAAeeLglsqpavsrqikrLEeelgvpL 45
                                  l+ l+++  v  eg    +AA ++g+s  a +  +k+ ++ l   L
  gi|91774070|ref|YP_566762.1| 39 LEELEALRLVDLEGlQQQEAATKMGISRRAFWEDLKNARKKLALAL 84
                                  577889999999999999*********************9998877 PP

>> HTH_11  HTH 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      0.16      16      43 ..      53      80 ..      39      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                        HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                  +  +e A ++++Srr+ + d+k  ++++
  gi|91774070|ref|YP_566762.1| 53 LQQQEAATKMGISRRAFWEDLKNARKKL 80
                                  66778899**************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 747.89
//
Query:       gi|91774071|ref|YP_566763.1|  [L=370]
Description: cell division control protein 6 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-10   39.1   0.0    5.9e-07   30.0   0.0    2.9  2  AAA_16           AAA ATPase domain
      8e-08   32.8   0.0    1.7e-07   31.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
    1.7e-06   27.7   0.1    0.00064   19.3   0.0    2.4  2  AAA_7            P-loop containing dynein motor region
    7.3e-06   26.0   0.0    1.3e-05   25.2   0.0    1.4  1  AAA_11           AAA domain
    8.5e-06   26.1   0.0      2e-05   24.9   0.0    1.5  1  AAA_22           AAA domain
    5.7e-05   23.0   0.0    0.00016   21.5   0.0    1.9  1  Cdc6_C           CDC6, C terminal winged helix domain
    6.4e-05   22.9   0.0    0.00013   22.0   0.0    1.4  1  NACHT            NACHT domain
    0.00019   20.7   0.0    0.00036   19.8   0.0    1.4  1  NB-ARC           NB-ARC domain
    0.00041   20.3   0.1     0.0014   18.6   0.1    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
    0.00047   19.3   0.0    0.00075   18.6   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
     0.0011   18.9   0.6     0.0046   17.0   0.1    2.2  2  AAA_14           AAA domain
     0.0016   18.8   0.0     0.0051   17.2   0.0    1.9  1  AAA_19           AAA domain
     0.0016   18.2   0.0     0.0031   17.2   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
     0.0016   18.2   0.0      0.013   15.2   0.0    2.1  2  AAA_24           AAA domain
      0.002   18.0   0.1      0.005   16.8   0.1    1.6  1  NTPase_1         NTPase
  ------ inclusion threshold ------
       0.01   15.0   0.0       0.13   11.4   0.0    2.1  2  DUF815           Protein of unknown function (DUF815)
      0.011   15.1   0.0      0.025   13.9   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.018   14.3   0.0      0.027   13.7   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.019   14.7   0.0      0.053   13.2   0.0    1.6  2  AAA_30           AAA domain
      0.021   14.1   0.0      0.047   12.9   0.0    1.6  1  KAP_NTPase       KAP family P-loop domain
      0.021   13.7   0.1          1    8.1   0.0    2.3  2  AAA_35           AAA-like domain
      0.023   13.7   0.0      0.037   13.0   0.0    1.2  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.024   14.8   0.0      0.082   13.1   0.0    1.9  1  TIP49_C          TIP49 AAA-lid domain
      0.026   14.5   0.0      0.063   13.3   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.031   13.6   0.1       0.19   11.1   0.1    2.1  2  ATPase           KaiC
      0.037   13.7   0.1        8.6    6.1   0.0    3.0  3  IstB_IS21        IstB-like ATP binding protein
      0.049   13.1   0.0      0.077   12.4   0.0    1.3  1  RecA             recA bacterial DNA recombination protein
      0.051   13.0   0.0       0.11   11.9   0.0    1.5  1  TniB             Bacterial TniB protein
      0.067   13.1   0.7       0.53   10.2   0.1    2.5  3  Rad17            Rad17 P-loop domain
      0.069   12.9   0.3       0.44   10.3   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.07   13.2   0.0      0.095   12.8   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.09   12.4   0.0       0.16   11.6   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
       0.11   12.5   0.1       0.37   10.8   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)
       0.11   11.2   0.0       0.71    8.6   0.0    1.9  2  AAA_32           AAA domain
       0.13   12.8   0.1       0.32   11.5   0.1    1.8  1  AAA_18           AAA 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 !   30.0   0.0   1.2e-09   5.9e-07       4     164 ..      30     165 ..      27     176 .. 0.67
   2 ?    0.0   0.1       1.9   9.8e+02     137     163 ..     264     291 ..     226     301 .. 0.62

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.2e-09
                        AAA_16   4 GReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalareel 81 
                                    Re +++ L   l+++ +g    + l+sG++G+GK++ v +++++++k+  +++f++ +c+        s+   ++ + ++
  gi|91774071|ref|YP_566763.1|  30 HRESQMQSLMYSLRPALRGMRpINSLISGPPGTGKTTTVLKVFEEMKKHseDIVFIKVNCQMD------STKFAVI-T-RV 102
                                   69999999999999888887767788**********************9977********999......3322222.1.34 PP

                        AAA_16  82 lrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade..aslqllaaLlr 160
                                   ++ l +     +++          +           ++  l+ + +++l ++e++lvl+lDd+  +    +  +++++Llr
  gi|91774071|ref|YP_566763.1| 103 YQGLFNV----SPPSS--------G----------VAFIKLFEKVMNYLIEKEKTLVLCLDDINYLYHegHADEVMYSLLR 161
                                   4444444....11111........1..........3566777777766666677788888877733332233334666666 PP

                        AAA_16 161 lles 164
                                   + e+
  gi|91774071|ref|YP_566763.1| 162 AHEQ 165
                                   6555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.9
                        AAA_16 137 lvlvlDdlqwadeaslql.laaLlrlle 163
                                     ++++d+++a e+s+ l l+  +++l+
  gi|91774071|ref|YP_566763.1| 264 KTILVEDVEKAYETSRLLhLRRSVQSLT 291
                                   3355566666666666665555444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   3.3e-10   1.7e-07       2     111 ..      55     179 ..      54     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.3e-10
                                   EEESSTTSSHHHHHHHHHHHHTHE.....EEEEETTTCSSS......................STTHHHHHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakelgve.....fleisgsellsk......................yvgesekkirelfkeake 55 
                                   l++GppGtGKT+++  v +e++ +     f+++++     k                      +++  ek ++ l+++   
  gi|91774071|ref|YP_566763.1|  55 LISGPPGTGKTTTVLKVFEEMKKHsedivFIKVNCQMDSTKfavitrvyqglfnvsppssgvaFIKLFEKVMNYLIEK--- 132
                                   799******************744444447888887776668888889999888877775554555555544444433... PP

                                   TSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                           AAA  56 kakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                   + k+ +l +D+i  l  +       ++++v+  Ll++ +++    +kv vi++  +
  gi|91774071|ref|YP_566763.1| 133 E-KTLVLCLDDINYLYHEG------HADEVMYSLLRAHEQYPG--AKVGVIAIVSD 179
                                   2.359**********9999......999999999999999999..46777776555 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 !   19.3   0.0   1.3e-06   0.00064      35      79 ..      53      97 ..      36     102 .. 0.90
   2 ?    5.9   0.0     0.016         8      94     132 ..     128     166 ..     121     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                         AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlq 79
                                  + l+ Gp GtGKt+++ +++++++k +  +++i+++ q++++++ 
  gi|91774071|ref|YP_566763.1| 53 NSLISGPPGTGKTTTVLKVFEEMKKHSEDIVFIKVNCQMDSTKFA 97
                                  6799***********************************999875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                         AAA_7  94 ygPpggkklvvFvDDlnmpakekygaqppiellRqlldy 132
                                   y   ++k+lv+ +DD+n    e   +     llR + +y
  gi|91774071|ref|YP_566763.1| 128 YLIEKEKTLVLCLDDINYLYHEGHADEVMYSLLRAHEQY 166
                                   666789****************************98665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.5e-08   1.3e-05      19      44 ..      53      78 ..      31     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-08
                        AAA_11 19 itliqGPPGtgKTktivellsqllsr 44
                                   +li+GPPGtgKT+t++++++++ ++
  gi|91774071|ref|YP_566763.1| 53 NSLISGPPGTGKTTTVLKVFEEMKKH 78
                                  59*********************644 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.8e-08     2e-05       9     113 ..      55     161 ..      53     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.8e-08
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseellealeqalra 88 
                                   ++ G++GtGKTt++ +++e+ ++++    e+  +++v+++ ++ + + + r     ++++  +++     l+e++ ++l +
  gi|91774071|ref|YP_566763.1|  55 LISGPPGTGKTTTVLKVFEEMKKHS----EDIVFIKVNCQMDStKFAVITRVYQGLFNVSPPSSGVAFIKLFEKVMNYLIE 131
                                   799*****************97653....3666679999999945555566666666666666778888888888888888 PP

                        AAA_22  89 ravielliiDEaqhlr...s..eealeeLr 113
                                   + ++ +l +D++ +l    +  e +++ Lr
  gi|91774071|ref|YP_566763.1| 132 KEKTLVLCLDDINYLYhegHadEVMYSLLR 161
                                   8889**********9765415344444443 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 !   21.5   0.0   3.2e-07   0.00016      37      83 ..     322     367 ..     296     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.2e-07
                                   --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHHH CS
                        Cdc6_C  37 ltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvle 83 
                                   l  ++++d++++L+  + +++  s+kG+r grtr i+ +++p+d+l+
  gi|91774071|ref|YP_566763.1| 322 LGYTRFYDMVNKLSEARYVDADFSGKGMR-GRTRIIKPRYQPEDILK 367
                                   789*************************7.**************985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.5e-07   0.00013       4     115 ..      55     162 ..      53     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-07
                                   EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C.....CHHHHCC CS
                         NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse.....vwavlle 78 
                                   ++ G++G GKTt + k+ +++++   +     +++ ++++++s++ ++ +++ + lf + p++++         v+++l+e
  gi|91774071|ref|YP_566763.1|  55 LISGPPGTGKTTTVLKVFEEMKKHSED----IVFIKVNCQMDSTKFAViTRVYQGLFNVSPPSSGVAFIklfekVMNYLIE 131
                                   799*******************99933....3556688888888765589999999999888776543355666******* PP

                                   SCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                         NACHT  79 lperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                    ++ l+l lD++++l  + ++      ++++ +l+r+
  gi|91774071|ref|YP_566763.1| 132 KEKTLVLCLDDINYLYHEGHA------DEVMYSLLRA 162
                                   ***************986655......7788888775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.9e-07   0.00036      25     112 ..      56     143 ..      45     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.9e-07
                                   EEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHH..HHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCT CS
                        NB-ARC  25 lvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdksee..iletilkeLslseddleekeeveslkrklvrlLltk 103
                                   ++G +G GKtt + +++++   ++++ + ++++ v  +++s +  ++ ++ + L + +   +  +  + l +k++++L++k
  gi|91774071|ref|YP_566763.1|  56 ISGPPGTGKTTTVLKVFEE---MKKHSEDIVFIKVNCQMDSTKfaVITRVYQGLFNVSPPSSGVAFIK-LFEKVMNYLIEK 132
                                   89*********99999999...6667777777777777766652277778888877755555555444.***********9 PP

                                   .TEEEE.EEEE CS
                        NB-ARC 104 .rfllv.lDDV 112
                                    ++l++ lDD+
  gi|91774071|ref|YP_566763.1| 133 eKTLVLcLDDI 143
                                   96665449**8 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.7e-06    0.0014      23     157 ..      54     171 ..      28     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.7e-06
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvf 103
                                    +i Gp g GKt+ + ++ e+ ++++++++++    + +++k+          +++ + l ++ p  ++            
  gi|91774071|ref|YP_566763.1|  54 SLISGPPGTGKTTTVLKVFEEMKKHSEDIVFIKVNCQMDSTKFAVI-------TRVYQGLFNVSPPSSG--------VAFI 119
                                   4799****************************99999999999998.......4455555566666555........3445 PP

                      ATPase_2 104 kaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekh 157
                                   k +e++++ + +k k +++ +D++ +l      +a +++++Ll++ e+ +  k 
  gi|91774071|ref|YP_566763.1| 120 KLFEKVMNYLIEKEKTLVLCLDDINYLY--HEGHADEVMYSLLRAHEQYPGAKV 171
                                   66899999999999*************9..556779999999999988766554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06   0.00075     112     163 ..      32      85 ..      19      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                         T2SSE 112 ealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinksderivtv 163
                                   e++ + +   lr a+r  +  + l+sG+ g+GKtt++  + +e++k++e iv +
  gi|91774071|ref|YP_566763.1|  32 ESQMQSLMYSLRPALRgmRPINSLISGPPGTGKTTTVLKVFEEMKKHSEDIVFI 85 
                                   55555555556666552145677****************************987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     9e-06    0.0046       6      76 ..      55     146 ..      52     185 .. 0.69
   2 ?   -1.6   0.1       4.9   2.5e+03      11      72 ..     260     318 ..     259     344 .. 0.45

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9e-06
                        AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderd...................kkladpe......kllelilek.l 60 
                                   +i+G+  +GKTt + ++++e   ++e+i++i+++ + d                         +      kl e +++  +
  gi|91774071|ref|YP_566763.1|  55 LISGPPGTGKTTTVLKVFEEMKKHSEDIVFIKVNCQMDstkfavitrvyqglfnvspP-----SsgvafiKLFEKVMNYlI 130
                                   799***************9999888999988777666644666666665555444430.....144433344444444433 PP

                        AAA_14  61 keekktylflDEiqev 76 
                                   ++ek+ +l+lD i ++
  gi|91774071|ref|YP_566763.1| 131 EKEKTLVLCLDDINYL 146
                                   3357778999999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.9
                        AAA_14  11 RrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek..lkeekktylflDE 72 
                                   Rr+ KT l++++ k +    ++ l +    ++++  ++   ll li e+  ++  ++ y+++ E
  gi|91774071|ref|YP_566763.1| 260 RRASKTILVEDVEKAYE--TSRLLHLRRSVQSLTPDEKL--LLCLIAENkdVQ-TGDLYILFHE 318
                                   56667777766644333..33333332222222222211..223333322222.3555555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   9.9e-06    0.0051      12      38 ..      53      79 ..      43      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.9e-06
                        AAA_19 12 vllvtaGpGtGKTrvlkhivallvelg 38
                                  + l+ ++pGtGKT+++ ++ +++++  
  gi|91774071|ref|YP_566763.1| 53 NSLISGPPGTGKTTTVLKVFEEMKKHS 79
                                  689*****************9999876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     6e-06    0.0031       5      59 ..      32      90 ..      28     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6e-06
                                  SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS..-EEEEETT CS
               Sigma54_activat  5 sealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskrkek..pfvavnca 59
                                  ++++++l+ +++ + +    ++ li G  GtGK++   +++e+ k++++   f++vnc 
  gi|91774071|ref|YP_566763.1| 32 ESQMQSLMYSLRPALRGMrpINSLISGPPGTGKTTTVLKVFEEMKKHSEdiVFIKVNCQ 90
                                  56677777777777654334999******************9776655423899****7 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.6e-05     0.013       3      77 ..      52     146 ..      50     158 .. 0.76
   2 ?    0.4   0.0      0.86   4.4e+02      48      80 ..     226     277 ..     197     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                        AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie................swedfldevvela 60 
                                   ++ li Gp+g+GKTt++++         ++++fi ++    ++d +kf  i+                +++++ ++v    
  gi|91774071|ref|YP_566763.1|  52 INSLISGPPGTGKTTTVLKVfeemkkhSEDIVFIKVNC---QMDSTKFAVITrvyqglfnvsppssgvAFIKLFEKVMNYL 129
                                   567899*************999999999999***9999...5555555555555588888888887776666666655556 PP

                        AAA_24  61 aeladyktlviDtidel 77 
                                    e+++  +l++D i+ l
  gi|91774071|ref|YP_566763.1| 130 IEKEKTLVLCLDDINYL 146
                                   66666677777777655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.86
                        AAA_24  48 swedfldevvel...................aaeladyktlviDtideleel 80 
                                    ++d++d++ve                    +ae +  kt+ +  +++++e 
  gi|91774071|ref|YP_566763.1| 226 VMDDVRDAIVEYvdltgdlrvgidllkrsglNAERRASKTILVEDVEKAYET 277
                                   567788888888888999999999999999999999999**99999999985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   9.7e-06     0.005       3      26 ..      55      78 ..      53      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.7e-06
                                  EEE--TTSSHHHHHHHHHHHH... CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkss 26
                                  +i+GppG+GKtT v kv e++k++
  gi|91774071|ref|YP_566763.1| 55 LISGPPGTGKTTTVLKVFEEMKKH 78
                                  69******************9875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.13      32      87 ..      30      87 ..      18     104 .. 0.85
   2 ?    1.3   0.1      0.32   1.6e+02      92     124 ..     119     151 ..     116     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                        DUF815 32 gidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrliev 87
                                    ++q ++l+   +  l+g++  n L+ G  GtGK ++v  +++e+++++  + +i+v
  gi|91774071|ref|YP_566763.1| 30 HRESQMQSLMYSLRPALRGMRPINSLISGPPGTGKTTTVLKVFEEMKKHSedIVFIKV 87
                                  568999999999*********************************9988744555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.32
                        DUF815  92 lkelpklvellrerperfilfvDDLsFeeeeee 124
                                   +k ++k+++ l e+++ ++l +DD+ +  +e +
  gi|91774071|ref|YP_566763.1| 119 IKLFEKVMNYLIEKEKTLVLCLDDINYLYHEGH 151
                                   567899******************998766655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.8e-05     0.025      12      48 ..      47      84 ..      38      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                    Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdele.rqgnvvr 48
                                  ++ rP+  l++G pG GK+++  ++ +e++ + +++v 
  gi|91774071|ref|YP_566763.1| 47 RGMRPINSLISGPPGTGKTTTVLKVFEEMKkHSEDIVF 84
                                  5679*************************944555554 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   5.2e-05     0.027       5      40 ..      55      88 ..      52     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                       DUF2075  5 lVtGvaGtGKtvvllnllaeleddeeertavylsvN 40
                                  l++G +GtGKt   l+++ e+  +++ +  v++ vN
  gi|91774071|ref|YP_566763.1| 55 LISGPPGTGKTTTVLKVFEEM--KKHSEDIVFIKVN 88
                                  89******************9..6666666666666 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    0.0001     0.053      21      46 ..      54      79 ..      45      90 .. 0.75
   2 ?   -2.3   0.0       5.9     3e+03      30      54 ..     263     292 ..     255     314 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                        AAA_30 21 avltGpAGtGKttalkalreaweaag 46
                                  +++ Gp+GtGKtt++ ++ e ++++ 
  gi|91774071|ref|YP_566763.1| 54 SLISGPPGTGKTTTVLKVFEEMKKHS 79
                                  6899*******998766655555444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                        AAA_30  30 GKttalkalreaweaag.....grviglAp 54 
                                    Kt +++ +++a+e++      ++v  l+p
  gi|91774071|ref|YP_566763.1| 263 SKTILVEDVEKAYETSRllhlrRSVQSLTP 292
                                   466666666666666544455444444444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.3e-05     0.047      20      93 ..      51     122 ..      31     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
                    KAP_NTPase  20 pivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkll 93 
                                   pi   ++g+ G+GK++ + k+ +e+k++  +++++f+++n    +++ +++ ++++ L+++ + ++g+  +kl+
  gi|91774071|ref|YP_566763.1|  51 PINSLISGPPGTGKTTTVLKVFEEMKKH--SEDIVFIKVNCQMDSTKFAVITRVYQGLFNVSPPSSGVAFIKLF 122
                                   5556789999******************..**********9998888888888888888887777777666666 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.071        37      36      80 ..      56     101 ..      51     109 .. 0.80
   2 ?    8.1   0.0     0.002         1     120     156 ..     128     163 ..     117     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.071
                        AAA_35  36 ikapkkmGKtSLlarilakakqqgyktvsldlq.ladkeilsdldk 80 
                                   i +p  +GKt  + ++ +++k+++   v ++++ ++d++ ++ + +
  gi|91774071|ref|YP_566763.1|  56 ISGPPGTGKTTTVLKVFEEMKKHSEDIVFIKVNcQMDSTKFAVITR 101
                                   789999******************9999998873455555665555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                        AAA_35 120 ylLkeidkplvLaldevdrlfeypeiakdflslLRsw 156
                                   yl+ e +k lvL+ld+++ l+++ +  + + slLR+ 
  gi|91774071|ref|YP_566763.1| 128 YLI-EKEKTLVLCLDDINYLYHEGHADEVMYSLLRAH 163
                                   444.45799*************999999999999975 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 ?   13.0   0.0   7.2e-05     0.037      35      83 ..      54     108 ..      41     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                         AAA_6  35 gapaGpagtGKtEtvkdLakalak.....qvvvfncs.dqldykslgkifkGlaq 83 
                                   + ++Gp gtGKt tv ++ +++ k     +++ +nc+ d+ ++  ++++++Gl +
  gi|91774071|ref|YP_566763.1|  54 SLISGPPGTGKTTTVLKVFEEMKKhsediVFIKVNCQmDSTKFAVITRVYQGLFN 108
                                   6789***********888777765222224566899757889999*******976 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00016     0.082      30      62 ..     244     276 ..     229     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                       TIP49_C  30 LRYaiqLltpasilakkrkkkevevedveevee 62 
                                   LR  i Ll+ + + a++r +k++ vedve+++e
  gi|91774071|ref|YP_566763.1| 244 LRVGIDLLKRSGLNAERRASKTILVEDVEKAYE 276
                                   9999***************************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 ?   13.3   0.0   0.00012     0.063      17      60 ..      44      85 ..      27     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                  ......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                        ResIII 17 eklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                   +l   r  + li  + GtGKT + +k+ e+++k+   e ++f+
  gi|91774071|ref|YP_566763.1| 44 PALRGMRPINSLISGPPGTGKTTTVLKVFEEMKKHS--EDIVFI 85
                                  455556677899********************9964..467776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00037      0.19      22      59 ..      54      90 ..      47     104 .. 0.84
   2 ?   -0.3   0.0       1.1   5.5e+02     105     144 ..     120     159 ..      92     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                        ATPase 22 vlitGepGtGKtifalqFlikgaekygepgvfvtveep 59
                                   li+G pGtGKt+ +l+ +++ ++k  e  vf+ v+ +
  gi|91774071|ref|YP_566763.1| 54 SLISGPPGTGKTTTVLK-VFEEMKKHSEDIVFIKVNCQ 90
                                  59*************99.56777888999999988655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                        ATPase 105 eelieelaeaikeikakrvviDsitglayeekeavaReil 144
                                   + + + +++ i++ k   + +D i+ l +e +++++   l
  gi|91774071|ref|YP_566763.1| 120 KLFEKVMNYLIEKEKTLVLCLDDINYLYHEGHADEVMYSL 159
                                   55677889999999999999*****994444444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.017       8.6      49      83 ..      53      87 ..      27      98 .. 0.81
   2 ?    3.8   0.0     0.084        43     106     136 ..     132     162 ..     120     174 .. 0.84
   3 ?   -1.0   0.0       2.5   1.3e+03      78      94 ..     322     338 ..     316     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                     IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrv 83
                                  n ++ Gp+G+GK+     +  e  ++   ++f++v
  gi|91774071|ref|YP_566763.1| 53 NSLISGPPGTGKTTTVLKVFEEMKKHSEDIVFIKV 87
                                  7899*********8777777777777777777766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.084
                     IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviek 136
                                     k+ +l lDd+ +l  + ++ e+++ ++ +
  gi|91774071|ref|YP_566763.1| 132 KEKTLVLCLDDINYLYHEGHADEVMYSLLRA 162
                                   5677899********************9975 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.5
                     IstB_IS21  78 vlfvrvedLveelkrar 94 
                                     ++r  d+v++l+ ar
  gi|91774071|ref|YP_566763.1| 322 LGYTRFYDMVNKLSEAR 338
                                   5699*********9998 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015     0.077      58     125 ..      56     124 ..      39     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                   EEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HH.HHHHTT--GGG-EEE--SSHHHHHHHHHH CS
                          RecA  58 iyGpessGkttlalhaiaeaqkkggvaafidaehaldpk.yakklGvdidellvsqpdtGeqaleiada 125
                                   i Gp  +Gktt  l++  e++k++  ++fi ++  +d++ +a    v    + vs p +G   +++ ++
  gi|91774071|ref|YP_566763.1|  56 ISGPPGTGKTTTVLKVFEEMKKHSEDIVFIKVNCQMDSTkFAVITRVYQGLFNVSPPSSGVAFIKLFEK 124
                                   6799*********************************86155555555555568888888776665555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.11      18      64 ..      34      81 ..      27     166 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                          TniB 18 eilerLeeLleypkrkrmpnlllvGdsnnGKtmiv.ekFarlhppekd 64
                                  ++ + + +L  + +  r+ n l+ G++ +GKt+ v + F++++++++d
  gi|91774071|ref|YP_566763.1| 34 QMQSLMYSLRPALRGMRPINSLISGPPGTGKTTTVlKVFEEMKKHSED 81
                                  455556677777888999*************97651667777666554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1     0.001      0.53      49      65 ..      55      71 ..      45     110 .. 0.77
   2 ?   -2.1   0.0       6.1   3.1e+03     153     178 ..     123     146 ..      69     154 .. 0.76
   3 ?   -0.6   0.0       2.1   1.1e+03     130     153 ..     260     284 ..     248     311 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                         Rad17 49 LisGPsGCgkstvvkvL 65
                                  LisGP+G gk+t+v  +
  gi|91774071|ref|YP_566763.1| 55 LISGPPGTGKTTTVLKV 71
                                  9*********9886433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.1
                         Rad17 153 revirkylrssealplilviteiesl 178
                                   ++v  +yl  +e  +l+l++ +i+ l
  gi|91774071|ref|YP_566763.1| 123 EKV-MNYLIEKEK-TLVLCLDDINYL 146
                                   333.345555555.688888888765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.1
                         Rad17 130 rtdkklilvedlPnkfyrds.dalr 153
                                   r   k ilved+   ++++    lr
  gi|91774071|ref|YP_566763.1| 260 RRASKTILVEDVEKAYETSRlLHLR 284
                                   45678999***98877765433333 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00086      0.44      35      60 ..      53      78 ..      24      92 .. 0.78
   2 ?    0.4   0.1      0.93   4.8e+02      73     108 ..     123     160 ..      77     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00086
                        RuvB_N 35 hvllyGpPGlGkttlakiiakelgvk 60
                                    l++GpPG Gktt    + +e++ +
  gi|91774071|ref|YP_566763.1| 53 NSLISGPPGTGKTTTVLKVFEEMKKH 78
                                  5699**********999999999765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.93
                        RuvB_N  73 gdlaalltnleekdvlfideihrlsr..aveevlysam 108
                                     ++  l + e++ vl +d+i  l +  +++ev+ys +
  gi|91774071|ref|YP_566763.1| 123 EKVMNYLIEKEKTLVLCLDDINYLYHegHADEVMYSLL 160
                                   55667788888899999****99976236899999865 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 ?   12.8   0.0   0.00018     0.095       5      44 ..      57      96 ..      54     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                                  ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  5 stkGGvGKTtlaanLaralarrglrVllvDaDpqannlai 44
                                  s+  G+GKTt++++    ++++  +++ +++  q+ +++ 
  gi|91774071|ref|YP_566763.1| 57 SGPPGTGKTTTVLKVFEEMKKHSEDIVFIKVNCQMDSTKF 96
                                  66669*************************9999988874 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.16       5      35 ..      55      85 ..      51      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                         SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllv 35
                                  l+ G+ G+GKTtt+ K+ + +kk+ ++++++
  gi|91774071|ref|YP_566763.1| 55 LISGPPGTGKTTTVLKVFEEMKKHSEDIVFI 85
                                  789********************99998876 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   0.00073      0.37       2      45 ..      54     100 ..      53     161 .. 0.65
   2 ?   -2.0   0.0       6.4   3.3e+03      40      77 ..     239     274 ..     233     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00073
                                   EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrr 45 
                                    l+ GppGtgK++ + ++ + +      ++ +  + ++ ++++   +
  gi|91774071|ref|YP_566763.1|  54 SLISGPPGTGKTTTVLKVFEEMkkhSEDIVFIKVNCQMDSTKFAVIT 100
                                   5889*********9998888875554444444555555555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.4
                                   HHH--B--.........--------G-SEEEEESGGG- CS
                         AAA_5  40 dlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                   dl+g +++  g   l+ s l  + r ++++++++ve+a
  gi|91774071|ref|YP_566763.1| 239 DLTGDLRV--GIDLLKRSGLNAERRASKTILVEDVEKA 274
                                   56666665..6666677777777778889999999987 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0014      0.71      34      66 ..      55      84 ..      49      94 .. 0.83
   2 ?    0.0   0.0      0.55   2.8e+02     481     511 ..     248     278 ..     240     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                        AAA_32 34 fvlGesgtGrttlvkrlleeiakkeptpdDwcY 66
                                   ++G++gtG+tt+v ++ ee++k+    +D+++
  gi|91774071|ref|YP_566763.1| 55 LISGPPGTGKTTTVLKVFEEMKKHS---EDIVF 84
                                  689***************9986654...56666 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.55
                        AAA_32 481 adllrEAdywakkegaevveaehVekAleek 511
                                   +dll+ +   a++++++++  e+VekA+e  
  gi|91774071|ref|YP_566763.1| 248 IDLLKRSGLNAERRASKTILVEDVEKAYETS 278
                                   7999999********************9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00063      0.32       2      25 ..      55      76 ..      55     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00063
                        AAA_18  2 lltGtpGvGKttlakeLskrlgfg 25
                                  l++G+pG+GKtt    + +++   
  gi|91774071|ref|YP_566763.1| 55 LISGPPGTGKTTTVLKVFEEM--K 76
                                  699*******99876664443..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 2403.74
//
Query:       gi|91774072|ref|YP_566764.1|  [L=195]
Description: molybdenum-pterin binding domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   43.9   0.2    1.2e-10   41.5   0.2    2.1  2  TOBE      TOBE domain
      6e-11   42.1   0.0    1.4e-10   40.9   0.0    1.6  2  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR


Domain annotation for each model (and alignments):
>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.21   1.9e+03      17      33 ..      92     108 ..      88     109 .. 0.80
   2 !   41.5   0.2   1.3e-14   1.2e-10       2      62 ..     116     175 ..     115     177 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                          TOBE  17 lgseveVrvdlgggatL 33 
                                    +s+++V+++ g++++L
  gi|91774072|ref|YP_566764.1|  92 EDSRSFVDITFGDETSL 108
                                   568999******99866 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 1.3e-14
                          TOBE   2 sarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakv 62 
                                   sa N l g++v +  ++  + V v++++   Lt+ +t ++ e+L+++ G+eVfa+ik+++v
  gi|91774072|ref|YP_566764.1| 116 SAHNKLSGRIVGIDKGNIVSKVKVEIDPDV-LTSIITSEALERLDVQEGDEVFATIKSTEV 175
                                   899***************************.****************************99 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 ?   -2.9   0.0      0.79   7.1e+03      50      59 ..       7      16 ..       2      17 .. 0.68
   2 !   40.9   0.0   1.6e-14   1.4e-10       4      60 .]      25      85 ..      23      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.79
                                  SSEEEE-HHH CS
                         HTH_1 50 grglrLTeaG 59
                                    ++ LTe G
  gi|91774072|ref|YP_566764.1|  7 RTKVWLTEDG 16
                                  3578899998 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1.6e-14
                                  HHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEE..ESSSE..EEE-HHHH CS
                         HTH_1  4 lrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfe..Rtgrg..lrLTeaGe 60
                                  ++l++a+ ee+s+++A+ +L +s+++++  +k+++e++g++ ++  R g+g  + LT++G+
  gi|91774072|ref|YP_566764.1| 25 VKLLKAIDEERSLRKACSKLDISYKHAWLILKKMNERVGHEVVTtiRGGKGqgTFLTDYGK 85
                                  799*****************************************777555455******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1456.14
//
Query:       gi|91774073|ref|YP_566765.1|  [L=251]
Description: exodeoxyribonuclease III [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-21   75.8   0.0    4.1e-21   75.6   0.0    1.0  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
      2e-05   24.4   0.0    5.1e-05   23.1   0.0    1.7  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   4.6e-25   4.1e-21      20     233 .]      10     238 ..       2     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4.6e-25
                                   HHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEEEEECSTEEEEEEEEEEETSSSSGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos  20 drladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggnggavlsrfpltslfrrtfiefndlvaa 100
                                   +   ++++a+++D+l+LQE++  e +++++l    g+++++ +      ++g+ g++++ + p+ ++++   +  +d+  +
  gi|91774073|ref|YP_566765.1|  10 KGFVEWMEATQPDILCLQETKATETQLPKELRHIHGYVPYFFS----AERKGYSGVGIYTKVPPVEVKYGLGVPRFDKEGR 86 
                                   55789***********************999999555555554....789******************************* PP

                                   EEEEEEEEEEEEEEE...CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTH.. CS
                                   xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                 Exo_endo_phos 101 lrreplaakleqlni...ashrdhdlvrdlqllalllqvealnadrgapvivaGDfNarpsdddsrvlrtrglalapap.. 176
                                   + +  +    +++ +       d++l  ++ ++  + +v++  +d g+ vi++GD N+++ + d  ++  + ++    p  
  gi|91774073|ref|YP_566765.1|  87 TLIVEFEDFALFNIYfpnGKASDERLEYKMDFYNAFMEVADSMKDAGKNVIICGDVNTAHKEIDLARPKQNERSSGFLPqe 167
                                   ************999****************************************************************77 PP

                                   ......H...............SSCESCETTTTTTTTTTTEB-BEEEEEECHHHCCEEEEEEECCHHEEC.....TSSCSS CS
                                   ......x...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxx RF
                 Exo_endo_phos 177 ......v...............glyllgggptptyvtraggsrlDrilaspalalfrsgvlppplalvrr.....ealtlS 231
                                         +                ++++++   + ++ r+ g+r+D+ +as +l+ +             r      ++++S
  gi|91774073|ref|YP_566765.1| 168 rewidtFlghgyldtlrmfepeSGNYTWWDMKTRARDRNVGWRIDYFFASVSLKDRI------------RsayilSDVMGS 236
                                   77666605566777888999******************************5444444............14555557889* PP

                                   SB CS
                                   xx RF
                 Exo_endo_phos 232 DH 233
                                   DH
  gi|91774073|ref|YP_566765.1| 237 DH 238
                                   *9 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   5.7e-09   5.1e-05       3     118 ..      97     241 ..      95     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.7e-09
               Exo_endo_phos_2   3 iisvYippsd..........elenlestlekllselksp..kiiilGDfNakhplWgsedtds.......sargeeLiefl 64 
                                   ++++Y p+ +          +++n+  ++ + +++      ++ii+GD+N  h++ +  + ++         +++e i+++
  gi|91774073|ref|YP_566765.1|  97 LFNIYFPNGKasderleykmDFYNAFMEVADSMKD---AgkNVIICGDVNTAHKEIDLARPKQnerssgfLPQEREWIDTF 174
                                   68889988888888887544444444455555555...4559************999865555667889967777777777 PP

               Exo_endo_phos_2  65 eehs.lsll..nllksg.ptfkssng.......sstiDltltsdnlals..kleleeedlgSDHrpi 118
                                     h+ l +l   +++sg  t+++ ++          iD +++s +l ++  +  +  + +gSDH pi
  gi|91774073|ref|YP_566765.1| 175 LGHGyLDTLrmFEPESGnYTWWDMKTrardrnvGWRIDYFFASVSLKDRirSAYILSDVMGSDHCPI 241
                                   777624555544455667999999988888766778************9998889999******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1427.12
//
Query:       gi|91774074|ref|YP_566766.1|  [L=542]
Description: thermosome, chaperonin Cpn60/TCP-1 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-180  601.5  24.0   1.2e-180  601.3  24.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
     0.0082   15.7   0.0      0.015   14.9   0.0    1.3  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 !  601.3  24.0  1.4e-184  1.2e-180       1     489 [.      36     524 ..      36     526 .. 0.99

  Alignments for each domain:
  == domain 1  score: 601.3 bits;  conditional E-value: 1.4e-184
                                   HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                   +a++v+ttlGPkGmdKmlv++ g+vv+TnDGatilke++iehPaak++ve+a++qd+evGDGTtt+++++geLl++ae++i
  gi|91774074|ref|YP_566766.1|  36 VAEAVRTTLGPKGMDKMLVDSLGDVVITNDGATILKEMDIEHPAAKMIVEVAKTQDDEVGDGTTTAAVITGELLKKAEEMI 116
                                   689****************************************************************************** PP

                                   HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS.EEC CS
                    Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene.kel 160
                                   ++++hpt i  gy++a  ka e+Lk+ a+++ ++  ++++L+++  t++++k  +++++ lsk++vdA+ ++++ ++ +++
  gi|91774074|ref|YP_566766.1| 117 EQDIHPTIIAAGYRMASVKAGEILKSLAKKVTID--NKDMLISISDTAMTGKGAEATKDILSKIAVDAIiSIVDRDNgNTV 195
                                   ***************************8888776..89*******************************888877779*** PP

                                   SCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHH CS
                    Cpn60_TCP1 161 dlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekql 241
                                   d++++kv+k+ gg+++dsel+eG++ldk+ ++++mpkk+e a+++ll+  +e ++te+++++ ++++e+l++++++ee +l
  gi|91774074|ref|YP_566766.1| 196 DIENVKVEKKVGGRIDDSELIEGMILDKERVHTNMPKKVEGARIALLNSAIELKETEVDAEISITSPEQLQSFLDQEESML 276
                                   ********************************************************************************* PP

                                   HHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETT CS
                    Cpn60_TCP1 242 eellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigs 322
                                   + l+ +i+k+g+nvv+cqkgidd+a+h+lak+gi+a+rrvkk+d+e+l++ t a++++++e++t e+lG a+ vee+kig 
  gi|91774074|ref|YP_566766.1| 277 KSLVTSITKTGANVVFCQKGIDDMAQHYLAKEGIFAVRRVKKSDMEKLVRSTSAKLITNIEEMTAEDLGAAELVEEKKIGG 357
                                   ********************************************************************************* PP

                                   CCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHH CS
                    Cpn60_TCP1 323 ekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaie 403
                                   +++t+i+++ ++k+++illrg t++v+d iera++dAl+vv+ aiede++v+GGGa e+e+a +l+eya+++sg+eqla++
  gi|91774074|ref|YP_566766.1| 358 DSMTFITGCVNPKSVSILLRGGTEHVIDNIERALNDALRVVAVAIEDEELVAGGGAPEVEVALRLNEYASTLSGREQLAVK 438
                                   ********************************************************************************* PP

                                   HHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEE CS
                    Cpn60_TCP1 404 afakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrid 484
                                   afa+ALev+p+tLaeNaGldpi++l +lra h+kg k++g++v +g++id++eagvv+pl+vk+qa++s teaa +iLrid
  gi|91774074|ref|YP_566766.1| 439 AFAEALEVVPRTLAENAGLDPIDMLVELRAHHEKGIKTAGLNVYTGTVIDMWEAGVVEPLRVKTQAINSGTEAAVMILRID 519
                                   ********************************************************************************* PP

                                   EEEXX CS
                    Cpn60_TCP1 485 eiika 489
                                   +ii  
  gi|91774074|ref|YP_566766.1| 520 DIIAS 524
                                   ***86 PP

>> TrwC  TrwC relaxase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.6e-06     0.015      43     124 ..     315     405 ..     295     419 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-06
                          TrwC  43 evteeqfeallegrhpd........tgerlgrakesaererkavagfDltf....saPKSvSllalvgdderraaieaahd 111
                                   +v++ ++e+l++ ++++        t+e lg+a+   e   k++ g  +tf      PKSvS+l   g++++  +ie+a +
  gi|91774074|ref|YP_566766.1| 315 RVKKSDMEKLVRSTSAKlitnieemTAEDLGAAELVEE---KKIGGDSMTFitgcVNPKSVSILLRGGTEHVIDNIERALN 392
                                   79999999999999999999999999999999777654...56666666662222459******99888888888888888 PP

                          TrwC 112 aAvkaalalleee 124
                                   +A + +   +e+e
  gi|91774074|ref|YP_566766.1| 393 DALRVVAVAIEDE 405
                                   8888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 3192.31
//
Query:       gi|91774075|ref|YP_566767.1|  [L=57]
Description: hypothetical protein Mbur_2147 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-27   96.0   3.4    1.4e-27   95.9   3.4    1.0  1  DUF5350   Family of unknown function (DUF5350)


Domain annotation for each model (and alignments):
>> DUF5350  Family of unknown function (DUF5350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   3.4   7.9e-32   1.4e-27       1      56 [.       1      56 [.       1      57 [] 0.98

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 7.9e-32
                       DUF5350  1 MGKTGsveWvkvKgrkgqirlVpkkegekkkpGPnQrfkssgkkrrikrrsakaiv 56
                                  MGKTGs++WvkvKgrkg+i++V+++ g+k++pGP+Qrf+ssg+krr+ +rs k+iv
  gi|91774075|ref|YP_566767.1|  1 MGKTGSINWVKVKGRKGKIIKVQRAFGAKAHPGPAQRFSSSGAKRRFLKRSPKSIV 56
                                  *****************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 377.27
//
Query:       gi|91774076|ref|YP_566768.1|  [L=420]
Description: hypothetical protein Mbur_2148 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-08   32.4   0.0    9.4e-08   32.0   0.0    1.3  1  NurA      NurA domain
  ------ inclusion threshold ------
      0.057   13.2   0.0        2.9    7.7   0.0    2.5  2  COQ9      COQ9


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 !   32.0   0.0     1e-11   9.4e-08      79     242 .]     185     388 ..      75     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1e-11
                                   SCEEEEECSHHCCCH............HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC...... CS
                          NurA  79 edllllDGsligslv............efdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnll..letl 141
                                   ++  ++DG+++++ +            +    +e +    +l+ +  +++     g +l+g +K+ +  +++ +l  +  +
  gi|91774076|ref|YP_566768.1| 185 KGFFIMDGPIYPKQLmywmvveskevrI----KEDPVAKNILQNYIDIMDYqmkkGMPLIGFVKNPEDMQIMITLrdKKGM 261
                                   56689**********8888887744443....44445555555555555557777********************999999 PP

                                   ..S--HHHHCCHHCCHCH.............................---STTS-HHHHTT-HCCHHHHHH-EEEEEEESS CS
                          NurA 142 ligesisDiallgallrk.............................pgytspllkilrekpllrealidkeiyfaYvrle 193
                                   ++ +++ D ++++ +l +                              + tsp+l+i+    +     +d++i+f+ + + 
  gi|91774076|ref|YP_566768.1| 262 KHLPWLRDSQFFKNVL-SlgngdngrngrwitytnwflqpnqfyegmINSTSPMLDID---LRHDLDPEDYAITFFMLYVP 338
                                   9***************.99**************************9999999999999...9999999************* PP

                                   TTTTEEEEEHHHHHHCCHHHHHHHHHH.....TTB-SSSBCCHHHHHHHHCC CS
                          NurA 194 gggsilrleipaevstakdedvlslla...sqrlsisGYprpLalAhelaki 242
                                     ++++++e p+  + +kde+v  l++   ++ +s +G+p  L ++++laki
  gi|91774076|ref|YP_566768.1| 339 MLDVLFKVEAPY--GFTKDESVRDLITrkvLFDISVNGIPLTLSKVDSLAKI 388
                                   *********775..5678888888888888*********************8 PP

>> COQ9  COQ9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.014   1.2e+02       8      28 ..       8      28 ..       5      31 .. 0.86
   2 ?    7.7   0.0   0.00033       2.9      27      54 ..     105     132 ..      95     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.014
                          COQ9  8 lrelarlaDdiwraagDkstD 28
                                  ++ + ++aD i   a+D stD
  gi|91774076|ref|YP_566768.1|  8 IKIMSEMADRIGMSAEDDSTD 28
                                  566789**************9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00033
                          COQ9  27 tDfnwYtkRatLsavyastelymlqdks 54 
                                   +D++ ++kR++++a y+ + l+ ++ +s
  gi|91774076|ref|YP_566768.1| 105 SDLELHSKRTIVAATYSPSPLVTIDTTS 132
                                   6999**************9999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2765.81
//
Query:       gi|91774077|ref|YP_566769.1|  [L=605]
Description: ATPase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-10   40.5   0.0    9.6e-10   38.9   0.0    2.0  1  DUF87          Helicase HerA, central domain
    2.2e-09   36.5   0.0      6e-06   25.1   0.0    2.2  2  DUF853         Bacterial protein of unknown function (DUF853)
    4.3e-06   26.6   0.0      0.013   15.3   0.0    2.3  2  DEAD           DEAD/DEAH box helicase
    9.8e-06   25.9   0.0      0.004   17.4   0.0    2.4  2  AAA_22         AAA domain
    1.8e-05   23.9   0.0        0.1   11.5   0.0    2.2  2  AAA_10         AAA-like domain
    4.1e-05   24.0   1.2       0.36   11.3   0.1    2.8  2  AAA            ATPase family associated with various cellular
    0.00036   21.0   0.0       0.17   12.2   0.0    2.4  2  AAA_16         AAA ATPase domain
    0.00048   19.2   0.0     0.0013   17.7   0.0    1.6  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00063   19.8   0.0        1.3    9.0   0.0    2.3  2  ResIII         Type III restriction enzyme, res subunit
     0.0068   15.9   0.0      0.012   15.1   0.0    1.3  1  AAA_7          P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.018   14.3   0.0        0.9    8.7   0.0    2.3  2  DUF2075        Uncharacterized conserved protein (DUF2075)
      0.045   13.1   0.0        0.5    9.7   0.0    2.1  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.047   13.3   0.0        0.1   12.2   0.0    1.5  2  Zot            Zonular occludens toxin (Zot)
      0.062   12.4   0.0       0.12   11.4   0.0    1.4  1  T2SSE          Type II/IV secretion system protein
        0.1   13.0   0.0       0.24   11.8   0.0    1.7  1  RNA_helicase   RNA 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 !   38.9   0.0     8e-13   9.6e-10      20      96 ..     225     345 ..     206     561 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 8e-13
                         DUF87  20 klvtrHlAilgsTGsGKSntvavLleelle..............kkga..tililDpHGEYgkalekllsekvkvitpsps 84 
                                    l+ rH+++ gsTG+GK+++++ +l++ ++              kk++   ++i Dp+ EY+++l    +++ ++ + +++
  gi|91774077|ref|YP_566769.1| 225 PLIFRHMLVCGSTGTGKTFLTKNILRQFMSpdnrynvrdtgdgsKKKLrpCVVIMDPQDEYSQFL----EDNPEISSSDEH 301
                                   6899***************************************96666668**************....666666666554 PP

                         DUF87  85 a................................kdkelkinpws 96 
                                                                    ++ e++i++  
  gi|91774077|ref|YP_566769.1| 302 NmhsedvefggvpstktfvakvdghsyngrsraQQVEFTIPFEM 345
                                   45555555555555555555555555666666666666666655 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 !    9.0   0.0   0.00039      0.46      21      45 ..     228     252 ..     218     257 .. 0.81
   2 !   25.1   0.0     5e-09     6e-06     171     319 ..     402     552 ..     384     569 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00039
                        DUF853  21 nrhGliaGatGtGktvtLqvlaesl 45 
                                    rh l++G+tGtGkt   + +  ++
  gi|91774077|ref|YP_566769.1| 228 FRHMLVCGSTGTGKTFLTKNILRQF 252
                                   69*************8777665555 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 5e-09
                        DUF853 171 gnvskasvgaiqreLltLeqqGaekffGePaLdledllrtdadGrGvislLaadkllq..sPklyatfLlWllseLfeeLP 249
                                   g+v +as + + r+   ++++  +++f +Pa  ++++l      +G + ++ ++ + +     l +  L+ +   + ++L 
  gi|91774077|ref|YP_566769.1| 402 GKVHEASYDGLVRK---VNNNSFKRVFDQPATPITEMLADI-FKEGQVCVFPTEYISStrIRDLITLTLMTV--AVDNKLN 476
                                   55555555555554...345555666666666666655443.334445444443322210223333333332..2234444 PP

                        DUF853 250 evGdl..dkPklvfffdeahLLfn....dapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqh 319
                                     G++      l++ +deah  +     + +k ++ k     r  r  G G++++tq+P+d+ dtv+ q+ +rv  
  gi|91774077|ref|YP_566769.1| 477 TSGETvvKETPLILVLDEAHRYLArgsgEHSKRIISKFADAARQGRKEGLGLFLITQDPQDIDDTVFKQINSRVIL 552
                                   444421133448999*****8765233356899****************************************965 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00097       1.2      15      58 ..     229     284 ..     221     315 .. 0.77
   2 !   15.3   0.0   1.1e-05     0.013     115     157 ..     479     522 ..     451     541 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00097
                                   CEEEEEESTTSSHHHHHHHHHHHHHHHS.............TTSTS-EEEEEESSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxx RF
                          DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyet.............kgktgpkalivePtre 58 
                                   +++lv++ TG+GKT      +  ++++              k+k +p ++i+ P  e
  gi|91774077|ref|YP_566769.1| 229 RHMLVCGSTGTGKTFLTKNILR-QFMSPdnrynvrdtgdgsKKKLRPCVVIMDPQDE 284
                                   789***********99554444.4434347777777777777777777777777665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.1e-05
                                   TSSHCTTE.EEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 115 gklnlsqv.rflVlDEadrlldqgfsdfinrilnqlpqitcdgk 157
                                   g+  +++   +lVlDEa+r+l  g +++ +ri+++++++  +g+
  gi|91774077|ref|YP_566769.1| 479 GETVVKETpLILVLDEAHRYLARGSGEHSKRIISKFADAARQGR 522
                                   444455552469***********************988877776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.4e-06     0.004       7      30 ..     230     253 ..     229     288 .. 0.72
   2 ?    5.8   0.0     0.013        15      91     128 ..     483     531 ..     450     539 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                   +++v+G +GtGKT+l +++l+q+ 
  gi|91774077|ref|YP_566769.1| 230 HMLVCGSTGTGKTFLTKNILRQFM 253
                                   799******************994 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                        AAA_22  91 v...ielliiDEaqh.lr..seealeeL.rsllnl....srkgvqliLv 128
                                   v   + +l++DEa++ l   s e+ + + +++++     ++ g+ l+L+
  gi|91774077|ref|YP_566769.1| 483 VketPLILVLDEAHRyLArgSGEHSKRIiSKFADAarqgRKEGLGLFLI 531
                                   1444579********9977756666666455555466566667776666 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00022      0.26      23      73 ..     230     297 ..     227     307 .. 0.88
   2 !   11.5   0.0   8.6e-05       0.1     237     294 ..     483     546 ..     448     584 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                        AAA_10  23 asliiGdlGnGKSvlakllvlyisllg.................gkaliiDpkkerekfketlpeiak 73 
                                   ++l+ G++G GK +l+k +  + +  +                   ++i+Dp+ e  +f e  pei +
  gi|91774077|ref|YP_566769.1| 230 HMLVCGSTGTGKTFLTKNILRQFMSPDnrynvrdtgdgskkklrPCVVIMDPQDEYSQFLEDNPEISS 297
                                   789**************99988777777999********9998878999*******9**999998754 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.6e-05
                        AAA_10 237 dkkefkvvifDEawiftssaeG...kkllkel...vRiGRsynaavylvtqsadDvlkeelknn 294
                                    k++  + ++DEa  +     G   k+++++     R+GR+    ++l+tq+++D+++   k+ 
  gi|91774077|ref|YP_566769.1| 483 VKETPLILVLDEAHRYLARGSGehsKRIISKFadaARQGRKEGLGLFLITQDPQDIDDTVFKQI 546
                                   455666889999998877666633356776542227********************99876654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00048      0.57       1      22 [.     231     252 ..     231     294 .. 0.86
   2 !   11.3   0.1    0.0003      0.36      55     125 ..     484     547 ..     454     554 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                                   EEEESSTTSSHHHHHHHHHHHH CS
                           AAA   1 vllyGppGtGKTllakavakel 22 
                                   +l++G  GtGKT l k + +++
  gi|91774077|ref|YP_566769.1| 231 MLVCGSTGTGKTFLTKNILRQF 252
                                   79****************9986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0003
                                   HTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSS CS
                           AAA  55 ekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfd 125
                                   ++ +p il++DE+++   +    + e+++r+++++  +  + +k+   + + ++t++p+++d+ +  + ++
  gi|91774077|ref|YP_566769.1| 484 KE-TPLILVLDEAHRYLARG---SGEHSKRIISKFADAARQGRKE--GLGLFLITQDPQDIDDTVF-KQIN 547
                                   33.59***********9888...8999***********9999994..699************9987.5555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00015      0.17      20      51 ..     221     255 ..     215     301 .. 0.80
   2 !    6.4   0.0    0.0088        11     117     164 ..     456     520 ..     363     531 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                        AAA_16  20 rsgrp...elvllsGesGvGKsslvrellralekd 51 
                                   ++g+p   + +l+ G  G+GK+ l + +lr++   
  gi|91774077|ref|YP_566769.1| 221 SMGDPlifRHMLVCGSTGTGKTFLTKNILRQFMSP 255
                                   678888889****************9999876544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0088
                        AAA_16 117 srllellkrllallsrder............plvlvlDdlq.....wadeaslqllaaLlrlles 164
                                   +r+++l++  l+  + d +            pl+lvlD+++        e+s  +++ +++++ +
  gi|91774077|ref|YP_566769.1| 456 TRIRDLITLTLMTVAVDNKlntsgetvvketPLILVLDEAHrylarGSGEHSKRIISKFADAARQ 520
                                   5666666666655555455566666666666**********554444445888888888888776 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 !   17.7   0.0   1.1e-06    0.0013      16      76 ..     229     287 ..     221     303 .. 0.83
   2 ?   -2.2   0.0       1.2   1.5e+03     258     308 ..     511     562 ..     507     571 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                 TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraivlDltGafvsrfydegkdillnPlDaRsa 76 
                                   +h+l+ G+tG+GKt  ++++lr+  +  +r  v D++    ++  ++   ++++P D+ s+
  gi|91774077|ref|YP_566769.1| 229 RHMLVCGSTGTGKTFLTKNILRQFMSPDNRYNVRDTGDGSKKK-LRPC-VVIMDPQDEYSQ 287
                                   8*********************************975544444.4444.599999998775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                 TrwB_AAD_bind 258 leelksllaegRkfGgavvlglqsiaqlre.vYGedaaqsilslvntklilr 308
                                   ++++++++ +gRk G  + l  q+ + + + v+ + +++ il+l n   i++
  gi|91774077|ref|YP_566769.1| 511 ISKFADAARQGRKEGLGLFLITQDPQDIDDtVFKQINSRVILNLSNDAAITA 562
                                   6788889999999999998888888888652556666666666666555554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0016       1.9      25      70 ..     229     288 ..     223     341 .. 0.72
   2 !    9.0   0.0    0.0011       1.3     105     159 ..     444     516 ..     410     521 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                                   SEEEEEESTTSTHHHHHHHHHHHH-S...................-EEEEESSHHHHHHH CS
                        ResIII  25 krglikmaTGtGKTlvaaklierllkkgkee..............kflflvprkslleqt 70 
                                   +++l+   TGtGKT++  ++ +++++  ++                ++++ + ++ ++q 
  gi|91774077|ref|YP_566769.1| 229 RHMLVCGSTGTGKTFLTKNILRQFMSPDNRYnvrdtgdgskkklrPCVVIMDPQDEYSQF 288
                                   57788889*********9999999875443345555555555555555555555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                   SEEEEEHHHHHHTH.......................HHHTTT-SEEEEETGGGTTS....TTTHHHHHT--- CS
                        ResIII 105 kilvttiqsldadseee...............eeeseellrdrfdviiiDEaHrlgak...kswreilekfke 159
                                   +++v+ ++ +++ + ++               +   e+  +++ ++++ DEaHr+ a    ++ ++i+ kf +
  gi|91774077|ref|YP_566769.1| 444 QVCVFPTEYISSTRIRDlitltlmtvavdnklNTSGETVVKETPLILVLDEAHRYLARgsgEHSKRIISKFAD 516
                                   5555555555555555555555555555444566667777778889*********998655577778888755 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     1e-05     0.012      34      58 ..     229     253 ..     227     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                         AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                   +++l++G+tGtGKt ++k++l+++ 
  gi|91774077|ref|YP_566769.1| 229 RHMLVCGSTGTGKTFLTKNILRQFM 253
                                   689****************998875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00075       0.9       4      26 ..     231     262 ..     229     337 .. 0.72
   2 ?    3.2   0.0     0.036        43      90     108 ..     488     506 ..     459     531 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00075
                       DUF2075   4 vlVtGvaGtGKtvvllnllael.........e 26 
                                   +lV G +GtGKt +  n+l +          +
  gi|91774077|ref|YP_566769.1| 231 MLVCGSTGTGKTFLTKNILRQFmspdnrynvR 262
                                   6899*****************95444444440 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.036
                       DUF2075  90 dvvivDEAhrlltksdqae 108
                                    +++ DEAhr l +++ ++
  gi|91774077|ref|YP_566769.1| 488 LILVLDEAHRYLARGSGEH 506
                                   5899******999665543 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00042       0.5      40      56 ..     229     245 ..     207     253 .. 0.79
   2 ?    0.8   0.0      0.21   2.6e+02     211     242 ..     505     536 ..     475     537 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                                   .SEEEE--TTSSHHHHH CS
                  FtsK_SpoIIIE  40 shllvaGatgsGKStal 56 
                                    h+lv+G+tg+GK+   
  gi|91774077|ref|YP_566769.1| 229 RHMLVCGSTGTGKTFLT 245
                                   5************9655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.21
                                   H....HHHHHHHHHHHCGGGTEEEEEEES--- CS
                  FtsK_SpoIIIE 211 dssvlvedaivRlarkgraaglHlllatqrls 242
                                   + s+++++ ++  ar+gr++gl l l+tq ++
  gi|91774077|ref|YP_566769.1| 505 EHSKRIISKFADAARQGRKEGLGLFLITQDPQ 536
                                   445666666666777799***********987 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.1   7.3e+03       4      15 ..     232     243 ..     231     254 .. 0.81
   2 ?   12.2   0.0   8.8e-05       0.1      83     142 ..     489     550 ..     452     577 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.1
                           Zot   4 lvtGapGsgKts 15 
                                   lv G  G+gKt 
  gi|91774077|ref|YP_566769.1| 232 LVCGSTGTGKTF 243
                                   67899*****96 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.8e-05
                           Zot  83 llviDEcqeifpvrakegrkd..pevi.naftehRhlgwDivlltqdiskihkevralaekav 142
                                   +lv+DE+++     ++e  k+   + + +a  + R+ g  + l+tqd+  i++ v + ++  v
  gi|91774077|ref|YP_566769.1| 489 ILVLDEAHRYLARGSGEHSKRiiSK-FaDAARQGRKEGLGLFLITQDPQDIDDTVFKQINSRV 550
                                   699********99999855443233.3366667799****************99977776655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.9e-05      0.12     131     158 ..     230     257 ..     225     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.9e-05
                         T2SSE 131 lilvsGgTgsGKttllyallkeinksde 158
                                    +lv G Tg+GKt l+  +l ++ + d+
  gi|91774077|ref|YP_566769.1| 230 HMLVCGSTGTGKTFLTKNILRQFMSPDN 257
                                   589*************999998887744 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.24       2      40 ..     232     265 ..     231     321 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpe 40 
                                   +++G++g+GK+ l+k++ +++++      ++++ +r + 
  gi|91774077|ref|YP_566769.1| 232 LVCGSTGTGKTFLTKNILRQFMSP-----DNRYNVRDTG 265
                                   69**************99888822.....2222223333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.74u 0.36s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 3485.15
//
Query:       gi|91774078|ref|YP_566770.1|  [L=56]
Description: hypothetical protein Mbur_2150 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0081   16.1   0.0      0.017   15.1   0.0    1.6  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.11   12.1   0.1    1.1  1  DUF1241   Protein of unknown function (DUF1241)


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 !   15.1   0.0   1.9e-06     0.017       2      36 ..       4      40 ..       3      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-06
                                  EEEEEEHHHHHHHHHHHHHHT..SSHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg..rSrSelIReAlrey 36
                                  vs+ +++ell+ L++++ + +  +++S++IR A+r  
  gi|91774078|ref|YP_566770.1|  4 VSVDIPQELLADLNKHVGDDKkfVNQSDAIRTAIRKM 40
                                  899**************998889***********975 PP

>> DUF1241  Protein of unknown function (DUF1241)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.2e-05      0.11     101     138 ..      12      49 ..       4      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                       DUF1241 101 iLsriPdeindRktfLetIkeiAsaIkklLdavnevlk 138
                                    L+ +   + d k+f++    i +aI+k+Ld+++++ +
  gi|91774078|ref|YP_566770.1|  12 LLADLNKHVGDDKKFVNQSDAIRTAIRKMLDMMDDIDR 49 
                                   6788888999**********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 338.47
//
Query:       gi|91774079|ref|YP_566771.1|  [L=257]
Description: xylose isomerase-like TIM barrel [Methanococcoides burtonii DSM 6242]
Scores for complete 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-31  108.0   0.0    5.4e-31  107.7   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 !  107.7   0.0     3e-35   5.4e-31       3     210 .]      23     221 ..      21     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 3e-35
                                   HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHT CS
                  AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLG 83 
                                   +++e+G++g E+   + + +    +e+l ++ + l+ ++l ++++ +f++ +  + + +     e ++++k+ +  a+++ 
  gi|91774079|ref|YP_566771.1|  23 ELEEIGYTGWEIVQEGSQCIN---RENLHRIEEVLETTNLYLTMHLPFSDMNLAGLNPGIQG--EVLRQMKHYLSVASDI- 97 
                                   6899****************8...69***************************998744433..77**************. PP

                                   BSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEEEEEEH CS
                  AP_endonuc_2  84 apllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvgvclDt 162
                                   ++l v+hpG  + ++++ +e aw+  ++s++el+d a+++g+ +a+E+++++++ +g+  +e++r+l++vd++nvg++lD+
  gi|91774079|ref|YP_566771.1|  98 VELAVVHPGYLSPYGGKIPEKAWDMNISSIQELCDTADEYGMSIAVENMPNFPMIFGRepDEMLRMLSDVDRDNVGMTLDV 178
                                   *********99999999999************************************************************* PP

                                   HHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                  AP_endonuc_2 163 gHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                   gH++   + v+++l++ ++ i hvHi+D+ g    +rd+h+p g G++
  gi|91774079|ref|YP_566771.1| 179 GHANTS-AMVEGFLKKCNKEIIHVHIHDNMG----KRDEHLPTGSGTV 221
                                   ****99.************************....***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1633.81
//
Query:       gi|91774080|ref|YP_566772.1|  [L=146]
Description: hypothetical protein Mbur_2152 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-17   63.0   0.0    5.8e-17   62.1   0.0    1.5  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 !   62.1   0.0   3.3e-21   5.8e-17       1     118 [.       3     114 ..       3     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.3e-21
                                   EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.....HHH CS
                   RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.....keL 76 
                                   +++v+++v++TE+e kV++a  n++pe+e     e  e  yg         le++ + ++lk++++l+r+e+i     +++
  gi|91774080|ref|YP_566772.1|   3 NVRVSVIVNPTENEGKVASATGNMFPEIE----LEMHERKYG-------NFLEGEGDINSLKNIHDLFRKERIidtarTQI 72 
                                   79************************774....444555566.......356677778***************97665555 PP

                                   HHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS...EEEEEEE CS
                   RNA_binding  77 lkeleervdekgklylrldKQaaylgklslvegdd...vIkvkik 118
                                   +k+  +   e +k++++++KQ a  g+l+++++++   +I+++i+
  gi|91774080|ref|YP_566772.1|  73 QKNRWG---EPEKTFFMINKQVATIGRLNFPAKEEplgSIQIEIN 114
                                   555555...9*************************9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 951.05
//
Query:       gi|91774081|ref|YP_566773.1|  [L=171]
Description: hypothetical protein Mbur_2153 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   51.0   0.1    2.5e-13   50.6   0.1    1.2  1  AAA_17    AAA domain
      2e-10   41.3   0.1    2.7e-10   40.9   0.1    1.1  1  AAA_18    AAA domain
     0.0042   17.3   0.0     0.0093   16.1   0.0    1.6  1  AAA_33    AAA domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   4.3e-17   2.5e-13       3     136 .]       1     129 [.       1     129 [. 0.80

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4.3e-17
                                   -TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHH..HHHHHSSEEEEEE- CS
                        AAA_17   3 gPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr..klpleekkelqkeaaeki..aeeakkkgvlvdgh 79 
                                   +P sGK+ ++ ++  + ++ ++++G ++ree+k++gl++++++     ++l+ k+ +++ a++ +   e  +k+ v+vdg 
  gi|91774081|ref|YP_566773.1|   1 MPASGKSVAS-EVIVDSNVDVVNMGNVIREEVKKRGLEPTDSNTGgvANDLRAKEGMDAVAKRCVpmIESLNKELVVVDGV 80 
                                   79*****666.888899********************99999988667799999999999999875344447888****** PP

                                   SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHHH CS
                        AAA_17  80 prikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesik 136
                                     i e +     +++++ e++   ++++++a+ e  +er+++ r+r++d +++e +k
  gi|91774081|ref|YP_566773.1|  81 RGIAEVNF----FKEQFGENF---TLVFIDAPLELRFERVAS-RGRSDDMTDIEALK 129
                                   **988766....456666777...899999999866666665.67777888888875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   4.5e-14   2.7e-10       6     120 ..       1     123 [.       1     135 [. 0.89

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 4.5e-14
                        AAA_18   6 tpGvGKttlakeLskrl.gf...gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleegknlvidg 81 
                                   +p++GK+  ++ + +++  +   g ++r+ +k++gl+ ++ +   + + +r++e++++++ +++  + s   + + +v+dg
  gi|91774081|ref|YP_566773.1|   1 MPASGKSVASEVIVDSNvDVvnmGNVIREEVKKRGLEPTDSNTgGVANDLRAKEGMDAVAKRCVPMIES--LNKELVVVDG 79 
                                   699**********9996454999*******************************************986..667777**** PP

                        AAA_18  82 hlaeleseaakdikk.....vvLtaspeelleRlekRgyeeaki 120
                                   +++  e   +k+  +     v+++a+ e ++eR++ Rg++++ +
  gi|91774081|ref|YP_566773.1|  80 VRGIAEVNFFKEQFGenftlVFIDAPLELRFERVASRGRSDDMT 123
                                   *****9999999888999********************887443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.6e-06    0.0093       7     125 ..       1     122 [.       1     135 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-06
                        AAA_33   7 lpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqskt..dytrvldrlyqilnelarkalsagrnvildatnl 80 
                                   +p+sGKs  +e ++  +      + ++++ + +r l++td ++    +  r+++ + +  ++ +    s ++ +++  + +
  gi|91774081|ref|YP_566773.1|   1 MPASGKSVASEVIVDSNVdvvnmGNVIREEVKKRGLEPTDSNTGGvaNDLRAKEGMDAVAKRCVPMIESLNKELVVVDGVR 81 
                                   699*********998887777778888888888888888887665444455555577777777777789999999999999 PP

                        AAA_33  81 srrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                     +e   f + +   g ++++v+++++ e+  eR+a R ++ d  
  gi|91774081|ref|YP_566773.1|  82 GIAEVNFFKEQF---GENFTLVFIDAPLELRFERVASRGRSDD-M 122
                                   999988887777...5689*********************754.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1005.17
//
Query:       gi|91774082|ref|YP_566774.1|  [L=318]
Description: dihydrouridine synthase, DuS [Methanococcoides burtonii DSM 6242]
Scores for complete 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-70  238.1   0.0    1.5e-70  237.7   0.0    1.1  1  Dus           Dihydrouridine synthase (Dus)
    1.5e-05   24.4   0.1    2.8e-05   23.6   0.1    1.4  2  ThiG          Thiazole biosynthesis protein ThiG
    0.00092   18.7   0.0     0.0029   17.1   0.0    1.7  2  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.7   0.0   2.6e-74   1.5e-70       2     288 ..      14     296 ..      13     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 2.6e-74
                                   E---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHH.TT-S CS
                           Dus   2 laPmagvtdlpfRelvrefgataLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaAklvad.lgad 81 
                                   laP+a+vt+l+fR +++++ga  L++tem+++ a+v+ ++++  +  + +ee+p  +Ql+g++p++++eaA + +d  + d
  gi|91774082|ref|YP_566774.1|  14 LAPLAEVTNLAFRLMCKKYGAS-LCFTEMISSDAVVYGNASSAMRGITCDEERPFGLQLFGNSPEVITEAALVLEDmFYPD 93 
                                   9*********************.****************99988888888888***********************7788* PP

                                   CEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SEEEEESSEC CS
                           Dus  82 eIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGaqaltvHgRtr 162
                                    Id+N+GCP++ +t+ g G+aLl+ p+lv +i +++ + v+ Pvt+kir+    +   +l++a+++e+aG+ a+tvHgRt 
  gi|91774082|ref|YP_566774.1|  94 MIDINLGCPAPVITNAGCGSALLESPELVSDIFSTLCEGVDTPVTAKIRVLE--SRAATLDMAHRLEDAGVCAITVHGRTC 172
                                   *************************************************975..58889********************** PP

                                   CCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHSC------HHH CS
                           Dus 163 aqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavktgeaepapplae 242
                                   +q+y+gtad +  k +k+++sipvi+NGdI+d  +a+++le+tG+dg+migr+a g+P +f++ s +++ ge    +  +e
  gi|91774082|ref|YP_566774.1| 173 EQGYSGTADHSYAKLIKEELSIPVIVNGDIRDGVSAEKVLEYTGCDGLMIGRAAMGDPHVFHRiSRYLDDGEVIG-C-GCE 251
                                   *************************************************************98777777655432.2.234 PP

                                   HHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHHHHH CS
                           Dus 243 eaeiveehlkkleeelgedkglrkirkhlawylkglkkaaelrrel 288
                                   +++     +  l+e++   ++  +   h++w   glk+++ +r+ +
  gi|91774082|ref|YP_566774.1| 252 QKRDDLLEYLDLLEKFDLSSH-INLKAHVQWFTRGLKGSRRMRSDI 296
                                   433333333334444433333.345567888888777777777655 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.87   5.2e+03     176     187 ..     103     114 ..      98     116 .. 0.85
   2 !   23.6   0.1   4.7e-09   2.8e-05     124     206 ..     141     225 ..     115     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.87
                                   S-BEEES---SH CS
                          ThiG 176 vPvivDAGigsp 187
                                    Pvi +AG gs+
  gi|91774082|ref|YP_566774.1| 103 APVITNAGCGSA 114
                                   599999999986 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4.7e-09
                                   -EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS-.---S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHT.T-SEEE CS
                          ThiG 124 FevlpYvsdDlvlarrleevGcaavmPlaapiGsg.lGllnkealkiiieeakvPvivDAGigspsdaaqamel.Gadavl 202
                                     vl    + l +a+rle++G+ a+   +     g  G +++   k+i ee+++Pviv+  i+    a +++e+ G+d+++
  gi|91774082|ref|YP_566774.1| 141 IRVLESRAATLDMAHRLEDAGVCAITVHGRTCEQGySGTADHSYAKLIKEELSIPVIVNGDIRDGVSAEKVLEYtGCDGLM 221
                                   5666667777889***************9999887469999999*****************************66*****9 PP

                                   ESHH CS
                          ThiG 203 lnta 206
                                   +  a
  gi|91774082|ref|YP_566774.1| 222 IGRA 225
                                   9766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.17     1e+03     102     164 ..     112     165 ..     106     171 .. 0.56
   2 !   17.1   0.0   4.9e-07    0.0029      59     120 ..     179     241 ..     142     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.17
                                   SHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT-SEE CS
                  His_biosynth 102 gtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelgagei 164
                                   g+a +++pel++++++   +     ++D+        k    e+   ++++a++le++g+++i
  gi|91774082|ref|YP_566774.1| 112 GSALLESPELVSDIFSTLCE-----GVDTPVT----AKIRVLESRAATLDMAHRLEDAGVCAI 165
                                   77888888888887774433.....5553322....222222223445666666666666555 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.9e-07
                                   HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHH.CT-SEEEESHHHHH-THHHHHHHHHHC CS
                  His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelle.agadkviigtaavknpelikelaekfg 120
                                   +a++++ + i ee++ipv v G Ir+  ++e++le  g+d ++ig aa+ +p++++++++   
  gi|91774082|ref|YP_566774.1| 179 TADHSYAKLIKEELSIPVIVNGDIRDGVSAEKVLEyTGCDGLMIGRAAMGDPHVFHRISRYLD 241
                                   5567788889************************9669******************9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 1655.87
//
Query:       gi|91774083|ref|YP_566775.1|  [L=180]
Description: pyruvate ferredoxin oxidoreductase subunit gamma [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-41  139.8   0.1    1.1e-40  139.6   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 !  139.6   0.1     6e-45   1.1e-40       1     177 []      10     175 ..      10     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 6e-45
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGGEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldglkpg 79 
                                   GGqG+vta+++la aa+  G+  qa++ +g e+rG+++ +  ri d+pi+ + +v+e+d++++ d+++l+  ++ +g k++
  gi|91774083|ref|YP_566775.1|  10 GGQGSVTAAELLAVAAFADGKFSQAFPAFGVERRGAPVQAFTRINDDPIRLRAQVYEPDYVIVQDPTLLEvvDVESGAKDD 90 
                                   9********************************************************************999********* PP

                                   EEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHHHHHCCS- CS
                           POR  80 giiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealeeaikkrfp 159
                                   g+i++ns +++p+ ++ +            +++ +v+atkia +i g ++++Ntv+lGa+a+++g +++e+++ a+k+rfp
  gi|91774083|ref|YP_566775.1|  91 GVILINS-DFEPEHFDLNTN----------AKIMTVNATKIALDIIG-RPIVNTVLLGAFAGASGlIDPESIKNAVKERFP 159
                                   *******.799999999886..........4799*************.********************************* PP

                                   CH.HHHHHHHHHHHHHHH CS
                           POR 160 kkkeviekNlkafragye 177
                                   +k  + ekN +a++++y+
  gi|91774083|ref|YP_566775.1| 160 GK--IGEKNAEAIQKAYD 175
                                   95..************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1093.38
//
Query:       gi|91774084|ref|YP_566776.1|  [L=86]
Description: pyruvate ferredoxin oxidoreductase, delta subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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   55.6  12.8    6.7e-09   35.2   3.1    2.4  2  Fer4      4Fe-4S binding domain
    1.1e-11   44.3  11.6    3.9e-06   26.7   2.2    2.2  2  Fer4_6    4Fe-4S binding domain
    2.1e-11   43.7   5.6    3.1e-11   43.2   5.6    1.3  1  Fer4_21   4Fe-4S dicluster domain
    2.2e-10   40.0   8.7      2e-05   24.4   1.1    2.3  2  Fer4_2    4Fe-4S binding domain
    2.2e-09   37.8   5.4    0.00024   21.6   0.4    2.2  2  Fer4_7    4Fe-4S dicluster domain
    4.2e-08   33.2   7.5    6.8e-08   32.6   7.5    1.4  1  Fer4_9    4Fe-4S dicluster domain
    2.6e-07   30.6  20.7    1.3e-05   25.2  11.1    2.0  2  Fer4_10   4Fe-4S dicluster domain
    5.1e-07   30.5   7.7    0.00024   21.9   1.9    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    2.3e-06   28.0   4.0      0.028   14.9   0.2    2.2  2  Fer4_17   4Fe-4S dicluster domain
     0.0015   18.8  15.1     0.0071   16.8   1.3    2.6  2  Fer4_4    4Fe-4S binding domain
     0.0044   17.4  12.5      0.097   13.1   1.4    2.2  2  Fer4_8    4Fe-4S dicluster domain
      0.008   16.9  13.7        0.2   12.4   2.6    2.6  2  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.011   16.3  13.5      0.019   15.5   2.0    2.5  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.039   14.9  14.4       0.79   10.8   2.1    2.4  2  Fer4_3    4Fe-4S binding domain
      0.069   14.0  11.4       0.25   12.2   1.7    2.1  2  Fer4_22   4Fe-4S dicluster domain
       0.29   11.3   8.6          1    9.6   8.7    1.7  1  Fer4_18   4Fe-4S dicluster domain
       0.58   10.3   3.7        3.6    7.8   0.6    2.1  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   2.2   6.3e-09   6.6e-06       1      19 [.      27      45 ..      27      48 .. 0.94
   2 !   35.2   3.1   6.3e-12   6.7e-09       2      24 .]      58      80 ..      57      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.3e-09
                                  EEEETTTSSS-THHHHHST CS
                          Fer4  1 vvideekCigCGaCvevCP 19
                                  +v+d++kCi+C++C+  CP
  gi|91774084|ref|YP_566776.1| 27 PVFDYDKCIKCKLCELLCP 45
                                  689**************** PP

  == domain 2  score: 35.2 bits;  conditional E-value: 6.3e-12
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  +++++ C gCG+C++ CP++AI+
  gi|91774084|ref|YP_566776.1| 58 EFNYDFCKGCGICANECPTDAIE 80
                                  689*******************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   2.2   5.5e-08   5.8e-05       2      21 ..      27      46 ..      26      51 .. 0.91
   2 !   26.7   2.2   3.7e-09   3.9e-06       2      24 .]      57      79 ..      56      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.5e-08
                        Fer4_6  2 veidpdkCigCgdCvrvCPe 21
                                  +++d+dkCi C  C+  CP 
  gi|91774084|ref|YP_566776.1| 27 PVFDYDKCIKCKLCELLCPD 46
                                  89*****************5 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 3.7e-09
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   e+++d C gCg C++ CP++ai
  gi|91774084|ref|YP_566776.1| 57 FEFNYDFCKGCGICANECPTDAI 79
                                  69*******************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   5.6     3e-14   3.1e-11       3      59 .]      29      81 ..      27      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3e-14
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                  +d dkCi+C++C + C+d s++a    ++  ++   d C GC +C++ CP+ d+iem
  gi|91774084|ref|YP_566776.1| 29 FDYDKCIKCKLCELLCPDMSVDA---RDDGFFEFNYDFCKGCGICANECPT-DAIEM 81
                                  689***************98887...568899******************6.***99 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.3   4.9e-07   0.00052       2      21 ..      26      45 ..      25      46 .. 0.94
   2 !   24.4   1.1   1.9e-08     2e-05       3      22 .]      57      76 ..      55      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.9e-07
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                  ++v+d d+Ci C+ C   CP
  gi|91774084|ref|YP_566776.1| 26 RPVFDYDKCIKCKLCELLCP 45
                                  699**************9*9 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.9e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  ++++ d C gCg+C + CP+
  gi|91774084|ref|YP_566776.1| 57 FEFNYDFCKGCGICANECPT 76
                                  689****************7 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.6   1.5e-06    0.0016      27      49 ..      23      45 ..       6      48 .. 0.79
   2 !   21.6   0.4   2.3e-07   0.00024       2      19 ..      64      81 ..      50      86 .] 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                        Fer4_7 27 gtekveidpekClgCgaCvavCP 49
                                  +t ++++d++kC+ C+ C+  CP
  gi|91774084|ref|YP_566776.1| 23 RTFRPVFDYDKCIKCKLCELLCP 45
                                  3467899***************9 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.3e-07
                        Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                  C gCg C++ Cp++aie+
  gi|91774084|ref|YP_566776.1| 64 CKGCGICANECPTDAIEM 81
                                  888888888888888877 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   7.5   6.5e-11   6.8e-08       1      51 []      33      79 ..      33      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.5e-11
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC++C+ C+  Cp + v  ++ + +  +  +    C gCg C++ Cp++ai
  gi|91774084|ref|YP_566776.1| 33 KCIKCKLCELLCPDMSVDARDDGFFEFNYDF----CKGCGICANECPTDAI 79
                                  7****************99999999888765....*************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2  11.1   1.2e-08   1.3e-05       2      56 .]      27      75 ..      26      75 .. 0.95
   2 !   16.6   2.0   5.9e-06    0.0063       4      23 ..      59      78 ..      56      86 .] 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +v+d d+Ci+C+ C   CP        +  a +++  + +++ C gcg C+ +CP
  gi|91774084|ref|YP_566776.1| 27 PVFDYDKCIKCKLCELLCPD------MSVDARDDGFFEFNYDFCKGCGICANECP 75
                                  5899****************......8999999999999***************9 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.9e-06
                       Fer4_10  4 idddtCirCgkCvkaCPadl 23
                                  ++ d C +Cg C + CP+d+
  gi|91774084|ref|YP_566776.1| 59 FNYDFCKGCGICANECPTDA 78
                                  67899************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 !   12.1   0.4   0.00027      0.29       1      18 [.      33      50 ..      33      60 .. 0.83
   2 !   21.9   1.9   2.3e-07   0.00024       1      20 [.      63      82 ..      63      86 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                       Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                  +C++C+ C   CP   ++
  gi|91774084|ref|YP_566776.1| 33 KCIKCKLCELLCPDMSVD 50
                                  5************87665 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.3e-07
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++Cg Ca+ CPt+ai++ 
  gi|91774084|ref|YP_566776.1| 63 FCKGCGICANECPTDAIEMV 82
                                  6****************976 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   2.7e-05     0.028      43      58 ..      31      46 ..      14      50 .. 0.87
   2 !   14.9   0.4   2.8e-05      0.03       1      14 [.      63      76 ..      53      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                       Fer4_17 43 aslCieCgeCerkCPq 58
                                   ++Ci+C++Ce  CP 
  gi|91774084|ref|YP_566776.1| 31 YDKCIKCKLCELLCPD 46
                                  689***********95 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.8e-05
                       Fer4_17  1 rCiqCgyClpeCps 14
                                  +C +Cg C++eCp+
  gi|91774084|ref|YP_566776.1| 63 FCKGCGICANECPT 76
                                  47777777777775 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   1.3   6.7e-06    0.0071       1      15 [.      31      45 ..      31      60 .. 0.90
   2 !   10.2   3.3   0.00089      0.93       4      16 ..      64      76 ..      59      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.7e-06
                        Fer4_4  1 qerCigCgsCvaaCP 15
                                  +++Ci C+ C+  CP
  gi|91774084|ref|YP_566776.1| 31 YDKCIKCKLCELLCP 45
                                  59************* PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00089
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C gCg C + CP+
  gi|91774084|ref|YP_566776.1| 64 CKGCGICANECPT 76
                                  9***********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 !   13.1   1.4   9.2e-05     0.097       3      20 ..      32      49 ..      30      62 .. 0.79
   2 !   10.1   3.6    0.0008      0.85       5      17 ..      64      76 ..      60      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-05
                        Fer4_8  3 ekCieCgaCqsaCpvlrr 20
                                  +kCi+C +C+  Cp ++ 
  gi|91774084|ref|YP_566776.1| 32 DKCIKCKLCELLCPDMSV 49
                                  79********99996555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0008
                        Fer4_8  5 CieCgaCqsaCpv 17
                                  C +Cg C ++Cp+
  gi|91774084|ref|YP_566776.1| 64 CKGCGICANECPT 76
                                  8888888888873 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.6   0.00019       0.2       2      28 ..      28      54 ..      28      59 .. 0.87
   2 !    9.4   3.4    0.0016       1.7       3      20 ..      59      76 ..      57      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                       Fer4_15  2 vvDrdaCigcglCvaeapevfeldedg 28
                                  v+D d+Ci c lC  ++p++ + + d+
  gi|91774084|ref|YP_566776.1| 28 VFDYDKCIKCKLCELLCPDMSVDARDD 54
                                  58****************998887754 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                       Fer4_15  3 vDrdaCigcglCvaeape 20
                                  ++ d C gcg C+ e+p+
  gi|91774084|ref|YP_566776.1| 59 FNYDFCKGCGICANECPT 76
                                  56789***********84 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   2.0   1.8e-05     0.019       2      19 ..      30      47 ..      29      60 .. 0.86
   2 ?    6.3   3.8     0.014        14       4      17 ..      62      75 ..      59      77 .. 0.89
   3 ?    4.9   0.9     0.036        38      48      57 ..      71      80 ..      70      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                       Fer4_13  2 DrdtCiacgaCvelaPdv 19
                                  D d+Ci c++C  l+Pd+
  gi|91774084|ref|YP_566776.1| 30 DYDKCIKCKLCELLCPDM 47
                                  679*************96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                       Fer4_13  4 dtCiacgaCvelaP 17
                                  d C +cg+C++ +P
  gi|91774084|ref|YP_566776.1| 62 DFCKGCGICANECP 75
                                  56************ PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.036
                       Fer4_13 48 adaCPvesIg 57
                                  a++CP+++I+
  gi|91774084|ref|YP_566776.1| 71 ANECPTDAIE 80
                                  689******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 ?   10.8   2.1   0.00075      0.79       1      12 [.      34      45 ..      34      51 .. 0.88
   2 ?    9.5   4.8     0.002       2.1       1      15 []      64      78 ..      64      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00075
                        Fer4_3  1 CtgCgaCvevCP 12
                                  C+ C +C+  CP
  gi|91774084|ref|YP_566776.1| 34 CIKCKLCELLCP 45
                                  ************ PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C gCg C + CP++A
  gi|91774084|ref|YP_566776.1| 64 CKGCGICANECPTDA 78
                                  9************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.3    0.0071       7.5       1      14 [.      33      46 ..      33      55 .. 0.87
   2 ?   12.2   1.7   0.00024      0.25      76      94 ..      58      76 ..      50      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0071
                       Fer4_22  1 rClsCgaCtlvCpt 14
                                  +C++C  C l+Cp 
  gi|91774084|ref|YP_566776.1| 33 KCIKCKLCELLCPD 46
                                  7***********96 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00024
                       Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                  +f+   C GCg C + cp+
  gi|91774084|ref|YP_566776.1| 58 EFNYDFCKGCGICANECPT 76
                                  578899***********97 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   8.7   0.00098         1      59      96 ..      32      75 ..      23      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00098
                       Fer4_18 59 gdcidcescvkvcP.tgidirkGlqle.....ciscllcidacd 96
                                   +ci+c+ c  +cP + +d r+   +e     c  c+ c + c 
  gi|91774084|ref|YP_566776.1| 32 DKCIKCKLCELLCPdMSVDARDDGFFEfnydfCKGCGICANECP 75
                                  68************779****85332222447999****99995 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 ?    7.8   0.6    0.0034       3.6      70      90 ..      29      49 ..       4      54 .. 0.80
   2 ?    4.6   0.3     0.032        34      64      93 ..      53      82 ..      44      86 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0034
                                  E-CCC--S--HHHHH-TT--E CS
                        ETF_QO 70 inaqnCvhCktCdikdpsqni 90
                                   +   C+ Ck C++  p+ ++
  gi|91774084|ref|YP_566776.1| 29 FDYDKCIKCKLCELLCPDMSV 49
                                  56689********98887665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.032
                                  SSEEEEE-CCC--S--HHHHH-TT--EEE- CS
                        ETF_QO 64 kekklqinaqnCvhCktCdikdpsqniewv 93
                                  ++  ++ n   C  C  C    p++ ie v
  gi|91774084|ref|YP_566776.1| 53 DDGFFEFNYDFCKGCGICANECPTDAIEMV 82
                                  56678999999*******999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 591.70
//
Query:       gi|91774085|ref|YP_566777.1|  [L=404]
Description: pyruvate ferredoxin oxidoreductase, alpha subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  232.9   0.1    4.9e-69  232.6   0.1    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.2e-30  105.8   0.1    2.7e-30  104.7   0.1    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    2.4e-08   33.9   0.0    5.1e-08   32.8   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.12   12.6   0.1       0.23   11.7   0.1    1.4  1  TetR_C_31        Tetracyclin repressor-like, C-terminal domai


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 !  232.6   0.1   1.1e-72   4.9e-69       2     225 ..      24     243 ..      23     249 .. 0.97

  Alignments for each domain:
  == domain 1  score: 232.6 bits;  conditional E-value: 1.1e-72
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   a++a++++vi+aYPITP++ i+e l++++a+ge+ + e++++esE++aisa +G++aaGar+  aT +qGl Lm+e l+ +
  gi|91774085|ref|YP_566777.1|  24 AVKACRPNVISAYPITPQTHIVEDLSQFIADGEIPNCEYINVESEFSAISALVGSSAAGARSYSATTSQGLELMHEVLFNV 104
                                   688999****************************89********************************************* PP

                                   HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEHHHH.HE CS
                         POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDgfllshe 161
                                   ag++lPvv++vv+Ra++++ ++i++dq+D +  rdtg+i+l++e+ qea d++++Af++Ae+  v +Pv+ ++Dgf+lsh 
  gi|91774085|ref|YP_566777.1| 105 AGMRLPVVMTVVNRAVSAP-INIWNDQQDSISQRDTGWIQLHAEDTQEAADMTAQAFKIAEDpdVLLPVLACMDGFILSHV 184
                                   *******************.************************************************************* PP

                                   EEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHH CS
                         POR_N 162 vekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekv 225
                                   +e+v l+de+    l+ e l++ e+k  +ldp++p ++g+ a p+ + e+r+ +++a+++a k 
  gi|91774085|ref|YP_566777.1| 185 YEPVVLLDED----LVAEYLPPFEPKF-KLDPKNPKTFGAFADPNSYTEFRYLQQQAMNKALKT 243
                                   **********....9999999999966.******************************987655 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 !  104.7   0.1   6.1e-34   2.7e-30       1      99 [.     271     372 ..     271     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 6.1e-34
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G.-HHHHHHHHHTGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse.Gqlveevkaalkk 80 
                                   A+++++amGs++gt+k++vd+lR++g+kvGll++r++rPFP+e++k+++k++k vv ld+nis+g + G+l++e k +l++
  gi|91774085|ref|YP_566777.1| 271 ADIILMAMGSIVGTIKDVVDKLRAQGVKVGLLKVRSFRPFPAEAIKNAIKGAKVVVALDKNISLGLNeGALFTETKGSLYN 351
                                   9******************************************************************************** PP

                                   G..TSEEEEEE--GGG----H CS
                       PFOR_II  81 s..kvkvvnfvaglgGrditv 99 
                                      +++++ f+ g+gGrdi +
  gi|91774085|ref|YP_566777.1| 352 TniNIPIIGFMIGHGGRDIPM 372
                                   9999**************976 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.1e-11   5.1e-08       7      79 ..     268     339 ..     265     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.1e-11
                                   ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHH CS
               Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigse 79 
                                    e  d++l a+Gs v +  +++++L+++g+++ ++ +r+++p+  e i+  + k  ++vv  +++++ G+ + 
  gi|91774085|ref|YP_566777.1| 268 TEDADIILMAMGSIVGTIKDVVDKLRAQGVKVGLLKVRSFRPFPAEAIK-NAIKGAKVVVALDKNISLGLNEG 339
                                   5789********************************************9.66778888888899998988664 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 ?   11.7   0.1   5.2e-05      0.23      48      99 ..     145     198 ..     141     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                                   HHHHHHHHHHHHHHHCS.S-HHHHHHHHHHHHHHHHHHHHHSG..TS-HHHHHHH CS
                     TetR_C_31  48 rralrealaallaalGl.pdpeeaarllvaaldGllldrLagp..aadpraevre 99 
                                    +++ + +a++ a++   +++ +    ++a++dG +l+++ +p     ++++v+e
  gi|91774085|ref|YP_566777.1| 145 HAEDTQEAADMTAQAFKiAEDPDVLLPVLACMDGFILSHVYEPvvL-LDEDLVAE 198
                                   577788888888877777555549999**************99642.22455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 2384.19
//
Query:       gi|91774086|ref|YP_566778.1|  [L=291]
Description: pyruvate ferredoxin oxidoreductase, beta subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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   86.5   0.2    2.1e-24   86.0   0.2    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 !   86.0   0.2   1.2e-28   2.1e-24       2     152 ..      38     200 ..      37     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.2e-28
                                   SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH......STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla......kpdrevvaivGDGgflmi.lqelatavrrnlpi 75 
                                   +Gcl++++  +    + +s+  + +++ + +  ++A+G+++a        + +++a+ GDG++l+i +  ++ a +r++++
  gi|91774086|ref|YP_566778.1|  38 TGCLEVMTTPY----PESSWNVPFIHSLFENNAAVASGIEAAlkakgeLGKTKIIAMGGDGATLDIgIRSISGAFERGHDF 114
                                   69999955555....5667777******************944443322358***************************** PP

                                   EEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSS CS
                  TPP_enzyme_C  76 tvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealkealekkg 147
                                   t+v+++Ne+y++tg q    +pf ++++++pagk     + +++++ +++ a+G + + + +  +++++ +++k+a++ +g
  gi|91774086|ref|YP_566778.1| 115 TYVCIDNEAYMNTGVQrsgATPFAASTTTSPAGKvsfgnIRPKKNMPAIMVAHGSPyVTTTSIGYPKDMIRKVKKAVDVEG 195
                                   **************************************8899**************88899999***************** PP

                                   EEEEE CS
                  TPP_enzyme_C 148 palie 152
                                   p++++
  gi|91774086|ref|YP_566778.1| 196 PTYVH 200
                                   ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2210.24
//
Query:       gi|91774087|ref|YP_566779.1|  [L=460]
Description: Na+/alanine symporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-141  472.2  34.7   2.1e-141  471.8  34.7    1.0  1  Na_Ala_symp  Sodium:alanine symporter family


Domain annotation for each model (and alignments):
>> Na_Ala_symp  Sodium:alanine symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.8  34.7  1.2e-145  2.1e-141       8     387 ..      65     459 ..      60     460 .] 0.97

  Alignments for each domain:
  == domain 1  score: 471.8 bits;  conditional E-value: 1.2e-145
                   Na_Ala_symp   8 ksegeissfqAlatalaarvGtGniaGvatAialGGpGAvfWmwvvallGmatkfvEstLaqlYkekdekgevrGGpayyi 88 
                                   k +g+issf Al+talaa++GtGni+GvatAi +GGpGA+fWmw++a++Gmatk++Es+La++Y++ de+g+++GGp+yyi
  gi|91774087|ref|YP_566779.1|  65 KYTGDISSFAALMTALAATIGTGNIVGVATAIKIGGPGALFWMWLAAFFGMATKYAESMLAVKYRNIDENGQMSGGPMYYI 145
                                   4689***************************************************************************** PP

                   Na_Ala_symp  89 ekglkkk....wlavlfavlliialglgi.navqansiasaleeafeveklvvgivlavllalvilggikriakvaevvvP 164
                                   +kgl  k     la++fa+  i ++ +gi  + q+n+ia+++  +f+v+++++++v++vl+alv +ggik+ia+va+vvvP
  gi|91774087|ref|YP_566779.1| 146 TKGLAGKfyarPLAAFFAFSGIGVAFFGIgIFPQVNAIADSAAITFNVPPIYTAAVVTVLVALVTIGGIKSIARVAQVVVP 226
                                   *****9988889**********9999***9999************************************************ PP

                   Na_Ala_symp 165 vmailYillalvvillniekvpevlalifksAFgleavagGilg....aaialGvkRglfSneAGlGsapiaaAaaevshp 241
                                   +mai+Y+l +l++i++n++ +p++++li++sAF+ +a++gG+lg     a+++G++Rg+fSne+GlGsapiaaAaa+v++p
  gi|91774087|ref|YP_566779.1| 227 FMAITYVLGCLLIIFTNLDMLPDTIRLIITSAFTQTAATGGFLGasmlLAVQMGIARGVFSNESGLGSAPIAAAAAKVKEP 307
                                   ********************************************99999******************************** PP

                   Na_Ala_symp 242 vkqGlvqalgvfidtlvvCtatalvill.......segvaltqaalesvlgsvgalfvaialllFafstilgnyyygeknl 315
                                   ++qGl++++g+f+dt++vCt+t++v+++        eg+ +t+ a+++ l++vga++v i l++Faf+tilg++yyge+++
  gi|91774087|ref|YP_566779.1| 308 ARQGLISMTGTFFDTIIVCTMTGIVLVMtgswtseYEGAYMTSYAFSTGLENVGAYIVGIGLIFFAFTTILGWNYYGERCV 388
                                   ****************************66555555********************************************* PP

                   Na_Ala_symp 316 eyllgkkkklliyrvlvlllvfvgavaslelvwnlaDialglmalvnliaillLskvvvkalkdYekqkkkg 387
                                   e+l+g  k +l y+++++llv  g + +le++w laDi+++lm+++nlia+l+L+kv+v+++++Y + ++k+
  gi|91774087|ref|YP_566779.1| 389 EFLVG-VKGILPYKIVYILLVGGGVFLTLETIWILADIVNALMVIPNLIALLALRKVIVNETRKYFEGLEKE 459
                                   ****9.5559*******************************************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3165.46
//
Query:       gi|91774088|ref|YP_566780.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91774088|ref|YP_566780.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91774088|ref|YP_566780.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91774088|ref|YP_566780.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91774088|ref|YP_566780.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91774088|ref|YP_566780.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91774088|ref|YP_566780.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91774088|ref|YP_566780.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91774088|ref|YP_566780.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2378.80
//
Query:       gi|91774089|ref|YP_566781.1|  [L=1065]
Description: helicase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-22   80.5   0.4      4e-22   78.6   0.1    2.2  2  Helicase_C  Helicase conserved C-terminal domain
    2.3e-09   37.5   0.6    3.4e-06   27.2   0.0    3.5  2  ResIII      Type III restriction enzyme, res subunit
    3.6e-07   30.1   0.0    1.4e-06   28.3   0.0    2.1  1  PLDc_2      PLD-like domain
    0.00014   20.7   0.0     0.0005   18.9   0.0    2.0  2  SNF2_N      SNF2 family N-terminal domain
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.37   10.8   0.0    1.6  1  Flavi_DEAD  Flavivirus DEAD domain
       0.25   11.4   2.4       0.91    9.6   0.0    3.0  3  TTRAP       Putative tranposon-transfer assisting protein
        6.3    7.2   6.5          3    8.3   1.7    2.5  2  CENP-H      Centromere protein H (CENP-H)


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 ?   -2.7   0.0       2.8   7.2e+03      47      73 ..     373     400 ..     370     408 .. 0.74
   2 !   78.6   0.1   1.6e-25     4e-22       2     110 ..     664     772 ..     663     773 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                                   STTSTHHHHHHHHHHHH.TTSSSEEEES CS
                    Helicase_C  47 hgelpqnereeileqfn.kgesdvLiat 73 
                                   h + ++n r+ i++  + +g+  vL+ t
  gi|91774089|ref|YP_566781.1| 373 HYRNENNRRKNIVNLIKsNGKAEVLLLT 400
                                   5566778888888888877888877655 PP

  == domain 2  score: 78.6 bits;  conditional E-value: 1.6e-25
                                   HHHHHHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                    Helicase_C   2 kleallell.kleeeggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                   k++ l+++l ++ ++g+ +++f++++d+++   k l   +    k+ ++hg  + +++++ ++qf+kg++d++++td++++
  gi|91774089|ref|YP_566781.1| 664 KIQNLKDILkNNLRDGKPTIVFSQYKDTIDYlYKSL---NgdIEKIDYIHG-SSDKSKDKLIDQFQKGDVDIILTTDILSE 740
                                   8889999996666788889**********6444444...233489999***.79999************************ PP

                                   SSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   G++ip++  +infdlp+n+  ++qr+GR+ R+
  gi|91774089|ref|YP_566781.1| 741 GVNIPRAVSIINFDLPYNPVLLVQRAGRALRI 772
                                   ******************************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 !   27.2   0.0   1.3e-09   3.4e-06      22     169 ..     273     403 ..     245     405 .. 0.70
   2 ?   -1.0   0.1       0.6   1.5e+03     121     148 ..     565     624 ..     506     651 .. 0.55

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.3e-09
                                   .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                                   ++   ++++   G GK++va ++++++lk+++ +k+l++ p      ++++e++++l+e        +s++ +++      
  gi|91774089|ref|YP_566781.1| 273 QKYGGYILANSVGLGKSYVAGQAMKAYLKQNPDKKCLLIYPP-----RMKTEWNSYLEEFG------ISDKVDMI------ 336
                                   45557889999****************************995.....67777777776532......22222222...... PP

                                   .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.....TTTHHHHHT---SEEEEEESS- CS
                        ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak....kswreilekfkeavllglTATp 169
                                     ++ + +  s  ++   e   ++++  d++ +i+ DEaH+++ +    k++ ++++++ +a +l lTATp
  gi|91774089|ref|YP_566781.1| 337 --SMGILQKPSYGEAD--EGIFDHRAYTDKYSLIVADEAHHYRNEnnrrKNIVNLIKSNGKAEVLLLTATP 403
                                   ..33333333333333..2348999******************98433335555566667799*******9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.6
                                   .......................................HHHTTT-SEEEEETGGGTTS.T CS
                        ResIII 121 e.................................eeeseellrdrfdviiiDEaHrlgakk 148
                                                                     ++e +   +++   +i+D  H   + +
  gi|91774089|ref|YP_566781.1| 565 VyylkirfalyreslekgtwingdnldilpfelgKQEYHAIIDETRHRVIFDSFHEQDS-S 624
                                   14444444444444445555555555555555555666666666666666666666555.3 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.3e-10   1.4e-06      32     133 .]      84     203 ..      46     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.3e-10
                        PLDc_2  32 aakrgvkvrilldskkd.............dagavdeaslkelkellleagvevrvfetllgslHaKlylid......gkt 93 
                                     +++  +ri+++++++             d ++ d+++   l+ l+ ++ +e rvf    + +H K++ +        + 
  gi|91774089|ref|YP_566781.1|  84 EWDSKAPIRIVMGRETSkftkeillsiikdDISTYDDETVELLEYLIKNNLIEFRVFLD--RKFHVKIFSFYyqssvfPDD 162
                                   56778899*****99889**********998899999999****************976..569*******8555555559 PP

                        PLDc_2  94 vivGSsNltkrgldlnlElnvviedk.elakeleeeFerlw 133
                                   +  GS+N++k gl+ n El + +    e  + ++e+F+ lw
  gi|91774089|ref|YP_566781.1| 163 LWAGSANFSKGGLTDNIELCIPMNVTgETRELFREWFDVLW 203
                                   999******************999887889999*****999 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 ?   -2.7   0.0      0.74   1.9e+03      54      69 ..     274     289 ..     267     352 .. 0.60
   2 !   18.9   0.0   1.9e-07    0.0005     178     233 ..     363     421 ..     288     494 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.74
                                   TT--EEE---TTS--H CS
                                   xxxxxxxxxxxxxxxx RF
                        SNF2_N  54 svrGGiLaDemGLGKT 69 
                                   +  G iLa   GLGK 
  gi|91774089|ref|YP_566781.1| 274 KYGGYILANSVGLGKS 289
                                   4555688888888884 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.9e-07
                                   -SEEEES-GGGT--TTSHHHHHHHH--...-S-EEEE-S--SSS-HHHHHHHHHHH-TT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 178 wkrvvlDEghtlknstskaaeavskLs...tsnrwiltGTPiqnsledlygLlkfLree 233
                                      +v DE+h  +n++++ +++v+ ++     + ++lt+TP+  s +dl+ L+++   +
  gi|91774089|ref|YP_566781.1| 363 YSLIVADEAHHYRNENNRRKNIVNLIKsngKAEVLLLTATPVNLSSKDLFNLIDLFYQG 421
                                   5689***********98888888877633356779*****************9976544 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.37      93     137 ..     360     404 ..     354     411 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                   ----SEEEEETTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-T CS
                    Flavi_DEAD  93 kknyeliimDeahflDPasiaarGyletkaeegeaalilltatPP 137
                                   + +y li+ Deah+   +    + +++  +++g+a+++lltatP 
  gi|91774089|ref|YP_566781.1| 360 TDKYSLIVADEAHHYRNENNRRKNIVNLIKSNGKAEVLLLTATPV 404
                                   5689***************9999*********************5 PP

>> TTRAP  Putative tranposon-transfer assisting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.7   9.4e+03      25      41 ..     641     659 ..     632     670 .. 0.46
   2 ?    9.6   0.0   0.00035      0.91       4      37 ..     900     932 ..     898     944 .. 0.80
   3 ?   -0.6   0.1      0.53   1.4e+03      18      42 ..     968     992 ..     965     999 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.7
                                   HHSTTTS.-..HHHHHHHH CS
                         TTRAP  25 kaalkyled..delreLae 41 
                                   +++l  l++   el e+ +
  gi|91774089|ref|YP_566781.1| 641 DEMLDTLKEvfGELEEIPY 659
                                   4444444221134444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00035
                                   HHHHHHHHH--SHHHHHHHHHHHSTTTS..-HHHH CS
                         TTRAP   4 eElnLiaiynegtRkelieelkaalkyl.eddelr 37 
                                   +E  L  i ++g+R ++i+e+++ lky+ ed   r
  gi|91774089|ref|YP_566781.1| 900 DEDDLFLIGKTGSRIKTINEIRESLKYVpED--AR 932
                                   6777888889******************554..44 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.53
                                   HHHHHHHHHSTTTS.-HHHHHHHHH CS
                         TTRAP  18 kelieelkaalkyleddelreLaes 42 
                                   k+l++++k+a   le +++    ++
  gi|91774089|ref|YP_566781.1| 968 KKLLNNIKEAKVKLESQDMCDCLDR 992
                                   6899**********99999876655 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 ?   -0.0   0.2      0.44   1.1e+03      44      87 ..     433     476 ..     424     480 .. 0.68
   2 ?    8.3   1.7    0.0012         3       8      69 ..     932     998 ..     928    1020 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.44
                        CENP-H  44 relaael.lelakekesekeklkeelekleaelkksrqrwrvvkn 87 
                                   rel  +  +el+  k + +++l e+++++e+el+ ++  wr+v+ 
  gi|91774089|ref|YP_566781.1| 433 RELYDTTsRELKDSKYKFNKDLLEKIKRIEKELNLKI-TWRIVQD 476
                                   5666666334444444444789999999999998866.6888876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0012
                        CENP-H   8 rdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek.....eklkeele 69 
                                   r  +s ++ k++++++++++e+++ + ++  + rk+++l++ + e + + es++     ++++e +e
  gi|91774089|ref|YP_566781.1| 932 RRLASADYSKIESQITSANAEIEKERTSSSLIGRKSKKLLNNIKEAKVKLESQDmcdclDRVRELVE 998
                                   778999*************************************988888888887777633333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1283  (0.07156); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.26s 00:00:01.05 Elapsed: 00:00:00.41
# Mc/sec: 7741.00
//
Query:       gi|91774090|ref|YP_566782.1|  [L=1104]
Description: hypothetical protein Mbur_2163 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-34  118.8   0.8    1.4e-34  118.8   0.8    2.6  3  TaqI_C    TaqI-like C-terminal specificity domain
    1.6e-12   47.3   5.0    5.8e-09   35.7   1.0    3.7  3  N6_Mtase  N-6 DNA Methylase
      2e-10   41.1   0.1    1.2e-09   38.6   0.1    2.4  1  Eco57I    Eco57I restriction-modification methylase


Domain annotation for each model (and alignments):
>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.2   6.9e+03      18      31 ..     102     115 ..      71     172 .. 0.60
   2 !  118.8   0.8   2.3e-38   1.4e-34       1     120 []     826     966 ..     826     966 .. 0.98
   3 ?   -3.7   0.2         2   1.2e+04      86     102 ..    1004    1020 ..     984    1030 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                        TaqI_C  18 gnYldlikkklkne 31 
                                   ++Y++  k+kl++ 
  gi|91774090|ref|YP_566782.1| 102 TEYIKSKKDKLSKF 115
                                   33333333333333 PP

  == domain 2  score: 118.8 bits;  conditional E-value: 2.3e-38
                        TaqI_C   1 kpllkGkdikrysieikgnYldlikkklknekakelfeekpKilvrdiskkld...aaydekayyvlntlylliakdele. 77 
                                   k++++Gkd++rysi+ +g Yld+++k++++++  e+fe +pK+++r++s+k+d   +++d+++yy+++ l++ +++++l+ 
  gi|91774090|ref|YP_566782.1| 826 KKFIEGKDLSRYSISDRGLYLDYLPKMMYGPRVPEFFE-SPKLITRHVSGKNDsliFTIDKMGYYSDHGLIMSTDYENLNs 905
                                   799***********************************.***********999999************************* PP

                        TaqI_C  78 ................vslkyllgiLNSklikfyykkiystl..rggysrlkrkeleklPi 120
                                                   +++++llgiLNSkl++f+y+++y+t   +g+ys++++++++++Pi
  gi|91774090|ref|YP_566782.1| 906 knrtsfsdytvdskhnYQIELLLGILNSKLMSFFYANVYATGslQGSYSHVYPQHVRNFPI 966
                                   ****************************************9888****************9 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2
                        TaqI_C   86 iLNSklikfyykkiyst 102 
                                    iL S +++ y+ + ++t
  gi|91774090|ref|YP_566782.1| 1004 ILDSLVYSLYFSSNFTT 1020
                                    88999999999988876 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   9.5e-05      0.56      22     104 ..     341     472 ..     335     488 .. 0.78
   2 !   35.7   1.0   9.7e-13   5.8e-09     122     291 ..     612     787 ..     579     808 .. 0.82
   3 ?   -4.3   0.2       1.4   8.6e+03     253     277 ..    1056    1080 ..    1048    1086 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 9.5e-05
                      N6_Mtase  22 gksgGeffTPrevsklivell....................................epksgesvyDpacGsggllvqaek 66 
                                    k+ G ++TP++++k i+e +                                    e  ++ +v+Dpa+Gsg++ + a++
  gi|91774090|ref|YP_566782.1| 341 NKKIGAYYTPEAITKYIAENTifpfamdkleldkkyenfadfheahnndadtlnrfnEALKHIKVLDPAVGSGAFPMAAAD 421
                                   578899999999999999987788999999999999999999999999888888887666777899999999999999998 PP

                      N6_Mtase  67 vlkee.............dgktkelsiyGqeknettyrLakmNlllhgiey 104
                                    l +                ++   +++G+++ e +++++ + l l  i+ 
  gi|91774090|ref|YP_566782.1| 422 ILFDWrrkcreklddyhlRREIIINNLHGVDIMEGAVEICMLRLWLWLIAS 472
                                   886656677777777655555555667788888888888888877766655 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 9.7e-13
                      N6_Mtase 122 kdkkfdvvvaNppfnqkew...kektlekde...rfreavapksnadla..fllhiieslkpkGraavvlangvLfrggke 194
                                   ++  fdvv+ Npp+ ++ w   + ++l+++     f+++++ ks+ dl   f+  ++e  +++G  + +l+n  + r+  +
  gi|91774090|ref|YP_566782.1| 612 EKGGFDVVIGNPPYVNA-WemeEGSKLIRTIlpkLFNDKCPLKSHWDLYipFIIQALEINSKQGYFSYILPNP-ICREKYG 690
                                   3778************9.*88766677776544468899999999998888*******************986.579999* PP

                      N6_Mtase 195 gkIrkalvekdlveavial.peklFyntsiptcilvlkkekaerkgkvlfidaseefkkkdrkknklteediekildtyke 274
                                    ++rk+++e+ +++ ++     ++F ++s + ++l++k  k+++ ++++ i+  +e ++  +  n+ ++ d +++ ++   
  gi|91774090|ref|YP_566782.1| 691 IEVRKYILENTNIKNILTSgVRNVFEGVSRQSIVLIIKNSKPKKVDNIISINYIDEDNNI-SILNSTKQSDWNNLFQCQFR 770
                                   ****************9872589**************************99999999988.68888888888888777555 PP

                      N6_Mtase 275 kskevdkfskvveleei 291
                                   ++ +  +f    +++++
  gi|91774090|ref|YP_566782.1| 771 YEMDSTSFDIISHIDKL 787
                                   55666666666666655 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 1.4
                      N6_Mtase  253 kdrkknklteediekildtykeksk 277 
                                    + ++k++l+e+++  i+ +y+  ++
  gi|91774090|ref|YP_566782.1| 1056 EMKEKQALEERNMTVIERVYQRLKN 1080
                                    3368899999999999999998733 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1     2e-13   1.2e-09       3     103 ..     616     729 ..     613     732 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2e-13
                        Eco57I   3 fdviiGNPPYqeseakkelkaleek..............akdiyqkFvekalkle..dkylaliiparflasgkglkefre 67 
                                   fdv+iGNPPY ++ +++e+++l ++              + d+y  F+ +al+++  ++y + i+p+    ++k++ e+r+
  gi|91774090|ref|YP_566782.1| 616 FDVVIGNPPYVNAWEMEEGSKLIRTilpklfndkcplksHWDLYIPFIIQALEINskQGYFSYILPNPIC-REKYGIEVRK 695
                                   9***********99777777666669************999*************98899*********99.********** PP

                        Eco57I  68 kllkdkklkklvefedskevFkdveikggilvflkd 103
                                    +l+++++k++ +    + vF++v+  ++i++++k+
  gi|91774090|ref|YP_566782.1| 696 YILENTNIKNILTSGVRN-VFEGVSR-QSIVLIIKN 729
                                   ***********9999888.****985.566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 7293.04
//
Query:       gi|91774091|ref|YP_566783.1|  [L=219]
Description: DNA-(apurinic or apyrimidinic site) lyase / endonuclease III [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-24   87.0   0.0    1.4e-24   86.6   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    0.00013   21.6   0.0    0.00034   20.3   0.0    1.7  1  HHH            Helix-hairpin-helix motif
     0.0064   17.2   0.1      0.017   15.9   0.0    1.7  2  DUF3349        Protein of unknown function (DUF3349)
  ------ inclusion threshold ------
      0.021   15.4   0.1        2.6    8.7   0.0    2.6  2  HHH_5          Helix-hairpin-helix domain
      0.022   15.3   0.4       0.12   13.0   0.1    2.0  2  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
      0.027   14.5   0.0       0.16   12.1   0.0    2.3  3  HTH_35         Winged helix-turn-helix DNA-binding
      0.094   12.8   0.1        2.5    8.3   0.0    2.3  2  HHH_2          Helix-hairpin-helix motif
      0.094   13.1   3.2       0.16   12.3   3.2    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   6.3e-28   1.4e-24       1     107 [.      44     179 ..      44     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 6.3e-28
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   +++ils+q++d+ +n+++++lf+++   ++e+la+ad + L++ i+++Gfyr K k+ik +++ ++               
  gi|91774091|ref|YP_566783.1|  44 IATILSAQCTDVQVNKVTNELFRKYT--NVEALAAADLDVLEKEIYSTGFYRAKSKNIKRTSQLILsdfngkvpdtmeelt 122
                                   789*********************85..***************************************************** PP

                                   ..................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                   ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ..................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                     gk + +i+vD+hv+r+ ++l++++++ ++kk+e++l++l e
  gi|91774091|ref|YP_566783.1| 123 tfpgvarktanivlargfGKVE-GIAVDTHVKRVSGKLGLTENT-DPKKIEQDLMKLAE 179
                                   ****************888765.******************996.*********99876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.5e-07   0.00034       2      28 ..     110     136 ..     109     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.5e-07
                                   HHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                           HHH   2 leglipasreeLlalPGVGpktAeaIl 28 
                                   ++g +p+++eeL++ PGV +ktA+ +l
  gi|91774091|ref|YP_566783.1| 110 FNGKVPDTMEELTTFPGVARKTANIVL 136
                                   89**********************887 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.4e-06     0.017       4      70 ..      17      87 ..      14     109 .. 0.68
   2 ?   -2.1   0.0       3.1     7e+03      57      57 ..     165     165 ..     143     192 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.4e-06
                                  HHHHHHHHHH-TT-B-HHHHHH...HH..HHHCTT--HHHHHHHHHHHHHH--.SSS.BSHHHCHHHHHHHC CS
                       DUF3349  4 asileWLragYPegvPeqdyvp...Ll..alLrrrLsdeevkevaeelvaeaaeadeavdeedieelitkvt 70
                                  ++i + L++ YP+  Pe dy     Ll   +L+ + +d +v++v++el ++  ++ ea+ ++d+ +l +++ 
  gi|91774091|ref|YP_566783.1| 17 DRIWSILKKEYPDPQPELDYSNefeLLiaTILSAQCTDVQVNKVTNELFRKY-TNVEALAAADLDVLEKEIY 87
                                  678889*************975333442247889999************999.4555566666555544443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                   B CS
                       DUF3349  57 v 57 
                                   +
  gi|91774091|ref|YP_566783.1| 165 T 165
                                   2 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.034        76      18      39 ..      64      84 ..      58      95 .. 0.84
   2 ?    8.7   0.0    0.0012       2.6       2      30 ..     119     147 ..     118     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.034
                                  HHTTT--SHHHHHHS-HHHHHT CS
                         HHH_5 18 llsaGiesvedlaaadveeLak 39
                                  l ++ ++ ve+laaad + L k
  gi|91774091|ref|YP_566783.1| 64 LFRK-YTNVEALAAADLDVLEK 84
                                  5666.789********999876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                                   HHHHTSTT--HHHHHHHHTTT--SHHHHH CS
                         HHH_5   2 eeLlsvsGiGpktAlallsaGiesvedla 30 
                                   eeL++ +G+ +ktA  +l  G++ ve +a
  gi|91774091|ref|YP_566783.1| 119 EELTTFPGVARKTANIVLARGFGKVEGIA 147
                                   799**********************9997 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.54   1.2e+03      29      52 ..      59      82 ..      56     109 .. 0.65
   2 ?   13.0   0.1   5.3e-05      0.12      15      81 ..     116     182 ..     106     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.54
                    5_3_exonuc 29 ktAakLlkeygsleeilenld.elk 52
                                  k   +L ++y ++e++ + +d ++ 
  gi|91774091|ref|YP_566783.1| 59 KVTNELFRKYTNVEALAA-ADlDVL 82
                                  566789999999999987.333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.3e-05
                    5_3_exonuc  15 DssDnipGvpgiGektAakLl.keygsleeilenldelkekklkekLeenkeearlskkLatiktdvp 81 
                                   D+ +++   pg+  ktA  +l + +g++e+i   ++ +k+ + k  L+en +  ++ ++L+++ ++ +
  gi|91774091|ref|YP_566783.1| 116 DTMEELTTFPGVARKTANIVLaRGFGKVEGIAVDTH-VKRVSGKLGLTENTDPKKIEQDLMKLAEQKD 182
                                   889999999********99883569******99776.4554556778999999999999999987644 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     7e-05      0.16      25      74 ..      53     102 ..      46     103 .. 0.88
   2 ?   -2.6   0.0       2.6   5.8e+03      17      44 ..     117     144 ..     116     148 .. 0.76
   3 ?   -3.1   0.0       3.8   8.5e+03      17      36 ..     173     192 ..     168     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                        HTH_35  25 aglssstlsnaltrpwpkgEalIAeaLgvppeeiwPsRYekdtkkilsrk 74 
                                    + + ++++n l r++++ Eal A  L+v  +ei+ + ++  ++k ++r+
  gi|91774091|ref|YP_566783.1|  53 TDVQVNKVTNELFRKYTNVEALAAADLDVLEKEIYSTGFYRAKSKNIKRT 102
                                   56777999*******************************99988888875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                        HTH_35  17 tLaalsreaglssstlsnaltrpwpkgE 44 
                                   t+ +l    g +++t + +l+r   k E
  gi|91774091|ref|YP_566783.1| 117 TMEELTTFPGVARKTANIVLARGFGKVE 144
                                   6677777778888888888988877777 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.8
                        HTH_35  17 tLaalsreaglssstlsnal 36 
                                    L +l+++ + +  +++ +l
  gi|91774091|ref|YP_566783.1| 173 DLMKLAEQKDWEDLSMTLIL 192
                                   57888888887776666555 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0011       2.5      14      38 ..      59      83 ..      58      90 .. 0.89
   2 ?    2.0   0.0       0.1   2.3e+02      33      51 ..     117     135 ..     116     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                         HHH_2 14 ktAklLakrFksldaLkkasleeLl 38
                                  k+ ++L +++ +++aL++a+l+ L 
  gi|91774091|ref|YP_566783.1| 59 KVTNELFRKYTNVEALAAADLDVLE 83
                                  56789****************9886 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.1
                         HHH_2  33 sleeLlevddiGeeiAqsi 51 
                                   ++eeL++ ++++ ++A+ +
  gi|91774091|ref|YP_566783.1| 117 TMEELTTFPGVARKTANIV 135
                                   5788888888888888765 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.2   7.3e-05      0.16       1      17 []     198     214 ..     198     214 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
                 EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                   C A+kP+C  C L+ lC
  gi|91774091|ref|YP_566783.1| 198 CDAKKPQCIVCLLSKLC 214
                                   99*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1654.83
//
Query:       gi|91774092|ref|YP_566784.1|  [L=247]
Description: hypothetical protein Mbur_2165 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.4   0.0       0.18   11.5   0.0    1.4  1  DUF3685   Protein of unknown function (DUF3685)
       0.14   12.2   0.0       0.27   11.4   0.0    1.5  1  DUF4819   Domain of unknown function (DUF4819)


Domain annotation for each model (and alignments):
>> DUF3685  Protein of unknown function (DUF3685)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     2e-05      0.18      16      85 ..      51     120 ..      42     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                       DUF3685  16 lekpllidntlyaaespealeraeallenlliqvanavvqelLnelaeveelkqnlykkellstReierf 85 
                                   l  +l+i++ l ++e+++ +e++++++  +  +v+n +++++ ++  +++++++++  k++ s +e++ f
  gi|91774092|ref|YP_566784.1|  51 LLASLIIHHFLERIENKHKMEKLNMIIGSFFSEVGNDLLAVISDADPHLDHVREKFVIKDVWSEKEFADF 120
                                   556899***********************************************************99987 PP

>> DUF4819  Domain of unknown function (DUF4819)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.27       2      50 ..      90     141 ..      89     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                       DUF4819   2 dvilDasPslsqvavgtrvcvrvdeseeaaekvyregvvvevktkp...vrf 50 
                                    vi+Da P l +v+    +    +e+e a+ +v+ +g++++v++++   v+f
  gi|91774092|ref|YP_566784.1|  90 AVISDADPHLDHVREKFVIKDVWSEKEFADFEVFLKGYIYKVDMNKidlVPF 141
                                   59***********99887776668999999*************998444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1559.47
//
Query:       gi|91774093|ref|YP_566785.1|  [L=364]
Description: DNA-directed DNA polymerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-41  142.1   0.1    2.4e-41  141.2   0.1    1.4  1  IMS       impB/mucB/samB family
    1.1e-09   39.0   0.3    2.4e-09   37.9   0.3    1.5  1  IMS_C     impB/mucB/samB family C-terminal domain
    8.4e-09   35.3   0.1    2.4e-08   33.8   0.1    1.8  1  IMS_HHH   IMS family HHH motif
     0.0018   18.5   0.0     0.0039   17.4   0.0    1.5  1  Cdd1      Pathogenicity locus
  ------ inclusion threshold ------
      0.014   16.0   0.5      0.091   13.4   0.1    2.4  2  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   0.1   6.6e-45   2.4e-41       1     149 [.       8     162 ..       8     163 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 6.6e-45
                                   EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHHHHHH CS
                           IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyrrask 78 
                                   +Dmd Fya++e+++dp+Lkgk vvv+ +s++   +g v +++y Ar +G++++m+ + ak++ pd+++++v+ + y ++s+
  gi|91774093|ref|YP_566785.1|   8 VDMDYFYAAIEEREDPSLKGKAVVVCMYSNRgeeGGAVSTCNYVARDAGIHSAMPCRLAKAVKPDAVFLPVRKTFYSEVSE 88 
                                   7***************************9999999********************************************** PP

                                   HHHHHHHHH-S.....EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHH CS
                           IMS  79 kileilkrfispk...vekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlas 149
                                   +i+ei++++ ++     ek++iDEa+l++t++ +   ++++++a+ +++++ke  glt+s+Gi++nk++AK+as
  gi|91774093|ref|YP_566785.1|  89 RIMEIIRSYADNDgelFEKLGIDEAFLEVTATSRGDIDKAQQIAQSIKDDVKELEGLTCSVGIGPNKIIAKMAS 162
                                   *********8744666***************888888888*********************************8 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.3   6.8e-13   2.4e-09       3     114 ..     245     358 ..     243     361 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 6.8e-13
                         IMS_C   3 earpepksissektfpepydesk.lkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtreilea 81 
                                   +++  + +i+   ++ +++ +s+ + + l eL +++  +  ++++  r+it+++ ys+f+  ++s+tL +p    + + e 
  gi|91774093|ref|YP_566785.1| 245 KEKTSSDQIGRMASLTHDTRKSDlVLSLLDELLDDVFSKVTARNVSFRSITVTVIYSNFKtVTKSHTLNHPMAEKAVLREV 325
                                   556667799999999994444446888888***************************8888******************** PP

                         IMS_C  82 alkLlrrlidepglpirligvsasnlvekaesq 114
                                     +++ +l d ++ +ir+igv+++nl e+++++
  gi|91774093|ref|YP_566785.1| 326 SYQIMGELLDSSTVNIRRIGVRVGNLHENKGQK 358
                                   *****999999****************888776 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   6.6e-12   2.4e-08       2      32 .]     176     206 ..     175     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 6.6e-12
                       IMS_HHH   2 ddvkefLwplpitkipGiGgklgekLeklGi 32 
                                   d+v  fL ++p+ k++GiG++++ekL+++Gi
  gi|91774093|ref|YP_566785.1| 176 DEVDGFLRKMPVAKLWGIGKVTEEKLANMGI 206
                                   78899*************************9 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0039      10      52 ..     189     231 ..     184     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                          Cdd1  10 diPniGkalaedlvelGirsveelkgedpeelyeklekltgar 52 
                                   ++ +iGk + e+l ++Gi  ve+l+g+d +el +++ k  g++
  gi|91774093|ref|YP_566785.1| 189 KLWGIGKVTEEKLANMGIDIVEDLAGHDVQELISAFGKTRGTW 231
                                   5779******************************999999987 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.56     2e+03      23      42 ..     125     144 ..     118     158 .. 0.63
   2 ?   13.4   0.1   2.5e-05     0.091       8      40 ..     191     223 ..     187     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.56
                                   --SHHHHHHS-HHHHHTSTT CS
                         HHH_5  23 iesvedlaaadveeLakipG 42 
                                   i+  +++a+  ++++ ++ G
  gi|91774093|ref|YP_566785.1| 125 IDKAQQIAQSIKDDVKELEG 144
                                   66667777765555555444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.5e-05
                                   TT--HHHHHHHHTTT--SHHHHHHS-HHHHHTS CS
                         HHH_5   8 sGiGpktAlallsaGiesvedlaaadveeLaki 40 
                                    GiG++t  +l++ Gi+ vedla  dv+eL ++
  gi|91774093|ref|YP_566785.1| 191 WGIGKVTEEKLANMGIDIVEDLAGHDVQELISA 223
                                   59***************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2789.89
//
Query:       gi|91774094|ref|YP_566786.1|  [L=298]
Description: hypothetical protein Mbur_2167 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   16.3   0.0        1.5    9.1   0.0    2.3  2  GP52      Phage gene product 52


Domain annotation for each model (and alignments):
>> GP52  Phage gene product 52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0018        31      37      56 ..     117     136 ..     111     140 .. 0.93
   2 !    9.1   0.0   8.1e-05       1.5      34      55 ..     210     231 ..     188     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0018
                          GP52  37 nwsqedlelyvGGiftPGyG 56 
                                   n+s+  l+  v   ftP yG
  gi|91774094|ref|YP_566786.1| 117 NYSRSHLNSIVSSAFTPMYG 136
                                   8999***************9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 8.1e-05
                          GP52  34 rlenwsqedlelyvGGiftPGy 55 
                                   +  nw q dle+y   + t G+
  gi|91774094|ref|YP_566786.1| 210 MDLNWKQADLEQYFDFLDTSGF 231
                                   4459*********988777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2139.61
//
Query:       gi|91774095|ref|YP_566787.1|  [L=80]
Description: hypothetical protein Mbur_2168 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 606.92
//
Query:       gi|91774096|ref|YP_566788.1|  [L=100]
Description: hypothetical protein Mbur_2169 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.057   13.1   0.1      0.067   12.8   0.1    1.2  1  Glyco_transf_7N  N-terminal region of glycosyl transferase gr


Domain annotation for each model (and alignments):
>> Glyco_transf_7N  N-terminal region of glycosyl transferase group 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.8e-06     0.067      64     109 ..      26      70 ..      15      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-06
               Glyco_transf_7N  64 illkrLhpllqrQqldykiyvieqagnetFnrakllnvgflealke 109
                                    + + ++++ ++Q+l  + +++e++ ++ F r k+l +g++e  k 
  gi|91774096|ref|YP_566788.1|  26 FWTYVFMQVHMHQKLPVAAVLVERN-DTDFQRKKILAIGYKEWKKM 70 
                                   46677889999******99999975.678************97664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 689.52
//
Query:       gi|91774097|ref|YP_566789.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91774097|ref|YP_566789.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91774097|ref|YP_566789.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91774097|ref|YP_566789.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91774097|ref|YP_566789.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91774097|ref|YP_566789.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91774097|ref|YP_566789.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91774097|ref|YP_566789.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91774097|ref|YP_566789.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2176.89
//
Query:       gi|91774098|ref|YP_566790.1|  [L=490]
Description: HEAT repeat-containing PBS lyase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-91  298.6  17.3    5.2e-14   52.4   0.1    6.8  9  HEAT_2         HEAT repeats
    6.6e-44  144.1   0.0    0.00025   21.4   0.0   12.5 12  HEAT_PBS       PBS lyase HEAT-like repeat
    1.5e-42  140.0   0.5     0.0032   17.6   0.0   13.4 13  HEAT           HEAT repeat
    2.3e-22   78.3   0.0      0.067   13.3   0.0   12.3 14  Arm            Armadillo/beta-catenin-like repeat
    6.7e-22   77.6   1.2       0.27   11.8   0.0   11.4 13  HEAT_EZ        HEAT-like repeat
    1.2e-19   70.7   7.0        0.1   13.2   0.0    8.3  8  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
    5.7e-12   46.0  15.6      0.087   12.9   0.2    7.9  7  Cnd1           non-SMC mitotic condensation complex subunit 1
    6.5e-10   39.4   9.7       0.16   12.4   0.0    7.2  7  RasGEF_N_2     Rapamycin-insensitive companion of mTOR RasGEF
      1e-06   28.9   3.4        2.2    8.3   0.0    7.1  7  Aconitase_B_N  Aconitate B N-terminal domain
    4.5e-06   25.5   8.5       0.12   10.9   0.2    5.1  6  Adaptin_N      Adaptin N terminal region
     0.0017   17.3   2.7       0.66    8.7   0.1    3.2  3  API5           Apoptosis inhibitory protein 5 (API5)
     0.0023   18.3   1.7          1    9.9   0.0    5.0  5  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
  ------ inclusion threshold ------
      0.012   15.7   3.8      0.092   12.8   0.3    2.9  3  IFS            Immunity factor for SPN
      0.016   14.8   0.4        1.6    8.2   0.0    3.5  3  CLASP_N        CLASP N terminal
      0.046   13.9   0.0        1.3    9.2   0.0    3.1  2  BRCC36_C       BRCC36 C-terminal helical domain
      0.066   13.3   1.0         12    6.0   0.1    3.0  3  ParcG          Parkin co-regulated protein
       0.07   13.1   0.0        2.7    8.1   0.0    3.4  4  SicP-binding   SicP binding


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 !   26.4   0.1   6.5e-09   6.9e-06       4      83 ..      24     102 ..      21     103 .. 0.86
   2 !   50.0   0.2   2.7e-16   2.8e-13       1      88 []      52     137 ..      52     137 .. 0.94
   3 !   52.4   0.1     5e-17   5.2e-14       1      87 [.      83     167 ..      83     168 .. 0.95
   4 !   32.5   0.0   7.7e-11   8.1e-08       1      69 [.     114     181 ..     114     187 .. 0.93
   5 !   32.7   0.0   7.1e-11   7.5e-08       1      83 [.     145     225 ..     145     230 .. 0.93
   6 !   51.7   0.0   8.4e-17   8.9e-14       1      82 [.     207     287 ..     207     287 .. 0.98
   7 !   34.0   0.0   2.8e-11   2.9e-08       2      75 ..     270     345 ..     269     346 .. 0.90
   8 !   38.3   0.1   1.2e-12   1.3e-09       2      75 ..     335     406 ..     334     413 .. 0.94
   9 !   46.0   0.0     5e-15   5.2e-12       1      87 [.     395     483 ..     395     484 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.5e-09
                        HEAT_2   4 LlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaA 83 
                                    l+al ++++ e+r +a ++  + +n   l++++e+l+++d+++Rr + + Lg ++d +a++ L ++l+d+d+ vv  aA
  gi|91774098|ref|YP_566790.1|  24 ILNAL-SHSNAEIRFQAEETFDEVANFNELETFIEALKSDDENIRRFVSRVLGGCDDLRAVEPLIQSLNDEDECVVDYAA 102
                                   57888.89999999999999999998888999999999999999999999999999999999999999999888887665 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 2.7e-16
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81 
                                   l+++++al ++ d+++rr + r+Lg +++ +a++ L++ l+ded+ v   aae+Lg ++d++a++ L + l ++ ++  R 
  gi|91774098|ref|YP_566790.1|  52 LETFIEAL-KSDDENIRRFVSRVLGGCDDLRAVEPLIQSLNDEDECVVDYAAESLGNLQDKRAVDPLIKVLSHKYWAA-RS 130
                                   57899***.99************************************************************9876666.88 PP

                        HEAT_2  82 aAaeaLa 88 
                                   +Aa +L+
  gi|91774098|ref|YP_566790.1| 131 SAALSLG 137
                                   9999985 PP

  == domain 3  score: 52.4 bits;  conditional E-value: 5e-17
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81 
                                   +++L+q l nd+d+ v   a+++Lg++++++a++ L+++l+++ +a R  aa +Lg igd++a++ L + l+ d+  +vR 
  gi|91774098|ref|YP_566790.1|  83 VEPLIQSL-NDEDECVVDYAAESLGNLQDKRAVDPLIKVLSHKYWAARSSAALSLGCIGDSRAIDPLVQTLN-DKYHEVRY 161
                                   589*****.************************************************************996.678888** PP

                        HEAT_2  82 aAaeaL 87 
                                    A+eaL
  gi|91774098|ref|YP_566790.1| 162 YAEEAL 167
                                   *****9 PP

  == domain 4  score: 32.5 bits;  conditional E-value: 7.7e-11
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLke 69 
                                   +d+L+++l +++ ++ r  a+ +Lg ig+ +a++ Lv+ l+d+  +vR+ a eaL +++d++a + L +
  gi|91774098|ref|YP_566790.1| 114 VDPLIKVL-SHKYWAARSSAALSLGCIGDSRAIDPLVQTLNDKYHEVRYYAEEALEKFDDDRATEELNK 181
                                   689*****.9****************************************************9998865 PP

  == domain 5  score: 32.7 bits;  conditional E-value: 7.1e-11
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81 
                                   +d+L+q l nd+ +evr+ a +aL ++++++a + L ++ e++ p   +++++a   +  +++++ L e+l+d++d+ vRe
  gi|91774098|ref|YP_566790.1| 145 IDPLVQTL-NDKYHEVRYYAEEALEKFDDDRATEELNKYHESQIPKHLKNVVNAFRTFEKSKSIDPLIEYLNDENDE-VRE 223
                                   689*****.**************************************************************877666.587 PP

                        HEAT_2  82 aA 83 
                                    A
  gi|91774098|ref|YP_566790.1| 224 YA 225
                                   76 PP

  == domain 6  score: 51.7 bits;  conditional E-value: 8.4e-17
                        HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81 
                                   +d+L+++l nd+++evr  a ++  +++++++++aL++ l+d++  v+r+aa +Lg+i++peal+ L + l++++++v+++
  gi|91774098|ref|YP_566790.1| 207 IDPLIEYL-NDENDEVREYASKCFYELNDKKSVDALIQSLNDPSKIVQRNAACSLGKIDTPEALEGLVQNLKSEKVEVRKN 286
                                   689*****.********************************************************************9987 PP

                        HEAT_2  82 a 82 
                                   a
  gi|91774098|ref|YP_566790.1| 287 A 287
                                   5 PP

  == domain 7  score: 34.0 bits;  conditional E-value: 2.8e-11
                        HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLg...aigdpealpaLkelldddd 75 
                                   + L+q l +++  evr++a+  +g+  ++ a +++++ l+ded++vR  aa+aL    ++ d++++++  e+l+++d
  gi|91774098|ref|YP_566790.1| 270 EGLVQNL-KSEKVEVRKNAVGGMGESESKLATKMIFQTLNDEDERVRLSAANALYfsdRLYDQQNIDSVIEALANKD 345
                                   779999*.9*********************************************72235569**********99876 PP

  == domain 8  score: 38.3 bits;  conditional E-value: 1.2e-12
                        HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddd 75 
                                   d  ++al   +d +vr+ a + L +i+++ a++ L+ +l+ded ++R  aa+aLg ig++ +++ L ++ldd++
  gi|91774098|ref|YP_566790.1| 335 DSVIEAL-ANKDVNVRKYATMGLIEIADEMAIKPLIYVLDDEDIRIRNYAAQALGNIGED-SIEPLVQILDDKN 406
                                   778999*.89************************************************96.*********8865 PP

  == domain 9  score: 46.0 bits;  conditional E-value: 5e-15
                        HEAT_2   1 ldaLlqalendpdpe....vrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                   +++L+q+l +d+++     + ra++ aLg i n ++++ L+++l+ +d+ v + a+ aLg++gdp++++ Lk++l+ d++ 
  gi|91774098|ref|YP_566790.1| 395 IEPLVQIL-DDKNTFgkkrLLRATVNALGFIENSKVVDSLIKALSIKDMFVKESACLALGEMGDPKSIEPLKACLN-DKHK 473
                                   58999999.88888555557799**************************************************996.5677 PP

                        HEAT_2  78 vvReaAaeaL 87 
                                    v+ aA ++L
  gi|91774098|ref|YP_566790.1| 474 KVQDAAKRSL 483
                                   7899998887 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 !    7.4   0.0    0.0076         8       2      27 .]      67      92 ..      66      92 .. 0.91
   2 !   21.4   0.0   2.3e-07   0.00025       4      26 ..     100     122 ..      97     123 .. 0.93
   3 !   14.5   0.0   4.1e-05     0.043       2      27 .]     129     154 ..     128     154 .. 0.94
   4 ?    2.0   0.0      0.44   4.7e+02       1      21 [.     159     179 ..     159     182 .. 0.90
   5 ?    2.1   0.0       0.4   4.3e+02       9      27 .]     198     216 ..     192     216 .. 0.77
   6 !   10.5   0.0   0.00082      0.86       1      27 []     221     247 ..     221     247 .. 0.96
   7 !   18.6   0.0   1.9e-06     0.002       1      26 [.     252     277 ..     252     278 .. 0.96
   8 ?    1.5   0.0      0.65   6.9e+02       1      11 [.     314     324 ..     314     343 .. 0.72
   9 !    8.0   0.0    0.0052       5.5       1      27 []     348     374 ..     348     374 .. 0.92
  10 !   16.5   0.0   9.1e-06    0.0096       2      27 .]     380     404 ..     379     404 .. 0.95
  11 ?    6.0   0.0     0.023        24       3      25 ..     415     437 ..     413     438 .. 0.92
  12 !   17.6   0.0   4.1e-06    0.0043       4      27 .]     447     470 ..     444     470 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0076
                                  HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS  2 RraAakaLgqlgdeeaipaLleaLqd 27
                                  Rr   + Lg + d +a+++L++ L+d
  gi|91774098|ref|YP_566790.1| 67 RRFVSRVLGGCDDLRAVEPLIQSLND 92
                                  8888899***************9987 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.3e-07
                                   HHHHHHHHCTSGGGHHHHHHHCT CS
                      HEAT_PBS   4 aAakaLgqlgdeeaipaLleaLq 26 
                                   +Aa++Lg+l+d++a+++L+++L 
  gi|91774098|ref|YP_566790.1| 100 YAAESLGNLQDKRAVDPLIKVLS 122
                                   8********************97 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                   R +Aa +Lg +gd +ai++L++ L+d
  gi|91774098|ref|YP_566790.1| 129 RSSAALSLGCIGDSRAIDPLVQTLND 154
                                   99*******************99887 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHHCTSGGGHHHH CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaL 21 
                                   vR++A +aL ++ d++a + L
  gi|91774098|ref|YP_566790.1| 159 VRYYAEEALEKFDDDRATEEL 179
                                   8***************99988 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.4
                                   HHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   9 LgqlgdeeaipaLleaLqd 27 
                                     ++    +i++L+e L+d
  gi|91774098|ref|YP_566790.1| 198 FRTFEKSKSIDPLIEYLND 216
                                   555666789********97 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00082
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   vR +A k  ++l+d+ +++aL++ L+d
  gi|91774098|ref|YP_566790.1| 221 VREYASKCFYELNDKKSVDALIQSLND 247
                                   8**********************9987 PP

  == domain 7  score: 18.6 bits;  conditional E-value: 1.9e-06
                                   HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                   v+r+Aa +Lg++ ++ea++ L+++L+
  gi|91774098|ref|YP_566790.1| 252 VQRNAACSLGKIDTPEALEGLVQNLK 277
                                   89**********************98 PP

  == domain 8  score: 1.5 bits;  conditional E-value: 0.65
                                   HHHHHHHHHHH CS
                      HEAT_PBS   1 vRraAakaLgq 11 
                                   vR +Aa aL+ 
  gi|91774098|ref|YP_566790.1| 314 VRLSAANALYF 324
                                   899*****985 PP

  == domain 9  score: 8.0 bits;  conditional E-value: 0.0052
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                   vR +A+ +L ++ de ai +L+ +L+d
  gi|91774098|ref|YP_566790.1| 348 VRKYATMGLIEIADEMAIKPLIYVLDD 374
                                   8********************977776 PP

  == domain 10  score: 16.5 bits;  conditional E-value: 9.1e-06
                                   HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                   R +Aa aLg++g  ++i++L++ L+d
  gi|91774098|ref|YP_566790.1| 380 RNYAAQALGNIGE-DSIEPLVQILDD 404
                                   889**********.**********98 PP

  == domain 11  score: 6.0 bits;  conditional E-value: 0.023
                                   HHHHHHHHHCTSGGGHHHHHHHC CS
                      HEAT_PBS   3 raAakaLgqlgdeeaipaLleaL 25 
                                   ra + aLg +    +++ L++aL
  gi|91774098|ref|YP_566790.1| 415 RATVNALGFIENSKVVDSLIKAL 437
                                   78899*****************9 PP

  == domain 12  score: 17.6 bits;  conditional E-value: 4.1e-06
                                   HHHHHHHHCTSGGGHHHHHHHCTC CS
                      HEAT_PBS   4 aAakaLgqlgdeeaipaLleaLqd 27 
                                   +A  aLg++gd+ +i++L+++L+d
  gi|91774098|ref|YP_566790.1| 447 SACLALGEMGDPKSIEPLKACLND 470
                                   5668******************98 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.037        39       5      26 ..      24      45 ..      21      49 .. 0.82
   2 ?    3.7   0.0     0.086        90       2      25 ..      52      75 ..      52      77 .. 0.90
   3 !   12.2   0.0   0.00016      0.17       4      28 ..      85     109 ..      82     111 .. 0.87
   4 !   11.0   0.0    0.0004      0.42       3      27 ..     115     139 ..     113     142 .. 0.89
   5 !    7.6   0.0     0.005       5.2       4      24 ..     147     167 ..     144     170 .. 0.82
   6 !   17.6   0.0     3e-06    0.0032       3      27 ..     208     232 ..     207     234 .. 0.92
   7 ?    6.1   0.0     0.015        15       3      22 ..     239     258 ..     238     263 .. 0.75
   8 !    7.1   0.0    0.0069       7.3       3      25 ..     270     292 ..     268     293 .. 0.86
   9 !   14.0   0.0   4.2e-05     0.044       5      24 ..     303     322 ..     301     323 .. 0.89
  10 ?    5.2   0.0      0.03        32       4      29 ..     336     361 ..     334     363 .. 0.89
  11 !   13.1   0.0   8.5e-05      0.09       3      29 ..     367     392 ..     365     394 .. 0.85
  12 !    8.5   0.0    0.0026       2.8       3      27 ..     431     455 ..     429     457 .. 0.84
  13 !    9.8   0.0   0.00096         1       4      29 ..     463     488 ..     461     489 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.037
                                  HHHHHT-SSHHHHHHHHHHHHH CS
                          HEAT  5 llkllsDpspeVReaAakaLga 26
                                  +l++ls++++e+R  A +++ +
  gi|91774098|ref|YP_566790.1| 24 ILNALSHSNAEIRFQAEETFDE 45
                                  899**********999777765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.086
                                  HHHHHHHHT-SSHHHHHHHHHHHH CS
                          HEAT  2 lPlllkllsDpspeVReaAakaLg 25
                                  l +++++l++++ ++R+ + + Lg
  gi|91774098|ref|YP_566790.1| 52 LETFIEALKSDDENIRRFVSRVLG 75
                                  57899************9999998 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00016
                                   HHHHHHT-SSHHHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                   +l++ l+D++  V + Aa++Lg+l 
  gi|91774098|ref|YP_566790.1|  85 PLIQSLNDEDECVVDYAAESLGNLQ 109
                                   577779****************996 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.0004
                                   HHHHHHHT-SSHHHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                   ++l+k ls++ +  R++Aa++Lg +
  gi|91774098|ref|YP_566790.1| 115 DPLIKVLSHKYWAARSSAALSLGCI 139
                                   679999*****************87 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.005
                                   HHHHHHT-SSHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaL 24 
                                   +l++ l+D+  eVR+ A +aL
  gi|91774098|ref|YP_566790.1| 147 PLVQTLNDKYHEVRYYAEEAL 167
                                   677779*********998887 PP

  == domain 6  score: 17.6 bits;  conditional E-value: 3e-06
                                   HHHHHHHT-SSHHHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                   ++l++ l+D++ eVRe A k++ +l
  gi|91774098|ref|YP_566790.1| 208 DPLIEYLNDENDEVREYASKCFYEL 232
                                   6799******************987 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.015
                                   HHHHHHHT-SSHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAak 22 
                                   ++l++ l+Dps  V ++Aa 
  gi|91774098|ref|YP_566790.1| 239 DALIQSLNDPSKIVQRNAAC 258
                                   579999*******9555553 PP

  == domain 8  score: 7.1 bits;  conditional E-value: 0.0069
                                   HHHHHHHT-SSHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAakaLg 25 
                                     l+++l+++  eVR++A+  +g
  gi|91774098|ref|YP_566790.1| 270 EGLVQNLKSEKVEVRKNAVGGMG 292
                                   568999************98776 PP

  == domain 9  score: 14.0 bits;  conditional E-value: 4.2e-05
                                   HHHHHT-SSHHHHHHHHHHH CS
                          HEAT   5 llkllsDpspeVReaAakaL 24 
                                   + + l+D++ +VR +Aa+aL
  gi|91774098|ref|YP_566790.1| 303 IFQTLNDEDERVRLSAANAL 322
                                   66779**************9 PP

  == domain 10  score: 5.2 bits;  conditional E-value: 0.03
                                   HHHHHHT-SSHHHHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaLgalae 29 
                                    ++++l  ++ +VR+ A   L ++a 
  gi|91774098|ref|YP_566790.1| 336 SVIEALANKDVNVRKYATMGLIEIAD 361
                                   6889999**************99985 PP

  == domain 11  score: 13.1 bits;  conditional E-value: 8.5e-05
                                   HHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAakaLgalae 29 
                                   Pl+   l D++ ++R  Aa+aLg++ e
  gi|91774098|ref|YP_566790.1| 367 PLIYV-LDDEDIRIRNYAAQALGNIGE 392
                                   55555.79****************987 PP

  == domain 12  score: 8.5 bits;  conditional E-value: 0.0026
                                   HHHHHHHT-SSHHHHHHHHHHHHHH CS
                          HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                   + l+k+ls ++++V e+A++aLg++
  gi|91774098|ref|YP_566790.1| 431 DSLIKALSIKDMFVKESACLALGEM 455
                                   5678888779*************98 PP

  == domain 13  score: 9.8 bits;  conditional E-value: 0.00096
                                   HHHHHHT-SSHHHHHHHHHHHHHHHH CS
                          HEAT   4 lllkllsDpspeVReaAakaLgalae 29 
                                   +l  +l+D++ +V +aA ++L +la+
  gi|91774098|ref|YP_566790.1| 463 PLKACLNDKHKKVQDAAKRSLKNLAK 488
                                   567789******************98 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.2   3.4e+03      18      32 ..      25      39 ..      21      39 .. 0.84
   2 ?    2.6   0.0      0.15   1.5e+02       6      30 ..      44      68 ..      41      68 .. 0.87
   3 !    6.9   0.0    0.0064       6.8      12      39 ..      81     108 ..      79     108 .. 0.94
   4 ?    0.1   0.0      0.86   9.1e+02      13      24 ..     113     124 ..     110     125 .. 0.88
   5 ?    4.1   0.0     0.047        50       8      29 ..     139     160 ..     137     166 .. 0.83
   6 ?    5.2   0.0     0.022        23      13      32 ..     206     225 ..     203     232 .. 0.87
   7 !    9.2   0.0    0.0012       1.3      14      37 ..     238     261 ..     233     263 .. 0.92
   8 !   10.2   0.0   0.00059      0.62      13      36 ..     268     291 ..     266     293 .. 0.89
   9 ?   -0.5   0.0       1.4   1.5e+03      21      36 ..     307     322 ..     305     323 .. 0.89
  10 ?   -1.2   0.0       2.2   2.3e+03      18      32 ..     338     352 ..     330     353 .. 0.62
  11 !   13.3   0.0   6.3e-05     0.067      13      39 ..     364     390 ..     357     392 .. 0.92
  12 ?    0.5   0.0      0.67   7.1e+02      14      25 ..     395     406 ..     393     422 .. 0.69
  13 ?    1.0   0.0      0.45   4.7e+02      11      38 ..     427     454 ..     426     457 .. 0.88
  14 ?    3.8   0.0     0.062        65      12      40 ..     459     487 ..     454     488 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.2
                                  HHHTTTSSHHHHHHH CS
                           Arm 18 vrLLssedeevqeeA 32
                                  ++ Ls+ + e++++A
  gi|91774098|ref|YP_566790.1| 25 LNALSHSNAEIRFQA 39
                                  6779999**999998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                                  HHHHHTTHHHHHHHHTTTSSHHHHH CS
                           Arm  6 davieaGavppLvrLLssedeevqe 30
                                  d+v + + ++ +++ L+s+de++++
  gi|91774098|ref|YP_566790.1| 44 DEVANFNELETFIEALKSDDENIRR 68
                                  5677888899************986 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0064
                                   THHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                           Arm  12 GavppLvrLLssedeevqeeAawALsNL 39 
                                    av+pL++ L++ede v+  Aa  L+NL
  gi|91774098|ref|YP_566790.1|  81 RAVEPLIQSLNDEDECVVDYAAESLGNL 108
                                   58*************************8 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.86
                                   HHHHHHHHTTTS CS
                           Arm  13 avppLvrLLsse 24 
                                   av+pL++ Ls++
  gi|91774098|ref|YP_566790.1| 113 AVDPLIKVLSHK 124
                                   8********985 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.047
                                   HHHTTHHHHHHHHTTTSSHHHH CS
                           Arm   8 vieaGavppLvrLLssedeevq 29 
                                   + ++ a++pLv+ L+++  ev+
  gi|91774098|ref|YP_566790.1| 139 IGDSRAIDPLVQTLNDKYHEVR 160
                                   67999*********98877765 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.022
                                   HHHHHHHHTTTSSHHHHHHH CS
                           Arm  13 avppLvrLLssedeevqeeA 32 
                                    ++pL++ L++e++ev+e A
  gi|91774098|ref|YP_566790.1| 206 SIDPLIEYLNDENDEVREYA 225
                                   599***************98 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.0012
                                   HHHHHHHTTTSSHHHHHHHHHHHH CS
                           Arm  14 vppLvrLLssedeevqeeAawALs 37 
                                   v++L++ L++++  vq++Aa+ L+
  gi|91774098|ref|YP_566790.1| 238 VDALIQSLNDPSKIVQRNAACSLG 261
                                   89*******************998 PP

  == domain 8  score: 10.2 bits;  conditional E-value: 0.00059
                                   HHHHHHHHTTTSSHHHHHHHHHHH CS
                           Arm  13 avppLvrLLssedeevqeeAawAL 36 
                                   a++ Lv+ L+se++ev+++A++ +
  gi|91774098|ref|YP_566790.1| 268 ALEGLVQNLKSEKVEVRKNAVGGM 291
                                   6888****************9976 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 1.4
                                   TTTSSHHHHHHHHHHH CS
                           Arm  21 LssedeevqeeAawAL 36 
                                   L++ede+v+  Aa AL
  gi|91774098|ref|YP_566790.1| 307 LNDEDERVRLSAANAL 322
                                   889**********998 PP

  == domain 10  score: -1.2 bits;  conditional E-value: 2.2
                                   HHHTTTSSHHHHHHH CS
                           Arm  18 vrLLssedeevqeeA 32 
                                   ++ L ++d++v++ A
  gi|91774098|ref|YP_566790.1| 338 IEALANKDVNVRKYA 352
                                   455667777777776 PP

  == domain 11  score: 13.3 bits;  conditional E-value: 6.3e-05
                                   HHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                           Arm  13 avppLvrLLssedeevqeeAawALsNL 39 
                                   a++pL+  L++ed +++  Aa AL+N+
  gi|91774098|ref|YP_566790.1| 364 AIKPLIYVLDDEDIRIRNYAAQALGNI 390
                                   89************************9 PP

  == domain 12  score: 0.5 bits;  conditional E-value: 0.67
                                   HHHHHHHTTTSS CS
                           Arm  14 vppLvrLLssed 25 
                                   ++pLv+ L++++
  gi|91774098|ref|YP_566790.1| 395 IEPLVQILDDKN 406
                                   89******9544 PP

  == domain 13  score: 1.0 bits;  conditional E-value: 0.45
                                   TTHHHHHHHHTTTSSHHHHHHHHHHHHH CS
                           Arm  11 aGavppLvrLLssedeevqeeAawALsN 38 
                                   + +v+ L++ Ls +d  v+e A+ AL+ 
  gi|91774098|ref|YP_566790.1| 427 SKVVDSLIKALSIKDMFVKESACLALGE 454
                                   6789999*****99999******99986 PP

  == domain 14  score: 3.8 bits;  conditional E-value: 0.062
                                   THHHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                           Arm  12 GavppLvrLLssedeevqeeAawALsNLa 40 
                                     ++pL ++L++++ +vq +A + L NLa
  gi|91774098|ref|YP_566790.1| 459 KSIEPLKACLNDKHKKVQDAAKRSLKNLA 487
                                   5599****************999888887 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.3   6.6e+03      31      45 ..      22      36 ..      18      36 .. 0.84
   2 ?    0.1   0.0       1.2   1.3e+03      31      53 ..      53      75 ..      50      75 .. 0.82
   3 ?    3.8   0.0     0.084        88      28      55 .]      81     108 ..      65     108 .. 0.83
   4 ?    3.7   0.0     0.086        91      28      52 ..     143     167 ..     126     170 .. 0.71
   5 !    8.3   0.0    0.0031       3.3      30      53 ..     207     230 ..     202     232 .. 0.85
   6 !   11.3   0.0   0.00037      0.39      30      55 .]     238     263 ..     235     263 .. 0.90
   7 !    7.0   0.0    0.0081       8.5      27      50 ..     266     289 ..     265     293 .. 0.91
   8 ?    5.3   0.0     0.027        29      36      52 ..     306     322 ..     300     324 .. 0.88
   9 !   11.8   0.0   0.00026      0.27       2      50 ..     313     354 ..     312     359 .. 0.88
  10 !    8.8   0.0    0.0022       2.3      34      55 .]     369     390 ..     361     390 .. 0.73
  11 ?   -1.8   0.0       4.6   4.9e+03      43      53 ..     412     422 ..     393     424 .. 0.53
  12 ?    3.4   0.0      0.11   1.1e+02      29      55 .]     429     455 ..     427     455 .. 0.74
  13 ?    4.1   0.1     0.066        70       4      48 ..     445     479 ..     443     486 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.3
                       HEAT_EZ 31 paLlalLnddsdeVR 45
                                  +  l++L+++++e+R
  gi|91774098|ref|YP_566790.1| 22 KGILNALSHSNAEIR 36
                                  56789999**99988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                       HEAT_EZ 31 paLlalLnddsdeVRaaAagaLg 53
                                    ++ +L++d+ ++R  + + Lg
  gi|91774098|ref|YP_566790.1| 53 ETFIEALKSDDENIRRFVSRVLG 75
                                  67999********9987777765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.084
                       HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                   +++ +L++ Lnd++  V  +Aa  Lgnl
  gi|91774098|ref|YP_566790.1|  81 RAVEPLIQSLNDEDECVVDYAAESLGNL 108
                                   46899999***999999********997 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.086
                       HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaL 52 
                                   +++++L+++Lnd+  eVR++A  aL
  gi|91774098|ref|YP_566790.1| 143 RAIDPLVQTLNDKYHEVRYYAEEAL 167
                                   5788999999998889999886666 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0031
                       HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLg 53 
                                   +++L+  Lnd++deVR++A  ++ 
  gi|91774098|ref|YP_566790.1| 207 IDPLIEYLNDENDEVREYASKCFY 230
                                   6789999************98876 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 0.00037
                       HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                                   ++aL++ Lnd+s+ V+ +Aa  Lg++
  gi|91774098|ref|YP_566790.1| 238 VDALIQSLNDPSKIVQRNAACSLGKI 263
                                   789************99999999986 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.0081
                       HEAT_EZ  27 peilpaLlalLnddsdeVRaaAag 50 
                                   pe+l  L++ L++++ eVR++A+g
  gi|91774098|ref|YP_566790.1| 266 PEALEGLVQNLKSEKVEVRKNAVG 289
                                   899**********999******98 PP

  == domain 8  score: 5.3 bits;  conditional E-value: 0.027
                       HEAT_EZ  36 lLnddsdeVRaaAagaL 52 
                                   +Lnd++ +VR  Aa aL
  gi|91774098|ref|YP_566790.1| 306 TLNDEDERVRLSAANAL 322
                                   7999999*********9 PP

  == domain 9  score: 11.8 bits;  conditional E-value: 0.00026
                       HEAT_EZ   2 rvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAag 50 
                                   rvR +Aa+aL    +  + ++q++++ ++ aL+      +d +VR++A  
  gi|91774098|ref|YP_566790.1| 313 RVRLSAANAL---YFSDRLYDQQNIDSVIEALA-----NKDvNVRKYATM 354
                                   89********...599*****************.....******777754 PP

  == domain 10  score: 8.8 bits;  conditional E-value: 0.0022
                       HEAT_EZ  34 lalLnddsdeVRaaAagaLgnl 55 
                                   +  L d++ ++R +Aa aLgn+
  gi|91774098|ref|YP_566790.1| 369 IYVLDDEDIRIRNYAAQALGNI 390
                                   444555555***********98 PP

  == domain 11  score: -1.8 bits;  conditional E-value: 4.6
                       HEAT_EZ  43 eVRaaAagaLg 53 
                                   +   a++ aLg
  gi|91774098|ref|YP_566790.1| 412 RLLRATVNALG 422
                                   55556666666 PP

  == domain 12  score: 3.4 bits;  conditional E-value: 0.11
                       HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgnl 55 
                                   +++ L+++L+ ++  V++ A+ aLg +
  gi|91774098|ref|YP_566790.1| 429 VVDSLIKALSIKDMFVKESACLALGEM 455
                                   666677777767778999999999976 PP

  == domain 13  score: 4.1 bits;  conditional E-value: 0.066
                       HEAT_EZ   4 RraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaA 48 
                                   +++A++aLG+   +++       p+ + +L a+Lnd++++V+ aA
  gi|91774098|ref|YP_566790.1| 445 KESACLALGE---MGD-------PKSIEPLKACLNDKHKKVQDAA 479
                                   5566666652...211.......1234455566777777888777 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 ?    2.8   0.0      0.17   1.8e+02      29      56 ..      21      48 ..       8      74 .. 0.83
   2 !    7.9   0.0    0.0044       4.6      29      56 ..      83     110 ..      77     133 .. 0.82
   3 !   12.7   0.1   0.00014      0.14      28      51 ..     144     167 ..     140     195 .. 0.91
   4 !   12.1   0.1   0.00021      0.22      27      68 ..     205     247 ..     186     263 .. 0.82
   5 !   11.2   0.0   0.00041      0.43      29      54 ..     300     325 ..     269     336 .. 0.81
   6 ?    3.9   0.0     0.076        80      26      55 ..     331     360 ..     325     364 .. 0.86
   7 !   13.2   0.0   9.6e-05       0.1      26      59 ..     362     395 ..     340     408 .. 0.77
   8 ?    3.4   0.0      0.11   1.2e+02      29      57 ..     461     489 ..     453     490 .] 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                 Vac14_Fab1_bd 29 vkpvlkcfsDkdsrvRyyacEslyniak 56
                                  +k +l+++s +++++R+ a E++  +a 
  gi|91774098|ref|YP_566790.1| 21 LKGILNALSHSNAEIRFQAEETFDEVAN 48
                                  78899**************999877665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0044
                 Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEslyniak 56 
                                   v+p++++++D+d+ v  ya+Esl n+  
  gi|91774098|ref|YP_566790.1|  83 VEPLIQSLNDEDECVVDYAAESLGNLQD 110
                                   89*********************99863 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00014
                 Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyacEsl 51 
                                    ++p++++++Dk ++vRyya E+l
  gi|91774098|ref|YP_566790.1| 144 AIDPLVQTLNDKYHEVRYYAEEAL 167
                                   589*******************98 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00021
                 Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEslynia.kvakgevlkllne 68 
                                   + ++p++++++D++++vR ya+ ++y +  k++ +++++ ln+
  gi|91774098|ref|YP_566790.1| 205 KSIDPLIEYLNDENDEVREYASKCFYELNdKKSVDALIQSLND 247
                                   5699**********************99636666777777776 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.00041
                 Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEslyni 54 
                                    k+++++++D+d+rvR  a+ +ly  
  gi|91774098|ref|YP_566790.1| 300 TKMIFQTLNDEDERVRLSAANALYFS 325
                                   57899*******************65 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.076
                 Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyacEslynia 55 
                                   ++ +++v++++  kd  vR ya+  l  ia
  gi|91774098|ref|YP_566790.1| 331 QQNIDSVIEALANKDVNVRKYATMGLIEIA 360
                                   667999****************99888876 PP

  == domain 7  score: 13.2 bits;  conditional E-value: 9.6e-05
                 Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyacEslyniakvak 59 
                                   e  +kp++ +++D+d r+R ya+ +l ni   + 
  gi|91774098|ref|YP_566790.1| 362 EMAIKPLIYVLDDEDIRIRNYAAQALGNIGEDSI 395
                                   4569**********************99976655 PP

  == domain 8  score: 3.4 bits;  conditional E-value: 0.11
                 Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEslyniakv 57 
                                   ++p+ +c++Dk ++v   a  sl n+ak+
  gi|91774098|ref|YP_566790.1| 461 IEPLKACLNDKHKKVQDAAKRSLKNLAKI 489
                                   789999********************996 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 ?    0.0   0.1      0.74   7.8e+02      59      90 ..      20      51 ..       6      74 .. 0.73
   2 ?    5.2   0.0     0.019        20      59      93 ..      82     117 ..      75     138 .. 0.79
   3 !   12.9   0.2   8.2e-05     0.087      55      95 ..     202     243 ..     127     247 .. 0.88
   4 ?    4.3   0.1     0.035        37       3      45 ..     253     291 ..     251     322 .. 0.53
   5 !   11.4   0.4   0.00022      0.24      23      88 ..     300     362 ..     283     370 .. 0.87
   6 !    9.8   0.1   0.00074      0.79      22      99 ..     333     404 ..     331     413 .. 0.85
   7 !    9.0   0.1    0.0012       1.3      27      86 ..     434     487 ..     414     490 .] 0.65

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.74
                          Cnd1 59 flselaklleDenprVvanalaalteisekse 90
                                   l+ ++++l+ +n++++  a   + e+++ +e
  gi|91774098|ref|YP_566790.1| 20 DLKGILNALSHSNAEIRFQAEETFDEVANFNE 51
                                  47778888999999999999999999888754 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                          Cnd1  59 flselaklleDenprVvanalaalteisek.senai 93 
                                    ++ l + l+De++ Vv+ a  +l ++++k + +++
  gi|91774098|ref|YP_566790.1|  82 AVEPLIQSLNDEDECVVDYAAESLGNLQDKrAVDPL 117
                                   56778899****************999999433444 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 8.2e-05
                          Cnd1  55 kekgflselaklleDenprVvanalaalteisek.senaiyn 95 
                                   ++++ ++ l + l+Den++V++ a  ++ e+++k s +a+++
  gi|91774098|ref|YP_566790.1| 202 EKSKSIDPLIEYLNDENDEVREYASKCFYELNDKkSVDALIQ 243
                                   5666899999999*****************999954455555 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.035
                          Cnd1   3 RalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivv 45 
                                     +a  +lg i  p+ +e lv++L++    e+  VRk+a+ ++
  gi|91774098|ref|YP_566790.1| 253 QRNAACSLGKIDTPEALEGLVQNLKS----EKVEVRKNAVGGM 291
                                   56666677777777776666665544....6677777776543 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00022
                          Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                   ++ + ++L+Ded+ VR  aa +   L+  d   +++ ++ + ++l +++ +V++ a + l ei+++
  gi|91774098|ref|YP_566790.1| 300 TKMIFQTLNDEDERVRLSAANA---LYFSDRLYDQQNIDSVIEALANKDVNVRKYATMGLIEIADE 362
                                   5667899************976...789999999999**************************986 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00074
                          Cnd1  22 lvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllpd 99 
                                   +++ + ++L  +d  VRk a ++++++ ++  +      + l   l+De+ r+++ a  al +i e s ++++++l d
  gi|91774098|ref|YP_566790.1| 333 NIDSVIEALANKDVNVRKYATMGLIEIADEMAI------KPLIYVLDDEDIRIRNYAAQALGNIGEDSIEPLVQILDD 404
                                   56777889999*************997666555......578999*******************99988888887765 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0012
                          Cnd1  27 rkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteis 86 
                                    k+L+ +d+ V++ a +++ ++ +++       ++ l+ +l+D++++V++ a+ +l++++
  gi|91774098|ref|YP_566790.1| 434 IKALSIKDMFVKESACLALGEMGDPK------SIEPLKACLNDKHKKVQDAAKRSLKNLA 487
                                   44444455555555555555544443......3567788888888888888888887776 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.2   9.7e+03      11      43 ..      25      56 ..      21      63 .. 0.68
   2 !    6.6   0.0    0.0096        10       7      36 ..      83     112 ..      82     125 .. 0.83
   3 !   12.4   0.0   0.00015      0.16       6      52 ..     144     191 ..     142     200 .. 0.80
   4 !    9.4   0.1    0.0012       1.3       7      44 ..     207     243 ..     204     285 .. 0.81
   5 ?    5.3   0.1     0.025        26       7      44 ..     300     339 ..     296     352 .. 0.83
   6 ?    1.4   0.0      0.38     4e+02       6      47 ..     364     406 ..     360     440 .. 0.81
   7 ?    2.2   0.0      0.23   2.4e+02       7      32 ..     461     486 ..     460     490 .] 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.2
                    RasGEF_N_2 11 vnqLydqsrevvaaaleiLeeacddkeslevlv 43
                                  +n L+ ++ e++ +a e ++e+ +  + le+++
  gi|91774098|ref|YP_566790.1| 25 LNALSHSNAEIRFQAEETFDEVANF-NELETFI 56
                                  6777888888888888888887443.3555555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0096
                    RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacddk 36 
                                   +e l+++L+d++++vv+ a+e L +  d++
  gi|91774098|ref|YP_566790.1|  83 VEPLIQSLNDEDECVVDYAAESLGNLQDKR 112
                                   789******************998885544 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00015
                    RasGEF_N_2   6 giellvnqLydqsrevvaaaleiLeeacddkeslevlvelkpsl..qhl 52 
                                   +i+ lv+ L+d+ +ev+  a e+Le++ dd++ +e+l ++++s   +hl
  gi|91774098|ref|YP_566790.1| 144 AIDPLVQTLNDKYHEVRYYAEEALEKF-DDDRATEELNKYHESQipKHL 191
                                   5899***********************.666788888777764325666 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0012
                    RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacddkeslevlve 44 
                                   i+ l++ L+d+++ev++ a ++++e  +dk+s+ +l++
  gi|91774098|ref|YP_566790.1| 207 IDPLIEYLNDENDEVREYASKCFYEL-NDKKSVDALIQ 243
                                   78999********************9.66667777766 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.025
                    RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeea..cddkeslevlve 44 
                                    +++++ L+d+++ v+  a+++L+    ++d++++ +++e
  gi|91774098|ref|YP_566790.1| 300 TKMIFQTLNDEDERVRLSAANALYFSdrLYDQQNIDSVIE 339
                                   58999******************96555777777777776 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.38
                    RasGEF_N_2   6 giellvnqLydqsrevvaaaleiLeeacddk.eslevlvelkp 47 
                                   +i+ l+  L d++  +++ a+++L ++ +d  e l ++++ k+
  gi|91774098|ref|YP_566790.1| 364 AIKPLIYVLDDEDIRIRNYAAQALGNIGEDSiEPLVQILDDKN 406
                                   78999999****************9997776666666665554 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.23
                    RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeea 32 
                                   ie l   L+d+ ++v++aa + L++ 
  gi|91774098|ref|YP_566790.1| 461 IEPLKACLNDKHKKVQDAAKRSLKNL 486
                                   7888899*************999876 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 ?    2.7   0.0      0.11   1.2e+02      94     119 ..      81     106 ..      68     109 .. 0.82
   2 ?    4.2   0.0     0.038        40      82     114 ..     100     132 ..      82     202 .. 0.70
   3 ?    0.5   0.0      0.53   5.6e+02      94     116 ..     205     227 ..     190     232 .. 0.84
   4 ?    1.6   0.1      0.25   2.6e+02      72     118 ..     310     356 ..     293     360 .. 0.72
   5 ?    3.5   0.1     0.065        68      83     120 ..     352     389 ..     335     391 .. 0.78
   6 ?   -0.7   0.0       1.2   1.3e+03      83     108 ..     383     407 ..     380     422 .. 0.73
   7 !    8.3   0.0    0.0021       2.2      68     121 ..     433     486 ..     425     489 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                 Aconitase_B_N  94 ynvksLidllkekdeelaeeaaeaLk 119
                                    +v++Li+ l+++de + + aae L 
  gi|91774098|ref|YP_566790.1|  81 RAVEPLIQSLNDEDECVVDYAAESLG 106
                                   479*******************9996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.038
                 Aconitase_B_N  82 eAvelLgtMlGGynvksLidllkekdeelaeea 114
                                    A e Lg+++   +v++Li++l++k  + +++a
  gi|91774098|ref|YP_566790.1| 100 YAAESLGNLQDKRAVDPLIKVLSHKYWAARSSA 132
                                   566666666666667777777663333333333 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.53
                 Aconitase_B_N  94 ynvksLidllkekdeelaeeaae 116
                                    ++++Li+ l+++++e++e a +
  gi|91774098|ref|YP_566790.1| 205 KSIDPLIEYLNDENDEVREYASK 227
                                   5899*******999999999987 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.25
                 Aconitase_B_N  72 eaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                   e e   +s+++A+ +   +    n++s+i++l +kd ++++ a+  L
  gi|91774098|ref|YP_566790.1| 310 EDERVRLSAANALYFSDRLYDQQNIDSVIEALANKDVNVRKYATMGL 356
                                   44555566666666666666677899999999988888888887665 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.065
                 Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekdeelaeeaaeaLkk 120
                                   A+  L ++   +++k+Li +l+++d ++++ aa+aL +
  gi|91774098|ref|YP_566790.1| 352 ATMGLIEIADEMAIKPLIYVLDDEDIRIRNYAAQALGN 389
                                   5555555566679**********************976 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 1.2
                 Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekde 108
                                   A + Lg+ +G  ++++L+++l++k++
  gi|91774098|ref|YP_566790.1| 383 AAQALGN-IGEDSIEPLVQILDDKNT 407
                                   6677776.48899********94443 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.0021
                 Aconitase_B_N  68 iakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkkt 121
                                   ++k     ++  +e+A   Lg+M    ++++L   l++k+++++++a++ Lk+ 
  gi|91774098|ref|YP_566790.1| 433 LIKALSIKDMFVKESACLALGEMGDPKSIEPLKACLNDKHKKVQDAAKRSLKNL 486
                                   556666667788999************************************985 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.069        73     233     344 ..      21     121 ..      13     125 .. 0.71
   2 ?    4.5   0.1      0.01        11      86     226 ..      88     220 ..      80     235 .. 0.67
   3 !    8.0   0.0   0.00089      0.94      79     134 ..     236     287 ..     223     291 .. 0.74
   4 !   10.9   0.2   0.00011      0.12     117     187 ..     301     365 ..     294     374 .. 0.88
   5 ?    0.7   0.0      0.14   1.5e+02      80      90 ..     429     439 ..     371     475 .. 0.56
   6 ?    0.8   0.0      0.13   1.4e+02      80     134 ..     429     479 ..     425     489 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.069
                                   HHHHCGGCGCSSCHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCCCSXX CS
                     Adaptin_N 233 lesllnllqssnnaVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlkifllk 313
                                   l+ +ln l++sn+ + + + +++ e+a+ nel     + +++ l+s den+r  + r l      +       +  i++l+
  gi|91774098|ref|YP_566790.1|  21 LKGILNALSHSNAEIRFQAEETFDEVANFNEL-----ETFIEALKSDDENIRRFVSRVLGGCDDLR-----AVEPLIQSLN 91 
                                   56788999999999999999999999999994.....66666778888888877766655443333.....4455566777 PP

                                   TTSXHHHHHHHHHHHCCCXXTTTHHHHHHHH CS
                     Adaptin_N 314 tdddvsirlkaldlllklvdesNvkeivkeL 344
                                    d+d+ +  +a + l +l d++ v+ ++k L
  gi|91774098|ref|YP_566790.1|  92 -DEDECVVDYAAESLGNLQDKRAVDPLIKVL 121
                                   .777777777777777777777777666665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                                   HHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSH CS
                     Adaptin_N  86 kDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdp 166
                                   ++l+d ++ ++  A  +L+++ +++ +    + + k+l+++    r++Aal++  + +       +  ++ +++ l+dk +
  gi|91774098|ref|YP_566790.1|  88 QSLNDEDECVVDYAAESLGNLQDKRAV----DPLIKVLSHKYWAARSSAALSLGCIGD----S--RA-IDPLVQTLNDKYH 157
                                   566666777777777777777766544....345566777777777777776554432....2..33.7889999****** PP

                                   HHHHHHHHHHHHHHCCCCCCCHHHHHHH....CCHHHHHHCS-HHHHHHHHHHHCC---SSHHH CS
                     Adaptin_N 167 gvvlaAvalleeikkndrlllkllpklv....rrLcnllteldpwlqvkiiklltrlarqepee 226
                                    v + A  +le+    dr++ +l +++     ++L+n+++ +  + + k i+ l ++ + e +e
  gi|91774098|ref|YP_566790.1| 158 EVRYYAEEALEKF-DDDRATEELNKYHEsqipKHLKNVVNAFRTFEKSKSIDPLIEYLNDENDE 220
                                   ************9.55555556666665111145667778888888888888888888766655 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00089
                                   CCCHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHH CS
                     Adaptin_N  79 LvtnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkA 134
                                    ++++l ++l+dp+++++ +A ++L++i +pe +e l++ +    k+++  vrk+A
  gi|91774098|ref|YP_566790.1| 236 KSVDALIQSLNDPSKIVQRNAACSLGKIDTPEALEGLVQNL----KSEKVEVRKNA 287
                                   57889999999999999999999999999999888777665....45555555555 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00011
                                   HHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHHHCCCCCCC CS
                     Adaptin_N 117 paikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleeikkndrlll 187
                                   + i+++l+d++  vr +Aa a++   +++ ++   + ++ ++e+l+ kd+ v   A++ l ei   d++++
  gi|91774098|ref|YP_566790.1| 301 KMIFQTLNDEDERVRLSAANALYFSDRLYDQQ---N-IDSVIEALANKDVNVRKYATMGLIEI--ADEMAI 365
                                   6799******************9999999998...5.9*************************..666654 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.14
                                   CCHHHHHHCCS CS
                     Adaptin_N  80 vtnslqkDlkd 90 
                                   v++sl k+l+ 
  gi|91774098|ref|YP_566790.1| 429 VVDSLIKALSI 439
                                   22333333333 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.13
                                   CCHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHH CS
                     Adaptin_N  80 vtnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkA 134
                                   v++sl k+l+ ++++++ +A  +L+ +++p+  e     +k++l+d++  v+ +A
  gi|91774098|ref|YP_566790.1| 429 VVDSLIKALSIKDMFVKESACLALGEMGDPKSIE----PLKACLNDKHKKVQDAA 479
                                   5778888888888888888888888888887554....46777777777766555 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00063      0.66      57     151 ..     203     288 ..     184     317 .. 0.80
   2 ?    0.8   0.0      0.16   1.7e+02      58      89 ..     331     362 ..     323     372 .. 0.87
   3 !    6.6   0.1    0.0027       2.8      58      99 ..     362     403 ..     358     404 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00063
                          API5  57 aekaidaqlDLiedddlgirkqAikdLpslckdtkeyvskiadiLaQlLitedaveldavhkallsllkldakasltalfk 137
                                   ++k+id +++ ++d++ ++r  A k   +l        +k +d+L Q L+  +++     ++a  sl k+d+ ++l++l +
  gi|91774098|ref|YP_566790.1| 203 KSKSIDPLIEYLNDENDEVREYASKCFYELND------KKSVDALIQSLNDPSKI---VQRNAACSLGKIDTPEALEGLVQ 274
                                   46789999999999999999999999888854......3569*****99865543...3368999**************** PP

                          API5 138 qieteeetvRekvl 151
                                   ++++e+ +vR+ ++
  gi|91774098|ref|YP_566790.1| 275 NLKSEKVEVRKNAV 288
                                   *****999999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                          API5  58 ekaidaqlDLiedddlgirkqAikdLpslckd 89 
                                   ++ id+ ++ + ++d+++rk A  +L +++ +
  gi|91774098|ref|YP_566790.1| 331 QQNIDSVIEALANKDVNVRKYATMGLIEIADE 362
                                   6889**********************999865 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0027
                          API5  58 ekaidaqlDLiedddlgirkqAikdLpslckdtkeyvskiad 99 
                                   e ai  ++ +++d+d+ ir  A ++L ++ +d+ e + +i d
  gi|91774098|ref|YP_566790.1| 362 EMAIKPLIYVLDDEDIRIRNYAAQALGNIGEDSIEPLVQILD 403
                                   5688889999***********************999988876 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 ?    1.5   0.0       0.4   4.3e+02      22      42 ..      83     103 ..      50     127 .. 0.62
   2 !    9.9   0.0   0.00095         1      19      83 ..     142     204 ..     140     216 .. 0.83
   3 ?    4.2   0.0     0.058        61       9      41 ..     194     226 ..     186     248 .. 0.74
   4 ?   -2.2   0.0       5.7     6e+03      18      67 ..     330     343 ..     297     349 .. 0.63
   5 ?   -1.7   0.0       3.8     4e+03      20      65 ..     393     437 ..     379     440 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHHHHHHHHHHHH CS
                   GlutR_dimer  22 vvptIkalrekaeeireeele 42 
                                   v+p+I++l+++ e +++   e
  gi|91774098|ref|YP_566790.1|  83 VEPLIQSLNDEDECVVDYAAE 103
                                   555555555554444433333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00095
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHHHHHHHHHHHHHSS-TT CS
                   GlutR_dimer  19 slevvptIkalrekaeeireeeleralkklaldgedreelekltrslvnkllheptarLkeaede 83 
                                   s++++p+++ l++k +e+r    e+al+k++ d++  eel+k  +s + k l++ +++ +  e++
  gi|91774098|ref|YP_566790.1| 142 SRAIDPLVQTLNDKYHEVRY-YAEEALEKFD-DDRATEELNKYHESQIPKHLKNVVNAFRTFEKS 204
                                   899**************996.5688999999.9999999*************9999999987333 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.058
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   GlutR_dimer   9 eveefeawlkslevvptIkalrekaeeireeel 41 
                                    v++f +  ks++++p+I  l+++ +e+re   
  gi|91774098|ref|YP_566790.1| 194 VVNAFRTFEKSKSIDPLIEYLNDENDEVREYAS 226
                                   5788999999*****************998654 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 5.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHH CS
                   GlutR_dimer  18 kslevvptIkalrekaeeireeeleralkklaldgedreelekltrslvn 67 
                                   ++++                                    +++++++l n
  gi|91774098|ref|YP_566790.1| 330 DQQN------------------------------------IDSVIEALAN 343
                                   3333....................................3333333333 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 3.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHH CS
                   GlutR_dimer  20 levvptIkalrekaeeireeeleralkklaldgedreelekltrsl 65 
                                    +++p+++ l +k    +++ l+ + + l+   e+ +++++l+++l
  gi|91774098|ref|YP_566790.1| 393 DSIEPLVQILDDKNTFGKKRLLRATVNALG-FIENSKVVDSLIKAL 437
                                   567788888888888888888888888888.666666688877776 PP

>> IFS  Immunity factor for SPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   8.8e-05     0.092      67     157 ..     185     281 ..     181     285 .. 0.82
   2 ?    2.6   0.1      0.12   1.3e+02      85     141 ..     330     384 ..     322     402 .. 0.78
   3 ?   -2.4   0.0       4.2   4.4e+03     107     132 ..     419     442 ..     397     477 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                           IFS  67 tdikerteeiLkelslSkdlvklyqvvsyinsqnllleeyeslpFi.idteelvsniiesiskLsd.ekkrekmkealvge 145
                                   ++i+++ +++   + + ++  +++  ++y+n +n  ++ey s  F+ ++ ++ v  +i+s   L+d  k++++ +   +g+
  gi|91774098|ref|YP_566790.1| 185 SQIPKHLKNVVNAFRTFEKSKSIDPLIEYLNDENDEVREYASKCFYeLNDKKSVDALIQS---LNDpSKIVQRNAACSLGK 262
                                   799999***********************************9999769************...665256778777888888 PP

                           IFS 146 las.......ykdsdlekv 157
                                   +++        ++ + ekv
  gi|91774098|ref|YP_566790.1| 263 IDTpealeglVQNLKSEKV 281
                                   8765555555555555555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                           IFS  85 dlvklyqvvsyinsqnllleeyeslpFiidteelvsniiesiskLsdekkrekmkea 141
                                   d  +++ v++ + +++ ++++y ++  i  ++e+   i+  i+ L+de++r + + a
  gi|91774098|ref|YP_566790.1| 330 DQQNIDSVIEALANKDVNVRKYATMGLIEIADEM--AIKPLIYVLDDEDIRIRNYAA 384
                                   6678999******************987555555..355556669999988666544 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.2
                           IFS 107 eslpFiidteelvsniiesiskLsde 132
                                   ++l F i++ ++v  +i++  +++d 
  gi|91774098|ref|YP_566790.1| 419 NALGF-IENSKVVDSLIKA-LSIKDM 442
                                   44444.6777777777777.344444 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0015       1.6     173     204 ..     197     233 ..     115     240 .. 0.65
   2 ?    0.1   0.0      0.47     5e+02     175     196 ..     297     318 ..     269     352 .. 0.82
   3 ?    1.1   0.0      0.23   2.4e+02     181     205 ..     464     488 ..     456     490 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                       CLASP_N 173 lldlieks.....lkkgleDanptVRetaRstfweff 204
                                    ++++eks     l++ l+D n +VRe a ++f e+ 
  gi|91774098|ref|YP_566790.1| 197 AFRTFEKSksidpLIEYLNDENDEVREYASKCFYELN 233
                                   3444444333344899*****************9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                       CLASP_N 175 dliekslkkgleDanptVReta 196
                                   +l+ k++ + l+D +  VR +a
  gi|91774098|ref|YP_566790.1| 297 KLATKMIFQTLNDEDERVRLSA 318
                                   6788999999999999999766 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.23
                       CLASP_N 181 lkkgleDanptVRetaRstfweffk 205
                                   lk++l+D   +V ++a+  + +++k
  gi|91774098|ref|YP_566790.1| 464 LKACLNDKHKKVQDAAKRSLKNLAK 488
                                   899**************98877766 PP

>> BRCC36_C  BRCC36 C-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.83   8.7e+02      53      66 ..     145     158 ..     130     169 .. 0.81
   2 ?    9.2   0.0    0.0012       1.3      43      71 ..     385     413 ..     379     417 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.83
                      BRCC36_C  53 avPllqtLesrlke 66 
                                     Pl+qtL+++  e
  gi|91774098|ref|YP_566790.1| 145 IDPLVQTLNDKYHE 158
                                   57*******99776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                      BRCC36_C  43 kslcalseviavPllqtLesrlkenknrl 71 
                                   ++l+++ e++  Pl+q L +++   k+rl
  gi|91774098|ref|YP_566790.1| 385 QALGNIGEDSIEPLVQILDDKNTFGKKRL 413
                                   79*******************99988886 PP

>> ParcG  Parkin co-regulated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.011        12      84     172 ..     147     242 ..     142     244 .. 0.67
   2 ?   -2.8   0.0       5.6   5.9e+03      44      86 ..     338     380 ..     329     412 .. 0.65
   3 ?    4.7   0.0     0.028        29      79     108 ..     458     487 ..     426     490 .] 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                         ParcG  84 plkeaLntrdeeviesaLkvlqklvkaseligeaLvpy........yrqlLpvlnlfknkrvnlgdkidy..rkkknikdl 154
                                   pl + Ln + +ev   a ++l+k+   ++   e+L+ y        ++++  ++++f++++ ++   i+y  ++++++++ 
  gi|91774098|ref|YP_566790.1| 147 PLVQTLNDKYHEVRYYAEEALEKF--DDDRATEELNKYhesqipkhLKNVVNAFRTFEKSK-SIDPLIEYlnDENDEVREY 224
                                   666666666666666666666666..45555555554411111111666677777666655.99999***9999999**** PP

                         ParcG 155 iqetlellerngGedali 172
                                    ++   +l+++   dali
  gi|91774098|ref|YP_566790.1| 225 ASKCFYELNDKKSVDALI 242
                                   *********999999998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.6
                         ParcG  44 fdGlretkhpyrflategikdlleaageekilpvlpklilplk 86 
                                   ++ l++++   r  at+g++++ ++ + + +++vl    + ++
  gi|91774098|ref|YP_566790.1| 338 IEALANKDVNVRKYATMGLIEIADEMAIKPLIYVLDDEDIRIR 380
                                   5667777777777788887777777766667766665555454 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.028
                         ParcG  79 pklilplkeaLntrdeeviesaLkvlqklv 108
                                   pk i plk+ Ln ++++v  +a + l++l 
  gi|91774098|ref|YP_566790.1| 458 PKSIEPLKACLNDKHKKVQDAAKRSLKNLA 487
                                   899***************999999998885 PP

>> SicP-binding  SicP binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.2   3.4e+03      34      48 ..      46      60 ..      23      62 .. 0.79
   2 ?    8.1   0.0    0.0025       2.7      30      71 ..     103     145 ..      88     158 .. 0.79
   3 ?   -0.6   0.0       1.3   1.3e+03      22      66 ..     218     264 ..     213     277 .. 0.73
   4 ?   -2.2   0.0         4   4.2e+03      34      50 ..     424     440 ..     423     466 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.2
                                  -S-HHHHHHHHHHHH CS
                  SicP-binding 34 vedrkiLevfllaLs 48
                                  v +   Le+f+ aL 
  gi|91774098|ref|YP_566790.1| 46 VANFNELETFIEALK 60
                                  567778999999995 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0025
                                   HCS.--S-HHHHHHHHHHHHHTTSCHHHHHHHHHHHH-----G CS
                  SicP-binding  30 eqv.rvedrkiLevfllaLskkyGeeavkdaldysairdnkPL 71 
                                   e +  ++d++ ++ +++ Ls+ky      +al ++ i d++ +
  gi|91774098|ref|YP_566790.1| 103 ESLgNLQDKRAVDPLIKVLSHKYWAARSSAALSLGCIGDSRAI 145
                                   554358***************************9998776533 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                                   HHHHHHHHHCS..--S-HHHHHHHHHHHHHTTSCHHHHHHHHHHHH- CS
                  SicP-binding  22 tevvrkyaeqv..rvedrkiLevfllaLskkyGeeavkdaldysair 66 
                                    + vr ya +    ++d+k+++ ++ +L +       ++a  +++i 
  gi|91774098|ref|YP_566790.1| 218 NDEVREYASKCfyELNDKKSVDALIQSLNDPSKIVQRNAACSLGKID 264
                                   57788888886335789999999999998766666666666666665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 4
                                   -S-HHHHHHHHHHHHHT CS
                  SicP-binding  34 vedrkiLevfllaLskk 50 
                                   +e+ k+++ +++aLs k
  gi|91774098|ref|YP_566790.1| 424 IENSKVVDSLIKALSIK 440
                                   68999999999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 3074.25
//
Query:       gi|91774099|ref|YP_566791.1|  [L=93]
Description: hypothetical protein Mbur_2176 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.7   0.8      0.083   13.0   0.1    2.0  2  RAP       RAP domain


Domain annotation for each model (and alignments):
>> RAP  RAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.6e-06     0.083      26      57 ..      38      66 ..      36      67 .. 0.79
   2 ?    1.0   0.1     0.027   4.8e+02      31      39 ..      83      91 ..      55      93 .] 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-06
                           RAP 26 iLsklGykvinIpyfeWnqlknkedkveylkk 57
                                  +L+k+   +i+Ipy +W+++   + +++y k+
  gi|91774099|ref|YP_566791.1| 38 LLRKM---IIDIPYAKWKKMGFSKGTLHYMKQ 66
                                  77888...9***********666667777776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.027
                           RAP 31 GykvinIpy 39
                                  +++v n++y
  gi|91774099|ref|YP_566791.1| 83 DWRVGNVNY 91
                                  588888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 693.57
//
Query:       gi|91774100|ref|YP_566792.1|  [L=1206]
Description: 5-oxoprolinase (ATP-hydrolyzing) [Methanococcoides burtonii DSM 6242]
Scores for complete 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-196  651.8   0.4   1.1e-195  651.0   0.4    1.3  1  Hydantoinase_B  Hydantoinase B/oxoprolinase
   2.2e-116  388.2   0.4   5.9e-116  386.8   0.4    1.8  1  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.9e-65  219.9   0.0    8.7e-64  214.5   0.0    2.6  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
      0.083   11.5   0.3        5.3    5.5   0.0    2.3  2  MutL            MutL protein
       0.13   12.5   0.2        0.4   10.8   0.2    1.8  1  Fib_alpha       Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.0   0.4    3e-199  1.1e-195       1     490 [.     696    1176 ..     696    1194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 651.0 bits;  conditional E-value: 3e-199
                Hydantoinase_B    1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelk 79  
                                    Dpi+levf+nr+msia++mg  lq+ta+S+nikerlDfsca+fd++g+l+a+aphipvhlgsm+e++kav+++++g+++
  gi|91774100|ref|YP_566792.1|  696 DPIMLEVFSNRFMSIAQQMGYSLQNTAYSVNIKERLDFSCAIFDHEGNLIANAPHIPVHLGSMEESIKAVIRNRKGRMN 774 
                                    9*************************************************************************99*** PP

                Hydantoinase_B   80 pGDvlltNdPyaggtHlpDitvitPvfhege.lvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege. 156 
                                    + D++++N+PyaggtHlpDitv++Pvf   + + f+vasr+HhaDiGGi+pGsmpp++++ifeEG++i+ +kl+++g  
  gi|91774100|ref|YP_566792.1|  775 KKDAYMLNSPYAGGTHLPDITVVSPVFCGCDeVQFYVASRGHHADIGGISPGSMPPKSRSIFEEGILIDDIKLMDRGYf 853 
                                    ***************************86557*********************************************** PP

                Hydantoinase_B  157 leedvlelllanv...RtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgty 232 
                                    +e++v+ell +     R+ ++n++Dl+Aq+aan++g+++l++++e+y+l tvea+m++++dnae+avr++++ l+dg  
  gi|91774100|ref|YP_566792.1|  854 RETEVTELLNSGEhpvRNHHQNIADLRAQVAANEKGIQQLEQMVEKYSLPTVEAYMQHVQDNAEEAVRKVIEVLHDG-- 930 
                                    9*******99877888*************************************************************.. PP

                Hydantoinase_B  233 eaedylddgipikvtvtidgde..atvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpe 309 
                                    e+++ ldd+++i+v+++id++e  at+D+tgtspq ++n+Nap++v+++av+yv+r+lv+++iplN+Gcl+p+++++pe
  gi|91774100|ref|YP_566792.1|  931 EFTYKLDDDSHIHVNIKIDKNErsATIDLTGTSPQQENNFNAPASVCKAAVLYVFRTLVKDNIPLNAGCLKPLNIIIPE 1009
                                    77788***9*********999889******************************************************* PP

                Hydantoinase_B  310 gsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGArpgk 388 
                                    g+llnps+paav++gnvetsq +vd++++al+      ++Aasqgtmnn+tfg   +  +e  +yyeti+gG+GA+ g+
  gi|91774100|ref|YP_566792.1| 1010 GCLLNPSHPAAVAAGNVETSQYIVDTLYGALG------IIAASQGTMNNFTFG---N--QEI-QYYETICGGSGAGDGF 1076
                                    ********************************......***************...4..445.**************** PP

                Hydantoinase_B  389 dGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvfapwGlaG 467 
                                    +G++av++hmtn+r+td+E+lE r+Pvl+e++++r++sgG+G+y GG+Gvvr+++fle+ ++++i+s++r+++p+G +G
  gi|91774100|ref|YP_566792.1| 1077 NGTDAVQTHMTNSRMTDPEVLELRFPVLLEEYSIRKESGGEGEYCGGNGVVRKVRFLEE-MKAAIISSHRKYPPFGSNG 1154
                                    **********************************************************7.******************* PP

                Hydantoinase_B  468 GepGargrvvlnllvr..geeenlg 490 
                                    G ++++g+   n+++r  g++ +++
  gi|91774100|ref|YP_566792.1| 1155 GSEAECGK---NMVIRkdGRKDTVA 1176
                                    ********...77776664444433 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.8   0.4  1.6e-119  5.9e-116       1     289 [.     207     498 ..     207     500 .. 0.99

  Alignments for each domain:
  == domain 1  score: 386.8 bits;  conditional E-value: 1.6e-119
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   r+et++v++ylsp+l++y++++ ++l+ +g  + l++mqs+Ggl++a  +++k  + ilSGPa+G+vgaa +s+ ag+k++
  gi|91774100|ref|YP_566792.1| 207 RGETTMVDGYLSPVLKRYVDRIHSALRSNGDDTSLLFMQSNGGLTQATSFKGK--NSILSGPAGGIVGAATVSEVAGFKEI 285
                                   89***************************************************..************************** PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkGgte 162
                                   I fDmGGTstDv++++ ge+e+s+e ei g+ +++p+++i+tv+agGgsil ++e+++++vgp+sag++pgpacyrkGg +
  gi|91774100|ref|YP_566792.1| 286 ISFDMGGTSTDVAHYN-GEYERSFENEIDGIHLYSPMMHIHTVAAGGGSIL-HYENERFQVGPDSAGSEPGPACYRKGG-P 363
                                   ****************.**********************************.***************************.* PP

                Hydantoinase_A 163 ltvTDanlvLGrlqpedfls..gpdgdqkldvelarrafeelakelnlk......veevAegilsvavenmanavrklsve 235
                                   ltvTD+n++L ++ pe+f++  g +g  +ld  +++++fee+a +++++      +eevAeg+l+vavenm na++k+s +
  gi|91774100|ref|YP_566792.1| 364 LTVTDCNVMLSKVIPEYFPQvfGESGTLPLDTGTVHAKFEEIASKVSEGsgksisPEEVAEGFLTVAVENMGNAIKKISTQ 444
                                   ***********************************************99******************************** PP

                Hydantoinase_A 236 rgldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvre 289
                                   rg+d k +tl++fGGaGaqha  +a++lg++k++++pyagvlsa+Gm+lAd+r 
  gi|91774100|ref|YP_566792.1| 445 RGYDLKSYTLCCFGGAGAQHAGLVADSLGMSKIFIHPYAGVLSAYGMGLADQRM 498
                                   ***************************************************996 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 !  214.5   0.0   2.4e-67   8.7e-64       2     178 .]       9     188 ..       8     188 .. 0.99
   2 ?    2.5   0.0     0.028     1e+02       3      18 ..     287     302 ..     285     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 214.5 bits;  conditional E-value: 2.4e-67
                    Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllst.....pdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                   ++ID+GGTfTD++  +++ ++++++Klls+     +dav+egir++l+  ++e+ p t++i+ ++mGTTv tNallerkge
  gi|91774100|ref|YP_566792.1|   9 FWIDRGGTFTDVIGRSPD-GTIVTHKLLSEnpehyEDAVIEGIRQMLDLGADEQLP-TREIECIKMGTTVGTNALLERKGE 87 
                                   8***************98.9*********************************999.************************ PP

                    Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvll 158
                                   + aL++tkgfrd+l+ig+qnrpd+f+l ik p+vly++v+e++er++ +ge+l pl+e+++r++lk+l+++g+ s+av+l+
  gi|91774100|ref|YP_566792.1|  88 KFALVVTKGFRDALRIGYQNRPDIFALDIKLPEVLYKTVIEAEERYSSRGEELIPLNEDKLRRNLKELHDSGIYSLAVALM 168
                                   ********************************************************************************* PP

                    Hydant_A_N 159 hSylnpehElrvaeiareig 178
                                   hSy++pehE+++++ia+eig
  gi|91774100|ref|YP_566792.1| 169 HSYRYPEHEIAIERIAKEIG 188
                                   *****************986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.028
                    Hydant_A_N   3 gIDvGGTfTDavalde 18 
                                     D+GGT TD+  +++
  gi|91774100|ref|YP_566792.1| 287 SFDMGGTSTDVAHYNG 302
                                   56********988775 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0015       5.3     221     264 ..     259     300 ..     243     316 .. 0.75
   2 ?    3.6   0.1    0.0056        20     197     244 ..     874     921 ..     865     928 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0015
                          MutL 221 saeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsv 264
                                   ++ i   Pa  + ++ +++e   +g+ +++ +D+GG++Tdv  +
  gi|91774100|ref|YP_566792.1| 259 KNSILSGPAGGIVGAATVSE--VAGFKEIISFDMGGTSTDVAHY 300
                                   45677778888888888888..55678**************987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0056
                          MutL 197 kaIrevFlehivkakglskleelvsaeimpTPaAvlkavellaeeeek 244
                                   + I ++ ++   + kg+++le++v++   pT +A ++ v+  aee  +
  gi|91774100|ref|YP_566792.1| 874 QNIADLRAQVAANEKGIQQLEQMVEKYSLPTVEAYMQHVQDNAEEAVR 921
                                   56666665555599************************9988885544 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 ?   10.8   0.2   0.00011       0.4      94     126 ..     866     898 ..     855     901 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                   HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  94 ketidaqesnirvLqnvlesneqkiqkLeqdid 126
                                   ++ + ++ +ni  L+  + +ne+ iq+Leq ++
  gi|91774100|ref|YP_566792.1| 866 EHPVRNHHQNIADLRAQVAANEKGIQQLEQMVE 898
                                   567999************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.96u 0.27s 00:00:01.23 Elapsed: 00:00:00.47
# Mc/sec: 7639.96
//
Query:       gi|91774101|ref|YP_566793.1|  [L=166]
Description: phosphoesterase, PA-phosphatase related [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-16   57.9  12.1    3.3e-15   56.0  12.1    1.9  1  PAP2      PAP2 superfamily
    5.6e-08   32.7   9.4    5.6e-08   32.7   9.4    2.0  2  PAP2_3    PAP2 superfamily
     0.0048   17.0   4.8      0.092   12.9   1.7    2.3  2  DUF212    Divergent PAP2 family
  ------ inclusion threshold ------
       0.32   11.6  12.9       0.07   13.7   3.7    2.3  2  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0  12.1   7.4e-19   3.3e-15       2     130 ..      52     157 ..      51     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 7.4e-19
                          PAP2   2 llalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkki 82 
                                   +l+++ ++++ +  + ++K+ +  pRP+ +    ++++               s+PS Hs++afa a++l+++  +  +  
  gi|91774101|ref|YP_566793.1|  52 VLYYCSMMLFLVGAVALIKSQLMVPRPEDVRFVVESSGY--------------SMPSAHSTAAFATAMFLHHVAIKYGIL- 117
                                   678999999999999999999999999888777777776..............9*******************9999999. PP

                          PAP2  83 glvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrl 130
                                           ++  a+ +alsR+++gvH++sDv+aG+++Gi++++l  ++
  gi|91774101|ref|YP_566793.1| 118 --------IWSGAIAMALSRVFAGVHYPSDVMAGVVLGIMIGYLWLQI 157
                                   ........9**********************************98776 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.9    0.0056        25      10      81 ..       6      76 ..       4      79 .. 0.82
   2 !   32.7   9.4   1.3e-11   5.6e-08     120     189 ..      85     152 ..      78     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0056
                        PAP2_3 10 lgldweaalnklllahpalavilalaYaslhfqvtllvlvllflrrrerlreflttlllatllgllvyalfP 81
                                  l  ++ ++ln   ++   + v+l++a + ++++++ ++l+l  +++   ++  + ++l+  +  + + +++P
  gi|91774101|ref|YP_566793.1|  6 LDVQILHILN-SYAGFDPIVVFLSVAGDDILWILIAAILFLSTSKEKVLYYCSMMLFLVGAVALIKSQLMVP 76
                                  6677778888.8888889999999999999999999999999999999999999999988887776666666 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.3e-11
                        PAP2_3 120 ienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalvaia 189
                                   +e++ +++PS H + a+ +a++l +++ k   ++l++  +++m+++ v  g HY  Dv+aGv+l++++ +
  gi|91774101|ref|YP_566793.1|  85 VESSGYSMPSAHSTAAFATAMFLHHVAIKY--GILIWSGAIAMALSRVFAGVHYPSDVMAGVVLGIMIGY 152
                                   5667789***************77777777..********************************998755 PP

>> DUF212  Divergent PAP2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.7   2.1e-05     0.092      18      76 ..      66     129 ..      48     134 .. 0.66
   2 !    5.3   0.1    0.0046        21     113     128 .]     135     150 ..     131     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                        DUF212  18 llKvliellkekkldlkllvstGg..mPSsHsalvtalata...vgleegldsslfalalvfal 76 
                                   +  +  +l++ +  d++ +v++ g  mPS+Hs++  a+a+    v++++g+     a+a++++ 
  gi|91774101|ref|YP_566793.1|  66 VALIKSQLMVPRPEDVRFVVESSGysMPSAHSTAAFATAMFlhhVAIKYGILIWSGAIAMALSR 129
                                   333344566777777888888876669*****99888877644578899988777777776664 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0046
                        DUF212 113 HtpleVlvGallGiiv 128
                                   H p +V++G++lGi++
  gi|91774101|ref|YP_566793.1| 135 HYPSDVMAGVVLGIMI 150
                                   99***********986 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.8     0.034   1.5e+02      14      50 ..      37      71 ..      34      73 .. 0.77
   2 ?   13.7   3.7   1.6e-05      0.07       7      69 ..      93     151 ..      89     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.034
                        PAP2_C 14 ltlavlfileyspkklailkvillllallglfliias 50
                                  +++a++++l++s++k+  l +++++l l+g + +i s
  gi|91774101|ref|YP_566793.1| 37 ILIAAILFLSTSKEKV--LYYCSMMLFLVGAVALIKS 71
                                  5566777777777777..9999999999999988865 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.6e-05
                        PAP2_C   7 fSGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvf 69 
                                    S H+++ + +++f+++++ k      ++++  a+   ++ + +  HY  DV+ g+++ +++ 
  gi|91774101|ref|YP_566793.1|  93 PSAHSTAAFATAMFLHHVAIKY----GILIWSGAIAMALSRVFAGVHYPSDVMAGVVLGIMIG 151
                                   5899999999999988887765....6999999*************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); 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:                         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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1146.89
//
Query:       gi|91774102|ref|YP_566794.1|  [L=462]
Description: amidophosphoribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-24   86.3   0.0    2.4e-24   85.6   0.0    1.4  1  GATase_7      Glutamine amidotransferase domain
    1.3e-22   80.4   0.0    2.3e-22   79.6   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    6.7e-07   28.5   0.0    1.1e-06   27.8   0.0    1.2  1  GATase_4      Glutamine amidotransferases class-II
    1.8e-06   27.6   0.0    3.1e-06   26.8   0.0    1.3  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 !   85.6   0.0   5.3e-28   2.4e-24      12     121 ..      93     208 ..      80     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 5.3e-28
                      GATase_7  12 gaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmfAfaiw 83 
                                   + QP++   ++g+l+i++nG ++N +elr+eLe++g  f t+sDtev+++ll +        e ++e++++l+G++++ai+
  gi|91774102|ref|YP_566794.1|  93 NCQPLMVnYKNGNLAIAHNGNLVNGQELRDELESEGRIFITSSDTEVIAHLLVKallihdplESIKEVMSMLKGSYSLAIM 173
                                   6799877689*****************************************9999************************** PP

                      GATase_7  84 deeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                    +++  l+++RD+lG+kPL +ge +g ++++aSe  a+
  gi|91774102|ref|YP_566794.1| 174 IDDR--LFAVRDPLGFKPLCVGEIDG-GYVVASESVAI 208
                                   9999..******************85.*******9987 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   5.2e-26   2.3e-22      10     134 .]      72     204 ..      64     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 5.2e-26
                      GATase_6  10 vedevalaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall...... 81 
                                    e++++++HvR +++g + +  + qP+    ++g+l+++hNG   n +elr+el++ +g+ f + sDtev+++ll      
  gi|91774102|ref|YP_566794.1|  72 LEGRLGVGHVRYSTTGDS-NIVNcQPLmvNYKNGNLAIAHNGNLVNGQELRDELES-EGRIFITSSDTEVIAHLLvkalli 150
                                   47889************9.77777***88889999*********************.****************88776665 PP

                      GATase_6  82 .eelG....eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                    +  +    +ev++ l+G ++ ai+    ++l+ +rd lg kpl++++ ++g ++ase
  gi|91774102|ref|YP_566794.1| 151 hD--PlesiKEVMSMLKGSYSLAIMI--DDRLFAVRDPLGFKPLCVGEIDGGYVVASE 204
                                   42..15688*********99999875..899**************************8 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.4e-10   1.1e-06      69     158 ..      72     163 ..      67     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.4e-10
                      GATase_4  69 iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdl...keykpkl.egrfePvGsTDsElafCelleelasrf 145
                                   ++ ++ v H+R  t+G+ +  n++p + ++++ +  +AHnG+l   +e++++l ++    + s D+E++   l+++l  + 
  gi|91774102|ref|YP_566794.1|  72 LEGRLGVGHVRYSTTGDSNIVNCQPLMVNYKNGNLAIAHNGNLvngQELRDELeSEGRIFITSSDTEVIAHLLVKALLIHD 152
                                   56778899***********************************53333667775444456889999998888888776655 PP

                      GATase_4 146 ekaepsaeelera 158
                                   +   +s++e++++
  gi|91774102|ref|YP_566794.1| 153 P--LESIKEVMSM 163
                                   3..4555555555 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   6.9e-10   3.1e-06      66     119 ..     292     380 ..     271     383 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 6.9e-10
                                   TT--EE...........................................EE----TTSEEEEE-SEESSSHHHHHHHHHHH CS
                  Pribosyltran  66 dgseeaargssdes...................................rlledpagkkVliVDDildtGgTllaalelLk 111
                                   d++ + a+g sdes                                   + +e+++++kV+i DD +  G+T ++++e ++
  gi|91774102|ref|YP_566794.1| 292 DSGITSAIGYSDESginyreglmknryigrtfilpgqemretavrlkmnTISENLRDRKVIILDDSIVRGTTSRRIIEMVR 372
                                   555555566666666666666666666666666666666777777778889****************************** PP

                                   CC-BSEEE CS
                  Pribosyltran 112 ekgpeevr 119
                                   ++g++ev+
  gi|91774102|ref|YP_566794.1| 373 NAGAKEVH 380
                                   ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3336.06
//
Query:       gi|91774103|ref|YP_566795.1|  [L=56]
Description: 50S ribosomal protein L37e [Methanococcoides burtonii DSM 6242]
Scores for complete 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   75.4  13.9    3.1e-21   75.3  13.9    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
       0.26   10.9   1.3       0.36   10.4   1.3    1.2  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
       0.41   10.2   0.2       0.41   10.2   0.2    2.6  3  zn-ribbon_14    Zinc-ribbon
       0.43   10.6   6.1       0.36   10.8   0.6    2.3  2  YhfH            YhfH-like protein
        6.4    4.6   7.1        6.5    4.5   7.1    1.0  1  Med16           Mediator complex subunit 16


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 !   75.3  13.9   8.6e-25   3.1e-21       1      54 []       2      55 ..       2      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 8.6e-25
                Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKak 54
                                  +kGt+s+Gkr +k+tH +CrrCg+ s ++++k+C scG+ +++++r+y+W++K k
  gi|91774103|ref|YP_566795.1|  2 SKGTPSMGKR-QKRTHAKCRRCGSVSLNIHTKQCTSCGFgRTSRMRSYQWQRKCK 55
                                  69********.555**************************************975 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|91774103|ref|YP_566795.1| 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 ?   10.2   0.2   0.00011      0.41       2      11 ..      18      27 ..      17      30 .. 0.87
   2 ?    4.1   0.9     0.009        32       2       8 ..      33      39 ..      32      41 .. 0.88
   3 ?   -4.0   0.2       3.1   1.1e+04       2       3 ..      53      54 ..      52      55 .. 0.42

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                  zn-ribbon_14  2 kCerCGylSS 11
                                  kC+rCG +S 
  gi|91774103|ref|YP_566795.1| 18 KCRRCGSVSL 27
                                  8*******95 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.009
                  zn-ribbon_14  2 kCerCGy 8 
                                  +C+ CG+
  gi|91774103|ref|YP_566795.1| 33 QCTSCGF 39
                                  8*****7 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.1
                  zn-ribbon_14  2 kC 3 
                                  kC
  gi|91774103|ref|YP_566795.1| 53 KC 54
                                  34 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4     0.018        65      15      21 ..      18      24 ..      13      28 .. 0.84
   2 ?   10.8   0.6    0.0001      0.36      10      20 ..      28      38 ..      24      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.018
                          YhfH 15 kCteCGk 21
                                  kC  CG+
  gi|91774103|ref|YP_566795.1| 18 KCRRCGS 24
                                  7999997 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0001
                          YhfH 10 nLPkKkCteCG 20
                                  n+ +K+Ct+CG
  gi|91774103|ref|YP_566795.1| 28 NIHTKQCTSCG 38
                                  7889******* PP

>> Med16  Mediator complex subunit 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   7.1    0.0018       6.5     707     750 ..       7      54 ..       2      55 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0018
                         Med16 707 qlakkkkql.RrCtRCgavslvgdplvrkatavkal.....wtmvflrtC 750
                                   +++k++k    +C RCg+vsl+ +   ++ t+             ++r+C
  gi|91774103|ref|YP_566795.1|   7 SMGKRQKRThAKCRRCGSVSLNIHT--KQCTSCGFGrtsrmRSYQWQRKC 54 
                                   55666666668**********9994..55444321112233666777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 372.34
//
Query:       gi|91774104|ref|YP_566796.1|  [L=72]
Description: small nuclear ribonucleoprotein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-22   78.2   0.4    2.9e-22   78.1   0.4    1.0  1  LSM       LSM domain
     0.0065   16.6   0.0     0.0073   16.4   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 !   78.1   0.4   3.3e-26   2.9e-22       3      67 .]       9      72 .]       7      72 .] 0.97

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 3.3e-26
                                  HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                           LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                  l++ +n  v+v+lk+ re+rG+L+g+D +mNlvL+++ee ++++  +rk+g v+iRG+n+v++s+
  gi|91774104|ref|YP_566796.1|  9 LNDALNTSVIVRLKGAREFRGVLQGYDVHMNLVLDEAEELKDGE-IVRKIGGVVIRGDNVVYVSP 72
                                  8899*************************************999.******************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 !   16.4   0.0   8.2e-07    0.0073      15      51 ..      16      50 ..       6      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.2e-07
                                  EEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                        SM-ATX 15 evevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                  +v v++k    ++G+++++++   +++vL+ a ++k+
  gi|91774104|ref|YP_566796.1| 16 SVIVRLKGAREFRGVLQGYDV--HMNLVLDEAEELKD 50
                                  799******************..***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 515.15
//
Query:       gi|91774105|ref|YP_566797.1|  [L=456]
Description: phosphomethylpyrimidine kinase [Methanococcoides burtonii DSM 6242]
Scores for 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-80  267.6   2.1    1.2e-79  267.1   2.1    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    2.4e-62  209.4   1.0    5.8e-62  208.2   1.0    1.6  1  ThiP_synth    Thiamine-phosphate synthase
    2.6e-10   40.1   0.6    4.2e-10   39.4   0.6    1.2  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 !  267.1   2.1   2.1e-83   1.2e-79       1     246 []      24     265 ..      24     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 267.1 bits;  conditional E-value: 2.1e-83
                                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHH CS
                  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaek 81 
                                   Ds+GGAGi+AD+kt+++l v+g+++it++t qnt+gv++ ++lp+++v++q++av++d++v+ +K+Gml+sa+i+++va+ 
  gi|91774105|ref|YP_566797.1|  24 DSGGGAGIEADIKTLASLYVHGACAITSVTSQNTTGVQSAYELPPTVVSDQMDAVCTDMDVRWAKTGMLSSANIVRAVADR 104
                                   9******************************************************************************** PP

                                   HHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEE CS
                  Phos_pyr_kin  82 lkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlik 162
                                   +kky+++vV+DPVm+a+ g +lle++av+ lk+eLlp++  +tPN+ Eae L+g++i+t ed+ eaak++++lg +aV+i+
  gi|91774105|ref|YP_566797.1| 105 VKKYGLKVVVDPVMAAEAGGDLLEKDAVSILKDELLPISYAVTPNISEAEILSGMSITTREDAMEAAKAIASLGLNAVIIT 185
                                   ********************************************************************************* PP

                                   EGGS-SSSEEEEEEEE..TSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSS CS
                  Phos_pyr_kin 163 Gghlegeeavvtdvly..dgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgkg 241
                                   Ggh    + v  d++y   ++e++e++++ ie   thG+GCt+s+a++++la+g+sl++A   Ake+v++ i  + ++gkg
  gi|91774105|ref|YP_566797.1| 186 GGHS---DGV--DLVYdsVTDEFTEVSGKLIE-GGTHGSGCTYSAALTSYLARGYSLQDAAIGAKEFVESGILLSKNIGKG 260
                                   ***5...555..99997667899*********.************************************************ PP

                                   S-B-- CS
                  Phos_pyr_kin 242 agpvn 246
                                   +gpvn
  gi|91774105|ref|YP_566797.1| 261 VGPVN 265
                                   ***97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   1.0   9.8e-66   5.8e-62       4     163 ..     285     444 ..     283     446 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 9.8e-66
                                   HHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT--EE CS
                    ThiP_synth   4 ralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpevraa 84 
                                   +a+++le++ +fa l+ evg+Nia+a+p+A +++Dvaav+GRIv+ +g++kvvg++++gasshvar++laam+fd+++ra 
  gi|91774105|ref|YP_566797.1| 285 EAVRMLEDDVNFASLVAEVGCNIAMAIPHAMEVKDVAAVNGRIVKLQGKPKVVGCVSLGASSHVARIVLAAMEFDSNMRAS 365
                                   79******************************************************************************* PP

                                   EEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESSHHHHHHHH CS
                    ThiP_synth  85 inirydekilealeelglkvvefdreeepeevgstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkdaeevvekv 163
                                   +ni+y++++l+++e++gl++++f+r+eepe+  +tm+wgv  ai+++ +vp +iydeGgvGkEpm++vlg+da+ev+  +
  gi|91774105|ref|YP_566797.1| 366 VNISYSKNVLAICEDMGLSISSFSRQEEPED-THTMDWGVTYAIDSYgRVPVIIYDEGGVGKEPMVRVLGRDAVEVAGIA 444
                                   *******************************.7**************99***************************9876 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.6     7e-14   4.2e-10     178     279 ..     137     240 ..      95     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 7e-14
                                   HHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEG.GGEEEEEE...TTEEEEEEE.SSSS-SBG CS
                          PfkB 178 lellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlG.keGalvve...kdgelkvpavpkvkvvDt 254
                                   +ell+ + +++pn +E+e+l+g+++++ e+a++a++++ + g + v++t G ++G+ +v    +d+  +v+   k     t
  gi|91774105|ref|YP_566797.1| 137 DELLPISYAVTPNISEAEILSGMSITTREDAMEAAKAIASLGLNAVIITGGhSDGVDLVYdsvTDEFTEVSG--KLIEGGT 215
                                   5899***********************************99**********779******544444444444..444567* PP

                                   TTHHHHHHHHHHHHHHTTHHHHHHH CS
                          PfkB 255 tGAGDsfvggflaallegksleeal 279
                                    G G ++ +++++ l++g sl++a+
  gi|91774105|ref|YP_566797.1| 216 HGSGCTYSAALTSYLARGYSLQDAA 240
                                   **********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3398.40
//
Query:       gi|91774106|ref|YP_566798.1|  [L=176]
Description: hypothetical protein Mbur_2183 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   93.5   0.7    2.2e-25   89.8   0.7    2.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.7   1.2e-29   2.2e-25       2     141 .]       6     176 .]       5     176 .] 0.94

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.2e-29
                                   -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH............ CS
                           Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada............ 70 
                                   yk+Il+a+Dgs +++kA+  +l+ a + ga + +l+vi+  + g ++++       + e +++e    +            
  gi|91774106|ref|YP_566798.1|   6 YKTILIATDGSVNAEKAVMSGLKIASSCGASVLALYVIEINSVGITPESVHRDNLTAMEVAATEHMTSEqwrefarvader 86 
                                   9******************************************99999888877777777776554444899********* PP

                                   ...................HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHH CS
                           Usp  71 ...................akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrh 132
                                                       k++ ++  ++v++++eeg+pa +il +a++e++d++V+G+ g+++   + lGSv+++v+r+
  gi|91774106|ref|YP_566798.1|  87 wkterhkllmekgeritayVKDMGKPLNIDVRTIIEEGHPAATILNTAKKENVDMVVIGTLGMTADGTFKLGSVADKVIRN 167
                                   **************************************************************999999************* PP

                                   TSSEEEEEE CS
                           Usp 133 apcpVlvVr 141
                                   +p+ Vl+Vr
  gi|91774106|ref|YP_566798.1| 168 SPVEVLAVR 176
                                   ********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1279.90
//
Query:       gi|91774107|ref|YP_566799.1|  [L=865]
Description: valyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-129  433.3   7.2   1.9e-128  429.4   7.2    2.0  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.9e-39  135.0   0.0    3.4e-39  134.2   0.0    1.3  1  Anticodon_1    Anticodon-binding domain of tRNA
      2e-22   79.5   2.6    2.1e-11   43.2   0.0    3.4  3  tRNA-synt_1g   tRNA synthetases class I (M)
    8.7e-07   28.6   0.0    0.00025   20.5   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    0.00027   20.5   0.0      0.017   14.6   0.0    2.4  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
     0.0075   15.2   0.1       0.53    9.1   0.0    2.5  2  tRNA-synt_1f   tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.028   14.6   1.1        4.2    7.6   0.2    2.8  2  DUF4451        Domain of unknown function (DUF4451)


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 !  429.4   7.2  7.3e-132  1.9e-128       2     600 ..      16     556 ..      12     558 .. 0.93

  Alignments for each domain:
  == domain 1  score: 429.4 bits;  conditional E-value: 7.3e-132
                   tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvek 82 
                                   +++ W+ +  ++    k+++++++i+  +PPy tG+ HiG++l+    d+v rykrm+G++v +  GwD++Gl++e kve+
  gi|91774107|ref|YP_566799.1|  16 WQNDWDMSM-YHFD-WKDESRPQYIIDTPPPYPTGNFHIGNSLNWCYIDFVARYKRMQGFNVMFPQGWDCHGLPTEVKVEE 94 
                                   556666554.4444.357779************************************************************ PP

                   tRNA-synt_1  83 klgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklv 163
                                   + g++++    ++ r+efr+ + e     ++++rk+++rlG s+D+++e +T+++e+   ++  fv++ d + +y+++++v
  gi|91774107|ref|YP_566799.1|  95 NHGITKN----QVPRTEFRQMCEELTVGNIDKMRKTMHRLGFSTDWSNEFVTMEPEYYVKTQTSFVKMKDMDRVYQSEHPV 171
                                   *999986....99******************************************************************** PP

                   tRNA-synt_1 164 nwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallkslv 244
                                   nw+++++ta++ +Evey   +  l +++f+       kl+iaTT+Pe l + +a+a+ pe                     
  gi|91774107|ref|YP_566799.1| 172 NWCPRCETAIAFAEVEYDSRDTKLNFLHFD-------KLEIATTRPELLAACVAIAISPE--------------------- 224
                                   *****************9999999999985.......699********************..................... PP

                   tRNA-synt_1 245 kkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedgtlte 325
                                             der+k+ +g++++ pl + ++ +iad+ vd  +GtG+V i    d++D +   ++nl++   +d++g +te
  gi|91774107|ref|YP_566799.1| 225 ----------DERYKQYIGQTMKVPLFGHDVEVIADKDVDPTFGTGAVMICTFGDKQDVRWWLEHNLPLRKGIDKSGIITE 295
                                   ..........9********************************************************************** PP

                   tRNA-synt_1 326 eaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkske 406
                                    a++++g+++ +++ +++++lk +g+l ++++ + +v++c+r k+pi+  + +qWfv++++  d++l++ +++++ p+  +
  gi|91774107|ref|YP_566799.1| 296 IAGKYAGMTIPECKAAIIKDLKSEGNLYEQNTLKQNVGMCWRCKTPIEILSEKQWFVKIDN--DEILRTADEIEWLPEYMK 374
                                   ************************************************************6..9***************** PP

                   tRNA-synt_1 407 kryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekdedv 486
                                    r ++w + ++ dWciSRqr+  ++ip+++ k+ +ev+v    +e+       +      +++     k++ +++e +edv
  gi|91774107|ref|YP_566799.1| 375 VRLQNWTNTMEwDWCISRQRIFATPIPVWYCKKCGEVMV--AEEEWLP--IDPT------QQQPPVACKCGCEDFEPEEDV 445
                                   *******99866**************************9..2233333..2222......222333457899********* PP

                   tRNA-synt_1 487 lDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKs 567
                                   lD+W +S+ +   + g+ +   +e++   p+++  +G Diir W   +il s+altg++P++++lv+g+v+ e+G+KmSKs
  gi|91774107|ref|YP_566799.1| 446 LDTWMDSSITALHVAGWLSD--KEMR--NPTQLRPQGHDIIRTWSFYSILRSMALTGKKPWESILVNGMVLGEDGHKMSKS 522
                                   ****************9877..6776..9**************************************************** PP

                   tRNA-synt_1 568 lgNvidpldvikkygadalRltli.lsdvgrdin 600
                                   lgNvi+p++vik ++ada R + +   ++g+d+ 
  gi|91774107|ref|YP_566799.1| 523 LGNVISPEEVIKDHSADAFRQWAAvGGSTGSDVM 556
                                   *********************9997888888876 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 !  134.2   0.0   1.3e-42   3.4e-39       1     150 [.     602     746 ..     602     749 .. 0.92

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 1.3e-42
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   d+w+ls ln+l+++vt++++ y+f++a++++  f w++l+d+y+elvk+rly+e++e +r+aq++l+ +++ l+r+laPf+
  gi|91774107|ref|YP_566799.1| 602 DKWLLSNLNRLISSVTASLDAYQFDEAYKSIRGFAWETLADNYIELVKSRLYGEDKEARRSAQYTLYVAIDGLSRMLAPFA 682
                                   9****************************************************99866655******************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                   Pf++Ee++     ++ +++si+++ewp  +++  ++++ e++ el+k+i   ir+++se +++ +++l++
  gi|91774107|ref|YP_566799.1| 683 PFFAEEMYS----RI-GERSIHVQEWPVvDKTLIDEAI-EKDGELIKDIAGSIRRYKSESGMALNAPLEK 746
                                   ********4....43.4578*******97776668888.9*************************99765 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 !   43.2   0.0   8.4e-15   2.1e-11       2     130 ..      38     181 ..      37     220 .. 0.67
   2 !    6.1   0.8    0.0015       3.9     133     238 ..     299     401 ..     294     412 .. 0.78
   3 !   27.7   0.0   4.3e-10   1.1e-06     290     373 ..     479     564 ..     460     567 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.4e-15
                                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-HHHH........HHHHH.. CS
                  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvtpeel........vekvh.. 71 
                                   ++ t+ pY++g+ H+G+ l+    D +aRykr++g +v+f  g D hG p+e+k e+ +g+t +++        +e+ +  
  gi|91774107|ref|YP_566799.1|  38 IIDTPPPYPTGNFHIGNSLNWCYIDFVARYKRMQGFNVMFPQGWDCHGLPTEVKVEEnHGITKNQVprtefrqmCEELTvg 118
                                   789999************************************************986257776655100000003332211 PP

                                   ..HHHHHHHHHTT---SEEEE..TTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE CS
                  tRNA-synt_1g  72 ..eeikelfkklnisfdkygr..ttseehkelvqeifkklkekgliyekeieqlycpkderfl 130
                                     +++++++++l+ s d  ++  t + e +  +q  f k+k+ + +y++e  + +cp++e+ +
  gi|91774107|ref|YP_566799.1| 119 niDKMRKTMHRLGFSTDWSNEfvTMEPEYYVKTQTSFVKMKDMDRVYQSEHPVNWCPRCETAI 181
                                   113344444444444442221114444555555555555555555555555555555555544 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0015
                                   GG-EE........-TTS-EE-TTSSB-E..................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHH CS
                  tRNA-synt_1g 133 ryvegtCPkckseeargdqceecgkkleptelinpk..saisgskpevketehlffklskfekklkewieeeekeleenvk 211
                                   +y  +t P+ck   a  +  ++ g+ +e ++l++ +  +  +++  e+ +++++f k+++  +++ +    e + l+e +k
  gi|91774107|ref|YP_566799.1| 299 KYAGMTIPECK--AAIIKDLKSEGNLYEQNTLKQNVgmCWRCKTPIEILSEKQWFVKIDN--DEILRTA-DEIEWLPEYMK 374
                                   56678889999..566677788999***9999987533888999999999*******986..4454444.33334788889 PP

                                   HHH.HHHHT----EE-ESS-SSS-EET CS
                  tRNA-synt_1g 212 kivkewlkegLkdlaisrdldwGipvP 238
                                     +++w ++   d++isr+  ++ p+P
  gi|91774107|ref|YP_566799.1| 375 VRLQNWTNTMEWDWCISRQRIFATPIP 401
                                   9999****9889*************99 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 4.3e-10
                                   GGGHHHHHTHHHHHHHH.TT----S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-H CS
                  tRNA-synt_1g 290 kdiikFHtifwPaillg.aelklpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfsw 368
                                    dii+  + +     ++ ++ k  +++ +++++   +g+K+SkS g+v+ ++e+++  +ad++R + a+ +++ +D+ f+w
  gi|91774107|ref|YP_566799.1| 479 HDIIRTWSFYSILRSMAlTGKKPWESILVNGMVLgEDGHKMSKSLGNVISPEEVIKDHSADAFRQWAAVGGSTGSDVMFRW 559
                                   555554443333333333444555788888887615689****************************************** PP

                                   HHHHH CS
                  tRNA-synt_1g 369 edfve 373
                                   +d+v 
  gi|91774107|ref|YP_566799.1| 560 KDVVS 564
                                   **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 !    5.6   0.0    0.0034       8.8      22      52 ..      49      79 ..      45     165 .. 0.87
   2 !   20.5   0.0   9.8e-08   0.00025     226     278 ..     490     543 ..     462     549 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0034
                                  --BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                  tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvq 52
                                  + h+G++ +   +D ++r+ +++g++v+f q
  gi|91774107|ref|YP_566799.1| 49 NFHIGNSLNWCYIDFVARYKRMQGFNVMFPQ 79
                                  57**************************976 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 9.8e-08
                                   HHHHHHHSSS--EEEEEEE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHHH CS
                  tRNA-synt_1e 226 laqseaafdkqlvkyflhnghlk.iegekmsksLknfitikdvlkkfdprqlRl 278
                                   + +s+a+++k+  +  l ng++   +g+kmsksL+n+i+ ++v+k +++ ++R 
  gi|91774107|ref|YP_566799.1| 490 ILRSMALTGKKPWESILVNGMVLgEDGHKMSKSLGNVISPEEVIKDHSADAFRQ 543
                                   668999999888888888888752679**********************99986 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 !    5.0   0.0    0.0059        15      21      65 ..     201     245 ..     184     254 .. 0.80
   2 !   14.6   0.0   6.8e-06     0.017      87     143 ..     234     290 ..     231     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0059
                 tRNA-synt_1_2  21 eklevfttrpdtlfGvtfvalapehplveklaekkkelaafieev 65 
                                   +kle+ ttrp+ l     +a++pe +  +++  ++ ++  f ++v
  gi|91774107|ref|YP_566799.1| 201 DKLEIATTRPELLAACVAIAISPEDERYKQYIGQTMKVPLFGHDV 245
                                   499**********************99999888887777776655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.8e-06
                 tRNA-synt_1_2  87 lkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpe 143
                                    ++  P+ g+++++   + v  ++gtgavm +   d++D +++ ++nlp+++ i ++
  gi|91774107|ref|YP_566799.1| 234 QTMKVPLFGHDVEVIADKDVDPTFGTGAVMICTFGDKQDVRWWLEHNLPLRKGIDKS 290
                                   5667799999999999999999****************************9988865 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 ?    3.4   0.0     0.012        30      33     131 ..      46     139 ..      16     175 .. 0.74
   2 !    9.1   0.0   0.00021      0.53     270     300 ..     507     537 ..     472     574 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.012
                  tRNA-synt_1f  33 pSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenlpek.llekylgkpltsiPdpk..gkhesyaeh 110
                                   p G  HiGn  +    d+var  r +g +v +   +D         + lp +  +e++ g   +++P ++  + +e+    
  gi|91774107|ref|YP_566799.1|  46 PTGNFHIGNSLNWCYIDFVARYKRMQGFNVMFPQGWDC--------HGLPTEvKVEENHGITKNQVPRTEfrQMCEELTVG 118
                                   88999999999999999999999999999877777763........23444444557777778888887633338888888 PP

                  tRNA-synt_1f 111 fnaelvesLdelgievefisa 131
                                   +  ++++++++lg+  ++ ++
  gi|91774107|ref|YP_566799.1| 119 NIDKMRKTMHRLGFSTDWSNE 139
                                   888888888888888877665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00021
                  tRNA-synt_1f 270 vYelillkggekmssSkGnvltledwlevae 300
                                   v  ++l + g+kms+S Gnv+++e++++  +
  gi|91774107|ref|YP_566799.1| 507 VNGMVLGEDGHKMSKSLGNVISPEEVIKDHS 537
                                   44678888899**************998655 PP

>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0016       4.2      59     119 ..     137     201 ..      89     204 .. 0.62
   2 ?    4.8   0.0     0.012        32      15      45 ..     324     357 ..     316     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0016
                       DUF4451  59 sngslvpePill........rskkrrkakekekegivCpkCneiievslsknkkekkvnellayfrHfk 119
                                   sn++ + eP ++        + k   + +++e+    Cp C+  i++  ++ ++    ++l   f Hf 
  gi|91774107|ref|YP_566799.1| 137 SNEFVTMEPEYYvktqtsfvKMKDMDRVYQSEHPVNWCPRCETAIAFAEVEYDSRD--TKLN--FLHFD 201
                                   5666666666664433333333333333333444445******9999988877775..3565..67775 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.012
                       DUF4451  15 ekdknekkeglCpiCeeev...ekkekflklkns 45 
                                   e++  ++++g+C  C++++   ++k+ f+k+ n 
  gi|91774107|ref|YP_566799.1| 324 EQNTLKQNVGMCWRCKTPIeilSEKQWFVKIDND 357
                                   44566789********999998888889988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (865 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.27s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 5408.30
//
Query:       gi|91774108|ref|YP_566800.1|  [L=356]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete 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-28   97.4   0.8    1.1e-27   96.4   0.8    1.5  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.8     6e-32   1.1e-27       1     111 [.     228     339 ..     228     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 6e-32
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +l+vdD+p++ el+r  l  e y +  +a +g++a+++  ee +dlillDi+mp+mdG+e++++++e++  +++ vi+++a
  gi|91774108|ref|YP_566800.1| 228 ILVVDDEPDIPELIRLSLATEPY-DFIVAYNGEDAVKKSIEELPDLILLDIMMPDMDGYEVVERLKEDPyaRDIAVIMVSA 307
                                   8**********************.9999*****************************************9899******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                   ++e ed+ +++++g+dd++sKpfd++e+ +++
  gi|91774108|ref|YP_566800.1| 308 KTEIEDKLKGMELGIDDYISKPFDKREINARI 339
                                   ****************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        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 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2267.94
//
Query:       gi|91774109|ref|YP_566801.1|  [L=923]
Description: alanyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-132  440.5   0.3   1.4e-131  439.8   0.0    1.5  2  tRNA-synt_2c   tRNA synthetases class II (A)
    5.1e-24   85.3   1.3    1.3e-23   83.9   1.3    1.8  1  DHHA1          DHHA1 domain
    2.7e-12   46.6   0.3    6.1e-12   45.5   0.3    1.7  1  tRNA_SAD       Threonyl and Alanyl tRNA synthetase second add
  ------ inclusion threshold ------
      0.013   15.5   0.6      0.033   14.2   0.6    1.6  1  DUF2205        Short coiled-coil protein
      0.027   13.7   0.0       0.15   11.2   0.0    2.0  2  Herpes_UL37_1  Herpesvirus UL37 tegument protein
       0.12   12.3   1.4       0.46   10.4   0.3    2.5  3  DUF2489        Protein of unknown function (DUF2489)
        2.4    7.8   6.5        1.6    8.3   0.1    2.6  3  Lebercilin     Ciliary protein causing Leber congenital amaur


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 !  439.8   0.0  5.4e-135  1.4e-131       1     552 []      62     603 ..      62     603 .. 0.93
   2 ?   -3.2   0.2      0.84   2.1e+03     408     477 ..     749     817 ..     744     824 .. 0.71

  Alignments for each domain:
  == domain 1  score: 439.8 bits;  conditional E-value: 5.4e-135
                                   HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS CS
                  tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGktar 81 
                                   ++re +l+fFe++gHt++++++v++++++++++++A++a+f+p++++++  p+++++++sQ+ciR++    Dl+ VGk +r
  gi|91774109|ref|YP_566801.1|  62 DMREFYLNFFEEQGHTRIERYPVIARWRDDIYLTIASIADFQPFVTSGQVPPPANPLTISQPCIRLS----DLDAVGKSGR 138
                                   59*****************************************************************....********** PP

                                   --SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHHH CS
                  tRNA-synt_2c  82 HhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekdn 155
                                   H+T FeM+++++f+     +Y+ke + e++  ll+ +lg d+  ++++++++++  +a+++ e l+g+ e ++l+f   +n
  gi|91774109|ref|YP_566801.1| 139 HLTTFEMMAHHAFNtkneeIYWKEHTLELCDGLLN-SLGADPMAVTYKEEPWAGggNAGACVEVLIGGLEVATLVF---MN 215
                                   **********************************9.*****************999*******************9...55 PP

                                   EE........ESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEEST....TSHEEEEEEEEEEE CS
                  tRNA-synt_2c 156 fw........emgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnree....dgtlkpLpkksidt 224
                                    +          gd + +++++++++++g e+ ++++++ ++++d+++  i+n ++  ++ e+    ++  ++L ++++ +
  gi|91774109|ref|YP_566801.1| 216 LKkdkngdidIKGDMYSKMENYIVDTGYGLERLVWASKGSPTIYDAIFPSIVNELMGLAGIEHelenNEYSHILSQNARLA 296
                                   552222222245666**************************************9986555444344399999********* PP

                                   EEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHH CS
                  tRNA-synt_2c 225 GmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrll 305
                                   G++++   a L e+r++++ +++++  ++ + + +          e++++iaDH+r+l+f+++dG++psn+++gY++R+++
  gi|91774109|ref|YP_566801.1| 297 GLMDISEKANLLELRKQVAASIGITADKLSSIMEP---------VENVYAIADHTRCLTFMIGDGIIPSNVKAGYLARLVI 368
                                   ************************99999988888.........689********************************** PP

                                   HHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCC.CSEEXHH CS
                  tRNA-synt_2c 306 RravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkk.kkelsge 385
                                   Rr++r++k+Lg+  + ++++++++++ l   ype++++ + +++i+e+Ee +Fa+TlerG++++e+++++ k+ ++++++e
  gi|91774109|ref|YP_566801.1| 369 RRTLRMMKDLGIMIP-ISEIIQMHINNLP-EYPEFQKRFDVIKDILEHEERKFAETLERGRRMMEKSARHYKEsGEKMPLE 447
                                   ***************.************7.7*****************************************999****** PP

                                   HHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTS CS
                  tRNA-synt_2c 386 dafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakv 466
                                   +++ +yd++G+P+++ k +a + g++vd +++++++++ ++++ +e+ke+k +   ++++++l+kt+  l+y+e       
  gi|91774109|ref|YP_566801.1| 448 TIIDMYDSHGIPPEISKAVASDVGVEVDLPDNFYSLVADKHSQ-SEEKEEK-VVPFADKIARLPKTKR-LFYDE------- 518
                                   **************************************99988.4445545.79999********999.9****....... PP

                                   XXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSX..XXTTSEEE CS
                  tRNA-synt_2c 467 lallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegk..lkvgdkvk 545
                                       ++  f + v e+ ++ +vLd+T +Y+e+GGq +D+G+++ e+  ++v+d+q ++gvv+h+++  e++  +++gd v 
  gi|91774109|ref|YP_566801.1| 519 ---PNRMDFDAVVLEVFDNHIVLDNTLMYPEGGGQPADHGTLTVEDVVLKVVDTQMYDGVVVHTINEIEDElhIRKGDMVV 596
                                   ...78899********************************************************998666633789***** PP

                                   EEEXHHH CS
                  tRNA-synt_2c 546 aevdeer 552
                                   ++v+e+r
  gi|91774109|ref|YP_566801.1| 597 GRVNEKR 603
                                   ***9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.84
                                   TTXEEXHHHHHHHHHHHHHHHCCHHSXSS.XXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEE CS
                  tRNA-synt_2c 408 kglkvdiegfekameeqrerskkekkekk.likkdvealkelkkteeflgyeeleaeakvlallkdkefve 477
                                   + + + +++ e + + + e+ + ++++   +i++ +++ kelkk+++ l+ e   a+++v +l++d e v+
  gi|91774109|ref|YP_566801.1| 749 EAAIIAMQDIETLVRDSSETLRVSAEQLPsTIERFFDEWKELKKENNKLKEEL--AHSRVSQLVNDAEDVN 817
                                   55667788888888888888776666655588888888888888888777776..6777777777776665 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   1.3   5.3e-27   1.3e-23       2     136 ..     781     916 ..     780     918 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 5.3e-27
                                   HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTE CS
                         DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdk 82 
                                   e++ +e+kel+ke ++lke+la+   ++l+++ae+v+g  ++++++ + +d   l   a++l +  ++ v++++++e +  
  gi|91774109|ref|YP_566801.1| 781 ERFFDEWKELKKENNKLKEELAHSRVSQLVNDAEDVNGIRIITKAI-PHADSEELTKTAGELTQ--ESNVVAILISEMD-G 857
                                   67899*****************************************.*****************..9977777776666.7 PP

                                   EEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHH CS
                         DHHA1  83 vkvsarskkd....gvdagelakeaaaklgggGGGH.dlAaGagipaekleealealee 136
                                   vk++a + +d    gv++g+++ke+++ +gggGGG+ ++A G+g++++ ++ al++  e
  gi|91774109|ref|YP_566801.1| 858 VKIVATAGDDavkrGVNVGAIVKEMSTMVGGGGGGRpNMARGGGTDPSGMDNALSRSVE 916
                                   999999998899******************************************98766 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 !   45.5   0.3   2.4e-15   6.1e-12       1      44 []     702     744 ..     702     744 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.4e-15
                                   EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                      tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                   +rv ++G+ ++e+C GtH+ nTg +g +kil+ e+i++g+ R++
  gi|91774109|ref|YP_566801.1| 702 IRVLQVGN-DIEACAGTHCTNTGLVGPIKILKTERIQDGVERLE 744
                                   79*****9.*********************************86 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   1.3e-05     0.033       7      52 ..     755     800 ..     751     803 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                       DUF2205   7 sedveklerearerLqqqakeLqssLqaLaervdeVkeehdKLese 52 
                                    +d+e l r+  e+L+  a++L s+ +  ++   e k+e++KL+ e
  gi|91774109|ref|YP_566801.1| 755 MQDIETLVRDSSETLRVSAEQLPSTIERFFDEWKELKKENNKLKEE 800
                                   589****************************************987 PP

>> Herpes_UL37_1  Herpesvirus UL37 tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.26   6.6e+02     124     161 ..     652     689 ..     629     714 .. 0.78
   2 ?   11.2   0.0   5.8e-05      0.15     113     171 ..     751     811 ..     740     843 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.26
                                   HHHHHTT--S--TTSHHHHHHHHHHHHHHHHHHHHHHH CS
                 Herpes_UL37_1 124 haLsankLrtsaklGPvsvrqliveWidvyetaiesal 161
                                    + +an++ + a+    + + +i++W+d+ e   +  +
  gi|91774109|ref|YP_566801.1| 652 TQEEANQIEIIANHTVMKNKRIISDWMDRTEAEQKYGF 689
                                   55567888888888888889999***999887666555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.8e-05
                                   HHHHHT-HHHHHHHHHTT--S--TTSHHHHHHHHHHHHHHHH..HHHHHHHHSS---SSS- CS
                 Herpes_UL37_1 113 lvaavtgsetlhaLsankLrtsaklGPvsvrqliveWidvye..taiesaltyapetllee 171
                                    + a+++ etl + s++ Lr+sa+  P+++     eW +  +  +  ++ l++++ + l +
  gi|91774109|ref|YP_566801.1| 751 AIIAMQDIETLVRDSSETLRVSAEQLPSTIERFFDEWKELKKenNKLKEELAHSRVSQLVN 811
                                   5789*********************************877654467788899998877655 PP

>> DUF2489  Protein of unknown function (DUF2489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.4   3.7e+03      53      90 ..     119     155 ..     117     161 .. 0.82
   2 ?   10.4   0.3   0.00018      0.46      67     117 ..     387     440 ..     382     447 .. 0.80
   3 ?   -2.3   0.0       1.6     4e+03      97     106 ..     787     796 ..     784     827 .. 0.46

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                       DUF2489  53 elsEgaiRikvLldaldlelsedseypalyelyekvkd 90 
                                   ++s  +iR++ L da++++ +  +++++++ ++  +k+
  gi|91774109|ref|YP_566801.1| 119 TISQPCIRLSDL-DAVGKSGRHLTTFEMMAHHAFNTKN 155
                                   567779999996.9999999988999999998877776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                       DUF2489  67 aldlelsedseypalyelyekvkdmptheark...alkkkermkldlereklEa 117
                                   +++++ ++  eyp +++ ++++kd+  he+rk   +l++  rm +  +r+ +E+
  gi|91774109|ref|YP_566801.1| 387 IIQMHINNLPEYPEFQKRFDVIKDILEHEERKfaeTLERGRRMMEKSARHYKES 440
                                   5667777779*********************95546777777888888877775 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.6
                       DUF2489  97 rkalkkkerm 106
                                   +k+lkk++ +
  gi|91774109|ref|YP_566801.1| 787 WKELKKENNK 796
                                   5555443321 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.4     6e+03      95     119 ..     286     310 ..     281     327 .. 0.75
   2 ?    8.3   0.1   0.00063       1.6     115     163 ..     394     443 ..     390     452 .. 0.87
   3 ?    2.1   0.5     0.053   1.4e+02      55      84 ..     773     802 ..     755     816 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                    Lebercilin  95 aellrlkdklkklkkLsedknLaer 119
                                   +++l+ +  l  l ++se+ nL+e 
  gi|91774109|ref|YP_566801.1| 286 SHILSQNARLAGLMDISEKANLLEL 310
                                   5778888888899999999999773 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00063
                    Lebercilin 115 nLaereeLqkkLeeleakleekeeki.keLerkleleeksfrrqlaaekk 163
                                   nL+e  e qk+ + +++ le++e+k+ ++Ler  +++eks r+  ++ +k
  gi|91774109|ref|YP_566801.1| 394 NLPEYPEFQKRFDVIKDILEHEERKFaETLERGRRMMEKSARHYKESGEK 443
                                   89***********************8357************997766555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.053
                    Lebercilin  55 eaeLpqllarhneEvrvlrerlRksqeker 84 
                                    ++Lp+ ++r  +E + l+++  k++e+  
  gi|91774109|ref|YP_566801.1| 773 AEQLPSTIERFFDEWKELKKENNKLKEELA 802
                                   445566666666666666666655555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.78u 0.25s 00:00:01.03 Elapsed: 00:00:00.44
# Mc/sec: 6276.38
//
Query:       gi|91774110|ref|YP_566802.1|  [L=91]
Description: hypothetical protein Mbur_2187 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       252  (0.0140554); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 593.94
//
Query:       gi|91774111|ref|YP_566803.1|  [L=261]
Description: stationary phase survival protein SurE [Methanococcoides burtonii DSM 6242]
Scores for complete 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-51  173.8   0.0    3.9e-51  173.6   0.0    1.1  1  SurE      Survival protein SurE
  ------ inclusion threshold ------
       0.14   11.4   0.0       0.19   10.9   0.0    1.2  1  SIL1      Nucleotide exchange factor SIL1
       0.24   11.5   0.5       0.42   10.7   0.5    1.4  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 !  173.6   0.0   6.6e-55   3.9e-51       1     192 [.       5     198 ..       5     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 6.6e-55
                                   EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHHHHTT CS
                          SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvklaleel 81 
                                   iLltNDDG+ a+gira ++++++ g +v+v aP++++Sg+g+++++ eplr+++++  ++ e  a+ GtP+d v l++ ++
  gi|91774111|ref|YP_566803.1|   5 ILLTNDDGVYAAGIRAAYRSVSDLG-DVTVSAPAQQQSGVGRSISIFEPLRITRTTI-DGIEVHAIGGTPTDSVILGIFTI 83 
                                   8*********************888.*************************996665.899999***************** PP

                                   TTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS.....SS-SSS---HHHHHHHHHHHHTTE CS
                          SurE  82 lkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk.....eeekkeedtfeaaakvaaklvekl 156
                                   +ke  pdl++SG N G+N++td+ ++SGT+gAale+a  g+paiA Sl++++     ++ ++ +++f+   k+++ +++k+
  gi|91774111|ref|YP_566803.1|  84 MKEL-PDLILSGFNIGENISTDTiTTSGTIGAALEGASYGVPAIAASLQVTEeglkfDDLRDFQHDFDVGIKFVNGVAKKV 163
                                   *875.******************9*************************99999999666667788*************** PP

                                   TTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCS CS
                          SurE 157 ieklllekvellnvNvPeleeeeikgvkvtrlgrrr 192
                                   +++ l e+v+lln+N+P+  ee+ + v++trl+r+ 
  gi|91774111|ref|YP_566803.1| 164 LKNGLPENVDLLNINIPHFVEEDSE-VEITRLARKF 198
                                   *****************77666655.88***99875 PP

>> SIL1  Nucleotide exchange factor SIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.2e-05      0.19      24      51 ..     133     160 ..     123     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.2e-05
                          SIL1  24 erlekaLddlielshDykfGvkiishef 51 
                                   ++   ++ddl ++ hD+++G+k ++   
  gi|91774111|ref|YP_566803.1| 133 TEEGLKFDDLRDFQHDFDVGIKFVNGVA 160
                                   555679****************987654 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   7.1e-05      0.42       6      19 ..     204     216 ..     204     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.1e-05
                                   EEEE-TTTT-EEEE CS
                            WW   6 eeqwdpdsGrvYYy 19 
                                   ee++dp+ Gr+YY+
  gi|91774111|ref|YP_566803.1| 204 EERRDPR-GRPYYW 216
                                   799****.*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1983.04
//
Query:       gi|91774112|ref|YP_566804.1|  [L=550]
Description: sulphate transporter [Methanococcoides burtonii DSM 6242]
Scores for 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  303.3  34.9    2.9e-90  302.8  34.9    1.2  1  Sulfate_transp  Sulfate permease family
    2.6e-11   43.2   0.0    4.8e-11   42.3   0.0    1.4  1  STAS            STAS domain
    8.4e-06   26.2   6.7    8.4e-06   26.2   6.7    4.3  4  MFS_MOT1        Molybdate transporter of MFS superfamily


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.8  34.9   4.9e-94   2.9e-90       1     379 [.      15     378 ..      15     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 302.8 bits;  conditional E-value: 4.9e-94
                Sulfate_transp   1 lkgDliaGitvallaiPqalayallaglppiygLyssvvpqlvyalfGtsrqlavGpvavlslivgeiiakvaeeepekgi 81 
                                   +++Dl aG+++a++a+P+a+a+a+++g++p++gLy++++++++ + fG+sr +++Gp++++++iv ++++         g+
  gi|91774112|ref|YP_566804.1|  15 FLSDLKAGLITAVVALPLAIAFAIASGVEPVMGLYTAIIAGMLVSTFGGSRYSISGPTGAMTVIVLSTVNGY-------GV 88 
                                   789*******************************************************************88.......** PP

                Sulfate_transp  82 eiattltllaGviqvllGllRLgflveflseavlsGfiaGaaivillsqikvllglervskkeslvsvlsslftnlekvnl 162
                                   e ++++ +laGv+q+l+G++RLg++v++++ +v+sGf++G++i+il+ q+++++gl     +e ++++++++ft+++ +n+
  gi|91774112|ref|YP_566804.1|  89 EGLLLAGVLAGVFQILFGIFRLGKVVKYIPLPVISGFTSGIGIIILIGQLSNVFGLV-LPAREHVWETVYDVFTSIDAMNI 168
                                   ********************************************************7.99********************9 PP

                Sulfate_transp 163 akvvlgllllvvLlvtkellkklkkllvipapaelvavivatlvsaifelkreagvkivgeipsglpelslpkvdwsllsa 243
                                   +++ + + +++++l+  ++l ++  + +  +pa ++ +++++++++ f+     ++ ivgeips +p++++ +++  l+ a
  gi|91774112|ref|YP_566804.1| 169 LALSMFAGTIILMLLLPKVLSNI--KYLKNIPASIITLVLSVILTYHFD----LKIPIVGEIPSIIPQIHMLDINIGLMYA 243
                                   99988777777777777777777..577889999**************4....45799*********************** PP

                Sulfate_transp 244 llpdalaialvglleaiavsksldkkkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGaktqlsglvsal 324
                                   +lp+a++ial+g +e+++ + + d+++++k++snkEL+++G++N++ ++f g+pat+a++rsavni+ Gakt++sg+++al
  gi|91774112|ref|YP_566804.1| 244 VLPAAFTIALLGTIESLLCAVVCDAMTNTKHNSNKELIGQGIANVILPFFAGIPATAAIARSAVNIREGAKTRMSGVIHAL 324
                                   ********************************************************************************* PP

                Sulfate_transp 325 vvllvllvltplleyiPkavLaaiiivagkglLvelkelkklwklskldflilla 379
                                   v+l +l++++p+++yiPka La+i++++ ++ +v+++e+  ++++sk+d+++ll 
  gi|91774112|ref|YP_566804.1| 325 VLLGILIFFGPIAQYIPKAYLAGILVLVSIK-MVNVDEIRTTINISKMDTFVLLT 378
                                   *******************************.********************986 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0     8e-15   4.8e-11       7      98 ..     436     518 ..     432     540 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 8e-15
                                   CTTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEEES CS
                          STAS   7 iegililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvevvlvn 87 
                                   ++++ +++++gp++f+    f+ k+++++  ++          ++i+ +  v+fiD++G++ Lk++++  k  g +v+l  
  gi|91774112|ref|YP_566804.1| 436 KDNVAVYTINGPFFFGAMAVFENKVDEHIHMSK---------PHIIIRMRYVPFIDTTGIERLKSFITTRKGTGEKVYLTT 507
                                   68999***************************8.........9************************************** PP

                                   --HHHHHHHHH CS
                          STAS  88 ikpevreklek 98 
                                   ++pev + ++ 
  gi|91774112|ref|YP_566804.1| 508 VQPEVMRSINS 518
                                   ******99654 PP

>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6  12.1   0.00041       2.4      14     109 ..      29     131 ..      19     133 .. 0.72
   2 ?   -0.9   1.2      0.35   2.1e+03      71     104 ..     171     206 ..     159     210 .. 0.70
   3 !   26.2   6.7   1.4e-09   8.4e-06      10     110 ..     254     355 ..     236     356 .. 0.85
   4 ?    0.8   0.2      0.11   6.5e+02      69      89 ..     392     412 ..     381     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00041
                      MFS_MOT1  14 llnlvialaalaslslta...lllsvG.lmnlltglfggvPmchgAgglaaqyrf....gartgaagillGlvllllgltg 86 
                                    l+l+ia a+ +++++     +++++G l+  ++g  + +  ++gA  ++   +      + +  ag+l G++ +l+g+++
  gi|91774112|ref|YP_566804.1|  29 ALPLAIAFAIASGVEPVMglyTAIIAGmLVSTFGGSRYSISGPTGAMTVIVLSTVngygVEGLLLAGVLAGVFQILFGIFR 109
                                   58889999988854443300023333335566666667777776665555442224488999******************8 PP

                      MFS_MOT1  87 llerllrliPksvlgglllgaGl 109
                                    l +++++iP +v+ g   g G+
  gi|91774112|ref|YP_566804.1| 110 -LGKVVKYIPLPVISGFTSGIGI 131
                                   .99*************9999886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.35
                      MFS_MOT1  71 agillGlvllllgltg..llerllrliPksvlggll 104
                                     ++ G ++l+l l    +  + l+ iP s++  +l
  gi|91774112|ref|YP_566804.1| 171 LSMFAGTIILMLLLPKvlSNIKYLKNIPASIITLVL 206
                                   456777777777776633556668889999998776 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 1.4e-09
                      MFS_MOT1  10 lglTllnlvialaala....slsltalllsvGlmnlltglfggvPmchgAgglaaqyrfgartgaagillGlvllllgltg 86 
                                   lg T+  l+ a+++ a    + + ++ l+  G++n+++ +f g+P  +  +  a + r+ga+t ++g++ +lvl  lg++ 
  gi|91774112|ref|YP_566804.1| 254 LG-TIESLLCAVVCDAmtntKHNSNKELIGQGIANVILPFFAGIPATAAIARSAVNIREGAKTRMSGVIHALVL--LGILI 331
                                   77.888888888888888886689999*******************9666666666799**********98876..56666 PP

                      MFS_MOT1  87 llerllrliPksvlgglllgaGle 110
                                    +  ++++iPk+ l g+l+ + ++
  gi|91774112|ref|YP_566804.1| 332 FFGPIAQYIPKAYLAGILVLVSIK 355
                                   67*****************99876 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.11
                      MFS_MOT1  69 gaagillGlvllllgltglle 89 
                                   + ag++l+++ll++ lt++++
  gi|91774112|ref|YP_566804.1| 392 IQAGMFLSIILLFIRLTNIID 412
                                   579***********9998664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4080.45
//
Query:       gi|91774113|ref|YP_566805.1|  [L=318]
Description: molybdenum cofactor biosynthesis protein A [Methanococcoides burtonii DSM 6242]
Scores for complete 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  109.0   0.1    8.3e-31  107.6   0.0    1.7  2  Radical_SAM    Radical SAM superfamily
    2.8e-18   66.1   0.1    5.7e-18   65.1   0.1    1.5  1  Mob_synth_C    Molybdenum Cofactor Synthesis C
    7.6e-07   29.5   0.1    2.4e-06   27.9   0.0    1.8  2  Fer4_12        4Fe-4S single cluster domain
    1.2e-06   28.6   0.0    2.5e-06   27.6   0.0    1.5  1  Fer4_14        4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.045   13.9   0.0      0.097   12.8   0.0    1.6  1  DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal do
       0.07   12.8   0.0       0.16   11.6   0.0    1.5  1  Imm9           Immunity protein 9
      0.083   13.4   1.4       0.67   10.4   1.4    2.1  1  PIN_12         PIN 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 !  107.6   0.0   3.3e-34   8.3e-31       1     167 []      21     179 ..      21     179 .. 0.97
   2 ?   -1.4   0.1       1.1   2.7e+03      53      53 ..     235     235 ..     197     298 .. 0.46

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 3.3e-34
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   +++t+ Cnl+C++C+      +eg  +++s   i  +v ++ a+ gv+ v ++ggepl+++df+++l++l kl      ++
  gi|91774113|ref|YP_566805.1|  21 ISITNRCNLDCIYCHSEG---DEGSRKEMSAKTISVIVSAA-AKFGVNKVKFSGGEPLVRKDFEDILRKLPKL----KDVS 93 
                                   689**************8...7*******************.8999**************************8....8*** PP

                                   EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeele 161
                                   v+tng+ + +e +  l+e+g+drv+++l+++d+ek+  +++  ++t+ +vle+++++ +ag+ +v+ ++v+l+G n++e+ 
  gi|91774113|ref|YP_566805.1|  94 VTTNGVFL-KERAFSLKEAGLDRVNVSLDTLDPEKYAYITHgSPETLHKVLEGIDAAISAGLTPVKLNMVLLKGINEDEIG 173
                                   ********.*********************************99************************************* PP

                                   HHHHHH CS
                                   xxxxxx RF
                   Radical_SAM 162 ellell 167
                                   ++l+l+
  gi|91774113|ref|YP_566805.1| 174 DMLDLV 179
                                   **9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                   E CS
                                   x RF
                   Radical_SAM  53 g 53 
                                   g
  gi|91774113|ref|YP_566805.1| 235 G 235
                                   2 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 !   65.1   0.1   2.2e-21   5.7e-18       3     120 ..     188     294 ..     186     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.2e-21
                                   EEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--EEEE-T CS
                   Mob_synth_C   3 lrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgkgeiglIapvsep.FCasCnRlRlta 82 
                                   l++I +m++++g++      + ad+i +++e++ + + +  ++++ +k+y i++++  +++++p++++ FCa+CnRlR+ta
  gi|91774113|ref|YP_566805.1| 188 LQIIQVMDFKDGKQY----DLDADKIEKKLEAHANNITI--RNMHHRKKYIIDGAE--VEFVRPIENTeFCANCNRLRITA 260
                                   788888888888754....56777777777777777777..569********9888..9********99************ PP

                                   TSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHH CS
                   Mob_synth_C  83 dGklktCLfaeee.idlrdllregaseeeLkelikeala 120
                                   dGklk+CL  +++ id+ ++       +eL el++++++
  gi|91774113|ref|YP_566805.1| 261 DGKLKPCLLVNNNlIDISEAEP-----DELPELLRRSVD 294
                                   *********9999888876522.....235555555555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   9.2e-10   2.4e-06      12     100 ..      24     105 ..      12     123 .. 0.80
   2 ?   -2.4   0.0       2.1   5.4e+03      28      50 ..     194     215 ..     191     224 .. 0.58

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 9.2e-10
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                   +++Cnl C +C+  +  +  s ke++ +++  i+  ++k  ++++ ++GGEPl+   ++++ ++++++ + k   + + ++
  gi|91774113|ref|YP_566805.1|  24 TNRCNLDCIYCH--SEGDEGSRKEMSAKTISVIVSAAAKFGVNKVKFSGGEPLV---RKDFEDILRKLPKLKD--VSVTTN 97 
                                   679*********..5568889999******************************...8888888888887776..677888 PP

                       Fer4_12  93 gytleels 100
                                   g+ l+e  
  gi|91774113|ref|YP_566805.1|  98 GVFLKERA 105
                                   88777654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                       Fer4_12  28 wsfksgkeftkelleeiiedlkk 50 
                                    +fk gk+++ ++ ++i ++l+ 
  gi|91774113|ref|YP_566805.1| 194 MDFKDGKQYDLDA-DKIEKKLEA 215
                                   6889999997443.444444432 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   9.7e-10   2.5e-06       5      94 ..      24     103 ..      21     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 9.7e-10
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwl 85 
                                   +++Cnl C  C  +   ++ + k+ + ++++ i+    + ++  +++ ++GGePL     k++ +++++l + +   ++ +
  gi|91774113|ref|YP_566805.1|  24 TNRCNLDCIYCHSEG--DEGSRKEMSAKTISVIV--SAAAKFGVNKVKFSGGEPLVR---KDFEDILRKLPKLK---DVSV 94 
                                   79*********9988..77788888899998899..6777777899*********55...89999999988766...9999 PP

                       Fer4_14  86 etngtleie 94 
                                    tng++ +e
  gi|91774113|ref|YP_566805.1|  95 TTNGVFLKE 103
                                   999998744 PP

>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.8e-05     0.097      70     117 ..      74     128 ..      40     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                                   EEHHHHHHHHHHSSTTSEEEEEEET.....TEEEEEEETTEE..EEEE-BEGGGS CS
                 DNA_pol3_beta  70 vparllldivkaLpndkkvkisvne.....qklliiksgssr..fslstlsaeey 117
                                   +  + + di+++Lp+ k+v++++n+      + +++++g +r   sl tl+ e y
  gi|91774113|ref|YP_566805.1|  74 LVRKDFEDILRKLPKLKDVSVTTNGvflkeRAFSLKEAGLDRvnVSLDTLDPEKY 128
                                   44589*******************9766544455666665551156778888887 PP

>> Imm9  Immunity protein 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.3e-05      0.16      49     112 ..      21      84 ..      14      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                          Imm9  49 illgk.anhigifkkgitdsstkekvlsisislPdskevrwGvkekekfagkpelnekkfkrild 112
                                   i++ +  n   i+ ++  d   +++  + +is+ +s  +++Gv++  kf g ++l +k f+ il 
  gi|91774113|ref|YP_566805.1|  21 ISITNrCNLDCIYCHSEGDEGSRKEMSAKTISVIVSAAAKFGVNKV-KFSGGEPLVRKDFEDILR 84 
                                   44444489999******9999988899999**************96.7*******9999998875 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.4   0.00026      0.67      20     141 ..     171     307 ..     161     312 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                        PIN_12  20 alkklleliesgkiklivpdivldEflknrekkieeskklekalks............lsklksakkklnekkkllslkei 88 
                                   ++  +l+l+ s+k+ li+  i ++ f+  ++ ++++  k+ek+l+              +k+  + ++++    ++  + +
  gi|91774113|ref|YP_566805.1| 171 EIGDMLDLVRSKKDDLILQIIQVMDFKDGKQYDLDAD-KIEKKLEAhannitirnmhhRKKYIIDGAEVEFVRPIENTEFC 250
                                   5556666666666666666666666666666666533.2222222220011211122233333333333333333333333 PP

                        PIN_12  89 kkkieekvees..lkklleklea.ikvipetndevkkilerafkkkpPf.skkkkkg 141
                                    +    ++ +   lk  l  +++ i+++++++de++++l+r+ +++ Pf ++ k+k+
  gi|91774113|ref|YP_566805.1| 251 ANCNRLRITADgkLKPCLLVNNNlIDISEAEPDELPELLRRSVDRRVPFyRDMKDKT 307
                                   2222222222233444444444479************************54447765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2232.18
//
Query:       gi|91774114|ref|YP_566806.1|  [L=452]
Description: cobyrinate a,c-diamide synthase / hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-34  118.9   0.0    3.1e-34  118.3   0.0    1.2  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    1.2e-19   71.0   3.8    2.1e-17   63.6   3.8    2.3  1  AAA_26    AAA domain
    1.8e-19   70.1   0.1    3.4e-19   69.2   0.1    1.5  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.011   15.0   0.9      0.021   14.1   0.9    1.5  1  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai
      0.064   12.7   0.7       0.12   11.8   0.7    1.4  1  ParA      NUBPL iron-transfer P-loop NTPase
      0.067   13.1   0.1       0.11   12.4   0.1    1.3  1  AAA_31    AAA domain
       0.12   12.3   0.4       0.42   10.5   0.2    2.0  2  NTPase_1  NTPase
       0.14   12.0   0.0       0.45   10.3   0.0    1.8  2  SNO       SNO glutamine amidotransferase 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 !  118.3   0.0   1.4e-37   3.1e-34       1     190 [.     253     433 ..     253     438 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 1.4e-37
                      GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvl 79 
                                   +i+v+r++a+ +y+   +d+ ++ +++  +f+p  d +l +d+d ++++Gg+++++ ++l+r+ ++ +++k+++++g+p++
  gi|91774114|ref|YP_566806.1| 253 NIGVARDSAFCFYYeeMFDMFRKCGANIEFFSP-LDGEL-PDVDGLYFGGGYPELHIAELERS-STTKKLKDLSADGMPIY 330
                                   69************988****************.8999*.56*******************99.88899************ PP

                      GATase_3  80 giCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevelaaeg....eevkGyEiHsGrtilkekak 156
                                   g+CGGlq+L++++e ++        +++ +l+ +et+ +k +l+    g++e +a+g     +v+G+E+H++ t  + + +
  gi|91774114|ref|YP_566806.1| 331 GECGGLQYLCSSYEIEDV------VYKMADLFSAETVQTK-RLQ--ALGYTEGVAKGkfikGPVRGHEFHYSLTECDSDSR 402
                                   *************98775......6************999.887..888888855555555899***********999999 PP

                      GATase_3 157 pllkvkvggnng.ekdGavkksedgnvlGtYlHgl 190
                                    ++++++g+++  +kdG+ ++    n l++Y+H +
  gi|91774114|ref|YP_566806.1| 403 LAYEMSRGKGIMnGKDGITEH----NSLASYMHAH 433
                                   9999988666556******88....********98 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   3.8   9.3e-21   2.1e-17       1     195 [.      16     194 ..      16     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 9.3e-21
                        AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaarq 81 
                                   ++++++gt  gvGKT+v++g+++al+++++kv+ +K    +i    d+ + + ++g+++ + +  ++++            
  gi|91774114|ref|YP_566806.1|  16 QSVLIAGTHSGVGKTTVAMGIMAALTKRNMKVQPYKVGPDYI----DPTHHTAICGVSSRNLD--TFMMG----------V 80 
                                   689*****************************9888544444....89999999999877774..45543..........4 PP

                        AAA_26  82 egedidlekivkelekdadivvVEGagglgvpitee..llnadiaknlgapvilVargglgtinqllltiealr.qknvrv 159
                                   +g+  ++++      kdadi v+EG+ gl ++  ++  ++ a +ak+lg+pvilV++++  +  + ++   +   +k+v++
  gi|91774114|ref|YP_566806.1|  81 DGVRRTVDNS----YKDADISVIEGVMGLYDGMDSTeiASSAHVAKSLGIPVILVVNVHGMSRSAGAIVKGFTEfDKDVEI 157
                                   5666666666....79**************99554434999*****************88766666666665555789*** PP

                        AAA_26 160 lGvilNkvrnpenvetlekksg.ipvlGvvPylpdle 195
                                   +GvilN+v +p+  + ++   + ipv+G+vP + d++
  gi|91774114|ref|YP_566806.1| 158 AGVILNRVGSPRHAKLIKDVLQdIPVVGTVPRNNDVK 194
                                   ******************99766**********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 !   69.2   0.1   1.5e-22   3.4e-19       1     126 [.      18     200 ..      18     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.5e-22
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH....................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx....................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep....................... 54 
                                   ++ia+t +GvGKTt+a ++++al +r+ +V++++++p+    ++                                     
  gi|91774114|ref|YP_566806.1|  18 VLIAGTHSGVGKTTVAMGIMAALTKRNMKVQPYKVGPDYIDPTHhtaiC--------Gvssrnldtfmmgvdgvrrtvdns 90 
                                   68************************************76666556541........03333344677777777788888* PP

                                   ..........................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...- CS
                                   ..........................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                          CbiA  55 ..........................................dlkrllellealgkkkall...lkiagvvlnrvdgenee 90 
                                                                             ++  +++++ a++k++  +   ++iagv+lnrv+++++ 
  gi|91774114|ref|YP_566806.1|  91 ykdadisviegvmglydgmdsteiassahvakslgipvilvvNVHGMSRSAGAIVKGFTEFdkdVEIAGVILNRVGSPRHA 171
                                   ******************************************9999999********999999***************888 PP

                                   TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  91 tllkealeelkqrygvpvlgviprdeavaeaparge 126
                                   +l+k+ l++      +pv+g +pr+ +v + p+r++
  gi|91774114|ref|YP_566806.1| 172 KLIKDVLQD------IPVVGTVPRNNDV-KVPSRHL 200
                                   877777766......7***********9.8998875 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   0.9   9.2e-06     0.021      10      56 ..      13      59 ..       4     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.2e-06
                       DUF1611 10 vkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili 56
                                    ++ vl+ GT + vGK t a+ + +al++r +k++    g+  i  
  gi|91774114|ref|YP_566806.1| 13 AMKQSVLIAGTHSGVGKTTVAMGIMAALTKRNMKVQPYKVGPDYIDP 59
                                  56788*****************************9988877766555 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 ?   11.8   0.7   5.2e-05      0.12       2      35 ..      14      47 ..      13      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                          ParA  2 vkkviavlSgKGGVGKStvavnlAlaLakkglkv 35
                                  +k+ ++++ +  GVGK+tva+ + +aL+k+++kv
  gi|91774114|ref|YP_566806.1| 14 MKQSVLIAGTHSGVGKTTVAMGIMAALTKRNMKV 47
                                  578999*************************998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.9e-05      0.11       7      33 ..      21      47 ..      15      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                        AAA_31  7 anqKGGvGKTTtsvnlaaalaklgkkv 33
                                  a    GvGKTT ++ + aal+k+++kv
  gi|91774114|ref|YP_566806.1| 21 AGTHSGVGKTTVAMGIMAALTKRNMKV 47
                                  55667*********************9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00019      0.42       3      31 ..      19      48 ..      17      51 .. 0.86
   2 ?   -1.9   0.0       1.2   2.7e+03     116     137 ..     172     192 ..     166     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                                  EEE-.-TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  3 fiTG.ppGvGKtTlvkkvlellkssgvkvg 31
                                  +i G ++GvGKtT+   ++ +l ++++kv+
  gi|91774114|ref|YP_566806.1| 19 LIAGtHSGVGKTTVAMGIMAALTKRNMKVQ 48
                                  5666257*********************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                   HHHHHHHTTTSEEEEE--SS-- CS
                      NTPase_1 116 eaveevLksekpvlavihrrkd 137
                                   + +++vL+ + pv+++++r++d
  gi|91774114|ref|YP_566806.1| 172 KLIKDVLQ-DIPVVGTVPRNND 192
                                   66777775.6899****99975 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   2.9e+03     112     144 ..     151     183 ..     118     224 .. 0.58
   2 ?   10.3   0.0    0.0002      0.45      29      91 ..     288     349 ..     265     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                                   EEEEEEETTTCSEEEEEESS--EEEEE-.TTTC CS
                           SNO 112 fekeldfknliekftavfiraPvieeilddeav 144
                                   f+k++++ ++i +  +    a  i+ +l+d+ v
  gi|91774114|ref|YP_566806.1| 151 FDKDVEIAGVILNRVGSPRHAKLIKDVLQDIPV 183
                                   444455555443333333344444444433333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                   GGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS- CS
                           SNO  29 edlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenelvk 91 
                                    +l +vd+l   GG        +er    ++l++  +++  +++G C Gl +l+   e+e+v 
  gi|91774114|ref|YP_566806.1| 288 GELPDVDGLYFGGGYPELHIAELERSSTTKKLKDLSADG-MPIYGECGGLQYLCSSYEIEDVV 349
                                   57999******9998876666678888899****99999.9*************999999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3136.22
//
Query:       gi|91774115|ref|YP_566807.1|  [L=364]
Description: DNA primase large subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-35  122.3   0.1    5.1e-35  121.2   0.1    1.5  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
      0.013   15.6   0.6       0.03   14.4   0.0    1.9  2  Skp1             Skp1 family, dimerisation domain
       0.12   12.7   0.0       0.25   11.6   0.0    1.5  1  zf-AD            Zinc-finger associated domain (zf-AD)


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 !  121.2   0.1   8.6e-39   5.1e-35       2     214 ..     136     324 ..     135     336 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 8.6e-39
                                   EEEEEHHHHHHHTT..-G......GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHH CS
               DNA_primase_lrg   2 fykvpfedvldlvk..rr......rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleel 74 
                                   f+ ++f+d+++l++  ++      ++ +kkGy+ + keel +ll e++r r++++l  t  ++   e +i +++      +
  gi|91774115|ref|YP_566807.1| 136 FFDLHFTDYIKLASplKDlnwklvNRKMKKGYVKISKEELARLLQEAIRLRIQNSLPVTVPKEI-CEACIPHTDT-----I 210
                                   7899**********9766999************************************9665544.3345555555.....4 PP

                                   HCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHS CS
               DNA_primase_lrg  75 lealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaf 155
                                    e+l+          +++++++  +++++  ++fPpC+ +++ +++++ +l+h+ r+++t+Fl +ig+s+de+++++  + 
  gi|91774115|ref|YP_566807.1| 211 SEELE----------KKKTEFGVGEFQRVESDLFPPCITQAIANVRAGVNLAHSMRFAMTSFLINIGMSVDEVVAMFNIS- 280
                                   44444..........4457999999******************************************************8. PP

                                   T..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-HHHH.HHHH CS
               DNA_primase_lrg 156 trteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cpfrhdpdkl 214
                                       ++Fd+ ++ry+i+h++G   ++t y+p+sC+++         +++g C     pd+l
  gi|91774115|ref|YP_566807.1| 281 ----PDFDEeKTRYQIEHIAG-TSSGTTYKPPSCNTM---------RTYGnCS---APDEL 324
                                   ....*****************.9**************.........9999994...67877 PP

>> Skp1  Skp1 family, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       1.5   9.2e+03      22      39 ..     198     215 ..     196     220 .. 0.47
   2 ?   14.4   0.0     5e-06      0.03      17      38 ..     267     288 ..     251     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                          Skp1  22 eiReiFnIenD.ftpEEee 39 
                                   ei+e     +D +  EE e
  gi|91774115|ref|YP_566807.1| 198 EICEACIPHTDtI-SEELE 215
                                   5555555556622.33333 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5e-06
                          Skp1  17 gktpeeiReiFnIenDftpEEe 38 
                                   g++++e+ ++FnI  Df +E+ 
  gi|91774115|ref|YP_566807.1| 267 GMSVDEVVAMFNISPDFDEEKT 288
                                   9*****************9975 PP

>> zf-AD  Zinc-finger associated domain (zf-AD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.25      21      53 ..     171     204 ..     154     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                         zf-AD  21 nssislaeileeltglele..pddslpekiCesCl 53 
                                   +++ +la++l+e  +l+++   + ++p+ iCe C+
  gi|91774115|ref|YP_566807.1| 171 SKE-ELARLLQEAIRLRIQnsLPVTVPKEICEACI 204
                                   445.8**************999999*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2545.15
//
Query:       gi|91774116|ref|YP_566808.1|  [L=245]
Description: DNA polymerase sliding clamp [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-14   52.2   0.7    4.7e-13   49.0   0.1    2.3  3  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    9.7e-10   38.7   0.0    2.9e-09   37.1   0.0    1.8  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
     0.0092   15.5   0.0      0.016   14.7   0.0    1.5  1  Rad9      Rad9


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1   7.9e-17   4.7e-13       4     101 ..       4      99 ..       1     104 [. 0.92
   2 ?    0.9   0.0     0.057   3.4e+02      83     114 ..     156     187 ..     145     200 .. 0.78
   3 ?   -2.2   0.0      0.53   3.2e+03      71      91 ..     194     214 ..     172     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 7.9e-17
                                   EEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTT CS
                        PCNA_N   4 arleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcann 84 
                                   a + +a llk  +e++  lv+ea f ++ +G+ ++a+D + va+vs+ l  e+f+++  + +  lg++l+ ++ il +a+ 
  gi|91774116|ref|YP_566808.1|   4 ATI-DAYLLKDSIETLSVLVDEARFRISPEGVVVRAVDPANVAMVSFDLTPEAFDDFEAN-DCELGLDLSRINDILGVADR 82 
                                   544.5889*************************************************975.799***************** PP

                                   TSEEEEEEETTSSEEEE CS
                        PCNA_N  85 edsvtlkaedeadtlal 101
                                   +d+v ++ ++e+ +l++
  gi|91774116|ref|YP_566808.1|  83 DDKVQMELDEESKKLKI 99 
                                   ********999988865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.057
                                   TTTSEEEEEEETTSSEEEEEEEECTSSEEEEE CS
                        PCNA_N  83 nnedsvtlkaedeadtlalvfesekkdkiaey 114
                                    + +s  ++ae ++d ++l++  ++   i+ +
  gi|91774116|ref|YP_566808.1| 156 VEGESFFMEAEGDTDRVKLTMTRDQLIDIKPS 187
                                   56688899***********9999887777655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.53
                                   EHHHHHHHHTTSTTTSEEEEE CS
                        PCNA_N  71 nlnslskilkcannedsvtlk 91 
                                   +l  ls i+k a +++ + l+
  gi|91774116|ref|YP_566808.1| 194 SLDYLSDIIKPASKSNEISLH 214
                                   566788888888887777775 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.92   5.5e+03      55      75 ..      72      92 ..      61      99 .. 0.68
   2 !   37.1   0.0   4.9e-13   2.9e-09       2     127 ..     122     240 ..     121     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.92
                                  EE--BEESSSGGGCBEEEESS CS
                        PCNA_C 55 vlkqvkdvdkeeeavklelke 75
                                   +++   v++ ++ v++el+e
  gi|91774116|ref|YP_566808.1| 72 RINDILGVADRDDKVQMELDE 92
                                  556666677777777777776 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 4.9e-13
                                   ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEE CS
                        PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfa 82 
                                   ip++e  a + l   + ++ ++   ++sd + + v  e+    a+Gd           k     ++ + ++ ++ v   f+
  gi|91774116|ref|YP_566808.1| 122 IPQLELPAEIVLNGKDLQKAVKAAEKISDHMLLGVEGESFFMEAEGDTDRV-------KLTMTRDQLIDIKPSQ-VRSLFS 194
                                   89999999***************************************7665.......3334567899999876.7888** PP

                                   HHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTC.EEEEEEE-B CS
                        PCNA_C  83 lkYlaeftkatsLservtlslssevPlvveykikdv.gllayllak 127
                                   l+Yl +++k +s s++++l+l ++ P++++++i+++ g + ylla+
  gi|91774116|ref|YP_566808.1| 195 LDYLSDIIKPASKSNEISLHLGNDFPIKINFSIANGkGTIGYLLAP 240
                                   *********************************9864788899987 PP

>> Rad9  Rad9
   #    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       4      99 ..      14     102 ..      11     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-06
                          Rad9   4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektvekvk 84 
                                   ++++ls + de  + is++g+ +r+v+ ++ a +++ l+++ Fd +     +++++ + +  +  ++ +++      +kv+
  gi|91774116|ref|YP_566808.1|  14 SIETLSVLVDEARFRISPEGVVVRAVDPANVAMVSFDLTPEAFDDF---EANDCELGLDLSRINDIL-GVA---DRDDKVQ 87 
                                   68899*****************************************...556788888888888888.666...3447788 PP

                          Rad9  85 isidekksrlivqll 99 
                                   +++de++ +l++q+ 
  gi|91774116|ref|YP_566808.1|  88 MELDEESKKLKIQIG 102
                                   888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 1852.96
//
Query:       gi|91774117|ref|YP_566809.1|  [L=103]
Description: DNA-directed RNA polymerase, subunit M [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-17   62.5   4.8    2.4e-17   62.5   4.8    3.1  3  TFIIS_C         Transcription factor S-II (TFIIS)
    5.8e-10   38.9   2.0    5.8e-10   38.9   2.0    3.2  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
    0.00053   19.7   6.2     0.0081   15.9   6.3    2.4  1  TackOD1         Thaumarchaeal output domain 1
     0.0028   17.6  10.6       0.15   12.1   0.6    2.6  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.7  10.1      0.017   15.1   1.4    2.6  2  DZR             Double zinc ribbon
      0.025   14.5   9.8       0.29   11.1   1.1    2.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.11   12.5   0.7       0.11   12.5   0.7    2.6  2  zinc-ribbons_6  zinc-ribbons
       0.16   12.0   8.0       0.74    9.9   3.7    2.8  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.19   11.7   6.0        9.6    6.2   0.1    3.6  3  Nudix_N_2       Nudix N-terminal
       0.38   10.5   9.9       0.94    9.2   1.7    2.9  3  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.39   11.0  13.0       0.13   12.5   2.5    3.0  2  IBR             IBR domain, a half RING-finger domain
        0.7   10.3   6.9         44    4.6   4.7    3.4  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.86    9.4   9.6         45    3.9   0.1    4.0  4  A2L_zn_ribbon   A2L zinc ribbon domain
        1.1    9.3   9.7        4.3    7.4   1.0    3.5  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        1.3    8.9   5.1       0.76    9.7   1.6    2.2  2  CxC3            CxC3 like cysteine cluster associated with KD
        1.5    8.8  15.8        7.7    6.5   0.4    4.1  4  zinc_ribbon_4   zinc-ribbon domain
        1.7    8.8  15.6        2.8    8.1   0.3    4.1  4  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        2.9    7.7  17.8        2.7    7.8   0.4    4.0  4  zinc_ribbon_2   zinc-ribbon domain
          3    7.4  15.8       0.17   11.3   3.8    2.9  2  zf-ribbon_3     zinc-ribbon domain
        3.6    7.4  18.9        1.9    8.3   1.7    4.0  4  Rubredoxin_2    Rubredoxin metal binding domain
        6.4    6.8   8.3       0.48   10.5   0.4    2.6  3  CpXC            CpXC protein
        9.6    6.1  13.3        3.1    7.6   0.2    3.3  4  zf-C2H2_11      zinc-finger C2H2-type


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 ?    3.7   0.3     0.067        55       3       8 ..       4       9 ..       2      12 .. 0.84
   2 ?    4.3   0.5     0.046        37       2      10 ..      19      27 ..      18      29 .. 0.69
   3 !   62.5   4.8   2.9e-20   2.4e-17       2      39 .]      63     100 ..      62     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.067
                       TFIIS_C 3 CpkCgs 8
                                 CpkC+s
  gi|91774117|ref|YP_566809.1| 4 CPKCKS 9
                                 ****98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.046
                       TFIIS_C  2 kCpkCgsre 10
                                  kC kCg ++
  gi|91774117|ref|YP_566809.1| 19 KCRKCGYEK 27
                                  677777666 PP

  == domain 3  score: 62.5 bits;  conditional E-value: 2.9e-20
                       TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                   +C++Cg++ ay++ +Q+RsaDE++t+f+kC+kC ++Wr
  gi|91774117|ref|YP_566809.1|  63 RCEECGNNTAYWWLRQLRSADESETRFFKCIKCSYTWR 100
                                   7************************************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   2.0   7.1e-13   5.8e-10       1      31 [.       1      27 [.       1      32 [. 0.93
   2 ?   -0.6   3.3       1.6   1.3e+03       4       9 ..      64      69 ..      64      70 .. 0.94
   3 !    7.2   0.1    0.0056       4.6      16      29 ..      83      97 ..      79      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 7.1e-13
                                  EEBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                  ++FCpkC++++ p e+ ++    Cr+CgYe+
  gi|91774117|ref|YP_566809.1|  1 MEFCPKCKSMMHPIEGTLK----CRKCGYEK 27
                                  99*****************....******98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                                  ESTTTS CS
                RNA_POL_M_15KD  4 CpkCgN 9 
                                  C +CgN
  gi|91774117|ref|YP_566809.1| 64 CEECGN 69
                                  9****9 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0056
                                  CSCCCE.EEESSSS- CS
                RNA_POL_M_15KD 16 dkegkn.feCrqCgY 29
                                  d++ ++ f C +C+Y
  gi|91774117|ref|YP_566809.1| 83 DESETRfFKCIKCSY 97
                                  5556667******** PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   6.3   9.9e-06    0.0081      88     156 ..       2      71 ..       1     100 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.9e-06
                       TackOD1  88 evCpkCkSidieeqelihhftCgnvgpeeeflke.gkleCpkCktkLrhiGvDYdrplevykCnsCkslf 156
                                   e CpkCkS+    + ++++ +Cg+ ++++   +  ++ +  + + ++ + + D   p ++ +C++C++ +
  gi|91774117|ref|YP_566809.1|   2 EFCPKCKSMMHPIEGTLKCRKCGYEKVKDAAPDLlSTSSREEREVTVLEGDTDIGLPTTTARCEECGNNT 71 
                                   78************************99998444044444555666677788999999999999999765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   3.6    0.0015       1.2      21      45 ..       4      25 ..       2      26 .. 0.78
   2 !   12.1   0.6   0.00018      0.15      19      46 .]      62      98 ..      54      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                 Zn_Tnp_IS1595 21 CPhCgsr.kayriktrglfqCkeCrk 45
                                  CP+C+s+ +++  ++   ++C++C++
  gi|91774117|ref|YP_566809.1|  4 CPKCKSMmHPI--EG--TLKCRKCGY 25
                                  *****776655..54..78*****98 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                 Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt........rglfqCkeCrkq 46
                                   +C  Cg+   ++ +++         + f+C +C+++
  gi|91774117|ref|YP_566809.1| 62 ARCEECGNNtAYWWLRQlrsadeseTRFFKCIKCSYT 98
                                  68*******66666666999**************985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.4   2.1e-05     0.017      13      37 ..       2      26 ..       1      33 [. 0.85
   2 ?    4.9   1.9     0.033        27      11      36 ..      60      97 ..      45     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                           DZR 13 rfCseCgtklkavaaedrCpsCgek 37
                                  +fC++C++ + + +   +C +Cg++
  gi|91774117|ref|YP_566809.1|  2 EFCPKCKSMMHPIEGTLKCRKCGYE 26
                                  69*******99999999*****997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.033
                           DZR 11 darfCseCgtk.....lkavaa..........edrCpsCge 36
                                      C+eCg++     l+   +            +C +C++
  gi|91774117|ref|YP_566809.1| 60 TTARCEECGNNtaywwLR---QlrsadesetrFFKCIKCSY 97
                                  455688888875555422...03335556666666777765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00035      0.29      31      56 ..       4      27 ..       2      32 .. 0.89
   2 ?    7.9   2.0    0.0035       2.8      27      56 ..      60      99 ..      42     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfea 56
                                  C++C s + +   + t+kC++Cg+e 
  gi|91774117|ref|YP_566809.1|  4 CPKCKSMMHP--IEGTLKCRKCGYEK 27
                                  **********..***********985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0035
                OrfB_Zn_ribbon 27 TSktCseCgsknke..........alsgrtfkCpnCgfea 56
                                  T  +C eCg +  +          + ++r fkC +C +++
  gi|91774117|ref|YP_566809.1| 60 TTARCEECGNNTAYwwlrqlrsadESETRFFKCIKCSYTW 99
                                  6779*****9999999999999999999********9986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00014      0.11       3      26 ..       4      27 ..       2      35 .. 0.86
   2 ?    2.9   2.0      0.13     1e+02       2      10 ..      63      71 ..      43     102 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                  -SSS-S--EE-SSEEE-TTT--EE CS
                zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedl 26
                                  Cp+C++ ++  + +++C++C  + 
  gi|91774117|ref|YP_566809.1|  4 CPKCKSMMHPIEGTLKCRKCGYEK 27
                                  *********9999*******8765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
                                  --SSS-S-- CS
                zinc-ribbons_6  2 kCpeCqqel 10
                                   C+eC +++
  gi|91774117|ref|YP_566809.1| 63 RCEECGNNT 71
                                  344444433 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.7   0.00091      0.74      64      95 ..      11      70 ..       2      75 .. 0.78
   2 ?    6.7   0.4    0.0084       6.9      64      93 ..      55      96 ..      31     103 .] 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00091
                                  EEEE--EEEETTTS-EEECHHH.HH...........................S-TTTSSS CS
                          HypA 64 ieevpvkvrCreCgkefeleek.al...........................rCpkCgsa 95
                                  ++ ++ +++Cr+Cg+e  ++++ +l                           rC++Cg++
  gi|91774117|ref|YP_566809.1| 11 MHPIEGTLKCRKCGYEKVKDAApDLlstssreerevtvlegdtdiglptttaRCEECGNN 70
                                  566788999999998877665333467889999999999999999999999999999986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0084
                                  EEEE--EEEETTTS-EEECHH.HHH...........S-TTTS CS
                          HypA 64 ieevpvkvrCreCgkefelee.kal...........rCpkCg 93
                                  i     ++rC+eCg+++     ++l           +C kC+
  gi|91774117|ref|YP_566809.1| 55 IGLPTTTARCEECGNNTAYWWlRQLrsadesetrffKCIKCS 96
                                  555667899999998776332112245566777777777775 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.071        58       2       8 ..       3       9 ..       2      13 .. 0.79
   2 ?    2.7   0.1      0.14   1.2e+02       3       9 ..      20      26 ..      19      34 .. 0.67
   3 ?    6.2   0.1     0.012       9.6       3      30 ..      64      97 ..      64      99 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.071
                                 B-TTT-- CS
                     Nudix_N_2 2 FCsqCGt 8
                                 FC++C +
  gi|91774117|ref|YP_566809.1| 3 FCPKCKS 9
                                 9999965 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                                  -TTT--B CS
                     Nudix_N_2  3 CsqCGtp 9 
                                  C++CG +
  gi|91774117|ref|YP_566809.1| 20 CRKCGYE 26
                                  8888865 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.012
                                  -TTT--B-E.....EE--TT-SS-EEE.ETTTTE CS
                     Nudix_N_2  3 CsqCGtpve.....lripdgDnreRlv.CpaCgt 30
                                  C++CG+ ++     +   ++++++R+  C +C++
  gi|91774117|ref|YP_566809.1| 64 CEECGNNTAywwlrQLRSADESETRFFkCIKCSY 97
                                  9*****9986665333446777777644777765 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 ?    9.2   1.7    0.0012      0.94       3      25 ..       4      25 ..       3      28 .. 0.81
   2 ?    5.9   0.0     0.012        10      19      24 ..      63      68 ..      57      73 .. 0.83
   3 ?   -1.3   0.2       2.3   1.8e+03       3       6 ..      92      95 ..      90      98 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                                  -SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGh 25
                                  C +C++ +  ++g  ++C++CG+
  gi|91774117|ref|YP_566809.1|  4 CPKCKSMMHPIEG-TLKCRKCGY 25
                                  8899999885555.5*******8 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                                  --SSS- CS
                DNA_RNApol_7kD 19 RCkeCG 24
                                  RC eCG
  gi|91774117|ref|YP_566809.1| 63 RCEECG 68
                                  9****9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.3
                                  -SSS CS
                DNA_RNApol_7kD  3 CgeC 6 
                                  C +C
  gi|91774117|ref|YP_566809.1| 92 CIKC 95
                                  4444 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 ?   12.5   2.5   0.00016      0.13      20      47 ..       3      26 ..       1      27 [. 0.87
   2 ?    2.1   2.9      0.28   2.3e+02      38      46 ..      87      97 ..      36     102 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                           IBR 20 wCprpdCeaiieksegcksvtCskCgfe 47
                                   Cp  +C++++++ eg+  ++C+kCg+e
  gi|91774117|ref|YP_566809.1|  3 FCP--KCKSMMHPIEGT--LKCRKCGYE 26
                                  7*9..***********5..56*****97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.28
                           IBR 38 s..vtCskCgf 46
                                  +   +C kC++
  gi|91774117|ref|YP_566809.1| 87 TrfFKCIKCSY 97
                                  12344555544 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 ?    4.6   4.7     0.054        44       3      17 ..       3      17 ..       2      38 .. 0.88
   2 ?    2.3   0.0      0.29   2.3e+02       3       9 ..      63      69 ..      61      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.054
                       zf-IS66  3 tCpcCGgllkpiged 17
                                   Cp+C + ++pi+++
  gi|91774117|ref|YP_566809.1|  3 FCPKCKSMMHPIEGT 17
                                  6******99***987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.29
                       zf-IS66  3 tCpcCGg 9 
                                   C +CG 
  gi|91774117|ref|YP_566809.1| 63 RCEECGN 69
                                  5999997 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.064        52      22      28 ..       2       8 ..       1      11 [. 0.84
   2 ?    3.9   0.1     0.055        45      23      30 ..      19      26 ..      15      29 .. 0.65
   3 ?    3.3   0.0     0.085        69       6      13 ..      64      71 ..      63      81 .. 0.68
   4 ?    2.4   0.2      0.16   1.3e+02      24      30 ..      92      98 ..      90      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.064
                 A2L_zn_ribbon 22 lvCieCg 28
                                  ++C++C 
  gi|91774117|ref|YP_566809.1|  2 EFCPKCK 8 
                                  89****5 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.055
                 A2L_zn_ribbon 23 vCieCgas 30
                                   C +Cg++
  gi|91774117|ref|YP_566809.1| 19 KCRKCGYE 26
                                  47777765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.085
                 A2L_zn_ribbon  6 CsvCggng 13
                                  C+ Cg+n 
  gi|91774117|ref|YP_566809.1| 64 CEECGNNT 71
                                  55555554 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.16
                 A2L_zn_ribbon 24 CieCgas 30
                                  Ci+C+++
  gi|91774117|ref|YP_566809.1| 92 CIKCSYT 98
                                  8899875 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.049        40       5      10 ..       4       9 ..       3      10 .. 0.76
   2 ?    1.2   0.1      0.44   3.6e+02      22      28 ..      20      26 ..      16      26 .. 0.67
   3 ?    7.4   1.0    0.0053       4.3       3      29 ..      62      99 ..      57     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.049
                PhnA_Zn_Ribbon  5 CplCaS 10
                                  Cp+C+S
  gi|91774117|ref|YP_566809.1|  4 CPKCKS 9 
                                  777776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.44
                PhnA_Zn_Ribbon 22 CpeCahE 28
                                  C +C++E
  gi|91774117|ref|YP_566809.1| 20 CRKCGYE 26
                                  6677766 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0053
                PhnA_Zn_Ribbon  3 pkCplCaSeytY...........edgallvCpeCahEw 29
                                    C++C+  ++Y            ++  + C +C++ w
  gi|91774117|ref|YP_566809.1| 62 ARCEECGNNTAYwwlrqlrsadeSETRFFKCIKCSYTW 99
                                  58*****9999999999999888888888899998877 PP

>> CxC3  CxC3 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.6   0.00093      0.76      10      55 ..      18      71 ..       2      82 .. 0.83
   2 ?   -0.7   0.1       1.6   1.3e+03      45      54 ..      89      98 ..      80     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00093
                          CxC3 10 sccgeCkktgt........ltlkageesiavvtkeGrfdlnsaafkCssCsavr 55
                                   +c +C   ++        +t++ +e++++v   +  + l++++ +C++C++++
  gi|91774117|ref|YP_566809.1| 18 LKCRKCGYEKVkdaapdllSTSSREEREVTVLEGDTDIGLPTTTARCEECGNNT 71
                                  678888877777778887778888888888888888888***********9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                          CxC3 45 afkCssCsav 54
                                   fkC +Cs++
  gi|91774117|ref|YP_566809.1| 89 FFKCIKCSYT 98
                                  5888888875 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5      0.23   1.9e+02       5       9 ..       4       8 ..       3      10 .. 0.73
   2 ?    5.1   0.8     0.026        22      24      32 ..      16      24 ..       8      26 .. 0.80
   3 ?    4.3   0.0     0.048        39      25      33 ..      61      69 ..      54      70 .. 0.81
   4 ?    6.5   0.4    0.0094       7.7      26      36 .]      90     100 ..      84     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.23
                 zinc_ribbon_4 5 CpsCk 9
                                 Cp+Ck
  gi|91774117|ref|YP_566809.1| 4 CPKCK 8
                                 77776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                 zinc_ribbon_4 24 vkvrCskCg 32
                                  + ++C kCg
  gi|91774117|ref|YP_566809.1| 16 GTLKCRKCG 24
                                  679*****9 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.048
                 zinc_ribbon_4 25 kvrCskCgh 33
                                   +rC  Cg+
  gi|91774117|ref|YP_566809.1| 61 TARCEECGN 69
                                  679999986 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0094
                 zinc_ribbon_4  26 vrCskCghvFr 36 
                                    +C kC+ ++r
  gi|91774117|ref|YP_566809.1|  90 FKCIKCSYTWR 100
                                   69********7 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0034       2.8       4      12 ..       4      12 ..       4      15 .. 0.90
   2 ?    1.9   0.4      0.29   2.4e+02       3       8 ..      19      24 ..      18      25 .. 0.85
   3 ?    4.6   0.2     0.044        36       3      10 ..      63      70 ..      62      73 .. 0.84
   4 ?    3.6   0.3     0.085        69       1       8 [.      89      96 ..      89      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0034
                        zf-ACC  4 CpsCgemly 12
                                  Cp+C++m++
  gi|91774117|ref|YP_566809.1|  4 CPKCKSMMH 12
                                  *******97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.29
                        zf-ACC  3 KCpsCg 8 
                                  KC +Cg
  gi|91774117|ref|YP_566809.1| 19 KCRKCG 24
                                  899998 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.044
                        zf-ACC  3 KCpsCgem 10
                                  +C++Cg+ 
  gi|91774117|ref|YP_566809.1| 63 RCEECGNN 70
                                  6*****86 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.085
                        zf-ACC  1 WtKCpsCg 8 
                                  ++KC +C+
  gi|91774117|ref|YP_566809.1| 89 FFKCIKCS 96
                                  79*****6 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.3     0.025        20      15      19 ..       3       7 ..       2       9 .. 0.73
   2 ?    7.8   0.4    0.0033       2.7       1      11 [.      19      29 ..      19      33 .. 0.75
   3 ?    4.9   0.2     0.028        23       2       7 ..      64      69 ..      57      70 .. 0.65
   4 ?    0.2   0.3      0.84   6.8e+02      16      19 ..      92      95 ..      84      97 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                 zinc_ribbon_2 15 FCpyC 19
                                  FCp+C
  gi|91774117|ref|YP_566809.1|  3 FCPKC 7 
                                  77777 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                 zinc_ribbon_2  1 fCpnCGaelqd 11
                                  +C +CG+e  +
  gi|91774117|ref|YP_566809.1| 19 KCRKCGYEKVK 29
                                  79999998655 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.028
                 zinc_ribbon_2  2 CpnCGa 7 
                                  C +CG+
  gi|91774117|ref|YP_566809.1| 64 CEECGN 69
                                  555554 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.84
                 zinc_ribbon_2 16 CpyC 19
                                  C +C
  gi|91774117|ref|YP_566809.1| 92 CIKC 95
                                  7777 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.8   0.00021      0.17       2      24 ..       1      25 [.       1      26 [. 0.91
   2 ?    4.7   0.2     0.025        21       2      11 ..      61      70 ..      60      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                   zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGt 24
                                  + +CP+C++   + ++  +C +CG+
  gi|91774117|ref|YP_566809.1|  1 MEFCPKCKSmMhPIEGTLKCRKCGY 25
                                  679******977************8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.025
                   zf-ribbon_3  2 tvrCPnCGap 11
                                  t rC +CG++
  gi|91774117|ref|YP_566809.1| 61 TARCEECGNN 70
                                  67999***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 ?    2.7   0.2      0.13     1e+02      17      22 ..       4       9 ..       3      10 .. 0.89
   2 ?    6.2   0.2      0.01       8.4       3      10 ..      20      27 ..      19      29 .. 0.83
   3 ?    8.3   1.7    0.0023       1.9       2      14 ..      63      75 ..      63      75 .. 0.92
   4 ?    1.3   0.5      0.37     3e+02       1       9 [.      90      98 ..      90     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                  Rubredoxin_2 17 CpsCgs 22
                                  Cp C+s
  gi|91774117|ref|YP_566809.1|  4 CPKCKS 9 
                                  ****98 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
                  Rubredoxin_2  3 CsqCGfes 10
                                  C++CG+e 
  gi|91774117|ref|YP_566809.1| 20 CRKCGYEK 27
                                  ******85 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0023
                  Rubredoxin_2  2 vCsqCGfesakwf 14
                                  +C++CG+ +a w+
  gi|91774117|ref|YP_566809.1| 63 RCEECGNNTAYWW 75
                                  8********9996 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.37
                  Rubredoxin_2  1 YvCsqCGfe 9 
                                  + C +C+++
  gi|91774117|ref|YP_566809.1| 90 FKCIKCSYT 98
                                  7899**997 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.86     7e+02       3       9 ..       4      10 ..       3      14 .. 0.62
   2 ?   10.5   0.4   0.00058      0.48       1      47 [.      18      71 ..      18      76 .. 0.79
   3 ?   -1.1   0.1       2.4   1.9e+03      36      46 ..      88      98 ..      76     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.86
                          CpXC  3 CpaCgke 9 
                                  Cp+C+++
  gi|91774117|ref|YP_566809.1|  4 CPKCKSM 10
                                  6666654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00058
                          CpXC  1 ltCpaCgkefeae.iwtsidadedpelkeklldgsl......featCpkCgata 47
                                  l+C +Cg e   + +++++ +++++e +  +l+g+       ++a+C++Cg+++
  gi|91774117|ref|YP_566809.1| 18 LKCRKCGYEKVKDaAPDLLSTSSREEREVTVLEGDTdiglptTTARCEECGNNT 71
                                  79*****8776651678999999999999*****85333333799******976 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.4
                          CpXC 36 featCpkCgat 46
                                  + ++C kC +t
  gi|91774117|ref|YP_566809.1| 88 RFFKCIKCSYT 98
                                  56788888775 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 ?   -2.9   0.4       7.4     6e+03       7      11 ..       4       8 ..       4       9 .. 0.80
   2 ?    7.6   0.2    0.0039       3.1       3      11 ..      16      24 ..      15      26 .. 0.87
   3 ?    6.6   0.2    0.0079       6.4       3      12 ..      60      69 ..      59      72 .. 0.87
   4 ?   -0.2   0.1         1   8.5e+02       5      10 ..      90      95 ..      89      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.4
                    zf-C2H2_11  7 CleCG 11
                                  C +C+
  gi|91774117|ref|YP_566809.1|  4 CPKCK 8 
                                  88897 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0039
                    zf-C2H2_11  3 stcqCleCG 11
                                   t++C++CG
  gi|91774117|ref|YP_566809.1| 16 GTLKCRKCG 24
                                  79******9 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0079
                    zf-C2H2_11  3 stcqCleCGl 12
                                  +t +C eCG 
  gi|91774117|ref|YP_566809.1| 60 TTARCEECGN 69
                                  79******95 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1
                    zf-C2H2_11  5 cqCleC 10
                                  ++C +C
  gi|91774117|ref|YP_566809.1| 90 FKCIKC 95
                                  58**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 729.94
//
Query:       gi|91774118|ref|YP_566810.1|  [L=139]
Description: NUDIX hydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-22   77.6   0.0      1e-21   77.4   0.0    1.0  1  NUDIX     NUDIX domain
    0.00029   20.4   0.0    0.00044   19.8   0.0    1.3  1  DUF4916   Domain of unknown function (DUF4916)


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 !   77.4   0.0   1.1e-25     1e-21       7     129 ..      13     126 ..       7     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1.1e-25
                                   EEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                         NUDIX   7 gvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheily 86 
                                   +v++ln+k  ++l++r+++pf++ ++lPgG+ve gEt e+AA+RE +EEtGl+ +l++l+g    +++++ ++++ h +++
  gi|91774118|ref|YP_566810.1|  13 AVIILNGK--IVLIKRNNYPFKNeFALPGGFVEVGETTEAAAIRESFEETGLSIDLVKLIG----VYSDPSRDPRGHTVSV 87 
                                   45599999..*************889**************************99*******....66777777779***** PP

                                   EEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                         NUDIX  87 vfleevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                   ++l+  +g++e n   + ++v ++++e+l  ++la ++rk+++
  gi|91774118|ref|YP_566810.1|  88 CYLATGHGNPEAN--TDAADVALFDPEKL--PELAFDHRKMID 126
                                   ***9999999988..7778899*******..888999998876 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     5e-08   0.00044     106     147 ..      76     117 ..      71     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5e-08
                                   SEE-TT-EEEEEEEEEEB-S-----TTEEEEEEE-HHHHTSH CS
                       DUF4916 106 eytdprqhavslayvvpvaGdceprqdaleleWltpeealse 147
                                   +  dpr h+vs++y+   +G+ e++ da +++ ++pe+  + 
  gi|91774118|ref|YP_566810.1|  76 PSRDPRGHTVSVCYLATGHGNPEANTDAADVALFDPEKLPEL 117
                                   568*********************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 951.83
//
Query:       gi|91774119|ref|YP_566811.1|  [L=270]
Description: hypothetical protein Mbur_2196 [Methanococcoides burtonii DSM 6242]
Scores for 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   48.3  15.9    1.9e-12   47.3  15.9    1.5  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
  ------ inclusion threshold ------
        1.5    8.7   5.0        5.9    6.8   0.4    3.5  3  Deltameth_res    Deltamethrin resistance


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3  15.9   2.1e-16   1.9e-12      74     254 ..      48     246 ..       4     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.1e-16
               Exosortase_EpsH  74 rvlllsalslvlillglvllllG...............................lralrlllfpllll.llalPlpavlva 122
                                    v++ + + ++                                             +l   + +++l  l+++P   + ++
  gi|91774119|ref|YP_566811.1|  48 YVAINDYFNVI-----------LtiaiaffclfmaqnmikgykgfsvseekghlNTVLMVTS-ATALGsLFYFP--FANIP 114
                                   22222222222...........0222222222234567777777888888776333333333.44444588888..66789 PP

               Exosortase_EpsH 123 qlslpLqllvaavagfllsllgipvereGnviqlptgqveVaeaCsGlrsllallalglllallfrrrlwkrkll.lllaa 202
                                    l+++++  v++ ++++l+ lg +v ++Gn i+ + + v++  aC+ +       +++l+ +l++  +++krkl+  ++++
  gi|91774119|ref|YP_566811.1| 115 SLNQWIISTVTNNTVWMLQTLGHDVLVSGNEIVYNGYAVSIILACTAI------ESIALFTGLIISINAPKRKLFqAFMVS 189
                                   99********************************9999*********5......556666666666666655444268899 PP

               Exosortase_EpsH 203 vpiaflaNlvRilllvlla..yhygpeaaegllH.....eiaGwllfgvalllllgllp 254
                                   vp+++ +Nl+R+++ +++   +++gpe++ + +H      ++G +lf++a ++++++lp
  gi|91774119|ref|YP_566811.1| 190 VPVIYSLNLIRNTFVIVAYgdQWFGPESF-EIAHhiiakFGSGIALFVIA-YVVMRILP 246
                                   ***************998733589*****.78884555445677888777.77777776 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4   0.00066       5.9      13      33 ..      47      67 ..      46      80 .. 0.89
   2 ?    0.9   0.0     0.046   4.1e+02      20      39 ..      89     108 ..      83     118 .. 0.79
   3 ?   -0.3   0.1      0.11   9.7e+02      26      40 ..     229     243 ..     226     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00066
                 Deltameth_res 13 qysakqrkYNavLaaGivili 33
                                  +y a +  +N +L ++i++++
  gi|91774119|ref|YP_566811.1| 47 HYVAINDYFNVILTIAIAFFC 67
                                  788999**************8 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.046
                 Deltameth_res  20 kYNavLaaGiviligTiala 39 
                                     N+vL++  ++  g+++++
  gi|91774119|ref|YP_566811.1|  89 HLNTVLMVTSATALGSLFYF 108
                                   56999999999999999986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.11
                 Deltameth_res  26 aaGiviligTialak 40 
                                    +Gi+ ++++ ++++
  gi|91774119|ref|YP_566811.1| 229 GSGIALFVIAYVVMR 243
                                   689*****9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1990.04
//
Query:       gi|91774120|ref|YP_566812.1|  [L=208]
Description: phosphatidylserine decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  102.3   5.1      1e-26   93.7   1.8    2.1  2  PS_Dcarbxylase  Phosphatidylserine decarboxylase
  ------ inclusion threshold ------
        0.1   13.3   0.0       0.17   12.6   0.0    1.3  1  Meiosis_expr    Meiosis-expressed


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   4.2e-05      0.37       4      34 ..      45      75 ..      42      78 .. 0.90
   2 !   93.7   1.8   1.2e-30     1e-26      70     199 ..      77     198 ..      74     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.2e-05
                PS_Dcarbxylase  4 ffvrklkdgaRpidddpgaivsPaDgrilqi 34
                                  f++++++d++R     +++++s aDg+++ +
  gi|91774120|ref|YP_566812.1| 45 FVIWFFRDPDRTTRICDHCMFSAADGKVMDV 75
                                  899**********999999********9876 PP

  == domain 2  score: 93.7 bits;  conditional E-value: 1.2e-30
                PS_Dcarbxylase  70 gyfvviyLspgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlvie.wkGkvavvpvGatnvgsivl 149
                                   g  v +++++ ++H+++ P+sg+v++++h +G +l++  ++ +++       eR+v+vi+ ++G+v v+++++ +v++iv 
  gi|91774120|ref|YP_566812.1|  77 GRRVCVFMNVHNVHVNRTPISGVVKSITHKKGGYLPAFHKDSERN-------ERTVTVIKsSHGEVNVTQIAGVMVRRIVS 150
                                   667899*****************************8877776665.......********659****************** PP

                PS_Dcarbxylase 150 nvlkgdelkkGeelGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                   +++ gdel  Ge++G+++fGS+v++ ++ +  ++   ++g++v++Ge+++
  gi|91774120|ref|YP_566812.1| 151 YINVGDELVNGEKIGMIRFGSRVDVTIPDD--FDIACKVGDRVYAGETVI 198
                                   ****************************99..7789************97 PP

>> Meiosis_expr  Meiosis-expressed
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05      0.17      28      73 ..      83     129 ..      74     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                  Meiosis_expr  28 ykevkkaeverWpetGfvkklq.rkdgtyyYynkeReCedkevhkvk 73 
                                   +++v++ +v+r p +G vk +  +k g+   ++k+ e +++ v+ +k
  gi|91774120|ref|YP_566812.1|  83 FMNVHNVHVNRTPISGVVKSIThKKGGYLPAFHKDSERNERTVTVIK 129
                                   8899999*************99455666679***********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1387.52
//
Query:       gi|91774121|ref|YP_566813.1|  [L=227]
Description: archaetidylserine synthase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-12   47.5   2.0    2.3e-12   47.5   2.0    3.4  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
        1.4    9.4   0.0        1.4    9.4   0.0    3.1  4  PhoR             Phosphate regulon sensor protein PhoR
        3.5    8.1   0.0        3.5    8.1   0.0    3.2  3  BatA             Aerotolerance regulator N-terminal


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 !   47.5   2.0   3.9e-16   2.3e-12       2      66 .]       9      71 ..       8      71 .. 0.92
   2 ?   -9.3  14.7         3   1.8e+04      11      35 ..     151     186 ..      75     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 3.9e-16
                                  -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
               CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                  +P+++Tl + ++++l+i+  ++ +   la++++l+a+++D+ DG+lARr+++ s +G+ lDslaD
  gi|91774121|ref|YP_566813.1|  9 IPDVVTLGNAMFGILSIFSAFSGK-ADLAFIFILFAAIADGADGFLARRMGS-SAIGENLDSLAD 71
                                  7****************8665554.6************************99.99*********9 PP

  == domain 2  score: -9.3 bits;  conditional E-value: 3
                                   HHHHHHHHHGGGS-H.............HHHHHHHH CS
               CDP-OH_P_transf  11 lllsvlailllltyyp...........lvlaillll 35 
                                   +++ +l +  l+++++           +++ai+++l
  gi|91774121|ref|YP_566813.1| 151 IVILMLLLSYLMISEHpypklrhpkamVIMAIIFML 186
                                   333222222223333366777777776444444443 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3      0.83   4.9e+03      18      38 ..      25      45 ..      14      47 .. 0.68
   2 ?    9.4   0.0   0.00023       1.4       9      50 ..      73     115 ..      66     126 .. 0.82
   3 ?   -1.8   0.3      0.72   4.3e+03      18      22 ..     153     157 ..     129     165 .. 0.52
   4 ?   -0.5   2.0      0.28   1.7e+03       6      39 ..     178     211 ..     173     220 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.83
                          PhoR 18 lvgllvgalaallllalllll 38
                                  ++++++g+  ++ +++l++++
  gi|91774121|ref|YP_566813.1| 25 IFSAFSGKADLAFIFILFAAI 45
                                  677788888888887777766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00023
                          PhoR   9 lallllaallvgllvgalaalll.lalllllawhlyqllrLsr 50 
                                   +++  ++a+++ l+ g+l++ l+  a+ ++++  + +l+r+++
  gi|91774121|ref|YP_566813.1|  73 ISFGTAPAVVIFLIYGHLQPYLVgTAACIYVLCGVLRLARFNT 115
                                   6778899****************99999999999999999953 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.72
                          PhoR  18 lvgll 22 
                                   +++ll
  gi|91774121|ref|YP_566813.1| 153 ILMLL 157
                                   22222 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.28
                          PhoR   6 llrlallllaallvgllvgalaallllallllla 39 
                                   ++  ++++l++l   +l ++l ++ +l+ ll+l+
  gi|91774121|ref|YP_566813.1| 178 VIMAIIFMLPVLSYFVLPEYLFIFATLIFLLMLL 211
                                   5556677777755555555555555544444443 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00059       3.5       4      41 ..      89     126 ..      87     131 .. 0.93
   2 ?   -1.3   0.6       0.5     3e+03      10      23 ..     148     160 ..     138     181 .. 0.62
   3 ?   -2.5   9.0       1.2   6.9e+03       4      25 ..     192     213 ..     162     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00059
                          BatA   4 FlnPllLlallllplpiillyllkrrpqevvfsslrll 41 
                                   +l+P+l + ++++ +++ +l+l + + + +++++++ l
  gi|91774121|ref|YP_566813.1|  89 HLQPYLVGTAACIYVLCGVLRLARFNTKHKEIPDFEGL 126
                                   899******************************99876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.5
                          BatA  10 Llallllplpiill 23 
                                   L + ++l l ++ +
  gi|91774121|ref|YP_566813.1| 148 LYGIVILML-LLSY 160
                                   444445555.2222 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.2
                          BatA   4 FlnPllLlallllplpiillyl 25 
                                   F  P++L+ ++ l+ +++llyl
  gi|91774121|ref|YP_566813.1| 192 FVLPEYLFIFATLIFLLMLLYL 213
                                   8889****99999998999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1434.47
//
Query:       gi|91774122|ref|YP_566814.1|  [L=869]
Description: ATPase AAA-2 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  206.8   1.8    2.4e-57  193.8   0.1    3.6  3  AAA_2            AAA domain (Cdc48 subfamily)
    6.5e-35  119.2   4.4    6.5e-35  119.2   4.4    3.9  3  AAA_lid_9        AAA lid domain
    2.6e-26   91.5   1.2    1.9e-15   56.7   0.2    3.2  2  Clp_N            Clp amino terminal domain, pathogenicity isl
    2.5e-23   83.0   0.1    4.7e-10   40.0   0.1    3.1  2  AAA              ATPase family associated with various cellul
    3.8e-23   81.4   1.0    3.8e-23   81.4   1.0    3.3  2  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    5.8e-17   62.0   0.3      1e-12   48.3   0.0    3.8  4  AAA_5            AAA domain (dynein-related subfamily)
    4.1e-09   36.4   0.1    3.8e-06   26.7   0.0    2.8  2  Sigma54_activat  Sigma-54 interaction domain
    7.3e-09   36.2   8.1    0.00014   22.3   0.0    5.0  4  AAA_16           AAA ATPase domain
    1.7e-08   34.8   0.8      0.043   14.1   0.1    4.7  3  AAA_22           AAA domain
    1.5e-07   31.1   0.0     0.0061   16.1   0.0    3.1  3  AAA_7            P-loop containing dynein motor region
    2.3e-07   30.7   0.0     0.0069   16.1   0.0    3.0  2  IstB_IS21        IstB-like ATP binding protein
    7.9e-07   29.2   0.0      0.019   15.0   0.0    2.9  2  AAA_14           AAA domain
    3.9e-06   26.9   0.0      0.018   14.9   0.0    3.0  2  NACHT            NACHT domain
    6.5e-06   26.2   7.6       0.14   12.0   0.0    4.8  4  ATPase_2         ATPase domain predominantly from Archaea
    7.6e-06   25.5   0.0     0.0048   16.3   0.0    3.6  2  TniB             Bacterial TniB protein
    1.2e-05   25.5   0.0      0.083   13.1   0.0    3.4  3  Roc              Ras of Complex, Roc, domain of DAPkinase
    4.3e-05   23.5   0.0       0.35   10.8   0.0    3.3  3  RsgA_GTPase      RsgA GTPase
    5.3e-05   23.8   0.1      0.037   14.6   0.0    3.8  2  AAA_18           AAA domain
    8.2e-05   22.9   0.1        0.3   11.5   0.0    3.2  2  RNA_helicase     RNA helicase
    9.7e-05   21.8   0.5       0.42    9.9   0.1    3.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00028   20.5   0.0       0.19   11.3   0.0    2.8  2  AAA_25           AAA domain
     0.0003   20.3   0.0       0.33   10.4   0.0    2.9  2  PhoH             PhoH-like protein
    0.00031   20.1   0.1     0.0084   15.4   0.0    3.0  2  Zeta_toxin       Zeta toxin
    0.00052   19.8   3.1      0.049   13.4   0.0    3.8  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00064   19.8   0.7        1.4    8.9   0.0    4.1  4  ResIII           Type III restriction enzyme, res subunit
     0.0007   18.8   2.1       0.52    9.4   0.1    3.5  3  DUF815           Protein of unknown function (DUF815)
    0.00079   19.9   0.5       0.14   12.7   0.0    3.5  3  ABC_tran         ABC transporter
     0.0011   19.1   0.0     0.0033   17.5   0.0    1.8  1  Torsin           Torsin
     0.0012   19.2   0.1       0.67   10.2   0.0    3.8  3  AAA_28           AAA domain
     0.0022   18.0   0.0        3.3    7.7   0.0    2.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0026   17.6   0.0        2.9    7.7   0.0    3.4  2  Bac_DnaA         Bacterial dnaA  protein
     0.0027   16.8   0.1      0.062   12.4   0.0    2.6  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.012   15.8   0.0       0.77    9.9   0.0    2.8  2  AAA_33           AAA domain
      0.016   14.9   0.0        6.3    6.5   0.0    3.2  2  AAA_30           AAA domain
       0.02   14.5   0.2          9    5.9   0.0    3.3  3  Ras              Ras family
      0.029   13.2   4.9      0.057   12.3   4.9    1.4  1  PV-1             PV-1 protein (PLVAP)
      0.032   14.0   0.0        9.2    6.1   0.0    2.8  2  AAA_29           P-loop containing region of AAA domain
      0.039   13.7   0.0        0.3   10.9   0.0    2.4  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.054   13.1   0.0         10    5.7   0.0    2.8  2  SRP54            SRP54-type protein, GTPase domain
      0.062   13.2   0.1        1.1    9.1   0.0    2.9  2  AAA_3            ATPase family associated with various cellul
      0.067   13.5   0.0        6.1    7.2   0.1    3.6  3  AAA_19           AAA domain
      0.074   12.8   0.0        1.9    8.3   0.0    2.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.31   11.5   0.0       0.31   11.5   0.0    5.1  2  AAA_23           AAA domain
        2.3    8.3   0.0        2.3    8.3   0.0    5.1  4  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.3   9.3e+02      10      57 ..      75     117 ..      66     139 .. 0.61
   2 !    9.8   0.1     0.002       0.8       5      82 ..     203     287 ..     199     331 .. 0.79
   3 !  193.8   0.1   5.9e-60   2.4e-57       1     170 [.     600     764 ..     600     765 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.3
                                   --TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHH CS
                         AAA_2  10 gptgvGktelakalaellfvkkekkliradaselleeeevehlvsrli 57 
                                     +g+G+t++++a +++l+   e++   ++  e++    veh++  l+
  gi|91774122|ref|YP_566814.1|  75 SGSGSGQTYVSQAYSRVLDT-AENEASSMND-EYIS---VEHVLIALL 117
                                   55789999999999999994.4444443332.3333...355544444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.002
                                   -EEEE--TTSSHHHHHHHHHHHTT-..........-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGG CS
                         AAA_2   5 silllgptgvGktelakalaellfv......kkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEid 78 
                                   +  l+g+ gvGkt + + la  +         k+kk+i +d+ +l+ + + +   ++ + a    v+  eg  i+++DE+ 
  gi|91774122|ref|YP_566814.1| 203 NPVLIGEAGVGKTAIVEGLALRIAKhdipedMKNKKIIALDMGALIAGAKFRGEFEERLKAVLKEVADSEGQiILFIDELH 283
                                   567899********888888666656888888999************999999998888888888877776657899**98 PP

                                   G--- CS
                         AAA_2  79 Kihp 82 
                                    i  
  gi|91774122|ref|YP_566814.1| 284 TIVG 287
                                   8776 PP

  == domain 3  score: 193.8 bits;  conditional E-value: 5.9e-60
                                   -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS........... CS
                         AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG........... 70 
                                   rpi+s+++lgptgvGktelakala  +f ++e+++ir+d+se++e    +h+vsrligappgy+g++egG           
  gi|91774122|ref|YP_566814.1| 600 RPIGSFIFLGPTGVGKTELAKALAAEMF-NDENNMIRIDMSEYME----KHTVSRLIGAPPGYIGHDEGGqlteavrrrpy 675
                                   699*************************.9***************....******************************** PP

                                   .EEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS-STTTTSGGG- CS
                         AAA_2  71 .ivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrskeeeeekkke 150
                                    +vl+DEi+K+h+           +V++++Lqil++g+ltd++gr+vd+kn+l+Imt+++ ++++ ++ + + e++ k++e
  gi|91774122|ref|YP_566814.1| 676 aVVLFDEIEKAHH-----------DVFNVMLQILDDGRLTDSHGRTVDFKNTLIIMTSNICVDRTLSKLE-EGEDYAKMQE 744
                                   *************...........****************************************999544.599******* PP

                                   -HHHHHHTT--HHHHTT--E CS
                         AAA_2 151 eveeelkkglipEllgRlpe 170
                                   ++++el k+++pE+++R++e
  gi|91774122|ref|YP_566814.1| 745 MAQNELAKHFRPEFINRIDE 764
                                   ******************97 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.9   1.2e+03      26      43 ..      11      28 ..       8      30 .. 0.88
   2 !  119.2   4.4   1.6e-37   6.5e-35       2     103 ..     345     446 ..     344     449 .. 0.97
   3 ?    3.0   0.2      0.24        98      61     101 ..     463     504 ..     451     507 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.9
                     AAA_lid_9 26 dealeaavklSkrYisdr 43
                                  +ea++++ ++++rY +++
  gi|91774122|ref|YP_566814.1| 11 QEAIQKSFSIAARYYNQQ 28
                                  79************9875 PP

  == domain 2  score: 119.2 bits;  conditional E-value: 1.6e-37
                     AAA_lid_9   2 eeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeeleklekelakle 82 
                                   +e+ti+iLrglkekye hHgv+i+d al+aa+ lS+rYisdrflPdkAIDl+Deaaa+vr++ +skp+el+++++++ +le
  gi|91774122|ref|YP_566814.1| 345 VENTISILRGLKEKYEVHHGVRIKDTALVAAAVLSNRYISDRFLPDKAIDLVDEAAAKVRTAIDSKPSELDEADRKILQLE 425
                                   799****************************************************************************** PP

                     AAA_lid_9  83 kekealekeeekekaerlkel 103
                                    e+eal+ke++  ++er+++l
  gi|91774122|ref|YP_566814.1| 426 IEREALKKEKDAVSKERVADL 446
                                   ***********9999998775 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.24
                     AAA_lid_9  61 rlkkes.kpeeleklekelaklekekealekeeekekaerlk 101
                                   + ++e+ + ++l +l++++++++ + e +e++ ++e a++lk
  gi|91774122|ref|YP_566814.1| 463 KWQSEKdTIANLGSLKQQIEDIKIQLELAENSGDFELASKLK 504
                                   333333044668899*****************9999999886 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   1.8e-10   7.3e-08       2      52 ..      18      68 ..      17      69 .. 0.95
   2 !   56.7   0.2   4.7e-18   1.9e-15       1      53 []      95     147 ..      95     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.8e-10
                                  HHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHH CS
                         Clp_N  2 qelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekll 52
                                  +++A ++ +q+ + EHLLlAL e+ +Gl   +L + G+  + + k++e++l
  gi|91774122|ref|YP_566814.1| 18 FSIAARYYNQQTECEHLLLALVEQTGGLVPTILDRIGAENQSIIKELEDHL 68
                                  57899999****************************************987 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 4.7e-18
                                   HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHHC CS
                         Clp_N   1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekllg 53 
                                   A+ +A s++++yis+EH+L+ALl+e++++  r+L++aG+++da  +ai+kl+g
  gi|91774122|ref|YP_566814.1|  95 AENEASSMNDEYISVEHVLIALLKEKESTSYRILEEAGITIDATLEAIKKLRG 147
                                   889************************************************97 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 !   40.0   0.1   1.1e-12   4.7e-10       2     111 ..     205     318 ..     204     338 .. 0.79
   2 !   39.5   0.0   1.6e-12   6.7e-10       2     113 ..     606     727 ..     605     740 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.1e-12
                                   EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                           AAA   2 llyGppGtGKTllakavakel..........gvefleisgsell..skyvgesekkirelfkeakekakpsilfiDEidal 70 
                                   +l+G  G+GKT++++ +a  +          + +++ +++  l+   k+ ge e+++++++ke+  ++++ ilfiDE++ +
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLALRIakhdipedmkNKKIIALDMGALIagAKFRGEFEERLKAVLKEVADSEGQIILFIDELHTI 285
                                   599***************997555555555457799999999997778***************7666658*********** PP

                                   HHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                           AAA  71 aksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                   +++    ++e ++++ n L ++l + +       +igat+ 
  gi|91774122|ref|YP_566814.1| 286 VGAG---ATEGAMDAGNLLKPMLARGEL-----HCIGATTL 318
                                   ***9...777777777777777777665.....57888775 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 1.6e-12
                                   EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS............STTHHHH.HHHHHHHHHHHTSTS.EEEEEE CS
                           AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk............yvgesek.kirelfkeakekakp.silfiD 65 
                                   ++ Gp G+GKT laka+a e+   + ++++i++se ++k            y+g+ e  ++ e +++      p  ++++D
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMfndENNMIRIDMSEYMEKhtvsrligappgYIGHDEGgQLTEAVRR---R--PyAVVLFD 681
                                   789*****************9766699**********999***********9998886134444433...3..559***** PP

                                   TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.GG CS
                           AAA  66 EidalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.pd 113
                                   Ei++ + +             n++l+ ld+ +           +++++i+++n  +d
  gi|91774122|ref|YP_566814.1| 682 EIEKAHHDV-----------FNVMLQILDDGRLTdshgrtvdFKNTLIIMTSNIcVD 727
                                   *****8777...........**********999999999999555899999997554 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       6.1   2.5e+03      14      33 ..     474     493 ..     470     502 .. 0.83
   2 !   81.4   1.0   9.2e-26   3.8e-23       1      81 []     771     851 ..     771     851 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.1
                                   HHHHHHHSCTTTEEEEEHHH CS
                 ClpB_D2-small  14 lkklekrlkergvelevtde 33 
                                   l  l++++++ +++le+ ++
  gi|91774122|ref|YP_566814.1| 474 LGSLKQQIEDIKIQLELAEN 493
                                   788999999999*9999886 PP

  == domain 2  score: 81.4 bits;  conditional E-value: 9.2e-26
                                   SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSSTTSEEEE CS
                 ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelkegdtvrv 81 
                                   Ltke+l+ Ivd++  +l +rlke+++ le++++a+ +lae+gy++ yGARpL+r+iq+e+e+++a++i+ g+  eg+t++v
  gi|91774122|ref|YP_566814.1| 771 LTKEQLVTIVDIKATDLIQRLKEKRMVLEISKKAKHYLAEAGYSETYGARPLKRVIQNEVETAVAKLIVGGQALEGSTIEV 851
                                   89***************************************************************************9986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       8.5   3.5e+03       8      29 ..      77      99 ..      76     126 .. 0.73
   2 !    9.1   0.0     0.003       1.2       3      24 ..     205     227 ..     203     287 .. 0.68
   3 !   48.3   0.0   2.4e-15     1e-12       2     122 ..     605     724 ..     604     736 .. 0.84
   4 ?   -1.3   0.0         5     2e+03      52      94 ..     743     785 ..     727     796 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.5
                                  SSSSHHHHHHHGGGGB.S--EEE CS
                         AAA_5  8 pGtgKselaerlaaal.nrevey 29
                                  +G+g + +++ ++++l ++e e 
  gi|91774122|ref|YP_566814.1| 77 SGSGQTYVSQAYSRVLdTAENEA 99
                                  69999*****9999997444444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.003
                                   EEE--SSSSHHHHHHHGGGGB.S CS
                         AAA_5   3 lLvGppGtgKselaerlaaal.n 24 
                                   +L+G+ G+gK+ ++e la ++ +
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLALRIaK 227
                                   79*************99988863 PP

  == domain 3  score: 48.3 bits;  conditional E-value: 2.4e-15
                                   EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--..........--------..G-SEEEEESGGG CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttsl.vdsplvraar..egeilvlDEver 76 
                                   ++ +Gp+G+gK+ela+ laa +   ++++  + +++++++ ++   +   +g   + + + l++a+r    +++++DE+e+
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMfndENNMIRIDMSEYMEKHTVSRLIGAPPGYIGHdEGGQLTEAVRrrPYAVVLFDEIEK 685
                                   799***************99999777777778899999999998888866555544155799999998888999******* PP

                                   --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS CS
                         AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanp 122
                                   a+ +v+n++l++l++ rl  ++ g+ v++kn      + +i+t+n 
  gi|91774122|ref|YP_566814.1| 686 AHHDVFNVMLQILDDGRLT-DSHGRTVDFKN------TLIIMTSNI 724
                                   ******************9.88888899999......789999985 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 5
                                   .....--------G-SEEEEESGGG--HHHHHHHHHHHHSSEE CS
                         AAA_5  52 tslvdsplvraaregeilvlDEveraesevlnsLlslleerrl 94 
                                   +++ +++l + +r   i ++DE+   ++ + + L ++ + +  
  gi|91774122|ref|YP_566814.1| 743 QEMAQNELAKHFRPEFINRIDELAIFRPLTKEQLVTIVDIKAT 785
                                   5677788888888888888888888788777777777776555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.013       5.1       2      60 ..     183     246 ..     182     257 .. 0.66
   2 !   26.7   0.0   9.4e-09   3.8e-06      23     147 ..     603     728 ..     574     746 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                                   ---SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH......HH.HSTTTTS-EEEEETTT CS
               Sigma54_activat   2 igesealkelleqikkvaktdlsvlitGesGtGKellarai......he.askrkekpfvavncaa 60 
                                   ig+++++++++e +++   ++ +vl  Ge G+GK+ + + +      h+  ++ k+k+++a++++a
  gi|91774122|ref|YP_566814.1| 183 IGRDQEIRHTIEILSRRR-KNNPVL-IGEAGVGKTAIVEGLalriakHDiPEDMKNKKIIALDMGA 246
                                   677777777777776653.445665.5********9988763333333343445666777777766 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 9.4e-09
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BE..HHHHHTTTSEEEEET CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekk..GlfekadgGtlfLDe 101
                                    s + +G +G+GK+ la+a+ ++  ++e+++++++++++ e+   s+L G   G + G ++  +   ++++    ++++De
  gi|91774122|ref|YP_566814.1| 603 GSFIFLGPTGVGKTELAKALAAEMFNDENNMIRIDMSEYMEKHTVSRLIGAPPG-YIGHDEGGQltEAVRRRPYAVVLFDE 682
                                   466789*********************************************999.778766544345566667799***** PP

                                   GGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HHH CS
               Sigma54_activat 102 igelplelQekLlrvlqegevervGsskeikvdvriiaatnedlee 147
                                   i++   ++ + +l++l++g+++   +++    ++ ii+++n  +++
  gi|91774122|ref|YP_566814.1| 683 IEKAHHDVFNVMLQILDDGRLTDSHGRTVDFKNTLIIMTSNICVDR 728
                                   *******************988765555555566677666655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       3.4   1.4e+03      57     130 ..      28      95 ..       6     148 .. 0.65
   2 !   22.3   0.0   3.4e-07   0.00014       2      51 ..     182     228 ..     181     253 .. 0.80
   3 ?    3.9   0.0      0.16        63     110     146 ..     252     284 ..     230     311 .. 0.69
   4 !   10.7   0.0    0.0012       0.5      23      49 ..     600     627 ..     573     655 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.4
                        AAA_16  57 rgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaea..srllellkrllall 130
                                   +++c++l     ++al+++    +l+  +ld+  + e +   ++le+ l++ p+++g+++  + + ++ +r l+ +
  gi|91774122|ref|YP_566814.1|  28 QTECEHL-----LLALVEQT-G-GLVPTILDRIGA-ENQSIIKELEDHLSELPQVSGSGSgqTYVSQAYSRVLDTA 95 
                                   3344444.....34566666.5.788888888555.5555555577777777777777777633333333333333 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.4e-07
                        AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                   ++GR++e+++  ++l+r r+   ++ +l+Ge+GvGK+++v+ l+ ++ k+
  gi|91774122|ref|YP_566814.1| 182 VIGRDQEIRHTIEILSRRRK---NNPVLIGEAGVGKTAIVEGLALRIAKH 228
                                   78******666666665555...55589************9888777766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.16
                        AAA_16 110 elagaeasrllellkrllallsrderplvlvlDdlqw 146
                                   + +g+ ++rl ++lk+ +    + e +++l++D+l+ 
  gi|91774122|ref|YP_566814.1| 252 KFRGEFEERLKAVLKEVA---DS-EGQIILFIDELHT 284
                                   444554556666666655...44.555********93 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0012
                        AAA_16  23 rp.elvllsGesGvGKsslvrellrale 49 
                                   rp ++ ++ G+ GvGK+ l+++l+ ++ 
  gi|91774122|ref|YP_566814.1| 600 RPiGSFIFLGPTGVGKTELAKALAAEMF 627
                                   3389999**************9997765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.3   5.3e+02      14      46 ..      77     110 ..      76     160 .. 0.73
   2 !   13.4   0.0   0.00017      0.07       4     102 ..     200     284 ..     197     320 .. 0.63
   3 !   14.1   0.1   0.00011     0.043       7     130 ..     604     720 ..     600     724 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                        AAA_22  14 sGtGKTtllrrlleqldeeakaee.erpevvfvt 46 
                                   sG+G T++ + + + ld +++ +  +++e+++v+
  gi|91774122|ref|YP_566814.1|  77 SGSGQTYVSQAYSRVLDTAENEASsMNDEYISVE 110
                                   79***********999988777778666666332 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00017
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelkaerlsseelleale 83 
                                   +++  v++Ge+G+GKT  ++ l+ +              ++ ++p++++ k++ + ++   +   + + +  +e+l + l 
  gi|91774122|ref|YP_566814.1| 200 RKNNPVLIGEAGVGKTAIVEGLALRI-------------AKHDIPEDMKNKKIiALDMGALIAGAKFR-GEFEERLKAVLK 266
                                   677789*****************997.............44555666633333244444444443333.333333333333 PP

                        AAA_22  84 qalraravielliiDEaqh 102
                                   + +++ +   +l iDE + 
  gi|91774122|ref|YP_566814.1| 267 EVADSEGQ-IILFIDELHT 284
                                   34444444.6666666665 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 0.00011
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                   + +  G++G+GKT l++ l+ +  ++      +   +++++++ ++  ++     r +g +  +     ++   +l++a+r
  gi|91774122|ref|YP_566814.1| 604 SFIFLGPTGVGKTELAKALAAEMFND------ENNMIRIDMSEYMEKHTV----SRLIGAPPGY---IGHDEGGQLTEAVR 671
                                   56778***************998665......888999999999965544....5666666666...56666789999999 PP

                        AAA_22  88 aravielliiDEaqhlrseealeeLrsllnl........srkgvqliLvGt 130
                                   +r   ++++ DE+++  ++++++   ++l++        ++ +++  L+++
  gi|91774122|ref|YP_566814.1| 672 RRPY-AVVLFDEIEKA-HHDVFNVMLQILDDgrltdshgRTVDFKNTLIIM 720
                                   9999.99999999999.8888888888888777766666666666666666 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       2.8   1.1e+03      29      68 ..      64     103 ..      46     118 .. 0.80
   2 !   10.8   0.0   0.00063      0.26      32     109 ..     200     282 ..     186     308 .. 0.63
   3 !   16.1   0.0   1.5e-05    0.0061      36      82 ..     605     651 ..     600     654 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.8
                         AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldkekylsltin 68 
                                   l ++  ++  v  +G+G t + + + + ld+ +    ++n
  gi|91774122|ref|YP_566814.1|  64 LEDHLSELPQVSGSGSGQTYVSQAYSRVLDTAENEASSMN 103
                                   55555555667789**************999888877776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00063
                         AAA_7  32 nkkpvllvGptGtGKtviikdllkkld....k...ekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvF 105
                                   +k++ +l+G++G+GKt+i++ l  ++     +   ++ +++ + + a    ++++  +e++l+   k+v     + ++++F
  gi|91774122|ref|YP_566814.1| 200 RKNNPVLIGEAGVGKTAIVEGLALRIAkhdiPedmKNKKIIALDMGALIAGAKFRGEFEERLKAVLKEVAD--SEGQIILF 278
                                   45567899************954443301121111233444455555555566655555555555555533..34456666 PP

                         AAA_7 106 vDDl 109
                                   +D+l
  gi|91774122|ref|YP_566814.1| 279 IDEL 282
                                   6666 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.5e-05
                         AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                                   +++ GptG+GKt ++k l  ++ +++ +++ i +s +++ +++ ++i
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMFNDENNMIRIDMSEYMEKHTVSRLI 651
                                   689**************9999999***************99999887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00063      0.26      45     108 ..     199     266 ..     185     282 .. 0.77
   2 !   16.1   0.0   1.7e-05    0.0069      50      80 ..     605     635 ..     587     653 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00063
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialg....veavraglsvlfvrvedLveelkrarrdgklaralkrllk 108
                                   ++k+n vl+G +GvGK+ +   l+    ++ + ++++   + + d+ + ++ a+  g+++++lk++lk
  gi|91774122|ref|YP_566814.1| 199 RRKNNPVLIGEAGVGKTAIVEGLAlriaKHDIPEDMKNKKIIALDMGALIAGAKFRGEFEERLKAVLK 266
                                   57899************976665500005556667777778888888888888888888888887665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.7e-05
                     IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlf 80 
                                   +++lGp+GvGK+ la al+ e  +++ +++ 
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMFNDENNMIR 635
                                   799*****************99987776655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00087      0.35       6      78 ..     205     287 ..     201     327 .. 0.70
   2 !   15.0   0.0   4.8e-05     0.019       6      90 ..     606     701 ..     603     714 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00087
                        AAA_14   6 vitGaRrvGKTtllkqlikell.......vkkesilyinldderd.kkla.dpekllelilek.lkeekktylflDEiqev 76 
                                   v+ G   vGKT +++ l+ +         +k+++i+ +++      +k++ ++e+ l+++l++ + +e++ +lf+DE + +
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLALRIAkhdipedMKNKKIIALDMGALIAgAKFRgEFEERLKAVLKEvADSEGQIILFIDELHTI 285
                                   5678889*****998774332244459777777777777666444333333455566677776344489999******998 PP

                        AAA_14  77 pe 78 
                                    +
  gi|91774122|ref|YP_566814.1| 286 VG 287
                                   44 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.8e-05
                        AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe...............kllelileklkeekktylflD 71 
                                   +  G+  vGKT l+k l+ e + ++++++ i++ +  +k     +               +l e++++    +   ++++D
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMFNDENNMIRIDMSEYMEKHTVS-RligappgyighdeggQLTEAVRR----RPYAVVLFD 681
                                   567999**************99999*******99977744321.122323333333222223333333....234569*** PP

                        AAA_14  72 Eiqev.pewekalkslvdeg 90 
                                   Ei ++  ++++++ +++d+g
  gi|91774122|ref|YP_566814.1| 682 EIEKAhHDVFNVMLQILDDG 701
                                   **998346888888888877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.5e-05     0.018       4      33 ..     205     234 ..     204     304 .. 0.91
   2 !    8.7   0.0    0.0037       1.5       4     161 ..     606     756 ..     604     761 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.5e-05
                                   EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC CS
                         NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqga 33 
                                   +l GeaG+GKT+ +++lal +a+ + p+++
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLALRIAKHDIPEDM 234
                                   689*********************999875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0037
                                   EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEE CS
                         NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelperlL 84 
                                   i  G+ G+GKT L++ la ++  ++ +  + +++ +++ +++sr   a  + ++ ++++ ++ ++v++        +  ++
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMFNDENNMIRIDMSEYMEKHTVSRLIGA-PPGYIGHDEGGQLTEAVRR--------RPYAV 677
                                   678***************999888877766777777766666665555.4555555555555555544........55555 PP

                                   EEEE-STT-SS-TCH..........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE...EEEE--TCCHHHHHHHH CS
                         NACHT  85 lilDglDelvtdlgq.kekqpvrtlLselirkkllpeasllltvrpralrdleeqleea.ivlevegfsesrrkqlvrk 161
                                    ++D +++++ d  + + +   +  L++   +++  +++l++ +++ ++ +  ++lee   +++++++ +++ ++ +r 
  gi|91774122|ref|YP_566814.1| 678 VLFDEIEKAHHDVFNvMLQILDDGRLTDSHGRTVDFKNTLIIMTSNICVDRTLSKLEEGeDYAKMQEMAQNELAKHFRP 756
                                   6677777666654444445555556666666666666666666666666554444444446666666666666666665 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 !    7.7   0.1    0.0072       2.9       4      40 ..     185     221 ..     183     231 .. 0.86
   2 !   12.0   0.0   0.00035      0.14     100     206 ..     255     356 ..     224     369 .. 0.70
   3 ?    5.8   0.0     0.029        12      25      62 ..     606     643 ..     597     670 .. 0.74
   4 ?    1.3   0.1      0.68   2.8e+02     119     223 ..     675     780 ..     664     790 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0072
                      ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkei 40 
                                   R++e++   eil+r +++  ++ G  g+GKta++  +
  gi|91774122|ref|YP_566814.1| 185 RDQEIRHTIEILSRRRKNNPVLIGEAGVGKTAIVEGL 221
                                   99*****9999999999999999*********98765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00035
                      ATPase_2 100 klvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSeglfiervynesel 180
                                    + ++ ++++l+++ ++  +ii++iDel  ++  g  + +    +Ll+ +      +   ++i ++     ++++++ + l
  gi|91774122|ref|YP_566814.1| 255 GEFEERLKAVLKEVADSEGQIILFIDELHTIVGAGATEGAMDAGNLLKPMLA----RGELHCIGATTLDEYRKYIEKDAAL 331
                                   5668899*************************76666444433333333333....4445667777777777777777777 PP

                      ATPase_2 181 egrhkyilvddldketalnflkegfk 206
                                   e r   +lvd  d e++  +l+ + k
  gi|91774122|ref|YP_566814.1| 332 ERRFLPVLVDQPDVENTISILRGL-K 356
                                   777777777777777777777765.4 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.029
                      ATPase_2  25 iY.GpegsGKtaLlkeiienledkdkyviyyialreesi 62 
                                   i+ Gp g+GKt L k ++ +  + + + +  i+++e+ +
  gi|91774122|ref|YP_566814.1| 606 IFlGPTGVGKTELAKALAAEMFNDENN-MIRIDMSEYME 643
                                   444*************99998554433.33444444444 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.68
                      ATPase_2 119 kiiiiiDelqklidlglngaellvkeL..lnliesl..tkekhlcvviclsSeglfiervyneselegrhkyilvddldke 195
                                     ++++De+ k+ +  +n    +++ L   +l +s+  t + + +++i++s   + +      s+le+  +y++++ + ++
  gi|91774122|ref|YP_566814.1| 675 YAVVLFDEIEKAHHDVFN---VMLQILddGRLTDSHgrTVDFKNTLIIMTSNICVDRT----LSKLEEGEDYAKMQEMAQN 748
                                   378889999998855555...3333331122333321155666777777777777777....8999999999999999654 PP

                      ATPase_2 196 t.alnflkegfkeleel...skedfeeiyryv 223
                                   + a+ f  e  + + el       +e+++ +v
  gi|91774122|ref|YP_566814.1| 749 ElAKHFRPEFINRIDELaifRPLTKEQLVTIV 780
                                   41556666655555555555444445555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0048      23     182 ..     189     338 ..     185     343 .. 0.80
   2 ?    1.6   0.0       0.4   1.6e+02      36      59 ..     603     626 ..     579     650 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                          TniB  23 LeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppek.dedaekvpvlvvqappkpdekrlyaaiLealgaplkara 102
                                   +++ +e  +r r +n +l+G+  +GKt+ive  a +  +++  ed ++ +++++++      +++  +  e+l+a l   +
  gi|91774122|ref|YP_566814.1| 189 IRHTIEILSRRRKNNPVLIGEAGVGKTAIVEGLALRIAKHDiPEDMKNKKIIALDMGALIAGAKFRGEFEERLKAVL---K 266
                                   56677888899999******************996655544268888899999999988888888888877777776...4 PP

                          TniB 103 rvskleqqvlrllrelkvrvLiiDEihnll.agsarkqreflnalksLgnelkipivlvGt.eealralrtDpqlasRFep 181
                                   +v++ e q+          +L iDE+h ++ ag  +    + n+lk +  + ++  +++ t +e  + +++D+ l++RF p
  gi|91774122|ref|YP_566814.1| 267 EVADSEGQI----------ILFIDELHTIVgAGATEGAMDAGNLLKPMLARGELHCIGATTlDEYRKYIEKDAALERRFLP 337
                                   555666665..........899******98456677788999***********999999983456679***********88 PP

                          TniB 182 i 182
                                   +
  gi|91774122|ref|YP_566814.1| 338 V 338
                                   7 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.4
                          TniB  36 pnlllvGdsnnGKtmivekFarlh 59 
                                    + +++G++ +GKt +++  a++ 
  gi|91774122|ref|YP_566814.1| 603 GSFIFLGPTGVGKTELAKALAAEM 626
                                   678899**********99877554 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       3.3   1.3e+03      59      93 ..      90     123 ..      70     133 .. 0.78
   2 ?    7.6   0.0      0.01       4.1       3      19 ..     205     221 ..     204     244 .. 0.85
   3 !   13.1   0.0    0.0002     0.083       3      38 ..     606     640 ..     604     650 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.3
                                   EEEEE-SGGCTTTT-HHHHCTSCEEEEEEEGHHHH CS
                           Roc  59 niWDtaGqerfrslhplylreaalailvydsrsse 93 
                                   ++ Dta + + +s+++ y++ ++++i+++++++s+
  gi|91774122|ref|YP_566814.1|  90 RVLDTAEN-EASSMNDEYISVEHVLIALLKEKEST 123
                                   56677754.56899999*******99999876654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.01
                                   EEESSTTSSHHHHHHCH CS
                           Roc   3 vlvGdsgvGKtsllkrf 19 
                                   vl+G++gvGKt +++ +
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGL 221
                                   79***********9866 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.0002
                                   EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEE CS
                           Roc   3 vlvGdsgvGKtsllkrfvedkfsekekstigvdflt 38 
                                   +++G +gvGKt l+k +  + f+++ +++i +d+++
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMFNDE-NNMIRIDMSE 640
                                   79********************876.5677777755 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     0.004       1.6      90     120 ..     192     222 ..     161     238 .. 0.79
   2 ?   -1.3   0.0       4.3   1.8e+03      65     101 ..     537     574 ..     526     580 .. 0.71
   3 !   10.8   0.0   0.00086      0.35     100     123 ..     603     626 ..     556     653 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.004
                                   HHHHHHHCTTSEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  90 leelkellkdktsvlvGqSGvGKStLinall 120
                                   + e+ ++ +++  vl+G+ GvGK+++++ l+
  gi|91774122|ref|YP_566814.1| 192 TIEILSRRRKNNPVLIGEAGVGKTAIVEGLA 222
                                   4456666677889*************99886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.3
                                   HHHHHHHHHHT.TSEEEE--TTTHTTHHHHHHHCTTSE CS
                   RsgA_GTPase  65 leelkeeleal.gyevllvsaktkegleelkellkdkt 101
                                    e++++ ++++ +++v+ + + ++e+l++l+e+l++++
  gi|91774122|ref|YP_566814.1| 537 EEDIAQVVSQWtNIPVTRLMEGEREKLTHLEEKLHERI 574
                                   444555555552578889999999**********9986 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00086
                                   SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpel 123
                                      +++G++GvGK+ L +al+ e+
  gi|91774122|ref|YP_566814.1| 603 GSFIFLGPTGVGKTELAKALAAEM 626
                                   5679****************9975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.13        52       3      40 ..     206     243 ..     205     285 .. 0.62
   2 !   14.6   0.0     9e-05     0.037       3      27 ..     607     628 ..     606     672 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.13
                        AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakengllle 40 
                                   l G +GvGKt + + L+ r + +++  d+  ++ + l+
  gi|91774122|ref|YP_566814.1| 206 LIGEAGVGKTAIVEGLALRIAKHDIPEDMKNKKIIALD 243
                                   7899***********97663224555555555444444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9e-05
                        AAA_18   3 ltGtpGvGKttlakeLskrlgfgvn 27 
                                     G+ GvGKt+lak+L+ ++ f  n
  gi|91774122|ref|YP_566814.1| 607 FLGPTGVGKTELAKALAAEM-F--N 628
                                   67**************9985.2..1 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.011       4.6       3      26 ..     206     229 ..     205     245 .. 0.80
   2 !   11.5   0.0   0.00073       0.3       2      25 ..     606     629 ..     605     649 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.011
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkkl 26 
                                   l G++g+GK+ +++ La +++k+ 
  gi|91774122|ref|YP_566814.1| 206 LIGEAGVGKTAIVEGLALRIAKHD 229
                                   78******************9775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00073
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkk 25 
                                   ++ Gp+g+GK+ lak La+++ ++
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMFND 629
                                   689***************999743 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.039        16      12      63 ..     190     242 ..     178     258 .. 0.74
   2 !    9.9   0.1     0.001      0.42      25     194 ..     605     763 ..     574     776 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.039
                  Mg_chelatase  12 kraleiaaa.GgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasv 63 
                                   ++++ei     + n +l+G +G GKt + + l+  +++ +  e ++ +ki ++
  gi|91774122|ref|YP_566814.1| 190 RHTIEILSRrRKNNPVLIGEAGVGKTAIVEGLALRIAKHDIPEDMKNKKIIAL 242
                                   5556654431456789*************999988888888888887777665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                  Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaskaalvGggskpkpGeisla 105
                                   ++++Gp G GKt lak+l++ + + +e++++ + + + + +k++ ++l+ ++p    h+        Gg+      ++ + 
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMFN-DENNMIRIDMSEYM-EKHTVSRLIGAPPGYIGHDE-------GGQ---LTEAVRRR 673
                                   789999999999999998765543.33344444443322.23444455555554444443.......222...23356666 PP

                  Mg_chelatase 106 hnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpc...gklkdkekectcsekeierYls 183
                                      v+++DE+ + +++v++v+ + l+dg++t s   ++v+f  ++ ++++ N c     +kl++ e+ ++++e ++++  +
  gi|91774122|ref|YP_566814.1| 674 PYAVVLFDEIEKAHHDVFNVMLQILDDGRLTDSH-GRTVDFK-NTLIIMTSNICVDrtlSKLEEGEDYAKMQEMAQNELAK 752
                                   6677788888888888888888888888887554.4567776.45677778888541113344444455555555556666 PP

                  Mg_chelatase 184 klsgplldRid 194
                                   +    +++Rid
  gi|91774122|ref|YP_566814.1| 753 HFRPEFINRID 763
                                   66666666666 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   0.00046      0.19      37     108 ..     205     279 ..     182     302 .. 0.76
   2 ?    5.9   0.0     0.021       8.7      37      58 ..     606     627 ..     598     637 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00046
                        AAA_25  37 llaGapgtGKttlaldlalavatGkpwlg.....pvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldl 108
                                   +l+G  g+GKt+++  lal +a+ +  ++     ++    +   ++++   + e+++Rl+av+++++d ++  +l +
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLALRIAK-HDIPEdmknkKIIALDMGA-LIAGAKFRGEFEERLKAVLKEVADSEGQIILFI 279
                                   799*******************5.5577734443221233444.455556666************999888877765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                        AAA_25  37 llaGapgtGKttlaldlalava 58 
                                   ++ G++g+GKt la  la+++ 
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMF 627
                                   778****************986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.012       4.9      10      46 ..     190     228 ..     182     302 .. 0.70
   2 !   10.4   0.0   0.00081      0.33      23      48 ..     606     631 ..     580     651 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                                   HHHHHHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                          PhoH  10 keylealk..kndivfaiGpaGtGKtylavalavealkk 46 
                                   ++++e+l+  +++  + iG+aG GKt +   la+++ k+
  gi|91774122|ref|YP_566814.1| 190 RHTIEILSrrRKNNPVLIGEAGVGKTAIVEGLALRIAKH 228
                                   56667776666667789**********988888776665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00081
                                   EEE--TTSSTTHHHHHHHHHHHHTTS CS
                          PhoH  23 faiGpaGtGKtylavalavealkkkk 48 
                                   + +Gp+G GKt la ala+e++++++
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMFNDEN 631
                                   678******************99854 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.73     3e+02      11      41 ..     196     226 ..     186     231 .. 0.74
   2 !   15.4   0.0   2.1e-05    0.0084      13      58 ..     598     645 ..     586     656 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.73
                    Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdele 41 
                                    s++r+   +l G  G GK+++ e l+ +++
  gi|91774122|ref|YP_566814.1| 196 LSRRRKNNPVLIGEAGVGKTAIVEGLALRIA 226
                                   5666677777889*********999887765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.1e-05
                    Zeta_toxin  13 qerPk.lillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh 58 
                                    +rP+ + +  G +G GK+ela++l++e+   ++n++r+d  ++ e h
  gi|91774122|ref|YP_566814.1| 598 PKRPIgSFIFLGPTGVGKTELAKALAAEMFnDENNMIRIDMSEYMEKH 645
                                   56665223345899***************98999******99998877 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.12        48      71      96 ..     257     285 ..     178     292 .. 0.72
   2 !   13.4   0.0   0.00012     0.049       8      58 ..     573     627 ..     566     645 .. 0.73
   3 ?   -2.4   0.0       8.6   3.5e+03      86     113 ..     676     703 ..     667     708 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.12
                        RuvB_N  71 kagdlaalltnleekd...vlfideihrl 96 
                                    +  l a+l+++ +++   +lfide+h +
  gi|91774122|ref|YP_566814.1| 257 FEERLKAVLKEVADSEgqiILFIDELHTI 285
                                   34567788888766544458999999976 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                        RuvB_N   8 eyigqekvkeklk.ifiea...akkreealdhvllyGpPGlGkttlakiiakelg 58 
                                     +gq++  + ++  +i+a    k  ++++   ++ Gp G+Gkt lak +a+e+ 
  gi|91774122|ref|YP_566814.1| 573 RIVGQNETVKAVSdAIIRAyagIKDPKRPIGSFIFLGPTGVGKTELAKALAAEMF 627
                                   467777655444314444421146677889999********************95 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.6
                        RuvB_N  86 dvlfideihrlsraveevlysamedfrl 113
                                    v++ dei + ++ v +v+ + ++d rl
  gi|91774122|ref|YP_566814.1| 676 AVVLFDEIEKAHHDVFNVMLQILDDGRL 703
                                   68889**********9999999999765 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 ?    4.6   0.0     0.072        30      10      50 ..     187     227 ..     178     242 .. 0.84
   2 ?    0.6   0.0       1.2   5.1e+02     124     146 ..     265     287 ..     252     302 .. 0.78
   3 !    8.9   0.0    0.0035       1.4      21      53 ..     590     631 ..     554     638 .. 0.69
   4 ?   -2.3   0.1       9.4   3.8e+03      55      88 ..     714     753 ..     701     805 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.072
                                   HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                        ResIII  10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierllk 50 
                                   + i+ ++e l+ +r+++ ++  + G+GKT +   l+ r++k
  gi|91774122|ref|YP_566814.1| 187 QEIRHTIEILSRRRKNNPVLIGEAGVGKTAIVEGLALRIAK 227
                                   5678888888878888899************9888888776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
                                   ...HHHTTT-SEEEEETGGGTTS CS
                        ResIII 124 eseellrdrfdviiiDEaHrlga 146
                                    +e ++++ + +++iDE H + +
  gi|91774122|ref|YP_566814.1| 265 LKEVADSEGQIILFIDELHTIVG 287
                                   56677888888********9876 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0035
                                   .......TTS....EEEEEESTTSTHHHHHHHHHHHH-S... CS
                        ResIII  21 s.....krdk....rglikmaTGtGKTlvaaklierllkkgk 53 
                                         k+ k     +++  +TG+GKT +a +l++++++ ++
  gi|91774122|ref|YP_566814.1| 590 RayagiKDPKrpigSFIFLGPTGVGKTELAKALAAEMFNDEN 631
                                   25555533333456788999**********999999998654 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 9.4
                                   .-EEEEESSHHHHHHHH......HHGGGGTGG....GEEE CS
                        ResIII  55 ekflflvprkslleqtl......eefkkflseaykeigkk 88 
                                   +++l++  +++ +++tl      e+++k+++ a++e  k 
  gi|91774122|ref|YP_566814.1| 714 KNTLIIMTSNICVDRTLskleegEDYAKMQEMAQNELAKH 753
                                   4888888888888888855555555555555555543333 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   0.1    0.0013      0.52      41     116 ..     189     282 ..     177     284 .. 0.72
   2 ?    6.1   0.0     0.013       5.4      54      96 ..     603     645 ..     549     658 .. 0.75
   3 ?   -0.7   0.1       1.6   6.4e+02      98     225 ..     666     805 ..     661     820 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                        DUF815  41 venteqfleglpannvLLwGarGtGKSslvkallneyaeeg..................Lrlievekedlkelpklvellr 103
                                   ++ t + l+ ++ nn +L+G+ G+GK ++v  l  ++a++                   ++  + + e  + l++++++++
  gi|91774122|ref|YP_566814.1| 189 IRHTIEILSRRRKNNPVLIGEAGVGKTAIVEGLALRIAKHDipedmknkkiialdmgalIAGAKFRGEFEERLKAVLKEVA 269
                                   56677888899999*******************999998887777777555553332222222233333456888888888 PP

                        DUF815 104 erperfilfvDDL 116
                                   +++ ++ilf+D L
  gi|91774122|ref|YP_566814.1| 270 DSEGQIILFIDEL 282
                                   8888888888876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                        DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrlievekedlkelp 96 
                                      ++ G  G+GK  l kal +e+ +++  +i ++ ++  e  
  gi|91774122|ref|YP_566814.1| 603 GSFIFLGPTGVGKTELAKALAAEMFNDENNMIRIDMSEYMEKH 645
                                   456889**********************9***99988766555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.6
                        DUF815  98 lvellrerperfilfvDDLsFeeeeeeyksLksvLeGsleakp......envliyaTsN...rRhLlpeklsdneeleeee 169
                                   l+e++r+rp+ ++lf D +   +++    +L+ + +G l+ +       +n li  TsN    R L + +  +    + +e
  gi|91774122|ref|YP_566814.1| 666 LTEAVRRRPYAVVLF-DEIEKAHHDVFNVMLQILDDGRLTDSHgrtvdfKNTLIIMTSNicvDRTLSKLEEGEDYA-KMQE 744
                                   667777777766655.777777777777777777777776543222233688888888843335555444433333.5566 PP

                        DUF815 170 ihaseavee.klsLsdRFGlwlgFykldqeeYleiveklakklglelek....eeleeeAl 225
                                   + ++e  +  +  + +R      F +l++e+ ++iv+  a++l  +l++     e++++A 
  gi|91774122|ref|YP_566814.1| 745 MAQNELAKHfRPEFINRIDELAIFRPLTKEQLVTIVDIKATDLIQRLKEkrmvLEISKKAK 805
                                   6666544432455667777667788888888888887777666555444233344555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.29   1.2e+02      15      32 ..     205     222 ..     196     239 .. 0.84
   2 ?   -1.4   0.2       7.5     3e+03      54      96 ..     467     492 ..     411     565 .. 0.54
   3 !   12.7   0.0   0.00034      0.14      16      51 ..     607     643 ..     603     750 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.29
                                   EEEESTTSSHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxx RF
                      ABC_tran  15 aivGenGaGKStLlklla 32 
                                   +++Ge G GK+ +++ la
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLA 222
                                   79**********998665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7.5
                                   HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCHHHHHHHSTTGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  54 leslrkeigvlpqepqlfpeltvrenesdeeiekalsklglke 96 
                                   ++ + +++g l                 +++ie++  +l+l e
  gi|91774122|ref|YP_566814.1| 467 EKDTIANLGSL-----------------KQQIEDIKIQLELAE 492
                                   22223333333.................333333333333332 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00034
                                   EEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                      ABC_tran  16 ivGenGaGKStLlkllagllkp.teGeilldgkdlke 51 
                                   ++G++G GK+ L+k+la ++ + ++  i++d+ +  e
  gi|91774122|ref|YP_566814.1| 607 FLGPTGVGKTELAKALAAEMFNdENNMIRIDMSEYME 643
                                   79**************988765267778888665544 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.1e-06    0.0033      15      81 ..     562     630 ..     556     644 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.1e-06
                                   -HHHHHHHHHHH--S-HHHHHHHHHH.HHHHHT-SS-SS-E.EEEEEE-TTSSHHHHHHHHHHHHSTTG CS
                        Torsin  15 nleeLekdlekklfGqhlvkklvvks.vkaylenekpkkpL.vlsfhGwtGtGknfvaeiiaenlyrdG 81 
                                   +l++Le+ l+++++Gq    k v  + ++ay   ++pk+p+  + f G tG Gk  +a+ +a ++++d 
  gi|91774122|ref|YP_566814.1| 562 KLTHLEEKLHERIVGQNETVKAVSDAiIRAYAGIKDPKRPIgSFIFLGPTGVGKTELAKALAAEMFNDE 630
                                   6899************99999998873699**********9458899*******************875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.39   1.6e+02       3      22 ..     205     224 ..     203     237 .. 0.82
   2 ?    1.4   0.1      0.82   3.4e+02      26      74 ..     387     436 ..     370     445 .. 0.77
   3 !   10.2   0.0    0.0017      0.67       2      22 ..     605     625 ..     604     681 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.39
                        AAA_28   3 vitGgestGKTtlleaLaar 22 
                                   v++G  + GKT ++e La r
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLALR 224
                                   899**************944 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.82
                        AAA_28  26 vvpEaareileeklakgedalpwv.edllafaervleeqleeeaaaaank 74 
                                    +p+ a ++++e +ak + a+++   +l +  +++l+ ++e+ea  ++++
  gi|91774122|ref|YP_566814.1| 387 FLPDKAIDLVDEAAAKVRTAIDSKpSELDEADRKILQLEIEREALKKEKD 436
                                   55777788888888888888888888999999999999999998875544 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0017
                        AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                   ++++G+ + GKT l++aLaa+
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAE 625
                                   6899***************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 ?    6.9   0.0     0.015       6.1      13      42 ..     195     224 ..     184     231 .. 0.73
   2 !    7.7   0.0    0.0081       3.3      21      43 ..     602     626 ..     562     635 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                                   HHHHCHTEEEEEEESTTSSHHHHHHHHHHH CS
                          TsaE  13 klakalgdvilLeGdLGaGKTtlvrglaka 42 
                                    l +  ++  +L G+ G+GKT++v gla  
  gi|91774122|ref|YP_566814.1| 195 ILSRRRKNNPVLIGEAGVGKTAIVEGLALR 224
                                   444444566799**************9865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0081
                                   E..EEEEESTTSSHHHHHHHHHHHT CS
                          TsaE  21 v..ilLeGdLGaGKTtlvrglakal 43 
                                   +  +++ G+ G+GKT l+++la+++
  gi|91774122|ref|YP_566814.1| 602 IgsFIFLGPTGVGKTELAKALAAEM 626
                                   1447788**************9987 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.027        11      32      61 ..     200     228 ..     183     289 .. 0.81
   2 !    7.7   0.0    0.0072       2.9      29      65 ..     597     633 ..     574     651 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                                   T.S--EEEE-SSSSSHHHHHHHHHHHHHHH CS
                      Bac_DnaA  32 kkynPlfiygevGlGktHLlkaignevlen 61 
                                   +k nP++i ge G+Gkt +++ ++ ++ ++
  gi|91774122|ref|YP_566814.1| 200 RKNNPVLI-GEAGVGKTAIVEGLALRIAKH 228
                                   46799988.**********99888777654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0072
                                   STTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
                      Bac_DnaA  29 apgkkynPlfiygevGlGktHLlkaignevlenapel 65 
                                    p++    +++ g++G+Gkt L ka++ e+ ++++++
  gi|91774122|ref|YP_566814.1| 597 DPKRPIGSFIFLGPTGVGKTELAKALAAEMFNDENNM 633
                                   455556667788***************9998887764 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 ?    1.2   0.1      0.39   1.6e+02      60     156 ..     126     228 ..      76     242 .. 0.71
   2 !   12.4   0.0   0.00015     0.062     129     201 ..     602     675 ..     570     684 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.39
                         T2SSE  60 ldiseerplqdarlpekgvrlrvvllPvvagealviRkksakeltlddlgaeealk......ekiaevlrkavr.erglil 133
                                   + ++e  + +da+l+    +lr++   ++++++ ++   ++  +++ +l+a+++l+      ++i+++++   r ++ + +
  gi|91774122|ref|YP_566814.1| 126 RILEEAGITIDATLE-AIKKLRGNRRITSENPEDTMEPLKKYGIDFTELAAQGKLDpvigrdQEIRHTIEILSRrRKNNPV 205
                                   444555666777776.77777777777777777777766777778888888888888888885555555544330566788 PP

                         T2SSE 134 vsGgTgsGKttllyallkeinks 156
                                   + G  g GKt ++  l   i+k+
  gi|91774122|ref|YP_566814.1| 206 LIGEAGVGKTAIVEGLALRIAKH 228
                                   899*******9988777777666 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00015
                         T2SSE 129 rglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak..kakvtfadllraaLRlrPD 201
                                    g++++ G+Tg GKt l+ al +e+ +++++++ + D  E+  ++     + a     + +    l +a+R+rP 
  gi|91774122|ref|YP_566814.1| 602 IGSFIFLGPTGVGKTELAKALAAEMFNDENNMIRI-DMSEYMEKHTVSRLIGAPpgYIGHDEGGQLTEAVRRRPY 675
                                   57899*******************99998999988.788887666544433333556666666666666666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.36   1.5e+02       4      26 ..     206     223 ..     205     278 .. 0.76
   2 ?    9.9   0.0    0.0019      0.77       3      38 ..     606     646 ..     605     701 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.36
                        AAA_33   4 lvGlpGsGKstlaerllkklgav 26 
                                   l+G +G+GK+  +e+l+      
  gi|91774122|ref|YP_566814.1| 206 LIGEAGVGKTAIVEGLA-----L 223
                                   799***********997.....4 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0019
                        AAA_33   3 llvGlpGsGKstlaerllkklg.....avllssdtlrrrlf 38 
                                   ++ G+ G+GK+ la+ l+++       +++++  +++++++
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALAAEMFndennMIRIDMSEYMEKHT 646
                                   899**************977666677788888777766655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.015       6.3      20      43 ..     203     226 ..     187     249 .. 0.79
   2 ?    4.5   0.0      0.06        24      22     109 ..     606     695 ..     603     704 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                        AAA_30  20 vavltGpAGtGKttalkalreawe 43 
                                     vl G AG GKt ++++l+  ++
  gi|91774122|ref|YP_566814.1| 203 NPVLIGEAGVGKTAIVEGLALRIA 226
                                   46899***********99965544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.06
                        AAA_30  22 vltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLaeelgi.eastiakllkrlkgrarlepgtllivDEagmv 100
                                   +  Gp G GKt + kal +e++++++  + +  ++    +++++ +g+ +++  +    +l++++r +p  +++ DE+  +
  gi|91774122|ref|YP_566814.1| 606 IFLGPTGVGKTELAKALaAEMFNDENNMIRIDMSEYMEKHTVSRLIGApPGYIGHDEGGQLTEAVRRRPYAVVLFDEIEKA 686
                                   5679************96677776665444444444444445555555344444555555555555555566666666666 PP

                        AAA_30 101 dtkqlaall 109
                                     + ++ +l
  gi|91774122|ref|YP_566814.1| 687 HHDVFNVML 695
                                   665555555 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.3   2.1e+03      52      92 ..      91     130 ..      85     178 .. 0.56
   2 ?    4.6   0.0     0.054        22       3      16 ..     205     218 ..     203     228 .. 0.92
   3 ?    5.9   0.0     0.022         9       2      30 ..     605     633 ..     604     649 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                                   EEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHH CS
                           Ras  52 iwDTAGqeefkslrelyyrdaegillvyditsresfenvkk 92 
                                   ++DTA  e  +s+++ y++  ++++ +   ++++s++ +++
  gi|91774122|ref|YP_566814.1|  91 VLDTAENE-ASSMNDEYISVEHVLIALLKEKESTSYRILEE 130
                                   66777544.46677777776666666666666666655444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.054
                                   EEEESTTSSHHHHH CS
                           Ras   3 vlvGdsavGKtsll 16 
                                   vl+G+ +vGKt+++
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIV 218
                                   89**********98 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.022
                                   EEEEESTTSSHHHHHHHHHHSSCSSSCTT CS
                           Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyes 30 
                                   ++++G ++vGKt l    + + F++e ++
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMFNDENNM 633
                                   589********************988654 PP

>> PV-1  PV-1 protein (PLVAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.9   0.00014     0.057     275     387 ..     388     496 ..     371     513 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                          PV-1 275 lPslmstkveelarslragiervarensdlqrqkleaeqslrasqeakekvekeaqareaklqaecarqtqlaleekaalr 355
                                   lP    + v+e a ++r++i++   e  +  r+ l+ e   +a +++k+ v+ke  a   k  a+       a   +a  +
  gi|91774122|ref|YP_566814.1| 388 LPDKAIDLVDEAAAKVRTAIDSKPSELDEADRKILQLEIEREALKKEKDAVSKERVADLEKELADIRAE-SDA--MRAKWQ 465
                                   67778889********************************************99777666666665433.334..467799 PP

                          PV-1 356 kerdnlakeleekkreveqlklqlavsnsald 387
                                    e+d++a +l   k+++e +k+ql+++  + d
  gi|91774122|ref|YP_566814.1| 466 SEKDTIA-NLGSLKQQIEDIKIQLELAENSGD 496
                                   ****998.699*************99876655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.023       9.2      21      41 ..     200     220 ..     189     225 .. 0.77
   2 ?    4.6   0.0     0.068        28      23      46 ..     603     626 ..     595     633 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                        AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                   +k++ +l+G+ G+GK++++  
  gi|91774122|ref|YP_566814.1| 200 RKNNPVLIGEAGVGKTAIVEG 220
                                   445889***********9965 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.068
                        AAA_29  23 gatlltGpsGsGKSTllDAiqalL 46 
                                   g++++ Gp+G+GK+ l  A++a +
  gi|91774122|ref|YP_566814.1| 603 GSFIFLGPTGVGKTELAKALAAEM 626
                                   57899*********9988887655 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 ?   10.9   0.0   0.00073       0.3      19     127 ..     602     698 ..     586     702 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00073
               DNA_pol3_delta2  19 ahayLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDvivieteekersikldqirelieelsrkp 99 
                                     +++f G++g+gk ela++la +++ +e+n        +  + +e+++++   +i+       i  d+  +l+e + r+p
  gi|91774122|ref|YP_566814.1| 602 IGSFIFLGPTGVGKTELAKALAAEMFNDENNMI-R---IDMSEYMEKHTVS--RLIGAPPG--YIGHDEGGQLTEAVRRRP 674
                                   5689**********************9999865.2...2222222222222..22233333..466666666666666666 PP

               DNA_pol3_delta2 100 reskkkiiiiedaekmtksAaNalLktl 127
                                   +     +++ +++ek ++   N +L++l
  gi|91774122|ref|YP_566814.1| 675 Y----AVVLFDEIEKAHHDVFNVMLQIL 698
                                   4....36666666666666666666666 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.074        30       5      28 ..     205     228 ..     201     249 .. 0.76
   2 ?    5.7   0.0     0.025        10       4      30 ..     605     631 ..     603     638 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.074
                                   EEEESTTSSHHHHHHHHHHHHHHT CS
                         SRP54   5 llvGlqGaGKTttlaKLaallkke 28 
                                   +l+G  G+GKT  +  La ++ k+
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGLALRIAKH 228
                                   799***************998876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS CS
                         SRP54   4 illvGlqGaGKTttlaKLaallkkegk 30 
                                   ++++G++G+GKT  +  Laa + ++++
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMFNDEN 631
                                   5899*********99999987766544 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.2   1.3e+03       4      23 ..     206     225 ..     205     230 .. 0.82
   2 ?    9.1   0.0    0.0028       1.1       7     110 ..     610     723 ..     605     736 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.2
                         AAA_3   4 legvPGlaktllvkalakal 23 
                                   l g  G++kt +v+ la  +
  gi|91774122|ref|YP_566814.1| 206 LIGEAGVGKTAIVEGLALRI 225
                                   55778*********999766 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0028
                         AAA_3   7 vPGlaktllvkalakal...dlefkriqftpdl...lPsdilGt...evfeekekefefkkGpvfanllladeinrappkt 78 
                                     G++kt l+kala  +   + ++ ri +   +     s ++G+    + +++  +++         ++l dei++a   +
  gi|91774122|ref|YP_566814.1| 610 PTGVGKTELAKALAAEMfndENNMIRIDMSEYMekhTVSRLIGAppgYIGHDEGGQLTEAVRRRPYAVVLFDEIEKAHHDV 690
                                   568888888888887663334456677766544111345666763322333334555444334446799************ PP

                         AAA_3  79 qsalleameerqvtv.egethklpepflvlatq 110
                                      +l+++++ ++t  +g+t ++++++++++ +
  gi|91774122|ref|YP_566814.1| 691 FNVMLQILDDGRLTDsHGRTVDFKNTLIIMTSN 723
                                   ************996257888888887777554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         9   3.7e+03      17      38 ..      75      96 ..      60     117 .. 0.82
   2 ?    7.2   0.1     0.015       6.1       9      36 ..     200     227 ..     192     401 .. 0.66
   3 ?    1.4   0.0      0.93   3.8e+02      13      36 ..     605     628 ..     597     641 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9
                        AAA_19 17 aGpGtGKTrvlkhivallvelg 38
                                   G G+G T+v ++  ++l  ++
  gi|91774122|ref|YP_566814.1| 75 SGSGSGQTYVSQAYSRVLDTAE 96
                                  699*****99888877776655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.015
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivallve 36 
                                   ++++ ++++ +G GKT ++++    + +
  gi|91774122|ref|YP_566814.1| 200 RKNNPVLIGEAGVGKTAIVEGLALRIAK 227
                                   5667789**********99875433333 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.93
                        AAA_19  13 llvtaGpGtGKTrvlkhivallve 36 
                                   ++ +++ G GKT++ k+  a++ +
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMFN 628
                                   5778999******99998887765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.67   2.7e+02       5      21 ..     205     221 ..     202     244 .. 0.85
   2 ?    8.3   0.0    0.0046       1.9       4      26 ..     605     627 ..     602     657 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.67
                     PduV-EutP   5 lliGkvgsGKttLtqal 21 
                                   +liG+ g+GKt++ + l
  gi|91774122|ref|YP_566814.1| 205 VLIGEAGVGKTAIVEGL 221
                                   69*********987765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0046
                     PduV-EutP   4 illiGkvgsGKttLtqalkgeel 26 
                                    +++G++g+GKt L++al  e +
  gi|91774122|ref|YP_566814.1| 605 FIFLGPTGVGKTELAKALAAEMF 627
                                   589***************98754 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       5.9   2.4e+03     154     184 ..      84     134 ..       8     150 .. 0.57
   2 ?   11.5   0.0   0.00075      0.31      20     188 ..     603     794 ..     599     810 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.9
                        AAA_23 154 rleelekeleeledekkllekl...........eqekekek...........e 184
                                     +++++ l+++e+e++ ++++           ++eke              +
  gi|91774122|ref|YP_566814.1|  84 VSQAYSRVLDTAENEASSMNDEyisvehvlialLKEKE--StsyrileeagiT 134
                                   44556666666666666666666666666654322222..1334444444443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00075
                        AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrks.grgfeksdveiese...........gkvkayvelt......fenk 82 
                                   g +++ Gp+G GKT +  A+   ++++ +++ r + ++ +ek+ v+   +           g+  + v+++      f  +
  gi|91774122|ref|YP_566814.1| 603 GSFIFLGPTGVGKTELAKALAAEMFNDENNMIRIDmSEYMEKHTVSRLIGappgyighdegGQLTEAVRRRpyavvlFDEI 683
                                   6799*********************98877777777668888888733334566666667544444466666666666555 PP

                        AAA_23  83 dgry......trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerlee 157
                                    +          +i ++  l+++ g+t++++++ ++ +++    +++ l++ ++  ++  ++   ++     +  k    e
  gi|91774122|ref|YP_566814.1| 684 EKAHhdvfnvMLQILDDGRLTDSHGRTVDFKNTLIIMTSNI--CVDRTLSKLEEGEDYAKMQEMAQN-----ELAKHFRPE 757
                                   55556667665555567777777777777777777766544..233333333332222222222222.....112234556 PP

                        AAA_23 158 lekeleeledekkllekl......eqekekekeleel 188
                                   +++ ++el  ++ l +++      +++ +  ++l+e+
  gi|91774122|ref|YP_566814.1| 758 FINRIDELAIFRPLTKEQlvtivdIKATDLIQRLKEK 794
                                   6666666666666666666666663444444444443 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.4   5.6e+02     120     193 ..      83     160 ..      53     179 .. 0.59
   2 ?    3.1   0.1      0.21        84      29      60 ..     207     244 ..     205     245 .. 0.93
   3 ?    8.3   0.0    0.0056       2.3      29      58 ..     608     636 ..     604     662 .. 0.85
   4 ?    0.5   0.2       1.3   5.3e+02     137     211 ..     720     788 ..     678     804 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                         DUF87 120 vleealdqaka.keekeklssde..pveklleelkkeke.elrklknqaiarlldkledllrkggsfsnsstdliall 193
                                   ++ +a++++ + +e++ +   de  +ve++l  l keke ++ ++ ++a  ++ ++le +++ +g++  +s+++++++
  gi|91774122|ref|YP_566814.1|  83 YVSQAYSRVLDtAENEASSMNDEyiSVEHVLIALLKEKEsTSYRILEEAGITIDATLEAIKKLRGNRRITSENPEDTM 160
                                   444444444442222333323331123444444444555488888888888999999999999988866666666665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.21
                         DUF87  29 lgsTGsGKSntvavLleelle......kkgatililDp 60 
                                   +g++G+GK+  v  L  ++++       k+ +i+ lD+
  gi|91774122|ref|YP_566814.1| 207 IGEAGVGKTAIVEGLALRIAKhdipedMKNKKIIALDM 244
                                   799******************99999999999999997 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0056
                         DUF87  29 lgsTGsGKSntvavLleellekkgatilil 58 
                                   lg TG+GK+ +++ L +e+ + +  +++ +
  gi|91774122|ref|YP_566814.1| 608 LGPTGVGKTELAKALAAEMFN-DENNMIRI 636
                                   899*****************5.44444444 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.3
                         DUF87 137 lssdepveklleelkkekeelrklknqaiarlldkle.dllrkggsfsnsstdliallleklekegkitiidlsg...v 211
                                   ++s+  v + l++l+ e e++ k++++a+++l ++++ +++++  +           +++ l+ke+ +ti+d++    +
  gi|91774122|ref|YP_566814.1| 720 MTSNICVDRTLSKLE-EGEDYAKMQEMAQNELAKHFRpEFINRIDEL---------AIFRPLTKEQLVTIVDIKAtdlI 788
                                   677777777788888.6667777777777777776653677777777.........78888899999999999885544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (869 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 1.01u 0.39s 00:00:01.40 Elapsed: 00:00:00.58
# Mc/sec: 4487.05
//
Query:       gi|91774123|ref|YP_566815.1|  [L=466]
Description: PAS sensor protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-15   56.2   0.0    7.9e-15   54.9   0.0    1.7  1  PAS_3     PAS fold
    3.2e-08   33.8   0.0    5.2e-08   33.1   0.0    1.3  1  PAS_4     PAS fold
    5.3e-07   29.6   0.0    9.9e-07   28.8   0.0    1.5  1  PAS       PAS fold
    1.2e-05   25.5   0.0    3.6e-05   24.0   0.0    1.8  1  PAS_9     PAS domain
    8.9e-05   22.6   0.0     0.0046   17.1   0.0    3.0  3  PAS_11    PAS domain


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   2.2e-18   7.9e-15       3      89 .]     308     391 ..     306     391 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 2.2e-18
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpv 83 
                                   y+s++v   +Gy+pe++ +   +wld+vhp+Dr r+ +++ + +k+     + +Ri+  dG+++w+e+ + ++ +++g+++
  gi|91774123|ref|YP_566815.1| 308 YISPQV-IFYGYTPEQISSG--NWLDIVHPDDRGRLIDSYRATVKNEFNEPTVFRIFDSDGHIYWMEEMGMPLLNSSGEVT 385
                                   677777.568**********..**********************888877888**************************** PP

                         PAS_3  84 rvigva 89 
                                    + g++
  gi|91774123|ref|YP_566815.1| 386 SISGII 391
                                   **9985 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.4e-11   5.2e-08       1     109 [.     290     398 ..     290     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.4e-11
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeer 79 
                                   ++++ d+++ +d d++ ly++++    +g++pe++    + +++ ++d++rl + +r+ ++ e     + ++ +  +g   
  gi|91774123|ref|YP_566815.1| 290 VENIKDMVYSIDVDMNLLYISPQVI-FYGYTPEQISSGNWLDIVHPDDRGRLIDSYRATVKNEFNE-PTVFRIFdsDGHIY 368
                                   6899******************955.59**************99999*************997444.44444446899999 PP

                         PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerr 109
                                   ++e   +Pl+++sGev  + +i+rD+Ter+
  gi|91774123|ref|YP_566815.1| 369 WMEEMGMPLLNSSGEVTSISGIIRDVTERK 398
                                   999999***********************8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.8e-10   9.9e-07       3     113 .]     286     394 ..     284     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.8e-10
                                   HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.. CS
                           PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl.. 81 
                                   +r ++e++ d++  +D d + ly+++    + G+++e++++ + ld +h++d   + +l+  ++++ +++ ++ + f+   
  gi|91774123|ref|YP_566815.1| 286 YRFLVENIKDMVYSIDVDMNLLYISPQVI-FYGYTPEQISSGNWLDIVHPDD---RGRLIDSYRATVKNEFNEPTVFRIfd 362
                                   899***********************986.89*************9999998...89999999999999999999999999 PP

                                   TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                           PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                    dg ++++e    p+++ +ge++ + g++rd+
  gi|91774123|ref|YP_566815.1| 363 SDGHIYWMEEMGMPLLNSSGEVTSISGIIRDV 394
                                   9******************************7 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     1e-08   3.6e-05       6     104 .]     300     396 ..     295     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                         PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvli..rkngetfwvlltasp 84 
                                   i + d ++ly++++++   Gy+pe++   ++ d++  +p+++ rl + +++  k+e+++++v++  +++g  +w +    p
  gi|91774123|ref|YP_566815.1| 300 I-DVDMNLLYISPQVIFY-GYTPEQISSGNWLDIV--HPDDRGRLIDSYRATVKNEFNEPTVFRifDSDGHIYWMEEMGMP 376
                                   4.4788899******966.****************..666666666666665557888887776336778******9999* PP

                         PAS_9  85 vkdddgelvgiivilrDite 104
                                   + +++ge+++i +i+rD+te
  gi|91774123|ref|YP_566815.1| 377 LLNSSGEVTSISGIIRDVTE 396
                                   *******************8 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.19   6.8e+02      24      78 ..     175     229 ..     170     241 .. 0.75
   2 ?    1.0   0.1      0.13   4.5e+02      54      81 ..     270     297 ..     249     299 .. 0.70
   3 !   17.1   0.0   1.3e-06    0.0046       7      83 ..     299     370 ..     293     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.19
                        PAS_11  24 asfslglekeelvgrsiydLchpqdlstlkshlrevi...ssngeatsslyRLrlsqd 78 
                                   +sf +  ++  +v+++ + ++hp+ +    +     +   + ++++ s++y  +l +d
  gi|91774123|ref|YP_566815.1| 175 ISFEQVAQR--IVEKIPFIFIHPDNVCACIDIQDSFYtssNFKRTNNSLSYNVSL-DD 229
                                   677777788..9999*********9887777777777655667777777887777.44 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                        PAS_11  54 shlrevissngeatsslyRLrl.sqdkfv 81 
                                     +r++  ++   ++++yR+ + + +++v
  gi|91774123|ref|YP_566815.1| 270 LMHRNMH-TSSFEKEQSYRFLVeNIKDMV 297
                                   4466666.777777888***996656666 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.3e-06
                        PAS_11   7 rldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkv 83 
                                    +d+d++ + + +    + +  g++ e+++   + d++hp+d+ +l + +r ++ +n+ ++ +++R+  s++++ ++
  gi|91774123|ref|YP_566815.1| 299 SIDVDMNLLYISP----QVIFYGYTPEQISSGNWLDIVHPDDRGRLIDSYRATV-KNEFNEPTVFRIFDSDGHIYWM 370
                                   5677777777777....6777899999***************************.************9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.51
# Mc/sec: 2761.91
//
Query:       gi|91774124|ref|YP_566816.1|  [L=633]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-22   78.6   0.5    4.3e-21   75.5   0.1    2.6  3  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.7e-12   47.1   0.2      9e-07   28.8   0.0    3.1  2  PAS_8        PAS domain
    3.9e-10   39.9   0.8    3.3e-06   27.3   0.1    2.7  2  PAS_9        PAS domain
    5.9e-08   32.9   0.0    2.6e-06   27.6   0.0    3.0  2  PAS_7        PAS fold
    8.9e-08   32.1   0.0    0.00017   21.6   0.0    2.6  2  PAS          PAS fold
    1.2e-05   25.9   0.0    6.5e-05   23.6   0.0    2.1  2  GAF          GAF domain
    7.6e-05   23.0   0.0    0.00017   21.9   0.0    1.6  1  GAF_2        GAF domain
    7.7e-05   22.9   0.0       0.11   12.7   0.0    2.6  2  PAS_4        PAS fold
    0.00029   21.2   0.0    0.00065   20.1   0.0    1.6  1  GAF_3        GAF domain
    0.00066   19.6   0.0     0.0017   18.3   0.0    1.7  2  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0032   17.5   0.1     0.0085   16.1   0.1    1.8  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0073   16.2   2.2      0.065   13.1   0.0    2.9  2  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
       0.05   13.7   0.0        1.2    9.2   0.0    2.6  2  SpoVT_C      Stage V sporulation protein T C-terminal, transc
      0.062   13.5   0.0       0.16   12.2   0.0    1.6  1  CNOT11       CCR4-NOT transcription complex subunit 11
       0.31   10.8   1.8        0.9    9.3   0.0    2.7  4  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain


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 ?   -1.3   0.0       2.5     3e+03      54      90 ..     182     218 ..      98     246 .. 0.62
   2 ?   -0.8   0.0       1.8   2.1e+03      35      59 ..     477     507 ..     451     520 .. 0.63
   3 !   75.5   0.1   3.6e-24   4.3e-21       6     110 ..     529     632 ..     525     633 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.5
                                   HTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTT CS
                     HATPase_c  54 lkklfekfsqddstkrggggtGlGlsivkklvelmgG 90 
                                   +k l ekf  ++s +++  g+ + +si+ ++v++ +G
  gi|91774124|ref|YP_566816.1| 182 RKVLSEKFAHSKSCMIRADGSIIDVSISSSFVDRNKG 218
                                   3344446666666666667777777777666665555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                                   E....TEEEEEEEESS..SSSTTHHHTGTCS CS
                     HATPase_c  35 e....ddlvisveDnG..iGipkedlkklfe 59 
                                   +    +++++sv D G  i i k +l  +f+
  gi|91774124|ref|YP_566816.1| 477 KldsvEEIEFSVIDIGlmINIAKTNLGAMFK 507
                                   134467999*****99555555555555554 PP

  == domain 3  score: 75.5 bits;  conditional E-value: 3.6e-24
                                   HHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHH CS
                     HATPase_c   6 LrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklve 86 
                                   +++++ nl++Na+k+++k+++i + i    d+ +++ +D G Gi+ e+ + +fe+f +   +k++ +gtG+Gl+iv+k+v+
  gi|91774124|ref|YP_566816.1| 529 VEEVFANLLSNAIKYSPKGSTIYIDILDAGDEWKVQFTDFGEGISDEEKDFVFERFKR--VNKTNIKGTGIGLAIVRKIVD 607
                                   5789***********99**********5449***************************..8899999************** PP

                                   HTTTEEEEEEET.TTEEEEEEEEES CS
                     HATPase_c  87 lmgGeiwvesep.grGttftftlpl 110
                                   l+gG++ ve++p g+G+ f++tl++
  gi|91774124|ref|YP_566816.1| 608 LHGGHFGVEDNPdGKGCVFWITLKK 632
                                   ********99999*********985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   7.5e-10     9e-07       2      40 ..     121     157 ..     120     185 .. 0.78
   2 !   15.0   0.1   1.6e-05     0.019       3      42 ..     283     322 ..     281     343 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.5e-10
                         PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadl 40 
                                   ++r+lfe s+d++++   +g+ i+ +N++a+e+lGy+   
  gi|91774124|ref|YP_566816.1| 121 YFRSLFEESNDAVLIHIqDGT-ILNINKKACEMLGYE--R 157
                                   8*************7333556.*************87..3 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-05
                         PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkg 42 
                                   l +++ess+dgia +d +++   +N ++  ++  ++d+ +
  gi|91774124|ref|YP_566816.1| 283 LSNVLESSSDGIAFFDMDNNTKLMNSQFRNMWEIPKDVVA 322
                                   7889************7777************97755444 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   2.8e-09   3.3e-06       2     103 ..     131     228 ..     130     229 .. 0.81
   2 !   10.4   0.1   0.00048      0.58       2     103 ..     292     394 ..     291     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.8e-09
                         PAS_9   2 dgili.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                   d++li +  dg+il +N++a+++lGy +  + + +   l++++ ++   + a     + k+ +    +ir +g+ + v ++
  gi|91774124|ref|YP_566816.1| 131 DAVLIhI-QDGTILNINKKACEMLGYERSTLCNINAYSLYDEKLYDGLPVFARKVLSE-KFAHSKSCMIRADGSIIDVSIS 209
                                   7888856.9*******************************444444444444444444.89******************** PP

                         PAS_9  82 aspvkdddgelvgiivilrDit 103
                                    s v  ++ +++   +i+rDit
  gi|91774124|ref|YP_566816.1| 210 SSFVDRNK-GVIQ--SIVRDIT 228
                                   *9995444.4555..7*****9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00048
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw..... 77 
                                   dgi++ ++d++   +N +++++    ++ v   ++ d+f    ++ + l++a   ++ k+r +   + +++g  ++     
  gi|91774124|ref|YP_566816.1| 292 DGIAFFDMDNNTKLMNSQFRNMWEIPKDVVADMNYIDIF--TNYGFQHLENAESVLS-KVRKFSSRYEKDSGLLYFkdgri 369
                                   678875577767799*******999999999***99999..8889999999998888.78888888888888333344444 PP

                         PAS_9  78 vlltaspvkdddgelvgiivilrDit 103
                                   ++ +++pv+  dg  +g+++ +rD+t
  gi|91774124|ref|YP_566816.1| 370 IEYNLFPVIK-DGVAQGHVCNCRDVT 394
                                   88******85.689999********9 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.25     3e+02      13      35 ..     138     160 ..     126     235 .. 0.51
   2 !   27.6   0.0   2.2e-09   2.6e-06       1     114 [.     287     400 ..     287     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.25
                         PAS_7  13 adlrLvawNrrylelldlpeelv 35 
                                   +d+ ++ +N++ +e+l++ ++ +
  gi|91774124|ref|YP_566816.1| 138 QDGTILNINKKACEMLGYERSTL 160
                                   55666666777777777666555 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.2e-09
                         PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfere 81 
                                   le+ s+Gi+ fD d++  ++N++++++ ++p+++v + +++ +++     ++  +a++v ++v+++ +++++   +s    
  gi|91774124|ref|YP_566816.1| 287 LESSSDGIAFFDMDNNTKLMNSQFRNMWEIPKDVV-ADMNYIDIFTNYGFQHLENAESVLSKVRKFSSRYEK---DSGLLY 363
                                   688899*****************************.677766665555444444447788888888766655...555566 PP

                         PAS_7  82 rpdgrvievrgnpl....pdgGfVttytDiTerrrae 114
                                    +dgr+ie +  p+       G V  + D+T +++ae
  gi|91774124|ref|YP_566816.1| 364 FKDGRIIEYNLFPVikdgVAQGHVCNCRDVTINKKAE 400
                                   78*********999654445799********999998 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.4e-07   0.00017       3      92 ..     122     209 ..     121     227 .. 0.71
   2 !    8.0   0.0    0.0024       2.8       3      89 ..     283     372 ..     281     393 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
                                   HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTT CS
                           PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrd 83 
                                   +r+++e + d++++   dg il +N++a+e+lG++r+ +++ + + l+ e+   +    + +  ++ + ++++   ++  d
  gi|91774124|ref|YP_566816.1| 122 FRSLFEESNDAVLIHIQDGTILNINKKACEMLGYERSTLCNINAYSLYDEKLY-DGLPVFARKVLSEKFAHSKSCMIRA-D 200
                                   6889999999999999*****************************99987633.3444444444444444444444555.6 PP

                                   SSEEEEEEE CS
                           PAS  84 grpihlevr 92 
                                   g++i + + 
  gi|91774124|ref|YP_566816.1| 201 GSIIDVSIS 209
                                   666666555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0024
                                   HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.. CS
                           PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl.. 81 
                                   l+++les+ d+i   D d +  ++N+ ++ +  ++ + v   +++d + +       ++le+++++ ++ r +  + ++  
  gi|91774124|ref|YP_566816.1| 283 LSNVLESSSDGIAFFDMDNNTKLMNSQFRNMWEIPKDVVADMNYIDIFTNY----GFQHLENAESVLSKVRKFSSRYEKds 359
                                   6789*****************************************877776....9****************999999988 PP

                                   .....TTSSEEEE CS
                           PAS  82 .....rdgrpihl 89 
                                        +dgr+i+ 
  gi|91774124|ref|YP_566816.1| 360 gllyfKDGRIIEY 372
                                   8998999988875 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.5e-08   6.5e-05      77     133 .]      48     106 ..      10     106 .. 0.80
   2 ?   -0.9   0.0       1.9   2.3e+03      12      43 ..     148     185 ..     144     230 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.5e-08
                                   HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHHH CS
                           GAF  77 nrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvaval 133
                                   ++  +++n ++rs++vvP++++++l+G + + n  +  ++++ e++++  ++  +++al
  gi|91774124|ref|YP_566816.1|  48 AEICQVDNCHVRSFVVVPMIVKNKLIGFIGFNNNEKevRWSDIEVDMFSFVGMIIGNAL 106
                                   34557899*************************555689**********9999999886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                                   HHHHHHTESEEEEEE.........EEETTEEECEEEEECC.E CS
                           GAF  12 elrellgadrvalyl.........pdydGlhydipqasrw.l 43 
                                   +++e+lg++r +l           + ydG    +p  +r  l
  gi|91774124|ref|YP_566816.1| 148 KACEMLGYERSTLCNinayslydeKLYDG----LPVFARKvL 185
                                   67899999998885445555555655666....555555532 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.4e-07   0.00017      85     138 .]      53     107 ..      29     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-07
                                   HHHHTT--EEEEEE-TTS---EEEEES.......--HHHHHHHHHHHHHHHHHHH CS
                         GAF_2  85 aghaglrsflavPlisegrvvGvlnlyankppa.fdeedlelLeelaeqiaiaie 138
                                    +  ++rsf++vP+i +++++G++++  n+++  +++ ++++++ ++  i+ a++
  gi|91774124|ref|YP_566816.1|  53 VDNCHVRSFVVVPMIVKNKLIGFIGFNNNEKEVrWSDIEVDMFSFVGMIIGNALQ 107
                                   677889999*******99*******9544444469*****************996 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0036       4.3       1      65 [.     126     190 ..     126     232 .. 0.80
   2 !   12.7   0.0   9.4e-05      0.11       1     107 [.     287     395 ..     287     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0036
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeep 65 
                                   ++ ++da+++   dg++l +N+ a+e++g+++ +l +   ++l+ e + ++l    r+vl+++ +
  gi|91774124|ref|YP_566816.1| 126 FEESNDAVLIHIQDGTILNINKKACEMLGYERSTLCNINAYSLYDEKLYDGLPVFARKVLSEKFA 190
                                   688999999999*********************99999999999999888888888888888543 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.4e-05
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll....pge 77 
                                   l+s++d++a++d d +   +N +++ +  +p + + ++ + ++++   + ++ ++ + vl+  +  ++  e +      ++
  gi|91774124|ref|YP_566816.1| 287 LESSSDGIAFFDMDNNTKLMNSQFRNMWEIPKDVVADMNYIDIFTN-YGFQHLENAESVLSKVRKFSSRYEKDSgllyFKD 366
                                   79*******************************************9.7777777778888888888888888777888999 PP

                         PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTe 107
                                   +r++e +l+P+   +G ++g+++ +rD+T 
  gi|91774124|ref|YP_566816.1| 367 GRIIEYNLFPVI-KDGVAQGHVCNCRDVTI 395
                                   ***********5.7**************96 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.4e-07   0.00065      75     129 .]      53     108 ..      35     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.4e-07
                         GAF_3  75 edglpdraalavPLvagrqviGvlalastkpr.afdaedlelleslArqiataier 129
                                    d+++ r+ ++vP+++++++iG+++++ ++++  +++ ++++++ ++  i++a+++
  gi|91774124|ref|YP_566816.1|  53 VDNCHVRSFVVVPMIVKNKLIGFIGFNNNEKEvRWSDIEVDMFSFVGMIIGNALQH 108
                                   689************************9998846******************9985 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.5     1e+04     106     117 ..     404     415 ..     403     419 .. 0.80
   2 !   18.3   0.0   1.5e-06    0.0017      31     112 ..     524     609 ..     508     630 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.5
                   HATPase_c_2 106 kglvDeveydge 117
                                   k+++D++ey++e
  gi|91774124|ref|YP_566816.1| 404 KKYADDLEYSNE 415
                                   789******766 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.5e-06
                   HATPase_c_2  31 eirlaveEactNavehayleap.egpvevrlesdeealtvevaDsGpg.fdpetlpdpteeep.....keslkegGrGlal 104
                                   + ++ veE+++N    a +  p   ++ + + +++++ +v+++D G+g  d e+    +         k++ k  G+Gla+
  gi|91774124|ref|YP_566816.1| 524 KANIMVEEVFANLLSNAIKYSPkGSTIYIDILDAGDEWKVQFTDFGEGiSDEEKDFVFE---RfkrvnKTNIKGTGIGLAI 601
                                   56799****************98899**********************77776533222...234566999********** PP

                   HATPase_c_2 105 ikglvDev 112
                                   ++++vD  
  gi|91774124|ref|YP_566816.1| 602 VRKIVDLH 609
                                   *****965 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 !   16.1   0.1   7.1e-06    0.0085       5      66 ..     420     480 ..     415     481 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.1e-06
                                   HHHHHHHHHHHHHHHHHHHHHHH.HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                         HisKA   5 flagvaHELrtPLsailgnaeaL.kregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                   ++  + H+L +P+  ++g++++L ++  +++++  ++l+++e +   + + +e +  ls++++
  gi|91774124|ref|YP_566816.1| 420 LADILRHDLLNPVGIVKGFLSVLiQK--EYDPKMLDMLRKAEMSNLKVIDTIEMVSKLSKLDS 480
                                   344579****************9755..58999999999999999999999999999998875 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.5      0.33   3.9e+02       4      47 ..      92     138 ..      90     153 .. 0.79
   2 !   13.1   0.0   5.4e-05     0.065       9      88 ..     532     616 ..     526     621 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.33
                   HATPase_c_5   4 ldlcvilgnlLdNAieacsk....ieeekrfIrltvrekkksliisie 47 
                                   +d+ + +g ++ NA++  +     + e++ + r  ++e++++++i+i+
  gi|91774124|ref|YP_566816.1|  92 VDMFSFVGMIIGNALQHERYnnvlC-ENEMYFRSLFEESNDAVLIHIQ 138
                                   799999********98777634422.4688888888999999999987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.4e-05
                   HATPase_c_5   9 ilgnlLdNAieacskieeekrfIrltvrekk.ksliisieNsyegek.....kkle.sskskkeehGiGlksireivkkyk 82 
                                   ++ nlL NAi  + k +  + +I++    ++ k  +  +   +++e+     ++++  +k++ +  GiGl  +r+iv+ ++
  gi|91774124|ref|YP_566816.1| 532 VFANLLSNAIKYSPKGS--TIYIDILDAGDEwKVQFTDFGEGISDEEkdfvfERFKrVNKTNIKGTGIGLAIVRKIVDLHG 610
                                   899*******9999977..566665544444133444444455555545566444435699999****************9 PP

                   HATPase_c_5  83 gnlsie 88 
                                   g++ +e
  gi|91774124|ref|YP_566816.1| 611 GHFGVE 616
                                   998776 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0     0.001       1.2      72     124 ..      53     105 ..      32     107 .. 0.85
   2 ?    1.4   0.0      0.27   3.2e+02      72     108 ..     366     400 ..     336     409 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                       SpoVT_C  72 eekeeysaqviaPIiaeGdviGaVillskeekkklgelekklaetaAsFLgkq 124
                                    ++ ++++ v++P i++   iG + + ++e++ + +++e+ +  ++   +g  
  gi|91774124|ref|YP_566816.1|  53 VDNCHVRSFVVVPMIVKNKLIGFIGFNNNEKEVRWSDIEVDMFSFVGMIIGNA 105
                                   455688999********************************999988887765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.27
                       SpoVT_C  72 eekeeysaqviaPIiaeGdviGaVillskeekkklge 108
                                   ++  ++ ++ ++P+i +G + G V+ + + + +k  e
  gi|91774124|ref|YP_566816.1| 366 DG--RIIEYNLFPVIKDGVAQGHVCNCRDVTINKKAE 400
                                   33..57788899************9985554443333 PP

>> CNOT11  CCR4-NOT transcription complex subunit 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.16       7     112 ..     434     544 ..     429     547 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                        CNOT11   7 iAielLlkllksseaneyldvlvkldvt....lhslevvnrlts.eaelpkefvhkyisnciksceeakdkeaqerlvrlv 82 
                                   i++ +L  l++++   + ld+l k +++    ++++e+v +l++ ++  + ef    i  +i+  ++      +++ +r +
  gi|91774124|ref|YP_566816.1| 434 IVKGFLSVLIQKEYDPKMLDMLRKAEMSnlkvIDTIEMVSKLSKlDSVEEIEFSVIDIGLMINIAKTNLGAMFKNKDMRAL 514
                                   88999999****999***********998777788888888888544444556556677777766666689999******* PP

                        CNOT11  83 cvflqsLirnkivdvkdllvevqaFClefs 112
                                   c+f  ++  +  + v+++++++ +  +++s
  gi|91774124|ref|YP_566816.1| 515 CRFSGNYPAKANIMVEEVFANLLSNAIKYS 544
                                   ****99999999999999999988888776 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.6   5.5e+03      40      57 ..     214     231 ..     213     233 .. 0.81
   2 ?   -3.5   0.0       7.2   8.6e+03      38      52 ..     337     351 ..     331     357 .. 0.69
   3 ?    9.3   0.0   0.00075       0.9       8      35 ..     412     440 ..     407     447 .. 0.80
   4 ?   -3.6   0.0       8.2   9.8e+03      51      62 .]     467     478 ..     464     484 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.6
                        SPOB_a  40 dkaeeyieevvkelkees 57 
                                   d+ + +i+++v++++ e+
  gi|91774124|ref|YP_566816.1| 214 DRNKGVIQSIVRDITVEK 231
                                   788889*****9998775 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.2
                        SPOB_a  38 kydkaeeyieevvke 52 
                                    +++ae+++ +v+k 
  gi|91774124|ref|YP_566816.1| 337 HLENAESVLSKVRKF 351
                                   567788888887765 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00075
                        SPOB_a   8 elkeliklL.rsqRHDflNhLQvIsGylq 35 
                                   + +el +lL   +RHD lN   +++G+l 
  gi|91774124|ref|YP_566816.1| 412 YSNELKDLLaDILRHDLLNPVGIVKGFLS 440
                                   4556666666669**************96 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 8.2
                        SPOB_a  51 kelkeeskilkl 62 
                                   + +++ sk++kl
  gi|91774124|ref|YP_566816.1| 467 DTIEMVSKLSKL 478
                                   445555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 3738.19
//
Query:       gi|91774125|ref|YP_566817.1|  [L=122]
Description: hypothetical protein Mbur_2202 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-43  145.3   0.0    9.7e-43  145.1   0.0    1.0  1  DHNA        Dihydroneopterin aldolase
     0.0092   16.1   0.1      0.018   15.2   0.1    1.4  1  Colipase_C  Colipase, C-terminal domain
  ------ inclusion threshold ------
       0.05   13.9   0.0       0.43   10.9   0.0    2.4  2  DUF3794     Domain of unknown function (DUF3794)
      0.065   13.2   0.0      0.078   12.9   0.0    1.1  1  RRF         Ribosome recycling factor
       0.09   12.7   0.0       0.16   12.0   0.0    1.3  1  TIR-like    Predicted nucleotide-binding protein containing T


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 !  145.1   0.0   2.7e-46   9.7e-43       1     107 [.      11     118 ..      11     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 2.7e-46
                                   -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-S.TS-EE--TTTEEEE CS
                          DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleeklee.fgYteLtgemldve 80 
                                   tdr++ +FEagiklgalyHqf+G+Pv+ +++ sle+ai++si++QP+ve+++v+idr+ l +kl++ fgY+eL+g+ml+v+
  gi|91774125|ref|YP_566817.1|  11 TDRDNVLFEAGIKLGALYHQFTGSPVNLRTVGSLETAIAQSISVQPCVENITVSIDRDILGSKLNDeFGYCELEGRMLNVQ 91 
                                   89**************************************************************999************** PP

                                   EEEEETTEEEEEEEEEETTTTEEEEEE CS
                          DHNA  81 itvkyeeaevkarleyieeldYplmkv 107
                                   i+ +ye+a+v++++e+++eldYplmk+
  gi|91774125|ref|YP_566817.1|  92 IDARYESAKVHVSMEFNKELDYPLMKI 118
                                   *************************99 PP

>> Colipase_C  Colipase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     5e-06     0.018      17      43 ..      56      82 ..      54      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-06
                    Colipase_C 17 pCEsGLtCeadktivGsitNtnfGiCe 43
                                  pC + +t   d+ i+Gs  N +fG+Ce
  gi|91774125|ref|YP_566817.1| 56 PCVENITVSIDRDILGSKLNDEFGYCE 82
                                  89999999******************6 PP

>> DUF3794  Domain of unknown function (DUF3794)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.43      11      74 ..       3      63 ..       1     104 [. 0.62
   2 ?    1.1   0.0      0.14     5e+02      63      76 ..      90     103 ..      80     119 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                       DUF3794 11 kieitevkvidgkviveGelkvkilY..........qnvhslegeipFsefieipgaepgmevdvkaevedisv 74
                                  +i ++++    ++v++e+ +k+  lY          ++v sle+ i  s             ++v+++ve+i+v
  gi|91774125|ref|YP_566817.1|  3 DIMVEDTITDRDNVLFEAGIKLGALYhqftgspvnlRTVGSLETAIAQS-------------ISVQPCVENITV 63
                                  566666767779**************99998777775566666665555.............222223333332 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.14
                       DUF3794  63 vdvkaevedisvel 76 
                                   v+++a+ e+ +v++
  gi|91774125|ref|YP_566817.1|  90 VQIDARYESAKVHV 103
                                   44444444444443 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05     0.078      26      84 ..      32      93 ..      20     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                  TTEEEEGGGTEEEEESSTTEEEEEESSCCHHHHHHHHHHHSCC-SEEEE...ESSEEEEE-- CS
                           RRF 26 ygkktpLnqlAqvsvkeartllitpfdkslvkaiekaIlksdlglnpqq...dgevlrvpip 84
                                   g++++L+++++ ++  a++++++p  ++++ +i + Il s+l+        +g++l+v+i 
  gi|91774125|ref|YP_566817.1| 32 TGSPVNLRTVGSLETAIAQSISVQPCVENITVSIDRDILGSKLNDEFGYcelEGRMLNVQID 93
                                  6889***************************************9554323347778887776 PP

>> TIR-like  Predicted nucleotide-binding protein containing TIR-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.3e-05      0.16      71      89 ..       9      27 ..       2      32 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-05
                      TIR-like 71 kkraRqNVifElGlflgkl 89
                                  + + R+NV+fE+G+ lg+l
  gi|91774125|ref|YP_566817.1|  9 TITDRDNVLFEAGIKLGAL 27
                                  6678**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 729.06
//
Query:       gi|91774126|ref|YP_566818.1|  [L=360]
Description: histidinol-phosphate aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for 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-60  203.6   0.0    5.6e-60  203.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      1e-10   41.1   0.1    7.7e-09   35.0   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    6.4e-10   38.9   0.4      1e-09   38.2   0.4    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      2e-08   33.2   0.1    3.2e-08   32.5   0.1    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0001   21.3   0.0    0.00035   19.6   0.0    1.7  2  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.092   11.5   0.0       0.14   11.0   0.0    1.2  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.4   0.0   1.9e-63   5.6e-60       2     362 ..      36     356 ..      35     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 203.4 bits;  conditional E-value: 1.9e-63
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                    vi+Lgsne++ +    ++p++++a +   +  +++ +y+  d + el  a+ ++        + +   v  g+G + l++
  gi|91774126|ref|YP_566818.1|  36 SVIKLGSNENPLG----PSPKAVEALI---ANAQGISIYPSAD-ARELVDAISEYTD------IPAANIVASGPGMDGLLD 102
                                   58***********....*********5...599**********.*************......44443466689******* PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    l++l  +  gde+++ +pt++ y+ ++r++g++ v++    e+df++++++l++al+        tk+i+++sp+NPtG 
  gi|91774126|ref|YP_566818.1| 103 GLARLV-IANGDEVVITTPTFSYYEIAARANGATTVYVQ--REKDFSINVDKLLAALTP------NTKMIFLCSPNNPTGN 174
                                   ******.********************************..67***************9......99************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlr 244
                                   v+++e++ k+   a++  +l+fvDeaY +f+ +     ++ ++v +++n+++ +++sKafGlaG R+Gy +  +++++   
  gi|91774126|ref|YP_566818.1| 175 VIPEEDILKI---ATATDALVFVDEAYVEFAEK-----NIAHLVLQHDNIIVGRTFSKAFGLAGMRMGYGIMPEWLREEYM 247
                                   **********...888899**************.....67999************************************** PP

                                   HHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHH CS
                 Aminotran_1_2 245 klsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLl 325
                                   k+++pf++s+++ aa  aalsd++    +l+++ +   k  k+l +eL    +kv++ q++++l+ + +++ a ++  +Ll
  gi|91774126|ref|YP_566818.1| 248 KIATPFNVSTAAMAAGIAALSDTE----HLNKSIELTVKGKKFLQEEL---PFKVYDTQANFVLVDVAPHK-ARDVTTELL 320
                                   ************************....9*******************...***********999777777.99******* PP

                                   HTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                 Aminotran_1_2 326 eevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                   ++ g++v+ +tsf     + +R+t+  +t+e++e++v+a
  gi|91774126|ref|YP_566818.1| 321 KK-GIIVRDCTSFAHagLSLIRVTI--GTKEQNEKVVKA 356
                                   **.***********999899*****..*********997 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   2.6e-12   7.7e-09      85     177 ..     109     197 ..      89     206 .. 0.86
   2 !    4.1   0.0    0.0062        19     282     367 ..     278     352 ..     238     355 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.6e-12
                                   -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHH CS
                   Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigkla 165
                                   + +gde+v+t+    +     + +a++ ga+ ++++ +++ ++++d+l ++l+++tk+++++  +n tG++ p e+i k+a
  gi|91774126|ref|YP_566818.1| 109 IANGDEVVITTP-TFSYY---EIAARANGATTVYVQREKDFSINVDKLLAALTPNTKMIFLCSPNNPTGNVIPEEDILKIA 185
                                   566677666643.33333...5567788***************************************************** PP

                                   HHTT-EEEEE-T CS
                   Aminotran_5 166 kkkgalvlvDaa 177
                                    + +alv+vD a
  gi|91774126|ref|YP_566818.1| 186 TATDALVFVDEA 197
                                   **********87 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0062
                                   HHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TT CS
                   Aminotran_5 282 elaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiy 362
                                   el+ + ++ l++   +++y     + +a+ v + ++ ++a+dv t L ++gI vr   + a      +a  + +R+ ++  
  gi|91774126|ref|YP_566818.1| 278 ELTVKGKKFLQEELPFKVY-----DTQANFVLVDVAPHKARDVTTELLKKGIIVRDCTSFA------HAGLSLIRVTIGTK 347
                                   4444455555554445554.....46899999**********************9755555......22225666666666 PP

                                   S-HHH CS
                   Aminotran_5 363 nteee 367
                                    ++e+
  gi|91774126|ref|YP_566818.1| 348 EQNEK 352
                                   66665 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 !   38.2   0.4   3.4e-13     1e-09      13     146 ..      57     197 ..      50     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.4e-13
                                   HHTSS-SSS...SHHHHHHHHHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEE CS
               DegT_DnrJ_EryC1  13 vlksgwlts...gpeveeFEkafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpv 88 
                                   ++ + + +s       +e+  a+++y+   +++ +a   G ++l+ +L  l + +gdeV++++ tF     a++ +ga++v
  gi|91774126|ref|YP_566818.1|  57 LIANAQGISiypSADARELVDAISEYTDipAANIVASGPGMDGLLDGLARLVIANGDEVVITTPTFSYYEIAARANGATTV 137
                                   55555555554455677888899999995566667777789**************************************** PP

                                   EE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB---HHHHHHHHHHCT-EEEEE-T CS
               DegT_DnrJ_EryC1  89 fvDvdpdtynidpaaieaaitertkaIl...pVhlyGqvadmdalkaiaakhglkvieDaA 146
                                   +v  + +++ i+++++ aa+t++tk I+   p +  G+v   + + +ia++++  v+ D A
  gi|91774126|ref|YP_566818.1| 138 YVQRE-KDFSINVDKLLAALTPNTKMIFlcsPNNPTGNVIPEEDILKIATATDALVFVDEA 197
                                   **987.99*******************9333457789***99*********9999998865 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 !   32.5   0.1   1.1e-11   3.2e-08      69     176 ..      87     198 ..      70     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.1e-11
                                   EEEEESS..HHHHHHHHHHTTS-T.TEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEE CS
               Cys_Met_Meta_PP  69 aalavss..GmaAiaaailallka.GdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklv 141
                                   aa +v+s  Gm  +   + +l+ a Gde+v+++    +t+++ +  ++  g ++ +v+       ++++l +a+++ntk++
  gi|91774126|ref|YP_566818.1|  87 AANIVASgpGMDGLLDGLARLVIAnGDEVVITT----PTFSYYEIAARANGATTVYVQRekdfsINVDKLLAALTPNTKMI 163
                                   4545555226777777777776555*****997....5777888888888888888887444445789999********** PP

                                   EEESS-TTTT----HHHHHHHHHHTT-EEEEEGTT CS
               Cys_Met_Meta_PP 142 ylEtptnpllkvvDiekiaklakkagvlvvvDntf 176
                                   +l +p np+ +v+  e+i+k+a + ++lv+vD ++
  gi|91774126|ref|YP_566818.1| 164 FLCSPNNPTGNVIPEEDILKIATATDALVFVDEAY 198
                                   ********************************976 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-07   0.00035      98     210 ..     114     240 ..      97     263 .. 0.72
   2 ?   -1.5   0.0      0.29   8.7e+02     297     347 ..     295     346 ..     291     356 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                                   EEEE-SS--THHH......HHTTTT-BTTEEEEEESTT-.--S..S-EEEEEESS-TTT---..-----...-TT-EEEEE CS
                   Alliinase_C  98 kvvaavPyysvyk......eqtslldsklykweGdaaayvkkknpeefielvtsPnnPdgll..reavv...kgseakviy 167
                                   +vv ++P +s y+        t+++ +++  ++ +  +     +p+  + +  sPnnP g++   e ++   + ++a v +
  gi|91774126|ref|YP_566818.1| 114 EVVITTPTFSYYEiaaranGATTVYVQREKDFSINVDKLLAALTPNTKMIFLCSPNNPTGNVipEEDILkiaTATDALVFV 194
                                   6777777777665111111235556666667777777777777888888899********985557788655677888999 PP

                                   E-TT-ST...TTS---S-B--SEEEEEHHHHHS-GGG-EEEEEES- CS
                   Alliinase_C 168 DlayYWP...hytpitskadedimLftlskltGhaGsrlGWalvkd 210
                                   D ay      + +++  + d+ i+  t+sk  G aG r+G++++ +
  gi|91774126|ref|YP_566818.1| 195 DEAYVEFaekNIAHLVLQHDNIIVGRTFSKAFGLAGMRMGYGIMPE 240
                                   ***97541114566666778888889***************99755 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.29
                                   EEE---SEEEEEESSSS..-HHHHHHTTTEEEEEGGGG.TS-TTEEEEESSS CS
                   Alliinase_C 297 vrepsPayaWlkcekeededcaevlrekkiltrsGevf.eaesryvrlsllk 347
                                   v +++  +  + +  ++ +d++  l +k+i+ r+ + f  a+ + +r+++  
  gi|91774126|ref|YP_566818.1| 295 VYDTQANFVLVDVAPHKARDVTTELLKKGIIVRDCTSFaHAGLSLIRVTIGT 346
                                   5667777888888888999999999999999999988724678888887654 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.5e-05      0.14     111     217 ..      99     199 ..      85     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.5e-05
                                   --TT-SS-GGGG.--EEEEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHHHHHHC-TTEEEEEE-SSS-TTT----- CS
                Aminotran_MocR 111 GvrdsegpwvkeekvkllvtvpGydrhfllleelGielltvdlqddGpdvdaveklvaedasvkGilavpkysnptGetis 191
                                   G+ d+    v  +   +++t+p +  + +  +  G   + v+ ++d   +++ + l+a  +  k ++++    nptG++i 
  gi|91774126|ref|YP_566818.1|  99 GLLDGLARLVIANGDEVVITTPTFSYYEIAARANGATTVYVQREKDF-SINVDKLLAALTPNTK-MIFLCSPNNPTGNVIP 177
                                   55555555566666678888888888888888888888888877764.4554455667777777.55677789******** PP

                                   HHHHHHHHT---SSTT-EEEEE-TTS CS
                Aminotran_MocR 192 eevarrlaalkaaapdfrifaddaya 217
                                   ee + ++a    +a d  +f+d+ay 
  gi|91774126|ref|YP_566818.1| 178 EEDILKIA----TATDALVFVDEAYV 199
                                   **999886....578999*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2402.76
//
Query:       gi|91774127|ref|YP_566819.1|  [L=390]
Description: acetylornithine aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-120  402.7   0.3   1.6e-120  402.5   0.3    1.0  1  Aminotran_3      Aminotransferase class-III
    0.00015   21.1   0.4    0.00071   18.9   0.4    1.9  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00026   20.4   1.4    0.00074   18.9   1.0    2.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0017   17.6   0.0     0.0039   16.4   0.0    1.6  2  Aminotran_1_2    Aminotransferase class I and II
     0.0032   16.5   0.0      0.012   14.6   0.0    1.8  2  Aminotran_5      Aminotransferase class-V


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 !  402.5   0.3  4.6e-124  1.6e-120       7     404 ..      27     389 ..      21     390 .] 0.97

  Alignments for each domain:
  == domain 1  score: 402.5 bits;  conditional E-value: 4.6e-124
                                   --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                   Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                   +  +l+++ ++G+++ d +g++++D v++iav+n+Gh+hPk+v+a+++qa kl h+s +++ ++ ++++ae+l+++ +   
  gi|91774127|ref|YP_566819.1|  27 TRQPLALESGQGSIVRDIEGREFIDCVAGIAVNNVGHCHPKIVEALSKQAGKLIHTS-NLYYTDVQANFAEELVNISGM-- 104
                                   455689999************************************************.*******************99.. PP

                                   SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGT CS
                   Aminotran_3  88 dkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevl 168
                                    + f++nsG+eAve+A+Klar       at k+++ia +++fHGrt+g+l vt + + y++ f+p++ +  +++y+     
  gi|91774127|ref|YP_566819.1| 105 GRAFFCNSGTEAVEAAMKLARV------ATGKKEFIATENSFHGRTMGSLTVTYK-STYRKPFEPLIQGERFVPYNS---- 174
                                   **********************......***************************.********************6.... PP

                                   B-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGG CS
                   Aminotran_3 169 keneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAleh 249
                                                ++a++++ ++++aAvivEpiqgegG++v+s+e+l+++re+c+++++lli+DEvqtGfGrTGk+f+ +h
  gi|91774127|ref|YP_566819.1| 175 -------------AQAIRDTVTEDTAAVIVEPIQGEGGINVPSDEYLREVREICDENEMLLIFDEVQTGFGRTGKWFCKDH 242
                                   .............78888999************************************************************ PP

                                   CTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH CS
                   Aminotran_3 250 agvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelgaalkegLee 330
                                     v+pD+mt+aKa++gG+p+ a++a++ +   +++++h+ TfgG placa+ala++++i +ekl+e+ +e+g+++ ++L++
  gi|91774127|ref|YP_566819.1| 243 SKVKPDIMTMAKAIGGGFPMGAIVARDGIS--FEKSQHAATFGGGPLACAAALASINVIRDEKLVERSAEMGQYFMNELNS 321
                                   ***************************995..888********************************************** PP

                                   HCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHHHHHH CS
                   Aminotran_3 331 lqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidelleilkk 404
                                   l+++   i evRg+Glmi++e+  +      +i++ a+++G+l+  + ++vir++ppliit+e+id+++ei+ +
  gi|91774127|ref|YP_566819.1| 322 LDND--SIVEVRGRGLMIGVEINRACA----DIVDLARDNGILLNCTSEKVIRIAPPLIITKEQIDKVVEIIGQ 389
                                   **77..5****************9999....9***********999999*********************9976 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4     2e-07   0.00071      36     210 ..      93     268 ..      67     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-07
                                   HHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-EBTT.TBE-HHH CS
               Beta_elim_lyase  36 rLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiael.agvklrdlknkea.Gkmdlek 113
                                   ++++++ ++ g+  a+f+ +Gt A + ++k+     g++ ++  ++ +h ++ g + +  ++   ++++   +   + + +
  gi|91774127|ref|YP_566819.1|  93 NFAEELVNISGMGRAFFCNSGTEAVEAAMKLARvATGKKEFIATENSFHGRTMGSLTVTyKSTYRKPFEPLIQgERFVPYN 173
                                   4566777899**************999996655355555566666668899998888774666555555433325788888 PP

                                   HHHHS--S-TTS-EEEEEEEESSBTTTTTB--.-HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTT.SSEE CS
               Beta_elim_lyase 114 leaaikevgaheekiklisltvTnntagGqvv.sleelrevaaiakkygiplhlDgARfanaakslgeivkemfsy.vDsv 192
                                    ++ai+++    e++++++++      gG  v s e+lrev++i++++++ l++D         + +   k+  ++  D++
  gi|91774127|ref|YP_566819.1| 174 SAQAIRDTVT--EDTAAVIVEPIQGE-GGINVpSDEYLREVREICDENEMLLIFDEVQTGFG-RTGKWFCKDHSKVkPDIM 250
                                   9999999777..99*******99886.7766615678******************7543222.455566666665446888 PP

                                   EEESSSTT--SS-EEEEE CS
               Beta_elim_lyase 193 tmslkKdllanvGgvlaf 210
                                   tm    ++++++G+++a 
  gi|91774127|ref|YP_566819.1| 251 TMAKAIGGGFPMGAIVAR 268
                                   888888888888888875 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.0   2.1e-07   0.00074      23     145 ..      89     226 ..      68     287 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-07
                                   HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTT.TT-EEEEESSS-THHHHHHHHTT-EEEEE-.....B-TTTS CS
               DegT_DnrJ_EryC1  23 peveeFEkafaaylgvkhaiavssGtaAlhlaLralgvg.pgdeVIvpsltFvatanavlelgakpvfvD.....vdpdty 97 
                                   +  ++F++++ +  g+  a  ++sGt+A++ a++   v   ++e I + ++F +     l + +k  +       ++ + +
  gi|91774127|ref|YP_566819.1|  89 DVQANFAEELVNISGMGRAFFCNSGTEAVEAAMKLARVAtGKKEFIATENSFHGRTMGSLTVTYKSTYRKpfeplIQGERF 169
                                   45679******************************888834579********87554444444443332211122666666 PP

                                   SB..-GGGCGGG--TTEEEEEEB-GGGB.....---..HHHHHHHHHHCT-EEEEE- CS
               DegT_DnrJ_EryC1  98 ni..dpaaieaaitertkaIlpVhlyGq.....vad..mdalkaiaakhglkvieDa 145
                                    +  +++ai+  +te t+a+++  + G+     ++d  + ++++i+++ ++ +i D 
  gi|91774127|ref|YP_566819.1| 170 VPynSAQAIRDTVTEDTAAVIVEPIQGEgginvPSDeyLREVREICDENEMLLIFDE 226
                                   653367899999999999999988888622222333447889999999999999985 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 ?   -1.8   0.0      0.38   1.4e+03      26      89 ..      71     125 ..      58     154 .. 0.53
   2 !   16.4   0.0   1.1e-06    0.0039     164     296 ..     202     325 ..     163     387 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.38
                                   HHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH CS
                 Aminotran_1_2  26 aeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllk 89 
                                   a  +  g l + ++  y++ +  + + e+l    g          +a  + sG+ a+ +a +  ++
  gi|91774127|ref|YP_566819.1|  71 ALSKqaGKLIHTSNLYYTDVQ--ANFAEELVNISG--------MGRAFFCNSGTEAVEAAMKL-AR 125
                                   444433334444444444333..666666666666........55344444444444333333.33 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-06
                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH.HHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgna.avvsql 243
                                   v++ e l+++ ++++++++ll++De+  gf  + + + + +++v++++      +++Ka G  G+ +G+i++ +    +  
  gi|91774127|ref|YP_566819.1| 202 VPSDEYLREVREICDENEMLLIFDEVQTGFGRTGKWFCKDHSKVKPDIM-----TMAKAIG-GGFPMGAIVARDgISFEKS 276
                                   566677999************************9988888******988.....******9.4888899999662444444 PP

                                   HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..T CS
                 Aminotran_1_2 244 rklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..g 296
                                   + ++++      ++ a+aaal   + +  + e+ ++r +++ +++ +eL++l  +
  gi|91774127|ref|YP_566819.1| 277 QHAATF----GGGPLACAAALASINVI--RDEKLVERSAEMGQYFMNELNSLdnD 325
                                   444444....66777777777776655..67889999999999999999988552 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.2e-06     0.012      45     179 ..      87     229 ..      57     234 .. 0.81
   2 ?   -1.2   0.0      0.21   7.7e+02     260     301 ..     288     329 ..     278     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-06
                                   HHHHHHHHH.HHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETT CS
                   Aminotran_5  45 veearekva.elinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldee 124
                                   ++++++++a el+n++   +  f+ ++tea++++++ + r    ++e++ te+  h+ ++    +  + +++  + pl ++
  gi|91774127|ref|YP_566819.1|  87 YTDVQANFAeELVNISGMGRAFFCNSGTEAVEAAMKLA-RVATGKKEFIATENSFHGRTMGSLTVTYKSTYRKPFEPLIQG 166
                                   5566666652588999999999**********998877.779999*********************999999887777666 PP

                                   SCBE....GGGHHHH--TTEEEEEEESBETTTTEB--....HHHHHHHHHHTT-EEEEE-TTT CS
                   Aminotran_5 125 geld....ldelekllnektklvaithvsnvtGtiqp....veeigklakkkgalvlvDaaqa 179
                                    +       ++++++++e+t++v++  ++ + G+  p    + e+ +++ ++++l++ D +q+
  gi|91774127|ref|YP_566819.1| 167 ERFVpynsAQAIRDTVTEDTAAVIVEPIQGEGGINVPsdeyLREVREICDENEMLLIFDEVQT 229
                                   66653345666777779*****************766233366788889999********997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES CS
                   Aminotran_5 260 glgaaleyleeigleaiekhekelaeyllerlkslpgvrlyg 301
                                   +++aal  ++ i  e+  ++++e+ +y +++l+sl++  +++
  gi|91774127|ref|YP_566819.1| 288 ACAAALASINVIRDEKLVERSAEMGQYFMNELNSLDNDSIVE 329
                                   788999999999999999999999999999999999877744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2877.33
//
Query:       gi|91774128|ref|YP_566820.1|  [L=276]
Description: hypothetical protein Mbur_2205 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-10   40.7  13.5    2.5e-06   27.7   1.6    3.9  3  Bactofilin  Polymer-forming cytoskeletal
    0.00046   19.8   4.6      0.013   15.2   0.4    6.5  7  Hexapep     Bacterial transferase hexapeptide (six repeats)
  ------ inclusion threshold ------
       0.23    9.8   0.0       0.44    8.9   0.0    1.4  2  DUF2863     Protein of unknown function (DUF2863)


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.3   4.9e-06     0.029       2      45 ..      30      75 ..       3      77 .. 0.51
   2 !   16.0   1.8   1.8e-06     0.011       2      54 ..      30      85 ..      29     105 .. 0.82
   3 !   27.7   1.6   4.2e-10   2.5e-06      22      96 ..     173     249 ..     149     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-06
                    Bactofilin  2 ligegtkikGelevegdlridG..kveGdieakgklvvgeggkveg 45
                                  ++ge ++++G++  ++d+rid   ++ G++++k++  +ge  +++g
  gi|91774128|ref|YP_566820.1| 30 ILGERVEVSGDIVASSDIRIDIwsHIGGNVKTKKNAYIGEFVTIDG 75
                                  4455555555555555555543325555555555555555555554 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-06
                    Bactofilin  2 ligegtkikGelevegdlridG..kveGdieakgklvvgeggkvegnika.eevvv 54
                                  ++ge ++++G++  ++d+rid   ++ G++++k++  +ge  +++g++ + +++++
  gi|91774128|ref|YP_566820.1| 30 ILGERVEVSGDIVASSDIRIDIwsHIGGNVKTKKNAYIGEFVTIDGRLVVkGDLDI 85
                                  78999********9999999755599******99******9999999665344555 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 4.2e-10
                    Bactofilin  22 dGkveGdieakgklvvgeggkvegnika.eevvvaGt...vkGnveaeekvelkktakveGdikaksleieegavfeGk 96 
                                   + ++ G+i+a+  l  g+++++ g+i+  ++v++ G+   ++Gn+ +++ v ++k ++v G+i+a+s++i+e a+++G 
  gi|91774128|ref|YP_566820.1| 173 NCRLVGNIRAS-MLEMGKNTTLYGSIRTlTNVDL-GEdniIHGNIVSRGDVYINKGTHVLGEINANSIKIHESARVDGV 249
                                   56778999888.8999999999999999677777.77677889999999999999999999999999999999999985 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3     0.022   1.3e+02      14      30 ..       6      22 ..       3      23 .. 0.83
   2 ?   -1.0   0.1      0.27   1.6e+03      16      28 ..      25      37 ..      24      39 .. 0.67
   3 !   13.7   0.3   6.7e-06      0.04       9      35 ..      48      74 ..      45      75 .. 0.89
   4 !   15.2   0.4   2.2e-06     0.013       1      31 [.      64      94 ..      64      94 .. 0.94
   5 !    3.8   0.1    0.0087        52       8      16 ..     168     176 ..     161     181 .. 0.57
   6 ?    2.4   0.2     0.023   1.4e+02      17      30 ..     200     213 ..     186     214 .. 0.78
   7 ?    2.3   1.5     0.026   1.6e+02       4      27 ..     205     228 ..     202     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.022
                                  EEEETTEEE-TTEEEET CS
                       Hexapep 14 aviggnVkIGdnvkIga 30
                                   v+ g++++G+++ I  
  gi|91774128|ref|YP_566820.1|  6 IVLDGDIVVGNHSDIRY 22
                                  68889*******99975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.27
                                  EETTEEE-TTEEE CS
                       Hexapep 16 iggnVkIGdnvkI 28
                                  i++ +++G++v +
  gi|91774128|ref|YP_566820.1| 25 IANAAILGERVEV 37
                                  6677777777765 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 6.7e-06
                                  EE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep  9 lIgpfaviggnVkIGdnvkIgagvvig 35
                                   I+ +++iggnVk  +n++Ig++v+i 
  gi|91774128|ref|YP_566820.1| 48 RIDIWSHIGGNVKTKKNAYIGEFVTID 74
                                  69999*******************996 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2.2e-06
                                  TEEEETTEEE-TTEEEETTEEE-TTEEEETT CS
                       Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgag 31
                                  ++ IG+ v+I+   v+ g+  IG++vkI +g
  gi|91774128|ref|YP_566820.1| 64 NAYIGEFVTIDGRLVVKGDLDIGNDVKISSG 94
                                  579*************************986 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.0087
                                   EEE-TTEEE CS
                       Hexapep   8 vlIgpfavi 16 
                                   ++Ig+++ +
  gi|91774128|ref|YP_566820.1| 168 ATIGNNCRL 176
                                   344444444 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.023
                                   ETTEEE-TTEEEET CS
                       Hexapep  17 ggnVkIGdnvkIga 30 
                                   + nV +G++ +I+ 
  gi|91774128|ref|YP_566820.1| 200 LTNVDLGEDNIIHG 213
                                   57999*******97 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.026
                                   EETTEEE-TTEEEETTEEE-TTEE CS
                       Hexapep   4 IGsnvlIgpfaviggnVkIGdnvk 27 
                                   +G++++I+ + v +g+V I ++++
  gi|91774128|ref|YP_566820.1| 205 LGEDNIIHGNIVSRGDVYINKGTH 228
                                   688888888888888888888776 PP

>> DUF2863  Protein of unknown function (DUF2863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   7.3e-05      0.44      42      71 ..     116     145 ..     111     159 .. 0.86
   2 ?   -3.5   0.0      0.43   2.5e+03     300     329 ..     179     208 ..     171     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 7.3e-05
                       DUF2863  42 llekllkegeeetldaaLdhlfkadseayd 71 
                                    l++ll+ g++e++++aLd+lf+++ e+ +
  gi|91774128|ref|YP_566820.1| 116 YLTELLRMGKDEEVEKALDELFDEEIETIG 145
                                   6899*******************9988765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.43
                       DUF2863 300 EyRigftlresneviyGvvWpllgeeeeee 329
                                    +R ++  +++n+ +yG +  l + + +e+
  gi|91774128|ref|YP_566820.1| 179 NIRASMLEMGKNTTLYGSIRTLTNVDLGED 208
                                   567778888888888888888877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 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:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2119.35
//
Query:       gi|91774129|ref|YP_566821.1|  [L=156]
Description: PUA domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-29  100.9   0.0      5e-29  100.2   0.0    1.3  1  TGT_C2           Patch-forming domain C2 of tRNA-guanine tran
    5.8e-14   51.8   0.1      1e-13   51.0   0.1    1.4  1  PUA              PUA domain
     0.0041   17.4   0.0      0.007   16.6   0.0    1.4  1  UPF0113          UPF0113 PUA domain
     0.0083   15.9   0.2      0.059   13.2   0.1    2.4  3  PUA_3            PUA-like domain
  ------ inclusion threshold ------
      0.032   14.5   0.0       0.13   12.5   0.0    1.9  2  Phage_CI_C       Bacteriophage CI repressor C-terminal domain
      0.057   13.5   0.0      0.068   13.2   0.0    1.2  1  MTS_N            Methyltransferase small domain N-terminal
       0.14   12.6   0.0       0.47   10.9   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1


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 !  100.2   0.0     2e-32     5e-29       2      71 .]      10      79 ..       9      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 2e-32
                        TGT_C2  2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                  ++r +adYqFG+g+gd Lfp+dvt+++s+t+rirq++v g+r+at+ra+dg++tLs+ +a  +h+++p+P
  gi|91774129|ref|YP_566821.1| 10 KVRVMADYQFGKGCGDILFPDDVTFQLSRTKRIRQIMVSGKRIATVRAKDGTFTLSMDAATAIHDHIPAP 79
                                  79******************************************************************98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.1     4e-17     1e-13       2      71 ..      82     151 ..      81     153 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 4e-17
                                   EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                           PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                   rv+v d Av ++++g+  +a+ v+ ++ +++ gd+V +vde+++++a G  ++s ee++  + g +v+++
  gi|91774129|ref|YP_566821.1|  82 RVTVCDDAVPFVSKGKTTFAKHVTAIDPELRSGDEVIVVDENDTVIATGQLMLSPEEIEALDTGAAVDVR 151
                                   799****************************************************************986 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06     0.007      15      53 ..      96     134 ..      91     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                       UPF0113  15 GrdvlkesilkitesvkenqvvvVlnengeplGiGkirk 53 
                                   G+  + +++  i++++++++ v+V++en+++++ G +  
  gi|91774129|ref|YP_566821.1|  96 GKTTFAKHVTAIDPELRSGDEVIVVDENDTVIATGQLML 134
                                   778899*****************************9854 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.56   1.4e+03      30      41 ..      77      88 ..      41      96 .. 0.63
   2 !   13.2   0.1   2.3e-05     0.059      19      49 ..     100     130 ..      85     133 .. 0.90
   3 ?   -1.3   0.0      0.79     2e+03      27      38 ..     140     150 ..     134     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.56
                         PUA_3 30 ledGdvVdvfse 41
                                  +++G+ V v ++
  gi|91774129|ref|YP_566821.1| 77 PAPGSRVTVCDD 88
                                  247777777775 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.3e-05
                         PUA_3  19 fsneiasvegeledGdvVdvfsekgkflGtG 49 
                                   f++ +  ++ el++Gd V v++e+++ ++tG
  gi|91774129|ref|YP_566821.1| 100 FAKHVTAIDPELRSGDEVIVVDENDTVIATG 130
                                   66777888889*******************9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.79
                         PUA_3  27 egeledGdvVdv 38 
                                   e +l +G +Vdv
  gi|91774129|ref|YP_566821.1| 140 E-ALDTGAAVDV 150
                                   3.6789999999 PP

>> Phage_CI_C  Bacteriophage CI repressor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.2e-05      0.13      52      87 ..      57      92 ..      43     105 .. 0.92
   2 ?   -0.8   0.0      0.72   1.8e+03      36      56 ..     111     131 ..      93     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                    Phage_CI_C 52 vsdGkwLvdieGrlsirelariPvkklrvsgdevsf 87
                                  ++dG++ + ++ ++ i++    P++++ v++d v+f
  gi|91774129|ref|YP_566821.1| 57 AKDGTFTLSMDAATAIHDHIPAPGSRVTVCDDAVPF 92
                                  68********************************99 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.72
                    Phage_CI_C  36 ieeekklylvdkkeadvsdGk 56 
                                   + +++++ +vd++ + +  G+
  gi|91774129|ref|YP_566821.1| 111 LRSGDEVIVVDENDTVIATGQ 131
                                   556677778888777777776 PP

>> MTS_N  Methyltransferase small domain N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.6e-05     0.068      68     114 ..      81     129 ..      31     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                                   H..TT-SEEEEE--SSHHHHHHHHHHHHTTS-TT-EEEEEEEGGGTGGG CS
                         MTS_N  68 e..skfdlvilylpKaKeeakylLalllsklkkgteilvVGenksGvks 114
                                   +  + +d ++ ++ K K  +  + +++ ++l++g e++vV en   +  
  gi|91774129|ref|YP_566821.1|  81 SrvTVCDDAVPFVSKGKTTFAKHVTAIDPELRSGDEVIVVDENDTVIAT 129
                                   234789*************************************876655 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5   3.8e+03      24      47 ..      34      56 ..      32      63 .. 0.68
   2 ?   10.9   0.0   0.00018      0.47      22      77 ..      96     150 ..      92     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
               Glyco_trans_1_2 24 faltddaegleelftpgkevilfe 47
                                  f+l+  ++ ++++   gk + +++
  gi|91774129|ref|YP_566821.1| 34 FQLSR-TKRIRQIMVSGKRIATVR 56
                                  55555.677777777777777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
               Glyco_trans_1_2  22 Gafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarerv 77 
                                   G +  +   ++++  ++ g+evi++ d+++ + + ++l+ +pee++a+ + a  +v
  gi|91774129|ref|YP_566821.1|  96 GKTTFAKHVTAIDPELRSGDEVIVV-DENDTVIATGQLMLSPEEIEALDTGAAVDV 150
                                   55667777789999999*******9.7799999*************9987776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1292.09
//
Query:       gi|91774130|ref|YP_566822.1|  [L=486]
Description: hypothetical protein Mbur_2207 [Methanococcoides burtonii DSM 6242]
Scores for 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-168  559.6   0.8   5.6e-168  559.4   0.8    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 !  559.4   0.8  3.1e-172  5.6e-168       1     412 []      52     486 .]      52     486 .] 0.99

  Alignments for each domain:
  == domain 1  score: 559.4 bits;  conditional E-value: 3.1e-172
                                   HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkeleka 77 
                                   q++nva+lpgi+k ++amPD+HlG+g+piG+V+a++   gvi+P++VG+DI CGvrll+ nlt +++++k+kel++++++a
  gi|91774130|ref|YP_566822.1|  52 QVANVAKLPGIQKFSMAMPDAHLGYGFPIGGVAAFDeeeGVISPGGVGFDInCGVRLLRSNLTVDDVRPKMKELTEKMFEA 132
                                   89******************************************************************************* PP

                                   S-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB  78 vpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFiEv 158
                                   vp+g+gsk+++k++++el++++ +g+kwave+g+ge++dle++e  g++++ d  ++s ka++r+r+q GtlGsGNHF+Ev
  gi|91774130|ref|YP_566822.1| 133 VPSGVGSKSRLKVTDSELDDIFLHGSKWAVENGYGEKTDLEHCEGGGCIEGGDVGNISIKARKRGRPQAGTLGSGNHFLEV 213
                                   ********************************************************************************* PP

                                   EEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 159 qlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkamqaa 239
                                   q+v++i+d+eaa+a+gleegqv +m+H+GSRg Ghqi++d +k++++a kk+gi+lpd++La++pa+see+q+Y+  m +a
  gi|91774130|ref|YP_566822.1| 214 QYVDKIYDQEAADAFGLEEGQVSFMIHCGSRGTGHQICTDNIKTMSQASKKYGIQLPDKQLACAPAQSEEAQNYFGSMICA 294
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-.............T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx.............x RF
                          RtcB 240 anyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA.............k 303
                                   anyA+ NRq+it+++r++++++++++ ++l+lelv+dvaHN+ak Eehe d   ++v+VhRKGAtrA             +
  gi|91774130|ref|YP_566822.1| 295 ANYAWNNRQMITHWTRDVIADTFRSDIDELGLELVYDVAHNVAKLEEHEvDgkkKNVYVHRKGATRAfpkghkevplkyrD 375
                                   ************************99999********************966889************************** PP

                                   T--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE-------------- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 304 vgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvleEapeaY 382
                                   vgqpv+ipGsmgt+Sy+++G ++++  sfgS++HGAGR+msR++akk+f++e++k +le++gi+v++++ ++++eEap+ Y
  gi|91774130|ref|YP_566822.1| 376 VGQPVLIPGSMGTASYVLHGGDRSMdiSFGSACHGAGRVMSRSHAKKEFQGEDIKMQLEKRGITVRSAHPAVIAEEAPGVY 456
                                   ********************************************************************************* PP

                                   ----HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 383 KdideVveaqaeaglvevvarlkpvlvvkg 412
                                   K+ ++Vv++++e +++++va++ p++v+kg
  gi|91774130|ref|YP_566822.1| 457 KSSSDVVNVVHELDIARKVAKMMPMGVIKG 486
                                   *****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 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:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3318.97
//
Query:       gi|91774131|ref|YP_566823.1|  [L=146]
Description: archease family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-44  149.5   3.2    7.2e-44  149.4   3.2    1.0  1  Archease  Archease protein family (MTH1598/TM1083)
  ------ inclusion threshold ------
       0.14   12.9   0.0        0.3   11.8   0.0    1.6  1  TTR-52    Transthyretin-like family


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 !  149.4   3.2     8e-48   7.2e-44       1     137 [.       8     145 ..       8     146 .] 0.98

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 8e-48
                                   EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----E CS
                      Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevk 81 
                                   yeyl+htAD +++a+Gk+ eeaf++aa+a+f++m+++skv+ k++++i v+a ++++lL+++L+ell+lf+++ ++f e+k
  gi|91774131|ref|YP_566823.1|   8 YEYLEHTADAKFRAYGKTKEEAFANAAEAMFNVMINTSKVDCKHKEDIIVNAPEIDELLVEWLSELLFLFEVDFLAFGEFK 88 
                                   9*******************************************************************************9 PP

                                   EEE..E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE CS
                      Archease  82 vde.eeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvD 137
                                   v++ +e++ e+el+++a ge++d e+he++tevKAvTy++lr+ee+++g+ ++v+vD
  gi|91774131|ref|YP_566823.1|  89 VENiTEKDGEFELSGHACGEEIDLERHEIDTEVKAVTYNDLRVEETENGFMVQVTVD 145
                                   966468999***********************************************9 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05       0.3      18      60 ..      76     124 ..      71     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                   EEEHHHHTS--EEEEEE--TTSEEEEEEEE-..--.....S--EEEEEE CS
                        TTR-52  18 LwekdtldpddlldetkTdedGnFelsgsen..el....tsidPylkiy 60 
                                   L+e d+l   +   e+ T++dG+Felsg+    e+    ++id  +k +
  gi|91774131|ref|YP_566823.1|  76 LFEVDFLAFGEFKVENITEKDGEFELSGHACgeEIdlerHEIDTEVKAV 124
                                   7788888888889999***********8865433322224666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1208.63
//
Query:       gi|91774132|ref|YP_566824.1|  [L=202]
Description: CDP-alcohol phosphatidyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-12   46.3   1.7    5.4e-12   46.3   1.7    2.7  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
      0.001   18.7   0.8      0.028   14.0   0.1    2.5  2  Doppel           Prion-like protein Doppel


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 !   46.3   1.7     6e-16   5.4e-12       2      66 .]      27      95 ..      26      95 .. 0.90
   2 ?   -0.9   2.7      0.32   2.9e+03      10      27 ..     152     174 ..     101     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6e-16
                                  -HHHHHHHHHHHHHHHHHGGGS-H.......HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
               CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyp.....lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   Pna+++++l+++ la + ++++        ++ai+++ + s++DalDG +AR l++ s+ G++lD+++D
  gi|91774132|ref|YP_566824.1| 27 SPNALSVASLVCAALAGISFYFS-VdnplgALIAIFFVALNSFLDALDGAVARYLRTDSKKGDFLDHVID 95
                                  6************9999877444.269999999999999******************999********99 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHGGGS-H......... CS
               CDP-OH_P_transf  10 rlllsvlailllltyyp.......l 27 
                                   rl+l+++a l +++  +       +
  gi|91774132|ref|YP_566824.1| 152 RLVLILIASLAYYI--YseaifgyT 174
                                   34444444432222..123555553 PP

>> Doppel  Prion-like protein Doppel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.013   1.2e+02       9      19 ..      57      67 ..      52      71 .. 0.77
   2 !   14.0   0.1   3.2e-06     0.028      10      28 ..     119     138 ..     115     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.013
                                  CHHHHHHHHHH CS
                        Doppel  9 wlAivCvLLfS 19
                                   +Ai++v L S
  gi|91774132|ref|YP_566824.1| 57 LIAIFFVALNS 67
                                  59*****8877 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.2e-06
                                   HHHHHHHHHHHCCT.TTS-S CS
                        Doppel  10 lAivCvLLfShLSl.VkARG 28 
                                   +AivCvLL S L + ++A G
  gi|91774132|ref|YP_566824.1| 119 IAIVCVLLTSYLGTqAQALG 138
                                   9*********9965366665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1601.91
//
Query:       gi|91774133|ref|YP_566825.1|  [L=183]
Description: L-fuculose phosphate aldolase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-36  126.2   0.0    1.6e-36  126.0   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 !  126.0   0.0   8.9e-41   1.6e-36       1     185 [.       3     175 ..       3     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 8.9e-41
                                   HHHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHH CS
                   Aldolase_II   1 eelaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiy 81 
                                   +e+a+ +++l ++glve + GniSvrv    s++it++g  ++e+++ ++v+v ++s + ++       +sse  +H+aiy
  gi|91774133|ref|YP_566825.1|   3 QEMAKFGKKLVDHGLVESNFGNISVRVG--RSMIITRTGAALDEIEEKSVVEVPIESTSELD-----VLASSEASVHRAIY 76 
                                   699***********************76..7999*********************9888883.....369*********** PP

                                   HH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEETTTEEE CS
                   Aldolase_II  82 karpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllrnHGll 162
                                   +  +da+a+vH+H p+ v+ +++++ + + p++ e++ +l  +e+p+++   +g++e+ge +++a++ +++++++ +HG++
  gi|91774133|ref|YP_566825.1|  77 QG-TDAKAIVHAHCPYSVTQTLITDSDRIIPIDSEGKLFL--KEIPIVK-GGIGSKEVGEGAVKAFE-EHRGMVVYSHGPF 152
                                   *6.9*****************9999999********9966..78***86.556*************8.77*********** PP

                                   EEESSHHHHHHHHHHHHHHHHHH CS
                   Aldolase_II 163 tvGetleeAvalaetleeaaeiq 185
                                   t G+tl eA+  ++ +e++++i 
  gi|91774133|ref|YP_566825.1| 153 TIGKTLPEAYIIMTQIEHSCRIK 175
                                   ********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1363.11
//
Query:       gi|91774134|ref|YP_566826.1|  [L=81]
Description: hypothetical protein Mbur_2211 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 457.59
//
Query:       gi|91774135|ref|YP_566827.1|  [L=184]
Description: hypothetical protein Mbur_2213 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   12.6   0.0       0.21   11.6   0.0    1.5  1  DUF982    Protein of unknown function (DUF982)


Domain annotation for each model (and alignments):
>> DUF982  Protein of unknown function (DUF982)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.2e-05      0.21      18      46 ..     124     153 ..     112     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                                   EHHHHHHHHHH--S--.-SHHHHHHHHHHH CS
                        DUF982  18 sveeAldfLleeWPvs.rgpayeaAlkaCr 46 
                                   ++ + +++L+e WP + +g+ +++A++ +r
  gi|91774135|ref|YP_566827.1| 124 TTGDVVELLKEFWPNNgDGTLRNRARSHIR 153
                                   7899*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1326.55
//
Query:       gi|91774136|ref|YP_566828.1|  [L=425]
Description: hypothetical protein Mbur_2214 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-10   38.3   7.0      7e-10   38.3   7.0    1.5  2  DUF2254   Predicted membrane protein (DUF2254)
  ------ inclusion threshold ------
      0.044   13.8   0.1       0.12   12.5   0.1    1.8  2  Nrap      Nrap protein domain 1
       0.49    9.7   3.2        1.1    8.6   3.2    1.5  1  TMEM43    Transmembrane protein 43


Domain annotation for each model (and alignments):
>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   7.0   1.2e-13     7e-10       5     156 ..      19     168 ..      16     198 .. 0.79
   2 ?   -3.4   0.0      0.53   3.2e+03     271     285 ..     314     328 ..     294     356 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.2e-13
                       DUF2254   5 wfipllivllavllallll.lldealslsldleelkegaeaaralLstiagsmltvagfvfSitvvalqlassqfsPRllr 84 
                                   w+  +++ +l +l+++ +l +++  +++s       ++  +ar ++s+++ s  +++++++S  +va++lass++s R++ 
  gi|91774136|ref|YP_566828.1|  19 WISRIAYYILLFLFSIGILhYINVLFGPST------YDMTSARYMISALIQSEAAIMAIIVSFSLVAVELASSSYSVRMID 93 
                                   665555555555544433303444433333......399****************************************** PP

                       DUF2254  85 nfmrdrvt.qvvLGtfigtfvYsllvlrairteee..vpqlsvlvalllaivsvllLiyFihhlarsiqvsnvia 156
                                   ++   ++   + + ++ig+++Ysl+vl +i  +e+    ql +++++   + s l+L  ++ ++ ++++ s++++
  gi|91774136|ref|YP_566828.1|  94 LLRAYNPDfWILMVIYIGSMTYSLFVLKSIPGNEGkyDMQLQIAISFYTGVYSFLTLFPYLFRTLHMLKPSTLLN 168
                                   **8866651566679***************9887777778******************99999999999988775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.53
                       DUF2254 271 efglrqLvEIAlRAL 285
                                   +  ++ L EI+ +A+
  gi|91774136|ref|YP_566828.1| 314 STVINHLYEIGQKAI 328
                                   456777888888887 PP

>> Nrap  Nrap protein domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.9e-05      0.12      48     106 ..     185     243 ..     167     279 .. 0.86
   2 ?   -2.8   0.0      0.96   5.8e+03      96     135 ..     368     411 ..     354     419 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                   EEEEEEGGG-TT-EEEEEEE---.----GGGTEEEEEEEE--TTSS-GGGGSTTS--S- CS
                          Nrap  48 kvsfeylngdelkpiLvirpkkeaekkfskskfririipvapsdlfklsklspsknnir 106
                                   +  ++++++d+++pi+ i +++  +++f+ ++  ++ii +  +++f  + l+p+k+ i 
  gi|91774136|ref|YP_566828.1| 185 SDAYTAHENDPIQPIIDIISSSLLNHDFETTRNGLNIIGMRAKEIFIRNNLEPTKQKII 243
                                   5568889************9998899****************************99885 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.96
                                   GGGSTTS--S----.............---------HHHHHHHHH CS
                          Nrap  96 sklspsknnirvetl..kee...kesseeeetlppTPlYNssils 135
                                    kl  + +  ++e +  k +    ++ + + +l +TP Y +  l+
  gi|91774136|ref|YP_566828.1| 368 GKLGIKASESDQELSvsK-SldsMNALKGSMELIETPEYQQLCLK 411
                                   555555555554444421.12224445566677788888766554 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.2   0.00019       1.1     174     244 ..       6      80 ..       3      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00019
                        TMEM43 174 mfakeksenklltwllRllGfllmflglllllsplsvlvslipll....gelvglglalvalllslslsllvial 244
                                   +++++ s  +l+ w+ R++ ++l+fl  + +l+ ++vl+   ++     + ++++ ++  a ++++++s+  +a+
  gi|91774136|ref|YP_566828.1|   6 IIKEAFSTDVLHLWISRIAYYILLFLFSIGILHYINVLFGPSTYDmtsaRYMISALIQSEAAIMAIIVSFSLVAV 80 
                                   788999999*****************8888999999888744441356655555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3064.10
//
Query:       gi|91774137|ref|YP_566829.1|  [L=59]
Description: hypothetical protein Mbur_2215 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 396.58
//
Query:       gi|91774138|ref|YP_566830.1|  [L=51]
Description: hypothetical protein Mbur_2216 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-14   52.0  16.3    7.4e-14   51.7  16.3    1.1  1  DUF1328          Protein of unknown function (DUF1328)
  ------ inclusion threshold ------
        2.8    8.1  14.1       0.71   10.0   4.9    2.0  2  SecG             Preprotein translocase SecG subunit
        3.1    6.5   7.6        3.3    6.5   7.6    1.0  1  TraG_N           TraG-like protein, N-terminal region
          7    7.2  13.0         97    3.5  13.0    2.0  1  DUF202           Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF1328  Protein of unknown function (DUF1328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7  16.3   1.7e-17   7.4e-14       1      39 []       9      47 ..       9      47 .. 0.99

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.7e-17
                       DUF1328  1 liFLviAliAgvLGFgGiagaaagiAkiLFfiFlvlfvi 39
                                  ++FL++Al+A vLG++G+ag +++iAk+L++iF+vl++i
  gi|91774138|ref|YP_566830.1|  9 IVFLIFALVAYVLGARGVAGLSMTIAKWLVIIFIVLAII 47
                                  89************************************8 PP

>> SecG  Preprotein translocase SecG subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.5     0.019        83      54      69 ..       5      20 ..       4      21 .. 0.85
   2 ?   10.0   4.9   0.00016      0.71      40      69 ..      21      50 ..      17      51 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.019
                                  HHHHHHHHHHHHHHHC CS
                          SecG 54 vilavlFfvlslvlal 69
                                  + la++F++ +lv  +
  gi|91774138|ref|YP_566830.1|  5 IGLAIVFLIFALVAYV 20
                                  579********99865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00016
                                  --SSCCCHHCCHHHHHHHHHHHHHHHHHHC CS
                          SecG 40 fgsrgaekfLtkiTvilavlFfvlslvlal 69
                                  +g+rg++++   i ++l+++F+vl++++ l
  gi|91774138|ref|YP_566830.1| 21 LGARGVAGLSMTIAKWLVIIFIVLAIITIL 50
                                  499***********************9865 PP

>> TraG_N  TraG-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.6   0.00073       3.3      35      73 ..       7      47 ..       1      50 [. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00073
                        TraG_N 35 lll.gilialiakvfee.kgalslrriekwllvaflvylll 73
                                  l + ++++al+a+v+ + ++a+ +++i kwl++ f+v +++
  gi|91774138|ref|YP_566830.1|  7 LAIvFLIFALVAYVLGArGVAGLSMTIAKWLVIIFIVLAII 47
                                  33335666666666633499999************998876 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5  13.0     0.022        97      18      56 ..       7      50 ..       5      51 .] 0.63

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.022
                        DUF202 18 lalialglallrffl.....tgepsalgkilglilivlgiltll 56
                                  la+++l +al++  l      g   +++k+l +i+ivl+i+t+l
  gi|91774138|ref|YP_566830.1|  7 LAIVFLIFALVAYVLgargvAGLSMTIAKWLVIIFIVLAIITIL 50
                                  5555555555554444344433344458**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 374.38
//
Query:       gi|91774139|ref|YP_566831.1|  [L=145]
Description: hypothetical protein Mbur_2217 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-09   36.1   1.9    9.3e-09   35.2   0.4    1.8  2  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.019   3.4e+02     151     174 ..      10      33 ..       3      36 .. 0.81
   2 !   35.2   0.4   5.2e-13   9.3e-09       4     108 ..      36     141 ..      33     145 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.019
                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlR 174
                                   v++++++  ++   +++ +ly++R
  gi|91774139|ref|YP_566831.1|  10 VTRTYSVVLDTIFKKTLDRLYKNR 33 
                                   455999999999**********99 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 5.2e-13
                     DDE_Tnp_1   4 revlivDattvrvpgtkedarwgykggkykygy.klhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgklvla 82 
                                   ++++++D+t ++    +   ++++  +k+++ y k  i v     +i++++i+ ++vhd k++k+ll +++++ ++ ++++
  gi|91774139|ref|YP_566831.1|  36 IDITAIDSTGFTSGYCS--NYYSWRIKKWRRSYvKTSISVVVSKFVITGYKISGKSVHDAKHAKTLLSQCHRNrRSIYYVM 114
                                   6899*******965555..556677888888888877777777778*********************************** PP

                     DDE_Tnp_1  83 DaGYasaelldtle.ekgvdyiirlkk 108
                                   D++Y+ +++++  + + g   i++l+k
  gi|91774139|ref|YP_566831.1| 115 DKAYDFENIHELARgKLGSIAIVPLRK 141
                                   *****8888888887777777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 950.14
//
Query:       gi|91774140|ref|YP_566832.1|  [L=289]
Description: nitrite and sulphite reductase 4Fe-4S subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  108.6   0.2    2.8e-31  108.2   0.2    1.1  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.5e-18   66.4   0.0    2.9e-18   65.4   0.0    1.4  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    1.2e-11   43.9  11.3    1.2e-05   24.9   2.0    2.9  2  Fer4          4Fe-4S binding domain
    5.5e-11   42.1  11.1      8e-06   25.7   2.4    3.0  2  Fer4_6        4Fe-4S binding domain
    7.7e-07   29.2  26.0    2.1e-06   27.8  11.9    2.6  3  Fer4_9        4Fe-4S dicluster domain
    9.6e-06   26.1  10.4    9.6e-06   26.1  10.4    2.7  3  Fer4_7        4Fe-4S dicluster domain
    0.00011   22.2  19.9    0.00014   21.9   2.2    2.9  3  Fer4_21       4Fe-4S dicluster domain
    0.00044   20.2  18.5      0.011   15.8   2.3    3.3  2  Fer4_2        4Fe-4S binding domain
    0.00064   19.8  14.2    0.00064   19.8  14.2    3.2  4  Fer4_10       4Fe-4S dicluster domain
     0.0079   16.9   0.4     0.0079   16.9   0.4    3.5  4  Fer4_15       4Fe-4S single cluster domain
     0.0088   16.5  18.4       0.15   12.6   1.6    3.5  3  Fer4_4        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   16.2  16.9       0.11   13.4   5.9    3.1  3  Fer4_16       4Fe-4S double cluster binding domain
      0.016   15.4   8.8      0.039   14.1   8.8    1.7  1  Fer4_18       4Fe-4S dicluster domain
      0.027   14.9   9.2       0.55   10.7   0.5    2.9  3  Fer4_8        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.2   2.2e-34   2.8e-31       2     150 ..      91     281 ..      90     287 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 2.2e-34
                                   SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei... 79 
                                   g+++r+v++c+g ++c + l+D + +a++++    + y   ++P+KfKia++gcp+ c + + nD+g++g+++++      
  gi|91774140|ref|YP_566832.1|  91 GKRVRAVVACQGDQVCNHGLIDCQTIAERLD----NLYFGADVPYKFKIAITGCPSACLKPQENDLGIMGTVHPKWSKdtc 167
                                   789****************************....**************************************99999*** PP

                                   .................................................EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHH CS
                                   .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  80 .................................................gfnilvGGglgrthgakktsarlgfvpeeevl 111
                                                                                    g +i+vGG++g+ +++++++++    + e+v+
  gi|91774140|ref|YP_566832.1| 168 tecgvcikhckanaitrsgstiridkdrcilcgdcilackkdalqaekiGHTIFVGGKVGKFPREGTKLVE--LFELEKVY 246
                                   **********************************************************************5..689999** PP

                                   HHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR 112 evveaivevyrdhgdrknrkkeRlkylverlGvekFrek 150
                                   ++v+  +++y     +++r+ eRl+++++r+G+ek ++ 
  gi|91774140|ref|YP_566832.1| 247 DIVDRTLDLYC----KHGREGERLGDVIDRIGIEKCKKG 281
                                   ***********....********************9875 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 !   65.4   0.0   2.3e-21   2.9e-18       2      62 ..      17      76 ..      16      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.3e-21
                  NIR_SIR_ferr  2 kqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleei 62
                                  +q++++  +++r+ v +G+++a ql+alad aekyg+g++++T+rQ+++++ ++ +d +++
  gi|91774140|ref|YP_566832.1| 17 PQRQKDL-FSMRIGVTGGHVDAGQLKALADAAEKYGEGYVHITSRQGIEIPFIDLNDTDAV 76
                                  6889665.5************************************************9997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   2.1   3.2e-08   4.1e-05       2      24 .]     161     183 ..     160     183 .. 0.93
   2 !   24.9   2.0   9.3e-09   1.2e-05       2      23 ..     190     211 ..     189     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.2e-08
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   ++ ++ C+ CG C++ C  +AIt
  gi|91774140|ref|YP_566832.1| 161 KWSKDTCTECGVCIKHCKANAIT 183
                                   7899******************7 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 9.3e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    id+++Ci CG C+ +C  +A+
  gi|91774140|ref|YP_566832.1| 190 RIDKDRCILCGDCILACKKDAL 211
                                   79*****************998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.6   3.3e-07   0.00043       2      24 .]     160     182 ..     159     182 .. 0.94
   2 !   25.7   2.4   6.2e-09     8e-06       2      24 .]     189     211 ..     188     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-07
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   + + +d C+ Cg C+++C ++ai
  gi|91774140|ref|YP_566832.1| 160 PKWSKDTCTECGVCIKHCKANAI 182
                                   7899*****************98 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 6.2e-09
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   ++id+d+Ci CgdC+ +C  +a+
  gi|91774140|ref|YP_566832.1| 189 IRIDKDRCILCGDCILACKKDAL 211
                                   89****************98875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       4.2   5.4e+03      10      10 ..     104     104 ..      76     118 .. 0.61
   2 !   14.7   6.2     2e-05     0.025      12      51 .]     140     182 ..     137     182 .. 0.56
   3 !   27.8  11.9   1.7e-09   2.1e-06       2      50 ..     167     210 ..     166     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.2
                        Fer4_9  10 e 10 
                                   +
  gi|91774140|ref|YP_566832.1| 104 Q 104
                                   1 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2e-05
                        Fer4_9  12 Cpagvvvedaaerkarlraase...eaCigCgaCveaCpkgai 51 
                                   Cp+   +++++   +  +   +   + C++Cg C+++C+ +ai
  gi|91774140|ref|YP_566832.1| 140 CPSACLKPQENDLGIMGTVHPKwskDTCTECGVCIKHCKANAI 182
                                   444444333333222222111124468************9987 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 1.7e-09
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   Ct+Cg C++ C+a++++++ ++  +  +     +Ci Cg+C+ aC+k+a
  gi|91774140|ref|YP_566832.1| 167 CTECGVCIKHCKANAITRSGSTIRIDKD-----RCILCGDCILACKKDA 210
                                   *****************99999888864.....6************997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2         6   7.7e+03      38      44 ..     100     106 ..      72     116 .. 0.64
   2 !   13.8   5.9     5e-05     0.064      11      52 .]     139     181 ..     137     181 .. 0.84
   3 !   26.1  10.4   7.5e-09   9.6e-06       1      52 []     166     210 ..     166     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6
                        Fer4_7  38 ClgCgaC 44 
                                   C+g ++C
  gi|91774140|ref|YP_566832.1| 100 CQGDQVC 106
                                   4443333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5e-05
                        Fer4_7  11 aCpvkaieldee.enekgtekveidpekClgCgaCvavCPtga 52 
                                    Cp+ +++ +e      gt +++ + ++C+ Cg+C++ C ++a
  gi|91774140|ref|YP_566832.1| 139 GCPSACLKPQENdLGIMGTVHPKWSKDTCTECGVCIKHCKANA 181
                                   6999999998752445588999999**************9986 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 7.5e-09
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C++Cg C + C+++ai+   +       +++id ++C+ Cg C+ +C ++a
  gi|91774140|ref|YP_566832.1| 166 TCTECGVCIKHCKANAITRSGS-------TIRIDKDRCILCGDCILACKKDA 210
                                   5*****************9775.......79*****************9986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       5.2   6.6e+03      11      13 ..     106     108 ..      92     118 .. 0.59
   2 !   10.2   4.3   0.00051      0.66      14      57 ..     140     182 ..     134     184 .. 0.66
   3 !   21.9   2.2   1.1e-07   0.00014       2      26 ..     190     214 ..     189     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.2
                       Fer4_21  11 Cgk 13 
                                   C++
  gi|91774140|ref|YP_566832.1| 106 CNH 108
                                   333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00051
                       Fer4_21  14 CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   C  aC +   + + i +  + k  +d+C+ C +C++ C   ++i
  gi|91774140|ref|YP_566832.1| 140 CPSACLKPQENDLGIMGTVHPKWSKDTCTECGVCIKHCKA-NAI 182
                                   6666666666666666666666777888888888877763.555 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 1.1e-07
                       Fer4_21   2 ridedkCigCgkCliaCedtshqai 26 
                                   rid+d+Ci Cg C++aC++ + qa 
  gi|91774140|ref|YP_566832.1| 190 RIDKDRCILCGDCILACKKDALQAE 214
                                   79****************9999985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   2.3   2.8e-05     0.036       3      22 .]     160     179 ..     159     179 .. 0.85
   2 !   15.8   2.3   8.7e-06     0.011       4      20 ..     190     206 ..     188     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                   ++   d+C++Cg C++ C a
  gi|91774140|ref|YP_566832.1| 160 PKWSKDTCTECGVCIKHCKA 179
                                   667789**********9975 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.7e-06
                        Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                    +d drCi Cg C+ aC
  gi|91774140|ref|YP_566832.1| 190 RIDKDRCILCGDCILAC 206
                                   589************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       8.1     1e+04      13      13 ..     104     104 ..      85     116 .. 0.59
   2 !    9.3   7.0   0.00092       1.2      19      55 ..     140     177 ..     136     178 .. 0.74
   3 !   19.8  14.2     5e-07   0.00064       5      55 ..     163     206 ..     159     207 .. 0.93
   4 !   14.7   5.2   1.9e-05     0.024       2      46 ..     189     279 ..     188     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.1
                       Fer4_10  13 g 13 
                                   +
  gi|91774140|ref|YP_566832.1| 104 Q 104
                                   1 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00092
                       Fer4_10  19 CPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   CP+   + +++   +++  + +   + Ct+cg C+++C
  gi|91774140|ref|YP_566832.1| 140 CPSAClKPQENDLGIMGTVHPKWSKDTCTECGVCIKHC 177
                                   44433478888888888888888888888888888888 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 5e-07
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    +dtC++Cg C k C       +a++++  ++++r++ ++C+ cg C+ aC
  gi|91774140|ref|YP_566832.1| 163 SKDTCTECGVCIKHC-------KANAITRSGSTIRIDKDRCILCGDCILAC 206
                                   689************.......789************************** PP

  == domain 4  score: 14.7 bits;  conditional E-value: 1.9e-05
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl................................................tsvgakgease 34 
                                   ++id+d+Ci Cg+C  aC  +                                                  ++g +ge+ +
  gi|91774140|ref|YP_566832.1| 189 IRIDKDRCILCGDCILAC--KKdalqaekightifvggkvgkfpregtklvelfelekvydivdrtldlyCKHGREGERLG 267
                                   789***************..5555777777777777777777777777777777777777777777777766677777777 PP

                       Fer4_10  35 eeavrkkvekCt 46 
                                   +  +r+++ekC 
  gi|91774140|ref|YP_566832.1| 268 DVIDRIGIEKCK 279
                                   777777777776 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3         5   6.4e+03       7      14 ..      99     106 ..      98     110 .. 0.89
   2 ?   -2.8   0.1       8.7   1.1e+04      55      64 ..     136     145 ..     131     146 .. 0.78
   3 ?    5.8   1.6     0.019        24       5      19 ..     164     178 ..     163     185 .. 0.89
   4 !   16.9   0.4   6.2e-06    0.0079       1      20 [.     189     208 ..     189     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5
                       Fer4_15   7 aCigcglC 14 
                                   aC+g+ +C
  gi|91774140|ref|YP_566832.1|  99 ACQGDQVC 106
                                   7******9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.7
                       Fer4_15  55 AaraCPvdAI 64 
                                   A   CP +++
  gi|91774140|ref|YP_566832.1| 136 AITGCPSACL 145
                                   6678999996 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.019
                       Fer4_15   5 rdaCigcglCvaeap 19 
                                   +d+C+ cg+C++ ++
  gi|91774140|ref|YP_566832.1| 164 KDTCTECGVCIKHCK 178
                                   69*********9996 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 6.2e-06
                       Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                   +++D+d+Ci cg C+ ++++
  gi|91774140|ref|YP_566832.1| 189 IRIDKDRCILCGDCILACKK 208
                                   79****************54 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       5.3   6.8e+03       6       9 ..     139     142 ..     138     145 .. 0.59
   2 !   12.2   4.1   0.00016      0.21       1      16 [.     164     179 ..     164     180 .. 0.90
   3 !   12.6   1.6   0.00012      0.15       1      15 [.     193     207 ..     193     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                        Fer4_4   6 gCgs 9  
                                   gC+s
  gi|91774140|ref|YP_566832.1| 139 GCPS 142
                                   7775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   +++C++Cg+C+  C+ 
  gi|91774140|ref|YP_566832.1| 164 KDTCTECGVCIKHCKA 179
                                   699***********85 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00012
                        Fer4_4   1 qerCigCgsCvaaCP 15 
                                   ++rCi Cg C+ aC+
  gi|91774140|ref|YP_566832.1| 193 KDRCILCGDCILACK 207
                                   69************8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       6.3     8e+03      11      20 ..     139     148 ..     136     152 .. 0.73
   2 ?   13.4   5.9   8.7e-05      0.11       1      30 [.     166     196 ..     166     197 .. 0.85
   3 ?   10.3   1.7   0.00085       1.1       1      20 [.     195     214 ..     195     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.3
                       Fer4_16  11 vCPtnaikek 20 
                                    CP++++k +
  gi|91774140|ref|YP_566832.1| 139 GCPSACLKPQ 148
                                   5888888876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.7e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaikek.kekeiearec 30 
                                   +C++Cg C++ C +nai+   +  +i++++c
  gi|91774140|ref|YP_566832.1| 166 TCTECGVCIKHCKANAITRSgSTIRIDKDRC 196
                                   5*****************8856777787777 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00085
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   rC+ Cg C+ +C  +a++++
  gi|91774140|ref|YP_566832.1| 195 RCILCGDCILACKKDALQAE 214
                                   6***************9987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   8.8   3.1e-05     0.039      57      97 ..     163     208 ..     139     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                       Fer4_18  57 gagdcidcescvkvcPtgidirkGlql.....eciscllcidacdk 97 
                                   ++  c++c++c+k c  +   r G  +      ci c+ ci ac+k
  gi|91774140|ref|YP_566832.1| 163 SKDTCTECGVCIKHCKANAITRSGSTIridkdRCILCGDCILACKK 208
                                   5678********************876334445***********86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       5.7   7.3e+03      48      57 ..      97     106 ..      73     116 .. 0.58
   2 ?   10.7   0.5   0.00043      0.55       4      16 ..     166     178 ..     153     191 .. 0.78
   3 ?    9.6   0.2   0.00096       1.2       3      17 ..     194     210 ..     192     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.7
                        Fer4_8  48 lwsCttcgaC 57 
                                   + +C++ + C
  gi|91774140|ref|YP_566832.1|  97 VVACQGDQVC 106
                                   3444444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00043
                        Fer4_8   4 kCieCgaCqsaCp 16 
                                    C+eCg C ++C 
  gi|91774140|ref|YP_566832.1| 166 TCTECGVCIKHCK 178
                                   5888888888775 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00096
                        Fer4_8   3 ekCieCgaCqsaCp..v 17 
                                   ++Ci Cg C  aC   +
  gi|91774140|ref|YP_566832.1| 194 DRCILCGDCILACKkdA 210
                                   68999999999994333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2067.54
//
Query:       gi|91774141|ref|YP_566833.1|  [L=384]
Description: major facilitator transporter [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-47  160.2  53.2    3.2e-45  154.6  39.4    2.0  2  MFS_1       Major Facilitator Superfamily
    1.2e-11   43.8  25.0    1.5e-11   43.4  25.0    1.1  1  MFS_3       Transmembrane secretion effector
    9.1e-05   21.1   6.6    9.1e-05   21.1   6.6    2.8  3  TRI12       Fungal trichothecene efflux pump (TRI12)
     0.0011   17.4  15.4      0.052   11.8  10.1    2.6  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami
     0.0054   15.6  26.0       0.25   10.1  26.0    2.1  1  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6  39.4   8.8e-49   3.2e-45       2     353 .]      12     346 ..      11     346 .. 0.88
   2 !   19.3   5.9   1.2e-07   0.00045     113     173 ..     321     379 ..     320     384 .] 0.88

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 8.8e-49
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   + +af+++++ +il+p+lp  +   lg  p+e+  l+t+y++ +a++sl++G+++dr+ r+ +l+ +l+l +l++ll +f 
  gi|91774141|ref|YP_566833.1|  12 AATAFFAMAGGAILAPVLP-QMVGPLGRMPHEVAQLMTVYTISTAIFSLVIGHFVDRVNRKTILVPCLVLNGLMGLLSFF- 90 
                                   6789***************.8*************************************9999************888889. PP

                         MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                   ++   +llvlr++qG+g ++++++++ +i d++ + +r   +g +s+++++G++ +pl+gg la  +gW ++f++  + + 
  gi|91774141|ref|YP_566833.1|  91 ATDLeTLLVLRFVQGVGIAGMMSLVMLVIGDVYEGLDRVHSMGRISMAIAIGSVTAPLIGGGLA-TVGWNYPFLFYVLSLP 170
                                   66677***********************************************************.8899999887777666 PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgl 243
                                   +++++  + l+ e ++++  ++++      + +l+  +k ++        ++ ++ +ff ++++ +++p++l++ +g++ +
  gi|91774141|ref|YP_566833.1| 171 FSLLM--WMLLPETKNNSHHETARG----LGEALRA-LKDIRIAY----TVFLSFAIFFLLFSIIVYIPFMLKDIFGFA-A 239
                                   66554..444444444444444444....4555555.66666666....77777777889999****************.8 PP

                         MFS_1 244 llaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllal 324
                                    +agl+l++ +++++ +a  + r++ +       +l++++l+l+a +++l++++   ++l l+l+++G g+g++++s  ++
  gi|91774141|ref|YP_566833.1| 240 KEAGLVLSIQGIAIILVASTIKRIASK---FSLPVLIGSGLFLMATSIFLISFSVQLPVLFLLLLVFGAGFGLTQTSTDTQ 317
                                   *************98887778888877...668999999999************999999999999*************** PP

                         MFS_1 325 asdlappeeagtasglfntagslggalgp 353
                                   + + ap +  g +++++nt+ +lg + +p
  gi|91774141|ref|YP_566833.1| 318 IIQIAPLRSKGGVLSIYNTMKYLGQSAAP 346
                                   ************************99987 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-07
                         MFS_1 113 wfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                                   ++p + +g ++++++++  lG   +p+  g+++ ++g +avf++ +i++ll++v    +++
  gi|91774141|ref|YP_566833.1| 321 IAPLRSKGGVLSIYNTMKYLGQSAAPITLGIILLYFGLQAVFILSGIFGLLVAVT--TFMV 379
                                   56778899********************************************984..4443 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4  25.0   4.3e-15   1.5e-11      40     393 ..      36     379 ..      10     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 4.3e-15
                         MFS_3  40 isasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaaln 120
                                   +   p  vA +    t+ + ++s++ G   D ++r+ +l+   +l++ + + l ++ a++     +ll+l ++ g+G a +
  gi|91774141|ref|YP_566833.1|  36 LGRMPHEVAQLMTVYTISTAIFSLVIGHFVDRVNRKTILV--PCLVLNGLMGLLSFFATD---LETLLVLRFVQGVGIAGM 111
                                   55667889999999999*****************999886..566666666666665555...567999************ PP

                         MFS_3 121 dPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkrevrksslprE 201
                                   +     ++g++ +  d    +   s+ i i     P +gG  +a+vG  + f + +ls  + ++   ++    +k++  + 
  gi|91774141|ref|YP_566833.1| 112 MSLVMLVIGDVYEGLDRVHSMGRISMAIAIGSVTAPLIGGG-LATVGWNYPFLFYVLSLPFSLLM--WMLLPETKNNSHH- 188
                                   *************9999999999****************97.699********999997554432..2222223333334. PP

                         MFS_3 202 kllealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvGAilgalllsrLRerls 282
                                   +  ++l ++lR  +  r   +v++  a+F+l   +++  +P++ +d  +  a   G++l+  G+  il a + +r+ +++s
  gi|91774141|ref|YP_566833.1| 189 ETARGLGEALRALKDIRIAYTVFLSFAIFFLL-FSIIVYIPFMLKDIFGFAAKEAGLVLSIQGIAIILVASTIKRIASKFS 268
                                   44678888899888877777777777777776.5677899***************************************** PP

                         MFS_3 283 serlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllW 363
                                      l+    + +A  ++ ++++ +l v++l ll+ Ga++ ++ ++ ++ +  + P   +g +l++Y t+ + g +a  +  
  gi|91774141|ref|YP_566833.1| 269 LPVLIGSGLFLMATSIFLISFSVQLPVLFLLLLVFGAGFGLTQTSTDTQIIQIAPLRSKGGVLSIYNTMKYLGQSAAPITL 349
                                   *************************************************9999**************************** PP

                         MFS_3 364 GavaealsvtlaLlaaaaalllaaaillll 393
                                   G +    +++   +++++  ll+a++++++
  gi|91774141|ref|YP_566833.1| 350 GIILLYFGLQAVFILSGIFGLLVAVTTFMV 379
                                   ****************99877777766665 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   6.6   2.5e-08   9.1e-05      64     205 ..      26     168 ..       3     184 .. 0.78
   2 ?    0.1   2.2     0.057     2e+02     191     252 ..     200     261 ..     186     308 .. 0.68
   3 ?    1.1   0.3     0.027        98      81     124 ..     332     375 ..     305     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.5e-08
                         TRI12  64 asalpnilqdvgqs.ensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgv 143
                                   a  lp+++  +g+   + + + t++t+  a+  lv+g + dr+ r+ +++   +l  +  ++   at ++tll    + gv
  gi|91774141|ref|YP_566833.1|  26 APVLPQMVGPLGRMpHEVAQLMTVYTISTAIFSLVIGHFVDRVNRKTILVPCLVLNGLMGLLSFFATDLETLLVLRFVQGV 106
                                   4456777777776524557789*************************999998885555577899***************9 PP

                         TRI12 144 a.agpagasplfvgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiit 205
                                     ag      l++g++     ++  +  +s+ + + s  +p +g  la  g w + f  y++ 
  gi|91774141|ref|YP_566833.1| 107 GiAGMMSLVMLVIGDVYEGLDRVHSMGRISMAIAIGSVTAPLIGGGLATVG-WNYPFLFYVLS 168
                                   53788888999*******999999999999999999999********9887.66666666554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.057
                         TRI12 191 iqgswrwifyiyiitsaiavllivvwyyppsfaqlhgkkvrkreelakldwigiilvivgvs 252
                                      + r  + +++  +   +l+ ++ y p  ++++ g  ++    +  ++ i iilv+  + 
  gi|91774141|ref|YP_566833.1| 200 ALKDIRIAYTVFLSFAIFFLLFSIIVYIPFMLKDIFGFAAKEAGLVLSIQGIAIILVASTIK 261
                                   5555666666666666666777899999**********999999999*********987753 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.027
                         TRI12  81 slfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaiv 124
                                   s++ t+  +gq+ + + +g +   fg + + il+ i+gl+ a+ 
  gi|91774141|ref|YP_566833.1| 332 SIYNTMKYLGQSAAPITLGIILLYFGLQAVFILSGIFGLLVAVT 375
                                   788999999*****************************998875 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 !    8.1   0.2    0.0002      0.71      38      83 ..      43      88 ..      10      95 .. 0.91
   2 !   11.8  10.1   1.5e-05     0.052       2      84 ..     208     288 ..     207     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0002
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 38 sgliassneignillilfvsYfggrghrPrwigigallmalgslll 83
                                  +  +++++ i++++++l++++f +r++r  ++  +++l +l  ll 
  gi|91774141|ref|YP_566833.1| 43 VAQLMTVYTISTAIFSLVIGHFVDRVNRKTILVPCLVLNGLMGLLS 88
                                  566899*************************999999999988775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.5e-05
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP   2 flvllsllglvq.amvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsl 81 
                                   + v+ls+++++    + +y+  +++ i   F++  ++ gl++s++ i+ il++  +  ++++   P +ig g++lma + +
  gi|91774141|ref|YP_566833.1| 208 YTVFLSFAIFFLlFSIIVYIPFMLKDI---FGFAAKEAGLVLSIQGIAIILVASTIKRIASKFSLPVLIGSGLFLMATSIF 285
                                   667888888877677888899988888...*************************************************** PP

                                   xxx RF
                          OATP  82 lla 84 
                                   l++
  gi|91774141|ref|YP_566833.1| 286 LIS 288
                                   987 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 !   10.1  26.0   7.1e-05      0.25       5     383 ..      12     362 ..       8     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.1e-05
                    MFS_1_like   5 kilyFfffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfi 85 
                                    ++ Ff  a  + l P l       g  ++e++ ++++  + + + ++++g  +Dr++ rk++++ +l+l+ ++ l  +  
  gi|91774141|ref|YP_566833.1|  12 AATAFFAMAGGAILAPVLPQMVGPLGRMPHEVAQLMTVYTISTAIFSLVIGHFVDRVN-RKTILVPCLVLNGLMGLLSF-- 89 
                                   5666777788888888888888888889999999999999999999999999999997.57788888888888877333.. PP

                    MFS_1_like  86 ppskerqeesklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyai.....f 161
                                                        + +++ +l++l+++  + +a+++    ++++  +g+  +   r+   G +++ai     +
  gi|91774141|ref|YP_566833.1|  90 ---------------------FATDLETLLVLRFVQGVGIAGMM----SLVMLVIGDVYEGLDRVHSMGRISMAIaigsvT 145
                                   .....................34555556666655444333333....334444444444444444455555544100004 PP

                    MFS_1_like 162 afitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswg 242
                                   a+++G  + ++  n+      ++++ + l  sll+ + l+et+ +s+ + +  l + l+ lk+ ++++ ++  + + ++  
  gi|91774141|ref|YP_566833.1| 146 APLIGGGLATVGWNY-----PFLFYVLSLPFSLLMWMLLPETKNNSHHETARGLGEALRALKDIRIAYTVFLSFAIFFLLF 221
                                   555666666666654.....466666777889999999*************************998764444443333333 PP

                    MFS_1_like 243 iienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievL 322
                                    i  ++   L +  g+    +G ++ ++ +a i +  + +++  k+++ +l+  +l++++   +l+++  ++ +++++ + 
  gi|91774141|ref|YP_566833.1| 222 SIIVYIPFMLkDIFGFAAKEAGLVLSIQGIAIILVASTIKRIASKFSLPVLIGSGLFLMATSIFLISFSVQLPVLFLLLLV 302
                                   34445555564779******************************************************************* PP

                    MFS_1_like 323 hgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                    g+ fgl+  +  + + +iap + ++ + ++++++ + lG+    ++ G++  +++++ +F
  gi|91774141|ref|YP_566833.1| 303 FGAGFGLTQTSTDTQIIQIAPLRSKGGVLSIYNTMKY-LGQSAAPITLGIILLYFGLQAVF 362
                                   *********999999*****************99976.67766666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2557.18
//
Query:       gi|91774142|ref|YP_566834.1|  [L=168]
Description: methylated-DNA--protein-cysteine methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-31  108.8   0.0    1.5e-31  108.3   0.0    1.2  1  DNA_binding_1    6-O-methylguanine DNA methyltransferase, DNA
     0.0076   17.0   0.0      0.013   16.3   0.0    1.4  1  Methyltransf_1N  6-O-methylguanine DNA methyltransferase, rib


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 !  108.3   0.0   1.7e-35   1.5e-31       1      80 [.      76     155 ..      76     156 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.7e-35
                                   HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTT CS
                 DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEg 80 
                                   +fq++Vw++lr+I +G++++Y++iAk++g+pka+raVg+a++anp++ ++PcHRVv+++gkl+g+++g++ k  lLe+Eg
  gi|91774142|ref|YP_566834.1|  76 DFQKKVWSALRNIQFGTTVSYSDIAKAIGNPKAVRAVGSAIGANPISTIIPCHRVVSSSGKLTGFSSGIDLKILLLEHEG 155
                                   59*****************************************************************************9 PP

>> Methyltransf_1N  6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-06     0.013       2      74 ..       1      69 [.       1      72 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                                  -EEEEEEETT.EEEEEEEETTCEEEEEEEC-HHHCCHHHCCCTTTSCCHCCHHHHHHHHHHHHHHHHS--B-SH CS
               Methyltransf_1N  2 lyytlidspl.grlllagdEkgllaidlldkdtselkelpkllkqdeelpalaelkqaleeYfageekpaltlP 74
                                  +yy ++ + l g++ll+gd + l  ++l++ +++ l+ +++++   +    +  +k +l++Yf+g +k  + l+
  gi|91774142|ref|YP_566834.1|  1 MYYDTMQTDLvGEILLVGDTDELKMVALQQGKKR-LSISSEWT--HD-GSLFSNAKEQLQQYFNGDLK-DFDLE 69
                                  79999999854**********************9.55555555..55.559***************99.77666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1234.47
//
Query:       gi|91774143|ref|YP_566835.1|  [L=292]
Description: hypothetical protein Mbur_2222 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-10   40.7   3.3    4.3e-10   39.2   3.3    1.8  1  PGF-CTERM    PGF-CTERM motif
    0.00046   21.0  10.6    0.00046   21.0  10.6    1.8  2  SGP          Sulphur globule protein
  ------ inclusion threshold ------
       0.12   11.8   0.6       0.35   10.2   0.0    2.0  3  DUF5305      Family of unknown function (DUF5305)
        1.9    8.4   5.7        4.1    7.4   5.7    1.6  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   3.3   9.5e-14   4.3e-10       2      23 .]     268     289 ..     267     289 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 9.5e-14
                     PGF-CTERM   2 PGFGavlAlaGLLaaalLaRRr 23 
                                   PGF+av+A+aGLLa+a+++RR+
  gi|91774143|ref|YP_566835.1| 268 PGFEAVFAIAGLLAVAYIVRRK 289
                                   *********************8 PP

>> SGP  Sulphur globule protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  10.6     1e-07   0.00046      41      76 ..     109     142 ..      73     156 .. 0.84
   2 ?   -4.7   0.7         4   1.8e+04      39      47 ..     201     209 ..     195     213 .. 0.52

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1e-07
                           SGP  41 grgygrGygrygygapygYgypygygaPygpYgaga 76 
                                   ++ yg+Gyg ygy++  gYgy +gyg  yg Yg+ga
  gi|91774143|ref|YP_566835.1| 109 SAEYGHGYG-YGYDSNVGYGYDFGYGYGYG-YGYGA 142
                                   567999999.9**********999999987.77665 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 4
                           SGP  39 grgrgygrG 47 
                                   ++g g+g+G
  gi|91774143|ref|YP_566835.1| 201 SSGGGSGSG 209
                                   333333333 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.1   5.1e+03     115     130 ..      15      31 ..       4      49 .. 0.52
   2 ?   -2.1   0.1      0.46     2e+03      17      56 ..      50      88 ..      40      99 .. 0.56
   3 ?   10.2   0.0   7.9e-05      0.35      91     137 ..     244     289 ..     240     292 .] 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
                       DUF5305 115 e.gilliilgllaligl 130
                                   + gi ++++++  l g 
  gi|91774143|ref|YP_566835.1|  15 SiGITIAVVIMMVLSGP 31 
                                   33333334444444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.46
                       DUF5305 17 skeltisesvsinlseyndrieeieeelglsvgtseltvv 56
                                  ++++t++ +++i   +    i+++  +  + + t+e++ +
  gi|91774143|ref|YP_566835.1| 50 GDSVTFDVTATIEDPDKYVPIDNFSLDITGAT-TTEVVFS 88
                                  44445555555555555555555555555444.5555555 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 7.9e-05
                       DUF5305  91 kdetdeengeitetvtvkespslaegilliilgllaliglvvlirri 137
                                   +++ +++ +++t+ +t++++ +l++ ++ +++++++l+++++++rr+
  gi|91774143|ref|YP_566835.1| 244 GTTDSDDGTNETTPETTEKPSGLLP-GFEAVFAIAGLLAVAYIVRRK 289
                                   4555589999999999999999999.9999************99994 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.7   0.00093       4.1      21      73 ..     210     263 ..     187     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00093
                   Trypan_PARP  21 gvgfaaaaegpedkgltkggkgkekgtkvsdddtngt.dp.epepepepepepep 73 
                                   gv + aa +  e +  t  g g   gt  sdd t+gt d+ +  +e  pe   +p
  gi|91774143|ref|YP_566835.1| 210 GVRIVAADDTEEPEDDTGSGDG-TDGTTDSDDGTDGTtDSdDGTNETTPETTEKP 263
                                   6667777666666666777888.58888899889888533134455555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1995.09
//
Query:       gi|91774144|ref|YP_566836.1|  [L=708]
Description: hypothetical protein Mbur_2223 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.016   15.5   1.9      0.016   15.5   1.9    3.6  4  DUF996      Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.9   8.9e-07     0.016       8      97 ..     141     236 ..     135     259 .. 0.67
   2 ?   -0.9   0.1      0.11   1.9e+03      42      73 ..     285     319 ..     271     341 .. 0.51
   3 ?    0.1   0.1     0.051   9.1e+02      37      87 ..     352     408 ..     349     416 .. 0.61
   4 ?   -1.0   0.1      0.11     2e+03     114     128 ..     682     696 ..     657     705 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.9e-07
                        DUF996   8 Lvlvalkeiskavndek.ifsnaliafilsiialvvailalllvlgalatalelpgleeaas.....lilllllvliiayv 82 
                                   +v +a+ ++s+ ++d++  ++ +l+ +i++i  + v+  ++ + l  ++ a+  ++ e+         ++l+ l++ ++++
  gi|91774144|ref|YP_566836.1| 141 FVPLAIRSFSDFLEDRTkWKRALLWTTIVGILDMHVLLTVFFIQLCIFVFAVYDKKEERKNIikstvHLGLVYLAVNMFWI 221
                                   6779*********99761566677889*****998885555444444444444444333333447656666666667899* PP

                        DUF996  83 lliisavflkksyel 97 
                                   l ++s+vf  +s+  
  gi|91774144|ref|YP_566836.1| 222 LPVFSSVFQGSSFLG 236
                                   ********9999854 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.11
                        DUF996  42 vailalllvlgalatalelpgleeaas...lilll 73 
                                   +++ a+l+ +++ + + +++ l+++++   +i+l+
  gi|91774144|ref|YP_566836.1| 285 LLFTAILFLAVHGFLYNTKKPLHKGLVlsaMISLV 319
                                   22333333334444444444444433333233333 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.051
                        DUF996  37 iialvvailalllvlgalatalelpgleeaas.......lilllllvliiayvlliis 87 
                                   +++++v++  +l++lg      ++++ +++         + ++ l+vl i++v+l+ s
  gi|91774144|ref|YP_566836.1| 352 FVGVLVLAYSFLGSLGVDELLNGFRNSKRIELasknkqkICSIALAVL-IIAVPLVYS 408
                                   577777777777777776666666666665446678886555555555.444555544 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.11
                        DUF996 114 yfiGaiLtivlvGli 128
                                   y+iGa+++i++  +i
  gi|91774144|ref|YP_566836.1| 682 YIIGAFISILMTAII 696
                                   333333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (708 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 3880.56
//
Query:       gi|91774145|ref|YP_566837.1|  [L=188]
Description: hypothetical protein Mbur_2224 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.9    7.0   7.9        1.4    9.0   0.1    2.7  3  DUF3278   Protein of unknown function (DUF3278)


Domain annotation for each model (and alignments):
>> DUF3278  Protein of unknown function (DUF3278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   7.6e-05       1.4      36      80 ..      10      51 ..       7      62 .. 0.78
   2 ?    0.4   0.3     0.035   6.3e+02      51      78 ..     122     149 ..     112     163 .. 0.59
   3 ?   -0.9   2.8     0.093   1.7e+03      64      86 ..     156     178 ..     135     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7.6e-05
                       DUF3278 36 nafillwlyllilslvalllakktpeselilglvltnlllvvlvs 80
                                  n  i+l+l+ll++++v+l++++++  ++l+   ++   llv++v+
  gi|91774145|ref|YP_566837.1| 10 NYPIFLALVLLAATAVTLAMGNESRAENLA---IYAYYLLVIGVT 51
                                  5669*****************999998888...555555555554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.035
                       DUF3278  51 valllakktpeselilglvltnlllvvl 78 
                                     l+l+k++ ++ +i+  vl+++l+v +
  gi|91774145|ref|YP_566837.1| 122 SHLVLMKSISKDVSINLGVLSVILYVYG 149
                                   5567777777776664444444444433 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.093
                       DUF3278  64 lilglvltnlllvvlvsglYili 86 
                                   ++ g++ ++ll+v++ s+lY+l+
  gi|91774145|ref|YP_566837.1| 156 IVRGYLEMILLVVIGFSSLYLLS 178
                                   45567778899999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1142.92
//
Query:       gi|91774146|ref|YP_566838.1|  [L=495]
Description: polysaccharide biosynthesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-20   72.4  72.3    7.3e-16   58.5  23.8    3.9  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
      1e-16   61.2  39.2      1e-16   61.2  39.2    2.8  3  Polysacc_synt    Polysaccharide biosynthesis protein
    1.7e-11   43.9  24.2    1.7e-11   43.9  24.2    2.0  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.3e-08   33.9  42.4    1.3e-08   33.9  42.4    2.3  2  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5  12.0    0.0037        16      32     128 ..      12     121 ..       3     125 .. 0.56
   2 !   18.3  22.6   4.1e-07    0.0018       6     112 ..     121     226 ..     116     272 .. 0.83
   3 ?   -2.2   2.9      0.87   3.9e+03      87     110 ..     255     277 ..     214     315 .. 0.60
   4 !   58.5  23.8   1.6e-19   7.3e-16       1     142 [.     325     458 ..     325     459 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0037
               Polysacc_synt_C  32 lkalvigalvklilnllli.....plfgivG..aaiatvlallvvavlnlyalrrllgikl.ellrrll.kpllaalvmgi 103
                                   + a++iga+++ ++n+++       +fg++G  a++  +l+l+v++++ l   + + g +  +   r++   l+a +++++
  gi|91774146|ref|YP_566838.1|  12 FAAFFIGAFLNYAFNVVMGwmltpAQFGMLGvsASFLLILSLFVTSAFPLTTTKFISGKHDrSTKHRVFkSALIANIGIAV 92 
                                   55666666655555555543333559***9954555567899999999999999988888873344444355555555555 PP

               Polysacc_synt_C 104 vvylllllllglllla.....al.alllavl 128
                                   ++  l+++  +++        +   l++++l
  gi|91774146|ref|YP_566838.1|  93 LLSVLFYISYTTN--IidlgaSYnLLVIGIL 121
                                   5332222222222..1233333344444444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.1e-07
               Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrrllgikl 85 
                                    l++i++++++++ siLqg+ r k ++ + +i++++kli  ++l+   fg++Ga+++  ++ ++++ l + + r  + +k 
  gi|91774146|ref|YP_566838.1| 121 LLATILTAMAVIYFSILQGTFRFKSFAFIGIITIFAKLISGVILVkMGFGALGAVLSFPISVFIGLSLAILLTRDFTFWKT 201
                                   57899****************************************999***************************999999 PP

               Polysacc_synt_C  86 ellrrllkpllaalvmgivvyllllll 112
                                   + + ++  ++++al m+  ++  + ll
  gi|91774146|ref|YP_566838.1| 202 KGWADT-NVYFFALPMFFGTL-GTTLL 226
                                   546666.66777777777733.22222 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.87
               Polysacc_synt_C  87 llrrllkpllaalvmgivvyllll 110
                                   +l +l  +++++++m+++  ++ +
  gi|91774146|ref|YP_566838.1| 255 ILAQL-PIFMVGALMSVLFPYISK 277
                                   33344.677777777776333333 PP

  == domain 4  score: 58.5 bits;  conditional E-value: 1.6e-19
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrll 81 
                                   +Lai+a+++ fl++++v+++i+q+ + ++i++++l +++++ +il +ll+p++givGaa++t++a  +++ ++  +  +++
  gi|91774146|ref|YP_566838.1| 325 ALAIVAIGMGFLVMTMVFTNIFQARNVPRIPAIVLPLAVIIEIILLILLVPSYGIVGAAASTTIACSIGCTVMAGLYVHTY 405
                                   69******************************************************************************* PP

               Polysacc_synt_C  82 giklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                   ++kl+ l  + k+l++  ++ +v+y+l +      l   + l+ ++ + ++vYl++l  +r
  gi|91774146|ref|YP_566838.1| 406 KLKLDHLAMV-KTLVSFCILLLVLYTLPHT----GL---FPLVGSLTLSGIVYLVVLASFR 458
                                   ****634444.7777777777774433333....33...3578888899999999998877 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2  39.2   2.3e-20     1e-16       3     272 ..       6     277 ..       5     279 .. 0.83
   2 ?    0.0  13.9       0.1   4.5e+02      66     213 ..     279     424 ..     276     429 .. 0.72
   3 ?   -2.3  10.5      0.51   2.3e+03      92     184 ..     362     454 ..     356     469 .. 0.76

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2.3e-20
                 Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvll 83 
                                   k+++v +++ +i + l + + v++ ++l+p++fG + + ++++ +l++++++ ++++ +++i+  ++++ ++++++++++ 
  gi|91774146|ref|YP_566838.1|   6 KNSFVMFAAFFIGAFLNYAFNVVMGWMLTPAQFGMLGVSASFLLILSLFVTSAFPLTTTKFISGKHDRSTKHRVFKSALIA 86 
                                   89******************************************************************************* PP

                 Polysacc_synt  84 vllvlvllfllllliaaflglpelavlylilalmll...llvgvasfrrglfqglermkyaavsqvveqlsrvilvliavf 161
                                    ++++vll +l++   ++++  +l   y +l + +l   +l+++a  + +++qg  r+k++a   +++  + +i  +i+v 
  gi|91774146|ref|YP_566838.1|  87 NIGIAVLLSVLFYIS-YTTNIIDLGASYNLLVIGILlatILTAMAVIYFSILQGTFRFKSFAFIGIITIFAKLISGVILVK 166
                                   *******99988777.77776666555555444444347788888888899999999999999999999999888888888 PP

                 Polysacc_synt 162 lfldivaavlgavlaalvggivslavlrkkfrprfvilslklv..rellsfsapltisslaillytyidsi...llglllg 237
                                   ++   ++avl+  +++++g+ +++++ r     +f++ ++k +  ++  +f++p+++++l+++l+ +id i   +l+  + 
  gi|91774146|ref|YP_566838.1| 167 MGFGALGAVLSFPISVFIGLSLAILLTR-----DFTFWKTKGWadTNVYFFALPMFFGTLGTTLLMNIDIIgvkFLTDVAL 242
                                   8887999999999999999777766666.....66666656662256789*******************884355566666 PP

                 Polysacc_synt 238 aeavGiYnaayqllvaisgllapivtaalfPvfse 272
                                   ++a+  Y +a+ +l  ++++++ +++++lfP++s+
  gi|91774146|ref|YP_566838.1| 243 SDALSGYYRAALILAQLPIFMVGALMSVLFPYISK 277
                                   667777777888888888899999999*******8 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.1
                 Polysacc_synt  66 kyrekkelvslillnvllvllvlvllfllllliaaflglpelavlylilalmll..llvgvasfrrglfqglermkyaavs 144
                                    +++ ++ +++i+  +l++l ++++++++ + +  ++  pe+    ++la++     ++ ++ +++++fq+ +  +  a+ 
  gi|91774146|ref|YP_566838.1| 279 TEND-RYASKSIKYGALFILPLALVIAAVPDAFILLMFPPEYIASAPALAIVAIgmGFLVMTMVFTNIFQARNVPRIPAIV 358
                                   4455.5889999999999999999999988777676666666666655555544456777777888899888888888888 PP

                 Polysacc_synt 145 qvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr.prfvilslklvrellsfsap 213
                                     + +++ +il++++v   + iv+a++++++a  +g  v + ++ + ++ +  +   l++v+ l+sf + 
  gi|91774146|ref|YP_566838.1| 359 LPLAVIIEIILLILLVPSYG-IVGAAASTTIACSIGCTVMAGLYVHTYKlKLDH---LAMVKTLVSFCIL 424
                                   88888888888888888888.999999999999999877776666555323333...5688888888665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.51
                 Polysacc_synt  92 fllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfld.ivaavl 171
                                   ++++  i  +l  p + ++  +++ +++   ++ ++ +gl+    + k   + +v + +s+ il+l++ +l+   ++ +v+
  gi|91774146|ref|YP_566838.1| 362 AVIIEIILLILLVPSYGIVGAAASTTIA-CSIGCTVMAGLYVHTYKLKLDHLAMVKTLVSFCILLLVLYTLPHTgLFPLVG 441
                                   3333333336788888888888887877.7777788888888889999999999999999999999999999988999999 PP

                 Polysacc_synt 172 gavlaalvggivs 184
                                   +++l+ +v ++v+
  gi|91774146|ref|YP_566838.1| 442 SLTLSGIVYLVVL 454
                                   8888888876665 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9  24.2   3.7e-15   1.7e-11       4     291 ..      31     322 ..      28     324 .. 0.80
   2 ?   -2.1   2.5      0.39   1.7e+03     120     185 ..     361     426 ..     321     434 .. 0.56

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 3.7e-15
               Polysacc_synt_3   4 RLLspedFGvvaialvvislanlfvdmGlssaliqke..dlteedlstvftfnlvlgllialvlfll..apliasfynqpe 80 
                                    +L+p+ FG++++   ++ +++lfv++ +   + +    + +++   +vf + l+  + ia++l +l    +  ++++   
  gi|91774146|ref|YP_566838.1|  31 WMLTPAQFGMLGVSASFLLILSLFVTSAFPLTTTKFIsgKHDRSTKHRVFKSALIANIGIAVLLSVLfyISYTTNIIDLGA 111
                                   58*************************996555443212344444567777777766555554433300334445555544 PP

               Polysacc_synt_3  81 lvtvlrv.lalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwla 160
                                    +++l + + l  il+++ ++  ++l+  ++Fk++++i ++++++ +i++++l+ +g+g+   v++  +s ++ l l +l 
  gi|91774146|ref|YP_566838.1| 112 SYNLLVIgILLATILTAMAVIYFSILQGTFRFKSFAFIGIITIFAKLISGVILVKMGFGALGAVLSFPISVFIGLSLAILL 192
                                   44444432234568899999***********************************************99999999999999 PP

               Polysacc_synt_3 161 skwrprlkfslkslkelfsfglklllsnllnylarnld....nlliGkvlssaaLGlYsvakrlaslpvaeitsviakVlf 237
                                   ++    +k +  + +++  f l +++ +l  +l +n+d    ++l   +ls+a  G+Y  a  la+lp+ ++  ++ +Vlf
  gi|91774146|ref|YP_566838.1| 193 TRDFTFWKTKGWADTNVYFFALPMFFGTLGTTLLMNIDiigvKFLTDVALSDALSGYYRAALILAQLPIFMV-GALMSVLF 272
                                   9988999999888899999******************943334677778888999*************9876.57889*** PP

               Polysacc_synt_3 238 PalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                   P +S+  ++     ++  k+++  al++lP+a ++a+v + ++ +++  ++  +
  gi|91774146|ref|YP_566838.1| 273 PYISKHTEN----DRYASKSIKYGALFILPLALVIAAVPDAFILLMFPPEYIAS 322
                                   *****9999....5678899**************************98887766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.39
               Polysacc_synt_3 120 vssvvgvivaivlAllglgvwALvigtllssllslvll.wlaskwrprlkfslkslkelfsfglkll 185
                                   +++++ +i+ i+l+  +  v A +  t+++s+  +v+  +++++++++l   l  +k l+sf++ ll
  gi|91774146|ref|YP_566838.1| 361 LAVIIEIILLILLVPSYGIVGAAASTTIACSIGCTVMAgLYVHTYKLKL-DHLAMVKTLVSFCILLL 426
                                   5566666666666666655666666666666544443313334444444.24677888888888766 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   4.6      0.34   1.5e+03     355     424 ..      12      92 ..       5     117 .. 0.52
   2 !   33.9  42.4   2.9e-12   1.3e-08      98     424 ..     113     427 ..      66     452 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.34
                          MurJ 355 vkislislvlnills.....llllpplgvvglalatslsaliglvllyvllrkrlk......lteargiktflaklvvlla 424
                                   + + +i ++ln +++     +l   ++g++g +++  l   + ++ ++ l++ ++        t+ r++k  l + +++++
  gi|91774146|ref|YP_566838.1|  12 FAAFFIGAFLNYAFNvvmgwMLTPAQFGMLGVSASFLLILSLFVTSAFPLTTTKFIsgkhdrSTKHRVFKSALIANIGIAV 92 
                                   555567777777777666676777777777777776655444444444333333332211113333333333333222222 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 2.9e-12
                          MurJ  98 vsllri.llpylllvslsavfgavLnarkkFfapafsPvllNvs.vIltllllanklgee.ailaLaiGvliGgvlqllvq 175
                                    +ll i +l+  +l  ++++ +++L+   +F ++af  ++  ++  I +++l++  +g   a+l+  i+v+iG+ l +l  
  gi|91774146|ref|YP_566838.1| 113 YNLLVIgILLATILTAMAVIYFSILQGTFRFKSFAFIGIITIFAkLISGVILVKMGFGALgAVLSFPISVFIGLSLAIL-- 191
                                   333333145566788999999**************99999888735666666677777211222344556666555544.. PP

                          MurJ 176 lpalkkaglllkprfafrdeglkkflklllptllgvsvs.qlnllvdtalAsflaegsvsilayadri.lqlPlglfgvsi 254
                                         +++ +  +++++d ++  f   +++ +lg      +  +   +l++++ + ++s ++ a +i +qlP+ + g ++
  gi|91774146|ref|YP_566838.1| 192 ----LTRDFTFWKTKGWADTNVYFFALPMFFGTLGTTLLmNIDIIGVKFLTDVALSDALSGYYRAALIlAQLPIFMVG-AL 267
                                   ....44555555778999999999988888877776554055555566888888888999888877652689987766.89 PP

                          MurJ 255 stvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipy 335
                                   ++vl+P +S++ +++         s++i+  +l ++p++ +++++ ++ + l+f      + +  a a +La+ a+g+ ++
  gi|91774146|ref|YP_566838.1| 268 MSVLFPYISKHTENDRYA------SKSIKYGALFILPLALVIAAVPDAFILLMF------PPEYIASAPALAIVAIGMGFL 336
                                   *********888776665......9*****************************......899999*************** PP

                          MurJ 336 alvklllrvfYAredtktPvkislislvlnillsllllpplgvvglalatslsaliglvll..yvllrkrlklteargikt 414
                                    ++ +++++f Ar+  + P+++  ++++++i+l +ll+p++g vg a++t+++  ig +++  +++ + +lkl+   ++kt
  gi|91774146|ref|YP_566838.1| 337 VMTMVFTNIFQARNVPRIPAIVLPLAVIIEIILLILLVPSYGIVGAAASTTIACSIGCTVMagLYVHTYKLKLDHLAMVKT 417
                                   *****************************************************9887655312344444557777777777 PP

                          MurJ 415 flaklvvlla 424
                                    +   ++ll+
  gi|91774146|ref|YP_566838.1| 418 LVSFCILLLV 427
                                   6666333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.80u 0.35s 00:00:01.14 Elapsed: 00:00:00.51
# Mc/sec: 2910.55
//
Query:       gi|91774147|ref|YP_566839.1|  [L=662]
Description: hypothetical protein Mbur_2226 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   15.2   0.4      0.059   13.6   0.4    1.9  1  CARDB      CARDB
      0.024   15.0   0.1       0.06   13.7   0.1    1.6  1  DUF961     Bacterial protein of unknown function (DUF961)
       0.06   13.6   0.4       0.23   11.7   0.4    2.1  1  FixG_C     IG-like fold at C-terminal of FixG, putative oxido
      0.065   13.3   0.4       0.23   11.5   0.1    2.1  2  DUF1573    Protein of unknown function (DUF1573)


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 ?   13.6   0.4   1.3e-05     0.059       3      86 ..     307     393 ..     305     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                   -EEE...EEEC-SEEETTSEEEEEEEEEE-.SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEE CS
                         CARDB   3 DLtv..tntlnpseafvgeentitvtvkNq.GtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtl 80 
                                   DL +  ++++ + + +++e+++i+++vkN  G  +  + ++++  dg++++  +   L +g+s+++++  +++ ++g+ ++
  gi|91774147|ref|YP_566839.1| 307 DLNIgvDEISIEPSYYQEEDMEIQFSVKNLdGGRYTAKPEITISTDGDSKTIYQELDLLSGDSEEIKVVLKAPQKQGSQKV 387
                                   888887888999999**************64999999999********97666667999**************88888889 PP

                                   EEEEST CS
                         CARDB  81 tvvvDp 86 
                                   tv++ +
  gi|91774147|ref|YP_566839.1| 388 TVTIRT 393
                                   888755 PP

>> DUF961  Bacterial protein of unknown function (DUF961)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.3e-05      0.06      42      87 ..     375     422 ..     352     432 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                        DUF961  42 klys.saq.gedieVtipaeagvkefeyedeVkLvnpkieavgnsing 87 
                                    l++ ++q +++++Vti +e   +e +++ +V ++np++++ +   ++
  gi|91774147|ref|YP_566839.1| 375 VLKApQKQgSQKVTVTIRTEYSTIEKSVDYQVRVINPTVTTLSADLQE 422
                                   55542577899******************************9988554 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4     5e-05      0.23      44     104 ..     324     396 ..     322     426 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                                   SS-EEEEEEEES-S........S-EE.......E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE..EG CS
                        FixG_C  44 ekprrytlsveglp........glel......agraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt..dd 104
                                   e+++++++sv++l+        ++++      +    +e+++ +g +++++v++++p+++   +s+++t++++  ++
  gi|91774147|ref|YP_566839.1| 324 EEDMEIQFSVKNLDggrytakpEITIstdgdsK-TIYQELDLLSGDSEEIKVVLKAPQKQ---GSQKVTVTIRteYS 396
                                   788999999999874545444444446665531.3369********************98...55666666642133 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         2   9.2e+03      73      84 ..     159     170 ..     135     178 .. 0.58
   2 ?   11.5   0.1   5.2e-05      0.23      46      88 ..     356     398 ..     312     408 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
                       DUF1573  73 gefnktvtvyan 84 
                                    + nk++ vy +
  gi|91774147|ref|YP_566839.1| 159 VRLNKNIYVYFD 170
                                   246777777766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.2e-05
                       DUF1573  46 tpeypkepiapGesgkikvtfnakgrpgefnktvtvyanteke 88 
                                   +  y++  +  G+s +ikv  +a +++g+++ tvt+ ++ ++ 
  gi|91774147|ref|YP_566839.1| 356 KTIYQELDLLSGDSEEIKVVLKAPQKQGSQKVTVTIRTEYSTI 398
                                   4446777899**************************9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 4064.58
//
Query:       gi|91774148|ref|YP_566840.1|  [L=767]
Description: hypothetical protein Mbur_2227 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1276  (0.0711696); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 4821.25
//
Query:       gi|91774149|ref|YP_566841.1|  [L=353]
Description: hypothetical protein Mbur_2228 [Methanococcoides burtonii DSM 6242]
Scores for 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-25   88.0   0.0    7.2e-25   87.2   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.055   12.3   0.0      0.093   11.6   0.0    1.3  1  Flavi_NS1        Flavivirus non-structural Protein NS1
       0.13   11.8   0.1       0.48    9.9   0.0    1.9  2  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> 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 !   87.2   0.0   1.2e-28   7.2e-25       3      92 .]     249     344 ..     247     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 1.2e-28
               Glyco_trans_1_2   3 Lnpsrs......espnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarerv 77 
                                   +n+++        ++n r+f ++ cG+f +tdd   ++++f++gke+i++++ e+++eki+y+++np++r ai ea+r +v
  gi|91774149|ref|YP_566841.1| 249 INVHEEyqkkygGDCNERTFKIPLCGGFEITDDVACIRKYFEDGKEIIIAKNREDWLEKIDYYMNNPDKRLAIIEAGRDKV 329
                                   555555666666779****************************************************************** PP

               Glyco_trans_1_2  78 laehtydhraeqlla 92 
                                   l+ehty++r+eq+l+
  gi|91774149|ref|YP_566841.1| 330 LKEHTYHNRVEQMLE 344
                                   ************985 PP

>> Flavi_NS1  Flavivirus 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   1.6e-05     0.093      14      48 ..     291     325 ..     283     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Flavi_NS1  14 cgdgifvtrevddwlekykyqaedpkklaaivkka 48 
                                    g+ i++ ++ +dwlek +y+ ++p k  ai+++ 
  gi|91774149|ref|YP_566841.1| 291 DGKEIIIAKNREDWLEKIDYYMNNPDKRLAIIEAG 325
                                   5889*********************9999999875 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 ?   -2.4   0.0      0.49     3e+03      76     101 ..      33      60 ..      25      61 .. 0.77
   2 ?    9.9   0.0   8.1e-05      0.48     120     171 ..     278     327 ..     273     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.49
                                   GEEECCHSSSHHHHHHC..ESEEEEEES CS
               Glycos_transf_1  76 iflgevsredleellkn..adifvlpsi 101
                                   +f+ ++  ++l+++l +   dif+ +s+
  gi|91774149|ref|YP_566841.1|  33 NFVTFSYGDNLDNFLDRnhIDIFITSSH 60 
                                   4555666669999999989999999886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.1e-05
                                   EEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
               Glycos_transf_1 120 iasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                   i+ ++  ++++++dg+   ++ ++n e++ e+i+ +++++++r +++e++r 
  gi|91774149|ref|YP_566841.1| 278 ITDDVACIRKYFEDGK--EIIIAKNREDWLEKIDYYMNNPDKRLAIIEAGRD 327
                                   5666788899999999..68888889***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2632.98
//
Query:       gi|91774150|ref|YP_566842.1|  [L=274]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-36  123.8   0.3    8.8e-36  123.3   0.3    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    3.9e-18   65.9   0.8      5e-18   65.6   0.8    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    9.9e-16   58.3   0.0    1.6e-15   57.7   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00014   22.3   0.1    0.00028   21.3   0.1    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.031   13.8   0.0       0.05   13.2   0.0    1.3  1  CobU             Cobinamide kinase / cobinamide phosphate gua


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 !  123.3   0.3   2.5e-39   8.8e-36       1     168 [.      10     172 ..      10     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 2.5e-39
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   svv+p+yN e++l+ ++es+l+q +y dfe i+vDD+StD+++ei+ee++k+d+r+ v+r+e n G a  + +g ++++g+
  gi|91774150|ref|YP_566842.1|  10 SVVMPAYNAEAYLKDSIESILDQ-TYTDFEFIIVDDASTDNSHEIIEEYSKKDKRIVVLRNEINLGIAETRTKGTKYSKGK 89 
                                   8**********************.********************************************************* PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEE CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallr 162
                                   yi++ DaDd+    +lek +++le++ + +v+g++   f++++ +        +  +    + r++      + ++ +++r
  gi|91774150|ref|YP_566842.1|  90 YIAVSDADDISILTRLEKQYNYLEEHKDCGVVGGFIELFDSDTSKIIGV----RKYYEDDANLRKRLFLYCPVAQPVCMMR 166
                                   *************************977666666666665555554432....3444444444444445555556666778 PP

                                   EHHHHH CS
               Glycos_transf_2 163 realee 168
                                   +e++e 
  gi|91774150|ref|YP_566842.1| 167 KEVFET 172
                                   887776 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 !   65.6   0.8   1.4e-21     5e-18       1     222 [.      10     215 ..      10     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.4e-21
               Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrGaska 80 
                                   svv+p ++ e   y+++ +  +  +   ++e+i+vdd S+++  e ++   ++ +++  l++e     + a +r +G++++
  gi|91774150|ref|YP_566842.1|  10 SVVMPAYNAEA--YLKDSIESILDQTYTDFEFIIVDDASTDNSHEIIEEYSKKDKRIvVLRNE--INLGIAETRTKGTKYS 86 
                                   79999999875..6***997766666689*************999999999999888566666..899************* PP

               Glyco_tranf_2_2  81 esdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkff 161
                                   ++ ++   DaD+   + ++ek+ +      l+e  d  vv  +++l + d+ ++  v   + +   l++ l  + ++++  
  gi|91774150|ref|YP_566842.1|  87 KGKYIAVSDADDISILTRLEKQYN-----YLEEHKDCGVVGGFIELFDSDTSKIIGVRKYYEDDANLRKRLFLYCPVAQP- 161
                                   **********************99.....9***************************99999999999999988888764. PP

               Glyco_tranf_2_2 162 apssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykaraksl 222
                                          +++++ f  +G yD ++  + aED dl  R++ ++k+ +     l y+ ++ks 
  gi|91774150|ref|YP_566842.1| 162 -----VCMMRKEVFETLGYYDPKY--PPAEDLDLWFRIGTKYKFANIQEILLKYRVHKKSA 215
                                   .....5799***************..********************9*********99975 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 !   57.7   0.0   4.3e-19   1.6e-15       4     194 ..       9     192 ..       6     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 4.3e-19
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealr 84 
                                   ++v+ p++n+e++l + +es+l q+y ++e+++v+d s++   e +ee     +d r++v++n+ nlg+    +    + +
  gi|91774150|ref|YP_566842.1|   9 ISVVMPAYNAEAYLKDSIESILDQTYTDFEFIIVDDASTDNSHEIIEEY--SKKDKRIVVLRNEINLGIA---ETRTKGTK 84 
                                   89********************************************994..3336799******999983...3446999* PP

               Glyco_tranf_2_3  85 avksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralgvltlnGs 163
                                     k++++++ D+D++   + l+++ +++ +++++g+vg+   +++ +++ +  + + + ++ +lr +++ +     +++  
  gi|91774150|ref|YP_566842.1|  85 YSKGKYIAVSDADDISILTRLEKQYNYLeEHKDCGVVGGFIeLFDSDTSKIIGVRKYYEDDANLRKRLFLYC----PVAQP 161
                                   **************************************6552778888777766664444455544444443....33446 PP

               Glyco_tranf_2_3 164 gslirrevlkelegldplflltdDyelglrl 194
                                    +++r ev++ l+  dp+  +++D++l++r+
  gi|91774150|ref|YP_566842.1| 162 VCMMRKEVFETLGYYDPKYPPAEDLDLWFRI 192
                                   9****************99999******985 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 !   21.3   0.1   7.8e-08   0.00028       1      84 [.      16     100 ..      16     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.8e-08
               Glyco_tranf_2_4   1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkel..pevkllhvdksyederrqvellkallaryaeadwvlv 77 
                                   +n++++L+  ++ +l+  +++  ++++d+ stD++ +i++e+  ++ +++  +++++    +++  ++   +y+++++++v
  gi|91774150|ref|YP_566842.1|  16 YNAEAYLKDSIESILDQTYTDfeFIIVDDASTDNSHEIIEEYskKDKRIVVLRNEIN---LGIAETRTKGTKYSKGKYIAV 93 
                                   5999999999**99999987444******************8435577999999885...776666666667999****** PP

               Glyco_tranf_2_4  78 vDaDEfl 84 
                                    DaD + 
  gi|91774150|ref|YP_566842.1|  94 SDADDIS 100
                                   ****875 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05      0.05      73     141 ..      18      86 ..       2      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                          CobU  73 kevvLvDcltlwltnllleeeaekveekleeeveellealkelkatvvlVsnEvglgvvpenalgrlfr 141
                                   +e++L D++  +l ++  + e   v+++ +++ +e++e  +++++++v+  nE+ lg+ ++   g ++ 
  gi|91774150|ref|YP_566842.1|  18 AEAYLKDSIESILDQTYTDFEFIIVDDASTDNSHEIIEEYSKKDKRIVVLRNEINLGIAETRTKGTKYS 86 
                                   478888888888888888877666999999******************************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1620.65
//
Query:       gi|91774151|ref|YP_566843.1|  [L=235]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  189.5   0.0    8.3e-56  189.3   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    4.8e-13   49.8   0.0    5.4e-13   49.6   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0078   16.0   0.0       0.22   11.2   0.0    2.1  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
       0.04   13.8   0.0      0.068   13.1   0.0    1.2  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 !  189.3   0.0   1.9e-59   8.3e-56       1     244 [.       2     231 ..       2     235 .] 0.94

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 1.9e-59
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   k++ILaGG+G+RL+PLt+ + k l+pv++k ++i+++l++l+++gi++i++v+ + h+  + e l++gs+fg + ++ +++
  gi|91774151|ref|YP_566843.1|   2 KGIILAGGTGSRLYPLTKVTNKHLLPVYDK-PMIYYPLQTLLDAGINDIMIVSGRGHAGHFLELLGSGSDFGARFTYEIQD 81 
                                   79****************************.************************************************** PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC.TTSBEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead.eegrver 161
                                   e  g+A+A+ l +++++d++    + v+ gD +++d +++av++++  a+     +++++v +a ++Gv+e+d ++++v +
  gi|91774151|ref|YP_566843.1|  82 EAGGIAQALNLTRDFADDDD----ITVILGDNIFQDIIRDAVQSFKTGAQ-----IFLKQVPDAARFGVAEIDeSSRQVLS 153
                                   *****************999....5666667777889********99999.....9*****************5555**** PP

                                   EECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHH CS
               NTP_transferase 162 fvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllean 242
                                   ++EKP+ +k s++a++G+Yv++s+v++++ + l+++ rge eitd++++++++g  +++   ++  +W D Gt+dsll+a 
  gi|91774151|ref|YP_566843.1| 154 IEEKPEVPK-SDYAVTGLYVYDSSVFEII-QTLKPSGRGELEITDVNNEYIRQGLMKYS-EIEG--QWTDAGTFDSLLRAG 229
                                   *********.*******************.78*************************98.6667..5***********997 PP

                                   HH CS
               NTP_transferase 243 ek 244
                                     
  gi|91774151|ref|YP_566843.1| 230 LM 231
                                   65 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 !   49.6   0.0   1.2e-16   5.4e-13       1     119 [.       3     129 ..       3     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.2e-16
                                   EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC......HHHHHHTTCTS-EEE-TTSS. CS
                  NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggde......evlaalarlgvrvvededpg. 69 
                                   ++iLAGG +sR+    +  +K llp+ +kp++ + l++l +ag++++++v g+       e+l    ++g+r++++ + + 
  gi|91774151|ref|YP_566843.1|   3 GIILAGGTGSRLYpltKvtNKHLLPVYDKPMIYYPLQTLLDAGINDIMIVSGRGhaghflELLGSGSDFGARFTYEIQDEa 83 
                                   79**********5433246*******************************98852343444444557889****9976652 PP

                                   -SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEE CS
                  NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvv 119
                                    g++++l    + a d+d + v+++D ++  +++++  +++++ +ga+++
  gi|91774151|ref|YP_566843.1|  84 GGIAQALNLTRDFA-DDDDITVILGDNIF--QDIIRDAVQSFK-TGAQIF 129
                                   55666666655656.************99..889999888885.555554 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 !   11.2   0.0     5e-05      0.22       4      65 ..       4      67 ..       1      85 [. 0.88
   2 ?    2.9   0.0     0.017        77      58     106 ..      92     142 ..      79     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
                                  EEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG CS
                          IspD  4 vipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld 65
                                  +i A G+G+R+    + ++K +l + +++++   +++ll+   ++ i++v  + + ++f +ll++
  gi|91774151|ref|YP_566843.1|  4 IILAGGTGSRLyplTKVTNKHLLPVYDKPMIYYPLQTLLD-AGINDIMIVSGRGHAGHFLELLGS 67
                                  899*******73336789**********************.789999999999999999999875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.017
                                   HHHHHHGGCCEEEEE--SSHHHHHHHHHHTTSSTTSEEE..E--TT-TT-- CS
                          IspD  58 efeqllldksiqlvaGGdeRaesVlnglkalegeakfVL..vHDaARpllk 106
                                    ++++  d +i+++ G +  ++ +  +++  +  a++ L  v DaAR  ++
  gi|91774151|ref|YP_566843.1|  92 LTRDFADDDDITVILGDNIFQDIIRDAVQSFKTGAQIFLkqVPDAARFGVA 142
                                   5566667789*************************99987899***95554 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.068      13      46 ..      20      53 ..      17      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                  STTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEE CS
                  CTP_transf_3 13 lpgKnlldlggkpliayvleaalkskafekviva 46
                                  + +K ll+  +kp+i y+l+ +l+++  +  iv+
  gi|91774151|ref|YP_566843.1| 20 VTNKHLLPVYDKPMIYYPLQTLLDAGINDIMIVS 53
                                  789*********************9987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1601.61
//
Query:       gi|91774152|ref|YP_566844.1|  [L=261]
Description: dTDP-4-dehydrorhamnose reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-90  301.0   0.0    7.7e-90  300.9   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
      6e-15   55.4   0.1    1.8e-14   53.8   0.1    1.7  1  Epimerase        NAD dependent epimerase/dehydratase family
      9e-10   38.5   0.0    1.4e-09   37.9   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.3e-08   32.6   2.0    1.7e-07   30.7   0.3    2.6  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.2e-07   29.2   2.9    7.7e-07   28.4   1.1    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.3e-05   24.5   0.2    5.2e-05   22.5   0.1    2.0  2  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 !  300.9   0.0   2.6e-93   7.7e-90       4     285 ..       1     259 [.       1     261 [] 0.96

  Alignments for each domain:
  == domain 1  score: 300.9 bits;  conditional E-value: 2.6e-93
                                   EEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHH CS
                 RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavea 84 
                                   +++Ga+G+lGs+L +++     +++ +t ++ld+t++++v + ++e+kp vv+naAAyt+vD +E+e++ a++vn +a++ 
  gi|91774152|ref|YP_566844.1|   1 MIIGASGMLGSDLSRAFP----DAVKFTHHDLDITNKQQVLKKIEEIKPYVVINAAAYTNVDGCEDEQDIAFKVNGHAPGY 77 
                                   689**************9....56899999*************************************************** PP

                                   HHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHH CS
                 RmlD_sub_bind  85 lAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygekgknfvktmlr 165
                                   +A+a++ +ga L+h StDyVFdG+kk+ Y e++ t+P+nvYG++Kl GEq + ++ +++ i+Rtsw++g++gknfv tmlr
  gi|91774152|ref|YP_566844.1|  78 IAQACSDIGAILVHFSTDYVFDGSKKE-YVESNITKPINVYGQSKLMGEQEIIKNTDNYRIIRTSWLFGKNGKNFVDTMLR 157
                                   ************************776.***************************************************** PP

                                   HHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS CS
                 RmlD_sub_bind 166 lakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevkpistaey 246
                                   l ke e++kvv+Dq+g+PT+++d+A+ ++++++         g+yH++neg ++w+efA +i++++        p+s++e+
  gi|91774152|ref|YP_566844.1| 158 LSKEMENVKVVNDQFGKPTHTADIARKTAEIINLNP------GIYHITNEGPCTWYEFASEIINNT-------VPCSSEEF 225
                                   *******************************98655......9********************976.......58****** PP

                                   --SS---SBE-B--HHHHHCCT----BHHHHHHHHHHHH CS
                 RmlD_sub_bind 247 ptpAkRPanSvLdtekleatfgiklrewrealkevlkel 285
                                   pt+AkRP +SvL ++k+      ++r+w++al+e+lke 
  gi|91774152|ref|YP_566844.1| 226 PTKAKRPTYSVLTNTKTT-----PMRHWKNALNEYLKEN 259
                                   ************998864.....66**********9985 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.1     6e-18   1.8e-14       3     186 ..       2     156 ..       1     175 [. 0.86

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 6e-18
                                   EETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHS CS
                     Epimerase   3 VtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassed 83 
                                   ++Ga+G++Gs l +a+ +     + +++                +ld+t+++++ + ++e +p +vi++Aa+ +v+   ++
  gi|91774152|ref|YP_566844.1|   2 IIGASGMLGSDLSRAFPD----AVKFTHH---------------DLDITNKQQVLKKIEEIKPYVVINAAAYTNVDGCEDE 63 
                                   899999999999999997....4778888...............9************************************ PP

                                   HHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EE CS
                     Epimerase  84 padfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglna 164
                                   +   ++ n +    +++a+++ g+  l+++s++ v+  +++    e++++  +kp + Y+ +Kl+ge+ + + ++ y    
  gi|91774152|ref|YP_566844.1|  64 QDIAFKVNGHAPGYIAQACSDIGA-ILVHFSTDYVFDGSKK----EYVESNITKPINVYGQSKLMGEQEIIKNTDNY---- 135
                                   ************************.***********95555....67755556***************999866666.... PP

                                   EEEEESEEESTTS-TTSTTSHH CS
                     Epimerase 165 iilrlfnlyGprngegevsrvi 186
                                    i+r + l+G++ g+++v+ ++
  gi|91774152|ref|YP_566844.1| 136 RIIRTSWLFGKN-GKNFVDTML 156
                                   79*********9.666655444 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 !   37.9   0.0   4.6e-13   1.4e-09      52     176 ..      21     140 ..      11     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.6e-13
                                   CCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGG CS
                 GDP_Man_Dehyd  52 enlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEv 132
                                    +++ h  D+t+++++ + ++e++p  v+n AA   Vd   ++ +  ++vn+ +   + +a+ ++g      +++ St+ v
  gi|91774152|ref|YP_566844.1|  21 VKFTHHDLDITNKQQVLKKIEEIKPYVVINAAAYTNVDGCEDEQDIAFKVNGHAPGYIAQACSDIGA----ILVHFSTDYV 97 
                                   47899***********************************************************984....79******** PP

                                   G-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EE CS
                 GDP_Man_Dehyd 133 YGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfav 176
                                   +    +  + E++ ++P + Y+ +Kl+ ++ +++  ++y +  +
  gi|91774152|ref|YP_566844.1|  98 FDGS-KKEYVESNITKPINVYGQSKLMGEQEIIKNTDNYRIIRT 140
                                   *444.45788******************9988888888887665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.47   1.4e+03       2      17 ..       1      16 [.       1      24 [. 0.87
   2 !   30.7   0.3   5.7e-11   1.7e-07      61     157 ..      28     136 ..      14     151 .. 0.82
   3 ?   -0.6   0.0       0.2   5.8e+02     214     251 ..     156     193 ..     147     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.47
                                  EEETTTSHHHHHHHHH CS
               Polysacc_synt_2  2 lvtGagGsiGselvrq 17
                                  ++ Ga+G +Gs l r 
  gi|91774152|ref|YP_566844.1|  1 MIIGASGMLGSDLSRA 16
                                  799********99876 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 5.7e-11
                                   --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG.......G.... CS
               Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD.......K.... 130
                                    d+++k+++ k +ee+k+ vv++aAA+ +V  +e +   a+k N ++   +++a+ + g   +v  StD       K    
  gi|91774152|ref|YP_566844.1|  28 LDITNKQQVLKKIEEIKPYVVINAAAYTNVDGCEDEQDIAFKVNGHAPGYIAQACSDIGA-ILVHFSTDyvfdgskKeyve 107
                                   599*****************************************************9996.68999**9444444312222 PP

                                   ..GSS--SHHHHHHHHHHHHHHHGGG--S CS
               Polysacc_synt_2 131 ..AvnPtnvmGatKrlaekllqalakese 157
                                       +P+nv+G +K++ e+ +++  ++ +
  gi|91774152|ref|YP_566844.1| 108 snITKPINVYGQSKLMGEQEIIKNTDNYR 136
                                   22368*************98888776654 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.2
                                   HHHHHH--SS-EEEE--.-EEEHHHHHHHH........ CS
               Polysacc_synt_2 214 lqalalakggeifvldmGepvkivdlakalielsglee 251
                                   l   +++++ ++   + G+p++ +d+a++  e+++l++
  gi|91774152|ref|YP_566844.1| 156 LRLSKEMENVKVVNDQFGKPTHTADIARKTAEIINLNP 193
                                   555677888888888999*********99999887765 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 ?   -1.9   0.0      0.43   1.3e+03       2      16 ..       2      16 ..       1      22 [. 0.84
   2 !   28.4   1.1   2.6e-10   7.7e-07      49     205 ..      25     166 ..      11     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.43
                     3Beta_HSD  2 vtGgaGFlGralvke 16
                                  ++G++G lG+ l ++
  gi|91774152|ref|YP_566844.1|  2 IIGASGMLGSDLSRA 16
                                  89*******998776 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.6e-10
                     3Beta_HSD  49 viegDvtdkdkleealegvd..vvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslg 126
                                    +  D+t+k+++ + +e+++  vvi  a++++v g ++++d   kvn +    + +ac + g  +lv+ S+ + v++ s++
  gi|91774152|ref|YP_566844.1|  25 HHDLDITNKQQVLKKIEEIKpyVVINAAAYTNVDGcEDEQDIAFKVNGHAPGYIAQACSDIG-AILVHFST-DYVFDGSKK 103
                                   6889*************995559************889999999**************9998.47787776.788995555 PP

                     3Beta_HSD 127 eeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfk 205
                                   e +          +++ ++y +sK + E+ ++k  +    n        +R + ++G   k +v ++ +l k  ++ +k
  gi|91774152|ref|YP_566844.1| 104 EYVE------SNITKPINVYGQSKLMGEQEIIKNTD----NY-----RIIRTSWLFGKNGKNFVDTMLRLSKEMEN-VK 166
                                   5554......33455789*************99877....33.....35788999998888888888888877633.33 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         1   3.1e+03       2      11 ..       3      12 ..       2      15 .. 0.82
   2 !   22.5   0.1   1.8e-08   5.2e-05      90     211 ..      47     148 ..      24     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                                  E-TTSHHHHH CS
                 NAD_binding_4  2 TGaTGFLGkv 11
                                   Ga+G+LG+ 
  gi|91774152|ref|YP_566844.1|  3 IGASGMLGSD 12
                                  69******85 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.8e-08
                                   EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEE CS
                 NAD_binding_4  90 viihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldedera 167
                                   v+i+ aA +n+d+   + + +++vN ++   + + ++ + +   l+h+ST yv + +++e                   ++
  gi|91774152|ref|YP_566844.1|  47 VVINAAAYTNVDGcedEQDIAFKVNGHAPGYIAQACSDIGAI--LVHFSTDYVFDGSKKE-----------------YVES 108
                                   89*********984445556*****************99766..******7777766643.................3457 PP

                                   ETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SS CS
                 NAD_binding_4 168 klkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesk 211
                                   + ++  n Y qsK ++E+ + +    +++   i+R s + g+  
  gi|91774152|ref|YP_566844.1| 109 NITKPINVYGQSKLMGEQEIIKNT--DNY--RIIRTSWLFGKNG 148
                                   888999************999999..455..6999999888444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1592.62
//
Query:       gi|91774153|ref|YP_566845.1|  [L=318]
Description: dTDP-glucose 4,6-dehydratase [Methanococcoides burtonii DSM 6242]
Scores for 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-82  275.1   0.0    1.1e-81  274.9   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.3e-63  211.9   0.0    1.2e-62  211.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.8e-23   82.9   0.0    2.8e-23   82.3   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.5e-20   71.7   0.0    3.7e-19   69.0   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.4e-17   63.8   0.0    5.3e-16   58.6   0.0    2.3  1  NAD_binding_4    Male sterility protein
    3.9e-17   62.3   0.0    2.8e-16   59.5   0.0    1.9  1  RmlD_sub_bind    RmlD substrate binding domain
    5.8e-10   39.4   0.0      9e-10   38.7   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00036   20.2   0.0    0.00053   19.6   0.0    1.3  1  NmrA             NmrA-like family
     0.0081   15.6   0.0      0.071   12.6   0.0    2.0  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
       0.22   11.4   0.0       0.49   10.3   0.0    1.6  1  KR               KR domain


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.9   0.0   5.9e-85   1.1e-81       1     330 [.       4     300 ..       4     302 .. 0.94

  Alignments for each domain:
  == domain 1  score: 274.9 bits;  conditional E-value: 5.9e-85
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG+ GfiGs++++++l+++ + + i+++++++++g+ e+l++    + ++n++++kgD++D + +e+++++v  d v++
  gi|91774153|ref|YP_566845.1|   4 LVTGGCGFIGSNFVRMMLQRYPD-CDITNLDKLTYAGNPENLKDI---RDNPNYSFIKGDICDPHVVEKAMENV--DIVIH 78 
                                   9******************9665.5899**************874...3579********************99..89*** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadw 162
                                   +AA+shVd+s+e+ + ++++nvlGt +LL+++ +  +   ++f+++St+EvYG+++   ++E+  ++P sPY+ +K+ +d 
  gi|91774153|ref|YP_566845.1|  79 FAAESHVDRSIEDGDVFVRTNVLGTNTLLNCALRSDI---KKFIHVSTDEVYGSTETGSFKEEDNLEPSSPYSSSKAGSDL 156
                                   ********************************98876...59*************************************** PP

                                   HHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS-- CS
                 GDP_Man_Dehyd 163 ivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpe 243
                                   ++++y+ +ygl+++++++ n+ +p++   +++++i++++++  +  ++v+++G + ++Rdw hv+D++++++ +lq+++  
  gi|91774153|ref|YP_566845.1| 157 LAMSYHTTYGLPVSITRCTNNFGPYQ---YPEKLIPLFITNLMES-EKVPVYGTGLNIRDWIHVDDHCSGIDFVLQNGN-- 231
                                   *************************6...9**********97776.58999**************************98.. PP

                                   -EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS- CS
                 GDP_Man_Dehyd 244 dyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvs 324
                                        +ge++++++ +el++l++  ++             k+ gk++  ++++ +r+g++ ++  d++k+k ++gWkp+++
  gi|91774153|ref|YP_566845.1| 232 -----SGEVYNIGGGNELTNLDITHRVL------------KDLGKDESMIRYVEDRKGHDFRYSLDCTKLK-KMGWKPEYD 294
                                   .....8*****************98754............456778888999******************9.9******** PP

                                   HHHHHH CS
                 GDP_Man_Dehyd 325 feelvr 330
                                   fe+ ++
  gi|91774153|ref|YP_566845.1| 295 FESALS 300
                                   **9876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.5   0.0   6.7e-66   1.2e-62       2     241 .]       4     239 ..       3     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 211.5 bits;  conditional E-value: 6.7e-66
                                   EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                     Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAav 74 
                                   lVtG+ GfiGs++v+ +l++    ++++ld+l++a+n ++l+d+      +++++d++d+  +e++++  ++d+vih+Aa+
  gi|91774153|ref|YP_566845.1|   4 LVTGGCGFIGSNFVRMMLQRYpdCDITNLDKLTYAGNPENLKDIrdnpnySFIKGDICDPHVVEKAME--NVDIVIHFAAE 82 
                                   9*******************98888*******************************************..9********** PP

                                   --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                     Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                   ++v++s+ed   f+++n+ gt +ll++a ++++k+++++s++evYG  ++   +e+    +l+p+spY+ +K+ ++ l+ +
  gi|91774153|ref|YP_566845.1|  83 SHVDRSIEDGDVFVRTNVLGTNTLLNCALRSDIKKFIHVSTDEVYGSTETGSFKEED---NLEPSSPYSSSKAGSDLLAMS 160
                                   **********************************************99995466666...79******************* PP

                                   HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTE CS
                     Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkge 236
                                   y+ +ygl++ i+r++n++Gp+   + ++++ip +i+++ e + +v ++g+g + Rd+++v+D++ +i +vl++   g++ge
  gi|91774153|ref|YP_566845.1| 161 YHTTYGLPVSITRCTNNFGPY---QYPEKLIPLFITNLMESE-KVPVYGTGLNIRDWIHVDDHCSGIDFVLQN---GNSGE 234
                                   *********************...88****************.******************************...9999* PP

                                   EEEES CS
                     Epimerase 237 iyniG 241
                                   +yniG
  gi|91774153|ref|YP_566845.1| 235 VYNIG 239
                                   ****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 !   82.3   0.0   1.6e-26   2.8e-23       1     219 [.       4     217 ..       4     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.6e-26
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvd 78 
                                   +vtGg+GF+G++ v++++++ +  ++  lD    + +pe l++++   + ++i+gD++d + +e+a+e+vd+vih a+ + 
  gi|91774153|ref|YP_566845.1|   4 LVTGGCGFIGSNFVRMMLQRYPDCDITNLDkltYAGNPENLKDIRDNPNYSFIKGDICDPHVVEKAMENVDIVIHFAAESH 84 
                                   69****************************555455666666666666666****************************** PP

                     3Beta_HSD  79 vagklte.deimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvl 158
                                   v   +++ d + + nv GT+++l+ ++++++++++++S+ ev g  ++      g  ++e +  ++++y++sKa ++ l +
  gi|91774153|ref|YP_566845.1|  85 VDRSIEDgDVFVRTNVLGTNTLLNCALRSDIKKFIHVSTDEVYGS-TE-----TGSFKEEDNLEPSSPYSSSKAGSDLLAM 159
                                   *99666526789*******************************99.33.....34444555667899*******9987777 PP

                     3Beta_HSD 159 kaNgrtlknggrlyTcaLRpagiyGegd..kllvp.llkqlaklglalfkigdeevlsdrvYvg 219
                                   +        g  l     R +  +G+++  ++l p ++ +l+ ++ ++  +g   ++ d++ v+
  gi|91774153|ref|YP_566845.1| 160 SYHT---TYG--LPVSITRCTNNFGPYQypEKLIPlFITNLMESE-KVPVYGTGLNIRDWIHVD 217
                                   6555...444..777777888889987533445551455555555.999999999999999886 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0     2e-22   3.7e-19       1     251 [.       3     261 ..       3     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 2e-22
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +lvtG+ G iGs++vr +l++ p    + + d l+     ++l++  ++ ++      + gd+ d + +eka+e  +vd+v
  gi|91774153|ref|YP_566845.1|   3 LLVTGGCGFIGSNFVRMMLQRYPD-CDITNLDKLTYAGNPENLKDIRDNPNY----SFIKGDICDPHVVEKAME--NVDIV 76 
                                   59******************9886.344455444444444445444444434....4568**************..***** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG..............SS--SHHHHHHHHHHHH CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA..............vnPtnvmGatKrlaekl 148
                                   +h AA  hV    e     ++tNvlgt++++++a+++++kk++ +StD                 +P + +  +K+ +++l
  gi|91774153|ref|YP_566845.1|  77 IHFAAESHVDRSIEDGDVFVRTNVLGTNTLLNCALRSDIKKFIHVSTDEVygstetgsfkeednLEPSSPYSSSKAGSDLL 157
                                   ***********999999*******************************862222222222222246777788888888888 PP

                                   HHHGGG--SSS--EEEEEEE-EETTGT...TSSHHHHHHHHHTTSSEEES-TT-.EEEEE-HHHHHHHHHHHHHH--SS-E CS
               Polysacc_synt_2 149 lqalakeseekktkfvvvRfGNVlgSr...GSviplFkkqikeggpvtvTdpem.tRyfmtieeavqLvlqalalakggei 225
                                   +++++++       ++++R  N +g       +iplF   + e ++v+v  + + +R ++ +++ ++ +   l+++++ge+
  gi|91774153|ref|YP_566845.1| 158 AMSYHTTY---GLPVSITRCTNNFGPYqypEKLIPLFITNLMESEKVPVYGTGLnIRDWIHVDDHCSGIDFVLQNGNSGEV 235
                                   88877777...688888998888886522268*****************88776469*********999999999****** PP

                                   EEE--.-EEEHHHHHHHH........ CS
               Polysacc_synt_2 226 fvldmGepvkivdlakalielsglee 251
                                   +    G+ ++ +d+ +++++  g++e
  gi|91774153|ref|YP_566845.1| 236 YNIGGGNELTNLDITHRVLKDLGKDE 261
                                   **999999999999999987777544 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   2.9e-19   5.3e-16       1     204 [.       5     175 ..       5     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.9e-19
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHH CS
                 NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedl 81 
                                   +TG+ GF+G+ +++ +L++ p++ i+ l          ++l+ +    +l++        + ++++GD+++p+       +
  gi|91774153|ref|YP_566845.1|   5 VTGGCGFIGSNFVRMMLQRYPDCDITNL----------DKLTYAGNPENLKDIR---DNPNYSFIKGDICDPH------VV 66 
                                   7********************9666554..........4453443334443333...47889********988......68 PP

                                   HHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H...... CS
                 NAD_binding_4  82 qelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekee 159
                                   ++ +e+vd++ih aA  ++d+++++   ++r+Nv+Gt  +l+ a +   +  ++hvST  v+g  e+              
  gi|91774153|ref|YP_566845.1|  67 EKAMENVDIVIHFAAESHVDRSIEDgdvFVRTNVLGTNTLLNCALRSDIK-KFIHVSTDEVYGSTETG------------- 133
                                   9999****************988776669****************98888.*******6666666633............. PP

                                   HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE- CS
                 NAD_binding_4 160 kldederaklkglpntYeqsKalaEklvrearrrsglpvvivRps 204
                                      + +++++ + +  Y+ sKa ++ l  +++   glpv+i R++
  gi|91774153|ref|YP_566845.1| 134 ---SFKEEDNLEPSSPYSSSKAGSDLLAMSYHTTYGLPVSITRCT 175
                                   ...3455566677889***************************97 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   1.5e-19   2.8e-16       1     282 [.       1     303 [.       1     307 [. 0.79

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.5e-19
                                   EEEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE- CS
                 RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae..eglevlaltre.....................eldltdaeavaellkeakpdvvvna 58 
                                   mk+lvtG+ G +Gs+ ++ + +   +++++ l++                      + d+ d++ v++++++   d+v++ 
  gi|91774153|ref|YP_566845.1|   1 MKLLVTGGCGFIGSNFVRMMLQryPDCDITNLDKLtyagnpenlkdirdnpnysfiKGDICDPHVVEKAMEN--VDIVIHF 79 
                                   89**************9998873457888888777999********************************99..899**** PP

                                   -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH CS
                 RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla 138
                                   AA   vD+  ++ +   + n+ ++++l + a + ++ ++ihvStD V+  +++  ++e+d+ +P + Y  +K+       +
  gi|91774153|ref|YP_566845.1|  80 AAESHVDRSIEDGDVFVRTNVLGTNTLLNCALRSDIkKFIHVSTDEVYGSTETGSFKEEDNLEPSSPYSSSKAGSDLLAMS 160
                                   *********************************99846**********************************877766665 PP

                                   ....H-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE CS
                 RmlD_sub_bind 139 ....agkkalivRtswvyge..kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyH 211
                                       +g  + i R +  +g   + + ++  ++  + e+e++ v      ++   +++d  + +  +l++  +     +vy 
  gi|91774153|ref|YP_566845.1| 161 yhttYGLPVSITRCTNNFGPyqYPEKLIPLFITNLMESEKVPVYGTglNIRDWIHVDDHCSGIDFVLQNGNS----GEVYN 237
                                   333334456788888888764466777777777777777777765411455566677777777777777776....77888 PP

                                   ---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHH CS
                 RmlD_sub_bind 212 lanegetswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevl 282
                                   +++ +e++ l++ + +lk++g+d++ ++ ++      + +  ++S Ld++kl++ +  +  ++++al +++
  gi|91774153|ref|YP_566845.1| 238 IGGGNELTNLDITHRVLKDLGKDESMIRYVEDR----KGHDFRYS-LDCTKLKKMGWKPEYDFESALSSTV 303
                                   888888888888888888888887777777433....33333444.6777777776666666766666655 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 !   38.7   0.0     5e-13     9e-10       1     131 [.       7     157 ..       7     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 5e-13
                                   TTTSHHHHHHHHHHHHC-.T-EEE.....EEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHH CS
                NAD_binding_10   1 GAtGkvGrllvkellarg.ghevt.....alvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkde 75 
                                   G+ G +G+  v+  l+r  + ++t      ++ npe l++++++++ + ++gd+ d+  +++a++++d+V+  ++ ++ d+
  gi|91774153|ref|YP_566845.1|   7 GGCGFIGSNFVRMMLQRYpDCDITnldklTYAGNPENLKDIRDNPNYSFIKGDICDPHVVEKAMENVDIVIHFAAESHVDR 87 
                                   7788899999999999988555551111145789***********************************998887777755 PP

                                   HH.............HHHHHHHHHHCT--EEEEEEETTTTSGCG.CHHHHHHHHCCHHHHHHHHHHHHHH CS
                NAD_binding_10  76 eg.............aknivdaakeagvkRfvlvsaigvgdevp.gefgewnkellkaylaakraaeell 131
                                    +             ++++++ a ++++k+f+ vs+  v+ +++ g+f+e ++   ++ +   +a  +ll
  gi|91774153|ref|YP_566845.1|  88 SIedgdvfvrtnvlgTNTLLNCALRSDIKKFIHVSTDEVYGSTEtGSFKEEDNLEPSSPYSSSKAGSDLL 157
                                   555667788888999*********************9999754314555544444455555555555555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.9e-07   0.00053       2      85 ..       4      95 ..       3     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.9e-07
                                  EESSTTSHHHHHHHHHHHH..HT-EEEEEES-S...-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEEE---GG..S CS
                          NmrA  2 lviGaTGrqGksvvrallk..aghkvralvRdt...kselakslkeaGvelv.kgdlddkeslvealkgvdvvfsvtgfy..s 76
                                  lv+G+ G +G+ +vr++l+   + ++  l + t   + e++k + ++++    kgd+ d  ++++a+++vd v+   +    +
  gi|91774153|ref|YP_566845.1|  4 LVTGGCGFIGSNFVRMMLQryPDCDITNLDKLTyagNPENLKDIRDNPNYSFiKGDICDPHVVEKAMENVDIVIHFAAEShvD 86
                                  8******************66455555544444777************96544********************9988866777 PP

                                  -HHHHHHHH CS
                          NmrA 77 keiedgkkl 85
                                    iedg   
  gi|91774153|ref|YP_566845.1| 87 RSIEDGDVF 95
                                  777777554 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0     4e-05     0.071       4     164 ..       4     162 ..       2     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                                   EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                     adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                   lvtG+++ IG ++++ ++++  ++ +++  + + +   ++lk+   + ++ +i++D+ d + ve+++e++       d+++
  gi|91774153|ref|YP_566845.1|   4 LVTGGCGFIGSNFVRMMLQRYPDCDITNLDKLTYAGNPENLKDIrdNPNYSFIKGDICDPHVVEKAMENV-------DIVI 77 
                                   8*******************99999999999999999999999988889***********9999888766.......9999 PP

                                   E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH........HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                     adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpaml........kqssGrIvnvsSvagkvpvagvaaYsAsKaa 155
                                   + A+ +      + s e+ +  + +N+ g+  l   +l+  +        ++  G+   ++S   +  ++  ++Ys+sKa+
  gi|91774153|ref|YP_566845.1|  78 HFAAES----HVDRSIEDGDVFVRTNVLGTNTLLNCALRSDIkkfihvstDEVYGS-TETGSFKEEDNLEPSSPYSSSKAG 153
                                   999883....4455666777788888888888888887772234445665555666.478888888888888899999998 PP

                                   HHHHHHHHH CS
                     adh_short 156 vagltrsla 164
                                    + l++s +
  gi|91774153|ref|YP_566845.1| 154 SDLLAMSYH 162
                                   888887765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.49       4      76 ..       4      74 ..       2     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                                  EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                            KR  4 litGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                  l+tGG+G +G  ++r+++++     +  l +   + + + ++++ +++ + + ++++ D+ d++ ve+++e+++
  gi|91774153|ref|YP_566845.1|  4 LVTGGCGFIGSNFVRMMLQRYpDCDITNLDKL--TYAGNPENLKDIRD-NPNYSFIKGDICDPHVVEKAMENVD 74
                                  9*****************98766677777766..44555556777776.5577888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1972.39
//
Query:       gi|91774154|ref|YP_566846.1|  [L=183]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-72  242.8   0.0    1.6e-72  242.7   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 !  242.7   0.0   8.9e-77   1.6e-72       2     168 ..       6     177 ..       5     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 242.7 bits;  conditional E-value: 8.9e-77
                                   -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHH.TS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEE CS
               dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaea.gleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaV 81 
                                   t+ie++++++pkvfgDeRG+f+es+n++ ++e+ g + +fvqdn+s+s+ gv+RGlH+q ep++q+klvrv++G+v+dv+V
  gi|91774154|ref|YP_566846.1|   6 TKIEDLYILKPKVFGDERGYFFESYNARVLDELvGKKYNFVQDNESRSSYGVIRGLHYQLEPYSQTKLVRVIQGTVYDVVV 86 
                                   89*****************************9978999******************************************* PP

                                   E-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---....SS.B-- CS
               dTDP_sugar_isom  82 DlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw....eelilS 158
                                   DlRk+S tfg+wvgveLs++nk+q++ip+gfahGf vls++a ++Yk+++yy+pese+gi+++Dp+l+idw    e++i++
  gi|91774154|ref|YP_566846.1|  87 DLRKESCTFGEWVGVELSEDNKKQFLIPKGFAHGFSVLSETAIFAYKCDDYYNPESEGGIMYDDPTLNIDWkvkkEDAIVA 167
                                   ***************************************************************************99**** PP

                                   HHHHT-B-HH CS
               dTDP_sugar_isom 159 ekDkaapsla 168
                                   +kDk++p+++
  gi|91774154|ref|YP_566846.1| 168 DKDKELPTFE 177
                                   *******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1269.37
//
Query:       gi|91774155|ref|YP_566847.1|  [L=313]
Description: NAD-dependent epimerase/dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-57  195.9   0.0    5.1e-57  193.8   0.0    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.1e-47  162.6   0.0    1.3e-47  162.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.2e-11   41.4   0.0    1.1e-10   41.0   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    3.2e-09   36.4   0.0    9.7e-05   21.6   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.4e-08   32.0   0.0    8.8e-08   31.6   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    2.8e-05   23.4   0.0     0.0047   16.1   0.0    2.3  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.072   12.5   0.0       0.12   11.9   0.0    1.3  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 !  193.8   0.0     2e-60   5.1e-57       1     332 []       4     302 ..       4     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 193.8 bits;  conditional E-value: 2e-60
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG+aGf  s++++lLl+kg+ev+ ++++     tg+++++a++     ++n++++++D++       l+ + ++d +++
  gi|91774155|ref|YP_566847.1|   4 LVTGGAGFMPSHMCDLLLSKGHEVVCVDNLV----TGNMDNMAHHM--ADKDNFTFINHDISK-----PLFLDEDIDYIFH 73 
                                   9***********************9987654....45555555433..34689********98.....789999******* PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.....S-----SHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.....tpfyPrsPYaaaK 157
                                   +A        +e P +t++v +lGt+++L ++++ g    +r++ aStsEvYG++   pq E+     + + Pr  Y  aK
  gi|91774155|ref|YP_566847.1|  74 MASPASPVDYLEFPIQTLKVGALGTYNMLGLAKEKG----ARILLASTSEVYGDPLVNPQPEEywgnvNTIGPRGVYDEAK 150
                                   ***9766666**********************9855....7*******************99888888999********** PP

                                   HHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHH CS
                 GDP_Man_Dehyd 158 lyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlq 238
                                    ya+ i+++y++ +++ + + ++fn+++pr+  +   r ++++v ++++g+ +++++G+++++R++ +v+D ve++ +++ 
  gi|91774155|ref|YP_566847.1| 151 RYAEAITMAYHRYHNIDTRIVRIFNTYGPRMRGN-DGRVVPNFVNQALKGE-DITVYGDGSQTRSFCYVSDEVEGIYRLMM 229
                                   ******************************9887.99*************8.8999************************* PP

                                   CSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH-- CS
                 GDP_Man_Dehyd 239 qdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgW 319
                                   +d  + ++i++ ++ sv ef+e  ++ +g                   ++  + +d  ++     + +  d++kak+ LgW
  gi|91774155|ref|YP_566847.1| 230 SDYCDPVNIGNPNEISVLEFAETVIELTGS------------------SSNIIYCDLPQDD---PKVRRPDITKAKKLLGW 289
                                   *****************9999965554443..................2334555554443...356778*********** PP

                                   --SS-HHHHHHHH CS
                 GDP_Man_Dehyd 320 kpkvsfeelvrem 332
                                   +pkv+++++++++
  gi|91774155|ref|YP_566847.1| 290 EPKVDLQDGLEKT 302
                                   *********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 !  162.3   0.0   5.2e-51   1.3e-47       2     228 ..       4     230 ..       3     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 5.2e-51
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                     Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                   lVtG++Gf+ s++++ ll+kg+ev+++d+l +++  +  ++       ++++ d+ +      lf +e++d+++h+A  ++
  gi|91774155|ref|YP_566847.1|   4 LVTGGAGFMPSHMCDLLLSKGHEVVCVDNLVTGNMDNMAHHMadkdnfTFINHDISK-----PLFLDEDIDYIFHMASPAS 79 
                                   8*****************************888888887777987777777777775.....567777************* PP

                                   HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS--.--SSHHHHHHHHHHHHHHH CS
                     Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgpl.kpnspYaaaKlageklvea 155
                                   + ++ e p ++++  + gt+n+l  a+++g+ r+l +s+sevYG++   p  ee+  + ++  p+  Y  aK+++e ++ a
  gi|91774155|ref|YP_566847.1|  80 PVDYLEFPIQTLKVGALGTYNMLGLAKEKGA-RILLASTSEVYGDPLVNPqPEEYWGNVNTiGPRGVYDEAKRYAEAITMA 159
                                   *******************************.************998866556776666667******************* PP

                                   HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                     Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                   y++ +++++ i+r+fn yGpr   g++ rv+p +++++l+g+ ++t++gdg++ R f+yv+D +e+i++++  
  gi|91774155|ref|YP_566847.1| 160 YHRYHNIDTRIVRIFNTYGPR-MRGNDGRVVPNFVNQALKGE-DITVYGDGSQTRSFCYVSDEVEGIYRLMMS 230
                                   ********************9.8888****************.*************************99977 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 !   41.0   0.0   4.3e-14   1.1e-10       1     219 [.       4     218 ..       4     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 4.3e-14
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegvdvvihlaslvd 78 
                                   +vtGgaGF+ ++++  L++ ++  ev  +D     ++ + ++++  k+   +i+ D+ +   l+e   ++d ++h+as   
  gi|91774155|ref|YP_566847.1|   4 LVTGGAGFMPSHMCDLLLSKGH--EVVCVDNLVTGNMDNMAHHMADKDnftFINHDISKPLFLDE---DIDYIFHMASPAS 79 
                                   69******************95..999999555555544444444444455************96...78999***99665 PP

                     3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngd..Eeleyesl..hqdaypesKalaE 154
                                            +  kv   GT n+l  ++++g r+l+  S+ ev g+     +++n +  E +   ++  +  +y e K+ aE
  gi|91774155|ref|YP_566847.1|  80 PVDyLEFPIQTLKVGALGTYNMLGLAKEKGARILL-ASTSEVYGD-----PLVNPQpeEYWGNVNTigPRGVYDEAKRYAE 154
                                   5551444456899*****************99875.9999*9999.....66655410555444446799*********** PP

                     3Beta_HSD 155 klvlkaNgrtlknggrlyTcaLRpagiyGeg....dkllvpllkqlaklglalfkigdeevlsdrvYvg 219
                                   ++ ++      +n   + T  +R    yG++    d ++vp +++ a +g+ +  +gd +++ ++ Yv 
  gi|91774155|ref|YP_566847.1| 155 AITMAYHR--YHN---IDTRIVRIFNTYGPRmrgnDGRVVPNFVNQALKGEDITVYGDGSQTRSFCYVS 218
                                   98776655..555...58999*********733334477888888888888****************96 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0     2e-05     0.052       2     127 ..       4     116 ..       3     127 .. 0.79
   2 !   21.6   0.0   3.8e-08   9.7e-05     133     251 ..     141     261 ..     137     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                   EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEE CS
               Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvf 82 
                                   lvtG++G + s++++ +l+k  + + + +    +++++++++    +k+++++          +++  + ++ + ++d++f
  gi|91774155|ref|YP_566847.1|   4 LVTGGAGFMPSHMCDLLLSKGHEVVCVDNLVTGNMDNMAHHMA---DKDNFTFI---------NHDISKPLFLDEDIDYIF 72 
                                   8******************999999998899999999999873...34344222.........455556666677899*** PP

                                   E----.--HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE CS
               Polysacc_synt_2  83 haAAl.KhVPlveenpleaiktNvlgtenvieaaieagvkkvvliS 127
                                   h A     V  +e +p++++k   lgt n++  a+e+g + ++l S
  gi|91774155|ref|YP_566847.1|  73 HMASPaSPVDYLE-FPIQTLKVGALGTYNMLGLAKEKGAR-ILLAS 116
                                   *998515577776.699*****************999865.44445 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 3.8e-08
                                   S--SHHHHHHHHHHHHHHHGGG--SSS--EE..EEEEE-EET.TGTTSSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHH CS
               Polysacc_synt_2 133 nPtnvmGatKrlaekllqalakeseekktkf..vvvRfGNVl.gSrGSviplFkkqikeggpvtv.TdpemtRyfmtieea 209
                                    P  v+  +Kr+ae +++a+++++ + +t++  ++  +G  + g  G v+p F +q  +g+++tv  d + tR f  +++ 
  gi|91774155|ref|YP_566847.1| 141 GPRGVYDEAKRYAEAITMAYHRYH-NIDTRIvrIFNTYGPRMrGNDGRVVPNFVNQALKGEDITVyGDGSQTRSFCYVSDE 220
                                   68889999**************99.444444113446887664778*******************55889*********** PP

                                   HHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH........ CS
               Polysacc_synt_2 210 vqLvlqalalakggeifvldmGepvkivdlakalielsglee 251
                                   v+ +   +       + + +  + +++++ a+++iel+g ++
  gi|91774155|ref|YP_566847.1| 221 VEGIYRLMMSDYCDPVNIGNP-NEISVLEFAETVIELTGSSS 261
                                   ***999998888888988888.88999999******999765 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 !   31.6   0.0   3.4e-11   8.8e-08       1     239 [.       1     264 [.       1     292 [. 0.84

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.4e-11
                                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT................T--TTSHHHHHHHHHHH--SEEEE------.H CS
                 RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre................eldltdaeavaellkeakpdvvvnaAAyta.v 64 
                                   m+ lvtG+ G + s++ ++l ++g+ev+ +++                 ++ + + +  + l+ + + d + ++A     v
  gi|91774155|ref|YP_566847.1|   1 MRTLVTGGAGFMPSHMCDLLLSKGHEVVCVDNLvtgnmdnmahhmadkdNFTFINHDISKPLFLDEDIDYIFHMASPASpV 81 
                                   899***************************88789999999999998887778888888889999**********976526 PP

                                   HHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-.....TTS-B-TTS----SSHHHHHHHHHHHHHHH.. CS
                 RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGe.....kkrpYeeddetsPlnvYGrtKlaGEqavla.. 138
                                   D  E  + +  +v a ++ ++  +a++ ga ++  St  V+         ++ + + ++ +P++vY ++K   E    a  
  gi|91774155|ref|YP_566847.1|  82 DYLE-FPIQTLKVGALGTYNMLGLAKEKGARILLASTSEVYGDPlvnpqPEEYWGNVNTIGPRGVYDEAKRYAEAITMAyh 161
                                   7776.58899******************************96658877455559999********************9944 PP

                                   ..H-SSEEEEEE-SEESS....SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE CS
                 RmlD_sub_bind 139 ..agkkalivRtswvyge....kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyH 211
                                     ++ ++ ivR+   yg     ++   v ++++ a + e ++v  D  q++s  ++ d  e +  l+    +         
  gi|91774155|ref|YP_566847.1| 162 ryHNIDTRIVRIFNTYGPrmrgNDGRVVPNFVNQALKGEDITVYGDgsQTRSFCYVSDEVEGIYRLMMSDYC-----DPVN 237
                                   434446678999999998764445568999*************99977888999999999999999998888.....4456 PP

                                   ---BS-EEHHHHHHHHHHHHCHTTSEEE CS
                 RmlD_sub_bind 212 lanegetswlefArailkeagadseevk 239
                                   ++n +e+s lefA+ +++ +g++s ++ 
  gi|91774155|ref|YP_566847.1| 238 IGNPNEISVLEFAETVIELTGSSS-NII 264
                                   899**************9999865.444 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0047        12       1      24 [.       5      29 ..       5      49 .. 0.82
   2 !   16.1   0.0   1.8e-06    0.0047      84     208 ..      64     178 ..      55     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0047
                                  EE-TTSHHHHHHHHHHHHHS-.T.E CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev.k 24
                                  +TG+ GF+ +++   LL++  ev  
  gi|91774155|ref|YP_566847.1|  5 VTGGAGFMPSHMCDLLLSKGHEVvC 29
                                  7****************99886534 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.8e-06
                                   HHHH--EEEE--SS...-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HH CS
                 NAD_binding_4  84 laeevdviihsaAt...vnfdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekl 161
                                   l e +d i+h+a     v++ e   + l+v  +Gt ++l lak+  +   +l  ST+ v+g+   + +            +
  gi|91774155|ref|YP_566847.1|  64 LDEDIDYIFHMASPaspVDYLEFPIQTLKVGALGTYNMLGLAKEKGA--RILLASTSEVYGDPLVNPQ-----------PE 131
                                   56889*****9865112666665567999**************6544..5999***999999996542...........24 PP

                                   H--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                 NAD_binding_4 162 dederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                   +     +  g    Y   K  aE +  +++r +++ + ivR+ + +g
  gi|91774155|ref|YP_566847.1| 132 EYWGNVNTIGPRGVYDEAKRYAEAITMAYHRYHNIDTRIVRIFNTYG 178
                                   45555566677889***************************866665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.5e-05      0.12       4      64 ..       4      64 ..       2      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                                  EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHH CS
                     adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreev 64
                                  lvtG+++ +   +++ l+++G +vv+vd+        +++  ++++++++i+ D+++   +
  gi|91774155|ref|YP_566847.1|  4 LVTGGAGFMPSHMCDLLLSKGHEVVCVDNLVTGNMDNMAHHMADKDNFTFINHDISKPLFL 64
                                  8*****99******************999887766666666667899********987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1951.64
//
Query:       gi|91774156|ref|YP_566848.1|  [L=95]
Description: hypothetical protein Mbur_2235 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 728.96
//
Query:       gi|91774157|ref|YP_566849.1|  [L=328]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-23   83.7   0.0    1.8e-23   83.4   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.5e-06   28.7   0.0    1.8e-06   28.4   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0058   15.6   1.3     0.0081   15.1   1.3    1.2  1  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
       0.12   12.1  15.9       0.19   11.5   5.9    3.8  2  Hexapep          Bacterial transferase hexapeptide (six repea
       0.19   12.1   3.7       0.39   11.1   3.7    1.5  1  Bactofilin       Polymer-forming cytoskeletal
       0.82    7.7   6.4        2.5    6.1   6.4    1.7  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 !   83.4   0.0   5.9e-27   1.8e-23      25     246 ..       2     213 ..       1     215 [. 0.89

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 5.9e-27
                                   SEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTSSE..E CS
               NTP_transferase  25 vpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelledeksdel 105
                                   v ++gk ++i + l r+++ + eeii+v+ +++++++  ++ +++    +++++ ++ + g+ +++++a++ ++d+     
  gi|91774157|ref|YP_566849.1|   2 VYIAGK-PVIGHILDRMIDLKPEEIILVVGYRKEQIIS-YVDRNYSDIFKITYVEQNHQLGLGHSIYVAKDAVGDSP---- 76 
                                   678888.*****************99999977776665.55555544458************************999.... PP

                                   EEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETT. CS
               NTP_transferase 106 vlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnse. 185
                                   +++  gD+++k  y ++ +k+ ++++ +  ++g+ +v+++++yG++e d+ + + ++vEKPk +  s+l  +G+Y+ ++  
  gi|91774157|ref|YP_566849.1|  77 IMITLGDMIFKAGYLDFYQKHFNNGN-CAGSIGVWEVDAPEKYGIVELDG-ECISKMVEKPKYPM-SNLGIAGVYFLKEPs 154
                                   9***********************99.9*********************8.59***********9.***********9651 PP

                                   HHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHHH CS
               NTP_transferase 186 vllflak.dleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanekla 246
                                   vl  +++  ++e +  e ++td+l+ ++++g++   f  +    W D G   slle n+ l+
  gi|91774157|ref|YP_566849.1| 155 VLFDILEkMVDEHTGNEIQLTDALQGMVSSGHRLKHFYVSS---WYDCGHSTSLLETNRVLL 213
                                   55555677999999*****************9999988888...************998665 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 !   28.4   0.0   5.9e-10   1.8e-06      21     110 ..       4      97 ..       1     173 [. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.9e-10
                                   CCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC.....TS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEET CS
                  NTP_transf_3  21 lggkpllervldalraagvdevvvvggd..eevlaalarl.....gvrvvededpgkgplaslaaalraaadadavlvlac 94 
                                   ++gkp++ ++ld++ +++ +e+++v+g+  e++ ++++r      ++++ve+  ++ g ++s++ a +a+ ++++++++++
  gi|91774157|ref|YP_566849.1|   4 IAGKPVIGHILDRMIDLKPEEIILVVGYrkEQIISYVDRNysdifKITYVEQN-HQLGLGHSIYVAKDAV-GDSPIMITLG 82 
                                   79************************996567888776665555578888886.699************9.9********* PP

                                   T-TT--HHHHHHHHHC CS
                  NTP_transf_3  95 DmPlltpelverllaa 110
                                   Dm++ ++  ++   ++
  gi|91774157|ref|YP_566849.1|  83 DMIF-KAGYLDFYQKH 97 
                                   **98.55555555555 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.3   2.7e-06    0.0081     268     318 ..     244     303 ..     184     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                    Fucokinase 268 ekk..........kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsgleless 318
                                   ++k           ++++++nSv+ ++vs++e+s i  s +  n  igs+s + g++l+ss
  gi|91774157|ref|YP_566849.1| 244 NTKesviiepvsiGNGVIITNSVVGPHVSIAENSNIDGSIVA-NSIIGSGSAIKGVNLRSS 303
                                   222455666666788999999999999999999999877665.666999999999999976 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.9   6.2e-05      0.19       4      35 ..     250     280 ..     247     281 .. 0.77
   2 ?    2.6   2.3      0.04   1.2e+02       2      28 ..     287     311 ..     283     313 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                                   EETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   I + v Ig++++i  n ++G++v I++++ i 
  gi|91774157|ref|YP_566849.1| 250 IIEPVSIGNGVII-TNSVVGPHVSIAENSNID 280
                                   5566889999999.666699999999999885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.04
                                   EEEETTEEE-TTEEEETTEEE-TTEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                   ++IGs++ I  ++ +    +IGd+v +
  gi|91774157|ref|YP_566849.1| 287 SIIGSGSAIK-GVNL-RSSIIGDDVNV 311
                                   5677777777.7777.44448888766 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.7   0.00013      0.39       8      65 ..     238     301 ..     235     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                    Bactofilin   8 kikGelevegdlri......dGkv.eGdieakgklvvgeggkvegnikaeevvvaGtvkGnveae 65 
                                   +++G+l++++++ i      +G + + +   + ++ ++e+++++g+i a++++ +G+    v+ +
  gi|91774157|ref|YP_566849.1| 238 EFNGNLNTKESVIIepvsigNGVIiTNS-VVGPHVSIAENSNIDGSIVANSIIGSGSAIKGVNLR 301
                                   699***********66666666542333.45669**********************965555555 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.4   0.00084       2.5     209     268 ..     245     308 ..     213     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00084
                       DUF4954 209 tinSskeapveiGegViledfiissGskik.....dgavisrcfvGqavklkkqfsaedsllfaN 268
                                   t +S   +pv+iG+gVi++++++    +i+     dg+++ ++++G +  +k +  +  s++++ 
  gi|91774157|ref|YP_566849.1| 245 TKESVIIEPVSIGNGVIITNSVVGPHVSIAensniDGSIVANSIIGSGSAIK-GVNLRSSIIGDD 308
                                   33566679**************998888863333368888889999888875.556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2390.81
//
Query:       gi|91774158|ref|YP_566850.1|  [L=267]
Description: glycosyl transferase family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   98.4   0.0      5e-28   98.0   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-08   34.6   0.0    2.5e-08   34.1   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.5e-07   30.4   0.1    3.7e-07   29.9   0.1    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0052   16.3   0.0     0.0084   15.6   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   1.1e-31     5e-28       1     167 [.       3     169 ..       3     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 1.1e-31
                                   EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH-- CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraat 79 
                                   sv+ip+yNe + +   l  + +   +  + feii+v+DgStD+t   ++++a++ +++++i  +en+Gk++a  +g +aa+
  gi|91774158|ref|YP_566850.1|   3 SVIIPAYNEGHHIHDNLLEINDElrTFCDSFEIIFVNDGSTDHTLVEAKRAAEKTDNIKIISYTENQGKGNATIEGYKAAS 83 
                                   8********777777777777777777****************************************************** PP

                                   SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCE CS
               Glycos_transf_2  80 gdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaal 160
                                     +i +lDaD+ ++p+ +e+l++ + ++gad v+++ ++  +  + ++  +r  + +r y+   k   +  +s+   +  l
  gi|91774158|ref|YP_566850.1|  84 KGFISILDADLDIPPKQIEPLLKMISETGADFVIQSKRHPHSCVKGFPIKRR--FLSRSYNLLIKLLFNLPVSDTQVGVKL 162
                                   ***********************************98877777777776665..89************************* PP

                                   EEEHHHH CS
               Glycos_transf_2 161 lrreale 167
                                   +r+++++
  gi|91774158|ref|YP_566850.1| 163 YRKDVVN 169
                                   **99985 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 !   34.1   0.0   5.5e-12   2.5e-08       4     120 ..       2     116 ..       1     142 [. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.5e-12
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey...prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                   l+v++p++ne   +++ l ++    +   +++e+++v d+s+++tl +a+ +a++ ++  ++++  ++n   +gk +a+ e
  gi|91774158|ref|YP_566850.1|   2 LSVIIPAYNEGHHIHDNLLEINDELRtfcDSFEIIFVNDGSTDHTLVEAKRAAEKTDN--IKIISYTEN---QGKGNATIE 77 
                                   89**********9999777766432224799*******************98888877..589988886...4689999** PP

               Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgav 120
                                   +++a++  ++ ++D+D  + P  ++ ll  +   ++++v
  gi|91774158|ref|YP_566850.1|  78 GYKAASKGFISILDADLDIPPKQIEPLLKMISETGADFV 116
                                   ************************999999855566666 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 !   29.9   0.1   8.3e-11   3.7e-07       1     107 [.       3     109 ..       3     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.3e-11
               Glyco_tranf_2_2   1 svviplraseerhyieervlqka...kyydeeielivvddgSsekfleevssiidlnllv...ylkdeddkayslaaarNr 75 
                                   sv+ip +++   h+i++ +l+++     + + +e+i+v+dgS++++l e +   ++  ++   ++ +      +++ a   
  gi|91774158|ref|YP_566850.1|   3 SVIIPAYNEG--HHIHDNLLEINdelRTFCDSFEIIFVNDGSTDHTLVEAKRAAEKTDNIkiiSYTE----NQGKGNATIE 77 
                                   799*999865..56*****7765111456899*****************999887766552133333....46999***** PP

               Glyco_tranf_2_2  76 GaskaesdlvlFlDaDcfissDkfekilklit 107
                                   G + a   +++ lDaD  i + ++e +lk+i 
  gi|91774158|ref|YP_566850.1|  78 GYKAASKGFISILDADLDIPPKQIEPLLKMIS 109
                                   *****************************986 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 !   15.6   0.0   1.9e-06    0.0084      18      65 ..      71     118 ..      61     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
               Glyco_transf_21  18 KvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVts 65 
                                   K n+ + +++aa + ++ i+D+d  ++p+ +e ll++++++++ +V +
  gi|91774158|ref|YP_566850.1|  71 KGNATIEGYKAASKGFISILDADLDIPPKQIEPLLKMISETGADFVIQ 118
                                   8999************************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1851.94
//
Query:       gi|91774159|ref|YP_566851.1|  [L=232]
Description: hypothetical protein Mbur_2238 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1681.60
//
Query:       gi|91774160|ref|YP_566852.1|  [L=88]
Description: hypothetical protein Mbur_2239 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-10   40.6   0.0    2.7e-10   40.4   0.0    1.1  1  DUF3303   Protein of unknown function (DUF3303)


Domain annotation for each model (and alignments):
>> DUF3303  Protein of unknown function (DUF3303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.5e-14   2.7e-10      25      89 ..      18      80 ..      10      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.5e-14
                       DUF3303 25 lesGaledkpegfellgrvhapgegrgfaiveaddakalfkhfapWralfGiefeitPvltdeev 89
                                  le +++  +p g+++++ ++    gr f++ e+dda+al+   +pW++   + +e  Pv+ + ++
  gi|91774160|ref|YP_566852.1| 18 LEHFKEIKMPAGIKVHNQWVDLTGGRYFILYECDDAEALATFNLPWSDV--CYIETVPVMGSTDF 80
                                  788888899****************************************..*********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 00:00:00.45
# Mc/sec: 593.45
//
Query:       gi|91774161|ref|YP_566853.1|  [L=88]
Description: hypothetical protein Mbur_2240 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-10   39.4   0.0    6.6e-10   39.1   0.0    1.1  1  DUF3303   Protein of unknown function (DUF3303)
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.013   15.4   0.0    1.3  1  GYD       GYD domain
      0.042   13.7   0.0      0.044   13.6   0.0    1.1  1  AUX_IAA   AUX/IAA family


Domain annotation for each model (and alignments):
>> DUF3303  Protein of unknown function (DUF3303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.1e-13   6.6e-10      25      89 ..      18      80 ..      11      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.1e-13
                       DUF3303 25 lesGaledkpegfellgrvhapgegrgfaiveaddakalfkhfapWralfGiefeitPvltdeev 89
                                  le +++  +p g++++  ++     r f++ e+dda+a++   +pW++   + +e  Pv+ + e+
  gi|91774161|ref|YP_566853.1| 18 LEHFKELKMPAGVKVHDQWIDLTGSRYFILYECDDAEAMATFNLPWSDV--CYIETVPVMKSTEF 80
                                  677888889****************************************..***********997 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.2e-06     0.013      26      88 ..      21      81 ..       7      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
                           GYD 26 kealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetlrafteeefd 88
                                   ++l+  +G+k++++++ l    +++++E +D e++a++ l  +       et+++++ +ef 
  gi|91774161|ref|YP_566853.1| 21 FKELKMPAGVKVHDQWIDLTGSRYFILYECDDAEAMATFNLPWSDVC--YIETVPVMKSTEFI 81
                                  45666778*******************************99877654..34677777777766 PP

>> AUX_IAA  AUX/IAA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.3e-06     0.044     189     237 .]      39      86 ..      16      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AUX_IAA 189 ldgseyvltYeDkdgDwmLvGDvPWemFvesvkrLrimkgseaiglapr 237
                                   l+gs y + Ye  d++ m    +PW+  v  +  + +mk+ e i+l  r
  gi|91774161|ref|YP_566853.1|  39 LTGSRYFILYECDDAEAMATFNLPWSD-VCYIETVPVMKSTEFISLMSR 86 
                                   789**********************84.55566678*******999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 590.70
//
Query:       gi|91774162|ref|YP_566854.1|  [L=345]
Description: hypothetical protein Mbur_2241 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-32  110.2   0.0    1.2e-31  109.6   0.0    1.3  1  DUF523    Protein of unknown function (DUF523)
    5.2e-19   68.6   2.1    1.1e-18   67.7   2.1    1.5  1  DUF1722   Protein of unknown function (DUF1722)


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 !  109.6   0.0   1.3e-35   1.2e-31       1     137 []      16     156 ..      16     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.3e-35
                        DUF523   1 ilvSaCLlgekvrydgkakksevleeelkelvkeelvpvCPEvaggLptPRepael.....akr.vlkkegedvtealekg 75 
                                   i+vS+CL +e+vrydg+  +++++++ +++++  ++++vCPEv++gL++PR+++++     +kr ++  +++d+te++ ++
  gi|91774162|ref|YP_566854.1|  16 IVVSKCLEFENVRYDGSVIHCQTVRD-MMQFA--DFIKVCPEVEIGLGVPRDSMRIvlvdgKKRlIQPITQNDLTEKMDNF 93 
                                   89******************877777.77777..**************************9778899************** PP

                        DUF523  76 aeealeelkeeeikgailkekSPSCGveki..Ydgtfskkl.vegeGvfaallkeegievpseee 137
                                   ++++l+el    ++g+i+k++SP+ G+++i  Y+ ++++    +g+G+fa+ + +++i++p+ee+
  gi|91774162|ref|YP_566854.1|  94 TNTFLKELP--PVDGFIFKSGSPTIGMRDIkiYSDKVKGLVvDRGNGFFAEKILRDYIDYPMEED 156
                                   ********9..5*****************999*99999988789*****************9985 PP

>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   2.1   1.2e-22   1.1e-18       2     117 .]     199     314 ..     198     314 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.2e-22
                       DUF1722   2 yllmahsqkeyrelgrlvanakkepleelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqelleliekYr 82 
                                   yl+  +++++  +l++lv+n+++ +++++++eYe+ + +++s++++ ++ i+v++  +  + ++l+  e+++l+++i+kY+
  gi|91774162|ref|YP_566854.1| 199 YLFRLYNHDISLKLDELVENKNSLKFDAILKEYERIMPHIFSREPKSNEFIDVANETFLNIVSSLNIVEEKYLAQIIKKYT 279
                                   99******************************************************************************* PP

                       DUF1722  83 egkvplsvpltlLkhyarkydneylleqtylnpyP 117
                                   +++++++++l++Lk y++++ ++  + ++++ pyP
  gi|91774162|ref|YP_566854.1| 280 DNRLTYDALLEILKFYVMRFSDSKKEYSRLFFPYP 314
                                   **********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2400.42
//
Query:       gi|91774163|ref|YP_566855.1|  [L=497]
Description: replication factor C large subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-11   42.9   0.0    1.6e-10   41.5   0.0    1.8  1  AAA              ATPase family associated with various cellul
    3.3e-08   33.7   0.0    6.5e-08   32.7   0.0    1.5  1  Rad17            Rad17 P-loop domain
    8.6e-08   32.5   0.4     0.0059   16.9   0.0    4.0  4  AAA_22           AAA domain
    2.1e-05   25.0   0.0    0.00073   20.0   0.0    2.4  2  AAA_16           AAA ATPase domain
    0.00017   21.4   0.0    0.00052   19.8   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00021   21.1   1.0    0.00061   19.6   1.0    1.8  1  AAA_30           AAA domain
     0.0008   19.4   0.0      0.002   18.2   0.0    1.7  1  AAA_14           AAA domain
     0.0021   18.2   0.0     0.0054   16.9   0.0    1.7  1  AAA_33           AAA domain
     0.0036   17.2   0.0      0.038   13.9   0.0    2.3  2  NACHT            NACHT domain
     0.0037   17.1   0.2        2.4    7.9   0.0    2.9  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0056   17.1   0.1      0.034   14.5   0.0    2.4  2  RNA_helicase     RNA helicase
     0.0075   16.4   0.0       0.02   15.0   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0077   16.0   0.0      0.017   14.8   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   16.3   0.3      0.048   14.2   0.0    2.2  2  AAA_18           AAA domain
      0.013   15.5   0.0      0.036   14.1   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      0.016   14.4   0.0      0.027   13.7   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
      0.023   15.0   0.0      0.076   13.4   0.0    1.9  1  AAA_assoc_2      AAA C-terminal domain
      0.024   14.2   0.0      0.049   13.2   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.037   12.9   0.0      0.057   12.2   0.0    1.2  1  PPV_E1_C         Papillomavirus helicase
      0.053   13.1   0.6       0.35   10.4   0.1    2.2  2  AAA_25           AAA domain
      0.059   13.4   0.0       0.14   12.1   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.06   13.1   0.0       0.21   11.3   0.0    1.9  2  Cytidylate_kin   Cytidylate kinase
      0.061   12.5   0.0       0.45    9.6   0.0    2.1  2  NB-ARC           NB-ARC domain
      0.066   13.1   0.0       0.13   12.2   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.085   11.8   0.0       0.16   10.9   0.0    1.3  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
       0.13   12.7   1.2       0.99    9.9   0.0    2.8  3  ABC_tran         ABC transporter
       0.36   11.1   2.8       0.73   10.1   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 !   41.5   0.0   2.4e-13   1.6e-10       1      74 [.      46     119 ..      46     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.4e-13
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS......TSEEEEEETGGGHHHHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka......kpsilfiDEidalaksr 74 
                                   ++l+Gp G+GKT++a+a+a++l+ e +e+++s+ +      ++  i+ +  +a++++      ++  +++DE+d+++++ 
  gi|91774163|ref|YP_566855.1|  46 IILHGPAGVGKTSAAHALARDLDWETIELNASDQR------TAGVIERVAGSASKMSsltgttAKRLIILDEADNIHGNA 119
                                   68*********************************......3444444444443333344443479**********9998 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   9.7e-11   6.5e-08       8      75 ..       6      73 ..       2     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.7e-11
                         Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75
                                  +W+eky+P+ + ++   kk + +++ew ++      +kr +++ GP+G gk+ + + L++ l  + +e
  gi|91774163|ref|YP_566855.1|  6 EWVEKYRPQSLTDIVGNKKSVVDMREWAQSWLSGTPEKRAIILHGPAGVGKTSAAHALARDLDWETIE 73
                                  7***************************99988888999*********************99888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.9e-06    0.0059       5      40 ..      43      79 ..      40     101 .. 0.74
   2 ?    5.6   0.0     0.028        18      91     105 ..     100     116 ..      73     124 .. 0.73
   3 ?    0.0   0.0       1.4   9.5e+02      44      80 ..     251     287 ..     225     298 .. 0.79
   4 ?    4.9   0.0     0.045        30      53     118 ..     351     424 ..     331     434 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.9e-06
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee..erp 40
                                  ++ ++++G++G+GKT  +  l++ ld ++ +e    + 
  gi|91774163|ref|YP_566855.1| 43 KRAIILHGPAGVGKTSAAHALARDLD-WETIELnaSDQ 79
                                  7899*******************995.66655555333 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.028
                        AAA_22  91 v...ielliiDEaqhlrs 105
                                       ++l+i+DEa+++ +
  gi|91774163|ref|YP_566855.1| 100 GttaKRLIILDEADNI-H 116
                                   044569*********9.4 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.4
                        AAA_22  44 fvtlpsstsskdllrellralglelkaerlsseelle 80 
                                   + t   ++++++l +++ ++l l+  +e++++e+l++
  gi|91774163|ref|YP_566855.1| 251 EATYGLDETPENLIHWIDENLPLQYGTEEGTQEDLIT 287
                                   55555667999**********9999998888888764 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.045
                        AAA_22  53 skdllrellralglelka....erlsseell.ealeqalrarav..ielliiDEaqhlr.seealeeLrsllnl 118
                                    +d++ ++++++ + +++    +r ++ +l+ ++le++  a++v     l iDE+ +l+ ++++ +++ ++++l
  gi|91774163|ref|YP_566855.1| 351 KRDMRDNIASKIADHANKsmrySRTDLAHLYgRMLEENEYAADVtfDLELSIDEMVYLTgKKKVTKDIQRIHDL 424
                                   67889999999999888899999********888888888888899899*********7668888888888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.1e-06   0.00073      18      49 ..      35      68 ..      26      83 .. 0.85
   2 ?    2.2   0.0      0.32   2.1e+02     117     168 ..      86     139 ..      69     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-06
                        AAA_16 18 rvrsgrp..elvllsGesGvGKsslvrellrale 49
                                  ++ sg+p  ++++l+G++GvGK+s + +l+r l 
  gi|91774163|ref|YP_566855.1| 35 SWLSGTPekRAIILHGPAGVGKTSAAHALARDLD 68
                                  567888888*******************999775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
                        AAA_16 117 srllellkrllallsrderplvlvlDdlq....wadeaslqllaaLlrlleskpll 168
                                   +r++   +++ +l+ ++++  +++lD+++     ad + + ++  + +++++ p++
  gi|91774163|ref|YP_566855.1|  86 ERVAGSASKMSSLTGTTAK-RLIILDEADnihgNADRGGARAIGGIIKNTDQ-PIV 139
                                   6777777778888888888.*********99998999888888888888776.555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   7.8e-07   0.00052       2      81 ..      12      97 ..      11     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.8e-07
                        RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl......kitsgPvlekagdlaal 78
                                  rP+sl++ +g +k   +++   ++  + + +   ++l+Gp G+Gkt+ a+ +a++l+ +        + ++ v+e+ +  a+ 
  gi|91774163|ref|YP_566855.1| 12 RPQSLTDIVGNKKSVVDMREWAQSWLSGTPEKRAIILHGPAGVGKTSAAHALARDLDWETielnasDQRTAGVIERVAGSASK 94
                                  9***********************99999999**********************99864311111122344566666555554 PP

                        RuvB_N 79 ltn 81
                                  +++
  gi|91774163|ref|YP_566855.1| 95 MSS 97
                                  444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.0   9.1e-07   0.00061      17      99 ..      42     114 ..      37     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.1e-07
                        AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEa 97 
                                   ++r  +l+GpAG GKt a  al++ ++ +  ++ + A+ ++ A v+++     as + +l+ ++++       +l+i DEa
  gi|91774163|ref|YP_566855.1|  42 EKRAIILHGPAGVGKTSAAHALARDLDWE--TIELNASDQRTAGVIERV-AGSASKMSSLTGTTAK-------RLIILDEA 112
                                   567899************99998877755..699************965.5589999999966665.......89999998 PP

                        AAA_30  98 gm 99 
                                     
  gi|91774163|ref|YP_566855.1| 113 DN 114
                                   54 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     3e-06     0.002       2      77 ..      43     116 ..      42     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3e-06
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklke.ekktylflDEiqevp 77 
                                   ++++++ G+  vGKT  ++ l+++l     +++++n  d+r++   +      + + ++  +   k++++lDE+ ++ 
  gi|91774163|ref|YP_566855.1|  43 KRAIILHGPAGVGKTSAAHALARDLD---WETIELNASDQRTAGVIERVaGSASKMSSLT-GtTAKRLIILDEADNIH 116
                                   6899******************9999...999******9999765533112223333332.246899******99985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.1e-06    0.0054       2      39 ..      46      90 ..      46     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.1e-06
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt.......lrrrlfg 39
                                  ++l+G++G+GK+  a+ l++ l++++++ ++       +++r++g
  gi|91774163|ref|YP_566855.1| 46 IILHGPAGVGKTSAAHALARDLDWETIELNAsdqrtagVIERVAG 90
                                  699********************9999888855555555555544 PP

>> NACHT  NACHT 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     0.038       1      26 [.      44      69 ..      44      79 .. 0.85
   2 ?    0.4   0.0       0.8   5.3e+02      73      99 ..      95     121 ..      75     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                                  SCEEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT  1 rlvilqGeaGsGKTtLlqklalawae 26
                                  r +il+G+aG+GKT  ++ la+++  
  gi|91774163|ref|YP_566855.1| 44 RAIILHGPAGVGKTSAAHALARDLDW 69
                                  579******************98865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.8
                                   HHHHCCSCCCEEEEEE-STT-SS-TCH CS
                         NACHT  73 wavllelperlLlilDglDelvtdlgq 99 
                                   ++ l+    + L+ilD +D ++   + 
  gi|91774163|ref|YP_566855.1|  95 MSSLTGTTAKRLIILDEADNIHGNADR 121
                                   667777788889********9985554 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.014       9.3      19      43 ..      43      67 ..      32      80 .. 0.86
   2 !    7.9   0.0    0.0036       2.4      85     162 ..      85     164 ..      68     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
               DNA_pol3_delta2 19 ahayLfeGdegigkkelalnlakal 43
                                  + a++++G++g+gk ++a +la+ l
  gi|91774163|ref|YP_566855.1| 43 KRAIILHGPAGVGKTSAAHALARDL 67
                                  579*******************987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
               DNA_pol3_delta2  85 ldqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsen..aifiLitsdtnklLktirSRcqelkfspl 162
                                   ++++    +++s  +    k++ii+++a++++ +A     + +    +n  + ++Li++d   l + +rS c elkf+++
  gi|91774163|ref|YP_566855.1|  85 IERVAGSASKMSSLTGTTAKRLIILDEADNIHGNADRGGARAIGGIIKNtdQPIVLIANDLYGLTPSVRSLCIELKFNSV 164
                                   4566666666667777788999999999999999876666666554333115699**********************975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   5.1e-05     0.034       1      25 [.      46      71 ..      46     119 .. 0.83
   2 ?   -1.6   0.1       5.4   3.6e+03      63      85 ..     446     469 ..     440     479 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakall.kk 25
                                  i+l+Gp+g+GK+++a+ La++l  ++
  gi|91774163|ref|YP_566855.1| 46 IILHGPAGVGKTSAAHALARDLDwET 71
                                  789******************97444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                  RNA_helicase  63 deenps.dlaelirlvsstpypln 85 
                                   ++++p+   ++l ++++stp + +
  gi|91774163|ref|YP_566855.1| 446 KKQTPDkKQMDLTQIINSTPQEDK 469
                                   444455588899999999987644 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     3e-05      0.02       5      83 ..      45     118 ..      42     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                                   -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...EEEEETGGG--- CS
                         AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...ivllDEidKihp 82 
                                    i+l gp gvGkt +a ala+ l+     + i ++as+  +    + +++r  g++  + +         + lDE d ih 
  gi|91774163|ref|YP_566855.1|  45 AIILHGPAGVGKTSAAHALARDLDW----ETIELNASDQRT----AGVIERVAGSASKMSSLTGTTakrLIILDEADNIHG 117
                                   68999*******************7....889999999988....888888888877777666666677***********8 PP

                                   - CS
                         AAA_2  83 k 83 
                                   +
  gi|91774163|ref|YP_566855.1| 118 N 118
                                   4 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.6e-05     0.017      46     117 ..      42     112 ..      21     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                     IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdl 117
                                   +k +i+l Gp+GvGK+  a al+++   + ++    + ++    ++r  +  +  + l+  ++ +l+ilD+ 
  gi|91774163|ref|YP_566855.1|  42 EKRAIILHGPAGVGKTSAAHALARDLDWETIELN-ASDQRTAGVIERVAGSASKMSSLTGTTAKRLIILDEA 112
                                   6889******************998755544433.3444455555566666666677788888888888885 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.2e-05     0.048       1      22 [.      46      67 ..      46      90 .. 0.88
   2 ?   -2.1   0.1       8.1   5.4e+03       9      62 ..     409     459 ..     409     476 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                  I+l G++GvGKt+ a++L++ l
  gi|91774163|ref|YP_566855.1| 46 IILHGPAGVGKTSAAHALARDL 67
                                  99****************9975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.1
                        AAA_18   9 vGKttlakeLskrlgfgvnlrdvakenglllevdpe....aldeskrldedkldklld 62 
                                   +GK  ++k +++         d+a+ ++ +l++d+     + +++k+  ++k++ l +
  gi|91774163|ref|YP_566855.1| 409 TGKKKVTKDIQRI-------HDLAQAKRRSLGRDEGkaffEKKPKKQTPDKKQMDLTQ 459
                                   5777777777665.......35555555555555554444344444444444444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.4e-05     0.036       2      78 ..      46     116 ..      45     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                   ++L Gp G+gK++ a  la+ l +e+ + + +++  ++ ++ r+     + + + s+l+   + +++++lDE ++++
  gi|91774163|ref|YP_566855.1|  46 IILHGPAGVGKTSAAHALARDLDWETIELNASDQR-TAGVIERVA----GSASKMSSLT-GTTAKRLIILDEADNIH 116
                                   79**********************99887776654.455666666....3444555566.66778888888888777 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     4e-05     0.027      16      83 ..       5      73 ..       1      97 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                        DUF815 16 lepveevdevklddLvgidkqkealventeqfleglpan.nvLLwGarGtGKSslvkallneyaeegLr 83
                                  +e ve++++ +l+d+vg +k   ++ e ++ +l+g+p +  ++L G  G+GK s  +al +++  e++ 
  gi|91774163|ref|YP_566855.1|  5 IEWVEKYRPQSLTDIVGNKKSVVDMREWAQSWLSGTPEKrAIILHGPAGVGKTSAAHALARDLDWETIE 73
                                  677899999999999**999999*************98625789***************9988777655 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.076      10      41 ..     187     219 ..     179     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..X CS
                   AAA_assoc_2  10 dalealaeladGDaRkaLnlLElaaeaaeak.e 41 
                                    +le lae a+GD R+a++ L+++a+  ++   
  gi|91774163|ref|YP_566855.1| 187 GVLEKLAESAGGDLRSAIKDLQAVATGRDEIhI 219
                                   5899******************99988765342 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.3e-05     0.049      32      76 ..      42      83 ..      26      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.3e-05
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsan 76
                                  +k+ ++l Gp+G+GKt+ ++ l + ld   + ++ +n s q +a 
  gi|91774163|ref|YP_566855.1| 42 EKRAIILHGPAGVGKTSAAHALARDLD---WETIELNASDQRTAG 83
                                  67899**********************...888888888888876 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.6e-05     0.057     253     289 ..      34      70 ..      22      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                      PPV_E1_C 253 kefLkgvPkknclvllGppntGkslfamslikfLkGk 289
                                   +++L g+P k +++l+Gp+  Gk+  a +l + L+ +
  gi|91774163|ref|YP_566855.1|  34 QSWLSGTPEKRAIILHGPAGVGKTSAAHALARDLDWE 70 
                                   78************************99999877755 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00053      0.35      27      55 ..      38      65 ..      27      68 .. 0.86
   2 ?    0.2   0.0      0.73   4.9e+02     143     172 ..     104     134 ..      68     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00053
                        AAA_25 27 kgllpagelallaGapgtGKttlaldlal 55
                                   g  p++  ++l G+ g+GKt +a  la 
  gi|91774163|ref|YP_566855.1| 38 SGT-PEKRAIILHGPAGVGKTSAAHALAR 65
                                  555.9999****************99997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.73
                        AAA_25 143 vrlvviDplsralgg.densnsdvgalveal 172
                                    rl+++D  + ++g+ d   ++++g ++++ 
  gi|91774163|ref|YP_566855.1| 104 KRLIILDEADNIHGNaDRGGARAIGGIIKNT 134
                                   589***********99988888888888765 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   0.00022      0.14       6      46 ..      28      70 ..      23      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                  HHHHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE  6 etealgkklakal..gdvilLeGdLGaGKTtlvrglakalgve 46
                                  ++++ +++  + +  +++i+L+G+ G+GKT  +++la+ l+ e
  gi|91774163|ref|YP_566855.1| 28 DMREWAQSWLSGTpeKRAIILHGPAGVGKTSAAHALARDLDWE 70
                                  566666666554566678********************99876 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.21       1      28 [.      46      73 ..      46      89 .. 0.90
   2 ?   -3.4   0.0       9.8   6.5e+03     103     121 ..     197     215 ..     183     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                  EEEE-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyld 28
                                  i + GPag GK s a+ala+ l+++ ++
  gi|91774163|ref|YP_566855.1| 46 IILHGPAGVGKTSAAHALARDLDWETIE 73
                                  5688*******************99876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.8
                                   HHHHHTT-BSSBEEEEESS CS
                Cytidylate_kin 103 vkklrelvkkarvvveGRD 121
                                      lr+++k+ + v+ GRD
  gi|91774163|ref|YP_566855.1| 197 GGDLRSAIKDLQAVATGRD 215
                                   5678999999999999999 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   0.00068      0.45       8      43 ..      33      66 ..      27      75 .. 0.77
   2 ?   -0.2   0.0       0.7   4.6e+02     140     185 ..     411     459 ..     403     467 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00068
                                  HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                   + +L+  + +++  + l+G +GvGKt  a+   ++
  gi|91774163|ref|YP_566855.1| 33 AQSWLS--GTPEKRAIILHGPAGVGKTSAAHALARD 66
                                  556777..55555699***********988877766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.7
                                   BCCCCCCS-S-..EEEEEESS--HHHHHHHHHHCCTS-GGCHH...CHH CS
                        NB-ARC 140 deevanavsat..sekievelLekdeawellenkvfekkleekes.lee 185
                                   +++v++ ++      + + ++L  de+  ++e+k  +++ ++k+  l +
  gi|91774163|ref|YP_566855.1| 411 KKKVTKDIQRIhdLAQAKRRSLGRDEGKAFFEKKPKKQTPDKKQMdLTQ 459
                                   56677777666323456789*************9988877766433444 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   0.00019      0.13      98     136 ..      42      80 ..       7      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                   TTSEEEEECSTTSSHHHHHHHHCTT-----S-------- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevseklgr 136
                                   +++ ++l G+ GvGK++   al+ +l+ +t e+ ++++r
  gi|91774163|ref|YP_566855.1|  42 EKRAIILHGPAGVGKTSAAHALARDLDWETIELNASDQR 80 
                                   56899************************9999888776 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 ?   10.9   0.0   0.00024      0.16      37      77 ..      48      88 ..      40      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                         AAA_6 37 paGpagtGKtEtvkdLakalakqvvvfncsdqldykslgki 77
                                  ++Gpag GKt +   La+ l   ++ +n sdq ++  ++++
  gi|91774163|ref|YP_566855.1| 48 LHGPAGVGKTSAAHALARDLDWETIELNASDQRTAGVIERV 88
                                  68*****************************9988877765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0015      0.99      11      45 ..      43      75 ..      38      99 .. 0.77
   2 ?   -2.3   0.0       9.1   6.1e+03     126     136 ..     103     113 ..      99     114 .. 0.82
   3 ?   -0.6   0.5       2.6   1.8e+03      38      51 ..     435     448 ..     343     494 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0015
                                  TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 11 gekvaivGenGaGKStLlkllagllkpteGeilld 45
                                   + + + G+ G GK++ + +la+ l+++  +i+l+
  gi|91774163|ref|YP_566855.1| 43 KRAIILHGPAGVGKTSAAHALARDLDWE--TIELN 75
                                  5678899******************995..44444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.1
                                   TSSEEEEESTT CS
                                   xxxxxxxxxxx RF
                      ABC_tran 126 kpkllllDEpt 136
                                   +++l++lDE+ 
  gi|91774163|ref|YP_566855.1| 103 AKRLIILDEAD 113
                                   6799*****96 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.6
                                   SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxx RF
                      ABC_tran  38 teGeilldgkdlke 51 
                                   +eG+  +++k+ k+
  gi|91774163|ref|YP_566855.1| 435 DEGKAFFEKKPKKQ 448
                                   34444444444444 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0011      0.73       1      23 [.      45      67 ..      45     106 .. 0.92
   2 ?    0.8   0.6      0.78   5.2e+02      92     146 ..     413     466 ..     362     493 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                     Hydin_ADK  1 aiivhGaPlsGKtatavtLakkY 23
                                  aii+hG+   GKt++a +La+  
  gi|91774163|ref|YP_566855.1| 45 AIILHGPAGVGKTSAAHALARDL 67
                                  8*******************975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.78
                     Hydin_ADK  92 ssaaeekaasskiskkkktsvvsgkkkaesegaksqkqkekktsetaqisssppl 146
                                   + +++  +  + ++++k+ s+  ++ ka  e++ ++++ +kk+ + +qi +s p+
  gi|91774163|ref|YP_566855.1| 413 KVTKDI-QRIHDLAQAKRRSLGRDEGKAFFEKKPKKQTPDKKQMDLTQIINSTPQ 466
                                   222222.222333333444444444444444444443333333333322222212 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 3503.44
//
Query:       gi|91774164|ref|YP_566856.1|  [L=285]
Description: N5-methyl-tetrahydromethanopterin--coenzyme M methyltransferase subunit X [Methanococcoides burtonii DSM 6242]
Scores for complete 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   22.2   0.0      0.092   12.0   0.0    2.2  2  PTA_PTB   Phosphate acetyl/butaryl transferase


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   7.9e-05       1.4       6      58 ..      14      67 ..      10      79 .. 0.74
   2 !   12.0   0.0   5.1e-06     0.092     111     207 ..      82     173 ..      70     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 7.9e-05
                                  HHHHHCTS--EEEES-.TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHC CS
                       PTA_PTB  6 ivekakkekkrivlpe.gedervlkAakelleegiadviLigdeaeikakalel 58
                                  ++++a  +++++++ + + + +++++++++++ g a+viL+gd++ei +  ++l
  gi|91774164|ref|YP_566856.1| 14 VSKRAILNMAKVAIGVrTPSAKMISSIENAHNSGYAHVILVGDKKEIDSVGTSL 67
                                  55666666666666542567899*********************9999855554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.1e-06
                                   HHHTTSSSEEEE-TTS-HHH..HHHHHHHCT-B-TT----EEEEEEEETTEEEEEESSSS-SS--HHHHHHHHHHHHHHHH CS
                       PTA_PTB 111 lvklgeaDglvsGavnttad..tlrpalqiiktkpgvklvSsvfimlledrlllfaDcavnvnPtaeelaeialesaktak 189
                                   l+++g +D++v G +n++ +  +l+++l i+k  +   ++   f+++  +  +++a + + +  +  +++  a   ++ ++
  gi|91774164|ref|YP_566856.1|  82 LLASGSVDAVVRGTANASGTlsHLKDVLGIEKLYR---MA---FLISADGVPFFLAPVGIDEGNDISDKITLAKLGVEHIR 156
                                   7899*********9998664115666666666665...33...666667778999************************** PP

                                   HCCSS--EEEEE-SSSTT CS
                       PTA_PTB 190 algeeeprvAlLSyStkg 207
                                   ++g +ep v +LS   +g
  gi|91774164|ref|YP_566856.1| 157 RFG-IEPVVGVLSGGRMG 173
                                   ***.********977766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1851.22
//
Query:       gi|161611176|ref|YP_566857.2|  [L=310]
Description: N5-methyltetrahydromethanopterin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-121  405.2   0.6   1.7e-121  405.0   0.6    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 !  405.0   0.6  9.5e-126  1.7e-121       1     295 [.       6     297 ..       6     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 405.0 bits;  conditional E-value: 9.5e-126
                           MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGeteeaiv 80 
                                    keq+v++iaGvk+GGqpGe Ptvl+gtify +hkived + Gifd+ aae+l++ q+ +sd+tGnP +v+++ +t  ++ 
  gi|161611176|ref|YP_566857.2|   6 KEQNVVNIAGVKMGGQPGELPTVLAGTIFYEGHKIVEDADVGIFDRFAAEDLVNVQDLISDETGNPSIVHIFANTVKSMQ 85 
                                    79****************************************************************************** PP

                           MtrH  81 kyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmdptvegk 160
                                    +yidfv+ vtd+P++ids + ev++a+a y+t++Glad++iynsin+si +ae eal  sd++++ivl+fn+md + eg+
  gi|161611176|ref|YP_566857.2|  86 EYIDFVSSVTDSPFIIDSPQPEVRMASAGYVTDIGLADKTIYNSINMSITEAECEALRLSDIDSSIVLGFNAMDSSLEGR 165
                                    ******************************************************************************** PP

                           MtrH 161 lkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdwlrefkkkek 240
                                    +++le+g++  +kgl+e+ae++Gi++ lid  +tp+g+gag+a++ ++a k+k+G+PvGsgihn+ps+W wl+e kk   
  gi|161611176|ref|YP_566857.2| 166 MSLLEDGGKLLDKGLIEVAEDCGISNILIDPSITPMGNGAGIALRMTMAAKEKWGFPVGSGIHNAPSSWRWLKEKKK--L 243
                                    *************************************************************************8544..5 PP

                           MtrH 241 ekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelg 295
                                    ++   y+++dvg++++q+++g+dfvlyGPiena  +fP  am+di+i+ea+ ++g
  gi|161611176|ref|YP_566857.2| 244 DPLV-YRMCDVGTVTMQQLVGGDFVLYGPIENAMYTFPMAAMADIMIAEASSDMG 297
                                    5665.88*******************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2206.10
//
Query:       gi|91774166|ref|YP_566858.1|  [L=334]
Description: hypothetical protein Mbur_2245 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      116  (0.00646996); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 2231.38
//
Query:       gi|91774167|ref|YP_566859.1|  [L=553]
Description: dihydroxy-acid dehydratase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-220  732.3   3.5   3.3e-220  732.1   3.5    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 !  732.1   3.5  1.8e-224  3.3e-220       1     517 []      31     550 ..      31     550 .. 0.97

  Alignments for each domain:
  == domain 1  score: 732.1 bits;  conditional E-value: 1.8e-224
                      ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqllD 81 
                                   kp+i+++ns++e++p+h hl+++aeavk+g+++aggvp+ef+tigv+Dgiamg+egm+ysLpsRe i d++e+m+++q++D
  gi|91774167|ref|YP_566859.1|  31 KPFIAVVNSWTEFIPGHIHLDKVAEAVKAGIRNAGGVPFEFHTIGVCDGIAMGHEGMKYSLPSREAIEDTIEIMIQGQQMD 111
                                   8******************************************************************************** PP

                      ILVD_EDD  82 alvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacpgaGsCs 160
                                   ++v++++CDKi+Pg+lmaa r++iPai+v+gGpm++g ++   +dl+svfe vg++++g +s+e+l++le+ +c gaGsC+
  gi|91774167|ref|YP_566859.1| 112 GMVMVTSCDKITPGHLMAAGRVDIPAIVVTGGPMLPGFVDdkYTDLVSVFEGVGSCQSGAVSSEKLKQLEDLCCCGAGSCA 192
                                   ************************************87555478************************************* PP

                      ILVD_EDD 161 gmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvllalGGStNavlH 241
                                   gm+TAntmac++ealGlslpg+a+++a++a+++++a+e+g+rive+v++ l++r+i+t ++feNAi v+la+GGStN++lH
  gi|91774167|ref|YP_566859.1| 193 GMFTANTMACMTEALGLSLPGCATAHAVDAKKMRMAKESGERIVEMVSEGLTARKIVTDKSFENAIRVDLAVGGSTNTTLH 273
                                   ********************************************************************************* PP

                      ILVD_EDD 242 llAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvltvtgktlaenlee... 319
                                   l+AiA+e+g+el l++f+els+++p+l+ l+P g+  m d++raGGv+a++k+L ++  l+ d +t+tgkt++en++e   
  gi|91774167|ref|YP_566859.1| 274 LPAIAHEFGLELPLEKFNELSKTTPHLIGLRPGGENFMIDFERAGGVQAIMKRLVTK--LNLDEKTITGKTVGENIDEfvi 352
                                   *******************************************************55..*****************98654 PP

                      ILVD_EDD 320 .aevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkikagdvvviry 399
                                    + +++ +vi ++e+pl++egg+avLkGnLap+G+vvK+sav+e++l+++gpArvfdseeea+e ilkg+ik+gdvvviry
  gi|91774167|ref|YP_566859.1| 353 vNPKTNARVITTIEEPLHEEGGIAVLKGNLAPDGSVVKQSAVHEKMLRHTGPARVFDSEEEAMETILKGDIKSGDVVVIRY 433
                                   44449**************************************************************************** PP

                      ILVD_EDD 400 eGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrtlelevs 480
                                   eGPkGgpGm+Eml+ptsa++g+gl ++valitDGRfSG+++g++igh+sPEA+egGpi+l+++GDiieid+++r+lel+vs
  gi|91774167|ref|YP_566859.1| 434 EGPKGGPGMREMLSPTSAIAGMGLIDSVALITDGRFSGGTRGPCIGHISPEAYEGGPIGLIQEGDIIEIDMPERRLELKVS 514
                                   ********************************************************************************* PP

                      ILVD_EDD 481 eeelaaRraawkp.ekkvktrgllakyaklvssaseGA 517
                                   ee+l++Rr  +kp ek+  ++g+l++y+k vssas+GA
  gi|91774167|ref|YP_566859.1| 515 EEDLEKRRVLFKPvEKE--ATGYLSRYRKIVSSASKGA 550
                                   ********99**94433..49****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3656.06
//
Query:       gi|91774168|ref|YP_566860.1|  [L=566]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-13   51.6   0.0      3e-13   50.5   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
     0.0066   16.4   0.1      0.024   14.6   0.1    2.0  1  PsbU         Photosystem II 12 kDa extrinsic protein (PsbU)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   3.3e-17     3e-13       2     166 ..     191     385 ..     190     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.3e-17
                                   EEESEESS-..-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS............TTHHHHHH CS
                                   xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlr..CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly............pdfvelle 68 
                                   +++rgC ++  CsfC+ ++    +g++ +++v ++++ev +l ++ g++++ +g + p+l                     
  gi|91774168|ref|YP_566860.1| 191 ETYRGCGRKvhCSFCTERF----YGHSDYRPVADVIAEVSSL-YDLGARNFRIGRQ-PDLLsyhakdigadvlQ------- 258
                                   789***************7....9******************.8**********77.55553444444444441....... PP

                                   HHHHTC..................CCTEEEEEEECSSCHG.....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCT CS
                                   xxxxxx..................xxxxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  69 rlakla..................vpgiritvetngtlpd.....eeklerllelg..vdrvslgleaaddekvlklmnrg 124
                                                            + +++  + ++t++       e+l+++++++   d  +lg+e+ad+  v   +  +
  gi|91774168|ref|YP_566860.1| 259 -----PspeileslysgirkvapeLKVLHMDNTNPATMVAypeqsFEILKTIVKYHtsGDIAALGIETADPA-VVSANDLK 333
                                   .....23334444444444557774555555555555544666668**************************.88888899 PP

                                   SHHHHHHHHHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 125 htfeevlealeklreagikr..........vvdrivglpGendeeleellel 166
                                     +++vl+++++++++g  r            +++ glpGe+++++e  ++l
  gi|91774168|ref|YP_566860.1| 334 VHPDDVLDVIKMINDVGSARgssglpellpGLNFVHGLPGETRKTFELNYDL 385
                                   *****************5555556666777***************9987776 PP

>> PsbU  Photosystem II 12 kDa extrinsic protein (PsbU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.7e-06     0.024      15      59 ..     512     556 ..     502     565 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                                   EETTTS-GGGGGGSTTTTTHHHHHHHHS---SSGGGGGG-TT--H CS
                          PsbU  15 vDlnnanvrafrqlrGlyPtlakkivknaPYdsvedvlniPgLse 59 
                                   +D+n + +++ r+++Gl     +ki+++ PY++++++++   L e
  gi|91774168|ref|YP_566860.1| 512 LDVNSTPLQVIREIPGLNAMDVSKIISGVPYANMDELVQKVALPE 556
                                   8**********************************9887656655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 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:                        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 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 4022.99
//
Query:       gi|91774169|ref|YP_566861.1|  [L=344]
Description: hypothetical protein Mbur_2249 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-43  147.0   9.9    1.3e-42  146.4   9.9    1.3  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   9.9   7.4e-47   1.3e-42       4     301 .]      11     324 ..       7     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 7.4e-47
               LPG_synthase_TM   4 glals.alllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnnv 83 
                                   +l++s +++++ll+ +vd +++++a+r++    +++a++l l+s+++++lr +++++slg+ i+ ++ + +   +l+v  v
  gi|91774169|ref|YP_566861.1|  11 SLVISfISIVLLLVFTVD-TTTIDAIRNIKKEAIVAAIALQLFSYVVWGLRTKFMCQSLGHDIKTLKTTEIAISSLLVAAV 90 
                                   555557444444444456.677899999999999*********************************************** PP

               LPG_synthase_TM  84 tPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa..vllllalallllavlall 162
                                   tP+++gGe++r++ll++ + ++ +ka+a+vv erl d + ++l+ ++al++l g +  ++   +l+++ l+++++++++++
  gi|91774169|ref|YP_566861.1|  91 TPSSAGGEALRIHLLSK-NEIPIGKATAVVVGERLTDAFLILLIAPFALYILRGFFPKENFdmLLIAGELFIFIILGILIY 170
                                   *****************.**********************************99988877687777777777888888888 PP

               LPG_synthase_TM 163 lllllrrrlarlarvlkrlarllarfarklasakr.......................klvlasprrlllafllslliwll 220
                                    +l   +++ +++ ++ +  r+    ++  ++                          k     ++ +   +++++++ ++
  gi|91774169|ref|YP_566861.1| 171 SILKPNKTKSTIHFFVNKTKRFHG--RKTDEA--LanvlekidieidnfqygiryftkK----GRKGVYYGIICTIIYRGT 243
                                   888888888888888888877632..222232..24699*************8744432....344588899999999*** PP

               LPG_synthase_TM 221 ealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                    +++l ++l++lg ++ ++l++ ++++lt ++++p++Pg +G++E+++ +l++ +  +++++++++l +r++t+y+ +++G
  gi|91774169|ref|YP_566861.1| 244 LYSILPVILAGLGQPPEILLSFMAQILLTCLMIIPATPGASGIAEFGASSLFSIVIATPSLIGITVLTWRALTYYMNIVVG 324
                                   *******************************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2204.81
//
Query:       gi|91774170|ref|YP_566862.1|  [L=399]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-47  162.2   0.0      2e-47  161.9   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    2.9e-17   61.6  26.0    1.2e-07   31.2   1.7    4.8  5  Hexapep          Bacterial transferase hexapeptide (six repea
    3.5e-08   34.0   0.0    5.1e-08   33.4   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    1.1e-05   25.1  24.8       0.01   15.6   4.4    4.6  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.18   10.7   2.2        1.1    8.2   2.3    2.0  1  Fucokinase       L-fucokinase
       0.85    7.7   3.9        1.3    7.1   3.9    1.3  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 !  161.9   0.0   6.6e-51     2e-47       1     243 [.      15     243 ..      15     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 6.6e-51
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   ka I++GG+GtRL+PLt +++k+ +p+l+k + + + ++ la++g++e iv++  + ++ +ee l++g  +gv +++++e+
  gi|91774170|ref|YP_566862.1|  15 KACIMCGGEGTRLRPLTFERPKPSIPILNK-PSVVHLVEHLAKEGFTE-IVITIGYMAEKIEECLGDGRMYGVYIEYVYEE 93 
                                   688***************************.9999*************.******************************** PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                   ++ gtA+ v+ a+e+l+de     ++++ggDh+++  ++ + ++++ ++a  ++t+g++  ++++e+G++ +d ++r++rf
  gi|91774170|ref|YP_566862.1|  94 KRLGTAGGVKNAEEFLKDEP----FMIVGGDHVMDLSLRSIYRQHEMNDA--MITIGLMSIDDPREFGIADMDVNNRIHRF 168
                                   *****************999....8*************************..***************************** PP

                                   ECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHH CS
               NTP_transferase 163 vEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllean 242
                                    EKP   +  s+las+GiY+  +e+++ +     + +++ d+ +d++p+++++gk+   +l ++   W DvG+  ++ +a+
  gi|91774170|ref|YP_566862.1| 169 LEKPGPGEIfSNLASTGIYMCSPEIFDWI-----PKDEKYDFAKDLFPALMSKGKKINGMLVRG--HWTDVGSSTAYRQAQ 242
                                   ****987777*******************.....8899**************************..5**********9998 PP

                                   H CS
               NTP_transferase 243 e 243
                                   +
  gi|91774170|ref|YP_566862.1| 243 R 243
                                   7 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.7   0.00013      0.39      13      32 ..     262     281 ..     259     285 .. 0.86
   2 !   17.3   3.7   9.6e-07    0.0029       2      30 ..     269     297 ..     268     298 .. 0.94
   3 !   31.2   1.7     4e-11   1.2e-07       1      28 [.     292     319 ..     292     322 .. 0.95
   4 !   17.2   4.1     1e-06     0.003       2      35 ..     322     360 ..     321     361 .. 0.91
   5 !   21.8   0.3   3.5e-08    0.0001       1      34 [.     356     389 ..     356     391 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                   TEEEETTEEE-TTEEEETTE CS
                       Hexapep  13 faviggnVkIGdnvkIgagv 32 
                                    a i g+ kIG+nv++g ++
  gi|91774170|ref|YP_566862.1| 262 DARIQGPLKIGNNVIVGTNS 281
                                   57899999********9987 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 9.6e-07
                                   EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                   ++IG+nv++g ++ + g+ +IG+n++Ig 
  gi|91774170|ref|YP_566862.1| 269 LKIGNNVIVGTNSALVGPMVIGNNTTIGD 297
                                   79*************************97 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 4e-11
                                   TEEEETTEEE-TTEEEETTEEE-TTEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                   +t+IG+nvlIgp++ ig+n++I dn++I
  gi|91774170|ref|YP_566862.1| 292 NTTIGDNVLIGPYTAIGSNCVIKDNCRI 319
                                   699************************9 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 1e-06
                                   EEEETTEEE-T.....TEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgp.....faviggnVkIGdnvkIgagvvig 35 
                                   + I ++v+Ig+     +++i +++++G n+ +++g+vig
  gi|91774170|ref|YP_566862.1| 322 SYIFNDVTIGSntnasGSIIDNHTIVGQNCNLENGTVIG 360
                                   6788999999999999**********************8 PP

  == domain 5  score: 21.8 bits;  conditional E-value: 3.5e-08
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   +tvIG  v+I+  a+i+++VkI + v I ag++i
  gi|91774170|ref|YP_566862.1| 356 GTVIGPRVIIRDDATIHSDVKIWPEVNIKAGSRI 389
                                   5778888888888888888888888888888777 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 !   33.4   0.0   1.7e-11   5.1e-08       1      98 [.      16     123 ..      16     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.7e-11
                                   EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHH...HHTTCT..S-EEE-TTSS CS
                  NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevla...alarlg..vrvvededpg 69 
                                   a+i++GG+++R+      ++K+ +p+ +kp + +++++l++ g+ e+v+  g+  e++++   + + +g  +++v++e + 
  gi|91774170|ref|YP_566862.1|  16 ACIMCGGEGTRLRpltfeRPKPSIPILNKPSVVHLVEHLAKEGFTEIVITIGYmaEKIEEclgDGRMYGvyIEYVYEE-KR 95 
                                   68**********6444436*********************************98754544111445555546678887.69 PP

                                   -SHHHHHHHHHHHH.SSSCEEEEETT-TT CS
                  NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmPl 98 
                                    g++++++ a + + ++++++++ +D+++
  gi|91774170|ref|YP_566862.1|  96 LGTAGGVKNAEEFL-KDEPFMIVGGDHVM 123
                                   9***********99.9**********975 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 !   14.1   6.0   9.8e-06     0.029       1      32 [.     268     301 ..     268     303 .. 0.69
   2 !   15.6   4.4   3.4e-06      0.01       2      29 ..     287     316 ..     286     321 .. 0.87
   3 ?    3.1   1.4     0.026        79       4      13 ..     307     316 ..     304     335 .. 0.57
   4 !   10.0   3.9   0.00019      0.57       8      33 ..     328     360 ..     326     361 .. 0.68
   5 !   10.7   0.7   0.00011      0.34       2      26 ..     345     371 ..     344     379 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.8e-06
                                   .EEE-TT-EE-TT-E.ES.EEE-TT-EE-TT-EE CS
                     Hexapep_2   1 pviIGdnCliGanag.iG.vslGdncvvgaGvvi 32 
                                   p++IG+n+++G n+  +G   +G+n ++g +v i
  gi|91774170|ref|YP_566862.1| 268 PLKIGNNVIVGTNSAlVGpMVIGNNTTIGDNVLI 301
                                   89***********876755555555555555544 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.4e-06
                                   EEE-TT-EE-TT-EES..EEE-TT-EE-TT CS
                     Hexapep_2   2 viIGdnCliGanagiG..vslGdncvvgaG 29 
                                     IG+n+ iG n  iG  + +G ncv+  +
  gi|91774170|ref|YP_566862.1| 287 MVIGNNTTIGDNVLIGpyTAIGSNCVIKDN 316
                                   679************99*********9755 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.026
                                   E-TT-EE-TT CS
                     Hexapep_2   4 IGdnCliGan 13 
                                   IG nC+i  n
  gi|91774170|ref|YP_566862.1| 307 IGSNCVIKDN 316
                                   5555555444 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00019
                                   -EE-TT...-E..ES..EEE-TT-EE-TT-EE- CS
                     Hexapep_2   8 CliGan...ag..iG..vslGdncvvgaGvvit 33 
                                   + iG+n   +g  i   +++G nc +++G vi 
  gi|91774170|ref|YP_566862.1| 328 VTIGSNtnaSGsiIDnhTIVGQNCNLENGTVIG 360
                                   55555522222425567**************96 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00011
                                   EEE-TT-EE-TT-EES..EEE-TT-EE CS
                     Hexapep_2   2 viIGdnCliGanagiG..vslGdncvv 26 
                                   +i+G+nC++    +iG  v+++d++++
  gi|91774170|ref|YP_566862.1| 345 TIVGQNCNLENGTVIGprVIIRDDATI 371
                                   466666666666666666666666665 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.3   0.00036       1.1     268     331 ..     311     372 ..     248     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00036
                    Fucokinase 268 ekkkesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilq 331
                                     +k+++ +++S + ++v++g ++    s +++++ +g+n+ + +  +     ++ ++dd  ++
  gi|91774170|ref|YP_566862.1| 311 CVIKDNCRILSSYIFNDVTIGSNTNASGSIIDNHTIVGQNCNLENGTVIGP--RVIIRDDATIH 372
                                   234888888999998899999888888888888888888888888888776..67888887777 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.9   0.00043       1.3     202     276 ..     286     358 ..     254     386 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00043
                       DUF4954 202 asklengtinSskeapveiG.egViledfiissGskikdgavisrcfvGqavklkkqfsaedsllfaNcqgengEa 276
                                      + n t +    + v iG +  i ++++i+  ++i  + + +++ +G +++ +     + +++++Nc++eng +
  gi|91774170|ref|YP_566862.1| 286 PMVIGNNTTIG---DNVLIGpYTAIGSNCVIKDNCRILSSYIFNDVTIGSNTNASGSIIDNHTIVGQNCNLENGTV 358
                                   44443333222...23444423344444444444444444444444444444444444444445555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2644.84
//
Query:       gi|91774171|ref|YP_566863.1|  [L=472]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-60  204.1   1.4    4.5e-59  200.2   0.0    2.7  2  DDE_Tnp_IS66     Transposase IS66 family
    8.3e-11   42.1   3.8    2.5e-10   40.6   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.5e-05   23.7   0.7    0.00016   22.2   0.7    1.8  1  SlyX             SlyX
     0.0001   22.6   0.1       0.18   12.0   0.2    2.7  2  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.034   14.2   1.0        6.5    6.8   0.4    2.5  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.054   14.1   1.8       0.26   11.9   1.8    2.2  1  BST2             Bone marrow stromal antigen 2
      0.068   13.7   0.7       0.27   11.7   0.4    2.1  2  DUF16            Protein of unknown function DUF16
       0.12   12.1   3.0       0.38   10.4   1.0    2.4  2  YkyA             Putative cell-wall binding lipoprotein
       0.12   12.3   2.7       0.79    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        0.4   10.8   2.0        4.1    7.6   0.0    2.6  3  GutM             Glucitol operon activator protein (GutM)
       0.48   10.8   7.0        1.1    9.7   5.2    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.91   10.2   8.9        6.7    7.5   1.5    3.5  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        1.5    8.5   4.2        5.1    6.7   0.6    2.9  3  LXG              LXG domain of WXG superfamily
        1.9    9.1   5.9       0.73   10.5   1.3    2.6  1  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.3      0.55     7e+02     174     225 ..      20      69 ..       4      84 .. 0.61
   2 !  200.2   0.0   3.5e-62   4.5e-59       2     280 ..     179     434 ..     178     436 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.55
                  DDE_Tnp_IS66 174 larigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   ++ + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91774171|ref|YP_566863.1|  20 VTLVTTLYDIIAEQQK--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   4446777777666532..3456666666666666666666666665544444 PP

  == domain 2  score: 200.2 bits;  conditional E-value: 3.5e-62
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91774171|ref|YP_566863.1| 179 TQYGLRLASLAVYLHDYQLLPYDRSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91774171|ref|YP_566863.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierearea....eaeerlalrqeesrpllaeleawleeqlkkvlpksklgkairyllk 236
                                   +e+++  q +++a++  + ++++  +++re+    ++e+ ++ +  + + ++  +e+     ++++ +            k
  gi|91774171|ref|YP_566863.1| 329 SENDD--QLWSKAMNIlLIDVKKSVDQIREMsgcmKPERIKEFEDWYGQIIHIGIEE-----NPQLQA------------K 390
                                   **977..*********99999999999974434555566666666666666666666.....333444............5 PP

                  DDE_Tnp_IS66 237 rweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                    ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91774171|ref|YP_566863.1| 391 SKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 434
                                   599****************************************9 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 !   40.6   3.8     2e-13   2.5e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91774171|ref|YP_566863.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.7   1.2e-07   0.00016      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91774171|ref|YP_566863.1| 22 LVTTLYDIIAEQQKIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0033       4.2       5      45 ..     249     287 ..     245     290 .. 0.84
   2 !   12.0   0.2   0.00014      0.18      86     138 ..     398     450 ..     384     452 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0033
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91774171|ref|YP_566863.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00014
                 DDE_Tnp_IS240  86 evshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                    ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91774171|ref|YP_566863.1| 398 FMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 450
                                   5667899*****************************98777776666666665 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4    0.0051       6.5     151     184 ..      23      56 ..       7      86 .. 0.74
   2 ?    5.5   0.0     0.012        16     105     159 ..     370     425 ..     270     433 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0051
                       UPF0242 151 lqeyqetieeqrsvlekrqdqieqLeskVrDlny 184
                                   + ++   i eq++ +e + ++i +Le +V+ l  
  gi|91774171|ref|YP_566863.1|  23 VTTLYDIIAEQQKIIELQAARITELEERVKKLEE 56 
                                   4555556667777777777777777766665543 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                       UPF0242 105 ldakeeelerlkeenqqLqekl.eaiaedfeelkleleeqLaekqellqeyqetie 159
                                    d   + ++   een qLq k  ++i + +++lk   e++Lae+  ++ + q++i+
  gi|91774171|ref|YP_566863.1| 370 EDWYGQIIHIGIEENPQLQAKSkNDILRFMHDLKVPFENNLAERDVRMMKVQQKIS 425
                                   4555566677779999**9885167889999**********************997 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.8    0.0002      0.26      44      87 ..      20      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 44 nqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                     v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91774171|ref|YP_566863.1| 20 VTLVTTLYDIIAEQQKIIELQAARITELEERVKKLEEQLKKNSR 63
                                  456788888888888999999*******************9876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00021      0.27      44      82 ..      24      62 ..      16      72 .. 0.83
   2 ?   -2.8   0.0       7.1   9.1e+03      42      57 ..     409     424 ..     400     442 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                  H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 44 dklgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  ++l   i+++++++e q ++i+el++++k+ +e+l+k  
  gi|91774171|ref|YP_566863.1| 24 TTLYDIIAEQQKIIELQAARITELEERVKKLEEQLKKNS 62
                                  5566678899999******************99998755 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.1
                                   HHH...HHHHHHHHHH CS
                         DUF16  42 kvdklgeqinkleqkv 57 
                                   +++ +++++ k++qk+
  gi|91774171|ref|YP_566863.1| 409 NLAERDVRMMKVQQKI 424
                                   4444444444444444 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0    0.0003      0.38      49      99 ..      16      66 ..       3      76 .. 0.85
   2 ?    0.3   0.0      0.37   4.7e+02      33      57 ..     368     392 ..     363     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                          YkyA 49 fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeel 99
                                   +++++l+  + +++ e+++++e + + i e +e ++k++e++++   ++ 
  gi|91774171|ref|YP_566863.1| 16 PEAVVTLVTTLYDIIAEQQKIIELQAARITELEERVKKLEEQLKKNSRNSS 66
                                  5679999*************************************9866554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                          YkyA  33 keqelyeeiielgmdefdkikklsd 57 
                                   + ++ y +ii  g++e+ +++++s+
  gi|91774171|ref|YP_566863.1| 368 EFEDWYGQIIHIGIEENPQLQAKSK 392
                                   556789***************9997 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.42   5.3e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00062      0.79      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.42
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91774171|ref|YP_566863.1| 116 KVHKCSNCER 125
                                   5566777654 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00062
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91774171|ref|YP_566863.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       7.2   9.2e+03      74     103 ..      30      58 ..      28      61 .. 0.66
   2 ?    7.6   0.0    0.0032       4.1      42      89 ..     331     378 ..     322     395 .. 0.81
   3 ?    1.9   0.1      0.18   2.3e+02      64      82 ..     427     445 ..     409     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.2
                          GutM  74 farfkeleelegksleeieeeklkkkdklt 103
                                   +a  +++ el+  +++e+ee+ +kk ++++
  gi|91774171|ref|YP_566863.1|  30 IAEQQKIIELQAARITELEER-VKKLEEQL 58 
                                   566667777777778888666.66666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0032
                          GutM  42 kkgrfragvivllavdedgiivearvmkGvTvfarfkeleelegksle 89 
                                   +  ++ ++++ +l +d ++ + ++r+m+G     r+ke+e+  g+ ++
  gi|91774171|ref|YP_566863.1| 331 NDDQLWSKAMNILLIDVKKSVDQIREMSGCMKPERIKEFEDWYGQIIH 378
                                   56677889999*******************999999999998888775 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.18
                          GutM  64 earvmkGvTvfarfkelee 82 
                                    +r m+G  +f+r+++  +
  gi|91774171|ref|YP_566863.1| 427 TFRSMQGALIFSRVRSYIS 445
                                   5689**********98654 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.8   2.3e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?    9.7   5.2   0.00088       1.1       2      28 ..     156     201 ..     155     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.8
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91774171|ref|YP_566863.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00088
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................c 28 
                                   e+k CP+Cg++++  +s++v++  ++                    
  gi|91774171|ref|YP_566863.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyD 201
                                   79***************99987544477777777777776666663 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 ?    3.4   0.1     0.098   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.5   1.5    0.0053       6.7       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.1   0.1      0.25   3.2e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.098
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91774171|ref|YP_566863.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0053
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91774171|ref|YP_566863.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.25
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91774171|ref|YP_566863.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.6     0.004       5.1     147     199 ..      12      64 ..       3      67 .. 0.84
   2 ?    1.2   0.1       0.2   2.5e+02     155     172 ..     225     242 ..     218     245 .. 0.80
   3 ?   -0.7   0.0      0.78     1e+03      10      62 ..     352     406 ..     344     430 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.004
                           LXG 147 lqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemtskgkis 199
                                   +++  + v + ++ l+d+ +eq+   + + + +++l+  v++Lee+ +k++ +
  gi|91774171|ref|YP_566863.1|  12 YEQGPEAVVTLVTTLYDIIAEQQKIIELQAARITELEERVKKLEEQLKKNSRN 64 
                                   566666777889999*****************************999999865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                           LXG 155 qetiekledfdqeqksal 172
                                   ++  ekledf+q+ k++l
  gi|91774171|ref|YP_566863.1| 225 KTCFEKLEDFEQQIKNFL 242
                                   45789********99987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.78
                           LXG  10 eaieqlksele.elkeqleqlkkaiqklveled.slkGkaaeaiknfyadlhlpl 62 
                                   ++i +++  ++ e  +++e+++ +i ++   e  +l+ k+ + i +f++dl +p+
  gi|91774171|ref|YP_566863.1| 352 DQIREMSGCMKpERIKEFEDWYGQIIHIGIEENpQLQAKSKNDILRFMHDLKVPF 406
                                   5555555544413346788888888887777778888888899999999988887 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.3   0.00057      0.73      34      71 ..      73     130 ..      19     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00057
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91774171|ref|YP_566863.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1616  (0.0901333); expected 358.6 (0.02)
Passed bias filter:                      871  (0.0485805); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.70u 0.25s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 3223.03
//
Query:       gi|91774172|ref|YP_566864.1|  [L=264]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-08   34.5   0.1    4.8e-08   33.3   0.1    1.6  1  OrfB_IS605  Probable transposase
     0.0035   17.3   1.4       0.01   15.7   0.8    1.9  2  CBM9_1      Carbohydrate family 9 binding domain-like
  ------ inclusion threshold ------
      0.022   15.0   0.6       0.13   12.6   0.8    2.2  2  NUMOD1      NUMOD1 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 !   33.3   0.1     8e-12   4.8e-08      14      99 ..     177     257 ..     163     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 8e-12
                    OrfB_IS605  14 kgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhk 94 
                                   + ++  g+D+Gin La+ +t+d + +++ g ++k+    ++  + +lqsk   s     a+r l+ ++ k +r +++  hk
  gi|91774172|ref|YP_566864.1| 177 EASTFMGVDVGINYLAVASTTDKKCKFFAGGKIKNLRNHYKSMRTRLQSKGTLS-----AKRILKYISGKEKRLMRDINHK 252
                                   567889*******************************************95555.....6888888888888888888888 PP

                    OrfB_IS605  95 lathl 99 
                                   +++++
  gi|91774172|ref|YP_566864.1| 253 ISKEI 257
                                   88887 PP

>> CBM9_1  Carbohydrate family 9 binding domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.18   1.1e+03     164     183 ..      30      49 ..      15      51 .. 0.78
   2 !   15.7   0.8   1.7e-06      0.01      72     155 ..     112     195 ..     105     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.18
                                   S-SSS-TTT-GGGSEEEEEE CS
                        CBM9_1 164 sdttgnnyqdpsvfGkltLk 183
                                   + ++++ +++ +++G ++L+
  gi|91774172|ref|YP_566864.1|  30 NHVSKVLFENGKTMGAMKLQ 49 
                                   455566699********998 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.7e-06
                                   EETT----SS--TTEEEEEEETT--E.EE-TT-...-GGGEEEEEEEETTEE....EEEEEEE-SS-.---TTEEEEEEEE CS
                        CBM9_1  72 lDennsktteynandfqyrvnldnea.svdegkkkliaegvtsaskkseggY....ivEaaiplktiatpaegkviGfdla 147
                                   +Den  k t++n++ ++y++   n+a  + +g+   ++ +  + +k+++g+Y     +E +ip k+i   ++ + +G d+ 
  gi|91774172|ref|YP_566864.1| 112 IDENTVKITTFNSSRKAYTILNYNHAkQYFDGS---WKYQASKIVKHNDGNYfihlSIEKEIPDKSI--IEASTFMGVDVG 187
                                   9******************97666660454555...9***************766667888888888..778889999999 PP

                                   EEEE-TTS CS
                        CBM9_1 148 inddddgg 155
                                   in  +   
  gi|91774172|ref|YP_566864.1| 188 INYLAVAS 195
                                   98744444 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   2.1e-05      0.13       8      30 ..     112     136 ..     110     138 .. 0.85
   2 ?   -1.8   0.0      0.71   4.2e+03      18      29 ..     174     185 ..     173     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                        NUMOD1   8 lntkt..igkFsSireAakyLgish 30 
                                   ++ +t  i++F+S r+A+ +L+++h
  gi|91774172|ref|YP_566864.1| 112 IDENTvkITTFNSSRKAYTILNYNH 136
                                   66666669****************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.71
                        NUMOD1  18 SireAakyLgis 29 
                                   Si eA+ ++g++
  gi|91774172|ref|YP_566864.1| 174 SIIEASTFMGVD 185
                                   8899*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1885.72
//
Query:       gi|91774173|ref|YP_566865.1|  [L=126]
Description: nucleic acid binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-05   23.7   0.1    4.8e-05   23.3   0.1    1.1  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.077   12.6   0.0      0.093   12.4   0.0    1.2  1  DUF4131          Domain of unknown function (DUF4131)


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 !   23.3   0.1   5.3e-09   4.8e-05       2      74 ..      49     121 ..      48     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.3e-09
                                   EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
               tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                    v+G v +++++ +g ++ ++++ +  +i+v++ + ++a+++ ++l ++d   + G + +++g+ le++v++ +
  gi|91774173|ref|YP_566865.1|  49 FVEGAVLNKRMTYSGDHLILEIEHEGEMITVFVPNnKGAKEIGKELAVNDMAHIAGVLDEYEGE-LEIIVKDKK 121
                                   589**********************************************************998.*****9855 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     1e-05     0.093      33      93 ..      10      71 ..       4     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1e-05
                       DUF4131 33 llllllllllallgfalrapqpna..ndlsqllesgqeviveGvvaslpeltgsgtrfvleve 93
                                  +ll++++l la+++f +   + +   ++ls+ +++g++v+veG v+++ +++ sg+ ++le+e
  gi|91774173|ref|YP_566865.1| 10 ILLAMAILSLAVAYFIYMPGELGGniEPLSDSTTLGEKVFVEGAVLNKRMTY-SGDHLILEIE 71
                                  67888888888888888877766634677777777*********99998888.7777888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 948.31
//
Query:       gi|91774174|ref|YP_566866.1|  [L=152]
Description: peptidylprolyl isomerase, FKBP-type [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-25   88.4   0.0    6.3e-25   87.3   0.0    1.5  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
      0.087   12.9   0.0       0.15   12.1   0.0    1.3  1  RNA_bind  RNA binding domain


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 !   87.3   0.0     7e-29   6.3e-25       5      94 .]       2     147 ..       1     147 [. 0.82

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 7e-29
                                   B-TTCEEEEEEEEEETTSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTT CS
                        FKBP_C   5 akegdtVtvhykgkledgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYg 72 
                                   ++egd ++v+y g+ledg++fd+s             ++ ++plef+vG+gq+i+Gf+ +++gm vGe++t+tip  +aYg
  gi|91774174|ref|YP_566866.1|   2 VQEGDLISVNYIGQLEDGTIFDTSledvakeagqhnpARGYEPLEFTVGAGQMIPGFDAGVVGMTVGEEKTVTIPAAEAYG 82 
                                   589*********************999999999988777****************************************** PP

                                   T.............................................TTBCTTTB.TTSEEEEEEEEE CS
                        FKBP_C  73 e.............................................kglaggvippnatLvFeveLl 94 
                                   e                                              ++++    +++tL F+++L+
  gi|91774174|ref|YP_566866.1|  83 EydeelvqpvprtqlkemgiepevgmplftqygqvtivridetnayVDYNH--HLAGETLTFKITLV 147
                                   *88888888888777666666666666666666666666644443333333..5566*******995 PP

>> RNA_bind  RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.6e-05      0.15      28      51 ..     110     133 ..     107     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                                   HTTTSEEEEEEEEETTEEEEEEEE CS
                      RNA_bind  28 lFspfGsvyvsWlddtsAfvaLhr 51 
                                   lF ++G+v +  +d+t A+v  ++
  gi|91774174|ref|YP_566866.1| 110 LFTQYGQVTIVRIDETNAYVDYNH 133
                                   8*******************8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.71
# Mc/sec: 650.19
//
Query:       gi|91774175|ref|YP_566867.1|  [L=181]
Description: peptidylprolyl isomerase, FKBP-type [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-22   78.5   0.0    6.4e-22   77.7   0.0    1.4  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
       0.71   10.5   4.5        1.3    9.6   4.5    1.5  1  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   7.1e-26   6.4e-22       4      94 .]      29     176 ..      26     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 7.1e-26
                                   BB-TTCEEEEEEEEEETTSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTT CS
                        FKBP_C   4 eakegdtVtvhykgkledgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippelaY 71 
                                    ++egd ++v+y g+l dg++fd+s             ++ ++plef+vG+ ++i Gf+ +++gm vGe++t+ ip  +aY
  gi|91774175|ref|YP_566867.1|  29 MVQEGDLISVNYIGQLDDGTIFDTSfedvakeagqynpARGYEPLEFTVGASRLIAGFDAGVVGMTVGEEKTVVIPAAEAY 109
                                   589**********************999999999966666***************************************** PP

                                   TT....................TTBCTTTB.TT.................................SEEEEEEEEE CS
                        FKBP_C  72 ge....................kglaggvippn.................................atLvFeveLl 94 
                                   ge                              +                                 +tL F+++L+
  gi|91774175|ref|YP_566867.1| 110 GEydeervqpvpisqlkekdieP---------EvgmllntisgqqvpivrmdetnayvdnnyplagETLTFQITLV 176
                                   **777666666665555555550.........24444445555555555555555555555666669999999985 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.5   0.00015       1.3       1      18 []       1      20 [.       1      20 [. 0.94

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                        LPAM_1  1 MKKi..llalgalllLsGCs 18
                                  M+K   ll+l+ +ll+sGC+
  gi|91774175|ref|YP_566867.1|  1 MRKAllLLILTGMLLVSGCA 20
                                  9999999************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1201.09
//
Query:       gi|91774176|ref|YP_566868.1|  [L=224]
Description: hypothetical protein Mbur_2257 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  232.6  26.6      4e-69  232.5  26.6    1.0  1  DUF2162          Predicted transporter (DUF2162)
  ------ inclusion threshold ------
       0.11   12.9   0.3       0.11   12.9   0.3    3.2  4  DUF2583          Protein of unknown function (DUF2583)
       0.54    9.3  34.2       0.17   10.9  15.2    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein


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 !  232.5  26.6   6.6e-73     4e-69       1     222 [.       6     219 ..       6     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 232.5 bits;  conditional E-value: 6.6e-73
                       DUF2162   1 llvlGiLfailifgiKtGlglglsnlsrkklllilllYlllflllalllssldekllesllrygmvlhllmAlllialGly 81 
                                   l+v+GiL+ail+fg+KtG+g+g+sn s+k +ll++++Yl+l+++l+ l++++d++ l+ + ++gm lh+l+Allli++G+y
  gi|91774176|ref|YP_566868.1|   6 LTVIGILMAILLFGVKTGIGCGFSNRSLKSILLLASSYLILSIVLGSLIGYVDQSNLDVIASMGMSLHVLVALLLIGAGIY 86 
                                   6899***************************************************************************** PP

                       DUF2162  82 tlkkwkkskkdvssrtflalvlPCPvCltailfsiillasslglspvevglvlglvflilvlvtyllsrkivkltktnypi 162
                                   t+k+w+ ++ dvs+rtfl+++lPCPvClta+++s++llas +++s++ +gl++g+vf+i+v++t+ll++k++k     +p+
  gi|91774176|ref|YP_566868.1|  87 TQKQWN-CGCDVSHRTFLVISLPCPVCLTALFISCMLLASYIDMSGTLIGLLVGVVFFISVVSTSLLCKKLGK-----TPE 161
                                   ******.**************************************************************9999.....*** PP

                       DUF2162 163 iLGnlmlfiGlyfLlsaliipniaqakaiylspltessieslllvlvlllallllGfllr 222
                                   +LGn+m+++G+y+L++a+i+p+++++k++++ ++t   +   +l++v+++++++ Gf+l+
  gi|91774176|ref|YP_566868.1| 162 TLGNIMMILGIYYLMGAIIVPAYIKTKQMNIPQYTA--PPIDILPFVVFAVFIAGGFVLN 219
                                   **********************************99..8999****************98 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.7      0.42   2.5e+03      16      56 ..      11      54 ..       3      60 .. 0.46
   2 ?   -1.0   0.8      0.42   2.5e+03      47      62 ..      68      84 ..      34      98 .. 0.53
   3 ?   -0.3   0.2      0.25   1.5e+03      43      58 ..     129     144 ..     103     152 .. 0.67
   4 ?   12.9   0.3   1.8e-05      0.11       5      54 ..     159     209 ..     155     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.42
                       DUF2583 16 lGlllmvaslaysvlnqlpelelpell...aeaallgifiGall 56
                                  + +++++ ++   +   + + +l  +l   ++  +l+i +G+l+
  gi|91774176|ref|YP_566868.1| 11 ILMAILLFGVKTGIGCGFSNRSLKSILllaSSYLILSIVLGSLI 54
                                  33334444444444444443333333211133345666666665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.42
                       DUF2583 47 l.lgifiGallWlaGar 62
                                  + +++ +   l l Ga+
  gi|91774176|ref|YP_566868.1| 68 MgMSLHVLVALLLIGAG 84
                                  21333333333444444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.25
                       DUF2583  43 aeaallgifiGallWl 58 
                                   ++++l+g+++G ++++
  gi|91774176|ref|YP_566868.1| 129 MSGTLIGLLVGVVFFI 144
                                   4566666666666654 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 1.8e-05
                       DUF2583   5 kalllGnvlmglGlllmvaslaysvlnqlpelelpellae.aallgifiGa 54 
                                   +   lGn++m lG+  +++++ +    +  ++++p++ a  +++l   + a
  gi|91774176|ref|YP_566868.1| 159 TPETLGNIMMILGIYYLMGAIIVPAYIKTKQMNIPQYTAPpIDILPFVVFA 209
                                   56789*******************************987425665544444 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 ?    4.5  11.0    0.0026        15     212     284 ..       5      79 ..       1      90 [. 0.63
   2 ?   10.9  15.2   2.9e-05      0.17     214     312 ..     102     211 ..     101     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0026
               ABC2_membrane_3 212 gdflvyllqlllilllafgl......gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgff 284
                                   ++ ++++l+++    l+fg+      g++  +l ++lll   +++++i+lg l++++ ++  ++++ +++ + +l +++
  gi|91774176|ref|YP_566868.1|   5 ILTVIGILMAI----LLFGVktgigcGFSNRSLKSILLLASSYLILSIVLGSLIGYVDQSNLDVIASMGMSLHVLVALL 79 
                                   33333333333....46666665555688889999**********************8888666665444433222222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 2.9e-05
               ABC2_membrane_3 214 flvyllqlllill.l.....afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivil..llsgffgg 286
                                   flv  l++ ++l  l     ++++ i++++ ++ ll+ ++f++++++ ++l+  l k++et   +++i+ +  l+++++++
  gi|91774176|ref|YP_566868.1| 102 FLVISLPCPVCLTaLfiscmLLASYIDMSGTLIGLLVGVVFFISVVSTSLLCKKLGKTPETLGNIMMILGIyyLMGAIIVP 182
                                   566666664443222113335555899**********************************88888888888889999999 PP

               ABC2_membrane_3 287 lfp...ledlpsalkwifsiiPffapglg 312
                                    ++     ++p +++    i+Pf+ ++++
  gi|91774176|ref|YP_566868.1| 183 AYIktkQMNIPQYTAPPIDILPFVVFAVF 211
                                   99995533466888888999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 1669.29
//
Query:       gi|91774177|ref|YP_566869.1|  [L=207]
Description: MotA/TolQ/ExbB proton channel [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.1   4.6    1.3e-09   37.9   3.8    1.7  1  MotA_ExbB        MotA/TolQ/ExbB proton channel family
  ------ inclusion threshold ------
      0.029   14.5   0.6        9.2    6.4   0.0    2.2  2  TMEM169          TMEM169 protein family
       0.07   11.7   0.3      0.088   11.4   0.3    1.0  1  Semenogelin      Semenogelin
      0.093   12.5   0.1       0.24   11.1   0.1    1.8  2  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like
       0.16   12.1   1.4       0.53   10.4   0.1    2.0  2  SLATT_3          SMODS and SLOG-associating 2TM effector doma
        0.7    9.8   5.6       0.61   10.0   0.4    2.3  2  DUF2975          Protein of unknown function (DUF2975)
        1.6    8.7   7.0         15    5.6   3.2    2.4  2  SpoIIM           Stage II sporulation protein M


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 !   37.9   3.8     5e-13   1.3e-09      35     110 ..     109     181 ..      36     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 5e-13
                                   HHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSGGCTHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MotA_ExbB  35 lsreeerlekglsilatigslaPllGLlGTVlGlieafqaladagsadlakvapgiaeALiaTalGlvvAipavla 110
                                    ++ e r+ k+l+  +++ ++aP+lGL+GT++ l  a+  la+    d+ ++a+++  A+ +T+lGl++ ++ +++
  gi|91774177|ref|YP_566869.1| 109 SEEYEVRMTKRLEQTKILSTVAPMLGLMGTLIPLGPALIGLAQ---GDILQLANNLMIAFATTVLGLFAGVVGYVL 181
                                   5667889999********************************9...788********************9887765 PP

>> TMEM169  TMEM169 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0036       9.2      53     104 ..       5      56 ..       2      61 .. 0.79
   2 ?    6.2   0.1    0.0041        10      63     103 ..     154     197 ..     147     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0036
                       TMEM169  53 sllhkillcPllillyPllivlvtlslglyaavkqlslsleeWlkevrdlek 104
                                   s+l +++++    llyP++i+l+    +  + +     ++++  ++vr+lek
  gi|91774177|ref|YP_566869.1|   5 SFLFQLMYTASAALLYPVVILLLLAVAASLGLIGEFISEYAKRHRNVRELEK 56 
                                   6788899999999*****9998776666666677777777777888888887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0041
                       TMEM169  63 llillyPllivlvtlslglyaavkq..lslsleeW.lkevrdle 103
                                   +l l+  l+i ++t  lgl+a+v+   l+l  ++W +++++d++
  gi|91774177|ref|YP_566869.1| 154 ILQLANNLMIAFATTVLGLFAGVVGyvLTLIRKRWyWQDMADID 197
                                   566777899**************853267777788689999886 PP

>> Semenogelin  Semenogelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   3.4e-05     0.088     288     357 ..      44     113 ..      36     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                   Semenogelin 288 ypssrteerqlhhgeksvqkdvskgsisiqteekihgksqnq.vtihsqdqehghkenkisyqsssteerh 357
                                   y     + r+l +  +svq  v   s+  ++ ek+h   qnq vt  ++d     k+n is     +ee  
  gi|91774177|ref|YP_566869.1|  44 YAKRHRNVRELEKVGRSVQESVKASSLD-NAAEKLHSLDQNQlVTSFAKDAGEYLKQNSISSIDWLSEEYE 113
                                   4555567799999999***999888876.67789*******967889999999999999997766666654 PP

>> 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 ?   11.1   0.1   9.6e-05      0.24      10      78 ..      16      85 ..       8     184 .. 0.73
   2 ?   -0.9   0.0      0.48   1.2e+03      11      47 ..     160     196 ..     153     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.6e-05
                    EMC3_TMCO1 10 dwvllPivivill.vgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqe 78
                                    +l+P+vi++ll v++  gl+ e+++++   + ++++ +k  + +q+ +++    +  +kl++l + q 
  gi|91774177|ref|YP_566869.1| 16 AALLYPVVILLLLaVAASLGLIGEFISEYAKRHRNVRELEKVGRSVQESVKASSLDNAAEKLHSLDQNQL 85
                                  46789997766543788889********997777788888999999999999999999999999988875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.48
                    EMC3_TMCO1  11 wvllPivivil.lvgiltgllsellqkllidkkkmeke 47 
                                   ++++ +  ++l l++ ++g++ +l++k   +++ m  +
  gi|91774177|ref|YP_566869.1| 160 NLMIAFATTVLgLFAGVVGYVLTLIRKRW-YWQDMADI 196
                                   45555555555345667788888888865.77766665 PP

>> SLATT_3  SMODS and SLOG-associating 2TM effector domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00021      0.53      28     145 ..       9     122 ..       2     130 .. 0.75
   2 ?    0.5   0.1      0.23     6e+02      47      77 ..     162     192 ..     142     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                       SLATT_3  28 llvvAAlaaalslkvgsvdlaallaalafllalvievvlarrrperkWyegRavAEsvKtlaWrYavrgepFeeelesaea 108
                                    l+  A aa+l   v  + l+a++a l++++ ++ e+  + r+ ++  + gR+v EsvK  +     ++e   ++l++++ 
  gi|91774177|ref|YP_566869.1|   9 QLMYTASAALLY-PVVILLLLAVAASLGLIGEFISEYAKRHRNVRELEKVGRSVQESVKASSLD--NAAEKL-HSLDQNQL 85 
                                   455555555555.44357789999999999999999999999999999***********99843..455666.77888888 PP

                       SLATT_3 109 eklfrerleevlrelrkvsselsresgeeaiteaMre 145
                                    + f+++  e l++++  s+   +e+ e+ +t++ ++
  gi|91774177|ref|YP_566869.1|  86 VTSFAKDAGEYLKQNSISSIDWLSEEYEVRMTKRLEQ 122
                                   8888888888888888877776667777777777766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.23
                       SLATT_3  47 laallaalafllalvievvlarrrperkWye 77 
                                   ++a+++ ++ l a v+++vl+  r++  W++
  gi|91774177|ref|YP_566869.1| 162 MIAFATTVLGLFAGVVGYVLTLIRKRWYWQD 192
                                   5666677777777888888888888777775 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.6     0.072   1.8e+02      14      39 ..      16      34 ..       5      61 .. 0.46
   2 ?   10.0   0.4   0.00024      0.61      57     117 ..     118     181 ..     110     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.072
                       DUF2975 14 aglrvpvlllgvlallafvvalvqlw 39
                                  a+l +pv++l +la++a        +
  gi|91774177|ref|YP_566869.1| 16 AALLYPVVILLLLAVAAS-------L 34
                                  333333333333333332.......2 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00024
                       DUF2975  57 rrLrriglaliaa.....alllaagivalallaelelapgvvllllgvafaslvigllvlvlaell 117
                                   +rL + + +  +a     + +l+++++al +la+   + +++  +l++afa+ v+gl++ v+  +l
  gi|91774177|ref|YP_566869.1| 118 KRLEQTKILSTVApmlglMGTLIPLGPALIGLAQ--GDILQLANNLMIAFATTVLGLFAGVVGYVL 181
                                   56666666666666777778899999********..999********************9998776 PP

>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.014        37      50      84 ..      10      44 ..       4      56 .. 0.69
   2 ?    5.6   3.2    0.0057        15      41      67 ..     157     182 ..     154     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                        SpoIIM 50 llfllGllllgiptilvl.linGfvlGavaalvaef 84
                                  l++ +   +l  p++++l l+ +++lG+++ +++e+
  gi|91774177|ref|YP_566869.1| 10 LMYTASA-ALLYPVVILLlLAVAASLGLIGEFISEY 44
                                  4555554.4444555555488888899999998887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0057
                        SpoIIM  41 fanNlrvalllfllGllllgiptilvl 67 
                                   +anNl++a+ + +lGl + g++  ++ 
  gi|91774177|ref|YP_566869.1| 157 LANNLMIAFATTVLGL-FAGVVGYVLT 182
                                   78*************7.6666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1244  (0.0693848); expected 358.6 (0.02)
Passed bias filter:                      815  (0.0454571); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1476.63
//
Query:       gi|91774178|ref|YP_566870.1|  [L=119]
Description: hypothetical protein Mbur_2259 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  118.4   0.2    1.5e-34  118.1   0.2    1.1  1  DUF2149   Uncharacterized conserved protein (DUF2149)


Domain annotation for each model (and alignments):
>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.2   8.5e-39   1.5e-34       1      92 []      21     112 ..      21     112 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 8.5e-39
                       DUF2149   1 lsgvaNLfDvalVlavallvalvsslnlqellsseedvtvvkkpgkekmeiivkegeelkkakesaekasgkGerlGtayr 81 
                                   l+gvaNLfD+a+V++val++alv+s++l ells++ d+t+vk+pg+++m+iivkeg++++  ++++++++g+Ge lGtay+
  gi|91774178|ref|YP_566870.1|  21 LTGVANLFDIAMVFSVALMIALVMSFQLPELLSPTADITIVKNPGQPDMKIIVKEGQNIEVLNMTDQIGGGTGEALGTAYQ 101
                                   79******************************************************************************* PP

                       DUF2149  82 lkdGkliyVPe 92 
                                   l+dG+++yVP+
  gi|91774178|ref|YP_566870.1| 102 LADGRVVYVPD 112
                                   **********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 899.75
//
Query:       gi|91774179|ref|YP_566871.1|  [L=1750]
Description: hydrogenobyrinic acid a,c-diamide cobaltochelatase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-280  932.4   0.2   6.4e-280  931.5   0.1    1.4  2  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 ?   -3.6   0.0     0.091   1.6e+03       7      28 ..     304     325 ..     302     357 .. 0.73
   2 !  931.5   0.1  3.6e-284  6.4e-280       8    1088 ..     458    1583 ..     448    1584 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.091
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel   7 ggveNlknllryladkllgkke 28 
                                    gv+N + +l ylad++ +k++
  gi|91774179|ref|YP_566871.1| 304 VGVKNAEDMLLYLADEYGNKPD 325
                                   689**************98555 PP

  == domain 2  score: 931.5 bits;  conditional E-value: 3.6e-284
                                    xxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx......xxxxxxxxxxx RF
                  CobN-Mg_chel    8 gveNlknllryladkllg......kkeeeveppvelpeegiyhpdake.lfesleeylewyk......kakkekaptvg 73  
                                    + +N ++ll y+a+++ g      + + +  + + lp++giyhpd+   +fe+++eylewy+      + +++++pt+g
  gi|91774179|ref|YP_566871.1|  458 ELRNAESLLVYIAKEYGGetaltaGWDYANVSSSGLPAVGIYHPDYGYkYFETTAEYLEWYQqesserRVYDPSRPTIG 536 
                                    568**************999998866666778999**********9977*****************9999********* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel   74 ilfyrahllagntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgpaeeeee 152 
                                    ++f+r+++++g+t v+dali+ +e++++nv++ f +      ++ ++ ++ +++e+ v+ +i++ sf+l+ +   +   
  gi|91774179|ref|YP_566871.1|  537 MWFHRNDVQNGQTGVVDALIEDIESKDCNVIVGFDTF-----DDIVQYYCDENEEPLVQSVISLKSFRLNYLDPLKG-- 608 
                                    *******************************887554.....78999999999****************87775443.. PP

                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  153 eaeeealkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetevekyepiper 230 
                                       ee+lk+lnvPvl + +   ++ ++ ++s++G+ + +++ + + p ldG  e + ++ +  +  e+   +y+pi+ +
  gi|91774179|ref|YP_566871.1|  609 ---EEELKKLNVPVLRGiVAEISDSTNVADSNSGIPNAQMVRKTISPNLDGIFEYILVGQSIYD-AESMSSEYVPIDGQ 683 
                                    ...4568**********888899999******************************99996444.78889********* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  231 vervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeLielll 309 
                                    v+++ ++  +wa+L+  +n++kkva+i++nyp+g++++g a++Ld++ S+  lL+++ ++ Y+v++lp++++eL+e++ 
  gi|91774179|ref|YP_566871.1|  684 VDWISNRSIKWAELKLAENEDKKVAVIYYNYPSGKDNIG-ASYLDTITSMRLLLDEMDDANYTVSDLPANNSELLERIW 761 
                                    ***************************************.55**********************989************ PP

                                    xxxxxxxxx.........xxxxx...xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx........xxxxxxxx RF
                  CobN-Mg_chel  310 eggtndpew.........eelkv...gaaallpaeeYeewfee.LpeelreeveerWgeppge........mveeeksg 367 
                                    ++g n  +w         e         ++l+p+e+Y++wfee Lpe+lr++v+e+Wgep  e        m+ e ++ 
  gi|91774179|ref|YP_566871.1|  762 AQGINAGSWapgvldemvE---NrteWGLQLIPMETYKQWFEEeLPEDLRNSVIEEWGEPWAEelpenksvMIWE-NET 836 
                                    *********9888864432...1445789*************99**************99655566668977775.666 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  368 ekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvgls 446 
                                    +++lvip++q+Gnv++++QParg+ +++++lyh++ +pPthqY+ fYlWl+++++ da++H+G+HGt EwlPGK+ gl 
  gi|91774179|ref|YP_566871.1|  837 GQYLVIPAVQYGNVLLMPQPARGFMQNDDTLYHSSVVPPTHQYIGFYLWLNNDWQPDAIIHFGTHGTHEWLPGKSYGLD 915 
                                    7****************************************************************************** PP

                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  447 .eecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkal 524 
                                     ++ +  +ll+dlP++YpYiv n+gEG++A  R++A i+dH+tP ++r+++yg+++eL++l + Y+  e + pe + a 
  gi|91774179|ref|YP_566871.1|  916 rKTEWAPLLLQDLPNIYPYIVANVGEGLTAEYRGNALIVDHMTPTLERSGSYGKIEELSRLTQIYYGPEMS-PETKAAY 993 
                                    9999***************************************************************7665.9999999 PP

                                    xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                  CobN-Mg_chel  525 reqilelveelnldkdlg...leeakeeeeeefeelle.kldgyleelkeaqirdglhilGeapegeq...lvdlvvai 596 
                                    ++qi+  + e+++d+dlg   + + ++ +e+ef+++++  l++y+ee++ ++i++g+hi+Ge+p+ +    l+d +  +
  gi|91774179|ref|YP_566871.1|  994 QAQIVYEIGETHIDSDLGlniT-DLASYNESEFSSFVKnVLHEYIEEIEGENIPYGMHIFGETPATNTtgyLHDELSLM 1071
                                    99****************6642.346778999****88468***********************765412233444444 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  597 lrleneegesltealaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee 675 
                                    +  +++ +++++ ++ +a+  + d       ++            ++  +++ e+++++++ +e+++    +++e+ + 
  gi|91774179|ref|YP_566871.1| 1072 V--RSMLKSGFEGSVLSAFYPEDDYPLGVPFND------------TRVDQMLWEVVTNGTDVNESQMMFYGKTNESVTV 1136
                                    4..223488888888888644444444444444............4444555555555555555555444444444443 PP

                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  676 .............eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeelle 741 
                                                 +++ E+++ll+aL++++ip+gp+ dp+ +++  +PTGrNfy+v+p+  P++a w vGk++a +l++
  gi|91774179|ref|YP_566871.1| 1137 dlvkglvyrdrlvDSSMEMDRLLSALNAGFIPAGPGTDPVMNPE-SVPTGRNFYGVNPELYPSKATWLVGKQMAIDLID 1214
                                    5555666666677888**************************66.*********************************8 PP

                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.........xxxxxxxx RF
                  CobN-Mg_chel  742 r.ylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaa.grvvdlelipleeL.........gRPRiDVt 809 
                                      y +e+g+yP ++++s +g+e++r +G  +A i++ lGvrPvwd+  g v ++e ip eeL         gRPRiD++
  gi|91774179|ref|YP_566871.1| 1215 AtYDSENGTYPDTIAFSRFGVEFIRDHGTLEAAIMYTLGVRPVWDEDnGYVIGVEEIPEEELlpnydpsvpGRPRIDIV 1293
                                    6266777************************************************************************ PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx....xxxxxxxxxxxxx RF
                  CobN-Mg_chel  810 vriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaelee.......keeae....eratyRvFgskpG 877 
                                      ++G+ RDafp+ ++++d+ ++l+ +++  ++ N+vr+h+ +++++  e       +e+a+    + +t+R +  ++G
  gi|91774179|ref|YP_566871.1| 1294 YLTAGM-RDAFPSKVQMIDDSIRLANSIEPVNYPNYVREHSDANYEQYYEelsktmdEETASnlarKLSTMRCYAVRDG 1371
                                    999995.************************************999998889988763322235569************ PP

                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  878 aYgagvqelies.snWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflG 955 
                                    +Y  g  +++ + ++We++e++ ++Yl+++++ Yg++  g e ++ + a+L +vd+ v++ +s+ ++ +d dd++q++G
  gi|91774179|ref|YP_566871.1| 1372 TYEIGTGNAMGAsGSWESDEEIVNIYLEKMGFLYGSELWGYEFSQSLIANLMNVDASVHSVNSNLYNSIDNDDFFQYFG 1450
                                    **********999****************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                  CobN-Mg_chel  956 GltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdata. 1033
                                     l++a+r+lsg++p++y++d s+pe +++ tlke + ++lr++ +NPkWiegm+ +Gy+G + +a+ +dn++  ++   
  gi|91774179|ref|YP_566871.1| 1451 ALNLAIRNLSGDNPDSYVVDGSDPEMTELSTLKEYFMKDLRTTAFNPKWIEGMKGSGYAGGRMFAEIIDNVWLAEVSDp 1529
                                    ******************************************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel 1034 dvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWeaseet 1088
                                    ++vdd ++e +++tYv+De +re+++e+Np A+++i+ r+lEaar+++W+a++e 
  gi|91774179|ref|YP_566871.1| 1530 ELVDDSTWEMLHNTYVNDE-MREWFNENNPGAYQSITGRMLEAARKDYWDAPQEV 1583
                                    ****************995.9******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.93u 0.34s 00:00:01.27 Elapsed: 00:00:00.49
# Mc/sec: 10741.36
//
Query:       gi|91774180|ref|YP_566872.1|  [L=389]
Description: coenzyme F420 hydrogenase/dehydrogenase beta subunit-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-34  119.0   0.0    1.5e-34  119.0   0.0    2.0  2  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    4.8e-25   87.5   0.2    1.5e-24   85.9   0.1    1.9  2  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    2.3e-11   43.6   2.9    5.7e-11   42.3   2.9    1.7  1  YHS          YHS domain
    3.4e-05   23.9  17.3     0.0011   19.1  12.8    3.2  4  Fer4_9       4Fe-4S dicluster domain
    3.6e-05   24.0  20.7     0.0093   16.4   2.2    3.7  3  Fer4_4       4Fe-4S binding domain
    6.4e-05   22.6  21.9      0.019   14.8   4.2    3.4  3  Fer4         4Fe-4S binding domain
    0.00012   22.6  17.1       0.08   13.5   1.6    3.6  5  Fer4_17      4Fe-4S dicluster domain
    0.00021   21.3  19.7    0.00067   19.7  13.4    2.9  2  Fer4_10      4Fe-4S dicluster domain
    0.00055   19.9  21.0        0.2   11.8   3.7    3.5  3  Fer4_2       4Fe-4S binding domain
    0.00099   19.5  17.4      0.094   13.2   2.7    3.5  5  Fer4_8       4Fe-4S dicluster domain
     0.0011   19.2   6.5      0.007   16.5   3.5    2.4  2  Fer4_18      4Fe-4S dicluster domain
     0.0069   17.3  11.1       0.44   11.5   1.0    3.5  3  Fer4_16      4Fe-4S double cluster binding domain
     0.0073   16.9  19.0        2.3    8.9  15.8    3.5  3  Fer4_7       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   15.4  12.9       0.58   10.9   0.5    3.5  3  Fer4_15      4Fe-4S single cluster domain
      0.053   13.6  20.1       0.19   11.8   2.5    3.4  3  Fer4_6       4Fe-4S binding domain
       0.15   12.6   0.5       0.15   12.6   0.5    3.5  3  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
       0.78    9.9  17.6       0.74   10.0  12.6    2.6  2  Fer4_21      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   2.1       7.1   7.5e+03      58     102 ..      56      84 ..      30     114 .. 0.40
   2 !  119.0   0.0   1.5e-37   1.5e-34       3     154 ..     213     363 ..     211     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.1
                   FrhB_FdhB_C  58 dvkklefrgk.gkfrvelkd.......ekeislkeleefirpsCkvCkdktae 102
                                   d +k+ f g   k ++++         +                       a+
  gi|91774180|ref|YP_566872.1|  56 DREKISF-GRlNKEIIKTGIctlcgacV-----------------------AS 84 
                                   3334444.33333333222233333332.......................22 PP

  == domain 2  score: 119.0 bits;  conditional E-value: 1.5e-37
                   FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk......kklkekilltiglfCggnfspealrklleelgvdpedvkklefrgkgkfrvelkd. 76 
                                    +++vG +C+i a++k+q       + + ++ +l  glfC+++f++++++++ e++g+d +d++++++r kg f++ +++ 
  gi|91774180|ref|YP_566872.1| 213 SIGFVGPSCNIDAVHKMQTssygflHLFLRARVLKFGLFCMDSFEHDGIKEFVESKGMDLNDIHSMKIR-KGLFELGTSEg 292
                                   589***************9999**97888888************************************7.******99999 PP

                   FrhB_FdhB_C  77 ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveageleleelde 154
                                    k+++l+el++++ +sCk+C+d+++e+ Dis+G v      g ++ g++tvl+r++ g e++++av++g+le+++l++
  gi|91774180|ref|YP_566872.1| 293 MKSYDLSELDQYRCSSCKYCTDMVSENTDISFGGV------G-TPVGWTTVLIRSSVGYEIFNEAVDSGYLEARPLEK 363
                                   999********************************......8.******************************99875 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 ?   -3.0   0.0       7.9   8.3e+03      63      72 ..     103     112 ..      79     114 .. 0.76
   2 !   85.9   0.1   1.4e-27   1.5e-24       2      77 ..     129     203 ..     128     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.9
                   FrhB_FdhB_N  63 aaGskYtlsp 72 
                                   a+G+ Y+++p
  gi|91774180|ref|YP_566872.1| 103 ACGVCYNQCP 112
                                   8899999987 PP

  == domain 2  score: 85.9 bits;  conditional E-value: 1.4e-27
                   FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvaps.kdpwrpkpviattkeellaaaGskYtlspnlklL 77 
                                   +aArs+ +    k+q+GG+vt++l+y+L+eg+ d+++v+++s ++pw+++pvi++t++e+l++aGs+Yt+s++l+ L
  gi|91774180|ref|YP_566872.1| 129 YAARSAIP--GVKGQDGGVVTSMLAYALDEGLLDCAVVTKRSkDEPWKAEPVIVRTSAEVLESAGSIYTHSMTLEPL 203
                                   99******..56******************************99****************************99866 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   2.9   5.4e-14   5.7e-11       2      39 ..       6      42 ..       5      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5.4e-14
                           YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFed 39
                                  +dP c+ +   ek+++ +eY+Gk+YyFcS +Ck+kF++
  gi|91774180|ref|YP_566872.1|  6 IDPICKVHM-SEKSDFVTEYGGKTYYFCSGKCKSKFDR 42
                                  7********.889***********************96 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   2.5   0.00037      0.39      33      47 ..      63      86 ..      30      91 .. 0.61
   2 !   19.1  12.8     1e-06    0.0011       2      49 ..      75     114 ..      74     116 .. 0.90
   3 !   13.9   3.5   4.2e-05     0.044       1      28 [.     100     127 ..     100     132 .. 0.80
   4 ?    4.6   0.1     0.036        38       1      10 [.     305     314 ..     286     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                        Fer4_9 33 e.........eaCigCgaCveaCp 47
                                              C+ CgaCv+ C+
  gi|91774180|ref|YP_566872.1| 63 GrlnkeiiktGICTLCGACVASCE 86
                                  044555555555888888888886 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1e-06
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   Ct CgaCv++C++ ++v+ + +   +        C+ Cg C++ Cp++
  gi|91774180|ref|YP_566872.1|  75 CTLCGACVASCEYVTFVDNKPKLVGK--------CTACGVCYNQCPRT 114
                                   ***************99888777755........************97 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 4.2e-05
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarl 28 
                                   kCt Cg C ++Cp ++++e++  +k+r+
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCPRTITKEEDLIGKIRY 127
                                   6999999999999999888887777765 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.036
                        Fer4_9   1 kCtgCgaCve 10 
                                   +C +C++C++
  gi|91774180|ref|YP_566872.1| 305 RCSSCKYCTD 314
                                   3666666654 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.4   3.8e-05     0.041       4      16 ..      75      87 ..      66      90 .. 0.92
   2 !   16.4   2.2   8.8e-06    0.0093       3      15 ..     100     112 ..      99     121 .. 0.92
   3 ?    3.2   2.3      0.16   1.6e+02       2      12 ..     304     314 ..     303     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C+ Cg+Cva+C++
  gi|91774180|ref|YP_566872.1| 75 CTLCGACVASCEY 87
                                  ***********85 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.8e-06
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                   +C+ Cg+C++ CP
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCP 112
                                   7************ PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                        Fer4_4   2 erCigCgsCva 12 
                                    rC  C+ C++
  gi|91774180|ref|YP_566872.1| 304 YRCSSCKYCTD 314
                                   69*******96 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.4     9e-05     0.095       3      19 ..      70      86 ..      68      89 .. 0.84
   2 !   14.8   4.2   1.8e-05     0.019       6      19 ..      99     112 ..      97     113 .. 0.93
   3 ?    5.1   0.5     0.021        22       4      16 ..     302     314 ..     300     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                                  EETTTSSS-THHHHHST CS
                          Fer4  3 ideekCigCGaCvevCP 19
                                  i +  C+ CGaCv  C 
  gi|91774180|ref|YP_566872.1| 70 IKTGICTLCGACVASCE 86
                                  55678***********5 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.8e-05
                                   TTSSS-THHHHHST CS
                          Fer4   6 ekCigCGaCvevCP 19 
                                    kC++CG C++ CP
  gi|91774180|ref|YP_566872.1|  99 GKCTACGVCYNQCP 112
                                   59************ PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.021
                                   ETTTSSS-THHHH CS
                          Fer4   4 deekCigCGaCve 16 
                                   d+ +C  C++C +
  gi|91774180|ref|YP_566872.1| 302 DQYRCSSCKYCTD 314
                                   8889*******86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   2.4   0.00048      0.51       8      58 ..      32      87 ..      29      89 .. 0.63
   2 !   11.1   1.2   0.00043      0.46       2      23 ..      75      96 ..      74     100 .. 0.87
   3 !   12.0   1.9   0.00022      0.24      41      59 ..      96     114 ..      88     116 .. 0.75
   4 !   13.5   1.6   7.6e-05      0.08       1      29 [.     100     131 ..     100     162 .. 0.71
   5 ?    5.4   0.5     0.025        26       1      11 [.     305     315 ..     305     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                       Fer4_17  8 ClpeCpsyeaydnepkkllraaklglleeaeke......ekaslCieCgeCerkCPq 58
                                  C  +C s  ++  e+  ++ + ++g+ e+++         k + C+ Cg C+++C +
  gi|91774180|ref|YP_566872.1| 32 CSGKCKSKFDRL-EKSVIRLKRNIGDREKISFGrlnkeiIKTGICTLCGACVASCEY 87
                                  666676654433.3555666666666666433334433458899***********76 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00043
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepk 23
                                  C+ Cg+C+++C +    dn+pk
  gi|91774180|ref|YP_566872.1| 75 CTLCGACVASCEYVTFVDNKPK 96
                                  999********99999888887 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00022
                       Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                   + +++C+ Cg C  +CP  
  gi|91774180|ref|YP_566872.1|  96 KLVGKCTACGVCYNQCPRT 114
                                   5677888888888888865 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 7.6e-05
                       Fer4_17   1 rCiqCgyClpeCpsyeaydne...pkkllraa 29 
                                   +C+ Cg C ++Cp+ +  +++   + ++++aa
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCPRTITKEEDligKIRYAYAA 131
                                   699**********9988766522222344443 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.025
                       Fer4_17   1 rCiqCgyClpe 11 
                                   rC++C+yC+++
  gi|91774180|ref|YP_566872.1| 305 RCSSCKYCTDM 315
                                   7*******985 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  13.4   6.4e-07   0.00067       3      56 .]      69     112 ..      67     112 .. 0.90
   2 ?    4.1   0.4     0.047        50       4      17 ..     301     314 ..     298     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.4e-07
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +i +  C+ Cg+Cv++C          ++ +  + + k v+kCt+cg C+ +CP
  gi|91774180|ref|YP_566872.1|  69 IIKTGICTLCGACVASC----------EYVTFVDNKPKLVGKCTACGVCYNQCP 112
                                   677889***********..........678888888899**************9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.047
                       Fer4_10   4 idddtCirCgkCvk 17 
                                   +d+ +C  C+ C++
  gi|91774180|ref|YP_566872.1| 301 LDQYRCSSCKYCTD 314
                                   57778999999986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   2.4   0.00029      0.31       6      20 ..      71      85 ..      68      87 .. 0.87
   2 !   11.8   3.7   0.00019       0.2       9      21 ..     100     112 ..      94     113 .. 0.92
   3 !    6.7   0.7    0.0084       8.8       6      18 ..     302     314 ..     300     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                        Fer4_2  6 dtdrCigCgaCvsaC 20
                                   t +C+ CgaCv +C
  gi|91774180|ref|YP_566872.1| 71 KTGICTLCGACVASC 85
                                  5779*********99 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00019
                        Fer4_2   9 rCigCgaCvsaCP 21 
                                   +C++Cg C++ CP
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCP 112
                                   8********99*9 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0084
                        Fer4_2   6 dtdrCigCgaCvs 18 
                                   d  rC +C+ C++
  gi|91774180|ref|YP_566872.1| 302 DQYRCSSCKYCTD 314
                                   7789*******85 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   4.1    0.0098        10      49      62 ..      73      86 ..      30      88 .. 0.65
   2 !    8.5   2.3    0.0025       2.6       5      18 ..      75      88 ..      71     100 .. 0.71
   3 !   12.4   3.2   0.00015      0.16      47      64 ..      97     114 ..      88     115 .. 0.78
   4 !   13.2   2.7   8.9e-05     0.094       4      18 ..     100     114 ..      97     165 .. 0.69
   5 ?    5.2   0.1     0.027        29      48      58 ..     303     313 ..     260     315 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0098
                        Fer4_8 49 wsCttcgaCtevCp 62
                                  + Ct cgaC+  C 
  gi|91774180|ref|YP_566872.1| 73 GICTLCGACVASCE 86
                                  55777777777774 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0025
                        Fer4_8  5 CieCgaCqsaCpvl 18
                                  C+ CgaC ++C  +
  gi|91774180|ref|YP_566872.1| 75 CTLCGACVASCEYV 88
                                  88888888888655 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00015
                        Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                    +++Ct+cg C ++Cp  
  gi|91774180|ref|YP_566872.1|  97 LVGKCTACGVCYNQCPRT 114
                                   578899999999999875 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 8.9e-05
                        Fer4_8   4 kCieCgaCqsaCpvl 18 
                                   kC+ Cg C ++Cp  
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCPRT 114
                                   677777777777633 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.027
                        Fer4_8  48 lwsCttcgaCt 58 
                                    ++C++c+ Ct
  gi|91774180|ref|YP_566872.1| 303 QYRCSSCKYCT 313
                                   57778887777 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.5   6.6e-06     0.007      55     111 ..      69     127 ..      44     130 .. 0.81
   2 ?    3.0   0.0       0.1   1.1e+02      81      95 ..     302     316 ..     289     328 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-06
                       Fer4_18  55 ekgagdcidcescvkvcP..tgidirkGlqleciscllcidacdkvmeklgkpkgliry 111
                                     ++g c+ c++cv+ c   t +d +  l  +c +c+ c + c + + k +   g iry
  gi|91774180|ref|YP_566872.1|  69 IIKTGICTLCGACVASCEyvTFVDNKPKLVGKCTACGVCYNQCPRTITKEEDLIGKIRY 127
                                   456889***********644889********************9988887776677777 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.1
                       Fer4_18  81 lqleciscllcidac 95 
                                    q+ c sc  c d  
  gi|91774180|ref|YP_566872.1| 302 DQYRCSSCKYCTDMV 316
                                   466666666666643 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 !    7.4   0.9    0.0078       8.2      53      64 ..      74      85 ..      26      96 .. 0.74
   2 !   11.5   1.0   0.00042      0.44       1      20 [.     100     119 ..     100     137 .. 0.85
   3 ?    3.3   0.1      0.15   1.6e+02      53      62 ..     305     314 ..     272     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0078
                       Fer4_16 53 aitgCdiCqdvC 64
                                   +t C++C++ C
  gi|91774180|ref|YP_566872.1| 74 ICTLCGACVASC 85
                                  556666666666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00042
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C+ Cg C + CP    ke+
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCPRTITKEE 119
                                   5************9887766 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                       Fer4_16  53 aitgCdiCqd 62 
                                   ++  C+ C+d
  gi|91774180|ref|YP_566872.1| 305 RCSSCKYCTD 314
                                   5555555554 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   4.1    0.0042       4.4      38      48 ..      75      85 ..      30      89 .. 0.65
   2 !    8.9  15.8    0.0022       2.3       2      50 ..      75     113 ..      74     115 .. 0.80
   3 ?    5.4   0.0     0.027        29       1      10 [.     305     314 ..     276     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                        Fer4_7 38 ClgCgaCvavC 48
                                  C+ CgaCva C
  gi|91774180|ref|YP_566872.1| 75 CTLCGACVASC 85
                                  55555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0022
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                   C+ CgaCva C + ++  ++               kC+ Cg+C + CP 
  gi|91774180|ref|YP_566872.1|  75 CTLCGACVASCEYVTFVDNKP----------KLVGKCTACGVCYNQCPR 113
                                   ************765554443..........24689************7 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.027
                        Fer4_7   1 rCigCgaCva 10 
                                   rC  C++C++
  gi|91774180|ref|YP_566872.1| 305 RCSSCKYCTD 314
                                   5666666665 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 ?    5.6   2.4     0.025        27       7      24 ..      74      90 ..      70      99 .. 0.80
   2 ?   10.9   0.5   0.00055      0.58       7      32 ..     100     125 ..      98     151 .. 0.83
   3 ?    4.5   0.1     0.055        58       3      20 ..     301     318 ..     300     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.025
                       Fer4_15  7 aCigcglCvaeapevfel 24
                                   C+ cg+Cva ++ ++++
  gi|91774180|ref|YP_566872.1| 74 ICTLCGACVASCE-YVTF 90
                                  5**********95.5554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00055
                       Fer4_15   7 aCigcglCvaeapevfeldedglasv 32 
                                   +C+ cg+C+  +p+ ++++ed + ++
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCPRTITKEEDLIGKI 125
                                   6*****************99955555 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.055
                       Fer4_15   3 vDrdaCigcglCvaeape 20 
                                   +D+ +C +c  C + ++e
  gi|91774180|ref|YP_566872.1| 301 LDQYRCSSCKYCTDMVSE 318
                                   89**********998876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.5   0.00018      0.19       7      21 ..      73      87 ..      69      88 .. 0.85
   2 ?   11.0   2.0   0.00033      0.35       8      20 ..     100     112 ..      99     122 .. 0.90
   3 ?    0.8   1.2      0.57   6.1e+02       5      16 ..     302     313 ..     300     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                        Fer4_6  7 dkCigCgdCvrvCPe 21
                                    C+ Cg+Cv+ C +
  gi|91774180|ref|YP_566872.1| 73 GICTLCGACVASCEY 87
                                  57***********75 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00033
                        Fer4_6   8 kCigCgdCvrvCP 20 
                                   kC+ Cg C++ CP
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCP 112
                                   8************ PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.57
                        Fer4_6   5 dpdkCigCgdCv 16 
                                   d+ +C +C  C+
  gi|91774180|ref|YP_566872.1| 302 DQYRCSSCKYCT 313
                                   5669*******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 ?    1.5   1.7      0.43   4.6e+02       6      17 ..      75      86 ..      72      94 .. 0.88
   2 ?   12.6   0.5   0.00014      0.15       5      19 ..     100     114 ..      98     127 .. 0.86
   3 ?    3.8   0.7     0.079        84       2      16 ..     302     316 ..     301     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.43
                       Fer4_13  6 CiacgaCvelaP 17
                                  C+ cgaCv+ + 
  gi|91774180|ref|YP_566872.1| 75 CTLCGACVASCE 86
                                  9*******9985 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                       Fer4_13   5 tCiacgaCvelaPdv 19 
                                   +C+acg+C++ +P +
  gi|91774180|ref|YP_566872.1| 100 KCTACGVCYNQCPRT 114
                                   7************87 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.079
                       Fer4_13   2 DrdtCiacgaCvela 16 
                                   D+ +C++c+ C ++ 
  gi|91774180|ref|YP_566872.1| 302 DQYRCSSCKYCTDMV 316
                                   7889*******9886 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  12.6    0.0007      0.74       3      52 ..      70     112 ..      68     117 .. 0.77
   2 ?    1.8   0.2      0.26   2.8e+02       4      48 ..     302     313 ..     293     321 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0007
                       Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                   i+   C  Cg C+ +Ce   ++ ++ +     + +  +C++C +C++ CP
  gi|91774180|ref|YP_566872.1|  70 IKTGICTLCGACVASCEY--VTFVDNK-----PKLVGKCTACGVCYNQCP 112
                                   77788************4..3444333.....345589************ PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                       Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCs 48 
                                   d+                                  +C  C+ C+
  gi|91774180|ref|YP_566872.1| 302 DQY---------------------------------RCSSCKYCT 313
                                   444.................................555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3009.58
//
Query:       gi|91774181|ref|YP_566873.1|  [L=116]
Description: hypothetical protein Mbur_2262 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00023   21.0   0.1    0.00037   20.3   0.1    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.046   13.3   0.0      0.054   13.1   0.0    1.2  1  RE_Bsp6I  Bsp6I restriction endonuclease


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 !   20.3   0.1   4.1e-08   0.00037       1      63 [.      12      82 ..      12      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.1e-08
                                  HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST........TTEEE CS
                          TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr........pklYr 63
                                  Lqkl+ s+  ak+ + Ll+ ++ t +e+  ++ + ++ v  +++ L++  +V++e+ +         k+Y+
  gi|91774181|ref|YP_566873.1| 12 LQKLNVSKPVAKALACLLSTERITSREVEMMSRLRQPEVSIAMNYLKENNWVDVEEIKkeqgkgrpIKVYS 82
                                  7899999999*********************************************9886666666444665 PP

>> RE_Bsp6I  Bsp6I restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     6e-06     0.054      38      88 ..      33      82 ..      16     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-06
                      RE_Bsp6I 38 qfggrnlnlPdefsealvaykldyvridgsavgfDavdkearkgieikaas 88
                                  ++++r++++ + + ++ v++ ++y++ ++  v  + ++ke +kg  ik  s
  gi|91774181|ref|YP_566873.1| 33 RITSREVEMMSRLRQPEVSIAMNYLKENNW-VDVEEIKKEQGKGRPIKVYS 82
                                  799*************************99.999**********8888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 874.90
//
Query:       gi|91774182|ref|YP_566874.1|  [L=413]
Description: 3-isopropylmalate dehydratase large subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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  323.9   5.3    5.1e-94  315.9   5.3    2.7  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.033   12.9   0.0      0.051   12.3   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.9   5.3   5.7e-98   5.1e-94       2     461 .]       7     405 ..       6     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 315.9 bits;  conditional E-value: 5.7e-98
                     Aconitase   2 kiwdahlvee.egiayv...pdrvllqdvtgvqalvdlaaareav.rrlggtlatidhlvpvdlvidhsvgaeealeknle 77 
                                   ki+++   ++ +  ++v   +d  + +d t+v a+  +++++ +  +++++ +   dhl+p++          ++ +++l+
  gi|91774182|ref|YP_566874.1|   7 KIFSKASGKDvKANEFVmakVDYAMAHDGTSVLAVRSFKNMGLENvWDPKRIVIPFDHLTPAN----------TETTADLH 77 
                                   6655443322212333334589*******************97655****************9..........11223333 PP

                     Aconitase  78 defernkeryefLksaakafgi.rvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgq 157
                                   +           +++     gi +++++g+GI+Hqv +E+g+a+pgk+vvg DSH++++g++G++++GvG +++ ++++  
  gi|91774182|ref|YP_566874.1|  78 HD----------IREWIGGQGIpNFFDVGEGICHQVLPENGFAMPGKLVVGADSHSCTYGAFGAFGTGVGATDMSEIFASG 148
                                   33..........3334444455589******************************************************** PP

                     Aconitase 158 plelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvde 238
                                   +l++++p++++v+ +Gklk+ v akD+ l+vig+++++g++ k+ Ef+G+++ +Ls+ +r+T++NMa+E+GA++g++p+d+
  gi|91774182|ref|YP_566874.1| 149 ELWFRVPETIKVTASGKLKKDVLAKDVTLKVIGTVGASGATYKAAEFYGDTITDLSISGRMTLSNMAIEMGAKAGIVPPDQ 229
                                   ********************************************************************************* PP

                     Aconitase 239 ktleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekea 319
                                   kt+++L+  gr+     ve y+       ++adedaey  ++++d ++lep++a p+++++++++ ++             
  gi|91774182|ref|YP_566874.1| 230 KTFDFLE--GRA-----VEGYEP------VYADEDAEYCAEYDIDGANLEPQIALPHQVDNVCDV-SE------------- 283
                                   *******..993.....355555......668*********************************.32............. PP

                     Aconitase 320 aekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiL 400
                                                 ++  kvd+++ig CTN+++ed++ aa++l+     g +v+   +t+v P+S+ +  ++ ++G+ e+L
  gi|91774182|ref|YP_566874.1| 284 --------------IEGKKVDQVFIGTCTNGRLEDLEVAAEILK-----GEQVAV--RTIVIPASRSIMLEAVRNGTAETL 343
                                   ..............334579************************.....999987..************************ PP

                     Aconitase 401 ekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaaAlaG 461
                                    +aG+++ ++gC++C+g   + + ege+++s+ NRNF+gR+g+++  yL SP+ ++a+A++G
  gi|91774182|ref|YP_566874.1| 344 LDAGVTLGSPGCGPCLGgHMGVIGEGEVCISTANRNFRGRMGKGGFIYLSSPATAAASAITG 405
                                   *****************999****************************************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.7e-06     0.051     284     357 ..     282     355 ..     253     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-06
                        DUF521 284 skakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtC 357
                                   s+ + +kvd v++G c    le+l+  ae+lkg+++   +++++ +sr+++ ea r g++e+l +aGv++ s  C
  gi|91774182|ref|YP_566874.1| 282 SEIEGKKVDQVFIGtCTNGRLEDLEVAAEILKGEQV-AVRTIVIPASRSIMLEAVRNGTAETLLDAGVTLGSPGC 355
                                   4567889******97888899**********55555.344566779**********************9877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2840.67
//
Query:       gi|91774183|ref|YP_566875.1|  [L=70]
Description: hypothetical protein Mbur_2264 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.039   14.2   0.0         11    6.4   0.0    2.1  2  DUF5388       Family of unknown function (DUF5388)
      0.057   13.6   0.1      0.073   13.2   0.1    1.2  1  Death         Death domain
       0.13   11.6   0.0       0.18   11.2   0.0    1.2  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0018        11      38      66 ..      10      37 ..       3      39 .. 0.89
   2 ?    6.1   0.0    0.0021        13      14      39 ..      43      69 ..      42      70 .] 0.91

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                       DUF5388 38 vkklveslidsLsesdkkrfkkqleiLEe 66
                                  +++l+e++i++ ses  k f++ ++ LE 
  gi|91774183|ref|YP_566875.1| 10 LEHLLEHWIEH-SESHSKSFNDWISKLEA 37
                                  67899****98.999**********9995 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0021
                       DUF5388 14 vdNHirNklqALa.aiGlaksqkeavk 39
                                  v  Hir +++ +   +G+ k +k++v 
  gi|91774183|ref|YP_566875.1| 43 VADHIRTAATKMDeCTGYLKQAKDVVR 69
                                  678*********989*********996 PP

>> Death  Death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.2e-05     0.073      46      84 ..      10      49 ..       4      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                  HHHHHHHHHHHHT.TTCSHHHHHHHHHHTTHHHHHHHHHH CS
                         Death 46 syalLqlWedreg.enatvgtLleaLrklgrddaaekles 84
                                  ++ lL +W+++      +++++++ L+ +g  ++a++++ 
  gi|91774183|ref|YP_566875.1| 10 LEHLLEHWIEHSEsHSKSFNDWISKLEAAGFKEVADHIRT 49
                                  5789****9988778899*******************986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     3e-05      0.18       5      41 ..      17      51 ..      14      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                  HTH_Tnp_ISL3  5 warrrsriTlrleayilelllesrsvkavArqlgvSw 41
                                  w+++  ++++ ++++i +l  e + +k+vA++ ++ +
  gi|91774183|ref|YP_566875.1| 17 WIEHSESHSKSFNDWISKL--EAAGFKEVADHIRTAA 51
                                  8999999************..999********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 483.64
//
Query:       gi|91774184|ref|YP_566876.1|  [L=396]
Description: hypothetical protein Mbur_2265 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-129  431.6   2.9     3e-129  431.4   2.9    1.0  1  DUF111      Protein of unknown function DUF111
  ------ inclusion threshold ------
      0.039   13.6   0.0       0.21   11.2   0.0    2.2  3  WcbI        Polysaccharide biosynthesis enzyme WcbI
      0.042   13.1   0.1      0.076   12.3   0.1    1.3  1  Zeta_toxin  Zeta toxin
       0.55   10.1   4.9        7.4    6.5   0.4    3.1  3  KH_2        KH domain


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 !  431.4   2.9  6.6e-133    3e-129       1     372 [.       4     381 ..       4     382 .. 0.98

  Alignments for each domain:
  == domain 1  score: 431.4 bits;  conditional E-value: 6.6e-133
                        DUF111   1 lyldcssGisGDmllgALldlgadkeeleealek.lgleeveleiekvkksgisatkvdveeeehehehrslaeieeiiea 80 
                                   l+++++sG+sGDm+l+ L+dlgadk e+ e +++ +   +v+++ie+ +k+gi+at+v++ +++++   rs+ e+ +ii++
  gi|91774184|ref|YP_566876.1|   4 LVFEPFSGASGDMILAGLIDLGADKGEIVEVIQAsV---DVSVTIEDITKCGIRATDVNI-HTKDSARIRSFGELIDIIKD 80 
                                   789****************************99944...579******************.66999999************ PP

                        DUF111  81 aslsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvasplalGsGtvrcahGil 161
                                   a+l+e+v+++a+a+f+++ +Aeakvhg++le++hfhEvG+ Da++d++g ++a+++++ve+++++p+++G+G+vr+ahG+l
  gi|91774184|ref|YP_566876.1|  81 ANLPEEVEKNAIAVFRIIGDAEAKVHGMSLEQLHFHEVGQDDALADVIGSCYAIHRMKVENILCTPVNVGGGSVRTAHGTL 161
                                   ********************************************************************************* PP

                        DUF111 162 PvPaPAvlellkelklkl.gevegElvTPTGaAilaalaeefgslpamkvekiGyGaGkrdleeipnvlRvlleeeeeele 241
                                   PvP+PA++e+l+++ l++ ++ ++El+TPTGaA+l+++a+  ++lp+ k+ ++GyGaG+ ++ ++pnvlR++l e++ +l+
  gi|91774184|ref|YP_566876.1| 162 PVPVPATTEILSGSGLEVhSNGDRELLTPTGAALLTYFANPSDQLPTGKILTTGYGAGDAET-DMPNVLRTMLMETTGNLS 241
                                   ****************999889****************************************.9*********99****** PP

                        DUF111 242 keevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleellfretttlGvRese.v 321
                                   ++++ vletn+DD+++evlg+++e+L+++GA Dv++tp++mKKgR++++++v++++e+ e++++ l+r+t+tlGvR  +  
  gi|91774184|ref|YP_566876.1| 242 RDHMEVLETNVDDVTGEVLGNLFETLMKEGAKDVTITPATMKKGRTGHIIHVIAHPENSERIARELIRQTGTLGVRILPtK 322
                                   ******************************************************************************989 PP

                        DUF111 322 erlvlereietvetelg....evrvKva....eevvkvkpEyedvkkiAeetglplkev 372
                                   +r+++er++e+v++ +g    +v+vK+a    +ev+++++E+ed+++i++e glplkev
  gi|91774184|ref|YP_566876.1| 323 HRFIAERKMEKVNIIIGkqtfQVTVKIAhdrsDEVLHISAEFEDCRRISQECGLPLKEV 381
                                   *****************9999*******987555************************9 PP

>> WcbI  Polysaccharide biosynthesis enzyme WcbI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.4   1.8e+03     105     137 ..       7      39 ..       5      49 .. 0.82
   2 ?   11.2   0.0   4.6e-05      0.21     150     202 ..     262     312 ..     235     315 .. 0.82
   3 ?   -2.8   0.0      0.92   4.1e+03     150     179 ..     363     390 ..     353     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                          WcbI 105 dpplvdYhdlrllaaaarglsaeeavalfrrdv 137
                                   +p  ++  d++l+ +++ g ++ e+v+++++ v
  gi|91774184|ref|YP_566876.1|   7 EPFSGASGDMILAGLIDLGADKGEIVEVIQASV 39 
                                   567778889*****************9998754 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.6e-05
                          WcbI 150 slaelrrreaahdvdlsdlleewsrrgqlmhtinHPgnavlldlarrvlaalg 202
                                   +l e   +e a dv++     + +r g+  h i+HP n+  +++ar ++++ g
  gi|91774184|ref|YP_566876.1| 262 NLFETLMKEGAKDVTITPATMKKGRTGHIIHVIAHPENS--ERIARELIRQTG 312
                                   556667789999*************************97..667777766665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.92
                          WcbI 150 slaelrrreaahdvdlsdlleewsrrgqlm 179
                                   + +  rr +++++++l+++++++ ++  ++
  gi|91774184|ref|YP_566876.1| 363 EFEDCRRISQECGLPLKEVIRRAEEK--AW 390
                                   56677888899999999999977655..55 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.7e-05     0.076      77     194 ..     241     359 ..     227     363 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                    Zeta_toxin  77 qkdaselvekllqeaiengyniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeeevaeg.Rlvpk 156
                                   ++d  e+ e+ ++ ++ +    ++e+ +++  +  +++ a  k+G++ +++ v++++e S   +++  +++++ g R+ p 
  gi|91774184|ref|YP_566876.1| 241 SRDHMEVLETNVDDVTGEVLGNLFETLMKEGAKDVTITPATMKKGRTGHIIHVIAHPENSERIARELIRQTGTLGvRILPT 321
                                   666777777888888888888899999*99999999999999******************998877777775568687776 PP

                    Zeta_toxin 157 eehdeafeglresvealeeekqldrvk.ik.drdgktvly 194
                                    +h  + e+ +e+v+++  +++++ ++ i+ dr++ +vl+
  gi|91774184|ref|YP_566876.1| 322 -KHRFIAERKMEKVNIIIGKQTFQVTVkIAhDRSD-EVLH 359
                                   .5667777777788888777777654445536776.4443 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2    0.0098        44       2      35 ..      35      64 ..      34      68 .. 0.85
   2 ?   -1.4   0.0      0.47   2.1e+03       6      37 ..     263     288 ..     261     291 .. 0.68
   3 ?    6.5   0.4    0.0016       7.4       6      43 ..     303     341 ..     300     345 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0098
                                  HHHHHHHHTECETEEEEEEECCSCEEEEEEEESC CS
                          KH_2  2 ipeslaveikkagvskveIertanrviiviresq 35
                                  i  s+ v+++ +++ k+ I    +++ + i++  
  gi|91774184|ref|YP_566876.1| 35 IQASVDVSVTIEDITKCGI----RATDVNIHTKD 64
                                  567999*************....89999999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.47
                                   HHHHTECETEEEEEEECCSCEEEEEEEESCHH CS
                          KH_2   6 laveikkagvskveIertanrviiviresqpg 37 
                                   l++++ k+g+++v I      +  ++++++ g
  gi|91774184|ref|YP_566876.1| 263 LFETLMKEGAKDVTI------TPATMKKGRTG 288
                                   678888999999999......33455555555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0016
                                   HHHHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGG CS
                          KH_2   6 lavei.kkagvskveIertanrviiviresqpgivIGkg 43 
                                   +a+e+ ++ g+ +v+I  t++r i   + ++  i+IGk+
  gi|91774184|ref|YP_566876.1| 303 IARELiRQTGTLGVRILPTKHRFIAERKMEKVNIIIGKQ 341
                                   66777799999**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2610.16
//
Query:       gi|91774185|ref|YP_566877.1|  [L=256]
Description: phosphoribosylaminoimidazole carboxylase related protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   66.8   4.0    2.1e-18   66.3   4.0    1.3  1  AIRC          AIR carboxylase
  ------ inclusion threshold ------
      0.082   12.3   0.0        1.4    8.3   0.0    2.1  2  Peripla_BP_1  Periplasmic binding proteins and sugar binding 
       0.18   12.1   0.0       0.33   11.3   0.0    1.4  1  La_HTH_kDCL   La HTH in kinetoplastid DICER domain


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 !   66.3   4.0   3.5e-22   2.1e-18       2     128 ..     122     249 ..     121     256 .] 0.86

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.5e-22
                                   EEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS CS
                          AIRC   2 VgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttl 78 
                                   V+ii + + D++v+++a  + +e+g      y+v v+  hr  +e++++ ++      ++i+++AG++  Lp vv+sl ++
  gi|91774185|ref|YP_566877.1| 122 VAIISAGTADIDVAEEARMAASEMGCntikIYDVGVAGFHRLISEMKSFEKN----RPDAIVVAAGREGTLPTVVSSLIDV 198
                                   9**********************998555557*************9988775....5679********************* PP

                                   -EEEEEE--...STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHT CS
                          AIRC  79 PVigvPvks...kalkgldsllSivqmPsgvpvatvaigkaknAallAaqila 128
                                   PVig Pv++      kg  +llS++q +s ++v++++   +  A+ +Aa+i  
  gi|91774185|ref|YP_566877.1| 199 PVIGLPVSTgygAGAKGEAALLSMLQSCSILSVVNID--AGFVAGAFAARIAN 249
                                   ********854346999***************98888..77777777777743 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 ?    1.8   0.0     0.022   1.3e+02     133     154 ..      40      61 ..      32      83 .. 0.73
   2 ?    8.3   0.0   0.00023       1.4      24      83 ..     139     201 ..     132     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.022
                                   HHHHHHHHHHHHHHHTT-GGGE CS
                  Peripla_BP_1 133 takervqGflaalaeaGlevkd 154
                                   t ++ ++Gf++a+ + G e  d
  gi|91774185|ref|YP_566877.1|  40 TFRKCRTGFMEAILAEGKEADD 61 
                                   6688899*******99995433 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00023
                                   HHHHHHHTEEEEEEE-SSHHHHH...HHHHHHHHTT-SEEEEE.-S-GGHHHHHHHHHHT-EEE CS
                  Peripla_BP_1  24 tkaakehgvdvlllaageeedla...kaidllkakgidgliia.tsdtsfdditakaesgipvi 83 
                                     aa+e g +++++ + + +  +   + +++ +++++d++++a ++ +  + ++     ++pvi
  gi|91774185|ref|YP_566877.1| 139 RMAASEMGCNTIKIYDVGVAGFHrliSEMKSFEKNRPDAIVVAaGREGTLPTVVSSLI-DVPVI 201
                                   5699************999999988999**************9778777776665433.47776 PP

>> La_HTH_kDCL  La HTH in kinetoplastid DICER domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.4e-05      0.33       5      43 ..       2      37 ..       1      52 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                   La_HTH_kDCL  5 klvriLRlvsvystalqnlgtlesillasGWvPleevls 43
                                  +l+ iLR+v   st+l+n    es++ + G vP++++ +
  gi|91774185|ref|YP_566877.1|  2 ELKNILRQVKDGSTELEN---AESQIRSMGYVPVSDIAK 37
                                  5799***********999...9**************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1830.12
//
Query:       gi|91774186|ref|YP_566878.1|  [L=1519]
Description: TPR repeat-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-25   85.9  13.4    2.6e-06   27.1   0.4    8.7  8  TPR_10           Tetratricopeptide repeat
    4.5e-20   71.7  27.3    7.3e-09   35.8   0.9   12.2 11  TPR_12           Tetratricopeptide repeat
    1.1e-12   47.0   4.6     0.0043   17.0   0.1    8.4  7  TPR_7            Tetratricopeptide repeat
    1.2e-10   40.7  24.4       0.42   10.8   0.3   12.4 12  TPR_2            Tetratricopeptide repeat
    1.8e-09   37.3  15.3       0.32   11.5   0.0   14.0 13  TPR_17           Tetratricopeptide repeat
    1.8e-08   34.5  18.2         10    7.3   0.0   13.1 12  TPR_14           Tetratricopeptide repeat
      8e-07   28.6  14.0      0.049   13.5   0.3    8.4 10  TPR_1            Tetratricopeptide repeat
      1e-05   25.5   9.2        6.1    7.0   0.0    8.3  9  MIT              MIT (microtubule interacting and transport) 
    2.9e-05   23.7  13.8        9.1    6.1   0.0   10.6 11  TPR_11           TPR repeat
      5e-05   23.2  28.3      0.025   14.8   0.3   11.4 13  TPR_8            Tetratricopeptide repeat
    0.00037   21.0  12.0         12    6.8   0.1    8.9  7  TPR_6            Tetratricopeptide repeat
    0.00051   19.8   6.6        6.3    6.5   0.0    6.9 10  TPR_21           Tetratricopeptide repeat-like domain
     0.0041   17.6  27.3        4.9    7.7   2.1   11.2 13  TPR_19           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.014   15.1   1.6       0.27   10.9   0.2    2.5  2  DUF2225          Uncharacterized protein conserved in bacteri
       0.12   12.8   0.3         15    6.1   0.0    3.3  2  3HCDH_RFF        3-hydroxybutyryl-CoA dehydrogenase reduced R
       0.15   11.8   1.0        0.8    9.4   0.2    2.7  2  TOM20_plant      Plant specific mitochondrial import receptor
       0.18   10.9  12.9        6.4    5.8   0.1    6.6  7  FANCI_S4         FANCI solenoid 4
       0.34   11.1   3.3         45    4.3   0.0    5.4  6  SesA             N-terminal domain on NACHT_NTPase and P-loop
       0.81    9.9   3.0        2.4    8.3   0.2    3.4  3  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
        8.5    6.0  12.6       0.75    9.5   0.4    5.0  6  UTP15_C          UTP15 C terminal


Domain annotation for each model (and alignments):
>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0045         4       2      38 ..      94     130 ..      94     134 .. 0.91
   2 !    9.0   0.0    0.0014       1.3       3      35 ..     143     175 ..     142     180 .. 0.90
   3 !    8.4   0.1    0.0022         2       2      22 ..     190     210 ..     189     226 .. 0.88
   4 ?   -1.7   0.0       3.4     3e+03       8      34 ..     580     606 ..     579     612 .. 0.81
   5 ?    2.7   0.0      0.13   1.2e+02       9      35 ..    1349    1375 ..    1341    1379 .. 0.84
   6 !   21.4   0.0   1.8e-07   0.00016       2      38 ..    1390    1426 ..    1389    1428 .. 0.93
   7 !   27.1   0.4   2.9e-09   2.6e-06       2      40 ..    1438    1476 ..    1437    1478 .. 0.95
   8 !    9.9   0.1   0.00074      0.66       4      28 ..    1488    1512 ..    1487    1519 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0045
                        TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllGp 38 
                                   A ++n  a +l + g+ + A  l+ee++ ++ +ll  
  gi|91774186|ref|YP_566878.1|  94 ALAMNKAATLLANKGDVEHAGYLFEETVKAYDKLLSK 130
                                   6699*****************************9975 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                        TPR_10   3 sslnNLanalrqrgrydeAealleealairrrl 35 
                                   s+ln+ a +l +rg+ ++A + +e++l +  +l
  gi|91774186|ref|YP_566878.1| 143 SALNDVATILAERGQQKDAKERFERSLKLSAKL 175
                                   69*************************987665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0022
                        TPR_10   2 AsslnNLanalrqrgrydeAe 22 
                                   +++++NLan+l+++g +++A 
  gi|91774186|ref|YP_566878.1| 190 LTIQTNLANLLYDMGLLEDAK 210
                                   689************999995 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.4
                        TPR_10   8 LanalrqrgrydeAealleealairrr 34 
                                   +++ l + gr+ +A+  +  +la+  +
  gi|91774186|ref|YP_566878.1| 580 MGRFLMDAGRLSAARSSYGSTLAVLTK 606
                                   589999********9988888877655 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.13
                        TPR_10    9 analrqrgrydeAealleealairrrl 35  
                                    +  l + gr  +A+  +e al+ir+ l
  gi|91774186|ref|YP_566878.1| 1349 GSFLMNAGRNVDARSSYEMALSIRKML 1375
                                    778999******************966 PP

  == domain 6  score: 21.4 bits;  conditional E-value: 1.8e-07
                        TPR_10    2 AsslnNLanalrqrgrydeAealleealairrrllGp 38  
                                    As++nNL+ +  q g+++eA a++e +l ++  l+ +
  gi|91774186|ref|YP_566878.1| 1390 ASIRNNLGTMFAQDGEFTEAKAMFEASLKTYVDLFDR 1426
                                    99*****************************988765 PP

  == domain 7  score: 27.1 bits;  conditional E-value: 2.9e-09
                        TPR_10    2 AsslnNLanalrqrgrydeAealleealairrrllGpdH 40  
                                    A +lnNLa +  ++gr+++A  ++e al+++ +ll++d+
  gi|91774186|ref|YP_566878.1| 1438 ALTLNNLAKLFADMGRHEDAKSIYESALEAYVELLNADP 1476
                                    679********************************9986 PP

  == domain 8  score: 9.9 bits;  conditional E-value: 0.00074
                        TPR_10    4 slnNLanalrqrgrydeAealleea 28  
                                    +l NL+ +l ++gr++++ +++e a
  gi|91774186|ref|YP_566878.1| 1488 TLDNLGSLLGEMGRGEDSIRMHEAA 1512
                                    799******************9987 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.64   5.7e+02      17      71 ..      23      75 ..       9      80 .. 0.70
   2 !   11.8   0.4   0.00026      0.23       6      74 ..      97     171 ..      92     174 .. 0.69
   3 ?    6.0   0.0     0.017        15       3      31 ..     190     218 ..     188     230 .. 0.81
   4 ?    2.3   0.0      0.23   2.1e+02       2      36 ..     237     271 ..     236     276 .. 0.89
   5 ?    1.0   0.0      0.58   5.2e+02       3      36 ..     574     607 ..     572     615 .. 0.84
   6 ?    3.2   0.1      0.12   1.1e+02       3      32 ..     670     699 ..     668     707 .. 0.80
   7 ?   -1.3   0.0       3.2   2.8e+03       6      27 ..     769     790 ..     764     795 .. 0.77
   8 ?   -1.5   0.1       3.5   3.1e+03      41      73 ..    1050    1082 ..    1036    1084 .. 0.76
   9 ?    4.5   0.0     0.047        43       2      35 ..    1341    1374 ..    1340    1384 .. 0.86
  10 !   35.8   0.9   8.1e-12   7.3e-09       2      75 ..    1389    1468 ..    1388    1470 .. 0.89
  11 !   28.0   1.7   2.3e-09     2e-06       3      76 ..    1438    1517 ..    1436    1518 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.64
                        TPR_12 17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71
                                  g+  +Ale l  a  +a+ +  +  +l++++ +  + + +  g+ ++Ale++  a
  gi|91774186|ref|YP_566878.1| 23 GQQKKALEVLLVAEKQAKDA--GSTDLLINIFQSVAKIMESNGEKDAALERYLGA 75
                                  55555666666666666555..556689999999999999999999999988655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00026
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpd......hpltattlrnLgrlyralgryeeAlelleealai 74 
                                   +n+ a++l+  g+ + A  l+e+ + ++ +ll ++          +++l++ ++++ ++g++++A e++e++l++
  gi|91774186|ref|YP_566878.1|  97 MNKAATLLANKGDVEHAGYLFEETVKAYDKLLSKEpnnvvhCSSMSSALNDVATILAERGQQKDAKERFERSLKL 171
                                   5455666666777777777777777777666554411111112356899************************97 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.017
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekale 31 
                                   +t+++nla++l+ +g +++A  ++e  + 
  gi|91774186|ref|YP_566878.1| 190 LTIQTNLANLLYDMGLLEDAKINFESTYG 218
                                   689999**************999997765 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.23
                        TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrl 36 
                                   +a +l +  +vl+ +++y+ + + l++ +++ +r 
  gi|91774186|ref|YP_566878.1| 237 IADTLEKQVNVLFDMQEYAASGKKLHELMDMLQRF 271
                                   78899899*********************999875 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.58
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrl 36 
                                   a++  +++ +l+ +gr+  A++ +   l++ ++l
  gi|91774186|ref|YP_566878.1| 574 AKLNERMGRFLMDAGRLSAARSSYGSTLAVLTKL 607
                                   5666689****************99999988776 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.12
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                   a +  +++++l+ +gr++ A++ ++ al +
  gi|91774186|ref|YP_566878.1| 670 AELNERVGSLLMNAGRLAAARSKYDSALTV 699
                                   556667899999999999999999988865 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 3.2
                        TPR_12   6 lnnlaavlrrlgrydeAlelle 27 
                                     ++++vl+++gr+   ++ +e
  gi|91774186|ref|YP_566878.1| 769 NQRMGNVLMKAGRLSAGRSKYE 790
                                   3369*********988887776 PP

  == domain 8  score: -1.5 bits;  conditional E-value: 3.5
                        TPR_12   41 hpltattlrnLgrlyralgryeeAlelleeala 73  
                                    h+  a+   ++  +++ +g++++A+++   +l+
  gi|91774186|ref|YP_566878.1| 1050 HAKIAELNEGMVLTLLTAGHLDAARAMSDSTLD 1082
                                    666666666666778889999999998777665 PP

  == domain 9  score: 4.5 bits;  conditional E-value: 0.047
                        TPR_12    2 vatalnnlaavlrrlgrydeAlellekaleiarr 35  
                                    va ++ + +++l+ +gr  +A++ +e al i++ 
  gi|91774186|ref|YP_566878.1| 1341 VADLYDRKGSFLMNAGRNVDARSSYEMALSIRKM 1374
                                    56777789*********************99865 PP

  == domain 10  score: 35.8 bits;  conditional E-value: 8.1e-12
                        TPR_12    2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpl......tattlrnLgrlyralgryeeAlelleealai 74  
                                    +a++ nnl+++ ++ g+++eA +++e++l  +  l++ d+++      +a tl+nL+ l+  +gr+e+A +++e al++
  gi|91774186|ref|YP_566878.1| 1389 IASIRNNLGTMFAQDGEFTEAKAMFEASLKTYVDLFDRDKEDaayqygAALTLNNLAKLFADMGRHEDAKSIYESALEA 1467
                                    689999***************************999998775222222689***************************8 PP

                        TPR_12   75 a 75  
                                    +
  gi|91774186|ref|YP_566878.1| 1468 Y 1468
                                    7 PP

  == domain 11  score: 28.0 bits;  conditional E-value: 2.3e-09
                        TPR_12    3 atalnnlaavlrrlgrydeAlellekaleiarrllGpd........hpltattlrnLgrlyralgryeeAlelleeala 73  
                                    a +lnnla + + +gr+++A +++e ale++ +ll+ d        h  +++tl nLg l+ ++gr e+ ++++e a +
  gi|91774186|ref|YP_566878.1| 1438 ALTLNNLAKLFADMGRHEDAKSIYESALEAYVELLNADpenvrykkH--ASITLDNLGSLLGEMGRGEDSIRMHEAAQE 1514
                                    78999**************************9999987333333223..799***********************9999 PP

                        TPR_12   74 iae 76  
                                    ++ 
  gi|91774186|ref|YP_566878.1| 1515 LRN 1517
                                    875 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      0.13   1.2e+02       1      29 [.     144     172 ..     144     184 .. 0.84
   2 ?   -1.4   0.0       3.6   3.2e+03       2      20 ..     680     698 ..     662     703 .. 0.68
   3 ?   -2.7   0.0         9   8.1e+03      13      32 ..    1219    1236 ..    1216    1239 .. 0.71
   4 ?   -0.8   0.0       2.2     2e+03       3      29 ..    1346    1372 ..    1344    1378 .. 0.84
   5 !   11.0   0.0    0.0004      0.36       3      35 ..    1394    1426 ..    1391    1427 .. 0.92
   6 !   17.0   0.1   4.8e-06    0.0043       1      28 [.    1440    1467 ..    1440    1478 .. 0.87
   7 !    7.6   0.0    0.0049       4.4       1      27 [.    1488    1512 ..    1488    1519 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                   aL+  a +  ++G+ ++A e +e+sL l 
  gi|91774186|ref|YP_566878.1| 144 ALNDVATILAERGQQKDAKERFERSLKLS 172
                                   5777789999**************99765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                         TPR_7   2 LlnLarlysrlGdyeeAie 20 
                                   L n +rl  ++ +y+ A++
  gi|91774186|ref|YP_566878.1| 680 LMNAGRLAAARSKYDSALT 698
                                   3455555555666666655 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9
                         TPR_7   13 GdyeeAielyeqsLaltkdp 32  
                                     d+  +i+ ye+    t  p
  gi|91774186|ref|YP_566878.1| 1219 ADFNFLISMYEK--LSTLNP 1236
                                    688889*****9..555444 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.2
                         TPR_7    3 lnLarlysrlGdyeeAielyeqsLalt 29  
                                    ++ ++   + G+  +A + ye +L ++
  gi|91774186|ref|YP_566878.1| 1346 DRKGSFLMNAGRNVDARSSYEMALSIR 1372
                                    56688889999999********88765 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.0004
                         TPR_7    3 lnLarlysrlGdyeeAielyeqsLaltkdpeda 35  
                                    +nL+ ++ ++G++ eA   +e+sL +  d +d+
  gi|91774186|ref|YP_566878.1| 1394 NNLGTMFAQDGEFTEAKAMFEASLKTYVDLFDR 1426
                                    8***********************999988875 PP

  == domain 6  score: 17.0 bits;  conditional E-value: 4.8e-06
                         TPR_7    1 aLlnLarlysrlGdyeeAielyeqsLal 28  
                                    +L+nLa l+ ++G++e+A ++ye +L+ 
  gi|91774186|ref|YP_566878.1| 1440 TLNNLAKLFADMGRHEDAKSIYESALEA 1467
                                    79**********************8854 PP

  == domain 7  score: 7.6 bits;  conditional E-value: 0.0049
                         TPR_7    1 aLlnLarlysrlGdyeeAielyeqsLa 27  
                                    +L+nL++l  ++G+ e+ i+ +e+  a
  gi|91774186|ref|YP_566878.1| 1488 TLDNLGSLLGEMGRGEDSIRMHEA--A 1512
                                    79*********************9..4 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.31   2.8e+02       4      27 ..      12      35 ..       9      42 .. 0.82
   2 ?    1.1   0.2      0.62   5.6e+02       1      30 [.      94     123 ..      94     127 .. 0.85
   3 ?    0.5   0.2         1   8.9e+02      21      34 .]     121     134 ..     101     134 .. 0.72
   4 !    7.4   0.0    0.0059       5.3       3      31 ..     144     172 ..     142     174 .. 0.92
   5 ?    2.6   0.0       0.2   1.8e+02       6      25 ..     195     214 ..     191     215 .. 0.89
   6 ?    0.4   0.0         1   9.3e+02       1      24 [.     574     597 ..     574     602 .. 0.88
   7 ?    5.8   0.0     0.019        17       1      28 [.     670     697 ..     670     702 .. 0.90
   8 ?    2.5   0.0      0.23     2e+02       1      24 [.     766     789 ..     766     791 .. 0.83
   9 ?    5.1   0.0     0.032        28       1      30 [.    1342    1371 ..    1342    1373 .. 0.92
  10 ?    6.5   0.0     0.011        10       5      29 ..    1394    1418 ..    1390    1420 .. 0.90
  11 !   10.8   0.3   0.00047      0.42       2      30 ..    1439    1467 ..    1438    1471 .. 0.93
  12 ?    4.1   0.1     0.066        59      17      34 .]    1461    1478 ..    1459    1478 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                         TPR_2  4 lynlGlayyklgdyeeAleafekA 27
                                  ++  G++ +++g+ ++Ale +  A
  gi|91774186|ref|YP_566878.1| 12 NFKKGMSFLEAGQQKKALEVLLVA 35
                                  6889**************988665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.62
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                   a a +  + +++++gd e A  +fe+ ++ 
  gi|91774186|ref|YP_566878.1|  94 ALAMNKAATLLANKGDVEHAGYLFEETVKA 123
                                   567888999***************998775 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1
                         TPR_2  21 leafekAleldPnn 34 
                                   ++a++k l+ +Pnn
  gi|91774186|ref|YP_566878.1| 121 VKAYDKLLSKEPNN 134
                                   57888888888886 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0059
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                   al+  + +++++g+ ++A+e fe++l+l 
  gi|91774186|ref|YP_566878.1| 144 ALNDVATILAERGQQKDAKERFERSLKLS 172
                                   7888999********************95 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.2
                         TPR_2   6 nlGlayyklgdyeeAleafe 25 
                                   nl++++y +g +e+A+  fe
  gi|91774186|ref|YP_566878.1| 195 NLANLLYDMGLLEDAKINFE 214
                                   9**************98886 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1
                         TPR_2   1 aealynlGlayyklgdyeeAleaf 24 
                                   a+++ ++G+ ++ +g++  A+  +
  gi|91774186|ref|YP_566878.1| 574 AKLNERMGRFLMDAGRLSAARSSY 597
                                   5677899*************9888 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.019
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAl 28 
                                   ae++ + G +++++g+++ A+  ++ Al
  gi|91774186|ref|YP_566878.1| 670 AELNERVGSLLMNAGRLAAARSKYDSAL 697
                                   67788999****************9998 PP

  == domain 8  score: 2.5 bits;  conditional E-value: 0.23
                         TPR_2   1 aealynlGlayyklgdyeeAleaf 24 
                                   ae++ ++G++++k+g++   +  +
  gi|91774186|ref|YP_566878.1| 766 AELNQRMGNVLMKAGRLSAGRSKY 789
                                   68899***********98766666 PP

  == domain 9  score: 5.1 bits;  conditional E-value: 0.032
                         TPR_2    1 aealynlGlayyklgdyeeAleafekAlel 30  
                                    a+++ + G  ++++g+  +A+  +e Al++
  gi|91774186|ref|YP_566878.1| 1342 ADLYDRKGSFLMNAGRNVDARSSYEMALSI 1371
                                    678999*********************987 PP

  == domain 10  score: 6.5 bits;  conditional E-value: 0.011
                         TPR_2    5 ynlGlayyklgdyeeAleafekAle 29  
                                    +nlG   ++ g++ eA++ fe++l+
  gi|91774186|ref|YP_566878.1| 1394 NNLGTMFAQDGEFTEAKAMFEASLK 1418
                                    89********************998 PP

  == domain 11  score: 10.8 bits;  conditional E-value: 0.00047
                         TPR_2    2 ealynlGlayyklgdyeeAleafekAlel 30  
                                      l+nl+++ + +g++e+A+  +e Ale 
  gi|91774186|ref|YP_566878.1| 1439 LTLNNLAKLFADMGRHEDAKSIYESALEA 1467
                                    679************************96 PP

  == domain 12  score: 4.1 bits;  conditional E-value: 0.066
                         TPR_2   17 yeeAleafekAleldPnn 34  
                                    ye Alea+ + l  dP+n
  gi|91774186|ref|YP_566878.1| 1461 YESALEAYVELLNADPEN 1478
                                    99**************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.82   7.3e+02      13      29 ..      94     110 ..      82     113 .. 0.83
   2 !   11.5   0.0   0.00036      0.32       1      34 []     123     163 ..     123     163 .. 0.96
   3 ?    0.5   0.1       1.1     1e+03      17      32 ..     194     209 ..     186     211 .. 0.69
   4 ?   -0.3   0.0         2   1.8e+03       5      16 ..     415     426 ..     412     428 .. 0.82
   5 ?    0.3   0.0       1.4   1.2e+03       2      29 ..     556     584 ..     555     593 .. 0.82
   6 ?    2.6   0.0      0.23   2.1e+02       2      33 ..     652     690 ..     651     691 .. 0.83
   7 ?    2.8   0.0      0.22   1.9e+02       1      31 [.     747     778 ..     747     782 .. 0.81
   8 ?   -0.6   0.0       2.6   2.4e+03       5      25 ..     991    1011 ..     988    1017 .. 0.86
   9 ?   -1.7   0.0       5.7   5.1e+03       1      32 [.    1035    1073 ..    1035    1075 .. 0.64
  10 ?   -0.3   0.0       2.1   1.9e+03       7      25 ..    1089    1107 ..    1087    1112 .. 0.87
  11 ?    2.0   0.0      0.37   3.3e+02       2      33 ..    1324    1362 ..    1323    1363 .. 0.73
  12 ?    0.5   0.0       1.1     1e+03      15      33 ..    1392    1410 ..    1389    1411 .. 0.87
  13 ?    5.4   0.1     0.031        28      14      33 ..    1439    1458 ..    1435    1459 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.82
                        TPR_17  13 adaynnLAelllknGdl 29 
                                   a a+n  A+ll+++Gd 
  gi|91774186|ref|YP_566878.1|  94 ALAMNKAATLLANKGDV 110
                                   7899999********95 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00036
                        TPR_17   1 lylkaleldPnn.......adaynnLAelllknGdlmtArq 34 
                                   +y k l ++Pnn       + a+n  A++l+++G+ ++A++
  gi|91774186|ref|YP_566878.1| 123 AYDKLLSKEPNNvvhcssmSSALNDVATILAERGQQKDAKE 163
                                   59************************************986 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.1
                        TPR_17  17 nnLAelllknGdlmtA 32 
                                   +nLA+ll+  G l++A
  gi|91774186|ref|YP_566878.1| 194 TNLANLLYDMGLLEDA 209
                                   4777777777766666 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2
                        TPR_17   5 aleldPnnaday 16 
                                    +++dPnn++++
  gi|91774186|ref|YP_566878.1| 415 LMQKDPNNVNLL 426
                                   5789*****986 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.4
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGd.l 29 
                                   y+   ++dP+++ ++   A+l ++ G+ l
  gi|91774186|ref|YP_566878.1| 556 YEMLSRIDPSDFSHHVKIAKLNERMGRfL 584
                                   6666789************9999888744 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.23
                        TPR_17   2 ylkaleldPnnadaynnLAelll.......knGdlmtAr 33 
                                   y+k   ldP++  +y   Ael +       ++G+l+ Ar
  gi|91774186|ref|YP_566878.1| 652 YEKLSILDPTDLSHYVKIAELNErvgsllmNAGRLAAAR 690
                                   8999999****9999999999886777777778887776 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.22
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGd.lmt 31 
                                   +y+k  +ldP++   y   Ael  + G+ lm+
  gi|91774186|ref|YP_566878.1| 747 MYEKLSQLDPSDLSYYVKIAELNQRMGNvLMK 778
                                   69**********99999999988887774544 PP

  == domain 8  score: -0.6 bits;  conditional E-value: 2.6
                        TPR_17    5 aleldPnnadaynnLAelllk 25  
                                     ++++P+n+ ++ + +++l +
  gi|91774186|ref|YP_566878.1|  991 LVQKEPDNFTFFSMIGTILTN 1011
                                    67899***********99976 PP

  == domain 9  score: -1.7 bits;  conditional E-value: 5.7
                        TPR_17    1 lylkaleldPnnadaynnLAelll.......knGdlmtA 32  
                                    +y+k   l+P++   +   Ael +        +G l+ A
  gi|91774186|ref|YP_566878.1| 1035 MYEKLSTLNPSDLSYHAKIAELNEgmvltllTAGHLDAA 1073
                                    588888999998777777776655444444466666665 PP

  == domain 10  score: -0.3 bits;  conditional E-value: 2.1
                        TPR_17    7 eldPnnadaynnLAelllk 25  
                                    +++P+n+ ++ + +++l +
  gi|91774186|ref|YP_566878.1| 1089 QKEPDNVTFLSMIGTILTN 1107
                                    689************9976 PP

  == domain 11  score: 2.0 bits;  conditional E-value: 0.37
                        TPR_17    2 ylkaleldPnn.......adaynnLAelllknGdlmtAr 33  
                                    y+k   +dP +       ad+y  ++ +l ++G+  +Ar
  gi|91774186|ref|YP_566878.1| 1324 YEKLSLIDPFDlshhtkvADLYDRKGSFLMNAGRNVDAR 1362
                                    777777788875555556788888888888999998887 PP

  == domain 12  score: 0.5 bits;  conditional E-value: 1.1
                        TPR_17   15 aynnLAelllknGdlmtAr 33  
                                      nnL++ +++ G++ +A+
  gi|91774186|ref|YP_566878.1| 1392 IRNNLGTMFAQDGEFTEAK 1410
                                    68************99997 PP

  == domain 13  score: 5.4 bits;  conditional E-value: 0.031
                        TPR_17   14 daynnLAelllknGdlmtAr 33  
                                      +nnLA+l++  G++++A+
  gi|91774186|ref|YP_566878.1| 1439 LTLNNLAKLFADMGRHEDAK 1458
                                    579**************997 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       5.6     5e+03      11      33 ..      19      41 ..      14      47 .. 0.82
   2 ?    0.9   0.0       1.3   1.1e+03      16      35 ..     116     135 ..      99     137 .. 0.77
   3 ?    3.4   0.1      0.19   1.7e+02       6      31 ..     147     172 ..     143     178 .. 0.86
   4 ?   -1.6   0.0       8.1   7.3e+03      11      34 ..     254     278 ..     249     281 .. 0.77
   5 ?    0.1   0.0       2.3   2.1e+03       6      23 ..     579     596 ..     575     615 .. 0.80
   6 ?    7.3   0.0     0.011        10       7      37 ..     683     713 ..     677     724 .. 0.80
   7 ?   -1.3   0.0       6.3   5.7e+03      21      43 ..     745     767 ..     743     768 .. 0.84
   8 ?   -1.3   0.0       6.4   5.8e+03      10      23 ..    1063    1076 ..    1059    1099 .. 0.76
   9 ?    0.1   0.0       2.3     2e+03      14      36 ..    1170    1192 ..    1155    1196 .. 0.63
  10 ?    4.2   0.0      0.11        97       2      30 ..    1343    1371 ..    1342    1373 .. 0.88
  11 ?    6.8   0.0     0.016        14       8      33 ..    1397    1422 ..    1395    1440 .. 0.79
  12 ?    5.8   0.1     0.032        29       7      31 ..    1444    1468 ..    1437    1484 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.6
                        TPR_14 11 llalGdpdeAiallrralalaPd 33
                                  +l++G+ ++A+++l  a ++a d
  gi|91774186|ref|YP_566878.1| 19 FLEAGQQKKALEVLLVAEKQAKD 41
                                  6899********99877777665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.3
                        TPR_14  16 dpdeAiallrralalaPdda 35 
                                    ++e +++++++l++ P++ 
  gi|91774186|ref|YP_566878.1| 116 LFEETVKAYDKLLSKEPNNV 135
                                   489999***********985 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.19
                        TPR_14   6 alaeallalGdpdeAiallrralala 31 
                                   + a +l+++G+ ++A + ++r l+l 
  gi|91774186|ref|YP_566878.1| 147 DVATILAERGQQKDAKERFERSLKLS 172
                                   67899*****************9976 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 8.1
                        TPR_14  11 llalG.dpdeAiallrralalaPdd 34 
                                   ++a+G ++ e +++l+r  ++ P +
  gi|91774186|ref|YP_566878.1| 254 YAASGkKLHELMDMLQRFAKDEPRF 278
                                   55555369999******99998876 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 2.3
                        TPR_14   6 alaeallalGdpdeAial 23 
                                   +++++l+ +G++ +A+  
  gi|91774186|ref|YP_566878.1| 579 RMGRFLMDAGRLSAARSS 596
                                   578999999999988755 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.011
                        TPR_14   7 laeallalGdpdeAiallrralalaPddaea 37 
                                   ++++ +a+ ++d A+++l ++++++Pd+ ++
  gi|91774186|ref|YP_566878.1| 683 AGRLAAARSKYDSALTVLMDLIQDDPDNFTF 713
                                   6788899999*****************9764 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 6.3
                        TPR_14  21 iallrralalaPddaeawlllaq 43 
                                   i +++++ +l+P+d+ ++   a+
  gi|91774186|ref|YP_566878.1| 745 ISMYEKLSQLDPSDLSYYVKIAE 767
                                   5699**********999887776 PP

  == domain 8  score: -1.3 bits;  conditional E-value: 6.4
                        TPR_14   10 allalGdpdeAial 23  
                                     ll++G +d+A+a+
  gi|91774186|ref|YP_566878.1| 1063 TLLTAGHLDAARAM 1076
                                    67888888888876 PP

  == domain 9  score: 0.1 bits;  conditional E-value: 2.3
                        TPR_14   14 lGdpdeAiallrralalaPddae 36  
                                      + d  +++l ++++++Pd+ +
  gi|91774186|ref|YP_566878.1| 1170 CSRSDSILDVLMDLVQKDPDNVT 1192
                                    33445588888888888888876 PP

  == domain 10  score: 4.2 bits;  conditional E-value: 0.11
                        TPR_14    2 eallalaeallalGdpdeAiallrralal 30  
                                    +++ + +++l+++G+  +A+  ++ al+ 
  gi|91774186|ref|YP_566878.1| 1343 DLYDRKGSFLMNAGRNVDARSSYEMALSI 1371
                                    5677889*******************985 PP

  == domain 11  score: 6.8 bits;  conditional E-value: 0.016
                        TPR_14    8 aeallalGdpdeAiallrralalaPd 33  
                                    +  +++ G++ eA a++++ l+++ d
  gi|91774186|ref|YP_566878.1| 1397 GTMFAQDGEFTEAKAMFEASLKTYVD 1422
                                    6678999**************97654 PP

  == domain 12  score: 5.8 bits;  conditional E-value: 0.032
                        TPR_14    7 laeallalGdpdeAiallrralala 31  
                                    la++++  G++++A  +++ al+++
  gi|91774186|ref|YP_566878.1| 1444 LAKLFADMGRHEDAKSIYESALEAY 1468
                                    8999******************965 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.3     3e+03       7      22 ..      15      30 ..      13      31 .. 0.89
   2 ?   -0.2   0.1       1.1     1e+03      17      34 .]     117     134 ..     116     134 .. 0.93
   3 ?   -0.6   0.0       1.5   1.3e+03       3      30 ..     144     171 ..     142     173 .. 0.89
   4 ?    4.4   0.0      0.04        36       5      21 ..     194     210 ..     191     215 .. 0.86
   5 ?   -2.8   0.0       7.3   6.6e+03      10      28 ..     679     697 ..     677     699 .. 0.54
   6 ?   -1.7   0.0       3.4   3.1e+03       6      17 ..     771     782 ..     767     784 .. 0.89
   7 ?    1.6   0.0       0.3   2.7e+02       6      30 ..    1347    1371 ..    1342    1373 .. 0.89
   8 !    8.3   0.0    0.0024       2.1       3      29 ..    1392    1418 ..    1390    1420 .. 0.90
   9 !   13.5   0.3   5.5e-05     0.049       1      29 [.    1438    1466 ..    1438    1468 .. 0.94
  10 ?   -0.8   0.0       1.7   1.6e+03       6      30 ..    1491    1515 ..    1491    1517 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.3
                                  HHHHHHHTT-HHHHHH CS
                         TPR_1  7 lGnayfklgkydeAle 22
                                  +G+ +++ g+ ++Ale
  gi|91774186|ref|YP_566878.1| 15 KGMSFLEAGQQKKALE 30
                                  79999*********97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHSTTH CS
                         TPR_1  17 ydeAleyyekALelnPnn 34 
                                   ++e +++y+k L+ +Pnn
  gi|91774186|ref|YP_566878.1| 117 FEETVKAYDKLLSKEPNN 134
                                   79999***********98 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                   al+  + ++ + g+ ++A e +e+ L+l
  gi|91774186|ref|YP_566878.1| 144 ALNDVATILAERGQQKDAKERFERSLKL 171
                                   7888899999**********9**99998 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.04
                                   HHHHHHHHHTT-HHHHH CS
                         TPR_1   5 ynlGnayfklgkydeAl 21 
                                    nl+n+++ +g +++A 
  gi|91774186|ref|YP_566878.1| 194 TNLANLLYDMGLLEDAK 210
                                   7**************97 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 7.3
                                   HHHHTT-HHHHHHHHHHHH CS
                         TPR_1  10 ayfklgkydeAleyyekAL 28 
                                   ++++ g++  A   y+ AL
  gi|91774186|ref|YP_566878.1| 679 LLMNAGRLAAARSKYDSAL 697
                                   5555566666655555555 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 3.4
                                   HHHHHHHHTT-H CS
                         TPR_1   6 nlGnayfklgky 17 
                                   ++Gn+++k g++
  gi|91774186|ref|YP_566878.1| 771 RMGNVLMKAGRL 782
                                   79*******996 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.3
                                    HHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1    6 nlGnayfklgkydeAleyyekALel 30  
                                    ++G  +++ g+  +A   ye AL++
  gi|91774186|ref|YP_566878.1| 1347 RKGSFLMNAGRNVDARSSYEMALSI 1371
                                    678889999**************98 PP

  == domain 8  score: 8.3 bits;  conditional E-value: 0.0024
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1    3 alynlGnayfklgkydeAleyyekALe 29  
                                    + +nlG ++ + g++ eA + +e  L+
  gi|91774186|ref|YP_566878.1| 1392 IRNNLGTMFAQDGEFTEAKAMFEASLK 1418
                                    679*******************99887 PP

  == domain 9  score: 13.5 bits;  conditional E-value: 5.5e-05
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1    1 akalynlGnayfklgkydeAleyyekALe 29  
                                    a +l+nl+ ++  +g++++A   ye ALe
  gi|91774186|ref|YP_566878.1| 1438 ALTLNNLAKLFADMGRHEDAKSIYESALE 1466
                                    6789************************8 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 1.7
                                    HHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1    6 nlGnayfklgkydeAleyyekALel 30  
                                    nlG ++ ++g+ ++ +   e A el
  gi|91774186|ref|YP_566878.1| 1491 NLGSLLGEMGRGEDSIRMHEAAQEL 1515
                                    9*************99999999887 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 ?   -2.3   0.1       5.4   4.8e+03       9      25 ..      14      30 ..       7      48 .. 0.57
   2 ?    4.1   0.7     0.054        48      13      55 ..      58     102 ..      52     105 .. 0.77
   3 ?    2.0   0.4      0.25   2.2e+02       3      40 ..      93     131 ..      91     137 .. 0.86
   4 ?   -1.1   0.0       2.3   2.1e+03       7      45 ..     289     325 ..     287     343 .. 0.81
   5 ?    1.1   0.0      0.48   4.3e+02      17      42 ..     587     614 ..     586     627 .. 0.80
   6 !    7.0   0.0    0.0068       6.1      16      40 ..     682     706 ..     680     727 .. 0.86
   7 ?    5.1   0.0     0.026        24      18      63 ..     876     919 ..     874     921 .. 0.79
   8 ?   -1.9   0.0         4   3.6e+03      17      41 ..    1259    1285 ..    1258    1292 .. 0.78
   9 ?    2.0   0.4      0.25   2.2e+02       4      40 ..    1438    1474 ..    1435    1488 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.4
                           MIT  9 kkAveeDnagnyeeAle 25
                                  kk +   +ag+ ++Ale
  gi|91774186|ref|YP_566878.1| 14 KKGMSFLEAGQQKKALE 30
                                  44444445555555544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.054
                           MIT  13 eeDnagnyeeAlelYkealelLlqalkekne...errellrekiee 55 
                                    ++++g+ ++Ale Y  a elL  + + +++   e++ l  +k+++
  gi|91774186|ref|YP_566878.1|  58 IMESNGEKDAALERYLGASELLDGLAN-SDPsfvEHKALAMNKAAT 102
                                   5799*****************998887.343456777777777666 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.25
                           MIT   3 kAlelvkkAveeDnagnyeeAlelYkealelLlqalk.e 40 
                                   kAl++ k+A+ + n+g+ e A  l++e ++   ++l+ e
  gi|91774186|ref|YP_566878.1|  93 KALAMNKAATLLANKGDVEHAGYLFEETVKAYDKLLSkE 131
                                   8********************999999988888888755 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.3
                           MIT   7 lvkkAveeDnagnyeeAlelYkealelLlqalkekneer 45 
                                   lvk A ++  +g +++A + Y+  l +L+ ++k  ++++
  gi|91774186|ref|YP_566878.1| 289 LVKLARDNADKGMFADARSGYELMLPVLMDLIK--DDQD 325
                                   7888888889999999*9999999999999999..4443 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.48
                           MIT  17 agnyeeAlelYkealelLlqalk.e.kn 42 
                                   ag  ++A + Y + l +L++++k e +n
  gi|91774186|ref|YP_566878.1| 587 AGRLSAARSSYGSTLAVLTKLIKeEpDN 614
                                   688999*****************44433 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0068
                           MIT  16 nagnyeeAlelYkealelLlqalke 40 
                                   nag  ++A ++Y +al +L+ +++ 
  gi|91774186|ref|YP_566878.1| 682 NAGRLAAARSKYDSALTVLMDLIQD 706
                                   79999******************93 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.026
                           MIT  18 gnyeeAlelYkealelLlqalkekneerrellrekieeYleRaeeL 63 
                                   g  ++A ++Y + l++L+ +l+  +e++  ++ + i++ l+ +e+L
  gi|91774186|ref|YP_566878.1| 876 GRLADARSKYDSTLNVLMDLLQ--KESDNVTFLSMIRTILSDMEYL 919
                                   67889*****************..6666777777777777777766 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 4
                           MIT   17 agnyeeAlelYkealelLlqalk.e.k 41  
                                    ag +++  ++Y + l++L+++++ e +
  gi|91774186|ref|YP_566878.1| 1259 AGRIDDVRSMYGSTLNILMKLMQgEpE 1285
                                    5666666789************96633 PP

  == domain 9  score: 2.0 bits;  conditional E-value: 0.25
                           MIT    4 AlelvkkAveeDnagnyeeAlelYkealelLlqalke 40  
                                    Al l + A      g  e+A + Y++ale  +++l+ 
  gi|91774186|ref|YP_566878.1| 1438 ALTLNNLAKLFADMGRHEDAKSIYESALEAYVELLNA 1474
                                    6666666666666788888999999999988888873 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.4   2.2e+03       3      19 ..      18      34 ..      16      40 .. 0.81
   2 ?   -1.6   0.1       2.5   2.3e+03       7      23 ..      62      78 ..      61      78 .. 0.83
   3 ?   -0.8   0.0       1.4   1.3e+03      10      28 ..     117     135 ..     108     135 .. 0.86
   4 ?   -0.1   0.0      0.84   7.5e+02       3      25 ..     151     173 ..     150     176 .. 0.89
   5 ?   -0.0   0.0      0.82   7.3e+02      19      36 ..     188     205 ..     187     206 .. 0.75
   6 ?    0.9   0.0       0.4   3.6e+02      21      42 .]     560     581 ..     555     581 .. 0.90
   7 ?    5.2   0.0     0.019        17       5      30 ..     688     713 ..     684     715 .. 0.87
   8 ?    6.1   0.0      0.01       9.1      17      42 .]     748     773 ..     745     773 .. 0.95
   9 ?   -1.0   0.0       1.7   1.5e+03      17      38 ..    1036    1057 ..    1035    1060 .. 0.88
  10 ?   -0.5   0.1       1.2   1.1e+03      11      24 ..    1429    1442 ..    1427    1452 .. 0.83
  11 ?    5.4   0.5     0.016        14      10      29 ..    1461    1480 ..    1457    1481 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                        TPR_11  3 ayyeqGkyeeAieaYkk 19
                                   + e G+ ++A+e++  
  gi|91774186|ref|YP_566878.1| 18 SFLEAGQQKKALEVLLV 34
                                  57899********9865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                        TPR_11  7 qGkyeeAieaYkkAlkl 23
                                   G+ ++A+e+Y  A +l
  gi|91774186|ref|YP_566878.1| 62 NGEKDAALERYLGASEL 78
                                  58889******988776 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.4
                        TPR_11  10 yeeAieaYkkAlkldPdna 28 
                                   +ee ++aY k l   P+n+
  gi|91774186|ref|YP_566878.1| 117 FEETVKAYDKLLSKEPNNV 135
                                   68899************95 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.84
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldP 25 
                                   ++ e+G+ ++A e++++ lkl+ 
  gi|91774186|ref|YP_566878.1| 151 ILAERGQQKDAKERFERSLKLSA 173
                                   6789****************986 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 0.82
                        TPR_11  19 kAlkldPdnaeayynLGl 36 
                                   kAl +  + a+++y +Gl
  gi|91774186|ref|YP_566878.1| 188 KALTIQTNLANLLYDMGL 205
                                   678888888888888886 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.4
                        TPR_11  21 lkldPdnaeayynLGlayykqG 42 
                                    ++dP++ + + +++++  ++G
  gi|91774186|ref|YP_566878.1| 560 SRIDPSDFSHHVKIAKLNERMG 581
                                   58****************9998 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.019
                        TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaea 30 
                                    ++ ky+ A++++   ++ dPdn ++
  gi|91774186|ref|YP_566878.1| 688 AARSKYDSALTVLMDLIQDDPDNFTF 713
                                   6789*******************976 PP

  == domain 8  score: 6.1 bits;  conditional E-value: 0.01
                        TPR_11  17 YkkAlkldPdnaeayynLGlayykqG 42 
                                   Y+k  +ldP++ + y +++++ +++G
  gi|91774186|ref|YP_566878.1| 748 YEKLSQLDPSDLSYYVKIAELNQRMG 773
                                   999********************998 PP

  == domain 9  score: -1.0 bits;  conditional E-value: 1.7
                        TPR_11   17 YkkAlkldPdnaeayynLGlay 38  
                                    Y+k   l+P++ + + +++++ 
  gi|91774186|ref|YP_566878.1| 1036 YEKLSTLNPSDLSYHAKIAELN 1057
                                    899999*********9999875 PP

  == domain 10  score: -0.5 bits;  conditional E-value: 1.2
                        TPR_11   11 eeAieaYkkAlkld 24  
                                    e+A  +Y +Al l+
  gi|91774186|ref|YP_566878.1| 1429 EDAAYQYGAALTLN 1442
                                    77889999999887 PP

  == domain 11  score: 5.4 bits;  conditional E-value: 0.016
                        TPR_11   10 yeeAieaYkkAlkldPdnae 29  
                                    ye A+eaY + l+ dP+n++
  gi|91774186|ref|YP_566878.1| 1461 YESALEAYVELLNADPENVR 1480
                                    9*****************85 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.3   3.9e+03       5      24 ..      13      32 ..      11      35 .. 0.88
   2 ?   -2.0   0.1       6.7     6e+03       4      20 ..      97     113 ..      95     127 .. 0.81
   3 ?    3.7   0.1     0.098        88       3      33 ..     144     174 ..     142     175 .. 0.90
   4 ?    3.3   0.0      0.13   1.2e+02       4      25 ..     193     214 ..     190     215 .. 0.89
   5 ?   -0.7   0.0       2.5   2.2e+03       3      24 ..     576     597 ..     574     598 .. 0.86
   6 ?    0.4   0.0       1.1     1e+03       4      28 ..     673     697 ..     670     704 .. 0.77
   7 ?   -1.6   0.0         5   4.5e+03      21      34 .]     745     758 ..     745     758 .. 0.86
   8 ?   -2.3   0.0       8.6   7.7e+03      22      34 .]    1034    1046 ..    1033    1046 .. 0.85
   9 ?   -2.1   0.0       6.9   6.2e+03      21      34 .]    1225    1238 ..    1225    1238 .. 0.86
  10 ?    3.3   0.0      0.13   1.2e+02       1      31 [.    1342    1372 ..    1342    1373 .. 0.93
  11 ?    6.5   0.0     0.013        11       2      29 ..    1391    1418 ..    1390    1420 .. 0.91
  12 !   14.8   0.3   2.8e-05     0.025       4      30 ..    1441    1467 ..    1438    1468 .. 0.93
  13 ?   -1.0   0.0       3.2   2.9e+03       6      30 ..    1491    1515 ..    1488    1518 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.3
                                  HHHHHHHHHTT-HHHHHHHH CS
                         TPR_8  5 ynlgsiylklgdyeeAkeyy 24
                                  +++g+  l+ g+ ++A e++
  gi|91774186|ref|YP_566878.1| 13 FKKGMSFLEAGQQKKALEVL 32
                                  789999**********9976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.7
                                   HHHHHHHHHHTT-HHHH CS
                         TPR_8   4 yynlgsiylklgdyeeA 20 
                                   +++ + ++ ++gd e A
  gi|91774186|ref|YP_566878.1|  97 MNKAATLLANKGDVEHA 113
                                   56778899999999988 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.098
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   a++  + i+ + g+ + Ake +e+ l+l+ +
  gi|91774186|ref|YP_566878.1| 144 ALNDVATILAERGQQKDAKERFERSLKLSAK 174
                                   77888999********************975 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHTT-HHHHHHHHH CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyye 25 
                                     nl++++ ++g +e Ak  +e
  gi|91774186|ref|YP_566878.1| 193 QTNLANLLYDMGLLEDAKINFE 214
                                   579***************9887 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 2.5
                                   HHHHHHHHHHHTT-HHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyy 24 
                                   +  ++g+ +++ g++ +A ++y
  gi|91774186|ref|YP_566878.1| 576 LNERMGRFLMDAGRLSAARSSY 597
                                   556899************9998 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekal 28 
                                     + gs++++ g++ +A + y  al
  gi|91774186|ref|YP_566878.1| 673 NERVGSLLMNAGRLAAARSKYDSAL 697
                                   5577999999999999987666555 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 5
                                   HHHHHHHHHHHHH. CS
                         TPR_8  21 keyyekaleldpdn 34 
                                   ++ yek  +ldp++
  gi|91774186|ref|YP_566878.1| 745 ISMYEKLSQLDPSD 758
                                   578********975 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 8.6
                                    HHHHHHHHHHHH. CS
                         TPR_8   22 eyyekaleldpdn 34  
                                    + yek  +l+p++
  gi|91774186|ref|YP_566878.1| 1034 SMYEKLSTLNPSD 1046
                                    68********975 PP

  == domain 9  score: -2.1 bits;  conditional E-value: 6.9
                                    HHHHHHHHHHHHH. CS
                         TPR_8   21 keyyekaleldpdn 34  
                                    ++ yek  +l+p++
  gi|91774186|ref|YP_566878.1| 1225 ISMYEKLSTLNPSD 1238
                                    578********975 PP

  == domain 10  score: 3.3 bits;  conditional E-value: 0.13
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8    1 aeayynlgsiylklgdyeeAkeyyekaleld 31  
                                    a++y ++gs +++ g+   A ++ye al+++
  gi|91774186|ref|YP_566878.1| 1342 ADLYDRKGSFLMNAGRNVDARSSYEMALSIR 1372
                                    67899***********************997 PP

  == domain 11  score: 6.5 bits;  conditional E-value: 0.013
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8    2 eayynlgsiylklgdyeeAkeyyekale 29  
                                    ++ +nlg    + g++ eAk+ +e  l+
  gi|91774186|ref|YP_566878.1| 1391 SIRNNLGTMFAQDGEFTEAKAMFEASLK 1418
                                    6789********************9987 PP

  == domain 12  score: 14.8 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8    4 yynlgsiylklgdyeeAkeyyekalel 30  
                                    ++nl+++  ++g++e Ak+ ye ale+
  gi|91774186|ref|YP_566878.1| 1441 LNNLAKLFADMGRHEDAKSIYESALEA 1467
                                    79***********************95 PP

  == domain 13  score: -1.0 bits;  conditional E-value: 3.2
                                    HHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8    6 nlgsiylklgdyeeAkeyyekalel 30  
                                    nlgs++ ++g+ e ++   e a el
  gi|91774186|ref|YP_566878.1| 1491 NLGSLLGEMGRGEDSIRMHEAAQEL 1515
                                    89********988887776666666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.14   1.2e+02       4      23 ..      13      32 ..      12      36 .. 0.91
   2 ?    1.8   0.0      0.54   4.8e+02      16      33 .]     117     134 ..      99     134 .. 0.86
   3 ?   -1.2   0.1       4.6   4.1e+03       9      25 ..     151     167 ..     148     171 .. 0.79
   4 ?   -0.8   0.0       3.4   3.1e+03      20      32 ..     601     613 ..     572     614 .. 0.75
   5 ?    5.3   0.0      0.04        36       3      33 .]     680     710 ..     678     710 .. 0.90
   6 ?    0.9   0.0      0.99   8.9e+02       6      30 ..    1396    1420 ..    1354    1422 .. 0.82
   7 ?    6.8   0.1     0.013        12       5      30 ..    1443    1468 ..    1442    1468 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
                                  HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  4 yklalsyrklgdtdkAleal 23
                                  +k ++s++++g+  kAle l
  gi|91774186|ref|YP_566878.1| 13 FKKGMSFLEAGQQKKALEVL 32
                                  789******99******976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.54
                                   HHHHHHHHHHHHHH-TT- CS
                         TPR_6  16 tdkAlealerlikeYPdS 33 
                                    ++ ++a+++l+++ P++
  gi|91774186|ref|YP_566878.1| 117 FEETVKAYDKLLSKEPNN 134
                                   57899***********95 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.6
                                   HHHHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAlealer 25 
                                    + + g+  +A+e +er
  gi|91774186|ref|YP_566878.1| 151 ILAERGQQKDAKERFER 167
                                   566777999******98 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.4
                                   HHHHHHHHHH-TT CS
                         TPR_6  20 lealerlikeYPd 32 
                                   l+ l +like Pd
  gi|91774186|ref|YP_566878.1| 601 LAVLTKLIKEEPD 613
                                   4578888888888 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.04
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPdS 33 
                                   l++++++  +  ++d Al+ l +li++ Pd+
  gi|91774186|ref|YP_566878.1| 680 LMNAGRLAAARSKYDSALTVLMDLIQDDPDN 710
                                   678999999977*****************95 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.99
                                    HHHHHHHHHHHHHHHHHHHHHHHH- CS
                         TPR_6    6 lalsyrklgdtdkAlealerlikeY 30  
                                    l+  + + g+ ++A++++e  +k Y
  gi|91774186|ref|YP_566878.1| 1396 LGTMFAQDGEFTEAKAMFEASLKTY 1420
                                    4455555489********9888777 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHHHHHHHHHHHHHHH- CS
                         TPR_6    5 klalsyrklgdtdkAlealerlikeY 30  
                                    +la+++  +g++++A+ ++e+ ++ Y
  gi|91774186|ref|YP_566878.1| 1443 NLAKLFADMGRHEDAKSIYESALEAY 1468
                                    589999999************99987 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4       1.1     1e+03      86     134 ..      19      70 ..       8      78 .. 0.80
   2 ?   -2.2   0.0       3.2   2.9e+03     155     174 ..     151     170 ..     147     175 .. 0.84
   3 ?   -0.8   0.0       1.2     1e+03     146     175 ..     574     603 ..     559     610 .. 0.87
   4 !    6.5   0.0     0.007       6.3     146     175 ..     670     699 ..     655     705 .. 0.89
   5 ?    0.5   0.0      0.46   4.2e+02     146     176 ..     766     796 ..     749     803 .. 0.83
   6 ?   -2.9   0.0       5.2   4.7e+03     156     174 ..     872     890 ..     867     895 .. 0.84
   7 ?    5.8   0.0     0.011       9.8     148     174 ..    1344    1370 ..    1336    1385 .. 0.88
   8 ?   -2.2   0.0       3.2   2.9e+03     153     174 ..    1397    1418 ..    1390    1423 .. 0.77
   9 ?    0.2   0.4      0.58   5.2e+02      83     174 ..    1445    1466 ..    1398    1480 .. 0.60
  10 ?   -0.5   0.0      0.97   8.7e+02     156     176 ..    1448    1468 ..    1446    1493 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                        TPR_21  86 aveagdlaaAkaqLewvlekakdeelkal...arlRLarvllaekkydeAlk 134
                                     eag+ ++A + L  + ++akd++ ++l   +   +a+++  +++ d+Al+
  gi|91774186|ref|YP_566878.1|  19 FLEAGQQKKALEVLLVAEKQAKDAGSTDLlinIFQSVAKIMESNGEKDAALE 70 
                                   6789999999999999999999999888732234589999999999999997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                        TPR_21 155 ilvaqgkldeAraaYqaAla 174
                                   il+++g++++A++ ++++l+
  gi|91774186|ref|YP_566878.1| 151 ILAERGQQKDAKERFERSLK 170
                                   78899999999999999886 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                        TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaa 175
                                   a+ +e+ G  l+  g+l  Ar+ Y   la 
  gi|91774186|ref|YP_566878.1| 574 AKLNERMGRFLMDAGRLSAARSSYGSTLAV 603
                                   6778999*****************988775 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.007
                        TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaa 175
                                   a+ +e+ G +l++ g+l+ Ar++Y+ Al+ 
  gi|91774186|ref|YP_566878.1| 670 AELNERVGSLLMNAGRLAAARSKYDSALTV 699
                                   6778999********************975 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.46
                        TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaal 176
                                   a+ +++ G++l++ g+l   r++Y+  +++l
  gi|91774186|ref|YP_566878.1| 766 AELNQRMGNVLMKAGRLSAGRSKYESTFNDL 796
                                   5567788******************988765 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 5.2
                        TPR_21 156 lvaqgkldeAraaYqaAla 174
                                   l++ g+l++Ar++Y+  l+
  gi|91774186|ref|YP_566878.1| 872 LISGGRLADARSKYDSTLN 890
                                   667899********99887 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.011
                        TPR_21  148 vaelrGDilvaqgkldeAraaYqaAla 174 
                                      +++G  l++ g++ +Ar+ Y+ Al+
  gi|91774186|ref|YP_566878.1| 1344 LYDRKGSFLMNAGRNVDARSSYEMALS 1370
                                    5699*********************96 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 3.2
                        TPR_21  153 GDilvaqgkldeAraaYqaAla 174 
                                    G ++++ g+++eA+a ++a+l+
  gi|91774186|ref|YP_566878.1| 1397 GTMFAQDGEFTEAKAMFEASLK 1418
                                    6677888889999998888876 PP

  == domain 9  score: 0.2 bits;  conditional E-value: 0.58
                        TPR_21   83 AkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgk 161 
                                    Ak  ++ g  ++Ak+ +e                                                             
  gi|91774186|ref|YP_566878.1| 1445 AKLFADMGRHEDAKSIYE------------------------------------------------------------- 1462
                                    455555555555554444............................................................. PP

                        TPR_21  162 ldeAraaYqaAla 174 
                                              Al+
  gi|91774186|ref|YP_566878.1| 1463 ---------SALE 1466
                                    .........4444 PP

  == domain 10  score: -0.5 bits;  conditional E-value: 0.97
                        TPR_21  156 lvaqgkldeAraaYqaAlaal 176 
                                    ++ +g+ ++A++ Y+ Al+a 
  gi|91774186|ref|YP_566878.1| 1448 FADMGRHEDAKSIYESALEAY 1468
                                    567899999******999875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       2.9   2.6e+03      36      57 ..      20      41 ..      19      49 .. 0.87
   2 ?   -2.2   0.0       6.9   6.1e+03      38      57 ..      69      88 ..      63      97 .. 0.81
   3 ?    1.5   0.1      0.49   4.4e+02      11      52 ..     121     169 ..     117     174 .. 0.67
   4 ?    5.0   0.3     0.039        35       2      45 ..     153     210 ..     152     211 .. 0.84
   5 ?    2.6   0.0      0.22     2e+02      29      46 ..     386     403 ..     361     427 .. 0.74
   6 ?    0.8   0.0      0.83   7.4e+02       1      26 [.     584     616 ..     580     621 .. 0.77
   7 ?    3.0   0.0      0.17   1.5e+02       3      24 ..     689     710 ..     666     723 .. 0.67
   8 ?   -1.2   0.0       3.3     3e+03      14      42 ..     748     783 ..     745     786 .. 0.65
   9 ?   -1.3   0.0       3.7   3.3e+03      27      45 ..     864     882 ..     858     900 .. 0.82
  10 ?   -0.1   0.0       1.5   1.4e+03      25      47 ..    1054    1076 ..    1034    1083 .. 0.78
  11 ?    2.7   0.0      0.21   1.8e+02      22      44 ..    1147    1169 ..    1131    1189 .. 0.83
  12 !    7.7   2.1    0.0055       4.9       3      54 ..    1402    1467 ..    1400    1470 .. 0.70
  13 ?    5.6   0.1     0.025        22       3      21 ..    1450    1468 ..    1448    1483 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.9
                        TPR_19 36 lalgqldeAealLdalpeedpd 57
                                  l++gq ++A ++L  + ++++d
  gi|91774186|ref|YP_566878.1| 20 LEAGQQKKALEVLLVAEKQAKD 41
                                  6899999******999999988 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.9
                        TPR_19 38 lgqldeAealLdalpeedpd 57
                                  l ++  A +lLd l ++dp 
  gi|91774186|ref|YP_566878.1| 69 LERYLGASELLDGLANSDPS 88
                                  6677789999**99999997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.49
                        TPR_19  11 lalleqalqedpk.......naearllLAeallalgqldeAealLdalp 52 
                                   ++++ ++l+++p+       ++ a+ + A +l + gq ++A++  ++ +
  gi|91774186|ref|YP_566878.1| 121 VKAYDKLLSKEPNnvvhcssMSSALNDVATILAERGQQKDAKERFERSL 169
                                   5667777777777777777777777777777777777777777766654 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.039
                        TPR_19   2 laegdyaeAlalleqalqedpk..............naearllLAeallalgqldeAe 45 
                                    ++g+  +A +++e+ l+ ++k               + ++ +LA++l+ +g l++A+
  gi|91774186|ref|YP_566878.1| 153 AERGQQKDAKERFERSLKLSAKlivldplnssnitkALTIQTNLANLLYDMGLLEDAK 210
                                   6899999999*****9999777777777777777778888889*************97 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.22
                        TPR_19  29 llLAeallalgqldeAea 46 
                                    +++++l+ +g++++A+ 
  gi|91774186|ref|YP_566878.1| 386 DRMVQLLIVAGRFEDARS 403
                                   4799************84 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.83
                        TPR_19   1 llaegdyaeA.......lalleqalqedpknae 26 
                                   l+++g++ +A       la l+++++e+p+n +
  gi|91774186|ref|YP_566878.1| 584 LMDAGRLSAArssygstLAVLTKLIKEEPDNTN 616
                                   567777777766666668999999999999976 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.17
                        TPR_19   3 aegdyaeAlalleqalqedpkn 24 
                                   a+ +y++Al  l  ++q+dp+n
  gi|91774186|ref|YP_566878.1| 689 ARSKYDSALTVLMDLIQDDPDN 710
                                   3445555555555555777776 PP

  == domain 8  score: -1.2 bits;  conditional E-value: 3.3
                        TPR_19  14 leqalqedpk.......naearllLAeallalgqld 42 
                                   +e++ q dp         ae+  ++ ++l+++g+l 
  gi|91774186|ref|YP_566878.1| 748 YEKLSQLDPSdlsyyvkIAELNQRMGNVLMKAGRLS 783
                                   555555555544444446788889999999999986 PP

  == domain 9  score: -1.3 bits;  conditional E-value: 3.7
                        TPR_19  27 arllLAeallalgqldeAe 45 
                                   +  +++++l++ g+l++A+
  gi|91774186|ref|YP_566878.1| 864 LNEGMIILLISGGRLADAR 882
                                   5557899999999999998 PP

  == domain 10  score: -0.1 bits;  conditional E-value: 1.5
                        TPR_19   25 aearllLAeallalgqldeAeal 47  
                                    ae+  +++  ll +g+ld+A+a+
  gi|91774186|ref|YP_566878.1| 1054 AELNEGMVLTLLTAGHLDAARAM 1076
                                    5666678888999*******997 PP

  == domain 11  score: 2.7 bits;  conditional E-value: 0.21
                        TPR_19   22 pknaearllLAeallalgqldeA 44  
                                    +k ae+  +++++l+++g+ld+A
  gi|91774186|ref|YP_566878.1| 1147 AKIAELNEGMIILLINAGRLDDA 1169
                                    5567778899************9 PP

  == domain 12  score: 7.7 bits;  conditional E-value: 0.0055
                        TPR_19    3 aegdyaeAlalleqal..........qedpk....naearl...lLAeallalgqldeAealLdalpee 54  
                                    ++g ++eA a++e+ l          +   +    +  a+l   +LA++   +g+ ++A+ + + ++e+
  gi|91774186|ref|YP_566878.1| 1402 QDGEFTEAKAMFEASLktyvdlfdrdK---EdaayQYGAALtlnNLAKLFADMGRHEDAKSIYESALEA 1467
                                    789999**9999999855555554432...2222444444445677**************999999887 PP

  == domain 13  score: 5.6 bits;  conditional E-value: 0.025
                        TPR_19    3 aegdyaeAlalleqalqed 21  
                                    ++g++++A +++e+al+++
  gi|91774186|ref|YP_566878.1| 1450 DMGRHEDAKSIYESALEAY 1468
                                    89*************9983 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.11     1e+02     115     190 ..      90     167 ..      54     189 .. 0.77
   2 ?   10.9   0.2    0.0003      0.27      86     185 ..    1399    1506 ..    1367    1517 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                       DUF2225 115 s.kkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegideat.vlYLiaeLerrlgnkeealrwlsk 190
                                     +kA  + ++A l  +k+d e   ++ ++ ++ y++ ++ke ++v   +  +  l  +a      g++++a++ +++
  gi|91774186|ref|YP_566878.1|  90 VeHKALAMNKAATLLANKGDVEHAGYLFEETVKAYDKLLSKEPNNVVHCSSMSsALNDVATILAERGQQKDAKERFER 167
                                   25899999**********************************999987776653344455555555666666666655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0003
                       DUF2225   86 dfskertldeaiesYkLallcye.lkkekks......kkAklalrlAWlyrdkedeekeklflkkAlelykeayekesf 157 
                                     f+++ +++ea + +  +l +y  l++  k         A ++ +lA l+ d + +e  k  ++ Ale y e ++ + +
  gi|91774186|ref|YP_566878.1| 1399 MFAQDGEFTEAKAMFEASLKTYVdLFDRDKEdaayqyGAALTLNNLAKLFADMGRHEDAKSIYESALEAYVELLNADPE 1477
                                    5777777777777777777775413333333445555667777899********************************* PP

                       DUF2225  158 pvegideatvlY.LiaeLerrlgnkeeal 185 
                                    +v+  ++a++++  ++ L   +g+ e+++
  gi|91774186|ref|YP_566878.1| 1478 NVRYKKHASITLdNLGSLLGEMGRGEDSI 1506
                                    99999999887634566666666666555 PP

>> 3HCDH_RFF  3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.017        15       5      29 ..     683     707 ..     679     716 .. 0.85
   2 ?    2.9   0.0      0.16   1.5e+02       2      27 ..     872     897 ..     871     907 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                     3HCDH_RFF   5 dGrtAtqraaeegrpvvlfDlaldy 29 
                                    Gr A+ r++ +++ +vl+Dl+ d 
  gi|91774186|ref|YP_566878.1| 683 AGRLAAARSKYDSALTVLMDLIQDD 707
                                   5********************9864 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                     3HCDH_RFF   2 alTdGrtAtqraaeegrpvvlfDlal 27 
                                    ++ Gr A  r++ ++   vl+Dl  
  gi|91774186|ref|YP_566878.1| 872 LISGGRLADARSKYDSTLNVLMDLLQ 897
                                   6899***********99999***975 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       2.4   2.2e+03      87     124 ..     108     145 ..      92     175 .. 0.81
   2 ?    9.4   0.2   0.00089       0.8      45     123 ..    1407    1488 ..    1399    1495 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
                                   --HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                   TOM20_plant  87 pdeeeakenfekatqffqqavdedPdndlyrkslelaa 124
                                    d e+a   fe + + +++   ++P+n ++  s+ +a 
  gi|91774186|ref|YP_566878.1| 108 GDVEHAGYLFEETVKAYDKLLSKEPNNVVHCSSMSSAL 145
                                   57788889999999999999999999999888887764 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00089
                                    HHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHH..HHHHH---H...HHHHHHHHHHHHHHHHHHHH-TT-HHHHH CS
                   TOM20_plant   45 aeakqmiqdaiskleeallidPkkhdalWcignayt..sfafltpde...eeakenfekatqffqqavdedPdndlyrk 118 
                                    +eak m + ++  + +  l d  k+da +  g a t    a l  d+   e+ak+ +e a + + +  ++dP+n  y+k
  gi|91774186|ref|YP_566878.1| 1407 TEAKAMFEASLKTYVD--LFDRDKEDAAYQYGAALTlnNLAKLFADMgrhEDAKSIYESALEAYVELLNADPENVRYKK 1483
                                    5677776555554444..5789999999999999874456788888544489**************************9 PP

                                    HHHHH CS
                   TOM20_plant  119 slela 123 
                                       ++
  gi|91774186|ref|YP_566878.1| 1484 HASIT 1488
                                    76655 PP

>> FANCI_S4  FANCI solenoid 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0071       6.4      83     131 ..     514     561 ..     472     563 .. 0.83
   2 ?   -1.1   0.0      0.96   8.6e+02      90     132 ..     713     754 ..     689     779 .. 0.85
   3 ?    2.3   0.1     0.085        76      57     131 ..     775     849 ..     759     851 .. 0.76
   4 ?    1.3   0.3      0.17   1.5e+02      38      98 ..     887     947 ..     879     965 .. 0.74
   5 ?   -1.3   0.0         1   9.2e+02      89     132 ..    1000    1042 ..     975    1052 .. 0.80
   6 ?    1.9   0.0      0.11     1e+02      87     136 ..    1094    1142 ..    1066    1165 .. 0.80
   7 ?   -0.1   0.0      0.45   4.1e+02      89     132 ..    1192    1234 ..    1169    1246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0071
                      FANCI_S4  83 lkerekslcsqlgtlvevlseLvqtalppgsavesllklltklYtlLtn 131
                                    + ++ +l s++  ++  +++L+ t++ +++  es l+ l+++Y++L++
  gi|91774186|ref|YP_566878.1| 514 EDPENVNLLSMIHEILDDMESLLDTEMDASKQ-ESSLNVLISMYEMLSR 561
                                   4556668999**********************.**************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.96
                      FANCI_S4  90 lcsqlgtlvevlseLvqtalppgsavesllklltklYtlLtnl 132
                                   + s++ tl+  +++L+++ + +++  e  l+ l+++Y+ L++l
  gi|91774186|ref|YP_566878.1| 713 FLSMFRTLLADMEHLLEVDCADSEK-EFDLNVLISMYEKLSQL 754
                                   5677889999999************.999**********9998 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.085
                      FANCI_S4  57 likklkaelaseklaeessqsevk.delkerekslcsqlgtlvevlseLvqtalppgsavesllklltklYtlLtn 131
                                   +++k+  ++a++ ++e++ ++ v+  + + ++ ++ s++ t+v+ ++ L++++  ++++ e  ++ l+++Y+ L+ 
  gi|91774186|ref|YP_566878.1| 775 VLMKAGRLSAGRSKYESTFNDLVElINEDPENVTFLSMVRTIVTDMEALIKMNDDDSEN-EYAFNVLISMYEKLSV 849
                                   555555555555555544444444566677777899***********************.***********99986 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.17
                      FANCI_S4  38 svlslllsalekvledvewlikklkaelaseklaeessqsevkdelkerekslcsqlgtlv 98 
                                   s+l++l++ l+k  ++v +l +  + ++ +e l e  s++++k++  ++ +s++++l+tlv
  gi|91774186|ref|YP_566878.1| 887 STLNVLMDLLQKESDNVTFLSMIRTILSDMEYLLETYSSETEKEAELNVLISMYEKLSTLV 947
                                   7778888888888888887766666666666666666677777777777778888887776 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1
                      FANCI_S4   89 slcsqlgtlvevlseLvqtalppgsavesllklltklYtlLtnl 132 
                                    ++ s++gt+++ +++L+ t+  +++  e+ ++ l ++Y+ L++l
  gi|91774186|ref|YP_566878.1| 1000 TFFSMIGTILTNMESLLGTENDASKK-EADFNFLMSMYEKLSTL 1042
                                    56678888888888888888888888.88888888888888876 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.11
                      FANCI_S4   87 ekslcsqlgtlvevlseLvqtalppgsavesllklltklYtlLtnltKyy 136 
                                    + ++ s++gt+++ +++L+ t+  +++  e+ l  l+++Y+ L++l+   
  gi|91774186|ref|YP_566878.1| 1094 NVTFLSMIGTILTNMESLLGTESDASKK-EADLDFLISMYEKLSTLVPSD 1142
                                    4467789999999999999999999999.999999999999999998655 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.45
                      FANCI_S4   89 slcsqlgtlvevlseLvqtalppgsavesllklltklYtlLtnl 132 
                                    ++ s++ t+++ +++L+ t++ +++  e+ ++ l+++Y+ L++l
  gi|91774186|ref|YP_566878.1| 1192 TFLSMVRTILTDMESLLDTEFDASKK-EADFNFLISMYEKLSTL 1234
                                    567888999999999*******9999.9999*******999987 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.05        45      30      66 ..     325     361 ..     316     370 .. 0.84
   2 ?   -0.6   0.0       1.6   1.4e+03      34      67 ..     425     458 ..     409     464 .. 0.89
   3 ?    0.8   0.0      0.61   5.5e+02      35      66 ..     522     553 ..     518     562 .. 0.85
   4 ?   -0.8   0.0       1.9   1.7e+03      35      69 ..     906     940 ..     879     947 .. 0.83
   5 ?   -2.7   0.0         7   6.2e+03      35      63 ..    1194    1222 ..    1193    1231 .. 0.80
   6 ?   -2.6   0.0       6.6   5.9e+03      37      66 ..    1292    1321 ..    1290    1326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.05
                          SesA  30 evgkrLplvqetLedaksqlesskldedtesaikpvl 66 
                                   + ++ +p+v+ +L+d +s le++++ +++e+ ++ ++
  gi|91774186|ref|YP_566878.1| 325 DYANYIPMVRTMLNDMESLLENDTDVSEKEADLTILI 361
                                   678899********************99988776665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                          SesA  34 rLplvqetLedaksqlesskldedtesaikpvle 67 
                                    L +++e+L+d +  le++++ ++ +s++++++ 
  gi|91774186|ref|YP_566878.1| 425 LLSMIREMLDDMEFLLETDRDVNEHKSNLNTLIY 458
                                   5899*******************99999988875 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.61
                          SesA  35 LplvqetLedaksqlesskldedtesaikpvl 66 
                                   L +++e+L+d +s l+++ + +++es+++ ++
  gi|91774186|ref|YP_566878.1| 522 LSMIHEILDDMESLLDTEMDASKQESSLNVLI 553
                                   899***************99999999776665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.9
                          SesA  35 LplvqetLedaksqlesskldedtesaikpvlesc 69 
                                   L +++ +L+d +  le+ ++++++e++++ ++  +
  gi|91774186|ref|YP_566878.1| 906 LSMIRTILSDMEYLLETYSSETEKEAELNVLISMY 940
                                   88999*************99999999887777655 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 7
                          SesA   35 LplvqetLedaksqlesskldedtesaik 63  
                                    L +v+ +L d +s l+++ + +++e+ ++
  gi|91774186|ref|YP_566878.1| 1194 LSMVRTILTDMESLLDTEFDASKKEADFN 1222
                                    789999*******9999999888777655 PP

  == domain 6  score: -2.6 bits;  conditional E-value: 6.6
                          SesA   37 lvqetLedaksqlesskldedtesaikpvl 66  
                                    +++++L+d +s le + +++++e+ ++ ++
  gi|91774186|ref|YP_566878.1| 1292 IFRNVLSDMESLLEIDCDESEKEEDLNVLI 1321
                                    7899**********9999999998777666 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0027       2.4      35      89 ..     397     452 ..     383     457 .. 0.87
   2 ?   -3.2   0.0       9.9   8.9e+03      35      78 ..     589     633 ..     586     636 .. 0.71
   3 ?   -2.8   0.0       7.6   6.8e+03      35      76 ..     877     919 ..     876     924 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                                   HHHHHHHHHHHHHHHHHHHH.T-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHT-- CS
               PEP-utilisers_N  35 rleeAlekvreelealaeka.lgeeeaaifeahlmlleDpelleeveerIreggln 89 
                                   r+e+A+ k+   l++l + +    ++ +++++ +++l+D e+l e+ + ++e++ n
  gi|91774186|ref|YP_566878.1| 397 RFEDARSKSDLTLDDLMDLMqKDPNNVNLLSMIREMLDDMEFLLETDRDVNEHKSN 452
                                   9**************9877764445788*******************999987755 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.9
                                   HHHHHHHHHHHHHHHHHHHH.T-HHHHHHHHHHHHHHT-HHHHHH CS
               PEP-utilisers_N  35 rleeAlekvreelealaeka.lgeeeaaifeahlmlleDpellee 78 
                                   rl +A+    + l+ l + + ++ ++ +++++ + +++D e l e
  gi|91774186|ref|YP_566878.1| 589 RLSAARSSYGSTLAVLTKLIkEEPDNTNFLSTFRTIVNDMEVLFE 633
                                   777777777777777654445444578899999999999887655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.6
                                   HHHHHHHHHHHHHHHHHHHH.T-HHHHHHHHHHHHHHT-HHHH CS
               PEP-utilisers_N  35 rleeAlekvreelealaeka.lgeeeaaifeahlmlleDpell 76 
                                   rl +A+ k  + l+ l + +  ++++  ++++ + +l+D e+l
  gi|91774186|ref|YP_566878.1| 877 RLADARSKYDSTLNVLMDLLqKESDNVTFLSMIRTILSDMEYL 919
                                   7888899999999887765543334577999999999998875 PP

>> UTP15_C  UTP15 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.6   2.3e+03      72     116 ..      25      69 ..      14      74 .. 0.70
   2 ?   -1.9   0.0       2.7   2.4e+03      73      99 ..     259     286 ..     236     299 .. 0.65
   3 ?   -1.3   0.2       1.8   1.6e+03      54      54 ..     485     485 ..     446     556 .. 0.57
   4 ?    9.5   0.4   0.00084      0.75      74     141 ..     888     961 ..     869     967 .. 0.74
   5 ?    0.8   0.1      0.38   3.4e+02      68     145 ..    1074    1158 ..    1051    1160 .. 0.80
   6 ?   -3.5   0.0       8.4   7.6e+03      73     102 ..    1175    1204 ..    1171    1252 .. 0.46

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                       UTP15_C  72 eeslepiLkfllkhitdpryvsllvdvanvlldlyseklgqseel 116
                                   +++ + +L    k+ +d   ++ll+++ + +  + +++ ++ + l
  gi|91774186|ref|YP_566878.1|  25 QKKALEVLLVAEKQAKDAGSTDLLINIFQSVAKIMESNGEKDAAL 69 
                                   444555666778888888888888888888888888777666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                       UTP15_C  73 eslepiLkfllkhit.dpryvsllvdva 99 
                                   ++l+ ++ +l +  + +pr+ + ++d +
  gi|91774186|ref|YP_566878.1| 259 KKLHELMDMLQRFAKdEPRFLERITDPI 286
                                   5566666666666643566666666655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                       UTP15_C  54 l 54 
                                   +
  gi|91774186|ref|YP_566878.1| 485 I 485
                                   2 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00084
                       UTP15_C  74 slepiLkfllk...hitdpryvsllvdvanvlldlyseklgqse...eldelvkrLkrkvreevelakellelk 141
                                   +l  ++  l k   ++t  +++++++  ++ ll++ys++ ++ +   +l ++ ++L++ v + ++ +++l+el+
  gi|91774186|ref|YP_566878.1| 888 TLNVLMDLLQKesdNVTFLSMIRTILSDMEYLLETYSSETEKEAelnVLISMYEKLSTLVPSDLSHHTKLTELN 961
                                   555555555550005555566677777899**********99973335667889***********999999987 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.38
                       UTP15_C   68 agrdeeslepiLkfllkhitdpryvsllvdvanvlldlyseklgqse......eldelvkrLkrkvreevelakellel 140 
                                       ++++l  ++  + k   ++ + s++ +++ ++  l++ + ++s+       l ++ ++L++ v + ++++ ++ el
  gi|91774186|ref|YP_566878.1| 1074 RAMSDSTLDVLMGLVQKEPDNVTFLSMIGTILTNMESLLGTESDASKkeadldFLISMYEKLSTLVPSDLSYHAKIAEL 1152
                                    567889999999999999999999999888888888888777777755666666889999******9999999999998 PP

                       UTP15_C  141 k.Gmle 145 
                                    + Gm+ 
  gi|91774186|ref|YP_566878.1| 1153 NeGMII 1158
                                    548875 PP

  == domain 6  score: -3.5 bits;  conditional E-value: 8.4
                       UTP15_C   73 eslepiLkfllkhitdpryvsllvdvanvl 102 
                                    + l  ++  + k   ++ + s++ +++  +
  gi|91774186|ref|YP_566878.1| 1175 SILDVLMDLVQKDPDNVTFLSMVRTILTDM 1204
                                    455555555555444444444333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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):              20  [number of targets reported over threshold]
# CPU time: 0.95u 0.27s 00:00:01.22 Elapsed: 00:00:00.47
# Mc/sec: 9702.51
//
Query:       gi|91774187|ref|YP_566879.1|  [L=826]
Description: peptidase U32 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-89  299.2   0.1    7.1e-77  257.7   0.0    2.5  2  Peptidase_U32  Peptidase family U32
    2.5e-22   79.5   0.1    5.5e-22   78.4   0.1    1.6  1  DUF3656        Collagenase
  ------ inclusion threshold ------
      0.035   13.7   0.1        4.4    6.8   0.0    3.1  3  DeoC           DeoC/LacD family aldolase
      0.068   13.7   1.3       0.11   13.0   0.1    1.9  2  DUF2190        Uncharacterized conserved protein (DUF2190)


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 !  257.7   0.0   1.6e-80   7.1e-77       3     231 ..      85     310 ..      83     312 .. 0.96
   2 !   38.7   0.1   1.3e-13   5.7e-10      20     197 ..     633     803 ..     615     808 .. 0.85

  Alignments for each domain:
  == domain 1  score: 257.7 bits;  conditional E-value: 1.6e-80
                 Peptidase_U32   3 klrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikekvp 83 
                                    + + ++++++lg+da+i+qD+g+l ++++ +p+l+lh+Stq++++++e+v+f+++ Ga rv+++REl+++ei++i ++  
  gi|91774187|ref|YP_566879.1|  85 HALDVVDRAYSLGIDAIILQDLGLLSILHRSYPDLALHASTQMTVHTPEGVDFIANAGAVRVIVSRELEVQEIEDIVKNS- 164
                                   5678899*************************************************************************. PP

                 Peptidase_U32  84 dvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkdlclieelpe 164
                                   dve+E+fvhGalc++ysG+cl+ss++++rsanrg+caqpcr++y ++ ++++ +e++     +g++ +s+ +lc+++e+ +
  gi|91774187|ref|YP_566879.1| 165 DVEIEIFVHGALCYSYSGKCLFSSFINDRSANRGACAQPCRRPYVFVVNGRTINEKI-----TGRFPISCAELCTLSEIGD 240
                                   **************************************************9887774.....488**************** PP

                 Peptidase_U32 165 lleaGvdslKIeGRmkspeyvatvvrvYreaidallagr...eevkeelkeeleklanrgltsgfllgrk 231
                                   +++ Gv+slKIeGRmk+peyv +   +Y+++++a++  +   e++ + ++++l++l+ rg+t+gf+lg++
  gi|91774187|ref|YP_566879.1| 241 IVKTGVKSLKIEGRMKRPEYVTESSLAYKQVVKAFCGSEeldEDEIKGFEKDLAQLFYRGFTKGFVLGDR 310
                                   ************************************99999999999*******************9986 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1.3e-13
                 Peptidase_U32  20 ivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikekvp....dvelEvfvhGalc 96 
                                    +  +g +elar++  ++++ +  + n+ ns + + +++ Ga rv l+ El+++e+k++++++     + +lE+  hG   
  gi|91774187|ref|YP_566879.1| 633 ACYTLGQVELARKM--SIPFVVQKEFNTFNSYTSDGFYRAGAFRVTLSSELNMDEMKDVADDIScrgeSHQLEAVAHGREL 711
                                   44557778999999..*********************************************99888989************ PP

                 Peptidase_U32  97 vaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkdlclieelpelleaGvdslKIeG 177
                                   + +  + ll  ++ +    +g+ +    ++   +  k+ ge          t +  +  + ++++++++ e G+d ++++ 
  gi|91774187|ref|YP_566879.1| 712 MLITEHDLLKPLIDNGITIEGSEVLLVDSKSDEYPVKRVGER---------TLIYDSMVTEMLDHVDKFEECGIDVIRLDL 783
                                   ************988666677777666666554444444444.........4777888899******************** PP

                 Peptidase_U32 178 RmkspeyvatvvrvYreaid 197
                                    ++ ++ v++++++Yr+++d
  gi|91774187|ref|YP_566879.1| 784 SLYGKKDVQEITSAYRRVMD 803
                                   ******************99 PP

>> DUF3656  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.1   1.2e-25   5.5e-22       1     106 [.     405     518 ..     405     519 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.2e-25
                       DUF3656   1 vyrtsdkklteelekslekseerkipvdlelaakegeplkltvtde...........leeAkkrplteenirkqLsklGgt 70 
                                   vy t+d+    +l ++l+++ ++ +pv++e+ a++ge lk++++++           +++A+++p+++e+i + ++klG+t
  gi|91774187|ref|YP_566879.1| 405 VYLTTDQ----RLLERLQRTRKQGLPVSIEVDASVGEVLKVRISSAsfsaefvdefvVQKAQNAPMSKEKIVEVIGKLGDT 481
                                   899****....6666666656667********9****999999866999999999************************** PP

                       DUF3656  71 pFeleeieidldgl.fiPvseLnelRRealekLeear 106
                                    Fe+++i+++++g  fiP+++L+++RR+a + L e++
  gi|91774187|ref|YP_566879.1| 482 SFEAKDIDVRINGDiFIPMGVLTNARRQAADMLLEKI 518
                                   ***********8555******************9997 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014        63      82     162 ..      20      99 ..       3     168 .. 0.85
   2 ?    6.8   0.0   0.00098       4.4     161     202 ..     567     606 ..     556     619 .. 0.84
   3 ?   -1.5   0.0      0.35   1.6e+03     161     191 ..     772     802 ..     769     811 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                                   TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE..EEE-CTTBSSTTCHHHHHHHHHHHH CS
                          DeoC  82 evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplile..lylrdeaikdekvdpdlvaeAarvs 160
                                   +v  +  a++ GAdav + v    +  ++++  ++++++     h++g++ +l+  + +++++ +    + d+v +A +++
  gi|91774187|ref|YP_566879.1|  20 DVDALMGAIKGGADAVYFGVTDLNARKGAKNFSVDDLGETIDLLHSHGIKAFLAlnIPVKQNELQH---ALDVVDRAYSLG 97 
                                   67777889************999999999**********************999545555555433...458888888887 PP

                                   TC CS
                          DeoC 161 ae 162
                                   ++
  gi|91774187|ref|YP_566879.1|  98 ID 99 
                                   76 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00098
                                   TCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEE CS
                          DeoC 161 aelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvls 202
                                   +++GaDi+  +++k +    ee ae+f+dv + +  + vvl+
  gi|91774187|ref|YP_566879.1| 567 VDCGADIVYLPMGKFSELLSEEYAETFRDVKETV--EIVVLA 606
                                   68*****************************955..555555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.35
                                   TCCT-SEEEE--SSCC.B.HHHHHHHHHHHH CS
                          DeoC 161 aelGaDiiKvevpkevvnateedaevfkdvi 191
                                    e+G+D+i  ++  ++++  +e   ++++v 
  gi|91774187|ref|YP_566879.1| 772 EECGIDVIRLDLSLYGKKDVQEITSAYRRVM 802
                                   589**********777777777777777765 PP

>> DUF2190  Uncharacterized conserved protein (DUF2190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       1.3   5.9e+03      27      42 ..      31      48 ..      15      54 .. 0.67
   2 ?   13.0   0.1   2.4e-05      0.11       6      74 ..     337     414 ..     331     443 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                       DUF2190 27 al..kvlGVAatdaaaGe 42
                                  ++   ++GV++ +a +G+
  gi|91774187|ref|YP_566879.1| 31 GAdaVYFGVTDLNARKGA 48
                                  334467999988998886 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.4e-05
                       DUF2190   6 sldvtvaaaaaitagqvvvlgal.kvlGVAa..t.daaaGetvtvaveGvf.....veaaaaiavGdkVywdasgkvl 74 
                                   + ++t++ +++i  +++v + +  +vlG A+    da+  e  + + ++++      +++ a++vG +Vy + + + l
  gi|91774187|ref|YP_566879.1| 337 NTSITLTLDEDIRLKDGVGIHTKaGVLGSAVnkLfDADGEEIKEANKRDIVtleisSKTGKAVSVGNEVYLTTDQRLL 414
                                   44555556779999999999985467776643333665555566788999999*999999***********9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (826 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 5708.50
//
Query:       gi|91774188|ref|YP_566880.1|  [L=195]
Description: Maf-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-51  173.6   0.0    3.3e-51  173.4   0.0    1.0  1  Maf       Maf-like protein


Domain annotation for each model (and alignments):
>> Maf  Maf-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.4   0.0   1.9e-55   3.3e-51       1     165 [.       3     186 ..       3     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 1.9e-55
                                   EEEEE---HHHHHHHHC.T-..EEEE------.......HHHHHHHHHHHHHHHHH.....TCEEEEEEEEEE...CE--- CS
                           Maf   1 kliLASaSprRkelLeq.lg..fevvpsdvde.......aeelvlrlAeaKaeava.....alvigaDtvvvl...ilgKP 63 
                                   k++LASaSprRkelL++ +g  fev++s+ +e        eelv+  + +Ka++va      ++i+aDtvv +   ilgKP
  gi|91774188|ref|YP_566880.1|   3 KVVLASASPRRKELLSKlIGnnFEVCVSSYEEtplqemnVEELVVFHSLEKAKDVAlrfdsGIIISADTVVFCdgaILGKP 83 
                                   68***************767999********9999989866789999*************988*********97767**** PP

                                   SSHHHHHHHHHHHTTSEEEEEEEEEEEE..EEE..EEEEEEEEEE----HHHHHHHHHCTSGCCSTTS--TTCGGGGGCEE CS
                           Maf  64 kdeeealemLkklsgrthevvTgvavlk..ekevksfvettevtfkelsdeeieaYvatgepldkAGaygiqgllglalve 142
                                   ++ ++a emL+++sg++   +Tg+++l+  +++++s++++t+v++k++s++ei++Yv++gepldkAGa++iqg+ g++lve
  gi|91774188|ref|YP_566880.1|  84 HTLNNAKEMLENISGKSVLAITGMTILDmdSGKCVSEYVSTDVNMKQMSSDEIASYVNSGEPLDKAGAFAIQGK-GAVLVE 163
                                   ******************************7788999************************************8.777*** PP

                                   EECS-HHHHHT--HHHHHHHHCC CS
                           Maf 143 rieGsysnVvGLPlaellelLke 165
                                   +i+G+++nVvGLPl++l ++L+e
  gi|91774188|ref|YP_566880.1| 164 SINGDFFNVVGLPLFRLGTILEE 186
                                   ******************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 1489.61
//
Query:       gi|91774189|ref|YP_566881.1|  [L=94]
Description: hypothetical protein Mbur_2270 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-32  109.6   0.1      6e-32  109.4   0.1    1.0  1  NTP_transf_9  Domain of unknown function (DUF427)


Domain annotation for each model (and alignments):
>> NTP_transf_9  Domain of unknown function (DUF427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.1   3.4e-36     6e-32       3      92 ..       4      88 ..       2      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 3.4e-36
                                  EE-SS-EEEEES--EEEEETTS--EEEB-GGGB-GGGEEEEEEEEEETTTEEEEEEEEEETTEEEEEEEEEESS--TT-GGGT CS
                  NTP_transf_9  3 vklngtvvaetddavvveetglppryYfppedvklellkpsdtttvCpwKGeasyyslavdgkevkdaaWsYpeptpeaaeik 85
                                  +k+ng+v+ae+++++ +e+     ++Yfppe+v+ e+l++sdt+++CpwKG a+y++++v+g++++daaWsYpep+++a+ei 
  gi|91774189|ref|YP_566881.1|  4 AKWNGVVLAESESVKEIEG-----NLYFPPESVNKEYLRESDTRSTCPWKGLAHYFDIVVNGEDNNDAAWSYPEPKEAAKEIT 81
                                  68*****************.....*********************************************************** PP

                                  T-BEE-T CS
                  NTP_transf_9 86 gyvaFya 92
                                  g++aF++
  gi|91774189|ref|YP_566881.1| 82 GHFAFWK 88
                                  ******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 726.79
//
Query:       gi|91774190|ref|YP_566882.1|  [L=211]
Description: hypothetical protein Mbur_2272 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-31  108.4   5.0    3.9e-15   55.8   0.3    2.6  2  zf-CDGSH  Iron-binding zinc finger CDGSH type
    1.5e-27   95.4   0.1    3.2e-27   94.4   0.1    1.6  1  Fer4_19   Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.3   4.3e-19   3.9e-15       1      47 [.      13      56 ..      13      57 .. 0.93
   2 !   54.1   0.6   1.4e-18   1.3e-14       1      47 [.     158     201 ..     158     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 4.3e-19
                      zf-CDGSH  1 nGPllVeGdvelvdadgesvelregrevvaLCrCgrSknkPfCDgsH 47
                                  nGP++ +   +l++++g+++e +     vaLCrCg+S+nkPfCDg+H
  gi|91774190|ref|YP_566882.1| 13 NGPYIAKELNDLKNSKGDTFEPQSM---VALCRCGHSSNKPFCDGTH 56
                                  8*****9888999999999999866...******************* PP

  == domain 2  score: 54.1 bits;  conditional E-value: 1.4e-18
                      zf-CDGSH   1 nGPllVeGdvelvdadgesvelregrevvaLCrCgrSknkPfCDgsH 47 
                                   +GP+   G++e  d+dg++ e +e+   ++LCrCg+SknkPfC g+H
  gi|91774190|ref|YP_566882.1| 158 DGPYDAVGRIEFDDPDGNTSEPKEH---FTLCRCGASKNKPFCSGEH 201
                                   7********************9998...******************* 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 !   94.4   0.1   3.6e-31   3.2e-27       1      63 [.      77     139 ..      77     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 3.6e-31
                       Fer4_19   1 yegeeitiednrelCihsgnCvkglpevFdpkrkpwikpdeasteeiievverCPSGALsyve 63 
                                   y g++iti+dnr++C+h g C+++lp+vF++k++pw++pd+as+++ii+vve+CPSGALsy++
  gi|91774190|ref|YP_566882.1|  77 YVGKDITIHDNRGVCSHRGYCTNNLPTVFRMKEEPWVDPDGASVKDIIRVVEMCPSGALSYTK 139
                                   78***********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1581.71
//
Query:       gi|91774191|ref|YP_566883.1|  [L=258]
Description: MscS mechanosensitive ion channel [Methanococcoides burtonii DSM 6242]
Scores for complete 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-49  166.1   0.1    1.1e-48  165.6   0.1    1.2  1  MS_channel       Mechanosensitive ion channel
    0.00059   19.8   3.7    0.00059   19.8   3.7    2.5  3  TM_helix         Conserved TM helix
  ------ inclusion threshold ------
       0.26   10.6   2.8       0.38   10.1   2.8    1.3  1  TssN             Type VI secretion system, TssN
       0.27   10.8   8.3       0.38   10.3   8.3    1.1  1  ABC2_membrane_5  ABC-2 family transporter protein
         10    6.7  14.3       0.85   10.1   6.1    2.2  2  FtsX             FtsX-like permease family


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 !  165.6   0.1     3e-52   1.1e-48       2     206 .]      48     246 ..      47     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 3e-52
                                   .HHHHHHHHHHHHHHHHTTT--SCCHHHHH.HHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                    MS_channel   2 kilkiliivvgilivlsllgvnvsallavl.GalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                   k ++ l++v +il++ s+lg ++s+++++l +++gl lg++++d++ n++aG+ + + +pf+ G+++e+ + +GtV ++g+
  gi|91774191|ref|YP_566883.1|  48 KFILALLYVAVILATVSMLGPDISSVIVGLsAVIGLILGFGMQDTLTNIAAGVWIATLRPFDKGEYLEVTGYSGTVHEVGI 128
                                   6788999***************999988873679*********************************************** PP

                                   SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEE CS
                    MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvlde 162
                                    +t++ t+d++++tiPn+ ++ s i+N +r ++trr++v++gv y+++   +e++l++ ++ +ke+p+v+ d+++ vv ++
  gi|91774191|ref|YP_566883.1| 129 MATDLLTPDNKLITIPNKLVWGSPIVNATR-MPTRRVDVDVGVSYDTK---PEDALKVAMKLMKENPMVHADPAPAVVTTA 205
                                   ******************************.*****************...****************************** PP

                                   E-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                    MS_channel 163 fgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                   ++dss+n+++r++++t   ++y+ v+ +++  i k+ +eegiei
  gi|91774191|ref|YP_566883.1| 206 LTDSSVNLQLRAWTNT---ADYWGVKGALTNGILKAYKEEGIEI 246
                                   ****************...***********************97 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   3.7   1.7e-07   0.00059      17      47 ..       8      38 ..       6      41 .. 0.94
   2 ?   -0.6   0.4      0.38   1.4e+03      10      22 ..      42      54 ..      38      64 .. 0.59
   3 ?   -2.2   0.1       1.2   4.3e+03      25      31 ..      80      86 ..      76     100 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.7e-07
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                      TM_helix 17 LvgAilILlvGwiiAkfvsrlvtkllaktgi 47
                                  L+ A+++L++G i+Ak++ ++ ++ l+kt++
  gi|91774191|ref|YP_566883.1|  8 LLSALIVLVLGIIVAKVLIKIFKNGLQKTNL 38
                                  899**************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                                  HHTTHSHHHHHHH CS
                      TM_helix 10 llsflPnLvgAil 22
                                  ++ fl + ++A+l
  gi|91774191|ref|YP_566883.1| 42 IVEFLSKFILALL 54
                                  5556666666654 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.2
                                  HHHHHHH CS
                      TM_helix 25 lvGwiiA 31
                                  ++G+i++
  gi|91774191|ref|YP_566883.1| 80 VIGLILG 86
                                  4555444 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.8   0.00011      0.38      63     115 ..       8      59 ..       2     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                          TssN  63 illqilylllGilhlylllkkffkelkekkilfeilltlivillglvlfvlvf 115
                                   +l+ +++l+lGi+ + +l+k f++ l++++ l e+++ +++ ++ ++l+v v 
  gi|91774191|ref|YP_566883.1|   8 LLSALIVLVLGIIVAKVLIKIFKNGLQKTN-LPELIVEFLSKFILALLYVAVI 59 
                                   577899********************9999.4455554444444444444433 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.3   0.00011      0.38      85     162 ..      10      87 ..       6     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
               ABC2_membrane_5  85 fvlililiailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivlii.iifgiifllv 162
                                   ++li+ +++i++  +l+ i +   ++ ++ e++  +l  +++al+++a++l  + ++g   + +++ + +++g+i  ++
  gi|91774191|ref|YP_566883.1|  10 SALIVLVLGIIVAKVLIKIFKNGLQKTNLPELIVEFLSKFILALLYVAVILATVSMLGPDISSVIVGLsAVIGLIL-GF 87 
                                   4556666666666666655555555599*********************************997554404444333.22 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   6.1   0.00024      0.85      26      85 ..       8      66 ..       3      72 .. 0.90
   2 ?    1.5   1.2      0.11   4.1e+02      27      47 ..      73      93 ..      70     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                          FtsX 26 llitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagl 85
                                  ll +l+ lv+G++++ ++++++ ++l++    +el + +    +l+++ ++++la++++l
  gi|91774191|ref|YP_566883.1|  8 LLSALIVLVLGIIVAKVLIKIFKNGLQKTNL-PELIVEFLSKFILALLYVAVILATVSML 66
                                  5678999999999999999999999999966.*************************997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                          FtsX 27 litlvalviGlglgllaaqll 47
                                  +i+ +++viGl+lg+ +   l
  gi|91774191|ref|YP_566883.1| 73 VIVGLSAVIGLILGFGMQDTL 93
                                  678889999999988776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1487.72
//
Query:       gi|91774192|ref|YP_566884.1|  [L=167]
Description: MarR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete 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   44.1   0.1    2.3e-11   43.4   0.1    1.4  1  MarR            MarR family
    7.2e-09   35.4   0.0    1.2e-08   34.8   0.0    1.3  1  MarR_2          MarR family
    4.5e-08   33.5   0.1    8.8e-08   32.5   0.1    1.5  1  HTH_27          Winged helix DNA-binding domain
    0.00057   20.0   0.0     0.0012   19.0   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0012   18.5   0.0     0.0037   17.0   0.0    1.8  2  FtsK_gamma      Ftsk gamma domain
     0.0013   18.4   0.0     0.0026   17.5   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
     0.0025   18.0   0.0     0.0043   17.2   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain
     0.0045   17.1   0.0     0.0076   16.4   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
       0.03   14.2   0.0      0.064   13.2   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.062   13.4   0.2       0.13   12.4   0.0    1.8  2  DUF2250         Uncharacterized protein conserved in archaea 
      0.081   12.8   0.5       0.23   11.4   0.1    2.0  2  TFIIE_alpha     TFIIE alpha subunit
       0.13   12.5   0.0       0.23   11.7   0.0    1.5  1  GAD             GAD 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 !   43.4   0.1   1.6e-14   2.3e-11       7      58 ..      43      94 ..      37      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.6e-14
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                  ++++ ++++g+   s Lak l+++ks++t ++d Le +Gl++R+ +p+DrR+
  gi|91774192|ref|YP_566884.1| 43 KAIHFIKREGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYRKDDPSDRRK 94
                                  567779999999***************************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   7.7e-12   1.2e-08      10      61 ..      44      93 ..      39      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 7.7e-12
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  +++++ r+++  + ++ la++l ++ks+++ +++ L+  GLv r+++p D+R
  gi|91774192|ref|YP_566884.1| 44 AIHFIKREGE--VMPSNLAKYLEIKKSSATSLIDSLETEGLVYRKDDPSDRR 93
                                  6799*****9..***************************************9 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   5.9e-11   8.8e-08       9      68 .]      45     103 ..      40     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.9e-11
                        HTH_27   9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                   +h i+ r++++  + l+++l + +s++ + ++ L+  GLv r+ d+ drr +++ lT+ G
  gi|91774192|ref|YP_566884.1|  45 IHFIK-REGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYRKDDPSDRRKTLLGLTENG 103
                                   57788.788888899*******************************************98 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 !   19.0   0.0   7.9e-07    0.0012      20      53 ..      51      84 ..      43      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.9e-07
                                  HSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 20 kkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                  ++ v +++la+ L++++ss++  +  Le +G+v 
  gi|91774192|ref|YP_566884.1| 51 EGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVY 84
                                  5668899*************************95 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.5e-06    0.0037       7      59 ..      41      94 ..      37      97 .. 0.88
   2 ?   -2.9   0.0       4.2   6.3e+03      34      43 ..     105     114 ..     103     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                    FtsK_gamma  7 feeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgpaeg.skpRe 59
                                   ++a++++ +eg++  S l + l+i  + A++lid Le eG+V  ++  s +R+
  gi|91774192|ref|YP_566884.1| 41 ANKAIHFIKREGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYRKDDpSDRRK 94
                                  689****************************************99887455555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.2
                    FtsK_gamma  34 nRAarlidqL 43 
                                    R+  +id++
  gi|91774192|ref|YP_566884.1| 105 ERSKYMIDKM 114
                                   6888999999 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.7e-06    0.0026      14      50 ..      49      85 ..      45      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.7e-06
                                  TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  ++ +e+  s lA+ + + kS++  l+ +L+ +G+v +
  gi|91774192|ref|YP_566884.1| 49 KREGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYR 85
                                  56677889***************************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 !   17.2   0.0   2.9e-06    0.0043       6      78 ..      45     116 ..      43     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                        HTH_34   6 lsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78 
                                   +++   + e+ +++l + le+ ++   + ++ Le+ g + ++ + +++ ++tll +T++G+e+ k  ++ ++s
  gi|91774192|ref|YP_566884.1|  45 IHFIKREGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYRKDDPSDR-RKTLLGLTENGLERSKYMIDKMCS 116
                                   5666678899999************************87666666666.**************9999999987 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.1e-06    0.0076      21      52 ..      56      87 ..      49     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.1e-06
                B-block_TFIIIC 21 qsdLakeskqdprslfyrlksLekkgLIvkqs 52
                                   s Lak+++++++s +++++sLe  gL++++ 
  gi|91774192|ref|YP_566884.1| 56 PSNLAKYLEIKKSSATSLIDSLETEGLVYRKD 87
                                  578**************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.064      20      57 ..      51      88 ..      48     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                  HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                  +g+   + +a+ l++ +s++ + + sLe  GlV+r++ 
  gi|91774192|ref|YP_566884.1| 51 EGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYRKDD 88
                                  56777889**************************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 ?   12.4   0.0   8.7e-05      0.13      17      57 ..      48      88 ..      33     114 .. 0.85
   2 ?   -3.0   0.0       5.5   8.3e+03      10      16 ..     136     142 ..     125     158 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.7e-05
                       DUF2250 17 lkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                  +k+ +   + ++ak+lei+++ +++l+++Le+ GL+ r++ 
  gi|91774192|ref|YP_566884.1| 48 IKREGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYRKDD 88
                                  555555567899************************99865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.5
                       DUF2250  10 alkvlkh 16 
                                   alk+l  
  gi|91774192|ref|YP_566884.1| 136 ALKILVK 142
                                   3444332 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00015      0.23      13      59 ..      39      85 ..      20     113 .. 0.86
   2 ?   -1.1   0.1       1.1   1.7e+03      26      38 ..     123     135 ..     112     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                  HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                   TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvky 59
                                  + a ++++ + ++gev   +lak l+i++    +l+  L  ++lv  
  gi|91774192|ref|YP_566884.1| 39 KTANKAIHFIKREGEVMPSNLAKYLEIKKSSATSLIDSLETEGLVYR 85
                                  56778999************************************953 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                                   TSEBHHHHHHHHT CS
                   TFIIE_alpha  26 gevteedlakelk 38 
                                   + +++ed+ + l+
  gi|91774192|ref|YP_566884.1| 123 SDLSDEDIDEALN 135
                                   6788999988875 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.23      21      75 ..      23      79 ..      13      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                  TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC..S-HHHHHHHHHHCT- CS
                           GAD 21 aklsrkeideleefakelgakglawikvegegltgpiakf..lteeevkklleavga 75
                                  ++++++ +++ +   ++ + k++ +ik ege + +++ak+  +++     l++ +++
  gi|91774192|ref|YP_566884.1| 23 SNIVGQFVEKDDICLNKTANKAIHFIKREGEVMPSNLAKYleIKKSSATSLIDSLET 79
                                  56777777777778889999********************88888888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1002.62
//
Query:       gi|91774193|ref|YP_566885.1|  [L=812]
Description: hydrophobe/amphiphile efflux-3 HAE3 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-56  192.1  25.8    2.1e-29  102.6   3.9    2.5  3  MMPL            MMPL family
    2.8e-13   50.0  10.5      8e-08   32.3   0.9    3.0  4  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    3.8e-11   41.4  24.7    8.5e-10   37.0   9.4    2.3  2  ACR_tran        AcrB/AcrD/AcrF family
    2.8e-10   39.0  24.8    3.2e-08   32.2   1.5    3.0  3  Patched         Patched family
    4.8e-10   39.1  11.2    4.8e-10   39.1  11.2    2.5  2  SecD_SecF       Protein export membrane protein
  ------ inclusion threshold ------
       0.46   10.0   3.1        0.9    9.1   3.1    1.4  1  Fzo_mitofusin   fzo-like conserved region
        2.2    8.0   6.1        3.7    7.3   0.1    2.9  3  Lectin_N        Hepatic lectin, N-terminal domain


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 ?   -4.0   0.5       2.1   5.3e+03     148     167 ..      30      49 ..      22      51 .. 0.77
   2 !  101.3   7.4     2e-32   5.1e-29      75     292 ..     155     367 ..      59     391 .. 0.80
   3 !  102.6   3.9     8e-33   2.1e-29      96     315 ..     568     783 ..     534     793 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.1
                          MMPL 148 ievvtlvvilviLlivyrSl 167
                                   ie  t+ +ilv Ll+v+ S+
  gi|91774193|ref|YP_566885.1|  30 IESNTIPIILVALLLVLVSV 49 
                                   67778888888888888776 PP

  == domain 2  score: 101.3 bits;  conditional E-value: 2e-32
                          MMPL  75 dvaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvv 155
                                   d+    + +D + a + v+++g++++++++e +++++  v+ a+ + + +v vtG +a +  +++a +++++++  +++++
  gi|91774193|ref|YP_566885.1| 155 DYVPEGLMPDATHALMYVEMAGSTSDEQKQEILRELEVSVSMAEFPPDYNVVVTGEPAFMVSMNNAMMSSMAVLLGLSVIL 235
                                   35555667999********************************************************************** PP

                          MMPL 156 ilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgl.lvvlliavGtDYallLvsRyreelaaged 235
                                    +v+L +v++ +   l+pl+ v+++++ ++g       +  le+ ++++++ ++ +li+ G+DYa+ +  R+ eel++ge+
  gi|91774193|ref|YP_566885.1| 236 MVVVLYLVFGHVRWRLMPLAIVLLGIIYTFGA------MGYLEIPMTMVSMaAFPVLIGLGIDYAIQFHNRIEEELERGES 310
                                   *******************************9......56667777777775899************************** PP

                          MMPL 236 reeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivl 292
                                    e+av ++++ tg++v++a ++ a+ +++L+++++p+++ ++  + +G+++ +l++l
  gi|91774193|ref|YP_566885.1| 311 PEAAVVDTIKHTGPAVLIALIITALGFFSLLTSSVPMIQDFAKLLLIGIAMCFLASL 367
                                   ******************************************************987 PP

  == domain 3  score: 102.6 bits;  conditional E-value: 8e-33
                          MMPL  96 gdpgsteadesvaairaaveear....pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaall 172
                                   gd+  ++++e ++a+ ++ve+      p+ g+ + +tG+ ++++++  a ++ + +++ ++l +++  Ll++yr l+ al+
  gi|91774193|ref|YP_566885.1| 568 GDAMGSLGMEGIEALIDVVEDDMvwmaPPPGVSATITGSNVVFTEVIGALTSGRVFMTYLGLGLVFGGLLLIYRDLLKALV 648
                                   599999**************99999*9****************************************************** PP

                          MMPL 173 plltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvta 253
                                   p++t  + ++ + gl     +llg++ + ++++l  +l+++vG+ Ya+l++ Ry ee ++g + eea+ +a +++gk+++ 
  gi|91774193|ref|YP_566885.1| 649 PVITMFMVVGWSGGL----MYLLGMDYTPMTATL-GALILGVGSEYAVLMMERYFEEKEKGATPEEAMSEAGTKIGKAIIT 724
                                   **************9....667788877777666.57889***************************************** PP

                          MMPL 254 aGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraalakprrkrk 315
                                   +Glt  + +++L+v+++ +++++G+   + v +++++++ + P ++v l  +   +++rk++
  gi|91774193|ref|YP_566885.1| 725 SGLTTLFGFCALAVSDFDIISSFGIITVIDVGLALFATFVIFPPVMVSLDNF---REKRKAA 783
                                   ************************************9999999999999888...5555544 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 ?   -5.7   2.4         7   1.8e+04      20      39 ..     219     238 ..     212     244 .. 0.44
   2 !   31.1   3.0   6.9e-11   1.8e-07      13     132 ..     254     373 ..     246     392 .. 0.87
   3 ?   -3.6   0.0       3.5   9.1e+03      42      50 ..     427     435 ..     417     441 .. 0.70
   4 !   32.3   0.9   3.1e-11     8e-08      10     144 ..     647     782 ..     643     788 .. 0.87

  Alignments for each domain:
  == domain 1  score: -5.7 bits;  conditional E-value: 7
                                   HHHHCCHHHHHHHHHHHHHH CS
                Sterol-sensing  20 vasslgllaylgltltliil 39 
                                    a+  ++  +lgl++ l+++
  gi|91774193|ref|YP_566885.1| 219 NAMMSSMAVLLGLSVILMVV 238
                                   34444444444544444433 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 6.9e-11
                                   HHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHH.HTTTCHHHHHHHHHHHHCCCCHHCCCHH CS
                Sterol-sensing  13 viivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrt.srsldeseriaealgevgpsilltslte 92 
                                   ++ivll ++ ++g + yl++++t++++  +P  ++  g+d    + + +++  +r ++ +  +  +++++gp++l+ ++  
  gi|91774193|ref|YP_566885.1| 254 LAIVLLGIIYTFGAMGYLEIPMTMVSMAAFPV-LIGLGIDYAIQFHNRIEEElERGESPEAAVVDTIKHTGPAVLIALIIT 333
                                   6899***********************99995.579****999999999765145555599******************** PP

                                   HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHH CS
                Sterol-sensing  93 llalllgaltdvpavqeFclfaavavlvdFllqitfFvav 132
                                   +l ++  + ++vp +q F+    +++++ Fl  +++ v+v
  gi|91774193|ref|YP_566885.1| 334 ALGFFSLLTSSVPMIQDFAKLLLIGIAMCFLASLFVGVTV 373
                                   **99977799*********************998877766 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.5
                                   HHHHHHHHC CS
                Sterol-sensing  42 lPflvlavg 50 
                                    Pfl+l++ 
  gi|91774193|ref|YP_566885.1| 427 HPFLILFIA 435
                                   588888875 PP

  == domain 4  score: 32.3 bits;  conditional E-value: 3.1e-11
                                   HHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHHCC CS
                Sterol-sensing  10 lagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsillts 89 
                                   l+ vi++ + v  s gl+++lg+++t++++  l  l+l vg +   ++++ + + +++    +e + ea +++g +i+ + 
  gi|91774193|ref|YP_566885.1| 647 LVPVITMFMVVGWSGGLMYLLGMDYTPMTA-TLGALILGVGSEYAVLMMERYFEEKEKGATpEEAMSEAGTKIGKAIITSG 726
                                   6779999**********************9.999*********9877777766655555444******************* PP

                                   CHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH.HHHHHHHHCTX CS
                Sterol-sensing  90 ltellall.lgaltdvpavqeFclfaavavlvdFllqitfFvavL.sldirreeser 144
                                   lt l+ +  l+ ++d+  +++F + +++ v +  +   ++F  v+ sld  re+++ 
  gi|91774193|ref|YP_566885.1| 727 LTTLFGFCaLA-VSDFDIISSFGIITVIDVGLALFATFVIFPPVMvSLDNFREKRKA 782
                                   ********555.******************************998578887776554 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   9.4   3.3e-13   8.5e-10     308     483 ..     197     375 ..      85     458 .. 0.80
   2 !   10.3   7.3   3.7e-05     0.095     862     983 ..     619     739 ..     580     773 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.3e-13
                                   GGSSTTEEEEEEEESHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCH CS
                      ACR_tran 308 eslPegveivvvydrtefvr...asieeVvktLleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNl 385
                                   +++P ++++vv+ + + +v+   a ++     L ++++L v+v++l  + +r  l+p+ +v l ++ tf ++  l++ + +
  gi|91774193|ref|YP_566885.1| 197 AEFPPDYNVVVTGEPAFMVSmnnAMMSSMAVLLGLSVILMVVVLYLVFGHVRWRLMPLAIVLLGIIYTFGAMGYLEIPMTM 277
                                   34999999999999998885221445667777889********************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHH.CTGGGGSB.HHHHHHHHHHH CS
                      ACR_tran 386 ltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllav.flPilflg.GveGklfrqfa 464
                                    ++ +  + iGl +D Ai     ie++le  ge+p +a+  ++k  + a+  ial+++a  f  +l+ +  ++  + + + 
  gi|91774193|ref|YP_566885.1| 278 VSMAAFPVLIGLGIDYAIQFHNRIEEELER-GESPEAAVVDTIKHTGPAV-LIALIITALgFFSLLTSSvPMIQDFAKLLL 356
                                   ******************************.************9976665.556666553144444333133444444456 PP

                                   HHHHHHHHHHHHHHHCCHH CS
                      ACR_tran 465 ltivlaillsvlvaltltP 483
                                   + i+++ l+s++v +t++ 
  gi|91774193|ref|YP_566885.1| 357 IGIAMCFLASLFVGVTVIY 375
                                   8999999999999999875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 3.7e-05
                                   CHHHHHHHHHHHHHHHHHHHHHTSSSTCHH..HHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ACR_tran 862 nsllilvalalllvflvLaalyeslsepll..illtvPlalvGallalllrglelsviaqvGlilliGlavkNaillvefa 940
                                   +  +++  l l lvf  L + y  l+++l+  i + + ++  G+l+ l l   +  ++a  G ++l G+ +  a+l++e +
  gi|91774193|ref|YP_566885.1| 619 SGRVFMTYLGLGLVFGGLLLIYRDLLKALVpvITMFMVVGWSGGLMYL-LGMDYTPMTATLGALIL-GVGSEYAVLMMERY 697
                                   344667778888888888999999988886324444557788888754.34445678999998765.99999999999999 PP

                                   HHHHHTTTTCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCT CS
                      ACR_tran 941 kelrekegksleeaileaakeRLrPiLMTalaailGvlPLals 983
                                    e++e +g ++eea+ ea+ +  ++i+   l++++G+  La+s
  gi|91774193|ref|YP_566885.1| 698 FEEKE-KGATPEEAMSEAGTKIGKAIITSGLTTLFGFCALAVS 739
                                   99988.8888999999999999999999999999999999987 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.023        58     427     518 ..      15     103 ..       5     150 .. 0.75
   2 !   12.8  11.7   9.1e-06     0.023     630     801 ..     196     369 ..     170     374 .. 0.85
   3 !   32.2   1.5   1.3e-11   3.2e-08     255     388 ..     644     778 ..     638     798 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.023
                       Patched 427 e.lkskffreiyapfllnksvrlvvlllfvvylaiaiyGcvnikegLepkklvledsplvevlkliekeiwkeglqvevvv 506
                                   e ++ k + e+++ f+ ++   ++ + l++v  ++++ G+ ni+ +   +  v + s+l + + ++  +i+   + v v+v
  gi|91774193|ref|YP_566885.1|  15 EvVIIKNLFEKLGVFIESNTIPIILVALLLV--LVSVQGAQNITMESGTDTFVEKTSQLYQDFDHLYMNIFGIEAIV-VIV 92 
                                   3366778888999999999999988888887..5799**************************99988888654443.344 PP

                       Patched 507 nNppdltikesr 518
                                   +  + ++ ++  
  gi|91774193|ref|YP_566885.1|  93 E-DGQVSDPAAL 103
                                   3.3445444433 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.1e-06
                       Patched 630 iadkeselnvtvfdedaafadqlltilpstiqnivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLD 710
                                   +a+  +++nv+v  e a+++++ + +++s+   + l++++m+vv  l   ++   l+    ++   i ++G +    + + 
  gi|91774193|ref|YP_566885.1| 196 MAEFPPDYNVVVTGEPAFMVSMNNAMMSSMAVLLGLSVILMVVVLYLVFGHVRWRLMPLAIVLLGIIYTFGAMGYLEIPMT 276
                                   45555779**************************************999999887764443333346789999999***** PP

                       Patched 711 pismitiimsiGfsvdlsaHiayafvrsekd..dakeRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvL 789
                                    +sm++  + iG  +d++     ++ ++ +   ++++ vv+++++ g  v+ + + T lg ++Ll+    m+q F+k +++
  gi|91774193|ref|YP_566885.1| 277 MVSMAAFPVLIGLGIDYAIQFHNRIEEELERgeSPEAAVVDTIKHTGPAVLIALIITALGFFSLLTSSVPMIQDFAKLLLI 357
                                   *****************9655555544433355************************************************ PP

                       Patched 790 vvvigllHgLli 801
                                    +++ +l  L++
  gi|91774193|ref|YP_566885.1| 358 GIAMCFLASLFV 369
                                   ***999999986 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 1.3e-11
                       Patched 255 ilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaaw.krteaklsvkkrigealseagvaiti 334
                                   + a++ v++ ++ +  s Gl+++lG+ +  ++     L+L++G   + lm++++ ++ e+  + ++ ++ea    g ai  
  gi|91774193|ref|YP_566885.1| 644 LKALVPVITMFMVVGWSGGLMYLLGMDYTPMTATLGALILGVGSEYAVLMMERYfEEKEKGATPEEAMSEAGTKIGKAIIT 724
                                   6789999*****************************************9999871455566679999************99 PP

                       Patched 335 TslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaakaea 388
                                     lT ++ F + a+++   i+ F i+t + + ++ + ++++f +v++   +   
  gi|91774193|ref|YP_566885.1| 725 SGLTTLFGFCALAVSDFDIISSFGIITVIDVGLALFATFVIFPPVMVSLDNFRE 778
                                   99********************************************98766533 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1  11.2   1.9e-13   4.8e-10      26     184 ..     218     375 ..     211     380 .. 0.89
   2 ?    2.1   6.8     0.041   1.1e+02      35     185 ..     623     772 ..     599     775 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.9e-13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHH CS
                     SecD_SecF  26 skelaekavlallialvliliyvalrF.ewrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvf 105
                                    + ++ + ++ l+++++l++++++l F + r+ l  ++ ++  +i t g++  l+i++++ ++aa  ++iG  ++  +   
  gi|91774193|ref|YP_566885.1| 218 NNAMMSSMAVLLGLSVILMVVVLYLVFgHVRWRLMPLAIVLLGIIYTFGAMGYLEIPMTMVSMAAFPVLIGLGIDYAIQFH 298
                                   5778899999999999999999999996345555555556668************************************** PP

                                   HHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHHHHHH CS
                     SecD_SecF 106 drvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifiasplll 184
                                   +r++e+l++   ++ + ++ + +++t    +++ ++t+l  ++ll     +++dfa  ll+G+++  + s+f+  ++++
  gi|91774193|ref|YP_566885.1| 299 NRIEEELER--GESPEAAVVDTIKHTGPAVLIALIITALGFFSLLTSSVPMIQDFAKLLLIGIAMCFLASLFVGVTVIY 375
                                   ******988..77788889999***************************************************988876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.041
                                   HHHHHHHHHHHHHHHHHT-HHH.HHHHHHHHHHHHHHHHHHHHHTT----HHH..HHHHHHHTTSSSHHHHHHHHHHHHHH CS
                     SecD_SecF  35 lallialvliliyvalrFewrv.alaaiialvhDviitvgvlsllgievdlat..vaalLtiiGYSvndtvvvfdrvrenl 112
                                   +   + l l++  + l++++ + al  +i+++  v    g++ llg++ ++ t  ++al  i+G   +  v++++r  e+ 
  gi|91774193|ref|YP_566885.1| 623 FMTYLGLGLVFGGLLLIYRDLLkALVPVITMFMVVGWSGGLMYLLGMDYTPMTatLGAL--ILGVGSEYAVLMMERYFEE- 700
                                   55555555555566666666543677788888888888899999999988754115555..7888889999*****9999. PP

                                   HH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
                     SecD_SecF 113 rkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifiaspllll 185
                                    k+k at +e++ ++ ++  +  i+  lttl+   al +   d++++f ++ ++ + +  + +  i  p+++ 
  gi|91774193|ref|YP_566885.1| 701 -KEKGATPEEAMSEAGTKIGKAIITSGLTTLFGFCALAVSDFDIISSFGIITVIDVGLALFATFVIFPPVMVS 772
                                   .8889**********988766555556899999********************99999888888887777765 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.1   0.00035       0.9       6      55 ..     217     266 ..     209     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00035
                 Fzo_mitofusin   6 lmvslalglasltsrtslgvlvvggvvlravgWrvialslalygllYlyE 55 
                                   +  ++++++a l   + + ++vv  +v   v Wr++ l+++l g++Y + 
  gi|91774193|ref|YP_566885.1| 217 MNNAMMSSMAVLLGLSVILMVVVLYLVFGHVRWRLMPLAIVLLGIIYTFG 266
                                   444566666777778889999999***********************986 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0014       3.7      28      63 ..      32      67 ..       7      93 .. 0.78
   2 ?    2.7   0.4     0.038        98      29      43 ..     225     239 ..     208     251 .. 0.76
   3 ?   -2.4   0.0       1.4   3.7e+03      33      50 ..     361     378 ..     347     420 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                      Lectin_N 28 llllslglsllLLVvvcVigsqnsqLqreLetLket 63
                                   + + + l  lLLV v+V g+qn  + +   t+ e+
  gi|91774193|ref|YP_566885.1| 32 SNTIPIILVALLLVLVSVQGAQNITMESGTDTFVEK 67
                                  5556677889*************9998876665554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.038
                      Lectin_N  29 lllslglsllLLVvv 43 
                                   + + lgls++L+Vvv
  gi|91774193|ref|YP_566885.1| 225 MAVLLGLSVILMVVV 239
                                   45779********98 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                      Lectin_N  33 lglsllLLVvvcVigsqn 50 
                                   + +   L V v Vi   n
  gi|91774193|ref|YP_566885.1| 361 MCFLASLFVGVTVIYGLN 378
                                   333334677777773322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.92u 0.34s 00:00:01.26 Elapsed: 00:00:00.52
# Mc/sec: 4683.26
//
Query:       gi|91774194|ref|YP_566886.1|  [L=369]
Description: hypothetical protein Mbur_2276 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0018   18.5   1.2       0.02   15.2   0.8    2.3  2  CARDB        CARDB
     0.0045   17.2   0.4        4.3    7.7   0.0    3.3  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
      0.062   13.5   0.1       0.63   10.3   0.0    2.5  2  ASH          Abnormal spindle-like microcephaly-assoc'd, ASPM
      0.086   13.2   1.1        2.2    8.6   1.0    2.9  3  DUF11        Domain of unknown function DUF11


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 ?    1.3   0.0     0.089     4e+02      12      72 ..      69     128 ..      59     149 .. 0.72
   2 !   15.2   0.8   4.4e-06      0.02       9      92 ..     232     320 ..     225     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.089
                                   -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                         CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                     e + ge+ +++v ++N G     + + ++  d+ l  + ++++L+ ++ +t  f +++e
  gi|91774194|ref|YP_566886.1|  69 DVEFERGETAQVRVVLSNRGVLHGFKARGNVGTDEGL-HSLSLKELEYESLRTTAFGIKAE 128
                                   556778999**********988877777777777777.66777777777777766666665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.4e-06
                                   EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE...SEE-CTEEEEEEEEEE-S..-S-CEEEEEEEE CS
                         CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv...psLaagesttvsftwtte..ategevtltvvv 84 
                                   +  ++e++ g++ ti+vt +N G+ ++++  ++++  + l ++ +v    ++a+ge +tvsf++  e  a e+ + +   +
  gi|91774194|ref|YP_566886.1| 232 SEVEGELTSGKSGTINVTYTNIGEVEAYDAYARIITMKPLSSSRSVvnlGNVAPGEDKTVSFNVASEisAVEKIYGIDSEI 312
                                   56678999**************************99999986666555599************999864344444466666 PP

                                   STT-SS-- CS
                         CARDB  85 DpdnevaE 92 
                                      n+ +E
  gi|91774194|ref|YP_566886.1| 313 KYRNDDDE 320
                                   66665555 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.93   4.2e+03       2      17 ..      73      88 ..      72      89 .. 0.81
   2 !    7.7   0.0   0.00096       4.3      55      78 ..     160     183 ..     142     184 .. 0.78
   3 !    6.0   0.1    0.0032        14       3      72 ..     240     308 ..     238     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.93
                   NPCBM_assoc  2 epGetvtltltvtndg 17
                                  e+Get +++++++n g
  gi|91774194|ref|YP_566886.1| 73 ERGETAQVRVVLSNRG 88
                                  7899999999998876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00096
                   NPCBM_assoc  55 atvkVtppagaaaGdyevtakarl 78 
                                     +++t++++a aG y++ + +++
  gi|91774194|ref|YP_566886.1| 160 MSFTITISDNAPAGSYMILLPVSY 183
                                   5799*************9887775 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0032
                   NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyev 72 
                                    G++ t+++t tn g+  a + + ++ + +  + ++ s+ ++  +apGe  ++ ++V +  +a+   y +
  gi|91774194|ref|YP_566886.1| 240 SGKSGTINVTYTNIGEVEAYDAYARIITMKPLS-SSRSVVNLGNVAPGEDKTVSFNVASEISAVEKIYGI 308
                                   677777777777777777777777776633334.679999999*************98877776655555 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00014      0.63      45      80 ..     221     256 ..     211     261 .. 0.86
   2 ?   -0.5   0.0      0.33   1.5e+03       4      28 ..     267     292 ..     264     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                   EEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           ASH  45 kvpaaekgfsveetelevqpgesvtltvtwtPteeg 80 
                                    +++++ +f v+e e e++ g+s t++vt+t+  e+
  gi|91774194|ref|YP_566886.1| 221 VIIEPSAKFVVSEVEGELTSGKSGTINVTYTNIGEV 256
                                   5788999************************97665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.33
                                   EE-TTB--.EEEEE-----EEEEEEE CS
                           ASH   4 llapfsrk.pfvsFgdvkvGssaerl 28 
                                   +++p s++   v++g+v+ G+ ++ +
  gi|91774194|ref|YP_566886.1| 267 TMKPLSSSrSVVNLGNVAPGEDKTVS 292
                                   56777777778888888888877654 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.24   1.1e+03       9      26 ..      71      88 ..      55      91 .. 0.78
   2 ?   -3.7   0.0       3.6   1.6e+04      12      25 ..     156     169 ..     151     173 .. 0.69
   3 ?    8.6   1.0    0.0005       2.2       9      81 ..     237     300 ..     226     306 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.24
                         DUF11  9 evrpGdtvtytltvtNtg 26
                                  e+  G+t ++ ++++N+g
  gi|91774194|ref|YP_566886.1| 71 EFERGETAQVRVVLSNRG 88
                                  556688888888888877 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.6
                         DUF11  12 pGdtvtytltvtNt 25 
                                   p d +++t+t + +
  gi|91774194|ref|YP_566886.1| 156 PDDPMSFTITISDN 169
                                   56777889887654 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0005
                         DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv..gsLeagesatlsftvrvtrt 81 
                                   e+++G   t ++t tN g + a+++  +      ++  s+s s         v  g++++ge +t+sf v    +
  gi|91774194|ref|YP_566886.1| 237 ELTSGKSGTINVTYTNIGEVEAYDAYARI---ITMKPLSSSRS------V--VnlGNVAPGEDKTVSFNVASEIS 300
                                   67899999999999999999997666665...45666666666......3..3459************9977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2123.12
//
Query:       gi|91774195|ref|YP_566887.1|  [L=370]
Description: hypothetical protein Mbur_2277 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0023   18.1   0.7        2.2    8.6   0.0    3.3  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
       0.13   12.1   0.1       0.21   11.4   0.1    1.3  1  DOCK-C2      C2 domain in Dock180 and Zizimin proteins
       0.23   11.7   3.2       0.49   10.7   0.1    2.9  2  CARDB        CARDB


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.8   4.8e+03       2      17 ..      68      83 ..      67      84 .. 0.87
   2 !    8.6   0.0   0.00037       2.2      37      76 ..     134     175 ..     104     178 .. 0.81
   3 ?   -2.4   0.1      0.97   5.8e+03       4      24 ..     208     228 ..     207     230 .. 0.84
   4 !    6.3   0.0    0.0019        12       3      78 ..     234     308 ..     232     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.8
                   NPCBM_assoc  2 epGetvtltltvtndg 17
                                  e+G++vtl++ + n+g
  gi|91774195|ref|YP_566887.1| 68 ERGDSVTLNIDLMNKG 83
                                  799*****99999987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00037
                   NPCBM_assoc  37 vevspasaaslapGetve..atvkVtppagaaaGdyevtaka 76 
                                   v++ p++a +l  G+++e  +++++ ++++a+ G y+ ++ +
  gi|91774195|ref|YP_566887.1| 134 VKSGPQEAGTLVSGQQTEspVQFNIEISNNAVSGNYPMRLDL 175
                                   56778888899999988745799**************99876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.97
                   NPCBM_assoc   4 Getvtltltvtndgtaaatnv 24 
                                   G+ +t+++ v ++ +  +tnv
  gi|91774195|ref|YP_566887.1| 208 GQNTTFNILVEDEARFEVTNV 228
                                   889999999999988888887 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0019
                   NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                   p+++  + +t +n g+ +a++  +++s+ +  + ++ + a + +l  Ge++ a +k+++ + a++  y +  ++++
  gi|91774195|ref|YP_566887.1| 234 PDSESMVYVTYKNVGDLPAKDATVRISAADPFS-TTDDQAFLGTLGSGESTVAIFKLKVDELAVPKAYALNSEVKY 308
                                   67888899999999*9****9999999999999.888888899**********************99*99998886 PP

>> DOCK-C2  C2 domain in Dock180 and Zizimin proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.5e-05      0.21     119     193 ..     262     335 ..     240     337 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                       DOCK-C2 119 flpLlkedgraflkd...gehelpvyk....kelppsgYlslpssrtssseeqkgpsekwldnskdtfkvrtklcSTiltq 192
                                     p+ ++d++afl +   ge ++ ++k    +   p++Y          ++e k +++k  d++ dt+k++t ++ST   +
  gi|91774195|ref|YP_566887.1| 262 ADPFSTTDDQAFLGTlgsGESTVAIFKlkvdELAVPKAYAL--------NSEVKYEDIKGHDQTSDTVKIKTDVLSTSAKS 334
                                   55777788899988665599999999866653334458883........34555678888999**************8766 PP

                       DOCK-C2 193 d 193
                                   d
  gi|91774195|ref|YP_566887.1| 335 D 335
                                   5 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5      0.14   8.6e+02      48      48 ..     101     101 ..      54     192 .. 0.59
   2 ?   10.7   0.1   8.1e-05      0.49       9      81 ..     226     303 ..     216     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                                   E CS
                         CARDB  48 l 48 
                                   +
  gi|91774195|ref|YP_566887.1| 101 E 101
                                   0 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.1e-05
                                   EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEE CS
                         CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..ategevtlt 81 
                                   t   +++++ +e+ ++vt kN G+  +++ +v++ + +      +++ +  L +gest   f+ +++  a ++ ++l+
  gi|91774195|ref|YP_566887.1| 226 TNVTGDLYPDSESMVYVTYKNVGDLPAKDATVRISAADPFSttdDQAFLGTLGSGESTVAIFKLKVDelAVPKAYALN 303
                                   666788999**************************99988766677778**********9999999876666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2431.03
//
Query:       gi|91774196|ref|YP_566888.1|  [L=408]
Description: translation initiation factor IF-2 subunit gamma [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-32  110.7   0.4    8.7e-32  109.2   0.4    1.9  1  eIF2_C         Initiation factor eIF2 gamma, C terminal
    8.8e-32  110.2   3.1    7.5e-31  107.2   3.1    2.0  1  GTP_EFTU       Elongation factor Tu GTP binding domain
    9.9e-07   29.1   0.2    4.1e-06   27.1   0.2    2.1  1  GTP_EFTU_D2    Elongation factor Tu domain 2
    3.9e-05   23.6   0.9    0.00053   19.9   0.2    2.3  2  RsgA_GTPase    RsgA GTPase
    0.00032   20.8   0.0    0.00095   19.2   0.0    1.8  1  MMR_HSR1       50S ribosome-binding GTPase
      0.002   18.1   0.1      0.004   17.1   0.1    1.5  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
     0.0023   15.9   0.2     0.0031   15.5   0.2    1.1  1  PolC_DP2       DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.019   14.7   2.8        3.4    7.4   0.7    2.6  3  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
      0.033   14.2   0.5      0.063   13.3   0.5    1.4  1  DZR            Double zinc ribbon
      0.072   12.7   0.4        0.8    9.3   0.1    2.2  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.076   12.5   1.3         12    5.4   0.0    2.7  2  FeoB_N         Ferrous iron transport protein B
       0.22   11.4   2.2       0.65    9.8   0.2    2.6  3  zf-ZPR1        ZPR1 zinc-finger domain
        2.7    7.8   4.7        9.1    6.2   4.7    1.9  1  zinc_ribbon_2  zinc-ribbon domain


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 !  109.2   0.4   6.3e-35   8.7e-32       2      86 .]     322     406 ..     321     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 6.3e-35
                                   EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEEE CS
                        eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLiG 82 
                                   ++++e++ller+vgv++e+++ k+k++E+Lmln+G+a+t+g+vts+++d+a+ kLk+Pvcae+g+ +a+sRr+++rWrLiG
  gi|91774196|ref|YP_566888.1| 322 SFTLELKLLERVVGVSDEESIGKIKTSEPLMLNVGTATTVGIVTSAREDVAEAKLKRPVCAEVGSMVAISRRIGSRWRLIG 402
                                   57899**************************************************************************** PP

                                   EEEE CS
                        eIF2_C  83 wGei 86 
                                   +G i
  gi|91774196|ref|YP_566888.1| 403 VGVI 406
                                   **87 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 !  107.2   3.1   5.4e-34   7.5e-31       3     193 ..       5     197 ..       3     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 5.4e-34
                                   EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................... CS
                      GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................... 64 
                                    +nig++ghvDhGKtTL+ +L                   +Dt++eE +rgi+i    + +                    
  gi|91774196|ref|YP_566888.1|   5 CVNIGMVGHVDHGKTTLVSALSGV---------------WTDTHSEEMKRGISIRLGYADTTfrkcptcpepqnlsvaktc 70 
                                   68*******************833...............367777777777777777776666677777777777778888 PP

                                   .....TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST.HH CS
                      GTP_EFTU  65 .....ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl.ka 137
                                        k+++ ++++++D+PGH+  + ++  g++++Dga+lv++a+e  ++pqt+e+l  ++  g++ i+++ NK+D + k+
  gi|91774196|ref|YP_566888.1|  71 ehcgtKTEEIRTVSFVDSPGHETLMATMLSGAAIMDGAILVIAANEEcPQPQTKEHLMALNIIGIKnIVIVQNKIDLVpKE 151
                                   8888668899***********************************9879*****************999999******999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                      GTP_EFTU 138 elkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                   ++ e  +++k ++      ++  +++   + pvv++Sa ++ +++ l++a+ e++p
  gi|91774196|ref|YP_566888.1| 152 KVIEHYHQIK-EF------VKGTVAE---DAPVVPISAQQNINIDVLISAMNEMIP 197
                                   9999999999.66......4444433...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 !   27.1   0.2   2.9e-09   4.1e-06       1      62 [.     229     297 ..     229     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.9e-09
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.......EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.......ivtrissletfhededeavaganaGvivaikg 62 
                                   G+v++g++  Gtlk Gd ++i++  ++ ++e       i t i  + + +e++dea +g+   +++++++
  gi|91774196|ref|YP_566888.1| 229 GGVIGGTLTAGTLKAGDDIEIRPgRKV-ESEnavrwepIFTNINLIIAGKEKVDEATPGGLLALGTGLDP 297
                                   89*********************6655.7778*************************9988888877755 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.16   2.2e+02     104     137 ..      10      40 ..       6      53 .. 0.80
   2 !   19.9   0.2   3.8e-07   0.00053      13      99 ..     102     194 ..      77     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.16
                                   EECSTTSSHHHHHHHHCTT-----S--------- CS
                   RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                   +vG+   GK+tL+ al +     t   se+++rG
  gi|91774196|ref|YP_566888.1|  10 MVGHVDHGKTTLVSALSGV---WTDTHSEEMKRG 40 
                                   6888899*********985...555555555555 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.8e-07
                                   EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTT CS
                   RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsakt 86 
                                   +a +d +++v++++ +e+ + + +  L++++  gi ++viv nKiDl+ +e+      +++e+ + + a + +v+ +sa++
  gi|91774196|ref|YP_566888.1| 102 AAIMDGAILVIAAN-EECPQPQTKEHLMALNIIGIkNIVIVQNKIDLVPKEKviehyhQIKEFVKGTVAEDAPVVPISAQQ 181
                                   8889**********.666666777888888889996789999**********99988888888888899999********9 PP

                                   HTTHHHHHHHCTT CS
                   RsgA_GTPase  87 kegleelkellkd 99 
                                   + +++ l +++++
  gi|91774196|ref|YP_566888.1| 182 NINIDVLISAMNE 194
                                   9999999887765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.9e-07   0.00095       1     113 [.       7     143 ..       7     144 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.9e-07
                                   EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE............................EEE CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke............................iel 50 
                                   +++ vG+   GK+tL++al+g  +   s++    + i+ g  +  ++  +                            + +
  gi|91774196|ref|YP_566888.1|   7 NIGMVGHVDHGKTTLVSALSGVwTDTHSEEMKRGISIRLGYADttFR--KcptcpepqnlsvaktcehcgtkteeirtVSF 85 
                                   5899****************975444455555555555554442222..12344455556666666666666677777*** PP

                                   EECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH.TTSEEEEEEE CS
                      MMR_HSR1  51 vDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleellee.akkplilvln 113
                                   vD pG  e       l  ++l+    +d ++lv+ a+ee  +p+ +e    l+    k++++v n
  gi|91774196|ref|YP_566888.1|  86 VDSPG-HE------TLMATMLSGAAiMDGAILVIAANEECPQPQTKEHLMALNIiGIKNIVIVQN 143
                                   *****.55......7889999877768*******9996655666555544443322344555555 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 !   17.1   0.1   2.9e-06     0.004      57     100 ..     137     192 ..      93     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                  MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                   + ++v NKiDl+ +e++ e +++              +v+iSa++++n+d L +++
  gi|91774196|ref|YP_566888.1| 137 NIVIVQNKIDLVPKEKVIEHYHQikefvkgtvaedAPVVPISAQQNINIDVLISAM 192
                                   457889*****99988877777667788899987668999************9887 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 !   15.5   0.2   2.2e-06    0.0031     615     758 ..      49     195 ..      30     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-06
                      PolC_DP2 615 eiarrkCkkC...gketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgereek 692
                                   + + rkC++C   ++ ++ ++Ce+Cg+ktee  + + +++  +e  +  + + a  ++   + + +  e  + + +e +  
  gi|91774196|ref|YP_566888.1|  49 DTTFRKCPTCpepQNLSVAKTCEHCGTKTEEIRTVSFVDSPGHETLMATMLSGAAIMDGAILVIAANEECPQPQTKE-HLM 128
                                   5667889988433567999************9999999998876665555555555555544444444444445555.446 PP

                      PolC_DP2 693 leelkgvkgltskekipEpleK.gilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrel 758
                                     ++ g+k+++  ++ ++ + K  ++   h++  f  gtv  D+  +p+++ +  +i+v ++ ++e+
  gi|91774196|ref|YP_566888.1| 129 ALNIIGIKNIVIVQNKIDLVPKeKVIEHYHQIKEFVKGTVAEDAPVVPISAQQNINIDVLISAMNEM 195
                                   6778899998776666666655269999******************************999998886 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    0.0044         6       4      23 ..       8      27 ..       6      39 .. 0.86
   2 ?    7.4   0.7    0.0025       3.4      39     142 ..      84     193 ..      66     194 .. 0.62
   3 ?   -3.0   0.0       3.9   5.3e+03      90     100 ..     358     368 ..     339     378 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0044
                     PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                  i ++G+v+ GKttL  al+g
  gi|91774196|ref|YP_566888.1|  8 IGMVGHVDHGKTTLVSALSG 27
                                  5589*************997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0025
                     PduV-EutP  39 eviDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi......itkidlaedeeniea... 110
                                   +++D+PG     ++l+ ++ + +a  d   lv  a +ee+  p++  ++++ ++iGi        kidl+ +e+ ie    
  gi|91774196|ref|YP_566888.1|  84 SFVDSPGH----ETLMATMLSGAAIMDGAILVI-AANEECPQPQTKEHLMALNIIGIknivivQNKIDLVPKEKVIEHyhq 159
                                   46888885....444445555555455444444.44456667777777777777775333211479****99988875111 PP

                     PduV-EutP 111 veelLksaGaek..ifevsavekegieellkyle 142
                                    +e++k   ae   +  +sa ++++i+ l++ ++
  gi|91774196|ref|YP_566888.1| 160 IKEFVKGTVAEDapVVPISAQQNINIDVLISAMN 193
                                   5556665555542269999999999999988776 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.9
                     PduV-EutP  90 keviGiitkid 100
                                     ++Gi+t + 
  gi|91774196|ref|YP_566888.1| 358 ATTVGIVTSAR 368
                                   45667776543 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   4.6e-05     0.063       1      27 [.      55      82 ..      55     127 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                           DZR  1 CpqCgee.lppdarfCseCgtklkavaa 27
                                  Cp+C e+ + + a++C++Cgtk ++  +
  gi|91774196|ref|YP_566888.1| 55 CPTCPEPqNLSVAKTCEHCGTKTEEIRT 82
                                  9***9996788899*******9876555 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 ?    1.2   0.0      0.18   2.5e+02       4      21 ..       9      26 ..       6      41 .. 0.77
   2 ?    9.3   0.1   0.00058       0.8     103     166 ..      96     161 ..      81     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                                  EEEESTTCCHHHHHHHHH CS
                          cobW  4 vltGflGsGKTtLlnhll 21
                                  +++G +  GKTtL+++l 
  gi|91774196|ref|YP_566888.1|  9 GMVGHVDHGKTTLVSALS 26
                                  57888889******9875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00058
                                   SHHHHHCCCECEEEEEEETTTH..CCHCCHHHHHHHHHHTSSE.EEEE-HHHHCHC..HHHHHHHH CS
                          cobW 103 eeelksdltldavvavvDaknl.eaeeekieekaedqlaaadl.lvlnKtDlldeeallekleerl 166
                                   ++ l+ ++ +d+ + v+ a++   + ++k++  a + +   ++ +v nK+Dl+++e+ +e+ +++ 
  gi|91774196|ref|YP_566888.1|  96 ATMLSGAAIMDGAILVIAANEEcPQPQTKEHLMALNIIGIKNIvIVQNKIDLVPKEKVIEHYHQIK 161
                                   55667778899999999997763444555555555666666651556*********8877776655 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 ?    5.4   0.0    0.0089        12       2      23 ..       7      28 ..       6      33 .. 0.89
   2 ?    5.3   0.4     0.009        12     106     155 ..     136     191 ..      66     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0089
                                  EEEEEESTTSSHHHHHHHHHTT CS
                        FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                  ++ +vG  + Gkttl+ al+g+
  gi|91774196|ref|YP_566888.1|  7 NIGMVGHVDHGKTTLVSALSGV 28
                                  6889***************996 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.009
                                   SSEEEEEETHHHHHHTTEEE-HHHHHHHH......TS-EEEEBTTTTBTHHHHHHH CS
                        FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekL......gvpvvktsakkkegieellka 155
                                   +++v++ n+id + k+++  + ++++e +      + pvv++sa+++ +i+ l++a
  gi|91774196|ref|YP_566888.1| 136 KNIVIVQNKIDLVPKEKVIEHYHQIKEFVkgtvaeDAPVVPISAQQNINIDVLISA 191
                                   4788999*******999998999999877333333589***********9998765 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00047      0.65      28      55 ..      65      92 ..      53      99 .. 0.84
   2 ?   -1.0   0.1         1   1.4e+03       5      30 ..     117     142 ..     116     145 .. 0.84
   3 ?   -2.9   0.0         4   5.5e+03     121     144 ..     256     279 ..     241     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00047
                       zf-ZPR1 28 imsfeCehCgyknnevksageieekGkr 55
                                   ++ +CehCg+k++e+++ + ++  G +
  gi|91774196|ref|YP_566888.1| 65 SVAKTCEHCGTKTEEIRTVSFVDSPGHE 92
                                  56789************99988887765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                       zf-ZPR1   5 sCgkengetrllltkiPyfkeviims 30 
                                   +C + +++++l+ ++i  +k+++i+ 
  gi|91774196|ref|YP_566888.1| 117 ECPQPQTKEHLMALNIIGIKNIVIVQ 142
                                   57777789999999********9975 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4
                       zf-ZPR1 121 edeekekieeflekleeliegeep 144
                                   e+e++ ++e ++++++ +i+g+e+
  gi|91774196|ref|YP_566888.1| 256 ESENAVRWEPIFTNINLIIAGKEK 279
                                   337788999999999999998876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.7    0.0066       9.1       9      22 ..      63      76 ..      54      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0066
                 zinc_ribbon_2  9 lqdnakFCpyCGtp 22
                                  +   ak C++CGt+
  gi|91774196|ref|YP_566888.1| 63 NLSVAKTCEHCGTK 76
                                  45789*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2584.03
//
Query:       gi|91774197|ref|YP_566889.1|  [L=122]
Description: hypothetical protein Mbur_2279 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-42  145.0   0.3    1.2e-42  144.9   0.3    1.0  1  PIN_9          PIN like domain
     0.0049   16.3   1.8       0.39   10.1   1.3    2.1  2  PIN_5          PINc domain ribonuclease
  ------ inclusion threshold ------
      0.045   13.5   0.3       0.12   12.2   0.3    1.8  1  DUF5615        Domain of unknown function (DUF5615)
       0.13   12.1   0.0       0.14   12.0   0.0    1.3  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN 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 !  144.9   0.3   2.7e-46   1.2e-42       1     116 []       3     115 ..       3     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 2.7e-46
                         PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDdail 81 
                                   vi+Dtn++mipvqf+vdif el rl g++e++vp+av++EL++l+k+ +g+++taakv+lsL++rc++++   + aDd+il
  gi|91774197|ref|YP_566889.1|   3 VIIDTNGFMIPVQFKVDIFGELGRL-GYDEFIVPQAVVNELKSLVKKYRGENKTAAKVGLSLSDRCTLLDRA-GIADDIIL 81 
                                   8************************.**********************************************.******** PP

                         PIN_9  82 elakeldaavlvTnDreLkkrllekgipvilLRqk 116
                                   +la ++daavl TnD +L krl++++ +v+ LRqk
  gi|91774197|ref|YP_566889.1|  82 QLALDMDAAVL-TNDVGLVKRLNDANATVVRLRQK 115
                                   ***********.**********************8 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0032        14      45      77 ..      32      64 ..      24      69 .. 0.84
   2 !   10.1   1.3   8.7e-05      0.39     162     183 ..      80     101 ..      66     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0032
                         PIN_5 45 cyippsvykElkeflkreeveeeviakldtwlv 77
                                  + +p++v +Elk+++k+++ e+++ ak+   l 
  gi|91774197|ref|YP_566889.1| 32 FIVPQAVVNELKSLVKKYRGENKTAAKVGLSLS 64
                                  457899*************99999999987665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 8.7e-05
                         PIN_5 162 vllLAkELdaavvssDeGikkw 183
                                   +l LA ++daav+++D G+ k 
  gi|91774197|ref|YP_566889.1|  80 ILQLALDMDAAVLTNDVGLVKR 101
                                   5669**************9875 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   2.6e-05      0.12      30      58 ..      70      98 ..      63     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                       DUF5615 30 lglegasDeeileyAkeedriivTkDkDF 58
                                  l+ +g+ D+ il++A + d++++T+D   
  gi|91774197|ref|YP_566889.1| 70 LDRAGIADDIILQLALDMDAAVLTNDVGL 98
                                  56789*********************665 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.1e-05      0.14      91     111 ..      76      96 ..      27     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                 RNase_Zc3h12a  91 ddrlilelAeekdGvivsndn 111
                                    d +il+lA + d+ +++nd 
  gi|91774197|ref|YP_566889.1|  76 ADDIILQLALDMDAAVLTNDV 96 
                                   499*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 842.47
//
Query:       gi|91774198|ref|YP_566890.1|  [L=192]
Description: DNA-directed RNA polymerase subunit E' [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-20   72.5   0.2    4.9e-20   71.7   0.2    1.4  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    2.1e-12   47.2   0.2    4.8e-12   46.1   0.2    1.6  1  S1             S1 RNA binding domain
     0.0099   16.1   0.0      0.014   15.6   0.0    1.3  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.2   8.2e-24   4.9e-20       1      70 []       8      77 ..       8      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 8.2e-24
                                  EEEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                   SHS2_Rpb7-N  1 edtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                  +dt+r++P  lg+++  +++++l+ek+eg+v+++lG iva++di+e++eg++l g+G+vy++V f+a++F
  gi|91774198|ref|YP_566890.1|  8 KDTIRVAPRLLGEDVGVSVKDALKEKLEGRVDKALGSIVAITDIEEVGEGHILVGDGAVYYDVIFEAIIF 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 !   46.1   0.2     8e-16   4.8e-12       3      69 ..      80     155 ..      78     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 8e-16
                                   TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTTTE CS
                            S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdrrr 69 
                                   +  ev+eG V++ +++GafV +g  ++g++++s++ +d             ++++++l++Gd+v++++  v  ++r+
  gi|91774198|ref|YP_566890.1|  80 QLQEVIEGLVVETVEFGAFVSIG-AMDGLLHVSQITDDfmsydgkngrLISKVGNRTLSEGDKVRARIVAVSTNERE 155
                                   6679*******************.***********************988999******************988886 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 !   15.6   0.0   2.4e-06     0.014       1      93 [.      79     174 ..      79     192 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                                   -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE----- CS
                 RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifvdvkp 81 
                                   P  +ev++g + ++ + g +vs+g +d ++   +   + +++d ++   + +v    +  l  g+++r r++ ++ ++++p
  gi|91774198|ref|YP_566890.1|  79 PQLQEVIEGLVVETVEFGAFVSIGAMDGLLHVSQITDDFMSYDGKNGRLISKV---GNRTLSEGDKVRARIVAVSTNEREP 156
                                   7789************************99999999999*************9...5556889****************** PP

                                   --HHHHHCHHH......C CS
                 RNA_pol_Rbc25  82 kspkeaeleee......e 93 
                                   +++k   + ++      e
  gi|91774198|ref|YP_566890.1| 157 RDSKIGLTMRQhalgrlE 174
                                   999876665555555441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1245.18
//
Query:       gi|91774199|ref|YP_566891.1|  [L=61]
Description: DNA-directed RNA polymerase, subunit E'' [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-13   49.6   0.3    3.7e-13   49.4   0.3    1.1  1  Spt4         Spt4/RpoE2 zinc finger
  ------ inclusion threshold ------
       0.01   15.7   1.8      0.014   15.2   1.8    1.2  1  Prok-RING_4  Prokaryotic RING finger family 4
      0.022   14.9   0.5      0.029   14.5   0.5    1.1  1  Laminin_EGF  Laminin EGF domain
      0.048   13.2   2.8      0.073   12.7   2.8    1.3  1  RecR         RecR protein
      0.082   12.3   2.9       0.15   11.5   0.3    2.1  2  zf-ribbon_3  zinc-ribbon domain
        7.9    6.3   8.0        8.6    6.1   0.5    2.2  2  zf-RRN7      Zinc-finger of RNA-polymerase I-specific TFIIB, 


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 !   49.4   0.3   1.3e-16   3.7e-13       2      77 .]       4      61 .]       3      61 .] 0.97

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.3e-16
                          Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                  + C++C+++++ ++     Cp+C            s+++s++++Glv+i+dp++S +A++  ++ +v+++YAlkv+
  gi|91774199|ref|YP_566891.1|  4 QVCRECHRIVSGQT-----CPVC-----------ASSNLSDDWSGLVIIVDPQRSIIAEM--IGVEVADKYALKVR 61
                                  58***********9.....****...........9*************************..************96 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.8   4.7e-06     0.014      20      38 ..       5      23 ..       3      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                   Prok-RING_4 20 vCkeCfdskdlssCPlCqr 38
                                  vC+eC      ++CP+C +
  gi|91774199|ref|YP_566891.1|  5 VCRECHRIVSGQTCPVCAS 23
                                  8****************86 PP

>> Laminin_EGF  Laminin EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   9.7e-06     0.029      19      41 ..       5      28 ..       2      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.7e-06
                                  CES.BTTTEESTTS-EE-TTEEEG CS
                   Laminin_EGF 19 qCl.CkenveGrkCdrCkpgyygl 41
                                  +C+ C++ v+G++C  C++    +
  gi|91774199|ref|YP_566891.1|  5 VCReCHRIVSGQTCPVCASSNLSD 28
                                  7****************9876655 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.8   2.4e-05     0.073      18      37 ..       5      24 ..       4      25 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                                  E-TTT--EESSSS-CCCCST CS
                          RecR 18 hCsrCgnlteedlCaICsdp 37
                                   C++C+ +     C++C+++
  gi|91774199|ref|YP_566891.1|  5 VCRECHRIVSGQTCPVCASS 24
                                  5****************986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.096   2.9e+02      16      22 ..       3       9 ..       3       9 .. 0.90
   2 ?   11.5   0.3     5e-05      0.15       3      16 ..      16      30 ..      14      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.096
                   zf-ribbon_3 16 dnvCpyC 22
                                  d+vC  C
  gi|91774199|ref|YP_566891.1|  3 DQVCREC 9 
                                  789**99 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5e-05
                   zf-ribbon_3  3 vrCPnCGa.plssdd 16
                                  ++CP C + +ls+d+
  gi|91774199|ref|YP_566891.1| 16 QTCPVCASsNLSDDW 30
                                  79******99***98 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   1.7      0.01        31      23      28 ..       5      10 ..       4      14 .. 0.90
   2 ?    6.1   0.5    0.0029       8.6       4      13 ..      15      28 ..      13      31 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.01
                       zf-RRN7 23 yCrrCh 28
                                  +Cr+Ch
  gi|91774199|ref|YP_566891.1|  5 VCRECH 10
                                  8***** PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0029
                       zf-RRN7  4 gppCgvCgc....r 13
                                  g  C+vC +    +
  gi|91774199|ref|YP_566891.1| 15 GQTCPVCASsnlsD 28
                                  678****9965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 368.81
//
Query:       gi|91774200|ref|YP_566892.1|  [L=188]
Description: hypothetical protein Mbur_2282 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-43  145.0   0.0    1.1e-42  144.6   0.0    1.1  1  DUF359        Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.057   13.1   0.1       0.08   12.6   0.1    1.3  1  MAF_flag10    Protein of unknown function DUF115
      0.078   13.0   0.1       0.14   12.2   0.1    1.5  1  RNase_P_pop3  RNase P subunit Pop3


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 !  144.6   0.0   1.8e-46   1.1e-42       1     125 [.      45     167 ..      45     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 1.8e-46
                        DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEEDL 81 
                                   +t +ll+++i+Pd+ ivD++tkR +++++      +k+k++ +i+v+Np+G+ite+li++i++a+ s+++v+i+V+GEEDL
  gi|91774200|ref|YP_566892.1|  45 TTFHLLDSNIIPDILIVDDRTKRAPASSQVVFG--TKHKGFAEITVDNPPGVITEDLINVISDAIVSDKNVRIFVQGEEDL 123
                                   799*********************777644433..4789****************************************** PP

                        DUF359  82 avlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                   a+lpail+ap +svv+YGqpdeGv+lv+vte++k+e+++l++k+
  gi|91774200|ref|YP_566892.1| 124 AALPAILMAPLNSVVLYGQPDEGVMLVRVTESLKAELKDLFDKI 167
                                   ****************************************9985 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.3e-05      0.08      43      80 ..      27      66 ..      22     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                    MAF_flag10 43 ll.kelrdkaviiaadtalk.aLlkegIkPDivvslDpqe 80
                                   l k+l++   +i+++  ++  Ll+ +I+PDi +  D+++
  gi|91774200|ref|YP_566892.1| 27 SLvKDLNNPTKLISVGDVTTfHLLDSNIIPDILIVDDRTK 66
                                  4449999999999998876637************999955 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.4e-05      0.14     104     151 ..     122     171 ..      95     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                  RNase_P_pop3 104 klvqlpksaqakldekl..Glskagmllvrkdasldkklaklvskkveel 151
                                    l  lp   +a l++++  G++++g++lvr ++sl+ +l++l +k +e++
  gi|91774200|ref|YP_566892.1| 122 DLAALPAILMAPLNSVVlyGQPDEGVMLVRVTESLKAELKDLFDKILEKQ 171
                                   5778999999999999889***********************99966664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1319.95
//
Query:       gi|91774201|ref|YP_566893.1|  [L=102]
Description: 30S ribosomal protein S24e [Methanococcoides burtonii DSM 6242]
Scores for complete 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   86.0   0.0    1.7e-24   85.6   0.0    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 !   85.6   0.0   9.4e-29   1.7e-24       1      77 [.      20      95 ..      20      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 9.4e-29
                                  EEEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS--- CS
                Ribosomal_S24e  1 vvdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekk 77
                                  ++d++++g +tps+ ++r kla+m++v+ +lv++++f++ +G+  ++G+akiY++++++k +E++++l+Rn+l+e++
  gi|91774201|ref|YP_566893.1| 20 KFDATFKG-STPSRLDVRGKLAAMLNVPLELVILQKFENTYGMSAANGYAKIYEDAARMKVVEKEYVLKRNELPEAE 95
                                  699*****.****************************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 00:00:00.44
# Mc/sec: 700.31
//
Query:       gi|91774202|ref|YP_566894.1|  [L=49]
Description: 30S ribosomal protein S27ae [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-21   73.8   3.4    9.7e-21   73.7   3.4    1.0  1  Ribosomal_S27   Ribosomal protein S27a
    8.9e-05   22.3   5.2    0.00033   20.5   4.1    2.1  2  Nudix_N_2       Nudix N-terminal
    0.00025   21.1   0.8    0.00029   20.9   0.8    1.2  1  Ribosomal_L37e  Ribosomal protein L37e
    0.00025   20.8   1.2    0.00043   20.1   1.2    1.3  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
     0.0047   17.1   0.1      0.005   17.0   0.1    1.1  1  IBR             IBR domain, a half RING-finger domain
     0.0048   16.5   3.5      0.038   13.7   0.2    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0053   16.9   0.2     0.0057   16.8   0.2    1.2  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
     0.0071   16.3   0.7      0.009   16.0   0.7    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0077   16.2   1.2      0.013   15.5   1.2    1.3  1  DZR             Double zinc ribbon
     0.0079   15.6   1.2       0.65    9.5   0.0    2.1  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.013   15.2   4.2       0.31   10.8   0.3    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.014   15.3   1.1      0.018   15.0   1.1    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.014   15.7   0.7      0.091   13.1   0.0    1.9  2  GFA             Glutathione-dependent formaldehyde-activating
      0.015   15.3   0.4      0.016   15.3   0.4    1.0  1  DUF1451         Zinc-ribbon containing domain
      0.036   14.1   0.2      0.037   14.1   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.07   13.1   0.9      0.086   12.9   0.1    1.6  2  zinc_ribbon_11  Probable zinc-ribbon
      0.084   13.0   2.8       0.38   11.0   0.6    2.1  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
      0.099   12.8   4.8       0.38   10.9   0.4    2.0  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        0.1   12.1   3.4       0.17   11.4   3.4    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
        1.3    8.7   4.7          2    8.1   0.3    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   3.4   1.1e-23   9.7e-21       1      45 []       3      45 ..       3      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.1e-23
                                  SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                 Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                  v  yYkv++ +++erlr+ Cpr CG+Gv++A+hkdR +CGkCg+T
  gi|91774202|ref|YP_566894.1|  3 VKDYYKVNG-ESIERLRQFCPR-CGDGVYLADHKDRLTCGKCGYT 45
                                  678******.9***********.*********************9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.8   0.00076      0.68      23      29 ..      19      25 ..       7      30 .. 0.68
   2 !   20.5   4.1   3.7e-07   0.00033       2      32 ..      20      46 ..      19      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00076
                                  EEETTTT CS
                     Nudix_N_2 23 lvCpaCg 29
                                    Cp+Cg
  gi|91774202|ref|YP_566894.1| 19 QFCPRCG 25
                                  5555555 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.7e-07
                                  B-TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                     Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgtih 32
                                  FC+ CG  v l+    D++ Rl+C +Cg++ 
  gi|91774202|ref|YP_566894.1| 20 FCPRCGDGVYLA----DHKDRLTCGKCGYTE 46
                                  ********8765....9***********975 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.8   3.3e-07   0.00029      17      43 ..      19      48 ..       9      49 .] 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.3e-07
                Ribosomal_L37e 17 ilCrrCgkrsy...hvqkktCascGypsak 43
                                   +C rCg   y   h  + tC++cGy + k
  gi|91774202|ref|YP_566894.1| 19 QFCPRCGDGVYladHKDRLTCGKCGYTEFK 48
                                  68*********776777779******7654 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 !   20.1   1.2   4.8e-07   0.00043       2      31 ..      19      46 ..      19      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.8e-07
                                  EBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                  +FCp Cg+  + ++ k    + C +CgY e
  gi|91774202|ref|YP_566894.1| 19 QFCPRCGDGVYLADHKDR--LTCGKCGYTE 46
                                  7*******9999887777..56******75 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 !   17.0   0.1   5.5e-06     0.005      15      46 ..      15      44 ..       2      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.5e-06
                           IBR 15 dpnlkwCprpdCeaiieksegcksvtCskCgf 46
                                  ++ ++ Cp   C+  +   ++++++tC kCg+
  gi|91774202|ref|YP_566894.1| 15 ERLRQFCP--RCGDGVYLADHKDRLTCGKCGY 44
                                  445889**..9**********99*******97 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   4.2e-05     0.038       4      11 ..      19      26 ..      16      33 .. 0.85
   2 ?    4.2   0.3     0.037        33       6      10 ..      39      43 ..      38      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                 zf-NADH-PPase  4 rFCgrCGa 11
                                  +FC+rCG 
  gi|91774202|ref|YP_566894.1| 19 QFCPRCGD 26
                                  9******6 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.037
                 zf-NADH-PPase  6 CgrCG 10
                                  Cg+CG
  gi|91774202|ref|YP_566894.1| 39 CGKCG 43
                                  99998 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 !   16.8   0.2   6.3e-06    0.0057      22      57 ..       7      41 ..       2      49 .] 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.3e-06
                MqsA_antitoxin 22 ykgektvikavtgdfCarCGegvldeeeedrlseel 57
                                  yk +   i+ ++ +fC+rCG+gv+ ++++drl+   
  gi|91774202|ref|YP_566894.1|  7 YKVNGESIERLR-QFCPRCGDGVYLADHKDRLTCGK 41
                                  666666666664.8*****************98665 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 !   16.0   0.7     1e-05     0.009      19      46 .]      19      45 ..       5      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                 Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrkq 46
                                  + CP+Cg + +y   +  ++ C +C+++
  gi|91774202|ref|YP_566894.1| 19 QFCPRCG-DGVYLADHKDRLTCGKCGYT 45
                                  45*****.8889999999*******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2   1.4e-05     0.013       8      36 ..      14      44 ..      11      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                           DZR  8 lppdarfCseCgtklkavaa..edrCpsCge 36
                                  ++   +fC++Cg  +  + +    +C +Cg+
  gi|91774202|ref|YP_566894.1| 14 IERLRQFCPRCGDGVYLADHkdRLTCGKCGY 44
                                  6666799****99976555566999999997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00073      0.65       4       9 ..      20      25 ..      11      32 .. 0.66
   2 ?    5.6   0.3     0.012        11      18      24 ..      38      44 ..      33      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00073
                   zf-ribbon_3  4 rCPnCG 9 
                                  +CP+CG
  gi|91774202|ref|YP_566894.1| 20 FCPRCG 25
                                  455555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                   zf-ribbon_3 18 vCpyCGt 24
                                  +C +CG+
  gi|91774202|ref|YP_566894.1| 38 TCGKCGY 44
                                  8*****7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00035      0.31      14      20 ..      19      25 ..      18      28 .. 0.75
   2 ?    6.2   0.3    0.0096       8.6      16      21 ..      39      44 ..      33      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                 zinc_ribbon_2 14 kFCpyCG 20
                                  +FCp+CG
  gi|91774202|ref|YP_566894.1| 19 QFCPRCG 25
                                  5888888 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0096
                 zinc_ribbon_2 16 CpyCGt 21
                                  C +CG+
  gi|91774202|ref|YP_566894.1| 39 CGKCGY 44
                                  888886 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.1     2e-05     0.018      30      55 ..      20      45 ..      18      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                   C++Cg  ++ a+++++++C +Cg++
  gi|91774202|ref|YP_566894.1| 20 FCPRCGDGVYLADHKDRLTCGKCGYT 45
                                  6***********************97 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.091      35      63 ..       4      32 ..       2      38 .. 0.65
   2 ?    3.0   0.1      0.15   1.3e+02      46      59 ..      33      46 ..      30      49 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                           GFA 35 keykktadsgnkvtrsfCpeCgsplysee 63
                                  k y k + ++ +  r+fCp+Cg  +y   
  gi|91774202|ref|YP_566894.1|  4 KDYYKVNGESIERLRQFCPRCGDGVYLAD 32
                                  5555554444445569*********9753 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                           GFA 46 kvtrsfCpeCgspl 59
                                  +++r  C +Cg + 
  gi|91774202|ref|YP_566894.1| 33 HKDRLTCGKCGYTE 46
                                  567899****9765 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.4   1.8e-05     0.016     106     144 ..      10      48 ..       2      49 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                       DUF1451 106 sGevvglGtlvCekCgkelalkkteeippCpkCgateFr 144
                                    Ge +   +  C +Cg  + l   +   +C kCg teF+
  gi|91774202|ref|YP_566894.1|  10 NGESIERLRQFCPRCGDGVYLADHKDRLTCGKCGYTEFK 48 
                                   68888888999***************9***********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 ?   14.1   0.2   4.1e-05     0.037      68      97 ..      16      47 ..       6      49 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                                  --EEEETTTS-EEECHH.H.HHS-TTTSSS-E CS
                          HypA 68 pvkvrCreCgkefelee.k.alrCpkCgsadv 97
                                  +++  C +Cg  + l++ k +l+C+kCg +++
  gi|91774202|ref|YP_566894.1| 16 RLRQFCPRCGDGVYLADhKdRLTCGKCGYTEF 47
                                  67889*****999977644689******8765 PP

>> zinc_ribbon_11  Probable zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.6e-05     0.086      96     122 ..       4      30 ..       1      36 [. 0.78
   2 ?   -0.6   0.0       1.4   1.3e+03      26      36 ..      34      44 ..      30      47 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-05
                zinc_ribbon_11  96 rkwycvlcdedyegkklcpackdgvys 122
                                   + +y v  +     ++ cp+c+dgvy 
  gi|91774202|ref|YP_566894.1|   4 KDYYKVNGESIERLRQFCPRCGDGVYL 30 
                                   6677777777777889**********6 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                zinc_ribbon_11 26 rqdvlcvscgc 36
                                  ++ ++c  cg 
  gi|91774202|ref|YP_566894.1| 34 KDRLTCGKCGY 44
                                  55678888886 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.17   1.5e+02       2      10 ..      21      29 ..      20      36 .. 0.77
   2 ?   11.0   0.6   0.00042      0.38      36      46 ..      37      47 ..      32      49 .] 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.17
                zinc_ribbon_13  2 CpKCgntea 10
                                  Cp+Cg   +
  gi|91774202|ref|YP_566894.1| 21 CPRCGDGVY 29
                                  999998766 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00042
                zinc_ribbon_13 36 vsCknCgYtel 46
                                   +C +CgYte+
  gi|91774202|ref|YP_566894.1| 37 LTCGKCGYTEF 47
                                  58********8 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00043      0.38      22      31 ..      17      26 ..       7      29 .. 0.85
   2 ?    9.9   4.9   0.00087      0.78       1      35 [.      14      48 ..      14      49 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                  NOB1_Zn_bind 22 tkkFCpkCGn 31
                                   ++FCp+CG 
  gi|91774202|ref|YP_566894.1| 17 LRQFCPRCGD 26
                                  69*******6 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00087
                  NOB1_Zn_bind  1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnktLk 35
                                  i+r++++  rC   + +  ++++  C kCG    k
  gi|91774202|ref|YP_566894.1| 14 IERLRQFCPRCGDGVYLADHKDRLTCGKCGYTEFK 48
                                  78999999999999999999999999999987766 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.4   0.00019      0.17       2      27 ..      20      44 ..      19      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                  EETTTTCEECHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                   CP Cg   ++ D++   l+C++CG+
  gi|91774202|ref|YP_566894.1| 20 FCPRCGDGVYLADHK-DRLTCGKCGY 44
                                  6*****944589977.567******7 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0022         2       3      12 ..      19      28 ..      18      35 .. 0.78
   2 ?    2.7   0.6      0.11        95       2       9 ..      36      43 ..      35      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                        zf_UBZ  3 ylCerCgkei 12
                                  ++C+rCg  +
  gi|91774202|ref|YP_566894.1| 19 QFCPRCGDGV 28
                                  69****9766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                        zf_UBZ  2 tylCerCg 9 
                                    +C +Cg
  gi|91774202|ref|YP_566894.1| 36 RLTCGKCG 43
                                  579****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 383.12
//
Query:       gi|91774203|ref|YP_566895.1|  [L=130]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-24   83.9   0.1    9.7e-24   83.7   0.1    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.1   5.4e-28   9.7e-24       1     111 [.       6     116 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 5.4e-28
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEEEESS CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpg.mdGlellkeireedpelpviiltah 80 
                                   +liv+D+++v+ +++++l++ gy +   a++g+ea+ +++   +dl+l+Di++ g mdG+e++++ir++  e+pv++lta+
  gi|91774203|ref|YP_566895.1|   6 ILIVEDEKIVALGIKKMLKNLGYLVPSIASSGEEAISKAEITFPDLVLMDIMLKGdMDGVEAADQIRKRF-EVPVVFLTAY 85 
                                   8**********************77779**************************99*************9.********** PP

                                   TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                   s+e+ +++a + + ++++ Kpf+++ L++ +
  gi|91774203|ref|YP_566895.1|  86 SDEKILERAKRTNPYGYIIKPFEENSLHATI 116
                                   ***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 959.29
//
Query:       gi|91774204|ref|YP_566896.1|  [L=834]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  102.0   1.7    1.3e-29  102.0   1.7    2.3  2  HisKA_2          Histidine kinase
    3.4e-24   86.0   4.2    1.3e-23   84.1   4.2    2.0  1  dCache_1         Cache domain
    2.8e-17   62.8   0.0    6.4e-17   61.6   0.0    1.7  1  PAS_3            PAS fold
    2.2e-10   41.0   1.7    4.2e-10   40.1   0.5    2.2  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    5.9e-06   26.6   0.1    0.00028   21.2   0.0    2.9  3  HAMP             HAMP domain
    1.6e-05   24.9   0.0      7e-05   22.8   0.0    2.1  2  PAS              PAS fold
    0.00034   20.0   0.1    0.00087   18.7   0.1    1.7  1  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
    0.00079   20.1   0.0     0.0023   18.6   0.0    1.8  1  HWE_HK           HWE histidine kinase
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.028   14.4   0.0    1.5  1  HATPase_c_2      Histidine kinase-like ATPase domain
      0.032   14.5   0.2        2.2    8.5   0.0    3.4  3  PAS_9            PAS domain
      0.034   14.1   0.1        0.1   12.5   0.1    1.8  1  DUF1869          Domain of unknown function (DUF1869)
       0.11   12.3   0.3        0.3   10.9   0.3    1.6  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       5.2   7.8e+03       7      15 ..     309     317 ..     308     319 .. 0.85
   2 !  102.0   1.7     9e-33   1.3e-29       1      76 []     637     712 ..     637     712 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.2
                       HisKA_2   7 kNnLqviss 15 
                                   +NnL vis+
  gi|91774204|ref|YP_566896.1| 309 RNNLIVIST 317
                                   7******97 PP

  == domain 2  score: 102.0 bits;  conditional E-value: 9e-33
                       HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                   EihHR+kNnLqvis+lL l+++k+kde+v++a+++sq+Rv+++al+he+Ly+sed+e++df +y ++L++ l +sy
  gi|91774204|ref|YP_566896.1| 637 EIHHRIKNNLQVISTLLYLESDKFKDEKVRDAFKNSQDRVRTMALVHEKLYQSEDMESIDFVDYTKNLINYLSQSY 712
                                   9***********************************************************************9997 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   4.2   8.9e-27   1.3e-23       8     247 ..      44     295 ..      33     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 8.9e-27
                      dCache_1   8 eeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvd....... 81 
                                   +eq+ + a++ an ++++++    + +t      +++++++++    ++r++++++lk+++ +np++ g y+ +       
  gi|91774204|ref|YP_566896.1|  44 YEQSIEKARGFANYFNSDMRANHVIGQT------IANSMNAYS---TSDRDEVNEILKEVAVRNPNLLGTYVCYepnafdg 115
                                   3334444444444444444444444444......555566555...599******************99999998888777 PP

                      dCache_1  82 ............adGqviassdpssppnleg.............tddpadrdwykealaggggkpvisdpyvdqtggkpvi 137
                                               + G++i                          + ++ ++d+yk ++ ++    +i dpy++ + g+ ++
  gi|91774204|ref|YP_566896.1| 116 ndqlfinaeghdETGRFI------------PywnringdlaidpLLNYEESDYYKLPKTTK--TDHIIDPYFY-E-GVFIV 180
                                   666666666666666665............033333345588889****************..78899***94.6.9**** PP

                      dCache_1 138 tiavpiyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd.kdllgknlrdelkaq.....ealek 212
                                   ++++pi++ + +f+G+ +ad++l++l++ +s++k+ +tgy+f+ +++G++i+ p+ kd++g   +++l+++       + +
  gi|91774204|ref|YP_566896.1| 181 SYVTPIFK-NDEFVGMGGADVSLTYLDEVVSEVKIFDTGYAFMTGNTGILISQPEqKDWIG---YKTLYDFdipeiSNMAD 257
                                   *******9.69*******************************************9999987...46666667766877777 PP

                      dCache_1 213 alakiesgvssvklng..eeylva.yapip.tglgWylv 247
                                   ++++  sg  +++     ++  v  y pi+ +++  +lv
  gi|91774204|ref|YP_566896.1| 258 EIKNGSSGYIDTIDPTtgKTV-VMfYEPIKtGNFSFILV 295
                                   777777777777644432566.556*****665666665 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   4.3e-20   6.4e-17       3      89 .]     528     614 ..     526     614 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4.3e-20
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +vs ++++  Gys e++ + + ++ dlv+p D++rv+e+lq+  ++g+ ++++eyRi++k G++ w ++r+++ rd +g++
  gi|91774204|ref|YP_566896.1| 528 FVSSNISQF-GYSLEDFSAGKVTYSDLVYPKDLPRVEEQLQKKCDEGAnEFTIEYRILTKYGQILWADERTFIRRDIDGNV 607
                                   667777666.*********************************************************************** PP

                         PAS_3  83 vrvigva 89 
                                   ++++g++
  gi|91774204|ref|YP_566896.1| 608 DHLQGII 614
                                   *****86 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 ?   -2.9   0.0       6.3   9.4e+03      28      54 ..     450     473 ..     430     485 .. 0.66
   2 !   40.1   0.5   2.8e-13   4.2e-10       6     111 ..     738     832 ..     734     833 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.3
                                   EEEEEEEETEEEEEEEESSSSSTTHHH CS
                     HATPase_c  28 eveikaseddlvisveDnGiGipkedl 54 
                                   ++++k   ++  +++  +Gi i+++ l
  gi|91774204|ref|YP_566896.1| 450 KINLK---GEGDFRILTDGIEITRQSL 473
                                   44444...4788888889999998876 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 2.8e-13
                                   HHHHHHHHHHHHHHH......HSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHH CS
                     HATPase_c   6 LrqiisnlvdNavkf......atkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGl 78 
                                   L  ii++lv+N++k+      ++++g i+v i+  +  d+++++v+DnG Gi++ d++     f +          + lGl
  gi|91774204|ref|YP_566896.1| 738 LGIIINELVSNSLKYafgdkdENEKGIISVDIE--NfgDEFMLTVSDNGNGISE-DID-----FRD---------TESLGL 801
                                   6679***********888765557778888888..4459**************8.667.....777.........788*** PP

                                   HHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                     HATPase_c  79 sivkklvelmgGeiwvesepgrGttftftlple 111
                                    +v +lve++gG+i+++ +   Gt+f++++ +e
  gi|91774204|ref|YP_566896.1| 802 QLVTNLVEQIGGDIELKRDN--GTKFIIQFTEE 832
                                   ****************6666..****9987665 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.2     3e+02       1      28 [.     329     360 ..     329     369 .. 0.79
   2 !   21.2   0.0   1.9e-07   0.00028       6      52 ..     383     429 ..     380     430 .. 0.96
   3 ?   -2.9   0.0       6.4   9.6e+03      21      51 ..     443     473 ..     438     474 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.2
                                   HHHHTTHHHHHHHHHHHHHHTT....TBTSST CS
                          HAMP   1 llarrilrPLrrLaraarriaa....Gdldtr 28 
                                   l+a+ ++rP++ +++  + +++    G+l++r
  gi|91774204|ref|YP_566896.1| 329 LIAGFVTRPINDIVADFKDLSDaavvGQLHAR 360
                                   68999********9988888876777777777 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.9e-07
                                   THHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                          HAMP   6 ilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                    +rP+ + +r+++++a+G+l tr p++ + E+  ++ +++ ++++L+
  gi|91774204|ref|YP_566896.1| 383 FTRPMTETMRVTNELAKGELQTRMPTDLKGEFKHIGDTLDSFATKLN 429
                                   68******************************************997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.4
                                   TTTBTSSTCCTTSSSHHHHHHHHHHHHHHHH CS
                          HAMP  21 aaGdldtrlpvsgrDEiGeLarafNaMldrL 51 
                                   ++ d+++ +  +g   ++ L   ++  +++L
  gi|91774204|ref|YP_566896.1| 443 QNEDFTHKINLKGEGDFRILTDGIEITRQSL 473
                                   5679999999999998888888887777766 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.5   3.8e+03      39      66 ..      65      95 ..      62     108 .. 0.70
   2 !   22.8   0.0   4.7e-08     7e-05       1     110 [.     502     614 ..     502     617 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                                  HHCTTSBGGGGBSTTHHH...HHHHHHHHHH CS
                           PAS 39 eevlgkslldliheedda...elaelleqll 66
                                  + v+g+++  +++  + +   e++e+l++++
  gi|91774204|ref|YP_566896.1| 65 NHVIGQTIANSMNAYSTSdrdEVNEILKEVA 95
                                  6788888887776665555547777777665 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 4.7e-08
                                   HHHHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEE CS
                           PAS   1 edlraileslpdpifvvD.edgrilyvNaaaeellGlsr.eevlgkslldliheedda.elaelleqlleqgeesrageis 78 
                                   e++++++es+p+ +f ++ e+g+ +++ ++  +++G+s  +   gk  + +++ ++d   + e+l++ + +g ++ + e +
  gi|91774204|ref|YP_566896.1| 502 EEMERVIESSPVVVFKWRaEKGWPIEFVSSNISQFGYSLeDFSAGKVTYSDLVYPKDLpRVEEQLQKKCDEGANEFTIEYR 582
                                   689************************************666789*9999999999999********************** PP

                                   EECTTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
                           PAS  79 fklrdgrpihlevraspvrdaggeilgflgvl 110
                                   + ++ g + +++ r+  +rd++g++ ++ g++
  gi|91774204|ref|YP_566896.1| 583 ILTKYGQILWADERTFIRRDIDGNVDHLQGII 614
                                   ************************99888775 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   5.8e-07   0.00087     155     291 ..     181     310 ..     170     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.8e-07
               Cache_3-Cache_2 155 TaYePikdadgkViGilyVgvdqsealkslrkelkklkvGktGylyvldgkgdkkgkliihptlk....gknvldlkdadg 231
                                   ++ +Pi  ++ + +G+   g d   +l  l +  +++k+ +tGy+++++++    g li  p++k     k+++d +    
  gi|91774204|ref|YP_566896.1| 181 SYVTPIF-KNDEFVGMG--GADV--SLTYLDEVVSEVKIFDTGYAFMTGNT----GILISQPEQKdwigYKTLYDFDI--- 249
                                   5566666.666667777..6666..677799********************....**********8885566666633... PP

               Cache_3-Cache_2 232 esvvkkllkk.ksgsleyelk..kdekgreklavftyfepwdWvivasvyedefqeevnrvrn 291
                                    + ++++ ++ k+gs  y     + ++g++ +++++  +  +  ++  v++de++++v+++rn
  gi|91774204|ref|YP_566896.1| 250 -PEISNMADEiKNGSSGYI-DtiDPTTGKTVVMFYEPIKTGNFSFILVVPKDEMLAGVTELRN 310
                                   .345556555544444442.22489999999*****************************998 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0023       1      53 [.     637     691 ..     637     712 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHHHHHHHHHHHHHSSS..XS-HHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                        HWE_HK   1 ElnHRvKNlLavvqsiarqtlrs..aesleefaeklsgRLqALsaahdllsreew 53 
                                   E++HR+KN L v++ +    + +   e+++++ ++ ++R+++++ +h+ l ++e 
  gi|91774204|ref|YP_566896.1| 637 EIHHRIKNNLQVISTLLYLESDKfkDEKVRDAFKNSQDRVRTMALVHEKLYQSED 691
                                   89**************9887664114556778888899*********99888764 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.9e-05     0.028      24     120 ..     730     824 ..     718     829 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                   HATPase_c_2  24 lseelldeirlaveEactNavehayleape...gpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrG 101
                                   l+ +++  + + ++E+++N  ++a  ++ e   g ++v +e  ++++ ++v+D+G+g               + ++++ +G
  gi|91774204|ref|YP_566896.1| 730 LNMDTAVPLGIIINELVSNSLKYAFGDKDEnekGIISVDIENFGDEFMLTVSDNGNGISEDI----------DFRDTESLG 800
                                   566666678899**********98665543334999*********************77653..........667778899 PP

                   HATPase_c_2 102 lalikglvDev..ey...dgegnv 120
                                   l l+++lv+++  ++   +++g++
  gi|91774204|ref|YP_566896.1| 801 LQLVTNLVEQIggDIelkRDNGTK 824
                                   999999998876644446666665 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.96   1.4e+03      20      69 ..      54     108 ..      52     115 .. 0.63
   2 ?    8.5   0.0    0.0015       2.2      10     102 ..     522     617 ..     512     619 .. 0.74
   3 ?    1.0   0.0      0.33     5e+02      50      80 ..     801     829 ..     743     830 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.96
                         PAS_9  20 alrllG..yspeevlgksitdlf.vtdpeanerlraaleqgrk..kerevevvli 69 
                                   +++ +   + ++ v+g+ i + + + + +++++++++l++     +   +++v++
  gi|91774204|ref|YP_566896.1|  54 FANYFNsdMRANHVIGQTIANSMnAYSTSDRDEVNEILKEVAVrnPNLLGTYVCY 108
                                   6777774455889******999985555555555555555543333555555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                         PAS_9  10 dg.rilyaNeaalrllGyspeevlgks..itdlf..vtdpeanerlraaleqgrk...kerevevvlirkngetfwvllta 82 
                                   +g +i++++    ++ Gys e++   +  ++dl+  ++ p+ +e l++      +   +e++ e+ + +k g+ +w++ + 
  gi|91774204|ref|YP_566896.1| 522 KGwPIEFVSSNISQF-GYSLEDFSAGKvtYSDLVypKDLPRVEEQLQKKC----DegaNEFTIEYRILTKYGQILWADERT 597
                                   563444777777777.9998888777767889994444444444555555....4555********************777 PP

                         PAS_9  83 spvkdddgelvgiivilrDi 102
                                   +  +d dg++ ++ +i+++i
  gi|91774204|ref|YP_566896.1| 598 FIRRDIDGNVDHLQGIIVNI 617
                                   7777789***9999999998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.33
                         PAS_9  50 lraaleqgrk..kerevevvlirkngetfwvll 80 
                                   l+ +     +  ++  ++++l r+ng++f +++
  gi|91774204|ref|YP_566896.1| 801 LQLVT----NlvEQIGGDIELKRDNGTKFIIQF 829
                                   22233....255599999**********99876 PP

>> DUF1869  Domain of unknown function (DUF1869)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.8e-05       0.1       3      28 ..     774     799 ..     773     809 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                                   --EEEEEEETTT--EEEEEE--SCGG CS
                       DUF1869   3 aelllTvTNknNGVSVDkefeslaeL 28 
                                   +e++lTv  + NG+S D +f   ++L
  gi|91774204|ref|YP_566896.1| 774 DEFMLTVSDNGNGISEDIDFRDTESL 799
                                   69*****************9887766 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 ?   10.9   0.3    0.0002       0.3       7      52 ..     742     795 ..     739     807 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                   HATPase_c_3   7 laelvdNsld...Adaen.......vkievnknrgktgeivieDdGkGmsee.elkn 52 
                                   + elv Nsl    +d  +       +++ +++  g++ ++++ D+G+G+se+ ++++
  gi|91774204|ref|YP_566896.1| 742 INELVSNSLKyafGD--KdenekgiISVDIEN-FGDEFMLTVSDNGNGISEDiDFRD 795
                                   569999999864433..244788887777777.5889**************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1355  (0.0755759); expected 358.6 (0.02)
Passed bias filter:                      766  (0.0427241); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.76u 0.25s 00:00:01.01 Elapsed: 00:00:00.43
# Mc/sec: 5872.23
//
Query:       gi|91774205|ref|YP_566897.1|  [L=262]
Description: hypothetical protein Mbur_2287 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-24   84.0   0.6    5.7e-24   84.0   0.6    1.9  2  DUF1724   Domain of unknown function (DUF1724)
  ------ inclusion threshold ------
      0.015   15.2   0.2      0.032   14.1   0.2    1.6  1  HTH_5     Bacterial regulatory protein, arsR family
      0.033   14.0   0.2        0.5   10.2   0.3    2.5  2  HxlR      HxlR-like helix-turn-helix
       0.16   12.1   2.7        5.9    7.1   0.1    2.8  3  Pro_sub2  Prodomain subtilisin 2


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 ?   -2.2   0.1       1.1   4.8e+03       6      22 ..     162     177 ..     159     177 .. 0.80
   2 !   84.0   0.6   1.3e-27   5.7e-24       2      61 ..     198     257 ..     197     258 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                       DUF1724   6 ydeeikplsltvtDkfl 22 
                                   +++ei  ++l+ tD+++
  gi|91774205|ref|YP_566897.1| 162 LSKEI-DFTLIFTDTVF 177
                                   57888.89999999875 PP

  == domain 2  score: 84.0 bits;  conditional E-value: 1.3e-27
                       DUF1724   2 klyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSe 61 
                                   +lyv+d+ ik+ ++ vt++f++l++f+k+g+ydh++++sfdesA kWGeeLF +Y + S+
  gi|91774205|ref|YP_566897.1| 198 DLYVCDDSIKLTTISVTERFTYLCFFNKEGMYDHRKIMSFDESASKWGEELFTHYQNLSR 257
                                   69*******************************************************998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   7.2e-06     0.032       2      45 ..      13      56 ..      12      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-06
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  ++R  +L lLaeg++ + ++   l+++  +   + k+L+e++++
  gi|91774205|ref|YP_566897.1| 13 EKRKNLLLLLAEGSRNIDQIKTSLNVTSKAMMPQIKILKEQDMI 56
                                  89**************************************9876 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00011       0.5      10      71 ..      18      72 ..      11      98 .. 0.75
   2 ?    0.7   0.0       0.1   4.7e+02      54      82 ..      99     129 ..      79     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                                  HHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGG CS
                          HxlR 10 ilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrs 71
                                  +l  l +g++   ++k+ l +++ k +  +++ L+++ +i +++++      +Y+l++ Gr 
  gi|91774205|ref|YP_566897.1| 18 LLLLLAEGSRNIDQIKTSL-NVTSKAMMPQIKILKEQDMIVQNELD------DYELSDVGRI 72
                                  4556999************.9*************877776554443......3666666654 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.1
                                   ESSSS-EEEEEE-TCGGG..GHHHHHHHHHH CS
                          HxlR  54 ypevPpkveYsltekGrs..lepvlqelkkw 82 
                                   ++++P+   Y++ e G+   +ep l+++ ++
  gi|91774205|ref|YP_566897.1|  99 LSSIPESLSYRIGELGQCmlIEPDLNHMFDL 129
                                   5788999999999999852256777777665 PP

>> Pro_sub2  Prodomain subtilisin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0013       5.9      66      86 ..      44      64 ..      34      65 .. 0.92
   2 ?    4.4   0.1    0.0096        43      49      78 ..     162     191 ..     126     201 .. 0.79
   3 ?   -3.2   0.0       2.2   9.8e+03      51      59 ..     215     223 ..     206     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0013
                      Pro_sub2 66 mnnlkllkeallilhkelkey 86
                                  m  +k+lke  +i+++el++y
  gi|91774205|ref|YP_566897.1| 44 MPQIKILKEQDMIVQNELDDY 64
                                  7899***************99 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0096
                      Pro_sub2  49 isspinflcffiptifdmnnlkllkealli 78 
                                   +s  i+f  +f  t+f+    + lke  li
  gi|91774205|ref|YP_566897.1| 162 LSKEIDFTLIFTDTVFERLKTDCLKELELI 191
                                   6889***************99*99997766 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.2
                      Pro_sub2  51 spinflcff 59 
                                       +lcff
  gi|91774205|ref|YP_566897.1| 215 ERFTYLCFF 223
                                   556789999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1926.72
//
Query:       gi|91774206|ref|YP_566898.1|  [L=168]
Description: dimethylamine corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   0.2    2.9e-27   95.1   0.2    1.1  1  B12-binding    B12 binding domain
    4.7e-10   39.8   1.4    2.3e-09   37.6   0.4    2.3  2  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.2   3.2e-31   2.9e-27       2     120 ..      48     160 ..      47     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 3.2e-31
                   B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrirp 80 
                                    ++ +tv+gd+h++G+ ++  +l++agfeV+++g +v++++++++i+++++d+vglSal+t++l++ ke++el  + + r+
  gi|91774206|ref|YP_566898.1|  48 VIVNGTVEGDVHDIGKSIVSTMLQAAGFEVHDIGRDVPVQNFIDKIKETNADMVGLSALMTTTLPGQKEVIELlkENGLRD 128
                                   57899********************************************************************8888999* PP

                   B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   +vkv+vGGa+++  ++    +  g+d+    ++e+a ea+
  gi|91774206|ref|YP_566898.1| 129 KVKVMVGGAPATDSWAK---K-CGADC----YAENASEAV 160
                                   *********98888888...6.99777....888888775 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.4   2.6e-13   2.3e-09      43      74 ..       1      32 [.       1      33 [. 0.97
   2 ?    0.9   0.0     0.071   6.3e+02      33      52 ..     104     123 ..      50     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 2.6e-13
                 B12-binding_2 43 mkeVGdlfgagelflpqvllsaevmkkavahL 74
                                  m+eVG lf++g+lflp+v+++a++m ++v+ L
  gi|91774206|ref|YP_566898.1|  1 MNEVGVLFERGKLFLPHVMMAADAMSAGVELL 32
                                  9****************************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.071
                 B12-binding_2  33 dvlndvllpamkeVGdlfga 52 
                                    +l +  lp+ keV +l ++
  gi|91774206|ref|YP_566898.1| 104 SALMTTTLPGQKEVIELLKE 123
                                   45667778999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.63
# Mc/sec: 810.02
//
Query:       gi|91774207|ref|YP_566899.1|  [L=500]
Description: amino acid transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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-73  247.6  47.4    2.6e-73  247.3  47.4    1.0  1  AA_permease_2  Amino acid permease
    3.8e-10   39.0  39.4    6.3e-10   38.2  39.4    1.4  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.3  47.4   2.8e-77   2.6e-73       1     424 [.      31     467 ..      31     470 .. 0.87

  Alignments for each domain:
  == domain 1  score: 247.3 bits;  conditional E-value: 2.8e-77
                 AA_permease_2   1 lsllsafalvigsv....igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf..... 72 
                                   +++ + +a++ig++      s ++++   + +  a+i+w++  v+ g +++ l+y El++++p+  G+ ++++++f     
  gi|91774207|ref|YP_566899.1|  31 IDWKQGLAIAIGVPllilP-SIGYFA--SYLWSFAIIVWGLS-VFQG-FMQNLAYGELATTFPNASGLPGFAQNVFkspdh 106
                                   799**********965322.445555..57899999988876.7778.79*********99***************99999 PP

                 AA_permease_2  73 ......gkkvaflsawfnwfayvpvlasilsvaasyllnalgpdlqgn..tw.ltyliaiaililvalinirgikesakiq 144
                                         gk+++ +saw++wfa+ pvl +i++++++++l+ l+p l g+  ++ l+++ +++i+ +++l+n+rg + +a + 
  gi|91774207|ref|YP_566899.1| 107 kgkydkGKLIGGFSAWSYWFAWNPVL-AIFAILVGFYLHSLFPVLAGTfsQYqLSMIAGVVIYGGLILVNYRGLSSGAAVG 186
                                   9999999*******************.66777777777778896555555442778888********************** PP

                 AA_permease_2 145 nilgilkillpliiliilglitvdgggfsslstetdtffpngwpgv.......llgllivlwsfdGfesaanvseevkk.. 216
                                    il+ +++ +p++i+ +++++t+d+ +++    +t+t++p+ w +        l+ +++++ws +++e+aa +  e k+  
  gi|91774207|ref|YP_566899.1| 187 YILAAFSL-IPMAIITLAPYFTGDFVMAN----ITSTWLPTDWAWDlshililLGIFAMAQWSACAWETAAIYGPEYKNpg 262
                                   ********.8******************9....8*******777633366665667888*****************99986 PP

                 AA_permease_2 217 kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssr 297
                                    dvpka+f++++i+lv y+lv+++++gv+++d+ian ++ ++++ ++++a+ g+v+++i++++++ +++++i ta++gssr
  gi|91774207|ref|YP_566899.1| 263 SDVPKALFSCGAICLVAYILVQMTVTGVLGIDGIAN-AP-IDPMLPVAQAALGDVGSTIAIVMLIAAMVLIIQTAYLGSSR 341
                                   79*********************************8.66.789************************************** PP

                 AA_permease_2 298 vlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrph 378
                                    ++++a++g lP++fak+n++g+pi a++++ i++lil  ++++++    +++l++s++g+++ +++ ++++++ +   ph
  gi|91774207|ref|YP_566899.1| 342 AMHSMATEGNLPKVFAKTNAHGTPILAMVVIGIFNLIL--ISMGTP----TAILAASAIGYVCANGISLFAYVKAKSS-PH 415
                                   ***********************************765..588887....*******************999988777.66 PP

                 AA_permease_2 379 l...kr....pgki.lvaiigalfllfllvalffppkgpatqssliytiiltva 424
                                   l    r    p+ +  va+++ lf+l l+ ++ +++++++   s++ t++++++
  gi|91774207|ref|YP_566899.1| 416 LaglDRpfkaPAGWkNVALMFGLFNLPLCLVGVIYLNTIEG--SWFSTVVGICV 467
                                   6566554444555779*******************988886..55555666554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2  39.4     7e-14   6.3e-10      31     389 ..      62     409 ..      35     486 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 7e-14
                   AA_permease  31 allayllagvviflvmlslgeiatngpksggfytyasrfl...........gpelGfviGlnylfswitvlaleltaasil 100
                                   a++++ l+++  f+  l+ ge+at +p+++g   +a+++            g+  G++ +++y+f w  vla+  + ++ +
  gi|91774207|ref|YP_566899.1|  62 AIIVWGLSVFQGFMQNLAYGELATTFPNASGLPGFAQNVFkspdhkgkydkGKLIGGFSAWSYWFAWNPVLAIFAILVGFY 142
                                   589999999999999************9999999999987333333333335679************88888877777777 PP

                   AA_permease 101 iqfwelvtdlpkawvt.......gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkgagfrf 174
                                   ++ +  ++ l  ++         g+v+++ l+++n+ g+   +++ +ila + +i ++   i++  + + g+   +     
  gi|91774207|ref|YP_566899.1| 143 LHSL--FPVLAGTFSQyqlsmiaGVVIYGGLILVNYRGLSSGAAVGYILAAFSLIPMA---IITLAPYFTGDFVMA----- 213
                                   7776..55555333335566667*********************99999998887765...556566666664444..... PP

                   AA_permease 175 lgdngsifknnlppgfa.keeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllli 254
                                      n +  + +lp ++a + +   ++  +++f+ +  ++   e  ai + E k+P  ++Pka  +   + +++Y+l+ +++
  gi|91774207|ref|YP_566899.1| 214 ---NIT--STWLPTDWAwDLSH--ILILLGIFAMAQWSACAWETAAIYGPEYKNPGSDVPKALFSCGAICLVAYILVQMTV 287
                                   ...444..77899999988888..9999999999999999***********************************987777 PP

                   AA_permease 255 gllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssanssly.sasRvlyslakdglaPkvlkkvskr 334
                                   + +++   +g+ n+ +++   + +++  +g    +++i++v l+aa+  ++   y  +sR+++s+a +g +Pkv++k + +
  gi|91774207|ref|YP_566899.1| 288 TGVLGI--DGIANAPIDP--MLPVAQAALGDV--GSTIAIVMLIAAMVLIIQTAYlGSSRAMHSMATEGNLPKVFAKTNAH 362
                                   766665..5688877988..666666666665..5566666666666555544441789********************** PP

                   AA_permease 335 gvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylr 389
                                   g P+ a+++  i+ l+++   s+ ++     + +la+sa+  +   ++++++y++
  gi|91774207|ref|YP_566899.1| 363 GTPILAMVVIGIFNLILI---SMGTP-----TAILAASAIGYVCANGISLFAYVK 409
                                   **********99999999...66666.....445555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2926.43
//
Query:       gi|91774208|ref|YP_566900.1|  [L=302]
Description: PAS sensor protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-16   59.0   0.1    6.7e-16   58.4   0.1    1.3  1  PAS_3     PAS fold
    6.5e-06   26.5   0.0      1e-05   25.8   0.0    1.3  1  GAF_2     GAF domain
    0.00018   21.7   0.0     0.0003   21.0   0.0    1.4  1  PAS_9     PAS domain


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   1.1e-19   6.7e-16       3      87 ..      35     119 ..      33     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.1e-19
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirdengkp 82 
                                   +vs++v  ++Gy++++++ k  ++ d++hp D+ervr+al  + ++    + +eyRi++ dG++rwv++++ +i+de+g  
  gi|91774208|ref|YP_566900.1|  35 FVSDNV-AMFGYDADDFMFKGLNYEDIIHPADLERVRKALSVYSESPDgIFVQEYRIFTSDGDVRWVREKMCIIYDEHGVM 114
                                   667777.789*******99999*******************9998777699****************************99 PP

                         PAS_3  83 vrvig 87 
                                    r+ +
  gi|91774208|ref|YP_566900.1| 115 ERLEC 119
                                   98865 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.7e-09     1e-05       4     137 ..     150     285 ..     148     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.7e-09
                                   HHHHHHHHHHHHHHSS...EEEEEEE-.TTS-EEEEEEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-GGG.-S-H CS
                         GAF_2   4 leelldlvldelvelg.aalgyillvd.ddgglrlaawgeaeeefgaaldrplgeg.lvgealrtgrpvilndlee.dpdk 80 
                                   le+ +d++l+  ++l+ + +g ++++d   ggl+l+ + +  ++f ++++  +++  +    +++g p++  ++ e  p  
  gi|91774208|ref|YP_566900.1| 150 LEDSMDALLKLTIQLDaINAGALYMLDdVTGGLVLVRYKGLSDGFLSCISY-FDHNsIQLNFAEKGFPIY-KHYSEiYPFI 228
                                   78899**********878888777755266779999999999999999944.455538889999999999.6655538888 PP

                                   HHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                         GAF_2  81 kglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                   +g  +g++gl+ ++++P+ +egr +G+l+ +++ +    e d++ L+ + +++++ i
  gi|91774208|ref|YP_566900.1| 229 SGTYLGDEGLQGTAIIPIHHEGRFMGMLFAASSSECIIPENDRDSLDVIKSLAGLMI 285
                                   8888*************************9888888899999999998888888877 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     5e-08    0.0003      11     104 .]      30     126 ..      19     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5e-08
                         PAS_9  11 g.rilyaNeaalrllGyspee..vlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltaspv 85 
                                   g +i+++++ ++ ++Gy++++  + g +++d++  +p + er+r+al   ++     + +e+ + +++g   wv+ +++ +
  gi|91774208|ref|YP_566900.1|  30 GwPIEFVSDNVA-MFGYDADDfmFKGLNYEDII--HPADLERVRKALSVYSEspdGIFVQEYRIFTSDGDVRWVREKMCII 107
                                   534558888887.99******8888999*****..9999999999999999899999************************ PP

                         PAS_9  86 kdddgelvgiivilrDite 104
                                   +d++g + ++ + ++Di++
  gi|91774208|ref|YP_566900.1| 108 YDEHGVMERLECSIIDISD 126
                                   *********99******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1929.67
//
Query:       gi|91774209|ref|YP_566901.1|  [L=134]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-18   67.4   0.2    1.3e-18   67.2   0.2    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.068   13.0   0.0      0.086   12.7   0.0    1.1  1  SIS           SIS 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 !   67.2   0.2   1.4e-22   1.3e-18       1     110 [.       6     115 ..       6     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.4e-22
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSS.SEHHHHHHHHHHCTTTSEEEEEESS CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpg.mdGlellkeireedpelpviiltah 80 
                                   +l+v+D+ +v + ++  l + gy +   a++g++a++++++ ++ l+l+Di++ g +dG+e++ +ir+ + ++p++++ta 
  gi|91774209|ref|YP_566901.1|   6 ILVVEDELIVGMMIKLKLAKMGYCVSCMASTGADAVAMVEKVRPELVLMDIRLKGsLDGVEAAMMIRKIS-NIPIVFITAD 85 
                                   8**********************7777****************************99***********99.********** PP

                                   TSHHHHHHHHHCTESEEEESSG-HHHHHHH CS
                  Response_reg  81 seeedavealkagaddflsKpfdpeeLlka 110
                                   s+ e++++a  a  ++fl Kpf  eeL + 
  gi|91774209|ref|YP_566901.1|  86 SSLETRERAELACPQGFLLKPFMDEELGSL 115
                                   ***********************9999665 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.6e-06     0.086      19      97 ..      15      91 ..      11     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
                                  HHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHH CS
                           SIS 19 iakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplare 97
                                  +++ ++lkl+++g++v+ + ++++    ++  ++++ +++ i   g    + aa    k  + +i+ IT  ++s+l ++
  gi|91774209|ref|YP_566901.1| 15 VGMMIKLKLAKMGYCVSCMASTGADAVAMVEKVRPELVLMDIRLKGSLDGVEAAMMIRKISNIPIVFIT--ADSSLETR 91
                                  8999********************88888*****************9999999999*************..56666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 933.54
//
Query:       gi|91774210|ref|YP_566902.1|  [L=92]
Description: hypothetical protein Mbur_2295 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   0.6        0.1   12.6   0.6    2.4  3  DUF2798   Protein of unknown function (DUF2798)


Domain annotation for each model (and alignments):
>> DUF2798  Protein of unknown function (DUF2798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   5.7e-06       0.1      26      39 ..      13      26 ..       1      27 [. 0.85
   2 ?   -0.4   0.2      0.07   1.3e+03       6      14 ..      47      55 ..      42      62 .. 0.49
   3 ?   -1.7   0.1      0.17   3.1e+03      36      44 ..      75      83 ..      70      90 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-06
                       DUF2798 26 flsaWlkawllAwp 39
                                  ++++Wl++w++++p
  gi|91774210|ref|YP_566902.1| 13 YIQQWLHSWSISMP 26
                                  89**********98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.07
                       DUF2798  6 lmslimSgi 14
                                    ++i ++i
  gi|91774210|ref|YP_566902.1| 47 AFAGIATFI 55
                                  233333333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.17
                       DUF2798 36 lAwpvAfpi 44
                                  +++ ++f +
  gi|91774210|ref|YP_566902.1| 75 IGFFAVFAL 83
                                  333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 615.63
//
Query:       gi|91774211|ref|YP_566903.1|  [L=81]
Description: AbrB family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00044   20.1   0.1    0.00084   19.2   0.0    1.5  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0042   17.1   0.0     0.0052   16.7   0.0    1.2  1  MraZ            MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.3e-08   0.00084       2      44 ..      10      51 ..       9      53 .. 0.93
   2 ?   -3.2   0.0      0.96   8.6e+03      35      43 ..      67      75 ..      65      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.3e-08
                                  EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHS CS
                MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrplksl 44
                                  +++++g+++iP  +r ++ ++ G +v ++ ++++i +rpl++ 
  gi|91774211|ref|YP_566903.1| 10 TITSKGQIVIPSSMR-KGSFDIGHRVAVIAKNNHIEIRPLSEI 51
                                  789************.7**********************9875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.96
                                  CCCCCCCHH CS
                MazE_antitoxin 35 kiilrplks 43
                                  k++++p ++
  gi|91774211|ref|YP_566903.1| 67 KLWDTPEED 75
                                  688888665 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.8e-07    0.0052      12      57 ..      13      60 ..       7      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.8e-07
                                  TTSEEE--CHHHHH.TTSCSEEEEEECCSEEEEEEHHHHHHHHHCH.H CS
                          MraZ 12 akGRlllPaklree.aklekevvviGvsncLeiwpraeWekyeeel.a 57
                                  +kG + +P++ r+  +     v vi++ n++ei+p+ e e++ e++ a
  gi|91774211|ref|YP_566903.1| 13 SKGQIVIPSSMRKGsFDIGHRVAVIAKNNHIEIRPLSEIEDQMETAiA 60
                                  79**********953788899*********************999632 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 515.61
//
Query:       gi|91774212|ref|YP_566904.1|  [L=493]
Description: transposase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-67  227.7   0.4    6.3e-67  226.0   0.0    1.8  2  DDE_Tnp_IS66     Transposase IS66 family
      9e-11   42.0   3.8    2.7e-10   40.5   3.8    1.9  1  zf-IS66          zinc-finger binding domain of transposase IS
    5.2e-05   23.8   0.7    0.00014   22.4   0.7    1.7  1  SlyX             SlyX
    0.00011   22.5   0.3       0.17   12.1   0.2    2.8  3  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.067   13.8   1.4        0.3   11.7   1.4    2.2  1  BST2             Bone marrow stromal antigen 2
       0.14   12.2   2.7       0.83    9.7   0.8    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.7   2.6       0.55   10.7   0.3    2.5  2  DUF16            Protein of unknown function DUF16
       0.36   11.2   6.9       0.52   10.7   4.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
          1   10.1   8.9        7.1    7.4   1.5    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        2.1    9.0   6.0       0.65   10.7   1.1    2.7  2  PLATZ            PLATZ transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.44   7.9e+02     175     225 ..      21      69 ..       5      84 .. 0.63
   2 !  226.0   0.0   3.5e-70   6.3e-67       2     280 ..     179     455 ..     178     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                  DDE_Tnp_IS66 175 arigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpks 225
                                   + + +ly+i +e ++    e +a+r +e ++ +++le++l++++++ ++ +
  gi|91774212|ref|YP_566904.1|  21 TLVTTLYDIIAEQQR--IIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69 
                                   446777777666532..3466666666666666666666666665554444 PP

  == domain 2  score: 226.0 bits;  conditional E-value: 3.5e-70
                  DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlk 81 
                                   +++g +l + +++l+ ++ lP++R +e+la++ G+e+s++tla+++k+++e+le + +++k+ l +s+vi++DET++r   
  gi|91774212|ref|YP_566904.1| 179 TQYGLRLASLAVYLHDYQLLPYERSCELLADVcGCEISPATLARAEKTCFEKLEDFEQQIKNFLIESPVINCDETGMR--- 256
                                   57999*************************************************************************... PP

                  DDE_Tnp_IS66  82 pgrgkgkksylWvyvtdkrkpavlfeyspsRggevaeal..LagfkGvlvsDgyagYnklaeeqvthalCwaHlrRkfvda 160
                                       +gk+++l+v++t+k   +++++ +++Rg+++++a+  L +f+G++v+D +++Y k+   +++h +C aHl+R+++++
  gi|91774212|ref|YP_566904.1| 257 ---IEGKRQWLHVASTNK---MTCYYPHQKRGSDAMNAMgiLPNFNGTVVHDFWKSYYKY---DCDHSICNAHLLRELTSV 328
                                   ...99***********99...***************99955666***************9...7***************** PP

                  DDE_Tnp_IS66 161 eeakkksqaaaealar.igklyaierear..ea..eaeerlalrqeesrpllaeleawleeql....kkvlpksklgkair 232
                                   +e+++  q +++a++  + ++++  +++r  +   ++e+ ++ +  + + ++  +e++ + q     ++ +++++++++++
  gi|91774212|ref|YP_566904.1| 329 SENDN--QLWSKAMNIlLIDVKKSVDQIRgmSGcmKPERIKEFEDWYGQIIHIGIEENPQLQAkskkRGRTKQTTAKNLLD 407
                                   **976..*********************964338888********************998554567799************ PP

                  DDE_Tnp_IS66 233 yllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   ++   ++++lrf++d +vp++NN+aER++R++++++K+s++++s++Ga
  gi|91774212|ref|YP_566904.1| 408 RFIGYKNDILRFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGA 455
                                   ***********************************************9 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 !   40.5   3.8   1.5e-13   2.7e-10       3      46 .]     119     164 ..     118     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                       zf-IS66   3 tCpcCGg.l.lkpigedrvreeldipPakfrViehirpkyaCpcCe 46 
                                   +C++C   l   ++++++ r+++dipP+k+ V+eh+ + ++Cp+C+
  gi|91774212|ref|YP_566904.1| 119 KCSNCERsLeDIEVKDHEKRQVFDIPPIKLQVTEHRAEIKSCPHCG 164
                                   6******8798899*******************************7 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7     8e-08   0.00014      18      65 ..      22      69 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65
                                  ++ +L d++aeqq+ i+ + +++ +l+er+k+lee+ +++ ++  +PP
  gi|91774212|ref|YP_566904.1| 22 LVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSRNSSKPP 69
                                  578999*******************************99998999998 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.6     1e+04      21      36 ..      27      42 ..      26      66 .. 0.57
   2 !    7.5   0.0    0.0025       4.5       5      45 ..     249     287 ..     245     290 .. 0.84
   3 !   12.1   0.2   9.3e-05      0.17      85     138 ..     418     471 ..     393     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
                 DDE_Tnp_IS240 21 yravDkegrildflvs 36
                                  y ++ +++ri++ +  
  gi|91774212|ref|YP_566904.1| 27 YDIIAEQQRIIELQAA 42
                                  6666666666666544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegrildflvskrRdtkaak 45 
                                   + DET ++i+Gk ++l  a  ++ ++ +++  ++R+ +a  
  gi|91774212|ref|YP_566904.1| 249 NCDETGMRIEGKRQWLHVA--STNKMTCYYPHQKRGSDAMN 287
                                   68************99866..77779999999999999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkg 138
                                   + ++ ++v+ +nn  E+d r +K++ + ++ f+s+++a  + +  + ++ ++k+
  gi|91774212|ref|YP_566904.1| 418 RFMHDLKVPFENNLAERDVRMMKVQQKISGTFRSMQGALIFSRVRSYISTVKKN 471
                                   45667899*****************************98777776666666665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017       0.3      45      87 ..      21      63 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2 45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                                    v tL + + +++   + q a++ el++ +kkL+++L++ + 
  gi|91774212|ref|YP_566904.1| 21 TLVTTLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNSR 63
                                  5678888888899999999********************9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   5.6e+02      36      45 ..     116     125 ..     109     140 .. 0.76
   2 ?    9.7   0.8   0.00046      0.83      21      34 ..     160     174 ..     153     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                 Zn_Tnp_IS1595  36 glfqCkeCrk 45 
                                   ++++C+ C +
  gi|91774212|ref|YP_566904.1| 116 KVHKCSNCER 125
                                   5566777755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595  21 CPhCgsr.kayrikt 34 
                                   CPhCg++ ka++ ++
  gi|91774212|ref|YP_566904.1| 160 CPHCGCKnKATFSEK 174
                                   *******99998876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00031      0.55      45      82 ..      25      62 ..      16      73 .. 0.82
   2 ?    0.9   0.1      0.34   6.2e+02      11      58 ..     392     446 ..     383     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82
                                  +l   i++++ ++e q ++i+el++++k+ +e+l+k  
  gi|91774212|ref|YP_566904.1| 25 TLYDIIAEQQRIIELQAARITELEERVKKLEEQLKKNS 62
                                  55667888999999999999999999999999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                   XX.X.XTTB-BHHHHHH....B-............BHHHHHHHHHHHH...HHHHHHHHHHH CS
                         DUF16  11 KkiPvkteYVTrkqlne....fkds..........nkqrLkkieakvdklgeqinkleqkve 58 
                                   Kk  ++t+  T k+l +    +k++                 +e++++ +++++ k++qk++
  gi|91774212|ref|YP_566904.1| 392 KK-RGRTKQTTAKNLLDrfigYKNDilrfmhdlkvP------FENNLAERDVRMMKVQQKIS 446
                                   44.467888888888777888999888854444440......55555555555555555553 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.4e+03      28      36 ..     117     125 ..      77     139 .. 0.60
   2 ?   10.7   4.5   0.00029      0.52       2      36 ..     156     213 ..     155     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
               Lar_restr_allev  28 cvyCadCga 36 
                                   +  C +C+ 
  gi|91774212|ref|YP_566904.1| 117 VHKCSNCER 125
                                   678999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
               Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigq...................cvyC...ad.Cga 36 
                                   e+k CP+Cg++++  +s++v++  ++                     +C   ad Cg+
  gi|91774212|ref|YP_566904.1| 156 EIKSCPHCGCKNKATFSEKVKQPTQYglrlaslavylhdyqllpyERSCellADvCGC 213
                                   79***************99987555588888888888888887775555444446666 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 ?    3.3   0.1     0.074   1.3e+02       2      23 ..     117     140 ..     116     144 .. 0.68
   2 ?    7.4   1.5     0.004       7.1       4      13 ..     159     168 ..     158     182 .. 0.68
   3 ?    2.0   0.1      0.19   3.3e+02       7      27 ..     249     267 ..     248     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                       zf-ISL3   2 phrCPnCgsk....tvvkhgkkerrv 23 
                                   +h+C nC +      v++h   +r+v
  gi|91774212|ref|YP_566904.1| 117 VHKCSNCERSlediEVKDHE--KRQV 140
                                   799*****998644446665..5665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                       zf-ISL3   4 rCPnCgsktv 13 
                                    CP+Cg+k++
  gi|91774212|ref|YP_566904.1| 159 SCPHCGCKNK 168
                                   5*******66 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                       zf-ISL3   7 nCgsktvvkhgkkerrvrhlp 27 
                                   nC ++ +++ g  +r+++h+ 
  gi|91774212|ref|YP_566904.1| 249 NCDETGMRIEG--KRQWLHVA 267
                                   79999999999..89999975 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00036      0.65      34      71 ..      73     130 ..      19     135 .. 0.89
   2 ?   -3.6   0.3        10   1.8e+04      55      66 ..     154     165 ..     144     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         PLATZ  34 vflnerpqarsakakakek.skkssse....................aCetCareLqde 71 
                                   vf+ne+p+++s+++k+ +k    ++ +                    +C+ C+r+L+d 
  gi|91774212|ref|YP_566904.1|  73 VFINEKPKTKSRRKKSGKKpG-GQKDHpgttlrmvdvpdeviihkvhKCSNCERSLEDI 130
                                   9*******9999988888743.33333568999***********************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                         PLATZ  55 kssseaCetCar 66 
                                   +++ ++C +C++
  gi|91774212|ref|YP_566904.1| 154 RAEIKSCPHCGC 165
                                   334478999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      874  (0.0487478); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.51
# Mc/sec: 2897.23
//
Query:       gi|91774213|ref|YP_566905.1|  [L=111]
Description: transcriptional modulator of MazE/toxin, MazF [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-09   37.8   0.0    2.3e-09   37.6   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.3e-13   2.3e-09       2     110 ..       6     107 ..       5     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.3e-13
                                   TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HHHCSS..SSSSSSEEEECCCE CS
                    PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhveleseildl..ngldkdswvkldqi 80 
                                   +G+Iv  ++ p +    +k+Rp +Vv + ++     vi +p+ts+++ +   ++++ l+s+  d    gl++ds ++   +
  gi|91774213|ref|YP_566905.1|   6 KGSIVVLPF-PFSDLAAAKKRPSLVVVDLKGD---DVILCPITSTHRGD---GYDISLKSG--DFiqGGLKHDSLIRSNRL 77 
                                   699******.85567778********999877...7**********777...******987..33447788********** PP

                                   EEEEGGGEEEEEEE--HHHHHHHHHHHHHH CS
                    PemK_toxin  81 rtvdkarlrkkigklsredlaevqralakl 110
                                   +t  ++ ++ k+g +++++++ev++ l kl
  gi|91774213|ref|YP_566905.1|  78 FTATTDIIAYKVGDITNTKMKEVEDVLVKL 107
                                   ***********************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 687.05
//
Query:       gi|91774214|ref|YP_566906.1|  [L=342]
Description: phage integrase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-17   63.5   0.0    3.5e-17   62.7   0.0    1.3  1  Phage_integrase  Phage integrase family
    3.1e-05   23.2   0.5    6.5e-05   22.2   0.5    1.5  1  zf-ribbon_3      zinc-ribbon domain
    0.00043   20.3   0.2    0.00094   19.2   0.2    1.5  1  DZR              Double zinc ribbon
     0.0014   18.3   3.6     0.0029   17.3   3.6    1.5  1  zinc_ribbon_2    zinc-ribbon domain
     0.0097   16.6   1.0     0.0097   16.6   1.0    2.1  2  zinc_ribbon_15   zinc-ribbon family
  ------ inclusion threshold ------
      0.046   12.7   0.0      0.079   11.9   0.0    1.3  1  DUF3435          Protein of unknown function (DUF3435)


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   1.2e-20   3.5e-17       4     170 ..      83     253 ..      82     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.2e-20
                                   HHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE....EEECSSSSEEEEECTHHHHHHH CS
               Phage_integrase   4 tedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvh....eregKgskeravplseealell 80 
                                   t++ev ++l+a+ +   +rd+++l++l + GlR++ l+s r+k+++ ++   ++      r +K+  +  +pl+ +   +l
  gi|91774214|ref|YP_566906.1|  83 TKEEVTSMLEACTN---ARDRAFLAILCDAGLRVGALASCRIKNVESNQYGSMIYisttSRSKKTTPAKGLPLTWS-SGYL 159
                                   689***********...***************************99888655553224334444444467777644.4579 PP

                                   HHHHHHH.CHCCTT.TSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SS CS
               Phage_integrase  81 kellska.leeaek.sellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHss 159
                                   +++++++ l+e+++   ++    +++pls +++  ++kr++e+ag++k+++ H +Rh++ t  +  g++ + + +  G++ 
  gi|91774214|ref|YP_566906.1| 160 QQWMAVHpLREDPEaPLWVTHTYKKEPLSYKSIGVTLKRIAERAGVKKNIHAHVFRHYAITGWILDGLSEQIINHRAGWAK 240
                                   99****96444444044555555********************************************************86 PP

                                   CC..HHHHHHCCC CS
               Phage_integrase 160 is..ttqiYthva 170
                                    s  + +iY++ +
  gi|91774214|ref|YP_566906.1| 241 DSnqMMKIYANFT 253
                                   5422669998765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.5   2.2e-08   6.5e-05       3      22 ..     278     297 ..     277     301 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                   zf-ribbon_3   3 vrCPnCGaplssddnvCpyC 22 
                                   +rCP+C+++l+++d++C  C
  gi|91774214|ref|YP_566906.1| 278 IRCPRCNNVLQESDRFCGQC 297
                                   79******99********99 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   3.1e-07   0.00094      29      48 ..     278     297 ..     256     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-07
                           DZR  29 drCpsCgekvdpearfCpeC 48 
                                   +rCp+C+  +++ +rfC++C
  gi|91774214|ref|YP_566906.1| 278 IRCPRCNNVLQESDRFCGQC 297
                                   67777777777777777777 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   3.6   9.8e-07    0.0029       1      19 [.     279     297 ..     279     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.8e-07
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyC 19 
                                   +Cp+C + lq+ ++FC +C
  gi|91774214|ref|YP_566906.1| 279 RCPRCNNVLQESDRFCGQC 297
                                   6****************** PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.2   3.5e+03       5      27 ..      32      53 ..      31      62 .. 0.79
   2 !   16.6   1.0   3.2e-06    0.0097      54      85 ..     266     297 ..     242     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                zinc_ribbon_15  5 kCgklskaelvkkkkvlklffip 27
                                  +C+ +sk e++++kk++k ff  
  gi|91774214|ref|YP_566906.1| 32 NCD-ISKGEIRNYKKCVKKFFKT 53
                                  677.6899999999999988855 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.2e-06
                zinc_ribbon_15  54 gkeiekkessekkeCknCgkeveeefkyCpkC 85 
                                   g ++e+k++++  +C++C+++++e+ ++C +C
  gi|91774214|ref|YP_566906.1| 266 GLKTEDKRHVTLIRCPRCNNVLQESDRFCGQC 297
                                   4455666667799******************* PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.6e-05     0.079     168     204 ..     182     218 ..     169     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                       DUF3435 168 lkdealtastlnsrlkrlgeiagfeepitpYklRrga 204
                                    k+e+l+++++   lkr++e ag ++ i+++ +R  a
  gi|91774214|ref|YP_566906.1| 182 YKKEPLSYKSIGVTLKRIAERAGVKKNIHAHVFRHYA 218
                                   5899******************************754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1924.10
//
Query:       gi|91774215|ref|YP_566907.1|  [L=415]
Description: proteasome-activating nucleotidase [Methanococcoides burtonii DSM 6242]
Scores for 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-43  146.7   0.2    1.8e-42  144.9   0.0    2.0  2  AAA              ATPase family associated with various cellul
    2.2e-13   49.7   0.1    8.6e-13   47.9   0.1    2.0  2  AAA_lid_3        AAA+ lid domain
    8.5e-05   22.7   0.0    0.00037   20.7   0.0    2.1  2  AAA_2            AAA domain (Cdc48 subfamily)
    0.00011   22.0   0.1    0.00056   19.7   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0002   21.3   0.0    0.00083   19.4   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00049   20.5   0.1      0.027   14.8   0.0    2.3  2  AAA_16           AAA ATPase domain
     0.0031   17.8   0.1       0.34   11.2   0.1    2.5  2  AAA_22           AAA domain
     0.0053   17.1   0.0      0.046   14.1   0.0    2.2  2  RNA_helicase     RNA helicase
     0.0093   15.3   0.7      0.055   12.8   0.0    2.4  3  ATPase           KaiC
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.094   12.4   0.0    2.3  3  Sigma54_activat  Sigma-54 interaction domain
      0.015   14.7   0.1      0.033   13.6   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.025   14.7   0.0      0.053   13.7   0.0    1.6  1  AAA_33           AAA domain
      0.032   13.4   0.0       0.06   12.5   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
      0.035   14.1   0.0       0.11   12.5   0.0    1.8  2  AAA_14           AAA domain
      0.043   13.7   0.0       0.09   12.6   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.044   13.0   0.0      0.078   12.2   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.072   12.8   0.0       0.14   11.8   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.074   12.3   0.0       0.15   11.3   0.0    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.11   12.2   0.0        0.3   10.8   0.0    1.8  1  AAA_24           AAA domain
       0.13   12.8   0.3        0.8   10.3   0.0    2.3  3  AAA_18           AAA domain
        0.4   11.1   2.3          2    8.8   0.0    2.8  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 ?   -1.2   0.0         3   2.6e+03      82      99 ..      58      75 ..      36     119 .. 0.72
   2 !  144.9   0.0   2.2e-45   1.8e-42       1     131 [.     197     329 ..     197     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3
                                  HHHHHHHHHHHHHHTTTS CS
                           AAA 82 eervvnqLlteldgvkkk 99
                                  ++ +vn+ l+e+d++k++
  gi|91774215|ref|YP_566907.1| 58 TSMMVNKYLSEMDQLKDQ 75
                                  455666667777776665 PP

  == domain 2  score: 144.9 bits;  conditional E-value: 2.2e-45
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgse 78 
                                   vl+yG pGtGKTl+akava+ ++++f+++sgs+l++k++ge+++ ++++f+ a+ek+ psilfiDEida+++ r    ++ 
  gi|91774215|ref|YP_566907.1| 197 VLMYGSPGTGKTLIAKAVASRAHATFIRMSGSDLVQKFIGEGARLVKDVFQLAREKS-PSILFIDEIDAVGGMRthdGTTG 276
                                   79******************************************************9.****************9876678 PP

                                   CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   s e +r++ qLl+e+dg++ + ++v +i+atnr+d ldpallr gRfdr+iei+
  gi|91774215|ref|YP_566907.1| 277 SAEVNRTMLQLLAEMDGFDPS-GNVKIIAATNRIDLLDPALLRpGRFDRIIEIP 329
                                   9999****************7.66***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.6   5.7e+03      14      21 ..     225     232 ..     225     232 .. 0.85
   2 !   47.9   0.1     1e-15   8.6e-13       1      45 []     352     396 ..     352     396 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.6
                     AAA_lid_3  14 ySGADlaa 21 
                                   +SG Dl++
  gi|91774215|ref|YP_566907.1| 225 MSGSDLVQ 232
                                   79***985 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 1e-15
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                   d+dl+++A +T+G SGADl  +++eA++  lrr  + i+m+df e
  gi|91774215|ref|YP_566907.1| 352 DIDLAKIANMTDGLSGADLNVIVKEAGMFVLRRRGDMIKMQDFLE 396
                                   89*****************************************75 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.3e-07   0.00037       5     104 ..     196     289 ..     192     307 .. 0.84
   2 ?   -2.0   0.0         4   3.4e+03      37      61 ..     388     410 ..     370     412 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.3e-07
                                   -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                         AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +l+ g+ g+Gkt++aka+a+  ++    ++ir+  s+l +    + + +     ++  + a e+   i+++DEid +   
  gi|91774215|ref|YP_566907.1| 196 GVLMYGSPGTGKTLIAKAVASRAHA----TFIRMSGSDLVQ----KFIGEGARLVKDVFQLAREKSpsILFIDEIDAVGGM 268
                                   57899******************96....************....77777777777777777777777**********998 PP

                                   ---------HHHHHHHHHHHH CS
                         AAA_2  84 essgadvSregVqrdLLqile 104
                                   ++      + +V r +Lq+l 
  gi|91774215|ref|YP_566907.1| 269 RTHDGTTGSAEVNRTMLQLLA 289
                                   77777778889********95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                   EEEGGG-------THHHHHHHHHTT CS
                         AAA_2  37 radaselleeeevehlvsrligapp 61 
                                   ++ ++++le  + e++vs+++++ p
  gi|91774215|ref|YP_566907.1| 388 MIKMQDFLE--AFEKVVSEEEVNTP 410
                                   455666666..99999999988876 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.6   5.7e+03      67      97 ..     136     166 ..     120     175 .. 0.60
   2 !   19.7   0.0   6.5e-07   0.00056      35      94 ..     196     263 ..     190     269 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.6
                        RuvB_N  67 Pvlekagdlaalltnleekdvlfideihrls 97 
                                    ++++a+d+ a +++l ++  +  d i  l+
  gi|91774215|ref|YP_566907.1| 136 AIISRAADVRAQMMELIDSPGIDYDMIGGLD 166
                                   4667777777777766665555555555555 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6.5e-07
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgP.vleka.gdlaalltnl......eekdvlfideih 94 
                                    vl+yG+PG Gkt +ak +a+  ++++   sg   ++k  g+ a l++++      ++  +lfidei 
  gi|91774215|ref|YP_566907.1| 196 GVLMYGSPGTGKTLIAKAVASRAHATFIRMSGSdLVQKFiGEGARLVKDVfqlareKSPSILFIDEID 263
                                   69******************9999886655555155553344444443321112214457******97 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   9.7e-07   0.00083       1     135 [.     196     317 ..     196     319 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.7e-07
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--.H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEverae.s 79 
                                   +vl+ G pGtgK+ +a+ +a++  +++        ++ +dl+++    +++++lv+ ++  a + +++il++DE++ +   
  gi|91774215|ref|YP_566907.1| 196 GVLMYGSPGTGKTLIAKAVASRAHATFIR------MSGSDLVQKFI--GEGARLVKDVFQLAREkSPSILFIDEIDAVGgM 268
                                   59*******************99888764......55678999999..6666777777764443699*********99888 PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                    + +      e +r +l  + e  ++++ +   ++ +ia++n+ d     l+pal+
  gi|91774215|ref|YP_566907.1| 269 RTHDGTTGSAEVNRTMLQLLAEMDGFDPSG---NVKIIAATNRID----LLDPALL 317
                                   888888888888888888888888888854...588999999888....6667665 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   3.2e-05     0.027      24      58 ..     194     225 ..     184     238 .. 0.78
   2 ?    3.2   0.0      0.12     1e+02     122     146 ..     241     272 ..     237     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrg 58 
                                   p+ vl +G +G+GK+ ++++++ ++ ++   f+r 
  gi|91774215|ref|YP_566907.1| 194 PSGVLMYGSPGTGKTLIAKAVASRAHAT---FIRM 225
                                   589*******************877665...6655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                        AAA_16 122 llkrllallsrderplvlvlDdlq........w 146
                                   l+k+ ++l+++ ++p +l++D+++        +
  gi|91774215|ref|YP_566907.1| 241 LVKDVFQLARE-KSPSILFIDEIDavggmrthD 272
                                   45566677887.889********9555555551 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    0.0004      0.34       9      40 ..     198     220 ..     192     235 .. 0.83
   2 ?    3.9   0.0      0.07        60      77     125 ..     240     302 ..     235     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                   + +G +GtGKT+ ++ ++++++         +
  gi|91774215|ref|YP_566907.1| 198 LMYGSPGTGKTLIAKAVASRAH---------A 220
                                   669****************994.........3 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.07
                        AAA_22  77 ellealeqalraravielliiDEaqhlr....s..........eealeeLrsllnl.srkgvql 125
                                   +l++ + q +r+++  ++l iDE++ +     +           ++l+ L ++  +  + +v++
  gi|91774215|ref|YP_566907.1| 240 RLVKDVFQLAREKSP-SILFIDEIDAVGgmrtHdgttgsaevnRTMLQLLAEMDGFdPSGNVKI 302
                                   566777788888888.**********97665414455666666777777766655555555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2       1.3   1.1e+03      49      93 ..      34      76 ..      14      88 .. 0.68
   2 !   14.1   0.0   5.3e-05     0.046       1      69 [.     197     256 ..     197     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
                  RNA_helicase 49 gqevvvidDfgqvkdeenpsdlaelirlvsstpyplnmasleekg 93
                                   q+v+   D+ +v++e   +  + l   +  ++y  +m++l+++ 
  gi|91774215|ref|YP_566907.1| 34 IQKVISENDLLKVQNE--TMKAKLLETSMMVNKYLSEMDQLKDQL 76
                                  5778888888888877..345555556666678888888888775 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.3e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenpsd 69 
                                   +++yG++g+GK+++ak             +++ +++r + +d ++++ g+ + ++ D+ q   e++ps+
  gi|91774215|ref|YP_566907.1| 197 VLMYGSPGTGKTLIAKA---------VASRAHATFIRMSGSDLVQKFIGEGARLVKDVFQLAREKSPSI 256
                                   679**************.........3355677888999999999999999999999999887755554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.93   7.9e+02      72     113 ..      32      78 ..      24     101 .. 0.68
   2 !   12.8   0.0   6.4e-05     0.055       5      37 ..     162     212 ..     160     221 .. 0.86
   3 ?   -2.6   0.0       3.3   2.8e+03     108     133 ..     242     269 ..     236     293 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.93
                        ATPase  72 wdlekleeegklaiidasesaeesaee.....kdkedleelieelae 113
                                   +d++k+ +e+ l  ++  +++++  e      k+ +++++l+++l +
  gi|91774215|ref|YP_566907.1|  32 VDIQKVISENDLLKVQNETMKAKLLETsmmvnKYLSEMDQLKDQLDH 78 
                                   78888888888887777777776555555555555555555555544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.4e-05
                        ATPase   5 IeglDeilk..................gGipegrvvlitGepGtGKtifal 37 
                                   I glD++lk                   Gi   + vl++G+pGtGKt++a+
  gi|91774215|ref|YP_566907.1| 162 IGGLDDVLKeviesvelpltepelfenIGIEPPSGVLMYGSPGTGKTLIAK 212
                                   77888888778888888888888888899*9*****************997 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.3
                        ATPase 108 ieelaeaikeikakrvviDsitgl..ay 133
                                   ++++ +  +e+  + + iD i+++  ++
  gi|91774215|ref|YP_566907.1| 242 VKDVFQLAREKSPSILFIDEIDAVggMR 269
                                   5566667777788888888887764223 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.094      22      60 ..     194     229 ..     184     238 .. 0.77
   2 ?   -2.5   0.0       4.3   3.7e+03      95     104 ..     255     264 ..     245     267 .. 0.79
   3 ?   -1.5   0.0       2.1   1.8e+03     134     143 ..     299     308 ..     295     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                   SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTT CS
               Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaa 60 
                                   ++ vl+ G  GtGK+l+a+a+ +   r+++ f+++  ++
  gi|91774215|ref|YP_566907.1| 194 PSGVLMYGSPGTGKTLIAKAVAS---RAHATFIRMSGSD 229
                                   5679***************9864...5556677666555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                                   SEEEEETGGG CS
               Sigma54_activat  95 GtlfLDeige 104
                                   ++lf+Dei  
  gi|91774215|ref|YP_566907.1| 255 SILFIDEIDA 264
                                   79*****975 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.1
                                   -EEEEEEESS CS
               Sigma54_activat 134 dvriiaatne 143
                                   +v+iiaatn+
  gi|91774215|ref|YP_566907.1| 299 NVKIIAATNR 308
                                   89******97 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.9e-05     0.033      25      43 ..     197     215 ..     190     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +l++G+pG+GKt++ak+++
  gi|91774215|ref|YP_566907.1| 197 VLMYGSPGTGKTLIAKAVA 215
                                   89*************9976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.2e-05     0.053       2      35 ..     197     232 ..     197     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrr 35 
                                   vl+ G pG+GK+  a+ ++ + +  +++ s  +l +
  gi|91774215|ref|YP_566907.1| 197 VLMYGSPGTGKTLIAKAVASRAHatFIRMSGSDLVQ 232
                                   79****************998885666666666554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05      0.06      52     115 ..     193     261 ..     158     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                        DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklve...llrerperfilfvDD 115
                                   p + vL++G+ GtGK  + ka+ ++++++ +r+   ++ ++ + e  +lv+   +l++++   ilf+D 
  gi|91774215|ref|YP_566907.1| 193 PPSGVLMYGSPGTGKTLIAKAVASRAHATFIRMSgsDLVQKFIGEGARLVKdvfQLAREKSPSILFIDE 261
                                   55679**********************999998422455555665555555111344555666777775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.9   5.9e+03      71      77 ..      27      33 ..      17      73 .. 0.67
   2 ?   12.5   0.0   0.00013      0.11       6      80 ..     198     269 ..     195     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.9
                        AAA_14 71 DEiqevp 77
                                  DEiqev+
  gi|91774215|ref|YP_566907.1| 27 DEIQEVD 33
                                  6666652 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00013
                        AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                   ++ G   +GKT ++k ++++       ++ ++  d  +k + + ++l + ++++++e+  ++lf+DEi  v +++
  gi|91774215|ref|YP_566907.1| 198 LMYGSPGTGKTLIAKAVASRAH---ATFIRMSGSDLVQKFIGEGARLVKDVFQLAREKSPSILFIDEIDAVGGMR 269
                                   56788889*********98888...899999999977765555556777777776566889*******9987665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001      0.09       2      36 ..     197     230 ..     196     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdl 36 
                                   vl+ g PG++ktl++ka+a+  +++f r+   +dl
  gi|91774215|ref|YP_566907.1| 197 VLMYGSPGTGKTLIAKAVASRAHATFIRMS-GSDL 230
                                   7999**********************9985.4555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.2e-05     0.078      14      53 ..     192     229 ..     183     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-05
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                                   e P  +l+ G+pG GK+ +a++++ +   +  ++r+++ d
  gi|91774215|ref|YP_566907.1| 192 EPPSGVLMYGSPGTGKTLIAKAVASRA--HATFIRMSGSD 229
                                   568899*****************9997..88888887644 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.14      48      74 ..     195     221 ..     184     265 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                     IstB_IS21  48 enivllGpsGvGKshlaialgveavra 74 
                                    ++++ G +G+GK+ +a a++ +a ++
  gi|91774215|ref|YP_566907.1| 195 SGVLMYGSPGTGKTLIAKAVASRAHAT 221
                                   67999***************9988654 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.15       4      43 ..     197     241 ..     195     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                       DUF2075   4 vlVtGvaGtGKtvvllnllael.....eddeeertavylsvNhpl 43 
                                   vl  G +GtGKt+++ +++ ++     +++ ++  ++++    +l
  gi|91774215|ref|YP_566907.1| 197 VLMYGSPGTGKTLIAKAVASRAhatfiRMSGSDLVQKFIGEGARL 241
                                   5789************99999866666555566666665555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00035       0.3       5      34 ..     197     228 ..     194     272 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekG 34 
                                   +l+yG++g+GKT +ak      ++ fi + ++
  gi|91774215|ref|YP_566907.1| 197 VLMYGSPGTGKTLIAKAVasRAHATFIRMSGS 228
                                   789************99966666666665554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1         2   1.7e+03      46      69 ..      26      49 ..      10     112 .. 0.61
   2 ?   10.3   0.0   0.00094       0.8       2      25 ..     198     229 ..     197     273 .. 0.68
   3 ?   -2.6   0.0         9   7.7e+03      13      39 ..     283     311 ..     282     361 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
                        AAA_18 46 ldeskrldedkldklldaleenss 69
                                  +de +++d++k+ +  d+l+ +++
  gi|91774215|ref|YP_566907.1| 26 TDEIQEVDIQKVISENDLLKVQNE 49
                                  444444444444444444444433 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00094
                        AAA_18   2 lltGtpGvGKttlakeLskrlgf........g 25 
                                   l  G pG+GKt +ak++++r +          
  gi|91774215|ref|YP_566907.1| 198 LMYGSPGTGKTLIAKAVASRAHAtfirmsgsD 229
                                   66899************998622357666543 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9
                        AAA_18  13 tlakeLskrlgf..gvnlrdvakenglll 39 
                                   t+ + L+++ gf  + n++ +a+ n++ l
  gi|91774215|ref|YP_566907.1| 283 TMLQLLAEMDGFdpSGNVKIIAATNRIDL 311
                                   55666777667777444444444433332 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.73   6.2e+02      38      90 ..      21      74 ..       3     108 .. 0.53
   2 ?    8.8   0.0    0.0024         2       1      34 [.     200     235 ..     200     264 .. 0.77
   3 ?   -2.2   0.1       6.2   5.3e+03     103     127 ..     323     347 ..     307     363 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.73
                                  TSHSSHHHHCTSHHHH...HHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEE CS
                        AAA_17 38 glakardemrklplee...kkelqkeaaekiaeeakkkgvlvdghprikeqagfld 90
                                  g + + de++++++++   +++l+k   e+++ +  ++ ++v+++ +  e++++ d
  gi|91774215|ref|YP_566907.1| 21 GEEHNTDEIQEVDIQKvisENDLLKVQNETMKAKLLETSMMVNKYLS--EMDQLKD 74
                                  33445566665544332224445555555555555555566655554..3333333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0024
                                   EE-TTSSHHHHHHHHHHHHTEEEE..EHHHHHHHHH CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthl..saGdllreea 34 
                                   +G PG GK+ +++ ++ + + t++  s +dl+ + +
  gi|91774215|ref|YP_566907.1| 200 YGSPGTGKTLIAKAVASRAHATFIrmSGSDLVQKFI 235
                                   799************998877776225577776555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.2
                                   SEEEEEE--HHHHHHHHHHHTTST- CS
                        AAA_17 103 daiilleadpeeilerrlkdrtrgr 127
                                   d ii + +++e+ +e+ lk +tr+ 
  gi|91774215|ref|YP_566907.1| 323 DRIIEIPIPDEKAREEILKIHTRKM 347
                                   5566666666667777766666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); 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: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2348.31
//
Query:       gi|91774216|ref|YP_566908.1|  [L=298]
Description: hypothetical protein Mbur_2302 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0011   19.3   0.3     0.0024   18.2   0.3    1.5  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   1.4e-07    0.0024      17      67 ..     226     279 ..     211     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-07
                                   -EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE---- CS
               Penicillinase_R  17 eatvkevveeleee.kelaysTVktllrrLvkKgllsreke..grafiYsplvs 67 
                                     t+k+++++ e+   e + sTV t l+r+++K+ll+r+ +  +r+++Y   ++
  gi|91774216|ref|YP_566908.1| 226 WSTSKKIQQHYESIyGEIKLSTVSTYLSRMYRKNLLERRGNrtQREYLYIGDME 279
                                   479999999999985678*******************97553388888866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2031.82
//
Query:       gi|91774217|ref|YP_566909.1|  [L=660]
Description: excinuclease ABC subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-30  103.8   0.1    1.4e-29  102.1   0.1    2.0  1  UvrB_inter  UvrB interaction domain
    7.9e-20   70.4   0.0      2e-19   69.2   0.0    1.7  1  UvrB        Ultra-violet resistance protein B
    5.9e-18   65.2   0.1    1.8e-17   63.6   0.1    1.8  1  Helicase_C  Helicase conserved C-terminal domain
    5.7e-13   49.2   0.0    6.6e-12   45.8   0.0    2.3  2  ResIII      Type III restriction enzyme, res subunit
    4.8e-09   35.7   3.0    4.8e-09   35.7   3.0    2.3  2  UVR         UvrB/uvrC motif
    0.00014   21.7   0.1     0.0037   17.1   0.0    3.0  3  DEAD        DEAD/DEAH box helicase
     0.0011   18.7   0.0      0.046   13.4   0.0    2.8  3  AAA_30      AAA domain
  ------ inclusion threshold ------
       0.02   15.2   0.1        6.1    7.2   0.0    2.9  2  AAA_19      AAA domain
      0.069   13.2   1.2       0.14   12.2   0.1    1.9  2  DUF87       Helicase HerA, central domain
       0.11   12.0   0.1       0.19   11.2   0.1    1.3  1  AAA_7       P-loop containing dynein motor region
       0.12   12.8   0.2          2    8.8   0.0    3.1  3  AAA         ATPase family associated with various cellular ac
       0.13   11.2   0.0       0.21   10.5   0.0    1.2  1  Kinesin     Kinesin motor domain


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.1   9.3e-33   1.4e-29       3      91 .]     160     250 ..     158     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 9.3e-33
                    UvrB_inter   3 lkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgkslek...l 80 
                                   l++g+++ r++l++ L++++Yernd+e  +G+Fr +Gdt+e+fpa+ +++ +rie+fgdei++i+++dp+tgk++++    
  gi|91774217|ref|YP_566909.1| 160 LRTGDEVGRSDLFAALINIHYERNDIESAKGSFRSKGDTIEVFPAQ-DNHGVRIELFGDEIDRISSFDPVTGKTIDEvkeD 239
                                   89********************************************.8**************************9763336 PP

                    UvrB_inter  81 eeitifPakhf 91 
                                   ++i+i+Pakhf
  gi|91774217|ref|YP_566909.1| 240 NSIVIYPAKHF 250
                                   79********9 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   1.3e-22     2e-19       1      42 [.     552     593 ..     552     594 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.3e-22
                                   EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXX CS
                          UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKki 42 
                                   lYA k+T+S+++A+ eT+rRR+iQ aYNe+hgI+P+ti+K++
  gi|91774217|ref|YP_566909.1| 552 LYAGKVTGSIEAALRETNRRRQIQLAYNEKHGIVPQTIHKAL 593
                                   8***************************************86 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 !   63.6   0.1   1.2e-20   1.8e-17       6     109 ..     435     544 ..     430     546 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.2e-20
                                   HHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                    Helicase_C   6 llell.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                   l+ ++ k +e+g+++l+ + t++++e+ +++ll + gi+v ++h+++ + er ei+++ +kg +dvL+  + + +G+dip+
  gi|91774217|ref|YP_566909.1| 435 LIGEVnKVTEKGYRTLVTTLTKRMAEDlTEYLL-EMGIRVRYMHSDIDTLERAEIIRDLRKGVFDVLVGINLLREGLDIPE 514
                                   4444468899***************99888985.447******************************************** PP

                                   ESEEEESSSS.....SSHHHHHHHHTTSSS CS
                    Helicase_C  85 vnlVinfdlp.....rnvtsyiqriGRtgR 109
                                   v +V ++d++     r+ +s+iq +GR+ R
  gi|91774217|ref|YP_566909.1| 515 VAFVAILDADkegflRSERSLIQTMGRASR 544
                                   **********88888889**********99 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   4.4e-15   6.6e-12       3     111 ..      11     141 ..       9     178 .. 0.73
   2 ?    1.0   0.0      0.26   3.8e+02     134     148 ..     327     355 ..     232     399 .. 0.61

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.4e-15
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                   e++  Q eai++l e l+ k+ k+ ++   TG+GKT++ a++i++++k      +l+++++k+l  q+ +ef++f+++++ 
  gi|91774217|ref|YP_566909.1|  11 EPKGDQPEAIRKLSEGLN-KGLKHQVLLGVTGSGKTFTVANVIQNVQK-----PTLVIAHNKTLAAQLFSEFREFFPNNAV 85 
                                   56668************9.****************************9.....8**********************99986 PP

                                   ......................GEEEESSS-B--..................-SEEEEEH CS
                        ResIII  84 e.....................igkkvsgdkkka...........kekdstnkkilvtti 111
                                   e                     i+k+ s     +           k+  + +  i+v+++
  gi|91774217|ref|YP_566909.1|  86 EyfvsyydyyqpeaylpttdtyIEKDSSV----NeeidrlrlsatKSLIERKDVIVVSSV 141
                                   66666444444444443333321111111....122223444444444444444555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                                   S.......EEEEETGGGTTS........T CS
                        ResIII 134 d.......viiiDEaHrlgak.......k 148
                                   +       +++iDE+H +  +       +
  gi|91774217|ref|YP_566909.1| 327 LeffpddfLLVIDESHVTIPQirgmhngD 355
                                   04444666899999998777655554440 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       2.9   4.3e+03      21      28 ..     484     491 ..     484     492 .. 0.91
   2 !   35.7   3.0   3.2e-12   4.8e-09       3      34 ..     624     655 ..     622     657 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.9
                           UVR  21 EkAAklRD 28 
                                   E+A  +RD
  gi|91774217|ref|YP_566909.1| 484 ERAEIIRD 491
                                   9******9 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 3.2e-12
                           UVR   3 likeLeeemeeAaenedFEkAAklRDqinalk 34 
                                   ++ eLe+em+ Aa+n++FE+AA lRD i++l+
  gi|91774217|ref|YP_566909.1| 624 MVIELEAEMHLAAKNLEFERAAALRDNIKELR 655
                                   678***************************98 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.5e-06    0.0037       4      74 ..      16      83 ..      14     131 .. 0.81
   2 ?   -1.1   0.0      0.94   1.4e+03     125     147 ..     336     353 ..     334     401 .. 0.43
   3 ?    0.2   0.0      0.38   5.6e+02      44     103 ..     443     502 ..     422     520 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                                  HHHHHHHHHTT.....CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                  xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  4 Qaeaiplilgg.....gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyi 74
                                  Q eai  + +g     ++ ++ + TGsGKT   +  v+q+v    +k    +l+++  + La q ++++++f+ + 
  gi|91774217|ref|YP_566909.1| 16 QPEAIRKLSEGlnkglKHQVLLGVTGSGKTFT-VANVIQNV----QK---PTLVIAHNKTLAAQLFSEFREFFPNN 83
                                  666777777555555677788899******98.78999999....34...56********************9854 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.94
                                   EEEETHHHHHHTTTHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 125 lVlDEadrlldqgfsdfinriln 147
                                   lV+DE +    q     i+ ++n
  gi|91774217|ref|YP_566909.1| 336 LVIDESHVTIPQ-----IRGMHN 353
                                   677777766555.....333333 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.38
                                   TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
                          DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvg 103
                                   +++g ++l+ + t+ +ae+  + l +++  +  r++ + i   ++ + +++l++g  d++vg
  gi|91774217|ref|YP_566909.1| 443 TEKGYRTLVTTLTKRMAEDLTEYLLEMGIRV--RYMhSDIDTLERAEIIRDLRKGvFDVLVG 502
                                   5677788888888888888777777777753..33335577778888888888887888887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.1e-05     0.046       5      65 ..      15      75 ..      12     144 .. 0.77
   2 ?    1.9   0.0      0.11   1.6e+02      42      77 ..     442     480 ..     435     504 .. 0.78
   3 ?   -2.7   0.0       2.8   4.2e+03      64      80 ..     580     596 ..     544     639 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                        AAA_30  5 eQaaaveal...ltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaee 65
                                  +Q +a+++l   l++g + +vl G+ G+GKt++++ + + ++   ++ +++A++++ A++L  e
  gi|91774217|ref|YP_566909.1| 15 DQPEAIRKLsegLNKGLKHQVLLGVTGSGKTFTVANVIQNVQ---KPTLVIAHNKTLAAQLFSE 75
                                  6777777663335667789**************999888777...5678999999988887654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                        AAA_30  42 weaaggrviglAptgkaAkvLae...elgieastiakll 77 
                                   ++++g+r ++ + t+++A++L+e   e+gi+ + +++ +
  gi|91774217|ref|YP_566909.1| 442 VTEKGYRTLVTTLTKRMAEDLTEyllEMGIRVRYMHSDI 480
                                   56689*****************87777788777766655 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.8
                        AAA_30  64 eelgieastiakllkrl 80 
                                   e+ gi  +ti+k l+r 
  gi|91774217|ref|YP_566909.1| 580 EKHGIVPQTIHKALQRE 596
                                   44555556666666443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0041       6.1      12      37 ..      33      58 ..      25     145 .. 0.87
   2 ?    5.0   0.1     0.019        28      41      74 ..     445     478 ..     431     647 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0041
                        AAA_19 12 vllvtaGpGtGKTrvlkhivallvel 37
                                  + ++++  G+GKT ++  +++ +++ 
  gi|91774217|ref|YP_566909.1| 33 HQVLLGVTGSGKTFTVANVIQNVQKP 58
                                  5689999************9988765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.019
                        AAA_19  41 kpeeillvaftgrAakelrerlaalgaeatTiHr 74 
                                   k  + l+ ++t+r a+ l+e l ++g + + +H+
  gi|91774217|ref|YP_566909.1| 445 KGYRTLVTTLTKRMAEDLTEYLLEMGIRVRYMHS 478
                                   347899**************99888888555553 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.3e-05      0.14      24      47 ..      32      55 ..      27      63 .. 0.84
   2 ?   -2.1   0.1       2.2   3.3e+03     115     177 ..     592     656 ..     574     659 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.3e-05
                         DUF87 24 rHlAilgsTGsGKSntvavLleel 47
                                  +H   lg TGsGK++tva  ++++
  gi|91774217|ref|YP_566909.1| 32 KHQVLLGVTGSGKTFTVANVIQNV 55
                                  68889************9888876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                         DUF87 115 avqrsvleealdqaka.....keekeklssdepveklleelkkekeelrklknqaiarlldkledllr 177
                                   a qr+++e  + ++++     +e+  ++ +++ v +l+ e++   + +++l  + +a+l d +++l +
  gi|91774217|ref|YP_566909.1| 592 ALQRELVETEYGEVVSevlgvAEDLSDIEIADMVIELEAEMH---LAAKNLEFERAAALRDNIKELRS 656
                                   446666666666666666667777788888888888888887...77777777777777777777765 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 ?   11.2   0.1   0.00013      0.19      28      63 ..      26      61 ..      18      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                         AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldkekyl 63
                                   l k  k+ +l G tG+GKt ++ +++++++k +++
  gi|91774217|ref|YP_566909.1| 26 GLNKGLKHQVLLGVTGSGKTFTVANVIQNVQKPTLV 61
                                  56666788999**************99999965544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0013         2       3      35 ..      36      68 ..      34     156 .. 0.85
   2 ?   -2.6   0.0       4.5   6.8e+03      62      73 ..     214     225 ..     193     247 .. 0.73
   3 ?   -0.7   0.0       1.2   1.8e+03      87     123 ..     533     570 ..     523     577 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                                  EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                           AAA  3 lyGppGtGKTllakavakelgvefleisgsell 35
                                  l G  G GKT ++  v+++++ + l i   + l
  gi|91774217|ref|YP_566909.1| 36 LLGVTGSGKTFTVANVIQNVQKPTLVIAHNKTL 68
                                  89*****************99887777666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.5
                                   EEEETGGGHHHH CS
                           AAA  62 lfiDEidalaks 73 
                                   lf DEid++ + 
  gi|91774217|ref|YP_566909.1| 214 LFGDEIDRISSF 225
                                   677888888654 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TT CS
                           AAA  87 nqLlteldgvkkkeskvivigatnrpdkldpallr.gR 123
                                     L++ + + +++ +  +++ a++   +++ al+  +R
  gi|91774217|ref|YP_566909.1| 533 RSLIQTMGRASRNADGYVILYAGKVTGSIEAALREtNR 570
                                   56888888888888878888888889999999996555 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.21      81     138 ..      37      98 ..      15     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                   EESTTSSHHHHHTBC..TTTSBSHH....HHHHHHHHHHHHHCTTTHEEEEEEEEEEEEEETTE CS
                       Kinesin  81 YGqtgsGKTyTmegk..eeeeeGii....praleelFesikkekeekekefsvkvsylEiYnee 138
                                    G+tgsGKT+T+     + +++ ++        ++lF++ ++   +  + ++  vsy++ Y+ e
  gi|91774217|ref|YP_566909.1|  37 LGVTGSGKTFTVANViqNVQKPTLViahnKTLAAQLFSEFREFFPN--NAVEYFVSYYDYYQPE 98 
                                   5***********9877733344443111124566788888776554..7788888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 3818.91
//
Query:       gi|91774218|ref|YP_566910.1|  [L=166]
Description: SOUL heme-binding protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-40  137.5   0.0    5.1e-40  137.4   0.0    1.0  1  SOUL      SOUL heme-binding protein


Domain annotation for each model (and alignments):
>> SOUL  SOUL heme-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.0   2.9e-44   5.1e-40       2     167 ..       4     163 ..       3     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 2.9e-44
                          SOUL   2 etpkYevlke..ekkyEvRryepavwaettvseasleearssgfrrLarYifgkNekeekiamtaPvvtkvkekevtmsfv 80 
                                   e+++Y+v++e  ++ +E+R+y  +++++++      +++++sgfr+L +YifgkN+++ kiamtaPv+++ +e+   msfv
  gi|91774218|ref|YP_566910.1|   4 EQLNYTVIEElgDG-VEIRQYGRSTFISADA-----KKDSNSGFRALSGYIFGKNKNGVKIAMTAPVISRQEEHVLHMSFV 78 
                                   899*****987555.**************95.....4566689************************98777799****** PP

                          SOUL  81 lpskyqaeepPkPtddsrVkleevpertvavrrFsGfateeevkeeaeeLreaLekdg.geekkdsyvlaqYnppftppfl 160
                                   lp+ y+++++P + d+ ++++++v++r++a +rFsG++te+++++++  L + L+++g +   k +++l++Ynpp+ pp+ 
  gi|91774218|ref|YP_566910.1|  79 LPEGYDVDNAPYSLDE-AISIHDVSPRKLAGIRFSGYVTENKIESRRLILEKNLSEHGlST--KGEFFLMRYNPPWFPPMI 156
                                   *************666.*******************99****************8888544..6789************** PP

                          SOUL 161 rrNEvwi 167
                                    rNE+++
  gi|91774218|ref|YP_566910.1| 157 MRNEIAV 163
                                   *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 942.24
//
Query:       gi|91774219|ref|YP_566911.1|  [L=467]
Description: deoxyribodipyrimidine photo-lyase type I [Methanococcoides burtonii DSM 6242]
Scores for 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  256.9   0.8    1.4e-76  256.5   0.8    1.2  1  FAD_binding_7   FAD binding domain of DNA photolyase
    1.1e-43  149.1   0.0    2.2e-43  148.1   0.0    1.5  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.5   0.8   1.6e-80   1.4e-76       2     200 ..     270     458 ..     269     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 256.5 bits;  conditional E-value: 1.6e-80
                                   HHHHHHHHHHHHHHHCSTTTTTSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHHHHHC CS
                 FAD_binding_7   2 lreLlwrefyyallaaepelaeralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmivasFlt 82 
                                   ++eL+wr+f++++ +++p++ ++a+k+kfd+++w++++   ++aW+ G+TGfP+vDA+mr+L++tG+mhnr+RmivasFl+
  gi|91774219|ref|YP_566911.1| 270 INELYWRDFFTQISFEFPDVFKHAFKKKFDHLSWDNDRI-FFDAWCLGKTGFPIVDAGMRELNTTGYMHNRVRMIVASFLV 349
                                   589*******************************66644.7**************************************** PP

                                   TTT-B-HHHHHHHHHHH-TT--CCHHHHHHHHHCT-STTS-STT----CCCCHHHCSTT-HHHHHH-GGGTTS-HHHHT-G CS
                 FAD_binding_7  83 kdLlidWregeevFeellvDadlasnagnwqwlagtgadaapafrifnpvkqgkkfDpegeyirrwvpeLkklpakyihep 163
                                   kdL+idW++ge++F+++lvD+d+++n+gnwqw+a+tgad++p+frifnp+ q+kkfD++++yi++w+peL++++ + ih+ 
  gi|91774219|ref|YP_566911.1| 350 KDLHIDWKRGERYFASKLVDYDPCVNNGNWQWAASTGADSQPYFRIFNPWLQQKKFDKDCKYIKKWIPELEDIEPQRIHKL 430
                                   *******************************************************************************75 PP

                                   GGSGCHHHHHHT--TTTSS---SS-HHHHHHHHHHHH CS
                 FAD_binding_7 164 wkapaeeqkkagvvlgkdYpkpivdhkearkraleay 200
                                    k         g      Yp+pivdh+++r+ al  +
  gi|91774219|ref|YP_566911.1| 431 EK---------GDMDIPGYPAPIVDHSKEREVALFMF 458
                                   53.........3445679*************998766 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   2.4e-47   2.2e-43       2     154 ..       9     163 ..       8     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 2.4e-47
                                   EEEESS---STT-HHHHHHHCTTSEEEEEEEE-HH..HHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHH CS
                DNA_photolyase   2 lvWfrrDlRlhDNpALaaAaasgepvipvfvldpe..kahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvl 80 
                                   l+ frrD+R+ DN AL aA++ ++ vip+f+ldp+  + +   ++++  +fllesL dL+ +L++ ++rL++++g p+ v+
  gi|91774219|ref|YP_566911.1|   9 LFVFRRDMRVDDNSALLAALDMSDVVIPCFILDPRlcDPKGKAFNSNALQFLLESLYDLKGQLEKVNGRLYLFSGLPEGVI 89 
                                   667********************************874444468************************************* PP

                                   HHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHCHHH CS
                DNA_photolyase  81 pelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkrwlk 154
                                    +l++ l+++av++n++y+p+  +rd ++++++ ++g+++ +f+d++l+epg+++tkkg+pykvFt+f++++ k
  gi|91774219|ref|YP_566911.1|  90 GQLLENLEIDAVFVNHDYTPFSIKRDMQIASICTDKGVDMLQFHDCLLHEPGSIRTKKGTPYKVFTQFFREASK 163
                                   **********************************************************************9887 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:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3452.60
//
Query:       gi|91774220|ref|YP_566912.1|  [L=143]
Description: MarR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-10   40.1   0.0    3.8e-10   39.5   0.0    1.3  1  MarR            MarR family
    3.6e-07   30.3   0.4      9e-07   29.0   0.4    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.7e-06   27.8   0.0    2.4e-06   27.3   0.0    1.3  1  MarR_2          MarR family
    7.8e-05   23.1   0.0    0.00015   22.2   0.0    1.5  2  HTH_27          Winged helix DNA-binding domain
     0.0016   18.3   1.7      0.002   18.0   0.1    2.0  3  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.034   14.2   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      0.059   13.2   0.0      0.096   12.5   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.067   13.2   0.0       0.13   12.2   0.0    1.4  1  HTH_36          Helix-turn-helix 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 !   39.5   0.0   1.7e-13   3.8e-10       2      58 ..      31      87 ..      30      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.7e-13
                                  -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                  +++ f+ L+ +++  ++++seLa+++ v+k++++ ++++L++ Gl+  ++s +D+R+
  gi|91774220|ref|YP_566912.1| 31 SYSSFSYLVVVRSLVNPTISELASAMDVKKPSASVMVKKLVDMGLLGVERSISDKRV 87
                                  7889****************************************************6 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 !   29.0   0.4     4e-10     9e-07      23      55 ..      47      79 ..      39      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4e-10
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyveye 55
                                  ++ ++la++++v+++s+s m+kkL ++G++ +e
  gi|91774220|ref|YP_566912.1| 47 PTISELASAMDVKKPSASVMVKKLVDMGLLGVE 79
                                  56799************************9776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.1e-09   2.4e-06      22      61 ..      47      86 ..      29      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-09
                                  EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                   t++ela +++++k+++s ++k+Lv+ GL+  +++  DkR
  gi|91774220|ref|YP_566912.1| 47 PTISELASAMDVKKPSASVMVKKLVDMGLLGVERSISDKR 86
                                  49****************************9999999*99 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 ?   -1.2   0.0       1.4     3e+03      27      39 ..      27      39 ..      20      47 .. 0.76
   2 !   22.2   0.0   6.7e-08   0.00015       9      68 .]      38      96 ..      30      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                        HTH_27 27 rlnvedshisysl 39
                                  + +v++s++sy +
  gi|91774220|ref|YP_566912.1| 27 YADVSYSSFSYLV 39
                                  7899999999865 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 6.7e-08
                        HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  L ++r  +   ++++l+ +++v + ++s ++kkL+ +GL+  +++  d+r   ++l+++G
  gi|91774220|ref|YP_566912.1| 38 LVVVR-SLVNPTISELASAMDVKKPSASVMVKKLVDMGLLGVERSISDKRVCNLTLSAEG 96
                                  66666.777789****************************99999999**9999999988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       4.1   9.2e+03      13      23 ..      13      24 ..      12      28 .. 0.61
   2 !   18.0   0.1     9e-07     0.002      14      56 ..      37      80 ..      30      89 .. 0.88
   3 ?   -1.5   0.0       1.1   2.5e+03       6      22 ..     118     134 ..     118     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.1
                                  HCHHHH.HHCCC CS
                          TrmB 13 vYlaLl.klgpa 23
                                   Y+++l k++++
  gi|91774220|ref|YP_566912.1| 13 YYQKILtKNEKL 24
                                  588888555555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9e-07
                                  CHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 14 YlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  Yl+++ +l + t++e+a++ +v ++++  ++++L+d+Gl  +e+
  gi|91774220|ref|YP_566912.1| 37 YLVVVrSLVNPTISELASAMDVKKPSASVMVKKLVDMGLLGVER 80
                                  88888899999****************************87776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                                   HHHHCCCHCHHHHHHCC CS
                          TrmB   6 LseyEakvYlaLlklgp 22 
                                   L ++E++v+  L ++  
  gi|91774220|ref|YP_566912.1| 118 LDDNEFEVFSGLWEKIT 134
                                   56899999999876655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.034      26      59 ..      48      81 ..      37      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                  -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20 26 taselaerldlskntlsyHLrvLeeagLvevvre 59
                                  t sela ++d++k ++s  +++L++ gL+ v+r+
  gi|91774220|ref|YP_566912.1| 48 TISELASAMDVKKPSASVMVKKLVDMGLLGVERS 81
                                  89***************************99885 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 ?   12.5   0.0   4.3e-05     0.096      20      48 ..      48      76 ..      41      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                                  BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyv 48
                                  t+selA + ++ k++++ +++ Lv +G++
  gi|91774220|ref|YP_566912.1| 48 TISELASAMDVKKPSASVMVKKLVDMGLL 76
                                  89*************************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 ?   12.2   0.0   5.8e-05      0.13      24      55 .]      45      76 ..      42      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                        HTH_36 24 cfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  ++p+ + la+++ ++k ++s  +k+L++ G++
  gi|91774220|ref|YP_566912.1| 45 VNPTISELASAMDVKKPSASVMVKKLVDMGLL 76
                                  689***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1091.73
//
Query:       gi|91774221|ref|YP_566913.1|  [L=451]
Description: MATE efflux family protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-35  119.8  32.2    4.6e-21   75.2  11.4    3.3  4  MatE             MatE
    1.4e-08   34.9  15.6    1.4e-08   34.9  15.6    4.4  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2  11.4   5.1e-25   4.6e-21       4     161 .]      24     182 ..      21     182 .. 0.95
   2 ?   -0.5   1.9     0.094   8.4e+02      74     103 ..     196     225 ..     190     252 .. 0.57
   3 !   58.6  12.8   6.3e-20   5.7e-16       1     158 [.     243     403 ..     243     406 .. 0.93
   4 ?   -3.6   0.3      0.85   7.6e+03      82      90 ..     422     430 ..     411     439 .. 0.46

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 5.1e-25
                          MatE   4 lenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglillllls 83 
                                   + +++  +  +id +++g+  g+  lA+v+++ ++l  +++ ++ ++t+ ++lv+ +lG++n+kra++++  +l l+++l+
  gi|91774221|ref|YP_566913.1|  24 VGFIIGGVQITIDGYFIGNGvGTLGLASVTLVYPLLIGMIATAMLIGTGGASLVAIELGKGNRKRAHRIASDMLPLMFVLG 104
                                   555555555679999999988************************************************************ PP

                          MatE  84 liiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161
                                    ++a+l+l+f+e++l++++++ +v  +a++ylri+++g + l+  + l+  +r  g++ +++ ++++++  n++l+yl
  gi|91774221|ref|YP_566913.1| 105 TFFAILGLFFTEPLLRMVGATGTVFVMANDYLRIMFIGSICLIAGIGLDPLVRNDGRPNFAMKMMVVGAMTNVVLDYL 182
                                   ****************************************************************************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.094
                          MatE  74 qglilllllsliiallvllfseqilslftq 103
                                   +++i+++++s i+++ +++ +   l+l+ +
  gi|91774221|ref|YP_566913.1| 196 IATIIAFAVSMIAFVSYFFSRYAQLRLYLS 225
                                   456677777777666655555555555544 PP

  == domain 3  score: 58.6 bits;  conditional E-value: 6.3e-20
                          MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                   P++++++   +l l  ++++ r+ ++ a++++++    + ++f+++ g+s+++++++g + Gak ++r+++a+ ++++  +
  gi|91774221|ref|YP_566913.1| 243 PAFVMQASLGVLVLSYNYMLLRYgSEIAVSSYGVIEYSFAIFFMIFEGISAGVQPIIGFNHGAKLYDRVYVATKMAILSCF 323
                                   7888888888999999*******999******************************************************* PP

                          MatE  81 llsliiallvllfseqilslft.qdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipl 158
                                   l++l  ++l++ f+e i++lf+ +d+e+l+ a + +ri i+gi++ ++ +  + +++++ k k++l+i +  + ++ +pl
  gi|91774221|ref|YP_566913.1| 324 LVGLSGFILLYTFPETIIQLFNrNDPELLATAVEGMRIFIFGIIVEGVIISVAVYYQSVNKIKPSLFIHFGKIfIFILPL 403
                                   *********************834677*****************************************998776665555 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 0.85
                          MatE  82 lsliiallv 90 
                                   +++ ++l+v
  gi|91774221|ref|YP_566913.1| 422 VGIYLMLIV 430
                                   333333322 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   4.1      0.18   1.6e+03      87     132 ..      14      63 ..       5      74 .. 0.59
   2 !   34.9  15.6   1.6e-12   1.4e-08       1     139 [.     135     284 ..     135     288 .. 0.75
   3 !    7.2   6.9   0.00054       4.8       2      83 ..     359     441 ..     358     447 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.18
               Polysacc_synt_C  87 llrrllkpllaalvmgivvylllllllglllla....alalllavlvgal 132
                                   l+r++  p+++++++g+v +++  +++g   +     +++l+  +l+g++
  gi|91774221|ref|YP_566913.1|  14 LFRKFALPAVVGFIIGGVQITIDGYFIGNGVGTlglaSVTLVYPLLIGMI 63 
                                   57888888888888888844455555555444433322344444444444 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.6e-12
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavln.lyalr 78 
                                   +L+i+ ++ i+l   + l  +    gr+ +a+k +v+ga+ +++l +l++  +  g+ Gaaiat++a++v+++    y+ +
  gi|91774221|ref|YP_566913.1| 135 YLRIMFIGSICLIAGIGLDPLVRNDGRPNFAMKMMVVGAMTNVVLDYLFVMCWgmGMQGAAIATIIAFAVSMIAFvSYFFS 215
                                   5889999999999999999999999*************************7772367************9988775899** PP

               Polysacc_synt_C  79 rllgikl.........ellrrllkpllaalvmgiv..vylllllllgllllaalalllavlvgalvYlllll 139
                                   r+ +++l         +++  +lk+ + a+vm +   v+ l +  + l+ +   +++++   g++ Y ++++
  gi|91774221|ref|YP_566913.1| 216 RYAQLRLylsdispdiKIIAGILKTGFPAFVMQASlgVLVLSYNYMLLRYG--SEIAVSS-YGVIEYSFAIF 284
                                   *******99977777766666667777777777664322222222222222..3555555.66666666665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.00054
               Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavlnlyalrrl 80 
                                   ++i++++ii+ ++++ ++ + q++++ k  l + +  +++ +il ll+i   ++g++G+ +a  ++  +++++  ++  ++
  gi|91774221|ref|YP_566913.1| 359 MRIFIFGIIVEGVIISVAVYYQSVNKIKPSLFIHFGKIFI-FILPLLFIlpRYYGLTGVWMAAPVGIYLMLIVVGVMFLKE 438
                                   79**************************988877766665.4455555542566****99998888888888887776666 PP

               Polysacc_synt_C  81 lgi 83 
                                   ++i
  gi|91774221|ref|YP_566913.1| 439 IKI 441
                                   665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3205.07
//
Query:       gi|91774222|ref|YP_566914.1|  [L=334]
Description: trimethylamine:corrinoid methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-53  179.8   0.0    6.2e-53  179.5   0.0    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   0.0   3.5e-57   6.2e-53      31     338 ..      18     332 ..      10     334 .] 0.93

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 3.5e-57
                          MTTB  31 yellseeeleaieeaalriLeeiGiefldpealellkaaGakv..egervrfdrglvreliakapreftlharnPerdvei 109
                                   ++ +s+++l ai++a ++++++ Gi++ d+e+++l+k+aG++v  ++  v++++++vr +i +ap+++tl +r+ +++ + 
  gi|91774222|ref|YP_566914.1|  18 IDFFSDADLRAIDSATMDVFQNPGIQVSDAESRALFKEAGCDVneKTMVVKIPEHVVRRAIMTAPSKITLYGREKQHTFTQ 98 
                                   67899**************************************7556669****************************976 PP

                          MTTB 110 g.gknvvfapvagaPfvrDlerg....rregtledfrnlvkLaqmldvlhhsggtvvepvDvpvnkr.hldvlyakltlsd 184
                                   + g +v+++  +  + +  +e        ++t ed++n +++++ +d++ +++   v ++D   +   +++ +++ l+ ++
  gi|91774222|ref|YP_566914.1|  99 QaGGKVHYTCFGTGVKMCKYEAPgvfkTVDSTEEDLANTARVCDWADNIDSYS-LAVSARDWAGKGAqDVHETFTPLMNTS 178
                                   537788888888888888777632343789**********************9.7788***9987655************* PP

                          MTTB 185 kvfmgsvtekeraedsiemlrivfGaeeeefranpvvttiinvnsPlkfdetmlealeayaragqavivtpfilaGAmaPv 265
                                   k+f+ +    e++e   ++l++  G +ee+ r++p+  ++   +sPlk+ +++++ + + ++ g+++ v++  ++GA  Pv
  gi|91774222|ref|YP_566914.1| 179 KHFFHIDPVGENVEYYWDILKAYYGGDEEQARSRPIFSELLCPTSPLKIGTNACQLILKSVNFGIPINVISMAMSGASCPV 259
                                   ********************************************************************************* PP

                          MTTB 266 tvagavaqalAEaLagialtqlvrpgapviyGtftssvdlksGApafGtpeaalatlvagqlArrlglPlrss 338
                                    +ag+++  +AE+L+gi+l+ql  pga+v yG+ t+  dlk G    G+pe  l+++++++l+++++lP+ ++
  gi|91774222|ref|YP_566914.1| 260 HLAGTLVTHNAEVLSGIVLAQLASPGAKVWYGSSTTAFDLKHGTAPVGSPELGLISAAVAKLGQYYDLPTYVA 332
                                   *********************************************************************8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2333.67
//
Query:       gi|91774223|ref|YP_566915.1|  [L=147]
Description: trimethylamine:corrinoid methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-29   99.8   0.0    9.8e-29   99.7   0.0    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   5.4e-33   9.8e-29     362     500 ..       6     142 ..       1     144 [. 0.94

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 5.4e-33
                          MTTB 362 avlaganlvlhaAGwleggLvasyekfilDadvlgmiarllegievseealaldairevgpgghflgtahTlaryetafye 442
                                    +lagan  +  AG+le g+++s+e++++D+d++ m +++++gi+v++e+l+l++i++vg g++fl+++ T ++ +    +
  gi|91774223|ref|YP_566915.1|   6 PALAGANTLY-GAGMLELGMTFSMEQLMIDNDIISMGKKVMKGIPVNDETLGLASIQKVGIGNNFLAHKETRDNINL-VSS 84 
                                   5789***987.79*************************************************************976.579 PP

                          MTTB 443 pelsdnknfeeWeeeGakdaeerAnekvkkiLaeyeepkldeaideeLrdfiarrkae 500
                                   p ++d+  f++W+++G+kd++++A+ekv +iL+++e  ++d+++ + ++++++r  a+
  gi|91774223|ref|YP_566915.1|  85 PDIFDRDMFGDWAAAGSKDIATVAHEKVTEILKNHEVTPIDSDLVRDMKAVVDRADAD 142
                                   *****************************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1140.18
//
Query:       gi|91774224|ref|YP_566916.1|  [L=216]
Description: trimethylamine corrinoid protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-21   76.1   3.7    1.3e-20   73.7   1.2    2.2  2  B12-binding    B12 binding domain
    9.7e-21   74.0   1.4    1.9e-20   73.1   1.1    1.7  2  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.015   1.4e+02      39      57 ..      21      40 ..       6      61 .. 0.75
   2 !   73.7   1.2   1.4e-24   1.3e-20       2     120 ..      96     208 ..      95     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.015
                   B12-binding 39 en.edivaairaekpdvvgl 57
                                  e  e+i +++++ k+d+v l
  gi|91774224|ref|YP_566916.1| 21 ELvEEICEEAIEAKVDMVSL 40
                                  33699************987 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 1.4e-24
                   B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrirp 80 
                                   +++++t++gd+h++G++++a +l+ agf+V++lg +v   + v+a++++kp +vg Sal+t+++    ++ e+  +++ir+
  gi|91774224|ref|YP_566916.1|  96 TIVIGTIEGDIHSIGKDIVATMLKIAGFKVVDLGRDVAIGTYVDAVKEHKPMIVGSSALMTTTMILQMNIEEQlkEAGIRD 176
                                   6899*********************************************************************9999**** PP

                   B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                    v ++vGGa+++ d+++   + +g  d    ++e+a +a+
  gi|91774224|ref|YP_566916.1| 177 SVMTMVGGAPVTQDWAD---K-IG-SD---IYAENATDAV 208
                                   ****************9...7.99.66...5888887765 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   1.1   2.1e-24   1.9e-20       5      74 ..      11      80 ..       7      81 .. 0.96
   2 ?   -2.9   0.0       1.1     1e+04      12      30 ..     169     185 ..     167     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2.1e-24
                 B12-binding_2  5 lhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                   + a++++d+e +ee+++ea++++ + v +++d+l ++m+eVGd f++g+lflp+v+ ++e+m ++va+L
  gi|91774224|ref|YP_566916.1| 11 AKAAVMDFDDELVEEICEEAIEAKVDMVSLIQDGLTAGMNEVGDQFEQGTLFLPHVIAASEAMSAGVAIL 80
                                  578*******************99********************************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                 B12-binding_2  12 gdkegieelidealaqgsa 30 
                                   ++++gi++ + +++  g a
  gi|91774224|ref|YP_566916.1| 169 LKEAGIRDSVMTMV--GGA 185
                                   68888888888877..555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1438.41
//
Query:       gi|91774225|ref|YP_566917.1|  [L=347]
Description: trimethylamine transporter [Methanococcoides burtonii DSM 6242]
Scores for complete 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   44.6  49.4      5e-06   26.7  17.0    3.1  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  24.3   1.2e-08   0.00021       2     136 ..      17     177 ..      16     178 .. 0.75
   2 !   26.7  17.0   2.8e-10     5e-06       2     136 ..     193     335 ..     192     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-08
                          EamA   2 lgillallaalfwaiyfvlskil..lrkvspltltf.......vrfliagilllii.............allkegkl.... 56 
                                   +g+l+al  a++w+++++   i+  +  +++++++        + ++i +il +++             a+     l    
  gi|91774225|ref|YP_566917.1|  17 KGYLWALFCAILWGMWYIPGTIIwaVPPFDSMWVAIeatngasMATVIVAILISAFnaatvllalfvwnAV-----Lgkfg 92 
                                   79****************99998555555555555444444444444444444444666666654444422.....13333 PP

                          EamA  57 .aklslkd....wllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGv 132
                                     k +l++     ++++  +++g+ +a l  f+a+  ++a++a+++ +  Pv+  il+  ++ge+++++++lgi++i+ G 
  gi|91774225|ref|YP_566917.1|  93 eMKRTLREfrpcSKWFFMASIFGGPVAILGSFIAMGFIGAGFAAVAALGYPVVGSILARQWYGEQISKRTWLGILVIIGGG 173
                                   33334444678889999***************************************************************9 PP

                          EamA 133 llil 136
                                   ++i+
  gi|91774225|ref|YP_566917.1| 174 FVIF 177
                                   9986 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.8e-10
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfl....iagillliiallkegkl...aklslkdwlll.lllgllg 74 
                                   lg++  l aal w+i + ++ ++l   +p   +++rfl    i  i+ +++ +l + ++   a   l+++ +l l ++ ++
  gi|91774225|ref|YP_566917.1| 193 LGYIGGLMAALGWGIEGAIAGKGLDIAEPDVGLTLRFLgeniIWWIIIVPVVALAGYPIfeyAIAALNPLSILvLSFAGIA 273
                                   69999*************************999999997777777777777777777777775566666555546677789 PP

                          EamA  75 tvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   + ++++++++++  +++++   i +l  ++++i+ +l+  + ++++ ++g +l++lG ++++
  gi|91774225|ref|YP_566917.1| 274 FGFCYVAWYKSFPLVGVARGQGIGNLYGLCSVIFLYLFVAQVPSWTVIVGGALCILGSFVMM 335
                                   9999******************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2434.38
//
Query:       gi|91774226|ref|YP_566918.1|  [L=98]
Description: hypothetical protein Mbur_2312 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 714.03
//
Query:       gi|91774227|ref|YP_566919.1|  [L=484]
Description: trimethylamine:corrinoid methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-87  292.2   0.0    5.8e-87  291.8   0.0    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.8   0.0   3.2e-91   5.8e-87      33     488 ..       7     468 ..       3     476 .. 0.94

  Alignments for each domain:
  == domain 1  score: 291.8 bits;  conditional E-value: 3.2e-91
                          MTTB  33 llseeeleaieeaalriLeeiGiefldpealellkaaGakv..egervrfdrglvreliakapreftlharnPerdveigg 111
                                    l++e+ ++i++++ +iL e G+++ ++ al++l + G+ v  ++ +v+f++ +++++++ apr+++l +r  + d++i+ 
  gi|91774227|ref|YP_566919.1|   7 FLTKEDCKEIHDTSVDILGECGVKIESEYALDKLSDFGCIVnrKNSIVKFPKYVIDDCLRYAPRSIKLYGRASKYDIKIES 87 
                                   5889*************************************988999********************************** PP

                          MTTB 112 knvvfapvagaPfvrDlerg.rregtledfrnlvkLaqmldvlhhsggtvvepvDvpvnkrhldvlyakltlsdkvfmgsv 191
                                    ++  ++++g   ++D++++  r+g l+d+++ + +a+ ld++h++   +    Dvp ++    +l +  + ++k++  + 
  gi|91774227|ref|YP_566919.1|  88 GRTYTSTASGYG-IIDRNKKiARDGILNDVAEGTLVAENLDNIHSVIPFLTGVHDVPSEIASPIILGETFKNTNKTVEFYL 167
                                   **9999888865.66777777**************************999999**************************** PP

                          MTTB 192 tekera.......edsiemlrivfGaeeeefranpvvttiinvnsPlkfdetmlealeayaragqavivtpfilaGAmaPv 265
                                   t+ +++        ++i++ +iv+G ++e +r++p+++ +i++ sPl++ e+    l + +++g +++++p+il+G ++Pv
  gi|91774227|ref|YP_566919.1| 168 TGGSNIsstlkdmDNVIKLSKIVAGSTFE-LRKKPFLMFLISSISPLTYTEDQSRILFRTVEEGLPLVIMPAILSGMTGPV 247
                                   *98875222222156899***********.8************************************************** PP

                          MTTB 266 tvagavaqalAEaLagialtqlvrpgapviyGtftssvdlksGApafGtpeaalatlvagqlArrlglPlrssggltaskl 346
                                   t+ag+++q++AE Lag+++++ +++gapv+yG+  +  d+ +G  ++G+ e  l+++ ++q++ ++++P+ s    ++s +
  gi|91774227|ref|YP_566919.1| 248 TIAGTLVQSNAEFLAGLVMANSMKKGAPVMYGHSNTILDMHTGIYSGGAVEMGLISACIAQMGEYYDIPTNSYCPKSDSHI 328
                                   ********************************************************************************* PP

                          MTTB 347 pDaQaayesanslwaavlaganlvlhaAGwleggLvasyekfilDadvlgmiarllegievseealaldairevgpgghfl 427
                                    D Q +ye+a+  +   l+g+++    AG + +   +s+e++++D++v+gm+ r+ +gi+++ee+la d i+ +gpgg+++
  gi|91774227|ref|YP_566919.1| 329 SDQQVGYEKAIQWILGSLSGVSYL-SGAGCVTSESLVSLEQLVIDNEVIGMVNRVNDGINITEETLAGDLIKYIGPGGNYM 408
                                   **********************95.68999999999********************************************* PP

                          MTTB 428 gtahTlaryetafyepelsdnknfeeWeeeGakdaeerAnekvkkiLaeyeepkldeaide 488
                                    t+hT    ++++++p++s + ++ +W ++ +kd+ ++A+ +v++iL+  ++p  ++ i +
  gi|91774227|ref|YP_566919.1| 409 KTNHTTFWLNSEHFKPKISQKDSYTQWLNNEEKDIVDVAAINVENILEIEQSPVNNDVI-K 468
                                   ***********************************************877666554444.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3219.33
//
Query:       gi|91774228|ref|YP_566920.1|  [L=117]
Description: hypothetical protein Mbur_2314 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 779.34
//
Query:       gi|91774229|ref|YP_566921.1|  [L=214]
Description: phage integrase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   82.2   0.7    4.3e-23   82.0   0.7    1.1  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.7   2.4e-27   4.3e-23      16     170 ..      49     195 ..      18     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2.4e-27
                                   GCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHHCHCCTTTSB CS
               Phage_integrase  16 eeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellskaleeaeksel 96 
                                   ++    r+k+l+ ++++tG R+s++ls++ +d+d+e+++i+    ++K++k +++ l +  +  l +++ +     + s l
  gi|91774229|ref|YP_566921.1|  49 RD----RNKILMITMWATGGRVSDVLSIHESDIDFEEKTIKF--FVSKRKKWHTISLDSDTTLRLSNYIRTW----NISGL 119
                                   33....7788899****************************9..99*************************9....89999 PP

                                   SSBET..TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHH.HHHHCCC CS
               Phage_integrase  97 lfask..rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssistt.qiYthva 170
                                   lf s    +k + rq+v+ ++  +++ agi   ++pH +Rh +at Ll +gv+++ +++ l H+s +tt   Y++v+
  gi|91774229|ref|YP_566921.1| 120 LFQSIngSKKAMIRQSVNYMLDDYAQIAGIR-SIHPHLFRHGLATYLLSKGVPMEIIAYRLKHASTRTTaAFYARVT 195
                                   99988778999********************.*************************************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1399.00
//
Query:       gi|91774230|ref|YP_566922.1|  [L=573]
Description: tetratricopeptide protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-100  325.0  59.2    7.6e-13   47.7   0.9   11.2 11  TPR_1            Tetratricopeptide repeat
    1.2e-87  281.1  36.1    3.8e-10   39.1   0.5   11.3 11  TPR_2            Tetratricopeptide repeat
    1.9e-69  229.1  44.8    1.5e-10   40.6   1.2   11.6 12  TPR_11           TPR repeat
    3.7e-69  223.2  45.8    1.3e-08   34.4   0.2   11.2 11  TPR_8            Tetratricopeptide repeat
    1.3e-52  172.5  44.9    3.3e-06   27.1   0.3   10.5 10  TPR_17           Tetratricopeptide repeat
    1.7e-52  171.7  19.2    0.00018   21.3   0.0   11.2 11  TPR_7            Tetratricopeptide repeat
    2.5e-49  165.4  23.3    7.1e-07   29.4   0.5    9.7  9  TPR_12           Tetratricopeptide repeat
      5e-37  126.3   0.0    5.9e-08   33.2   0.1    6.3  6  TPR_16           Tetratricopeptide repeat
    3.3e-34  114.6   0.0     0.0093   16.7   0.1   10.6 10  TPR_14           Tetratricopeptide repeat
    4.7e-32  110.3   6.3      3e-05   24.4   0.5    6.5  7  TPR_19           Tetratricopeptide repeat
    3.8e-31  106.1  25.3     0.0032   17.3   0.3    9.9 10  TPR_10           Tetratricopeptide repeat
      2e-20   72.8  31.7    2.7e-06   27.5   3.2    5.4  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    5.2e-20   71.4   0.0    4.5e-05   23.5   0.0    6.2  9  TPR_9            Tetratricopeptide repeat
    1.7e-16   59.6   9.6        3.2    8.6   0.0   10.4 10  TPR_6            Tetratricopeptide repeat
    1.4e-13   50.6  22.1     0.0041   16.1   0.1    7.0  9  NARP1            NMDA receptor-regulated protein 1
    1.5e-12   47.5  22.0       0.57   10.4   0.1    9.4  9  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    5.6e-12   45.7  13.7      0.022   14.8   1.0    6.3  6  SRP_TPR_like     Putative TPR-like repeat
    3.6e-11   42.4   5.0        5.7    6.6   0.0    9.2  9  HTH_Bact         Helix-turn-helix bacterial domain
    3.7e-11   43.1   5.3        1.5    8.5   0.0    8.1  9  TPR_21           Tetratricopeptide repeat-like domain
      4e-10   39.6  19.8       0.56   10.3   0.0    8.7 10  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    9.4e-10   38.7   8.3        9.3    6.3   0.0    9.5  8  DUF3856          Domain of Unknown Function (DUF3856)
    9.4e-10   38.4  46.2       0.74    9.9   0.3   10.5 10  MIT              MIT (microtubule interacting and transport) 
    9.6e-09   34.9  22.8        9.1    6.8   0.0   10.2 10  PPR              PPR repeat
    2.3e-08   33.9  12.8         12    6.0   0.1    8.8  9  TPR_3            Tetratricopeptide repeat
    7.6e-08   32.9   0.1        1.8    9.0   0.1    5.1  4  BTAD             Bacterial transcriptional activator domain
      1e-05   24.9  10.4         39    3.8   0.0    8.7  9  SHNi-TPR         SHNi-TPR
     0.0004   20.6   0.6     0.0035   17.6   0.4    2.5  2  TPR_20           Tetratricopeptide repeat
     0.0017   19.0  13.2         92    3.9   0.0    9.0  9  Sel1             Sel1 repeat
     0.0034   17.5  17.4         64    3.9   0.0    8.7  8  PPR_2            PPR repeat family
     0.0069   15.6   0.0          3    7.0   0.1    3.8  5  TPR_15           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   15.9  14.7    2.5e+02    1.8  14.7    4.8  1  RhoGEF           RhoGEF domain
      0.023   13.7   0.9       0.43    9.5   0.1    2.9  4  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
       0.14   13.0  42.8         32    5.9   0.3    9.9  9  NSF              Aromatic-di-Alanine (AdAR) repeat
       0.31   11.4   3.3       0.93    9.8   0.3    2.5  2  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
       0.34   10.3   8.1      0.057   12.8   0.5    3.1  3  Coatomer_E       Coatomer epsilon subunit
        1.7    8.5  39.2         21    5.0   0.1    9.8 10  Sda              Sporulation inhibitor A


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 !   11.8   0.2   0.00032      0.16      21      34 .]     196     209 ..     196     209 .. 0.95
   2 !   29.0   0.1   1.2e-09     6e-07       4      30 ..     213     239 ..     211     243 .. 0.94
   3 !   45.9   0.7   5.6e-15   2.8e-12       4      34 .]     247     277 ..     245     277 .. 0.97
   4 !   40.7   0.5   2.5e-13   1.3e-10       4      34 .]     281     311 ..     278     311 .. 0.95
   5 !   28.9   0.2   1.3e-09   6.6e-07       4      30 ..     315     341 ..     312     345 .. 0.93
   6 !   47.7   0.9   1.5e-15   7.6e-13       4      34 .]     349     379 ..     347     379 .. 0.97
   7 !   40.7   0.5   2.5e-13   1.3e-10       4      34 .]     383     413 ..     380     413 .. 0.95
   8 !   31.2   0.0   2.5e-10   1.2e-07       3      30 ..     416     443 ..     414     447 .. 0.93
   9 !   33.9   1.6   3.4e-11   1.7e-08       4      34 .]     451     481 ..     449     481 .. 0.96
  10 !   46.2   1.4   4.4e-15   2.2e-12       3      34 .]     484     515 ..     482     515 .. 0.96
  11 ?    6.6   0.1     0.014       7.1       2      31 ..     517     546 ..     516     549 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHHSTTH CS
                         TPR_1  21 leyyekALelnPnn 34 
                                   l+yy kALe+nP+n
  gi|91774230|ref|YP_566922.1| 196 LDYYTKALEHNPDN 209
                                   79**********98 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.2e-09
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALel 30 
                                   + n+G a+ +l+kydeA+ +y+kA+e+
  gi|91774230|ref|YP_566922.1| 213 WSNKGDALCNLEKYDEAIGCYDKAIEI 239
                                   9*************************8 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 5.6e-15
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++n+Gna+ +l++ydeA+e+y+kA+e++P++
  gi|91774230|ref|YP_566922.1| 247 WNNKGNALCNLERYDEAIECYDKAIEIDPDF 277
                                   *****************************97 PP

  == domain 4  score: 40.7 bits;  conditional E-value: 2.5e-13
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++n+G a+ +l+kydeA+e+y+kA+e++P++
  gi|91774230|ref|YP_566922.1| 281 CNNKGDALCNLEKYDEAIECYDKAIEIDPDF 311
                                   79***************************97 PP

  == domain 5  score: 28.9 bits;  conditional E-value: 1.3e-09
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALel 30 
                                   ++n+G a+ +l++y+eA+e+y+kA+e 
  gi|91774230|ref|YP_566922.1| 315 CNNKGDALCNLERYNEAIECYDKAIEM 341
                                   79***********************96 PP

  == domain 6  score: 47.7 bits;  conditional E-value: 1.5e-15
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++n+Gna+f+l+ky++A+e+y+kA+e++P++
  gi|91774230|ref|YP_566922.1| 349 WNNKGNAHFNLEKYNKAIECYDKAIEIDPDF 379
                                   *****************************97 PP

  == domain 7  score: 40.7 bits;  conditional E-value: 2.5e-13
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++n+G a+ +l+kydeA+e+y+kA+e++P++
  gi|91774230|ref|YP_566922.1| 383 CNNKGDALCNLEKYDEAIECYDKAIEIDPDF 413
                                   79***************************97 PP

  == domain 8  score: 31.2 bits;  conditional E-value: 2.5e-10
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                    + n+G a+ +l+++deA+e+y+kALe+
  gi|91774230|ref|YP_566922.1| 416 YWGNKGDALCNLERHDEAIECYDKALEI 443
                                   69*************************9 PP

  == domain 9  score: 33.9 bits;  conditional E-value: 3.4e-11
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++n+Gna+ +l++y+eA+e+y+k Le++P++
  gi|91774230|ref|YP_566922.1| 451 CNNKGNALCNLERYNEAIECYDKTLEIYPDF 481
                                   79***************************97 PP

  == domain 10  score: 46.2 bits;  conditional E-value: 4.4e-15
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +++n+Gna+++l++y+eA+e+y+kALe +Pn+
  gi|91774230|ref|YP_566922.1| 484 CWNNKGNALYYLERYNEAIECYDKALEMDPND 515
                                   7*****************************97 PP

  == domain 11  score: 6.6 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                   +a+y  + ++ k+g+ +eAl    k +el+
  gi|91774230|ref|YP_566922.1| 517 DAWYASASIFSKNGNKEEALYRLAKSIELD 546
                                   79*****************97666666666 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1      0.01       5.1      21      34 .]     196     209 ..     196     209 .. 0.92
   2 !   24.8   0.0   2.8e-08   1.4e-05       3      31 ..     212     240 ..     211     243 .. 0.94
   3 !   36.6   0.2   4.8e-12   2.4e-09       3      33 ..     246     276 ..     245     277 .. 0.96
   4 !   33.4   0.1   5.1e-11   2.5e-08       3      33 ..     280     310 ..     278     311 .. 0.95
   5 !   25.1   0.0   2.3e-08   1.1e-05       3      30 ..     314     341 ..     312     345 .. 0.92
   6 !   36.3   0.2   6.1e-12     3e-09       3      33 ..     348     378 ..     347     379 .. 0.96
   7 !   33.4   0.1   5.1e-11   2.5e-08       3      33 ..     382     412 ..     380     413 .. 0.95
   8 !   25.0   0.0   2.5e-08   1.2e-05       3      31 ..     416     444 ..     414     447 .. 0.92
   9 !   28.0   0.2   2.6e-09   1.3e-06       3      33 ..     450     480 ..     448     481 .. 0.95
  10 !   39.1   0.5   7.6e-13   3.8e-10       3      34 .]     484     515 ..     482     515 .. 0.96
  11 !   11.4   0.1   0.00057      0.29       2      32 ..     517     547 ..     516     549 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                         TPR_2  21 leafekAleldPnn 34 
                                   l+++ kAle++P+n
  gi|91774230|ref|YP_566922.1| 196 LDYYTKALEHNPDN 209
                                   58**********98 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 2.8e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                   ++ n G+a+ +l +y+eA+ +++kA+e+ 
  gi|91774230|ref|YP_566922.1| 212 YWSNKGDALCNLEKYDEAIGCYDKAIEIS 240
                                   79*************************86 PP

  == domain 3  score: 36.6 bits;  conditional E-value: 4.8e-12
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   +++n G+a+ +l +y+eA+e+++kA+e+dP+
  gi|91774230|ref|YP_566922.1| 246 YWNNKGNALCNLERYDEAIECYDKAIEIDPD 276
                                   7*****************************8 PP

  == domain 4  score: 33.4 bits;  conditional E-value: 5.1e-11
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   +++n G+a+ +l +y+eA+e+++kA+e+dP+
  gi|91774230|ref|YP_566922.1| 280 YCNNKGDALCNLEKYDEAIECYDKAIEIDPD 310
                                   799***************************8 PP

  == domain 5  score: 25.1 bits;  conditional E-value: 2.3e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                   +++n G+a+ +l +y+eA+e+++kA+e 
  gi|91774230|ref|YP_566922.1| 314 YCNNKGDALCNLERYNEAIECYDKAIEM 341
                                   799***********************97 PP

  == domain 6  score: 36.3 bits;  conditional E-value: 6.1e-12
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   +++n G+a+++l +y++A+e+++kA+e+dP+
  gi|91774230|ref|YP_566922.1| 348 YWNNKGNAHFNLEKYNKAIECYDKAIEIDPD 378
                                   7*****************************8 PP

  == domain 7  score: 33.4 bits;  conditional E-value: 5.1e-11
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   +++n G+a+ +l +y+eA+e+++kA+e+dP+
  gi|91774230|ref|YP_566922.1| 382 YCNNKGDALCNLEKYDEAIECYDKAIEIDPD 412
                                   799***************************8 PP

  == domain 8  score: 25.0 bits;  conditional E-value: 2.5e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                   ++ n G+a+ +l +++eA+e+++kAle+ 
  gi|91774230|ref|YP_566922.1| 416 YWGNKGDALCNLERHDEAIECYDKALEIS 444
                                   799************************86 PP

  == domain 9  score: 28.0 bits;  conditional E-value: 2.6e-09
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   +++n G+a+ +l +y+eA+e+++k le++P+
  gi|91774230|ref|YP_566922.1| 450 YCNNKGNALCNLERYNEAIECYDKTLEIYPD 480
                                   689***************************8 PP

  == domain 10  score: 39.1 bits;  conditional E-value: 7.6e-13
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +++n G+a+y+l +y+eA+e+++kAle dPn+
  gi|91774230|ref|YP_566922.1| 484 CWNNKGNALYYLERYNEAIECYDKALEMDPND 515
                                   7*****************************97 PP

  == domain 11  score: 11.4 bits;  conditional E-value: 0.00057
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                   +a+y+ + +  k+g+ eeAl  + k++eld 
  gi|91774230|ref|YP_566922.1| 517 DAWYASASIFSKNGNKEEALYRLAKSIELDD 547
                                   69***************************96 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.9   1.9e+03      21      34 ..     175     188 ..     175     188 .. 0.89
   2 !    9.4   0.2    0.0017      0.84      17      38 ..     199     220 ..     196     223 .. 0.92
   3 !   26.6   0.2   6.8e-09   3.4e-06       1      38 [.     217     254 ..     217     257 .. 0.96
   4 !   33.3   0.4   5.8e-11   2.9e-08       1      37 [.     251     287 ..     251     288 .. 0.93
   5 !   34.0   0.3   3.3e-11   1.7e-08       1      38 [.     285     322 ..     285     324 .. 0.93
   6 !   30.0   0.1   6.2e-10   3.1e-07       1      41 [.     319     359 ..     319     360 .. 0.97
   7 !   31.7   0.8   1.8e-10   8.8e-08       1      37 [.     353     389 ..     353     390 .. 0.93
   8 !   33.8   0.3   3.9e-11     2e-08       1      37 [.     387     423 ..     387     424 .. 0.93
   9 !   19.3   0.0   1.3e-06   0.00067       1      26 [.     421     446 ..     421     447 .. 0.93
  10 !   25.3   0.8   1.8e-08   8.9e-06       1      39 [.     455     493 ..     455     494 .. 0.98
  11 !   40.6   1.2   2.9e-13   1.5e-10       1      42 []     489     530 ..     489     530 .. 0.97
  12 ?    2.7   0.1      0.21     1e+02       4      26 ..     526     548 ..     523     551 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.9
                        TPR_11  21 lkldPdnaeayynL 34 
                                   l++d+d a++++n+
  gi|91774230|ref|YP_566922.1| 175 LEFDSDAATIFLNI 188
                                   799*******9985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0017
                        TPR_11  17 YkkAlkldPdnaeayynLGlay 38 
                                   Y kAl+ +Pdn + ++n G+a+
  gi|91774230|ref|YP_566922.1| 199 YTKALEHNPDNDSYWSNKGDAL 220
                                   89*****************997 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 6.8e-09
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                   Gda++ + ky+eAi +Y kA++++ d+   ++n G+a+
  gi|91774230|ref|YP_566922.1| 217 GDALCNLEKYDEAIGCYDKAIEISTDFDMYWNNKGNAL 254
                                   9***********************************97 PP

  == domain 4  score: 33.3 bits;  conditional E-value: 5.8e-11
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                   G+a++ + +y+eAie+Y kA+++dPd+ +  +n G+a
  gi|91774230|ref|YP_566922.1| 251 GNALCNLERYDEAIECYDKAIEIDPDFSSYCNNKGDA 287
                                   9*************************99888888877 PP

  == domain 5  score: 34.0 bits;  conditional E-value: 3.3e-11
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                   Gda++ + ky+eAie+Y kA+++dPd+ +  +n G+a+
  gi|91774230|ref|YP_566922.1| 285 GDALCNLEKYDEAIECYDKAIEIDPDFSSYCNNKGDAL 322
                                   9*************************999998888875 PP

  == domain 6  score: 30.0 bits;  conditional E-value: 6.2e-10
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   Gda++ + +y+eAie+Y kA++ + d+   ++n G+a++++
  gi|91774230|ref|YP_566922.1| 319 GDALCNLERYNEAIECYDKAIEMSTDFDMYWNNKGNAHFNL 359
                                   9*************************************975 PP

  == domain 7  score: 31.7 bits;  conditional E-value: 1.8e-10
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                   G+a + + ky++Aie+Y kA+++dPd+ +  +n G+a
  gi|91774230|ref|YP_566922.1| 353 GNAHFNLEKYNKAIECYDKAIEIDPDFSSYCNNKGDA 389
                                   9*************************99888888877 PP

  == domain 8  score: 33.8 bits;  conditional E-value: 3.9e-11
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                   Gda++ + ky+eAie+Y kA+++dPd+ + + n G+a
  gi|91774230|ref|YP_566922.1| 387 GDALCNLEKYDEAIECYDKAIEIDPDFSSYWGNKGDA 423
                                   9*************************99988888877 PP

  == domain 9  score: 19.3 bits;  conditional E-value: 1.3e-06
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                                   Gda++ + + +eAie+Y kAl+++ d
  gi|91774230|ref|YP_566922.1| 421 GDALCNLERHDEAIECYDKALEISTD 446
                                   9*********************9865 PP

  == domain 10  score: 25.3 bits;  conditional E-value: 1.8e-08
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                   G+a++ + +y+eAie+Y k l++ Pd+ + ++n G+a+y
  gi|91774230|ref|YP_566922.1| 455 GNALCNLERYNEAIECYDKTLEIYPDFSSCWNNKGNALY 493
                                   9************************************98 PP

  == domain 11  score: 40.6 bits;  conditional E-value: 2.9e-13
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G+a+y + +y+eAie+Y kAl+ dP++ +a+y+ + ++ k+G
  gi|91774230|ref|YP_566922.1| 489 GNALYYLERYNEAIECYDKALEMDPNDDDAWYASASIFSKNG 530
                                   9********************************999999988 PP

  == domain 12  score: 2.7 bits;  conditional E-value: 0.21
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPd 26 
                                   + + G+ eeA+ ++ k ++ld +
  gi|91774230|ref|YP_566922.1| 526 FSKNGNKEEALYRLAKSIELDDS 548
                                   5678999*************966 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.5   1.2e+03      23      34 .]     198     209 ..     196     209 .. 0.87
   2 !   17.2   0.1   8.3e-06    0.0042       3      32 ..     212     241 ..     210     243 .. 0.93
   3 !   30.6   0.2   4.2e-10   2.1e-07       3      33 ..     246     276 ..     246     277 .. 0.96
   4 !   30.4   0.2     5e-10   2.5e-07       2      33 ..     279     310 ..     278     311 .. 0.95
   5 !   23.9   0.2     6e-08     3e-05       2      31 ..     313     342 ..     312     345 .. 0.92
   6 !   34.4   0.2   2.6e-11   1.3e-08       3      33 ..     348     378 ..     348     379 .. 0.97
   7 !   30.4   0.2     5e-10   2.5e-07       2      33 ..     381     412 ..     380     413 .. 0.95
   8 !   24.0   0.0   5.6e-08   2.8e-05       2      32 ..     415     445 ..     414     447 .. 0.93
   9 !   19.0   0.3   2.2e-06    0.0011       3      33 ..     450     480 ..     450     481 .. 0.95
  10 !   31.7   0.5   1.9e-10   9.7e-08       3      34 .]     484     515 ..     482     515 .. 0.95
  11 !    9.2   0.1     0.003       1.5       2      31 ..     517     546 ..     516     549 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.5
                                   HHHHHHHHHHH. CS
                         TPR_8  23 yyekaleldpdn 34 
                                   yy kale +pdn
  gi|91774230|ref|YP_566922.1| 198 YYTKALEHNPDN 209
                                   9******99986 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 8.3e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                   ++ n+g+++ +l++y+eA+ +y ka+e++ 
  gi|91774230|ref|YP_566922.1| 212 YWSNKGDALCNLEKYDEAIGCYDKAIEIST 241
                                   799************************985 PP

  == domain 3  score: 30.6 bits;  conditional E-value: 4.2e-10
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +++n+g+++ +l++y+eA+e+y ka+e+dpd
  gi|91774230|ref|YP_566922.1| 246 YWNNKGNALCNLERYDEAIECYDKAIEIDPD 276
                                   69****************************8 PP

  == domain 4  score: 30.4 bits;  conditional E-value: 5e-10
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++++n+g+++ +l++y+eA+e+y ka+e+dpd
  gi|91774230|ref|YP_566922.1| 279 SYCNNKGDALCNLEKYDEAIECYDKAIEIDPD 310
                                   589****************************8 PP

  == domain 5  score: 23.9 bits;  conditional E-value: 6e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   ++++n+g+++ +l++y+eA+e+y ka+e++
  gi|91774230|ref|YP_566922.1| 313 SYCNNKGDALCNLERYNEAIECYDKAIEMS 342
                                   589*************************98 PP

  == domain 6  score: 34.4 bits;  conditional E-value: 2.6e-11
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +++n+g+++++l++y++A+e+y ka+e+dpd
  gi|91774230|ref|YP_566922.1| 348 YWNNKGNAHFNLEKYNKAIECYDKAIEIDPD 378
                                   69****************************8 PP

  == domain 7  score: 30.4 bits;  conditional E-value: 5e-10
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++++n+g+++ +l++y+eA+e+y ka+e+dpd
  gi|91774230|ref|YP_566922.1| 381 SYCNNKGDALCNLEKYDEAIECYDKAIEIDPD 412
                                   589****************************8 PP

  == domain 8  score: 24.0 bits;  conditional E-value: 5.6e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                   +++ n+g+++ +l++++eA+e+y kale++ 
  gi|91774230|ref|YP_566922.1| 415 SYWGNKGDALCNLERHDEAIECYDKALEIST 445
                                   58**************************985 PP

  == domain 9  score: 19.0 bits;  conditional E-value: 2.2e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +++n+g+++ +l++y+eA+e+y k le+ pd
  gi|91774230|ref|YP_566922.1| 450 YCNNKGNALCNLERYNEAIECYDKTLEIYPD 480
                                   599**************************98 PP

  == domain 10  score: 31.7 bits;  conditional E-value: 1.9e-10
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    ++n+g+++  l++y+eA+e+y kale+dp++
  gi|91774230|ref|YP_566922.1| 484 CWNNKGNALYYLERYNEAIECYDKALEMDPND 515
                                   7*****************************96 PP

  == domain 11  score: 9.2 bits;  conditional E-value: 0.003
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   +a+y  +si +k g++eeA   + k +eld
  gi|91774230|ref|YP_566922.1| 517 DAWYASASIFSKNGNKEEALYRLAKSIELD 546
                                   69*****************76666666665 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.4     5e-08   2.5e-05       1      33 [.     198     230 ..     198     231 .. 0.97
   2 !   20.4   0.2   8.8e-07   0.00044       1      34 []     232     265 ..     232     265 .. 0.97
   3 !   21.2   0.2     5e-07   0.00025       1      34 []     266     299 ..     266     299 .. 0.97
   4 !   19.2   0.2   2.3e-06    0.0011       1      34 []     300     333 ..     300     333 .. 0.97
   5 !   12.9   0.3   0.00023      0.11       1      34 []     334     367 ..     334     367 .. 0.97
   6 !   21.2   0.2     5e-07   0.00025       1      34 []     368     401 ..     368     401 .. 0.97
   7 !   24.2   0.0   5.4e-08   2.7e-05       1      34 []     402     435 ..     402     435 .. 0.97
   8 !   10.5   0.5    0.0013      0.66       1      34 []     436     469 ..     436     469 .. 0.97
   9 !   19.6   0.5   1.6e-06   0.00078       1      34 []     470     503 ..     470     503 .. 0.96
  10 !   27.1   0.3   6.6e-09   3.3e-06       1      33 [.     504     536 ..     504     537 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5e-08
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +y+kale++P+n   + n++ +l+++ ++++A+
  gi|91774230|ref|YP_566922.1| 198 YYTKALEHNPDNDSYWSNKGDALCNLEKYDEAI 230
                                   6******************************97 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 8.8e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y ka+e+  +    +nn++++l+++ ++++A++
  gi|91774230|ref|YP_566922.1| 232 CYDKAIEISTDFDMYWNNKGNALCNLERYDEAIE 265
                                   8*******************************86 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 5e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y ka+e+dP+ +   nn++ +l+++ ++++A++
  gi|91774230|ref|YP_566922.1| 266 CYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIE 299
                                   8*******************************86 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 2.3e-06
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y ka+e+dP+ +   nn++ +l+++ ++ +A++
  gi|91774230|ref|YP_566922.1| 300 CYDKAIEIDPDFSSYCNNKGDALCNLERYNEAIE 333
                                   8*******************************86 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.00023
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y ka+e   +    +nn+++++ ++ ++ +A++
  gi|91774230|ref|YP_566922.1| 334 CYDKAIEMSTDFDMYWNNKGNAHFNLEKYNKAIE 367
                                   8******************************986 PP

  == domain 6  score: 21.2 bits;  conditional E-value: 5e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y ka+e+dP+ +   nn++ +l+++ ++++A++
  gi|91774230|ref|YP_566922.1| 368 CYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIE 401
                                   8*******************************86 PP

  == domain 7  score: 24.2 bits;  conditional E-value: 5.4e-08
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y ka+e+dP+ +  + n++ +l+++ ++++A++
  gi|91774230|ref|YP_566922.1| 402 CYDKAIEIDPDFSSYWGNKGDALCNLERHDEAIE 435
                                   8*******************************86 PP

  == domain 8  score: 10.5 bits;  conditional E-value: 0.0013
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y kale+  +     nn++++l+++ ++ +A++
  gi|91774230|ref|YP_566922.1| 436 CYDKALEISTDFGMYCNNKGNALCNLERYNEAIE 469
                                   8*******************************86 PP

  == domain 9  score: 19.6 bits;  conditional E-value: 1.6e-06
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y k le++P+ +  +nn++++l+ + ++ +A++
  gi|91774230|ref|YP_566922.1| 470 CYDKTLEIYPDFSSCWNNKGNALYYLERYNEAIE 503
                                   8*****************************9986 PP

  == domain 10  score: 27.1 bits;  conditional E-value: 6.6e-09
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +y kale dPn+ da++  A +++knG++++A+
  gi|91774230|ref|YP_566922.1| 504 CYDKALEMDPNDDDAWYASASIFSKNGNKEEAL 536
                                   8******************************97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.9     2e+03      20      33 ..     197     208 ..     196     212 .. 0.72
   2 !   16.7   0.0   1.1e-05    0.0055       3      28 ..     214     239 ..     211     244 .. 0.86
   3 !   21.1   0.0   4.2e-07   0.00021       2      31 ..     247     276 ..     247     280 .. 0.87
   4 !   21.3   0.0   3.5e-07   0.00018       2      31 ..     281     310 ..     279     314 .. 0.87
   5 !   17.6   0.1   5.6e-06    0.0028       2      29 ..     315     342 ..     313     346 .. 0.87
   6 !   19.4   0.0   1.5e-06   0.00073       2      31 ..     349     378 ..     349     382 .. 0.87
   7 !   21.3   0.0   3.7e-07   0.00018       2      31 ..     383     412 ..     381     415 .. 0.87
   8 !   17.8   0.1   4.7e-06    0.0023       3      30 ..     418     445 ..     415     448 .. 0.88
   9 !   16.1   0.0   1.7e-05    0.0085       2      29 ..     451     478 ..     451     483 .. 0.88
  10 !   17.9   0.1   4.2e-06    0.0021       1      34 [.     484     515 ..     484     517 .. 0.87
  11 ?    4.8   0.0     0.065        32       1      32 [.     518     549 ..     518     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.9
                         TPR_7  20 elyeqsLaltkdpe 33 
                                   ++y++  al+  p+
  gi|91774230|ref|YP_566922.1| 197 DYYTK--ALEHNPD 208
                                   79999..7776665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.1e-05
                         TPR_7   3 lnLarlysrlGdyeeAielyeqsLal 28 
                                   +n +++ ++l +y+eAi++y +++++
  gi|91774230|ref|YP_566922.1| 214 SNKGDALCNLEKYDEAIGCYDKAIEI 239
                                   799*******************7665 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 4.2e-07
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   ++n +++ ++l +y+eAie+y ++++++ d
  gi|91774230|ref|YP_566922.1| 247 WNNKGNALCNLERYDEAIECYDKAIEIDPD 276
                                   6899*******************7777665 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 3.5e-07
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   ++n +++ ++l +y+eAie+y ++++++ d
  gi|91774230|ref|YP_566922.1| 281 CNNKGDALCNLEKYDEAIECYDKAIEIDPD 310
                                   699********************7777665 PP

  == domain 5  score: 17.6 bits;  conditional E-value: 5.6e-06
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                   ++n +++ ++l +y eAie+y +++++ 
  gi|91774230|ref|YP_566922.1| 315 CNNKGDALCNLERYNEAIECYDKAIEMS 342
                                   699********************66654 PP

  == domain 6  score: 19.4 bits;  conditional E-value: 1.5e-06
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   ++n ++++++l +y +Aie+y ++++++ d
  gi|91774230|ref|YP_566922.1| 349 WNNKGNAHFNLEKYNKAIECYDKAIEIDPD 378
                                   6899*******************7777665 PP

  == domain 7  score: 21.3 bits;  conditional E-value: 3.7e-07
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   ++n +++ ++l +y+eAie+y ++++++ d
  gi|91774230|ref|YP_566922.1| 383 CNNKGDALCNLEKYDEAIECYDKAIEIDPD 412
                                   699********************7776655 PP

  == domain 8  score: 17.8 bits;  conditional E-value: 4.7e-06
                         TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltk 30 
                                    n +++ ++l +++eAie+y ++L++  
  gi|91774230|ref|YP_566922.1| 418 GNKGDALCNLERHDEAIECYDKALEIST 445
                                   799*******************998865 PP

  == domain 9  score: 16.1 bits;  conditional E-value: 1.7e-05
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                   ++n +++ ++l +y eAie+y + L++ 
  gi|91774230|ref|YP_566922.1| 451 CNNKGNALCNLERYNEAIECYDKTLEIY 478
                                   799********************77765 PP

  == domain 10  score: 17.9 bits;  conditional E-value: 4.2e-06
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                   +++n +++   l +y eAie+y +  al+ dp+d
  gi|91774230|ref|YP_566922.1| 484 CWNNKGNALYYLERYNEAIECYDK--ALEMDPND 515
                                   789*********************..77766665 PP

  == domain 11  score: 4.8 bits;  conditional E-value: 0.065
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                   a+++ a+++s+ G+ eeA+  + +s++l++++
  gi|91774230|ref|YP_566922.1| 518 AWYASASIFSKNGNKEEALYRLAKSIELDDSD 549
                                   67899**************9999977777665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.9e-05    0.0097       6      33 ..     213     240 ..     209     244 .. 0.91
   2 !   21.6   0.1   3.9e-07   0.00019       6      32 ..     247     273 ..     241     275 .. 0.91
   3 !   17.5   0.0   7.8e-06    0.0039       7      32 ..     282     307 ..     277     309 .. 0.91
   4 !   16.2   0.1   1.9e-05    0.0097       7      33 ..     316     342 ..     311     346 .. 0.89
   5 !   15.5   0.0   3.2e-05     0.016       6      32 ..     349     375 ..     344     376 .. 0.91
   6 !   17.4   0.0   8.1e-06     0.004       7      32 ..     384     409 ..     379     410 .. 0.91
   7 !   22.0   0.0   2.9e-07   0.00014       5      34 ..     416     445 ..     412     449 .. 0.88
   8 !   18.2   0.1   4.4e-06    0.0022       7      33 ..     452     478 ..     447     481 .. 0.91
   9 !   29.4   0.5   1.4e-09   7.1e-07       6      75 ..     485     546 ..     480     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-05
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleia 33 
                                   ++n +++l+ l++ydeA+ +++ka+ei 
  gi|91774230|ref|YP_566922.1| 213 WSNKGDALCNLEKYDEAIGCYDKAIEIS 240
                                   6799**********************97 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 3.9e-07
                        TPR_12   6 lnnlaavlrrlgrydeAlellekalei 32 
                                   +nn +++l+ l+rydeA+e+++ka+ei
  gi|91774230|ref|YP_566922.1| 247 WNNKGNALCNLERYDEAIECYDKAIEI 273
                                   568**********************98 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 7.8e-06
                        TPR_12   7 nnlaavlrrlgrydeAlellekalei 32 
                                   nn +++l+ l++ydeA+e+++ka+ei
  gi|91774230|ref|YP_566922.1| 282 NNKGDALCNLEKYDEAIECYDKAIEI 307
                                   479*********************98 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 1.9e-05
                        TPR_12   7 nnlaavlrrlgrydeAlellekaleia 33 
                                   nn +++l+ l+ry eA+e+++ka+e+ 
  gi|91774230|ref|YP_566922.1| 316 NNKGDALCNLERYNEAIECYDKAIEMS 342
                                   479*********************986 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 3.2e-05
                        TPR_12   6 lnnlaavlrrlgrydeAlellekalei 32 
                                   +nn +++++ l++y +A+e+++ka+ei
  gi|91774230|ref|YP_566922.1| 349 WNNKGNAHFNLEKYNKAIECYDKAIEI 375
                                   668**********************98 PP

  == domain 6  score: 17.4 bits;  conditional E-value: 8.1e-06
                        TPR_12   7 nnlaavlrrlgrydeAlellekalei 32 
                                   nn +++l+ l++ydeA+e+++ka+ei
  gi|91774230|ref|YP_566922.1| 384 NNKGDALCNLEKYDEAIECYDKAIEI 409
                                   479*********************98 PP

  == domain 7  score: 22.0 bits;  conditional E-value: 2.9e-07
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiar 34 
                                    + n +++l+ l+r+deA+e+++kalei +
  gi|91774230|ref|YP_566922.1| 416 YWGNKGDALCNLERHDEAIECYDKALEIST 445
                                   4679***********************975 PP

  == domain 8  score: 18.2 bits;  conditional E-value: 4.4e-06
                        TPR_12   7 nnlaavlrrlgrydeAlellekaleia 33 
                                   nn +++l+ l+ry eA+e+++k lei+
  gi|91774230|ref|YP_566922.1| 452 NNKGNALCNLERYNEAIECYDKTLEIY 478
                                   379**********************98 PP

  == domain 9  score: 29.4 bits;  conditional E-value: 1.4e-09
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                   +nn +++l++l+ry eA+e+++kale+    +++d      + ++ + ++++ g+ eeAl++l ++++++
  gi|91774230|ref|YP_566922.1| 485 WNNKGNALYYLERYNEAIECYDKALEMD---PNDDD-----AWYASASIFSKNGNKEEALYRLAKSIELD 546
                                   679*************************...66666.....6788999******************9986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0014      0.68      19      63 ..     198     239 ..     196     243 .. 0.91
   2 !   22.3   0.0     3e-07   0.00015       3      66 ..     250     310 ..     247     312 .. 0.96
   3 !   19.2   0.0   2.8e-06    0.0014       3      66 ..     318     378 ..     316     378 .. 0.95
   4 !   26.4   0.0   1.6e-08   8.2e-06       3      64 ..     386     444 ..     384     446 .. 0.94
   5 !   11.3   0.0   0.00083      0.41       3      45 ..     454     493 ..     452     493 .. 0.93
   6 !   33.2   0.1   1.2e-10   5.9e-08       2      57 ..     487     540 ..     486     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0014
                        TPR_16  19 aleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                   +++ al+ +   Pd+   + ++gda+  +  ++eA+  y++a++ 
  gi|91774230|ref|YP_566922.1| 198 YYTKALEHN---PDNDSYWSNKGDALCNLEKYDEAIGCYDKAIEI 239
                                   7999*****...************************999999875 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3e-07
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   +++a+ ++ +yd+A++ ++ a++ d   Pd     +++gda+  +  ++eA++ y++a++ +pd
  gi|91774230|ref|YP_566922.1| 250 KGNALCNLERYDEAIECYDKAIEID---PDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPD 310
                                   7899999******************...**99*****************************997 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 2.8e-06
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   +++a+ ++ +y +A++ ++ a+++     d    ++++g+a++ +  + +A++ y++a++ +pd
  gi|91774230|ref|YP_566922.1| 318 KGDALCNLERYNEAIECYDKAIEMS---TDFDMYWNNKGNAHFNLEKYNKAIECYDKAIEIDPD 378
                                   7899999******************...88888****************************997 PP

  == domain 4  score: 26.4 bits;  conditional E-value: 1.6e-08
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                   +++a+ ++ +yd+A++ ++ a++ d   Pd    + ++gda+  + r++eA++ y++al+ +
  gi|91774230|ref|YP_566922.1| 386 KGDALCNLEKYDEAIECYDKAIEID---PDFSSYWGNKGDALCNLERHDEAIECYDKALEIS 444
                                   7899999******************...******************************9865 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00083
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45 
                                   +++a+ ++ +y +A++ ++ +l+ +   Pd    ++++g+a++
  gi|91774230|ref|YP_566922.1| 454 KGNALCNLERYNEAIECYDKTLEIY---PDFSSCWNNKGNALY 493
                                   7899999******************...99999*******997 PP

  == domain 6  score: 33.2 bits;  conditional E-value: 1.2e-10
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.aly 57 
                                   ++++a++++ +y +A++ ++ al++d   P + +A+++++ ++ ++g+ +eA+  l 
  gi|91774230|ref|YP_566922.1| 487 NKGNALYYLERYNEAIECYDKALEMD---PNDDDAWYASASIFSKNGNKEEALyRLA 540
                                   579***********************...***********************95555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.21   1.1e+02      22      39 ..     197     214 ..     196     219 .. 0.84
   2 !    9.2   0.0    0.0049       2.4       8      38 ..     217     247 ..     212     253 .. 0.87
   3 !   13.4   0.0   0.00021       0.1       9      34 ..     252     277 ..     247     282 .. 0.89
   4 !   12.4   0.0   0.00047      0.23       9      34 ..     286     311 ..     284     316 .. 0.89
   5 ?    5.7   0.0     0.067        33       9      38 ..     320     349 ..     318     355 .. 0.86
   6 !    9.8   0.0    0.0031       1.5       8      34 ..     353     379 ..     348     383 .. 0.91
   7 !   15.7   0.0   3.8e-05     0.019       9      42 ..     388     421 ..     386     423 .. 0.88
   8 !    9.0   0.0    0.0057       2.8       9      33 ..     422     446 ..     420     450 .. 0.86
   9 ?    5.6   0.0      0.07        35       9      38 ..     456     485 ..     454     491 .. 0.86
  10 !   16.7   0.1   1.9e-05    0.0093       8      42 ..     489     523 ..     485     525 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.21
                        TPR_14  22 allrralalaPddaeawl 39 
                                   +++ +al+++Pd++ +w 
  gi|91774230|ref|YP_566922.1| 197 DYYTKALEHNPDNDSYWS 214
                                   7899**********9995 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0049
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                                   ++al +l+++deAi ++++a++   d++ +w
  gi|91774230|ref|YP_566922.1| 217 GDALCNLEKYDEAIGCYDKAIEISTDFDMYW 247
                                   56888999****************9999988 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00021
                        TPR_14   9 eallalGdpdeAiallrralalaPdd 34 
                                    al +l+++deAi+++++a++ +Pd+
  gi|91774230|ref|YP_566922.1| 252 NALCNLERYDEAIECYDKAIEIDPDF 277
                                   678899******************97 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00047
                        TPR_14   9 eallalGdpdeAiallrralalaPdd 34 
                                   +al +l+++deAi+++++a++ +Pd+
  gi|91774230|ref|YP_566922.1| 286 DALCNLEKYDEAIECYDKAIEIDPDF 311
                                   6778899*****************97 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.067
                        TPR_14   9 eallalGdpdeAiallrralalaPddaeaw 38 
                                   +al +l+++ eAi+++++a++   d++ +w
  gi|91774230|ref|YP_566922.1| 320 DALCNLERYNEAIECYDKAIEMSTDFDMYW 349
                                   6778899**************999998888 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.0031
                        TPR_14   8 aeallalGdpdeAiallrralalaPdd 34 
                                   + a+++l+++ +Ai+++++a++ +Pd+
  gi|91774230|ref|YP_566922.1| 353 GNAHFNLEKYNKAIECYDKAIEIDPDF 379
                                   67999********************97 PP

  == domain 7  score: 15.7 bits;  conditional E-value: 3.8e-05
                        TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                   +al +l+++deAi+++++a++ +Pd+  +w   +
  gi|91774230|ref|YP_566922.1| 388 DALCNLEKYDEAIECYDKAIEIDPDFSSYWGNKG 421
                                   6778899*******************99997765 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.0057
                        TPR_14   9 eallalGdpdeAiallrralalaPd 33 
                                   +al +l+++deAi+++++al+   d
  gi|91774230|ref|YP_566922.1| 422 DALCNLERHDEAIECYDKALEISTD 446
                                   678899**************98765 PP

  == domain 9  score: 5.6 bits;  conditional E-value: 0.07
                        TPR_14   9 eallalGdpdeAiallrralalaPddaeaw 38 
                                    al +l+++ eAi+++++ l+ +Pd+   w
  gi|91774230|ref|YP_566922.1| 456 NALCNLERYNEAIECYDKTLEIYPDFSSCW 485
                                   5777899******************87766 PP

  == domain 10  score: 16.7 bits;  conditional E-value: 1.9e-05
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                   + al+ l+++ eAi+++++al+ +P+d++aw++ a
  gi|91774230|ref|YP_566922.1| 489 GNALYYLERYNEAIECYDKALEMDPNDDDAWYASA 523
                                   56888999***********************9877 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.9e-05     0.039      12      57 ..     197     242 ..     196     250 .. 0.90
   2 !   10.5   0.0    0.0014      0.69      33      59 ..     252     278 ..     245     284 .. 0.88
   3 !   23.9   0.0   8.9e-08   4.4e-05       6      60 ..     259     313 ..     257     316 .. 0.94
   4 !   20.1   0.0   1.3e-06   0.00067       6      57 ..     293     344 ..     291     352 .. 0.92
   5 !   22.2   0.0     3e-07   0.00015       6      62 ..     361     417 ..     359     421 .. 0.94
   6 !   14.7   0.0   6.7e-05     0.033       6      57 ..     429     480 ..     427     486 .. 0.95
   7 !   24.4   0.5   6.1e-08     3e-05       4      58 ..     495     549 ..     492     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.9e-05
                        TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   +++++al+++p+n+  + +  +al +l  +deA+ + d++ e   d
  gi|91774230|ref|YP_566922.1| 197 DYYTKALEHNPDNDSYWSNKGDALCNLEKYDEAIGCYDKAIEISTD 242
                                   789**********************************999887776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                        TPR_19  33 eallalgqldeAealLdalpeedpdda 59 
                                   +al +l ++deA+++ d++ e dpd +
  gi|91774230|ref|YP_566922.1| 252 NALCNLERYDEAIECYDKAIEIDPDFS 278
                                   79999*******************964 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 8.9e-08
                        TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                   +y+eA++ + +a++ dp+ +    +  +al +l  +deA+++ d++ e dpd + 
  gi|91774230|ref|YP_566922.1| 259 RYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPDFSS 313
                                   8***************************************************644 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 1.3e-06
                        TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   +y+eA++ + +a++ dp+ +    +  +al +l +++eA+++ d++ e+  d
  gi|91774230|ref|YP_566922.1| 293 KYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLERYNEAIECYDKAIEMSTD 344
                                   8********************************************9999888 PP

  == domain 5  score: 22.2 bits;  conditional E-value: 3e-07
                        TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   +y  A++ + +a++ dp+ +    +  +al +l  +deA+++ d++ e dpd + y+
  gi|91774230|ref|YP_566922.1| 361 KYNKAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPDFSSYW 417
                                   799*************************************************87665 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 6.7e-05
                        TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   +++eA++ + +al+ + + +    +  +al +l +++eA+++ d+ +e +pd
  gi|91774230|ref|YP_566922.1| 429 RHDEAIECYDKALEISTDFGMYCNNKGNALCNLERYNEAIECYDKTLEIYPD 480
                                   79***********************************************999 PP

  == domain 7  score: 24.4 bits;  conditional E-value: 6.1e-08
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                    ++y eA++ + +al+ dp++++a+++ A +  ++g+ +eA   L++  e d  d
  gi|91774230|ref|YP_566922.1| 495 LERYNEAIECYDKALEMDPNDDDAWYASASIFSKNGNKEEALYRLAKSIELDDSD 549
                                   579**************************************99998888777665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0075       3.7       7      31 ..     215     239 ..     214     241 .. 0.91
   2 !   15.7   0.2   2.1e-05      0.01       6      31 ..     248     273 ..     248     273 .. 0.97
   3 !   12.9   0.0   0.00016     0.078       4      31 ..     280     307 ..     278     307 .. 0.94
   4 !   13.4   0.1   0.00011     0.055       4      31 ..     314     341 ..     312     343 .. 0.93
   5 !   10.5   0.1   0.00088      0.44       6      31 ..     350     375 ..     350     375 .. 0.97
   6 !   12.9   0.0   0.00016     0.078       4      31 ..     382     409 ..     380     409 .. 0.94
   7 !   10.7   0.0   0.00078      0.39       9      31 ..     421     443 ..     418     445 .. 0.90
   8 !   17.3   0.3   6.5e-06    0.0032       3      32 ..     449     478 ..     448     478 .. 0.95
   9 !   14.7   0.3     4e-05      0.02       6      31 ..     486     511 ..     483     511 .. 0.94
  10 ?   -1.8   0.0       6.6   3.3e+03      13      30 ..     527     544 ..     523     545 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0075
                        TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                   N + al+++ +ydeA   +++a++i
  gi|91774230|ref|YP_566922.1| 215 NKGDALCNLEKYDEAIGCYDKAIEI 239
                                   66889******************98 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.1e-05
                        TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                   nN +nal+++ rydeA + +++a++i
  gi|91774230|ref|YP_566922.1| 248 NNKGNALCNLERYDEAIECYDKAIEI 273
                                   899*********************97 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00016
                        TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                    +nN + al+++ +ydeA + +++a++i
  gi|91774230|ref|YP_566922.1| 280 YCNNKGDALCNLEKYDEAIECYDKAIEI 307
                                   579***********************97 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 0.00011
                        TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                    +nN + al+++ ry+eA + +++a+++
  gi|91774230|ref|YP_566922.1| 314 YCNNKGDALCNLERYNEAIECYDKAIEM 341
                                   579***********************98 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00088
                        TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                   nN +na++++ +y++A + +++a++i
  gi|91774230|ref|YP_566922.1| 350 NNKGNAHFNLEKYNKAIECYDKAIEI 375
                                   899*********************97 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.00016
                        TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                    +nN + al+++ +ydeA + +++a++i
  gi|91774230|ref|YP_566922.1| 382 YCNNKGDALCNLEKYDEAIECYDKAIEI 409
                                   579***********************97 PP

  == domain 7  score: 10.7 bits;  conditional E-value: 0.00078
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   + al+++ r+deA + +++al+i
  gi|91774230|ref|YP_566922.1| 421 GDALCNLERHDEAIECYDKALEI 443
                                   779******************98 PP

  == domain 8  score: 17.3 bits;  conditional E-value: 6.5e-06
                        TPR_10   3 sslnNLanalrqrgrydeAealleealair 32 
                                   + +nN +nal+++ ry+eA + ++++l+i+
  gi|91774230|ref|YP_566922.1| 449 MYCNNKGNALCNLERYNEAIECYDKTLEIY 478
                                   568*************************98 PP

  == domain 9  score: 14.7 bits;  conditional E-value: 4e-05
                        TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                   nN +nal+ + ry+eA + +++al++
  gi|91774230|ref|YP_566922.1| 486 NNKGNALYYLERYNEAIECYDKALEM 511
                                   99**********************96 PP

  == domain 10  score: -1.8 bits;  conditional E-value: 6.6
                        TPR_10  13 rqrgrydeAealleeala 30 
                                   ++ g+ +eA+  l ++++
  gi|91774230|ref|YP_566922.1| 527 SKNGNKEEALYRLAKSIE 544
                                   678999999988877776 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.8   2.1e-07   0.00011      16      81 ..     198     269 ..     180     270 .. 0.82
   2 !   21.7   3.2   3.4e-07   0.00017       4      81 ..     225     303 ..     223     304 .. 0.92
   3 !   21.5   3.9     4e-07    0.0002       4      81 ..     259     337 ..     258     338 .. 0.95
   4 !   27.5   3.2   5.4e-09   2.7e-06       3      81 ..     326     405 ..     324     406 .. 0.91
   5 !   22.9   4.6   1.5e-07   7.4e-05       3      81 ..     428     507 ..     426     508 .. 0.92
   6 !   19.9   0.2   1.3e-06   0.00064       4      58 ..     497     552 ..     496     554 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.1e-07
                                   H....HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  16 l...aaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +   a e++ ++d+y+  ++ +l+++++y++A+  ++ka ++      ++  ++ +l  L++y+eAi +++k
  gi|91774230|ref|YP_566922.1| 198 YytkALEHNPDNDSYWsnKGDALCNLEKYDEAIGCYDKAiEISTDFDMYWNNKGNALCNLERYDEAIECYDK 269
                                   0454468999999***666********************777666669********************9987 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 3.4e-07
                                   -HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   4 nyknAiflaerllaaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +y++Ai +++++   e   + d y+  ++ +l+++++y++A+e ++ka ++++    ++  ++ +l  L+ky+eAi +++k
  gi|91774230|ref|YP_566922.1| 225 KYDEAIGCYDKAI--EISTDFDMYWnnKGNALCNLERYDEAIECYDKAiEIDPDFSSYCNNKGDALCNLEKYDEAIECYDK 303
                                   79***********..7777788888557********************99999999*********************9987 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 4e-07
                                   -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +y++Ai +++++ + +++ ++    ++ +l+++++y++A+e ++ka ++++    ++  ++ +l  L++y+eAi +++k
  gi|91774230|ref|YP_566922.1| 259 RYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIECYDKAiEIDPDFSSYCNNKGDALCNLERYNEAIECYDK 337
                                   8************999999999999*********************99999999*********************9987 PP

  == domain 4  score: 27.5 bits;  conditional E-value: 5.4e-09
                                   T-HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   ++y++Ai +++++   e   + d y+  ++ +++++++y++A+e ++ka ++++    ++  ++ +l  L+ky+eAi +++
  gi|91774230|ref|YP_566922.1| 326 ERYNEAIECYDKAI--EMSTDFDMYWnnKGNAHFNLEKYNKAIECYDKAiEIDPDFSSYCNNKGDALCNLEKYDEAIECYD 404
                                   79************..6666777888557********************99999999*********************998 PP

                                   S CS
                        ANAPC3  81 k 81 
                                   k
  gi|91774230|ref|YP_566922.1| 405 K 405
                                   7 PP

  == domain 5  score: 22.9 bits;  conditional E-value: 1.5e-07
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +++++Ai +++++l+ +t+       ++ +l+++++y++A+e ++k+ ++++    c+  ++ +l+ L++y+eAi +++k
  gi|91774230|ref|YP_566922.1| 428 ERHDEAIECYDKALEISTDFGMYCNNKGNALCNLERYNEAIECYDKTlEIYPDFSSCWNNKGNALYYLERYNEAIECYDK 507
                                   689***********8777777777779*************************************************9987 PP

  == domain 6  score: 19.9 bits;  conditional E-value: 1.3e-06
                                   -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHH CS
                        ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgc 58 
                                   +y++Ai +++++l+++++++++ y+ A  + +ng+ ++A++ l k+ +l+++++++
  gi|91774230|ref|YP_566922.1| 497 RYNEAIECYDKALEMDPNDDDAWYASASIFSKNGNKEEALYRLAKSiELDDSDKNS 552
                                   89*******************************************98998888766 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.58   2.9e+02      22      59 ..     203     240 ..     195     244 .. 0.81
   2 !    8.0   0.0    0.0063       3.1       8      61 ..     223     276 ..     218     287 .. 0.89
   3 !   14.5   0.0   5.8e-05     0.029       6      61 ..     255     310 ..     251     312 .. 0.95
   4 !   12.0   0.0   0.00037      0.18       7      59 ..     290     342 ..     285     346 .. 0.93
   5 !    8.6   0.0     0.004         2       8      61 ..     325     378 ..     320     388 .. 0.90
   6 !   15.3   0.0   3.4e-05     0.017       4      61 ..     355     412 ..     353     413 .. 0.96
   7 !   12.5   0.0   0.00025      0.12       7      59 ..     392     444 ..     387     447 .. 0.93
   8 !   23.5   0.0     9e-08   4.5e-05       6      65 ..     459     518 ..     455     525 .. 0.94
   9 ?    1.8   0.0      0.53   2.6e+02      25      64 ..     512     551 ..     511     557 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.58
                         TPR_9  22 lllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   l  +Pd  + +   G +l  l+ + +A+ + + +++++
  gi|91774230|ref|YP_566922.1| 203 LEHNPDNDSYWSNKGDALCNLEKYDEAIGCYDKAIEIS 240
                                   5667777788999999************9999999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0063
                         TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    e++++a+ +++  + +  d    +   G +l  l+++ +A+++ + +++++pd
  gi|91774230|ref|YP_566922.1| 223 LEKYDEAIGCYDKAIEISTDFDMYWNNKGNALCNLERYDEAIECYDKAIEIDPD 276
                                   5788889999999999988888899999************************97 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 5.8e-05
                         TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    + e++++a+++++  + ++Pd  +     G +l  l+ + +A+++ + +++++pd
  gi|91774230|ref|YP_566922.1| 255 CNLERYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPD 310
                                   57799*************************************************97 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00037
                         TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   + e++++a+++++  + ++Pd  +     G +l  l+++++A+++ + +++++
  gi|91774230|ref|YP_566922.1| 290 NLEKYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLERYNEAIECYDKAIEMS 342
                                   56899*******************************************99986 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.004
                         TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    e++ +a+++++  + +  d    +   G +++ l+ +++A+++ + +++++pd
  gi|91774230|ref|YP_566922.1| 325 LERYNEAIECYDKAIEMSTDFDMYWNNKGNAHFNLEKYNKAIECYDKAIEIDPD 378
                                   578889999999999999998899999************************997 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 3.4e-05
                         TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   ++ + e++ +a+++++  + ++Pd  +     G +l  l+ + +A+++ + +++++pd
  gi|91774230|ref|YP_566922.1| 355 AHFNLEKYNKAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPD 412
                                   78999***************************************************97 PP

  == domain 7  score: 12.5 bits;  conditional E-value: 0.00025
                         TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   + e++++a+++++  + ++Pd  + +   G +l  l++  +A+++ + +l+++
  gi|91774230|ref|YP_566922.1| 392 NLEKYDEAIECYDKAIEIDPDFSSYWGNKGDALCNLERHDEAIECYDKALEIS 444
                                   56899*******************************************99876 PP

  == domain 8  score: 23.5 bits;  conditional E-value: 9e-08
                         TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                    + e++ +a+++++  l + Pd  + +   G +l+ l+++++A+++ + +l+++p+++da
  gi|91774230|ref|YP_566922.1| 459 CNLERYNEAIECYDKTLEIYPDFSSCWNNKGNALYYLERYNEAIECYDKALEMDPNDDDA 518
                                   57799**************************************************99998 PP

  == domain 9  score: 1.8 bits;  conditional E-value: 0.53
                         TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                   +P+d + ++  + +  + G+ ++Al  L   ++l++++  
  gi|91774230|ref|YP_566922.1| 512 DPNDDDAWYASASIFSKNGNKEEALYRLAKSIELDDSDKN 551
                                   799999***********************99999987765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.73   3.7e+02       8      28 ..     218     238 ..     215     240 .. 0.80
   2 ?    7.6   0.0     0.013       6.4       9      32 ..     253     276 ..     249     276 .. 0.83
   3 ?    7.7   0.0     0.012         6       8      32 ..     286     310 ..     283     310 .. 0.84
   4 ?    1.8   0.0      0.92   4.6e+02       9      28 ..     321     340 ..     317     340 .. 0.79
   5 !    8.6   0.0    0.0064       3.2       7      32 ..     353     378 ..     351     378 .. 0.91
   6 ?    7.7   0.0     0.012         6       8      32 ..     388     412 ..     385     412 .. 0.84
   7 ?    2.4   0.0      0.59     3e+02       9      28 ..     423     442 ..     419     443 .. 0.78
   8 ?    7.8   0.0     0.011       5.5       9      32 ..     457     480 ..     453     480 .. 0.84
   9 ?    5.1   0.1     0.081        40       9      32 ..     491     514 ..     487     515 .. 0.80
  10 ?    1.9   0.0      0.84   4.2e+02       1       9 [.     534     542 ..     517     550 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.73
                                   HHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   8 lsyrklgdtdkAlealerlik 28 
                                    ++ +l ++d+A+  +++ i+
  gi|91774230|ref|YP_566922.1| 218 DALCNLEKYDEAIGCYDKAIE 238
                                   55666569*********9997 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                   ++ +l ++d+A+e +++ i+  Pd
  gi|91774230|ref|YP_566922.1| 253 ALCNLERYDEAIECYDKAIEIDPD 276
                                   5556569*************9997 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                    ++ +l ++d+A+e +++ i+  Pd
  gi|91774230|ref|YP_566922.1| 286 DALCNLEKYDEAIECYDKAIEIDPD 310
                                   56666569*************9997 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.92
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAlealerlik 28 
                                   ++ +l ++ +A+e +++ i+
  gi|91774230|ref|YP_566922.1| 321 ALCNLERYNEAIECYDKAIE 340
                                   56665699********9985 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0064
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                   + ++++l ++ kA+e +++ i+  Pd
  gi|91774230|ref|YP_566922.1| 353 GNAHFNLEKYNKAIECYDKAIEIDPD 378
                                   78999988**************9997 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                    ++ +l ++d+A+e +++ i+  Pd
  gi|91774230|ref|YP_566922.1| 388 DALCNLEKYDEAIECYDKAIEIDPD 412
                                   56666569*************9997 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.59
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAlealerlik 28 
                                   ++ +l ++d+A+e +++ ++
  gi|91774230|ref|YP_566922.1| 423 ALCNLERHDEAIECYDKALE 442
                                   56665699*******99876 PP

  == domain 8  score: 7.8 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                   ++ +l ++ +A+e +++ ++ YPd
  gi|91774230|ref|YP_566922.1| 457 ALCNLERYNEAIECYDKTLEIYPD 480
                                   55565599***************8 PP

  == domain 9  score: 5.1 bits;  conditional E-value: 0.081
                                   HHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                   +++ l ++ +A+e +++ ++  P+
  gi|91774230|ref|YP_566922.1| 491 ALYYLERYNEAIECYDKALEMDPN 514
                                   555555************998887 PP

  == domain 10  score: 1.9 bits;  conditional E-value: 0.84
                                   HHHHHHHHH CS
                         TPR_6   1 dAlyklals 9  
                                   +Aly+la+s
  gi|91774230|ref|YP_566922.1| 534 EALYRLAKS 542
                                   466666655 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.8         3   1.5e+03     401     426 ..     127     152 ..     112     182 .. 0.52
   2 ?    3.7   0.2     0.047        23      25      83 ..     165     221 ..     150     241 .. 0.66
   3 !    7.7   0.5    0.0029       1.5      35      98 ..     207     269 ..     184     272 .. 0.80
   4 !   12.7   0.2   8.9e-05     0.044      18      99 ..     224     304 ..     215     310 .. 0.82
   5 !   12.4   0.6   0.00011     0.056      18      99 ..     258     338 ..     252     343 .. 0.80
   6 !   13.1   1.1   6.7e-05     0.034      18      99 ..     292     372 ..     288     377 .. 0.81
   7 !   12.8   0.4     8e-05      0.04      19      98 ..     361     439 ..     358     442 .. 0.82
   8 !    9.9   0.0    0.0006       0.3      17      73 ..     427     483 ..     420     493 .. 0.77
   9 !   16.1   0.1   8.3e-06    0.0041     204     260 ..     494     550 ..     484     555 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3
                                   HHT-S-HHHHHHHHHHHHHHHHHHHH CS
                         NARP1 401 ksaelseaerkklrkkakkaekkaek 426
                                   +++e+s  +rk +r k k+ ek+++ 
  gi|91774230|ref|YP_566922.1| 127 EKKEISRLNRKIARDKRKRTEKELDV 152
                                   23344444444444444444444433 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.047
                                   HHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHH.HHHHHHHHH-TT-CHHHHHHHHHT. CS
                         NARP1  25 ehLeekekqivDklavketkaelllkLgrkeeAe.atyeaLlernpenskYyeglekakk 83 
                                   + L   e++   +l++    a + l++++  + e  +y++ le+np+n +Y+++   a+ 
  gi|91774230|ref|YP_566922.1| 165 NSL---ERRKNTNLEFDSDAATIFLNIEKIVNLElDYYTKALEHNPDNDSYWSNKGDALC 221
                                   333...44444567888888999999998877653789999**********998877774 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0029
                                   --HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHH CS
                         NARP1  35 vDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyde 98 
                                    D+ ++  +k++ l++L++++eA   y + +e  ++   Y+++  +a+  + e  ++  ++yd+
  gi|91774230|ref|YP_566922.1| 207 PDNDSYWSNKGDALCNLEKYDEAIGCYDKAIEISTDFDMYWNNKGNALC-NLERYDEAIECYDK 269
                                   567778889********************************99998885.33335666677765 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 8.9e-05
                                   THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHH CS
                         NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyde 98 
                                   +k++eA+   +++ +  +D   + ++k++ l++L+r++eA + y + +e  p+ s+Y ++   a+  + e+ ++  ++yd+
  gi|91774230|ref|YP_566922.1| 224 EKYDEAIGCYDKAIEISTDFDMYWNNKGNALCNLERYDEAIECYDKAIEIDPDFSSYCNNKGDALC-NLEKYDEAIECYDK 303
                                   6777888888888888889999999********************************999999985.33335677777776 PP

                                   T CS
                         NARP1  99 l 99 
                                   +
  gi|91774230|ref|YP_566922.1| 304 A 304
                                   5 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00011
                                   THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHH CS
                         NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyde 98 
                                   ++++eA+e  +++ +   D  ++ ++k++ l++L++++eA + y + +e  p+ s+Y ++   a+  + e  ++  ++yd+
  gi|91774230|ref|YP_566922.1| 258 ERYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPDFSSYCNNKGDALC-NLERYNEAIECYDK 337
                                   56777777777777777888999999*******************************999988885.33345777777777 PP

                                   T CS
                         NARP1  99 l 99 
                                   +
  gi|91774230|ref|YP_566922.1| 338 A 338
                                   6 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 6.7e-05
                                   THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHH CS
                         NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyde 98 
                                   +k++eA+e  +++ +   D  ++ ++k++ l++L+r++eA + y + +e+ ++   Y+++  +a+  + e+ ++  ++yd+
  gi|91774230|ref|YP_566922.1| 292 EKYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLERYNEAIECYDKAIEMSTDFDMYWNNKGNAHF-NLEKYNKAIECYDK 371
                                   567778877777777778889999999***************************999999888874.44446777788877 PP

                                   T CS
                         NARP1  99 l 99 
                                   +
  gi|91774230|ref|YP_566922.1| 372 A 372
                                   5 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 8e-05
                                   HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHH CS
                         NARP1  19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyde 98 
                                   k+++A+e  +++ +   D  ++ ++k++ l++L++++eA + y + +e  p+ s+Y+ +   a+  + e +++  ++yd+
  gi|91774230|ref|YP_566922.1| 361 KYNKAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPDFSSYWGNKGDALC-NLERHDEAIECYDK 439
                                   66777777777777777889999**********************************99999986.34446777888876 PP

  == domain 8  score: 9.9 bits;  conditional E-value: 0.0006
                                   HTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                         NARP1  17 agkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk 73 
                                    ++++eA+e  +++ +  +D   + ++k++ l++L+r++eA + y + le  p+ s+
  gi|91774230|ref|YP_566922.1| 427 LERHDEAIECYDKALEISTDFGMYCNNKGNALCNLERYNEAIECYDKTLEIYPDFSS 483
                                   467788888888888888888888888888888888888888888888888887655 PP

  == domain 9  score: 16.1 bits;  conditional E-value: 8.3e-06
                                   HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H CS
                         NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR 260
                                   +l+++++A+e+ dka+e +p+  + +++ a i+ + G+ ++A   + ++ +lD  D+
  gi|91774230|ref|YP_566922.1| 494 YLERYNEAIECYDKALEMDPNDDDAWYASASIFSKNGNKEEALYRLAKSIELDDSDK 550
                                   578999************************************************996 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 !   10.4   0.1    0.0012      0.58      12      40 ..     214     242 ..     207     258 .. 0.87
   2 ?    5.0   0.1     0.056        28      14      36 ..     250     272 ..     245     277 .. 0.83
   3 !    8.6   0.1    0.0044       2.2      12      36 ..     282     306 ..     274     313 .. 0.88
   4 !   10.4   0.1    0.0012      0.57      12      55 ..     316     360 ..     310     367 .. 0.84
   5 ?    2.6   0.1      0.32   1.6e+02      22      36 ..     360     374 ..     350     380 .. 0.83
   6 !    8.5   0.1    0.0047       2.3      12      36 ..     384     408 ..     377     413 .. 0.87
   7 ?    4.2   0.1     0.099        49      14      40 ..     420     446 ..     412     462 .. 0.83
   8 ?    3.1   0.0      0.22   1.1e+02      14      36 ..     454     476 ..     449     482 .. 0.81
   9 ?    4.2   0.1       0.1        52      14      36 ..     488     510 ..     480     514 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                     NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaaylse 40 
                                   s k d l    ky+eai c+ ka ++ ++
  gi|91774230|ref|YP_566922.1| 214 SNKGDALCNLEKYDEAIGCYDKAIEISTD 242
                                   6788999999*************998776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.056
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaaa 36 
                                   k + l    +y+eai c+ ka +
  gi|91774230|ref|YP_566922.1| 250 KGNALCNLERYDEAIECYDKAIE 272
                                   6677778889**********976 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0044
                     NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaa 36 
                                   + k d l    ky+eai c+ ka +
  gi|91774230|ref|YP_566922.1| 282 NNKGDALCNLEKYDEAIECYDKAIE 306
                                   6788999999************976 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0012
                     NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaaylse.amkltkseqaqlsle 55 
                                   + k d l    +y+eai c+ ka ++ ++  m   +  +a++ le
  gi|91774230|ref|YP_566922.1| 316 NNKGDALCNLERYNEAIECYDKAIEMSTDfDMYWNNKGNAHFNLE 360
                                   67889999999**************99994477788888888887 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.32
                     NRBF2_MIT  22 Gkyeeaischkkaaa 36 
                                    ky++ai c+ ka +
  gi|91774230|ref|YP_566922.1| 360 EKYNKAIECYDKAIE 374
                                   69**********976 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0047
                     NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaa 36 
                                   + k d l    ky+eai c+ ka +
  gi|91774230|ref|YP_566922.1| 384 NNKGDALCNLEKYDEAIECYDKAIE 408
                                   6788999999************976 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.099
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaaaylse 40 
                                   k d l    +++eai c+ ka ++ ++
  gi|91774230|ref|YP_566922.1| 420 KGDALCNLERHDEAIECYDKALEISTD 446
                                   67788888899**********998776 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.22
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaaa 36 
                                   k + l    +y+eai c+ k+ +
  gi|91774230|ref|YP_566922.1| 454 KGNALCNLERYNEAIECYDKTLE 476
                                   6677778889********99866 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.1
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaaa 36 
                                   k + l    +y+eai c+ ka +
  gi|91774230|ref|YP_566922.1| 488 KGNALYYLERYNEAIECYDKALE 510
                                   6666777789**********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 !   11.0   0.0   0.00066      0.33       6      66 ..     189     265 ..     186     270 .. 0.82
   2 ?    5.8   0.1     0.028        14       3      41 ..     265     305 ..     264     318 .. 0.75
   3 !   14.8   1.0   4.5e-05     0.022       3      68 ..     299     369 ..     297     375 .. 0.78
   4 ?    6.1   0.1     0.022        11       3      41 ..     367     407 ..     365     433 .. 0.79
   5 !   14.3   0.6   6.1e-05      0.03       3      69 ..     435     506 ..     400     518 .. 0.64
   6 !   14.3   1.1   6.2e-05     0.031       3      71 ..     435     508 ..     433     557 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00066
                  SRP_TPR_like   6 ekilrlegkelkkf.............kvvaliklekyeeaLkllkkgsalsedvrf...EkaYvlYklkkykkalk 66 
                                   eki++le + ++k              k  al +leky+ea+   +k+ ++s d  +    k  +l  l++y +a +
  gi|91774230|ref|YP_566922.1| 189 EKIVNLELDYYTKAlehnpdndsywsnKGDALCNLEKYDEAIGCYDKAIEISTDFDMywnNKGNALCNLERYDEAIE 265
                                   899999999999999999999999999******************99998887754322367788888888888865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.028
                  SRP_TPR_like   3 eeyekilrlegk..elkkfkvvaliklekyeeaLkllkkgs 41 
                                   e+y+k ++++ +   + + k  al +leky+ea++  +k+ 
  gi|91774230|ref|YP_566922.1| 265 ECYDKAIEIDPDfsSYCNNKGDALCNLEKYDEAIECYDKAI 305
                                   5688888886531145555999************9998875 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 4.5e-05
                  SRP_TPR_like   3 eeyekilrlegk..elkkfkvvaliklekyeeaLkllkkgsalsedvrf...EkaYvlYklkkykkalkil 68 
                                   e+y+k ++++ +   + + k  al +le+y+ea++  +k+ ++s d  +    k  +++ l+ky+ka +  
  gi|91774230|ref|YP_566922.1| 299 ECYDKAIEIDPDfsSYCNNKGDALCNLERYNEAIECYDKAIEMSTDFDMywnNKGNAHFNLEKYNKAIECY 369
                                   6788888887541145555999*****************9999987643234799************8765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.022
                  SRP_TPR_like   3 eeyekilrlegk..elkkfkvvaliklekyeeaLkllkkgs 41 
                                   e+y+k ++++ +   + + k  al +leky+ea++  +k+ 
  gi|91774230|ref|YP_566922.1| 367 ECYDKAIEIDPDfsSYCNNKGDALCNLEKYDEAIECYDKAI 407
                                   6788888887541145555999************9998875 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 6.1e-05
                  SRP_TPR_like   3 eeyekilrlegk..elkkfkvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkilk 69 
                                   e+y+k l+++++   + + k  al +le+y+ea++  +k+ ++    +++   k  +lY l++y++a +  +
  gi|91774230|ref|YP_566922.1| 435 ECYDKALEISTDfgMYCNNKGNALCNLERYNEAIECYDKTLEIYpdfSSCWNNKGNALYYLERYNEAIECYD 506
                                   456666665554223444477777777777777777777764431114566777777777777777766544 PP

  == domain 6  score: 14.3 bits;  conditional E-value: 6.2e-05
                  SRP_TPR_like   3 eeyekilrlegk..elkkfkvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkilkkv 71 
                                   e+y+k l+++++   + + k  al +le+y+ea++  +k+ ++    +++   k  +lY l++y++a +  +k+
  gi|91774230|ref|YP_566922.1| 435 ECYDKALEISTDfgMYCNNKGNALCNLERYNEAIECYDKTLEIYpdfSSCWNNKGNALYYLERYNEAIECYDKA 508
                                   678888888776335666799****************9998554222678999**************9887664 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 ?    5.4   0.0     0.027        14       1      17 [.     225     241 ..     225     244 .. 0.92
   2 ?    5.1   0.0     0.033        16       1      15 [.     259     273 ..     259     279 .. 0.93
   3 ?    4.5   0.0     0.052        26       1      15 [.     293     307 ..     293     313 .. 0.93
   4 ?    6.6   0.0     0.011       5.7       1      17 [.     327     343 ..     327     346 .. 0.92
   5 ?    3.7   0.0     0.096        48       1      15 [.     361     375 ..     361     381 .. 0.92
   6 ?    4.4   0.0     0.055        27       1      15 [.     395     409 ..     395     414 .. 0.94
   7 ?    1.8   0.0      0.37   1.9e+02       2      17 ..     430     445 ..     429     448 .. 0.88
   8 ?   -0.9   0.0       2.6   1.3e+03       1      15 [.     463     477 ..     463     480 .. 0.90
   9 ?    1.3   0.0      0.51   2.6e+02       1      15 [.     497     511 ..     497     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.027
                                   -HHHHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAieiSi 17 
                                   +Y+ea+   +kAieiS 
  gi|91774230|ref|YP_566922.1| 225 KYDEAIGCYDKAIEIST 241
                                   6**************95 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.033
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   rY+ea+e  +kAiei
  gi|91774230|ref|YP_566922.1| 259 RYDEAIECYDKAIEI 273
                                   7************98 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.052
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   +Y+ea+e  +kAiei
  gi|91774230|ref|YP_566922.1| 293 KYDEAIECYDKAIEI 307
                                   6************98 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.011
                                   -HHHHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAieiSi 17 
                                   rY+ea+e  +kAie+S 
  gi|91774230|ref|YP_566922.1| 327 RYNEAIECYDKAIEMST 343
                                   7*************995 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.096
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   +Y++a+e  +kAiei
  gi|91774230|ref|YP_566922.1| 361 KYNKAIECYDKAIEI 375
                                   6************98 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.055
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   +Y+ea+e  +kAiei
  gi|91774230|ref|YP_566922.1| 395 KYDEAIECYDKAIEI 409
                                   6************98 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHHHHHHH CS
                      HTH_Bact   2 YeeaLeqvnkAieiSi 17 
                                    +ea+e  +kA+eiS 
  gi|91774230|ref|YP_566922.1| 430 HDEAIECYDKALEIST 445
                                   699***********95 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 2.6
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   rY+ea+e  +k +ei
  gi|91774230|ref|YP_566922.1| 463 RYNEAIECYDKTLEI 477
                                   7******99999886 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 0.51
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   rY+ea+e  +kA+e+
  gi|91774230|ref|YP_566922.1| 497 RYNEAIECYDKALEM 511
                                   7***********985 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.051        25     151     174 ..     215     238 ..     203     244 .. 0.90
   2 ?    2.2   0.0      0.26   1.3e+02     150     174 ..     248     272 ..     243     277 .. 0.89
   3 !    8.5   0.0    0.0031       1.5     143     174 ..     276     306 ..     254     314 .. 0.73
   4 ?    5.2   0.0     0.031        15     148     175 ..     314     341 ..     309     348 .. 0.88
   5 ?    0.3   0.0         1     5e+02     150     174 ..     350     374 ..     344     380 .. 0.89
   6 !    7.6   0.0    0.0057       2.8     148     174 ..     382     408 ..     356     414 .. 0.84
   7 ?    6.6   0.0     0.011       5.6     150     174 ..     418     442 ..     412     459 .. 0.90
   8 ?   -1.2   0.0       2.9   1.4e+03     148     174 ..     450     476 ..     442     483 .. 0.88
   9 ?    1.9   0.0      0.33   1.6e+02     151     179 ..     487     515 ..     480     528 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.051
                        TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                    +GD+l + +k deA   Y++A++
  gi|91774230|ref|YP_566922.1| 215 NKGDALCNLEKYDEAIGCYDKAIE 238
                                   69********************97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.26
                        TPR_21 150 elrGDilvaqgkldeAraaYqaAla 174
                                   + +G++l + ++ deA + Y++A++
  gi|91774230|ref|YP_566922.1| 248 NNKGNALCNLERYDEAIECYDKAIE 272
                                   679********************97 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0031
                        TPR_21 143 afaalvaelrGDilvaqgkldeAraaYqaAla 174
                                    f+ ++ + +GD+l + +k deA + Y++A++
  gi|91774230|ref|YP_566922.1| 276 DFS-SYCNNKGDALCNLEKYDEAIECYDKAIE 306
                                   444.46678*********************97 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.031
                        TPR_21 148 vaelrGDilvaqgkldeAraaYqaAlaa 175
                                   + + +GD+l + ++ +eA + Y++A++ 
  gi|91774230|ref|YP_566922.1| 314 YCNNKGDALCNLERYNEAIECYDKAIEM 341
                                   55679********************985 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1
                        TPR_21 150 elrGDilvaqgkldeAraaYqaAla 174
                                   + +G+++++ +k ++A + Y++A++
  gi|91774230|ref|YP_566922.1| 350 NNKGNAHFNLEKYNKAIECYDKAIE 374
                                   679********************97 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0057
                        TPR_21 148 vaelrGDilvaqgkldeAraaYqaAla 174
                                   + + +GD+l + +k deA + Y++A++
  gi|91774230|ref|YP_566922.1| 382 YCNNKGDALCNLEKYDEAIECYDKAIE 408
                                   5678*********************97 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.011
                        TPR_21 150 elrGDilvaqgkldeAraaYqaAla 174
                                     +GD+l + ++ deA + Y++Al+
  gi|91774230|ref|YP_566922.1| 418 GNKGDALCNLERHDEAIECYDKALE 442
                                   579********************97 PP

  == domain 8  score: -1.2 bits;  conditional E-value: 2.9
                        TPR_21 148 vaelrGDilvaqgkldeAraaYqaAla 174
                                   + + +G++l + ++ +eA + Y++ l+
  gi|91774230|ref|YP_566922.1| 450 YCNNKGNALCNLERYNEAIECYDKTLE 476
                                   56789*****************99875 PP

  == domain 9  score: 1.9 bits;  conditional E-value: 0.33
                        TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleek 179
                                    +G++l+  ++ +eA + Y++Al+   ++
  gi|91774230|ref|YP_566922.1| 487 NKGNALYYLERYNEAIECYDKALEMDPND 515
                                   69*********************987765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.1     2e+03      23      35 ..     198     210 ..     196     212 .. 0.81
   2 ?   -1.4   0.0       5.2   2.6e+03      13      31 ..     222     240 ..     219     244 .. 0.79
   3 ?    6.8   0.0     0.014         7      13      35 ..     256     278 ..     252     280 .. 0.89
   4 ?    6.6   0.0     0.017       8.3      13      35 ..     290     312 ..     287     314 .. 0.89
   5 ?   -0.5   0.0       2.6   1.3e+03      13      31 ..     324     342 ..     321     346 .. 0.81
   6 !   10.3   0.0    0.0011      0.56      10      35 ..     355     380 ..     353     382 .. 0.94
   7 ?    6.6   0.0     0.017       8.3      13      35 ..     392     414 ..     389     416 .. 0.89
   8 ?   -1.4   0.0       5.2   2.6e+03      13      31 ..     426     444 ..     423     447 .. 0.82
   9 ?    5.1   0.1     0.047        23      13      35 ..     460     482 ..     456     484 .. 0.89
  10 !    9.2   0.1    0.0026       1.3      10      37 ..     491     518 ..     489     519 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.1
                                   HHHHHHHHTTS-H CS
                    Fis1_TPR_C  23 yvdalLeiEPenr 35 
                                   y    Le+ P+n 
  gi|91774230|ref|YP_566922.1| 198 YYTKALEHNPDND 210
                                   777899*****96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.2
                                   HHT-HHHHHHHHHHHHHHT CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiE 31 
                                    l +Y+eA  + d  +ei 
  gi|91774230|ref|YP_566922.1| 222 NLEKYDEAIGCYDKAIEIS 240
                                   6889999999999888875 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.014
                                   HHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                    l +Y+eA ++ d  +ei+P+++
  gi|91774230|ref|YP_566922.1| 256 NLERYDEAIECYDKAIEIDPDFS 278
                                   7899****************986 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.017
                                   HHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                    l +Y+eA ++ d  +ei+P+++
  gi|91774230|ref|YP_566922.1| 290 NLEKYDEAIECYDKAIEIDPDFS 312
                                   6899****************986 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.6
                                   HHT-HHHHHHHHHHHHHHT CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiE 31 
                                    l +Y+eA ++ d  +e+ 
  gi|91774230|ref|YP_566922.1| 324 NLERYNEAIECYDKAIEMS 342
                                   6899******999988875 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.0011
                                   HHHHHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenr 35 
                                   +h+ l +Y++A ++ d  +ei+P+++
  gi|91774230|ref|YP_566922.1| 355 AHFNLEKYNKAIECYDKAIEIDPDFS 380
                                   89*********************986 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.017
                                   HHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                    l +Y+eA ++ d  +ei+P+++
  gi|91774230|ref|YP_566922.1| 392 NLEKYDEAIECYDKAIEIDPDFS 414
                                   6899****************986 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 5.2
                                   HHT-HHHHHHHHHHHHHHT CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiE 31 
                                    l +++eA ++ d  Lei 
  gi|91774230|ref|YP_566922.1| 426 NLERHDEAIECYDKALEIS 444
                                   6889999999999999986 PP

  == domain 9  score: 5.1 bits;  conditional E-value: 0.047
                                   HHT-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                    l +Y+eA ++ d  Lei P+++
  gi|91774230|ref|YP_566922.1| 460 NLERYNEAIECYDKTLEIYPDFS 482
                                   7899****************986 PP

  == domain 10  score: 9.2 bits;  conditional E-value: 0.0026
                                   HHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQa 37 
                                   + y l +Y+eA ++ d  Le++P+   a
  gi|91774230|ref|YP_566922.1| 491 ALYYLERYNEAIECYDKALEMDPNDDDA 518
                                   568899*****************98765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.66   3.3e+02      94     118 ..      82     106 ..      76     130 .. 0.85
   2 ?    3.9   0.0       0.1        52      81     129 ..     195     239 ..     187     244 .. 0.77
   3 ?    4.9   0.0      0.05        25     105     128 ..     249     272 ..     213     276 .. 0.58
   4 ?    5.0   0.0     0.049        24      64     128 ..     253     272 ..     240     310 .. 0.57
   5 ?    6.3   0.0     0.019       9.3     103     130 ..     315     342 ..     276     352 .. 0.71
   6 ?    6.0   0.1     0.024        12      63     129 ..     388     443 ..     344     447 .. 0.74
   7 ?    5.6   0.1     0.032        16      66     129 ..     459     511 ..     447     514 .. 0.57
   8 ?    4.9   0.1      0.05        25      59     129 ..     486     511 ..     478     559 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.66
                                   THHHHHHHHHHHHHHHHHHTT-HHH CS
                       DUF3856  94 deGklWiaavfsravaleelGrkde 118
                                     G+ W+++ ++r++al +l r +e
  gi|91774230|ref|YP_566922.1|  82 KLGRTWMSVNIKRGQALPDLMRWAE 106
                                   5699*************99988766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                                   HHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  81 alryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                    l y+ +  e + d+ + W     +++ al +l ++dea+  + +a e+
  gi|91774230|ref|YP_566922.1| 195 ELDYYTKALEHNPDNDSYW----SNKGDALCNLEKYDEAIGCYDKAIEI 239
                                   5677777777777777777....47899999999999999999988886 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.05
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 105 sravaleelGrkdealkafrmage 128
                                   +++ al +l r+dea++ + +a e
  gi|91774230|ref|YP_566922.1| 249 NKGNALCNLERYDEAIECYDKAIE 272
                                   456666666666666666665555 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.049
                                   HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                   al++l rydea+e+ dka+                                             e
  gi|91774230|ref|YP_566922.1| 253 ALCNLERYDEAIECYDKAI---------------------------------------------E 272
                                   4444444444444444443.............................................2 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                       DUF3856 103 vfsravaleelGrkdealkafrmagemi 130
                                     +++ al +l r++ea++ + +a em 
  gi|91774230|ref|YP_566922.1| 315 CNNKGDALCNLERYNEAIECYDKAIEMS 342
                                   4567788888888888888888888875 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.024
                                   HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                   +al++l +ydea+e+ dka+       e++ d  + W     +++ al +l r+dea++ + +a e+
  gi|91774230|ref|YP_566922.1| 388 DALCNLEKYDEAIECYDKAI-------EIDPDFSSYW----GNKGDALCNLERHDEAIECYDKALEI 443
                                   45556666666665555554.......5666666666....46788888888888888888877775 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.032
                                   HHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  66 aklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                   ++l ry+ea+e+ dk+l+ +        d  + W     +++ al  l r++ea++ + +a em
  gi|91774230|ref|YP_566922.1| 459 CNLERYNEAIECYDKTLEIY-------PDFSSCW----NNKGNALYYLERYNEAIECYDKALEM 511
                                   55555555555555555332.......3333334....35666666666666666666666665 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.05
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  59 aglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       +al  l ry+ea+e+ dkal+                                             m
  gi|91774230|ref|YP_566922.1| 486 NNKGNALYYLERYNEAIECYDKALE---------------------------------------------M 511
                                   4455666666666666666666663.............................................3 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 ?   -1.2   0.0       4.3   2.2e+03      44      63 ..     112     131 ..      96     133 .. 0.72
   2 ?    7.2   0.1      0.01       5.1      17      32 ..     223     238 ..     222     240 .. 0.90
   3 !    8.6   0.2     0.004         2      18      32 ..     258     272 ..     256     273 .. 0.88
   4 !    9.9   0.3    0.0015      0.74      17      32 ..     291     306 ..     290     307 .. 0.89
   5 !    7.7   0.1    0.0074       3.7      18      32 ..     326     340 ..     324     342 .. 0.89
   6 !    7.5   0.3    0.0087       4.3      17      32 ..     359     374 ..     358     375 .. 0.89
   7 !    9.9   0.3    0.0015      0.74      17      32 ..     393     408 ..     392     409 .. 0.89
   8 ?    5.1   0.0     0.047        23      19      32 ..     429     442 ..     426     445 .. 0.86
   9 ?    3.7   0.0      0.13        63      18      32 ..     462     476 ..     459     485 .. 0.88
  10 ?    6.5   0.5     0.018       8.7      19      32 ..     497     510 ..     494     511 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.3
                           MIT  44 errellrekieeYleRaeeL 63 
                                    ++  +r+ +e+Yl+  +e+
  gi|91774230|ref|YP_566922.1| 112 LTKGDIRNIVEKYLKEKKEI 131
                                   67778999*****9976665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.01
                           MIT  17 agnyeeAlelYkeale 32 
                                    ++y+eA+ +Y +a+e
  gi|91774230|ref|YP_566922.1| 223 LEKYDEAIGCYDKAIE 238
                                   589************8 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.004
                           MIT  18 gnyeeAlelYkeale 32 
                                   + y+eA+e+Y +a+e
  gi|91774230|ref|YP_566922.1| 258 ERYDEAIECYDKAIE 272
                                   78************8 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0015
                           MIT  17 agnyeeAlelYkeale 32 
                                    ++y+eA+e+Y +a+e
  gi|91774230|ref|YP_566922.1| 291 LEKYDEAIECYDKAIE 306
                                   589************8 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0074
                           MIT  18 gnyeeAlelYkeale 32 
                                   + y eA+e+Y +a+e
  gi|91774230|ref|YP_566922.1| 326 ERYNEAIECYDKAIE 340
                                   68***********98 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.0087
                           MIT  17 agnyeeAlelYkeale 32 
                                    ++y +A+e+Y +a+e
  gi|91774230|ref|YP_566922.1| 359 LEKYNKAIECYDKAIE 374
                                   589************8 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0015
                           MIT  17 agnyeeAlelYkeale 32 
                                    ++y+eA+e+Y +a+e
  gi|91774230|ref|YP_566922.1| 393 LEKYDEAIECYDKAIE 408
                                   589************8 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.047
                           MIT  19 nyeeAlelYkeale 32 
                                     +eA+e+Y +ale
  gi|91774230|ref|YP_566922.1| 429 RHDEAIECYDKALE 442
                                   679*********98 PP

  == domain 9  score: 3.7 bits;  conditional E-value: 0.13
                           MIT  18 gnyeeAlelYkeale 32 
                                   + y eA+e+Y + le
  gi|91774230|ref|YP_566922.1| 462 ERYNEAIECYDKTLE 476
                                   68********99876 PP

  == domain 10  score: 6.5 bits;  conditional E-value: 0.018
                           MIT  19 nyeeAlelYkeale 32 
                                    y eA+e+Y +ale
  gi|91774230|ref|YP_566922.1| 497 RYNEAIECYDKALE 510
                                   7***********98 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.079        39       8      26 ..     218     236 ..     218     239 .. 0.88
   2 ?    6.8   0.0     0.018       9.1       8      27 ..     252     271 ..     252     274 .. 0.89
   3 ?    6.7   0.1     0.019       9.4       8      27 ..     286     305 ..     286     308 .. 0.88
   4 ?    4.8   0.1     0.077        39       8      28 ..     320     340 ..     320     342 .. 0.89
   5 ?   -0.4   0.0       3.5   1.8e+03       9      26 ..     355     372 ..     354     375 .. 0.78
   6 ?    6.7   0.1     0.019       9.4       8      27 ..     388     407 ..     388     410 .. 0.88
   7 ?    5.4   0.1      0.05        25       8      25 ..     422     439 ..     422     443 .. 0.89
   8 ?    4.1   0.0      0.13        65       8      25 ..     456     473 ..     456     477 .. 0.91
   9 ?   -0.5   0.1       3.8   1.9e+03      14      28 ..     496     510 ..     490     512 .. 0.76
  10 ?    0.9   0.0       1.3   6.7e+02       9      20 ..     525     536 ..     523     537 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.079
                           PPR   8 sgycknGkleeAlelfkeM 26 
                                   +++c   k++eA+ ++++ 
  gi|91774230|ref|YP_566922.1| 218 DALCNLEKYDEAIGCYDKA 236
                                   699************9985 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.018
                           PPR   8 sgycknGkleeAlelfkeMk 27 
                                   +++c   +++eA+e++++ +
  gi|91774230|ref|YP_566922.1| 252 NALCNLERYDEAIECYDKAI 271
                                   79**************9865 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.019
                           PPR   8 sgycknGkleeAlelfkeMk 27 
                                   +++c   k++eA+e++++ +
  gi|91774230|ref|YP_566922.1| 286 DALCNLEKYDEAIECYDKAI 305
                                   699*************9865 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.077
                           PPR   8 sgycknGkleeAlelfkeMke 28 
                                   +++c   ++ eA+e++++ +e
  gi|91774230|ref|YP_566922.1| 320 DALCNLERYNEAIECYDKAIE 340
                                   699*************98765 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 3.5
                           PPR   9 gycknGkleeAlelfkeM 26 
                                   ++    k+ +A+e++++ 
  gi|91774230|ref|YP_566922.1| 355 AHFNLEKYNKAIECYDKA 372
                                   6667789999***99985 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.019
                           PPR   8 sgycknGkleeAlelfkeMk 27 
                                   +++c   k++eA+e++++ +
  gi|91774230|ref|YP_566922.1| 388 DALCNLEKYDEAIECYDKAI 407
                                   699*************9865 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.05
                           PPR   8 sgycknGkleeAlelfke 25 
                                   +++c   +++eA+e++++
  gi|91774230|ref|YP_566922.1| 422 DALCNLERHDEAIECYDK 439
                                   699*************98 PP

  == domain 8  score: 4.1 bits;  conditional E-value: 0.13
                           PPR   8 sgycknGkleeAlelfke 25 
                                   +++c   ++ eA+e++++
  gi|91774230|ref|YP_566922.1| 456 NALCNLERYNEAIECYDK 473
                                   79**************97 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 3.8
                           PPR  14 GkleeAlelfkeMke 28 
                                    ++ eA+e++++ +e
  gi|91774230|ref|YP_566922.1| 496 ERYNEAIECYDKALE 510
                                   578999999998655 PP

  == domain 10  score: 0.9 bits;  conditional E-value: 1.3
                           PPR   9 gycknGkleeAl 20 
                                    ++knG+ eeAl
  gi|91774230|ref|YP_566922.1| 525 IFSKNGNKEEAL 536
                                   699********7 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.19        95      13      25 ..     222     234 ..     220     237 .. 0.87
   2 ?    4.1   0.0     0.095        48      13      25 ..     256     268 ..     254     276 .. 0.79
   3 ?    5.2   0.0     0.043        21      13      25 ..     290     302 ..     288     310 .. 0.80
   4 ?    2.0   0.0      0.45   2.2e+02      13      25 ..     324     336 ..     322     339 .. 0.87
   5 ?    5.0   0.1      0.05        25      12      25 ..     357     370 ..     355     378 .. 0.81
   6 ?    5.2   0.0     0.043        21      13      25 ..     392     404 ..     390     412 .. 0.80
   7 ?   -2.3   0.0       9.7   4.8e+03      18      25 ..     431     438 ..     426     442 .. 0.69
   8 ?    2.0   0.0      0.43   2.2e+02      13      25 ..     460     472 ..     458     476 .. 0.88
   9 ?    6.0   0.1     0.024        12      11      36 .]     492     515 ..     489     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.19
                                   HTT-HHHHHHH.. CS
                         TPR_3  13 nkkkyqeArelfs 25 
                                   n +ky+eA++ ++
  gi|91774230|ref|YP_566922.1| 222 NLEKYDEAIGCYD 234
                                   568******9976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.095
                                   HTT-HHHHHHH.. CS
                         TPR_3  13 nkkkyqeArelfs 25 
                                   n ++y+eA+e ++
  gi|91774230|ref|YP_566922.1| 256 NLERYDEAIECYD 268
                                   5689*******77 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.043
                                   HTT-HHHHHHH.. CS
                         TPR_3  13 nkkkyqeArelfs 25 
                                   n +ky+eA+e ++
  gi|91774230|ref|YP_566922.1| 290 NLEKYDEAIECYD 302
                                   568********77 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.45
                                   HTT-HHHHHHH.. CS
                         TPR_3  13 nkkkyqeArelfs 25 
                                   n ++y+eA+e ++
  gi|91774230|ref|YP_566922.1| 324 NLERYNEAIECYD 336
                                   5689******976 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.05
                                   HHTT-HHHHHHH.. CS
                         TPR_3  12 ynkkkyqeArelfs 25 
                                   +n +ky++A+e ++
  gi|91774230|ref|YP_566922.1| 357 FNLEKYNKAIECYD 370
                                   6889********77 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.043
                                   HTT-HHHHHHH.. CS
                         TPR_3  13 nkkkyqeArelfs 25 
                                   n +ky+eA+e ++
  gi|91774230|ref|YP_566922.1| 392 NLEKYDEAIECYD 404
                                   568********77 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 9.7
                                   HHHHHH.. CS
                         TPR_3  18 qeArelfs 25 
                                   +eA+e ++
  gi|91774230|ref|YP_566922.1| 431 DEAIECYD 438
                                   77887765 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.43
                                   HTT-HHHHHHH.. CS
                         TPR_3  13 nkkkyqeArelfs 25 
                                   n ++y+eA+e ++
  gi|91774230|ref|YP_566922.1| 460 NLERYNEAIECYD 472
                                   5689******976 PP

  == domain 9  score: 6.0 bits;  conditional E-value: 0.024
                                   HHHTT-HHHHHHH..HHHHHHH-TT- CS
                         TPR_3  11 fynkkkyqeArelfsYallaildken 36 
                                   +y  ++y+eA+e ++   +  +d+++
  gi|91774230|ref|YP_566922.1| 492 LYYLERYNEAIECYD--KALEMDPND 515
                                   78889********77..999888876 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.65   3.3e+02      83     124 ..     197     238 ..     186     245 .. 0.90
   2 ?    7.2   0.0     0.013       6.4      58     123 ..     274     339 ..     250     345 .. 0.82
   3 ?    7.3   0.0     0.012       5.9      60     124 ..     378     442 ..     358     449 .. 0.87
   4 !    9.0   0.1    0.0035       1.8      63     116 ..     483     536 ..     454     543 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.65
                                   HHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  83 aelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                   ++++++++++P ++ ++     Al+ +++  eA++ Y+++ +
  gi|91774230|ref|YP_566922.1| 197 DYYTKALEHNPDNDSYWSNKGDALCNLEKYDEAIGCYDKAIE 238
                                   6788999******************************98866 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          BTAD  58 eelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                   + ++ + +    +a+  l++++ea++ ++++++ +P    ++     Al+ ++r +eA+e Y+++ 
  gi|91774230|ref|YP_566922.1| 274 DPDFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLERYNEAIECYDKAI 339
                                   55566677788889999999999999999999999999999999999************9999876 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  60 lrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                   ++ + +    +a+  l++++ea++ ++++++ +P    ++     Al+ ++r  eA+e Y+++ +
  gi|91774230|ref|YP_566922.1| 378 DFSSYCNNKGDALCNLEKYDEAIECYDKAIEIDPDFSSYWGNKGDALCNLERHDEAIECYDKALE 442
                                   55667778889999**********************************************98865 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0035
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
                          BTAD  63 ealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                                   ++     +a+ +l+r++ea++ ++++++++P +++++ +      + G+++eAL
  gi|91774230|ref|YP_566922.1| 483 SCWNNKGNALYYLERYNEAIECYDKALEMDPNDDDAWYASASIFSKNGNKEEAL 536
                                   444555667777888888888888888888888888888888888888888887 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.1   5.5e+02      15      30 ..     224     239 ..     221     241 .. 0.90
   2 ?    3.8   0.0     0.079        39      15      30 ..     258     273 ..     255     273 .. 0.93
   3 ?    3.6   0.0      0.09        45      15      30 ..     292     307 ..     289     307 .. 0.93
   4 ?    1.5   0.0       0.4     2e+02      15      29 ..     326     340 ..     323     341 .. 0.90
   5 ?   -0.2   0.0       1.4   6.8e+02      15      30 ..     360     375 ..     357     375 .. 0.90
   6 ?    3.6   0.0      0.09        45      15      30 ..     394     409 ..     391     409 .. 0.93
   7 ?    1.6   0.0       0.4     2e+02      15      30 ..     428     443 ..     425     445 .. 0.91
   8 ?    2.0   0.0      0.28   1.4e+02      15      31 ..     462     478 ..     459     479 .. 0.91
   9 ?    3.4   0.0       0.1        52      15      29 ..     496     510 ..     495     511 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   e++++A+  ++ka+e+
  gi|91774230|ref|YP_566922.1| 224 EKYDEAIGCYDKAIEI 239
                                   99*****999999987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.079
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   e++++A+e ++ka+e+
  gi|91774230|ref|YP_566922.1| 258 ERYDEAIECYDKAIEI 273
                                   9************997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.09
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   e++++A+e ++ka+e+
  gi|91774230|ref|YP_566922.1| 292 EKYDEAIECYDKAIEI 307
                                   9************997 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.4
                      SHNi-TPR  15 enFpqAveDlrkaLe 29 
                                   e++++A+e ++ka+e
  gi|91774230|ref|YP_566922.1| 326 ERYNEAIECYDKAIE 340
                                   9*******9999987 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.4
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   e+++ A+e ++ka+e+
  gi|91774230|ref|YP_566922.1| 360 EKYNKAIECYDKAIEI 375
                                   89999***99999997 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.09
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   e++++A+e ++ka+e+
  gi|91774230|ref|YP_566922.1| 394 EKYDEAIECYDKAIEI 409
                                   9************997 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.4
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   e+ ++A+e ++kaLe+
  gi|91774230|ref|YP_566922.1| 428 ERHDEAIECYDKALEI 443
                                   7889**********98 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.28
                      SHNi-TPR  15 enFpqAveDlrkaLeLr 31 
                                   e++++A+e ++k Le++
  gi|91774230|ref|YP_566922.1| 462 ERYNEAIECYDKTLEIY 478
                                   9**********999996 PP

  == domain 9  score: 3.4 bits;  conditional E-value: 0.1
                      SHNi-TPR  15 enFpqAveDlrkaLe 29 
                                   e++++A+e ++kaLe
  gi|91774230|ref|YP_566922.1| 496 ERYNEAIECYDKALE 510
                                   9*************8 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.6   1.8e+03       7      42 ..     195     230 ..     192     241 .. 0.84
   2 !   17.6   0.4     7e-06    0.0035       7      62 ..     501     556 ..     496     562 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.6
                        TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAl 42 
                                   el+   +al+ npd+     +  +al   ++y+eA+
  gi|91774230|ref|YP_566922.1| 195 ELDYYTKALEHNPDNDSYWSNKGDALCNLEKYDEAI 230
                                   5666778999*****999999999999999999887 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7e-06
                        TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaark 62 
                                    ++  ++al+ +p+d da ++ A    ++g++eeAl +L + ++ d ++++ a+ +
  gi|91774230|ref|YP_566922.1| 501 AIECYDKALEMDPNDDDAWYASASIFSKNGNKEEALYRLAKSIELDDSDKNSAMND 556
                                   56677899**************************************9999888765 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0         1     5e+02      11      35 ..     246     272 ..     244     273 .. 0.70
   2 ?    2.4   0.0      0.54   2.7e+02      11      35 ..     280     306 ..     279     308 .. 0.76
   3 ?    3.9   0.0      0.18        92      11      36 ..     314     341 ..     313     342 .. 0.78
   4 ?    3.1   0.0      0.33   1.7e+02      11      35 ..     348     374 ..     346     376 .. 0.72
   5 ?    2.4   0.0      0.54   2.7e+02      11      35 ..     382     408 ..     381     410 .. 0.76
   6 ?   -0.2   0.0       3.7   1.9e+03      24      34 ..     431     441 ..     416     442 .. 0.82
   7 ?   -1.1   0.0       6.9   3.4e+03      10      32 ..     449     473 ..     448     474 .. 0.76
   8 ?    2.9   0.1      0.39     2e+02      23      37 ..     498     512 ..     486     513 .. 0.85
   9 ?   -1.3   0.0       8.2   4.1e+03       2       8 ..     534     540 ..     533     546 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1
                          Sel1  11 ylylnGl...gvpkDpekAiewyekAAe 35 
                                   y+  +G     +++ +++Aie+y kA e
  gi|91774230|ref|YP_566922.1| 246 YWNNKGNalcNLER-YDEAIECYDKAIE 272
                                   55555555533666.899*******975 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.54
                          Sel1  11 ylylnGl...gvpkDpekAiewyekAAe 35 
                                   y+  +G+    ++k +++Aie+y kA e
  gi|91774230|ref|YP_566922.1| 280 YCNNKGDalcNLEK-YDEAIECYDKAIE 306
                                   66677777633666.99********975 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.18
                          Sel1  11 ylylnGl...gvpkDpekAiewyekAAeq 36 
                                   y+  +G+    +++ +++Aie+y kA e+
  gi|91774230|ref|YP_566922.1| 314 YCNNKGDalcNLER-YNEAIECYDKAIEM 341
                                   67777777644777.99*********987 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.33
                          Sel1  11 ylylnGl..g.vpkDpekAiewyekAAe 35 
                                   y+  +G     ++k ++kAie+y kA e
  gi|91774230|ref|YP_566922.1| 348 YWNNKGNahFnLEK-YNKAIECYDKAIE 374
                                   56666665533566.99********975 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.54
                          Sel1  11 ylylnGl...gvpkDpekAiewyekAAe 35 
                                   y+  +G+    ++k +++Aie+y kA e
  gi|91774230|ref|YP_566922.1| 382 YCNNKGDalcNLEK-YDEAIECYDKAIE 408
                                   66677777633666.99********975 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 3.7
                          Sel1  24 ekAiewyekAA 34 
                                   ++Aie+y kA 
  gi|91774230|ref|YP_566922.1| 431 DEAIECYDKAL 441
                                   79*******96 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 6.9
                          Sel1  10 fylylnGl...gvpkDpekAiewyek 32 
                                   +y+  +G     +++ +++Aie+y k
  gi|91774230|ref|YP_566922.1| 449 MYCNNKGNalcNLER-YNEAIECYDK 473
                                   688888887744888.9999999965 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.39
                          Sel1  23 pekAiewyekAAeqG 37 
                                   +++Aie+y kA e++
  gi|91774230|ref|YP_566922.1| 498 YNEAIECYDKALEMD 512
                                   689********9986 PP

  == domain 9  score: -1.3 bits;  conditional E-value: 8.2
                          Sel1   2 eAmyrLG 8  
                                   eA+yrL+
  gi|91774230|ref|YP_566922.1| 534 EALYRLA 540
                                   79****9 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.71   3.5e+02      11      27 ..     218     234 ..     218     238 .. 0.89
   2 ?    3.5   0.0      0.17        82      11      28 ..     252     269 ..     248     281 .. 0.89
   3 ?    3.9   0.0      0.13        64      11      28 ..     286     303 ..     286     315 .. 0.87
   4 ?    3.2   0.1       0.2     1e+02      11      28 ..     320     337 ..     320     348 .. 0.84
   5 ?   -0.2   0.0       2.4   1.2e+03      12      28 ..     355     371 ..     354     383 .. 0.83
   6 ?    3.7   0.0      0.14        70      11      28 ..     388     405 ..     388     416 .. 0.90
   7 ?    1.7   0.1      0.58   2.9e+02      11      27 ..     422     438 ..     422     441 .. 0.91
   8 ?    2.6   0.0      0.32   1.6e+02      11      27 ..     456     472 ..     456     474 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.71
                         PPR_2  11 sglckkgkveeAfklfn 27 
                                   ++lc+ +k++eA+  ++
  gi|91774230|ref|YP_566922.1| 218 DALCNLEKYDEAIGCYD 234
                                   589**********9998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.17
                         PPR_2  11 sglckkgkveeAfklfne 28 
                                   ++lc+ ++++eA++ +++
  gi|91774230|ref|YP_566922.1| 252 NALCNLERYDEAIECYDK 269
                                   689************986 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.13
                         PPR_2  11 sglckkgkveeAfklfne 28 
                                   ++lc+ +k++eA++ +++
  gi|91774230|ref|YP_566922.1| 286 DALCNLEKYDEAIECYDK 303
                                   589************986 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.2
                         PPR_2  11 sglckkgkveeAfklfne 28 
                                   ++lc+ ++++eA++ +++
  gi|91774230|ref|YP_566922.1| 320 DALCNLERYNEAIECYDK 337
                                   589*************97 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2.4
                         PPR_2  12 glckkgkveeAfklfne 28 
                                   ++++ +k+++A++ +++
  gi|91774230|ref|YP_566922.1| 355 AHFNLEKYNKAIECYDK 371
                                   7888999******9986 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.14
                         PPR_2  11 sglckkgkveeAfklfne 28 
                                   ++lc+ +k++eA++ +++
  gi|91774230|ref|YP_566922.1| 388 DALCNLEKYDEAIECYDK 405
                                   589************985 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.58
                         PPR_2  11 sglckkgkveeAfklfn 27 
                                   ++lc+ ++ +eA++ ++
  gi|91774230|ref|YP_566922.1| 422 DALCNLERHDEAIECYD 438
                                   589************98 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.32
                         PPR_2  11 sglckkgkveeAfklfn 27 
                                   ++lc+ ++++eA++ ++
  gi|91774230|ref|YP_566922.1| 456 NALCNLERYNEAIECYD 472
                                   689***********998 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         2     1e+03     186     239 ..     183     235 ..     175     248 .. 0.62
   2 ?    0.2   0.0      0.71   3.6e+02     156     182 ..     254     280 ..     240     345 .. 0.58
   3 ?    0.2   0.0      0.71   3.5e+02     164     238 ..     296     370 ..     285     378 .. 0.47
   4 ?    4.2   0.0     0.043        21     146     242 ..     346     442 ..     319     449 .. 0.82
   5 !    7.0   0.1     0.006         3     158     267 ..     426     535 ..     412     542 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                        TPR_15 186 llWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrk 239
                                    ++l i+   + eL ++ ka++ +   + s+w   + Al  L+++++A   + k
  gi|91774230|ref|YP_566922.1| 183 TIFLNIEKIVNLELDYYTKALEHN-PDNDSYWSNKGDALCNLEKYDEAIGCYDK 235
                                   566666666666666666666655.44555666666666666666666655555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.71
                        TPR_15 156 yrqegqtdaAlrdyreAlalapdssel 182
                                     +  + d+A+++y +A++ +pd s+ 
  gi|91774230|ref|YP_566922.1| 254 LCNLERYDEAIECYDKAIEIDPDFSSY 280
                                   555556667777777777777765544 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.71
                        TPR_15 164 aAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara..esd.asLwgplaaAlllLgrpkkALeylr 238
                                   +A+++y +A++ +pd s+  ++   +l +l+r++e   +++ + ++   ++d   +w+  + A   L++++kA e + 
  gi|91774230|ref|YP_566922.1| 296 EAIECYDKAIEIDPDFSSYCNNKGDALCNLERYNE---AIECYDKAIemSTDfDMYWNNKGNAHFNLEKYNKAIECYD 370
                                   55555555555555555444444444444444443...4444444442222202234444444444444444444444 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.043
                        TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaA 223
                                    +++   ++++ +  + ++A+++y +A++ +pd s+  ++   +l +l++++e   +++ + ++       +s+wg  + A
  gi|91774230|ref|YP_566922.1| 346 DMYWNNKGNAHFNLEKYNKAIECYDKAIEIDPDFSSYCNNKGDALCNLEKYDE---AIECYDKAIeidPDFSSYWGNKGDA 423
                                   57788888888888999999999999999999999999999999999999997...8888888885555567889999999 PP

                        TPR_15 224 lllLgrpkkALeylrkqak 242
                                   l  L+r ++A e + k ++
  gi|91774230|ref|YP_566922.1| 424 LCNLERHDEAIECYDKALE 442
                                   9999999999999888765 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.006
                        TPR_15 158 qegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaAlllLgrpkkALe 235
                                   +  ++d+A+++y +Al+ + d     ++   +l +l+r++e   +++ + +        +s w+  + Al +L+r+++A e
  gi|91774230|ref|YP_566922.1| 426 NLERHDEAIECYDKALEISTDFGMYCNNKGNALCNLERYNE---AIECYDKTLeiyPDFSSCWNNKGNALYYLERYNEAIE 503
                                   55677778888888887777777777777777888888887...444444444344778889999999************* PP

                        TPR_15 236 ylrkqakenrkdplwllaYADaleqagradeA 267
                                    + k ++  ++d     a A +  ++g+ +eA
  gi|91774230|ref|YP_566922.1| 504 CYDKALEMDPNDDDAWYASASIFSKNGNKEEA 535
                                   ****9999998887777789999999999998 PP

>> RhoGEF  RhoGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  14.7       0.5   2.5e+02      32     107 ..     175     299 ..     116     517 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.5
                                   CCHHHHHHHHCTTHHHHHHHHHHHHHHHHHHHH.............................................HHH CS
                        RhoGEF  32 vlseeeikiiFsnieeilelhrsflleeLeerl............................................kese 68 
                                   +  +++  +iF nie+i++l  + + ++Le++                                             +  +
  gi|91774230|ref|YP_566922.1| 175 LEFDSDAATIFLNIEKIVNLELDYYTKALEHNPdndsywsnkgdalcnlekydeaigcydkaieistdfdmywnnkgNALC 255
                                   455677889************888899999999999999999999999999999999888888888877776665442555 PP

                                   TTSS-S-SHHHHHHHHSTHHHHHHHHHCHHHHHHHHHH.....H CS
                        RhoGEF  69 eqkeaqsigdvflkfadkfkkYseYcsnypnalkllke.....l 107
                                   + +++++  ++++k ++    +s+Yc+n+ +al  l++     +
  gi|91774230|ref|YP_566922.1| 256 NLERYDEAIECYDKAIEIDPDFSSYCNNKGDALCNLEKydeaiE 299
                                   56666777777777775555588888888888888888333330 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.49   2.4e+02     185     272 ..     157     248 ..     149     270 .. 0.51
   2 ?   -1.5   0.0       1.9   9.3e+02     218     287 ..     296     365 ..     252     373 .. 0.65
   3 ?   -1.2   0.0       1.6     8e+02     237     287 ..     383     433 ..     356     436 .. 0.74
   4 ?    9.5   0.1   0.00086      0.43     247     291 ..     495     539 ..     465     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.49
                                   HHHHHHHHHHH...HTT-GGGHHHHHHHHHHTT-HHH.HHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHH CS
                         ChAPs 185 ydralellekL...keeepevvillarvllladeEvd.avkllneeleeeekdaelLllqaefllskkkeelAlevakrav 261
                                   ++r+ ++++ L   k+++ e  +  a ++l  ++ v+  ++   ++le+++++ +  + + + l + +k++ A+ + ++a+
  gi|91774230|ref|YP_566922.1| 157 IERCKTMINSLerrKNTNLEFDSDAATIFLNIEKIVNlELDYYTKALEHNPDNDSYWSNKGDALCNLEKYDEAIGCYDKAI 237
                                   334444433331002333444444555555554444423445555666666666666666666666666666666666666 PP

                                   HH-TT-HHHHH CS
                         ChAPs 262 ksaPsefktWa 272
                                   +++    + W 
  gi|91774230|ref|YP_566922.1| 238 EISTDFDMYWN 248
                                   66655555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                   HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHH CS
                         ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienA 287
                                   +a++   +++e +++ ++    + + l + ++++ A+e+ ++a++++    + W    + + +le +++A
  gi|91774230|ref|YP_566922.1| 296 EAIECYDKAIEIDPDFSSYCNNKGDALCNLERYNEAIECYDKAIEMSTDFDMYWNNKGNAHFNLEKYNKA 365
                                   4555555555555555555666666777778888888888888888877777788777777777777776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHH CS
                         ChAPs 237 LllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienA 287
                                      + + l + +k++ A+e+ ++a+++ P  ++ W    +   +le  ++A
  gi|91774230|ref|YP_566922.1| 383 CNNKGDALCNLEKYDEAIECYDKAIEIDPDFSSYWGNKGDALCNLERHDEA 433
                                   5555666788889999*************9999998777777777766666 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00086
                                   SS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                         ChAPs 247 kkkeelAlevakravksaPsefktWalLvkvYikledienALltL 291
                                    ++++ A+e+ ++a ++ P++   W+  + ++ k ++ e+AL+ L
  gi|91774230|ref|YP_566922.1| 495 LERYNEAIECYDKALEMDPNDDDAWYASASIFSKNGNKEEALYRL 539
                                   467788************************************988 PP

>> NSF  Aromatic-di-Alanine (AdAR) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       1.5   7.4e+02       1      11 [.     229     239 ..     229     239 .. 0.86
   2 ?    5.6   0.3     0.082        41       1      11 [.     263     273 ..     263     273 .. 0.93
   3 ?    5.6   0.3     0.082        41       1      11 [.     297     307 ..     297     307 .. 0.93
   4 ?    5.9   0.3     0.064        32       1      11 [.     331     341 ..     331     341 .. 0.94
   5 ?    5.6   0.3     0.082        41       1      11 [.     365     375 ..     365     375 .. 0.93
   6 ?    5.6   0.3     0.082        41       1      11 [.     399     409 ..     399     409 .. 0.93
   7 ?    3.2   0.1      0.52   2.6e+02       1      10 [.     433     442 ..     433     443 .. 0.86
   8 ?    2.4   0.2      0.94   4.7e+02       1      12 []     467     478 ..     464     478 .. 0.82
   9 ?    3.5   0.1      0.43   2.2e+02       1      11 [.     501     511 ..     501     511 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 1.5
                           NSF   1 AakhyekAaei 11 
                                   A+ +y kA+ei
  gi|91774230|ref|YP_566922.1| 229 AIGCYDKAIEI 239
                                   677*****997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.082
                           NSF   1 AakhyekAaei 11 
                                   A+++y kA+ei
  gi|91774230|ref|YP_566922.1| 263 AIECYDKAIEI 273
                                   9*******997 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.082
                           NSF   1 AakhyekAaei 11 
                                   A+++y kA+ei
  gi|91774230|ref|YP_566922.1| 297 AIECYDKAIEI 307
                                   9*******997 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.064
                           NSF   1 AakhyekAaei 11 
                                   A+++y kA+e+
  gi|91774230|ref|YP_566922.1| 331 AIECYDKAIEM 341
                                   9********97 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.082
                           NSF   1 AakhyekAaei 11 
                                   A+++y kA+ei
  gi|91774230|ref|YP_566922.1| 365 AIECYDKAIEI 375
                                   9*******997 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.082
                           NSF   1 AakhyekAaei 11 
                                   A+++y kA+ei
  gi|91774230|ref|YP_566922.1| 399 AIECYDKAIEI 409
                                   9*******997 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.52
                           NSF   1 AakhyekAae 10 
                                   A+++y kA e
  gi|91774230|ref|YP_566922.1| 433 AIECYDKALE 442
                                   9******966 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.94
                           NSF   1 AakhyekAaeiy 12 
                                   A+++y k  eiy
  gi|91774230|ref|YP_566922.1| 467 AIECYDKTLEIY 478
                                   889999888877 PP

  == domain 9  score: 3.5 bits;  conditional E-value: 0.43
                           NSF   1 AakhyekAaei 11 
                                   A+++y kA e+
  gi|91774230|ref|YP_566922.1| 501 AIECYDKALEM 511
                                   9*******775 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.58   2.9e+02      15      29 ..     126     140 ..     120     142 .. 0.79
   2 ?    9.8   0.3    0.0019      0.93       5      28 ..     142     165 ..     139     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.58
               Val_tRNA-synt_C  15 klekeiervqkKLan 29 
                                   k +kei r+++K+a+
  gi|91774230|ref|YP_566922.1| 126 KEKKEISRLNRKIAR 140
                                   5589999***99996 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
               Val_tRNA-synt_C   5 eraRLeKeLaklekeiervqkKLa 28 
                                    r+R eKeL+ ++ eier++++++
  gi|91774230|ref|YP_566922.1| 142 KRKRTEKELDVIRREIERCKTMIN 165
                                   699*****************9998 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.97   4.8e+02     202     248 ..     245     291 ..     218     313 .. 0.64
   2 ?   -0.3   0.2       1.1   5.6e+02     181     247 ..     326     392 ..     319     413 .. 0.74
   3 ?   12.8   0.5   0.00012     0.057     181     265 ..     462     546 ..     422     563 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.97
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHT CS
                    Coatomer_E 202 lllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhl 248
                                   +  n k  +   l+ry+eA +   +a++ d+       N   a  +l
  gi|91774230|ref|YP_566922.1| 245 MYWNNKGNALCNLERYDEAIECYDKAIEIDPDFSSYCNNKGDALCNL 291
                                   44455555555678999999999999988876655555544444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                   THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHH CS
                    Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqh 247
                                   e++++A   ++   e      +  n k  ++  l++y++A +   +a++ d+       N   a  +
  gi|91774230|ref|YP_566922.1| 326 ERYNEAIECYDKAIEMSTDFDMYWNNKGNAHFNLEKYNKAIECYDKAIEIDPDFSSYCNNKGDALCN 392
                                   6778888888877777777778889999999999999999999999988887665555554444444 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00012
                                   THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHH CS
                    Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsq 261
                                   e++++A   ++   e y+  +   n k  +   l+ry+eA +   +aL+ d++d ++   +     ++g  +e+  r  ++
  gi|91774230|ref|YP_566922.1| 462 ERYNEAIECYDKTLEIYPDFSSCWNNKGNALYYLERYNEAIECYDKALEMDPNDDDAWYASASIFSKNGNKEEALYRLAKS 542
                                   8999******************************************************99999999999999998887666 PP

                                   HHHH CS
                    Coatomer_E 262 lkls 265
                                   + l 
  gi|91774230|ref|YP_566922.1| 543 IELD 546
                                   5554 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       6.3   3.1e+03      11      24 ..     197     210 ..     196     210 .. 0.81
   2 ?   -0.1   0.0       1.6   7.8e+02      10      21 ..     230     241 ..     227     244 .. 0.75
   3 ?    4.6   0.1     0.054        27      10      25 ..     264     277 ..     261     278 .. 0.83
   4 ?    4.6   0.1     0.054        27      10      25 ..     298     311 ..     295     312 .. 0.83
   5 ?    4.3   0.1     0.066        33      10      22 ..     332     344 ..     330     346 .. 0.83
   6 ?    4.5   0.1     0.058        29      10      25 ..     366     379 ..     361     380 .. 0.85
   7 ?    4.6   0.1     0.054        27      10      25 ..     400     413 ..     397     414 .. 0.83
   8 ?    3.3   0.1      0.14        71      10      24 ..     434     446 ..     430     447 .. 0.77
   9 ?   -1.6   0.1       4.6   2.3e+03      11      19 ..     462     470 ..     461     481 .. 0.61
  10 ?    5.0   0.1     0.042        21      10      24 ..     502     516 ..     501     516 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.3
                           Sda  11 eaYekAlelnLdpD 24 
                                     Y kAle n d D
  gi|91774230|ref|YP_566922.1| 197 DYYTKALEHNPDND 210
                                   579*****997776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                           Sda  10 ieaYekAlelnL 21 
                                   i +Y+kA+e   
  gi|91774230|ref|YP_566922.1| 230 IGCYDKAIEIST 241
                                   669*****9754 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.054
                           Sda  10 ieaYekAlelnLdpDF 25 
                                   ie+Y+kA+e   dpDF
  gi|91774230|ref|YP_566922.1| 264 IECYDKAIEI--DPDF 277
                                   9*******96..5666 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.054
                           Sda  10 ieaYekAlelnLdpDF 25 
                                   ie+Y+kA+e   dpDF
  gi|91774230|ref|YP_566922.1| 298 IECYDKAIEI--DPDF 311
                                   9*******96..5666 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.066
                           Sda  10 ieaYekAlelnLd 22 
                                   ie+Y+kA+e+  d
  gi|91774230|ref|YP_566922.1| 332 IECYDKAIEMSTD 344
                                   8********8654 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.058
                           Sda  10 ieaYekAlelnLdpDF 25 
                                   ie+Y+kA+e   dpDF
  gi|91774230|ref|YP_566922.1| 366 IECYDKAIEI--DPDF 379
                                   8*******96..5666 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.054
                           Sda  10 ieaYekAlelnLdpDF 25 
                                   ie+Y+kA+e   dpDF
  gi|91774230|ref|YP_566922.1| 400 IECYDKAIEI--DPDF 413
                                   9*******96..5666 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.14
                           Sda  10 ieaYekAlelnLdpD 24 
                                   ie+Y+kAle   ++D
  gi|91774230|ref|YP_566922.1| 434 IECYDKALEI--STD 446
                                   9******985..444 PP

  == domain 9  score: -1.6 bits;  conditional E-value: 4.6
                           Sda  11 eaYekAlel 19 
                                   e Y +A+e+
  gi|91774230|ref|YP_566922.1| 462 ERYNEAIEC 470
                                   556666665 PP

  == domain 10  score: 5.0 bits;  conditional E-value: 0.042
                           Sda  10 ieaYekAlelnLdpD 24 
                                   ie+Y+kAle++ ++D
  gi|91774230|ref|YP_566922.1| 502 IECYDKALEMDPNDD 516
                                   8*********97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1082  (0.0603492); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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):              36  [number of targets reported over threshold]
# CPU time: 0.90u 0.31s 00:00:01.21 Elapsed: 00:00:00.56
# Mc/sec: 3064.77
//
Query:       gi|91774231|ref|YP_566923.1|  [L=125]
Description: hypothetical protein Mbur_2319 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 792.18
//
Query:       gi|91774232|ref|YP_566924.1|  [L=379]
Description: phage integrase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-21   75.0   0.0    1.2e-20   74.0   0.0    1.5  1  Phage_integrase  Phage integrase family
      1e-15   57.9   0.7    2.1e-15   56.9   0.7    1.5  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    0.00025   21.3   0.0    0.00082   19.6   0.0    1.9  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    0.00086   19.3   0.6     0.0018   18.3   0.6    1.4  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.016   14.1   0.0      0.027   13.4   0.0    1.3  1  DUF3435          Protein of unknown function (DUF3435)
      0.044   14.5   0.5      0.091   13.5   0.5    1.5  1  zinc_ribbon_15   zinc-ribbon family
       0.16   11.4   0.6       0.33   10.4   0.6    1.5  1  Mu-like_Com      Mu-like prophage protein Com
       0.23   11.8   4.0       0.44   10.9   2.3    2.5  2  Phage_int_SAM_3  Phage integrase, N-terminal SAM-like domain
       0.61    9.9   4.4        1.2    9.0   4.4    1.4  1  zinc_ribbon_2    zinc-ribbon domain
       0.77    9.3   3.0        1.5    8.3   2.1    1.9  2  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   6.7e-24   1.2e-20       5     169 ..     116     280 ..     112     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 6.7e-24
                                   HHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHH CS
               Phage_integrase   5 edeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkells 85 
                                   + +v++l+ a+++    rd++++++l+++++R+ E+l+L+++++++++  + +   egK++  r+  +  ea++ l+ +++
  gi|91774232|ref|YP_566924.1| 116 PADVKKLIPACKT---QRDRAIIMTLWDSAARATEVLNLNIGHVEIDKYGAVI-VVEGKTGMRRIRLI--EAVPDLQAWIN 190
                                   67899********...***************************9998754444.47999999887665..799******** PP

                                   HHCHCCTTTSBSSBET.....TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCC CS
               Phage_integrase  86 kaleeaeksellfask.....rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssis 161
                                   ++  ++++++ lf+       + k+l  +tv+ ++k+++e agi+k+++pH +Rh   t+L+++g+   ++  + G++  s
  gi|91774232|ref|YP_566924.1| 191 QHPYKNNPESPLFVTFrntgnEPKRLDIRTVQNTLKKVAEDAGIKKNIHPHAFRHGKLTDLVKRGFKETELRIIAGWEADS 271
                                   **8888888888888878898899******************************************************999 PP

                                   HH.HHHHCC CS
               Phage_integrase 162 tt.qiYthv 169
                                       +Y+h+
  gi|91774232|ref|YP_566924.1| 272 KMpATYIHL 280
                                   888***997 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.7   1.2e-18   2.1e-15       2      79 ..      15      90 ..      14      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.2e-18
               Phage_int_SAM_4  2 lerfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffykkvl 79
                                  le++ + l l++++e+Ti++ l++++ fl+++++k+++e+tk+die+Y+   + +++ +++t++n++  l+ f+k++ 
  gi|91774232|ref|YP_566924.1| 15 LEDYARSLGLNNFKETTINTKLWKVYTFLKHHDNKKINEITKKDIESYILFRR-KNN-KPKTVHNDIVDLRLFFKWLK 90
                                  7899999********************************************88.666.9*****************75 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.37   6.7e+02      45      77 ..      11      43 ..       5      45 .. 0.80
   2 !   19.6   0.0   4.6e-07   0.00082      24      81 ..      34      90 ..      15      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.37
                                  -HHHHHHHHHS----------HHHHHHHHHHHH CS
               Phage_int_SAM_1 45 ttedvraflaeleeeglsatslarrlsalrsFf 77
                                  + e + ++ + l  +++++t+++ +l  + +F+
  gi|91774232|ref|YP_566924.1| 11 NKEVLEDYARSLGLNNFKETTINTKLWKVYTFL 43
                                  6677789999999999*******9987776665 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 4.6e-07
                                  HHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHH CS
               Phage_int_SAM_1 24 rdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflv 81
                                   +L ++ +fl+++  ++++++t +d+ +++  ++++ ++ +++++ +  lr Ff++l+
  gi|91774232|ref|YP_566924.1| 34 TKLWKVYTFLKHHDNKKINEITKKDIESYILFRRKN-NKPKTVHNDIVDLRLFFKWLK 90
                                  556667788888899******************996.7******************95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.6   9.9e-07    0.0018       1      23 [.     312     334 ..     312     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.9e-07
                           DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                   Cp+C++ +p+d+++Cs C   l+
  gi|91774232|ref|YP_566924.1| 312 CPRCKTLNPHDSKYCSSCSMVLD 334
                                   ******************87775 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.027     171     203 ..     214     246 ..     198     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                       DUF3435 171 ealtastlnsrlkrlgeiagfeepitpYklRrg 203
                                   ++l+ +t+++ lk+++e+ag+++ i+p+ +R g
  gi|91774232|ref|YP_566924.1| 214 KRLDIRTVQNTLKKVAEDAGIKKNIHPHAFRHG 246
                                   68999**************************98 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   5.1e-05     0.091      60      85 ..     304     329 ..     283     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                zinc_ribbon_15  60 kessekkeCknCgkeveeefkyCpkC 85 
                                   k + +  eC++C++   +++kyC++C
  gi|91774232|ref|YP_566924.1| 304 KLELKPIECPRCKTLNPHDSKYCSSC 329
                                   23344789****************** PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00018      0.33      24      34 ..     309     319 ..     300     329 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                   Mu-like_Com  24 tiKCPRCGtLn 34 
                                    i CPRC tLn
  gi|91774232|ref|YP_566924.1| 309 PIECPRCKTLN 319
                                   599*******9 PP

>> Phage_int_SAM_3  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.3   0.00024      0.44       3      54 ..      12      63 ..      10      64 .. 0.89
   2 ?   -2.8   0.0       4.7   8.3e+03      47      55 ..     182     190 ..     174     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                  HHHHHHHHHHHH.HHH-HHHHHHHHHHHTTTHHHHTTSSBGGG--HHHHHHHH CS
               Phage_int_SAM_3  3 sefleeWleeyk.prvkesTyatyksiiknhIlPyFgniklkkItpadiqkfq 54
                                  +e+le +      ++ ke+T++t+   + +  l +  n+k+++It++di  ++
  gi|91774232|ref|YP_566924.1| 12 KEVLEDYARSLGlNNFKETTINTKLWKVYT-FLKHHDNKKINEITKKDIESYI 63
                                  577888888877799**************7.99999*************9876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                                   HHHHHHHHH CS
               Phage_int_SAM_3  47 padiqkfqn 55 
                                     d+q ++n
  gi|91774232|ref|YP_566924.1| 182 VPDLQAWIN 190
                                   679999*99 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.4   0.00066       1.2       2      19 ..     312     329 ..     311     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00066
                 zinc_ribbon_2   2 CpnCGaelqdnakFCpyC 19 
                                   Cp+C + ++ ++k+C+ C
  gi|91774232|ref|YP_566924.1| 312 CPRCKTLNPHDSKYCSSC 329
                                   *****************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 ?   -1.3   0.0      0.91   1.6e+03       6      17 ..     124     134 ..     124     135 .. 0.82
   2 ?    8.3   2.1   0.00085       1.5       3      22 ..     310     329 ..     309     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.91
                   zf-ribbon_3   6 PnCGaplssddn 17 
                                   P+C+++ +++++
  gi|91774232|ref|YP_566924.1| 124 PACKTQ-RDRAI 134
                                   899999.88886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00085
                   zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                   ++CP+C++ +   d + C +C
  gi|91774232|ref|YP_566924.1| 310 IECPRCKTlN-PHDSKYCSSC 329
                                   68******99.********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2629.50
//
Query:       gi|91774233|ref|YP_566925.1|  [L=240]
Description: hypothetical protein Mbur_2321 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   26.0   0.0     0.0025   17.1   0.0    2.1  2  Zeta_toxin    Zeta toxin
     0.0053   16.7   0.0     0.0073   16.3   0.0    1.6  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
       0.02   15.9   4.9        0.1   13.6   0.7    3.0  3  DUF3986       Protein of unknown function (DUF3986)
      0.038   14.3   0.0       0.18   12.1   0.0    2.0  2  AAA_22        AAA domain
      0.059   13.5   0.0       0.24   11.6   0.0    2.0  1  AAA_33        AAA domain
      0.098   13.1   0.0       0.26   11.8   0.0    1.7  2  AAA_23        AAA domain
       0.11   12.9   0.0         11    6.5   0.0    2.8  3  RNA_helicase  RNA helicase
       0.13   11.7   0.0       0.28   10.7   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
       0.14   11.5   0.1       0.51    9.7   0.0    1.9  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.22   11.2   4.7        0.3   10.7   4.7    1.4  1  AAA_15        AAA ATPase domain


Domain annotation for each model (and alignments):
>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0017       3.1      20      53 ..       7      41 ..       2      44 .. 0.72
   2 !   17.1   0.0   1.4e-06    0.0025      98     189 ..     118     204 ..      54     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                    Zeta_toxin 20 llgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                  + +G  G+GK+++ +++ ++ +   +   +++pDd
  gi|91774233|ref|YP_566925.1|  7 VFAGPNGSGKTAIVSEFIEKRDeLIDPNRHVNPDD 41
                                  679************99988653233334555555 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.4e-06
                    Zeta_toxin  98 iivegtlrspdvvkklaealkkaGYevevvvvavk.kelSrlgvldRyeeevae.gRlvpkeehdeafeglresvealeee 176
                                   + +e+ l++p++++ + +++k+ G++v +++v ++ +e+   +v++R++  ++  +R    ++  ++ ++l e+++     
  gi|91774233|ref|YP_566925.1| 118 FSFETVLSHPSKID-FLKDAKELGWDVYLYFVSTNdPEINCVRVAQRVQMGGHDvPREKIYDRYTKTNNNLFEALKH---- 193
                                   569***********.*****************98648**************55534444444444444444444444.... PP

                    Zeta_toxin 177 kqldrvkikdrdg 189
                                     + r  i+d+++
  gi|91774233|ref|YP_566925.1| 194 --CRRAYIFDNSE 204
                                   ..44444555555 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 !   16.3   0.0   4.1e-06    0.0073      24      68 ..       7      53 ..       2     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                      ATPase_2 24 fiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldef 68
                                  +  Gp gsGKta++ e+ie+++++ +  +++  ++l+  +  ++d+f
  gi|91774233|ref|YP_566925.1|  7 VFAGPNGSGKTAIVSEFIEKRDELIDpnRHVNPDDLNLLDVLNFDNF 53
                                  556******************88766456666667777777777776 PP

>> DUF3986  Protein of unknown function (DUF3986)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   5.7e-05       0.1      37      72 ..      48      86 ..      40     106 .. 0.83
   2 ?    1.4   0.0      0.36   6.5e+02      24      41 ..     132     149 ..     128     171 .. 0.78
   3 ?    0.8   0.0      0.57     1e+03       3      30 ..     188     216 ..     185     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-05
                       DUF3986 37 fdfedygvekdelslskf.dkyalfdkyGykv..ysika 72
                                  ++f+++gv++de  ++ f  +y++++k G+++  ++ik 
  gi|91774233|ref|YP_566925.1| 48 LNFDNFGVKVDESDFRDFvLQYHFYEKLGITIeyLKIKD 86
                                  78999**************************96556644 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.36
                       DUF3986  24 ayKrknedvWvvyfdfed 41 
                                   ++K  +e  W+vy+ f +
  gi|91774233|ref|YP_566925.1| 132 FLKDAKELGWDVYLYFVS 149
                                   578889999****98743 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.57
                       DUF3986   3 fdesiHlhlgy.ykdnldlEaiayKrkne 30 
                                   f+   H    y +++ +++E ia K+ ++
  gi|91774233|ref|YP_566925.1| 188 FEALKHCRRAYiFDNSEEMELIAKKNPDG 216
                                   5666777777734667899***9998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.18       5      38 ..       3      40 ..       1     117 [. 0.70
   2 ?   -0.3   0.0      0.66   1.2e+03      84     104 ..     189     207 ..     162     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee....e 38
                                  +++ v  G+ G+GKT  + ++ e+ de +++++     
  gi|91774233|ref|YP_566925.1|  3 QRMRVFAGPNGSGKTAIVSEFIEKRDELIDPNRhvnpD 40
                                  6777889*****************99877776666540 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.66
                        AAA_22  84 qalraravielliiDEaqhlr 104
                                   +al+++++  + i D+ + + 
  gi|91774233|ref|YP_566925.1| 189 EALKHCRR--AYIFDNSEEME 207
                                   56677766..88888888874 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   0.00013      0.24       3     130 ..       7     173 ..       5     202 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                        AAA_33   3 llvGlpGsGKstlaerllkklg.....avllssdt..........................................lrrr 36 
                                   ++ G++GsGK+  + + ++k++       +++ d+                                          ++++
  gi|91774233|ref|YP_566925.1|   7 VFAGPNGSGKTAIVSEFIEKRDelidpNRHVNPDDlnlldvlnfdnfgvkvdesdfrdfvlqyhfyeklgitieylkIKDN 87 
                                   799*************99887777776666777777777776666666666666666664444433333333333322222 PP

                        AAA_33  37 lfgtdqqsktdytrvldr.lyqilnelarkalsagrnvil.datnlsrrerarflklarrlgvpvrivvvetdeetlk.eR 114
                                   +f+         ++ +++ + ++l++++r +l + +  ++   t ls+    +flk a++lg  v + +v+t + +++  R
  gi|91774233|ref|YP_566925.1|  88 CFY---------INQKSSyMGAMLSDYLRHCLIKTNERLFsFETVLSHPSKIDFLKDAKELGWDVYLYFVSTNDPEINcVR 159
                                   222.........221111133345555555554444433324566666666677777777777777766666555554357 PP

                        AAA_33 115 lakRaangddrsevpe 130
                                   +a+R + g+++  vp+
  gi|91774233|ref|YP_566925.1| 160 VAQRVQMGGHD--VPR 173
                                   77776666654..555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.26      23      36 ..       7      20 ..       2      25 .. 0.84
   2 ?   -1.5   0.0       1.7     3e+03      80      80 ..     148     148 ..      67     214 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                        AAA_23 23 lItGpNGaGKTTil 36
                                  ++ GpNG+GKT+i+
  gi|91774233|ref|YP_566925.1|  7 VFAGPNGSGKTAIV 20
                                  789*********97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                        AAA_23  80 e 80 
                                    
  gi|91774233|ref|YP_566925.1| 148 V 148
                                   0 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.006        11       2      21 ..       7      26 ..       6      41 .. 0.85
   2 ?   -1.6   0.0         2   3.6e+03      11      36 ..      94     119 ..      90     129 .. 0.79
   3 ?    3.0   0.0     0.073   1.3e+02      39      75 ..     172     210 ..     161     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.006
                  RNA_helicase  2 wlyGpsgeGKStlakeLaka 21
                                  ++ Gp+g GK+ ++ e++++
  gi|91774233|ref|YP_566925.1|  7 VFAGPNGSGKTAIVSEFIEK 26
                                  588***********998875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                  RNA_helicase  11 KStlakeLakallkklklkkkdsvys 36 
                                   KS+++  + ++ l++   k++++++s
  gi|91774233|ref|YP_566925.1|  94 KSSYMGAMLSDYLRHCLIKTNERLFS 119
                                   89999999999998887777766665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.073
                  RNA_helicase  39 peddfwdgYtgqevvvidDfgqvkdee.nps.dlaelir 75 
                                   p+++++d Yt+ + ++++ ++ ++  +  ++ +++eli 
  gi|91774233|ref|YP_566925.1| 172 PREKIYDRYTKTNNNLFEALKHCRRAYiFDNsEEMELIA 210
                                   78999*******************999977779999986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.28      35      58 ..       5      28 ..       1      36 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                         AAA_7 35 pvllvGptGtGKtviikdllkkld 58
                                    ++ Gp G+GKt+i++++++k d
  gi|91774233|ref|YP_566925.1|  5 MRVFAGPNGSGKTAIVSEFIEKRD 28
                                  55799*************999877 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 ?    9.7   0.0   0.00028      0.51      24      41 ..       3      20 ..       1      24 [. 0.85
   2 ?   -1.6   0.0      0.82   1.5e+03      95     133 ..      73     112 ..      55     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                                  SSEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxxx RF
                         SMC_N 24 ksftaivGpNGSGKsnll 41
                                  +++ +  GpNGSGK+ ++
  gi|91774233|ref|YP_566925.1|  3 QRMRVFAGPNGSGKTAIV 20
                                  6788999********997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.82
                                   SCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                         SMC_N  95 eevsisrrvkrkgeseykingkevtk.kevsellesagis 133
                                   e++ i+ +  + +++ ++in+k+    + +s+ l++  i+
  gi|91774233|ref|YP_566925.1|  73 EKLGITIEYLKIKDNCFYINQKSSYMgAMLSDYLRHCLIK 112
                                   6677788888888888999998877656667777766665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.7   0.00017       0.3      26     126 ..       6      98 ..       2     234 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                        AAA_15  26 tvliGkNnsGKSsilealdlFlnnkekkn.............kkvikiekedleifeniseskdikIdvef.......... 83 
                                    v+ G+N+sGK+ i+  +   +++ +  +             +  ++++ +++ ++ ++s ++d+ ++++f          
  gi|91774233|ref|YP_566925.1|   6 RVFAGPNGSGKTAIVSEF---IEKRD--ElidpnrhvnpddlNLLDVLNFDNFGVKVDESDFRDFVLQYHFyeklgitiey 81 
                                   5899**********9766...33222..1345778888***9666666666677777788888888888883333333322 PP

                        AAA_15  84 .......aekekakeyektlkskekkkadlllkkkesdlkktikdkklkl 126
                                                                            +i++k  + 
  gi|91774233|ref|YP_566925.1|  82 lkikdncF---------------------------------YINQKSSYM 98 
                                   33322220.................................222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1610.23
//
Query:       gi|91774234|ref|YP_566926.1|  [L=474]
Description: ribulose bisphosphate carboxylase [Methanococcoides burtonii DSM 6242]
Scores for 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-94  314.0   0.0    1.1e-67  228.4   0.0    2.1  2  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.1e-30  106.2   0.0    2.8e-30  104.9   0.0    1.7  1  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.4   0.0   1.2e-71   1.1e-67       2     221 ..     147     364 ..     146     369 .. 0.96
   2 !   83.9   0.0   1.3e-27   1.1e-23     200     299 .]     371     471 ..     365     471 .. 0.90

  Alignments for each domain:
  == domain 1  score: 228.4 bits;  conditional E-value: 1.2e-71
                                   HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHHHSS- CS
                 RuBisCO_large   2 iaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqdetGek 82 
                                   + ++r++l++++rpilGti+KPk+GL++++ya+v+y+++ gg Df+K+DE++++q f+++++ ++ v ea+++a +etG+k
  gi|91774234|ref|YP_566926.1| 147 VDDMRKYLDVYDRPILGTIVKPKMGLTSAEYAEVCYDFWVGGGDFVKNDEPQANQDFCPYEKMVAHVKEAMDKAVKETGQK 227
                                   5689***************************************************************************** PP

                                   -EEEEE---SSHHHHHHHHHHHHHHHGG....EEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHS.T--SEE-H CS
                 RuBisCO_large  83 klyalnitaddleemlrraefvketgge....ivlvdvlviGfaaitslrkafrknelllHlHraghgaltr.qskhGisf 158
                                   k++++n++a+d + m++r e++ ++g e    ++l+d++++G+ a+++lr++ ++  ++lH+Hra hga+tr ++  G+s+
  gi|91774234|ref|YP_566926.1| 228 KVHSFNVSAADFDTMIERCEMITNAGFEpgsyAFLIDGITAGWMAVQTLRRRYPD--VFLHFHRAAHGAFTRqENPIGFSV 306
                                   ***********************999888888********************665..5**************66679**** PP

                                   HHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT--- CS
                 RuBisCO_large 159 rvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslka 221
                                    vl+k++RL+G++++htgt+g+gk++g ++     +d + +++++  ++ g ffeq + ++ +
  gi|91774234|ref|YP_566926.1| 307 LVLSKFARLAGASGIHTGTAGIGKMKGTPA-----EDVVAAHSIQYLKSPGHFFEQTWSKIMD 364
                                   ******************************.....89999******************98765 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 1.3e-27
                                   HHHHSSEEE-SS-E.EE-TT----EEEEESS--TTTHHHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT CS
                 RuBisCO_large 200 kmleedeaegiffe.qdlaslkavlpvasgGihagqlpellenlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveG 279
                                   + ++ed a+  ++e  ++  +k++ p++sgG++ ++l+ +++ + + d i+++G G+++Hp g+++Gakal qa +a ++G
  gi|91774234|ref|YP_566926.1| 371 NLVNEDLAHHVILEdDSWRAMKKCCPIVSGGLNPVKLKPFIDVMENVDFITTMGSGVHSHPGGTQSGAKALVQACDAYLQG 451
                                   55677777776665156999************************************************************* PP

                                   --HHHHHTT-HHHHHHHHHX CS
                 RuBisCO_large 280 adleeyAkehkeLarAlesw 299
                                    d+eeyAk+hkeLa+A+e +
  gi|91774234|ref|YP_566926.1| 452 MDIEEYAKDHKELAEAIEFY 471
                                   *****************975 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 !  104.9   0.0   3.1e-34   2.8e-30      10     120 .]      29     136 ..      18     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 3.1e-34
               RuBisCO_large_N  10 ketdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvkiAYplelFeeg.si 89 
                                   +++ lla+f++ P  +++v +aaa++AaeSStgt+ +vst++  + ++++a+vy+++    e+elv+iAYp +lF++g ++
  gi|91774234|ref|YP_566926.1|  29 NGEFLLAVFHMIPGGDLNVLQAAAEIAAESSTGTNIKVSTETA-FSRTMNARVYQLDL---ERELVWIAYPWRLFDRGgNV 105
                                   456689************************************9.************77...79**************88** PP

               RuBisCO_large_N  90 pqllssiaGnifgmkavkalrleDirlPkay 120
                                    ++l+ i+Gni+gmk+++al+l Di++P+++
  gi|91774234|ref|YP_566926.1| 106 QNILTYIIGNILGMKEIQALKLMDIWFPPSM 136
                                   ****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3133.24
//
Query:       gi|91774235|ref|YP_566927.1|  [L=76]
Description: ferredoxin [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-15   56.9   2.2    2.7e-15   56.6   2.2    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00083   20.0   0.4     0.0012   19.5   0.4    1.2  1  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   2.2     3e-19   2.7e-15       1      57 [.      18      73 ..      18      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3e-19
                       Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57
                                  V+ ++ i c++C + aP+ F+++d+g+ ++v++qp++++ek+++ee +d+C  e+Ig
  gi|91774235|ref|YP_566927.1| 18 VE-NEFITCQKCIDEAPNNFKMNDNGSSVFVFKQPENDTEKKNCEEVMDSCSAEAIG 73
                                  56.899**************************************************8 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 !   19.5   0.4   1.4e-07    0.0012       9      64 ..      23      72 ..      20      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                       Fer4_15  9 igcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                  i c  C++eap+ f+++++g ++++ +      ++ +d+e+++ +e +++C ++AI
  gi|91774235|ref|YP_566927.1| 23 ITCQKCIDEAPNNFKMNDNGSSVFVFK------QPENDTEKKNCEEVMDSCSAEAI 72
                                  5799******************99986......6669******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 513.30
//
Query:       gi|91774236|ref|YP_566928.1|  [L=99]
Description: carboxymuconolactone decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   34.9   0.0    1.3e-08   34.8   0.0    1.0  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
       0.11   12.3   0.1       0.18   11.6   0.1    1.4  1  SinI      Anti-repressor SinI


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 !   34.8   0.0   1.4e-12   1.3e-08       1      84 [.      14      96 ..      14      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.4e-12
                                  HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHH CS
                           CMD  1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaa 83
                                  pe+ ++l +  ++++  e+g++ k++ L+al   a+ g ++ v++ + +Al+aG+t+eei++++++    +g   +  A++a+
  gi|91774236|ref|YP_566928.1| 14 PEFVKLLDENLHNAFP-ENGIPYKYKLLMALSLDASKGAVNGVRSLALQALDAGATKEEIMQTIRITQYICGIGSVYVAANAL 95
                                  8999999999999998.999****************************************************99999999988 PP

                                  H CS
                           CMD 84 e 84
                                  +
  gi|91774236|ref|YP_566928.1| 96 Q 96
                                  7 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     2e-05      0.18       8      22 ..      58      72 ..      56      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                                  HHHHHHHHT--SHHH CS
                          SinI  8 LikEAkesGlskeEf 22
                                  L ++A+++G +keE+
  gi|91774236|ref|YP_566928.1| 58 LALQALDAGATKEEI 72
                                  899***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 671.19
//
Query:       gi|91774237|ref|YP_566929.1|  [L=107]
Description: small multidrug resistance protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-24   86.4   7.8      2e-24   86.1   7.8    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein
     0.0049   17.0  11.1      0.012   15.7  11.1    1.7  1  EamA            EamA-like transporter family
  ------ inclusion threshold ------
      0.041   13.7   1.6      0.041   13.7   1.6    1.8  2  DUF5381         Family of unknown function (DUF5381)
        2.2    7.8   6.0       0.51    9.9   0.5    1.9  2  SLATT_6         SMODS and SLOG-associating 2TM effector domai
        7.1    6.9   7.7       0.21   11.8   0.5    2.0  3  DUF4040         Domain of unknown function (DUF4040)


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   7.8   5.6e-28     2e-24       1      93 []       1      93 [.       1      93 [. 0.98

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 5.6e-28
                                  XX-HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH----- CS
                Multi_Drug_Res  1 mnwvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillfgesls 83
                                  m++ ll++ i++e+ g++ +k+s+g ++   sl++ v+ygisf+++ +alk+++vs+AYa+wsG+Gt+ ++l+g+++f+e++ 
  gi|91774237|ref|YP_566929.1|  1 MSYSLLAISIFFEICGTVCMKISDGYSNISASLMIFVFYGISFSIFPFALKNIDVSLAYAIWSGVGTASMTLIGVYYFKEPAT 83
                                  7899******************************************************************************* PP

                                  ---HHHHHHH CS
                Multi_Drug_Res 84 lkkliglali 93
                                    k++++ ++
  gi|91774237|ref|YP_566929.1| 84 TIKMVSIFIV 93
                                  ******9875 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  11.1   3.5e-06     0.012      65     136 ..      29     101 ..       1     102 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.5e-06
                          EamA  65 llllllgllgtvlafllffyalkktsasnasli.tslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   ++  l+ ++   + f++f  alk++++s a  i + +  + +++++v++++e+ t +++++i+++++Gvl ++
  gi|91774237|ref|YP_566929.1|  29 ISASLMIFVFYGISFSIFPFALKNIDVSLAYAIwSGVGTASMTLIGVYYFKEPATTIKMVSIFIVMAGVLGLN 101
                                   5556778888899999**************999899*********************************9986 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.0      0.28     1e+03      38      59 ..      22      43 ..       1      52 [. 0.42
   2 ?   13.7   1.6   1.1e-05     0.041       5      52 ..      53     100 ..      49     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.28
                       DUF5381 38 skysllyiiigiigtifgliil 59
                                   +  +  i ++++  +f+ i++
  gi|91774237|ref|YP_566929.1| 22 ISDGYSNISASLMIFVFYGISF 43
                                  2223333444444444444333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                       DUF5381   5 vksrkflrvllflatvglglaglfllfeglkfeskysllyiiigiigt 52 
                                   + ++  ++++  ++t+ ++l+g++ ++e  ++    s++ +++g++g+
  gi|91774237|ref|YP_566929.1|  53 IDVSLAYAIWSGVGTASMTLIGVYYFKEPATTIKMVSIFIVMAGVLGL 100
                                   56678899*************************************985 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.6     0.082   2.9e+02      41      76 ..       8      45 ..       2      54 .. 0.79
   2 ?    9.9   0.5   0.00014      0.51      42      75 ..      69     103 ..      55     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.082
                       SLATT_6 41 islavGilalvieels..tkllsalliiigiialyisa 76
                                  is+++ i + v+ ++s   + +sa l+i+   ++ +s+
  gi|91774237|ref|YP_566929.1|  8 ISIFFEICGTVCMKISdgYSNISASLMIFVFYGISFSI 45
                                  78888888888888886667899999998888887765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00014
                       SLATT_6  42 sl.avGilalvieelstkllsalliiigiialyis 75 
                                   s+  +G++ +  ++ + k++s++++++g+++l +s
  gi|91774237|ref|YP_566929.1|  69 SMtLIGVYYFKEPATTIKMVSIFIVMAGVLGLNLS 103
                                   44158***************************987 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.6   9.3e+03      17      26 ..       6      15 ..       3      20 .. 0.51
   2 ?   11.8   0.5   5.8e-05      0.21      15      60 ..      28      72 ..      25      79 .. 0.90
   3 ?   -1.0   0.2      0.55     2e+03      20      28 ..      92     100 ..      82     103 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                       DUF4040 17 laavillgvv 26
                                  la  i++ ++
  gi|91774237|ref|YP_566929.1|  6 LAISIFFEIC 15
                                  4444444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.8e-05
                       DUF4040 15 drlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllll 60
                                  +  a+++++  +G+  +++ + l+  Dv l++a + +g+ t+ + l
  gi|91774237|ref|YP_566929.1| 28 NISASLMIFVFYGISFSIFPFALKNIDVSLAYA-IWSGVGTASMTL 72
                                  56789****************************.****99997766 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.55
                       DUF4040  20 villgvvGl 28 
                                   +++ gv+Gl
  gi|91774237|ref|YP_566929.1|  92 IVMAGVLGL 100
                                   566677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 778.33
//
Query:       gi|91774238|ref|YP_566930.1|  [L=147]
Description: hypothetical protein Mbur_2326 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   18.0  10.1     0.0028   18.0  10.1    1.8  2  DUF420        Protein of unknown function (DUF420)
     0.0088   16.0   5.8      0.039   13.9   0.5    2.4  2  Ninjurin      Ninjurin
  ------ inclusion threshold ------
       0.35   10.7   0.0       0.35   10.7   0.0    3.5  4  Adeno_E3_CR2  Adenovirus E3 region protein CR2
          2    7.8  11.0        2.9    7.3  11.0    1.3  1  GPI2          Phosphatidylinositol N-acetylglucosaminyltransf
        6.8    4.9  16.4        8.1    4.6  16.4    1.0  1  DUF2070       Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  10.1   7.7e-07    0.0028       2     131 ..       6     119 ..       5     120 .. 0.85
   2 ?   -3.7   0.2       3.8   1.4e+04      41      41 ..     129     129 ..     121     141 .. 0.48

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.7e-07
                        DUF420   2 palnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalagetkfggpeeegvirpvYlaiLitHi 82 
                                   ++l+ +l ++a+v+ll ++ + +k+  + H ++  la+ ++ +  +lY+ + +  g   f          p Y +iL +H 
  gi|91774238|ref|YP_566930.1|   6 ADLSLTLQVIAFVMLLYAINL-RKEGLKEHGRASSLAVYVM-VPTILYMFYSISLG---FR--------LPEYGIILGMHR 73 
                                   67899999*******999865.7778999999999887765.55778888888874...44........356********* PP

                        DUF420  83 vLavvvvplvlvtlvlalkgkfekHrkiaritvpiwlyvavtGvvvYll 131
                                   +L  +v++++++ +++ ++ k + H  i+    ++w +++++G++vYl+
  gi|91774238|ref|YP_566930.1|  74 LLGSIVLIFIILFVTNRWRFKKKFHMDIVT---VCWTLTLMMGIAVYLI 119
                                   *************************98875...68************95 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.8
                        DUF420  41 l 41 
                                   +
  gi|91774238|ref|YP_566930.1| 129 I 129
                                   1 PP

>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.5   1.1e-05     0.039      45      98 ..       4      56 ..       1      59 [. 0.76
   2 !    4.6   0.4    0.0084        30      29      65 ..      83     120 ..      77     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                      Ninjurin 45 vLislSllLqvvvgilliliasklnlekekkerrlnklnnaatilvfvitvini 98
                                  vL  lSl Lqv++ ++l++ a +l  e  k++ r+  l  ++++ +++ ++  i
  gi|91774238|ref|YP_566930.1|  4 VLADLSLTLQVIAFVMLLY-AINLRKEGLKEHGRASSLAVYVMVPTILYMFYSI 56
                                  67789**************.6455555566666888888888888887777665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0084
                      Ninjurin  29 avlesgekskfy.iallvLislSllLqvvvgillilia 65 
                                   ++l ++++++f   + + +++++  L +++gi+++li+
  gi|91774238|ref|YP_566930.1|  83 IILFVTNRWRFKkKFHMDIVTVCWTLTLMMGIAVYLIS 120
                                   45556667999889999999999999999999988753 PP

>> Adeno_E3_CR2  Adenovirus E3 region protein CR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.7e-05      0.35       5      34 ..       1      30 [.       1      35 [. 0.78
   2 ?   -2.7   0.3       1.4   5.2e+03      15      25 ..      44      54 ..      41      55 .. 0.64
   3 ?    1.7   0.2     0.062   2.2e+02      17      34 ..      78      94 ..      66      99 .. 0.58
   4 ?   -3.9   2.9       3.5   1.2e+04      21      29 ..     129     137 ..     123     141 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.7e-05
                  Adeno_E3_CR2  5 tiaIivaVvvGlaiIiicmlyYaCcYrkhr 34
                                  +i+  +   + l +I+++ml+Ya   rk  
  gi|91774238|ref|YP_566930.1|  1 MISVLADLSLTLQVIAFVMLLYAINLRKEG 30
                                  5666666667789**********9988865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                  Adeno_E3_CR2 15 GlaiIiicmly 25
                                  +++  i+ m+y
  gi|91774238|ref|YP_566930.1| 44 VMVPTILYMFY 54
                                  45556777776 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.062
                  Adeno_E3_CR2 17 aiIiicmlyYaCcYrkhr 34
                                  +++ i +++++  + +++
  gi|91774238|ref|YP_566930.1| 78 IVL-IFIILFVTNRWRFK 94
                                  344.44555555555555 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 3.5
                  Adeno_E3_CR2  21 icmlyYaCc 29 
                                   i ++ +a c
  gi|91774238|ref|YP_566930.1| 129 ISLFFFAIC 137
                                   444555544 PP

>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  11.0   0.00081       2.9     143     266 ..      11     144 ..       3     147 .] 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00081
                          GPI2 143 wlllinifffdysiekkkskekeek......lvaslStnaalmastvLASRLpstlqVFsl..llfsi.evfglfPvfrrs 214
                                   +l +i  ++  y i+  k+  ke++      +   + t + ++ s+ L  RLp+ + +  +  ll si  +f+++ v +r 
  gi|91774238|ref|YP_566930.1|  11 TLQVIAFVMLLYAINLRKEGLKEHGrasslaVYVMVPTILYMFYSISLGFRLPEYGIILGMhrLLGSIvLIFIILFVTNRW 91 
                                   555555555555544444443333344455577788899999***********9887755422444441455555555554 PP

                          GPI2 215 lrhrswrl.hvvltvllvllagagvgiilklllavvlllllalimgvcpwwli 266
                                     ++++++  v++ ++l+l++g++v+ i++ + +++++ l++++++++p+  +
  gi|91774238|ref|YP_566930.1|  92 RFKKKFHMdIVTVCWTLTLMMGIAVYLISHAISCYLMISLFFFAICLFPYHTL 144
                                   44455555356677788899999999999988888999999999999888765 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  16.4    0.0023       8.1      49     169 ..      14     138 ..       2     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0023
                       DUF2070  49 lvaflltlpvlrilggr.ltykrslflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesll 128
                                   ++af+++l ++++ ++   ++ r+  la+  +++ ++ ++ +i l + l+++ +   +  l  +++l +++l+++ +++++
  gi|91774238|ref|YP_566930.1|  14 VIAFVMLLYAINLRKEGlKEHGRASSLAVYVMVPTILYMFYSISLGFRLPEYGIILGMHRLLGSIVLIFIILFVTNRWRFK 94 
                                   778888888888877667999999*************88888888866666666666666888888888899999999988 PP

                       DUF2070 129 kav...lpaliqpllailllvlyfspesfllllllslifalavy 169
                                   k     ++++  +l++++ + +y+ ++ +  +l++sl+f+++++
  gi|91774238|ref|YP_566930.1|  95 KKFhmdIVTVCWTLTLMMGIAVYLISHAISCYLMISLFFFAICL 138
                                   87777755555555555555555446666666666776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 998.00
//
Query:       gi|91774239|ref|YP_566931.1|  [L=95]
Description: hypothetical protein Mbur_2327 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-16   60.3   1.5    1.3e-16   60.3   1.5    1.6  2  zf_CopZ   Zinc binding domain


Domain annotation for each model (and alignments):
>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.0   5.6         1   1.8e+04      40      40 ..      26      26 ..       9      33 .. 0.57
   2 !   60.3   1.5     7e-21   1.3e-16       2      51 ..      45      94 ..      44      95 .] 0.96

  Alignments for each domain:
  == domain 1  score: -8.0 bits;  conditional E-value: 1
                                  - CS
                       zf_CopZ 40 k 40
                                  +
  gi|91774239|ref|YP_566931.1| 26 S 26
                                  2 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 7e-21
                                  -B-TTT--B-EEE-HHHHHHHB-GGGGGG--S-EE.E---TT-SEEEE-S CS
                       zf_CopZ  2 kkCPvCgkkGkkVkliTvkhllkpellekvkeedYylCknedCdVvYFna 51
                                  + CP Cg ++++V +iTvkhl+k+e +e + +e++ lC+ne+C+V+YF +
  gi|91774239|ref|YP_566931.1| 45 TACPICGYSSEQVGSITVKHLVKKEKMEDNIDENHLLCMNEECEVAYFTE 94
                                  78**********************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 559.20
//
Query:       gi|91774240|ref|YP_566932.1|  [L=153]
Description: peptide methionine sulfoxide reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-60  203.9   0.5    1.6e-60  203.7   0.5    1.0  1  PMSR      Peptide methionine sulfoxide reductase


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.7   0.5   8.8e-65   1.6e-60       2     146 ..       4     148 ..       3     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.7 bits;  conditional E-value: 8.8e-65
                                   EEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT-SSE CS
                          PMSR   2 avlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDptqlnr 82 
                                   a++a+GCFWgve++f+k++Gv+st+vGY+gG+ ++ptY++v++g+tghaE++++++d++++++ elle+++++hDpt+++ 
  gi|91774240|ref|YP_566932.1|   4 ATFAAGCFWGVEAAFSKVEGVISTKVGYTGGTLKDPTYKDVSTGSTGHAESIDIIFDESVITYGELLEVLWNTHDPTTKDS 84 
                                   89******************************************************************************* PP

                                   ETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH CS
                          PMSR  83 qgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYlek 146
                                   qg D+G+qYrsai+y++++q+e+a +++e+l+++ +++++i tei +++ef +ae+yHq+Y++k
  gi|91774240|ref|YP_566932.1|  85 QGPDHGSQYRSAIFYHDDAQREAALRSREQLERSGKYDSTIKTEIVKASEFSPAEDYHQKYFQK 148
                                   **************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 889.62
//
Query:       gi|91774241|ref|YP_566933.1|  [L=142]
Description: methionine sulfoxide reductase B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-51  171.4   0.0      8e-51  171.2   0.0    1.0  1  SelR            SelR domain
    0.00069   19.8   0.6     0.0013   18.9   0.6    1.6  1  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
     0.0092   15.8   0.1        4.3    7.3   0.0    2.3  2  ADD_ATRX        Cysteine Rich ADD domain
  ------ inclusion threshold ------
      0.021   14.2   1.9       0.47    9.9   0.2    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.022   14.3   1.6        5.7    6.5   0.3    3.2  3  TF_Zn_Ribbon    TFIIB zinc-binding
      0.028   14.7   0.2       0.81   10.0   0.1    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
      0.053   13.2   2.1        5.2    6.8   0.2    2.4  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.11   12.2   2.0        3.8    7.4   0.1    2.6  2  zinc_ribbon_2   zinc-ribbon domain
       0.27   10.7   1.2       0.31   10.5   0.0    1.6  2  Mu-like_Com     Mu-like prophage protein Com


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0     4e-54     8e-51       1     120 [.      11     129 ..      11     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 4e-54
                                   HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEECTTSE CS
                          SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdtslgme 81 
                                   e+kk Ltpeqy++lrek+te pftge+ ++ + Gvy+c +cg+++fss++kfds +GwpsF+e+i++++v+ + d s+ m+
  gi|91774241|ref|YP_566933.1|  11 EWKKLLTPEQYAILREKKTEIPFTGELLRNDRPGVYSCGACGQEIFSSKNKFDSSSGWPSFYEVISNDRVELVIDDSYFMK 91 
                                   7******************************************************************************** PP

                                   EEEEEETTCECEEEEEECTSSSSS.SEEEEE-CCCEEEE CS
                          SelR  82 rtevvcakcdahlGhvFedgpkpttgkrycinsvslkfk 120
                                   r+e++c++c++hlGhvF+dgp++ tgkrycins+sl f+
  gi|91774241|ref|YP_566933.1|  92 RIEIQCSNCGSHLGHVFDDGPQS-TGKRYCINSASLGFT 129
                                   **********************9.5***********996 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.6   6.7e-07    0.0013      36     103 ..      81     139 ..      44     141 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.7e-07
                                   CEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCCCCCCCTCEEEEGGGEEEEESSSSXXXXX CS
                  Yippee-Mis18  36 nvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteeelkykrglfiletkaitsyslgekeeeke 103
                                   ++v+++   ++        +++C++C+s+lG ++ + +++ + kr  ++++++++  ++  eke+ek+
  gi|91774241|ref|YP_566933.1|  81 ELVIDDSYFMK------RIEIQCSNCGSHLGHVFDDGPQS-TGKR--YCINSASLGFTEGSEKEKEKK 139
                                   24444444444......568****************9998.6666..9*****999999888888775 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0022       4.3      12      25 ..      46      59 ..      39      64 .. 0.79
   2 !    6.4   0.0    0.0042       8.3      11      24 ..      94     107 ..      88     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0022
                      ADD_ATRX 12 vsCtaCgqqvnhfq 25
                                   sC aCgq+++  +
  gi|91774241|ref|YP_566933.1| 46 YSCGACGQEIFSSK 59
                                  69*******98754 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0042
                      ADD_ATRX  11 ivsCtaCgqqvnhf 24 
                                    ++C+ Cg ++ h+
  gi|91774241|ref|YP_566933.1|  94 EIQCSNCGSHLGHV 107
                                   499********997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.024        48      17      25 ..      46      54 ..      42      58 .. 0.70
   2 ?    9.9   0.2   0.00023      0.47       2      12 ..      94     104 ..      93     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.024
                   zf-ribbon_3 17 nvCpyCGtk 25
                                    C  CG++
  gi|91774241|ref|YP_566933.1| 46 YSCGACGQE 54
                                  568888876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00023
                   zf-ribbon_3   2 tvrCPnCGapl 12 
                                   +++C+nCG++l
  gi|91774241|ref|YP_566933.1|  94 EIQCSNCGSHL 104
                                   789*****964 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0095        19      12      27 ..      38      53 ..      33      71 .. 0.79
   2 ?    0.6   0.0      0.21   4.1e+02      27      40 ..      82      95 ..      81      96 .. 0.87
   3 ?    6.5   0.3    0.0029       5.7       2      22 ..      96     120 ..      95     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0095
                                  HEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon 12 veDpergelvCtdCGl 27
                                  +++   g + C++CG 
  gi|91774241|ref|YP_566933.1| 38 LRNDRPGVYSCGACGQ 53
                                  566666889*****96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                                  BEEEECCCCCCCHH CS
                  TF_Zn_Ribbon 27 lVlednsidegpew 40
                                  lV++d + ++++e 
  gi|91774241|ref|YP_566933.1| 82 LVIDDSYFMKRIEI 95
                                  8*********9985 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0029
                                   EETTTTCEE.CHEE...TSTTCEEE CS
                  TF_Zn_Ribbon   2 kCPnCgstn.lveD...pergelvC 22 
                                   +C nCgs    v+D    ++g  +C
  gi|91774241|ref|YP_566933.1|  96 QCSNCGSHLgHVFDdgpQSTGKRYC 120
                                   7999999877788866556666565 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 ?    2.6   0.0     0.084   1.7e+02       5      17 ..      45      57 ..      41      69 .. 0.67
   2 ?   10.0   0.1   0.00041      0.81      52      68 ..      90     106 ..      87     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.084
                 zf-LITAF-like  5 qvdCpaCqqrvvT 17
                                     C aC+q++ +
  gi|91774241|ref|YP_566933.1| 45 VYSCGACGQEIFS 57
                                  4556666666554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00041
                 zf-LITAF-like  52 lkdvehyCpnCgallgt 68 
                                   +k +e +C+nCg++lg+
  gi|91774241|ref|YP_566933.1|  90 MKRIEIQCSNCGSHLGH 106
                                   6899***********97 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0026       5.2       1      10 [.      46      55 ..      46      61 .. 0.86
   2 ?    5.9   0.1    0.0051        10      18      25 ..      95     102 ..      89     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0026
                                  -B-SSS--B- CS
                DNA_RNApol_7kD  1 YiCgeCgaev 10
                                  Y Cg Cg+e 
  gi|91774241|ref|YP_566933.1| 46 YSCGACGQEI 55
                                  99*****985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0051
                                   ---SSS-- CS
                DNA_RNApol_7kD  18 iRCkeCGh 25 
                                   i+C +CG+
  gi|91774241|ref|YP_566933.1|  95 IQCSNCGS 102
                                   99*****7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.025        50      16      22 ..      48      54 ..      42      62 .. 0.60
   2 ?    7.4   0.1    0.0019       3.8      16      23 .]      97     104 ..      94     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.025
                 zinc_ribbon_2 16 CpyCGtp 22
                                  C  CG +
  gi|91774241|ref|YP_566933.1| 48 CGACGQE 54
                                  5555544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0019
                 zinc_ribbon_2  16 CpyCGtpl 23 
                                   C++CG++l
  gi|91774241|ref|YP_566933.1|  97 CSNCGSHL 104
                                   88888876 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       2.1   4.2e+03       7      10 ..      48      51 ..      46      55 .. 0.73
   2 ?   10.5   0.0   0.00016      0.31      22      50 ..      92     121 ..      87     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                   Mu-like_Com  7 CGeC 10
                                  CG C
  gi|91774241|ref|YP_566933.1| 48 CGAC 51
                                  7777 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                   Mu-like_Com  22 eltiKCPRCGt.LnHlkaesldaegrReri 50 
                                    ++i+C  CG  L H+    +++ g+R  i
  gi|91774241|ref|YP_566933.1|  92 RIEIQCSNCGShLGHVFDDGPQSTGKRYCI 121
                                   589*******669*************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 880.64
//
Query:       gi|91774242|ref|YP_566934.1|  [L=138]
Description: hypothetical protein Mbur_2330 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score 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   13.8   1.2       0.11   12.2   0.1    2.1  2  Neurensin       Neurensin
      0.037   14.0   6.4       0.06   13.4   6.4    1.4  1  Gly-zipper_Omp  Glycine zipper
       0.28   11.1   3.6        4.9    7.0   1.1    2.3  2  DUF2721         Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.091   5.4e+02     105     130 ..       5      31 ..       1      34 [. 0.69
   2 ?   12.2   0.1   1.8e-05      0.11      27      60 ..      96     129 ..      80     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.091
                     Neurensin 105 lGglllalsll.vpalsksdkkeeele 130
                                   l+++ la++l  ++++++++ k++ ++
  gi|91774242|ref|YP_566934.1|   5 LAAVFLAFVLCvLSIFLANVVKKRVAD 31 
                                   677888888874677777777777665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.8e-05
                     Neurensin  27 lllqrakqksesllwkvslvvgtlvlllGvtall 60 
                                   ++  r+  + es l +v++v+ + vl+lGvt+l 
  gi|91774242|ref|YP_566934.1|  96 VKNIRPLTEKESRLQRVFIVFTISVLILGVTVLF 129
                                   56677778899********************995 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.4     1e-05      0.06       5      45 ..      54      94 ..      46      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                Gly-zipper_Omp  5 iGAaaGaliGgavggrgtGaliGAavGaavGgliGaamdkq 45
                                  +G  +G  iG a g+ ++G++iG a+G   G +iG+ ++k+
  gi|91774242|ref|YP_566934.1| 54 LGMPLGISIGIALGNVAIGIAIGPALGMGFGTMIGYVLEKK 94
                                  55557888999999*9********************99886 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.1   0.00082       4.9      67      96 ..       2      31 ..       1      38 [. 0.80
   2 ?    4.2   0.1    0.0062        37      62      85 ..     108     131 ..      90     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00082
                       DUF2721 67 illlvlsallvvlvvlllflsallsldlsl 96
                                   l+l++ +l++vl+vl +fl+++++ +++ 
  gi|91774242|ref|YP_566934.1|  2 SLFLAAVFLAFVLCVLSIFLANVVKKRVAD 31
                                  577888899999999999999988777665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0062
                       DUF2721  62 lirrailllvlsallvvlvvlllf 85 
                                    ++r +++ ++s+l++ ++vl+ +
  gi|91774242|ref|YP_566934.1| 108 RLQRVFIVFTISVLILGVTVLFSL 131
                                   556666666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 877.78
//
Query:       gi|91774243|ref|YP_566935.1|  [L=307]
Description: MscS mechanosensitive ion channel [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.3e-42  143.7   0.8    8.8e-42  143.0   0.8    1.3  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.58    8.2   3.2       0.75    7.8   3.2    1.1  1  UPF0182     Uncharacterised protein family (UPF0182)


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 !  143.0   0.8   9.8e-46   8.8e-42       4     206 .]      64     277 ..      61     277 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 9.8e-46
                                   HHHHHHHHHHHHHHHTTT--...SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                    MS_channel   4 lkiliivvgilivlsllgvn...vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                   +  ++++ g+l++++++        al+a++G++g+++g+a+++++sn++aG+ l + +pf++GDl++i +  G+V+di+l
  gi|91774243|ref|YP_566935.1|  64 IVAVVYFAGLLVIIFHFESLrdlSIALFAGAGFAGIVVGMAAQNTLSNIIAGVALATFRPFRVGDLLTIHGEYGRVTDITL 144
                                   55566666666666666554454779******************************************************* PP

                                   SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T.......... CS
                    MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk.......... 152
                                     tkirt+d+r + iPn  +++++i+N+s  ++t+  +v+ig+ y+s+   ++ +++++ ++++++++v +          
  gi|91774243|ref|YP_566935.1| 145 GYTKIRTWDNRRLNIPNHVISDEAIINWSIDDPTVNWTVDIGISYDSN---IDLARRIMIDEASKHKNVMSyenlqkhnsh 222
                                   ************************************************...9999999*********************** PP

                                   ...TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                    MS_channel 153 ...dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       +e  v+l+e+gd ++n++++v+v++   +  + +  ++ + ikk +++egiei
  gi|91774243|ref|YP_566935.1| 223 ekkGEEVSVLLTELGDFAVNLRLYVWVRD--RSVCFTTGCDLKEAIKKRFDAEGIEI 277
                                   *999999**********************..8***********************97 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.2   8.4e-05      0.75     146     250 ..      18     123 ..       2     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 8.4e-05
                       UPF0182 146 lslllalvllaliavllvyllsgeslgirl.........kfaelskaarrhlsvllallllllalsywLdryellys.krg 216
                                    ++++++v+l+++++ l+           l         k++++++++   +  ++++++ + +l +++  +e l + +  
  gi|91774243|ref|YP_566935.1|  18 IFFAFFVVILTFFTARLTDR---------LlkayfvlasKKMNIDETTYGLVRRIIVAVVYFAGLLVIIFHFESLRDlSIA 89 
                                   22333333333333333333.........1233445555667788887777777778888888888888888888874445 PP

                       UPF0182 217 vvtGagYtdvnavlpaktilavialvvavlllva 250
                                   +++Gag+  + + + a++ l+ i + va++ +  
  gi|91774243|ref|YP_566935.1|  90 LFAGAGFAGIVVGMAAQNTLSNIIAGVALATFRP 123
                                   9********************9999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1891.66
//
Query:       gi|91774244|ref|YP_566936.1|  [L=208]
Description: UbiE/COQ5 methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   66.2   0.0    4.8e-18   65.7   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    5.1e-18   65.2   0.0    6.9e-18   64.8   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.9e-18   65.3   0.0    8.7e-18   64.8   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.1e-16   60.9   0.0    1.3e-16   60.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    2.2e-09   38.0   0.0    3.4e-09   37.3   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    3.2e-08   33.6   0.0    4.1e-08   33.2   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    4.8e-08   32.6   0.0      6e-08   32.3   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      7e-07   29.0   0.0    9.1e-07   28.6   0.0    1.1  1  MTS              Methyltransferase small domain
    8.3e-07   27.9   0.0    9.4e-07   27.7   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    2.1e-05   24.5   0.1    0.00017   21.5   0.1    1.9  1  Methyltransf_8   Hypothetical methyltransferase
    0.00012   21.8   0.1    0.00029   20.5   0.1    1.7  1  MetW             Methionine biosynthesis protein MetW
    0.00094   18.7   0.0     0.0013   18.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0024   17.5   0.0      0.006   16.3   0.0    1.5  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0029   17.3   0.0     0.0038   16.9   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0037   17.3   0.0      0.005   16.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.036   13.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.028   14.0   0.0      0.039   13.5   0.0    1.2  1  DOT1             Histone methylation protein DOT1
      0.029   14.5   0.0      0.055   13.6   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
      0.047   13.6   0.0      0.075   13.0   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.071   12.7   0.0      0.098   12.3   0.0    1.1  1  NodS             Nodulation protein S (NodS)
       0.13   11.9   0.0       0.17   11.5   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit


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 !   65.7   0.0   5.6e-21   4.8e-18       1      97 []      46     143 ..      46     143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 5.6e-21
                                   EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                   vLdlGcGt  l +++ k+  + +kv+g+D+s+++l++a+++ +  + ++++++g +++lpf+++ fD+vv s a++ +++e
  gi|91774244|ref|YP_566936.1|  46 VLDLGCGTASLDIEIEKKAeHTCKVYGIDLSDTQLKYAHSKTKGMEEEISLYKGTMDELPFKNDAFDIVVTSVAFCETDEE 126
                                   9*****************9659********************76666************************9889999*** PP

                                   HHHHHHHHHHHHEEEEE CS
               Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    ++  +ke +rvL++gG
  gi|91774244|ref|YP_566936.1| 127 VRRGSIKETSRVLRNGG 143
                                   ****************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 !   64.8   0.0     8e-21   6.9e-18      19     164 ..      16     160 ..      13     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 8e-21
                                   HHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSST CS
               Ubie_methyltran  19 kyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkin 99 
                                   +yD    +l +g h  + k   +l    +g kvlD+ +Gt+ l +++ ++++++ kv ++D++++ Lk ++ k k     +
  gi|91774244|ref|YP_566936.1|  16 NYDIFATLLGFG-HSYYEKAAGEL-PLEKGMKVLDLGCGTASLDIEIEKKAEHTCKVYGIDLSDTQLKYAHSKTKGM-EEE 93 
                                   788888888887.66666555554.45689****************************************9997643.459 PP

                                   EEEEE--TTT-TTS-T-EEEEEEES-GGG-S-..HHHHHHHHHHHEEEEEEEEEEEE----SHHHHH CS
               Ubie_methyltran 100 ieflqanaeeLpfeddsfDvvtvsfGlrnvtD..klkaLkeayrvlkpGGrlvvlefskvelpllsq 164
                                   i + ++   eLpf++d+fD+v  s  +  + +  +  ++ke  rvl+ GG +v ++ +++ + l s 
  gi|91774244|ref|YP_566936.1|  94 ISLYKGTMDELPFKNDAFDIVVTSVAFCETDEevRRGSIKETSRVLRNGGYFVLIDCARPRMALTSA 160
                                   *******************9987777666655115679**********************9988765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0     1e-20   8.7e-18       1      96 []      47     147 ..      47     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1e-20
                                   EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CC CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..ed 76 
                                   Ld+GcGt +l  +++k++   ++v+g+Dls+++lk+a++k+++ ++++++ ++++ +lpf+++ fD+vv s +++    e 
  gi|91774244|ref|YP_566936.1|  47 LDLGCGTASLDIEIEKKAehtCKVYGIDLSDTQLKYAHSKTKGMEEEISLYKGTMDELPFKNDAFDIVVTSVAFCETdeEV 127
                                   8**********9999666677****************9999999999******************************9888 PP

                                   HHHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                   ++  +ke  RvL++gG++v+
  gi|91774244|ref|YP_566936.1| 128 RRGSIKETSRVLRNGGYFVL 147
                                   999**************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   1.6e-19   1.3e-16       2     114 ..      41     157 ..      40     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.6e-19
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                   +kg++vlDlGCGt  l +e+ +++   ++v+GiD s + +++A ++   +g + ++++ +g + el+  ++ + fD++++ 
  gi|91774244|ref|YP_566936.1|  41 EKGMKVLDLGCGTASLDIEIEKKAEHTCKVYGIDLSDTQLKYAHSK--TKGMEeEISLYKGTMDELP--FKNDAFDIVVTS 117
                                   79*******************99999*****************996..6688879************..***********9 PP

               Methyltransf_31  82 evl..naladpdkileeiervlkpggilliedpr.....l 114
                                    ++   +       ++e +rvl++gg++++ d+      l
  gi|91774244|ref|YP_566936.1| 118 VAFceTDEEVRRGSIKETSRVLRNGGYFVLIDCArprmaL 157
                                   8886666666778899*****************9444430 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0     4e-12   3.4e-09       1      99 []      47     145 ..      47     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4e-12
               Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhl 79 
                                   L++GcGt+sl  ++++k  ++++++g+D+s  +++ a  k++  e+   + ++ + ++   l+ + ++fD+vv s +++ +
  gi|91774244|ref|YP_566936.1|  47 LDLGCGTASLDIEIEKKAeHTCKVYGIDLSDTQLKYAHSKTKGMEE-EISLYKGTMDE---LPFKnDAFDIVVTSVAFCET 123
                                   8****************99***************888888888775.44445544444...444458********999999 PP

               Methyltransf_12  80 ..kdirevldnirklLkpgGrl 99 
                                     + +r ++++  ++L++gG++
  gi|91774244|ref|YP_566936.1| 124 deEVRRGSIKETSRVLRNGGYF 145
                                   977777**************85 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   4.8e-11   4.1e-08      20     159 ..      40     187 ..      27     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.8e-11
               Methyltransf_23  20 lraggrvLdiGcGtGillevl...rengfsvtgvDlspeaveiae........kakkaqkdqfdeq........eaaepqg 81 
                                   l++g++vLd+GcGt +l  ++   +e+ ++v+g+Dls+ + + a         +           +        e +++++
  gi|91774244|ref|YP_566936.1|  40 LEKGMKVLDLGCGTASLDIEIekkAEHTCKVYGIDLSDTQLKYAHsktkgmeeE-----------IslykgtmdELPFKND 109
                                   8999************9999954445578********98777653444444433...........1344444437777*** PP

               Methyltransf_23  82 kfdlIvlrevlehvpd..ppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaG 159
                                    fd++v +  ++  +       ++   + l+ gGy++l + +++  ++ +++  ++   + +    ++  ++ e+++++G
  gi|91774244|ref|YP_566936.1| 110 AFDIVVTSVAFCETDEevRRGSIKETSRVLRNGGYFVLIDCARPRMALTSAMLLPFFMLK-TNEDNWN-NTYVEICKNNG 187
                                   **************96447799****************9998876444444444444444.4445555.45555555555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0     7e-11     6e-08      53     166 ..      33     149 ..      27     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 7e-11
                                   HHHTTTT--TT-EEEEES-TTSHHHHH..HHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-..--.-- CS
                          CMAS  53 lileklelkpGmtlLdiGcGWGslvrr..averydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl..de.kv 128
                                    + + l l++Gm++Ld+GcG  sl ++    +++  kv g+ lS+ q k+a+ + + ++  ++ +++     +l  ++  +
  gi|91774244|ref|YP_566936.1|  33 KAAGELPLEKGMKVLDLGCGTASLDIEieKKAEHTCKVYGIDLSDTQLKYAHSKTKGME--EEISLYKGTMDELpfKNdAF 111
                                   5677899**************99865411556679****************99988777..5555555555555114469* PP

                                   SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEE CS
                          CMAS 129 drvvsvgafehvgkenydtffkklkkllkedGllllht 166
                                   d vv+  af    +e     +k+++++l+++G ++l  
  gi|91774244|ref|YP_566936.1| 112 DIVVTSVAFCETDEEVRRGSIKETSRVLRNGGYFVLID 149
                                   ***99999999999999999************998754 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.1e-09   9.1e-07      27     138 ..      38     148 ..      35     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.1e-09
                                   CHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE-- CS
                           MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivsNP 105
                                   lp e+  kvlDlGcG+  l +++ k+ +++  v  +d +   l+ a+   +  + e+++++  + e  ++++ fd++v+  
  gi|91774244|ref|YP_566936.1|  38 LPLEKGMKVLDLGCGTASLDIEIEKKAEHTCkVYGIDLSDTQLKYAHSKTKGMEEEISLYKGTMDElPFKNDAFDIVVTSV 118
                                   56667889***************999988756999****************99999******9998456799********9 PP

                                   -STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                           MTS 106 PfhagkatelavaeeliaeAkeaLkegGeLliV 138
                                    f +  +   +v +  i+e  ++L++gG ++++
  gi|91774244|ref|YP_566936.1| 119 AFCETDE---EVRRGSIKETSRVLRNGGYFVLI 148
                                   9988777...99****************99887 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.1e-09   9.4e-07     120     217 ..      45     147 ..      27     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.1e-09
               Methyltransf_29 120 tvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLe..Rgvpailavl.gt.krlpyPsrsfdlihCsr..Cridw 194
                                   +vlD+GCg as+   + ++   t  +   D  + q+++a    +g+   +++  gt   lp+   +fd++  s   C  d 
  gi|91774244|ref|YP_566936.1|  45 KVLDLGCGTASLDIEIEKKAEHTCKVYGIDLSDTQLKYAHSktKGMEEEISLYkGTmDELPFKNDAFDIVVTSVafCETDE 125
                                   69************************************975226888888876333268**********987652277777 PP

               Methyltransf_29 195 teedgilllevdRvlRpgGyfvl 217
                                   + + g  + e  RvlR gGyfvl
  gi|91774244|ref|YP_566936.1| 126 EVRRG-SIKETSRVLRNGGYFVL 147
                                   77777.579*************8 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1     2e-07   0.00017      74     157 ..      44     148 ..      39     164 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-07
                                   S-EEEES-TT-HHH....HH--S-..EEEEESS-SS............TTE..EES-TTS-S--TT-EEEEEEES---SS- CS
                Methyltransf_8  74 lvvadlGcGeakia....eavrekekvrsfdlvavn............erv..vacdlakvPledesvdvavfclslmgtn 136
                                   + v dlGcG a +     ++ +++ kv  +dl   +            e++      + ++P ++++ d++v  +++  t+
  gi|91774244|ref|YP_566936.1|  44 MKVLDLGCGTASLDieieKKAEHTCKVYGIDLSDTQlkyahsktkgmeEEIslYKGTMDELPFKNDAFDIVVTSVAFCETD 124
                                   5799*****99887433233445568999999754311111111111133311456899******************9998 PP

                                   HHH...HHHHHHHHEEEEEEEEEE CS
                Methyltransf_8 137 lad...flkeanrvlkvGGllkva 157
                                    ++    +ke  rvl++GG++ + 
  gi|91774244|ref|YP_566936.1| 125 EEVrrgSIKETSRVLRNGGYFVLI 148
                                   6542238************98765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.3e-07   0.00029      12      90 ..      41     125 ..      37     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.3e-07
                          MetW  12 kpgsrvldlGcGdGellell..keekqvdgrGleldeegvaec..vakG....lsviqgdldkdlenfedksfdyvvlsqt 84 
                                   ++g +vldlGcG  +l   +  k e+  + +G++l+++ ++ +   +kG    +s+ +g +d+    f++++fd+vv s +
  gi|91774244|ref|YP_566936.1|  41 EKGMKVLDLGCGTASLDIEIekKAEHTCKVYGIDLSDTQLKYAhsKTKGmeeeISLYKGTMDE--LPFKNDAFDIVVTSVA 119
                                   6789***********955441134567899******998865511455622224556666654..4699*********999 PP

                          MetW  85 lqatrn 90 
                                   + +t +
  gi|91774244|ref|YP_566936.1| 120 FCETDE 125
                                   877754 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0013     159     232 ..      40     116 ..      32     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLgak..kvvavDiDevAvkvakeNaelNkveakleva..lseell.keekadviva 232
                                   +++g +vlD+G+G++ L i   k + +  kv+++D+ +  +k a++     ++e++++++  + +el+ k+  +d++v 
  gi|91774244|ref|YP_566936.1|  40 LEKGMKVLDLGCGTASLDIEIEKKAEHtcKVYGIDLSDTQLKYAHSK--TKGMEEEISLYkgTMDELPfKNDAFDIVVT 116
                                   56789**************999876543389***********99975..5578888887633455555568999*9997 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     7e-06     0.006      33     154 ..      38     148 ..      27     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7e-06
                                   .T-S--EEEEEET-TT-...HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--...........-TTT-- CS
                          TPMT  33 lkakaglrvlvPlCGka...ldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvkeysageiellcgdvFtlr 110
                                   l +++g +vl  +CG a   +++   Ae+  +v G++ls+  ++ +    +     ++ +g++e    ei+l+ g +  l+
  gi|91774244|ref|YP_566936.1|  38 LPLEKGMKVLDLGCGTAsldIEIEKKAEHTCKVYGIDLSDTQLKYA----H-----SKTKGMEE----EISLYKGTMDELP 105
                                   5667788999999**8743346778899999*********999983....2.....34556666....899*****99999 PP

                                   -SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE..EE CS
                          TPMT 111 aeelgkfdliydraalvAlppelreryakslaelLkpdgeglLv 154
                                    ++   fd++   +a++  ++e+r    k+  ++L+++g  +L+
  gi|91774244|ref|YP_566936.1| 106 FKND-AFDIVVTSVAFCETDEEVRRGSIKETSRVLRNGGYFVLI 148
                                   8887.8********************************997776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.5e-06    0.0038      65     131 ..      56     120 ..      30     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                                   HHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---- CS
                       UPF0020  65 lkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY 131
                                   l  e+e++a+++ k+yg+Dl    ++ a ++ +  g++++i++++  + +L+ k++ +d++vt   +
  gi|91774244|ref|YP_566936.1|  56 LDIEIEKKAEHTCKVYGIDLSDTQLKYAHSKTK--GMEEEISLYKGTMDELPFKNDAFDIVVTSVAF 120
                                   667999**********************99765..899**************9999******97655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.8e-06     0.005      25      75 ..      42      91 ..      29     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
               Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                  + ++v+D+G+G + L   ++  ++e+ +kv+gid+++   + a    + ++
  gi|91774244|ref|YP_566936.1| 42 KGMKVLDLGCGTASLDIEIEK-KAEHTCKVYGIDLSDTQLKYAHSKTKGME 91
                                  5678***************99.7779*********9998887777666555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.2e-05     0.036      69     117 ..      38      86 ..      30     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                   TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH CS
                          PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn 117
                                   l l+kg++vL++G+G+  l   + +  +++++v +i+ +    + a+ +
  gi|91774244|ref|YP_566936.1|  38 LPLEKGMKVLDLGCGTASLDIEIEKKAEHTCKVYGIDLSDTQLKYAHSK 86 
                                   669*********************************9887766666555 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.6e-05     0.039      36     110 ..      36     111 ..      22     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                                   HHTT--TT-EEEEES-TTSHHHHHH..HHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEEESS-S CS
                          DOT1  36 dkvnlkkedvFvDLGSGvGnvvlqa..alevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakiefirksF 110
                                    ++ l+k    +DLG G   + + +   +e  ck  +G++++d+  ++a+++++ +++ ++l+   + ++ f+++ F
  gi|91774244|ref|YP_566936.1|  36 GELPLEKGMKVLDLGCGTASLDIEIekKAEHTCK-VYGIDLSDTQLKYAHSKTKGMEEEISLYKGTMDELPFKNDAF 111
                                   56778999999*******9877655116778888.9***************************88888888877666 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.4e-05     0.055      19     101 ..      40     123 ..      30     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-05
                                   S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH...TTEEEECS-C.CCSSHHHHHCHCHHHSSEEEEEE-- CS
                          FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl...pgvttiqgdi.tdpetiekikealserkvdlvvsDg 95 
                                   +++g++v+Dlg+++ +    + ++ ++++kv+++Dl   ++    ++ + ++  i + + t++++   +++  +d+vv  +
  gi|91774244|ref|YP_566936.1|  40 LEKGMKVLDLGCGTASLDIEIEKKAEHTCKVYGIDLSDTQLKyahSKTKGMEEEIsLYKGTMDELP--FKNDAFDIVVTSV 118
                                   56899************99999998889********999554445888888999988888999877..6778999999999 PP

                                   S-SS-C CS
                          FtsJ  96 apdvsg 101
                                   a +++ 
  gi|91774244|ref|YP_566936.1| 119 A-FCET 123
                                   9.6554 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.8e-05     0.075      13      72 ..      41      99 ..      37     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-05
               Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrls 72
                                  ekg +v+D G+  + l+i++ k+ +++ kv+ +D+++  l+ a+++ +  g+e++i+++ +
  gi|91774244|ref|YP_566936.1| 41 EKGMKVLDLGCGTASLDIEIEKKaEHTCKVYGIDLSDTQLKYAHSKTK--GMEEEISLYKG 99
                                  67889**************9865167789**************98875..57777777655 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011     0.098      46     144 ..      45     147 ..      36     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                          NodS  46 dalevGcaaGalt...erlapyckrltvvdvveeaiararervkes.shiswivsdvqqfst.dekfdlivvaevlyyied 121
                                   ++l++Gc + +l    e+ a ++ ++  +d+ +  ++ a+ ++k +  +is  +  + ++   ++ fd ivv+ v +  +d
  gi|91774244|ref|YP_566936.1|  45 KVLDLGCGTASLDieiEKKAEHTCKVYGIDLSDTQLKYAHSKTKGMeEEISLYKGTMDELPFkNDAFD-IVVTSVAFCETD 124
                                   68999**999985222677888888899********99999999762579999988888875156777.78899*999999 PP

                          NodS 122 vaelraavrnlvsllapdgqlvf 144
                                    +  r+++++  ++l+ +g++v+
  gi|91774244|ref|YP_566936.1| 125 EEVRRGSIKETSRVLRNGGYFVL 147
                                   9999****************996 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.17      35      95 ..      37      95 ..      34     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                         GCD14 35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvt 95
                                  +L l++G +v++ G G++sl   i +  + t +++ ++  +++ + a  +   +++++ + 
  gi|91774244|ref|YP_566936.1| 37 ELPLEKGMKVLDLGCGTASLDIEIEKKAEHTCKVYGIDLSDTQLKYAHSK--TKGMEEEIS 95
                                  57899*************************************99999864..445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1291.77
//
Query:       gi|91774245|ref|YP_566937.1|  [L=245]
Description: 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-73  244.9   0.0    7.9e-73  244.7   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.7   0.0   4.4e-77   7.9e-73       1     217 [.      48     244 ..      48     245 .] 0.97

  Alignments for each domain:
  == domain 1  score: 244.7 bits;  conditional E-value: 4.4e-77
                                   .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHH CS
                 FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeA 81 
                                   kivc+glny +h+ e+g   +++p      epv+f+k++ss++g+gd+i++Pa s+++dyE+ELavvigk++r++ + e+A
  gi|91774245|ref|YP_566937.1|  48 KIVCIGLNYIDHAVELG---MDVPV-----EPVIFMKPPSSVIGSGDKIVYPAMSQRVDYEAELAVVIGKRCRNI-DYEDA 119
                                   69**************8...66777.....999******************************************.99*** PP

                                   HTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSHHH CS
                 FAA_hydrolase  82 edaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifspae 162
                                    d+iaGyt +nDv+aRdlq+++    +w+++ksfdtf+p+Gp+iv+  +++ p+d+++++rvnge++qds+t+++if+++ 
  gi|91774245|ref|YP_566937.1| 120 GDVIAGYTCFNDVTARDLQQKDG---QWTRAKSFDTFAPLGPFIVPEGDFD-PSDVSIKCRVNGEVRQDSSTSNLIFDIPH 196
                                   ***********************...************************5.68*************************** PP

                                   HHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                 FAA_hydrolase 163 liahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                   li+ +s ++tLe Gd+i+tGTp+gvg  e     l  gD+veve+eg+G+l+n+V
  gi|91774245|ref|YP_566937.1| 197 LIEFISDIMTLEVGDVISTGTPPGVG--E-----LLRGDVVEVEVEGIGTLANEV 244
                                   ************************99..4.....99*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1512.41
//
Query:       gi|91774246|ref|YP_566938.1|  [L=99]
Description: hypothetical protein Mbur_2334 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00077   19.0   0.1     0.0014   18.1   0.1    1.5  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0016   18.3   0.1     0.0025   17.6   0.1    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.014   15.7   0.1      0.019   15.3   0.1    1.2  1  Rrf2           Transcriptional regulator
      0.019   14.9   0.3      0.057   13.3   0.2    1.9  2  HTH_5          Bacterial regulatory protein, arsR family
      0.031   13.6   0.1      0.042   13.2   0.1    1.1  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
      0.061   13.7   0.1       0.11   12.9   0.0    1.5  2  FaeA           FaeA-like protein
      0.074   12.6   0.0      0.095   12.3   0.0    1.3  1  HTH_47         winged helix-turn-helix
      0.075   13.0   0.1       0.18   11.7   0.0    1.9  1  HTH_12         Ribonuclease R winged-helix domain
       0.11   12.0   0.0       0.12   11.8   0.0    1.3  1  RepL           Firmicute plasmid replication protein (RepL)
       0.11   12.5   0.2        1.4    9.1   0.0    2.6  2  MerR_1         MerR HTH family regulatory protein


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 !   18.1   0.1   7.8e-07    0.0014       5      48 .]      16      59 ..      12      59 .. 0.88
   2 ?   -3.2   0.0       3.7   6.6e+03      18      26 ..      65      73 ..      64      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.8e-07
                        HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ++ +L+ + +n+ i +  LAe++g++   v++ l+ Le+e lIk
  gi|91774246|ref|YP_566938.1| 16 HLLVLKKVIENGPIGILKLAEETGMPTHKVRYSLRVLEQEHLIK 59
                                  5666666789********************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.7
                        HTH_24 18 isqreLAer 26
                                   +  +LAe+
  gi|91774246|ref|YP_566938.1| 65 ATAGDLAEE 73
                                  677899995 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.4e-06    0.0025       3      54 ..       9      60 ..       7      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                  HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                          TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                  +l L+e    v ++++++gp  + ++aee+g p  kv  +Lr Le+  l++ 
  gi|91774246|ref|YP_566938.1|  9 ELELTERHLLVLKKVIENGPIGILKLAEETGMPTHKVRYSLRVLEQEHLIKP 60
                                  6899*****************************************9988875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.1e-05     0.019       3      64 ..       6      68 ..       5      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                  --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE.EETTT-TC CS
                          Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk.svrGkgGG 64
                                  +++++e+  + ll+L+k  e++p+ + ++ae+++++ + ++  l+ L+++ l+k s  G+  G
  gi|91774246|ref|YP_566938.1|  6 INRELELTERHLLVLKKVIENGPIGILKLAEETGMPTHKVRYSLRVLEQEHLIKpSSHGATAG 68
                                  67888888899******************************************8677777666 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 ?   13.3   0.2   3.2e-05     0.057       5      45 ..      17      58 ..      13      59 .. 0.87
   2 ?   -2.3   0.0       2.3   4.2e+03      17      25 ..      66      74 ..      65      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                  HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  l +Lk + e g+  +  laee+g++  +v++ L++L+++ L+
  gi|91774246|ref|YP_566938.1| 17 LLVLKKVIEnGPIGILKLAEETGMPTHKVRYSLRVLEQEHLI 58
                                  67788888888899999********************99887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                                  EHHHHHHHH CS
                         HTH_5 17 cvcelaeel 25
                                  ++++laee+
  gi|91774246|ref|YP_566938.1| 66 TAGDLAEEF 74
                                  789***985 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.4e-05     0.042      83     133 ..      11      59 ..       4      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                   TSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXE CS
                 RNA_pol_Rpc34  83 slsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyik 133
                                   +l+e   lV++ + e G  GI   ++ + ++++ + v+ +L++Le++ +ik
  gi|91774246|ref|YP_566938.1|  11 ELTERHLLVLKKVIENGPIGIL--KLAEETGMPTHKVRYSLRVLEQEHLIK 59 
                                   56777779**********9997..599***********************9 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     6e-05      0.11      10      49 ..      24      62 ..      15      70 .. 0.83
   2 ?   -3.4   0.1       7.3   1.3e+04       5      12 ..      85      92 ..      84      95 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                                  HH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                          FaeA 10 nsikapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49
                                  ++ ++p     +A+ +g+    +Ry L  Le+e  ik s 
  gi|91774246|ref|YP_566938.1| 24 IE-NGPIGILKLAEETGMPTHKVRYSLRVLEQEHLIKPSS 62
                                  44.677777889**********************999775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.3
                                  HHHHHHH. CS
                          FaeA  5 Ileylnsi 12
                                  Ile +++i
  gi|91774246|ref|YP_566938.1| 85 ILEKITQI 92
                                  56656555 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.3e-05     0.095      44      77 ..      26      59 ..       2      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                                  EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 44 DGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                   G  ++l++Ae++g+p ++v   +r L+++ l++
  gi|91774246|ref|YP_566938.1| 26 NGPIGILKLAEETGMPTHKVRYSLRVLEQEHLIK 59
                                  588899*************************996 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.18      30      53 ..      40      63 ..      17      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                        HTH_12 30 igeravRyrLrkleergltrrvgy 53
                                  + +  vRy Lr+le++ l++  + 
  gi|91774246|ref|YP_566938.1| 40 MPTHKVRYSLRVLEQEHLIKPSSH 63
                                  456789************996655 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.8e-05      0.12      80     112 ..      33      65 ..      19      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.8e-05
                          RepL  80 elaeetgislktvsetlkileeanilkkkanGv 112
                                   +laeetg+ ++ v+  l++le+  ++k  + G+
  gi|91774246|ref|YP_566938.1|  33 KLAEETGMPTHKVRYSLRVLEQEHLIKPSSHGA 65 
                                   79*************************998887 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 ?   -0.5   0.1      0.73   1.3e+03      39      50 ..      13      24 ..       5      25 .. 0.79
   2 ?    9.1   0.0   0.00078       1.4       5      29 ..      33      61 ..      30      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.73
                                  EHHHHHHHHHHH CS
                        MerR_1 39 tdedierLklik 50
                                  t++++ +Lk++ 
  gi|91774246|ref|YP_566938.1| 13 TERHLLVLKKVI 24
                                  789999999885 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00078
                                  HHHHHHTS-HHHHHH....HHHHTT-S-E CS
                        MerR_1  5 evakilgvtthtlry....wekegllkpk 29
                                  ++a+++g++th +ry     e+e l+kp+
  gi|91774246|ref|YP_566938.1| 33 KLAEETGMPTHKVRYslrvLEQEHLIKPS 61
                                  69*******99887733336677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 694.67
//
Query:       gi|91774247|ref|YP_566939.1|  [L=569]
Description: glutamyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-61  207.6   0.0    2.8e-61  207.1   0.0    1.2  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    1.3e-27   96.8   0.0    2.1e-27   96.1   0.0    1.4  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 !  207.1   0.0   3.1e-65   2.8e-61       2     312 ..     104     411 ..     103     413 .. 0.95

  Alignments for each domain:
  == domain 1  score: 207.1 bits;  conditional E-value: 3.1e-65
                                   -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCC..C--HHHHHHHHHHHHHTT---SSEEEEGGGGHHH CS
                  tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpe..rekeeaeesiledlkwlgikwdekptyqsdrfde 80 
                                   V+ RfaP+P+G + +G+ + +++n  + k+++Gkfi+R++DTdp+  r   ea +  led +wl+ k+ ++++ +sd ++ 
  gi|91774247|ref|YP_566939.1| 104 VVMRFAPNPNGPPTLGSTRGIVVNSEYVKRYGGKFIIRFDDTDPQtkRPMLEAYDWYLEDCEWLDAKP-DEVVIASDNMEV 183
                                   899****************************************9721555689999************.66999******* PP

                                   HHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGGSS CS
                  tRNA-synt_1c  81 lkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vefrD 160
                                   +++ya +L++ G+AYvc+c+    ++ + +  k  +++r +  e nl+ + ++m  g++e+++avvR+k d e++  ++rD
  gi|91774247|ref|YP_566939.1| 184 YYDYARQLLEMGHAYVCFCEGGDFKKFKDA--KEPCPHRGHAPEVNLEHW-DKMLAGEYEEKAAVVRIKTDIEHKdPAMRD 261
                                   ****************************99..89999*************.89******************99999***** PP

                                   TEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEETT CS
                  tRNA-synt_1c 161 lvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrlnlek 241
                                     + ri  +  +  + v +k+ + P  df  +i D++ ++th++r+++ +d+++++  ++++lg+e p+  h   +   e 
  gi|91774247|ref|YP_566939.1| 262 FGAFRIVKTA-HPRPEVDDKYVVWPLLDFEGAIEDHVLGMTHIIRGKDLMDSEKRQGYIYNYLGWEYPKTTHWGRVKMHEF 341
                                   ******9988.66788********************************************************999999999 PP

                                   SB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHHHHH CS
                  tRNA-synt_1c 242 kklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdrkkL 312
                                    k S   l +++++ ++ +wdd+r+++l++lrr+G++pe++r+++   ++ + + ++ +++ l a +rk +
  gi|91774247|ref|YP_566939.1| 342 GKFSTSGLRQSIEDGEYSGWDDPRLPTLRALRRRGIKPEAIRKFMIDMGVGETD-VSLSMDTLYAENRKII 411
                                   **************************************************9998.9988888888777765 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 !   96.1   0.0   2.4e-31   2.1e-27       1     174 []     415     556 ..     415     556 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 2.4e-31
                tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveevekde 81 
                                   A+Ry++V+dpv++++e+   +  ++++ +lhp+ +++g r + +++++++ ++D+++ + g+++r+k+lyni++++v    
  gi|91774247|ref|YP_566939.1| 415 ANRYFFVWDPVELEVED---AVCCTVNPSLHPS-EDRGVRCIDIGSKLLVCKSDVESAELGDMLRMKYLYNIEITSV---- 487
                                   89**************4...4689*********.9***************************************999.... PP

                tRNA-synt_1c_C  82 sgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepalanlkkgd 161
                                       + lk+++ g+s+e+a+++k+ iihWv+ e+ +++                ++l p+++ +   g++e+++ + + ++
  gi|91774247|ref|YP_566939.1| 488 ----SPLKCKCIGDSMEDAKSNKMrIIHWVP-EDGIPV----------------KVLAPQGEFI---GMGEKQIVD-ELDN 543
                                   ....4688***********99999*******.59****................9*******74...9********.9*** PP

                tRNA-synt_1c_C 162 ivQfeRiGyfrvd 174
                                   +vQfeR+G++r+d
  gi|91774247|ref|YP_566939.1| 544 VVQFERFGFCRID 556
                                   ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3712.64
//
Query:       gi|91774248|ref|YP_566940.1|  [L=235]
Description: 30S ribosomal protein S3Ae [Methanococcoides burtonii DSM 6242]
Scores for 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-69  232.2   4.8    5.3e-69  231.9   4.8    1.1  1  Ribosomal_S3Ae  Ribosomal S3Ae family


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 !  231.9   4.8   2.9e-73   5.3e-69       3     199 ..       6     191 ..       4     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 231.9 bits;  conditional E-value: 2.9e-73
                                   ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEEEESSE CS
                Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkieevqgkn 82 
                                    +++ Dk+k K+Wy++ aP+++g+++iG t+        +++e+l+gr+ve+++++Ltnd+ k+  ++klkl+i++v+g+ 
  gi|91774248|ref|YP_566940.1|   6 VQRKLDKWKLKQWYNIVAPKFIGSNHIGLTPT-------DDPESLIGRIVETTVGELTNDFsKH--NIKLKLEIDNVTGDV 77 
                                   67899***************************.......**********************555..*************** PP

                                   EEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-HH CS
                Ribosomal_S3Ae  83 altnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldlk 163
                                   a t+F g+e+t+D+lrs+v++++s+I+++++vktkDgy++rv++++fT kr   a++sq+ka+r +m+e++ ++aseld++
  gi|91774248|ref|YP_566940.1|  78 ANTRFIGHEITTDYLRSIVKRQTSRIDTNLNVKTKDGYKIRVKPICFTVKR---ARTSQIKALRDIMTETTAKRASELDFE 155
                                   ***************************************************...*************************** PP

                                   HHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEE CS
                Ribosomal_S3Ae 164 elvkklipeslgkeiekeakkIyplrnveirKvkvl 199
                                   ++v++ i  +l+++i+++ak+Iyplr+veirK++v 
  gi|91774248|ref|YP_566940.1| 156 QFVEEAIVGKLSANIYRKAKSIYPLRRVEIRKTEVQ 191
                                   ********77***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1520.14
//
Query:       gi|91774249|ref|YP_566941.1|  [L=502]
Description: seryl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for 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-60  201.1   0.1    1.3e-59  200.6   0.1    1.2  1  tRNA_bind_4   tRNA-binding domain
    3.6e-06   27.1   0.0    8.9e-06   25.8   0.0    1.6  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 


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 !  200.6   0.1   1.4e-63   1.3e-59       1     160 [.       3     158 ..       3     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 1.4e-63
                                   EEEEEEEEEEESS-SCCCHHHHHHHHHHHCCTGGGTTSSTTT.S.SSEEEEEEE-SSEEEEEEEEESSS-HHHHHHHHHHH CS
                   tRNA_bind_4   1 lkfelkgklklskdieeaeeeieefieeanktiLkkGvpegkeeegakitewkiegnelkleieSgryvRahdallrlkkp 81 
                                   lkf+lkg++k+s+d + a+e i+++++ean+tiLkkG+peg+   gakit+w+i + +++l+ieSgryvRahda++rlkkp
  gi|91774249|ref|YP_566941.1|   3 LKFNLKGAFKTSTDPTGAKEVIAQYFDEANNTILKKGAPEGQ---GAKITQWDIVDGSIELTIESGRYVRAHDAIMRLKKP 80 
                                   69***************************************9...************************************ PP

                                   HHHHCCCCCS--EEEEEEEEEEEEEE-SS--HH---TTECEEEEETTEEEEEEES--HHHHHTTHHHHHHHHHHHHHCC CS
                   tRNA_bind_4  82 laeklGkkyriGvRgikveeyeieiesekelkaekipeveeveveegkitlelkdvdeselkkrvvdRiiklveekiek 160
                                   la+klGk++riG+Rg++v++++i++++e e+ +++ip+v+++++ eg ++lel +v+esel++r++dRi++l+eek+++
  gi|91774249|ref|YP_566941.1|  81 LAAKLGKEFRIGIRGVDVKKFTISMPAEGEIGNMNIPHVSNISKVEGGLILEL-NVGESELERRIPDRILTLMEEKVRA 158
                                   *****************************************************.**********************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 !   25.8   0.0   9.9e-10   8.9e-06      18      95 ..     306     384 ..     301     477 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.9e-10
                                   HHHHHHHHHHHEEEBGGSSEEEEE.EEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  18 eetfvelirdevlrskrLPlklyq.iqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlg 95 
                                   +++f    + e++   + P+k+++  +t +R+E   ++G+ Rv eFh  + +  ++++++ +  r+l + + +if++++
  gi|91774249|ref|YP_566941.1| 306 CPPFWMYLQGETIPTDEFPIKVFDkSGTSHRYESGGIHGIERVDEFHRVEIVWLGTKEQVIETARKLHERYMHIFNEIL 384
                                   566666666666766679***986368*******99***************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3282.56
//
Query:       gi|91774250|ref|YP_566942.1|  [L=184]
Description: phage SPO1 DNA polymerase-related protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-38  130.3   0.0    7.2e-38  130.0   0.0    1.0  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.0     4e-42   7.2e-38       4     139 ..      35     167 ..      32     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 4e-42
                                   -CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCCHHHH CS
                           UDG   4 gppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeikacapll 84 
                                   g  ++kv+++GeaPg++ed+tg pF+grag++l++l++ +gl+       +  ++n++kcrpp nr +p+++e++ c+p+l
  gi|91774250|ref|YP_566942.1|  35 GSDEPKVLFIGEAPGKKEDETGVPFCGRAGKILDELIEYMGLES-----SDWAVINTIKCRPPNNR-NPNKKELDCCKPFL 109
                                   7899****************************************.....*****************.************** PP

                                   HHHHHHHHSSEEEEESHHHHHH...HHHHSCESCCCSCT.SEEEEES-SSTTTTT...T CS
                           UDG  85 eeeiellkprlivllGktaakall.geklgklrgklleakirvlplphPsplnrn...f 139
                                    ++i+ll p+livllG+ta ka++ g+k++    + le   +vl+ +hP++l ++   +
  gi|91774250|ref|YP_566942.1| 110 IRQIQLLDPNLIVLLGNTAEKAYCsGHKMKWGAVEMLEG-KNVLKIFHPAALIYTrsrT 167
                                   **********************96655555444445555.8**************4422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1272.65
//
Query:       gi|91774251|ref|YP_566943.1|  [L=79]
Description: hypothetical protein Mbur_2339 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       786  (0.0438396); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 517.05
//
Query:       gi|91774252|ref|YP_566944.1|  [L=437]
Description: phosphoesterase, RecJ-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-17   62.5   1.4    1.4e-16   61.2   0.4    2.3  2  DHHA1     DHHA1 domain
     0.0018   18.4   0.6     0.0056   16.9   0.6    1.8  1  DHH       DHH family
  ------ inclusion threshold ------
      0.012   15.8   0.2      0.081   13.2   0.0    2.5  2  EIIA-man  PTS system fructose IIA component
      0.071   13.3   0.3       0.95    9.7   0.0    2.8  4  ALS_ss_C  Small subunit of acetolactate synthase
       0.18   10.3   0.0       0.25    9.8   0.0    1.1  1  Nic96     Nup93/Nic96


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3   8.2e+03      23      45 ..     257     279 ..     233     297 .. 0.54
   2 !   61.2   0.4   3.9e-20   1.4e-16      27     138 .]     315     432 ..     301     432 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHTCEEECTCEEEEE CS
                         DHHA1  23 aklkaeellekaeevkgvkvlva 45 
                                    ++  + ++ ++e vk+v  lva
  gi|91774252|ref|YP_566944.1| 257 DAAVGDVYILNNEVVKNVYDLVA 279
                                   33333344444444444444444 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 3.9e-20
                                   HHHHHHTCEEEC.....TCEEEEEECHCCHHH.HHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HH CS
                         DHHA1  27 aeellekaeevk.....gvkvlvaevgeewda.galgiaadklksklkkpvivfvakeegdkvkvsarskkd....gvdag 97 
                                   ++++++++ +++     g+++++    ++ +  g++++ + +     +++  v++ k eg kvk+s r +++    g+d++
  gi|91774252|ref|YP_566944.1| 315 QKAIVNDINKAEgllqkGKSIYYLIG-DDLEStGMIASTVIRYIH--PDMPFVAINKVEG-KVKISSRGTRElvskGLDLA 391
                                   33333333333444433555555555.444443666666666666..7788888888888.*********99********* PP

                                   HHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                         DHHA1  98 elakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                    +++ aa+++gg GGGH+ A+Ga++++ek+ee+++++++++
  gi|91774252|ref|YP_566944.1| 392 YAMRTAADAVGGQGGGHNIASGASVEPEKIEEFIALVDDIV 432
                                   *************************************9875 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   1.5e-06    0.0056       8      56 ..      28     108 ..      24     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-06
                                   CSSSHHHHHH.HHHHHH..................................CECS--TCGGCGCCHHCCCSEEEEEEE-S- CS
                                   xxxxxxxxxx.xxxxxx..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH   8 knpDtDsigS.aialan..................................llvDhneksqavegeakeeaedviiiDHHr 53 
                                    + D+D+i S ai  ++                                  + +D+++ + + +g   +   d+i+iDHH+
  gi|91774252|ref|YP_566944.1|  28 SHNDADGISSaAIICQAllrknipyhltivsrledsvaeminettnegdivIFCDMGSGQPDIIG---KVLHDTIVIDHHK 105
                                   688*******666666688888888888888888888888888888888877***********99...88899*******9 PP

                                   --S CS
                                   xxx RF
                           DHH  54 lge 56 
                                   +  
  gi|91774252|ref|YP_566944.1| 106 PVG 108
                                   965 PP

>> EIIA-man  PTS system fructose IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   5.4e+03       9      21 ..       9      21 ..       3      34 .. 0.63
   2 ?   13.2   0.0   2.2e-05     0.081      43      71 ..      60      88 ..      55      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                                  CHHHHHHHHHHCC CS
                      EIIA-man  9 elAeglaelleel 21
                                  elAe++a+++ee 
  gi|91774252|ref|YP_566944.1|  9 ELAEQIADIIEEY 21
                                  4555555555543 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.2e-05
                                  HHHHHHHHHCTS--TTEEEEEESSCCCHH CS
                      EIIA-man 43 laekikeaieevdsedevlvLvDlggatp 71
                                  l++ ++e i+e+++e ++++++D+g+++p
  gi|91774252|ref|YP_566944.1| 60 LEDSVAEMINETTNEGDIVIFCDMGSGQP 88
                                  67889999999999*************98 PP

>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.2   1.1e+04      16      29 ..      12      26 ..       4      30 .. 0.59
   2 ?   -3.7   0.0       4.2   1.5e+04      61      74 .]     173     186 ..     163     186 .. 0.73
   3 ?    9.7   0.0   0.00026      0.95      39      59 ..     206     226 ..     187     231 .. 0.84
   4 ?   -0.6   0.0      0.44   1.6e+03      44      56 ..     417     429 ..     413     435 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.2
                                  HHHHHHHHHT.T-EE CS
                      ALS_ss_C 16 seileiaeif.raki 29
                                  ++i +i+e + +a++
  gi|91774252|ref|YP_566944.1| 12 EQIADIIEEYsHARV 26
                                  456666665555555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.2
                                   EEEEEEEEEEEEST CS
                      ALS_ss_C  61 levvRtGrvAleRG 74 
                                    e v  G++ +++G
  gi|91774252|ref|YP_566944.1| 173 DEAVEAGVISIKKG 186
                                   57788899999886 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00026
                                   EEEEE-HHHHHHHHHHS-GGG CS
                      ALS_ss_C  39 ieltgteekidaliellkpfg 59 
                                   + +tg++ekid+++++l+ +g
  gi|91774252|ref|YP_566944.1| 206 LDITGDREKIDSFLDMLEIHG 226
                                   689**************9766 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.44
                                   -HHHHHHHHHHS- CS
                      ALS_ss_C  44 teekidaliellk 56 
                                   ++eki+++i l++
  gi|91774252|ref|YP_566944.1| 417 EPEKIEEFIALVD 429
                                   689******9986 PP

>> Nic96  Nup93/Nic96
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   6.9e-05      0.25     505     585 ..     212     292 ..     192     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.9e-05
                                   HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHTT-S--.-HHH...HHHHHHCGCCS-HHHHTTHHHHHHHHHHHHHHHHHH CS
                         Nic96 505 retcelLldlleifdlyeagqweealdeiekldllPl.aegdleevrekveefkslseevakvipdlLlatmtclskqyeq 584
                                   re ++  ld+lei+  + + + ++ l+++ ++ +l l ++ ++e+++++v  +  l++ev+k++ dl+ ++ tc +k++  
  gi|91774252|ref|YP_566944.1| 212 REKIDSFLDMLEIHGDIDSMDSDK-LQKLISTIVLKLtKRASPEAIDAAVGDVYILNNEVVKNVYDLVAIMNTCGKKKVPG 291
                                   677888899999999998888765.88888888999999999************************998888887777666 PP

                                   H CS
                         Nic96 585 l 585
                                   l
  gi|91774252|ref|YP_566944.1| 292 L 292
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2646.09
//
Query:       gi|91774253|ref|YP_566945.1|  [L=396]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-46  157.0   0.0    8.9e-46  156.5   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    8.2e-16   57.0  25.6    6.8e-09   35.1   3.7    5.7  5  Hexapep          Bacterial transferase hexapeptide (six repea
    3.9e-15   56.6   0.0    5.1e-15   56.2   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    3.9e-05   23.3   4.0    3.9e-05   23.3   4.0    5.0  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
     0.0001   20.6   0.5    0.00017   19.9   0.5    1.3  1  DUF4954          Domain of unknown function (DUF4954)
    0.00074   19.3   0.0     0.0011   18.7   0.0    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.048   13.6   0.0      0.094   12.6   0.0    1.4  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 !  156.5   0.0   3.5e-49   8.9e-46       1     246 [.       2     230 ..       2     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 3.5e-49
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   kavILa G+GtR++PLt++++k ++pv++k +++++ +  ++++gi+   v +t +h++ +e+++++g++++v++  ++++
  gi|91774253|ref|YP_566945.1|   2 KAVILAAGEGTRMRPLTSSIPKVMLPVANK-PMLEHIVDSAIEAGIDG-FVFITGYHEEVIEQYFGNGDRWNVTIDHVHQE 80 
                                   79****************************.*****************.5555669************************* PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                   e+ gtA+A+  a+  +++++     +vL+gD+l++   ++ +++ ie+++  ++++ +++v++++++Gvie+d++ +v+++
  gi|91774253|ref|YP_566945.1|  81 EQLGTANAIGYAKGHVKEKF-----IVLNGDVLVS---SDHIEHMIERKE--DAVITVKRVDNPSDFGVIETDGN-KVINI 150
                                   ***********999999666.....9*********...888999999999..89999****************95.9**** PP

                                   ECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHH CS
               NTP_transferase 163 vEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleane 243
                                   +EKP+ ++ ++la++GiY+f + +++ + ++ + ++r+e eitd l+ +++++ +  + + +    W D+G + ++l+an+
  gi|91774253|ref|YP_566945.1| 151 IEKPEFPP-TDLANAGIYLFSEAIFDLI-EQTTLSPREEYEITDSLQMLINSDADVGYEILEE--EWIDIGRPWDMLDANA 227
                                   ********.9******************.7799999**************9987776655555..4*************98 PP

                                   HHH CS
               NTP_transferase 244 kla 246
                                    l+
  gi|91774253|ref|YP_566945.1| 228 VLL 230
                                   765 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   9.6e-08   0.00025       9      36 .]     240     267 ..     240     267 .. 0.94
   2 !   35.1   3.7   2.6e-12   6.8e-09       2      35 ..     251     284 ..     250     285 .. 0.95
   3 !   22.0   1.3   3.6e-08   9.3e-05       4      29 ..     277     302 ..     275     304 .. 0.90
   4 !   16.1   0.5   2.7e-06    0.0068       1      35 [.     303     336 ..     303     337 .. 0.92
   5 ?    1.9   0.3     0.081   2.1e+02       2      17 ..     363     378 ..     362     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.6e-08
                                   EE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   9 lIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   +I p+a++ g+V +G+++ I +g++i g
  gi|91774253|ref|YP_566945.1| 240 VIEPNATLIGDVSVGRGTLIRNGAYIIG 267
                                   599**********************975 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 2.6e-12
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   + +G ++lI+++a+i g+V+IG+++ Ig+++ i+
  gi|91774253|ref|YP_566945.1| 251 VSVGRGTLIRNGAYIIGPVIIGNDCDIGPNCFIR 284
                                   789****************************997 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 3.6e-08
                                   EETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIg 29 
                                   IG n++I+p + ig++V+IG+ v + 
  gi|91774253|ref|YP_566945.1| 277 IGPNCFIRPSTAIGNDVHIGNAVEVK 302
                                   9*******************988775 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 2.7e-06
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   +++I +++ Ig+ +++ g+ +IG+ +  gag+ ++
  gi|91774253|ref|YP_566945.1| 303 NSIIMDGTNIGHLTYL-GDSIIGRKCNFGAGTKVA 336
                                   579*************.9999***********987 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.081
                                   EEEETTEEE-TTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfavig 17 
                                   ++ G++v+ g ++ i 
  gi|91774253|ref|YP_566945.1| 363 VIMGDDVHTGINSSIN 378
                                   6788888888888875 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0     2e-18   5.1e-15       1     121 [.       3     128 ..       3     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 2e-18
                                   EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHHHHTTCT..S-EEE-TTSS-SHH CS
                  NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd.eevlaalarlg..vrvvededpgkgpl 73 
                                   aviLA+G+++Rm    +  +K +lp+++kp+le+++d++ +ag+d  v ++g+ eev +++ + g  + v+ d  +++ +l
  gi|91774253|ref|YP_566945.1|   3 AVILAAGEGTRMRpltSsiPKVMLPVANKPMLEHIVDSAIEAGIDGFVFITGYhEEVIEQYFGNGdrWNVTIDHVHQEEQL 83 
                                   79**********7554269*************************9988888884677777755543477888877666555 PP

                                   HHHHHHHHHH..SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEE CS
                  NTP_transf_3  74 aslaaalraaa.dadavlvlacDmPlltpelverllaaaaasgadvvvp 121
                                   ++  a   a +  ++ ++vl +D+ l++++++e+++++ +   ++v+ +
  gi|91774253|ref|YP_566945.1|  84 GTANAIGYAKGhVKEKFIVLNGDV-LVSSDHIEHMIERKE---DAVITV 128
                                   55444333322368**********.88**********954...333333 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 !    5.3   0.5    0.0064        17      12      32 ..     243     265 ..     240     266 .. 0.90
   2 !   23.3   4.0   1.5e-08   3.9e-05       1      28 [.     268     297 ..     268     301 .. 0.95
   3 ?   -1.0   0.0       0.6   1.5e+03      13      21 ..     303     313 ..     302     314 .. 0.86
   4 ?    3.8   0.2     0.019        48       3      13 ..     322     332 ..     321     335 .. 0.90
   5 ?    0.4   0.1      0.22   5.7e+02       2      17 ..     363     380 ..     357     389 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0064
                                   TT-E.ES.EEE-TT-EE-TT-EE CS
                     Hexapep_2  12 anag.iG.vslGdncvvgaGvvi 32 
                                   +na+ iG vs+G++  + +G +i
  gi|91774253|ref|YP_566945.1| 243 PNATlIGdVSVGRGTLIRNGAYI 265
                                   79998977************998 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.5e-08
                                   .EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                     Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvga 28 
                                   pviIG++C iG+n+ i   + +G+++++g+
  gi|91774253|ref|YP_566945.1| 268 PVIIGNDCDIGPNCFIrpSTAIGNDVHIGN 297
                                   8****************99*********98 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.6
                                   T-EE..SEEE- CS
                     Hexapep_2  13 nagi..GvslG 21 
                                   n++i  G+++G
  gi|91774253|ref|YP_566945.1| 303 NSIImdGTNIG 313
                                   99988999999 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.019
                                   EE-TT-EE-TT CS
                     Hexapep_2   3 iIGdnCliGan 13 
                                   iIG  C++Ga 
  gi|91774253|ref|YP_566945.1| 322 IIGRKCNFGAG 332
                                   8********96 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.22
                                   EEE-TT-EE-TT-EE..S CS
                     Hexapep_2   2 viIGdnCliGanagi..G 17 
                                   vi Gd++  G n+ i  G
  gi|91774253|ref|YP_566945.1| 363 VIMGDDVHTGINSSInvG 380
                                   555666666666654445 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.5   6.6e-08   0.00017     176     259 ..     253     334 ..     220     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.6e-08
                       DUF4954 176 igekvkilnag.likNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqavklk 255
                                   +g+ + i+n   +i  v ig+ + i     ++  t + +    v+iG+ V+++++ii+ G++i + + + ++++G+ ++++
  gi|91774253|ref|YP_566945.1| 253 VGRGTLIRNGAyIIGPVIIGNDCDIGPNCFIRPSTAIGN---DVHIGNAVEVKNSIIMDGTNIGHLTYLGDSIIGRKCNFG 330
                                   577777777541567789999999988888888887765...69***********************************98 PP

                       DUF4954 256 kqfs 259
                                    + +
  gi|91774253|ref|YP_566945.1| 331 AGTK 334
                                   7765 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 !   18.7   0.0   4.5e-07    0.0011       2      42 ..       2      45 ..       1     142 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.5e-07
                                  EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTT CS
                          IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallask 42
                                   +vi AAG+G+Rm+   +  pK  l ++++++leh vd++ + +
  gi|91774253|ref|YP_566945.1|  2 KAVILAAGEGTRMRpltSSIPKVMLPVANKPMLEHIVDSAIEAG 45
                                  69**********96444899******************988744 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.7e-05     0.094      16      52 ..      23      59 ..      20     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                                  GGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHH CS
                  CTP_transf_3 16 KnlldlggkpliayvleaalkskafekvivaTDseei 52
                                  K++l+ ++kp+++++++ a++++    v++   +ee+
  gi|91774253|ref|YP_566945.1| 23 KVMLPVANKPMLEHIVDSAIEAGIDGFVFITGYHEEV 59
                                  9********************9885558887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2414.55
//
Query:       gi|91774254|ref|YP_566946.1|  [L=433]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-40  136.0   0.0      2e-39  134.4   0.0    1.9  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.4e-25   89.8   0.0      4e-25   88.4   0.0    1.8  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    7.1e-20   71.3   0.0    1.3e-19   70.4   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.9e-11   42.7   0.1      1e-10   41.6   0.1    1.5  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 !  134.4   0.0   4.5e-43     2e-39       2     136 ..       2     127 ..       1     129 [. 0.96

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 4.5e-43
                                   GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHH CS
                     PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPav 82 
                                   ++fg sG+Rg+ + +e+t++l++k+g a++++ ++       vvGrD R+ ++++++a+++gl+++G++v+++g+++tP +
  gi|91774254|ref|YP_566946.1|   2 KLFGSSGIRGITN-KEVTTDLALKVGLALGKTKRS------AVVGRDPRIAGEMIEHAIISGLLSAGCDVVRIGMVSTPTL 75 
                                   68********999.779*************88776......7*************************************** PP

                                   HHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-E CS
                     PGM_PMM_I  83 sfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeee 136
                                   ++a++   +d+g+mitaSHnp+ey giK+ +++G+ ++++++e+Ie++ieke++
  gi|91774254|ref|YP_566946.1|  76 AYATKD--YDCGVMITASHNPAEYVGIKLWNPDGMAFDSSQQEEIEECIEKEDF 127
                                   *****9..799****************************************987 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0     9e-29     4e-25       5     103 .]     150     242 ..     143     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 9e-29
                                   HHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SE CS
                    PGM_PMM_II   5 ealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadl 85 
                                   ++++++      k+s+ +v+id++ Gag++i++ +l+++g++v++ln++pd+ fp ++p+p++  +l ll  +vk+ gad+
  gi|91774254|ref|YP_566946.1| 150 NMILQN-----VKRSSKRVIIDCGCGAGSTITPYVLRKMGCEVITLNSQPDGYFPARNPEPND-TNLTLLKIAVKEFGADI 224
                                   344444.....4555568*********************************************.***************** PP

                                   EEEE-TTS-BEEEEETTE CS
                    PGM_PMM_II  86 glafDgDaDRlgvvderG 103
                                   g+a DgDaDR++++de+G
  gi|91774254|ref|YP_566946.1| 225 GIAQDGDADRMMAIDEKG 242
                                   ****************98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0     3e-23   1.3e-19       1     111 [.     246     348 ..     246     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 3e-23
                                   HHHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                   PGM_PMM_III   1 dgdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                   +gd++lal+a++ ++    +ga +v +v ts+++++++   g ++++t+vGd yv+ee+k+ +a +GgE Sg +if++ ++
  gi|91774254|ref|YP_566946.1| 246 TGDEMLALFARHECD----EGAIIVVPVDTSMMVDDALP--GSTVIRTRVGDVYVAEEIKRCNADIGGEPSGSWIFPKISY 320
                                   59*********8877....4667**************65..999************************************* PP

                                   S--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                   PGM_PMM_III  82 tkDGilaallvleilaetgkslselleell 111
                                   + DGi a+++++e++ +  ++lsel +el+
  gi|91774254|ref|YP_566946.1| 321 CPDGIFASAKIMELIEN--RTLSELKKELP 348
                                   ***************76..69****98876 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 !   41.6   0.1   2.3e-14     1e-10       9      67 ..     362     425 ..     356     431 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.3e-14
                                   -TT....EECCCCCTTH.....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHHHHHHHHH CS
                    PGM_PMM_IV   9 kak..vvaalaallkva.....sikeglkilledGrrlavRpSGTepllrvyvEak.sdeelarlae 67 
                                   ++k  v++ +   l  +     s ++g+++   +G++l vRpSGTep++r+ +Ea+   ++l  +ae
  gi|91774254|ref|YP_566946.1| 362 ERKahVMEVVHSKL--EkcgkiSDIDGIRVEMDNGWVL-VRPSGTEPKIRITAEAReGADRLFSMAE 425
                                   43322333333333..134677999*************.****************977777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2651.91
//
Query:       gi|91774255|ref|YP_566947.1|  [L=614]
Description: glucosamine--fructose-6-phosphate aminotransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-58  194.8   0.4    4.3e-28   97.8   0.0    2.8  3  SIS       SIS domain
    3.6e-20   72.5   0.0    8.2e-20   71.4   0.0    1.5  1  GATase_6  Glutamine amidotransferase domain
    5.5e-16   58.6   0.0    4.1e-15   55.8   0.0    2.3  2  GATase_7  Glutamine amidotransferase domain
    3.3e-05   22.9   0.0    5.4e-05   22.2   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II
  ------ inclusion threshold ------
      0.015   16.1   0.0       0.14   13.0   0.0    2.4  2  DUF5124   Domain of unknown function (DUF5124)
      0.018   15.1   0.2        1.5    8.9   0.0    3.0  3  Imm3      Immunity protein Imm3


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.94   2.8e+03       9      40 ..     183     214 ..     174     222 .. 0.63
   2 !   94.1   0.1     2e-30   5.8e-27       2     129 ..     295     421 ..     294     423 .. 0.97
   3 !   97.8   0.0   1.4e-31   4.3e-28       2     129 ..     467     595 ..     466     597 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.94
                                   EEEESHHHHHHHHHHHHHHHHHHTSEEEEEEH CS
                           SIS   9 yvlGaGtsyaiakelalkleeiggivveveda 40 
                                   +++G+G     a+    ++ +++++vv+v+d 
  gi|91774255|ref|YP_566947.1| 183 LIIGMGNGEYYAASDVTAFLSHTKKVVFVDDL 214
                                   56666665554444455566888888888765 PP

  == domain 2  score: 94.1 bits;  conditional E-value: 2e-30
                                   HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                           SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                   +++ +ri ++++Gts ++++ +++ +e+++gi+ +v+  se+++g  + ++++ l i+i++sget+d++aa++ +k+ g +
  gi|91774255|ref|YP_566947.1| 295 IRNIDRIEIIACGTSWNAGLLGKYLFEKLAGIHTDVDIGSEFRYG-NPIMRNNVLSIAITQSGETADTLAAVKSCKAYGCN 374
                                   67889****************************************.*********************************** PP

                                   EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                           SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                    iaIT+  gs++ r  d +ly++a+pe++va+tk++taql+ l++l 
  gi|91774255|ref|YP_566947.1| 375 SIAITNVVGSSITRVVDSVLYTRAGPEIGVAATKTFTAQLIILYLLS 421
                                   ******************************************99985 PP

  == domain 3  score: 97.8 bits;  conditional E-value: 1.4e-31
                                   HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTS CS
                           SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakerga 81 
                                   +a+++  +++G+  +y++a+e+alkl+ei++i++e+ + +elkhg+lal+de+++v++i++ g+  d+++++  ++k+r a
  gi|91774255|ref|YP_566947.1| 467 FAEERDYFFVGRNVNYPVALEGALKLKEISYIHAEGFAGGELKHGPLALLDEGTPVVAIATKGHVYDKILSNIkEVKAREA 547
                                   6788999*****************************************************************99******* PP

                                   EEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                           SIS  82 kiiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                   ++ia++ + ++ + ++ d++l+i+   e l+++++s+++ql+a+++++
  gi|91774255|ref|YP_566947.1| 548 RVIAVAEKGDTEIEKYVDYVLRIPPTHEMLAPILSSVVLQLLAYYTAL 595
                                   ********************************************9987 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   2.7e-23   8.2e-20      11     133 ..      62     196 ..      50     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 2.7e-23
                      GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall..eelG.... 85 
                                   +++++++H+R+a++g + +   +P   ++g++++vhNG i+ny +++e+l++ +g++f s++Dtev+++l+  + +G    
  gi|91774255|ref|YP_566947.1|  62 KGNIGIGHTRWATHGVPSTINSHPH--NSGNISVVHNGIIENYLSIKEQLQK-EGYTFLSETDTEVIAHLIhsKLYGsatn 139
                                   4569*************88888***..*************************.****************998944555566 PP

                      GATase_6  86 ...........eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafas 133
                                              +++l++l+G +a+a + + +++t+  ar +   +pl+++  ++  + as
  gi|91774255|ref|YP_566947.1| 140 tkkicdfftalQQALKELEGSYAIATVCSsEPDTMLAARKD---SPLIIGMGNGEYYAAS 196
                                   667778999999999**********9999666666665433...8888887776666666 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   1.4e-18   4.1e-15      20     122 ..      87     202 ..      69     203 .. 0.90
   2 ?   -0.4   0.0      0.34     1e+03      24      57 ..     523     560 ..     507     570 .. 0.67

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.4e-18
                      GATase_7  20 edgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea................ewgeealerlnGmfAfaiwd 84 
                                   ++g++ +v+nG i Ny +++e+L+++g++f +++Dtev+++l+++                  +++al++l+G++A+a + 
  gi|91774255|ref|YP_566947.1|  87 NSGNISVVHNGIIENYLSIKEQLQKEGYTFLSETDTEVIAHLIHSklygsatntkkicdffTALQQALKELEGSYAIATVC 167
                                   6799***************************************99****************99***************997 PP

                      GATase_7  85 eeek.rlllaRDrlGikPLyygedkgdallfaSelkall 122
                                   ++e  ++l+aR      PL++g  +g +++ aS + a+l
  gi|91774255|ref|YP_566947.1| 168 SSEPdTMLAARK---DSPLIIGMGNG-EYYAASDVTAFL 202
                                   666537888887...59*******85.*******99986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                      GATase_7  24 lvivfnGeiy.....NykelreeLeakghrfrtksDtev 57 
                                   ++i++ G +y     N ke++++ ea+ +++++k+Dte+
  gi|91774255|ref|YP_566947.1| 523 VAIATKGHVYdkilsNIKEVKAR-EARVIAVAEKGDTEI 560
                                   55666666662222266777777.566688899999997 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.8e-08   5.4e-05      61     177 ..      54     168 ..      46     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-08
                      GATase_4  61 aelvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpkl.egrfePvGsTDsElafCel 137
                                    +++++ +ik ++ + H R at+G  +  n+hp        ++   HnG +++   +k++l ++ ++ + +TD+E++   +
  gi|91774255|ref|YP_566947.1|  54 EKILKD-DIKGNIGIGHTRWATHGVPSTINSHPHN----SGNISVVHNGIIENylsIKEQLqKEGYTFLSETDTEVIAHLI 129
                                   567777.9*************************75....5577889*****98444566667889*************999 PP

                      GATase_4 138 leelasrfekaepsaeeleralaelakeiaelGvfnllls 177
                                    ++l  +++ +++++ + ++al++ +ke++    + ++ s
  gi|91774255|ref|YP_566947.1| 130 HSKLYGSAT-NTKKICDFFTALQQALKELEGSYAIATVCS 168
                                   9****9995.579999***********9986555544443 PP

>> DUF5124  Domain of unknown function (DUF5124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.66     2e+03      49      80 ..     220     252 ..     200     269 .. 0.75
   2 ?   13.0   0.0   4.6e-05      0.14      20      66 ..     459     508 ..     450     535 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.66
                       DUF5124  49 klscialvdtkGsvagkwnst.dfkldsgqGlg 80 
                                   + +++ + d +G+v  k  +t ++ +++ + +g
  gi|91774255|ref|YP_566947.1| 220 QPNGVEFYDIDGNVIEKETTTiNWDIEAAEKAG 252
                                   5588999999***99887554477777766655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.6e-05
                       DUF5124  20 aiydclekyskaevyylvG...dfmqlessdaklscialvdtkGsvagkw 66 
                                    i +c+e +++++ y+ vG   ++  + ++  kl+ i+++  +G   g+ 
  gi|91774255|ref|YP_566947.1| 459 EIRECAEIFAEERDYFFVGrnvNYPVALEGALKLKEISYIHAEGFAGGEL 508
                                   6889***************5444555689***************888765 PP

>> Imm3  Immunity protein Imm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00049       1.5      18      64 ..      25      71 ..      17      83 .. 0.87
   2 ?   -2.5   0.0       1.7     5e+03      84     108 ..     104     128 ..      89     158 .. 0.66
   3 ?    2.6   0.0     0.044   1.3e+02      55     104 ..     399     446 ..     377     459 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00049
                          Imm3 18 eykaeerslseaiartsdefenveklgeiekvvvdvaigeialkhak 64
                                  ey+  + +    + +t+d ++ + k++++ek++ d + g+i + h++
  gi|91774255|ref|YP_566947.1| 25 EYRGYDSAGITLLNKTIDTYKTIGKINDLEKILKDDIKGNIGIGHTR 71
                                  66666666777799*****************************9998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                          Imm3  84 elkgelteeeikdlleRrdkVledl 108
                                    +k++l++e ++ l+e   +V+  l
  gi|91774255|ref|YP_566947.1| 104 SIKEQLQKEGYTFLSETDTEVIAHL 128
                                   4555566666665555555555554 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.044
                          Imm3  55 igeialkhakvfvklkegiikrLsslnleelkgelteeeikdlleRrdkV 104
                                     ei +  +k+f+   + ii  L s+ +   +g ++++e kdll   +++
  gi|91774255|ref|YP_566947.1| 399 GPEIGVAATKTFTA--QLIILYLLSIRFARTRGTINTNEAKDLLIELKRI 446
                                   45888888999875..569999*********************8765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3752.29
//
Query:       gi|91774256|ref|YP_566948.1|  [L=405]
Description: nucleotidyl transferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-43  149.4   0.1    1.8e-43  148.9   0.1    1.2  1  NTP_transferase  Nucleotidyl transferase
    4.2e-19   67.5  32.4    8.2e-09   34.9   0.6    4.8  4  Hexapep          Bacterial transferase hexapeptide (six repea
    5.3e-14   52.9   0.0    7.1e-14   52.5   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    5.4e-07   29.3  24.6    0.00017   21.3   5.7    4.9  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    0.00016   21.5   1.0    0.00083   19.2   0.1    2.6  4  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00083   19.3   0.3     0.0014   18.6   0.3    1.4  1  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
      0.045   13.6   1.2       0.25   11.2   1.2    2.3  1  Arg_repressor_C  Arginine repressor, C-terminal domain
      0.057   13.5   0.5       0.37   10.9   0.1    2.4  3  DUF1694          Protein of unknown function (DUF1694)
      0.064   12.6   0.1       0.11   11.7   0.1    1.4  1  PTA_PTB          Phosphate acetyl/butaryl transferase
        1.5    7.6  10.6        4.8    6.0   4.1    3.3  3  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   0.1     1e-46   1.8e-43       1     231 [.       2     219 ..       2     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 1e-46
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   kavILa G+G R +PLt t++k ++pv++k ++i++++  la+++i+++i+v+  ++++++ +++++g +fg+++++++++
  gi|91774256|ref|YP_566948.1|   2 KAVILAAGEGLRCRPLTLTRSKVMLPVANK-PIIEHVIDSLAKNEIKDLILVVG-YEKERIMDYFEDGIDFGINITYVHQK 80 
                                   79****************************.*****************666666.77788899****************** PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrver 161
                                    + gtA+A++++ael+++e+  e++lvL+gD +i+  +++++++++        +t+++ ++e+ ++yGvi  d+ ++v++
  gi|91774256|ref|YP_566948.1|  81 AQLGTAHAIKQVAELMGEED--ETFLVLNGDNVIEAnTIKDLLDNHNG-----NATILTARKENTRGYGVIVCDG-KKVKK 153
                                   *****************999..5************7677777777754.....567999***************9.6**** PP

                                   EECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
               NTP_transferase 162 fvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                   +vEKP ++  s+++++GiY+f++++++ + ++   ++ ge  itd+l++++++g +   ++ +    W D
  gi|91774256|ref|YP_566948.1| 154 IVEKPTAEV-SHVINTGIYMFDQNIFERI-EQTPISQMGEFAITDTLQQMIDDGLQVDHTITNS--LWID 219
                                   *******99.*******************.66777888999************97766655555..6877 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.5   1.2e-06    0.0021      12      35 ..     248     271 ..     241     272 .. 0.89
   2 !   34.9   0.6   4.6e-12   8.2e-09       2      34 ..     274     306 ..     273     308 .. 0.93
   3 !   17.6   2.4   1.3e-06    0.0023       1      30 [.     308     336 ..     308     337 .. 0.91
   4 !   13.3   3.3   2.9e-05     0.051       1      34 [.     361     394 ..     361     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                   TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep  12 pfaviggnVkIGdnvkIgagvvig 35 
                                    +a+i+gnV IG+n++I +g++i 
  gi|91774256|ref|YP_566948.1| 248 EGAIIRGNVSIGNNTIIRSGCYIV 271
                                   589******************995 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 4.6e-12
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   ++IG+n+ I p +vi++ ++IGdnv+Ig+++ +
  gi|91774256|ref|YP_566948.1| 274 AIIGDNCEIAPTVVILPSTTIGDNVTIGSFSHL 306
                                   79***************************9875 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.3e-06
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEET CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                   +++I +n+ Ig+ ++i +n +IG n  Ig+
  gi|91774256|ref|YP_566948.1| 308 NSIIMNNTRIGNHSHI-SNSVIGMNNSIGP 336
                                   579*************.8888********9 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 2.9e-05
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   +t++G++++Ig+++ + ++V I +n+ I +g  i
  gi|91774256|ref|YP_566948.1| 361 GTITGDDTIIGHGVLVKAGVMISSNCNIDSGKII 394
                                   689***********************99887665 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 !   52.5   0.0     4e-17   7.1e-14       1     132 [.       3     144 ..       3     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 4e-17
                                   EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC.....TS-EEE-TTSS CS
                  NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl.....gvrvvededpg 69 
                                   aviLA+G++ R       + K +lp+++kp++e+v+d+l++ +++++++v+g+  e + +++++      ++++v+++ ++
  gi|91774256|ref|YP_566948.1|   3 AVILAAGEGLRCRpltltRSKVMLPVANKPIIEHVIDSLAKNEIKDLILVVGYekERIMDYFEDGidfgiNITYVHQK-AQ 82 
                                   79**********6554436*******************************9995446777776555554456667665.68 PP

                                   -SHHHHHHHHHHHH..SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCE CS
                  NTP_transf_3  70 kgplaslaaalraaa.dadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpll 132
                                    g++++++  ++  + +++ +lvl +D + +++++++ ll+++ + +a ++ ++ e++rg+ ++
  gi|91774256|ref|YP_566948.1|  83 LGTAHAIKQVAELMGeEDETFLVLNGDNV-IEANTIKDLLDNH-NGNATILTARKENTRGYGVI 144
                                   99999999999986668999********6.6***********7.57789999999999987664 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 !   21.3   5.7   9.4e-08   0.00017       1      33 [.     255     289 ..     255     290 .. 0.92
   2 !    8.8   1.4   0.00073       1.3       2      15 ..     292     305 ..     291     336 .. 0.69
   3 !    7.9   2.5    0.0015       2.6       4      32 ..     364     394 ..     361     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.4e-08
                                   .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                     Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                   +v+IG+n++i + ++i  + ++Gdnc +++ vvi 
  gi|91774256|ref|YP_566948.1| 255 NVSIGNNTIIRSGCYIvgPAIIGDNCEIAPTVVIL 289
                                   69*************8855***********99995 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00073
                                   EEE-TT-EE-TT-E CS
                     Hexapep_2   2 viIGdnCliGanag 15 
                                   ++IGdn+ iG+++ 
  gi|91774256|ref|YP_566948.1| 292 TTIGDNVTIGSFSH 305
                                   68*********986 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0015
                                   E-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                     Hexapep_2   4 IGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                    Gd+++iG    +  Gv +  nc +++G +i
  gi|91774256|ref|YP_566948.1| 364 TGDDTIIGHGVLVkaGVMISSNCNIDSGKII 394
                                   5888888888887778888888888888555 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   4.6e-07   0.00083       2      64 ..       2      65 ..       1     133 [. 0.64
   2 ?   -0.6   0.0      0.52   9.3e+02      18      57 ..      99     139 ..      87     167 .. 0.71
   3 ?   -2.8   0.0       2.4   4.4e+03     127     153 ..     191     217 ..     175     229 .. 0.67
   4 ?   -1.3   0.0      0.85   1.5e+03     199     216 ..     341     358 ..     332     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.6e-07
                                  EEEEECTTSSCT...T-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHG CS
                          IspD  2 vvvipAAGsGkR...mkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqlll 64
                                   +vi AAG+G R   +   + K  l +++++++eh +d+l++++ ++ +++vv  ++ e++++   
  gi|91774256|ref|YP_566948.1|  2 KAVILAAGEGLRcrpLTLTRSKVMLPVANKPIIEHVIDSLAKNE-IKDLILVVGYEK-ERIMDYFE 65
                                  69********9944446799*******************99955.555555554433.45554444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.52
                                   S-GGGSEETTEEHHH.HHHHHHHCTTTEEEEEEEE-GGGHH CS
                          IspD  18 lpKqflelkgqtlle.htvdallaskavdkivvvvseddte 57 
                                    +  fl l+g+ ++e +t++ ll++++ +  ++  ++++t 
  gi|91774256|ref|YP_566948.1|  99 EDETFLVLNGDNVIEaNTIKDLLDNHNGNATILTARKENTR 139
                                   55678899999999735888888877766666666555544 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.4
                                   EEE-SSEEEEEETTT.BEEEEETGTTEE CS
                          IspD 127 alpvkDtikrveadg.lvaetedRegLw 153
                                     +++Dt+++   dg +v +t+  ++Lw
  gi|91774256|ref|YP_566948.1| 191 EFAITDTLQQMIDDGlQVDHTIT-NSLW 217
                                   56789999877666646666654.4555 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.85
                                   --TTG----SHHHHHHHH CS
                          IspD 199 GeednlKittpeDlalAe 216
                                    +++n+Ki  ++D+ +Ae
  gi|91774256|ref|YP_566948.1| 341 EDKENIKIELEDDIQTAE 358
                                   5789**********9998 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3     8e-07    0.0014      15     152 ..      22     161 ..      20     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8e-07
                                   TGGGSEETTEEHHHHHHHHHHHTTTTSE..EEEEES-HHHHHHHHH...TTSEEEE--TTCSSHHHHHHHHHHHHTTT.TT CS
                  CTP_transf_3  15 gKnlldlggkpliayvleaalkskafek..vivaTDseeiknvake...fgasvlvtrsslesdterflevvkaflmsene 90 
                                    K++l+ ++kp+i++v++ + k  ++++  ++v   +e+i++  ++   fg+ +    ++++ +t+   + v+++  + ++
  gi|91774256|ref|YP_566948.1|  22 SKVMLPVANKPIIEHVIDSLAK-NEIKDliLVVGYEKERIMDYFEDgidFGINITYVHQKAQLGTAHAIKQVAELMGE-ED 100
                                   59********************.5556667889999999**9999633377************************999.66 PP

                                   SEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETTSHHHHTSTTSTEEEETTTSBE CS
                  CTP_transf_3  91 eiivnlqGdnPllqeevikkaietlkenqedylstlvkkvgkeeevlnandlkvllddagka 152
                                   e+ + l Gdn+ ++  +ik ++++++ n    ++ +    g    v + +++k++++++ ++
  gi|91774256|ref|YP_566948.1| 101 ETFLVLNGDNV-IEANTIKDLLDNHNGNATILTARKENTRGYGVIVCDGKKVKKIVEKPTAE 161
                                   67777899*97.78899999999999985443333333334445555566666666665444 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 ?   11.2   1.2   0.00014      0.25      32      50 ..     352     370 ..     350     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                   HH-..TTEEEEEE-SSEEE CS
               Arg_repressor_C  32 DslelpeilGtiAGdDTil 50 
                                   D+++  e lGti GdDTi+
  gi|91774256|ref|YP_566948.1| 352 DDIQTAEKLGTITGDDTII 370
                                   67888999*********96 PP

>> DUF1694  Protein of unknown function (DUF1694)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.28     5e+02      43      95 ..      28      80 ..      24      85 .. 0.87
   2 ?   10.9   0.1   0.00021      0.37      40     112 ..      80     152 ..      74     155 .. 0.88
   3 ?   -3.0   0.0       4.1   7.4e+03      74     102 ..     333     361 ..     324     368 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.28
                                  HTSSS--HHHHHHHHC-SSEEEEEETTS-HHHHHHHHHHHHHTT--EEEE--- CS
                       DUF1694 43 veekkvykeleealkkkkalkllingkldedilskyiklakkenikftivnde 95
                                  v +k + +++ ++l+k++ + l++    +++ +++y +   + +i++t+v+++
  gi|91774256|ref|YP_566948.1| 28 VANKPIIEHVIDSLAKNEIKDLILVVGYEKERIMDYFEDGIDFGINITYVHQK 80
                                  567788899999************99999999999999999999999999876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
                                   HHHHTSSS--HHHHHHHHC-SSEEEEEETTS-HHHHHHHHHHHHHTT--EEEE---.SS--SEEEEEEESS--- CS
                       DUF1694  40 keqveekkvykeleealkkkkalkllingkldedilskyiklakkenikftivnde.eaesdiglvvasdeAvn 112
                                   k+q+ ++++ k++ e++ +++++ l++ng+ +   ++++ +l +++n ++ti++   e++  +g++v++ + v+
  gi|91774256|ref|YP_566948.1|  80 KAQLGTAHAIKQVAELMGEEDETFLVLNGD-NVIEANTIKDLLDNHNGNATILTARkENTRGYGVIVCDGKKVK 152
                                   78999999*********************9.6667788899999*******99998788999*****9877665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.1
                                   HHHHHHHHHHHTT--EEEE---SS--SEE CS
                       DUF1694  74 ilskyiklakkenikftivndeeaesdig 102
                                   ++++y  + +kenik+++ +d ++ +++g
  gi|91774256|ref|YP_566948.1| 333 SIGPYFITEDKENIKIELEDDIQTAEKLG 361
                                   56667777777777777777766666666 PP

>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.4e-05      0.11      14      91 ..      21     100 ..      16     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                                   --EEEES-TTSHHHHHHHHHHHHTTSSEEEEES.-HHHHHHHHHHCTB--TT.-EEE-TTT-CCHHHHHHHHHHHCCCC. CS
                       PTA_PTB  14 kkrivlpegedervlkAakelleegiadviLig.deaeikakaleldldlsg.ieivdpetsekleeyadelyelrkrkg 91 
                                    +++ lp+++ + + + +++l++++i d+iL+   e+e     +e ++d +  i+ v  + +  + + +++++el++++ 
  gi|91774256|ref|YP_566948.1|  21 RSKVMLPVANKPIIEHVIDSLAKNEIKDLILVVgYEKERIMDYFEDGIDFGInITYVHQKAQLGTAHAIKQVAELMGEED 100
                                   579*************************9987667777778899999***999999999999999*******99998765 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.028        51      47     150 ..      98     180 ..      80     203 .. 0.73
   2 ?    6.0   4.1    0.0027       4.8     266     320 ..     278     333 ..     230     357 .. 0.77
   3 ?   -3.2   0.2       1.7   3.1e+03     289     328 ..     366     402 ..     361     404 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.028
                    Fucokinase  47 rmkpGvlvtssDvlllf..dseeisfdkagvtalavpstldigtnHGVfvlddqsseeeeleirsvkkflhKpseeelqas 125
                                   +  +++lv+++D ++     +  ++ ++  +t+l+ +++ +  +  GV+v d++          +vkk++ Kp++e  +  
  gi|91774256|ref|YP_566948.1|  98 EEDETFLVLNGDNVIEAntIKDLLDNHNGNATILTARKENT--RGYGVIVCDGK----------KVKKIVEKPTAEVSH-- 164
                                   55677888888877633122344444555888888877765..45699999998..........899999999998777.. PP

                    Fucokinase 126 gavlkdekvlldsGvvffdhktaek 150
                                            ++ +G+++fd++++e+
  gi|91774256|ref|YP_566948.1| 165 ---------VINTGIYMFDQNIFER 180
                                   .........6777777777777765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0027
                    Fucokinase 266 kkekkkesavvinS.vlessvsvgegsviehsslkgnvsigsnsivsglelessee 320
                                   ++ ++++++v++ S  +  +v++g  s +++s + +n++ig++s +s+  +  +++
  gi|91774256|ref|YP_566948.1| 278 DNCEIAPTVVILPStTIGDNVTIGSFSHLQNSIIMNNTRIGNHSHISNSVIGMNNS 333
                                   34445777788765257799999999999999999999999999999988877765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.7
                    Fucokinase 289 egsviehsslk.gnvsigsnsivsglelesseeslelpddt 328
                                   ++++i h  l  ++v i sn+ + + ++ s     +lp+++
  gi|91774256|ref|YP_566948.1| 366 DDTIIGHGVLVkAGVMISSNCNIDSGKIISR----NLPENS 402
                                   5666666666556666777776655555543....356555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2353.50
//
Query:       gi|91774257|ref|YP_566949.1|  [L=152]
Description: 30S ribosomal protein S15P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-25   87.2   0.4    1.2e-24   86.1   0.4    1.6  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    3.1e-15   56.1   0.4    4.2e-15   55.7   0.4    1.2  1  Ribosomal_S15    Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.4   1.4e-28   1.2e-24       1      60 []       1      60 [.       1      60 [. 1.00

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 1.4e-28
                                  X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
               Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                  Ma+mh+r kGkSgS++P+r e+p+W++ ++ee+++ +++l+k+G ++S IG++LRD+yGv
  gi|91774257|ref|YP_566949.1|  1 MAKMHTRTKGKSGSTKPIRSESPAWSTATTEEITKVVLDLWKQGNSTSVIGMVLRDNYGV 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 !   55.7   0.4   4.7e-19   4.2e-15       3      79 ..      73     147 ..      69     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4.7e-19
                                   HHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCT CS
                 Ribosomal_S15   3 elikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklg 79 
                                   e+++++ +++    ++++++++l+ ++  l++hl  n+kD+h++r+L+  +sk+r+l+kY+++++v   ++k+  e+++
  gi|91774257|ref|YP_566949.1|  73 EILRDNSEEP----NVPEDLYNLIVKAIGLRKHLVVNNKDVHNKRSLQSAESKIRRLVKYYQSTKVlpIDWKYKPETAE 147
                                   4556666666....99**************************************************9999**9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 968.47
//
Query:       gi|91774258|ref|YP_566950.1|  [L=243]
Description: hypothetical protein Mbur_2346 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.34   11.3   2.9       0.47   10.8   1.5    1.8  2  Sec3_C_2  Sec3 exocyst complex subunit


Domain annotation for each model (and alignments):
>> Sec3_C_2  Sec3 exocyst complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.19   3.3e+03      29      57 ..      35      65 ..      19      71 .. 0.62
   2 ?   10.8   1.5   2.6e-05      0.47       8      66 ..     174     232 ..     170     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.19
                      Sec3_C_2 29 aiiesveelaeekielk..evkdilqdsilG 57
                                  + i++v+ +a  + e     +   l+ +i+G
  gi|91774258|ref|YP_566950.1| 35 STIQTVDPIAISHKEQTriAIDTYLDKCIAG 65
                                  4566666655333332201567788888888 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.6e-05
                      Sec3_C_2   8 dWseedaikdvlkelefsldeaiiesveelaeekielkevkdilqdsilGCeslfstln 66 
                                     +e+d i+ ++k++ + l++++ e++++ + +    +++++i q      es++  +n
  gi|91774258|ref|YP_566950.1| 174 TITEQDMIRANQKNIANYLKNSMSEEINDTVSQMATTNDINKIRQLRDEKIESIYNKIN 232
                                   56799*****************************9999999887766666777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1618.12
//
Query:       gi|91774259|ref|YP_566951.1|  [L=113]
Description: hypothetical protein Mbur_2347 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00095   19.3   0.2     0.0013   18.9   0.2    1.2  1  Clavanin  Clavanin


Domain annotation for each model (and alignments):
>> Clavanin  Clavanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   7.2e-08    0.0013       3      44 ..      25      66 ..      23      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.2e-08
                      Clavanin  3 tiilillilglgidaksleerkaeeekvlrllgkvihgvgnl 44
                                  t il+lli+ l i a +  ++ka+e+  l  + k++h+  ++
  gi|91774259|ref|YP_566951.1| 25 TAILVLLIMALAITAMADLKEKANEDSALIEISKIVHNSEQI 66
                                  89**************99999****************87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 779.65
//
Query:       gi|91774260|ref|YP_566952.1|  [L=377]
Description: histidyl-tRNA synthetase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-64  218.3   0.0    1.8e-64  218.0   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.1e-15   58.1   0.0    1.9e-15   57.3   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      4e-05   22.9   2.1      0.057   12.5   0.6    2.9  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)
     0.0011   18.6   0.0     0.0074   15.8   0.0    2.0  2  tRNA-synt_2d    tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.054   14.0   0.5        4.2    8.0   0.0    3.2  3  EF-G-binding_N  Elongation factor G-binding protein, N-termin
      0.068   13.3   0.1       0.14   12.3   0.1    1.5  1  HGTP_anticodon  Anticodon binding 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 !  218.0   0.0     6e-68   1.8e-64       1     310 []       8     310 ..       8     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 218.0 bits;  conditional E-value: 6e-68
                                   T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHHHHHH CS
                 tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqvaRiaa 80 
                                   g+rd+lpee ++++++++ + +++++w+Y++V++P++E l+ ++ ++ge    +++ + D+ +r+++lR+++T+ v R++ 
  gi|91774260|ref|YP_566952.1|   8 GTRDFLPEETARRRNIENIMRNVVNKWDYKEVITPTFENLELFTLKSGEGvIGELYNFNDKGNRNMALRPELTAPVMRMYV 88 
                                   78*****************************************9999999456**************************** PP

                                   HHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHHHH CS
                 tRNA-synt_His  81 hrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvral 160
                                   + ++  ++pl+l Y+++++r ++ + gr re+ Q+G+E+iG++  +ad+E++ l++ +l+ aag+ +  l +gh g++r +
  gi|91774260|ref|YP_566952.1|  89 NEMQaTPKPLKLFYFENCFRYERPQKGRFREFWQFGVEVIGSNRADADAEIIALATTMLN-AAGI-KGDLHVGHLGIIRHI 167
                                   ***99******************************************************6.****.789999********* PP

                                   HHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC...HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHHHHHH CS
                 tRNA-synt_His 161 leaaglsesleeallaalarkdlaelkelaaeaglkealrellkalelygdaevleealealaaapalqaaldeleelaal 241
                                   l++++  +++++++++++++kd ++l+e  +e +++ +lr+ l  l +  + +++++a+e l + +     +d++e+l + 
  gi|91774260|ref|YP_566952.1| 168 LRELE--PEQQSKIMRLVDKKDDSGLEEYFEEINAPVELRRNLLELICITGTDAITKAREILGDIE----EIDKFEQLLTF 242
                                   **866..99***************************9*99999999999999******99776664....59********* PP

                                   HHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-SEEEEEECTTTGGG.T---EEEEEEEEHHHH CS
                 tRNA-synt_His 242 lealakpevrvtlDlaelrgyeYytGlvFaayaegvgq..aiarGGrYdelgaaf.grarpAtGfsldleal 310
                                   l+a++   ++++++l+  rg++YytG+vF++yaeg g+  ++ +GG Y +l++ f g   p+tGf l  +++
  gi|91774260|ref|YP_566952.1| 243 LNAYE---IDYSINLGIARGLDYYTGMVFEIYAEGLGAqnQVCGGGSY-QLISLFgGGDVPSTGFGLGFDRI 310
                                   ***85...**************************988555********.9*****999*******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 !   57.3   0.0   6.3e-19   1.9e-15       1     131 [.      63     281 ..      63     334 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 6.3e-19
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddsl 80 
                                   Y ++d+ +r+++L+P+ ++++++++ +e+    k  Plkl+++  ++R+E++ ++G  R reF q + +v++++    d +
  gi|91774260|ref|YP_566952.1|  63 YNFNDKGNRNMALRPELTAPVMRMYVNEMQATpK--PLKLFYFENCFRYERP-QKG--RFREFWQFGVEVIGSNR--ADAD 136
                                   899*************************543336..****************.***..***************87..8*** PP

                                   HHHHHHHHHHHHHTT.SC..........EEEEEEGTTSC.......................................... CS
                                   xxxxxxxxxxxxxxxxxx..........xxxxxxxxxxx.......................................... RF
                  tRNA-synt_2b  81 rdlikaisriferlglef..........raiielmsaks.......................................... 109
                                   +++i ++ +++++ g++           r+i+                                                 
  gi|91774260|ref|YP_566952.1| 137 AEIIALATTMLNAAGIKGdlhvghlgiiRHIL------Relepeqqskimrlvdkkddsgleeyfeeinapvelrrnllel 211
                                   ****************9966666555554444......0444555778999999999999999999999999999999999 PP

                                   ................................................BTTSEEEEEEEEETTTSEEEEE CS
                                   ................................................xxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 110 ................................................adykdkkefeavsesltkgiei 131
                                                                                   +dy+   +fe++ e l+++ ++
  gi|91774260|ref|YP_566952.1| 212 icitgtdaitkareilgdieeidkfeqlltflnayeidysinlgiargLDYYTGMVFEIYAEGLGAQNQV 281
                                   9999999999999999999999999999999999999999999999999999999999999999988876 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 !   12.5   0.6   1.9e-05     0.057      25     122 ..      20     127 ..      10     157 .. 0.72
   2 !    8.1   0.0   0.00041       1.2     272     297 ..     288     313 ..     278     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT..TEEE..............-E-S.-SHHH.HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..............xxxx.xxxxx.xxxxxx RF
                   tRNA-synt_2  25 rstvtkavrkyleengfieietPiLsksdteegarlFkvksrek.ekeff..............aLtq.spqly.lelliv 88 
                                   r ++ +++r++ ++ ++ e+ tP++ +       +lF++ks e   +e++               Lt   + +y  e+ + 
  gi|91774260|ref|YP_566952.1|  20 RRNIENIMRNVVNKWDYKEVITPTFENL------ELFTLKSGEGvIGELYnfndkgnrnmalrpELTApVMRMYvNEMQAT 94 
                                   7788999999999999999999998877......66666555544223333345555544456634331455662456666 PP

                                   CTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  89 agidrvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                    +  + f + ++FR E+ ++ r   EF+q+ +e+
  gi|91774260|ref|YP_566952.1|  95 PKPLKLFYFENCFRYERPQKGRFR-EFWQFGVEV 127
                                   6788*****************999.*****9997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00041
                                   HHHHHHHCT--SEEEEEEEHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 272 wylealeyGapphgGlglGldRlvml 297
                                   +++ ++  G +p  G+glG+dR++ +
  gi|91774260|ref|YP_566952.1| 288 QLISLFGGGDVPSTGFGLGFDRIMEV 313
                                   68889999**************8754 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 !   15.8   0.0   2.5e-06    0.0074      77     135 ..      69     131 ..      18     156 .. 0.80
   2 ?    0.2   0.0      0.15   4.4e+02     208     222 ..     297     311 ..     287     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-06
                                   ECESEEE-SSTHHHHHHHH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT CS
                  tRNA-synt_2d  77 veekllLRthttavqirtl....ekkkppikiisigrvfRrdavDathlaeFhqveglvvden 135
                                    ++++ LR   ta  +r+     ++  +p+k++ ++++fR +   + +  eF q    v+++n
  gi|91774260|ref|YP_566952.1|  69 GNRNMALRPELTAPVMRMYvnemQATPKPLKLFYFENCFRYERPQKGRFREFWQFGVEVIGSN 131
                                   367899999999877776555559999**************************9887777765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                                   TSEEEEEEEEHHHHH CS
                  tRNA-synt_2d 208 evsgfafGlGveRla 222
                                   +v+  +fGlG++R+ 
  gi|91774260|ref|YP_566952.1| 297 DVPSTGFGLGFDRIM 311
                                   678899*******85 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0014       4.2      41      79 ..     164     202 ..     127     204 .. 0.93
   2 ?    0.3   0.0      0.36   1.1e+03      50      73 ..     221     244 ..     205     248 .. 0.65
   3 ?    1.6   0.0      0.14     4e+02      40      76 ..     309     344 ..     306     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0014
                EF-G-binding_N  41 IlelfpelseeqkelLeqiddiktkekaeklLeeLkeyV 79 
                                   I++++ el++eq++ ++ + d k+ +  e+++ee++  V
  gi|91774260|ref|YP_566952.1| 164 IRHILRELEPEQQSKIMRLVDKKDDSGLEEYFEEINAPV 202
                                   7889**********9*9*****************99876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                EF-G-binding_N  50 eeqkelLeqiddiktkekaeklLe 73 
                                   ++++e+L +i++i++ e+   +L+
  gi|91774260|ref|YP_566952.1| 221 TKAREILGDIEEIDKFEQLLTFLN 244
                                   566777766666666555555554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.14
                EF-G-binding_N  40 kIlelfpelseeqkelLeqiddiktkekaeklLeeLk 76 
                                   +I+e+ + + e+qk+ +  i++ +t+ +a ++ ++L+
  gi|91774260|ref|YP_566952.1| 309 RIMEVCEIMPEKQKSVV-VISTDETRIDAIQVTTSLR 344
                                   78998877777777777.999999*****99999986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.8e-05      0.14       2      60 ..     324     377 .]     317     377 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                                   EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE- CS
                HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvG 60 
                                   vvvi   e        a ++   Lr++ + v ld  +++++ ++++a+++   +av+vG
  gi|91774260|ref|YP_566952.1| 324 VVVISTDE----TRIDAIQVTTSLRKE-LTVYLDIMQRNFKTQLSHANNIEADYAVIVG 377
                                   33333333....455689999999977.99****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2310.95
//
Query:       gi|91774261|ref|YP_566953.1|  [L=389]
Description: amidohydrolase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-29  103.5   0.1    5.1e-29  101.7   0.1    1.8  1  Amidohydro_1  Amidohydrolase family
    2.2e-11   43.7   0.0    3.1e-11   43.2   0.0    1.1  1  A_deaminase   Adenosine/AMP deaminase
    3.2e-09   36.8   0.0    4.2e-08   33.1   0.0    2.2  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.065   13.4   0.1       0.24   11.7   0.2    1.8  2  Phage_DsbA    Transcriptional regulator DsbA
      0.099   12.2   0.0       0.15   11.6   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein


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 !  101.7   0.1   1.4e-32   5.1e-29       1     328 [.      63     372 ..      63     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 1.4e-32
                                   EEEE-EEEEEEECETTECSSS............GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEE CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga............tledwl.............vppetaaealesgiktalksGtttvadmg 56 
                                   i+ P +I++H+H+ +s  +++            +l+ ++             ++  ++   ++  i+ +l+ Gt  +ad++
  gi|91774261|ref|YP_566953.1|  63 IIAPCFINSHTHIGDSICKDPvlgecnnfkvskDLDALVrppgglkhkilenTSYPDLVRSMRMTIQDMLQTGTSAFADFR 143
                                   6889************99999888565555555555555*********99887777788899999**************** PP

                                   HSSTHHHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHH CS
                  Amidohydro_1  57 attstgiealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkea 137
                                   +  + g+ al ea++++ ++  i+g   + d +  +  + +  ++++ a              +l+ ++   +  + l + 
  gi|91774261|ref|YP_566953.1| 144 EGGVLGALALEEAVSDQDIDHLIFGRPKCTD-RPLDEIMSELDRILQHA-------------DGLGMSGTNDLDMDILIKS 210
                                   **999***********866766666666666.66666666666666666.............6777799999999988888 PP

                                   HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHH CS
                  Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahc 218
                                    ++ak+ ++ +aiHa+e +++  d+e+a+     +             d+    l h++  + +++  + e   ++ ++ c
  gi|91774261|ref|YP_566953.1| 211 KRKAKDFNKLFAIHAGEKDNT--DIEKAIS---LD-----P-------DI----LIHMTKAMRSDLQAISES--NIPIVVC 268
                                   899************995555..9999999...44.....2.......44....778888888889999999..******* PP

                                   HHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT- CS
                  Amidohydro_1 219 pfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalgl 299
                                   p+sn i + g++++  +l+eGv+vg+gtD + + ns+n++ e+ ++           +  gl+  ++++m+T+ngA  lgl
  gi|91774261|ref|YP_566953.1| 269 PRSNFITDAGMAPICGMLEEGVNVGVGTD-NVMLNSVNMFSEMEVLS----------KVFGLEDRQVFKMCTLNGASLLGL 338
                                   *****************************.*****************..........6888******************** PP

                                   TTTSSSS-TTSB--EEEECCCT......CGGGTTT CS
                  Amidohydro_1 300 ddkvGsievGkdADlvvvdldi......laafvgl 328
                                   + ++Gsi++G +ADl ++++++        ++ g+
  gi|91774261|ref|YP_566953.1| 339 E-NTGSIKKGNKADLMILNGNSnnlvgiSDPISGM 372
                                   5.****************87332233434444444 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   8.7e-15   3.1e-11     180     304 ..     208     324 ..     181     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.7e-15
                                   HHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT- CS
                   A_deaminase 180 lklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyaen 260
                                    k +++a + + l+++HaGE    + + +A+ l + + + H +++  + +Lq   ++ +ip+ vcP SN  +    +    
  gi|91774261|ref|YP_566953.1| 208 IKSKRKAKDFNKLFAIHAGEKD-NTDIEKAISL-DPDILIHMTKAMRS-DLQ-AISESNIPIVVCPRSNFIT----DAGMA 280
                                   34556666667789******85.56799**998.99*****8887765.566.5799***************....88999 PP

                                   CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHHT--HHHH CS
                   A_deaminase 261 PlkeflerglnvslntDDPlqfgttLieeYaiaaqvfklseedl 304
                                   P+   le+g+nv ++tD+ ++ ++++  e++++++vf+l++++ 
  gi|91774261|ref|YP_566953.1| 281 PICGMLEEGVNVGVGTDNVMLNSVNMFSEMEVLSKVFGLEDRQV 324
                                   ***************************************99874 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.054   1.9e+02       8      21 ..      62      75 ..      60      80 .. 0.85
   2 !   33.1   0.0   1.2e-11   4.2e-08     318     447 ..     251     360 ..     198     378 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.054
                  Amidohydro_3  8 rlvlPGFvDsHtHl 21
                                   + +P F+ sHtH+
  gi|91774261|ref|YP_566953.1| 62 NIIAPCFINSHTHI 75
                                  5789*********5 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.2e-11
                  Amidohydro_3 318 tesqiervaalqvaagvqpvfnf..edelldsrlgperargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrkt 395
                                     s+++++ + ++ + v+p++nf  +              g +p+  +l+ gv+v  g+D         +     ++    
  gi|91774261|ref|YP_566953.1| 251 MRSDLQAISESNIPIVVCPRSNFitD-------------AGMAPICGMLEEGVNVGVGTDnV-------MLNSVNMF--SE 309
                                   55666666666666666777777432.............34589999*************32.......22222222..22 PP

                  Amidohydro_3 396 rrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld...a 447
                                   +   evl     l+ +++++++T ++A +lgle + G++++G +ADl++l+   +
  gi|91774261|ref|YP_566953.1| 310 M---EVLSKVFGLEDRQVFKMCTLNGASLLGLENT-GSIKKGNKADLMILNgnsN 360
                                   2...666666677889******************9.**************95544 PP

>> Phage_DsbA  Transcriptional regulator DsbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.8   9.9e+03       9      30 ..     112     133 ..     109     139 .. 0.73
   2 ?   11.7   0.2   6.6e-05      0.24       9      53 ..     194     236 ..     190     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
                    Phage_DsbA   9 LkidsereLikDiaiRakeele 30 
                                   L   s+ +L++ +++  ++ l+
  gi|91774261|ref|YP_566953.1| 112 LENTSYPDLVRSMRMTIQDMLQ 133
                                   5557899999999887777665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.6e-05
                    Phage_DsbA   9 LkidsereLikDiaiRakeelevdgkdFnkllklY..hkdnRdveea 53 
                                   L +++ ++L  Di i+ k     ++kdFnkl +++   kdn d e+a
  gi|91774261|ref|YP_566953.1| 194 LGMSGTNDLDMDILIKSKR----KAKDFNKLFAIHagEKDNTDIEKA 236
                                   7789*************97....89*******99844699*999988 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.15      43      95 ..     224     284 ..     197     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                   BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS.........H CS
                  Peripla_BP_2  43 evgadgeidvEklaalkPDlvilskglgltdedeellksgiptvivessntg.........e 95 
                                    +g  ++ d+Ek + l+PD++i  ++   +++   + +s+ip v+ + sn++          
  gi|91774261|ref|YP_566953.1| 224 HAGEKDNTDIEKAISLDPDILIHMTKA-MRSDLQAISESNIPIVVCPRSNFItdagmapicG 284
                                   57788899**************99999.8999999***********9999986666655550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2443.45
//
Query:       gi|91774262|ref|YP_566954.1|  [L=150]
Description: hypothetical protein Mbur_2350 [Methanococcoides burtonii DSM 6242]
Scores for 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-37  128.3   0.0    3.4e-37  128.1   0.0    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.12   12.6   0.2         17    5.7   0.0    2.7  3  PCP_red   Proto-chlorophyllide reductase 57 kD subunit


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 !  128.1   0.0   3.8e-41   3.4e-37       2     141 .]       6     145 ..       5     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 3.8e-41
                                   -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                           Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                   yk+I+Va+Dgse+ kkA+ +++e+ak +ga+l++++v+d+ a+++ ++ +  +   el ++e +++  + ++ a+ +g + 
  gi|91774262|ref|YP_566954.1|   6 YKKIMVATDGSEQNKKAISYGVEFAKLSGAKLYVVYVVDTAAFASIPMDAGWEMMYELLETEGKNASMQVEEFARSQGLEL 86 
                                   9*********************************************999988888888888888888889*********** PP

                                   EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                   e +v+eg+p+ ei+++aee+++d+iV+G+ g++g++r+llGSv+e+v r++++pVlvVr
  gi|91774262|ref|YP_566954.1|  87 ESTVLEGHPSNEIIKFAEENGIDMIVIGTLGKTGIDRFLLGSVAEKVTRNSKVPVLVVR 145
                                   **********************************************************8 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 ?    5.7   0.0    0.0019        17      22      34 ..      73      85 ..      69      86 .. 0.83
   2 ?    4.1   0.0    0.0062        56      24      39 ..      99     114 ..      97     118 .. 0.82
   3 ?   -2.7   0.0      0.83   7.4e+03      11      16 ..     138     143 ..     134     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0019
                                  HHHHHHHHHHT-S CS
                       PCP_red 22 raaEklArerGle 34
                                    +E++Ar +Gle
  gi|91774262|ref|YP_566954.1| 73 MQVEEFARSQGLE 85
                                  689********87 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0062
                                   HHHHHHHHT-SEE-HH CS
                       PCP_red  24 aEklArerGleeVtve 39 
                                   + k+A+e+G++++ + 
  gi|91774262|ref|YP_566954.1|  99 IIKFAEENGIDMIVIG 114
                                   679*********9765 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.83
                                   TS-HHH CS
                       PCP_red  11 kiPffv 16 
                                   k+P++v
  gi|91774262|ref|YP_566954.1| 138 KVPVLV 143
                                   899887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1026.25
//
Query:       gi|91774263|ref|YP_566955.1|  [L=283]
Description: CBS domain-containing protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-42  142.0  12.0    1.3e-12   47.9   0.6    4.3  4  CBS            CBS domain
     0.0081   16.0   0.0      0.017   14.9   0.0    1.5  1  SNURF          SNURF/RPN4 protein
  ------ inclusion threshold ------
      0.056   13.4   0.1        1.7    8.6   0.0    2.2  2  Peptidase_S55  SpoIVB peptidase S55
      0.076   13.6   0.1         29    5.3   0.0    3.0  3  GAF            GAF domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.3   2.8e-14   1.3e-10       1      53 [.       7      58 ..       7      61 .. 0.96
   2 !   47.9   0.6   2.9e-16   1.3e-12       4      55 ..      68     118 ..      63     120 .. 0.92
   3 !   24.4   0.1   6.4e-09   2.9e-05      11      54 ..     137     180 ..     127     182 .. 0.83
   4 !   33.9   0.0   7.3e-12   3.3e-08       1      56 [.     226     281 ..     226     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.8e-14
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                  V+dim +dv +++   +  e+l ++++k+vs+lPV+ +d+klvGiv+++ ll+
  gi|91774263|ref|YP_566955.1|  7 VRDIMVKDVACISLPGSRDEVLSILKDKKVSGLPVI-KDNKLVGIVSRSNLLK 58
                                  89***********************9999*******.7999**********98 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 2.9e-16
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   +m rd+++++pd++l+ a+ ++ ++g++rlPVV e++klvG++t  D++  l
  gi|91774263|ref|YP_566955.1|  68 LMVRDPISISPDEDLSVAAHILLKHGIRRLPVV-ENEKLVGLITVADVVGSL 118
                                   499******************99**********.8999*********99776 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 6.4e-09
                                   EEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS  11 tvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllra 54 
                                    v  +t+l+ +++ m e + v ++PV+d +  +vG++t+rD+++a
  gi|91774263|ref|YP_566955.1| 137 PVWYETPLHVVARNM-ELAhVKAVPVIDTNLDIVGLITDRDIISA 180
                                   68899**********.5444*******86779***********98 PP

  == domain 4  score: 33.9 bits;  conditional E-value: 7.3e-12
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V+d+m +++++++ ++ ++e++ +m++++++++PVV  + k++G++ +r ll+a+l
  gi|91774263|ref|YP_566955.1| 226 VKDVMVKELISASSNMGVSECALKMKRNRIDQVPVVSANQKFIGLLRDRYLLKAIL 281
                                   89***********************9999*******76779*************97 PP

>> SNURF  SNURF/RPN4 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.8e-06     0.017      11      53 ..     218     262 ..     206     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-06
                         SNURF  11 rtaeqhvPevevqvkrrrras..lsnqecqlyPrrsrqqqvPvvd 53 
                                   r   + vP  +v vk    as  +   ec l  +r r  qvPvv 
  gi|91774263|ref|YP_566955.1| 218 RIKVPSVPVKDVMVKELISASsnMGVSECALKMKRNRIDQVPVVS 262
                                   667788999999999998888335568****************96 PP

>> Peptidase_S55  SpoIVB peptidase S55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00037       1.7     175     192 ..      36      53 ..      34      62 .. 0.86
   2 ?    2.4   0.0      0.03   1.3e+02     178     192 ..      97     111 ..      82     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00037
                 Peptidase_S55 175 mSGsPiiqngklvGavth 192
                                   +SG P+i+++klvG v+ 
  gi|91774263|ref|YP_566955.1|  36 VSGLPVIKDNKLVGIVSR 53 
                                   69************9975 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.03
                 Peptidase_S55 178 sPiiqngklvGavth 192
                                    P++ n+klvG +t 
  gi|91774263|ref|YP_566955.1|  97 LPVVENEKLVGLITV 111
                                   6**********9995 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0064        29      90     123 ..      36      69 ..      19      71 .. 0.86
   2 ?    5.2   0.0    0.0069        31      59     109 ..      71     113 ..      67     130 .. 0.85
   3 ?   -1.4   0.0      0.75   3.4e+03      81     105 ..     147     172 ..     136     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0064
                                   EEEEEEEETTEEEEEEEEEE..SSSCSHHHHHHHHH CS
                           GAF  90 slvvPlvndgelwGllvlhn..psppftreelellq 123
                                   + ++P++ d++l+G+++  n  ++p  t+e+l+ll+
  gi|91774263|ref|YP_566955.1|  36 VSGLPVIKDNKLVGIVSRSNllKKP--TEEQLALLM 69 
                                   5689***************986666..999999986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0069
                                   SSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE CS
                           GAF  59 gqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn 109
                                   ++p++i+   pd++ +     ++l  +gir    +P+v +++l+Gl+++ +
  gi|91774263|ref|YP_566955.1|  71 RDPISIS---PDEDLSV--AAHILLKHGIR---RLPVVENEKLVGLITVAD 113
                                   6789999...8888777..56899999**9...99************9976 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.75
                                   HHHHTTESEEEEEEEEE.TTEEEEEE CS
                           GAF  81 llenmgirsslvvPlvn.dgelwGll 105
                                   +++nm+   + +vP+++ + +++Gl+
  gi|91774263|ref|YP_566955.1| 147 VARNMELAHVKAVPVIDtNLDIVGLI 172
                                   567899999999***98566678876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1645.65
//
Query:       gi|91774264|ref|YP_566956.1|  [L=226]
Description: 5-amino-6-(5-phosphoribosylamino)uracil reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  178.7   0.0    1.3e-52  178.6   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 !  178.6   0.0   7.3e-57   1.3e-52       2     200 .]       5     219 ..       4     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 7.3e-57
                                   EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS-EEEE CS
                        RibD_C   2 yvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearqpvrvV 81 
                                   +  +++a+S+DGk++++++++ +i+g+ +  +++elra +dai+vG+gtvlad+psltv+ +  r ++ +++  ++pvr++
  gi|91774264|ref|YP_566956.1|   5 FTFINSAMSADGKISTKERKQVRISGDIDFDRMDELRASSDAIMVGIGTVLADDPSLTVKSRYRRDTRkNKGLDEDPVRII 85 
                                   66799***********************************************************9888555666******* PP

                                   EETTS-S-TTSHHHHSS.S-EEEEESSCSCHHHHHHCC....E......SE-HHHHHHHHHHTT--EEEEEETHHHHHHHH CS
                        RibD_C  82 vdstlrvpldakvltdd.aptlvatteeadkekveklk....v......rvdlkelleeLkergirsllveGGatLagsll 151
                                   vds+ r+pl+a++++++    +va++++a+kekv+ l+    +      +vdl+ l+ +L+ +gi++l+veGGatL++ ll
  gi|91774264|ref|YP_566956.1|  86 VDSKARTPLNADIFKKGtGMRIVAVSSSAPKEKVDALSkkatIitagdeKVDLVLLMGQLSSMGIQRLMVEGGATLNWGLL 166
                                   **************************************98872578999******************************** PP

                                   HTTT-SEEEEEEESCE--T.TSBCSSSSST-SS...EEEEEEEEEEETTEEEE CS
                        RibD_C 152 raglvDelrlyiaPkllGg.agktlfdgegfka...lklklvksealgegvvl 200
                                    +glvDe+  +i  +++Gg   +tl+dgegf++   l l+l +se++ egv+l
  gi|91774264|ref|YP_566956.1| 167 SNGLVDEVFSFIGNIFIGGnSSPTLVDGEGFLKgdfLPLELISSETIEEGVLL 219
                                   **************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1215.54
//
Query:       gi|91774265|ref|YP_566957.1|  [L=165]
Description: thioredoxin [Methanococcoides burtonii DSM 6242]
Scores for complete 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   38.5   0.0    1.2e-09   38.1   0.0    1.2  1  Thioredoxin    Thioredoxin
     0.0014   18.9   0.0     0.0025   18.1   0.0    1.4  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
       0.03   13.9   0.0       0.04   13.5   0.0    1.2  1  DUF953         Eukaryotic protein of unknown function (DUF953
      0.063   13.5   0.0        0.1   12.8   0.0    1.4  1  Thioredoxin_7  Thioredoxin-like
       0.13   12.7   0.0       0.28   11.7   0.0    1.5  2  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   3.4e-13   1.2e-09       4      78 ..      41     113 ..      38     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.4e-13
                                   ESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                   Thioredoxin   4 vltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78 
                                   v++k++ ++++ +   +vl++  A+wC++C +l P+l++la +++++ +++ +d    + la++++  +iP   +
  gi|91774265|ref|YP_566957.1|  41 VTEKQQIDDALVN--GPVLLKIGAEWCPPCTQLDPVLDELAMDYEGRATIMYIDSGITSGLAAQFKYYSIPDTTV 113
                                   5666777777777..9**************************************************999998665 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   7.1e-07    0.0025       3      42 ..      55      92 ..      53     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.1e-07
                                  EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE CS
                 Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvs 42
                                   vlL +ga+wcppc++  p l+el  +++   +  i y+ 
  gi|91774265|ref|YP_566957.1| 55 PVLLKIGAEWCPPCTQLDPVLDELAMDYE--GRATIMYID 92
                                  69**********************99998..777777776 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 ?   13.5   0.0   1.1e-05      0.04      17      67 ..      43      94 ..      29     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                  TSSSEEEEEEB--B-.TTS-BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE-- CS
                        DUF953 17 keskivfilFlgekd.teGesWCPdCvkaepvieealkeapedvklvrvdvG 67
                                  ++++i  +l  g    + G  WCP C + +pv+ e   +    ++++++d G
  gi|91774265|ref|YP_566957.1| 43 EKQQIDDALVNGPVLlKIGAEWCPPCTQLDPVLDELAMDYEGRATIMYIDSG 94
                                  4556666666776666889***************999998888888888877 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.8e-05       0.1      19      37 ..      55      73 ..      50     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                                  -EEEEE--TT-HHHHHHHH CS
                 Thioredoxin_7 19 pvlvffgaswcftCqaler 37
                                  pvl+ +ga+wc++C+ l+ 
  gi|91774265|ref|YP_566957.1| 55 PVLLKIGAEWCPPCTQLDP 73
                                  9*************99875 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.8e-05      0.28       6      34 ..      54      85 ..      50     116 .. 0.76
   2 ?   -2.6   0.0       2.1   7.6e+03      92     107 ..     136     151 ..     130     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
                 Thioredoxin_2  6 kpvlvvftdpdCpyCkklkkelkel...ddvt 34
                                   pvl+ + +++Cp C +l  +l+el    + +
  gi|91774265|ref|YP_566957.1| 54 GPVLLKIGAEWCPPCTQLDPVLDELamdYEGR 85
                                  6899999**************99997443333 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                 Thioredoxin_2  92 ivarlpGyvpaeelea 107
                                     ar+ Gyv+   le 
  gi|91774265|ref|YP_566957.1| 136 NKARILGYVDISVLET 151
                                   4579999998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 985.96
//
Query:       gi|91774266|ref|YP_566958.1|  [L=214]
Description: cytochrome c biogenesis protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-33  116.9  29.5    2.3e-33  115.9  29.5    1.4  1  DsbD       Cytochrome C biogenesis protein transmembrane regi
  ------ inclusion threshold ------
        3.4    7.6  11.8        0.5   10.3   1.0    2.7  3  MerE       MerE protein


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 !  115.9  29.5   2.6e-37   2.3e-33       1     212 [.      11     206 ..      11     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 2.6e-37
                          DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevirrv 81 
                                   af aG++s lsPC+lpl+P+ ++y +         +k+k+    + l  v Glsl fv +g+ ++  g+l++++  +++  
  gi|91774266|ref|YP_566958.1|  11 AFIAGVISILSPCVLPLLPVIFAYST---------SKGKL----RPLAIVSGLSLSFVFMGIITSVFGSLFQQYLIYLTAF 78 
                                   699*********************76.........44555....67899******************************** PP

                          DsbD  82 aglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskeslakgallll 162
                                   ag+ivil+Gl++l  f++  ++    l   + k++   +g lllG++ +++w PC+gP+las+l l+a +++l++ga ll+
  gi|91774266|ref|YP_566958.1|  79 AGIIVILMGLTLL--FDLGTFNSIGGLSGKQFKENG-LMGGLLLGISLGIIWIPCVGPILASILSLVAIEGDLLYGAFLLF 156
                                   ***********99..998887777666554444444.7******************************************* PP

                          DsbD 163 vyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvlll 212
                                   vy++Gl+ip+ll++  ++    kl ++ ky  +++++ g +lvl+G+ +l
  gi|91774266|ref|YP_566958.1| 157 VYSMGLGIPMLLIAYSANISSSKLGMIAKYDMYLKKVVGFILVLVGMWML 206
                                   **********************************************9886 PP

>> MerE  MerE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   5.6e-05       0.5      14      64 ..       8      57 ..       4      67 .. 0.86
   2 ?   -3.5   0.3       1.1     1e+04      54      65 ..      83      94 ..      75      96 .. 0.62
   3 ?    5.0   0.4    0.0026        24      16      40 ..     115     140 ..     109     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.6e-05
                          MerE 14 pltGylwGalavltcPchlpilaivlaGttaGaflgeywviaalaltGlfv 64
                                  pl+ ++ G++++l+ Pc lp+l +++a +t+   l    ++++l+l+ +f+
  gi|91774266|ref|YP_566958.1|  8 PLAAFIAGVISILS-PCVLPLLPVIFAYSTSKGKLRPLAIVSGLSLSFVFM 57
                                  7888999***9997.************999998999999999999988886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                          MerE 54 iaalaltGlfvl 65
                                  ++ ++lt lf l
  gi|91774266|ref|YP_566958.1| 83 VILMGLTLLFDL 94
                                  344566767755 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0026
                          MerE  16 tGylwGa.lavltcPchlpilaivla 40 
                                    G l G+ l ++  Pc  pila +l+
  gi|91774266|ref|YP_566958.1| 115 GGLLLGIsLGIIWIPCVGPILASILS 140
                                   5677775589999*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1451.44
//
Query:       gi|91774267|ref|YP_566959.1|  [L=249]
Description: precorrin-8X methylmutase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-65  219.3   2.7    4.4e-65  219.0   2.7    1.1  1  CbiC      Precorrin-8X methylmutase
  ------ inclusion threshold ------
       0.05   14.0   0.3        7.2    7.1   0.2    3.3  2  DUF4258   Domain of unknown function (DUF4258)


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 !  219.0   2.7   4.9e-69   4.4e-65       2     195 ..      45     234 ..      44     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 4.9e-69
                                   HHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHHHTT CS
                          CbiC   2 IeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkrlekl 82 
                                   I+ +S +i ++ + + e ++ ee+v++R++ +t+d+++a+++r+++da+eag++a+k+gapi++D++mvkaG+tkk ++  
  gi|91774267|ref|YP_566959.1|  45 IYMTSRRIAHDLIVKGEKETPEERVTQRCVISTGDPSIADIMRYTDDAIEAGVKAIKNGAPIFVDINMVKAGVTKKGHD-- 123
                                   8999********999999********************************************************99976.. PP

                                   C-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHHHHH CS
                          CbiC  83 gnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaaesK 163
                                    +ev+c+l++++ ae ak+ gitr+aa++ +a+++ eg+iv+iGnAP+A l+++++ie+g +kpal++g+PvGFv+aaesK
  gi|91774267|ref|YP_566959.1| 124 -CEVICVLDEDQNAEVAKKYGITRTAAGFLLARDRIEGSIVAIGNAPSAALAVCRMIEHG-IKPALIVGTPVGFVNAAESK 202
                                   .58******************************************************998.6******************* PP

                                   HHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
                          CbiC 164 ealaesevpyitveGrkGGsavAaaivnaLle 195
                                   e+++++evp+it+ G++GG+++A+a+vn+L++
  gi|91774267|ref|YP_566959.1| 203 EEIRKMEVPSITCVGTRGGTPMAVACVNELVA 234
                                   ******************************86 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2   0.00081       7.2      21      56 ..      98     135 ..      15     140 .. 0.85
   2 ?    3.3   0.0     0.012   1.1e+02       5      20 ..     174     189 ..     174     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00081
                       DUF4258  21 evlenGeiieeys.......lvlgktsegrplhvvvapdedpv 56 
                                   ++++nG      +       + +g+t++g+  +v++++ded  
  gi|91774267|ref|YP_566959.1|  98 KAIKNGA-----PifvdinmVKAGVTKKGHDCEVICVLDEDQN 135
                                   4667774.....23444467667****************9965 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.012
                       DUF4258   5 ArermaeRgIseedie 20 
                                   A++rm e gI+ + i 
  gi|91774267|ref|YP_566959.1| 174 AVCRMIEHGIKPALIV 189
                                   7899999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1561.02
//
Query:       gi|91774268|ref|YP_566960.1|  [L=267]
Description: precorrin-3 methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  126.6   0.2    1.5e-36  126.4   0.2    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.051   13.2   0.1       0.12   12.0   0.0    1.7  2  IMP_cyclohyd  IMP cyclohydrolase-like protein


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 !  126.4   0.2   1.6e-40   1.5e-36       1     212 [.      16     224 ..      16     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1.6e-40
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                   kl+++G+GpG+ e+lT+rA++++ ++d ++g +  +l+ + +ll++       ++   +++ ++  + a++ +e++++ k 
  gi|91774268|ref|YP_566960.1|  16 KLFIIGIGPGSVEQLTIRARDVILNSDYIVGNG-TYLDQMAELLDK-------QKII-RSAMGKEVDRAKKAVELAKENKV 87 
                                   799******************************.888888788765.......3344.44445555577778999999999 PP

                  TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallan 160
                                   V ++++GD +vyg+++ ++e ++ ++ +++vev+PGv++++a a+ lg+p+++++ v s++  l++++ +e+r+ +a++a 
  gi|91774268|ref|YP_566960.1|  88 VSMISGGDANVYGMAGLVMEVAEHADLEVDVEVLPGVTAITAGASVLGAPIVNDFAVISLSdlLTPWEVIEKRLNAAASA- 167
                                   ************************99******************************************999999999888. PP

                  TP_methylase 161 gdtlvllkapr.k.....laelaelLkealyddttpvavveragted.ervvrgtleel 212
                                    d+++ l++p+ +     ++++++++k++ +d   pv +v++a + + +  +++tlee+
  gi|91774268|ref|YP_566960.1| 168 -DFVISLYNPKsRqrhsnFSRAIDIIKQH-KDGSVPVGLVKNALRGEsQDYIVTTLEEV 224
                                   .**********7478999***********.999************85488999***996 PP

>> IMP_cyclohyd  IMP cyclohydrolase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05      0.12      63      94 ..      39      70 ..      30      90 .. 0.91
   2 ?   -2.7   0.0      0.43   3.9e+03     139     161 ..     212     236 ..     181     258 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                                  ETTEEEEESSTHHHHHHHHHHTSB-HHHHHHH CS
                  IMP_cyclohyd 63 lddkavvtNGsqtdtiaeklekgltardalal 94
                                  l++  +v+NG+  d +ae l+k++ +r a+ +
  gi|91774268|ref|YP_566960.1| 39 LNSDYIVGNGTYLDQMAELLDKQKIIRSAMGK 70
                                  67889************************876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.43
                                   TTS-EEEESSS-..-S-EE-----S CS
                  IMP_cyclohyd 139 agegtliatYek..gepkeveleae 161
                                   + + +++ t e+  ++++ v++++ 
  gi|91774268|ref|YP_566960.1| 212 ESQDYIVTTLEEvlDHNDWVDMSTM 236
                                   3344555555555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1997.36
//
Query:       gi|91774269|ref|YP_566961.1|  [L=243]
Description: precorrin-4 C11-methyltransferase / cobalt-factor II C20-methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for 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-45  154.0   0.4    5.8e-45  153.8   0.4    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    0.00014   22.3   0.1    0.00048   20.6   0.1    1.9  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.091   13.4   0.1        3.3    8.5   0.0    2.6  2  GTP-bdg_N     GTP-binding GTPase N-terminal
       0.13   11.9   0.0        0.2   11.3   0.0    1.4  1  ApbA          Ketopantoate reductase PanE/ApbA


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 !  153.8   0.4   1.3e-48   5.8e-45       2     212 ..       6     204 ..       5     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 1.3e-48
                  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdV 82 
                                   +++VG+GpG+p+l+T+ + + l++ad+v++++s++   + d+++         g+++++ + + e+i++++a al++gk+V
  gi|91774269|ref|YP_566961.1|   6 VTFVGAGPGNPKLITLLGKEKLEEADLVVYAGSLVNPVVVDYCK---------GEKVDSYGLTLEDISKRIANALEEGKKV 77 
                                   89******************************99******9995.........68999*********************** PP

                  TP_methylase  83 vllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallang 161
                                   v+l+sGDP++yg + e +e+l+    g+ ve +PGvss+ a aa+l++ lt +g++ +++  +p+ ++ ee++l++l+ ++
  gi|91774269|ref|YP_566961.1|  78 VRLHSGDPSLYGNVVEQMEELKT--YGVTVERVPGVSSVFATAAALNTQLTLNGVSDTLIitRPAGKTLEEDKLKELSRHN 156
                                   ***********************..******************************************************** PP

                  TP_methylase 162 dtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                    t++++ +++k++e++e        d+tpvavv +a+++d++++ gt++++
  gi|91774269|ref|YP_566961.1| 157 ATMAVFLGTQKIEEIMEKVEY---SDDTPVAVVFHASWPDQKIIYGTVADI 204
                                   *******************44...5677*******************9987 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.1e-07   0.00048      23     115 ..      52     167 ..      46     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...............CCTEEEEEEECSSC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxx RF
                   Radical_SAM  23 egrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...............vpgiritvetngtl 88 
                                    ++++ l++e+i + +  +  e g+k+v l++g+p+ly + ve +e+l+                   + +++ ++ ng+ 
  gi|91774269|ref|YP_566961.1|  52 KVDSYGLTLEDISKRIANA-LEEGKKVVRLHSGDPSLYGNVVEQMEELKTYGvtvervpgvssvfatAAALNTQLTLNGVS 131
                                   4778889************.7999*************************99999999777777777777777777777777 PP

                                   HG............HHHHHHHHHTT.-SEEEEEEBSSSHH CS
                                   xx............xxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   Radical_SAM  89 pd............eeklerllelg.vdrvslgleaadde 115
                                   ++            e+kl++l + + +    + +  ++ +
  gi|91774269|ref|YP_566961.1| 132 DTliitrpagktleEDKLKELSRHNaT----MAVFLGTQK 167
                                   669999999888888888888886633....333333333 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.065   2.9e+02      29      57 ..      16      45 ..       4      48 .. 0.73
   2 ?    8.5   0.0   0.00073       3.3      25      58 ..     153     188 ..     143     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.065
                     GTP-bdg_N 29 pdpatyiGkGkveeikelveeee.adlvif 57
                                  p+  t++Gk k+ee   +v + + ++ v++
  gi|91774269|ref|YP_566961.1| 16 PKLITLLGKEKLEEADLVVYAGSlVNPVVV 45
                                  5667999******99988866332566665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00073
                     GTP-bdg_N  25 krekpdpatyiGkGkveeikelveeee..adlvifd 58 
                                   +r++   a+++G+ k+eei e+ve  +    +v+f+
  gi|91774269|ref|YP_566961.1| 153 SRHNATMAVFLGTQKIEEIMEKVEYSDdtPVAVVFH 188
                                   567888999**************8743113455554 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   4.4e-05       0.2      26     126 ..      87     202 ..      62     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                                   EE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEEEESSSS CS
                          ApbA  26 lilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKayqteealeeikplldpntvvlllqNGl 105
                                   l+++   ++e+lk+ G++++++ g   +  ++a+ +++   ++  d +i+t +a  t e  +++k+l  +n+++ +++ + 
  gi|91774269|ref|YP_566961.1|  87 LYGNVVeQMEELKTYGVTVERVPGVSSVFATAAALNTQLTLNGVSDTLIITRPAGKTLE-EDKLKELSRHNATMAVFLGTQ 166
                                   55555557899************777777777776665788999***************.677************999999 PP

                                   CHHHHHTTTS...............TTSEEEEEEEE CS
                          ApbA 106 gheeelreal...............pkprvlggvtt 126
                                   + ee++++                 p++++++g++ 
  gi|91774269|ref|YP_566961.1| 167 KIEEIMEKVEysddtpvavvfhaswPDQKIIYGTVA 202
                                   999988887767666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1659.29
//
Query:       gi|91774270|ref|YP_566962.1|  [L=203]
Description: cobalt-precorrin-2 C(20)-methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  119.1   0.0    3.2e-34  118.8   0.0    1.1  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 !  118.8   0.0   1.8e-38   3.2e-34       1     167 [.       1     170 [.       1     189 [. 0.90

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.8e-38
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                   +l++VG+GpGdpellT++A+++lk++d v+ +++ a +++++++ +e  l +pm ++ ++l+e+++++a+++a+++r+g +
  gi|91774270|ref|YP_566962.1|   1 MLIGVGLGPGDPELLTLKAVNILKNSDKVYVPGNMAAKLVKPYATPE-ILDFPMLRDYDVLNEVWKKNADIIADEARNG-T 79 
                                   79*******************************77*******99776.99*****************************.6 PP

                  TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeeereleal 157
                                   Vv+  +GDP++++t+ +l +   ++++++e+ ++PG+ss+++ aar++++++ ++ev++ +      + +a+++++++e++
  gi|91774270|ref|YP_566962.1|  80 VVFGLIGDPNFFSTFTHLKRVMNKHYPDVETSTVPGISSITSFAARADAEVDTSFEVSDGSetkhkIRLKANRPRQLIEEF 160
                                   ***********************************************************9988777333446677778887 PP

                  TP_methylase 158 langdtlvll 167
                                   +++g+t +++
  gi|91774270|ref|YP_566962.1| 161 SEEGYTDFIF 170
                                   7777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1406.13
//
Query:       gi|91774271|ref|YP_566963.1|  [L=183]
Description: precorrin-8W decarboxylase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   48.0   0.1    1.2e-12   47.9   0.1    1.1  1  Methyltransf_31  Methyltransferase domain
    4.4e-09   36.4   0.5    1.1e-08   35.2   0.5    1.5  1  Methyltransf_18  Methyltransferase domain
    1.6e-08   35.2   0.1    2.5e-08   34.5   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    1.7e-08   34.2   0.1    2.1e-08   33.9   0.1    1.2  1  MTS              Methyltransferase small domain
    1.7e-07   31.2   0.1    2.2e-07   30.8   0.1    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.2e-07   29.5   0.6    5.1e-07   29.3   0.6    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    7.5e-07   28.8   0.3    7.5e-07   28.8   0.3    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.1e-06   26.3   0.1    4.5e-06   26.1   0.1    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    2.3e-05   25.1   0.1    3.3e-05   24.6   0.1    1.3  1  Methyltransf_12  Methyltransferase domain
    2.8e-05   23.8   0.0    3.6e-05   23.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    6.7e-05   23.5   0.1    0.00011   22.7   0.1    1.5  1  Methyltransf_11  Methyltransferase domain
    0.00032   20.5   0.1     0.0015   18.2   0.1    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    0.00072   19.1   0.1     0.0013   18.3   0.1    1.6  1  DOT1             Histone methylation protein DOT1
     0.0008   19.4   0.0     0.0013   18.8   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
    0.00089   19.0   0.1     0.0012   18.6   0.1    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0011   18.6   0.5     0.0017   18.0   0.5    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0014   17.7   0.1      0.015   14.4   0.0    1.9  2  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0024   17.5   0.0     0.0027   17.2   0.0    1.2  1  Methyltransf_5   MraW methylase family
     0.0025   17.7   0.0     0.0029   17.5   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
     0.0058   16.1   0.4       0.01   15.3   0.0    1.5  2  Methyltransf_4   Putative methyltransferase
     0.0089   17.0   0.0      0.017   16.1   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.078   12.6   0.0       0.13   11.9   0.0    1.3  1  GATase_3         CobB/CobQ-like glutamine amidotransferase do
      0.093   12.2   0.0       0.12   11.8   0.0    1.4  1  AviRa            RRNA methyltransferase AviRa
      0.094   12.0   0.0       0.11   11.8   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.1   1.6e-15   1.2e-12       2      81 ..      27     106 ..      26     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.6e-15
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklled.ekfDlils 80 
                                   ++g++++D+GCGtG+ ++e+  +   + +vv iD  eeaie++r+n ++ g+d v++ +g+  e ++k+ +d  ++D  + 
  gi|91774271|ref|YP_566963.1|  27 KDGITFYDVGCGTGAVSIEAS-KTARNFKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHGESSEaIDKN-ADiGSIDCAFV 105
                                   68999****************.77889***********************************9988865.33355555444 PP

               Methyltransf_31  81 n 81 
                                    
  gi|91774271|ref|YP_566963.1| 106 G 106
                                   3 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.5   1.4e-11   1.1e-08      15     149 ..      29     162 ..      25     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.4e-11
               Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvviaGmGg. 93 
                                   g ++ D+G+  g ++i++ k+ +  kv+a+D +e+++e +++n ++ g+ d+++++ ++  e+++++  +  + +a +Gg 
  gi|91774271|ref|YP_566963.1|  29 GITFYDVGCGTGAVSIEASKTARNFKVVAIDAREEAIEVSRTNFRNFGI-DDVTLIHGESSEAIDKNAdIGSIDCAFVGGt 108
                                   56789*******************************************9.67************97755889999988873 PP

               Methyltransf_18  94 elileILeeakeklkkikklilqpnseaeelRkylvengfkiedEelvkeegkiYe 149
                                   ++i+++L+   ek+  ++++++++ + +  +  +   ++  i +E +     + Ye
  gi|91774271|ref|YP_566963.1| 109 KNISKVLDVLYEKK--TRNIVVNAVRIETVVTTMNKMKELGIFSEVVHVTITRGYE 162
                                   57899998874443..3456666555555555555555555555544444443333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   3.4e-11   2.5e-08       3      70 ..      34     105 ..      32     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3.4e-11
                                   EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBS..SSTTTEEEEEE CS
               Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgda.edlp..fedgsfDlvvs 70 
                                   d+GcGtG ++++++k   + kv+++D  ee++e  r+++++ g+ +v++++g+  e+++   + gs+D+ ++
  gi|91774271|ref|YP_566963.1|  34 DVGCGTGAVSIEASKTARNFKVVAIDAREEAIEVSRTNFRNFGIdDVTLIHGESsEAIDknADIGSIDCAFV 105
                                   9***************989********************99999******9998344552234457777776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.1   2.8e-11   2.1e-08      26      99 ..      23      96 ..      18     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.8e-11
                                  HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EE CS
                           MTS 26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfd 99
                                  +l+ +   +  D+GcG+G++++++ k   + +v+++d+  +A+e++++n+++ +++ v++++ +  e+++ k+ d
  gi|91774271|ref|YP_566963.1| 23 KLDLKDGITFYDVGCGTGAVSIEASKTARNFKVVAIDAREEAIEVSRTNFRNFGIDdVTLIHGESSEAID-KNAD 96
                                  55555566688********************************************999999999888887.6666 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 !   30.8   0.1     3e-10   2.2e-07      58     143 ..      13      97 ..       4     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3e-10
                                   -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTG CS
                          PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGye 138
                                   +p ++a+ l  l+lk+g    +vG+G+G  + + a    ++++vv+i+  +e +e ++ n ++ ++++v++++g+  +  +
  gi|91774271|ref|YP_566963.1|  13 KPEVIAISLSKLDLKDGITFYDVGCGTGAVS-IEASKTARNFKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHGESSEAID 92 
                                   68999***********************765.56666788999*******************************9988888 PP

                                   GG-SE CS
                          PCMT 139 ekaPY 143
                                   ++a  
  gi|91774271|ref|YP_566963.1|  93 KNADI 97 
                                   77755 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.6   6.8e-10   5.1e-07      46     138 ..      27     120 ..      18     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.8e-10
                                   --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--T.TT-TTS-..T-EEEEEEE CS
               Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqana.eeLpfed..dsfDvvtvs 123
                                   k g ++ Dv +Gtg ++++ s++++ ++kvv +D  e+ ++v++   ++ g  ++ ++++++ e+++ +   +s D+  v+
  gi|91774271|ref|YP_566963.1|  27 KDGITFYDVGCGTGAVSIEASKTAR-NFKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHGESsEAIDKNAdiGSIDCAFVG 106
                                   78999**************999886.69*******************************9761455544336899999888 PP

                                   S-GGG-S-HHHHHHH CS
               Ubie_methyltran 124 fGlrnvtDklkaLke 138
                                    G +n++  l +L e
  gi|91774271|ref|YP_566963.1| 107 -GTKNISKVLDVLYE 120
                                   .99999999988865 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.3     1e-09   7.5e-07     159     228 ..      26      96 ..      16     100 .. 0.77
   2 ?   -3.1   0.1       5.2   3.9e+03     203     213 ..     125     135 ..     109     156 .. 0.51

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1e-09
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkveakleva.lseellkeekad 228
                                   +k g ++ DvG+G+G  +i a+k + + kvva+D  e A++v++ N++  ++++   ++  s+e+++ ++ad
  gi|91774271|ref|YP_566963.1|  26 LKDGITFYDVGCGTGAVSIEASKTARNfKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHgESSEAID-KNAD 96 
                                   45566889**************9987659******************99999985545523344444.5565 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.2
                          PrmA 203 NaelNkveakl 213
                                   N+ +N v+ + 
  gi|91774271|ref|YP_566963.1| 125 NIVVNAVRIET 135
                                   23333332222 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   6.1e-09   4.5e-06      52     155 ..      18     121 ..      13     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.1e-09
                                   HHHHTTTT--TT-EEEEES-TTSHHHHHHHHH.H--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEE CS
                          CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraver.ydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrv 131
                                    + l kl+lk+G t  d+GcG G++ ++a +   + kvv++   +e  ++++ ++ + ++++ + ++    e +d++ d +
  gi|91774271|ref|YP_566963.1|  18 AISLSKLDLKDGITFYDVGCGTGAVSIEASKTaRNFKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHGESSEAIDKNAD-I 97 
                                   56799********************999976414899**********************99988888888888877766.7 PP

                                   EEES-GGGTSGGGHHHHHHHHHHH CS
                          CMAS 132 vsvgafehvgkenydtffkklkkl 155
                                    s++     g++n  +  ++l+++
  gi|91774271|ref|YP_566963.1|  98 GSIDCAFVGGTKNISKVLDVLYEK 121
                                   777766666777776666666655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   4.4e-08   3.3e-05       2      77 ..      34     116 ..      33     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.4e-08
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvv......asnv 75 
                                   ++GcGtG+++ +  +  ++ +++++D  ++aie  ++ ++  + ++++ ++ e  +++d+    +s D  +      +s v
  gi|91774271|ref|YP_566963.1|  34 DVGCGTGAVSIEASKTARNFKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHGESSEAIDKNADiGSIDCAFvggtknISKV 114
                                   9****************************************************9999988766778887774444444444 PP

               Methyltransf_12  76 lh 77 
                                   l 
  gi|91774271|ref|YP_566963.1| 115 LD 116
                                   44 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.8e-08   3.6e-05      43     119 ..      30     105 ..      20     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.8e-08
                                   -EEEETT-TTSHHHHHH..HHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE CS
                 Cons_hypoth95  43 arvLDlfaGsGalglEA..lSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivfl 119
                                    ++ D+ +G+Ga+++EA    R+  k+v+++  +ea+++ ++n +++++++ ++ +  +++ea++k+a   +++d  f+
  gi|91774271|ref|YP_566963.1|  30 ITFYDVGCGTGAVSIEAskTARN-FKVVAIDAREEAIEVSRTNFRNFGIDD-VTLIHGESSEAIDKNA-DIGSIDCAFV 105
                                   5688999*********9333454.4799********************997.9999999999999994.3345555554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.5e-07   0.00011       2      66 ..      34     104 ..      33     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-07
                                   EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC.T.SS-T.T-EEEEE CS
               Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaek.l.pfed.nsfDlvv 66 
                                   dvGcGtG+++ +  k++   +vv++D  +e++++++++ ++ g+  v++++++ ++ + + +d +s+D+ +
  gi|91774271|ref|YP_566963.1|  34 DVGCGTGAVSIEASKTArnFKVVAIDAREEAIEVSRTNFRNFGIdDVTLIHGESSEaIdKNADiGSIDCAF 104
                                   9*************888889********************9999888888877765233333335666555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.1e-06    0.0015      17     103 ..      18      79 ..       8     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-06
                                   HHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHH CS
                       UPF0020  17 AaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNae 97 
                                   A +l +l ++k+g +++D  CG+G++ IEa   ++n         ++ +++ea e  r++ +++g+D              
  gi|91774271|ref|YP_566963.1|  18 AISLSKL-DLKDGITFYDVGCGTGAVSIEASKTARNFK-----VVAIDAREEAIEVSRTNFRNFGID-------------- 78 
                                   5555444.899********************9999988.....223345555555555555555555.............. PP

                                   HTT-GG CS
                       UPF0020  98 kagvgd 103
                                        d
  gi|91774271|ref|YP_566963.1|  79 -----D 79 
                                   .....4 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.7e-06    0.0013      24      87 ..      10      73 ..       7     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                                  --B-HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHH CS
                          DOT1 24 GEllpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqke 87
                                  G ++pe+++  l+k++lk+  +F+D G G G v + a+  ++  + v ++  ++a e+++++ +
  gi|91774271|ref|YP_566963.1| 10 GPTKPEVIAISLSKLDLKDGITFYDVGCGTGAVSIEASKTARNFKVVAIDAREEAIEVSRTNFR 73
                                  67899999********************************999999999999999888877665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-06    0.0013      22      90 ..      25      88 ..      15     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
               Methyltransf_32 22 kesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsie 90
                                  + ++ +t  DvG+G g  s   +   +  ++kvv+ida+ee +e +++  +++g  + +++  ++++++
  gi|91774271|ref|YP_566963.1| 25 DLKDGITFYDVGCGTGAVSIEASK--TARNFKVVAIDAREEAIEVSRTNFRNFG--I-DDVTLIHGESS 88
                                  456678999*******99888887..5579****************99988888..5.55555555554 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.5e-06    0.0012      29     172 ..      17     157 ..      14     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                         GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdee 109
                                   i++   kL+lk G    + G G+g++s   ++t     ++ +++  e+ +e +r +fr+ ++++++ ++         +++
  gi|91774271|ref|YP_566963.1|  17 IAISLSKLDLKDGITFYDVGCGTGAVSIEASKTAR-NFKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHGESSEAIDKNAD 96 
                                   6777899**********************999965.67999*********************9976666555444444678 PP

                         GCD14 110 vsgkvDavfLDlPaPweaiphaakal.kkeggrlCsfsPCieqvqrtceaLrelg.fteietlev 172
                                   + g++D+ f+      + i ++ ++l +k+   +   +  ie v  t+++++elg f e+  + +
  gi|91774271|ref|YP_566963.1|  97 I-GSIDCAFVG---GTKNISKVLDVLyEKKTRNIVVNAVRIETVVTTMNKMKELGiFSEVVHVTI 157
                                   8.899999985...67899999999955555568888889************9986777776655 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   2.2e-06    0.0017       6      77 ..      34     105 ..      30     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
               Methyltransf_15   6 DlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklk.lekikvdlvfl 77 
                                   D+ +G+G  +i+  ++   f kv+ai+  +e ++++  N + +g++  +tl++g+  e++ k       ++d+ f+
  gi|91774271|ref|YP_566963.1|  34 DVGCGTGAVSIEASKTarnF-KVVAIDAREEAIEVSRTNFRNFGID-DVTLIHGESSEAIDKNAdIG--SIDCAFV 105
                                   9999**99999876655547.9*********************996.59*******99776632022..3476664 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.9e-05     0.015      16      82 ..      14      84 ..      12      95 .. 0.85
   2 ?    1.4   0.0      0.19   1.4e+02     211     257 ..     101     146 ..      97     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                  HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE- CS
                        RrnaAD 16 kkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvh 82
                                  + vi+  l+kl+l++  t +++g G+G+ + e  k a   +vv++  +e+ +++ +++++      ++++h
  gi|91774271|ref|YP_566963.1| 14 PEVIAISLSKLDLKDGITFYDVGCGTGAVSIEASKTArnFKVVAIDAREEAIEVSRTNFRnfGIDDVTLIH 84
                                  67888889*****************************65689*******9999999988755555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
                                   HHHHCTTTSBCCCHCCCTSTCHHHHHCTT.T--TTTCCCCSGHHHHH CS
                        RrnaAD 211 rkllnrkrktlstslksllpggelqalsstgindnalvkklsaeqtl 257
                                    ++++   k++s++l+ l++++ ++ + +  + +++ v+  ++ + l
  gi|91774271|ref|YP_566963.1| 101 DCAFVGGTKNISKVLDVLYEKKTRNIVVN-AVRIETVVTTMNKMKEL 146
                                   67899999********9999999888877.57777777766665555 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.7e-06    0.0027      12      83 ..      20      93 ..      13     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                                  HHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....-.--EEEEES-G.GGHHH CS
                Methyltransf_5 12 vvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefe.krltlvkgnf.kelke 83
                                  +++ l+ k++ ++ D+  G+g  s +  +  ++ ++++id  ++a++++++++++f  +++tl++g++ +++++
  gi|91774271|ref|YP_566963.1| 20 SLSKLDLKDGITFYDVGCGTGAVSIEASKTARNFKVVAIDAREEAIEVSRTNFRNFGiDDVTLIHGESsEAIDK 93
                                  5788999******************999999999**********************8467******99444444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-06    0.0029      28      62 ..      34      86 ..      20     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
               Methyltransf_23 28 diGcGtGillevlren..gfsvtgvDlspeaveiae................k 62
                                  d+GcGtG ++ ++++    f+v+++D+++ea+e  +                +
  gi|91774271|ref|YP_566963.1| 34 DVGCGTGAVSIEASKTarNFKVVAIDAREEAIEVSRtnfrnfgiddvtlihgE 86
                                  9************6643389************987776666666444444441 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05      0.01       4      64 ..      31      91 ..      28     105 .. 0.89
   2 ?   -2.3   0.1       3.4   2.5e+03      38      60 ..     111     133 ..     108     149 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                  EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64
                                  ++ ++GcG G + ++ +k   + ++++i+ r++ ++    + ++ ++  + +++g+  + +
  gi|91774271|ref|YP_566963.1| 31 TFYDVGCGTGAVSIEASKTARNFKVVAIDAREEAIEVSRTNFRNFGIDDVTLIHGESSEAI 91
                                  789*********************************9999999999999999999886665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                                   HHHHHHHHHHCTTSSEEEEES-C CS
                Methyltransf_4  38 vakvlkkiealelkNlrilrgda 60 
                                   + kvl+   +++ +N+ +     
  gi|91774271|ref|YP_566963.1| 111 ISKVLDVLYEKKTRNIVVNAVRI 133
                                   56666666666667766544443 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-05     0.017       4      86 ..      36     116 ..      34     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-05
               Methyltransf_24   4 GvysGvstlwllralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikadseealasla.agsiDllfiDggha 80 
                                   G  +G  ++ + +a + +++ ++va+d  +   ea ++ r+   +   d v+li+++s+ea+ + a  gsiD++f+ g  +
  gi|91774271|ref|YP_566963.1|  36 G--CGTGAVSI-EASKTARNFKVVAIDARE---EAIEVSRTnfrNFGIDDVTLIHGESSEAIDKNAdIGSIDCAFVGGTKN 110
                                   6..66666655.5677777789******99...66666666444344455*************777789*******99887 PP

               Methyltransf_24  81 aeavle 86 
                                    ++vl+
  gi|91774271|ref|YP_566963.1| 111 ISKVLD 116
                                   777765 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.13       9      78 ..      71     137 ..      65     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                      GATase_3   9 aisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpv 78 
                                    + n++  d+ +++ e+    + ++ k+ ++g+ +d  +++G+k+  + l +l e+++++ + +a++ ++ v
  gi|91774271|ref|YP_566963.1|  71 NFRNFGidDVTLIHGES---SEAID-KNADIGS-IDCAFVGGTKNISKVLDVLYEKKTRNIVVNAVRIETVV 137
                                   56777776666665554...45566.7889987.**************************999999877665 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.12      37     100 ..      15      73 ..      13     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                         AviRa  37 EilqralellekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLs 100
                                   E+++ +l+ l+ k+   ++t yD  CG++ +   +   ++++  kv+a D  ee++e++++N++
  gi|91774271|ref|YP_566963.1|  15 EVIAISLSKLDLKD---GITFYDVGCGTGAV--SIEASKTARNFKVVAIDAREEAIEVSRTNFR 73 
                                   56666666665444...5***********65..566667777789*****************87 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.11      55     129 ..      21      96 ..      14     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                   HHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS-----TTEEEEES-TTTS---.--S CS
                Methyltransf_2  55 leafdleglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsageeervefvgGdffkdslP.eaD 129
                                   l + dl+   +++DvG GtGa+  +++++  + kv+  D   e +e  ++ +     ++v+ + G+   +++  +aD
  gi|91774271|ref|YP_566963.1|  21 LSKLDLKDGITFYDVGCGTGAVSIEASKTARNFKVVAIDAReEAIEVSRTNFRNFGIDDVTLIHGESS-EAIDkNAD 96 
                                   677788888899***************************86268999999997777788999988876.66654555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1278.90
//
Query:       gi|91774272|ref|YP_566964.1|  [L=495]
Description: cobyric acid synthase [Methanococcoides burtonii DSM 6242]
Scores for 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-50  169.8   0.0    7.4e-50  169.3   0.0    1.3  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
      4e-19   68.9   0.0    6.3e-19   68.3   0.0    1.3  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    8.8e-19   68.1   0.1    9.9e-18   64.7   0.1    2.1  1  AAA_26    AAA domain
    7.8e-05   22.5   0.0    0.00016   21.5   0.0    1.5  1  GATase    Glutamine amidotransferase class-I
     0.0015   18.4   0.0     0.0026   17.6   0.0    1.3  1  SNO       SNO glutamine amidotransferase 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 !  169.3   0.0   2.1e-53   7.4e-50       1     195 [.     258     440 ..     258     441 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 2.1e-53
                      GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgi 81 
                                   +iavirl +isn+td++pLe  +  +vr+v+   ++lg+ +d++i+pG+k+t++dl+ l esg++++ik+++   +p+lgi
  gi|91774272|ref|YP_566964.1| 258 DIAVIRLTRISNFTDFEPLEHMA--KVRYVD-LSDDLGN-PDAIIIPGTKNTTSDLNDLVESGMADKIKSFYG-MVPILGI 333
                                   69*****************9977..788999.7788987.******************************996.99***** PP

                      GATase_3  82 CGGlqmLGeeiedpegveg.eageveglglLdietefek.ekltgqvegevel......aaegeevkGyEiHsGrtilkek 154
                                   CGG+qmLG++i+d+ g+eg e+ +++glglLdiet+f   ek+t qv+++v+       + +ge vkGyEiH+G +++   
  gi|91774272|ref|YP_566964.1| 334 CGGYQMLGKSIVDS-GIEGgESARLDGLGLLDIETVFDAyEKRTVQVTKTVKEsgpifdSIKGEDVKGYEIHMGISSS--- 410
                                   *************6.67773566****************9**********998*****98899***********6664... PP

                      GATase_3 155 akpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrn 195
                                   ++p +          +dG+   + +g v+GtYlHglfdn n
  gi|91774272|ref|YP_566964.1| 411 KRPVFG---------DDGCA--DDSGLVIGTYLHGLFDNVN 440
                                   567775.........59***..77**************966 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 !   68.3   0.0   1.8e-22   6.3e-19       2     116 ..      12     233 ..      11     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.8e-22
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........................... RF
                          CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep........................... 54 
                                   ++ +t + vGK+ ++++L+r+++   ++V++++a++++ n+ i ++g+e+ i++                           
  gi|91774272|ref|YP_566964.1|  12 LVLGTASHVGKSAIVTALCRIFSA-DHKVAPFKAQNMSLNSWItVDGKEIGIAQaiqakaagveptadmnpvllkpkgdrv 91 
                                   799*********************.****************99************************************** PP

                                   ..............................................................................CCH CS
                                   ..............................................................................xxx RF
                          CbiA  55 ..............................................................................dlk 57 
                                                                                                                 d++
  gi|91774272|ref|YP_566964.1|  92 sqvillgepyadksagayydsieethdvlkgalkrleaeydlivmegaggaaeinlydrdivnigtaritdapiilvgDIE 172
                                   ********************************************************************************* PP

                                   CCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                   xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  58 rllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprde 116
                                   r ++++++l+++ +ll      ++ g+++n+++g+   + l+++l+el++ +g+pvlgv+p+ +
  gi|91774272|ref|YP_566964.1| 173 R-GGVFASLYGTIQLLpedvrKNVRGLIINKFRGD--PAILESGLTELEELTGIPVLGVMPYFK 233
                                   *.************99*******************..************999*********965 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.1   2.8e-21   9.9e-18       1     190 [.       9     231 ..       9     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 2.8e-21
                        AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....................ededselikellgldqt 60 
                                   ++++v gt  +vGK+++ ++L+r++ + + kv+ fK  +  ++                       e ++++  +l  ++ 
  gi|91774272|ref|YP_566964.1|   9 KHLLVLGTASHVGKSAIVTALCRIF-SADHKVAPFKAQNMSLNswitvdgkeigiaqaiqakaaGVEPTADMNPVLLKPKG 88 
                                   689**********************.89999**9*9887777788887665444444444333222233333334433443 PP

                        AAA_26  61 yelpeplalsaplspelaarqegedidlekiv....kelekdadivvVEGagglgvpitee..llnadiaknlgapvilVa 135
                                       + ++l +p++++ a++  +   +  ++     k+le+++d++v EGagg  +  +++   +n+  a+  +ap+ilV+
  gi|91774272|ref|YP_566964.1|  89 DRVSQVILLGEPYADKSAGAYYDSIEETHDVLkgalKRLEAEYDLIVMEGAGGAAEINLYDrdIVNIGTARITDAPIILVG 169
                                   444566666677777777766665555555557889*******************8765554589**************** PP

                        AAA_26 136 rggl.gtinqllltieal.rqknvrvlGvilNkvrnp.....envetlekksgipvlGvvPy 190
                                    +++ g ++ l+ ti++l  +  ++v+G+i+Nk+r +       +++le+ +gipvlGv+Py
  gi|91774272|ref|YP_566964.1| 170 DIERgGVFASLYGTIQLLpEDVRKNVRGLIINKFRGDpaileSGLTELEELTGIPVLGVMPY 231
                                   **994589**********4456889*********999777765******************9 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.4e-08   0.00016      39      90 ..     290     346 ..     249     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.4e-08
                                   THHSTSEEEEEEESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT CS
                        GATase  39 llknpdgilvsgGpgspg......vegkieaikearenkiPiLGICLGmQllaiefgr 90 
                                    l npd+i+++g  ++ +        g+ + ik + +  +PiLGIC G Q+l++++  
  gi|91774272|ref|YP_566964.1| 290 DLGNPDAIIIPGTKNTTSdlndlvESGMADKIKSFYG-MVPILGICGGYQMLGKSIVD 346
                                   3789*******9999999****98889**********.**************988765 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.2e-07    0.0026      23     117 ..     283     384 ..     271     405 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.2e-07
                                   EEE-SGGGGCC-SEEEE-SS-HHH..HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB........SS-SS CS
                           SNO  23 ktvkrkedlaevdaliiPGGesta..mskliertglyedllefvknsekvvlGtCaGlillskelene........lvktl 93 
                                   + v   +dl + da+iiPG   t+  ++ l+ + g+ ++++ f      ++lG C G  +l k +  +            l
  gi|91774272|ref|YP_566964.1| 283 RYVDLSDDLGNPDAIIIPGTKNTTsdLNDLV-ESGMADKIKSFYGM--VPILGICGGYQMLGKSIVDSgieggesaRLDGL 360
                                   5677789*************99982334455.46889999988755..5*************9987654445555566779 PP

                                   --CCEEEETTTT-SCCGEEEEEEE CS
                           SNO  94 ellkvkvkrnafGrqvdsfekeld 117
                                   +ll+++   +a+ ++    +k+++
  gi|91774272|ref|YP_566964.1| 361 GLLDIETVFDAYEKRTVQVTKTVK 384
                                   999999999999877666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3385.74
//
Query:       gi|91774273|ref|YP_566965.1|  [L=353]
Description: anthranilate phosphoribosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-94  315.9   2.0    2.7e-94  315.5   2.0    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    7.6e-17   60.9   0.4    3.7e-16   58.7   0.3    2.2  2  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 !  315.5   2.0     3e-98   2.7e-94       3     252 ..      73     321 ..      71     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 315.5 bits;  conditional E-value: 3e-98
                                   TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHHS CS
               Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfape 83 
                                    lvD++gTGGd++nt+NiStaaaiv+AaaGv+vakhgn s +s sGsaDv  +lgv+++l+p+ v++++e+ g+gf++ap+
  gi|91774273|ref|YP_566965.1|  73 ILVDTCGTGGDRHNTINISTAAAIVAAAAGVTVAKHGNHSFTSLSGSADVFKELGVKIDLEPDLVKSSIEDIGIGFMLAPK 153
                                   58******************************************************************************* PP

                                   SSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHHHHHHHH CS
               Glycos_transf_3  84 yhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsllakttva 164
                                   +h+amk ++++r+el +rT+fn+LGPL+np  +k+q++gv++k+l++ +aevlk+lg e+++v+hgdG+de+s+l++t va
  gi|91774273|ref|YP_566965.1| 154 FHPAMKRMVGPRKELAVRTMFNILGPLTNPTGAKAQVIGVFDKDLCNLMAEVLKKLGKEHVMVFHGDGMDEISTLSETFVA 234
                                   ********************************************************************************* PP

                                   HHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHHH CS
               Glycos_transf_3 165 elkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvakaee 245
                                   elkdg i +ytl+pe++g++ra+  ++ gg+p+ena+ l  +l+g+k+a  rd+v++na+aa+++ag a s+k+++  aee
  gi|91774273|ref|YP_566965.1| 235 ELKDGIISNYTLTPEELGVARAKATDIVGGTPEENAHDLLYILNGEKGAK-RDIVVVNAAAAIYVAGLAISIKDAIPLAEE 314
                                   ************************************************85.****************************** PP

                                   HHHTSHH CS
               Glycos_transf_3 246 vidsGkA 252
                                   +ids kA
  gi|91774273|ref|YP_566965.1| 315 AIDSRKA 321
                                   ***9888 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 !   58.7   0.3   4.1e-20   3.7e-16       3      61 ..       4      61 ..       2      63 .. 0.96
   2 ?   -1.6   0.0      0.28   2.5e+03      11      18 ..     244     251 ..     232     255 .. 0.68

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 4.1e-20
                                  HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHH CS
               Glycos_trans_3N  3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmre 61
                                  +++kl+dg++L+  e ++a+ +il+ ++tdaq++Af m +++kGet +E+a++a+ m++
  gi|91774273|ref|YP_566965.1|  4 YLQKLIDGHDLSMVESEAAMGQILE-SATDAQVGAFVMGMKMKGETSDEVAGFAKGMLN 61
                                  89**********************9.9******************************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.28
                                   .---HHHH CS
               Glycos_trans_3N  11 eeLtaeei 18 
                                    +Lt+ee+
  gi|91774273|ref|YP_566965.1| 244 YTLTPEEL 251
                                   59999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2278.38
//
Query:       gi|91774274|ref|YP_566966.1|  [L=222]
Description: phosphoribosylanthranilate isomerase [Methanococcoides burtonii DSM 6242]
Scores for 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-34  116.9   1.7    1.1e-33  116.7   1.7    1.0  1  PRAI            N-(5'phosphoribosyl)anthranilate (PRA) isomer
  ------ inclusion threshold ------
      0.029   14.4   0.0       0.04   13.9   0.0    1.2  1  Glyco_transf_4  Glycosyltransferase Family 4


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 !  116.7   1.7   1.2e-37   1.1e-33       1     193 [.       7     216 ..       7     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 1.2e-37
                                   TCE----SHHHHHHHHHHTSSEEEEE--T..TBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTECEEEE CS
                          PRAI   1 akicgltrasdvkaavkagadelglifae..sskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgldvvQL 77 
                                   +k+cg+++a+dv  +v +g+d++g+i+++   ++r+++ ++a+el+ +vp     V V +  +++e  + +++ + dvvQ+
  gi|91774274|ref|YP_566966.1|   7 VKVCGMKSAEDVDLSVRSGVDAVGFITDVpvDTPRKIDLQKAKELIASVPFFvdSVLVIMPGSAQEAIDMIRTAKPDVVQI 87 
                                   699***********************9752268*****************5445999************************ PP

                                   -CGG.-HHHHHHH.HHHS-TTSEEEEEEE-S......SS--S-SSTT-SEEEEE....SSS-SSSXXXXGGGGTTSXX... CS
                          PRAI  78 HGdedeqeyeell.ktelpvikalkvaesvd......evkearradhvdllllD....sgaGGtGelldwsliskllks.. 145
                                   H + d +e++ l  +t++++i+ ++v+ +v+      +++ ++  + +d +llD     + GGtG+l d+s+ + + +   
  gi|91774274|ref|YP_566966.1|  88 HSQLDIEEMRILRdNTDVSIIRTFHVQGDVSaddlcnNINMFTSENLIDGVLLDsyvsGKVGGTGQLHDLSVSKRVVDLvd 168
                                   ****8777766651689**********9987555544566667777778899999997789*********99888875588 PP

                                   TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHHH CS
                          PRAI 146 lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfvq 193
                                   +++iLAGGL+p+Nv+  ++   +++vD +sGVEt+G kD +k+++fv+
  gi|91774274|ref|YP_566966.1| 169 VPAILAGGLNPDNVKACVNEVIPFAVDTASGVETDGLKDVDKVAAFVN 216
                                   **********************************************98 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.5e-06      0.04      41     106 ..      50     114 ..      22     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-06
                Glyco_transf_4  41 vrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHgl 106
                                     + +vp++ +  l +++ +++ +  +++  kpDvv +hs    +  ++ lr  +++ ++ t+H  
  gi|91774274|ref|YP_566966.1|  50 ELIASVPFFVDSVLVIMPGSAQEAIDMIRTAKPDVVQIHSQLD-IEEMRILRDNTDVSIIRTFHVQ 114
                                   456788999999999*********************9999666.5888889999**********65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1706.17
//
Query:       gi|91774275|ref|YP_566967.1|  [L=523]
Description: anthranilate synthase, component I [Methanococcoides burtonii DSM 6242]
Scores for complete 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-95  318.5   0.0    2.3e-92  309.2   0.0    2.9  3  Chorismate_bind  chorismate binding enzyme
    8.6e-24   84.4   0.1      3e-22   79.4   0.0    2.9  3  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0018        17      30      86 ..      26      85 ..      21     106 .. 0.78
   2 ?    0.4   0.0     0.045     4e+02     160     180 ..     115     135 ..     112     140 .. 0.87
   3 !  309.2   0.0   2.6e-96   2.3e-92       5     258 .]     261     511 ..     257     511 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0018
                                  EEECESS-B-HHHHHHHHHCTBSSSEEEEEEETT....EEEEEEESSEEEEEETTSEEEEE CS
               Chorismate_bind 30 lkaeleaavdplalyralrarnpapysflleled....sellgaSPElllkveggrriete 86
                                  l a+++++ +pl+ly +l++   ++    +e e+    ++++ga P+ ++k++g+ +++ e
  gi|91774275|ref|YP_566967.1| 26 LMAKVRSDCSPLQLYTTLQKDRYSYLLESVEKEKrharFSFVGAYPDGVVKISGR-TLVLE 85
                                  5567788999********9966555555554433566699************965.66655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.045
                                   EEEESTT--HHHHHHHCSS-C CS
               Chorismate_bind 160 egelkedvslldllkalfPtg 180
                                   ++ +++++++ld+l+a+fPt+
  gi|91774275|ref|YP_566967.1| 115 KAVIRDGHDVLDALRAVFPTA 135
                                   6778999************97 PP

  == domain 3  score: 309.2 bits;  conditional E-value: 2.6e-96
                                   HHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSEEEE CS
               Chorismate_bind   5 YaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrriet 85 
                                   +++av ++k++i +gd+++vvlsrr++++l  + +pl+lyr+lr+ np+py++l++++d +++gaSPE+l++v+++ ++ t
  gi|91774275|ref|YP_566967.1| 261 FEKAVMTAKQHIIDGDIFQVVLSRRYSVRL--QQSPLELYRTLREINPSPYMYLFSFDDLSIVGASPETLMTVHKK-NVIT 338
                                   899**************************5..5689**************************************77.**** PP

                                   ECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEEEESTT CS
               Chorismate_bind  86 epiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstiegelked 166
                                   +piaGT +rgk+++ed+++++++++deKeraEh+m+vdl rnd++ v+++gsvkv++l++v +ys+v+h+ st+ g l+++
  gi|91774275|ref|YP_566967.1| 339 NPIAGTCPRGKDKAEDAKYAAHMMADEKERAEHVMLVDLGRNDVRMVSQSGSVKVKDLMSVVKYSHVQHIESTVCGVLRPE 419
                                   ********************************************************************************* PP

                                   --HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEEEEETT-- CS
               Chorismate_bind 167 vslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGaGIvadSd 247
                                   ++ +d+ +a+fP+g+++GaPk rameiide+E++ RgvY+G vgy + +g++++a+vIRt+v++ ++++++aGaGIvadSd
  gi|91774275|ref|YP_566967.1| 420 CDQFDATRAIFPAGTLSGAPKIRAMEIIDEFETSARGVYGGGVGYYSWNGDVDTAIVIRTVVINGDTAYIQAGAGIVADSD 500
                                   ***************************************************************9999************** PP

                                   HHHHHHHHHHH CS
               Chorismate_bind 248 peaEyeEtlaK 258
                                   p  EyeEt+ K
  gi|91774275|ref|YP_566967.1| 501 PTYEYEETERK 511
                                   ********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 !   79.4   0.0   3.3e-26     3e-22       3     142 .]      34     202 ..      32     202 .. 0.79
   2 ?   -1.3   0.0      0.26   2.4e+03       5      51 ..     294     336 ..     291     371 .. 0.61
   3 ?    1.4   0.0     0.039   3.5e+02      86     100 ..     452     467 ..     384     475 .. 0.82

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 3.3e-26
                 Anth_synt_I_N   3 ltplsvylklaeeehkflLeSaeneggegrySfigldpflelkskngeveveg...........................p 56 
                                    +pl++y  l+++++++lLeS+e+e++ +r+Sf+g+ p +++k+ ++ + +e                             
  gi|91774275|ref|YP_566967.1|  34 CSPLQLYTTLQKDRYSYLLESVEKEKRHARFSFVGAYPDGVVKISGRTLVLECttdsplisnvrqniasecdiiedtdglL 114
                                   78*********************99999**********9998866555555555677888888888888888888876744 PP

                 Anth_synt_I_N  57 egeeleeeepldalrellerfrsaedse.....ptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydtliv 132
                                   +   ++  ++ldalr+++ ++  +         +    f gG++Gy gYD+v     l+ ++  + ++pd+++il+ +++v
  gi|91774275|ref|YP_566967.1| 115 KAVIRDGHDVLDALRAVFPTANGTVL-LngerfDR-QTFLGGAIGYNGYDIVYDC-WLDAERSHNSDIPDMQFILTTKTFV 192
                                   44444444499999999999995543.25776433.34*************8887.56655555667************** PP

                 Anth_synt_I_N 133 fDhkerrlyl 142
                                   fDh+++++y+
  gi|91774275|ref|YP_566967.1| 193 FDHLTEETYI 202
                                   ******9997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.26
                 Anth_synt_I_N   5 plsvylklaeee...hkflLeSaeneggegrySfigldpflelkskngev 51 
                                   pl++y+ l+e +   + + L S +        S++g++p   ++++++ v
  gi|91774275|ref|YP_566967.1| 294 PLELYRTLREINpspYMY-LFSFD------DLSIVGASPETLMTVHKKNV 336
                                   666676666665542222.33332......45777777766655555554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.039
                 Anth_synt_I_N  86 telp.fvgGlvGylgY 100
                                   t+ + ++gG vGy++ 
  gi|91774275|ref|YP_566967.1| 452 TSARgVYGGGVGYYSW 467
                                   3333389******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3439.47
//
Query:       gi|91774276|ref|YP_566968.1|  [L=196]
Description: anthranilate synthase component II [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-45  153.8   0.0      5e-45  153.6   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    2.7e-17   63.3   0.1    6.9e-17   61.9   0.1    1.6  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.6   0.0   5.6e-49     5e-45       2     187 ..       5     187 ..       4     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 5.6e-49
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-EEEET CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiPiLGIC 78 
                                   +i+n ds+++nlv+++   + ++ vvp++ s ee +    +pd+i++s+Gpg+pg    +++++ +i+e+   ++PiLG+C
  gi|91774276|ref|YP_566968.1|   5 FINNRDSFVWNLVDYVSMYESDTVVVPNTISVEEVR--DIKPDAIVISPGPGNPGnardIGNCLYIIREFGV-NVPILGVC 82 
                                   6899******************************96..689****************************777.******** PP

                                   HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEE CS
                        GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiie 159
                                   LG+Q +   +g+++ +  + + hg+ + + +d+++l++g + ++ + ++H++ + +   + +++ v+a+++++  +m+i +
  gi|91774276|ref|YP_566968.1|  83 LGHQSINTVYGGTIGHSPDGPVHGKASMISHDGSELFEGISGTFAAGRYHSLSIHE---LAKDVNVIAENDNG-LIMGIKH 159
                                   ********************************************************...***********887.9****** PP

                                   ETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                        GATase 160 kknpfvgvQFHPEststpegpellfnfl 187
                                   +++p++gvQFHPEs++tpeg +l+ nfl
  gi|91774276|ref|YP_566968.1| 160 RSYPVYGVQFHPESILTPEGLKLVGNFL 187
                                   ***********************99996 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1   7.7e-21   6.9e-17      86     216 .]      56     172 ..      38     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 7.7e-21
                 Peptidase_C26  86 adpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgse 166
                                     ++Rd+ ++  i ++   +vPilg+C+G+q +n ++GGt+  + +       h       ++  ++ + + l++ + g  
  gi|91774276|ref|YP_566968.1|  56 PGNARDIGNCLYIIREFGVNVPILGVCLGHQSINTVYGGTIGHSPD----GPVH------GKASMISHDGSELFEGISG-- 124
                                   5679************************************987666....3434......2233455556666666666.. PP

                 Peptidase_C26 167 eievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   +++   +H+ +i+ela++++v+A  + g+i  i++++  ++v+gvQ+HPE
  gi|91774276|ref|YP_566968.1| 125 TFAAGRYHSLSIHELAKDVNVIAENDNGLIMGIKHRS--YPVYGVQFHPE 172
                                   9*******************************99999..78********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1375.57
//
Query:       gi|91774277|ref|YP_566969.1|  [L=190]
Description: hypothetical protein Mbur_2367 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-24   84.8   0.1      1e-23   84.3   0.1    1.2  1  AAA_18           AAA domain
    5.9e-05   23.5   0.2     0.0016   18.8   0.2    2.2  1  AAA_17           AAA domain
    0.00015   22.1   0.3    0.00034   20.9   0.1    1.8  2  AAA_28           AAA domain
    0.00038   20.2   0.1     0.0014   18.4   0.0    1.9  2  CoaE             Dephospho-CoA kinase
      0.006   16.7   0.3       0.13   12.4   0.0    2.1  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.026   14.2   0.2      0.042   13.6   0.2    1.5  1  AAA_24           AAA domain
      0.033   14.5   0.0      0.064   13.5   0.0    1.5  1  AAA_22           AAA domain
      0.037   13.0   0.3       0.38    9.7   0.1    2.1  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.076   12.7   0.1       0.29   10.9   0.0    1.9  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.084   13.0   0.0       0.14   12.3   0.0    1.3  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.098   13.1   0.2       0.28   11.6   0.2    1.6  1  AAA              ATPase family associated with various cellul
       0.13   12.3   0.0       0.31   11.0   0.0    1.6  2  AAA_5            AAA domain (dynein-related subfamily)
       0.14   12.5   0.2       0.26   11.7   0.1    1.5  1  AAA_16           AAA ATPase domain
       0.44   10.9   1.8       0.62   10.4   0.6    1.9  2  AAA_19           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 !   84.3   0.1   7.9e-27     1e-23       1     130 []      12     129 ..      12     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 7.9e-27
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvid 80 
                                   I+ltGtpG+GKt++++ L+++ g+    l+d++k++ l+ evd+   ++++++d+d++ + + +l + ++     ++ +id
  gi|91774277|ref|YP_566969.1|  12 IGLTGTPGTGKTSVSRLLQEH-GYnMLYLTDLIKDECLYSEVDEG--RDTLVADMDRVFSRVCELVGDDE-----GVNIID 84 
                                   89******************9.6779*******************..**********9999999999764.....555*** PP

                        AAA_18  81 ghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                   +h+a+++ +       +vL++ p+ l+eRl+ R+y++aki+en eae+ld
  gi|91774277|ref|YP_566969.1|  85 SHMAHHIADVV-----IVLRTAPSDLRERLNLRDYSDAKIEENVEAECLD 129
                                   *******9943.....9******************************985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.3e-06    0.0016       1      80 [.      15      87 ..      15     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                                  EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                        AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghp 80
                                  +G PG GK+ ++ +l ++ g+ +l   dl+ +e+  ++     de r+    + +++  ++ e + ++  ++  ++d h+
  gi|91774277|ref|YP_566969.1| 15 TGTPGTGKTSVS-RLLQEHGYNMLYLTDLIKDECLYSEV----DEGRDTLVADMDRVFSRVCELVGDD--EGVNIIDSHM 87
                                  69********99.********************988887....4555444555555555555555543..4455666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.6e-07   0.00034       3      27 ..      13      37 ..      11      78 .. 0.81
   2 ?   -0.8   0.0       1.3   1.6e+03     119     119 ..     102     102 ..      44     153 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.6e-07
                        AAA_28  3 vitGgestGKTtlleaLaargypvv 27
                                   +tG+++tGKT++++ L+++gy+++
  gi|91774277|ref|YP_566969.1| 13 GLTGTPGTGKTSVSRLLQEHGYNML 37
                                  59******************99865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                        AAA_28 119 p 119
                                   p
  gi|91774277|ref|YP_566969.1| 102 P 102
                                   2 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0014       1      28 [.      10      37 ..      10      60 .. 0.91
   2 ?   -0.5   0.0      0.68   8.7e+02     116     131 ..      85     100 ..      68     141 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                  EEEEEEESTTSSHHHHHHHHHHTT-EEE CS
                          CoaE  1 livgltGgiasGKstvanlfadlgvpiv 28
                                  +i+gltG  ++GK+ v++l++++g++++
  gi|91774277|ref|YP_566969.1| 10 MIIGLTGTPGTGKTSVSRLLQEHGYNML 37
                                  69**********************9986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                                   TTGGGGSSEEEEEE-- CS
                          CoaE 116 kqlekliervlvvdve 131
                                   +++++ i  v++v  +
  gi|91774277|ref|YP_566969.1|  85 SHMAHHIADVVIVLRT 100
                                   4444444444444333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0    0.0001      0.13       4      35 ..      14      44 ..      11      72 .. 0.74
   2 ?    2.7   0.0     0.099   1.3e+02      95     125 ..      89     118 ..      55     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                        AAA_33  4 lvGlpGsGKstlaerllkklgavllssdtlrr 35
                                  l G pG+GK+ +++ ll+++g+  l   +l++
  gi|91774277|ref|YP_566969.1| 14 LTGTPGTGKTSVSR-LLQEHGYNMLYLTDLIK 44
                                  679*******9987.899***88876555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.099
                        AAA_33  95 lgvpvrivvvetdeetlkeRlakRaangddr 125
                                   ++ ++ ++v++t ++ l+eRl  R  + d++
  gi|91774277|ref|YP_566969.1|  89 HHIADVVIVLRTAPSDLRERLNLRDYS-DAK 118
                                   45678999*************999985.444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.3e-05     0.042       3      79 ..      10     141 ..       8     161 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                        AAA_24   3 lkiliyGpsgiGKTtlakel...gpkplfi...................................dtekGlksldadkfpd 45 
                                   + i ++G +g+GKT++ + l   g++ l++                                     ++G++ +d +    
  gi|91774277|ref|YP_566969.1|  10 MIIGLTGTPGTGKTSVSRLLqehGYNMLYLtdlikdeclysevdegrdtlvadmdrvfsrvcelvGDDEGVNIIDSHMAHH 90 
                                   67899***************9998888888777777777774444444444433333333333333333333333333333 PP

                        AAA_24  46 ie........swedfldevvel...................aaeladyktlviDtidelee 79 
                                   i         +                              + e + ++++ + ++++  +
  gi|91774277|ref|YP_566969.1|  91 IAdvvivlrtA----------PsdlrerlnlrdysdakieeNVEAECLDVILVESVEWCQK 141
                                   33444444442..........0333444444455566665466666677777777777655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-05     0.064       7      66 ..      11      76 ..       7     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee.erpevv..fvtlpsst...sskdllrellralgl 66
                                  i+ +tG +GtGKT + r l+e   +  + ++  ++e++  +v+   +t   + + +++++++ +g+
  gi|91774277|ref|YP_566969.1| 11 IIGLTGTPGTGKTSVSRLLQEHGYNMLYLTDlIKDECLysEVDEGRDTlvaDMDRVFSRVCELVGD 76
                                  7779*************9999865555555574555552344444444665666666666666664 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0003      0.38      30      50 ..      10      29 ..       6      36 .. 0.78
   2 ?    1.3   0.0       0.1   1.3e+02     116     135 ..     122     141 ..      81     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                                  EEEEEEE-TTSSHHHHHHHHH CS
                          MeaB 30 qvvGltGvPGaGkstlvealg 50
                                    +GltG+PG+Gk   v++l 
  gi|91774277|ref|YP_566969.1| 10 MIIGLTGTPGTGKT-SVSRLL 29
                                  579**********5.556654 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                   HHHHTT-SEEEEEEESSTTH CS
                          MeaB 116 lleaaGfDvvlietvGvGqs 135
                                    +ea   Dv+l+e v   q 
  gi|91774277|ref|YP_566969.1| 122 NVEAECLDVILVESVEWCQK 141
                                   57899999999999987775 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.29       1      21 [.      11      31 ..      11      46 .. 0.93
   2 ?   -0.9   0.1      0.89   1.1e+03     136     165 ..     130     158 ..     113     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                           PRK  1 vIgvagsSGaGkttvarklek 21
                                  +Ig++g  G Gkt+v+r l++
  gi|91774277|ref|YP_566969.1| 11 IIGLTGTPGTGKTSVSRLLQE 31
                                  8****************9976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.89
                           PRK 136 vdisidlelarklqRDiaeRGrsleavlds 165
                                   v  ++ +e+ +k+   i + Gr  e+v++ 
  gi|91774277|ref|YP_566969.1| 130 VILVESVEWCQKVY-EIDTTGRMAEDVVSD 158
                                   45567788999876.566777777777765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.14      24      57 ..      12      45 ..       5      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                  EEEEEETT--HHHHHHCC--TTS-EE--SSTTHH CS
               Sigma54_activ_2 24 vfltGekGsgkelvArlLhknsgpwleifvverl 57
                                  + ltG +G+gk++v+rlL++ + + l +++++++
  gi|91774277|ref|YP_566969.1| 12 IGLTGTPGTGKTSVSRLLQEHGYNMLYLTDLIKD 45
                                  559*****************99988888877655 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   0.2   0.00022      0.28       3      20 ..      14      31 ..      12      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                  EESSTTSSHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavak 20
                                  l+G+pGtGKT++ + + +
  gi|91774277|ref|YP_566969.1| 14 LTGTPGTGKTSVSRLLQE 31
                                  89*********9987754 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   0.0   0.00024      0.31       4      40 ..      14      51 ..      12      72 .. 0.74
   2 ?   -2.4   0.0       3.4   4.3e+03      36      49 ..     100     122 ..      94     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                  EE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHH CS
                         AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltrdtteed 40
                                  L G pGtgK+++++ l +   n  +++ ++++   +++
  gi|91774277|ref|YP_566969.1| 14 LTGTPGTGKTSVSRLLQEHGyNMLYLTDLIKDECLYSE 51
                                  89*************99876566666655555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                                   --HHHHH--B--........... CS
                         AAA_5  36 tteedlkgrreik.........n 49 
                                   t ++dl+ r++++         n
  gi|91774277|ref|YP_566969.1| 100 TAPSDLRERLNLRdysdakieeN 122
                                   55666666666654333222223 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0002      0.26      27      46 ..      12      31 ..       5      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                        AAA_16 27 vllsGesGvGKsslvrellr 46
                                  + l+G +G+GK+s+ r l++
  gi|91774277|ref|YP_566969.1| 12 IGLTGTPGTGKTSVSRLLQE 31
                                  669************99986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00048      0.62       9      29 ..       8      28 ..       3      49 .. 0.82
   2 ?   -1.6   0.0       2.3     3e+03     111     138 ..      49      77 ..      29      78 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                        AAA_19  9 kekvllvtaGpGtGKTrvlkh 29
                                  ++ ++ +t+ pGtGKT v + 
  gi|91774277|ref|YP_566969.1|  8 SNMIIGLTGTPGTGKTSVSRL 28
                                  5667889*********98665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                        AAA_19 111 fqdvdelqyrLlkallgekkkll.lvGDp 138
                                   +++vde   +L+  +     +++ lvGD+
  gi|91774277|ref|YP_566969.1|  49 YSEVDEGRDTLVADMDRVFSRVCeLVGDD 77 
                                   45566666666555553334443367775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1178.12
//
Query:       gi|91774278|ref|YP_566970.1|  [L=64]
Description: hypothetical protein Mbur_2368 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 493.15
//
Query:       gi|91774279|ref|YP_566971.1|  [L=151]
Description: hypothetical protein Mbur_2369 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0051   16.4   2.3      0.016   14.8   2.3    1.8  1  tRNA_anti-like  tRNA_anti-like
  ------ inclusion threshold ------
       0.04   13.3   0.1       0.27   10.6   0.0    2.0  2  Slp             Outer membrane lipoprotein Slp family
       0.06   13.9   0.9       0.14   12.7   0.9    1.6  1  LPAM_1          Prokaryotic membrane lipoprotein lipid attach
      0.065   11.9   0.0      0.088   11.5   0.0    1.2  1  DUF5018         Domain of unknown function (DUF5018)


Domain annotation for each model (and alignments):
>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.3   3.6e-06     0.016      81     151 ..      68     137 ..       1     144 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-06
                                   HHHHTT-EEEEEEEEEEEEE-STT-E.EEEEE-TT-S-S--EEEEEEGGHHHHHH--TTSEEEEEEE----- CS
                tRNA_anti-like  81 dkkYkGkiieVeGvvsdikkieassv.vvlardddgltnVrclledeateasaakiskGqkvtivGqvngvs 151
                                   d+ YkG  ++ +G+v  +++ +++s+ v       +l++   ++++++ +  + k+ kGq +t  G ++ ++
  gi|91774279|ref|YP_566971.1|  68 DEGYKGNFVQWTGTVFAVTN-NGDSYtVQVQHCPGSLSDAGVTFSQDQ-NDVVSKLIKGQEITYLGRITRYQ 137
                                   778***************99.666663666666789999*********.5556699********99998886 PP

>> Slp  Outer membrane lipoprotein Slp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.1e-05      0.27      28      60 ..      68     100 ..      53     116 .. 0.87
   2 ?    0.5   0.0     0.077   3.4e+02      92     107 ..     123     138 ..     117     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.1e-05
                           Slp  28 peaykgkevrlGGkivkvenkkdktrleivslp 60 
                                   +e ykg+ v++ G++ +v+n+ d+ ++++ + p
  gi|91774279|ref|YP_566971.1|  68 DEGYKGNFVQWTGTVFAVTNNGDSYTVQVQHCP 100
                                   4679**********************9998877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.077
                           Slp  92 kgrlvTvvGtlkgset 107
                                   kg+++T +G+++  ++
  gi|91774279|ref|YP_566971.1| 123 KGQEITYLGRITRYQK 138
                                   8999***999998775 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 ?   12.7   0.9   3.1e-05      0.14       4      18 .]       8      22 ..       5      22 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                        LPAM_1  4 illalgalllLsGCs 18
                                  i+l+l ++l++sGCs
  gi|91774279|ref|YP_566971.1|  8 IVLLLMLVLMVSGCS 22
                                  589***********9 PP

>> DUF5018  Domain of unknown function (DUF5018)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     2e-05     0.088       3      64 ..       9      96 ..       7     112 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                       DUF5018  3 sllaalalllagChepee..lvpdv.erqginsitaqFak........................gefkdeeaakytitdedkd 58
                                   ll +l+l+++gC + ee  +v++v ++ g++ i+ +F +                        g+f++ + + +++t+ + d
  gi|91774279|ref|YP_566971.1|  9 VLLLMLVLMVSGCSDSEEsdVVSEVaDDLGVDVISTSFDDlddaycdpevtqdeiatlidegykGNFVQWTGTVFAVTN-NGD 90
                                  678899*******9988644555551567*********99997777777777777777776666666666666666554.566 PP

                       DUF5018 59 eiviei 64
                                  ++++++
  gi|91774279|ref|YP_566971.1| 91 SYTVQV 96
                                  666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1303.95
//
Query:       gi|91774280|ref|YP_566972.1|  [L=170]
Description: nicotinamide-nucleotide adenylyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-18   67.3   0.2    2.2e-17   63.6   0.2    2.0  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.051   13.0   0.2        1.5    8.3   0.0    2.1  2  ATP-sulfurylase  ATP-sulfurylase
      0.087   12.0   0.0        2.8    7.0   0.1    2.0  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
       0.12   12.0   0.0       0.62    9.7   0.0    2.0  1  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
       0.13   12.1   0.1       0.21   11.5   0.1    1.3  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.2     6e-21   2.2e-17       1     143 []       7     135 ..       7     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 6e-21
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
               CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                   ++ G+F+p+HlGH  ++  ++k+++e li+g+ s+++++    ++++a eR+ m+++a e+ +   v ++ l  +   +++
  gi|91774280|ref|YP_566972.1|   7 FYIGRFQPFHLGHHSVITSIAKEVDE-LIIGIGSAQTSHEV-NNPFTAGERVMMIRHALEDID---VHFYALPIDD-IQQN 81 
                                   589***********************.************98.****************55555...4455544322.2334 PP

                                   TTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
               CTP_transf_like  82 pdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                   p   ++v    + +       ++++++n++lv++ ++e+   v+ ++++++n++S+t+ir+r
  gi|91774280|ref|YP_566972.1|  82 P---IWVSYVTSRTP-----PFDTVYANNPLVIELFEETGVMVKQPPMYHRNEYSGTEIRRR 135
                                   4...77777754333.....8****************9999999****************97 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.019        69      29      57 ..      13      39 ..       5      83 .. 0.72
   2 ?    8.3   0.0   0.00041       1.5     173     209 ..     119     154 ..     107     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.019
                                  S---HHHHHHHHHHHHHTSEEEEEEEB-S CS
               ATP-sulfurylase 29 nplHraHeellkraleeeadglllhplvg 57
                                  +p+H +H+ +++ +++ e+d l++  +  
  gi|91774280|ref|YP_566972.1| 13 QPFHLGHHSVITSIAK-EVDELIIG-IGS 39
                                  799***********99.68855543.444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00041
                                   GCCGGEEE--HHHHHCCHHTT----TTTS-HHHHHHH CS
               ATP-sulfurylase 173 hkkeevesisgtelrkllregeeipewfsrpevlkvL 209
                                    +  +++++sgte+r+++ egee  ++++ + v++v+
  gi|91774280|ref|YP_566972.1| 119 PPMYHRNEYSGTEIRRRMLEGEEW-KHLVPNAVADVI 154
                                   5667899***************97.556666666666 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00079       2.8       7      30 ..       9      32 ..       3      41 .. 0.76
   2 ?    3.1   0.0     0.012        44     203     236 ..     126     156 ..     113     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00079
                   HIGH_NTase1  7 IaEYNPfHnGHlyhlekakeltga 30
                                  I  + PfH GH   ++++ +++++
  gi|91774280|ref|YP_566972.1|  9 IGRFQPFHLGHHSVITSIAKEVDE 32
                                  66689************9998543 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.012
                   HIGH_NTase1 203 iaSAtaiRkalkeekkleelkklvPestleilke 236
                                     S t iR+ + e    ee k+lvP++++++++e
  gi|91774280|ref|YP_566972.1| 126 EYSGTEIRRRMLEG---EEWKHLVPNAVADVIEE 156
                                   4699******9666...78*********999976 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00017      0.62       9      58 ..      13      67 ..       9      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00017
                Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfvvkedksl.....fsyeerlklvkkGikdlk 58
                                   Pf lGh+ ++   ake d +++ + + ++s+     f++ er+ ++++ ++d++
  gi|91774280|ref|YP_566972.1| 13 QPFHLGHHSVITSIAKEVDELIIGIGSAQTSHevnnpFTAGERVMMIRHALEDID 67
                                  69*********************99887766433444888999999999888876 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.9e-05      0.21       8      33 ..       5      30 ..       1      38 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                       FAD_syn  8 avvtlGnFDGvHlGHqallkkaveaa 33
                                   +  +G F  +HlGH+++++++ ++ 
  gi|91774280|ref|YP_566972.1|  5 RAFYIGRFQPFHLGHHSVITSIAKEV 30
                                  5678****************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 1317.80
//
Query:       gi|91774281|ref|YP_566973.1|  [L=343]
Description: F420H2 dehydrogenase subunit F [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-37  126.2   0.0    2.1e-36  125.1   0.0    1.6  1  FrhB_FdhB_C      Coenzyme F420 hydrogenase/dehydrogenase, bet
    2.8e-15   56.2   0.0    4.8e-15   55.5   0.0    1.4  1  FrhB_FdhB_N      Coenzyme F420 hydrogenase/dehydrogenase, bet
    1.6e-09   37.2  18.3    4.7e-08   32.5   5.3    2.6  2  Fer4             4Fe-4S binding domain
      6e-09   35.9   8.1    9.7e-06   25.6   0.5    2.8  3  Fer4_10          4Fe-4S dicluster domain
    2.9e-07   31.0   9.2    2.9e-07   31.0   9.2    2.1  2  Fer4_7           4Fe-4S dicluster domain
    5.8e-07   29.6  10.4    7.8e-07   29.2   7.8    2.3  2  Fer4_9           4Fe-4S dicluster domain
    3.7e-06   26.7  17.4    1.9e-05   24.5   4.1    2.6  2  Fer4_2           4Fe-4S binding domain
    5.5e-05   24.0  13.5    9.4e-05   23.3  10.8    2.6  1  Fer4_16          4Fe-4S double cluster binding domain
    0.00033   20.6  21.4    0.00045   20.2   4.9    3.3  3  Fer4_6           4Fe-4S binding domain
    0.00072   19.6  26.1     0.0039   17.3  14.9    2.8  3  Fer4_21          4Fe-4S dicluster domain
     0.0008   19.7   1.9     0.0008   19.7   1.9    2.8  2  Fer4_4           4Fe-4S binding domain
     0.0013   19.2   8.1     0.0013   19.2   8.1    2.1  1  Fer4_8           4Fe-4S dicluster domain
     0.0045   17.5  10.6      0.016   15.7   9.2    2.5  4  Fer4_17          4Fe-4S dicluster domain
     0.0073   17.0   4.4       0.31   11.8   0.4    2.7  2  Fer4_15          4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.034   14.3   0.0    1.3  1  CTP_transf_like  Cytidylyltransferase-like
      0.077   13.6  10.3       0.42   11.2   3.8    2.6  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
       0.14   12.1   0.0       0.39   10.7   0.0    1.7  2  Phage-tail_2     Baseplate structural protein, domain 2
        9.1    7.5  28.8       0.35   11.9   8.5    3.6  3  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 !  125.1   0.0   2.1e-39   2.1e-36       2     147 ..     162     302 ..     161     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 2.1e-39
                   FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqkkklkekilltiglfCggnfspealrk..lleelgvdpedvkklefrgkgkfrvelkd..ek 78 
                                   +k+av+G+PCq+++ r + + ++++ki+l+igl+C+++f +e++ +  + e +gv+ edv+k++f gkgkf++++kd  e+
  gi|91774281|ref|YP_566973.1| 162 EKIAVIGVPCQAHGARLISE-NVNDKIVLIIGLLCMESFHQEVMTDkiIPEIMGVKAEDVVKMDF-GKGKFWAYTKDgeEH 240
                                   79******************.9*****************99988888999***************.************999 PP

                   FrhB_FdhB_C  79 eislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveagel 147
                                   +++++++    r+ C+ C+d+t+ +ADi+vG+v      g +++g++ vl+rt+ ge+ ++ ++++ e+
  gi|91774281|ref|YP_566973.1| 241 SVPIAKVAPHARNPCHHCNDYTSVFADIAVGSV------G-TPDGWNSVLIRTDAGEKYFKMVESELEF 302
                                   9********************************......8.********************87666554 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 !   55.5   0.0   4.9e-18   4.8e-15      14      77 ..      92     154 ..      85     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 4.9e-18
                   FrhB_FdhB_N  14 kaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlklL 77 
                                    +q+GG+++a++ +lL++g+id+v+ ++++ ++w+++  + t++e++ +a G+kYt+ ++l++L
  gi|91774281|ref|YP_566973.1|  92 AGQDGGVTSAIARSLLRQGEIDCVVGITRN-EKWETELELFTSAEDVEKAKGTKYTYDSVLSVL 154
                                   59****************************.79****************************999 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   5.3   4.8e-11   4.7e-08       2      24 .]       9      31 ..       8      31 .. 0.96
   2 !   10.1   5.0   0.00056      0.56       5      20 ..      54      69 ..      53      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 4.8e-11
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  vi+ + C++CGaCv++CP gAIt
  gi|91774281|ref|YP_566973.1|  9 VINFDVCTACGACVSACPAGAIT 31
                                  79********************7 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00056
                                  TTTSSS-THHHHHSTT CS
                          Fer4  5 eekCigCGaCvevCPv 20
                                  ++ C gC +C  +CPv
  gi|91774281|ref|YP_566973.1| 54 PNVCEGCLTCSRICPV 69
                                  578************8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.5   9.8e-09   9.7e-06       2      30 ..       8      36 ..       7      47 .. 0.73
   2 !   14.6   0.1   2.7e-05     0.027       6      26 ..      54      70 ..      50      99 .. 0.80
   3 ?   -2.8   0.1       7.4   7.4e+03       7      13 ..     253     259 ..     249     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.8e-09
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakg 30
                                   vi+ d C+ Cg+Cv+aCPa + ++g k+
  gi|91774281|ref|YP_566973.1|  8 DVINFDVCTACGACVSACPAGAITMGDKK 36
                                  6899****************553333322 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.7e-05
                       Fer4_10  6 ddtCirCgkCvkaCPadltsv 26
                                  ++ C +C +C + CP+    v
  gi|91774281|ref|YP_566973.1| 54 PNVCEGCLTCSRICPV----V 70
                                  689************9....3 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.4
                       Fer4_10   7 dtCirCg 13 
                                   + C +C+
  gi|91774281|ref|YP_566973.1| 253 NPCHHCN 259
                                   4577776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   9.2   2.9e-10   2.9e-07       2      50 ..      15      69 ..      14      70 .. 0.74
   2 ?   -1.5   0.0       4.1   4.1e+03      37      42 ..     254     259 ..     229     262 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.9e-10
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekv........eidpekClgCgaCvavCPt 50
                                  C+ CgaCv+aCp++ai++ +++ e +   +           p+ C gC  C + CP+
  gi|91774281|ref|YP_566973.1| 15 CTACGACVSACPAGAITMGDKKAEIRD--PdslelythGAAPNVCEGCLTCSRICPV 69
                                  ******************987333222..222233332456899************7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.1
                        Fer4_7  37 kClgCg 42 
                                    C +C+
  gi|91774281|ref|YP_566973.1| 254 PCHHCN 259
                                   466664 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   7.8   7.8e-10   7.8e-07       2      48 ..      15      69 ..      14      71 .. 0.92
   2 ?   -0.0   0.0         1     1e+03      33      40 ..     243     259 ..     195     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.8e-10
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpk 48
                                  Ct CgaCv+aCpag++++ +++ ++r     e        + C gC +C  +Cp 
  gi|91774281|ref|YP_566973.1| 15 CTACGACVSACPAGAITMGDKKAEIRDPDSLElythgaapNVCEGCLTCSRICPV 69
                                  ****************99999999998665559*******99***********95 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1
                        Fer4_9  33 e.........eaCigCg 40 
                                             + C++C+
  gi|91774281|ref|YP_566973.1| 243 PiakvapharNPCHHCN 259
                                   04444445556688886 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   4.1   1.9e-08   1.9e-05       4      22 .]       9      27 ..       7      27 .. 0.94
   2 !    7.4   5.4    0.0052       5.1       7      21 ..      54      68 ..      52      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.9e-08
                        Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                  v++ d C++CgaCvsaCPa
  gi|91774281|ref|YP_566973.1|  9 VINFDVCTACGACVSACPA 27
                                  6899**************8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0052
                        Fer4_2  7 tdrCigCgaCvsaCP 21
                                  ++ C gC +C   CP
  gi|91774281|ref|YP_566973.1| 54 PNVCEGCLTCSRICP 68
                                  689************ 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 !   23.3  10.8   9.4e-08   9.4e-05       2      66 ..      15      69 ..      14      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.4e-08
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                  C+ Cg+C+++CP++ai++  +k++e+r+          +l+++ ++ +    + gC +C ++CP+
  gi|91774281|ref|YP_566973.1| 15 CTACGACVSACPAGAITMG-DKKAEIRDPD------SLELYTHGAAPN---VCEGCLTCSRICPV 69
                                  *******************.5555555554......445666665555...799**********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 !   20.2   4.9   4.5e-07   0.00045       7      24 .]      13      30 ..       9      30 .. 0.91
   2 !    8.4   2.8    0.0023       2.3       6      21 ..      54      69 ..      53      74 .. 0.89
   3 ?    1.2   0.3      0.45   4.5e+02       6      14 ..     252     260 ..     250     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.5e-07
                        Fer4_6  7 dkCigCgdCvrvCPegai 24
                                  d C+ Cg+Cv++CP+gai
  gi|91774281|ref|YP_566973.1| 13 DVCTACGACVSACPAGAI 30
                                  56***************8 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0023
                        Fer4_6  6 pdkCigCgdCvrvCPe 21
                                  p+ C gC  C r+CP 
  gi|91774281|ref|YP_566973.1| 54 PNVCEGCLTCSRICPV 69
                                  577************5 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.45
                        Fer4_6   6 pdkCigCgd 14 
                                   +++C +C+d
  gi|91774281|ref|YP_566973.1| 252 RNPCHHCND 260
                                   799****86 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.4   1.2e-05     0.012      35      59 .]       8      32 ..       1      32 [. 0.79
   2 !   17.3  14.9   3.9e-06    0.0039       3      55 ..      10      71 ..       9      73 .. 0.68
   3 ?   -2.7   0.0       6.7   6.7e+03      39      45 ..     253     259 ..     245     265 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                       Fer4_21 35 kvv.edeCvGCnlCssvCPvedciem 59
                                   v+  d C++C  C+s CP  ++i+m
  gi|91774281|ref|YP_566973.1|  8 DVInFDVCTACGACVSACPA-GAITM 32
                                  4442599************5.***98 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.9e-06
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidakt............vlkvvedeCvGCnlCssvCPved 55
                                  i+ d C  Cg C+ aC+     ai++ +k+            ++    + C GC  Cs +CPv d
  gi|91774281|ref|YP_566973.1| 10 INFDVCTACGACVSACPA---GAITMGDKKaeirdpdslelyTHGAAPNVCEGCLTCSRICPVVD 71
                                  8889*************6...55543333312233333333233456899*************76 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.7
                       Fer4_21  39 deCvGCn 45 
                                   + C  Cn
  gi|91774281|ref|YP_566973.1| 253 NPCHHCN 259
                                   3444443 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.9     8e-07    0.0008       2      17 .]      13      28 ..      12      33 .. 0.91
   2 !    7.1   1.4    0.0086       8.6       2      16 ..      55      69 ..      54      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8e-07
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  + C+ Cg+Cv+aCP g
  gi|91774281|ref|YP_566973.1| 13 DVCTACGACVSACPAG 28
                                  78************65 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0086
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  + C gC  C ++CP+
  gi|91774281|ref|YP_566973.1| 55 NVCEGCLTCSRICPV 69
                                  779***********4 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   8.1   1.3e-06    0.0013       2      63 ..      12      69 ..      11      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                  ++ C+ CgaC saCp+   t  + + + r+  +  +  +++     a + C +c  C++ Cpv
  gi|91774281|ref|YP_566973.1| 12 FDVCTACGACVSACPAGAITMgDKKAEIRDPDSL-ELYTHG----AAPNVCEGCLTCSRICPV 69
                                  567************9998876666666666666.333333....589**************7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.8   0.00011      0.11      42      59 ..      11      28 ..       4      30 .. 0.81
   2 !   15.7   9.2   1.6e-05     0.016       2      57 ..      15      68 ..      14      71 .. 0.83
   3 ?    6.7   1.4     0.011        10       2      19 ..      57      74 ..      56      97 .. 0.75
   4 ?   -2.0   0.0       5.7   5.7e+03      44      50 ..     253     259 ..     235     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                       Fer4_17 42 kaslCieCgeCerkCPqg 59
                                  +++ C+ Cg C+++CP+g
  gi|91774281|ref|YP_566973.1| 11 NFDVCTACGACVSACPAG 28
                                  567899999999999976 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.6e-05
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57
                                  C+ Cg+C+ +Cp ++++  ++k  +r+  + +le      + + C +C  C+r CP
  gi|91774281|ref|YP_566973.1| 15 CTACGACVSACPAGAITMGDKKAEIRD--PDSLELYTHGAAPNVCEGCLTCSRICP 68
                                  ****************88877776666..3455555567899*************9 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.011
                       Fer4_17  2 CiqCgyClpeCpsyeayd 19
                                  C +C  C + Cp    y 
  gi|91774281|ref|YP_566973.1| 57 CEGCLTCSRICPVVDGYF 74
                                  999999999999877654 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5.7
                       Fer4_17  44 slCieCg 50 
                                   + C++C+
  gi|91774281|ref|YP_566973.1| 253 NPCHHCN 259
                                   5566665 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.4   0.00031      0.31       3      33 ..      10      40 ..       9      51 .. 0.81
   2 ?    6.1   0.3     0.019        19       8      34 ..      57      86 ..      54     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                       Fer4_15  3 vDrdaCigcglCvaeapevfeldedglasvl 33
                                  ++ d C+ cg+Cv ++p      +d +a+++
  gi|91774281|ref|YP_566973.1| 10 INFDVCTACGACVSACPAGAITMGDKKAEIR 40
                                  66689***********987777778888777 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                       Fer4_15  8 CigcglCvaea...pevfeldedglasvll 34
                                  C+gc  C + +   + +fe + + + s+l+
  gi|91774281|ref|YP_566973.1| 57 CEGCLTCSRICpvvDGYFEDEFANVRSFLA 86
                                  ***********5555666665544444444 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05     0.034      16     108 ..     102     210 ..     100     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH.................HHHHH CS
               CTP_transf_like  16 lleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltr.................evlkk 79 
                                   +++ +++++e d +vg++ +e+   +  +l++++e +e  +  k++ + +    +++                   +++ +
  gi|91774281|ref|YP_566973.1| 102 IARSLLRQGEIDCVVGITRNEKWETE-LELFTSAEDVEKAKGTKYTYDSVLSVLRDPFSkyekiavigvpcqahgaRLISE 181
                                   7888999*****************99.****************77776655555555555777*********999888888 PP

                                   TTTTEEEEEEEHHHHHHHHCHHHHHHHHH CS
               CTP_transf_like  80 lkpdklylvigadvledfsewkeleeilg 108
                                      dk++l+ig  ++e+f+++   ++i+ 
  gi|91774281|ref|YP_566973.1| 182 NVNDKIVLIIGLLCMESFHQEVMTDKIIP 210
                                   8788**************87775555554 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 ?   11.2   3.8   0.00042      0.42       2      18 ..      11      27 ..      10      29 .. 0.88
   2 ?    5.6   0.5     0.024        24       5      19 ..      56      70 ..      54      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                       Fer4_13  2 DrdtCiacgaCvelaPd 18
                                  + d C+acgaCv+++P 
  gi|91774281|ref|YP_566973.1| 11 NFDVCTACGACVSACPA 27
                                  5688************5 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.024
                       Fer4_13  5 tCiacgaCvelaPdv 19
                                   C +c +C  ++P v
  gi|91774281|ref|YP_566973.1| 56 VCEGCLTCSRICPVV 70
                                  599**********76 PP

>> Phage-tail_2  Baseplate structural protein, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.1   8.1e+03     138     165 ..     113     140 ..     111     145 .. 0.73
   2 ?   10.7   0.0   0.00039      0.39      33      77 ..     242     286 ..     233     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.1
                                   EEEEEEEESS-EEEEEEEEE-SS----S CS
                  Phage-tail_2 138 devihelsnnnsvthlymftnatkleti 165
                                   d v+    n++  t l +ft a  +e  
  gi|91774281|ref|YP_566973.1| 113 DCVVGITRNEKWETELELFTSAEDVEKA 140
                                   5566666777788999999999888765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00039
                                   EEEES--CGGCSGGGSEEEEEE-TTSS---EEEETT--EEEEEE- CS
                  Phage-tail_2  33 vwltksnphkrdpmknatiyahsfldssipmittgkgensivvsr 77 
                                   v ++k  ph r+p + +  y+  f d ++  + t  g ns+++  
  gi|91774281|ref|YP_566973.1| 242 VPIAKVAPHARNPCHHCNDYTSVFADIAVGSVGTPDGWNSVLIRT 286
                                   567899**********************************98754 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.5   0.00035      0.35       1      15 []      15      29 ..      15      29 .. 0.96
   2 ?    6.3   3.7     0.022        22       1      13 [.      57      69 ..      57      72 .. 0.91
   3 ?   -0.1   1.4       2.3   2.3e+03       1       5 [.     255     259 ..     255     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  Ct CgaCv +CP gA
  gi|91774281|ref|YP_566973.1| 15 CTACGACVSACPAGA 29
                                  9***********998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.022
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C gC +C + CPv
  gi|91774281|ref|YP_566973.1| 57 CEGCLTCSRICPV 69
                                  99**99******6 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.3
                        Fer4_3   1 CtgCg 5  
                                   C++C+
  gi|91774281|ref|YP_566973.1| 255 CHHCN 259
                                   ****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2724.30
//
Query:       gi|91774282|ref|YP_566974.1|  [L=328]
Description: methylenetetrahydromethanopterin reductase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-62  211.2   0.0    2.9e-62  210.9   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.015   15.6   0.0    1.3  1  PHP             PHP domain


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 !  210.9   0.0   3.2e-66   2.9e-62      25     314 .]      16     302 ..       8     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 3.2e-66
                Bac_luciferase  25 lvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglgl 105
                                   ++++a++aE+ Gfd vw+++h+++    +d +++la+la+ T+ i++gt+vt++ytr+ a++A ++  ++++sgGR++lgl
  gi|91774282|ref|YP_566974.1|  16 IAHYAKLAEQQGFDNVWITDHYNN----RDVYSTLAVLAMNTNSIKIGTGVTNPYTRNAAITASSIGAINEISGGRAILGL 92 
                                   6889*******************9....***************************************************** PP

                Bac_luciferase 106 gtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglelaarha 186
                                   g g  a+  +++G+++++++  ++E + +lr  ++ge+v+ +G+ ++  ga l  ++g+  +P+y++a +p++lela+++a
  gi|91774282|ref|YP_566974.1|  93 GPGDKATF-DAMGIEWEKPLTTTKENISALRSFFAGEKVTMDGDMVQFSGAKLAFKTGD--VPIYMGAQGPKMLELAGEVA 170
                                   ***99888.999*********************************************55..6******************* PP

                Bac_luciferase 187 dglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagldfyaldsegagreaea 264
                                   dg+l++ ++p + + +++++ +ga++agrdp d++v++ + +++++++++Ar+ a    a+i  +    +  e++g + +a
  gi|91774282|ref|YP_566974.1| 171 DGVLINASHPNDFEVAVKQITSGAKKAGRDPKDVDVAAYACFSIDKDAAKARSAAkvvVAFIVAG-SPDMVLERHGIDVAA 250
                                   *******************************************************7776666444.444444455444444 PP

                Bac_luciferase 265 a.eiqeeedanlwagaadav.pdelvaatalvGtpeqvaerlaayaeagvde 314
                                   +  i+ + +++++ + +  + ++++++++ + Gtp+++ +r+ ++ + gv++
  gi|91774282|ref|YP_566974.1| 251 KaDIGGAIAKGDFGALMGDMvTNNMMESFSISGTPDDCKARINELLDIGVTQ 302
                                   426677777777766665555*************************999985 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.7e-06     0.015      12      65 ..      11      63 ..       6     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                                  .S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP 12 dgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGle 65
                                  d +l+i  ++k a+++g++ + iTDh n  +++     +   + + ik+  G+ 
  gi|91774282|ref|YP_566974.1| 11 DPVLKIAHYAKLAEQQGFDNVWITDHYNNRDVYSTLAVLAM-NTNSIKIGTGVT 63
                                  678999**********************9999999988844.447899988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2216.47
//
Query:       gi|91774283|ref|YP_566975.1|  [L=78]
Description: hypothetical protein Mbur_2373 [Methanococcoides burtonii DSM 6242]
Scores for complete 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  107.4  11.5      3e-31  107.2  11.5    1.0  1  DUF2180       Uncharacterized protein conserved in archaea (D
     0.0062   16.3   0.6      0.013   15.3   0.6    1.4  1  zf-UBP_var    Variant UBP zinc finger
  ------ inclusion threshold ------
      0.028   14.6   9.9      0.075   13.2   1.6    2.3  2  zf-AN1        AN1-like Zinc finger
       0.41   10.3   6.4       0.34   10.6   0.8    2.0  2  TackOD1       Thaumarchaeal output domain 1
        1.4    9.3   8.2         10    6.6   2.2    2.3  2  Transp_Tc5_C  Tc5 transposase C-terminal domain
        1.7    8.8   7.0        4.1    7.6   7.0    1.7  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 !  107.2  11.5     1e-34     3e-31       1      67 [.       1      75 [.       1      76 [. 0.98

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 1e-34
                       DUF2180  1 mkCYeCakegkdtdavaiCivCGkGvCkdHlvreeievweGgypfpak........klkktlprilCkeClealk 67
                                  mkCYeCak++kd+d+++iCivCG+GvCkdHl+re+i++w+G+y+++++        k+++++ +i+C++C++al+
  gi|91774283|ref|YP_566975.1|  1 MKCYECAKNEKDSDVLGICIVCGRGVCKDHLMREKIPKWDGEYDIKLScmgdsckiKDMQPMLKIVCTPCHDALI 75
                                  9***********************************************************************997 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 !   15.3   0.6   4.2e-06     0.013      15      44 ..       3      32 ..       2      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-06
                    zf-UBP_var 15 CvycFdtpesedGlyvcLkcFlgfckkhae 44
                                  C  c +++++ d l +c+ c +g+ck+h+ 
  gi|91774283|ref|YP_566975.1|  3 CYECAKNEKDSDVLGICIVCGRGVCKDHLM 32
                                  999*************************85 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.6   2.5e-05     0.075       1      31 [.       3      34 ..       3      35 .. 0.74
   2 ?    6.1   1.5    0.0042        12       1      20 [.      49      71 ..      49      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                        zf-AN1  1 CsfksCkkkd...flpfkCryCgkvFClkHrlpe 31
                                  C   +C k++    + + C  Cg+  C++H + e
  gi|91774283|ref|YP_566975.1|  3 CY--ECAKNEkdsDVLGICIVCGRGVCKDHLMRE 34
                                  55..476666434355**************9887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0042
                        zf-AN1  1 CsfksCkkkdflp...fkCryCg 20
                                  C  +sCk kd+ p   + C  C+
  gi|91774283|ref|YP_566975.1| 49 CMGDSCKIKDMQPmlkIVCTPCH 71
                                  8899******777777****997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   0.00011      0.34     148     185 ..       2      39 ..       1      41 [. 0.94
   2 ?    3.7   0.4     0.014        43     150     170 ..      52      72 ..      39      78 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                       TackOD1 148 kCnsCkslfsepevkarClsCekesesddlkvreiysy 185
                                   kC +C +  ++++v   C+ C++ + +d+l  ++i ++
  gi|91774283|ref|YP_566975.1|   2 KCYECAKNEKDSDVLGICIVCGRGVCKDHLMREKIPKW 39 
                                   7*****************************99999887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                       TackOD1 150 nsCkslfsepevkarClsCek 170
                                   +sCk    +p +k++C+ C++
  gi|91774283|ref|YP_566975.1|  52 DSCKIKDMQPMLKIVCTPCHD 72 
                                   689999999999999999986 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 ?    6.6   2.2    0.0033        10      30      56 ..       6      32 ..       1      36 [. 0.73
   2 ?    6.5   0.4    0.0036        11      27      50 ..      51      74 ..      41      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0033
                  Transp_Tc5_C 30 CkiegCselafikCarCkellCFdHfv 56
                                  C+ ++ ++  +  C+ C + +C dH++
  gi|91774283|ref|YP_566975.1|  6 CAKNEKDSDVLGICIVCGRGVCKDHLM 32
                                  5555555555556************98 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0036
                  Transp_Tc5_C 27 sedCkiegCselafikCarCkell 50
                                   + Cki++ + +  i C  C++ l
  gi|91774283|ref|YP_566975.1| 51 GDSCKIKDMQPMLKIVCTPCHDAL 74
                                  467*****************9865 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   7.0    0.0014       4.1      12      65 ..       3      73 ..       1      76 [. 0.61

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                                  -TTT--B--SSS--EE-TTT--EE-STTS.-EEE.EE................GGGTEEEEEEE-HHHHHH CS
                          FYVE 12 CeiCakkFsllrrrhhCrlCGkvvCekCs.sklvall................ekeaeeksvrvCkeClae 65
                                  C +Cak+ + +     C +CG+ vC+++  +++++++                 k  +     vC+ C++ 
  gi|91774283|ref|YP_566975.1|  3 CYECAKNEKDSDVLGICIVCGRGVCKDHLmREKIPKWdgeydiklscmgdsckIKDMQPMLKIVCTPCHDA 73
                                  7777777666666677*********7765233444445555555555544432234444445899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); 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:                         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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 510.70
//
Query:       gi|91774284|ref|YP_566976.1|  [L=75]
Description: hypothetical protein Mbur_2374 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-26   92.2   5.8    1.6e-26   92.0   5.8    1.0  1  DUF2180          Uncharacterized protein conserved in archaea
    6.6e-05   23.6   4.5    0.00093   20.0   1.1    2.1  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
      0.006   16.7   3.6      0.016   15.3   3.6    1.7  1  FYVE             FYVE zinc finger
  ------ inclusion threshold ------
        0.8    9.8   8.5         11    6.1   0.1    2.8  2  zf-BED           BED zinc finger
       0.99    9.8   5.3       0.57   10.6   2.1    1.9  2  Transp_Tc5_C     Tc5 transposase C-terminal domain
        9.3    6.9   7.7        1.5    9.3   0.3    2.5  3  zf-H2C2_2        Zinc-finger double domain


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 !   92.0   5.8   5.5e-30   1.6e-26       1      67 [.       5      70 ..       5      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 5.5e-30
                       DUF2180  1 mkCYeCakegkdtdavaiCivCGkGvCkdHlvreeievweGgypfpakklkktlprilCkeClealk 67
                                  mkCY+C++eg+dt+a+a+Ci+CGkG+C++H+++  ++v++G++p+++ ++++ l++ilCk+Cl++++
  gi|91774284|ref|YP_566976.1|  5 MKCYDCMEEGNDTEAAAVCILCGKGICVNHSKELLLSVSAGAPPHTK-RMHNGLTKILCKYCLSNTI 70
                                  9*******************************************997.9**************9875 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 !   20.0   1.1   3.1e-07   0.00093       2      30 ..       6      34 ..       5      34 .. 0.97
   2 ?    5.1   0.1     0.013        40      12      22 ..      54      65 ..      48      71 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.1e-07
               Tnp_zf-ribbon_2  2 RCkvClkkkikkeTriiCqeCdvplCrnh 30
                                   C++C   ++ +e+   C  C++++C+nh
  gi|91774284|ref|YP_566976.1|  6 KCYDCMEEGNDTEAAAVCILCGKGICVNH 34
                                  5***************************9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
               Tnp_zf-ribbon_2 12 kke.TriiCqeC 22
                                   +  T+i C+ C
  gi|91774284|ref|YP_566976.1| 54 HNGlTKILCKYC 65
                                  444699999999 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.6   5.4e-06     0.016       8      65 ..       3      68 ..       1      73 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                                  --SB-TTT--B--SSS--EE-TTT--EE-STTS-EEE.EE........GGGTEEEEEEE-HHHHHH CS
                          FYVE  8 evkkCeiCakkFsllrrrhhCrlCGkvvCekCssklvall........ekeaeeksvrvCkeClae 65
                                  ++ kC  C ++ + ++    C lCGk +C ++s++l+ ++        +++++     +Ck Cl++
  gi|91774284|ref|YP_566976.1|  3 TMMKCYDCMEEGNDTEAAAVCILCGKGICVNHSKELLLSVsagapphtKRMHNGLTKILCKYCLSN 68
                                  5679********999******************999877777777764444444555679999865 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.8    0.0063        19      13      26 ..      17      30 ..       1      39 [. 0.82
   2 ?    6.1   0.1    0.0038        11       9      22 ..      52      65 ..      48      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0063
                                  GSS--EETTTTEE- CS
                        zf-BED 13 keqkavCryCgkil 26
                                  +e  avC+ Cgk +
  gi|91774284|ref|YP_566976.1| 17 TEAAAVCILCGKGI 30
                                  6788*******965 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0038
                                  ---GGSS--EETTT CS
                        zf-BED  9 pvslkeqkavCryC 22
                                  ++    +k+ C+yC
  gi|91774284|ref|YP_566976.1| 52 RMHNGLTKILCKYC 65
                                  55567799****** 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 ?   10.6   2.1   0.00019      0.57      27      54 ..       7      34 ..       1      39 [. 0.90
   2 ?    0.3   0.1       0.3     9e+02      40      47 ..      59      66 ..      52      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                  Transp_Tc5_C 27 sedCkiegCselafikCarCkellCFdH 54
                                    dC  eg +  a   C+ C + +C +H
  gi|91774284|ref|YP_566976.1|  7 CYDCMEEGNDTEAAAVCILCGKGICVNH 34
                                  569999**9999***************9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                  Transp_Tc5_C 40 fikCarCk 47
                                   i C +C 
  gi|91774284|ref|YP_566976.1| 59 KILCKYCL 66
                                  58899995 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 ?   -3.2   0.6       4.9   1.5e+04      16      20 ..       6      10 ..       6      12 .. 0.71
   2 ?    2.0   0.0      0.11   3.2e+02      17      22 ..      23      28 ..      18      29 .. 0.89
   3 ?    9.3   0.3   0.00052       1.5       5      22 ..      49      67 ..      49      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.9
                     zf-H2C2_2 16 eCplC 20
                                  +C  C
  gi|91774284|ref|YP_566976.1|  6 KCYDC 10
                                  57777 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                     zf-H2C2_2 17 CplCdk 22
                                  C lC+k
  gi|91774284|ref|YP_566976.1| 23 CILCGK 28
                                  ****99 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00052
                     zf-H2C2_2  5 Hir.kHtgekpyeCplCdk 22
                                  H++  H g ++  C++C  
  gi|91774284|ref|YP_566976.1| 49 HTKrMHNGLTKILCKYCLS 67
                                  87626************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.44
# Mc/sec: 515.03
//
Query:       gi|91774285|ref|YP_566977.1|  [L=116]
Description: alkylhydroperoxidase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-17   62.7   0.2    3.1e-17   62.4   0.2    1.1  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.029   13.3   0.0      0.033   13.1   0.0    1.1  1  PA26      PA26 p53-induced protein (sestrin)
      0.066   13.3   1.8        0.2   11.7   1.3    2.1  2  SapB_1    Saposin-like type B, region 1
       0.14   12.5   0.0       0.43   11.0   0.0    1.7  2  UXS1_N    UDP-glucuronate decarboxylase N-terminal


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 !   62.4   0.2   6.9e-21   3.1e-17       1      84 [.      31     113 ..      31     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 6.9e-21
                                   HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHH CS
                           CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAla 81 
                                   p + + +t+ ++ +l  +g+L++k + L+alav a+ +ce C  a ++ Al++G+t+eei+e++ +  +++g pa+ a ++
  gi|91774285|ref|YP_566977.1|  31 PHFVKKYTRCDHKILT-DGALPAKVKILMALAVVASKQCESCTVAQMKSALKNGATKEEIMETMEVISVTSGAPAVAACRD 110
                                   788999*********9.***********************************************************99998 PP

                                   HHH CS
                           CMD  82 aae 84 
                                   a++
  gi|91774285|ref|YP_566977.1| 111 ALK 113
                                   876 PP

>> PA26  PA26 p53-induced protein (sestrin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.3e-06     0.033      37     102 ..      21      86 ..       2      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-06
                          PA26  37 qvtqvl.glHPqylesflrtqnfllrgdgpLpleyRhYiailaaaRhqcsyLvklhekeFlekggds 102
                                   q+ ++l  l P++ ++++r+ + +l  dg Lp++++  +a+   a  qc++    ++k+ l++g  +
  gi|91774285|ref|YP_566977.1|  21 QILETLhELDPHFVKKYTRCDHKILT-DGALPAKVKILMALAVVASKQCESCTVAQMKSALKNGATK 86 
                                   4444441358**************95.8*************9999****998888888888877655 PP

>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         1   4.6e+03      25      32 ..      21      28 ..      18      29 .. 0.83
   2 ?   11.7   1.3   4.4e-05       0.2      10      31 ..      73      94 ..      67      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                  HHHHHHHH CS
                        SapB_1 25 eIieaLek 32
                                  +I+e L++
  gi|91774285|ref|YP_566977.1| 21 QILETLHE 28
                                  89999997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.4e-05
                                  HHHHHHHH-SS--HHHHHHHHH CS
                        SapB_1 10 VkeveklLkdNkTeeeIieaLe 31
                                  V ++++ Lk+ +T+eeI+e +e
  gi|91774285|ref|YP_566977.1| 73 VAQMKSALKNGATKEEIMETME 94
                                  8899**************9876 PP

>> UXS1_N  UDP-glucuronate decarboxylase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.6   2.7e+03      61      74 ..      24      37 ..       6      38 .. 0.73
   2 ?   11.0   0.0   9.5e-05      0.43      14      48 ..      53      87 ..      39      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.6
                        UXS1_N 61 ekirdlekSftqKy 74
                                  e +++l+  f++Ky
  gi|91774285|ref|YP_566977.1| 24 ETLHELDPHFVKKY 37
                                  56677888888888 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.5e-05
                        UXS1_N 14 rmklLlalaliaYvasvwGtfvnmrsiqenGdvKv 48
                                  ++k+L+ala++a   +   t ++m+s   nG  K 
  gi|91774285|ref|YP_566977.1| 53 KVKILMALAVVASKQCESCTVAQMKSALKNGATKE 87
                                  48*****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 902.60
//
Query:       gi|91774286|ref|YP_566978.1|  [L=457]
Description: hypothetical protein Mbur_2376 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-09   37.5   4.4    7.5e-07   30.0   0.8    2.5  2  Cytochrome_C554  Cytochrome c554 and c-prime
    6.4e-06   26.1  10.3     0.0081   16.1   4.0    3.2  3  Cytochrome_C7    Cytochrome c7 and related cytochrome c
      0.001   18.7  14.4      0.081   12.7   2.4    4.4  4  Paired_CXXCH_1   Doubled CXXCH motif (Paired_CXXCH_1)
  ------ inclusion threshold ------
      0.017   15.5  15.1        3.4    8.2   3.0    3.8  3  Cytochrom_c3_2   Cytochrome c3
      0.022   13.7   0.4      0.022   13.7   0.4    2.7  3  Cytochrom_C552   Cytochrome c552
      0.095   12.7   7.2        1.4    9.0   0.2    3.4  3  DZR              Double zinc ribbon
       0.11   12.4   5.3        1.5    8.7   0.1    3.4  3  C1_1             Phorbol esters/diacylglycerol binding domain
       0.77   10.1  18.5         16    5.9   0.0    5.3  5  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
        1.7    8.3  13.7        1.9    8.2   0.2    3.4  4  Cytochrom_NNT    NapC/NirT cytochrome c family, N-terminal re
        6.1    6.7   6.4        5.5    6.9   0.2    3.3  3  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Cytochrome_C554  Cytochrome c554 and c-prime
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.8   4.2e-10   7.5e-07       1      84 []      38     120 ..      38     120 .. 0.70
   2 !    8.4   0.1    0.0022       3.9      45      83 ..     160     204 ..     145     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.2e-10
                                   HHHHHTHHHHHHHTTSTGGGTTGGGSTTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTTSTT--....-SSS--GGGBSS CS
               Cytochrome_C554   1 aCaeCHeeqyeswkkskhakaleslkkekkaeakkkakldpakdaeeapeClkCHatgagkdkgf....vlkektkllagV 77 
                                   +Ca+CH+   ++ ++s+ha a++    +k+a  +++   d   + ++++ C +CH++     + +     +  ++ +++gV
  gi|91774286|ref|YP_566978.1|  38 KCANCHAILRSQHEGSMHAFAYSDPLYQKEALLASE---D--TNGQTDEFCSRCHTPIGVVSGEVppidGSMISDVAAEGV 113
                                   6*********************97766665443333...2..34567999******96543333322223333455678** PP

                                   -HHHHH- CS
               Cytochrome_C554  78 qCesCHg 84 
                                   qC+ CH+
  gi|91774286|ref|YP_566978.1| 114 QCDFCHT 120
                                   ******5 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                                   -TT-TTTGGGSBSTTT......STT---SSS--GGGBSS-HHHHH CS
               Cytochrome_C554  45 aeeapeClkCHatgag......kdkgfvlkektkllagVqCesCH 83 
                                   ++ea+ C  CH  +        +d  +  +e++ +++gV C+ CH
  gi|91774286|ref|YP_566978.1| 160 YTEAEYCGMCHNVNSPfnglplDDTYTFWSESSYAEEGVVCQDCH 204
                                   6788999999998874233443444445556677789******** PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   4.0   4.5e-06    0.0081      12      73 .]      35     120 ..      25     120 .. 0.63
   2 !   12.7   5.1   5.5e-05     0.099       9      73 .]     108     171 ..      71     205 .. 0.49
   3 !    5.9   0.2     0.007        13      10      23 ..     194     207 ..     185     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.5e-06
                 Cytochrome_C7  12 tgykCtdCHsklfeskak........kkmaemekgkskkaeves.lt...CgaCHdgknaf..............svakka 66 
                                   t+ kC++CH  l  s+ +        + +  ++k+ + + e ++  t   C  CH+   +                 a+  
  gi|91774286|ref|YP_566978.1|  35 TNSKCANCHAILR-SQHEgsmhafayS-DPLYQKEALLASEDTNgQTdefCSRCHTPIGVVsgevppidgsmisdVAAEGV 113
                                   5789*****9994.2221124343221.3333333333333333344889*******999667777777778877556799 PP

                 Cytochrome_C7  67 eCakCHt 73 
                                   +C+ CHt
  gi|91774286|ref|YP_566978.1| 114 QCDFCHT 120
                                   ******7 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.5e-05
                 Cytochrome_C7   9 lkatgykCtdCHsklfeskakkkmaemekgkskkaevesltCgaCHdgknaf............................. 60 
                                   ++a+g                                  ++C+ CH+ ++                               
  gi|91774286|ref|YP_566978.1| 108 VAAEG----------------------------------VQCDFCHTVSESAgigdgsfvsspgdvkwgprddapsafhes 154
                                   22233..................................556666665555444444444444444445555555555555 PP

                 Cytochrome_C7  61 ....svakkaeCakCHt 73 
                                        +++++ C+ CH+
  gi|91774286|ref|YP_566978.1| 155 efngLYTEAEYCGMCHN 171
                                   55553334555555553 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.007
                 Cytochrome_C7  10 katgykCtdCHskl 23 
                                   +++g  C+dCH ++
  gi|91774286|ref|YP_566978.1| 194 AEEGVVCQDCHMSP 207
                                   33577899999876 PP

>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   2.4   4.5e-05     0.081       4      38 ..      34      88 ..      33      92 .. 0.88
   2 ?    2.9   0.1     0.053        95       5      18 ..     110     124 ..     107     132 .. 0.80
   3 ?    3.4   0.2     0.035        63      28      38 ..     161     171 ..     151     175 .. 0.63
   4 !    7.3   1.6    0.0022         4       8      39 ..     165     206 ..     157     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                Paired_CXXCH_1  4 vaegeClsCHnphgsdnpkll....................kkakgaalCysCHd 38
                                  v++ +C +CH    s++++ +                    ++ ++ + C  CH+
  gi|91774286|ref|YP_566978.1| 34 VTNSKCANCHAILRSQHEGSMhafaysdplyqkeallasedTNGQTDEFCSRCHT 88
                                  67789*****88888888888888889999*********99889999*******7 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.053
                Paired_CXXCH_1   5 aeg.eClsCHnphgs 18 
                                   aeg +C  CH    s
  gi|91774286|ref|YP_566978.1| 110 AEGvQCDFCHTVSES 124
                                   66768*****87666 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.035
                Paired_CXXCH_1  28 kgaalCysCHd 38 
                                   ++a+ C  CH+
  gi|91774286|ref|YP_566978.1| 161 TEAEYCGMCHN 171
                                   56677777776 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0022
                Paired_CXXCH_1   8 eClsCHnphgsdnpkll............kkakgaalCysCHde 39 
                                    C  CHn   s++++l             + a++  +C++CH +
  gi|91774286|ref|YP_566978.1| 165 YCGMCHNVN-SPFNGLPlddtytfwsessY-AEEGVVCQDCHMS 206
                                   4999**987.66777777999999999966.888899*****75 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.0    0.0019       3.4      21      66 ..      31      88 ..      24      90 .. 0.60
   2 ?    7.6   5.0     0.003       5.3       4      66 ..     110     205 ..     107     207 .. 0.70
   3 ?    5.2   0.2     0.016        29       3      17 ..     194     208 ..     192     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                                  TTHHHHHHHHHHH--HHHCHTTSST.............TSSBTTSSCTSSS-GGGTS- CS
                Cytochrom_c3_2 21 dkaveeekClsCHgkleelakktkea............keanphkshekeleCteCHk 66
                                  ++ v+++kC +CH  l++ ++ + +a              a+++++ +++  C++CH+
  gi|91774286|ref|YP_566978.1| 31 EDFVTNSKCANCHAILRSQHEGSMHAfaysdplyqkeaLLASEDTNGQTDEFCSRCHT 88
                                  56788999*****988877766554455666776543211222222235555777774 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.003
                                   CCT.TGGGTSSSST-SSTTHHHHHH...............................HHHHH--HHHCHTTSST..TSSBTT CS
                Cytochrom_c3_2   4 kegvkCadCHtkekpkkdkaveeek...............................ClsCHgkleelakktkea.keanph 52 
                                   +egv+C+ CHt +++    + +  +                               C  CH+  + ++    +   +   +
  gi|91774286|ref|YP_566978.1| 110 AEGVQCDFCHTVSESAGIGDGSFVSspgdvkwgprddapsafhesefnglyteaeyCGMCHNVNSPFNGLPLDDtYTFWSE 190
                                   689999999997765433333332245788888888888888888899999999999999999998888554441444444 PP

                                   SSC.TSSS-GGGTS- CS
                Cytochrom_c3_2  53 ksh.ekeleCteCHk 66 
                                   +s+ e+ + C++CH+
  gi|91774286|ref|YP_566978.1| 191 SSYaEEGVVCQDCHM 205
                                   455357788999996 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.016
                                   HCCT.TGGGTSSSST CS
                Cytochrom_c3_2   3 akegvkCadCHtkek 17 
                                   a+egv C+dCH +  
  gi|91774286|ref|YP_566978.1| 194 AEEGVVCQDCHMSPG 208
                                   678999999998755 PP

>> Cytochrom_C552  Cytochrome c552
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.027        49      62      97 ..      55      90 ..      47      97 .. 0.91
   2 ?    1.7   0.4     0.053        95     242     288 ..      77     124 ..      69     125 .. 0.81
   3 ?   13.7   0.4   1.2e-05     0.022     233     254 ..     185     206 ..     183     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.027
                                  GGGHHHHHHHSGGG---SSTT-SSSBGGGGTTT-TH CS
                Cytochrom_C552 62 HayaveDvletlrtgapkeaeegkqpaaCltCkspd 97
                                  Ha+a +D l  +    ++e+++g++   C  C++p 
  gi|91774286|ref|YP_566978.1| 55 HAFAYSDPLYQKEALLASEDTNGQTDEFCSRCHTPI 90
                                  99999***9999999999****************95 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.053
                                   HHTT--HHHHHS-EEE.TTSEEEE----S-GGGGCCCTGGGT--S-HH CS
                Cytochrom_C552 242 akngvsCaDCHmPkvk.egakkvtdHkvtsPlksiekaCksCHkqsee 288
                                   ++ +  C  CH P     g+    d  + s +++   +C  CH+ se+
  gi|91774286|ref|YP_566978.1|  77 GQTDEFCSRCHTPIGVvSGEVPPIDGSMISDVAAEGVQCDFCHTVSES 124
                                   666777999999986647778888999999999999999999998875 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 1.2e-05
                                   HHHHHTSHHHHTT--HHHHHS- CS
                Cytochrom_C552 233 fElysegvHakngvsCaDCHmP 254
                                   + ++se+  a++gv C DCHm 
  gi|91774286|ref|YP_566978.1| 185 YTFWSESSYAEEGVVCQDCHMS 206
                                   789******************5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.066   1.2e+02      28      41 ..      36      49 ..      14      53 .. 0.70
   2 ?    9.0   0.2   0.00079       1.4       9      37 ..      77     121 ..      71     126 .. 0.82
   3 ?    3.2   0.3      0.05        90      10      35 ..     161     204 ..     156     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.066
                           DZR 28 edrCpsCgekvdpe 41
                                  + +C +C++ + ++
  gi|91774286|ref|YP_566978.1| 36 NSKCANCHAILRSQ 49
                                  67899999887665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00079
                           DZR   9 ppdarfCseCgtklkavaa................edrCpsCgek 37 
                                    + ++fCs+C t++  v+                   +C+ C++ 
  gi|91774286|ref|YP_566978.1|  77 GQTDEFCSRCHTPIGVVSGevppidgsmisdvaaeGVQCDFCHTV 121
                                   57789********97666688899999999999998999999886 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.05
                           DZR  10 pdarfCseCgtklkavaa..................edrCpsCg 35 
                                    +a++C+ C +  ++ +                     +C  C+
  gi|91774286|ref|YP_566978.1| 161 TEAEYCGMCHNVNSPFNGlplddtytfwsessyaeeGVVCQDCH 204
                                   57899999998766555566777777888888877777788886 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 ?    1.3   0.1      0.18   3.3e+02      12      21 ..      37      46 ..      29      57 .. 0.65
   2 ?    8.7   0.1   0.00086       1.5       9      36 ..      78     120 ..      73     123 .. 0.88
   3 ?    2.6   0.4     0.071   1.3e+02      24      36 ..     193     205 ..     158     207 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.18
                                  -B-TTT-SB- CS
                          C1_1 12 tfCkhCgefl 21
                                  ++C+ C  +l
  gi|91774286|ref|YP_566978.1| 37 SKCANCHAIL 46
                                  4555555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00086
                                   SS--B-TTT-SB-...............-SSSS-EEEETTT-- CS
                          C1_1   9 kqptfCkhCgefl...............wgkekqglkCswCkl 36 
                                   +   fC+ C  ++               +  +  g++C+ C+ 
  gi|91774286|ref|YP_566978.1|  78 QTDEFCSRCHTPIgvvsgevppidgsmiSDVAAEGVQCDFCHT 120
                                   5678*********************996669**********96 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.071
                                   SSS-EEEETTT-- CS
                          C1_1  24 kekqglkCswCkl 36 
                                    +  g+ C++C++
  gi|91774286|ref|YP_566978.1| 193 YAEEGVVCQDCHM 205
                                   4567999****98 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.8     0.022        39      11      20 ..      36      48 ..      31      75 .. 0.74
   2 ?    5.9   0.0    0.0089        16      11      30 ..      80     103 ..      70     114 .. 0.69
   3 ?    2.8   0.2     0.085   1.5e+02      13      25 ..     114     134 ..     108     158 .. 0.64
   4 ?    4.5   0.1     0.025        45      10      28 ..     160     182 ..     154     198 .. 0.63
   5 ?    2.7   0.5     0.092   1.6e+02      13      24 ..     199     210 ..     189     254 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.022
               Cytochrome_CBB3 11 kknCasCHg...k 20
                                  +++Ca CH+   +
  gi|91774286|ref|YP_566978.1| 36 NSKCANCHAilrS 48
                                  789*****96642 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0089
               Cytochrome_CBB3  11 kknCasCHg.kggag...pslagr 30 
                                   ++ C++CH+  g +    p++ g+
  gi|91774286|ref|YP_566978.1|  80 DEFCSRCHTpIGVVSgevPPIDGS 103
                                   579*****9644443466666655 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.085
               Cytochrome_CBB3  13 nCasCHg.kggag.......p 25 
                                   +C  CH+ ++ ag        
  gi|91774286|ref|YP_566978.1| 114 QCDFCHTvSESAGigdgsfvS 134
                                   8*****986655554644431 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.025
               Cytochrome_CBB3  10 ykk..nCasCHg..kggagpsla 28 
                                   y++  +C  CH   +  +g +l 
  gi|91774286|ref|YP_566978.1| 160 YTEaeYCGMCHNvnSPFNGLPLD 182
                                   55445******943333344444 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.092
               Cytochrome_CBB3  13 nCasCHgkggag 24 
                                    C+ CH + g  
  gi|91774286|ref|YP_566978.1| 199 VCQDCHMSPGIT 210
                                   7*****955543 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.7      0.11     2e+02     121     135 ..      32      46 ..       2      60 .. 0.60
   2 ?   -0.3   5.3      0.43   7.6e+02      34      43 ..      78      87 ..      24      90 .. 0.49
   3 ?    5.3   0.7     0.008        14      34      67 ..      78     111 ..      64     126 .. 0.59
   4 ?    8.2   0.2     0.001       1.9      35      76 ..     162     208 ..     154     216 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                 Cytochrom_NNT 121 kandsreCrnCHsee 135
                                     + +++C nCH   
  gi|91774286|ref|YP_566978.1|  32 DFVTNSKCANCHAIL 46 
                                   334445555555443 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                 Cytochrom_NNT 34 steeFCvsCH 43
                                   t+eFC  CH
  gi|91774286|ref|YP_566978.1| 78 QTDEFCSRCH 87
                                  2444444444 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.008
                 Cytochrom_NNT  34 steeFCvsCHemednveeykesiHysnrsgvrae 67 
                                    t+eFC  CH+    v+     i  s  s v ae
  gi|91774286|ref|YP_566978.1|  78 QTDEFCSRCHTPIGVVSGEVPPIDGSMISDVAAE 111
                                   4788999999765555544445555555555543 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.001
                 Cytochrom_NNT  35 teeFCvsCHemednveey..kesiHysnrsg...vraeCsdCHvPke 76 
                                   ++e+C  CH+++++++ +   ++  +  +s      + C+dCH+   
  gi|91774286|ref|YP_566978.1| 162 EAEYCGMCHNVNSPFNGLplDDTYTFWSESSyaeEGVVCQDCHMSPG 208
                                   56788888888887665421444444333331112356888888654 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.25   4.5e+02       1       7 [.      38      44 ..      38      48 .. 0.77
   2 ?    6.9   0.2     0.003       5.5      11      23 .]      78      90 ..      75      90 .. 0.79
   3 ?   -0.6   0.2      0.69   1.2e+03      15      19 ..     165     169 ..     160     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.25
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +C nC+a
  gi|91774286|ref|YP_566978.1| 38 KCANCHA 44
                                  7999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.003
                 zinc_ribbon_2 11 dnakFCpyCGtpl 23
                                   ++ FC++C tp+
  gi|91774286|ref|YP_566978.1| 78 QTDEFCSRCHTPI 90
                                  6789999999985 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.69
                 zinc_ribbon_2  15 FCpyC 19 
                                   +C  C
  gi|91774286|ref|YP_566978.1| 165 YCGMC 169
                                   45444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 3542.93
//
Query:       gi|91774287|ref|YP_566979.1|  [L=209]
Description: NADPH-dependent FMN reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-34  118.6   0.0    2.5e-34  118.3   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    2.1e-06   27.6   0.0    3.1e-06   27.0   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.047   13.9   0.0      0.088   13.0   0.0    1.5  1  Flavodoxin_5  Flavodoxin domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0   4.2e-38   2.5e-34       2     149 ..       7     160 ..       6     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 4.2e-38
                                   EEEEEES--STT-HHHHHHHHHHCCT-T..T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                       FMN_red   2 kilvisGSlrkgsntrklaewaaealkea.gaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaadali 77 
                                   k+l+isGS+r ++ t++++++a++ ++e+ g+e+e++  +++  + c   + c+ ++ + + ++dd+ el+ek+++ada+i
  gi|91774287|ref|YP_566979.1|   7 KLLGISGSPR-KKATDRMVREALKYAEEKyGVEIEYFSAKGKdLKFCihcDHCVRTK-QGCIHKDDIVELYEKMEWADAWI 85 
                                   99*******8.778************99999*******9999888886666666454.34********************* PP

                                   EEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSEEE CS
                       FMN_red  78 ivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraava 149
                                   i+tP+Y+g++sg+ K+++Dr+++   r++k + +K++a++a gg+r gg++ + q  + +  + ++i+v+++ + 
  gi|91774287|ref|YP_566979.1|  86 IGTPVYQGTVSGQTKTIMDRCRAvvARDPKVFMNKVGAGMADGGDRVGGQEPALQVIHNFYiISEMIPVSGGSFG 160
                                   *********************99**************************************88******998875 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   5.2e-10   3.1e-06       2     102 ..       7     105 ..       6     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.2e-10
                                   EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHC....C..HHHHTT..C.HHHHHHHHH CS
                  Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaa....k..layeek..p.adveseqie 73 
                                   k+L i ++pr+  + + ++ +++++ +e++   e++++                     +    ++++     d+ +   e
  gi|91774287|ref|YP_566979.1|   7 KLLGISGSPRK--KATDRMVREALKYAEEKYGVEIEYFSAKGKD-LK-------FcihcDhcVRTKQGciHkDDIVELY-E 76 
                                   77889999999..5667777777777777665667776655532.22.......2222232334445566437777777.* PP

                                   HHHCSSEEEEEEE-BTTB--HHHHHHHHH CS
                  Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDr 102
                                   k+++ada ++++P++  +v+ + K  +Dr
  gi|91774287|ref|YP_566979.1|  77 KMEWADAWIIGTPVYQGTVSGQTKTIMDR 105
                                   ****************************9 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.088      36      80 ..      73     117 ..      39     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                  Flavodoxin_5  36 kesedlesydavvigasvyygkllpelakFvekhreaLstkpval 80 
                                   +  e++e++da +ig++vy+g ++++ +   ++ r+ +++ p ++
  gi|91774287|ref|YP_566979.1|  73 ELYEKMEWADAWIIGTPVYQGTVSGQTKTIMDRCRAVVARDPKVF 117
                                   345899*******************99999999988888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1660.88
//
Query:       gi|91774288|ref|YP_566980.1|  [L=232]
Description: oxidoreductase FAD/NAD(P)-binding [Methanococcoides burtonii DSM 6242]
Scores for complete 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   73.6   0.0    2.6e-20   73.1   0.0    1.3  1  NAD_binding_1  Oxidoreductase NAD-binding domain
    2.1e-13   50.5   0.0    2.9e-13   50.0   0.0    1.2  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    2.4e-06   27.8   0.0    0.00043   20.4   0.0    2.2  2  NAD_binding_6  Ferric reductase NAD binding domain
    8.3e-06   25.9   0.0    1.5e-05   25.0   0.0    1.5  1  FAD_binding_8  FAD-binding domain
  ------ inclusion threshold ------
      0.062   14.0   0.0       0.12   13.1   0.0    1.5  1  TTR-52         Transthyretin-like family


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 !   73.1   0.0   7.2e-24   2.6e-20       1     108 [.     107     211 ..     107     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 7.2e-24
                                   EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHH CS
                 NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdal 81 
                                   +i+gG Gi+P+ s+ r + +  k  t +v++  n+ e d+++ +el+e+ +++p+ +kvv++++r + +w g +gr+ + +
  gi|91774288|ref|YP_566980.1| 107 LISGGIGITPMISICRYCSDS-KTGTDIVFLDSNKVESDIAFGDELDEMGRSHPN-MKVVHTLTRADTDWLGCTGRICEPM 185
                                   79******************8.999******************************.8************************ PP

                                   HHHHHHHSSTTEEEEEECSHHHHHHHH CS
                 NAD_binding_1  82 leellslkkeethvyvCGppgMikavr 108
                                   + +++s +  e  vyvCGpp+M+k v+
  gi|91774288|ref|YP_566980.1| 186 ILDYIS-DILERTVYVCGPPPMMKSVE 211
                                   ******.788999***********986 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 !   50.0   0.0   8.1e-17   2.9e-13       2      98 ..       5      97 ..       4      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 8.1e-17
                                  EEEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-T CS
                 FAD_binding_6  2 lkltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelki 84
                                  +++te  e ++d++ frfk p   +++++ +Gq++f++++++ge   ++ t+ ss++ek +le+  k++ g + s aLd + +
  gi|91774288|ref|YP_566980.1|  5 APITEIIEQTHDVKSFRFKRP---EDFEYKAGQYLFVSIPVNGEMQRKPLTISSSPTEKDHLEFT-KKLTGHEYSDALDAMVP 83
                                  568888999**********99...5567***********************************97.888999*********** PP

                                  T-EEEEEEEE-SEE CS
                 FAD_binding_6 85 gdtleikGPlGkfe 98
                                  gd+l i+GP G+f+
  gi|91774288|ref|YP_566980.1| 84 GDVLIINGPNGRFT 97
                                  ************97 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.2e-07   0.00043       1      27 [.     102     128 ..     102     170 .. 0.76
   2 !    5.3   0.0    0.0053        19     138     154 ..     197     213 ..     189     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-07
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_6   1 yenvllvagGiGitpfisilkdllkks 27 
                                   y+ + l++gGiGitp+isi++ +    
  gi|91774288|ref|YP_566980.1| 102 YNKIALISGGIGITPMISICRYCSDSK 128
                                   6889****************9876554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0053
                                   xxxxxxxxxxxxxxxxx RF
                 NAD_binding_6 138 gvfvCGppklvkevkkl 154
                                   +v+vCGpp ++k v++l
  gi|91774288|ref|YP_566980.1| 197 TVYVCGPPPMMKSVEEL 213
                                   699*********99875 PP

>> FAD_binding_8  FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.2e-09   1.5e-05       9      66 ..      10      65 ..       3      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.2e-09
                 FAD_binding_8  9 valleedliklkvskpkkslkykaGqyvyinipslsklfwqsHPFtiasape.ddklsl 66
                                  +    +d+ + ++++p+  ++ykaGqy++++ip   ++  q  P ti s+p   d+l+ 
  gi|91774288|ref|YP_566980.1| 10 IIEQTHDVKSFRFKRPED-FEYKAGQYLFVSIPVNGEM--QRKPLTISSSPTeKDHLEF 65
                                  55556889999******9.*************999967..**********986677765 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.4e-05      0.12      37      68 ..      92     129 ..      58     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                                   TTSEEEEEEEE---.......S--EEEEEE-----T.. CS
                        TTR-52  37 edGnFelsgsenelt......sidPylkiyhkCndkek 68 
                                    +G+F+ +g+ n++        i+P++ i  +C+d+++
  gi|91774288|ref|YP_566980.1|  92 PNGRFTFEGEYNKIAlisggiGITPMISICRYCSDSKT 129
                                   69**********996666667**************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1620.07
//
Query:       gi|91774289|ref|YP_566981.1|  [L=191]
Description: rubrerythrin [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-33  114.2   4.7      7e-33  113.9   4.7    1.1  1  Rubrerythrin    Rubrerythrin
      2e-09   37.5   0.9    2.8e-09   37.0   0.9    1.2  1  Ferritin        Ferritin-like domain
     0.0012   18.9   2.8      0.027   14.5   0.1    2.2  2  DUF892          Domain of unknown function (DUF892)
     0.0067   16.6   1.1      0.012   15.8   1.1    1.4  1  Ferritin_2      Ferritin-like domain
  ------ inclusion threshold ------
       0.05   13.2   0.0      0.083   12.5   0.0    1.3  1  DUF3231         Protein of unknown function (DUF3231)
      0.051   13.6   0.0      0.092   12.8   0.0    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.057   12.8   0.3        5.4    6.4   0.1    2.3  2  zf-TFIIB        Transcription factor zinc-finger
        0.1   12.5   6.6       0.18   11.7   0.4    2.6  3  HalOD2          Halobacterial output domain 2
       0.21   11.8   1.7        0.5   10.5   1.7    1.6  1  Zn-ribbon_8     Zinc ribbon domain
       0.34   10.8   0.0       0.34   10.8   0.0    1.8  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        1.6    8.8   4.9        6.1    7.0   0.2    2.4  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        2.4    8.0   7.0       0.83    9.4   0.5    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   4.7   4.7e-36     7e-33       1     136 [.      11     138 ..      11     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 4.7e-36
                                   HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGG CS
                  Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflt 80 
                                   ++L kA+agEs+ar++Y+++a+ a+ +gy qi+++F e+A++E+eHak+l+k+le  + e           + +++  +++
  gi|91774289|ref|YP_566981.1|  11 KNLLKAFAGESQARNRYTYFASVARkAGYDQISAIFAETADNEKEHAKRLFKFLEGGDVEVT---------ASFPAGVISS 82 
                                   69******************************************************666666.........99999***** PP

                                   HHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  81 taknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                   t++nLe+a++g+ +e+++my++++++ae eg+ e++ +f+ +a aEk+Heer+ kl
  gi|91774289|ref|YP_566981.1|  83 TRDNLEAAAAGENYEHTTMYPEFAKIAESEGFLEIASVFRHIAVAEKGHEERYLKL 138
                                   ******************************************************98 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.9   1.9e-12   2.8e-09       2     139 ..      11     142 ..      10     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.9e-12
                                   HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSSHH CS
                      Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefgsve 82 
                                   k L +++a e +a + y ++a++++  g++++++ f e a+ e eha++l++++   Gg     ++e+ +  +    +s++
  gi|91774289|ref|YP_566981.1|  11 KNLLKAFAGESQARNRYTYFASVARKAGYDQISAIFAETADNEKEHAKRLFKFLE--GG-----DVEVTASFPAGVISSTR 84 
                                   68999***********************************************986..77.....77777755555568*** PP

                                   HHHHHHHHHHH.HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  83 evleaalehek.kvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                   + leaa + e+ + t+++ e +++ae+eg    a+ + ++   +  he+   +l  +l
  gi|91774289|ref|YP_566981.1|  85 DNLEAAAAGENyEHTTMYPEFAKIAESEGFLEIASVFRHIAVAEKGHEERYLKLAANL 142
                                   *****999885379***********************999999999988877776665 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.8e-05     0.027     111     152 ..      25      66 ..       3      75 .. 0.86
   2 ?    4.8   0.4     0.017        25     100     151 ..      88     140 ..      77     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF892 111 AsYgtLialAeqlgekeaaklLeqtleeekatdekltelaes 152
                                    +Y+  +++A+++g++++ +++ +t ++ek+ +++l +++e 
  gi|91774289|ref|YP_566981.1|  25 NRYTYFASVARKAGYDQISAIFAETADNEKEHAKRLFKFLEG 66 
                                   589*********************************999874 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                                   .HHHHHHHHHH.HHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF892 100 aaaqavehyEi.AsYgtLialAeqlgekeaaklLeqtleeekatdekltelae 151
                                    aa a e+yE  + Y   +++Ae  g  e+a++++++   ek  +e+  +la 
  gi|91774289|ref|YP_566981.1|  88 EAAAAGENYEHtTMYPEFAKIAESEGFLEIASVFRHIAVAEKGHEERYLKLAA 140
                                   68888999996257***************************999998888876 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   8.3e-06     0.012      10      98 ..      17     127 ..      10     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.3e-06
                    Ferritin_2  10 lnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaavakptfdf................ 74 
                                    + E ++ + Yt+ ++ a     ++  +++ +++ e a++e++H++ l + leG+    + t  f                
  gi|91774289|ref|YP_566981.1|  17 FAGESQARNRYTYFASVA----RKAGYDQISAIFAETADNEKEHAKRLFKFLEGGDV--EVTASFpagvisstrdnleaaa 91 
                                   555666777777777643....4555567899*********************6665..3444554455666777778888 PP

                    Ferritin_2  75 ............afdpfadeksflalaavlEdvgvs 98 
                                               +f ++a+++ fl+ a v+ +++v+
  gi|91774289|ref|YP_566981.1|  92 agenyehttmypEFAKIAESEGFLEIASVFRHIAVA 127
                                   888888888999999999999999999999888875 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05     0.083      31      86 ..      23      81 ..      11      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                       DUF3231 31 gialitgFlqvaed...keikelleralelsnkhikelkelLkeenlpiPsgfsesdvt 86
                                  +   +t+F++va++     i++++ ++ ++ ++h k+l ++L+  ++ + ++f+   ++
  gi|91774289|ref|YP_566981.1| 23 ARNRYTYFASVARKagyDQISAIFAETADNEKEHAKRLFKFLEGGDVEVTASFPAGVIS 81
                                  5566788888776633369**********************************765554 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.2e-05     0.092      66      95 ..     151     180 ..     116     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                   EE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                          HypA  66 evpvkvrCreCgkefeleekalrCpkCgsa 95 
                                   +  v  rCr+Cg+  e  ++  +Cp+C++ 
  gi|91774289|ref|YP_566981.1| 151 DGTVAWRCRNCGYIHEGPAAPDKCPACDHP 180
                                   446889******99995443348****875 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.019        28       9      26 ..     144     162 ..     141     162 .. 0.80
   2 ?    6.4   0.1    0.0036       5.4       1      10 [.     173     182 ..     173     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                      zf-TFIIB   9 leeser.ggveidyCpqCr 26 
                                   le++ r +g   ++C +C+
  gi|91774289|ref|YP_566981.1| 144 LEMVFRkDGTVAWRCRNCG 162
                                   6666665999********7 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0036
                      zf-TFIIB   1 kCPkCqdele 10 
                                   kCP+C +++ 
  gi|91774289|ref|YP_566981.1| 173 KCPACDHPMG 182
                                   8******996 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.5   8.2e+03      22      29 ..      37      44 ..      31      45 .. 0.76
   2 ?   11.7   0.4   0.00012      0.18      25      43 ..     149     167 ..     145     170 .. 0.84
   3 ?    3.2   1.0     0.056        84       2       9 ..     171     178 ..     170     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.5
                        HalOD2 22 eGyrqLGa 29
                                  +Gy+q+ a
  gi|91774289|ref|YP_566981.1| 37 AGYDQISA 44
                                  69999865 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                        HalOD2  25 rqLGayvWkCtrCGevqaa 43 
                                   r+ G+  W+C +CG +  +
  gi|91774289|ref|YP_566981.1| 149 RKDGTVAWRCRNCGYIHEG 167
                                   677999********98765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.056
                        HalOD2   2 PekCseCs 9  
                                   P+kC++C 
  gi|91774289|ref|YP_566981.1| 171 PDKCPACD 178
                                   9******7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.7   0.00033       0.5       7      34 ..     157     179 ..     155     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                   Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgs 34 
                                   rC++Cg  +e       ++ ++ CP+C +
  gi|91774289|ref|YP_566981.1| 157 RCRNCGYIHEG------PAAPDkCPACDH 179
                                   9*****99992......334555****75 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 ?   10.8   0.0   0.00023      0.34      19      32 ..     152     166 ..     145     167 .. 0.73
   2 ?   -3.5   0.6       6.8     1e+04       4       7 ..     174     177 ..     174     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                   CCE.EEESSSS-EEE CS
                RNA_POL_M_15KD  19 gkn.feCrqCgYeep 32 
                                   g++   Cr+CgY+ +
  gi|91774289|ref|YP_566981.1| 152 GTVaWRCRNCGYIHE 166
                                   444456******987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.8
                                   ESTT CS
                RNA_POL_M_15KD   4 CpkC 7  
                                   Cp C
  gi|91774289|ref|YP_566981.1| 174 CPAC 177
                                   8888 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0041       6.1       9      22 ..     147     160 ..     145     162 .. 0.87
   2 ?    3.2   1.0     0.062        92       1       8 [.     173     180 ..     173     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0041
                DNA_ligase_ZBD   9 vvReegeaiyRCtn 22 
                                   v R++g +++RC n
  gi|91774289|ref|YP_566981.1| 147 VFRKDGTVAWRCRN 160
                                   559*********87 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.062
                DNA_ligase_ZBD   1 hCPvCGsa 8  
                                   +CP+C+++
  gi|91774289|ref|YP_566981.1| 173 KCPACDHP 180
                                   6****986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5   0.00056      0.83       1       8 [.     156     163 ..     152     167 .. 0.75
   2 ?    1.6   1.2      0.16   2.4e+02      16      21 ..     173     178 ..     173     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00056
                  Rubredoxin_2   1 YvCsqCGf 8  
                                   ++C++CG+
  gi|91774289|ref|YP_566981.1| 156 WRCRNCGY 163
                                   67777777 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                  Rubredoxin_2  16 rCpsCg 21 
                                   +Cp+C 
  gi|91774289|ref|YP_566981.1| 173 KCPACD 178
                                   7****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1276.77
//
Query:       gi|91774290|ref|YP_566982.1|  [L=180]
Description: flavoprotein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-17   62.3   0.0    7.4e-17   61.6   0.0    1.4  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   4.1e-21   7.4e-17       1     105 [.       2     123 ..       2     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4.1e-21
                                   EEEEEEE-SSCGGGCH.HHHHHHHHH.TTEEEEEEESCHHHHCCHHGGS.....TCSSHHHHHHCT............... CS
                  Flavoprotein   1 kkillgiTGsvaaika.lellekLkk.egievqvvltkaAkkfiskeklklaa.redpilhielrr............... 63 
                                   k+i++giTGs + i +  ++++ ++k  + e+ v+l+k+++ +++    ++ + +         +r               
  gi|91774290|ref|YP_566982.1|   2 KRIAWGITGSGDQIVEtYQVMKDIQKrTDLEFMVFLSKEGETVMKWY--RIWDdI---------QRdfpnfktgvgpnspf 71 
                                   79**********99998*********78*****************44..332221.........22344445555666777 PP

                                   ........TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEE CS
                  Flavoprotein  64 ........wadllviaPasantlakianGiadnlltlilra..takkpilia 105
                                           ++d+l+i Pa+an++aki++Giad+l+t+++    + ++pi+i+
  gi|91774290|ref|YP_566982.1|  72 iagplqvgHYDALIISPATANSVAKIVHGIADTLVTNVVAQtaKGDTPIYIL 123
                                   77777778*******************************3334666777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1134.85
//
Query:       gi|91774291|ref|YP_566983.1|  [L=367]
Description: myo-inositol-1-phosphate synthase [Methanococcoides burtonii DSM 6242]
Scores for complete 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  115.6   0.0      2e-33  114.9   0.0    1.3  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.059   12.7   0.0       0.12   11.7   0.0    1.7  2  NAD_binding_5   Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   2.2e-37     2e-33       1     109 []     199     307 ..     199     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 2.2e-37
                                   SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE-GGG CS
                Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kYvpyl 78 
                                   G+T+++++La+l+ +rg+k++++++lN +Gn+D++n+ +++r++sKk sK+++v++++ + +l  +dh+++i   +Yvp+ 
  gi|91774291|ref|YP_566983.1| 199 GATITHRTLADLFNKRGVKLERTYQLNTGGNTDFLNMLNRDRLSSKKTSKTEAVQSVLTE-RL--DDHNIHIgpsDYVPWQ 276
                                   9********************************************************998.44..58************** PP

                                   TTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                Inos-1-P_synth  79 gDsKvaldeieseiflggkntielkleceDS 109
                                   +D+K ++ ++e+++f++++++iel+l++eDS
  gi|91774291|ref|YP_566983.1| 277 QDNKLCFLRMEGKLFGDVPMNIELRLSVEDS 307
                                   ******************************9 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.37   3.3e+03      58      96 ..      29      68 ..       7      85 .. 0.65
   2 ?   11.7   0.0   1.3e-05      0.12     207     274 ..     151     217 ..     119     357 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.37
                                  xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                 NAD_binding_5 58 egedvyvpikdllplvnpndl.vfgGwDisslnlaeamer 96
                                  e++d+   ++  +  + p d+ v+ ++Di + ++ + +++
  gi|91774291|ref|YP_566983.1| 29 EEKDAIGLMHWEIGGYRPFDIeVVAAFDIDERKVGKDVSE 68
                                  3445555555555666666776667777777766666555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.3e-05
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_5 207 tiyavAailegvpyingsPqntl.vpglvelAekkgvfiaGdDfKtlLAaPlilDLvllveLaqrvevk 274
                                     ya  a+ ++v+++n  P      p   +    kg++i+GdD+K  L a +      l++L+++ +vk
  gi|91774291|ref|YP_566983.1| 151 KFYAQCALDANVAFVNNMPVFIAsNPEWAQKFADKGIPIIGDDIKAQLGATIT--HRTLADLFNKRGVK 217
                                   579****************8877667666666678***********7776554..34555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2280.14
//
Query:       gi|91774292|ref|YP_566984.1|  [L=404]
Description: beta-lactamase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-12   48.5   0.0    1.6e-12   47.8   0.0    1.3  1  Flavodoxin_1   Flavodoxin
    7.6e-10   39.1   0.0    1.1e-09   38.5   0.0    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.1e-06   26.2   0.0    1.1e-05   25.0   0.0    1.6  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   2.7e-16   1.6e-12       1     141 [.     260     390 ..     260     392 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.7e-16
                                   EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGH.HHHHHHHHHHCHHG CS
                  Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppenge.sffqdllelkgdel 80 
                                   ++Y+++ G+te +Ak++ e+++e g++a++++l++ d  +s + +e l   v++   +G+p+++g  +f+ + +  +    
  gi|91774292|ref|YP_566984.1| 260 VIYDTMWGSTEIMAKEIVEGVSECGVEARMFHLRKND--WSMMLRELLSSPVIA---VGSPTMHGTmFFTISGFLTYL--- 332
                                   89***********************************..788888888888888...999999999999999999994... PP

                                   CCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTST.HGHHHHHH CS
                  Flavodoxin_1  81 edgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednq.egqeeafr 141
                                   +   l  +  + +++G+ ++ +   a+k ++e++  +G e++ ++l+++  +  ++++++++
  gi|91774292|ref|YP_566984.1| 333 K--GLRPKGKSAVAFGSFGWGG--GAVKHVEEMMASAGLEVIEPGLQAKYRPYeDDLKACRE 390
                                   3..577888999**********..**************************998777777665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.9e-13   1.1e-09       4     163 ..      36     198 ..      33     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.9e-13
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                   +  n+yli  d++v LiDt  +  a+ + +   ++ ++p ++d++i  H   DH +gl+ ++e ++ +++ + + ++++++
  gi|91774292|ref|YP_566984.1|  36 GTYNAYLI-VDDKVTLIDTVKGDFAPEMIK-RIRKVVNPSKIDHIICNHVEMDHSSGLPAIMELAKDAKIFCTKRGKVGLE 114
                                   5679****.5*********87777777665.77999********************************************* PP

                                   HHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC... CS
                   Lactamase_B  85 eeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl... 162
                                   e+ +           g sa + ++++ +++++ g+r +       +h +++++ +++++++lf+ Da+ ++   ++++   
  gi|91774292|ref|YP_566984.1| 115 EHYEA---------NGCSAWDFEIVDTGYELDIGSRTLMFLETPMLHWPDSMQTYLKEDRILFSNDAFGQHLATSVRFede 186
                                   ***65.........57999************************************************99877777666555 PP

                                   ............ CS
                   Lactamase_B 163 ...........t 163
                                               
  gi|91774292|ref|YP_566984.1| 187 vecgaledaaiY 198
                                   555544444443 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 !   25.0   0.0   1.9e-09   1.1e-05       4     114 ..      50     154 ..      48     184 .. 0.80
   2 ?   -3.1   0.0      0.77   4.6e+03      99     146 ..     218     267 ..     216     282 .. 0.58

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.9e-09
                                   EES--TTHHHH..HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT CS
                 Lactamase_B_2   4 LiDagpdlrqq..alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee 82 
                                   LiD++ + +++       ++ +++ ++++id ++  h ++DH  gl+ + el++ +++++++k+    le++  y+a +  
  gi|91774292|ref|YP_566984.1|  50 LIDTVKGDFAPemI----KRIRKVVNPSKIDHIICNHVEMDHSSGLPAIMELAK-DAKIFCTKRGKVGLEEH--YEANGCS 123
                                   78999985555322....2334666789***********************765.699****9999999999..5555555 PP

                                   TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE- CS
                 Lactamase_B_2  83 pavnvheldwgesfelgdggleitatparhks 114
                                    a +++ +d+g ++++g+  l +  tp  h+ 
  gi|91774292|ref|YP_566984.1| 124 -AWDFEIVDTGYELDIGSRTLMFLETPMLHWP 154
                                   .6789999999999999888888878877775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.77
                                   CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE....CTTEEEEEESS-S-- CS
                 Lactamase_B_2  99 gdggleitatparhksgrrldrnagdtlGlrie....gggkrvyyigDtgyi 146
                                   ++ gle+ +++ +h+  +  ++++++++   i+    ++  +v+ i Dt   
  gi|91774292|ref|YP_566984.1| 218 AELGLEFDMIAPSHGVIW--RKEPMRVVEAYIKwakgEAVPKVLVIYDTMWG 267
                                   566778888888888877..44555554444443222333446666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2863.68
//
Query:       gi|91774293|ref|YP_566985.1|  [L=91]
Description: hypothetical protein Mbur_2384 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   62.8   3.0    2.8e-17   62.7   3.0    1.0  1  FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta ch


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 !   62.7   3.0   1.6e-21   2.8e-17       4      86 ..      10      90 ..       6      91 .] 0.95

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.6e-21
                                  HHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HHHHHH....---TTSSSB CS
                     FeThRed_B  4 ktrkflekvakklgtkfnpdeevtevvieglarnkeeyGkrlCPCrlvedkeeeekkavwnCPCvplreeldeekeChCglfv 86
                                  ++ + ++k a+++g+ +npd +v ++ ++g+ +nk+eyG+ +C C+  +++ e++kk++  CPC  ++ +++ +++C Cgl++
  gi|91774293|ref|YP_566985.1| 10 EFYNRSKKNAETTGYRLNPDYDVITIAVKGICNNKREYGEWYCFCQKRTGDVEKDKKII--CPCAARSRDVEMRGSCKCGLYI 90
                                  566788999**************************************************..*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 619.17
//
Query:       gi|91774294|ref|YP_566986.1|  [L=523]
Description: D-3-phosphoglycerate dehydrogenase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-61  204.4   0.1    1.3e-60  203.8   0.1    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    5.6e-40  136.1   2.9    2.1e-39  134.3   1.0    2.2  2  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    1.7e-05   24.4   0.1      8e-05   22.3   0.1    2.3  1  ACT            ACT domain
    4.6e-05   23.0   0.5    0.00012   21.7   0.0    1.9  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    9.8e-05   22.6   1.5    0.00022   21.4   0.2    2.2  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.066   13.8   1.2       0.66   10.6   0.0    3.2  4  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.8   0.1   4.2e-64   1.3e-60       1     178 []     104     278 ..     104     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.8 bits;  conditional E-value: 4.2e-64
                                   HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                  2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81 
                                   +a++++++r++++a++++++++w ++k+++g e++gkt+G+iGlGrIG +vakr+++++m ++ayd++ ++++ ++++gve
  gi|91774294|ref|YP_566986.1| 104 IAMMMSMARNIPQANASLKAKKW-ERKNFMGVEVNGKTLGVIGLGRIGAEVAKRAQGLEMSILAYDPFVTEDR-AKDMGVE 182
                                   689********************.99******************************************99766.******* PP

                                   ECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTC CS
                  2-Hacid_dh_C  82 lvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplped 162
                                   l++++++ +++D++++h+pl +etr++++++++++mk++  +iN+aRGg+++eeaL++a ++gkiagaa+Dvf +ep+  d
  gi|91774294|ref|YP_566986.1| 183 LTTVDDIAQRADFITVHTPLIKETRNILDKAQFDMMKSSTRVINCARGGIINEEALADAARNGKIAGAAIDVFTSEPPF-D 262
                                   *****************************************************************************99.7 PP

                                   HHHHHSTTEEE-SS-T CS
                  2-Hacid_dh_C 163 spllelpnviltPHia 178
                                    p++ l+nvi+tPH++
  gi|91774294|ref|YP_566986.1| 263 CPFIGLDNVIVTPHLG 278
                                   7*************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 !  134.3   1.0     7e-43   2.1e-39       1     134 []       3     310 ..       3     310 .. 0.99
   2 ?    1.3   0.0     0.085   2.5e+02      20      65 ..     351     397 ..     327     401 .. 0.71

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 7e-43
                                   EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaak 81 
                                   vl++++l+ee++  l+e +++v+v + l+++el+ek+  +dal++rs t+vt++v+ea+++Lk+i+ragvGvDnvD+daa+
  gi|91774294|ref|YP_566986.1|   3 VLVSDSLSEEGVSKLSE-HFDVDVSTGLSEDELVEKIGIFDALVIRSGTHVTKRVIEAADNLKIIGRAGVGVDNVDVDAAT 82 
                                   79999************.66************************************************************* PP

                                   HTT-EEEE-TTTTHHHHHHHH............................................................ CS
                                   xxxxxxxxxxxxxxxxxxxxx............................................................ RF
                    2-Hacid_dh  82 erGilVtnvpgystesvAElt............................................................ 102
                                   e+Gi+V+n+p+ +  s+AE+t                                                            
  gi|91774294|ref|YP_566986.1|  83 EKGIIVVNAPEGNMLSAAEHTiammmsmarnipqanaslkakkwerknfmgvevngktlgviglgrigaevakraqglems 163
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                    2-Hacid_dh 103 ................................................................................. 102
                                                                                                                    
  gi|91774294|ref|YP_566986.1| 164 ilaydpfvtedrakdmgvelttvddiaqradfitvhtpliketrnildkaqfdmmksstrvincarggiineealadaarn 244
                                   ********************************************************************************* PP

                                   ..................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                   ..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 103 ..................................aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                                                     a+Teeaq n+a  +ae+++++l+g+s++n +n
  gi|91774294|ref|YP_566986.1| 245 gkiagaaidvftseppfdcpfigldnvivtphlgASTEEAQVNVAVSVAEEIISVLNGGSARNTIN 310
                                   **************************************************************9987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.085
                                   EEEEEESCSSHHHCHHHHTT..ESEEEE-TTS-BSHHHHHHHTT--EE CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh  20 vevevkdellteellekakd..adalivrsntkvtaevlealpkLkvi 65 
                                   ++ e+ d+ +++ +++++k+   da+  ++n  v+a  l++  +++v+
  gi|91774294|ref|YP_566986.1| 351 YNGEIADKDTRAVTVAALKGilEDAVGSAVNY-VNAPSLAKSRNVEVV 397
                                   24444558999999999999766888888888.999999999999988 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   2.7e-08     8e-05      20      65 ..     469     512 ..     467     514 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.7e-08
                                   HHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT  20 aladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                   +l++++iNi  ++++++e   +g +++ + vd e+ e +l++++++
  gi|91774294|ref|YP_566986.1| 469 VLGENNINISGMQVGRVEV--GGNTIMALNVDNEVSEGILDEIRAI 512
                                   79*****************..9*********************997 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.5   4.5e+03      47      82 ..      69     105 ..      43     114 .. 0.55
   2 !   21.7   0.0     4e-08   0.00012       2      99 ..     136     233 ..     135     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                   TT-EEEEHH.HHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                          IlvN  47 egfevltva.eavkkadvvmiliPDelqkevyeeeie 82 
                                   +g+ v +v+ +a+++  ++++ +P+  + +  e++i+
  gi|91774294|ref|YP_566986.1|  69 AGVGVDNVDvDAATEKGIIVVNAPEGNMLSAAEHTIA 105
                                   4444444432455555566666666555555555555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 4e-08
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-H.HHHHHHHHHHT CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPD.elqkevyeeei 81 
                                   ++gk++ viG G  G   a+  r +gl++ +  ++   + ++Ak+ g+e +tv++++++ad++++ +P  +  +++++++ 
  gi|91774294|ref|YP_566986.1| 136 VNGKTLGVIGLGRIGAEVAK--RAQGLEMSILAYDPFVTEDRAKDMGVELTTVDDIAQRADFITVHTPLiKETRNILDKAQ 214
                                   579************99998..789******9999999******************************6245677888777 PP

                                   GGG--TT-.EEEESSSHHH CS
                          IlvN  82 epnlkegk.alafahGfni 99 
                                    + +k+ + ++ +a G  i
  gi|91774294|ref|YP_566986.1| 215 FDMMKSSTrVINCARGGII 233
                                   7777765436777777555 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      0.62   1.9e+03      37     131 ..      80     107 ..      32     124 .. 0.62
   2 !   21.4   0.2   7.4e-08   0.00022       2     106 ..     141     244 ..     140     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.62
                                   HHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEE CS
                 NAD_binding_2  37 elvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspedtrelakelkekglkfldaPVS 117
                                   ++                                                                  +ekg+ +++aP  
  gi|91774294|ref|YP_566986.1|  80 AA------------------------------------------------------------------TEKGIIVVNAP-E 93 
                                   33..................................................................33333333333.2 PP

                                   SHHHHHHHT-EEEE CS
                 NAD_binding_2 118 GGeegAekGtLsim 131
                                   G    A++ t+++m
  gi|91774294|ref|YP_566986.1|  94 GNMLSAAEHTIAMM 107
                                   33333333333333 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 7.4e-08
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC-- CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealk 81 
                                   +g+iGlG +G++ a++ +  ++++ +y+  +  +e+ +++  + ++++ ++++++d++ +  +  k++++++++  ++ +k
  gi|91774294|ref|YP_566986.1| 141 LGVIGLGRIGAEVAKRAQGLEMSILAYD--PFVTEDRAKDMGVELTTVDDIAQRADFITVHTPLIKETRNILDKaQFDMMK 219
                                   8***************999999999998..558888888888999*****************************7789999 PP

                                   TT-EEEE-S---HHHHHHHHHHHHH CS
                 NAD_binding_2  82 kgdilidgstsspedtrelakelke 106
                                   +++ +i+++   + + + la+++++
  gi|91774294|ref|YP_566986.1| 220 SSTRVINCARGGIINEEALADAARN 244
                                   9999999988777777777776655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.8   2.4e+03      27      54 ..       2      29 ..       1      65 [. 0.78
   2 ?   -1.9   0.0       1.7   5.1e+03      45      70 ..      68      92 ..      43     107 .. 0.57
   3 ?   10.6   0.0   0.00022      0.66       2      70 ..     141     201 ..     140     225 .. 0.83
   4 ?   -2.5   0.0       2.6   7.8e+03      26      60 ..     392     425 ..     374     429 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.8
                                  CEEEEEESSCCCHHHHHHHHC-EEECEC CS
                 F420_oxidored 27 eivvansrnpekaeelaeelgvkvtavd 54
                                  +++v  s ++e + +l e++ v+v+++ 
  gi|91774294|ref|YP_566986.1|  2 KVLVSDSLSEEGVSKLSEHFDVDVSTGL 29
                                  5778888999999999999999987753 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                  HHC-EEECECHHHHHHH-SEEEE-S- CS
                 F420_oxidored 45 elgvkvtavdneeaaeeadvvvlavk 70
                                  ++gv+v      +aa+e  ++v+  +
  gi|91774294|ref|YP_566986.1| 68 RAGVGVDN-VDVDAATEKGIIVVNAP 92
                                  33466666.34455555666666544 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00022
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S- CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavk 70 
                                   +g+iG G++g+ +a++++       +i+     +p   e  a+++gv++t+    + a++ad++ +  +
  gi|91774294|ref|YP_566986.1| 141 LGVIGLGRIGAEVAKRAQGLE---MSIL---AYDPFVTEDRAKDMGVELTT--VDDIAQRADFITVHTP 201
                                   89*************877666...5555...589999999999**999999..999******9866554 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.6
                                   GCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH CS
                 F420_oxidored  26 heivvansrnpekaeelaeelgvkvtavdneeaae 60 
                                   +++ v+ +++ e+    a+++ +++++++n + ++
  gi|91774294|ref|YP_566986.1| 392 RNVEVV-ESKSETSGDHASTIRITLFQGTNTKSVS 425
                                   455545.4444444555566666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.49
# Mc/sec: 3215.62
//
Query:       gi|91774295|ref|YP_566987.1|  [L=160]
Description: hypothetical protein Mbur_2386 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1016.84
//
Query:       gi|91774296|ref|YP_566988.1|  [L=155]
Description: hypothetical protein Mbur_2387 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-53  180.6   0.0    1.4e-53  180.4   0.0    1.0  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22


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 !  180.4   0.0   7.9e-58   1.4e-53       1     144 []       3     146 ..       3     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 7.9e-58
                       DUF2240   1 elkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpdeell 81 
                                   el ++va+pfk++++++ls +df+f+ls+d+kw+sp qa+k+ d++ ++g+l+ ++g+lv+n+d+++++iP+gFkp+++l+
  gi|91774296|ref|YP_566988.1|   3 ELFFVVASPFKNNATTSLSIKDFEFSLSFDLKWMSPAQASKVRDQGIMSGILKFDEGELVLNMDASSIDIPAGFKPSSDLF 83 
                                   6789***************************************************************************** PP

                       DUF2240  82 kekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddlieev 144
                                   +ek t+++i+d+i++++gi+k+evv++in++qe+l+gl+d+e+aal+va++ g+d+ +l+++v
  gi|91774296|ref|YP_566988.1|  84 REKGTIDMIMDTIVSNGGIDKREVVSRINQKQETLGGLLDAEVAALLVAHELGCDAGSLFNDV 146
                                   **********************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 971.20
//
Query:       gi|91774297|ref|YP_566989.1|  [L=126]
Description: 50S ribosomal protein L18e [Methanococcoides burtonii DSM 6242]
Scores for complete 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    1.5e-12   47.3   0.0    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    1.7e-07   32.0   0.4      4e-07   30.7   0.4    1.8  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   1.6e-16   1.5e-12      10     138 ..       3     125 ..       1     126 [] 0.93

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.6e-16
                 Ribosomal_L18  10 kkskrkapksenvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvr 90 
                                   kk++ k ++ +n+ +  L+ + +  ar  d+   k + krL +  +  + + ls++ ++      e+ ++ v g+v+    
  gi|91774297|ref|YP_566989.1|   3 KKTQMKITRKTNPRIPALISVLKDTARENDAPIWKDMAKRLEKPSRIYAEVNLSKINRHAA----ENDLVLVPGKVLGAGA 79 
                                   788999999**********************************99999********99988....5689999******999 PP

                 Ribosomal_L18  91 llevPklsvaALrftetararilkaGGeiltlDqLalraPtGkntvLl 138
                                   l +  +++vaAL f++ta ++i++aGG+++t++q+  ++P G+   ++
  gi|91774297|ref|YP_566989.1|  80 LGH--AVTVAALTFSTTAVDKITNAGGKCMTIEQILEENPAGSGIRIM 125
                                   987..69***********************************988766 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 !   30.7   0.4   4.5e-11     4e-07      71     127 ..      49     107 ..       4     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.5e-11
                                   ---EEEGGGTTTTSSS.......SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  71 eaeeidleelaeaglikk...kdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                     +e++l+++ +++ +++       Kvlg g l ++++v a  fS +A+ kI +aGGk++
  gi|91774297|ref|YP_566989.1|  49 IYAEVNLSKI-NRHAAENdlvLVPGKVLGAGALGHAVTVAALTFSTTAVDKITNAGGKCM 107
                                   3567888888.33333334433344*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 788.35
//
Query:       gi|91774298|ref|YP_566990.1|  [L=139]
Description: 50S ribosomal protein L13P [Methanococcoides burtonii DSM 6242]
Scores for complete 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   45.5   0.0    1.1e-09   38.6   0.0    2.2  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 !   38.6   0.0   6.1e-14   1.1e-09       4     118 ..       3     103 ..       1     109 [. 0.85

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 6.1e-14
                                   EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSH CS
                 Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkp 84 
                                   viDA+g ++grlas++ak+L              G+ v ++nae+ +++g+k+++   y     ++++ ++++   + ++p
  gi|91774298|ref|YP_566990.1|   3 VIDANGLIMGRLASNVAKMLL------------SGEEVSIVNAERAVISGSKVTTFEEYD---VIRNMGTREFGPYFPRRP 68 
                                   89***************9996............6999***************99766554...55666677899999**** PP

                                   HHHHHHHHHCCS-SSH.HHHHHGCTEEEESSSTTS CS
                 Ribosomal_L13  85 eeilekaVkgmLpknk.lgrrrlkrLkvyageehp 118
                                   ++il+++V+gmLp ++  g++ + rLkvy g   +
  gi|91774298|ref|YP_566990.1|  69 DRILKRTVRGMLPYKRaRGKDAMGRLKVYVGIPYE 103
                                   *************6662688888******996555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 895.60
//
Query:       gi|91774299|ref|YP_566991.1|  [L=134]
Description: 30S ribosomal protein S9P [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-33  116.1   0.2    1.5e-33  115.9   0.2    1.0  1  Ribosomal_S9   Ribosomal protein S9/S16
  ------ inclusion threshold ------
       0.12   11.9   0.1       0.12   11.9   0.1    1.1  1  F_bP_aldolase  Fructose-bisphosphate aldolase class-II


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 !  115.9   0.2   1.7e-37   1.5e-33       1     121 []      10     134 .]      10     134 .] 0.94

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 1.7e-37
                                   EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHHHHHH CS
                  Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiaraLva 80 
                                   G+ K+++Ar+++  g+gk ++n+k+++ Y + e a+ k++epl l+++  + +d+ vkv+gGG++gqa+Air++iar++v+
  gi|91774299|ref|YP_566991.1|  10 GKNKTAIARATVSVGTGKARINKKPVDIYEP-EFAKLKIIEPLMLAKEAVSgLDIDVKVSGGGIMGQANAIRTAIARGIVE 89 
                                   899*************************888.89999*********998878***************************** PP

                                   HHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                  Ribosomal_S9  81 lekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                   +++   + L+      +++ll++D+R++E kK+g ++AR+kyq+s+R
  gi|91774299|ref|YP_566991.1|  90 WTN--DTDLRdafmayDRNLLVNDSRQTETKKFGGPGARAKYQKSYR 134
                                   *88..466665555788****************************99 PP

>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.3e-05      0.12     172     263 ..      19     128 ..       2     134 .] 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                   EE--SS---SS--SS......--THHHHHHHHHH..........--S.EE-SGTTS-HHHHHHHHHTTEEEEEE-HHHHHH CS
                 F_bP_aldolase 172 lAvaiGnvHGvykpkpk....Ldferlkeiqkav..........vpl.VlHGgsgvpdeeirkaiklGvvKiNidtdlrla 237
                                     v++G+     ++kp      +f  lk i+  +          + + V  Gg   + + ir+ai++G+v    dtdlr+a
  gi|91774299|ref|YP_566991.1|  19 ATVSVGTGKARINKKPVdiyePEFAKLKIIEPLMlakeavsgldIDVkVSGGGIMGQANAIRTAIARGIVEWTNDTDLRDA 99 
                                   55677776666666644443323333333333333333336655555788888888999********************** PP

                                   HHHHHHHG..GE-HHH-HHHHHHH.HHHH CS
                 F_bP_aldolase 238 ytkavkke..kenkkydprkllke.aeea 263
                                   +++  ++   +++ +++ +k+  + a+++
  gi|91774299|ref|YP_566991.1| 100 FMAYDRNLlvNDSRQTETKKFGGPgARAK 128
                                   *9988666542222245555555545555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 877.60
//
Query:       gi|91774300|ref|YP_566992.1|  [L=62]
Description: DNA-directed RNA polymerase subunit N [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-28   96.7   0.3    7.9e-28   96.5   0.3    1.0  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.3   4.4e-32   7.9e-28       2      58 ..       1      57 [.       1      58 [. 0.98

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 4.4e-32
                                  ---SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                     RNA_pol_N  2 iiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                                  +iPVrCFtCGkvi+  weey+++  +ge+p+ +Ld+L++ ryCCrrm+l+hv+l+++
  gi|91774300|ref|YP_566992.1|  1 MIPVRCFTCGKVIAGSWEEYKRRTGEGEDPATVLDDLKFVRYCCRRMFLAHVELVDT 57
                                  8******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 432.43
//
Query:       gi|91774301|ref|YP_566993.1|  [L=63]
Description: DNA-directed RNA polymerase, subunit K [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-10   40.8   0.1    1.7e-10   40.7   0.1    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6
  ------ inclusion threshold ------
      0.083   11.9   0.0      0.089   11.8   0.0    1.0  1  DUF4026       Protein of unknown function (DUF4026)


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 !   40.7   0.1   1.9e-14   1.7e-10       3      49 .]       6      56 ..       4      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.9e-14
                                  TTSS--HHHHHHHHHHHHHHH....HT.......S.S-SSSSTTCHHHHTT-S-- CS
                  RNA_pol_Rpb6  3 tskvltrYelvriaakRArQieegesl.......e.tqkpvviAlrEiaegkipi 49
                                   + + trYe +ri+++R +Qi     +       + +++ +  A+ E ++g ipi
  gi|91774301|ref|YP_566993.1|  6 SNEKYTRYERARIIGARSLQI----AMgapilieDdNTDALYLATLEFEKGVIPI 56
                                  56778****************....6666666665589***************97 PP

>> DUF4026  Protein of unknown function (DUF4026)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.9e-06     0.089     217     252 ..      24      59 ..      18      63 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.9e-06
                       DUF4026 217 gqvelnePiligqtekgleylvalPyeeGirqinkk 252
                                    q+ ++ Pili + + +  yl +l +e+G+  i  k
  gi|91774301|ref|YP_566993.1|  24 LQIAMGAPILIEDDNTDALYLATLEFEKGVIPITVK 59 
                                   599**************************9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 384.51
//
Query:       gi|91774302|ref|YP_566994.1|  [L=214]
Description: 30S ribosomal protein S2 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-24   86.5   0.4    3.8e-15   55.7   0.3    2.1  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
       0.13   11.8   0.2       0.21   11.1   0.2    1.3  1  Peripla_BP_4  Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0     5e-11   4.5e-07       2      95 ..      33     123 ..      32     129 .. 0.92
   2 !   55.7   0.3   4.2e-19   3.8e-15     148     213 ..     131     196 ..     124     198 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5e-11
                  Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakrang 81 
                                   L+agvh+G q++  +++m +++y +r +g +++d++ t + +r ++++++  + + ++il v+ ++  +   +  +k +++
  gi|91774302|ref|YP_566994.1|  33 LAAGVHIGTQQK--TQNMMKFVYRVRtDGLYVLDIQSTDERIRSIAHFLS--MYDPSRILVVSARQYGQYPATMFSKSVGA 109
                                   89******7766..788******999569********************8..67899*********99999999******* PP

                  Ribosomal_S2  82 yyvnerWlgGtLTN 95 
                                   +    r+++G+LTN
  gi|91774302|ref|YP_566994.1| 110 VSKVGRFIPGSLTN 123
                                   ************** PP

  == domain 2  score: 55.7 bits;  conditional E-value: 4.2e-19
                  Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                    Pd+v+v+dp  +  +++Ea ++gipv+a++Dtn  +++vd +Ip N++  ++++l++ +la+ i+
  gi|91774302|ref|YP_566994.1| 131 EPDVVIVTDPAGDAQVIREAVNVGIPVVALCDTNNMTSNVDLVIPTNNKGRKALSLVYWLLAREIA 196
                                   6*************************************************************9886 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 ?   11.1   0.2   2.3e-05      0.21      56     105 ..     132     179 ..     121     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                                   -SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HH CS
                  Peripla_BP_4  56 vdgiivapvdstalapalkkakaaGIpVvafdsddapsgerlayvgfdne 105
                                   +d++iv+  d+++ a+++ +a + GIpVva    ++ +++++ ++ ++n+
  gi|91774302|ref|YP_566994.1| 132 PDVVIVT--DPAGDAQVIREAVNVGIPVVALCDTNNMTSNVDLVIPTNNK 179
                                   7777776..888889***************65554999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1437.30
//
Query:       gi|91774303|ref|YP_566995.1|  [L=264]
Description: hypothetical protein Mbur_2394 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-76  255.3   0.0    6.1e-76  255.1   0.0    1.0  1  Memo      Memo-like protein
    3.1e-06   26.5   0.0    6.3e-06   25.5   0.0    1.4  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio
  ------ inclusion threshold ------
      0.072   12.8   0.0       0.11   12.2   0.0    1.3  1  GATase    Glutamine amidotransferase class-I


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.1   0.0     1e-79   6.1e-76       1     270 [.       3     261 ..       3     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 255.1 bits;  conditional E-value: 1e-79
                          Memo   1 eaavAGsfYpedeeelkkqleeflekntgkkeiarviisPHagyvysgevaakayaelesskvervvilGpsHtilgskvs 81 
                                   +++vAG+fYp  +++l+k + ++++      e     ++PHagyvysg+vaa+a+a+l ++  ++ vi+Gp+Ht++gs+v+
  gi|91774303|ref|YP_566995.1|   3 QPTVAGKFYPLSTKALRKEIVKCFHGLEIMSEDVIGAVVPHAGYVYSGPVAAHAFARLPKA--DTYVIFGPNHTGYGSPVA 81 
                                   599******************888765555444555667*******************998..9***************** PP

                          Memo  82 vlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseetakevgea 162
                                   +++ + ++TP+Gd++ D el + L     i+d+de+a+++EHS+Evq+pfL++l+ +  fk++Pi++++q+e+ta evg  
  gi|91774303|ref|YP_566995.1|  82 MSQ-DVWNTPFGDVETDRELGKLLAG--TIIDMDEVAHRYEHSVEVQIPFLQYLFGS-DFKVLPICMGMQDEDTAVEVGLE 158
                                   **9.****************998888..6****************************.5********************** PP

                          Memo 163 lakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGekpiavilkalkkl 241
                                   +a+++k++   +++i+SsDlsHy      pqe ae+  D+++i+a+ +++  e++   +++++t cG++pi+++l a+k+ 
  gi|91774303|ref|YP_566995.1| 159 VARAVKESGkkVVFIASSDLSHYV-----PQEKAEKS-DNYLIDAILDMDVPEIYRRKYEKDITACGYGPITAMLTAAKEC 233
                                   *******99989************.....******99.******************************************* PP

                          Memo 242 gakkakllkYaqssdvtsdtdsvVsyasl 270
                                   gak+ +l+kY +s+dvt+ +  vV+ya++
  gi|91774303|ref|YP_566995.1| 234 GAKNTELVKYGTSGDVTG-DPMVVGYAAI 261
                                   *****************5.6789****87 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 !   25.5   0.0     1e-09   6.3e-06     124     214 ..     129     210 ..      91     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1e-09
                          LigB 124 LelmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakadaqtlllneefd 204
                                   L+++++     +v+++ +        +     ++G  +++av+e+ k+v++++s +lsH+ ++++a k d    l+++++d
  gi|91774303|ref|YP_566995.1| 129 LQYLFG--SDFKVLPICMGM-----QDEDTAVEVGLEVARAVKESGKKVVFIASSDLSHYVPQEKAEKSDN--YLIDAILD 200
                                   577777..357777776655.....899999**********************************887777..66888888 PP

                          LigB 205 eelldllkeg 214
                                   + + ++ +  
  gi|91774303|ref|YP_566995.1| 201 MDVPEIYRRK 210
                                   7776666654 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05      0.11      56      96 ..     121     163 ..     111     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                                   TTTTHHHHHHHHCTSTS-EEEETHHHHH..HHHHTTTEEEEEE CS
                        GATase  56 gvegkieaikearenkiPiLGICLGmQl..laiefgrkvvkek 96 
                                   +ve +i +++++++++  +L IC+GmQ   +a e+g +v ++ 
  gi|91774303|ref|YP_566995.1| 121 SVEVQIPFLQYLFGSDFKVLPICMGMQDedTAVEVGLEVARAV 163
                                   3999***********************4336666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1787.44
//
Query:       gi|91774304|ref|YP_566996.1|  [L=303]
Description: mevalonate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-18   64.7   0.1    1.4e-17   63.7   0.1    1.6  1  GHMP_kinases_N   GHMP kinases N terminal domain
    7.1e-14   51.9   1.1      2e-13   50.5   0.4    1.9  2  GHMP_kinases_C   GHMP kinases C terminal
    0.00094   18.7   0.1     0.0026   17.3   0.1    1.8  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
  ------ inclusion threshold ------
      0.069   13.1   0.0       0.11   12.4   0.0    1.2  1  SpoIIE           Stage II sporulation protein E (SpoIIE)


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 !   63.7   0.1     3e-21   1.4e-17       1      66 []      79     146 ..      79     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 3e-21
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                   d++i+s+iPvg+GLGSSAA++va+++A+  ll+l le+   ak++ e e+ +q g  s+ D +++++Gg
  gi|91774304|ref|YP_566996.1|  79 DLRISSDIPVGSGLGSSAAVTVATIKAMDTLLDLGLELddiAKMGHEVEQNIQ-GTASPTDTYVCTMGG 146
                                   689*****************************888644449************.**************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 ?   -1.3   0.0      0.67     3e+03      55      65 ..      89      99 ..      88     122 .. 0.71
   2 !   50.5   0.4   4.5e-17     2e-13       5      79 ..     210     281 ..     207     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.67
                GHMP_kinases_C 55 GaGgGptvfal 65
                                  G+G+G++ ++ 
  gi|91774304|ref|YP_566996.1| 89 GSGLGSSAAVT 99
                                  77777776654 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 4.5e-17
                GHMP_kinases_C   5 lergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                   ++ +d+ ++gel+n  q   l++ +g+++ el +l+ a++e Ga+g+k++GaGgG++ +a+   +++++ va+a+
  gi|91774304|ref|YP_566996.1| 210 VNDRDYVSVGELMNIDQG--LLDAIGVSCAELSSLIYAARESGAYGSKITGAGGGGCMVAIS-PRENVDSVAEAI 281
                                   4569999***********..9****************************************9.********9987 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 !   17.3   0.1   5.8e-07    0.0026      14      49 .]       4      39 ..       2      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.8e-07
                                  EEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEEEE CS
               GalKase_gal_bdg 14 asAPGRvnLiGEHtDYngGfVlpmAieqdiyiavsp 49
                                   sAPG v L GEH    g   + +A++ ++ + vsp
  gi|91774304|ref|YP_566996.1|  4 CSAPGKVYLFGEHAVVYGEPAICCAVDIRTRVTVSP 39
                                  69****************************999986 PP

>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.11      14      82 ..      89     162 ..      87     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                   SSSHH.HHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT......TTCEEEEEEEETTTTEEEEEEES CS
                        SpoIIE  14 GhGle.Aalimgllrsalrelataglepaevlkrlnralardleee.....erfaTavlavydpstgkleyanaG 82 
                                   G Gl+ +a++++++++a+++l++ gle+++++k  +++  ++++ +       ++T+  +v+ p+++kle++ +G
  gi|91774304|ref|YP_566996.1|  89 GSGLGsSAAVTVATIKAMDTLLDLGLELDDIAKMGHEVE-QNIQGTasptdTYVCTMGGVVLIPQRKKLELIDCG 162
                                   66775157889999*************777776554444.555555566778899999999************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1776.22
//
Query:       gi|91774305|ref|YP_566997.1|  [L=257]
Description: aspartate/glutamate/uridylate kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-40  139.2   2.5    1.9e-40  139.0   2.5    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 !  139.0   2.5     1e-44   1.9e-40       2     241 .]       7     234 ..       6     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 1e-44
                                   EEEEEE-TTCCCCTCC....HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHH CS
                     AA_kinase   2 rvVvKlGGssltdkee....aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevat 78 
                                   ++++K+GGs++tdk      a+ ++++++ ++++  + kl++VhG+gs+++ ++++ + l++g++a         +g v+t
  gi|91774305|ref|YP_566997.1|   7 ITILKIGGSVITDKRSedglAWEEEIVRIAREISGFEGKLIIVHGAGSYGHPQAKR-YALTEGFHA---------EGAVVT 77 
                                   689*********88778***777777777777777799******************.********9.........8***** PP

                                   HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE- CS
                     AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgs 159
                                   + a+ +l++++v  l ++g++a+++++  +++ ++gr       ++      i+ +le+g vpvl+g++++de +++ ++s
  gi|91774305|ref|YP_566997.1|  78 HNAVKALNRIVVGILNDEGVNAISVHPMCCTVAKNGR-------ISDMYLGSIRLMLEKGLVPVLHGDVVMDEVKGVSIIS 151
                                   ****************************999998888.......99999***************************99*** PP

                                   HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH....CSSS.TTTHHHHCHHHHHHHHHCTT-E CS
                     AA_kinase 160 sDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee....saselatgGmkvkhpaalaaarrggip 236
                                   +D+++ +lA  l+A ++ + +  dGV+d+ +  +    +++ +++de+++    sa++++tgGm  k++++l++ + + i 
  gi|91774305|ref|YP_566997.1| 152 GDQVIPYLATQLKASRIGVGSAADGVFDDKGVTI---PVITSMNFDEIKAyiggSAGTDVTGGMLGKVLEMLELGKTSSIT 229
                                   *******************************999...9***************************************99** PP

                                   EEEEE CS
                     AA_kinase 237 vvItn 241
                                    +I+n
  gi|91774305|ref|YP_566997.1| 230 SYIFN 234
                                   ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1523.70
//
Query:       gi|91774306|ref|YP_566998.1|  [L=362]
Description: isopentenyl pyrophosphate isomerase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-28   99.5   1.4    4.1e-26   91.8   1.4    2.1  1  FMN_dh        FMN-dependent dehydrogenase
    4.7e-07   29.1   9.4      0.014   14.4   0.1    3.6  3  IMPDH         IMP dehydrogenase / GMP reductase domain
    0.00016   21.2   0.1    0.00016   21.2   0.1    2.1  3  NMO           Nitronate monooxygenase
     0.0082   15.3   0.9      0.017   14.3   0.9    1.6  1  Glu_synthase  Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.023   13.9   1.6        0.5    9.5   0.0    2.8  4  DHO_dh        Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   1.4   1.1e-29   4.1e-26       6     344 ..       4     333 ..       2     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.1e-29
                                   -HHHHHHHH--STTSHHHHHHHHGGGGEEE---SSSS-S..S-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHH CS
                        FMN_dh   6 pkkafayvaggagdevtlrenraaferirlrprvlrdvs..kvdlsttllGqklslPvliaPvglaklahpdgelalaraa 84 
                                   +k+++++++ +a++ v  r+ ++ f+++ l +++l +++  ++dlst++lG++l++P+lia++          + ala+aa
  gi|91774306|ref|YP_566998.1|   4 SKRKIEHLELCAKRPVESRNVTSGFDDVMLIHKALPQIHmdEIDLSTDFLGKSLKAPFLIASITGGHPDTTPVNAALAEAA 84 
                                   57789999***************************98752277********************88888888899******* PP

                                   HHHTS-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHC.....TESEEEEESSTSS---BHHHHHCT- CS
                        FMN_dh  85 akagipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaa.....gykalvltvDtpvlgkRerdlrngf 160
                                   +++g+ ++++++ ++++e+  ++       +++v++d++ ++ +  ++ aa     g++a+   vD+  +     +     
  gi|91774306|ref|YP_566998.1|  85 EELGVGIGVGSQ-RAAIEDPEQE------SSFSVVRDKAPNAFVYGNVGAAqikeyGIEAIEKLVDMLDAD----A----- 149
                                   ***********9.8999999774......468889999999888888887733333566666666654333....2..... PP

                                   -BSTT-T.G.TTGGGSTSGSCCTTH..THHHHHHCCCHB-TC--HHHHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTE CS
                        FMN_dh 161 slppklklrnllqelakpewaaealkkasaaaefvgkqldpsltwddikwlreqtklplvvKGv...ltaedakraveaGv 238
                                    l  +l+   +lqe+ +pe+  +a                     + ik++ + +++p++ K+    +++eda ++ eaGv
  gi|91774306|ref|YP_566998.1| 150 -LAVHLN---FLQEAIQPEGDRDAT-----------G------VLEMIKEVCS-LNVPIIAKETgagISKEDAALLKEAGV 208
                                   .333434...999*******99998...........2......2466788777.78999999998899************* PP

                                   SEEEE--GGG.........TSSTT---HHHCH.........HHH..HHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEE CS
                        FMN_dh 239 dgivvSNHGG.........RqldgapatidvL.........pei..veavggrievlvDgGirrGsDvlkAlalGAdavll 299
                                   ++i v   GG         R  d+  a  + L         p++  v ++++ ++v++ gG+r+G D++k l lGA a   
  gi|91774306|ref|YP_566998.1| 209 SAIDVGGVGGtswsgvevyRAHDSGDAISEDLgnlywdfgiPTVssVLECRSFVPVVATGGVRTGLDIAKSLSLGAYAASA 289
                                   *******************888888888888866566655555544555556799************************** PP

                                   SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCG CS
                        FMN_dh 300 GRpflyglaagGeeGvervleilraelertmallGvksvaeldrs 344
                                   + pf +g a+ G++ v + l+ + +el+ +m l+G+ +++el+ s
  gi|91774306|ref|YP_566998.1| 290 ALPF-VGPALIGADEVVSSLSKMLNELRVAMFLCGCGNINELRTS 333
                                   ****.899*********************************9876 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   3.7    0.0009       3.2       3     176 ..      27     218 ..      25     226 .. 0.65
   2 !   14.4   0.1     4e-06     0.014     189     232 ..     248     286 ..     242     306 .. 0.79
   3 !    9.8   0.0   9.9e-05      0.36     298     332 ..     303     337 ..     294     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0009
                                   -GGGEEEE---B.-S-GGGSB--EESSTTEEESSSEEE-SS.....T.TT-SHHHHHHHHHTT.SEEEE-SSS-HHH..HH CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxx.xxxxxxxxxxxxx..xx RF
                         IMPDH   3 tfddvllvpaks.evlpkevdlktkltkkiklniPlvsaam.....d.tvtesemAialareG.gigvihknlsiee..qa 73 
                                    fddv+l+ ++  ++  +e+dl+t++  k +l+ P++ a++     d t  ++ +A a  + G gigv  +   ie+  q 
  gi|91774306|ref|YP_566998.1|  27 GFDDVMLIHKALpQIHMDEIDLSTDFLGK-SLKAPFLIASItgghpDtTPVNAALAEAAEELGvGIGVGSQRAAIEDpeQE 106
                                   59***9999887689999*******9977.899999888763333332445777777777777788888888888752155 PP

                                   HHHHHHHTSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHT.T-SEEEEE-S........TS..SSHHHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........xx..xxxxxxxxxxxxxxxx RF
                         IMPDH  74 eevkkvkrspnaakdekgrllvgaavgvkedalervkalvea.gvdvlvvdsa........hg..hsekvleavkeikkkv 143
                                   ++ + v+   ++a ++     vgaa  +ke  +e +++lv+  ++d+l+v           +g    ++vle++ke+ +  
  gi|91774306|ref|YP_566998.1| 107 SSFSVVR---DKAPNAFVYGNVGAA-QIKEYGIEAIEKLVDMlDADALAVHLNflqeaiqpEGdrDATGVLEMIKEVCSLN 183
                                   5555665...334444555566766.4455667777777775367777776431111122233113345666666666444 PP

                                   TTSEEEE...EEE-SHHHHHHHHHTT-SEEEE-.SS- CS
                                   xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                         IMPDH 144 eevevia...GnvataegakaLieagadavkvG.iGp 176
                                     v +ia   G   ++e a+ L eag+ a+ vG +G 
  gi|91774306|ref|YP_566998.1| 184 --VPIIAketGAGISKEDAALLKEAGVSAIDVGgVGG 218
                                   ..777743338889999***************72444 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4e-06
                                   ---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 189 GvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGada 232
                                   G+p +++v+e+ ++     vpv+a GG+++  di+k+l++Ga a
  gi|91774306|ref|YP_566998.1| 248 GIPTVSSVLECRSF-----VPVVATGGVRTGLDIAKSLSLGAYA 286
                                   67777777777554.....9*********************976 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 9.9e-05
                                   -HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 298 svkevveqlvgglrsgmgylGaktieelkekakfv 332
                                   +v + +++++++lr +m  +G+ +i+el++++k++
  gi|91774306|ref|YP_566998.1| 303 EVVSSLSKMLNELRVAMFLCGCGNINELRTSSKVT 337
                                   56778999*********************988765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       1.2   4.4e+03     199     217 ..      67      85 ..      54      93 .. 0.77
   2 ?   -0.8   0.2      0.23   8.1e+02     177     220 ..     165     212 ..     157     217 .. 0.64
   3 !   21.2   0.1   4.5e-08   0.00016     185     227 ..     249     295 ..     245     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.2
                           NMO 199 aGGiidrrgvaaaLalGAs 217
                                   +GG  d   v+aaLa  A+
  gi|91774306|ref|YP_566998.1|  67 TGGHPDTTPVNAALAEAAE 85 
                                   6899999999999998887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.23
                           NMO 177 gdkglfaLvpqvldavd..iPviA..aGGiidrrgvaaaLalGAsgvq 220
                                   gd++ + +++ ++++ +  +P+iA  +G  i +++ a    +G s++ 
  gi|91774306|ref|YP_566998.1| 165 GDRDATGVLEMIKEVCSlnVPIIAkeTGAGISKEDAALLKEAGVSAID 212
                                   45677778888888888889**99554544444444333345555555 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 4.5e-08
                           NMO 185 vpqvldavd....iPviAaGGiidrrgvaaaLalGAsgvqigtrfLl 227
                                   +p+v ++++    +Pv+A+GG+ ++ ++a  L+lGA ++  +  f++
  gi|91774306|ref|YP_566998.1| 249 IPTVSSVLEcrsfVPVVATGGVRTGLDIAKSLSLGAYAASAALPFVG 295
                                   578888888888************************99986655554 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 !   14.3   0.9   4.6e-06     0.017     203     300 ..     183     287 ..     164     300 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-06
                                   TSEEEEE.EE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHH..........HHHHB-.--HHHHHHHHHHHHHHTT- CS
                  Glu_synthase 203 eakvsvK.lvaeagvetiaagvakanadiilidGleGGTGAspks..........sikhaG.lPlelalaevdqtlkeegl 271
                                   ++++  K  +a+   e+ a+ + +a++ +i + G+ GGT  s  +          + +  G l +  +++ v  +l   + 
  gi|91774306|ref|YP_566998.1| 183 NVPIIAKeTGAGISKEDAAL-LKEAGVSAIDVGGV-GGTSWSGVEvyrahdsgdaISEDLGnLYWDFGIPTVSSVL---EC 258
                                   56666652234444444444.66677777777665.3443222210000010111222223367889999999988...57 PP

                                   GGG-EEEEESS--SHHHHHHHHHHT-SEE CS
                  Glu_synthase 272 rdrvsliadGglktgadvvkalalGAdav 300
                                   r+ v + a+Gg++tg d++k+l lGA a 
  gi|91774306|ref|YP_566998.1| 259 RSFVPVVATGGVRTGLDIAKSLSLGAYAA 287
                                   999***********************765 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.79   2.8e+03       2      19 ..      48      65 ..      48      90 .. 0.78
   2 ?   -2.3   0.0      0.56     2e+03     217     242 ..     121     146 ..     105     149 .. 0.77
   3 ?    2.2   0.3     0.024        86     230     274 ..     169     215 ..     166     229 .. 0.80
   4 ?    9.5   0.0   0.00014       0.5     242     270 ..     259     287 ..     241     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.79
                                  G-EEETTEEESSSEEE-T CS
                        DHO_dh  2 latkvlglkfknpiglAa 19
                                  l+t++lg+ +k p+++A+
  gi|91774306|ref|YP_566998.1| 48 LSTDFLGKSLKAPFLIAS 65
                                  6789999*******9998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.56
                                   SSEEEEEGGGHHHHHHHHHHHHHHTT CS
                        DHO_dh 217 ktGGlsGkalkdialkvirelykrlk 242
                                     G ++ +++k+ +++ i +l ++l+
  gi|91774306|ref|YP_566998.1| 121 VYGNVGAAQIKEYGIEAIEKLVDMLD 146
                                   56888899999999999999988776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHTTT.S-EEE..ESS--SHHHHHHHHHHTECEEEESH CS
                        DHO_dh 230 alkvirelykrlkkeipiIg..vGGiesgeDalekieaGAslvqvyt 274
                                   a+ v+  ++++ + ++piI+  +G   s eDa    eaG s++ v+ 
  gi|91774306|ref|YP_566998.1| 169 ATGVLEMIKEVCSLNVPIIAkeTGAGISKEDAALLKEAGVSAIDVGG 215
                                   566777778888889****86567667899999999******99984 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00014
                                   TT.S-EEEESS--SHHHHHHHHHHTECEE CS
                        DHO_dh 242 kkeipiIgvGGiesgeDalekieaGAslv 270
                                   ++ +p++++GG+ +g D    +  GA + 
  gi|91774306|ref|YP_566998.1| 259 RSFVPVVATGGVRTGLDIAKSLSLGAYAA 287
                                   4479******************9999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2080.27
//
Query:       gi|91774307|ref|YP_566999.1|  [L=447]
Description: beta-lactamase-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-09   38.0   1.6    4.3e-09   36.2   0.1    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    9.9e-09   35.0   0.4    4.1e-08   33.0   0.1    2.1  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    9.8e-08   32.2   2.0    4.6e-07   30.0   2.0    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0061   16.7   0.0      0.016   15.3   0.0    1.7  1  Nkap_C         NF-kappa-B-activating protein C-terminal domai


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 !   36.2   0.1   9.6e-13   4.3e-09      30     143 ..      74     175 ..      62     191 .. 0.85
   2 ?    0.3   0.1     0.094   4.2e+02     167     200 ..     380     410 ..     356     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 9.6e-13
                                   SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE CS
                 Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatpa 110
                                    ++a++ th+H DH+  ++ l++++   +p+++++ ++a +++++  + +    + ++ ++++g++ +++d +++i+++ +
  gi|91774307|ref|YP_566999.1|  74 NVAAIVCTHGHLDHIGAIPKLAHRYT--APIIGTPYTAALIKQQIESERKFGV-KNKIIPIEAGGTYQIND-DVSIELIRV 150
                                   799********************544..89**************988888887.9**************97.89******* PP

                                   -EE--CTCCE-TTTSEEEEEECTTEEEEEESS- CS
                 Lactamase_B_2 111 rhksgrrldrnagdtlGlriegggkrvyyigDt 143
                                   +h+           ++ +++ ++  +v+y+ D 
  gi|91774307|ref|YP_566999.1| 151 QHSIID--------AVFVAVHTPVGAVLYACDF 175
                                   **9877........6666666666666666665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.094
                                   SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                 Lactamase_B_2 167 yeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                   y+d       gH+  e+ +e++++++++ +++ H
  gi|91774307|ref|YP_566999.1| 380 YDDVH---VSGHAYREDHWELLRMINPEHVIPAH 410
                                   44444...5688888*****************99 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.64   2.9e+03      34      50 ..      78      94 ..      71     126 .. 0.68
   2 !   33.0   0.1   9.2e-12   4.1e-08       9      54 ..     381     425 ..     376     436 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.64
                         RMMBL 34 vilvHGeeeatsalarl 50
                                  ++  HG+ +++ a  +l
  gi|91774307|ref|YP_566999.1| 78 IVCTHGHLDHIGAIPKL 94
                                  56667776666655444 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 9.2e-12
                         RMMBL   9 eeidfSgHadknellelirklkprnvilvHGeeeatsalarllkee 54 
                                   +++++SgHa+++++ el+r+++p++vi+ HG   + sa+ + + e+
  gi|91774307|ref|YP_566999.1| 381 DDVHVSGHAYREDHWELLRMINPEHVIPAHGNIGMHSAYIEMA-ED 425
                                   5789***************************999988887777.55 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   2.0     1e-10   4.6e-07       6      96 ..      17     126 ..      12     191 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1e-10
                                   SEEEEEEETTCEEEES--SCHHHHHHHH...................HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                   Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraal...................elaalglkpkdvdavilTHlHlDHiGglgglvea 67 
                                    n++ i+ d++ i++D G+  ++ ++ +                   +    +    +v a++ TH+HlDHiG+ ++l+++
  gi|91774307|ref|YP_566999.1|  17 RNMTAIRVDEDIIIVDMGLRLDRVQIHEdveidkmhsleliemgaipDDTIMKQVNGNVAAIVCTHGHLDHIGAIPKLAHR 97 
                                   677788888888888888888888877788888888888887777664444555567899********************* PP

                                   HCCEETCCEHHHHCCHCHHHHHHHHHCCH CS
                   Lactamase_B  68 tdvpvgavaeeapalfmeeaddaasrkgl 96 
                                   + +p++  + +a+  +   +       ++
  gi|91774307|ref|YP_566999.1|  98 YTAPIIGTPYTAALIKQQIESERKFGVKN 126
                                   ******99999988888888554444433 PP

>> Nkap_C  NF-kappa-B-activating protein C-terminal 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     0.016      18      54 ..     399     435 ..     386     443 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
                        Nkap_C  18 qyvqegkRiPrRGevGltseeiekfekaGyvmsGsrh 54 
                                   + ++ ++ iP  G++G++s  ie  e+aGy++  + h
  gi|91774307|ref|YP_566999.1| 399 RMINPEHVIPAHGNIGMHSAYIEMAEDAGYILGDTVH 435
                                   56788899***********************976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2831.02
//
Query:       gi|91774308|ref|YP_567000.1|  [L=322]
Description: farnesyltranstransferase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-69  232.1   0.0    7.1e-69  231.7   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
       0.12   11.9   0.0       0.23   10.9   0.0    1.5  1  SPO22            Meiosis protein SPO22/ZIP4 like
       0.19   11.5   0.0       0.33   10.7   0.0    1.4  1  DUF1131          Protein of unknown function (DUF1131)


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 !  231.7   0.0   1.2e-72   7.1e-69       2     227 ..      28     250 ..      27     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 1.2e-72
                                   HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHH CS
               polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnkl 82 
                                   e+l++a++yl +agGKrlRp++++l+ ea++ ++    ++  +a+++el+h+++LvhDDimD++++RRG p++h ++G + 
  gi|91774308|ref|YP_567000.1|  28 EELYRASRYLPDAGGKRLRPAVLMLSTEAVGGDP---MSVIPAAVALELVHNFTLVHDDIMDNDDVRRGMPAVHVKWGSEG 105
                                   68999**************************444...78****************************************** PP

                                   HHHHHHHHHHHHHHHHHHHH..STT..HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHH CS
               polyprenyl_synt  83 Aindgdfllarafellaklf..eks..lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpv 159
                                   Ai++gd l+++afe+l+ +     +  l++++l+s+++++++eGq +d+e e++d++s   +eeyle+v++KT++l+ +++
  gi|91774308|ref|YP_567000.1| 106 AILAGDTLYSKAFEILSVMEkdP-EriLKCVALLSRTCTEICEGQWMDIEFENRDTVS---EEEYLEMVEKKTSVLYGAAA 182
                                   *****************998752.3469*********************999999999...******************** PP

                                   HHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT CS
               polyprenyl_synt 160 alaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalela 227
                                   +++all+gasde+++a++++g+ +G+ FQiqDD++D+++ ++ lgK+ g+D+ egk tl++++al++ 
  gi|91774308|ref|YP_567000.1| 183 KVGALLGGASDEVADAMYEFGRLVGISFQIQDDVIDMVTPEDILGKVRGSDLIEGKRTLIAIHALNHG 250
                                   *********99******************************************************954 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.9e-05      0.23     100     164 ..     125     187 ..     114     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.9e-05
                         SPO22 100 eesyekalkavellqkeygkkehpsllllklkillkreadeeeieealeemidsvelseanfkli 164
                                   e++ e+ lk+v ll+  ++  e  ++ ++ ++   +++++eee++e++e+  + + ++ a++ ++
  gi|91774308|ref|YP_567000.1| 125 EKDPERILKCVALLSRTCT--EICEGQWMDIEFENRDTVSEEEYLEMVEKKTSVLYGAAAKVGAL 187
                                   6788***********8888..**************************998766555555555555 PP

>> DUF1131  Protein of unknown function (DUF1131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.5e-05      0.33     106     146 ..     111     151 ..      80     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.5e-05
                       DUF1131 106 sdlyskafgaCkkgseddeesveCkapqskhvsyvfsGeWe 146
                                   + lyskaf+  +  ++d e+ ++C+a  s+  + + +G+W 
  gi|91774308|ref|YP_567000.1| 111 DTLYSKAFEILSVMEKDPERILKCVALLSRTCTEICEGQWM 151
                                   469*************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2021.78
//
Query:       gi|91774309|ref|YP_567001.1|  [L=549]
Description: type II secretion system protein E [Methanococcoides burtonii DSM 6242]
Scores for complete 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-41  141.2   0.0      6e-41  140.3   0.0    1.4  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
        0.2   11.4   0.4       0.52   10.1   0.0    1.8  2  AAA_29    P-loop containing region of 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 !  140.3   0.0   6.7e-45     6e-41      36     248 ..     190     408 ..     160     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 6.7e-45
                         T2SSE  36 lreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvag..ealviRkksakeltlddlgaeeal 114
                                   +++  + e++ l+ ++ ++ + ++++is   p++da+lp +g rl++ l   + +   ++ iRk ++  +t  dl   ++ 
  gi|91774309|ref|YP_567001.1| 190 IKTNISFEESRLNSFVINLCQKSGKHISIGDPMIDATLP-DGSRLQATLGKEITTrgSSFDIRKFKSDPITPIDLLEFGTC 269
                                   555566777888888899999******************.*******998766665699********************** PP

                         T2SSE 115 kekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak.......kakvtf 188
                                   + ++      a+++  + +++GgT sGKt ll+a+  +i+    +iv +ED++E+ l+++n ++  ++       +++vt+
  gi|91774309|ref|YP_567001.1| 270 SSEMLGYFWLAIENGFSAIFAGGTASGKTSLLNAVSLFIPPL-SKIVSIEDTREVMLHHDNWIAGLTResvtdsgAGEVTM 349
                                   ******************************************.********************9888889999999***** PP

                         T2SSE 189 adllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeqlga 248
                                    dll+a+LR+rP  i+vGE+R+ke+l++ +A++TGH    sT+Ha++++ +++rLe+   
  gi|91774309|ref|YP_567001.1| 350 FDLLKASLRQRPESILVGEVRGKEALTLFQALSTGHTT-YSTMHAGDVQTVVNRLENEPI 408
                                   **************************************.****************98654 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 ?   10.1   0.0   5.8e-05      0.52      22      48 ..     283     310 ..     275     315 .. 0.81
   2 ?   -2.9   0.1      0.67     6e+03      30      42 ..     341     353 ..     340     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.8e-05
                        AAA_29  22 kg.atlltGpsGsGKSTllDAiqalLvp 48 
                                   +g + +++G + sGK++ll A++  + p
  gi|91774309|ref|YP_567001.1| 283 NGfSAIFAGGTASGKTSLLNAVSLFIPP 310
                                   5667899**************9866555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.67
                        AAA_29  30 psGsGKSTllDAi 42 
                                   +sG+G  T++D +
  gi|91774309|ref|YP_567001.1| 341 DSGAGEVTMFDLL 353
                                   699******9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3579.07
//
Query:       gi|91774310|ref|YP_567002.1|  [L=647]
Description: type II secretion system protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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  118.4   4.4    5.6e-16   58.6   2.5    3.1  2  T2SSF        Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.011   16.3   1.8        3.2    8.4   0.4    3.1  2  DUF1279      Protein of unknown function (DUF1279)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   7.7e-20   6.9e-16       5     124 ..     137     263 ..     134     264 .. 0.92
   2 !   58.6   2.5   6.2e-20   5.6e-16       1     124 [.     444     570 ..     444     571 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 7.7e-20
                                   HHHHHH.TT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HH CS
                         T2SSF   5 latlls.aGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnLa 78 
                                   ++ l++ +Gv++ +a+++l+e+++ +g  a+e+ +i+r++++ g ++  a++     t s+ ++ +++ ++ ++++gg+L 
  gi|91774310|ref|YP_567002.1| 137 MYALTKsGGVTVHDAFRSLSEHSHvYGLAADEFGYIVRDMDYFGmDVLSAIRncssTTSSTNLKAFLDGILFVISSGGDLN 217
                                   666666599*********************************987888888899976666899****************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  79 evLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                    +L+   +++  ++  ++k ++++l++l++++va++v++++++i++
  gi|91774310|ref|YP_567002.1| 218 SYLRSKTDQFHLDATKQQKTFLEMLGVLAEAYVAVFVVGPIFMIII 263
                                   *****************************************99986 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 6.2e-20
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT- CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageeggn 76 
                                   fl+ la+  +aG+ l +a+ ++a+++  g+l+ e++r+ + l++G++ls ++     r + + + ++ ++ l+ a e++++
  gi|91774310|ref|YP_567002.1| 444 FLNRLASINEAGILLIDAINMVAQTK-IGVLQSEVRRMQKGLSWGQDLSSVFMefesRVK-TTMnSRIITLLVKASESTSD 522
                                   8999**********************.**************************7774333.6888**************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                   +  vL+ +a++ e +++lr+++ ++++ +l+++++ ++v+l+++ +l+
  gi|91774310|ref|YP_567002.1| 523 IIGVLHIAAKDAELQQNLRKERSTEMAVYLFIVYISFAVFLFIIYVLT 570
                                   *******************************************99875 PP

>> DUF1279  Protein of unknown function (DUF1279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0019        17      30      87 ..     207     264 ..     134     269 .. 0.91
   2 ?    8.4   0.4   0.00036       3.2      33      91 ..     517     575 ..     500     576 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0019
                       DUF1279  30 YllvksgvdveelleklklsvkvsskkvekksksswgefaiAYaihKilipiRlpiTl 87 
                                    ++++sg d++++l++   +++ + +k +k   +++g +a AY++  ++ pi + i l
  gi|91774310|ref|YP_567002.1| 207 LFVISSGGDLNSYLRSKTDQFHLDATKQQKTFLEMLGVLAEAYVAVFVVGPIFMIIIL 264
                                   467788**********99999*999999999999**********99888888766655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00036
                       DUF1279  33 vksgvdveelleklklsvkvsskkvekksksswgefaiAYaihKilipiRlpiTlaitp 91 
                                    +s  d++ +l++   + + +++  +++s++++  ++i Y+   ++++i +++T+  +p
  gi|91774310|ref|YP_567002.1| 517 SESTSDIIGVLHIAAKDAELQQNLRKERSTEMAVYLFIVYISFAVFLFIIYVLTAYFIP 575
                                   334889999999999999999**********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4145.35
//
Query:       gi|91774311|ref|YP_567003.1|  [L=301]
Description: hypothetical protein Mbur_2402 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   16.4   0.2     0.0083   15.1   0.0    1.7  2  Arylsulfotrans  Arylsulfotransferase (ASST)
  ------ inclusion threshold ------
      0.037   15.0   1.3       0.13   13.2   0.6    2.2  2  Pilin_N         Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0     0.098   8.7e+02      67      82 ..      44      60 ..      29      74 .. 0.75
   2 !   15.1   0.0   9.2e-07    0.0083      14      68 ..     113     166 ..     102     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.098
                Arylsulfotrans 67 qklaefdllGrvike.y 82
                                  + +aefd++G v+++  
  gi|91774311|ref|YP_567003.1| 44 KTAAEFDHMGDVYEDmS 60
                                  67899*****9998744 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.2e-07
                Arylsulfotrans  14 drLylvnnlewdekknnlivDtkGevrWyldqdkisdnklkrlkngkllilsgqk 68 
                                    ++y+  + +++ + +n+++D+ G +r+  ++  ++d++   l+ng+l+i++g++
  gi|91774311|ref|YP_567003.1| 113 VGMYITAEDQSNGTIYNYVLDDLGSIRYSSNNRYFMDQS-FVLENGALFIVQGNR 166
                                   567888888999*************************98.579*********954 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   1.4e-05      0.13       2      26 ..      14      38 ..      13      72 .. 0.89
   2 ?   -0.9   0.0      0.37   3.4e+03      39      65 ..     251     277 ..     244     281 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                       Pilin_N  2 AVSpViGviLmvaitvIlaAviaaf 26
                                  A+S V+ viL++ + v ++Av+ + 
  gi|91774311|ref|YP_567003.1| 14 AISTVVSVILLLGLAVAMMAVFNVT 38
                                  9********************9875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                       Pilin_N  39 qasievkidssastgknavslehkgGd 65 
                                   +a +    +++ +t++n+v+l   +G+
  gi|91774311|ref|YP_567003.1| 251 KAGLVSPAEYNVTTSNNNVTLSLYSGN 277
                                   555544467777788888999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1570.29
//
Query:       gi|91774312|ref|YP_567004.1|  [L=371]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-33  115.1   1.3    2.4e-33  115.0   0.1    1.7  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.3e-18   66.8   0.1    2.5e-18   65.9   0.1    1.5  1  HisKA        His Kinase A (phospho-acceptor) domain
    4.1e-09   36.6   0.1    1.1e-08   35.2   0.1    1.8  1  PAS_9        PAS domain
    4.7e-08   33.3   0.0    7.2e-08   32.7   0.0    1.3  1  PAS_4        PAS fold
    5.4e-08   32.8   0.0    1.3e-07   31.6   0.0    1.7  1  PAS          PAS fold
    7.1e-07   29.1   0.0    1.4e-06   28.2   0.0    1.4  1  PAS_8        PAS domain
    0.00054   19.9   0.0     0.0013   18.7   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
    0.00085   19.2   0.0     0.0023   17.8   0.0    1.7  1  HATPase_c_5  GHKL domain
      0.003   17.4   0.2     0.0084   15.9   0.0    1.8  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.039   14.0   0.5      0.088   12.8   0.5    1.5  1  DUF1216      Protein of unknown function (DUF1216)


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 ?   -3.5   0.1       7.9   1.4e+04       6      31 ..     186     208 ..     176     223 .. 0.51
   2 !  115.0   0.1   1.3e-36   2.4e-33       2     109 ..     249     357 ..     248     360 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.9
                                   HHHHHHHHHHHHHHHHSTTTEEEEEE CS
                     HATPase_c   6 LrqiisnlvdNavkfatkageievei 31 
                                   L  ii+ +++++  +   +g+ e++i
  gi|91774312|ref|YP_567004.1| 186 LLNIINDILSASQIE---TGKMELHI 208
                                   444444444444433...33333333 PP

  == domain 2  score: 115.0 bits;  conditional E-value: 1.3e-36
                                   HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHH CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsiv 81 
                                   d ++++qii nlv Na+kf+++++++e++ + s+d ++isv+D+GiGi+++d++klf++f q d+s++r++ggtGlGl+iv
  gi|91774312|ref|YP_567004.1| 249 DATKFEQIIYNLVNNAIKFTNEGEKVEIRGEISDDFVHISVKDSGIGISPDDQNKLFTPFFQvDSSNTREYGGTGLGLAIV 329
                                   78899**************7788899998887789********************************************** PP

                                   HHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  82 kklvelmgGeiwvesepgrGttftftlp 109
                                   kk+ve++gG++wvese g+G+tf f++p
  gi|91774312|ref|YP_567004.1| 330 KKYVEMHGGKVWVESEVGKGSTFGFRMP 357
                                   ***********************99988 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 !   65.9   0.1   1.4e-21   2.5e-18       1      67 []     134     202 ..     134     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.4e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                         HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                   s+++fla+++HELrtPL++i+g+++++++e  g+l+e +k+++  ++s++++l+++++d+L  s+ie+g
  gi|91774312|ref|YP_567004.1| 134 SKSEFLANMSHELRTPLNSIIGFSDVISNEshGSLNELQKKFISNVISNGKHLLNIINDILSASQIETG 202
                                   799************************88899**********************************987 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   6.3e-12   1.1e-08       2     104 .]      14     113 ..      13     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 6.3e-12
                         PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                   dgili++ dgr l +N+  ++ lGy++ e+l+  + d+  +++ ++   ++++  +++    ve++ i k+g+ ++++l++
  gi|91774312|ref|YP_567004.1|  14 DGILIITLDGRFLEVNQITCDDLGYQRHELLQMTVMDIT-PPEFREMARENVIGKMKQGGGIVETISICKDGSLVPIELNI 93 
                                   89***99********************************.33333344444444444499********************* PP

                         PAS_9  83 spvkdddgelvgiivilrDite 104
                                    p+  ++   ++  ++ r+ite
  gi|91774312|ref|YP_567004.1|  94 HPIEYNGAPAIL--AVARNITE 113
                                   ***888877777..*******8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     4e-11   7.2e-08       1     109 [.       9     115 ..       9     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4e-11
                         PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleral.rrvlegeepiefleelllpgeerh 80 
                                   ++s++d+++++  dgr+l +N+  ++ +g++++ell +t+ ++ p+e ++  ++++  ++ +g+  +e+  + + +g+ ++
  gi|91774312|ref|YP_567004.1|   9 FNSVNDGILIITLDGRFLEVNQITCDDLGYQRHELLQMTVMDITPPEFREMARENViGKMKQGGGIVETISICK-DGSLVP 88 
                                   789********************************************777766665156666665555555555.5***** PP

                         PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                   +el+++P+ + +G   ++l+++r iTer+
  gi|91774312|ref|YP_567004.1|  89 IELNIHPI-EYNGA-PAILAVARNITERK 115
                                   ********.45666.*************8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   7.3e-11   1.3e-07       3     101 ..       5     101 ..       3     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.3e-11
                                   HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTT CS
                           PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrd 83 
                                   ++++++s  d+i+++  dgr+l+vN+ +++ lG++r e+l  +++ +i +++ +e+a++       +  +  + is+++ d
  gi|91774312|ref|YP_567004.1|   5 YETVFNSVNDGILIITLDGRFLEVNQITCDDLGYQRHELLQMTVM-DITPPEFREMARENVIGKMKQGGGIVETISICK-D 83 
                                   88999**********************************977777.555554443333333333333333333455555.* PP

                                   SSEEEEEEEEEEEEETTE CS
                           PAS  84 grpihlevraspvrdagg 101
                                   g+ +++e++ +p+   g 
  gi|91774312|ref|YP_567004.1|  84 GSLVPIELNIHPIEYNGA 101
                                   ************987765 PP

>> 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   7.6e-10   1.4e-06       3      57 ..       5      57 ..       3      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 7.6e-10
                         PAS_8  3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57
                                  ++++f+s++dgi+++ l++r+++vNq +++ lGy   +l+ +   ++++  +p+++
  gi|91774312|ref|YP_567004.1|  5 YETVFNSVNDGILIITLDGRFLEVNQITCDDLGYQrHELLQM---TVMDITPPEFR 57
                                  99************998889*************883333333...66666666666 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     7e-07    0.0013      39     110 ..     260     334 ..     248     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7e-07
                   HATPase_c_2  39 actNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGlalikglvD 110
                                   +++Na++  ++    ++ve+r e++++ ++++v+DsG g  p ++++     p        + +    G+Gla++k++v+
  gi|91774312|ref|YP_567004.1| 260 LVNNAIKFTNE---GEKVEIRGEISDDFVHISVKDSGIGISPDDQNKLFT--PffqvdssnTREYGGTGLGLAIVKKYVE 334
                                   35566666665...688**********************99987776554..3468888777777888999999999985 PP

>> HATPase_c_5  GHKL 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    0.0023       6      90 ..     253     345 ..     248     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                   HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek.......kklesskskkeehGiGlksi 74 
                                   +  i+ nl +NAi   ++ e    ++++  + +++++ is++ s  g     ++       +   s++++ +  G+Gl  +
  gi|91774312|ref|YP_567004.1| 253 FEQIIYNLVNNAIKFTNEGE----KVEIRGEISDDFVHISVKDSGIGispddQNklftpffQVDSSNTREYGGTGLGLAIV 329
                                   567999*******9888866....6888888999999999999966655554222344343444466777888999***** PP

                   HATPase_c_5  75 reivkkykgnlsieae 90 
                                   ++ v+ ++g++++e e
  gi|91774312|ref|YP_567004.1| 330 KKYVEMHGGKVWVESE 345
                                   ************9986 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 ?   -2.6   0.0       2.6   4.6e+03      80     119 ..     103     142 ..     100     153 .. 0.66
   2 !   15.9   0.0   4.7e-06    0.0084       3      81 ..     253     328 ..     251     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                   HATPase_c_3  80 Aslslgkkltvitkkegesstltldvdkidkenekvleel 119
                                   A+l +++++t   k+e+ +  ++l  ++ +k++++ l+++
  gi|91774312|ref|YP_567004.1| 103 AILAVARNITERKKAEEAMLSAKLAAEDANKSKSEFLANM 142
                                   5666777777777777777777777777666666666555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.7e-06
                   HATPase_c_3   3 lekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlklAs 81 
                                   +e+ +  lv+N++    + e+v+i  +  + +   i+++D G G+s+++  + +++  +  +  ++ + +G  G+G  lA+
  gi|91774312|ref|YP_567004.1| 253 FEQIIYNLVNNAIKftNEGEKVEIRGEISD-DFVHISVKDSGIGISPDDQNKLFTPFFQVDS--SNTREYGGTGLG--LAI 328
                                   56778899****984344555666555443.4589*****************9998888877..478899999999..555 PP

>> DUF1216  Protein of unknown function (DUF1216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   4.9e-05     0.088      20     120 ..     172     268 ..     157     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                       DUF1216  20 ekeyvsdmkskagklseamavlasklsksgevkkslqeeqqevmktlkelqsvaskivsekkskkegsltltseqqkeike 100
                                   +k++ s+++s  ++l + ++ + s  s+ +  k +l+ ++  v ++++e++ ++  i sek+ + +  + +      +i+ 
  gi|91774312|ref|YP_567004.1| 172 QKKFISNVISNGKHLLNIINDILS-ASQIETGKMELHISEFHVSESINEIEVLMIPIASEKNIELKFNIDIG---MPNIRA 248
                                   899****************99998.78888899999999*********************999955444444...468*** PP

                       DUF1216 101 tilkweqvitqfvetavese 120
                                     +k+eq+i  +v++a++ +
  gi|91774312|ref|YP_567004.1| 249 DATKFEQIIYNLVNNAIKFT 268
                                   ****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); 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:                        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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2031.72
//
Query:       gi|91774313|ref|YP_567005.1|  [L=353]
Description: radical SAM family Fe-S protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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-20   71.8   0.0    8.2e-20   71.8   0.0    2.6  2  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.015   15.3   0.2      0.015   15.3   0.2    2.8  3  DZR            Double zinc ribbon
       0.04   14.2   0.9          6    7.3   0.4    3.5  2  GFA            Glutathione-dependent formaldehyde-activating 
      0.044   14.1   2.0       0.13   12.5   0.0    2.6  3  Fer4_12        4Fe-4S single cluster domain
       0.11   11.1   0.1       0.13   10.9   0.1    1.2  1  Prismane       Prismane/CO dehydrogenase family
       0.45   10.1   8.7        1.7    8.3   0.0    2.9  3  zf_C2H2_13     Zinc finger domain
       0.73    9.9   4.6         24    5.1   0.1    3.2  3  Elf1           Transcription elongation factor Elf1 like
       0.98    9.5   0.1       0.98    9.5   0.1    3.0  3  Ogr_Delta      Ogr/Delta-like zinc finger
          1    9.4   7.6        1.4    8.9   0.2    3.3  3  Nudix_N_2      Nudix N-terminal
        1.1    9.1  14.4       0.99    9.2   0.8    3.5  3  zinc_ribbon_2  zinc-ribbon domain
        4.5    7.5   7.4        2.8    8.1   0.4    3.1  3  DiS_P_DiS      Bacterial Peptidase A24 N-terminal domain
        4.6    6.8  17.9       0.62    9.5   0.2    3.7  4  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   5.5e-23   8.2e-20       5     166 ..      93     245 ..      91     249 .. 0.89
   2 ?   -0.1   0.0       0.7     1e+03     119     148 ..     269     299 ..     257     307 .. 0.72

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 5.5e-23
                                   SEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                    gCn+rC++C+++     + +e  + ++++e+ +e + +     g++ + ++  ep+ +++++ + ++lak+  +g+ +++
  gi|91774313|ref|YP_567005.1|  93 IGCNFRCKHCQNWIIsqvGLDEANSIEITPEQAVERALAT----GCRSIAWTYNEPTIWYEYTYDSAKLAKE--AGLDTVY 167
                                   59***********986655556666666666666666555....5***************************..7****** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleel 163
                                   +tng+   +e le + ++  d + ++++a++++ + k +  g  +  vle+ ++++e+g++ v ++ +++p  nd+e +el
  gi|91774313|ref|YP_567005.1| 168 VTNGYIT-PEALEHISPYL-DAFRVDIKAFSEK-FYKEV-VGARLAPVLESAKLAKELGMH-VEVVNLVIPTLNDSE-DEL 242
                                   ******8.*********99.*************.*****.99*******************.9***********988.777 PP

                                   HHH CS
                                   xxx RF
                   Radical_SAM 164 lel 166
                                   +el
  gi|91774313|ref|YP_567005.1| 243 REL 245
                                   664 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.7
                                   HHHT.CTSHHHHHHHHHHHHHHTTSETEEEE CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 119 klmn.rghtfeevlealeklreagikrvvdr 148
                                   k+++ ++  +e + +a +++ +ag+k v+++
  gi|91774313|ref|YP_567005.1| 269 KMNHlPPTPVETLEKAHQIALDAGLKYVYIG 299
                                   5555677788999999999999999964443 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.76   1.1e+03      28      41 ..      27      40 ..       9      48 .. 0.67
   2 ?   -0.4   0.1       0.8   1.2e+03      31      35 ..      99     103 ..      75     109 .. 0.78
   3 ?   15.3   0.2     1e-05     0.015      13      40 ..     309     346 ..     303     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.76
                           DZR 28 edrCpsCgekvdpe 41
                                  + rC  C++ +   
  gi|91774313|ref|YP_567005.1| 27 NVRCNLCNHRCRIS 40
                                  56777777776554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.8
                           DZR  31 CpsCg 35 
                                   C +C+
  gi|91774313|ref|YP_567005.1|  99 CKHCQ 103
                                   44443 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1e-05
                           DZR  13 rfCseCgtklkavaa...........edrCpsCgekvdp 40 
                                    fC+ Cg+++                 ++C +Cg++++ 
  gi|91774313|ref|YP_567005.1| 309 TFCPSCGKPVIVR-GvfdvqdqaltpDNKCRNCGAPISI 346
                                   69*******9844.358999999**999******99875 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.34     5e+02      51      61 ..      98     108 ..      56     123 .. 0.78
   2 ?    7.3   0.4     0.004         6      44      62 ..     303     321 ..     279     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                           GFA  51 fCpeCgsplys 61 
                                    C++C+  ++s
  gi|91774313|ref|YP_567005.1|  98 RCKHCQNWIIS 108
                                   46666666654 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.004
                           GFA  44 gnkvtrsfCpeCgsplyse 62 
                                   g++ + +fCp+Cg p++++
  gi|91774313|ref|YP_567005.1| 303 GHEYEITFCPSCGKPVIVR 321
                                   6677789*******99875 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 ?   -2.2   0.6       3.1   4.7e+03      12      20 ..      30      38 ..      23      45 .. 0.71
   2 ?   12.5   0.0   8.7e-05      0.13       6     101 ..      86     179 ..      82     201 .. 0.68
   3 ?   -0.7   0.0       1.1   1.6e+03      64      94 ..     234     264 ..     233     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                       Fer4_12 12 vsgCnlsCk 20
                                   + Cn++C+
  gi|91774313|ref|YP_567005.1| 30 CNLCNHRCR 38
                                  445888887 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.7e-05
                       Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                   +++sl + gCn++Ck C n  + ++   +  + + + e+++e++  +  + +  +  EP     +e  ++ +k  ke++++
  gi|91774313|ref|YP_567005.1|  86 LVYSLGTIGCNFRCKHCQNWIISQVGLDEANSiEITPEQAVERALATGCRSIAWTYNEPTI--WYEYTYDSAKLAKEAGLD 164
                                   56777789**********9998877655444434444555555556677778888888888..556667777777777774 PP

                       Fer4_12  86 kdiwlytgytleelsk 101
                                    ++ +++gy+  e ++
  gi|91774313|ref|YP_567005.1| 165 -TVYVTNGYITPEALE 179
                                   .777888887777665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                       Fer4_12  64 llpenaeallelvkevkeekpekdiwlytgy 94 
                                    l    ++l el k+v e+  e++ + +t +
  gi|91774313|ref|YP_567005.1| 234 TLNDSEDELRELSKWVFENLGENTPVHFTRF 264
                                   5656678999********9999899988865 PP

>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1     9e-05      0.13       3      88 ..      30     116 ..      28     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9e-05
                                   E-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTS..TTTB-SHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                      Prismane   3 CrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktl..tnvnfddekklkrlaea 81 
                                   C++C+   Cri+k k+G+CG+ ++       li+++    a+    ++ + ++   +l  +l     nf+ ++  +++  +
  gi|91774313|ref|YP_567005.1|  30 CNLCN-HRCRISKGKTGICGVRENRDGTLYSLIYAMVSSEAVDPIEKKPLFHFNPGSLVYSLgtIGCNFRCKHCQNWIISQ 109
                                   88886.68************9998777777777766554444433333333333333322220025566666666666666 PP

                                   HCHHHCC CS
                                   xxxxxxx RF
                      Prismane  82 lgieeel 88 
                                   +g++e+ 
  gi|91774313|ref|YP_567005.1| 110 VGLDEAN 116
                                   6666555 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.7       5.7   8.5e+03      15      23 ..      95     102 ..      89     104 .. 0.67
   2 ?    8.3   0.0    0.0011       1.7      19      32 ..     310     323 ..     298     326 .. 0.77
   3 ?    6.7   0.4    0.0036       5.3      20      30 ..     337     347 ..     336     348 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.7
                    zf_C2H2_13  15 lnYRvCnkC 23 
                                    n+R C++C
  gi|91774313|ref|YP_567005.1|  95 CNFR-CKHC 102
                                   5677.7777 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                    zf_C2H2_13  19 vCnkCGkPisleai 32 
                                    C +CGkP+ +  +
  gi|91774313|ref|YP_567005.1| 310 FCPSCGKPVIVRGV 323
                                   5*******987655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0036
                    zf_C2H2_13  20 CnkCGkPisle 30 
                                   C +CG Pis++
  gi|91774313|ref|YP_567005.1| 337 CRNCGAPISIY 347
                                   9*******986 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.062        92      40      57 ..      22      39 ..      12      44 .. 0.79
   2 ?    1.6   0.0      0.19   2.9e+02      21      40 ..      96     115 ..      89     122 .. 0.73
   3 ?    5.1   0.1     0.016        24      24      54 ..     311     343 ..     304     350 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.062
                          Elf1 40 kekiaevsCkvCgesfet 57
                                  k + ++v+C+ C+ ++++
  gi|91774313|ref|YP_567005.1| 22 KLEGGNVRCNLCNHRCRI 39
                                  556789999999998875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.19
                          Elf1  21 kFdCpfCnheksvevkldkk 40 
                                   +F+C +C++    +v ld+ 
  gi|91774313|ref|YP_567005.1|  96 NFRCKHCQNWIISQVGLDEA 115
                                   79999999875556666655 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.016
                          Elf1  24 CpfCnheksvevkldkkek..iaevsCkvCges 54 
                                   Cp C++   v+  +d +++  +   +C++Cg+ 
  gi|91774313|ref|YP_567005.1| 311 CPSCGKPVIVRGVFDVQDQalTPDNKCRNCGAP 343
                                   *******999988888888778999*****985 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   1.3       1.3     2e+03       1      13 [.      29      41 ..      29      44 .. 0.87
   2 ?   -1.0   0.1       1.2   1.9e+03       1       9 [.      98     106 ..      98     108 .. 0.83
   3 ?    9.5   0.1   0.00065      0.98       2      35 ..     311     342 ..     310     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                     Ogr_Delta  1 rCPhCgapaaart 13
                                  rC +C ++ ++++
  gi|91774313|ref|YP_567005.1| 29 RCNLCNHRCRISK 41
                                  7999***999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                     Ogr_Delta   1 rCPhCgapa 9  
                                   rC hC++++
  gi|91774313|ref|YP_567005.1|  98 RCKHCQNWI 106
                                   799**9875 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00065
                     Ogr_Delta   2 CPhCgapaaartsrnlskdvreryyqCsnfeCga 35 
                                   CP Cg+p  +r +     +     + C+n  Cga
  gi|91774313|ref|YP_567005.1| 311 CPSCGKPVIVRGVFDVQDQALTPDNKCRN--CGA 342
                                   ****************************9..998 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       1.8   2.7e+03      24      29 ..      98     103 ..      97     104 .. 0.74
   2 ?    8.9   0.2   0.00094       1.4       2      11 ..     310     319 ..     309     324 .. 0.87
   3 ?    3.3   0.1     0.054        80       3      11 ..     337     345 ..     336     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                                   EETTTT CS
                     Nudix_N_2  24 vCpaCg 29 
                                   +C++C+
  gi|91774313|ref|YP_567005.1|  98 RCKHCQ 103
                                   688886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00094
                                   B-TTT--B-E CS
                     Nudix_N_2   2 FCsqCGtpve 11 
                                   FC++CG+pv 
  gi|91774313|ref|YP_567005.1| 310 FCPSCGKPVI 319
                                   9*******85 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.054
                                   -TTT--B-E CS
                     Nudix_N_2   3 CsqCGtpve 11 
                                   C++CG+p++
  gi|91774313|ref|YP_567005.1| 337 CRNCGAPIS 345
                                   9*****976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.3       1.1   1.6e+03       1       6 [.      98     103 ..      98     104 .. 0.80
   2 ?    9.2   0.8   0.00066      0.99      15      22 ..     310     317 ..     309     318 .. 0.53
   3 ?    7.6   0.4    0.0021       3.1       1       9 [.     336     344 ..     335     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                 zinc_ribbon_2   1 fCpnCG 6  
                                   +C++C 
  gi|91774313|ref|YP_567005.1|  98 RCKHCQ 103
                                   6****6 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00066
                 zinc_ribbon_2  15 FCpyCGtp 22 
                                   FCp CG p
  gi|91774313|ref|YP_567005.1| 310 FCPSCGKP 317
                                   55555555 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0021
                 zinc_ribbon_2   1 fCpnCGael 9  
                                   +C nCGa++
  gi|91774313|ref|YP_567005.1| 336 KCRNCGAPI 344
                                   799999987 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 ?   -1.3   0.2       1.6   2.4e+03      28      38 ..      28      38 ..      20      42 .. 0.70
   2 ?    1.9   0.1      0.16   2.4e+02      52      68 ..      96     112 ..      86     120 .. 0.75
   3 ?    8.1   0.4    0.0019       2.8      29      64 ..     310     346 ..     299     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                     DiS_P_DiS 28 SrCpkCghklk 38
                                   rC+ C+h+ +
  gi|91774313|ref|YP_567005.1| 28 VRCNLCNHRCR 38
                                  46777777655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                     DiS_P_DiS  52 rgrCraCkakislrypl 68 
                                     rC++C++ i  +  l
  gi|91774313|ref|YP_567005.1|  96 NFRCKHCQNWIISQVGL 112
                                   56999999988766655 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0019
                     DiS_P_DiS  29 rCpkCghklkwleliPvlSy.lllrgrCraCkakisl 64 
                                    Cp+Cg+++ ++    v    l+   +Cr+C+a+is+
  gi|91774313|ref|YP_567005.1| 310 FCPSCGKPVIVRGVFDVQDQaLTPDNKCRNCGAPISI 346
                                   6888888888888888886525567899999999997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.9      0.93   1.4e+03       3      10 ..      28      35 ..      26      43 .. 0.81
   2 ?   -1.3   0.5       1.1   1.6e+03      19      23 ..      99     103 ..      98     104 .. 0.84
   3 ?    9.5   0.2   0.00042      0.62       4      11 ..     310     317 ..     308     321 .. 0.71
   4 ?    8.7   0.4   0.00079       1.2      16      26 .]     334     344 ..     332     344 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.93
                   zf-ribbon_3  3 vrCPnCGa 10
                                  vrC+ C++
  gi|91774313|ref|YP_567005.1| 28 VRCNLCNH 35
                                  89**9*98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                   zf-ribbon_3  19 CpyCG 23 
                                   C++C+
  gi|91774313|ref|YP_567005.1|  99 CKHCQ 103
                                   99996 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00042
                   zf-ribbon_3   4 rCPnCGap 11 
                                   +CP+CG+p
  gi|91774313|ref|YP_567005.1| 310 FCPSCGKP 317
                                   67777775 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00079
                   zf-ribbon_3  16 dnvCpyCGtkl 26 
                                   dn+C +CG+++
  gi|91774313|ref|YP_567005.1| 334 DNKCRNCGAPI 344
                                   89******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 1949.96
//
Query:       gi|91774314|ref|YP_567006.1|  [L=110]
Description: ArsR family transcriptional regulator [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-12   46.5   1.9    3.9e-12   45.8   1.9    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    2.2e-08   34.1   0.0    2.8e-08   33.7   0.0    1.2  1  HTH_20           Helix-turn-helix domain
    5.8e-05   23.2   0.1      9e-05   22.6   0.1    1.3  1  HTH_34           Winged helix DNA-binding domain
     0.0025   17.5   0.0      0.003   17.2   0.0    1.1  1  SMC_ScpB         Segregation and condensation complex subunit
     0.0034   17.7   0.0     0.0055   17.0   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.025   14.1   0.1      0.027   14.0   0.1    1.1  1  DUF1700          Protein of unknown function (DUF1700)
      0.026   14.4   0.0      0.046   13.6   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.026   14.2   0.2      0.032   13.9   0.2    1.1  1  OFeT_1           Ferrous iron uptake permease, iron-lead tran
      0.028   14.1   0.0      0.039   13.6   0.0    1.3  1  RP-C             Replication protein C N-terminal domain
      0.034   13.7   0.1       0.64    9.6   0.0    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.059   13.9   0.0       0.11   13.0   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
      0.063   13.2   0.1       0.16   11.9   0.0    1.7  2  MarR             MarR family
      0.082   12.7   0.2       0.96    9.3   0.0    2.3  3  DUF1495          Winged helix DNA-binding domain (DUF1495)
       0.11   12.8   0.1        0.3   11.3   0.0    1.7  2  Rio2_N           Rio2, N-terminal
       0.16   11.9   0.0       0.27   11.2   0.0    1.3  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 !   45.8   1.9   3.3e-15   3.9e-12       3      46 ..      44      87 ..      42      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 3.3e-15
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   RlkIL+l   ++lcvc + +++++s s++S+HL+ L ++GLV+
  gi|91774314|ref|YP_567006.1| 44 IRLKILSLILVQPLCVCLIKDIMKMSDSKLSYHLSTLVDSGLVK 87
                                  5******************************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.3e-11   2.8e-08       2      60 ..      35      92 ..      34      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.3e-11
                                  HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   i++AL++  R++il+++   ++l++  +++ + +s++ lsyHL +L++ gLv++++ g
  gi|91774314|ref|YP_567006.1| 35 AIHHALSSTIRLKILSLI-LVQPLCVCLIKDIMKMSDSKLSYHLSTLVDSGLVKREKKG 92
                                  589***************.************************************9987 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 !   22.6   0.1   7.6e-08     9e-05       1      49 [.      44      91 ..      44      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.6e-08
                        HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                  +Rl++ls L+ v+  +   +k+ ++++d++Ls hl++L + g ++++k+
  gi|91774314|ref|YP_567006.1| 44 IRLKILS-LILVQPLCVCLIKDIMKMSDSKLSYHLSTLVDSGLVKREKK 91
                                  7999997.6778889999****************************996 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 !   17.2   0.0   2.5e-06     0.003      84     144 ..      44     102 ..      26     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-06
                      SMC_ScpB  84 aaletLaiIaykq..pvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTek 144
                                     l++L++I ++    +  ++i ++ +++ +++++tL++ gl+++++    +g+ i+Y+ Tek
  gi|91774314|ref|YP_567006.1|  44 IRLKILSLILVQPlcVCLIKDIMKMSDSKLSYHLSTLVDSGLVKREK----KGNWIIYHPTEK 102
                                   468899999876632345678888899999***************99....9*********97 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.6e-06    0.0055      41      72 ..      76     107 ..      59     110 .] 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.6e-06
                                   HHHHHHHTTS-EEEEETTEEEEE----XXXXX CS
               Penicillinase_R  41 llrrLvkKgllsrekegrafiYsplvseeeav 72 
                                    l+ Lv+ gl++rek+g+ +iY+p+ + e+++
  gi|91774314|ref|YP_567006.1|  76 HLSTLVDSGLVKREKKGNWIIYHPTEKAEKYK 107
                                   6899***********************99997 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.3e-05     0.027      65     110 ..      23      68 ..       4      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                       DUF1700  65 aikkaekkkslknvskailavigLsllnlilvlipliviislvlsl 110
                                   +i +++k  +++ + +a+ ++i L +l+lilv + ++++i  ++ +
  gi|91774314|ref|YP_567006.1|  23 RIANEDKLAEQSAIHHALSSTIRLKILSLILVQPLCVCLIKDIMKM 68 
                                   678889999******************************9877766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.046      28      66 ..      62     101 ..      49     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                                   HCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                          TrmB  28 iaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66 
                                   i  + + + sk    L+ L+d GlV+rek g+  +Y++++
  gi|91774314|ref|YP_567006.1|  62 IKDIMKMSDSKLSYHLSTLVDSGLVKREKkGNWIIYHPTE 101
                                   6778899999999***************956688999875 PP

>> OFeT_1  Ferrous iron uptake permease, iron-lead transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.6e-05     0.032     111     171 ..      21      81 ..       5      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                        OFeT_1 111 savealeaalvilalipqsyssallGtllasilvvaltavlkdqiarirlphlkfvlsall 171
                                   ++  a e+ l   + i ++ ss++   +l+ ilv  l + l ++i+++   +l + ls+l+
  gi|91774314|ref|YP_567006.1|  21 ALRIANEDKLAEQSAIHHALSSTIRLKILSLILVQPLCVCLIKDIMKMSDSKLSYHLSTLV 81 
                                   55567788888889999*****************************************997 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 ?   13.6   0.0   3.3e-05     0.039      79     107 ..      64      92 ..      31      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                          RP-C  79 ralglsestlrrhlaaLveaGliirrDsp 107
                                     +++s+s+l++hl+ Lv+ Gl+ r    
  gi|91774314|ref|YP_567006.1|  64 DIMKMSDSKLSYHLSTLVDSGLVKREKKG 92 
                                   6679*******************987665 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      0.13   1.6e+02       3      14 ..      43      54 ..      41      58 .. 0.81
   2 ?    9.6   0.0   0.00053      0.64      28      48 .]      67      87 ..      64      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.13
                        HTH_24  3 etdrkILelLqk 14
                                   +++kIL+l+  
  gi|91774314|ref|YP_567006.1| 43 TIRLKILSLILV 54
                                  689*****9975 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00053
                        HTH_24 28 glSpstvnrrlkrLeeeGlIk 48
                                   +S s ++++l  L+++Gl+k
  gi|91774314|ref|YP_567006.1| 67 KMSDSKLSYHLSTLVDSGLVK 87
                                  6899***************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 ?   13.0   0.0   9.1e-05      0.11      24      53 ..      62      91 ..      61     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-05
                        HTH_27 24 lcgrlnvedshisyslkkLtekGLvertgd 53
                                  + + ++++ds  sy l+ L+  GLv+r+++
  gi|91774314|ref|YP_567006.1| 62 IKDIMKMSDSKLSYHLSTLVDSGLVKREKK 91
                                  67899********************77765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9   3.4e+03      20      30 ..      27      37 ..      23      44 .. 0.69
   2 ?   11.9   0.0   0.00013      0.16      24      52 ..      63      91 ..      55      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                                  HHHHHHHHTS- CS
                          MarR 20 vseLakklgvs 30
                                    +La+++ ++
  gi|91774314|ref|YP_567006.1| 27 EDKLAEQSAIH 37
                                  56788887766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                                  HHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR 24 akklgvskstvtrvldrLekkGlieRsks 52
                                   + +++s s ++  l +L++ Gl++R+k+
  gi|91774314|ref|YP_567006.1| 63 KDIMKMSDSKLSYHLSTLVDSGLVKREKK 91
                                  56799*********************996 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 ?    0.8   0.1      0.35   4.2e+02      41      65 ..      12      36 ..       7      51 .. 0.71
   2 ?   -0.2   0.0      0.75   8.9e+02       7      19 ..      41      53 ..      33      74 .. 0.71
   3 ?    9.3   0.0    0.0008      0.96      57      86 ..      78     106 ..      62     110 .] 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.35
                       DUF1495 41 nvkGaleGmgkrynsessLielGLv 65
                                  ++ G +eG + r  +e+ L e+  +
  gi|91774314|ref|YP_567006.1| 12 KLLGGIEGIALRIANEDKLAEQSAI 36
                                  5678888888888888877776544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.75
                       DUF1495  7 kSkvRkkvllyLy 19
                                  +S +R k+l  ++
  gi|91774314|ref|YP_567006.1| 41 SSTIRLKILSLIL 53
                                  6899999998765 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0008
                       DUF1495  57 ssLielGLveeeeeseglklYklteeGiei 86 
                                   s L+  GLv+ +e++ +  +Y+ te+ +++
  gi|91774314|ref|YP_567006.1|  78 STLVDSGLVK-REKKGNWIIYHPTEKAEKY 106
                                   45*******6.68899999***99998776 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1   2.5e+03      37      50 ..      31      45 ..      10      52 .. 0.59
   2 ?   11.3   0.0   0.00025       0.3      28      59 ..      60      91 ..      54      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                        Rio2_N 37 k.eeevkkrlsrllk 50
                                    ++ ++++ls+ ++
  gi|91774314|ref|YP_567006.1| 31 AeQSAIHHALSSTIR 45
                                  324445555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00025
                        Rio2_N 28 elieeisrlkeeevkkrlsrllkaklisrkta 59
                                   li+ i +++ ++++++ls+l++ +l++r+++
  gi|91774314|ref|YP_567006.1| 60 CLIKDIMKMSDSKLSYHLSTLVDSGLVKREKK 91
                                  58999************************754 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.27      29      55 ..      64      90 ..      59      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                  HHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 29 rrlglsksavsrilkrLvaaGLverrp 55
                                  + +++s s +s++l  Lv+ GLv r++
  gi|91774314|ref|YP_567006.1| 64 DIMKMSDSKLSYHLSTLVDSGLVKREK 90
                                  67899*******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 606.10
//
Query:       gi|91774315|ref|YP_567007.1|  [L=199]
Description: CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00017   21.4   8.9    0.00053   19.8   8.6    1.8  1  CTP_transf_1  Cytidylyltransferase family
     0.0015   19.0   1.8     0.0015   19.0   1.8    2.5  2  DUF2061       Predicted membrane protein (DUF2061)


Domain annotation for each model (and alignments):
>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   8.6   5.9e-08   0.00053      56     197 ..      14     158 ..       1     177 [. 0.62

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-08
                                   H....HHHHHHHHHHTTTSSSHHHHHHHHHHHHHHHHHH---................HHHHHHHHHHHHHHHHHTHHHH. CS
                  CTP_transf_1  56 l.llslvlllllllflylesliallklvlllvlvllllvlkvl.............kskskklervilallallyvvlllq 122
                                   +   s++++ l+++f y+ +  ++  ++l+lvl+ +ll+   +              ++ k+ ++++ ++  +++      
  gi|91774315|ref|YP_567007.1|  14 FvRKSIHFISLSIVFIYYYMGKEFTLNFLTLVLCCILLIDY-FrveknlkipvvwkLYRAKEKDKLSGTTYFMIG------ 87 
                                   44456677777777777766666666666666666666664.336665666555542222222222222222222...... PP

                                   TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH---B-S-TTS---BHHHHHHHHHHHHHHHHHHHHHHHCT CS
                  CTP_transf_1 123 slllienikeglllvllllalvvaaDigaYffGklfGktkllpkiSPkKTveGfigGlvaavvvglllalvlska 197
                                     ++i+    +  ++ ++++++ + D++a ++G+ +Gk+  ++k  P+  +eG+i  +++ +++g+l+ +    a
  gi|91774315|ref|YP_567007.1|  88 --SIIAISIFSKEVASAAILMTTFGDSAAALIGIRYGKR--WIKNLPNRAWEGVISEFIVNLIIGYLFLSNWIVA 158
                                   ..333333333444556778999****************..************************9997654443 PP

>> DUF2061  Predicted membrane protein (DUF2061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.6      0.22   1.9e+03       6      32 ..      82      94 ..      80     109 .. 0.53
   2 !   19.0   1.8   1.7e-07    0.0015      12      44 ..     141     173 ..     137     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.22
                       DUF2061  6 swrvihtvvtflvaylltgslalAgai 32
                                  ++ +i++++++               i
  gi|91774315|ref|YP_567007.1| 82 TYFMIGSIIAIS--------------I 94
                                  444444444444..............3 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.7e-07
                       DUF2061  12 tvvtflvaylltgslalAgaialvEpvvktvlY 44 
                                   ++v ++++yl+ +++ +A+++al+ +++ t++Y
  gi|91774315|ref|YP_567007.1| 141 FIVNLIIGYLFLSNWIVALTMALAATIIETLIY 173
                                   89999***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1091.58
//
Query:       gi|91774316|ref|YP_567008.1|  [L=383]
Description: glycosyltransferase [Methanococcoides burtonii DSM 6242]
Scores for 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   66.8   0.0    1.6e-08   34.2   0.0    2.2  2  Glyco_trans_1_3  Glycosyl transferase family 1
    6.6e-14   52.2   0.0    1.1e-13   51.6   0.0    1.3  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    3.3e-06   26.2   0.0    5.7e-06   25.4   0.0    1.3  1  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas
    2.8e-05   24.2   0.0    7.3e-05   22.8   0.0    1.7  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00031   20.8   0.0    0.00059   19.9   0.0    1.5  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
    0.00045   20.7   0.0    0.00074   19.9   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.09   11.9   0.0        2.2    7.3   0.0    2.2  2  Mito_fiss_Elm1   Mitochondrial fission ELM1
      0.091   12.3   0.0       0.19   11.2   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
       0.11   12.9   0.0       0.32   11.4   0.0    1.7  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 !   34.2   0.0     8e-12   1.6e-08       1     129 [.       1     130 [.       1     168 [. 0.87
   2 !   30.4   0.0   1.1e-10   2.2e-07     241     316 ..     263     336 ..     247     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8e-12
               Glyco_trans_1_3   1 arilYgvsGeGaGhasRsrvvlehL.arghevkvvvsgraldvLekef..dvneivglsivyeenrvrklktllknlqvaa 78 
                                   ++i+  v GeG Gh+sR   +++++ + ghev + ++g ++d ++k+   +   i+ +++v +  ++     +++ ++   
  gi|91774316|ref|YP_567008.1|   1 MKIMIFVCGEGLGHTSRCISLAQQMkTAGHEVLMGAYGYSKDLIKKKGlkTAEIIPEIQLVGDSGSLDLKSSVIATIKS-- 79 
                                   799999*******************777****************999655566678999999999**999999998854.. PP

               Glyco_trans_1_3  79 klaknvkalvelvedfrpdlvvtDFealtallakrhkLPvisvdnqqvvnr 129
                                   +    + ++   +++f+pdlv++D     + +a  +k Pv  + nq  +++
  gi|91774316|ref|YP_567008.1|  80 GQFMGIGKIHRTLKEFKPDLVISDSYYTGIFFAWLRKKPVYLMVNQSNMEE 130
                                   5566788899999***********999999999999999988877776655 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 1.1e-10
               Glyco_trans_1_3 241 afseegFleDLataraviagagftLmtealyLkkPlLavPvarqFeqvlnalyLerlgyGaavdakdldkedvkdF 316
                                   +f +e F   L+++  via +g+++m eal  + P+L+ P  +  eq  na+ Le +g+G  ++   +++e++ + 
  gi|91774316|ref|YP_567008.1| 263 EFIDEQF-PYLKASDIVIAPGGHSMMMEALSFGVPILSFPDMGHIEQENNATSLEEEGCGKRLE-YSISPEKLLEH 336
                                   4444444.35889999********************************************9976.77888877655 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 !   51.6   0.0   5.3e-17   1.1e-13      49     146 ..     250     345 ..     224     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 5.3e-17
                                   T.-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE CS
               Glyco_tran_28_C  49 k.veeltlkvevfefidkmaeaikaadLvIsRAGagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqke 128
                                   + + +l ++v+++efid+   ++ka+d+vI  +G+++ +E+l++g+p + +p   +   +q+nNa +le++g++  le++ 
  gi|91774316|ref|YP_567008.1| 250 DkYTDLPENVTIMEFIDEQFPYLKASDIVIAPGGHSMMMEALSFGVPILSFPDMGHI--EQENNATSLEEEGCGKRLEYSI 328
                                   3344444889*********************************************88..*******************999 PP

                                   -STTCHHHHHHHHCCS-- CS
               Glyco_tran_28_C 129 ltpekLeeallelaaekl 146
                                     pekL e + +l +++ 
  gi|91774316|ref|YP_567008.1| 329 S-PEKLLEHIHQLIEDDA 345
                                   9.*******999988775 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.9e-09   5.7e-06     345     423 ..     279     358 ..     268     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-09
                         UDPGT 345 vtHaGangvyEaisnGvPmvglPlFg..dqrdNikrmeakgaavtlnvkemtsedllnAlkevindksykenimrLsslhk 423
                                   ++ +G   ++Ea+s GvP+   P  g  +q++N+ ++e  g + +l+   ++ e ll+ ++++i+d+ yk+    L sl +
  gi|91774316|ref|YP_567008.1| 279 IAPGGHSMMMEALSFGVPILSFPDMGhiEQENNATSLEEEGCGKRLEY-SISPEKLLEHIHQLIEDDAYKDKTQYLRSLSH 358
                                   677899999**************999667****************987.5899******************9999988866 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.7e-08   7.3e-05       6     155 ..      16     177 ..      13     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.7e-08
                Glyco_transf_4   6 rhvleLaraLarrGheVtvvtpgddgpleeev................elvvrvprvplpllkrllrslaflrrlrrllkr 70 
                                     +  La+++  +GheV + + g++++l ++                     ++++  +         +  + ++ r lk+
  gi|91774316|ref|YP_567008.1|  16 SRCISLAQQMKTAGHEVLMGAYGYSKDLIKKKglktaeiipeiqlvgdSGSLDLKSSVIA--TIKSGQFMGIGKIHRTLKE 94 
                                   56789**********************999999988855554433322121222222222..2222234446799****** PP

                Glyco_transf_4  71 ekpDvvHahspaalgaallalrrrlgiplVltvHglye...krllkarlkplsrllralerrllrradrviavSeatadel 148
                                   +kpD+v + s++++++ ++  +  +++p+ l v  +         +   + l ++ ++++ r++r++d +i +   + + +
  gi|91774316|ref|YP_567008.1|  95 FKPDLVISDSYYTGIFFAW--L--RKKPVYLMVNQSNMeefFMGKGILMGCLGNVTKRFYTRVFRKVDGIIIPDFPMPNTI 171
                                   *************987744..3..46677666666555567666667778899999999999********99887777777 PP

                Glyco_transf_4 149 rerygvp 155
                                   ++ y+++
  gi|91774316|ref|YP_567008.1| 172 CK-YNLD 177
                                   77.6665 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.9e-07   0.00059       2      94 ..       4     102 ..       3     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                                   EEEE-SSH.HHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---G..........HCTT..CHHHHCCHH CS
               Glyco_transf_28   2 vllggGTg.GhvfPalAlakeLkkegheVrylgtkrgleerlveeaglefepiage..........klrrklspknlkeil 71 
                                   ++ ++G g Gh    ++la+++k  gheV  l+   g+ + l++++gl++ +i  e           l      + + +i+
  gi|91774316|ref|YP_567008.1|   4 MIFVCGEGlGHTSRCISLAQQMKTAGHEV--LMGAYGYSKDLIKKKGLKTAEIIPEiqlvgdsgslDL----KSSVIATIK 78 
                                   5666666669*******************..555677777777********98777777777643333....333333333 PP

                                   H.HHHHHHHHHHHHHHHHHCCCCC CS
               Glyco_transf_28  72 k.vlkavvkakkilkeakpdavvg 94 
                                   + ++ ++ k+ ++lke+kpd+v++
  gi|91774316|ref|YP_567008.1|  79 SgQFMGIGKIHRTLKEFKPDLVIS 102
                                   32456999*************997 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 !   19.9   0.0   3.7e-07   0.00074      36     134 .]     241     343 ..     209     343 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.7e-07
                                   EES---....HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE--.---SHHHHHHHHTT-EEEE-.TGGGTTT--... CS
               Glyco_trans_1_4  36 ivGdgp..rpeeleelaagleerveftGfvedlaellaaadvfvaPs.egfglkllEamaaglpvVat.dvggiaevv... 109
                                   +   gp  +p+++     +l e+v+++ f+++  ++l+a+d+++aP        ++Ea+++g+p+ ++ d+g i++     
  gi|91774316|ref|YP_567008.1| 241 LLS-GPsiKPDKYT----DLPENVTIMEFIDEQFPYLKASDIVIAPGgH---SMMMEALSFGVPILSFpDMGHIEQ-Enna 312
                                   444.4433333333....46699*******99**************843...5799************55655544.1111 PP

                                   ...TTSSEE--TT.........-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4 110 ...gengllvppg.........dpealaeailrLled 134
                                      +e+      g         +pe+l e+i +L+ed
  gi|91774316|ref|YP_567008.1| 313 tslEEE------GcgkrleysiSPEKLLEHIHQLIED 343
                                   122233......1333333333677888888887776 PP

>> Mito_fiss_Elm1  Mitochondrial fission ELM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.041        81       2      74 ..      13     116 ..      13     131 .. 0.65
   2 ?    7.3   0.0    0.0011       2.2     228     281 ..     273     325 ..     268     342 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.041
                Mito_fiss_Elm1   2 GaenQalGLaeaLgleievkrislkkllrvl.rprg............................adakei..aklaretle 51 
                                   G+++ ++ La++++++ +++++      + l +++g                            ++  +    +  ++tl+
  gi|91774316|ref|YP_567008.1|  13 GHTSRCISLAQQMKTAGHEVLMGAYGYSKDLiKKKGlktaeiipeiqlvgdsgsldlkssviatIKSGQFmgIGKIHRTLK 93 
                                   889999999999996666664544444433324444666667777778888888886666665522222200233345566 PP

                Mito_fiss_Elm1  52 kpgPdlviaaGrrtaslalalkr 74 
                                   +  Pdlvi+    t ++  +l++
  gi|91774316|ref|YP_567008.1|  94 EFKPDLVISDSYYTGIFFAWLRK 116
                                   67999999999999999999998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                Mito_fiss_Elm1 228 lAdaivvTaDSvSMlsEAastgkpVyvlglegkskKfarfhksLrergvvrpft 281
                                    A+ iv+ +   SM++EA+s g+p+  ++ +  +   ++   sL+e+g  ++++
  gi|91774316|ref|YP_567008.1| 273 KASDIVIAPGGHSMMMEALSFGVPILSFP-DMGHIEQENNATSLEEEGCGKRLE 325
                                   477799999999*************9998.555555666666666666666665 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.6e-05      0.19      71     161 ..     255     346 ..     249     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                                   TTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......SEEEE-TT.- CS
               Glycos_transf_1  71 lsdnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......tGllvkpn.n 144
                                   l +nv++  +++  +   +lk++di+++p    g     +EA+++g+p+++    g  e+ +++        G   +   +
  gi|91774316|ref|YP_567008.1| 255 LPENVTIMEFID--EQFPYLKASDIVIAP----GGHSMMMEALSFGVPILSFPDMGHIEQENNATsleeegCGKRLEYSiS 329
                                   778888888887..555678899******....7777889*************8888888888877999886666666679 PP

                                   HHHHHHHHHHHHHSHHH CS
               Glycos_transf_1 145 aealaeairklledeel 161
                                   +e+l e+i +l+ed+  
  gi|91774316|ref|YP_567008.1| 330 PEKLLEHIHQLIEDDAY 346
                                   99999999999999843 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.32       7     136 ..      18     163 ..      13     183 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
               Glyco_trans_4_4   7 vaelaraLaarGheVtvltpapapgapeleedgvrvh....rlpvprrpspladlaal.............ralrrllrqr 70 
                                   +  la+++  +GheV + + ++  +       g+ +      + +   + +  dl+++                 r+l  +
  gi|91774316|ref|YP_567008.1|  18 CISLAQQMKTAGHEVLMGAYGYSKDLI--KKKGLKTAeiipEIQLVGDS-GSLDLKSSviatiksgqfmgiGKIHRTL--K 93 
                                   556666666666666666654443322..22233222111123333333.3344443333444444443445558999..* PP

               Glyco_trans_4_4  71 rerpdvvhahsptaglaarlarrrrgiplvvtlhgll...lrrg..sgavrrlyralerrllrradavlvv 136
                                   +++pd+v++ s+++g++ +++r ++ + l+v+  + +     +g  +g+++++ +++  r++r +d+++ +
  gi|91774316|ref|YP_567008.1|  94 EFKPDLVISDSYYTGIFFAWLR-KKPVYLMVNQSNMEeffMGKGilMGCLGNVTKRFYTRVFRKVDGIIIP 163
                                   ***********99999999999.766777776665444333334889999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2211.81
//
Query:       gi|91774317|ref|YP_567009.1|  [L=281]
Description: hypothetical protein Mbur_2408 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-15   54.9  16.4    6.3e-14   52.1  16.4    2.2  1  PAP2_3    PAP2 superfamily
      2e-09   37.3   5.6      2e-09   37.3   5.6    2.1  2  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
        0.6    9.1  12.7       0.14   11.2   3.0    2.3  2  DUF973    Protein of unknown function (DUF973)
        2.8    8.5  11.0       0.33   11.5   4.4    2.4  2  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1  16.4   1.4e-17   6.3e-14      23     190 .]      94     253 ..      83     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.4e-17
                        PAP2_3  23 lahpalavilalaYaslh.fqvtllvlvllflrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaasl 102
                                    a+p+l+++ a++Y + + ++++ ++l++l+ ++ + l+ef +++ l+ l+++ +y+lfP+      ++    ++   + l
  gi|91774317|ref|YP_567009.1|  94 FANPWLTYFSAFIYMIGFsVLLIGTFLIFLYKKDAKGLQEFSIAFTLIYLVAYPFYILFPVSVT---SNTLPNMAPLLYGL 171
                                   578***********98651566778999999******************************999...22222222333333 PP

                        PAP2_3 103 agalrdgasravllrgtienglaa..fPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGv 181
                                   +          ++   +i ++     fPSlH+a++l+++l++    ++  l++la++  + + ++++++g H ++D+i+G+
  gi|91774317|ref|YP_567009.1| 172 DP--------SIVKIMHICDPTLDncFPSLHTALSLMTMLIVLARTKNYGLKALAVFTTISIQFTILYLGIHWITDLIGGI 244
                                   33........3444444555554445*************99888888889******************************* PP

                        PAP2_3 182 alalvaial 190
                                   +la+ ++++
  gi|91774317|ref|YP_567009.1| 245 MLAFTSYYI 253
                                   *****9985 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.24   1.1e+03     124     124 ..     121     121 ..      88     158 .. 0.59
   2 !   37.3   5.6   4.4e-13     2e-09      50     131 ..     184     258 ..     136     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.24
                          PAP2 124 a 124
                                   +
  gi|91774317|ref|YP_567009.1| 121 I 121
                                   2 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 4.4e-13
                          PAP2  50 keakesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrl 130
                                    + +++fPS H+a +++ +l++ +  ++   k       +++++ ++ + ++ lylg+H+ +D+++G++++++  ++a+r+
  gi|91774317|ref|YP_567009.1| 184 PTLDNCFPSLHTALSLMTMLIVLARTKNYGLK-------ALAVFTTISIQFTILYLGIHWITDLIGGIMLAFTSYYIATRY 257
                                   45578**********99999999999999998.......89999999*****************************99998 PP

                          PAP2 131 v 131
                                   +
  gi|91774317|ref|YP_567009.1| 258 R 258
                                   6 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.2    0.0077        35     127     153 ..      97     123 ..      49     154 .. 0.81
   2 ?   11.2   3.0   3.1e-05      0.14     123     176 ..     207     271 ..     193     274 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0077
                        DUF973 127 lslillgviilligiilaliGqillgl 153
                                     l  ++++i++ig+ ++liG  l++l
  gi|91774317|ref|YP_567009.1|  97 PWLTYFSAFIYMIGFSVLLIGTFLIFL 123
                                   456678889999999999999988876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.1e-05
                        DUF973 123 l...........slilslillgviilligiilaliGqillglsfyklGevYnnglikigGiliii 176
                                                 ++++i + ++ l i  i  liG i+l+++ y + ++Y + ++  ++ li +
  gi|91774317|ref|YP_567009.1| 207 ArtknyglkalaVFTTISIQFTILYLGIHWITDLIGGIMLAFTSYYIATRYRELIVTRSSKLITV 271
                                   144444444422445556666666666666**************************999999987 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.5      0.26   1.2e+03      30      47 ..     100     121 ..      79     127 .. 0.51
   2 ?   11.5   4.4   7.3e-05      0.33       8      71 ..     192     253 ..     188     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.26
                        PAP2_C  30 a....ilkvillllallglfli 47 
                                   +    ++ +i + ++l+g fli
  gi|91774317|ref|YP_567009.1| 100 TyfsaFIYMIGFSVLLIGTFLI 121
                                   1222234555555555555555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.3e-05
                        PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvfll 71 
                                   S Ht+  ++++l++l  +++    lk +++++++++ f i++   H+  D + g++++++ +++
  gi|91774317|ref|YP_567009.1| 192 SLHTALSLMTMLIVLARTKNYG--LKALAVFTTISIQFTILYLGIHWITDLIGGIMLAFTSYYI 253
                                   5699999999999999988887..********************************99988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1618.68
//
Query:       gi|91774318|ref|YP_567010.1|  [L=342]
Description: hypothetical protein Mbur_2409 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-45  154.0  31.1    7.9e-45  153.7  31.1    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.7  31.1   4.4e-49   7.9e-45       3     301 .]      10     323 ..       8     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 4.4e-49
               LPG_synthase_TM   3 lglals.alllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnn 82 
                                   ++l +s ++++a++++++d+++l  ++r+++  +lllal l+lls+ll++lr r++++ lg+ +s+ r++ +++ ++f+ +
  gi|91774318|ref|YP_567010.1|  10 ISLFISvISIIAVMFYTLDPQTL-VSIRNIRTEFLLLALCLHLLSYLLWGLRTRAMCKFLGFDVSITRAFEIVTSSTFLAS 89 
                                   566666778888889999*9877.579****************************************************** PP

               LPG_synthase_TM  83 vtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa..vllllalallllavlal 161
                                   vtP+++gGe++r++ll + e+v++++a+a+v+ erlld++ +++  ++al l+ g   + a   v++ + l+l+l +++++
  gi|91774318|ref|YP_567010.1|  90 VTPSSIGGEPLRVHLLGQ-ENVPVGSATAVVLGERLLDGILILVSAPVALHLFRGVISTSALstVVVMGELLLFLTFLTII 169
                                   ******************.********************************999988766669888888888888888888 PP

               LPG_synthase_TM 162 llllllrrrlarlarvlkrlarllarfarklasakr....................klvlasprrlllafllslliwllea 222
                                   ++++  ++++++l  ++ r a    +         r                     +v + ++ l+    +++l w++e+
  gi|91774318|ref|YP_567010.1| 170 YAVWHPHYTKKTLNYIIHRTAVVTGTAE-----SGRledltrkldmiiddfhnsmaFFVTKGRKGLFFGSVYTILFWIVEF 245
                                   8999999999999988888866543332.....2223445789*************999999999**************** PP

               LPG_synthase_TM 223 ltlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                   +++ ++l +l+ ++ ++ +++++++l++++++p++Pg +Gv+E ++++l++l+ v+ ++++++++++r++tlyl l++G
  gi|91774318|ref|YP_567010.1| 246 AMIPVILIGLNQPPAIVMSFAAQVLLMILLVIPITPGSSGVAELGATSLFSLF-VPVYLIGIVVVAWRAFTLYLNLIVG 323
                                   *****************************************************.***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 1805.26
//
Query:       gi|91774319|ref|YP_567011.1|  [L=130]
Description: hypothetical protein Mbur_2410 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-50  171.0   0.3    1.3e-50  170.8   0.3    1.0  1  DUF2209   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2209  Uncharacterized protein conserved in archaea (DUF2209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.3   7.1e-55   1.3e-50       1     121 []       5     124 ..       5     124 .. 0.99

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 7.1e-55
                       DUF2209   1 vavDiSGRHkekdgeylmvcaaVslevsadriekveqvkilvvaseeepkledvvklieeaveelkeegtivaEkGelyne 81 
                                   +avDiSGRHk+kdg y+mvcaaV+levsa++ie+++qv+i+++ s+++ ++ d+v++ie +v+e++  gtiv+EkG+lyn+
  gi|91774319|ref|YP_567011.1|   5 IAVDISGRHKIKDG-YYMVCAAVALEVSASHIESISQVAIKPFLSHDPLAVLDIVRIIEVTVSEIAFPGTIVVEKGDLYNQ 84 
                                   8***********99.****************************************************************** PP

                       DUF2209  82 pewlveailkkefkyqeslgEreaielAHhvslsarklli 121
                                   pewl+++++++++kyqesl+E+ aie+AH+vsls+rkll+
  gi|91774319|ref|YP_567011.1|  85 PEWLSKNMFSRDIKYQESLSEMLAIEFAHYVSLSSRKLLM 124
                                   **************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 733.16
//
Query:       gi|91774320|ref|YP_567012.1|  [L=413]
Description: small GTP-binding protein [Methanococcoides burtonii DSM 6242]
Scores for 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-27   93.5   0.2    1.9e-26   92.5   0.2    1.5  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    8.9e-20   70.9   0.1    2.5e-19   69.4   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
    5.4e-12   46.1   0.2    9.7e-12   45.3   0.2    1.4  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    1.6e-06   27.7   0.2    5.7e-06   25.9   0.0    2.0  2  FeoB_N        Ferrous iron transport protein B
    7.2e-06   25.7   0.1    0.00073   19.1   0.1    2.6  1  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0001   22.3   0.0       0.57   10.1   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
    0.00011   22.1   0.0     0.0003   20.8   0.0    1.7  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0039   16.6   0.0     0.0086   15.5   0.0    1.6  1  Arf           ADP-ribosylation factor family
      0.007   16.9   0.2      0.084   13.4   0.0    2.6  3  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.095   12.7   0.1       0.43   10.6   0.0    2.0  2  Dynamin_N     Dynamin family
       0.17   11.6   0.1        3.2    7.5   0.0    2.8  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.2   1.2e-29   1.9e-26       3      89 .]      22     107 ..      20     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.2e-29
                     GTP-bdg_N   3 sleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqL 83 
                                   +  El+eLa++a+++vvg ++q r  pd+++ +G+Gkv+e++elve+ +a+ vif+++Ls++q+ n++++++++ViDR +L
  gi|91774320|ref|YP_567012.1|  22 KFVELKELARAAHYNVVGVLTQTR-YPDRKYQVGRGKVDELAELVEALDAEKVIFNHQLSTTQIYNISETCKCEVIDRFNL 101
                                   678*******************97.9******************************************************* PP

                     GTP-bdg_N  84 ILdIFA 89 
                                   IL+IFA
  gi|91774320|ref|YP_567012.1| 102 ILEIFA 107
                                   *****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 ?   -2.7   0.0       3.9   6.3e+03      23      41 ..      72      90 ..      59     140 .. 0.60
   2 !   69.4   0.0   1.5e-22   2.5e-19       2     114 .]     193     311 ..     192     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.9
                                  TEEESSSTTSSSSEEEEEE CS
                      MMR_HSR1 23 kaivsdkpgtTrdinegrv 41
                                  k+i +++  tT+  n  + 
  gi|91774320|ref|YP_567012.1| 72 KVIFNHQLSTTQIYNISET 90
                                  5555555555555444433 PP

  == domain 2  score: 69.4 bits;  conditional E-value: 1.5e-22
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC....TSE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee....adl 78 
                                   va++G++N+GKStL+++l++e ++v+d+ +tT+ ++++ +++k++++ l+Dt+G+ie  +  +++ +af++  +    ad+
  gi|91774320|ref|YP_567012.1| 193 VALAGYTNAGKSTLFQSLVKEGVEVEDMLFTTLSPTTRSLSIKQRRVLLTDTVGFIE--DLPHWMVDAFRSTLDeiflADV 271
                                   89****************************************************998..66668999999966558889** PP

                                   EEEEEETTTTCSHHHHHHH.....HHHHHHTTSEEEEEEES CS
                      MMR_HSR1  79 illvvdaseeklkpldeel.....eelleeakkplilvlnk 114
                                   illvvd+s + l+ ++++l       +++ ++ +++ vlnk
  gi|91774320|ref|YP_567012.1| 272 ILLVVDMS-DPLDVIRQKLvvshdIFWKRTEGAEIVAVLNK 311
                                   ******98.43433333331111112223356666667776 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.2   5.9e-15   9.7e-12       1      77 [.     109     183 ..     109     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5.9e-15
                                   H--SHHHHHHHHHHHHHHHHHHHC...XXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                     GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLe...glgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrk 77 
                                   rA+t+ aklQVelA+l+y+lp+ +   +l k+ +r     g++G G ++ +++++ +++ri ++++e+ +  k  e +r+
  gi|91774320|ref|YP_567012.1| 109 RATTRRAKLQVELAKLQYELPKARaivSLLKKDERP----GFMGLGGYE-DSYEQDVKKRIVRIRNEIHNSCKGGESLRS 183
                                   9*********************97345555555666....59*******.******************998888777776 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.3   2.1e+03      77     106 ..      97     126 ..      81     140 .. 0.77
   2 !   25.9   0.0   3.5e-09   5.7e-06       3     156 .]     193     352 ..     191     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.3
                                   TSSSEEEEEEEGGGHHHHHHHHHHHHHTTS CS
                        FeoB_N  77 eepdvvvnvvdatnlernLyLtlqllelgv 106
                                   +++++++++  +    r   L ++l+ l+ 
  gi|91774320|ref|YP_567012.1|  97 DRFNLILEIFASRATTRRAKLQVELAKLQY 126
                                   567888888888888888888888887765 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3.5e-09
                                   EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----S.SSSSSSHHH..HHHHHHHHCTSSS CS
                        FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiY.slsayseee..kvardflleeepd 80 
                                   val+G  n+Gk+tlf +l +   +v     +t   ++ +l++k+++v ++D  G   +l +   +   +   +++l + + 
  gi|91774320|ref|YP_567012.1| 193 VALAGYTNAGKSTLFQSLVKEGVEVEDMLFTTLSPTTRSLSIKQRRVLLTDTVGFIeDLPHWMVDAfrSTLDEIFLADVIL 273
                                   89****************************************************752565555554112233344433334 PP

                                   EEEEEEEGGG.HHHHHHHHHHHH...HTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                        FeoB_N  81 vvvnvvdatn.lernLyLtlqll...elgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                   +vv++ d    ++++L++  +++     g+++v +ln+ d ++ + +e  ++++s  L  + v +sa++++g+e ll++i
  gi|91774320|ref|YP_567012.1| 274 LVVDMSDPLDvIRQKLVVSHDIFwkrTEGAEIVAVLNKADMVDPDDLERKVDAIS-YLAPHLVLVSASSGDGFEVLLDTI 352
                                   55555554443678899999997332456899****************9999997.5899999**********9999876 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 !   19.1   0.1   4.5e-07   0.00073      44     193 ..     222     357 ..     190     358 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.5e-07
                                   CHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG....GHHHHHHH....HHT-SEEEEEEETTTB..STHHHHHH CS
                      GTP_EFTU  44 DtlkeErergiTiksaaisleketkkylinliDtPGHvd....Fskevirg....lrvlDgavlvvdaveG..vepqteev 114
                                    t+     r ++ik           ++++ l Dt G ++    ++ +  r+    +  +D+ +lvvd ++   v  q   v
  gi|91774320|ref|YP_567012.1| 222 FTTLSPTTRSLSIK-----------QRRVLLTDTVGFIEdlphWMVDAFRStldeIFLADVILLVVDMSDPldVIRQKLVV 291
                                   34444444444444...........444444444444322222333333333333889***********985533343333 PP

                                   ...HHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                      GTP_EFTU 115 ...lrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                      +   ++eg +i+ ++NK+D++  ++l++ v+++++                    ++v +Sa +g+g++ ll++++e+
  gi|91774320|ref|YP_567012.1| 292 shdIFWKRTEGAEIVAVLNKADMVdPDDLERKVDAISYLA-------------P----HLVLVSASSGDGFEVLLDTIYEN 355
                                   1115566788888***********7688999999999444.............3....5999****************999 PP

                                   SH CS
                      GTP_EFTU 192 lp 193
                                   lp
  gi|91774320|ref|YP_567012.1| 356 LP 357
                                   98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00048      0.78      82     127 ..     173     217 ..     129     249 .. 0.73
   2 !   10.1   0.0   0.00035      0.57      42      97 ..     298     352 ..     263     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00048
                                   --TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT----- CS
                   RsgA_GTPase  82 vsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelkt 127
                                    s k +e+l++ +++   ++++l+G + +GKStL  +l+ e  +++
  gi|91774320|ref|YP_567012.1| 173 NSCKGGESLRSFRHERGFSLVALAGYTNAGKSTLFQSLVKE-GVEV 217
                                   445667777777777777999*****************987.4444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                                   HHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                   RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                     ++g+e+v vlnK+D+++ ++ le+  ++++ l  +++lvsa++++g+e l + +
  gi|91774320|ref|YP_567012.1| 298 KRTEGAEIVAVLNKADMVDPDD-LERKVDAISYLAPHLVLVSASSGDGFEVLLDTI 352
                                   5678899***************.9**9*********************99998766 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 !   20.8   0.0   1.8e-07    0.0003      58     104 ..     305     356 ..     293     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                  MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiweeL 104
                                    + vlNK+D+++ ++l++         p+ v +Sa+++ +++ L+++i+e+L
  gi|91774320|ref|YP_567012.1| 305 IVAVLNKADMVDPDDLERKVDAisylaPHLVLVSASSGDGFEVLLDTIYENL 356
                                   689**********999987775567779**********************98 PP

>> Arf  ADP-ribosylation factor 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    0.0086      19     130 ..     195     317 ..     179     356 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.3e-06
                                   EEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGG.GGCTTE.......SEEEEE CS
                           Arf  19 llGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvGGqeklRplWk.nYfekt.......davifv 88 
                                   l G  naGK+T+ + l +e ++       T+ +++++l+ik+ ++ + D  G  +  p W  + f++t       d+++ v
  gi|91774320|ref|YP_567012.1| 195 LAGYTNAGKSTLFQSLVKEGVEVedmLFTTLSPTTRSLSIKQRRVLLTDTVGFIEDLPHWMvDAFRSTldeiflaDVILLV 275
                                   45999***********99877654557899*******************88887777888535566653333444677888 PP

                                   EETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTS CS
                           Arf  89 vDsadreRleeakeeLkalleeeelkevallvlaNKqDlpea 130
                                   vD +d   +   k  +++ +  ++ + + ++ + NK D+ + 
  gi|91774320|ref|YP_567012.1| 276 VDMSDPLDVIRQKLVVSHDIFWKRTEGAEIVAVLNKADMVDP 317
                                   888887666666666666677788999**********99764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.2   5.2e+03      28      39 ..      70      81 ..      26     108 .. 0.48
   2 !   13.4   0.0   5.2e-05     0.084       1      35 [.     193     224 ..     193     244 .. 0.88
   3 ?    0.2   0.0      0.64     1e+03      69     108 ..     361     406 ..     291     411 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.2
                        AAA_18 28 lrdvakenglll 39
                                    +v+++++l++
  gi|91774320|ref|YP_567012.1| 70 AEKVIFNHQLST 81
                                  222333333333 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.2e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvaken 35 
                                   ++l+G+  +GK+tl + L k+   gv++ d+++  
  gi|91774320|ref|YP_567012.1| 193 VALAGYTNAGKSTLFQSLVKE---GVEVEDMLFTT 224
                                   689******************...99999999875 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.64
                        AAA_18  69 s.....aleegknlvidghlaeleseaakdikkvvLtasp.eelle 108
                                   +     ++ e +  +++++  e + ++   + ++vL+++  ee l+
  gi|91774320|ref|YP_567012.1| 361 RssislDMSEDSLSIVSWLYDEGIVHSIDYGEYIVLEVEArEEILR 406
                                   2555555666666688888888888888777778888877555554 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00027      0.43       1      37 [.     193     229 ..     193     238 .. 0.86
   2 ?   -0.5   0.0      0.71   1.2e+03      97     150 ..     233     289 ..     228     312 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EE CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrple 37 
                                   +a+ G +++GKS++  +L++e + + +   tT  p++
  gi|91774320|ref|YP_567012.1| 193 VALAGYTNAGKSTLFQSLVKEGVEVEDMLFTTLSPTT 229
                                   6889*****************9999999999888876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.71
                                   ETTS-SEEEEE---B-SSSGTTS....HHHHHHHSTTEEEEEEEETTS-CCC-CHHHH CS
                     Dynamin_N  97 sllvkgltlvDlPGldsvnkrdq....elvkeyikkadiilavtsanhdlsnsealfl 150
                                   s+++ ++ l D+ G+++   + +    + +   i  ad+il+v++++  l  + +++l
  gi|91774320|ref|YP_567012.1| 233 SIKQRRVLLTDTVGFIEDLPHWMvdafRSTLDEIFLADVILLVVDMSDPLD-VIRQKL 289
                                   566666777777777775555555445555555667899999999988776.555555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.85   1.4e+03      88     108 ..      33      53 ..      20      91 .. 0.74
   2 ?    7.5   0.0     0.002       3.2       4     139 ..     193     350 ..     191     354 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.85
                     PduV-EutP  88 fnkeviGiitkidlaedeeni 108
                                    + +v+G++t++  ++ + ++
  gi|91774320|ref|YP_567012.1|  33 AHYNVVGVLTQTRYPDRKYQV 53 
                                   556789999988877665554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                     PduV-EutP   4 illiGkvgsGKttLtqalkg.....eelkYk....ktqaiefsdev...iDtPGeylenrkly.salivtsae...advia 68 
                                   + l G +++GK tL q+l +     e++ ++     t ++ ++++     Dt G   +  +++  a+++t  e   advi 
  gi|91774320|ref|YP_567012.1| 193 VALAGYTNAGKSTLFQSLVKegvevEDMLFTtlspTTRSLSIKQRRvllTDTVGFIEDLPHWMvDAFRSTLDEiflADVIL 273
                                   568899999999999999874555544444322224666666655322347777433334444134433332233378888 PP

                     PduV-EutP  69 lvqdateeesvfppgfa...svfnk.....eviGiitkidlaedeenieaveelLksaGaekifevsavekegieellk 139
                                   lv+d++++  v+ ++++    +f k     e++ ++ k+d++ d +++e   + ++   a ++  vsa + +g+e ll+
  gi|91774320|ref|YP_567012.1| 274 LVVDMSDPLDVIRQKLVvshDIFWKrtegaEIVAVLNKADMV-DPDDLERKVDAISYL-APHLVLVSASSGDGFEVLLD 350
                                   888888888887776542224565533334577778888887.777777766665554.45666677777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2405.90
//
Query:       gi|91774321|ref|YP_567013.1|  [L=223]
Description: PHP-like protein [Methanococcoides burtonii DSM 6242]
Scores for complete 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   66.4   0.0    2.6e-18   65.5   0.0    1.5  1  PHP_C     PHP-associated
    5.3e-06   26.8   0.0    8.3e-06   26.2   0.0    1.4  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   2.9e-22   2.6e-18       1      56 []     137     192 ..     137     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 2.9e-22
                         PHP_C   1 geaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56 
                                   g+aN +Ar++A +lglp +gGSD+H +++VG+ yT +++  +t +++leair g++
  gi|91774321|ref|YP_567013.1| 137 GVANNKARKVAGELGLPQVGGSDSHEARMVGCSYTKIDATDRTLESVLEAIRDGKV 192
                                   579***************************************************85 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   9.2e-10   8.3e-06       1      72 [.       4      73 ..       4     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.2e-10
                                  EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE....... CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvadds 72
                                  dlHvH+ +s   ++  +  +++ ak  gl+ +ai Dh+ + g +   + ak+ + ++i +i G+e++  +++
  gi|91774321|ref|YP_567013.1|  4 DLHVHSWFSKD-SNSDPASILEYAKMNGLDGVAICDHDTREGGLVCSRLAKDTN-SDIIVIPGVEVTSSKGH 73
                                  89*******66.677779************************999999997655.89********5544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1346.18
//
Query:       gi|91774322|ref|YP_567014.1|  [L=345]
Description: hypothetical protein Mbur_2413 [Methanococcoides burtonii DSM 6242]
Scores for complete 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-39  134.4  50.6    5.8e-39  134.1  50.6    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1  50.6   3.2e-43   5.8e-39       4     323 ..      13     335 ..      10     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 3.2e-43
               AI-2E_transport   4 ilvllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvplliaqltqlv 83 
                                   +l +++l+++l++++ +++  +l A++l+++++pv+  L ++ ++k  ++++lv++l ++l+vl+++++++l+i  ++ ++
  gi|91774322|ref|YP_567014.1|  13 LLSIIVLAVVLSYALLPYINAFLGAFILYVIFKPVYILLtERLKLKENISAILVMILSMILVVLPIYYMFTLIIGEIEMVI 93 
                                   44555555555555555999**********************************************************999 PP

               AI-2E_transport  84 kslp..ayidslqnilnelpslleele.n...liqalkqslskilsnilssilnsllsllasllglilslvlvllllffll 158
                                   +++       s+ +i+n ++   +  + n    + +++ ++ + +s + s++ + l+++++++ gl++s++++++ll++l+
  gi|91774322|ref|YP_567014.1|  94 TNIItnL---SYVDITNYFDIVKNIDYiNeiaPDIDIQGKIVTLISTLGSYLSKHLIGAVQNISGLLISVIIMFFLLYYLF 171
                                   9999441...33344444444444444444456899999****************************************99 PP

               AI-2E_transport 159 ldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliPyiGa 239
                                       +     l+ l + ++++++++l e+++++ ++l++++l+a+++g + +i +++ g++   l+a ++ +++++P++Ga
  gi|91774322|ref|YP_567014.1| 172 TSTNTNISNQLQDLIPFNKKNTNKLLTEIKNIIHSTLIATLLIAVLQGTIIGITFYAVGINGVALWAAVTTVLSFLPVVGA 252
                                   988877777777777777*************************************************************** PP

               AI-2E_transport 240 vivlipiaiialltggikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlilavpltavik 320
                                    +v++p++++ l+t++ + + iv++v+ ++   ++n+l+P++ +k   +hp+v ll +++g+ lfGlvG+ ++++l + + 
  gi|91774322|ref|YP_567014.1| 253 PLVWAPAVLFKLITQD-YVAAIVILVAGIILSNIDNVLRPYIQKKVGAMHPFVSLLGIFVGIYLFGLVGIVVGPLLISSFL 332
                                   ****************.999999999999999999****************************************998776 PP

               AI-2E_transport 321 ail 323
                                    il
  gi|91774322|ref|YP_567014.1| 333 LIL 335
                                   555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1393  (0.0776954); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2170.41
//
Query:       gi|91774323|ref|YP_567015.1|  [L=505]
Description: multisensor signal transduction histidine kinase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-30  104.3   0.2    1.3e-29  103.0   0.2    1.7  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    2.3e-17   63.2   0.7      5e-17   62.1   0.7    1.6  1  Response_reg  Response regulator receiver domain
    1.7e-13   50.4   3.6    1.8e-13   50.3   0.5    2.6  2  HisKA         His Kinase A (phospho-acceptor) domain
    6.6e-09   36.0   0.0    1.5e-08   34.8   0.0    1.7  1  PAS_4         PAS fold
    1.7e-07   31.4   0.1    5.4e-07   29.8   0.1    1.9  1  PAS_9         PAS domain
    2.1e-05   24.5   0.0    7.3e-05   22.7   0.0    1.9  2  PAS           PAS fold
    0.00015   22.0   0.0     0.0004   20.6   0.0    1.8  1  PAS_3         PAS fold
    0.00028   20.8   0.0    0.00069   19.5   0.0    1.6  1  HATPase_c_5   GHKL domain
    0.00082   19.3   0.0     0.0028   17.6   0.0    1.9  1  PAS_8         PAS domain
     0.0088   15.9   0.0      0.019   14.8   0.0    1.5  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
       0.13   10.8   0.3       0.31    9.5   0.1    1.6  2  GshA          Glutamate-cysteine ligase


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 !  103.0   0.2   7.9e-33   1.3e-29       1     109 [.     395     504 ..     395     505 .] 0.96

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 7.9e-33
                                   EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHH CS
                     HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsi 80 
                                   gd+++L+++i++l+dNa+kf++++g+i ++   +++ + i +eD+GiGip+e l+++f +f+q d+st+r++ggtG+Gl i
  gi|91774323|ref|YP_567015.1| 395 GDKDHLKRMINHLLDNAIKFTPEGGKIGISALHDSESVIINIEDTGIGIPEELLPNIFSRFYQvDGSTRRKYGGTGVGLHI 475
                                   799*****************88*****999887668********************************************* PP

                                   HHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlp 109
                                   +kk++e ++G+++v+s+ g+Gt + ++lp
  gi|91774323|ref|YP_567015.1| 476 CKKIIEAHKGSLSVSSKIGEGTIISVKLP 504
                                   **************************998 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.7   3.1e-20     5e-17       1     111 [.      16     126 ..      16     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.1e-20
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEES CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviilta 79 
                                   +li++ d++ +e+l + l   +y ++  a +g+ea+ ++ke+++dl+ll+  +p++dG+e+++ +++++  + lpvi++t+
  gi|91774323|ref|YP_567015.1|  16 ILIAEADEKDAEALVSHLS-PNY-DIIRAVNGNEAVIITKEKHPDLVLLNSTLPEIDGYEVCRLLKRDEsnKVLPVIMITS 94 
                                   7999999999999999998.889.888999***********************************88886788******** PP

                                   STSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                  Response_reg  80 hseeedavealkagaddflsKpfdpeeLlkal 111
                                    ++e+++++a++  add l+ p+d+ eL++++
  gi|91774323|ref|YP_567015.1|  95 ITDEDEKTKAIESKADDLLVRPVDILELTTRV 126
                                   ****************************9998 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 !   50.3   0.5   1.1e-16   1.8e-13       2      62 ..     282     344 ..     281     348 .. 0.92
   2 ?   -1.0   0.1       1.2   1.9e+03      41      60 ..     390     409 ..     380     411 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.1e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                         HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdls 62 
                                   + +fl ++ HELrtPL +i+g++e++ ++  g+ ++ +k +++t+ ++++rl+hlve lL  s
  gi|91774323|ref|YP_567015.1| 282 KDQFLTNLTHELRTPLISIKGFTELMLEDhmGPINDAQKNAIHTVLRNSERLRHLVESLLYVS 344
                                   789**********************85555*8888************************9766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHHHH CS
                         HisKA  41 letiesearrldhlvedlLd 60 
                                   l ti    ++l ++++ lLd
  gi|91774323|ref|YP_567015.1| 390 LPTILGDKDHLKRMINHLLD 409
                                   567777778999****9998 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   9.4e-12   1.5e-08       4     109 ..     153     262 ..     150     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 9.4e-12
                         PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelll.....pgee 78 
                                      ++ v+++d++v+ +N+ a++++g++ +e++Gk +++ + ++ +++r+ + +  v+eg+  +e +e+          ee
  gi|91774323|ref|YP_567015.1| 153 AGSIIGVISKDLKVTLVNQKACDVLGYEKDEIIGKNWFDAFLPGyVRERIKEGYIGVIEGK--LEPPEYSEKpilnkTNEE 231
                                   567899********************************8666666***************6..44444433345568**** PP

                         PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                   r + ++ + lrd +  +ig++  + DiTer+
  gi|91774323|ref|YP_567015.1| 232 RLIFWHDVVLRDKDNNIIGTISSGDDITERK 262
                                   *****************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   3.3e-10   5.4e-07       6     104 .]     159     260 ..     153     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.3e-10
                         PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirkngetfwvllta 82 
                                   ++ +d +++ +N++a+++lGy ++e++gk+++d f  + + +er+++ +    +    +++  e  + +k++e+ ++  + 
  gi|91774323|ref|YP_567015.1| 159 VISKDLKVTLVNQKACDVLGYEKDEIIGKNWFDAF-LPGYVRERIKEGYIGVIEgklePPEYSEKPILNKTNEERLIFWHD 238
                                   36799******************************.444444444444444444456566677777777777777778899 PP

                         PAS_9  83 spvkdddgelvgiivilrDite 104
                                   + ++d+d++++g i+   Dite
  gi|91774323|ref|YP_567015.1| 239 VVLRDKDNNIIGTISSGDDITE 260
                                   999*****************98 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.5e-08   7.3e-05      11      64 ..     154     204 ..     145     213 .. 0.86
   2 ?   -3.7   0.0       7.2   1.2e+04      45      70 ..     247     272 ..     240     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.5e-08
                                   SSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHH CS
                           PAS  11 pdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleq 64 
                                    + i v+ +d ++++vN++a++ lG++ +e++gk+ +d + + +   ++e++++
  gi|91774323|ref|YP_567015.1| 154 GSIIGVISKDLKVTLVNQKACDVLGYEKDEIIGKNWFDAFLPGY---VRERIKE 204
                                   56677999******************************998876...7776665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.2
                                   BGGGGBSTTHHHHHHHHHHHHHHHTT CS
                           PAS  45 slldliheeddaelaelleqlleqge 70 
                                   ++++ i+  dd + +++ e+++e+++
  gi|91774323|ref|YP_567015.1| 247 NIIGTISSGDDITERKIAEKAMEEAN 272
                                   56667777777777777777777666 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.4e-07    0.0004       3      86 ..     168     252 ..     166     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.4e-07
                         PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge..pyegeyRirrkdGeyrwveararvirdeng 80 
                                    v+++ +++lGy+++e++gk  +w d+  p   rer++e +  +++++   p   e  i++k  e r + ++ +v+rd+++
  gi|91774323|ref|YP_567015.1| 168 LVNQKACDVLGYEKDEIIGK--NWFDAFLPGYvRERIKEGYIGVIEGKLepPEYSEKPILNKTNEERLIFWHDVVLRDKDN 246
                                   5899****************..***********************7777755588899*********************** PP

                         PAS_3  81 kpvrvi 86 
                                   +++  i
  gi|91774323|ref|YP_567015.1| 247 NIIGTI 252
                                   988765 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.3e-07   0.00069       5      90 ..     399     492 ..     396     498 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.3e-07
                   HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek.....kklesskskkeehGiGlks 73 
                                   +l +++  lLdNAi    +      +I +++  +++s+ii+ie +  g       ++     +   s+ +k +  G+Gl+ 
  gi|91774323|ref|YP_567015.1| 399 HLKRMINHLLDNAIKFTPEGG----KIGISALHDSESVIINIEDTGIGipeellpNIfsrfyQVDGSTRRKYGGTGVGLHI 475
                                   67889999******8877655....7*******************7776655555225434344448899999******** PP

                   HATPase_c_5  74 ireivkkykgnlsieae 90 
                                    ++i++ +kg+ls++ +
  gi|91774323|ref|YP_567015.1| 476 CKKIIEAHKGSLSVSSK 492
                                   ***********998765 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.7e-06    0.0028      21      55 ..     164     196 ..     150     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                         PAS_8  21 drivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                    +++ vNq+a++ lGy+ ++++g+   ++++ + p+
  gi|91774323|ref|YP_567015.1| 164 LKVTLVNQKACDVLGYEkDEIIGK---NWFDAFLPG 196
                                   37***************7777772...666666665 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 !   14.8   0.0   1.2e-05     0.019      10      78 ..     407     474 ..     400     491 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                   HATPase_c_3  10 lvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlk 78 
                                   l+dN++    +  ++ i++ ++  ++  i ieD G G++ee l n + r+ + + +   +++++G  G+Gl 
  gi|91774323|ref|YP_567015.1| 407 LLDNAIKftPEGGKIGISALHDS-ESVIINIEDTGIGIPEELLPNIFsRFYQVDGS---TRRKYGGTGVGLH 474
                                   77888773344556777777764.67899****************87578888888...79*********54 PP

>> GshA  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.78   1.3e+03     138     162 ..      42      66 ..      19      72 .. 0.77
   2 ?    9.5   0.1   0.00019      0.31      59     107 ..     319     367 ..     312     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.78
                                   E-EEETTEEEETTEE-SEEEEES-- CS
                          GshA 138 plvrkgerlglkdfdpclillNnDl 162
                                   ++  ++  + +k+ +p+l+llN  l
  gi|91774323|ref|YP_567015.1|  42 AVNGNEAVIITKEKHPDLVLLNSTL 66 
                                   44445666799999*******9866 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHHHHHHSTT-SEEEEEE-S-SS-HHHHHHHHHHHHHHHHT CS
                          GshA  59 lplavqaaqeaiekicpeakklllipEnhtrNtfYlenvaalkeileka 107
                                   ++ a++ + ++ e++ + +++ll +  +ht+N +Y  +v  l++i e+ 
  gi|91774323|ref|YP_567015.1| 319 QKNAIHTVLRNSERLRHLVESLLYVSGEHTKNIKYNMDVLSLTKITEEI 367
                                   5667777777788888999*************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.71u 0.39s 00:00:01.10 Elapsed: 00:00:00.56
# Mc/sec: 2722.64
//
Query:       gi|91774324|ref|YP_567016.1|  [L=375]
Description: gamma-glutamyl kinase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-39  135.1   0.1    4.1e-39  134.6   0.1    1.2  1  AA_kinase  Amino acid kinase family
    5.6e-16   58.3   0.3      1e-15   57.4   0.3    1.5  1  PUA        PUA 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 !  134.6   0.1   4.5e-43   4.1e-39       2     241 .]      13     244 ..      12     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 4.5e-43
                                   EEEEEE-TTCCCCTCC....HHHHHHHHHHHHHHHHTTEEEEEE--H.HHHHHHHHHTCCCCCHHHC....E..HHHHHHH CS
                     AA_kinase   2 rvVvKlGGssltdkee....aslrrlaeqiaalkesgnklvvVhGgg.sftdgllalksglssgelaaglrstleeageva 77 
                                   ++V+K+G +s++ +++    ++++ +a q+++l+++g+++++V++g+ +++ ++l+l  g  ++e+               
  gi|91774324|ref|YP_567016.1|  13 KIVIKIGTTSISREDGslnnEFMDTIASQVSELHRAGKQIILVSSGSiGIGIEILDL--GCRPKEIP-------------- 77 
                                   79**********77778*****************************33555555555..66666666.............. PP

                                   HHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE.EEE CS
                     AA_kinase  78 trdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeege.lgr 157
                                    r+a+a++g+ ++++ ++++++++gl++a++++t + +   +++  + + ++ i +ll+ gv+p++++++ + +++   + 
  gi|91774324|ref|YP_567016.1|  78 VRQAAAAVGQGVLMQHWTEAFQKYGLNVAQILLTYDSF---TNRLTYLNLRNSISTLLSYGVIPIINENDPICVHEIeATL 155
                                   56************************************...***************************995555555599* PP

                                   E-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH......CSSS.TTTHHHHCHHHHHHHHHC CS
                     AA_kinase 158 gssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee......saselatgGmkvkhpaalaaarr 232
                                   g++D ++a++A +++Ad li++td+dG+yd++pk ++da+ll++++  +          +s  + gGm++k++aa  +  +
  gi|91774324|ref|YP_567016.1| 156 GDNDKLSAMVASKMEADLLILFTDIDGLYDKNPKRHDDAVLLRTVEEITPTIesyggnPTSMKGVGGMRTKIDAAKICNIS 236
                                   ********************************************955544444688898899999**********999999 PP

                                   TT-EEEEEE CS
                     AA_kinase 233 ggipvvItn 241
                                   g + +vI+n
  gi|91774324|ref|YP_567016.1| 237 G-CYMVIAN 244
                                   9.****998 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.3   1.2e-19     1e-15       1      74 []     285     357 ..     285     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.2e-19
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                   g +vvd gA +al+++ sLl+ Gv++v g+f +gd+V +    g + ++G++ y+seel+ ikg+ + ei ++l
  gi|91774324|ref|YP_567016.1| 285 GSIVVDTGAKEALAKRMSLLPSGVLGVAGTFDRGDIVKLECD-GVVFGKGITDYTSEELKAIKGKQTNEIADIL 357
                                   689**********************************99888.***************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2055.40
//
Query:       gi|91774325|ref|YP_567017.1|  [L=449]
Description: gamma-glutamyl phosphate reductase [Methanococcoides burtonii DSM 6242]
Scores for complete 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   70.2   0.6    1.1e-14   53.9   0.1    2.5  2  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.04   14.0   3.5        5.1    7.3   0.0    3.8  4  DUF3911   Protein of unknown function (DUF3911)


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 !   53.9   0.1   1.2e-18   1.1e-14      29     304 ..       3     294 ..       1     314 [. 0.78
   2 !   14.1   0.1   1.4e-06     0.012     374     430 ..     324     380 ..     309     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.2e-18
                                   HHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH..HHHHHHHHHHHHHHHHHH. CS
                        Aldedh  29 edvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara..eveeaidvlryyaelaek. 106
                                   +d+++ v +Ak a    a+++ +++ + L+++a++l ++++++ e+  ++     +   +    +  +d l+ +   ++  
  gi|91774325|ref|YP_567017.1|   3 TDIEQKVMEAKMASIVLASVDTQTKDNALEAMAKALDANRNKILEANKADLEEAERMKNEgkLSQALVDRLKVTDPKIDGm 83 
                                   567777777777777777777777777777777776666666655544433322222222202233344444444444433 PP

                                   HSE.EE..............EEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHH CS
                        Aldedh 107 leg.ev..............lpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalll 172
                                   ++g +               l+ ++g + + +  P+G +g+I  ++    ++ + +  +l  GN++v+K  +e+  s  ++
  gi|91774325|ref|YP_567017.1|  84 ISGiRDvikledpsgrtintLELDKGLELYQVSSPIGLIGVI--FESRPDVVPQVMSLCLKSGNATVFKGGSEALNSNRVI 162
                                   333211333333333333324445999***************..88888888899999*********************** PP

                                   HHHHHHT.....TS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTS CS
                        Aldedh 173 aelfeea.....glPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivleda 248
                                   ++++ ea     g+Pkg+++++ +  +ev + l+ ++ +d++   Gs++  + i+ + +     v+    G  ++ v  +a
  gi|91774325|ref|YP_567017.1| 163 FNILVEAledtpGIPKGAFQLMET-REEVMDILALDEYIDLLIPRGSNDFVKFIQDNTK---ISVLGHADGICHVYVDTNA 239
                                   ****9999999**********988.999****************************988...89999************** PP

                                   HHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTST CS
                        Aldedh 249 DldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplde 304
                                   Dl+ka + +  + + +   vC a++ ll++++i++ef+ ++v +++++ v   +de
  gi|91774325|ref|YP_567017.1| 240 DLNKAYDVCFDSKVQYP-AVCNAMETLLINREIAEEFLPEMVRRYEEVGVELRFDE 294
                                   ***********999886.8***************************9988777665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.4e-06
                                   EEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST-- CS
                        Aldedh 374 VlsvikfkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttga 430
                                   +ls+  ++++eeai+  N+     + +++t++ ++ +++++ ++  +v++N st++a
  gi|91774325|ref|YP_567017.1| 324 ILSIKLVDSIEEAIDHINKYGSHHTDAIITENKTKRKQFIALVDSSSVMVNASTRFA 380
                                   899************************************************997765 PP

>> DUF3911  Protein of unknown function (DUF3911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.4   3.6e+03      47      59 ..      18      30 ..       5      35 .. 0.70
   2 ?    7.3   0.0   0.00057       5.1       4      38 ..     181     215 ..     178     250 .. 0.76
   3 ?    2.2   0.1     0.022     2e+02      41      65 ..     317     341 ..     309     347 .. 0.88
   4 ?    2.9   0.0     0.014   1.2e+02      38      68 ..     353     383 ..     342     385 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.4
                       DUF3911 47 fvasidlqaness 59
                                   +as+d q++++ 
  gi|91774325|ref|YP_567017.1| 18 VLASVDTQTKDNA 30
                                  5688998888765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00057
                       DUF3911   4 vqikGtrkevvemlqlfdlmdtkGfckfknyveve 38 
                                    q+  tr+ev+++l l + +d       +++v   
  gi|91774325|ref|YP_567017.1| 181 FQLMETREEVMDILALDEYIDLLIPRGSNDFVKFI 215
                                   68999*********997776654333334444433 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.022
                       DUF3911  41 etkhnefvasidlqanessaqdtln 65 
                                   +t+ n+f+ si l    ++a d++n
  gi|91774325|ref|YP_567017.1| 317 KTEYNDFILSIKLVDSIEEAIDHIN 341
                                   5899*********999999999998 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.014
                       DUF3911  38 eanetkhnefvasidlqanessaqdtlndql 68 
                                     n+tk+++f+a +d  +   +a   + d +
  gi|91774325|ref|YP_567017.1| 353 TENKTKRKQFIALVDSSSVMVNASTRFADGF 383
                                   57999***********999999999888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.77u 0.37s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 2370.32
//
Query:       gi|91774326|ref|YP_567018.1|  [L=572]
Description: methyl-coenzyme M reductase, alpha subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-145  482.0   1.0   5.8e-145  481.7   1.0    1.1  1  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
    1.8e-65  219.1   5.3    1.8e-65  219.1   5.3    2.0  2  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 !  481.7   1.0  6.5e-149  5.8e-145       2     270 .]      15     283 ..      14     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 481.7 bits;  conditional E-value: 6.5e-149
                                   X--HHHHHHH-S.S.-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH-S----TTS....S--S-SS---EEEBTTS- CS
                   MCR_alpha_N   2 klflkalkkkfkke.dpeekktkfykfeGlkqserkrefveaakkiakkrgislynpdilhl.GvplGqrklmpykvsgtd 80 
                                    +f+ka  +++ ++ ++++kk ++y + G++q++rk e+ +a+++ia krg++ ynp ++h+ G+plGqr+l+p+ +sgtd
  gi|91774326|ref|YP_567018.1|  15 IKFTKAHGDNKMEGgEITDKKVTYY-RLGVDQNPRKVEMRKAGQEIADKRGLVGYNP-MMHCgGIPLGQRALTPSFISGTD 93 
                                   5899999876655449*****9996.78*****************************.88**9****************** PP

                                   -EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT-----TTT-T CS
                   MCR_alpha_N  81 vlvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehmvethPalve 161
                                   ++ve+ddlh+vnnaa+qq+wddirrt ivg+d+ahe+lekrlG+evtPetin+ylevlnhalPGgavvqehmvethPalv+
  gi|91774326|ref|YP_567018.1|  94 IMVESDDLHYVNNAAMQQMWDDIRRTTIVGMDMAHETLEKRLGIEVTPETINHYLEVLNHALPGGAVVQEHMVETHPALVD 174
                                   ********************************************************************************* PP

                                   T-EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHHHHHHHHHHHHHHT CS
                   MCR_alpha_N 162 dcyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrwsamqigmsfisayk 242
                                   dcy k+ftGddeladeid+qfli+ink+fpeeqae+lk+aiGk+++q+++iPtivsrt+dG++tsrw+amq+gmsfi+ay+
  gi|91774326|ref|YP_567018.1| 175 DCYCKIFTGDDELADEIDDQFLININKQFPEEQAEALKAAIGKTTWQAAHIPTIVSRTTDGAQTSRWMAMQVGMSFIAAYN 255
                                   ********************************************************************************* PP

                                   --SS-TTHHHHHHHHHTTSEEES---B- CS
                   MCR_alpha_N 243 lcaGeaavadlayaakhaeviemgellP 270
                                   +caGeaavadl+yaakha vi+mg++lP
  gi|91774326|ref|YP_567018.1| 256 MCAGEAAVADLSYAAKHAGVISMGDMLP 283
                                   ***************************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 ?   -2.2   0.0      0.59   5.3e+03      72      99 ..     223     250 ..     189     267 .. 0.72
   2 !  219.1   5.3     2e-69   1.8e-65       1     127 []     331     463 ..     331     463 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.59
                     MCR_alpha  72 ekyptlledhfGGsqraavlaaaagist 99 
                                    ++pt++     G+q +  +a   g+s 
  gi|91774326|ref|YP_567018.1| 223 AHIPTIVSRTTDGAQTSRWMAMQVGMSF 250
                                   4678888888888888888777777664 PP

  == domain 2  score: 219.1 bits;  conditional E-value: 2e-69
                     MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdky......gglakvkatlevvkdiatevtlyaleqyekyp 75 
                                   dqiwlGsymsGGvGftqyataayt+nildd +yy+vdy++dky      g+ +kvkat++vvkdiate t+y++e+yekyp
  gi|91774326|ref|YP_567018.1| 331 DQIWLGSYMSGGVGFTQYATAAYTNNILDDNLYYNVDYINDKYdgaankGADNKVKATMDVVKDIATESTIYGIENYEKYP 411
                                   9******************************************999999999***************************** PP

                     MCR_alpha  76 tlledhfGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                   t+ledhfGGsqra+vl+aaag +talatgn+naGl+gwylsm+lhkea +rl
  gi|91774326|ref|YP_567018.1| 412 TALEDHFGGSQRATVLSAAAGSATALATGNGNAGLSGWYLSMYLHKEALGRL 463
                                   **************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3210.37
//
Query:       gi|91774327|ref|YP_567019.1|  [L=248]
Description: methyl-coenzyme M reductase, gamma subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-116  387.6   0.3   2.1e-116  387.5   0.3    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 !  387.5   0.3  1.2e-120  2.1e-116       1     246 []       5     246 ..       5     246 .. 0.99

  Alignments for each domain:
  == domain 1  score: 387.5 bits;  conditional E-value: 1.2e-120
                     MCR_gamma   1 aqyyPGeskvaenrrkfmdpeaeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGakaGdrv 81 
                                   aqyyPG ++vaenrrk+m  + ++eklre+sd+d+  +lghraPG++y+s+hPPl+em epe+++re+ve ++GakaGdrv
  gi|91774327|ref|YP_567019.1|   5 AQYYPGATSVAENRRKHM--SGKVEKLREVSDDDLTLVLGHRAPGSDYPSTHPPLAEMGEPECSVREMVEATPGAKAGDRV 83 
                                   6*****************..899********************************************************** PP

                     MCR_gamma  82 ryiqfadsmyfaPaqPyqrarlellryrgvdtGtlsGrqiievrerdlekiskelletelfdpartgirGatvhGhslrld 162
                                   ry+qf+dsmy+aP++Py r+++ ++++rgvd+GtlsGrq++e+rerd+e+++k  lete+++pa +++rGatvhGhslrl 
  gi|91774327|ref|YP_567019.1|  84 RYVQFVDSMYNAPSTPYFRSYAVAINHRGVDPGTLSGRQVVEARERDMEEVAKFQLETEMTCPALASLRGATVHGHSLRLP 164
                                   ********************************************************************************* PP

                     MCR_gamma 163 enGlmfdalqrlvldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgvalrddkevvevvkrihelrtkl 243
                                   e+G+mfd+l+r+ l+  +g v + kdqvg+ +dkkvd Gkp++e+e  k+ttiyr+d++a+rdd+ev+e+v++i+e+rt +
  gi|91774327|ref|YP_567019.1| 165 EDGIMFDMLDRCRLE--NGVVIMHKDQVGRAIDKKVDFGKPMSEEEAAKRTTIYRVDNIAFRDDAEVIEWVHTIFEKRTAY 243
                                   **************5..9*************************************************************** PP

                     MCR_gamma 244 gfk 246
                                   gfk
  gi|91774327|ref|YP_567019.1| 244 GFK 246
                                   *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1364.47
//
Query:       gi|91774328|ref|YP_567020.1|  [L=200]
Description: methyl-coenzyme M reductase operon protein C [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-06   25.5   1.0    1.1e-05   24.7   1.0    1.4  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 !   24.7   1.0     6e-10   1.1e-05      72     175 ..      37     146 ..      32     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6e-10
                         MCR_C  72 iavvsptLarhhlPhsaCDvaeylrraGaktnmiGlarGvg.......kriaqikeeekrlinehDlavfvlGnfkdCikk 145
                                   +  v+++  r+h+  + C+++  +rr+  +  ++ l  G g            i+ ee + i  h lav   Gn +d + k
  gi|91774328|ref|YP_567020.1|  37 VIAVAMSPGRRHITKPICELTYGMRREEIQVSVLVLNSGSGipdtpmrSGSFGITPEEIAQISRHKLAVIHTGNIRDHVVK 117
                                   556899999******************************994444331123358899************************ PP

                         MCR_C 146 kkeklfedievPvvvtggPeelkleevpga 175
                                   k ++++++ + P +v++   +++ e+++ +
  gi|91774328|ref|YP_567020.1| 118 KVREILKEADTPAIVVCQA-NIDFEDLARV 146
                                   *****************99.8999987443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1110.39
//
Query:       gi|91774329|ref|YP_567021.1|  [L=162]
Description: methyl-coenzyme M reductase, protein D [Methanococcoides burtonii DSM 6242]
Scores for complete 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-55  187.0   0.0    1.6e-55  186.9   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 !  186.9   0.0     9e-60   1.6e-55       1     141 [.      13     152 ..      13     154 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.9 bits;  conditional E-value: 9e-60
                         MCR_D   1 dveifpeRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGrillele 81 
                                   ++ei+p+R+L+pet+++lLnel+++egi+r+++hGprLPk+vpygpa+G++v+hk  k+i++++++++L v vGri+le+ 
  gi|91774329|ref|YP_567021.1|  13 QIEICPARFLSPETAQRLLNELSNIEGITRAFVHGPRLPKTVPYGPATGHDVDHKFSKNIQIGETDMDLAVIVGRIRLEIL 93 
                                   89******************************************************************************* PP

                         MCR_D  82 deeviekieeiceevlpfsyeikegkfirkkktvsDyakyGeeeadkrllGlvDpkskle 141
                                   +ee+ e+i+e+ce++lp++ye+++g fi++++tvsDyak+G+  ad+++lGl+Dpk k+ 
  gi|91774329|ref|YP_567021.1|  94 NEEIRENIREVCERTLPMGYEFRQGLFIQRRQTVSDYAKRGPG-ADPTTLGLADPKGKVG 152
                                   *******************************************.************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 939.22
//
Query:       gi|91774330|ref|YP_567022.1|  [L=434]
Description: methyl-coenzyme M reductase, beta subunit [Methanococcoides burtonii DSM 6242]
Scores for complete 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-132  439.6   8.6   6.3e-132  438.7   8.6    1.4  1  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    7.9e-82  273.3   2.6    7.9e-82  273.3   2.6    1.6  2  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi


Domain annotation for each model (and alignments):
>> MCR_beta  Methyl-coenzyme M reductase beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.7   8.6    7e-136  6.3e-132       1     246 [.     186     431 ..     186     434 .] 0.99

  Alignments for each domain:
  == domain 1  score: 438.7 bits;  conditional E-value: 7e-136
                      MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtvGtvv 81 
                                   G++lrni++nhv+ait ++a+naaalssi+eq++++emG+avG+fer++llg+ayqGlnann+vyd+vkengk+gt+Gtv+
  gi|91774330|ref|YP_567022.1| 186 GFSLRNIMTNHVAAITGRKAMNAAALSSIYEQAGMYEMGNAVGSFERHQLLGFAYQGLNANNVVYDIVKENGKTGTIGTVI 266
                                   8******************************************************************************** PP

                      MCR_beta  82 eslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleketglpGvdf 162
                                   ++++e+ai+ +vi+v+++ psgyk+y+++dv++wna aaaG+laa++vn+ga+raaq+vsst++y+nd+lek+tglpG+d+
  gi|91774330|ref|YP_567022.1| 267 DTVIEKAIDLGVIEVDHTAPSGYKFYKANDVSMWNACAAAGQLAATLVNCGAGRAAQNVSSTIVYFNDILEKQTGLPGCDM 347
                                   ********************************************************************************* PP

                      MCR_beta 163 GrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgevfgeidefreplk 243
                                   Gr++Gt+vGfsffshsiyGGGGpGifnGnhvvtrhs+Gfaipcv+aa+a+daGtq+ ++e+ts+lvg+vfg+i+efrep+k
  gi|91774330|ref|YP_567022.1| 348 GRAQGTGVGFSFFSHSIYGGGGPGIFNGNHVVTRHSRGFAIPCVSAACAIDAGTQMITIEKTSALVGNVFGSIEEFREPIK 428
                                   ********************************************************************************* PP

                      MCR_beta 244 ava 246
                                   ava
  gi|91774330|ref|YP_567022.1| 429 AVA 431
                                   *98 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 !  273.3   2.6   8.8e-86   7.9e-82       1     182 []       3     184 ..       3     184 .. 1.00
   2 ?   -2.9   0.1      0.49   4.4e+03      49      75 ..     254     280 ..     247     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 273.3 bits;  conditional E-value: 8.8e-86
                    MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivenadaia 81 
                                   Dk+d+ydd+G+llesdv++ +++P++n+ai ki+kd+krtva+nlagiek+l+tgk+ggk+++ilGr+l++div nadaia
  gi|91774330|ref|YP_567022.1|   3 DKVDIYDDRGTLLESDVDILNLAPTTNTAIGKIIKDTKRTVAINLAGIEKGLATGKYGGKGRQILGRSLEYDIVGNADAIA 83 
                                   9******************************************************************************** PP

                    MCR_beta_N  82 ekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaavlGryPqt 162
                                   e++ +lv+v++dddt vk+++gGkqllvqvPs+R++a+a++ +++++++aavve+ii++f++dmfda++vk+av+G+yPqt
  gi|91774330|ref|YP_567022.1|  84 ESVANLVKVSNDDDTVVKVIGGGKQLLVQVPSARTDAGADFVSGSTVSGAAVVETIINTFNTDMFDAPLVKGAVWGSYPQT 164
                                   ********************************************************************************* PP

                    MCR_beta_N 163 vdlaggnvasilsipqkneG 182
                                   +d++ggnvasilsipq+neG
  gi|91774330|ref|YP_567022.1| 165 MDMSGGNVASILSIPQQNEG 184
                                   *******************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.49
                    MCR_beta_N  49 ekalktgkvggkaskilGreldldive 75 
                                   ++  ktg++g+   ++  + +dl ++e
  gi|91774330|ref|YP_567022.1| 254 KENGKTGTIGTVIDTVIEKAIDLGVIE 280
                                   556688888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2462.40
//
Query:       gi|91774331|ref|YP_567023.1|  [L=409]
Description: hypothetical protein Mbur_2422 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-14   54.7   6.7    2.2e-12   47.6   5.1    3.3  3  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.097   12.4   0.1       0.26   11.0   0.0    1.7  2  MIX          Mitochondrial membrane-anchored proteins


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   5.1   2.5e-16   2.2e-12       7     158 ..      15     188 ..      10     195 .. 0.86
   2 ?   -0.2   0.0      0.13   1.1e+03      28     142 ..     232     249 ..     211     315 .. 0.64
   3 ?   -2.1   0.0      0.48   4.3e+03     126     143 ..     391     408 ..     350     409 .] 0.68

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.5e-16
                                   ESS--TTTSCCTT.......................HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEE.SSTGGGST CS
                                   xxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxx.xxxxxxxx RF
                   Radical_SAM   7 CnlrCsfCarpet.......................vrregrgrslsveeileevkelk.aekg.vkevilg.ggepllyp 61 
                                   C++ Cs+C++++                        + +e ++ +++ ++++ ev ++  ++ g  + ++++ +g+++ yp
  gi|91774331|ref|YP_567023.1|  15 CRGFCSYCYFKKVkdvpafgckhcfpfskgcdyctrGVKELYSGFKPAQYVMGEVSQAIhFSSGeLDKITISgSGDVSCYP 95 
                                   666666666666666666666666666666666666669****************9998899999666666538******* PP

                                   THHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  62 dfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                   d+ el+  l++ + + i++ +++  +  +ee +  + e gv+ vs+++ a+d+e   k+m   +++e  l++l+ + ++ +
  gi|91774331|ref|YP_567023.1|  96 DLKELVYLLSQFQ-KPIHLGYTSGKGFTSEEDASFFIENGVTEVSFTVFATDPEIRGKYM-NDPEPEISLAVLREFCAN-C 173
                                   ***********97.*************99*************************777777.67****************.* PP

                                   ETEEEEEEEBTTTSHH CS
                                   xxxxxxxxxxxxxxxx RF
                   Radical_SAM 143 krvvdrivglpGende 158
                                   + v+  iv++pG nd 
  gi|91774331|ref|YP_567023.1| 174 E-VYGAIVVIPGINDG 188
                                   *.************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  28 slsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslg 108
                                   + +v+e  ++v+e+                                                                   
  gi|91774331|ref|YP_567023.1| 232 THTVDEFTQIVREA------------------------------------------------------------------- 245
                                   33445555555555................................................................... PP

                                   EBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 109 leaaddekvlklmnrghtfeevlealeklreagi 142
                                                                +++  
  gi|91774331|ref|YP_567023.1| 246 -----------------------------ASK-H 249
                                   .............................433.2 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.48
                                   HHHHHHHHHHHHHHTTSE CS
                                   xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 126 tfeevlealeklreagik 143
                                   +fe ++e++e +++ g++
  gi|91774331|ref|YP_567023.1| 391 EFENFKELIEHINAIGMP 408
                                   467788888887777776 PP

>> MIX  Mitochondrial membrane-anchored proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.62   5.5e+03      64      83 ..      61      79 ..      55      86 .. 0.77
   2 ?   11.0   0.0   2.9e-05      0.26      93     150 ..     280     343 ..     270     345 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.62
                           MIX 64 padwlvpleltqvlkytsga 83
                                  pa+++   e++q ++++sg 
  gi|91774331|ref|YP_567023.1| 61 PAQYV-MGEVSQAIHFSSGE 79
                                  66654.46999999999997 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.9e-05
                           MIX  93 dqlrkevllqllnvkygrvkdpn...ggrv.....nrdveeiismavddleamdlspsadavlvpt 150
                                    ++rk+  +   nv  gr+++     gg v     n+d+  +i  ++ddl+++dls  +++vl+p 
  gi|91774331|ref|YP_567023.1| 280 PEVRKKATILTSNVAAGRLSEIFgklGGTVnviglNKDIGCLI--TIDDLNDIDLSEVTETVLIPG 343
                                   5678888888888888888875411256662122256776665..69*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2263.05
//
Query:       gi|91774332|ref|YP_567024.1|  [L=1185]
Description: DNA polymerase II large subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
          0 1328.3   0.0          0 1327.6   0.0    1.3  2  PolC_DP2         DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
       0.18   11.8  19.2          3    8.0   0.4    3.3  3  DZR              Double zinc ribbon
       0.95    9.9   0.0       0.95    9.9   0.0    3.8  4  Lar_restr_allev  Restriction alleviation protein Lar
        2.4    8.2  14.3        2.2    8.3   0.2    3.1  2  HypA             Hydrogenase/urease nickel incorporation, met
        6.9    7.0   9.7        3.5    8.0   2.4    3.2  3  Ribosomal_L32p   Ribosomal L32p protein family
        7.9    6.6  10.3       0.59   10.3   4.0    2.2  2  TerY_C           TerY-C metal binding domain


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1327.6   0.0         0         0       1     864 []      52     935 ..      52     935 .. 0.97
   2 ?   -4.3   0.1         1     3e+03     619     653 ..    1102    1140 ..    1099    1169 .. 0.48

  Alignments for each domain:
  == domain 1  score: 1327.6 bits;  conditional E-value: 0
                      PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeiaegkv 81 
                                   eYf++le +l++ ++i ++ars+g+dpk++vEiplAkdladRve+l+g+kgvae ir+le+++sree+al++++e+a+gkv
  gi|91774332|ref|YP_567024.1|  52 EYFNTLEGTLKKEIDIVNDARSRGKDPKPHVEIPLAKDLADRVENLIGVKGVAELIRKLEETMSREEAALALGREVAQGKV 132
                                   6******************************************************************************** PP

                      PolC_DP2  82 geaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDyvrkklgld 162
                                   ge++sk+ea++ a+r+++a+ltegvvaAP+eGi++ +i+knddg+ey++++yaGPiRsaGGtaqalsvLv+Dyvr+ +g+d
  gi|91774332|ref|YP_567024.1| 133 GEFDSKSEAIEAAIRVSVAMLTEGVVAAPIEGIDRASIGKNDDGSEYVSIFYAGPIRSAGGTAQALSVLVGDYVRRGVGID 213
                                   ********************************************************************************* PP

                      PolC_DP2 163 rykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrvRGGmllvlaeGi 243
                                   rykpr+ee+eRy+eEi lY+rvaslqy+ps+eeirliv+n+p++idGe+te eev+g+r+ler++tnrvRGGm+lvlaeG+
  gi|91774332|ref|YP_567024.1| 214 RYKPRKEEVERYIEEIMLYKRVASLQYTPSEEEIRLIVENCPICIDGEPTEAEEVEGHRNLERIDTNRVRGGMALVLAEGL 294
                                   ********************************************************************************* PP

                      PolC_DP2 244 alkakKikkkvkklklegWewleelika....ekeekkeeeeekkevkpkekylrdliaGRpvlshpsrkGGfRLrYGRsr 320
                                   alka+Ki+k+vk+lk++gWewle+li++    ++++++ee++ k+++kpk+ky+rdliaGRpv+shpsr+GGfRLrYGRsr
  gi|91774332|ref|YP_567024.1| 295 ALKAPKIQKHVKNLKIDGWEWLEQLISGvkssSESDEDEETDGKPKIKPKDKYMRDLIAGRPVFSHPSRPGGFRLRYGRSR 375
                                   ***************************954433333334444459************************************ PP

                      PolC_DP2 321 ntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddveealeikkeveeildlGei 401
                                   nt++a+agi Pa m ++d+f+a GtqlkverPgKaa+++pvdsiegPtv+l+nGdv+rid+++ea ++++eveei+d+Gei
  gi|91774332|ref|YP_567024.1| 376 NTSFAAAGISPAGMIVMDDFIAPGTQLKVERPGKAAGMAPVDSIEGPTVRLNNGDVIRIDTIDEAYALRSEVEEIIDIGEI 456
                                   ********************************************************************************* PP

                      PolC_DP2 402 LvayGeflennhpLvpasyveewwiqelekaaakkeaee....kpsaeealelseeldvpLhPkytylwhdisveelekLa 478
                                   L++yG+flennhpL+p++y++ewwiqe++kaa ++e++e    +p++e al+l++el++pLhPk+tylwhdi+++++++La
  gi|91774332|ref|YP_567024.1| 457 LINYGDFLENNHPLAPSPYCFEWWIQEYRKAAPDTETNEaelkEPTQEVALDLCKELNIPLHPKFTYLWHDIDNSQYTALA 537
                                   *****************************999998877788889************************************* PP

                      PolC_DP2 479 eavaekkkl..eeeklvleleee....vkeiLekllvehkvkeekivieealallkslgldleeekleke.eekdalelvn 552
                                   + +++++ l  + + l+l+l+++    +k++Le+llv+hk++++ ++iee l+l++slgld+e +k  ++  +++ le +n
  gi|91774332|ref|YP_567024.1| 538 DLISKDGLLeaDGSFLKLPLQRTidtgMKKVLEDLLVQHKIQGQALTIEEPLPLIHSLGLDEELSKGWDSlGHEELLENIN 618
                                   *******877666677777777677889*********************************99887655567789****** PP

                      PolC_DP2 553 elsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaak.k......kgeieveiarrkCkkCgk 626
                                   e++g+ vr +aptrigaRmGRPeKs++Rkm+pa+h+Lfpi eagg++rs+++aa+ k       g+i vei++r C++Cg 
  gi|91774332|ref|YP_567024.1| 619 EIAGFVVRPRAPTRIGARMGRPEKSDKRKMTPAPHALFPIAEAGGNTRSLEKAANfKvntnskAGTIPVEIGNRICPACGV 699
                                   ******************************************************9758899989999************** PP

                      PolC_DP2 627 etlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgereekleelkgvkgltskek 707
                                   e++e+rCe Cge t +kl C++c+ +v++ekc+kc++++++++ +kid+k++++ka+e++ger+ +l+++kgvk+++sk++
  gi|91774332|ref|YP_567024.1| 700 EGFEFRCE-CGEYTLPKLFCPRCGISVNKEKCPKCNSKTTCTSMRKIDFKSIYQKAFESIGERD-HLDSFKGVKKMMSKHM 778
                                   ********.*****************************************************66.9*************** PP

                      PolC_DP2 708 ipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsed 788
                                   +pEpleKgilRakh++++fkdgtvRyDm+d+plth+rp+eigvs+e++ elGY +Di+Gkpl +++q+++lkvqD+v+s d
  gi|91774332|ref|YP_567024.1| 779 TPEPLEKGILRAKHGLFTFKDGTVRYDMSDIPLTHIRPAEIGVSCERMIELGYLKDIYGKPLIDSEQVLCLKVQDLVISYD 859
                                   ********************************************************************************* PP

                      PolC_DP2 789 aaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                   aa+y+l++++++DdlL+k+y++ ++Yn+++ +d++G l++glaPHtsagvlgR+iGft+asvgyahPyfHaakRRn
  gi|91774332|ref|YP_567024.1| 860 AADYILRITQYIDDLLVKYYKVAPYYNAKHIDDIVGVLLMGLAPHTSAGVLGRLIGFTTASVGYAHPYFHAAKRRN 935
                                   ***************************************************************************9 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1
                      PolC_DP2  619 rkCkkCgke....tlearCeeCgekteeklvCkkceeev 653 
                                    ++C kC ++     l+  C++Cg ++  +++   +++  
  gi|91774332|ref|YP_567024.1| 1102 TRCVKCAAKfrrpPLTGSCPKCGGRVILTVHEGAVKKYL 1140
                                    455555543111134556777776666544444444433 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.8      0.12   3.5e+02      11      19 ..     690     698 ..     683     714 .. 0.73
   2 ?    3.9  14.0     0.018        55       1      39 [.     694     738 ..     694     742 .. 0.83
   3 ?    8.0   0.4   0.00099         3      12      38 ..    1101    1127 ..    1094    1131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.12
                           DZR  11 darfCseCg 19 
                                   ++r C++Cg
  gi|91774332|ref|YP_567024.1| 690 GNRICPACG 698
                                   556666666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.018
                           DZR   1 CpqCgee..........lppdarfCseCgtklkavaaedrCpsCgekvd 39 
                                   Cp Cg e           +  + fC++Cg +++    +++Cp+C++k++
  gi|91774332|ref|YP_567024.1| 694 CPACGVEgfefrcecgeYTLPKLFCPRCGISVN----KEKCPKCNSKTT 738
                                   78888888888877777777788**********....8******99865 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00099
                           DZR   12 arfCseCgtklkavaaedrCpsCgekv 38  
                                       C +C +k ++++    Cp+Cg  v
  gi|91774332|ref|YP_567024.1| 1101 RTRCVKCAAKFRRPPLTGSCPKCGGRV 1127
                                    456999999998888899999998766 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         3     9e+03       4       9 ..     252     257 ..     251     270 .. 0.75
   2 ?   -2.2   5.2         2   5.8e+03       6      36 ..     694     723 ..     691     729 .. 0.81
   3 ?   -2.6   4.4       2.6   7.8e+03       5      19 ..     729     743 ..     718     751 .. 0.78
   4 ?    9.9   0.0   0.00032      0.95       6      27 ..    1120    1141 ..    1118    1158 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
               Lar_restr_allev   4 kpCPfC 9  
                                   + CP C
  gi|91774332|ref|YP_567024.1| 252 ENCPIC 257
                                   57**** PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
               Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCga 36 
                                   CP Cg ++  +r + + +   +  +C  Cg 
  gi|91774332|ref|YP_567024.1| 694 CPACGVEGFEFRCECGEY-TLPKLFCPRCGI 723
                                   9****9999998888877.567999999998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.6
               Lar_restr_allev   5 pCPfCggravlersq 19 
                                    CP C+++ +   + 
  gi|91774332|ref|YP_567024.1| 729 KCPKCNSKTTCTSMR 743
                                   699999988876655 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00032
               Lar_restr_allev    6 CPfCggravlersqrvvaeigq 27  
                                    CP Cggr +l  +++ v+++ q
  gi|91774332|ref|YP_567024.1| 1120 CPKCGGRVILTVHEGAVKKYLQ 1141
                                    ***************9998776 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 ?    1.1   9.0      0.13     4e+02      69     101 ..     714     741 ..     673     751 .. 0.82
   2 ?    8.3   0.2   0.00075       2.2      69      97 ..    1100    1128 ..    1091    1139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                                   -EEEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                          HypA  69 vkvrCreCgkefeleekalrCpkCgsadveivs 101
                                    k+ C +Cg ++++e    +CpkC+s+  +++s
  gi|91774332|ref|YP_567024.1| 714 PKLFCPRCGISVNKE----KCPKCNSKT-TCTS 741
                                   5789*****877755....8****9964.5555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00075
                                    -EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                          HypA   69 vkvrCreCgkefeleekalrCpkCgsadv 97  
                                     ++rC +C ++f+    + +CpkCg++ +
  gi|91774332|ref|YP_567024.1| 1100 QRTRCVKCAAKFRRPPLTGSCPKCGGRVI 1128
                                    5789********97754679*****9743 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.13     4e+02      35      47 ..     687     699 ..     665     702 .. 0.73
   2 ?    8.0   2.4    0.0012       3.5      31      51 ..     707     727 ..     705     734 .. 0.85
   3 ?   -0.7   0.5       0.6   1.8e+03       8      33 ..    1098    1124 ..    1097    1129 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                                   EECTTC-BTTTTB CS
                Ribosomal_L32p  35 lklpHrvcpscGy 47 
                                   + +  r+cp+cG+
  gi|91774332|ref|YP_567024.1| 687 VEIGNRICPACGV 699
                                   56789******96 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0012
                                   TTCCEECTTC-BTTTTBSSSB CS
                Ribosomal_L32p  31 ncgelklpHrvcpscGyYkgr 51 
                                   +cge++lp+  cp cG   ++
  gi|91774332|ref|YP_567024.1| 707 ECGEYTLPKLFCPRCGISVNK 727
                                   5***************65554 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.6
                                    -HHHHHHHGGGT-----.-EEEETTTC CS
                Ribosomal_L32p    8 SksrrrkRrahwklkap.nlvecpncg 33  
                                    S++r+r    + k + p     cp+cg
  gi|91774332|ref|YP_567024.1| 1098 SRQRTRCVKCAAKFRRPpLTGSCPKCG 1124
                                    667777666565666662557999999 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.0    0.0002      0.59      57     119 ..     667     744 ..     653     750 .. 0.66
   2 ?   -1.5   0.4      0.83   2.5e+03      75      87 ..    1118    1130 ..    1104    1137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                        TerY_C  57 sderasnlkvntseL.......eGapgCPhCgnalafavCeCg.....kllCid...geeeatCpwCgkevkfgease 119
                                   s e+a n kvnt++        +G+  CP Cg +     CeCg     kl+C       +++ Cp+C+++++ +++ +
  gi|91774332|ref|YP_567024.1| 667 SLEKAANFKVNTNSKagtipveIGNRICPACGVEGFEFRCECGeytlpKLFCPRcgiSVNKEKCPKCNSKTTCTSMRK 744
                                   555666677777665111111246778*****9988889****55555588854212478899*****9998876554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                        TerY_C   75 pgCPhCgnalafa 87  
                                    ++CP Cg ++ ++
  gi|91774332|ref|YP_567024.1| 1118 GSCPKCGGRVILT 1130
                                    4688888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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):               6  [number of targets reported over threshold]
# CPU time: 0.99u 0.39s 00:00:01.38 Elapsed: 00:00:00.57
# Mc/sec: 6213.67
//
Query:       gi|91774333|ref|YP_567025.1|  [L=155]
Description: hypothetical protein Mbur_2424 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 858.41
//
Query:       gi|91774334|ref|YP_567026.1|  [L=571]
Description: pyruvate carboxylase subunit B [Methanococcoides burtonii DSM 6242]
Scores for complete 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-57  193.0   0.3    8.1e-57  192.2   0.3    1.4  1  PYC_OADA         Conserved carboxylase domain
    2.8e-50  171.3   0.0      4e-50  170.8   0.0    1.2  1  HMGL-like        HMGL-like
    7.3e-15   54.6   5.2    7.3e-15   54.6   5.2    2.0  2  Biotin_lipoyl    Biotin-requiring enzyme
    8.6e-05   22.3   0.3      0.096   12.5   0.0    2.5  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0017   19.1   1.3        1.3    9.8   0.0    3.3  3  HlyD_3           HlyD family secretion protein
     0.0017   18.3   3.2     0.0057   16.6   2.0    2.4  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0028   16.9   1.0       0.39    9.9   0.1    2.4  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
  ------ inclusion threshold ------
        2.4    8.1   5.6        3.1    7.7   0.5    2.5  2  GCV_H            Glycine cleavage H-protein


Domain annotation for each model (and alignments):
>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   0.3   3.6e-60   8.1e-57       1     195 [.     291     479 ..     291     483 .. 0.91

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 3.6e-60
                                   HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TTSS-- CS
                      PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegrykdip 81 
                                   V+ ++iPGG+l+nl +q+keq++ldk+e+vl+e+++v+++lG++++VTP+S++vg++Av+nvl+        +e ryk ip
  gi|91774334|ref|YP_567026.1| 291 VLLYQIPGGMLSNLVSQLKEQNALDKYEAVLEEMPKVREELGYPPLVTPTSQIVGTQAVLNVLM--------GE-RYKVIP 362
                                   789*************************************************************........86.****** PP

                                   HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHHHHHHHHHH CS
                      PYC_OADA  82 dsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypkvaekflkf 160
                                   ++v+d+++G +G+ p+++  e+++k++ +e pit+rpad+l+p ++e+l+ke+eek   k+eedvl+y+lyp++a kfl  
  gi|91774334|ref|YP_567026.1| 363 KEVKDYVRGLYGRSPAPISSEMIAKIIGDEMPITVRPADLLKP-EYESLKKEAEEKGlvKKEEDVLTYILYPAIAPKFLLG 442
                                   *******************************************.***********99667*******************98 PP

                                   HHHHHHHH..CTTTS........-SEEEEEETTEEEE CS
                      PYC_OADA 161 reeygdvsvlptkvffe..glkvgeeveveveggkyl 195
                                   ++e +++ + +  + ++    ++++++ ve+eg+ ++
  gi|91774334|ref|YP_567026.1| 443 EAEEEELVATKAATGVApvNVAIPTDYIVEIEGEVFE 479
                                   8877776644444444411555799999999999876 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.0   1.8e-53     4e-50       2     263 ..       3     268 ..       2     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 1.8e-53
                                   -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B........ CS
                     HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkka......r. 66 
                                   vki++t LRD++q+l ++++++ ++l+i+++Lde+g+ ++E+        +++ + ed++e++r++++ ++k+      r 
  gi|91774334|ref|YP_567026.1|   3 VKITETILRDAHQSLlATRMRTRNMLPIIDKLDEVGYYSLEMwggatfdtCIRYLNEDPWERLRELKSRMEKTpaqmllRg 83 
                                   89************99*******************************************************9977766625 PP

                                   ...--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT-BTTTBS- CS
                     HMGL-like  67 ..ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..velsledasrt 143
                                     +++++++ +++++++v +++++g +++++f+a+++              ++++e+a+  a++ g++   ++s++ ++ +
  gi|91774334|ref|YP_567026.1|  84 qnLVGYRHYSDDVVEKFVTKAHENGIDIFRIFDAVND--------------IRNMEKAISVAKNVGAHvqGTISYTISPVH 150
                                   67***********************************..............*****************66789******** PP

                                   -HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBT CS
                     HMGL-like 144 dleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtv 224
                                   ++e+ +e +++++e  +++i i+D+ G+l P+ea+eli  lk++v   +++++HcH + G+A +  laA +aG+d +d+++
  gi|91774334|ref|YP_567026.1| 151 TVEKYVEFANELAERDCDSICIKDMAGLLAPHEAYELITSLKKEVG--LPVALHCHCTSGMASMSYLAACKAGVDILDTAL 229
                                   **********************************************..********************************* PP

                                   TS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                     HMGL-like 225 nGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                   + l +++  +++e +vaal+++++dtgldl k+++++++
  gi|91774334|ref|YP_567026.1| 230 SPLAGGTSQPPTESVVAALQRTKYDTGLDLGKFTAASKY 268
                                   *********************************999875 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.0       7.8   1.7e+04      18      28 ..     129     139 ..     125     142 .. 0.65
   2 !   54.6   5.2   3.2e-18   7.3e-15      14      73 .]     510     570 ..     503     570 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 7.8
                                   SESSSTTCEE- CS
                 Biotin_lipoyl  18 evlvkvGdkVk 28 
                                   +v ++vG +V+
  gi|91774334|ref|YP_567026.1| 129 SVAKNVGAHVQ 139
                                   56666776665 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 3.2e-18
                                   E..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                 Biotin_lipoyl  14 eg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                   +g v+++ v+vGd+V++g+ ++++eamKme+ i a + Gvvk i v+eGd v+  ++l++i
  gi|91774334|ref|YP_567026.1| 510 QGmVLSINVSVGDTVEEGDKVCVIEAMKMENAIHASHGGVVKGIFVSEGDLVSKVEVLMTI 570
                                   367889************************************************9999987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   4.3e-05     0.096       5      42 ..     505     542 ..     504     545 .. 0.88
   2 !    8.5   0.1   0.00078       1.8       5      33 ..     542     570 ..     541     571 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
               Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqlal 42 
                                   +++   G V ++nV  G+ V++Gd   +++  + ++a+
  gi|91774334|ref|YP_567026.1| 505 VTSHMQGMVLSINVSVGDTVEEGDKVCVIEAMKMENAI 542
                                   56677899****************99999999998887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00078
               Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                   I+a+  G+V+ ++V +G+ V +  vL+++
  gi|91774334|ref|YP_567026.1| 542 IHASHGGVVKGIFVSEGDLVSKVEVLMTI 570
                                   788889****************9999998 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.6   3.6e+03      35      50 ..     458     473 ..     445     493 .. 0.53
   2 !    9.8   0.0   0.00057       1.3       2      31 ..     505     534 ..     504     539 .. 0.91
   3 !    6.2   0.1    0.0072        16       2      30 ..     542     570 ..     541     571 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                        HlyD_3  35 tllveakvpaadlgsi 50 
                                    + v +++p +++  i
  gi|91774334|ref|YP_567026.1| 458 VAPVNVAIPTDYIVEI 473
                                   3344444444444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00057
                        HlyD_3   2 lrApvdGvvvelnveegevvqagdelleii 31 
                                   +++  +G v ++nv++g+ v++gd++  i 
  gi|91774334|ref|YP_567026.1| 505 VTSHMQGMVLSINVSVGDTVEEGDKVCVIE 534
                                   789999*******************99885 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0072
                        HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                   + A+ +Gvv+ + v+eg+ v++ ++l++i
  gi|91774334|ref|YP_567026.1| 542 IHASHGGVVKGIFVSEGDLVSKVEVLMTI 570
                                   789************************99 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 ?   -1.2   0.0      0.86   1.9e+03      30      51 ..     336     357 ..     325     360 .. 0.85
   2 !   16.6   2.0   2.6e-06    0.0057      39      83 ..     511     556 ..     482     570 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.86
                        RnfC_N  30 lvlplsqhiGapakplvkvgdk 51 
                                   lv p sq +G++a + v  g++
  gi|91774334|ref|YP_567026.1| 336 LVTPTSQIVGTQAVLNVLMGER 357
                                   799**********999988876 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.6e-06
                        RnfC_N  39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekr 83 
                                   G+  ++ v+vgd+V++G+k+   e+  +  ++has  G Vk i   
  gi|91774334|ref|YP_567026.1| 511 GMVLSINVSVGDTVEEGDKVCVIEAmKMENAIHASHGGVVKGIFVS 556
                                   7777889**************9998667999**********99655 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00017      0.39     108     142 ..     502     536 ..     488     538 .. 0.82
   2 !    5.7   0.1    0.0033       7.3     109     139 ..     540     570 ..     534     571 .] 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlftiadl 142
                                   +  v++ ++G+V++ nv  G++v++gd++  i  +
  gi|91774334|ref|YP_567026.1| 502 EGAVTSHMQGMVLSINVSVGDTVEEGDKVCVIEAM 536
                                   557899999****************9999988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0033
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 109 vtvkapisGvVteknvreGqyvqpgdtlfti 139
                                     ++a+  GvV    v eG+ v++ ++l+ti
  gi|91774334|ref|YP_567026.1| 540 NAIHASHGGVVKGIFVSEGDLVSKVEVLMTI 570
                                   5689999999999999999999999999998 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.5     0.011        24      23      78 ..     467     520 ..     444     522 .. 0.81
   2 ?    7.7   0.5    0.0014       3.1      28      71 ..     508     550 ..     503     554 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
                                   -HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGG CS
                         GCV_H  23 tdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekl 78 
                                   td+  e  g+v  v++ ++g +v   e+ +  E v   + v + ++G v+ +N  +
  gi|91774334|ref|YP_567026.1| 467 TDYIVEIEGEVFEVKVEPAGGSVTVAEKSS--EVVECEGAVTSHMQGMVLSINVSV 520
                                   89999999***************9888755..6677889999**********9876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                                   HHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEE CS
                         GCV_H  28 eelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGev 71 
                                   ++ g v+++++  vg++v++g+++ ++E+ K+   + a   G v
  gi|91774334|ref|YP_567026.1| 508 HMQGMVLSINV-SVGDTVEEGDKVCVIEAMKMENAIHASHGGVV 550
                                   55667777776.69******************999999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 3171.73
//
Query:       gi|91774335|ref|YP_567027.1|  [L=498]
Description: pyruvate carboxylase subunit A [Methanococcoides burtonii DSM 6242]
Scores for complete 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-79  265.7   0.0    3.8e-79  265.1   0.0    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.6e-47  160.6   0.0    5.5e-47  158.9   0.0    1.9  2  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    1.2e-45  154.0   0.0    2.7e-45  152.9   0.0    1.7  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    1.7e-12   47.3   0.1    4.1e-12   46.1   0.1    1.6  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    4.7e-07   29.5   0.1    9.3e-07   28.6   0.1    1.5  1  ATP-grasp        ATP-grasp domain
    1.8e-06   28.1   0.0    3.5e-06   27.2   0.0    1.5  1  ATP-grasp_3      ATP-grasp domain
    1.3e-05   25.1   0.1    2.9e-05   23.9   0.1    1.7  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00035   20.2   0.0     0.0025   17.5   0.0    2.2  1  RimK             RimK-like ATP-grasp domain
     0.0087   15.8   0.0      0.019   14.7   0.0    1.5  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.058   12.8   0.0    1.5  1  ATP-grasp_5      ATP-grasp domain
      0.039   13.6   0.1      0.073   12.7   0.1    1.5  1  ATP-grasp_4      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.1   0.0   2.3e-82   3.8e-79       2     209 ..     116     321 ..     115     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 265.1 bits;  conditional E-value: 2.3e-82
                                   HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS- CS
                   CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkq 82 
                                   k +a++++ +++vpvvp+ ++++e+++eal++a++igyPv+ika++g+GG Gm+v+++++e++ ++++ ++ a++afg+++
  gi|91774335|ref|YP_567027.1| 116 KIAARKLMIEAGVPVVPGYDKAIEDVDEALEMADSIGYPVMIKASAGGGGIGMKVVYSKDEFQSSLESIQSVAQSAFGDPT 196
                                   67899**************************************************************************** PP

                                   EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEE CS
                   CPSase_L_D2  83 vlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtvefl 163
                                   v++ek++++p++iE+++l+D++gn+++v +re+s+q+r+qk++e+APs++L++e r++++eaavk+v+++g+++agtvefl
  gi|91774335|ref|YP_567027.1| 197 VFIEKYVEEPRHIEFQILADSHGNTVYVSDRECSIQRRHQKLMEEAPSPVLSPELRKKMGEAAVKAVKSIGYENAGTVEFL 277
                                   ********************************************************************************* PP

                                   EETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                   CPSase_L_D2 164 ldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                   ++  ++++y++EvNtRl+ve+ ++e +TGldlvk++++ia g++L+
  gi|91774335|ref|YP_567027.1| 278 YS--KGDFYFLEVNTRLQVEHCITELVTGLDLVKQQLHIACGKELP 321
                                   **..5**************************************997 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 !  158.9   0.0   3.4e-50   5.5e-47       1     110 []       1     110 [.       1     110 [. 0.99
   2 ?   -2.6   0.0       5.1   8.2e+03      11      30 ..     256     275 ..     254     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 3.4e-50
                                   ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE-- CS
                 Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpG 81 
                                   ++kkvlianrGeiA+ri+ra+rel+++tvavys++d+n+l+ ++adea+++gp+++s+sYln++ki+++akesga+ +hpG
  gi|91774335|ref|YP_567027.1|   1 MFKKVLIANRGEIAIRIMRACRELDVSTVAVYSDADKNALFPKYADEAYHIGPSPSSQSYLNMDKIIEVAKESGAEGIHPG 81 
                                   79******************************************************************************* PP

                                   SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                 Biotin_carb_N  82 yGflsEnaefaeaveeagivfiGPsaeal 110
                                   yGflsEn+ fa+++++agivfiGPs+e++
  gi|91774335|ref|YP_567027.1|  82 YGFLSENPVFAKKCKAAGIVFIGPSSEVI 110
                                   **************************987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.1
                                   HHHHHHHHHHHHHTT-EEEE CS
                 Biotin_carb_N  11 GeiAvriiravrelgietva 30 
                                   Ge+Av+ ++++   +  tv 
  gi|91774335|ref|YP_567027.1| 256 GEAAVKAVKSIGYENAGTVE 275
                                   89999999998877777664 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 !  152.9   0.0   1.7e-48   2.7e-45       1     107 [.     335     441 ..     335     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 1.7e-48
                                   EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS- CS
                 Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGvk 81 
                                   e+RinaEdp ++f+ps+Gk+t+++ p+gpgvR+dsgv+ g++++p+yDs++aKl+++getreea++r++raL e++i Gv+
  gi|91774335|ref|YP_567027.1| 335 ECRINAEDPLNDFAPSPGKITRYRSPGGPGVRIDSGVYMGYTIPPFYDSMIAKLCTWGETREEAISRMKRALYEFVIVGVT 415
                                   8******************************************************************************** PP

                                   BSHHHHHHHHH-HHHHHT---TTTCC CS
                 Biotin_carb_C  82 tnieflrailedeefakgeldtkfle 107
                                   tni+f++a+l++e+f++g+l+t+f+e
  gi|91774335|ref|YP_567027.1| 416 TNIPFHKAVLSNEAFVRGDLTTHFIE 441
                                   *************************8 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 !   46.1   0.1   2.5e-15   4.1e-12      28     174 ..     144     290 ..     122     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2.5e-15
                                   HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEEEEE CS
               Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklevsev 101
                                     ++ +++gypv++K++  G  +G++ v s++e+++ +e+  +       d +v++E+++ e r ie  +l + + ++  v
  gi|91774335|ref|YP_567027.1| 144 ALEMADSIGYPVMIKASAGGGGIGMKVVYSKDEFQSSLESIQSVaqsafgDPTVFIEKYVeEPRHIEFQILADSHGNTVYV 224
                                   4478899**************************9988765433222233399********999*********777666555 PP

                                   EEEE-SSSSS-HHHHHC.TT-EEESS-.---HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
               Dala_Dala_lig_C 102 geivvkkgfydyeakysddkaqlevpa.klekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                    ++    ++ + ++k +      e p   l++e ++k+ e+a+ka k ++ +  + v f+++ +g++++ EvNt
  gi|91774335|ref|YP_567027.1| 225 SDREC--SIQRRHQKLM-----EEAPSpVLSPELRKKMGEAAVKAVKSIGYENAGTVEFLYS-KGDFYFLEVNT 290
                                   55443..3445555554.....3333314899**************************9997.9*********9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   5.7e-10   9.3e-07      12     159 ..     136     291 ..     123     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.7e-10
                                   EEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEE CS
                     ATP-grasp  12 laveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvr 84 
                                    a+e+ +e+ e+a+++g+pv++K +  g  G G +vv s+++ ++ le +        ++ +v +E++v+  + +   +  
  gi|91774335|ref|YP_567027.1| 136 KAIEDVDEALEMADSIGYPVMIK-ASAGGGGIGMKVVYSKDEFQSSLESIqsvaqsafGDPTVFIEKYVEEPRHIEFQILA 215
                                   4689999****************.677779**************99999999999999999******************** PP

                                   ETTC-EEE-.-EEEEEEETTEEEEEEECEE-.SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
                     ATP-grasp  85 saeGetafy.pvvetvqedgilrlsvapaev.sekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                                   + +G+t+ + +    +q++    +  ap++v s +  kk  e a k+v+++g+    +vE+ +  +g+ ++ E+  R
  gi|91774335|ref|YP_567027.1| 216 DSHGNTVYVsDRECSIQRRHQKLMEEAPSPVlSPELRKKMGEAAVKAVKSIGYENAGTVEFLYS-KGDFYFLEVNTR 291
                                   ****9766514555677777666677777661567889999*******************8777.999999998877 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.1e-09   3.5e-06      25     159 ..     146     293 ..     114     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.1e-09
                                   EESS--SSSEEEEESS-------B--SS--TTE...................EEEE---.SEEEEEEEEE.SSSEEEEEEE CS
                   ATP-grasp_3  25 eeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefie.GkplSvsllsdgekvlvlavn 92 
                                   e +++  +++ +K + G+gg ++ vv  k+e ++++e+++             + +++e  +++  ++l+d + + v +  
  gi|91774335|ref|YP_567027.1| 146 EMADSIGYPVMIKASAGGGGIGMKVVYSKDEFQSSLESIQsvaqsafgdptvFIEKYVEePRHIEFQILADSHGNTVYVSD 226
                                   34455699****************************9999999********9888899626999******99988888888 PP

                                   EEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                   ATP-grasp_3  93 rqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                   r+   +++++       +p+   + ++++ e+a ++v+++ g      v++++++++ y++EvN Rl+
  gi|91774335|ref|YP_567027.1| 227 RECSIQRRHQKLMEEAPSPVLSPElRKKMGEAAVKAVKSI-GYENAGTVEFLYSKGDFYFLEVNTRLQ 293
                                   8877666776777777777765555***************.9999999******************97 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 !   23.9   0.1   1.8e-08   2.9e-05       1     106 [.     114     223 ..     114     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.8e-08
                                   HBHHHHHHHHHHTT--B-.-E.EEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHH..CTS-TTC CS
                        GARS_A   1 asKsfakdllkkagipta.ey.eaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkei..lekkkfG 77 
                                   +sK  a++l+ +ag+p    y +a++d++ea e+ ++ + ++  +Ka+   +g g++v+ s++e  + +++i  + + +fG
  gi|91774335|ref|YP_567027.1| 114 GSKIAARKLMIEAGVPVVpGYdKAIEDVDEALEMADSIGYPV-MIKASAGGGGIGMKVVYSKDEFQSSLESIqsVAQSAFG 193
                                   589999**********87666367899***************.9***************9999987777777223457788 PP

                                   CCCSSEEEEE---S...EEEEEEEEECTTEEE CS
                        GARS_A  78 eagekvviEelleG...eEvsllalvdgktvk 106
                                       +v iE+++e    +E+ +la + g+tv+
  gi|91774335|ref|YP_567027.1| 194 --DPTVFIEKYVEEprhIEFQILADSHGNTVY 223
                                   ..89*******985222688888888888875 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-06    0.0025      26     175 ..     137     300 ..     114     314 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                   S-S-HHHHHHTT-..-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH....GGG--.....EEEEE--SS-SEEEEEEE.. CS
                          RimK  26 deedaekliekik.lrfPvvvKsvegsqGikvvlakkeqklkqvlea....lkeai.....lvqeyieeaenediRvlv.. 94 
                                     ed+++ +e+ + ++ Pv++K + g  Gi++ +   +++ ++ le+     + a      ++ +y+ee    +  +l   
  gi|91774335|ref|YP_567027.1| 137 AIEDVDEALEMADsIGYPVMIKASAGGGGIGMKVVYSKDEFQSSLESiqsvAQSAFgdptvFIEKYVEEPRHIEFQILAds 217
                                   3455555555555568********99877665555555555555555333333332666669*******999999998632 PP

                                   ETTEEEEEEEEE--SSS----TTTT-EEEE-....---HHHHHHHHHHHHHCT-SEEE.EEEEEETTEEEEEEEESS--SH CS
                          RimK  95 vddevvaalrrvskeGdFRsnlhrGgvaekl....qlseeekelAikaakamelvvaG.vDllrakrgllvlEvnsspgle 170
                                    ++ v  + r  s +   R   ++   a       +l ++  e A+ka k ++   aG v+ l +k ++++lEvn+  ++e
  gi|91774335|ref|YP_567027.1| 218 HGNTVYVSDRECSIQ---RRHQKLMEEAPSPvlspELRKKMGEAAVKAVKSIGYENAGtVEFLYSKGDFYFLEVNTRLQVE 295
                                   344444443333333...33333333333330112455666689*************9678****************9999 PP

                                   HHHHH CS
                          RimK 171 kiekt 175
                                   +   +
  gi|91774335|ref|YP_567027.1| 296 HCITE 300
                                   86433 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 !   14.7   0.0   1.2e-05     0.019      44     113 ..     250     320 ..     213     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                  ATPgrasp_Ter  44 ekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllglet 113
                                   e ++++ e+a + ++++g +    v + + ++  + LE+N+R +    ++  ++G++l++  l+ + g+e 
  gi|91774335|ref|YP_567027.1| 250 ELRKKMGEAAVKAVKSIGYENAGTVEFLYSKGDFYFLEVNTRLQVEHCITeLVTGLDLVKQQLHIACGKEL 320
                                   55678899************************************9877772557**********9999633 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-05     0.058      13      54 ..     117     160 ..     111     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                   ATP-grasp_5  13 aeakelleaygipvvetrl..assaeeaveaaeeigypvvlKiv 54 
                                     a++l+   g+pvv+     +++++ea+e+a++igypv +K  
  gi|91774335|ref|YP_567027.1| 117 IAARKLMIEAGVPVVPGYDkaIEDVDEALEMADSIGYPVMIKAS 160
                                   5688999999*****9754449********************85 PP

>> ATP-grasp_4  ATP-grasp 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     0.073       1     159 [.     151     299 ..     151     300 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                   ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieG.eEfavdayfdeeGepvi 80 
                                   i +Pv iK s g + +G+ ++ +++e+++ +++i++    a     +++  + ++ +E+y+e    +   ++ d++G++v 
  gi|91774335|ref|YP_567027.1| 151 IGYPVMIKASAGGGGIGMKVVYSKDEFQSSLESIQSV---A-----QSAFGDPTVFIEKYVEEpRHIEFQILADSHGNTVY 223
                                   579*******************************954...3.....33344556689999975245677788888888886 PP

                   ATP-grasp_4  81 lnilkkefaseedvsdrl.yvtsakvieetlealeellkevnallglknfpvHiElrvsedgkiipiEvnplrfaglcst 159
                                   ++   +e + ++  ++ +    s+ ++ e  +++ e+  ++ + +g +n  + +E+  s+ g+ + +Evn +   + c+t
  gi|91774335|ref|YP_567027.1| 224 VSD--RECSIQRRHQKLMeEAPSPVLSPELRKKMGEAAVKAVKSIGYENAGT-VEFLYSK-GDFYFLEVNTRLQVEHCIT 299
                                   554..44444444444441234445556666777666666666777766554.7777664.6777777777766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 2793.06
//
Query:       gi|91774336|ref|YP_567028.1|  [L=321]
Description: biotin--acetyl-CoA-carboxylase ligase [Methanococcoides burtonii DSM 6242]
Scores for complete 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-17   61.6   0.0    4.6e-16   58.9   0.0    2.0  2  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
    6.5e-12   45.2   0.0    1.4e-11   44.1   0.0    1.6  1  HTH_11           HTH domain
    1.6e-09   37.5   0.9    3.8e-09   36.3   0.9    1.7  1  BPL_C            Biotin protein ligase C terminal domain
    3.8e-07   29.6   0.0    1.1e-06   28.0   0.0    1.9  1  HTH_24           Winged helix-turn-helix DNA-binding
    4.6e-07   29.5   0.0    9.4e-07   28.5   0.0    1.4  2  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
      0.006   16.4   0.0       0.44   10.4   0.0    3.1  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0063   16.5   0.0      0.062   13.3   0.0    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0097   16.2   0.0      0.071   13.5   0.0    2.2  2  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
       0.09   12.7   0.0       0.22   11.5   0.0    1.7  1  MarR             MarR family
       0.13   12.1   0.0       0.28   11.1   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm


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 ?   -0.1   0.0      0.46   8.3e+02      68      92 ..      32      60 ..      19      71 .. 0.72
   2 !   58.9   0.0   2.5e-19   4.6e-16       4     131 .]      90     210 ..      87     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.46
                                  HHHHHHHHHHHH..........HHTT-TT CS
                 BPL_LplA_LipB 68 vsllvlavlealg...y.rdskpgiegip 92
                                   +++v+++++alg   y + s pg   + 
  gi|91774336|ref|YP_567028.1| 32 SRTMVWKYMKALGeegYvIRSSPGSGHVL 60
                                  67899*******86543544556555555 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 2.5e-19
                                   EES-HHHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH. CS
                 BPL_LplA_LipB   4 vikstntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealg 80 
                                    ++stn+++k ++ ss  + g++v+++ q +Gr     +w sp g++++s++l+   +++ +++++++++   +av++a+ 
  gi|91774336|ref|YP_567028.1|  90 EVDSTNDVAK-KMGSS-SDEGTVVIAEMQDSGRgrkgGHWMSPRGGVWMSVILK---PNVVPAYAPRFTLMAGVAVAKAI- 164
                                   5789999888.44444.5899*********************************...67799******************. PP

                                   .....HHTT-TTEEEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                 BPL_LplA_LipB  81 yrdskpgiegipvfikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                         +  g+ ++ kwpnD++++++K+ Gi+++      ++  ++ig+g+n
  gi|91774336|ref|YP_567028.1| 165 ------RGLGVEASLKWPNDVLIGDKKVCGILTEMDAeCDQINFVIIGIGIN 210
                                   ......99**************************999778888889999988 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   7.8e-15   1.4e-11       3      54 ..       6      58 ..       4      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 7.8e-15
                        HTH_11  3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGY 54
                                   +i++ L++a ++ isgeeL   L++Sr+ v++++kaL e g+ I s+pg+G 
  gi|91774336|ref|YP_567028.1|  6 MDIIRALKRAGNNpISGEELGGILGISRTMVWKYMKALGEEGYVIRSSPGSGH 58
                                  69************************************************995 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.9   2.1e-12   3.8e-09       1      48 []     275     321 .]     275     321 .] 0.97

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.1e-12
                                   STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEEE CS
                         BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdislr 48 
                                   ++G+ V + +++++++G+avGI++ G Ll++t++g ++ i +G+++++
  gi|91774336|ref|YP_567028.1| 275 TIGRDVDVVTPQRIIRGKAVGITENGTLLVETAEG-LEEIVAGSCIHG 321
                                   69*********************************.*********986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   6.3e-10   1.1e-06       2      47 ..       2      49 ..       1      50 [. 0.95

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.3e-10
                        HTH_24  2 detdrkILelLqk..nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +++ +I+++L++  n  is  eL   lg+S++ v++++k L eeG++
  gi|91774336|ref|YP_567028.1|  2 TDKKMDIIRALKRagNNPISGEELGGILGISRTMVWKYMKALGEEGYV 49
                                  67899*********99*******************************9 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 ?   -3.2   0.0       2.8     5e+03      21      40 ..      98     117 ..      90     121 .. 0.70
   2 !   28.5   0.0   5.2e-10   9.4e-07      42     181 ..     134     270 ..     124     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
               BPL_LplA_LipB_2  21 vaaaaegcdagtvvyslaad 40 
                                    +++ +++d gtvv+++ +d
  gi|91774336|ref|YP_567028.1|  98 AKKMGSSSDEGTVVIAEMQD 117
                                   44555667999999988777 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 5.2e-10
               BPL_LplA_LipB_2  42 leaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilv.ngarvGgvrlaaseadeeevPdwlvvgle 121
                                   + ++++l+P+v  a A +   +++va++ A++ l+   v   l+wp+++l+ ++ ++G ++ + +e+d+    +++++g+ 
  gi|91774336|ref|YP_567028.1| 134 VWMSVILKPNVVPAYAPRFTLMAGVAVAKAIRGLG---VEASLKWPNDVLIgDKKVCGILTEMDAECDQ---INFVIIGIG 208
                                   5689******************************9...6899******998355667766655555544...467777766 PP

               BPL_LplA_LipB_2 122 lalekese..epGetpdetaLeeEGcaeveavalleslarhllawinrweedGfrpvhaewl 181
                                   ++++   e  +++ + ++t+L+e   +e+++ a +++l r l     r + +Gf+++ +ew+
  gi|91774336|ref|YP_567028.1| 209 INVNVLIEelSEDLRSSSTSLSEIKGEELDRIAFVQALLRALEDEYIRSKTSGFDSILEEWR 270
                                   665554443499999999*******************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00025      0.44       8      39 ..       8      41 ..       2      43 .. 0.88
   2 ?   -2.3   0.0       2.2     4e+03       1       9 [.      73      81 ..      73      82 .. 0.91
   3 ?    2.0   0.0       0.1   1.9e+02       8      25 ..     214     231 ..     212     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                 HTH_AsnC-type  8 ILeaLqed..aRisyaeLAervGlSestvlrRvr 39
                                  I++aL +     is +eL+  +G+S++ v++ ++
  gi|91774336|ref|YP_567028.1|  8 IIRALKRAgnNPISGEELGGILGISRTMVWKYMK 41
                                  999999998899*****************98665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                 HTH_AsnC-type  1 LDeiDrkIL 9 
                                  +D +D  I+
  gi|91774336|ref|YP_567028.1| 73 MDGLDTSII 81
                                  9*****998 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.1
                 HTH_AsnC-type   8 ILeaLqedaRisyaeLAe 25 
                                   ++e+L ed R s + L+e
  gi|91774336|ref|YP_567028.1| 214 LIEELSEDLRSSSTSLSE 231
                                   89******9999999887 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.5e-05     0.062      20      65 ..      18      67 ..       7      68 .. 0.80
   2 ?   -0.3   0.0      0.58     1e+03       2      41 ..     185     232 ..     184     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                                  EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE...TEE.EEES-HHHH CS
                     HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr...grr.irildleaL 65
                                   p++ eel+ +lG++r  v + +++L +eg++ r   g + + +  +++L
  gi|91774336|ref|YP_567028.1| 18 NPISGEELGGILGISRTMVWKYMKALGEEGYVIRsspGSGhVLVSAPDKL 67
                                  5999**************************98742334334877777776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHCTTT.......C.EEEEEHHHHHHHHHTTSSHHHHHHH CS
                     HTH_Crp_2   2 RlArfLlrlaerag.......g.eielpltqeelAsmlGltretvsri 41 
                                   +++  L +++++ +       g  i++++  eel++ l ++  ++s i
  gi|91774336|ref|YP_567028.1| 185 KVCGILTEMDAECDqinfviiGiGINVNVLIEELSEDLRSSSTSLSEI 232
                                   688888888443222334444466788999999999999999998875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   3.9e-05     0.071      20      73 ..      14      66 ..       6      74 .. 0.84
   2 ?   -0.7   0.0         1   1.8e+03      56      67 ..     117     128 ..     109     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                                  SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE.EEETTT-TCEEESSHCCC CS
                          Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglv.ksvrGkgGGyrLakppee 73
                                  +++++p+s ee+    +is++++ k ++ L ++g+v +s  G   G +L  +p++
  gi|91774336|ref|YP_567028.1| 14 RAGNNPISGEELGGILGISRTMVWKYMKALGEEGYViRSSPGS--GHVLVSAPDK 66
                                  566778****************************864899998..8888888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1
                                   EEETTT-TCEEE CS
                          Rrf2  56 ksvrGkgGGyrL 67 
                                    s rG++GG ++
  gi|91774336|ref|YP_567028.1| 117 DSGRGRKGGHWM 128
                                   5889*****876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.22       2      50 ..       2      52 ..       1      55 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                  -HHHHHHHHHHHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  2 tltqfviLrilyeqgplsvs..eLakklgvskstvtrvldrLekkGlieRs 50
                                  t   ++i+r l++ g+  +s  eL+  lg+s+++v +  ++L ++G++ Rs
  gi|91774336|ref|YP_567028.1|  2 TDKKMDIIRALKRAGNNPISgeELGGILGISRTMVWKYMKALGEEGYVIRS 52
                                  6667899999*****9888889**************************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 ?   11.1   0.0   0.00016      0.28      22      56 ..      19      53 ..      15      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                  CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  p + +e+  +lg++r+ v ++++ L + G+V r+ 
  gi|91774336|ref|YP_567028.1| 19 PISGEELGGILGISRTMVWKYMKALGEEGYVIRSS 53
                                  5567889999*********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1865.18
//
Query:       gi|91774337|ref|YP_567029.1|  [L=186]
Description: hypothetical protein Mbur_2428 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   22.8   1.8    5.8e-05   22.3   1.8    1.1  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 !   22.3   1.8   3.2e-09   5.8e-05     104     203 ..      36     125 ..      32     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.2e-09
                       S-layer 104 vlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyvyekdlgdeddvviiavhv 184
                                   vl+d  +   +++  +++  +gY   +k++  dg +vw+eL  dg  + ++++++    s ++y ++ ++     i+ + +
  gi|91774337|ref|YP_567029.1|  36 VLMDG-KGIFIETKGEWHFSQGYLFVVKDVSDDG-NVWVELLLDGVLLKDEILNE---GSVFIYLHNSKE-----IFNITL 106
                                   56665.3444556666************998777.5*******************...******876554.....899999 PP

                       S-layer 185 devfrgtedslvviegifq 203
                                   d+v+ g++ +l+++  ++q
  gi|91774337|ref|YP_567029.1| 107 DSVYYGSDGDLITFIPVYQ 125
                                   9999999999999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1049.88
//
Query:       gi|91774338|ref|YP_567030.1|  [L=307]
Description: phosphoserine phosphatase [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0003   20.5  14.5      0.036   13.6   1.2    3.4  3  PspA_IM30        PspA/IM30 family
     0.0004   20.4  12.3       0.13   12.3   4.6    3.1  3  DUF1664          Protein of unknown function (DUF1664)
    0.00056   19.3  11.3       0.25   10.6   5.0    3.2  3  DUF3450          Protein of unknown function (DUF3450)
     0.0031   17.0   2.1     0.0031   17.0   2.1    3.0  2  DUF4618          Domain of unknown function (DUF4618)
  ------ inclusion threshold ------
      0.012   15.9   2.7       0.17   12.2   0.1    2.5  2  IL5              Interleukin 5
      0.027   14.3  12.3       0.16   11.8   4.8    2.4  2  Spc29            Spindle Pole Component 29
       0.03   14.9   4.5        1.1    9.9   0.5    3.4  2  SlyX             SlyX
       0.03   13.7  24.6      0.058   12.8  11.2    2.3  2  GAS              Growth-arrest specific micro-tubule binding
      0.031   14.4  22.2       0.03   14.4   2.8    3.4  3  DUF848           Gammaherpesvirus protein of unknown function
       0.04   13.0   5.8      0.044   12.8   0.9    2.2  2  Perilipin        Perilipin family
       0.04   13.9  17.2       0.48   10.4   0.8    2.9  4  Laminin_II       Laminin Domain II
      0.049   13.9  21.3       0.63   10.3   0.8    4.0  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.057   13.9   9.4        0.5   10.9   1.1    3.3  3  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.082   13.3  22.3        0.5   10.8   3.4    2.3  2  Fez1             Fez1
      0.083   12.3  11.8       0.54    9.6   3.1    3.0  3  DUF4527          Protein of unknown function (DUF4527)
      0.087   12.9   3.2         29    4.7   0.6    3.1  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        0.1   12.5  19.1        1.5    8.7   0.1    3.5  3  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
       0.18   10.9  23.3       0.25   10.4   4.3    2.4  2  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.18   12.1   1.3       0.87    9.9   0.4    2.6  2  TetR_C_24        Tetracyclin repressor-like, C-terminal domai
       0.22   10.9  15.5    1.3e+02    1.7  15.5    2.2  1  DUF4407          Domain of unknown function (DUF4407)
       0.23   11.8  12.8       0.65   10.3   0.4    4.0  3  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.45   11.2  21.3       0.45   11.2   1.2    3.9  3  YabA             Initiation control protein YabA
        0.5   10.9  22.9        1.2    9.7   5.6    3.1  3  APG6_N           Apg6 coiled-coil region
       0.51   10.1  23.3        0.9    9.3   8.5    2.8  3  DUF724           Protein of unknown function (DUF724)
       0.58   10.0  13.8        1.1    9.0   2.3    4.1  4  DivIC            Septum formation initiator
       0.68   10.4  13.7        1.9    8.9   4.1    3.6  2  Snapin_Pallidin  Snapin/Pallidin
       0.69   10.0  20.5        1.4    9.0   9.2    3.7  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.69    8.7  10.2       0.19   10.6   1.8    2.4  2  5_nucleotid      5' nucleotidase family
       0.93    9.9   5.9        2.3    8.6   0.9    3.7  3  kleA_kleC        Uncharacterized KorC regulated protein A
        1.1    9.7  10.9       0.44   11.0   1.5    4.0  5  UPF0184          Uncharacterised protein family (UPF0184)
        1.1    9.1   5.6         33    4.4   0.1    3.8  3  HSBP1            Heat shock factor binding protein 1
        1.1    8.9  24.9        4.5    7.0  12.8    3.0  2  DUF4201          Domain of unknown function (DUF4201)
        1.7    9.0  10.5        1.2    9.5   0.1    4.1  3  TSC22            TSC-22/dip/bun family
        1.7    8.4   8.8        6.5    6.5   0.4    3.0  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        2.6    8.2  20.2          1    9.6   5.2    2.7  2  ATG16            Autophagy protein 16 (ATG16)
          3    8.2  17.9        1.8    8.9   2.3    3.2  3  DUF641           Plant protein of unknown function (DUF641)
          3    8.4  18.1        9.2    6.8   7.5    3.7  2  DUF16            Protein of unknown function DUF16
        3.4    8.3  14.4        7.1    7.2   0.7    4.3  3  YtxH             YtxH-like protein
        4.4    7.8  20.3        2.1    8.9   1.3    3.9  3  ZapB             Cell division protein ZapB
        4.5    7.6  10.5         19    5.6   0.1    3.8  3  DUF948           Bacterial protein of unknown function (DUF94
        5.7    7.7  16.2        2.6    8.8   1.5    3.9  4  Occludin_ELL     Occludin homology domain
          6    7.6  16.2        4.4    8.0   0.3    3.9  4  DUF2203          Uncharacterized conserved protein (DUF2203)
          8    6.0  17.5       0.51    9.9   2.5    2.8  3  HAUS-augmin3     HAUS augmin-like complex subunit 3
        9.8    6.4  20.3         12    6.1   1.2    3.9  4  Fib_alpha        Fibrinogen alpha/beta chain family


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 !   10.3   2.3   0.00096      0.39      93     144 ..      11      62 ..       5      83 .. 0.86
   2 ?    3.2   1.2      0.14        56      96     135 ..      77     116 ..      61     133 .. 0.78
   3 !   13.6   1.2   8.8e-05     0.036      91     146 ..     211     266 ..     206     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00096
                     PspA_IM30  93 ikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkareka 144
                                    k+l++++++++t+ +  + + + + + l+   t+i+elk+k+++l a+ k 
  gi|91774338|ref|YP_567030.1|  11 EKDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKE 62 
                                   5899******************************************999764 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                     PspA_IM30  96 lekqaealetqlaqqrsaveqlrkqlealetkieelkakk 135
                                   + +++ + +   ++ rs   ++++++++l+tk +e+ ++ 
  gi|91774338|ref|YP_567030.1|  77 ANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQS 116
                                   5677888888899999999999999999999999988775 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 8.8e-05
                     PspA_IM30  91 aeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaak 146
                                   ++i +l k+a  +++q ++  + v  +r++++ l++ki+el+++  +++ +++ ++
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQ 266
                                   5788999**************************************99998877665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   4.6   0.00032      0.13      55     119 ..      47     111 ..      29     116 .. 0.91
   2 ?   -0.4   0.0       2.7   1.1e+03      59      94 ..     162     197 ..     146     203 .. 0.50
   3 !   11.9   0.2   0.00043      0.17      41     121 ..     183     266 ..     174     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00032
                       DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                   ++l++ +++L+++++++ +k  e k++    +e+++e+++  +ei+++ ++v   +++l++k ++
  gi|91774338|ref|YP_567030.1|  47 DELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDE 111
                                   7899*******************************************************999665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.7
                       DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevre 94 
                                   ++ ++L s+i +  ++ ++  ++   + ++v+ + e
  gi|91774338|ref|YP_567030.1| 162 SQADELHSKIVETYRSSESIYKADGTVGKDVKGLAE 197
                                   233455555555555555555555555555555444 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00043
                       DUF1664  41 davesvskqleqvseslaatkrhLs.....sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                   +a  +v+k+++ + e+  ++k+hLs     ++id++ k+ d   + +ke+ + v+ +re+++ ++ +++++++  +    k
  gi|91774338|ref|YP_567030.1| 183 KADGTVGKDVKGLAEE--SQKHHLSmlasyKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDK 261
                                   5666778888887775..66777754445579**************************************99999998889 PP

                       DUF1664 117 lerie 121
                                   l++i+
  gi|91774338|ref|YP_567030.1| 262 LNEIQ 266
                                   98886 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.8     0.021       8.6      51      98 ..      44      91 ..       4      99 .. 0.75
   2 !   10.6   5.0    0.0006      0.25      28     153 ..      49     175 ..      38     183 .. 0.82
   3 !   10.1   0.2   0.00091      0.37      15      93 ..     189     267 ..     181     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.021
                       DUF3450 51 aeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98
                                   ++ +lke+ ++l+++ ++l+   ++ ++ ++  +e+i+ei+ +++e+
  gi|91774338|ref|YP_567030.1| 44 TNIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEI 91
                                  456667777777777777777777777777777777777777777766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0006
                       DUF3450  28 avaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmi.d 107
                                     +++ + ++++++l+ +++e ++    ++e +++++  +++ ++  +++  +i++l+++ +e ++ +r+ v  l +   +
  gi|91774338|ref|YP_567030.1|  49 LKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSVESLSRAYaA 129
                                   55677788888899999888888888888999999******************************9999999999987626 PP

                       DUF3450 108 rLeqfveldlPflle.eRqarlakLkelmdradvslaekyrrvleay 153
                                   +L++f ++d+P + e +  ++l +L e +d a+ ++ e   +++e+y
  gi|91774338|ref|YP_567030.1| 130 ELDKFLNADIPLKHEiDIFEKLSDLGERIDAAS-QADELHSKIVETY 175
                                   8***********998777788888887776644.4556666677766 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00091
                       DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                    ++++ + +e++k + +  +s kkid+l +e++ + a++++  + ++ ++ + + l++ +++++ e++    +++ei+ 
  gi|91774338|ref|YP_567030.1| 189 GKDVKGLAEESQKHHLSMLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQV 267
                                   5677778888888888888889999999999999999999998888888888888888888888888888888888875 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.1   7.6e-06    0.0031     165     228 ..       9      72 ..       2      76 .. 0.86
   2 ?    4.2   4.1     0.062        25     162     228 ..     188     253 ..      71     265 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.6e-06
                       DUF4618 165 llkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepre 228
                                   + ++  ++t++ +++ ++++ +  + + + ++ +r +i+el+e+ ++L+a+v++L+ +a+e ++
  gi|91774338|ref|YP_567030.1|   9 MSEKDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDKK 72 
                                   5555567888999999999999999999******************************998765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.062
                       DUF4618 162 kekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepre 228
                                     k +k lae+++k+ + ++l+   +  +l+ke + +  +i+e    ++ ++++++ L+a++ e r+
  gi|91774338|ref|YP_567030.1| 188 VGKDVKGLAEESQKH-HLSMLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRD 253
                                   445567788888777.556666778888999999999999999999999999999999999888886 PP

>> IL5  Interleukin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.19        79      54      93 ..      22      62 ..       5      99 .. 0.77
   2 ?   12.2   0.1   0.00042      0.17      35     101 ..     198     265 ..     167     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.19
                                  HTTS--.SSTHHHHHHHHHHHHHHHHHHHHTTTSSEEEHHH CS
                           IL5 54 knqtvq.geaveklfqnlslikkyidlqkkkcgeerrrvkq 93
                                  ++++++ + +++ +f++l+l +  id  k+k  +   +vk+
  gi|91774338|ref|YP_567030.1| 22 RTKITHnERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKE 62
                                  44444414578888888888888888888876666666654 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00042
                                   SSS-GGGGHHHHHHHHHHHHTTS.--SSTHHHHHHHHHHHHHHHHHHHHTTTSSEEEHHHHHHHHHHH CS
                           IL5  35 vhknhqlcieeifqGidtlknqt.vqgeaveklfqnlslikkyidlqkkkcgeerrrvkqfldylqef 101
                                   + ++h+l +   ++ id l++     +  +++ ++ +s i++ id  k k +e r +   +ld l+e 
  gi|91774338|ref|YP_567030.1| 198 ESQKHHLSMLASYKKIDELRKEAdLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEI 265
                                   6789***************87762567789**********************************9985 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.8    0.0004      0.16     117     208 ..      16     115 ..       1     136 [. 0.74
   2 ?    7.4   0.8    0.0087       3.5     111     162 ..     205     256 ..     149     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                         Spc29 117 kkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaalehSnrkfrsys............sapsnst 185
                                   +++++   k+ +++ ++k   r l+ +rt ++eL+ek ++l+ +vk+la+    ++k+r  +            +++s + 
  gi|91774338|ref|YP_567030.1|  16 NTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDIAneniseikgtrdEIRSEK- 95 
                                   3333455699****************************************999999999888888887776655555544. PP

                         Spc29 186 tkefvgslyensddtrWdqpslr 208
                                    ++  gs+ e  ++t+ d++ ++
  gi|91774338|ref|YP_567030.1|  96 -NKVTGSITE--LKTKRDEYNKQ 115
                                   .445555443..46665555543 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0087
                         Spc29 111 siyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevk 162
                                   s+  s kki+el k  d  + +Ike    +   r  ++ L+ k+ el +e+ 
  gi|91774338|ref|YP_567030.1| 205 SMLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELS 256
                                   45578899****************************************9982 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5    0.0027       1.1      10      58 ..      23      71 ..      14      81 .. 0.88
   2 ?    4.7   0.3      0.11        47      17      48 ..     225     256 ..     210     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0027
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                          SlyX 10 iklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58
                                  +k+++ e+t++   + +  ++  id+l+++ ++l+ ++kel++++++++
  gi|91774338|ref|YP_567030.1| 23 TKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDK 71
                                  8999*************************************99987665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                          SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlk 48 
                                    +i+e  dvv   +++id l++++ +l+++l+
  gi|91774338|ref|YP_567030.1| 225 AQIKETYDVVSPIREKIDPLKAKISELRDELS 256
                                   56778888888899999999999999998884 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  11.2   0.00014     0.058      29     136 ..      12     123 ..       9     130 .. 0.83
   2 ?    6.7   5.5      0.01       4.2      39     128 ..     182     275 ..     164     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                           GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk....dlk 105
                                   k lK+ +++ ++k ++ne+ l+ +  + k  + ++ +++e++++L++q+k+   +  + k+l+   +e  +e+k    +++
  gi|91774338|ref|YP_567030.1|  12 KDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKgtrdEIR 92 
                                   78*********************************************9998887777777777777777777761111555 PP

                           GAS 106 wehevleqrfekvekerdelykkfeaaiqev 136
                                    e++ +   +++++ +rde +k+ + +++ +
  gi|91774338|ref|YP_567030.1|  93 SEKNKVTGSITELKTKRDEYNKQSRGSVESL 123
                                   666667777899********99999888765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                           GAS  39 kkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqs....lknlkarlkelekelkdlkwehevleqrf 115
                                    k +    k+++ +++e ++    + +  ++++eLrk++  y+ + ++       +++++  l+ ++++l+ e  v  +++
  gi|91774338|ref|YP_567030.1| 182 YKADGTVGKDVKGLAEESQKHHLSMLASYKKIDELRKEADLYHAQIKEtydvVSPIREKIDPLKAKISELRDELSVYLDKL 262
                                   566667778888899999999999999999999999999999877665222245679999999****************** PP

                           GAS 116 ekvekerdelykk 128
                                   ++++ e+de +  
  gi|91774338|ref|YP_567030.1| 263 NEIQVEKDEKKLD 275
                                   *999999986544 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.9     0.094        38      51     104 ..       7      60 ..       2      62 .. 0.81
   2 ?    7.0   6.8     0.015       5.9      51     126 ..      45     118 ..      37     131 .. 0.88
   3 ?   14.4   2.8   7.3e-05      0.03      88     127 ..     239     278 ..     195     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.094
                        DUF848  51 qlkrtkeikalveavdteieakkkelslLkk.lnrkkvarveeLtdkvlelkeev 104
                                   ++  +k++k++v+ + t+i+++++ l+ + + l  ++ ++++eL++k   l+++v
  gi|91774338|ref|YP_567030.1|   7 STMSEKDLKNTVNDYRTKITHNERTLKGVFRdLKLHR-TNIDELKEKRDKLNAQV 60 
                                   5667899**************9999998766466665.67999999999988877 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.015
                        DUF848  51 qlkrtkeikalveavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsleeaqeeyqegesset 126
                                   ++ + ke +++++a  +e+ +k +e ++L+ +  +++ ++   +d++   k+ v+  + +l+ + +ey+++  s  
  gi|91774338|ref|YP_567030.1|  45 NIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQ--SRG 118
                                   6778899999**********************************************************944..333 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 7.3e-05
                        DUF848  88 arveeLtdkvlelkeevsleldsleeaqeeyqegessets 127
                                   ++++ L+ k+ el++e+s+ ld+l+e q e+ e++ +e +
  gi|91774338|ref|YP_567030.1| 239 EKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKKLDEKH 278
                                   68999*************************9988766655 PP

>> Perilipin  Perilipin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.12        47     292     351 ..      49     107 ..       8     135 .. 0.60
   2 ?   12.8   0.9   0.00011     0.044     223     304 ..     203     287 ..     166     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                   -----..SHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHH CS
                     Perilipin 292 eeeeeeeeeqvEsrtLsllrsltqqLqttcqslvssiqglPssvqekvqqarrsaeelqa 351
                                     +e++++ ++  + L++     ++L++  ++ +s+i+g  ++++ + ++++ s++el++
  gi|91774338|ref|YP_567030.1|  49 L-KEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKT 107
                                   2.2222345555555666666666666666666666666666666666666666666655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--...---------------------------------.....SH CS
                     Perilipin 223 erAyqhsleklrqakqraqealaqlsstldLielakkglsaanqklseaqekllqswlewkkkqqeeseeeeeeee...ee 300
                                   + ++  s +k+ + +++a    aq+++t d+++ ++++++ ++ k+se +++l   + + ++ q e++e++ +e++   +e
  gi|91774338|ref|YP_567030.1| 203 HLSMLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKKLDEKHivaKE 283
                                   55778899*********************************************9999999999999999988887777755 PP

                                   HHHH CS
                     Perilipin 301 qvEs 304
                                   + E+
  gi|91774338|ref|YP_567030.1| 284 KFEK 287
                                   5554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.8    0.0051       2.1      19     109 ..      11      98 ..       2     116 .. 0.79
   2 ?    4.3   0.7     0.092        38       1      84 [.      77     160 ..      77     181 .. 0.67
   3 ?   -1.5   0.0       5.6   2.3e+03      31      54 ..     162     185 ..     145     201 .. 0.49
   4 ?   10.4   0.8    0.0012      0.48      24      84 ..     211     271 ..     192     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0051
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHH CS
                    Laminin_II  19 laplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseikelI 99 
                                    ++l++ ++  + k+ + +r+++ +  ++k   + i++ +++  kL+ ++ +L  k +e k+l++      +niseik   
  gi|91774338|ref|YP_567030.1|  11 EKDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDI---ANENISEIKGTR 88 
                                   567888888888888888888888888888888888888888888888888888888888888888...568999999877 PP

                                   HHHHHHHHT- CS
                    Laminin_II 100 aqARkaAnki 109
                                      R+  nk+
  gi|91774338|ref|YP_567030.1|  89 DEIRSEKNKV 98 
                                   7777777776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.092
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                    Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldklkelkq 80 
                                   ++e+++e++ t  e+ + ++++   + ++k k  e n++ +   e ++ ++   ++   ++   L++++ ++++kl+ l +
  gi|91774338|ref|YP_567030.1|  77 ANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSVESLSrAYAAELDKFLNADIPLKHEI-DIFEKLSDLGE 156
                                   678999999999999999999999999999999999988666666665233333333333334444444.46666666666 PP

                                   HHHH CS
                    Laminin_II  81 leea 84 
                                   + +a
  gi|91774338|ref|YP_567030.1| 157 RIDA 160
                                   6555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.6
                                   XXXXXXXXXXXXXXXXXXXXXXXX CS
                    Laminin_II  31 eklseinrsveetnekvkdankai 54 
                                   +++ e+++++ et    ++  ka 
  gi|91774338|ref|YP_567030.1| 162 SQADELHSKIVETYRSSESIYKAD 185
                                   234444445445544444444444 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0012
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II  24 qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                   ++++++++++   +++++et ++v+   + i+  + ++++L  ++ + ldkl+e++  +++
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDE 271
                                   578899999999999999**********************************999877665 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 ?    6.4  10.9     0.025        10       3      70 ..      38     114 ..      36     142 .. 0.58
   2 ?    0.6   0.2       1.6   6.4e+02      57      98 ..     179     221 ..     120     227 .. 0.60
   3 ?   10.3   0.8    0.0015      0.63      43      98 ..     211     270 ..     198     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.025
                                   -HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHH........HHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TC CS
                  Seryl_tRNA_N   3 DiklirenpeavkeklkkRgedkadvdelleldekrr........elqveleelqaerNelskeIgkakkkk.edae 70 
                                   D+kl r+n++++kek  k +++++++++    d+k r        e++ + +e+++e+N+++ +I ++k k  e  +
  gi|91774338|ref|YP_567030.1|  38 DLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRdianenisEIKGTRDEIRSEKNKVTGSITELKTKRdEYNK 114
                                   67777777777777777666555555555555555551111111133445677777777777777777766533333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.6
                                   HHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  57 keIgkakkkk....edaeeliaevkelkeelkaleaelkeleaele 98 
                                   ++I ka   +    +d + l +e+++    + a  ++ +el++e +
  gi|91774338|ref|YP_567030.1| 179 ESIYKA---DgtvgKDVKGLAEESQKHHLSMLASYKKIDELRKEAD 221
                                   333333...2233566666666666666666666666666666655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaele 98 
                                   ++++el++e     ++I++  +      e+++ l+a+++el +el+ + ++l+e++ e +
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQIKETYDVVspirEKIDPLKAKISELRDELSVYLDKLNEIQVEKD 270
                                   578889999999999999988876777788999999999999999999999999988765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1    0.0012       0.5      17      57 ..      22      72 ..      12      85 .. 0.65
   2 ?   -1.4   0.0         8   3.3e+03      48      48 ..      99      99 ..      73     125 .. 0.55
   3 ?    7.0   0.3      0.02       8.2      28      66 ..     225     263 ..     207     277 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                       NPV_P10 17 ddkVdalqqqv....ddvqenlpdvtelnekLdaqsaqLaelet......k 57
                                   +k++  +  +     d++    +++el+ek d+++aq++el t      k
  gi|91774338|ref|YP_567030.1| 22 RTKITHNERTLkgvfRDLKLHRTNIDELKEKRDKLNAQVKELATkaredkK 72
                                  555555444442222566666779999999999999999999994444443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 8
                       NPV_P10 48 s 48
                                  +
  gi|91774338|ref|YP_567030.1| 99 T 99
                                  1 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.02
                       NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   ++++e    v+ + ek+d + a++ el ++++   d Ln
  gi|91774338|ref|YP_567030.1| 225 AQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLN 263
                                   466666667777888888888888888775444444333 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  10.1    0.0049         2      32     134 ..      24     124 ..       5     149 .. 0.47
   2 ?   10.8   3.4    0.0012       0.5      41     131 ..     193     283 ..     187     304 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0049
                          Fez1  32 eivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeee 112
                                    i +   +l+ +  +l+ + ++i+el+e++++    l+   +el+ k  e + lr+ +++  +e+k++r+e+++ +++ + 
  gi|91774338|ref|YP_567030.1|  24 KITHNERTLKGVFRDLKLHRTNIDELKEKRDK----LNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTG 100
                                   22333333333333344444444444444443....444444555556666666666666666666666666664433333 PP

                          Fez1 113 aalesdeakaqrqe.....aeeleelk 134
                                   +    +e k++r+e     + ++e+l+
  gi|91774338|ref|YP_567030.1| 101 S---ITELKTKRDEynkqsRGSVESLS 124
                                   2...33333333331111133333333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0012
                          Fez1  41 relrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeak 121
                                   + l ++ +++  ++    ++++e  +e + ++++++++ + ++ +rek++ l+++++elr+els    + +e ++e+de+k
  gi|91774338|ref|YP_567030.1| 193 KGLAEESQKHHLSMLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKK 273
                                   45555555666666667777888889999999999******************************9999999999999988 PP

                          Fez1 122 aqrqeaeele 131
                                     +++  + e
  gi|91774338|ref|YP_567030.1| 274 LDEKHIVAKE 283
                                   7776632222 PP

>> DUF4527  Protein of unknown function (DUF4527)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.1    0.0013      0.54       7      68 ..       8      69 ..       2      71 .. 0.81
   2 ?    6.7   0.1      0.01       4.1      30      70 ..      72     113 ..      70     116 .. 0.86
   3 ?    0.4   0.2      0.85   3.5e+02      67      89 ..     228     250 ..     198     277 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                       DUF4527  7 easeedlrlrvk....qLhHqvltLqcqLRdqasahreLqasreeaerlreelqekleElqkkqhE 68
                                   +se+dl+  v+    ++ H  +tL+   Rd + +hr   +  +e ++ r++l+ +++El  k +E
  gi|91774338|ref|YP_567030.1|  8 TMSEKDLKNTVNdyrtKITHNERTLKGVFRDLK-LHR---TNIDELKEKRDKLNAQVKELATKARE 69
                                  4678888888753333689************86.787...899*****************999887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                       DUF4527  30 qLRdqas.ahreLqasreeaerlreelqekleElqkkqhEan 70 
                                   +LRd a    +e++ +r+e +  ++++++ ++El+ k++E n
  gi|91774338|ref|YP_567030.1|  72 KLRDIANeNISEIKGTRDEIRSEKNKVTGSITELKTKRDEYN 113
                                   688876514589999***********************9976 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.85
                       DUF4527  67 hEanlAvtPLkAklAsLvqkCre 89 
                                   +E    v+P++ k+  L  k  e
  gi|91774338|ref|YP_567030.1| 228 KETYDVVSPIREKIDPLKAKISE 250
                                   44444455555555444444433 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 ?    4.7   0.6     0.072        29      35      83 ..      20      67 ..       9      84 .. 0.56
   2 ?    3.5   0.0      0.16        66      17      70 ..      83     136 ..      71     146 .. 0.81
   3 ?    2.7   0.0      0.29   1.2e+02      61      92 ..     233     264 ..     207     279 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.072
                  Baculo_PEP_C 35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtl 83
                                  +  t +++ e++L+ +  dlk   +++d +l++  ++L++++++l+++ 
  gi|91774338|ref|YP_567030.1| 20 DYRTKITHNERTLKGVFRDLKLHRTNID-ELKEKRDKLNAQVKELATKA 67
                                  4444455555555555555554444443.45555555555555555443 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                  Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtllt 70 
                                   ++  + + ir+ + ++++ +++l+++ ++  ++   +++sl+ + +++ld++l+
  gi|91774338|ref|YP_567030.1|  83 EIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSVESLSRAYAAELDKFLN 136
                                   556666789999999999999999999888888888999999998888888876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.29
                  Baculo_PEP_C  61 ldtrldtlltnLtdalnalqdtlrneLtnlns 92 
                                   + + + + ++ L++++ +l d+l+  L+ ln 
  gi|91774338|ref|YP_567030.1| 233 VVSPIREKIDPLKAKISELRDELSVYLDKLNE 264
                                   33334444444444444444444444444443 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.7      0.13        51       1      34 [.      53      86 ..      53      96 .. 0.89
   2 ?    8.7   0.1    0.0036       1.5       5      57 ..      96     148 ..      92     155 .. 0.85
   3 ?    8.3   4.0     0.005       2.1       9      70 ..     211     270 ..     206     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                  .HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Phage_Mu_Gam  1 reeanwalrkiaelkreleeieaeaneeiaaike 34
                                  r+++n+ ++++a   re +++ + ane+i +ik 
  gi|91774338|ref|YP_567030.1| 53 RDKLNAQVKELATKAREDKKLRDIANENISEIKG 86
                                  57999*************************9985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                  Phage_Mu_Gam   5 nwalrkiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqY 57 
                                   n++ + i elk++ +e++++   +++ +  +++ael++  +    l++++  +
  gi|91774338|ref|YP_567030.1|  96 NKVTGSITELKTKRDEYNKQSRGSVESLSRAYAAELDKFLNADIPLKHEIDIF 148
                                   778889*******************************9977776666666655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.005
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTHHHH-..-- CS
                  Phage_Mu_Gam   9 rkiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYaeankdeLfkdgk 70 
                                   +ki el++e + + a+++e  +       ++++plk++i++l ++l  Y +++  e++ +++
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQIKETYDV-VSPIREKIDPLKAKISELRDELSVYLDKLN-EIQVEKD 270
                                   67888888888888888776654.4567899*******************9998.5543333 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 ?    3.0  14.8      0.11        44      30     152 ..      45     150 ..      11     209 .. 0.53
   2 ?   10.4   4.3   0.00061      0.25      57     128 ..     201     272 ..     161     297 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                         Atg14  30 rlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdk 110
                                    +  lk+                 + ++l++++k +++k++e k+l+ + +e+++e+k ++++ ++e ++    + +l+ k
  gi|91774338|ref|YP_567030.1|  45 NIDELKE-----------------KRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTK 108
                                   3333333.................335666666666666666666666666666666655555544444444333333333 PP

                         Atg14 111 lkkRrsdleslqneleerrkkqiaklqdaikrieqklsslss 152
                                     + +++ +   ++l+ + +++++k+++a ++ ++ ++ +++
  gi|91774338|ref|YP_567030.1| 109 RDEYNKQSRGSVESLSRAYAAELDKFLNADIPLKHEIDIFEK 150
                                   332222222333444444444444444444444444444433 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00061
                         Atg14  57 qledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleer 128
                                   +       + +k++el+++  + +++++e  d +s  +++i+  k+k+++l+d+l+    +l+ +q e  e+
  gi|91774338|ref|YP_567030.1| 201 KHHLSMLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEK 272
                                   334444556679999999999999999999999999999999999999999999995555545555444443 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4    0.0021      0.87       8      71 ..      14      76 ..       7      84 .. 0.88
   2 ?   -1.6   0.0       7.5   3.1e+03      43      62 ..     104     123 ..      94     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0021
                                  HHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS CS
                     TetR_C_24  8 LralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedl 71
                                  L++ v ++   i+++ ++   ++r+l+ L+  + +e++++r+++ +++++l ++++++++++d 
  gi|91774338|ref|YP_567030.1| 14 LKNTVNDYRTKITHNERTLKGVFRDLK-LHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDI 76
                                  7888899999999999999999***65.9*****************************999654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.5
                                   HHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_24  43 eiralrreyerllrdlieeG 62 
                                   e++++r+ey ++ r  +e  
  gi|91774338|ref|YP_567030.1| 104 ELKTKRDEYNKQSRGSVESL 123
                                   67778888888777766654 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7  15.5      0.33   1.3e+02     134     208 ..      38     137 ..       3     288 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.33
                       DUF4407 134 elaeleaqiaalqaeidaaearldalraeaqkeldgtk................gtgttgvaGkgpaakekkaqldaaqa. 197
                                   +l+  +++i++l+++ d+++a++++l ++a++  +                    ++ ++v G  ++ k+k+++++++++ 
  gi|91774338|ref|YP_567030.1|  38 DLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDianeniseikgtrdeiRSEKNKVTGSITELKTKRDEYNKQSRg 118
                                   333333333344444444444444444444433332223311111111111444333333444444444443333332220 PP

                       DUF4407 198 elaelkakld........a 208
                                    +++l++           a
  gi|91774338|ref|YP_567030.1| 119 SVESLSRAYAaeldkflnA 137
                                   2222222211333333330 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.0     0.034        14      41      84 ..      16      63 ..       2      79 .. 0.43
   2 ?    0.0   0.1       2.6     1e+03      54      54 ..     106     106 ..      71     160 .. 0.59
   3 ?   10.3   0.4    0.0016      0.65      32      79 ..     206     253 ..     193     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.034
                       BLOC1_2 41 dvaaslekklek....lnekyeelqpylqqidqiekqvteLeeavseL 84
                                  + +++ ++k+ +    l+     l+ + ++id+++++ ++L + v+eL
  gi|91774338|ref|YP_567030.1| 16 NTVNDYRTKITHnertLKGVFRDLKLHRTNIDELKEKRDKLNAQVKEL 63
                                  333333333332000022222233333333333333333333333333 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.6
                       BLOC1_2  54 n 54 
                                   +
  gi|91774338|ref|YP_567030.1| 106 K 106
                                   2 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0016
                       BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                   + + ykk+++  +++     +++e+y+ ++p  ++id ++++++eL +
  gi|91774338|ref|YP_567030.1| 206 MLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRD 253
                                   5678999999999999999*************************9975 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   7.5      0.71   2.9e+02       4      77 ..      54     127 ..       9     130 .. 0.50
   2 ?    4.6   0.2      0.13        52       5      79 ..     146     219 ..     143     224 .. 0.87
   3 ?   11.2   1.2    0.0011      0.45       4      72 ..     228     295 ..     225     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.71
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlY 77 
                                   ++l ++++el ++ +e ++  +  +e+++e+    +e++ e++k+   ++e ++k++e +k+++ + e+L+r Y
  gi|91774338|ref|YP_567030.1|  54 DKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSVESLSRAY 127
                                   22333444444443333222222233444444444455555555555555555555555555555556665555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlYee 79 
                                   ++f+kl++l e++++  ++ +el+++++e++   +++     ++ + ++   +++++++ ++  +++++ +l +e
  gi|91774338|ref|YP_567030.1| 146 DIFEKLSDLGERIDAA-SQADELHSKIVETYRSSESIYKADGTVGKDVKGLAEESQKHHLSMLASYKKIDELRKE 219
                                   7999*******99865.6789***************999999999999989999999999999999998888665 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXX CS
                          YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegken 72 
                                   ke +d ++ + e+++ l+++++el++el+  l++ +e+++e+++ +    ++  ++++ +k+ + + e 
  gi|91774338|ref|YP_567030.1| 228 KETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKKLDE-KHIVAKEKFEKTGRMSLED 295
                                   788999***********************************87633222.2333333333333444444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.1     0.023       9.5      77     128 ..      11      62 ..       5      67 .. 0.72
   2 ?    5.6   8.1     0.051        21      16      93 ..      44     125 ..      39     153 .. 0.73
   3 ?    9.7   5.6     0.003       1.2      48     116 ..     205     273 ..     161     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.023
                        APG6_N  77 reeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyeh 128
                                   +++l++ +++++ +  + e+  +  +r+ + ++++  el+e++d+l+aq++ 
  gi|91774338|ref|YP_567030.1|  11 EKDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKE 62 
                                   5677777777777777777777777788888888888888888888887754 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.051
                        APG6_N  16 kqleqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                   + +++++++rd++++  k+l ++++e++k     +e++ e++   +++++e+++    + el+++r+e +++ +   e l+
  gi|91774338|ref|YP_567030.1|  44 TNIDELKEKRDKLNAQVKELATKAREDKKlrdiANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSVESLS 124
                                   567899999999999999999998777666666666777777778888888888888888888888888887665444444 PP

                        APG6_N  93 a 93 
                                   +
  gi|91774338|ref|YP_567030.1| 125 R 125
                                   3 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.003
                        APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellele 116
                                   ++ ++ +++++l+ke +   +++ke+ +  + +++++  l+++ ++l +e   ++ + ne q+e+ e++
  gi|91774338|ref|YP_567030.1| 205 SMLASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKK 273
                                   445555667777777777777777777777777777777777777777777777777777777766654 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   8.5    0.0022       0.9      97     177 ..      39     119 ..      24     130 .. 0.86
   2 ?    1.2   0.5      0.69   2.8e+02     109     170 ..     162     223 ..     146     229 .. 0.61
   3 ?    7.2   4.7    0.0098         4      96     184 ..     206     288 ..     198     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0022
                        DUF724  97 Llslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledv 177
                                   L   +++ ++l+e+r kl+ +++e +++ r+ ++  d  +++i+e++  ++ ++++k++   +i +lk++ ++++++ +  
  gi|91774338|ref|YP_567030.1|  39 LKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGS 119
                                   555677889999***************9999999999999*********************************99987755 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.69
                        DUF724 109 eerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekl 170
                                   ++  +l++ki e   +++++ +    + k ++ l ++++     + a+ k+i +l++ea+ +
  gi|91774338|ref|YP_567030.1| 162 SQADELHSKIVETYRSSESIYKADGTVGKDVKGLAEESQKHHLSMLASYKKIDELRKEADLY 223
                                   44555666666666666666666666666666666666666666666666666666666555 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0098
                        DUF724  96 kLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeled 176
                                     l+  ++ ++l++e   ++ +i+e  +  + + e+id l+ ki+el+ +l +      ++ +e  +++++++kl+e++  
  gi|91774338|ref|YP_567030.1| 206 M-LASYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYL----DKLNE-IQVEKDEKKLDEKHIV 280
                                   3.344456788888999999*******************************8766....33334.4677788888888888 PP

                        DUF724 177 veqeFeav 184
                                   ++++Fe++
  gi|91774338|ref|YP_567030.1| 281 AKEKFEKT 288
                                   88888876 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.3    0.0028       1.1      23      55 ..      36      67 ..      25      77 .. 0.77
   2 ?    1.7   0.4      0.53   2.2e+02      24      60 ..      79     115 ..      72     121 .. 0.66
   3 ?    0.7   0.0       1.1   4.4e+02      30      50 ..     210     230 ..     200     235 .. 0.80
   4 ?    4.7   0.0     0.061        25      23      54 ..     224     254 ..     221     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0028
                                  HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                         DivIC 23 kqeiaalqaelaklkaeneeLeaevkdLksded 55
                                   ++++    ++++lk+++++L+a+vk+L  +++
  gi|91774338|ref|YP_567030.1| 36 FRDLKLHRTNIDELKEKRDKLNAQVKEL-ATKA 67
                                  56667778899***************99.4554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.53
                                   HHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                         DivIC  24 qeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                   ++i +++ + ++++ e+++ +  + +Lk  +d   ++
  gi|91774338|ref|YP_567030.1|  79 ENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQ 115
                                   5666666666777777777777777776655555555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHCC- CS
                         DivIC  30 qaelaklkaeneeLeaevkdL 50 
                                    +++++l++e +   a++k+ 
  gi|91774338|ref|YP_567030.1| 210 YKKIDELRKEADLYHAQIKET 230
                                   688999999999888888865 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.061
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                         DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                   +++i++  + +  ++++++ L+a++++L+ de
  gi|91774338|ref|YP_567030.1| 224 HAQIKETYDVVSPIREKIDPLKAKISELR-DE 254
                                   67889999999999999999999999996.43 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.1    0.0047       1.9      15      74 ..      39     100 ..      35     114 .. 0.87
   2 ?    5.3   0.2     0.063        26      10      57 ..     222     266 ..     216     278 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0047
               Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmss 74 
                                   l+ +++++ el+++ ++L++q+++l++k +e +++ +  +e ++++k  ++ +++ k++++ 
  gi|91774338|ref|YP_567030.1|  39 LKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDiaNENISEIKGTRDEIRSEKNKVTG 100
                                   5667899***********************999999998899******99999999999985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.063
               Snapin_Pallidin  10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpd 57 
                                   l++ +++e+ + ++ +r++ + L++++++l+++L  + +  +     +
  gi|91774338|ref|YP_567030.1| 222 LYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLN---EIQ 266
                                   555556666666666666666666666666666655544444...333 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 ?    9.0   9.2    0.0035       1.4      20     118 ..      14     115 ..       2     118 .. 0.57
   2 ?    4.5   2.5     0.081        33      57     109 ..     211     263 ..     195     289 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0035
                    TPR_MLP1_2  20 aeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreel....nelkaeiaelkaeaesakaelee...sees 93 
                                   ++++++ ++++++  ++ +k       r l +h ++++el++ r++l    +el ++++e k+ ++ a+++++e    + +
  gi|91774338|ref|YP_567030.1|  14 LKNTVNDYRTKITHNERTLKGVF----RDLKLHRTNIDELKEKRDKLnaqvKELATKAREDKKLRDIANENISEikgTRDE 90 
                                   33333333333333333333333....477788888888876665553333666666666555555555554441115667 PP

                    TPR_MLP1_2  94 weeqkeelekelselekriedlneq 118
                                   + ++k++    ++el++++++ n+q
  gi|91774338|ref|YP_567030.1|  91 IRSEKNKVTGSITELKTKRDEYNKQ 115
                                   7778888888888888888888887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.081
                    TPR_MLP1_2  57 kelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelsele 109
                                   k++ +lr+e++ + a+i+e  + +   +++++  +++++e ++el   l++l+
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLN 263
                                   55555555555555555555555555555555555555555555554444443 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.8   0.00046      0.19     346     440 ..      42     137 ..      16     141 .. 0.79
   2 ?    3.3   1.2     0.079        32     333     407 ..     141     214 ..     139     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                                   H.HHHHHHHHHHHHHHHHHHHHHHHT.TTHHHHHHHHHHHHHHHHHHHHHHHHHHCCS-TTT--SSEETTEEBHHHHH... CS
                   5_nucleotid 346 k.eeleelekleelledelkklksseeeskekleeleedleelkkeirelreelkelfnkqfGslfrtgseksrFarq... 422
                                   + ++++el++++++l+ ++k+l ++     +++++l++ ++e  +ei+ +r+e++++ nk+ Gs+   ++++  +++q   
  gi|91774338|ref|YP_567030.1|  42 HrTNIDELKEKRDKLNAQVKELATK----AREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQsrg 118
                                   338899***********99999999....4556778888888889999999999999999999999888777777766444 PP

                                   .HHHH-SEEESSHHHHHTS CS
                   5_nucleotid 423 .veryAdlYtssvsnLlky 440
                                    ve  +  Y++++ ++l+ 
  gi|91774338|ref|YP_567030.1| 119 sVESLSRAYAAELDKFLNA 137
                                   4777777777777777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.079
                                   HHHHHHHHHHTHHH.HHHHHHHHHHHHHHHHHHHHHHH.................T.TTHHHHHHHHHHHHHHHHHHHHHH CS
                   5_nucleotid 333 LeeElevleekkek.eeleelekleelledelkklkss.................eeeskekleeleedleelkkeirelr 395
                                   L++E++++e+ ++  e+++  ++ +el ++++++++ss                 +                  +e ++ +
  gi|91774338|ref|YP_567030.1| 141 LKHEIDIFEKLSDLgERIDAASQADELHSKIVETYRSSesiykadgtvgkdvkglA------------------EESQKHH 203
                                   78888888888888888888888888888888888888555555555555444441..................3333333 PP

                                   HHHHCCS-TTT- CS
                   5_nucleotid 396 eelkelfnkqfG 407
                                    ++ +++ k++ 
  gi|91774338|ref|YP_567030.1| 204 LSMLASY-KKID 214
                                   3333333.2222 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 ?    8.6   0.9    0.0055       2.3      12      51 ..      32      71 ..      29      81 .. 0.83
   2 ?   -0.2   0.0       3.1   1.3e+03      10      28 ..      82     100 ..      75     124 .. 0.70
   3 ?   -1.3   0.0       6.8   2.8e+03      38      53 ..     211     226 ..     206     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0055
                     kleA_kleC 12 LpevatdlvarRdkiAaklaeAeeLvrqaeeLRakvyees 51
                                  L +v  dl+ +R +i ++ ++ + L  q++eL +k++e++
  gi|91774338|ref|YP_567030.1| 32 LKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDK 71
                                  6778888999999999999999999999999999988764 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.1
                     kleA_kleC  10 DeLpevatdlvarRdkiAa 28 
                                    e+ +  ++++++++k+  
  gi|91774338|ref|YP_567030.1|  82 SEIKGTRDEIRSEKNKVTG 100
                                   5677777888888887653 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.8
                     kleA_kleC  38 rqaeeLRakvyeesaa 53 
                                   ++++eLR+++ +  a 
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQ 226
                                   6777888777665555 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.5    0.0011      0.44      41      69 ..      45      73 ..      33      85 .. 0.83
   2 ?   -1.7   0.0       9.7   3.9e+03      39      59 ..      85     105 ..      72     126 .. 0.54
   3 ?   -0.6   0.0       4.5   1.8e+03      42      62 ..     158     177 ..     138     184 .. 0.69
   4 ?    0.2   0.0       2.4   9.8e+02      41      67 ..     212     238 ..     183     249 .. 0.74
   5 ?    0.9   0.1       1.5     6e+02      31      47 ..     248     264 ..     241     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                       UPF0184 41 aLDalEernDdlnskLrELlesnRqiRle 69
                                   +D+l e+ D+ln++++EL    R+ +++
  gi|91774338|ref|YP_567030.1| 45 NIDELKEKRDKLNAQVKELATKAREDKKL 73
                                  68******************999997754 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 9.7
                       UPF0184  39 nsaLDalEernDdlnskLrEL 59 
                                     + D++   ++++ + + EL
  gi|91774338|ref|YP_567030.1|  85 KGTRDEIRSEKNKVTGSITEL 105
                                   444444444444444444444 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 4.5
                       UPF0184  42 LDalEernDdlnskLrELles 62 
                                   +Da   + D+l+sk+ E   s
  gi|91774338|ref|YP_567030.1| 158 IDAA-SQADELHSKIVETYRS 177
                                   5554.4579999999887666 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.4
                       UPF0184  41 aLDalEernDdlnskLrELlesnRqiR 67 
                                    +D+l +  D  +++++E  +    iR
  gi|91774338|ref|YP_567030.1| 212 KIDELRKEADLYHAQIKETYDVVSPIR 238
                                   479999999999999999766555555 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.5
                       UPF0184  31 insmLDqinsaLDalEe 47 
                                   i +  D+++ +LD+l+e
  gi|91774338|ref|YP_567030.1| 248 ISELRDELSVYLDKLNE 264
                                   66677999*****9987 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 ?    4.0   0.1      0.11        44      29      50 ..      46      67 ..      43      68 .. 0.92
   2 ?    4.4   0.1     0.082        33      24      37 ..     146     159 ..     144     161 .. 0.92
   3 ?    0.5   0.0       1.4   5.5e+02      34      48 ..     239     253 ..     234     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                         HSBP1 29 iDdMssriDdLEksiadlmtqa 50
                                  iD++ ++ D L +++++l t+a
  gi|91774338|ref|YP_567030.1| 46 IDELKEKRDKLNAQVKELATKA 67
                                  9******************998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.082
                         HSBP1  24 qilsriDdMssriD 37 
                                   +i++++ d+++riD
  gi|91774338|ref|YP_567030.1| 146 DIFEKLSDLGERID 159
                                   599*********** PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.4
                         HSBP1  34 sriDdLEksiadlmt 48 
                                   ++iD L + i++l +
  gi|91774338|ref|YP_567030.1| 239 EKIDPLKAKISELRD 253
                                   678888888888765 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  12.8     0.011       4.5      47     133 ..      14     100 ..      11     129 .. 0.91
   2 ?    6.6   4.1     0.015         6      56     126 ..     211     281 ..     181     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                       DUF4201  47 lqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkq 127
                                   l++ ++ +++kI   +  Lk   +  + +   + +lkek++ l+++++el ++ +e ++ ++   +++++ k  rd +r +
  gi|91774338|ref|YP_567030.1|  14 LKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSE 94 
                                   789999999999999999999999999999999************************************************ PP

                       DUF4201 128 neklkq 133
                                   ++k+  
  gi|91774338|ref|YP_567030.1|  95 KNKVTG 100
                                   *99865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                       DUF4201  56 kkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrk 126
                                   kkI+e  ke    + +++ t  +++ ++ek + l+++ sel++el+   ++l++++ e  + kl+ +++ +
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKKLDEKHIVA 281
                                   899999999999999999999999*********************99999999999888888888777654 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.2      0.37   1.5e+02      15      35 ..      45      65 ..      42      89 .. 0.57
   2 ?   -0.3   0.1       3.4   1.4e+03       5      22 ..     201     219 ..     200     231 .. 0.66
   3 ?    9.5   0.1     0.003       1.2      12      31 ..     237     256 ..     231     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.37
                         TSC22 15 eVevLkekIkeLeernselee 35
                                   +++Lkek   L ++++el +
  gi|91774338|ref|YP_567030.1| 45 NIDELKEKRDKLNAQVKELAT 65
                                  456666666666666666543 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3.4
                         TSC22   5 KsHL.mfAVrEeVevLkek 22 
                                   K HL m+A    +++L+++
  gi|91774338|ref|YP_567030.1| 201 KHHLsMLASYKKIDELRKE 219
                                   6666667777777777764 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.003
                         TSC22  12 VrEeVevLkekIkeLeerns 31 
                                   +rE ++ Lk kI eL ++ s
  gi|91774338|ref|YP_567030.1| 237 IREKIDPLKAKISELRDELS 256
                                   68888888888888877665 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       1.1   4.3e+02     104     163 ..       6      65 ..       2      69 .. 0.66
   2 ?    5.2   0.9     0.042        17      73     131 ..      66     124 ..      60     131 .. 0.81
   3 ?    6.5   0.4     0.016       6.5      73     152 ..     188     270 ..     156     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
                                   ......HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 104 dsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                    s+ s ++ ++ v+   +++ + +++lk +    +   + ++e++   +++ a ++e ++
  gi|91774338|ref|YP_567030.1|   6 ASTMSEKDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELAT 65 
                                   455555666667777777777777777777777777777777777777777777766665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.042
                                   HHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHH CS
                     MCPsignal  73 VAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealk 131
                                    A E +kL + + +   ei+    ei  e n+++ s++e +++ +e  ++ + + e+l+
  gi|91774338|ref|YP_567030.1|  66 KAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSVESLS 124
                                   57888888888999999999999999999999999999999998887777776666665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHHHH...HHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  73 VAdEVrkLAersaqaakei...ealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaa 150
                                   V ++V+ LAe+s++    +    + i e+ ke +   + ++et   v+   e+++  + +++e+ ++ +   d ++ei++ 
  gi|91774338|ref|YP_567030.1| 188 VGKDVKGLAEESQKHHLSMlasYKKIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVE 268
                                   677888888888876554411134455666666666677777777777777777777777777776666666666666665 PP

                                   HH CS
                     MCPsignal 151 se 152
                                    +
  gi|91774338|ref|YP_567030.1| 269 KD 270
                                   55 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5  10.8       1.5     6e+02      73     138 ..      29      94 ..       2     124 .. 0.54
   2 ?    9.6   5.2    0.0025         1      69     183 ..     157     273 ..      93     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.5
                         ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletk 138
                                   + +++     l+ +r+   el  +r +l+ +++el ++ +++++     +e++ e++ +r +++ +
  gi|91774338|ref|YP_567030.1|  29 ERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSE 94 
                                   333344444444455555555555555555555555555555555555555555444444444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0025
                         ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                     + +++  +l++k++++    +  yk+ g+  + ++ l ee qk   ++ +  ++++el++e      ++k+  + +   
  gi|91774338|ref|YP_567030.1| 157 RIDAASQADELHSKIVETYRSSESIYKADGTVGKDVKGLAEESQKHHLSMLASYKKIDELRKEADLYHAQIKETYDVVSPI 237
                                   455677889999**************************************************************9999999 PP

                         ATG16 150 eklvqdlqDElsaLqlqlnqaEeklr..klekENke 183
                                   ++ ++ l+  +s L+ +l+   +kl+  ++ek+ k+
  gi|91774338|ref|YP_567030.1| 238 REKIDPLKAKISELRDELSVYLDKLNeiQVEKDEKK 273
                                   999998888888888888888777773334444444 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 ?    8.9   2.3    0.0045       1.8      69     126 ..       7      64 ..       1      66 [. 0.89
   2 ?    0.8   0.4       1.4   5.8e+02      37      90 ..      89     148 ..      85     183 .. 0.60
   3 ?    7.7   2.3      0.01       4.1      36     123 ..     178     270 ..     174     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0045
                        DUF641  69 seaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkkle 126
                                   s+++e+ l++ +++ r ++   e t+k + ++lk  +++i+eLkek ++++++ k+l 
  gi|91774338|ref|YP_567030.1|   7 STMSEKDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELA 64 
                                   35789999****************************************9999988876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.4
                        DUF641  37 ekiqaADkavvseLkklselkrlyrkkqkkkaseaeeseleaeiqe.......qrsllkty 90 
                                   ++i++  + v   +++l   ++ y k+++ + +   +++ +ae+++       +++ ++  
  gi|91774338|ref|YP_567030.1|  89 DEIRSEKNKVTGSITELKTKRDEYNKQSRGSVE-SLSRAYAAELDKflnadipLKHEIDIF 148
                                   677777778888888888888888888776654.344444444444333344444444444 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.01
                        DUF641  36 pekiqaADkavvseLkklselkrlyrkkqkkkase.....aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeL 111
                                   +e+i +AD  v ++ k l+e  ++   +  ++ ++     +e    +a+i+e  +++ +    ++ l+a++++ + e++  
  gi|91774338|ref|YP_567030.1| 178 SESIYKADGTVGKDVKGLAEESQKHHLSMLASYKKidelrKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVY 258
                                   577888888888888888776555544444333322344478888899999999999999999999999999999999999 PP

                        DUF641 112 kekLeeaeksnk 123
                                    +kL+e++ ++ 
  gi|91774338|ref|YP_567030.1| 259 LDKLNEIQVEKD 270
                                   999998876544 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.5     0.023       9.2      25      76 ..      18      72 ..       7     161 .. 0.84
   2 ?    3.9   3.6      0.19        77      43      88 ..     220     265 ..     129     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.023
                                  HHHB-.....BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DUF16 25 lnefkds...nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqge 76
                                   n+++     n+  Lk +   ++ +  +i++l++k +k+++++kel  +    ++
  gi|91774338|ref|YP_567030.1| 18 VNDYRTKithNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQVKELATKAREDKK 72
                                  45555556668888888888999**********************9987665554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.19
                                   HH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHH CS
                         DUF16  43 vdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleli 88 
                                    d    qi++  + v+   eki+ lk+++   ++el    + l+ i
  gi|91774338|ref|YP_567030.1| 220 ADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEI 265
                                   3344444444555555555555555555544444444333333332 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.7     0.017       7.1      28      73 ..      12      70 ..       7      72 .. 0.72
   2 ?    4.3   4.2      0.15        61      28      70 ..      47      91 ..      44     126 .. 0.70
   3 ?    4.4   2.2      0.13        53      32      70 ..     211     255 ..     145     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.017
                          YtxH 28 kdlkekaddlkekakelleeakeka....................kekaedlkekvkekadelkek 73
                                  kdlk++++d++ k++                              kek ++l  +vke a +++e+
  gi|91774338|ref|YP_567030.1| 12 KDLKNTVNDYRTKITHN-------ErtlkgvfrdlklhrtnidelKEKRDKLNAQVKELATKARED 70
                                  56666777776666322.......123455789999999998889999999999999998888876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.15
                          YtxH 28 kdlkekaddlkekakelleeakeka......kekaedlkekvkekadel 70
                                  ++lkek d+l  ++kel+++a+e        +    +  +++k + de+
  gi|91774338|ref|YP_567030.1| 47 DELKEKRDKLNAQVKELATKAREDKklrdiaN----ENISEIKGTRDEI 91
                                  56888888888888888888888877855553....3333333333333 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.13
                          YtxH  32 ekaddlkekakelleeakeka......kekaedlkekvkekadel 70 
                                   +k d+l++ a+ ++ ++ke+       +ek++ lk k++e  del
  gi|91774338|ref|YP_567030.1| 211 KKIDELRKEADLYHAQIKETYdvvspiREKIDPLKAKISELRDEL 255
                                   567777777877777777777887888666666666666666655 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   8.2      0.15        59      19      60 ..      45     100 ..      40     125 .. 0.66
   2 ?   -1.0   0.0         6   2.5e+03       4      33 ..     149     177 ..     147     215 .. 0.61
   3 ?    8.9   1.3    0.0051       2.1      18      61 ..     239     284 ..     225     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.15
                          ZapB  19 titlLqmeieeLkeeneelkeenrele..........eeneqlk....eereawqe 60 
                                   +i++L+++ ++L ++++el+ ++re +          +e++  +     e+++++ 
  gi|91774338|ref|YP_567030.1|  45 NIDELKEKRDKLNAQVKELATKAREDKklrdianeniSEIKGTRdeirSEKNKVTG 100
                                   56777777777777777777777777777776665543333333333344444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 6
                          ZapB   4 elLeqLEskiqkaidtitlLqmeieeLkee 33 
                                   e L+ L ++i++a  + ++L  +i e  + 
  gi|91774338|ref|YP_567030.1| 149 EKLSDLGERIDAA-SQADELHSKIVETYRS 177
                                   6677777777665.3445555555554444 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0051
                          ZapB  18 dtitlLqmeieeLkeeneelkeenrele..eeneqlkeereawqer 61 
                                   ++i+ L+ +i+eL+ e + + ++ +e++  +  ++l e +   +e+
  gi|91774338|ref|YP_567030.1| 239 EKIDPLKAKISELRDELSVYLDKLNEIQveKDEKKLDEKHIVAKEK 284
                                   6899999999999999999999999999655566666666665555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.1      0.22        90      23      78 ..      13      64 ..       4      69 .. 0.64
   2 ?    2.7   0.2      0.38   1.5e+02      22      67 ..      71     116 ..      70     128 .. 0.82
   3 ?    5.6   0.1     0.046        19      23      73 ..     215     265 ..     204     276 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.22
                        DUF948 23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteava 78
                                   lk+t++  ++ i++ e+ ++++ ++++   + +n   ++++ek +k+++ ++++a
  gi|91774338|ref|YP_567030.1| 13 DLKNTVNDYRTKITHNERTLKGVFRDLKL--HRTNI--DELKEKRDKLNAQVKELA 64
                                  56777777777777777777777777764..44444..446666666666665554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.38
                        DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvnekl 67 
                                   +kl+++++e+ + i+++++++++  ++v++ +++ ++  ++ n+++
  gi|91774338|ref|YP_567030.1|  71 KKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQS 116
                                   5888899999999999999999999999999998888777777765 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.046
                        DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73 
                                   +l+k +d   a+i+e+ + v pi ++++ l ak+ el ++++  l+k++++
  gi|91774338|ref|YP_567030.1| 215 ELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEI 265
                                   566777777777777777777777777777777777777777777777665 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.6      0.53   2.1e+02      28      81 ..      43      97 ..      12     114 .. 0.75
   2 ?    0.2   0.1       3.1   1.3e+03      28      61 ..      92     126 ..      89     139 .. 0.69
   3 ?    2.2   0.0      0.75   3.1e+02      18      69 ..     128     178 ..     115     191 .. 0.57
   4 ?    8.8   1.5    0.0065       2.6      20      83 ..     223     286 ..     204     293 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.53
                  Occludin_ELL 28 haeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkr 81
                                   ++++e+++k  +L++++kel+++ +e kk+ +   ++ +++k    e +++k++
  gi|91774338|ref|YP_567030.1| 43 RTNIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGtRDEIRSEKNK 97
                                  4567888888888888888888888877777666556666666545556666655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.1
                  Occludin_ELL  28 haeleevskkfseLerelkelkegsk.eykkieee 61 
                                    +e ++v+  ++eL+++ +e++++s+  ++++ + 
  gi|91774338|ref|YP_567030.1|  92 RSEKNKVTGSITELKTKRDEYNKQSRgSVESLSRA 126
                                   55667788888888888888888877666666555 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.75
                  Occludin_ELL  18 nkeYkeYkelhaeleevskkfseLe...relkelkegskeykkieeeilqeykkl 69 
                                    +e +++ +    l++  + f++L+   +++++++    + ++++++i+++y++ 
  gi|91774338|ref|YP_567030.1| 128 AAELDKFLNADIPLKHEIDIFEKLSdlgERIDAAS----QADELHSKIVETYRSS 178
                                   55555555555555544455555540004444444....4556666666666654 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0065
                  Occludin_ELL  20 eYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrce 83 
                                    +++ ke ++ ++ +++k+  L+++++el+++ + y +  +ei+ e  ++k d+++  +k+++e
  gi|91774338|ref|YP_567030.1| 223 YHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKKLDEKHIVAKEKFE 286
                                   3555666667777777777777777777777777777777777777777777888888888776 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.6       0.4   1.6e+02      18      57 ..      35      72 ..       2      85 .. 0.48
   2 ?    8.0   0.3     0.011       4.4       8      66 ..      77     135 ..      73     148 .. 0.80
   3 ?    3.9   1.0       0.2        82      21      74 ..     212     267 ..     141     269 .. 0.68
   4 ?    5.1   0.5     0.087        35      13      68 ..     232     287 ..     224     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.4
                       DUF2203 18 lleelralrkeleeleeeleeakaeaekseaaeleaelee 57
                                  ++++l+  r+++ el+e+ ++ +a+ ++   a++++e ++
  gi|91774338|ref|YP_567030.1| 35 VFRDLKLHRTNIDELKEKRDKLNAQVKE--LATKAREDKK 72
                                  3333333333333333333333333221..3333333333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.011
                       DUF2203   8 AnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelv 66 
                                   An+ + ++k + +e+r+ +++++   +el+++++e++k+++ + e+  ++++ae+++++
  gi|91774338|ref|YP_567030.1|  77 ANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSVESLSRAYAAELDKFL 135
                                   99999******************************987775555555555555555544 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.2
                       DUF2203  21 elralrkeleeleeeleeakaeaekse.........aaeleaeleeleaeieelveeieelGv 74 
                                   ++ +lrke+    ++++e+                    l+a+++el++e++ ++++++e+ v
  gi|91774338|ref|YP_567030.1| 212 KIDELRKEADLYHAQIKET-------YdvvspirekIDPLKAKISELRDELSVYLDKLNEIQV 267
                                   2223333333333333332.......1333333344666777888888888888877777766 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.087
                       DUF2203  13 pllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelvee 68 
                                    +++++ e++  l++++ el++el+   ++ ++ + +++e++l+e    ++e +e+
  gi|91774338|ref|YP_567030.1| 232 DVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKKLDEKHIVAKEKFEK 287
                                   56777778888888888888888888888877777777777777777766666554 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 ?    2.4   5.4      0.24        98      65     140 ..      38     113 ..       3     139 .. 0.47
   2 ?    1.0   0.4      0.64   2.6e+02      59      98 ..     184     224 ..     120     234 .. 0.54
   3 ?    9.9   2.5    0.0013      0.51      53     124 ..     210     285 ..     198     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.24
                  HAUS-augmin3  65 dvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraen 140
                                   d +l +  ++e++e+  +L+++++eL    +   k ++  +  +++++ ++ +  +e++++++ ++e++ +  + n
  gi|91774338|ref|YP_567030.1|  38 DLKLHRTNIDELKEKRDKLNAQVKELATKAREDKKLRDIANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYN 113
                                   3333344444444444444444444443333333333333333334444444444444444444444444433333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.64
                  HAUS-augmin3  59 sdlkq.edvellevileeeeesleaLeqelqeLqkekalkl 98 
                                    d++  +dv+ l ++ ++   s  a  ++++eL+ke +l  
  gi|91774338|ref|YP_567030.1| 184 ADGTVgKDVKGLAEESQKHHLSMLASYKKIDELRKEADLYH 224
                                   22222445555555555555555555555555555555554 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0013
                  HAUS-augmin3  53 Lktie....psdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeeke 124
                                   +k+i+    + dl + + +++   ++ ++e++  L+++++eL+ e    l +ln++qv   + +  ++   ++ek 
  gi|91774338|ref|YP_567030.1| 210 YKKIDelrkEADLYHAQIKETYDVVSPIREKIDPLKAKISELRDELSVYLDKLNEIQVEKDEKKLDEKHIVAKEKF 285
                                   555555545666777888999999999*******************************999999888888888764 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.2     0.029        12      81     132 ..       9      60 ..       2      70 .. 0.72
   2 ?    3.5   2.2      0.19        77      33      92 ..      77     136 ..      70     178 .. 0.75
   3 ?    5.2   2.9     0.053        22      56     107 ..     201     251 ..     135     275 .. 0.48
   4 ?    4.8   1.6      0.07        29      36      99 ..     212     287 ..     208     306 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.029
                                   HHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                     Fib_alpha  81 ksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqkerkC 132
                                    s+k+l++ +++++ +i+++e++++     l+  + +i +L+++ d+++++ 
  gi|91774338|ref|YP_567030.1|   9 MSEKDLKNTVNDYRTKITHNERTLKGVFRDLKLHRTNIDELKEKRDKLNAQV 60 
                                   5677788888888888888888888777778888888888888877776654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                                   CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCH CS
                     Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilr 92 
                                    ++++++++ + +ei+++++++   ++e+k++  e +k+++++ +++ + ++ el+ + l+
  gi|91774338|ref|YP_567030.1|  77 ANENISEIKGTRDEIRSEKNKVTGSITELKTKRDEYNKQSRGSvESLSRAYAAELD-KFLN 136
                                   57889999999999999999999999999999999999999887888888888888.4444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.053
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                     Fib_alpha  56 elvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                   ++  ++  s+++  +  k+ d +  +++++ +  ++ ++e+id    +i +L
  gi|91774338|ref|YP_567030.1| 201 KHHLSMLASYKKIDELRKEADLYHAQIKETYD-VVSPIREKIDPLKAKISEL 251
                                   22222222222222222222333333333333.3333333333333333333 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.07
                                   HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH............HHHHHHHHHHHHHHCCCHHHHHHHC CS
                     Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkd............ndnvikksskeleeeilrlketida 99 
                                   ++++l++e + ++ + ke++++v+ i++++ + +++ ++            n+  ++k +k+l+e+++  ke+  +
  gi|91774338|ref|YP_567030.1| 212 KIDELRKEADLYHAQIKETYDVVSPIREKIDPLKAKISElrdelsvyldklNEIQVEKDEKKLDEKHIVAKEKFEK 287
                                   5666666666666666666666666666666655555554445555554445666666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2073  (0.115623); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        60  (0.00334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 1.19u 0.37s 00:00:01.56 Elapsed: 00:00:00.59
# Mc/sec: 1560.45
//
Query:       gi|91774339|ref|YP_567031.1|  [L=237]
Description: hypothetical protein Mbur_2430 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.023   14.9  13.5      0.045   14.0   0.6    2.1  2  ATG16         Autophagy protein 16 (ATG16)
       0.27   11.5   7.0         11    6.4   0.5    3.3  3  DUF948        Bacterial protein of unknown function (DUF948)
          1    8.9  10.6          4    6.9  10.7    1.8  1  Exonuc_VII_L  Exonuclease VII, large subunit
        1.2    9.2   6.9        1.4    8.9   1.8    2.7  3  DUF4446       Protein of unknown function (DUF4446)
          2    8.5  19.2        4.2    7.4   9.6    3.0  2  DHR10         Designed helical repeat protein 10 domain
        3.5    6.9  15.9        2.6    7.3   8.6    2.2  2  Cluap1        Clusterin-associated protein-1
        3.7    7.3  14.6       0.33   10.8   7.3    2.1  2  DUF724        Protein of unknown function (DUF724)
        9.1    6.3  19.7         12    5.9   0.9    2.3  2  UPF0242       Uncharacterised protein family (UPF0242) N-term


Domain annotation for each model (and alignments):
>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   6.6     0.009        20      80     138 ..      38      96 ..      14     101 .. 0.81
   2 ?   14.0   0.6     2e-05     0.045      24     123 ..     128     231 ..     114     236 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.009
                         ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletk 138
                                   ++ +a+++  l+e  k+ +el  r ++lne+++  ++k +   +r++ l+++r++l  +
  gi|91774339|ref|YP_567031.1|  38 KSVIAKHKRLLEEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVLKEKRQQLYHQ 96 
                                   56688999999999999999999999999999999999999999999999999999766 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2e-05
                         ATG16  24 ynrLldrtsaleaenaklekaaasaks....sksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgel 100
                                    +rL+d +++ +   + l k    +++    +++++ +ak + a +++++ + +  i++le++ ++  eel++   ++g l
  gi|91774339|ref|YP_567031.1| 128 VRRLIDISEEKQVVDELLTKLNGMSTHgtvqNSVQQIKAKVNGAIEASNELAGTIGIKALEENFHKASEELKTISPRHGWL 208
                                   56777777776666666654444444444433333333333333333377889999************************* PP

                         ATG16 101 aqrllelneelqkleeklkedee 123
                                   ++r+++ ne+l+  e++  ++e+
  gi|91774339|ref|YP_567031.1| 209 ENRIKSHNEALEHWEKNPATEEN 231
                                   ***********998887666655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5    0.0048        11      22      73 ..      49      93 ..      36     112 .. 0.57
   2 ?    3.1   0.1     0.052   1.2e+02      44      82 ..     116     153 ..     113     155 .. 0.85
   3 ?    5.1   0.7     0.012        27      35      63 ..     154     182 ..     138     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0048
                        DUF948 22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73
                                   + +k ++e+ a+ + l++q+++  ++ ed+l+ +++l        ek ++l
  gi|91774339|ref|YP_567031.1| 49 EEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVL-------KEKRQQL 93
                                  33355566666666666666666666666666666553.......3333333 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.052
                        DUF948  44 pilkevedllakvnelledvneklekvdplteavadlge 82 
                                   ++++ ++d  +kv++ l d++e+ + vd+l ++++ +++
  gi|91774339|ref|YP_567031.1| 116 KLMHAANDGFTKVRR-LIDISEEKQVVDELLTKLNGMST 153
                                   577888888899999.999**********9999888776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.012
                        DUF948  35 ieelekqvdpilkevedllakvnelledv 63 
                                     ++++ v++i  +v+++++ +nel+  +
  gi|91774339|ref|YP_567031.1| 154 HGTVQNSVQQIKAKVNGAIEASNELAGTI 182
                                   33455777777777777777777766655 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 ?    6.9  10.7    0.0018         4     144     267 ..      35     159 ..      17     236 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0018
                  Exonuc_VII_L 144 eleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k. 222
                                   el +++ + ++rl ++ ++ ++e  +r ++l+++++s++++ e+   r++ l+e+ ++            l + +e++   
  gi|91774339|ref|YP_567031.1|  35 ELIKSVIAKHKRLLEEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVLKEKRQQ------------LYHQAENVlGn 103
                                   4444444444444444444444444444444444433333333333333332222222............22222222111 PP

                  Exonuc_VII_L 223 ...........ekleekkerl.kklkerlelleekkerleeleeklealsplkvLkr 267
                                              +kl +++++  +k+ +rl  ++e+k+ ++el +kl+ +s + + ++
  gi|91774339|ref|YP_567031.1| 104 mftdiddklldNKLMHAANDGfTKV-RRLIDISEEKQVVDELLTKLNGMSTHGTVQN 159
                                   1111112222222222222221222.3333577777777777777777766666554 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.8   0.00063       1.4      41      86 ..      42      87 ..       9     112 .. 0.76
   2 ?   -0.0   0.0      0.35   7.9e+02      26      56 ..     136     166 ..     116     184 .. 0.52
   3 ?    1.8   0.1     0.093   2.1e+02      34      76 ..     178     220 ..     161     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00063
                       DUF4446 41 ksleellkekleeveelkeeseelekeieeleeklkkslqkvglvr 86
                                  ++ ++ll+e+ +e  el+++s++l+++ie+ ++k + +l+++++++
  gi|91774339|ref|YP_567031.1| 42 AKHKRLLEEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVLK 87
                                  3456778888888888888888888888888888888888888765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.35
                       DUF4446  26 klkkkykklmkgkdgksleellkekleevee 56 
                                   + k+ +++l+++ +g s   ++++ ++++++
  gi|91774339|ref|YP_567031.1| 136 EEKQVVDELLTKLNGMSTHGTVQNSVQQIKA 166
                                   3333334444444444444444444444433 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.093
                       DUF4446  34 lmkgkdgksleellkekleeveelkeeseelekeieeleeklk 76 
                                   l      k lee +++  ee+++++ ++  le++i++ +e l+
  gi|91774339|ref|YP_567031.1| 178 LAGTIGIKALEENFHKASEELKTISPRHGWLENRIKSHNEALE 220
                                   5555567899999999999999999999999999999988876 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.6    0.0019       4.2      55     115 ..      37      97 ..      23      99 .. 0.82
   2 ?    4.6   2.0     0.014        31      59     102 ..     184     227 ..     133     236 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0019
                         DHR10  55 akkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleel 115
                                    k+ +++++  lee ++e +el+++ + l+ q+e+ ++k e    + e  +e+ ++ ++++
  gi|91774339|ref|YP_567031.1|  37 IKSVIAKHKRLLEEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVLKEKRQQLYHQA 97 
                                   5677899999999999999999999999999999999999998888887777777766665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                         DHR10  59 lkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                   +k+l+++ ++ ++el+ ++ ++  l+ ++++++e le+ +++ +
  gi|91774339|ref|YP_567031.1| 184 IKALEENFHKASEELKTISPRHGWLENRIKSHNEALEHWEKNPA 227
                                   46677777777777777777777777777777777777766554 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.6    0.0012       2.6     154     223 ..      21      90 ..      12     107 .. 0.89
   2 ?    4.1   0.8     0.012        26     122     214 ..     134     224 ..      95     231 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                        Cluap1 154 tkalsrqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsvr 223
                                   ++ +++++++ + ++ +k+ i k k+ le+++k+ ++l++  ++L+++ie  kq  e + +r++ l++ r
  gi|91774339|ref|YP_567031.1|  21 ESNMNKETSILDKDELIKSVIAKHKRLLEEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVLKEKR 90 
                                   5667888889999999************************************************999866 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                        Cluap1 122 lkaarqlaseitekgasLydlLekevelreartkalsrqleleeiekalkea..ikkvkeelektkkalenlesdeanLea 200
                                   + + +q++ e+ +k    ++ ++++ +++++ +++ ++     e  ++l+ +  ik+++e+ +k +++l++++  +  Le+
  gi|91774339|ref|YP_567031.1| 134 ISEEKQVVDELLTK----LNGMSTHGTVQNSVQQIKAKVNGAIEASNELAGTigIKALEENFHKASEELKTISPRHGWLEN 210
                                   44444444444443....222333333444444444444444444444443311688899999999999999999999999 PP

                        Cluap1 201 kiekkkqeleraqk 214
                                   +i+ +++ le+ +k
  gi|91774339|ref|YP_567031.1| 211 RIKSHNEALEHWEK 224
                                   99999998888776 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   7.3   0.00015      0.33     102     177 ..      25     100 ..      14     108 .. 0.93
   2 ?    1.2   0.7      0.13   2.9e+02      63     151 ..     134     224 ..     118     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                        DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledv 177
                                   ++ t++l++ + +++ i++++   +++++e++el+ + + l++q ++ k+kke+   +i  lk + ++l ++ e+v
  gi|91774339|ref|YP_567031.1|  25 NKETSILDKDELIKSVIAKHKRLLEEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVLKEKRQQLYHQAENV 100
                                   678999************************************************************9999988876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                        DUF724  63 iddsrseleslkeslaeLekhGF...dVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkil 140
                                   i +++++ ++l+++l+ + +hG    +V+++++++n  ++  +e + +   +k+le+++ ++++e + ++  +  le++i+
  gi|91774339|ref|YP_567031.1| 134 ISEEKQVVDELLTKLNGMSTHGTvqnSVQQIKAKVNGAIEASNELAGTI-GIKALEENFHKASEELKTISPRHGWLENRIK 213
                                   5555566666666666666666322255666666666666555555443.4677788888888888888888888888887 PP

                        DUF724 141 elerqlallke 151
                                    +++ l++  +
  gi|91774339|ref|YP_567031.1| 214 SHNEALEHWEK 224
                                   77777766553 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  13.0     0.016        35      96     165 ..      26     101 ..      13     147 .. 0.81
   2 ?    5.9   0.9    0.0054        12      64     118 ..     171     225 ..     115     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                       UPF0242  96 eeeeeLkee......ldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvl 165
                                   +e+  L +       +++ +++le++++e  +L  + +a  e++e +k++ e++L + + l ++ q+  ++  +vl
  gi|91774339|ref|YP_567031.1|  26 KETSILDKDeliksvIAKHKRLLEEYNKEFSELDARSKALNEQIESSKQKKEDTLTRIEVLKEKRQQLYHQAENVL 101
                                   4444443334444447888889999999999999999999999999999999999999888888888777766665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0054
                       UPF0242  64 klekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkee 118
                                    +e+s+  +    +++l+e++++  e+l+    ++  L++++++ +e+le+ +++
  gi|91774339|ref|YP_567031.1| 171 AIEASNELAGTIGIKALEENFHKASEELKTISPRHGWLENRIKSHNEALEHWEKN 225
                                   336666666666678888*******************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2247  (0.125328); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.74u 0.36s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 1227.96
//
Query:       gi|91774340|ref|YP_567032.1|  [L=96]
Description: hypothetical protein Mbur_2431 [Methanococcoides burtonii DSM 6242]
Scores for 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-32  110.3   0.1    4.5e-32  110.2   0.1    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.1   2.5e-36   4.5e-32       1      92 []       6      96 .]       6      96 .] 0.99

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 2.5e-36
                                  EEETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETT CS
                        DUF424  1 yrtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidg 83
                                  +r++++  lvavcdkel+gk++++ge+++ +segfy+ge+asee++++++++a  aNi+g +++++a++ G vdp++V++i+g
  gi|91774340|ref|YP_567032.1|  6 HRSTNQ-ILVAVCDKELVGKKLTKGEIVIDISEGFYKGEIASEETIVQAIRNAPSANIFGTRSIQCAIDSGAVDPECVIYIEG 87
                                  799999.**************************************************************************** PP

                                  EEEEEEEE- CS
                        DUF424 84 vphaqigkl 92
                                  +phaqi+kl
  gi|91774340|ref|YP_567032.1| 88 TPHAQIYKL 96
                                  *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 554.72
//
Query:       gi|91774341|ref|YP_567033.1|  [L=696]
Description: replicative DNA helicase Mcm [Methanococcoides burtonii DSM 6242]
Scores for complete 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-91  303.8   0.0    6.8e-91  303.3   0.0    1.2  1  MCM              MCM P-loop domain
    5.5e-36  123.2   0.0    9.8e-36  122.4   0.0    1.4  1  MCM_OB           MCM OB domain
    1.7e-27   95.7   0.4    4.4e-27   94.3   0.4    1.8  1  MCM_lid          MCM AAA-lid domain
    4.6e-11   43.2   1.3    1.2e-10   41.9   0.4    2.1  2  MCM_N            MCM N-terminal domain
    5.3e-07   29.2   0.0    0.00014   21.3   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.3e-05   25.2   0.0    3.2e-05   23.9   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0032   17.3   0.0      0.013   15.4   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.085   13.2   0.0    2.4  2  AAA_16           AAA ATPase domain
      0.058   13.9   0.1       0.18   12.3   0.1    1.9  1  DUF4072          Domain of unknown function (DUF4072)
       0.17   11.6   0.1        1.6    8.4   0.1    2.2  1  Sigma54_activat  Sigma-54 interaction 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 !  303.3   0.0   3.8e-94   6.8e-91       2     223 ..     261     483 ..     260     484 .. 0.97

  Alignments for each domain:
  == domain 1  score: 303.3 bits;  conditional E-value: 3.8e-94
                                   HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSS CS
                           MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklap 82 
                                   +e+i e+ k+++i +++  siapsiyg+ed+k+a+ lqlf++v k l+d++++rgdi++llvgdpg+aKsqlL+y+ k++p
  gi|91774341|ref|YP_567033.1| 261 EERIVEMGKDPEINKMIRGSIAPSIYGYEDIKEALSLQLFSAVPKMLPDGSRVRGDIHILLVGDPGIAKSQLLRYMVKISP 341
                                   7899***************************************************************************** PP

                                   SEEEEESSSSSSSHSSSEEEEESSSSS.EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE CS
                           MCM  83 ravytsgkgssaagLtaavvrdeetge.fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLn 162
                                   r+v++sgk++s++gLtaa v+d+  +  ++leaGalv+ad G++++De+dkm++ed+s+lhEamEqqtis+aKaGi atL+
  gi|91774341|ref|YP_567033.1| 342 RGVFASGKSASSSGLTAAAVKDDLGDGrWTLEAGALVMADMGLAAVDEMDKMSKEDKSSLHEAMEQQTISVAKAGILATLK 422
                                   ****************999998876544***************************************************** PP

                                   --EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                           MCM 163 artsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                   +r+++l Aanpk+gr+dk + +ae+in+++al+srFDlif+llD +d+ kD+++a+hi+++
  gi|91774341|ref|YP_567033.1| 423 SRCALLGAANPKYGRFDKYEGLAEQINMPPALISRFDLIFILLDVPDRIKDSNIAHHILKS 483
                                   **********************************************************986 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   0.0   5.5e-39   9.8e-36       2     125 ..      95     223 ..      94     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 5.5e-39
                                   XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSEEEEE CS
                        MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkletekskfvdf 77 
                                   +R+lrs+h+ k++++eG++ +a+ev+pk+++a+f+c +c++t        ++ eP+ Ce+++C++k+pfkl +++s+f d 
  gi|91774341|ref|YP_567033.1|  95 IRELRSKHLLKFISIEGMIRKATEVRPKITNAAFMCMRCENTSFEpqggpKFVEPTDCENESCGKKGPFKLLIDQSTFLDA 175
                                   8***************************************96653678888999*************************** PP

                                   EEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                        MCM_OB  78 qklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                   qkl++QEspe++  G+ P+sl+v +eddl   vkPGdr  + G++r+ 
  gi|91774341|ref|YP_567033.1| 176 QKLQVQESPESLKGGSQPQSLDVDAEDDLAGLVKPGDRLVINGVLRSH 223
                                   ********************************************9975 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.4   2.4e-30   4.4e-27       1      86 [.     520     604 ..     520     605 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.4e-30
                                   HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                       MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                   +llrkY+ayar++i+P+++++a++++ ++Y++lRk+ e++ ++ +p+t+RqLe+l+RL+eA+A++rls+vvt +d+++ +r
  gi|91774341|ref|YP_567033.1| 520 DLLRKYVAYARRRIFPIMEDDARDHIINYYLDLRKQGEGK-DSPVPVTARQLEALVRLAEASARIRLSNVVTIDDAKRTTR 599
                                   58*********************************99655.99************************************** PP

                                   HHHHH CS
                       MCM_lid  82 llkes 86 
                                   + +++
  gi|91774341|ref|YP_567033.1| 600 ISMAC 604
                                   98876 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.4   6.7e-14   1.2e-10       2      85 ..       8      81 ..       7     121 .. 0.89
   2 ?   -1.9   0.0       2.9   5.1e+03      62      84 ..     531     553 ..     516     583 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.7e-14
                         MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealkevvkkleps 82
                                  ekF+dFL+ +            Y d++  +a++  e +++ vd+ dL++fd +La ++le+p +++p+ e+al+e+   +e++
  gi|91774341|ref|YP_567033.1|  8 EKFRDFLKRY------------YWDEILLLANEypELRSIVVDFPDLEQFDADLAYELLEHPDDVIPYAEQALREIDIPIEKD 78
                                  89******88............*********998999*************************************987766665 PP

                         MCM_N 83 ykd 85
                                    d
  gi|91774341|ref|YP_567033.1| 79 LDD 81
                                  544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                         MCM_N  62 keylplleealkevvkklepsyk 84 
                                   +++ p++e+ +++ + +++ +  
  gi|91774341|ref|YP_567033.1| 531 RRIFPIMEDDARDHIINYYLDLR 553
                                   46679999999998888776544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0     0.006        11      21      48 ..     315     342 ..     312     355 .. 0.89
   2 !   21.3   0.0   7.9e-08   0.00014      92     159 ..     366     434 ..     356     458 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.006
                  Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllpp 48 
                                   G  ++llvG pG  K+ l + + ++ p+
  gi|91774341|ref|YP_567033.1| 315 GDIHILLVGDPGIAKSQLLRYMVKISPR 342
                                   7889***************999999875 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 7.9e-08
                  Mg_chelatase  92 Gggs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                   G g+ + + G++ +a  G+  +DE+ +++++   +L e +e++++++++a   ++  +r+ l+ a+Np 
  gi|91774341|ref|YP_567033.1| 366 GDGRwTLEAGALVMADMGLAAVDEMDKMSKEDKSSLHEAMEQQTISVAKAGILATLKSRCALLGAANPK 434
                                   555558899**********************************************************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 !   23.9   0.0   1.8e-08   3.2e-05       1     138 []     318     458 ..     318     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.8e-08
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEE...E--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyv...qltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                   ++lLvG+pG++Ks+l +++ +   r v+     + ++++t++ +k  +   +g+  l+ ++lv  +    ++ +DE ++++
  gi|91774341|ref|YP_567033.1| 318 HILLVGDPGIAKSQLLRYMVKISPRGVFASgksASSSGLTAAAVKDDLG--DGRWTLEAGALV--MADMGLAAVDEMDKMS 394
                                   79*********************88888752226777888888888888..99999*******..88999999******** PP

                                   HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..........-TT-TTHHHHTT- CS
                         AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.........rslnelspalrsRf 138
                                   +e  +sL+  +e++++++++ g l   k+        ++++anp +          ++ ++ pal+sRf
  gi|91774341|ref|YP_567033.1| 395 KEDKSSLHEAMEQQTISVAKAGILATLKSR-----CALLGAANPKYgrfdkyeglAEQINMPPALISRF 458
                                   ***********************9999986.....9********9988777766556666778888887 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.1e-06     0.013       1     112 [.     318     433 ..     318     443 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftp.dllPsdilGtevfeeke.kefefkkGp.vfanllla..deinrapp 76 
                                   h+ll g PG+ak +l + + k+     + +         s ++ + v ++    ++++++G+ v+a++ la  de+++ + 
  gi|91774341|ref|YP_567033.1| 318 HILLVGDPGIAKSQLLRYMVKIS---PRGVFASGkSASSSGLTAAAVKDDLGdGRWTLEAGAlVMADMGLAavDEMDKMSK 395
                                   999*********99999876654...44443333034456777777776543489******845677777555******** PP

                         AAA_3  77 ktqsalleameerqvtveget..hklpepflvlatqnP 112
                                     +s+l eame+++++v+++    +l++   +l + nP
  gi|91774341|ref|YP_567033.1| 396 EDKSSLHEAMEQQTISVAKAGilATLKSRCALLGAANP 433
                                   **************999876411577777777777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.8e-05     0.085      26      78 ..     318     362 ..     302     418 .. 0.68
   2 ?   -0.8   0.0      0.97   1.7e+03      75     144 ..     528     594 ..     478     606 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                        AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalar 78 
                                    +ll+G++G+ Ks l+r     ++ + g+f++gk  ++      s l+ a+ +
  gi|91774341|ref|YP_567033.1| 318 HILLVGDPGIAKSQLLRYMV-KISPR-GVFASGKSASS------SGLTAAAVK 362
                                   699*****************.69988.9******9999......333333323 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.97
                        AAA_16  75 alareellrqlldeaesaeleawrekleealaavpelagaea.....srllellkrll.allsrderplvlvlDdl 144
                                   ++ r++++  ++d+a++   +++ +  ++  +       +++      r le+l rl+ a ++ + +  v+++Dd+
  gi|91774341|ref|YP_567033.1| 528 YA-RRRIFPIMEDDARDHIINYYLDLRKQGEG-------KDSpvpvtARQLEALVRLAeASARIRLS-NVVTIDDA 594
                                   34.55666666666555555555553333222.......2223333466677777777555555444.78888886 PP

>> DUF4072  Domain of unknown function (DUF4072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.9e-05      0.18       5      35 ..     561     591 ..     561     612 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.9e-05
                       DUF4072   5 spaPLsaahletLaaLagAsrieridaqAaR 35 
                                   sp P+ a +le+L++La+As+  r++++ ++
  gi|91774341|ref|YP_567033.1| 561 SPVPVTARQLEALVRLAEASARIRLSNVVTI 591
                                   899******************9999998775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0009       1.6      82     142 ..     370     432 ..     305     444 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0009
                                   SS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEES CS
               Sigma54_activat  82 ekekkGlfekadgGtlfLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatn 142
                                    + ++G++  ad G   +De+ +++ e  + L ++++++++   + G  ++ k  + ++ a+n
  gi|91774341|ref|YP_567033.1| 370 WTLEAGALVMADMGLAAVDEMDKMSKEDKSSLHEAMEQQTIsvAKAGILATLKSRCALLGAAN 432
                                   445789******************************999861156777777777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.81u 0.39s 00:00:01.20 Elapsed: 00:00:00.58
# Mc/sec: 3591.91
//
Query:       gi|91774342|ref|YP_567034.1|  [L=231]
Description: RNA methyltransferase TrmH, group 1 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-32  111.7   0.0    4.3e-32  111.2   0.0    1.2  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.0   2.4e-36   4.3e-32       2     142 .]       5     156 ..       4     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 2.4e-36
                                   EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEEE CS
                SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalvat 81 
                                   l ++lve+ ++gN+G++aR++k+fg+s+l+lv+p++    + ea+++a++a ++le +k+v+++eeal+  + + +a++++
  gi|91774342|ref|YP_567034.1|   5 LKIILVEPLYQGNIGSVARAMKNFGFSDLILVNPCEL---KMEARAFASHAYDILEsAKTVETIEEALEGSDLV-IATTGI 81 
                                   679******************************8875...9999****************************99.777777 PP

                                   ST..T-SEGC.......CSHHH.......TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                SpoU_methylase  82 sl..kgksls.......eidlk.......ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                   ++   +++++       ++  k       + +a++fG+Ed+G +ne+l+l d +v+Ip+s+ ++ +N+++Av i+ly
  gi|91774342|ref|YP_567034.1|  82 TGmkIDEHIRmppytprDL--KvkfsgmsGTIAVIFGREDHGFTNEELKLSDVIVSIPTSKIYPIMNLSHAVTIILY 156
                                   7753222222333333322..24466999**********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1285.94
//
Query:       gi|91774343|ref|YP_567035.1|  [L=124]
Description: rubrerythrin [Methanococcoides burtonii DSM 6242]
Scores for complete 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-11   42.8   7.4    2.3e-09   37.8   7.4    2.0  1  Rubrerythrin     Rubrerythrin
    0.00088   18.9   0.5       0.35   10.4   0.1    2.1  2  Phenol_Hydrox    Methane/Phenol/Toluene Hydroxylase
     0.0036   17.8   0.3     0.0086   16.6   0.3    1.6  2  AAA_assoc_C      C-terminal AAA-associated domain
      0.007   16.3   6.7       0.45   10.5   6.7    2.1  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.042   12.7   1.6        1.7    7.4   0.1    2.0  2  FA_desaturase_2  Fatty acid desaturase


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 !   37.8   7.4   6.4e-13   2.3e-09       1     136 [.       5     119 ..       5     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 6.4e-13
                                   HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGG CS
                  Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflt 80 
                                   +iL++ ++gE ++   Y +++++a+ eg  + a +F+++A +E+ Ha+ +++ll+ ++ +                     
  gi|91774343|ref|YP_567035.1|   5 DILKATFKGETTEVGWYFAMSRQAErEGHFEAALYFRQIAMDEAWHAAEVAELLGLVKDTTI------------------- 66 
                                   79****************************************************99777777................... PP

                                   HHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  81 taknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                     +n+e+++eg++ +e e   + +++a++egne a+ +f+k++ +E +H+  l+ l
  gi|91774343|ref|YP_567035.1|  67 --ENIEMMLEGETMAEGEK-AEAAKIAREEGNEAAALFFAKASLDEARHKSGLAGL 119
                                   ..9**************99.7889*************************9887765 PP

>> Phenol_Hydrox  Methane/Phenol/Toluene Hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   9.8e-05      0.35     186     225 ..      21      60 ..      10      64 .. 0.91
   2 !    7.1   0.0   0.00098       3.5     190     224 ..      87     121 ..      83     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.8e-05
                                   HHHTHHHGGGGT-SHHHHHHHHHHHHHHHHHHHHHHHHII CS
                 Phenol_Hydrox 186 fvafaevaaangDeltpslissaqsdearharwgdallkv 225
                                   + a++++a ++g +  ++ ++++  dea+ha+ +++ll +
  gi|91774343|ref|YP_567035.1|  21 YFAMSRQAEREGHFEAALYFRQIAMDEAWHAAEVAELLGL 60 
                                   557999******************************9865 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00098
                                   HHHGGGGT-SHHHHHHHHHHHHHHHHHHHHHHHHI CS
                 Phenol_Hydrox 190 aevaaangDeltpslissaqsdearharwgdallk 224
                                   a+ a+++g e+ ++++ +a  dearh+   + llk
  gi|91774343|ref|YP_567035.1|  87 AKIAREEGNEAAALFFAKASLDEARHKSGLAGLLK 121
                                   567999********************987777665 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 ?   -1.5   0.0         1   3.6e+03      36      58 ..      15      37 ..      12      41 .. 0.80
   2 !   16.6   0.3   2.4e-06    0.0086       8      77 ..      42     111 ..      36     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                   AAA_assoc_C 36 lTelGrkfveadikerKeifreq 58
                                   Te+G  f+ +   er   f+ +
  gi|91774343|ref|YP_567035.1| 15 TTEVGWYFAMSRQAEREGHFEAA 37
                                  58999999999999998877765 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.4e-06
                   AAA_assoc_C   8 elevddLlpiveaaelLglve.veegdielTelGrkfveadikerKeifreqllklvplaaairrvLdere 77 
                                   ++ +d+  +++e+aelLglv+ ++  +ie+  +G++++e++  e  +i re+  +   l+ a  + Lde +
  gi|91774343|ref|YP_567035.1|  42 QIAMDEAWHAAEVAELLGLVKdTTIENIEMMLEGETMAEGEKAEAAKIAREEGNEAAALFFAKAS-LDEAR 111
                                   5679****************737889*************************98887777765544.56555 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   6.7   0.00012      0.45      17     139 ..      20     123 ..       4     124 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSSHHHHHHHHHHHHHHHHH CS
                      Ferritin  17 qylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefgsveevleaalehekkvte 97 
                                    y+am++ ++ +g ++ a +f++ a +e  ha ++ae +                       +++ e +e +le e+ +  
  gi|91774343|ref|YP_567035.1|  20 WYFAMSRQAEREGHFEAALYFRQIAMDEAWHAAEVAELLGLVK-------------------DTTIENIEMMLEGETMAEG 81 
                                   6************************************875444...................2555666778888888888 PP

                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  98 slrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                   +  e++++a+eeg  a a f+ +   ++ +h   l+ ll+k+
  gi|91774343|ref|YP_567035.1|  82 EKAEAAKIAREEGNEAAALFFAKASLDEARHKSGLAGLLKKM 123
                                   888888888888888888888777777788888888888776 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0023       8.4     162     226 ..      13      74 ..       3      86 .. 0.73
   2 ?    7.4   0.1   0.00047       1.7     171     201 ..      85     115 ..      79     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0023
               FA_desaturase_2 162 ErATkvsH.rntaklakeagdellakicgaiaadEkrHeaaYtrvvekllevdpdeavlaladmmr 226
                                      T+v     ++++a+++g   +a   ++ia dE+ H+a     v++ll +  d+++  ++ m++
  gi|91774343|ref|YP_567035.1|  13 GETTEVGWyFAMSRQAEREGHFEAALYFRQIAMDEAWHAAE----VAELLGLVKDTTIENIEMMLE 74 
                                   55555553146789999999999999************975....555666666666666666655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00047
               FA_desaturase_2 171 ntaklakeagdellakicgaiaadEkrHeaa 201
                                   + ak+a+e+g+e++a   ++ + dE+rH+  
  gi|91774343|ref|YP_567035.1|  85 EAAKIAREEGNEAAALFFAKASLDEARHKSG 115
                                   679*************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 718.37
//
Query:       gi|91774344|ref|YP_567036.1|  [L=219]
Description: nitrite and sulphite reductase 4Fe-4S subunit [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-25   88.1   0.0    5.3e-25   87.8   0.0    1.1  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.3e-13   50.6   0.0    2.1e-13   49.9   0.0    1.4  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.058   13.4   0.0    1.5  1  Carla_C4      Carlavirus putative nucleic acid binding protei


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 !   87.8   0.0   8.9e-29   5.3e-25       2     152 ..      83     217 ..      82     219 .] 0.94

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 8.9e-29
                                   SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeigfn 82 
                                   g ++r+++ cpg + c+ a  D+  l  +++    + y+  +lP KfK+avsgc n c    ++Dig++g+ +     gf+
  gi|91774344|ref|YP_567036.1|  83 GRCVRSIKVCPGITNCKRAQQDAMALGLKLD----ELYHGIELPSKFKMAVSGCMNSCSGPAVKDIGVMGTPR-----GFT 154
                                   689****************************....**************************************.....*** PP

                                   EEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  83 ilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                   +l GG++g++++ +  +a+ g ++e e le+v  i+e+y+    r   kk Rl+ l++++G++ F+++v+
  gi|91774344|ref|YP_567036.1| 155 LLAGGNAGIRPRIGDVIAE-G-LDEVEALEMVGRIIEFYM----R-SAKKYRLGRLIDDIGLDVFKNEVR 217
                                   ******************7.5.55555*************....5.55677****************995 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 !   49.9   0.0   3.6e-17   2.1e-13       3      66 ..      13      74 ..      11      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3.6e-17
                  NIR_SIR_ferr  3 qkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66
                                  q+d ++y ++  ++p+G+i+a++l+ + d+a+kyg  +i++T+ Q + l g++e+dle+ ++eL
  gi|91774344|ref|YP_567036.1| 13 QRDRESY-AIVPHTPAGIISADELQCVVDVARKYG-ATIKFTSAQRVALIGLKENDLEDAWSEL 74
                                  8998888.***************************.**************************99 PP

>> Carla_C4  Carlavirus putative nucleic acid binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.6e-06     0.058      49      71 ..      78     100 ..      30     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.6e-06
                      Carla_C4  49 RArsigRCeRCyRvyPpfvftkk 71 
                                    A sigRC+R  +v P+++  k+
  gi|91774344|ref|YP_567036.1|  78 PASSIGRCVRSIKVCPGITNCKR 100
                                   589**************776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.34s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1270.36
//
Query:       gi|91774345|ref|YP_567037.1|  [L=268]
Description: CoB-CoM heterodisulfide reductase, subunit E [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0069   16.0   4.9     0.0069   16.0   4.9    3.2  3  Nitrate_red_gam  Nitrate reductase gamma subunit
  ------ inclusion threshold ------
      0.087   13.0   0.6      0.087   13.0   0.6    3.4  4  DUF5367          Family of unknown function (DUF5367)


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 ?   -0.5   0.1     0.085   7.6e+02     125     142 ..      32      50 ..      13     101 .. 0.60
   2 !   16.0   4.9   7.6e-07    0.0069      92     146 ..     161     215 ..     123     228 .. 0.85
   3 !    8.2   1.9   0.00018       1.6     180     209 ..     232     262 ..     222     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.085
               Nitrate_red_gam 125 vvlllLllqi.llGllttl 142
                                   ++++ ++++i ++G+++ l
  gi|91774345|ref|YP_567037.1|  32 MIMATIAIAIfMIGMYINL 50 
                                   2222222222033444333 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.6e-07
               Nitrate_red_gam  92 liagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsal 146
                                    ++  ++l+G+++ ++RRl++++ r++t a D v+l+ L++ +++G+++  + + 
  gi|91774345|ref|YP_567037.1| 161 DVFSYILLTGIIIAIFRRLFVAKARESTIAFDSVLLIGLTIIVVTGFVADGIRNG 215
                                   5678899***************************************998766655 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00018
               Nitrate_red_gam 180 klHvllg.lllfalfPFtrLvHvlsapleYl 209
                                    +Hv++  +  +a +PF++ +H+++ pl+ +
  gi|91774345|ref|YP_567037.1| 232 LFHVVISlFFCIAYIPFSKYMHMFAGPLTLM 262
                                   578877615567899************9865 PP

>> DUF5367  Family of unknown function (DUF5367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.5     0.047   4.2e+02      73      90 ..      25      42 ..      15      53 .. 0.43
   2 ?   -1.7   0.3      0.36   3.2e+03      84      88 ..     128     132 ..     114     158 .. 0.58
   3 ?   13.0   0.6   9.7e-06     0.087      54      94 ..     169     209 ..     162     211 .. 0.89
   4 ?   -0.6   0.4      0.17   1.5e+03      49      73 ..     229     253 ..     225     263 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.047
                       DUF5367 73 aslFaswlLwayslvllt 90
                                     Fa+ ++ a  ++ ++
  gi|91774345|ref|YP_567037.1| 25 RITFAAVMIMATIAIAIF 42
                                  344444333322222111 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
                       DUF5367  84 yslvl 88 
                                   +  + 
  gi|91774345|ref|YP_567037.1| 128 IMSIA 132
                                   22221 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 9.7e-06
                       DUF5367  54 DvlilvfFeeifpnlqpeaaslFaswlLwayslvlltgvvl 94 
                                     +i++ F  +f+   +e+  +F s lL ++ ++++tg+v 
  gi|91774345|ref|YP_567037.1| 169 TGIIIAIFRRLFVAKARESTIAFDSVLLIGLTIIVVTGFVA 209
                                   5578999*******999999******************985 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.17
                       DUF5367  49 pgmllDvlilvfFeeifpnlqpeaa 73 
                                   p+ l+ v+i +fF   ++ +++ ++
  gi|91774345|ref|YP_567037.1| 229 PASLFHVVISLFFCIAYIPFSKYMH 253
                                   6777778888888777766554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1529.20
//
Query:       gi|91774346|ref|YP_567038.1|  [L=415]
Description: CoB-CoM heterodisulfide reductase, subunit D [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-28   97.2   7.8    2.4e-15   56.5   0.0    2.7  3  CCG              Cysteine-rich domain
    3.1e-12   46.8   2.3    3.1e-12   46.8   2.3    3.0  3  Fer4_8           4Fe-4S dicluster domain
    9.9e-07   29.2   3.3    9.9e-07   29.2   3.3    3.0  2  Fer4_17          4Fe-4S dicluster domain
    7.7e-06   25.9  16.5    9.9e-06   25.6  11.4    3.4  3  Fer4_10          4Fe-4S dicluster domain
    1.6e-05   25.4   9.8    1.6e-05   25.4   9.8    2.7  3  Fer4_7           4Fe-4S dicluster domain
    5.8e-05   23.9   6.3    5.8e-05   23.9   6.3    2.5  2  Fer4_16          4Fe-4S double cluster binding domain
    0.00013   22.0   8.8      0.096   12.8   0.8    3.2  3  Fer4_21          4Fe-4S dicluster domain
    0.00021   21.4  22.7    0.00045   20.3  12.1    3.5  4  Fer4_9           4Fe-4S dicluster domain
    0.00071   19.8   5.3       0.47   10.7   0.5    2.5  2  Fer4_18          4Fe-4S dicluster domain
      0.003   17.3  21.3      0.011   15.6   3.4    3.2  3  Fer4             4Fe-4S binding domain
     0.0069   16.4  20.3      0.023   14.7   2.7    3.4  3  Fer4_6           4Fe-4S binding domain
     0.0099   15.9  21.0       0.01   15.9   2.0    3.5  4  Fer4_2           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   16.2   2.6        3.7    8.3   0.1    3.0  2  Fer4_15          4Fe-4S single cluster domain
      0.021   14.5   2.0      0.021   14.5   2.0    3.1  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.033   15.0  12.4        0.4   11.5   0.5    3.5  3  Fer4_22          4Fe-4S dicluster domain
      0.068   14.1   3.5      0.068   14.1   3.5    3.5  2  Fer4_3           4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       7.4   8.2e+03      74      80 ..      89      95 ..      73      98 .. 0.57
   2 !   44.3   1.3   1.4e-14   1.6e-11       2      81 ..     165     247 ..     164     250 .. 0.96
   3 !   56.5   0.0   2.1e-18   2.4e-15       1      84 [.     293     380 ..     293     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.4
                           CCG 74 vtacpgC 80
                                  +t+c+ C
  gi|91774346|ref|YP_567038.1| 89 CTTCGMC 95
                                  4566666 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 1.4e-14
                           CCG   2 ayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkee...laealakrnvetaeetgadaivtacp 78 
                                   +yf gC  ++ +++++  a++++l+ lg+e+  l e+e CC ++ +r+g++e   +a++ a++nv+ +  +ga+ ++ ac+
  gi|91774346|ref|YP_567038.1| 165 LYFGGC-TAELRQQKLAFATARVLNHLGIEFAMLgEDEVCCCSALVRTGQHEiedIARRAARKNVDGIVAKGAKTVLYACA 244
                                   79****.9******************************************88777999*********************** PP

                           CCG  79 gCl 81 
                                   gC+
  gi|91774346|ref|YP_567038.1| 245 GCY 247
                                   **8 PP

  == domain 3  score: 56.5 bits;  conditional E-value: 2.1e-18
                           CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadaivtac 77 
                                   v+y+d+Chl+r+   y+ +r +l ++++ ++ e+++  e++ CCGaggg++   + la+ +a+ +v+ a  +++d++ +ac
  gi|91774346|ref|YP_567038.1| 293 VTYHDPCHLGRHVgvYEPPRFVLNAIPGLNLKEMDRIkENQRCCGAGGGVKAGVPdLALGVAETRVQDALAKNPDILSSAC 373
                                   89**********************************************99988777************************* PP

                           CCG  78 pgCllql 84 
                                   p+C+ +l
  gi|91774346|ref|YP_567038.1| 374 PFCKRNL 380
                                   ***9876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   2.3   2.7e-15   3.1e-12       2      65 .]      20     103 ..      19     103 .. 0.81
   2 ?    1.3   0.6      0.42   4.7e+02      16      55 ..     206     247 ..     200     248 .. 0.51
   3 ?   -0.1   0.0       1.2   1.4e+03      13      34 ..     371     392 ..     369     414 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.7e-15
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvlee.....................eealwsCttc 54 
                                   +++C++Cg C + Cp++ +++k++  a+ +++        +        +                     ++ +++Cttc
  gi|91774346|ref|YP_567038.1|  20 IDACVRCGECVKWCPTYDASNKDPGLAPRDKILrwgqfmnK--------SyglrarlfgpkaipeediaqfKDDVYKCTTC 92 
                                   689******************99999998877734443330........3556667777778888888888********** PP

                        Fer4_8  55 gaCtevCpvgi 65 
                                   g+C++vC vgi
  gi|91774346|ref|YP_567038.1|  93 GMCATVCEVGI 103
                                   ********997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.42
                        Fer4_8  16 pvlrrtkkhlldargeaaedvqeeqvlee...eealwsCttcg 55 
                                    +l rt++h  +   ++a+++  +  + +   ++ l++C +c 
  gi|91774346|ref|YP_567038.1| 206 SALVRTGQHEIEDIARRAARKNVDGIV-AkgaKTVLYACAGCY 247
                                   444455544333333333312222222.2356999****9996 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.2
                        Fer4_8  13 saCpvlrrtkkhlldargeaae 34 
                                   saCp+++r   +  d+ g  + 
  gi|91774346|ref|YP_567038.1| 371 SACPFCKRNLSDGRDSLGADEL 392
                                   6899999998887777777665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   3.3   8.8e-10   9.9e-07       1      60 [.      22     103 ..      22     104 .. 0.67
   2 ?   -0.6   0.6       1.8     2e+03      12      49 ..     205     246 ..     202     248 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 8.8e-10
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepk.....kllraakl...............glleeaeke..ekaslCieCgeCerkCPqg 59 
                                   +C +Cg C++ Cp+y a +++p      k+lr  ++               ++ ee +++  + + +C++Cg+C+++C  g
  gi|91774346|ref|YP_567038.1|  22 ACVRCGECVKWCPTYDASNKDPGlaprdKILRWGQFmnksyglrarlfgpkAIPEEDIAQfkDDVYKCTTCGMCATVCEVG 102
                                   5****************87754432222333322224455556666677764555555545479**************987 PP

                       Fer4_17  60 l 60 
                                   +
  gi|91774346|ref|YP_567038.1| 103 I 103
                                   7 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                       Fer4_17  12 Cpsyeaydnepk.kllraaklglleeaeke...ekaslCieC 49 
                                   C+ + ++++++   ++r+a+ + ++++ ++   ++   C++C
  gi|91774346|ref|YP_567038.1| 205 CSALVRTGQHEIeDIARRAARKNVDGIVAKgakTVLYACAGC 246
                                   444555554333157777766667776444454688999999 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6  11.4   8.9e-09   9.9e-06       7      55 ..      21      99 ..      17     100 .. 0.87
   2 ?   -1.7   0.0       2.9   3.2e+03      39      49 ..     237     247 ..     220     249 .. 0.71
   3 ?   -1.2   0.0         2   2.3e+03      38      49 ..     366     377 ..     355     383 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 8.9e-09
                       Fer4_10  7 dtCirCgkCvkaCPadl.............................tsvgakgeaseeeavrk.kvekCtgcgaCveaC 55
                                  d C+rCg+Cvk CP++                              +  g k++ +e+ a+ k +v+kCt+cg+C+ +C
  gi|91774346|ref|YP_567038.1| 21 DACVRCGECVKWCPTYDasnkdpglaprdkilrwgqfmnksyglraRLFGPKAIPEEDIAQFKdDVYKCTTCGMCATVC 99
                                  79*************889**************************986666666666666666669************** PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.9
                       Fer4_10  39 rkkvekCtgcg 49 
                                   ++++++C gc 
  gi|91774346|ref|YP_567038.1| 237 KTVLYACAGCY 247
                                   44677777774 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                       Fer4_10  38 vrkkvekCtgcg 49 
                                    ++ +++C++c 
  gi|91774346|ref|YP_567038.1| 366 PDILSSACPFCK 377
                                   555677787775 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   3.2   0.00029      0.32      35      50 ..      20      35 ..      13      38 .. 0.71
   2 !   25.4   9.8   1.5e-08   1.6e-05       1      52 []      22     103 ..      22     103 .. 0.62
   3 ?   -2.3   0.2       6.4   7.2e+03      34      42 ..     239     247 ..     204     249 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                        Fer4_7 35 pekClgCgaCvavCPt 50
                                   + C+ Cg+Cv+ CPt
  gi|91774346|ref|YP_567038.1| 20 IDACVRCGECVKWCPT 35
                                  5667777777777775 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.5e-08
                        Fer4_7   1 rCigCgaCvaaCp.vkaieldeeenek...........................gt..ekveidpekClgCgaCvavCPtg 51 
                                   +C+ Cg Cv+ Cp ++a + d+   ++                           +   ++ + d  kC++Cg+C++vC +g
  gi|91774346|ref|YP_567038.1|  22 ACVRCGECVKWCPtYDASNKDPGLAPRdkilrwgqfmnksyglrarlfgpkaipEEdiAQFKDDVYKCTTCGMCATVCEVG 102
                                   5***********9666666665433333444454444444555555554444432211333556779***********998 PP

                        Fer4_7  52 a 52 
                                   +
  gi|91774346|ref|YP_567038.1| 103 I 103
                                   6 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.4
                        Fer4_7  34 dpekClgCg 42 
                                   +   C gC+
  gi|91774346|ref|YP_567038.1| 239 VLYACAGCY 247
                                   445577775 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   6.3   5.2e-08   5.8e-05       2      65 ..      23     100 ..      22     102 .. 0.74
   2 ?   -1.4   0.5       4.3   4.9e+03      11      57 ..     202     246 ..     201     248 .. 0.42

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.2e-08
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.............ntaekkdlaedeekckkq..eaitgCdiCqdvCP 65 
                                   C++Cg+C++ CPt   ++k ++ +++r++i               +  + k ++e+  ++ k   +++t C++C++vC 
  gi|91774346|ref|YP_567038.1|  23 CVRCGECVKWCPTYDASNK-DPGLAPRDKILRwgqfmnksyglraRLFGPKAIPEEDIAQFKDdvYKCTTCGMCATVCE 100
                                   *************998888.677777774433455555556999988888887776655443333899**********6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.3
                       Fer4_16  11 vCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgC 57 
                                   vC  +a+  + + eie  +  ++  +++ d +  + +++  +a++gC
  gi|91774346|ref|YP_567038.1| 202 VCCCSALVRTGQHEIEDIARRAA--RKNVDGIVAKGAKTVLYACAGC 246
                                   66666666664444433333222..3332222222333335666666 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.8   8.5e-05     0.096      36      55 ..      17      37 ..       4      41 .. 0.66
   2 !   12.4   0.5   0.00011      0.13      39      53 ..      87     101 ..      72     115 .. 0.71
   3 ?   -1.3   0.0       2.3   2.6e+03      32      45 ..     234     247 ..     219     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-05
                       Fer4_21 36 vve.deCvGCnlCssvCPved 55
                                  ++e d Cv C  C++ CP+ d
  gi|91774346|ref|YP_567038.1| 17 LMEiDACVRCGECVKWCPTYD 37
                                  443378888888888888765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                       Fer4_21  39 deCvGCnlCssvCPv 53 
                                    +C+ C +C++vC v
  gi|91774346|ref|YP_567038.1|  87 YKCTTCGMCATVCEV 101
                                   378888888888877 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.3
                       Fer4_21  32 tvlkvvedeCvGCn 45 
                                   + +k+v   C GC 
  gi|91774346|ref|YP_567038.1| 234 KGAKTVLYACAGCY 247
                                   45566667888885 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.8   2.4e-05     0.026      33      48 ..      17      35 ..       2      39 .. 0.71
   2 !   20.3  12.1     4e-07   0.00045       1      49 [.      22     102 ..      22     104 .. 0.95
   3 ?   -1.2   0.8       2.1   2.4e+03      33      39 ..     226     246 ..     201     248 .. 0.55
   4 ?   -2.4   0.0         5   5.6e+03      34      40 ..     371     377 ..     347     379 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                        Fer4_9 33 e...eaCigCgaCveaCpk 48
                                      +aC+ Cg+Cv+ Cp+
  gi|91774346|ref|YP_567038.1| 17 LmeiDACVRCGECVKWCPT 35
                                  144568************8 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4e-07
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase................................eaCigCgaCveaCpkg 49 
                                   +C++Cg+Cv+ Cp+  +++++ +   r ++ ++                                 +C++Cg C+ +C+ g
  gi|91774346|ref|YP_567038.1|  22 ACVRCGECVKWCPTYDASNKDPGLAPRDKILRWgqfmnksyglrarlfgpkaipeediaqfkddvYKCTTCGMCATVCEVG 102
                                   6************9999999999999999999999******************************99***********987 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.1
                        Fer4_9  33 e..............eaCigC 39 
                                   +               aC gC
  gi|91774346|ref|YP_567038.1| 226 KnvdgivakgaktvlYACAGC 246
                                   345555555666666678777 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 5
                        Fer4_9  34 eaCigCg 40 
                                   +aC +C+
  gi|91774346|ref|YP_567038.1| 371 SACPFCK 377
                                   5677775 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.4   0.00044      0.49      52      73 ..      14      35 ..       2      40 .. 0.78
   2 !   10.7   0.5   0.00042      0.47      55      76 ..      83     104 ..      70     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                       Fer4_18 52 erkekgagdcidcescvkvcPt 73
                                    +  +   c+ c+ cvk cPt
  gi|91774346|ref|YP_567038.1| 14 AVQLMEIDACVRCGECVKWCPT 35
                                  555667789************9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00042
                       Fer4_18  55 ekgagdcidcescvkvcPtgid 76 
                                   ++++ +c++c++c +vc +gi+
  gi|91774346|ref|YP_567038.1|  83 KDDVYKCTTCGMCATVCEVGIN 104
                                   556779*************997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   4.4   0.00019      0.21       6      20 ..      21      35 ..      20      36 .. 0.93
   2 !   15.6   3.4   9.6e-06     0.011       4      21 ..      85     102 ..      82     103 .. 0.88
   3 ?   -2.5   0.3       4.9   5.5e+03      16      20 ..     371     375 ..     370     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                  TTSSS-THHHHHSTT CS
                          Fer4  6 ekCigCGaCvevCPv 20
                                  + C++CG+Cv+ CP+
  gi|91774346|ref|YP_567038.1| 21 DACVRCGECVKWCPT 35
                                  79***********98 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 9.6e-06
                                   ETTTSSS-THHHHHSTTT CS
                          Fer4   4 deekCigCGaCvevCPvg 21 
                                   d  kC+ CG C+ vC vg
  gi|91774346|ref|YP_567038.1|  85 DVYKCTTCGMCATVCEVG 102
                                   6679***********987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.9
                                   HHSTT CS
                          Fer4  16 evCPv 20 
                                   ++CP+
  gi|91774346|ref|YP_567038.1| 371 SACPF 375
                                   57885 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   2.7   2.1e-05     0.023       7      21 ..      21      35 ..      18      39 .. 0.89
   2 !   11.3   3.7   0.00026      0.29       8      23 ..      88     103 ..      85     104 .. 0.89
   3 ?   -1.5   0.4       2.7   3.1e+03       8      14 ..     242     248 ..     242     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                        Fer4_6  7 dkCigCgdCvrvCPe 21
                                  d+C+ Cg+Cv+ CP+
  gi|91774346|ref|YP_567038.1| 21 DACVRCGECVKWCPT 35
                                  89************7 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00026
                        Fer4_6   8 kCigCgdCvrvCPega 23 
                                   kC+ Cg C++vC  g+
  gi|91774346|ref|YP_567038.1|  88 KCTTCGMCATVCEVGI 103
                                   8***********9875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.7
                        Fer4_6   8 kCigCgd 14 
                                   +C gC++
  gi|91774346|ref|YP_567038.1| 242 ACAGCYR 248
                                   5999985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.0     9e-06      0.01       8      22 .]      21      35 ..      14      35 .. 0.89
   2 !   11.9   2.8   0.00017      0.19       5      20 ..      84      99 ..      80     101 .. 0.86
   3 ?   -2.0   0.1       4.4   4.9e+03       9      13 ..     242     246 ..     239     248 .. 0.79
   4 ?   -2.5   0.1       6.4   7.2e+03      18      21 ..     371     374 ..     370     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                        Fer4_2  8 drCigCgaCvsaCPa 22
                                  d+C++Cg Cv+ CP+
  gi|91774346|ref|YP_567038.1| 21 DACVRCGECVKWCPT 35
                                  89************7 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                        Fer4_2  5 vdtdrCigCgaCvsaC 20
                                   d  +C+ Cg C ++C
  gi|91774346|ref|YP_567038.1| 84 DDVYKCTTCGMCATVC 99
                                  56779*********** PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.4
                        Fer4_2   9 rCigC 13 
                                   +C gC
  gi|91774346|ref|YP_567038.1| 242 ACAGC 246
                                   69999 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 6.4
                        Fer4_2  18 saCP 21 
                                   saCP
  gi|91774346|ref|YP_567038.1| 371 SACP 374
                                   79*9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0033       3.7       5      30 ..      20      46 ..      17      81 .. 0.88
   2 ?    6.6   0.6     0.012        14       7      19 ..      88     100 ..      83     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
                       Fer4_15  5 rdaCigcglCvaeapevfelded.gla 30
                                   daC  cg Cv+ +p++   ++d gla
  gi|91774346|ref|YP_567038.1| 20 IDACVRCGECVKWCPTYDASNKDpGLA 46
                                  59*************998887765666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                       Fer4_15   7 aCigcglCvaeap 19 
                                   +C+ cg+C+++++
  gi|91774346|ref|YP_567038.1|  88 KCTTCGMCATVCE 100
                                   8*********995 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.6      0.49   5.5e+02       8      17 ..      22      31 ..      16      32 .. 0.79
   2 ?   14.5   2.0   1.8e-05     0.021       4      24 ..      84     104 ..      82     106 .. 0.89
   3 ?   -3.9   1.8        10   1.1e+04      27      29 ..     202     204 ..     198     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.49
                                  E-TTT--EEE CS
               Desulfoferrod_N  8 kCevCGniVe 17
                                   C  CG+ V+
  gi|91774346|ref|YP_567038.1| 22 ACVRCGECVK 31
                                  69****9996 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.8e-05
                                   T-EEE-TTT--EEEECC--SS CS
               Desulfoferrod_N   4 levYkCevCGniVeVleaGgG 24 
                                    +vYkC+ CG   +V e+G+ 
  gi|91774346|ref|YP_567038.1|  84 DDVYKCTTCGMCATVCEVGIN 104
                                   59****************985 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 10
                                   EET CS
               Desulfoferrod_N  27 VCC 29 
                                   VCC
  gi|91774346|ref|YP_567038.1| 202 VCC 204
                                   777 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00036       0.4      75      94 ..      16      35 ..       7      37 .. 0.80
   2 ?    9.2   0.6     0.002       2.2      78      96 .]      85     103 ..      71     103 .. 0.76
   3 ?    0.3   0.5       1.1   1.3e+03      57      88 ..     218     249 ..     200     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                       Fer4_22 75 ekfgesgCvGCgRCieacpv 94
                                  + ++  +Cv Cg C+++cp+
  gi|91774346|ref|YP_567038.1| 16 QLMEIDACVRCGECVKWCPT 35
                                  45678899999999999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                       Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                   + ++C+ Cg C ++c v+i
  gi|91774346|ref|YP_567038.1|  85 DVYKCTTCGMCATVCEVGI 103
                                   6678888888888888765 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.1
                       Fer4_22  57 ekkerlrqrllhklsefkekfgesgCvGCgRC 88 
                                   + ++r  ++ ++ +    +k+  ++C GC R 
  gi|91774346|ref|YP_567038.1| 218 DIARRAARKNVDGIVAKGAKTVLYACAGCYRT 249
                                   44455555555555566666777899999885 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.5   6.1e-05     0.068       1      13 [.      23      35 ..      23      38 .. 0.86
   2 ?    4.9   5.7     0.053        59       1      14 [.      89     102 ..      89     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C+ Cg Cv++CP+
  gi|91774346|ref|YP_567038.1| 23 CVRCGECVKWCPT 35
                                  99**********5 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.053
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   Ct Cg C  vC vg
  gi|91774346|ref|YP_567038.1|  89 CTTCGMCATVCEVG 102
                                   ***********776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2363.12
//
Query:       gi|91774347|ref|YP_567039.1|  [L=211]
Description: hypothetical protein Mbur_2438 [Methanococcoides burtonii DSM 6242]
Scores for 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-43  147.0   3.6    3.6e-43  146.7   3.6    1.1  1  DUF116           Protein of unknown function DUF116
  ------ inclusion threshold ------
        1.9    7.5   8.1        2.7    7.0   8.1    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein


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 !  146.7   3.6     4e-47   3.6e-43       3     154 ..      56     205 ..      54     206 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 4e-47
                        DUF116   3 lkllgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklte.eglnCkrCgkCkigelkklaek 82 
                                   +k+++ +++++++ +++++ie++n+++ ++f +  +  r+++lP+C+r+ +C+a++++  g++Ck+Cg C+ig ++k+a++
  gi|91774347|ref|YP_567039.1|  56 AKWMCGVFSIRDTLVDEILIEIRNAVMLDDFIN-AKGPRAVFLPQCMRHPNCRARCDPiLGYECKKCGLCDIGIICKAADE 135
                                   799******************************.6999********************99********************* PP

                        DUF116  83 lgykvyivtggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveeleel 154
                                   +g++vy+++gg++++ki+k +kp ++igvaC+++l+e++++++   +++q+v+l k+gC+nTkvdv e+ e+
  gi|91774347|ref|YP_567039.1| 136 HGFTVYVIPGGSFVKKIMKAHKPGSCIGVACYNELSESMEEISF--MPVQGVCLLKDGCFNTKVDVLEVIEK 205
                                   *******************************************9..556778899***********999886 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 ?    7.0   8.1    0.0003       2.7     237     302 ..       7      64 ..       2      68 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0003
               ABC2_membrane_3 237 nlglllllfllfglayialgyllssl.fknsetaqilifivilllsgffgglfpledlpsalkwifs 302
                                    lg l++++llf+l+ i++++l+++  fkn            + +s+++++l+++ ++++++  +fs
  gi|91774347|ref|YP_567039.1|   7 LLGKLFVYMLLFALLGIVVALLVGFYsFKNKMVI--------F-PSFVLFMLYLFYSPAKWMCGVFS 64 
                                   5566777777777777777777777766666332........2.34444444444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1219  (0.0679904); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1222.19
//
Query:       gi|91774348|ref|YP_567040.1|  [L=208]
Description: hypothetical protein Mbur_2439 [Methanococcoides burtonii DSM 6242]
Scores for 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-44  149.8   0.0    4.9e-44  149.6   0.0    1.0  1  DUF116    Protein of unknown function DUF116
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.22   11.4   0.0    1.4  1  DUF1686   Protein of unknown function (DUF1686)


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 !  149.6   0.0   5.4e-48   4.9e-44      10     153 ..      59     199 ..      51     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 5.4e-48
                        DUF116  10 lgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklteeglnCkrCgkCkigelkklaeklgykvyiv 90 
                                   ++ d +kl++++++++n++++++f+k  ++krl+++PhC+r+ dCpa  t+ g++C++CgkC +++lk+ aek+gy++yiv
  gi|91774348|ref|YP_567040.1|  59 FS-DPRKLDMWMVSLKNSAHMSDFAK--TKKRLMFVPHCMRSLDCPAYATKYGIQCRSCGKCVFDQLKEDAEKYGYEFYIV 136
                                   44.7899*******************..8**************************************************** PP

                        DUF116  91 tggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveelee 153
                                   tg++++++i+k++  ++++ +aC +++++g+++l +++vi++++++ ++gC+nTkvd   +e+
  gi|91774348|ref|YP_567040.1| 137 TGSSFVKNILKDRPADGVLVIACDYEINKGMRSLAGTGVITYGIPMLNDGCYNTKVDEVFVED 199
                                   *********************************************************877776 PP

>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.5e-05      0.22       5      40 ..     162     197 ..     158     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.5e-05
                       DUF1686   5 swntalyvlavaGtiiyqiwvLakeyrdkgveevlr 40 
                                    +n+++ +la +G i+y+i +L   +++ +v ev  
  gi|91774348|ref|YP_567040.1| 162 EINKGMRSLAGTGVITYGIPMLNDGCYNTKVDEVFV 197
                                   5899****************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1153.45
//
Query:       gi|91774349|ref|YP_567041.1|  [L=94]
Description: hypothetical protein Mbur_2440 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 535.41
//
Query:       gi|91774350|ref|YP_567042.1|  [L=193]
Description: hypothetical protein Mbur_2441 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1073.70
//
Query:       gi|91774351|ref|YP_567043.1|  [L=313]
Description: transposase, IS4 [Methanococcoides burtonii DSM 6242]
Scores for complete 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   76.6   0.0    2.1e-21   75.7   0.0    1.5  1  DUF772       Transposase domain (DUF772)
      2e-16   60.3   2.2    5.8e-16   58.8   2.2    1.7  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   17.5   0.1     0.0091   16.2   0.1    1.7  1  DDE_Tnp_1_6  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.035   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
      0.035   13.8   0.1      0.071   12.8   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     6e-25   2.1e-21       1      72 [.      50     121 ..      50     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6e-25
                        DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                   Grp+++  +mlk+l+lq+++glSd ele++  +++sfr flg+     ++pdh+t + fR+r+ +    +++++e
  gi|91774351|ref|YP_567043.1|  50 GRPNVDEIVMLKMLVLQQWHGLSDPELERQATDRISFRKFLGFP---AKIPDHTTVWAFRERISQagkEDEIWNE 121
                                   9*****************************************96...78****************9988888775 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   2.2   1.6e-19   5.8e-16       5     214 .]     135     301 ..     132     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
                     DDE_Tnp_1   5 evlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqll 69 
                                   ++ i Dat++ +   +                +d+ w++k+ k+++gyklh++ dt+  li ++++t+++vhds++     
  gi|91774351|ref|YP_567043.1| 135 QGMIQDATFIHADPGHanldtprgneaktrrcKDGTWTKKASKSHFGYKLHTIEDTEYDLIRRYRTTTASVHDSQVDLS-- 213
                                   67788******988889*********************************************************97333.. PP

                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgd 150
                                   +     +g +v++D+GY+  ++ +  +                           ++ +  r++++  ++k rnk       
  gi|91774351|ref|YP_567043.1| 214 E-----EGEVVYRDRGYF-GAISKGYD--------------------------ATMQRGVRGHPIGIRDKMRNK------- 255
                                   4.....9**********9.44444433..........................6788*****************....... PP

                     DDE_Tnp_1 151 vyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                     +++r+R+  Er  + +k++f  + +r+ +l+rv  ++ ++++++nl
  gi|91774351|ref|YP_567043.1| 256 ------------------RISRKRAKGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNL 301
                                   ..................*********************************************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.5e-06    0.0091      71     124 ..     252     304 ..     230     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   DDE_Tnp_1_6  71 eegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                    + k+  +kRa + E+  a ik+      +r++ l++v++++ ++a+ +Nl +l
  gi|91774351|ref|YP_567043.1| 252 MRNKRISRKRA-KGERPYAVIKNVFTSGFVRVTTLARVNVKMAITAFSYNLYQL 304
                                   45567778887.99*************************************997 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.035      37     118 ..     173     255 ..     156     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                   DDE_Tnp_1_3  37 kssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgy...iskklaeelleegie.litklr 112
                                   k +    +G+kLh i + + ++++ ++ t++ v+D +  + l++e  + ++ D+gy   isk    ++ ++g++     +r
  gi|91774351|ref|YP_567043.1| 173 KKASKSHFGYKLHTIEDTEYDLIRrYRTTTASVHDSQV-D-LSEE-GEVVYRDRGYfgaISKGYDATM-QRGVRgHPIGIR 249
                                   55555679*************99637889999999875.3.6665.6789******444455544444.334431334566 PP

                   DDE_Tnp_1_3 113 knmkkk 118
                                    +m++k
  gi|91774351|ref|YP_567043.1| 250 DKMRNK 255
                                   666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.071      72     132 ..     213     276 ..     167     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     DDE_Tnp_4  72 vkpgdvilaDkgFk..lsekl.lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++g+v+  D+g+   +s+ +  +++++ +++++  +++ +n++i++ r   Er  + +k+ f+
  gi|91774351|ref|YP_567043.1| 213 SEEGEVVYRDRGYFgaISKGYdATMQRGVRGHPIGIRDKMRNKRISRKRAKGERPYAVIKNVFT 276
                                   35789999999997546665646999999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1800.62
//
Query:       gi|91774352|ref|YP_567044.1|  [L=93]
Description: hypothetical protein Mbur_2443 [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0005   20.1   0.0    0.00063   19.8   0.0    1.2  1  DASH_Dad3    DASH complex subunit Dad3
     0.0017   17.9   0.0     0.0018   17.8   0.0    1.1  1  ComA         (2R)-phospho-3-sulfolactate synthase (ComA)
  ------ inclusion threshold ------
      0.015   14.1   0.1      0.016   14.0   0.1    1.0  1  Tht1         Tht1-like nuclear fusion protein
      0.041   13.2   0.1      0.046   13.1   0.1    1.1  1  Helo_like_N  Fungal N-terminal domain of STAND proteins


Domain annotation for each model (and alignments):
>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.4e-07   0.00063       5      33 ..      17      53 ..      14      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-07
                     DASH_Dad3  5 eqevLdeYerLaenlktLaselkeLasn........s 33
                                  +q vLd+Y+++ e+ k+L sel eL+s+         
  gi|91774352|ref|YP_567044.1| 17 DQIVLDQYKEMVEKTKQLHSELVELSSKmgsiadtiD 53
                                  688************************9765444440 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     4e-07    0.0018      63     126 ..       3      66 ..       1      91 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-07
                                   CTT-EEEE-HHHHHHHHHTT-HHHHHHHHHHCT-SEEEE--SSS---HHHHHHHHHHHCCTTSE CS
                          ComA  63 ehgvyvstGgtlfEaalaqgkvdeyleeckelgfdviEvsdgtlelpeeeklrliekakkeglk 126
                                   + ++ v+ Gg  +   ++ ++++e++e++k+l+ + +E+s+ + ++ +     l e+a ++ + 
  gi|91774352|ref|YP_567044.1|   3 QVDIFVYSGGGNMADQIVLDQYKEMVEKTKQLHSELVELSSKMGSIADTIDNGLPERAVSDKFD 66 
                                   67999****99999999999*************************9988877777777777665 PP

>> Tht1  Tht1-like nuclear fusion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.5e-06     0.016     229     304 ..      17      91 ..      12      93 .] 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-06
                          Tht1 229 eqegmvlekeilekikqlksevddvnsiladlieelagykndlkek.lnekddsena.ialsaigkytsefsafmekr 304
                                   +q  + + ke++ek kql+se+ ++ s +  +++      n l e+ + +k+ds +  + +s     +  +s++ ekr
  gi|91774352|ref|YP_567044.1|  17 DQIVLDQYKEMVEKTKQLHSELVELSSKMGSIADTID---NGLPERaVSDKFDSIDHdVHMSDDPLSSRRVSTLSEKR 91 
                                   565666889************************9887...9998873678***9863144555444455556666665 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     1e-05     0.046     144     181 ..      17      53 ..      13      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                   Helo_like_N 144 taevleeykeliedttsdLeehLedideklealtekse 181
                                   ++ vl++yke++e+t+ +L++ L ++ +k+ +++++ +
  gi|91774352|ref|YP_567044.1|  17 DQIVLDQYKEMVEKTK-QLHSELVELSSKMGSIADTID 53 
                                   5679*********986.69***********99985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 549.10
//
Query:       gi|91774353|ref|YP_567045.1|  [L=175]
Description: heat shock protein [Methanococcoides burtonii DSM 6242]
Scores for 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   24.1   0.0    4.6e-05   22.9   0.0    1.7  1  ArsA_HSP20     HSP20-like domain found in ArsA
     0.0001   22.4   0.2      0.001   19.2   0.2    2.0  1  HSP20          Hsp20/alpha crystallin family
  ------ inclusion threshold ------
      0.041   13.1   0.0       0.05   12.8   0.0    1.2  1  RuBisCO_large  Ribulose bisphosphate carboxylase large chain,
      0.074   14.1   0.0       0.12   13.5   0.0    1.2  1  CS             CS domain
       0.11   12.5   0.2        6.9    6.7   0.0    2.3  2  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated


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 !   22.9   0.0   1.3e-08   4.6e-05       1      63 []      96     161 ..      96     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-08
                    ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                   dd++   +dL  v+ke+i+l  ++ +L +++     ++ R++ L   +  + + +A+f++gvL + F
  gi|91774353|ref|YP_567045.1|  96 DDHVHFMVDLSCVEKEDIKLNAEEMTLHVTASrghwSYVRTFDLLVPVYPESA-KATFKNGVLDVIF 161
                                   7899999*************************9***********999****77.**********987 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   2.9e-07     0.001       2      87 ..      92     163 ..      91     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.9e-07
                                   --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEE CS
                         HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLt 82 
                                    +e++++ ++ +d++ ++ke++k++ e+ ++ v++ +         +++      ++r+f L   v +++ ka++k+GvL 
  gi|91774353|ref|YP_567045.1|  92 LIETDDHVHFMVDLSCVEKEDIKLNAEEMTLHVTASRG--------HWS------YVRTFDLLVPVYPESAKATFKNGVLD 158
                                   6899******************************9988........555......778888888999*************9 PP

                                   EEEEB CS
                         HSP20  83 vtvpk 87 
                                   v  ++
  gi|91774353|ref|YP_567045.1| 159 VIFKR 163
                                   96655 PP

>> 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 ?   12.8   0.0   1.4e-05      0.05      54      96 ..      15      58 ..      11     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                  SSBTTB-HHHHHHHHHHHHH.HHHHHHSS--EEEEE---SSHHH CS
                 RuBisCO_large 54 nsqpfarlkdrieavaeaik.raqdetGekklyalnitaddlee 96
                                  ++  f  ++d ie++++a++ +  d +G+ k+y + it++  ee
  gi|91774353|ref|YP_567045.1| 15 ENDSFEDVRDMIENIMDAMNvDLGDLSGKPKVYGFSITHHPGEE 58
                                  7899***************9567899************998777 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05      0.12       7      73 ..      94     160 ..      89     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                   EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE..TS.CEEEEECEBSS-BETTTEEEEEETTEEEEE CS
                            CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki..gk.eklliegeLfgpIdpeesswtieskkveit 73 
                                   +t+d+V   + ++  +++k+d+k++ +e +l+v    g+  ++    +L+ p+ pe+++ t+++  ++++
  gi|91774353|ref|YP_567045.1|  94 ETDDHVHFMVDLS--CVEKEDIKLNAEEMTLHVTAsrGHwSYVR-TFDLLVPVYPESAKATFKNGVLDVI 160
                                   5666666666664..56******************966666665.445**************99888875 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0019       6.9       3      27 ..      39      58 ..      38      68 .. 0.83
   2 ?    3.4   0.0     0.021        74      33      56 ..      92     115 ..      88     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0019
                                  EE-GG-EEEEEEEEEE-TTS-EEEE CS
                 OB_aCoA_assoc  3 elsgrGtvysftvvhrappgfaeea 27
                                  +lsg+ +vy f+++h++      e+
  gi|91774353|ref|YP_567045.1| 39 DLSGKPKVYGFSITHHPG-----EE 58
                                  589999***********9.....33 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.021
                                   EEE-TT...-EE-EEEEEEES..T CS
                 OB_aCoA_assoc  33 vVeLdegvrimarlvgvdpdevri 56 
                                   ++e d+ v  m++l +v+ +++++
  gi|91774353|ref|YP_567045.1|  92 LIETDDHVHFMVDLSCVEKEDIKL 115
                                   7999**************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1114.56
//
Query:       gi|91774354|ref|YP_567046.1|  [L=125]
Description: response regulator receiver [Methanococcoides burtonii DSM 6242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-27   94.2   0.1    5.8e-27   94.1   0.1    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.059   13.6   0.0      0.099   12.9   0.0    1.4  1  PLDc          Phospholipase D Active site motif


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 !   94.1   0.1   6.5e-31   5.8e-27       1     111 [.      10     120 ..      10     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 6.5e-31
                                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESST CS
                  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahs 81 
                                   +l+vdD+ + + l++++le eg+ ev  a+ g+e+l++l++ k+d+illDi+mp+mdG e++ +ir ed ++p+ i++ +s
  gi|91774354|ref|YP_567046.1|  10 ILVVDDEADTIFLISSILEPEGF-EVIGADGGAECLKILESVKPDVILLDIMMPDMDGWETFHKIRSEDVDVPICIISVKS 89 
                                   8**********************.8888***************************************************** PP

                                   SHHHHHHHH.HCTESEEEESSG-HHHHHHHH CS
                  Response_reg  82 eeedaveal.kagaddflsKpfdpeeLlkal 111
                                   ++ d+  +l  ++a+d++ Kpf+ e+L+ ++
  gi|91774354|ref|YP_567046.1|  90 QSFDRMLGLnVLNANDYINKPFSAEDLIGRI 120
                                   *99999999678***************9887 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05     0.099       3      21 ..       4      25 ..       2      26 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                  BEE---EEEETTT...EEEEE- CS
                          PLDc  3 gthHqKivivDdr...vafvGg 21
                                  gt++ Ki++vDd+   ++++++
  gi|91774354|ref|YP_567046.1|  4 GTLNKKILVVDDEadtIFLISS 25
                                  89***********999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 829.37
//
Query:       gi|91774355|ref|YP_567047.1|  [L=357]
Description: methyltransferase [Methanococcoides burtonii DSM 6242]
Scores for 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   48.1   0.1    1.9e-12   47.1   0.1    1.7  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      2e-08   34.2   0.1    4.3e-08   33.1   0.1    1.6  1  Methyltransf_31  Methyltransferase domain
      5e-07   30.3   0.0    1.4e-06   28.9   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    5.3e-07   29.3   0.0    1.1e-06   28.3   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
    5.8e-05   22.2   0.4    0.00029   19.9   0.1    2.2  3  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0002   20.9   0.0    0.00038   20.1   0.0    1.4  1  MTS              Methyltransferase small domain
    0.00037   21.1   0.0    0.00094   19.8   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
     0.0004   20.4   0.0    0.00091   19.2   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
      0.004   16.5   0.2      0.013   14.8   0.0    1.8  2  GidB             rRNA small subunit methyltransferase G
     0.0074   16.0   0.0      0.013   15.2   0.0    1.3  1  CmcI             Cephalosporin hydroxylase
      0.009   15.1   0.0      0.022   13.8   0.0    1.7  2  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.023   14.8   0.0      0.032   14.3   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
      0.031   13.9   0.0      0.068   12.8   0.0    1.5  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.04   13.7   0.0      0.087   12.6   0.0    1.5  1  Met_10           Met-10+ like-protein
      0.097   12.0   0.0       0.15   11.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.15   11.7   0.0       0.27   11.0   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   1.7e-15   1.9e-12       2      77 ..      47     119 ..      46     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.7e-15
               Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvfl 77 
                                   r+i D+ +G GG++i fa++ +kv+aiei+l+k++ a+ N+e Yg  d++ +++gd ++     +  k+  d++f 
  gi|91774355|ref|YP_567047.1|  47 RTIADISCGIGGQTIFFAKECKKVYAIEIDLKKIEYAEINCERYG-LDNVEFICGDALSEEVINQIPKL--DVLFS 119
                                   7899****************************************7.589*******9884433344444..55443 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   3.8e-11   4.3e-08       6      81 ..      48     120 ..      45     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.8e-11
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled.ekfDlilsn 81 
                                   ++ D+ CG G  t+ +a+e +  ++v+ i+i+ + ie+A+ n+++ gldnveF  gd+ + e   ++  k D+++s+
  gi|91774355|ref|YP_567047.1|  48 TIADISCGIGGQTIFFAKE-C--KKVYAIEIDLKKIEYAEINCERYGLDNVEFICGDALSEEVI-NQiPKLDVLFSD 120
                                   578**************65.3..58***********************************7743.334799999988 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.2e-09   1.4e-06       1      57 [.      49     104 ..      49     130 .. 0.86
   2 ?   -2.8   0.0       9.8   1.1e+04      41      67 ..     247     274 ..     229     298 .. 0.54

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.2e-09
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed 57 
                                   + d+ cG G  t+ +ak++  +kv++++i+ + +e+a+ ++e+ gl nvef++gda +
  gi|91774355|ref|YP_567047.1|  49 IADISCGIGGQTIFFAKEC--KKVYAIEIDLKKIEYAEINCERYGLdNVEFICGDALS 104
                                   78****************9..9*********************************954 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.8
                                   HHHTTTTEEEEESBCCG.BSSSTTTEEE CS
               Methyltransf_25  41 aeeeglnvefvqgdaed.lpfedgsfDl 67 
                                   +e++  +v++++ d ++ l   ++  D 
  gi|91774355|ref|YP_567047.1| 247 NENNTTQVQLYEIDQKRsLFTSEEPLDH 274
                                   3333345555555553313334444444 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   9.5e-10   1.1e-06       4      93 ..      48     131 ..      45     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.5e-10
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEES---- CS
                Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifilFPDPw 84 
                                   ++++i cG G+ ++  Ak+   k++ +iEi  k ++++  + e+++l N++ ++gda   l+e + + ++ k+ +lF+DP 
  gi|91774355|ref|YP_567047.1|  48 TIADISCGIGGQTIFFAKEC--KKVYAIEIDLKKIEYAEINCERYGLDNVEFICGDA---LSEEVIN-QIPKLDVLFSDPA 122
                                   689**************986..667899*****************************...7777766.89**********6 PP

                                   -SGGGGGGS CS
                Methyltransf_4  85 fKkrhhKrR 93 
                                          rR
  gi|91774355|ref|YP_567047.1| 123 RPPSEDERR 131
                                   655555555 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 !   19.9   0.1   2.6e-07   0.00029     205     255 ..      49      99 ..      37     114 .. 0.87
   2 ?   -1.3   0.0      0.74   8.3e+02      75     101 ..     235     261 ..     213     272 .. 0.81
   3 ?   -1.9   0.0       1.1   1.2e+03      89     115 ..     273     299 ..     264     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
               tRNA_U5-meth_tr 205 llelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiir 255
                                   + ++ cG G  ++ +a++ +kv a ei    +e a +n++   +dnv++i 
  gi|91774355|ref|YP_567047.1|  49 IADISCGIGGQTIFFAKECKKVYAIEIDLKKIEYAEINCERYGLDNVEFIC 99 
                                   56788*******************************************995 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.74
               tRNA_U5-meth_tr  75 inelmkallaalkqdeklreklfqvdf 101
                                    +el+++l + l+++++ + +l+++d 
  gi|91774355|ref|YP_567047.1| 235 KAELLPELANDLNENNTTQVQLYEIDQ 261
                                   468999999999999999999999985 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
               tRNA_U5-meth_tr  89 deklreklfqvdflstlsgellvslly 115
                                   d+ l ++ +++++++ +  +++ sll 
  gi|91774355|ref|YP_567047.1| 273 DHPLAKNSYEIKYVTEMDAKIINSLLK 299
                                   567889999**********99999985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.4e-07   0.00038      31      93 ..      45     106 ..      28     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.4e-07
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTS CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleev 93 
                                   + ++++D+ cG+G  ++ +ake+++  v ++++d + +e a+ n+e+ +l+ ve++  d+l+e 
  gi|91774355|ref|YP_567047.1|  45 KCRTIADISCGIGGQTIFFAKECKK--VYAIEIDLKKIEYAEINCERYGLDnVEFICGDALSEE 106
                                   45789*****************999..9***********************9999999988764 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.4e-07   0.00094       2      53 ..      51     103 ..      50     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.4e-07
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECC CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadae 53 
                                   d+ cG G  +  +ak +++v++++++ + +++a+ + ++ gl +vef+++da 
  gi|91774355|ref|YP_567047.1|  51 DISCGIGGQTIFFAKECKKVYAIEIDLKKIEYAEINCERYGLdNVEFICGDAL 103
                                   89*************************************************85 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.1e-07   0.00091      14      77 ..      45     105 ..      37     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.1e-07
               Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlek 77 
                                   k++++aDi +  g  +i+ +  + +kkv+a++i  + +e a+ n+e++gl d++e++++d l++
  gi|91774355|ref|YP_567047.1|  45 KCRTIADISCGIGGQTIFFA--KECKKVYAIEIDLKKIEYAEINCERYGL-DNVEFICGDALSE 105
                                   5889*******999999998..6899************************.68*******9975 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-05     0.013      52     109 ..      49     104 ..      34     119 .. 0.77
   2 ?   -1.1   0.0      0.92     1e+03      82     104 ..     233     255 ..     230     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                   EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC CS
                          GidB  52 viDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee 109
                                   ++D+  G G  G  + +a++ +k++ +e + kki++ e  +e+ +l+nve+++ +a +
  gi|91774355|ref|YP_567047.1|  49 IADISCGIG--GQTIFFAKECKKVYAIEIDLKKIEYAEINCERYGLDNVEFICGDALS 104
                                   778877776..566667888999*******************************9965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.92
                                   HHHHHHHHHHHHHCT-SSEEEEE CS
                          GidB  82 ekkiaFLeevkeelklenveive 104
                                     k++ L e+ ++l+ +n++ v+
  gi|91774355|ref|YP_567047.1| 233 VTKAELLPELANDLNENNTTQVQ 255
                                   56778888888888888888776 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.013      31     105 ..      44     113 ..      35     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                          CmcI  31 lkPdliietGiahGGsalfsasllallkskrkvlaididireknrqaieahpl.asrieliegssvdpeiveqvks 105
                                   lk ++i ++    GG  +f+a+ +       kv ai+id ++ + ++i++ +   +++e+i g++++ e+++q+ +
  gi|91774355|ref|YP_567047.1|  44 LKCRTIADISCGIGGQTIFFAKEC------KKVYAIEIDLKKIEYAEINCERYgLDNVEFICGDALSEEVINQIPK 113
                                   6778898999999*******9865......567****************98873699****************976 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     2e-05     0.022      22      92 ..      35     109 ..      29     153 .. 0.79
   2 ?   -2.4   0.0       1.8     2e+03      57      84 ..     235     260 ..     217     278 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                                   HHHHH-GG..TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHH CS
                        RrnaAD  22 Ildklnle..ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpe 92 
                                   I+ k   +  +  t+ +i  G G +T  +ak +k+v ++E+d + ++  + + +     +++ +  D+l  e+ +
  gi|91774355|ref|YP_567047.1|  35 IVAKYRAKrlKCRTIADISCGIGGQTIFFAKECKKVYAIEIDLKKIEYAEINCEryGLDNVEFICGDALSEEVIN 109
                                   66666655667789****************************987776666555555566777777766666655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                   EE-S-HHHHHHHHCHTTTCCCEEEE-S- CS
                        RrnaAD  57 vlElderLakllqkklskdeklkvvhqD 84 
                                     El ++La+ l++  ++ +++++++ D
  gi|91774355|ref|YP_567047.1| 235 KAELLPELANDLNE--NNTTQVQLYEID 260
                                   55555555555555..445555555544 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.9e-05     0.032      11      96 ..      34     122 ..      29     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                                   HHHHHHT-S-.TT-EEEECT-TTSHHHHHHCCT.T.-SEEEE..EESSSS.......HHH...TTEEEECS-CCCSSHHHH CS
                          FtsJ  11 eidekfklfk.pgktvvDlgaaPGgwsqvllqrlgakgkvva..vDlqpm.......apl...pgvttiqgditdpetiek 78 
                                   ei +k++  + + +t+ D+ ++ Gg + + +++++   kv+a  +Dl+++       + +   ++v++i+gd +++e+i++
  gi|91774355|ref|YP_567047.1|  34 EIVAKYRAKRlKCRTIADISCGIGGQTIFFAKECK---KVYAieIDLKKIeyaeincE-RyglDNVEFICGDALSEEVINQ 110
                                   567788844478999******************64...56662267788888766552.13558****************9 PP

                                   HCHCHHHSSEEEEEE--S CS
                          FtsJ  79 ikealserkvdlvvsDga 96 
                                   i +       d+  sD a
  gi|91774355|ref|YP_567047.1| 111 IPK------LDVLFSDPA 122
                                   995......788888877 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.068      11      70 ..      48     104 ..      43     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                                   EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTC CS
               Methyltr_RsmB-F  11 tilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDark 70 
                                   ti D++++ Gg+T + a+   + ++v+A++++ ++++  + n +r g+ n+  +++Da  
  gi|91774355|ref|YP_567047.1|  48 TIADISCGIGGQTIFFAK---ECKKVYAIEIDLKKIEYAEINCERYGLDNVEFICGDALS 104
                                   789***********9985...5889********************************865 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-05     0.087     103     160 ..      48     102 ..      35     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-05
                                   EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-G CS
                        Met_10 103 vVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDg 160
                                   ++ d+  GiG  +i  ak  + k+v+ai+++ + ++y + n ++  +++ v+ i++D+
  gi|91774355|ref|YP_567047.1|  48 TIADISCGIGGQTIFFAK--ECKKVYAIEIDLKKIEYAEINCERYGLDN-VEFICGDA 102
                                   678999************..8999*****************99988876.56888875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.15      45     109 ..      43     104 ..      28     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                   S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT CS
               Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee 109
                                    ++ +++ D+++G g  ++ ++++ +   kv  ++i+ + ++ +e   ++ g  n+ef++++a  
  gi|91774355|ref|YP_567047.1|  43 RLKCRTIADISCGIGGQTIFFAKECK---KVYAIEIDLKKIEYAEINCERYGLDNVEFICGDALS 104
                                   45667999************998776...67888899999*********************9865 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024      0.27      76     133 ..      48     102 ..      35     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                   EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-G CS
                          PCMT  76 rvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDG 133
                                    + ++ +G G +t  +a+  +++    +ie   + +e a+ n ++ +l+nv +++gD 
  gi|91774355|ref|YP_567047.1|  48 TIADISCGIGGQTIFFAKECKKVY---AIEIDLKKIEYAEINCERYGLDNVEFICGDA 102
                                   5789*************9988877...7787778899*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2235.07
//
[ok]
